Multiple sequence alignment - TraesCS7D01G085400

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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 TraesCS7D01G085400 chr7D 100.000 4536 0 0 1 4536 52356675 52352140 0.000000e+00 8377
1 TraesCS7D01G085400 chr7D 94.141 1758 93 4 2783 4536 52470631 52468880 0.000000e+00 2667
2 TraesCS7D01G085400 chr7D 92.358 916 55 8 351 1266 52483549 52482649 0.000000e+00 1290
3 TraesCS7D01G085400 chr7D 96.100 718 22 3 1855 2570 52474416 52473703 0.000000e+00 1166
4 TraesCS7D01G085400 chr7D 95.425 306 12 2 1268 1573 52475417 52475114 1.900000e-133 486
5 TraesCS7D01G085400 chr7D 94.737 190 8 1 2602 2789 52473702 52473513 1.230000e-75 294
6 TraesCS7D01G085400 chr7D 95.429 175 7 1 1574 1748 71982547 71982374 1.240000e-70 278
7 TraesCS7D01G085400 chr7D 93.333 165 7 2 232 392 52483634 52483470 1.630000e-59 241
8 TraesCS7D01G085400 chr7D 96.748 123 4 0 1748 1870 52475121 52474999 5.950000e-49 206
9 TraesCS7D01G085400 chr4A 95.740 1925 71 9 2614 4536 666951337 666949422 0.000000e+00 3090
10 TraesCS7D01G085400 chr4A 95.011 882 40 2 1748 2625 666952272 666951391 0.000000e+00 1382
11 TraesCS7D01G085400 chr4A 87.530 1243 93 34 351 1573 666953465 666952265 0.000000e+00 1380
12 TraesCS7D01G085400 chr4A 82.661 744 102 17 836 1566 17898669 17897940 6.400000e-178 634
13 TraesCS7D01G085400 chr4A 77.140 1028 212 18 3509 4527 18273966 18274979 3.940000e-160 575
14 TraesCS7D01G085400 chr4A 82.081 173 25 4 405 576 17899567 17899400 4.730000e-30 143
15 TraesCS7D01G085400 chr5D 84.653 1427 193 16 3120 4526 4052711 4051291 0.000000e+00 1399
16 TraesCS7D01G085400 chr5D 82.371 1004 162 11 3537 4530 4253154 4252156 0.000000e+00 859
17 TraesCS7D01G085400 chr5D 84.827 837 125 2 3506 4342 27351020 27350186 0.000000e+00 841
18 TraesCS7D01G085400 chr5D 84.006 719 100 12 1749 2457 4054309 4053596 0.000000e+00 676
19 TraesCS7D01G085400 chr5D 83.971 680 76 16 909 1573 4054964 4054303 4.980000e-174 621
20 TraesCS7D01G085400 chr5D 85.059 589 75 11 1760 2341 27354997 27354415 5.050000e-164 588
21 TraesCS7D01G085400 chr5D 83.096 491 58 18 2640 3120 4053381 4052906 1.510000e-114 424
22 TraesCS7D01G085400 chr5D 89.542 306 32 0 1224 1529 27355347 27355042 5.500000e-104 388
23 TraesCS7D01G085400 chr5D 80.247 162 22 5 436 588 4055989 4055829 3.710000e-21 113
24 TraesCS7D01G085400 chr5A 83.883 1030 155 9 3504 4530 4289127 4290148 0.000000e+00 972
25 TraesCS7D01G085400 chr5B 82.191 1123 179 13 3406 4514 7022459 7021344 0.000000e+00 946
26 TraesCS7D01G085400 chr5B 84.456 772 101 9 3760 4530 19737217 19736464 0.000000e+00 743
27 TraesCS7D01G085400 chr5B 85.042 595 76 9 1760 2346 19744471 19743882 1.090000e-165 593
28 TraesCS7D01G085400 chr5B 82.353 663 89 14 919 1572 19745120 19744477 6.630000e-153 551
29 TraesCS7D01G085400 chr5B 80.848 637 102 13 938 1570 6927803 6927183 2.450000e-132 483
30 TraesCS7D01G085400 chr5B 75.461 1031 209 21 3512 4530 64736877 64735879 3.200000e-126 462
31 TraesCS7D01G085400 chr5B 79.167 384 73 6 3383 3762 19742501 19742121 4.500000e-65 259
32 TraesCS7D01G085400 chr7A 96.000 550 21 1 1024 1573 54853468 54852920 0.000000e+00 893
33 TraesCS7D01G085400 chr7A 95.683 556 18 3 2020 2575 54852000 54851451 0.000000e+00 889
34 TraesCS7D01G085400 chr7A 93.189 602 28 4 431 1032 54854131 54853543 0.000000e+00 872
35 TraesCS7D01G085400 chr7A 96.071 280 8 1 1748 2024 54852927 54852648 1.920000e-123 453
36 TraesCS7D01G085400 chr7A 90.594 202 16 3 1562 1761 495505183 495505383 9.680000e-67 265
37 TraesCS7D01G085400 chr7A 93.750 112 4 2 20 128 54854762 54854651 1.010000e-36 165
38 TraesCS7D01G085400 chr3D 84.448 598 87 5 963 1557 418560560 418561154 6.540000e-163 584
39 TraesCS7D01G085400 chr3D 82.660 594 90 6 964 1557 418443145 418443725 8.700000e-142 514
40 TraesCS7D01G085400 chr3D 81.495 535 85 13 1779 2309 418704339 418704863 1.170000e-115 427
41 TraesCS7D01G085400 chr3D 81.781 494 77 12 1779 2269 418481031 418481514 7.070000e-108 401
42 TraesCS7D01G085400 chr3D 95.402 174 7 1 1574 1747 604800472 604800300 4.470000e-70 276
43 TraesCS7D01G085400 chr3B 79.830 471 83 10 1777 2245 545000842 545001302 2.620000e-87 333
44 TraesCS7D01G085400 chr3B 84.242 330 52 0 965 1294 544927683 544928012 5.660000e-84 322
45 TraesCS7D01G085400 chr3B 85.586 111 16 0 965 1075 544835315 544835425 2.870000e-22 117
46 TraesCS7D01G085400 chr6D 92.574 202 10 4 1564 1761 426639476 426639276 7.430000e-73 285
47 TraesCS7D01G085400 chr6D 93.122 189 12 1 1572 1760 345628808 345628621 4.470000e-70 276
48 TraesCS7D01G085400 chr4D 95.977 174 7 0 1574 1747 17560281 17560454 2.670000e-72 283
49 TraesCS7D01G085400 chr4D 95.402 174 7 1 1574 1747 507858196 507858368 4.470000e-70 276
50 TraesCS7D01G085400 chr2A 94.118 187 10 1 1563 1749 207465035 207465220 2.670000e-72 283
51 TraesCS7D01G085400 chr2D 94.944 178 5 3 1574 1751 23041031 23041204 4.470000e-70 276
52 TraesCS7D01G085400 chrUn 85.586 111 16 0 965 1075 438150892 438151002 2.870000e-22 117


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 TraesCS7D01G085400 chr7D 52352140 52356675 4535 True 8377.000000 8377 100.000000 1 4536 1 chr7D.!!$R1 4535
1 TraesCS7D01G085400 chr7D 52468880 52475417 6537 True 963.800000 2667 95.430200 1268 4536 5 chr7D.!!$R3 3268
2 TraesCS7D01G085400 chr7D 52482649 52483634 985 True 765.500000 1290 92.845500 232 1266 2 chr7D.!!$R4 1034
3 TraesCS7D01G085400 chr4A 666949422 666953465 4043 True 1950.666667 3090 92.760333 351 4536 3 chr4A.!!$R2 4185
4 TraesCS7D01G085400 chr4A 18273966 18274979 1013 False 575.000000 575 77.140000 3509 4527 1 chr4A.!!$F1 1018
5 TraesCS7D01G085400 chr4A 17897940 17899567 1627 True 388.500000 634 82.371000 405 1566 2 chr4A.!!$R1 1161
6 TraesCS7D01G085400 chr5D 4252156 4253154 998 True 859.000000 859 82.371000 3537 4530 1 chr5D.!!$R1 993
7 TraesCS7D01G085400 chr5D 4051291 4055989 4698 True 646.600000 1399 83.194600 436 4526 5 chr5D.!!$R2 4090
8 TraesCS7D01G085400 chr5D 27350186 27355347 5161 True 605.666667 841 86.476000 1224 4342 3 chr5D.!!$R3 3118
9 TraesCS7D01G085400 chr5A 4289127 4290148 1021 False 972.000000 972 83.883000 3504 4530 1 chr5A.!!$F1 1026
10 TraesCS7D01G085400 chr5B 7021344 7022459 1115 True 946.000000 946 82.191000 3406 4514 1 chr5B.!!$R2 1108
11 TraesCS7D01G085400 chr5B 19736464 19737217 753 True 743.000000 743 84.456000 3760 4530 1 chr5B.!!$R3 770
12 TraesCS7D01G085400 chr5B 6927183 6927803 620 True 483.000000 483 80.848000 938 1570 1 chr5B.!!$R1 632
13 TraesCS7D01G085400 chr5B 19742121 19745120 2999 True 467.666667 593 82.187333 919 3762 3 chr5B.!!$R5 2843
14 TraesCS7D01G085400 chr5B 64735879 64736877 998 True 462.000000 462 75.461000 3512 4530 1 chr5B.!!$R4 1018
15 TraesCS7D01G085400 chr7A 54851451 54854762 3311 True 654.400000 893 94.938600 20 2575 5 chr7A.!!$R1 2555
16 TraesCS7D01G085400 chr3D 418560560 418561154 594 False 584.000000 584 84.448000 963 1557 1 chr3D.!!$F3 594
17 TraesCS7D01G085400 chr3D 418443145 418443725 580 False 514.000000 514 82.660000 964 1557 1 chr3D.!!$F1 593
18 TraesCS7D01G085400 chr3D 418704339 418704863 524 False 427.000000 427 81.495000 1779 2309 1 chr3D.!!$F4 530

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
19 20 0.111061 ATCCAGCTTGTTCCAGCACA 59.889 50.0 0.00 0.00 42.84 4.57 F
1680 2628 0.039180 TAGCCTGCTATAGCCCGCTA 59.961 55.0 26.87 26.87 42.16 4.26 F
1718 2666 0.035820 TTTTGAGGTCCGCCGCTATT 60.036 50.0 0.00 0.00 40.50 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1699 2647 0.035820 AATAGCGGCGGACCTCAAAA 60.036 50.0 9.78 0.0 0.0 2.44 R
3022 10331 1.065031 CCGCATTTCTTGTTTCGCCG 61.065 55.0 0.00 0.0 0.0 6.46 R
3630 11329 2.526304 TTGGAAGGACAGTGAACTCG 57.474 50.0 0.00 0.0 0.0 4.18 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
18 19 2.952714 ATCCAGCTTGTTCCAGCAC 58.047 52.632 0.00 0.00 42.84 4.40
19 20 0.111061 ATCCAGCTTGTTCCAGCACA 59.889 50.000 0.00 0.00 42.84 4.57
20 21 0.819259 TCCAGCTTGTTCCAGCACAC 60.819 55.000 0.00 0.00 42.84 3.82
21 22 1.102809 CCAGCTTGTTCCAGCACACA 61.103 55.000 0.00 0.00 42.84 3.72
22 23 0.309922 CAGCTTGTTCCAGCACACAG 59.690 55.000 0.00 0.00 42.84 3.66
23 24 0.181114 AGCTTGTTCCAGCACACAGA 59.819 50.000 0.00 0.00 42.84 3.41
38 39 5.986135 AGCACACAGAGTAATCGGATATTTC 59.014 40.000 0.00 0.00 0.00 2.17
96 99 6.239064 GGATCTAGATCGAACCTCTTTGCTTA 60.239 42.308 23.30 0.00 38.69 3.09
128 131 3.390311 TCATGCCTGCAGATCAATCTACT 59.610 43.478 17.39 0.00 34.85 2.57
129 132 3.465742 TGCCTGCAGATCAATCTACTC 57.534 47.619 17.39 0.00 34.85 2.59
130 133 3.036819 TGCCTGCAGATCAATCTACTCT 58.963 45.455 17.39 0.00 34.85 3.24
131 134 3.069300 TGCCTGCAGATCAATCTACTCTC 59.931 47.826 17.39 0.00 34.85 3.20
133 136 3.307674 CTGCAGATCAATCTACTCTCGC 58.692 50.000 8.42 0.00 34.85 5.03
134 137 2.689983 TGCAGATCAATCTACTCTCGCA 59.310 45.455 0.00 0.00 34.85 5.10
135 138 3.049206 GCAGATCAATCTACTCTCGCAC 58.951 50.000 0.00 0.00 34.85 5.34
136 139 3.295785 CAGATCAATCTACTCTCGCACG 58.704 50.000 0.00 0.00 34.85 5.34
137 140 2.946329 AGATCAATCTACTCTCGCACGT 59.054 45.455 0.00 0.00 34.85 4.49
138 141 2.826979 TCAATCTACTCTCGCACGTC 57.173 50.000 0.00 0.00 0.00 4.34
139 142 2.357075 TCAATCTACTCTCGCACGTCT 58.643 47.619 0.00 0.00 0.00 4.18
141 144 3.556365 TCAATCTACTCTCGCACGTCTAG 59.444 47.826 0.00 0.00 0.00 2.43
142 145 2.955477 TCTACTCTCGCACGTCTAGA 57.045 50.000 0.00 0.00 0.00 2.43
145 148 1.080298 ACTCTCGCACGTCTAGACAG 58.920 55.000 22.37 16.39 0.00 3.51
146 149 1.080298 CTCTCGCACGTCTAGACAGT 58.920 55.000 22.37 16.99 0.00 3.55
147 150 0.796927 TCTCGCACGTCTAGACAGTG 59.203 55.000 28.30 28.30 38.18 3.66
191 313 7.484035 AGACAGACAATGAGAAAAGTGTAAC 57.516 36.000 0.00 0.00 0.00 2.50
230 353 2.093341 ACGTCTCTCCTCACCTACTCTC 60.093 54.545 0.00 0.00 0.00 3.20
303 450 3.447586 GTCTAGACAGTGGGCAACATCTA 59.552 47.826 18.20 0.35 39.74 1.98
317 464 6.460123 GGGCAACATCTAAAATTCATGATCGT 60.460 38.462 0.00 0.00 39.74 3.73
353 507 5.423015 CAGCTGAGCTTCTTAAGGTAATCA 58.577 41.667 8.42 2.43 39.77 2.57
381 535 2.634940 AGGACTGCAGTTGAGCTTCTTA 59.365 45.455 22.65 0.00 34.99 2.10
383 537 4.006319 GGACTGCAGTTGAGCTTCTTAAT 58.994 43.478 22.65 0.00 34.99 1.40
496 717 5.479306 TGCTGTCTTTACTTACAGGACATC 58.521 41.667 4.79 0.00 42.72 3.06
527 757 2.542020 TCGTGTTCAGGATGCTTTGA 57.458 45.000 0.00 0.00 34.76 2.69
674 905 3.323979 TGGAGTACTCTGTTCTTTGGGAC 59.676 47.826 21.88 1.78 0.00 4.46
731 982 6.173339 ACTGAGAACCATATGAATTTCACGT 58.827 36.000 3.65 0.00 0.00 4.49
745 1012 5.888412 ATTTCACGTGCAATTCAAAAGAC 57.112 34.783 11.67 0.00 0.00 3.01
746 1013 4.630894 TTCACGTGCAATTCAAAAGACT 57.369 36.364 11.67 0.00 0.00 3.24
748 1015 5.940192 TCACGTGCAATTCAAAAGACTAT 57.060 34.783 11.67 0.00 0.00 2.12
751 1018 6.855914 TCACGTGCAATTCAAAAGACTATTTC 59.144 34.615 11.67 0.00 0.00 2.17
752 1019 6.636447 CACGTGCAATTCAAAAGACTATTTCA 59.364 34.615 0.82 0.00 0.00 2.69
753 1020 6.636850 ACGTGCAATTCAAAAGACTATTTCAC 59.363 34.615 0.00 0.00 0.00 3.18
754 1021 6.183359 CGTGCAATTCAAAAGACTATTTCACG 60.183 38.462 5.94 5.94 39.68 4.35
756 1023 6.636447 TGCAATTCAAAAGACTATTTCACGTG 59.364 34.615 9.94 9.94 0.00 4.49
768 1035 6.734137 ACTATTTCACGTGCAATTCAAAAGA 58.266 32.000 18.30 4.95 0.00 2.52
786 1053 5.428184 AAAGAAGAGTCTAACCTCATGGG 57.572 43.478 0.00 0.00 35.66 4.00
816 1632 7.581213 TCCATTCAAAAGTGACATGTTAAGT 57.419 32.000 0.00 0.00 31.90 2.24
842 1671 3.686241 TGTGACATGTCTCATGCTAAAGC 59.314 43.478 25.55 0.00 42.50 3.51
1107 2054 2.040813 ACTTCTGGAGCACATCACCAAT 59.959 45.455 0.00 0.00 34.98 3.16
1165 2112 5.090757 GCTTTGCAACGGTTTATAAGGTAC 58.909 41.667 0.00 0.00 0.00 3.34
1168 2115 2.030823 GCAACGGTTTATAAGGTACGCC 59.969 50.000 0.00 0.00 0.00 5.68
1193 2140 9.175312 CCTATACAGTAACTCTCAGTTAGTCAA 57.825 37.037 1.46 0.00 41.14 3.18
1350 2298 5.622378 AGAAATTCAGCGAAGAAATTCGTC 58.378 37.500 11.52 0.00 45.45 4.20
1549 2497 7.465353 TGATGTCACATGTATTTGGTTCAAT 57.535 32.000 0.00 0.00 0.00 2.57
1559 2507 9.386010 CATGTATTTGGTTCAATCATCCATTTT 57.614 29.630 0.00 0.00 0.00 1.82
1589 2537 8.757164 AGTGTTTAGCAATGTTTTAAATAGCC 57.243 30.769 0.00 0.00 0.00 3.93
1590 2538 7.540745 AGTGTTTAGCAATGTTTTAAATAGCCG 59.459 33.333 0.00 0.00 0.00 5.52
1591 2539 6.809196 TGTTTAGCAATGTTTTAAATAGCCGG 59.191 34.615 0.00 0.00 0.00 6.13
1592 2540 3.780902 AGCAATGTTTTAAATAGCCGGC 58.219 40.909 21.89 21.89 0.00 6.13
1593 2541 3.447229 AGCAATGTTTTAAATAGCCGGCT 59.553 39.130 34.85 34.85 0.00 5.52
1594 2542 4.642885 AGCAATGTTTTAAATAGCCGGCTA 59.357 37.500 36.88 36.88 0.00 3.93
1595 2543 5.301805 AGCAATGTTTTAAATAGCCGGCTAT 59.698 36.000 37.79 37.79 40.63 2.97
1596 2544 6.488683 AGCAATGTTTTAAATAGCCGGCTATA 59.511 34.615 41.53 28.18 38.20 1.31
1597 2545 6.801862 GCAATGTTTTAAATAGCCGGCTATAG 59.198 38.462 41.53 23.03 38.20 1.31
1598 2546 5.934935 TGTTTTAAATAGCCGGCTATAGC 57.065 39.130 41.53 29.25 38.20 2.97
1599 2547 5.617252 TGTTTTAAATAGCCGGCTATAGCT 58.383 37.500 41.53 30.77 43.20 3.32
1600 2548 5.699458 TGTTTTAAATAGCCGGCTATAGCTC 59.301 40.000 41.53 28.73 40.56 4.09
1601 2549 4.467198 TTAAATAGCCGGCTATAGCTCC 57.533 45.455 41.53 12.16 40.56 4.70
1602 2550 0.818296 AATAGCCGGCTATAGCTCCG 59.182 55.000 41.53 18.50 44.89 4.63
1603 2551 1.668101 ATAGCCGGCTATAGCTCCGC 61.668 60.000 41.03 20.23 44.01 5.54
1604 2552 2.766306 TAGCCGGCTATAGCTCCGCT 62.766 60.000 32.24 25.87 44.01 5.52
1605 2553 2.341101 GCCGGCTATAGCTCCGCTA 61.341 63.158 22.15 0.00 45.55 4.26
1612 2560 3.998156 TAGCTCCGCTATAGCCCG 58.002 61.111 19.00 9.44 41.02 6.13
1613 2561 2.341101 TAGCTCCGCTATAGCCCGC 61.341 63.158 19.00 17.12 41.02 6.13
1614 2562 2.766306 TAGCTCCGCTATAGCCCGCT 62.766 60.000 24.41 24.41 41.02 5.52
1615 2563 2.341101 GCTCCGCTATAGCCCGCTA 61.341 63.158 19.00 0.00 37.91 4.26
1616 2564 1.668101 GCTCCGCTATAGCCCGCTAT 61.668 60.000 19.00 13.46 41.58 2.97
1617 2565 1.676746 CTCCGCTATAGCCCGCTATA 58.323 55.000 19.00 14.20 39.65 1.31
1618 2566 2.231529 CTCCGCTATAGCCCGCTATAT 58.768 52.381 19.00 0.00 39.77 0.86
1619 2567 3.409570 CTCCGCTATAGCCCGCTATATA 58.590 50.000 19.00 0.00 39.77 0.86
1620 2568 3.409570 TCCGCTATAGCCCGCTATATAG 58.590 50.000 19.00 5.30 39.77 1.31
1622 2570 3.579335 GCTATAGCCCGCTATATAGCC 57.421 52.381 25.48 13.82 45.81 3.93
1623 2571 3.158676 GCTATAGCCCGCTATATAGCCT 58.841 50.000 25.48 19.31 45.81 4.58
1624 2572 3.574826 GCTATAGCCCGCTATATAGCCTT 59.425 47.826 25.48 12.81 45.81 4.35
1625 2573 4.039366 GCTATAGCCCGCTATATAGCCTTT 59.961 45.833 25.48 15.29 45.81 3.11
1626 2574 5.453480 GCTATAGCCCGCTATATAGCCTTTT 60.453 44.000 25.48 13.42 45.81 2.27
1627 2575 3.336138 AGCCCGCTATATAGCCTTTTC 57.664 47.619 25.48 12.31 46.34 2.29
1628 2576 2.637872 AGCCCGCTATATAGCCTTTTCA 59.362 45.455 25.48 0.00 46.34 2.69
1629 2577 3.003480 GCCCGCTATATAGCCTTTTCAG 58.997 50.000 25.48 11.73 46.34 3.02
1630 2578 3.003480 CCCGCTATATAGCCTTTTCAGC 58.997 50.000 25.48 3.90 46.34 4.26
1631 2579 3.557054 CCCGCTATATAGCCTTTTCAGCA 60.557 47.826 25.48 0.00 46.34 4.41
1632 2580 3.681897 CCGCTATATAGCCTTTTCAGCAG 59.318 47.826 25.48 9.82 46.34 4.24
1633 2581 3.681897 CGCTATATAGCCTTTTCAGCAGG 59.318 47.826 25.48 6.35 46.34 4.85
1634 2582 4.006319 GCTATATAGCCTTTTCAGCAGGG 58.994 47.826 22.02 0.00 43.39 4.45
1635 2583 4.505742 GCTATATAGCCTTTTCAGCAGGGT 60.506 45.833 22.02 0.00 44.56 4.34
1636 2584 2.134789 ATAGCCTTTTCAGCAGGGTG 57.865 50.000 2.17 0.00 42.32 4.61
1637 2585 0.609131 TAGCCTTTTCAGCAGGGTGC 60.609 55.000 2.17 0.00 42.32 5.01
1638 2586 2.935740 GCCTTTTCAGCAGGGTGCC 61.936 63.158 0.00 0.00 46.52 5.01
1639 2587 2.629656 CCTTTTCAGCAGGGTGCCG 61.630 63.158 0.00 0.00 46.52 5.69
1640 2588 3.273080 CTTTTCAGCAGGGTGCCGC 62.273 63.158 0.00 0.00 46.52 6.53
1641 2589 3.790416 TTTTCAGCAGGGTGCCGCT 62.790 57.895 0.00 0.00 46.52 5.52
1642 2590 2.404566 TTTTCAGCAGGGTGCCGCTA 62.405 55.000 0.00 0.00 46.52 4.26
1643 2591 2.404566 TTTCAGCAGGGTGCCGCTAA 62.405 55.000 0.00 0.00 46.52 3.09
1644 2592 2.359850 CAGCAGGGTGCCGCTAAA 60.360 61.111 0.00 0.00 46.52 1.85
1645 2593 1.750399 CAGCAGGGTGCCGCTAAAT 60.750 57.895 0.00 0.00 46.52 1.40
1646 2594 0.463654 CAGCAGGGTGCCGCTAAATA 60.464 55.000 0.00 0.00 46.52 1.40
1647 2595 0.179045 AGCAGGGTGCCGCTAAATAG 60.179 55.000 0.00 0.00 46.52 1.73
1648 2596 0.463833 GCAGGGTGCCGCTAAATAGT 60.464 55.000 0.00 0.00 37.42 2.12
1649 2597 1.583054 CAGGGTGCCGCTAAATAGTC 58.417 55.000 0.00 0.00 0.00 2.59
1650 2598 0.468648 AGGGTGCCGCTAAATAGTCC 59.531 55.000 0.00 0.00 0.00 3.85
1651 2599 0.534427 GGGTGCCGCTAAATAGTCCC 60.534 60.000 0.00 0.00 0.00 4.46
1652 2600 0.179468 GGTGCCGCTAAATAGTCCCA 59.821 55.000 0.00 0.00 0.00 4.37
1653 2601 1.202770 GGTGCCGCTAAATAGTCCCAT 60.203 52.381 0.00 0.00 0.00 4.00
1654 2602 1.873591 GTGCCGCTAAATAGTCCCATG 59.126 52.381 0.00 0.00 0.00 3.66
1655 2603 1.488812 TGCCGCTAAATAGTCCCATGT 59.511 47.619 0.00 0.00 0.00 3.21
1656 2604 2.701423 TGCCGCTAAATAGTCCCATGTA 59.299 45.455 0.00 0.00 0.00 2.29
1657 2605 3.064931 GCCGCTAAATAGTCCCATGTAC 58.935 50.000 0.00 0.00 0.00 2.90
1658 2606 3.493699 GCCGCTAAATAGTCCCATGTACA 60.494 47.826 0.00 0.00 0.00 2.90
1659 2607 4.699637 CCGCTAAATAGTCCCATGTACAA 58.300 43.478 0.00 0.00 0.00 2.41
1660 2608 5.120399 CCGCTAAATAGTCCCATGTACAAA 58.880 41.667 0.00 0.00 0.00 2.83
1661 2609 5.763204 CCGCTAAATAGTCCCATGTACAAAT 59.237 40.000 0.00 0.00 0.00 2.32
1662 2610 6.932400 CCGCTAAATAGTCCCATGTACAAATA 59.068 38.462 0.00 0.00 0.00 1.40
1663 2611 7.117812 CCGCTAAATAGTCCCATGTACAAATAG 59.882 40.741 0.00 0.00 0.00 1.73
1664 2612 7.360101 CGCTAAATAGTCCCATGTACAAATAGC 60.360 40.741 0.00 0.38 0.00 2.97
1665 2613 7.094762 GCTAAATAGTCCCATGTACAAATAGCC 60.095 40.741 0.00 0.00 0.00 3.93
1666 2614 6.515512 AATAGTCCCATGTACAAATAGCCT 57.484 37.500 0.00 0.00 0.00 4.58
1667 2615 4.156455 AGTCCCATGTACAAATAGCCTG 57.844 45.455 0.00 0.00 0.00 4.85
1668 2616 2.618709 GTCCCATGTACAAATAGCCTGC 59.381 50.000 0.00 0.00 0.00 4.85
1669 2617 2.509548 TCCCATGTACAAATAGCCTGCT 59.490 45.455 0.00 0.00 0.00 4.24
1670 2618 3.714280 TCCCATGTACAAATAGCCTGCTA 59.286 43.478 0.00 0.64 0.00 3.49
1671 2619 4.350816 TCCCATGTACAAATAGCCTGCTAT 59.649 41.667 0.00 5.84 40.63 2.97
1672 2620 5.546110 TCCCATGTACAAATAGCCTGCTATA 59.454 40.000 11.81 0.00 38.20 1.31
1673 2621 5.877012 CCCATGTACAAATAGCCTGCTATAG 59.123 44.000 11.81 10.15 38.20 1.31
1674 2622 5.352569 CCATGTACAAATAGCCTGCTATAGC 59.647 44.000 18.18 18.18 38.20 2.97
1675 2623 4.894784 TGTACAAATAGCCTGCTATAGCC 58.105 43.478 21.84 6.81 38.20 3.93
1676 2624 3.425162 ACAAATAGCCTGCTATAGCCC 57.575 47.619 21.84 10.22 38.20 5.19
1677 2625 2.289694 ACAAATAGCCTGCTATAGCCCG 60.290 50.000 21.84 12.41 38.20 6.13
1678 2626 0.250513 AATAGCCTGCTATAGCCCGC 59.749 55.000 21.84 20.87 38.20 6.13
1679 2627 0.616111 ATAGCCTGCTATAGCCCGCT 60.616 55.000 28.43 28.43 43.69 5.52
1680 2628 0.039180 TAGCCTGCTATAGCCCGCTA 59.961 55.000 26.87 26.87 42.16 4.26
1681 2629 0.616111 AGCCTGCTATAGCCCGCTAT 60.616 55.000 25.96 13.46 40.93 2.97
1682 2630 1.112113 GCCTGCTATAGCCCGCTATA 58.888 55.000 21.84 14.20 39.65 1.31
1688 2636 3.980646 CTATAGCCCGCTATAGCTCTG 57.019 52.381 23.85 11.16 46.26 3.35
1689 2637 0.820871 ATAGCCCGCTATAGCTCTGC 59.179 55.000 21.98 19.32 40.56 4.26
1690 2638 0.251386 TAGCCCGCTATAGCTCTGCT 60.251 55.000 25.64 25.64 43.41 4.24
1691 2639 0.251386 AGCCCGCTATAGCTCTGCTA 60.251 55.000 22.97 1.60 45.55 3.49
1705 2653 5.594724 GCTCTGCTATAGCTGATTTTGAG 57.405 43.478 28.09 18.62 45.61 3.02
1706 2654 4.451774 GCTCTGCTATAGCTGATTTTGAGG 59.548 45.833 28.09 18.05 45.61 3.86
1707 2655 5.609423 CTCTGCTATAGCTGATTTTGAGGT 58.391 41.667 28.09 0.00 45.61 3.85
1708 2656 5.605534 TCTGCTATAGCTGATTTTGAGGTC 58.394 41.667 25.38 0.00 42.71 3.85
1709 2657 4.708177 TGCTATAGCTGATTTTGAGGTCC 58.292 43.478 24.61 0.00 42.66 4.46
1710 2658 3.743396 GCTATAGCTGATTTTGAGGTCCG 59.257 47.826 17.75 0.00 38.21 4.79
1711 2659 2.024176 TAGCTGATTTTGAGGTCCGC 57.976 50.000 0.00 0.00 0.00 5.54
1712 2660 0.678048 AGCTGATTTTGAGGTCCGCC 60.678 55.000 0.00 0.00 0.00 6.13
1713 2661 1.982073 GCTGATTTTGAGGTCCGCCG 61.982 60.000 0.00 0.00 40.50 6.46
1714 2662 1.982073 CTGATTTTGAGGTCCGCCGC 61.982 60.000 0.00 0.00 40.50 6.53
1715 2663 1.745489 GATTTTGAGGTCCGCCGCT 60.745 57.895 0.00 0.00 40.50 5.52
1716 2664 0.461339 GATTTTGAGGTCCGCCGCTA 60.461 55.000 0.00 0.00 40.50 4.26
1717 2665 0.180406 ATTTTGAGGTCCGCCGCTAT 59.820 50.000 0.00 0.00 40.50 2.97
1718 2666 0.035820 TTTTGAGGTCCGCCGCTATT 60.036 50.000 0.00 0.00 40.50 1.73
1719 2667 0.035820 TTTGAGGTCCGCCGCTATTT 60.036 50.000 0.00 0.00 40.50 1.40
1720 2668 0.742990 TTGAGGTCCGCCGCTATTTG 60.743 55.000 0.00 0.00 40.50 2.32
1721 2669 1.887707 GAGGTCCGCCGCTATTTGG 60.888 63.158 0.00 0.00 40.50 3.28
1743 2691 4.927422 GCAATAGCCCGCTATTTAAAACA 58.073 39.130 17.30 0.00 44.18 2.83
2063 4269 6.678568 AGCTTGCTATGACTCCTGTAATAT 57.321 37.500 0.00 0.00 0.00 1.28
2171 4384 3.729462 GCACCAGAATTTTATACGCGCAA 60.729 43.478 5.73 0.00 0.00 4.85
2245 4458 1.939980 ACTAACAGGAGACAGGGGAC 58.060 55.000 0.00 0.00 0.00 4.46
2301 4514 9.060347 TGCTCTAATATAAAGGCTTGATTTCAG 57.940 33.333 1.55 0.00 0.00 3.02
2334 4739 8.813282 TGTGTTACACTGCTTTGTATAATATCG 58.187 33.333 16.79 0.00 35.11 2.92
2540 4957 9.803315 CTAGATGAGCAGTGTTATAAGTGTAAA 57.197 33.333 0.00 0.00 0.00 2.01
2706 7101 1.308783 GGCCTGTTGCTTCTAGGTGC 61.309 60.000 0.00 0.00 40.92 5.01
2722 7120 1.202348 GGTGCCATGAGGTTTTGCTAC 59.798 52.381 0.00 0.00 37.19 3.58
2756 7169 5.546526 TCCTTTAACAAACATTTCATGCCC 58.453 37.500 0.00 0.00 0.00 5.36
2922 10231 3.102972 TGGAGAAATCTCAGGGAGACAG 58.897 50.000 12.21 0.00 41.76 3.51
2977 10286 0.368227 CGATTGAGTGCGCTGACTTC 59.632 55.000 3.44 0.00 0.00 3.01
3027 10336 4.682787 CATATAATTGATAGGCTCGGCGA 58.317 43.478 10.14 10.14 0.00 5.54
3110 10419 7.973402 AGCAAAGGTATGGTCACATATACATA 58.027 34.615 4.43 0.00 41.34 2.29
3381 11071 4.377021 TGTACTTACAACTTGCAGTCAGG 58.623 43.478 0.00 0.00 32.40 3.86
3437 11127 8.986847 CAGAGAATACAATGGCTAATGAGTTAG 58.013 37.037 0.00 0.00 40.25 2.34
3533 11229 4.074259 TGTGCAGCAAGAAACTGACATAT 58.926 39.130 0.00 0.00 37.32 1.78
3539 11235 6.094048 GCAGCAAGAAACTGACATATAGGAAA 59.906 38.462 0.00 0.00 37.32 3.13
3540 11236 7.467623 CAGCAAGAAACTGACATATAGGAAAC 58.532 38.462 0.00 0.00 37.32 2.78
3630 11329 4.902448 ACTTTATCTGGGAGTATCTCACCC 59.098 45.833 0.00 0.00 36.46 4.61
4107 11839 7.096599 GCCTTTAAAGATCGAGTTGACAAAAAC 60.097 37.037 16.98 0.00 0.00 2.43
4338 12070 1.338105 CCTGAATGCTTGAGGTCGTGA 60.338 52.381 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.819259 GTGTGCTGGAACAAGCTGGA 60.819 55.000 0.00 0.00 38.70 3.86
2 3 1.102809 TGTGTGCTGGAACAAGCTGG 61.103 55.000 2.83 0.00 38.70 4.85
4 5 0.181114 TCTGTGTGCTGGAACAAGCT 59.819 50.000 2.83 0.00 38.70 3.74
5 6 0.590195 CTCTGTGTGCTGGAACAAGC 59.410 55.000 0.00 0.00 38.70 4.01
6 7 1.959042 ACTCTGTGTGCTGGAACAAG 58.041 50.000 0.00 0.00 38.70 3.16
7 8 3.552132 TTACTCTGTGTGCTGGAACAA 57.448 42.857 0.00 0.00 38.70 2.83
8 9 3.664107 GATTACTCTGTGTGCTGGAACA 58.336 45.455 0.00 0.00 0.00 3.18
9 10 2.668457 CGATTACTCTGTGTGCTGGAAC 59.332 50.000 0.00 0.00 0.00 3.62
10 11 2.353704 CCGATTACTCTGTGTGCTGGAA 60.354 50.000 0.00 0.00 0.00 3.53
11 12 1.204704 CCGATTACTCTGTGTGCTGGA 59.795 52.381 0.00 0.00 0.00 3.86
12 13 1.204704 TCCGATTACTCTGTGTGCTGG 59.795 52.381 0.00 0.00 0.00 4.85
13 14 2.654749 TCCGATTACTCTGTGTGCTG 57.345 50.000 0.00 0.00 0.00 4.41
14 15 5.537300 AATATCCGATTACTCTGTGTGCT 57.463 39.130 0.00 0.00 0.00 4.40
15 16 5.986135 AGAAATATCCGATTACTCTGTGTGC 59.014 40.000 0.00 0.00 0.00 4.57
16 17 7.203218 TCAGAAATATCCGATTACTCTGTGTG 58.797 38.462 10.65 0.00 32.52 3.82
17 18 7.348080 TCAGAAATATCCGATTACTCTGTGT 57.652 36.000 10.65 0.00 32.52 3.72
18 19 7.148672 GCATCAGAAATATCCGATTACTCTGTG 60.149 40.741 10.65 9.73 32.52 3.66
19 20 6.870965 GCATCAGAAATATCCGATTACTCTGT 59.129 38.462 10.65 0.00 32.52 3.41
20 21 6.870439 TGCATCAGAAATATCCGATTACTCTG 59.130 38.462 6.84 6.84 0.00 3.35
21 22 6.997655 TGCATCAGAAATATCCGATTACTCT 58.002 36.000 0.00 0.00 0.00 3.24
22 23 6.870965 ACTGCATCAGAAATATCCGATTACTC 59.129 38.462 0.29 0.00 35.18 2.59
23 24 6.763355 ACTGCATCAGAAATATCCGATTACT 58.237 36.000 0.29 0.00 35.18 2.24
59 62 6.878317 TCGATCTAGATCCTGAACACAAATT 58.122 36.000 23.97 0.00 34.40 1.82
109 112 3.036819 AGAGTAGATTGATCTGCAGGCA 58.963 45.455 15.13 10.01 41.27 4.75
128 131 0.796927 CACTGTCTAGACGTGCGAGA 59.203 55.000 24.50 5.96 32.51 4.04
129 132 0.794981 GCACTGTCTAGACGTGCGAG 60.795 60.000 34.74 23.09 44.62 5.03
130 133 1.209383 GCACTGTCTAGACGTGCGA 59.791 57.895 34.74 15.25 44.62 5.10
131 134 3.755404 GCACTGTCTAGACGTGCG 58.245 61.111 34.74 20.63 44.62 5.34
133 136 0.109086 CCCAGCACTGTCTAGACGTG 60.109 60.000 28.30 28.30 38.18 4.49
134 137 0.539901 ACCCAGCACTGTCTAGACGT 60.540 55.000 17.85 14.92 0.00 4.34
135 138 0.603569 AACCCAGCACTGTCTAGACG 59.396 55.000 17.85 14.32 0.00 4.18
136 139 1.338200 CCAACCCAGCACTGTCTAGAC 60.338 57.143 16.32 16.32 0.00 2.59
137 140 0.976641 CCAACCCAGCACTGTCTAGA 59.023 55.000 0.00 0.00 0.00 2.43
138 141 0.687354 ACCAACCCAGCACTGTCTAG 59.313 55.000 0.00 0.00 0.00 2.43
139 142 0.396435 CACCAACCCAGCACTGTCTA 59.604 55.000 0.00 0.00 0.00 2.59
141 144 1.898574 CCACCAACCCAGCACTGTC 60.899 63.158 0.00 0.00 0.00 3.51
142 145 1.719063 ATCCACCAACCCAGCACTGT 61.719 55.000 0.00 0.00 0.00 3.55
145 148 2.639327 GCATCCACCAACCCAGCAC 61.639 63.158 0.00 0.00 0.00 4.40
146 149 2.283101 GCATCCACCAACCCAGCA 60.283 61.111 0.00 0.00 0.00 4.41
147 150 2.036256 AGCATCCACCAACCCAGC 59.964 61.111 0.00 0.00 0.00 4.85
148 151 0.327924 TACAGCATCCACCAACCCAG 59.672 55.000 0.00 0.00 0.00 4.45
149 152 0.327924 CTACAGCATCCACCAACCCA 59.672 55.000 0.00 0.00 0.00 4.51
191 313 1.990060 TGCGAGAGGGGAAAGGAGG 60.990 63.158 0.00 0.00 0.00 4.30
230 353 4.261994 GGAGATGAGGAATCGAGGAAGAAG 60.262 50.000 0.00 0.00 40.54 2.85
303 450 4.701651 TCCTCTGCAACGATCATGAATTTT 59.298 37.500 0.00 0.00 0.00 1.82
381 535 4.437239 CAGTCCTCTGAAGCGATTACATT 58.563 43.478 0.00 0.00 43.76 2.71
383 537 2.417379 GCAGTCCTCTGAAGCGATTACA 60.417 50.000 0.00 0.00 43.76 2.41
496 717 3.372206 CCTGAACACGATAAAGAAGCAGG 59.628 47.826 0.00 0.00 35.04 4.85
657 888 4.618920 GGAAGTCCCAAAGAACAGAGTA 57.381 45.455 0.00 0.00 34.14 2.59
687 920 4.446385 CAGTCCAACAAATCAAACATGCTG 59.554 41.667 0.00 0.00 0.00 4.41
691 924 6.461509 GGTTCTCAGTCCAACAAATCAAACAT 60.462 38.462 0.00 0.00 0.00 2.71
731 982 6.636447 CACGTGAAATAGTCTTTTGAATTGCA 59.364 34.615 10.90 0.00 0.00 4.08
745 1012 7.591057 TCTTCTTTTGAATTGCACGTGAAATAG 59.409 33.333 22.08 14.79 37.85 1.73
746 1013 7.421599 TCTTCTTTTGAATTGCACGTGAAATA 58.578 30.769 22.08 4.85 37.85 1.40
748 1015 5.645624 TCTTCTTTTGAATTGCACGTGAAA 58.354 33.333 22.23 17.29 37.85 2.69
751 1018 4.601019 ACTCTTCTTTTGAATTGCACGTG 58.399 39.130 12.28 12.28 37.85 4.49
752 1019 4.576463 AGACTCTTCTTTTGAATTGCACGT 59.424 37.500 0.00 0.00 37.85 4.49
753 1020 5.100751 AGACTCTTCTTTTGAATTGCACG 57.899 39.130 0.00 0.00 37.85 5.34
754 1021 6.858478 GGTTAGACTCTTCTTTTGAATTGCAC 59.142 38.462 0.00 0.00 37.85 4.57
756 1023 7.041098 TGAGGTTAGACTCTTCTTTTGAATTGC 60.041 37.037 0.00 0.00 37.85 3.56
816 1632 3.479489 AGCATGAGACATGTCACAAACA 58.521 40.909 26.30 17.40 43.51 2.83
842 1671 3.241995 GGAAAACATTAGACAGCGCTACG 60.242 47.826 10.99 0.00 0.00 3.51
1165 2112 5.502153 AACTGAGAGTTACTGTATAGGCG 57.498 43.478 0.00 0.00 36.52 5.52
1168 2115 9.991388 GTTGACTAACTGAGAGTTACTGTATAG 57.009 37.037 0.00 0.00 39.51 1.31
1193 2140 1.134580 CATGATCAAGACGAGGGCAGT 60.135 52.381 0.00 0.00 0.00 4.40
1350 2298 1.135859 GTGCTTTGCCTTCATCAGACG 60.136 52.381 0.00 0.00 0.00 4.18
1563 2511 9.849166 GGCTATTTAAAACATTGCTAAACACTA 57.151 29.630 0.00 0.00 0.00 2.74
1564 2512 7.540745 CGGCTATTTAAAACATTGCTAAACACT 59.459 33.333 0.00 0.00 0.00 3.55
1565 2513 7.201401 CCGGCTATTTAAAACATTGCTAAACAC 60.201 37.037 0.00 0.00 0.00 3.32
1566 2514 6.809196 CCGGCTATTTAAAACATTGCTAAACA 59.191 34.615 0.00 0.00 0.00 2.83
1567 2515 6.237728 GCCGGCTATTTAAAACATTGCTAAAC 60.238 38.462 22.15 0.00 0.00 2.01
1568 2516 5.808030 GCCGGCTATTTAAAACATTGCTAAA 59.192 36.000 22.15 0.00 0.00 1.85
1569 2517 5.126384 AGCCGGCTATTTAAAACATTGCTAA 59.874 36.000 31.86 0.00 0.00 3.09
1570 2518 4.642885 AGCCGGCTATTTAAAACATTGCTA 59.357 37.500 31.86 0.00 0.00 3.49
1571 2519 3.447229 AGCCGGCTATTTAAAACATTGCT 59.553 39.130 31.86 0.00 0.00 3.91
1572 2520 3.780902 AGCCGGCTATTTAAAACATTGC 58.219 40.909 31.86 0.00 0.00 3.56
1573 2521 6.801862 GCTATAGCCGGCTATTTAAAACATTG 59.198 38.462 44.65 25.37 39.65 2.82
1574 2522 6.715264 AGCTATAGCCGGCTATTTAAAACATT 59.285 34.615 44.65 25.26 43.38 2.71
1575 2523 6.238648 AGCTATAGCCGGCTATTTAAAACAT 58.761 36.000 44.65 26.89 43.38 2.71
1576 2524 5.617252 AGCTATAGCCGGCTATTTAAAACA 58.383 37.500 44.65 27.89 43.38 2.83
1577 2525 5.121925 GGAGCTATAGCCGGCTATTTAAAAC 59.878 44.000 44.65 30.15 43.38 2.43
1578 2526 5.243207 GGAGCTATAGCCGGCTATTTAAAA 58.757 41.667 44.65 29.19 43.38 1.52
1579 2527 4.619863 CGGAGCTATAGCCGGCTATTTAAA 60.620 45.833 44.65 29.52 43.67 1.52
1580 2528 3.119245 CGGAGCTATAGCCGGCTATTTAA 60.119 47.826 44.65 29.85 43.67 1.52
1581 2529 2.426024 CGGAGCTATAGCCGGCTATTTA 59.574 50.000 44.65 30.51 43.67 1.40
1582 2530 1.204941 CGGAGCTATAGCCGGCTATTT 59.795 52.381 44.65 31.93 43.67 1.40
1583 2531 0.818296 CGGAGCTATAGCCGGCTATT 59.182 55.000 44.65 31.45 43.67 1.73
1584 2532 2.494677 CGGAGCTATAGCCGGCTAT 58.505 57.895 42.09 42.09 43.67 2.97
1585 2533 3.998156 CGGAGCTATAGCCGGCTA 58.002 61.111 36.88 36.88 43.67 3.93
1597 2545 1.668101 ATAGCGGGCTATAGCGGAGC 61.668 60.000 22.13 22.13 42.31 4.70
1598 2546 1.676746 TATAGCGGGCTATAGCGGAG 58.323 55.000 18.30 12.52 43.26 4.63
1599 2547 2.359981 ATATAGCGGGCTATAGCGGA 57.640 50.000 21.13 4.91 42.57 5.54
1600 2548 2.095161 GCTATATAGCGGGCTATAGCGG 60.095 54.545 18.61 13.46 42.57 5.52
1601 2549 3.204597 GCTATATAGCGGGCTATAGCG 57.795 52.381 18.61 15.96 42.57 4.26
1613 2561 4.999950 CACCCTGCTGAAAAGGCTATATAG 59.000 45.833 5.30 5.30 33.07 1.31
1614 2562 4.746702 GCACCCTGCTGAAAAGGCTATATA 60.747 45.833 0.00 0.00 40.96 0.86
1615 2563 3.825328 CACCCTGCTGAAAAGGCTATAT 58.175 45.455 0.00 0.00 33.07 0.86
1616 2564 2.683742 GCACCCTGCTGAAAAGGCTATA 60.684 50.000 0.00 0.00 40.96 1.31
1617 2565 1.957113 GCACCCTGCTGAAAAGGCTAT 60.957 52.381 0.00 0.00 40.96 2.97
1618 2566 0.609131 GCACCCTGCTGAAAAGGCTA 60.609 55.000 0.00 0.00 40.96 3.93
1619 2567 1.905354 GCACCCTGCTGAAAAGGCT 60.905 57.895 0.00 0.00 40.96 4.58
1620 2568 2.653115 GCACCCTGCTGAAAAGGC 59.347 61.111 0.00 0.00 40.96 4.35
1621 2569 3.369921 GGCACCCTGCTGAAAAGG 58.630 61.111 0.00 0.00 44.28 3.11
1628 2576 0.179045 CTATTTAGCGGCACCCTGCT 60.179 55.000 1.45 2.32 44.28 4.24
1629 2577 0.463833 ACTATTTAGCGGCACCCTGC 60.464 55.000 1.45 0.00 44.08 4.85
1630 2578 1.583054 GACTATTTAGCGGCACCCTG 58.417 55.000 1.45 0.00 0.00 4.45
1631 2579 0.468648 GGACTATTTAGCGGCACCCT 59.531 55.000 1.45 0.00 0.00 4.34
1632 2580 0.534427 GGGACTATTTAGCGGCACCC 60.534 60.000 1.45 0.00 0.00 4.61
1633 2581 0.179468 TGGGACTATTTAGCGGCACC 59.821 55.000 1.45 0.00 0.00 5.01
1634 2582 1.873591 CATGGGACTATTTAGCGGCAC 59.126 52.381 1.45 0.00 0.00 5.01
1635 2583 1.488812 ACATGGGACTATTTAGCGGCA 59.511 47.619 1.45 0.00 0.00 5.69
1636 2584 2.256117 ACATGGGACTATTTAGCGGC 57.744 50.000 0.00 0.00 0.00 6.53
1637 2585 4.330944 TGTACATGGGACTATTTAGCGG 57.669 45.455 0.00 0.00 0.00 5.52
1638 2586 6.861065 ATTTGTACATGGGACTATTTAGCG 57.139 37.500 0.00 0.00 0.00 4.26
1639 2587 7.094762 GGCTATTTGTACATGGGACTATTTAGC 60.095 40.741 0.00 7.68 0.00 3.09
1640 2588 8.157476 AGGCTATTTGTACATGGGACTATTTAG 58.843 37.037 0.00 0.00 0.00 1.85
1641 2589 7.936847 CAGGCTATTTGTACATGGGACTATTTA 59.063 37.037 0.00 0.00 0.00 1.40
1642 2590 6.772716 CAGGCTATTTGTACATGGGACTATTT 59.227 38.462 0.00 0.00 0.00 1.40
1643 2591 6.299141 CAGGCTATTTGTACATGGGACTATT 58.701 40.000 0.00 0.00 0.00 1.73
1644 2592 5.746065 GCAGGCTATTTGTACATGGGACTAT 60.746 44.000 0.00 0.00 0.00 2.12
1645 2593 4.444306 GCAGGCTATTTGTACATGGGACTA 60.444 45.833 0.00 0.00 0.00 2.59
1646 2594 3.685550 GCAGGCTATTTGTACATGGGACT 60.686 47.826 0.00 0.00 0.00 3.85
1647 2595 2.618709 GCAGGCTATTTGTACATGGGAC 59.381 50.000 0.00 0.00 0.00 4.46
1648 2596 2.509548 AGCAGGCTATTTGTACATGGGA 59.490 45.455 0.00 0.00 0.00 4.37
1649 2597 2.936202 AGCAGGCTATTTGTACATGGG 58.064 47.619 0.00 0.00 0.00 4.00
1650 2598 5.352569 GCTATAGCAGGCTATTTGTACATGG 59.647 44.000 20.01 0.00 39.65 3.66
1651 2599 5.352569 GGCTATAGCAGGCTATTTGTACATG 59.647 44.000 25.53 0.00 46.26 3.21
1652 2600 5.491982 GGCTATAGCAGGCTATTTGTACAT 58.508 41.667 25.53 0.00 46.26 2.29
1653 2601 4.894784 GGCTATAGCAGGCTATTTGTACA 58.105 43.478 25.53 0.00 46.26 2.90
1661 2609 3.999066 CTATAGCGGGCTATAGCAGGCTA 60.999 52.174 32.94 32.94 46.26 3.93
1662 2610 3.274250 CTATAGCGGGCTATAGCAGGCT 61.274 54.545 31.51 31.51 46.26 4.58
1663 2611 1.067821 CTATAGCGGGCTATAGCAGGC 59.932 57.143 26.16 24.65 46.26 4.85
1683 2631 4.451774 CCTCAAAATCAGCTATAGCAGAGC 59.548 45.833 26.07 1.38 45.16 4.09
1684 2632 5.609423 ACCTCAAAATCAGCTATAGCAGAG 58.391 41.667 26.07 17.72 45.16 3.35
1685 2633 5.453903 GGACCTCAAAATCAGCTATAGCAGA 60.454 44.000 26.07 23.24 45.16 4.26
1686 2634 4.754114 GGACCTCAAAATCAGCTATAGCAG 59.246 45.833 26.07 18.60 45.16 4.24
1687 2635 4.708177 GGACCTCAAAATCAGCTATAGCA 58.292 43.478 26.07 7.38 45.16 3.49
1688 2636 3.743396 CGGACCTCAAAATCAGCTATAGC 59.257 47.826 17.33 17.33 42.49 2.97
1689 2637 3.743396 GCGGACCTCAAAATCAGCTATAG 59.257 47.826 0.00 0.00 33.80 1.31
1690 2638 3.494398 GGCGGACCTCAAAATCAGCTATA 60.494 47.826 0.00 0.00 36.44 1.31
1691 2639 2.565841 GCGGACCTCAAAATCAGCTAT 58.434 47.619 0.00 0.00 33.80 2.97
1692 2640 1.406887 GGCGGACCTCAAAATCAGCTA 60.407 52.381 0.00 0.00 36.44 3.32
1693 2641 0.678048 GGCGGACCTCAAAATCAGCT 60.678 55.000 0.00 0.00 36.44 4.24
1694 2642 1.803289 GGCGGACCTCAAAATCAGC 59.197 57.895 0.00 0.00 35.57 4.26
1695 2643 1.982073 GCGGCGGACCTCAAAATCAG 61.982 60.000 9.78 0.00 0.00 2.90
1696 2644 2.038269 GCGGCGGACCTCAAAATCA 61.038 57.895 9.78 0.00 0.00 2.57
1697 2645 0.461339 TAGCGGCGGACCTCAAAATC 60.461 55.000 9.78 0.00 0.00 2.17
1698 2646 0.180406 ATAGCGGCGGACCTCAAAAT 59.820 50.000 9.78 0.00 0.00 1.82
1699 2647 0.035820 AATAGCGGCGGACCTCAAAA 60.036 50.000 9.78 0.00 0.00 2.44
1700 2648 0.035820 AAATAGCGGCGGACCTCAAA 60.036 50.000 9.78 0.00 0.00 2.69
1701 2649 0.742990 CAAATAGCGGCGGACCTCAA 60.743 55.000 9.78 0.00 0.00 3.02
1702 2650 1.153449 CAAATAGCGGCGGACCTCA 60.153 57.895 9.78 0.00 0.00 3.86
1703 2651 1.887707 CCAAATAGCGGCGGACCTC 60.888 63.158 9.78 0.00 0.00 3.85
1704 2652 2.189521 CCAAATAGCGGCGGACCT 59.810 61.111 9.78 0.00 0.00 3.85
1705 2653 3.583086 GCCAAATAGCGGCGGACC 61.583 66.667 9.78 0.00 40.35 4.46
1721 2669 4.927422 TGTTTTAAATAGCGGGCTATTGC 58.073 39.130 22.61 12.89 45.37 3.56
1722 2670 6.420604 CCAATGTTTTAAATAGCGGGCTATTG 59.579 38.462 22.61 11.73 45.37 1.90
1724 2672 5.596772 ACCAATGTTTTAAATAGCGGGCTAT 59.403 36.000 7.36 7.36 40.63 2.97
1725 2673 4.951094 ACCAATGTTTTAAATAGCGGGCTA 59.049 37.500 2.42 2.42 0.00 3.93
1726 2674 3.767131 ACCAATGTTTTAAATAGCGGGCT 59.233 39.130 0.00 0.00 0.00 5.19
1727 2675 3.862845 CACCAATGTTTTAAATAGCGGGC 59.137 43.478 0.00 0.00 0.00 6.13
1728 2676 5.066968 ACACCAATGTTTTAAATAGCGGG 57.933 39.130 0.00 0.00 34.46 6.13
1741 2689 5.995897 GTCCTTAGTCACTAAACACCAATGT 59.004 40.000 0.00 0.00 42.46 2.71
1742 2690 6.231211 AGTCCTTAGTCACTAAACACCAATG 58.769 40.000 0.00 0.00 0.00 2.82
1743 2691 6.435292 AGTCCTTAGTCACTAAACACCAAT 57.565 37.500 0.00 0.00 0.00 3.16
2092 4304 9.987272 CTAATCAATTAATGGAAAAGGGGATTC 57.013 33.333 0.00 0.00 0.00 2.52
2171 4384 8.627208 AATGTCTAACTTGAATGTGATCTGTT 57.373 30.769 0.00 0.00 0.00 3.16
2245 4458 8.780249 TCATCTTACATTGTCAATATCAGCATG 58.220 33.333 0.00 0.00 37.54 4.06
2301 4514 6.725246 ACAAAGCAGTGTAACACAGTAATTC 58.275 36.000 0.00 0.00 41.43 2.17
2334 4739 9.109393 TGTTATGCTATGTCTAAATGGAAGAAC 57.891 33.333 0.00 0.00 0.00 3.01
2627 5340 5.796935 GCAACACACTAACATAATGAGCAAG 59.203 40.000 0.00 0.00 0.00 4.01
2706 7101 4.701956 AAATCGTAGCAAAACCTCATGG 57.298 40.909 0.00 0.00 39.83 3.66
2722 7120 9.840427 AATGTTTGTTAAAGGAGACATAAATCG 57.160 29.630 0.00 0.00 0.00 3.34
2836 10145 6.615316 TCCTGAGTTATGATTTATGTGGAGGA 59.385 38.462 0.00 0.00 0.00 3.71
2922 10231 4.234530 ACTCGTACTTGTACCAGTTGTC 57.765 45.455 4.74 0.00 0.00 3.18
2977 10286 3.719144 GGTCGTTTCGCCGGGTTG 61.719 66.667 2.18 0.00 0.00 3.77
3022 10331 1.065031 CCGCATTTCTTGTTTCGCCG 61.065 55.000 0.00 0.00 0.00 6.46
3027 10336 4.613622 CGAACTCATCCGCATTTCTTGTTT 60.614 41.667 0.00 0.00 0.00 2.83
3110 10419 6.594159 CGGACACATAAGAAGTTTCATAAGGT 59.406 38.462 0.00 0.00 0.00 3.50
3347 11025 7.907214 AGTTGTAAGTACATGGAAAGATCAC 57.093 36.000 0.00 0.00 35.89 3.06
3381 11071 4.416738 GACCAGGGGCCACAGCTC 62.417 72.222 8.31 0.00 39.56 4.09
3437 11127 8.001881 TCATATAGTCCTTCTGTCAACTTCTC 57.998 38.462 0.00 0.00 0.00 2.87
3630 11329 2.526304 TTGGAAGGACAGTGAACTCG 57.474 50.000 0.00 0.00 0.00 4.18
3927 11639 2.442413 GCACCAACCCTTAACATAGCA 58.558 47.619 0.00 0.00 0.00 3.49
4107 11839 5.634118 TCCCTTCCTATATGCTTCAATTGG 58.366 41.667 5.42 0.00 0.00 3.16
4263 11995 3.928992 GCACTTCATGATCTCTTGACGAA 59.071 43.478 0.00 0.00 31.00 3.85
4338 12070 5.772672 TGGAAACACTGCACAATAGGTAAAT 59.227 36.000 0.00 0.00 33.40 1.40


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

AutoCloner maintained by Alex Coulton.