Multiple sequence alignment - TraesCS6A01G106100

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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 TraesCS6A01G106100 chr6A 100.000 2624 0 0 1 2624 74138087 74140710 0.000000e+00 4846
1 TraesCS6A01G106100 chr4D 94.887 1017 48 3 1611 2624 106322044 106321029 0.000000e+00 1587
2 TraesCS6A01G106100 chr4D 94.887 1017 47 4 1611 2624 380012885 380011871 0.000000e+00 1585
3 TraesCS6A01G106100 chr5D 94.882 1016 49 3 1611 2624 133383209 133384223 0.000000e+00 1585
4 TraesCS6A01G106100 chr5D 94.286 1015 54 4 1611 2624 212415898 212416909 0.000000e+00 1550
5 TraesCS6A01G106100 chr1D 94.882 1016 49 3 1611 2624 291125763 291126777 0.000000e+00 1585
6 TraesCS6A01G106100 chr2D 94.494 1017 52 4 1611 2624 436459774 436458759 0.000000e+00 1565
7 TraesCS6A01G106100 chr2D 94.106 1018 54 6 1611 2624 429878653 429877638 0.000000e+00 1543
8 TraesCS6A01G106100 chr2D 94.094 1016 57 3 1611 2624 256946012 256944998 0.000000e+00 1541
9 TraesCS6A01G106100 chr6D 94.395 1017 53 3 1611 2624 417443723 417444738 0.000000e+00 1559
10 TraesCS6A01G106100 chr6D 92.252 413 31 1 1194 1605 460216917 460217329 3.760000e-163 584
11 TraesCS6A01G106100 chr6D 89.778 225 18 2 1043 1262 460215790 460216014 1.540000e-72 283
12 TraesCS6A01G106100 chr1B 92.691 903 51 8 1 888 93946133 93947035 0.000000e+00 1288
13 TraesCS6A01G106100 chr7D 97.594 748 16 2 143 888 101553066 101552319 0.000000e+00 1280
14 TraesCS6A01G106100 chr7D 96.262 107 3 1 1 106 101553172 101553066 9.650000e-40 174
15 TraesCS6A01G106100 chr6B 93.491 507 32 1 1 506 678296532 678296026 0.000000e+00 752
16 TraesCS6A01G106100 chr6B 95.641 390 15 1 501 888 678293573 678293184 2.220000e-175 625
17 TraesCS6A01G106100 chr6B 91.579 95 8 0 884 978 707846772 707846866 5.890000e-27 132
18 TraesCS6A01G106100 chr4B 85.577 520 67 5 193 706 169932580 169933097 2.970000e-149 538
19 TraesCS6A01G106100 chr1A 84.158 505 67 9 211 706 590827171 590827671 6.570000e-131 477
20 TraesCS6A01G106100 chr3A 87.097 279 32 3 193 471 22136935 22137209 1.960000e-81 313
21 TraesCS6A01G106100 chr3A 85.417 192 28 0 884 1075 446666280 446666089 1.590000e-47 200
22 TraesCS6A01G106100 chr3A 82.902 193 33 0 1413 1605 29104031 29104223 9.650000e-40 174
23 TraesCS6A01G106100 chr3A 90.526 95 9 0 884 978 34253641 34253547 2.740000e-25 126
24 TraesCS6A01G106100 chr4A 87.500 192 24 0 885 1076 639244305 639244496 3.400000e-54 222
25 TraesCS6A01G106100 chr7A 85.492 193 28 0 884 1076 639657710 639657518 4.430000e-48 202


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 TraesCS6A01G106100 chr6A 74138087 74140710 2623 False 4846.0 4846 100.000 1 2624 1 chr6A.!!$F1 2623
1 TraesCS6A01G106100 chr4D 106321029 106322044 1015 True 1587.0 1587 94.887 1611 2624 1 chr4D.!!$R1 1013
2 TraesCS6A01G106100 chr4D 380011871 380012885 1014 True 1585.0 1585 94.887 1611 2624 1 chr4D.!!$R2 1013
3 TraesCS6A01G106100 chr5D 133383209 133384223 1014 False 1585.0 1585 94.882 1611 2624 1 chr5D.!!$F1 1013
4 TraesCS6A01G106100 chr5D 212415898 212416909 1011 False 1550.0 1550 94.286 1611 2624 1 chr5D.!!$F2 1013
5 TraesCS6A01G106100 chr1D 291125763 291126777 1014 False 1585.0 1585 94.882 1611 2624 1 chr1D.!!$F1 1013
6 TraesCS6A01G106100 chr2D 436458759 436459774 1015 True 1565.0 1565 94.494 1611 2624 1 chr2D.!!$R3 1013
7 TraesCS6A01G106100 chr2D 429877638 429878653 1015 True 1543.0 1543 94.106 1611 2624 1 chr2D.!!$R2 1013
8 TraesCS6A01G106100 chr2D 256944998 256946012 1014 True 1541.0 1541 94.094 1611 2624 1 chr2D.!!$R1 1013
9 TraesCS6A01G106100 chr6D 417443723 417444738 1015 False 1559.0 1559 94.395 1611 2624 1 chr6D.!!$F1 1013
10 TraesCS6A01G106100 chr6D 460215790 460217329 1539 False 433.5 584 91.015 1043 1605 2 chr6D.!!$F2 562
11 TraesCS6A01G106100 chr1B 93946133 93947035 902 False 1288.0 1288 92.691 1 888 1 chr1B.!!$F1 887
12 TraesCS6A01G106100 chr7D 101552319 101553172 853 True 727.0 1280 96.928 1 888 2 chr7D.!!$R1 887
13 TraesCS6A01G106100 chr6B 678293184 678296532 3348 True 688.5 752 94.566 1 888 2 chr6B.!!$R1 887
14 TraesCS6A01G106100 chr4B 169932580 169933097 517 False 538.0 538 85.577 193 706 1 chr4B.!!$F1 513
15 TraesCS6A01G106100 chr1A 590827171 590827671 500 False 477.0 477 84.158 211 706 1 chr1A.!!$F1 495

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
920 3405 0.031721 GCTACGGGCGTAAGTGCTAT 59.968 55.0 0.0 0.0 41.68 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2476 5944 1.006043 AGGAGATCGAGTCTTGTGGGA 59.994 52.381 0.0 0.0 37.29 4.37 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
108 111 0.912006 GACCTCCTTGCCTCCTCCTT 60.912 60.000 0.00 0.00 0.00 3.36
127 130 1.379576 GCCCCAGATCAAGCAGCTT 60.380 57.895 0.21 0.21 0.00 3.74
138 141 1.841302 AAGCAGCTTGTCCGGATCCA 61.841 55.000 7.81 0.00 0.00 3.41
149 152 1.895707 CGGATCCAATGCAGGCTCC 60.896 63.158 13.41 5.06 39.95 4.70
233 238 1.561643 TCGCACATTCTTCCTCCTCT 58.438 50.000 0.00 0.00 0.00 3.69
284 289 1.775877 CCATGGGATAGCCAGGGGT 60.776 63.158 2.85 0.00 35.74 4.95
401 416 1.293763 TCAGATGTGGATGGGGTAGGA 59.706 52.381 0.00 0.00 0.00 2.94
626 3107 3.207265 TGTGTGTGCTGGTCATTTAGT 57.793 42.857 0.00 0.00 0.00 2.24
770 3254 4.956700 TCCTATGTTCCTCTTGTCGATTCT 59.043 41.667 0.00 0.00 0.00 2.40
825 3309 7.819900 TGCTTACTCTATTCTCTCTGGTTTTTC 59.180 37.037 0.00 0.00 0.00 2.29
826 3310 7.819900 GCTTACTCTATTCTCTCTGGTTTTTCA 59.180 37.037 0.00 0.00 0.00 2.69
827 3311 9.145865 CTTACTCTATTCTCTCTGGTTTTTCAC 57.854 37.037 0.00 0.00 0.00 3.18
863 3348 2.668632 CCTATGCGTGGTGGTGGT 59.331 61.111 0.00 0.00 0.00 4.16
872 3357 1.066502 CGTGGTGGTGGTGTATGATCA 60.067 52.381 0.00 0.00 0.00 2.92
888 3373 3.365472 TGATCAGATCAAGGTCTCCGAA 58.635 45.455 10.93 0.00 36.11 4.30
889 3374 3.769300 TGATCAGATCAAGGTCTCCGAAA 59.231 43.478 10.93 0.00 36.11 3.46
890 3375 3.594603 TCAGATCAAGGTCTCCGAAAC 57.405 47.619 0.00 0.00 0.00 2.78
891 3376 3.165875 TCAGATCAAGGTCTCCGAAACT 58.834 45.455 0.00 0.00 0.00 2.66
892 3377 3.578716 TCAGATCAAGGTCTCCGAAACTT 59.421 43.478 0.00 0.00 0.00 2.66
893 3378 4.770531 TCAGATCAAGGTCTCCGAAACTTA 59.229 41.667 0.00 0.00 0.00 2.24
894 3379 4.865365 CAGATCAAGGTCTCCGAAACTTAC 59.135 45.833 0.00 0.00 0.00 2.34
895 3380 3.293311 TCAAGGTCTCCGAAACTTACG 57.707 47.619 0.00 0.00 0.00 3.18
896 3381 2.886523 TCAAGGTCTCCGAAACTTACGA 59.113 45.455 0.00 0.00 0.00 3.43
897 3382 2.985139 CAAGGTCTCCGAAACTTACGAC 59.015 50.000 0.00 0.00 0.00 4.34
898 3383 2.233271 AGGTCTCCGAAACTTACGACA 58.767 47.619 0.00 0.00 0.00 4.35
899 3384 2.624838 AGGTCTCCGAAACTTACGACAA 59.375 45.455 0.00 0.00 0.00 3.18
900 3385 3.257624 AGGTCTCCGAAACTTACGACAAT 59.742 43.478 0.00 0.00 0.00 2.71
901 3386 3.367025 GGTCTCCGAAACTTACGACAATG 59.633 47.826 0.00 0.00 0.00 2.82
902 3387 2.991190 TCTCCGAAACTTACGACAATGC 59.009 45.455 0.00 0.00 0.00 3.56
903 3388 2.993899 CTCCGAAACTTACGACAATGCT 59.006 45.455 0.00 0.00 0.00 3.79
904 3389 4.082625 TCTCCGAAACTTACGACAATGCTA 60.083 41.667 0.00 0.00 0.00 3.49
905 3390 3.922240 TCCGAAACTTACGACAATGCTAC 59.078 43.478 0.00 0.00 0.00 3.58
906 3391 3.241552 CCGAAACTTACGACAATGCTACG 60.242 47.826 0.00 0.00 0.00 3.51
907 3392 3.241552 CGAAACTTACGACAATGCTACGG 60.242 47.826 0.00 0.00 0.00 4.02
908 3393 2.288961 ACTTACGACAATGCTACGGG 57.711 50.000 0.00 0.00 0.00 5.28
909 3394 0.928229 CTTACGACAATGCTACGGGC 59.072 55.000 0.00 0.00 42.22 6.13
910 3395 0.802994 TTACGACAATGCTACGGGCG 60.803 55.000 0.00 0.00 45.43 6.13
911 3396 1.936436 TACGACAATGCTACGGGCGT 61.936 55.000 0.00 0.00 45.43 5.68
912 3397 1.226745 CGACAATGCTACGGGCGTA 60.227 57.895 0.00 0.00 45.43 4.42
913 3398 0.802994 CGACAATGCTACGGGCGTAA 60.803 55.000 0.00 0.00 45.43 3.18
914 3399 0.928229 GACAATGCTACGGGCGTAAG 59.072 55.000 0.00 0.00 45.43 2.34
915 3400 0.248289 ACAATGCTACGGGCGTAAGT 59.752 50.000 0.00 0.00 45.43 2.24
916 3401 0.650512 CAATGCTACGGGCGTAAGTG 59.349 55.000 0.00 0.00 45.43 3.16
917 3402 1.087771 AATGCTACGGGCGTAAGTGC 61.088 55.000 0.00 0.00 45.43 4.40
918 3403 1.956629 ATGCTACGGGCGTAAGTGCT 61.957 55.000 0.00 0.00 45.43 4.40
919 3404 1.314534 TGCTACGGGCGTAAGTGCTA 61.315 55.000 0.00 0.00 45.43 3.49
920 3405 0.031721 GCTACGGGCGTAAGTGCTAT 59.968 55.000 0.00 0.00 41.68 2.97
921 3406 1.929482 GCTACGGGCGTAAGTGCTATC 60.929 57.143 0.00 0.00 41.68 2.08
922 3407 1.607628 CTACGGGCGTAAGTGCTATCT 59.392 52.381 0.00 0.00 41.68 1.98
923 3408 0.822164 ACGGGCGTAAGTGCTATCTT 59.178 50.000 0.00 0.00 41.68 2.40
924 3409 1.206371 ACGGGCGTAAGTGCTATCTTT 59.794 47.619 0.00 0.00 41.68 2.52
925 3410 1.593006 CGGGCGTAAGTGCTATCTTTG 59.407 52.381 0.00 0.00 41.68 2.77
926 3411 1.330829 GGGCGTAAGTGCTATCTTTGC 59.669 52.381 0.00 0.00 41.68 3.68
927 3412 2.280628 GGCGTAAGTGCTATCTTTGCT 58.719 47.619 0.00 0.00 41.68 3.91
928 3413 2.030946 GGCGTAAGTGCTATCTTTGCTG 59.969 50.000 0.00 0.00 41.68 4.41
929 3414 2.030946 GCGTAAGTGCTATCTTTGCTGG 59.969 50.000 0.00 0.00 41.68 4.85
930 3415 3.521560 CGTAAGTGCTATCTTTGCTGGA 58.478 45.455 0.00 0.00 0.00 3.86
931 3416 3.553511 CGTAAGTGCTATCTTTGCTGGAG 59.446 47.826 0.00 0.00 0.00 3.86
932 3417 2.035530 AGTGCTATCTTTGCTGGAGC 57.964 50.000 0.00 0.00 42.50 4.70
933 3418 0.654683 GTGCTATCTTTGCTGGAGCG 59.345 55.000 0.00 0.00 45.83 5.03
934 3419 0.536724 TGCTATCTTTGCTGGAGCGA 59.463 50.000 0.00 0.00 45.83 4.93
935 3420 1.066215 TGCTATCTTTGCTGGAGCGAA 60.066 47.619 1.36 1.36 45.83 4.70
936 3421 2.009774 GCTATCTTTGCTGGAGCGAAA 58.990 47.619 2.96 0.73 43.25 3.46
937 3422 2.031437 GCTATCTTTGCTGGAGCGAAAG 59.969 50.000 13.17 13.17 43.25 2.62
938 3423 2.479566 ATCTTTGCTGGAGCGAAAGA 57.520 45.000 19.42 19.42 43.25 2.52
939 3424 2.254546 TCTTTGCTGGAGCGAAAGAA 57.745 45.000 16.89 7.24 43.25 2.52
940 3425 2.146342 TCTTTGCTGGAGCGAAAGAAG 58.854 47.619 16.89 7.50 43.25 2.85
941 3426 0.593128 TTTGCTGGAGCGAAAGAAGC 59.407 50.000 0.00 0.00 45.83 3.86
942 3427 1.568612 TTGCTGGAGCGAAAGAAGCG 61.569 55.000 0.00 0.00 45.83 4.68
943 3428 1.738099 GCTGGAGCGAAAGAAGCGA 60.738 57.895 0.00 0.00 40.04 4.93
944 3429 1.086634 GCTGGAGCGAAAGAAGCGAT 61.087 55.000 0.00 0.00 40.04 4.58
945 3430 1.802880 GCTGGAGCGAAAGAAGCGATA 60.803 52.381 0.00 0.00 40.04 2.92
946 3431 2.123342 CTGGAGCGAAAGAAGCGATAG 58.877 52.381 0.00 0.00 40.04 2.08
958 3443 3.786101 CGATAGCTGCGTGTGCTT 58.214 55.556 0.00 0.00 43.34 3.91
959 3444 1.346197 CGATAGCTGCGTGTGCTTG 59.654 57.895 0.00 0.00 43.34 4.01
960 3445 1.078201 CGATAGCTGCGTGTGCTTGA 61.078 55.000 0.00 0.00 43.34 3.02
961 3446 0.371645 GATAGCTGCGTGTGCTTGAC 59.628 55.000 0.00 0.00 43.34 3.18
962 3447 1.021390 ATAGCTGCGTGTGCTTGACC 61.021 55.000 0.00 0.00 43.34 4.02
963 3448 2.376228 TAGCTGCGTGTGCTTGACCA 62.376 55.000 0.00 0.00 43.34 4.02
964 3449 2.620112 GCTGCGTGTGCTTGACCAT 61.620 57.895 0.00 0.00 43.34 3.55
965 3450 1.208358 CTGCGTGTGCTTGACCATG 59.792 57.895 0.00 0.00 43.34 3.66
966 3451 2.191354 CTGCGTGTGCTTGACCATGG 62.191 60.000 11.19 11.19 43.34 3.66
967 3452 1.965930 GCGTGTGCTTGACCATGGA 60.966 57.895 21.47 0.00 38.39 3.41
968 3453 1.915614 GCGTGTGCTTGACCATGGAG 61.916 60.000 21.47 6.66 38.39 3.86
969 3454 0.320683 CGTGTGCTTGACCATGGAGA 60.321 55.000 21.47 0.13 0.00 3.71
970 3455 1.877680 CGTGTGCTTGACCATGGAGAA 60.878 52.381 21.47 9.36 0.00 2.87
971 3456 1.808945 GTGTGCTTGACCATGGAGAAG 59.191 52.381 21.47 19.25 0.00 2.85
972 3457 0.807496 GTGCTTGACCATGGAGAAGC 59.193 55.000 30.02 30.02 41.03 3.86
973 3458 0.401356 TGCTTGACCATGGAGAAGCA 59.599 50.000 33.00 33.00 46.49 3.91
974 3459 1.093159 GCTTGACCATGGAGAAGCAG 58.907 55.000 30.93 16.02 40.47 4.24
975 3460 1.612726 GCTTGACCATGGAGAAGCAGT 60.613 52.381 30.93 7.18 40.47 4.40
976 3461 2.354259 CTTGACCATGGAGAAGCAGTC 58.646 52.381 21.47 2.93 0.00 3.51
977 3462 1.649321 TGACCATGGAGAAGCAGTCT 58.351 50.000 21.47 0.00 40.25 3.24
986 3471 2.540265 AGAAGCAGTCTCTGTGTTGG 57.460 50.000 0.00 0.00 33.43 3.77
987 3472 1.765314 AGAAGCAGTCTCTGTGTTGGT 59.235 47.619 0.00 0.00 33.43 3.67
988 3473 2.139118 GAAGCAGTCTCTGTGTTGGTC 58.861 52.381 0.00 0.00 33.43 4.02
989 3474 1.123077 AGCAGTCTCTGTGTTGGTCA 58.877 50.000 0.00 0.00 33.43 4.02
990 3475 1.486310 AGCAGTCTCTGTGTTGGTCAA 59.514 47.619 0.00 0.00 33.43 3.18
991 3476 1.599542 GCAGTCTCTGTGTTGGTCAAC 59.400 52.381 6.87 6.87 35.57 3.18
992 3477 2.743183 GCAGTCTCTGTGTTGGTCAACT 60.743 50.000 13.96 0.00 35.81 3.16
993 3478 2.868583 CAGTCTCTGTGTTGGTCAACTG 59.131 50.000 13.96 5.82 41.67 3.16
994 3479 2.158900 AGTCTCTGTGTTGGTCAACTGG 60.159 50.000 13.96 5.52 41.67 4.00
995 3480 2.115427 TCTCTGTGTTGGTCAACTGGA 58.885 47.619 13.96 8.73 41.67 3.86
996 3481 2.103094 TCTCTGTGTTGGTCAACTGGAG 59.897 50.000 13.96 15.53 41.67 3.86
997 3482 2.103094 CTCTGTGTTGGTCAACTGGAGA 59.897 50.000 13.96 10.81 41.67 3.71
998 3483 2.503765 TCTGTGTTGGTCAACTGGAGAA 59.496 45.455 13.96 0.00 41.67 2.87
999 3484 2.874701 CTGTGTTGGTCAACTGGAGAAG 59.125 50.000 13.96 1.33 41.67 2.85
1000 3485 2.503765 TGTGTTGGTCAACTGGAGAAGA 59.496 45.455 13.96 0.00 41.67 2.87
1001 3486 3.136443 TGTGTTGGTCAACTGGAGAAGAT 59.864 43.478 13.96 0.00 41.67 2.40
1002 3487 3.499918 GTGTTGGTCAACTGGAGAAGATG 59.500 47.826 13.96 0.00 41.67 2.90
1003 3488 2.479566 TGGTCAACTGGAGAAGATGC 57.520 50.000 0.00 0.00 0.00 3.91
1004 3489 1.003580 TGGTCAACTGGAGAAGATGCC 59.996 52.381 0.00 0.00 0.00 4.40
1005 3490 1.680249 GGTCAACTGGAGAAGATGCCC 60.680 57.143 0.00 0.00 0.00 5.36
1006 3491 0.250234 TCAACTGGAGAAGATGCCCG 59.750 55.000 0.00 0.00 0.00 6.13
1007 3492 0.036010 CAACTGGAGAAGATGCCCGT 60.036 55.000 0.00 0.00 0.00 5.28
1008 3493 1.207089 CAACTGGAGAAGATGCCCGTA 59.793 52.381 0.00 0.00 0.00 4.02
1009 3494 1.115467 ACTGGAGAAGATGCCCGTAG 58.885 55.000 0.00 0.00 0.00 3.51
1022 3507 4.570663 CGTAGGCGGCCCGAAGAG 62.571 72.222 17.02 0.00 35.76 2.85
1023 3508 4.893601 GTAGGCGGCCCGAAGAGC 62.894 72.222 17.02 0.00 35.76 4.09
1027 3512 4.280494 GCGGCCCGAAGAGCGATA 62.280 66.667 7.68 0.00 44.57 2.92
1028 3513 2.651361 CGGCCCGAAGAGCGATAT 59.349 61.111 0.00 0.00 44.57 1.63
1029 3514 1.880894 CGGCCCGAAGAGCGATATA 59.119 57.895 0.00 0.00 44.57 0.86
1030 3515 0.242825 CGGCCCGAAGAGCGATATAA 59.757 55.000 0.00 0.00 44.57 0.98
1031 3516 1.336517 CGGCCCGAAGAGCGATATAAA 60.337 52.381 0.00 0.00 44.57 1.40
1032 3517 2.762745 GGCCCGAAGAGCGATATAAAA 58.237 47.619 0.00 0.00 44.57 1.52
1033 3518 2.737252 GGCCCGAAGAGCGATATAAAAG 59.263 50.000 0.00 0.00 44.57 2.27
1034 3519 3.391049 GCCCGAAGAGCGATATAAAAGT 58.609 45.455 0.00 0.00 44.57 2.66
1035 3520 3.808174 GCCCGAAGAGCGATATAAAAGTT 59.192 43.478 0.00 0.00 44.57 2.66
1036 3521 4.272748 GCCCGAAGAGCGATATAAAAGTTT 59.727 41.667 0.00 0.00 44.57 2.66
1037 3522 5.558463 GCCCGAAGAGCGATATAAAAGTTTC 60.558 44.000 0.00 0.00 44.57 2.78
1038 3523 5.332355 CCCGAAGAGCGATATAAAAGTTTCG 60.332 44.000 0.00 0.00 44.57 3.46
1039 3524 5.457799 CCGAAGAGCGATATAAAAGTTTCGA 59.542 40.000 4.58 0.00 44.57 3.71
1040 3525 6.337914 CGAAGAGCGATATAAAAGTTTCGAC 58.662 40.000 0.00 0.00 44.57 4.20
1041 3526 6.196724 CGAAGAGCGATATAAAAGTTTCGACT 59.803 38.462 0.00 0.00 44.57 4.18
1092 3577 4.816385 CAGGACATAAAGTATGCCGATGTT 59.184 41.667 0.00 0.00 39.79 2.71
1095 3580 5.756347 GGACATAAAGTATGCCGATGTTGTA 59.244 40.000 0.00 0.00 39.79 2.41
1102 3587 2.813179 GCCGATGTTGTAGCGCTGG 61.813 63.158 22.90 11.28 36.74 4.85
1133 3618 3.723348 GGGACGAAACGCTGGTGC 61.723 66.667 0.00 0.00 0.00 5.01
1151 3636 2.028484 AGCAAGAAACGCCGACGA 59.972 55.556 0.00 0.00 43.93 4.20
1171 3656 3.181510 CGATGCATGCATGTCTGATATGG 60.182 47.826 36.73 8.81 36.70 2.74
1173 3658 2.882137 TGCATGCATGTCTGATATGGTG 59.118 45.455 26.79 0.00 0.00 4.17
1178 3668 3.708121 TGCATGTCTGATATGGTGAGTCT 59.292 43.478 14.96 0.00 0.00 3.24
1206 3696 3.192844 CGAGGGAAGCTAACTCACACTTA 59.807 47.826 11.35 0.00 0.00 2.24
1259 4720 4.060900 ACTGCGCATTATAGTCCAATCTG 58.939 43.478 12.24 0.00 0.00 2.90
1285 4746 0.611200 AGGCACGTACATGGTTGCTA 59.389 50.000 0.00 0.00 0.00 3.49
1313 4774 6.775088 ACAAGTCGTATAATGCAACTTCATG 58.225 36.000 0.00 0.00 0.00 3.07
1326 4787 0.617413 CTTCATGTGGGAGCTCACCT 59.383 55.000 14.84 0.00 36.87 4.00
1383 4845 5.840693 AGGAAAAAGAAAAGGACATGATGGT 59.159 36.000 0.00 0.00 0.00 3.55
1411 4873 4.766375 TCCTAATGGCTTAGCTACAACAC 58.234 43.478 3.59 0.00 34.21 3.32
1423 4885 2.216263 GCTACAACACGCAAAGCAAAAG 59.784 45.455 0.00 0.00 33.38 2.27
1440 4902 4.021104 GCAAAAGGGTTAGGCTTTTCTGAT 60.021 41.667 0.00 0.00 0.00 2.90
1458 4920 2.493675 TGATGGGTCAGAAGAGAAGACG 59.506 50.000 0.00 0.00 33.18 4.18
1487 4949 3.395702 AAGCCATACCGCGGGTGA 61.396 61.111 31.76 15.07 36.19 4.02
1516 4978 2.442087 GCCCATTACCTGGTGGCC 60.442 66.667 10.23 0.00 44.30 5.36
1525 4987 4.371417 CTGGTGGCCTGCATGGGT 62.371 66.667 3.32 0.00 36.00 4.51
1529 4991 1.293179 GTGGCCTGCATGGGTTTTC 59.707 57.895 3.32 0.00 36.00 2.29
1563 5025 0.315568 GTGTGGACGAGAACTCAGCT 59.684 55.000 0.00 0.00 0.00 4.24
1569 5031 0.528470 ACGAGAACTCAGCTACAGCC 59.472 55.000 0.00 0.00 43.38 4.85
1605 5067 1.589630 TCCAACAGGGATGTCGACG 59.410 57.895 11.62 0.00 42.15 5.12
1606 5068 1.447838 CCAACAGGGATGTCGACGG 60.448 63.158 11.62 0.00 40.01 4.79
1607 5069 2.100631 CAACAGGGATGTCGACGGC 61.101 63.158 11.62 4.95 0.00 5.68
1608 5070 2.579657 AACAGGGATGTCGACGGCA 61.580 57.895 3.85 3.85 0.00 5.69
1609 5071 2.509336 CAGGGATGTCGACGGCAC 60.509 66.667 3.27 6.33 0.00 5.01
1644 5106 3.635373 AGTGACTTCCTTCAAGTGTCGTA 59.365 43.478 0.00 0.00 46.10 3.43
1645 5107 4.098960 AGTGACTTCCTTCAAGTGTCGTAA 59.901 41.667 0.00 0.00 46.10 3.18
1691 5155 2.833794 CAAACTTGTTCCTCGAGTCCA 58.166 47.619 12.31 1.65 39.66 4.02
1825 5290 2.745100 CGACCCGACCTCAGACGA 60.745 66.667 0.00 0.00 32.72 4.20
1862 5327 1.227674 GTGTCATCCCTGGATCGGC 60.228 63.158 0.00 0.00 31.62 5.54
1927 5393 8.040727 AGTAGCAATCACACACTTATTACATCA 58.959 33.333 0.00 0.00 0.00 3.07
2012 5479 4.766375 CGGAAGGCTTGGAAGATAAAGTA 58.234 43.478 3.46 0.00 0.00 2.24
2016 5483 7.336396 GGAAGGCTTGGAAGATAAAGTAAGTA 58.664 38.462 3.46 0.00 0.00 2.24
2207 5674 2.337849 TGCATATATGGCTGGTGGAGA 58.662 47.619 14.51 0.00 0.00 3.71
2317 5785 4.292186 TCATTGAGAAGGTTCCTCCAAG 57.708 45.455 0.00 0.00 39.02 3.61
2333 5801 6.318913 TCCTCCAAGTCAATCCCAATTAAAA 58.681 36.000 0.00 0.00 0.00 1.52
2455 5923 9.542462 GCTAACCATGATTAGTTTATACACTCA 57.458 33.333 8.66 0.00 35.05 3.41
2472 5940 0.107263 TCAGCAGAGGTTTGCACACA 60.107 50.000 5.20 0.00 46.47 3.72
2476 5944 2.431782 AGCAGAGGTTTGCACACATTTT 59.568 40.909 5.20 0.00 46.47 1.82
2538 6006 3.888930 ACATGGTGTTTGAGAAACGGATT 59.111 39.130 0.00 0.00 44.28 3.01
2549 6017 3.692576 AGAAACGGATTATCGAGACACG 58.307 45.455 0.00 0.00 44.09 4.49
2594 6062 2.621070 ACTCTGGGTGGACAGTTACAT 58.379 47.619 0.00 0.00 39.48 2.29
2598 6066 4.620723 TCTGGGTGGACAGTTACATCTAT 58.379 43.478 0.00 0.00 39.48 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 57 2.531483 TAGCCTGAGGGGAGGTGGAC 62.531 65.000 0.00 0.00 37.23 4.02
59 61 1.237458 GGATAGCCTGAGGGGAGGT 59.763 63.158 0.00 0.00 37.23 3.85
108 111 2.044650 GCTGCTTGATCTGGGGCA 60.045 61.111 0.00 0.00 0.00 5.36
127 130 1.224315 CCTGCATTGGATCCGGACA 59.776 57.895 6.12 0.00 0.00 4.02
233 238 3.075005 GGCAGAGGACCGGTAGCA 61.075 66.667 7.34 0.00 0.00 3.49
284 289 0.836606 TGACTCAAGCACAAGGTGGA 59.163 50.000 0.00 0.00 33.64 4.02
401 416 1.229625 TCCAGTGATGGCTGACCCT 60.230 57.895 0.00 0.00 38.70 4.34
492 510 2.802816 CCGCCTCTGTAATAGCAACATC 59.197 50.000 0.00 0.00 0.00 3.06
496 514 1.202371 CGTCCGCCTCTGTAATAGCAA 60.202 52.381 0.00 0.00 0.00 3.91
611 3087 3.232213 TCGAGACTAAATGACCAGCAC 57.768 47.619 0.00 0.00 0.00 4.40
626 3107 6.318396 TGCCATGTTTCAATTCATAATCGAGA 59.682 34.615 0.00 0.00 0.00 4.04
660 3141 2.307049 CATTTTCTTCACCAACGCGAC 58.693 47.619 15.93 0.00 0.00 5.19
825 3309 0.320683 TCACATTCTGCTCCCACGTG 60.321 55.000 9.08 9.08 0.00 4.49
826 3310 0.320771 GTCACATTCTGCTCCCACGT 60.321 55.000 0.00 0.00 0.00 4.49
827 3311 1.021390 GGTCACATTCTGCTCCCACG 61.021 60.000 0.00 0.00 0.00 4.94
863 3348 4.279420 CGGAGACCTTGATCTGATCATACA 59.721 45.833 20.16 5.83 39.39 2.29
872 3357 4.380655 CGTAAGTTTCGGAGACCTTGATCT 60.381 45.833 0.00 0.00 34.32 2.75
888 3373 2.613691 CCCGTAGCATTGTCGTAAGTT 58.386 47.619 0.00 0.00 39.48 2.66
889 3374 1.738030 GCCCGTAGCATTGTCGTAAGT 60.738 52.381 0.00 0.00 42.97 2.24
890 3375 0.928229 GCCCGTAGCATTGTCGTAAG 59.072 55.000 0.00 0.00 42.97 2.34
891 3376 0.802994 CGCCCGTAGCATTGTCGTAA 60.803 55.000 0.00 0.00 44.04 3.18
892 3377 1.226745 CGCCCGTAGCATTGTCGTA 60.227 57.895 0.00 0.00 44.04 3.43
893 3378 1.936436 TACGCCCGTAGCATTGTCGT 61.936 55.000 0.00 0.00 44.04 4.34
894 3379 0.802994 TTACGCCCGTAGCATTGTCG 60.803 55.000 0.60 0.00 44.04 4.35
895 3380 0.928229 CTTACGCCCGTAGCATTGTC 59.072 55.000 0.60 0.00 44.04 3.18
896 3381 0.248289 ACTTACGCCCGTAGCATTGT 59.752 50.000 0.60 0.00 44.04 2.71
897 3382 0.650512 CACTTACGCCCGTAGCATTG 59.349 55.000 0.60 0.00 44.04 2.82
898 3383 1.087771 GCACTTACGCCCGTAGCATT 61.088 55.000 0.60 0.00 44.04 3.56
899 3384 1.520787 GCACTTACGCCCGTAGCAT 60.521 57.895 0.60 0.00 44.04 3.79
900 3385 1.314534 TAGCACTTACGCCCGTAGCA 61.315 55.000 11.39 0.00 44.04 3.49
901 3386 0.031721 ATAGCACTTACGCCCGTAGC 59.968 55.000 0.60 2.12 38.52 3.58
902 3387 1.607628 AGATAGCACTTACGCCCGTAG 59.392 52.381 0.60 0.00 31.71 3.51
903 3388 1.683943 AGATAGCACTTACGCCCGTA 58.316 50.000 0.00 0.00 0.00 4.02
904 3389 0.822164 AAGATAGCACTTACGCCCGT 59.178 50.000 0.00 0.00 0.00 5.28
905 3390 1.593006 CAAAGATAGCACTTACGCCCG 59.407 52.381 0.00 0.00 0.00 6.13
906 3391 1.330829 GCAAAGATAGCACTTACGCCC 59.669 52.381 0.00 0.00 0.00 6.13
907 3392 2.030946 CAGCAAAGATAGCACTTACGCC 59.969 50.000 0.00 0.00 32.48 5.68
908 3393 2.030946 CCAGCAAAGATAGCACTTACGC 59.969 50.000 0.00 0.00 0.00 4.42
909 3394 3.521560 TCCAGCAAAGATAGCACTTACG 58.478 45.455 0.00 0.00 0.00 3.18
910 3395 3.311048 GCTCCAGCAAAGATAGCACTTAC 59.689 47.826 0.00 0.00 41.59 2.34
911 3396 3.535561 GCTCCAGCAAAGATAGCACTTA 58.464 45.455 0.00 0.00 41.59 2.24
912 3397 2.363683 GCTCCAGCAAAGATAGCACTT 58.636 47.619 0.00 0.00 41.59 3.16
913 3398 1.741732 CGCTCCAGCAAAGATAGCACT 60.742 52.381 0.00 0.00 42.21 4.40
914 3399 0.654683 CGCTCCAGCAAAGATAGCAC 59.345 55.000 0.00 0.00 42.21 4.40
915 3400 0.536724 TCGCTCCAGCAAAGATAGCA 59.463 50.000 0.00 0.00 42.21 3.49
916 3401 1.656652 TTCGCTCCAGCAAAGATAGC 58.343 50.000 0.00 0.00 42.21 2.97
917 3402 3.525537 TCTTTCGCTCCAGCAAAGATAG 58.474 45.455 15.99 4.90 40.11 2.08
918 3403 3.610040 TCTTTCGCTCCAGCAAAGATA 57.390 42.857 15.99 3.31 40.11 1.98
919 3404 2.479566 TCTTTCGCTCCAGCAAAGAT 57.520 45.000 15.99 0.00 40.11 2.40
920 3405 2.146342 CTTCTTTCGCTCCAGCAAAGA 58.854 47.619 15.99 15.99 41.57 2.52
921 3406 1.400759 GCTTCTTTCGCTCCAGCAAAG 60.401 52.381 13.17 13.17 42.21 2.77
922 3407 0.593128 GCTTCTTTCGCTCCAGCAAA 59.407 50.000 0.00 0.00 42.21 3.68
923 3408 1.568612 CGCTTCTTTCGCTCCAGCAA 61.569 55.000 0.00 0.00 42.21 3.91
924 3409 2.029288 CGCTTCTTTCGCTCCAGCA 61.029 57.895 0.00 0.00 42.21 4.41
925 3410 1.086634 ATCGCTTCTTTCGCTCCAGC 61.087 55.000 0.00 0.00 37.78 4.85
926 3411 2.123342 CTATCGCTTCTTTCGCTCCAG 58.877 52.381 0.00 0.00 0.00 3.86
927 3412 1.802880 GCTATCGCTTCTTTCGCTCCA 60.803 52.381 0.00 0.00 0.00 3.86
928 3413 0.855995 GCTATCGCTTCTTTCGCTCC 59.144 55.000 0.00 0.00 0.00 4.70
929 3414 1.520590 CAGCTATCGCTTCTTTCGCTC 59.479 52.381 0.00 0.00 46.47 5.03
930 3415 1.565305 CAGCTATCGCTTCTTTCGCT 58.435 50.000 0.00 0.00 46.47 4.93
931 3416 0.042621 GCAGCTATCGCTTCTTTCGC 60.043 55.000 0.00 0.00 46.47 4.70
932 3417 0.228238 CGCAGCTATCGCTTCTTTCG 59.772 55.000 0.00 0.00 46.47 3.46
933 3418 1.005557 CACGCAGCTATCGCTTCTTTC 60.006 52.381 7.38 0.00 46.47 2.62
934 3419 1.002366 CACGCAGCTATCGCTTCTTT 58.998 50.000 7.38 0.00 46.47 2.52
935 3420 0.108615 ACACGCAGCTATCGCTTCTT 60.109 50.000 7.38 0.00 46.47 2.52
936 3421 0.803768 CACACGCAGCTATCGCTTCT 60.804 55.000 7.38 0.00 46.47 2.85
937 3422 1.633171 CACACGCAGCTATCGCTTC 59.367 57.895 7.38 0.00 46.47 3.86
938 3423 2.456119 GCACACGCAGCTATCGCTT 61.456 57.895 7.38 0.00 46.47 4.68
940 3425 2.456119 AAGCACACGCAGCTATCGC 61.456 57.895 7.38 0.00 42.53 4.58
941 3426 1.078201 TCAAGCACACGCAGCTATCG 61.078 55.000 6.07 6.07 42.53 2.92
942 3427 0.371645 GTCAAGCACACGCAGCTATC 59.628 55.000 0.00 0.00 42.53 2.08
943 3428 1.021390 GGTCAAGCACACGCAGCTAT 61.021 55.000 0.00 0.00 42.53 2.97
944 3429 1.667830 GGTCAAGCACACGCAGCTA 60.668 57.895 0.00 0.00 42.53 3.32
945 3430 2.974698 GGTCAAGCACACGCAGCT 60.975 61.111 0.00 0.00 45.97 4.24
946 3431 2.620112 ATGGTCAAGCACACGCAGC 61.620 57.895 0.00 0.00 42.27 5.25
947 3432 1.208358 CATGGTCAAGCACACGCAG 59.792 57.895 0.00 0.00 42.27 5.18
948 3433 2.260154 CCATGGTCAAGCACACGCA 61.260 57.895 2.57 0.00 42.27 5.24
949 3434 1.915614 CTCCATGGTCAAGCACACGC 61.916 60.000 12.58 0.00 38.99 5.34
950 3435 0.320683 TCTCCATGGTCAAGCACACG 60.321 55.000 12.58 0.00 0.00 4.49
951 3436 1.808945 CTTCTCCATGGTCAAGCACAC 59.191 52.381 12.58 0.00 0.00 3.82
952 3437 1.883638 GCTTCTCCATGGTCAAGCACA 60.884 52.381 30.02 5.64 40.86 4.57
953 3438 0.807496 GCTTCTCCATGGTCAAGCAC 59.193 55.000 30.02 13.03 40.86 4.40
954 3439 0.401356 TGCTTCTCCATGGTCAAGCA 59.599 50.000 32.11 32.11 46.96 3.91
955 3440 1.093159 CTGCTTCTCCATGGTCAAGC 58.907 55.000 29.09 29.09 41.43 4.01
956 3441 2.027377 AGACTGCTTCTCCATGGTCAAG 60.027 50.000 12.58 15.19 0.00 3.02
957 3442 1.980765 AGACTGCTTCTCCATGGTCAA 59.019 47.619 12.58 4.81 0.00 3.18
958 3443 1.552337 GAGACTGCTTCTCCATGGTCA 59.448 52.381 12.58 0.00 44.74 4.02
959 3444 2.307934 GAGACTGCTTCTCCATGGTC 57.692 55.000 12.58 0.00 44.74 4.02
967 3452 1.765314 ACCAACACAGAGACTGCTTCT 59.235 47.619 0.00 0.00 37.23 2.85
968 3453 2.139118 GACCAACACAGAGACTGCTTC 58.861 52.381 0.00 0.00 34.37 3.86
969 3454 1.486310 TGACCAACACAGAGACTGCTT 59.514 47.619 0.00 0.00 34.37 3.91
970 3455 1.123077 TGACCAACACAGAGACTGCT 58.877 50.000 0.00 0.00 34.37 4.24
971 3456 1.599542 GTTGACCAACACAGAGACTGC 59.400 52.381 7.92 0.00 40.84 4.40
972 3457 2.868583 CAGTTGACCAACACAGAGACTG 59.131 50.000 14.42 0.00 43.47 3.51
973 3458 2.158900 CCAGTTGACCAACACAGAGACT 60.159 50.000 14.42 0.00 43.47 3.24
974 3459 2.158957 TCCAGTTGACCAACACAGAGAC 60.159 50.000 14.42 0.00 43.47 3.36
975 3460 2.103094 CTCCAGTTGACCAACACAGAGA 59.897 50.000 14.42 3.80 43.47 3.10
976 3461 2.103094 TCTCCAGTTGACCAACACAGAG 59.897 50.000 14.42 14.73 43.47 3.35
977 3462 2.115427 TCTCCAGTTGACCAACACAGA 58.885 47.619 14.42 9.19 43.47 3.41
978 3463 2.620251 TCTCCAGTTGACCAACACAG 57.380 50.000 14.42 7.32 43.47 3.66
979 3464 2.503765 TCTTCTCCAGTTGACCAACACA 59.496 45.455 14.42 0.00 43.47 3.72
980 3465 3.194005 TCTTCTCCAGTTGACCAACAC 57.806 47.619 14.42 0.00 43.47 3.32
981 3466 3.743521 CATCTTCTCCAGTTGACCAACA 58.256 45.455 14.42 0.00 43.47 3.33
982 3467 2.485814 GCATCTTCTCCAGTTGACCAAC 59.514 50.000 4.81 4.81 41.45 3.77
983 3468 2.553028 GGCATCTTCTCCAGTTGACCAA 60.553 50.000 0.00 0.00 0.00 3.67
984 3469 1.003580 GGCATCTTCTCCAGTTGACCA 59.996 52.381 0.00 0.00 0.00 4.02
985 3470 1.680249 GGGCATCTTCTCCAGTTGACC 60.680 57.143 0.00 0.00 42.30 4.02
986 3471 1.743996 GGGCATCTTCTCCAGTTGAC 58.256 55.000 0.00 0.00 30.00 3.18
987 3472 0.250234 CGGGCATCTTCTCCAGTTGA 59.750 55.000 0.00 0.00 0.00 3.18
988 3473 0.036010 ACGGGCATCTTCTCCAGTTG 60.036 55.000 0.00 0.00 0.00 3.16
989 3474 1.482593 CTACGGGCATCTTCTCCAGTT 59.517 52.381 0.00 0.00 33.06 3.16
990 3475 1.115467 CTACGGGCATCTTCTCCAGT 58.885 55.000 0.00 0.00 35.11 4.00
991 3476 0.390860 CCTACGGGCATCTTCTCCAG 59.609 60.000 0.00 0.00 0.00 3.86
992 3477 2.516448 CCTACGGGCATCTTCTCCA 58.484 57.895 0.00 0.00 0.00 3.86
1005 3490 4.570663 CTCTTCGGGCCGCCTACG 62.571 72.222 23.83 5.49 39.67 3.51
1006 3491 4.893601 GCTCTTCGGGCCGCCTAC 62.894 72.222 23.83 5.48 0.00 3.18
1010 3495 2.209064 TATATCGCTCTTCGGGCCGC 62.209 60.000 23.83 5.53 39.05 6.53
1011 3496 0.242825 TTATATCGCTCTTCGGGCCG 59.757 55.000 22.51 22.51 39.05 6.13
1012 3497 2.450609 TTTATATCGCTCTTCGGGCC 57.549 50.000 0.00 0.00 39.05 5.80
1013 3498 3.391049 ACTTTTATATCGCTCTTCGGGC 58.609 45.455 0.00 0.00 39.05 6.13
1014 3499 5.332355 CGAAACTTTTATATCGCTCTTCGGG 60.332 44.000 0.00 0.00 39.05 5.14
1015 3500 5.457799 TCGAAACTTTTATATCGCTCTTCGG 59.542 40.000 0.00 0.00 39.05 4.30
1016 3501 6.196724 AGTCGAAACTTTTATATCGCTCTTCG 59.803 38.462 0.00 0.00 35.39 3.79
1017 3502 7.432838 AGAGTCGAAACTTTTATATCGCTCTTC 59.567 37.037 12.02 0.00 41.43 2.87
1018 3503 7.259161 AGAGTCGAAACTTTTATATCGCTCTT 58.741 34.615 12.02 2.49 41.43 2.85
1019 3504 6.797454 AGAGTCGAAACTTTTATATCGCTCT 58.203 36.000 12.02 12.02 40.47 4.09
1020 3505 7.324135 CCTAGAGTCGAAACTTTTATATCGCTC 59.676 40.741 0.00 0.00 38.02 5.03
1021 3506 7.140048 CCTAGAGTCGAAACTTTTATATCGCT 58.860 38.462 0.00 0.00 35.28 4.93
1022 3507 6.129141 GCCTAGAGTCGAAACTTTTATATCGC 60.129 42.308 0.00 0.00 35.28 4.58
1023 3508 6.086502 CGCCTAGAGTCGAAACTTTTATATCG 59.913 42.308 0.00 0.00 35.28 2.92
1024 3509 7.137426 TCGCCTAGAGTCGAAACTTTTATATC 58.863 38.462 0.00 0.00 35.28 1.63
1025 3510 7.035840 TCGCCTAGAGTCGAAACTTTTATAT 57.964 36.000 0.00 0.00 35.28 0.86
1026 3511 6.441093 TCGCCTAGAGTCGAAACTTTTATA 57.559 37.500 0.00 0.00 35.28 0.98
1027 3512 5.320549 TCGCCTAGAGTCGAAACTTTTAT 57.679 39.130 0.00 0.00 35.28 1.40
1028 3513 4.771590 TCGCCTAGAGTCGAAACTTTTA 57.228 40.909 0.00 0.00 35.28 1.52
1029 3514 3.655276 TCGCCTAGAGTCGAAACTTTT 57.345 42.857 0.00 0.00 35.28 2.27
1030 3515 3.005578 ACTTCGCCTAGAGTCGAAACTTT 59.994 43.478 12.85 0.00 42.99 2.66
1031 3516 2.557490 ACTTCGCCTAGAGTCGAAACTT 59.443 45.455 12.85 2.33 42.99 2.66
1032 3517 2.161030 ACTTCGCCTAGAGTCGAAACT 58.839 47.619 12.85 0.00 42.99 2.66
1033 3518 2.095364 TGACTTCGCCTAGAGTCGAAAC 60.095 50.000 12.85 10.87 42.99 2.78
1034 3519 2.156917 TGACTTCGCCTAGAGTCGAAA 58.843 47.619 12.85 0.68 42.99 3.46
1035 3520 1.817357 TGACTTCGCCTAGAGTCGAA 58.183 50.000 11.78 11.78 41.65 3.71
1036 3521 1.671328 CATGACTTCGCCTAGAGTCGA 59.329 52.381 5.20 2.20 33.00 4.20
1037 3522 1.268794 CCATGACTTCGCCTAGAGTCG 60.269 57.143 0.00 0.06 33.00 4.18
1038 3523 1.537135 GCCATGACTTCGCCTAGAGTC 60.537 57.143 0.00 3.01 0.00 3.36
1039 3524 0.461961 GCCATGACTTCGCCTAGAGT 59.538 55.000 0.00 0.00 0.00 3.24
1040 3525 0.596083 CGCCATGACTTCGCCTAGAG 60.596 60.000 0.00 0.00 0.00 2.43
1041 3526 1.437573 CGCCATGACTTCGCCTAGA 59.562 57.895 0.00 0.00 0.00 2.43
1061 3546 5.525378 GCATACTTTATGTCCTGGACTTCTG 59.475 44.000 26.03 15.21 38.43 3.02
1092 3577 2.177394 TGTGATTTTCCAGCGCTACA 57.823 45.000 10.99 5.24 0.00 2.74
1095 3580 0.883833 CCTTGTGATTTTCCAGCGCT 59.116 50.000 2.64 2.64 0.00 5.92
1102 3587 0.168128 CGTCCCGCCTTGTGATTTTC 59.832 55.000 0.00 0.00 0.00 2.29
1133 3618 1.626654 ATCGTCGGCGTTTCTTGCTG 61.627 55.000 10.18 0.00 40.13 4.41
1151 3636 3.506067 CACCATATCAGACATGCATGCAT 59.494 43.478 27.46 27.46 37.08 3.96
1171 3656 1.444553 CCCTCGCGACAAGACTCAC 60.445 63.158 3.71 0.00 0.00 3.51
1173 3658 0.456995 CTTCCCTCGCGACAAGACTC 60.457 60.000 3.71 0.00 0.00 3.36
1178 3668 0.389426 GTTAGCTTCCCTCGCGACAA 60.389 55.000 3.71 0.00 0.00 3.18
1206 3696 1.202710 TGCTTCACGTTACCCACATGT 60.203 47.619 0.00 0.00 0.00 3.21
1214 3704 1.154469 GCGCCTTGCTTCACGTTAC 60.154 57.895 0.00 0.00 41.73 2.50
1215 3705 1.595655 TGCGCCTTGCTTCACGTTA 60.596 52.632 4.18 0.00 46.63 3.18
1216 3706 2.899838 TGCGCCTTGCTTCACGTT 60.900 55.556 4.18 0.00 46.63 3.99
1242 3732 4.214971 CCTGCACAGATTGGACTATAATGC 59.785 45.833 0.00 0.00 0.00 3.56
1244 3734 5.221803 CCTCCTGCACAGATTGGACTATAAT 60.222 44.000 0.00 0.00 0.00 1.28
1245 3735 4.101585 CCTCCTGCACAGATTGGACTATAA 59.898 45.833 0.00 0.00 0.00 0.98
1249 4710 0.617413 CCTCCTGCACAGATTGGACT 59.383 55.000 0.00 0.00 0.00 3.85
1285 4746 5.404946 AGTTGCATTATACGACTTGTACGT 58.595 37.500 0.00 0.00 45.75 3.57
1313 4774 1.374758 CGTGAAGGTGAGCTCCCAC 60.375 63.158 19.56 9.97 36.37 4.61
1326 4787 1.145156 CACCAGGACACCACGTGAA 59.855 57.895 19.30 0.00 36.96 3.18
1347 4808 1.791103 TTTTTCCTGGGCGTTGCTCG 61.791 55.000 0.00 0.00 43.12 5.03
1411 4873 1.934849 GCCTAACCCTTTTGCTTTGCG 60.935 52.381 0.00 0.00 0.00 4.85
1423 4885 2.291605 ACCCATCAGAAAAGCCTAACCC 60.292 50.000 0.00 0.00 0.00 4.11
1440 4902 1.203013 TCCGTCTTCTCTTCTGACCCA 60.203 52.381 0.00 0.00 0.00 4.51
1458 4920 1.134371 GTATGGCTTGTCTCCTGGTCC 60.134 57.143 0.00 0.00 0.00 4.46
1547 5009 1.813178 CTGTAGCTGAGTTCTCGTCCA 59.187 52.381 0.00 0.00 0.00 4.02
1548 5010 1.468395 GCTGTAGCTGAGTTCTCGTCC 60.468 57.143 0.00 0.00 38.21 4.79
1569 5031 4.081030 CTGTTCAGCAGCACCGCG 62.081 66.667 0.00 0.00 38.52 6.46
1591 5053 2.994995 TGCCGTCGACATCCCTGT 60.995 61.111 17.16 0.00 38.67 4.00
1598 5060 2.354188 CTGAACGTGCCGTCGACA 60.354 61.111 17.16 0.00 39.99 4.35
1605 5067 2.426024 TCACTAGATACCTGAACGTGCC 59.574 50.000 0.00 0.00 0.00 5.01
1606 5068 3.128938 AGTCACTAGATACCTGAACGTGC 59.871 47.826 0.00 0.00 0.00 5.34
1607 5069 4.966965 AGTCACTAGATACCTGAACGTG 57.033 45.455 0.00 0.00 0.00 4.49
1608 5070 4.398673 GGAAGTCACTAGATACCTGAACGT 59.601 45.833 0.00 0.00 0.00 3.99
1609 5071 4.641094 AGGAAGTCACTAGATACCTGAACG 59.359 45.833 0.00 0.00 0.00 3.95
1644 5106 3.117131 ACCAGATGAAGACACCCCTTTTT 60.117 43.478 0.00 0.00 0.00 1.94
1645 5107 2.447047 ACCAGATGAAGACACCCCTTTT 59.553 45.455 0.00 0.00 0.00 2.27
1691 5155 9.218525 TCTCCATTTTCTACTCTTTAGGATGAT 57.781 33.333 0.00 0.00 0.00 2.45
1862 5327 3.133691 AGTACTGTGTGTGTCAGCATTG 58.866 45.455 0.00 0.00 36.50 2.82
2012 5479 2.224426 TGCCGTTGGAGTTGATGTACTT 60.224 45.455 0.00 0.00 0.00 2.24
2016 5483 2.632377 CTATGCCGTTGGAGTTGATGT 58.368 47.619 0.00 0.00 0.00 3.06
2207 5674 8.902540 TCGCAAAAATCATATAACCATAGAGT 57.097 30.769 0.00 0.00 0.00 3.24
2344 5812 8.871629 TCACTCTAAATTAATTTGTTGGGCTA 57.128 30.769 21.19 0.41 0.00 3.93
2346 5814 8.250332 TCATCACTCTAAATTAATTTGTTGGGC 58.750 33.333 21.19 0.00 0.00 5.36
2392 5860 6.662865 ATGGACATCTTGAGTATCTGGTAG 57.337 41.667 0.00 0.00 34.92 3.18
2455 5923 1.696063 AATGTGTGCAAACCTCTGCT 58.304 45.000 4.11 0.00 43.07 4.24
2472 5940 4.508662 GAGATCGAGTCTTGTGGGAAAAT 58.491 43.478 0.00 0.00 37.29 1.82
2476 5944 1.006043 AGGAGATCGAGTCTTGTGGGA 59.994 52.381 0.00 0.00 37.29 4.37
2538 6006 3.340928 TCTGAAAGACCGTGTCTCGATA 58.659 45.455 6.96 0.00 42.59 2.92
2594 6062 6.015010 GCTAGCAGATGTAGAGGGAAAATAGA 60.015 42.308 10.63 0.00 0.00 1.98
2598 6066 3.134804 GGCTAGCAGATGTAGAGGGAAAA 59.865 47.826 18.24 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.