Multiple sequence alignment - TraesCS5D01G567700

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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 TraesCS5D01G567700 chr5D 100.000 4376 0 0 1 4376 565199023 565203398 0.000000e+00 8082.0
1 TraesCS5D01G567700 chr5D 79.866 298 35 14 1147 1421 6542726 6542431 1.240000e-45 195.0
2 TraesCS5D01G567700 chr5B 91.030 2854 193 27 1002 3811 707957097 707954263 0.000000e+00 3794.0
3 TraesCS5D01G567700 chr5B 84.935 385 44 8 47 419 707958959 707958577 1.150000e-100 377.0
4 TraesCS5D01G567700 chr4A 92.906 1903 85 21 708 2593 606623943 606625812 0.000000e+00 2721.0
5 TraesCS5D01G567700 chr4A 86.032 630 44 19 3190 3811 606626121 606626714 1.720000e-178 636.0
6 TraesCS5D01G567700 chr4A 88.333 420 44 4 1 417 606623177 606623594 2.350000e-137 499.0
7 TraesCS5D01G567700 chr4A 93.077 260 18 0 2822 3081 606625812 606626071 8.880000e-102 381.0
8 TraesCS5D01G567700 chr4A 78.113 530 83 27 1143 1651 708652321 708651804 5.500000e-79 305.0
9 TraesCS5D01G567700 chr4A 84.188 234 23 5 502 723 606623694 606623925 9.530000e-52 215.0
10 TraesCS5D01G567700 chr4A 82.917 240 31 8 3998 4232 606627368 606627602 1.600000e-49 207.0
11 TraesCS5D01G567700 chr4A 85.496 131 14 4 3801 3929 606627056 606627183 9.880000e-27 132.0
12 TraesCS5D01G567700 chr4A 81.609 87 14 2 456 541 588583236 588583151 2.180000e-08 71.3
13 TraesCS5D01G567700 chr4A 80.460 87 17 0 456 542 625686716 625686630 2.820000e-07 67.6
14 TraesCS5D01G567700 chr4A 80.682 88 15 2 456 542 732285686 732285600 2.820000e-07 67.6
15 TraesCS5D01G567700 chr7D 72.701 1359 252 79 1149 2413 127292158 127290825 1.170000e-90 344.0
16 TraesCS5D01G567700 chr7D 79.206 529 79 24 1143 1651 24521319 24520802 5.420000e-89 339.0
17 TraesCS5D01G567700 chr7D 84.091 88 12 2 456 542 309509014 309509100 2.800000e-12 84.2
18 TraesCS5D01G567700 chr7D 80.899 89 17 0 456 544 532599548 532599460 2.180000e-08 71.3
19 TraesCS5D01G567700 chr7A 78.450 529 83 23 1143 1651 25133690 25133173 2.540000e-82 316.0
20 TraesCS5D01G567700 chr7A 74.260 878 160 46 1149 1972 128051068 128050203 4.250000e-80 309.0
21 TraesCS5D01G567700 chr7A 82.222 270 45 2 1141 1407 25360402 25360133 3.400000e-56 230.0
22 TraesCS5D01G567700 chr7A 81.053 95 16 2 451 544 616935546 616935453 1.690000e-09 75.0
23 TraesCS5D01G567700 chr7B 74.215 892 148 50 1143 1972 89204358 89205229 9.200000e-77 298.0
24 TraesCS5D01G567700 chr6D 85.263 95 9 5 456 547 100540719 100540811 4.660000e-15 93.5
25 TraesCS5D01G567700 chr3B 82.353 85 15 0 456 540 25057526 25057610 1.690000e-09 75.0
26 TraesCS5D01G567700 chr6A 80.000 90 18 0 455 544 557970047 557970136 2.820000e-07 67.6
27 TraesCS5D01G567700 chr1A 87.755 49 6 0 3662 3710 361069875 361069923 1.700000e-04 58.4


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 TraesCS5D01G567700 chr5D 565199023 565203398 4375 False 8082.000000 8082 100.000000 1 4376 1 chr5D.!!$F1 4375
1 TraesCS5D01G567700 chr5B 707954263 707958959 4696 True 2085.500000 3794 87.982500 47 3811 2 chr5B.!!$R1 3764
2 TraesCS5D01G567700 chr4A 606623177 606627602 4425 False 684.428571 2721 87.564143 1 4232 7 chr4A.!!$F1 4231
3 TraesCS5D01G567700 chr4A 708651804 708652321 517 True 305.000000 305 78.113000 1143 1651 1 chr4A.!!$R3 508
4 TraesCS5D01G567700 chr7D 127290825 127292158 1333 True 344.000000 344 72.701000 1149 2413 1 chr7D.!!$R2 1264
5 TraesCS5D01G567700 chr7D 24520802 24521319 517 True 339.000000 339 79.206000 1143 1651 1 chr7D.!!$R1 508
6 TraesCS5D01G567700 chr7A 25133173 25133690 517 True 316.000000 316 78.450000 1143 1651 1 chr7A.!!$R1 508
7 TraesCS5D01G567700 chr7A 128050203 128051068 865 True 309.000000 309 74.260000 1149 1972 1 chr7A.!!$R3 823
8 TraesCS5D01G567700 chr7B 89204358 89205229 871 False 298.000000 298 74.215000 1143 1972 1 chr7B.!!$F1 829

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
911 1966 0.594602 CATGTGCACTGTGTTGGGAG 59.405 55.0 19.41 0.0 0.0 4.30 F
2149 3346 0.037326 CAACTACTTGCTGCTCCCGA 60.037 55.0 0.00 0.0 0.0 5.14 F
2796 3997 0.172803 ACAGTGTCGCCGAGGTTATC 59.827 55.0 0.00 0.0 0.0 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2685 3886 0.251916 TAGGGTTGCCATGAAGGTCG 59.748 55.0 0.0 0.0 40.61 4.79 R
3132 4333 0.259647 CCCCAGAATCCTTGGCATCA 59.740 55.0 0.0 0.0 0.00 3.07 R
4063 5770 0.409876 TAGTGAGGAGTGGCTGAGGT 59.590 55.0 0.0 0.0 0.00 3.85 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
84 85 9.635404 TGTCTTATTTTCTCCCACTTTAAAAGA 57.365 29.630 0.00 0.00 0.00 2.52
166 173 5.354234 GTGTGTGTACTTATTTCCATGGAGG 59.646 44.000 15.53 6.84 39.47 4.30
170 177 5.239525 GTGTACTTATTTCCATGGAGGCATC 59.760 44.000 15.53 0.00 37.29 3.91
189 196 5.088739 GCATCCTTGAAAACTCAATGTACG 58.911 41.667 0.00 0.00 0.00 3.67
227 234 3.614092 ACGCAATGAATGTTCCAGAGAT 58.386 40.909 0.00 0.00 0.00 2.75
243 250 4.646572 CAGAGATATAAACTGGAAGGGGC 58.353 47.826 0.00 0.00 39.30 5.80
253 264 1.221213 TGGAAGGGGCCCTGCTTATT 61.221 55.000 30.12 11.71 32.13 1.40
288 299 8.492673 TGTTATGGATATTGCCTCGATATTTC 57.507 34.615 0.00 0.00 0.00 2.17
311 322 9.998106 TTTCTGGACTAAAATATATGGTAGAGC 57.002 33.333 9.04 2.90 0.00 4.09
379 390 6.773638 ACATGTCTGGAATACCATAAGGATC 58.226 40.000 0.00 0.00 45.87 3.36
405 418 9.498307 CCCGTATTTAGTGTTTTAGCTTTTATG 57.502 33.333 0.00 0.00 0.00 1.90
440 503 7.201848 CCAATAATTGTGAGTGATGGTGCTAAT 60.202 37.037 0.00 0.00 0.00 1.73
443 506 6.683974 ATTGTGAGTGATGGTGCTAATAAC 57.316 37.500 0.00 0.00 0.00 1.89
468 531 7.778382 ACCAAATTACATTTACTCCCTACATCC 59.222 37.037 0.00 0.00 0.00 3.51
469 532 7.230712 CCAAATTACATTTACTCCCTACATCCC 59.769 40.741 0.00 0.00 0.00 3.85
470 533 7.460214 AATTACATTTACTCCCTACATCCCA 57.540 36.000 0.00 0.00 0.00 4.37
471 534 6.494666 TTACATTTACTCCCTACATCCCAG 57.505 41.667 0.00 0.00 0.00 4.45
472 535 4.631234 ACATTTACTCCCTACATCCCAGA 58.369 43.478 0.00 0.00 0.00 3.86
474 537 5.672194 ACATTTACTCCCTACATCCCAGAAT 59.328 40.000 0.00 0.00 0.00 2.40
476 539 7.517604 ACATTTACTCCCTACATCCCAGAATAT 59.482 37.037 0.00 0.00 0.00 1.28
477 540 9.046846 CATTTACTCCCTACATCCCAGAATATA 57.953 37.037 0.00 0.00 0.00 0.86
479 542 8.666129 TTACTCCCTACATCCCAGAATATAAG 57.334 38.462 0.00 0.00 0.00 1.73
481 544 7.491681 ACTCCCTACATCCCAGAATATAAGAT 58.508 38.462 0.00 0.00 0.00 2.40
482 545 7.621683 ACTCCCTACATCCCAGAATATAAGATC 59.378 40.741 0.00 0.00 0.00 2.75
483 546 6.607600 TCCCTACATCCCAGAATATAAGATCG 59.392 42.308 0.00 0.00 0.00 3.69
484 547 6.381420 CCCTACATCCCAGAATATAAGATCGT 59.619 42.308 0.00 0.00 0.00 3.73
485 548 7.093289 CCCTACATCCCAGAATATAAGATCGTT 60.093 40.741 0.00 0.00 0.00 3.85
486 549 7.976734 CCTACATCCCAGAATATAAGATCGTTC 59.023 40.741 0.00 0.00 0.00 3.95
487 550 6.702329 ACATCCCAGAATATAAGATCGTTCC 58.298 40.000 0.00 0.00 0.00 3.62
488 551 6.498651 ACATCCCAGAATATAAGATCGTTCCT 59.501 38.462 0.00 0.00 0.00 3.36
489 552 6.591750 TCCCAGAATATAAGATCGTTCCTC 57.408 41.667 0.00 0.00 0.00 3.71
490 553 6.075315 TCCCAGAATATAAGATCGTTCCTCA 58.925 40.000 0.00 0.00 0.00 3.86
491 554 6.553476 TCCCAGAATATAAGATCGTTCCTCAA 59.447 38.462 0.00 0.00 0.00 3.02
492 555 6.870965 CCCAGAATATAAGATCGTTCCTCAAG 59.129 42.308 0.00 0.00 0.00 3.02
493 556 6.367422 CCAGAATATAAGATCGTTCCTCAAGC 59.633 42.308 0.00 0.00 0.00 4.01
494 557 7.151308 CAGAATATAAGATCGTTCCTCAAGCT 58.849 38.462 0.00 0.00 0.00 3.74
495 558 8.300286 CAGAATATAAGATCGTTCCTCAAGCTA 58.700 37.037 0.00 0.00 0.00 3.32
496 559 8.861086 AGAATATAAGATCGTTCCTCAAGCTAA 58.139 33.333 0.00 0.00 0.00 3.09
497 560 8.819643 AATATAAGATCGTTCCTCAAGCTAAC 57.180 34.615 0.00 0.00 0.00 2.34
498 561 4.537135 AAGATCGTTCCTCAAGCTAACA 57.463 40.909 0.00 0.00 0.00 2.41
499 562 4.744795 AGATCGTTCCTCAAGCTAACAT 57.255 40.909 0.00 0.00 0.00 2.71
500 563 5.854010 AGATCGTTCCTCAAGCTAACATA 57.146 39.130 0.00 0.00 0.00 2.29
501 564 5.837437 AGATCGTTCCTCAAGCTAACATAG 58.163 41.667 0.00 0.00 0.00 2.23
556 619 4.201980 GGGAGTAGTTTGTTGCGAACTTTT 60.202 41.667 7.03 0.00 38.77 2.27
557 620 5.337554 GGAGTAGTTTGTTGCGAACTTTTT 58.662 37.500 7.03 0.00 38.77 1.94
585 648 5.587844 AGCATGACATCCAACTATTTCAGAC 59.412 40.000 0.00 0.00 0.00 3.51
679 752 4.023291 TGAAAAACAGAAGGTTCTTGCCT 58.977 39.130 0.00 0.00 39.29 4.75
744 1388 3.211045 GGTTTGAAGGCTGTACACAGAA 58.789 45.455 13.50 0.00 46.59 3.02
746 1390 4.261197 GGTTTGAAGGCTGTACACAGAAAG 60.261 45.833 13.50 0.00 46.59 2.62
747 1391 4.415881 TTGAAGGCTGTACACAGAAAGA 57.584 40.909 13.50 0.00 46.59 2.52
748 1392 3.995199 TGAAGGCTGTACACAGAAAGAG 58.005 45.455 13.50 0.00 46.59 2.85
749 1393 3.641436 TGAAGGCTGTACACAGAAAGAGA 59.359 43.478 13.50 0.00 46.59 3.10
750 1394 3.951775 AGGCTGTACACAGAAAGAGAG 57.048 47.619 13.50 0.00 46.59 3.20
751 1395 3.501349 AGGCTGTACACAGAAAGAGAGA 58.499 45.455 13.50 0.00 46.59 3.10
763 1407 7.708752 ACACAGAAAGAGAGAGTGTCTTTTTAG 59.291 37.037 5.87 5.17 42.95 1.85
768 1412 9.923786 GAAAGAGAGAGTGTCTTTTTAGTTTTC 57.076 33.333 5.87 0.00 42.95 2.29
791 1437 5.248477 TCTGTACTGCTCCCTTGAGTTAAAT 59.752 40.000 0.00 0.00 40.95 1.40
799 1445 6.015434 TGCTCCCTTGAGTTAAATTCCTTTTC 60.015 38.462 0.00 0.00 40.95 2.29
852 1500 6.090483 AGTACTACATATGCATGTGAGGTC 57.910 41.667 27.77 16.93 45.17 3.85
859 1507 2.047002 TGCATGTGAGGTCATCATGG 57.953 50.000 17.04 6.34 40.92 3.66
904 1953 1.538075 TGCATTCTCATGTGCACTGTG 59.462 47.619 19.41 16.40 45.60 3.66
905 1954 1.538512 GCATTCTCATGTGCACTGTGT 59.461 47.619 19.41 0.00 40.94 3.72
906 1955 2.030540 GCATTCTCATGTGCACTGTGTT 60.031 45.455 19.41 5.03 40.94 3.32
908 1957 1.596603 TCTCATGTGCACTGTGTTGG 58.403 50.000 19.41 11.11 0.00 3.77
911 1966 0.594602 CATGTGCACTGTGTTGGGAG 59.405 55.000 19.41 0.00 0.00 4.30
913 1968 0.747644 TGTGCACTGTGTTGGGAGTG 60.748 55.000 19.41 0.00 42.18 3.51
925 1980 0.694771 TGGGAGTGCTTGATCTGCTT 59.305 50.000 11.38 2.13 0.00 3.91
926 1981 1.908619 TGGGAGTGCTTGATCTGCTTA 59.091 47.619 11.38 0.00 0.00 3.09
927 1982 2.284190 GGGAGTGCTTGATCTGCTTAC 58.716 52.381 11.38 4.08 0.00 2.34
928 1983 2.355108 GGGAGTGCTTGATCTGCTTACA 60.355 50.000 11.38 0.00 0.00 2.41
929 1984 3.539604 GGAGTGCTTGATCTGCTTACAT 58.460 45.455 11.38 0.00 0.00 2.29
930 1985 4.443457 GGGAGTGCTTGATCTGCTTACATA 60.443 45.833 11.38 0.00 0.00 2.29
931 1986 5.303971 GGAGTGCTTGATCTGCTTACATAT 58.696 41.667 11.38 0.00 0.00 1.78
932 1987 6.459066 GGAGTGCTTGATCTGCTTACATATA 58.541 40.000 11.38 0.00 0.00 0.86
933 1988 7.102346 GGAGTGCTTGATCTGCTTACATATAT 58.898 38.462 11.38 0.00 0.00 0.86
934 1989 8.253810 GGAGTGCTTGATCTGCTTACATATATA 58.746 37.037 11.38 0.00 0.00 0.86
935 1990 9.814899 GAGTGCTTGATCTGCTTACATATATAT 57.185 33.333 11.38 0.00 0.00 0.86
974 2037 1.592131 GCGCTGAGCTGAGATGAGG 60.592 63.158 3.62 0.00 44.04 3.86
990 2053 1.064389 TGAGGTGAGCTAGCTAGAGCA 60.064 52.381 25.15 17.07 45.43 4.26
993 2056 1.478510 GGTGAGCTAGCTAGAGCACAA 59.521 52.381 30.63 9.91 43.32 3.33
995 2058 2.165437 GTGAGCTAGCTAGAGCACAAGT 59.835 50.000 27.63 4.68 43.32 3.16
996 2059 2.425312 TGAGCTAGCTAGAGCACAAGTC 59.575 50.000 25.15 6.36 45.43 3.01
997 2060 1.403679 AGCTAGCTAGAGCACAAGTCG 59.596 52.381 25.15 0.00 45.43 4.18
998 2061 1.402259 GCTAGCTAGAGCACAAGTCGA 59.598 52.381 25.15 0.00 45.16 4.20
1025 2103 4.219725 GGGCTTCTTGCACTTTAATACCAA 59.780 41.667 0.00 0.00 43.01 3.67
1028 2106 7.196331 GGCTTCTTGCACTTTAATACCAATAG 58.804 38.462 0.00 0.00 45.15 1.73
1074 2152 5.371629 GCACACGACTACACAGATTTTAAC 58.628 41.667 0.00 0.00 0.00 2.01
1076 2154 6.352526 CACACGACTACACAGATTTTAACAC 58.647 40.000 0.00 0.00 0.00 3.32
1077 2155 5.174398 ACACGACTACACAGATTTTAACACG 59.826 40.000 0.00 0.00 0.00 4.49
1086 2164 7.262048 ACACAGATTTTAACACGACCATTTTT 58.738 30.769 0.00 0.00 0.00 1.94
1130 2208 1.455383 GCCCAGTTCAACCACACCAG 61.455 60.000 0.00 0.00 0.00 4.00
1338 2419 3.423154 GCCCGCTCCAAGTTCACG 61.423 66.667 0.00 0.00 0.00 4.35
1624 2732 0.108992 CGGTGTAGGCAAGAACGCTA 60.109 55.000 0.00 0.00 0.00 4.26
1985 3123 2.677836 TCATCTTCAAAGGTATGCGCAC 59.322 45.455 14.90 0.00 0.00 5.34
2009 3147 4.681744 GACATAGAGAAAGAGACAGCAGG 58.318 47.826 0.00 0.00 0.00 4.85
2149 3346 0.037326 CAACTACTTGCTGCTCCCGA 60.037 55.000 0.00 0.00 0.00 5.14
2160 3357 2.725008 CTCCCGATGCTCGTCCTC 59.275 66.667 5.15 0.00 38.40 3.71
2203 3400 4.228567 TCTGCACCAACGGCGACA 62.229 61.111 16.62 0.46 0.00 4.35
2394 3595 0.471211 TGTGGGAGTTCCTCGTCCTT 60.471 55.000 0.00 0.00 36.20 3.36
2427 3628 1.696884 TGGTTCATGGTGTCACTGCTA 59.303 47.619 2.35 0.00 0.00 3.49
2474 3675 4.697756 CCTTGGCCGCGTCTTCCA 62.698 66.667 4.92 3.80 0.00 3.53
2595 3796 1.623973 CGTTTTCGTTCTCGCTCCCC 61.624 60.000 0.00 0.00 38.65 4.81
2619 3820 1.419762 ACGCTGCCCATCATACCATTA 59.580 47.619 0.00 0.00 0.00 1.90
2623 3824 3.415212 CTGCCCATCATACCATTACCAG 58.585 50.000 0.00 0.00 0.00 4.00
2624 3825 2.162681 GCCCATCATACCATTACCAGC 58.837 52.381 0.00 0.00 0.00 4.85
2630 3831 1.888512 CATACCATTACCAGCCATGCC 59.111 52.381 0.00 0.00 0.00 4.40
2677 3878 2.754472 TCATGGAATATCTCGCCAACG 58.246 47.619 0.00 0.00 42.01 4.10
2688 3889 2.248431 GCCAACGAGTTGCACGAC 59.752 61.111 10.25 0.00 39.16 4.34
2703 3904 1.002134 CGACCTTCATGGCAACCCT 60.002 57.895 0.00 0.00 40.22 4.34
2718 3919 3.864921 GCAACCCTACCTCACTTACACTG 60.865 52.174 0.00 0.00 0.00 3.66
2746 3947 4.090057 GGTTCGCGCTTGCAGACC 62.090 66.667 5.56 0.25 39.07 3.85
2749 3950 4.600576 TCGCGCTTGCAGACCACA 62.601 61.111 5.56 0.00 39.07 4.17
2772 3973 1.932511 GATCTCTTGCCTTTCTGCGAG 59.067 52.381 0.00 0.00 43.01 5.03
2781 3982 1.000283 CCTTTCTGCGAGAGTGACAGT 60.000 52.381 0.00 0.00 33.12 3.55
2796 3997 0.172803 ACAGTGTCGCCGAGGTTATC 59.827 55.000 0.00 0.00 0.00 1.75
2898 4099 1.621814 TCCAAGTACTGCGCTTACCTT 59.378 47.619 9.73 2.91 0.00 3.50
3013 4214 3.258290 GGCGCTGCTACTTCTCGC 61.258 66.667 7.64 0.00 44.39 5.03
3018 4219 2.126071 TGCTACTTCTCGCCGTGC 60.126 61.111 0.00 0.00 0.00 5.34
3048 4249 1.670811 CGGTACAACAAGATCATGGGC 59.329 52.381 2.59 0.00 0.00 5.36
3052 4253 1.754234 AACAAGATCATGGGCGCCC 60.754 57.895 39.40 39.40 0.00 6.13
3071 4272 3.783580 AGAGCAGCCGAGCAGCAT 61.784 61.111 13.83 1.94 43.44 3.79
3072 4273 3.574445 GAGCAGCCGAGCAGCATG 61.574 66.667 13.83 0.00 43.44 4.06
3108 4309 2.167398 AAAGAGGCGCGGAGTTAGCA 62.167 55.000 8.83 0.00 34.19 3.49
3109 4310 2.125673 GAGGCGCGGAGTTAGCAA 60.126 61.111 8.83 0.00 34.19 3.91
3111 4312 1.696832 GAGGCGCGGAGTTAGCAAAG 61.697 60.000 8.83 0.00 34.19 2.77
3119 4320 2.612972 CGGAGTTAGCAAAGAAGCTGGA 60.613 50.000 0.00 0.00 46.11 3.86
3123 4324 4.322567 AGTTAGCAAAGAAGCTGGAGAAG 58.677 43.478 0.00 0.00 46.11 2.85
3131 4332 1.999024 GAAGCTGGAGAAGAAAGCTCG 59.001 52.381 0.00 0.00 46.36 5.03
3132 4333 0.972883 AGCTGGAGAAGAAAGCTCGT 59.027 50.000 0.00 0.00 43.76 4.18
3133 4334 1.074752 GCTGGAGAAGAAAGCTCGTG 58.925 55.000 0.00 0.00 34.05 4.35
3139 4340 1.002430 AGAAGAAAGCTCGTGATGCCA 59.998 47.619 0.00 0.00 0.00 4.92
3255 4459 1.608283 GGGCACGAGAAACTGCTAGTT 60.608 52.381 0.00 0.00 40.80 2.24
3337 4544 2.431942 CCGATATACCACGGGCGC 60.432 66.667 0.00 0.00 44.59 6.53
3363 4570 2.639751 GCAATTGAACGTGTGACTGAC 58.360 47.619 10.34 0.00 0.00 3.51
3413 4620 8.985315 TCTAGGTCGGTCTGTATCTATTTTAA 57.015 34.615 0.00 0.00 0.00 1.52
3415 4622 9.843334 CTAGGTCGGTCTGTATCTATTTTAATC 57.157 37.037 0.00 0.00 0.00 1.75
3417 4624 8.578151 AGGTCGGTCTGTATCTATTTTAATCTC 58.422 37.037 0.00 0.00 0.00 2.75
3487 4694 1.737236 GTGTGTGTGTGTGTGTGATGT 59.263 47.619 0.00 0.00 0.00 3.06
3491 4698 3.851403 GTGTGTGTGTGTGTGATGTTTTC 59.149 43.478 0.00 0.00 0.00 2.29
3560 4780 0.969149 TCTTGAGTCGGCAGTGATGT 59.031 50.000 0.00 0.00 0.00 3.06
3561 4781 1.067565 TCTTGAGTCGGCAGTGATGTC 60.068 52.381 0.00 0.00 0.00 3.06
3607 4832 4.301628 GGGCAGAAGAAGAAAACACAATG 58.698 43.478 0.00 0.00 0.00 2.82
3639 4864 1.001815 CACACAAGGGACGCGAATTTT 60.002 47.619 15.93 0.00 0.00 1.82
3644 4869 0.889186 AGGGACGCGAATTTTGTGCT 60.889 50.000 15.93 0.00 0.00 4.40
3646 4871 0.517316 GGACGCGAATTTTGTGCTCT 59.483 50.000 15.93 0.00 0.00 4.09
3648 4873 0.163788 ACGCGAATTTTGTGCTCTCG 59.836 50.000 15.93 0.00 0.00 4.04
3649 4874 0.519175 CGCGAATTTTGTGCTCTCGG 60.519 55.000 0.00 0.00 0.00 4.63
3650 4875 0.179189 GCGAATTTTGTGCTCTCGGG 60.179 55.000 0.00 0.00 0.00 5.14
3651 4876 0.447801 CGAATTTTGTGCTCTCGGGG 59.552 55.000 0.00 0.00 0.00 5.73
3652 4877 0.811281 GAATTTTGTGCTCTCGGGGG 59.189 55.000 0.00 0.00 0.00 5.40
3653 4878 0.112412 AATTTTGTGCTCTCGGGGGT 59.888 50.000 0.00 0.00 0.00 4.95
3654 4879 0.988832 ATTTTGTGCTCTCGGGGGTA 59.011 50.000 0.00 0.00 0.00 3.69
3655 4880 0.323629 TTTTGTGCTCTCGGGGGTAG 59.676 55.000 0.00 0.00 0.00 3.18
3656 4881 1.550130 TTTGTGCTCTCGGGGGTAGG 61.550 60.000 0.00 0.00 0.00 3.18
3657 4882 3.851128 GTGCTCTCGGGGGTAGGC 61.851 72.222 0.00 0.00 0.00 3.93
3658 4883 4.392166 TGCTCTCGGGGGTAGGCA 62.392 66.667 0.00 0.00 0.00 4.75
3659 4884 3.851128 GCTCTCGGGGGTAGGCAC 61.851 72.222 0.00 0.00 0.00 5.01
3660 4885 2.363795 CTCTCGGGGGTAGGCACA 60.364 66.667 0.00 0.00 0.00 4.57
3661 4886 2.682494 TCTCGGGGGTAGGCACAC 60.682 66.667 0.00 0.00 0.00 3.82
3662 4887 3.000819 CTCGGGGGTAGGCACACA 61.001 66.667 0.00 0.00 0.00 3.72
3723 4948 7.576861 AAGGTCAAAAAGAACCGAATCTTAA 57.423 32.000 3.55 0.00 38.69 1.85
3767 4993 7.272037 ACCATTGTACTCAGGTAAAAAGTTG 57.728 36.000 0.00 0.00 30.00 3.16
3784 5010 6.686484 AAAGTTGGGCCAAAGAATTATTCT 57.314 33.333 22.82 7.51 43.15 2.40
3805 5031 5.003804 TCTCATAGACTTCAGGGCAAAAAC 58.996 41.667 0.00 0.00 0.00 2.43
3817 5395 6.229733 TCAGGGCAAAAACAAAAATCTATGG 58.770 36.000 0.00 0.00 0.00 2.74
3821 5399 5.351189 GGCAAAAACAAAAATCTATGGCGAT 59.649 36.000 0.00 0.00 0.00 4.58
3833 5411 4.607955 TCTATGGCGATAATATAGCGTGC 58.392 43.478 0.00 0.00 40.16 5.34
3837 5415 4.109766 TGGCGATAATATAGCGTGCATAC 58.890 43.478 0.00 0.00 40.16 2.39
3843 5421 7.096966 GCGATAATATAGCGTGCATACTACTTC 60.097 40.741 0.00 0.00 40.16 3.01
3844 5422 8.123575 CGATAATATAGCGTGCATACTACTTCT 58.876 37.037 0.00 0.00 32.13 2.85
3851 5429 6.439599 AGCGTGCATACTACTTCTATAAGTG 58.560 40.000 3.86 0.00 45.63 3.16
3852 5430 5.117287 GCGTGCATACTACTTCTATAAGTGC 59.883 44.000 3.86 0.00 45.63 4.40
3853 5431 6.439599 CGTGCATACTACTTCTATAAGTGCT 58.560 40.000 3.86 0.00 45.63 4.40
3855 5433 8.074370 CGTGCATACTACTTCTATAAGTGCTTA 58.926 37.037 3.86 0.00 45.63 3.09
3856 5434 9.745880 GTGCATACTACTTCTATAAGTGCTTAA 57.254 33.333 3.86 0.00 45.63 1.85
3871 5449 6.941218 AGTGCTTAAAGTAACTACTAACGC 57.059 37.500 0.00 0.00 34.99 4.84
3873 5451 7.150640 AGTGCTTAAAGTAACTACTAACGCTT 58.849 34.615 0.00 0.00 34.99 4.68
3875 5453 6.587608 TGCTTAAAGTAACTACTAACGCTTCC 59.412 38.462 0.00 0.00 34.99 3.46
3878 5456 4.107363 AGTAACTACTAACGCTTCCTGC 57.893 45.455 0.00 0.00 34.13 4.85
3908 5486 1.215924 AGTCTCCTACTAGGTCTGGCC 59.784 57.143 0.00 0.00 36.36 5.36
3922 5500 2.105477 GTCTGGCCATATGATGTGTCCT 59.895 50.000 5.51 0.00 0.00 3.85
3925 5503 1.242076 GCCATATGATGTGTCCTGGC 58.758 55.000 3.65 0.00 42.00 4.85
3929 5507 1.190643 TATGATGTGTCCTGGCGTCA 58.809 50.000 0.00 0.00 35.44 4.35
3930 5508 0.543277 ATGATGTGTCCTGGCGTCAT 59.457 50.000 0.00 2.72 36.75 3.06
3931 5509 1.190643 TGATGTGTCCTGGCGTCATA 58.809 50.000 0.00 0.00 0.00 2.15
3933 5511 2.138320 GATGTGTCCTGGCGTCATATG 58.862 52.381 0.00 0.00 0.00 1.78
3934 5512 1.190643 TGTGTCCTGGCGTCATATGA 58.809 50.000 0.00 0.00 0.00 2.15
3968 5675 0.028505 GCGCTCATGCCACACTTATG 59.971 55.000 0.00 0.00 35.36 1.90
3969 5676 0.028505 CGCTCATGCCACACTTATGC 59.971 55.000 0.00 0.00 35.36 3.14
3970 5677 1.386533 GCTCATGCCACACTTATGCT 58.613 50.000 0.00 0.00 0.00 3.79
3977 5684 0.396139 CCACACTTATGCTGGCCCAT 60.396 55.000 0.00 0.00 0.00 4.00
3978 5685 0.742505 CACACTTATGCTGGCCCATG 59.257 55.000 0.00 0.00 0.00 3.66
3988 5695 1.074405 GCTGGCCCATGAGGATAATCA 59.926 52.381 0.00 0.00 38.24 2.57
3991 5698 2.373169 TGGCCCATGAGGATAATCACTC 59.627 50.000 0.00 0.00 38.24 3.51
3992 5699 2.373169 GGCCCATGAGGATAATCACTCA 59.627 50.000 0.00 0.00 46.62 3.41
3993 5700 3.181440 GGCCCATGAGGATAATCACTCAA 60.181 47.826 0.00 0.00 45.81 3.02
3994 5701 4.464008 GCCCATGAGGATAATCACTCAAA 58.536 43.478 0.00 0.00 45.81 2.69
3995 5702 4.889409 GCCCATGAGGATAATCACTCAAAA 59.111 41.667 0.00 0.00 45.81 2.44
3996 5703 5.360714 GCCCATGAGGATAATCACTCAAAAA 59.639 40.000 0.00 0.00 45.81 1.94
4012 5719 1.713830 AAAAATCGCTCGGCTACGC 59.286 52.632 0.00 0.00 40.69 4.42
4043 5750 1.817099 GAGCCACCTCATTCGCTGG 60.817 63.158 0.00 0.00 38.03 4.85
4046 5753 0.392461 GCCACCTCATTCGCTGGTTA 60.392 55.000 0.00 0.00 30.72 2.85
4053 5760 0.106719 CATTCGCTGGTTACCCCCAT 60.107 55.000 0.00 0.00 33.00 4.00
4054 5761 0.106719 ATTCGCTGGTTACCCCCATG 60.107 55.000 0.00 0.00 33.00 3.66
4093 5800 5.682730 GCCACTCCTCACTATCTAGGAAAAC 60.683 48.000 0.00 0.00 41.33 2.43
4101 5808 7.928706 CCTCACTATCTAGGAAAACACCAATAG 59.071 40.741 0.00 0.00 34.58 1.73
4113 5820 1.741706 CACCAATAGCTGCTGGTTCTG 59.258 52.381 16.67 5.10 43.62 3.02
4114 5821 1.630369 ACCAATAGCTGCTGGTTCTGA 59.370 47.619 13.43 0.00 43.62 3.27
4115 5822 2.040278 ACCAATAGCTGCTGGTTCTGAA 59.960 45.455 13.43 0.00 43.62 3.02
4215 5923 9.596677 AAACATAAATTTGCATCAAAAATCACG 57.403 25.926 0.00 0.00 36.90 4.35
4216 5924 8.531622 ACATAAATTTGCATCAAAAATCACGA 57.468 26.923 0.00 0.00 36.90 4.35
4217 5925 8.986847 ACATAAATTTGCATCAAAAATCACGAA 58.013 25.926 0.00 0.00 36.90 3.85
4218 5926 9.976255 CATAAATTTGCATCAAAAATCACGAAT 57.024 25.926 0.00 0.00 36.90 3.34
4220 5928 8.716619 AAATTTGCATCAAAAATCACGAATTG 57.283 26.923 0.00 0.00 36.90 2.32
4221 5929 5.842619 TTGCATCAAAAATCACGAATTGG 57.157 34.783 0.00 0.00 0.00 3.16
4272 5980 6.534475 TCCTGATTTTTCATGGATTTGAGG 57.466 37.500 0.00 0.00 0.00 3.86
4273 5981 6.255287 TCCTGATTTTTCATGGATTTGAGGA 58.745 36.000 0.00 0.00 0.00 3.71
4274 5982 6.725369 TCCTGATTTTTCATGGATTTGAGGAA 59.275 34.615 0.00 0.00 0.00 3.36
4275 5983 7.235193 TCCTGATTTTTCATGGATTTGAGGAAA 59.765 33.333 0.00 0.00 0.00 3.13
4276 5984 7.332678 CCTGATTTTTCATGGATTTGAGGAAAC 59.667 37.037 0.00 0.00 0.00 2.78
4277 5985 7.733969 TGATTTTTCATGGATTTGAGGAAACA 58.266 30.769 0.00 0.00 0.00 2.83
4278 5986 8.209584 TGATTTTTCATGGATTTGAGGAAACAA 58.790 29.630 0.00 0.00 0.00 2.83
4279 5987 9.223099 GATTTTTCATGGATTTGAGGAAACAAT 57.777 29.630 0.00 0.00 0.00 2.71
4280 5988 8.977267 TTTTTCATGGATTTGAGGAAACAATT 57.023 26.923 0.00 0.00 0.00 2.32
4282 5990 9.709495 TTTTCATGGATTTGAGGAAACAATTAG 57.291 29.630 0.00 0.00 0.00 1.73
4283 5991 6.866480 TCATGGATTTGAGGAAACAATTAGC 58.134 36.000 0.00 0.00 0.00 3.09
4284 5992 6.436847 TCATGGATTTGAGGAAACAATTAGCA 59.563 34.615 0.00 0.00 0.00 3.49
4285 5993 6.662865 TGGATTTGAGGAAACAATTAGCAA 57.337 33.333 0.00 0.00 0.00 3.91
4286 5994 7.243604 TGGATTTGAGGAAACAATTAGCAAT 57.756 32.000 0.00 0.00 0.00 3.56
4287 5995 7.678837 TGGATTTGAGGAAACAATTAGCAATT 58.321 30.769 0.00 0.00 0.00 2.32
4288 5996 8.811017 TGGATTTGAGGAAACAATTAGCAATTA 58.189 29.630 0.00 0.00 0.00 1.40
4289 5997 9.087424 GGATTTGAGGAAACAATTAGCAATTAC 57.913 33.333 0.00 0.00 0.00 1.89
4290 5998 9.638239 GATTTGAGGAAACAATTAGCAATTACA 57.362 29.630 0.00 0.00 0.00 2.41
4291 5999 9.995003 ATTTGAGGAAACAATTAGCAATTACAA 57.005 25.926 0.00 0.00 0.00 2.41
4292 6000 9.823647 TTTGAGGAAACAATTAGCAATTACAAA 57.176 25.926 0.00 0.00 0.00 2.83
4293 6001 9.823647 TTGAGGAAACAATTAGCAATTACAAAA 57.176 25.926 0.00 0.00 0.00 2.44
4294 6002 9.823647 TGAGGAAACAATTAGCAATTACAAAAA 57.176 25.926 0.00 0.00 0.00 1.94
4296 6004 9.830975 AGGAAACAATTAGCAATTACAAAAAGT 57.169 25.926 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
143 144 5.496556 CCTCCATGGAAATAAGTACACACA 58.503 41.667 17.00 0.00 38.35 3.72
166 173 5.088739 CGTACATTGAGTTTTCAAGGATGC 58.911 41.667 8.67 0.00 45.45 3.91
170 177 5.007234 TGTGACGTACATTGAGTTTTCAAGG 59.993 40.000 0.00 0.93 45.89 3.61
189 196 9.549509 TTCATTGCGTAAATATAAACTTGTGAC 57.450 29.630 0.00 0.00 0.00 3.67
207 214 5.936686 ATATCTCTGGAACATTCATTGCG 57.063 39.130 0.00 0.00 38.20 4.85
227 234 1.850345 CAGGGCCCCTTCCAGTTTATA 59.150 52.381 21.43 0.00 0.00 0.98
238 245 1.001140 ATGGAATAAGCAGGGCCCCT 61.001 55.000 21.43 6.41 0.00 4.79
242 249 2.276732 TAGCATGGAATAAGCAGGGC 57.723 50.000 0.00 0.00 0.00 5.19
243 250 4.147321 ACAATAGCATGGAATAAGCAGGG 58.853 43.478 0.00 0.00 0.00 4.45
288 299 7.542477 CACGCTCTACCATATATTTTAGTCCAG 59.458 40.741 0.00 0.00 0.00 3.86
311 322 4.813161 AGGAATGCATTGAGTAGAATCACG 59.187 41.667 18.59 0.00 0.00 4.35
363 374 5.952347 ATACGGGATCCTTATGGTATTCC 57.048 43.478 12.58 1.05 34.23 3.01
367 378 6.783977 ACACTAAATACGGGATCCTTATGGTA 59.216 38.462 12.58 7.10 34.23 3.25
379 390 9.498307 CATAAAAGCTAAAACACTAAATACGGG 57.502 33.333 0.00 0.00 0.00 5.28
405 418 8.450578 TCACTCACAATTATTGGGAATACATC 57.549 34.615 11.27 0.00 43.64 3.06
420 433 5.590259 GGTTATTAGCACCATCACTCACAAT 59.410 40.000 0.00 0.00 34.04 2.71
450 513 4.631234 TCTGGGATGTAGGGAGTAAATGT 58.369 43.478 0.00 0.00 0.00 2.71
464 527 6.940739 AGGAACGATCTTATATTCTGGGATG 58.059 40.000 0.00 0.00 0.00 3.51
465 528 6.726299 TGAGGAACGATCTTATATTCTGGGAT 59.274 38.462 0.00 0.00 0.00 3.85
468 531 6.367422 GCTTGAGGAACGATCTTATATTCTGG 59.633 42.308 0.00 0.00 0.00 3.86
469 532 7.151308 AGCTTGAGGAACGATCTTATATTCTG 58.849 38.462 0.00 0.00 0.00 3.02
470 533 7.296628 AGCTTGAGGAACGATCTTATATTCT 57.703 36.000 0.00 0.00 0.00 2.40
471 534 8.917655 GTTAGCTTGAGGAACGATCTTATATTC 58.082 37.037 0.00 0.00 0.00 1.75
472 535 8.421784 TGTTAGCTTGAGGAACGATCTTATATT 58.578 33.333 0.00 0.00 0.00 1.28
474 537 7.342769 TGTTAGCTTGAGGAACGATCTTATA 57.657 36.000 0.00 0.00 0.00 0.98
476 539 5.654603 TGTTAGCTTGAGGAACGATCTTA 57.345 39.130 0.00 0.00 0.00 2.10
477 540 4.537135 TGTTAGCTTGAGGAACGATCTT 57.463 40.909 0.00 0.00 0.00 2.40
509 572 9.284968 CCCTCCGTCTCATAATATAAAAATGTT 57.715 33.333 0.00 0.00 0.00 2.71
510 573 8.656806 TCCCTCCGTCTCATAATATAAAAATGT 58.343 33.333 0.00 0.00 0.00 2.71
511 574 9.155975 CTCCCTCCGTCTCATAATATAAAAATG 57.844 37.037 0.00 0.00 0.00 2.32
512 575 8.881262 ACTCCCTCCGTCTCATAATATAAAAAT 58.119 33.333 0.00 0.00 0.00 1.82
513 576 8.258850 ACTCCCTCCGTCTCATAATATAAAAA 57.741 34.615 0.00 0.00 0.00 1.94
514 577 7.850935 ACTCCCTCCGTCTCATAATATAAAA 57.149 36.000 0.00 0.00 0.00 1.52
515 578 8.168725 ACTACTCCCTCCGTCTCATAATATAAA 58.831 37.037 0.00 0.00 0.00 1.40
526 589 2.299297 CAACAAACTACTCCCTCCGTCT 59.701 50.000 0.00 0.00 0.00 4.18
527 590 2.685100 CAACAAACTACTCCCTCCGTC 58.315 52.381 0.00 0.00 0.00 4.79
556 619 8.801299 TGAAATAGTTGGATGTCATGCTAAAAA 58.199 29.630 5.87 0.00 0.00 1.94
557 620 8.347004 TGAAATAGTTGGATGTCATGCTAAAA 57.653 30.769 5.87 0.00 0.00 1.52
565 628 6.650807 GTGAAGTCTGAAATAGTTGGATGTCA 59.349 38.462 0.00 0.00 0.00 3.58
566 629 6.876257 AGTGAAGTCTGAAATAGTTGGATGTC 59.124 38.462 0.00 0.00 0.00 3.06
630 693 2.866726 AAAAAGTGGCCCGCGCATT 61.867 52.632 8.75 0.00 36.38 3.56
631 694 3.302344 AAAAAGTGGCCCGCGCAT 61.302 55.556 8.75 0.00 36.38 4.73
688 761 8.964476 AGTTCTAGACACAAAAGAATTCTTCA 57.036 30.769 20.71 0.00 34.61 3.02
724 1368 4.574828 TCTTTCTGTGTACAGCCTTCAAAC 59.425 41.667 7.14 0.00 43.46 2.93
744 1388 9.103861 CAGAAAACTAAAAAGACACTCTCTCTT 57.896 33.333 0.00 0.00 0.00 2.85
746 1390 8.426881 ACAGAAAACTAAAAAGACACTCTCTC 57.573 34.615 0.00 0.00 0.00 3.20
747 1391 9.315525 GTACAGAAAACTAAAAAGACACTCTCT 57.684 33.333 0.00 0.00 0.00 3.10
748 1392 9.315525 AGTACAGAAAACTAAAAAGACACTCTC 57.684 33.333 0.00 0.00 0.00 3.20
749 1393 9.099454 CAGTACAGAAAACTAAAAAGACACTCT 57.901 33.333 0.00 0.00 0.00 3.24
750 1394 7.851472 GCAGTACAGAAAACTAAAAAGACACTC 59.149 37.037 0.00 0.00 0.00 3.51
751 1395 7.553044 AGCAGTACAGAAAACTAAAAAGACACT 59.447 33.333 0.00 0.00 0.00 3.55
763 1407 3.740115 TCAAGGGAGCAGTACAGAAAAC 58.260 45.455 0.00 0.00 0.00 2.43
768 1412 4.537135 TTAACTCAAGGGAGCAGTACAG 57.463 45.455 0.00 0.00 45.42 2.74
791 1437 7.123098 ACTTTTTCTTTTACCGGAGAAAAGGAA 59.877 33.333 29.23 26.78 46.50 3.36
799 1445 6.622833 TTACCACTTTTTCTTTTACCGGAG 57.377 37.500 9.46 0.00 0.00 4.63
830 1476 5.842907 TGACCTCACATGCATATGTAGTAC 58.157 41.667 4.61 0.00 45.53 2.73
831 1477 6.267471 TGATGACCTCACATGCATATGTAGTA 59.733 38.462 4.61 0.00 45.53 1.82
833 1479 5.544650 TGATGACCTCACATGCATATGTAG 58.455 41.667 4.61 1.51 45.53 2.74
836 1482 4.156008 CCATGATGACCTCACATGCATATG 59.844 45.833 0.00 0.00 39.68 1.78
852 1500 2.089201 TCTTGAGTGCTTGCCATGATG 58.911 47.619 0.00 0.00 0.00 3.07
859 1507 1.889545 AGGTTCTCTTGAGTGCTTGC 58.110 50.000 0.00 0.00 0.00 4.01
904 1953 0.807496 GCAGATCAAGCACTCCCAAC 59.193 55.000 5.41 0.00 0.00 3.77
905 1954 0.694771 AGCAGATCAAGCACTCCCAA 59.305 50.000 11.97 0.00 0.00 4.12
906 1955 0.694771 AAGCAGATCAAGCACTCCCA 59.305 50.000 11.97 0.00 0.00 4.37
908 1957 2.977914 TGTAAGCAGATCAAGCACTCC 58.022 47.619 11.97 0.00 0.00 3.85
932 1987 9.737025 CGCGCGCGTACATATATATATATATAT 57.263 33.333 42.49 21.99 37.23 0.86
960 2015 0.822811 GCTCACCTCATCTCAGCTCA 59.177 55.000 0.00 0.00 0.00 4.26
961 2016 1.113788 AGCTCACCTCATCTCAGCTC 58.886 55.000 0.00 0.00 35.46 4.09
966 2029 3.750371 TCTAGCTAGCTCACCTCATCTC 58.250 50.000 23.26 0.00 0.00 2.75
969 2032 2.238521 GCTCTAGCTAGCTCACCTCAT 58.761 52.381 23.26 0.00 39.50 2.90
974 2037 2.165437 ACTTGTGCTCTAGCTAGCTCAC 59.835 50.000 23.26 22.14 43.50 3.51
990 2053 0.687354 AGAAGCCCATGTCGACTTGT 59.313 50.000 24.70 10.50 0.00 3.16
993 2056 0.674895 GCAAGAAGCCCATGTCGACT 60.675 55.000 17.92 0.00 37.23 4.18
995 2058 0.955428 GTGCAAGAAGCCCATGTCGA 60.955 55.000 0.00 0.00 44.83 4.20
996 2059 0.957395 AGTGCAAGAAGCCCATGTCG 60.957 55.000 0.00 0.00 44.83 4.35
997 2060 1.251251 AAGTGCAAGAAGCCCATGTC 58.749 50.000 0.00 0.00 44.83 3.06
998 2061 1.708341 AAAGTGCAAGAAGCCCATGT 58.292 45.000 0.00 0.00 44.83 3.21
1017 2095 7.334858 TGTGCAAGATGTCACTATTGGTATTA 58.665 34.615 0.00 0.00 34.49 0.98
1049 2127 0.879090 ATCTGTGTAGTCGTGTGCGA 59.121 50.000 0.00 0.00 45.79 5.10
1050 2128 1.698165 AATCTGTGTAGTCGTGTGCG 58.302 50.000 0.00 0.00 39.92 5.34
1086 2164 6.572898 CGACATAGGAGTTGGTTAGGTTGTAA 60.573 42.308 0.00 0.00 0.00 2.41
1095 2173 0.252197 GGGCGACATAGGAGTTGGTT 59.748 55.000 0.00 0.00 0.00 3.67
1099 2177 1.207329 GAACTGGGCGACATAGGAGTT 59.793 52.381 0.00 0.00 0.00 3.01
1107 2185 1.525077 GTGGTTGAACTGGGCGACA 60.525 57.895 0.00 0.00 0.00 4.35
1130 2208 1.001641 ATGGAGGTGAGCAAGGTGC 60.002 57.895 0.00 0.00 45.46 5.01
1551 2659 1.214673 ACGATCCTCTGTACCAGCCTA 59.785 52.381 0.00 0.00 0.00 3.93
1624 2732 2.045524 CATGTAGGAGGTGATGAGCCT 58.954 52.381 0.00 0.00 39.42 4.58
1985 3123 3.129462 TGCTGTCTCTTTCTCTATGTCGG 59.871 47.826 0.00 0.00 0.00 4.79
2149 3346 1.077357 AGAGGACGAGGACGAGCAT 60.077 57.895 0.00 0.00 42.66 3.79
2160 3357 2.752238 AGGACGAGGCAGAGGACG 60.752 66.667 0.00 0.00 0.00 4.79
2394 3595 1.112916 TGAACCAGTCGGAGAGCACA 61.113 55.000 0.00 0.00 36.95 4.57
2427 3628 1.535462 GGTTTCACAGCGTACTTGCAT 59.465 47.619 0.00 0.00 37.31 3.96
2595 3796 1.227234 TATGATGGGCAGCGTCACG 60.227 57.895 0.00 0.00 0.00 4.35
2630 3831 3.177194 TTCACCTGGTCCGGCACAG 62.177 63.158 15.75 15.75 34.54 3.66
2671 3872 2.248431 GTCGTGCAACTCGTTGGC 59.752 61.111 11.35 4.97 40.74 4.52
2677 3878 0.798776 CCATGAAGGTCGTGCAACTC 59.201 55.000 0.00 0.00 32.19 3.01
2682 3883 1.210155 GTTGCCATGAAGGTCGTGC 59.790 57.895 0.00 0.00 40.61 5.34
2685 3886 0.251916 TAGGGTTGCCATGAAGGTCG 59.748 55.000 0.00 0.00 40.61 4.79
2688 3889 0.625849 AGGTAGGGTTGCCATGAAGG 59.374 55.000 0.00 0.00 41.84 3.46
2728 3929 4.090057 GTCTGCAAGCGCGAACCC 62.090 66.667 12.10 0.00 42.97 4.11
2731 3932 3.345808 GTGGTCTGCAAGCGCGAA 61.346 61.111 12.10 0.00 42.97 4.70
2746 3947 1.734465 GAAAGGCAAGAGATCCGTGTG 59.266 52.381 0.00 0.00 0.00 3.82
2749 3950 1.677217 GCAGAAAGGCAAGAGATCCGT 60.677 52.381 0.00 0.00 0.00 4.69
2772 3973 1.442857 CTCGGCGACACTGTCACTC 60.443 63.158 4.99 0.00 32.09 3.51
2781 3982 4.349682 AGGATAACCTCGGCGACA 57.650 55.556 4.99 0.00 44.13 4.35
2834 4035 2.040145 TCATCAGAGGTTGTGGAATGCA 59.960 45.455 0.00 0.00 0.00 3.96
2982 4183 2.967397 CGCCAGAACCCGAGTACA 59.033 61.111 0.00 0.00 0.00 2.90
2985 4186 4.379243 CAGCGCCAGAACCCGAGT 62.379 66.667 2.29 0.00 0.00 4.18
3018 4219 0.530211 TGTTGTACCGGGTGTTGACG 60.530 55.000 10.66 0.00 0.00 4.35
3071 4272 3.629855 TCTTTTCACGACATTTCTTGGCA 59.370 39.130 0.00 0.00 29.94 4.92
3072 4273 4.222114 CTCTTTTCACGACATTTCTTGGC 58.778 43.478 0.00 0.00 0.00 4.52
3108 4309 4.071423 GAGCTTTCTTCTCCAGCTTCTTT 58.929 43.478 0.00 0.00 44.12 2.52
3109 4310 3.673902 GAGCTTTCTTCTCCAGCTTCTT 58.326 45.455 0.00 0.00 44.12 2.52
3111 4312 1.999024 CGAGCTTTCTTCTCCAGCTTC 59.001 52.381 0.00 0.00 44.12 3.86
3119 4320 1.002430 TGGCATCACGAGCTTTCTTCT 59.998 47.619 0.00 0.00 0.00 2.85
3123 4324 0.449388 CCTTGGCATCACGAGCTTTC 59.551 55.000 0.00 0.00 0.00 2.62
3129 4330 1.407299 CCAGAATCCTTGGCATCACGA 60.407 52.381 0.00 0.00 0.00 4.35
3131 4332 1.396653 CCCAGAATCCTTGGCATCAC 58.603 55.000 0.00 0.00 0.00 3.06
3132 4333 0.259647 CCCCAGAATCCTTGGCATCA 59.740 55.000 0.00 0.00 0.00 3.07
3133 4334 0.552848 TCCCCAGAATCCTTGGCATC 59.447 55.000 0.00 0.00 0.00 3.91
3139 4340 1.208165 ACCGCTTCCCCAGAATCCTT 61.208 55.000 0.00 0.00 0.00 3.36
3255 4459 1.066430 GTGATGAACTCGCCACCCTTA 60.066 52.381 0.00 0.00 0.00 2.69
3380 4587 3.394940 ACAGACCGACCTAGATCCATCTA 59.605 47.826 0.00 0.00 38.32 1.98
3382 4589 2.588620 ACAGACCGACCTAGATCCATC 58.411 52.381 0.00 0.00 0.00 3.51
3383 4590 2.757894 ACAGACCGACCTAGATCCAT 57.242 50.000 0.00 0.00 0.00 3.41
3384 4591 3.394940 AGATACAGACCGACCTAGATCCA 59.605 47.826 0.00 0.00 0.00 3.41
3385 4592 4.023726 AGATACAGACCGACCTAGATCC 57.976 50.000 0.00 0.00 0.00 3.36
3387 4594 9.584008 TTAAAATAGATACAGACCGACCTAGAT 57.416 33.333 0.00 0.00 0.00 1.98
3413 4620 0.530744 ATGCACACGTACCACGAGAT 59.469 50.000 5.61 0.00 46.05 2.75
3415 4622 0.388006 TCATGCACACGTACCACGAG 60.388 55.000 5.61 0.00 46.05 4.18
3514 4733 1.323412 CCCCAAACCGTTTGTGATGA 58.677 50.000 20.03 0.00 38.98 2.92
3560 4780 1.337728 CCATGGCAACGACAGTACAGA 60.338 52.381 0.00 0.00 42.51 3.41
3561 4781 1.078709 CCATGGCAACGACAGTACAG 58.921 55.000 0.00 0.00 42.51 2.74
3607 4832 2.287788 CCCTTGTGTGTGTTGCTTCATC 60.288 50.000 0.00 0.00 0.00 2.92
3639 4864 2.363795 CCTACCCCCGAGAGCACA 60.364 66.667 0.00 0.00 0.00 4.57
3644 4869 2.682494 GTGTGCCTACCCCCGAGA 60.682 66.667 0.00 0.00 0.00 4.04
3646 4871 2.285069 ATGTGTGCCTACCCCCGA 60.285 61.111 0.00 0.00 0.00 5.14
3648 4873 0.693092 TAGGATGTGTGCCTACCCCC 60.693 60.000 0.00 0.00 36.96 5.40
3649 4874 1.435256 ATAGGATGTGTGCCTACCCC 58.565 55.000 0.00 0.00 40.60 4.95
3650 4875 3.619979 GCATATAGGATGTGTGCCTACCC 60.620 52.174 0.00 0.00 40.60 3.69
3651 4876 3.600388 GCATATAGGATGTGTGCCTACC 58.400 50.000 0.00 0.00 40.60 3.18
3652 4877 3.254060 CGCATATAGGATGTGTGCCTAC 58.746 50.000 0.00 0.00 40.60 3.18
3653 4878 3.592898 CGCATATAGGATGTGTGCCTA 57.407 47.619 0.00 0.00 41.91 3.93
3654 4879 2.462456 CGCATATAGGATGTGTGCCT 57.538 50.000 0.00 0.00 39.56 4.75
3657 4882 2.168326 TGGCGCATATAGGATGTGTG 57.832 50.000 10.83 0.00 35.35 3.82
3658 4883 2.928801 TTGGCGCATATAGGATGTGT 57.071 45.000 10.83 0.00 32.53 3.72
3659 4884 5.878332 TTATTTGGCGCATATAGGATGTG 57.122 39.130 10.83 0.00 0.00 3.21
3660 4885 7.466746 AAATTATTTGGCGCATATAGGATGT 57.533 32.000 10.83 0.00 0.00 3.06
3661 4886 8.677300 ACTAAATTATTTGGCGCATATAGGATG 58.323 33.333 10.83 0.00 0.00 3.51
3662 4887 8.807948 ACTAAATTATTTGGCGCATATAGGAT 57.192 30.769 10.83 0.00 0.00 3.24
3723 4948 9.772973 CAATGGTTGATCATATTTGATTCCAAT 57.227 29.630 16.01 9.68 42.73 3.16
3767 4993 7.001073 AGTCTATGAGAATAATTCTTTGGCCC 58.999 38.462 0.00 0.00 40.87 5.80
3784 5010 4.724399 TGTTTTTGCCCTGAAGTCTATGA 58.276 39.130 0.00 0.00 0.00 2.15
3805 5031 8.604035 ACGCTATATTATCGCCATAGATTTTTG 58.396 33.333 0.00 0.00 32.39 2.44
3817 5395 6.200100 AGTAGTATGCACGCTATATTATCGC 58.800 40.000 0.00 0.00 0.00 4.58
3845 5423 9.080915 GCGTTAGTAGTTACTTTAAGCACTTAT 57.919 33.333 3.21 0.00 37.73 1.73
3846 5424 8.299570 AGCGTTAGTAGTTACTTTAAGCACTTA 58.700 33.333 3.21 0.00 37.73 2.24
3847 5425 7.150640 AGCGTTAGTAGTTACTTTAAGCACTT 58.849 34.615 3.21 0.00 37.73 3.16
3849 5427 6.941218 AGCGTTAGTAGTTACTTTAAGCAC 57.059 37.500 0.00 0.00 37.73 4.40
3850 5428 6.587608 GGAAGCGTTAGTAGTTACTTTAAGCA 59.412 38.462 0.00 0.00 37.73 3.91
3851 5429 6.810676 AGGAAGCGTTAGTAGTTACTTTAAGC 59.189 38.462 0.00 1.63 37.73 3.09
3852 5430 7.201418 GCAGGAAGCGTTAGTAGTTACTTTAAG 60.201 40.741 0.00 0.00 37.73 1.85
3853 5431 6.587608 GCAGGAAGCGTTAGTAGTTACTTTAA 59.412 38.462 0.00 0.00 37.73 1.52
3855 5433 4.928020 GCAGGAAGCGTTAGTAGTTACTTT 59.072 41.667 0.00 0.00 37.73 2.66
3856 5434 4.492611 GCAGGAAGCGTTAGTAGTTACTT 58.507 43.478 0.00 0.00 37.73 2.24
3871 5449 3.870419 GAGACTAAGATGCAAGCAGGAAG 59.130 47.826 0.00 0.00 0.00 3.46
3873 5451 2.169352 GGAGACTAAGATGCAAGCAGGA 59.831 50.000 0.00 0.00 0.00 3.86
3875 5453 3.540314 AGGAGACTAAGATGCAAGCAG 57.460 47.619 0.00 0.00 40.61 4.24
3878 5456 5.830991 ACCTAGTAGGAGACTAAGATGCAAG 59.169 44.000 23.50 0.00 46.54 4.01
3908 5486 2.138320 GACGCCAGGACACATCATATG 58.862 52.381 0.00 0.00 0.00 1.78
3922 5500 3.615155 TCCAAAACATCATATGACGCCA 58.385 40.909 7.78 0.00 0.00 5.69
3925 5503 6.029607 CCAGTTTCCAAAACATCATATGACG 58.970 40.000 7.78 1.51 0.00 4.35
3929 5507 4.677779 GCGCCAGTTTCCAAAACATCATAT 60.678 41.667 0.00 0.00 0.00 1.78
3930 5508 3.366883 GCGCCAGTTTCCAAAACATCATA 60.367 43.478 0.00 0.00 0.00 2.15
3931 5509 2.610232 GCGCCAGTTTCCAAAACATCAT 60.610 45.455 0.00 0.00 0.00 2.45
3933 5511 1.000274 AGCGCCAGTTTCCAAAACATC 60.000 47.619 2.29 0.00 0.00 3.06
3934 5512 1.000274 GAGCGCCAGTTTCCAAAACAT 60.000 47.619 2.29 0.00 0.00 2.71
3964 5671 1.151760 ATCCTCATGGGCCAGCATAA 58.848 50.000 13.78 0.00 34.39 1.90
3968 5675 1.074405 TGATTATCCTCATGGGCCAGC 59.926 52.381 13.78 0.00 34.39 4.85
3969 5676 2.374504 AGTGATTATCCTCATGGGCCAG 59.625 50.000 13.78 4.37 34.39 4.85
3970 5677 2.373169 GAGTGATTATCCTCATGGGCCA 59.627 50.000 9.61 9.61 34.39 5.36
4060 5767 1.834263 GTGAGGAGTGGCTGAGGTTAT 59.166 52.381 0.00 0.00 0.00 1.89
4061 5768 1.203187 AGTGAGGAGTGGCTGAGGTTA 60.203 52.381 0.00 0.00 0.00 2.85
4062 5769 0.472734 AGTGAGGAGTGGCTGAGGTT 60.473 55.000 0.00 0.00 0.00 3.50
4063 5770 0.409876 TAGTGAGGAGTGGCTGAGGT 59.590 55.000 0.00 0.00 0.00 3.85
4064 5771 1.686052 GATAGTGAGGAGTGGCTGAGG 59.314 57.143 0.00 0.00 0.00 3.86
4066 5773 2.836636 AGATAGTGAGGAGTGGCTGA 57.163 50.000 0.00 0.00 0.00 4.26
4067 5774 2.890311 CCTAGATAGTGAGGAGTGGCTG 59.110 54.545 0.00 0.00 34.46 4.85
4068 5775 2.786445 TCCTAGATAGTGAGGAGTGGCT 59.214 50.000 0.00 0.00 36.92 4.75
4069 5776 3.231207 TCCTAGATAGTGAGGAGTGGC 57.769 52.381 0.00 0.00 36.92 5.01
4071 5778 6.334202 GTGTTTTCCTAGATAGTGAGGAGTG 58.666 44.000 0.00 0.00 42.80 3.51
4072 5779 5.422650 GGTGTTTTCCTAGATAGTGAGGAGT 59.577 44.000 0.00 0.00 42.80 3.85
4249 5957 6.255287 TCCTCAAATCCATGAAAAATCAGGA 58.745 36.000 0.00 0.00 0.00 3.86
4250 5958 6.534475 TCCTCAAATCCATGAAAAATCAGG 57.466 37.500 0.00 0.00 0.00 3.86
4252 5960 7.733969 TGTTTCCTCAAATCCATGAAAAATCA 58.266 30.769 0.00 0.00 0.00 2.57
4253 5961 8.606040 TTGTTTCCTCAAATCCATGAAAAATC 57.394 30.769 0.00 0.00 0.00 2.17
4254 5962 9.577222 AATTGTTTCCTCAAATCCATGAAAAAT 57.423 25.926 0.00 0.00 0.00 1.82
4255 5963 8.977267 AATTGTTTCCTCAAATCCATGAAAAA 57.023 26.923 0.00 0.00 0.00 1.94
4256 5964 9.709495 CTAATTGTTTCCTCAAATCCATGAAAA 57.291 29.630 0.00 0.00 0.00 2.29
4257 5965 7.818930 GCTAATTGTTTCCTCAAATCCATGAAA 59.181 33.333 0.00 0.00 0.00 2.69
4258 5966 7.039152 TGCTAATTGTTTCCTCAAATCCATGAA 60.039 33.333 0.00 0.00 0.00 2.57
4259 5967 6.436847 TGCTAATTGTTTCCTCAAATCCATGA 59.563 34.615 0.00 0.00 0.00 3.07
4260 5968 6.632909 TGCTAATTGTTTCCTCAAATCCATG 58.367 36.000 0.00 0.00 0.00 3.66
4261 5969 6.855763 TGCTAATTGTTTCCTCAAATCCAT 57.144 33.333 0.00 0.00 0.00 3.41
4262 5970 6.662865 TTGCTAATTGTTTCCTCAAATCCA 57.337 33.333 0.00 0.00 0.00 3.41
4263 5971 9.087424 GTAATTGCTAATTGTTTCCTCAAATCC 57.913 33.333 4.89 0.00 32.38 3.01
4264 5972 9.638239 TGTAATTGCTAATTGTTTCCTCAAATC 57.362 29.630 0.00 0.00 32.38 2.17
4265 5973 9.995003 TTGTAATTGCTAATTGTTTCCTCAAAT 57.005 25.926 0.00 0.00 32.38 2.32
4266 5974 9.823647 TTTGTAATTGCTAATTGTTTCCTCAAA 57.176 25.926 0.00 0.00 32.38 2.69
4267 5975 9.823647 TTTTGTAATTGCTAATTGTTTCCTCAA 57.176 25.926 0.00 0.00 32.38 3.02
4268 5976 9.823647 TTTTTGTAATTGCTAATTGTTTCCTCA 57.176 25.926 0.00 0.00 32.38 3.86
4270 5978 9.830975 ACTTTTTGTAATTGCTAATTGTTTCCT 57.169 25.926 0.00 0.00 32.38 3.36


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

AutoCloner maintained by Alex Coulton.