Multiple sequence alignment - TraesCS4A01G446400

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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 TraesCS4A01G446400 chr4A 100.000 5791 0 0 1 5791 713930231 713936021 0.000000e+00 10695.0
1 TraesCS4A01G446400 chr4A 83.709 1952 217 56 3479 5364 713895006 713893090 0.000000e+00 1749.0
2 TraesCS4A01G446400 chr4A 90.698 559 26 10 1354 1912 713898481 713897949 0.000000e+00 721.0
3 TraesCS4A01G446400 chr4A 89.573 211 22 0 945 1155 713901949 713901739 9.560000e-68 268.0
4 TraesCS4A01G446400 chr4A 76.453 344 25 22 646 952 713902457 713902133 1.010000e-27 135.0
5 TraesCS4A01G446400 chr7D 95.461 1498 61 5 3896 5391 18809321 18807829 0.000000e+00 2383.0
6 TraesCS4A01G446400 chr7D 94.022 1472 50 16 517 1961 18812937 18811477 0.000000e+00 2196.0
7 TraesCS4A01G446400 chr7D 89.426 1759 107 38 2167 3884 18811216 18809496 0.000000e+00 2145.0
8 TraesCS4A01G446400 chr7D 92.695 835 33 9 1149 1965 18833672 18834496 0.000000e+00 1179.0
9 TraesCS4A01G446400 chr7D 83.311 761 57 19 2538 3247 18834622 18835363 6.330000e-179 638.0
10 TraesCS4A01G446400 chr7D 97.695 347 5 2 1 347 18813749 18813406 1.390000e-165 593.0
11 TraesCS4A01G446400 chr7D 92.347 196 15 0 957 1152 18832227 18832422 4.420000e-71 279.0
12 TraesCS4A01G446400 chr7D 91.549 142 11 1 357 497 18813422 18813281 1.650000e-45 195.0
13 TraesCS4A01G446400 chr7D 77.650 349 24 20 646 959 18830582 18830911 4.640000e-36 163.0
14 TraesCS4A01G446400 chr7D 83.590 195 8 11 1970 2154 18811438 18811258 1.670000e-35 161.0
15 TraesCS4A01G446400 chr7D 89.610 77 5 1 5390 5463 18807655 18807579 1.720000e-15 95.3
16 TraesCS4A01G446400 chr7D 97.143 35 1 0 540 574 462139966 462139932 6.270000e-05 60.2
17 TraesCS4A01G446400 chr7A 90.920 1685 70 35 536 2154 19178990 19177323 0.000000e+00 2187.0
18 TraesCS4A01G446400 chr7A 91.301 1161 77 9 4005 5158 19175343 19174200 0.000000e+00 1563.0
19 TraesCS4A01G446400 chr7A 91.042 1094 81 10 2167 3247 19176865 19175776 0.000000e+00 1461.0
20 TraesCS4A01G446400 chr7A 88.278 691 61 9 1041 1731 19145620 19146290 0.000000e+00 809.0
21 TraesCS4A01G446400 chr7A 89.803 304 17 6 1 304 19179417 19179128 1.520000e-100 377.0
22 TraesCS4A01G446400 chr7A 87.613 331 26 13 5464 5791 710542597 710542279 2.550000e-98 370.0
23 TraesCS4A01G446400 chr7A 86.707 331 29 13 5464 5791 707761345 707761663 2.570000e-93 353.0
24 TraesCS4A01G446400 chr7A 85.833 240 14 1 3323 3542 19175620 19175381 2.700000e-58 237.0
25 TraesCS4A01G446400 chr7A 82.883 222 12 9 641 852 19144260 19144465 5.960000e-40 176.0
26 TraesCS4A01G446400 chr7A 96.923 65 2 0 989 1053 19144591 19144655 6.140000e-20 110.0
27 TraesCS4A01G446400 chr7A 95.000 40 1 1 4029 4068 19175374 19175336 1.740000e-05 62.1
28 TraesCS4A01G446400 chr6D 86.368 939 119 8 988 1920 3314865 3315800 0.000000e+00 1016.0
29 TraesCS4A01G446400 chr6D 89.118 680 74 0 4142 4821 3317518 3318197 0.000000e+00 846.0
30 TraesCS4A01G446400 chr6D 80.357 504 74 18 988 1484 3311409 3311894 5.520000e-95 359.0
31 TraesCS4A01G446400 chr6D 79.755 163 24 7 3849 4003 3317267 3317428 6.140000e-20 110.0
32 TraesCS4A01G446400 chr6B 85.745 940 116 10 988 1916 6602542 6603474 0.000000e+00 977.0
33 TraesCS4A01G446400 chr6B 85.563 942 119 13 990 1920 6683087 6682152 0.000000e+00 970.0
34 TraesCS4A01G446400 chr6B 81.931 1046 139 28 3836 4861 6604929 6605944 0.000000e+00 839.0
35 TraesCS4A01G446400 chr6B 87.517 729 82 1 4142 4861 6681935 6681207 0.000000e+00 833.0
36 TraesCS4A01G446400 chr6B 90.260 308 25 3 5484 5789 18756493 18756189 1.170000e-106 398.0
37 TraesCS4A01G446400 chr6B 87.143 70 9 0 999 1068 6601571 6601640 4.810000e-11 80.5
38 TraesCS4A01G446400 chr6A 85.714 938 121 6 988 1916 2130365 2131298 0.000000e+00 977.0
39 TraesCS4A01G446400 chr6A 82.448 1054 135 31 3836 4869 2132640 2133663 0.000000e+00 876.0
40 TraesCS4A01G446400 chr6A 82.874 508 75 7 988 1484 2127541 2128047 4.120000e-121 446.0
41 TraesCS4A01G446400 chr2B 86.050 638 86 1 4154 4791 727221831 727221197 0.000000e+00 682.0
42 TraesCS4A01G446400 chr2B 91.909 309 21 2 5484 5791 68371894 68372199 4.150000e-116 429.0
43 TraesCS4A01G446400 chr2B 87.915 331 22 8 5464 5791 12252119 12252434 1.970000e-99 374.0
44 TraesCS4A01G446400 chr2D 85.827 635 87 1 4157 4791 598729002 598728371 0.000000e+00 671.0
45 TraesCS4A01G446400 chr3A 90.705 312 22 4 5484 5791 705336677 705336985 5.400000e-110 409.0
46 TraesCS4A01G446400 chr1B 90.291 309 26 2 5484 5791 564122657 564122352 9.040000e-108 401.0
47 TraesCS4A01G446400 chr1B 82.927 328 44 11 5464 5783 509053344 509053021 9.500000e-73 285.0
48 TraesCS4A01G446400 chr1B 97.143 35 1 0 540 574 368707651 368707617 6.270000e-05 60.2
49 TraesCS4A01G446400 chr7B 91.724 290 19 3 5503 5790 624264243 624263957 1.170000e-106 398.0
50 TraesCS4A01G446400 chr5B 89.644 309 25 3 5484 5791 546131043 546130741 2.530000e-103 387.0
51 TraesCS4A01G446400 chr3B 84.100 239 21 3 1607 1842 145882457 145882233 1.260000e-51 215.0
52 TraesCS4A01G446400 chr3B 79.042 167 33 2 1 167 96728646 96728810 4.740000e-21 113.0


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 TraesCS4A01G446400 chr4A 713930231 713936021 5790 False 10695.000000 10695 100.000000 1 5791 1 chr4A.!!$F1 5790
1 TraesCS4A01G446400 chr4A 713893090 713902457 9367 True 718.250000 1749 85.108250 646 5364 4 chr4A.!!$R1 4718
2 TraesCS4A01G446400 chr7D 18807579 18813749 6170 True 1109.757143 2383 91.621857 1 5463 7 chr7D.!!$R2 5462
3 TraesCS4A01G446400 chr7D 18830582 18835363 4781 False 564.750000 1179 86.500750 646 3247 4 chr7D.!!$F1 2601
4 TraesCS4A01G446400 chr7A 19174200 19179417 5217 True 981.183333 2187 90.649833 1 5158 6 chr7A.!!$R2 5157
5 TraesCS4A01G446400 chr7A 19144260 19146290 2030 False 365.000000 809 89.361333 641 1731 3 chr7A.!!$F2 1090
6 TraesCS4A01G446400 chr6D 3311409 3318197 6788 False 582.750000 1016 83.899500 988 4821 4 chr6D.!!$F1 3833
7 TraesCS4A01G446400 chr6B 6681207 6683087 1880 True 901.500000 970 86.540000 990 4861 2 chr6B.!!$R2 3871
8 TraesCS4A01G446400 chr6B 6601571 6605944 4373 False 632.166667 977 84.939667 988 4861 3 chr6B.!!$F1 3873
9 TraesCS4A01G446400 chr6A 2127541 2133663 6122 False 766.333333 977 83.678667 988 4869 3 chr6A.!!$F1 3881
10 TraesCS4A01G446400 chr2B 727221197 727221831 634 True 682.000000 682 86.050000 4154 4791 1 chr2B.!!$R1 637
11 TraesCS4A01G446400 chr2D 598728371 598729002 631 True 671.000000 671 85.827000 4157 4791 1 chr2D.!!$R1 634

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
122 123 0.240945 GCCATCCTTGGTTCAACACG 59.759 55.0 0.00 0.0 45.57 4.49 F
2086 11740 0.250038 GAGTGAAGCTGCTGTGGTCA 60.250 55.0 1.35 0.0 0.00 4.02 F
2087 11741 0.250209 AGTGAAGCTGCTGTGGTCAG 60.250 55.0 1.35 0.0 43.87 3.51 F
2342 12503 0.325296 TGCGGTCCTCCACCTAGATT 60.325 55.0 0.00 0.0 44.21 2.40 F
3745 16157 0.030504 TGCACACAACCAATGCTTCG 59.969 50.0 0.00 0.0 40.13 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2090 11744 0.037590 TATTGCACCACCACCAGTCC 59.962 55.0 0.0 0.0 0.00 3.85 R
3193 13684 0.041238 ACCAGAGGGCACTACTAGCA 59.959 55.0 0.0 0.0 37.90 3.49 R
3343 14156 0.376152 GCTGATGCAACCACGAGATG 59.624 55.0 0.0 0.0 39.41 2.90 R
3827 16239 0.471022 TAGCCCACCACTCTCACACA 60.471 55.0 0.0 0.0 0.00 3.72 R
5529 18380 0.174617 GCCTAGCCTCCGCATATCTC 59.825 60.0 0.0 0.0 37.52 2.75 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
122 123 0.240945 GCCATCCTTGGTTCAACACG 59.759 55.000 0.00 0.00 45.57 4.49
194 195 6.311935 GCCGTAATGTTATTGACTTCAGTACA 59.688 38.462 0.00 0.00 33.10 2.90
195 196 7.148540 GCCGTAATGTTATTGACTTCAGTACAA 60.149 37.037 0.00 0.00 33.10 2.41
311 312 0.524862 CATGTGCTTGCTCCAAGTCC 59.475 55.000 6.80 0.00 42.77 3.85
431 435 2.910579 AGGTACGGCCTCTGCATAA 58.089 52.632 0.00 0.00 46.96 1.90
435 439 0.899019 TACGGCCTCTGCATAACACA 59.101 50.000 0.00 0.00 40.13 3.72
483 487 9.816787 AACAAACCTAAAAATATACTCCCTTCA 57.183 29.630 0.00 0.00 0.00 3.02
534 862 5.481105 ACGTTTTATATTGTGGGACGAAGA 58.519 37.500 0.00 0.00 33.67 2.87
575 903 1.739067 AAGTAAATCAGTCCAGCCGC 58.261 50.000 0.00 0.00 0.00 6.53
579 907 1.888436 AAATCAGTCCAGCCGCGAGA 61.888 55.000 8.23 0.00 0.00 4.04
656 998 2.654912 GAACCGCGACAAGGACACG 61.655 63.158 8.23 0.00 0.00 4.49
735 1091 3.037549 AGGATTGTCCATCACTCTCCTC 58.962 50.000 0.00 0.00 39.61 3.71
740 1096 0.413434 TCCATCACTCTCCTCCACCA 59.587 55.000 0.00 0.00 0.00 4.17
905 1315 1.602851 GCTCATCACCTTGCTATGCTG 59.397 52.381 0.00 0.00 0.00 4.41
906 1316 2.219458 CTCATCACCTTGCTATGCTGG 58.781 52.381 0.00 0.00 0.00 4.85
959 2878 2.202932 CCATTGAGGAGTCCGCGG 60.203 66.667 22.12 22.12 41.22 6.46
965 2884 3.708220 GAGGAGTCCGCGGCTTCAG 62.708 68.421 23.51 0.00 0.00 3.02
1077 7413 2.202851 CTGCTCCACCTAGCGCTG 60.203 66.667 22.90 6.70 45.85 5.18
1103 7448 2.281761 CCTGAACCACCGCAGCTT 60.282 61.111 0.00 0.00 0.00 3.74
1374 10880 0.535335 ACATGGTGTTCGCCGACTAT 59.465 50.000 0.00 0.00 0.00 2.12
1377 10883 1.217244 GGTGTTCGCCGACTATGGT 59.783 57.895 0.00 0.00 0.00 3.55
1916 11453 1.269309 CCTCATCTTCGTAAGCTCCCG 60.269 57.143 0.00 0.00 37.18 5.14
1968 11552 3.813143 CGGCCGCATGCATCAACA 61.813 61.111 14.67 0.00 43.89 3.33
2000 11618 2.224113 TGGTTCTCCGTCAACTTGTACC 60.224 50.000 0.00 0.00 36.30 3.34
2009 11635 2.281762 GTCAACTTGTACCGATCGATGC 59.718 50.000 18.66 2.76 0.00 3.91
2010 11636 1.255342 CAACTTGTACCGATCGATGCG 59.745 52.381 18.66 6.46 0.00 4.73
2085 11739 1.287730 CGAGTGAAGCTGCTGTGGTC 61.288 60.000 1.35 0.00 0.00 4.02
2086 11740 0.250038 GAGTGAAGCTGCTGTGGTCA 60.250 55.000 1.35 0.00 0.00 4.02
2087 11741 0.250209 AGTGAAGCTGCTGTGGTCAG 60.250 55.000 1.35 0.00 43.87 3.51
2088 11742 1.071987 TGAAGCTGCTGTGGTCAGG 59.928 57.895 1.35 0.00 41.57 3.86
2089 11743 1.072159 GAAGCTGCTGTGGTCAGGT 59.928 57.895 1.35 0.00 43.28 4.00
2090 11744 1.228063 AAGCTGCTGTGGTCAGGTG 60.228 57.895 1.35 0.00 40.91 4.00
2091 11745 2.670934 GCTGCTGTGGTCAGGTGG 60.671 66.667 0.00 0.00 41.57 4.61
2092 11746 3.150949 CTGCTGTGGTCAGGTGGA 58.849 61.111 0.00 0.00 41.57 4.02
2093 11747 1.302033 CTGCTGTGGTCAGGTGGAC 60.302 63.158 0.00 0.00 46.20 4.02
2094 11748 1.762522 CTGCTGTGGTCAGGTGGACT 61.763 60.000 0.00 0.00 46.16 3.85
2128 11782 1.213296 ATAATTGTGGGGTCGGAGCT 58.787 50.000 7.19 0.00 0.00 4.09
2134 11788 2.359169 TGGGGTCGGAGCTTAGCTG 61.359 63.158 13.01 0.00 39.88 4.24
2147 11801 1.347707 CTTAGCTGGTGGAGTGGTTGA 59.652 52.381 0.00 0.00 0.00 3.18
2150 11804 0.954452 GCTGGTGGAGTGGTTGAAAG 59.046 55.000 0.00 0.00 0.00 2.62
2151 11805 1.476833 GCTGGTGGAGTGGTTGAAAGA 60.477 52.381 0.00 0.00 0.00 2.52
2163 11822 5.297776 AGTGGTTGAAAGAGAGACAAATGTG 59.702 40.000 0.00 0.00 0.00 3.21
2213 12313 6.474751 GGTTTCGTTACCATGATGAGTACTAC 59.525 42.308 0.00 0.00 38.12 2.73
2291 12395 1.160137 GTGTGACCGTCCGTACTACT 58.840 55.000 0.00 0.00 0.00 2.57
2295 12399 2.289002 GTGACCGTCCGTACTACTATGG 59.711 54.545 0.00 0.00 0.00 2.74
2342 12503 0.325296 TGCGGTCCTCCACCTAGATT 60.325 55.000 0.00 0.00 44.21 2.40
2351 12528 6.284459 GTCCTCCACCTAGATTAAGACAATG 58.716 44.000 0.00 0.00 0.00 2.82
2352 12529 5.366768 TCCTCCACCTAGATTAAGACAATGG 59.633 44.000 0.00 0.00 0.00 3.16
2353 12530 5.036117 TCCACCTAGATTAAGACAATGGC 57.964 43.478 0.00 0.00 0.00 4.40
2400 12604 2.482142 GGTGTTGGAAAATTGCCGTCAA 60.482 45.455 0.00 0.00 36.51 3.18
2469 12692 8.085296 AGAATTAGGCTATCGTAGAAATGACTG 58.915 37.037 0.00 0.00 43.58 3.51
2502 12838 5.192327 ACCACTACGTGCCATATAGTTAC 57.808 43.478 0.00 0.00 31.34 2.50
2577 12913 5.986135 TCTGTAGCAAGTCTCAAGAGTTTTC 59.014 40.000 0.00 0.00 35.65 2.29
2648 12986 1.546923 CATCAACAAATGCTGAGGCCA 59.453 47.619 5.01 0.00 37.74 5.36
2649 12987 1.927487 TCAACAAATGCTGAGGCCAT 58.073 45.000 5.01 0.00 37.74 4.40
2707 13046 4.352600 CGGTTACGTATCTGTCACTCTT 57.647 45.455 0.00 0.00 34.81 2.85
2713 13052 3.191581 ACGTATCTGTCACTCTTGGTCTG 59.808 47.826 0.00 0.00 0.00 3.51
2749 13088 2.623416 TCGGTCGATAGCAATCACTCAT 59.377 45.455 0.00 0.00 31.93 2.90
2849 13188 6.039493 TGAAGGTGATACCGATTTCTCTAGTC 59.961 42.308 0.00 0.00 44.90 2.59
2911 13319 4.763793 CCCCTTGAAATGATATAGGCACAG 59.236 45.833 0.00 0.00 0.00 3.66
3058 13477 8.696043 AATCTGATGTGGCAGCTTATTTAATA 57.304 30.769 0.00 0.00 35.86 0.98
3087 13506 9.346725 GAAAGTGAGTTTTATTGCCTCTTATTG 57.653 33.333 0.00 0.00 0.00 1.90
3135 13598 7.648039 AAGAGTACCTTTAGATGGAGTACAG 57.352 40.000 0.00 0.00 36.58 2.74
3137 13600 3.802948 ACCTTTAGATGGAGTACAGCG 57.197 47.619 0.00 0.00 41.32 5.18
3270 13761 5.633655 TTAAATATTACTCCCTGCCGGAA 57.366 39.130 5.05 0.00 41.40 4.30
3271 13762 3.487120 AATATTACTCCCTGCCGGAAC 57.513 47.619 5.05 0.00 41.40 3.62
3297 13846 7.826918 TTTGTAAGTAATTACCACTTTGCCT 57.173 32.000 12.05 0.00 37.42 4.75
3315 14106 3.519510 TGCCTTTCTAGTGCTTCATACCT 59.480 43.478 0.00 0.00 0.00 3.08
3343 14156 4.894114 ACATAGGAGTACCATACACAGGAC 59.106 45.833 0.00 0.00 38.94 3.85
3352 14165 2.481969 CCATACACAGGACATCTCGTGG 60.482 54.545 0.00 0.00 36.72 4.94
3381 14194 5.072055 TCAGCCATTCATTGAGTTGAAGAA 58.928 37.500 1.45 0.00 38.90 2.52
3388 14201 7.482743 CCATTCATTGAGTTGAAGAATTGTACG 59.517 37.037 0.00 0.00 38.90 3.67
3438 15545 1.202521 TGGTAGCACACACTGACACAG 60.203 52.381 0.00 0.00 37.52 3.66
3452 15559 8.950210 CACACTGACACAGAAGGAAATATTATT 58.050 33.333 5.76 0.00 35.18 1.40
3453 15560 9.520515 ACACTGACACAGAAGGAAATATTATTT 57.479 29.630 5.76 1.25 35.18 1.40
3512 15912 2.225167 ACATTGTGGTAAACCCCGGAAT 60.225 45.455 0.73 0.00 34.29 3.01
3745 16157 0.030504 TGCACACAACCAATGCTTCG 59.969 50.000 0.00 0.00 40.13 3.79
3810 16222 7.319646 AGAGTGAAGACATTTGTGAGATAGAC 58.680 38.462 0.00 0.00 0.00 2.59
3822 16234 4.400567 TGTGAGATAGACATGGAGTGAGTG 59.599 45.833 0.00 0.00 0.00 3.51
3827 16239 2.603021 AGACATGGAGTGAGTGTGACT 58.397 47.619 0.00 0.00 0.00 3.41
3884 16318 2.329379 GTAGGACAGTGTTCTCAAGCG 58.671 52.381 7.55 0.00 0.00 4.68
3885 16319 0.601311 AGGACAGTGTTCTCAAGCGC 60.601 55.000 0.00 0.00 0.00 5.92
3886 16320 1.488957 GACAGTGTTCTCAAGCGCG 59.511 57.895 0.00 0.00 0.00 6.86
3890 16324 1.201825 GTGTTCTCAAGCGCGTGAC 59.798 57.895 22.28 13.73 0.00 3.67
3892 16326 2.027024 TTCTCAAGCGCGTGACGT 59.973 55.556 22.28 0.00 46.11 4.34
3893 16327 1.000233 GTTCTCAAGCGCGTGACGTA 61.000 55.000 22.28 7.97 46.11 3.57
3894 16328 1.000233 TTCTCAAGCGCGTGACGTAC 61.000 55.000 22.28 0.00 46.11 3.67
3969 16576 8.638873 TGTGAGGTGGTTATACATAATACAGAG 58.361 37.037 0.00 0.00 0.00 3.35
4082 16703 5.299949 TCTCGAACACATATAAGCATGCAT 58.700 37.500 21.98 11.22 0.00 3.96
4121 16742 5.410355 AATGCAGCAAAAACATAGTGGAT 57.590 34.783 0.00 0.00 0.00 3.41
4126 16747 4.860907 CAGCAAAAACATAGTGGATCTTGC 59.139 41.667 0.00 0.00 38.51 4.01
4141 16762 5.477291 TGGATCTTGCAATTTTAAACCCGTA 59.523 36.000 0.00 0.00 0.00 4.02
4805 17426 3.003275 ACGCATGATTGTTCGTGTTTCTT 59.997 39.130 0.00 0.00 40.41 2.52
5042 17683 4.593206 ACAAACAGTTGGGATCTCTACTCA 59.407 41.667 6.72 0.00 39.22 3.41
5133 17774 6.072452 TGTTTGCCGTACACATTGATGAATTA 60.072 34.615 0.00 0.00 0.00 1.40
5202 17850 6.543831 ACATACCTCAAAATTCCATGCTCTAC 59.456 38.462 0.00 0.00 0.00 2.59
5206 17854 6.769822 ACCTCAAAATTCCATGCTCTACATAG 59.230 38.462 0.00 0.00 36.64 2.23
5209 17857 6.767902 TCAAAATTCCATGCTCTACATAGGAC 59.232 38.462 0.00 0.00 36.64 3.85
5355 18028 6.155827 CGTGAATTAGAGCCCAAATCAAAAA 58.844 36.000 0.00 0.00 0.00 1.94
5383 18056 2.363276 ACGTCATAGCCGTCCCCA 60.363 61.111 0.00 0.00 31.97 4.96
5400 18248 5.654497 GTCCCCATCACTTTGAATTTCATC 58.346 41.667 0.00 0.00 0.00 2.92
5419 18267 8.776376 TTTCATCAAAAATTTATCTGGCTTCC 57.224 30.769 0.00 0.00 0.00 3.46
5425 18273 9.651913 TCAAAAATTTATCTGGCTTCCAATAAC 57.348 29.630 0.00 0.00 30.80 1.89
5430 18281 4.660789 ATCTGGCTTCCAATAACAATGC 57.339 40.909 0.00 0.00 30.80 3.56
5433 18284 1.134946 GGCTTCCAATAACAATGCGCT 59.865 47.619 9.73 0.00 0.00 5.92
5463 18314 2.768527 AGGGTGTGATCTCATCGTTCAT 59.231 45.455 0.02 0.00 0.00 2.57
5464 18315 2.868583 GGGTGTGATCTCATCGTTCATG 59.131 50.000 0.02 0.00 0.00 3.07
5465 18316 3.525537 GGTGTGATCTCATCGTTCATGT 58.474 45.455 0.02 0.00 33.66 3.21
5466 18317 3.935203 GGTGTGATCTCATCGTTCATGTT 59.065 43.478 0.02 0.00 33.66 2.71
5467 18318 4.201753 GGTGTGATCTCATCGTTCATGTTG 60.202 45.833 0.02 0.00 33.66 3.33
5468 18319 3.934579 TGTGATCTCATCGTTCATGTTGG 59.065 43.478 0.00 0.00 33.66 3.77
5469 18320 4.183865 GTGATCTCATCGTTCATGTTGGA 58.816 43.478 0.00 0.00 33.66 3.53
5470 18321 4.631377 GTGATCTCATCGTTCATGTTGGAA 59.369 41.667 0.00 0.00 33.66 3.53
5471 18322 5.122239 GTGATCTCATCGTTCATGTTGGAAA 59.878 40.000 0.00 0.00 33.66 3.13
5484 18335 3.343380 GTTGGAAACGGTTTGTACCTG 57.657 47.619 11.43 0.00 42.66 4.00
5485 18336 2.684374 GTTGGAAACGGTTTGTACCTGT 59.316 45.455 11.43 0.00 42.66 4.00
5486 18337 2.563702 TGGAAACGGTTTGTACCTGTC 58.436 47.619 11.43 0.00 42.66 3.51
5487 18338 1.528161 GGAAACGGTTTGTACCTGTCG 59.472 52.381 11.43 0.00 42.66 4.35
5488 18339 2.204237 GAAACGGTTTGTACCTGTCGT 58.796 47.619 11.43 0.00 42.66 4.34
5489 18340 3.380142 GAAACGGTTTGTACCTGTCGTA 58.620 45.455 11.43 0.00 42.66 3.43
5490 18341 3.665745 AACGGTTTGTACCTGTCGTAT 57.334 42.857 0.00 0.00 42.66 3.06
5491 18342 3.665745 ACGGTTTGTACCTGTCGTATT 57.334 42.857 0.00 0.00 42.66 1.89
5492 18343 3.319755 ACGGTTTGTACCTGTCGTATTG 58.680 45.455 0.00 0.00 42.66 1.90
5493 18344 3.243839 ACGGTTTGTACCTGTCGTATTGT 60.244 43.478 0.00 0.00 42.66 2.71
5494 18345 4.022416 ACGGTTTGTACCTGTCGTATTGTA 60.022 41.667 0.00 0.00 42.66 2.41
5495 18346 4.922692 CGGTTTGTACCTGTCGTATTGTAA 59.077 41.667 0.00 0.00 42.66 2.41
5496 18347 5.164061 CGGTTTGTACCTGTCGTATTGTAAC 60.164 44.000 0.00 0.00 42.66 2.50
5497 18348 5.695816 GGTTTGTACCTGTCGTATTGTAACA 59.304 40.000 0.00 0.00 41.53 2.41
5498 18349 6.369615 GGTTTGTACCTGTCGTATTGTAACAT 59.630 38.462 0.00 0.00 41.53 2.71
5499 18350 7.545265 GGTTTGTACCTGTCGTATTGTAACATA 59.455 37.037 0.00 0.00 41.53 2.29
5500 18351 8.924691 GTTTGTACCTGTCGTATTGTAACATAA 58.075 33.333 0.00 0.00 0.00 1.90
5501 18352 9.656040 TTTGTACCTGTCGTATTGTAACATAAT 57.344 29.630 0.00 0.00 0.00 1.28
5502 18353 9.656040 TTGTACCTGTCGTATTGTAACATAATT 57.344 29.630 0.00 0.00 0.00 1.40
5503 18354 9.304731 TGTACCTGTCGTATTGTAACATAATTC 57.695 33.333 0.00 0.00 0.00 2.17
5504 18355 9.525409 GTACCTGTCGTATTGTAACATAATTCT 57.475 33.333 0.00 0.00 0.00 2.40
5505 18356 8.420374 ACCTGTCGTATTGTAACATAATTCTG 57.580 34.615 0.00 0.00 0.00 3.02
5506 18357 8.038944 ACCTGTCGTATTGTAACATAATTCTGT 58.961 33.333 0.00 0.00 0.00 3.41
5507 18358 9.524106 CCTGTCGTATTGTAACATAATTCTGTA 57.476 33.333 0.00 0.00 0.00 2.74
5517 18368 9.733556 TGTAACATAATTCTGTATTGTTGGTCT 57.266 29.630 0.00 0.00 0.00 3.85
5543 18394 3.992260 ATATACGAGATATGCGGAGGC 57.008 47.619 0.00 0.00 40.52 4.70
5544 18395 1.840737 ATACGAGATATGCGGAGGCT 58.159 50.000 0.00 0.00 40.82 4.58
5545 18396 2.484742 TACGAGATATGCGGAGGCTA 57.515 50.000 0.00 0.00 40.82 3.93
5546 18397 1.169577 ACGAGATATGCGGAGGCTAG 58.830 55.000 0.00 0.00 40.82 3.42
5547 18398 0.453793 CGAGATATGCGGAGGCTAGG 59.546 60.000 0.00 0.00 40.82 3.02
5548 18399 0.174617 GAGATATGCGGAGGCTAGGC 59.825 60.000 8.55 8.55 40.82 3.93
5558 18409 2.820037 GGCTAGGCCTCACGCAAC 60.820 66.667 9.68 0.00 46.69 4.17
5559 18410 2.820037 GCTAGGCCTCACGCAACC 60.820 66.667 9.68 0.00 40.31 3.77
5560 18411 2.125106 CTAGGCCTCACGCAACCC 60.125 66.667 9.68 0.00 40.31 4.11
5561 18412 2.606519 TAGGCCTCACGCAACCCT 60.607 61.111 9.68 0.00 40.31 4.34
5562 18413 1.305465 TAGGCCTCACGCAACCCTA 60.305 57.895 9.68 0.00 40.31 3.53
5563 18414 0.905809 TAGGCCTCACGCAACCCTAA 60.906 55.000 9.68 0.00 40.31 2.69
5564 18415 1.302993 GGCCTCACGCAACCCTAAA 60.303 57.895 0.00 0.00 40.31 1.85
5565 18416 0.679960 GGCCTCACGCAACCCTAAAT 60.680 55.000 0.00 0.00 40.31 1.40
5566 18417 0.733150 GCCTCACGCAACCCTAAATC 59.267 55.000 0.00 0.00 37.47 2.17
5567 18418 1.948611 GCCTCACGCAACCCTAAATCA 60.949 52.381 0.00 0.00 37.47 2.57
5568 18419 2.432444 CCTCACGCAACCCTAAATCAA 58.568 47.619 0.00 0.00 0.00 2.57
5569 18420 2.817258 CCTCACGCAACCCTAAATCAAA 59.183 45.455 0.00 0.00 0.00 2.69
5570 18421 3.365969 CCTCACGCAACCCTAAATCAAAC 60.366 47.826 0.00 0.00 0.00 2.93
5571 18422 3.482436 TCACGCAACCCTAAATCAAACT 58.518 40.909 0.00 0.00 0.00 2.66
5572 18423 3.500680 TCACGCAACCCTAAATCAAACTC 59.499 43.478 0.00 0.00 0.00 3.01
5573 18424 2.482721 ACGCAACCCTAAATCAAACTCG 59.517 45.455 0.00 0.00 0.00 4.18
5574 18425 2.159572 CGCAACCCTAAATCAAACTCGG 60.160 50.000 0.00 0.00 0.00 4.63
5575 18426 2.817844 GCAACCCTAAATCAAACTCGGT 59.182 45.455 0.00 0.00 0.00 4.69
5576 18427 4.004982 GCAACCCTAAATCAAACTCGGTA 58.995 43.478 0.00 0.00 0.00 4.02
5577 18428 4.638865 GCAACCCTAAATCAAACTCGGTAT 59.361 41.667 0.00 0.00 0.00 2.73
5578 18429 5.818857 GCAACCCTAAATCAAACTCGGTATA 59.181 40.000 0.00 0.00 0.00 1.47
5579 18430 6.238293 GCAACCCTAAATCAAACTCGGTATAC 60.238 42.308 0.00 0.00 0.00 1.47
5580 18431 6.549433 ACCCTAAATCAAACTCGGTATACA 57.451 37.500 5.01 0.00 0.00 2.29
5581 18432 7.133133 ACCCTAAATCAAACTCGGTATACAT 57.867 36.000 5.01 0.00 0.00 2.29
5582 18433 8.253867 ACCCTAAATCAAACTCGGTATACATA 57.746 34.615 5.01 0.00 0.00 2.29
5583 18434 8.365647 ACCCTAAATCAAACTCGGTATACATAG 58.634 37.037 5.01 3.82 0.00 2.23
5584 18435 7.331193 CCCTAAATCAAACTCGGTATACATAGC 59.669 40.741 5.01 0.00 0.00 2.97
5585 18436 7.331193 CCTAAATCAAACTCGGTATACATAGCC 59.669 40.741 5.01 0.00 0.00 3.93
5586 18437 5.801531 ATCAAACTCGGTATACATAGCCA 57.198 39.130 5.01 0.00 0.00 4.75
5587 18438 4.940463 TCAAACTCGGTATACATAGCCAC 58.060 43.478 5.01 0.00 0.00 5.01
5588 18439 4.647853 TCAAACTCGGTATACATAGCCACT 59.352 41.667 5.01 0.00 0.00 4.00
5589 18440 5.128171 TCAAACTCGGTATACATAGCCACTT 59.872 40.000 5.01 0.00 0.00 3.16
5590 18441 5.609533 AACTCGGTATACATAGCCACTTT 57.390 39.130 5.01 0.00 0.00 2.66
5591 18442 5.609533 ACTCGGTATACATAGCCACTTTT 57.390 39.130 5.01 0.00 0.00 2.27
5592 18443 5.985911 ACTCGGTATACATAGCCACTTTTT 58.014 37.500 5.01 0.00 0.00 1.94
5593 18444 6.047231 ACTCGGTATACATAGCCACTTTTTC 58.953 40.000 5.01 0.00 0.00 2.29
5594 18445 5.362263 TCGGTATACATAGCCACTTTTTCC 58.638 41.667 5.01 0.00 0.00 3.13
5595 18446 5.129815 TCGGTATACATAGCCACTTTTTCCT 59.870 40.000 5.01 0.00 0.00 3.36
5596 18447 5.465724 CGGTATACATAGCCACTTTTTCCTC 59.534 44.000 5.01 0.00 0.00 3.71
5597 18448 5.465724 GGTATACATAGCCACTTTTTCCTCG 59.534 44.000 5.01 0.00 0.00 4.63
5598 18449 2.084546 ACATAGCCACTTTTTCCTCGC 58.915 47.619 0.00 0.00 0.00 5.03
5599 18450 1.062587 CATAGCCACTTTTTCCTCGCG 59.937 52.381 0.00 0.00 0.00 5.87
5600 18451 1.296056 TAGCCACTTTTTCCTCGCGC 61.296 55.000 0.00 0.00 0.00 6.86
5601 18452 2.561373 CCACTTTTTCCTCGCGCC 59.439 61.111 0.00 0.00 0.00 6.53
5602 18453 2.173382 CACTTTTTCCTCGCGCCG 59.827 61.111 0.00 0.00 0.00 6.46
5603 18454 2.280592 ACTTTTTCCTCGCGCCGT 60.281 55.556 0.00 0.00 0.00 5.68
5604 18455 2.315386 ACTTTTTCCTCGCGCCGTC 61.315 57.895 0.00 0.00 0.00 4.79
5605 18456 3.348967 CTTTTTCCTCGCGCCGTCG 62.349 63.158 0.00 0.00 39.07 5.12
5624 18475 2.202932 CCCCCTCTTGACATCGCG 60.203 66.667 0.00 0.00 0.00 5.87
5625 18476 2.892425 CCCCTCTTGACATCGCGC 60.892 66.667 0.00 0.00 0.00 6.86
5626 18477 2.892425 CCCTCTTGACATCGCGCC 60.892 66.667 0.00 0.00 0.00 6.53
5627 18478 3.257561 CCTCTTGACATCGCGCCG 61.258 66.667 0.00 0.00 0.00 6.46
5628 18479 3.918220 CTCTTGACATCGCGCCGC 61.918 66.667 0.00 0.00 0.00 6.53
5653 18504 3.034878 ATCGCCACCTCGATCTCG 58.965 61.111 0.00 0.00 44.97 4.04
5654 18505 3.200887 ATCGCCACCTCGATCTCGC 62.201 63.158 0.00 0.00 44.97 5.03
5656 18507 4.194720 GCCACCTCGATCTCGCGT 62.195 66.667 5.77 0.00 39.60 6.01
5657 18508 2.024871 CCACCTCGATCTCGCGTC 59.975 66.667 5.77 0.00 39.60 5.19
5658 18509 2.351322 CACCTCGATCTCGCGTCG 60.351 66.667 5.77 8.86 40.30 5.12
5659 18510 4.239203 ACCTCGATCTCGCGTCGC 62.239 66.667 12.20 7.29 38.88 5.19
5660 18511 4.965858 CCTCGATCTCGCGTCGCC 62.966 72.222 12.44 0.00 38.88 5.54
5704 18555 4.880537 CTCCGCGCGATGGCTTCT 62.881 66.667 34.63 0.00 36.88 2.85
5708 18559 3.127533 GCGCGATGGCTTCTGGTT 61.128 61.111 12.10 0.00 36.88 3.67
5709 18560 3.093278 CGCGATGGCTTCTGGTTC 58.907 61.111 0.00 0.00 36.88 3.62
5710 18561 2.464459 CGCGATGGCTTCTGGTTCC 61.464 63.158 0.00 0.00 36.88 3.62
5711 18562 1.078143 GCGATGGCTTCTGGTTCCT 60.078 57.895 0.00 0.00 35.83 3.36
5712 18563 1.092345 GCGATGGCTTCTGGTTCCTC 61.092 60.000 0.00 0.00 35.83 3.71
5713 18564 0.462759 CGATGGCTTCTGGTTCCTCC 60.463 60.000 0.00 0.00 0.00 4.30
5714 18565 0.915364 GATGGCTTCTGGTTCCTCCT 59.085 55.000 0.00 0.00 37.07 3.69
5715 18566 0.915364 ATGGCTTCTGGTTCCTCCTC 59.085 55.000 0.00 0.00 37.07 3.71
5716 18567 1.201429 TGGCTTCTGGTTCCTCCTCC 61.201 60.000 0.00 0.00 37.07 4.30
5717 18568 1.219393 GCTTCTGGTTCCTCCTCCG 59.781 63.158 0.00 0.00 37.07 4.63
5718 18569 1.219393 CTTCTGGTTCCTCCTCCGC 59.781 63.158 0.00 0.00 37.07 5.54
5719 18570 2.564553 CTTCTGGTTCCTCCTCCGCG 62.565 65.000 0.00 0.00 37.07 6.46
5720 18571 4.148825 CTGGTTCCTCCTCCGCGG 62.149 72.222 22.12 22.12 37.07 6.46
5737 18588 3.962421 GCGATGCAGCTGGCCATC 61.962 66.667 17.12 18.30 43.89 3.51
5738 18589 2.515290 CGATGCAGCTGGCCATCA 60.515 61.111 24.88 12.68 43.89 3.07
5739 18590 1.897137 CGATGCAGCTGGCCATCAT 60.897 57.895 24.88 16.18 43.89 2.45
5740 18591 1.853114 CGATGCAGCTGGCCATCATC 61.853 60.000 24.88 21.01 43.89 2.92
5741 18592 1.853114 GATGCAGCTGGCCATCATCG 61.853 60.000 22.25 0.00 43.89 3.84
5742 18593 3.285215 GCAGCTGGCCATCATCGG 61.285 66.667 17.12 0.00 36.11 4.18
5750 18601 2.203252 CCATCATCGGCCCTGTGG 60.203 66.667 0.00 2.49 0.00 4.17
5751 18602 2.591753 CATCATCGGCCCTGTGGT 59.408 61.111 0.00 0.00 0.00 4.16
5752 18603 1.820906 CATCATCGGCCCTGTGGTG 60.821 63.158 0.00 0.00 0.00 4.17
5753 18604 1.995066 ATCATCGGCCCTGTGGTGA 60.995 57.895 0.00 0.00 0.00 4.02
5754 18605 2.257409 ATCATCGGCCCTGTGGTGAC 62.257 60.000 0.00 0.00 0.00 3.67
5755 18606 4.082523 ATCGGCCCTGTGGTGACG 62.083 66.667 0.00 0.00 0.00 4.35
5760 18611 4.394712 CCCTGTGGTGACGCCTCC 62.395 72.222 6.60 0.00 41.24 4.30
5761 18612 4.742201 CCTGTGGTGACGCCTCCG 62.742 72.222 6.60 0.00 41.24 4.63
5762 18613 4.742201 CTGTGGTGACGCCTCCGG 62.742 72.222 6.60 0.00 41.24 5.14
5789 18640 4.969196 CGCCGGTCCCATCCATCG 62.969 72.222 1.90 0.00 0.00 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 3.025978 CCAAGATTTGCCATGCTTCCTA 58.974 45.455 0.00 0.00 0.00 2.94
414 417 0.177141 TGTTATGCAGAGGCCGTACC 59.823 55.000 0.00 0.00 40.13 3.34
416 419 0.899019 TGTGTTATGCAGAGGCCGTA 59.101 50.000 0.00 0.00 40.13 4.02
417 420 0.036164 TTGTGTTATGCAGAGGCCGT 59.964 50.000 0.00 0.00 40.13 5.68
419 422 2.857592 CATTGTGTTATGCAGAGGCC 57.142 50.000 0.00 0.00 40.13 5.19
431 435 4.523943 ACTTATTGGATGTGTGCATTGTGT 59.476 37.500 0.00 0.00 35.07 3.72
435 439 5.981088 TGAACTTATTGGATGTGTGCATT 57.019 34.783 0.00 0.00 35.07 3.56
476 480 8.097038 GCTATGTTACATTATGAGATGAAGGGA 58.903 37.037 2.23 0.00 0.00 4.20
483 487 9.851686 TTTCCAAGCTATGTTACATTATGAGAT 57.148 29.630 2.23 0.00 0.00 2.75
512 534 5.808540 TCTCTTCGTCCCACAATATAAAACG 59.191 40.000 0.00 0.00 0.00 3.60
523 851 3.814283 ACGATATACTCTCTTCGTCCCAC 59.186 47.826 0.00 0.00 40.51 4.61
575 903 1.132453 TGACACTAATCGCTGGTCTCG 59.868 52.381 0.00 0.00 0.00 4.04
579 907 2.695666 AGCTATGACACTAATCGCTGGT 59.304 45.455 0.00 0.00 0.00 4.00
656 998 0.892358 ATGATGCATCCATGGCGACC 60.892 55.000 23.67 0.00 0.00 4.79
735 1091 1.303643 GAGCAAGGGGAGTTGGTGG 60.304 63.158 0.00 0.00 38.25 4.61
758 1124 1.674322 ATTGGTAGTGCGGTGTGCC 60.674 57.895 0.00 0.00 45.60 5.01
959 2878 0.664761 TGTGCAAAGTGAGCTGAAGC 59.335 50.000 0.00 0.00 42.49 3.86
965 2884 4.937781 CAGCTGTGCAAAGTGAGC 57.062 55.556 5.25 0.41 0.00 4.26
1077 7413 4.329545 TGGTTCAGGGAGTGGCGC 62.330 66.667 0.00 0.00 0.00 6.53
1125 7470 4.241555 CCGAGAATGGGGAGGCCG 62.242 72.222 0.00 0.00 0.00 6.13
1377 10883 0.322816 GCATCAGCTTCCACTTGGGA 60.323 55.000 0.00 0.00 46.61 4.37
1916 11453 2.128771 TGGCAGAGGGAATAAAGTGC 57.871 50.000 0.00 0.00 0.00 4.40
1968 11552 6.045072 TGACGGAGAACCAAAATGTACTAT 57.955 37.500 0.00 0.00 35.59 2.12
2009 11635 1.253800 GTATAGATGATGATGCGCGCG 59.746 52.381 28.44 28.44 0.00 6.86
2010 11636 1.253800 CGTATAGATGATGATGCGCGC 59.746 52.381 27.26 27.26 0.00 6.86
2085 11739 2.431683 CCACCACCAGTCCACCTG 59.568 66.667 0.00 0.00 41.15 4.00
2086 11740 2.039831 ACCACCACCAGTCCACCT 60.040 61.111 0.00 0.00 0.00 4.00
2087 11741 2.113139 CACCACCACCAGTCCACC 59.887 66.667 0.00 0.00 0.00 4.61
2088 11742 2.594592 GCACCACCACCAGTCCAC 60.595 66.667 0.00 0.00 0.00 4.02
2089 11743 2.005606 ATTGCACCACCACCAGTCCA 62.006 55.000 0.00 0.00 0.00 4.02
2090 11744 0.037590 TATTGCACCACCACCAGTCC 59.962 55.000 0.00 0.00 0.00 3.85
2091 11745 2.128771 ATATTGCACCACCACCAGTC 57.871 50.000 0.00 0.00 0.00 3.51
2092 11746 3.730215 TTATATTGCACCACCACCAGT 57.270 42.857 0.00 0.00 0.00 4.00
2093 11747 4.402155 ACAATTATATTGCACCACCACCAG 59.598 41.667 0.00 0.00 0.00 4.00
2094 11748 4.159321 CACAATTATATTGCACCACCACCA 59.841 41.667 0.00 0.00 0.00 4.17
2095 11749 4.441356 CCACAATTATATTGCACCACCACC 60.441 45.833 0.00 0.00 0.00 4.61
2096 11750 4.441356 CCCACAATTATATTGCACCACCAC 60.441 45.833 0.00 0.00 0.00 4.16
2097 11751 3.703556 CCCACAATTATATTGCACCACCA 59.296 43.478 0.00 0.00 0.00 4.17
2128 11782 1.429930 TCAACCACTCCACCAGCTAA 58.570 50.000 0.00 0.00 0.00 3.09
2134 11788 2.368875 TCTCTCTTTCAACCACTCCACC 59.631 50.000 0.00 0.00 0.00 4.61
2147 11801 3.809832 CGTGTCCACATTTGTCTCTCTTT 59.190 43.478 0.00 0.00 0.00 2.52
2150 11804 3.026630 TCGTGTCCACATTTGTCTCTC 57.973 47.619 0.00 0.00 0.00 3.20
2151 11805 3.685139 ATCGTGTCCACATTTGTCTCT 57.315 42.857 0.00 0.00 0.00 3.10
2163 11822 2.736682 CCGACGGCAAATCGTGTCC 61.737 63.158 0.00 0.00 43.96 4.02
2213 12313 4.509230 TGAACGTACTACGATAGCTACTGG 59.491 45.833 15.49 0.00 46.05 4.00
2280 12381 3.119388 TGTTGCACCATAGTAGTACGGAC 60.119 47.826 0.00 0.00 0.00 4.79
2291 12395 5.048364 GGTGTACTGAAATTGTTGCACCATA 60.048 40.000 0.00 0.00 39.59 2.74
2295 12399 3.067461 TGGGTGTACTGAAATTGTTGCAC 59.933 43.478 0.00 0.00 0.00 4.57
2342 12503 7.517614 TTAAAGTTGACATGCCATTGTCTTA 57.482 32.000 11.39 1.92 45.07 2.10
2351 12528 3.181496 GCTAGGCTTAAAGTTGACATGCC 60.181 47.826 0.00 0.00 39.19 4.40
2352 12529 3.691609 AGCTAGGCTTAAAGTTGACATGC 59.308 43.478 0.00 0.00 33.89 4.06
2353 12530 5.007136 GCTAGCTAGGCTTAAAGTTGACATG 59.993 44.000 22.10 0.00 40.44 3.21
2358 12535 3.873952 CCAGCTAGCTAGGCTTAAAGTTG 59.126 47.826 18.86 4.42 40.44 3.16
2400 12604 4.223923 TCCACCACCAACAAAAGAAATGTT 59.776 37.500 0.00 0.00 41.50 2.71
2441 12664 8.704234 GTCATTTCTACGATAGCCTAATTCTTG 58.296 37.037 0.00 0.00 42.67 3.02
2469 12692 1.944709 ACGTAGTGGTTTGGTTGCTTC 59.055 47.619 0.00 0.00 42.51 3.86
2502 12838 2.551459 AGCACTGCTTTTAGCTCTTGTG 59.449 45.455 0.00 5.59 42.97 3.33
2600 12938 8.569641 ACATAGCACACGGTTATAAAAAGAAAA 58.430 29.630 0.00 0.00 0.00 2.29
2601 12939 8.018520 CACATAGCACACGGTTATAAAAAGAAA 58.981 33.333 0.00 0.00 0.00 2.52
2602 12940 7.523219 CACATAGCACACGGTTATAAAAAGAA 58.477 34.615 0.00 0.00 0.00 2.52
2638 12976 1.072806 GGATGTATCATGGCCTCAGCA 59.927 52.381 3.32 0.00 42.56 4.41
2641 12979 4.524802 AAAAGGATGTATCATGGCCTCA 57.475 40.909 3.32 0.00 0.00 3.86
2707 13046 2.115427 TCAAGTGTGGACTTCAGACCA 58.885 47.619 0.00 0.00 40.68 4.02
2713 13052 2.338500 GACCGATCAAGTGTGGACTTC 58.662 52.381 0.00 0.00 40.68 3.01
2749 13088 3.117888 GTGATTGCTATCAAGGGGAAGGA 60.118 47.826 12.50 0.00 42.23 3.36
2849 13188 0.179145 CTACGCTACACCAACCGAGG 60.179 60.000 0.00 0.00 0.00 4.63
2911 13319 3.871594 CCACTAATCCGTTGAGAATGACC 59.128 47.826 0.00 0.00 0.00 4.02
3058 13477 6.071320 AGAGGCAATAAAACTCACTTTCCTT 58.929 36.000 0.00 0.00 33.76 3.36
3079 13498 6.145534 TGTGTTTTGCGAGTCTACAATAAGAG 59.854 38.462 0.00 0.00 0.00 2.85
3087 13506 9.262472 CTTATTTAATGTGTTTTGCGAGTCTAC 57.738 33.333 0.00 0.00 0.00 2.59
3135 13598 8.716619 TTTTACAATGTGTTGTATCTTAACGC 57.283 30.769 0.00 0.00 46.91 4.84
3191 13682 0.101399 CAGAGGGCACTACTAGCACG 59.899 60.000 0.00 0.00 41.23 5.34
3193 13684 0.041238 ACCAGAGGGCACTACTAGCA 59.959 55.000 0.00 0.00 37.90 3.49
3195 13686 2.145397 TGACCAGAGGGCACTACTAG 57.855 55.000 0.00 0.00 34.69 2.57
3271 13762 8.357402 AGGCAAAGTGGTAATTACTTACAAAAG 58.643 33.333 15.05 7.75 39.23 2.27
3297 13846 5.932303 GTGTTCAGGTATGAAGCACTAGAAA 59.068 40.000 0.00 0.00 45.96 2.52
3315 14106 5.717654 TGTGTATGGTACTCCTATGTGTTCA 59.282 40.000 0.00 0.00 34.23 3.18
3343 14156 0.376152 GCTGATGCAACCACGAGATG 59.624 55.000 0.00 0.00 39.41 2.90
3352 14165 3.119245 ACTCAATGAATGGCTGATGCAAC 60.119 43.478 0.00 0.00 41.91 4.17
3691 16096 2.239907 GAGGCTGGGAGTTATCCTGTTT 59.760 50.000 0.00 0.00 45.85 2.83
3692 16097 1.840635 GAGGCTGGGAGTTATCCTGTT 59.159 52.381 0.00 0.00 45.85 3.16
3694 16099 1.415659 CAGAGGCTGGGAGTTATCCTG 59.584 57.143 0.00 0.00 45.85 3.86
3810 16222 2.224137 ACACAGTCACACTCACTCCATG 60.224 50.000 0.00 0.00 0.00 3.66
3822 16234 1.539065 CCACCACTCTCACACAGTCAC 60.539 57.143 0.00 0.00 0.00 3.67
3827 16239 0.471022 TAGCCCACCACTCTCACACA 60.471 55.000 0.00 0.00 0.00 3.72
3884 16318 2.251869 TGTCATGTAGTACGTCACGC 57.748 50.000 0.00 0.00 0.00 5.34
3885 16319 5.152923 ACTATGTCATGTAGTACGTCACG 57.847 43.478 0.00 0.00 30.91 4.35
3886 16320 5.964168 GTGACTATGTCATGTAGTACGTCAC 59.036 44.000 14.07 14.07 44.63 3.67
3890 16324 5.277876 GGAGGTGACTATGTCATGTAGTACG 60.278 48.000 3.65 0.00 44.63 3.67
3891 16325 5.009811 GGGAGGTGACTATGTCATGTAGTAC 59.990 48.000 3.65 0.00 44.63 2.73
3892 16326 5.138276 GGGAGGTGACTATGTCATGTAGTA 58.862 45.833 3.65 0.00 44.63 1.82
3893 16327 3.961408 GGGAGGTGACTATGTCATGTAGT 59.039 47.826 3.65 0.00 44.63 2.73
3894 16328 3.960755 TGGGAGGTGACTATGTCATGTAG 59.039 47.826 3.65 0.00 44.63 2.74
3969 16576 9.598517 TCAAAATACATGCAAATTATTTCTCCC 57.401 29.630 9.68 0.00 0.00 4.30
4082 16703 3.057666 TGCATTTTTCTACAATCTGCGCA 60.058 39.130 10.98 10.98 0.00 6.09
4121 16742 4.275443 ACGTACGGGTTTAAAATTGCAAGA 59.725 37.500 21.06 0.00 0.00 3.02
4126 16747 5.508922 GCATACACGTACGGGTTTAAAATTG 59.491 40.000 30.42 14.98 32.06 2.32
4805 17426 2.239400 ACACTGATCGTCCTGAACTCA 58.761 47.619 0.00 0.00 0.00 3.41
5133 17774 3.054875 TGCTCAGCCTGTACATCAATCTT 60.055 43.478 0.00 0.00 0.00 2.40
5145 17786 1.088340 CGATTGGAGTGCTCAGCCTG 61.088 60.000 0.00 0.00 0.00 4.85
5202 17850 2.016318 TCAATTGCGGCAAGTCCTATG 58.984 47.619 21.11 11.92 0.00 2.23
5206 17854 1.795162 CGAATCAATTGCGGCAAGTCC 60.795 52.381 21.11 6.46 0.00 3.85
5209 17857 2.261037 TTCGAATCAATTGCGGCAAG 57.739 45.000 21.11 8.53 0.00 4.01
5243 17908 6.046593 TGTAGACTTTCTTCGTTTGACACAT 58.953 36.000 0.00 0.00 0.00 3.21
5355 18028 3.728845 GGCTATGACGTGGACACATATT 58.271 45.455 0.00 0.00 0.00 1.28
5400 18248 9.434420 TGTTATTGGAAGCCAGATAAATTTTTG 57.566 29.630 0.00 0.00 33.81 2.44
5419 18267 6.798476 CCTATAATGTGAGCGCATTGTTATTG 59.202 38.462 11.47 8.29 39.20 1.90
5425 18273 3.058708 CACCCTATAATGTGAGCGCATTG 60.059 47.826 11.47 4.95 39.20 2.82
5474 18325 6.768029 TGTTACAATACGACAGGTACAAAC 57.232 37.500 0.00 0.00 32.95 2.93
5475 18326 9.656040 ATTATGTTACAATACGACAGGTACAAA 57.344 29.630 0.00 0.00 32.95 2.83
5476 18327 9.656040 AATTATGTTACAATACGACAGGTACAA 57.344 29.630 0.00 0.00 32.95 2.41
5477 18328 9.304731 GAATTATGTTACAATACGACAGGTACA 57.695 33.333 0.00 0.00 32.95 2.90
5478 18329 9.525409 AGAATTATGTTACAATACGACAGGTAC 57.475 33.333 0.00 0.00 32.95 3.34
5479 18330 9.524106 CAGAATTATGTTACAATACGACAGGTA 57.476 33.333 0.00 0.00 35.11 3.08
5480 18331 8.038944 ACAGAATTATGTTACAATACGACAGGT 58.961 33.333 0.00 0.00 0.00 4.00
5481 18332 8.420374 ACAGAATTATGTTACAATACGACAGG 57.580 34.615 0.00 0.00 0.00 4.00
5491 18342 9.733556 AGACCAACAATACAGAATTATGTTACA 57.266 29.630 11.55 0.00 34.56 2.41
5517 18368 8.890718 GCCTCCGCATATCTCGTATATATATAA 58.109 37.037 3.96 0.00 34.03 0.98
5518 18369 8.265764 AGCCTCCGCATATCTCGTATATATATA 58.734 37.037 0.00 0.00 37.52 0.86
5519 18370 7.113437 AGCCTCCGCATATCTCGTATATATAT 58.887 38.462 0.00 0.00 37.52 0.86
5520 18371 6.473758 AGCCTCCGCATATCTCGTATATATA 58.526 40.000 0.00 0.00 37.52 0.86
5521 18372 5.317808 AGCCTCCGCATATCTCGTATATAT 58.682 41.667 0.00 0.00 37.52 0.86
5522 18373 4.715713 AGCCTCCGCATATCTCGTATATA 58.284 43.478 0.00 0.00 37.52 0.86
5523 18374 3.556999 AGCCTCCGCATATCTCGTATAT 58.443 45.455 0.00 0.00 37.52 0.86
5524 18375 3.000684 AGCCTCCGCATATCTCGTATA 57.999 47.619 0.00 0.00 37.52 1.47
5525 18376 1.840737 AGCCTCCGCATATCTCGTAT 58.159 50.000 0.00 0.00 37.52 3.06
5526 18377 2.357075 CTAGCCTCCGCATATCTCGTA 58.643 52.381 0.00 0.00 37.52 3.43
5527 18378 1.169577 CTAGCCTCCGCATATCTCGT 58.830 55.000 0.00 0.00 37.52 4.18
5528 18379 0.453793 CCTAGCCTCCGCATATCTCG 59.546 60.000 0.00 0.00 37.52 4.04
5529 18380 0.174617 GCCTAGCCTCCGCATATCTC 59.825 60.000 0.00 0.00 37.52 2.75
5530 18381 1.261238 GGCCTAGCCTCCGCATATCT 61.261 60.000 0.00 0.00 46.69 1.98
5531 18382 1.219393 GGCCTAGCCTCCGCATATC 59.781 63.158 0.00 0.00 46.69 1.63
5532 18383 3.393360 GGCCTAGCCTCCGCATAT 58.607 61.111 0.00 0.00 46.69 1.78
5542 18393 2.820037 GGTTGCGTGAGGCCTAGC 60.820 66.667 4.42 13.20 42.61 3.42
5543 18394 1.327690 TAGGGTTGCGTGAGGCCTAG 61.328 60.000 4.42 0.65 42.61 3.02
5544 18395 0.905809 TTAGGGTTGCGTGAGGCCTA 60.906 55.000 4.42 0.00 42.61 3.93
5545 18396 1.774894 TTTAGGGTTGCGTGAGGCCT 61.775 55.000 3.86 3.86 42.61 5.19
5546 18397 0.679960 ATTTAGGGTTGCGTGAGGCC 60.680 55.000 0.00 0.00 42.61 5.19
5547 18398 0.733150 GATTTAGGGTTGCGTGAGGC 59.267 55.000 0.00 0.00 43.96 4.70
5548 18399 2.107950 TGATTTAGGGTTGCGTGAGG 57.892 50.000 0.00 0.00 0.00 3.86
5549 18400 3.502211 AGTTTGATTTAGGGTTGCGTGAG 59.498 43.478 0.00 0.00 0.00 3.51
5550 18401 3.482436 AGTTTGATTTAGGGTTGCGTGA 58.518 40.909 0.00 0.00 0.00 4.35
5551 18402 3.666902 CGAGTTTGATTTAGGGTTGCGTG 60.667 47.826 0.00 0.00 0.00 5.34
5552 18403 2.482721 CGAGTTTGATTTAGGGTTGCGT 59.517 45.455 0.00 0.00 0.00 5.24
5553 18404 2.159572 CCGAGTTTGATTTAGGGTTGCG 60.160 50.000 0.00 0.00 0.00 4.85
5554 18405 2.817844 ACCGAGTTTGATTTAGGGTTGC 59.182 45.455 0.00 0.00 0.00 4.17
5555 18406 6.819649 TGTATACCGAGTTTGATTTAGGGTTG 59.180 38.462 0.00 0.00 0.00 3.77
5556 18407 6.949715 TGTATACCGAGTTTGATTTAGGGTT 58.050 36.000 0.00 0.00 0.00 4.11
5557 18408 6.549433 TGTATACCGAGTTTGATTTAGGGT 57.451 37.500 0.00 0.00 0.00 4.34
5558 18409 7.331193 GCTATGTATACCGAGTTTGATTTAGGG 59.669 40.741 0.00 0.00 0.00 3.53
5559 18410 7.331193 GGCTATGTATACCGAGTTTGATTTAGG 59.669 40.741 0.00 0.00 0.00 2.69
5560 18411 7.870954 TGGCTATGTATACCGAGTTTGATTTAG 59.129 37.037 0.00 0.00 0.00 1.85
5561 18412 7.654520 GTGGCTATGTATACCGAGTTTGATTTA 59.345 37.037 0.00 0.00 0.00 1.40
5562 18413 6.482308 GTGGCTATGTATACCGAGTTTGATTT 59.518 38.462 0.00 0.00 0.00 2.17
5563 18414 5.989777 GTGGCTATGTATACCGAGTTTGATT 59.010 40.000 0.00 0.00 0.00 2.57
5564 18415 5.304614 AGTGGCTATGTATACCGAGTTTGAT 59.695 40.000 0.00 0.00 0.00 2.57
5565 18416 4.647853 AGTGGCTATGTATACCGAGTTTGA 59.352 41.667 0.00 0.00 0.00 2.69
5566 18417 4.945246 AGTGGCTATGTATACCGAGTTTG 58.055 43.478 0.00 0.00 0.00 2.93
5567 18418 5.609533 AAGTGGCTATGTATACCGAGTTT 57.390 39.130 0.00 0.00 0.00 2.66
5568 18419 5.609533 AAAGTGGCTATGTATACCGAGTT 57.390 39.130 0.00 0.00 0.00 3.01
5569 18420 5.609533 AAAAGTGGCTATGTATACCGAGT 57.390 39.130 0.00 0.00 0.00 4.18
5570 18421 5.465724 GGAAAAAGTGGCTATGTATACCGAG 59.534 44.000 0.00 0.00 0.00 4.63
5571 18422 5.129815 AGGAAAAAGTGGCTATGTATACCGA 59.870 40.000 0.00 0.00 0.00 4.69
5572 18423 5.365619 AGGAAAAAGTGGCTATGTATACCG 58.634 41.667 0.00 0.00 0.00 4.02
5573 18424 5.465724 CGAGGAAAAAGTGGCTATGTATACC 59.534 44.000 0.00 0.00 0.00 2.73
5574 18425 5.050295 GCGAGGAAAAAGTGGCTATGTATAC 60.050 44.000 0.00 0.00 0.00 1.47
5575 18426 5.054477 GCGAGGAAAAAGTGGCTATGTATA 58.946 41.667 0.00 0.00 0.00 1.47
5576 18427 3.877508 GCGAGGAAAAAGTGGCTATGTAT 59.122 43.478 0.00 0.00 0.00 2.29
5577 18428 3.267483 GCGAGGAAAAAGTGGCTATGTA 58.733 45.455 0.00 0.00 0.00 2.29
5578 18429 2.084546 GCGAGGAAAAAGTGGCTATGT 58.915 47.619 0.00 0.00 0.00 2.29
5579 18430 1.062587 CGCGAGGAAAAAGTGGCTATG 59.937 52.381 0.00 0.00 0.00 2.23
5580 18431 1.369625 CGCGAGGAAAAAGTGGCTAT 58.630 50.000 0.00 0.00 0.00 2.97
5581 18432 1.296056 GCGCGAGGAAAAAGTGGCTA 61.296 55.000 12.10 0.00 0.00 3.93
5582 18433 2.617274 GCGCGAGGAAAAAGTGGCT 61.617 57.895 12.10 0.00 0.00 4.75
5583 18434 2.126850 GCGCGAGGAAAAAGTGGC 60.127 61.111 12.10 0.00 0.00 5.01
5584 18435 2.561373 GGCGCGAGGAAAAAGTGG 59.439 61.111 12.10 0.00 0.00 4.00
5585 18436 2.173382 CGGCGCGAGGAAAAAGTG 59.827 61.111 12.10 0.00 0.00 3.16
5586 18437 2.280592 ACGGCGCGAGGAAAAAGT 60.281 55.556 12.10 0.00 0.00 2.66
5587 18438 2.474712 GACGGCGCGAGGAAAAAG 59.525 61.111 12.10 0.00 0.00 2.27
5588 18439 3.408020 CGACGGCGCGAGGAAAAA 61.408 61.111 12.10 0.00 0.00 1.94
5607 18458 2.202932 CGCGATGTCAAGAGGGGG 60.203 66.667 0.00 0.00 0.00 5.40
5608 18459 2.892425 GCGCGATGTCAAGAGGGG 60.892 66.667 12.10 0.00 0.00 4.79
5609 18460 2.892425 GGCGCGATGTCAAGAGGG 60.892 66.667 12.10 0.00 0.00 4.30
5610 18461 3.257561 CGGCGCGATGTCAAGAGG 61.258 66.667 12.10 0.00 0.00 3.69
5611 18462 3.918220 GCGGCGCGATGTCAAGAG 61.918 66.667 19.09 0.00 0.00 2.85
5637 18488 3.889044 GCGAGATCGAGGTGGCGA 61.889 66.667 6.39 0.00 45.22 5.54
5639 18490 4.194720 ACGCGAGATCGAGGTGGC 62.195 66.667 15.93 0.00 43.37 5.01
5640 18491 2.024871 GACGCGAGATCGAGGTGG 59.975 66.667 15.93 0.00 43.37 4.61
5641 18492 2.351322 CGACGCGAGATCGAGGTG 60.351 66.667 15.93 0.00 43.37 4.00
5642 18493 4.239203 GCGACGCGAGATCGAGGT 62.239 66.667 20.01 2.74 43.37 3.85
5643 18494 4.965858 GGCGACGCGAGATCGAGG 62.966 72.222 20.01 0.00 43.37 4.63
5687 18538 4.880537 AGAAGCCATCGCGCGGAG 62.881 66.667 31.69 21.85 41.18 4.63
5691 18542 3.100862 GAACCAGAAGCCATCGCGC 62.101 63.158 0.00 0.00 41.18 6.86
5692 18543 2.464459 GGAACCAGAAGCCATCGCG 61.464 63.158 0.00 0.00 41.18 5.87
5693 18544 1.078143 AGGAACCAGAAGCCATCGC 60.078 57.895 0.00 0.00 0.00 4.58
5694 18545 0.462759 GGAGGAACCAGAAGCCATCG 60.463 60.000 0.00 0.00 38.79 3.84
5695 18546 0.915364 AGGAGGAACCAGAAGCCATC 59.085 55.000 0.00 0.00 42.04 3.51
5696 18547 0.915364 GAGGAGGAACCAGAAGCCAT 59.085 55.000 0.00 0.00 42.04 4.40
5697 18548 1.201429 GGAGGAGGAACCAGAAGCCA 61.201 60.000 0.00 0.00 42.04 4.75
5698 18549 1.604915 GGAGGAGGAACCAGAAGCC 59.395 63.158 0.00 0.00 42.04 4.35
5699 18550 1.219393 CGGAGGAGGAACCAGAAGC 59.781 63.158 0.00 0.00 42.04 3.86
5700 18551 1.219393 GCGGAGGAGGAACCAGAAG 59.781 63.158 0.00 0.00 42.04 2.85
5701 18552 2.646175 CGCGGAGGAGGAACCAGAA 61.646 63.158 0.00 0.00 42.04 3.02
5702 18553 3.068691 CGCGGAGGAGGAACCAGA 61.069 66.667 0.00 0.00 42.04 3.86
5703 18554 4.148825 CCGCGGAGGAGGAACCAG 62.149 72.222 24.07 0.00 45.00 4.00
5720 18571 3.962421 GATGGCCAGCTGCATCGC 61.962 66.667 15.35 10.59 43.89 4.58
5721 18572 1.853114 GATGATGGCCAGCTGCATCG 61.853 60.000 23.69 6.59 43.89 3.84
5722 18573 1.853114 CGATGATGGCCAGCTGCATC 61.853 60.000 23.69 22.31 43.89 3.91
5723 18574 1.897137 CGATGATGGCCAGCTGCAT 60.897 57.895 23.69 16.69 43.89 3.96
5724 18575 2.515290 CGATGATGGCCAGCTGCA 60.515 61.111 23.69 12.47 43.89 4.41
5725 18576 3.285215 CCGATGATGGCCAGCTGC 61.285 66.667 23.69 12.87 40.16 5.25
5733 18584 2.203252 CCACAGGGCCGATGATGG 60.203 66.667 13.16 12.00 0.00 3.51
5734 18585 1.820906 CACCACAGGGCCGATGATG 60.821 63.158 13.16 0.86 37.90 3.07
5735 18586 1.995066 TCACCACAGGGCCGATGAT 60.995 57.895 13.16 0.00 37.90 2.45
5736 18587 2.606213 TCACCACAGGGCCGATGA 60.606 61.111 13.16 3.28 37.90 2.92
5737 18588 2.436646 GTCACCACAGGGCCGATG 60.437 66.667 0.00 0.00 37.90 3.84
5738 18589 4.082523 CGTCACCACAGGGCCGAT 62.083 66.667 0.00 0.00 37.90 4.18
5743 18594 4.394712 GGAGGCGTCACCACAGGG 62.395 72.222 8.91 0.00 43.14 4.45
5744 18595 4.742201 CGGAGGCGTCACCACAGG 62.742 72.222 8.91 0.00 43.14 4.00
5745 18596 4.742201 CCGGAGGCGTCACCACAG 62.742 72.222 8.91 0.00 46.14 3.66
5772 18623 4.969196 CGATGGATGGGACCGGCG 62.969 72.222 0.00 0.00 0.00 6.46


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

AutoCloner maintained by Alex Coulton.