Multiple sequence alignment - TraesCS7A01G227000

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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 TraesCS7A01G227000 chr7A 100.000 5949 0 0 3424 9372 197291455 197297403 0.000000e+00 10986.0
1 TraesCS7A01G227000 chr7A 100.000 3124 0 0 1 3124 197288032 197291155 0.000000e+00 5770.0
2 TraesCS7A01G227000 chr7A 93.165 673 42 4 5 674 26792778 26793449 0.000000e+00 985.0
3 TraesCS7A01G227000 chr7A 92.878 674 46 2 1 672 284739155 284738482 0.000000e+00 977.0
4 TraesCS7A01G227000 chr7A 92.456 676 47 4 1 674 514885939 514885266 0.000000e+00 963.0
5 TraesCS7A01G227000 chr7A 77.855 578 85 21 3424 3998 538523234 538522697 1.520000e-82 318.0
6 TraesCS7A01G227000 chr7A 91.398 93 6 2 2968 3060 432684660 432684750 9.880000e-25 126.0
7 TraesCS7A01G227000 chr7A 91.176 68 4 2 2072 2138 197289905 197289971 3.600000e-14 91.6
8 TraesCS7A01G227000 chr7A 91.176 68 4 2 1874 1940 197290103 197290169 3.600000e-14 91.6
9 TraesCS7A01G227000 chr7D 93.597 5982 250 62 3424 9354 187206212 187200313 0.000000e+00 8802.0
10 TraesCS7A01G227000 chr7D 92.899 1690 69 21 697 2361 187208864 187207201 0.000000e+00 2409.0
11 TraesCS7A01G227000 chr7D 93.413 501 23 3 2355 2847 187207040 187206542 0.000000e+00 734.0
12 TraesCS7A01G227000 chr7D 96.484 256 7 2 2842 3097 187206513 187206260 1.130000e-113 422.0
13 TraesCS7A01G227000 chr7D 80.035 576 78 25 3426 3998 461647495 461648036 8.820000e-105 392.0
14 TraesCS7A01G227000 chr7D 84.018 219 31 4 3741 3956 208219922 208219705 3.430000e-49 207.0
15 TraesCS7A01G227000 chr7D 89.552 67 7 0 3044 3110 88334999 88335065 1.680000e-12 86.1
16 TraesCS7A01G227000 chr7D 84.375 64 9 1 3929 3992 133314063 133314125 2.830000e-05 62.1
17 TraesCS7A01G227000 chr7B 96.532 3201 82 12 5491 8683 330537063 330533884 0.000000e+00 5269.0
18 TraesCS7A01G227000 chr7B 88.817 1708 88 36 706 2361 330541291 330539635 0.000000e+00 2001.0
19 TraesCS7A01G227000 chr7B 87.893 1082 67 29 4399 5459 330538500 330537462 0.000000e+00 1214.0
20 TraesCS7A01G227000 chr7B 88.922 677 40 13 3747 4399 330539506 330538841 0.000000e+00 802.0
21 TraesCS7A01G227000 chr7B 91.089 303 12 4 9014 9316 330532868 330532581 6.820000e-106 396.0
22 TraesCS7A01G227000 chr7B 87.245 196 11 4 8664 8846 330533868 330533674 2.650000e-50 211.0
23 TraesCS7A01G227000 chr7B 87.611 113 11 3 8822 8931 330533674 330533562 2.750000e-25 128.0
24 TraesCS7A01G227000 chr7B 90.217 92 9 0 2969 3060 50982269 50982360 4.600000e-23 121.0
25 TraesCS7A01G227000 chr7B 89.231 65 5 2 8933 8996 330533331 330533268 7.800000e-11 80.5
26 TraesCS7A01G227000 chr5A 93.917 674 38 3 1 672 285360662 285359990 0.000000e+00 1014.0
27 TraesCS7A01G227000 chr5A 92.962 682 45 3 1 679 489918181 489917500 0.000000e+00 990.0
28 TraesCS7A01G227000 chr5A 92.151 688 46 8 1 684 19266309 19265626 0.000000e+00 965.0
29 TraesCS7A01G227000 chr5A 92.391 92 7 0 2969 3060 207080064 207079973 2.120000e-26 132.0
30 TraesCS7A01G227000 chr5A 79.874 159 10 8 2972 3109 356499357 356499200 7.750000e-16 97.1
31 TraesCS7A01G227000 chr1A 93.491 676 42 2 1 674 494819942 494820617 0.000000e+00 1003.0
32 TraesCS7A01G227000 chr1A 80.645 310 51 7 3433 3739 145990159 145990462 2.040000e-56 231.0
33 TraesCS7A01G227000 chr3A 93.175 674 43 3 1 672 215470044 215469372 0.000000e+00 987.0
34 TraesCS7A01G227000 chr3A 83.178 107 13 3 3596 3701 666227261 666227363 1.000000e-14 93.5
35 TraesCS7A01G227000 chr2A 92.160 676 50 3 1 674 653029332 653030006 0.000000e+00 952.0
36 TraesCS7A01G227000 chr2A 79.368 475 82 11 3433 3907 680540209 680540667 4.220000e-83 320.0
37 TraesCS7A01G227000 chr2A 81.395 172 31 1 3737 3908 102106427 102106597 1.270000e-28 139.0
38 TraesCS7A01G227000 chr2A 92.553 94 6 1 2967 3060 442379978 442379886 5.900000e-27 134.0
39 TraesCS7A01G227000 chr2B 79.531 469 82 12 3426 3891 641186179 641186636 1.170000e-83 322.0
40 TraesCS7A01G227000 chr2B 76.379 580 108 17 3426 3998 798619843 798619286 1.540000e-72 285.0
41 TraesCS7A01G227000 chr2B 81.633 245 40 4 3715 3956 317239197 317238955 2.060000e-46 198.0
42 TraesCS7A01G227000 chr2D 80.556 432 69 13 3434 3862 538316203 538316622 1.520000e-82 318.0
43 TraesCS7A01G227000 chr2D 90.323 93 7 1 2968 3060 41287615 41287525 4.600000e-23 121.0
44 TraesCS7A01G227000 chr6A 83.969 262 40 2 3737 3998 29959465 29959724 5.620000e-62 250.0
45 TraesCS7A01G227000 chr1B 79.430 316 54 6 3426 3739 193003001 193002695 7.370000e-51 213.0
46 TraesCS7A01G227000 chr1B 90.217 92 9 0 2969 3060 99769782 99769873 4.600000e-23 121.0
47 TraesCS7A01G227000 chr1B 92.063 63 4 1 3044 3105 24801471 24801533 4.660000e-13 87.9
48 TraesCS7A01G227000 chr5B 83.929 224 32 4 3737 3957 401937398 401937620 2.650000e-50 211.0
49 TraesCS7A01G227000 chr3B 83.482 224 33 4 3737 3957 368958260 368958482 1.230000e-48 206.0
50 TraesCS7A01G227000 chr3B 80.247 162 12 7 2969 3110 28571018 28570857 4.630000e-18 104.0
51 TraesCS7A01G227000 chr6D 81.967 244 40 4 3757 3998 211700858 211701099 4.440000e-48 204.0
52 TraesCS7A01G227000 chr4A 89.051 137 14 1 2969 3104 729218249 729218385 1.620000e-37 169.0
53 TraesCS7A01G227000 chr4B 89.130 92 10 0 2969 3060 167336554 167336645 2.140000e-21 115.0
54 TraesCS7A01G227000 chr4B 80.576 139 26 1 4361 4498 80064796 80064934 1.290000e-18 106.0
55 TraesCS7A01G227000 chr1D 80.473 169 13 6 2962 3110 280996295 280996463 2.770000e-20 111.0
56 TraesCS7A01G227000 chr1D 94.030 67 4 0 3044 3110 322270766 322270832 1.670000e-17 102.0
57 TraesCS7A01G227000 chr6B 89.706 68 5 2 3044 3110 520275113 520275047 1.680000e-12 86.1
58 TraesCS7A01G227000 chr5D 76.829 164 23 6 3741 3904 491012786 491012638 2.810000e-10 78.7


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 TraesCS7A01G227000 chr7A 197288032 197297403 9371 False 4234.8000 10986 95.58800 1 9372 4 chr7A.!!$F3 9371
1 TraesCS7A01G227000 chr7A 26792778 26793449 671 False 985.0000 985 93.16500 5 674 1 chr7A.!!$F1 669
2 TraesCS7A01G227000 chr7A 284738482 284739155 673 True 977.0000 977 92.87800 1 672 1 chr7A.!!$R1 671
3 TraesCS7A01G227000 chr7A 514885266 514885939 673 True 963.0000 963 92.45600 1 674 1 chr7A.!!$R2 673
4 TraesCS7A01G227000 chr7A 538522697 538523234 537 True 318.0000 318 77.85500 3424 3998 1 chr7A.!!$R3 574
5 TraesCS7A01G227000 chr7D 187200313 187208864 8551 True 3091.7500 8802 94.09825 697 9354 4 chr7D.!!$R2 8657
6 TraesCS7A01G227000 chr7D 461647495 461648036 541 False 392.0000 392 80.03500 3426 3998 1 chr7D.!!$F3 572
7 TraesCS7A01G227000 chr7B 330532581 330541291 8710 True 1262.6875 5269 89.66750 706 9316 8 chr7B.!!$R1 8610
8 TraesCS7A01G227000 chr5A 285359990 285360662 672 True 1014.0000 1014 93.91700 1 672 1 chr5A.!!$R3 671
9 TraesCS7A01G227000 chr5A 489917500 489918181 681 True 990.0000 990 92.96200 1 679 1 chr5A.!!$R5 678
10 TraesCS7A01G227000 chr5A 19265626 19266309 683 True 965.0000 965 92.15100 1 684 1 chr5A.!!$R1 683
11 TraesCS7A01G227000 chr1A 494819942 494820617 675 False 1003.0000 1003 93.49100 1 674 1 chr1A.!!$F2 673
12 TraesCS7A01G227000 chr3A 215469372 215470044 672 True 987.0000 987 93.17500 1 672 1 chr3A.!!$R1 671
13 TraesCS7A01G227000 chr2A 653029332 653030006 674 False 952.0000 952 92.16000 1 674 1 chr2A.!!$F2 673
14 TraesCS7A01G227000 chr2B 798619286 798619843 557 True 285.0000 285 76.37900 3426 3998 1 chr2B.!!$R2 572

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
103 104 1.517832 GGATACGACAGCTGCTGGT 59.482 57.895 31.00 22.21 35.51 4.00 F
1366 1381 1.197721 CTTGCTCCTAGTTTTGCCACG 59.802 52.381 0.00 0.00 0.00 4.94 F
2189 2247 0.330267 ATTAACTCCACCCCAACCGG 59.670 55.000 0.00 0.00 0.00 5.28 F
3880 4159 0.109781 CACCGGAAAACGCCATTCAG 60.110 55.000 9.46 0.00 42.52 3.02 F
4008 4309 0.313987 TCATCCCTACGTGCATAGCG 59.686 55.000 0.00 0.00 0.00 4.26 F
4060 4361 0.457851 GTGCATGTAGCTCTCTCGGT 59.542 55.000 0.00 0.00 45.94 4.69 F
4654 5298 0.542805 CATGGAAATTTGGCCCCCTG 59.457 55.000 0.00 0.00 0.00 4.45 F
5262 5922 0.899717 GGTTTGAATCCTGCCTGGCA 60.900 55.000 21.96 21.96 36.92 4.92 F
5427 6094 0.916086 AGTTTGTGGTGGTGGAGTCA 59.084 50.000 0.00 0.00 0.00 3.41 F
5772 6806 1.133792 GTGCCCTATGCCCAGTGTTAT 60.134 52.381 0.00 0.00 40.16 1.89 F
7438 8480 1.406539 CTGCTGAACAACTTGGCTGTT 59.593 47.619 0.00 0.00 39.69 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1412 1427 1.654220 CTGCAACACCAAACCTCGG 59.346 57.895 0.00 0.00 0.00 4.63 R
2817 3053 0.241213 CGGAGTCGACTTCTGCAAGA 59.759 55.000 21.08 0.00 39.30 3.02 R
4078 4379 0.999406 TGTTTTAGCTGATCGCGAGC 59.001 50.000 19.12 19.12 45.59 5.03 R
5213 5873 0.530744 CCTGGTCGTACAAGCTAGCA 59.469 55.000 18.83 0.00 0.00 3.49 R
5247 5907 0.991146 TTAGTGCCAGGCAGGATTCA 59.009 50.000 16.83 0.00 40.08 2.57 R
5452 6119 1.133253 CTTGCGCGGTCTGTGATTG 59.867 57.895 8.83 0.00 0.00 2.67 R
6458 7493 1.403249 CGAGTAAACACCCAGGTACCG 60.403 57.143 6.18 1.26 0.00 4.02 R
6707 7747 3.463944 ACGACGAACAATTTCAAGGTCT 58.536 40.909 0.00 0.00 0.00 3.85 R
6918 7959 5.533903 CAGGCTGTTATTTGCAAGGAGATAT 59.466 40.000 6.28 0.00 0.00 1.63 R
7492 8534 1.967779 TCAGTTTCTGGGATGTCACGA 59.032 47.619 0.00 0.00 31.51 4.35 R
8652 9700 0.679640 TCCCATGTTTCCGGATGCAC 60.680 55.000 4.15 3.19 0.00 4.57 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
50 51 1.722034 GGCACTGGGATCCTATCTGA 58.278 55.000 12.58 0.00 0.00 3.27
103 104 1.517832 GGATACGACAGCTGCTGGT 59.482 57.895 31.00 22.21 35.51 4.00
554 558 3.517140 GGGCCGCAAATGCATCGA 61.517 61.111 0.00 0.00 42.21 3.59
619 624 3.645975 CGCCACTTTTGTCCGCGT 61.646 61.111 4.92 0.00 40.96 6.01
652 658 2.332654 GCAGCGGACGAAATGGGTT 61.333 57.895 0.00 0.00 0.00 4.11
662 668 3.292460 ACGAAATGGGTTGGTCTTTTGA 58.708 40.909 0.00 0.00 0.00 2.69
681 687 6.892658 TTTGAAGTTGCTCTAAATTAGCCA 57.107 33.333 0.00 0.00 39.30 4.75
682 688 7.466746 TTTGAAGTTGCTCTAAATTAGCCAT 57.533 32.000 0.00 0.00 39.30 4.40
684 690 6.855836 TGAAGTTGCTCTAAATTAGCCATTG 58.144 36.000 0.00 0.00 39.30 2.82
685 691 6.434028 TGAAGTTGCTCTAAATTAGCCATTGT 59.566 34.615 0.00 0.00 39.30 2.71
686 692 7.609918 TGAAGTTGCTCTAAATTAGCCATTGTA 59.390 33.333 0.00 0.00 39.30 2.41
687 693 7.321745 AGTTGCTCTAAATTAGCCATTGTAC 57.678 36.000 0.00 0.00 39.30 2.90
688 694 6.884295 AGTTGCTCTAAATTAGCCATTGTACA 59.116 34.615 0.00 0.00 39.30 2.90
689 695 7.557719 AGTTGCTCTAAATTAGCCATTGTACAT 59.442 33.333 0.00 0.00 39.30 2.29
690 696 8.836413 GTTGCTCTAAATTAGCCATTGTACATA 58.164 33.333 0.00 0.00 39.30 2.29
691 697 8.378172 TGCTCTAAATTAGCCATTGTACATAC 57.622 34.615 0.00 0.00 39.30 2.39
692 698 7.444183 TGCTCTAAATTAGCCATTGTACATACC 59.556 37.037 0.00 0.00 39.30 2.73
693 699 7.094762 GCTCTAAATTAGCCATTGTACATACCC 60.095 40.741 0.00 0.00 33.73 3.69
694 700 8.041143 TCTAAATTAGCCATTGTACATACCCT 57.959 34.615 0.00 0.00 0.00 4.34
695 701 9.161572 TCTAAATTAGCCATTGTACATACCCTA 57.838 33.333 0.00 0.00 0.00 3.53
696 702 9.787435 CTAAATTAGCCATTGTACATACCCTAA 57.213 33.333 0.00 3.02 0.00 2.69
697 703 8.691661 AAATTAGCCATTGTACATACCCTAAG 57.308 34.615 0.00 0.00 0.00 2.18
698 704 6.818281 TTAGCCATTGTACATACCCTAAGT 57.182 37.500 0.00 0.00 0.00 2.24
699 705 5.710409 AGCCATTGTACATACCCTAAGTT 57.290 39.130 0.00 0.00 0.00 2.66
700 706 6.074698 AGCCATTGTACATACCCTAAGTTT 57.925 37.500 0.00 0.00 0.00 2.66
701 707 6.120220 AGCCATTGTACATACCCTAAGTTTC 58.880 40.000 0.00 0.00 0.00 2.78
702 708 6.069615 AGCCATTGTACATACCCTAAGTTTCT 60.070 38.462 0.00 0.00 0.00 2.52
703 709 6.602009 GCCATTGTACATACCCTAAGTTTCTT 59.398 38.462 0.00 0.00 0.00 2.52
704 710 7.415206 GCCATTGTACATACCCTAAGTTTCTTG 60.415 40.741 0.00 0.00 0.00 3.02
862 868 4.035102 GCTCCTCCCACCCACCAC 62.035 72.222 0.00 0.00 0.00 4.16
863 869 3.330720 CTCCTCCCACCCACCACC 61.331 72.222 0.00 0.00 0.00 4.61
881 887 2.750350 CCAGAGTCCCACACCCAC 59.250 66.667 0.00 0.00 0.00 4.61
882 888 2.146724 CCAGAGTCCCACACCCACA 61.147 63.158 0.00 0.00 0.00 4.17
959 973 2.517402 CCCGGACGGAGAGAGAGG 60.517 72.222 13.13 0.00 37.50 3.69
962 976 1.820481 CGGACGGAGAGAGAGGGAC 60.820 68.421 0.00 0.00 0.00 4.46
1321 1335 3.691326 AGGTTCGCCCCCTCCCTA 61.691 66.667 0.00 0.00 38.27 3.53
1322 1336 3.162154 GGTTCGCCCCCTCCCTAG 61.162 72.222 0.00 0.00 0.00 3.02
1364 1379 1.247567 GCTTGCTCCTAGTTTTGCCA 58.752 50.000 0.00 0.00 0.00 4.92
1366 1381 1.197721 CTTGCTCCTAGTTTTGCCACG 59.802 52.381 0.00 0.00 0.00 4.94
1412 1427 9.952188 GTTAATTTCTTGCTGAGTATTTATCCC 57.048 33.333 0.00 0.00 0.00 3.85
1426 1442 1.364269 TATCCCCGAGGTTTGGTGTT 58.636 50.000 0.00 0.00 0.00 3.32
1638 1654 2.650778 CCCCCTTTTGTTGAGCGC 59.349 61.111 0.00 0.00 0.00 5.92
1709 1726 4.362932 TTGCGTTGAAATTGTGAACTCA 57.637 36.364 0.00 0.00 0.00 3.41
1785 1826 5.449314 CCGGACTGACTAGTAAGATTGTCTG 60.449 48.000 14.67 6.71 37.25 3.51
1794 1835 7.536855 ACTAGTAAGATTGTCTGTTAACTCCG 58.463 38.462 7.22 0.00 0.00 4.63
2032 2076 4.168101 TCCTCAAAGTTCACCACTAGGAT 58.832 43.478 0.00 0.00 34.13 3.24
2188 2246 3.570912 ATATTAACTCCACCCCAACCG 57.429 47.619 0.00 0.00 0.00 4.44
2189 2247 0.330267 ATTAACTCCACCCCAACCGG 59.670 55.000 0.00 0.00 0.00 5.28
2190 2248 1.061324 TTAACTCCACCCCAACCGGT 61.061 55.000 0.00 0.00 36.18 5.28
2261 2319 8.138712 GGTTCTCGATCAGATATTTAACTCAGT 58.861 37.037 0.00 0.00 0.00 3.41
2271 2329 7.380870 CAGATATTTAACTCAGTCACCAGATCG 59.619 40.741 0.00 0.00 0.00 3.69
2304 2364 4.697352 AGTTGAACAGAGCCATATGTTGTC 59.303 41.667 1.24 0.00 40.84 3.18
2382 2610 7.206687 TCCACATGAAACCTTACATTTTTGTC 58.793 34.615 0.00 0.00 0.00 3.18
2441 2669 8.842280 TCTATTGTCCGACAAACAGTTATTTTT 58.158 29.630 17.64 0.03 41.96 1.94
2566 2802 6.003326 TGAAAAATGCTGATACTGGTTCTGA 58.997 36.000 0.00 0.00 0.00 3.27
2574 2810 5.049818 GCTGATACTGGTTCTGACAATATGC 60.050 44.000 0.00 0.00 0.00 3.14
2578 2814 4.511527 ACTGGTTCTGACAATATGCTCTG 58.488 43.478 0.00 0.00 0.00 3.35
2592 2828 7.781693 ACAATATGCTCTGGTTAAATGATTCCT 59.218 33.333 0.00 0.00 0.00 3.36
2596 2832 5.415701 TGCTCTGGTTAAATGATTCCTTGAC 59.584 40.000 0.00 0.00 0.00 3.18
2607 2843 5.828299 TGATTCCTTGACGAAAACAAGTT 57.172 34.783 0.00 0.00 41.88 2.66
2618 2854 8.973835 TGACGAAAACAAGTTAAAATTGTCTT 57.026 26.923 7.55 1.51 39.91 3.01
2664 2900 6.697019 CGAAAACAAGTGAAAATGGTCTCAAT 59.303 34.615 0.00 0.00 0.00 2.57
2673 2909 9.753674 AGTGAAAATGGTCTCAATAAAGGATAA 57.246 29.630 0.00 0.00 0.00 1.75
2713 2949 0.623723 TCTATGGGCCACCTTCAACC 59.376 55.000 9.28 0.00 37.76 3.77
2736 2972 5.821470 CCAGTTATCATCATGTCTTTCTGCT 59.179 40.000 0.00 0.00 0.00 4.24
2753 2989 5.411831 TCTGCTCAGAAGTGTGTTCATAT 57.588 39.130 0.00 0.00 33.91 1.78
2795 3031 0.884704 TGTCCAGAAACTTGCTCGCC 60.885 55.000 0.00 0.00 0.00 5.54
2797 3033 1.302832 CCAGAAACTTGCTCGCCCT 60.303 57.895 0.00 0.00 0.00 5.19
2817 3053 3.765511 CCTGTGATGATTTGGTCCACAAT 59.234 43.478 0.00 0.00 39.21 2.71
2824 3060 3.256383 TGATTTGGTCCACAATCTTGCAG 59.744 43.478 19.12 0.00 39.21 4.41
2836 3072 0.241213 TCTTGCAGAAGTCGACTCCG 59.759 55.000 20.33 11.30 37.07 4.63
2847 3083 2.358737 GACTCCGCCACCCACAAG 60.359 66.667 0.00 0.00 0.00 3.16
2868 3137 2.643551 CCAATCCTAAGCCGACATGTT 58.356 47.619 0.00 0.00 0.00 2.71
2902 3171 2.683211 ATACCTTTGCATGATCCCCC 57.317 50.000 0.00 0.00 0.00 5.40
2944 3213 6.801367 TTCAACTATGTATACGAAGCGTTC 57.199 37.500 0.00 0.00 41.54 3.95
2991 3260 2.095212 GGGATGAAAACAGAGCGGAAAC 60.095 50.000 0.00 0.00 0.00 2.78
3012 3281 2.351336 GACGGATCTGGGTGCTACCG 62.351 65.000 6.47 0.00 39.83 4.02
3092 3361 3.476181 GAAACAAACACGGAGCGAATAC 58.524 45.455 0.00 0.00 0.00 1.89
3093 3362 1.065358 ACAAACACGGAGCGAATACG 58.935 50.000 0.00 0.00 42.79 3.06
3094 3363 0.368907 CAAACACGGAGCGAATACGG 59.631 55.000 0.00 0.00 40.71 4.02
3095 3364 1.356527 AAACACGGAGCGAATACGGC 61.357 55.000 0.00 0.00 40.71 5.68
3096 3365 3.320078 CACGGAGCGAATACGGCG 61.320 66.667 4.80 4.80 40.71 6.46
3097 3366 3.818787 ACGGAGCGAATACGGCGT 61.819 61.111 19.64 19.64 40.71 5.68
3098 3367 3.320078 CGGAGCGAATACGGCGTG 61.320 66.667 24.86 6.78 40.15 5.34
3099 3368 2.960129 GGAGCGAATACGGCGTGG 60.960 66.667 24.86 10.22 40.15 4.94
3100 3369 2.103538 GAGCGAATACGGCGTGGA 59.896 61.111 24.86 3.21 40.15 4.02
3101 3370 2.202703 AGCGAATACGGCGTGGAC 60.203 61.111 24.86 12.07 40.15 4.02
3102 3371 2.507547 GCGAATACGGCGTGGACA 60.508 61.111 24.86 1.82 40.15 4.02
3528 3798 9.217278 TGCATTTGTGCATATTTTATTCAACTT 57.783 25.926 0.00 0.00 40.23 2.66
3573 3843 3.347077 AATCAGAAGGACAAGCTCCAG 57.653 47.619 0.00 0.00 42.46 3.86
3593 3863 7.362056 GCTCCAGATGTAAAGAAAAGCACAATA 60.362 37.037 0.00 0.00 0.00 1.90
3595 3865 8.677300 TCCAGATGTAAAGAAAAGCACAATATC 58.323 33.333 0.00 0.00 0.00 1.63
3683 3953 1.305930 GCCCGGTCTCAATTGTGGTC 61.306 60.000 5.13 0.89 0.00 4.02
3732 4002 5.355071 TGCTATTAGAAATTGAGCCACACAG 59.645 40.000 0.00 0.00 31.98 3.66
3741 4011 3.070576 GCCACACAGGGGCCAATC 61.071 66.667 4.39 0.00 45.87 2.67
3742 4012 2.765969 CCACACAGGGGCCAATCT 59.234 61.111 4.39 0.00 0.00 2.40
3743 4013 1.998530 CCACACAGGGGCCAATCTA 59.001 57.895 4.39 0.00 0.00 1.98
3744 4014 0.394352 CCACACAGGGGCCAATCTAC 60.394 60.000 4.39 0.00 0.00 2.59
3745 4015 0.620556 CACACAGGGGCCAATCTACT 59.379 55.000 4.39 0.00 0.00 2.57
3879 4158 1.519751 CCACCGGAAAACGCCATTCA 61.520 55.000 9.46 0.00 42.52 2.57
3880 4159 0.109781 CACCGGAAAACGCCATTCAG 60.110 55.000 9.46 0.00 42.52 3.02
3973 4274 0.820074 TCTGCCGGAAAAGCGGAAAA 60.820 50.000 5.05 0.00 42.56 2.29
3974 4275 0.387239 CTGCCGGAAAAGCGGAAAAG 60.387 55.000 5.05 0.00 39.03 2.27
3975 4276 1.733041 GCCGGAAAAGCGGAAAAGC 60.733 57.895 5.05 0.00 37.41 3.51
4008 4309 0.313987 TCATCCCTACGTGCATAGCG 59.686 55.000 0.00 0.00 0.00 4.26
4011 4312 1.661821 CCCTACGTGCATAGCGCTC 60.662 63.158 16.34 0.00 43.06 5.03
4060 4361 0.457851 GTGCATGTAGCTCTCTCGGT 59.542 55.000 0.00 0.00 45.94 4.69
4097 4398 0.999406 GCTCGCGATCAGCTAAAACA 59.001 50.000 10.36 0.00 45.59 2.83
4111 4412 7.168219 TCAGCTAAAACAGATTACAGATTGGT 58.832 34.615 0.00 0.00 0.00 3.67
4135 4436 9.838339 GGTAGACTATATAATAGCCAAATGCAT 57.162 33.333 0.00 0.00 44.83 3.96
4156 4457 8.228035 TGCATGTGTAGTACCTTTTAAGTTTT 57.772 30.769 0.00 0.00 0.00 2.43
4207 4508 1.197036 GCAACTTCCTTCGGTGCTTAC 59.803 52.381 0.00 0.00 0.00 2.34
4222 4523 2.228582 TGCTTACACACATGTTCATGCC 59.771 45.455 12.00 0.00 40.48 4.40
4227 4528 2.156917 CACACATGTTCATGCCTGACT 58.843 47.619 12.00 0.00 0.00 3.41
4262 4563 9.418839 GACTAGGACTAGGAAACCTAATTCTTA 57.581 37.037 10.81 0.00 35.49 2.10
4272 4573 8.715842 AGGAAACCTAATTCTTATACTCCTTCC 58.284 37.037 0.00 0.00 28.47 3.46
4314 4616 9.556030 GCCTATAAAGTCAAACAGTGTAAAATC 57.444 33.333 0.00 0.00 0.00 2.17
4458 5101 5.639757 ACAAGCTTTTTCAAAATTTGCACC 58.360 33.333 0.00 0.00 31.26 5.01
4464 5107 5.862924 TTTTCAAAATTTGCACCGTTTGA 57.137 30.435 11.80 11.80 38.01 2.69
4468 5111 4.564769 TCAAAATTTGCACCGTTTGACTTC 59.435 37.500 11.80 0.00 35.60 3.01
4469 5112 2.399396 ATTTGCACCGTTTGACTTCG 57.601 45.000 0.00 0.00 0.00 3.79
4529 5172 2.104669 GGACTTATCCCTACAGCCCT 57.895 55.000 0.00 0.00 39.39 5.19
4530 5173 2.409570 GGACTTATCCCTACAGCCCTT 58.590 52.381 0.00 0.00 39.39 3.95
4531 5174 3.584294 GGACTTATCCCTACAGCCCTTA 58.416 50.000 0.00 0.00 39.39 2.69
4532 5175 3.324268 GGACTTATCCCTACAGCCCTTAC 59.676 52.174 0.00 0.00 39.39 2.34
4589 5232 2.169663 GCATTCAAGTGTCATGCTCG 57.830 50.000 9.57 0.00 40.23 5.03
4629 5273 0.959553 ACGTCATCTCACCGTGACTT 59.040 50.000 0.00 0.00 41.90 3.01
4630 5274 1.340248 ACGTCATCTCACCGTGACTTT 59.660 47.619 0.00 0.00 41.90 2.66
4654 5298 0.542805 CATGGAAATTTGGCCCCCTG 59.457 55.000 0.00 0.00 0.00 4.45
4663 5307 3.451894 GGCCCCCTGTTGATTGCG 61.452 66.667 0.00 0.00 0.00 4.85
4677 5321 1.157257 ATTGCGTGTCACACAGCGAA 61.157 50.000 15.61 12.40 36.96 4.70
4731 5375 6.161855 TCAAGAATGTATATCAGGCGACTT 57.838 37.500 0.00 0.00 40.21 3.01
4837 5482 7.028361 GGAGCTAGTACAAAAGTACACAGTAG 58.972 42.308 8.32 3.02 32.56 2.57
4847 5492 9.120538 ACAAAAGTACACAGTAGACAATCAAAT 57.879 29.630 0.00 0.00 0.00 2.32
4854 5499 6.094048 ACACAGTAGACAATCAAATATGGCAC 59.906 38.462 0.00 0.00 0.00 5.01
4915 5560 7.014615 ACTGAAAATTCCAATCAGGCATATACC 59.985 37.037 6.92 0.00 43.79 2.73
4947 5592 3.848272 ATAAACATTGAAGCCACGTGG 57.152 42.857 30.66 30.66 38.53 4.94
5000 5645 4.081862 TCCACGAGGAGTTACCACATTAAG 60.082 45.833 0.00 0.00 39.61 1.85
5009 5654 7.834342 GGAGTTACCACATTAAGCAAGAGCTC 61.834 46.154 5.27 5.27 44.38 4.09
5066 5711 2.172082 AGAGCTCTTGCATGGAAGCATA 59.828 45.455 21.14 4.48 45.19 3.14
5067 5712 2.548904 GAGCTCTTGCATGGAAGCATAG 59.451 50.000 21.14 14.55 45.19 2.23
5082 5742 2.097142 AGCATAGACGTGACCTTCGTAC 59.903 50.000 0.00 0.00 41.64 3.67
5094 5754 7.171678 ACGTGACCTTCGTACTTATACCTATAC 59.828 40.741 0.00 0.00 39.78 1.47
5099 5759 8.989980 ACCTTCGTACTTATACCTATACGTTAC 58.010 37.037 0.00 0.00 40.88 2.50
5135 5795 1.022982 CATGCATGCAGACCGTGAGT 61.023 55.000 26.69 2.26 31.89 3.41
5151 5811 3.561310 CGTGAGTTGCAGCATGGTATTAT 59.439 43.478 2.55 0.00 35.86 1.28
5213 5873 4.141756 TGAATTGATTTGGTGCAGTGGTTT 60.142 37.500 0.00 0.00 0.00 3.27
5256 5916 2.202479 GCGCGGTTTGAATCCTGC 60.202 61.111 8.83 0.00 0.00 4.85
5260 5920 1.937546 GCGGTTTGAATCCTGCCTGG 61.938 60.000 0.00 0.00 37.10 4.45
5262 5922 0.899717 GGTTTGAATCCTGCCTGGCA 60.900 55.000 21.96 21.96 36.92 4.92
5290 5950 4.663636 TTTTTCTCCGAATTCTTCTCGC 57.336 40.909 3.52 0.00 34.95 5.03
5331 5994 2.159014 TCGTAGCCCGTGCATAAATTCT 60.159 45.455 0.00 0.00 41.13 2.40
5427 6094 0.916086 AGTTTGTGGTGGTGGAGTCA 59.084 50.000 0.00 0.00 0.00 3.41
5453 6120 8.068892 ACTTTTACAAGTTTATGGACCAAACA 57.931 30.769 10.89 0.00 40.66 2.83
5472 6139 1.291877 AATCACAGACCGCGCAAGTC 61.292 55.000 17.46 17.46 41.68 3.01
5703 6737 5.296780 TGCCTGTGCTTAATATCTTGCTAAC 59.703 40.000 0.00 0.00 38.71 2.34
5757 6791 4.586235 ACCACCTGCAGTGTGCCC 62.586 66.667 22.61 0.00 45.74 5.36
5772 6806 1.133792 GTGCCCTATGCCCAGTGTTAT 60.134 52.381 0.00 0.00 40.16 1.89
6097 7132 7.092137 TCTAATCAACATTTTGCTGGATCTG 57.908 36.000 0.00 0.00 32.17 2.90
6099 7134 2.231964 TCAACATTTTGCTGGATCTGCC 59.768 45.455 8.34 0.00 32.17 4.85
6153 7188 3.319137 TCGTAGTTGCTGCTTTGAGAT 57.681 42.857 0.00 0.00 0.00 2.75
6220 7255 9.290483 CATATAATTAGTACTATCACACTGCCG 57.710 37.037 2.79 0.00 0.00 5.69
6307 7342 8.697846 TTTATTTACTCATCCTGACTTACGTG 57.302 34.615 0.00 0.00 0.00 4.49
6707 7747 2.170166 CATGCTACAAGGGGCAAAGAA 58.830 47.619 0.00 0.00 41.90 2.52
7132 8173 3.039252 ACTGATCTCCCAGGTAAGAGG 57.961 52.381 0.00 0.00 38.44 3.69
7438 8480 1.406539 CTGCTGAACAACTTGGCTGTT 59.593 47.619 0.00 0.00 39.69 3.16
7492 8534 5.702670 TCTTCTTTCGAATGTCAAAGCAGAT 59.297 36.000 10.48 0.00 30.11 2.90
7597 8639 9.787435 TGGATTAGTTGGGTACAAACATATATC 57.213 33.333 11.82 8.50 38.54 1.63
7610 8652 7.963532 ACAAACATATATCGAGGAGGTATGTT 58.036 34.615 13.35 13.35 43.79 2.71
7731 8773 4.994217 GCTATTTTCTCAGCCCTAGTCATC 59.006 45.833 0.00 0.00 0.00 2.92
7906 8949 3.701205 TGGCAGAAGTTCTAAGATGCA 57.299 42.857 4.74 0.00 35.40 3.96
7914 8957 7.466590 GCAGAAGTTCTAAGATGCAGTTATTCC 60.467 40.741 4.74 0.00 33.92 3.01
7958 9001 2.661176 TCCTGTAATGAACCCCCTCT 57.339 50.000 0.00 0.00 0.00 3.69
7983 9026 3.454812 AGGTTACTGACTGTTGTTCCACT 59.545 43.478 0.00 0.00 0.00 4.00
7999 9042 5.705441 TGTTCCACTCACCATTTGATAAGTC 59.295 40.000 0.00 0.00 32.17 3.01
8537 9585 4.006319 GCCTTGACTTTGAGTAGCAGAAT 58.994 43.478 0.00 0.00 0.00 2.40
8633 9681 3.892588 TGGAAAACCCTTGTGTTGGATAC 59.107 43.478 0.00 0.00 35.38 2.24
8637 9685 6.127730 GGAAAACCCTTGTGTTGGATACTATG 60.128 42.308 0.00 0.00 37.61 2.23
8652 9700 1.492176 ACTATGGGCTGTTGATCTGGG 59.508 52.381 0.00 0.00 0.00 4.45
8662 9710 1.271127 TTGATCTGGGTGCATCCGGA 61.271 55.000 29.62 29.62 45.35 5.14
8675 9756 0.999712 ATCCGGAAACATGGGAGGTT 59.000 50.000 9.01 0.00 32.43 3.50
8686 9768 2.465860 TGGGAGGTTGTATGTTGACG 57.534 50.000 0.00 0.00 0.00 4.35
8735 9817 2.080286 TCTACTGTTGAGCCGCTTTC 57.920 50.000 0.00 0.00 0.00 2.62
8736 9818 1.618837 TCTACTGTTGAGCCGCTTTCT 59.381 47.619 0.00 0.00 0.00 2.52
8737 9819 2.037251 TCTACTGTTGAGCCGCTTTCTT 59.963 45.455 0.00 0.00 0.00 2.52
8738 9820 0.947244 ACTGTTGAGCCGCTTTCTTG 59.053 50.000 0.00 0.00 0.00 3.02
8739 9821 0.386478 CTGTTGAGCCGCTTTCTTGC 60.386 55.000 0.00 0.00 0.00 4.01
8743 9834 1.515736 GAGCCGCTTTCTTGCATGC 60.516 57.895 11.82 11.82 0.00 4.06
8861 9983 2.049888 TGCAATGGAATGATACGCCA 57.950 45.000 0.00 0.00 35.91 5.69
8872 9994 1.217882 GATACGCCATCCGAAACAGG 58.782 55.000 0.00 0.00 41.02 4.00
8885 10007 3.125316 CCGAAACAGGTATGCTCACTTTC 59.875 47.826 0.00 0.00 0.00 2.62
8935 10276 6.369890 CAGTTGCTAAAAGCTCTCTCAACATA 59.630 38.462 15.97 0.00 42.97 2.29
8936 10277 6.370166 AGTTGCTAAAAGCTCTCTCAACATAC 59.630 38.462 15.97 0.00 42.97 2.39
8944 10295 9.678260 AAAAGCTCTCTCAACATACAGATAAAT 57.322 29.630 0.00 0.00 0.00 1.40
8993 10645 6.266168 ACTCTTCTACAAGATGAGACACTG 57.734 41.667 20.49 0.00 44.65 3.66
8998 10650 3.690475 ACAAGATGAGACACTGCATCA 57.310 42.857 0.00 0.00 42.52 3.07
9047 10780 1.209128 CGCCAGAGTAATAGCCAACG 58.791 55.000 0.00 0.00 0.00 4.10
9048 10781 1.470979 CGCCAGAGTAATAGCCAACGT 60.471 52.381 0.00 0.00 0.00 3.99
9109 10842 5.769835 ACATATGATGTCCTTGTCCCAATT 58.230 37.500 10.38 0.00 39.92 2.32
9199 10932 8.664079 AGAATCTATATCCAGTTATGCAAGGTT 58.336 33.333 0.00 0.00 0.00 3.50
9264 10997 8.180267 CCATCTGATCTTGTAGTAAGCTTTTTG 58.820 37.037 3.20 0.00 0.00 2.44
9272 11005 9.950680 TCTTGTAGTAAGCTTTTTGAAAATCAG 57.049 29.630 3.20 0.00 0.00 2.90
9316 11049 9.481340 GGAAGTTGAATTATTTTTCTCTGCTTT 57.519 29.630 0.00 0.00 0.00 3.51
9327 11060 7.823745 TTTTTCTCTGCTTTGAATCTTACCT 57.176 32.000 0.00 0.00 0.00 3.08
9328 11061 7.823745 TTTTCTCTGCTTTGAATCTTACCTT 57.176 32.000 0.00 0.00 0.00 3.50
9354 11087 9.764363 TCCTTTATATGCATTTAGTGTAGAGTG 57.236 33.333 3.54 0.00 0.00 3.51
9355 11088 9.547753 CCTTTATATGCATTTAGTGTAGAGTGT 57.452 33.333 3.54 0.00 0.00 3.55
9357 11090 6.851222 ATATGCATTTAGTGTAGAGTGTGC 57.149 37.500 3.54 0.00 0.00 4.57
9358 11091 2.993220 TGCATTTAGTGTAGAGTGTGCG 59.007 45.455 0.00 0.00 34.28 5.34
9359 11092 3.250744 GCATTTAGTGTAGAGTGTGCGA 58.749 45.455 0.00 0.00 0.00 5.10
9360 11093 3.865745 GCATTTAGTGTAGAGTGTGCGAT 59.134 43.478 0.00 0.00 0.00 4.58
9361 11094 4.259970 GCATTTAGTGTAGAGTGTGCGATG 60.260 45.833 0.00 0.00 0.00 3.84
9362 11095 4.514781 TTTAGTGTAGAGTGTGCGATGT 57.485 40.909 0.00 0.00 0.00 3.06
9363 11096 2.354109 AGTGTAGAGTGTGCGATGTG 57.646 50.000 0.00 0.00 0.00 3.21
9364 11097 1.886542 AGTGTAGAGTGTGCGATGTGA 59.113 47.619 0.00 0.00 0.00 3.58
9365 11098 2.493675 AGTGTAGAGTGTGCGATGTGAT 59.506 45.455 0.00 0.00 0.00 3.06
9366 11099 3.694566 AGTGTAGAGTGTGCGATGTGATA 59.305 43.478 0.00 0.00 0.00 2.15
9367 11100 4.339530 AGTGTAGAGTGTGCGATGTGATAT 59.660 41.667 0.00 0.00 0.00 1.63
9368 11101 4.442403 GTGTAGAGTGTGCGATGTGATATG 59.558 45.833 0.00 0.00 0.00 1.78
9369 11102 2.477825 AGAGTGTGCGATGTGATATGC 58.522 47.619 0.00 0.00 0.00 3.14
9370 11103 2.102084 AGAGTGTGCGATGTGATATGCT 59.898 45.455 0.00 0.00 0.00 3.79
9371 11104 2.474359 GAGTGTGCGATGTGATATGCTC 59.526 50.000 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 0.745845 GCACGACTGGCATCTGGATT 60.746 55.000 0.00 0.00 0.00 3.01
97 98 2.113774 CTGGCAGAACCACCAGCA 59.886 61.111 9.42 0.00 46.36 4.41
179 181 0.983378 CCCCTCCGAGTTTCTCCCAT 60.983 60.000 0.00 0.00 0.00 4.00
406 410 4.871557 ACGCGGTCAGCTTAATTTATTACA 59.128 37.500 12.47 0.00 45.59 2.41
409 413 3.064820 CCACGCGGTCAGCTTAATTTATT 59.935 43.478 12.47 0.00 45.59 1.40
534 538 1.144496 GATGCATTTGCGGCCCAAT 59.856 52.632 0.00 0.00 45.83 3.16
581 585 2.040544 CCAAGCGCCGATCCAAACT 61.041 57.895 2.29 0.00 0.00 2.66
652 658 6.959639 ATTTAGAGCAACTTCAAAAGACCA 57.040 33.333 0.00 0.00 0.00 4.02
662 668 6.840780 ACAATGGCTAATTTAGAGCAACTT 57.159 33.333 7.63 0.00 41.98 2.66
681 687 9.802039 TTTCAAGAAACTTAGGGTATGTACAAT 57.198 29.630 0.00 0.00 0.00 2.71
682 688 9.629878 TTTTCAAGAAACTTAGGGTATGTACAA 57.370 29.630 0.00 0.00 0.00 2.41
685 691 9.856162 ACTTTTTCAAGAAACTTAGGGTATGTA 57.144 29.630 0.00 0.00 33.72 2.29
686 692 8.762481 ACTTTTTCAAGAAACTTAGGGTATGT 57.238 30.769 0.00 0.00 33.72 2.29
695 701 9.803315 GTGGAGATAAACTTTTTCAAGAAACTT 57.197 29.630 0.00 0.00 33.72 2.66
696 702 8.129211 CGTGGAGATAAACTTTTTCAAGAAACT 58.871 33.333 0.00 0.00 33.72 2.66
697 703 7.913821 ACGTGGAGATAAACTTTTTCAAGAAAC 59.086 33.333 0.00 0.00 33.72 2.78
698 704 7.913297 CACGTGGAGATAAACTTTTTCAAGAAA 59.087 33.333 7.95 0.00 33.72 2.52
699 705 7.281324 TCACGTGGAGATAAACTTTTTCAAGAA 59.719 33.333 17.00 0.00 33.72 2.52
700 706 6.764085 TCACGTGGAGATAAACTTTTTCAAGA 59.236 34.615 17.00 0.00 33.72 3.02
701 707 6.954944 TCACGTGGAGATAAACTTTTTCAAG 58.045 36.000 17.00 0.00 35.92 3.02
702 708 6.928979 TCACGTGGAGATAAACTTTTTCAA 57.071 33.333 17.00 0.00 0.00 2.69
703 709 6.708502 TGATCACGTGGAGATAAACTTTTTCA 59.291 34.615 17.00 0.00 0.00 2.69
704 710 7.117812 TCTGATCACGTGGAGATAAACTTTTTC 59.882 37.037 17.00 0.00 0.00 2.29
861 867 2.529389 GGTGTGGGACTCTGGGGT 60.529 66.667 0.00 0.00 0.00 4.95
862 868 3.330720 GGGTGTGGGACTCTGGGG 61.331 72.222 0.00 0.00 0.00 4.96
863 869 2.529136 TGGGTGTGGGACTCTGGG 60.529 66.667 0.00 0.00 0.00 4.45
1311 1325 3.452919 AGGGAGCTAGGGAGGGGG 61.453 72.222 0.00 0.00 0.00 5.40
1312 1326 2.202899 GAGGGAGCTAGGGAGGGG 59.797 72.222 0.00 0.00 0.00 4.79
1316 1330 3.028683 CAGGGAGGGAGCTAGGGA 58.971 66.667 0.00 0.00 0.00 4.20
1321 1335 3.726144 GCAAGCAGGGAGGGAGCT 61.726 66.667 0.00 0.00 41.03 4.09
1322 1336 4.811364 GGCAAGCAGGGAGGGAGC 62.811 72.222 0.00 0.00 0.00 4.70
1366 1381 3.652539 TAGGTGCTACGCCAACCGC 62.653 63.158 0.00 0.00 41.76 5.68
1412 1427 1.654220 CTGCAACACCAAACCTCGG 59.346 57.895 0.00 0.00 0.00 4.63
1638 1654 6.108687 TCAGCACATCTCAATAACCAGTTAG 58.891 40.000 0.00 0.00 0.00 2.34
1674 1691 4.784329 TCAACGCAAATTACACGCATTTA 58.216 34.783 0.00 0.00 0.00 1.40
1785 1826 2.740447 CCTTTAGTGCACCGGAGTTAAC 59.260 50.000 14.63 0.00 0.00 2.01
1794 1835 4.092968 CGAAACTATCACCTTTAGTGCACC 59.907 45.833 14.63 0.00 46.81 5.01
1871 1912 9.057089 CATGATACCCTTTAGTGAATTTAGGAC 57.943 37.037 0.00 0.00 0.00 3.85
1873 1914 8.980481 ACATGATACCCTTTAGTGAATTTAGG 57.020 34.615 0.00 0.00 0.00 2.69
1880 1921 9.832445 GATCTTTTACATGATACCCTTTAGTGA 57.168 33.333 0.00 0.00 0.00 3.41
1881 1922 9.838339 AGATCTTTTACATGATACCCTTTAGTG 57.162 33.333 0.00 0.00 0.00 2.74
1882 1923 9.838339 CAGATCTTTTACATGATACCCTTTAGT 57.162 33.333 0.00 0.00 0.00 2.24
1883 1924 9.838339 ACAGATCTTTTACATGATACCCTTTAG 57.162 33.333 0.00 0.00 0.00 1.85
1990 2031 3.785051 AAAAACAGGGGGTGGGGGC 62.785 63.158 0.00 0.00 0.00 5.80
2011 2052 4.559862 ATCCTAGTGGTGAACTTTGAGG 57.440 45.455 0.00 0.00 40.56 3.86
2203 2261 4.562757 CCCCAGAAGTAGTGACGAATTTCA 60.563 45.833 0.00 0.00 0.00 2.69
2261 2319 6.656270 TCAACTACTAGTTAACGATCTGGTGA 59.344 38.462 0.00 4.08 36.03 4.02
2271 2329 6.453092 TGGCTCTGTTCAACTACTAGTTAAC 58.547 40.000 0.00 0.00 36.03 2.01
2304 2364 1.464687 CGCGAACAGCTGGATTCTTTG 60.465 52.381 19.93 7.74 45.59 2.77
2348 2409 3.081804 GGTTTCATGTGGAACTACCCAG 58.918 50.000 4.31 0.00 36.78 4.45
2382 2610 3.861276 TTCATGGCAATTGCAGAAGAG 57.139 42.857 30.32 14.00 44.36 2.85
2441 2669 6.582295 GCTTAGCATTTTTCATGAGAACGAAA 59.418 34.615 0.00 0.00 32.39 3.46
2444 2672 4.795278 GGCTTAGCATTTTTCATGAGAACG 59.205 41.667 6.53 0.00 32.39 3.95
2481 2709 0.808125 AAACAAAGCAGCACACGACA 59.192 45.000 0.00 0.00 0.00 4.35
2566 2802 7.781693 AGGAATCATTTAACCAGAGCATATTGT 59.218 33.333 0.00 0.00 0.00 2.71
2574 2810 5.874810 TCGTCAAGGAATCATTTAACCAGAG 59.125 40.000 0.00 0.00 0.00 3.35
2578 2814 7.142680 TGTTTTCGTCAAGGAATCATTTAACC 58.857 34.615 0.00 0.00 0.00 2.85
2592 2828 8.973835 AGACAATTTTAACTTGTTTTCGTCAA 57.026 26.923 2.37 0.00 36.98 3.18
2618 2854 9.496873 TTTTCGTCTAGGAATCATTTGAAGTTA 57.503 29.630 0.00 0.00 0.00 2.24
2677 2913 7.335422 GGCCCATAGATATTATCACTCAACTTG 59.665 40.741 6.46 0.00 0.00 3.16
2713 2949 6.537660 TGAGCAGAAAGACATGATGATAACTG 59.462 38.462 0.00 3.62 0.00 3.16
2736 2972 9.219603 CCTCTTAAAATATGAACACACTTCTGA 57.780 33.333 0.00 0.00 0.00 3.27
2753 2989 6.378848 ACACCTTGTGCTTTTACCTCTTAAAA 59.621 34.615 0.00 0.00 35.90 1.52
2771 3007 2.291741 GAGCAAGTTTCTGGACACCTTG 59.708 50.000 0.00 0.00 36.47 3.61
2772 3008 2.576615 GAGCAAGTTTCTGGACACCTT 58.423 47.619 0.00 0.00 0.00 3.50
2773 3009 1.541233 CGAGCAAGTTTCTGGACACCT 60.541 52.381 0.00 0.00 0.00 4.00
2795 3031 2.794103 TGTGGACCAAATCATCACAGG 58.206 47.619 0.00 0.00 34.01 4.00
2797 3033 4.665451 AGATTGTGGACCAAATCATCACA 58.335 39.130 21.39 0.00 36.44 3.58
2817 3053 0.241213 CGGAGTCGACTTCTGCAAGA 59.759 55.000 21.08 0.00 39.30 3.02
2824 3060 2.126031 GGTGGCGGAGTCGACTTC 60.126 66.667 21.08 17.62 46.40 3.01
2836 3072 2.649129 GGATTGGCTTGTGGGTGGC 61.649 63.158 0.00 0.00 0.00 5.01
2847 3083 0.947244 CATGTCGGCTTAGGATTGGC 59.053 55.000 0.00 0.00 0.00 4.52
2868 3137 5.507482 GCAAAGGTATACATCGAGCTAGACA 60.507 44.000 5.01 0.00 0.00 3.41
2944 3213 1.613317 TACGTGATGGGCTGGACCAG 61.613 60.000 17.83 17.83 45.20 4.00
2991 3260 2.125326 TAGCACCCAGATCCGTCCG 61.125 63.158 0.00 0.00 0.00 4.79
3012 3281 6.737750 CCGCAGAAAAATATGAAAACAAATGC 59.262 34.615 0.00 0.00 0.00 3.56
3051 3320 6.209192 TGTTTCCGGTAGTATCTGTTTCTGTA 59.791 38.462 0.00 0.00 0.00 2.74
3085 3354 2.507547 TGTCCACGCCGTATTCGC 60.508 61.111 0.00 0.00 35.54 4.70
3096 3365 2.025418 CTACCGTTGCCGTGTCCAC 61.025 63.158 0.00 0.00 0.00 4.02
3097 3366 2.340809 CTACCGTTGCCGTGTCCA 59.659 61.111 0.00 0.00 0.00 4.02
3098 3367 3.116531 GCTACCGTTGCCGTGTCC 61.117 66.667 0.00 0.00 0.00 4.02
3099 3368 2.356553 TGCTACCGTTGCCGTGTC 60.357 61.111 2.42 0.00 0.00 3.67
3100 3369 2.357034 CTGCTACCGTTGCCGTGT 60.357 61.111 2.42 0.00 0.00 4.49
3101 3370 3.118454 CCTGCTACCGTTGCCGTG 61.118 66.667 2.42 0.00 0.00 4.94
3102 3371 3.622826 ACCTGCTACCGTTGCCGT 61.623 61.111 2.42 0.00 0.00 5.68
3573 3843 9.713740 CTGAGATATTGTGCTTTTCTTTACATC 57.286 33.333 0.00 0.00 0.00 3.06
3683 3953 1.211457 AGGAAGCTAGCCCTGATTGTG 59.789 52.381 12.13 0.00 0.00 3.33
3732 4002 2.736670 ACAATGAGTAGATTGGCCCC 57.263 50.000 0.00 0.00 37.60 5.80
3974 4275 1.131315 GGATGAAAACGGAGCAGAAGC 59.869 52.381 0.00 0.00 42.56 3.86
3975 4276 1.740025 GGGATGAAAACGGAGCAGAAG 59.260 52.381 0.00 0.00 0.00 2.85
4008 4309 5.082059 CACATACACAAAAATCAGTCGAGC 58.918 41.667 0.00 0.00 0.00 5.03
4011 4312 4.782156 TGCACATACACAAAAATCAGTCG 58.218 39.130 0.00 0.00 0.00 4.18
4078 4379 0.999406 TGTTTTAGCTGATCGCGAGC 59.001 50.000 19.12 19.12 45.59 5.03
4135 4436 9.895138 AGAGAAAAACTTAAAAGGTACTACACA 57.105 29.630 0.00 0.00 38.49 3.72
4156 4457 9.119418 TGTACATCAACAAAAATTGAGAGAGAA 57.881 29.630 0.00 0.00 41.76 2.87
4173 4474 5.376625 AGGAAGTTGCTTCTTGTACATCAA 58.623 37.500 0.00 0.00 40.07 2.57
4207 4508 2.156917 AGTCAGGCATGAACATGTGTG 58.843 47.619 0.92 12.26 40.80 3.82
4213 4514 0.770499 TCCCAAGTCAGGCATGAACA 59.230 50.000 0.92 0.00 37.14 3.18
4222 4523 3.056465 GTCCTAGTCAACTCCCAAGTCAG 60.056 52.174 0.00 0.00 33.48 3.51
4227 4528 3.335786 TCCTAGTCCTAGTCAACTCCCAA 59.664 47.826 0.96 0.00 0.00 4.12
4420 5063 8.691661 AAAAAGCTTGTAGGAAGAACTATCAA 57.308 30.769 0.00 0.00 0.00 2.57
4429 5072 7.852454 GCAAATTTTGAAAAAGCTTGTAGGAAG 59.148 33.333 13.26 0.00 31.99 3.46
4458 5101 8.889849 ATATAAATTTTGTCCGAAGTCAAACG 57.110 30.769 0.00 0.00 34.05 3.60
4464 5107 9.901172 AGAAGGTATATAAATTTTGTCCGAAGT 57.099 29.630 0.00 0.00 0.00 3.01
4492 5135 3.052338 AGTCCTACTCCCCGGAATCTAAA 60.052 47.826 0.73 0.00 0.00 1.85
4498 5141 2.425392 GGATAAGTCCTACTCCCCGGAA 60.425 54.545 0.73 0.00 41.60 4.30
4501 5144 1.630223 GGGATAAGTCCTACTCCCCG 58.370 60.000 0.00 0.00 44.44 5.73
4524 5167 9.567702 AGGAATATATGATTAGAAGTAAGGGCT 57.432 33.333 0.00 0.00 0.00 5.19
4580 5223 3.804873 GGGAAATAAGAGACGAGCATGAC 59.195 47.826 0.00 0.00 0.00 3.06
4589 5232 6.909909 ACGTTGAATTTGGGAAATAAGAGAC 58.090 36.000 0.00 0.00 0.00 3.36
4654 5298 1.921573 GCTGTGTGACACGCAATCAAC 60.922 52.381 21.44 3.38 38.24 3.18
4663 5307 1.560860 GGAGCTTCGCTGTGTGACAC 61.561 60.000 9.14 9.14 39.88 3.67
4679 5323 5.258456 TGATAAACTAACCAGTAGCGGAG 57.742 43.478 0.00 0.00 33.48 4.63
4714 5358 8.367911 TCAGAAAATAAGTCGCCTGATATACAT 58.632 33.333 0.00 0.00 0.00 2.29
4722 5366 7.721286 ATCTATTCAGAAAATAAGTCGCCTG 57.279 36.000 0.00 0.00 33.50 4.85
4957 5602 9.893634 TCGTGGAACTAGGATTCAATTTATTTA 57.106 29.630 0.00 0.00 31.75 1.40
4958 5603 8.801882 TCGTGGAACTAGGATTCAATTTATTT 57.198 30.769 0.00 0.00 31.75 1.40
4959 5604 8.438676 CTCGTGGAACTAGGATTCAATTTATT 57.561 34.615 0.00 0.00 31.75 1.40
4981 5626 3.857052 TGCTTAATGTGGTAACTCCTCG 58.143 45.455 0.00 0.00 37.07 4.63
5066 5711 4.333926 GGTATAAGTACGAAGGTCACGTCT 59.666 45.833 0.00 0.00 43.62 4.18
5067 5712 4.333926 AGGTATAAGTACGAAGGTCACGTC 59.666 45.833 0.00 0.00 43.62 4.34
5213 5873 0.530744 CCTGGTCGTACAAGCTAGCA 59.469 55.000 18.83 0.00 0.00 3.49
5247 5907 0.991146 TTAGTGCCAGGCAGGATTCA 59.009 50.000 16.83 0.00 40.08 2.57
5394 6060 3.486383 CACAAACTTACATCCCAGGTGT 58.514 45.455 0.00 0.00 0.00 4.16
5427 6094 8.532819 TGTTTGGTCCATAAACTTGTAAAAGTT 58.467 29.630 5.12 5.12 44.25 2.66
5452 6119 1.133253 CTTGCGCGGTCTGTGATTG 59.867 57.895 8.83 0.00 0.00 2.67
5453 6120 1.291877 GACTTGCGCGGTCTGTGATT 61.292 55.000 20.92 0.00 0.00 2.57
5480 6147 4.171103 CGAGGTAAAGGCCCCGGG 62.171 72.222 15.80 15.80 0.00 5.73
5485 6156 5.295292 GGAGTTAAAATACGAGGTAAAGGCC 59.705 44.000 0.00 0.00 0.00 5.19
5497 6531 4.099419 CCATTGGGCAGGGAGTTAAAATAC 59.901 45.833 0.00 0.00 0.00 1.89
5544 6578 5.532406 GTCCAATATCAGCTAGGATGCAAAA 59.468 40.000 0.00 0.00 34.99 2.44
5545 6579 5.065914 GTCCAATATCAGCTAGGATGCAAA 58.934 41.667 0.00 0.00 34.99 3.68
5546 6580 4.102996 TGTCCAATATCAGCTAGGATGCAA 59.897 41.667 0.00 0.00 34.99 4.08
5555 6589 8.844244 GTGATTTTTCTATGTCCAATATCAGCT 58.156 33.333 0.00 0.00 0.00 4.24
5725 6759 3.576982 CAGGTGGTTGTTCAGTAGGAGTA 59.423 47.826 0.00 0.00 0.00 2.59
5757 6791 2.172505 TCCACCATAACACTGGGCATAG 59.827 50.000 0.00 0.00 40.85 2.23
5941 6975 3.932710 TCACTGCATAAGAATTCACGGAC 59.067 43.478 8.44 0.00 0.00 4.79
6097 7132 4.307432 GAAGGGAAACTAAAAGCAAAGGC 58.693 43.478 0.00 0.00 41.61 4.35
6099 7134 5.791336 AGGAAGGGAAACTAAAAGCAAAG 57.209 39.130 0.00 0.00 0.00 2.77
6153 7188 6.366340 AGCTACTAGTATAAGAGCTGAACCA 58.634 40.000 14.83 0.00 41.82 3.67
6220 7255 8.887036 AACAAAAGGAACATGGAATTTTAGAC 57.113 30.769 0.00 0.00 0.00 2.59
6307 7342 2.288213 GGCGCTTCAAAATAATAGGCCC 60.288 50.000 7.64 0.00 32.02 5.80
6458 7493 1.403249 CGAGTAAACACCCAGGTACCG 60.403 57.143 6.18 1.26 0.00 4.02
6707 7747 3.463944 ACGACGAACAATTTCAAGGTCT 58.536 40.909 0.00 0.00 0.00 3.85
6918 7959 5.533903 CAGGCTGTTATTTGCAAGGAGATAT 59.466 40.000 6.28 0.00 0.00 1.63
7132 8173 5.587289 TCAGGTTGATTTGCAAAACAGTAC 58.413 37.500 19.65 16.14 38.44 2.73
7205 8246 6.178607 TGCTTCATCCTTGCTGATAAGATA 57.821 37.500 0.00 0.00 0.00 1.98
7492 8534 1.967779 TCAGTTTCTGGGATGTCACGA 59.032 47.619 0.00 0.00 31.51 4.35
7906 8949 3.200165 GCAACAGGAGGTAGGGAATAACT 59.800 47.826 0.00 0.00 32.57 2.24
7958 9001 5.818857 GTGGAACAACAGTCAGTAACCTAAA 59.181 40.000 0.00 0.00 44.16 1.85
7983 9026 4.009675 GGCACAGACTTATCAAATGGTGA 58.990 43.478 0.00 0.00 41.67 4.02
8026 9069 6.506538 AGATCCAACTATAAGGCATGACTT 57.493 37.500 19.84 19.84 34.52 3.01
8537 9585 1.301716 GCTCCTGAACGGCTGAACA 60.302 57.895 0.00 0.00 0.00 3.18
8633 9681 1.492176 ACCCAGATCAACAGCCCATAG 59.508 52.381 0.00 0.00 0.00 2.23
8637 9685 2.048603 GCACCCAGATCAACAGCCC 61.049 63.158 0.00 0.00 0.00 5.19
8652 9700 0.679640 TCCCATGTTTCCGGATGCAC 60.680 55.000 4.15 3.19 0.00 4.57
8662 9710 4.522789 GTCAACATACAACCTCCCATGTTT 59.477 41.667 0.00 0.00 39.06 2.83
8675 9756 4.687018 AGCGATAAACAACGTCAACATACA 59.313 37.500 0.00 0.00 0.00 2.29
8686 9768 5.059221 GCACATTGTAACAGCGATAAACAAC 59.941 40.000 0.00 0.00 33.27 3.32
8735 9817 3.248266 GTGGCTCTTTAAAGCATGCAAG 58.752 45.455 21.98 14.49 44.35 4.01
8736 9818 2.351641 CGTGGCTCTTTAAAGCATGCAA 60.352 45.455 21.98 2.08 44.35 4.08
8737 9819 1.199789 CGTGGCTCTTTAAAGCATGCA 59.800 47.619 21.98 0.00 44.35 3.96
8738 9820 1.468054 CCGTGGCTCTTTAAAGCATGC 60.468 52.381 10.51 10.51 44.35 4.06
8739 9821 2.083774 TCCGTGGCTCTTTAAAGCATG 58.916 47.619 10.51 8.16 44.35 4.06
8743 9834 2.762535 TCCTCCGTGGCTCTTTAAAG 57.237 50.000 9.04 9.04 35.26 1.85
8819 9911 6.407074 GCAATAGTGACTAGAAAGGAGGCTAA 60.407 42.308 0.00 0.00 0.00 3.09
8861 9983 2.501723 AGTGAGCATACCTGTTTCGGAT 59.498 45.455 0.00 0.00 0.00 4.18
8900 10022 5.409826 AGCTTTTAGCAACTGTCTATGACAC 59.590 40.000 1.09 0.00 45.56 3.67
8901 10023 5.551233 AGCTTTTAGCAACTGTCTATGACA 58.449 37.500 1.09 0.37 45.56 3.58
9027 10760 1.583054 GTTGGCTATTACTCTGGCGG 58.417 55.000 0.00 0.00 0.00 6.13
9047 10780 3.066900 ACATGTCTGATAGTCGCCTACAC 59.933 47.826 0.00 0.00 0.00 2.90
9048 10781 3.288092 ACATGTCTGATAGTCGCCTACA 58.712 45.455 0.00 0.00 0.00 2.74
9109 10842 7.777095 ACATGGTTACTTGCAAACTAAGAAAA 58.223 30.769 0.00 0.00 0.00 2.29
9178 10911 6.533730 TCCAACCTTGCATAACTGGATATAG 58.466 40.000 4.47 0.00 0.00 1.31
9272 11005 8.522830 TCAACTTCCATCATCCAATAAGAAAAC 58.477 33.333 0.00 0.00 0.00 2.43
9316 11049 9.866655 AATGCATATAAAGGAAGGTAAGATTCA 57.133 29.630 0.00 0.00 0.00 2.57
9325 11058 9.778741 TCTACACTAAATGCATATAAAGGAAGG 57.221 33.333 0.00 0.00 0.00 3.46
9328 11061 9.764363 CACTCTACACTAAATGCATATAAAGGA 57.236 33.333 0.00 0.00 0.00 3.36
9344 11077 1.886542 TCACATCGCACACTCTACACT 59.113 47.619 0.00 0.00 0.00 3.55
9346 11079 4.610945 CATATCACATCGCACACTCTACA 58.389 43.478 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.