Multiple sequence alignment - TraesCS2A01G384700

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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 TraesCS2A01G384700 chr2A 100.000 3877 0 0 1 3877 630094025 630090149 0.000000e+00 7160.0
1 TraesCS2A01G384700 chr2A 86.207 87 7 3 2950 3034 31014078 31014161 5.340000e-14 89.8
2 TraesCS2A01G384700 chr2D 93.480 2178 57 18 904 3034 485491295 485489156 0.000000e+00 3157.0
3 TraesCS2A01G384700 chr2D 97.176 779 20 2 3100 3877 485489156 485488379 0.000000e+00 1315.0
4 TraesCS2A01G384700 chr2D 95.146 103 4 1 3019 3121 564674215 564674114 1.110000e-35 161.0
5 TraesCS2A01G384700 chr2D 95.833 96 4 0 3782 3877 485465935 485465840 5.190000e-34 156.0
6 TraesCS2A01G384700 chr2D 95.918 49 2 0 109 157 485491440 485491392 3.210000e-11 80.5
7 TraesCS2A01G384700 chr2B 90.047 1497 84 24 797 2269 570094465 570093010 0.000000e+00 1879.0
8 TraesCS2A01G384700 chr2B 86.946 812 74 14 10 801 570107508 570106709 0.000000e+00 883.0
9 TraesCS2A01G384700 chr2B 86.771 703 44 15 2289 2955 570091004 570090315 0.000000e+00 737.0
10 TraesCS2A01G384700 chr2B 88.690 504 51 5 3117 3619 570090317 570089819 9.210000e-171 610.0
11 TraesCS2A01G384700 chr2B 90.160 437 30 7 1 425 570115084 570114649 1.220000e-154 556.0
12 TraesCS2A01G384700 chr2B 89.474 437 33 9 1 425 570136990 570136555 1.230000e-149 540.0
13 TraesCS2A01G384700 chr2B 86.770 257 29 4 3621 3873 570089778 570089523 8.200000e-72 281.0
14 TraesCS2A01G384700 chr2B 94.393 107 3 3 3033 3137 85695571 85695676 1.110000e-35 161.0
15 TraesCS2A01G384700 chr4D 100.000 91 0 0 3031 3121 507164696 507164786 6.660000e-38 169.0
16 TraesCS2A01G384700 chr4D 96.842 95 1 2 3024 3118 9991726 9991634 1.440000e-34 158.0
17 TraesCS2A01G384700 chr4D 89.831 118 9 3 3005 3120 484742779 484742663 8.680000e-32 148.0
18 TraesCS2A01G384700 chr3B 96.078 102 2 1 3030 3131 293523524 293523623 8.620000e-37 165.0
19 TraesCS2A01G384700 chr3B 91.489 94 2 4 2944 3034 325848093 325848183 1.460000e-24 124.0
20 TraesCS2A01G384700 chr3B 84.146 82 10 2 2953 3034 325848202 325848124 4.150000e-10 76.8
21 TraesCS2A01G384700 chr1B 97.917 96 1 1 3024 3118 618002453 618002548 8.620000e-37 165.0
22 TraesCS2A01G384700 chr7D 96.875 96 3 0 3026 3121 18013099 18013194 1.110000e-35 161.0
23 TraesCS2A01G384700 chr7D 92.661 109 5 2 3017 3125 4798915 4798810 1.870000e-33 154.0
24 TraesCS2A01G384700 chr7D 94.444 72 3 1 2943 3013 465477957 465477886 4.100000e-20 110.0
25 TraesCS2A01G384700 chr7B 96.040 101 1 2 3034 3134 11532988 11532891 1.110000e-35 161.0
26 TraesCS2A01G384700 chr7B 94.444 72 3 1 2943 3013 490208162 490208091 4.100000e-20 110.0
27 TraesCS2A01G384700 chr6D 96.842 95 3 0 3027 3121 95714144 95714238 4.010000e-35 159.0
28 TraesCS2A01G384700 chr4A 96.875 96 2 1 3028 3123 741030478 741030572 4.010000e-35 159.0
29 TraesCS2A01G384700 chr1D 96.842 95 3 0 3026 3120 84569148 84569242 4.010000e-35 159.0
30 TraesCS2A01G384700 chr1D 89.773 88 3 4 2953 3034 23007882 23007795 1.470000e-19 108.0
31 TraesCS2A01G384700 chr1A 93.333 75 4 1 2940 3013 441240928 441240854 4.100000e-20 110.0
32 TraesCS2A01G384700 chr5D 92.308 78 3 3 2938 3013 326457696 326457620 1.470000e-19 108.0
33 TraesCS2A01G384700 chr5A 90.244 82 4 4 2934 3013 429984492 429984571 1.910000e-18 104.0
34 TraesCS2A01G384700 chr6A 87.912 91 5 3 2950 3034 83356592 83356682 6.850000e-18 102.0
35 TraesCS2A01G384700 chr6B 85.542 83 8 3 2953 3034 488218641 488218720 2.480000e-12 84.2


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 TraesCS2A01G384700 chr2A 630090149 630094025 3876 True 7160.00 7160 100.000000 1 3877 1 chr2A.!!$R1 3876
1 TraesCS2A01G384700 chr2D 485488379 485491440 3061 True 1517.50 3157 95.524667 109 3877 3 chr2D.!!$R3 3768
2 TraesCS2A01G384700 chr2B 570106709 570107508 799 True 883.00 883 86.946000 10 801 1 chr2B.!!$R1 791
3 TraesCS2A01G384700 chr2B 570089523 570094465 4942 True 876.75 1879 88.069500 797 3873 4 chr2B.!!$R4 3076

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
767 811 0.038892 AACGCTCAATGCCTTGCAAG 60.039 50.0 19.93 19.93 43.62 4.01 F
1004 1048 0.034059 CTCCCACAGAAGACAAGCGT 59.966 55.0 0.00 0.00 0.00 5.07 F
1674 1759 0.543277 TGTTCCTAGGCCAGCTGATG 59.457 55.0 17.39 0.00 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1632 1717 2.066340 TGGTTGTCCAGTAGCCAGG 58.934 57.895 0.00 0.0 39.03 4.45 R
2790 4900 0.107897 ACGCCCAACATAATCTGCGA 60.108 50.000 8.79 0.0 44.32 5.10 R
3105 5230 0.981183 TGCAATGTACTCCCTCCGTT 59.019 50.000 0.00 0.0 0.00 4.44 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
91 92 0.698238 TGGAAACCACCCTCTCCATG 59.302 55.000 0.00 0.00 32.97 3.66
99 100 2.619074 CCACCCTCTCCATGAAAACTCC 60.619 54.545 0.00 0.00 0.00 3.85
100 101 1.279271 ACCCTCTCCATGAAAACTCCG 59.721 52.381 0.00 0.00 0.00 4.63
101 102 1.373570 CCTCTCCATGAAAACTCCGC 58.626 55.000 0.00 0.00 0.00 5.54
102 103 1.065854 CCTCTCCATGAAAACTCCGCT 60.066 52.381 0.00 0.00 0.00 5.52
122 123 7.784037 TCCGCTGTTTATAAGTAATAACCTCA 58.216 34.615 0.00 0.00 29.54 3.86
266 290 6.321435 AGCCCTTGCAGAAATAAATAGTAACC 59.679 38.462 0.00 0.00 41.13 2.85
282 306 8.953368 AATAGTAACCTAACAATACCTTTCCG 57.047 34.615 0.00 0.00 0.00 4.30
292 316 0.393808 TACCTTTCCGCAAGATGGCC 60.394 55.000 0.00 0.00 43.02 5.36
309 333 1.882623 GGCCACCTCTGAAAACTCTTG 59.117 52.381 0.00 0.00 0.00 3.02
314 338 4.035675 CCACCTCTGAAAACTCTTGACAAC 59.964 45.833 0.00 0.00 0.00 3.32
326 350 2.560981 TCTTGACAACGCCATCAGAGTA 59.439 45.455 0.00 0.00 0.00 2.59
328 352 2.167662 TGACAACGCCATCAGAGTAGA 58.832 47.619 0.00 0.00 0.00 2.59
331 355 2.760650 ACAACGCCATCAGAGTAGATGA 59.239 45.455 5.57 0.00 46.51 2.92
350 374 4.970662 TGAAAGCAATATCTTCAGCACC 57.029 40.909 0.00 0.00 0.00 5.01
351 375 4.334552 TGAAAGCAATATCTTCAGCACCA 58.665 39.130 0.00 0.00 0.00 4.17
352 376 4.951715 TGAAAGCAATATCTTCAGCACCAT 59.048 37.500 0.00 0.00 0.00 3.55
353 377 5.066893 TGAAAGCAATATCTTCAGCACCATC 59.933 40.000 0.00 0.00 0.00 3.51
354 378 4.434545 AGCAATATCTTCAGCACCATCT 57.565 40.909 0.00 0.00 0.00 2.90
356 380 4.579340 AGCAATATCTTCAGCACCATCTTG 59.421 41.667 0.00 0.00 0.00 3.02
357 381 4.337555 GCAATATCTTCAGCACCATCTTGT 59.662 41.667 0.00 0.00 0.00 3.16
358 382 5.732528 GCAATATCTTCAGCACCATCTTGTG 60.733 44.000 0.00 0.00 39.29 3.33
394 427 1.064463 CACACCATCTGGCCCAACTAT 60.064 52.381 0.00 0.00 39.32 2.12
403 436 1.633432 TGGCCCAACTATGCAGTTAGT 59.367 47.619 0.00 0.00 43.30 2.24
425 458 0.754957 ATCTCAGGTCCTCCAGCGAG 60.755 60.000 0.00 0.00 35.89 5.03
430 463 2.052690 GGTCCTCCAGCGAGCTACA 61.053 63.158 0.00 0.00 34.49 2.74
434 467 0.179124 CCTCCAGCGAGCTACAAGAC 60.179 60.000 0.00 0.00 34.49 3.01
435 468 0.524392 CTCCAGCGAGCTACAAGACG 60.524 60.000 0.00 0.00 0.00 4.18
444 477 3.381949 GAGCTACAAGACGTCAAACTGT 58.618 45.455 19.50 16.33 0.00 3.55
447 480 1.014352 ACAAGACGTCAAACTGTGGC 58.986 50.000 19.50 0.00 0.00 5.01
453 486 2.203480 TCAAACTGTGGCAGGCCC 60.203 61.111 8.02 0.00 35.51 5.80
466 499 1.997874 AGGCCCAGACCCACATCTC 60.998 63.158 0.00 0.00 0.00 2.75
486 519 2.883267 ATTTCAGGCTCGGAGCTGGC 62.883 60.000 27.47 12.70 41.99 4.85
510 543 6.573289 GCGTTCCTCTGATCCTATCATTGTAT 60.573 42.308 0.00 0.00 38.85 2.29
512 545 8.523658 CGTTCCTCTGATCCTATCATTGTATAA 58.476 37.037 0.00 0.00 38.85 0.98
513 546 9.868277 GTTCCTCTGATCCTATCATTGTATAAG 57.132 37.037 0.00 0.00 38.85 1.73
515 548 9.607333 TCCTCTGATCCTATCATTGTATAAGTT 57.393 33.333 0.00 0.00 38.85 2.66
547 580 0.530650 CATAGTCTTGCCCGCACGAT 60.531 55.000 0.00 0.00 0.00 3.73
554 587 2.819595 GCCCGCACGATGACATGT 60.820 61.111 0.00 0.00 0.00 3.21
560 593 1.266356 CGCACGATGACATGTACAACG 60.266 52.381 18.86 18.86 38.93 4.10
571 604 0.319083 TGTACAACGGAATCGGCACT 59.681 50.000 0.00 0.00 41.39 4.40
593 626 2.105466 GCCGCTGGCTTCTTCAGAG 61.105 63.158 11.61 0.00 46.69 3.35
599 632 2.211806 CTGGCTTCTTCAGAGCATAGC 58.788 52.381 0.00 0.00 34.36 2.97
608 641 7.601886 GCTTCTTCAGAGCATAGCAAGATATAA 59.398 37.037 0.00 0.00 0.00 0.98
609 642 9.656040 CTTCTTCAGAGCATAGCAAGATATAAT 57.344 33.333 0.00 0.00 0.00 1.28
610 643 9.650539 TTCTTCAGAGCATAGCAAGATATAATC 57.349 33.333 0.00 0.00 0.00 1.75
611 644 8.810041 TCTTCAGAGCATAGCAAGATATAATCA 58.190 33.333 0.00 0.00 0.00 2.57
621 664 4.649692 CAAGATATAATCACCTGCCTGCT 58.350 43.478 0.00 0.00 0.00 4.24
624 667 2.062971 ATAATCACCTGCCTGCTTGG 57.937 50.000 0.00 0.00 39.35 3.61
649 692 1.203428 TGTCTCTCCCCCTTCCATGAA 60.203 52.381 0.00 0.00 0.00 2.57
654 697 2.677228 CCCCTTCCATGAAGCCGT 59.323 61.111 0.00 0.00 38.24 5.68
704 747 4.008933 GCTGACCACCTGACGCCT 62.009 66.667 0.00 0.00 0.00 5.52
711 754 3.382832 ACCTGACGCCTCTTCCCG 61.383 66.667 0.00 0.00 0.00 5.14
721 764 2.007547 GCCTCTTCCCGTTGCTACTTC 61.008 57.143 0.00 0.00 0.00 3.01
722 765 1.275291 CCTCTTCCCGTTGCTACTTCA 59.725 52.381 0.00 0.00 0.00 3.02
723 766 2.611518 CTCTTCCCGTTGCTACTTCAG 58.388 52.381 0.00 0.00 0.00 3.02
724 767 2.231478 CTCTTCCCGTTGCTACTTCAGA 59.769 50.000 0.00 0.00 0.00 3.27
725 768 2.231478 TCTTCCCGTTGCTACTTCAGAG 59.769 50.000 0.00 0.00 0.00 3.35
726 769 1.629043 TCCCGTTGCTACTTCAGAGT 58.371 50.000 0.00 0.00 39.97 3.24
727 770 1.272490 TCCCGTTGCTACTTCAGAGTG 59.728 52.381 0.00 0.00 36.60 3.51
728 771 1.272490 CCCGTTGCTACTTCAGAGTGA 59.728 52.381 0.00 0.00 36.60 3.41
765 809 1.286570 CAACGCTCAATGCCTTGCA 59.713 52.632 0.00 0.00 44.86 4.08
767 811 0.038892 AACGCTCAATGCCTTGCAAG 60.039 50.000 19.93 19.93 43.62 4.01
770 814 0.458025 GCTCAATGCCTTGCAAGCTC 60.458 55.000 21.43 14.49 43.62 4.09
772 816 1.804326 CAATGCCTTGCAAGCTCGC 60.804 57.895 21.43 18.61 43.62 5.03
773 817 2.998279 AATGCCTTGCAAGCTCGCC 61.998 57.895 21.43 6.63 43.62 5.54
831 875 2.099062 CATGCGCTTCGACTTGCC 59.901 61.111 9.73 0.00 0.00 4.52
853 897 4.056125 CCGGTGACTGCGAGCTGA 62.056 66.667 8.91 0.00 0.00 4.26
854 898 2.807045 CGGTGACTGCGAGCTGAC 60.807 66.667 8.91 3.48 0.00 3.51
855 899 2.433318 GGTGACTGCGAGCTGACC 60.433 66.667 8.91 3.45 0.00 4.02
856 900 2.340078 GTGACTGCGAGCTGACCA 59.660 61.111 8.91 3.91 0.00 4.02
857 901 1.079543 GTGACTGCGAGCTGACCAT 60.080 57.895 8.91 0.00 0.00 3.55
858 902 1.079612 TGACTGCGAGCTGACCATG 60.080 57.895 8.91 0.00 0.00 3.66
859 903 2.435586 ACTGCGAGCTGACCATGC 60.436 61.111 8.91 0.00 0.00 4.06
882 926 3.663176 CGGTGTGCCTGGCAAGTG 61.663 66.667 25.23 9.96 41.47 3.16
883 927 3.297620 GGTGTGCCTGGCAAGTGG 61.298 66.667 25.23 0.00 41.47 4.00
902 946 3.749981 AAGTGGCAACGGCTTGAG 58.250 55.556 0.00 0.00 40.87 3.02
935 979 2.538222 TGGGTGTAATTACCGGACTGA 58.462 47.619 9.46 0.00 41.79 3.41
953 997 3.314331 CCCTGTCTCTGCCCGTGT 61.314 66.667 0.00 0.00 0.00 4.49
954 998 2.047844 CCTGTCTCTGCCCGTGTG 60.048 66.667 0.00 0.00 0.00 3.82
955 999 2.740055 CTGTCTCTGCCCGTGTGC 60.740 66.667 0.00 0.00 0.00 4.57
1004 1048 0.034059 CTCCCACAGAAGACAAGCGT 59.966 55.000 0.00 0.00 0.00 5.07
1005 1049 1.272490 CTCCCACAGAAGACAAGCGTA 59.728 52.381 0.00 0.00 0.00 4.42
1006 1050 1.899814 TCCCACAGAAGACAAGCGTAT 59.100 47.619 0.00 0.00 0.00 3.06
1007 1051 2.301870 TCCCACAGAAGACAAGCGTATT 59.698 45.455 0.00 0.00 0.00 1.89
1008 1052 3.074412 CCCACAGAAGACAAGCGTATTT 58.926 45.455 0.00 0.00 0.00 1.40
1009 1053 3.125316 CCCACAGAAGACAAGCGTATTTC 59.875 47.826 0.00 0.00 0.00 2.17
1010 1054 3.181530 CCACAGAAGACAAGCGTATTTCG 60.182 47.826 0.00 0.00 43.12 3.46
1011 1055 2.993899 ACAGAAGACAAGCGTATTTCGG 59.006 45.455 0.00 0.00 40.26 4.30
1029 1073 1.001393 GTTTCCTCGATTGCCCCCA 60.001 57.895 0.00 0.00 0.00 4.96
1146 1196 4.830765 GCAGACATGGCGCCCGTA 62.831 66.667 26.77 5.45 0.00 4.02
1381 1446 1.335132 TGGGTCGCTTACTCCATCCC 61.335 60.000 0.00 0.00 0.00 3.85
1397 1462 2.281761 CCCCGTTGTTCTGCTGCT 60.282 61.111 0.00 0.00 0.00 4.24
1415 1480 1.376543 CTCATGTGCCAGGTGATGAC 58.623 55.000 0.00 0.00 0.00 3.06
1505 1570 4.682334 TCGGTGGTGGGCGAGGTA 62.682 66.667 0.00 0.00 0.00 3.08
1559 1624 2.363683 CAGAAGCAGGTCCAGGAATTC 58.636 52.381 0.00 0.00 0.00 2.17
1567 1632 2.197465 GGTCCAGGAATTCCAGGTACT 58.803 52.381 29.38 5.86 42.71 2.73
1601 1666 0.901580 CTTGCTTTGCTCCCCATGGT 60.902 55.000 11.73 0.00 0.00 3.55
1632 1717 7.725818 ACTAGTGTTTAGCTTTACCTTCAAC 57.274 36.000 0.00 0.00 0.00 3.18
1674 1759 0.543277 TGTTCCTAGGCCAGCTGATG 59.457 55.000 17.39 0.00 0.00 3.07
1800 1886 2.721090 GCACACGCTTTAGCTTTTTGAG 59.279 45.455 0.00 0.00 39.32 3.02
1812 1898 8.635765 TTTAGCTTTTTGAGGTCACATAATCT 57.364 30.769 0.00 0.00 37.30 2.40
2080 2166 1.676678 ATCGTGACGCCTGCACCTAT 61.677 55.000 0.00 0.00 32.74 2.57
2082 2168 1.079127 GTGACGCCTGCACCTATGT 60.079 57.895 0.00 0.00 0.00 2.29
2163 2249 1.898472 AGTGCTGCATGTAGACTCACT 59.102 47.619 15.68 14.64 0.00 3.41
2287 4347 3.868757 TGGTACAAGTTCCGAGATGAG 57.131 47.619 0.00 0.00 31.92 2.90
2354 4427 9.897744 AATAATTTTATTGCCTGTATGATGTCG 57.102 29.630 0.00 0.00 32.42 4.35
2398 4471 2.618709 AGGAAACAGCTTCAAAGAACCG 59.381 45.455 0.00 0.00 35.55 4.44
2416 4489 6.056884 AGAACCGTTACAACCAGAAACAATA 58.943 36.000 0.00 0.00 0.00 1.90
2494 4601 2.826725 GGGTGACTGTAGCAGTAGAACT 59.173 50.000 1.43 0.00 45.44 3.01
2541 4648 1.601419 CTGGTGGCCTTTGCATCTGG 61.601 60.000 3.32 0.00 40.13 3.86
3030 5155 4.778427 ACGGAGGGATCTCTAAAAAGACTT 59.222 41.667 0.00 0.00 39.86 3.01
3034 5159 8.083462 CGGAGGGATCTCTAAAAAGACTTATAC 58.917 40.741 0.00 0.00 39.86 1.47
3037 5162 9.150028 AGGGATCTCTAAAAAGACTTATACTCC 57.850 37.037 0.00 0.00 0.00 3.85
3038 5163 8.369424 GGGATCTCTAAAAAGACTTATACTCCC 58.631 40.741 0.00 0.00 0.00 4.30
3039 5164 9.150028 GGATCTCTAAAAAGACTTATACTCCCT 57.850 37.037 0.00 0.00 0.00 4.20
3041 5166 8.536340 TCTCTAAAAAGACTTATACTCCCTCC 57.464 38.462 0.00 0.00 0.00 4.30
3042 5167 7.284944 TCTCTAAAAAGACTTATACTCCCTCCG 59.715 40.741 0.00 0.00 0.00 4.63
3043 5168 6.894103 TCTAAAAAGACTTATACTCCCTCCGT 59.106 38.462 0.00 0.00 0.00 4.69
3044 5169 6.370186 AAAAAGACTTATACTCCCTCCGTT 57.630 37.500 0.00 0.00 0.00 4.44
3045 5170 5.595257 AAAGACTTATACTCCCTCCGTTC 57.405 43.478 0.00 0.00 0.00 3.95
3046 5171 3.564264 AGACTTATACTCCCTCCGTTCC 58.436 50.000 0.00 0.00 0.00 3.62
3047 5172 3.053095 AGACTTATACTCCCTCCGTTCCA 60.053 47.826 0.00 0.00 0.00 3.53
3048 5173 3.703052 GACTTATACTCCCTCCGTTCCAA 59.297 47.826 0.00 0.00 0.00 3.53
3049 5174 4.098894 ACTTATACTCCCTCCGTTCCAAA 58.901 43.478 0.00 0.00 0.00 3.28
3050 5175 4.720273 ACTTATACTCCCTCCGTTCCAAAT 59.280 41.667 0.00 0.00 0.00 2.32
3051 5176 5.191124 ACTTATACTCCCTCCGTTCCAAATT 59.809 40.000 0.00 0.00 0.00 1.82
3052 5177 6.384886 ACTTATACTCCCTCCGTTCCAAATTA 59.615 38.462 0.00 0.00 0.00 1.40
3053 5178 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
3054 5179 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
3055 5180 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
3056 5181 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
3057 5182 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
3058 5183 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
3059 5184 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
3060 5185 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
3061 5186 2.091588 CCGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
3062 5187 2.091588 CGTTCCAAATTACTCGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
3063 5188 3.062042 GTTCCAAATTACTCGTCGTGGT 58.938 45.455 0.00 0.00 0.00 4.16
3064 5189 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
3065 5190 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
3066 5191 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
3067 5192 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
3068 5193 5.406175 TCCAAATTACTCGTCGTGGTTTTAG 59.594 40.000 0.00 0.00 0.00 1.85
3069 5194 5.178067 CCAAATTACTCGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 0.00 2.24
3070 5195 6.293027 CCAAATTACTCGTCGTGGTTTTAGTT 60.293 38.462 0.00 0.00 0.00 2.24
3071 5196 6.457851 AATTACTCGTCGTGGTTTTAGTTC 57.542 37.500 0.00 0.00 0.00 3.01
3072 5197 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
3073 5198 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
3074 5199 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
3075 5200 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
3076 5201 5.295045 ACTCGTCGTGGTTTTAGTTCAAATT 59.705 36.000 0.00 0.00 0.00 1.82
3077 5202 6.121613 TCGTCGTGGTTTTAGTTCAAATTT 57.878 33.333 0.00 0.00 0.00 1.82
3078 5203 5.966503 TCGTCGTGGTTTTAGTTCAAATTTG 59.033 36.000 12.15 12.15 0.00 2.32
3079 5204 5.966503 CGTCGTGGTTTTAGTTCAAATTTGA 59.033 36.000 16.91 16.91 34.92 2.69
3080 5205 6.469595 CGTCGTGGTTTTAGTTCAAATTTGAA 59.530 34.615 26.01 26.01 44.31 2.69
3093 5218 7.743520 TTCAAATTTGAACTAAAACCACGAC 57.256 32.000 26.01 0.00 41.88 4.34
3094 5219 5.966503 TCAAATTTGAACTAAAACCACGACG 59.033 36.000 18.45 0.00 33.55 5.12
3095 5220 5.738118 AATTTGAACTAAAACCACGACGA 57.262 34.783 0.00 0.00 0.00 4.20
3096 5221 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
3097 5222 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
3098 5223 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
3099 5224 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
3100 5225 5.531634 TGAACTAAAACCACGACGAGTAAT 58.468 37.500 0.00 0.00 0.00 1.89
3101 5226 5.984926 TGAACTAAAACCACGACGAGTAATT 59.015 36.000 0.00 1.08 0.00 1.40
3102 5227 6.479660 TGAACTAAAACCACGACGAGTAATTT 59.520 34.615 0.00 0.34 0.00 1.82
3103 5228 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
3104 5229 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
3105 5230 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
3106 5231 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
3107 5232 3.062042 ACCACGACGAGTAATTTGGAAC 58.938 45.455 0.00 0.00 0.00 3.62
3108 5233 2.091588 CCACGACGAGTAATTTGGAACG 59.908 50.000 0.00 0.00 0.00 3.95
3109 5234 2.091588 CACGACGAGTAATTTGGAACGG 59.908 50.000 0.00 0.00 0.00 4.44
3110 5235 2.030007 ACGACGAGTAATTTGGAACGGA 60.030 45.455 0.00 0.00 0.00 4.69
3259 5384 6.199342 GCGTTGTTAGGAATTTGCAAAGTAAA 59.801 34.615 18.19 7.61 0.00 2.01
3382 5507 3.385193 AAATGTTGCAGTTTAGGGTGC 57.615 42.857 0.00 0.00 40.29 5.01
3575 5701 0.654160 GCACGGGAAATAAGGTACGC 59.346 55.000 0.00 0.00 0.00 4.42
3594 5720 5.290493 ACGCCTTTACATGATATTCCTGA 57.710 39.130 0.00 0.00 0.00 3.86
3772 5937 6.149308 ACAAATCGTGAGCTGAATATGTGAAA 59.851 34.615 0.00 0.00 0.00 2.69
3774 5939 5.723492 TCGTGAGCTGAATATGTGAAATG 57.277 39.130 0.00 0.00 0.00 2.32
3864 6033 1.272592 TGCAGCTGGGATCCATTTTGA 60.273 47.619 17.12 0.00 30.82 2.69
3873 6042 5.256474 TGGGATCCATTTTGAAACTCTCTC 58.744 41.667 15.23 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 2.050144 GGGCACTGGATATCTTCCTGA 58.950 52.381 2.05 0.00 45.68 3.86
51 52 2.053244 CTGGGCACTGGATATCTTCCT 58.947 52.381 2.05 0.00 45.68 3.36
52 53 1.771255 ACTGGGCACTGGATATCTTCC 59.229 52.381 2.05 0.00 45.69 3.46
62 63 1.152777 TGGTTTCCACTGGGCACTG 60.153 57.895 0.00 0.00 0.00 3.66
81 82 2.014068 GCGGAGTTTTCATGGAGAGGG 61.014 57.143 0.00 0.00 0.00 4.30
99 100 9.256477 TGATGAGGTTATTACTTATAAACAGCG 57.744 33.333 0.00 0.00 38.62 5.18
157 181 9.121517 CATGAAAACTCTCAAAATCATGTGTAC 57.878 33.333 0.00 0.00 39.34 2.90
163 187 8.521176 CCTTCTCATGAAAACTCTCAAAATCAT 58.479 33.333 0.00 0.00 0.00 2.45
170 194 4.103153 ACCACCTTCTCATGAAAACTCTCA 59.897 41.667 0.00 0.00 0.00 3.27
222 246 4.530875 GGCTTATCCCAATCATCCTATGG 58.469 47.826 0.00 0.00 0.00 2.74
266 290 5.220854 CCATCTTGCGGAAAGGTATTGTTAG 60.221 44.000 0.00 0.00 36.46 2.34
281 305 2.110967 CAGAGGTGGCCATCTTGCG 61.111 63.158 22.29 7.97 0.00 4.85
282 306 0.322816 TTCAGAGGTGGCCATCTTGC 60.323 55.000 22.29 8.48 0.00 4.01
292 316 4.260375 CGTTGTCAAGAGTTTTCAGAGGTG 60.260 45.833 0.00 0.00 0.00 4.00
309 333 2.941453 TCTACTCTGATGGCGTTGTC 57.059 50.000 0.00 0.00 0.00 3.18
314 338 2.799412 GCTTTCATCTACTCTGATGGCG 59.201 50.000 4.91 0.00 42.82 5.69
326 350 5.298777 GGTGCTGAAGATATTGCTTTCATCT 59.701 40.000 0.00 0.00 0.00 2.90
328 352 4.951715 TGGTGCTGAAGATATTGCTTTCAT 59.048 37.500 0.00 0.00 0.00 2.57
331 355 5.198965 AGATGGTGCTGAAGATATTGCTTT 58.801 37.500 0.00 0.00 0.00 3.51
350 374 4.327357 CGTAAGACTACAAGGCACAAGATG 59.673 45.833 0.00 0.00 43.02 2.90
351 375 4.495422 CGTAAGACTACAAGGCACAAGAT 58.505 43.478 0.00 0.00 43.02 2.40
352 376 3.859627 GCGTAAGACTACAAGGCACAAGA 60.860 47.826 0.00 0.00 43.02 3.02
353 377 2.412089 GCGTAAGACTACAAGGCACAAG 59.588 50.000 0.00 0.00 43.02 3.16
354 378 2.224090 TGCGTAAGACTACAAGGCACAA 60.224 45.455 0.00 0.00 43.02 3.33
356 380 1.725164 GTGCGTAAGACTACAAGGCAC 59.275 52.381 11.85 11.85 36.44 5.01
357 381 1.341852 TGTGCGTAAGACTACAAGGCA 59.658 47.619 0.00 0.00 43.02 4.75
358 382 1.725164 GTGTGCGTAAGACTACAAGGC 59.275 52.381 0.00 0.00 43.02 4.35
360 384 3.021269 TGGTGTGCGTAAGACTACAAG 57.979 47.619 0.00 0.00 43.02 3.16
362 386 2.823747 AGATGGTGTGCGTAAGACTACA 59.176 45.455 0.00 0.00 43.02 2.74
363 387 3.179830 CAGATGGTGTGCGTAAGACTAC 58.820 50.000 0.00 0.00 43.02 2.73
394 427 3.055819 GGACCTGAGATGAACTAACTGCA 60.056 47.826 0.00 0.00 0.00 4.41
403 436 1.198713 GCTGGAGGACCTGAGATGAA 58.801 55.000 0.00 0.00 37.31 2.57
425 458 2.221055 CCACAGTTTGACGTCTTGTAGC 59.779 50.000 17.92 2.06 0.00 3.58
430 463 1.299541 CTGCCACAGTTTGACGTCTT 58.700 50.000 17.92 0.00 0.00 3.01
434 467 2.639286 GCCTGCCACAGTTTGACG 59.361 61.111 0.00 0.00 0.00 4.35
435 468 2.564721 GGGCCTGCCACAGTTTGAC 61.565 63.158 10.86 0.00 37.98 3.18
447 480 2.262774 GAGATGTGGGTCTGGGCCTG 62.263 65.000 4.53 4.06 0.00 4.85
453 486 3.276857 CCTGAAATGAGATGTGGGTCTG 58.723 50.000 0.00 0.00 0.00 3.51
466 499 1.094073 CCAGCTCCGAGCCTGAAATG 61.094 60.000 16.99 7.36 43.77 2.32
486 519 5.207110 ACAATGATAGGATCAGAGGAACG 57.793 43.478 0.00 0.00 43.53 3.95
510 543 9.742144 AAGACTATGACTCTAGTTCAGAACTTA 57.258 33.333 21.05 9.15 42.81 2.24
512 545 7.362574 GCAAGACTATGACTCTAGTTCAGAACT 60.363 40.741 19.81 19.81 45.40 3.01
513 546 6.750039 GCAAGACTATGACTCTAGTTCAGAAC 59.250 42.308 5.00 5.00 32.11 3.01
515 548 5.358442 GGCAAGACTATGACTCTAGTTCAGA 59.642 44.000 3.70 0.00 32.11 3.27
529 562 0.530650 CATCGTGCGGGCAAGACTAT 60.531 55.000 11.32 0.00 37.27 2.12
547 580 2.612604 CCGATTCCGTTGTACATGTCA 58.387 47.619 0.00 0.00 0.00 3.58
554 587 0.319083 ACAGTGCCGATTCCGTTGTA 59.681 50.000 0.00 0.00 0.00 2.41
560 593 4.126524 GGCTACAGTGCCGATTCC 57.873 61.111 0.00 0.00 43.74 3.01
577 610 0.743701 ATGCTCTGAAGAAGCCAGCG 60.744 55.000 0.00 0.00 30.09 5.18
593 626 5.065731 GGCAGGTGATTATATCTTGCTATGC 59.934 44.000 0.00 0.00 34.57 3.14
599 632 4.649692 AGCAGGCAGGTGATTATATCTTG 58.350 43.478 0.00 0.00 0.00 3.02
621 664 1.201429 GGGGGAGAGACAAGAGCCAA 61.201 60.000 0.00 0.00 0.00 4.52
624 667 0.539518 GAAGGGGGAGAGACAAGAGC 59.460 60.000 0.00 0.00 0.00 4.09
649 692 1.531149 CTGTTTGACGAAATGACGGCT 59.469 47.619 0.00 0.00 42.29 5.52
654 697 2.548057 GACCAGCTGTTTGACGAAATGA 59.452 45.455 13.81 0.00 0.00 2.57
688 731 1.821061 AAGAGGCGTCAGGTGGTCAG 61.821 60.000 9.41 0.00 0.00 3.51
694 737 3.382832 CGGGAAGAGGCGTCAGGT 61.383 66.667 9.41 0.00 0.00 4.00
704 747 2.231478 CTCTGAAGTAGCAACGGGAAGA 59.769 50.000 0.00 0.00 0.00 2.87
711 754 4.233789 CTCTGTCACTCTGAAGTAGCAAC 58.766 47.826 0.00 0.00 33.25 4.17
721 764 1.445754 CTGCGGCTCTGTCACTCTG 60.446 63.158 0.00 0.00 0.00 3.35
722 765 2.969016 CTGCGGCTCTGTCACTCT 59.031 61.111 0.00 0.00 0.00 3.24
723 766 2.813042 GCTGCGGCTCTGTCACTC 60.813 66.667 11.21 0.00 35.22 3.51
724 767 4.385405 GGCTGCGGCTCTGTCACT 62.385 66.667 18.85 0.00 38.73 3.41
801 845 3.873883 GCATGGTCAGCTCGCTGC 61.874 66.667 13.83 8.99 43.31 5.25
847 891 3.260483 CTCGCGCATGGTCAGCTC 61.260 66.667 8.75 0.00 0.00 4.09
875 919 2.795110 TTGCCACTTGCCACTTGCC 61.795 57.895 0.00 0.00 40.16 4.52
876 920 1.592400 GTTGCCACTTGCCACTTGC 60.592 57.895 0.00 0.00 40.16 4.01
877 921 1.299316 CGTTGCCACTTGCCACTTG 60.299 57.895 0.00 0.00 40.16 3.16
878 922 2.489275 CCGTTGCCACTTGCCACTT 61.489 57.895 0.00 0.00 40.16 3.16
879 923 2.906897 CCGTTGCCACTTGCCACT 60.907 61.111 0.00 0.00 40.16 4.00
880 924 4.645921 GCCGTTGCCACTTGCCAC 62.646 66.667 0.00 0.00 40.16 5.01
881 925 4.892965 AGCCGTTGCCACTTGCCA 62.893 61.111 0.00 0.00 40.16 4.92
882 926 3.605664 AAGCCGTTGCCACTTGCC 61.606 61.111 0.00 0.00 40.16 4.52
883 927 2.355009 CAAGCCGTTGCCACTTGC 60.355 61.111 0.00 0.00 38.69 4.01
884 928 1.283793 CTCAAGCCGTTGCCACTTG 59.716 57.895 0.00 0.00 41.70 3.16
899 943 2.621055 CACCCAAAACAAATCGTCCTCA 59.379 45.455 0.00 0.00 0.00 3.86
902 946 4.571372 TTACACCCAAAACAAATCGTCC 57.429 40.909 0.00 0.00 0.00 4.79
935 979 3.314331 CACGGGCAGAGACAGGGT 61.314 66.667 0.00 0.00 0.00 4.34
953 997 4.323477 GGCTGGTGTACCACGGCA 62.323 66.667 16.55 0.00 42.01 5.69
954 998 3.835790 TTGGCTGGTGTACCACGGC 62.836 63.158 15.21 15.21 42.01 5.68
955 999 1.671054 CTTGGCTGGTGTACCACGG 60.671 63.158 0.00 0.00 42.01 4.94
993 1037 4.392216 GAAACCGAAATACGCTTGTCTTC 58.608 43.478 0.00 0.00 41.07 2.87
1004 1048 2.940410 GGCAATCGAGGAAACCGAAATA 59.060 45.455 0.00 0.00 39.62 1.40
1005 1049 1.743394 GGCAATCGAGGAAACCGAAAT 59.257 47.619 0.00 0.00 39.62 2.17
1006 1050 1.161843 GGCAATCGAGGAAACCGAAA 58.838 50.000 0.00 0.00 39.62 3.46
1007 1051 0.675522 GGGCAATCGAGGAAACCGAA 60.676 55.000 0.00 0.00 39.62 4.30
1008 1052 1.078708 GGGCAATCGAGGAAACCGA 60.079 57.895 0.00 0.00 40.53 4.69
1009 1053 2.112815 GGGGCAATCGAGGAAACCG 61.113 63.158 0.00 0.00 0.00 4.44
1010 1054 1.753078 GGGGGCAATCGAGGAAACC 60.753 63.158 0.00 0.00 0.00 3.27
1011 1055 0.610785 TTGGGGGCAATCGAGGAAAC 60.611 55.000 0.00 0.00 0.00 2.78
1012 1056 0.334676 ATTGGGGGCAATCGAGGAAA 59.665 50.000 0.00 0.00 0.00 3.13
1013 1057 0.106719 GATTGGGGGCAATCGAGGAA 60.107 55.000 0.00 0.00 32.74 3.36
1014 1058 1.531748 GATTGGGGGCAATCGAGGA 59.468 57.895 0.00 0.00 32.74 3.71
1015 1059 1.529244 GGATTGGGGGCAATCGAGG 60.529 63.158 0.00 0.00 41.23 4.63
1016 1060 1.893808 CGGATTGGGGGCAATCGAG 60.894 63.158 0.00 0.00 41.23 4.04
1232 1294 0.389025 AAACCTGCGAAGGCTTTTGG 59.611 50.000 10.27 4.32 40.82 3.28
1235 1297 1.363807 GCAAACCTGCGAAGGCTTT 59.636 52.632 10.27 6.77 39.20 3.51
1381 1446 0.957395 ATGAGCAGCAGAACAACGGG 60.957 55.000 0.00 0.00 0.00 5.28
1397 1462 0.391528 CGTCATCACCTGGCACATGA 60.392 55.000 0.00 0.00 38.20 3.07
1415 1480 3.764466 AGGACGGCCTTGCTCTCG 61.764 66.667 2.12 0.00 43.90 4.04
1505 1570 3.989698 CTGCCCGACGACGCTGAAT 62.990 63.158 0.64 0.00 38.29 2.57
1559 1624 2.434884 CGGCTGTGCAGTACCTGG 60.435 66.667 0.00 0.00 31.21 4.45
1632 1717 2.066340 TGGTTGTCCAGTAGCCAGG 58.934 57.895 0.00 0.00 39.03 4.45
1800 1886 5.880332 TGGAAAGCAGTTAGATTATGTGACC 59.120 40.000 0.00 0.00 0.00 4.02
1812 1898 8.750515 TGATGATTAATCATGGAAAGCAGTTA 57.249 30.769 30.86 2.69 46.84 2.24
1915 2001 4.754372 TGCAATTTAGAAGTGAGTGCAG 57.246 40.909 0.00 0.00 35.72 4.41
2080 2166 6.078664 GGAATATTAGGAGAAGGAGGAGACA 58.921 44.000 0.00 0.00 0.00 3.41
2082 2168 5.137949 TGGGAATATTAGGAGAAGGAGGAGA 59.862 44.000 0.00 0.00 0.00 3.71
2163 2249 4.644234 TCATCACTTTCTTGGAGCACAAAA 59.356 37.500 0.00 0.00 38.91 2.44
2541 4648 6.861065 TGACAGAATAAAGACACCAAGAAC 57.139 37.500 0.00 0.00 0.00 3.01
2743 4850 4.682787 TGAAGACCTGCATTCTATGTACG 58.317 43.478 0.00 0.00 0.00 3.67
2744 4851 5.525378 CCTTGAAGACCTGCATTCTATGTAC 59.475 44.000 0.00 0.00 0.00 2.90
2745 4852 5.396772 CCCTTGAAGACCTGCATTCTATGTA 60.397 44.000 0.00 0.00 0.00 2.29
2746 4853 4.521146 CCTTGAAGACCTGCATTCTATGT 58.479 43.478 0.00 0.00 0.00 2.29
2790 4900 0.107897 ACGCCCAACATAATCTGCGA 60.108 50.000 8.79 0.00 44.32 5.10
3003 5128 5.897824 TCTTTTTAGAGATCCCTCCGTATGT 59.102 40.000 0.00 0.00 40.30 2.29
3030 5155 5.901276 AGTAATTTGGAACGGAGGGAGTATA 59.099 40.000 0.00 0.00 0.00 1.47
3034 5159 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
3036 5161 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
3037 5162 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
3038 5163 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
3039 5164 2.030007 ACGACGAGTAATTTGGAACGGA 60.030 45.455 0.00 0.00 0.00 4.69
3040 5165 2.091588 CACGACGAGTAATTTGGAACGG 59.908 50.000 0.00 0.00 0.00 4.44
3041 5166 2.091588 CCACGACGAGTAATTTGGAACG 59.908 50.000 0.00 0.00 0.00 3.95
3042 5167 3.062042 ACCACGACGAGTAATTTGGAAC 58.938 45.455 0.00 0.00 0.00 3.62
3043 5168 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
3044 5169 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
3045 5170 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
3046 5171 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
3047 5172 6.479660 TGAACTAAAACCACGACGAGTAATTT 59.520 34.615 0.00 0.34 0.00 1.82
3048 5173 5.984926 TGAACTAAAACCACGACGAGTAATT 59.015 36.000 0.00 1.08 0.00 1.40
3049 5174 5.531634 TGAACTAAAACCACGACGAGTAAT 58.468 37.500 0.00 0.00 0.00 1.89
3050 5175 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
3051 5176 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
3052 5177 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
3053 5178 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
3054 5179 5.738118 AATTTGAACTAAAACCACGACGA 57.262 34.783 0.00 0.00 0.00 4.20
3055 5180 5.966503 TCAAATTTGAACTAAAACCACGACG 59.033 36.000 18.45 0.00 33.55 5.12
3056 5181 7.743520 TTCAAATTTGAACTAAAACCACGAC 57.256 32.000 26.01 0.00 41.88 4.34
3069 5194 6.469595 CGTCGTGGTTTTAGTTCAAATTTGAA 59.530 34.615 26.01 26.01 44.31 2.69
3070 5195 5.966503 CGTCGTGGTTTTAGTTCAAATTTGA 59.033 36.000 16.91 16.91 34.92 2.69
3071 5196 5.966503 TCGTCGTGGTTTTAGTTCAAATTTG 59.033 36.000 12.15 12.15 0.00 2.32
3072 5197 6.121613 TCGTCGTGGTTTTAGTTCAAATTT 57.878 33.333 0.00 0.00 0.00 1.82
3073 5198 5.295045 ACTCGTCGTGGTTTTAGTTCAAATT 59.705 36.000 0.00 0.00 0.00 1.82
3074 5199 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
3075 5200 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
3076 5201 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
3077 5202 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
3078 5203 6.457851 AATTACTCGTCGTGGTTTTAGTTC 57.542 37.500 0.00 0.00 0.00 3.01
3079 5204 6.293027 CCAAATTACTCGTCGTGGTTTTAGTT 60.293 38.462 0.00 0.00 0.00 2.24
3080 5205 5.178067 CCAAATTACTCGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 0.00 2.24
3081 5206 5.406175 TCCAAATTACTCGTCGTGGTTTTAG 59.594 40.000 0.00 0.00 0.00 1.85
3082 5207 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
3083 5208 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
3084 5209 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
3085 5210 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
3086 5211 3.062042 GTTCCAAATTACTCGTCGTGGT 58.938 45.455 0.00 0.00 0.00 4.16
3087 5212 2.091588 CGTTCCAAATTACTCGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
3088 5213 2.091588 CCGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
3089 5214 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
3090 5215 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
3091 5216 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
3092 5217 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
3093 5218 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
3094 5219 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
3095 5220 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
3096 5221 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
3097 5222 3.839490 TGTACTCCCTCCGTTCCAAATTA 59.161 43.478 0.00 0.00 0.00 1.40
3098 5223 2.640826 TGTACTCCCTCCGTTCCAAATT 59.359 45.455 0.00 0.00 0.00 1.82
3099 5224 2.262637 TGTACTCCCTCCGTTCCAAAT 58.737 47.619 0.00 0.00 0.00 2.32
3100 5225 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
3101 5226 1.946984 ATGTACTCCCTCCGTTCCAA 58.053 50.000 0.00 0.00 0.00 3.53
3102 5227 1.553248 CAATGTACTCCCTCCGTTCCA 59.447 52.381 0.00 0.00 0.00 3.53
3103 5228 1.742750 GCAATGTACTCCCTCCGTTCC 60.743 57.143 0.00 0.00 0.00 3.62
3104 5229 1.066430 TGCAATGTACTCCCTCCGTTC 60.066 52.381 0.00 0.00 0.00 3.95
3105 5230 0.981183 TGCAATGTACTCCCTCCGTT 59.019 50.000 0.00 0.00 0.00 4.44
3106 5231 1.204146 ATGCAATGTACTCCCTCCGT 58.796 50.000 0.00 0.00 0.00 4.69
3107 5232 2.548067 GGTATGCAATGTACTCCCTCCG 60.548 54.545 0.00 0.00 0.00 4.63
3108 5233 2.706190 AGGTATGCAATGTACTCCCTCC 59.294 50.000 0.00 0.00 0.00 4.30
3109 5234 3.733337 CAGGTATGCAATGTACTCCCTC 58.267 50.000 0.00 0.00 0.00 4.30
3110 5235 3.845781 CAGGTATGCAATGTACTCCCT 57.154 47.619 0.00 0.00 0.00 4.20
3382 5507 8.723942 AGTATCTAACAGAGTTTGGCATAAAG 57.276 34.615 0.00 0.00 0.00 1.85
3575 5701 9.730705 ATATGTGTCAGGAATATCATGTAAAGG 57.269 33.333 0.00 0.00 29.15 3.11
3594 5720 4.502105 TGCTTGTACCATCCATATGTGT 57.498 40.909 1.24 0.00 0.00 3.72
3634 5799 1.002033 GCCAGTTCACAGTTGCTCAAG 60.002 52.381 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.