Multiple sequence alignment - TraesCS5A01G086300

Loading Multiple Alignment...

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 TraesCS5A01G086300 chr5A 100.000 7538 0 0 1 7538 115026476 115018939 0.000000e+00 13921.0
1 TraesCS5A01G086300 chr5A 98.359 2620 29 3 2645 5264 328721020 328723625 0.000000e+00 4588.0
2 TraesCS5A01G086300 chr5A 96.242 479 3 2 1726 2190 64378881 64378404 0.000000e+00 771.0
3 TraesCS5A01G086300 chr5A 93.946 479 15 1 1726 2190 245959803 245959325 0.000000e+00 712.0
4 TraesCS5A01G086300 chr5A 100.000 45 0 0 2542 2586 115023875 115023831 4.850000e-12 84.2
5 TraesCS5A01G086300 chr5A 100.000 45 0 0 2602 2646 115023935 115023891 4.850000e-12 84.2
6 TraesCS5A01G086300 chr7A 98.282 2619 45 0 2647 5265 201423244 201420626 0.000000e+00 4588.0
7 TraesCS5A01G086300 chr7A 98.167 2618 48 0 2646 5263 383179315 383176698 0.000000e+00 4569.0
8 TraesCS5A01G086300 chr7A 97.899 2618 55 0 2646 5263 19254624 19257241 0.000000e+00 4530.0
9 TraesCS5A01G086300 chr1A 98.280 2617 44 1 2647 5263 566646564 566643949 0.000000e+00 4582.0
10 TraesCS5A01G086300 chr1A 97.746 2618 57 2 2646 5263 569898961 569901576 0.000000e+00 4506.0
11 TraesCS5A01G086300 chr1A 77.239 268 56 3 2191 2457 495183804 495184067 1.310000e-32 152.0
12 TraesCS5A01G086300 chr2A 98.054 2621 49 2 2645 5263 86901917 86904537 0.000000e+00 4556.0
13 TraesCS5A01G086300 chr2A 91.423 478 25 9 1726 2188 690313278 690312802 6.380000e-180 641.0
14 TraesCS5A01G086300 chr6B 98.014 2618 52 0 2646 5263 308522257 308519640 0.000000e+00 4547.0
15 TraesCS5A01G086300 chr7B 97.975 2617 53 0 2647 5263 727535230 727532614 0.000000e+00 4540.0
16 TraesCS5A01G086300 chr5D 95.648 2298 70 10 5264 7538 112047261 112044971 0.000000e+00 3663.0
17 TraesCS5A01G086300 chr5D 94.433 1473 57 7 1 1453 112050317 112048850 0.000000e+00 2242.0
18 TraesCS5A01G086300 chr5D 88.090 487 39 11 1721 2190 551309551 551310035 1.840000e-155 560.0
19 TraesCS5A01G086300 chr5D 98.033 305 5 1 2342 2646 112047560 112047257 5.180000e-146 529.0
20 TraesCS5A01G086300 chr5D 90.119 253 8 2 1487 1723 112048857 112048606 5.680000e-81 313.0
21 TraesCS5A01G086300 chr5D 100.000 59 0 0 2543 2601 112047300 112047242 8.000000e-20 110.0
22 TraesCS5A01G086300 chr5D 100.000 42 0 0 2605 2646 112047358 112047317 2.260000e-10 78.7
23 TraesCS5A01G086300 chr5B 94.780 1571 61 10 5264 6816 121204060 121202493 0.000000e+00 2427.0
24 TraesCS5A01G086300 chr5B 90.508 1770 113 24 1 1723 121206325 121204564 0.000000e+00 2287.0
25 TraesCS5A01G086300 chr5B 93.207 736 34 7 6813 7538 121202257 121201528 0.000000e+00 1068.0
26 TraesCS5A01G086300 chr5B 90.000 140 14 0 2458 2597 121204184 121204045 1.670000e-41 182.0
27 TraesCS5A01G086300 chr6A 94.154 479 14 1 1726 2190 489858455 489857977 0.000000e+00 717.0
28 TraesCS5A01G086300 chr6A 90.828 338 15 3 1721 2044 565417305 565417640 8.980000e-119 438.0
29 TraesCS5A01G086300 chr6A 90.801 337 16 4 1721 2043 489842927 489842592 3.230000e-118 436.0
30 TraesCS5A01G086300 chr1D 94.409 465 20 3 1726 2185 228812243 228811780 0.000000e+00 710.0
31 TraesCS5A01G086300 chr3A 92.292 480 21 3 1726 2190 160077169 160077647 0.000000e+00 667.0
32 TraesCS5A01G086300 chr3A 93.373 332 7 6 1728 2044 160079319 160079650 1.900000e-130 477.0
33 TraesCS5A01G086300 chr4D 90.985 477 27 9 1729 2190 357411758 357412233 4.960000e-176 628.0
34 TraesCS5A01G086300 chr4D 90.041 482 29 11 1726 2190 8619137 8618658 2.330000e-169 606.0
35 TraesCS5A01G086300 chr3B 91.421 373 5 3 4920 5266 774721945 774721574 3.160000e-133 486.0
36 TraesCS5A01G086300 chr3D 80.519 308 27 15 1726 2002 571620363 571620058 9.910000e-49 206.0
37 TraesCS5A01G086300 chr7D 80.226 177 29 6 2191 2364 279728930 279728757 2.210000e-25 128.0
38 TraesCS5A01G086300 chr7D 76.226 265 46 11 2191 2454 220988150 220988398 2.860000e-24 124.0


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 TraesCS5A01G086300 chr5A 115018939 115026476 7537 True 4696.466667 13921 100.000000 1 7538 3 chr5A.!!$R3 7537
1 TraesCS5A01G086300 chr5A 328721020 328723625 2605 False 4588.000000 4588 98.359000 2645 5264 1 chr5A.!!$F1 2619
2 TraesCS5A01G086300 chr7A 201420626 201423244 2618 True 4588.000000 4588 98.282000 2647 5265 1 chr7A.!!$R1 2618
3 TraesCS5A01G086300 chr7A 383176698 383179315 2617 True 4569.000000 4569 98.167000 2646 5263 1 chr7A.!!$R2 2617
4 TraesCS5A01G086300 chr7A 19254624 19257241 2617 False 4530.000000 4530 97.899000 2646 5263 1 chr7A.!!$F1 2617
5 TraesCS5A01G086300 chr1A 566643949 566646564 2615 True 4582.000000 4582 98.280000 2647 5263 1 chr1A.!!$R1 2616
6 TraesCS5A01G086300 chr1A 569898961 569901576 2615 False 4506.000000 4506 97.746000 2646 5263 1 chr1A.!!$F2 2617
7 TraesCS5A01G086300 chr2A 86901917 86904537 2620 False 4556.000000 4556 98.054000 2645 5263 1 chr2A.!!$F1 2618
8 TraesCS5A01G086300 chr6B 308519640 308522257 2617 True 4547.000000 4547 98.014000 2646 5263 1 chr6B.!!$R1 2617
9 TraesCS5A01G086300 chr7B 727532614 727535230 2616 True 4540.000000 4540 97.975000 2647 5263 1 chr7B.!!$R1 2616
10 TraesCS5A01G086300 chr5D 112044971 112050317 5346 True 1155.950000 3663 96.372167 1 7538 6 chr5D.!!$R1 7537
11 TraesCS5A01G086300 chr5B 121201528 121206325 4797 True 1491.000000 2427 92.123750 1 7538 4 chr5B.!!$R1 7537
12 TraesCS5A01G086300 chr3A 160077169 160079650 2481 False 572.000000 667 92.832500 1726 2190 2 chr3A.!!$F1 464

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
115 117 0.249489 AGATATCGGGCGTTGTCAGC 60.249 55.000 0.00 0.00 0.00 4.26 F
1305 1322 0.037590 TAGAGCGTTGGCATTTGGGT 59.962 50.000 0.00 0.00 43.41 4.51 F
2226 2563 0.107703 GGGACATTGCCGAGATGTGA 60.108 55.000 3.54 0.00 37.83 3.58 F
2328 2881 0.100682 GCCATGCAGCATCACAGAAG 59.899 55.000 4.38 0.00 0.00 2.85 F
3371 4173 0.616395 TGGGACGGTGATTCCTGCTA 60.616 55.000 0.00 0.00 33.17 3.49 F
5674 6700 0.249955 TCCATCATTCTGCAGTGCGA 59.750 50.000 14.67 8.07 0.00 5.10 F
5779 6808 3.626217 TCGATACTCACGCATCACTTACT 59.374 43.478 0.00 0.00 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2056 2393 0.597637 CGAGGACGAGCTGTTTGTGT 60.598 55.000 0.00 0.00 42.66 3.72 R
2309 2862 0.100682 CTTCTGTGATGCTGCATGGC 59.899 55.000 21.53 12.47 0.00 4.40 R
3477 4279 1.303091 GCGCCGAGTTATTTGTGGGT 61.303 55.000 0.00 0.00 0.00 4.51 R
5331 6348 5.467902 TTTTTCTGCAAAACAATCAGCAC 57.532 34.783 0.00 0.00 30.89 4.40 R
5891 6920 2.370189 CTCCAGAAGAGTGTCAAACCCT 59.630 50.000 0.00 0.00 37.87 4.34 R
6516 7545 0.969894 ACCTCAAGACCTTCTCCACG 59.030 55.000 0.00 0.00 0.00 4.94 R
7049 8327 1.308047 AGCATTTTGTCACGCACAGA 58.692 45.000 0.00 0.00 35.97 3.41 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
44 46 1.073763 TGAGAATCAACCCACCCACAG 59.926 52.381 0.00 0.00 45.97 3.66
106 108 1.078759 CGGCGAATGAGATATCGGGC 61.079 60.000 0.00 0.00 39.38 6.13
114 116 1.067060 TGAGATATCGGGCGTTGTCAG 59.933 52.381 0.00 0.00 0.00 3.51
115 117 0.249489 AGATATCGGGCGTTGTCAGC 60.249 55.000 0.00 0.00 0.00 4.26
182 184 8.340618 AGAACAGCATTAGACACAATGTAATT 57.659 30.769 0.00 0.00 38.04 1.40
268 270 1.289800 GAACCTTGACGAGCCGAACC 61.290 60.000 1.50 0.00 0.00 3.62
274 276 2.672307 ACGAGCCGAACCGAGAGT 60.672 61.111 1.50 0.00 0.00 3.24
432 434 1.154469 GCTACCAGCGCAAAACGTC 60.154 57.895 11.47 0.00 46.11 4.34
459 461 3.606687 GAATTCAAGTACCCACCACGAT 58.393 45.455 0.00 0.00 0.00 3.73
520 522 2.696187 GGAGAACTAGAAAGAGGCGGAT 59.304 50.000 0.00 0.00 0.00 4.18
665 667 3.382832 AGGAGCACGCCGTAGCTT 61.383 61.111 13.75 0.00 42.04 3.74
830 840 2.361230 CCGGCTTTCCCAGAACCC 60.361 66.667 0.00 0.00 0.00 4.11
923 940 1.006832 CCTTATCTGCCCACGTTTCG 58.993 55.000 0.00 0.00 0.00 3.46
931 948 1.203313 CCCACGTTTCGTTTCGCTC 59.797 57.895 0.00 0.00 38.32 5.03
972 989 1.139947 CGCGAGAACCTTCCTCCTC 59.860 63.158 0.00 0.00 0.00 3.71
973 990 1.316706 CGCGAGAACCTTCCTCCTCT 61.317 60.000 0.00 0.00 0.00 3.69
974 991 0.458260 GCGAGAACCTTCCTCCTCTC 59.542 60.000 0.00 0.00 0.00 3.20
975 992 1.107945 CGAGAACCTTCCTCCTCTCC 58.892 60.000 0.00 0.00 32.35 3.71
976 993 1.341581 CGAGAACCTTCCTCCTCTCCT 60.342 57.143 0.00 0.00 32.35 3.69
986 1003 1.388547 CTCCTCTCCTCTTCTCACCG 58.611 60.000 0.00 0.00 0.00 4.94
987 1004 0.992695 TCCTCTCCTCTTCTCACCGA 59.007 55.000 0.00 0.00 0.00 4.69
989 1006 1.614583 CCTCTCCTCTTCTCACCGACA 60.615 57.143 0.00 0.00 0.00 4.35
1038 1055 3.418744 GACGCGGCCTCTCTTCCTC 62.419 68.421 12.47 0.00 0.00 3.71
1305 1322 0.037590 TAGAGCGTTGGCATTTGGGT 59.962 50.000 0.00 0.00 43.41 4.51
1310 1327 1.667510 GTTGGCATTTGGGTTGCGG 60.668 57.895 0.00 0.00 41.07 5.69
1364 1386 6.683974 ACTCCCTTTGACGAATATCAAATG 57.316 37.500 1.68 0.03 45.21 2.32
1366 1388 7.335627 ACTCCCTTTGACGAATATCAAATGTA 58.664 34.615 1.68 0.00 45.21 2.29
1425 1447 2.467566 TAGACCTTGGACCGAAAAGC 57.532 50.000 0.00 0.00 0.00 3.51
1426 1448 0.765510 AGACCTTGGACCGAAAAGCT 59.234 50.000 0.00 0.00 0.00 3.74
1489 1511 7.439356 CAGCTTTCCGTATCTGAATTCTGAATA 59.561 37.037 17.62 8.96 0.00 1.75
1492 1514 8.607441 TTTCCGTATCTGAATTCTGAATATGG 57.393 34.615 17.62 20.04 0.00 2.74
1493 1515 7.303182 TCCGTATCTGAATTCTGAATATGGT 57.697 36.000 23.52 12.20 0.00 3.55
1494 1516 7.154656 TCCGTATCTGAATTCTGAATATGGTG 58.845 38.462 23.52 12.25 0.00 4.17
1539 1561 7.212976 TGGTATCATTCTCTGCTCATAGTTTC 58.787 38.462 0.00 0.00 0.00 2.78
1675 1761 8.116651 TCTATTTTGCTAAAATGCTGGTAACA 57.883 30.769 13.65 0.00 42.52 2.41
1723 1809 5.183904 CCCTCATCTTTCGTTTGGAAGAAAT 59.816 40.000 0.00 0.00 36.02 2.17
1748 2070 5.021458 TGGTAGAAACTAGGGTTCTACTGG 58.979 45.833 29.15 0.00 36.90 4.00
1827 2163 4.116328 TCGTGCGCGAGGGAAGAG 62.116 66.667 20.10 0.00 42.81 2.85
1866 2202 1.746322 GCGGCTAGGGTTAGGTCTCC 61.746 65.000 0.00 0.00 0.00 3.71
1922 2258 7.596248 TGATTGCTTCTTGCTTAATCTCAAAAC 59.404 33.333 0.00 0.00 43.37 2.43
1970 2306 7.777889 ATCCTCCTAATGATATAATTGGGCT 57.222 36.000 9.88 0.00 37.91 5.19
2051 2388 2.222027 CCGCTCATAACATTTCTCCCC 58.778 52.381 0.00 0.00 0.00 4.81
2056 2393 3.042682 TCATAACATTTCTCCCCGCCTA 58.957 45.455 0.00 0.00 0.00 3.93
2122 2459 1.407258 GGAACTCCTCGAGGTGATCAG 59.593 57.143 34.06 24.12 33.75 2.90
2128 2465 1.657751 CTCGAGGTGATCAGCCGTCA 61.658 60.000 24.76 12.93 0.00 4.35
2147 2484 3.283684 CAAACACCTCCGCGGCAA 61.284 61.111 23.51 2.44 35.61 4.52
2194 2531 3.534056 GCGGCGGCTTCCTAGGTA 61.534 66.667 9.78 0.00 35.83 3.08
2198 2535 0.389757 GGCGGCTTCCTAGGTAGAAG 59.610 60.000 18.94 11.46 42.99 2.85
2199 2536 1.400737 GCGGCTTCCTAGGTAGAAGA 58.599 55.000 18.94 0.00 42.80 2.87
2200 2537 1.755380 GCGGCTTCCTAGGTAGAAGAA 59.245 52.381 18.94 0.00 42.80 2.52
2201 2538 2.223852 GCGGCTTCCTAGGTAGAAGAAG 60.224 54.545 18.94 10.06 42.80 2.85
2204 2541 3.719173 CTTCCTAGGTAGAAGAAGCCG 57.281 52.381 9.78 0.00 42.80 5.52
2205 2542 2.068834 TCCTAGGTAGAAGAAGCCGG 57.931 55.000 9.08 0.00 0.00 6.13
2206 2543 1.041437 CCTAGGTAGAAGAAGCCGGG 58.959 60.000 2.18 0.00 0.00 5.73
2207 2544 1.041437 CTAGGTAGAAGAAGCCGGGG 58.959 60.000 2.18 0.00 0.00 5.73
2208 2545 0.398098 TAGGTAGAAGAAGCCGGGGG 60.398 60.000 2.18 0.00 0.00 5.40
2222 2559 2.919043 GGGGGACATTGCCGAGAT 59.081 61.111 0.00 0.00 0.00 2.75
2223 2560 1.526917 GGGGGACATTGCCGAGATG 60.527 63.158 0.00 0.00 0.00 2.90
2225 2562 1.097547 GGGGACATTGCCGAGATGTG 61.098 60.000 3.54 0.00 37.83 3.21
2226 2563 0.107703 GGGACATTGCCGAGATGTGA 60.108 55.000 3.54 0.00 37.83 3.58
2227 2564 1.678728 GGGACATTGCCGAGATGTGAA 60.679 52.381 3.54 0.00 37.83 3.18
2228 2565 2.083774 GGACATTGCCGAGATGTGAAA 58.916 47.619 3.54 0.00 37.83 2.69
2229 2566 2.684881 GGACATTGCCGAGATGTGAAAT 59.315 45.455 3.54 0.00 37.83 2.17
2232 2569 2.634982 TTGCCGAGATGTGAAATTGC 57.365 45.000 0.00 0.00 0.00 3.56
2234 2571 1.469703 TGCCGAGATGTGAAATTGCTG 59.530 47.619 0.00 0.00 0.00 4.41
2236 2573 2.358957 CCGAGATGTGAAATTGCTGGA 58.641 47.619 0.00 0.00 0.00 3.86
2237 2574 2.947652 CCGAGATGTGAAATTGCTGGAT 59.052 45.455 0.00 0.00 0.00 3.41
2238 2575 4.129380 CCGAGATGTGAAATTGCTGGATA 58.871 43.478 0.00 0.00 0.00 2.59
2239 2576 4.758674 CCGAGATGTGAAATTGCTGGATAT 59.241 41.667 0.00 0.00 0.00 1.63
2240 2577 5.334646 CCGAGATGTGAAATTGCTGGATATG 60.335 44.000 0.00 0.00 0.00 1.78
2241 2578 5.449107 AGATGTGAAATTGCTGGATATGC 57.551 39.130 0.00 0.00 0.00 3.14
2242 2579 5.138276 AGATGTGAAATTGCTGGATATGCT 58.862 37.500 0.00 0.00 0.00 3.79
2243 2580 4.642445 TGTGAAATTGCTGGATATGCTG 57.358 40.909 0.00 0.00 0.00 4.41
2244 2581 4.271661 TGTGAAATTGCTGGATATGCTGA 58.728 39.130 5.27 0.00 0.00 4.26
2245 2582 4.891168 TGTGAAATTGCTGGATATGCTGAT 59.109 37.500 5.27 0.00 0.00 2.90
2247 2584 5.690409 GTGAAATTGCTGGATATGCTGATTG 59.310 40.000 5.27 0.00 0.00 2.67
2249 2586 5.864418 AATTGCTGGATATGCTGATTGTT 57.136 34.783 5.27 0.00 0.00 2.83
2250 2587 4.906065 TTGCTGGATATGCTGATTGTTC 57.094 40.909 5.27 0.00 0.00 3.18
2251 2588 4.160642 TGCTGGATATGCTGATTGTTCT 57.839 40.909 5.27 0.00 0.00 3.01
2252 2589 3.881089 TGCTGGATATGCTGATTGTTCTG 59.119 43.478 5.27 0.00 0.00 3.02
2253 2590 4.132336 GCTGGATATGCTGATTGTTCTGA 58.868 43.478 5.27 0.00 0.00 3.27
2255 2592 5.505324 GCTGGATATGCTGATTGTTCTGAAC 60.505 44.000 13.49 13.49 0.00 3.18
2258 2595 5.008415 GGATATGCTGATTGTTCTGAACCTG 59.992 44.000 17.26 7.69 0.00 4.00
2259 2596 2.507484 TGCTGATTGTTCTGAACCTGG 58.493 47.619 17.26 0.00 0.00 4.45
2261 2598 3.245016 TGCTGATTGTTCTGAACCTGGAT 60.245 43.478 17.26 6.76 0.00 3.41
2262 2599 3.128242 GCTGATTGTTCTGAACCTGGATG 59.872 47.826 17.26 5.40 0.00 3.51
2265 2602 5.005740 TGATTGTTCTGAACCTGGATGAAG 58.994 41.667 17.26 0.00 0.00 3.02
2266 2603 4.705110 TTGTTCTGAACCTGGATGAAGA 57.295 40.909 17.26 0.00 0.00 2.87
2267 2604 4.008074 TGTTCTGAACCTGGATGAAGAC 57.992 45.455 17.26 0.00 0.00 3.01
2268 2605 3.648067 TGTTCTGAACCTGGATGAAGACT 59.352 43.478 17.26 0.00 0.00 3.24
2269 2606 4.249661 GTTCTGAACCTGGATGAAGACTC 58.750 47.826 9.38 0.00 0.00 3.36
2272 2609 2.978978 TGAACCTGGATGAAGACTCCAA 59.021 45.455 0.00 0.00 42.12 3.53
2279 2832 2.948315 GGATGAAGACTCCAATTCCTGC 59.052 50.000 0.00 0.00 32.72 4.85
2282 2835 3.349927 TGAAGACTCCAATTCCTGCATG 58.650 45.455 0.00 0.00 0.00 4.06
2285 2838 3.771216 AGACTCCAATTCCTGCATGTTT 58.229 40.909 0.00 0.00 0.00 2.83
2292 2845 4.704540 CCAATTCCTGCATGTTTAGTACCA 59.295 41.667 0.00 0.00 0.00 3.25
2293 2846 5.360714 CCAATTCCTGCATGTTTAGTACCAT 59.639 40.000 0.00 0.00 0.00 3.55
2296 2849 5.372343 TCCTGCATGTTTAGTACCATCAT 57.628 39.130 0.00 0.00 0.00 2.45
2298 2851 5.130975 TCCTGCATGTTTAGTACCATCATCT 59.869 40.000 0.00 0.00 0.00 2.90
2310 2863 3.885484 CCATCATCTGGTTGTATTCGC 57.115 47.619 0.00 0.00 40.49 4.70
2311 2864 2.549754 CCATCATCTGGTTGTATTCGCC 59.450 50.000 0.00 0.00 40.49 5.54
2312 2865 3.205338 CATCATCTGGTTGTATTCGCCA 58.795 45.455 0.00 0.00 0.00 5.69
2313 2866 3.558931 TCATCTGGTTGTATTCGCCAT 57.441 42.857 0.00 0.00 0.00 4.40
2314 2867 3.205338 TCATCTGGTTGTATTCGCCATG 58.795 45.455 0.00 0.00 0.00 3.66
2315 2868 1.378531 TCTGGTTGTATTCGCCATGC 58.621 50.000 0.00 0.00 0.00 4.06
2318 2871 0.248621 GGTTGTATTCGCCATGCAGC 60.249 55.000 0.00 0.00 0.00 5.25
2319 2872 0.451383 GTTGTATTCGCCATGCAGCA 59.549 50.000 0.00 0.00 30.36 4.41
2320 2873 1.066002 GTTGTATTCGCCATGCAGCAT 59.934 47.619 0.52 0.52 30.36 3.79
2321 2874 0.946528 TGTATTCGCCATGCAGCATC 59.053 50.000 4.38 0.00 0.00 3.91
2323 2876 0.946528 TATTCGCCATGCAGCATCAC 59.053 50.000 4.38 0.00 0.00 3.06
2326 2879 2.110352 CGCCATGCAGCATCACAGA 61.110 57.895 4.38 0.00 0.00 3.41
2327 2880 1.650314 CGCCATGCAGCATCACAGAA 61.650 55.000 4.38 0.00 0.00 3.02
2328 2881 0.100682 GCCATGCAGCATCACAGAAG 59.899 55.000 4.38 0.00 0.00 2.85
2329 2882 1.746470 CCATGCAGCATCACAGAAGA 58.254 50.000 4.38 0.00 0.00 2.87
2330 2883 2.298610 CCATGCAGCATCACAGAAGAT 58.701 47.619 4.38 0.00 0.00 2.40
2331 2884 3.473625 CCATGCAGCATCACAGAAGATA 58.526 45.455 4.38 0.00 0.00 1.98
2332 2885 3.498777 CCATGCAGCATCACAGAAGATAG 59.501 47.826 4.38 0.00 0.00 2.08
2334 2887 2.093341 TGCAGCATCACAGAAGATAGCA 60.093 45.455 0.00 0.00 31.48 3.49
2335 2888 3.139850 GCAGCATCACAGAAGATAGCAT 58.860 45.455 0.00 0.00 0.00 3.79
2336 2889 3.564644 GCAGCATCACAGAAGATAGCATT 59.435 43.478 0.00 0.00 0.00 3.56
2337 2890 4.554919 GCAGCATCACAGAAGATAGCATTG 60.555 45.833 0.00 0.00 0.00 2.82
2338 2891 3.564644 AGCATCACAGAAGATAGCATTGC 59.435 43.478 0.00 0.00 0.00 3.56
2339 2892 3.304525 GCATCACAGAAGATAGCATTGCC 60.305 47.826 4.70 0.00 0.00 4.52
2340 2893 3.920231 TCACAGAAGATAGCATTGCCT 57.080 42.857 4.70 0.00 0.00 4.75
2406 3203 0.921347 GTAAGTACGTCGCAGCATGG 59.079 55.000 0.00 0.00 35.86 3.66
2444 3241 4.766891 TGCTCCTTCTAATTTGGTTCCTTG 59.233 41.667 0.00 0.00 0.00 3.61
2940 3737 7.612065 TGCCTAAGATAACTTGCCTAATCTA 57.388 36.000 0.00 0.00 37.53 1.98
3371 4173 0.616395 TGGGACGGTGATTCCTGCTA 60.616 55.000 0.00 0.00 33.17 3.49
3919 4733 4.865761 GCGCGTATGCTGGGTCGA 62.866 66.667 8.43 0.00 39.65 4.20
4533 5485 3.467226 CCCGGTGCCGAGTACCAT 61.467 66.667 12.71 0.00 38.20 3.55
5213 6229 7.612065 TGCCTAAGATAACTTGCCTAATCTA 57.388 36.000 0.00 0.00 37.53 1.98
5448 6465 2.224018 TGGTCCTTTTTGTGCTTGATGC 60.224 45.455 0.00 0.00 43.25 3.91
5476 6500 3.428452 CGCGATCTGTCTAACCCAACTAA 60.428 47.826 0.00 0.00 0.00 2.24
5618 6644 3.317608 CATCATTGCACGCCTGTTC 57.682 52.632 0.00 0.00 0.00 3.18
5674 6700 0.249955 TCCATCATTCTGCAGTGCGA 59.750 50.000 14.67 8.07 0.00 5.10
5778 6807 3.948851 TCGATACTCACGCATCACTTAC 58.051 45.455 0.00 0.00 0.00 2.34
5779 6808 3.626217 TCGATACTCACGCATCACTTACT 59.374 43.478 0.00 0.00 0.00 2.24
5780 6809 3.969352 CGATACTCACGCATCACTTACTC 59.031 47.826 0.00 0.00 0.00 2.59
5781 6810 4.495844 CGATACTCACGCATCACTTACTCA 60.496 45.833 0.00 0.00 0.00 3.41
5838 6867 8.263940 TGTTTGTATGTACTTAAATCCTCAGC 57.736 34.615 0.00 0.00 0.00 4.26
6044 7073 9.477484 AAGGTATGCTATAAACTATGTTCTTCG 57.523 33.333 0.00 0.00 0.00 3.79
6389 7418 4.774726 TGATGAGGCTGAACTAGAGTCTTT 59.225 41.667 0.00 0.00 0.00 2.52
6402 7431 4.574599 AGAGTCTTTTGGCAATGTTGAC 57.425 40.909 0.00 7.44 36.50 3.18
6516 7545 5.678955 AGGTGAAACTGGAGAAGTATACC 57.321 43.478 0.00 0.00 38.56 2.73
6739 7773 5.533528 TGATCATTCCCTTGTAGATGCATTG 59.466 40.000 0.00 0.00 0.00 2.82
6788 7824 4.824289 AGCATCAAAAGCCAAAATACCAG 58.176 39.130 0.00 0.00 0.00 4.00
6789 7825 4.284234 AGCATCAAAAGCCAAAATACCAGT 59.716 37.500 0.00 0.00 0.00 4.00
6803 7839 6.413783 AAATACCAGTGTGGGTTAAAAAGG 57.586 37.500 0.00 0.00 43.37 3.11
6809 7845 4.749598 CAGTGTGGGTTAAAAAGGCAAATC 59.250 41.667 0.00 0.00 0.00 2.17
6860 8135 8.034215 TGTAAAACTCATGCATCCTTTTATTGG 58.966 33.333 0.00 0.00 0.00 3.16
6868 8143 8.922237 TCATGCATCCTTTTATTGGCTTAATTA 58.078 29.630 0.00 0.00 0.00 1.40
6890 8165 7.966246 TTAGTAAAACTAATTGCCGAAGTCA 57.034 32.000 0.00 0.00 35.89 3.41
6900 8175 8.150945 ACTAATTGCCGAAGTCATTACATATCT 58.849 33.333 0.00 0.00 0.00 1.98
6912 8187 9.314133 AGTCATTACATATCTAGATGCTTGGTA 57.686 33.333 15.79 7.41 0.00 3.25
6930 8205 6.127619 GCTTGGTAGTTGGAATAGATGCTTTT 60.128 38.462 0.00 0.00 0.00 2.27
6976 8252 7.930865 AGAGCTGGTCTATAATTTGATCAAGAC 59.069 37.037 7.75 10.87 31.71 3.01
6978 8254 6.480320 GCTGGTCTATAATTTGATCAAGACGT 59.520 38.462 8.41 0.00 35.34 4.34
6983 8259 9.031360 GTCTATAATTTGATCAAGACGTGCTTA 57.969 33.333 8.41 1.06 34.31 3.09
7049 8327 3.427098 CGATGCATTCAGTTGCTGTTGAT 60.427 43.478 0.00 0.00 43.18 2.57
7079 8357 3.253188 TGACAAAATGCTTAGTGACTGGC 59.747 43.478 0.00 0.00 0.00 4.85
7080 8358 3.221771 ACAAAATGCTTAGTGACTGGCA 58.778 40.909 15.05 15.05 39.06 4.92
7089 8374 4.379918 GCTTAGTGACTGGCAAATTCCTTC 60.380 45.833 0.00 0.00 0.00 3.46
7102 8387 5.694910 GCAAATTCCTTCATATTCTGCATGG 59.305 40.000 0.00 0.00 0.00 3.66
7109 8394 5.824624 CCTTCATATTCTGCATGGTAGTTGT 59.175 40.000 0.00 0.00 0.00 3.32
7145 8430 1.808945 GTCCTCATGTTTGCTGGACTG 59.191 52.381 0.00 0.00 40.21 3.51
7370 8656 3.504906 CCAATATGGTGGCAATCTAGCAG 59.495 47.826 0.00 0.00 31.84 4.24
7389 8675 3.877559 CAGTGTGGAAGATGATTGGCTA 58.122 45.455 0.00 0.00 0.00 3.93
7472 8766 2.621998 CTCCATGCTCAATAAAGGCTGG 59.378 50.000 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 46 0.033504 TTCCACTCGGTGCTTCAGAC 59.966 55.000 0.00 0.00 31.34 3.51
106 108 1.497278 CAACCCATCGCTGACAACG 59.503 57.895 0.00 0.00 0.00 4.10
114 116 0.388520 GCTTTGTTCCAACCCATCGC 60.389 55.000 0.00 0.00 0.00 4.58
115 117 0.109781 CGCTTTGTTCCAACCCATCG 60.110 55.000 0.00 0.00 0.00 3.84
182 184 0.464036 AGCACCGTGAAGTCTTGTCA 59.536 50.000 1.65 0.00 0.00 3.58
221 223 4.057406 TCCTCACAAGGCAAATGTTTTG 57.943 40.909 0.00 0.00 43.02 2.44
268 270 1.797933 CGGCTTCACGTCACTCTCG 60.798 63.158 0.00 0.00 0.00 4.04
274 276 2.355837 GAGTGCGGCTTCACGTCA 60.356 61.111 0.00 0.00 41.61 4.35
423 425 0.659123 AATTCGTGGCGACGTTTTGC 60.659 50.000 20.82 0.00 46.20 3.68
432 434 0.725117 GGGTACTTGAATTCGTGGCG 59.275 55.000 0.04 0.00 0.00 5.69
438 440 3.048337 TCGTGGTGGGTACTTGAATTC 57.952 47.619 0.00 0.00 0.00 2.17
520 522 1.965930 GTCAATGCCACGGTGAGCA 60.966 57.895 20.96 20.96 44.45 4.26
732 734 2.202690 CGTAGCCATGGACGCGAA 60.203 61.111 18.40 0.00 31.49 4.70
830 840 0.518636 CGCTCAATCAATATGGGCCG 59.481 55.000 0.00 0.00 41.33 6.13
882 899 3.615509 TTAACGGGCCGGGCTCTTG 62.616 63.158 31.78 17.08 0.00 3.02
931 948 2.491022 TTTTGGTTTGGGGACGCGG 61.491 57.895 12.47 0.00 0.00 6.46
972 989 1.067495 GGTTGTCGGTGAGAAGAGGAG 60.067 57.143 0.00 0.00 0.00 3.69
973 990 0.966920 GGTTGTCGGTGAGAAGAGGA 59.033 55.000 0.00 0.00 0.00 3.71
974 991 0.388649 CGGTTGTCGGTGAGAAGAGG 60.389 60.000 0.00 0.00 34.75 3.69
975 992 0.314302 ACGGTTGTCGGTGAGAAGAG 59.686 55.000 0.00 0.00 44.45 2.85
976 993 0.313043 GACGGTTGTCGGTGAGAAGA 59.687 55.000 0.00 0.00 44.45 2.87
986 1003 1.078759 CTCCATGAGCGACGGTTGTC 61.079 60.000 0.00 0.00 41.91 3.18
987 1004 1.079819 CTCCATGAGCGACGGTTGT 60.080 57.895 0.00 0.00 0.00 3.32
989 1006 2.579201 CCTCCATGAGCGACGGTT 59.421 61.111 0.00 0.00 0.00 4.44
1274 1291 3.307242 CCAACGCTCTACAGAATTAGTGC 59.693 47.826 0.00 0.00 35.93 4.40
1305 1322 4.458989 AGCTAACATCAAAATTCTCCGCAA 59.541 37.500 0.00 0.00 0.00 4.85
1425 1447 3.777106 TGCCTCCAATAATCTGCCTAG 57.223 47.619 0.00 0.00 0.00 3.02
1426 1448 4.729552 ATTGCCTCCAATAATCTGCCTA 57.270 40.909 0.00 0.00 39.81 3.93
1489 1511 3.928005 ATGCTCAGAGAATGACACCAT 57.072 42.857 0.00 0.00 33.22 3.55
1492 1514 5.064452 CCAAACTATGCTCAGAGAATGACAC 59.936 44.000 0.00 0.00 33.22 3.67
1493 1515 5.181009 CCAAACTATGCTCAGAGAATGACA 58.819 41.667 0.00 0.00 33.22 3.58
1494 1516 5.181748 ACCAAACTATGCTCAGAGAATGAC 58.818 41.667 0.00 0.00 33.22 3.06
1723 1809 6.837568 CCAGTAGAACCCTAGTTTCTACCATA 59.162 42.308 24.63 3.58 37.34 2.74
1748 2070 1.614413 CTACAATCTCCGCCCTAGACC 59.386 57.143 0.00 0.00 0.00 3.85
1922 2258 9.367444 GATTATATAAACTCATGTAAGGACCCG 57.633 37.037 0.00 0.00 0.00 5.28
1970 2306 6.552350 AGTTATCTTATCGTGTTAGGGGCTTA 59.448 38.462 0.00 0.00 0.00 3.09
2005 2341 0.618458 TTACAGCCAGGCAGTTAGGG 59.382 55.000 15.73 0.00 29.63 3.53
2006 2342 2.717639 ATTACAGCCAGGCAGTTAGG 57.282 50.000 15.73 0.00 29.63 2.69
2051 2388 0.944311 ACGAGCTGTTTGTGTAGGCG 60.944 55.000 0.00 0.00 0.00 5.52
2056 2393 0.597637 CGAGGACGAGCTGTTTGTGT 60.598 55.000 0.00 0.00 42.66 3.72
2097 2434 1.292223 CCTCGAGGAGTTCCGCAAA 59.708 57.895 28.21 0.00 42.08 3.68
2122 2459 2.258726 GGAGGTGTTTGGTGACGGC 61.259 63.158 0.00 0.00 0.00 5.68
2177 2514 3.501458 CTACCTAGGAAGCCGCCGC 62.501 68.421 17.98 0.00 0.00 6.53
2178 2515 1.389609 TTCTACCTAGGAAGCCGCCG 61.390 60.000 17.98 0.00 0.00 6.46
2179 2516 0.389757 CTTCTACCTAGGAAGCCGCC 59.610 60.000 17.98 0.00 34.66 6.13
2180 2517 1.400737 TCTTCTACCTAGGAAGCCGC 58.599 55.000 17.98 0.00 39.75 6.53
2181 2518 3.719173 CTTCTTCTACCTAGGAAGCCG 57.281 52.381 17.98 0.63 39.75 5.52
2184 2521 2.362717 CCGGCTTCTTCTACCTAGGAAG 59.637 54.545 17.98 9.15 40.85 3.46
2185 2522 2.385803 CCGGCTTCTTCTACCTAGGAA 58.614 52.381 17.98 0.00 0.00 3.36
2186 2523 1.411216 CCCGGCTTCTTCTACCTAGGA 60.411 57.143 17.98 0.00 0.00 2.94
2187 2524 1.041437 CCCGGCTTCTTCTACCTAGG 58.959 60.000 7.41 7.41 0.00 3.02
2188 2525 1.041437 CCCCGGCTTCTTCTACCTAG 58.959 60.000 0.00 0.00 0.00 3.02
2189 2526 0.398098 CCCCCGGCTTCTTCTACCTA 60.398 60.000 0.00 0.00 0.00 3.08
2205 2542 1.526917 CATCTCGGCAATGTCCCCC 60.527 63.158 0.00 0.00 0.00 5.40
2206 2543 1.097547 CACATCTCGGCAATGTCCCC 61.098 60.000 0.00 0.00 35.19 4.81
2207 2544 0.107703 TCACATCTCGGCAATGTCCC 60.108 55.000 0.00 0.00 35.19 4.46
2208 2545 1.737838 TTCACATCTCGGCAATGTCC 58.262 50.000 0.00 0.00 35.19 4.02
2209 2546 4.100529 CAATTTCACATCTCGGCAATGTC 58.899 43.478 0.00 0.00 35.19 3.06
2210 2547 3.674138 GCAATTTCACATCTCGGCAATGT 60.674 43.478 0.00 0.00 37.85 2.71
2211 2548 2.855963 GCAATTTCACATCTCGGCAATG 59.144 45.455 0.00 0.00 0.00 2.82
2214 2551 1.469703 CAGCAATTTCACATCTCGGCA 59.530 47.619 0.00 0.00 0.00 5.69
2215 2552 1.202222 CCAGCAATTTCACATCTCGGC 60.202 52.381 0.00 0.00 0.00 5.54
2216 2553 2.358957 TCCAGCAATTTCACATCTCGG 58.641 47.619 0.00 0.00 0.00 4.63
2217 2554 5.686834 CATATCCAGCAATTTCACATCTCG 58.313 41.667 0.00 0.00 0.00 4.04
2218 2555 5.241064 AGCATATCCAGCAATTTCACATCTC 59.759 40.000 0.00 0.00 0.00 2.75
2219 2556 5.009710 CAGCATATCCAGCAATTTCACATCT 59.990 40.000 0.00 0.00 0.00 2.90
2220 2557 5.009310 TCAGCATATCCAGCAATTTCACATC 59.991 40.000 0.00 0.00 0.00 3.06
2221 2558 4.891168 TCAGCATATCCAGCAATTTCACAT 59.109 37.500 0.00 0.00 0.00 3.21
2222 2559 4.271661 TCAGCATATCCAGCAATTTCACA 58.728 39.130 0.00 0.00 0.00 3.58
2223 2560 4.906065 TCAGCATATCCAGCAATTTCAC 57.094 40.909 0.00 0.00 0.00 3.18
2225 2562 5.839621 ACAATCAGCATATCCAGCAATTTC 58.160 37.500 0.00 0.00 0.00 2.17
2226 2563 5.864418 ACAATCAGCATATCCAGCAATTT 57.136 34.783 0.00 0.00 0.00 1.82
2227 2564 5.597182 AGAACAATCAGCATATCCAGCAATT 59.403 36.000 0.00 0.00 0.00 2.32
2228 2565 5.009710 CAGAACAATCAGCATATCCAGCAAT 59.990 40.000 0.00 0.00 0.00 3.56
2229 2566 4.337274 CAGAACAATCAGCATATCCAGCAA 59.663 41.667 0.00 0.00 0.00 3.91
2232 2569 5.008415 GGTTCAGAACAATCAGCATATCCAG 59.992 44.000 15.36 0.00 0.00 3.86
2234 2571 5.008415 CAGGTTCAGAACAATCAGCATATCC 59.992 44.000 15.36 0.00 0.00 2.59
2236 2573 4.885907 CCAGGTTCAGAACAATCAGCATAT 59.114 41.667 15.36 0.00 0.00 1.78
2237 2574 4.019411 TCCAGGTTCAGAACAATCAGCATA 60.019 41.667 15.36 0.00 0.00 3.14
2238 2575 3.087031 CCAGGTTCAGAACAATCAGCAT 58.913 45.455 15.36 0.00 0.00 3.79
2239 2576 2.106338 TCCAGGTTCAGAACAATCAGCA 59.894 45.455 15.36 0.00 0.00 4.41
2240 2577 2.783135 TCCAGGTTCAGAACAATCAGC 58.217 47.619 15.36 0.00 0.00 4.26
2241 2578 4.582869 TCATCCAGGTTCAGAACAATCAG 58.417 43.478 15.36 0.80 0.00 2.90
2242 2579 4.639078 TCATCCAGGTTCAGAACAATCA 57.361 40.909 15.36 0.00 0.00 2.57
2243 2580 5.123027 GTCTTCATCCAGGTTCAGAACAATC 59.877 44.000 15.36 0.00 0.00 2.67
2244 2581 5.006386 GTCTTCATCCAGGTTCAGAACAAT 58.994 41.667 15.36 0.04 0.00 2.71
2245 2582 4.103153 AGTCTTCATCCAGGTTCAGAACAA 59.897 41.667 15.36 0.00 0.00 2.83
2247 2584 4.249661 GAGTCTTCATCCAGGTTCAGAAC 58.750 47.826 4.52 4.52 0.00 3.01
2249 2586 2.834549 GGAGTCTTCATCCAGGTTCAGA 59.165 50.000 0.00 0.00 36.79 3.27
2250 2587 2.568956 TGGAGTCTTCATCCAGGTTCAG 59.431 50.000 0.00 0.00 41.96 3.02
2251 2588 2.619931 TGGAGTCTTCATCCAGGTTCA 58.380 47.619 0.00 0.00 41.96 3.18
2258 2595 2.948315 GCAGGAATTGGAGTCTTCATCC 59.052 50.000 0.00 0.00 37.35 3.51
2259 2596 3.614092 TGCAGGAATTGGAGTCTTCATC 58.386 45.455 0.00 0.00 0.00 2.92
2261 2598 3.245016 ACATGCAGGAATTGGAGTCTTCA 60.245 43.478 4.84 0.00 0.00 3.02
2262 2599 3.350833 ACATGCAGGAATTGGAGTCTTC 58.649 45.455 4.84 0.00 0.00 2.87
2265 2602 4.702131 ACTAAACATGCAGGAATTGGAGTC 59.298 41.667 4.84 0.00 0.00 3.36
2266 2603 4.666512 ACTAAACATGCAGGAATTGGAGT 58.333 39.130 4.84 0.00 0.00 3.85
2267 2604 5.066505 GGTACTAAACATGCAGGAATTGGAG 59.933 44.000 4.84 0.00 0.00 3.86
2268 2605 4.947388 GGTACTAAACATGCAGGAATTGGA 59.053 41.667 4.84 0.00 0.00 3.53
2269 2606 4.704540 TGGTACTAAACATGCAGGAATTGG 59.295 41.667 4.84 4.44 0.00 3.16
2272 2609 5.754782 TGATGGTACTAAACATGCAGGAAT 58.245 37.500 4.84 0.00 0.00 3.01
2292 2845 3.558931 TGGCGAATACAACCAGATGAT 57.441 42.857 0.00 0.00 0.00 2.45
2293 2846 3.205338 CATGGCGAATACAACCAGATGA 58.795 45.455 0.00 0.00 36.78 2.92
2296 2849 1.339535 TGCATGGCGAATACAACCAGA 60.340 47.619 0.00 0.00 36.78 3.86
2298 2851 1.093972 CTGCATGGCGAATACAACCA 58.906 50.000 0.00 0.00 37.99 3.67
2300 2853 0.451383 TGCTGCATGGCGAATACAAC 59.549 50.000 0.00 0.00 34.52 3.32
2301 2854 1.334556 GATGCTGCATGGCGAATACAA 59.665 47.619 21.53 0.00 34.52 2.41
2303 2856 0.946528 TGATGCTGCATGGCGAATAC 59.053 50.000 21.53 3.24 34.52 1.89
2304 2857 0.946528 GTGATGCTGCATGGCGAATA 59.053 50.000 21.53 0.00 34.52 1.75
2305 2858 1.033202 TGTGATGCTGCATGGCGAAT 61.033 50.000 21.53 0.00 34.52 3.34
2306 2859 1.650314 CTGTGATGCTGCATGGCGAA 61.650 55.000 21.53 0.11 34.52 4.70
2307 2860 2.046120 TGTGATGCTGCATGGCGA 60.046 55.556 21.53 0.00 34.52 5.54
2309 2862 0.100682 CTTCTGTGATGCTGCATGGC 59.899 55.000 21.53 12.47 0.00 4.40
2310 2863 1.746470 TCTTCTGTGATGCTGCATGG 58.254 50.000 21.53 7.43 0.00 3.66
2311 2864 3.058846 GCTATCTTCTGTGATGCTGCATG 60.059 47.826 21.53 5.56 0.00 4.06
2312 2865 3.139850 GCTATCTTCTGTGATGCTGCAT 58.860 45.455 16.20 16.20 0.00 3.96
2313 2866 2.093341 TGCTATCTTCTGTGATGCTGCA 60.093 45.455 4.13 4.13 0.00 4.41
2314 2867 2.558378 TGCTATCTTCTGTGATGCTGC 58.442 47.619 0.00 0.00 0.00 5.25
2315 2868 4.554919 GCAATGCTATCTTCTGTGATGCTG 60.555 45.833 0.00 0.00 0.00 4.41
2318 2871 4.023963 CAGGCAATGCTATCTTCTGTGATG 60.024 45.833 4.82 0.00 0.00 3.07
2319 2872 4.135306 CAGGCAATGCTATCTTCTGTGAT 58.865 43.478 4.82 0.00 0.00 3.06
2320 2873 3.538591 CAGGCAATGCTATCTTCTGTGA 58.461 45.455 4.82 0.00 0.00 3.58
2321 2874 3.965292 CAGGCAATGCTATCTTCTGTG 57.035 47.619 4.82 0.00 0.00 3.66
2642 3439 6.606395 GGTAGAGTACTTGATCCTACCAGAAA 59.394 42.308 23.37 0.00 45.25 2.52
2643 3440 6.127793 GGTAGAGTACTTGATCCTACCAGAA 58.872 44.000 23.37 0.00 45.25 3.02
2746 3543 3.470888 GCCCTTCTCCTAGCCGCA 61.471 66.667 0.00 0.00 0.00 5.69
3477 4279 1.303091 GCGCCGAGTTATTTGTGGGT 61.303 55.000 0.00 0.00 0.00 4.51
5331 6348 5.467902 TTTTTCTGCAAAACAATCAGCAC 57.532 34.783 0.00 0.00 30.89 4.40
5448 6465 3.050619 GGTTAGACAGATCGCGTATTGG 58.949 50.000 5.77 0.00 0.00 3.16
5618 6644 5.303845 TCCTGATCTTAGATCACCACATCTG 59.696 44.000 19.74 8.48 34.75 2.90
5778 6807 8.131100 ACAAAATCACATCTTTGTACAACTGAG 58.869 33.333 8.07 3.50 42.47 3.35
5779 6808 7.995289 ACAAAATCACATCTTTGTACAACTGA 58.005 30.769 8.07 10.14 42.47 3.41
5780 6809 7.379529 GGACAAAATCACATCTTTGTACAACTG 59.620 37.037 8.07 8.89 43.88 3.16
5781 6810 7.425606 GGACAAAATCACATCTTTGTACAACT 58.574 34.615 8.07 0.00 43.88 3.16
5891 6920 2.370189 CTCCAGAAGAGTGTCAAACCCT 59.630 50.000 0.00 0.00 37.87 4.34
5905 6934 2.679092 CAGGCCATGGCTCCAGAA 59.321 61.111 34.70 0.00 41.60 3.02
5906 6935 4.119363 GCAGGCCATGGCTCCAGA 62.119 66.667 34.70 0.00 41.60 3.86
6389 7418 1.196581 CGTCATCGTCAACATTGCCAA 59.803 47.619 0.00 0.00 0.00 4.52
6402 7431 0.298707 CGCCATCTTCAACGTCATCG 59.701 55.000 0.00 0.00 43.34 3.84
6516 7545 0.969894 ACCTCAAGACCTTCTCCACG 59.030 55.000 0.00 0.00 0.00 4.94
6621 7650 2.359848 CCATCGTAATAGTGGTCACCGA 59.640 50.000 0.00 0.29 0.00 4.69
6766 7802 4.284234 ACTGGTATTTTGGCTTTTGATGCT 59.716 37.500 0.00 0.00 0.00 3.79
6788 7824 4.956085 AGATTTGCCTTTTTAACCCACAC 58.044 39.130 0.00 0.00 0.00 3.82
6789 7825 6.325286 ACTTAGATTTGCCTTTTTAACCCACA 59.675 34.615 0.00 0.00 0.00 4.17
6803 7839 8.669243 AGAGTTGTGCTAATTACTTAGATTTGC 58.331 33.333 4.14 0.00 37.16 3.68
6837 8112 5.876460 GCCAATAAAAGGATGCATGAGTTTT 59.124 36.000 2.46 9.47 0.00 2.43
6868 8143 7.448748 AATGACTTCGGCAATTAGTTTTACT 57.551 32.000 0.00 0.00 0.00 2.24
6884 8159 9.149225 CCAAGCATCTAGATATGTAATGACTTC 57.851 37.037 4.54 0.00 0.00 3.01
6889 8164 9.935241 AACTACCAAGCATCTAGATATGTAATG 57.065 33.333 4.54 0.00 0.00 1.90
6890 8165 9.935241 CAACTACCAAGCATCTAGATATGTAAT 57.065 33.333 4.54 0.00 0.00 1.89
6900 8175 7.445121 CATCTATTCCAACTACCAAGCATCTA 58.555 38.462 0.00 0.00 0.00 1.98
6946 8221 8.489489 TGATCAAATTATAGACCAGCTCTTCTT 58.511 33.333 0.00 0.00 0.00 2.52
6976 8252 6.311445 AGAACATCAGAAGTAACATAAGCACG 59.689 38.462 0.00 0.00 0.00 5.34
6978 8254 6.818644 GGAGAACATCAGAAGTAACATAAGCA 59.181 38.462 0.00 0.00 0.00 3.91
6983 8259 6.773638 ACAAGGAGAACATCAGAAGTAACAT 58.226 36.000 0.00 0.00 0.00 2.71
7049 8327 1.308047 AGCATTTTGTCACGCACAGA 58.692 45.000 0.00 0.00 35.97 3.41
7079 8357 6.812998 ACCATGCAGAATATGAAGGAATTTG 58.187 36.000 0.00 0.00 0.00 2.32
7080 8358 7.781693 ACTACCATGCAGAATATGAAGGAATTT 59.218 33.333 0.00 0.00 0.00 1.82
7089 8374 6.682423 TCAACAACTACCATGCAGAATATG 57.318 37.500 0.00 0.00 0.00 1.78
7102 8387 4.154918 CCTGCAGAGGAATTCAACAACTAC 59.845 45.833 17.39 0.00 42.93 2.73
7109 8394 1.988107 AGGACCTGCAGAGGAATTCAA 59.012 47.619 17.39 0.00 42.93 2.69
7145 8430 9.842775 AGGCTACCAAGGTTTAATTAACTATAC 57.157 33.333 0.00 0.00 36.93 1.47
7210 8496 9.397280 CTGGATAAATGATGAAGATATGCTGAT 57.603 33.333 0.00 0.00 0.00 2.90
7370 8656 3.209410 CCTAGCCAATCATCTTCCACAC 58.791 50.000 0.00 0.00 0.00 3.82
7389 8675 4.323417 TCATTCGTGAAGTTTGCATACCT 58.677 39.130 3.47 0.00 0.00 3.08
7472 8766 2.805099 GGCGAATCCACTCAATCATCTC 59.195 50.000 0.00 0.00 34.01 2.75
7503 8797 6.327934 TCTCTACGACCAAAGTTATTGCTAC 58.672 40.000 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.