Multiple sequence alignment - TraesCS1D01G430700

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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 TraesCS1D01G430700 chr1D 100.000 4231 0 0 1 4231 481454961 481450731 0.000000e+00 7814.0
1 TraesCS1D01G430700 chr1D 91.646 2011 129 16 1254 3236 481550718 481552717 0.000000e+00 2747.0
2 TraesCS1D01G430700 chr1D 83.551 1380 189 21 1224 2596 481501658 481500310 0.000000e+00 1256.0
3 TraesCS1D01G430700 chr1D 84.106 453 49 13 2599 3047 481500228 481499795 2.350000e-112 416.0
4 TraesCS1D01G430700 chr1D 82.292 384 57 7 2599 2982 481488611 481488239 5.280000e-84 322.0
5 TraesCS1D01G430700 chr1D 86.498 237 32 0 2358 2594 481488935 481488699 1.170000e-65 261.0
6 TraesCS1D01G430700 chr1D 76.369 347 34 25 305 628 481461899 481462220 4.410000e-30 143.0
7 TraesCS1D01G430700 chr1D 84.906 53 6 2 1585 1636 326909113 326909062 8.000000e-03 52.8
8 TraesCS1D01G430700 chr1A 91.534 2008 133 12 1254 3236 577985497 577987492 0.000000e+00 2732.0
9 TraesCS1D01G430700 chr1A 83.772 1368 184 21 1236 2596 578208280 578206944 0.000000e+00 1262.0
10 TraesCS1D01G430700 chr1A 85.809 451 45 11 2599 3047 578206862 578206429 1.070000e-125 460.0
11 TraesCS1D01G430700 chr1A 100.000 28 0 0 1585 1612 410156049 410156076 8.000000e-03 52.8
12 TraesCS1D01G430700 chr1B 87.146 2365 208 52 762 3076 670158601 670160919 0.000000e+00 2595.0
13 TraesCS1D01G430700 chr1B 89.072 2068 165 35 1063 3096 669922584 669924624 0.000000e+00 2510.0
14 TraesCS1D01G430700 chr1B 83.303 1114 163 14 1224 2333 670142808 670143902 0.000000e+00 1005.0
15 TraesCS1D01G430700 chr1B 90.094 424 36 3 304 727 670158184 670158601 2.880000e-151 545.0
16 TraesCS1D01G430700 chr1B 90.536 317 12 6 464 774 670139322 670139018 1.830000e-108 403.0
17 TraesCS1D01G430700 chr1B 92.576 229 17 0 2368 2596 670149475 670149703 3.150000e-86 329.0
18 TraesCS1D01G430700 chr1B 87.879 264 28 2 2599 2862 670149778 670150037 1.480000e-79 307.0
19 TraesCS1D01G430700 chr1B 81.413 269 43 5 40 306 570244564 570244827 3.310000e-51 213.0
20 TraesCS1D01G430700 chr1B 81.111 270 42 6 40 306 41264508 41264771 1.540000e-49 207.0
21 TraesCS1D01G430700 chr1B 80.370 270 43 9 40 306 579292844 579293106 3.340000e-46 196.0
22 TraesCS1D01G430700 chr1B 77.358 265 38 13 305 549 669920305 669920567 2.050000e-28 137.0
23 TraesCS1D01G430700 chr1B 91.753 97 6 2 802 897 670139012 670138917 2.650000e-27 134.0
24 TraesCS1D01G430700 chr5D 93.182 880 36 19 3366 4231 390548427 390547558 0.000000e+00 1271.0
25 TraesCS1D01G430700 chr5D 85.239 901 85 31 3370 4231 542465369 542466260 0.000000e+00 883.0
26 TraesCS1D01G430700 chr7B 92.512 868 41 14 3370 4231 34164344 34165193 0.000000e+00 1221.0
27 TraesCS1D01G430700 chr7B 83.260 227 35 1 2599 2825 520417958 520418181 5.550000e-49 206.0
28 TraesCS1D01G430700 chr6B 92.423 871 43 14 3368 4231 413938200 413939054 0.000000e+00 1221.0
29 TraesCS1D01G430700 chr6B 89.163 203 15 6 111 308 512177980 512177780 3.270000e-61 246.0
30 TraesCS1D01G430700 chr5B 91.294 873 54 16 3367 4231 36406217 36407075 0.000000e+00 1171.0
31 TraesCS1D01G430700 chr5B 91.349 867 60 9 3369 4231 347392871 347393726 0.000000e+00 1171.0
32 TraesCS1D01G430700 chr5B 85.000 380 37 16 3859 4231 11304636 11304270 6.680000e-98 368.0
33 TraesCS1D01G430700 chr5B 86.792 265 29 4 42 305 398078636 398078377 1.490000e-74 291.0
34 TraesCS1D01G430700 chr2B 91.076 874 56 15 3367 4231 166813101 166812241 0.000000e+00 1162.0
35 TraesCS1D01G430700 chr2B 92.157 663 41 10 3369 4023 166834816 166835475 0.000000e+00 926.0
36 TraesCS1D01G430700 chr2B 81.935 620 78 22 3439 4049 666727519 666728113 1.060000e-135 494.0
37 TraesCS1D01G430700 chr2B 81.215 362 49 12 2211 2564 245130060 245130410 1.500000e-69 274.0
38 TraesCS1D01G430700 chr2B 82.251 231 35 6 2362 2589 245299393 245299620 1.200000e-45 195.0
39 TraesCS1D01G430700 chr3A 83.854 384 38 15 3859 4231 549911701 549912071 1.130000e-90 344.0
40 TraesCS1D01G430700 chr3A 83.764 271 35 6 42 307 12975942 12975676 9.080000e-62 248.0
41 TraesCS1D01G430700 chr6D 90.411 219 12 7 79 294 315365383 315365595 3.220000e-71 279.0
42 TraesCS1D01G430700 chr6D 85.091 275 34 5 42 315 299051750 299052018 1.500000e-69 274.0
43 TraesCS1D01G430700 chr2A 81.648 267 41 6 42 305 16024522 16024783 9.210000e-52 215.0
44 TraesCS1D01G430700 chr4A 91.139 79 5 1 4153 4231 655514933 655515009 5.790000e-19 106.0


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 TraesCS1D01G430700 chr1D 481450731 481454961 4230 True 7814.0 7814 100.0000 1 4231 1 chr1D.!!$R2 4230
1 TraesCS1D01G430700 chr1D 481550718 481552717 1999 False 2747.0 2747 91.6460 1254 3236 1 chr1D.!!$F2 1982
2 TraesCS1D01G430700 chr1D 481499795 481501658 1863 True 836.0 1256 83.8285 1224 3047 2 chr1D.!!$R4 1823
3 TraesCS1D01G430700 chr1D 481488239 481488935 696 True 291.5 322 84.3950 2358 2982 2 chr1D.!!$R3 624
4 TraesCS1D01G430700 chr1A 577985497 577987492 1995 False 2732.0 2732 91.5340 1254 3236 1 chr1A.!!$F2 1982
5 TraesCS1D01G430700 chr1A 578206429 578208280 1851 True 861.0 1262 84.7905 1236 3047 2 chr1A.!!$R1 1811
6 TraesCS1D01G430700 chr1B 670158184 670160919 2735 False 1570.0 2595 88.6200 304 3076 2 chr1B.!!$F7 2772
7 TraesCS1D01G430700 chr1B 669920305 669924624 4319 False 1323.5 2510 83.2150 305 3096 2 chr1B.!!$F5 2791
8 TraesCS1D01G430700 chr1B 670142808 670143902 1094 False 1005.0 1005 83.3030 1224 2333 1 chr1B.!!$F4 1109
9 TraesCS1D01G430700 chr1B 670149475 670150037 562 False 318.0 329 90.2275 2368 2862 2 chr1B.!!$F6 494
10 TraesCS1D01G430700 chr5D 390547558 390548427 869 True 1271.0 1271 93.1820 3366 4231 1 chr5D.!!$R1 865
11 TraesCS1D01G430700 chr5D 542465369 542466260 891 False 883.0 883 85.2390 3370 4231 1 chr5D.!!$F1 861
12 TraesCS1D01G430700 chr7B 34164344 34165193 849 False 1221.0 1221 92.5120 3370 4231 1 chr7B.!!$F1 861
13 TraesCS1D01G430700 chr6B 413938200 413939054 854 False 1221.0 1221 92.4230 3368 4231 1 chr6B.!!$F1 863
14 TraesCS1D01G430700 chr5B 36406217 36407075 858 False 1171.0 1171 91.2940 3367 4231 1 chr5B.!!$F1 864
15 TraesCS1D01G430700 chr5B 347392871 347393726 855 False 1171.0 1171 91.3490 3369 4231 1 chr5B.!!$F2 862
16 TraesCS1D01G430700 chr2B 166812241 166813101 860 True 1162.0 1162 91.0760 3367 4231 1 chr2B.!!$R1 864
17 TraesCS1D01G430700 chr2B 166834816 166835475 659 False 926.0 926 92.1570 3369 4023 1 chr2B.!!$F1 654
18 TraesCS1D01G430700 chr2B 666727519 666728113 594 False 494.0 494 81.9350 3439 4049 1 chr2B.!!$F4 610

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
458 471 0.030908 GAGACGATAGACCGGGCAAG 59.969 60.0 11.69 0.0 41.38 4.01 F
1823 3369 0.325860 TTGCGTACCTGGATACCCCT 60.326 55.0 0.00 0.0 35.38 4.79 F
2021 3570 0.606604 GAAGCCTAGACGTCCACCAA 59.393 55.0 13.01 0.0 0.00 3.67 F
3024 4804 0.034477 GGCCAAGCTTTGCTACCCTA 60.034 55.0 20.64 0.0 38.25 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1870 3416 0.602638 TTGCCCGCTAACAGTGTCAG 60.603 55.000 0.00 0.00 0.00 3.51 R
2994 4763 0.113190 AGCTTGGCCTTGGCTAGTTT 59.887 50.000 14.17 1.04 34.07 2.66 R
3081 4873 0.843309 TCAAAGGACCAAGCCAGACA 59.157 50.000 0.00 0.00 0.00 3.41 R
3838 5660 7.385752 AGTGGCATTTGTTATGAAAATGAAGTG 59.614 33.333 11.91 0.00 44.30 3.16 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
17 18 2.476499 GCGAACTCGAAGCAAGGC 59.524 61.111 2.69 0.00 43.02 4.35
18 19 2.029844 GCGAACTCGAAGCAAGGCT 61.030 57.895 2.69 0.00 43.02 4.58
19 20 1.960994 GCGAACTCGAAGCAAGGCTC 61.961 60.000 2.69 0.00 43.02 4.70
20 21 0.389166 CGAACTCGAAGCAAGGCTCT 60.389 55.000 0.00 0.00 38.25 4.09
21 22 1.355005 GAACTCGAAGCAAGGCTCTC 58.645 55.000 0.00 0.00 38.25 3.20
22 23 0.389166 AACTCGAAGCAAGGCTCTCG 60.389 55.000 13.00 13.00 38.25 4.04
23 24 1.518133 CTCGAAGCAAGGCTCTCGG 60.518 63.158 16.60 8.58 38.25 4.63
24 25 3.191539 CGAAGCAAGGCTCTCGGC 61.192 66.667 11.98 0.00 38.25 5.54
31 32 2.267324 AGGCTCTCGGCTTTGCTC 59.733 61.111 0.00 0.00 44.74 4.26
32 33 3.191539 GGCTCTCGGCTTTGCTCG 61.192 66.667 0.00 0.00 41.46 5.03
33 34 3.858989 GCTCTCGGCTTTGCTCGC 61.859 66.667 0.00 0.00 38.06 5.03
34 35 3.549150 CTCTCGGCTTTGCTCGCG 61.549 66.667 0.00 0.00 0.00 5.87
35 36 4.357947 TCTCGGCTTTGCTCGCGT 62.358 61.111 5.77 0.00 0.00 6.01
36 37 3.843240 CTCGGCTTTGCTCGCGTC 61.843 66.667 5.77 0.00 0.00 5.19
39 40 3.353836 GGCTTTGCTCGCGTCCAA 61.354 61.111 5.77 8.09 0.00 3.53
40 41 2.127232 GCTTTGCTCGCGTCCAAC 60.127 61.111 5.77 0.00 0.00 3.77
41 42 2.607892 GCTTTGCTCGCGTCCAACT 61.608 57.895 5.77 0.00 0.00 3.16
42 43 1.289109 GCTTTGCTCGCGTCCAACTA 61.289 55.000 5.77 0.00 0.00 2.24
43 44 0.438830 CTTTGCTCGCGTCCAACTAC 59.561 55.000 5.77 0.00 0.00 2.73
44 45 0.032952 TTTGCTCGCGTCCAACTACT 59.967 50.000 5.77 0.00 0.00 2.57
45 46 0.388134 TTGCTCGCGTCCAACTACTC 60.388 55.000 5.77 0.00 0.00 2.59
46 47 1.516603 GCTCGCGTCCAACTACTCC 60.517 63.158 5.77 0.00 0.00 3.85
47 48 1.139095 CTCGCGTCCAACTACTCCC 59.861 63.158 5.77 0.00 0.00 4.30
48 49 1.303888 TCGCGTCCAACTACTCCCT 60.304 57.895 5.77 0.00 0.00 4.20
49 50 1.139095 CGCGTCCAACTACTCCCTC 59.861 63.158 0.00 0.00 0.00 4.30
50 51 1.313812 CGCGTCCAACTACTCCCTCT 61.314 60.000 0.00 0.00 0.00 3.69
51 52 0.173708 GCGTCCAACTACTCCCTCTG 59.826 60.000 0.00 0.00 0.00 3.35
52 53 1.546961 CGTCCAACTACTCCCTCTGT 58.453 55.000 0.00 0.00 0.00 3.41
53 54 1.893801 CGTCCAACTACTCCCTCTGTT 59.106 52.381 0.00 0.00 0.00 3.16
54 55 2.299297 CGTCCAACTACTCCCTCTGTTT 59.701 50.000 0.00 0.00 0.00 2.83
55 56 3.614390 CGTCCAACTACTCCCTCTGTTTC 60.614 52.174 0.00 0.00 0.00 2.78
56 57 3.323979 GTCCAACTACTCCCTCTGTTTCA 59.676 47.826 0.00 0.00 0.00 2.69
57 58 4.020128 GTCCAACTACTCCCTCTGTTTCAT 60.020 45.833 0.00 0.00 0.00 2.57
58 59 5.187186 GTCCAACTACTCCCTCTGTTTCATA 59.813 44.000 0.00 0.00 0.00 2.15
59 60 5.783360 TCCAACTACTCCCTCTGTTTCATAA 59.217 40.000 0.00 0.00 0.00 1.90
60 61 6.443849 TCCAACTACTCCCTCTGTTTCATAAT 59.556 38.462 0.00 0.00 0.00 1.28
61 62 6.540189 CCAACTACTCCCTCTGTTTCATAATG 59.460 42.308 0.00 0.00 0.00 1.90
62 63 6.875972 ACTACTCCCTCTGTTTCATAATGT 57.124 37.500 0.00 0.00 0.00 2.71
63 64 7.973048 ACTACTCCCTCTGTTTCATAATGTA 57.027 36.000 0.00 0.00 0.00 2.29
64 65 8.012957 ACTACTCCCTCTGTTTCATAATGTAG 57.987 38.462 0.00 0.00 0.00 2.74
65 66 6.875972 ACTCCCTCTGTTTCATAATGTAGT 57.124 37.500 0.00 0.00 0.00 2.73
66 67 6.644347 ACTCCCTCTGTTTCATAATGTAGTG 58.356 40.000 0.00 0.00 0.00 2.74
67 68 6.213600 ACTCCCTCTGTTTCATAATGTAGTGT 59.786 38.462 0.00 0.00 0.00 3.55
68 69 7.399191 ACTCCCTCTGTTTCATAATGTAGTGTA 59.601 37.037 0.00 0.00 0.00 2.90
69 70 8.319057 TCCCTCTGTTTCATAATGTAGTGTAT 57.681 34.615 0.00 0.00 0.00 2.29
70 71 9.429109 TCCCTCTGTTTCATAATGTAGTGTATA 57.571 33.333 0.00 0.00 0.00 1.47
108 109 8.825667 AAAAAGTCAAACTAAGCAAACTTTGA 57.174 26.923 5.65 0.00 37.12 2.69
109 110 7.812309 AAAGTCAAACTAAGCAAACTTTGAC 57.188 32.000 16.37 16.37 46.84 3.18
111 112 5.646606 GTCAAACTAAGCAAACTTTGACCA 58.353 37.500 14.47 0.00 43.35 4.02
112 113 6.096695 GTCAAACTAAGCAAACTTTGACCAA 58.903 36.000 14.47 0.00 43.35 3.67
113 114 6.253512 GTCAAACTAAGCAAACTTTGACCAAG 59.746 38.462 14.47 0.09 43.35 3.61
126 127 7.696992 ACTTTGACCAAGTTTACAGAGAAAA 57.303 32.000 0.00 0.00 43.89 2.29
127 128 7.535997 ACTTTGACCAAGTTTACAGAGAAAAC 58.464 34.615 0.00 0.00 43.89 2.43
128 129 7.393515 ACTTTGACCAAGTTTACAGAGAAAACT 59.606 33.333 0.00 0.00 43.89 2.66
129 130 8.795842 TTTGACCAAGTTTACAGAGAAAACTA 57.204 30.769 1.96 0.00 44.35 2.24
130 131 8.974060 TTGACCAAGTTTACAGAGAAAACTAT 57.026 30.769 1.96 0.00 44.35 2.12
131 132 8.974060 TGACCAAGTTTACAGAGAAAACTATT 57.026 30.769 1.96 0.00 44.35 1.73
132 133 9.403583 TGACCAAGTTTACAGAGAAAACTATTT 57.596 29.630 1.96 0.00 44.35 1.40
260 261 9.868277 TGATCAAAGTTTGTAATGTTTGACTTT 57.132 25.926 15.08 0.00 40.67 2.66
299 300 5.422666 TGCGCTACATTATGAAATGAAGG 57.577 39.130 9.73 0.00 44.50 3.46
300 301 4.275689 TGCGCTACATTATGAAATGAAGGG 59.724 41.667 9.73 0.00 44.50 3.95
301 302 4.515191 GCGCTACATTATGAAATGAAGGGA 59.485 41.667 0.00 0.00 44.50 4.20
302 303 5.334414 GCGCTACATTATGAAATGAAGGGAG 60.334 44.000 0.00 0.00 44.50 4.30
395 399 4.634703 TTGGCGCACGGGACACAT 62.635 61.111 10.83 0.00 0.00 3.21
419 423 5.813157 TGATCGCAAATGACGTTTTCCTATA 59.187 36.000 0.00 0.00 0.00 1.31
420 424 5.459110 TCGCAAATGACGTTTTCCTATAC 57.541 39.130 0.00 0.00 0.00 1.47
429 442 5.860182 TGACGTTTTCCTATACGAGACAAAG 59.140 40.000 0.00 0.00 40.03 2.77
430 443 5.166398 ACGTTTTCCTATACGAGACAAAGG 58.834 41.667 0.00 0.00 40.03 3.11
446 459 4.836825 ACAAAGGTCATGAATGAGACGAT 58.163 39.130 0.00 0.00 37.51 3.73
448 461 6.045318 ACAAAGGTCATGAATGAGACGATAG 58.955 40.000 0.00 0.00 37.51 2.08
458 471 0.030908 GAGACGATAGACCGGGCAAG 59.969 60.000 11.69 0.00 41.38 4.01
460 473 1.027357 GACGATAGACCGGGCAAGTA 58.973 55.000 11.69 0.00 41.38 2.24
490 1395 1.963515 GGGACAGATGGTTGCAAAAGT 59.036 47.619 0.00 0.00 0.00 2.66
500 1405 2.601314 GGTTGCAAAAGTGACGTTTTCC 59.399 45.455 0.00 0.00 0.00 3.13
513 1418 4.513692 TGACGTTTTCCATACAAGACAAGG 59.486 41.667 0.00 0.00 0.00 3.61
589 1498 1.186917 TTGACCGGCGTCTTCCCTAA 61.187 55.000 6.01 0.00 39.94 2.69
666 2045 2.612972 GGTTCTCTGCGTTTGATCCAGA 60.613 50.000 0.00 0.00 34.68 3.86
740 2119 0.405973 AAGACAAGAGAAAGGGCCCC 59.594 55.000 21.43 2.42 0.00 5.80
742 2121 2.125766 GACAAGAGAAAGGGCCCCGT 62.126 60.000 21.43 6.26 0.00 5.28
744 2123 2.907179 AAGAGAAAGGGCCCCGTGG 61.907 63.158 21.43 0.00 0.00 4.94
791 2248 6.519891 GCATTTTGTCTTTTGGATTTAGGGGA 60.520 38.462 0.00 0.00 0.00 4.81
793 2250 6.664428 TTTGTCTTTTGGATTTAGGGGAAG 57.336 37.500 0.00 0.00 0.00 3.46
849 2318 0.804933 GTGTATCAAGGCGTCCCGAC 60.805 60.000 0.00 0.00 35.76 4.79
879 2349 1.270625 CCAAGTCCAAGTTAGGCACGA 60.271 52.381 0.00 0.00 0.00 4.35
884 2354 1.290955 CAAGTTAGGCACGACCGGA 59.709 57.895 9.46 0.00 46.52 5.14
892 2362 1.641677 GCACGACCGGAATACATGC 59.358 57.895 9.46 5.23 0.00 4.06
1057 2572 3.440415 AGCTCGATCGTCGCCACA 61.440 61.111 21.97 0.11 40.21 4.17
1062 2577 1.517276 CTCGATCGTCGCCACATTTAC 59.483 52.381 15.94 0.00 40.21 2.01
1068 2583 2.030096 TCGTCGCCACATTTACACACTA 60.030 45.455 0.00 0.00 0.00 2.74
1069 2584 2.091588 CGTCGCCACATTTACACACTAC 59.908 50.000 0.00 0.00 0.00 2.73
1070 2585 2.414138 GTCGCCACATTTACACACTACC 59.586 50.000 0.00 0.00 0.00 3.18
1071 2586 1.392168 CGCCACATTTACACACTACCG 59.608 52.381 0.00 0.00 0.00 4.02
1072 2587 2.690786 GCCACATTTACACACTACCGA 58.309 47.619 0.00 0.00 0.00 4.69
1073 2588 2.671396 GCCACATTTACACACTACCGAG 59.329 50.000 0.00 0.00 0.00 4.63
1154 2696 1.406205 GCTCTTCTCCCTTGCAGGTAC 60.406 57.143 0.00 0.00 31.93 3.34
1155 2697 0.895530 TCTTCTCCCTTGCAGGTACG 59.104 55.000 0.00 0.00 31.93 3.67
1156 2698 0.608640 CTTCTCCCTTGCAGGTACGT 59.391 55.000 0.00 0.00 31.93 3.57
1157 2699 1.822990 CTTCTCCCTTGCAGGTACGTA 59.177 52.381 0.00 0.00 31.93 3.57
1188 2730 3.725740 GCCGAGCGTTATGAAATGAAATG 59.274 43.478 0.00 0.00 0.00 2.32
1206 2748 4.974368 AATGTGTGTTTTCGAGGTTTCA 57.026 36.364 0.00 0.00 0.00 2.69
1239 2781 5.759506 AATGACGATGTTTGTTGGTGTAA 57.240 34.783 0.00 0.00 0.00 2.41
1248 2794 6.343226 TGTTTGTTGGTGTAAACGTACTAC 57.657 37.500 0.00 0.00 39.11 2.73
1252 2798 4.099266 TGTTGGTGTAAACGTACTACCTGT 59.901 41.667 11.04 0.00 34.79 4.00
1298 2844 3.083997 GGGAGGGTGGCGACTGAT 61.084 66.667 0.00 0.00 0.00 2.90
1328 2874 2.356553 GCGTCCGTGGTGCAACTA 60.357 61.111 2.04 0.00 36.74 2.24
1480 3026 2.108700 CCAAAATAATTTCGCGCTCCG 58.891 47.619 5.56 0.00 38.61 4.63
1571 3117 2.092699 GGTCTTCAAAGAGGCTAGCCAT 60.093 50.000 34.70 20.48 38.92 4.40
1625 3171 3.499737 CAGGCGGCGTTGGCTAAG 61.500 66.667 9.37 0.00 43.82 2.18
1694 3240 1.006571 GCTCAAGACGTCGTTCCCA 60.007 57.895 10.46 0.00 0.00 4.37
1727 3273 1.358877 CGTTCAAGGATGACATCGCA 58.641 50.000 9.31 0.00 34.61 5.10
1816 3362 1.597797 CCGTACCTTGCGTACCTGGA 61.598 60.000 0.00 0.00 43.93 3.86
1823 3369 0.325860 TTGCGTACCTGGATACCCCT 60.326 55.000 0.00 0.00 35.38 4.79
1832 3378 0.623031 TGGATACCCCTGGCATGTCA 60.623 55.000 0.00 0.00 35.38 3.58
1870 3416 3.514362 CCCCAATAACGGCGTGCC 61.514 66.667 15.70 0.00 0.00 5.01
1892 3438 1.170290 ACACTGTTAGCGGGCAAACC 61.170 55.000 0.00 0.00 0.00 3.27
1914 3460 3.626680 TTCAGCCTCTTCGACGCCG 62.627 63.158 0.00 0.00 37.07 6.46
2021 3570 0.606604 GAAGCCTAGACGTCCACCAA 59.393 55.000 13.01 0.00 0.00 3.67
2052 3601 1.965754 GCACCCAAACAAAGGCCACA 61.966 55.000 5.01 0.00 0.00 4.17
2054 3603 1.065854 CACCCAAACAAAGGCCACAAA 60.066 47.619 5.01 0.00 0.00 2.83
2057 3606 1.474855 CCAAACAAAGGCCACAAAGGG 60.475 52.381 5.01 0.00 38.09 3.95
2155 3704 3.591835 CGCAAACGGGCACAACCT 61.592 61.111 0.00 0.00 39.10 3.50
2243 3792 2.427506 GCCCTCTTCAACGAGAACAAT 58.572 47.619 0.00 0.00 32.74 2.71
2451 4024 3.965539 GACTGCAGCGCCATCCAGT 62.966 63.158 15.27 16.40 40.92 4.00
2540 4113 3.952628 GAAGAACGGCCGGGTCAGG 62.953 68.421 31.76 0.00 0.00 3.86
2873 4610 7.384115 CCAAGTAAGTTCACTTCTGAATTCGTA 59.616 37.037 0.04 0.00 38.69 3.43
2874 4611 7.870588 AGTAAGTTCACTTCTGAATTCGTAC 57.129 36.000 0.04 0.00 38.69 3.67
2875 4612 5.824243 AAGTTCACTTCTGAATTCGTACG 57.176 39.130 9.53 9.53 38.69 3.67
2876 4613 4.868067 AGTTCACTTCTGAATTCGTACGT 58.132 39.130 16.05 0.00 38.69 3.57
2992 4761 1.005215 CAAGGGCCTGAGGTGAAGAAT 59.995 52.381 6.92 0.00 0.00 2.40
2993 4762 1.376649 AGGGCCTGAGGTGAAGAATT 58.623 50.000 4.50 0.00 0.00 2.17
2994 4763 2.562296 AGGGCCTGAGGTGAAGAATTA 58.438 47.619 4.50 0.00 0.00 1.40
2995 4764 2.919602 AGGGCCTGAGGTGAAGAATTAA 59.080 45.455 4.50 0.00 0.00 1.40
3022 4802 0.900182 AAGGCCAAGCTTTGCTACCC 60.900 55.000 20.64 5.55 38.25 3.69
3023 4803 1.304464 GGCCAAGCTTTGCTACCCT 60.304 57.895 20.64 0.00 38.25 4.34
3024 4804 0.034477 GGCCAAGCTTTGCTACCCTA 60.034 55.000 20.64 0.00 38.25 3.53
3025 4805 1.095600 GCCAAGCTTTGCTACCCTAC 58.904 55.000 14.95 0.00 38.25 3.18
3026 4806 1.751437 CCAAGCTTTGCTACCCTACC 58.249 55.000 0.00 0.00 38.25 3.18
3077 4869 7.218963 GCTGTCAACAAAGTCTAGTTTTCAAAG 59.781 37.037 0.00 0.00 0.00 2.77
3078 4870 8.106247 TGTCAACAAAGTCTAGTTTTCAAAGT 57.894 30.769 0.00 0.00 0.00 2.66
3081 4873 9.974980 TCAACAAAGTCTAGTTTTCAAAGTTTT 57.025 25.926 0.00 0.00 0.00 2.43
3147 4939 2.594592 GCGTGGCCAGTTTCAGGT 60.595 61.111 5.11 0.00 0.00 4.00
3152 4944 2.359531 CGTGGCCAGTTTCAGGTTTTTA 59.640 45.455 5.11 0.00 0.00 1.52
3156 4948 5.820423 GTGGCCAGTTTCAGGTTTTTATTTT 59.180 36.000 5.11 0.00 0.00 1.82
3157 4949 6.317642 GTGGCCAGTTTCAGGTTTTTATTTTT 59.682 34.615 5.11 0.00 0.00 1.94
3159 4951 8.214364 TGGCCAGTTTCAGGTTTTTATTTTTAT 58.786 29.630 0.00 0.00 0.00 1.40
3160 4952 9.062524 GGCCAGTTTCAGGTTTTTATTTTTATT 57.937 29.630 0.00 0.00 0.00 1.40
3197 4989 4.551729 GGCATGGCCTTAACGCTA 57.448 55.556 8.35 0.00 46.69 4.26
3236 5028 7.094848 GCTTTGGCTTGCTCCATTTTAATAAAA 60.095 33.333 0.25 0.25 35.77 1.52
3237 5029 8.682936 TTTGGCTTGCTCCATTTTAATAAAAA 57.317 26.923 2.03 0.00 38.87 1.94
3318 5110 9.859427 TTAAGTAAATTCATGCTTTTCATCAGG 57.141 29.630 0.00 0.00 31.79 3.86
3319 5111 7.472334 AGTAAATTCATGCTTTTCATCAGGT 57.528 32.000 0.00 0.00 31.79 4.00
3320 5112 7.318141 AGTAAATTCATGCTTTTCATCAGGTG 58.682 34.615 0.00 0.00 31.79 4.00
3321 5113 3.581024 TTCATGCTTTTCATCAGGTGC 57.419 42.857 0.00 0.00 31.79 5.01
3322 5114 2.799017 TCATGCTTTTCATCAGGTGCT 58.201 42.857 0.00 0.00 31.79 4.40
3323 5115 3.159472 TCATGCTTTTCATCAGGTGCTT 58.841 40.909 0.00 0.00 31.79 3.91
3324 5116 4.334552 TCATGCTTTTCATCAGGTGCTTA 58.665 39.130 0.00 0.00 31.79 3.09
3325 5117 4.951715 TCATGCTTTTCATCAGGTGCTTAT 59.048 37.500 0.00 0.00 31.79 1.73
3326 5118 6.121590 TCATGCTTTTCATCAGGTGCTTATA 58.878 36.000 0.00 0.00 31.79 0.98
3327 5119 6.774170 TCATGCTTTTCATCAGGTGCTTATAT 59.226 34.615 0.00 0.00 31.79 0.86
3328 5120 7.286087 TCATGCTTTTCATCAGGTGCTTATATT 59.714 33.333 0.00 0.00 31.79 1.28
3329 5121 8.570488 CATGCTTTTCATCAGGTGCTTATATTA 58.430 33.333 0.00 0.00 31.79 0.98
3330 5122 8.696043 TGCTTTTCATCAGGTGCTTATATTAT 57.304 30.769 0.00 0.00 0.00 1.28
3331 5123 9.791801 TGCTTTTCATCAGGTGCTTATATTATA 57.208 29.630 0.00 0.00 0.00 0.98
3385 5177 8.635765 TCCTCAAATCACTTTAGCTACATTTT 57.364 30.769 0.00 0.00 0.00 1.82
3510 5306 2.607499 TGGGCTGTGTGGAATCAATTT 58.393 42.857 0.00 0.00 0.00 1.82
3546 5342 2.038426 TCAGTCGAATTGCTTCTTGGGA 59.962 45.455 0.00 0.00 0.00 4.37
3729 5542 5.414144 TCATGATAAAGTGCAATTTCGGTGA 59.586 36.000 16.40 12.82 0.00 4.02
3786 5606 6.877322 TCTCTTCTTAAAGGAAATACCAACGG 59.123 38.462 0.00 0.00 42.04 4.44
3879 5709 7.894376 AAATGCCACTATTCATTTGTTCTTG 57.106 32.000 0.00 0.00 40.27 3.02
4000 5835 9.586435 CAGTTTTGTTTTAGATTCTGTTTTCCT 57.414 29.630 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.960994 GAGCCTTGCTTCGAGTTCGC 61.961 60.000 0.00 0.00 39.88 4.70
1 2 0.389166 AGAGCCTTGCTTCGAGTTCG 60.389 55.000 0.00 0.00 39.88 3.95
2 3 1.355005 GAGAGCCTTGCTTCGAGTTC 58.645 55.000 0.00 0.00 39.88 3.01
3 4 0.389166 CGAGAGCCTTGCTTCGAGTT 60.389 55.000 12.20 0.00 39.88 3.01
4 5 1.214062 CGAGAGCCTTGCTTCGAGT 59.786 57.895 12.20 0.00 39.88 4.18
6 7 2.573869 CCGAGAGCCTTGCTTCGA 59.426 61.111 16.52 0.00 39.88 3.71
7 8 3.191539 GCCGAGAGCCTTGCTTCG 61.192 66.667 11.20 11.20 39.88 3.79
8 9 0.957888 AAAGCCGAGAGCCTTGCTTC 60.958 55.000 10.85 0.00 42.85 3.86
9 10 1.073897 AAAGCCGAGAGCCTTGCTT 59.926 52.632 0.00 0.00 45.40 3.91
10 11 1.673665 CAAAGCCGAGAGCCTTGCT 60.674 57.895 0.00 0.00 45.47 3.91
11 12 2.873288 CAAAGCCGAGAGCCTTGC 59.127 61.111 0.00 0.00 45.47 4.01
12 13 1.642952 GAGCAAAGCCGAGAGCCTTG 61.643 60.000 0.00 0.00 44.40 3.61
13 14 1.376553 GAGCAAAGCCGAGAGCCTT 60.377 57.895 0.00 0.00 45.47 4.35
14 15 2.267324 GAGCAAAGCCGAGAGCCT 59.733 61.111 0.00 0.00 45.47 4.58
15 16 3.191539 CGAGCAAAGCCGAGAGCC 61.192 66.667 0.00 0.00 45.47 4.70
16 17 3.858989 GCGAGCAAAGCCGAGAGC 61.859 66.667 0.00 0.00 44.25 4.09
17 18 3.549150 CGCGAGCAAAGCCGAGAG 61.549 66.667 0.00 0.00 0.00 3.20
18 19 4.357947 ACGCGAGCAAAGCCGAGA 62.358 61.111 15.93 0.00 0.00 4.04
19 20 3.843240 GACGCGAGCAAAGCCGAG 61.843 66.667 15.93 3.83 0.00 4.63
22 23 3.353836 TTGGACGCGAGCAAAGCC 61.354 61.111 15.93 2.58 0.00 4.35
23 24 1.289109 TAGTTGGACGCGAGCAAAGC 61.289 55.000 15.93 0.00 0.00 3.51
24 25 0.438830 GTAGTTGGACGCGAGCAAAG 59.561 55.000 15.93 0.00 0.00 2.77
25 26 0.032952 AGTAGTTGGACGCGAGCAAA 59.967 50.000 15.93 0.35 0.00 3.68
26 27 0.388134 GAGTAGTTGGACGCGAGCAA 60.388 55.000 15.93 0.00 0.00 3.91
27 28 1.211969 GAGTAGTTGGACGCGAGCA 59.788 57.895 15.93 0.00 0.00 4.26
28 29 1.516603 GGAGTAGTTGGACGCGAGC 60.517 63.158 15.93 3.71 0.00 5.03
29 30 1.139095 GGGAGTAGTTGGACGCGAG 59.861 63.158 15.93 0.00 0.00 5.03
30 31 1.303888 AGGGAGTAGTTGGACGCGA 60.304 57.895 15.93 0.00 0.00 5.87
31 32 1.139095 GAGGGAGTAGTTGGACGCG 59.861 63.158 3.53 3.53 0.00 6.01
32 33 0.173708 CAGAGGGAGTAGTTGGACGC 59.826 60.000 0.00 0.00 0.00 5.19
33 34 1.546961 ACAGAGGGAGTAGTTGGACG 58.453 55.000 0.00 0.00 0.00 4.79
34 35 3.323979 TGAAACAGAGGGAGTAGTTGGAC 59.676 47.826 0.00 0.00 0.00 4.02
35 36 3.583228 TGAAACAGAGGGAGTAGTTGGA 58.417 45.455 0.00 0.00 0.00 3.53
36 37 4.559862 ATGAAACAGAGGGAGTAGTTGG 57.440 45.455 0.00 0.00 0.00 3.77
37 38 7.106239 ACATTATGAAACAGAGGGAGTAGTTG 58.894 38.462 0.00 0.00 0.00 3.16
38 39 7.259088 ACATTATGAAACAGAGGGAGTAGTT 57.741 36.000 0.00 0.00 0.00 2.24
39 40 6.875972 ACATTATGAAACAGAGGGAGTAGT 57.124 37.500 0.00 0.00 0.00 2.73
40 41 7.923344 CACTACATTATGAAACAGAGGGAGTAG 59.077 40.741 0.00 0.00 0.00 2.57
41 42 7.399191 ACACTACATTATGAAACAGAGGGAGTA 59.601 37.037 0.00 0.00 0.00 2.59
42 43 6.213600 ACACTACATTATGAAACAGAGGGAGT 59.786 38.462 0.00 0.00 0.00 3.85
43 44 6.644347 ACACTACATTATGAAACAGAGGGAG 58.356 40.000 0.00 0.00 0.00 4.30
44 45 6.620877 ACACTACATTATGAAACAGAGGGA 57.379 37.500 0.00 0.00 0.00 4.20
83 84 8.825667 TCAAAGTTTGCTTAGTTTGACTTTTT 57.174 26.923 10.90 0.00 40.64 1.94
89 90 5.906113 TGGTCAAAGTTTGCTTAGTTTGA 57.094 34.783 10.90 13.93 42.30 2.69
90 91 6.573617 CTTGGTCAAAGTTTGCTTAGTTTG 57.426 37.500 10.90 10.74 38.97 2.93
103 104 7.762382 AGTTTTCTCTGTAAACTTGGTCAAAG 58.238 34.615 0.00 0.00 41.69 2.77
104 105 7.696992 AGTTTTCTCTGTAAACTTGGTCAAA 57.303 32.000 0.00 0.00 41.69 2.69
105 106 8.974060 ATAGTTTTCTCTGTAAACTTGGTCAA 57.026 30.769 6.33 0.00 41.69 3.18
106 107 8.974060 AATAGTTTTCTCTGTAAACTTGGTCA 57.026 30.769 6.33 0.00 41.69 4.02
234 235 9.868277 AAAGTCAAACATTACAAACTTTGATCA 57.132 25.926 8.55 0.00 36.06 2.92
273 274 8.882736 CCTTCATTTCATAATGTAGCGCATATA 58.117 33.333 11.47 0.00 41.54 0.86
274 275 7.148188 CCCTTCATTTCATAATGTAGCGCATAT 60.148 37.037 11.47 0.00 41.54 1.78
275 276 6.149308 CCCTTCATTTCATAATGTAGCGCATA 59.851 38.462 11.47 0.00 41.54 3.14
276 277 5.048504 CCCTTCATTTCATAATGTAGCGCAT 60.049 40.000 11.47 0.00 41.54 4.73
277 278 4.275689 CCCTTCATTTCATAATGTAGCGCA 59.724 41.667 11.47 0.00 41.54 6.09
278 279 4.515191 TCCCTTCATTTCATAATGTAGCGC 59.485 41.667 0.00 0.00 41.54 5.92
279 280 5.760253 ACTCCCTTCATTTCATAATGTAGCG 59.240 40.000 0.00 0.00 41.54 4.26
280 281 8.854614 ATACTCCCTTCATTTCATAATGTAGC 57.145 34.615 0.00 0.00 41.54 3.58
286 287 9.967451 TTGTGTAATACTCCCTTCATTTCATAA 57.033 29.630 0.00 0.00 0.00 1.90
287 288 9.967451 TTTGTGTAATACTCCCTTCATTTCATA 57.033 29.630 0.00 0.00 0.00 2.15
288 289 8.877864 TTTGTGTAATACTCCCTTCATTTCAT 57.122 30.769 0.00 0.00 0.00 2.57
289 290 7.393234 CCTTTGTGTAATACTCCCTTCATTTCA 59.607 37.037 0.00 0.00 0.00 2.69
290 291 7.148069 CCCTTTGTGTAATACTCCCTTCATTTC 60.148 40.741 0.00 0.00 0.00 2.17
291 292 6.663523 CCCTTTGTGTAATACTCCCTTCATTT 59.336 38.462 0.00 0.00 0.00 2.32
292 293 6.187682 CCCTTTGTGTAATACTCCCTTCATT 58.812 40.000 0.00 0.00 0.00 2.57
293 294 5.755849 CCCTTTGTGTAATACTCCCTTCAT 58.244 41.667 0.00 0.00 0.00 2.57
294 295 4.566907 GCCCTTTGTGTAATACTCCCTTCA 60.567 45.833 0.00 0.00 0.00 3.02
295 296 3.945921 GCCCTTTGTGTAATACTCCCTTC 59.054 47.826 0.00 0.00 0.00 3.46
296 297 3.332485 TGCCCTTTGTGTAATACTCCCTT 59.668 43.478 0.00 0.00 0.00 3.95
297 298 2.916934 TGCCCTTTGTGTAATACTCCCT 59.083 45.455 0.00 0.00 0.00 4.20
298 299 3.359695 TGCCCTTTGTGTAATACTCCC 57.640 47.619 0.00 0.00 0.00 4.30
299 300 5.758784 GTCTATGCCCTTTGTGTAATACTCC 59.241 44.000 0.00 0.00 0.00 3.85
300 301 6.346096 TGTCTATGCCCTTTGTGTAATACTC 58.654 40.000 0.00 0.00 0.00 2.59
301 302 6.308015 TGTCTATGCCCTTTGTGTAATACT 57.692 37.500 0.00 0.00 0.00 2.12
302 303 6.598064 ACTTGTCTATGCCCTTTGTGTAATAC 59.402 38.462 0.00 0.00 0.00 1.89
395 399 2.811431 AGGAAAACGTCATTTGCGATCA 59.189 40.909 0.00 0.00 35.96 2.92
419 423 4.021104 TCTCATTCATGACCTTTGTCTCGT 60.021 41.667 0.00 0.00 42.28 4.18
420 424 4.328440 GTCTCATTCATGACCTTTGTCTCG 59.672 45.833 0.00 0.00 42.28 4.04
429 442 4.551388 GGTCTATCGTCTCATTCATGACC 58.449 47.826 0.00 0.00 35.39 4.02
430 443 4.222886 CGGTCTATCGTCTCATTCATGAC 58.777 47.826 0.00 0.00 32.50 3.06
446 459 1.382146 CCCCTACTTGCCCGGTCTA 60.382 63.158 0.00 0.00 0.00 2.59
448 461 4.484872 GCCCCTACTTGCCCGGTC 62.485 72.222 0.00 0.00 0.00 4.79
478 1383 3.246619 GAAAACGTCACTTTTGCAACCA 58.753 40.909 0.00 0.00 0.00 3.67
490 1395 4.513692 CCTTGTCTTGTATGGAAAACGTCA 59.486 41.667 0.00 0.00 0.00 4.35
513 1418 9.443283 GTGCTTCATTTTTATGATAGACACATC 57.557 33.333 0.00 0.00 0.00 3.06
557 1466 1.202639 CCGGTCAATGCAGCACCTATA 60.203 52.381 0.00 0.00 0.00 1.31
558 1467 0.464373 CCGGTCAATGCAGCACCTAT 60.464 55.000 0.00 0.00 0.00 2.57
589 1498 3.275143 TGTCAACACGTGTGGAAAAGAT 58.725 40.909 26.95 3.11 34.19 2.40
708 2087 3.162666 TCTTGTCTTCTACACCCGATGT 58.837 45.455 0.00 0.00 46.06 3.06
744 2123 1.367840 CTAGTGGCAGTATCCCGGC 59.632 63.158 1.83 0.00 0.00 6.13
745 2124 0.389391 CACTAGTGGCAGTATCCCGG 59.611 60.000 15.49 0.00 0.00 5.73
746 2125 1.338337 CTCACTAGTGGCAGTATCCCG 59.662 57.143 22.48 0.00 0.00 5.14
747 2126 1.069358 GCTCACTAGTGGCAGTATCCC 59.931 57.143 22.48 0.00 0.00 3.85
748 2127 1.757118 TGCTCACTAGTGGCAGTATCC 59.243 52.381 25.71 7.22 33.85 2.59
750 2129 4.494091 AAATGCTCACTAGTGGCAGTAT 57.506 40.909 29.87 20.56 39.08 2.12
751 2130 3.981071 AAATGCTCACTAGTGGCAGTA 57.019 42.857 29.87 19.54 39.08 2.74
754 2133 2.813754 GACAAAATGCTCACTAGTGGCA 59.186 45.455 29.15 29.15 39.66 4.92
755 2134 3.077359 AGACAAAATGCTCACTAGTGGC 58.923 45.455 22.48 22.32 0.00 5.01
756 2135 5.695851 AAAGACAAAATGCTCACTAGTGG 57.304 39.130 22.48 13.97 0.00 4.00
757 2136 5.916883 CCAAAAGACAAAATGCTCACTAGTG 59.083 40.000 17.17 17.17 0.00 2.74
758 2137 5.827797 TCCAAAAGACAAAATGCTCACTAGT 59.172 36.000 0.00 0.00 0.00 2.57
800 2260 2.594303 CAAGCTTGGACCGGCACA 60.594 61.111 19.14 0.00 0.00 4.57
849 2318 2.900546 ACTTGGACTTGGACTGGTCTAG 59.099 50.000 0.67 2.23 33.46 2.43
879 2349 1.610038 CATGCATGCATGTATTCCGGT 59.390 47.619 40.30 14.19 46.20 5.28
1057 2572 4.683832 GATGCTCTCGGTAGTGTGTAAAT 58.316 43.478 0.00 0.00 0.00 1.40
1062 2577 3.242268 CGATGCTCTCGGTAGTGTG 57.758 57.895 1.87 0.00 43.82 3.82
1071 2586 2.050533 AGCGCGATCGATGCTCTC 60.051 61.111 24.12 3.36 38.10 3.20
1072 2587 2.354422 CAGCGCGATCGATGCTCT 60.354 61.111 26.14 9.78 45.29 4.09
1188 2730 6.128742 ACGTATATGAAACCTCGAAAACACAC 60.129 38.462 0.00 0.00 0.00 3.82
1206 2748 8.812147 ACAAACATCGTCATTATCACGTATAT 57.188 30.769 0.00 0.00 38.45 0.86
1239 2781 2.357569 CCCCCTCTACAGGTAGTACGTT 60.358 54.545 0.00 0.00 38.30 3.99
1328 2874 3.953612 TGGTGATGCTGTTTTTCTTGAGT 59.046 39.130 0.00 0.00 0.00 3.41
1361 2907 2.703798 CGTGGGGTCGGTGTCGTAT 61.704 63.158 0.00 0.00 37.69 3.06
1480 3026 3.357079 CGTTGCTCTGCACCCACC 61.357 66.667 0.00 0.00 38.71 4.61
1571 3117 2.093106 GGGACGAGCTGAGAGTTTAGA 58.907 52.381 0.00 0.00 0.00 2.10
1727 3273 2.660064 GGGGCTCATCACCGACAGT 61.660 63.158 0.00 0.00 0.00 3.55
1816 3362 4.079212 AGTTAATTGACATGCCAGGGGTAT 60.079 41.667 2.93 0.00 0.00 2.73
1823 3369 5.435686 AGAGGTAGTTAATTGACATGCCA 57.564 39.130 2.93 0.00 0.00 4.92
1832 3378 4.259356 GGCGGAACAAGAGGTAGTTAATT 58.741 43.478 0.00 0.00 0.00 1.40
1870 3416 0.602638 TTGCCCGCTAACAGTGTCAG 60.603 55.000 0.00 0.00 0.00 3.51
1892 3438 2.181426 CGTCGAAGAGGCTGAAGTAG 57.819 55.000 0.00 0.00 36.95 2.57
1955 3501 2.562912 CCAACGTGCATGCTGGAC 59.437 61.111 21.60 7.96 35.21 4.02
2015 3564 2.046892 CCGTGCTCTCCTTGGTGG 60.047 66.667 0.00 0.00 37.10 4.61
2028 3577 1.067250 CTTTGTTTGGGTGCCCGTG 59.933 57.895 2.44 0.00 39.42 4.94
2192 3741 2.435938 TTCAGATCGGCGTTGGGC 60.436 61.111 6.85 0.00 42.51 5.36
2408 3957 4.351938 TTGCCGCACGCGTAGTCT 62.352 61.111 13.44 0.00 42.08 3.24
2540 4113 2.774774 CTGAAGTCGCAAGCGCTC 59.225 61.111 12.06 0.00 39.59 5.03
2576 4149 1.380302 ACCTGATGGTGCCTGGTTC 59.620 57.895 0.00 0.00 46.51 3.62
2873 4610 7.083875 TCTTTTCTTGAAACAAGAATCACGT 57.916 32.000 21.82 0.00 36.30 4.49
2874 4611 7.969387 TTCTTTTCTTGAAACAAGAATCACG 57.031 32.000 21.82 13.18 36.30 4.35
2912 4657 7.222999 GTGGAACGAAATCACCATTAACAAAAA 59.777 33.333 0.00 0.00 34.87 1.94
2913 4658 6.697892 GTGGAACGAAATCACCATTAACAAAA 59.302 34.615 0.00 0.00 34.87 2.44
2992 4761 2.167662 GCTTGGCCTTGGCTAGTTTAA 58.832 47.619 11.71 0.00 34.07 1.52
2993 4762 1.354368 AGCTTGGCCTTGGCTAGTTTA 59.646 47.619 14.17 0.00 34.07 2.01
2994 4763 0.113190 AGCTTGGCCTTGGCTAGTTT 59.887 50.000 14.17 1.04 34.07 2.66
2995 4764 0.113190 AAGCTTGGCCTTGGCTAGTT 59.887 50.000 15.64 4.97 35.06 2.24
3022 4802 9.862371 ATGATTATTGCTTAATCTCGTAGGTAG 57.138 33.333 16.06 0.00 44.43 3.18
3023 4803 9.856488 GATGATTATTGCTTAATCTCGTAGGTA 57.144 33.333 16.06 0.94 44.43 3.08
3024 4804 8.589338 AGATGATTATTGCTTAATCTCGTAGGT 58.411 33.333 16.06 0.00 44.43 3.08
3025 4805 8.867935 CAGATGATTATTGCTTAATCTCGTAGG 58.132 37.037 16.06 3.84 44.43 3.18
3026 4806 8.379161 GCAGATGATTATTGCTTAATCTCGTAG 58.621 37.037 16.06 7.77 44.43 3.51
3077 4869 1.692411 AGGACCAAGCCAGACAAAAC 58.308 50.000 0.00 0.00 0.00 2.43
3078 4870 2.430332 CAAAGGACCAAGCCAGACAAAA 59.570 45.455 0.00 0.00 0.00 2.44
3081 4873 0.843309 TCAAAGGACCAAGCCAGACA 59.157 50.000 0.00 0.00 0.00 3.41
3164 4956 1.275666 TGCCAGAGTAGCTAAGCCAA 58.724 50.000 0.00 0.00 0.00 4.52
3190 4982 5.018539 AGCCATGACAGTTTATAGCGTTA 57.981 39.130 0.00 0.00 0.00 3.18
3197 4989 3.434309 AGCCAAAGCCATGACAGTTTAT 58.566 40.909 0.00 0.00 41.25 1.40
3292 5084 9.859427 CCTGATGAAAAGCATGAATTTACTTAA 57.141 29.630 0.00 0.00 37.34 1.85
3293 5085 9.023962 ACCTGATGAAAAGCATGAATTTACTTA 57.976 29.630 0.00 0.00 37.34 2.24
3294 5086 7.816031 CACCTGATGAAAAGCATGAATTTACTT 59.184 33.333 0.00 0.00 37.34 2.24
3295 5087 7.318141 CACCTGATGAAAAGCATGAATTTACT 58.682 34.615 0.00 0.00 37.34 2.24
3296 5088 6.035327 GCACCTGATGAAAAGCATGAATTTAC 59.965 38.462 0.00 0.00 37.34 2.01
3297 5089 6.071221 AGCACCTGATGAAAAGCATGAATTTA 60.071 34.615 0.00 0.00 37.34 1.40
3298 5090 4.933400 GCACCTGATGAAAAGCATGAATTT 59.067 37.500 0.00 0.00 37.34 1.82
3299 5091 4.222145 AGCACCTGATGAAAAGCATGAATT 59.778 37.500 0.00 0.00 37.34 2.17
3300 5092 3.767673 AGCACCTGATGAAAAGCATGAAT 59.232 39.130 0.00 0.00 37.34 2.57
3301 5093 3.159472 AGCACCTGATGAAAAGCATGAA 58.841 40.909 0.00 0.00 37.34 2.57
3302 5094 2.799017 AGCACCTGATGAAAAGCATGA 58.201 42.857 0.00 0.00 37.34 3.07
3303 5095 3.587797 AAGCACCTGATGAAAAGCATG 57.412 42.857 0.00 0.00 37.34 4.06
3304 5096 7.592885 AATATAAGCACCTGATGAAAAGCAT 57.407 32.000 0.00 0.00 40.77 3.79
3305 5097 8.696043 ATAATATAAGCACCTGATGAAAAGCA 57.304 30.769 0.00 0.00 0.00 3.91
3346 5138 9.965902 AGTGATTTGAGGAACAGTCTTATAATT 57.034 29.630 0.00 0.00 0.00 1.40
3347 5139 9.965902 AAGTGATTTGAGGAACAGTCTTATAAT 57.034 29.630 0.00 0.00 0.00 1.28
3348 5140 9.793259 AAAGTGATTTGAGGAACAGTCTTATAA 57.207 29.630 0.00 0.00 0.00 0.98
3350 5142 9.442047 CTAAAGTGATTTGAGGAACAGTCTTAT 57.558 33.333 0.00 0.00 0.00 1.73
3351 5143 7.387948 GCTAAAGTGATTTGAGGAACAGTCTTA 59.612 37.037 0.00 0.00 0.00 2.10
3352 5144 6.205658 GCTAAAGTGATTTGAGGAACAGTCTT 59.794 38.462 0.00 0.00 0.00 3.01
3353 5145 5.703130 GCTAAAGTGATTTGAGGAACAGTCT 59.297 40.000 0.00 0.00 0.00 3.24
3354 5146 5.703130 AGCTAAAGTGATTTGAGGAACAGTC 59.297 40.000 0.00 0.00 0.00 3.51
3355 5147 5.625150 AGCTAAAGTGATTTGAGGAACAGT 58.375 37.500 0.00 0.00 0.00 3.55
3356 5148 6.650807 TGTAGCTAAAGTGATTTGAGGAACAG 59.349 38.462 0.00 0.00 0.00 3.16
3357 5149 6.530120 TGTAGCTAAAGTGATTTGAGGAACA 58.470 36.000 0.00 0.00 0.00 3.18
3358 5150 7.617041 ATGTAGCTAAAGTGATTTGAGGAAC 57.383 36.000 0.00 0.00 0.00 3.62
3359 5151 8.635765 AAATGTAGCTAAAGTGATTTGAGGAA 57.364 30.769 0.00 0.00 0.00 3.36
3360 5152 8.635765 AAAATGTAGCTAAAGTGATTTGAGGA 57.364 30.769 0.00 0.00 0.00 3.71
3361 5153 9.994432 CTAAAATGTAGCTAAAGTGATTTGAGG 57.006 33.333 0.00 0.00 0.00 3.86
3483 5279 2.202395 CCACACAGCCCAACCCAAG 61.202 63.158 0.00 0.00 0.00 3.61
3572 5376 8.561738 AAGAAAAGGGAAAAAGGAAAAAGAAC 57.438 30.769 0.00 0.00 0.00 3.01
3786 5606 6.515272 TCCTGAAAAGGAATGAATTAGTGC 57.485 37.500 0.00 0.00 34.56 4.40
3838 5660 7.385752 AGTGGCATTTGTTATGAAAATGAAGTG 59.614 33.333 11.91 0.00 44.30 3.16


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

AutoCloner maintained by Alex Coulton.