Multiple sequence alignment - TraesCS2A01G057000

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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 TraesCS2A01G057000 chr2A 100.000 8129 0 0 1 8129 24127527 24135655 0.000000e+00 15012.0
1 TraesCS2A01G057000 chr2A 79.449 1416 242 38 5898 7276 23804954 23806357 0.000000e+00 957.0
2 TraesCS2A01G057000 chr2A 80.897 1293 147 47 4599 5849 24130286 24131520 0.000000e+00 928.0
3 TraesCS2A01G057000 chr2A 80.897 1293 147 47 2760 3994 24132125 24133375 0.000000e+00 928.0
4 TraesCS2A01G057000 chr2A 81.130 885 123 16 985 1853 23803091 23803947 0.000000e+00 669.0
5 TraesCS2A01G057000 chr2D 91.185 3823 247 46 4309 8087 22423108 22426884 0.000000e+00 5110.0
6 TraesCS2A01G057000 chr2D 89.128 3440 194 76 709 4019 22419364 22422752 0.000000e+00 4115.0
7 TraesCS2A01G057000 chr2D 83.083 1200 157 30 4598 5768 22421481 22422663 0.000000e+00 1050.0
8 TraesCS2A01G057000 chr2D 81.948 1263 148 32 2770 3994 22423407 22424627 0.000000e+00 996.0
9 TraesCS2A01G057000 chr2D 83.087 881 105 19 985 1852 21607733 21608582 0.000000e+00 761.0
10 TraesCS2A01G057000 chr2D 94.118 289 17 0 4023 4311 22422790 22423078 2.690000e-119 440.0
11 TraesCS2A01G057000 chr2D 79.208 505 53 24 7667 8129 22480728 22480234 3.690000e-78 303.0
12 TraesCS2A01G057000 chr2D 83.471 242 11 6 2193 2411 22422788 22423023 1.790000e-46 198.0
13 TraesCS2A01G057000 chrUn 89.062 2496 153 56 821 3214 16951142 16953619 0.000000e+00 2987.0
14 TraesCS2A01G057000 chrUn 89.062 2496 153 56 821 3214 266455388 266457865 0.000000e+00 2987.0
15 TraesCS2A01G057000 chrUn 89.739 2027 145 28 4498 6503 360308869 360306885 0.000000e+00 2532.0
16 TraesCS2A01G057000 chrUn 90.708 1356 75 24 821 2136 282234149 282232805 0.000000e+00 1759.0
17 TraesCS2A01G057000 chrUn 88.475 833 66 8 3212 4019 16953991 16954818 0.000000e+00 979.0
18 TraesCS2A01G057000 chrUn 88.475 833 66 8 3212 4019 266458237 266459064 0.000000e+00 979.0
19 TraesCS2A01G057000 chrUn 80.983 1262 157 35 2770 3995 360308758 360307544 0.000000e+00 924.0
20 TraesCS2A01G057000 chrUn 95.031 483 21 1 6861 7343 428228220 428228699 0.000000e+00 756.0
21 TraesCS2A01G057000 chrUn 95.031 483 21 1 6861 7343 464457278 464457757 0.000000e+00 756.0
22 TraesCS2A01G057000 chrUn 82.407 756 89 26 5040 5768 16953991 16954729 3.220000e-173 619.0
23 TraesCS2A01G057000 chrUn 82.407 756 89 26 5040 5768 266458237 266458975 3.220000e-173 619.0
24 TraesCS2A01G057000 chrUn 79.570 465 68 19 4598 5042 16953162 16953619 2.850000e-79 307.0
25 TraesCS2A01G057000 chrUn 79.570 465 68 19 4598 5042 266457408 266457865 2.850000e-79 307.0
26 TraesCS2A01G057000 chrUn 91.351 185 14 2 4309 4493 16955076 16955258 1.350000e-62 252.0
27 TraesCS2A01G057000 chrUn 91.351 185 14 2 4309 4493 266459322 266459504 1.350000e-62 252.0
28 TraesCS2A01G057000 chrUn 84.337 249 27 10 585 829 16949566 16949806 4.910000e-57 233.0
29 TraesCS2A01G057000 chrUn 84.337 249 27 10 585 829 266453812 266454052 4.910000e-57 233.0
30 TraesCS2A01G057000 chrUn 84.337 249 27 10 585 829 282235725 282235485 4.910000e-57 233.0
31 TraesCS2A01G057000 chrUn 89.542 153 16 0 143 295 16915258 16915410 2.310000e-45 195.0
32 TraesCS2A01G057000 chrUn 96.364 110 4 0 4023 4132 16954856 16954965 1.800000e-41 182.0
33 TraesCS2A01G057000 chrUn 96.364 110 4 0 4023 4132 266459102 266459211 1.800000e-41 182.0
34 TraesCS2A01G057000 chrUn 87.500 128 10 6 19 144 16948693 16948816 8.500000e-30 143.0
35 TraesCS2A01G057000 chrUn 87.500 128 10 6 19 144 266452939 266453062 8.500000e-30 143.0
36 TraesCS2A01G057000 chrUn 87.500 128 10 6 19 144 282236598 282236475 8.500000e-30 143.0
37 TraesCS2A01G057000 chrUn 87.000 100 10 2 2571 2669 360308861 360308764 8.630000e-20 110.0
38 TraesCS2A01G057000 chrUn 87.037 54 2 5 174 227 31563470 31563518 1.000000e-03 56.5
39 TraesCS2A01G057000 chr2B 88.365 1908 167 27 5393 7280 39237969 39239841 0.000000e+00 2242.0
40 TraesCS2A01G057000 chr2B 82.480 879 116 16 985 1853 35030406 35029556 0.000000e+00 736.0
41 TraesCS2A01G057000 chr2B 86.036 444 44 9 3560 3994 39237970 39238404 2.070000e-125 460.0
42 TraesCS2A01G057000 chr2B 97.619 42 1 0 5314 5355 39237929 39237970 1.130000e-08 73.1
43 TraesCS2A01G057000 chr3A 86.770 257 32 2 1932 2187 108468814 108468559 1.340000e-72 285.0
44 TraesCS2A01G057000 chr6D 79.182 269 34 7 1926 2188 461386494 461386746 5.050000e-37 167.0


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 TraesCS2A01G057000 chr2A 24127527 24135655 8128 False 15012.000000 15012 100.000000 1 8129 1 chr2A.!!$F1 8128
1 TraesCS2A01G057000 chr2A 24130286 24133375 3089 False 928.000000 928 80.897000 2760 5849 2 chr2A.!!$F3 3089
2 TraesCS2A01G057000 chr2A 23803091 23806357 3266 False 813.000000 957 80.289500 985 7276 2 chr2A.!!$F2 6291
3 TraesCS2A01G057000 chr2D 22419364 22426884 7520 False 1984.833333 5110 87.155500 709 8087 6 chr2D.!!$F2 7378
4 TraesCS2A01G057000 chr2D 21607733 21608582 849 False 761.000000 761 83.087000 985 1852 1 chr2D.!!$F1 867
5 TraesCS2A01G057000 chrUn 360306885 360308869 1984 True 1188.666667 2532 85.907333 2571 6503 3 chrUn.!!$R2 3932
6 TraesCS2A01G057000 chrUn 16948693 16955258 6565 False 712.750000 2987 87.383250 19 5768 8 chrUn.!!$F5 5749
7 TraesCS2A01G057000 chrUn 266452939 266459504 6565 False 712.750000 2987 87.383250 19 5768 8 chrUn.!!$F6 5749
8 TraesCS2A01G057000 chrUn 282232805 282236598 3793 True 711.666667 1759 87.515000 19 2136 3 chrUn.!!$R1 2117
9 TraesCS2A01G057000 chr2B 39237929 39239841 1912 False 925.033333 2242 90.673333 3560 7280 3 chr2B.!!$F1 3720
10 TraesCS2A01G057000 chr2B 35029556 35030406 850 True 736.000000 736 82.480000 985 1853 1 chr2B.!!$R1 868

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
514 611 0.608130 ATGACACTGCAAGCGGTAGA 59.392 50.000 6.16 0.00 37.60 2.59 F
1855 3566 0.036306 CCACTCCACAGGTAACCCAC 59.964 60.000 0.00 0.00 37.17 4.61 F
2265 3980 0.170339 GCCTATTTGTTGGTGCGGAC 59.830 55.000 0.00 0.00 0.00 4.79 F
2543 4277 0.819582 ATTTGGCTGCATTTCCCTCG 59.180 50.000 0.50 0.00 0.00 4.63 F
2562 4307 2.165234 TCGATATAGCTCTCCTGCATGC 59.835 50.000 11.82 11.82 34.99 4.06 F
2707 4455 2.524569 AAAAATGGGTCGTGGCTTTG 57.475 45.000 0.00 0.00 0.00 2.77 F
6315 8633 1.153086 GGTGAAGGAGATGCGGCAT 60.153 57.895 16.65 16.65 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2157 3869 0.108281 GACCCTCCTAACTGGCGAAC 60.108 60.000 0.00 0.0 35.26 3.95 R
2694 4441 1.515521 CTGAACCAAAGCCACGACCC 61.516 60.000 0.00 0.0 0.00 4.46 R
5909 8210 5.264395 TCTGTGTGAGATGGATCTGTTAGA 58.736 41.667 0.00 0.0 37.25 2.10 R
6019 8320 4.526650 ACCGTCTTGGCCTTTTCATAAATT 59.473 37.500 3.32 0.0 43.94 1.82 R
6204 8522 3.764434 TCCTATCTTGCGAGAAGTTGTCT 59.236 43.478 7.99 0.0 40.25 3.41 R
6329 8647 1.336609 GCACGTAGTTCTTCCGGTTCT 60.337 52.381 0.00 0.0 41.61 3.01 R
7599 9932 0.034186 CACCCAATGCCCAGCTTCTA 60.034 55.000 0.00 0.0 0.00 2.10 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
25 26 2.882170 GGTAGAAACCCCACCATGC 58.118 57.895 0.00 0.00 40.21 4.06
42 43 6.206243 CCACCATGCCAAATTTCATGTTTTTA 59.794 34.615 15.10 0.00 38.63 1.52
43 44 7.255381 CCACCATGCCAAATTTCATGTTTTTAA 60.255 33.333 15.10 0.00 38.63 1.52
97 99 9.699410 AAACCATTAATCTCCATATTGTTCAGA 57.301 29.630 0.00 0.00 0.00 3.27
98 100 8.915057 ACCATTAATCTCCATATTGTTCAGAG 57.085 34.615 0.00 0.00 0.00 3.35
99 101 8.497745 ACCATTAATCTCCATATTGTTCAGAGT 58.502 33.333 0.00 0.00 0.00 3.24
100 102 8.997323 CCATTAATCTCCATATTGTTCAGAGTC 58.003 37.037 0.00 0.00 0.00 3.36
101 103 8.706936 CATTAATCTCCATATTGTTCAGAGTCG 58.293 37.037 0.00 0.00 0.00 4.18
133 135 3.510459 CCCTGAGGTTTGGAATTCCTTT 58.490 45.455 24.73 6.30 36.82 3.11
152 228 7.948034 TCCTTTCCTTTTCTTGTAGTTCAAA 57.052 32.000 0.00 0.00 35.48 2.69
237 332 8.834465 CAAATTTTGACATGAAAAATGGTACCA 58.166 29.630 18.99 18.99 37.32 3.25
246 341 6.656632 TGAAAAATGGTACCAACATGCTAA 57.343 33.333 20.76 0.00 0.00 3.09
249 344 7.178274 TGAAAAATGGTACCAACATGCTAATCT 59.822 33.333 20.76 0.00 0.00 2.40
268 363 3.999046 TCTTTGTTAAAGAGTCGGTCCC 58.001 45.455 0.14 0.00 42.31 4.46
295 390 5.310409 TGGGGATTTCTAATGAGGTGATC 57.690 43.478 0.00 0.00 0.00 2.92
299 394 6.296145 GGGGATTTCTAATGAGGTGATCTAGG 60.296 46.154 0.00 0.00 0.00 3.02
302 397 8.093927 GGATTTCTAATGAGGTGATCTAGGAAG 58.906 40.741 0.00 0.00 0.00 3.46
306 401 9.527157 TTCTAATGAGGTGATCTAGGAAGATAG 57.473 37.037 0.00 0.00 42.73 2.08
307 402 8.674173 TCTAATGAGGTGATCTAGGAAGATAGT 58.326 37.037 0.00 0.00 42.73 2.12
344 439 2.120312 TGCCAATTCGAGGGGTATACA 58.880 47.619 5.01 0.00 0.00 2.29
355 451 5.756347 TCGAGGGGTATACATTTCATTTTCG 59.244 40.000 5.01 1.58 0.00 3.46
357 453 6.008696 AGGGGTATACATTTCATTTTCGGA 57.991 37.500 5.01 0.00 0.00 4.55
370 466 7.579589 TTCATTTTCGGATTTGCTAAACATG 57.420 32.000 0.00 0.00 0.00 3.21
372 468 7.374272 TCATTTTCGGATTTGCTAAACATGAA 58.626 30.769 0.00 0.00 0.00 2.57
383 479 4.340666 TGCTAAACATGAAGTGCCTGAAAA 59.659 37.500 0.00 0.00 0.00 2.29
397 493 3.499157 GCCTGAAAATTTTGCAAGCATCA 59.501 39.130 8.47 1.17 0.00 3.07
409 505 1.667724 CAAGCATCAGTCGATTCCACC 59.332 52.381 0.00 0.00 0.00 4.61
426 522 3.470567 CGACGCTGAAGACGGTGC 61.471 66.667 0.00 0.00 36.47 5.01
443 539 2.429930 CCAACGTGAGGAGCCCAA 59.570 61.111 1.12 0.00 0.00 4.12
495 591 4.361971 ACCTCGCTGGAGACGGGA 62.362 66.667 1.32 0.00 43.27 5.14
496 592 2.835431 CCTCGCTGGAGACGGGAT 60.835 66.667 0.00 0.00 43.27 3.85
497 593 2.415010 CTCGCTGGAGACGGGATG 59.585 66.667 0.00 0.00 43.27 3.51
509 606 2.743752 CGGGATGACACTGCAAGCG 61.744 63.158 0.00 0.00 37.60 4.68
514 611 0.608130 ATGACACTGCAAGCGGTAGA 59.392 50.000 6.16 0.00 37.60 2.59
518 615 1.073216 CACTGCAAGCGGTAGAGACG 61.073 60.000 6.16 0.00 37.60 4.18
519 616 1.517257 CTGCAAGCGGTAGAGACGG 60.517 63.158 0.00 0.00 0.00 4.79
521 618 1.226717 GCAAGCGGTAGAGACGGAG 60.227 63.158 0.00 0.00 0.00 4.63
523 620 1.001145 AAGCGGTAGAGACGGAGGT 60.001 57.895 0.00 0.00 0.00 3.85
538 647 4.741239 GGTGAGGAGGGAGGGGCA 62.741 72.222 0.00 0.00 0.00 5.36
540 649 2.209809 TGAGGAGGGAGGGGCAAA 59.790 61.111 0.00 0.00 0.00 3.68
554 663 1.028130 GGCAAAGCTTAGAGGGATGC 58.972 55.000 0.00 3.66 0.00 3.91
556 665 1.683011 GCAAAGCTTAGAGGGATGCCA 60.683 52.381 5.86 0.00 0.00 4.92
557 666 2.726821 CAAAGCTTAGAGGGATGCCAA 58.273 47.619 5.86 0.00 0.00 4.52
560 669 4.796110 AAGCTTAGAGGGATGCCAATTA 57.204 40.909 5.86 0.00 0.00 1.40
583 764 3.680156 GGCACGGCATGAGGAAAA 58.320 55.556 0.00 0.00 0.00 2.29
594 905 3.244181 GCATGAGGAAAATTGGGTGTGTT 60.244 43.478 0.00 0.00 0.00 3.32
613 924 8.198109 GGTGTGTTTAGCTCTCATCTAGATAAA 58.802 37.037 4.54 0.00 33.66 1.40
645 956 6.949352 ATGTATCATCTGTTGGATTTCACC 57.051 37.500 0.00 0.00 31.27 4.02
646 957 5.814481 TGTATCATCTGTTGGATTTCACCA 58.186 37.500 0.00 0.00 38.24 4.17
647 958 6.425735 TGTATCATCTGTTGGATTTCACCAT 58.574 36.000 0.00 0.00 39.82 3.55
712 1025 8.657729 GTTAATCAAGGAGTGTAAAAGCTAGAC 58.342 37.037 0.00 0.00 0.00 2.59
713 1026 6.613153 ATCAAGGAGTGTAAAAGCTAGACT 57.387 37.500 0.00 0.00 0.00 3.24
770 1084 7.496263 GGGGACTTTGTTAATTCTCATCTAGAC 59.504 40.741 0.00 0.00 32.51 2.59
771 1085 8.041323 GGGACTTTGTTAATTCTCATCTAGACA 58.959 37.037 0.00 0.00 32.51 3.41
907 2563 4.786994 TGTCTCTAGGGTCTTAGTCCACTA 59.213 45.833 0.00 0.00 0.00 2.74
971 2630 2.596904 GCATGAGCAAGCCAAATGAT 57.403 45.000 0.00 0.00 41.58 2.45
1315 3014 2.202797 CCATCGTCCAGGACAGCG 60.203 66.667 20.13 6.00 32.09 5.18
1509 3214 3.231736 ACTCGCTGGAACCACGGT 61.232 61.111 12.78 8.72 0.00 4.83
1743 3454 0.977627 ACGCCACCATGGATCTCAGA 60.978 55.000 21.47 0.00 40.96 3.27
1747 3458 2.113807 CCACCATGGATCTCAGAGACA 58.886 52.381 21.47 0.00 40.96 3.41
1855 3566 0.036306 CCACTCCACAGGTAACCCAC 59.964 60.000 0.00 0.00 37.17 4.61
1875 3586 5.163854 CCCACTTCAAATCTAACGATGTCAC 60.164 44.000 0.00 0.00 0.00 3.67
1876 3587 5.408299 CCACTTCAAATCTAACGATGTCACA 59.592 40.000 0.00 0.00 0.00 3.58
1877 3588 6.299604 CACTTCAAATCTAACGATGTCACAC 58.700 40.000 0.00 0.00 0.00 3.82
1878 3589 5.408604 ACTTCAAATCTAACGATGTCACACC 59.591 40.000 0.00 0.00 0.00 4.16
1879 3590 4.888917 TCAAATCTAACGATGTCACACCA 58.111 39.130 0.00 0.00 0.00 4.17
1880 3591 4.929211 TCAAATCTAACGATGTCACACCAG 59.071 41.667 0.00 0.00 0.00 4.00
1881 3592 2.363788 TCTAACGATGTCACACCAGC 57.636 50.000 0.00 0.00 0.00 4.85
1902 3613 5.680229 CAGCTGCATGAACGAATTTCTAATC 59.320 40.000 0.00 0.00 34.97 1.75
1907 3618 6.183360 TGCATGAACGAATTTCTAATCTTCCC 60.183 38.462 0.00 0.00 34.97 3.97
1915 3626 8.053355 ACGAATTTCTAATCTTCCCATAAGGTT 58.947 33.333 0.00 0.00 36.75 3.50
1945 3656 0.975135 TCAACGGTAATTGTCCCCGA 59.025 50.000 12.62 0.00 44.41 5.14
1947 3658 0.390209 AACGGTAATTGTCCCCGACG 60.390 55.000 12.62 0.00 44.41 5.12
1975 3686 2.142292 CTGTAAGGGGGCTGGCAAGT 62.142 60.000 2.88 0.00 0.00 3.16
1989 3700 4.306600 CTGGCAAGTGAACCATTTTTACC 58.693 43.478 0.00 0.00 34.82 2.85
2019 3730 8.806177 GTTTTAGTTGTAAAACGGGATCAAAT 57.194 30.769 5.30 0.00 44.94 2.32
2023 3734 5.048294 AGTTGTAAAACGGGATCAAATGACC 60.048 40.000 0.00 0.00 0.00 4.02
2027 3738 2.706636 CGGGATCAAATGACCGCAT 58.293 52.632 0.00 0.00 39.85 4.73
2029 3740 2.217750 CGGGATCAAATGACCGCATTA 58.782 47.619 0.00 0.00 43.71 1.90
2041 3752 6.671614 ATGACCGCATTATTTAGACGAAAA 57.328 33.333 0.00 0.00 0.00 2.29
2042 3753 6.671614 TGACCGCATTATTTAGACGAAAAT 57.328 33.333 0.00 0.00 33.69 1.82
2044 3755 6.964370 TGACCGCATTATTTAGACGAAAATTG 59.036 34.615 0.00 0.00 31.63 2.32
2046 3757 5.173131 CCGCATTATTTAGACGAAAATTGCC 59.827 40.000 0.00 0.00 31.63 4.52
2047 3758 5.971202 CGCATTATTTAGACGAAAATTGCCT 59.029 36.000 0.00 0.00 31.63 4.75
2048 3759 6.472163 CGCATTATTTAGACGAAAATTGCCTT 59.528 34.615 0.00 0.00 31.63 4.35
2049 3760 7.305418 CGCATTATTTAGACGAAAATTGCCTTC 60.305 37.037 0.00 0.00 31.63 3.46
2050 3761 7.702348 GCATTATTTAGACGAAAATTGCCTTCT 59.298 33.333 0.00 0.00 31.63 2.85
2051 3762 9.226345 CATTATTTAGACGAAAATTGCCTTCTC 57.774 33.333 0.00 0.00 31.63 2.87
2052 3763 4.921470 TTAGACGAAAATTGCCTTCTCG 57.079 40.909 0.00 0.00 35.68 4.04
2053 3764 2.076863 AGACGAAAATTGCCTTCTCGG 58.923 47.619 0.00 0.00 33.89 4.63
2054 3765 1.130561 GACGAAAATTGCCTTCTCGGG 59.869 52.381 0.00 0.00 33.89 5.14
2055 3766 1.271163 ACGAAAATTGCCTTCTCGGGA 60.271 47.619 0.00 0.00 33.89 5.14
2079 3790 7.173907 GGAAGAAAATGTCATGTCTTCTGAAGA 59.826 37.037 24.87 15.82 43.56 2.87
2112 3824 4.104086 TCTCCCCACTTCATCACAACTAT 58.896 43.478 0.00 0.00 0.00 2.12
2143 3855 0.961019 AATTGTTCGCATGTGCCACT 59.039 45.000 0.00 0.00 37.91 4.00
2147 3859 2.324330 TTCGCATGTGCCACTTCCG 61.324 57.895 0.00 0.00 37.91 4.30
2157 3869 3.777925 CACTTCCGCTGGCGAACG 61.778 66.667 16.79 6.24 42.83 3.95
2160 3872 3.011760 CTTCCGCTGGCGAACGTTC 62.012 63.158 18.47 18.47 42.83 3.95
2242 3957 7.453126 TCCCCAATAATTTGTCACTTTATGTGT 59.547 33.333 0.00 0.00 46.27 3.72
2243 3958 7.545265 CCCCAATAATTTGTCACTTTATGTGTG 59.455 37.037 0.00 0.00 46.27 3.82
2244 3959 8.087750 CCCAATAATTTGTCACTTTATGTGTGT 58.912 33.333 0.00 0.00 46.27 3.72
2265 3980 0.170339 GCCTATTTGTTGGTGCGGAC 59.830 55.000 0.00 0.00 0.00 4.79
2288 4003 2.411547 CCATTCGACTTCGCTCACAAAC 60.412 50.000 0.00 0.00 39.60 2.93
2293 4008 0.940126 ACTTCGCTCACAAACAGCAG 59.060 50.000 0.00 0.00 36.61 4.24
2296 4011 1.202568 CGCTCACAAACAGCAGACG 59.797 57.895 0.00 0.00 36.61 4.18
2323 4038 6.201044 CACGTACCAAGAGTCCATAATTGATC 59.799 42.308 0.00 0.00 0.00 2.92
2324 4039 5.402568 CGTACCAAGAGTCCATAATTGATCG 59.597 44.000 0.00 0.00 0.00 3.69
2503 4237 4.649088 AGTTTAAAACTCACCAGCCAAC 57.351 40.909 0.00 0.00 37.02 3.77
2534 4268 4.400251 CCTCTTAATCTGAATTTGGCTGCA 59.600 41.667 0.50 0.00 0.00 4.41
2538 4272 7.037438 TCTTAATCTGAATTTGGCTGCATTTC 58.963 34.615 0.50 0.00 0.00 2.17
2541 4275 2.235402 CTGAATTTGGCTGCATTTCCCT 59.765 45.455 0.50 0.00 0.00 4.20
2542 4276 2.234414 TGAATTTGGCTGCATTTCCCTC 59.766 45.455 0.50 0.00 0.00 4.30
2543 4277 0.819582 ATTTGGCTGCATTTCCCTCG 59.180 50.000 0.50 0.00 0.00 4.63
2562 4307 2.165234 TCGATATAGCTCTCCTGCATGC 59.835 50.000 11.82 11.82 34.99 4.06
2620 4366 7.678837 ACAACCCAAATAATCACATGTCAAAT 58.321 30.769 0.00 0.00 0.00 2.32
2707 4455 2.524569 AAAAATGGGTCGTGGCTTTG 57.475 45.000 0.00 0.00 0.00 2.77
2753 4527 7.937700 TGGATTGAGGGAGTATTTTCTAGAT 57.062 36.000 0.00 0.00 0.00 1.98
5930 8231 6.358974 TTTCTAACAGATCCATCTCACACA 57.641 37.500 0.00 0.00 34.22 3.72
5963 8264 3.780294 TGTGGGTGATATTCCTAGCTGTT 59.220 43.478 0.00 0.00 0.00 3.16
5964 8265 4.227300 TGTGGGTGATATTCCTAGCTGTTT 59.773 41.667 0.00 0.00 0.00 2.83
6019 8320 6.425721 GCTCTTCTCGCTCTTCTCTATACTAA 59.574 42.308 0.00 0.00 0.00 2.24
6272 8590 1.544691 CGTGTACAGAGGGTTGCTACT 59.455 52.381 0.00 0.00 0.00 2.57
6315 8633 1.153086 GGTGAAGGAGATGCGGCAT 60.153 57.895 16.65 16.65 0.00 4.40
6329 8647 0.527113 CGGCATCCAACATTGAAGCA 59.473 50.000 0.00 0.00 0.00 3.91
6364 8682 0.101219 CGTGCATGAGATCGAGACCA 59.899 55.000 0.00 0.00 0.00 4.02
6366 8684 2.030805 CGTGCATGAGATCGAGACCATA 60.031 50.000 0.00 0.00 0.00 2.74
6405 8723 1.528542 CCTCCTACGGCTCATCGGA 60.529 63.158 0.00 0.00 0.00 4.55
6495 8816 2.280389 CATGATGGCGGCGCTAGT 60.280 61.111 32.30 17.54 0.00 2.57
6679 9000 0.387622 CGGCGACTTTGGACTCGTAA 60.388 55.000 0.00 0.00 32.30 3.18
6988 9309 0.460811 GCAGATGGAGCGTGTCATGA 60.461 55.000 0.00 0.00 0.00 3.07
6999 9320 0.464036 GTGTCATGATCACCGGGCTA 59.536 55.000 6.32 0.00 0.00 3.93
7012 9333 0.172578 CGGGCTAACATGTGTCGAGA 59.827 55.000 0.00 0.00 0.00 4.04
7118 9439 5.188434 CCTCAAAGATACTTCAATGAGGCA 58.812 41.667 13.90 0.00 43.78 4.75
7126 9447 3.771216 ACTTCAATGAGGCACAAGGATT 58.229 40.909 0.00 0.00 0.00 3.01
7175 9499 1.308069 GCTCTCGCAAATGCAAGGGA 61.308 55.000 0.00 0.00 42.21 4.20
7202 9526 4.491676 TCTTTAGCGTAGTGAACATGTCC 58.508 43.478 0.00 0.00 0.00 4.02
7217 9547 8.064222 GTGAACATGTCCGTGAAATAATATGAG 58.936 37.037 0.00 0.00 0.00 2.90
7280 9610 5.450965 GCTCTATAGGCGTGTACAAGGTTAA 60.451 44.000 10.87 0.00 0.00 2.01
7289 9619 6.423604 GGCGTGTACAAGGTTAAGTTAAGTAA 59.576 38.462 10.87 0.00 0.00 2.24
7306 9636 9.819267 AGTTAAGTAAAATATCTCTAGTGTGGC 57.181 33.333 0.00 0.00 0.00 5.01
7325 9655 5.636965 TGTGGCAAATATTTTTGAATCACGG 59.363 36.000 12.18 0.00 44.11 4.94
7355 9687 3.389329 TGGGCACAATGGTTGTAACATTT 59.611 39.130 0.00 0.00 43.23 2.32
7358 9690 3.672867 GCACAATGGTTGTAACATTTCCG 59.327 43.478 0.00 0.00 43.23 4.30
7377 9709 2.286950 CCGAAAACACCATGTCACTGTG 60.287 50.000 0.17 0.17 36.11 3.66
7411 9743 6.388435 TCGTCTATTCTTAAAGTAGGGAGC 57.612 41.667 0.00 0.00 0.00 4.70
7485 9818 4.778143 GGCAGGTACCCAGTGCCG 62.778 72.222 23.55 0.33 46.95 5.69
7490 9823 2.280552 GGTACCCAGTGCCGACTCA 61.281 63.158 0.00 0.00 0.00 3.41
7493 9826 1.327690 TACCCAGTGCCGACTCATCC 61.328 60.000 0.00 0.00 0.00 3.51
7510 9843 4.246978 TCATCCAGATCTAGGGAGAGAGA 58.753 47.826 7.76 1.61 36.45 3.10
7511 9844 4.289410 TCATCCAGATCTAGGGAGAGAGAG 59.711 50.000 7.76 0.00 36.45 3.20
7521 9854 4.890499 AGGGAGAGAGAGAAATACTGGA 57.110 45.455 0.00 0.00 0.00 3.86
7529 9862 6.775629 AGAGAGAGAAATACTGGACTGGTATC 59.224 42.308 0.00 0.00 0.00 2.24
7565 9898 4.481368 TGTGTATATTGTGTCTGGGACC 57.519 45.455 0.00 0.00 0.00 4.46
7592 9925 8.637108 TCCATGTGGGGATATATTGTGTATAT 57.363 34.615 0.00 0.00 37.22 0.86
7593 9926 9.067963 TCCATGTGGGGATATATTGTGTATATT 57.932 33.333 0.00 0.00 37.22 1.28
7594 9927 9.123902 CCATGTGGGGATATATTGTGTATATTG 57.876 37.037 0.00 0.00 31.80 1.90
7595 9928 9.685276 CATGTGGGGATATATTGTGTATATTGT 57.315 33.333 0.00 0.00 31.80 2.71
7596 9929 9.685276 ATGTGGGGATATATTGTGTATATTGTG 57.315 33.333 0.00 0.00 31.80 3.33
7597 9930 8.664992 TGTGGGGATATATTGTGTATATTGTGT 58.335 33.333 0.00 0.00 31.80 3.72
7613 9946 3.931907 TGTGTATAGAAGCTGGGCATT 57.068 42.857 0.00 0.00 0.00 3.56
7624 9957 1.346068 GCTGGGCATTGGGTGTAAAAA 59.654 47.619 0.00 0.00 0.00 1.94
7643 9976 9.155975 TGTAAAAATAGAAAGCAAAAACAAGCA 57.844 25.926 0.00 0.00 0.00 3.91
7649 9982 2.328819 AGCAAAAACAAGCATGCCAA 57.671 40.000 15.66 0.00 39.59 4.52
7653 9986 3.559242 GCAAAAACAAGCATGCCAAGTTA 59.441 39.130 15.66 0.00 32.73 2.24
7657 9990 6.588719 AAAACAAGCATGCCAAGTTAGATA 57.411 33.333 15.66 0.00 0.00 1.98
7670 10003 8.980596 TGCCAAGTTAGATATTCAATGGATTTT 58.019 29.630 0.00 0.00 0.00 1.82
7801 10136 9.515020 TTGTTCATGAAATTTAGAAGTGTTCAC 57.485 29.630 10.35 0.00 31.45 3.18
7806 10141 6.370593 TGAAATTTAGAAGTGTTCACGCATC 58.629 36.000 0.00 0.00 0.00 3.91
7921 10271 2.073776 ACCCTGGGAGGAACAGAAAAT 58.926 47.619 22.23 0.00 37.67 1.82
7965 10315 7.886629 ATGCAGTCATAATACCTCACAATTT 57.113 32.000 0.00 0.00 0.00 1.82
7983 10333 6.084939 CACAATTTATCGTCACAAAGTCAACG 59.915 38.462 0.00 0.00 36.50 4.10
8003 10353 6.690957 TCAACGAACTGAATGTAAGCAAAAAG 59.309 34.615 0.00 0.00 0.00 2.27
8112 10466 6.397831 CACCTTTGTGTGAAAATATGCATG 57.602 37.500 10.16 0.00 38.55 4.06
8113 10467 6.157904 CACCTTTGTGTGAAAATATGCATGA 58.842 36.000 10.16 0.00 38.55 3.07
8114 10468 6.645827 CACCTTTGTGTGAAAATATGCATGAA 59.354 34.615 10.16 0.00 38.55 2.57
8115 10469 6.869913 ACCTTTGTGTGAAAATATGCATGAAG 59.130 34.615 10.16 0.00 0.00 3.02
8116 10470 6.869913 CCTTTGTGTGAAAATATGCATGAAGT 59.130 34.615 10.16 0.00 0.00 3.01
8117 10471 7.148705 CCTTTGTGTGAAAATATGCATGAAGTG 60.149 37.037 10.16 0.00 0.00 3.16
8118 10472 5.712004 TGTGTGAAAATATGCATGAAGTGG 58.288 37.500 10.16 0.00 0.00 4.00
8119 10473 5.104374 GTGTGAAAATATGCATGAAGTGGG 58.896 41.667 10.16 0.00 0.00 4.61
8120 10474 4.771577 TGTGAAAATATGCATGAAGTGGGT 59.228 37.500 10.16 0.00 0.00 4.51
8121 10475 5.245751 TGTGAAAATATGCATGAAGTGGGTT 59.754 36.000 10.16 0.00 0.00 4.11
8122 10476 6.165577 GTGAAAATATGCATGAAGTGGGTTT 58.834 36.000 10.16 0.00 0.00 3.27
8123 10477 6.650390 GTGAAAATATGCATGAAGTGGGTTTT 59.350 34.615 10.16 4.00 0.00 2.43
8124 10478 6.873076 TGAAAATATGCATGAAGTGGGTTTTC 59.127 34.615 10.16 12.00 35.03 2.29
8125 10479 6.610075 AAATATGCATGAAGTGGGTTTTCT 57.390 33.333 10.16 0.00 0.00 2.52
8126 10480 6.610075 AATATGCATGAAGTGGGTTTTCTT 57.390 33.333 10.16 0.00 0.00 2.52
8127 10481 4.961438 ATGCATGAAGTGGGTTTTCTTT 57.039 36.364 0.00 0.00 0.00 2.52
8128 10482 4.751767 TGCATGAAGTGGGTTTTCTTTT 57.248 36.364 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.683179 GGCATGGTGGGGTTTCTACC 60.683 60.000 0.00 0.00 44.22 3.18
8 9 0.039035 TGGCATGGTGGGGTTTCTAC 59.961 55.000 0.00 0.00 0.00 2.59
9 10 0.780637 TTGGCATGGTGGGGTTTCTA 59.219 50.000 0.00 0.00 0.00 2.10
10 11 0.105246 TTTGGCATGGTGGGGTTTCT 60.105 50.000 0.00 0.00 0.00 2.52
11 12 0.983467 ATTTGGCATGGTGGGGTTTC 59.017 50.000 0.00 0.00 0.00 2.78
12 13 1.443852 AATTTGGCATGGTGGGGTTT 58.556 45.000 0.00 0.00 0.00 3.27
13 14 1.350684 GAAATTTGGCATGGTGGGGTT 59.649 47.619 0.00 0.00 0.00 4.11
14 15 0.983467 GAAATTTGGCATGGTGGGGT 59.017 50.000 0.00 0.00 0.00 4.95
15 16 0.982704 TGAAATTTGGCATGGTGGGG 59.017 50.000 0.00 0.00 0.00 4.96
16 17 2.027007 ACATGAAATTTGGCATGGTGGG 60.027 45.455 18.79 0.83 44.64 4.61
17 18 3.337694 ACATGAAATTTGGCATGGTGG 57.662 42.857 18.79 1.11 44.64 4.61
18 19 5.692613 AAAACATGAAATTTGGCATGGTG 57.307 34.783 18.79 2.52 41.29 4.17
19 20 7.814264 TTAAAAACATGAAATTTGGCATGGT 57.186 28.000 18.79 12.63 43.82 3.55
20 21 8.566260 TCTTTAAAAACATGAAATTTGGCATGG 58.434 29.630 18.79 6.39 44.64 3.66
21 22 9.384682 GTCTTTAAAAACATGAAATTTGGCATG 57.615 29.630 14.97 14.97 45.56 4.06
22 23 9.341078 AGTCTTTAAAAACATGAAATTTGGCAT 57.659 25.926 0.00 0.00 0.00 4.40
23 24 8.729805 AGTCTTTAAAAACATGAAATTTGGCA 57.270 26.923 0.00 0.00 0.00 4.92
77 79 8.007405 TCGACTCTGAACAATATGGAGATTAA 57.993 34.615 0.00 0.00 0.00 1.40
81 83 4.950475 ACTCGACTCTGAACAATATGGAGA 59.050 41.667 0.00 0.00 0.00 3.71
88 90 3.862642 GCCAAGACTCGACTCTGAACAAT 60.863 47.826 0.00 0.00 0.00 2.71
90 92 1.000163 GCCAAGACTCGACTCTGAACA 60.000 52.381 0.00 0.00 0.00 3.18
91 93 1.000163 TGCCAAGACTCGACTCTGAAC 60.000 52.381 0.00 0.00 0.00 3.18
92 94 1.000163 GTGCCAAGACTCGACTCTGAA 60.000 52.381 0.00 0.00 0.00 3.02
93 95 0.598562 GTGCCAAGACTCGACTCTGA 59.401 55.000 0.00 0.00 0.00 3.27
94 96 0.389166 GGTGCCAAGACTCGACTCTG 60.389 60.000 0.00 0.00 0.00 3.35
95 97 1.536943 GGGTGCCAAGACTCGACTCT 61.537 60.000 0.00 0.00 0.00 3.24
96 98 1.079750 GGGTGCCAAGACTCGACTC 60.080 63.158 0.00 0.00 0.00 3.36
97 99 1.534235 AGGGTGCCAAGACTCGACT 60.534 57.895 0.00 0.00 0.00 4.18
98 100 1.374758 CAGGGTGCCAAGACTCGAC 60.375 63.158 0.00 0.00 0.00 4.20
99 101 1.533033 TCAGGGTGCCAAGACTCGA 60.533 57.895 0.00 0.00 0.00 4.04
100 102 1.079543 CTCAGGGTGCCAAGACTCG 60.080 63.158 0.00 0.00 0.00 4.18
101 103 1.298014 CCTCAGGGTGCCAAGACTC 59.702 63.158 0.00 0.00 0.00 3.36
221 316 5.481105 AGCATGTTGGTACCATTTTTCATG 58.519 37.500 17.17 21.97 35.85 3.07
222 317 5.743636 AGCATGTTGGTACCATTTTTCAT 57.256 34.783 17.17 12.24 0.00 2.57
237 332 8.230486 CGACTCTTTAACAAAGATTAGCATGTT 58.770 33.333 2.04 0.00 45.75 2.71
246 341 4.041198 TGGGACCGACTCTTTAACAAAGAT 59.959 41.667 2.04 0.00 45.75 2.40
249 344 3.842007 TGGGACCGACTCTTTAACAAA 57.158 42.857 0.00 0.00 0.00 2.83
268 363 6.380846 TCACCTCATTAGAAATCCCCATTTTG 59.619 38.462 0.00 0.00 31.94 2.44
283 378 9.083422 CAACTATCTTCCTAGATCACCTCATTA 57.917 37.037 0.00 0.00 41.38 1.90
302 397 7.388776 TGGCATGTTATGATAGCTTCAACTATC 59.611 37.037 0.00 4.90 45.86 2.08
306 401 5.756195 TGGCATGTTATGATAGCTTCAAC 57.244 39.130 0.00 0.00 38.03 3.18
307 402 6.964807 ATTGGCATGTTATGATAGCTTCAA 57.035 33.333 0.00 0.00 38.03 2.69
320 415 0.039618 ACCCCTCGAATTGGCATGTT 59.960 50.000 0.00 0.00 0.00 2.71
344 439 8.658609 CATGTTTAGCAAATCCGAAAATGAAAT 58.341 29.630 0.00 0.00 0.00 2.17
355 451 4.082026 AGGCACTTCATGTTTAGCAAATCC 60.082 41.667 0.00 0.00 27.25 3.01
357 453 4.523943 TCAGGCACTTCATGTTTAGCAAAT 59.476 37.500 0.00 0.00 34.60 2.32
370 466 4.553351 GCTTGCAAAATTTTCAGGCACTTC 60.553 41.667 21.32 9.83 34.60 3.01
372 468 2.874086 GCTTGCAAAATTTTCAGGCACT 59.126 40.909 21.32 0.00 43.88 4.40
383 479 4.418392 GAATCGACTGATGCTTGCAAAAT 58.582 39.130 0.00 0.00 34.24 1.82
409 505 3.470567 GCACCGTCTTCAGCGTCG 61.471 66.667 0.00 0.00 0.00 5.12
412 508 2.664851 TTGGCACCGTCTTCAGCG 60.665 61.111 0.00 0.00 0.00 5.18
424 520 4.329545 GGGCTCCTCACGTTGGCA 62.330 66.667 0.00 0.00 0.00 4.92
426 522 1.966451 GTTGGGCTCCTCACGTTGG 60.966 63.158 0.00 0.00 0.00 3.77
443 539 0.036952 CCAGAGTTGATGCTCACCGT 60.037 55.000 0.00 0.00 37.94 4.83
470 566 3.710722 CCAGCGAGGTCCTGGCTT 61.711 66.667 24.55 8.62 42.60 4.35
482 578 2.105128 GTCATCCCGTCTCCAGCG 59.895 66.667 0.00 0.00 0.00 5.18
495 591 0.608130 TCTACCGCTTGCAGTGTCAT 59.392 50.000 0.00 0.00 0.00 3.06
496 592 0.038251 CTCTACCGCTTGCAGTGTCA 60.038 55.000 0.00 0.00 0.00 3.58
497 593 0.243907 TCTCTACCGCTTGCAGTGTC 59.756 55.000 0.00 0.00 0.00 3.67
509 606 0.255318 TCCTCACCTCCGTCTCTACC 59.745 60.000 0.00 0.00 0.00 3.18
514 611 2.218115 CTCCCTCCTCACCTCCGTCT 62.218 65.000 0.00 0.00 0.00 4.18
518 615 2.041405 CCCTCCCTCCTCACCTCC 60.041 72.222 0.00 0.00 0.00 4.30
519 616 2.041405 CCCCTCCCTCCTCACCTC 60.041 72.222 0.00 0.00 0.00 3.85
521 618 4.741239 TGCCCCTCCCTCCTCACC 62.741 72.222 0.00 0.00 0.00 4.02
523 620 1.925455 CTTTGCCCCTCCCTCCTCA 60.925 63.158 0.00 0.00 0.00 3.86
538 647 3.677156 ATTGGCATCCCTCTAAGCTTT 57.323 42.857 3.20 0.00 0.00 3.51
540 649 3.976654 TCTAATTGGCATCCCTCTAAGCT 59.023 43.478 0.00 0.00 0.00 3.74
554 663 2.180204 CCGTGCCGCCTCTAATTGG 61.180 63.158 0.00 0.00 0.00 3.16
556 665 2.513897 GCCGTGCCGCCTCTAATT 60.514 61.111 0.00 0.00 0.00 1.40
557 666 3.106986 ATGCCGTGCCGCCTCTAAT 62.107 57.895 0.00 0.00 0.00 1.73
571 752 1.901833 ACACCCAATTTTCCTCATGCC 59.098 47.619 0.00 0.00 0.00 4.40
572 753 2.299867 ACACACCCAATTTTCCTCATGC 59.700 45.455 0.00 0.00 0.00 4.06
573 754 4.605640 AACACACCCAATTTTCCTCATG 57.394 40.909 0.00 0.00 0.00 3.07
583 764 3.788227 TGAGAGCTAAACACACCCAAT 57.212 42.857 0.00 0.00 0.00 3.16
620 931 7.716560 TGGTGAAATCCAACAGATGATACATAG 59.283 37.037 0.00 0.00 37.61 2.23
690 1001 6.613153 AGTCTAGCTTTTACACTCCTTGAT 57.387 37.500 0.00 0.00 0.00 2.57
691 1002 6.946583 TCTAGTCTAGCTTTTACACTCCTTGA 59.053 38.462 1.60 0.00 0.00 3.02
692 1003 7.030768 GTCTAGTCTAGCTTTTACACTCCTTG 58.969 42.308 1.60 0.00 0.00 3.61
694 1005 6.486941 AGTCTAGTCTAGCTTTTACACTCCT 58.513 40.000 1.60 0.00 0.00 3.69
695 1006 6.762702 AGTCTAGTCTAGCTTTTACACTCC 57.237 41.667 1.60 0.00 0.00 3.85
696 1007 8.083462 ACAAAGTCTAGTCTAGCTTTTACACTC 58.917 37.037 18.71 0.00 33.22 3.51
697 1008 7.953752 ACAAAGTCTAGTCTAGCTTTTACACT 58.046 34.615 18.71 7.55 33.22 3.55
698 1009 8.590719 AACAAAGTCTAGTCTAGCTTTTACAC 57.409 34.615 18.71 5.84 33.22 2.90
736 1049 1.196012 AACAAAGTCCCCCGCAAAAA 58.804 45.000 0.00 0.00 0.00 1.94
743 1056 5.510430 AGATGAGAATTAACAAAGTCCCCC 58.490 41.667 0.00 0.00 0.00 5.40
830 2486 8.928733 TGGATTAGTCAAGTCAAACGTTTATAC 58.071 33.333 14.20 14.48 0.00 1.47
832 2488 7.972832 TGGATTAGTCAAGTCAAACGTTTAT 57.027 32.000 14.20 0.00 0.00 1.40
935 2591 3.402681 CAGGACGATGCTGGGGGT 61.403 66.667 0.00 0.00 31.71 4.95
938 2594 2.184830 CATGCAGGACGATGCTGGG 61.185 63.158 0.00 0.78 46.63 4.45
971 2630 7.512580 GCAGCTAGCTAGTGATCAGCACATA 62.513 48.000 18.86 0.00 44.71 2.29
1315 3014 0.244178 GAGAGGTTGTCCGTCCTGTC 59.756 60.000 0.00 0.00 37.06 3.51
1494 3196 2.280524 CAACCGTGGTTCCAGCGA 60.281 61.111 0.16 0.00 36.00 4.93
1509 3214 3.305314 CCGTTCGAGGGATCCCAA 58.695 61.111 32.69 15.71 38.92 4.12
1628 3336 4.746951 CGTACGTGACGCTCGCCA 62.747 66.667 4.25 0.00 46.27 5.69
1747 3458 2.358247 CTGTACAAGGCCGGCGTT 60.358 61.111 27.85 27.85 0.00 4.84
1842 3553 4.398319 AGATTTGAAGTGGGTTACCTGTG 58.602 43.478 0.00 0.00 37.76 3.66
1855 3566 5.408299 TGGTGTGACATCGTTAGATTTGAAG 59.592 40.000 0.00 0.00 34.23 3.02
1875 3586 0.806868 ATTCGTTCATGCAGCTGGTG 59.193 50.000 17.12 1.76 0.00 4.17
1876 3587 1.538047 AATTCGTTCATGCAGCTGGT 58.462 45.000 17.12 0.00 0.00 4.00
1877 3588 2.163010 AGAAATTCGTTCATGCAGCTGG 59.837 45.455 17.12 0.00 38.86 4.85
1878 3589 3.482722 AGAAATTCGTTCATGCAGCTG 57.517 42.857 10.11 10.11 38.86 4.24
1879 3590 5.587844 AGATTAGAAATTCGTTCATGCAGCT 59.412 36.000 0.00 0.00 38.86 4.24
1880 3591 5.814783 AGATTAGAAATTCGTTCATGCAGC 58.185 37.500 0.00 0.00 38.86 5.25
1881 3592 6.909357 GGAAGATTAGAAATTCGTTCATGCAG 59.091 38.462 0.00 0.00 38.86 4.41
1907 3618 9.280174 ACCGTTGATATATTGGTAAACCTTATG 57.720 33.333 0.02 0.00 36.82 1.90
1915 3626 9.275398 GGACAATTACCGTTGATATATTGGTAA 57.725 33.333 15.92 15.92 46.04 2.85
1947 3658 1.017701 CCCCCTTACAGCGAACGTTC 61.018 60.000 18.47 18.47 0.00 3.95
1962 3673 2.991540 GTTCACTTGCCAGCCCCC 60.992 66.667 0.00 0.00 0.00 5.40
1967 3678 4.306600 GGTAAAAATGGTTCACTTGCCAG 58.693 43.478 0.00 0.00 38.27 4.85
1975 3686 5.838531 AAACTGACGGTAAAAATGGTTCA 57.161 34.783 0.00 0.00 0.00 3.18
1989 3700 5.006552 TCCCGTTTTACAACTAAAACTGACG 59.993 40.000 12.10 0.00 45.21 4.35
2019 3730 6.671614 ATTTTCGTCTAAATAATGCGGTCA 57.328 33.333 0.00 0.00 0.00 4.02
2023 3734 5.971202 AGGCAATTTTCGTCTAAATAATGCG 59.029 36.000 0.00 0.00 34.03 4.73
2027 3738 7.413657 CCGAGAAGGCAATTTTCGTCTAAATAA 60.414 37.037 11.23 0.00 42.38 1.40
2029 3740 5.163754 CCGAGAAGGCAATTTTCGTCTAAAT 60.164 40.000 11.23 0.00 42.38 1.40
2047 3758 4.651778 ACATGACATTTTCTTCCCGAGAA 58.348 39.130 0.00 0.00 42.56 2.87
2048 3759 4.020218 AGACATGACATTTTCTTCCCGAGA 60.020 41.667 0.00 0.00 0.00 4.04
2049 3760 4.256920 AGACATGACATTTTCTTCCCGAG 58.743 43.478 0.00 0.00 0.00 4.63
2050 3761 4.286297 AGACATGACATTTTCTTCCCGA 57.714 40.909 0.00 0.00 0.00 5.14
2051 3762 4.697352 AGAAGACATGACATTTTCTTCCCG 59.303 41.667 22.30 0.00 43.36 5.14
2052 3763 5.707298 TCAGAAGACATGACATTTTCTTCCC 59.293 40.000 22.30 8.81 43.36 3.97
2053 3764 6.808008 TCAGAAGACATGACATTTTCTTCC 57.192 37.500 22.30 11.79 43.36 3.46
2054 3765 8.092521 TCTTCAGAAGACATGACATTTTCTTC 57.907 34.615 20.13 20.13 42.88 2.87
2055 3766 8.455903 TTCTTCAGAAGACATGACATTTTCTT 57.544 30.769 12.75 8.28 37.23 2.52
2079 3790 2.065799 AGTGGGGAGAGGTGACATTTT 58.934 47.619 0.00 0.00 0.00 1.82
2143 3855 3.039588 GAACGTTCGCCAGCGGAA 61.040 61.111 13.36 2.67 40.25 4.30
2157 3869 0.108281 GACCCTCCTAACTGGCGAAC 60.108 60.000 0.00 0.00 35.26 3.95
2160 3872 2.901042 GGACCCTCCTAACTGGCG 59.099 66.667 0.00 0.00 32.53 5.69
2206 3921 9.659135 TGACAAATTATTGGGGATAATCTCAAT 57.341 29.630 0.00 0.00 39.47 2.57
2241 3956 2.159572 CGCACCAACAAATAGGCTACAC 60.160 50.000 0.00 0.00 0.00 2.90
2242 3957 2.080693 CGCACCAACAAATAGGCTACA 58.919 47.619 0.00 0.00 0.00 2.74
2243 3958 1.400494 CCGCACCAACAAATAGGCTAC 59.600 52.381 0.00 0.00 0.00 3.58
2244 3959 1.279558 TCCGCACCAACAAATAGGCTA 59.720 47.619 0.00 0.00 0.00 3.93
2265 3980 1.805539 TGAGCGAAGTCGAATGGCG 60.806 57.895 4.59 4.33 43.02 5.69
2269 3984 2.476619 CTGTTTGTGAGCGAAGTCGAAT 59.523 45.455 4.59 0.00 43.02 3.34
2272 3987 0.111089 GCTGTTTGTGAGCGAAGTCG 60.111 55.000 0.00 0.00 43.27 4.18
2288 4003 0.318360 TTGGTACGTGACGTCTGCTG 60.318 55.000 16.19 6.26 41.54 4.41
2293 4008 1.400759 GGACTCTTGGTACGTGACGTC 60.401 57.143 16.19 9.11 41.54 4.34
2296 4011 4.445452 TTATGGACTCTTGGTACGTGAC 57.555 45.455 0.00 0.00 0.00 3.67
2323 4038 2.435685 ATTAATTTCTGTCGCACGCG 57.564 45.000 3.53 3.53 41.35 6.01
2324 4039 6.087028 TGTTTTTATTAATTTCTGTCGCACGC 59.913 34.615 0.00 0.00 0.00 5.34
2420 4151 7.715266 TGTCACATCAATTTTGGGATGATTA 57.285 32.000 9.74 0.00 42.73 1.75
2496 4230 8.186821 CAGATTAAGAGGATTTAAAGTTGGCTG 58.813 37.037 0.00 0.00 0.00 4.85
2534 4268 4.709397 CAGGAGAGCTATATCGAGGGAAAT 59.291 45.833 0.00 0.00 0.00 2.17
2538 4272 1.748493 GCAGGAGAGCTATATCGAGGG 59.252 57.143 0.00 0.00 0.00 4.30
2541 4275 2.165234 GCATGCAGGAGAGCTATATCGA 59.835 50.000 14.21 0.00 34.99 3.59
2542 4276 2.166050 AGCATGCAGGAGAGCTATATCG 59.834 50.000 21.98 0.00 35.19 2.92
2543 4277 3.448301 AGAGCATGCAGGAGAGCTATATC 59.552 47.826 21.98 3.43 37.48 1.63
2645 4391 5.860648 ATAAAATATCAGACCGGGGGATT 57.139 39.130 6.32 0.00 0.00 3.01
2647 4393 5.132985 TCAAATAAAATATCAGACCGGGGGA 59.867 40.000 6.32 0.00 0.00 4.81
2648 4394 5.381757 TCAAATAAAATATCAGACCGGGGG 58.618 41.667 6.32 0.00 0.00 5.40
2693 4440 1.527380 GAACCAAAGCCACGACCCA 60.527 57.895 0.00 0.00 0.00 4.51
2694 4441 1.515521 CTGAACCAAAGCCACGACCC 61.516 60.000 0.00 0.00 0.00 4.46
2707 4455 2.888834 AAATGTGTTGTGGCTGAACC 57.111 45.000 0.00 0.00 39.84 3.62
2753 4527 7.853929 GCAAAAGAAAACATCGAACTACTACAA 59.146 33.333 0.00 0.00 0.00 2.41
2758 4532 6.636850 ACATGCAAAAGAAAACATCGAACTAC 59.363 34.615 0.00 0.00 0.00 2.73
5909 8210 5.264395 TCTGTGTGAGATGGATCTGTTAGA 58.736 41.667 0.00 0.00 37.25 2.10
5930 8231 6.378280 GGAATATCACCCACATTTTTGTCTCT 59.622 38.462 0.00 0.00 0.00 3.10
6019 8320 4.526650 ACCGTCTTGGCCTTTTCATAAATT 59.473 37.500 3.32 0.00 43.94 1.82
6121 8431 8.952278 TGATTGAATAACATGGTTAGTTGGTAC 58.048 33.333 0.00 0.00 0.00 3.34
6123 8433 7.361713 CGTGATTGAATAACATGGTTAGTTGGT 60.362 37.037 0.00 0.00 0.00 3.67
6204 8522 3.764434 TCCTATCTTGCGAGAAGTTGTCT 59.236 43.478 7.99 0.00 40.25 3.41
6315 8633 1.879380 CGGTTCTGCTTCAATGTTGGA 59.121 47.619 0.00 0.00 0.00 3.53
6329 8647 1.336609 GCACGTAGTTCTTCCGGTTCT 60.337 52.381 0.00 0.00 41.61 3.01
6405 8723 2.125147 CCACCATCGTCGCACCAT 60.125 61.111 0.00 0.00 0.00 3.55
6435 8753 1.062206 GGGTTCGAGCTCGTAGACG 59.938 63.158 33.33 10.06 40.80 4.18
6495 8816 2.487086 CGGCCATGTCAATATTCTCCCA 60.487 50.000 2.24 0.00 0.00 4.37
6679 9000 1.524002 CATGGCGGATGACCTGTCT 59.476 57.895 0.00 0.00 33.31 3.41
6699 9020 4.835891 CGAGGAGTACCCCCGCCT 62.836 72.222 0.00 0.00 37.34 5.52
6735 9056 0.335705 TGGGGTCCATGTAGTCCGTA 59.664 55.000 0.00 0.00 0.00 4.02
6737 9058 0.178068 CTTGGGGTCCATGTAGTCCG 59.822 60.000 0.00 0.00 31.53 4.79
6783 9104 5.280164 CCCAAAGCTGTATATATCAGAGGCA 60.280 44.000 13.25 0.00 35.20 4.75
6930 9251 2.420890 CCTCTCAGCCGCTCATCC 59.579 66.667 0.00 0.00 0.00 3.51
6988 9309 0.618458 ACACATGTTAGCCCGGTGAT 59.382 50.000 0.00 0.00 33.82 3.06
6999 9320 1.733041 CGCCGTCTCGACACATGTT 60.733 57.895 0.00 0.00 0.00 2.71
7091 9412 7.500559 GCCTCATTGAAGTATCTTTGAGGTAAT 59.499 37.037 20.31 0.00 46.32 1.89
7098 9419 5.885230 TGTGCCTCATTGAAGTATCTTTG 57.115 39.130 0.00 0.00 0.00 2.77
7175 9499 6.426937 ACATGTTCACTACGCTAAAGATGTTT 59.573 34.615 0.00 0.00 33.38 2.83
7280 9610 9.819267 GCCACACTAGAGATATTTTACTTAACT 57.181 33.333 0.00 0.00 0.00 2.24
7316 9646 2.490115 GCCCACAAATTACCGTGATTCA 59.510 45.455 4.59 0.00 35.02 2.57
7343 9673 4.741185 GGTGTTTTCGGAAATGTTACAACC 59.259 41.667 3.67 6.48 0.00 3.77
7355 9687 2.217750 CAGTGACATGGTGTTTTCGGA 58.782 47.619 0.00 0.00 0.00 4.55
7358 9690 2.358898 AGCACAGTGACATGGTGTTTTC 59.641 45.455 4.15 0.00 35.05 2.29
7411 9743 6.019075 TCTCGGAAAAATACATCACAATAGCG 60.019 38.462 0.00 0.00 0.00 4.26
7452 9785 1.327690 TGCCCGTATCAGGTGTCTCC 61.328 60.000 0.00 0.00 0.00 3.71
7485 9818 4.042809 TCTCTCCCTAGATCTGGATGAGTC 59.957 50.000 18.42 0.00 32.45 3.36
7490 9823 4.512298 TCTCTCTCTCCCTAGATCTGGAT 58.488 47.826 7.81 0.00 0.00 3.41
7493 9826 7.391554 CAGTATTTCTCTCTCTCCCTAGATCTG 59.608 44.444 5.18 0.00 0.00 2.90
7510 9843 6.875972 AAGTGATACCAGTCCAGTATTTCT 57.124 37.500 0.00 0.00 30.57 2.52
7511 9844 7.103641 TGAAAGTGATACCAGTCCAGTATTTC 58.896 38.462 0.00 0.00 30.57 2.17
7521 9854 4.623932 TTCTGCTGAAAGTGATACCAGT 57.376 40.909 3.21 0.00 35.30 4.00
7529 9862 8.239314 ACAATATACACAATTCTGCTGAAAGTG 58.761 33.333 26.21 26.21 42.60 3.16
7565 9898 4.043310 ACACAATATATCCCCACATGGAGG 59.957 45.833 0.00 0.00 37.96 4.30
7592 9925 3.931907 ATGCCCAGCTTCTATACACAA 57.068 42.857 0.00 0.00 0.00 3.33
7593 9926 3.544684 CAATGCCCAGCTTCTATACACA 58.455 45.455 0.00 0.00 0.00 3.72
7594 9927 2.880890 CCAATGCCCAGCTTCTATACAC 59.119 50.000 0.00 0.00 0.00 2.90
7595 9928 2.158623 CCCAATGCCCAGCTTCTATACA 60.159 50.000 0.00 0.00 0.00 2.29
7596 9929 2.158608 ACCCAATGCCCAGCTTCTATAC 60.159 50.000 0.00 0.00 0.00 1.47
7597 9930 2.135189 ACCCAATGCCCAGCTTCTATA 58.865 47.619 0.00 0.00 0.00 1.31
7598 9931 0.929244 ACCCAATGCCCAGCTTCTAT 59.071 50.000 0.00 0.00 0.00 1.98
7599 9932 0.034186 CACCCAATGCCCAGCTTCTA 60.034 55.000 0.00 0.00 0.00 2.10
7600 9933 1.304713 CACCCAATGCCCAGCTTCT 60.305 57.895 0.00 0.00 0.00 2.85
7605 9938 3.979101 ATTTTTACACCCAATGCCCAG 57.021 42.857 0.00 0.00 0.00 4.45
7613 9946 8.041323 TGTTTTTGCTTTCTATTTTTACACCCA 58.959 29.630 0.00 0.00 0.00 4.51
7624 9957 4.692155 GGCATGCTTGTTTTTGCTTTCTAT 59.308 37.500 18.92 0.00 35.46 1.98
7643 9976 8.716674 AATCCATTGAATATCTAACTTGGCAT 57.283 30.769 0.00 0.00 0.00 4.40
7921 10271 2.477845 TTGCATGCTCTGTAGAAGCA 57.522 45.000 20.33 0.00 43.04 3.91
7965 10315 4.443063 CAGTTCGTTGACTTTGTGACGATA 59.557 41.667 0.00 0.00 43.09 2.92
7983 10333 6.642131 TCATGCTTTTTGCTTACATTCAGTTC 59.358 34.615 0.00 0.00 43.37 3.01
8090 10444 6.343716 TCATGCATATTTTCACACAAAGGT 57.656 33.333 0.00 0.00 0.00 3.50
8091 10445 6.869913 ACTTCATGCATATTTTCACACAAAGG 59.130 34.615 0.00 0.00 0.00 3.11
8092 10446 7.148705 CCACTTCATGCATATTTTCACACAAAG 60.149 37.037 0.00 0.00 0.00 2.77
8093 10447 6.645827 CCACTTCATGCATATTTTCACACAAA 59.354 34.615 0.00 0.00 0.00 2.83
8094 10448 6.157904 CCACTTCATGCATATTTTCACACAA 58.842 36.000 0.00 0.00 0.00 3.33
8095 10449 5.336610 CCCACTTCATGCATATTTTCACACA 60.337 40.000 0.00 0.00 0.00 3.72
8096 10450 5.104374 CCCACTTCATGCATATTTTCACAC 58.896 41.667 0.00 0.00 0.00 3.82
8097 10451 4.771577 ACCCACTTCATGCATATTTTCACA 59.228 37.500 0.00 0.00 0.00 3.58
8098 10452 5.329035 ACCCACTTCATGCATATTTTCAC 57.671 39.130 0.00 0.00 0.00 3.18
8099 10453 5.999205 AACCCACTTCATGCATATTTTCA 57.001 34.783 0.00 0.00 0.00 2.69
8100 10454 7.099120 AGAAAACCCACTTCATGCATATTTTC 58.901 34.615 0.00 6.26 35.01 2.29
8101 10455 7.008021 AGAAAACCCACTTCATGCATATTTT 57.992 32.000 0.00 0.00 0.00 1.82
8102 10456 6.610075 AGAAAACCCACTTCATGCATATTT 57.390 33.333 0.00 0.00 0.00 1.40
8103 10457 6.610075 AAGAAAACCCACTTCATGCATATT 57.390 33.333 0.00 0.00 0.00 1.28
8104 10458 6.610075 AAAGAAAACCCACTTCATGCATAT 57.390 33.333 0.00 0.00 0.00 1.78
8105 10459 6.418057 AAAAGAAAACCCACTTCATGCATA 57.582 33.333 0.00 0.00 0.00 3.14
8106 10460 4.961438 AAAGAAAACCCACTTCATGCAT 57.039 36.364 0.00 0.00 0.00 3.96
8107 10461 4.751767 AAAAGAAAACCCACTTCATGCA 57.248 36.364 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.