Multiple sequence alignment - TraesCS1A01G026300

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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 TraesCS1A01G026300 chr1A 100.000 5223 0 0 1 5223 12573420 12568198 0.000000e+00 9646.0
1 TraesCS1A01G026300 chr1A 88.162 2002 185 15 3225 5220 13415026 13416981 0.000000e+00 2337.0
2 TraesCS1A01G026300 chr1A 87.879 1782 177 13 3443 5220 13348567 13350313 0.000000e+00 2058.0
3 TraesCS1A01G026300 chr1A 89.393 1565 150 6 3659 5220 13570986 13572537 0.000000e+00 1956.0
4 TraesCS1A01G026300 chr1A 94.611 1169 52 10 1192 2354 23184343 23183180 0.000000e+00 1799.0
5 TraesCS1A01G026300 chr1A 88.751 1449 143 15 3778 5220 13454591 13456025 0.000000e+00 1755.0
6 TraesCS1A01G026300 chr1A 95.388 1019 41 3 2368 3380 13569710 13570728 0.000000e+00 1616.0
7 TraesCS1A01G026300 chr1A 86.690 1450 178 12 3778 5223 22614518 22613080 0.000000e+00 1594.0
8 TraesCS1A01G026300 chr1A 93.032 1019 52 4 2368 3380 13347566 13348571 0.000000e+00 1471.0
9 TraesCS1A01G026300 chr1A 81.697 1049 102 47 173 1191 13346592 13347580 0.000000e+00 791.0
10 TraesCS1A01G026300 chr1A 83.467 375 43 11 835 1191 13453097 13453470 1.080000e-86 331.0
11 TraesCS1A01G026300 chr1A 90.244 123 7 3 225 347 22617917 22617800 7.000000e-34 156.0
12 TraesCS1A01G026300 chr1A 91.346 104 9 0 468 571 13413519 13413622 5.450000e-30 143.0
13 TraesCS1A01G026300 chr1A 83.962 106 8 4 786 890 22616330 22616233 5.570000e-15 93.5
14 TraesCS1A01G026300 chr1B 92.071 2863 205 15 2368 5223 17018756 17015909 0.000000e+00 4010.0
15 TraesCS1A01G026300 chr1B 85.637 738 96 7 2368 3098 16856576 16857310 0.000000e+00 767.0
16 TraesCS1A01G026300 chr1B 85.346 737 101 4 2368 3098 16530206 16530941 0.000000e+00 756.0
17 TraesCS1A01G026300 chr1B 91.131 327 29 0 867 1193 16876556 16876882 1.330000e-120 444.0
18 TraesCS1A01G026300 chr1B 88.767 365 28 6 445 800 16876183 16876543 8.030000e-118 435.0
19 TraesCS1A01G026300 chr1B 87.739 261 20 3 943 1191 16518177 16518437 1.420000e-75 294.0
20 TraesCS1A01G026300 chr1B 92.746 193 14 0 999 1191 17018934 17018742 3.980000e-71 279.0
21 TraesCS1A01G026300 chr1B 80.952 378 37 18 848 1191 16529844 16530220 3.100000e-67 267.0
22 TraesCS1A01G026300 chr1B 85.057 261 27 5 943 1191 16839484 16839744 6.710000e-64 255.0
23 TraesCS1A01G026300 chr1B 78.818 203 20 12 73 275 16875878 16876057 1.190000e-21 115.0
24 TraesCS1A01G026300 chr1B 90.361 83 3 3 256 337 16528355 16528433 2.570000e-18 104.0
25 TraesCS1A01G026300 chr1D 89.700 2000 190 7 3225 5219 11289045 11291033 0.000000e+00 2538.0
26 TraesCS1A01G026300 chr1D 92.330 1356 70 12 2368 3707 11273291 11274628 0.000000e+00 1897.0
27 TraesCS1A01G026300 chr1D 88.003 1417 159 9 3808 5220 11319548 11320957 0.000000e+00 1664.0
28 TraesCS1A01G026300 chr1D 86.552 1450 180 14 3776 5220 11455521 11456960 0.000000e+00 1583.0
29 TraesCS1A01G026300 chr1D 88.173 1319 149 4 3904 5220 11495875 11497188 0.000000e+00 1565.0
30 TraesCS1A01G026300 chr1D 85.655 1450 192 13 3778 5220 11178354 11179794 0.000000e+00 1511.0
31 TraesCS1A01G026300 chr1D 82.976 793 129 5 2368 3159 11288239 11289026 0.000000e+00 712.0
32 TraesCS1A01G026300 chr1D 87.406 397 37 4 795 1191 11494082 11494465 1.330000e-120 444.0
33 TraesCS1A01G026300 chr1D 83.862 378 40 9 835 1191 11176863 11177240 1.800000e-89 340.0
34 TraesCS1A01G026300 chr1D 84.762 105 8 3 786 890 11452840 11452936 1.200000e-16 99.0
35 TraesCS1A01G026300 chr2B 94.234 1162 53 9 1198 2354 765485890 765484738 0.000000e+00 1762.0
36 TraesCS1A01G026300 chr2B 93.579 1168 61 11 1193 2354 493261534 493262693 0.000000e+00 1729.0
37 TraesCS1A01G026300 chr6B 94.002 1167 61 7 1193 2354 23290612 23291774 0.000000e+00 1759.0
38 TraesCS1A01G026300 chr2A 94.062 1162 60 8 1199 2354 578666691 578667849 0.000000e+00 1755.0
39 TraesCS1A01G026300 chr2D 93.729 1164 65 6 1195 2354 21619631 21620790 0.000000e+00 1738.0
40 TraesCS1A01G026300 chr7D 92.876 1165 74 7 1194 2354 382650647 382651806 0.000000e+00 1683.0
41 TraesCS1A01G026300 chr5B 94.301 1088 53 8 1192 2274 262051122 262052205 0.000000e+00 1657.0
42 TraesCS1A01G026300 chr5B 87.324 71 5 2 3703 3772 623210517 623210584 1.560000e-10 78.7
43 TraesCS1A01G026300 chr5B 87.324 71 5 2 3703 3772 626871913 626871980 1.560000e-10 78.7
44 TraesCS1A01G026300 chr5B 88.889 63 4 3 3700 3762 576291932 576291991 2.020000e-09 75.0
45 TraesCS1A01G026300 chr3B 93.060 1124 68 9 1192 2310 880511 881629 0.000000e+00 1635.0
46 TraesCS1A01G026300 chrUn 86.111 684 83 7 2368 3045 317005059 317004382 0.000000e+00 726.0
47 TraesCS1A01G026300 chrUn 86.111 684 83 7 2368 3045 317984859 317984182 0.000000e+00 726.0
48 TraesCS1A01G026300 chrUn 90.659 182 17 0 1010 1191 317005226 317005045 5.230000e-60 243.0
49 TraesCS1A01G026300 chrUn 81.281 203 33 5 3778 3976 2473980 2473779 5.410000e-35 159.0
50 TraesCS1A01G026300 chrUn 81.281 203 33 5 3778 3976 317983600 317983399 5.410000e-35 159.0
51 TraesCS1A01G026300 chr4A 89.706 68 6 1 3706 3772 608607690 608607623 9.320000e-13 86.1
52 TraesCS1A01G026300 chr6D 86.567 67 8 1 3706 3772 93529420 93529485 7.260000e-09 73.1
53 TraesCS1A01G026300 chr3A 85.507 69 7 1 3706 3774 568019717 568019782 9.390000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G026300 chr1A 12568198 12573420 5222 True 9646.000000 9646 100.000000 1 5223 1 chr1A.!!$R1 5222
1 TraesCS1A01G026300 chr1A 23183180 23184343 1163 True 1799.000000 1799 94.611000 1192 2354 1 chr1A.!!$R2 1162
2 TraesCS1A01G026300 chr1A 13569710 13572537 2827 False 1786.000000 1956 92.390500 2368 5220 2 chr1A.!!$F4 2852
3 TraesCS1A01G026300 chr1A 13346592 13350313 3721 False 1440.000000 2058 87.536000 173 5220 3 chr1A.!!$F1 5047
4 TraesCS1A01G026300 chr1A 13413519 13416981 3462 False 1240.000000 2337 89.754000 468 5220 2 chr1A.!!$F2 4752
5 TraesCS1A01G026300 chr1A 13453097 13456025 2928 False 1043.000000 1755 86.109000 835 5220 2 chr1A.!!$F3 4385
6 TraesCS1A01G026300 chr1A 22613080 22617917 4837 True 614.500000 1594 86.965333 225 5223 3 chr1A.!!$R3 4998
7 TraesCS1A01G026300 chr1B 17015909 17018934 3025 True 2144.500000 4010 92.408500 999 5223 2 chr1B.!!$R1 4224
8 TraesCS1A01G026300 chr1B 16856576 16857310 734 False 767.000000 767 85.637000 2368 3098 1 chr1B.!!$F3 730
9 TraesCS1A01G026300 chr1B 16528355 16530941 2586 False 375.666667 756 85.553000 256 3098 3 chr1B.!!$F4 2842
10 TraesCS1A01G026300 chr1B 16875878 16876882 1004 False 331.333333 444 86.238667 73 1193 3 chr1B.!!$F5 1120
11 TraesCS1A01G026300 chr1D 11273291 11274628 1337 False 1897.000000 1897 92.330000 2368 3707 1 chr1D.!!$F1 1339
12 TraesCS1A01G026300 chr1D 11319548 11320957 1409 False 1664.000000 1664 88.003000 3808 5220 1 chr1D.!!$F2 1412
13 TraesCS1A01G026300 chr1D 11288239 11291033 2794 False 1625.000000 2538 86.338000 2368 5219 2 chr1D.!!$F4 2851
14 TraesCS1A01G026300 chr1D 11494082 11497188 3106 False 1004.500000 1565 87.789500 795 5220 2 chr1D.!!$F6 4425
15 TraesCS1A01G026300 chr1D 11176863 11179794 2931 False 925.500000 1511 84.758500 835 5220 2 chr1D.!!$F3 4385
16 TraesCS1A01G026300 chr1D 11452840 11456960 4120 False 841.000000 1583 85.657000 786 5220 2 chr1D.!!$F5 4434
17 TraesCS1A01G026300 chr2B 765484738 765485890 1152 True 1762.000000 1762 94.234000 1198 2354 1 chr2B.!!$R1 1156
18 TraesCS1A01G026300 chr2B 493261534 493262693 1159 False 1729.000000 1729 93.579000 1193 2354 1 chr2B.!!$F1 1161
19 TraesCS1A01G026300 chr6B 23290612 23291774 1162 False 1759.000000 1759 94.002000 1193 2354 1 chr6B.!!$F1 1161
20 TraesCS1A01G026300 chr2A 578666691 578667849 1158 False 1755.000000 1755 94.062000 1199 2354 1 chr2A.!!$F1 1155
21 TraesCS1A01G026300 chr2D 21619631 21620790 1159 False 1738.000000 1738 93.729000 1195 2354 1 chr2D.!!$F1 1159
22 TraesCS1A01G026300 chr7D 382650647 382651806 1159 False 1683.000000 1683 92.876000 1194 2354 1 chr7D.!!$F1 1160
23 TraesCS1A01G026300 chr5B 262051122 262052205 1083 False 1657.000000 1657 94.301000 1192 2274 1 chr5B.!!$F1 1082
24 TraesCS1A01G026300 chr3B 880511 881629 1118 False 1635.000000 1635 93.060000 1192 2310 1 chr3B.!!$F1 1118
25 TraesCS1A01G026300 chrUn 317004382 317005226 844 True 484.500000 726 88.385000 1010 3045 2 chrUn.!!$R2 2035
26 TraesCS1A01G026300 chrUn 317983399 317984859 1460 True 442.500000 726 83.696000 2368 3976 2 chrUn.!!$R3 1608

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
408 1547 0.037326 CGCCTGGTATACATCCGCAT 60.037 55.0 5.01 0.00 0.00 4.73 F
1245 3505 0.394488 TCCAAAGCAACCAACACCGA 60.394 50.0 0.00 0.00 0.00 4.69 F
1719 3983 0.536460 ATGGCAAACGAAACGGGACT 60.536 50.0 0.00 0.00 0.00 3.85 F
2366 4639 0.104671 GGAGGAGAGCAGCTCATGTC 59.895 60.0 24.64 15.66 45.81 3.06 F
2895 5177 0.604243 CATTTGTCCCCGTCGGTCAA 60.604 55.0 11.06 9.73 37.81 3.18 F
3662 6153 1.372582 GCAAATCAGTGCTCCGATCA 58.627 50.0 0.00 0.00 41.51 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2357 4630 0.035630 GACTTGCCTGGACATGAGCT 60.036 55.0 0.00 0.0 0.00 4.09 R
2363 4636 0.183492 AAGCTTGACTTGCCTGGACA 59.817 50.0 0.00 0.0 37.17 4.02 R
3454 5913 0.409484 AAGGGTAGCCTTTGGTGCAT 59.591 50.0 20.62 0.0 0.00 3.96 R
3638 6129 0.610232 GGAGCACTGATTTGCCCACT 60.610 55.0 0.00 0.0 44.14 4.00 R
4151 6744 0.958822 AACAATTCGGGCTTGGTGAC 59.041 50.0 0.00 0.0 0.00 3.67 R
5009 7609 0.676782 CAGGGTGCTACTTTTCCCCG 60.677 60.0 0.00 0.0 40.70 5.73 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 2.715536 GGCAAACCGAACAGAACCT 58.284 52.632 0.00 0.00 0.00 3.50
21 22 0.310854 GGCAAACCGAACAGAACCTG 59.689 55.000 0.00 0.00 37.52 4.00
22 23 1.305201 GCAAACCGAACAGAACCTGA 58.695 50.000 0.45 0.00 35.18 3.86
23 24 1.002792 GCAAACCGAACAGAACCTGAC 60.003 52.381 0.45 0.00 35.18 3.51
24 25 2.285083 CAAACCGAACAGAACCTGACA 58.715 47.619 0.45 0.00 35.18 3.58
25 26 2.878406 CAAACCGAACAGAACCTGACAT 59.122 45.455 0.45 0.00 35.18 3.06
26 27 2.930826 ACCGAACAGAACCTGACATT 57.069 45.000 0.45 0.00 35.18 2.71
27 28 3.208747 ACCGAACAGAACCTGACATTT 57.791 42.857 0.45 0.00 35.18 2.32
28 29 3.551846 ACCGAACAGAACCTGACATTTT 58.448 40.909 0.45 0.00 35.18 1.82
29 30 3.564225 ACCGAACAGAACCTGACATTTTC 59.436 43.478 0.45 0.00 35.18 2.29
30 31 3.363970 CCGAACAGAACCTGACATTTTCG 60.364 47.826 0.45 5.55 35.91 3.46
31 32 3.493129 CGAACAGAACCTGACATTTTCGA 59.507 43.478 9.54 0.00 37.24 3.71
32 33 4.608445 CGAACAGAACCTGACATTTTCGAC 60.608 45.833 9.54 0.00 37.24 4.20
33 34 3.804036 ACAGAACCTGACATTTTCGACA 58.196 40.909 0.45 0.00 35.18 4.35
34 35 4.389374 ACAGAACCTGACATTTTCGACAT 58.611 39.130 0.45 0.00 35.18 3.06
35 36 4.452455 ACAGAACCTGACATTTTCGACATC 59.548 41.667 0.45 0.00 35.18 3.06
36 37 4.692625 CAGAACCTGACATTTTCGACATCT 59.307 41.667 0.00 0.00 32.44 2.90
37 38 5.180117 CAGAACCTGACATTTTCGACATCTT 59.820 40.000 0.00 0.00 32.44 2.40
38 39 5.180117 AGAACCTGACATTTTCGACATCTTG 59.820 40.000 0.00 0.00 0.00 3.02
39 40 4.389374 ACCTGACATTTTCGACATCTTGT 58.611 39.130 0.00 0.00 0.00 3.16
40 41 4.452455 ACCTGACATTTTCGACATCTTGTC 59.548 41.667 0.00 0.00 43.65 3.18
50 51 2.489971 GACATCTTGTCGACCCAAACA 58.510 47.619 14.12 0.00 37.67 2.83
51 52 2.875933 GACATCTTGTCGACCCAAACAA 59.124 45.455 14.12 0.00 37.67 2.83
52 53 3.283751 ACATCTTGTCGACCCAAACAAA 58.716 40.909 14.12 0.00 35.13 2.83
53 54 3.066203 ACATCTTGTCGACCCAAACAAAC 59.934 43.478 14.12 0.00 35.13 2.93
54 55 2.712709 TCTTGTCGACCCAAACAAACA 58.287 42.857 14.12 0.00 35.13 2.83
55 56 3.082548 TCTTGTCGACCCAAACAAACAA 58.917 40.909 14.12 0.00 35.13 2.83
56 57 3.506455 TCTTGTCGACCCAAACAAACAAA 59.494 39.130 14.12 0.00 35.13 2.83
57 58 3.936372 TGTCGACCCAAACAAACAAAA 57.064 38.095 14.12 0.00 0.00 2.44
58 59 4.252971 TGTCGACCCAAACAAACAAAAA 57.747 36.364 14.12 0.00 0.00 1.94
81 82 0.678395 AACCAAATCCGTGCAATGCA 59.322 45.000 2.72 2.72 35.60 3.96
87 88 1.184431 ATCCGTGCAATGCATTCCAA 58.816 45.000 12.38 0.00 41.91 3.53
111 112 1.725641 CACAAGCGGTGCATCTTCTA 58.274 50.000 0.00 0.00 41.36 2.10
112 113 1.662629 CACAAGCGGTGCATCTTCTAG 59.337 52.381 0.00 0.00 41.36 2.43
113 114 1.276421 ACAAGCGGTGCATCTTCTAGT 59.724 47.619 0.00 0.00 0.00 2.57
114 115 2.496070 ACAAGCGGTGCATCTTCTAGTA 59.504 45.455 0.00 0.00 0.00 1.82
115 116 2.860735 CAAGCGGTGCATCTTCTAGTAC 59.139 50.000 0.00 0.00 0.00 2.73
132 133 7.228314 TCTAGTACAGTAGTGCTTTGTGATT 57.772 36.000 0.00 0.00 41.21 2.57
133 134 7.090808 TCTAGTACAGTAGTGCTTTGTGATTG 58.909 38.462 0.00 0.00 41.21 2.67
134 135 5.853936 AGTACAGTAGTGCTTTGTGATTGA 58.146 37.500 0.00 0.00 37.41 2.57
135 136 5.696724 AGTACAGTAGTGCTTTGTGATTGAC 59.303 40.000 0.00 0.00 37.41 3.18
136 137 3.494626 ACAGTAGTGCTTTGTGATTGACG 59.505 43.478 0.00 0.00 0.00 4.35
137 138 3.740832 CAGTAGTGCTTTGTGATTGACGA 59.259 43.478 0.00 0.00 0.00 4.20
138 139 4.389992 CAGTAGTGCTTTGTGATTGACGAT 59.610 41.667 0.00 0.00 0.00 3.73
139 140 3.818961 AGTGCTTTGTGATTGACGATG 57.181 42.857 0.00 0.00 0.00 3.84
140 141 3.402110 AGTGCTTTGTGATTGACGATGA 58.598 40.909 0.00 0.00 0.00 2.92
141 142 4.005650 AGTGCTTTGTGATTGACGATGAT 58.994 39.130 0.00 0.00 0.00 2.45
142 143 4.093514 GTGCTTTGTGATTGACGATGATG 58.906 43.478 0.00 0.00 0.00 3.07
143 144 3.103738 GCTTTGTGATTGACGATGATGC 58.896 45.455 0.00 0.00 0.00 3.91
144 145 3.181503 GCTTTGTGATTGACGATGATGCT 60.182 43.478 0.00 0.00 0.00 3.79
145 146 4.340263 CTTTGTGATTGACGATGATGCTG 58.660 43.478 0.00 0.00 0.00 4.41
146 147 2.282407 TGTGATTGACGATGATGCTGG 58.718 47.619 0.00 0.00 0.00 4.85
147 148 1.003116 GTGATTGACGATGATGCTGGC 60.003 52.381 0.00 0.00 0.00 4.85
148 149 0.590195 GATTGACGATGATGCTGGCC 59.410 55.000 0.00 0.00 0.00 5.36
149 150 0.107066 ATTGACGATGATGCTGGCCA 60.107 50.000 4.71 4.71 0.00 5.36
150 151 1.026182 TTGACGATGATGCTGGCCAC 61.026 55.000 0.00 0.00 0.00 5.01
151 152 2.124570 ACGATGATGCTGGCCACC 60.125 61.111 0.00 0.00 0.00 4.61
152 153 2.124612 CGATGATGCTGGCCACCA 60.125 61.111 0.00 0.52 0.00 4.17
153 154 1.750018 CGATGATGCTGGCCACCAA 60.750 57.895 0.00 0.00 30.80 3.67
157 158 4.666253 ATGCTGGCCACCAAGCGT 62.666 61.111 0.00 1.49 32.91 5.07
162 163 3.683937 GGCCACCAAGCGTTGCAT 61.684 61.111 0.00 0.00 34.79 3.96
194 195 3.434179 ACCCACCCACCCAAAGCA 61.434 61.111 0.00 0.00 0.00 3.91
195 196 2.917227 CCCACCCACCCAAAGCAC 60.917 66.667 0.00 0.00 0.00 4.40
196 197 2.198426 CCACCCACCCAAAGCACT 59.802 61.111 0.00 0.00 0.00 4.40
197 198 1.903404 CCACCCACCCAAAGCACTC 60.903 63.158 0.00 0.00 0.00 3.51
198 199 1.903404 CACCCACCCAAAGCACTCC 60.903 63.158 0.00 0.00 0.00 3.85
200 201 2.845345 CCCACCCAAAGCACTCCCT 61.845 63.158 0.00 0.00 0.00 4.20
201 202 1.153756 CCACCCAAAGCACTCCCTT 59.846 57.895 0.00 0.00 0.00 3.95
203 204 0.961753 CACCCAAAGCACTCCCTTTC 59.038 55.000 0.00 0.00 32.97 2.62
239 246 1.745115 CCCACATCCAACGCATCGT 60.745 57.895 0.00 0.00 43.97 3.73
288 295 6.202188 CCAAAAGCATTACGTACTATTCCGAT 59.798 38.462 0.00 0.00 0.00 4.18
320 334 3.748048 TCTATCTTGACTGCTGTTGTTGC 59.252 43.478 0.00 0.00 0.00 4.17
350 1467 2.764547 CCTCCGTCTCCCCTTCCC 60.765 72.222 0.00 0.00 0.00 3.97
368 1485 2.248423 TCCCCTCATTCTCATCTCCTCA 59.752 50.000 0.00 0.00 0.00 3.86
373 1490 4.082625 CCTCATTCTCATCTCCTCATCTCG 60.083 50.000 0.00 0.00 0.00 4.04
381 1498 2.739943 TCTCCTCATCTCGTCCATTGT 58.260 47.619 0.00 0.00 0.00 2.71
394 1533 3.112075 ATTGTGTCGCGTCGCCTG 61.112 61.111 12.44 0.00 0.00 4.85
397 1536 4.409218 GTGTCGCGTCGCCTGGTA 62.409 66.667 12.44 0.00 0.00 3.25
398 1537 3.445687 TGTCGCGTCGCCTGGTAT 61.446 61.111 12.44 0.00 0.00 2.73
400 1539 1.656569 GTCGCGTCGCCTGGTATAC 60.657 63.158 12.44 0.00 0.00 1.47
401 1540 2.114051 TCGCGTCGCCTGGTATACA 61.114 57.895 12.44 0.00 0.00 2.29
404 1543 0.666577 GCGTCGCCTGGTATACATCC 60.667 60.000 5.75 0.00 0.00 3.51
405 1544 0.386858 CGTCGCCTGGTATACATCCG 60.387 60.000 5.01 2.04 0.00 4.18
407 1546 1.110518 TCGCCTGGTATACATCCGCA 61.111 55.000 5.01 0.00 0.00 5.69
408 1547 0.037326 CGCCTGGTATACATCCGCAT 60.037 55.000 5.01 0.00 0.00 4.73
409 1548 1.442769 GCCTGGTATACATCCGCATG 58.557 55.000 5.01 0.00 35.92 4.06
411 1550 1.270785 CCTGGTATACATCCGCATGCA 60.271 52.381 19.57 0.00 32.57 3.96
414 1553 2.009774 GGTATACATCCGCATGCATCC 58.990 52.381 19.57 2.88 32.57 3.51
415 1554 2.615240 GGTATACATCCGCATGCATCCA 60.615 50.000 19.57 0.00 32.57 3.41
418 1557 1.007734 CATCCGCATGCATCCAAGC 60.008 57.895 19.57 0.00 32.59 4.01
419 1558 1.152819 ATCCGCATGCATCCAAGCT 60.153 52.632 19.57 0.00 33.71 3.74
423 1562 1.734137 GCATGCATCCAAGCTCCAG 59.266 57.895 14.21 0.00 33.14 3.86
433 1572 0.673022 CAAGCTCCAGTGAGTGCTCC 60.673 60.000 8.11 0.00 40.95 4.70
434 1573 2.125753 GCTCCAGTGAGTGCTCCG 60.126 66.667 0.00 0.00 40.95 4.63
440 1579 4.767255 GTGAGTGCTCCGCCCCTG 62.767 72.222 0.00 0.00 0.00 4.45
526 1679 6.474751 GCAATGCTTGGATCTAAAAACTGATC 59.525 38.462 0.00 0.00 38.56 2.92
528 1681 7.707624 ATGCTTGGATCTAAAAACTGATCAA 57.292 32.000 0.00 0.00 40.41 2.57
540 1702 5.893897 AAACTGATCAATTCTCCTGCTTC 57.106 39.130 0.00 0.00 0.00 3.86
560 1743 3.603532 TCAGAGTCTCATCCATTTGTGC 58.396 45.455 1.94 0.00 0.00 4.57
597 1794 3.114606 TCCAGGGTAGCAAGAATCATGA 58.885 45.455 0.00 0.00 0.00 3.07
637 1837 1.871676 CAGGATGCATCGAATCCACTG 59.128 52.381 20.15 14.97 45.24 3.66
639 1839 2.371179 AGGATGCATCGAATCCACTGAT 59.629 45.455 20.15 0.00 45.24 2.90
710 1918 5.707298 ACATCCACACCTTCTTGTTAATCTG 59.293 40.000 0.00 0.00 0.00 2.90
732 1947 3.671702 GCACCTTCTTGTTAATCTGCTGC 60.672 47.826 0.00 0.00 0.00 5.25
745 1960 5.747951 AATCTGCTGCTTTGCTAGATTAC 57.252 39.130 8.38 0.00 38.14 1.89
752 1967 5.453587 GCTGCTTTGCTAGATTACAAATTCG 59.546 40.000 0.00 0.00 35.38 3.34
763 1981 7.979444 AGATTACAAATTCGTCTTCTTCCAA 57.021 32.000 0.00 0.00 0.00 3.53
804 2115 2.673523 GCATCTGGCCTCTGGTGT 59.326 61.111 3.32 0.00 36.11 4.16
805 2116 1.748122 GCATCTGGCCTCTGGTGTG 60.748 63.158 3.32 0.00 36.11 3.82
806 2117 1.748122 CATCTGGCCTCTGGTGTGC 60.748 63.158 3.32 0.00 0.00 4.57
834 2157 1.667830 CGCTTCCGCTTCCTTGTCA 60.668 57.895 0.00 0.00 0.00 3.58
1014 3274 1.873270 CGGTCATGGAGGTCGTCACA 61.873 60.000 0.00 0.00 0.00 3.58
1040 3300 2.774351 GGGCTGCCTACTCCCCAT 60.774 66.667 19.68 0.00 37.46 4.00
1044 3304 1.410850 GCTGCCTACTCCCCATGCTA 61.411 60.000 0.00 0.00 0.00 3.49
1089 3349 1.298264 CTTGCACAAGCGCGTCAAA 60.298 52.632 8.43 0.00 46.23 2.69
1193 3453 1.334869 CGACAGGCAAGTCAAGCTTTT 59.665 47.619 0.00 0.00 38.43 2.27
1194 3454 2.223572 CGACAGGCAAGTCAAGCTTTTT 60.224 45.455 0.00 0.00 38.43 1.94
1243 3503 2.908688 ATTCCAAAGCAACCAACACC 57.091 45.000 0.00 0.00 0.00 4.16
1244 3504 0.457851 TTCCAAAGCAACCAACACCG 59.542 50.000 0.00 0.00 0.00 4.94
1245 3505 0.394488 TCCAAAGCAACCAACACCGA 60.394 50.000 0.00 0.00 0.00 4.69
1246 3506 0.673437 CCAAAGCAACCAACACCGAT 59.327 50.000 0.00 0.00 0.00 4.18
1247 3507 1.883275 CCAAAGCAACCAACACCGATA 59.117 47.619 0.00 0.00 0.00 2.92
1248 3508 2.351350 CCAAAGCAACCAACACCGATAC 60.351 50.000 0.00 0.00 0.00 2.24
1249 3509 2.264005 AAGCAACCAACACCGATACA 57.736 45.000 0.00 0.00 0.00 2.29
1250 3510 1.808411 AGCAACCAACACCGATACAG 58.192 50.000 0.00 0.00 0.00 2.74
1251 3511 0.802494 GCAACCAACACCGATACAGG 59.198 55.000 0.00 0.00 37.30 4.00
1254 3514 2.467566 ACCAACACCGATACAGGAAC 57.532 50.000 0.00 0.00 34.73 3.62
1291 3553 3.618150 CACAACAAGCCCAAAAGAAACAG 59.382 43.478 0.00 0.00 0.00 3.16
1297 3559 6.179756 ACAAGCCCAAAAGAAACAGAAAAAT 58.820 32.000 0.00 0.00 0.00 1.82
1300 3562 8.672815 CAAGCCCAAAAGAAACAGAAAAATAAA 58.327 29.630 0.00 0.00 0.00 1.40
1326 3588 3.882888 AGAGAAAAGAATGCCAACAACGA 59.117 39.130 0.00 0.00 0.00 3.85
1396 3660 1.293498 CACCACGCTCCTAGCACTT 59.707 57.895 0.00 0.00 42.58 3.16
1512 3776 0.843343 GGGTGAGGTGGAAGGGGTAA 60.843 60.000 0.00 0.00 0.00 2.85
1526 3790 2.818274 GTAAGCCCGACGCCCTTG 60.818 66.667 8.05 0.00 38.78 3.61
1630 3894 1.391933 CGACCCCAGACGATCCATCA 61.392 60.000 0.00 0.00 32.72 3.07
1719 3983 0.536460 ATGGCAAACGAAACGGGACT 60.536 50.000 0.00 0.00 0.00 3.85
1737 4001 1.135527 ACTGACGGAAACAAGACGACA 59.864 47.619 0.00 0.00 0.00 4.35
1912 4176 3.485431 CTGCAGAACGCGAGCCAG 61.485 66.667 15.93 7.85 46.97 4.85
2285 4553 2.040359 GAAGGGGAGGAGGGGGAG 60.040 72.222 0.00 0.00 0.00 4.30
2286 4554 3.711782 AAGGGGAGGAGGGGGAGG 61.712 72.222 0.00 0.00 0.00 4.30
2361 4634 3.160748 GGGGGAGGAGAGCAGCTC 61.161 72.222 15.25 15.25 43.17 4.09
2362 4635 2.364842 GGGGAGGAGAGCAGCTCA 60.365 66.667 24.64 0.00 45.81 4.26
2363 4636 1.765657 GGGGAGGAGAGCAGCTCAT 60.766 63.158 24.64 9.77 45.81 2.90
2364 4637 1.446791 GGGAGGAGAGCAGCTCATG 59.553 63.158 24.64 0.00 45.81 3.07
2365 4638 1.336632 GGGAGGAGAGCAGCTCATGT 61.337 60.000 24.64 7.64 45.81 3.21
2366 4639 0.104671 GGAGGAGAGCAGCTCATGTC 59.895 60.000 24.64 15.66 45.81 3.06
2446 4719 1.462283 TCGTCGACAAGTTCCTCGTAG 59.538 52.381 17.16 0.00 0.00 3.51
2515 4794 4.470664 AGGAGCTCAAGAACAAGATGATCT 59.529 41.667 17.19 0.00 30.32 2.75
2555 4834 4.000331 AGAATCACCATCGAATAGCTGG 58.000 45.455 0.00 0.36 41.73 4.85
2571 4850 0.819582 CTGGCGCCATCAAGGAAATT 59.180 50.000 32.87 0.00 41.22 1.82
2693 4972 2.076863 GGCTTTGTACACAGAAGCGAT 58.923 47.619 19.45 0.00 45.04 4.58
2895 5177 0.604243 CATTTGTCCCCGTCGGTCAA 60.604 55.000 11.06 9.73 37.81 3.18
2964 5269 4.524328 GGAAAATCCCACTCAGATGTTGTT 59.476 41.667 0.00 0.00 0.00 2.83
3066 5376 9.587772 AAAATGATACTACTATGATATGTCCGC 57.412 33.333 0.00 0.00 0.00 5.54
3084 5394 2.101582 CCGCTTCCTATGCTAGTTGTCT 59.898 50.000 0.00 0.00 0.00 3.41
3308 5710 6.909357 GCAATTGGTCTAAGAAATTCATCTCG 59.091 38.462 7.72 0.00 0.00 4.04
3330 5750 4.612712 CGGCGTTGTACATTTCATCAAAGT 60.613 41.667 0.00 0.00 0.00 2.66
3441 5898 4.777366 CCCACCCCATTAAAACAAAGATCT 59.223 41.667 0.00 0.00 0.00 2.75
3454 5913 4.323417 ACAAAGATCTAAACGGTGCATCA 58.677 39.130 0.00 0.00 0.00 3.07
3552 6037 3.799963 CCTTTTCGCCTTGTTTACAAACC 59.200 43.478 2.55 0.00 38.11 3.27
3620 6111 2.233922 GAGTCTCCGGGAAGTTCATCAA 59.766 50.000 0.00 0.00 0.00 2.57
3638 6129 7.234661 TCATCAACGGCCATACAGTATATTA 57.765 36.000 2.24 0.00 0.00 0.98
3662 6153 1.372582 GCAAATCAGTGCTCCGATCA 58.627 50.000 0.00 0.00 41.51 2.92
3671 6208 4.129380 CAGTGCTCCGATCATTCCAATAA 58.871 43.478 0.00 0.00 0.00 1.40
3746 6283 4.870221 AAGTGTCGTGGTTTTAGTTCAC 57.130 40.909 0.00 0.00 0.00 3.18
3768 6306 5.123820 CACACAATATTTTGGATCAGACGGT 59.876 40.000 6.56 0.00 37.15 4.83
3781 6319 6.148150 TGGATCAGACGGTGTAACAAATTAAC 59.852 38.462 0.00 0.00 39.98 2.01
3787 6325 7.170320 CAGACGGTGTAACAAATTAACTGTACT 59.830 37.037 0.00 0.00 39.98 2.73
3932 6524 2.037121 TGTCAAGATTGAGACGCCTGAA 59.963 45.455 0.00 0.00 37.98 3.02
3936 6528 3.176552 AGATTGAGACGCCTGAATCTG 57.823 47.619 12.28 0.00 46.69 2.90
4037 6630 7.956328 TGTGATGTCTATAGACCTTACACTT 57.044 36.000 26.37 2.56 44.15 3.16
4255 6849 2.172293 ACTGATGATTCCAGAAGGCTCC 59.828 50.000 0.00 0.00 35.69 4.70
4287 6881 6.214412 AGAGAATATTTCCTGACAAGAGTGGT 59.786 38.462 0.00 0.00 0.00 4.16
4460 7054 6.398918 GCTCTGGACTAACAGAAGATAACAA 58.601 40.000 0.00 0.00 46.05 2.83
4479 7073 3.452627 ACAATTTAGAGGAGATGCGGAGT 59.547 43.478 0.00 0.00 0.00 3.85
4495 7089 4.022242 TGCGGAGTATACTATCTTTCAGCC 60.022 45.833 5.09 0.00 0.00 4.85
4632 7226 2.557229 CCACCATGGAAATCAAGGGACA 60.557 50.000 21.47 0.00 40.96 4.02
4655 7249 3.191371 AGCCTGTTTTTGCTCGGATTAAG 59.809 43.478 0.00 0.00 30.33 1.85
4815 7409 6.871035 TGTATTGGATGGTACTAGGGATAGT 58.129 40.000 0.00 0.00 0.00 2.12
4849 7449 1.263217 GCAATGTTCGTCGTTTGTCCT 59.737 47.619 0.00 0.00 0.00 3.85
4962 7562 7.899172 TCTGCTATTAATATCTTACCAGCCCTA 59.101 37.037 0.00 0.00 0.00 3.53
4996 7596 3.058914 AGTTTTGCGTGTACTTGATCTGC 60.059 43.478 0.00 0.00 0.00 4.26
4998 7598 0.608130 TGCGTGTACTTGATCTGCCT 59.392 50.000 0.00 0.00 0.00 4.75
5003 7603 3.128764 CGTGTACTTGATCTGCCTCACTA 59.871 47.826 0.00 0.00 0.00 2.74
5005 7605 5.665459 GTGTACTTGATCTGCCTCACTATT 58.335 41.667 0.00 0.00 0.00 1.73
5009 7609 6.107901 ACTTGATCTGCCTCACTATTATCC 57.892 41.667 0.00 0.00 0.00 2.59
5024 7624 2.994186 TATCCGGGGAAAAGTAGCAC 57.006 50.000 0.00 0.00 0.00 4.40
5155 7755 4.826274 TTGGAGGTGTTGGATCTTAGAG 57.174 45.455 0.00 0.00 0.00 2.43
5162 7762 4.706962 GGTGTTGGATCTTAGAGGCAATTT 59.293 41.667 0.00 0.00 0.00 1.82
5172 7772 5.877012 TCTTAGAGGCAATTTTGAGCTACAG 59.123 40.000 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.002792 GTCAGGTTCTGTTCGGTTTGC 60.003 52.381 0.00 0.00 32.61 3.68
6 7 2.930826 ATGTCAGGTTCTGTTCGGTT 57.069 45.000 0.00 0.00 32.61 4.44
7 8 2.930826 AATGTCAGGTTCTGTTCGGT 57.069 45.000 0.00 0.00 32.61 4.69
8 9 3.363970 CGAAAATGTCAGGTTCTGTTCGG 60.364 47.826 8.66 0.00 34.04 4.30
9 10 3.493129 TCGAAAATGTCAGGTTCTGTTCG 59.507 43.478 9.70 9.70 36.78 3.95
10 11 4.272504 TGTCGAAAATGTCAGGTTCTGTTC 59.727 41.667 0.00 0.00 32.61 3.18
11 12 4.196193 TGTCGAAAATGTCAGGTTCTGTT 58.804 39.130 0.00 0.00 32.61 3.16
12 13 3.804036 TGTCGAAAATGTCAGGTTCTGT 58.196 40.909 0.00 0.00 32.61 3.41
13 14 4.692625 AGATGTCGAAAATGTCAGGTTCTG 59.307 41.667 0.00 0.00 0.00 3.02
14 15 4.899502 AGATGTCGAAAATGTCAGGTTCT 58.100 39.130 0.00 0.00 0.00 3.01
15 16 5.049405 ACAAGATGTCGAAAATGTCAGGTTC 60.049 40.000 0.00 0.00 0.00 3.62
16 17 4.821805 ACAAGATGTCGAAAATGTCAGGTT 59.178 37.500 0.00 0.00 0.00 3.50
17 18 4.389374 ACAAGATGTCGAAAATGTCAGGT 58.611 39.130 0.00 0.00 0.00 4.00
18 19 4.962693 GACAAGATGTCGAAAATGTCAGG 58.037 43.478 12.24 0.00 37.67 3.86
30 31 2.489971 TGTTTGGGTCGACAAGATGTC 58.510 47.619 18.91 0.39 43.65 3.06
31 32 2.631160 TGTTTGGGTCGACAAGATGT 57.369 45.000 18.91 0.00 0.00 3.06
32 33 3.066064 TGTTTGTTTGGGTCGACAAGATG 59.934 43.478 18.91 0.00 37.12 2.90
33 34 3.283751 TGTTTGTTTGGGTCGACAAGAT 58.716 40.909 18.91 0.00 37.12 2.40
34 35 2.712709 TGTTTGTTTGGGTCGACAAGA 58.287 42.857 18.91 0.00 37.12 3.02
35 36 3.495670 TTGTTTGTTTGGGTCGACAAG 57.504 42.857 18.91 0.00 37.12 3.16
36 37 3.936372 TTTGTTTGTTTGGGTCGACAA 57.064 38.095 18.91 0.40 34.22 3.18
37 38 3.936372 TTTTGTTTGTTTGGGTCGACA 57.064 38.095 18.91 0.00 0.00 4.35
55 56 4.065321 TGCACGGATTTGGTTCATTTTT 57.935 36.364 0.00 0.00 0.00 1.94
56 57 3.742433 TGCACGGATTTGGTTCATTTT 57.258 38.095 0.00 0.00 0.00 1.82
57 58 3.742433 TTGCACGGATTTGGTTCATTT 57.258 38.095 0.00 0.00 0.00 2.32
58 59 3.587923 CATTGCACGGATTTGGTTCATT 58.412 40.909 0.00 0.00 0.00 2.57
59 60 2.674747 GCATTGCACGGATTTGGTTCAT 60.675 45.455 3.15 0.00 0.00 2.57
60 61 1.336702 GCATTGCACGGATTTGGTTCA 60.337 47.619 3.15 0.00 0.00 3.18
61 62 1.336702 TGCATTGCACGGATTTGGTTC 60.337 47.619 7.38 0.00 31.71 3.62
62 63 0.678395 TGCATTGCACGGATTTGGTT 59.322 45.000 7.38 0.00 31.71 3.67
63 64 0.896923 ATGCATTGCACGGATTTGGT 59.103 45.000 14.66 0.00 43.04 3.67
64 65 1.928503 GAATGCATTGCACGGATTTGG 59.071 47.619 18.59 0.00 43.04 3.28
65 66 1.928503 GGAATGCATTGCACGGATTTG 59.071 47.619 24.25 0.00 43.04 2.32
66 67 1.549620 TGGAATGCATTGCACGGATTT 59.450 42.857 27.41 3.60 43.04 2.17
67 68 1.184431 TGGAATGCATTGCACGGATT 58.816 45.000 27.41 4.02 43.04 3.01
68 69 1.184431 TTGGAATGCATTGCACGGAT 58.816 45.000 30.36 0.00 43.04 4.18
69 70 0.964700 TTTGGAATGCATTGCACGGA 59.035 45.000 30.36 15.56 43.04 4.69
70 71 1.067706 TCTTTGGAATGCATTGCACGG 60.068 47.619 30.36 23.95 43.04 4.94
71 72 2.350899 TCTTTGGAATGCATTGCACG 57.649 45.000 30.36 23.30 43.04 5.34
81 82 2.034558 CACCGCTTGTGTTCTTTGGAAT 59.965 45.455 0.00 0.00 40.26 3.01
111 112 5.696724 GTCAATCACAAAGCACTACTGTACT 59.303 40.000 0.00 0.00 0.00 2.73
112 113 5.388475 CGTCAATCACAAAGCACTACTGTAC 60.388 44.000 0.00 0.00 0.00 2.90
113 114 4.684242 CGTCAATCACAAAGCACTACTGTA 59.316 41.667 0.00 0.00 0.00 2.74
114 115 3.494626 CGTCAATCACAAAGCACTACTGT 59.505 43.478 0.00 0.00 0.00 3.55
115 116 3.740832 TCGTCAATCACAAAGCACTACTG 59.259 43.478 0.00 0.00 0.00 2.74
132 133 1.450134 GTGGCCAGCATCATCGTCA 60.450 57.895 5.11 0.00 0.00 4.35
133 134 2.182842 GGTGGCCAGCATCATCGTC 61.183 63.158 29.70 1.66 0.00 4.20
134 135 2.124570 GGTGGCCAGCATCATCGT 60.125 61.111 29.70 0.00 0.00 3.73
135 136 1.721664 CTTGGTGGCCAGCATCATCG 61.722 60.000 36.37 18.68 38.73 3.84
136 137 2.012902 GCTTGGTGGCCAGCATCATC 62.013 60.000 36.37 21.16 38.73 2.92
137 138 2.056223 GCTTGGTGGCCAGCATCAT 61.056 57.895 36.37 0.00 38.73 2.45
138 139 2.677524 GCTTGGTGGCCAGCATCA 60.678 61.111 36.37 22.50 38.73 3.07
139 140 3.818787 CGCTTGGTGGCCAGCATC 61.819 66.667 36.37 27.63 38.73 3.91
140 141 4.666253 ACGCTTGGTGGCCAGCAT 62.666 61.111 36.37 20.28 38.73 3.79
141 142 4.892965 AACGCTTGGTGGCCAGCA 62.893 61.111 33.13 33.13 33.81 4.41
142 143 4.347453 CAACGCTTGGTGGCCAGC 62.347 66.667 28.15 28.15 33.81 4.85
143 144 4.347453 GCAACGCTTGGTGGCCAG 62.347 66.667 5.11 0.00 39.89 4.85
145 146 2.713927 AAATGCAACGCTTGGTGGCC 62.714 55.000 0.00 0.00 45.63 5.36
146 147 1.284297 GAAATGCAACGCTTGGTGGC 61.284 55.000 0.00 0.00 46.45 5.01
147 148 0.314935 AGAAATGCAACGCTTGGTGG 59.685 50.000 0.00 0.00 0.00 4.61
148 149 2.138596 AAGAAATGCAACGCTTGGTG 57.861 45.000 0.00 0.00 0.00 4.17
149 150 2.545742 GGAAAGAAATGCAACGCTTGGT 60.546 45.455 0.00 0.00 0.00 3.67
150 151 2.061028 GGAAAGAAATGCAACGCTTGG 58.939 47.619 0.00 0.00 0.00 3.61
151 152 2.472488 GTGGAAAGAAATGCAACGCTTG 59.528 45.455 0.00 0.00 0.00 4.01
152 153 2.742774 GTGGAAAGAAATGCAACGCTT 58.257 42.857 0.00 0.00 0.00 4.68
153 154 1.334960 CGTGGAAAGAAATGCAACGCT 60.335 47.619 0.00 0.00 0.00 5.07
157 158 0.316841 GGGCGTGGAAAGAAATGCAA 59.683 50.000 0.00 0.00 0.00 4.08
161 162 0.898326 GGGTGGGCGTGGAAAGAAAT 60.898 55.000 0.00 0.00 0.00 2.17
162 163 1.529713 GGGTGGGCGTGGAAAGAAA 60.530 57.895 0.00 0.00 0.00 2.52
194 195 4.914581 AGGTAAAGAAGAAGGAAAGGGAGT 59.085 41.667 0.00 0.00 0.00 3.85
195 196 5.506730 AGGTAAAGAAGAAGGAAAGGGAG 57.493 43.478 0.00 0.00 0.00 4.30
196 197 5.133830 ACAAGGTAAAGAAGAAGGAAAGGGA 59.866 40.000 0.00 0.00 0.00 4.20
197 198 5.386060 ACAAGGTAAAGAAGAAGGAAAGGG 58.614 41.667 0.00 0.00 0.00 3.95
198 199 5.473846 GGACAAGGTAAAGAAGAAGGAAAGG 59.526 44.000 0.00 0.00 0.00 3.11
200 201 5.103855 TGGGACAAGGTAAAGAAGAAGGAAA 60.104 40.000 0.00 0.00 31.92 3.13
201 202 4.414182 TGGGACAAGGTAAAGAAGAAGGAA 59.586 41.667 0.00 0.00 31.92 3.36
203 204 4.072839 GTGGGACAAGGTAAAGAAGAAGG 58.927 47.826 0.00 0.00 44.16 3.46
239 246 4.459330 TCATGTGTTTGTTCATCAGTGGA 58.541 39.130 0.00 0.00 0.00 4.02
288 295 5.536538 AGCAGTCAAGATAGATACGAATCCA 59.463 40.000 0.00 0.00 31.98 3.41
320 334 0.682855 ACGGAGGAGCAGAGGAAGAG 60.683 60.000 0.00 0.00 0.00 2.85
350 1467 4.082625 CGAGATGAGGAGATGAGAATGAGG 60.083 50.000 0.00 0.00 0.00 3.86
368 1485 0.802222 CGCGACACAATGGACGAGAT 60.802 55.000 0.00 0.00 0.00 2.75
373 1490 2.769617 CGACGCGACACAATGGAC 59.230 61.111 15.93 0.00 0.00 4.02
381 1498 2.114051 TATACCAGGCGACGCGACA 61.114 57.895 15.93 0.00 37.34 4.35
394 1533 2.009774 GGATGCATGCGGATGTATACC 58.990 52.381 19.63 17.26 35.26 2.73
396 1535 3.337358 CTTGGATGCATGCGGATGTATA 58.663 45.455 19.63 3.51 35.26 1.47
397 1536 2.156917 CTTGGATGCATGCGGATGTAT 58.843 47.619 19.69 19.69 37.59 2.29
398 1537 1.596603 CTTGGATGCATGCGGATGTA 58.403 50.000 18.65 14.78 31.50 2.29
400 1539 1.007734 GCTTGGATGCATGCGGATG 60.008 57.895 13.21 13.21 0.00 3.51
401 1540 1.152819 AGCTTGGATGCATGCGGAT 60.153 52.632 17.39 0.91 34.99 4.18
404 1543 2.060004 CTGGAGCTTGGATGCATGCG 62.060 60.000 17.39 1.08 34.99 4.73
405 1544 1.035932 ACTGGAGCTTGGATGCATGC 61.036 55.000 16.02 16.02 34.99 4.06
407 1546 0.622136 TCACTGGAGCTTGGATGCAT 59.378 50.000 0.00 0.00 34.99 3.96
408 1547 0.035725 CTCACTGGAGCTTGGATGCA 60.036 55.000 0.00 0.00 33.67 3.96
409 1548 0.035630 ACTCACTGGAGCTTGGATGC 60.036 55.000 0.00 0.00 45.42 3.91
411 1550 0.035630 GCACTCACTGGAGCTTGGAT 60.036 55.000 0.00 0.00 45.42 3.41
414 1553 0.673022 GGAGCACTCACTGGAGCTTG 60.673 60.000 0.00 0.00 45.42 4.01
415 1554 1.676384 GGAGCACTCACTGGAGCTT 59.324 57.895 0.00 0.00 45.42 3.74
439 1578 0.035739 GTAAACAAGGTCTCCCGGCA 59.964 55.000 0.00 0.00 35.12 5.69
440 1579 0.675837 GGTAAACAAGGTCTCCCGGC 60.676 60.000 0.00 0.00 35.12 6.13
442 1581 1.017701 GCGGTAAACAAGGTCTCCCG 61.018 60.000 0.00 0.00 37.08 5.14
443 1582 1.017701 CGCGGTAAACAAGGTCTCCC 61.018 60.000 0.00 0.00 0.00 4.30
526 1679 4.183101 GAGACTCTGAAGCAGGAGAATTG 58.817 47.826 0.00 0.00 31.51 2.32
528 1681 3.439154 TGAGACTCTGAAGCAGGAGAAT 58.561 45.455 3.68 0.00 31.51 2.40
540 1702 3.374367 CAGCACAAATGGATGAGACTCTG 59.626 47.826 3.68 0.00 0.00 3.35
560 1743 3.698040 CCCTGGATTCAAGATTCAACCAG 59.302 47.826 0.00 0.00 41.79 4.00
627 1827 1.536922 CCAGGTCGATCAGTGGATTCG 60.537 57.143 0.00 5.14 32.67 3.34
637 1837 2.935481 ACGAAGTTACCAGGTCGATC 57.065 50.000 0.00 0.00 37.78 3.69
710 1918 3.671702 GCAGCAGATTAACAAGAAGGTGC 60.672 47.826 0.00 0.00 40.92 5.01
732 1947 8.660373 AGAAGACGAATTTGTAATCTAGCAAAG 58.340 33.333 9.93 0.00 37.89 2.77
745 1960 3.364964 CGGGTTGGAAGAAGACGAATTTG 60.365 47.826 0.00 0.00 0.00 2.32
752 1967 0.036294 CTCCCGGGTTGGAAGAAGAC 60.036 60.000 22.86 0.00 42.00 3.01
995 3216 1.153823 GTGACGACCTCCATGACCG 60.154 63.158 0.00 0.00 0.00 4.79
1027 3287 0.764369 CCTAGCATGGGGAGTAGGCA 60.764 60.000 0.00 0.00 30.00 4.75
1032 3292 2.042762 TGGCCTAGCATGGGGAGT 59.957 61.111 3.32 0.00 37.12 3.85
1044 3304 2.384433 ATCCATGAGCAGCTGGCCT 61.384 57.895 17.12 4.45 46.50 5.19
1227 3487 0.673437 ATCGGTGTTGGTTGCTTTGG 59.327 50.000 0.00 0.00 0.00 3.28
1228 3488 2.292016 TGTATCGGTGTTGGTTGCTTTG 59.708 45.455 0.00 0.00 0.00 2.77
1237 3497 0.719465 GCGTTCCTGTATCGGTGTTG 59.281 55.000 0.00 0.00 0.00 3.33
1239 3499 0.108804 CAGCGTTCCTGTATCGGTGT 60.109 55.000 7.62 0.00 44.32 4.16
1243 3503 1.227263 CCCCAGCGTTCCTGTATCG 60.227 63.158 0.00 0.00 40.06 2.92
1244 3504 1.523938 GCCCCAGCGTTCCTGTATC 60.524 63.158 0.00 0.00 40.06 2.24
1245 3505 2.590092 GCCCCAGCGTTCCTGTAT 59.410 61.111 0.00 0.00 40.06 2.29
1263 3523 0.459489 TTGGGCTTGTTGTGCTGTTC 59.541 50.000 0.00 0.00 0.00 3.18
1264 3524 0.901124 TTTGGGCTTGTTGTGCTGTT 59.099 45.000 0.00 0.00 0.00 3.16
1297 3559 7.950512 TGTTGGCATTCTTTTCTCTTCATTTA 58.049 30.769 0.00 0.00 0.00 1.40
1300 3562 6.218746 GTTGTTGGCATTCTTTTCTCTTCAT 58.781 36.000 0.00 0.00 0.00 2.57
1312 3574 0.802494 ATCCGTCGTTGTTGGCATTC 59.198 50.000 0.00 0.00 0.00 2.67
1326 3588 3.188460 CCTCATTGTTTTCGTTGATCCGT 59.812 43.478 0.00 0.00 0.00 4.69
1641 3905 3.591835 GTTGGTGGGCGGTGTGTG 61.592 66.667 0.00 0.00 0.00 3.82
1719 3983 1.135053 TGTGTCGTCTTGTTTCCGTCA 60.135 47.619 0.00 0.00 0.00 4.35
1737 4001 1.299976 GCTCCTGGTTCCCGATTGT 59.700 57.895 0.00 0.00 0.00 2.71
2129 4397 2.189521 GGCGACAATGGATCCGGT 59.810 61.111 7.39 5.18 0.00 5.28
2354 4627 2.133359 TTGCCTGGACATGAGCTGCT 62.133 55.000 0.00 0.00 0.00 4.24
2355 4628 1.654954 CTTGCCTGGACATGAGCTGC 61.655 60.000 0.00 0.00 0.00 5.25
2356 4629 0.322277 ACTTGCCTGGACATGAGCTG 60.322 55.000 0.00 0.00 0.00 4.24
2357 4630 0.035630 GACTTGCCTGGACATGAGCT 60.036 55.000 0.00 0.00 0.00 4.09
2358 4631 0.321919 TGACTTGCCTGGACATGAGC 60.322 55.000 0.00 0.00 0.00 4.26
2359 4632 2.082231 CTTGACTTGCCTGGACATGAG 58.918 52.381 0.00 0.00 0.00 2.90
2360 4633 1.883638 GCTTGACTTGCCTGGACATGA 60.884 52.381 0.00 0.00 0.00 3.07
2361 4634 0.524862 GCTTGACTTGCCTGGACATG 59.475 55.000 0.00 0.00 0.00 3.21
2362 4635 0.403271 AGCTTGACTTGCCTGGACAT 59.597 50.000 0.00 0.00 0.00 3.06
2363 4636 0.183492 AAGCTTGACTTGCCTGGACA 59.817 50.000 0.00 0.00 37.17 4.02
2364 4637 1.000938 CAAAGCTTGACTTGCCTGGAC 60.001 52.381 0.00 0.00 39.09 4.02
2365 4638 1.321474 CAAAGCTTGACTTGCCTGGA 58.679 50.000 0.00 0.00 39.09 3.86
2366 4639 0.316204 CCAAAGCTTGACTTGCCTGG 59.684 55.000 0.00 0.00 39.09 4.45
2446 4719 2.271800 CTGCTGAATACCTTCGACACC 58.728 52.381 0.00 0.00 33.86 4.16
2515 4794 4.431416 TCTTGCCCTTCTTGAACAAGTA 57.569 40.909 13.15 4.44 38.99 2.24
2529 4808 1.750193 TTCGATGGTGATTCTTGCCC 58.250 50.000 0.00 0.00 0.00 5.36
2555 4834 2.687935 TCCTTAATTTCCTTGATGGCGC 59.312 45.455 0.00 0.00 35.26 6.53
2693 4972 2.158623 CCATAAATGCCCACCAGCTCTA 60.159 50.000 0.00 0.00 0.00 2.43
2964 5269 3.370840 AGCTGCCTTTCATCCAACATA 57.629 42.857 0.00 0.00 0.00 2.29
3308 5710 4.794169 ACTTTGATGAAATGTACAACGCC 58.206 39.130 0.00 0.00 0.00 5.68
3454 5913 0.409484 AAGGGTAGCCTTTGGTGCAT 59.591 50.000 20.62 0.00 0.00 3.96
3552 6037 9.767684 CTTTCGAGTATATTCTGCTGATAGTAG 57.232 37.037 0.00 0.00 0.00 2.57
3620 6111 4.222145 CCCACTAATATACTGTATGGCCGT 59.778 45.833 10.51 1.35 0.00 5.68
3638 6129 0.610232 GGAGCACTGATTTGCCCACT 60.610 55.000 0.00 0.00 44.14 4.00
3662 6153 9.936329 ACAATGGTTAGGTAGATTTATTGGAAT 57.064 29.630 0.00 0.00 0.00 3.01
3693 6230 3.370978 CGGAGCGAGTACAACATTTCAAT 59.629 43.478 0.00 0.00 0.00 2.57
3710 6247 3.001330 CGACACTTATTTTGGATCGGAGC 59.999 47.826 0.00 0.00 0.00 4.70
3746 6283 5.123820 ACACCGTCTGATCCAAAATATTGTG 59.876 40.000 0.00 0.00 34.60 3.33
3781 6319 9.138062 GCATCAATGACATAGATAGAAGTACAG 57.862 37.037 0.00 0.00 0.00 2.74
3787 6325 6.527423 TGCTGCATCAATGACATAGATAGAA 58.473 36.000 0.00 0.00 0.00 2.10
4004 6596 6.406400 GGTCTATAGACATCACAAAGCTGAGT 60.406 42.308 29.36 0.00 46.47 3.41
4151 6744 0.958822 AACAATTCGGGCTTGGTGAC 59.041 50.000 0.00 0.00 0.00 3.67
4255 6849 9.270640 CTTGTCAGGAAATATTCTCTTATGGAG 57.729 37.037 0.00 0.00 43.12 3.86
4389 6983 2.290367 CTCATGCTTTGGTTTCACGTGA 59.710 45.455 15.76 15.76 0.00 4.35
4460 7054 6.249951 AGTATACTCCGCATCTCCTCTAAAT 58.750 40.000 0.00 0.00 0.00 1.40
4632 7226 1.620822 ATCCGAGCAAAAACAGGCTT 58.379 45.000 0.00 0.00 41.22 4.35
4655 7249 8.718102 TCTATTAATGAGCTGGTTGAAGTAAC 57.282 34.615 0.00 0.00 38.60 2.50
4807 7401 5.606749 TGCCATGTAAAGACATACTATCCCT 59.393 40.000 0.00 0.00 44.82 4.20
4815 7409 5.645929 ACGAACATTGCCATGTAAAGACATA 59.354 36.000 3.50 0.00 44.82 2.29
4887 7487 9.881649 ACTCGTGATATATCCGTAATACTTCTA 57.118 33.333 17.52 1.43 0.00 2.10
4892 7492 7.065563 ACCTCACTCGTGATATATCCGTAATAC 59.934 40.741 17.52 6.18 39.13 1.89
4896 7496 4.903054 ACCTCACTCGTGATATATCCGTA 58.097 43.478 17.52 8.41 39.13 4.02
4951 7551 3.589735 TCAAACCTTGATAGGGCTGGTAA 59.410 43.478 0.00 0.00 46.58 2.85
4953 7553 1.992557 TCAAACCTTGATAGGGCTGGT 59.007 47.619 0.00 0.00 46.58 4.00
4962 7562 4.111916 CACGCAAAACTTCAAACCTTGAT 58.888 39.130 0.00 0.00 39.84 2.57
4996 7596 4.102681 ACTTTTCCCCGGATAATAGTGAGG 59.897 45.833 0.73 0.00 0.00 3.86
4998 7598 5.221581 GCTACTTTTCCCCGGATAATAGTGA 60.222 44.000 0.73 0.00 0.00 3.41
5003 7603 3.434596 GGTGCTACTTTTCCCCGGATAAT 60.435 47.826 0.73 0.00 0.00 1.28
5005 7605 1.487558 GGTGCTACTTTTCCCCGGATA 59.512 52.381 0.73 0.00 0.00 2.59
5009 7609 0.676782 CAGGGTGCTACTTTTCCCCG 60.677 60.000 0.00 0.00 40.70 5.73
5024 7624 2.162681 CCTTGAGGTTAAGTTGCAGGG 58.837 52.381 0.00 0.00 0.00 4.45
5058 7658 2.775384 ACCAAGGTACCTCAAGTGAACA 59.225 45.455 16.64 0.00 0.00 3.18
5065 7665 2.832129 CTGCTAGACCAAGGTACCTCAA 59.168 50.000 16.64 0.00 0.00 3.02
5155 7755 4.725790 ATTCCTGTAGCTCAAAATTGCC 57.274 40.909 0.00 0.00 0.00 4.52
5162 7762 3.347216 GAAGGCAATTCCTGTAGCTCAA 58.653 45.455 0.00 0.00 46.94 3.02
5188 7788 9.535878 GTAGATTAATCTTCTCAACTTCCGAAT 57.464 33.333 22.60 0.00 38.32 3.34
5191 7791 7.493367 AGGTAGATTAATCTTCTCAACTTCCG 58.507 38.462 22.60 0.00 38.32 4.30


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

AutoCloner maintained by Alex Coulton.