Multiple sequence alignment - TraesCS1A01G273800

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1A01G273800 chr1A 100.000 3762 0 0 1 3762 467254799 467258560 0.000000e+00 6948.0
1 TraesCS1A01G273800 chr1A 88.516 566 50 10 100 659 536244291 536244847 0.000000e+00 671.0
2 TraesCS1A01G273800 chr1A 88.339 566 54 7 100 661 581261698 581262255 0.000000e+00 669.0
3 TraesCS1A01G273800 chr1A 97.959 98 0 2 3 99 141334745 141334649 6.460000e-38 169.0
4 TraesCS1A01G273800 chr1D 90.152 2427 121 23 660 3022 368317675 368320047 0.000000e+00 3049.0
5 TraesCS1A01G273800 chr1D 90.816 392 19 3 3044 3418 368320261 368320652 3.350000e-140 508.0
6 TraesCS1A01G273800 chr1D 85.757 337 29 5 3101 3418 369899385 369899721 4.650000e-89 339.0
7 TraesCS1A01G273800 chr1D 86.061 330 18 13 3414 3715 368320724 368321053 2.800000e-86 329.0
8 TraesCS1A01G273800 chr1D 94.891 137 7 0 3411 3547 369899790 369899926 8.180000e-52 215.0
9 TraesCS1A01G273800 chr1D 86.131 137 14 5 3564 3695 369902291 369902427 3.920000e-30 143.0
10 TraesCS1A01G273800 chr1D 96.386 83 1 1 3020 3102 369899223 369899303 6.550000e-28 135.0
11 TraesCS1A01G273800 chr1B 93.778 1125 67 1 1887 3008 492334716 492335840 0.000000e+00 1687.0
12 TraesCS1A01G273800 chr1B 88.846 1291 56 32 660 1890 492333132 492334394 0.000000e+00 1506.0
13 TraesCS1A01G273800 chr1B 90.263 380 23 9 3044 3418 492355783 492356153 5.650000e-133 484.0
14 TraesCS1A01G273800 chr1B 83.654 312 21 14 3414 3695 492356225 492356536 2.230000e-67 267.0
15 TraesCS1A01G273800 chr1B 100.000 28 0 0 3020 3047 492355623 492355650 7.000000e-03 52.8
16 TraesCS1A01G273800 chrUn 95.907 562 19 4 100 659 335004373 335003814 0.000000e+00 907.0
17 TraesCS1A01G273800 chr3A 95.552 562 22 3 100 659 585547801 585548361 0.000000e+00 896.0
18 TraesCS1A01G273800 chr3A 95.434 219 7 3 443 659 585504581 585504798 2.780000e-91 346.0
19 TraesCS1A01G273800 chr3A 97.959 98 2 0 3 100 138427134 138427037 1.800000e-38 171.0
20 TraesCS1A01G273800 chr3A 91.667 96 8 0 3603 3698 627277387 627277292 2.360000e-27 134.0
21 TraesCS1A01G273800 chr4A 88.277 563 54 9 100 659 22726842 22727395 0.000000e+00 664.0
22 TraesCS1A01G273800 chr4A 96.154 104 2 2 3 105 287119645 287119747 6.460000e-38 169.0
23 TraesCS1A01G273800 chr4A 96.970 99 2 1 3 101 137088491 137088588 8.360000e-37 165.0
24 TraesCS1A01G273800 chr4A 96.000 100 2 2 1 99 681558130 681558228 1.080000e-35 161.0
25 TraesCS1A01G273800 chr7D 88.078 562 57 7 100 659 33949165 33949718 0.000000e+00 658.0
26 TraesCS1A01G273800 chr7D 96.875 32 1 0 3043 3074 75800876 75800907 2.000000e-03 54.7
27 TraesCS1A01G273800 chr3B 88.028 568 51 10 101 661 207299183 207299740 0.000000e+00 656.0
28 TraesCS1A01G273800 chr3B 96.970 33 1 0 3043 3075 39451120 39451088 5.250000e-04 56.5
29 TraesCS1A01G273800 chr4B 81.037 849 132 18 1920 2755 642457835 642457003 0.000000e+00 649.0
30 TraesCS1A01G273800 chr4B 77.389 628 125 15 1134 1745 642458726 642458100 1.290000e-94 357.0
31 TraesCS1A01G273800 chr4B 82.917 240 31 8 1149 1380 642463184 642462947 1.370000e-49 207.0
32 TraesCS1A01G273800 chr4B 81.008 258 32 12 1149 1398 642537199 642536951 4.960000e-44 189.0
33 TraesCS1A01G273800 chr4B 92.000 50 4 0 1696 1745 642774607 642774558 1.870000e-08 71.3
34 TraesCS1A01G273800 chr4D 80.165 847 143 10 1920 2755 499503747 499502915 8.930000e-171 610.0
35 TraesCS1A01G273800 chr4D 81.667 240 34 8 1149 1380 499547312 499547075 1.380000e-44 191.0
36 TraesCS1A01G273800 chr4D 100.000 31 0 0 3044 3074 213840223 213840193 1.460000e-04 58.4
37 TraesCS1A01G273800 chr7A 86.501 563 61 9 104 659 110815730 110815176 4.160000e-169 604.0
38 TraesCS1A01G273800 chr5A 79.433 846 152 9 1920 2755 680503836 680503003 2.520000e-161 579.0
39 TraesCS1A01G273800 chr5A 76.989 704 126 21 1053 1739 680504792 680504108 1.650000e-98 370.0
40 TraesCS1A01G273800 chr5A 85.477 241 25 7 1148 1380 680512096 680511858 3.750000e-60 243.0
41 TraesCS1A01G273800 chr5A 81.781 247 35 6 1142 1380 627014975 627015219 8.240000e-47 198.0
42 TraesCS1A01G273800 chr5A 94.393 107 4 2 1 106 106280862 106280967 3.010000e-36 163.0
43 TraesCS1A01G273800 chr5A 92.857 112 4 4 3 112 160111183 160111292 3.890000e-35 159.0
44 TraesCS1A01G273800 chr5A 77.037 270 58 4 2090 2357 680669321 680669054 6.510000e-33 152.0
45 TraesCS1A01G273800 chr2D 89.499 419 38 6 100 514 619039574 619039990 3.330000e-145 525.0
46 TraesCS1A01G273800 chr2A 96.970 99 1 2 3 99 327953934 327954032 8.360000e-37 165.0
47 TraesCS1A01G273800 chr2A 91.379 116 4 6 3 113 467207883 467207997 1.810000e-33 154.0
48 TraesCS1A01G273800 chr3D 91.667 96 8 0 3603 3698 484347388 484347293 2.360000e-27 134.0
49 TraesCS1A01G273800 chr3D 100.000 33 0 0 3045 3077 67062420 67062388 1.130000e-05 62.1
50 TraesCS1A01G273800 chr6D 97.059 34 1 0 3046 3079 15700720 15700687 1.460000e-04 58.4
51 TraesCS1A01G273800 chr5B 100.000 29 0 0 3046 3074 98664887 98664859 2.000000e-03 54.7


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 TraesCS1A01G273800 chr1A 467254799 467258560 3761 False 6948.000000 6948 100.000000 1 3762 1 chr1A.!!$F1 3761
1 TraesCS1A01G273800 chr1A 536244291 536244847 556 False 671.000000 671 88.516000 100 659 1 chr1A.!!$F2 559
2 TraesCS1A01G273800 chr1A 581261698 581262255 557 False 669.000000 669 88.339000 100 661 1 chr1A.!!$F3 561
3 TraesCS1A01G273800 chr1D 368317675 368321053 3378 False 1295.333333 3049 89.009667 660 3715 3 chr1D.!!$F1 3055
4 TraesCS1A01G273800 chr1D 369899223 369902427 3204 False 208.000000 339 90.791250 3020 3695 4 chr1D.!!$F2 675
5 TraesCS1A01G273800 chr1B 492333132 492335840 2708 False 1596.500000 1687 91.312000 660 3008 2 chr1B.!!$F1 2348
6 TraesCS1A01G273800 chr1B 492355623 492356536 913 False 267.933333 484 91.305667 3020 3695 3 chr1B.!!$F2 675
7 TraesCS1A01G273800 chrUn 335003814 335004373 559 True 907.000000 907 95.907000 100 659 1 chrUn.!!$R1 559
8 TraesCS1A01G273800 chr3A 585547801 585548361 560 False 896.000000 896 95.552000 100 659 1 chr3A.!!$F2 559
9 TraesCS1A01G273800 chr4A 22726842 22727395 553 False 664.000000 664 88.277000 100 659 1 chr4A.!!$F1 559
10 TraesCS1A01G273800 chr7D 33949165 33949718 553 False 658.000000 658 88.078000 100 659 1 chr7D.!!$F1 559
11 TraesCS1A01G273800 chr3B 207299183 207299740 557 False 656.000000 656 88.028000 101 661 1 chr3B.!!$F1 560
12 TraesCS1A01G273800 chr4B 642457003 642458726 1723 True 503.000000 649 79.213000 1134 2755 2 chr4B.!!$R4 1621
13 TraesCS1A01G273800 chr4D 499502915 499503747 832 True 610.000000 610 80.165000 1920 2755 1 chr4D.!!$R2 835
14 TraesCS1A01G273800 chr7A 110815176 110815730 554 True 604.000000 604 86.501000 104 659 1 chr7A.!!$R1 555
15 TraesCS1A01G273800 chr5A 680503003 680504792 1789 True 474.500000 579 78.211000 1053 2755 2 chr5A.!!$R3 1702

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
983 1076 0.687354 AGGAACGAACCTCACTGCAT 59.313 50.0 0.0 0.0 34.98 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2769 3374 0.035725 CAGGCTCATCTCAACAGGCA 60.036 55.0 0.0 0.0 35.19 4.75 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
20 21 1.873591 CAGAGACAAAACCTGAACCCG 59.126 52.381 0.00 0.00 0.00 5.28
21 22 1.766496 AGAGACAAAACCTGAACCCGA 59.234 47.619 0.00 0.00 0.00 5.14
22 23 2.143925 GAGACAAAACCTGAACCCGAG 58.856 52.381 0.00 0.00 0.00 4.63
23 24 1.202770 AGACAAAACCTGAACCCGAGG 60.203 52.381 0.00 0.00 36.57 4.63
24 25 0.841289 ACAAAACCTGAACCCGAGGA 59.159 50.000 0.00 0.00 34.37 3.71
25 26 1.213430 ACAAAACCTGAACCCGAGGAA 59.787 47.619 0.00 0.00 34.37 3.36
26 27 2.303175 CAAAACCTGAACCCGAGGAAA 58.697 47.619 0.00 0.00 34.37 3.13
27 28 2.691011 CAAAACCTGAACCCGAGGAAAA 59.309 45.455 0.00 0.00 34.37 2.29
28 29 2.971901 AACCTGAACCCGAGGAAAAT 57.028 45.000 0.00 0.00 34.37 1.82
29 30 4.376225 AAACCTGAACCCGAGGAAAATA 57.624 40.909 0.00 0.00 34.37 1.40
30 31 4.376225 AACCTGAACCCGAGGAAAATAA 57.624 40.909 0.00 0.00 34.37 1.40
31 32 4.376225 ACCTGAACCCGAGGAAAATAAA 57.624 40.909 0.00 0.00 34.37 1.40
32 33 4.930696 ACCTGAACCCGAGGAAAATAAAT 58.069 39.130 0.00 0.00 34.37 1.40
33 34 6.069705 ACCTGAACCCGAGGAAAATAAATA 57.930 37.500 0.00 0.00 34.37 1.40
34 35 6.669631 ACCTGAACCCGAGGAAAATAAATAT 58.330 36.000 0.00 0.00 34.37 1.28
35 36 7.808218 ACCTGAACCCGAGGAAAATAAATATA 58.192 34.615 0.00 0.00 34.37 0.86
36 37 8.276477 ACCTGAACCCGAGGAAAATAAATATAA 58.724 33.333 0.00 0.00 34.37 0.98
37 38 8.565416 CCTGAACCCGAGGAAAATAAATATAAC 58.435 37.037 0.00 0.00 31.48 1.89
38 39 9.338622 CTGAACCCGAGGAAAATAAATATAACT 57.661 33.333 0.00 0.00 0.00 2.24
39 40 9.689501 TGAACCCGAGGAAAATAAATATAACTT 57.310 29.630 0.00 0.00 0.00 2.66
44 45 9.590088 CCGAGGAAAATAAATATAACTTAACGC 57.410 33.333 0.00 0.00 0.00 4.84
45 46 9.590088 CGAGGAAAATAAATATAACTTAACGCC 57.410 33.333 0.00 0.00 0.00 5.68
46 47 9.590088 GAGGAAAATAAATATAACTTAACGCCG 57.410 33.333 0.00 0.00 0.00 6.46
47 48 8.562052 AGGAAAATAAATATAACTTAACGCCGG 58.438 33.333 0.00 0.00 0.00 6.13
48 49 8.558700 GGAAAATAAATATAACTTAACGCCGGA 58.441 33.333 5.05 0.00 0.00 5.14
49 50 9.934190 GAAAATAAATATAACTTAACGCCGGAA 57.066 29.630 5.05 0.00 0.00 4.30
51 52 9.720667 AAATAAATATAACTTAACGCCGGAAAC 57.279 29.630 5.05 0.00 0.00 2.78
66 67 3.397849 GGAAACGGTAAGAGTTGGAGT 57.602 47.619 0.00 0.00 31.43 3.85
67 68 4.525912 GGAAACGGTAAGAGTTGGAGTA 57.474 45.455 0.00 0.00 31.43 2.59
68 69 4.240888 GGAAACGGTAAGAGTTGGAGTAC 58.759 47.826 0.00 0.00 31.43 2.73
69 70 4.262164 GGAAACGGTAAGAGTTGGAGTACA 60.262 45.833 0.00 0.00 31.43 2.90
70 71 4.942761 AACGGTAAGAGTTGGAGTACAA 57.057 40.909 0.00 0.00 36.54 2.41
71 72 4.942761 ACGGTAAGAGTTGGAGTACAAA 57.057 40.909 0.00 0.00 41.58 2.83
72 73 5.479124 ACGGTAAGAGTTGGAGTACAAAT 57.521 39.130 0.00 0.00 41.58 2.32
73 74 5.861727 ACGGTAAGAGTTGGAGTACAAATT 58.138 37.500 0.00 0.00 41.58 1.82
74 75 5.699458 ACGGTAAGAGTTGGAGTACAAATTG 59.301 40.000 0.00 0.00 41.58 2.32
75 76 5.121768 CGGTAAGAGTTGGAGTACAAATTGG 59.878 44.000 0.00 0.00 41.58 3.16
76 77 6.235664 GGTAAGAGTTGGAGTACAAATTGGA 58.764 40.000 0.00 0.00 41.58 3.53
77 78 6.713450 GGTAAGAGTTGGAGTACAAATTGGAA 59.287 38.462 0.00 0.00 41.58 3.53
78 79 7.229907 GGTAAGAGTTGGAGTACAAATTGGAAA 59.770 37.037 0.00 0.00 41.58 3.13
79 80 6.884280 AGAGTTGGAGTACAAATTGGAAAG 57.116 37.500 0.00 0.00 41.58 2.62
80 81 6.365520 AGAGTTGGAGTACAAATTGGAAAGT 58.634 36.000 0.00 0.00 41.58 2.66
81 82 6.833933 AGAGTTGGAGTACAAATTGGAAAGTT 59.166 34.615 0.00 0.00 41.58 2.66
82 83 7.996644 AGAGTTGGAGTACAAATTGGAAAGTTA 59.003 33.333 0.00 0.00 41.58 2.24
83 84 7.937649 AGTTGGAGTACAAATTGGAAAGTTAC 58.062 34.615 0.00 0.00 41.58 2.50
84 85 7.558444 AGTTGGAGTACAAATTGGAAAGTTACA 59.442 33.333 0.00 0.00 41.58 2.41
85 86 8.357402 GTTGGAGTACAAATTGGAAAGTTACAT 58.643 33.333 0.00 0.00 41.58 2.29
86 87 8.106247 TGGAGTACAAATTGGAAAGTTACATC 57.894 34.615 0.00 0.00 29.22 3.06
87 88 7.175990 TGGAGTACAAATTGGAAAGTTACATCC 59.824 37.037 0.00 1.00 29.22 3.51
88 89 7.141100 AGTACAAATTGGAAAGTTACATCCG 57.859 36.000 0.00 0.00 38.63 4.18
89 90 5.385509 ACAAATTGGAAAGTTACATCCGG 57.614 39.130 0.00 0.00 38.63 5.14
90 91 4.219725 ACAAATTGGAAAGTTACATCCGGG 59.780 41.667 0.00 0.00 38.63 5.73
91 92 2.500392 TTGGAAAGTTACATCCGGGG 57.500 50.000 0.00 0.00 38.63 5.73
92 93 1.364269 TGGAAAGTTACATCCGGGGT 58.636 50.000 0.00 2.79 38.63 4.95
93 94 1.003812 TGGAAAGTTACATCCGGGGTG 59.996 52.381 5.55 5.55 38.63 4.61
94 95 1.003928 GGAAAGTTACATCCGGGGTGT 59.996 52.381 18.45 18.45 0.00 4.16
95 96 2.553685 GGAAAGTTACATCCGGGGTGTT 60.554 50.000 19.71 0.00 0.00 3.32
96 97 3.307621 GGAAAGTTACATCCGGGGTGTTA 60.308 47.826 19.71 6.65 0.00 2.41
97 98 3.339253 AAGTTACATCCGGGGTGTTAC 57.661 47.619 19.71 19.44 31.30 2.50
98 99 2.259012 AGTTACATCCGGGGTGTTACA 58.741 47.619 26.16 4.90 33.02 2.41
203 204 0.981183 TCTATGGCCGTGGTCTTGTT 59.019 50.000 8.05 0.00 0.00 2.83
240 241 4.980805 GTCTTCGGTGGTGCGGCA 62.981 66.667 0.00 0.00 0.00 5.69
278 279 4.314440 GGTCACCTGCGCTCCACA 62.314 66.667 9.73 0.00 0.00 4.17
575 593 6.066054 GATGATCGCTAGGATTCATCGATA 57.934 41.667 0.00 0.00 39.59 2.92
576 594 5.236655 TGATCGCTAGGATTCATCGATAC 57.763 43.478 0.00 0.00 39.59 2.24
577 595 4.700213 TGATCGCTAGGATTCATCGATACA 59.300 41.667 0.00 0.00 39.59 2.29
578 596 5.358160 TGATCGCTAGGATTCATCGATACAT 59.642 40.000 0.00 0.00 39.59 2.29
643 663 8.541234 AGGGAGGTTTAGATTACAAGAGTTTAG 58.459 37.037 0.00 0.00 0.00 1.85
734 762 8.891671 AAAAACATGAGATTTGTGCAAATAGT 57.108 26.923 9.78 1.77 40.77 2.12
801 848 1.064611 TCGGAGAGGAGATCGAAACCT 60.065 52.381 7.89 7.89 36.68 3.50
802 849 1.751924 CGGAGAGGAGATCGAAACCTT 59.248 52.381 9.21 1.84 33.89 3.50
803 850 2.950309 CGGAGAGGAGATCGAAACCTTA 59.050 50.000 9.21 0.00 33.89 2.69
820 867 2.435805 CCTTAGGCCTCTACATCAAGCA 59.564 50.000 9.68 0.00 0.00 3.91
827 874 2.415491 CCTCTACATCAAGCAACGACGA 60.415 50.000 0.00 0.00 0.00 4.20
850 920 2.801077 TAGTCGACATCACCCTCTGA 57.199 50.000 19.50 0.00 0.00 3.27
862 932 8.511604 ACATCACCCTCTGAAATAAGTAAATG 57.488 34.615 0.00 0.00 30.60 2.32
887 957 2.578021 AGATGTGAGTGGGCTAAACCAT 59.422 45.455 0.00 0.00 43.59 3.55
983 1076 0.687354 AGGAACGAACCTCACTGCAT 59.313 50.000 0.00 0.00 34.98 3.96
990 1092 2.159653 CGAACCTCACTGCATGTAAAGC 60.160 50.000 0.00 0.00 0.00 3.51
1004 1106 2.224744 TGTAAAGCAGCACTGGAATGGA 60.225 45.455 0.00 0.00 0.00 3.41
1128 1240 6.204495 CCCCTGAACTAGTAGTACGAATAGTC 59.796 46.154 14.99 9.99 0.00 2.59
1129 1241 6.991531 CCCTGAACTAGTAGTACGAATAGTCT 59.008 42.308 14.99 7.12 0.00 3.24
1130 1242 7.041916 CCCTGAACTAGTAGTACGAATAGTCTG 60.042 44.444 14.99 11.94 0.00 3.51
1131 1243 7.244166 TGAACTAGTAGTACGAATAGTCTGC 57.756 40.000 14.99 9.31 0.00 4.26
1132 1244 6.820152 TGAACTAGTAGTACGAATAGTCTGCA 59.180 38.462 14.99 11.28 0.00 4.41
1309 1421 1.203441 ATGCCTCTCCAACCTCTGCA 61.203 55.000 0.00 0.00 0.00 4.41
1408 1520 2.676471 ATGAGTTTGGTGGCCGGC 60.676 61.111 21.18 21.18 0.00 6.13
1435 1547 5.823353 GGTACGTATCTTCTCTTCTCCTTG 58.177 45.833 0.00 0.00 0.00 3.61
1469 1603 4.703645 AATGCATGCATGATGATCTAGC 57.296 40.909 32.79 11.74 36.68 3.42
1480 1614 3.445450 TGATGATCTAGCTAGCCCGATTC 59.555 47.826 16.35 9.34 0.00 2.52
1482 1616 1.478916 GATCTAGCTAGCCCGATTCCC 59.521 57.143 16.35 0.00 0.00 3.97
1554 1699 2.693591 CTCGGGCTCAGGTACAATCTTA 59.306 50.000 0.00 0.00 0.00 2.10
1720 1865 0.374758 CGGTTTGTGATCAGCGATGG 59.625 55.000 0.00 0.00 35.95 3.51
1733 1878 1.141665 CGATGGCTGGACGATCACA 59.858 57.895 0.00 0.00 33.34 3.58
1843 2000 2.829120 GGCCCAAGGTAGCACAATTTAA 59.171 45.455 0.00 0.00 0.00 1.52
1845 2002 4.441495 GGCCCAAGGTAGCACAATTTAATC 60.441 45.833 0.00 0.00 0.00 1.75
1846 2003 4.159506 GCCCAAGGTAGCACAATTTAATCA 59.840 41.667 0.00 0.00 0.00 2.57
1847 2004 5.163416 GCCCAAGGTAGCACAATTTAATCAT 60.163 40.000 0.00 0.00 0.00 2.45
1848 2005 6.507023 CCCAAGGTAGCACAATTTAATCATC 58.493 40.000 0.00 0.00 0.00 2.92
1849 2006 6.096705 CCCAAGGTAGCACAATTTAATCATCA 59.903 38.462 0.00 0.00 0.00 3.07
1850 2007 7.363705 CCCAAGGTAGCACAATTTAATCATCAA 60.364 37.037 0.00 0.00 0.00 2.57
1988 2580 3.404899 TCACCGATGTTTTTCTACCCAC 58.595 45.455 0.00 0.00 0.00 4.61
2007 2599 2.346365 GGAACCGGTGGTCAGGAC 59.654 66.667 8.52 0.00 33.12 3.85
2034 2626 1.497278 CACCGTGAAACCGAGCATG 59.503 57.895 0.00 0.00 0.00 4.06
2040 2632 1.606668 GTGAAACCGAGCATGAACCAA 59.393 47.619 0.00 0.00 0.00 3.67
2332 2934 3.114616 CCGCTGAGACGTTGCTGG 61.115 66.667 0.00 0.00 0.00 4.85
2337 2939 0.803768 CTGAGACGTTGCTGGATCCG 60.804 60.000 7.39 3.14 0.00 4.18
2384 2986 1.202806 TGACTGCTCCACTCCCAAAAG 60.203 52.381 0.00 0.00 0.00 2.27
2427 3029 3.967987 ACTTCATGGGTCTGGTATCCTAC 59.032 47.826 0.00 0.00 0.00 3.18
2454 3056 3.606846 CGTGTGTTGGCTGTTGTTATGAG 60.607 47.826 0.00 0.00 0.00 2.90
2496 3098 0.461548 TGGTGGACGATGATCTGCTC 59.538 55.000 0.00 0.00 0.00 4.26
2769 3374 1.238439 CATTCAACTTGACGGCCACT 58.762 50.000 2.24 0.00 0.00 4.00
2790 3395 0.747283 CCTGTTGAGATGAGCCTGGC 60.747 60.000 11.65 11.65 0.00 4.85
2792 3397 1.452833 GTTGAGATGAGCCTGGCCC 60.453 63.158 16.57 3.45 0.00 5.80
2811 3416 2.416836 CCCTGCATTTGCTTGATCAGTG 60.417 50.000 3.94 0.00 42.66 3.66
2824 3429 0.979665 ATCAGTGAGTCCTGGTGGTG 59.020 55.000 0.00 0.00 33.14 4.17
2877 3482 2.740055 GTGCCGTGCTCTCCTGTG 60.740 66.667 0.00 0.00 0.00 3.66
2912 3517 4.412858 TGTCCAGTCCCCTTACAAACTTAA 59.587 41.667 0.00 0.00 0.00 1.85
2945 3550 1.000060 TGCATGAGGCTTCTGTTTTGC 60.000 47.619 0.00 0.06 45.15 3.68
2946 3551 1.670967 GCATGAGGCTTCTGTTTTGCC 60.671 52.381 0.00 0.00 46.42 4.52
2968 3573 1.888512 TGGTTTCCTTGCTCTGAATGC 59.111 47.619 0.00 0.00 0.00 3.56
2991 3596 6.917477 TGCAAAACTGTGATGAATTACAAGAC 59.083 34.615 0.00 0.00 0.00 3.01
2994 3599 6.808008 AACTGTGATGAATTACAAGACCAG 57.192 37.500 0.00 0.00 0.00 4.00
3008 3613 9.654663 ATTACAAGACCAGTGAACTCTTATTAC 57.345 33.333 0.00 0.00 0.00 1.89
3015 3620 9.303537 GACCAGTGAACTCTTATTACTGATAAC 57.696 37.037 0.00 0.00 40.80 1.89
3169 4187 5.977635 TCAGAATCACCATAACACTACCTG 58.022 41.667 0.00 0.00 0.00 4.00
3184 4220 6.289064 ACACTACCTGAGGAGTTTAACTTTG 58.711 40.000 4.99 0.00 0.00 2.77
3191 4227 7.067129 ACCTGAGGAGTTTAACTTTGTTCTTTC 59.933 37.037 4.99 0.00 0.00 2.62
3222 4259 4.655027 GATGCAGAACATGTGTATGTGTG 58.345 43.478 0.00 0.00 46.54 3.82
3234 4271 3.918591 GTGTATGTGTGTTCAGGTACTCG 59.081 47.826 0.00 0.00 34.60 4.18
3267 4304 1.868251 CGACTCCGAAGCGTACAGC 60.868 63.158 0.00 0.00 41.97 4.40
3331 4368 3.571590 GGAGACCTCTGGTGTATCTCAT 58.428 50.000 0.00 0.00 35.25 2.90
3357 4394 0.109132 CGATTTCAAGGGCCTGCAAC 60.109 55.000 6.92 0.00 0.00 4.17
3402 4439 1.075542 TTACAGCACGCCAAAGATCG 58.924 50.000 0.00 0.00 0.00 3.69
3428 4541 6.484540 CAATAACATAAAGTGCTGCTCTGAG 58.515 40.000 4.83 0.00 0.00 3.35
3429 4542 2.354259 ACATAAAGTGCTGCTCTGAGC 58.646 47.619 22.38 22.38 42.82 4.26
3503 4616 2.515523 CCTCCGGCTTGCTCCATG 60.516 66.667 0.00 0.00 0.00 3.66
3547 4660 5.347907 CCTCGTACAGAACACTGAAAATACC 59.652 44.000 0.00 0.00 35.80 2.73
3550 4663 5.694910 CGTACAGAACACTGAAAATACCACT 59.305 40.000 0.00 0.00 35.80 4.00
3553 4666 5.885912 ACAGAACACTGAAAATACCACTTGT 59.114 36.000 0.00 0.00 35.80 3.16
3554 4667 6.038271 ACAGAACACTGAAAATACCACTTGTC 59.962 38.462 0.00 0.00 35.80 3.18
3555 4668 6.038161 CAGAACACTGAAAATACCACTTGTCA 59.962 38.462 0.00 0.00 33.94 3.58
3559 7021 8.635765 ACACTGAAAATACCACTTGTCAATAT 57.364 30.769 0.00 0.00 0.00 1.28
3561 7023 7.970061 CACTGAAAATACCACTTGTCAATATGG 59.030 37.037 12.44 12.44 38.26 2.74
3562 7024 7.888021 ACTGAAAATACCACTTGTCAATATGGA 59.112 33.333 18.49 6.75 36.04 3.41
3577 7039 4.851639 ATATGGATAATCAGCTGGGGAC 57.148 45.455 15.13 2.26 0.00 4.46
3586 7048 2.668550 GCTGGGGACACCACGAAC 60.669 66.667 0.00 0.00 46.80 3.95
3587 7049 3.148084 CTGGGGACACCACGAACT 58.852 61.111 0.00 0.00 46.80 3.01
3589 7051 0.246635 CTGGGGACACCACGAACTAG 59.753 60.000 0.00 0.00 46.80 2.57
3590 7052 0.178955 TGGGGACACCACGAACTAGA 60.179 55.000 0.00 0.00 46.80 2.43
3592 7054 1.254954 GGGACACCACGAACTAGAGT 58.745 55.000 0.00 0.00 36.50 3.24
3594 7056 1.612463 GGACACCACGAACTAGAGTGT 59.388 52.381 0.00 0.00 43.99 3.55
3596 7058 1.612463 ACACCACGAACTAGAGTGTCC 59.388 52.381 0.00 0.00 37.05 4.02
3602 7072 1.828832 GAACTAGAGTGTCCGCATCG 58.171 55.000 0.00 0.00 0.00 3.84
3638 7108 0.955919 CGTTGGGGCTCTTCTTGTCC 60.956 60.000 0.00 0.00 0.00 4.02
3715 7185 7.175104 ACCATACTAAAATTCAGAAGGAGCAA 58.825 34.615 0.00 0.00 0.00 3.91
3716 7186 7.836183 ACCATACTAAAATTCAGAAGGAGCAAT 59.164 33.333 0.00 0.00 0.00 3.56
3717 7187 8.348507 CCATACTAAAATTCAGAAGGAGCAATC 58.651 37.037 0.00 0.00 0.00 2.67
3718 7188 8.896744 CATACTAAAATTCAGAAGGAGCAATCA 58.103 33.333 0.00 0.00 0.00 2.57
3719 7189 7.388460 ACTAAAATTCAGAAGGAGCAATCAG 57.612 36.000 0.00 0.00 0.00 2.90
3720 7190 7.170965 ACTAAAATTCAGAAGGAGCAATCAGA 58.829 34.615 0.00 0.00 0.00 3.27
3721 7191 5.893897 AAATTCAGAAGGAGCAATCAGAC 57.106 39.130 0.00 0.00 0.00 3.51
3722 7192 4.840716 ATTCAGAAGGAGCAATCAGACT 57.159 40.909 0.00 0.00 0.00 3.24
3723 7193 3.606595 TCAGAAGGAGCAATCAGACTG 57.393 47.619 0.00 0.00 0.00 3.51
3724 7194 3.168292 TCAGAAGGAGCAATCAGACTGA 58.832 45.455 7.80 7.80 0.00 3.41
3725 7195 3.580022 TCAGAAGGAGCAATCAGACTGAA 59.420 43.478 9.70 0.00 31.69 3.02
3726 7196 4.224594 TCAGAAGGAGCAATCAGACTGAAT 59.775 41.667 9.70 0.00 31.69 2.57
3727 7197 4.942483 CAGAAGGAGCAATCAGACTGAATT 59.058 41.667 9.70 2.04 0.00 2.17
3728 7198 6.070596 TCAGAAGGAGCAATCAGACTGAATTA 60.071 38.462 9.70 0.00 31.69 1.40
3729 7199 6.258287 CAGAAGGAGCAATCAGACTGAATTAG 59.742 42.308 9.70 1.15 0.00 1.73
3730 7200 4.450053 AGGAGCAATCAGACTGAATTAGC 58.550 43.478 9.70 10.85 0.00 3.09
3731 7201 4.163839 AGGAGCAATCAGACTGAATTAGCT 59.836 41.667 18.30 18.30 0.00 3.32
3732 7202 4.272991 GGAGCAATCAGACTGAATTAGCTG 59.727 45.833 21.37 9.83 34.14 4.24
3733 7203 4.841422 AGCAATCAGACTGAATTAGCTGT 58.159 39.130 9.70 0.00 34.35 4.40
3734 7204 4.634883 AGCAATCAGACTGAATTAGCTGTG 59.365 41.667 9.70 0.00 34.35 3.66
3735 7205 4.201891 GCAATCAGACTGAATTAGCTGTGG 60.202 45.833 9.70 0.00 34.35 4.17
3736 7206 5.181009 CAATCAGACTGAATTAGCTGTGGA 58.819 41.667 9.70 0.00 34.35 4.02
3737 7207 4.890158 TCAGACTGAATTAGCTGTGGAA 57.110 40.909 1.64 0.00 34.35 3.53
3738 7208 4.825422 TCAGACTGAATTAGCTGTGGAAG 58.175 43.478 1.64 0.00 34.35 3.46
3739 7209 4.528206 TCAGACTGAATTAGCTGTGGAAGA 59.472 41.667 1.64 0.00 34.35 2.87
3740 7210 4.869297 CAGACTGAATTAGCTGTGGAAGAG 59.131 45.833 0.00 0.00 0.00 2.85
3741 7211 4.530161 AGACTGAATTAGCTGTGGAAGAGT 59.470 41.667 0.00 0.00 0.00 3.24
3742 7212 5.012561 AGACTGAATTAGCTGTGGAAGAGTT 59.987 40.000 0.00 0.00 0.00 3.01
3743 7213 5.625150 ACTGAATTAGCTGTGGAAGAGTTT 58.375 37.500 0.00 0.00 0.00 2.66
3744 7214 5.703130 ACTGAATTAGCTGTGGAAGAGTTTC 59.297 40.000 0.00 0.00 0.00 2.78
3745 7215 5.620206 TGAATTAGCTGTGGAAGAGTTTCA 58.380 37.500 0.00 0.00 34.90 2.69
3746 7216 5.702670 TGAATTAGCTGTGGAAGAGTTTCAG 59.297 40.000 0.00 0.00 34.90 3.02
3747 7217 4.689612 TTAGCTGTGGAAGAGTTTCAGT 57.310 40.909 0.00 0.00 34.90 3.41
3748 7218 3.567478 AGCTGTGGAAGAGTTTCAGTT 57.433 42.857 0.00 0.00 34.90 3.16
3749 7219 3.891049 AGCTGTGGAAGAGTTTCAGTTT 58.109 40.909 0.00 0.00 34.90 2.66
3750 7220 3.629398 AGCTGTGGAAGAGTTTCAGTTTG 59.371 43.478 0.00 0.00 34.90 2.93
3751 7221 3.793465 GCTGTGGAAGAGTTTCAGTTTGC 60.793 47.826 0.00 0.00 34.90 3.68
3752 7222 3.620488 TGTGGAAGAGTTTCAGTTTGCT 58.380 40.909 0.00 0.00 34.90 3.91
3753 7223 3.378112 TGTGGAAGAGTTTCAGTTTGCTG 59.622 43.478 0.00 0.00 43.87 4.41
3754 7224 3.378427 GTGGAAGAGTTTCAGTTTGCTGT 59.622 43.478 0.00 0.00 43.05 4.40
3755 7225 3.627577 TGGAAGAGTTTCAGTTTGCTGTC 59.372 43.478 0.00 0.00 43.05 3.51
3756 7226 3.627577 GGAAGAGTTTCAGTTTGCTGTCA 59.372 43.478 0.00 0.00 43.05 3.58
3757 7227 4.260948 GGAAGAGTTTCAGTTTGCTGTCAG 60.261 45.833 0.00 0.00 43.05 3.51
3758 7228 4.142609 AGAGTTTCAGTTTGCTGTCAGA 57.857 40.909 3.32 0.00 43.05 3.27
3759 7229 3.873952 AGAGTTTCAGTTTGCTGTCAGAC 59.126 43.478 3.32 0.00 43.05 3.51
3760 7230 3.609853 AGTTTCAGTTTGCTGTCAGACA 58.390 40.909 3.32 2.48 43.05 3.41
3761 7231 4.009675 AGTTTCAGTTTGCTGTCAGACAA 58.990 39.130 4.41 4.88 43.05 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.873591 CGGGTTCAGGTTTTGTCTCTG 59.126 52.381 0.00 0.00 0.00 3.35
2 3 2.143925 CTCGGGTTCAGGTTTTGTCTC 58.856 52.381 0.00 0.00 0.00 3.36
3 4 1.202770 CCTCGGGTTCAGGTTTTGTCT 60.203 52.381 0.00 0.00 0.00 3.41
4 5 1.202722 TCCTCGGGTTCAGGTTTTGTC 60.203 52.381 0.00 0.00 32.20 3.18
6 7 1.975660 TTCCTCGGGTTCAGGTTTTG 58.024 50.000 0.00 0.00 32.20 2.44
7 8 2.740506 TTTCCTCGGGTTCAGGTTTT 57.259 45.000 0.00 0.00 32.20 2.43
8 9 2.740506 TTTTCCTCGGGTTCAGGTTT 57.259 45.000 0.00 0.00 32.20 3.27
9 10 2.971901 ATTTTCCTCGGGTTCAGGTT 57.028 45.000 0.00 0.00 32.20 3.50
10 11 4.376225 TTTATTTTCCTCGGGTTCAGGT 57.624 40.909 0.00 0.00 32.20 4.00
11 12 8.565416 GTTATATTTATTTTCCTCGGGTTCAGG 58.435 37.037 0.00 0.00 0.00 3.86
12 13 9.338622 AGTTATATTTATTTTCCTCGGGTTCAG 57.661 33.333 0.00 0.00 0.00 3.02
13 14 9.689501 AAGTTATATTTATTTTCCTCGGGTTCA 57.310 29.630 0.00 0.00 0.00 3.18
18 19 9.590088 GCGTTAAGTTATATTTATTTTCCTCGG 57.410 33.333 0.00 0.00 0.00 4.63
19 20 9.590088 GGCGTTAAGTTATATTTATTTTCCTCG 57.410 33.333 0.00 0.00 0.00 4.63
20 21 9.590088 CGGCGTTAAGTTATATTTATTTTCCTC 57.410 33.333 0.00 0.00 0.00 3.71
21 22 8.562052 CCGGCGTTAAGTTATATTTATTTTCCT 58.438 33.333 6.01 0.00 0.00 3.36
22 23 8.558700 TCCGGCGTTAAGTTATATTTATTTTCC 58.441 33.333 6.01 0.00 0.00 3.13
23 24 9.934190 TTCCGGCGTTAAGTTATATTTATTTTC 57.066 29.630 6.01 0.00 0.00 2.29
25 26 9.720667 GTTTCCGGCGTTAAGTTATATTTATTT 57.279 29.630 6.01 0.00 0.00 1.40
26 27 8.063630 CGTTTCCGGCGTTAAGTTATATTTATT 58.936 33.333 6.01 0.00 0.00 1.40
27 28 7.566709 CGTTTCCGGCGTTAAGTTATATTTAT 58.433 34.615 6.01 0.00 0.00 1.40
28 29 6.932051 CGTTTCCGGCGTTAAGTTATATTTA 58.068 36.000 6.01 0.00 0.00 1.40
29 30 5.798910 CGTTTCCGGCGTTAAGTTATATTT 58.201 37.500 6.01 0.00 0.00 1.40
30 31 5.393902 CGTTTCCGGCGTTAAGTTATATT 57.606 39.130 6.01 0.00 0.00 1.28
45 46 2.288640 ACTCCAACTCTTACCGTTTCCG 60.289 50.000 0.00 0.00 0.00 4.30
46 47 3.397849 ACTCCAACTCTTACCGTTTCC 57.602 47.619 0.00 0.00 0.00 3.13
47 48 4.874970 TGTACTCCAACTCTTACCGTTTC 58.125 43.478 0.00 0.00 0.00 2.78
48 49 4.942761 TGTACTCCAACTCTTACCGTTT 57.057 40.909 0.00 0.00 0.00 3.60
49 50 4.942761 TTGTACTCCAACTCTTACCGTT 57.057 40.909 0.00 0.00 0.00 4.44
50 51 4.942761 TTTGTACTCCAACTCTTACCGT 57.057 40.909 0.00 0.00 31.20 4.83
51 52 5.121768 CCAATTTGTACTCCAACTCTTACCG 59.878 44.000 0.00 0.00 31.20 4.02
52 53 6.235664 TCCAATTTGTACTCCAACTCTTACC 58.764 40.000 0.00 0.00 31.20 2.85
53 54 7.739498 TTCCAATTTGTACTCCAACTCTTAC 57.261 36.000 0.00 0.00 31.20 2.34
54 55 7.996644 ACTTTCCAATTTGTACTCCAACTCTTA 59.003 33.333 0.00 0.00 31.20 2.10
55 56 6.833933 ACTTTCCAATTTGTACTCCAACTCTT 59.166 34.615 0.00 0.00 31.20 2.85
56 57 6.365520 ACTTTCCAATTTGTACTCCAACTCT 58.634 36.000 0.00 0.00 31.20 3.24
57 58 6.635030 ACTTTCCAATTTGTACTCCAACTC 57.365 37.500 0.00 0.00 31.20 3.01
58 59 7.558444 TGTAACTTTCCAATTTGTACTCCAACT 59.442 33.333 0.00 0.00 31.20 3.16
59 60 7.708998 TGTAACTTTCCAATTTGTACTCCAAC 58.291 34.615 0.00 0.00 31.20 3.77
60 61 7.883391 TGTAACTTTCCAATTTGTACTCCAA 57.117 32.000 0.00 0.00 0.00 3.53
61 62 7.175990 GGATGTAACTTTCCAATTTGTACTCCA 59.824 37.037 0.00 0.00 31.99 3.86
62 63 7.535997 GGATGTAACTTTCCAATTTGTACTCC 58.464 38.462 0.00 0.00 31.99 3.85
63 64 7.241376 CGGATGTAACTTTCCAATTTGTACTC 58.759 38.462 0.00 0.00 31.99 2.59
64 65 6.150474 CCGGATGTAACTTTCCAATTTGTACT 59.850 38.462 0.00 0.00 31.99 2.73
65 66 6.319399 CCGGATGTAACTTTCCAATTTGTAC 58.681 40.000 0.00 0.00 31.99 2.90
66 67 5.416326 CCCGGATGTAACTTTCCAATTTGTA 59.584 40.000 0.73 0.00 31.99 2.41
67 68 4.219725 CCCGGATGTAACTTTCCAATTTGT 59.780 41.667 0.73 0.00 31.99 2.83
68 69 4.381505 CCCCGGATGTAACTTTCCAATTTG 60.382 45.833 0.73 0.00 31.99 2.32
69 70 3.767131 CCCCGGATGTAACTTTCCAATTT 59.233 43.478 0.73 0.00 31.99 1.82
70 71 3.245479 ACCCCGGATGTAACTTTCCAATT 60.245 43.478 0.73 0.00 31.99 2.32
71 72 2.310647 ACCCCGGATGTAACTTTCCAAT 59.689 45.455 0.73 0.00 31.99 3.16
72 73 1.706305 ACCCCGGATGTAACTTTCCAA 59.294 47.619 0.73 0.00 31.99 3.53
73 74 1.003812 CACCCCGGATGTAACTTTCCA 59.996 52.381 0.73 0.00 31.99 3.53
74 75 1.003928 ACACCCCGGATGTAACTTTCC 59.996 52.381 0.73 0.00 0.00 3.13
75 76 2.484742 ACACCCCGGATGTAACTTTC 57.515 50.000 0.73 0.00 0.00 2.62
76 77 2.963599 AACACCCCGGATGTAACTTT 57.036 45.000 0.73 0.00 0.00 2.66
77 78 2.638855 TGTAACACCCCGGATGTAACTT 59.361 45.455 0.73 0.00 0.00 2.66
78 79 2.235402 CTGTAACACCCCGGATGTAACT 59.765 50.000 0.73 0.00 0.00 2.24
79 80 2.234414 TCTGTAACACCCCGGATGTAAC 59.766 50.000 0.73 0.05 0.00 2.50
80 81 2.498481 CTCTGTAACACCCCGGATGTAA 59.502 50.000 0.73 0.00 0.00 2.41
81 82 2.104967 CTCTGTAACACCCCGGATGTA 58.895 52.381 0.73 0.00 0.00 2.29
82 83 0.902531 CTCTGTAACACCCCGGATGT 59.097 55.000 0.73 3.79 0.00 3.06
83 84 0.178068 CCTCTGTAACACCCCGGATG 59.822 60.000 0.73 2.98 0.00 3.51
84 85 0.042131 TCCTCTGTAACACCCCGGAT 59.958 55.000 0.73 0.00 0.00 4.18
85 86 0.042131 ATCCTCTGTAACACCCCGGA 59.958 55.000 0.73 0.00 0.00 5.14
86 87 0.464452 GATCCTCTGTAACACCCCGG 59.536 60.000 0.00 0.00 0.00 5.73
87 88 1.409427 GAGATCCTCTGTAACACCCCG 59.591 57.143 0.00 0.00 0.00 5.73
88 89 1.763545 GGAGATCCTCTGTAACACCCC 59.236 57.143 0.00 0.00 0.00 4.95
89 90 1.409427 CGGAGATCCTCTGTAACACCC 59.591 57.143 0.00 0.00 32.64 4.61
90 91 1.409427 CCGGAGATCCTCTGTAACACC 59.591 57.143 0.00 0.00 35.27 4.16
91 92 1.409427 CCCGGAGATCCTCTGTAACAC 59.591 57.143 0.73 0.00 35.27 3.32
92 93 1.688311 CCCCGGAGATCCTCTGTAACA 60.688 57.143 0.73 0.00 35.27 2.41
93 94 1.041437 CCCCGGAGATCCTCTGTAAC 58.959 60.000 0.73 0.00 35.27 2.50
94 95 0.635009 ACCCCGGAGATCCTCTGTAA 59.365 55.000 0.73 0.00 35.27 2.41
95 96 0.185416 GACCCCGGAGATCCTCTGTA 59.815 60.000 0.73 0.00 35.27 2.74
96 97 1.075896 GACCCCGGAGATCCTCTGT 60.076 63.158 0.73 0.00 35.27 3.41
97 98 1.075970 TGACCCCGGAGATCCTCTG 60.076 63.158 0.73 0.00 36.69 3.35
98 99 1.231641 CTGACCCCGGAGATCCTCT 59.768 63.158 0.73 0.00 0.00 3.69
203 204 2.919839 TGGAAACCACCAAGGCGA 59.080 55.556 0.00 0.00 43.14 5.54
240 241 1.147824 CCTCCTTGATGGCAGCGAT 59.852 57.895 0.00 0.00 35.26 4.58
278 279 4.704833 AAGTGATGCCGGCGCTGT 62.705 61.111 23.90 7.64 35.36 4.40
303 304 1.763968 GGGGGAATTACCTTCTGTGC 58.236 55.000 6.68 0.00 38.98 4.57
323 324 2.620115 TCTCCAACAGAAAAGCTTGCAG 59.380 45.455 0.00 0.00 0.00 4.41
376 377 0.747644 ATCATCGCCATGGACGCAAA 60.748 50.000 18.40 7.38 0.00 3.68
382 383 1.434188 AACCCTATCATCGCCATGGA 58.566 50.000 18.40 0.00 0.00 3.41
575 593 1.006043 TCCTTCTCGGACTCCTCATGT 59.994 52.381 0.00 0.00 36.69 3.21
576 594 1.769026 TCCTTCTCGGACTCCTCATG 58.231 55.000 0.00 0.00 36.69 3.07
577 595 2.498078 GTTTCCTTCTCGGACTCCTCAT 59.502 50.000 0.00 0.00 42.97 2.90
578 596 1.893801 GTTTCCTTCTCGGACTCCTCA 59.106 52.381 0.00 0.00 42.97 3.86
747 794 8.281212 AGAAAAATGACAGCCGTCTAATTAAT 57.719 30.769 1.05 0.00 43.06 1.40
757 804 2.704572 AGAGGAGAAAAATGACAGCCG 58.295 47.619 0.00 0.00 0.00 5.52
794 841 3.132289 TGATGTAGAGGCCTAAGGTTTCG 59.868 47.826 4.42 0.00 0.00 3.46
801 848 3.678806 CGTTGCTTGATGTAGAGGCCTAA 60.679 47.826 4.42 0.00 0.00 2.69
802 849 2.159099 CGTTGCTTGATGTAGAGGCCTA 60.159 50.000 4.42 0.00 0.00 3.93
803 850 1.406069 CGTTGCTTGATGTAGAGGCCT 60.406 52.381 3.86 3.86 0.00 5.19
827 874 3.634448 CAGAGGGTGATGTCGACTAAGAT 59.366 47.826 17.92 0.83 0.00 2.40
862 932 5.163343 TGGTTTAGCCCACTCACATCTATAC 60.163 44.000 0.00 0.00 36.04 1.47
983 1076 2.161855 CCATTCCAGTGCTGCTTTACA 58.838 47.619 0.00 0.00 0.00 2.41
990 1092 1.271543 TGTTCCTCCATTCCAGTGCTG 60.272 52.381 0.00 0.00 0.00 4.41
1004 1106 3.005791 CGAATTTGAGGGCTTTTGTTCCT 59.994 43.478 0.00 0.00 0.00 3.36
1113 1225 4.201930 GCAGTGCAGACTATTCGTACTACT 60.202 45.833 11.09 0.00 0.00 2.57
1114 1226 4.036352 GCAGTGCAGACTATTCGTACTAC 58.964 47.826 11.09 0.00 0.00 2.73
1115 1227 3.692593 TGCAGTGCAGACTATTCGTACTA 59.307 43.478 15.37 0.00 33.32 1.82
1128 1240 0.968901 AATCCATGGGTGCAGTGCAG 60.969 55.000 20.42 6.15 40.08 4.41
1129 1241 0.966875 GAATCCATGGGTGCAGTGCA 60.967 55.000 15.37 15.37 35.60 4.57
1130 1242 1.669999 GGAATCCATGGGTGCAGTGC 61.670 60.000 13.02 8.58 0.00 4.40
1131 1243 0.323633 TGGAATCCATGGGTGCAGTG 60.324 55.000 13.02 0.00 0.00 3.66
1132 1244 0.632835 ATGGAATCCATGGGTGCAGT 59.367 50.000 14.96 0.00 43.39 4.40
1213 1325 0.826672 AGGAGGACGTCGACCAAGTT 60.827 55.000 24.31 7.55 0.00 2.66
1408 1520 3.626670 AGAAGAGAAGATACGTACCGGTG 59.373 47.826 19.93 3.27 0.00 4.94
1432 1544 5.745514 CATGCATTAATTCGTCTCTCCAAG 58.254 41.667 0.00 0.00 0.00 3.61
1435 1547 3.561310 TGCATGCATTAATTCGTCTCTCC 59.439 43.478 18.46 0.00 0.00 3.71
1469 1603 0.760945 AGGTCAGGGAATCGGGCTAG 60.761 60.000 0.00 0.00 0.00 3.42
1480 1614 5.990120 AAATCAAGAATTCAAGGTCAGGG 57.010 39.130 8.44 0.00 0.00 4.45
1482 1616 9.007901 AGAACTAAATCAAGAATTCAAGGTCAG 57.992 33.333 8.44 0.00 0.00 3.51
1554 1699 2.434884 CGCATCGTGGGTGAAGCT 60.435 61.111 0.00 0.00 30.73 3.74
1580 1725 0.323629 CCTTCAGGTTCGGCTGGTTA 59.676 55.000 0.00 0.00 0.00 2.85
1720 1865 2.509336 CCGGTGTGATCGTCCAGC 60.509 66.667 0.00 0.00 0.00 4.85
1768 1925 3.682292 AAGGCGGCCTCGGATTCAC 62.682 63.158 24.08 0.00 36.79 3.18
1845 2002 8.394121 GCTTCAACTTCTAGGAGTAAATTGATG 58.606 37.037 3.45 7.91 0.00 3.07
1846 2003 8.103305 TGCTTCAACTTCTAGGAGTAAATTGAT 58.897 33.333 3.45 0.00 0.00 2.57
1847 2004 7.450074 TGCTTCAACTTCTAGGAGTAAATTGA 58.550 34.615 3.45 1.37 0.00 2.57
1848 2005 7.672983 TGCTTCAACTTCTAGGAGTAAATTG 57.327 36.000 3.45 0.00 0.00 2.32
1849 2006 8.870075 AATGCTTCAACTTCTAGGAGTAAATT 57.130 30.769 3.45 0.00 0.00 1.82
1850 2007 8.870075 AAATGCTTCAACTTCTAGGAGTAAAT 57.130 30.769 3.45 0.00 0.00 1.40
2019 2611 0.165944 GGTTCATGCTCGGTTTCACG 59.834 55.000 0.00 0.00 0.00 4.35
2040 2632 3.502211 CACTGGGAGTTGCTACGATTTTT 59.498 43.478 0.00 0.00 0.00 1.94
2148 2746 0.721718 GAAGCAGGTCCACGAAATCG 59.278 55.000 0.48 0.48 46.33 3.34
2160 2758 1.160137 CCAAGAAACCGAGAAGCAGG 58.840 55.000 0.00 0.00 0.00 4.85
2332 2934 4.315941 CGGGCTAAGGGGCGGATC 62.316 72.222 0.00 0.00 42.03 3.36
2337 2939 2.124695 CAGAACGGGCTAAGGGGC 60.125 66.667 0.00 0.00 40.05 5.80
2384 2986 1.566018 CTTTGGTTCCACGGCGTCTC 61.566 60.000 10.85 0.23 0.00 3.36
2427 3029 2.941333 CAGCCAACACACGAGCTG 59.059 61.111 0.00 0.00 45.92 4.24
2496 3098 3.138798 GCAGAGGCCTGGTGCATG 61.139 66.667 25.51 10.12 43.89 4.06
2769 3374 0.035725 CAGGCTCATCTCAACAGGCA 60.036 55.000 0.00 0.00 35.19 4.75
2790 3395 1.822990 ACTGATCAAGCAAATGCAGGG 59.177 47.619 8.28 0.00 45.16 4.45
2792 3397 3.190744 ACTCACTGATCAAGCAAATGCAG 59.809 43.478 8.28 0.00 45.16 4.41
2811 3416 0.182775 AACAACCACCACCAGGACTC 59.817 55.000 0.00 0.00 38.69 3.36
2824 3429 8.172484 GTCAAATTAAACAGAACCAAAACAACC 58.828 33.333 0.00 0.00 0.00 3.77
2877 3482 3.621715 GGGACTGGACAAAACGATCATAC 59.378 47.826 0.00 0.00 0.00 2.39
2912 3517 3.021695 CCTCATGCATTCAGACACCAAT 58.978 45.455 0.00 0.00 0.00 3.16
2945 3550 0.250295 TCAGAGCAAGGAAACCACGG 60.250 55.000 0.00 0.00 0.00 4.94
2946 3551 1.593196 TTCAGAGCAAGGAAACCACG 58.407 50.000 0.00 0.00 0.00 4.94
2968 3573 7.424803 TGGTCTTGTAATTCATCACAGTTTTG 58.575 34.615 0.00 0.00 0.00 2.44
2991 3596 8.188799 TCGTTATCAGTAATAAGAGTTCACTGG 58.811 37.037 0.00 0.00 37.72 4.00
2994 3599 9.731819 TCATCGTTATCAGTAATAAGAGTTCAC 57.268 33.333 0.00 0.00 30.39 3.18
3008 3613 5.527582 CCCCCTTACTTTTCATCGTTATCAG 59.472 44.000 0.00 0.00 0.00 2.90
3015 3620 2.747446 CACACCCCCTTACTTTTCATCG 59.253 50.000 0.00 0.00 0.00 3.84
3125 4141 1.869767 GATCATTGTCATGGCCTCGAC 59.130 52.381 15.78 15.78 0.00 4.20
3169 4187 6.913132 GCTGAAAGAACAAAGTTAAACTCCTC 59.087 38.462 0.00 0.00 34.07 3.71
3184 4220 1.595609 CATCGCGTTGCTGAAAGAAC 58.404 50.000 5.77 0.00 34.07 3.01
3191 4227 1.510623 GTTCTGCATCGCGTTGCTG 60.511 57.895 34.25 32.69 43.18 4.41
3222 4259 1.202428 GCCTGATCCGAGTACCTGAAC 60.202 57.143 0.00 0.00 0.00 3.18
3234 4271 3.838271 TCGAGCACCGCCTGATCC 61.838 66.667 0.00 0.00 38.37 3.36
3267 4304 5.347093 CGATGATGTGGAGGAGATTAAATCG 59.653 44.000 0.00 0.00 0.00 3.34
3331 4368 2.307686 AGGCCCTTGAAATCGTTCCTTA 59.692 45.455 0.00 0.00 32.28 2.69
3402 4439 4.096984 AGAGCAGCACTTTATGTTATTGCC 59.903 41.667 0.00 0.00 33.48 4.52
3503 4616 1.810755 GTTTTCCCCATGTCGTTCCTC 59.189 52.381 0.00 0.00 0.00 3.71
3547 4660 7.308408 CCAGCTGATTATCCATATTGACAAGTG 60.308 40.741 17.39 0.00 0.00 3.16
3550 4663 6.005823 CCCAGCTGATTATCCATATTGACAA 58.994 40.000 17.39 0.00 0.00 3.18
3553 4666 4.851540 TCCCCAGCTGATTATCCATATTGA 59.148 41.667 17.39 0.00 0.00 2.57
3554 4667 4.946157 GTCCCCAGCTGATTATCCATATTG 59.054 45.833 17.39 0.00 0.00 1.90
3555 4668 4.603171 TGTCCCCAGCTGATTATCCATATT 59.397 41.667 17.39 0.00 0.00 1.28
3559 7021 1.490490 GTGTCCCCAGCTGATTATCCA 59.510 52.381 17.39 0.83 0.00 3.41
3561 7023 1.490490 TGGTGTCCCCAGCTGATTATC 59.510 52.381 17.39 2.18 38.72 1.75
3562 7024 1.212935 GTGGTGTCCCCAGCTGATTAT 59.787 52.381 17.39 0.00 46.45 1.28
3577 7039 1.401148 CGGACACTCTAGTTCGTGGTG 60.401 57.143 11.97 0.00 35.79 4.17
3611 7081 0.250770 AGAGCCCCAACGGAAAACTC 60.251 55.000 0.00 0.00 0.00 3.01
3614 7084 0.476771 AGAAGAGCCCCAACGGAAAA 59.523 50.000 0.00 0.00 0.00 2.29
3638 7108 0.865769 GCATATTTCTGTACCCCGCG 59.134 55.000 0.00 0.00 0.00 6.46
3677 7147 6.494893 TTTAGTATGGTTGCTGATGTTCAC 57.505 37.500 0.00 0.00 0.00 3.18
3715 7185 5.188555 TCTTCCACAGCTAATTCAGTCTGAT 59.811 40.000 2.68 0.00 34.45 2.90
3716 7186 4.528206 TCTTCCACAGCTAATTCAGTCTGA 59.472 41.667 0.00 0.00 34.45 3.27
3717 7187 4.825422 TCTTCCACAGCTAATTCAGTCTG 58.175 43.478 0.00 0.00 35.66 3.51
3718 7188 4.530161 ACTCTTCCACAGCTAATTCAGTCT 59.470 41.667 0.00 0.00 0.00 3.24
3719 7189 4.826556 ACTCTTCCACAGCTAATTCAGTC 58.173 43.478 0.00 0.00 0.00 3.51
3720 7190 4.899352 ACTCTTCCACAGCTAATTCAGT 57.101 40.909 0.00 0.00 0.00 3.41
3721 7191 5.702670 TGAAACTCTTCCACAGCTAATTCAG 59.297 40.000 0.00 0.00 0.00 3.02
3722 7192 5.620206 TGAAACTCTTCCACAGCTAATTCA 58.380 37.500 0.00 0.00 0.00 2.57
3723 7193 5.703130 ACTGAAACTCTTCCACAGCTAATTC 59.297 40.000 0.00 0.00 32.67 2.17
3724 7194 5.625150 ACTGAAACTCTTCCACAGCTAATT 58.375 37.500 0.00 0.00 32.67 1.40
3725 7195 5.234466 ACTGAAACTCTTCCACAGCTAAT 57.766 39.130 0.00 0.00 32.67 1.73
3726 7196 4.689612 ACTGAAACTCTTCCACAGCTAA 57.310 40.909 0.00 0.00 32.67 3.09
3727 7197 4.689612 AACTGAAACTCTTCCACAGCTA 57.310 40.909 0.00 0.00 32.67 3.32
3728 7198 3.567478 AACTGAAACTCTTCCACAGCT 57.433 42.857 0.00 0.00 32.67 4.24
3729 7199 3.793465 GCAAACTGAAACTCTTCCACAGC 60.793 47.826 0.00 0.00 32.67 4.40
3730 7200 3.629398 AGCAAACTGAAACTCTTCCACAG 59.371 43.478 0.00 0.00 35.14 3.66
3731 7201 3.620488 AGCAAACTGAAACTCTTCCACA 58.380 40.909 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.