Multiple sequence alignment - TraesCS6B01G191600

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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 TraesCS6B01G191600 chr6B 100.000 4578 0 0 1 4578 225868127 225872704 0.000000e+00 8455.0
1 TraesCS6B01G191600 chr6B 99.174 121 1 0 868 988 341547695 341547815 7.710000e-53 219.0
2 TraesCS6B01G191600 chr6B 99.167 120 1 0 868 987 171973686 171973805 2.770000e-52 217.0
3 TraesCS6B01G191600 chr6B 88.235 102 10 2 437 536 457218398 457218499 2.240000e-23 121.0
4 TraesCS6B01G191600 chr6B 95.775 71 3 0 4508 4578 487209572 487209502 1.040000e-21 115.0
5 TraesCS6B01G191600 chr6A 95.327 3552 106 16 988 4524 152060190 152056684 0.000000e+00 5585.0
6 TraesCS6B01G191600 chr6A 95.506 445 14 3 1 439 152061003 152060559 0.000000e+00 706.0
7 TraesCS6B01G191600 chr6D 94.575 3539 122 19 989 4514 126872423 126875904 0.000000e+00 5408.0
8 TraesCS6B01G191600 chr6D 97.931 435 9 0 2 436 126871595 126872029 0.000000e+00 754.0
9 TraesCS6B01G191600 chr6D 94.798 173 5 2 530 701 126872049 126872218 2.720000e-67 267.0
10 TraesCS6B01G191600 chr6D 91.515 165 11 3 707 869 126872272 126872435 1.660000e-54 224.0
11 TraesCS6B01G191600 chr3A 100.000 121 0 0 868 988 708952472 708952352 1.660000e-54 224.0
12 TraesCS6B01G191600 chr3A 87.037 54 5 2 4354 4406 434843979 434843927 4.950000e-05 60.2
13 TraesCS6B01G191600 chr2B 100.000 121 0 0 868 988 492706898 492707018 1.660000e-54 224.0
14 TraesCS6B01G191600 chr2B 86.139 101 12 2 436 535 40493837 40493738 1.740000e-19 108.0
15 TraesCS6B01G191600 chr1A 100.000 121 0 0 868 988 204838153 204838033 1.660000e-54 224.0
16 TraesCS6B01G191600 chr1A 85.106 141 17 4 25 163 566564801 566564939 1.720000e-29 141.0
17 TraesCS6B01G191600 chr1A 98.485 66 1 0 4513 4578 320523098 320523033 2.890000e-22 117.0
18 TraesCS6B01G191600 chr1A 94.737 38 2 0 4357 4394 191861270 191861307 4.950000e-05 60.2
19 TraesCS6B01G191600 chr5D 99.174 121 1 0 868 988 519818286 519818166 7.710000e-53 219.0
20 TraesCS6B01G191600 chr5D 83.688 141 19 4 25 163 438360600 438360738 3.720000e-26 130.0
21 TraesCS6B01G191600 chr5D 93.902 82 4 1 4497 4578 357878333 357878413 6.220000e-24 122.0
22 TraesCS6B01G191600 chr5D 93.671 79 5 0 4500 4578 128577685 128577607 8.050000e-23 119.0
23 TraesCS6B01G191600 chr4A 99.174 121 1 0 868 988 275123024 275122904 7.710000e-53 219.0
24 TraesCS6B01G191600 chr4A 86.301 73 6 2 4326 4394 227091290 227091218 4.910000e-10 76.8
25 TraesCS6B01G191600 chr1B 99.174 121 1 0 868 988 15344006 15343886 7.710000e-53 219.0
26 TraesCS6B01G191600 chr1B 84.507 142 16 6 25 163 657272693 657272831 7.990000e-28 135.0
27 TraesCS6B01G191600 chr1B 97.101 69 2 0 4510 4578 151363654 151363722 2.890000e-22 117.0
28 TraesCS6B01G191600 chr1B 95.122 41 2 0 4357 4397 429763272 429763232 1.060000e-06 65.8
29 TraesCS6B01G191600 chr2A 94.245 139 6 2 860 997 716884420 716884283 1.290000e-50 211.0
30 TraesCS6B01G191600 chr2A 89.524 105 10 1 433 536 515503784 515503680 1.030000e-26 132.0
31 TraesCS6B01G191600 chr2A 89.773 88 5 4 4493 4578 745552743 745552828 4.840000e-20 110.0
32 TraesCS6B01G191600 chr1D 85.816 141 16 4 25 163 472561544 472561682 3.690000e-31 147.0
33 TraesCS6B01G191600 chr1D 95.833 72 3 0 4507 4578 250511530 250511459 2.890000e-22 117.0
34 TraesCS6B01G191600 chr5A 85.106 141 17 4 25 163 553421511 553421649 1.720000e-29 141.0
35 TraesCS6B01G191600 chr5B 84.397 141 18 4 25 163 532877282 532877420 7.990000e-28 135.0
36 TraesCS6B01G191600 chr5B 93.671 79 5 0 4500 4578 140966027 140965949 8.050000e-23 119.0
37 TraesCS6B01G191600 chr5B 80.576 139 25 2 26 163 638344605 638344468 6.260000e-19 106.0
38 TraesCS6B01G191600 chr5B 88.525 61 6 1 4335 4394 564511981 564512041 6.350000e-09 73.1
39 TraesCS6B01G191600 chr7D 90.099 101 9 1 437 536 412475276 412475176 3.720000e-26 130.0
40 TraesCS6B01G191600 chr7D 94.595 74 4 0 4505 4578 423587098 423587171 1.040000e-21 115.0
41 TraesCS6B01G191600 chr7D 94.872 39 2 0 4356 4394 47415536 47415574 1.380000e-05 62.1
42 TraesCS6B01G191600 chr7D 84.906 53 8 0 4356 4408 47415509 47415457 2.000000e-03 54.7
43 TraesCS6B01G191600 chr7B 90.099 101 9 1 437 536 158013597 158013697 3.720000e-26 130.0
44 TraesCS6B01G191600 chr4D 87.619 105 11 2 433 536 82567651 82567754 2.240000e-23 121.0
45 TraesCS6B01G191600 chr4D 86.275 102 11 3 437 536 166011968 166011868 1.740000e-19 108.0
46 TraesCS6B01G191600 chr3B 88.119 101 11 1 437 536 24919135 24919035 8.050000e-23 119.0
47 TraesCS6B01G191600 chr3B 88.119 101 11 1 437 536 519364395 519364295 8.050000e-23 119.0


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 TraesCS6B01G191600 chr6B 225868127 225872704 4577 False 8455.00 8455 100.00000 1 4578 1 chr6B.!!$F2 4577
1 TraesCS6B01G191600 chr6A 152056684 152061003 4319 True 3145.50 5585 95.41650 1 4524 2 chr6A.!!$R1 4523
2 TraesCS6B01G191600 chr6D 126871595 126875904 4309 False 1663.25 5408 94.70475 2 4514 4 chr6D.!!$F1 4512

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
952 1019 0.108615 GGTCCATCAGTCAGTGGTCG 60.109 60.0 0.0 0.0 36.84 4.79 F
957 1024 0.243907 ATCAGTCAGTGGTCGAACGG 59.756 55.0 0.0 0.0 0.00 4.44 F
1678 1747 0.676151 TTGCTGATGTATGCCGCACA 60.676 50.0 0.0 0.0 0.00 4.57 F
2895 2969 0.621082 AGAAAACTAGGAGCTGGGCC 59.379 55.0 0.0 0.0 0.00 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2510 2579 2.437651 TCCACAGGAAACATCAGACACA 59.562 45.455 0.00 0.0 0.0 3.72 R
2654 2723 4.104086 ACCTTGAGAGAGAGAGAGAGAGA 58.896 47.826 0.00 0.0 0.0 3.10 R
2964 3038 1.480137 GCTGTGCACTCCTATCTCTGT 59.520 52.381 19.41 0.0 0.0 3.41 R
3955 4037 2.418746 GGAGAGCCGAGATGTTAGCAAA 60.419 50.000 0.00 0.0 0.0 3.68 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
198 199 2.678336 CAAGTTCCACTAGGCGAAATCC 59.322 50.000 0.00 0.00 33.74 3.01
389 390 4.115401 TCTCTCATCATCTTCACCAACG 57.885 45.455 0.00 0.00 0.00 4.10
426 433 1.486726 CCCGCTCCTCTTCTGGTTATT 59.513 52.381 0.00 0.00 0.00 1.40
436 443 4.827692 TCTTCTGGTTATTGTACGTGCAT 58.172 39.130 7.30 0.56 0.00 3.96
439 446 5.950758 TCTGGTTATTGTACGTGCATTTT 57.049 34.783 7.30 0.00 0.00 1.82
440 447 6.320494 TCTGGTTATTGTACGTGCATTTTT 57.680 33.333 7.30 0.00 0.00 1.94
461 468 7.892778 TTTTTGCATAGTAATACGTGTCTCA 57.107 32.000 0.00 0.00 0.00 3.27
462 469 8.487313 TTTTTGCATAGTAATACGTGTCTCAT 57.513 30.769 0.00 0.00 0.00 2.90
463 470 8.487313 TTTTGCATAGTAATACGTGTCTCATT 57.513 30.769 0.00 0.00 0.00 2.57
464 471 8.487313 TTTGCATAGTAATACGTGTCTCATTT 57.513 30.769 0.00 0.00 0.00 2.32
465 472 9.589111 TTTGCATAGTAATACGTGTCTCATTTA 57.411 29.630 0.00 0.00 0.00 1.40
466 473 9.758651 TTGCATAGTAATACGTGTCTCATTTAT 57.241 29.630 0.00 0.00 0.00 1.40
478 485 9.477484 ACGTGTCTCATTTATATCATAAAGGTC 57.523 33.333 0.00 0.00 0.00 3.85
479 486 9.476202 CGTGTCTCATTTATATCATAAAGGTCA 57.524 33.333 3.97 1.43 0.00 4.02
492 499 8.732746 ATCATAAAGGTCATAGTACAAACCAC 57.267 34.615 0.00 0.00 34.09 4.16
493 500 6.814644 TCATAAAGGTCATAGTACAAACCACG 59.185 38.462 0.00 0.00 34.09 4.94
494 501 4.612264 AAGGTCATAGTACAAACCACGT 57.388 40.909 0.00 0.00 34.09 4.49
495 502 5.726980 AAGGTCATAGTACAAACCACGTA 57.273 39.130 0.00 0.00 34.09 3.57
496 503 5.064441 AGGTCATAGTACAAACCACGTAC 57.936 43.478 0.00 0.00 39.64 3.67
497 504 4.523943 AGGTCATAGTACAAACCACGTACA 59.476 41.667 0.00 0.00 41.40 2.90
498 505 5.010922 AGGTCATAGTACAAACCACGTACAA 59.989 40.000 0.00 0.00 41.40 2.41
499 506 5.695816 GGTCATAGTACAAACCACGTACAAA 59.304 40.000 0.00 0.00 41.40 2.83
500 507 6.346838 GGTCATAGTACAAACCACGTACAAAC 60.347 42.308 0.00 0.00 41.40 2.93
501 508 5.695816 TCATAGTACAAACCACGTACAAACC 59.304 40.000 0.00 0.00 41.40 3.27
502 509 2.865551 AGTACAAACCACGTACAAACCG 59.134 45.455 0.00 0.00 41.40 4.44
503 510 2.021355 ACAAACCACGTACAAACCGA 57.979 45.000 0.00 0.00 0.00 4.69
504 511 2.563702 ACAAACCACGTACAAACCGAT 58.436 42.857 0.00 0.00 0.00 4.18
505 512 2.545106 ACAAACCACGTACAAACCGATC 59.455 45.455 0.00 0.00 0.00 3.69
506 513 2.803956 CAAACCACGTACAAACCGATCT 59.196 45.455 0.00 0.00 0.00 2.75
507 514 2.074547 ACCACGTACAAACCGATCTG 57.925 50.000 0.00 0.00 0.00 2.90
508 515 1.614903 ACCACGTACAAACCGATCTGA 59.385 47.619 0.00 0.00 0.00 3.27
509 516 2.036217 ACCACGTACAAACCGATCTGAA 59.964 45.455 0.00 0.00 0.00 3.02
510 517 3.061322 CCACGTACAAACCGATCTGAAA 58.939 45.455 0.00 0.00 0.00 2.69
511 518 3.495377 CCACGTACAAACCGATCTGAAAA 59.505 43.478 0.00 0.00 0.00 2.29
512 519 4.024725 CCACGTACAAACCGATCTGAAAAA 60.025 41.667 0.00 0.00 0.00 1.94
532 539 5.509605 AAAACTGAAAAGACAACAAACGC 57.490 34.783 0.00 0.00 0.00 4.84
540 547 1.202651 AGACAACAAACGCTAGTGGCT 60.203 47.619 8.42 0.00 39.13 4.75
548 560 3.611766 AACGCTAGTGGCTGTATCTTT 57.388 42.857 8.42 0.00 39.13 2.52
711 777 1.486997 ATCTGAGTGGCTGTGGCTGT 61.487 55.000 0.00 0.00 38.73 4.40
730 796 4.938226 GCTGTGGTTTCTTCTATGCTTACT 59.062 41.667 0.00 0.00 0.00 2.24
777 843 1.601914 GCCAAGAAACGCGTTGGAATT 60.602 47.619 27.40 16.23 45.35 2.17
790 856 2.301583 GTTGGAATTGGGCCAGCTTTTA 59.698 45.455 6.23 0.00 36.64 1.52
818 885 0.311165 AGGTTAGATCATCCGCGACG 59.689 55.000 8.23 0.00 0.00 5.12
847 914 1.733061 GCCGTCTTCTTTCGTCTCTCC 60.733 57.143 0.00 0.00 0.00 3.71
881 948 4.479993 CCAGAAGCGGCTCCCCTG 62.480 72.222 1.45 11.05 0.00 4.45
882 949 3.393970 CAGAAGCGGCTCCCCTGA 61.394 66.667 16.88 0.00 0.00 3.86
883 950 3.394836 AGAAGCGGCTCCCCTGAC 61.395 66.667 1.45 0.00 0.00 3.51
884 951 4.821589 GAAGCGGCTCCCCTGACG 62.822 72.222 1.45 0.00 42.16 4.35
927 994 2.362889 CCATGTGGGCCTGTTCCC 60.363 66.667 4.53 0.00 46.73 3.97
928 995 2.362889 CATGTGGGCCTGTTCCCC 60.363 66.667 4.53 0.00 45.97 4.81
929 996 4.047125 ATGTGGGCCTGTTCCCCG 62.047 66.667 4.53 0.00 45.95 5.73
931 998 3.728373 GTGGGCCTGTTCCCCGAT 61.728 66.667 4.53 0.00 45.95 4.18
932 999 3.727258 TGGGCCTGTTCCCCGATG 61.727 66.667 4.53 0.00 45.95 3.84
933 1000 4.506255 GGGCCTGTTCCCCGATGG 62.506 72.222 0.84 0.00 40.51 3.51
949 1016 0.914644 ATGGGTCCATCAGTCAGTGG 59.085 55.000 0.00 0.00 36.82 4.00
950 1017 0.473694 TGGGTCCATCAGTCAGTGGT 60.474 55.000 0.00 0.00 36.84 4.16
951 1018 0.250513 GGGTCCATCAGTCAGTGGTC 59.749 60.000 0.00 0.00 36.84 4.02
952 1019 0.108615 GGTCCATCAGTCAGTGGTCG 60.109 60.000 0.00 0.00 36.84 4.79
953 1020 0.888619 GTCCATCAGTCAGTGGTCGA 59.111 55.000 0.00 0.00 36.84 4.20
954 1021 1.272490 GTCCATCAGTCAGTGGTCGAA 59.728 52.381 0.00 0.00 36.84 3.71
955 1022 1.272490 TCCATCAGTCAGTGGTCGAAC 59.728 52.381 0.00 0.00 36.84 3.95
956 1023 1.340658 CATCAGTCAGTGGTCGAACG 58.659 55.000 0.00 0.00 0.00 3.95
957 1024 0.243907 ATCAGTCAGTGGTCGAACGG 59.756 55.000 0.00 0.00 0.00 4.44
958 1025 2.022129 CAGTCAGTGGTCGAACGGC 61.022 63.158 0.00 0.00 0.00 5.68
959 1026 2.028484 GTCAGTGGTCGAACGGCA 59.972 61.111 0.00 0.00 0.00 5.69
960 1027 2.028484 TCAGTGGTCGAACGGCAC 59.972 61.111 0.00 0.00 0.00 5.01
961 1028 3.041940 CAGTGGTCGAACGGCACC 61.042 66.667 0.00 0.00 0.00 5.01
962 1029 4.309950 AGTGGTCGAACGGCACCC 62.310 66.667 0.00 0.00 0.00 4.61
963 1030 4.309950 GTGGTCGAACGGCACCCT 62.310 66.667 0.00 0.00 0.00 4.34
964 1031 4.308458 TGGTCGAACGGCACCCTG 62.308 66.667 0.00 0.00 0.00 4.45
982 1049 2.107141 CCGAACGGCAGAGGATCC 59.893 66.667 2.48 2.48 33.66 3.36
983 1050 2.427245 CCGAACGGCAGAGGATCCT 61.427 63.158 16.13 16.13 33.66 3.24
984 1051 1.066587 CGAACGGCAGAGGATCCTC 59.933 63.158 31.27 31.27 43.03 3.71
985 1052 1.066587 GAACGGCAGAGGATCCTCG 59.933 63.158 31.51 26.20 46.90 4.63
986 1053 1.668101 GAACGGCAGAGGATCCTCGT 61.668 60.000 31.51 24.57 46.90 4.18
987 1054 1.668101 AACGGCAGAGGATCCTCGTC 61.668 60.000 31.51 25.76 46.90 4.20
988 1055 1.826054 CGGCAGAGGATCCTCGTCT 60.826 63.158 31.51 15.40 46.90 4.18
991 1058 4.268720 AGAGGATCCTCGTCTGCC 57.731 61.111 31.51 10.89 46.90 4.85
992 1059 1.456705 AGAGGATCCTCGTCTGCCC 60.457 63.158 31.51 10.16 46.90 5.36
1407 1474 9.886132 CTAAATGAGTTGGTGTTACTTACCTAT 57.114 33.333 0.00 0.00 39.01 2.57
1450 1517 7.148340 GCAATTTTACTGAAGTCTGCAGAGTAT 60.148 37.037 24.13 14.08 36.86 2.12
1451 1518 8.386606 CAATTTTACTGAAGTCTGCAGAGTATC 58.613 37.037 24.13 20.92 36.86 2.24
1452 1519 6.590234 TTTACTGAAGTCTGCAGAGTATCA 57.410 37.500 24.13 23.63 37.82 2.15
1453 1520 6.782082 TTACTGAAGTCTGCAGAGTATCAT 57.218 37.500 24.13 17.81 37.82 2.45
1454 1521 5.008619 ACTGAAGTCTGCAGAGTATCATG 57.991 43.478 24.13 20.11 37.82 3.07
1455 1522 4.708909 ACTGAAGTCTGCAGAGTATCATGA 59.291 41.667 24.13 0.00 37.82 3.07
1456 1523 5.363292 ACTGAAGTCTGCAGAGTATCATGAT 59.637 40.000 24.13 13.81 37.82 2.45
1678 1747 0.676151 TTGCTGATGTATGCCGCACA 60.676 50.000 0.00 0.00 0.00 4.57
1756 1825 5.860941 TCAAACCTTAACATGGAAAGCAA 57.139 34.783 0.00 0.00 0.00 3.91
1757 1826 5.841810 TCAAACCTTAACATGGAAAGCAAG 58.158 37.500 0.00 0.00 0.00 4.01
1767 1836 2.250031 TGGAAAGCAAGCATCAACCAT 58.750 42.857 0.00 0.00 0.00 3.55
1864 1933 6.715347 AAATTGTAGCTCAAAACCTCAACT 57.285 33.333 0.00 0.00 39.62 3.16
2100 2169 1.368579 CCAACTTGGGCTTGGCAAG 59.631 57.895 22.75 22.75 32.03 4.01
2158 2227 1.737793 CCCTTGCTGGTTACGATGTTC 59.262 52.381 0.00 0.00 0.00 3.18
2200 2269 5.127682 GCCCTGAAATGAACTAATTGGATGT 59.872 40.000 0.00 0.00 0.00 3.06
2205 2274 7.315142 TGAAATGAACTAATTGGATGTTGCTC 58.685 34.615 0.00 0.00 0.00 4.26
2373 2442 3.327757 AGCACCTTCTCCACAAGAATACA 59.672 43.478 0.00 0.00 43.06 2.29
2386 2455 6.646240 CCACAAGAATACATTGGGAAAACAAG 59.354 38.462 0.00 0.00 32.60 3.16
2393 2462 7.660030 ATACATTGGGAAAACAAGGGATAAG 57.340 36.000 0.00 0.00 34.21 1.73
2399 2468 5.883673 TGGGAAAACAAGGGATAAGTATTCG 59.116 40.000 0.00 0.00 0.00 3.34
2510 2579 6.470278 TGTTCATGAAGTGACTCATCTTGAT 58.530 36.000 8.80 0.00 36.32 2.57
2531 2600 2.437651 TGTGTCTGATGTTTCCTGTGGA 59.562 45.455 0.00 0.00 0.00 4.02
2546 2615 3.455910 CCTGTGGACTTGATCATTCCCTA 59.544 47.826 17.37 8.41 0.00 3.53
2623 2692 6.558009 CACTTGCTATGCATAATGTTTCTGT 58.442 36.000 8.00 0.00 38.76 3.41
2649 2718 8.958119 TGTACTTATTTCTCTCTCTCTCTCTC 57.042 38.462 0.00 0.00 0.00 3.20
2650 2719 8.768397 TGTACTTATTTCTCTCTCTCTCTCTCT 58.232 37.037 0.00 0.00 0.00 3.10
2651 2720 9.262358 GTACTTATTTCTCTCTCTCTCTCTCTC 57.738 40.741 0.00 0.00 0.00 3.20
2652 2721 8.095452 ACTTATTTCTCTCTCTCTCTCTCTCT 57.905 38.462 0.00 0.00 0.00 3.10
2653 2722 8.207545 ACTTATTTCTCTCTCTCTCTCTCTCTC 58.792 40.741 0.00 0.00 0.00 3.20
2654 2723 6.821616 ATTTCTCTCTCTCTCTCTCTCTCT 57.178 41.667 0.00 0.00 0.00 3.10
2655 2724 5.860941 TTCTCTCTCTCTCTCTCTCTCTC 57.139 47.826 0.00 0.00 0.00 3.20
2656 2725 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
2657 2726 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2658 2727 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2659 2728 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2660 2729 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2661 2730 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2662 2731 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2663 2732 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2664 2733 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2665 2734 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2666 2735 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2667 2736 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2668 2737 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2669 2738 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2670 2739 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2671 2740 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2695 2764 8.890410 TCAAGGTAGTAGTGTTTAATAGGACT 57.110 34.615 0.00 0.00 0.00 3.85
2839 2913 1.888512 TCAAGCACCAGCATTCTTTCC 59.111 47.619 0.00 0.00 45.49 3.13
2895 2969 0.621082 AGAAAACTAGGAGCTGGGCC 59.379 55.000 0.00 0.00 0.00 5.80
2968 3042 2.798976 GCATGAGCACCAAAAACAGA 57.201 45.000 0.00 0.00 41.58 3.41
2969 3043 2.669364 GCATGAGCACCAAAAACAGAG 58.331 47.619 0.00 0.00 41.58 3.35
2970 3044 2.294233 GCATGAGCACCAAAAACAGAGA 59.706 45.455 0.00 0.00 41.58 3.10
3083 3164 8.534333 TTATATTCCTCTCATGTGATTTACGC 57.466 34.615 0.00 0.00 0.00 4.42
3172 3253 1.547472 GCTGGGCCAAATTGCTTCCT 61.547 55.000 8.04 0.00 0.00 3.36
3200 3281 6.506538 ACATAAGCTACATCCCATTCTCTT 57.493 37.500 0.00 0.00 0.00 2.85
3253 3334 5.104151 TCTGTGCCATATATCAACCAAAGGA 60.104 40.000 0.00 0.00 0.00 3.36
3367 3448 4.932200 GTCAACTATCTGGTTGGTGAGAAG 59.068 45.833 6.59 0.00 44.52 2.85
3379 3460 1.745653 GGTGAGAAGCCAATAACAGCC 59.254 52.381 0.00 0.00 0.00 4.85
3472 3553 1.308783 GCAGACTAGGTTTGGGCAGC 61.309 60.000 0.00 0.00 0.00 5.25
3617 3698 5.271598 AGGGAAGGATATTGATTGTTGCAA 58.728 37.500 0.00 0.00 0.00 4.08
3624 3705 8.701908 AGGATATTGATTGTTGCAATAGTCAT 57.298 30.769 19.38 12.89 40.39 3.06
3708 3789 4.579454 ACTACTACTCACACGCTTTCAA 57.421 40.909 0.00 0.00 0.00 2.69
3720 3801 3.061006 CACGCTTTCAAAATTGTGTCTGC 60.061 43.478 0.00 0.00 0.00 4.26
3727 3808 3.068024 TCAAAATTGTGTCTGCCACCTTC 59.932 43.478 0.00 0.00 43.85 3.46
3747 3829 5.105756 CCTTCCACTTCCATGTAATGTTTCC 60.106 44.000 0.00 0.00 44.81 3.13
3852 3934 4.294347 TGGTCTTGGAAGGGAAAATGTTT 58.706 39.130 0.00 0.00 0.00 2.83
3896 3978 2.165998 GCTTCCTCCTGTGCAATTCTT 58.834 47.619 0.00 0.00 0.00 2.52
3923 4005 6.310467 AGCTTGTCTGTTTACATGTACATACG 59.690 38.462 8.32 0.00 0.00 3.06
3927 4009 8.367943 TGTCTGTTTACATGTACATACGTTTT 57.632 30.769 8.32 0.00 0.00 2.43
3949 4031 9.434559 GTTTTAATCCTATTGCGAATGTTCTAC 57.565 33.333 0.00 0.00 0.00 2.59
3950 4032 8.958119 TTTAATCCTATTGCGAATGTTCTACT 57.042 30.769 0.00 0.00 0.00 2.57
3951 4033 6.851222 AATCCTATTGCGAATGTTCTACTG 57.149 37.500 0.00 0.00 0.00 2.74
3952 4034 5.339008 TCCTATTGCGAATGTTCTACTGT 57.661 39.130 0.00 0.00 0.00 3.55
3953 4035 6.459670 TCCTATTGCGAATGTTCTACTGTA 57.540 37.500 0.00 0.00 0.00 2.74
3954 4036 6.869695 TCCTATTGCGAATGTTCTACTGTAA 58.130 36.000 0.00 0.00 0.00 2.41
3955 4037 7.497595 TCCTATTGCGAATGTTCTACTGTAAT 58.502 34.615 0.00 0.00 0.00 1.89
4118 4200 8.946085 TGAATTGTGTAATAAGCACTTTCCTAG 58.054 33.333 0.00 0.00 37.70 3.02
4294 4377 7.148018 GCTCAATTCAAAGACCATGGAGATTTA 60.148 37.037 21.47 2.73 0.00 1.40
4331 4414 7.984475 TGCATAGTACTCCCACCATTAATAAT 58.016 34.615 0.00 0.00 0.00 1.28
4354 4437 7.678947 ATTACTTCCTCTGTCTCAAAATGTG 57.321 36.000 0.00 0.00 0.00 3.21
4478 4563 8.853345 GCATGTTACTTGACAAAACATCAATAG 58.147 33.333 13.06 5.81 40.83 1.73
4486 4571 6.907741 TGACAAAACATCAATAGAATTGCGA 58.092 32.000 0.00 0.00 0.00 5.10
4489 4574 8.398491 ACAAAACATCAATAGAATTGCGATTC 57.602 30.769 17.64 17.64 41.63 2.52
4521 4606 7.290813 ACAATGTTTTCTTTTCTACTCCCTCT 58.709 34.615 0.00 0.00 0.00 3.69
4524 4609 7.369551 TGTTTTCTTTTCTACTCCCTCTGTA 57.630 36.000 0.00 0.00 0.00 2.74
4525 4610 7.798071 TGTTTTCTTTTCTACTCCCTCTGTAA 58.202 34.615 0.00 0.00 0.00 2.41
4526 4611 8.269317 TGTTTTCTTTTCTACTCCCTCTGTAAA 58.731 33.333 0.00 0.00 0.00 2.01
4527 4612 8.775527 GTTTTCTTTTCTACTCCCTCTGTAAAG 58.224 37.037 0.00 0.00 0.00 1.85
4528 4613 7.850935 TTCTTTTCTACTCCCTCTGTAAAGA 57.149 36.000 0.00 0.00 0.00 2.52
4529 4614 7.850935 TCTTTTCTACTCCCTCTGTAAAGAA 57.149 36.000 0.00 0.00 0.00 2.52
4530 4615 8.258850 TCTTTTCTACTCCCTCTGTAAAGAAA 57.741 34.615 0.00 0.00 0.00 2.52
4531 4616 8.881262 TCTTTTCTACTCCCTCTGTAAAGAAAT 58.119 33.333 0.00 0.00 0.00 2.17
4539 4624 8.425703 ACTCCCTCTGTAAAGAAATATAAGAGC 58.574 37.037 0.00 0.00 0.00 4.09
4540 4625 7.434492 TCCCTCTGTAAAGAAATATAAGAGCG 58.566 38.462 0.00 0.00 0.00 5.03
4541 4626 7.069578 TCCCTCTGTAAAGAAATATAAGAGCGT 59.930 37.037 0.00 0.00 0.00 5.07
4542 4627 7.711339 CCCTCTGTAAAGAAATATAAGAGCGTT 59.289 37.037 0.00 0.00 0.00 4.84
4543 4628 9.099454 CCTCTGTAAAGAAATATAAGAGCGTTT 57.901 33.333 0.00 0.00 0.00 3.60
4558 4643 9.953697 ATAAGAGCGTTTAGATCACTAAAGTAG 57.046 33.333 0.00 0.00 45.42 2.57
4559 4644 7.393841 AGAGCGTTTAGATCACTAAAGTAGT 57.606 36.000 0.00 0.00 45.42 2.73
4571 4656 5.718724 ACTAAAGTAGTGACCTAAACGCT 57.281 39.130 0.00 0.00 37.69 5.07
4572 4657 5.707931 ACTAAAGTAGTGACCTAAACGCTC 58.292 41.667 0.00 0.00 37.69 5.03
4573 4658 4.868314 AAAGTAGTGACCTAAACGCTCT 57.132 40.909 0.00 0.00 0.00 4.09
4574 4659 4.868314 AAGTAGTGACCTAAACGCTCTT 57.132 40.909 0.00 0.00 0.00 2.85
4575 4660 5.972107 AAGTAGTGACCTAAACGCTCTTA 57.028 39.130 0.00 0.00 0.00 2.10
4576 4661 6.527057 AAGTAGTGACCTAAACGCTCTTAT 57.473 37.500 0.00 0.00 0.00 1.73
4577 4662 7.636150 AAGTAGTGACCTAAACGCTCTTATA 57.364 36.000 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 1.300963 GGTGAAGATGGCCTGCAGA 59.699 57.895 17.39 0.00 28.87 4.26
114 115 0.905337 CGAGGAGGTTCTGGAAGGGT 60.905 60.000 0.00 0.00 0.00 4.34
198 199 1.153939 GCTCGGATCGGATCGGATG 60.154 63.158 23.23 18.36 37.87 3.51
389 390 2.143925 CGGGGAAAGAAAGACACAGAC 58.856 52.381 0.00 0.00 0.00 3.51
439 446 8.487313 AAATGAGACACGTATTACTATGCAAA 57.513 30.769 0.00 0.00 0.00 3.68
440 447 9.758651 ATAAATGAGACACGTATTACTATGCAA 57.241 29.630 0.00 0.00 0.00 4.08
453 460 9.476202 TGACCTTTATGATATAAATGAGACACG 57.524 33.333 0.00 0.00 0.00 4.49
466 473 9.826574 GTGGTTTGTACTATGACCTTTATGATA 57.173 33.333 0.00 0.00 33.33 2.15
467 474 7.494625 CGTGGTTTGTACTATGACCTTTATGAT 59.505 37.037 0.00 0.00 33.33 2.45
468 475 6.814644 CGTGGTTTGTACTATGACCTTTATGA 59.185 38.462 0.00 0.00 33.33 2.15
469 476 6.592607 ACGTGGTTTGTACTATGACCTTTATG 59.407 38.462 0.00 0.00 33.33 1.90
470 477 6.704310 ACGTGGTTTGTACTATGACCTTTAT 58.296 36.000 0.00 0.00 33.33 1.40
471 478 6.100404 ACGTGGTTTGTACTATGACCTTTA 57.900 37.500 0.00 0.00 33.33 1.85
472 479 4.964593 ACGTGGTTTGTACTATGACCTTT 58.035 39.130 0.00 0.00 33.33 3.11
473 480 4.612264 ACGTGGTTTGTACTATGACCTT 57.388 40.909 0.00 0.00 33.33 3.50
474 481 4.523943 TGTACGTGGTTTGTACTATGACCT 59.476 41.667 0.00 0.00 42.09 3.85
475 482 4.808558 TGTACGTGGTTTGTACTATGACC 58.191 43.478 0.00 0.00 42.09 4.02
476 483 6.346838 GGTTTGTACGTGGTTTGTACTATGAC 60.347 42.308 0.00 0.00 42.09 3.06
477 484 5.695816 GGTTTGTACGTGGTTTGTACTATGA 59.304 40.000 0.00 0.00 42.09 2.15
478 485 5.388682 CGGTTTGTACGTGGTTTGTACTATG 60.389 44.000 0.00 0.00 42.09 2.23
479 486 4.685628 CGGTTTGTACGTGGTTTGTACTAT 59.314 41.667 0.00 0.00 42.09 2.12
480 487 4.047822 CGGTTTGTACGTGGTTTGTACTA 58.952 43.478 0.00 0.00 42.09 1.82
481 488 2.865551 CGGTTTGTACGTGGTTTGTACT 59.134 45.455 0.00 0.00 42.09 2.73
482 489 2.863137 TCGGTTTGTACGTGGTTTGTAC 59.137 45.455 0.00 0.00 41.97 2.90
483 490 3.170791 TCGGTTTGTACGTGGTTTGTA 57.829 42.857 0.00 0.00 0.00 2.41
484 491 2.021355 TCGGTTTGTACGTGGTTTGT 57.979 45.000 0.00 0.00 0.00 2.83
485 492 2.803956 AGATCGGTTTGTACGTGGTTTG 59.196 45.455 0.00 0.00 0.00 2.93
486 493 2.803956 CAGATCGGTTTGTACGTGGTTT 59.196 45.455 0.00 0.00 0.00 3.27
487 494 2.036217 TCAGATCGGTTTGTACGTGGTT 59.964 45.455 0.00 0.00 0.00 3.67
488 495 1.614903 TCAGATCGGTTTGTACGTGGT 59.385 47.619 0.00 0.00 0.00 4.16
489 496 2.357327 TCAGATCGGTTTGTACGTGG 57.643 50.000 0.00 0.00 0.00 4.94
490 497 4.718858 TTTTCAGATCGGTTTGTACGTG 57.281 40.909 0.00 0.00 0.00 4.49
509 516 5.694458 AGCGTTTGTTGTCTTTTCAGTTTTT 59.306 32.000 0.00 0.00 0.00 1.94
510 517 5.227152 AGCGTTTGTTGTCTTTTCAGTTTT 58.773 33.333 0.00 0.00 0.00 2.43
511 518 4.805219 AGCGTTTGTTGTCTTTTCAGTTT 58.195 34.783 0.00 0.00 0.00 2.66
512 519 4.434713 AGCGTTTGTTGTCTTTTCAGTT 57.565 36.364 0.00 0.00 0.00 3.16
513 520 4.634443 ACTAGCGTTTGTTGTCTTTTCAGT 59.366 37.500 0.00 0.00 0.00 3.41
514 521 4.963953 CACTAGCGTTTGTTGTCTTTTCAG 59.036 41.667 0.00 0.00 0.00 3.02
515 522 4.201871 CCACTAGCGTTTGTTGTCTTTTCA 60.202 41.667 0.00 0.00 0.00 2.69
516 523 4.279659 CCACTAGCGTTTGTTGTCTTTTC 58.720 43.478 0.00 0.00 0.00 2.29
517 524 3.488553 GCCACTAGCGTTTGTTGTCTTTT 60.489 43.478 0.00 0.00 0.00 2.27
518 525 2.032924 GCCACTAGCGTTTGTTGTCTTT 59.967 45.455 0.00 0.00 0.00 2.52
519 526 1.602377 GCCACTAGCGTTTGTTGTCTT 59.398 47.619 0.00 0.00 0.00 3.01
520 527 1.226746 GCCACTAGCGTTTGTTGTCT 58.773 50.000 0.00 0.00 0.00 3.41
521 528 3.748021 GCCACTAGCGTTTGTTGTC 57.252 52.632 0.00 0.00 0.00 3.18
648 664 3.801594 CCTTTTCCCAAAATTCACGTGTG 59.198 43.478 16.51 5.75 0.00 3.82
711 777 5.932303 GTCACAGTAAGCATAGAAGAAACCA 59.068 40.000 0.00 0.00 0.00 3.67
730 796 3.991773 CCCGATTTAAGAACTTCGTCACA 59.008 43.478 0.00 0.00 0.00 3.58
777 843 1.605165 CCGGTTAAAAGCTGGCCCA 60.605 57.895 0.00 0.00 0.00 5.36
864 931 4.479993 CAGGGGAGCCGCTTCTGG 62.480 72.222 3.01 0.00 37.10 3.86
865 932 3.393970 TCAGGGGAGCCGCTTCTG 61.394 66.667 3.01 5.91 37.10 3.02
866 933 3.394836 GTCAGGGGAGCCGCTTCT 61.395 66.667 3.01 0.00 37.10 2.85
867 934 4.821589 CGTCAGGGGAGCCGCTTC 62.822 72.222 3.01 0.00 37.10 3.86
930 997 0.914644 CCACTGACTGATGGACCCAT 59.085 55.000 0.32 0.32 38.34 4.00
931 998 0.473694 ACCACTGACTGATGGACCCA 60.474 55.000 0.00 0.00 39.46 4.51
932 999 0.250513 GACCACTGACTGATGGACCC 59.749 60.000 0.00 0.00 39.46 4.46
933 1000 0.108615 CGACCACTGACTGATGGACC 60.109 60.000 0.00 0.00 39.46 4.46
934 1001 0.888619 TCGACCACTGACTGATGGAC 59.111 55.000 0.00 0.00 39.46 4.02
935 1002 1.272490 GTTCGACCACTGACTGATGGA 59.728 52.381 0.00 0.00 39.46 3.41
936 1003 1.714794 GTTCGACCACTGACTGATGG 58.285 55.000 0.00 0.00 42.13 3.51
937 1004 1.340658 CGTTCGACCACTGACTGATG 58.659 55.000 0.00 0.00 0.00 3.07
938 1005 0.243907 CCGTTCGACCACTGACTGAT 59.756 55.000 0.00 0.00 0.00 2.90
939 1006 1.658114 CCGTTCGACCACTGACTGA 59.342 57.895 0.00 0.00 0.00 3.41
940 1007 2.022129 GCCGTTCGACCACTGACTG 61.022 63.158 0.00 0.00 0.00 3.51
941 1008 2.338984 GCCGTTCGACCACTGACT 59.661 61.111 0.00 0.00 0.00 3.41
942 1009 2.028484 TGCCGTTCGACCACTGAC 59.972 61.111 0.00 0.00 0.00 3.51
943 1010 2.028484 GTGCCGTTCGACCACTGA 59.972 61.111 0.00 0.00 0.00 3.41
944 1011 3.041940 GGTGCCGTTCGACCACTG 61.042 66.667 12.56 0.00 31.97 3.66
945 1012 4.309950 GGGTGCCGTTCGACCACT 62.310 66.667 12.56 0.00 33.48 4.00
946 1013 4.309950 AGGGTGCCGTTCGACCAC 62.310 66.667 5.67 6.47 33.48 4.16
947 1014 4.308458 CAGGGTGCCGTTCGACCA 62.308 66.667 5.67 0.00 33.48 4.02
965 1032 2.107141 GGATCCTCTGCCGTTCGG 59.893 66.667 3.84 6.90 0.00 4.30
966 1033 1.066587 GAGGATCCTCTGCCGTTCG 59.933 63.158 31.11 0.00 39.80 3.95
967 1034 1.066587 CGAGGATCCTCTGCCGTTC 59.933 63.158 33.70 11.23 40.69 3.95
968 1035 1.668101 GACGAGGATCCTCTGCCGTT 61.668 60.000 33.70 15.24 40.69 4.44
969 1036 2.043852 ACGAGGATCCTCTGCCGT 60.044 61.111 33.70 25.82 40.69 5.68
970 1037 1.826054 AGACGAGGATCCTCTGCCG 60.826 63.158 33.70 25.21 40.69 5.69
971 1038 1.739049 CAGACGAGGATCCTCTGCC 59.261 63.158 33.70 23.03 40.41 4.85
973 1040 1.739049 GGCAGACGAGGATCCTCTG 59.261 63.158 33.70 28.14 46.62 3.35
974 1041 1.456705 GGGCAGACGAGGATCCTCT 60.457 63.158 33.70 22.77 40.69 3.69
975 1042 1.456705 AGGGCAGACGAGGATCCTC 60.457 63.158 29.15 29.15 39.55 3.71
976 1043 1.760086 CAGGGCAGACGAGGATCCT 60.760 63.158 16.13 16.13 0.00 3.24
977 1044 2.818132 CAGGGCAGACGAGGATCC 59.182 66.667 2.48 2.48 0.00 3.36
978 1045 2.107953 GCAGGGCAGACGAGGATC 59.892 66.667 0.00 0.00 0.00 3.36
979 1046 3.474570 GGCAGGGCAGACGAGGAT 61.475 66.667 0.00 0.00 0.00 3.24
982 1049 4.463879 CTGGGCAGGGCAGACGAG 62.464 72.222 0.00 0.00 0.00 4.18
984 1051 3.790437 ATCTGGGCAGGGCAGACG 61.790 66.667 0.00 0.00 0.00 4.18
985 1052 2.124403 CATCTGGGCAGGGCAGAC 60.124 66.667 0.00 0.00 0.00 3.51
986 1053 4.119363 GCATCTGGGCAGGGCAGA 62.119 66.667 0.00 0.00 32.19 4.26
987 1054 3.657038 AAGCATCTGGGCAGGGCAG 62.657 63.158 0.00 0.00 35.83 4.85
988 1055 3.650298 GAAGCATCTGGGCAGGGCA 62.650 63.158 0.00 0.00 35.83 5.36
989 1056 2.832201 GAAGCATCTGGGCAGGGC 60.832 66.667 0.00 0.00 35.83 5.19
990 1057 2.123982 GGAAGCATCTGGGCAGGG 60.124 66.667 0.00 0.00 35.83 4.45
991 1058 2.123982 GGGAAGCATCTGGGCAGG 60.124 66.667 0.00 0.00 35.83 4.85
992 1059 2.123982 GGGGAAGCATCTGGGCAG 60.124 66.667 0.00 0.00 35.83 4.85
1451 1518 9.117183 CATACATAACCCCTATCATGAATCATG 57.883 37.037 16.63 16.63 42.60 3.07
1452 1519 7.776969 GCATACATAACCCCTATCATGAATCAT 59.223 37.037 0.00 0.00 0.00 2.45
1453 1520 7.112122 GCATACATAACCCCTATCATGAATCA 58.888 38.462 0.00 0.00 0.00 2.57
1454 1521 6.543831 GGCATACATAACCCCTATCATGAATC 59.456 42.308 0.00 0.00 0.00 2.52
1455 1522 6.011717 TGGCATACATAACCCCTATCATGAAT 60.012 38.462 0.00 0.00 0.00 2.57
1456 1523 5.311913 TGGCATACATAACCCCTATCATGAA 59.688 40.000 0.00 0.00 0.00 2.57
1524 1591 1.620323 GGCCAGAAAGAAATGGTGCTT 59.380 47.619 0.00 0.00 38.91 3.91
1716 1785 6.766944 AGGTTTGAATGCTCTGATCAGAATAG 59.233 38.462 25.09 15.26 36.94 1.73
1767 1836 8.532186 AAAAATATGGTTGCATCATACCAGTA 57.468 30.769 13.20 6.92 46.82 2.74
1782 1851 3.776417 AGCATGGGCAAGAAAAATATGGT 59.224 39.130 0.00 0.00 44.61 3.55
2158 2227 5.710099 TCAGGGCAAAAGTTATCACCTTAAG 59.290 40.000 0.00 0.00 0.00 1.85
2205 2274 5.647658 TCATTAAACCATTGCCTCACTAGTG 59.352 40.000 17.17 17.17 0.00 2.74
2221 2290 6.617879 ACCTACCATTTTCGCTTCATTAAAC 58.382 36.000 0.00 0.00 0.00 2.01
2373 2442 7.068226 CGAATACTTATCCCTTGTTTTCCCAAT 59.932 37.037 0.00 0.00 0.00 3.16
2386 2455 7.254795 CCAACATTGAACTCGAATACTTATCCC 60.255 40.741 0.00 0.00 0.00 3.85
2393 2462 4.201822 GCCTCCAACATTGAACTCGAATAC 60.202 45.833 0.00 0.00 0.00 1.89
2399 2468 2.508526 ACAGCCTCCAACATTGAACTC 58.491 47.619 0.00 0.00 0.00 3.01
2453 2522 4.030314 CCAGATGATGGGCATATTGTCT 57.970 45.455 0.00 0.00 46.36 3.41
2510 2579 2.437651 TCCACAGGAAACATCAGACACA 59.562 45.455 0.00 0.00 0.00 3.72
2531 2600 6.060788 GCAGAGAATTAGGGAATGATCAAGT 58.939 40.000 0.00 0.00 0.00 3.16
2546 2615 7.992754 AAAGAAATACTCACAGCAGAGAATT 57.007 32.000 7.69 0.00 38.98 2.17
2623 2692 9.391006 GAGAGAGAGAGAGAGAAATAAGTACAA 57.609 37.037 0.00 0.00 0.00 2.41
2649 2718 4.892345 TGAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
2650 2719 4.871822 TGAGAGAGAGAGAGAGAGAGAGA 58.128 47.826 0.00 0.00 0.00 3.10
2651 2720 5.453057 CCTTGAGAGAGAGAGAGAGAGAGAG 60.453 52.000 0.00 0.00 0.00 3.20
2652 2721 4.406972 CCTTGAGAGAGAGAGAGAGAGAGA 59.593 50.000 0.00 0.00 0.00 3.10
2653 2722 4.163078 ACCTTGAGAGAGAGAGAGAGAGAG 59.837 50.000 0.00 0.00 0.00 3.20
2654 2723 4.104086 ACCTTGAGAGAGAGAGAGAGAGA 58.896 47.826 0.00 0.00 0.00 3.10
2655 2724 4.494091 ACCTTGAGAGAGAGAGAGAGAG 57.506 50.000 0.00 0.00 0.00 3.20
2656 2725 5.030147 ACTACCTTGAGAGAGAGAGAGAGA 58.970 45.833 0.00 0.00 0.00 3.10
2657 2726 5.359194 ACTACCTTGAGAGAGAGAGAGAG 57.641 47.826 0.00 0.00 0.00 3.20
2658 2727 5.962031 ACTACTACCTTGAGAGAGAGAGAGA 59.038 44.000 0.00 0.00 0.00 3.10
2659 2728 6.049149 CACTACTACCTTGAGAGAGAGAGAG 58.951 48.000 0.00 0.00 0.00 3.20
2660 2729 5.486063 ACACTACTACCTTGAGAGAGAGAGA 59.514 44.000 0.00 0.00 0.00 3.10
2661 2730 5.741011 ACACTACTACCTTGAGAGAGAGAG 58.259 45.833 0.00 0.00 0.00 3.20
2662 2731 5.765576 ACACTACTACCTTGAGAGAGAGA 57.234 43.478 0.00 0.00 0.00 3.10
2663 2732 6.827586 AAACACTACTACCTTGAGAGAGAG 57.172 41.667 0.00 0.00 0.00 3.20
2664 2733 8.880991 ATTAAACACTACTACCTTGAGAGAGA 57.119 34.615 0.00 0.00 0.00 3.10
2666 2735 9.186837 CCTATTAAACACTACTACCTTGAGAGA 57.813 37.037 0.00 0.00 0.00 3.10
2667 2736 9.186837 TCCTATTAAACACTACTACCTTGAGAG 57.813 37.037 0.00 0.00 0.00 3.20
2668 2737 8.964772 GTCCTATTAAACACTACTACCTTGAGA 58.035 37.037 0.00 0.00 0.00 3.27
2669 2738 8.968969 AGTCCTATTAAACACTACTACCTTGAG 58.031 37.037 0.00 0.00 0.00 3.02
2670 2739 8.890410 AGTCCTATTAAACACTACTACCTTGA 57.110 34.615 0.00 0.00 0.00 3.02
2735 2809 6.024049 GCTATTTCCAAGTTCGAACTCATTG 58.976 40.000 29.82 23.07 38.57 2.82
2912 2986 4.424626 CGTCATACTACATGCACAAGACT 58.575 43.478 0.00 0.00 0.00 3.24
2964 3038 1.480137 GCTGTGCACTCCTATCTCTGT 59.520 52.381 19.41 0.00 0.00 3.41
2965 3039 1.755959 AGCTGTGCACTCCTATCTCTG 59.244 52.381 19.41 0.00 0.00 3.35
2966 3040 2.157640 AGCTGTGCACTCCTATCTCT 57.842 50.000 19.41 0.66 0.00 3.10
2967 3041 2.935201 CAAAGCTGTGCACTCCTATCTC 59.065 50.000 19.41 0.00 0.00 2.75
2968 3042 2.355513 CCAAAGCTGTGCACTCCTATCT 60.356 50.000 19.41 3.09 0.00 1.98
2969 3043 2.012673 CCAAAGCTGTGCACTCCTATC 58.987 52.381 19.41 0.75 0.00 2.08
2970 3044 1.630369 TCCAAAGCTGTGCACTCCTAT 59.370 47.619 19.41 0.00 0.00 2.57
3172 3253 3.028130 TGGGATGTAGCTTATGTCGACA 58.972 45.455 22.48 22.48 0.00 4.35
3253 3334 6.405397 GGACACCAGTTTTAACATTGTCAGTT 60.405 38.462 16.37 0.00 36.61 3.16
3367 3448 2.102946 GCTGCGGCTGTTATTGGC 59.897 61.111 11.21 0.00 35.22 4.52
3617 3698 7.611467 TGATAGCAAAACTGTTCCAATGACTAT 59.389 33.333 0.00 3.84 0.00 2.12
3624 3705 5.830912 CAGTTGATAGCAAAACTGTTCCAA 58.169 37.500 4.92 0.00 45.30 3.53
3720 3801 3.433306 TTACATGGAAGTGGAAGGTGG 57.567 47.619 0.00 0.00 0.00 4.61
3727 3808 4.085733 TGGGAAACATTACATGGAAGTGG 58.914 43.478 0.00 0.00 33.60 4.00
3747 3829 4.996758 TGATGGACGAGCATAAATACATGG 59.003 41.667 0.00 0.00 0.00 3.66
3837 3919 8.575649 TGAACTATCTAAACATTTTCCCTTCC 57.424 34.615 0.00 0.00 0.00 3.46
3852 3934 5.455183 CCTGGGAATGCACATGAACTATCTA 60.455 44.000 0.00 0.00 0.00 1.98
3896 3978 9.146984 GTATGTACATGTAAACAGACAAGCTAA 57.853 33.333 18.81 0.00 37.67 3.09
3923 4005 9.434559 GTAGAACATTCGCAATAGGATTAAAAC 57.565 33.333 0.00 0.00 0.00 2.43
3927 4009 7.497595 ACAGTAGAACATTCGCAATAGGATTA 58.502 34.615 0.00 0.00 0.00 1.75
3934 4016 6.747280 GCAAATTACAGTAGAACATTCGCAAT 59.253 34.615 0.00 0.00 0.00 3.56
3949 4031 4.572389 AGCCGAGATGTTAGCAAATTACAG 59.428 41.667 0.00 0.00 0.00 2.74
3950 4032 4.513442 AGCCGAGATGTTAGCAAATTACA 58.487 39.130 0.00 0.00 0.00 2.41
3951 4033 4.811557 AGAGCCGAGATGTTAGCAAATTAC 59.188 41.667 0.00 0.00 0.00 1.89
3952 4034 5.023533 AGAGCCGAGATGTTAGCAAATTA 57.976 39.130 0.00 0.00 0.00 1.40
3953 4035 3.873952 GAGAGCCGAGATGTTAGCAAATT 59.126 43.478 0.00 0.00 0.00 1.82
3954 4036 3.462021 GAGAGCCGAGATGTTAGCAAAT 58.538 45.455 0.00 0.00 0.00 2.32
3955 4037 2.418746 GGAGAGCCGAGATGTTAGCAAA 60.419 50.000 0.00 0.00 0.00 3.68
4097 4179 5.800296 TGCTAGGAAAGTGCTTATTACACA 58.200 37.500 0.00 0.00 40.59 3.72
4118 4200 8.925700 CCACCTTCTAAAAATGTTTTCTTATGC 58.074 33.333 0.00 0.00 0.00 3.14
4137 4220 8.732746 ATTTATCACTATACAACACCACCTTC 57.267 34.615 0.00 0.00 0.00 3.46
4227 4310 6.446781 AATTTTGATGGACATCACTAGCTG 57.553 37.500 14.12 0.00 46.49 4.24
4294 4377 5.359194 AGTACTATGCATGGCAAGTAGTT 57.641 39.130 10.16 0.00 43.62 2.24
4331 4414 5.997746 CCACATTTTGAGACAGAGGAAGTAA 59.002 40.000 0.00 0.00 0.00 2.24
4375 4458 6.889177 TGCAATATACTCCCATTGTCTCAAAA 59.111 34.615 0.00 0.00 35.12 2.44
4376 4459 6.422333 TGCAATATACTCCCATTGTCTCAAA 58.578 36.000 0.00 0.00 35.12 2.69
4410 4495 5.713792 TGTCAAAACTTGAAGTTGGACAA 57.286 34.783 28.41 18.51 43.77 3.18
4478 4563 6.422223 ACATTGTCGAATAGAATCGCAATTC 58.578 36.000 12.90 0.00 42.21 2.17
4495 4580 7.445707 AGAGGGAGTAGAAAAGAAAACATTGTC 59.554 37.037 0.00 0.00 0.00 3.18
4497 4582 7.229506 ACAGAGGGAGTAGAAAAGAAAACATTG 59.770 37.037 0.00 0.00 0.00 2.82
4499 4584 6.842676 ACAGAGGGAGTAGAAAAGAAAACAT 58.157 36.000 0.00 0.00 0.00 2.71
4532 4617 9.953697 CTACTTTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 40.05 1.73
4533 4618 8.954350 ACTACTTTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 40.05 2.10
4534 4619 7.828712 ACTACTTTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 40.05 2.85
4535 4620 7.393841 ACTACTTTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 40.05 4.09
4549 4634 5.707931 GAGCGTTTAGGTCACTACTTTAGT 58.292 41.667 0.00 0.00 46.08 2.24


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

AutoCloner maintained by Alex Coulton.