Multiple sequence alignment - TraesCS7A01G398900

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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 TraesCS7A01G398900 chr7A 100.000 3596 0 0 1 3596 578716381 578719976 0.000000e+00 6641.0
1 TraesCS7A01G398900 chr7A 90.892 538 49 0 1 538 563873106 563873643 0.000000e+00 723.0
2 TraesCS7A01G398900 chr7A 89.683 252 26 0 3124 3375 578970360 578970611 4.480000e-84 322.0
3 TraesCS7A01G398900 chr7B 93.342 2448 97 27 536 2924 536638736 536641176 0.000000e+00 3557.0
4 TraesCS7A01G398900 chr7B 90.217 460 33 4 2920 3375 536642528 536642979 1.110000e-164 590.0
5 TraesCS7A01G398900 chr2B 90.589 2274 130 37 613 2840 157372338 157374573 0.000000e+00 2937.0
6 TraesCS7A01G398900 chr2B 83.806 247 33 6 2878 3121 157374731 157374973 1.000000e-55 228.0
7 TraesCS7A01G398900 chr2B 83.004 253 37 4 3122 3371 485913094 485913343 1.300000e-54 224.0
8 TraesCS7A01G398900 chr7D 91.776 2067 99 25 603 2623 508334158 508332117 0.000000e+00 2809.0
9 TraesCS7A01G398900 chr7D 89.925 536 50 2 1 534 602028253 602028786 0.000000e+00 688.0
10 TraesCS7A01G398900 chr7D 85.957 235 18 4 3376 3596 184534236 184534003 1.670000e-58 237.0
11 TraesCS7A01G398900 chr2D 91.602 2072 111 24 538 2587 107027193 107029223 0.000000e+00 2804.0
12 TraesCS7A01G398900 chr2D 91.589 535 44 1 1 534 429202432 429202966 0.000000e+00 737.0
13 TraesCS7A01G398900 chr2D 90.892 538 45 3 1 538 201456082 201456615 0.000000e+00 719.0
14 TraesCS7A01G398900 chr2D 90.093 535 52 1 1 534 511531833 511532367 0.000000e+00 693.0
15 TraesCS7A01G398900 chr2D 83.796 432 36 12 2416 2843 107133596 107133997 2.620000e-101 379.0
16 TraesCS7A01G398900 chr2D 76.585 615 118 21 1187 1788 382380402 382381003 7.490000e-82 315.0
17 TraesCS7A01G398900 chr2D 78.755 273 24 8 567 837 107136562 107136802 6.220000e-33 152.0
18 TraesCS7A01G398900 chr2A 88.860 1149 99 10 1697 2843 103380998 103382119 0.000000e+00 1386.0
19 TraesCS7A01G398900 chr2A 90.667 375 25 5 2330 2702 103366020 103366386 1.160000e-134 490.0
20 TraesCS7A01G398900 chr2A 82.745 255 39 5 3121 3372 114298100 114297848 4.670000e-54 222.0
21 TraesCS7A01G398900 chr2A 82.661 248 34 8 2878 3121 103375844 103376086 1.010000e-50 211.0
22 TraesCS7A01G398900 chr2A 81.377 247 39 6 2878 3121 103382273 103382515 1.020000e-45 195.0
23 TraesCS7A01G398900 chr4D 91.312 541 41 2 1 540 488494425 488494960 0.000000e+00 734.0
24 TraesCS7A01G398900 chr4D 83.203 256 43 0 3120 3375 507972447 507972702 6.000000e-58 235.0
25 TraesCS7A01G398900 chr4D 83.784 222 25 5 3376 3596 445238414 445238625 2.190000e-47 200.0
26 TraesCS7A01G398900 chr4D 82.993 147 19 4 3364 3509 172204549 172204690 1.050000e-25 128.0
27 TraesCS7A01G398900 chr1D 90.280 535 50 2 1 534 407802565 407803098 0.000000e+00 699.0
28 TraesCS7A01G398900 chr1D 84.646 254 39 0 3122 3375 410067195 410067448 1.660000e-63 254.0
29 TraesCS7A01G398900 chr1D 85.517 145 18 2 3375 3519 23166170 23166311 8.040000e-32 148.0
30 TraesCS7A01G398900 chr5D 89.815 540 50 4 1 539 493829823 493829288 0.000000e+00 688.0
31 TraesCS7A01G398900 chr5D 83.399 253 42 0 3123 3375 93264956 93265208 6.000000e-58 235.0
32 TraesCS7A01G398900 chr5D 95.105 143 5 2 3454 3596 561696035 561696175 1.300000e-54 224.0
33 TraesCS7A01G398900 chr5D 82.051 156 24 4 3369 3522 506736945 506736792 2.910000e-26 130.0
34 TraesCS7A01G398900 chr5D 81.529 157 21 6 3369 3522 506701255 506701104 4.880000e-24 122.0
35 TraesCS7A01G398900 chr5A 89.591 538 54 1 1 538 631062831 631062296 0.000000e+00 682.0
36 TraesCS7A01G398900 chr5A 85.433 254 37 0 3122 3375 681859300 681859553 7.660000e-67 265.0
37 TraesCS7A01G398900 chr3D 79.062 597 113 10 1196 1786 448497005 448496415 2.010000e-107 399.0
38 TraesCS7A01G398900 chr3D 89.691 194 16 3 3403 3596 217903937 217903748 9.970000e-61 244.0
39 TraesCS7A01G398900 chr3D 85.202 223 27 4 3375 3596 380826030 380826247 1.300000e-54 224.0
40 TraesCS7A01G398900 chr3D 93.750 144 7 2 3454 3596 217035892 217036034 7.820000e-52 215.0
41 TraesCS7A01G398900 chr3D 82.474 97 17 0 1890 1986 95563812 95563908 6.400000e-13 86.1
42 TraesCS7A01G398900 chr3A 79.062 597 113 10 1196 1786 589826413 589825823 2.010000e-107 399.0
43 TraesCS7A01G398900 chr3A 82.828 99 13 4 1890 1986 113713000 113713096 6.400000e-13 86.1
44 TraesCS7A01G398900 chr3B 78.763 598 115 10 1196 1787 588696522 588695931 1.210000e-104 390.0
45 TraesCS7A01G398900 chr3B 87.838 222 21 3 3376 3596 55879511 55879295 4.610000e-64 255.0
46 TraesCS7A01G398900 chr3B 84.667 150 19 2 3374 3522 229987008 229986862 2.890000e-31 147.0
47 TraesCS7A01G398900 chr3B 80.921 152 26 2 3371 3522 382019716 382019864 2.270000e-22 117.0
48 TraesCS7A01G398900 chr3B 82.474 97 17 0 1890 1986 146552911 146553007 6.400000e-13 86.1
49 TraesCS7A01G398900 chr1B 88.235 221 13 8 3376 3596 629603715 629603922 5.960000e-63 252.0
50 TraesCS7A01G398900 chr1B 83.333 138 18 3 3372 3508 76382439 76382306 4.880000e-24 122.0
51 TraesCS7A01G398900 chr1B 81.169 154 23 4 3354 3506 250954575 250954723 6.310000e-23 119.0
52 TraesCS7A01G398900 chr5B 83.137 255 41 2 3122 3375 514664769 514665022 7.760000e-57 231.0
53 TraesCS7A01G398900 chr4A 83.929 224 24 8 3376 3596 722142279 722142493 1.690000e-48 204.0
54 TraesCS7A01G398900 chrUn 85.294 136 15 3 3375 3509 111199475 111199344 6.260000e-28 135.0
55 TraesCS7A01G398900 chr6A 81.879 149 25 2 3372 3519 528484419 528484566 1.360000e-24 124.0
56 TraesCS7A01G398900 chr4B 82.857 140 18 4 3372 3509 584174233 584174368 1.750000e-23 121.0


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 TraesCS7A01G398900 chr7A 578716381 578719976 3595 False 6641.0 6641 100.0000 1 3596 1 chr7A.!!$F2 3595
1 TraesCS7A01G398900 chr7A 563873106 563873643 537 False 723.0 723 90.8920 1 538 1 chr7A.!!$F1 537
2 TraesCS7A01G398900 chr7B 536638736 536642979 4243 False 2073.5 3557 91.7795 536 3375 2 chr7B.!!$F1 2839
3 TraesCS7A01G398900 chr2B 157372338 157374973 2635 False 1582.5 2937 87.1975 613 3121 2 chr2B.!!$F2 2508
4 TraesCS7A01G398900 chr7D 508332117 508334158 2041 True 2809.0 2809 91.7760 603 2623 1 chr7D.!!$R2 2020
5 TraesCS7A01G398900 chr7D 602028253 602028786 533 False 688.0 688 89.9250 1 534 1 chr7D.!!$F1 533
6 TraesCS7A01G398900 chr2D 107027193 107029223 2030 False 2804.0 2804 91.6020 538 2587 1 chr2D.!!$F1 2049
7 TraesCS7A01G398900 chr2D 429202432 429202966 534 False 737.0 737 91.5890 1 534 1 chr2D.!!$F4 533
8 TraesCS7A01G398900 chr2D 201456082 201456615 533 False 719.0 719 90.8920 1 538 1 chr2D.!!$F2 537
9 TraesCS7A01G398900 chr2D 511531833 511532367 534 False 693.0 693 90.0930 1 534 1 chr2D.!!$F5 533
10 TraesCS7A01G398900 chr2D 382380402 382381003 601 False 315.0 315 76.5850 1187 1788 1 chr2D.!!$F3 601
11 TraesCS7A01G398900 chr2D 107133596 107136802 3206 False 265.5 379 81.2755 567 2843 2 chr2D.!!$F6 2276
12 TraesCS7A01G398900 chr2A 103380998 103382515 1517 False 790.5 1386 85.1185 1697 3121 2 chr2A.!!$F3 1424
13 TraesCS7A01G398900 chr4D 488494425 488494960 535 False 734.0 734 91.3120 1 540 1 chr4D.!!$F3 539
14 TraesCS7A01G398900 chr1D 407802565 407803098 533 False 699.0 699 90.2800 1 534 1 chr1D.!!$F2 533
15 TraesCS7A01G398900 chr5D 493829288 493829823 535 True 688.0 688 89.8150 1 539 1 chr5D.!!$R1 538
16 TraesCS7A01G398900 chr5A 631062296 631062831 535 True 682.0 682 89.5910 1 538 1 chr5A.!!$R1 537
17 TraesCS7A01G398900 chr3D 448496415 448497005 590 True 399.0 399 79.0620 1196 1786 1 chr3D.!!$R2 590
18 TraesCS7A01G398900 chr3A 589825823 589826413 590 True 399.0 399 79.0620 1196 1786 1 chr3A.!!$R1 590
19 TraesCS7A01G398900 chr3B 588695931 588696522 591 True 390.0 390 78.7630 1196 1787 1 chr3B.!!$R3 591

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
218 219 0.109458 CCGACGTTGATCGACCTCAA 60.109 55.000 3.74 0.0 45.13 3.02 F
1407 1490 0.249120 TCGACATCTTCACGGCCAAT 59.751 50.000 2.24 0.0 0.00 3.16 F
1896 1982 1.532868 CAAGACAAGAACAAGCTCCGG 59.467 52.381 0.00 0.0 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1876 1959 1.532868 CCGGAGCTTGTTCTTGTCTTG 59.467 52.381 0.00 0.00 0.00 3.02 R
2574 2663 0.253820 AGGGTGAGATGGGGTGGAAT 60.254 55.000 0.00 0.00 0.00 3.01 R
3436 7230 0.232303 GCGTGATAATAGTGGCGCAC 59.768 55.000 10.83 5.73 43.62 5.34 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
167 168 1.239296 CCCGATATCACCGCCGTCTA 61.239 60.000 3.12 0.00 0.00 2.59
171 172 2.161808 CGATATCACCGCCGTCTAGAAT 59.838 50.000 3.12 0.00 0.00 2.40
172 173 3.502920 GATATCACCGCCGTCTAGAATG 58.497 50.000 0.00 0.00 0.00 2.67
218 219 0.109458 CCGACGTTGATCGACCTCAA 60.109 55.000 3.74 0.00 45.13 3.02
258 259 3.818787 GCCGACGAGGACGCCTAA 61.819 66.667 0.00 0.00 45.00 2.69
341 343 2.477189 CGTGGCCGGCTTTTATGTTTAG 60.477 50.000 28.56 1.05 0.00 1.85
349 351 6.809689 GCCGGCTTTTATGTTTAGTTAAATGT 59.190 34.615 22.15 0.00 0.00 2.71
415 419 2.355115 GAAATGGGTCGGGCCAGT 59.645 61.111 4.39 0.00 39.65 4.00
420 424 3.948719 GGGTCGGGCCAGTGTTGA 61.949 66.667 4.39 0.00 39.65 3.18
443 447 2.590575 CGTGCCGACCCAAACACT 60.591 61.111 0.00 0.00 0.00 3.55
460 464 1.154413 CTGCGTCGGATGTTTGTGC 60.154 57.895 0.00 0.00 0.00 4.57
508 512 1.088306 ACAGACAAAAACGCCGTTCA 58.912 45.000 1.60 0.00 0.00 3.18
513 517 3.109619 GACAAAAACGCCGTTCATTTGA 58.890 40.909 25.45 0.00 31.63 2.69
534 538 2.635443 CGGCCCGTTGGAATTGCTT 61.635 57.895 0.00 0.00 0.00 3.91
564 568 2.357034 TTTCTGGTCGAGCACGGC 60.357 61.111 14.39 0.37 43.86 5.68
620 628 3.124270 CGCCATGCAGCACGGTTA 61.124 61.111 9.74 0.00 0.00 2.85
635 643 1.359459 GGTTAAAGGCCGAGCGTGAG 61.359 60.000 0.00 0.00 0.00 3.51
659 667 0.756294 TCCTTGAGAGCGGTCAAACA 59.244 50.000 18.15 10.84 36.01 2.83
685 695 2.591429 CACCAACCAGCGCAGTCA 60.591 61.111 11.47 0.00 0.00 3.41
686 696 1.968017 CACCAACCAGCGCAGTCAT 60.968 57.895 11.47 0.00 0.00 3.06
687 697 1.228245 ACCAACCAGCGCAGTCATT 60.228 52.632 11.47 0.00 0.00 2.57
688 698 1.237285 ACCAACCAGCGCAGTCATTC 61.237 55.000 11.47 0.00 0.00 2.67
690 700 0.445436 CAACCAGCGCAGTCATTCTC 59.555 55.000 11.47 0.00 0.00 2.87
691 701 1.016130 AACCAGCGCAGTCATTCTCG 61.016 55.000 11.47 0.00 0.00 4.04
692 702 2.699809 CAGCGCAGTCATTCTCGC 59.300 61.111 11.47 0.00 40.33 5.03
806 846 0.318614 AACCATCAACTTTTGCCGCG 60.319 50.000 0.00 0.00 0.00 6.46
821 863 3.423154 GCGTCCCCTCGTGCTTTG 61.423 66.667 0.00 0.00 0.00 2.77
822 864 3.423154 CGTCCCCTCGTGCTTTGC 61.423 66.667 0.00 0.00 0.00 3.68
823 865 2.032681 GTCCCCTCGTGCTTTGCT 59.967 61.111 0.00 0.00 0.00 3.91
824 866 1.600916 GTCCCCTCGTGCTTTGCTT 60.601 57.895 0.00 0.00 0.00 3.91
835 877 1.533753 CTTTGCTTGGCCTTCCCCA 60.534 57.895 3.32 0.00 0.00 4.96
837 879 3.826265 TTGCTTGGCCTTCCCCACC 62.826 63.158 3.32 0.00 33.82 4.61
838 880 3.984732 GCTTGGCCTTCCCCACCT 61.985 66.667 3.32 0.00 33.82 4.00
841 883 2.211468 CTTGGCCTTCCCCACCTACC 62.211 65.000 3.32 0.00 33.82 3.18
842 884 2.612746 GGCCTTCCCCACCTACCA 60.613 66.667 0.00 0.00 0.00 3.25
843 885 2.006991 GGCCTTCCCCACCTACCAT 61.007 63.158 0.00 0.00 0.00 3.55
845 887 0.395724 GCCTTCCCCACCTACCATTG 60.396 60.000 0.00 0.00 0.00 2.82
846 888 0.999712 CCTTCCCCACCTACCATTGT 59.000 55.000 0.00 0.00 0.00 2.71
925 993 1.680735 TCACAGCAACCAACAACATCC 59.319 47.619 0.00 0.00 0.00 3.51
926 994 0.667993 ACAGCAACCAACAACATCCG 59.332 50.000 0.00 0.00 0.00 4.18
957 1033 3.058708 CACCAGCTCAAACACACATACTG 60.059 47.826 0.00 0.00 0.00 2.74
960 1037 4.389992 CCAGCTCAAACACACATACTGTAG 59.610 45.833 0.00 0.00 0.00 2.74
961 1038 4.991056 CAGCTCAAACACACATACTGTAGT 59.009 41.667 0.00 0.00 0.00 2.73
962 1039 6.156519 CAGCTCAAACACACATACTGTAGTA 58.843 40.000 0.00 0.00 34.67 1.82
1159 1242 4.475135 GAGGGAAGCGTGGAGGCC 62.475 72.222 0.00 0.00 0.00 5.19
1407 1490 0.249120 TCGACATCTTCACGGCCAAT 59.751 50.000 2.24 0.00 0.00 3.16
1494 1577 4.612412 TTCTTCACGGCGCGGGTT 62.612 61.111 19.75 0.00 0.00 4.11
1855 1938 2.358015 ACTACGTCGAGAAGAGAAGGG 58.642 52.381 0.00 0.00 0.00 3.95
1896 1982 1.532868 CAAGACAAGAACAAGCTCCGG 59.467 52.381 0.00 0.00 0.00 5.14
2289 2375 4.149019 TGGCTGGCCAACAACCCA 62.149 61.111 12.27 5.76 44.12 4.51
2493 2582 1.880340 GAGCTTCGAGATGGTGCCG 60.880 63.158 0.00 0.00 0.00 5.69
2574 2663 2.024868 CAACCATTCCGTCGTCGCA 61.025 57.895 0.00 0.00 35.54 5.10
2592 2684 0.106519 CATTCCACCCCATCTCACCC 60.107 60.000 0.00 0.00 0.00 4.61
2602 2694 2.022195 CCATCTCACCCTGAGCAATTG 58.978 52.381 0.00 0.00 43.95 2.32
2604 2696 0.401356 TCTCACCCTGAGCAATTGCA 59.599 50.000 30.89 11.63 43.95 4.08
2617 2709 3.262405 AGCAATTGCATCTTCAACCCAAT 59.738 39.130 30.89 3.18 45.16 3.16
2631 2723 1.922447 ACCCAATAGCCTGATCCACAA 59.078 47.619 0.00 0.00 0.00 3.33
2640 2732 2.028748 GCCTGATCCACAAGCACAATTT 60.029 45.455 0.00 0.00 36.13 1.82
2641 2733 3.555586 GCCTGATCCACAAGCACAATTTT 60.556 43.478 0.00 0.00 36.13 1.82
2647 2741 5.336150 TCCACAAGCACAATTTTTCTTCA 57.664 34.783 0.00 0.00 0.00 3.02
2704 2806 6.951198 TGTCAGTTGATTTATGGGGTTTACAT 59.049 34.615 0.00 0.00 0.00 2.29
2789 2893 7.567571 GCTTTTCAGCTTTAAGAAATTGGTTC 58.432 34.615 0.00 0.00 43.51 3.62
2867 2976 7.814264 TTTTTATGGGTGCAAATTGAAATGT 57.186 28.000 0.00 0.00 0.00 2.71
2883 2992 7.522901 TTGAAATGTTATTGCCATTCATTCG 57.477 32.000 0.00 0.00 31.49 3.34
2886 2995 5.833406 ATGTTATTGCCATTCATTCGACA 57.167 34.783 0.00 0.00 0.00 4.35
2894 3003 3.853671 GCCATTCATTCGACAAATGTGAC 59.146 43.478 10.84 0.00 44.36 3.67
2910 3138 1.878522 GACGTATGGTGCTCCGCTG 60.879 63.158 0.00 0.00 36.30 5.18
2954 6743 1.157870 AACTGAAACCGAGGCACGTG 61.158 55.000 12.28 12.28 40.78 4.49
2991 6781 6.601613 TCTGGTCGGCACATCTTTTATAAAAT 59.398 34.615 10.97 0.00 0.00 1.82
2994 6784 8.740906 TGGTCGGCACATCTTTTATAAAATTTA 58.259 29.630 10.97 1.44 0.00 1.40
3028 6821 2.399396 ATGTTGAACCTTCGCAAACG 57.601 45.000 0.00 0.00 42.01 3.60
3043 6836 2.381589 CAAACGAAGCTTCCGGTTTTC 58.618 47.619 22.30 0.71 34.37 2.29
3044 6837 0.584876 AACGAAGCTTCCGGTTTTCG 59.415 50.000 20.62 21.45 45.62 3.46
3062 6855 1.065491 TCGCAAGTAAGGTGGATGCAT 60.065 47.619 0.00 0.00 36.84 3.96
3112 6906 5.049612 CACTCATTCATAGCTCGATTGCATT 60.050 40.000 0.00 0.00 34.99 3.56
3121 6915 5.269505 AGCTCGATTGCATTCTAACTACT 57.730 39.130 7.00 0.00 34.99 2.57
3122 6916 5.046529 AGCTCGATTGCATTCTAACTACTG 58.953 41.667 7.00 0.00 34.99 2.74
3235 7029 5.508153 GCGGATCACTACAGTAGATGAACAT 60.508 44.000 14.94 0.62 0.00 2.71
3250 7044 7.468141 AGATGAACATATCGTATCTAAGCCA 57.532 36.000 0.00 0.00 32.33 4.75
3264 7058 7.040617 CGTATCTAAGCCACAGACTAGGAATAA 60.041 40.741 0.00 0.00 0.00 1.40
3298 7092 5.180117 CACGATCTCAAACAAAGAGGACAAT 59.820 40.000 0.00 0.00 33.92 2.71
3318 7112 4.805231 CACATACGGTGCGGCGGA 62.805 66.667 9.78 1.34 41.36 5.54
3335 7129 0.669625 GGAAGCAGAACCGTTAGCGT 60.670 55.000 0.00 0.66 36.15 5.07
3345 7139 2.215196 ACCGTTAGCGTTGATGTTGTT 58.785 42.857 0.00 0.00 36.15 2.83
3347 7141 2.570169 CGTTAGCGTTGATGTTGTTGG 58.430 47.619 0.00 0.00 0.00 3.77
3364 7158 0.327924 TGGCCATGTCGTTGAGGAAT 59.672 50.000 0.00 0.00 0.00 3.01
3375 7169 2.007608 GTTGAGGAATAGGTTGCCGAC 58.992 52.381 0.00 0.00 0.00 4.79
3376 7170 1.271856 TGAGGAATAGGTTGCCGACA 58.728 50.000 0.00 0.00 0.00 4.35
3377 7171 1.066430 TGAGGAATAGGTTGCCGACAC 60.066 52.381 0.00 0.00 0.00 3.67
3378 7172 1.207329 GAGGAATAGGTTGCCGACACT 59.793 52.381 0.00 0.00 0.00 3.55
3379 7173 2.429610 GAGGAATAGGTTGCCGACACTA 59.570 50.000 0.00 0.00 0.00 2.74
3380 7174 2.167900 AGGAATAGGTTGCCGACACTAC 59.832 50.000 0.00 0.00 0.00 2.73
3381 7175 2.167900 GGAATAGGTTGCCGACACTACT 59.832 50.000 0.00 0.00 0.00 2.57
3382 7176 3.382546 GGAATAGGTTGCCGACACTACTA 59.617 47.826 0.00 0.00 0.00 1.82
3383 7177 4.499357 GGAATAGGTTGCCGACACTACTAG 60.499 50.000 0.00 0.00 0.00 2.57
3384 7178 2.211250 AGGTTGCCGACACTACTAGA 57.789 50.000 0.00 0.00 0.00 2.43
3385 7179 2.522185 AGGTTGCCGACACTACTAGAA 58.478 47.619 0.00 0.00 0.00 2.10
3386 7180 2.895404 AGGTTGCCGACACTACTAGAAA 59.105 45.455 0.00 0.00 0.00 2.52
3387 7181 3.322828 AGGTTGCCGACACTACTAGAAAA 59.677 43.478 0.00 0.00 0.00 2.29
3388 7182 4.060205 GGTTGCCGACACTACTAGAAAAA 58.940 43.478 0.00 0.00 0.00 1.94
3406 7200 4.499037 AAAAAGATTGTTAGGGACGCAC 57.501 40.909 0.00 0.00 0.00 5.34
3407 7201 2.109425 AAGATTGTTAGGGACGCACC 57.891 50.000 0.00 0.00 38.08 5.01
3408 7202 1.276622 AGATTGTTAGGGACGCACCT 58.723 50.000 3.80 3.80 44.75 4.00
3409 7203 2.463752 AGATTGTTAGGGACGCACCTA 58.536 47.619 1.81 1.81 42.09 3.08
3410 7204 3.039011 AGATTGTTAGGGACGCACCTAT 58.961 45.455 6.55 0.00 42.45 2.57
3411 7205 3.454812 AGATTGTTAGGGACGCACCTATT 59.545 43.478 6.55 0.00 42.45 1.73
3412 7206 3.706600 TTGTTAGGGACGCACCTATTT 57.293 42.857 6.55 0.00 42.45 1.40
3413 7207 3.706600 TGTTAGGGACGCACCTATTTT 57.293 42.857 6.55 0.00 42.45 1.82
3414 7208 3.340034 TGTTAGGGACGCACCTATTTTG 58.660 45.455 6.55 0.00 42.45 2.44
3415 7209 2.681344 GTTAGGGACGCACCTATTTTGG 59.319 50.000 6.55 0.00 42.45 3.28
3416 7210 0.679960 AGGGACGCACCTATTTTGGC 60.680 55.000 0.00 0.00 39.65 4.52
3417 7211 0.679960 GGGACGCACCTATTTTGGCT 60.680 55.000 0.00 0.00 38.98 4.75
3418 7212 1.407712 GGGACGCACCTATTTTGGCTA 60.408 52.381 0.00 0.00 38.98 3.93
3419 7213 2.572290 GGACGCACCTATTTTGGCTAT 58.428 47.619 0.00 0.00 35.41 2.97
3420 7214 2.949644 GGACGCACCTATTTTGGCTATT 59.050 45.455 0.00 0.00 35.41 1.73
3421 7215 4.131596 GGACGCACCTATTTTGGCTATTA 58.868 43.478 0.00 0.00 35.41 0.98
3422 7216 4.577283 GGACGCACCTATTTTGGCTATTAA 59.423 41.667 0.00 0.00 35.41 1.40
3423 7217 5.240844 GGACGCACCTATTTTGGCTATTAAT 59.759 40.000 0.00 0.00 35.41 1.40
3424 7218 6.072112 ACGCACCTATTTTGGCTATTAATG 57.928 37.500 0.00 0.00 0.00 1.90
3425 7219 5.009610 ACGCACCTATTTTGGCTATTAATGG 59.990 40.000 0.00 0.00 0.00 3.16
3426 7220 5.230182 GCACCTATTTTGGCTATTAATGGC 58.770 41.667 14.96 14.96 0.00 4.40
3427 7221 5.460646 CACCTATTTTGGCTATTAATGGCG 58.539 41.667 16.49 4.03 34.82 5.69
3428 7222 4.022329 ACCTATTTTGGCTATTAATGGCGC 60.022 41.667 16.49 0.00 34.82 6.53
3429 7223 4.022416 CCTATTTTGGCTATTAATGGCGCA 60.022 41.667 16.49 12.78 34.82 6.09
3430 7224 2.861462 TTTGGCTATTAATGGCGCAC 57.139 45.000 16.49 4.89 34.82 5.34
3431 7225 2.051334 TTGGCTATTAATGGCGCACT 57.949 45.000 16.49 0.00 34.82 4.40
3432 7226 2.920724 TGGCTATTAATGGCGCACTA 57.079 45.000 16.49 0.00 34.82 2.74
3433 7227 3.417069 TGGCTATTAATGGCGCACTAT 57.583 42.857 16.49 0.00 34.82 2.12
3434 7228 4.545208 TGGCTATTAATGGCGCACTATA 57.455 40.909 16.49 0.00 34.82 1.31
3435 7229 4.503910 TGGCTATTAATGGCGCACTATAG 58.496 43.478 16.49 9.49 34.82 1.31
3436 7230 3.871594 GGCTATTAATGGCGCACTATAGG 59.128 47.826 16.49 0.00 34.82 2.57
3437 7231 4.504858 GCTATTAATGGCGCACTATAGGT 58.495 43.478 10.83 0.00 0.00 3.08
3448 7242 3.386768 CACTATAGGTGCGCCACTATT 57.613 47.619 20.59 0.00 39.22 1.73
3449 7243 4.514781 CACTATAGGTGCGCCACTATTA 57.485 45.455 20.59 1.31 39.22 0.98
3450 7244 5.073311 CACTATAGGTGCGCCACTATTAT 57.927 43.478 20.59 9.55 39.22 1.28
3451 7245 5.103000 CACTATAGGTGCGCCACTATTATC 58.897 45.833 20.59 0.00 39.22 1.75
3452 7246 4.770531 ACTATAGGTGCGCCACTATTATCA 59.229 41.667 20.59 7.17 37.19 2.15
3453 7247 2.240493 AGGTGCGCCACTATTATCAC 57.760 50.000 20.59 0.00 37.19 3.06
3454 7248 0.859232 GGTGCGCCACTATTATCACG 59.141 55.000 12.58 0.00 34.40 4.35
3455 7249 0.232303 GTGCGCCACTATTATCACGC 59.768 55.000 4.18 0.00 46.05 5.34
3456 7250 0.878523 TGCGCCACTATTATCACGCC 60.879 55.000 4.18 0.00 45.32 5.68
3457 7251 0.878523 GCGCCACTATTATCACGCCA 60.879 55.000 0.00 0.00 40.43 5.69
3458 7252 1.795768 CGCCACTATTATCACGCCAT 58.204 50.000 0.00 0.00 0.00 4.40
3459 7253 2.143122 CGCCACTATTATCACGCCATT 58.857 47.619 0.00 0.00 0.00 3.16
3460 7254 3.322369 CGCCACTATTATCACGCCATTA 58.678 45.455 0.00 0.00 0.00 1.90
3461 7255 3.367932 CGCCACTATTATCACGCCATTAG 59.632 47.826 0.00 0.00 0.00 1.73
3462 7256 4.315803 GCCACTATTATCACGCCATTAGT 58.684 43.478 0.00 0.00 0.00 2.24
3463 7257 5.475719 GCCACTATTATCACGCCATTAGTA 58.524 41.667 0.00 0.00 0.00 1.82
3464 7258 6.106673 GCCACTATTATCACGCCATTAGTAT 58.893 40.000 0.00 0.00 0.00 2.12
3465 7259 6.594159 GCCACTATTATCACGCCATTAGTATT 59.406 38.462 0.00 0.00 0.00 1.89
3466 7260 7.413000 GCCACTATTATCACGCCATTAGTATTG 60.413 40.741 0.00 0.00 0.00 1.90
3467 7261 7.413000 CCACTATTATCACGCCATTAGTATTGC 60.413 40.741 0.00 0.00 0.00 3.56
3468 7262 7.117667 CACTATTATCACGCCATTAGTATTGCA 59.882 37.037 0.00 0.00 0.00 4.08
3469 7263 5.922739 TTATCACGCCATTAGTATTGCAG 57.077 39.130 0.00 0.00 0.00 4.41
3470 7264 2.560504 TCACGCCATTAGTATTGCAGG 58.439 47.619 0.00 0.00 0.00 4.85
3471 7265 2.093181 TCACGCCATTAGTATTGCAGGT 60.093 45.455 0.00 0.00 0.00 4.00
3472 7266 3.133183 TCACGCCATTAGTATTGCAGGTA 59.867 43.478 0.00 0.00 0.00 3.08
3473 7267 3.874543 CACGCCATTAGTATTGCAGGTAA 59.125 43.478 0.00 0.00 0.00 2.85
3474 7268 3.875134 ACGCCATTAGTATTGCAGGTAAC 59.125 43.478 0.00 0.00 0.00 2.50
3475 7269 3.874543 CGCCATTAGTATTGCAGGTAACA 59.125 43.478 0.00 0.00 41.41 2.41
3476 7270 4.024893 CGCCATTAGTATTGCAGGTAACAG 60.025 45.833 0.00 0.00 41.41 3.16
3477 7271 4.881850 GCCATTAGTATTGCAGGTAACAGT 59.118 41.667 0.00 0.00 41.41 3.55
3478 7272 5.220854 GCCATTAGTATTGCAGGTAACAGTG 60.221 44.000 0.00 0.00 41.41 3.66
3479 7273 5.296780 CCATTAGTATTGCAGGTAACAGTGG 59.703 44.000 0.00 0.00 41.41 4.00
3480 7274 2.711542 AGTATTGCAGGTAACAGTGGC 58.288 47.619 0.00 0.00 41.41 5.01
3481 7275 1.396996 GTATTGCAGGTAACAGTGGCG 59.603 52.381 0.00 0.00 41.41 5.69
3482 7276 1.586154 ATTGCAGGTAACAGTGGCGC 61.586 55.000 0.00 0.00 41.41 6.53
3483 7277 2.668212 GCAGGTAACAGTGGCGCA 60.668 61.111 10.83 0.00 41.41 6.09
3484 7278 2.040544 GCAGGTAACAGTGGCGCAT 61.041 57.895 10.83 0.00 41.41 4.73
3485 7279 1.982073 GCAGGTAACAGTGGCGCATC 61.982 60.000 10.83 0.41 41.41 3.91
3486 7280 0.391661 CAGGTAACAGTGGCGCATCT 60.392 55.000 10.83 3.31 41.41 2.90
3487 7281 0.324943 AGGTAACAGTGGCGCATCTT 59.675 50.000 10.83 0.00 41.41 2.40
3488 7282 0.447801 GGTAACAGTGGCGCATCTTG 59.552 55.000 10.83 4.17 0.00 3.02
3489 7283 1.156736 GTAACAGTGGCGCATCTTGT 58.843 50.000 10.83 4.89 0.00 3.16
3490 7284 2.343101 GTAACAGTGGCGCATCTTGTA 58.657 47.619 10.83 0.00 0.00 2.41
3491 7285 1.442769 AACAGTGGCGCATCTTGTAG 58.557 50.000 10.83 0.00 0.00 2.74
3492 7286 0.321671 ACAGTGGCGCATCTTGTAGT 59.678 50.000 10.83 0.00 0.00 2.73
3493 7287 0.723414 CAGTGGCGCATCTTGTAGTG 59.277 55.000 10.83 0.00 0.00 2.74
3494 7288 1.021390 AGTGGCGCATCTTGTAGTGC 61.021 55.000 10.83 0.00 40.36 4.40
3502 7296 4.183539 GCATCTTGTAGTGCGTCATTAC 57.816 45.455 5.85 5.85 0.00 1.89
3503 7297 3.865745 GCATCTTGTAGTGCGTCATTACT 59.134 43.478 11.55 0.00 29.79 2.24
3504 7298 5.041287 GCATCTTGTAGTGCGTCATTACTA 58.959 41.667 11.55 5.71 29.79 1.82
3505 7299 5.692204 GCATCTTGTAGTGCGTCATTACTAT 59.308 40.000 11.55 3.68 32.55 2.12
3506 7300 6.201044 GCATCTTGTAGTGCGTCATTACTATT 59.799 38.462 11.55 0.00 32.55 1.73
3507 7301 7.558991 CATCTTGTAGTGCGTCATTACTATTG 58.441 38.462 11.55 4.66 32.55 1.90
3508 7302 5.518847 TCTTGTAGTGCGTCATTACTATTGC 59.481 40.000 11.55 0.00 32.55 3.56
3509 7303 5.006153 TGTAGTGCGTCATTACTATTGCT 57.994 39.130 11.55 0.00 32.55 3.91
3510 7304 6.139048 TGTAGTGCGTCATTACTATTGCTA 57.861 37.500 11.55 0.00 32.55 3.49
3511 7305 5.975344 TGTAGTGCGTCATTACTATTGCTAC 59.025 40.000 11.55 0.00 32.55 3.58
3512 7306 5.006153 AGTGCGTCATTACTATTGCTACA 57.994 39.130 0.00 0.00 0.00 2.74
3513 7307 5.043903 AGTGCGTCATTACTATTGCTACAG 58.956 41.667 0.00 0.00 0.00 2.74
3514 7308 4.209288 GTGCGTCATTACTATTGCTACAGG 59.791 45.833 0.00 0.00 0.00 4.00
3515 7309 4.142026 TGCGTCATTACTATTGCTACAGGT 60.142 41.667 0.00 0.00 0.00 4.00
3516 7310 4.209288 GCGTCATTACTATTGCTACAGGTG 59.791 45.833 0.00 0.00 0.00 4.00
3517 7311 4.209288 CGTCATTACTATTGCTACAGGTGC 59.791 45.833 0.00 0.00 0.00 5.01
3518 7312 4.209288 GTCATTACTATTGCTACAGGTGCG 59.791 45.833 0.00 0.00 0.00 5.34
3519 7313 2.218953 TACTATTGCTACAGGTGCGC 57.781 50.000 0.00 0.00 0.00 6.09
3520 7314 0.462047 ACTATTGCTACAGGTGCGCC 60.462 55.000 8.71 8.71 0.00 6.53
3521 7315 0.461870 CTATTGCTACAGGTGCGCCA 60.462 55.000 20.59 0.00 37.19 5.69
3522 7316 0.742990 TATTGCTACAGGTGCGCCAC 60.743 55.000 20.59 2.79 37.19 5.01
3523 7317 2.469465 ATTGCTACAGGTGCGCCACT 62.469 55.000 20.59 4.91 37.19 4.00
3524 7318 3.121030 GCTACAGGTGCGCCACTG 61.121 66.667 20.59 22.18 37.19 3.66
3525 7319 2.434884 CTACAGGTGCGCCACTGG 60.435 66.667 25.77 7.40 37.19 4.00
3526 7320 3.238497 TACAGGTGCGCCACTGGT 61.238 61.111 25.77 13.05 37.19 4.00
3527 7321 1.884075 CTACAGGTGCGCCACTGGTA 61.884 60.000 25.77 13.48 37.19 3.25
3528 7322 1.473497 TACAGGTGCGCCACTGGTAA 61.473 55.000 25.77 12.56 37.19 2.85
3529 7323 2.032071 AGGTGCGCCACTGGTAAC 59.968 61.111 20.59 0.00 37.19 2.50
3530 7324 2.032071 GGTGCGCCACTGGTAACT 59.968 61.111 12.58 0.00 34.40 2.24
3531 7325 1.599797 GGTGCGCCACTGGTAACTT 60.600 57.895 12.58 0.00 34.40 2.66
3532 7326 1.170290 GGTGCGCCACTGGTAACTTT 61.170 55.000 12.58 0.00 34.40 2.66
3533 7327 0.666374 GTGCGCCACTGGTAACTTTT 59.334 50.000 4.18 0.00 37.61 2.27
3534 7328 1.066454 GTGCGCCACTGGTAACTTTTT 59.934 47.619 4.18 0.00 37.61 1.94
3581 7375 7.625828 TTTTTAAATTTTGAAGGCGGGAAAA 57.374 28.000 0.00 0.00 0.00 2.29
3582 7376 7.809546 TTTTAAATTTTGAAGGCGGGAAAAT 57.190 28.000 0.00 0.00 32.01 1.82
3583 7377 8.904099 TTTTAAATTTTGAAGGCGGGAAAATA 57.096 26.923 0.00 0.00 30.81 1.40
3584 7378 8.541133 TTTAAATTTTGAAGGCGGGAAAATAG 57.459 30.769 0.00 0.00 30.81 1.73
3585 7379 5.738619 AATTTTGAAGGCGGGAAAATAGT 57.261 34.783 0.00 0.00 30.81 2.12
3586 7380 6.844097 AATTTTGAAGGCGGGAAAATAGTA 57.156 33.333 0.00 0.00 30.81 1.82
3587 7381 5.890424 TTTTGAAGGCGGGAAAATAGTAG 57.110 39.130 0.00 0.00 0.00 2.57
3588 7382 4.563140 TTGAAGGCGGGAAAATAGTAGT 57.437 40.909 0.00 0.00 0.00 2.73
3589 7383 5.680594 TTGAAGGCGGGAAAATAGTAGTA 57.319 39.130 0.00 0.00 0.00 1.82
3590 7384 5.272283 TGAAGGCGGGAAAATAGTAGTAG 57.728 43.478 0.00 0.00 0.00 2.57
3591 7385 3.747854 AGGCGGGAAAATAGTAGTAGC 57.252 47.619 0.00 0.00 0.00 3.58
3592 7386 2.035576 AGGCGGGAAAATAGTAGTAGCG 59.964 50.000 0.00 0.00 0.00 4.26
3593 7387 1.791204 GCGGGAAAATAGTAGTAGCGC 59.209 52.381 0.00 0.00 0.00 5.92
3594 7388 2.800629 GCGGGAAAATAGTAGTAGCGCA 60.801 50.000 11.47 0.00 0.00 6.09
3595 7389 2.793232 CGGGAAAATAGTAGTAGCGCAC 59.207 50.000 11.47 5.97 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
153 154 1.000607 GCATTCTAGACGGCGGTGATA 60.001 52.381 13.24 0.00 0.00 2.15
218 219 2.573869 CGTCTGCGTCAGGACCAT 59.426 61.111 6.95 0.00 31.51 3.55
258 259 2.125912 CTAGACAACGCGCTGCCT 60.126 61.111 9.87 6.48 0.00 4.75
443 447 2.612567 GGCACAAACATCCGACGCA 61.613 57.895 0.00 0.00 0.00 5.24
489 493 1.088306 TGAACGGCGTTTTTGTCTGT 58.912 45.000 27.48 0.00 0.00 3.41
499 503 1.289109 CCGACTCAAATGAACGGCGT 61.289 55.000 6.77 6.77 37.30 5.68
508 512 1.674322 CCAACGGGCCGACTCAAAT 60.674 57.895 35.78 4.66 0.00 2.32
513 517 1.674322 CAATTCCAACGGGCCGACT 60.674 57.895 35.78 16.74 0.00 4.18
534 538 5.430007 TCGACCAGAAACAGTTTCCTTAAA 58.570 37.500 20.47 2.20 40.54 1.52
564 568 7.282332 AGATCCTTTTCTTTCTTTCAACCAG 57.718 36.000 0.00 0.00 0.00 4.00
620 628 4.314440 TGCTCACGCTCGGCCTTT 62.314 61.111 0.00 0.00 36.97 3.11
635 643 2.125350 CCGCTCTCAAGGACCTGC 60.125 66.667 0.00 0.00 0.00 4.85
645 653 2.726241 GCAAATTTGTTTGACCGCTCTC 59.274 45.455 19.03 0.00 33.95 3.20
659 667 0.108396 GCTGGTTGGTGGGCAAATTT 59.892 50.000 0.00 0.00 0.00 1.82
685 695 1.532007 GAGATAGACGACGGCGAGAAT 59.468 52.381 22.49 6.93 41.64 2.40
686 696 0.935898 GAGATAGACGACGGCGAGAA 59.064 55.000 22.49 0.64 41.64 2.87
687 697 0.179092 TGAGATAGACGACGGCGAGA 60.179 55.000 22.49 0.78 41.64 4.04
688 698 0.869068 ATGAGATAGACGACGGCGAG 59.131 55.000 22.49 10.00 41.64 5.03
690 700 0.386100 CCATGAGATAGACGACGGCG 60.386 60.000 10.39 10.39 44.79 6.46
691 701 0.664767 GCCATGAGATAGACGACGGC 60.665 60.000 0.00 0.00 0.00 5.68
692 702 0.668535 TGCCATGAGATAGACGACGG 59.331 55.000 0.00 0.00 0.00 4.79
806 846 1.600916 AAGCAAAGCACGAGGGGAC 60.601 57.895 0.00 0.00 0.00 4.46
818 860 1.836604 GTGGGGAAGGCCAAGCAAA 60.837 57.895 5.01 0.00 35.15 3.68
821 863 2.612493 TAGGTGGGGAAGGCCAAGC 61.612 63.158 5.01 0.00 35.15 4.01
822 864 1.303282 GTAGGTGGGGAAGGCCAAG 59.697 63.158 5.01 0.00 35.15 3.61
823 865 2.235761 GGTAGGTGGGGAAGGCCAA 61.236 63.158 5.01 0.00 35.15 4.52
824 866 2.612746 GGTAGGTGGGGAAGGCCA 60.613 66.667 5.01 0.00 35.15 5.36
835 877 4.041567 TGACTGACAATGACAATGGTAGGT 59.958 41.667 0.00 0.00 0.00 3.08
837 879 6.373779 GTTTGACTGACAATGACAATGGTAG 58.626 40.000 0.00 0.00 38.36 3.18
838 880 5.240623 GGTTTGACTGACAATGACAATGGTA 59.759 40.000 0.00 0.00 38.36 3.25
841 883 4.037803 TGGGTTTGACTGACAATGACAATG 59.962 41.667 0.00 0.00 38.36 2.82
842 884 4.037923 GTGGGTTTGACTGACAATGACAAT 59.962 41.667 0.00 0.00 38.36 2.71
843 885 3.380004 GTGGGTTTGACTGACAATGACAA 59.620 43.478 0.00 0.00 38.36 3.18
845 887 2.032030 CGTGGGTTTGACTGACAATGAC 60.032 50.000 0.00 0.00 38.36 3.06
846 888 2.217750 CGTGGGTTTGACTGACAATGA 58.782 47.619 0.00 0.00 38.36 2.57
894 961 1.808531 TTGCTGTGAAGGTGCCATGC 61.809 55.000 0.00 0.00 0.00 4.06
957 1033 1.202031 GCTTGGCGTGCAATGTACTAC 60.202 52.381 0.00 0.00 0.00 2.73
960 1037 1.062587 CTAGCTTGGCGTGCAATGTAC 59.937 52.381 0.00 0.00 0.00 2.90
961 1038 1.368641 CTAGCTTGGCGTGCAATGTA 58.631 50.000 0.00 0.00 0.00 2.29
962 1039 1.926511 GCTAGCTTGGCGTGCAATGT 61.927 55.000 7.70 0.00 33.60 2.71
1407 1490 3.950794 GAAGACCATGTCGGCGCCA 62.951 63.158 28.98 11.20 39.03 5.69
1869 1952 2.638480 TGTTCTTGTCTTGTCCTGGG 57.362 50.000 0.00 0.00 0.00 4.45
1876 1959 1.532868 CCGGAGCTTGTTCTTGTCTTG 59.467 52.381 0.00 0.00 0.00 3.02
1896 1982 2.860628 GATGTGGTCGATCGCGCAC 61.861 63.158 11.09 14.70 37.46 5.34
2289 2375 1.118356 CCGGCTTCTCCCATAGCTCT 61.118 60.000 0.00 0.00 37.54 4.09
2318 2404 2.294078 CCCAAGAACCTCTCCGGCT 61.294 63.158 0.00 0.00 35.61 5.52
2574 2663 0.253820 AGGGTGAGATGGGGTGGAAT 60.254 55.000 0.00 0.00 0.00 3.01
2592 2684 3.508762 GGTTGAAGATGCAATTGCTCAG 58.491 45.455 29.37 0.00 42.66 3.35
2602 2694 2.360165 CAGGCTATTGGGTTGAAGATGC 59.640 50.000 0.00 0.00 0.00 3.91
2604 2696 4.446889 GGATCAGGCTATTGGGTTGAAGAT 60.447 45.833 0.00 0.00 0.00 2.40
2631 2723 9.768662 ATTTGTAATCTGAAGAAAAATTGTGCT 57.231 25.926 0.00 0.00 0.00 4.40
2671 2771 7.409697 CCCATAAATCAACTGACATACTTTCG 58.590 38.462 0.00 0.00 0.00 3.46
2716 2819 2.936498 CACGCGTGATCCTCCTTTTTAT 59.064 45.455 34.93 0.00 0.00 1.40
2760 2864 8.562052 CCAATTTCTTAAAGCTGAAAAGCATTT 58.438 29.630 1.54 0.00 42.41 2.32
2784 2888 3.304391 GCTGAAAAGCGTTATGTGAACCA 60.304 43.478 0.00 0.00 0.00 3.67
2789 2893 6.370593 TCTTAAAGCTGAAAAGCGTTATGTG 58.629 36.000 14.27 6.98 38.23 3.21
2846 2955 8.944029 CAATAACATTTCAATTTGCACCCATAA 58.056 29.630 0.00 0.00 0.00 1.90
2848 2957 6.127952 GCAATAACATTTCAATTTGCACCCAT 60.128 34.615 0.00 0.00 0.00 4.00
2849 2958 5.180868 GCAATAACATTTCAATTTGCACCCA 59.819 36.000 0.00 0.00 0.00 4.51
2860 2969 6.751425 GTCGAATGAATGGCAATAACATTTCA 59.249 34.615 0.00 0.00 38.57 2.69
2867 2976 6.530887 CACATTTGTCGAATGAATGGCAATAA 59.469 34.615 18.09 0.00 46.59 1.40
2883 2992 2.742053 AGCACCATACGTCACATTTGTC 59.258 45.455 0.00 0.00 0.00 3.18
2886 2995 2.356135 GGAGCACCATACGTCACATTT 58.644 47.619 0.00 0.00 35.97 2.32
2910 3138 0.738762 GGGACGCTAAGAACGAACCC 60.739 60.000 0.00 0.00 40.73 4.11
2954 6743 2.257034 CCGACCAGAGTAAACTTACGC 58.743 52.381 0.00 0.00 38.65 4.42
3028 6821 0.309612 TTGCGAAAACCGGAAGCTTC 59.690 50.000 18.54 18.54 43.60 3.86
3043 6836 1.331756 GATGCATCCACCTTACTTGCG 59.668 52.381 16.23 0.00 36.11 4.85
3044 6837 1.678101 GGATGCATCCACCTTACTTGC 59.322 52.381 35.93 8.03 46.38 4.01
3062 6855 5.761205 AGCTCTCTTATGAACTAGTGAGGA 58.239 41.667 0.00 0.00 34.31 3.71
3191 6985 7.209471 TCCGCATGATTAGTTTAAACTTTGT 57.791 32.000 25.07 11.97 40.37 2.83
3197 6991 7.766738 TGTAGTGATCCGCATGATTAGTTTAAA 59.233 33.333 0.00 0.00 32.41 1.52
3235 7029 5.938710 CCTAGTCTGTGGCTTAGATACGATA 59.061 44.000 0.00 0.00 0.00 2.92
3250 7044 8.417884 GTGCTAGAATTCTTATTCCTAGTCTGT 58.582 37.037 14.36 0.00 40.91 3.41
3264 7058 5.724328 TGTTTGAGATCGTGCTAGAATTCT 58.276 37.500 13.56 13.56 0.00 2.40
3318 7112 0.865769 CAACGCTAACGGTTCTGCTT 59.134 50.000 13.99 5.08 46.04 3.91
3331 7125 1.106351 TGGCCAACAACATCAACGCT 61.106 50.000 0.61 0.00 0.00 5.07
3335 7129 1.269174 CGACATGGCCAACAACATCAA 59.731 47.619 10.96 0.00 0.00 2.57
3345 7139 0.327924 ATTCCTCAACGACATGGCCA 59.672 50.000 8.56 8.56 0.00 5.36
3347 7141 2.213499 CCTATTCCTCAACGACATGGC 58.787 52.381 0.00 0.00 0.00 4.40
3364 7158 3.354948 TCTAGTAGTGTCGGCAACCTA 57.645 47.619 0.00 0.00 0.00 3.08
3385 7179 3.254903 GGTGCGTCCCTAACAATCTTTTT 59.745 43.478 0.00 0.00 0.00 1.94
3386 7180 2.817844 GGTGCGTCCCTAACAATCTTTT 59.182 45.455 0.00 0.00 0.00 2.27
3387 7181 2.039879 AGGTGCGTCCCTAACAATCTTT 59.960 45.455 0.00 0.00 36.75 2.52
3388 7182 1.628846 AGGTGCGTCCCTAACAATCTT 59.371 47.619 0.00 0.00 36.75 2.40
3389 7183 1.276622 AGGTGCGTCCCTAACAATCT 58.723 50.000 0.00 0.00 36.75 2.40
3390 7184 2.973694 TAGGTGCGTCCCTAACAATC 57.026 50.000 0.36 0.00 34.11 2.67
3391 7185 3.926058 AATAGGTGCGTCCCTAACAAT 57.074 42.857 6.36 0.00 40.42 2.71
3392 7186 3.706600 AAATAGGTGCGTCCCTAACAA 57.293 42.857 6.36 0.00 40.42 2.83
3393 7187 3.340034 CAAAATAGGTGCGTCCCTAACA 58.660 45.455 6.36 0.00 40.42 2.41
3394 7188 2.681344 CCAAAATAGGTGCGTCCCTAAC 59.319 50.000 6.36 0.00 40.42 2.34
3395 7189 2.942306 GCCAAAATAGGTGCGTCCCTAA 60.942 50.000 6.36 0.00 40.42 2.69
3396 7190 1.407712 GCCAAAATAGGTGCGTCCCTA 60.408 52.381 4.94 4.94 41.26 3.53
3397 7191 0.679960 GCCAAAATAGGTGCGTCCCT 60.680 55.000 0.67 0.67 38.70 4.20
3398 7192 0.679960 AGCCAAAATAGGTGCGTCCC 60.680 55.000 0.00 0.00 36.75 4.46
3399 7193 2.032680 TAGCCAAAATAGGTGCGTCC 57.967 50.000 0.00 0.00 0.00 4.79
3400 7194 5.744666 TTAATAGCCAAAATAGGTGCGTC 57.255 39.130 0.00 0.00 0.00 5.19
3401 7195 5.009610 CCATTAATAGCCAAAATAGGTGCGT 59.990 40.000 0.00 0.00 0.00 5.24
3402 7196 5.460646 CCATTAATAGCCAAAATAGGTGCG 58.539 41.667 0.00 0.00 0.00 5.34
3403 7197 5.230182 GCCATTAATAGCCAAAATAGGTGC 58.770 41.667 0.00 0.00 0.00 5.01
3404 7198 5.460646 CGCCATTAATAGCCAAAATAGGTG 58.539 41.667 0.03 0.00 0.00 4.00
3405 7199 4.022329 GCGCCATTAATAGCCAAAATAGGT 60.022 41.667 0.00 0.00 0.00 3.08
3406 7200 4.022416 TGCGCCATTAATAGCCAAAATAGG 60.022 41.667 4.18 0.00 0.00 2.57
3407 7201 4.917415 GTGCGCCATTAATAGCCAAAATAG 59.083 41.667 4.18 0.00 0.00 1.73
3408 7202 4.582656 AGTGCGCCATTAATAGCCAAAATA 59.417 37.500 4.18 0.00 0.00 1.40
3409 7203 3.384467 AGTGCGCCATTAATAGCCAAAAT 59.616 39.130 4.18 0.00 0.00 1.82
3410 7204 2.757868 AGTGCGCCATTAATAGCCAAAA 59.242 40.909 4.18 0.00 0.00 2.44
3411 7205 2.374184 AGTGCGCCATTAATAGCCAAA 58.626 42.857 4.18 0.00 0.00 3.28
3412 7206 2.051334 AGTGCGCCATTAATAGCCAA 57.949 45.000 4.18 0.00 0.00 4.52
3413 7207 2.920724 TAGTGCGCCATTAATAGCCA 57.079 45.000 4.18 0.00 0.00 4.75
3414 7208 3.871594 CCTATAGTGCGCCATTAATAGCC 59.128 47.826 4.18 0.00 0.00 3.93
3415 7209 4.330074 CACCTATAGTGCGCCATTAATAGC 59.670 45.833 4.18 0.00 40.28 2.97
3429 7223 4.770531 TGATAATAGTGGCGCACCTATAGT 59.229 41.667 10.83 6.09 34.49 2.12
3430 7224 5.103000 GTGATAATAGTGGCGCACCTATAG 58.897 45.833 10.83 0.00 34.49 1.31
3431 7225 4.380128 CGTGATAATAGTGGCGCACCTATA 60.380 45.833 10.83 3.93 34.49 1.31
3432 7226 3.614150 CGTGATAATAGTGGCGCACCTAT 60.614 47.826 10.83 11.02 34.49 2.57
3433 7227 2.287970 CGTGATAATAGTGGCGCACCTA 60.288 50.000 10.83 8.88 34.49 3.08
3434 7228 1.538204 CGTGATAATAGTGGCGCACCT 60.538 52.381 10.83 6.50 34.49 4.00
3435 7229 0.859232 CGTGATAATAGTGGCGCACC 59.141 55.000 10.83 0.00 34.49 5.01
3436 7230 0.232303 GCGTGATAATAGTGGCGCAC 59.768 55.000 10.83 5.73 43.62 5.34
3437 7231 0.878523 GGCGTGATAATAGTGGCGCA 60.879 55.000 10.83 0.00 45.58 6.09
3438 7232 0.878523 TGGCGTGATAATAGTGGCGC 60.879 55.000 0.00 0.00 43.46 6.53
3439 7233 1.795768 ATGGCGTGATAATAGTGGCG 58.204 50.000 0.00 0.00 0.00 5.69
3440 7234 4.315803 ACTAATGGCGTGATAATAGTGGC 58.684 43.478 0.00 0.00 0.00 5.01
3441 7235 7.413000 GCAATACTAATGGCGTGATAATAGTGG 60.413 40.741 0.00 0.00 0.00 4.00
3442 7236 7.117667 TGCAATACTAATGGCGTGATAATAGTG 59.882 37.037 0.00 0.00 34.42 2.74
3443 7237 7.158697 TGCAATACTAATGGCGTGATAATAGT 58.841 34.615 0.00 0.00 34.42 2.12
3444 7238 7.201556 CCTGCAATACTAATGGCGTGATAATAG 60.202 40.741 0.00 0.00 34.42 1.73
3445 7239 6.593770 CCTGCAATACTAATGGCGTGATAATA 59.406 38.462 0.00 0.00 34.42 0.98
3446 7240 5.412594 CCTGCAATACTAATGGCGTGATAAT 59.587 40.000 0.00 0.00 34.42 1.28
3447 7241 4.754618 CCTGCAATACTAATGGCGTGATAA 59.245 41.667 0.00 0.00 34.42 1.75
3448 7242 4.202315 ACCTGCAATACTAATGGCGTGATA 60.202 41.667 0.00 0.00 34.42 2.15
3449 7243 3.141398 CCTGCAATACTAATGGCGTGAT 58.859 45.455 0.00 0.00 34.42 3.06
3450 7244 2.093181 ACCTGCAATACTAATGGCGTGA 60.093 45.455 0.00 0.00 34.42 4.35
3451 7245 2.288666 ACCTGCAATACTAATGGCGTG 58.711 47.619 0.00 0.00 34.42 5.34
3452 7246 2.710096 ACCTGCAATACTAATGGCGT 57.290 45.000 0.00 0.00 34.42 5.68
3453 7247 3.874543 TGTTACCTGCAATACTAATGGCG 59.125 43.478 0.00 0.00 34.42 5.69
3454 7248 4.881850 ACTGTTACCTGCAATACTAATGGC 59.118 41.667 0.00 0.00 32.05 4.40
3455 7249 5.296780 CCACTGTTACCTGCAATACTAATGG 59.703 44.000 0.00 0.00 0.00 3.16
3456 7250 5.220854 GCCACTGTTACCTGCAATACTAATG 60.221 44.000 0.00 0.00 0.00 1.90
3457 7251 4.881850 GCCACTGTTACCTGCAATACTAAT 59.118 41.667 0.00 0.00 0.00 1.73
3458 7252 4.258543 GCCACTGTTACCTGCAATACTAA 58.741 43.478 0.00 0.00 0.00 2.24
3459 7253 3.677700 CGCCACTGTTACCTGCAATACTA 60.678 47.826 0.00 0.00 0.00 1.82
3460 7254 2.711542 GCCACTGTTACCTGCAATACT 58.288 47.619 0.00 0.00 0.00 2.12
3461 7255 1.396996 CGCCACTGTTACCTGCAATAC 59.603 52.381 0.00 0.00 0.00 1.89
3462 7256 1.732941 CGCCACTGTTACCTGCAATA 58.267 50.000 0.00 0.00 0.00 1.90
3463 7257 1.586154 GCGCCACTGTTACCTGCAAT 61.586 55.000 0.00 0.00 0.00 3.56
3464 7258 2.258013 GCGCCACTGTTACCTGCAA 61.258 57.895 0.00 0.00 0.00 4.08
3465 7259 2.668212 GCGCCACTGTTACCTGCA 60.668 61.111 0.00 0.00 0.00 4.41
3466 7260 1.982073 GATGCGCCACTGTTACCTGC 61.982 60.000 4.18 0.00 0.00 4.85
3467 7261 0.391661 AGATGCGCCACTGTTACCTG 60.392 55.000 4.18 0.00 0.00 4.00
3468 7262 0.324943 AAGATGCGCCACTGTTACCT 59.675 50.000 4.18 0.00 0.00 3.08
3469 7263 0.447801 CAAGATGCGCCACTGTTACC 59.552 55.000 4.18 0.00 0.00 2.85
3470 7264 1.156736 ACAAGATGCGCCACTGTTAC 58.843 50.000 4.18 0.00 0.00 2.50
3471 7265 2.028476 ACTACAAGATGCGCCACTGTTA 60.028 45.455 4.18 0.00 0.00 2.41
3472 7266 1.270839 ACTACAAGATGCGCCACTGTT 60.271 47.619 4.18 0.00 0.00 3.16
3473 7267 0.321671 ACTACAAGATGCGCCACTGT 59.678 50.000 4.18 5.82 0.00 3.55
3474 7268 0.723414 CACTACAAGATGCGCCACTG 59.277 55.000 4.18 0.00 0.00 3.66
3475 7269 1.021390 GCACTACAAGATGCGCCACT 61.021 55.000 4.18 0.28 30.97 4.00
3476 7270 1.425428 GCACTACAAGATGCGCCAC 59.575 57.895 4.18 0.00 30.97 5.01
3477 7271 3.889227 GCACTACAAGATGCGCCA 58.111 55.556 4.18 0.00 30.97 5.69
3481 7275 3.865745 AGTAATGACGCACTACAAGATGC 59.134 43.478 2.35 0.00 38.52 3.91
3482 7276 7.558991 CAATAGTAATGACGCACTACAAGATG 58.441 38.462 2.35 0.00 30.36 2.90
3483 7277 6.201044 GCAATAGTAATGACGCACTACAAGAT 59.799 38.462 2.35 0.00 30.36 2.40
3484 7278 5.518847 GCAATAGTAATGACGCACTACAAGA 59.481 40.000 2.35 0.00 30.36 3.02
3485 7279 5.520288 AGCAATAGTAATGACGCACTACAAG 59.480 40.000 2.35 0.00 30.36 3.16
3486 7280 5.416083 AGCAATAGTAATGACGCACTACAA 58.584 37.500 2.35 0.00 30.36 2.41
3487 7281 5.006153 AGCAATAGTAATGACGCACTACA 57.994 39.130 2.35 0.00 30.36 2.74
3488 7282 5.975344 TGTAGCAATAGTAATGACGCACTAC 59.025 40.000 0.00 0.00 30.36 2.73
3489 7283 6.139048 TGTAGCAATAGTAATGACGCACTA 57.861 37.500 0.00 0.00 0.00 2.74
3490 7284 5.006153 TGTAGCAATAGTAATGACGCACT 57.994 39.130 0.00 0.00 0.00 4.40
3491 7285 4.209288 CCTGTAGCAATAGTAATGACGCAC 59.791 45.833 0.00 0.00 0.00 5.34
3492 7286 4.142026 ACCTGTAGCAATAGTAATGACGCA 60.142 41.667 0.00 0.00 0.00 5.24
3493 7287 4.209288 CACCTGTAGCAATAGTAATGACGC 59.791 45.833 0.00 0.00 0.00 5.19
3494 7288 4.209288 GCACCTGTAGCAATAGTAATGACG 59.791 45.833 0.00 0.00 0.00 4.35
3495 7289 4.209288 CGCACCTGTAGCAATAGTAATGAC 59.791 45.833 0.00 0.00 0.00 3.06
3496 7290 4.368315 CGCACCTGTAGCAATAGTAATGA 58.632 43.478 0.00 0.00 0.00 2.57
3497 7291 3.059597 GCGCACCTGTAGCAATAGTAATG 60.060 47.826 0.30 0.00 0.00 1.90
3498 7292 3.131396 GCGCACCTGTAGCAATAGTAAT 58.869 45.455 0.30 0.00 0.00 1.89
3499 7293 2.546778 GCGCACCTGTAGCAATAGTAA 58.453 47.619 0.30 0.00 0.00 2.24
3500 7294 1.202486 GGCGCACCTGTAGCAATAGTA 60.202 52.381 10.83 0.00 0.00 1.82
3501 7295 0.462047 GGCGCACCTGTAGCAATAGT 60.462 55.000 10.83 0.00 0.00 2.12
3502 7296 0.461870 TGGCGCACCTGTAGCAATAG 60.462 55.000 10.83 0.00 36.63 1.73
3503 7297 0.742990 GTGGCGCACCTGTAGCAATA 60.743 55.000 10.83 0.00 36.63 1.90
3504 7298 2.040544 GTGGCGCACCTGTAGCAAT 61.041 57.895 10.83 0.00 36.63 3.56
3505 7299 2.668212 GTGGCGCACCTGTAGCAA 60.668 61.111 10.83 0.00 36.63 3.91
3506 7300 3.625897 AGTGGCGCACCTGTAGCA 61.626 61.111 10.83 0.00 34.49 3.49
3507 7301 3.121030 CAGTGGCGCACCTGTAGC 61.121 66.667 10.83 0.00 34.49 3.58
3508 7302 1.884075 TACCAGTGGCGCACCTGTAG 61.884 60.000 20.00 10.95 34.49 2.74
3509 7303 1.473497 TTACCAGTGGCGCACCTGTA 61.473 55.000 20.00 12.34 34.49 2.74
3510 7304 2.813726 TTACCAGTGGCGCACCTGT 61.814 57.895 20.00 13.10 34.49 4.00
3511 7305 2.031919 TTACCAGTGGCGCACCTG 59.968 61.111 10.83 14.20 34.49 4.00
3512 7306 2.032071 GTTACCAGTGGCGCACCT 59.968 61.111 10.83 0.00 34.49 4.00
3513 7307 1.170290 AAAGTTACCAGTGGCGCACC 61.170 55.000 10.83 0.00 34.49 5.01
3514 7308 0.666374 AAAAGTTACCAGTGGCGCAC 59.334 50.000 10.83 5.73 34.10 5.34
3515 7309 1.394618 AAAAAGTTACCAGTGGCGCA 58.605 45.000 10.83 0.00 0.00 6.09
3557 7351 7.625828 TTTTCCCGCCTTCAAAATTTAAAAA 57.374 28.000 0.00 0.00 0.00 1.94
3558 7352 7.809546 ATTTTCCCGCCTTCAAAATTTAAAA 57.190 28.000 0.00 0.00 0.00 1.52
3559 7353 8.151596 ACTATTTTCCCGCCTTCAAAATTTAAA 58.848 29.630 0.00 0.00 33.02 1.52
3560 7354 7.672240 ACTATTTTCCCGCCTTCAAAATTTAA 58.328 30.769 0.00 0.00 33.02 1.52
3561 7355 7.234661 ACTATTTTCCCGCCTTCAAAATTTA 57.765 32.000 0.00 0.00 33.02 1.40
3562 7356 6.109156 ACTATTTTCCCGCCTTCAAAATTT 57.891 33.333 0.00 0.00 33.02 1.82
3563 7357 5.738619 ACTATTTTCCCGCCTTCAAAATT 57.261 34.783 0.00 0.00 33.02 1.82
3564 7358 5.949952 ACTACTATTTTCCCGCCTTCAAAAT 59.050 36.000 0.00 0.00 34.75 1.82
3565 7359 5.318630 ACTACTATTTTCCCGCCTTCAAAA 58.681 37.500 0.00 0.00 0.00 2.44
3566 7360 4.913784 ACTACTATTTTCCCGCCTTCAAA 58.086 39.130 0.00 0.00 0.00 2.69
3567 7361 4.563140 ACTACTATTTTCCCGCCTTCAA 57.437 40.909 0.00 0.00 0.00 2.69
3568 7362 4.442472 GCTACTACTATTTTCCCGCCTTCA 60.442 45.833 0.00 0.00 0.00 3.02
3569 7363 4.056740 GCTACTACTATTTTCCCGCCTTC 58.943 47.826 0.00 0.00 0.00 3.46
3570 7364 3.492137 CGCTACTACTATTTTCCCGCCTT 60.492 47.826 0.00 0.00 0.00 4.35
3571 7365 2.035576 CGCTACTACTATTTTCCCGCCT 59.964 50.000 0.00 0.00 0.00 5.52
3572 7366 2.401351 CGCTACTACTATTTTCCCGCC 58.599 52.381 0.00 0.00 0.00 6.13
3573 7367 1.791204 GCGCTACTACTATTTTCCCGC 59.209 52.381 0.00 0.00 0.00 6.13
3574 7368 2.793232 GTGCGCTACTACTATTTTCCCG 59.207 50.000 9.73 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.