Multiple sequence alignment - TraesCS2A01G508300

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 TraesCS2A01G508300 chr2A 100.000 5941 0 0 1 5941 734897481 734891541 0.000000e+00 10972.0
1 TraesCS2A01G508300 chr2A 85.068 1614 221 16 3337 4939 735342411 735344015 0.000000e+00 1628.0
2 TraesCS2A01G508300 chr2A 93.750 64 4 0 1432 1495 735389137 735389200 4.900000e-16 97.1
3 TraesCS2A01G508300 chr2A 97.059 34 1 0 315 348 735379495 735379528 2.310000e-04 58.4
4 TraesCS2A01G508300 chr2D 93.810 2084 125 4 3575 5654 601603435 601601352 0.000000e+00 3131.0
5 TraesCS2A01G508300 chr2D 88.262 1772 127 36 777 2512 601693684 601691958 0.000000e+00 2045.0
6 TraesCS2A01G508300 chr2D 87.114 1521 177 14 3328 4842 601717637 601716130 0.000000e+00 1705.0
7 TraesCS2A01G508300 chr2D 86.207 1508 197 10 3338 4840 602703933 602705434 0.000000e+00 1622.0
8 TraesCS2A01G508300 chr2D 90.987 699 44 9 67 755 601694368 601693679 0.000000e+00 924.0
9 TraesCS2A01G508300 chr2D 91.748 618 32 10 2713 3327 601691923 601691322 0.000000e+00 841.0
10 TraesCS2A01G508300 chr2D 81.415 947 94 36 1606 2513 601657248 601656345 0.000000e+00 699.0
11 TraesCS2A01G508300 chr2D 94.056 286 12 3 5656 5941 601601302 601601022 4.250000e-116 429.0
12 TraesCS2A01G508300 chr2D 79.022 634 88 32 888 1490 601729831 601729212 5.580000e-105 392.0
13 TraesCS2A01G508300 chr2D 80.138 579 58 27 964 1496 601967261 601966694 4.350000e-101 379.0
14 TraesCS2A01G508300 chr2D 87.705 244 28 2 1076 1317 602739808 602740051 3.500000e-72 283.0
15 TraesCS2A01G508300 chr2D 95.522 67 3 0 1 67 601694482 601694416 2.260000e-19 108.0
16 TraesCS2A01G508300 chr2D 76.596 188 28 11 1432 1617 602766826 602766999 8.200000e-14 89.8
17 TraesCS2A01G508300 chr2D 82.979 94 13 2 2713 2803 601656311 601656218 1.370000e-11 82.4
18 TraesCS2A01G508300 chr2B 93.317 2095 119 10 3575 5654 731897107 731895019 0.000000e+00 3073.0
19 TraesCS2A01G508300 chr2B 91.294 1700 123 15 3345 5039 732013876 732012197 0.000000e+00 2296.0
20 TraesCS2A01G508300 chr2B 90.893 1724 125 17 3328 5039 732018666 732016963 0.000000e+00 2285.0
21 TraesCS2A01G508300 chr2B 91.125 1555 101 12 992 2512 732020910 732019359 0.000000e+00 2073.0
22 TraesCS2A01G508300 chr2B 89.526 1499 135 15 3337 4829 732040170 732038688 0.000000e+00 1879.0
23 TraesCS2A01G508300 chr2B 87.647 1619 181 15 3328 4931 732046262 732044648 0.000000e+00 1864.0
24 TraesCS2A01G508300 chr2B 90.598 936 56 12 1606 2512 732015524 732014592 0.000000e+00 1212.0
25 TraesCS2A01G508300 chr2B 88.337 926 66 15 94 996 732024222 732023316 0.000000e+00 1074.0
26 TraesCS2A01G508300 chr2B 93.053 619 30 8 2713 3327 732019324 732018715 0.000000e+00 893.0
27 TraesCS2A01G508300 chr2B 92.730 619 32 8 2713 3327 732014557 732013948 0.000000e+00 881.0
28 TraesCS2A01G508300 chr2B 78.487 846 88 40 1269 2097 732016941 732016173 9.020000e-128 468.0
29 TraesCS2A01G508300 chr2B 94.464 289 12 2 5656 5941 731894969 731894682 5.460000e-120 442.0
30 TraesCS2A01G508300 chr2B 77.896 846 93 35 1269 2097 732012175 732011407 1.970000e-119 440.0
31 TraesCS2A01G508300 chr2B 84.334 383 35 13 2883 3257 732046764 732046399 9.470000e-93 351.0
32 TraesCS2A01G508300 chr2B 78.975 566 74 27 949 1490 732049942 732049398 1.590000e-90 344.0
33 TraesCS2A01G508300 chr2B 84.179 335 43 9 3001 3330 732040549 732040220 3.460000e-82 316.0
34 TraesCS2A01G508300 chr2B 79.355 465 66 20 1050 1495 732042156 732041703 3.480000e-77 300.0
35 TraesCS2A01G508300 chr2B 88.400 250 27 1 1076 1323 733179066 733179315 3.480000e-77 300.0
36 TraesCS2A01G508300 chr2B 80.523 421 44 13 2123 2509 731945518 731945102 7.530000e-74 289.0
37 TraesCS2A01G508300 chrUn 85.333 450 45 13 2883 3327 296303196 296302763 4.220000e-121 446.0
38 TraesCS2A01G508300 chrUn 85.333 450 45 13 2883 3327 376650187 376649754 4.220000e-121 446.0
39 TraesCS2A01G508300 chrUn 85.235 447 45 13 2883 3324 15296091 15296521 1.970000e-119 440.0
40 TraesCS2A01G508300 chrUn 85.202 446 46 12 2883 3324 258621104 258621533 1.970000e-119 440.0
41 TraesCS2A01G508300 chrUn 77.919 471 71 19 1044 1492 15283066 15283525 4.570000e-66 263.0
42 TraesCS2A01G508300 chrUn 77.919 471 71 19 1044 1492 15302550 15303009 4.570000e-66 263.0
43 TraesCS2A01G508300 chrUn 91.620 179 14 1 2536 2714 42253715 42253892 4.600000e-61 246.0
44 TraesCS2A01G508300 chr7A 96.045 177 7 0 2536 2712 722229558 722229382 7.530000e-74 289.0
45 TraesCS2A01G508300 chr7D 82.243 321 53 3 5045 5365 596241337 596241021 2.110000e-69 274.0
46 TraesCS2A01G508300 chr7B 81.734 323 54 4 5045 5366 674310338 674310020 1.270000e-66 265.0
47 TraesCS2A01G508300 chr7B 86.897 145 18 1 5783 5927 674307409 674307266 1.710000e-35 161.0
48 TraesCS2A01G508300 chr5A 93.370 181 8 2 2536 2712 25124009 25124189 1.270000e-66 265.0
49 TraesCS2A01G508300 chr3B 92.778 180 10 1 2536 2712 754454791 754454612 2.120000e-64 257.0
50 TraesCS2A01G508300 chr3A 91.398 186 12 4 2534 2717 679300297 679300114 9.880000e-63 252.0
51 TraesCS2A01G508300 chr4A 92.045 176 13 1 2537 2712 715606091 715605917 4.600000e-61 246.0
52 TraesCS2A01G508300 chr4B 85.641 195 22 6 2529 2719 19559603 19559411 3.630000e-47 200.0
53 TraesCS2A01G508300 chr4B 85.475 179 23 3 2536 2712 488145110 488145287 3.660000e-42 183.0
54 TraesCS2A01G508300 chr1B 86.111 180 23 2 2534 2712 250062641 250062819 6.080000e-45 193.0


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 TraesCS2A01G508300 chr2A 734891541 734897481 5940 True 10972.000000 10972 100.000000 1 5941 1 chr2A.!!$R1 5940
1 TraesCS2A01G508300 chr2A 735342411 735344015 1604 False 1628.000000 1628 85.068000 3337 4939 1 chr2A.!!$F1 1602
2 TraesCS2A01G508300 chr2D 601601022 601603435 2413 True 1780.000000 3131 93.933000 3575 5941 2 chr2D.!!$R4 2366
3 TraesCS2A01G508300 chr2D 601716130 601717637 1507 True 1705.000000 1705 87.114000 3328 4842 1 chr2D.!!$R1 1514
4 TraesCS2A01G508300 chr2D 602703933 602705434 1501 False 1622.000000 1622 86.207000 3338 4840 1 chr2D.!!$F1 1502
5 TraesCS2A01G508300 chr2D 601691322 601694482 3160 True 979.500000 2045 91.629750 1 3327 4 chr2D.!!$R6 3326
6 TraesCS2A01G508300 chr2D 601729212 601729831 619 True 392.000000 392 79.022000 888 1490 1 chr2D.!!$R2 602
7 TraesCS2A01G508300 chr2D 601656218 601657248 1030 True 390.700000 699 82.197000 1606 2803 2 chr2D.!!$R5 1197
8 TraesCS2A01G508300 chr2D 601966694 601967261 567 True 379.000000 379 80.138000 964 1496 1 chr2D.!!$R3 532
9 TraesCS2A01G508300 chr2B 731894682 731897107 2425 True 1757.500000 3073 93.890500 3575 5941 2 chr2B.!!$R2 2366
10 TraesCS2A01G508300 chr2B 732011407 732024222 12815 True 1291.333333 2296 88.268111 94 5039 9 chr2B.!!$R3 4945
11 TraesCS2A01G508300 chr2B 732038688 732049942 11254 True 842.333333 1879 84.002667 949 4931 6 chr2B.!!$R4 3982
12 TraesCS2A01G508300 chr7B 674307266 674310338 3072 True 213.000000 265 84.315500 5045 5927 2 chr7B.!!$R1 882

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
287 336 0.035439 TCCCTTTCGTGAGGCCATTC 60.035 55.0 5.01 0.00 35.37 2.67 F
293 342 0.320374 TCGTGAGGCCATTCGAGTTT 59.680 50.0 5.01 0.00 0.00 2.66 F
1323 3839 0.389166 GTCCAGAGCAAGACCGTGAG 60.389 60.0 0.00 0.00 0.00 3.51 F
1750 4275 0.041576 CCGCGTTCATAGTCGATCGA 60.042 55.0 15.15 15.15 31.29 3.59 F
2672 5517 0.613012 ATGTTTGCCTCCCCTTCAGC 60.613 55.0 0.00 0.00 0.00 4.26 F
2705 5550 0.677731 TGATTTGGGCTCAAGCTCCG 60.678 55.0 0.00 0.00 41.95 4.63 F
4544 16296 0.251354 GGCTGAAGATGCTGAGGTGA 59.749 55.0 0.00 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1302 3818 0.946221 CACGGTCTTGCTCTGGACAC 60.946 60.000 0.00 0.00 34.49 3.67 R
1709 4234 1.354506 CCGACTCCGACGGTATGTC 59.645 63.158 14.79 17.86 44.57 3.06 R
2966 6979 0.108992 CTACCGCAAGTCCGCAACTA 60.109 55.000 0.00 0.00 37.17 2.24 R
2969 6982 0.317799 TAACTACCGCAAGTCCGCAA 59.682 50.000 0.00 0.00 0.00 4.85 R
4338 16090 0.098025 GCTCTTCTCCGTGAGTCGAG 59.902 60.000 0.00 12.77 42.86 4.04 R
4692 16444 3.616956 TGCTTCCCTTGTATGACTGAG 57.383 47.619 0.00 0.00 0.00 3.35 R
5771 19910 1.423921 AGTGACCCCCGAGATTTTTGT 59.576 47.619 0.00 0.00 0.00 2.83 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
128 177 4.803426 GTCGCTGGAGAGCACCGG 62.803 72.222 0.00 0.00 46.62 5.28
155 204 3.087781 GAGGGAGAAAGAAAATGCAGCT 58.912 45.455 0.00 0.00 0.00 4.24
180 229 2.938798 TCGGATTGGGGCCTGGTT 60.939 61.111 0.84 0.00 0.00 3.67
281 330 1.137086 ACATCGATCCCTTTCGTGAGG 59.863 52.381 0.00 0.61 40.03 3.86
287 336 0.035439 TCCCTTTCGTGAGGCCATTC 60.035 55.000 5.01 0.00 35.37 2.67
293 342 0.320374 TCGTGAGGCCATTCGAGTTT 59.680 50.000 5.01 0.00 0.00 2.66
294 343 1.156736 CGTGAGGCCATTCGAGTTTT 58.843 50.000 5.01 0.00 0.00 2.43
295 344 2.028839 TCGTGAGGCCATTCGAGTTTTA 60.029 45.455 5.01 0.00 0.00 1.52
297 346 2.678336 GTGAGGCCATTCGAGTTTTAGG 59.322 50.000 5.01 0.00 0.00 2.69
342 391 4.849926 CGAGTTGTTTGATGAAATGCTCAG 59.150 41.667 0.00 0.00 37.52 3.35
375 424 1.298713 CGCGGAGAGGAGTTCGATG 60.299 63.158 0.00 0.00 0.00 3.84
376 425 1.066587 GCGGAGAGGAGTTCGATGG 59.933 63.158 0.00 0.00 0.00 3.51
377 426 1.066587 CGGAGAGGAGTTCGATGGC 59.933 63.158 0.00 0.00 0.00 4.40
378 427 1.066587 GGAGAGGAGTTCGATGGCG 59.933 63.158 0.00 0.00 39.35 5.69
379 428 1.590259 GAGAGGAGTTCGATGGCGC 60.590 63.158 0.00 0.00 37.46 6.53
396 450 2.759973 CCTAGGCGGGTGCTGAGA 60.760 66.667 0.00 0.00 42.25 3.27
422 476 6.950619 AGCATTGAGGTAATTTCCTTTTCTCT 59.049 34.615 4.96 0.00 38.02 3.10
526 583 2.027192 ACGGTGCAAGATGGTGACTATT 60.027 45.455 0.00 0.00 0.00 1.73
556 615 4.441634 GCTTAGTCCACCGACATCACTATT 60.442 45.833 0.00 0.00 41.87 1.73
577 638 9.548631 ACTATTGGCATAGTAGTACATAGGATT 57.451 33.333 2.52 0.00 43.39 3.01
605 672 3.670122 AGGACATGGGGTATCTATCTCCT 59.330 47.826 0.00 0.00 0.00 3.69
616 683 3.066208 TCTATCTCCTTGCCCTGGATT 57.934 47.619 0.00 0.00 32.56 3.01
617 684 2.707791 TCTATCTCCTTGCCCTGGATTG 59.292 50.000 0.00 0.00 32.56 2.67
618 685 0.554792 ATCTCCTTGCCCTGGATTGG 59.445 55.000 0.00 0.00 32.56 3.16
619 686 0.549902 TCTCCTTGCCCTGGATTGGA 60.550 55.000 0.00 0.00 32.56 3.53
620 687 0.554792 CTCCTTGCCCTGGATTGGAT 59.445 55.000 0.00 0.00 32.56 3.41
679 747 1.302033 GCCCCATAGTCCATGAGCG 60.302 63.158 0.00 0.00 36.69 5.03
683 751 1.345741 CCCATAGTCCATGAGCGTCAT 59.654 52.381 0.00 0.00 37.65 3.06
707 775 3.500448 TGGCATAGACAAGTTGGACAA 57.500 42.857 7.96 0.00 0.00 3.18
727 795 1.065418 AGAGCTTCCATGTAAACCCGG 60.065 52.381 0.00 0.00 0.00 5.73
739 807 3.315749 TGTAAACCCGGAAATTGTCACAC 59.684 43.478 0.73 0.00 0.00 3.82
760 828 1.935873 CACTGATTATGCCACACTCGG 59.064 52.381 0.00 0.00 0.00 4.63
846 914 8.175716 AGCTGAAGTTTAATAACGAAATACTGC 58.824 33.333 0.00 0.00 39.31 4.40
874 942 2.946990 CGCCGGACCAATAAAACCTATT 59.053 45.455 5.05 0.00 0.00 1.73
875 943 4.128643 CGCCGGACCAATAAAACCTATTA 58.871 43.478 5.05 0.00 0.00 0.98
913 982 5.112129 AGTCAACTTAGTGGACCAAAGTT 57.888 39.130 15.63 15.66 42.60 2.66
966 1043 8.300286 AGATCGATTACTAGTATCACCATTGTG 58.700 37.037 2.79 0.00 44.18 3.33
1046 3539 1.600663 CGGTAAGCCTGTATCTCGCAG 60.601 57.143 0.00 0.00 0.00 5.18
1125 3636 3.775654 GCGGCTGTCCCACTAGCT 61.776 66.667 0.00 0.00 39.80 3.32
1225 3736 0.951040 CTTCAACCTCACCTGCGACC 60.951 60.000 0.00 0.00 0.00 4.79
1227 3738 1.961277 CAACCTCACCTGCGACCAC 60.961 63.158 0.00 0.00 0.00 4.16
1258 3773 3.397613 GAAGCTGCTCCTGGGCGAT 62.398 63.158 1.00 0.00 34.52 4.58
1323 3839 0.389166 GTCCAGAGCAAGACCGTGAG 60.389 60.000 0.00 0.00 0.00 3.51
1353 3869 1.747355 GTCCGACCCTATCAGAAACGA 59.253 52.381 0.00 0.00 0.00 3.85
1508 4024 1.524008 CGTTGCCCCAGACCCTTTTC 61.524 60.000 0.00 0.00 0.00 2.29
1641 4160 5.242838 TGTTCAAGGGTGATTTGGACAATAC 59.757 40.000 0.00 0.00 40.22 1.89
1750 4275 0.041576 CCGCGTTCATAGTCGATCGA 60.042 55.000 15.15 15.15 31.29 3.59
1873 4398 1.398692 TTTGGTGGCTGGAACAAGAC 58.601 50.000 0.00 0.00 38.70 3.01
1876 4401 1.070786 GTGGCTGGAACAAGACCGA 59.929 57.895 0.00 0.00 38.70 4.69
1897 4661 5.333952 CCGAGACCGTGATATAGTGTTCTAC 60.334 48.000 0.00 0.00 0.00 2.59
1900 4664 5.236047 AGACCGTGATATAGTGTTCTACGAC 59.764 44.000 0.00 0.00 0.00 4.34
1907 4671 8.021973 GTGATATAGTGTTCTACGACCCTAATG 58.978 40.741 0.00 0.00 0.00 1.90
1951 4715 2.336554 TGAACAGCGTCGTTACCTAC 57.663 50.000 0.00 0.00 0.00 3.18
1989 4753 2.050985 GTGCAGTTGCTTGGACGC 60.051 61.111 5.62 0.00 42.66 5.19
2017 4781 1.331756 GGCAATCCTTACATGCGTCAG 59.668 52.381 0.00 0.00 40.94 3.51
2250 5033 5.480422 AGCTTCTATTTTTGTGGGGGTTAAG 59.520 40.000 0.00 0.00 0.00 1.85
2377 5185 5.012664 TCACCATGTAGTAAATGTGGTCTGT 59.987 40.000 0.00 0.00 41.01 3.41
2387 5195 7.871853 AGTAAATGTGGTCTGTTATGTCAAAC 58.128 34.615 0.00 0.00 0.00 2.93
2390 5198 5.029807 TGTGGTCTGTTATGTCAAACTCA 57.970 39.130 0.00 0.00 0.00 3.41
2394 5202 6.912591 GTGGTCTGTTATGTCAAACTCAAAAG 59.087 38.462 0.00 0.00 0.00 2.27
2409 5222 4.836125 TCAAAAGATGAGGCAGTTCAAC 57.164 40.909 0.00 0.00 33.04 3.18
2440 5266 7.986085 AGCAAAGATTATTGTGTGTTCTAGT 57.014 32.000 0.00 0.00 32.80 2.57
2458 5284 7.666388 TGTTCTAGTAAGAGCTAAGACTGTCTT 59.334 37.037 24.80 24.80 34.62 3.01
2459 5285 9.165035 GTTCTAGTAAGAGCTAAGACTGTCTTA 57.835 37.037 24.42 24.42 33.97 2.10
2481 5307 8.556589 TCTTACCTATGAAATTTCATCTTCCCA 58.443 33.333 31.70 15.77 44.17 4.37
2493 5319 6.899393 TTCATCTTCCCAATATAACATGCC 57.101 37.500 0.00 0.00 0.00 4.40
2505 5331 7.310664 CAATATAACATGCCATCCTGCTAAAG 58.689 38.462 0.00 0.00 0.00 1.85
2535 5380 3.335579 CCCTGCAACTTTAGTCACTACC 58.664 50.000 0.00 0.00 0.00 3.18
2536 5381 3.244422 CCCTGCAACTTTAGTCACTACCA 60.244 47.826 0.00 0.00 0.00 3.25
2537 5382 3.997021 CCTGCAACTTTAGTCACTACCAG 59.003 47.826 0.00 0.00 0.00 4.00
2538 5383 4.503296 CCTGCAACTTTAGTCACTACCAGT 60.503 45.833 0.00 0.00 0.00 4.00
2540 5385 3.746492 GCAACTTTAGTCACTACCAGTGG 59.254 47.826 7.91 7.91 45.94 4.00
2544 5389 3.373226 GTCACTACCAGTGGCGGA 58.627 61.111 9.78 0.00 45.94 5.54
2545 5390 1.215647 GTCACTACCAGTGGCGGAG 59.784 63.158 9.78 6.94 45.94 4.63
2558 5403 4.883354 CGGAGCTTCATGGGGGCC 62.883 72.222 0.00 0.00 0.00 5.80
2559 5404 3.743017 GGAGCTTCATGGGGGCCA 61.743 66.667 4.39 0.00 38.19 5.36
2560 5405 2.360191 GAGCTTCATGGGGGCCAA 59.640 61.111 4.39 0.00 36.95 4.52
2561 5406 2.037847 AGCTTCATGGGGGCCAAC 59.962 61.111 4.39 0.00 36.95 3.77
2562 5407 3.076916 GCTTCATGGGGGCCAACC 61.077 66.667 4.39 6.97 36.95 3.77
2563 5408 2.772924 CTTCATGGGGGCCAACCT 59.227 61.111 15.84 0.48 36.95 3.50
2564 5409 1.683365 CTTCATGGGGGCCAACCTG 60.683 63.158 15.84 11.47 36.95 4.00
2565 5410 3.236769 TTCATGGGGGCCAACCTGG 62.237 63.158 15.84 8.58 41.55 4.45
2566 5411 4.783501 CATGGGGGCCAACCTGGG 62.784 72.222 15.84 3.09 38.19 4.45
2593 5438 2.115343 CCCCCTAGCTCACAAGAAAC 57.885 55.000 0.00 0.00 0.00 2.78
2594 5439 1.340114 CCCCCTAGCTCACAAGAAACC 60.340 57.143 0.00 0.00 0.00 3.27
2595 5440 1.351017 CCCCTAGCTCACAAGAAACCA 59.649 52.381 0.00 0.00 0.00 3.67
2596 5441 2.025887 CCCCTAGCTCACAAGAAACCAT 60.026 50.000 0.00 0.00 0.00 3.55
2597 5442 3.012518 CCCTAGCTCACAAGAAACCATG 58.987 50.000 0.00 0.00 0.00 3.66
2598 5443 2.421424 CCTAGCTCACAAGAAACCATGC 59.579 50.000 0.00 0.00 0.00 4.06
2599 5444 1.985473 AGCTCACAAGAAACCATGCA 58.015 45.000 0.00 0.00 0.00 3.96
2600 5445 2.522185 AGCTCACAAGAAACCATGCAT 58.478 42.857 0.00 0.00 0.00 3.96
2601 5446 3.689347 AGCTCACAAGAAACCATGCATA 58.311 40.909 0.00 0.00 0.00 3.14
2602 5447 4.275810 AGCTCACAAGAAACCATGCATAT 58.724 39.130 0.00 0.00 0.00 1.78
2603 5448 4.097437 AGCTCACAAGAAACCATGCATATG 59.903 41.667 0.00 0.00 0.00 1.78
2604 5449 4.142315 GCTCACAAGAAACCATGCATATGT 60.142 41.667 0.00 0.00 32.21 2.29
2605 5450 5.622914 GCTCACAAGAAACCATGCATATGTT 60.623 40.000 0.00 3.18 32.21 2.71
2606 5451 6.343716 TCACAAGAAACCATGCATATGTTT 57.656 33.333 20.45 20.45 32.21 2.83
2607 5452 6.389091 TCACAAGAAACCATGCATATGTTTC 58.611 36.000 29.19 29.19 36.13 2.78
2608 5453 6.209192 TCACAAGAAACCATGCATATGTTTCT 59.791 34.615 31.37 31.37 41.26 2.52
2609 5454 6.869913 CACAAGAAACCATGCATATGTTTCTT 59.130 34.615 35.39 35.39 44.32 2.52
2611 5456 5.969423 AGAAACCATGCATATGTTTCTTGG 58.031 37.500 31.37 18.53 39.19 3.61
2612 5457 5.481473 AGAAACCATGCATATGTTTCTTGGT 59.519 36.000 31.37 19.05 39.19 3.67
2613 5458 6.663093 AGAAACCATGCATATGTTTCTTGGTA 59.337 34.615 31.37 0.00 39.19 3.25
2614 5459 7.342799 AGAAACCATGCATATGTTTCTTGGTAT 59.657 33.333 31.37 19.14 39.19 2.73
2615 5460 7.422465 AACCATGCATATGTTTCTTGGTATT 57.578 32.000 15.23 3.87 37.30 1.89
2616 5461 8.532186 AACCATGCATATGTTTCTTGGTATTA 57.468 30.769 15.23 0.00 37.30 0.98
2617 5462 8.169977 ACCATGCATATGTTTCTTGGTATTAG 57.830 34.615 14.01 0.00 36.76 1.73
2618 5463 7.231317 ACCATGCATATGTTTCTTGGTATTAGG 59.769 37.037 14.01 0.00 36.76 2.69
2619 5464 6.633500 TGCATATGTTTCTTGGTATTAGGC 57.367 37.500 4.29 0.00 0.00 3.93
2620 5465 5.534654 TGCATATGTTTCTTGGTATTAGGCC 59.465 40.000 4.29 0.00 0.00 5.19
2621 5466 5.770162 GCATATGTTTCTTGGTATTAGGCCT 59.230 40.000 11.78 11.78 0.00 5.19
2622 5467 6.940298 GCATATGTTTCTTGGTATTAGGCCTA 59.060 38.462 8.91 8.91 0.00 3.93
2623 5468 7.611855 GCATATGTTTCTTGGTATTAGGCCTAT 59.388 37.037 14.74 6.63 0.00 2.57
2624 5469 9.520515 CATATGTTTCTTGGTATTAGGCCTATT 57.479 33.333 14.74 13.01 0.00 1.73
2626 5471 8.838649 ATGTTTCTTGGTATTAGGCCTATTTT 57.161 30.769 14.74 4.46 0.00 1.82
2627 5472 8.288689 TGTTTCTTGGTATTAGGCCTATTTTC 57.711 34.615 14.74 7.09 0.00 2.29
2628 5473 7.340999 TGTTTCTTGGTATTAGGCCTATTTTCC 59.659 37.037 14.74 15.34 0.00 3.13
2629 5474 6.584471 TCTTGGTATTAGGCCTATTTTCCA 57.416 37.500 14.74 17.47 0.00 3.53
2630 5475 7.161715 TCTTGGTATTAGGCCTATTTTCCAT 57.838 36.000 14.74 5.42 0.00 3.41
2631 5476 8.282801 TCTTGGTATTAGGCCTATTTTCCATA 57.717 34.615 14.74 4.34 0.00 2.74
2632 5477 8.729047 TCTTGGTATTAGGCCTATTTTCCATAA 58.271 33.333 14.74 10.06 0.00 1.90
2633 5478 9.362151 CTTGGTATTAGGCCTATTTTCCATAAA 57.638 33.333 14.74 7.13 0.00 1.40
2634 5479 9.716556 TTGGTATTAGGCCTATTTTCCATAAAA 57.283 29.630 14.74 3.28 38.87 1.52
2635 5480 9.716556 TGGTATTAGGCCTATTTTCCATAAAAA 57.283 29.630 14.74 0.00 40.98 1.94
2661 5506 6.973229 AAGCTGAAATTTGATATGTTTGCC 57.027 33.333 0.00 0.00 0.00 4.52
2662 5507 6.290294 AGCTGAAATTTGATATGTTTGCCT 57.710 33.333 0.00 0.00 0.00 4.75
2663 5508 6.335777 AGCTGAAATTTGATATGTTTGCCTC 58.664 36.000 0.00 0.00 0.00 4.70
2664 5509 5.521372 GCTGAAATTTGATATGTTTGCCTCC 59.479 40.000 0.00 0.00 0.00 4.30
2665 5510 5.976458 TGAAATTTGATATGTTTGCCTCCC 58.024 37.500 0.00 0.00 0.00 4.30
2666 5511 5.104982 TGAAATTTGATATGTTTGCCTCCCC 60.105 40.000 0.00 0.00 0.00 4.81
2667 5512 3.756082 TTTGATATGTTTGCCTCCCCT 57.244 42.857 0.00 0.00 0.00 4.79
2668 5513 3.756082 TTGATATGTTTGCCTCCCCTT 57.244 42.857 0.00 0.00 0.00 3.95
2669 5514 3.297134 TGATATGTTTGCCTCCCCTTC 57.703 47.619 0.00 0.00 0.00 3.46
2670 5515 2.580322 TGATATGTTTGCCTCCCCTTCA 59.420 45.455 0.00 0.00 0.00 3.02
2671 5516 2.806945 TATGTTTGCCTCCCCTTCAG 57.193 50.000 0.00 0.00 0.00 3.02
2672 5517 0.613012 ATGTTTGCCTCCCCTTCAGC 60.613 55.000 0.00 0.00 0.00 4.26
2673 5518 1.979155 GTTTGCCTCCCCTTCAGCC 60.979 63.158 0.00 0.00 0.00 4.85
2674 5519 3.224007 TTTGCCTCCCCTTCAGCCC 62.224 63.158 0.00 0.00 0.00 5.19
2676 5521 3.424105 GCCTCCCCTTCAGCCCAT 61.424 66.667 0.00 0.00 0.00 4.00
2677 5522 2.599597 CCTCCCCTTCAGCCCATG 59.400 66.667 0.00 0.00 0.00 3.66
2678 5523 2.123982 CTCCCCTTCAGCCCATGC 60.124 66.667 0.00 0.00 37.95 4.06
2679 5524 3.728292 CTCCCCTTCAGCCCATGCC 62.728 68.421 0.00 0.00 38.69 4.40
2680 5525 4.847367 CCCCTTCAGCCCATGCCC 62.847 72.222 0.00 0.00 38.69 5.36
2681 5526 4.847367 CCCTTCAGCCCATGCCCC 62.847 72.222 0.00 0.00 38.69 5.80
2682 5527 4.847367 CCTTCAGCCCATGCCCCC 62.847 72.222 0.00 0.00 38.69 5.40
2702 5547 1.481871 CCATGATTTGGGCTCAAGCT 58.518 50.000 0.00 0.00 42.33 3.74
2703 5548 1.407979 CCATGATTTGGGCTCAAGCTC 59.592 52.381 0.00 1.35 42.33 4.09
2704 5549 1.407979 CATGATTTGGGCTCAAGCTCC 59.592 52.381 0.00 1.28 41.95 4.70
2705 5550 0.677731 TGATTTGGGCTCAAGCTCCG 60.678 55.000 0.00 0.00 41.95 4.63
2706 5551 1.997928 GATTTGGGCTCAAGCTCCGC 61.998 60.000 0.00 0.00 41.95 5.54
2707 5552 4.722700 TTGGGCTCAAGCTCCGCC 62.723 66.667 11.30 11.30 41.95 6.13
2710 5555 4.400961 GGCTCAAGCTCCGCCACT 62.401 66.667 14.03 0.00 43.25 4.00
2711 5556 3.123620 GCTCAAGCTCCGCCACTG 61.124 66.667 0.00 0.00 38.21 3.66
2712 5557 2.435586 CTCAAGCTCCGCCACTGG 60.436 66.667 0.00 0.00 0.00 4.00
2713 5558 3.241530 TCAAGCTCCGCCACTGGT 61.242 61.111 0.00 0.00 0.00 4.00
2714 5559 2.743928 CAAGCTCCGCCACTGGTC 60.744 66.667 0.00 0.00 0.00 4.02
2715 5560 3.241530 AAGCTCCGCCACTGGTCA 61.242 61.111 0.00 0.00 0.00 4.02
2716 5561 3.537206 AAGCTCCGCCACTGGTCAC 62.537 63.158 0.00 0.00 0.00 3.67
2717 5562 4.008933 GCTCCGCCACTGGTCACT 62.009 66.667 0.00 0.00 0.00 3.41
2718 5563 2.646175 GCTCCGCCACTGGTCACTA 61.646 63.158 0.00 0.00 0.00 2.74
2719 5564 1.215647 CTCCGCCACTGGTCACTAC 59.784 63.158 0.00 0.00 0.00 2.73
2770 5615 4.051661 TGCTTGGAATCTTGGAAAGGAT 57.948 40.909 0.00 0.00 46.24 3.24
2779 5624 9.099071 TGGAATCTTGGAAAGGATTTTGAATTA 57.901 29.630 0.00 0.00 46.24 1.40
2893 6906 6.268158 ACTCTGATACTAGACTCGAGGATACA 59.732 42.308 18.41 5.05 41.41 2.29
2936 6949 2.500392 TGGGTGCCAAGGTATGTTAC 57.500 50.000 0.00 0.00 0.00 2.50
2959 6972 4.737855 TGTAGATTCTGCTGGGTTCTAC 57.262 45.455 15.18 15.18 39.33 2.59
2964 6977 5.735766 AGATTCTGCTGGGTTCTACTTTAC 58.264 41.667 0.00 0.00 0.00 2.01
2965 6978 4.967084 TTCTGCTGGGTTCTACTTTACA 57.033 40.909 0.00 0.00 0.00 2.41
2966 6979 5.499004 TTCTGCTGGGTTCTACTTTACAT 57.501 39.130 0.00 0.00 0.00 2.29
2967 6980 6.614694 TTCTGCTGGGTTCTACTTTACATA 57.385 37.500 0.00 0.00 0.00 2.29
2968 6981 6.222038 TCTGCTGGGTTCTACTTTACATAG 57.778 41.667 0.00 0.00 0.00 2.23
2969 6982 5.720041 TCTGCTGGGTTCTACTTTACATAGT 59.280 40.000 0.00 0.00 0.00 2.12
2970 6983 6.212791 TCTGCTGGGTTCTACTTTACATAGTT 59.787 38.462 0.00 0.00 0.00 2.24
2971 6984 6.170506 TGCTGGGTTCTACTTTACATAGTTG 58.829 40.000 0.00 0.00 0.00 3.16
2974 6987 4.569564 GGGTTCTACTTTACATAGTTGCGG 59.430 45.833 0.00 0.00 0.00 5.69
2976 6989 5.290400 GGTTCTACTTTACATAGTTGCGGAC 59.710 44.000 0.00 0.00 0.00 4.79
3011 7024 2.325761 ACGTTACGAGAGAACATGCAC 58.674 47.619 13.03 0.00 0.00 4.57
3108 7124 2.185350 CGAGTGCCTACAGCCAGG 59.815 66.667 0.00 0.00 42.71 4.45
3261 7314 5.821204 AGAGAAAAGTCCATGTTTTGTTCG 58.179 37.500 0.00 0.00 0.00 3.95
3307 7360 4.974645 TGCCCCTGAACTAATATACAGG 57.025 45.455 0.00 0.00 46.37 4.00
3376 7484 5.564550 ACTCAAAGCATCAGTAGGATTGTT 58.435 37.500 0.00 0.00 32.57 2.83
3407 7517 8.352942 AGTCAGACATGGATAACAAAAAGAAAC 58.647 33.333 2.66 0.00 0.00 2.78
3510 7623 6.153067 AGTTGAGTAGTCTGAAACAGATTCG 58.847 40.000 4.79 0.00 42.73 3.34
3978 8091 3.821033 ACTTTCACAGACAAACCATAGGC 59.179 43.478 0.00 0.00 0.00 3.93
4137 15888 1.702182 TGCATTGGAAACTGCAAGGA 58.298 45.000 0.00 0.00 44.87 3.36
4184 15935 7.423844 TGCTTCCATATCTGTATACCATAGG 57.576 40.000 0.00 0.00 0.00 2.57
4323 16075 5.373812 ACTTATGGTTACCTTGATCCTGG 57.626 43.478 2.07 0.00 0.00 4.45
4338 16090 7.122948 CCTTGATCCTGGATACTACTATACCAC 59.877 44.444 9.66 0.00 37.61 4.16
4453 16205 1.271656 GAAAGCACAAGCCTTGCATCT 59.728 47.619 3.88 0.00 42.83 2.90
4477 16229 8.328758 TCTCATTTTGTGTCACTTATAAGGGAT 58.671 33.333 20.13 0.00 41.20 3.85
4544 16296 0.251354 GGCTGAAGATGCTGAGGTGA 59.749 55.000 0.00 0.00 0.00 4.02
4563 16315 3.188048 GTGATTGCAAGACTCACAGAAGG 59.812 47.826 21.28 0.00 39.24 3.46
4692 16444 4.878397 AGTGAACCAGAGTGCTATAAATGC 59.122 41.667 0.00 0.00 0.00 3.56
4800 16552 6.392354 CAAGATGATTTTGCTTACATGGTGT 58.608 36.000 0.00 0.00 0.00 4.16
4809 16561 3.074412 GCTTACATGGTGTAGTGTTGCT 58.926 45.455 0.00 0.00 33.92 3.91
5185 16947 6.532988 TCAGATGATCAAAATGGCAATTCA 57.467 33.333 0.00 0.00 0.00 2.57
5187 16949 6.378848 TCAGATGATCAAAATGGCAATTCAGA 59.621 34.615 0.00 0.00 0.00 3.27
5290 17052 1.273048 GGCCTGAAATGATTGTGTGCA 59.727 47.619 0.00 0.00 0.00 4.57
5376 17141 7.255486 CGAAGGGAGAGAAAAAGGTAAATTTGT 60.255 37.037 0.00 0.00 0.00 2.83
5539 17306 3.057315 GCTATGCCACTTGTGTCAATTGT 60.057 43.478 5.13 0.00 0.00 2.71
5556 17323 5.241506 TCAATTGTAGGGACAGCTGAAAAAG 59.758 40.000 23.35 0.00 36.76 2.27
5654 17431 8.956426 CATTTTTAAGGCCTGATCTAACACTTA 58.044 33.333 5.69 0.00 0.00 2.24
5660 17485 4.253685 GCCTGATCTAACACTTAGTTGCA 58.746 43.478 0.00 0.00 41.50 4.08
5767 19906 5.393962 AGAATGCTAAAATGTGAAGCGAAC 58.606 37.500 0.00 0.00 39.14 3.95
5771 19910 5.344066 TGCTAAAATGTGAAGCGAACAAAA 58.656 33.333 0.00 0.00 39.14 2.44
5772 19911 5.231147 TGCTAAAATGTGAAGCGAACAAAAC 59.769 36.000 0.00 0.00 39.14 2.43
5773 19912 5.231147 GCTAAAATGTGAAGCGAACAAAACA 59.769 36.000 0.00 0.00 0.00 2.83
5814 19953 8.642432 CACTAACCTGATAGATCCAAGATTACA 58.358 37.037 0.00 0.00 0.00 2.41
5827 19966 4.695455 CCAAGATTACAACACGGAGTTCAT 59.305 41.667 0.00 0.00 41.61 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 3.261951 CGCCAGTGCCGATTACCG 61.262 66.667 0.00 0.00 38.18 4.02
128 177 4.394610 GCATTTTCTTTCTCCCTCAGTCTC 59.605 45.833 0.00 0.00 0.00 3.36
261 310 1.137086 CCTCACGAAAGGGATCGATGT 59.863 52.381 0.54 0.00 46.45 3.06
281 330 1.327764 CTCGCCTAAAACTCGAATGGC 59.672 52.381 0.00 0.00 37.24 4.40
287 336 2.860735 CAAGATCCTCGCCTAAAACTCG 59.139 50.000 0.00 0.00 0.00 4.18
293 342 0.465705 CAGCCAAGATCCTCGCCTAA 59.534 55.000 0.00 0.00 0.00 2.69
294 343 1.402896 CCAGCCAAGATCCTCGCCTA 61.403 60.000 0.00 0.00 0.00 3.93
295 344 2.739996 CCAGCCAAGATCCTCGCCT 61.740 63.158 0.00 0.00 0.00 5.52
297 346 2.203126 CCCAGCCAAGATCCTCGC 60.203 66.667 0.00 0.00 0.00 5.03
323 372 4.583907 TCACCTGAGCATTTCATCAAACAA 59.416 37.500 0.00 0.00 34.68 2.83
360 409 1.066587 CGCCATCGAACTCCTCTCC 59.933 63.158 0.00 0.00 38.10 3.71
378 427 4.537433 CTCAGCACCCGCCTAGGC 62.537 72.222 24.75 24.75 39.83 3.93
379 428 2.303549 CTTCTCAGCACCCGCCTAGG 62.304 65.000 3.67 3.67 39.83 3.02
396 450 7.452813 AGAGAAAAGGAAATTACCTCAATGCTT 59.547 33.333 0.00 0.00 39.62 3.91
422 476 2.227865 GCAGTGGCAATTCGAAAACCTA 59.772 45.455 0.00 0.00 40.72 3.08
470 524 0.678048 GAGATGCCCAGTTGACCACC 60.678 60.000 0.00 0.00 0.00 4.61
497 554 3.803082 CTTGCACCGTGCCATCCG 61.803 66.667 20.67 1.14 44.23 4.18
512 569 4.018960 AGCTGGTCAAATAGTCACCATCTT 60.019 41.667 0.00 0.00 39.51 2.40
519 576 4.530553 TGGACTAAGCTGGTCAAATAGTCA 59.469 41.667 17.12 5.72 42.59 3.41
526 583 0.320374 CGGTGGACTAAGCTGGTCAA 59.680 55.000 17.93 7.54 35.61 3.18
556 615 6.951778 TGCTAATCCTATGTACTACTATGCCA 59.048 38.462 0.00 0.00 0.00 4.92
577 638 4.419984 AGATACCCCATGTCCTATGCTA 57.580 45.455 0.00 0.00 0.00 3.49
605 672 1.381599 GCCATCCAATCCAGGGCAA 60.382 57.895 0.00 0.00 44.01 4.52
616 683 2.983030 GTTGCACCGTGCCATCCA 60.983 61.111 20.67 0.00 44.23 3.41
617 684 4.101790 CGTTGCACCGTGCCATCC 62.102 66.667 20.67 5.09 44.23 3.51
618 685 3.047280 TCGTTGCACCGTGCCATC 61.047 61.111 20.67 9.78 44.23 3.51
619 686 3.353836 GTCGTTGCACCGTGCCAT 61.354 61.111 20.67 0.00 44.23 4.40
631 698 0.108585 ATGCTGGTCACTTGGTCGTT 59.891 50.000 0.00 0.00 0.00 3.85
679 747 6.318648 TCCAACTTGTCTATGCCAATAATGAC 59.681 38.462 0.00 0.00 0.00 3.06
683 751 5.565509 TGTCCAACTTGTCTATGCCAATAA 58.434 37.500 0.00 0.00 0.00 1.40
707 775 1.065418 CCGGGTTTACATGGAAGCTCT 60.065 52.381 2.61 0.00 0.00 4.09
727 795 5.801947 GCATAATCAGTGGTGTGACAATTTC 59.198 40.000 0.00 0.00 0.00 2.17
739 807 1.935873 CGAGTGTGGCATAATCAGTGG 59.064 52.381 12.06 0.00 0.00 4.00
760 828 2.294449 AGCAAGAAGGGAAGGGAAAC 57.706 50.000 0.00 0.00 0.00 2.78
853 921 2.027003 TAGGTTTTATTGGTCCGGCG 57.973 50.000 0.00 0.00 0.00 6.46
874 942 3.230976 TGACTTCAAGTCTCCAGTGCTA 58.769 45.455 18.49 0.00 45.27 3.49
875 943 2.042464 TGACTTCAAGTCTCCAGTGCT 58.958 47.619 18.49 0.00 45.27 4.40
921 990 8.563123 TCGATCTCCTATATAAGTTGTGTAGG 57.437 38.462 14.07 14.07 34.55 3.18
1046 3539 2.256461 CGAGCTTTGCTTGTGGCC 59.744 61.111 0.00 0.00 39.88 5.36
1110 3615 1.308783 GCAAAGCTAGTGGGACAGCC 61.309 60.000 0.00 0.00 41.80 4.85
1225 3736 4.308458 TTCGGAGGGTGGCGTGTG 62.308 66.667 0.00 0.00 0.00 3.82
1300 3816 1.367840 GGTCTTGCTCTGGACACGT 59.632 57.895 0.00 0.00 34.49 4.49
1302 3818 0.946221 CACGGTCTTGCTCTGGACAC 60.946 60.000 0.00 0.00 34.49 3.67
1353 3869 2.214181 GAGAGATGGCGTCCGTGTGT 62.214 60.000 2.37 0.00 0.00 3.72
1641 4160 2.283529 ACCTGGTACACGGCCTCTG 61.284 63.158 0.00 0.00 31.39 3.35
1709 4234 1.354506 CCGACTCCGACGGTATGTC 59.645 63.158 14.79 17.86 44.57 3.06
1750 4275 1.882352 GCATTCCCGTTGAACCACTCT 60.882 52.381 0.00 0.00 35.31 3.24
1873 4398 3.564644 AGAACACTATATCACGGTCTCGG 59.435 47.826 0.00 0.00 41.39 4.63
1876 4401 5.236047 GTCGTAGAACACTATATCACGGTCT 59.764 44.000 0.00 0.00 39.69 3.85
1897 4661 3.384789 TCCAATGAGAGACATTAGGGTCG 59.615 47.826 0.00 0.00 46.01 4.79
1951 4715 5.231991 GCACCTTATTGCAAATCCATTAACG 59.768 40.000 1.71 0.00 42.49 3.18
2017 4781 1.692173 TAGCGGTACCTTGGCATCCC 61.692 60.000 10.90 0.00 0.00 3.85
2190 4963 7.796054 TCGGAAGAGATTCTAGGATTGAATTT 58.204 34.615 0.00 0.00 32.73 1.82
2208 4981 1.550976 GCTCCCTTTTCTCTCGGAAGA 59.449 52.381 0.00 0.00 35.16 2.87
2390 5198 3.319122 GTGGTTGAACTGCCTCATCTTTT 59.681 43.478 0.00 0.00 0.00 2.27
2394 5202 2.191128 AGTGGTTGAACTGCCTCATC 57.809 50.000 0.00 0.00 0.00 2.92
2409 5222 7.370383 ACACACAATAATCTTTGCTAAAGTGG 58.630 34.615 0.00 0.00 39.52 4.00
2481 5307 7.233632 TCTTTAGCAGGATGGCATGTTATATT 58.766 34.615 3.81 0.00 35.86 1.28
2493 5319 4.202090 GGGCAGAATTTCTTTAGCAGGATG 60.202 45.833 8.83 0.00 40.87 3.51
2505 5331 3.391506 AAAGTTGCAGGGCAGAATTTC 57.608 42.857 0.00 0.00 40.61 2.17
2535 5380 2.110967 CCATGAAGCTCCGCCACTG 61.111 63.158 0.00 0.00 0.00 3.66
2536 5381 2.270205 CCATGAAGCTCCGCCACT 59.730 61.111 0.00 0.00 0.00 4.00
2537 5382 2.825836 CCCATGAAGCTCCGCCAC 60.826 66.667 0.00 0.00 0.00 5.01
2538 5383 4.113815 CCCCATGAAGCTCCGCCA 62.114 66.667 0.00 0.00 0.00 5.69
2539 5384 4.883354 CCCCCATGAAGCTCCGCC 62.883 72.222 0.00 0.00 0.00 6.13
2541 5386 4.883354 GGCCCCCATGAAGCTCCG 62.883 72.222 0.00 0.00 0.00 4.63
2542 5387 3.301222 TTGGCCCCCATGAAGCTCC 62.301 63.158 0.00 0.00 31.53 4.70
2543 5388 2.054453 GTTGGCCCCCATGAAGCTC 61.054 63.158 0.00 0.00 31.53 4.09
2544 5389 2.037847 GTTGGCCCCCATGAAGCT 59.962 61.111 0.00 0.00 31.53 3.74
2545 5390 3.076916 GGTTGGCCCCCATGAAGC 61.077 66.667 0.00 0.00 31.53 3.86
2546 5391 1.683365 CAGGTTGGCCCCCATGAAG 60.683 63.158 10.93 0.00 31.53 3.02
2547 5392 2.444696 CAGGTTGGCCCCCATGAA 59.555 61.111 10.93 0.00 31.53 2.57
2548 5393 3.671410 CCAGGTTGGCCCCCATGA 61.671 66.667 10.93 0.00 31.53 3.07
2549 5394 4.783501 CCCAGGTTGGCCCCCATG 62.784 72.222 10.93 4.05 35.79 3.66
2574 5419 1.340114 GGTTTCTTGTGAGCTAGGGGG 60.340 57.143 0.00 0.00 0.00 5.40
2575 5420 1.351017 TGGTTTCTTGTGAGCTAGGGG 59.649 52.381 0.00 0.00 0.00 4.79
2576 5421 2.859165 TGGTTTCTTGTGAGCTAGGG 57.141 50.000 0.00 0.00 0.00 3.53
2577 5422 2.421424 GCATGGTTTCTTGTGAGCTAGG 59.579 50.000 0.00 0.00 0.00 3.02
2578 5423 3.076621 TGCATGGTTTCTTGTGAGCTAG 58.923 45.455 0.00 0.00 0.00 3.42
2579 5424 3.138884 TGCATGGTTTCTTGTGAGCTA 57.861 42.857 0.00 0.00 0.00 3.32
2580 5425 1.985473 TGCATGGTTTCTTGTGAGCT 58.015 45.000 0.00 0.00 0.00 4.09
2581 5426 4.142315 ACATATGCATGGTTTCTTGTGAGC 60.142 41.667 10.16 0.00 36.39 4.26
2582 5427 5.571784 ACATATGCATGGTTTCTTGTGAG 57.428 39.130 10.16 0.00 36.39 3.51
2583 5428 5.981088 AACATATGCATGGTTTCTTGTGA 57.019 34.783 10.16 0.00 36.39 3.58
2584 5429 6.392354 AGAAACATATGCATGGTTTCTTGTG 58.608 36.000 33.27 12.86 42.27 3.33
2585 5430 6.594788 AGAAACATATGCATGGTTTCTTGT 57.405 33.333 33.27 22.40 42.27 3.16
2586 5431 7.285783 CAAGAAACATATGCATGGTTTCTTG 57.714 36.000 41.88 41.88 46.48 3.02
2587 5432 6.014327 ACCAAGAAACATATGCATGGTTTCTT 60.014 34.615 37.01 37.01 42.27 2.52
2588 5433 5.481473 ACCAAGAAACATATGCATGGTTTCT 59.519 36.000 33.27 33.27 42.27 2.52
2589 5434 5.723295 ACCAAGAAACATATGCATGGTTTC 58.277 37.500 31.20 31.20 42.27 2.78
2590 5435 5.743636 ACCAAGAAACATATGCATGGTTT 57.256 34.783 23.21 23.21 42.27 3.27
2591 5436 7.422465 AATACCAAGAAACATATGCATGGTT 57.578 32.000 10.16 10.96 44.95 3.67
2592 5437 7.231317 CCTAATACCAAGAAACATATGCATGGT 59.769 37.037 10.16 17.25 42.09 3.55
2593 5438 7.596494 CCTAATACCAAGAAACATATGCATGG 58.404 38.462 10.16 2.10 36.39 3.66
2594 5439 7.086376 GCCTAATACCAAGAAACATATGCATG 58.914 38.462 10.16 0.00 38.21 4.06
2595 5440 6.209391 GGCCTAATACCAAGAAACATATGCAT 59.791 38.462 3.79 3.79 0.00 3.96
2596 5441 5.534654 GGCCTAATACCAAGAAACATATGCA 59.465 40.000 1.58 0.00 0.00 3.96
2597 5442 5.770162 AGGCCTAATACCAAGAAACATATGC 59.230 40.000 1.29 0.00 0.00 3.14
2598 5443 9.520515 AATAGGCCTAATACCAAGAAACATATG 57.479 33.333 18.42 0.00 0.00 1.78
2600 5445 9.930158 AAAATAGGCCTAATACCAAGAAACATA 57.070 29.630 18.42 0.00 0.00 2.29
2601 5446 8.838649 AAAATAGGCCTAATACCAAGAAACAT 57.161 30.769 18.42 0.00 0.00 2.71
2602 5447 7.340999 GGAAAATAGGCCTAATACCAAGAAACA 59.659 37.037 18.42 0.00 0.00 2.83
2603 5448 7.340999 TGGAAAATAGGCCTAATACCAAGAAAC 59.659 37.037 18.42 0.00 0.00 2.78
2604 5449 7.415086 TGGAAAATAGGCCTAATACCAAGAAA 58.585 34.615 18.42 0.00 0.00 2.52
2605 5450 6.975949 TGGAAAATAGGCCTAATACCAAGAA 58.024 36.000 18.42 0.00 0.00 2.52
2606 5451 6.584471 TGGAAAATAGGCCTAATACCAAGA 57.416 37.500 18.42 0.00 0.00 3.02
2607 5452 8.934023 TTATGGAAAATAGGCCTAATACCAAG 57.066 34.615 24.50 0.00 0.00 3.61
2608 5453 9.716556 TTTTATGGAAAATAGGCCTAATACCAA 57.283 29.630 24.50 15.78 29.38 3.67
2609 5454 9.716556 TTTTTATGGAAAATAGGCCTAATACCA 57.283 29.630 18.42 21.81 34.54 3.25
2635 5480 9.101655 GGCAAACATATCAAATTTCAGCTTATT 57.898 29.630 0.00 0.00 0.00 1.40
2636 5481 8.480501 AGGCAAACATATCAAATTTCAGCTTAT 58.519 29.630 0.00 0.00 0.00 1.73
2637 5482 7.839907 AGGCAAACATATCAAATTTCAGCTTA 58.160 30.769 0.00 0.00 0.00 3.09
2638 5483 6.704310 AGGCAAACATATCAAATTTCAGCTT 58.296 32.000 0.00 0.00 0.00 3.74
2639 5484 6.290294 AGGCAAACATATCAAATTTCAGCT 57.710 33.333 0.00 0.00 0.00 4.24
2640 5485 5.521372 GGAGGCAAACATATCAAATTTCAGC 59.479 40.000 0.00 0.00 0.00 4.26
2641 5486 6.044682 GGGAGGCAAACATATCAAATTTCAG 58.955 40.000 0.00 0.00 0.00 3.02
2642 5487 5.104982 GGGGAGGCAAACATATCAAATTTCA 60.105 40.000 0.00 0.00 0.00 2.69
2643 5488 5.129320 AGGGGAGGCAAACATATCAAATTTC 59.871 40.000 0.00 0.00 0.00 2.17
2644 5489 5.032170 AGGGGAGGCAAACATATCAAATTT 58.968 37.500 0.00 0.00 0.00 1.82
2645 5490 4.623863 AGGGGAGGCAAACATATCAAATT 58.376 39.130 0.00 0.00 0.00 1.82
2646 5491 4.270317 AGGGGAGGCAAACATATCAAAT 57.730 40.909 0.00 0.00 0.00 2.32
2647 5492 3.756082 AGGGGAGGCAAACATATCAAA 57.244 42.857 0.00 0.00 0.00 2.69
2648 5493 3.011144 TGAAGGGGAGGCAAACATATCAA 59.989 43.478 0.00 0.00 0.00 2.57
2649 5494 2.580322 TGAAGGGGAGGCAAACATATCA 59.420 45.455 0.00 0.00 0.00 2.15
2650 5495 3.217626 CTGAAGGGGAGGCAAACATATC 58.782 50.000 0.00 0.00 0.00 1.63
2651 5496 2.687914 GCTGAAGGGGAGGCAAACATAT 60.688 50.000 0.00 0.00 0.00 1.78
2652 5497 1.340991 GCTGAAGGGGAGGCAAACATA 60.341 52.381 0.00 0.00 0.00 2.29
2653 5498 0.613012 GCTGAAGGGGAGGCAAACAT 60.613 55.000 0.00 0.00 0.00 2.71
2654 5499 1.228552 GCTGAAGGGGAGGCAAACA 60.229 57.895 0.00 0.00 0.00 2.83
2655 5500 1.979155 GGCTGAAGGGGAGGCAAAC 60.979 63.158 0.00 0.00 36.06 2.93
2656 5501 2.440599 GGCTGAAGGGGAGGCAAA 59.559 61.111 0.00 0.00 36.06 3.68
2657 5502 3.661648 GGGCTGAAGGGGAGGCAA 61.662 66.667 0.00 0.00 37.74 4.52
2659 5504 3.424105 ATGGGCTGAAGGGGAGGC 61.424 66.667 0.00 0.00 35.29 4.70
2660 5505 2.599597 CATGGGCTGAAGGGGAGG 59.400 66.667 0.00 0.00 0.00 4.30
2661 5506 2.123982 GCATGGGCTGAAGGGGAG 60.124 66.667 0.00 0.00 36.96 4.30
2662 5507 3.743017 GGCATGGGCTGAAGGGGA 61.743 66.667 0.00 0.00 40.87 4.81
2663 5508 4.847367 GGGCATGGGCTGAAGGGG 62.847 72.222 0.00 0.00 40.87 4.79
2664 5509 4.847367 GGGGCATGGGCTGAAGGG 62.847 72.222 0.00 0.00 40.87 3.95
2665 5510 4.847367 GGGGGCATGGGCTGAAGG 62.847 72.222 0.00 0.00 40.87 3.46
2684 5529 1.407979 GGAGCTTGAGCCCAAATCATG 59.592 52.381 0.00 0.00 43.38 3.07
2685 5530 1.772836 GGAGCTTGAGCCCAAATCAT 58.227 50.000 0.00 0.00 43.38 2.45
2686 5531 0.677731 CGGAGCTTGAGCCCAAATCA 60.678 55.000 0.00 0.00 43.38 2.57
2687 5532 2.101700 CGGAGCTTGAGCCCAAATC 58.898 57.895 0.00 0.00 43.38 2.17
2688 5533 4.326255 CGGAGCTTGAGCCCAAAT 57.674 55.556 0.00 0.00 43.38 2.32
2701 5546 1.215647 GTAGTGACCAGTGGCGGAG 59.784 63.158 9.78 0.00 0.00 4.63
2702 5547 2.632544 CGTAGTGACCAGTGGCGGA 61.633 63.158 9.78 0.00 0.00 5.54
2703 5548 2.126071 CGTAGTGACCAGTGGCGG 60.126 66.667 9.78 0.00 0.00 6.13
2704 5549 2.126071 CCGTAGTGACCAGTGGCG 60.126 66.667 9.78 3.10 0.00 5.69
2705 5550 0.250166 AAACCGTAGTGACCAGTGGC 60.250 55.000 9.78 2.56 0.00 5.01
2706 5551 3.604875 ATAAACCGTAGTGACCAGTGG 57.395 47.619 7.91 7.91 0.00 4.00
2707 5552 3.682858 CCAATAAACCGTAGTGACCAGTG 59.317 47.826 0.00 0.00 0.00 3.66
2708 5553 3.325716 ACCAATAAACCGTAGTGACCAGT 59.674 43.478 0.00 0.00 0.00 4.00
2709 5554 3.934068 ACCAATAAACCGTAGTGACCAG 58.066 45.455 0.00 0.00 0.00 4.00
2710 5555 4.527816 ACTACCAATAAACCGTAGTGACCA 59.472 41.667 0.00 0.00 40.82 4.02
2711 5556 5.077134 ACTACCAATAAACCGTAGTGACC 57.923 43.478 0.00 0.00 40.82 4.02
2712 5557 4.795278 CGACTACCAATAAACCGTAGTGAC 59.205 45.833 3.96 0.00 42.04 3.67
2713 5558 4.458989 ACGACTACCAATAAACCGTAGTGA 59.541 41.667 3.96 0.00 42.04 3.41
2714 5559 4.737054 ACGACTACCAATAAACCGTAGTG 58.263 43.478 3.96 0.80 42.04 2.74
2715 5560 5.391312 AACGACTACCAATAAACCGTAGT 57.609 39.130 0.00 0.00 44.07 2.73
2716 5561 5.863397 TGAAACGACTACCAATAAACCGTAG 59.137 40.000 0.00 0.00 36.40 3.51
2717 5562 5.777802 TGAAACGACTACCAATAAACCGTA 58.222 37.500 0.00 0.00 0.00 4.02
2718 5563 4.630111 TGAAACGACTACCAATAAACCGT 58.370 39.130 0.00 0.00 0.00 4.83
2719 5564 5.390145 CCTTGAAACGACTACCAATAAACCG 60.390 44.000 0.00 0.00 0.00 4.44
2770 5615 5.007682 CCCCTCCTCGAGTTTAATTCAAAA 58.992 41.667 12.31 0.00 0.00 2.44
2779 5624 3.391382 CGCCCCCTCCTCGAGTTT 61.391 66.667 12.31 0.00 0.00 2.66
2844 5696 9.978336 AGTAAAGGATAGTAGTTGAGTCTAGTT 57.022 33.333 0.00 0.00 0.00 2.24
2893 6906 1.080638 TGATGTTAGGGGTTGCCCTT 58.919 50.000 0.00 0.00 44.66 3.95
2906 6919 0.405198 TGGCACCCATCAGTGATGTT 59.595 50.000 27.27 14.03 40.34 2.71
2936 6949 4.213564 AGAACCCAGCAGAATCTACAAG 57.786 45.455 0.00 0.00 0.00 3.16
2959 6972 3.483574 CGCAAGTCCGCAACTATGTAAAG 60.484 47.826 0.00 0.00 37.17 1.85
2964 6977 1.019278 ACCGCAAGTCCGCAACTATG 61.019 55.000 0.00 0.00 37.17 2.23
2965 6978 0.533491 TACCGCAAGTCCGCAACTAT 59.467 50.000 0.00 0.00 37.17 2.12
2966 6979 0.108992 CTACCGCAAGTCCGCAACTA 60.109 55.000 0.00 0.00 37.17 2.24
2967 6980 1.374252 CTACCGCAAGTCCGCAACT 60.374 57.895 0.00 0.00 41.10 3.16
2968 6981 1.226030 AACTACCGCAAGTCCGCAAC 61.226 55.000 0.00 0.00 0.00 4.17
2969 6982 0.317799 TAACTACCGCAAGTCCGCAA 59.682 50.000 0.00 0.00 0.00 4.85
2970 6983 0.533491 ATAACTACCGCAAGTCCGCA 59.467 50.000 0.00 0.00 0.00 5.69
2971 6984 2.497107 TATAACTACCGCAAGTCCGC 57.503 50.000 0.00 0.00 0.00 5.54
2974 6987 5.053025 CGTAACGTTATAACTACCGCAAGTC 60.053 44.000 11.86 0.00 0.00 3.01
2976 6989 5.027737 TCGTAACGTTATAACTACCGCAAG 58.972 41.667 11.86 0.00 0.00 4.01
3033 7046 6.130569 AGCACGGGGGTTTATAAATTGAATA 58.869 36.000 0.31 0.00 0.00 1.75
3038 7051 4.160814 GGAAAGCACGGGGGTTTATAAATT 59.839 41.667 7.50 0.00 46.57 1.82
3076 7092 2.290916 GCACTCGTCGATATCTGAAGGA 59.709 50.000 0.00 1.58 0.00 3.36
3376 7484 5.937975 TGTTATCCATGTCTGACTGATCA 57.062 39.130 9.51 0.00 0.00 2.92
3509 7622 1.400846 AGAAATCAAGCTGCTGCATCG 59.599 47.619 18.42 5.52 42.74 3.84
3510 7623 3.119602 TCAAGAAATCAAGCTGCTGCATC 60.120 43.478 18.42 0.00 42.74 3.91
3618 7731 3.515901 CCTAGGACTGAAAACAGTAGGCT 59.484 47.826 1.05 0.00 35.23 4.58
3978 8091 1.068055 GCCAAAGAGCTTCACCACATG 60.068 52.381 0.00 0.00 0.00 3.21
4184 15935 5.061311 GCATATATTTGCGCATTTGATGTCC 59.939 40.000 12.75 0.00 32.06 4.02
4323 16075 6.089283 CGTGAGTCGAGTGGTATAGTAGTATC 59.911 46.154 0.00 0.00 42.86 2.24
4338 16090 0.098025 GCTCTTCTCCGTGAGTCGAG 59.902 60.000 0.00 12.77 42.86 4.04
4453 16205 9.967451 TTATCCCTTATAAGTGACACAAAATGA 57.033 29.630 11.50 0.00 0.00 2.57
4544 16296 3.777106 TCCTTCTGTGAGTCTTGCAAT 57.223 42.857 0.00 0.00 0.00 3.56
4563 16315 9.744468 TTTCTTCACCTTTTAAACTTAAGCATC 57.256 29.630 1.29 0.00 0.00 3.91
4692 16444 3.616956 TGCTTCCCTTGTATGACTGAG 57.383 47.619 0.00 0.00 0.00 3.35
4939 16698 8.833493 ACATGTTTAACTGTAGAAACTGTAACC 58.167 33.333 15.22 0.00 36.84 2.85
4976 16738 3.546271 GCAAACTTTTGAACTTCGGTGTC 59.454 43.478 5.87 0.00 40.55 3.67
5185 16947 4.338400 GCAACACCTTAGAGTGGTTTTTCT 59.662 41.667 5.98 0.00 42.28 2.52
5187 16949 3.383505 GGCAACACCTTAGAGTGGTTTTT 59.616 43.478 5.98 0.00 42.28 1.94
5248 17010 2.371841 AGACAGCCTGTATTTGACCACA 59.628 45.455 0.00 0.00 0.00 4.17
5290 17052 5.006746 GGAGAAAATACAACGAGCGAATGAT 59.993 40.000 0.00 0.00 0.00 2.45
5376 17141 8.311109 TCACAAGCTATCAGTTAAGTTATGTGA 58.689 33.333 4.46 4.46 39.70 3.58
5539 17306 2.344592 TCCCTTTTTCAGCTGTCCCTA 58.655 47.619 14.67 0.00 0.00 3.53
5556 17323 5.470098 ACTGACGCATCATACATATTTTCCC 59.530 40.000 0.00 0.00 33.22 3.97
5767 19906 3.068873 TGACCCCCGAGATTTTTGTTTTG 59.931 43.478 0.00 0.00 0.00 2.44
5771 19910 1.423921 AGTGACCCCCGAGATTTTTGT 59.576 47.619 0.00 0.00 0.00 2.83
5772 19911 2.200373 AGTGACCCCCGAGATTTTTG 57.800 50.000 0.00 0.00 0.00 2.44
5773 19912 3.560668 GGTTAGTGACCCCCGAGATTTTT 60.561 47.826 0.00 0.00 43.06 1.94
5814 19953 6.921307 GGAATAAACAAAATGAACTCCGTGTT 59.079 34.615 0.00 0.00 42.38 3.32
5827 19966 8.754080 TGAAAGTTCTTCAGGGAATAAACAAAA 58.246 29.630 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.