Multiple sequence alignment - TraesCS2D01G540100

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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 TraesCS2D01G540100 chr2D 100.000 3019 0 0 1 3019 620158889 620161907 0.000000e+00 5576.0
1 TraesCS2D01G540100 chr2D 91.813 342 24 4 1978 2319 620187773 620188110 9.800000e-130 473.0
2 TraesCS2D01G540100 chr2D 83.585 463 71 2 2525 2982 610174311 610174773 2.150000e-116 429.0
3 TraesCS2D01G540100 chr2D 86.154 325 24 8 1404 1710 620193975 620194296 6.240000e-87 331.0
4 TraesCS2D01G540100 chr2D 94.937 79 4 0 1158 1236 620193798 620193876 1.140000e-24 124.0
5 TraesCS2D01G540100 chr2D 91.250 80 7 0 1156 1235 620447875 620447954 3.180000e-20 110.0
6 TraesCS2D01G540100 chr2D 91.139 79 7 0 1156 1234 620295783 620295861 1.140000e-19 108.0
7 TraesCS2D01G540100 chr2B 91.543 1076 71 10 1355 2414 759757222 759758293 0.000000e+00 1465.0
8 TraesCS2D01G540100 chr2B 88.739 444 34 9 846 1274 759756752 759757194 2.060000e-146 529.0
9 TraesCS2D01G540100 chr2B 85.538 325 26 9 1404 1710 759765664 759765985 1.350000e-83 320.0
10 TraesCS2D01G540100 chr2B 75.544 597 72 29 1404 1944 759677141 759677719 3.030000e-55 226.0
11 TraesCS2D01G540100 chr2B 86.070 201 16 3 46 244 759753685 759753875 3.950000e-49 206.0
12 TraesCS2D01G540100 chr2B 86.471 170 9 8 244 401 759756155 759756322 1.110000e-39 174.0
13 TraesCS2D01G540100 chr2B 86.667 120 16 0 2409 2528 503942141 503942022 1.890000e-27 134.0
14 TraesCS2D01G540100 chr2B 92.405 79 6 0 1158 1236 759765492 759765570 2.460000e-21 113.0
15 TraesCS2D01G540100 chr2B 91.139 79 7 0 1156 1234 760263969 760264047 1.140000e-19 108.0
16 TraesCS2D01G540100 chr2A 85.349 703 54 22 1353 2043 751553065 751553730 0.000000e+00 682.0
17 TraesCS2D01G540100 chr2A 92.508 307 17 4 2083 2386 751553722 751554025 4.620000e-118 435.0
18 TraesCS2D01G540100 chr2A 87.829 304 16 10 127 411 751551966 751552267 1.340000e-88 337.0
19 TraesCS2D01G540100 chr2A 84.451 328 27 11 1404 1710 751609251 751609575 4.890000e-78 302.0
20 TraesCS2D01G540100 chr2A 97.015 134 4 0 1102 1235 751552894 751553027 3.030000e-55 226.0
21 TraesCS2D01G540100 chr2A 84.865 185 28 0 1404 1588 751546905 751547089 1.430000e-43 187.0
22 TraesCS2D01G540100 chr2A 84.946 186 25 2 1404 1589 751662865 751663047 5.140000e-43 185.0
23 TraesCS2D01G540100 chr2A 81.095 201 17 10 928 1110 751552672 751552869 1.130000e-29 141.0
24 TraesCS2D01G540100 chr2A 92.553 94 7 0 439 532 751552332 751552425 5.250000e-28 135.0
25 TraesCS2D01G540100 chr2A 93.671 79 5 0 1158 1236 751609057 751609135 5.290000e-23 119.0
26 TraesCS2D01G540100 chr1A 83.167 600 79 10 2410 2988 91171015 91170417 2.060000e-146 529.0
27 TraesCS2D01G540100 chr1A 100.000 29 0 0 2991 3019 256027040 256027068 2.000000e-03 54.7
28 TraesCS2D01G540100 chr1A 100.000 29 0 0 2991 3019 297885329 297885357 2.000000e-03 54.7
29 TraesCS2D01G540100 chr1A 100.000 29 0 0 2991 3019 554465909 554465937 2.000000e-03 54.7
30 TraesCS2D01G540100 chr5D 83.250 597 72 12 2414 2983 435582836 435583431 9.590000e-145 523.0
31 TraesCS2D01G540100 chr5D 85.082 429 62 2 2554 2982 532074760 532074334 1.290000e-118 436.0
32 TraesCS2D01G540100 chr5D 84.262 413 65 0 2570 2982 436203384 436203796 1.300000e-108 403.0
33 TraesCS2D01G540100 chr5D 81.996 461 75 6 2528 2983 176089841 176089384 4.720000e-103 385.0
34 TraesCS2D01G540100 chr5D 81.500 200 9 10 2410 2581 532757415 532757614 4.060000e-29 139.0
35 TraesCS2D01G540100 chr5D 78.392 199 13 12 2412 2581 443306631 443306434 5.320000e-18 102.0
36 TraesCS2D01G540100 chr1D 84.816 461 63 5 2525 2983 445206135 445206590 9.860000e-125 457.0
37 TraesCS2D01G540100 chr1D 100.000 29 0 0 2991 3019 244401293 244401265 2.000000e-03 54.7
38 TraesCS2D01G540100 chr1D 100.000 29 0 0 2991 3019 244407743 244407715 2.000000e-03 54.7
39 TraesCS2D01G540100 chr1D 100.000 29 0 0 2991 3019 244423281 244423253 2.000000e-03 54.7
40 TraesCS2D01G540100 chr1D 100.000 29 0 0 2991 3019 394176976 394176948 2.000000e-03 54.7
41 TraesCS2D01G540100 chr1D 100.000 29 0 0 2991 3019 394177492 394177464 2.000000e-03 54.7
42 TraesCS2D01G540100 chr1D 100.000 29 0 0 2991 3019 394178029 394178001 2.000000e-03 54.7
43 TraesCS2D01G540100 chr3A 84.096 459 68 4 2528 2982 505528738 505528281 3.570000e-119 438.0
44 TraesCS2D01G540100 chr1B 83.224 459 71 4 2528 2982 543078968 543078512 1.670000e-112 416.0
45 TraesCS2D01G540100 chr1B 97.500 40 1 0 142 181 577994303 577994264 5.400000e-08 69.4
46 TraesCS2D01G540100 chrUn 75.456 603 74 29 1404 1950 23148846 23148262 3.030000e-55 226.0
47 TraesCS2D01G540100 chr7B 84.348 115 17 1 2416 2529 367490312 367490426 8.850000e-21 111.0
48 TraesCS2D01G540100 chr7B 90.909 66 5 1 2410 2475 661471760 661471696 1.490000e-13 87.9
49 TraesCS2D01G540100 chr3D 93.750 64 4 0 2412 2475 434891039 434891102 2.480000e-16 97.1
50 TraesCS2D01G540100 chr3D 91.935 62 5 0 2414 2475 349646250 349646311 1.490000e-13 87.9
51 TraesCS2D01G540100 chr5B 92.063 63 5 0 2412 2474 271098767 271098705 4.150000e-14 89.8
52 TraesCS2D01G540100 chr4A 88.889 72 6 2 2406 2475 284626868 284626939 1.490000e-13 87.9
53 TraesCS2D01G540100 chr3B 88.571 70 6 2 2525 2592 809168271 809168340 1.930000e-12 84.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G540100 chr2D 620158889 620161907 3018 False 5576.0 5576 100.00000 1 3019 1 chr2D.!!$F2 3018
1 TraesCS2D01G540100 chr2B 759753685 759758293 4608 False 593.5 1465 88.20575 46 2414 4 chr2B.!!$F3 2368
2 TraesCS2D01G540100 chr2B 759677141 759677719 578 False 226.0 226 75.54400 1404 1944 1 chr2B.!!$F1 540
3 TraesCS2D01G540100 chr2A 751551966 751554025 2059 False 326.0 682 89.39150 127 2386 6 chr2A.!!$F3 2259
4 TraesCS2D01G540100 chr2A 751609057 751609575 518 False 210.5 302 89.06100 1158 1710 2 chr2A.!!$F4 552
5 TraesCS2D01G540100 chr1A 91170417 91171015 598 True 529.0 529 83.16700 2410 2988 1 chr1A.!!$R1 578
6 TraesCS2D01G540100 chr5D 435582836 435583431 595 False 523.0 523 83.25000 2414 2983 1 chr5D.!!$F1 569
7 TraesCS2D01G540100 chrUn 23148262 23148846 584 True 226.0 226 75.45600 1404 1950 1 chrUn.!!$R1 546

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
79 80 0.027194 CACGGCGCATGAGAATTCAG 59.973 55.0 10.83 0.0 36.61 3.02 F
401 2700 0.107508 CTTGAGGACACGCCATGGAT 60.108 55.0 18.40 0.0 40.02 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1200 3630 0.036010 AGACGACCTTGATGGCCTTG 60.036 55.0 3.32 0.0 40.22 3.61 R
2040 4567 0.179059 TTTGTGGCTGACTCGCTCAA 60.179 50.0 0.00 0.0 0.00 3.02 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
22 23 2.846371 GCCTCATATGCTTAGGCGG 58.154 57.895 15.86 0.00 45.82 6.13
23 24 0.674895 GCCTCATATGCTTAGGCGGG 60.675 60.000 15.86 1.90 45.82 6.13
24 25 0.674895 CCTCATATGCTTAGGCGGGC 60.675 60.000 0.00 0.00 42.25 6.13
25 26 0.674895 CTCATATGCTTAGGCGGGCC 60.675 60.000 0.18 0.18 42.25 5.80
26 27 2.034879 CATATGCTTAGGCGGGCCG 61.035 63.158 24.35 24.35 42.25 6.13
27 28 2.214216 ATATGCTTAGGCGGGCCGA 61.214 57.895 33.44 5.73 42.25 5.54
28 29 2.450479 ATATGCTTAGGCGGGCCGAC 62.450 60.000 33.44 30.87 42.25 4.79
39 40 4.148825 GGCCGACCGATCACTGCT 62.149 66.667 0.00 0.00 0.00 4.24
40 41 2.583593 GCCGACCGATCACTGCTC 60.584 66.667 0.00 0.00 0.00 4.26
41 42 2.278206 CCGACCGATCACTGCTCG 60.278 66.667 0.00 0.00 35.92 5.03
50 51 2.303549 ATCACTGCTCGGGCACTAGC 62.304 60.000 5.44 5.33 44.28 3.42
59 60 4.840005 GGCACTAGCGGACCCTGC 62.840 72.222 0.00 0.00 43.41 4.85
79 80 0.027194 CACGGCGCATGAGAATTCAG 59.973 55.000 10.83 0.00 36.61 3.02
92 94 2.040813 AGAATTCAGGCTTTCAGCAGGA 59.959 45.455 8.44 0.00 44.75 3.86
95 97 1.073722 CAGGCTTTCAGCAGGACCA 59.926 57.895 0.00 0.00 44.75 4.02
114 116 0.392998 AGTCAATGGACCATGCGGAC 60.393 55.000 19.26 19.26 45.48 4.79
149 151 2.740055 GTGACGCTCAGCCAGGTG 60.740 66.667 0.00 0.00 0.00 4.00
197 201 3.542046 GGACTCCAGCTTTGTCCTC 57.458 57.895 17.55 0.00 44.84 3.71
205 209 1.741770 GCTTTGTCCTCGCACGGAT 60.742 57.895 0.00 0.00 35.11 4.18
208 212 3.982372 TTGTCCTCGCACGGATCGC 62.982 63.158 0.00 0.00 35.11 4.58
275 2560 2.586648 AGAAAAGAAGACCGGGCATT 57.413 45.000 11.69 0.00 0.00 3.56
280 2576 1.002624 GAAGACCGGGCATTCCACA 60.003 57.895 11.69 0.00 34.36 4.17
357 2653 2.476499 GCCTCTTCTTGCGCGTTC 59.524 61.111 8.43 0.00 0.00 3.95
361 2657 1.070821 CTCTTCTTGCGCGTTCATCA 58.929 50.000 8.43 0.00 0.00 3.07
401 2700 0.107508 CTTGAGGACACGCCATGGAT 60.108 55.000 18.40 0.00 40.02 3.41
402 2701 0.327924 TTGAGGACACGCCATGGATT 59.672 50.000 18.40 0.00 40.02 3.01
404 2703 1.017387 GAGGACACGCCATGGATTTC 58.983 55.000 18.40 4.94 40.02 2.17
405 2704 0.744414 AGGACACGCCATGGATTTCG 60.744 55.000 18.40 12.21 40.02 3.46
407 2706 0.802494 GACACGCCATGGATTTCGTT 59.198 50.000 18.40 6.49 32.38 3.85
408 2707 0.802494 ACACGCCATGGATTTCGTTC 59.198 50.000 18.40 0.00 32.38 3.95
419 2738 2.552373 GGATTTCGTTCCTCAACCCTGT 60.552 50.000 0.00 0.00 32.68 4.00
422 2741 0.471211 TCGTTCCTCAACCCTGTCCT 60.471 55.000 0.00 0.00 0.00 3.85
437 2756 3.262915 CCTGTCCTTGTGGAAGAGAAGAT 59.737 47.826 0.00 0.00 45.18 2.40
452 2792 6.371595 AGAGAAGATTGTCCAGAGTTGAAT 57.628 37.500 0.00 0.00 0.00 2.57
458 2798 2.672714 TGTCCAGAGTTGAATCGTTCG 58.327 47.619 0.00 0.00 0.00 3.95
461 2801 1.359848 CAGAGTTGAATCGTTCGGGG 58.640 55.000 0.00 0.00 0.00 5.73
492 2832 3.727258 TCCCCAAGACCGGGCATG 61.727 66.667 11.69 8.24 45.90 4.06
505 2845 3.127533 GCATGCCGTGTCCAGACC 61.128 66.667 6.36 0.00 0.00 3.85
544 2914 1.335964 GGCGCAACTTTTTCTTCTCCC 60.336 52.381 10.83 0.00 0.00 4.30
553 2923 4.998033 ACTTTTTCTTCTCCCTTGATCGAC 59.002 41.667 0.00 0.00 0.00 4.20
556 2926 1.195115 CTTCTCCCTTGATCGACCCA 58.805 55.000 0.00 0.00 0.00 4.51
557 2927 1.555075 CTTCTCCCTTGATCGACCCAA 59.445 52.381 0.00 0.00 0.00 4.12
558 2928 1.879575 TCTCCCTTGATCGACCCAAT 58.120 50.000 2.99 0.00 0.00 3.16
559 2929 2.196595 TCTCCCTTGATCGACCCAATT 58.803 47.619 2.99 0.00 0.00 2.32
560 2930 2.170607 TCTCCCTTGATCGACCCAATTC 59.829 50.000 2.99 0.00 0.00 2.17
561 2931 1.134521 TCCCTTGATCGACCCAATTCG 60.135 52.381 2.99 0.00 40.53 3.34
562 2932 0.657840 CCTTGATCGACCCAATTCGC 59.342 55.000 2.99 0.00 38.95 4.70
563 2933 0.657840 CTTGATCGACCCAATTCGCC 59.342 55.000 2.99 0.00 38.95 5.54
564 2934 0.251916 TTGATCGACCCAATTCGCCT 59.748 50.000 0.00 0.00 38.95 5.52
565 2935 0.461870 TGATCGACCCAATTCGCCTG 60.462 55.000 0.00 0.00 38.95 4.85
571 2941 2.345760 CCCAATTCGCCTGCTTGCT 61.346 57.895 0.00 0.00 0.00 3.91
575 2945 0.961019 AATTCGCCTGCTTGCTTTGA 59.039 45.000 0.00 0.00 0.00 2.69
581 2951 0.251077 CCTGCTTGCTTTGACCCTCT 60.251 55.000 0.00 0.00 0.00 3.69
590 2960 2.769095 GCTTTGACCCTCTAGGAGACAT 59.231 50.000 0.00 0.00 39.89 3.06
598 2968 4.085733 CCCTCTAGGAGACATCATACAGG 58.914 52.174 0.00 0.00 38.24 4.00
614 2984 3.021451 AGGTTTGTTCCTGAAGCGG 57.979 52.632 0.00 0.00 36.35 5.52
617 2987 1.228429 TTTGTTCCTGAAGCGGGGG 60.228 57.895 0.00 0.00 0.00 5.40
641 3011 4.443266 GGAGGCGCGCTCAACTCT 62.443 66.667 32.29 18.48 0.00 3.24
642 3012 3.184683 GAGGCGCGCTCAACTCTG 61.185 66.667 32.29 0.00 0.00 3.35
645 3015 3.716006 GCGCGCTCAACTCTGCAA 61.716 61.111 26.67 0.00 0.00 4.08
646 3016 2.171940 CGCGCTCAACTCTGCAAC 59.828 61.111 5.56 0.00 0.00 4.17
647 3017 2.558313 GCGCTCAACTCTGCAACC 59.442 61.111 0.00 0.00 0.00 3.77
648 3018 2.253758 GCGCTCAACTCTGCAACCA 61.254 57.895 0.00 0.00 0.00 3.67
649 3019 1.864862 CGCTCAACTCTGCAACCAG 59.135 57.895 0.00 0.00 40.54 4.00
650 3020 1.578423 GCTCAACTCTGCAACCAGC 59.422 57.895 0.00 0.00 45.96 4.85
651 3021 0.888285 GCTCAACTCTGCAACCAGCT 60.888 55.000 0.00 0.00 45.94 4.24
652 3022 1.602311 CTCAACTCTGCAACCAGCTT 58.398 50.000 0.00 0.00 45.94 3.74
653 3023 2.771089 CTCAACTCTGCAACCAGCTTA 58.229 47.619 0.00 0.00 45.94 3.09
654 3024 2.481952 CTCAACTCTGCAACCAGCTTAC 59.518 50.000 0.00 0.00 45.94 2.34
655 3025 1.537202 CAACTCTGCAACCAGCTTACC 59.463 52.381 0.00 0.00 45.94 2.85
656 3026 1.059913 ACTCTGCAACCAGCTTACCT 58.940 50.000 0.00 0.00 45.94 3.08
657 3027 1.002544 ACTCTGCAACCAGCTTACCTC 59.997 52.381 0.00 0.00 45.94 3.85
658 3028 0.324943 TCTGCAACCAGCTTACCTCC 59.675 55.000 0.00 0.00 45.94 4.30
681 3051 3.977134 AGTGATCAGTCAATGTGCTCT 57.023 42.857 0.00 0.00 35.80 4.09
682 3052 3.859443 AGTGATCAGTCAATGTGCTCTC 58.141 45.455 0.00 0.00 35.80 3.20
693 3063 4.699626 TGCTCTCGCAATCAAGCA 57.300 50.000 0.00 0.00 44.62 3.91
817 3193 3.755628 GCCTACACACGGCTCCGA 61.756 66.667 15.95 0.00 44.17 4.55
818 3194 3.077519 GCCTACACACGGCTCCGAT 62.078 63.158 15.95 0.00 44.17 4.18
819 3195 1.065928 CCTACACACGGCTCCGATC 59.934 63.158 15.95 0.00 42.83 3.69
820 3196 1.065928 CTACACACGGCTCCGATCC 59.934 63.158 15.95 0.00 42.83 3.36
821 3197 2.351336 CTACACACGGCTCCGATCCC 62.351 65.000 15.95 0.00 42.83 3.85
822 3198 4.530857 CACACGGCTCCGATCCCC 62.531 72.222 15.95 0.00 42.83 4.81
824 3200 4.530857 CACGGCTCCGATCCCCAC 62.531 72.222 15.95 0.00 42.83 4.61
827 3203 2.122989 GGCTCCGATCCCCACCTA 60.123 66.667 0.00 0.00 0.00 3.08
828 3204 2.508751 GGCTCCGATCCCCACCTAC 61.509 68.421 0.00 0.00 0.00 3.18
829 3205 2.857744 GCTCCGATCCCCACCTACG 61.858 68.421 0.00 0.00 0.00 3.51
830 3206 1.455217 CTCCGATCCCCACCTACGT 60.455 63.158 0.00 0.00 0.00 3.57
831 3207 1.735376 CTCCGATCCCCACCTACGTG 61.735 65.000 0.00 0.00 39.91 4.49
896 3272 1.294659 GCAAGGTCTCACAGAAGCGG 61.295 60.000 0.00 0.00 0.00 5.52
902 3278 2.989253 TCACAGAAGCGGCCGAGA 60.989 61.111 33.48 11.03 0.00 4.04
904 3280 3.303135 ACAGAAGCGGCCGAGACA 61.303 61.111 33.48 0.00 0.00 3.41
911 3287 4.778415 CGGCCGAGACAGACACCG 62.778 72.222 24.07 0.00 0.00 4.94
918 3294 2.546373 CCGAGACAGACACCGGTTTTTA 60.546 50.000 2.97 0.00 37.40 1.52
924 3300 2.220133 CAGACACCGGTTTTTACTGTCG 59.780 50.000 2.97 0.66 37.03 4.35
925 3301 0.939419 ACACCGGTTTTTACTGTCGC 59.061 50.000 2.97 0.00 0.00 5.19
967 3343 4.265056 GGTCGCCACCCCACTTGT 62.265 66.667 0.00 0.00 36.54 3.16
984 3360 0.250295 TGTCTCTGAAAACAGCCCGG 60.250 55.000 0.00 0.00 0.00 5.73
996 3375 2.671963 GCCCGGCCGAGACTTTTT 60.672 61.111 30.73 0.00 0.00 1.94
1022 3405 2.550699 TAAATCCACCTGCCTGCCCG 62.551 60.000 0.00 0.00 0.00 6.13
1048 3444 0.872021 CAGATTACACCGCGCTCTCC 60.872 60.000 5.56 0.00 0.00 3.71
1057 3453 3.535962 GCGCTCTCCTCCTCCCTG 61.536 72.222 0.00 0.00 0.00 4.45
1200 3630 1.215655 ACGACGACAAGCAGAAGCAC 61.216 55.000 0.00 0.00 45.49 4.40
1275 3705 5.997129 CCTGCTTCTTCTTCTTCTTCTTCTT 59.003 40.000 0.00 0.00 0.00 2.52
1276 3706 6.147656 CCTGCTTCTTCTTCTTCTTCTTCTTC 59.852 42.308 0.00 0.00 0.00 2.87
1277 3707 6.825610 TGCTTCTTCTTCTTCTTCTTCTTCT 58.174 36.000 0.00 0.00 0.00 2.85
1278 3708 7.278875 TGCTTCTTCTTCTTCTTCTTCTTCTT 58.721 34.615 0.00 0.00 0.00 2.52
1279 3709 7.440856 TGCTTCTTCTTCTTCTTCTTCTTCTTC 59.559 37.037 0.00 0.00 0.00 2.87
1280 3710 7.657354 GCTTCTTCTTCTTCTTCTTCTTCTTCT 59.343 37.037 0.00 0.00 0.00 2.85
1281 3711 9.196552 CTTCTTCTTCTTCTTCTTCTTCTTCTC 57.803 37.037 0.00 0.00 0.00 2.87
1282 3712 7.666623 TCTTCTTCTTCTTCTTCTTCTTCTCC 58.333 38.462 0.00 0.00 0.00 3.71
1283 3713 6.019779 TCTTCTTCTTCTTCTTCTTCTCCG 57.980 41.667 0.00 0.00 0.00 4.63
1284 3714 5.536916 TCTTCTTCTTCTTCTTCTTCTCCGT 59.463 40.000 0.00 0.00 0.00 4.69
1285 3715 5.379732 TCTTCTTCTTCTTCTTCTCCGTC 57.620 43.478 0.00 0.00 0.00 4.79
1291 3721 1.136984 CTTCTTCTCCGTCCCGTCG 59.863 63.158 0.00 0.00 0.00 5.12
1294 3724 0.321564 TCTTCTCCGTCCCGTCGTAA 60.322 55.000 0.00 0.00 0.00 3.18
1295 3725 0.179179 CTTCTCCGTCCCGTCGTAAC 60.179 60.000 0.00 0.00 0.00 2.50
1300 3730 2.162754 CGTCCCGTCGTAACCATGC 61.163 63.158 0.00 0.00 0.00 4.06
1302 3732 0.461339 GTCCCGTCGTAACCATGCAT 60.461 55.000 0.00 0.00 0.00 3.96
1310 3740 2.822758 TAACCATGCATGCGCTCGC 61.823 57.895 21.69 12.13 39.64 5.03
1317 3747 2.586914 CATGCGCTCGCTGATCCA 60.587 61.111 9.73 0.00 42.51 3.41
1336 3766 2.224621 CCAGTCTGAATTCCACACCAGT 60.225 50.000 0.00 0.00 0.00 4.00
1338 3768 3.499918 CAGTCTGAATTCCACACCAGTTC 59.500 47.826 2.27 0.00 0.00 3.01
1339 3769 3.392616 AGTCTGAATTCCACACCAGTTCT 59.607 43.478 2.27 0.00 0.00 3.01
1340 3770 3.499918 GTCTGAATTCCACACCAGTTCTG 59.500 47.826 2.27 0.00 0.00 3.02
1341 3771 3.136443 TCTGAATTCCACACCAGTTCTGT 59.864 43.478 2.27 0.00 0.00 3.41
1342 3772 3.476552 TGAATTCCACACCAGTTCTGTC 58.523 45.455 2.27 0.00 0.00 3.51
1343 3773 3.118075 TGAATTCCACACCAGTTCTGTCA 60.118 43.478 2.27 0.00 0.00 3.58
1344 3774 2.325583 TTCCACACCAGTTCTGTCAC 57.674 50.000 0.00 0.00 0.00 3.67
1345 3775 0.104120 TCCACACCAGTTCTGTCACG 59.896 55.000 0.00 0.00 0.00 4.35
1346 3776 1.498865 CCACACCAGTTCTGTCACGC 61.499 60.000 0.00 0.00 0.00 5.34
1347 3777 1.591594 ACACCAGTTCTGTCACGCG 60.592 57.895 3.53 3.53 0.00 6.01
1348 3778 2.661866 ACCAGTTCTGTCACGCGC 60.662 61.111 5.73 0.00 0.00 6.86
1349 3779 2.356313 CCAGTTCTGTCACGCGCT 60.356 61.111 5.73 0.00 0.00 5.92
1350 3780 2.375766 CCAGTTCTGTCACGCGCTC 61.376 63.158 5.73 0.00 0.00 5.03
1351 3781 2.429236 AGTTCTGTCACGCGCTCG 60.429 61.111 5.73 0.00 42.43 5.03
1374 3804 4.302455 CTGATCCGTATCTGAATTTCGCT 58.698 43.478 0.00 0.00 33.98 4.93
1382 3813 3.238108 TCTGAATTTCGCTCTCTGACC 57.762 47.619 0.00 0.00 0.00 4.02
1387 3818 2.662006 TTTCGCTCTCTGACCATGAG 57.338 50.000 0.00 0.00 0.00 2.90
1493 3924 3.036084 CACGTCGTCGGCAAGCTT 61.036 61.111 7.05 0.00 41.85 3.74
1559 3990 2.240921 GGCCAAGGAGGAGAAGAAAGAT 59.759 50.000 0.00 0.00 41.22 2.40
1834 4322 2.202987 GGTGATCCGGCAGCTCAG 60.203 66.667 0.00 0.00 33.68 3.35
1835 4323 2.894387 GTGATCCGGCAGCTCAGC 60.894 66.667 0.00 0.00 0.00 4.26
1836 4324 3.079478 TGATCCGGCAGCTCAGCT 61.079 61.111 0.00 0.00 40.77 4.24
1864 4377 6.183360 GCATCTGCTTAGTTTGTAACGTGTAT 60.183 38.462 0.00 0.00 38.21 2.29
1944 4469 2.168728 GGTGTGGAGAAGGACCAGATAC 59.831 54.545 0.00 0.00 38.14 2.24
2051 4578 0.738762 GCAGCAGATTGAGCGAGTCA 60.739 55.000 0.00 0.00 37.01 3.41
2055 4582 0.108472 CAGATTGAGCGAGTCAGCCA 60.108 55.000 3.79 0.51 36.21 4.75
2067 4594 3.616076 CGAGTCAGCCACAAAGAGAAGAT 60.616 47.826 0.00 0.00 0.00 2.40
2073 4600 7.120432 AGTCAGCCACAAAGAGAAGATAATTTC 59.880 37.037 0.00 0.00 0.00 2.17
2110 4637 0.517316 GGTCGCTCGTGCATCTTTTT 59.483 50.000 10.43 0.00 39.64 1.94
2148 4675 3.391296 AGTTTGAACTCTCAAGCCCACTA 59.609 43.478 0.00 0.00 42.15 2.74
2170 4697 0.514691 GAGTTGCTTTCAGTCAGCCG 59.485 55.000 0.00 0.00 36.33 5.52
2181 4708 1.153549 GTCAGCCGGTCAGTCATCC 60.154 63.158 1.90 0.00 0.00 3.51
2252 4779 0.375454 CGTGTGTTTTCTTCGGCACA 59.625 50.000 0.00 0.00 39.21 4.57
2338 4865 1.579698 ATCGCTGCTCTAACTGCATG 58.420 50.000 0.00 0.00 39.86 4.06
2340 4867 1.434622 CGCTGCTCTAACTGCATGGG 61.435 60.000 0.00 0.00 39.86 4.00
2341 4868 1.099879 GCTGCTCTAACTGCATGGGG 61.100 60.000 0.00 0.00 39.86 4.96
2361 4891 7.552050 TGGGGTTTTCATTTTCTATGATTGT 57.448 32.000 0.00 0.00 0.00 2.71
2386 4916 9.659830 GTATCGAAACATCTTTTGTGTTTTACT 57.340 29.630 5.80 0.00 46.51 2.24
2395 4925 3.612472 TTGTGTTTTACTAACGGCTGC 57.388 42.857 0.00 0.00 0.00 5.25
2399 4929 2.477375 TGTTTTACTAACGGCTGCGAAG 59.523 45.455 0.00 0.00 0.00 3.79
2507 5047 1.580059 AGATGGGCTCCTTAAACGGA 58.420 50.000 0.00 0.00 0.00 4.69
2508 5048 2.127708 AGATGGGCTCCTTAAACGGAT 58.872 47.619 0.00 0.00 31.43 4.18
2521 5061 2.162338 AACGGATCTCAAACGCCCGA 62.162 55.000 0.00 0.00 42.49 5.14
2526 5082 0.535335 ATCTCAAACGCCCGAGCTAA 59.465 50.000 0.00 0.00 36.60 3.09
2554 5110 0.258774 AATATGGGGCGGATATGGGC 59.741 55.000 0.00 0.00 0.00 5.36
2594 5152 0.406750 TAGGACTGACGAAGGGGTCA 59.593 55.000 0.00 0.00 44.25 4.02
2598 5156 1.046472 ACTGACGAAGGGGTCACACA 61.046 55.000 0.00 0.00 41.76 3.72
2605 5163 1.073923 GAAGGGGTCACACATGGACTT 59.926 52.381 0.00 0.00 35.61 3.01
2610 5168 1.074775 TCACACATGGACTTGCCCC 59.925 57.895 0.00 0.00 34.97 5.80
2655 5213 4.764336 CTTCGTCGCCGCGGTGTA 62.764 66.667 35.52 20.86 0.00 2.90
2737 5295 1.551019 GGAGTCCCGCAACCCTAGTT 61.551 60.000 0.00 0.00 36.33 2.24
2747 5305 2.681097 GCAACCCTAGTTCATCCACCTC 60.681 54.545 0.00 0.00 32.45 3.85
2773 5331 1.583495 ATCTGCGTCGTCAGTCCGAA 61.583 55.000 13.75 0.00 38.80 4.30
2781 5339 0.458543 CGTCAGTCCGAACCCATCTG 60.459 60.000 0.00 0.00 0.00 2.90
2871 5431 4.452114 TCACGTACTACACAATACTCACGT 59.548 41.667 0.00 0.00 41.58 4.49
2881 5441 4.391869 ACTCACGTCGGAGTGCTA 57.608 55.556 13.43 0.00 46.02 3.49
2892 5452 1.015109 GGAGTGCTACGTCGAGATCA 58.985 55.000 0.00 0.00 0.00 2.92
2893 5453 1.604755 GGAGTGCTACGTCGAGATCAT 59.395 52.381 0.00 0.00 0.00 2.45
2988 5548 3.082701 AGCAGGAGGAGCTGGAGC 61.083 66.667 0.00 0.00 41.61 4.70
2989 5549 4.173924 GCAGGAGGAGCTGGAGCC 62.174 72.222 0.00 0.00 43.38 4.70
2990 5550 2.686470 CAGGAGGAGCTGGAGCCA 60.686 66.667 0.00 0.00 43.38 4.75
2991 5551 2.686835 AGGAGGAGCTGGAGCCAC 60.687 66.667 0.00 0.00 43.38 5.01
2992 5552 4.154347 GGAGGAGCTGGAGCCACG 62.154 72.222 0.00 0.00 43.38 4.94
2993 5553 3.071206 GAGGAGCTGGAGCCACGA 61.071 66.667 0.00 0.00 43.38 4.35
2994 5554 3.073735 AGGAGCTGGAGCCACGAG 61.074 66.667 0.00 0.00 43.38 4.18
2995 5555 3.386237 GGAGCTGGAGCCACGAGT 61.386 66.667 0.00 0.00 43.38 4.18
2996 5556 2.052690 GGAGCTGGAGCCACGAGTA 61.053 63.158 0.00 0.00 43.38 2.59
2997 5557 1.395826 GGAGCTGGAGCCACGAGTAT 61.396 60.000 0.00 0.00 43.38 2.12
2998 5558 0.461961 GAGCTGGAGCCACGAGTATT 59.538 55.000 0.00 0.00 43.38 1.89
2999 5559 0.905357 AGCTGGAGCCACGAGTATTT 59.095 50.000 0.00 0.00 43.38 1.40
3000 5560 1.134670 AGCTGGAGCCACGAGTATTTC 60.135 52.381 0.00 0.00 43.38 2.17
3001 5561 1.405526 GCTGGAGCCACGAGTATTTCA 60.406 52.381 0.00 0.00 34.31 2.69
3002 5562 2.271800 CTGGAGCCACGAGTATTTCAC 58.728 52.381 0.00 0.00 0.00 3.18
3003 5563 1.278238 GGAGCCACGAGTATTTCACG 58.722 55.000 0.00 0.00 36.30 4.35
3004 5564 1.278238 GAGCCACGAGTATTTCACGG 58.722 55.000 0.00 0.00 34.65 4.94
3005 5565 0.892755 AGCCACGAGTATTTCACGGA 59.107 50.000 0.00 0.00 34.65 4.69
3006 5566 1.274167 AGCCACGAGTATTTCACGGAA 59.726 47.619 0.00 0.00 34.65 4.30
3007 5567 2.070783 GCCACGAGTATTTCACGGAAA 58.929 47.619 0.00 2.25 35.94 3.13
3008 5568 2.093783 GCCACGAGTATTTCACGGAAAG 59.906 50.000 0.00 0.00 34.92 2.62
3009 5569 2.093783 CCACGAGTATTTCACGGAAAGC 59.906 50.000 0.00 2.20 34.92 3.51
3010 5570 2.093783 CACGAGTATTTCACGGAAAGCC 59.906 50.000 0.00 0.00 34.92 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.704572 GCCTAAGCATATGAGGCGAAT 58.295 47.619 15.86 0.00 45.94 3.34
1 2 2.169832 GCCTAAGCATATGAGGCGAA 57.830 50.000 15.86 0.00 45.94 4.70
2 3 3.914984 GCCTAAGCATATGAGGCGA 57.085 52.632 15.86 0.00 45.94 5.54
5 6 0.674895 GCCCGCCTAAGCATATGAGG 60.675 60.000 6.97 5.72 39.83 3.86
6 7 0.674895 GGCCCGCCTAAGCATATGAG 60.675 60.000 6.97 0.00 39.83 2.90
7 8 1.374947 GGCCCGCCTAAGCATATGA 59.625 57.895 6.97 0.00 39.83 2.15
8 9 2.034879 CGGCCCGCCTAAGCATATG 61.035 63.158 3.84 0.00 39.83 1.78
9 10 2.214216 TCGGCCCGCCTAAGCATAT 61.214 57.895 0.00 0.00 39.83 1.78
10 11 2.840572 TCGGCCCGCCTAAGCATA 60.841 61.111 0.00 0.00 39.83 3.14
11 12 4.547367 GTCGGCCCGCCTAAGCAT 62.547 66.667 0.00 0.00 39.83 3.79
22 23 4.148825 AGCAGTGATCGGTCGGCC 62.149 66.667 0.00 0.00 0.00 6.13
23 24 2.583593 GAGCAGTGATCGGTCGGC 60.584 66.667 0.00 0.00 0.00 5.54
37 38 4.874977 GTCCGCTAGTGCCCGAGC 62.875 72.222 0.00 0.00 36.12 5.03
38 39 4.208686 GGTCCGCTAGTGCCCGAG 62.209 72.222 0.00 0.00 35.36 4.63
41 42 4.162690 CAGGGTCCGCTAGTGCCC 62.163 72.222 10.22 10.22 41.36 5.36
42 43 4.840005 GCAGGGTCCGCTAGTGCC 62.840 72.222 0.00 0.00 35.36 5.01
43 44 4.840005 GGCAGGGTCCGCTAGTGC 62.840 72.222 0.00 0.00 0.00 4.40
44 45 3.390521 TGGCAGGGTCCGCTAGTG 61.391 66.667 0.00 0.00 0.00 2.74
59 60 1.353103 GAATTCTCATGCGCCGTGG 59.647 57.895 4.18 0.00 0.00 4.94
92 94 0.677731 CGCATGGTCCATTGACTGGT 60.678 55.000 0.00 0.00 46.08 4.00
95 97 0.392998 GTCCGCATGGTCCATTGACT 60.393 55.000 0.00 0.00 41.47 3.41
114 116 4.549680 CGTCACGAGTACTATACGTCAAGG 60.550 50.000 5.22 0.65 38.18 3.61
149 151 1.270041 GGCTGACTGATAGCTACTGGC 60.270 57.143 0.00 0.00 40.92 4.85
275 2560 3.815809 AGGAACGATTCAACTTTGTGGA 58.184 40.909 0.00 0.00 0.00 4.02
280 2576 3.432252 CGTGCTAGGAACGATTCAACTTT 59.568 43.478 0.00 0.00 43.68 2.66
336 2632 3.793144 GCGCAAGAAGAGGCCGTG 61.793 66.667 0.30 0.00 43.02 4.94
357 2653 1.683943 ATCAAGGGGACGCAATGATG 58.316 50.000 8.01 0.00 30.00 3.07
361 2657 1.463674 GTCAATCAAGGGGACGCAAT 58.536 50.000 0.00 0.00 0.00 3.56
366 2662 1.354368 TCAAGGGTCAATCAAGGGGAC 59.646 52.381 0.00 0.00 0.00 4.46
401 2700 1.202722 GGACAGGGTTGAGGAACGAAA 60.203 52.381 0.00 0.00 32.28 3.46
402 2701 0.395312 GGACAGGGTTGAGGAACGAA 59.605 55.000 0.00 0.00 32.28 3.85
404 2703 0.396811 AAGGACAGGGTTGAGGAACG 59.603 55.000 0.00 0.00 32.28 3.95
405 2704 1.143073 ACAAGGACAGGGTTGAGGAAC 59.857 52.381 0.00 0.00 0.00 3.62
407 2706 0.764890 CACAAGGACAGGGTTGAGGA 59.235 55.000 0.00 0.00 0.00 3.71
408 2707 0.250901 CCACAAGGACAGGGTTGAGG 60.251 60.000 0.00 0.00 36.89 3.86
419 2738 4.263068 GGACAATCTTCTCTTCCACAAGGA 60.263 45.833 0.00 0.00 43.93 3.36
422 2741 4.347876 TCTGGACAATCTTCTCTTCCACAA 59.652 41.667 0.00 0.00 32.79 3.33
437 2756 3.057019 CGAACGATTCAACTCTGGACAA 58.943 45.455 0.00 0.00 0.00 3.18
452 2792 3.315140 TGACCATGCCCCGAACGA 61.315 61.111 0.00 0.00 0.00 3.85
458 2798 4.344865 ACACGGTGACCATGCCCC 62.345 66.667 16.29 0.00 0.00 5.80
461 2801 2.746277 GGGACACGGTGACCATGC 60.746 66.667 26.40 9.66 33.85 4.06
492 2832 4.394712 CTGGGGTCTGGACACGGC 62.395 72.222 3.10 0.00 35.00 5.68
505 2845 1.008424 CGATCGATCCGTGTCTGGG 60.008 63.158 19.51 0.00 0.00 4.45
544 2914 0.657840 GGCGAATTGGGTCGATCAAG 59.342 55.000 0.00 0.00 43.86 3.02
553 2923 1.880819 AAGCAAGCAGGCGAATTGGG 61.881 55.000 0.00 0.00 39.27 4.12
556 2926 0.961019 TCAAAGCAAGCAGGCGAATT 59.039 45.000 0.00 0.00 39.27 2.17
557 2927 0.242017 GTCAAAGCAAGCAGGCGAAT 59.758 50.000 0.00 0.00 39.27 3.34
558 2928 1.654220 GTCAAAGCAAGCAGGCGAA 59.346 52.632 0.00 0.00 39.27 4.70
559 2929 2.260869 GGTCAAAGCAAGCAGGCGA 61.261 57.895 0.00 0.00 39.27 5.54
560 2930 2.256461 GGTCAAAGCAAGCAGGCG 59.744 61.111 0.00 0.00 39.27 5.52
561 2931 1.871126 GAGGGTCAAAGCAAGCAGGC 61.871 60.000 0.00 0.00 0.00 4.85
562 2932 0.251077 AGAGGGTCAAAGCAAGCAGG 60.251 55.000 0.00 0.00 0.00 4.85
563 2933 2.354259 CTAGAGGGTCAAAGCAAGCAG 58.646 52.381 0.00 0.00 0.00 4.24
564 2934 1.003580 CCTAGAGGGTCAAAGCAAGCA 59.996 52.381 0.00 0.00 0.00 3.91
565 2935 1.279271 TCCTAGAGGGTCAAAGCAAGC 59.721 52.381 0.00 0.00 36.25 4.01
571 2941 4.061131 TGATGTCTCCTAGAGGGTCAAA 57.939 45.455 0.00 0.00 36.25 2.69
575 2945 4.448493 CCTGTATGATGTCTCCTAGAGGGT 60.448 50.000 0.00 0.00 32.59 4.34
581 2951 6.351881 GGAACAAACCTGTATGATGTCTCCTA 60.352 42.308 0.00 0.00 33.45 2.94
598 2968 1.524008 CCCCCGCTTCAGGAACAAAC 61.524 60.000 0.00 0.00 0.00 2.93
624 2994 4.443266 AGAGTTGAGCGCGCCTCC 62.443 66.667 30.33 18.04 39.98 4.30
625 2995 3.184683 CAGAGTTGAGCGCGCCTC 61.185 66.667 30.33 25.64 41.15 4.70
628 2998 3.716006 TTGCAGAGTTGAGCGCGC 61.716 61.111 26.66 26.66 0.00 6.86
629 2999 2.171940 GTTGCAGAGTTGAGCGCG 59.828 61.111 0.00 0.00 0.00 6.86
630 3000 2.180131 CTGGTTGCAGAGTTGAGCGC 62.180 60.000 0.00 0.00 0.00 5.92
631 3001 1.864862 CTGGTTGCAGAGTTGAGCG 59.135 57.895 0.00 0.00 0.00 5.03
632 3002 0.888285 AGCTGGTTGCAGAGTTGAGC 60.888 55.000 0.00 0.00 45.94 4.26
633 3003 1.602311 AAGCTGGTTGCAGAGTTGAG 58.398 50.000 0.00 0.00 45.94 3.02
634 3004 2.494059 GTAAGCTGGTTGCAGAGTTGA 58.506 47.619 1.72 0.00 45.94 3.18
635 3005 1.537202 GGTAAGCTGGTTGCAGAGTTG 59.463 52.381 9.75 0.00 45.94 3.16
636 3006 1.421646 AGGTAAGCTGGTTGCAGAGTT 59.578 47.619 9.75 0.00 45.94 3.01
637 3007 1.002544 GAGGTAAGCTGGTTGCAGAGT 59.997 52.381 9.75 0.00 45.94 3.24
638 3008 1.677217 GGAGGTAAGCTGGTTGCAGAG 60.677 57.143 9.75 0.00 45.94 3.35
639 3009 0.324943 GGAGGTAAGCTGGTTGCAGA 59.675 55.000 9.75 0.00 45.94 4.26
640 3010 0.678048 GGGAGGTAAGCTGGTTGCAG 60.678 60.000 9.75 0.00 45.94 4.41
641 3011 1.378762 GGGAGGTAAGCTGGTTGCA 59.621 57.895 9.75 0.00 45.94 4.08
642 3012 0.251165 TTGGGAGGTAAGCTGGTTGC 60.251 55.000 1.72 0.14 43.29 4.17
643 3013 1.073923 ACTTGGGAGGTAAGCTGGTTG 59.926 52.381 1.72 0.00 0.00 3.77
644 3014 1.073923 CACTTGGGAGGTAAGCTGGTT 59.926 52.381 0.00 0.00 0.00 3.67
645 3015 0.693049 CACTTGGGAGGTAAGCTGGT 59.307 55.000 0.00 0.00 0.00 4.00
646 3016 0.984230 TCACTTGGGAGGTAAGCTGG 59.016 55.000 0.00 0.00 0.00 4.85
647 3017 2.237143 TGATCACTTGGGAGGTAAGCTG 59.763 50.000 0.00 0.00 0.00 4.24
648 3018 2.503356 CTGATCACTTGGGAGGTAAGCT 59.497 50.000 0.00 0.00 0.00 3.74
649 3019 2.237392 ACTGATCACTTGGGAGGTAAGC 59.763 50.000 0.00 0.00 0.00 3.09
650 3020 3.515502 TGACTGATCACTTGGGAGGTAAG 59.484 47.826 0.00 0.00 0.00 2.34
651 3021 3.516586 TGACTGATCACTTGGGAGGTAA 58.483 45.455 0.00 0.00 0.00 2.85
652 3022 3.184382 TGACTGATCACTTGGGAGGTA 57.816 47.619 0.00 0.00 0.00 3.08
653 3023 2.030027 TGACTGATCACTTGGGAGGT 57.970 50.000 0.00 0.00 0.00 3.85
654 3024 3.276857 CATTGACTGATCACTTGGGAGG 58.723 50.000 0.00 0.00 33.38 4.30
655 3025 3.688185 CACATTGACTGATCACTTGGGAG 59.312 47.826 0.00 0.00 33.38 4.30
656 3026 3.678289 CACATTGACTGATCACTTGGGA 58.322 45.455 0.00 0.00 33.38 4.37
657 3027 2.163010 GCACATTGACTGATCACTTGGG 59.837 50.000 0.00 0.00 33.38 4.12
658 3028 3.079578 AGCACATTGACTGATCACTTGG 58.920 45.455 0.00 0.00 33.38 3.61
681 3051 1.573932 CGTGGTTGCTTGATTGCGA 59.426 52.632 0.00 0.00 35.36 5.10
682 3052 1.442520 CCGTGGTTGCTTGATTGCG 60.443 57.895 0.00 0.00 35.36 4.85
754 3130 1.272715 CGTATCATCGTGTTGGCGC 59.727 57.895 0.00 0.00 0.00 6.53
756 3132 0.928229 GGACGTATCATCGTGTTGGC 59.072 55.000 0.00 0.00 44.21 4.52
802 3178 1.065928 GGATCGGAGCCGTGTGTAG 59.934 63.158 8.96 0.00 40.74 2.74
880 3256 2.659610 GCCGCTTCTGTGAGACCT 59.340 61.111 0.00 0.00 0.00 3.85
882 3258 2.811317 CGGCCGCTTCTGTGAGAC 60.811 66.667 14.67 0.00 0.00 3.36
883 3259 2.989253 TCGGCCGCTTCTGTGAGA 60.989 61.111 23.51 0.00 0.00 3.27
884 3260 2.507992 CTCGGCCGCTTCTGTGAG 60.508 66.667 23.51 5.96 0.00 3.51
885 3261 2.989253 TCTCGGCCGCTTCTGTGA 60.989 61.111 23.51 6.58 0.00 3.58
896 3272 2.710724 AAACCGGTGTCTGTCTCGGC 62.711 60.000 8.52 0.00 45.65 5.54
902 3278 3.200483 GACAGTAAAAACCGGTGTCTGT 58.800 45.455 15.58 15.58 35.64 3.41
904 3280 2.476821 CGACAGTAAAAACCGGTGTCT 58.523 47.619 8.52 0.00 36.24 3.41
911 3287 1.154543 CCGCGCGACAGTAAAAACC 60.155 57.895 34.63 0.00 0.00 3.27
993 3372 4.161377 GGCAGGTGGATTTATAGGCAAAAA 59.839 41.667 0.00 0.00 0.00 1.94
996 3375 2.513738 AGGCAGGTGGATTTATAGGCAA 59.486 45.455 0.00 0.00 0.00 4.52
1022 3405 0.179081 GCGGTGTAATCTGGGACTCC 60.179 60.000 0.00 0.00 0.00 3.85
1048 3444 4.247380 GCGATGGCCAGGGAGGAG 62.247 72.222 13.05 0.00 41.22 3.69
1200 3630 0.036010 AGACGACCTTGATGGCCTTG 60.036 55.000 3.32 0.00 40.22 3.61
1283 3713 0.461339 ATGCATGGTTACGACGGGAC 60.461 55.000 0.00 0.00 0.00 4.46
1284 3714 0.461163 CATGCATGGTTACGACGGGA 60.461 55.000 19.40 0.00 0.00 5.14
1285 3715 2.013807 CATGCATGGTTACGACGGG 58.986 57.895 19.40 0.00 0.00 5.28
1291 3721 1.010797 CGAGCGCATGCATGGTTAC 60.011 57.895 27.34 10.17 46.23 2.50
1295 3725 4.607606 CAGCGAGCGCATGCATGG 62.608 66.667 27.34 17.93 46.23 3.66
1300 3730 2.586914 TGGATCAGCGAGCGCATG 60.587 61.111 17.68 11.88 44.88 4.06
1302 3732 3.706563 GACTGGATCAGCGAGCGCA 62.707 63.158 17.68 0.00 44.88 6.09
1310 3740 3.937706 GTGTGGAATTCAGACTGGATCAG 59.062 47.826 7.93 0.00 36.78 2.90
1317 3747 3.392616 AGAACTGGTGTGGAATTCAGACT 59.607 43.478 7.93 0.00 39.36 3.24
1345 3775 2.049985 ATACGGATCAGCGAGCGC 60.050 61.111 6.78 6.78 42.33 5.92
1346 3776 0.727457 CAGATACGGATCAGCGAGCG 60.727 60.000 10.99 0.00 34.17 5.03
1347 3777 0.593618 TCAGATACGGATCAGCGAGC 59.406 55.000 10.99 0.00 34.17 5.03
1348 3778 3.567576 ATTCAGATACGGATCAGCGAG 57.432 47.619 10.99 0.00 34.17 5.03
1349 3779 4.299155 GAAATTCAGATACGGATCAGCGA 58.701 43.478 10.99 0.04 34.17 4.93
1350 3780 3.120286 CGAAATTCAGATACGGATCAGCG 59.880 47.826 10.99 0.00 34.17 5.18
1351 3781 3.120854 GCGAAATTCAGATACGGATCAGC 60.121 47.826 10.99 0.00 34.17 4.26
1359 3789 4.742659 GGTCAGAGAGCGAAATTCAGATAC 59.257 45.833 0.00 0.00 0.00 2.24
1374 3804 5.080337 AGTAACAGTTCTCATGGTCAGAGA 58.920 41.667 0.00 0.00 40.20 3.10
1387 3818 9.828852 CGATACCTGAGAATATAGTAACAGTTC 57.171 37.037 0.00 0.00 0.00 3.01
1520 3951 3.917760 GGGCCGACGGAGAGGATG 61.918 72.222 20.50 0.00 0.00 3.51
1559 3990 1.006571 GTCGTCCTTCTTGGCGTCA 60.007 57.895 0.00 0.00 36.93 4.35
1757 4237 4.408821 TCCATCACCGGTGCAGGC 62.409 66.667 30.25 0.00 33.69 4.85
1832 4320 1.735386 ACTAAGCAGATGCACAGCTG 58.265 50.000 13.48 13.48 46.77 4.24
1833 4321 2.486472 AACTAAGCAGATGCACAGCT 57.514 45.000 7.68 3.74 45.16 4.24
1834 4322 2.227388 ACAAACTAAGCAGATGCACAGC 59.773 45.455 7.68 0.00 45.16 4.40
1835 4323 5.385617 GTTACAAACTAAGCAGATGCACAG 58.614 41.667 7.68 5.92 45.16 3.66
1836 4324 4.084066 CGTTACAAACTAAGCAGATGCACA 60.084 41.667 7.68 0.00 45.16 4.57
1919 4443 1.353091 GGTCCTTCTCCACACCTCTT 58.647 55.000 0.00 0.00 0.00 2.85
1920 4444 0.191064 TGGTCCTTCTCCACACCTCT 59.809 55.000 0.00 0.00 0.00 3.69
1921 4445 0.610687 CTGGTCCTTCTCCACACCTC 59.389 60.000 0.00 0.00 0.00 3.85
2025 4552 1.078918 TCAATCTGCTGCACCTCCG 60.079 57.895 0.00 0.00 0.00 4.63
2040 4567 0.179059 TTTGTGGCTGACTCGCTCAA 60.179 50.000 0.00 0.00 0.00 3.02
2051 4578 6.376581 CCTGAAATTATCTTCTCTTTGTGGCT 59.623 38.462 0.00 0.00 0.00 4.75
2055 4582 5.355350 CCGCCTGAAATTATCTTCTCTTTGT 59.645 40.000 0.00 0.00 0.00 2.83
2067 4594 2.963101 TCTAGCTAGCCGCCTGAAATTA 59.037 45.455 16.35 0.00 40.39 1.40
2073 4600 0.320247 CCAATCTAGCTAGCCGCCTG 60.320 60.000 16.35 7.88 40.39 4.85
2084 4611 0.179137 TGCACGAGCGACCAATCTAG 60.179 55.000 0.00 0.00 46.23 2.43
2138 4665 1.277557 AGCAACTCTCTAGTGGGCTTG 59.722 52.381 0.00 0.00 41.75 4.01
2148 4675 2.549778 GGCTGACTGAAAGCAACTCTCT 60.550 50.000 8.21 0.00 42.69 3.10
2181 4708 0.512952 CCTTTCGCTTTGTCAGTCGG 59.487 55.000 0.00 0.00 0.00 4.79
2338 4865 9.750125 GATACAATCATAGAAAATGAAAACCCC 57.250 33.333 0.00 0.00 0.00 4.95
2382 4912 2.745728 GCTTCGCAGCCGTTAGTAA 58.254 52.632 0.00 0.00 40.61 2.24
2395 4925 2.009051 TCTAACATGTGCATGGCTTCG 58.991 47.619 15.52 0.41 42.91 3.79
2399 4929 1.097232 TGCTCTAACATGTGCATGGC 58.903 50.000 15.52 9.48 42.91 4.40
2486 5026 3.109151 TCCGTTTAAGGAGCCCATCTAA 58.891 45.455 0.00 0.00 34.92 2.10
2487 5027 2.754465 TCCGTTTAAGGAGCCCATCTA 58.246 47.619 0.00 0.00 34.92 1.98
2507 5047 0.535335 TTAGCTCGGGCGTTTGAGAT 59.465 50.000 0.00 0.93 44.37 2.75
2508 5048 0.389426 GTTAGCTCGGGCGTTTGAGA 60.389 55.000 0.00 0.00 44.37 3.27
2594 5152 2.034066 CGGGGCAAGTCCATGTGT 59.966 61.111 0.00 0.00 36.21 3.72
2598 5156 1.304134 GGTTTCGGGGCAAGTCCAT 60.304 57.895 0.00 0.00 36.21 3.41
2684 5242 2.897350 CCGATTTGCTCTCCGGCC 60.897 66.667 0.00 0.00 35.29 6.13
2688 5246 2.262423 AATAGGCCGATTTGCTCTCC 57.738 50.000 5.09 0.00 0.00 3.71
2754 5312 1.583495 TTCGGACTGACGACGCAGAT 61.583 55.000 20.87 9.12 43.37 2.90
2757 5315 2.050714 GTTCGGACTGACGACGCA 60.051 61.111 0.00 0.00 43.37 5.24
2761 5319 0.611062 AGATGGGTTCGGACTGACGA 60.611 55.000 0.00 0.00 41.76 4.20
2764 5322 1.596934 GCAGATGGGTTCGGACTGA 59.403 57.895 0.00 0.00 0.00 3.41
2773 5331 2.367512 GGGAGGAGGCAGATGGGT 60.368 66.667 0.00 0.00 0.00 4.51
2871 5431 0.461516 ATCTCGACGTAGCACTCCGA 60.462 55.000 0.00 0.00 0.00 4.55
2881 5441 0.383590 CTCCTGCATGATCTCGACGT 59.616 55.000 0.00 0.00 0.00 4.34
2884 5444 2.557490 CAGATCTCCTGCATGATCTCGA 59.443 50.000 18.22 3.39 45.13 4.04
2892 5452 1.756408 CTCGCCCAGATCTCCTGCAT 61.756 60.000 0.00 0.00 41.57 3.96
2893 5453 2.364186 TCGCCCAGATCTCCTGCA 60.364 61.111 0.00 0.00 41.57 4.41
2973 5533 2.686470 TGGCTCCAGCTCCTCCTG 60.686 66.667 0.00 0.00 41.70 3.86
2983 5543 1.403647 CGTGAAATACTCGTGGCTCCA 60.404 52.381 0.00 0.00 0.00 3.86
2988 5548 2.093783 GCTTTCCGTGAAATACTCGTGG 59.906 50.000 0.48 0.00 34.31 4.94
2989 5549 2.093783 GGCTTTCCGTGAAATACTCGTG 59.906 50.000 0.48 0.00 34.31 4.35
2990 5550 2.344025 GGCTTTCCGTGAAATACTCGT 58.656 47.619 0.48 0.00 34.31 4.18


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

AutoCloner maintained by Alex Coulton.