Multiple sequence alignment - TraesCS3A01G395200

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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 TraesCS3A01G395200 chr3A 100.000 7053 0 0 1 7053 642364180 642371232 0.000000e+00 13025
1 TraesCS3A01G395200 chr3A 99.225 129 1 0 1887 2015 642365941 642366069 4.250000e-57 233
2 TraesCS3A01G395200 chr3A 99.225 129 1 0 1762 1890 642366066 642366194 4.250000e-57 233
3 TraesCS3A01G395200 chr3D 95.895 5189 178 16 1887 7053 504055774 504060949 0.000000e+00 8370
4 TraesCS3A01G395200 chr3D 90.240 1168 53 25 748 1890 504054771 504055902 0.000000e+00 1469
5 TraesCS3A01G395200 chr3B 94.540 5201 200 28 1887 7053 665465291 665470441 0.000000e+00 7954
6 TraesCS3A01G395200 chr3B 92.764 1147 41 17 748 1890 665464311 665465419 0.000000e+00 1620
7 TraesCS3A01G395200 chr3B 88.513 679 50 12 1 679 665463436 665464086 0.000000e+00 797
8 TraesCS3A01G395200 chr6D 87.682 893 93 9 3093 3981 454487822 454488701 0.000000e+00 1024
9 TraesCS3A01G395200 chr6D 83.107 882 112 13 4402 5253 454489182 454490056 0.000000e+00 769
10 TraesCS3A01G395200 chr6D 87.107 636 68 7 4055 4683 454488697 454489325 0.000000e+00 708
11 TraesCS3A01G395200 chr6D 80.765 863 94 36 2213 3051 454487011 454487825 6.050000e-170 608
12 TraesCS3A01G395200 chr6D 84.696 477 63 5 5587 6059 454490579 454491049 1.070000e-127 468
13 TraesCS3A01G395200 chr6D 80.556 540 55 30 959 1480 454486290 454486797 3.110000e-98 370
14 TraesCS3A01G395200 chr6D 83.228 316 34 10 5288 5589 454490061 454490371 9.010000e-69 272
15 TraesCS3A01G395200 chr6D 94.488 127 7 0 6560 6686 267532962 267532836 5.580000e-46 196
16 TraesCS3A01G395200 chr6A 87.556 900 90 9 3093 3981 600695193 600696081 0.000000e+00 1022
17 TraesCS3A01G395200 chr6A 84.790 881 101 9 4402 5251 600696562 600697440 0.000000e+00 854
18 TraesCS3A01G395200 chr6A 86.950 636 69 7 4055 4683 600696077 600696705 0.000000e+00 702
19 TraesCS3A01G395200 chr6A 82.808 698 80 18 2377 3051 600694516 600695196 7.880000e-164 588
20 TraesCS3A01G395200 chr6A 84.277 477 65 5 5587 6059 600697951 600698421 2.320000e-124 457
21 TraesCS3A01G395200 chr6A 80.303 528 61 25 958 1462 600693346 600693853 6.730000e-95 359
22 TraesCS3A01G395200 chr6A 95.276 127 6 0 6560 6686 381088855 381088729 1.200000e-47 202
23 TraesCS3A01G395200 chr6B 87.293 905 95 9 3093 3981 690963611 690964511 0.000000e+00 1016
24 TraesCS3A01G395200 chr6B 84.199 886 104 12 4402 5253 690964992 690965875 0.000000e+00 828
25 TraesCS3A01G395200 chr6B 86.529 631 71 7 4055 4678 690964507 690965130 0.000000e+00 682
26 TraesCS3A01G395200 chr6B 83.772 684 72 21 2395 3051 690962943 690963614 4.680000e-171 612
27 TraesCS3A01G395200 chr6B 84.277 477 64 6 5587 6059 690966398 690966867 8.340000e-124 455
28 TraesCS3A01G395200 chr6B 77.439 820 126 38 959 1760 690961589 690962367 1.090000e-117 435
29 TraesCS3A01G395200 chr5B 94.316 651 29 4 1887 2530 540406271 540405622 0.000000e+00 990
30 TraesCS3A01G395200 chr5B 91.757 461 29 4 1435 1890 540406596 540406140 3.590000e-177 632
31 TraesCS3A01G395200 chr1B 94.788 614 24 4 1889 2495 35063555 35064167 0.000000e+00 950
32 TraesCS3A01G395200 chr1B 91.522 460 30 4 1436 1890 35063229 35063684 6.010000e-175 625
33 TraesCS3A01G395200 chr1A 93.985 133 8 0 6560 6692 242003471 242003339 1.200000e-47 202
34 TraesCS3A01G395200 chr1A 92.857 140 9 1 6560 6699 357773039 357773177 1.200000e-47 202
35 TraesCS3A01G395200 chr1D 93.182 132 9 0 6561 6692 194467446 194467315 2.010000e-45 195
36 TraesCS3A01G395200 chr7D 93.077 130 9 0 6557 6686 493569746 493569875 2.600000e-44 191
37 TraesCS3A01G395200 chr2D 92.481 133 9 1 6560 6692 380416677 380416546 9.340000e-44 189


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 TraesCS3A01G395200 chr3A 642364180 642371232 7052 False 13025.000000 13025 100.000000 1 7053 1 chr3A.!!$F1 7052
1 TraesCS3A01G395200 chr3D 504054771 504060949 6178 False 4919.500000 8370 93.067500 748 7053 2 chr3D.!!$F1 6305
2 TraesCS3A01G395200 chr3B 665463436 665470441 7005 False 3457.000000 7954 91.939000 1 7053 3 chr3B.!!$F1 7052
3 TraesCS3A01G395200 chr6D 454486290 454491049 4759 False 602.714286 1024 83.877286 959 6059 7 chr6D.!!$F1 5100
4 TraesCS3A01G395200 chr6A 600693346 600698421 5075 False 663.666667 1022 84.447333 958 6059 6 chr6A.!!$F1 5101
5 TraesCS3A01G395200 chr6B 690961589 690966867 5278 False 671.333333 1016 83.918167 959 6059 6 chr6B.!!$F1 5100
6 TraesCS3A01G395200 chr5B 540405622 540406596 974 True 811.000000 990 93.036500 1435 2530 2 chr5B.!!$R1 1095
7 TraesCS3A01G395200 chr1B 35063229 35064167 938 False 787.500000 950 93.155000 1436 2495 2 chr1B.!!$F1 1059

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
349 350 0.392706 TCATGGCGCTACGGATGATT 59.607 50.000 7.64 0.0 0.00 2.57 F
1878 2440 0.037697 AGCGACAATAGCCACGAACA 60.038 50.000 0.00 0.0 34.64 3.18 F
1916 2478 0.106719 CCACGGATGGGGCTTGTTAT 60.107 55.000 0.00 0.0 43.04 1.89 F
2969 3729 0.179156 CAATGGCATTGACCAGTCGC 60.179 55.000 31.50 0.0 44.71 5.19 F
4496 5430 1.197430 AGAACCTGGTGAGCAGAGGG 61.197 60.000 14.03 0.0 0.00 4.30 F
5106 6061 1.340889 GCCTTCACCATCAAGCAAACA 59.659 47.619 0.00 0.0 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1897 2459 0.106719 ATAACAAGCCCCATCCGTGG 60.107 55.0 0.00 0.0 45.61 4.94 R
2969 3729 0.249120 TCCGGGTTGATACTGCACAG 59.751 55.0 0.00 0.0 0.00 3.66 R
3572 4350 1.192146 ACGCCTGTACCATCCACAGT 61.192 55.0 2.17 0.0 41.52 3.55 R
4621 5561 0.178921 TCCTCTGCTGACCAGGTTCT 60.179 55.0 0.00 0.0 42.05 3.01 R
5691 6883 0.679002 CCAGGTGGTGCAAGAGGATG 60.679 60.0 0.00 0.0 0.00 3.51 R
6686 7884 0.464452 GGGAGGTGATACAACCCTCG 59.536 60.0 0.00 0.0 44.71 4.63 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
67 68 5.560760 GCTTGTGCTATGCTTATTATTCGCA 60.561 40.000 0.00 0.00 35.67 5.10
180 181 4.783242 GCAATTTGCGTACTCTCAGAAAA 58.217 39.130 5.49 0.00 31.71 2.29
263 264 1.461091 GCACTGCCATGCATGCCTAT 61.461 55.000 21.69 0.00 45.39 2.57
300 301 8.997323 CAAGGTTTTTATTTGCATCCAATAACA 58.003 29.630 2.26 0.00 0.00 2.41
302 303 7.334171 AGGTTTTTATTTGCATCCAATAACAGC 59.666 33.333 2.26 3.09 0.00 4.40
303 304 7.118971 GGTTTTTATTTGCATCCAATAACAGCA 59.881 33.333 2.26 0.00 0.00 4.41
313 314 3.633525 TCCAATAACAGCATGCCAGATTC 59.366 43.478 15.66 0.00 42.53 2.52
331 332 1.154035 CGCCGCCAAGGTTTTGATC 60.154 57.895 0.00 0.00 43.70 2.92
349 350 0.392706 TCATGGCGCTACGGATGATT 59.607 50.000 7.64 0.00 0.00 2.57
372 373 1.340405 GGTACGACTCTACCACCAGGA 60.340 57.143 0.00 0.00 36.84 3.86
411 412 6.311723 GCTAAATTTGCGAAACTACTGCTTA 58.688 36.000 0.00 0.00 0.00 3.09
652 653 1.374758 CTGACGACCAGGGTGAAGC 60.375 63.158 0.00 0.00 39.23 3.86
658 659 4.379243 CCAGGGTGAAGCGAGCGT 62.379 66.667 0.00 0.00 0.00 5.07
660 661 3.303135 AGGGTGAAGCGAGCGTCA 61.303 61.111 9.49 9.49 32.43 4.35
667 668 1.002366 GAAGCGAGCGTCAATGTGAT 58.998 50.000 6.16 0.00 0.00 3.06
671 718 0.926155 CGAGCGTCAATGTGATGAGG 59.074 55.000 1.62 0.00 35.46 3.86
680 727 5.063186 CGTCAATGTGATGAGGAGAAGAAAG 59.937 44.000 0.00 0.00 37.38 2.62
684 731 7.551974 TCAATGTGATGAGGAGAAGAAAGAATC 59.448 37.037 0.00 0.00 0.00 2.52
695 742 2.898705 AGAAAGAATCGAGCGCTTGAT 58.101 42.857 30.61 30.61 35.28 2.57
744 791 4.208686 GGCTCTACGGACGGGCAG 62.209 72.222 0.00 0.00 0.00 4.85
745 792 4.874977 GCTCTACGGACGGGCAGC 62.875 72.222 0.00 0.00 0.00 5.25
746 793 4.554363 CTCTACGGACGGGCAGCG 62.554 72.222 0.00 0.00 0.00 5.18
784 941 2.958576 GCGGAATTGTTTCGGCCA 59.041 55.556 2.24 0.00 46.71 5.36
785 942 1.154035 GCGGAATTGTTTCGGCCAG 60.154 57.895 2.24 0.00 46.71 4.85
864 1034 2.642254 CCAGCCCACGTACGGAGAA 61.642 63.158 21.06 0.00 0.00 2.87
865 1035 1.290955 CAGCCCACGTACGGAGAAA 59.709 57.895 21.06 0.00 0.00 2.52
880 1050 4.149396 ACGGAGAAAAGTAACGAAATGACG 59.851 41.667 0.00 0.00 39.31 4.35
931 1104 3.093278 CGCTCCGTTTGATCTGCC 58.907 61.111 0.00 0.00 0.00 4.85
932 1105 1.741401 CGCTCCGTTTGATCTGCCA 60.741 57.895 0.00 0.00 0.00 4.92
933 1106 1.298157 CGCTCCGTTTGATCTGCCAA 61.298 55.000 0.00 0.00 0.00 4.52
934 1107 0.881118 GCTCCGTTTGATCTGCCAAA 59.119 50.000 0.00 0.00 34.03 3.28
935 1108 1.474077 GCTCCGTTTGATCTGCCAAAT 59.526 47.619 0.00 0.00 38.18 2.32
936 1109 2.682856 GCTCCGTTTGATCTGCCAAATA 59.317 45.455 0.00 0.00 38.18 1.40
998 1176 2.640316 AACTCCTCTGGGTGTTTCAC 57.360 50.000 0.00 0.00 44.03 3.18
999 1177 1.507140 ACTCCTCTGGGTGTTTCACA 58.493 50.000 2.41 0.00 36.05 3.58
1006 1184 0.466372 TGGGTGTTTCACAATGCCGA 60.466 50.000 2.41 0.00 35.86 5.54
1118 1302 1.938657 ATCAGCACCGTGAGAGGACG 61.939 60.000 1.65 0.00 39.13 4.79
1481 1693 9.757227 CAGATTTTTGGTTTACCTTTTGTCATA 57.243 29.630 0.00 0.00 36.82 2.15
1527 1739 8.912988 AGTAAAGTGATTGAAATTTGGTTCAGA 58.087 29.630 0.00 0.00 38.69 3.27
1551 2105 7.335422 AGACACAAAAGTATAGCAAGATGGAAG 59.665 37.037 0.00 0.00 0.00 3.46
1580 2134 5.363939 GTCTCTGCATTTGCTCCTAAGTAT 58.636 41.667 3.94 0.00 42.66 2.12
1844 2406 9.979270 GTAGAGTTATGTTTTCACTGATTCATG 57.021 33.333 0.00 0.00 0.00 3.07
1858 2420 6.800408 CACTGATTCATGAAGTGATTGTGTTC 59.200 38.462 17.54 5.94 43.22 3.18
1862 2424 3.187022 TCATGAAGTGATTGTGTTCAGCG 59.813 43.478 0.00 0.00 33.83 5.18
1863 2425 2.832563 TGAAGTGATTGTGTTCAGCGA 58.167 42.857 0.00 0.00 0.00 4.93
1864 2426 2.543848 TGAAGTGATTGTGTTCAGCGAC 59.456 45.455 0.00 0.00 0.00 5.19
1865 2427 2.238942 AGTGATTGTGTTCAGCGACA 57.761 45.000 0.00 0.00 0.00 4.35
1866 2428 2.560504 AGTGATTGTGTTCAGCGACAA 58.439 42.857 0.00 0.00 36.54 3.18
1867 2429 3.141398 AGTGATTGTGTTCAGCGACAAT 58.859 40.909 0.00 0.00 43.82 2.71
1868 2430 4.314961 AGTGATTGTGTTCAGCGACAATA 58.685 39.130 0.00 0.00 41.74 1.90
1869 2431 4.389992 AGTGATTGTGTTCAGCGACAATAG 59.610 41.667 0.00 0.00 41.74 1.73
1870 2432 3.125146 TGATTGTGTTCAGCGACAATAGC 59.875 43.478 0.00 0.00 41.74 2.97
1871 2433 1.438651 TGTGTTCAGCGACAATAGCC 58.561 50.000 0.00 0.00 34.64 3.93
1872 2434 1.270571 TGTGTTCAGCGACAATAGCCA 60.271 47.619 0.00 0.00 34.64 4.75
1873 2435 1.128692 GTGTTCAGCGACAATAGCCAC 59.871 52.381 0.00 0.00 34.64 5.01
1874 2436 0.370273 GTTCAGCGACAATAGCCACG 59.630 55.000 0.00 0.00 34.64 4.94
1875 2437 0.245266 TTCAGCGACAATAGCCACGA 59.755 50.000 0.00 0.00 34.64 4.35
1876 2438 0.245266 TCAGCGACAATAGCCACGAA 59.755 50.000 0.00 0.00 34.64 3.85
1877 2439 0.370273 CAGCGACAATAGCCACGAAC 59.630 55.000 0.00 0.00 34.64 3.95
1878 2440 0.037697 AGCGACAATAGCCACGAACA 60.038 50.000 0.00 0.00 34.64 3.18
1879 2441 1.006832 GCGACAATAGCCACGAACAT 58.993 50.000 0.00 0.00 0.00 2.71
1880 2442 2.159156 AGCGACAATAGCCACGAACATA 60.159 45.455 0.00 0.00 34.64 2.29
1881 2443 2.605818 GCGACAATAGCCACGAACATAA 59.394 45.455 0.00 0.00 0.00 1.90
1882 2444 3.543460 GCGACAATAGCCACGAACATAAC 60.543 47.826 0.00 0.00 0.00 1.89
1883 2445 3.615056 CGACAATAGCCACGAACATAACA 59.385 43.478 0.00 0.00 0.00 2.41
1884 2446 4.092237 CGACAATAGCCACGAACATAACAA 59.908 41.667 0.00 0.00 0.00 2.83
1885 2447 5.545658 ACAATAGCCACGAACATAACAAG 57.454 39.130 0.00 0.00 0.00 3.16
1886 2448 5.242434 ACAATAGCCACGAACATAACAAGA 58.758 37.500 0.00 0.00 0.00 3.02
1887 2449 5.351465 ACAATAGCCACGAACATAACAAGAG 59.649 40.000 0.00 0.00 0.00 2.85
1888 2450 2.076863 AGCCACGAACATAACAAGAGC 58.923 47.619 0.00 0.00 0.00 4.09
1889 2451 1.804151 GCCACGAACATAACAAGAGCA 59.196 47.619 0.00 0.00 0.00 4.26
1890 2452 2.225491 GCCACGAACATAACAAGAGCAA 59.775 45.455 0.00 0.00 0.00 3.91
1891 2453 3.119849 GCCACGAACATAACAAGAGCAAT 60.120 43.478 0.00 0.00 0.00 3.56
1892 2454 4.615912 GCCACGAACATAACAAGAGCAATT 60.616 41.667 0.00 0.00 0.00 2.32
1893 2455 4.853196 CCACGAACATAACAAGAGCAATTG 59.147 41.667 0.00 0.00 36.22 2.32
1894 2456 5.334802 CCACGAACATAACAAGAGCAATTGA 60.335 40.000 10.34 0.00 34.20 2.57
1895 2457 6.317088 CACGAACATAACAAGAGCAATTGAT 58.683 36.000 10.34 1.34 34.20 2.57
1896 2458 6.803320 CACGAACATAACAAGAGCAATTGATT 59.197 34.615 10.34 0.00 34.20 2.57
1897 2459 7.007725 CACGAACATAACAAGAGCAATTGATTC 59.992 37.037 10.34 5.96 34.20 2.52
1898 2460 6.470235 CGAACATAACAAGAGCAATTGATTCC 59.530 38.462 10.34 0.00 34.20 3.01
1899 2461 6.839124 ACATAACAAGAGCAATTGATTCCA 57.161 33.333 10.34 0.00 34.20 3.53
1900 2462 6.624423 ACATAACAAGAGCAATTGATTCCAC 58.376 36.000 10.34 0.00 34.20 4.02
1901 2463 3.837213 ACAAGAGCAATTGATTCCACG 57.163 42.857 10.34 0.59 34.20 4.94
1902 2464 2.489329 ACAAGAGCAATTGATTCCACGG 59.511 45.455 10.34 0.00 34.20 4.94
1903 2465 2.749076 CAAGAGCAATTGATTCCACGGA 59.251 45.455 10.34 0.00 31.55 4.69
1904 2466 3.287867 AGAGCAATTGATTCCACGGAT 57.712 42.857 10.34 0.00 0.00 4.18
1905 2467 2.947652 AGAGCAATTGATTCCACGGATG 59.052 45.455 10.34 0.00 0.00 3.51
1906 2468 7.667797 CAAGAGCAATTGATTCCACGGATGG 62.668 48.000 10.34 0.00 38.74 3.51
1914 2476 2.035626 CCACGGATGGGGCTTGTT 59.964 61.111 0.00 0.00 43.04 2.83
1915 2477 1.301623 CCACGGATGGGGCTTGTTA 59.698 57.895 0.00 0.00 43.04 2.41
1916 2478 0.106719 CCACGGATGGGGCTTGTTAT 60.107 55.000 0.00 0.00 43.04 1.89
1917 2479 1.684869 CCACGGATGGGGCTTGTTATT 60.685 52.381 0.00 0.00 43.04 1.40
1918 2480 2.099405 CACGGATGGGGCTTGTTATTT 58.901 47.619 0.00 0.00 0.00 1.40
1919 2481 3.283751 CACGGATGGGGCTTGTTATTTA 58.716 45.455 0.00 0.00 0.00 1.40
1920 2482 3.315191 CACGGATGGGGCTTGTTATTTAG 59.685 47.826 0.00 0.00 0.00 1.85
1921 2483 3.053917 ACGGATGGGGCTTGTTATTTAGT 60.054 43.478 0.00 0.00 0.00 2.24
1922 2484 3.951680 CGGATGGGGCTTGTTATTTAGTT 59.048 43.478 0.00 0.00 0.00 2.24
1923 2485 4.401202 CGGATGGGGCTTGTTATTTAGTTT 59.599 41.667 0.00 0.00 0.00 2.66
1924 2486 5.105513 CGGATGGGGCTTGTTATTTAGTTTT 60.106 40.000 0.00 0.00 0.00 2.43
1925 2487 6.106003 GGATGGGGCTTGTTATTTAGTTTTG 58.894 40.000 0.00 0.00 0.00 2.44
1926 2488 4.888917 TGGGGCTTGTTATTTAGTTTTGC 58.111 39.130 0.00 0.00 0.00 3.68
1927 2489 4.345257 TGGGGCTTGTTATTTAGTTTTGCA 59.655 37.500 0.00 0.00 0.00 4.08
1928 2490 5.012561 TGGGGCTTGTTATTTAGTTTTGCAT 59.987 36.000 0.00 0.00 0.00 3.96
1929 2491 5.937540 GGGGCTTGTTATTTAGTTTTGCATT 59.062 36.000 0.00 0.00 0.00 3.56
1930 2492 6.429692 GGGGCTTGTTATTTAGTTTTGCATTT 59.570 34.615 0.00 0.00 0.00 2.32
1931 2493 7.360861 GGGGCTTGTTATTTAGTTTTGCATTTC 60.361 37.037 0.00 0.00 0.00 2.17
1932 2494 7.387673 GGGCTTGTTATTTAGTTTTGCATTTCT 59.612 33.333 0.00 0.00 0.00 2.52
1933 2495 8.773645 GGCTTGTTATTTAGTTTTGCATTTCTT 58.226 29.630 0.00 0.00 0.00 2.52
1934 2496 9.797473 GCTTGTTATTTAGTTTTGCATTTCTTC 57.203 29.630 0.00 0.00 0.00 2.87
1936 2498 9.823647 TTGTTATTTAGTTTTGCATTTCTTCCA 57.176 25.926 0.00 0.00 0.00 3.53
1937 2499 9.995003 TGTTATTTAGTTTTGCATTTCTTCCAT 57.005 25.926 0.00 0.00 0.00 3.41
1941 2503 7.775053 TTAGTTTTGCATTTCTTCCATAGGT 57.225 32.000 0.00 0.00 0.00 3.08
1942 2504 6.029346 AGTTTTGCATTTCTTCCATAGGTG 57.971 37.500 0.00 0.00 0.00 4.00
1944 2506 3.737559 TGCATTTCTTCCATAGGTGGT 57.262 42.857 0.00 0.00 46.16 4.16
1945 2507 4.853468 TGCATTTCTTCCATAGGTGGTA 57.147 40.909 0.00 0.00 46.16 3.25
1946 2508 4.780815 TGCATTTCTTCCATAGGTGGTAG 58.219 43.478 0.00 0.00 46.16 3.18
1947 2509 4.473196 TGCATTTCTTCCATAGGTGGTAGA 59.527 41.667 0.36 0.36 46.44 2.59
1953 2515 6.978674 TCTTCCATAGGTGGTAGAGTTATG 57.021 41.667 0.36 0.00 44.20 1.90
1954 2516 6.441222 TCTTCCATAGGTGGTAGAGTTATGT 58.559 40.000 0.36 0.00 44.20 2.29
1955 2517 6.901300 TCTTCCATAGGTGGTAGAGTTATGTT 59.099 38.462 0.36 0.00 44.20 2.71
1956 2518 7.402071 TCTTCCATAGGTGGTAGAGTTATGTTT 59.598 37.037 0.36 0.00 44.20 2.83
1957 2519 7.504926 TCCATAGGTGGTAGAGTTATGTTTT 57.495 36.000 0.00 0.00 46.16 2.43
1958 2520 7.562135 TCCATAGGTGGTAGAGTTATGTTTTC 58.438 38.462 0.00 0.00 46.16 2.29
1959 2521 7.181305 TCCATAGGTGGTAGAGTTATGTTTTCA 59.819 37.037 0.00 0.00 46.16 2.69
1960 2522 7.280205 CCATAGGTGGTAGAGTTATGTTTTCAC 59.720 40.741 0.00 0.00 40.83 3.18
1961 2523 6.435292 AGGTGGTAGAGTTATGTTTTCACT 57.565 37.500 0.00 0.00 0.00 3.41
1962 2524 6.231211 AGGTGGTAGAGTTATGTTTTCACTG 58.769 40.000 0.00 0.00 0.00 3.66
1963 2525 6.042781 AGGTGGTAGAGTTATGTTTTCACTGA 59.957 38.462 0.00 0.00 0.00 3.41
1964 2526 6.879458 GGTGGTAGAGTTATGTTTTCACTGAT 59.121 38.462 0.00 0.00 0.00 2.90
1965 2527 7.390718 GGTGGTAGAGTTATGTTTTCACTGATT 59.609 37.037 0.00 0.00 0.00 2.57
1966 2528 8.443937 GTGGTAGAGTTATGTTTTCACTGATTC 58.556 37.037 0.00 0.00 0.00 2.52
1967 2529 8.154203 TGGTAGAGTTATGTTTTCACTGATTCA 58.846 33.333 0.00 0.00 0.00 2.57
1968 2530 9.167311 GGTAGAGTTATGTTTTCACTGATTCAT 57.833 33.333 0.00 0.00 0.00 2.57
1969 2531 9.979270 GTAGAGTTATGTTTTCACTGATTCATG 57.021 33.333 0.00 0.00 0.00 3.07
1970 2532 8.853077 AGAGTTATGTTTTCACTGATTCATGA 57.147 30.769 0.00 0.00 0.00 3.07
1971 2533 9.288576 AGAGTTATGTTTTCACTGATTCATGAA 57.711 29.630 11.26 11.26 33.03 2.57
1972 2534 9.552114 GAGTTATGTTTTCACTGATTCATGAAG 57.448 33.333 14.54 2.68 36.26 3.02
1973 2535 9.071276 AGTTATGTTTTCACTGATTCATGAAGT 57.929 29.630 14.54 3.37 36.26 3.01
1974 2536 9.121517 GTTATGTTTTCACTGATTCATGAAGTG 57.878 33.333 16.66 16.66 42.17 3.16
1975 2537 6.940831 TGTTTTCACTGATTCATGAAGTGA 57.059 33.333 20.02 20.02 46.44 3.41
1980 2542 6.490566 TCACTGATTCATGAAGTGATTGTG 57.509 37.500 20.02 17.09 44.01 3.33
1981 2543 5.999600 TCACTGATTCATGAAGTGATTGTGT 59.000 36.000 20.02 6.31 44.01 3.72
1982 2544 6.487668 TCACTGATTCATGAAGTGATTGTGTT 59.512 34.615 20.02 0.00 44.01 3.32
1983 2545 6.800408 CACTGATTCATGAAGTGATTGTGTTC 59.200 38.462 17.54 5.94 43.22 3.18
1984 2546 6.487668 ACTGATTCATGAAGTGATTGTGTTCA 59.512 34.615 14.54 7.47 36.54 3.18
1985 2547 6.905578 TGATTCATGAAGTGATTGTGTTCAG 58.094 36.000 14.54 0.00 36.54 3.02
1986 2548 6.487668 TGATTCATGAAGTGATTGTGTTCAGT 59.512 34.615 14.54 0.00 36.54 3.41
2046 2608 8.616942 TGCGTATTGTTTGCAGTATGTAATAAT 58.383 29.630 0.00 0.00 41.29 1.28
2047 2609 8.891928 GCGTATTGTTTGCAGTATGTAATAATG 58.108 33.333 0.00 0.00 46.84 1.90
2052 2614 7.026562 TGTTTGCAGTATGTAATAATGTGTGC 58.973 34.615 0.00 0.00 45.92 4.57
2079 2642 0.740149 TGGCTCAAAATATGGCAGCG 59.260 50.000 0.00 0.00 31.34 5.18
2172 2737 7.264373 AGCAAGCATACACCTTTAATATGTC 57.736 36.000 0.00 0.00 0.00 3.06
2246 2811 3.149196 CCAGTGCTGTAGTTCACCAATT 58.851 45.455 0.00 0.00 33.90 2.32
2556 3301 4.080807 TCCGGTGCTCTTTTATGATTACCA 60.081 41.667 0.00 0.00 0.00 3.25
2563 3308 6.599244 TGCTCTTTTATGATTACCACTCCTTG 59.401 38.462 0.00 0.00 0.00 3.61
2697 3451 6.765989 TGAATGTAATATCTGCAGGTTGGTAC 59.234 38.462 15.13 10.23 0.00 3.34
2969 3729 0.179156 CAATGGCATTGACCAGTCGC 60.179 55.000 31.50 0.00 44.71 5.19
2993 3753 2.146342 GCAGTATCAACCCGGATCATG 58.854 52.381 0.73 0.00 0.00 3.07
3004 3764 3.181440 ACCCGGATCATGATGTAAATGCT 60.181 43.478 14.30 0.00 0.00 3.79
3067 3827 4.090066 CGAGAGAGTGTAACCGATTTTGTG 59.910 45.833 0.00 0.00 37.80 3.33
3069 3829 5.230942 AGAGAGTGTAACCGATTTTGTGAG 58.769 41.667 0.00 0.00 37.80 3.51
3072 3832 2.477375 GTGTAACCGATTTTGTGAGCGA 59.523 45.455 0.00 0.00 0.00 4.93
3138 3898 4.350816 TCCCGATTTCCATGAACCATCTAT 59.649 41.667 0.00 0.00 0.00 1.98
3169 3938 1.757699 GACCGCCCTCAAGAAGATACT 59.242 52.381 0.00 0.00 0.00 2.12
3233 4011 8.552034 GTCCAAGTAGTGATAATAGAAACATGC 58.448 37.037 0.00 0.00 0.00 4.06
3294 4072 3.309954 GCTTTGCTTCGAGGTAATACTGG 59.690 47.826 0.00 0.00 0.00 4.00
3403 4181 8.306761 GGAGACAAGTACAAAAATTCATTCCAT 58.693 33.333 0.00 0.00 0.00 3.41
3516 4294 2.235650 TGGCTCCAGATTCTGACAGAAG 59.764 50.000 21.78 9.27 37.69 2.85
3537 4315 3.207474 CACTGATGCTTTACTGGCAAC 57.793 47.619 0.00 0.00 43.14 4.17
3572 4350 4.640771 AGATCCTTGCCTGAGTTTGTTA 57.359 40.909 0.00 0.00 0.00 2.41
3695 4473 3.052869 TGAGGGTAGTGCTAGGATTGAGA 60.053 47.826 0.00 0.00 0.00 3.27
3820 4598 3.691609 CCAACCTTCTACAAGAGAATGCC 59.308 47.826 0.00 0.00 43.39 4.40
3853 4631 9.284968 CCTTCTACATTGTTTAAGGAGAAGAAA 57.715 33.333 19.38 0.00 39.26 2.52
3879 4660 4.779993 AGGTTCTTCTGGAAGTCAGTTT 57.220 40.909 9.73 0.00 43.76 2.66
3941 4722 8.416329 GCAACATCTTGGAAAATAATACATCCT 58.584 33.333 0.00 0.00 33.02 3.24
3963 4744 3.741245 TGGTAGGAAGACTGCTCTAGT 57.259 47.619 0.00 0.00 44.02 2.57
4052 4839 4.813161 CCGCTTGTCTTCTATCATTGATGT 59.187 41.667 9.46 0.00 0.00 3.06
4053 4840 5.295292 CCGCTTGTCTTCTATCATTGATGTT 59.705 40.000 9.46 0.00 0.00 2.71
4123 4910 4.698304 CAGGGCTTTACGGAACAAGATTTA 59.302 41.667 0.00 0.00 0.00 1.40
4131 4918 9.221775 CTTTACGGAACAAGATTTATGCATAAC 57.778 33.333 18.70 8.65 0.00 1.89
4147 4934 4.097741 TGCATAACATGTGGTAAAGATGGC 59.902 41.667 0.00 0.00 33.81 4.40
4337 5124 1.251251 ATCTGCTTTCCTTGGCACAC 58.749 50.000 0.00 0.00 39.29 3.82
4496 5430 1.197430 AGAACCTGGTGAGCAGAGGG 61.197 60.000 14.03 0.00 0.00 4.30
4668 5608 4.445385 GCAGAAAACAAATGCTACAAGTGG 59.555 41.667 0.00 0.00 37.00 4.00
4751 5691 5.447279 GCACCCAATAAAGATTGTGTACTCG 60.447 44.000 0.00 0.00 40.87 4.18
4782 5737 3.065925 AGAAAACAAGTTGAGCAGTCTGC 59.934 43.478 17.48 17.48 45.46 4.26
4830 5785 7.658575 AGATGGTAATGGCAATTCATTTTATGC 59.341 33.333 0.00 0.00 38.24 3.14
4833 5788 6.762661 GGTAATGGCAATTCATTTTATGCTGT 59.237 34.615 0.00 0.00 38.24 4.40
5046 6001 5.799213 AGAAAAGGAGACAGTGGTATCTTG 58.201 41.667 0.00 0.00 35.59 3.02
5106 6061 1.340889 GCCTTCACCATCAAGCAAACA 59.659 47.619 0.00 0.00 0.00 2.83
5115 6079 6.015603 TCACCATCAAGCAAACAATATCAACA 60.016 34.615 0.00 0.00 0.00 3.33
5135 6099 6.534436 TCAACACAAGCGTTAGTAAGTGTTAA 59.466 34.615 13.96 1.99 45.25 2.01
5311 6280 2.039746 TGTAGGGTGGATGTTTGTGAGG 59.960 50.000 0.00 0.00 0.00 3.86
5554 6535 9.056005 TCATGGTTAGAATGAAGTTACATATGC 57.944 33.333 1.58 0.00 31.17 3.14
5570 6552 9.119329 GTTACATATGCGATAGTGAAGTTAGAG 57.881 37.037 1.58 0.00 39.35 2.43
5657 6849 7.203910 TGTAATGGCGTCTGTTTTTGTAATTT 58.796 30.769 0.00 0.00 0.00 1.82
5688 6880 2.019249 GCCATATCTGTCTTTGCAGCA 58.981 47.619 0.00 0.00 36.49 4.41
5689 6881 2.621998 GCCATATCTGTCTTTGCAGCAT 59.378 45.455 0.00 0.00 36.49 3.79
5691 6883 4.792057 GCCATATCTGTCTTTGCAGCATTC 60.792 45.833 0.00 0.00 36.49 2.67
5808 7004 7.065563 ACTGACATTACTGATGCTGAAATCTTC 59.934 37.037 0.00 0.00 39.47 2.87
5878 7074 5.294306 GTGTTCTTGCTAGCATGCTAACATA 59.706 40.000 26.80 17.24 35.29 2.29
6114 7310 2.283298 CACCTAGTGCAGCTATTGTGG 58.717 52.381 0.00 0.00 32.86 4.17
6440 7638 4.196193 CAAAGACAACACCAACAGGTCTA 58.804 43.478 0.00 0.00 37.82 2.59
6441 7639 4.706842 AAGACAACACCAACAGGTCTAT 57.293 40.909 0.00 0.00 37.82 1.98
6532 7730 5.239525 GCACATAGGATTACCAGACCATTTC 59.760 44.000 0.00 0.00 38.94 2.17
6535 7733 2.172717 AGGATTACCAGACCATTTCCCG 59.827 50.000 0.00 0.00 38.94 5.14
6537 7735 3.617284 GATTACCAGACCATTTCCCGTT 58.383 45.455 0.00 0.00 0.00 4.44
6589 7787 3.010584 ACCAAAGAACTAGCCATGGACAT 59.989 43.478 18.40 2.45 0.00 3.06
6662 7860 6.512415 GCGAGATCTTATGGGTTTCATTTCTG 60.512 42.308 0.00 0.00 37.30 3.02
6686 7884 2.670019 ACCCTAACTTGTTTGGGACC 57.330 50.000 29.81 0.00 42.11 4.46
6720 7929 6.786967 TCACCTCCCTAGTTAGAACAATAC 57.213 41.667 0.00 0.00 0.00 1.89
6785 7994 3.845781 TCTGCATCCCTAATCCACTTC 57.154 47.619 0.00 0.00 0.00 3.01
6794 8003 5.285401 TCCCTAATCCACTTCTAATGACCA 58.715 41.667 0.00 0.00 0.00 4.02
6882 8091 2.027377 GCCCACCATATCTCATCAGGAG 60.027 54.545 0.00 0.00 45.49 3.69
7016 8225 6.952773 TTTACAGCACACTCAGGTTTTATT 57.047 33.333 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.397832 TAGTCAAACGGCGGCCCC 62.398 66.667 14.55 0.00 0.00 5.80
17 18 3.497031 GGCTAGTCAAACGGCGGC 61.497 66.667 13.24 0.00 0.00 6.53
18 19 3.186047 CGGCTAGTCAAACGGCGG 61.186 66.667 13.24 0.00 42.10 6.13
19 20 2.901051 ATCCGGCTAGTCAAACGGCG 62.901 60.000 4.80 4.80 45.58 6.46
53 54 2.539688 CACTCGCTGCGAATAATAAGCA 59.460 45.455 25.86 0.00 34.74 3.91
61 62 0.179134 GACTACCACTCGCTGCGAAT 60.179 55.000 25.86 14.10 34.74 3.34
144 145 9.445786 GTACGCAAATTGCATGTAATAGTTTAT 57.554 29.630 18.65 0.00 45.36 1.40
145 146 8.670135 AGTACGCAAATTGCATGTAATAGTTTA 58.330 29.630 18.65 0.00 45.36 2.01
153 154 4.249661 TGAGAGTACGCAAATTGCATGTA 58.750 39.130 18.65 9.89 45.36 2.29
227 228 5.157067 GCAGTGCCTTCTTATTTCTTTGTC 58.843 41.667 2.85 0.00 0.00 3.18
263 264 3.878160 AAAAACCTTGCACGGAAGAAA 57.122 38.095 17.43 0.00 0.00 2.52
300 301 2.898840 CGGCGAATCTGGCATGCT 60.899 61.111 18.92 0.00 0.00 3.79
302 303 3.957535 GGCGGCGAATCTGGCATG 61.958 66.667 12.98 0.00 45.28 4.06
313 314 1.154035 GATCAAAACCTTGGCGGCG 60.154 57.895 0.51 0.51 35.61 6.46
331 332 0.514255 CAATCATCCGTAGCGCCATG 59.486 55.000 2.29 0.00 0.00 3.66
372 373 8.934973 GCAAATTTAGCGATCGTTCTAATTAT 57.065 30.769 17.81 5.60 0.00 1.28
398 399 8.443937 AGTCGATCAAATTTAAGCAGTAGTTTC 58.556 33.333 0.00 0.00 0.00 2.78
402 403 6.313905 ACCAGTCGATCAAATTTAAGCAGTAG 59.686 38.462 0.00 0.00 0.00 2.57
411 412 4.636206 GGCTCTTACCAGTCGATCAAATTT 59.364 41.667 0.00 0.00 0.00 1.82
469 470 8.059461 TCTCTCCTGGTAATTGAGAATACAGTA 58.941 37.037 0.00 0.00 34.91 2.74
472 473 7.255625 CGATCTCTCCTGGTAATTGAGAATACA 60.256 40.741 0.00 0.00 37.34 2.29
530 531 1.738432 GTGCGTGTTCCGAACTTTTC 58.262 50.000 12.43 0.81 42.22 2.29
531 532 3.909957 GTGCGTGTTCCGAACTTTT 57.090 47.368 12.43 0.00 42.22 2.27
564 565 3.554692 GATTGACCGGCACTCGCG 61.555 66.667 0.00 0.00 39.92 5.87
566 567 2.456119 GCTGATTGACCGGCACTCG 61.456 63.158 0.00 3.10 38.29 4.18
646 647 0.179240 CACATTGACGCTCGCTTCAC 60.179 55.000 0.00 0.00 0.00 3.18
647 648 0.319469 TCACATTGACGCTCGCTTCA 60.319 50.000 0.00 0.00 0.00 3.02
650 651 0.108662 TCATCACATTGACGCTCGCT 60.109 50.000 0.00 0.00 0.00 4.93
652 653 0.926155 CCTCATCACATTGACGCTCG 59.074 55.000 0.00 0.00 0.00 5.03
658 659 6.364568 TCTTTCTTCTCCTCATCACATTGA 57.635 37.500 0.00 0.00 0.00 2.57
660 661 6.538021 CGATTCTTTCTTCTCCTCATCACATT 59.462 38.462 0.00 0.00 0.00 2.71
667 668 3.428180 CGCTCGATTCTTTCTTCTCCTCA 60.428 47.826 0.00 0.00 0.00 3.86
671 718 2.535331 AGCGCTCGATTCTTTCTTCTC 58.465 47.619 2.64 0.00 0.00 2.87
680 727 3.299020 CACAAAAATCAAGCGCTCGATTC 59.701 43.478 23.04 0.00 30.64 2.52
684 731 0.704551 GCACAAAAATCAAGCGCTCG 59.295 50.000 12.06 0.00 0.00 5.03
695 742 0.941542 CGAGGTTCCTCGCACAAAAA 59.058 50.000 24.74 0.00 47.00 1.94
731 778 3.636313 TTTCGCTGCCCGTCCGTAG 62.636 63.158 0.00 0.00 38.35 3.51
735 782 3.423154 CAGTTTCGCTGCCCGTCC 61.423 66.667 0.00 0.00 38.52 4.79
743 790 2.357517 CGGGCAGACAGTTTCGCT 60.358 61.111 0.00 0.00 0.00 4.93
744 791 4.090057 GCGGGCAGACAGTTTCGC 62.090 66.667 0.00 0.00 36.51 4.70
745 792 3.777925 CGCGGGCAGACAGTTTCG 61.778 66.667 0.00 0.00 0.00 3.46
746 793 4.090057 GCGCGGGCAGACAGTTTC 62.090 66.667 20.76 0.00 39.62 2.78
793 950 4.228567 GAGGGAGCGCTACAGCCC 62.229 72.222 23.75 22.44 41.00 5.19
864 1034 1.808343 GGGCCGTCATTTCGTTACTTT 59.192 47.619 0.00 0.00 0.00 2.66
865 1035 1.270947 TGGGCCGTCATTTCGTTACTT 60.271 47.619 0.00 0.00 0.00 2.24
919 1092 6.863126 ACTTCTTTTATTTGGCAGATCAAACG 59.137 34.615 0.00 0.00 39.13 3.60
998 1176 1.452108 GAGAAGGGGGTCGGCATTG 60.452 63.158 0.00 0.00 0.00 2.82
999 1177 2.680370 GGAGAAGGGGGTCGGCATT 61.680 63.158 0.00 0.00 0.00 3.56
1118 1302 0.530870 GTGGTCGGAATAGGCAGAGC 60.531 60.000 0.00 0.00 0.00 4.09
1527 1739 7.119846 GTCTTCCATCTTGCTATACTTTTGTGT 59.880 37.037 0.00 0.00 0.00 3.72
1551 2105 0.166814 GCAAATGCAGAGACGGTGTC 59.833 55.000 0.00 0.00 41.59 3.67
1580 2134 9.162764 GGACAAGATTTAATCTAACTAGCACAA 57.837 33.333 7.98 0.00 39.08 3.33
1844 2406 2.543848 TGTCGCTGAACACAATCACTTC 59.456 45.455 0.00 0.00 0.00 3.01
1858 2420 0.370273 GTTCGTGGCTATTGTCGCTG 59.630 55.000 0.00 0.00 0.00 5.18
1862 2424 5.350365 TCTTGTTATGTTCGTGGCTATTGTC 59.650 40.000 0.00 0.00 0.00 3.18
1863 2425 5.242434 TCTTGTTATGTTCGTGGCTATTGT 58.758 37.500 0.00 0.00 0.00 2.71
1864 2426 5.727791 GCTCTTGTTATGTTCGTGGCTATTG 60.728 44.000 0.00 0.00 0.00 1.90
1865 2427 4.332819 GCTCTTGTTATGTTCGTGGCTATT 59.667 41.667 0.00 0.00 0.00 1.73
1866 2428 3.871594 GCTCTTGTTATGTTCGTGGCTAT 59.128 43.478 0.00 0.00 0.00 2.97
1867 2429 3.259064 GCTCTTGTTATGTTCGTGGCTA 58.741 45.455 0.00 0.00 0.00 3.93
1868 2430 2.076863 GCTCTTGTTATGTTCGTGGCT 58.923 47.619 0.00 0.00 0.00 4.75
1869 2431 1.804151 TGCTCTTGTTATGTTCGTGGC 59.196 47.619 0.00 0.00 0.00 5.01
1870 2432 4.685169 ATTGCTCTTGTTATGTTCGTGG 57.315 40.909 0.00 0.00 0.00 4.94
1871 2433 5.688823 TCAATTGCTCTTGTTATGTTCGTG 58.311 37.500 0.00 0.00 0.00 4.35
1872 2434 5.940192 TCAATTGCTCTTGTTATGTTCGT 57.060 34.783 0.00 0.00 0.00 3.85
1873 2435 6.470235 GGAATCAATTGCTCTTGTTATGTTCG 59.530 38.462 0.00 0.00 0.00 3.95
1874 2436 7.274250 GTGGAATCAATTGCTCTTGTTATGTTC 59.726 37.037 0.00 0.00 0.00 3.18
1875 2437 7.092716 GTGGAATCAATTGCTCTTGTTATGTT 58.907 34.615 0.00 0.00 0.00 2.71
1876 2438 6.623549 CGTGGAATCAATTGCTCTTGTTATGT 60.624 38.462 0.00 0.00 0.00 2.29
1877 2439 5.740569 CGTGGAATCAATTGCTCTTGTTATG 59.259 40.000 0.00 0.00 0.00 1.90
1878 2440 5.163622 CCGTGGAATCAATTGCTCTTGTTAT 60.164 40.000 0.00 0.00 0.00 1.89
1879 2441 4.155826 CCGTGGAATCAATTGCTCTTGTTA 59.844 41.667 0.00 0.00 0.00 2.41
1880 2442 3.057315 CCGTGGAATCAATTGCTCTTGTT 60.057 43.478 0.00 0.00 0.00 2.83
1881 2443 2.489329 CCGTGGAATCAATTGCTCTTGT 59.511 45.455 0.00 0.00 0.00 3.16
1882 2444 2.749076 TCCGTGGAATCAATTGCTCTTG 59.251 45.455 0.00 0.00 0.00 3.02
1883 2445 3.071874 TCCGTGGAATCAATTGCTCTT 57.928 42.857 0.00 0.00 0.00 2.85
1884 2446 2.787473 TCCGTGGAATCAATTGCTCT 57.213 45.000 0.00 0.00 0.00 4.09
1885 2447 3.344904 CATCCGTGGAATCAATTGCTC 57.655 47.619 0.00 0.00 0.00 4.26
1897 2459 0.106719 ATAACAAGCCCCATCCGTGG 60.107 55.000 0.00 0.00 45.61 4.94
1898 2460 1.762708 AATAACAAGCCCCATCCGTG 58.237 50.000 0.00 0.00 0.00 4.94
1899 2461 2.525105 AAATAACAAGCCCCATCCGT 57.475 45.000 0.00 0.00 0.00 4.69
1900 2462 3.551846 ACTAAATAACAAGCCCCATCCG 58.448 45.455 0.00 0.00 0.00 4.18
1901 2463 5.932619 AAACTAAATAACAAGCCCCATCC 57.067 39.130 0.00 0.00 0.00 3.51
1902 2464 5.580691 GCAAAACTAAATAACAAGCCCCATC 59.419 40.000 0.00 0.00 0.00 3.51
1903 2465 5.012561 TGCAAAACTAAATAACAAGCCCCAT 59.987 36.000 0.00 0.00 0.00 4.00
1904 2466 4.345257 TGCAAAACTAAATAACAAGCCCCA 59.655 37.500 0.00 0.00 0.00 4.96
1905 2467 4.888917 TGCAAAACTAAATAACAAGCCCC 58.111 39.130 0.00 0.00 0.00 5.80
1906 2468 7.387673 AGAAATGCAAAACTAAATAACAAGCCC 59.612 33.333 0.00 0.00 0.00 5.19
1907 2469 8.310406 AGAAATGCAAAACTAAATAACAAGCC 57.690 30.769 0.00 0.00 0.00 4.35
1908 2470 9.797473 GAAGAAATGCAAAACTAAATAACAAGC 57.203 29.630 0.00 0.00 0.00 4.01
1910 2472 9.823647 TGGAAGAAATGCAAAACTAAATAACAA 57.176 25.926 0.00 0.00 0.00 2.83
1911 2473 9.995003 ATGGAAGAAATGCAAAACTAAATAACA 57.005 25.926 0.00 0.00 30.96 2.41
1915 2477 8.815912 ACCTATGGAAGAAATGCAAAACTAAAT 58.184 29.630 0.00 0.00 30.96 1.40
1916 2478 8.087750 CACCTATGGAAGAAATGCAAAACTAAA 58.912 33.333 0.00 0.00 30.96 1.85
1917 2479 7.601856 CACCTATGGAAGAAATGCAAAACTAA 58.398 34.615 0.00 0.00 30.96 2.24
1918 2480 7.156876 CACCTATGGAAGAAATGCAAAACTA 57.843 36.000 0.00 0.00 30.96 2.24
1919 2481 6.029346 CACCTATGGAAGAAATGCAAAACT 57.971 37.500 0.00 0.00 30.96 2.66
1935 2497 8.041323 AGTGAAAACATAACTCTACCACCTATG 58.959 37.037 0.00 0.00 0.00 2.23
1936 2498 8.041323 CAGTGAAAACATAACTCTACCACCTAT 58.959 37.037 0.00 0.00 0.00 2.57
1937 2499 7.233962 TCAGTGAAAACATAACTCTACCACCTA 59.766 37.037 0.00 0.00 0.00 3.08
1938 2500 6.042781 TCAGTGAAAACATAACTCTACCACCT 59.957 38.462 0.00 0.00 0.00 4.00
1939 2501 6.228258 TCAGTGAAAACATAACTCTACCACC 58.772 40.000 0.00 0.00 0.00 4.61
1940 2502 7.907214 ATCAGTGAAAACATAACTCTACCAC 57.093 36.000 0.00 0.00 0.00 4.16
1941 2503 8.154203 TGAATCAGTGAAAACATAACTCTACCA 58.846 33.333 0.00 0.00 0.00 3.25
1942 2504 8.547967 TGAATCAGTGAAAACATAACTCTACC 57.452 34.615 0.00 0.00 0.00 3.18
1943 2505 9.979270 CATGAATCAGTGAAAACATAACTCTAC 57.021 33.333 0.00 0.00 0.00 2.59
1944 2506 9.942850 TCATGAATCAGTGAAAACATAACTCTA 57.057 29.630 0.00 0.00 0.00 2.43
1945 2507 8.853077 TCATGAATCAGTGAAAACATAACTCT 57.147 30.769 0.00 0.00 0.00 3.24
1946 2508 9.552114 CTTCATGAATCAGTGAAAACATAACTC 57.448 33.333 8.96 0.00 34.26 3.01
1947 2509 9.071276 ACTTCATGAATCAGTGAAAACATAACT 57.929 29.630 8.96 0.00 34.26 2.24
1948 2510 9.121517 CACTTCATGAATCAGTGAAAACATAAC 57.878 33.333 17.54 0.00 40.43 1.89
1949 2511 9.065798 TCACTTCATGAATCAGTGAAAACATAA 57.934 29.630 21.13 2.20 43.12 1.90
1950 2512 8.620116 TCACTTCATGAATCAGTGAAAACATA 57.380 30.769 21.13 2.79 43.12 2.29
1951 2513 7.514784 TCACTTCATGAATCAGTGAAAACAT 57.485 32.000 21.13 0.63 43.12 2.71
1952 2514 6.940831 TCACTTCATGAATCAGTGAAAACA 57.059 33.333 21.13 3.97 43.12 2.83
1958 2520 6.250344 ACACAATCACTTCATGAATCAGTG 57.750 37.500 16.66 16.66 41.93 3.66
1959 2521 6.487668 TGAACACAATCACTTCATGAATCAGT 59.512 34.615 8.96 0.00 41.93 3.41
1960 2522 6.905578 TGAACACAATCACTTCATGAATCAG 58.094 36.000 8.96 0.00 41.93 2.90
1961 2523 6.487668 ACTGAACACAATCACTTCATGAATCA 59.512 34.615 8.96 4.87 41.93 2.57
1962 2524 6.800408 CACTGAACACAATCACTTCATGAATC 59.200 38.462 8.96 0.06 41.93 2.52
1963 2525 6.487668 TCACTGAACACAATCACTTCATGAAT 59.512 34.615 8.96 0.00 41.93 2.57
1964 2526 5.821995 TCACTGAACACAATCACTTCATGAA 59.178 36.000 8.12 8.12 41.93 2.57
1965 2527 5.237127 GTCACTGAACACAATCACTTCATGA 59.763 40.000 0.00 0.00 43.13 3.07
1966 2528 5.007921 TGTCACTGAACACAATCACTTCATG 59.992 40.000 0.00 0.00 0.00 3.07
1967 2529 5.125356 TGTCACTGAACACAATCACTTCAT 58.875 37.500 0.00 0.00 0.00 2.57
1968 2530 4.512484 TGTCACTGAACACAATCACTTCA 58.488 39.130 0.00 0.00 0.00 3.02
1969 2531 5.484173 TTGTCACTGAACACAATCACTTC 57.516 39.130 0.00 0.00 0.00 3.01
1970 2532 6.293626 GCTATTGTCACTGAACACAATCACTT 60.294 38.462 0.67 0.00 41.37 3.16
1971 2533 5.180117 GCTATTGTCACTGAACACAATCACT 59.820 40.000 0.67 0.00 41.37 3.41
1972 2534 5.385617 GCTATTGTCACTGAACACAATCAC 58.614 41.667 0.67 0.00 41.37 3.06
1973 2535 4.455533 GGCTATTGTCACTGAACACAATCA 59.544 41.667 0.67 0.00 41.37 2.57
1974 2536 4.455533 TGGCTATTGTCACTGAACACAATC 59.544 41.667 0.67 0.00 41.37 2.67
1975 2537 4.216257 GTGGCTATTGTCACTGAACACAAT 59.784 41.667 4.56 3.04 44.72 2.71
1976 2538 3.563808 GTGGCTATTGTCACTGAACACAA 59.436 43.478 4.56 0.00 44.72 3.33
1977 2539 3.138304 GTGGCTATTGTCACTGAACACA 58.862 45.455 4.56 0.00 44.72 3.72
1978 2540 2.157668 CGTGGCTATTGTCACTGAACAC 59.842 50.000 10.11 0.00 45.84 3.32
1979 2541 2.036604 TCGTGGCTATTGTCACTGAACA 59.963 45.455 10.11 0.00 45.84 3.18
1980 2542 2.683968 TCGTGGCTATTGTCACTGAAC 58.316 47.619 10.11 0.00 45.84 3.18
1981 2543 3.064207 GTTCGTGGCTATTGTCACTGAA 58.936 45.455 10.11 11.35 45.84 3.02
1982 2544 2.036604 TGTTCGTGGCTATTGTCACTGA 59.963 45.455 10.11 6.38 45.84 3.41
1983 2545 2.412870 TGTTCGTGGCTATTGTCACTG 58.587 47.619 10.11 4.26 45.84 3.66
1984 2546 2.831685 TGTTCGTGGCTATTGTCACT 57.168 45.000 10.11 0.00 45.84 3.41
1985 2547 4.390603 TGTTATGTTCGTGGCTATTGTCAC 59.609 41.667 1.49 1.49 44.68 3.67
1986 2548 4.570930 TGTTATGTTCGTGGCTATTGTCA 58.429 39.130 0.00 0.00 0.00 3.58
2046 2608 3.070476 TGAGCCATTGATAAGCACACA 57.930 42.857 0.00 0.00 0.00 3.72
2047 2609 4.439305 TTTGAGCCATTGATAAGCACAC 57.561 40.909 0.00 0.00 0.00 3.82
2052 2614 6.751157 TGCCATATTTTGAGCCATTGATAAG 58.249 36.000 0.00 0.00 0.00 1.73
2079 2642 5.877012 TGAGATGCCTGTCAGAATTTAGAAC 59.123 40.000 0.00 0.00 0.00 3.01
2193 2758 5.238583 ACAACTCATTAGGTACAAGCAGAC 58.761 41.667 0.00 0.00 0.00 3.51
2556 3301 1.053424 TTCGCCAAGGTACAAGGAGT 58.947 50.000 0.00 0.00 0.00 3.85
2563 3308 3.438781 TGATGATTGTTTCGCCAAGGTAC 59.561 43.478 0.00 0.00 0.00 3.34
2697 3451 4.013267 TCTTTCTCCAAGCTTCCTGAAG 57.987 45.455 0.00 2.48 41.24 3.02
2958 3718 1.595109 CTGCACAGCGACTGGTCAA 60.595 57.895 10.80 0.00 35.51 3.18
2969 3729 0.249120 TCCGGGTTGATACTGCACAG 59.751 55.000 0.00 0.00 0.00 3.66
3038 3798 2.729467 CGGTTACACTCTCTCGCTGAAG 60.729 54.545 0.00 0.00 0.00 3.02
3067 3827 5.273944 ACATTTCTTGTGAAAGTTTCGCTC 58.726 37.500 25.23 12.62 44.25 5.03
3169 3938 3.118223 TGACACTGACACCAACACCAATA 60.118 43.478 0.00 0.00 0.00 1.90
3233 4011 1.524621 CAGGCTCGGCTGTAATGGG 60.525 63.158 11.87 0.00 0.00 4.00
3294 4072 3.667960 CGCAACCTGCTTTGACATAAGTC 60.668 47.826 0.00 0.00 42.25 3.01
3403 4181 7.310485 CCATGTGATCTCTCTCCATCATTATCA 60.310 40.741 0.00 0.00 31.71 2.15
3537 4315 5.065731 GGCAAGGATCTTGTTTCAGATGTAG 59.934 44.000 9.07 0.00 33.36 2.74
3572 4350 1.192146 ACGCCTGTACCATCCACAGT 61.192 55.000 2.17 0.00 41.52 3.55
3695 4473 3.138283 TGACCAGAATCCTTTTCCACTGT 59.862 43.478 0.00 0.00 0.00 3.55
3820 4598 2.496899 ACAATGTAGAAGGCCCTGTG 57.503 50.000 0.00 0.00 0.00 3.66
3853 4631 5.782845 ACTGACTTCCAGAAGAACCTTATCT 59.217 40.000 14.19 0.00 45.78 1.98
3913 4694 6.559810 TGTATTATTTTCCAAGATGTTGCCG 58.440 36.000 0.00 0.00 31.64 5.69
3941 4722 5.390087 ACTAGAGCAGTCTTCCTACCATA 57.610 43.478 0.00 0.00 33.84 2.74
3963 4744 0.241749 CGCATTGCAGCAAGGAGAAA 59.758 50.000 23.70 0.00 27.31 2.52
4052 4839 3.449377 TGACTACAGGACGGCATATTGAA 59.551 43.478 0.00 0.00 0.00 2.69
4053 4840 3.028130 TGACTACAGGACGGCATATTGA 58.972 45.455 0.00 0.00 0.00 2.57
4123 4910 5.221303 GCCATCTTTACCACATGTTATGCAT 60.221 40.000 3.79 3.79 38.60 3.96
4131 4918 2.726821 ACTGGCCATCTTTACCACATG 58.273 47.619 5.51 0.00 0.00 3.21
4496 5430 8.078596 ACTTGTATCATTTGTTCTCTGCTTTTC 58.921 33.333 0.00 0.00 0.00 2.29
4617 5557 3.030291 CTCTGCTGACCAGGTTCTAGAT 58.970 50.000 0.00 0.00 42.05 1.98
4618 5558 2.451490 CTCTGCTGACCAGGTTCTAGA 58.549 52.381 0.00 0.00 42.05 2.43
4619 5559 1.480137 CCTCTGCTGACCAGGTTCTAG 59.520 57.143 0.00 0.00 42.05 2.43
4620 5560 1.077169 TCCTCTGCTGACCAGGTTCTA 59.923 52.381 0.00 0.00 42.05 2.10
4621 5561 0.178921 TCCTCTGCTGACCAGGTTCT 60.179 55.000 0.00 0.00 42.05 3.01
4622 5562 0.687354 TTCCTCTGCTGACCAGGTTC 59.313 55.000 0.00 0.00 42.05 3.62
4751 5691 9.906111 CTGCTCAACTTGTTTTCTTTTATTTTC 57.094 29.630 0.00 0.00 0.00 2.29
4782 5737 2.747855 GGGCTTCTGCACCTTCCG 60.748 66.667 0.00 0.00 41.91 4.30
4830 5785 5.562506 ATTCTGAGATGAATGTTGCACAG 57.437 39.130 0.00 0.00 35.57 3.66
5106 6061 7.386848 ACACTTACTAACGCTTGTGTTGATATT 59.613 33.333 9.49 0.00 35.47 1.28
5115 6079 6.423001 CCTTCTTAACACTTACTAACGCTTGT 59.577 38.462 0.00 0.00 0.00 3.16
5197 6165 9.723601 TGTCGTTTAATTATAGGTTAACCAGTT 57.276 29.630 26.26 14.31 38.89 3.16
5268 6236 9.376075 CTACAGCTTTTTCTTTATCTCAGATCA 57.624 33.333 0.00 0.00 0.00 2.92
5282 6250 3.421844 ACATCCACCCTACAGCTTTTTC 58.578 45.455 0.00 0.00 0.00 2.29
5285 6254 3.157087 CAAACATCCACCCTACAGCTTT 58.843 45.455 0.00 0.00 0.00 3.51
5286 6255 2.108250 ACAAACATCCACCCTACAGCTT 59.892 45.455 0.00 0.00 0.00 3.74
5554 6535 9.488124 GTTAACTACACTCTAACTTCACTATCG 57.512 37.037 0.00 0.00 0.00 2.92
5633 6825 7.380065 TGAAATTACAAAAACAGACGCCATTAC 59.620 33.333 0.00 0.00 0.00 1.89
5638 6830 5.516090 TCTGAAATTACAAAAACAGACGCC 58.484 37.500 0.00 0.00 31.02 5.68
5657 6849 4.713814 AGACAGATATGGCTCAGTTTCTGA 59.286 41.667 0.00 0.00 38.25 3.27
5688 6880 1.637553 AGGTGGTGCAAGAGGATGAAT 59.362 47.619 0.00 0.00 0.00 2.57
5689 6881 1.067295 AGGTGGTGCAAGAGGATGAA 58.933 50.000 0.00 0.00 0.00 2.57
5691 6883 0.679002 CCAGGTGGTGCAAGAGGATG 60.679 60.000 0.00 0.00 0.00 3.51
5775 6971 7.661437 TCAGCATCAGTAATGTCAGTTAACTTT 59.339 33.333 5.07 0.18 37.71 2.66
5776 6972 7.161404 TCAGCATCAGTAATGTCAGTTAACTT 58.839 34.615 5.07 0.00 37.71 2.66
5777 6973 6.701340 TCAGCATCAGTAATGTCAGTTAACT 58.299 36.000 1.12 1.12 37.71 2.24
5808 7004 5.727434 AGGAAATTTAGCAAAAGATGGCAG 58.273 37.500 0.00 0.00 0.00 4.85
5878 7074 4.263462 TGAGTCAGAATAGCCAATGGTGTT 60.263 41.667 0.00 0.00 0.00 3.32
6001 7197 5.362143 CCTCCATTTGACTCTCAGATCACTA 59.638 44.000 0.00 0.00 0.00 2.74
6214 7410 5.499313 TGCAATCTACATGTTTCATCCAGA 58.501 37.500 2.30 0.00 0.00 3.86
6484 7682 4.280677 TCATTTCATGACCAGGTTGAAACC 59.719 41.667 18.08 3.91 40.88 3.27
6532 7730 0.978146 AGGGAGGTGATGAGAACGGG 60.978 60.000 0.00 0.00 0.00 5.28
6535 7733 4.342665 CCTAACTAGGGAGGTGATGAGAAC 59.657 50.000 4.39 0.00 39.86 3.01
6537 7735 4.186077 CCTAACTAGGGAGGTGATGAGA 57.814 50.000 4.39 0.00 39.86 3.27
6589 7787 3.390521 CTAGCTCCCACGCACCCA 61.391 66.667 0.00 0.00 0.00 4.51
6662 7860 2.443416 CCAAACAAGTTAGGGTAGGCC 58.557 52.381 0.00 0.00 0.00 5.19
6686 7884 0.464452 GGGAGGTGATACAACCCTCG 59.536 60.000 0.00 0.00 44.71 4.63
6767 7976 5.369404 TCATTAGAAGTGGATTAGGGATGCA 59.631 40.000 0.00 0.00 33.24 3.96
6785 7994 2.425143 ACATGGCTGGTGGTCATTAG 57.575 50.000 0.00 0.00 38.32 1.73
6794 8003 1.656587 TGGAGAGTAACATGGCTGGT 58.343 50.000 0.00 0.00 0.00 4.00
6882 8091 1.264295 ACCGTTCCTCTTGACCCTAC 58.736 55.000 0.00 0.00 0.00 3.18
7016 8225 5.136828 TCCCTCAACTTTTCAGTATTTGCA 58.863 37.500 0.00 0.00 30.68 4.08


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

AutoCloner maintained by Alex Coulton.