Multiple sequence alignment - TraesCS1D01G125100

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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 TraesCS1D01G125100 chr1D 100.000 9650 0 0 1 9650 132205538 132215187 0.000000e+00 17821.0
1 TraesCS1D01G125100 chr1A 94.555 3012 94 19 191 3138 159515969 159518974 0.000000e+00 4590.0
2 TraesCS1D01G125100 chr1A 94.654 1085 51 7 4221 5302 159522293 159523373 0.000000e+00 1676.0
3 TraesCS1D01G125100 chr1A 93.580 1106 43 11 7772 8859 159527525 159528620 0.000000e+00 1624.0
4 TraesCS1D01G125100 chr1A 93.917 822 24 4 3140 3951 159518944 159519749 0.000000e+00 1218.0
5 TraesCS1D01G125100 chr1A 92.622 637 45 2 9016 9650 506269365 506268729 0.000000e+00 915.0
6 TraesCS1D01G125100 chr1A 91.506 624 19 6 7210 7805 159526907 159527524 0.000000e+00 828.0
7 TraesCS1D01G125100 chr1A 93.640 456 23 3 6703 7156 159524578 159525029 0.000000e+00 676.0
8 TraesCS1D01G125100 chr1A 86.804 485 39 9 5329 5793 159523358 159523837 1.440000e-142 518.0
9 TraesCS1D01G125100 chr1A 84.199 443 38 16 5794 6215 159524158 159524589 1.510000e-107 401.0
10 TraesCS1D01G125100 chr1A 92.683 164 9 2 1 161 159514433 159514596 5.830000e-57 233.0
11 TraesCS1D01G125100 chr1A 91.083 157 13 1 8860 9015 506269548 506269392 2.730000e-50 211.0
12 TraesCS1D01G125100 chr1A 96.721 122 2 1 4104 4225 159521822 159521941 1.640000e-47 202.0
13 TraesCS1D01G125100 chr1B 94.451 2433 81 24 823 3237 205418894 205421290 0.000000e+00 3696.0
14 TraesCS1D01G125100 chr1B 96.635 1278 30 5 7471 8743 205427315 205428584 0.000000e+00 2109.0
15 TraesCS1D01G125100 chr1B 92.239 786 46 4 4442 5217 205423943 205424723 0.000000e+00 1099.0
16 TraesCS1D01G125100 chr1B 89.254 791 61 19 8858 9641 645945208 645945981 0.000000e+00 968.0
17 TraesCS1D01G125100 chr1B 90.595 723 43 14 5348 6055 205425947 205426659 0.000000e+00 935.0
18 TraesCS1D01G125100 chr1B 91.948 621 29 11 191 796 205418147 205418761 0.000000e+00 850.0
19 TraesCS1D01G125100 chr1B 96.480 483 17 0 3228 3710 205422451 205422933 0.000000e+00 798.0
20 TraesCS1D01G125100 chr1B 89.897 485 13 13 3777 4225 205422940 205423424 8.350000e-165 592.0
21 TraesCS1D01G125100 chr1B 94.795 365 16 3 6311 6675 205426957 205427318 5.060000e-157 566.0
22 TraesCS1D01G125100 chr1B 95.706 163 7 0 4221 4383 205423778 205423940 7.430000e-66 263.0
23 TraesCS1D01G125100 chr1B 96.154 52 2 0 8808 8859 205428583 205428634 1.730000e-12 86.1
24 TraesCS1D01G125100 chr2B 90.342 818 50 14 8859 9650 306906452 306905638 0.000000e+00 1046.0
25 TraesCS1D01G125100 chr2B 92.801 639 35 5 9016 9650 797075536 797074905 0.000000e+00 915.0
26 TraesCS1D01G125100 chr2B 86.823 812 75 15 8866 9650 528842282 528841476 0.000000e+00 878.0
27 TraesCS1D01G125100 chr2B 92.647 68 3 2 95 161 423777979 423778045 7.980000e-16 97.1
28 TraesCS1D01G125100 chr4D 93.636 660 30 9 8992 9647 215464627 215465278 0.000000e+00 976.0
29 TraesCS1D01G125100 chr4B 88.228 824 66 14 8854 9647 57172348 57171526 0.000000e+00 955.0
30 TraesCS1D01G125100 chr4B 92.647 68 3 2 95 162 653416354 653416419 7.980000e-16 97.1
31 TraesCS1D01G125100 chr6A 93.691 634 37 3 9019 9650 191240994 191240362 0.000000e+00 946.0
32 TraesCS1D01G125100 chr6A 87.826 115 13 1 6250 6363 590025887 590025773 6.080000e-27 134.0
33 TraesCS1D01G125100 chr5D 91.667 660 46 7 8992 9647 42233291 42233945 0.000000e+00 905.0
34 TraesCS1D01G125100 chr3B 91.168 668 50 7 8986 9650 637530589 637529928 0.000000e+00 898.0
35 TraesCS1D01G125100 chr3B 92.754 69 5 0 95 163 24930173 24930241 6.170000e-17 100.0
36 TraesCS1D01G125100 chr3B 90.667 75 6 1 3309 3383 189670834 189670761 2.220000e-16 99.0
37 TraesCS1D01G125100 chr7B 91.252 663 49 9 8992 9650 633894379 633895036 0.000000e+00 894.0
38 TraesCS1D01G125100 chr7B 91.429 70 4 2 95 162 18960818 18960749 2.870000e-15 95.3
39 TraesCS1D01G125100 chr5B 85.091 825 82 15 8859 9647 551514481 551515300 0.000000e+00 804.0
40 TraesCS1D01G125100 chr5B 90.826 109 4 5 8858 8962 450837890 450837784 3.630000e-29 141.0
41 TraesCS1D01G125100 chr7D 82.927 164 20 5 1 159 266365910 266365750 3.630000e-29 141.0
42 TraesCS1D01G125100 chr6B 75.796 314 54 11 8858 9155 478906248 478905941 1.310000e-28 139.0
43 TraesCS1D01G125100 chr6B 86.364 66 6 3 8859 8922 124388776 124388840 1.740000e-07 69.4
44 TraesCS1D01G125100 chr6B 94.286 35 1 1 5860 5894 656516804 656516771 1.800000e-02 52.8
45 TraesCS1D01G125100 chr7A 80.952 168 24 5 1 162 326507621 326507456 1.020000e-24 126.0
46 TraesCS1D01G125100 chr7A 86.538 52 4 2 8679 8727 271723304 271723355 5.000000e-03 54.7
47 TraesCS1D01G125100 chr2D 91.781 73 4 2 95 166 52847869 52847798 6.170000e-17 100.0
48 TraesCS1D01G125100 chr2D 91.549 71 4 2 95 164 553908282 553908351 7.980000e-16 97.1
49 TraesCS1D01G125100 chr2D 89.062 64 6 1 8853 8915 631943399 631943462 2.890000e-10 78.7
50 TraesCS1D01G125100 chr3D 90.667 75 6 1 3309 3383 133542934 133542861 2.220000e-16 99.0
51 TraesCS1D01G125100 chr3A 90.667 75 6 1 3309 3383 147291405 147291332 2.220000e-16 99.0


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 TraesCS1D01G125100 chr1D 132205538 132215187 9649 False 17821.00 17821 100.0000 1 9650 1 chr1D.!!$F1 9649
1 TraesCS1D01G125100 chr1A 159514433 159528620 14187 False 1196.60 4590 92.2259 1 8859 10 chr1A.!!$F1 8858
2 TraesCS1D01G125100 chr1A 506268729 506269548 819 True 563.00 915 91.8525 8860 9650 2 chr1A.!!$R1 790
3 TraesCS1D01G125100 chr1B 205418147 205428634 10487 False 1099.41 3696 93.8900 191 8859 10 chr1B.!!$F2 8668
4 TraesCS1D01G125100 chr1B 645945208 645945981 773 False 968.00 968 89.2540 8858 9641 1 chr1B.!!$F1 783
5 TraesCS1D01G125100 chr2B 306905638 306906452 814 True 1046.00 1046 90.3420 8859 9650 1 chr2B.!!$R1 791
6 TraesCS1D01G125100 chr2B 797074905 797075536 631 True 915.00 915 92.8010 9016 9650 1 chr2B.!!$R3 634
7 TraesCS1D01G125100 chr2B 528841476 528842282 806 True 878.00 878 86.8230 8866 9650 1 chr2B.!!$R2 784
8 TraesCS1D01G125100 chr4D 215464627 215465278 651 False 976.00 976 93.6360 8992 9647 1 chr4D.!!$F1 655
9 TraesCS1D01G125100 chr4B 57171526 57172348 822 True 955.00 955 88.2280 8854 9647 1 chr4B.!!$R1 793
10 TraesCS1D01G125100 chr6A 191240362 191240994 632 True 946.00 946 93.6910 9019 9650 1 chr6A.!!$R1 631
11 TraesCS1D01G125100 chr5D 42233291 42233945 654 False 905.00 905 91.6670 8992 9647 1 chr5D.!!$F1 655
12 TraesCS1D01G125100 chr3B 637529928 637530589 661 True 898.00 898 91.1680 8986 9650 1 chr3B.!!$R2 664
13 TraesCS1D01G125100 chr7B 633894379 633895036 657 False 894.00 894 91.2520 8992 9650 1 chr7B.!!$F1 658
14 TraesCS1D01G125100 chr5B 551514481 551515300 819 False 804.00 804 85.0910 8859 9647 1 chr5B.!!$F1 788

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
561 1916 0.040425 GCAAACCGTGTGATTTCGCT 60.040 50.000 0.00 0.00 0.00 4.93 F
1001 2470 0.916845 AAGAGGAGAGGGAAAGGGGC 60.917 60.000 0.00 0.00 0.00 5.80 F
1063 2532 1.686587 AGCAAAAGGAAGGGGAAAACG 59.313 47.619 0.00 0.00 0.00 3.60 F
1395 2866 1.993391 ACTGGGGATGGTGGTACCG 60.993 63.158 7.57 0.00 42.58 4.02 F
2134 3626 0.884704 GTTGCTGGTGACGGACATGT 60.885 55.000 0.00 0.00 39.98 3.21 F
3557 6252 0.105964 TCACTTGAGGGGTTGTGTCG 59.894 55.000 0.00 0.00 0.00 4.35 F
5099 10120 1.497278 CTCATGTTTGTCGTGGCCG 59.503 57.895 0.00 0.00 34.14 6.13 F
5475 11595 0.250338 GCTTAGAATAGGGCCCACCG 60.250 60.000 27.56 3.97 46.96 4.94 F
5478 11598 0.325860 TAGAATAGGGCCCACCGTGT 60.326 55.000 27.56 3.89 46.96 4.49 F
6877 13426 1.134220 TCGACATATCACTTTGGGGCC 60.134 52.381 0.00 0.00 0.00 5.80 F
8127 16570 0.657840 CTACCTTAACTGCGGCATGC 59.342 55.000 9.90 9.90 46.70 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1950 3442 0.466124 GTGGTGCTGTATCCCTCTCC 59.534 60.000 0.00 0.00 0.00 3.71 R
2115 3607 0.884704 ACATGTCCGTCACCAGCAAC 60.885 55.000 0.00 0.00 0.00 4.17 R
2134 3626 1.541118 TGGGACTTGGGCTGGATCA 60.541 57.895 0.00 0.00 0.00 2.92 R
2215 3707 1.800586 TGTTTGAGAAGTCGAGCATGC 59.199 47.619 10.51 10.51 0.00 4.06 R
3946 6651 0.720232 AGTCCCACACCCATACCCTA 59.280 55.000 0.00 0.00 0.00 3.53 R
5474 11594 0.179227 CACACACACACACACACACG 60.179 55.000 0.00 0.00 0.00 4.49 R
6413 12962 0.634465 ACCAAACCCTTTGACCCAGT 59.366 50.000 0.00 0.00 43.26 4.00 R
6744 13293 0.933097 GAGTAGCCGCACATGACATG 59.067 55.000 14.02 14.02 0.00 3.21 R
7369 15745 1.002502 GTGGTAACCCCCTGCTGTC 60.003 63.158 0.00 0.00 0.00 3.51 R
8523 16976 0.034574 AATAGACCGGCCATGCACAA 60.035 50.000 0.00 0.00 0.00 3.33 R
9575 18091 0.865111 CATTGTCGAGGTCGTTGCAA 59.135 50.000 0.00 0.00 40.80 4.08 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
75 76 0.386113 GTAGGTGTCTGATCGAGCCC 59.614 60.000 0.00 0.00 0.00 5.19
82 83 1.880340 CTGATCGAGCCCTGTTCGC 60.880 63.158 0.00 0.00 36.29 4.70
91 92 1.576421 CCCTGTTCGCAGCTTGTTC 59.424 57.895 0.00 0.00 43.67 3.18
92 93 1.165907 CCCTGTTCGCAGCTTGTTCA 61.166 55.000 0.00 0.00 43.67 3.18
141 145 9.878599 CTTCTATAAAAATATGGTACGCCTTTG 57.121 33.333 0.00 0.00 35.27 2.77
196 1543 6.012745 AGGATGAGTTTATTCTTTTGCAGGT 58.987 36.000 0.00 0.00 0.00 4.00
368 1715 4.388577 ACAAGACTTGCTTTCCCCTAAT 57.611 40.909 15.24 0.00 33.60 1.73
397 1744 0.465705 TGGGCTAATCGAGGAAGCAG 59.534 55.000 15.66 0.00 38.01 4.24
404 1751 3.616956 AATCGAGGAAGCAGAACATCA 57.383 42.857 0.00 0.00 0.00 3.07
425 1772 9.225436 ACATCAAATATTTGGCGGTTTATTTTT 57.775 25.926 24.40 0.00 38.66 1.94
426 1773 9.488124 CATCAAATATTTGGCGGTTTATTTTTG 57.512 29.630 24.40 0.00 38.66 2.44
433 1780 5.736486 TGGCGGTTTATTTTTGTTTTTCC 57.264 34.783 0.00 0.00 0.00 3.13
434 1781 5.429130 TGGCGGTTTATTTTTGTTTTTCCT 58.571 33.333 0.00 0.00 0.00 3.36
437 1784 6.689241 GGCGGTTTATTTTTGTTTTTCCTTTG 59.311 34.615 0.00 0.00 0.00 2.77
452 1799 1.662122 CCTTTGGCCGACACGTAATAC 59.338 52.381 0.00 0.00 0.00 1.89
484 1831 3.406512 ACATTCCTAGTGAGGGCTACT 57.593 47.619 0.00 0.00 43.94 2.57
529 1884 3.618997 GCACTCGTATTTCCTTCCCTTGA 60.619 47.826 0.00 0.00 0.00 3.02
561 1916 0.040425 GCAAACCGTGTGATTTCGCT 60.040 50.000 0.00 0.00 0.00 4.93
569 1924 2.417719 GTGTGATTTCGCTGTTCTCCT 58.582 47.619 0.00 0.00 0.00 3.69
572 1927 2.413453 GTGATTTCGCTGTTCTCCTCAC 59.587 50.000 0.00 0.00 0.00 3.51
815 2260 9.233649 AGTACTAATTATCAGCTCGCTACTTAT 57.766 33.333 0.00 0.00 0.00 1.73
1001 2470 0.916845 AAGAGGAGAGGGAAAGGGGC 60.917 60.000 0.00 0.00 0.00 5.80
1063 2532 1.686587 AGCAAAAGGAAGGGGAAAACG 59.313 47.619 0.00 0.00 0.00 3.60
1395 2866 1.993391 ACTGGGGATGGTGGTACCG 60.993 63.158 7.57 0.00 42.58 4.02
1406 2877 3.225104 TGGTGGTACCGGTAGTATCATC 58.775 50.000 16.41 11.86 43.91 2.92
1670 3161 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1950 3442 2.619074 GGATTGGTTGGAGGTCAAGAGG 60.619 54.545 0.00 0.00 35.80 3.69
2115 3607 3.287867 ACAACTTCTATGGGAGCCATG 57.712 47.619 0.00 0.00 44.84 3.66
2134 3626 0.884704 GTTGCTGGTGACGGACATGT 60.885 55.000 0.00 0.00 39.98 3.21
2215 3707 3.371063 CACAAGCCTGGGCAGCAG 61.371 66.667 14.39 3.15 44.88 4.24
2308 3800 5.048643 ACTCATCCGAGGTGAATAACGATAG 60.049 44.000 0.00 0.00 44.17 2.08
2311 3803 7.834625 CTCATCCGAGGTGAATAACGATAGTAC 60.835 44.444 0.00 0.00 42.02 2.73
2680 4202 7.756722 CACATGTTCTGATATTCCTTTGGAAAC 59.243 37.037 0.00 0.00 45.41 2.78
2825 4350 8.752005 TCCTCACCCTGAATTCTTTTATATTG 57.248 34.615 7.05 0.00 0.00 1.90
2917 4442 0.915364 ATGGAGAGGAGGGTTCTTGC 59.085 55.000 0.00 0.00 0.00 4.01
2923 4448 0.551131 AGGAGGGTTCTTGCTGGGAT 60.551 55.000 0.00 0.00 0.00 3.85
3126 4651 6.042552 CCATTACTCTCTCTCTCTCTCTCTCT 59.957 46.154 0.00 0.00 0.00 3.10
3128 4653 4.877773 ACTCTCTCTCTCTCTCTCTCTCT 58.122 47.826 0.00 0.00 0.00 3.10
3130 4655 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
3132 4657 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3134 4659 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3136 4661 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3138 4663 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3140 4665 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3142 4667 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3144 4669 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3146 4671 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3148 4673 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3166 4691 3.885901 TCTCTCTCTCTCTCTCTCTCTCG 59.114 52.174 0.00 0.00 0.00 4.04
3168 4693 2.101415 CTCTCTCTCTCTCTCTCTCGCA 59.899 54.545 0.00 0.00 0.00 5.10
3170 4695 1.552792 TCTCTCTCTCTCTCTCGCACA 59.447 52.381 0.00 0.00 0.00 4.57
3258 5953 9.897744 GAAAATGACTCTCACAATTGACATTTA 57.102 29.630 13.59 0.00 35.34 1.40
3427 6122 0.940833 TGACGATTCTTGCGTTGCAA 59.059 45.000 0.00 0.00 46.80 4.08
3440 6135 2.479837 CGTTGCAACAGTAGTGGAGAA 58.520 47.619 28.01 0.00 0.00 2.87
3557 6252 0.105964 TCACTTGAGGGGTTGTGTCG 59.894 55.000 0.00 0.00 0.00 4.35
3667 6362 2.307098 CTCCTGGGTCAAATTGAGGTCT 59.693 50.000 0.00 0.00 0.00 3.85
3747 6444 5.916661 TGGTACCTTGATCAGAAGAGTAC 57.083 43.478 14.36 12.87 33.41 2.73
4015 6853 1.509463 CTGTGTGCATGCATGGGAC 59.491 57.895 25.64 17.62 0.00 4.46
4197 8847 2.679342 ATACATGGGCCACGGCAGT 61.679 57.895 9.28 5.47 44.11 4.40
4433 9443 6.681729 ACGAAGGATCCAAATAGGCTATTA 57.318 37.500 19.53 5.48 37.29 0.98
4439 9449 5.817816 GGATCCAAATAGGCTATTATGGACG 59.182 44.000 31.21 17.03 37.75 4.79
4484 9494 3.326297 TCCCCAGGGTTTTAAGCAAAATG 59.674 43.478 4.22 0.00 36.10 2.32
4502 9512 8.562052 AGCAAAATGAATGGAATTTCAACTTTC 58.438 29.630 0.00 0.00 38.98 2.62
4503 9513 8.344098 GCAAAATGAATGGAATTTCAACTTTCA 58.656 29.630 4.16 4.16 38.98 2.69
4598 9608 2.159382 AGGGTGAGTGCCGTAAAAATG 58.841 47.619 0.00 0.00 0.00 2.32
4751 9771 7.794810 CGTTTGGAAATATAATTGCATGCATTG 59.205 33.333 23.37 0.00 30.43 2.82
4785 9805 4.764172 CACCCTGATTCAAGACTCCTTAG 58.236 47.826 0.00 0.00 0.00 2.18
4869 9889 3.479006 CGCATGTAACGAAAGGTGAAAG 58.521 45.455 0.00 0.00 0.00 2.62
5099 10120 1.497278 CTCATGTTTGTCGTGGCCG 59.503 57.895 0.00 0.00 34.14 6.13
5120 10141 7.996644 TGGCCGAGGTTATAGAAAAATTTATCT 59.003 33.333 0.00 0.00 0.00 1.98
5148 10169 8.709646 CGTCTAGAATAACCAATAAATACCAGC 58.290 37.037 0.00 0.00 0.00 4.85
5160 10182 8.465999 CCAATAAATACCAGCAAACTTGTGATA 58.534 33.333 0.00 0.00 0.00 2.15
5167 10189 7.524717 ACCAGCAAACTTGTGATAAATTACT 57.475 32.000 0.00 0.00 0.00 2.24
5168 10190 7.370383 ACCAGCAAACTTGTGATAAATTACTG 58.630 34.615 0.00 0.00 0.00 2.74
5308 10330 9.197306 AGAATAAAACTTGTTCTAAAACAGGGT 57.803 29.630 5.57 0.00 43.59 4.34
5311 10333 7.706100 AAAACTTGTTCTAAAACAGGGTACA 57.294 32.000 5.57 0.00 41.14 2.90
5312 10334 7.706100 AAACTTGTTCTAAAACAGGGTACAA 57.294 32.000 5.57 0.00 41.14 2.41
5313 10335 7.706100 AACTTGTTCTAAAACAGGGTACAAA 57.294 32.000 5.57 0.00 45.72 2.83
5314 10336 7.706100 ACTTGTTCTAAAACAGGGTACAAAA 57.294 32.000 5.57 0.00 45.72 2.44
5315 10337 8.301252 ACTTGTTCTAAAACAGGGTACAAAAT 57.699 30.769 5.57 0.00 45.72 1.82
5316 10338 9.411189 ACTTGTTCTAAAACAGGGTACAAAATA 57.589 29.630 5.57 0.00 45.72 1.40
5389 11508 9.635404 AACCCTATTTCGGAATTAATTATCACA 57.365 29.630 0.00 0.00 0.00 3.58
5471 11591 2.373502 ACTCATGCTTAGAATAGGGCCC 59.626 50.000 16.46 16.46 0.00 5.80
5472 11592 2.373169 CTCATGCTTAGAATAGGGCCCA 59.627 50.000 27.56 10.89 0.00 5.36
5474 11594 0.843984 TGCTTAGAATAGGGCCCACC 59.156 55.000 27.56 9.71 40.67 4.61
5475 11595 0.250338 GCTTAGAATAGGGCCCACCG 60.250 60.000 27.56 3.97 46.96 4.94
5476 11596 1.129058 CTTAGAATAGGGCCCACCGT 58.871 55.000 27.56 5.28 46.96 4.83
5477 11597 0.834612 TTAGAATAGGGCCCACCGTG 59.165 55.000 27.56 0.00 46.96 4.94
5478 11598 0.325860 TAGAATAGGGCCCACCGTGT 60.326 55.000 27.56 3.89 46.96 4.49
5479 11599 1.451387 GAATAGGGCCCACCGTGTG 60.451 63.158 27.56 0.00 46.96 3.82
5480 11600 2.193087 GAATAGGGCCCACCGTGTGT 62.193 60.000 27.56 2.06 46.96 3.72
5481 11601 2.478335 AATAGGGCCCACCGTGTGTG 62.478 60.000 27.56 0.00 46.96 3.82
5611 11754 9.767684 TTTGTGAATATAACTAAATGCGAGTTG 57.232 29.630 0.00 0.00 37.68 3.16
5629 11772 5.173131 CGAGTTGCACAAAAACATAAAGTCC 59.827 40.000 0.00 0.00 0.00 3.85
5630 11773 5.040635 AGTTGCACAAAAACATAAAGTCCG 58.959 37.500 0.00 0.00 0.00 4.79
5632 11775 2.403698 GCACAAAAACATAAAGTCCGCG 59.596 45.455 0.00 0.00 0.00 6.46
5747 11890 5.016173 TGAAACTCATTTTGGGGGTATCTG 58.984 41.667 0.00 0.00 0.00 2.90
5864 12327 8.144478 AGTGCACGAAATATTATCACATACTCT 58.856 33.333 12.01 0.00 0.00 3.24
5865 12328 8.765219 GTGCACGAAATATTATCACATACTCTT 58.235 33.333 0.00 0.00 0.00 2.85
5967 12432 8.732746 ACTAATTGGCGACTTGATAGTAATTT 57.267 30.769 0.00 0.00 33.84 1.82
6351 12900 7.652300 TTCATTTATGTGGTATATGACGAGC 57.348 36.000 0.00 0.00 32.65 5.03
6352 12901 5.861787 TCATTTATGTGGTATATGACGAGCG 59.138 40.000 0.00 0.00 29.36 5.03
6373 12922 5.365895 AGCGGGAGTACATAACTATTTTCCT 59.634 40.000 0.00 0.00 39.07 3.36
6450 12999 6.972901 GGTTTGGTACTTGACTTTTGAGAAAG 59.027 38.462 0.00 0.00 46.17 2.62
6702 13251 9.812347 ATAAAATATGTGGATTAAGCTGGATGA 57.188 29.630 0.00 0.00 0.00 2.92
6703 13252 8.716674 AAAATATGTGGATTAAGCTGGATGAT 57.283 30.769 0.00 0.00 0.00 2.45
6704 13253 9.812347 AAAATATGTGGATTAAGCTGGATGATA 57.188 29.630 0.00 0.00 0.00 2.15
6705 13254 9.812347 AAATATGTGGATTAAGCTGGATGATAA 57.188 29.630 0.00 0.00 0.00 1.75
6706 13255 9.986157 AATATGTGGATTAAGCTGGATGATAAT 57.014 29.630 0.00 0.00 0.00 1.28
6772 13321 3.403968 TGTGCGGCTACTCATTAAACAA 58.596 40.909 0.00 0.00 0.00 2.83
6817 13366 8.876275 ATAGTTTACATGCCAAATTAATGCTG 57.124 30.769 0.00 0.00 0.00 4.41
6818 13367 5.581874 AGTTTACATGCCAAATTAATGCTGC 59.418 36.000 0.00 0.00 0.00 5.25
6841 13390 8.188531 TGCCACGTGTATAGTAATTAACTTTC 57.811 34.615 15.65 0.00 39.80 2.62
6842 13391 7.009448 TGCCACGTGTATAGTAATTAACTTTCG 59.991 37.037 15.65 0.00 39.80 3.46
6877 13426 1.134220 TCGACATATCACTTTGGGGCC 60.134 52.381 0.00 0.00 0.00 5.80
6880 13429 3.365472 GACATATCACTTTGGGGCCTTT 58.635 45.455 0.84 0.00 0.00 3.11
6890 13439 6.671779 TCACTTTGGGGCCTTTTTATAATCAT 59.328 34.615 0.84 0.00 0.00 2.45
6963 13514 7.530426 AGAGAAGCATAAAACAATGAAGGTT 57.470 32.000 0.00 0.00 0.00 3.50
6998 13549 2.280933 CGCCACCCACCGTTAACA 60.281 61.111 6.39 0.00 0.00 2.41
7035 13586 8.622948 AGTCTCCTCGTTTGAATTATTTTCTT 57.377 30.769 0.00 0.00 0.00 2.52
7135 13686 3.824133 AGCACAATAGCCATCATTGCTA 58.176 40.909 0.00 0.00 44.78 3.49
7281 15656 5.832539 ACCCCATAGGATGAAGTTATGAG 57.167 43.478 0.00 0.00 39.89 2.90
7284 15659 6.183361 ACCCCATAGGATGAAGTTATGAGTTC 60.183 42.308 0.00 0.00 39.89 3.01
7354 15730 8.215954 ACTCAGTAAAATAACTAAGGGGAACT 57.784 34.615 0.00 0.00 0.00 3.01
7366 15742 5.878669 ACTAAGGGGAACTTTTAACATAGCG 59.121 40.000 0.00 0.00 40.64 4.26
7367 15743 3.014623 AGGGGAACTTTTAACATAGCGC 58.985 45.455 0.00 0.00 0.00 5.92
7368 15744 2.223180 GGGGAACTTTTAACATAGCGCG 60.223 50.000 0.00 0.00 0.00 6.86
7369 15745 2.223180 GGGAACTTTTAACATAGCGCGG 60.223 50.000 8.83 0.00 0.00 6.46
7388 15764 1.772567 ACAGCAGGGGGTTACCACA 60.773 57.895 5.81 0.00 45.22 4.17
7411 15787 8.720562 CACATAGTTACATGACTGAACAAATGA 58.279 33.333 0.00 0.00 0.00 2.57
8030 16473 5.750484 TGAGTTGCAATTAAGTACGTACG 57.250 39.130 19.49 15.01 0.00 3.67
8038 16481 1.962412 TAAGTACGTACGTGTTGGCG 58.038 50.000 30.25 0.00 37.94 5.69
8083 16526 8.495554 TTTTATTTACATTGTGCAACGTACAG 57.504 30.769 0.00 0.00 42.39 2.74
8085 16528 6.788684 ATTTACATTGTGCAACGTACAGTA 57.211 33.333 0.00 0.00 42.39 2.74
8120 16563 3.891056 AACGTTTGCTACCTTAACTGC 57.109 42.857 0.00 0.00 0.00 4.40
8127 16570 0.657840 CTACCTTAACTGCGGCATGC 59.342 55.000 9.90 9.90 46.70 4.06
8216 16668 1.972223 CCTCGTCCCAGTCTCGTGT 60.972 63.158 0.00 0.00 0.00 4.49
8220 16672 1.505353 GTCCCAGTCTCGTGTACGG 59.495 63.158 4.44 0.00 40.29 4.02
8337 16789 1.779221 ATATGTGTTGTGCATGGGGG 58.221 50.000 0.00 0.00 0.00 5.40
8479 16931 2.159379 GGGTGAAAGCGATTAAGCCTTG 60.159 50.000 9.33 0.00 37.11 3.61
8517 16970 2.681848 CTGCGAAGAGGCTTTTCATGAT 59.318 45.455 16.86 0.00 0.00 2.45
8523 16976 4.313020 AGAGGCTTTTCATGATGGAAGT 57.687 40.909 0.00 0.00 0.00 3.01
8745 17200 7.395489 AGGAAGAATGAGATACAAAAGTGCAAT 59.605 33.333 0.00 0.00 0.00 3.56
8763 17218 3.585862 CAATGTCCTACGTACACAAGCT 58.414 45.455 6.68 0.00 0.00 3.74
8766 17221 0.892755 TCCTACGTACACAAGCTGGG 59.107 55.000 0.00 0.00 0.00 4.45
8769 17224 0.393448 TACGTACACAAGCTGGGCAA 59.607 50.000 0.00 0.00 0.00 4.52
8798 17253 0.165295 CACATGAGCACAAGACAGCG 59.835 55.000 0.00 0.00 35.48 5.18
8800 17255 2.037136 ATGAGCACAAGACAGCGCC 61.037 57.895 2.29 0.00 35.48 6.53
8813 17268 1.669115 AGCGCCAACACAGCTACAG 60.669 57.895 2.29 0.00 39.74 2.74
8888 17345 1.152183 GGAGGAATACCCCGGCCTA 60.152 63.158 0.00 0.00 36.73 3.93
8964 17431 6.823689 TCATAAGGTCCAAAGAAGCTCATAAC 59.176 38.462 0.00 0.00 0.00 1.89
9010 17509 2.050442 GAAAAGCGCCACAACCGG 60.050 61.111 2.29 0.00 0.00 5.28
9047 17547 9.751542 GAATAATAAGCTACGATGCCTATACAT 57.248 33.333 0.00 0.00 0.00 2.29
9144 17646 0.111253 ACCAAAGGCTCCCTGAAGTG 59.889 55.000 0.00 0.00 32.13 3.16
9641 18159 9.770097 GAATACATGGATTTCACTGAGAAGATA 57.230 33.333 4.21 0.00 37.57 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 5.344884 CACTAAAGCTACTCTCTGGCTAAC 58.655 45.833 0.00 0.00 35.06 2.34
21 22 6.369890 TGAAAATGCACTAAAGCTACTCTCTG 59.630 38.462 0.00 0.00 34.99 3.35
82 83 7.864379 AGACAATTTACAAGATTGAACAAGCTG 59.136 33.333 6.09 4.04 37.11 4.24
91 92 7.814642 AGAGAGCAAGACAATTTACAAGATTG 58.185 34.615 0.00 0.00 39.73 2.67
92 93 7.992754 AGAGAGCAAGACAATTTACAAGATT 57.007 32.000 0.00 0.00 0.00 2.40
169 1505 7.121168 CCTGCAAAAGAATAAACTCATCCTACA 59.879 37.037 0.00 0.00 0.00 2.74
184 1520 7.575414 TGTAAACTTGATACCTGCAAAAGAA 57.425 32.000 0.00 0.00 0.00 2.52
368 1715 4.442893 CCTCGATTAGCCCATAACAAGTGA 60.443 45.833 0.00 0.00 0.00 3.41
397 1744 8.419076 AATAAACCGCCAAATATTTGATGTTC 57.581 30.769 26.32 10.62 40.55 3.18
425 1772 1.135333 GTGTCGGCCAAAGGAAAAACA 59.865 47.619 2.24 0.00 0.00 2.83
426 1773 1.847818 GTGTCGGCCAAAGGAAAAAC 58.152 50.000 2.24 0.00 0.00 2.43
431 1778 0.322322 ATTACGTGTCGGCCAAAGGA 59.678 50.000 2.24 0.00 0.00 3.36
433 1780 2.339418 TGTATTACGTGTCGGCCAAAG 58.661 47.619 2.24 0.00 0.00 2.77
434 1781 2.452295 TGTATTACGTGTCGGCCAAA 57.548 45.000 2.24 0.00 0.00 3.28
437 1784 2.124903 CTCATGTATTACGTGTCGGCC 58.875 52.381 14.19 0.00 36.53 6.13
452 1799 5.536538 TCACTAGGAATGTAGGTAGCTCATG 59.463 44.000 0.00 0.00 0.00 3.07
498 1853 3.241995 GGAAATACGAGTGCGCTACAAAG 60.242 47.826 9.73 3.75 42.48 2.77
529 1884 1.269726 CGGTTTGCTTGCTTGGATTGT 60.270 47.619 0.00 0.00 0.00 2.71
561 1916 1.070134 CGTCCTTTGGTGAGGAGAACA 59.930 52.381 0.00 0.00 46.18 3.18
569 1924 7.276658 TGCTTAATATATTCGTCCTTTGGTGA 58.723 34.615 0.00 0.00 0.00 4.02
572 1927 7.042321 TCGTTGCTTAATATATTCGTCCTTTGG 60.042 37.037 0.00 0.00 0.00 3.28
815 2260 4.701171 ACGAGTACCTTTCAAACAACCAAA 59.299 37.500 0.00 0.00 0.00 3.28
1001 2470 1.226746 ACTTTCCGTTGCTTTCCTCG 58.773 50.000 0.00 0.00 0.00 4.63
1027 2496 6.879458 TCCTTTTGCTTCACTCCTTTATCTAC 59.121 38.462 0.00 0.00 0.00 2.59
1063 2532 1.550524 GGGGAATCTGGGCTTTGTTTC 59.449 52.381 0.00 0.00 0.00 2.78
1141 2610 4.263506 GGGGTATATGATGTTCTTGGGAGG 60.264 50.000 0.00 0.00 0.00 4.30
1395 2866 5.923684 GCTTCAAGCTACTGATGATACTACC 59.076 44.000 0.71 0.00 38.45 3.18
1406 2877 0.737219 GGCATGGCTTCAAGCTACTG 59.263 55.000 12.86 5.74 41.99 2.74
1670 3161 7.440198 TCTTCTTATCTGAATCACTAGCATGG 58.560 38.462 0.00 0.00 0.00 3.66
1716 3208 5.295292 AGCTACACATACTCACGTACGTAAT 59.705 40.000 22.34 11.76 0.00 1.89
1721 3213 4.879104 AGAGCTACACATACTCACGTAC 57.121 45.455 0.00 0.00 32.71 3.67
1733 3225 2.456073 TCCTTCCCCTAGAGCTACAC 57.544 55.000 0.00 0.00 0.00 2.90
1818 3310 4.924305 AGTGAAATGAACATGCAACAGT 57.076 36.364 0.00 0.00 0.00 3.55
1950 3442 0.466124 GTGGTGCTGTATCCCTCTCC 59.534 60.000 0.00 0.00 0.00 3.71
2088 3580 5.104900 GGCTCCCATAGAAGTTGTAAGAAGA 60.105 44.000 0.00 0.00 0.00 2.87
2115 3607 0.884704 ACATGTCCGTCACCAGCAAC 60.885 55.000 0.00 0.00 0.00 4.17
2134 3626 1.541118 TGGGACTTGGGCTGGATCA 60.541 57.895 0.00 0.00 0.00 2.92
2215 3707 1.800586 TGTTTGAGAAGTCGAGCATGC 59.199 47.619 10.51 10.51 0.00 4.06
2252 3744 4.704103 TGGCTCCTCAGCTCCGGT 62.704 66.667 0.00 0.00 46.03 5.28
2372 3889 6.857437 AAATAAAGCCAGCCATAGAAAACT 57.143 33.333 0.00 0.00 0.00 2.66
2548 4066 9.725206 AAACCTGAACCTAGAGGATTATTACTA 57.275 33.333 1.60 0.00 38.94 1.82
2680 4202 6.940298 TCAATTAACTAGTTCACCAAAGAGGG 59.060 38.462 12.39 0.00 43.89 4.30
2772 4297 3.691609 GCAAAACATCCAGTAGCTAGCTT 59.308 43.478 24.88 1.98 0.00 3.74
2825 4350 7.203910 ACAGCTGAACACTTATACTATAGCAC 58.796 38.462 23.35 0.00 0.00 4.40
2917 4442 6.372931 TGACCCCATTTTTATCTTATCCCAG 58.627 40.000 0.00 0.00 0.00 4.45
3126 4651 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3128 4653 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3130 4655 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3132 4657 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3134 4659 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3136 4661 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3138 4663 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3140 4665 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3142 4667 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
3144 4669 3.885901 CGAGAGAGAGAGAGAGAGAGAGA 59.114 52.174 0.00 0.00 0.00 3.10
3146 4671 2.362397 GCGAGAGAGAGAGAGAGAGAGA 59.638 54.545 0.00 0.00 0.00 3.10
3148 4673 2.107366 TGCGAGAGAGAGAGAGAGAGA 58.893 52.381 0.00 0.00 0.00 3.10
3258 5953 6.134535 TGTAAACTGGATGGTAGTGGAAAT 57.865 37.500 0.00 0.00 0.00 2.17
3427 6122 8.908903 CATTTAGATCTAGTTCTCCACTACTGT 58.091 37.037 6.60 0.00 36.88 3.55
3440 6135 4.647853 TGCGGGTACACATTTAGATCTAGT 59.352 41.667 2.02 0.00 0.00 2.57
3521 6216 4.110036 AGTGAACTGAAACAGGCAAAAC 57.890 40.909 0.00 0.00 35.51 2.43
3557 6252 6.564125 CGTGTGTCAGAGATAAACTTTGGTTC 60.564 42.308 0.00 0.00 34.14 3.62
3667 6362 7.301420 AGAGAGAGAGAGAGAGAGAGAGATTA 58.699 42.308 0.00 0.00 0.00 1.75
3747 6444 3.055819 CCCATATGTCCTCTATTCACCCG 60.056 52.174 1.24 0.00 0.00 5.28
3852 6549 1.374947 GCAGTGGTGGGCTCAACTA 59.625 57.895 1.77 0.00 0.00 2.24
3946 6651 0.720232 AGTCCCACACCCATACCCTA 59.280 55.000 0.00 0.00 0.00 3.53
4197 8847 2.516227 TTTGAATGGATGCCCCGTTA 57.484 45.000 0.27 0.00 44.02 3.18
4433 9443 1.978580 ACCCTGAAGTCTTTCGTCCAT 59.021 47.619 0.00 0.00 36.04 3.41
4439 9449 2.155279 GGCTCAACCCTGAAGTCTTTC 58.845 52.381 0.00 0.00 0.00 2.62
4525 9535 0.934436 GCACACGCGAAAACATGCTT 60.934 50.000 15.93 0.00 0.00 3.91
4598 9608 6.313905 CAGGTCACAAGGTTTACTATGACATC 59.686 42.308 11.44 0.16 38.54 3.06
4761 9781 1.680249 GGAGTCTTGAATCAGGGTGCC 60.680 57.143 0.63 0.00 0.00 5.01
4869 9889 9.750125 CCTTCCATAATAAGGTTATTCAAAAGC 57.250 33.333 0.00 0.00 38.98 3.51
4873 9893 7.724061 GGCTCCTTCCATAATAAGGTTATTCAA 59.276 37.037 0.00 0.00 43.42 2.69
5074 10095 2.226200 CACGACAAACATGAGCATCCAA 59.774 45.455 0.00 0.00 0.00 3.53
5148 10169 9.897744 ATGACACAGTAATTTATCACAAGTTTG 57.102 29.630 0.00 0.00 0.00 2.93
5286 10308 8.804912 TGTACCCTGTTTTAGAACAAGTTTTA 57.195 30.769 0.03 0.00 44.65 1.52
5290 10312 7.706100 TTTTGTACCCTGTTTTAGAACAAGT 57.294 32.000 0.03 3.97 44.65 3.16
5330 10352 9.838339 AGATAGCAGCTAATTTACTACATTGTT 57.162 29.630 6.13 0.00 0.00 2.83
5350 11465 9.498176 TCCGAAATAGGGTTTTTATTAGATAGC 57.502 33.333 0.00 0.00 0.00 2.97
5472 11592 1.004320 ACACACACACACACACGGT 60.004 52.632 0.00 0.00 0.00 4.83
5474 11594 0.179227 CACACACACACACACACACG 60.179 55.000 0.00 0.00 0.00 4.49
5475 11595 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
5476 11596 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
5477 11597 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
5478 11598 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
5479 11599 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
5480 11600 2.289133 ACTACACACACACACACACACA 60.289 45.455 0.00 0.00 0.00 3.72
5481 11601 2.343101 ACTACACACACACACACACAC 58.657 47.619 0.00 0.00 0.00 3.82
5588 11730 7.822575 GCAACTCGCATTTAGTTATATTCAC 57.177 36.000 0.00 0.00 41.79 3.18
5606 11749 5.173131 CGGACTTTATGTTTTTGTGCAACTC 59.827 40.000 0.00 0.00 38.04 3.01
5611 11754 2.403698 CGCGGACTTTATGTTTTTGTGC 59.596 45.455 0.00 0.00 0.00 4.57
5615 11758 2.096119 CGGACGCGGACTTTATGTTTTT 60.096 45.455 12.47 0.00 0.00 1.94
5629 11772 0.918619 CCACATAAACTACGGACGCG 59.081 55.000 3.53 3.53 0.00 6.01
5630 11773 2.000429 ACCACATAAACTACGGACGC 58.000 50.000 0.00 0.00 0.00 5.19
5632 11775 9.538508 AAAAGATATACCACATAAACTACGGAC 57.461 33.333 0.00 0.00 0.00 4.79
6010 12476 8.587608 CACCCCCTCGTAACACTATATATAAAA 58.412 37.037 0.00 0.00 0.00 1.52
6012 12478 7.240897 ACACCCCCTCGTAACACTATATATAA 58.759 38.462 0.00 0.00 0.00 0.98
6147 12695 8.842280 AGGTTCAACTATTTATTTCGTGAAACA 58.158 29.630 0.00 0.00 35.74 2.83
6164 12712 4.385825 TGCATTAACGAGAAGGTTCAACT 58.614 39.130 0.00 0.00 0.00 3.16
6291 12840 9.827411 CCTCTTTAGCTTTTTAACATACTTCAC 57.173 33.333 0.00 0.00 0.00 3.18
6292 12841 9.569122 ACCTCTTTAGCTTTTTAACATACTTCA 57.431 29.630 0.00 0.00 0.00 3.02
6299 12848 9.796180 TGGTTATACCTCTTTAGCTTTTTAACA 57.204 29.630 0.00 0.00 39.58 2.41
6304 12853 9.528489 TGAATTGGTTATACCTCTTTAGCTTTT 57.472 29.630 0.00 0.00 39.58 2.27
6305 12854 9.700831 ATGAATTGGTTATACCTCTTTAGCTTT 57.299 29.630 0.00 0.00 39.58 3.51
6306 12855 9.700831 AATGAATTGGTTATACCTCTTTAGCTT 57.299 29.630 0.00 0.00 39.58 3.74
6307 12856 9.700831 AAATGAATTGGTTATACCTCTTTAGCT 57.299 29.630 0.00 0.00 39.58 3.32
6413 12962 0.634465 ACCAAACCCTTTGACCCAGT 59.366 50.000 0.00 0.00 43.26 4.00
6676 13225 9.812347 TCATCCAGCTTAATCCACATATTTTAT 57.188 29.630 0.00 0.00 0.00 1.40
6677 13226 9.812347 ATCATCCAGCTTAATCCACATATTTTA 57.188 29.630 0.00 0.00 0.00 1.52
6678 13227 8.716674 ATCATCCAGCTTAATCCACATATTTT 57.283 30.769 0.00 0.00 0.00 1.82
6679 13228 9.812347 TTATCATCCAGCTTAATCCACATATTT 57.188 29.630 0.00 0.00 0.00 1.40
6680 13229 9.986157 ATTATCATCCAGCTTAATCCACATATT 57.014 29.630 0.00 0.00 0.00 1.28
6744 13293 0.933097 GAGTAGCCGCACATGACATG 59.067 55.000 14.02 14.02 0.00 3.21
6816 13365 7.009448 CGAAAGTTAATTACTATACACGTGGCA 59.991 37.037 21.57 7.60 35.54 4.92
6817 13366 7.332530 CGAAAGTTAATTACTATACACGTGGC 58.667 38.462 21.57 0.00 35.54 5.01
6818 13367 7.489113 ACCGAAAGTTAATTACTATACACGTGG 59.511 37.037 21.57 4.06 35.54 4.94
6841 13390 4.655440 TGTCGATACATGTTTTCAACCG 57.345 40.909 2.30 0.00 0.00 4.44
6842 13391 7.850982 GTGATATGTCGATACATGTTTTCAACC 59.149 37.037 2.30 0.00 45.99 3.77
6858 13407 1.134098 AGGCCCCAAAGTGATATGTCG 60.134 52.381 0.00 0.00 0.00 4.35
6890 13439 9.360093 CGCTTGTTAATTTAATGGGAATAAACA 57.640 29.630 0.00 0.00 0.00 2.83
6901 13450 5.121768 ACTGCTCGTCGCTTGTTAATTTAAT 59.878 36.000 0.00 0.00 40.11 1.40
6963 13514 2.420722 GGCGACCCGATAAAAATGAACA 59.579 45.455 0.00 0.00 0.00 3.18
6991 13542 2.289444 ACTCCTGGTGGACATGTTAACG 60.289 50.000 0.00 0.00 37.46 3.18
6998 13549 2.998493 GGAGACTCCTGGTGGACAT 58.002 57.895 14.72 0.00 37.46 3.06
7059 13610 8.557450 AGTGTACTTTCCTCCCATTGTTATAAT 58.443 33.333 0.00 0.00 0.00 1.28
7199 13750 9.724839 CAGCAAAGAAATTTGTTTTTCATGAAT 57.275 25.926 9.40 0.00 37.93 2.57
7200 13751 8.944029 TCAGCAAAGAAATTTGTTTTTCATGAA 58.056 25.926 10.39 3.38 37.93 2.57
7201 13752 8.489990 TCAGCAAAGAAATTTGTTTTTCATGA 57.510 26.923 10.39 9.32 37.93 3.07
7203 13754 8.496707 ACTCAGCAAAGAAATTTGTTTTTCAT 57.503 26.923 10.39 0.00 37.93 2.57
7204 13755 7.903995 ACTCAGCAAAGAAATTTGTTTTTCA 57.096 28.000 10.39 0.00 37.93 2.69
7206 13757 9.964303 AAAAACTCAGCAAAGAAATTTGTTTTT 57.036 22.222 10.39 12.03 39.01 1.94
7265 15640 6.127054 CCCAGTGAACTCATAACTTCATCCTA 60.127 42.308 0.00 0.00 0.00 2.94
7278 15653 1.611977 CGTACTGTCCCAGTGAACTCA 59.388 52.381 7.13 0.00 45.01 3.41
7281 15656 3.508762 CATACGTACTGTCCCAGTGAAC 58.491 50.000 7.13 0.00 45.01 3.18
7284 15659 1.203758 TGCATACGTACTGTCCCAGTG 59.796 52.381 7.13 0.00 45.01 3.66
7297 15672 7.239166 ACATCTTAATTTCTGAGTGCATACG 57.761 36.000 0.00 0.00 0.00 3.06
7352 15728 2.671396 CTGTCCGCGCTATGTTAAAAGT 59.329 45.455 5.56 0.00 0.00 2.66
7354 15730 1.395608 GCTGTCCGCGCTATGTTAAAA 59.604 47.619 5.56 0.00 0.00 1.52
7366 15742 3.712907 TAACCCCCTGCTGTCCGC 61.713 66.667 0.00 0.00 39.77 5.54
7367 15743 2.267961 GTAACCCCCTGCTGTCCG 59.732 66.667 0.00 0.00 0.00 4.79
7368 15744 2.228480 TGGTAACCCCCTGCTGTCC 61.228 63.158 0.00 0.00 0.00 4.02
7369 15745 1.002502 GTGGTAACCCCCTGCTGTC 60.003 63.158 0.00 0.00 0.00 3.51
7380 15756 7.601130 TGTTCAGTCATGTAACTATGTGGTAAC 59.399 37.037 0.00 0.00 0.00 2.50
7388 15764 7.066284 GCCTCATTTGTTCAGTCATGTAACTAT 59.934 37.037 0.00 0.00 0.00 2.12
7411 15787 1.134521 TGTCGACTTTCAGTGTTGCCT 60.135 47.619 17.92 0.00 0.00 4.75
7829 16266 2.189191 CTGCTGCTCTGGTTGGCCTA 62.189 60.000 3.32 0.00 35.27 3.93
8030 16473 4.591998 ATTTTGTTTGTTTCGCCAACAC 57.408 36.364 0.00 0.00 45.54 3.32
8083 16526 4.600012 ACGTTAACTGATGCAGCAATAC 57.400 40.909 5.96 0.83 34.37 1.89
8085 16528 4.229096 CAAACGTTAACTGATGCAGCAAT 58.771 39.130 5.96 0.00 34.37 3.56
8098 16541 4.084433 CGCAGTTAAGGTAGCAAACGTTAA 60.084 41.667 0.00 11.01 42.93 2.01
8099 16542 3.429543 CGCAGTTAAGGTAGCAAACGTTA 59.570 43.478 0.00 0.00 37.39 3.18
8100 16543 2.222445 CGCAGTTAAGGTAGCAAACGTT 59.778 45.455 0.00 0.00 39.44 3.99
8101 16544 1.796459 CGCAGTTAAGGTAGCAAACGT 59.204 47.619 0.00 0.00 0.00 3.99
8102 16545 1.127951 CCGCAGTTAAGGTAGCAAACG 59.872 52.381 0.00 0.00 0.00 3.60
8120 16563 0.740149 ACACATGGTATTGCATGCCG 59.260 50.000 16.68 0.00 37.93 5.69
8127 16570 6.371548 GCACCCTGTATATACACATGGTATTG 59.628 42.308 19.29 13.27 43.16 1.90
8337 16789 0.604578 TTACGTACTCCTGCACCACC 59.395 55.000 0.00 0.00 0.00 4.61
8338 16790 1.271656 AGTTACGTACTCCTGCACCAC 59.728 52.381 0.00 0.00 28.23 4.16
8479 16931 3.125146 TCGCAGAAACAATGCAGATACAC 59.875 43.478 0.00 0.00 44.05 2.90
8517 16970 2.267351 CGGCCATGCACAACTTCCA 61.267 57.895 2.24 0.00 0.00 3.53
8523 16976 0.034574 AATAGACCGGCCATGCACAA 60.035 50.000 0.00 0.00 0.00 3.33
8643 17098 2.741985 CATGGCGCAGACGGACAA 60.742 61.111 10.83 0.00 41.59 3.18
8656 17111 5.824904 AAAATCAGCTAGTAAGTGCATGG 57.175 39.130 0.00 0.00 0.00 3.66
8745 17200 1.271379 CCAGCTTGTGTACGTAGGACA 59.729 52.381 0.00 0.00 0.00 4.02
8763 17218 1.070786 GTGACGTCTCCTTTGCCCA 59.929 57.895 17.92 0.00 0.00 5.36
8766 17221 1.728971 CTCATGTGACGTCTCCTTTGC 59.271 52.381 17.92 0.00 0.00 3.68
8769 17224 0.969149 TGCTCATGTGACGTCTCCTT 59.031 50.000 17.92 2.92 0.00 3.36
8798 17253 4.035675 GGATAATTCTGTAGCTGTGTTGGC 59.964 45.833 0.00 0.00 0.00 4.52
8800 17255 6.108687 TCTGGATAATTCTGTAGCTGTGTTG 58.891 40.000 0.00 0.00 0.00 3.33
8970 17438 5.932303 TCAGATATATTTGCTTTCGGCTACC 59.068 40.000 0.00 0.00 42.39 3.18
8981 17453 4.676924 GTGGCGCTTTTCAGATATATTTGC 59.323 41.667 7.64 0.00 0.00 3.68
8982 17454 5.820131 TGTGGCGCTTTTCAGATATATTTG 58.180 37.500 7.64 0.00 0.00 2.32
8987 17459 2.423538 GGTTGTGGCGCTTTTCAGATAT 59.576 45.455 7.64 0.00 0.00 1.63
8990 17462 1.781025 CGGTTGTGGCGCTTTTCAGA 61.781 55.000 7.64 0.00 0.00 3.27
8991 17463 1.370414 CGGTTGTGGCGCTTTTCAG 60.370 57.895 7.64 0.00 0.00 3.02
8992 17464 2.718731 CGGTTGTGGCGCTTTTCA 59.281 55.556 7.64 0.00 0.00 2.69
8993 17465 2.050442 CCGGTTGTGGCGCTTTTC 60.050 61.111 7.64 0.00 0.00 2.29
9010 17509 5.957910 AGCTTATTATTCTATCGCATCGC 57.042 39.130 0.00 0.00 0.00 4.58
9011 17510 6.905609 TCGTAGCTTATTATTCTATCGCATCG 59.094 38.462 0.00 0.00 0.00 3.84
9012 17511 8.686418 CATCGTAGCTTATTATTCTATCGCATC 58.314 37.037 0.00 0.00 0.00 3.91
9013 17512 7.168302 GCATCGTAGCTTATTATTCTATCGCAT 59.832 37.037 0.00 0.00 0.00 4.73
9014 17513 6.472486 GCATCGTAGCTTATTATTCTATCGCA 59.528 38.462 0.00 0.00 0.00 5.10
9043 17543 7.827729 TGGCGAGCTAATAATAGACTAGATGTA 59.172 37.037 0.00 0.00 0.00 2.29
9047 17547 5.415077 GGTGGCGAGCTAATAATAGACTAGA 59.585 44.000 0.00 0.00 0.00 2.43
9093 17594 1.667151 CGTTGGGAGACGGTACCAA 59.333 57.895 13.54 0.00 41.66 3.67
9144 17646 1.281899 GTCCTTACTCACTCATGCGC 58.718 55.000 0.00 0.00 0.00 6.09
9575 18091 0.865111 CATTGTCGAGGTCGTTGCAA 59.135 50.000 0.00 0.00 40.80 4.08


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

AutoCloner maintained by Alex Coulton.