Multiple sequence alignment - TraesCS7A01G159700

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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 TraesCS7A01G159700 chr7A 100.000 4288 0 0 1 4288 116004223 116008510 0.000000e+00 7919.0
1 TraesCS7A01G159700 chr7A 89.720 107 8 1 4038 4144 116018608 116018711 2.690000e-27 134.0
2 TraesCS7A01G159700 chr7A 96.875 32 1 0 4038 4069 116008232 116008263 2.000000e-03 54.7
3 TraesCS7A01G159700 chr7B 94.048 3108 122 23 975 4041 69819147 69822232 0.000000e+00 4656.0
4 TraesCS7A01G159700 chr7B 84.027 601 67 19 335 914 25657309 25656717 6.270000e-153 551.0
5 TraesCS7A01G159700 chr7B 89.147 258 15 6 4038 4288 69822201 69822452 4.160000e-80 309.0
6 TraesCS7A01G159700 chr7B 91.096 146 13 0 624 769 69818942 69819087 9.410000e-47 198.0
7 TraesCS7A01G159700 chr7B 93.388 121 7 1 3921 4041 69912531 69912650 1.230000e-40 178.0
8 TraesCS7A01G159700 chr7B 93.388 121 7 1 3921 4041 70068914 70069033 1.230000e-40 178.0
9 TraesCS7A01G159700 chr7D 94.293 2944 103 22 978 3865 110881629 110884563 0.000000e+00 4446.0
10 TraesCS7A01G159700 chr7D 86.095 525 57 9 335 844 78304376 78303853 6.270000e-153 551.0
11 TraesCS7A01G159700 chr7D 93.125 160 7 3 3882 4041 110884544 110884699 9.270000e-57 231.0
12 TraesCS7A01G159700 chr7D 82.545 275 24 7 4038 4288 110884668 110884942 2.010000e-53 220.0
13 TraesCS7A01G159700 chr7D 97.521 121 2 1 3921 4041 110890316 110890435 5.620000e-49 206.0
14 TraesCS7A01G159700 chr7D 95.327 107 5 0 4038 4144 110890404 110890510 2.050000e-38 171.0
15 TraesCS7A01G159700 chr6D 87.741 881 73 16 60 915 1589908 1589038 0.000000e+00 996.0
16 TraesCS7A01G159700 chr6D 93.103 87 4 2 4203 4288 101213189 101213274 4.500000e-25 126.0
17 TraesCS7A01G159700 chr6D 96.552 58 2 0 1 58 388228851 388228908 3.530000e-16 97.1
18 TraesCS7A01G159700 chr6D 92.308 39 2 1 4157 4195 469319499 469319462 2.000000e-03 54.7
19 TraesCS7A01G159700 chr6A 87.144 879 82 19 60 914 1028964 1029835 0.000000e+00 968.0
20 TraesCS7A01G159700 chr6A 92.143 140 11 0 61 200 40220809 40220670 9.410000e-47 198.0
21 TraesCS7A01G159700 chr6A 85.393 89 7 2 194 276 40220367 40220279 2.120000e-13 87.9
22 TraesCS7A01G159700 chr3B 87.811 845 74 17 60 881 720955073 720955911 0.000000e+00 963.0
23 TraesCS7A01G159700 chr3B 86.765 136 15 2 4156 4288 812336917 812336782 9.610000e-32 148.0
24 TraesCS7A01G159700 chr3A 87.758 727 61 11 60 758 681457622 681458348 0.000000e+00 824.0
25 TraesCS7A01G159700 chr3A 81.609 609 69 18 1231 1825 326495006 326495585 8.400000e-127 464.0
26 TraesCS7A01G159700 chr3A 81.433 614 68 27 1228 1825 137587790 137588373 1.090000e-125 460.0
27 TraesCS7A01G159700 chr3A 98.214 56 1 0 1 56 95538510 95538455 9.810000e-17 99.0
28 TraesCS7A01G159700 chr5B 84.581 668 74 16 246 896 558711655 558711000 1.680000e-178 636.0
29 TraesCS7A01G159700 chr5B 88.372 129 11 2 4160 4288 325960719 325960595 7.430000e-33 152.0
30 TraesCS7A01G159700 chr4D 80.069 873 125 26 60 914 484616753 484617594 1.710000e-168 603.0
31 TraesCS7A01G159700 chr1A 88.142 506 52 5 60 558 132487651 132487147 2.850000e-166 595.0
32 TraesCS7A01G159700 chr1A 89.744 117 10 1 4166 4282 571718906 571719020 9.610000e-32 148.0
33 TraesCS7A01G159700 chr1A 86.719 128 14 2 4161 4288 320328631 320328507 5.780000e-29 139.0
34 TraesCS7A01G159700 chrUn 82.013 606 68 18 1231 1825 109548373 109548948 1.080000e-130 477.0
35 TraesCS7A01G159700 chrUn 93.388 121 7 1 3921 4041 426294616 426294735 1.230000e-40 178.0
36 TraesCS7A01G159700 chrUn 89.873 79 8 0 4049 4127 16657285 16657363 7.590000e-18 102.0
37 TraesCS7A01G159700 chrUn 78.571 84 16 1 4161 4244 96035161 96035080 2.000000e-03 54.7
38 TraesCS7A01G159700 chr3D 86.605 433 37 5 357 771 544780416 544780845 3.910000e-125 459.0
39 TraesCS7A01G159700 chr3D 96.386 83 3 0 4206 4288 562531704 562531622 2.080000e-28 137.0
40 TraesCS7A01G159700 chr3D 96.552 58 2 0 1 58 129016731 129016788 3.530000e-16 97.1
41 TraesCS7A01G159700 chr3D 96.552 58 2 0 1 58 384561006 384560949 3.530000e-16 97.1
42 TraesCS7A01G159700 chr2B 81.937 382 37 14 566 930 253278493 253278127 1.170000e-75 294.0
43 TraesCS7A01G159700 chr6B 93.388 121 7 1 3921 4041 548948317 548948436 1.230000e-40 178.0
44 TraesCS7A01G159700 chr6B 93.388 121 7 1 3921 4041 549028829 549028948 1.230000e-40 178.0
45 TraesCS7A01G159700 chr1D 92.800 125 5 3 3917 4041 382909297 382909417 1.230000e-40 178.0
46 TraesCS7A01G159700 chr1D 89.781 137 12 2 3665 3800 382909148 382909283 1.580000e-39 174.0
47 TraesCS7A01G159700 chr1D 96.552 58 2 0 1 58 203950039 203950096 3.530000e-16 97.1
48 TraesCS7A01G159700 chr4B 87.662 154 15 3 60 212 616957848 616957998 4.410000e-40 176.0
49 TraesCS7A01G159700 chr5A 88.028 142 14 2 60 200 665442992 665443131 9.540000e-37 165.0
50 TraesCS7A01G159700 chr2D 91.489 94 7 1 4191 4283 592290286 592290379 1.250000e-25 128.0
51 TraesCS7A01G159700 chr2D 96.552 58 2 0 1 58 172999833 172999776 3.530000e-16 97.1
52 TraesCS7A01G159700 chr2D 96.552 58 2 0 1 58 459810794 459810737 3.530000e-16 97.1
53 TraesCS7A01G159700 chr2D 96.552 58 2 0 1 58 461370822 461370879 3.530000e-16 97.1
54 TraesCS7A01G159700 chr5D 83.582 134 20 2 4157 4288 312479604 312479471 1.620000e-24 124.0
55 TraesCS7A01G159700 chr2A 89.873 79 8 0 4049 4127 17299864 17299942 7.590000e-18 102.0
56 TraesCS7A01G159700 chr2A 88.608 79 9 0 4049 4127 20365207 20365285 3.530000e-16 97.1
57 TraesCS7A01G159700 chr2A 97.059 34 0 1 4156 4188 198857584 198857617 5.990000e-04 56.5
58 TraesCS7A01G159700 chr4A 93.846 65 2 2 1 65 583691881 583691819 3.530000e-16 97.1
59 TraesCS7A01G159700 chr1B 94.872 39 1 1 4157 4195 310944008 310944045 4.630000e-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 TraesCS7A01G159700 chr7A 116004223 116008510 4287 False 3986.850000 7919 98.437500 1 4288 2 chr7A.!!$F2 4287
1 TraesCS7A01G159700 chr7B 69818942 69822452 3510 False 1721.000000 4656 91.430333 624 4288 3 chr7B.!!$F3 3664
2 TraesCS7A01G159700 chr7B 25656717 25657309 592 True 551.000000 551 84.027000 335 914 1 chr7B.!!$R1 579
3 TraesCS7A01G159700 chr7D 110881629 110884942 3313 False 1632.333333 4446 89.987667 978 4288 3 chr7D.!!$F1 3310
4 TraesCS7A01G159700 chr7D 78303853 78304376 523 True 551.000000 551 86.095000 335 844 1 chr7D.!!$R1 509
5 TraesCS7A01G159700 chr6D 1589038 1589908 870 True 996.000000 996 87.741000 60 915 1 chr6D.!!$R1 855
6 TraesCS7A01G159700 chr6A 1028964 1029835 871 False 968.000000 968 87.144000 60 914 1 chr6A.!!$F1 854
7 TraesCS7A01G159700 chr3B 720955073 720955911 838 False 963.000000 963 87.811000 60 881 1 chr3B.!!$F1 821
8 TraesCS7A01G159700 chr3A 681457622 681458348 726 False 824.000000 824 87.758000 60 758 1 chr3A.!!$F3 698
9 TraesCS7A01G159700 chr3A 326495006 326495585 579 False 464.000000 464 81.609000 1231 1825 1 chr3A.!!$F2 594
10 TraesCS7A01G159700 chr3A 137587790 137588373 583 False 460.000000 460 81.433000 1228 1825 1 chr3A.!!$F1 597
11 TraesCS7A01G159700 chr5B 558711000 558711655 655 True 636.000000 636 84.581000 246 896 1 chr5B.!!$R2 650
12 TraesCS7A01G159700 chr4D 484616753 484617594 841 False 603.000000 603 80.069000 60 914 1 chr4D.!!$F1 854
13 TraesCS7A01G159700 chr1A 132487147 132487651 504 True 595.000000 595 88.142000 60 558 1 chr1A.!!$R1 498
14 TraesCS7A01G159700 chrUn 109548373 109548948 575 False 477.000000 477 82.013000 1231 1825 1 chrUn.!!$F2 594

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
958 1009 0.102300 CGACAGACCACACACTGACA 59.898 55.0 0.00 0.00 37.54 3.58 F
964 1015 0.107703 ACCACACACTGACACACCTG 60.108 55.0 0.00 0.00 0.00 4.00 F
965 1016 0.177836 CCACACACTGACACACCTGA 59.822 55.0 0.00 0.00 0.00 3.86 F
1102 1153 0.398381 CCTCCTCCTCCTCCTTCTGG 60.398 65.0 0.00 0.00 0.00 3.86 F
1373 1426 0.601311 GAAAGTGTGACCGCTCTGCT 60.601 55.0 0.00 0.00 0.00 4.24 F
1544 1606 1.099879 GCTGCAGTAGGCCAATCTGG 61.100 60.0 16.64 8.17 43.89 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2834 2940 0.734889 GCACTACGATGCCAAATGCT 59.265 50.000 0.00 0.0 39.86 3.79 R
2893 2999 6.151480 ACTCTAGAAGGTGTCTGCTAGTTAAC 59.849 42.308 7.94 0.0 45.50 2.01 R
3021 3127 7.814642 AGAATTTGATGTGACTGAAAGATGAC 58.185 34.615 0.00 0.0 37.43 3.06 R
3141 3247 6.409704 ACAGTTTTGAGATGCAGATTAGCTA 58.590 36.000 0.00 0.0 34.99 3.32 R
3186 3292 6.376299 ACATCGTACTCTTCTACATACCACAA 59.624 38.462 0.00 0.0 0.00 3.33 R
3558 3680 0.105224 TCGACAAAAAGGACTCGGCA 59.895 50.000 0.00 0.0 0.00 5.69 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
31 32 5.712217 CGCAATCGGTCTTGATAGTTAAA 57.288 39.130 0.00 0.00 0.00 1.52
32 33 6.287107 CGCAATCGGTCTTGATAGTTAAAT 57.713 37.500 0.00 0.00 0.00 1.40
33 34 6.715464 CGCAATCGGTCTTGATAGTTAAATT 58.285 36.000 0.00 0.00 0.00 1.82
34 35 7.186804 CGCAATCGGTCTTGATAGTTAAATTT 58.813 34.615 0.00 0.00 0.00 1.82
35 36 8.332464 CGCAATCGGTCTTGATAGTTAAATTTA 58.668 33.333 0.00 0.00 0.00 1.40
36 37 9.434559 GCAATCGGTCTTGATAGTTAAATTTAC 57.565 33.333 0.00 0.00 0.00 2.01
37 38 9.632969 CAATCGGTCTTGATAGTTAAATTTACG 57.367 33.333 0.00 0.00 0.00 3.18
38 39 7.760131 TCGGTCTTGATAGTTAAATTTACGG 57.240 36.000 0.00 0.00 0.00 4.02
39 40 7.322664 TCGGTCTTGATAGTTAAATTTACGGT 58.677 34.615 0.00 0.00 0.00 4.83
40 41 7.489113 TCGGTCTTGATAGTTAAATTTACGGTC 59.511 37.037 0.00 0.00 0.00 4.79
41 42 7.276218 CGGTCTTGATAGTTAAATTTACGGTCA 59.724 37.037 0.00 0.00 0.00 4.02
42 43 8.938906 GGTCTTGATAGTTAAATTTACGGTCAA 58.061 33.333 0.00 6.02 0.00 3.18
51 52 8.680001 AGTTAAATTTACGGTCAAAGTTGAAGT 58.320 29.630 0.00 2.51 39.21 3.01
52 53 9.934190 GTTAAATTTACGGTCAAAGTTGAAGTA 57.066 29.630 0.00 1.61 39.21 2.24
53 54 9.934190 TTAAATTTACGGTCAAAGTTGAAGTAC 57.066 29.630 0.00 0.00 39.21 2.73
54 55 5.640218 TTTACGGTCAAAGTTGAAGTACG 57.360 39.130 9.02 7.98 39.21 3.67
55 56 2.476821 ACGGTCAAAGTTGAAGTACGG 58.523 47.619 0.00 0.00 39.21 4.02
56 57 2.101249 ACGGTCAAAGTTGAAGTACGGA 59.899 45.455 0.00 0.00 39.21 4.69
57 58 2.729882 CGGTCAAAGTTGAAGTACGGAG 59.270 50.000 0.00 0.00 39.21 4.63
58 59 3.725490 GGTCAAAGTTGAAGTACGGAGT 58.275 45.455 0.00 0.00 41.62 3.85
65 66 7.170320 TCAAAGTTGAAGTACGGAGTATCAAAC 59.830 37.037 2.81 0.00 41.65 2.93
200 204 6.283161 ACGACAAAAGAAGTAGTGCTTAAC 57.717 37.500 0.00 0.00 37.59 2.01
353 369 9.675464 AATCTAAAACCTCGGTATTCAATTACA 57.325 29.630 0.00 0.00 0.00 2.41
391 407 7.193595 ACTTCAGTTTCGAAAAACCATAGTTG 58.806 34.615 13.10 0.00 44.87 3.16
506 531 6.323739 AGTGATATTTGTTGAACCCAAACACT 59.676 34.615 0.00 0.00 34.49 3.55
516 545 5.474825 TGAACCCAAACACTTCAAAGTTTC 58.525 37.500 0.00 0.00 37.08 2.78
724 772 7.744087 ACTTGCATCACTTTGTTAGTCAATA 57.256 32.000 0.00 0.00 33.85 1.90
822 872 7.813852 AAACTCGTGTATTATGAAGTCACTC 57.186 36.000 0.00 0.00 0.00 3.51
823 873 6.510879 ACTCGTGTATTATGAAGTCACTCA 57.489 37.500 0.00 0.00 0.00 3.41
844 894 7.010738 CACTCACAATTCAAGAAAAAGTTGCAT 59.989 33.333 0.00 0.00 0.00 3.96
845 895 7.550196 ACTCACAATTCAAGAAAAAGTTGCATT 59.450 29.630 0.00 0.00 0.00 3.56
848 898 9.424659 CACAATTCAAGAAAAAGTTGCATTAAC 57.575 29.630 0.00 0.00 39.65 2.01
859 909 8.871686 AAAAGTTGCATTAACCTCAAAACTAG 57.128 30.769 0.00 0.00 40.24 2.57
861 911 8.685838 AAGTTGCATTAACCTCAAAACTAGTA 57.314 30.769 0.00 0.00 40.24 1.82
865 915 8.453238 TGCATTAACCTCAAAACTAGTAACAA 57.547 30.769 0.00 0.00 0.00 2.83
866 916 8.347035 TGCATTAACCTCAAAACTAGTAACAAC 58.653 33.333 0.00 0.00 0.00 3.32
867 917 8.347035 GCATTAACCTCAAAACTAGTAACAACA 58.653 33.333 0.00 0.00 0.00 3.33
868 918 9.878599 CATTAACCTCAAAACTAGTAACAACAG 57.121 33.333 0.00 0.00 0.00 3.16
869 919 9.623000 ATTAACCTCAAAACTAGTAACAACAGT 57.377 29.630 0.00 0.00 0.00 3.55
889 940 2.409948 AGTGGCTTAGATTCTGGTGC 57.590 50.000 0.00 0.00 0.00 5.01
935 986 5.557703 CGTTATCGACACGATGCTACTAGAA 60.558 44.000 12.56 0.00 46.43 2.10
940 991 4.144902 CGACACGATGCTACTAGAAAATCG 59.855 45.833 15.25 15.25 44.26 3.34
954 1005 2.910688 AAATCGACAGACCACACACT 57.089 45.000 0.00 0.00 0.00 3.55
955 1006 2.154854 AATCGACAGACCACACACTG 57.845 50.000 0.00 0.00 39.65 3.66
956 1007 1.328279 ATCGACAGACCACACACTGA 58.672 50.000 0.00 0.00 37.54 3.41
957 1008 0.384309 TCGACAGACCACACACTGAC 59.616 55.000 0.00 0.00 37.54 3.51
958 1009 0.102300 CGACAGACCACACACTGACA 59.898 55.000 0.00 0.00 37.54 3.58
959 1010 1.571919 GACAGACCACACACTGACAC 58.428 55.000 0.00 0.00 37.54 3.67
960 1011 0.901827 ACAGACCACACACTGACACA 59.098 50.000 0.00 0.00 37.54 3.72
961 1012 1.290203 CAGACCACACACTGACACAC 58.710 55.000 0.00 0.00 36.38 3.82
962 1013 0.178068 AGACCACACACTGACACACC 59.822 55.000 0.00 0.00 0.00 4.16
963 1014 0.178068 GACCACACACTGACACACCT 59.822 55.000 0.00 0.00 0.00 4.00
964 1015 0.107703 ACCACACACTGACACACCTG 60.108 55.000 0.00 0.00 0.00 4.00
965 1016 0.177836 CCACACACTGACACACCTGA 59.822 55.000 0.00 0.00 0.00 3.86
966 1017 1.406751 CCACACACTGACACACCTGAA 60.407 52.381 0.00 0.00 0.00 3.02
967 1018 1.665679 CACACACTGACACACCTGAAC 59.334 52.381 0.00 0.00 0.00 3.18
968 1019 1.277842 ACACACTGACACACCTGAACA 59.722 47.619 0.00 0.00 0.00 3.18
969 1020 1.665679 CACACTGACACACCTGAACAC 59.334 52.381 0.00 0.00 0.00 3.32
970 1021 1.277842 ACACTGACACACCTGAACACA 59.722 47.619 0.00 0.00 0.00 3.72
971 1022 1.665679 CACTGACACACCTGAACACAC 59.334 52.381 0.00 0.00 0.00 3.82
972 1023 1.277842 ACTGACACACCTGAACACACA 59.722 47.619 0.00 0.00 0.00 3.72
973 1024 1.665679 CTGACACACCTGAACACACAC 59.334 52.381 0.00 0.00 0.00 3.82
1102 1153 0.398381 CCTCCTCCTCCTCCTTCTGG 60.398 65.000 0.00 0.00 0.00 3.86
1125 1176 2.440817 CCCGACCATGGACCCCTAC 61.441 68.421 21.47 0.00 0.00 3.18
1365 1418 4.919754 GCATGAATTTCTGAAAGTGTGACC 59.080 41.667 7.92 0.00 33.76 4.02
1373 1426 0.601311 GAAAGTGTGACCGCTCTGCT 60.601 55.000 0.00 0.00 0.00 4.24
1377 1430 2.813042 GTGACCGCTCTGCTGCTC 60.813 66.667 0.00 0.00 0.00 4.26
1378 1431 3.305516 TGACCGCTCTGCTGCTCA 61.306 61.111 0.00 0.00 0.00 4.26
1379 1432 2.186384 GACCGCTCTGCTGCTCAT 59.814 61.111 0.00 0.00 0.00 2.90
1380 1433 1.882167 GACCGCTCTGCTGCTCATC 60.882 63.158 0.00 0.00 0.00 2.92
1381 1434 2.295472 GACCGCTCTGCTGCTCATCT 62.295 60.000 0.00 0.00 0.00 2.90
1392 1445 1.332889 TGCTCATCTCATCAGGCCGT 61.333 55.000 0.00 0.00 0.00 5.68
1544 1606 1.099879 GCTGCAGTAGGCCAATCTGG 61.100 60.000 16.64 8.17 43.89 3.86
1586 1651 9.369904 CATTCTTTGTAATAAATGGGACCAAAG 57.630 33.333 0.00 0.00 38.91 2.77
1613 1678 8.882736 CAGTGCTAATTGAGTATGATTTGTACA 58.117 33.333 0.00 0.00 30.61 2.90
1744 1828 6.406370 TGGATAAAATAGATATGACCGCCTG 58.594 40.000 0.00 0.00 0.00 4.85
1818 1911 4.318831 GCACACTTGTGTAAGTACTGCTTC 60.319 45.833 10.95 0.00 45.12 3.86
1861 1954 5.009010 CGGTCATTTCTTATTGCCAGCTATT 59.991 40.000 0.00 0.00 0.00 1.73
1885 1978 4.083003 TGGTTCCAAAATTCGAGCATGTAC 60.083 41.667 0.00 0.00 0.00 2.90
1891 1984 5.460646 CAAAATTCGAGCATGTACCACTTT 58.539 37.500 0.00 0.00 0.00 2.66
2016 2109 8.798859 ACTTTTTGCTGATGTATCTTCTATGT 57.201 30.769 0.00 0.00 0.00 2.29
2019 2112 7.776933 TTTGCTGATGTATCTTCTATGTGTC 57.223 36.000 0.00 0.00 0.00 3.67
2078 2171 1.807142 GGAGTTACTGAGGCTGTTTGC 59.193 52.381 0.00 0.00 41.94 3.68
2093 2186 4.504864 GCTGTTTGCCCCCTTAAAATTTCT 60.505 41.667 0.00 0.00 35.15 2.52
2136 2229 2.439507 TCAACTGGAGTTCTTCTTGGCT 59.560 45.455 0.00 0.00 35.83 4.75
2210 2303 3.080300 TGGACACCTGTCTTTGTTTGT 57.920 42.857 5.44 0.00 44.20 2.83
2211 2304 4.223556 TGGACACCTGTCTTTGTTTGTA 57.776 40.909 5.44 0.00 44.20 2.41
2212 2305 4.787551 TGGACACCTGTCTTTGTTTGTAT 58.212 39.130 5.44 0.00 44.20 2.29
2213 2306 5.931294 TGGACACCTGTCTTTGTTTGTATA 58.069 37.500 5.44 0.00 44.20 1.47
2214 2307 5.761234 TGGACACCTGTCTTTGTTTGTATAC 59.239 40.000 5.44 0.00 44.20 1.47
2215 2308 5.761234 GGACACCTGTCTTTGTTTGTATACA 59.239 40.000 0.08 0.08 44.20 2.29
2439 2533 6.092533 TGTGAACATATAGCATCATATTGGCG 59.907 38.462 0.00 0.00 0.00 5.69
2706 2800 1.734163 GTAGCCCGCTACAACACAAT 58.266 50.000 19.53 0.00 45.90 2.71
2801 2903 7.495934 TGGTCTAGCAAGCTTCTTCAATATAAC 59.504 37.037 0.00 0.00 0.00 1.89
2834 2940 3.128589 GCCTGCTAATTTGGATTGTTCGA 59.871 43.478 0.00 0.00 0.00 3.71
3021 3127 2.561569 ACACTTTTTCAGGAGGACACG 58.438 47.619 0.00 0.00 0.00 4.49
3109 3215 4.261994 GCTTCCAGGTAAACTTTTGCATCA 60.262 41.667 0.00 0.00 0.00 3.07
3120 3226 6.651755 AACTTTTGCATCACAGAAAGTTTG 57.348 33.333 15.57 0.00 41.50 2.93
3125 3231 4.713553 TGCATCACAGAAAGTTTGTCCTA 58.286 39.130 0.00 0.00 0.00 2.94
3186 3292 2.551270 TCCAGGCAAAGGTATCAGAGT 58.449 47.619 0.00 0.00 0.00 3.24
3558 3680 3.573110 GTCGTTATGCCTACCAGGAGTAT 59.427 47.826 0.00 0.00 37.67 2.12
3609 3731 3.685756 CCGATAACTTTTTGCCGAGGTTA 59.314 43.478 0.00 0.00 0.00 2.85
3618 3740 5.715434 TTTTGCCGAGGTTAAATTTAGCT 57.285 34.783 11.26 5.74 0.00 3.32
3624 3746 5.321516 CCGAGGTTAAATTTAGCTTTCACG 58.678 41.667 11.26 4.87 0.00 4.35
3647 3769 5.527033 GGTGTAGTCTTCGTACTTGACTTT 58.473 41.667 14.36 0.00 40.86 2.66
3649 3771 6.204359 GTGTAGTCTTCGTACTTGACTTTCA 58.796 40.000 14.36 11.94 40.86 2.69
3652 3774 4.040376 GTCTTCGTACTTGACTTTCACGT 58.960 43.478 0.00 0.00 33.29 4.49
3682 3804 6.043243 TCCTGTAATGAAAGAGAGGAAGTGTT 59.957 38.462 0.00 0.00 32.46 3.32
3711 3833 4.882671 ACGGATTCCTTGATCAAAATCG 57.117 40.909 19.48 17.27 34.39 3.34
3737 3859 3.928779 GGATCCCATCGCGCTGGA 61.929 66.667 29.54 20.38 38.69 3.86
3738 3860 2.345244 GATCCCATCGCGCTGGAT 59.655 61.111 29.54 23.87 41.54 3.41
3744 3866 0.249447 CCATCGCGCTGGATGACTTA 60.249 55.000 24.25 0.00 45.27 2.24
3751 3873 2.301577 GCTGGATGACTTAGCGAACT 57.698 50.000 0.00 0.00 0.00 3.01
3762 3884 0.108804 TAGCGAACTACAGCTGCCAC 60.109 55.000 15.27 0.21 44.32 5.01
3763 3885 1.667830 GCGAACTACAGCTGCCACA 60.668 57.895 15.27 0.00 0.00 4.17
3865 4027 6.925718 GCTCAAACTTTGGCTCTATTTTTCTT 59.074 34.615 1.62 0.00 0.00 2.52
3866 4028 7.439356 GCTCAAACTTTGGCTCTATTTTTCTTT 59.561 33.333 1.62 0.00 0.00 2.52
3867 4029 9.317936 CTCAAACTTTGGCTCTATTTTTCTTTT 57.682 29.630 1.62 0.00 0.00 2.27
3868 4030 9.665719 TCAAACTTTGGCTCTATTTTTCTTTTT 57.334 25.926 1.62 0.00 0.00 1.94
3891 4053 9.673454 TTTTTCTTTTAAAGATAAGTTCGGCTC 57.327 29.630 8.31 0.00 37.38 4.70
3892 4054 8.617290 TTTCTTTTAAAGATAAGTTCGGCTCT 57.383 30.769 8.31 0.00 37.38 4.09
3893 4055 9.715121 TTTCTTTTAAAGATAAGTTCGGCTCTA 57.285 29.630 8.31 0.00 37.38 2.43
3894 4056 9.886132 TTCTTTTAAAGATAAGTTCGGCTCTAT 57.114 29.630 8.31 0.00 37.38 1.98
3895 4057 9.886132 TCTTTTAAAGATAAGTTCGGCTCTATT 57.114 29.630 2.94 0.00 31.20 1.73
3900 4062 8.794335 AAAGATAAGTTCGGCTCTATTTTTCT 57.206 30.769 0.00 0.00 0.00 2.52
3954 4116 1.768870 AGGACTGTCGGGGGATAATTG 59.231 52.381 1.07 0.00 0.00 2.32
3985 4147 2.612221 GGAGTTGTTACGTGGAAGAGGG 60.612 54.545 0.00 0.00 0.00 4.30
3986 4148 1.346722 AGTTGTTACGTGGAAGAGGGG 59.653 52.381 0.00 0.00 0.00 4.79
3987 4149 0.035739 TTGTTACGTGGAAGAGGGGC 59.964 55.000 0.00 0.00 0.00 5.80
3988 4150 0.834687 TGTTACGTGGAAGAGGGGCT 60.835 55.000 0.00 0.00 0.00 5.19
4022 4184 3.737850 GATCCTTTGGCTAGGTGATGAG 58.262 50.000 6.21 0.00 36.63 2.90
4023 4185 1.839994 TCCTTTGGCTAGGTGATGAGG 59.160 52.381 6.21 0.00 36.63 3.86
4024 4186 1.839994 CCTTTGGCTAGGTGATGAGGA 59.160 52.381 0.00 0.00 0.00 3.71
4025 4187 2.239654 CCTTTGGCTAGGTGATGAGGAA 59.760 50.000 0.00 0.00 0.00 3.36
4026 4188 3.539604 CTTTGGCTAGGTGATGAGGAAG 58.460 50.000 0.00 0.00 0.00 3.46
4027 4189 2.550277 TGGCTAGGTGATGAGGAAGA 57.450 50.000 0.00 0.00 0.00 2.87
4028 4190 2.832838 TGGCTAGGTGATGAGGAAGAA 58.167 47.619 0.00 0.00 0.00 2.52
4029 4191 3.181329 TGGCTAGGTGATGAGGAAGAAA 58.819 45.455 0.00 0.00 0.00 2.52
4030 4192 3.782523 TGGCTAGGTGATGAGGAAGAAAT 59.217 43.478 0.00 0.00 0.00 2.17
4031 4193 4.228210 TGGCTAGGTGATGAGGAAGAAATT 59.772 41.667 0.00 0.00 0.00 1.82
4032 4194 4.578105 GGCTAGGTGATGAGGAAGAAATTG 59.422 45.833 0.00 0.00 0.00 2.32
4033 4195 5.431765 GCTAGGTGATGAGGAAGAAATTGA 58.568 41.667 0.00 0.00 0.00 2.57
4034 4196 5.295540 GCTAGGTGATGAGGAAGAAATTGAC 59.704 44.000 0.00 0.00 0.00 3.18
4035 4197 5.246981 AGGTGATGAGGAAGAAATTGACA 57.753 39.130 0.00 0.00 0.00 3.58
4036 4198 5.006386 AGGTGATGAGGAAGAAATTGACAC 58.994 41.667 0.00 0.00 0.00 3.67
4037 4199 4.142816 GGTGATGAGGAAGAAATTGACACG 60.143 45.833 0.00 0.00 0.00 4.49
4038 4200 4.002982 TGATGAGGAAGAAATTGACACGG 58.997 43.478 0.00 0.00 0.00 4.94
4039 4201 2.151202 TGAGGAAGAAATTGACACGGC 58.849 47.619 0.00 0.00 0.00 5.68
4040 4202 1.468914 GAGGAAGAAATTGACACGGCC 59.531 52.381 0.00 0.00 0.00 6.13
4041 4203 1.202879 AGGAAGAAATTGACACGGCCA 60.203 47.619 2.24 0.00 0.00 5.36
4042 4204 1.200020 GGAAGAAATTGACACGGCCAG 59.800 52.381 2.24 0.00 0.00 4.85
4043 4205 1.200020 GAAGAAATTGACACGGCCAGG 59.800 52.381 2.24 0.00 0.00 4.45
4044 4206 0.110486 AGAAATTGACACGGCCAGGT 59.890 50.000 2.24 0.00 0.00 4.00
4045 4207 0.240945 GAAATTGACACGGCCAGGTG 59.759 55.000 2.24 6.37 43.54 4.00
4046 4208 0.179004 AAATTGACACGGCCAGGTGA 60.179 50.000 16.64 0.00 40.38 4.02
4047 4209 0.038166 AATTGACACGGCCAGGTGAT 59.962 50.000 16.64 2.34 40.38 3.06
4048 4210 0.677731 ATTGACACGGCCAGGTGATG 60.678 55.000 16.64 0.67 40.38 3.07
4049 4211 1.763546 TTGACACGGCCAGGTGATGA 61.764 55.000 16.64 0.42 40.38 2.92
4101 4264 2.512515 GCACGGCCAGAGATGGAC 60.513 66.667 2.24 0.00 0.00 4.02
4127 4290 1.620822 AAGGTCTGCACCCAAATCAC 58.379 50.000 0.74 0.00 45.12 3.06
4129 4292 1.076024 AGGTCTGCACCCAAATCACAT 59.924 47.619 0.74 0.00 45.12 3.21
4146 4309 3.829224 TGGTTCGGCCACCCTATT 58.171 55.556 9.69 0.00 43.61 1.73
4153 4323 0.035458 CGGCCACCCTATTCTCATCC 59.965 60.000 2.24 0.00 0.00 3.51
4164 4334 8.407064 CACCCTATTCTCATCCGATATAACTAC 58.593 40.741 0.00 0.00 0.00 2.73
4244 4430 6.447162 CATGATCATATTTTGCTGCATCACT 58.553 36.000 8.15 0.00 0.00 3.41
4269 4455 9.814899 CTGAGATACACTATCACTCTCAATTTT 57.185 33.333 0.00 0.00 41.14 1.82
4273 4459 6.808008 ACACTATCACTCTCAATTTTGTGG 57.192 37.500 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 5.712217 TTTAACTATCAAGACCGATTGCG 57.288 39.130 0.00 0.00 37.24 4.85
10 11 9.434559 GTAAATTTAACTATCAAGACCGATTGC 57.565 33.333 0.00 0.00 0.00 3.56
11 12 9.632969 CGTAAATTTAACTATCAAGACCGATTG 57.367 33.333 0.00 0.00 0.00 2.67
12 13 8.823818 CCGTAAATTTAACTATCAAGACCGATT 58.176 33.333 0.00 0.00 0.00 3.34
13 14 7.983484 ACCGTAAATTTAACTATCAAGACCGAT 59.017 33.333 0.00 0.00 0.00 4.18
14 15 7.322664 ACCGTAAATTTAACTATCAAGACCGA 58.677 34.615 0.00 0.00 0.00 4.69
15 16 7.276218 TGACCGTAAATTTAACTATCAAGACCG 59.724 37.037 0.00 0.00 0.00 4.79
16 17 8.483307 TGACCGTAAATTTAACTATCAAGACC 57.517 34.615 0.00 0.00 0.00 3.85
25 26 8.680001 ACTTCAACTTTGACCGTAAATTTAACT 58.320 29.630 0.00 0.00 36.83 2.24
26 27 8.845942 ACTTCAACTTTGACCGTAAATTTAAC 57.154 30.769 0.00 0.00 36.83 2.01
27 28 9.934190 GTACTTCAACTTTGACCGTAAATTTAA 57.066 29.630 0.00 0.00 36.83 1.52
28 29 8.274939 CGTACTTCAACTTTGACCGTAAATTTA 58.725 33.333 0.00 0.00 36.83 1.40
29 30 7.127686 CGTACTTCAACTTTGACCGTAAATTT 58.872 34.615 0.00 0.00 36.83 1.82
30 31 6.293027 CCGTACTTCAACTTTGACCGTAAATT 60.293 38.462 0.00 0.00 36.83 1.82
31 32 5.178067 CCGTACTTCAACTTTGACCGTAAAT 59.822 40.000 0.00 0.00 36.83 1.40
32 33 4.507388 CCGTACTTCAACTTTGACCGTAAA 59.493 41.667 0.00 0.00 36.83 2.01
33 34 4.050553 CCGTACTTCAACTTTGACCGTAA 58.949 43.478 0.00 0.00 36.83 3.18
34 35 3.317711 TCCGTACTTCAACTTTGACCGTA 59.682 43.478 0.00 0.00 36.83 4.02
35 36 2.101249 TCCGTACTTCAACTTTGACCGT 59.899 45.455 0.00 0.00 36.83 4.83
36 37 2.729882 CTCCGTACTTCAACTTTGACCG 59.270 50.000 0.00 0.00 36.83 4.79
37 38 3.725490 ACTCCGTACTTCAACTTTGACC 58.275 45.455 0.00 0.00 36.83 4.02
38 39 6.154445 TGATACTCCGTACTTCAACTTTGAC 58.846 40.000 0.00 0.00 36.83 3.18
39 40 6.335471 TGATACTCCGTACTTCAACTTTGA 57.665 37.500 0.00 0.00 34.92 2.69
40 41 7.288672 GTTTGATACTCCGTACTTCAACTTTG 58.711 38.462 0.00 0.00 0.00 2.77
41 42 6.426025 GGTTTGATACTCCGTACTTCAACTTT 59.574 38.462 0.00 0.00 0.00 2.66
42 43 5.930569 GGTTTGATACTCCGTACTTCAACTT 59.069 40.000 0.00 0.00 0.00 2.66
43 44 5.245526 AGGTTTGATACTCCGTACTTCAACT 59.754 40.000 0.00 0.00 0.00 3.16
44 45 5.476614 AGGTTTGATACTCCGTACTTCAAC 58.523 41.667 0.00 0.00 0.00 3.18
45 46 5.733620 AGGTTTGATACTCCGTACTTCAA 57.266 39.130 0.00 0.00 0.00 2.69
46 47 5.475719 CAAGGTTTGATACTCCGTACTTCA 58.524 41.667 0.00 0.00 0.00 3.02
47 48 4.329256 GCAAGGTTTGATACTCCGTACTTC 59.671 45.833 0.00 0.00 0.00 3.01
48 49 4.020485 AGCAAGGTTTGATACTCCGTACTT 60.020 41.667 0.00 0.00 0.00 2.24
49 50 3.514309 AGCAAGGTTTGATACTCCGTACT 59.486 43.478 0.00 0.00 0.00 2.73
50 51 3.858247 AGCAAGGTTTGATACTCCGTAC 58.142 45.455 0.00 0.00 0.00 3.67
51 52 4.708421 ACTAGCAAGGTTTGATACTCCGTA 59.292 41.667 0.00 0.00 0.00 4.02
52 53 3.514309 ACTAGCAAGGTTTGATACTCCGT 59.486 43.478 0.00 0.00 0.00 4.69
53 54 4.124851 ACTAGCAAGGTTTGATACTCCG 57.875 45.455 0.00 0.00 0.00 4.63
54 55 6.043411 CAGTACTAGCAAGGTTTGATACTCC 58.957 44.000 0.00 0.00 0.00 3.85
55 56 6.043411 CCAGTACTAGCAAGGTTTGATACTC 58.957 44.000 0.00 0.00 0.00 2.59
56 57 5.627040 GCCAGTACTAGCAAGGTTTGATACT 60.627 44.000 8.52 0.00 0.00 2.12
57 58 4.571176 GCCAGTACTAGCAAGGTTTGATAC 59.429 45.833 8.52 0.00 0.00 2.24
58 59 4.383770 GGCCAGTACTAGCAAGGTTTGATA 60.384 45.833 15.30 0.00 0.00 2.15
65 66 1.765314 AGATGGCCAGTACTAGCAAGG 59.235 52.381 13.05 3.75 0.00 3.61
115 118 9.911788 ACAGTTAATCACATAATCAATCTTCCT 57.088 29.630 0.00 0.00 0.00 3.36
182 186 6.228258 TCCATCGTTAAGCACTACTTCTTTT 58.772 36.000 0.00 0.00 39.97 2.27
200 204 9.435688 TGGTTGATAATACAAATATCTCCATCG 57.564 33.333 0.00 0.00 33.77 3.84
481 506 6.323739 AGTGTTTGGGTTCAACAAATATCACT 59.676 34.615 0.00 0.00 39.68 3.41
506 531 5.379732 ACCACAGTTTTCGAAACTTTGAA 57.620 34.783 10.79 0.00 31.50 2.69
516 545 4.875544 TTCTCAGAAACCACAGTTTTCG 57.124 40.909 0.00 0.00 46.25 3.46
633 680 5.582689 GGCAACTTACAATAGAAAGGCAT 57.417 39.130 0.00 0.00 0.00 4.40
692 740 4.398988 ACAAAGTGATGCAAGTTCTCAACA 59.601 37.500 0.00 0.00 0.00 3.33
698 746 6.060028 TGACTAACAAAGTGATGCAAGTTC 57.940 37.500 0.00 0.00 39.07 3.01
724 772 1.194547 CGCAGCACGTTTAACTCACAT 59.805 47.619 0.00 0.00 36.87 3.21
797 846 8.517056 TGAGTGACTTCATAATACACGAGTTTA 58.483 33.333 0.00 0.00 36.71 2.01
802 851 6.262193 TGTGAGTGACTTCATAATACACGA 57.738 37.500 0.00 0.00 36.71 4.35
822 872 9.424659 GTTAATGCAACTTTTTCTTGAATTGTG 57.575 29.630 0.00 0.00 30.70 3.33
823 873 8.611757 GGTTAATGCAACTTTTTCTTGAATTGT 58.388 29.630 0.00 0.00 37.30 2.71
845 895 9.754382 CTACTGTTGTTACTAGTTTTGAGGTTA 57.246 33.333 0.00 0.00 0.00 2.85
848 898 7.170998 CCACTACTGTTGTTACTAGTTTTGAGG 59.829 40.741 0.00 0.00 0.00 3.86
859 909 7.063544 CAGAATCTAAGCCACTACTGTTGTTAC 59.936 40.741 0.00 0.00 0.00 2.50
861 911 5.934625 CAGAATCTAAGCCACTACTGTTGTT 59.065 40.000 0.00 0.00 0.00 2.83
865 915 4.081420 CACCAGAATCTAAGCCACTACTGT 60.081 45.833 0.00 0.00 0.00 3.55
866 916 4.437239 CACCAGAATCTAAGCCACTACTG 58.563 47.826 0.00 0.00 0.00 2.74
867 917 3.118592 GCACCAGAATCTAAGCCACTACT 60.119 47.826 0.00 0.00 0.00 2.57
868 918 3.198872 GCACCAGAATCTAAGCCACTAC 58.801 50.000 0.00 0.00 0.00 2.73
869 919 2.159099 CGCACCAGAATCTAAGCCACTA 60.159 50.000 0.00 0.00 0.00 2.74
935 986 2.102420 TCAGTGTGTGGTCTGTCGATTT 59.898 45.455 0.00 0.00 33.89 2.17
940 991 1.134818 TGTGTCAGTGTGTGGTCTGTC 60.135 52.381 0.00 0.00 33.89 3.51
954 1005 1.002544 TGTGTGTGTTCAGGTGTGTCA 59.997 47.619 0.00 0.00 0.00 3.58
955 1006 1.396996 GTGTGTGTGTTCAGGTGTGTC 59.603 52.381 0.00 0.00 0.00 3.67
956 1007 1.271108 TGTGTGTGTGTTCAGGTGTGT 60.271 47.619 0.00 0.00 0.00 3.72
957 1008 1.130373 GTGTGTGTGTGTTCAGGTGTG 59.870 52.381 0.00 0.00 0.00 3.82
958 1009 1.271108 TGTGTGTGTGTGTTCAGGTGT 60.271 47.619 0.00 0.00 0.00 4.16
959 1010 1.130373 GTGTGTGTGTGTGTTCAGGTG 59.870 52.381 0.00 0.00 0.00 4.00
960 1011 1.271108 TGTGTGTGTGTGTGTTCAGGT 60.271 47.619 0.00 0.00 0.00 4.00
961 1012 1.130373 GTGTGTGTGTGTGTGTTCAGG 59.870 52.381 0.00 0.00 0.00 3.86
962 1013 1.803555 TGTGTGTGTGTGTGTGTTCAG 59.196 47.619 0.00 0.00 0.00 3.02
963 1014 1.533299 GTGTGTGTGTGTGTGTGTTCA 59.467 47.619 0.00 0.00 0.00 3.18
964 1015 1.533299 TGTGTGTGTGTGTGTGTGTTC 59.467 47.619 0.00 0.00 0.00 3.18
965 1016 1.598882 TGTGTGTGTGTGTGTGTGTT 58.401 45.000 0.00 0.00 0.00 3.32
966 1017 1.598882 TTGTGTGTGTGTGTGTGTGT 58.401 45.000 0.00 0.00 0.00 3.72
967 1018 2.695613 TTTGTGTGTGTGTGTGTGTG 57.304 45.000 0.00 0.00 0.00 3.82
968 1019 3.717400 TTTTTGTGTGTGTGTGTGTGT 57.283 38.095 0.00 0.00 0.00 3.72
1137 1188 3.391382 GACACGGGACCAGGAGGG 61.391 72.222 0.00 0.00 44.81 4.30
1142 1193 2.663196 GGGAAGACACGGGACCAG 59.337 66.667 0.00 0.00 0.00 4.00
1365 1418 0.249531 ATGAGATGAGCAGCAGAGCG 60.250 55.000 0.00 0.00 40.15 5.03
1373 1426 1.332889 ACGGCCTGATGAGATGAGCA 61.333 55.000 0.00 0.00 0.00 4.26
1377 1430 0.596083 GTCGACGGCCTGATGAGATG 60.596 60.000 0.00 0.00 0.00 2.90
1378 1431 1.736586 GTCGACGGCCTGATGAGAT 59.263 57.895 0.00 0.00 0.00 2.75
1379 1432 2.415608 GGTCGACGGCCTGATGAGA 61.416 63.158 12.24 0.00 0.00 3.27
1380 1433 2.105128 GGTCGACGGCCTGATGAG 59.895 66.667 12.24 0.00 0.00 2.90
1381 1434 3.458163 GGGTCGACGGCCTGATGA 61.458 66.667 19.55 0.00 0.00 2.92
1544 1606 7.486647 ACAAAGAATGAGCAATATTGTCATCC 58.513 34.615 22.56 15.87 32.06 3.51
1586 1651 6.789262 ACAAATCATACTCAATTAGCACTGC 58.211 36.000 0.00 0.00 0.00 4.40
1613 1678 0.323178 CCTTCACAGCCTTCCTGCAT 60.323 55.000 0.00 0.00 45.78 3.96
1736 1820 3.113260 AGCAATATAGAACAGGCGGTC 57.887 47.619 0.00 0.00 0.00 4.79
1818 1911 2.664568 CCGAGCAAAGCAAATCAACATG 59.335 45.455 0.00 0.00 0.00 3.21
1861 1954 3.320541 ACATGCTCGAATTTTGGAACCAA 59.679 39.130 1.83 1.83 0.00 3.67
1885 1978 5.066505 GGAGGCATGAAACATACTAAAGTGG 59.933 44.000 0.00 0.00 0.00 4.00
1891 1984 4.411869 TGATGGGAGGCATGAAACATACTA 59.588 41.667 0.00 0.00 0.00 1.82
2016 2109 4.391830 GGCTTCAATCTCAACAATACGACA 59.608 41.667 0.00 0.00 0.00 4.35
2019 2112 3.616821 TCGGCTTCAATCTCAACAATACG 59.383 43.478 0.00 0.00 0.00 3.06
2078 2171 5.420739 TCGATCCAAAGAAATTTTAAGGGGG 59.579 40.000 0.00 0.00 0.00 5.40
2093 2186 2.367241 TGTCAAGACCACTCGATCCAAA 59.633 45.455 0.00 0.00 0.00 3.28
2136 2229 3.703556 TCAAAGATTCAAACCTGCCACAA 59.296 39.130 0.00 0.00 0.00 3.33
2213 2306 9.178758 GGAGGATGAAACACTAAGATTAATTGT 57.821 33.333 0.00 0.00 0.00 2.71
2214 2307 9.177608 TGGAGGATGAAACACTAAGATTAATTG 57.822 33.333 0.00 0.00 0.00 2.32
2215 2308 9.178758 GTGGAGGATGAAACACTAAGATTAATT 57.821 33.333 0.00 0.00 0.00 1.40
2221 2315 5.087323 AGAGTGGAGGATGAAACACTAAGA 58.913 41.667 0.00 0.00 43.61 2.10
2229 2323 5.825593 ACTTGTAAGAGTGGAGGATGAAA 57.174 39.130 0.00 0.00 0.00 2.69
2343 2437 1.675641 CTTTTGGGGTGCTCGAGGG 60.676 63.158 15.58 0.00 0.00 4.30
2439 2533 6.173339 TGAGTTCCCTTCTCAATGTTATCAC 58.827 40.000 0.00 0.00 38.71 3.06
2834 2940 0.734889 GCACTACGATGCCAAATGCT 59.265 50.000 0.00 0.00 39.86 3.79
2893 2999 6.151480 ACTCTAGAAGGTGTCTGCTAGTTAAC 59.849 42.308 7.94 0.00 45.50 2.01
3021 3127 7.814642 AGAATTTGATGTGACTGAAAGATGAC 58.185 34.615 0.00 0.00 37.43 3.06
3109 3215 9.793259 TCATTATCTTTAGGACAAACTTTCTGT 57.207 29.630 0.00 0.00 0.00 3.41
3141 3247 6.409704 ACAGTTTTGAGATGCAGATTAGCTA 58.590 36.000 0.00 0.00 34.99 3.32
3186 3292 6.376299 ACATCGTACTCTTCTACATACCACAA 59.624 38.462 0.00 0.00 0.00 3.33
3558 3680 0.105224 TCGACAAAAAGGACTCGGCA 59.895 50.000 0.00 0.00 0.00 5.69
3609 3731 5.995897 AGACTACACCGTGAAAGCTAAATTT 59.004 36.000 5.28 0.00 0.00 1.82
3618 3740 3.565482 AGTACGAAGACTACACCGTGAAA 59.435 43.478 5.28 0.00 36.58 2.69
3624 3746 4.762956 AGTCAAGTACGAAGACTACACC 57.237 45.455 13.75 0.00 40.59 4.16
3682 3804 3.904800 TCAAGGAATCCGTTGCTATCA 57.095 42.857 0.00 0.00 34.65 2.15
3696 3818 3.259064 GTCGTCCGATTTTGATCAAGGA 58.741 45.455 8.41 9.02 0.00 3.36
3697 3819 3.000041 TGTCGTCCGATTTTGATCAAGG 59.000 45.455 8.41 6.68 0.00 3.61
3700 3822 3.000041 CCTTGTCGTCCGATTTTGATCA 59.000 45.455 0.00 0.00 0.00 2.92
3711 3833 0.249489 CGATGGGATCCTTGTCGTCC 60.249 60.000 12.58 0.00 0.00 4.79
3737 3859 3.775202 CAGCTGTAGTTCGCTAAGTCAT 58.225 45.455 5.25 0.00 34.58 3.06
3738 3860 2.671351 GCAGCTGTAGTTCGCTAAGTCA 60.671 50.000 16.64 0.00 34.58 3.41
3744 3866 1.374758 GTGGCAGCTGTAGTTCGCT 60.375 57.895 16.64 0.00 36.83 4.93
3751 3873 3.316029 GCATAAATGATGTGGCAGCTGTA 59.684 43.478 16.64 1.73 37.90 2.74
3762 3884 2.607180 TCGGTCACACGCATAAATGATG 59.393 45.455 0.00 0.00 38.73 3.07
3763 3885 2.899976 TCGGTCACACGCATAAATGAT 58.100 42.857 0.00 0.00 0.00 2.45
3800 3927 0.037326 GTTCGCTCACCTGGACATGA 60.037 55.000 0.00 0.00 0.00 3.07
3802 3929 1.079819 CGTTCGCTCACCTGGACAT 60.080 57.895 0.00 0.00 0.00 3.06
3865 4027 9.673454 GAGCCGAACTTATCTTTAAAAGAAAAA 57.327 29.630 0.00 0.00 41.63 1.94
3866 4028 9.063615 AGAGCCGAACTTATCTTTAAAAGAAAA 57.936 29.630 0.00 0.00 41.63 2.29
3867 4029 8.617290 AGAGCCGAACTTATCTTTAAAAGAAA 57.383 30.769 0.00 0.00 41.63 2.52
3868 4030 9.886132 ATAGAGCCGAACTTATCTTTAAAAGAA 57.114 29.630 0.00 0.00 41.63 2.52
3869 4031 9.886132 AATAGAGCCGAACTTATCTTTAAAAGA 57.114 29.630 0.00 0.00 42.69 2.52
3874 4036 9.886132 AGAAAAATAGAGCCGAACTTATCTTTA 57.114 29.630 0.00 0.00 0.00 1.85
3875 4037 8.669243 CAGAAAAATAGAGCCGAACTTATCTTT 58.331 33.333 0.00 0.00 0.00 2.52
3876 4038 8.041323 TCAGAAAAATAGAGCCGAACTTATCTT 58.959 33.333 0.00 0.00 0.00 2.40
3877 4039 7.556844 TCAGAAAAATAGAGCCGAACTTATCT 58.443 34.615 0.00 0.00 0.00 1.98
3878 4040 7.772332 TCAGAAAAATAGAGCCGAACTTATC 57.228 36.000 0.00 0.00 0.00 1.75
3879 4041 7.770897 ACATCAGAAAAATAGAGCCGAACTTAT 59.229 33.333 0.00 0.00 0.00 1.73
3880 4042 7.064609 CACATCAGAAAAATAGAGCCGAACTTA 59.935 37.037 0.00 0.00 0.00 2.24
3881 4043 5.940470 ACATCAGAAAAATAGAGCCGAACTT 59.060 36.000 0.00 0.00 0.00 2.66
3882 4044 5.352569 CACATCAGAAAAATAGAGCCGAACT 59.647 40.000 0.00 0.00 0.00 3.01
3883 4045 5.122396 ACACATCAGAAAAATAGAGCCGAAC 59.878 40.000 0.00 0.00 0.00 3.95
3884 4046 5.245531 ACACATCAGAAAAATAGAGCCGAA 58.754 37.500 0.00 0.00 0.00 4.30
3885 4047 4.832248 ACACATCAGAAAAATAGAGCCGA 58.168 39.130 0.00 0.00 0.00 5.54
3886 4048 5.551760 AACACATCAGAAAAATAGAGCCG 57.448 39.130 0.00 0.00 0.00 5.52
3887 4049 6.024049 CGAAACACATCAGAAAAATAGAGCC 58.976 40.000 0.00 0.00 0.00 4.70
3888 4050 5.509622 GCGAAACACATCAGAAAAATAGAGC 59.490 40.000 0.00 0.00 0.00 4.09
3889 4051 6.835914 AGCGAAACACATCAGAAAAATAGAG 58.164 36.000 0.00 0.00 0.00 2.43
3890 4052 6.801539 AGCGAAACACATCAGAAAAATAGA 57.198 33.333 0.00 0.00 0.00 1.98
3891 4053 7.858052 AAAGCGAAACACATCAGAAAAATAG 57.142 32.000 0.00 0.00 0.00 1.73
3892 4054 8.020819 CCTAAAGCGAAACACATCAGAAAAATA 58.979 33.333 0.00 0.00 0.00 1.40
3893 4055 6.863126 CCTAAAGCGAAACACATCAGAAAAAT 59.137 34.615 0.00 0.00 0.00 1.82
3894 4056 6.205784 CCTAAAGCGAAACACATCAGAAAAA 58.794 36.000 0.00 0.00 0.00 1.94
3895 4057 5.278266 CCCTAAAGCGAAACACATCAGAAAA 60.278 40.000 0.00 0.00 0.00 2.29
3896 4058 4.215399 CCCTAAAGCGAAACACATCAGAAA 59.785 41.667 0.00 0.00 0.00 2.52
3897 4059 3.751175 CCCTAAAGCGAAACACATCAGAA 59.249 43.478 0.00 0.00 0.00 3.02
3898 4060 3.244422 ACCCTAAAGCGAAACACATCAGA 60.244 43.478 0.00 0.00 0.00 3.27
3899 4061 3.074412 ACCCTAAAGCGAAACACATCAG 58.926 45.455 0.00 0.00 0.00 2.90
3900 4062 3.134574 ACCCTAAAGCGAAACACATCA 57.865 42.857 0.00 0.00 0.00 3.07
3954 4116 3.376546 ACGTAACAACTCCTACTCGATCC 59.623 47.826 0.00 0.00 0.00 3.36
3998 4160 1.144057 ACCTAGCCAAAGGATCGCG 59.856 57.895 0.00 0.00 39.15 5.87
4022 4184 1.200020 CTGGCCGTGTCAATTTCTTCC 59.800 52.381 0.00 0.00 0.00 3.46
4023 4185 1.200020 CCTGGCCGTGTCAATTTCTTC 59.800 52.381 0.00 0.00 0.00 2.87
4024 4186 1.247567 CCTGGCCGTGTCAATTTCTT 58.752 50.000 0.00 0.00 0.00 2.52
4025 4187 0.110486 ACCTGGCCGTGTCAATTTCT 59.890 50.000 0.00 0.00 0.00 2.52
4026 4188 0.240945 CACCTGGCCGTGTCAATTTC 59.759 55.000 0.00 0.00 0.00 2.17
4027 4189 0.179004 TCACCTGGCCGTGTCAATTT 60.179 50.000 10.17 0.00 35.18 1.82
4028 4190 0.038166 ATCACCTGGCCGTGTCAATT 59.962 50.000 10.17 0.00 35.18 2.32
4029 4191 0.677731 CATCACCTGGCCGTGTCAAT 60.678 55.000 10.17 0.00 35.18 2.57
4030 4192 1.302431 CATCACCTGGCCGTGTCAA 60.302 57.895 10.17 0.00 35.18 3.18
4031 4193 2.171209 CTCATCACCTGGCCGTGTCA 62.171 60.000 10.17 0.00 35.18 3.58
4032 4194 1.448540 CTCATCACCTGGCCGTGTC 60.449 63.158 10.17 0.00 35.18 3.67
4033 4195 2.665000 CTCATCACCTGGCCGTGT 59.335 61.111 10.17 0.85 35.18 4.49
4034 4196 2.124983 CCTCATCACCTGGCCGTG 60.125 66.667 4.50 4.50 34.93 4.94
4035 4197 1.903877 CTTCCTCATCACCTGGCCGT 61.904 60.000 0.00 0.00 0.00 5.68
4036 4198 1.153289 CTTCCTCATCACCTGGCCG 60.153 63.158 0.00 0.00 0.00 6.13
4037 4199 0.620556 TTCTTCCTCATCACCTGGCC 59.379 55.000 0.00 0.00 0.00 5.36
4038 4200 2.496899 TTTCTTCCTCATCACCTGGC 57.503 50.000 0.00 0.00 0.00 4.85
4039 4201 4.397417 GTCAATTTCTTCCTCATCACCTGG 59.603 45.833 0.00 0.00 0.00 4.45
4040 4202 5.005740 TGTCAATTTCTTCCTCATCACCTG 58.994 41.667 0.00 0.00 0.00 4.00
4041 4203 5.006386 GTGTCAATTTCTTCCTCATCACCT 58.994 41.667 0.00 0.00 0.00 4.00
4042 4204 4.142816 CGTGTCAATTTCTTCCTCATCACC 60.143 45.833 0.00 0.00 0.00 4.02
4043 4205 4.142816 CCGTGTCAATTTCTTCCTCATCAC 60.143 45.833 0.00 0.00 0.00 3.06
4044 4206 4.002982 CCGTGTCAATTTCTTCCTCATCA 58.997 43.478 0.00 0.00 0.00 3.07
4045 4207 3.181506 GCCGTGTCAATTTCTTCCTCATC 60.182 47.826 0.00 0.00 0.00 2.92
4046 4208 2.749621 GCCGTGTCAATTTCTTCCTCAT 59.250 45.455 0.00 0.00 0.00 2.90
4047 4209 2.151202 GCCGTGTCAATTTCTTCCTCA 58.849 47.619 0.00 0.00 0.00 3.86
4048 4210 1.468914 GGCCGTGTCAATTTCTTCCTC 59.531 52.381 0.00 0.00 0.00 3.71
4049 4211 1.534729 GGCCGTGTCAATTTCTTCCT 58.465 50.000 0.00 0.00 0.00 3.36
4101 4264 1.207089 TGGGTGCAGACCTTATCGAAG 59.793 52.381 8.68 0.00 42.66 3.79
4144 4307 9.712305 CTTTTGGTAGTTATATCGGATGAGAAT 57.288 33.333 0.00 0.00 0.00 2.40
4145 4308 8.148351 CCTTTTGGTAGTTATATCGGATGAGAA 58.852 37.037 0.00 0.00 34.07 2.87
4146 4309 7.256190 CCCTTTTGGTAGTTATATCGGATGAGA 60.256 40.741 0.00 0.00 38.10 3.27
4153 4323 4.070009 GGGCCCTTTTGGTAGTTATATCG 58.930 47.826 17.04 0.00 38.10 2.92
4200 4370 7.421087 TCATGGCCATTGAAGATTATCAAAA 57.579 32.000 17.92 0.00 42.22 2.44
4201 4371 7.288158 TGATCATGGCCATTGAAGATTATCAAA 59.712 33.333 17.92 0.00 42.22 2.69
4244 4430 9.591792 CAAAATTGAGAGTGATAGTGTATCTCA 57.408 33.333 0.00 0.00 43.38 3.27


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

AutoCloner maintained by Alex Coulton.