Multiple sequence alignment - TraesCS4A01G041500

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 TraesCS4A01G041500 chr4A 100.000 3708 0 0 1 3708 35149987 35153694 0.000000e+00 6848.0
1 TraesCS4A01G041500 chr4A 98.054 411 7 1 3299 3708 545240149 545240559 0.000000e+00 713.0
2 TraesCS4A01G041500 chr4A 81.443 194 21 4 29 207 40103630 40103437 1.070000e-30 145.0
3 TraesCS4A01G041500 chr4D 93.072 3089 138 33 1 3038 433698345 433701408 0.000000e+00 4449.0
4 TraesCS4A01G041500 chr4D 91.882 271 20 2 3032 3301 342524491 342524222 9.720000e-101 377.0
5 TraesCS4A01G041500 chr4D 83.226 155 12 5 72 212 97449115 97449269 3.010000e-26 130.0
6 TraesCS4A01G041500 chr4D 89.583 96 9 1 125 219 445738734 445738639 1.810000e-23 121.0
7 TraesCS4A01G041500 chr4D 93.671 79 5 0 127 205 433698297 433698375 6.510000e-23 119.0
8 TraesCS4A01G041500 chr4B 89.616 2552 162 57 335 2837 532254619 532257116 0.000000e+00 3149.0
9 TraesCS4A01G041500 chr4B 84.685 222 18 6 1 207 2014618 2014398 1.350000e-49 207.0
10 TraesCS4A01G041500 chr2B 86.763 1171 100 23 1523 2674 451890801 451891935 0.000000e+00 1253.0
11 TraesCS4A01G041500 chr2B 90.842 273 22 3 3030 3301 637570505 637570235 2.720000e-96 363.0
12 TraesCS4A01G041500 chr2B 86.758 219 14 3 5 208 383640207 383639989 2.880000e-56 230.0
13 TraesCS4A01G041500 chr2A 86.139 1176 100 31 1523 2674 516025020 516026156 0.000000e+00 1210.0
14 TraesCS4A01G041500 chr2A 97.368 418 9 2 3292 3708 441528247 441528663 0.000000e+00 710.0
15 TraesCS4A01G041500 chr2A 96.698 424 12 2 3286 3708 500537384 500537806 0.000000e+00 704.0
16 TraesCS4A01G041500 chr2A 81.014 690 99 29 3036 3708 495245785 495245111 1.530000e-143 520.0
17 TraesCS4A01G041500 chr2A 89.216 102 11 0 2751 2852 303736301 303736402 1.080000e-25 128.0
18 TraesCS4A01G041500 chr2A 81.579 114 21 0 2747 2860 559070091 559069978 1.100000e-15 95.3
19 TraesCS4A01G041500 chr2D 87.683 958 71 21 1737 2674 380577852 380578782 0.000000e+00 1072.0
20 TraesCS4A01G041500 chr2D 84.979 233 19 7 1 218 315978291 315978060 4.820000e-54 222.0
21 TraesCS4A01G041500 chr2D 88.525 183 20 1 1523 1705 380577598 380577779 1.730000e-53 220.0
22 TraesCS4A01G041500 chr2D 82.328 232 35 4 2804 3034 308905139 308905365 2.920000e-46 196.0
23 TraesCS4A01G041500 chr2D 88.235 102 12 0 2751 2852 262454577 262454678 5.030000e-24 122.0
24 TraesCS4A01G041500 chr7A 97.826 414 8 1 3296 3708 87799736 87799323 0.000000e+00 713.0
25 TraesCS4A01G041500 chr7A 91.513 271 20 3 3032 3301 383864835 383865103 1.630000e-98 370.0
26 TraesCS4A01G041500 chr7A 94.737 76 3 1 2680 2754 412481487 412481412 2.340000e-22 117.0
27 TraesCS4A01G041500 chr5A 97.826 414 8 1 3295 3708 705336953 705337365 0.000000e+00 713.0
28 TraesCS4A01G041500 chr5A 91.111 270 21 3 3034 3301 90709437 90709705 2.720000e-96 363.0
29 TraesCS4A01G041500 chr5A 87.500 96 9 2 2657 2749 591364492 591364587 1.410000e-19 108.0
30 TraesCS4A01G041500 chr1A 97.143 420 10 2 3290 3708 590666866 590666448 0.000000e+00 708.0
31 TraesCS4A01G041500 chr1A 82.960 223 22 6 1 208 62391936 62391715 1.760000e-43 187.0
32 TraesCS4A01G041500 chrUn 96.919 422 10 3 3288 3708 36061101 36061520 0.000000e+00 704.0
33 TraesCS4A01G041500 chrUn 84.685 222 18 5 1 207 270511078 270511298 1.350000e-49 207.0
34 TraesCS4A01G041500 chrUn 84.793 217 17 7 1 202 98278072 98277857 1.750000e-48 204.0
35 TraesCS4A01G041500 chrUn 84.305 223 19 4 1 208 362324419 362324198 1.750000e-48 204.0
36 TraesCS4A01G041500 chrUn 84.234 222 19 5 1 206 89675210 89675431 6.280000e-48 202.0
37 TraesCS4A01G041500 chrUn 83.784 222 20 7 1 207 60670476 60670696 2.920000e-46 196.0
38 TraesCS4A01G041500 chrUn 83.857 223 19 7 1 207 269657074 269657295 2.920000e-46 196.0
39 TraesCS4A01G041500 chrUn 82.960 223 22 7 1 208 92967795 92968016 1.760000e-43 187.0
40 TraesCS4A01G041500 chrUn 85.714 175 20 4 1 171 292135335 292135508 2.940000e-41 180.0
41 TraesCS4A01G041500 chrUn 83.010 206 16 12 17 207 13920313 13920514 6.370000e-38 169.0
42 TraesCS4A01G041500 chrUn 80.631 222 27 5 1 207 49116949 49117169 1.380000e-34 158.0
43 TraesCS4A01G041500 chrUn 89.381 113 12 0 1 113 7918787 7918899 3.860000e-30 143.0
44 TraesCS4A01G041500 chrUn 88.496 113 13 0 1 113 7865777 7865889 1.800000e-28 137.0
45 TraesCS4A01G041500 chrUn 81.503 173 16 4 48 205 10698301 10698130 1.080000e-25 128.0
46 TraesCS4A01G041500 chrUn 88.889 81 9 0 127 207 246321719 246321639 2.360000e-17 100.0
47 TraesCS4A01G041500 chrUn 88.889 81 9 0 127 207 350761357 350761437 2.360000e-17 100.0
48 TraesCS4A01G041500 chr3B 96.919 422 10 3 3288 3708 6050797 6051216 0.000000e+00 704.0
49 TraesCS4A01G041500 chr3B 78.058 278 32 18 2745 3011 815860091 815859832 8.300000e-32 148.0
50 TraesCS4A01G041500 chr3B 75.618 283 51 11 2744 3025 245294432 245294697 1.400000e-24 124.0
51 TraesCS4A01G041500 chr5D 90.813 283 20 6 3022 3301 520897121 520896842 1.260000e-99 374.0
52 TraesCS4A01G041500 chr5D 90.876 274 21 4 3026 3297 44832344 44832615 7.570000e-97 364.0
53 TraesCS4A01G041500 chr5D 80.080 251 45 3 2784 3034 494076942 494076697 8.180000e-42 182.0
54 TraesCS4A01G041500 chr5D 80.252 238 41 4 2774 3011 493841868 493842099 1.370000e-39 174.0
55 TraesCS4A01G041500 chr1D 91.176 272 21 3 3031 3301 390369469 390369200 2.100000e-97 366.0
56 TraesCS4A01G041500 chr1D 85.135 222 17 6 1 207 62799248 62799468 2.900000e-51 213.0
57 TraesCS4A01G041500 chr1D 85.135 222 17 3 1 207 62800385 62800165 2.900000e-51 213.0
58 TraesCS4A01G041500 chr1D 85.135 222 17 6 1 207 323930167 323930387 2.900000e-51 213.0
59 TraesCS4A01G041500 chr1D 84.753 223 18 4 1 207 481633650 481633872 3.750000e-50 209.0
60 TraesCS4A01G041500 chr1D 83.857 223 19 5 1 207 204999849 205000070 2.920000e-46 196.0
61 TraesCS4A01G041500 chr1D 94.737 76 3 1 2680 2754 31420449 31420374 2.340000e-22 117.0
62 TraesCS4A01G041500 chr1D 94.737 76 3 1 2677 2751 396411366 396411441 2.340000e-22 117.0
63 TraesCS4A01G041500 chr1B 91.111 270 22 2 3027 3295 623196175 623196443 7.570000e-97 364.0
64 TraesCS4A01G041500 chr1B 90.698 86 6 2 2667 2751 660674434 660674518 3.030000e-21 113.0
65 TraesCS4A01G041500 chr6B 82.105 285 44 5 2751 3034 170346728 170347006 1.720000e-58 237.0
66 TraesCS4A01G041500 chr6B 85.586 222 16 6 1 207 272401704 272401484 6.240000e-53 219.0
67 TraesCS4A01G041500 chr5B 87.019 208 25 2 1 208 626438248 626438043 2.230000e-57 233.0
68 TraesCS4A01G041500 chr6D 86.486 222 14 6 1 207 255009591 255009371 2.880000e-56 230.0
69 TraesCS4A01G041500 chr6D 85.333 225 17 6 1 210 414926813 414927036 6.240000e-53 219.0
70 TraesCS4A01G041500 chr6D 84.753 223 18 3 1 208 273973906 273973685 3.750000e-50 209.0
71 TraesCS4A01G041500 chr6D 84.305 223 19 4 1 208 458198938 458198717 1.750000e-48 204.0
72 TraesCS4A01G041500 chr6D 84.305 223 19 4 1 208 458229311 458229090 1.750000e-48 204.0
73 TraesCS4A01G041500 chr6D 84.305 223 19 4 1 208 458263303 458263082 1.750000e-48 204.0
74 TraesCS4A01G041500 chr6D 83.929 224 20 6 1 209 18165207 18164985 2.260000e-47 200.0
75 TraesCS4A01G041500 chr6D 83.857 223 20 7 1 208 458143529 458143308 8.120000e-47 198.0
76 TraesCS4A01G041500 chr6D 93.902 82 5 0 126 207 445184354 445184435 1.400000e-24 124.0
77 TraesCS4A01G041500 chr6D 90.909 88 5 3 2669 2754 4356992 4356906 8.420000e-22 115.0
78 TraesCS4A01G041500 chr6D 88.421 95 11 0 114 208 437410935 437411029 8.420000e-22 115.0
79 TraesCS4A01G041500 chr7D 86.036 222 16 9 1 208 296642903 296642683 1.340000e-54 224.0
80 TraesCS4A01G041500 chr7D 85.135 222 17 6 1 207 388040949 388040729 2.900000e-51 213.0
81 TraesCS4A01G041500 chr7B 85.455 220 17 3 1 205 595064872 595064653 8.070000e-52 215.0
82 TraesCS4A01G041500 chr7B 96.104 77 2 1 2676 2751 606560256 606560332 1.400000e-24 124.0
83 TraesCS4A01G041500 chr3D 84.821 224 18 6 1 209 75350928 75351150 1.040000e-50 211.0
84 TraesCS4A01G041500 chr3D 83.857 223 21 6 1 208 111983479 111983701 8.120000e-47 198.0
85 TraesCS4A01G041500 chr3D 83.186 226 18 7 1 207 587308499 587308275 4.890000e-44 189.0
86 TraesCS4A01G041500 chr3D 84.058 207 17 6 1 192 92747820 92747615 6.320000e-43 185.0
87 TraesCS4A01G041500 chr3D 94.318 88 5 0 123 210 560947248 560947335 6.460000e-28 135.0
88 TraesCS4A01G041500 chr6A 94.737 76 3 1 2680 2754 611109141 611109066 2.340000e-22 117.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G041500 chr4A 35149987 35153694 3707 False 6848 6848 100.0000 1 3708 1 chr4A.!!$F1 3707
1 TraesCS4A01G041500 chr4D 433698297 433701408 3111 False 2284 4449 93.3715 1 3038 2 chr4D.!!$F2 3037
2 TraesCS4A01G041500 chr4B 532254619 532257116 2497 False 3149 3149 89.6160 335 2837 1 chr4B.!!$F1 2502
3 TraesCS4A01G041500 chr2B 451890801 451891935 1134 False 1253 1253 86.7630 1523 2674 1 chr2B.!!$F1 1151
4 TraesCS4A01G041500 chr2A 516025020 516026156 1136 False 1210 1210 86.1390 1523 2674 1 chr2A.!!$F4 1151
5 TraesCS4A01G041500 chr2A 495245111 495245785 674 True 520 520 81.0140 3036 3708 1 chr2A.!!$R1 672
6 TraesCS4A01G041500 chr2D 380577598 380578782 1184 False 646 1072 88.1040 1523 2674 2 chr2D.!!$F3 1151

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
852 955 0.591659 GGGCACTCGAAAACAAGGAC 59.408 55.000 0.00 0.00 0.0 3.85 F
948 1054 1.202486 GGCTGATCATTAACCGGTCGA 60.202 52.381 8.04 2.55 0.0 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2479 2683 1.006337 GGAAAAATGGCAGCGCACA 60.006 52.632 11.47 5.96 0.0 4.57 R
2901 3108 0.603065 GCAGCCCGAACTCCAAAAAT 59.397 50.000 0.00 0.00 0.0 1.82 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
31 80 2.478831 GGCTAGAGCATGCACTTCTAC 58.521 52.381 22.83 12.67 44.36 2.59
41 90 4.024556 GCATGCACTTCTACATGGTATCAC 60.025 45.833 14.21 0.00 43.13 3.06
101 150 6.616947 CAATTAAATTGTAGCCCACTTTCGA 58.383 36.000 0.00 0.00 35.57 3.71
115 179 3.367025 CACTTTCGATCCACGTTTAGACC 59.633 47.826 0.00 0.00 43.13 3.85
118 182 2.165167 TCGATCCACGTTTAGACCTGT 58.835 47.619 0.00 0.00 43.13 4.00
122 186 0.682852 CCACGTTTAGACCTGTGGGA 59.317 55.000 2.34 0.00 46.37 4.37
147 211 7.906160 AGAGTGTTGACGTATAAATGTATTGC 58.094 34.615 0.00 0.00 0.00 3.56
166 230 5.537300 TTGCCTAGTCTCTTCCATCATAC 57.463 43.478 0.00 0.00 0.00 2.39
197 261 2.421073 TGTTGCATTGACTAGAGCATGC 59.579 45.455 10.51 10.51 36.80 4.06
209 273 2.969990 AGAGCATGCACTTCTACACAG 58.030 47.619 21.98 0.00 0.00 3.66
213 277 2.871637 GCATGCACTTCTACACAGTCCA 60.872 50.000 14.21 0.00 0.00 4.02
217 281 2.417719 CACTTCTACACAGTCCAAGCC 58.582 52.381 0.00 0.00 0.00 4.35
220 284 1.198759 TCTACACAGTCCAAGCCCCC 61.199 60.000 0.00 0.00 0.00 5.40
235 299 1.562783 CCCCCGGAGAGGAGATAATC 58.437 60.000 0.73 0.00 45.00 1.75
255 319 3.934068 TCGGTGACAAGGAAATAGGAAC 58.066 45.455 0.00 0.00 0.00 3.62
266 330 3.381949 GAAATAGGAACTCGACGATGGG 58.618 50.000 0.00 0.00 41.75 4.00
279 343 1.072159 GATGGGGGAATCGCCTCTG 59.928 63.158 16.09 0.00 45.28 3.35
343 408 5.665812 AGGTTACCCATATTAGTTGCTCTCA 59.334 40.000 0.00 0.00 0.00 3.27
370 436 4.815846 GGTGGTTGTTGCATCAATTTTCTT 59.184 37.500 13.07 0.00 0.00 2.52
408 474 1.266178 GCTTTGGGTTACTGGCCATT 58.734 50.000 5.51 2.21 0.00 3.16
411 477 1.540267 TTGGGTTACTGGCCATTTCG 58.460 50.000 5.51 0.00 0.00 3.46
444 522 2.989253 GACCAGGCCCGGTTTTGG 60.989 66.667 13.21 8.66 40.22 3.28
522 606 1.001378 ACATCTTTTTCGCTGCACACC 60.001 47.619 0.00 0.00 0.00 4.16
532 617 0.810031 GCTGCACACCTGTATACCCG 60.810 60.000 0.00 0.00 0.00 5.28
536 621 1.112113 CACACCTGTATACCCGAGCT 58.888 55.000 0.00 0.00 0.00 4.09
543 628 4.838986 ACCTGTATACCCGAGCTTTATGAT 59.161 41.667 0.00 0.00 0.00 2.45
546 631 6.812160 CCTGTATACCCGAGCTTTATGATTAC 59.188 42.308 0.00 0.00 0.00 1.89
557 642 7.601886 CGAGCTTTATGATTACCATCAAGAGAT 59.398 37.037 0.00 0.00 42.93 2.75
770 864 2.322355 ACCAGTGCTATGATGTCAGC 57.678 50.000 0.00 0.00 38.31 4.26
852 955 0.591659 GGGCACTCGAAAACAAGGAC 59.408 55.000 0.00 0.00 0.00 3.85
882 985 2.544069 GGCTAACATCGCTAGGACAGAC 60.544 54.545 0.00 0.00 0.00 3.51
909 1015 7.201591 CCGACGAATACCAGTATATACCAGTAG 60.202 44.444 9.32 3.55 0.00 2.57
911 1017 9.658799 GACGAATACCAGTATATACCAGTAGTA 57.341 37.037 9.32 5.21 34.76 1.82
912 1018 9.442047 ACGAATACCAGTATATACCAGTAGTAC 57.558 37.037 9.32 0.00 32.46 2.73
913 1019 9.664332 CGAATACCAGTATATACCAGTAGTACT 57.336 37.037 9.32 0.00 32.46 2.73
945 1051 3.379650 CGGCTGATCATTAACCGGT 57.620 52.632 0.00 0.00 40.18 5.28
948 1054 1.202486 GGCTGATCATTAACCGGTCGA 60.202 52.381 8.04 2.55 0.00 4.20
949 1055 2.548067 GGCTGATCATTAACCGGTCGAT 60.548 50.000 8.04 8.08 0.00 3.59
950 1056 2.731976 GCTGATCATTAACCGGTCGATC 59.268 50.000 20.83 20.83 34.40 3.69
952 1058 2.619646 TGATCATTAACCGGTCGATCGA 59.380 45.455 21.90 15.15 36.17 3.59
953 1059 3.254903 TGATCATTAACCGGTCGATCGAT 59.745 43.478 21.90 10.69 36.17 3.59
995 1103 1.207089 CATCCCTGAGCTCCACGTAAA 59.793 52.381 12.15 0.00 0.00 2.01
1027 1140 2.047274 TTGGAGTAGGCAGCGTGC 60.047 61.111 0.00 0.00 44.08 5.34
1330 1443 1.327764 GTTGCTGACTAATACGGCTGC 59.672 52.381 0.00 0.00 39.95 5.25
1354 1467 4.082136 GGTGTGATCTCTAGGAAGAAACGT 60.082 45.833 0.00 0.00 0.00 3.99
1367 1480 1.764134 AGAAACGTCCACCACTAACCA 59.236 47.619 0.00 0.00 0.00 3.67
1646 1781 1.857217 CTTCATCGTCGCAATCCTGAG 59.143 52.381 0.00 0.00 0.00 3.35
1670 1805 4.028131 AGGTGGGTCGTCATACTAATCAA 58.972 43.478 0.00 0.00 0.00 2.57
1861 2051 2.044806 CTACAAGGGCCCGGAGATGG 62.045 65.000 18.44 0.00 0.00 3.51
2108 2298 2.186384 GCTCACGCTCTGCATCCT 59.814 61.111 0.00 0.00 0.00 3.24
2224 2414 2.440796 CCTTCACGCCCATGCCAT 60.441 61.111 0.00 0.00 0.00 4.40
2304 2502 3.907260 ATGTCGTGGTGCCTGCAGG 62.907 63.158 29.34 29.34 38.53 4.85
2312 2510 1.376466 GTGCCTGCAGGAGAAAGGA 59.624 57.895 37.21 6.18 37.39 3.36
2437 2635 6.375455 CCTATTCAGTAACTCACATGCCTTTT 59.625 38.462 0.00 0.00 0.00 2.27
2524 2728 0.669318 GCGTACTTGGTGCTGTGCTA 60.669 55.000 0.00 0.00 0.00 3.49
2714 2921 9.602568 TCATAGTGAGAGTAACTTAGACTAGTG 57.397 37.037 0.00 0.00 0.00 2.74
2782 2989 3.652057 ATAGCATAGCCAACAACAGGT 57.348 42.857 0.00 0.00 0.00 4.00
2935 3142 1.937546 GCTGCAGCCGGCTGTTAATT 61.938 55.000 46.58 17.48 45.24 1.40
2955 3162 3.685139 TTACAGTCTGCTTCCCTTCTG 57.315 47.619 0.00 0.00 0.00 3.02
2980 3187 5.995282 TCTCCTCTTCTATCTCATCGAACTC 59.005 44.000 0.00 0.00 0.00 3.01
2985 3192 4.827304 TCTATCTCATCGAACTCAGCAG 57.173 45.455 0.00 0.00 0.00 4.24
2996 3203 8.768019 TCATCGAACTCAGCAGAAATATAATTG 58.232 33.333 0.00 0.00 0.00 2.32
3019 3226 7.843490 TGTTTAATCCTTATAGTGTGCTGAC 57.157 36.000 0.00 0.00 0.00 3.51
3024 3231 5.578005 TCCTTATAGTGTGCTGACTGTAC 57.422 43.478 0.00 0.00 0.00 2.90
3038 3245 7.004691 TGCTGACTGTACCATATCATAGTACT 58.995 38.462 0.00 0.00 37.76 2.73
3039 3246 7.175119 TGCTGACTGTACCATATCATAGTACTC 59.825 40.741 0.00 0.00 37.76 2.59
3040 3247 7.362229 GCTGACTGTACCATATCATAGTACTCC 60.362 44.444 0.00 0.00 37.76 3.85
3041 3248 6.946583 TGACTGTACCATATCATAGTACTCCC 59.053 42.308 0.00 0.00 37.76 4.30
3042 3249 7.104974 ACTGTACCATATCATAGTACTCCCT 57.895 40.000 0.00 0.00 37.76 4.20
3104 3311 6.573434 TGCATCTATACAAGACCACTAACAG 58.427 40.000 0.00 0.00 36.93 3.16
3108 3315 9.517609 CATCTATACAAGACCACTAACAGTAAC 57.482 37.037 0.00 0.00 36.93 2.50
3110 3317 3.986277 ACAAGACCACTAACAGTAACCG 58.014 45.455 0.00 0.00 0.00 4.44
3113 3320 3.759581 AGACCACTAACAGTAACCGAGA 58.240 45.455 0.00 0.00 0.00 4.04
3114 3321 3.505293 AGACCACTAACAGTAACCGAGAC 59.495 47.826 0.00 0.00 0.00 3.36
3119 3326 5.699458 CCACTAACAGTAACCGAGACAAAAT 59.301 40.000 0.00 0.00 0.00 1.82
3129 3336 9.010029 AGTAACCGAGACAAAATTTAATGATGT 57.990 29.630 0.00 0.00 0.00 3.06
3132 3339 8.742554 ACCGAGACAAAATTTAATGATGTTTC 57.257 30.769 0.00 0.00 0.00 2.78
3137 3344 7.542130 AGACAAAATTTAATGATGTTTCCTCGC 59.458 33.333 0.00 0.00 0.00 5.03
3141 3348 4.944962 TTAATGATGTTTCCTCGCACTG 57.055 40.909 0.00 0.00 0.00 3.66
3143 3350 0.955428 TGATGTTTCCTCGCACTGGC 60.955 55.000 0.00 0.00 0.00 4.85
3200 3407 4.072131 TGACATTGTGCTACTTTCTTCCC 58.928 43.478 0.00 0.00 0.00 3.97
3202 3409 4.666512 ACATTGTGCTACTTTCTTCCCAT 58.333 39.130 0.00 0.00 0.00 4.00
3205 3412 4.365514 TGTGCTACTTTCTTCCCATTCA 57.634 40.909 0.00 0.00 0.00 2.57
3217 3424 1.758280 TCCCATTCATTCCTTGCATGC 59.242 47.619 11.82 11.82 28.73 4.06
3229 3436 3.333414 GCATGCATGCGGACGTAT 58.667 55.556 33.99 0.00 44.67 3.06
3232 3439 1.262950 GCATGCATGCGGACGTATTAA 59.737 47.619 33.99 0.00 44.67 1.40
3237 3444 3.431912 TGCATGCGGACGTATTAATGATC 59.568 43.478 14.09 0.00 0.00 2.92
3242 3449 2.029649 CGGACGTATTAATGATCCCGGT 60.030 50.000 0.00 0.00 32.84 5.28
3247 3454 6.165700 ACGTATTAATGATCCCGGTTAACT 57.834 37.500 5.42 0.00 0.00 2.24
3249 3456 7.373493 ACGTATTAATGATCCCGGTTAACTAG 58.627 38.462 5.42 0.22 0.00 2.57
3252 3459 9.768662 GTATTAATGATCCCGGTTAACTAGAAA 57.231 33.333 5.42 0.00 0.00 2.52
3416 3624 5.964958 AGGAAACTCAAATACATGTGTGG 57.035 39.130 9.11 0.00 32.90 4.17
3438 3647 5.396324 TGGATACATAGACAACACCATGTCC 60.396 44.000 3.95 0.00 46.44 4.02
3445 3654 4.546829 GACAACACCATGTCCCTAGTAA 57.453 45.455 0.00 0.00 43.11 2.24
3453 3662 3.829601 CCATGTCCCTAGTAAGCCTCTAG 59.170 52.174 0.00 0.00 35.86 2.43
3457 3666 3.637694 GTCCCTAGTAAGCCTCTAGTTGG 59.362 52.174 0.00 0.00 34.72 3.77
3465 3674 0.031449 GCCTCTAGTTGGCTAGCTCG 59.969 60.000 15.72 0.00 46.38 5.03
3467 3676 1.751924 CCTCTAGTTGGCTAGCTCGTT 59.248 52.381 15.72 1.22 43.30 3.85
3468 3677 2.480416 CCTCTAGTTGGCTAGCTCGTTG 60.480 54.545 15.72 1.50 43.30 4.10
3474 3683 2.939103 GTTGGCTAGCTCGTTGATCAAT 59.061 45.455 15.72 0.00 0.00 2.57
3475 3684 4.119862 GTTGGCTAGCTCGTTGATCAATA 58.880 43.478 15.72 2.38 0.00 1.90
3476 3685 3.982475 TGGCTAGCTCGTTGATCAATAG 58.018 45.455 15.72 13.07 0.00 1.73
3477 3686 3.636764 TGGCTAGCTCGTTGATCAATAGA 59.363 43.478 15.72 16.55 0.00 1.98
3478 3687 4.281941 TGGCTAGCTCGTTGATCAATAGAT 59.718 41.667 15.72 16.66 37.13 1.98
3480 3689 4.624882 GCTAGCTCGTTGATCAATAGATGG 59.375 45.833 19.51 16.76 33.72 3.51
3482 3691 4.626042 AGCTCGTTGATCAATAGATGGTC 58.374 43.478 19.51 9.51 39.79 4.02
3493 3702 3.543680 ATAGATGGTCACGGTTTCCTG 57.456 47.619 0.00 0.00 0.00 3.86
3494 3703 1.348064 AGATGGTCACGGTTTCCTGA 58.652 50.000 0.00 0.00 0.00 3.86
3495 3704 1.276421 AGATGGTCACGGTTTCCTGAG 59.724 52.381 0.00 0.00 0.00 3.35
3504 3713 1.679944 CGGTTTCCTGAGCATGGACAT 60.680 52.381 0.00 0.00 32.65 3.06
3505 3714 2.450476 GGTTTCCTGAGCATGGACATT 58.550 47.619 0.00 0.00 32.65 2.71
3507 3716 2.133281 TTCCTGAGCATGGACATTGG 57.867 50.000 0.00 0.00 32.65 3.16
3508 3717 1.288188 TCCTGAGCATGGACATTGGA 58.712 50.000 0.00 0.00 0.00 3.53
3510 3719 1.954382 CCTGAGCATGGACATTGGATG 59.046 52.381 0.00 0.00 0.00 3.51
3556 3768 5.955961 TTAGGAGAATGATGTGATGGACA 57.044 39.130 0.00 0.00 39.53 4.02
3557 3769 4.849813 AGGAGAATGATGTGATGGACAA 57.150 40.909 0.00 0.00 38.36 3.18
3564 3776 2.374839 TGATGTGATGGACAAGACCCAA 59.625 45.455 0.00 0.00 38.36 4.12
3565 3777 3.010472 TGATGTGATGGACAAGACCCAAT 59.990 43.478 0.00 0.00 38.36 3.16
3567 3779 2.290896 TGTGATGGACAAGACCCAATCC 60.291 50.000 0.00 0.00 37.22 3.01
3569 3781 3.199946 GTGATGGACAAGACCCAATCCTA 59.800 47.826 0.00 0.00 37.22 2.94
3573 3785 2.644676 GACAAGACCCAATCCTAAGCC 58.355 52.381 0.00 0.00 0.00 4.35
3580 3792 1.490490 CCCAATCCTAAGCCTAGCACA 59.510 52.381 0.00 0.00 0.00 4.57
3582 3794 3.209410 CCAATCCTAAGCCTAGCACAAG 58.791 50.000 0.00 0.00 0.00 3.16
3583 3795 3.118261 CCAATCCTAAGCCTAGCACAAGA 60.118 47.826 0.00 0.00 0.00 3.02
3584 3796 4.445448 CCAATCCTAAGCCTAGCACAAGAT 60.445 45.833 0.00 0.00 0.00 2.40
3585 3797 4.615588 ATCCTAAGCCTAGCACAAGATC 57.384 45.455 0.00 0.00 0.00 2.75
3586 3798 3.374764 TCCTAAGCCTAGCACAAGATCA 58.625 45.455 0.00 0.00 0.00 2.92
3587 3799 3.969976 TCCTAAGCCTAGCACAAGATCAT 59.030 43.478 0.00 0.00 0.00 2.45
3588 3800 4.063689 CCTAAGCCTAGCACAAGATCATG 58.936 47.826 0.00 0.00 0.00 3.07
3594 3808 4.509600 GCCTAGCACAAGATCATGTAGTTC 59.490 45.833 2.77 0.00 30.84 3.01
3595 3809 4.742167 CCTAGCACAAGATCATGTAGTTCG 59.258 45.833 2.77 0.00 30.84 3.95
3596 3810 4.193826 AGCACAAGATCATGTAGTTCGT 57.806 40.909 2.77 0.00 30.84 3.85
3597 3811 5.324784 AGCACAAGATCATGTAGTTCGTA 57.675 39.130 2.77 0.00 30.84 3.43
3603 3817 7.435192 CACAAGATCATGTAGTTCGTATGCTAA 59.565 37.037 2.77 0.00 30.84 3.09
3604 3818 7.979537 ACAAGATCATGTAGTTCGTATGCTAAA 59.020 33.333 0.80 0.00 0.00 1.85
3610 3824 7.333423 TCATGTAGTTCGTATGCTAAAGCTTTT 59.667 33.333 18.47 1.19 42.66 2.27
3611 3825 7.057149 TGTAGTTCGTATGCTAAAGCTTTTC 57.943 36.000 18.47 10.34 42.66 2.29
3613 3827 8.030692 TGTAGTTCGTATGCTAAAGCTTTTCTA 58.969 33.333 18.47 4.25 42.66 2.10
3617 3831 7.843490 TCGTATGCTAAAGCTTTTCTAATGT 57.157 32.000 18.47 0.66 42.66 2.71
3619 3833 7.547722 TCGTATGCTAAAGCTTTTCTAATGTCA 59.452 33.333 18.47 4.72 42.66 3.58
3620 3834 8.175069 CGTATGCTAAAGCTTTTCTAATGTCAA 58.825 33.333 18.47 0.00 42.66 3.18
3621 3835 9.495754 GTATGCTAAAGCTTTTCTAATGTCAAG 57.504 33.333 18.47 5.49 42.66 3.02
3624 3838 9.231297 TGCTAAAGCTTTTCTAATGTCAAGTAT 57.769 29.630 18.47 0.00 42.66 2.12
3625 3839 9.709600 GCTAAAGCTTTTCTAATGTCAAGTATC 57.290 33.333 18.47 0.00 38.21 2.24
3638 3852 8.738645 AATGTCAAGTATCATTTCCTTAGACC 57.261 34.615 0.00 0.00 31.35 3.85
3641 3855 8.988060 TGTCAAGTATCATTTCCTTAGACCATA 58.012 33.333 0.00 0.00 0.00 2.74
3658 3872 2.355756 CCATAAGATTGTGCAACTCCCG 59.644 50.000 0.00 0.00 38.04 5.14
3659 3873 2.107950 TAAGATTGTGCAACTCCCGG 57.892 50.000 0.00 0.00 38.04 5.73
3666 3880 1.985662 TGCAACTCCCGGATACCGT 60.986 57.895 0.73 0.00 46.80 4.83
3683 3897 0.034896 CGTAGGAGTGCTTTGGGTGT 59.965 55.000 0.00 0.00 0.00 4.16
3684 3898 1.523758 GTAGGAGTGCTTTGGGTGTG 58.476 55.000 0.00 0.00 0.00 3.82
3685 3899 0.250727 TAGGAGTGCTTTGGGTGTGC 60.251 55.000 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.465287 TGCTCTAGCCGATGCAATCA 59.535 50.000 0.00 0.00 41.33 2.57
2 3 1.463831 CATGCTCTAGCCGATGCAATC 59.536 52.381 0.00 0.00 41.13 2.67
3 4 1.520494 CATGCTCTAGCCGATGCAAT 58.480 50.000 0.00 0.00 41.13 3.56
10 59 0.179089 AGAAGTGCATGCTCTAGCCG 60.179 55.000 21.70 0.00 41.18 5.52
31 80 2.092753 ACCTCTTGGCTGTGATACCATG 60.093 50.000 0.00 0.00 35.42 3.66
67 116 2.230992 ACAATTTAATTGCGCCAGCTGA 59.769 40.909 17.39 0.00 43.98 4.26
68 117 2.609350 ACAATTTAATTGCGCCAGCTG 58.391 42.857 16.57 6.78 43.98 4.24
115 179 0.389391 ACGTCAACACTCTCCCACAG 59.611 55.000 0.00 0.00 0.00 3.66
118 182 5.046878 ACATTTATACGTCAACACTCTCCCA 60.047 40.000 0.00 0.00 0.00 4.37
122 186 7.011109 GGCAATACATTTATACGTCAACACTCT 59.989 37.037 0.00 0.00 0.00 3.24
147 211 3.508012 CCGGTATGATGGAAGAGACTAGG 59.492 52.174 0.00 0.00 0.00 3.02
176 240 2.421073 GCATGCTCTAGTCAATGCAACA 59.579 45.455 11.37 0.00 38.96 3.33
182 246 4.484537 AGAAGTGCATGCTCTAGTCAAT 57.515 40.909 21.70 5.92 0.00 2.57
190 254 2.670414 GACTGTGTAGAAGTGCATGCTC 59.330 50.000 20.33 15.94 0.00 4.26
197 261 2.417719 GGCTTGGACTGTGTAGAAGTG 58.582 52.381 0.00 0.00 0.00 3.16
209 273 3.787001 CTCTCCGGGGGCTTGGAC 61.787 72.222 0.00 0.00 0.00 4.02
213 277 1.665948 TATCTCCTCTCCGGGGGCTT 61.666 60.000 0.00 0.00 32.36 4.35
217 281 1.178276 CGATTATCTCCTCTCCGGGG 58.822 60.000 0.00 0.00 32.98 5.73
220 284 2.226912 GTCACCGATTATCTCCTCTCCG 59.773 54.545 0.00 0.00 0.00 4.63
235 299 3.933332 GAGTTCCTATTTCCTTGTCACCG 59.067 47.826 0.00 0.00 0.00 4.94
255 319 1.007271 CGATTCCCCCATCGTCGAG 60.007 63.158 0.00 0.00 41.03 4.04
266 330 1.068434 CTTCTCTCAGAGGCGATTCCC 59.932 57.143 0.57 0.00 34.51 3.97
323 388 6.464322 CCATGTGAGAGCAACTAATATGGGTA 60.464 42.308 12.88 0.00 41.97 3.69
343 408 1.702182 TGATGCAACAACCACCATGT 58.298 45.000 0.00 0.00 0.00 3.21
370 436 4.796110 AGCATCCTCTTTTAGCCCAATA 57.204 40.909 0.00 0.00 0.00 1.90
408 474 3.345414 GTCTCTCCTTCACTACTCCGAA 58.655 50.000 0.00 0.00 0.00 4.30
411 477 3.020984 CTGGTCTCTCCTTCACTACTCC 58.979 54.545 0.00 0.00 37.07 3.85
512 596 0.810031 GGGTATACAGGTGTGCAGCG 60.810 60.000 5.01 0.00 0.00 5.18
522 606 6.812160 GGTAATCATAAAGCTCGGGTATACAG 59.188 42.308 5.01 0.00 0.00 2.74
532 617 8.845413 ATCTCTTGATGGTAATCATAAAGCTC 57.155 34.615 0.00 0.00 41.90 4.09
536 621 7.600375 GCTCGATCTCTTGATGGTAATCATAAA 59.400 37.037 0.00 0.00 42.41 1.40
543 628 4.736126 TTGCTCGATCTCTTGATGGTAA 57.264 40.909 0.00 0.00 32.19 2.85
546 631 3.063180 GTGTTTGCTCGATCTCTTGATGG 59.937 47.826 0.00 0.00 32.19 3.51
557 642 7.305705 CGTCAATTTTAAAATGTGTTTGCTCGA 60.306 33.333 14.04 0.00 0.00 4.04
621 706 9.166222 TGTGTACTGATTATATTTATGGGAGGT 57.834 33.333 0.00 0.00 0.00 3.85
687 780 1.014044 CCCACGTCAGTTCATCGGTG 61.014 60.000 0.00 0.00 0.00 4.94
852 955 0.316442 CGATGTTAGCCAAGCGCATG 60.316 55.000 11.47 8.27 41.38 4.06
882 985 4.701651 TGGTATATACTGGTATTCGTCGGG 59.298 45.833 12.54 0.00 0.00 5.14
909 1015 3.131755 AGCCGGTAGATTTACACCAGTAC 59.868 47.826 1.90 0.00 34.25 2.73
911 1017 2.093658 CAGCCGGTAGATTTACACCAGT 60.094 50.000 1.90 0.00 34.25 4.00
912 1018 2.167693 TCAGCCGGTAGATTTACACCAG 59.832 50.000 1.90 0.00 34.25 4.00
913 1019 2.181125 TCAGCCGGTAGATTTACACCA 58.819 47.619 1.90 0.00 34.25 4.17
914 1020 2.973694 TCAGCCGGTAGATTTACACC 57.026 50.000 1.90 0.00 0.00 4.16
945 1051 2.227626 GCTCAGGAATGAGATCGATCGA 59.772 50.000 21.86 21.86 38.13 3.59
948 1054 2.964464 ACAGCTCAGGAATGAGATCGAT 59.036 45.455 9.38 0.00 38.13 3.59
949 1055 2.382882 ACAGCTCAGGAATGAGATCGA 58.617 47.619 9.38 0.00 38.13 3.59
950 1056 2.886862 ACAGCTCAGGAATGAGATCG 57.113 50.000 9.38 1.41 38.13 3.69
952 1058 3.181456 GGCTAACAGCTCAGGAATGAGAT 60.181 47.826 9.38 0.00 41.99 2.75
953 1059 2.169352 GGCTAACAGCTCAGGAATGAGA 59.831 50.000 9.38 0.00 41.99 3.27
995 1103 1.411977 CTCCAACGATCCTCATGCTCT 59.588 52.381 0.00 0.00 0.00 4.09
1323 1436 3.649277 GAGATCACACCGCAGCCGT 62.649 63.158 0.00 0.00 0.00 5.68
1330 1443 4.425520 GTTTCTTCCTAGAGATCACACCG 58.574 47.826 0.00 0.00 0.00 4.94
1367 1480 4.657814 ATAACCCTGTCACAACCTTGAT 57.342 40.909 0.00 0.00 0.00 2.57
1646 1781 1.108776 TAGTATGACGACCCACCTGC 58.891 55.000 0.00 0.00 0.00 4.85
1652 1787 7.711339 AGAAATCTTTGATTAGTATGACGACCC 59.289 37.037 0.00 0.00 0.00 4.46
1861 2051 2.663196 CAGACGGTGGAGGAACCC 59.337 66.667 0.00 0.00 36.84 4.11
2108 2298 4.988716 AGTGGTCGGCGTCCCTGA 62.989 66.667 20.02 0.00 0.00 3.86
2206 2396 4.738998 TGGCATGGGCGTGAAGGG 62.739 66.667 0.00 0.00 42.47 3.95
2224 2414 5.464057 ACGTACGAATCAAACATCAGAAACA 59.536 36.000 24.41 0.00 0.00 2.83
2304 2502 1.750206 GACGTAGAGGGGTCCTTTCTC 59.250 57.143 0.00 0.45 31.76 2.87
2312 2510 2.043248 ATGGCGACGTAGAGGGGT 60.043 61.111 0.00 0.00 0.00 4.95
2437 2635 2.107378 TCAAACAGGCTCCACCATGTTA 59.893 45.455 0.00 0.00 43.14 2.41
2479 2683 1.006337 GGAAAAATGGCAGCGCACA 60.006 52.632 11.47 5.96 0.00 4.57
2524 2728 3.395702 TACAGCCCCGCCACGATT 61.396 61.111 0.00 0.00 0.00 3.34
2745 2952 3.194755 TGCTATTAACCGTGCTCTGAAGA 59.805 43.478 0.00 0.00 0.00 2.87
2801 3008 9.726232 TGTTGACTATTACGTTGACTATATGTC 57.274 33.333 0.00 0.00 45.54 3.06
2887 3094 9.171877 GAACTCCAAAAATGAGTGAATCTAGAT 57.828 33.333 0.00 0.00 42.10 1.98
2890 3097 6.371548 CCGAACTCCAAAAATGAGTGAATCTA 59.628 38.462 0.00 0.00 42.10 1.98
2891 3098 5.182001 CCGAACTCCAAAAATGAGTGAATCT 59.818 40.000 0.00 0.00 42.10 2.40
2892 3099 5.393962 CCGAACTCCAAAAATGAGTGAATC 58.606 41.667 0.00 0.00 42.10 2.52
2895 3102 3.146066 CCCGAACTCCAAAAATGAGTGA 58.854 45.455 0.00 0.00 42.10 3.41
2896 3103 2.351738 GCCCGAACTCCAAAAATGAGTG 60.352 50.000 0.00 0.00 42.10 3.51
2897 3104 1.886542 GCCCGAACTCCAAAAATGAGT 59.113 47.619 0.00 0.00 44.75 3.41
2898 3105 2.095059 CAGCCCGAACTCCAAAAATGAG 60.095 50.000 0.00 0.00 35.92 2.90
2899 3106 1.885887 CAGCCCGAACTCCAAAAATGA 59.114 47.619 0.00 0.00 0.00 2.57
2900 3107 1.669795 GCAGCCCGAACTCCAAAAATG 60.670 52.381 0.00 0.00 0.00 2.32
2901 3108 0.603065 GCAGCCCGAACTCCAAAAAT 59.397 50.000 0.00 0.00 0.00 1.82
2935 3142 2.972713 ACAGAAGGGAAGCAGACTGTAA 59.027 45.455 3.99 0.00 36.94 2.41
2955 3162 5.763204 AGTTCGATGAGATAGAAGAGGAGAC 59.237 44.000 0.00 0.00 0.00 3.36
2996 3203 7.549488 ACAGTCAGCACACTATAAGGATTAAAC 59.451 37.037 0.00 0.00 32.17 2.01
3024 3231 6.098982 GGGAATGAGGGAGTACTATGATATGG 59.901 46.154 0.00 0.00 0.00 2.74
3094 3301 3.225104 TGTCTCGGTTACTGTTAGTGGT 58.775 45.455 0.00 0.00 0.00 4.16
3104 3311 9.620660 AACATCATTAAATTTTGTCTCGGTTAC 57.379 29.630 0.00 0.00 0.00 2.50
3108 3315 8.028938 AGGAAACATCATTAAATTTTGTCTCGG 58.971 33.333 0.00 0.00 0.00 4.63
3110 3317 9.065871 CGAGGAAACATCATTAAATTTTGTCTC 57.934 33.333 0.00 0.00 0.00 3.36
3113 3320 7.116233 GTGCGAGGAAACATCATTAAATTTTGT 59.884 33.333 0.00 0.00 0.00 2.83
3114 3321 7.329226 AGTGCGAGGAAACATCATTAAATTTTG 59.671 33.333 0.00 0.00 0.00 2.44
3119 3326 4.155826 CCAGTGCGAGGAAACATCATTAAA 59.844 41.667 0.00 0.00 0.00 1.52
3137 3344 5.382303 CAAGTATTAAACAAGTCGCCAGTG 58.618 41.667 0.00 0.00 0.00 3.66
3141 3348 4.413495 TGCAAGTATTAAACAAGTCGCC 57.587 40.909 0.00 0.00 0.00 5.54
3143 3350 5.389778 TGCATGCAAGTATTAAACAAGTCG 58.610 37.500 20.30 0.00 0.00 4.18
3144 3351 6.808212 ACATGCATGCAAGTATTAAACAAGTC 59.192 34.615 25.90 0.00 0.00 3.01
3183 3390 4.724399 TGAATGGGAAGAAAGTAGCACAA 58.276 39.130 0.00 0.00 0.00 3.33
3185 3392 5.163612 GGAATGAATGGGAAGAAAGTAGCAC 60.164 44.000 0.00 0.00 0.00 4.40
3186 3393 4.949856 GGAATGAATGGGAAGAAAGTAGCA 59.050 41.667 0.00 0.00 0.00 3.49
3187 3394 5.196695 AGGAATGAATGGGAAGAAAGTAGC 58.803 41.667 0.00 0.00 0.00 3.58
3194 3401 3.454719 TGCAAGGAATGAATGGGAAGA 57.545 42.857 0.00 0.00 0.00 2.87
3217 3424 3.370978 GGGATCATTAATACGTCCGCATG 59.629 47.826 0.00 0.00 0.00 4.06
3221 3428 2.029649 ACCGGGATCATTAATACGTCCG 60.030 50.000 6.32 10.58 36.43 4.79
3222 3429 3.672767 ACCGGGATCATTAATACGTCC 57.327 47.619 6.32 4.98 0.00 4.79
3224 3431 6.165700 AGTTAACCGGGATCATTAATACGT 57.834 37.500 6.32 0.00 0.00 3.57
3226 3433 9.768662 TTTCTAGTTAACCGGGATCATTAATAC 57.231 33.333 6.32 0.00 0.00 1.89
3298 3505 4.437682 CCTCTAGGGCATATTTCCAACA 57.562 45.455 0.00 0.00 0.00 3.33
3388 3596 9.466497 ACACATGTATTTGAGTTTCCTATCAAT 57.534 29.630 0.00 0.00 35.47 2.57
3389 3597 8.729756 CACACATGTATTTGAGTTTCCTATCAA 58.270 33.333 0.00 0.00 33.73 2.57
3391 3599 7.552687 TCCACACATGTATTTGAGTTTCCTATC 59.447 37.037 0.00 0.00 0.00 2.08
3393 3601 6.774673 TCCACACATGTATTTGAGTTTCCTA 58.225 36.000 0.00 0.00 0.00 2.94
3394 3602 5.630121 TCCACACATGTATTTGAGTTTCCT 58.370 37.500 0.00 0.00 0.00 3.36
3395 3603 5.957842 TCCACACATGTATTTGAGTTTCC 57.042 39.130 0.00 0.00 0.00 3.13
3396 3604 8.039603 TGTATCCACACATGTATTTGAGTTTC 57.960 34.615 0.00 0.00 0.00 2.78
3397 3605 7.994425 TGTATCCACACATGTATTTGAGTTT 57.006 32.000 0.00 0.00 0.00 2.66
3400 3608 8.982685 GTCTATGTATCCACACATGTATTTGAG 58.017 37.037 0.00 0.00 39.46 3.02
3401 3609 8.482128 TGTCTATGTATCCACACATGTATTTGA 58.518 33.333 0.00 0.00 39.46 2.69
3402 3610 8.661352 TGTCTATGTATCCACACATGTATTTG 57.339 34.615 0.00 0.00 39.46 2.32
3403 3611 9.109393 GTTGTCTATGTATCCACACATGTATTT 57.891 33.333 0.00 0.00 39.46 1.40
3405 3613 7.710907 GTGTTGTCTATGTATCCACACATGTAT 59.289 37.037 0.00 0.00 39.46 2.29
3416 3624 5.057149 GGGACATGGTGTTGTCTATGTATC 58.943 45.833 0.00 0.00 44.39 2.24
3424 3632 4.504858 CTTACTAGGGACATGGTGTTGTC 58.495 47.826 0.00 0.00 44.27 3.18
3429 3637 2.103263 GAGGCTTACTAGGGACATGGTG 59.897 54.545 0.00 0.00 0.00 4.17
3430 3638 2.022918 AGAGGCTTACTAGGGACATGGT 60.023 50.000 0.00 0.00 0.00 3.55
3431 3639 2.683768 AGAGGCTTACTAGGGACATGG 58.316 52.381 0.00 0.00 0.00 3.66
3432 3640 4.475345 ACTAGAGGCTTACTAGGGACATG 58.525 47.826 13.13 0.00 40.86 3.21
3453 3662 2.010145 TGATCAACGAGCTAGCCAAC 57.990 50.000 12.13 2.48 0.00 3.77
3457 3666 4.624882 CCATCTATTGATCAACGAGCTAGC 59.375 45.833 11.07 6.62 0.00 3.42
3465 3674 4.442706 ACCGTGACCATCTATTGATCAAC 58.557 43.478 11.07 0.00 0.00 3.18
3467 3676 4.753516 AACCGTGACCATCTATTGATCA 57.246 40.909 0.00 0.00 0.00 2.92
3468 3677 4.511826 GGAAACCGTGACCATCTATTGATC 59.488 45.833 0.00 0.00 0.00 2.92
3474 3683 2.496070 CTCAGGAAACCGTGACCATCTA 59.504 50.000 0.00 0.00 0.00 1.98
3475 3684 1.276421 CTCAGGAAACCGTGACCATCT 59.724 52.381 0.00 0.00 0.00 2.90
3476 3685 1.726853 CTCAGGAAACCGTGACCATC 58.273 55.000 0.00 0.00 0.00 3.51
3477 3686 0.321653 GCTCAGGAAACCGTGACCAT 60.322 55.000 0.00 0.00 0.00 3.55
3478 3687 1.070786 GCTCAGGAAACCGTGACCA 59.929 57.895 0.00 0.00 0.00 4.02
3480 3689 0.798776 CATGCTCAGGAAACCGTGAC 59.201 55.000 0.00 0.00 0.00 3.67
3482 3691 0.321564 TCCATGCTCAGGAAACCGTG 60.322 55.000 0.00 0.00 30.71 4.94
3484 3693 0.321564 TGTCCATGCTCAGGAAACCG 60.322 55.000 0.00 0.00 36.80 4.44
3485 3694 2.134789 ATGTCCATGCTCAGGAAACC 57.865 50.000 0.00 0.00 36.80 3.27
3513 3722 6.147821 CCTAATGATGTGATCCCGTTATCAAC 59.852 42.308 0.00 0.00 37.61 3.18
3514 3723 6.042666 TCCTAATGATGTGATCCCGTTATCAA 59.957 38.462 0.00 0.00 37.61 2.57
3516 3725 6.037786 TCCTAATGATGTGATCCCGTTATC 57.962 41.667 0.00 0.00 0.00 1.75
3517 3726 5.780282 TCTCCTAATGATGTGATCCCGTTAT 59.220 40.000 0.00 0.00 0.00 1.89
3518 3727 5.144832 TCTCCTAATGATGTGATCCCGTTA 58.855 41.667 0.00 0.00 0.00 3.18
3520 3729 3.576861 TCTCCTAATGATGTGATCCCGT 58.423 45.455 0.00 0.00 0.00 5.28
3521 3730 4.607293 TTCTCCTAATGATGTGATCCCG 57.393 45.455 0.00 0.00 0.00 5.14
3522 3731 6.119240 TCATTCTCCTAATGATGTGATCCC 57.881 41.667 0.00 0.00 32.21 3.85
3536 3748 4.472470 TCTTGTCCATCACATCATTCTCCT 59.528 41.667 0.00 0.00 33.90 3.69
3552 3764 2.644676 GCTTAGGATTGGGTCTTGTCC 58.355 52.381 0.00 0.00 0.00 4.02
3556 3768 2.439880 GCTAGGCTTAGGATTGGGTCTT 59.560 50.000 4.88 0.00 0.00 3.01
3557 3769 2.050918 GCTAGGCTTAGGATTGGGTCT 58.949 52.381 4.88 0.00 0.00 3.85
3564 3776 3.969976 TGATCTTGTGCTAGGCTTAGGAT 59.030 43.478 4.88 0.00 29.47 3.24
3565 3777 3.374764 TGATCTTGTGCTAGGCTTAGGA 58.625 45.455 4.88 0.00 0.00 2.94
3567 3779 4.701765 ACATGATCTTGTGCTAGGCTTAG 58.298 43.478 13.08 0.00 0.00 2.18
3569 3781 3.641434 ACATGATCTTGTGCTAGGCTT 57.359 42.857 13.08 0.00 0.00 4.35
3573 3785 5.344066 ACGAACTACATGATCTTGTGCTAG 58.656 41.667 21.20 14.16 0.00 3.42
3580 3792 7.169982 GCTTTAGCATACGAACTACATGATCTT 59.830 37.037 0.00 0.00 41.59 2.40
3582 3794 6.642950 AGCTTTAGCATACGAACTACATGATC 59.357 38.462 0.00 0.00 45.16 2.92
3583 3795 6.516718 AGCTTTAGCATACGAACTACATGAT 58.483 36.000 0.00 0.00 45.16 2.45
3584 3796 5.902681 AGCTTTAGCATACGAACTACATGA 58.097 37.500 0.00 0.00 45.16 3.07
3585 3797 6.589830 AAGCTTTAGCATACGAACTACATG 57.410 37.500 4.33 0.00 45.16 3.21
3586 3798 7.549488 AGAAAAGCTTTAGCATACGAACTACAT 59.451 33.333 13.10 0.00 45.16 2.29
3587 3799 6.872020 AGAAAAGCTTTAGCATACGAACTACA 59.128 34.615 13.10 0.00 45.16 2.74
3588 3800 7.292129 AGAAAAGCTTTAGCATACGAACTAC 57.708 36.000 13.10 0.00 45.16 2.73
3594 3808 7.684670 TGACATTAGAAAAGCTTTAGCATACG 58.315 34.615 13.10 1.72 45.16 3.06
3595 3809 9.495754 CTTGACATTAGAAAAGCTTTAGCATAC 57.504 33.333 13.10 1.75 45.16 2.39
3596 3810 9.231297 ACTTGACATTAGAAAAGCTTTAGCATA 57.769 29.630 13.10 0.54 45.16 3.14
3597 3811 8.115490 ACTTGACATTAGAAAAGCTTTAGCAT 57.885 30.769 13.10 0.00 45.16 3.79
3613 3827 8.328758 TGGTCTAAGGAAATGATACTTGACATT 58.671 33.333 0.00 0.00 38.18 2.71
3624 3838 7.283127 GCACAATCTTATGGTCTAAGGAAATGA 59.717 37.037 0.00 0.00 0.00 2.57
3625 3839 7.067372 TGCACAATCTTATGGTCTAAGGAAATG 59.933 37.037 0.00 0.00 0.00 2.32
3626 3840 7.118723 TGCACAATCTTATGGTCTAAGGAAAT 58.881 34.615 0.00 0.00 0.00 2.17
3627 3841 6.480763 TGCACAATCTTATGGTCTAAGGAAA 58.519 36.000 0.00 0.00 0.00 3.13
3638 3852 2.355756 CCGGGAGTTGCACAATCTTATG 59.644 50.000 0.00 0.00 0.00 1.90
3641 3855 0.400213 TCCGGGAGTTGCACAATCTT 59.600 50.000 0.00 0.00 0.00 2.40
3647 3861 1.520787 CGGTATCCGGGAGTTGCAC 60.521 63.158 0.00 0.00 44.15 4.57
3658 3872 2.483188 CCAAAGCACTCCTACGGTATCC 60.483 54.545 0.00 0.00 0.00 2.59
3659 3873 2.483188 CCCAAAGCACTCCTACGGTATC 60.483 54.545 0.00 0.00 0.00 2.24
3666 3880 0.250727 GCACACCCAAAGCACTCCTA 60.251 55.000 0.00 0.00 0.00 2.94
3669 3883 1.827789 TGGCACACCCAAAGCACTC 60.828 57.895 0.00 0.00 41.82 3.51
3679 3893 0.524604 GTTGTGACGTTTGGCACACC 60.525 55.000 2.92 0.00 43.97 4.16


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

AutoCloner maintained by Alex Coulton.