Multiple sequence alignment - TraesCS4A01G449700

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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 TraesCS4A01G449700 chr4A 100.000 8075 0 0 1 8075 715712866 715720940 0.000000e+00 14875.0
1 TraesCS4A01G449700 chr4A 94.287 2328 96 11 976 3278 715880112 715877797 0.000000e+00 3528.0
2 TraesCS4A01G449700 chr4A 94.510 929 26 2 3271 4174 715877410 715876482 0.000000e+00 1410.0
3 TraesCS4A01G449700 chr4A 98.204 724 12 1 254 976 159497377 159496654 0.000000e+00 1264.0
4 TraesCS4A01G449700 chr4A 88.841 699 58 9 4176 4873 715876397 715875718 0.000000e+00 841.0
5 TraesCS4A01G449700 chr4A 96.484 256 8 1 1 255 715880353 715880098 9.690000e-114 422.0
6 TraesCS4A01G449700 chr7D 92.294 6553 327 64 1282 7717 17869444 17862953 0.000000e+00 9140.0
7 TraesCS4A01G449700 chr7D 94.839 310 15 1 976 1284 17869846 17869537 4.380000e-132 483.0
8 TraesCS4A01G449700 chr7D 94.677 263 6 2 1 255 17870094 17869832 1.260000e-107 401.0
9 TraesCS4A01G449700 chr7A 91.275 4298 210 50 976 5182 17364209 17359986 0.000000e+00 5707.0
10 TraesCS4A01G449700 chr7A 93.215 2093 115 17 5173 7248 17359955 17357873 0.000000e+00 3053.0
11 TraesCS4A01G449700 chr7A 89.834 482 39 7 7239 7718 17353810 17353337 1.930000e-170 610.0
12 TraesCS4A01G449700 chr7A 95.367 259 8 1 1 255 17364453 17364195 7.540000e-110 409.0
13 TraesCS4A01G449700 chr2B 81.723 2566 355 78 2089 4561 629102903 629105447 0.000000e+00 2036.0
14 TraesCS4A01G449700 chr2B 97.787 723 16 0 254 976 64337168 64336446 0.000000e+00 1247.0
15 TraesCS4A01G449700 chr2B 88.719 851 86 6 5693 6543 629106501 629107341 0.000000e+00 1031.0
16 TraesCS4A01G449700 chr2B 85.816 987 109 20 5595 6564 629024126 629025098 0.000000e+00 1018.0
17 TraesCS4A01G449700 chr2B 78.000 1100 175 49 2140 3186 629020544 629021629 5.320000e-176 628.0
18 TraesCS4A01G449700 chr2B 88.305 419 42 5 5179 5590 629105908 629106326 5.630000e-136 496.0
19 TraesCS4A01G449700 chr2B 83.894 416 47 11 5179 5584 629023652 629024057 5.910000e-101 379.0
20 TraesCS4A01G449700 chr2B 76.445 692 147 11 3738 4418 629123362 629124048 2.140000e-95 361.0
21 TraesCS4A01G449700 chr2B 78.481 395 61 20 1344 1734 629019412 629019786 3.770000e-58 237.0
22 TraesCS4A01G449700 chr2B 85.211 142 19 2 1052 1192 629101705 629101845 2.350000e-30 145.0
23 TraesCS4A01G449700 chr2D 81.347 2584 351 93 2089 4568 529544682 529547238 0.000000e+00 1980.0
24 TraesCS4A01G449700 chr2D 85.466 977 116 17 5595 6557 529537807 529538771 0.000000e+00 994.0
25 TraesCS4A01G449700 chr2D 88.263 835 86 8 5707 6540 529548228 529549051 0.000000e+00 989.0
26 TraesCS4A01G449700 chr2D 81.818 1155 172 23 3366 4509 529535693 529536820 0.000000e+00 935.0
27 TraesCS4A01G449700 chr2D 78.735 1091 172 38 2140 3186 529534350 529535424 0.000000e+00 675.0
28 TraesCS4A01G449700 chr2D 88.164 414 47 1 5179 5590 529547754 529548167 7.280000e-135 492.0
29 TraesCS4A01G449700 chr2D 86.761 423 44 6 5179 5590 529537324 529537745 2.050000e-125 460.0
30 TraesCS4A01G449700 chr2D 78.338 397 58 22 1344 1734 529533263 529533637 1.750000e-56 231.0
31 TraesCS4A01G449700 chr2D 84.146 82 11 2 1677 1757 46686627 46686707 2.420000e-10 78.7
32 TraesCS4A01G449700 chr2A 81.240 2564 353 91 2089 4568 674047108 674049627 0.000000e+00 1953.0
33 TraesCS4A01G449700 chr2A 97.787 723 11 1 254 976 733694944 733695661 0.000000e+00 1242.0
34 TraesCS4A01G449700 chr2A 88.372 860 88 7 5688 6545 674050651 674051500 0.000000e+00 1024.0
35 TraesCS4A01G449700 chr2A 85.121 988 115 20 5595 6564 674031015 674031988 0.000000e+00 981.0
36 TraesCS4A01G449700 chr2A 77.807 1131 187 44 2127 3214 674027504 674028613 2.460000e-179 640.0
37 TraesCS4A01G449700 chr2A 88.889 414 44 1 5179 5590 674050066 674050479 7.230000e-140 508.0
38 TraesCS4A01G449700 chr2A 86.493 422 46 5 5179 5590 674030533 674030953 3.440000e-123 453.0
39 TraesCS4A01G449700 chr2A 75.679 810 135 40 976 1757 674045887 674046662 1.670000e-91 348.0
40 TraesCS4A01G449700 chr2A 76.081 694 148 13 3738 4419 674059768 674060455 6.000000e-91 346.0
41 TraesCS4A01G449700 chr2A 80.797 276 40 11 1464 1734 674026489 674026756 3.820000e-48 204.0
42 TraesCS4A01G449700 chrUn 99.904 1044 1 0 6825 7868 50879843 50878800 0.000000e+00 1923.0
43 TraesCS4A01G449700 chrUn 100.000 898 0 0 6971 7868 50897671 50896774 0.000000e+00 1659.0
44 TraesCS4A01G449700 chrUn 98.340 723 12 0 254 976 55786967 55786245 0.000000e+00 1269.0
45 TraesCS4A01G449700 chrUn 98.340 723 12 0 254 976 302514790 302515512 0.000000e+00 1269.0
46 TraesCS4A01G449700 chrUn 100.000 197 0 0 7879 8075 50870067 50869871 1.660000e-96 364.0
47 TraesCS4A01G449700 chrUn 100.000 197 0 0 7879 8075 50888373 50888177 1.660000e-96 364.0
48 TraesCS4A01G449700 chr3B 98.064 723 14 0 254 976 797016598 797015876 0.000000e+00 1258.0
49 TraesCS4A01G449700 chr3B 97.925 723 15 0 254 976 101644228 101644950 0.000000e+00 1253.0
50 TraesCS4A01G449700 chr3B 94.949 198 9 1 7879 8075 42164383 42164186 7.870000e-80 309.0
51 TraesCS4A01G449700 chr3B 91.457 199 15 2 7879 8075 799451613 799451811 1.030000e-68 272.0
52 TraesCS4A01G449700 chr3A 98.064 723 14 0 254 976 146779231 146779953 0.000000e+00 1258.0
53 TraesCS4A01G449700 chr3A 97.925 723 15 0 254 976 203840545 203841267 0.000000e+00 1253.0
54 TraesCS4A01G449700 chr3A 78.900 673 99 12 5696 6362 25406300 25406935 4.510000e-112 416.0
55 TraesCS4A01G449700 chr3A 89.756 205 13 1 7879 8075 744756271 744756475 1.040000e-63 255.0
56 TraesCS4A01G449700 chr3A 86.517 178 20 3 7901 8075 28154096 28153920 8.270000e-45 193.0
57 TraesCS4A01G449700 chr1B 79.073 669 99 16 5696 6360 175892765 175892134 9.690000e-114 422.0
58 TraesCS4A01G449700 chr1B 94.444 198 10 1 7879 8075 84409601 84409404 3.660000e-78 303.0
59 TraesCS4A01G449700 chr1B 92.386 197 15 0 7879 8075 624008024 624007828 1.720000e-71 281.0
60 TraesCS4A01G449700 chr1B 90.741 54 3 2 4778 4829 566020040 566020093 4.040000e-08 71.3
61 TraesCS4A01G449700 chr5B 93.434 198 12 1 7879 8075 265446375 265446572 7.930000e-75 292.0
62 TraesCS4A01G449700 chr5B 83.636 55 9 0 4739 4793 634674454 634674508 1.500000e-02 52.8


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 TraesCS4A01G449700 chr4A 715712866 715720940 8074 False 14875.000000 14875 100.000000 1 8075 1 chr4A.!!$F1 8074
1 TraesCS4A01G449700 chr4A 715875718 715880353 4635 True 1550.250000 3528 93.530500 1 4873 4 chr4A.!!$R2 4872
2 TraesCS4A01G449700 chr4A 159496654 159497377 723 True 1264.000000 1264 98.204000 254 976 1 chr4A.!!$R1 722
3 TraesCS4A01G449700 chr7D 17862953 17870094 7141 True 3341.333333 9140 93.936667 1 7717 3 chr7D.!!$R1 7716
4 TraesCS4A01G449700 chr7A 17357873 17364453 6580 True 3056.333333 5707 93.285667 1 7248 3 chr7A.!!$R2 7247
5 TraesCS4A01G449700 chr2B 64336446 64337168 722 True 1247.000000 1247 97.787000 254 976 1 chr2B.!!$R1 722
6 TraesCS4A01G449700 chr2B 629101705 629107341 5636 False 927.000000 2036 85.989500 1052 6543 4 chr2B.!!$F3 5491
7 TraesCS4A01G449700 chr2B 629019412 629025098 5686 False 565.500000 1018 81.547750 1344 6564 4 chr2B.!!$F2 5220
8 TraesCS4A01G449700 chr2B 629123362 629124048 686 False 361.000000 361 76.445000 3738 4418 1 chr2B.!!$F1 680
9 TraesCS4A01G449700 chr2D 529544682 529549051 4369 False 1153.666667 1980 85.924667 2089 6540 3 chr2D.!!$F3 4451
10 TraesCS4A01G449700 chr2D 529533263 529538771 5508 False 659.000000 994 82.223600 1344 6557 5 chr2D.!!$F2 5213
11 TraesCS4A01G449700 chr2A 733694944 733695661 717 False 1242.000000 1242 97.787000 254 976 1 chr2A.!!$F2 722
12 TraesCS4A01G449700 chr2A 674045887 674051500 5613 False 958.250000 1953 83.545000 976 6545 4 chr2A.!!$F4 5569
13 TraesCS4A01G449700 chr2A 674026489 674031988 5499 False 569.500000 981 82.554500 1464 6564 4 chr2A.!!$F3 5100
14 TraesCS4A01G449700 chr2A 674059768 674060455 687 False 346.000000 346 76.081000 3738 4419 1 chr2A.!!$F1 681
15 TraesCS4A01G449700 chrUn 50878800 50879843 1043 True 1923.000000 1923 99.904000 6825 7868 1 chrUn.!!$R2 1043
16 TraesCS4A01G449700 chrUn 50896774 50897671 897 True 1659.000000 1659 100.000000 6971 7868 1 chrUn.!!$R4 897
17 TraesCS4A01G449700 chrUn 55786245 55786967 722 True 1269.000000 1269 98.340000 254 976 1 chrUn.!!$R5 722
18 TraesCS4A01G449700 chrUn 302514790 302515512 722 False 1269.000000 1269 98.340000 254 976 1 chrUn.!!$F1 722
19 TraesCS4A01G449700 chr3B 797015876 797016598 722 True 1258.000000 1258 98.064000 254 976 1 chr3B.!!$R2 722
20 TraesCS4A01G449700 chr3B 101644228 101644950 722 False 1253.000000 1253 97.925000 254 976 1 chr3B.!!$F1 722
21 TraesCS4A01G449700 chr3A 146779231 146779953 722 False 1258.000000 1258 98.064000 254 976 1 chr3A.!!$F2 722
22 TraesCS4A01G449700 chr3A 203840545 203841267 722 False 1253.000000 1253 97.925000 254 976 1 chr3A.!!$F3 722
23 TraesCS4A01G449700 chr3A 25406300 25406935 635 False 416.000000 416 78.900000 5696 6362 1 chr3A.!!$F1 666
24 TraesCS4A01G449700 chr1B 175892134 175892765 631 True 422.000000 422 79.073000 5696 6360 1 chr1B.!!$R2 664

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
942 957 1.133598 GGCCGGGTGTAATGCTTAAAC 59.866 52.381 2.18 0.0 0.00 2.01 F
1492 1753 1.133668 AGTCAGCCCCTTATCCAATGC 60.134 52.381 0.00 0.0 0.00 3.56 F
1744 2013 1.348036 GGTACCTGGAGCAGTTTGACT 59.652 52.381 4.06 0.0 0.00 3.41 F
1851 2150 3.676291 TTTATTTGCAGGGAGGTTTGC 57.324 42.857 0.00 0.0 40.67 3.68 F
3536 5081 1.817357 TCTGTTCTCTCGCCTCGTAA 58.183 50.000 0.00 0.0 0.00 3.18 F
4135 5710 1.191535 TATGTTCAGGTAGGCTGCGT 58.808 50.000 0.00 0.0 0.00 5.24 F
5418 7314 1.140312 ACTGGGCAAAGGAGAAGTCA 58.860 50.000 0.00 0.0 0.00 3.41 F
5859 7843 1.261989 TCGCGACGGAAATAGAAACG 58.738 50.000 3.71 0.0 0.00 3.60 F
6814 8808 1.985116 AGGCTGGAGGACTTCGACC 60.985 63.158 0.00 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 2296 4.024048 GGAGATTCAGCACGTTCAAGAAAA 60.024 41.667 0.00 0.0 0.00 2.29 R
2583 3413 5.572126 GGCTATAGTTCATCGTCGGAATAAC 59.428 44.000 0.84 0.0 0.00 1.89 R
3513 5058 2.356382 ACGAGGCGAGAGAACAGAATAG 59.644 50.000 0.00 0.0 0.00 1.73 R
3824 5399 1.066286 AGTGATGCAGCTCCAAGACTC 60.066 52.381 2.53 0.0 0.00 3.36 R
5268 7152 0.464036 CCACGCCAACTATAGCTCCA 59.536 55.000 0.00 0.0 0.00 3.86 R
5538 7438 1.701847 CCATATCCTCCCTGACCAAGG 59.298 57.143 0.00 0.0 46.94 3.61 R
6816 8810 0.406750 TGACCCGAAGTACCTCCTCA 59.593 55.000 0.00 0.0 0.00 3.86 R
6969 8963 4.776322 TCGCCGCCACCCTTGATG 62.776 66.667 0.00 0.0 0.00 3.07 R
8033 10040 0.320374 ACCGAATCTTCACGAGGCAA 59.680 50.000 0.00 0.0 0.00 4.52 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
58 59 1.903877 CGGAACCTCACAGCCCTGAT 61.904 60.000 1.69 0.00 0.00 2.90
141 150 3.724374 TGTCCTAACTTGAAACCGACAG 58.276 45.455 0.00 0.00 0.00 3.51
197 207 8.858003 TTACTCGTCTATCTGATTCAATGTTC 57.142 34.615 0.00 0.00 0.00 3.18
240 250 1.145571 ACTTGACAGGGCCTTTACCA 58.854 50.000 1.32 0.00 0.00 3.25
241 251 1.710809 ACTTGACAGGGCCTTTACCAT 59.289 47.619 1.32 0.00 0.00 3.55
242 252 2.290960 ACTTGACAGGGCCTTTACCATC 60.291 50.000 1.32 0.00 0.00 3.51
243 253 1.668826 TGACAGGGCCTTTACCATCT 58.331 50.000 1.32 0.00 0.00 2.90
244 254 1.992557 TGACAGGGCCTTTACCATCTT 59.007 47.619 1.32 0.00 0.00 2.40
245 255 2.378547 TGACAGGGCCTTTACCATCTTT 59.621 45.455 1.32 0.00 0.00 2.52
246 256 3.017442 GACAGGGCCTTTACCATCTTTC 58.983 50.000 1.32 0.00 0.00 2.62
247 257 2.378547 ACAGGGCCTTTACCATCTTTCA 59.621 45.455 1.32 0.00 0.00 2.69
248 258 3.011708 ACAGGGCCTTTACCATCTTTCAT 59.988 43.478 1.32 0.00 0.00 2.57
249 259 3.633986 CAGGGCCTTTACCATCTTTCATC 59.366 47.826 1.32 0.00 0.00 2.92
250 260 2.618709 GGGCCTTTACCATCTTTCATCG 59.381 50.000 0.84 0.00 0.00 3.84
251 261 2.618709 GGCCTTTACCATCTTTCATCGG 59.381 50.000 0.00 0.00 0.00 4.18
252 262 2.618709 GCCTTTACCATCTTTCATCGGG 59.381 50.000 0.00 0.00 0.00 5.14
455 470 4.603989 TCTTTCAATGCAAATTGGCTCA 57.396 36.364 6.34 0.00 32.65 4.26
728 743 2.771943 TGGAGAATCGAGGCCTGTTTAT 59.228 45.455 12.00 1.18 34.37 1.40
748 763 4.842531 ATGGAGGTGTGTACATGATTGA 57.157 40.909 0.00 0.00 0.00 2.57
942 957 1.133598 GGCCGGGTGTAATGCTTAAAC 59.866 52.381 2.18 0.00 0.00 2.01
1038 1053 8.456471 TGAGATTCACAACTCAAATCATGATTC 58.544 33.333 20.95 4.41 39.68 2.52
1073 1089 5.245075 ACAATGAATACATTTGTTTCCCCGT 59.755 36.000 0.00 0.00 43.17 5.28
1106 1122 7.615757 TCTCACAGTTCCTCTCTTCAACATATA 59.384 37.037 0.00 0.00 0.00 0.86
1423 1680 9.148104 GGAACTGTACGTATTTACTGAATTCTT 57.852 33.333 7.05 0.00 0.00 2.52
1492 1753 1.133668 AGTCAGCCCCTTATCCAATGC 60.134 52.381 0.00 0.00 0.00 3.56
1658 1924 6.017605 GCTCCACACCATTCAATCTTATGTAG 60.018 42.308 0.00 0.00 0.00 2.74
1662 1931 8.184192 CCACACCATTCAATCTTATGTAGTTTC 58.816 37.037 0.00 0.00 0.00 2.78
1672 1941 9.454859 CAATCTTATGTAGTTTCCCTCTCTTTT 57.545 33.333 0.00 0.00 0.00 2.27
1741 2010 2.270352 TTGGTACCTGGAGCAGTTTG 57.730 50.000 14.36 0.00 0.00 2.93
1744 2013 1.348036 GGTACCTGGAGCAGTTTGACT 59.652 52.381 4.06 0.00 0.00 3.41
1787 2056 5.874810 TGTTCCAAGTCATAGTAATGCTGTC 59.125 40.000 0.00 0.00 32.76 3.51
1851 2150 3.676291 TTTATTTGCAGGGAGGTTTGC 57.324 42.857 0.00 0.00 40.67 3.68
1955 2296 7.333672 GGAAGATTCATTTTAGTTACGTGAGGT 59.666 37.037 0.00 0.00 0.00 3.85
2009 2355 9.890629 GGCCTCTTAAGAAAATTTCCATTTAAT 57.109 29.630 6.63 0.00 31.89 1.40
2133 2696 5.772825 TCTTTCACTACTTTGCTGCATTT 57.227 34.783 1.84 0.00 0.00 2.32
2397 3190 4.395542 GCTCTTCTTCACTTGCATTCATCT 59.604 41.667 0.00 0.00 0.00 2.90
2398 3191 5.447548 GCTCTTCTTCACTTGCATTCATCTC 60.448 44.000 0.00 0.00 0.00 2.75
2548 3378 9.973450 TCTGATAAGCTTGTATCAATAGACTTC 57.027 33.333 9.86 0.00 39.43 3.01
2558 3388 8.561932 TGTATCAATAGACTTCTCGAAATTCG 57.438 34.615 9.38 9.38 42.10 3.34
2560 3390 5.407502 TCAATAGACTTCTCGAAATTCGCA 58.592 37.500 10.93 0.00 40.21 5.10
2583 3413 8.365210 CGCAAGTTTAAATTTACTGTAAGCATG 58.635 33.333 0.00 0.00 37.60 4.06
2597 3427 4.506288 TGTAAGCATGTTATTCCGACGATG 59.494 41.667 0.00 0.00 0.00 3.84
3248 4130 7.506938 AGGCTGTTTTGGTGCATATATCTAAAT 59.493 33.333 0.00 0.00 0.00 1.40
3536 5081 1.817357 TCTGTTCTCTCGCCTCGTAA 58.183 50.000 0.00 0.00 0.00 3.18
3702 5271 4.353777 AGGAACTATAGACCTGCAACTGA 58.646 43.478 17.55 0.00 36.02 3.41
3782 5357 2.373169 TGCTGTGGACTCTGGAAAATCT 59.627 45.455 0.00 0.00 0.00 2.40
3824 5399 1.588404 GTGTATGAACCTGATCGTGCG 59.412 52.381 0.00 0.00 0.00 5.34
3843 5418 1.367659 GAGTCTTGGAGCTGCATCAC 58.632 55.000 9.39 8.86 0.00 3.06
4130 5705 8.870879 GTTTTCGATATATATGTTCAGGTAGGC 58.129 37.037 0.00 0.00 0.00 3.93
4135 5710 1.191535 TATGTTCAGGTAGGCTGCGT 58.808 50.000 0.00 0.00 0.00 5.24
4536 6248 9.559958 CAATCTTATGCGTCTTGAAATAAAAGT 57.440 29.630 0.00 0.00 0.00 2.66
4561 6275 9.221775 GTAACCGAAAATACTAAAGCATCAATG 57.778 33.333 0.00 0.00 0.00 2.82
4570 6284 6.655078 ACTAAAGCATCAATGTGAAAAGGT 57.345 33.333 0.00 0.00 0.00 3.50
4571 6285 7.054491 ACTAAAGCATCAATGTGAAAAGGTT 57.946 32.000 0.00 0.00 0.00 3.50
4596 6310 3.309682 CACTATGTGGCGATGGTTACTTG 59.690 47.826 0.00 0.00 0.00 3.16
4608 6322 5.352293 CGATGGTTACTTGTTTAGGGGTAAC 59.648 44.000 0.00 0.00 41.56 2.50
4613 6327 8.277918 TGGTTACTTGTTTAGGGGTAACTAAAA 58.722 33.333 12.42 0.00 42.63 1.52
4616 6330 9.919416 TTACTTGTTTAGGGGTAACTAAAAAGT 57.081 29.630 18.51 18.51 42.63 2.66
4621 6335 8.219868 TGTTTAGGGGTAACTAAAAAGTAGCTT 58.780 33.333 0.00 0.00 42.63 3.74
4622 6336 8.725148 GTTTAGGGGTAACTAAAAAGTAGCTTC 58.275 37.037 0.00 0.00 42.63 3.86
4623 6337 6.443995 AGGGGTAACTAAAAAGTAGCTTCA 57.556 37.500 0.00 0.00 0.00 3.02
4637 6351 1.341852 AGCTTCACATTGCATGCACAA 59.658 42.857 22.58 7.32 0.00 3.33
4649 6363 3.125316 GCATGCACAAAATGACACAAGT 58.875 40.909 14.21 0.00 0.00 3.16
4654 6368 6.389830 TGCACAAAATGACACAAGTAAGAT 57.610 33.333 0.00 0.00 0.00 2.40
4655 6369 6.207928 TGCACAAAATGACACAAGTAAGATG 58.792 36.000 0.00 0.00 0.00 2.90
4684 6419 4.669206 AGATGTCATCAAGATTCGCTCT 57.331 40.909 15.20 0.00 34.96 4.09
4690 6425 5.755375 TGTCATCAAGATTCGCTCTAATTCC 59.245 40.000 0.00 0.00 32.41 3.01
4694 6429 7.336679 TCATCAAGATTCGCTCTAATTCCAAAA 59.663 33.333 0.00 0.00 32.41 2.44
4696 6431 8.055279 TCAAGATTCGCTCTAATTCCAAAAAT 57.945 30.769 0.00 0.00 32.41 1.82
4697 6432 8.522830 TCAAGATTCGCTCTAATTCCAAAAATT 58.477 29.630 0.00 0.00 32.41 1.82
4698 6433 8.801913 CAAGATTCGCTCTAATTCCAAAAATTC 58.198 33.333 0.00 0.00 32.41 2.17
4699 6434 8.055279 AGATTCGCTCTAATTCCAAAAATTCA 57.945 30.769 0.00 0.00 30.26 2.57
4700 6435 8.522830 AGATTCGCTCTAATTCCAAAAATTCAA 58.477 29.630 0.00 0.00 30.26 2.69
4701 6436 9.305925 GATTCGCTCTAATTCCAAAAATTCAAT 57.694 29.630 0.00 0.00 0.00 2.57
4757 6544 9.847224 ATAATATCCGTTTTCACCACTAAATCT 57.153 29.630 0.00 0.00 0.00 2.40
4758 6545 5.880054 ATCCGTTTTCACCACTAAATCTG 57.120 39.130 0.00 0.00 0.00 2.90
4760 6547 4.753107 TCCGTTTTCACCACTAAATCTGTC 59.247 41.667 0.00 0.00 0.00 3.51
4776 6563 5.808042 ATCTGTCATGACGAGATTTTTGG 57.192 39.130 23.71 7.13 30.56 3.28
4782 6569 6.368791 TGTCATGACGAGATTTTTGGAACTAG 59.631 38.462 20.54 0.00 0.00 2.57
4863 6651 5.242795 ACTTGAGTTACCAGGCTAAACAT 57.757 39.130 8.65 0.00 0.00 2.71
4876 6664 7.155328 CCAGGCTAAACATAGGTAGTTATCAG 58.845 42.308 0.00 0.00 0.00 2.90
4877 6665 6.647067 CAGGCTAAACATAGGTAGTTATCAGC 59.353 42.308 0.00 0.00 0.00 4.26
4878 6666 5.634020 GGCTAAACATAGGTAGTTATCAGCG 59.366 44.000 0.00 0.00 0.00 5.18
4880 6668 7.365741 GCTAAACATAGGTAGTTATCAGCGTA 58.634 38.462 0.00 0.00 0.00 4.42
4910 6698 8.408601 AGTACATGTCATTTGAGATATTTTGGC 58.591 33.333 0.00 0.00 0.00 4.52
4911 6699 7.172868 ACATGTCATTTGAGATATTTTGGCA 57.827 32.000 0.00 0.00 0.00 4.92
4914 6702 7.230849 TGTCATTTGAGATATTTTGGCAACT 57.769 32.000 0.00 0.00 37.61 3.16
4950 6738 4.584327 AAGTTTTCACCTGGTAATGTGC 57.416 40.909 0.00 0.00 32.51 4.57
4971 6759 5.231568 GTGCGAGTTACCATACTATTCACAC 59.768 44.000 0.00 0.00 0.00 3.82
4972 6760 4.440103 GCGAGTTACCATACTATTCACACG 59.560 45.833 0.00 0.00 0.00 4.49
4985 6799 7.807687 ACTATTCACACGTTGTTAGATGTAC 57.192 36.000 0.00 0.00 0.00 2.90
4993 6807 3.174375 GTTGTTAGATGTACCGTCGACC 58.826 50.000 10.58 0.00 0.00 4.79
5039 6856 1.392168 CGCTACAACATGTGGGTTACG 59.608 52.381 4.95 7.78 28.80 3.18
5101 6920 9.766277 GTCATTTGAGATGTTTAGATTTCTGTC 57.234 33.333 0.00 0.00 0.00 3.51
5117 6937 9.512588 AGATTTCTGTCAAAAGTATGTCATTCT 57.487 29.630 0.00 0.00 0.00 2.40
5120 6940 9.778741 TTTCTGTCAAAAGTATGTCATTCTAGT 57.221 29.630 0.00 0.00 0.00 2.57
5123 6943 9.862371 CTGTCAAAAGTATGTCATTCTAGTAGT 57.138 33.333 0.00 0.00 0.00 2.73
5124 6944 9.639601 TGTCAAAAGTATGTCATTCTAGTAGTG 57.360 33.333 0.00 0.00 0.00 2.74
5177 7012 9.845740 AGCAACCAGTTTACATATAATCATACA 57.154 29.630 0.00 0.00 0.00 2.29
5195 7079 9.725019 AATCATACATTTCTGACAAGTGAACTA 57.275 29.630 0.00 0.00 0.00 2.24
5268 7152 4.760204 GGTAGTAAAACAGGTGTGATTGCT 59.240 41.667 5.34 5.34 0.00 3.91
5283 7167 2.332063 TTGCTGGAGCTATAGTTGGC 57.668 50.000 0.84 0.90 42.66 4.52
5286 7170 1.858091 CTGGAGCTATAGTTGGCGTG 58.142 55.000 0.84 0.00 33.93 5.34
5312 7196 8.520351 GGTAGTTTTAGGATTGTTAGCATTTGT 58.480 33.333 0.00 0.00 0.00 2.83
5387 7278 4.109765 AGGTATGGGATACACTAGGACCAT 59.890 45.833 0.00 0.00 41.28 3.55
5413 7309 2.708861 TGTTCTAACTGGGCAAAGGAGA 59.291 45.455 0.00 0.00 0.00 3.71
5418 7314 1.140312 ACTGGGCAAAGGAGAAGTCA 58.860 50.000 0.00 0.00 0.00 3.41
5421 7317 2.958355 CTGGGCAAAGGAGAAGTCAAAA 59.042 45.455 0.00 0.00 0.00 2.44
5469 7369 5.185056 TCTTGCAGAGCTGTACAGTATTGTA 59.815 40.000 23.44 14.87 38.76 2.41
5559 7459 2.694397 CTTGGTCAGGGAGGATATGGA 58.306 52.381 0.00 0.00 0.00 3.41
5574 7474 6.296803 AGGATATGGATCGGTTTTTAAGGTC 58.703 40.000 0.00 0.00 32.28 3.85
5575 7475 6.059484 GGATATGGATCGGTTTTTAAGGTCA 58.941 40.000 0.00 0.00 32.28 4.02
5613 7577 8.816894 ACAGTCTTAAATATCAGAAGGAAGACA 58.183 33.333 12.79 0.00 42.31 3.41
5624 7588 7.406031 TCAGAAGGAAGACATCTTTATACGT 57.594 36.000 0.00 0.00 36.11 3.57
5627 7592 8.936864 CAGAAGGAAGACATCTTTATACGTTTT 58.063 33.333 0.00 0.00 36.11 2.43
5724 7700 2.937519 TGATGTTTGGCAGTGTGGTAA 58.062 42.857 0.00 0.00 0.00 2.85
5859 7843 1.261989 TCGCGACGGAAATAGAAACG 58.738 50.000 3.71 0.00 0.00 3.60
5892 7876 5.220892 GGTTCAACACCGTAATCTTGTGAAA 60.221 40.000 0.00 0.00 35.12 2.69
6058 8046 9.758651 AGACAACTAAAAATTTAAACCCACATC 57.241 29.630 0.00 0.00 0.00 3.06
6322 8312 4.884164 AGTGCATTTCTATCTTGCTAACCC 59.116 41.667 0.00 0.00 37.28 4.11
6338 8328 7.562454 TGCTAACCCTTTATGTTTATGTAGC 57.438 36.000 0.00 0.00 0.00 3.58
6347 8337 9.567848 CCTTTATGTTTATGTAGCATTTTCGTT 57.432 29.630 0.00 0.00 0.00 3.85
6545 8539 2.004583 TTCGAATGGGTAAGCTCACG 57.995 50.000 0.00 0.00 0.00 4.35
6604 8598 9.550406 CTATCGGTAAAACCCATAGTGAAAATA 57.450 33.333 3.37 0.00 35.53 1.40
6641 8635 6.753180 TGGAAATATAGAGCTCACATGTCTC 58.247 40.000 17.77 0.00 0.00 3.36
6643 8637 5.384063 AATATAGAGCTCACATGTCTCCG 57.616 43.478 17.77 0.00 0.00 4.63
6717 8711 2.637521 CATCCTGTGCACAGTGCTT 58.362 52.632 37.55 20.44 45.31 3.91
6814 8808 1.985116 AGGCTGGAGGACTTCGACC 60.985 63.158 0.00 0.00 0.00 4.79
6816 8810 2.637383 GCTGGAGGACTTCGACCGT 61.637 63.158 0.00 0.00 0.00 4.83
6969 8963 0.657840 GCTACATCACGGAATGGCAC 59.342 55.000 0.00 0.00 0.00 5.01
7864 9871 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
7865 9872 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
7866 9873 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
7867 9874 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
7897 9904 4.838152 GGCGGCGCAGAAGATCCA 62.838 66.667 34.36 0.00 0.00 3.41
7898 9905 3.267860 GCGGCGCAGAAGATCCAG 61.268 66.667 29.21 0.00 0.00 3.86
7899 9906 3.267860 CGGCGCAGAAGATCCAGC 61.268 66.667 10.83 0.00 0.00 4.85
7900 9907 2.899339 GGCGCAGAAGATCCAGCC 60.899 66.667 10.83 0.00 37.61 4.85
7901 9908 3.267860 GCGCAGAAGATCCAGCCG 61.268 66.667 0.30 0.00 0.00 5.52
7902 9909 3.267860 CGCAGAAGATCCAGCCGC 61.268 66.667 0.00 0.00 0.00 6.53
7903 9910 2.899339 GCAGAAGATCCAGCCGCC 60.899 66.667 0.00 0.00 0.00 6.13
7904 9911 2.906458 CAGAAGATCCAGCCGCCT 59.094 61.111 0.00 0.00 0.00 5.52
7905 9912 1.523258 CAGAAGATCCAGCCGCCTG 60.523 63.158 0.00 0.00 38.85 4.85
7906 9913 2.899339 GAAGATCCAGCCGCCTGC 60.899 66.667 0.00 0.00 37.77 4.85
7927 9934 4.176752 GGATGGGCCCCTGTCGTC 62.177 72.222 22.27 4.26 0.00 4.20
7928 9935 3.083997 GATGGGCCCCTGTCGTCT 61.084 66.667 22.27 0.00 0.00 4.18
7929 9936 3.083997 ATGGGCCCCTGTCGTCTC 61.084 66.667 22.27 0.00 0.00 3.36
7934 9941 4.477975 CCCCTGTCGTCTCGCGTC 62.478 72.222 5.77 0.00 42.13 5.19
7935 9942 3.432588 CCCTGTCGTCTCGCGTCT 61.433 66.667 5.77 0.00 42.13 4.18
7936 9943 2.202362 CCTGTCGTCTCGCGTCTG 60.202 66.667 5.77 0.00 42.13 3.51
7937 9944 2.202362 CTGTCGTCTCGCGTCTGG 60.202 66.667 5.77 0.00 42.13 3.86
7938 9945 4.400109 TGTCGTCTCGCGTCTGGC 62.400 66.667 5.77 0.00 42.13 4.85
7939 9946 4.400109 GTCGTCTCGCGTCTGGCA 62.400 66.667 5.77 0.00 43.84 4.92
7940 9947 3.440415 TCGTCTCGCGTCTGGCAT 61.440 61.111 5.77 0.00 43.84 4.40
7941 9948 2.110352 TCGTCTCGCGTCTGGCATA 61.110 57.895 5.77 0.00 43.84 3.14
7942 9949 1.655654 CGTCTCGCGTCTGGCATAG 60.656 63.158 5.77 0.00 43.84 2.23
7943 9950 1.728069 GTCTCGCGTCTGGCATAGA 59.272 57.895 5.77 0.00 43.84 1.98
7950 9957 3.536917 TCTGGCATAGACCCGCGG 61.537 66.667 21.04 21.04 0.00 6.46
7951 9958 3.849951 CTGGCATAGACCCGCGGT 61.850 66.667 26.12 12.57 39.44 5.68
7952 9959 4.155733 TGGCATAGACCCGCGGTG 62.156 66.667 26.12 16.57 35.25 4.94
7953 9960 4.157120 GGCATAGACCCGCGGTGT 62.157 66.667 26.12 21.39 35.25 4.16
7954 9961 2.585247 GCATAGACCCGCGGTGTC 60.585 66.667 28.69 28.69 35.25 3.67
7955 9962 2.889617 CATAGACCCGCGGTGTCA 59.110 61.111 33.59 24.24 35.25 3.58
7956 9963 1.226974 CATAGACCCGCGGTGTCAG 60.227 63.158 33.59 23.73 35.25 3.51
7957 9964 2.423898 ATAGACCCGCGGTGTCAGG 61.424 63.158 33.59 19.09 35.25 3.86
7963 9970 4.025401 CGCGGTGTCAGGCCAAAC 62.025 66.667 5.01 2.43 0.00 2.93
7964 9971 3.670377 GCGGTGTCAGGCCAAACC 61.670 66.667 5.01 5.76 39.61 3.27
7966 9973 3.670377 GGTGTCAGGCCAAACCGC 61.670 66.667 5.01 0.00 46.52 5.68
7967 9974 4.025401 GTGTCAGGCCAAACCGCG 62.025 66.667 5.01 0.00 46.52 6.46
7968 9975 4.555709 TGTCAGGCCAAACCGCGT 62.556 61.111 5.01 0.00 46.52 6.01
7969 9976 3.723348 GTCAGGCCAAACCGCGTC 61.723 66.667 5.01 0.00 46.52 5.19
8008 10015 3.706373 CCCCCAGGTGGAGACGTG 61.706 72.222 0.00 0.00 37.65 4.49
8009 10016 2.923035 CCCCAGGTGGAGACGTGT 60.923 66.667 0.00 0.00 36.42 4.49
8010 10017 2.657237 CCCAGGTGGAGACGTGTC 59.343 66.667 3.66 3.66 36.42 3.67
8011 10018 2.258591 CCAGGTGGAGACGTGTCG 59.741 66.667 6.62 0.00 36.42 4.35
8012 10019 2.265904 CCAGGTGGAGACGTGTCGA 61.266 63.158 6.62 0.00 36.42 4.20
8013 10020 1.210413 CAGGTGGAGACGTGTCGAG 59.790 63.158 6.62 0.00 33.99 4.04
8014 10021 2.126424 GGTGGAGACGTGTCGAGC 60.126 66.667 10.88 10.88 34.09 5.03
8015 10022 2.502080 GTGGAGACGTGTCGAGCG 60.502 66.667 6.62 7.64 34.09 5.03
8016 10023 2.667199 TGGAGACGTGTCGAGCGA 60.667 61.111 14.99 0.00 34.09 4.93
8017 10024 2.098680 GGAGACGTGTCGAGCGAG 59.901 66.667 14.99 0.00 34.09 5.03
8018 10025 2.098680 GAGACGTGTCGAGCGAGG 59.901 66.667 14.99 0.00 34.09 4.63
8019 10026 2.358369 AGACGTGTCGAGCGAGGA 60.358 61.111 14.99 0.00 34.09 3.71
8020 10027 2.098680 GACGTGTCGAGCGAGGAG 59.901 66.667 14.99 0.00 0.00 3.69
8021 10028 3.384014 GACGTGTCGAGCGAGGAGG 62.384 68.421 14.99 0.00 0.00 4.30
8022 10029 4.180946 CGTGTCGAGCGAGGAGGG 62.181 72.222 3.52 0.00 0.00 4.30
8023 10030 3.827898 GTGTCGAGCGAGGAGGGG 61.828 72.222 0.00 0.00 0.00 4.79
8043 10050 4.980805 GCCCGTGTTGCCTCGTGA 62.981 66.667 0.00 0.00 0.00 4.35
8044 10051 2.280524 CCCGTGTTGCCTCGTGAA 60.281 61.111 0.00 0.00 0.00 3.18
8045 10052 2.317609 CCCGTGTTGCCTCGTGAAG 61.318 63.158 0.00 0.00 0.00 3.02
8046 10053 1.300620 CCGTGTTGCCTCGTGAAGA 60.301 57.895 0.00 0.00 0.00 2.87
8047 10054 0.670546 CCGTGTTGCCTCGTGAAGAT 60.671 55.000 0.00 0.00 0.00 2.40
8048 10055 1.148310 CGTGTTGCCTCGTGAAGATT 58.852 50.000 0.00 0.00 0.00 2.40
8049 10056 1.126846 CGTGTTGCCTCGTGAAGATTC 59.873 52.381 0.00 0.00 0.00 2.52
8050 10057 1.126846 GTGTTGCCTCGTGAAGATTCG 59.873 52.381 0.00 0.00 0.00 3.34
8051 10058 0.721718 GTTGCCTCGTGAAGATTCGG 59.278 55.000 0.00 0.00 0.00 4.30
8052 10059 0.320374 TTGCCTCGTGAAGATTCGGT 59.680 50.000 0.00 0.00 0.00 4.69
8053 10060 0.389817 TGCCTCGTGAAGATTCGGTG 60.390 55.000 0.00 0.00 0.00 4.94
8054 10061 1.084370 GCCTCGTGAAGATTCGGTGG 61.084 60.000 0.00 0.00 0.00 4.61
8055 10062 1.084370 CCTCGTGAAGATTCGGTGGC 61.084 60.000 0.00 0.00 0.00 5.01
8056 10063 1.413767 CTCGTGAAGATTCGGTGGCG 61.414 60.000 0.00 0.00 0.00 5.69
8057 10064 2.785258 GTGAAGATTCGGTGGCGC 59.215 61.111 0.00 0.00 0.00 6.53
8058 10065 2.032634 GTGAAGATTCGGTGGCGCA 61.033 57.895 10.83 0.00 0.00 6.09
8059 10066 1.741401 TGAAGATTCGGTGGCGCAG 60.741 57.895 10.83 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 6.325596 CAAGTTGAGAGTTCATACAGATCGA 58.674 40.000 0.00 0.00 32.27 3.59
141 150 8.076178 GGTGTGCAATTGGAATTATATACAGAC 58.924 37.037 7.72 1.35 0.00 3.51
197 207 5.682234 ATTTTGCCCTAAATCCCTGAAAG 57.318 39.130 0.00 0.00 0.00 2.62
240 250 1.477558 GGCACATCCCCGATGAAAGAT 60.478 52.381 8.57 0.00 42.09 2.40
241 251 0.107214 GGCACATCCCCGATGAAAGA 60.107 55.000 8.57 0.00 42.09 2.52
242 252 0.394216 TGGCACATCCCCGATGAAAG 60.394 55.000 8.57 0.18 42.09 2.62
243 253 0.394216 CTGGCACATCCCCGATGAAA 60.394 55.000 8.57 0.00 42.09 2.69
244 254 1.224315 CTGGCACATCCCCGATGAA 59.776 57.895 8.57 0.00 42.09 2.57
245 255 1.561769 AACTGGCACATCCCCGATGA 61.562 55.000 8.57 0.00 42.09 2.92
246 256 1.077501 AACTGGCACATCCCCGATG 60.078 57.895 0.08 0.08 44.71 3.84
247 257 1.077501 CAACTGGCACATCCCCGAT 60.078 57.895 0.00 0.00 38.20 4.18
248 258 2.063015 AACAACTGGCACATCCCCGA 62.063 55.000 0.00 0.00 38.20 5.14
249 259 0.322098 TAACAACTGGCACATCCCCG 60.322 55.000 0.00 0.00 38.20 5.73
250 260 1.917872 TTAACAACTGGCACATCCCC 58.082 50.000 0.00 0.00 38.20 4.81
251 261 4.461081 TGTTATTAACAACTGGCACATCCC 59.539 41.667 6.79 0.00 38.72 3.85
252 262 5.637006 TGTTATTAACAACTGGCACATCC 57.363 39.130 6.79 0.00 38.72 3.51
324 339 1.306148 TGACTCCGCGACGAAGATAT 58.694 50.000 8.23 0.00 0.00 1.63
728 743 4.565444 CCTTCAATCATGTACACACCTCCA 60.565 45.833 0.00 0.00 0.00 3.86
748 763 1.152610 TATCCCTCGCCGTAGCCTT 60.153 57.895 0.00 0.00 34.57 4.35
942 957 4.643334 AGGGGCGCTTTATTACTTAAAAGG 59.357 41.667 7.64 0.00 34.07 3.11
1038 1053 7.424227 AATGTATTCATTGTTGCAAACTTGG 57.576 32.000 0.00 0.00 41.95 3.61
1073 1089 9.035890 TGAAGAGAGGAACTGTGAGATTAATTA 57.964 33.333 0.00 0.00 41.55 1.40
1106 1122 6.610075 AATGCATTGATACCAAAAGTCCTT 57.390 33.333 12.09 0.00 35.67 3.36
1219 1235 9.908152 ACCAAAAGTAAATCTAAACTTGTATGC 57.092 29.630 0.00 0.00 36.12 3.14
1435 1693 1.000938 CAACTGGCTTGGCAGAAGAAC 60.001 52.381 27.00 0.00 0.00 3.01
1604 1866 8.896320 ATAATATATCAACAACACGGCAACTA 57.104 30.769 0.00 0.00 0.00 2.24
1672 1941 8.945195 AATCATTATCTGATGCCCATCTAAAA 57.055 30.769 9.44 0.74 44.03 1.52
1741 2010 6.568869 ACATAAGTGATCTTACAGCTCAGTC 58.431 40.000 0.00 0.00 38.71 3.51
1744 2013 6.070824 TGGAACATAAGTGATCTTACAGCTCA 60.071 38.462 0.00 0.00 38.71 4.26
1768 2037 8.453320 TCATTTTGACAGCATTACTATGACTTG 58.547 33.333 0.00 0.00 33.37 3.16
1822 2118 8.838649 ACCTCCCTGCAAATAAATATACTTTT 57.161 30.769 0.00 0.00 0.00 2.27
1926 2236 7.118680 TCACGTAACTAAAATGAATCTTCCACC 59.881 37.037 0.00 0.00 0.00 4.61
1955 2296 4.024048 GGAGATTCAGCACGTTCAAGAAAA 60.024 41.667 0.00 0.00 0.00 2.29
2009 2355 9.918630 GAAAGTACTAATCTAACACCTTACACA 57.081 33.333 0.00 0.00 0.00 3.72
2017 2363 8.654215 CCGAAAAGGAAAGTACTAATCTAACAC 58.346 37.037 0.00 0.00 45.00 3.32
2133 2696 7.177216 AGTCATTTAAAGCATCATTTCCTGACA 59.823 33.333 10.88 0.00 36.48 3.58
2397 3190 6.013379 AGGGTGTTCAAAGATGTCAGATTAGA 60.013 38.462 0.00 0.00 0.00 2.10
2398 3191 6.093219 CAGGGTGTTCAAAGATGTCAGATTAG 59.907 42.308 0.00 0.00 0.00 1.73
2507 3337 6.151985 AGCTTATCAGATATCCTACAGTTCCG 59.848 42.308 0.00 0.00 0.00 4.30
2548 3378 9.113876 AGTAAATTTAAACTTGCGAATTTCGAG 57.886 29.630 22.25 13.46 43.74 4.04
2558 3388 9.191995 ACATGCTTACAGTAAATTTAAACTTGC 57.808 29.630 0.00 2.15 0.00 4.01
2583 3413 5.572126 GGCTATAGTTCATCGTCGGAATAAC 59.428 44.000 0.84 0.00 0.00 1.89
2597 3427 6.261118 CAAGAAATGCACTTGGCTATAGTTC 58.739 40.000 7.49 0.00 45.15 3.01
2849 3705 8.738645 ATTATTCCCAAGAAATCTAGTGACAC 57.261 34.615 0.00 0.00 35.09 3.67
2853 3709 8.160106 AGGCTATTATTCCCAAGAAATCTAGTG 58.840 37.037 0.00 0.00 35.09 2.74
3513 5058 2.356382 ACGAGGCGAGAGAACAGAATAG 59.644 50.000 0.00 0.00 0.00 1.73
3518 5063 2.853731 ATTACGAGGCGAGAGAACAG 57.146 50.000 0.00 0.00 0.00 3.16
3536 5081 8.800370 AACAAAGTGACATTTTAAACCCAAAT 57.200 26.923 0.00 0.00 0.00 2.32
3824 5399 1.066286 AGTGATGCAGCTCCAAGACTC 60.066 52.381 2.53 0.00 0.00 3.36
3843 5418 5.670485 TGTTGGTGCTCCTGTAACATATAG 58.330 41.667 6.34 0.00 34.23 1.31
4130 5705 9.388346 TGTTTAATTTGTCACTTAATAACGCAG 57.612 29.630 0.00 0.00 0.00 5.18
4200 5899 7.838771 ACGTTCACCCTATACAAATAAGAAC 57.161 36.000 0.00 0.00 0.00 3.01
4517 6228 6.148150 TCGGTTACTTTTATTTCAAGACGCAT 59.852 34.615 0.00 0.00 0.00 4.73
4536 6248 8.952278 ACATTGATGCTTTAGTATTTTCGGTTA 58.048 29.630 0.00 0.00 0.00 2.85
4593 6307 8.509690 GCTACTTTTTAGTTACCCCTAAACAAG 58.490 37.037 0.00 0.00 36.81 3.16
4596 6310 8.627208 AAGCTACTTTTTAGTTACCCCTAAAC 57.373 34.615 0.00 0.00 36.81 2.01
4608 6322 7.502177 CATGCAATGTGAAGCTACTTTTTAG 57.498 36.000 0.00 0.00 40.20 1.85
4637 6351 8.225603 ACAGTTTCATCTTACTTGTGTCATTT 57.774 30.769 0.00 0.00 0.00 2.32
4649 6363 9.591792 CTTGATGACATCTACAGTTTCATCTTA 57.408 33.333 16.25 0.43 42.04 2.10
4654 6368 7.276438 CGAATCTTGATGACATCTACAGTTTCA 59.724 37.037 16.25 0.00 0.00 2.69
4655 6369 7.616673 CGAATCTTGATGACATCTACAGTTTC 58.383 38.462 16.25 15.66 0.00 2.78
4697 6432 9.585099 GTGCCATTTGAGATTAAAACATATTGA 57.415 29.630 0.00 0.00 0.00 2.57
4698 6433 9.368674 TGTGCCATTTGAGATTAAAACATATTG 57.631 29.630 0.00 0.00 0.00 1.90
4700 6435 9.754382 GATGTGCCATTTGAGATTAAAACATAT 57.246 29.630 0.00 0.00 0.00 1.78
4701 6436 8.196771 GGATGTGCCATTTGAGATTAAAACATA 58.803 33.333 0.00 0.00 36.34 2.29
4702 6437 7.043565 GGATGTGCCATTTGAGATTAAAACAT 58.956 34.615 0.00 0.00 36.34 2.71
4731 6466 9.847224 AGATTTAGTGGTGAAAACGGATATTAT 57.153 29.630 0.00 0.00 0.00 1.28
4740 6527 7.078228 GTCATGACAGATTTAGTGGTGAAAAC 58.922 38.462 21.07 0.00 0.00 2.43
4757 6544 5.063204 AGTTCCAAAAATCTCGTCATGACA 58.937 37.500 24.93 11.49 0.00 3.58
4758 6545 5.613358 AGTTCCAAAAATCTCGTCATGAC 57.387 39.130 16.21 16.21 0.00 3.06
4760 6547 6.968131 TCTAGTTCCAAAAATCTCGTCATG 57.032 37.500 0.00 0.00 0.00 3.07
4776 6563 8.153550 AGAACATATCAACATGGGATCTAGTTC 58.846 37.037 19.80 19.80 34.11 3.01
4782 6569 6.057533 TGACAGAACATATCAACATGGGATC 58.942 40.000 5.52 0.00 0.00 3.36
4822 6610 5.470098 TCAAGTTCTGCAGGTTGATAACTTC 59.530 40.000 20.19 0.00 35.57 3.01
4863 6651 8.739039 TGTACTTTTTACGCTGATAACTACCTA 58.261 33.333 0.00 0.00 0.00 3.08
4876 6664 7.295201 TCTCAAATGACATGTACTTTTTACGC 58.705 34.615 0.00 0.00 0.00 4.42
4924 6712 7.530010 CACATTACCAGGTGAAAACTTATGAG 58.470 38.462 0.76 0.00 37.18 2.90
4931 6719 2.550606 TCGCACATTACCAGGTGAAAAC 59.449 45.455 0.76 0.00 37.18 2.43
4950 6738 5.575957 ACGTGTGAATAGTATGGTAACTCG 58.424 41.667 0.00 0.00 37.61 4.18
4971 6759 2.842485 GTCGACGGTACATCTAACAACG 59.158 50.000 0.00 0.00 0.00 4.10
4972 6760 3.119708 AGGTCGACGGTACATCTAACAAC 60.120 47.826 9.92 0.00 0.00 3.32
5132 6967 7.173562 TGGTTGCTGTATTACGTCTTAAATGTT 59.826 33.333 0.00 0.00 0.00 2.71
5143 6978 5.849357 TGTAAACTGGTTGCTGTATTACG 57.151 39.130 0.00 0.00 0.00 3.18
5195 7079 7.056635 CACTGTAGGGGTGAAATCTGATAAAT 58.943 38.462 0.00 0.00 36.89 1.40
5268 7152 0.464036 CCACGCCAACTATAGCTCCA 59.536 55.000 0.00 0.00 0.00 3.86
5283 7167 5.640357 TGCTAACAATCCTAAAACTACCACG 59.360 40.000 0.00 0.00 0.00 4.94
5286 7170 8.520351 ACAAATGCTAACAATCCTAAAACTACC 58.480 33.333 0.00 0.00 0.00 3.18
5312 7196 3.303938 TGCCTCCAAACAAAGATTCCAA 58.696 40.909 0.00 0.00 0.00 3.53
5387 7278 6.071984 TCCTTTGCCCAGTTAGAACAAAATA 58.928 36.000 0.00 0.00 30.51 1.40
5538 7438 1.701847 CCATATCCTCCCTGACCAAGG 59.298 57.143 0.00 0.00 46.94 3.61
5547 7447 3.790089 AAAACCGATCCATATCCTCCC 57.210 47.619 0.00 0.00 0.00 4.30
5559 7459 5.414765 GGATGAACTGACCTTAAAAACCGAT 59.585 40.000 0.00 0.00 0.00 4.18
5574 7474 9.784531 ATATTTAAGACTGTATGGGATGAACTG 57.215 33.333 0.00 0.00 0.00 3.16
5724 7700 4.464008 TCAGCAATGGAAGAAGTTTCAGT 58.536 39.130 0.00 0.00 0.00 3.41
5871 7855 6.038825 ACAATTTCACAAGATTACGGTGTTGA 59.961 34.615 0.00 0.00 34.27 3.18
5892 7876 2.756760 CTCAAGGCAGCAACCATACAAT 59.243 45.455 0.00 0.00 0.00 2.71
6058 8046 2.276732 TGACTTCCCTTTTCCTGCAG 57.723 50.000 6.78 6.78 0.00 4.41
6233 8223 5.000591 TCATCATAAAGTTTTGCGAGTCCA 58.999 37.500 0.00 0.00 0.00 4.02
6338 8328 5.052436 CGCCATTAGCATACAAACGAAAATG 60.052 40.000 0.00 0.00 44.04 2.32
6347 8337 5.050634 GTCGATAAACGCCATTAGCATACAA 60.051 40.000 0.00 0.00 44.04 2.41
6545 8539 2.706112 ATAGGGCCTAGAGTTCCTCC 57.294 55.000 19.74 0.00 0.00 4.30
6568 8562 6.433404 TGGGTTTTACCGATAGCACATAAAAA 59.567 34.615 0.00 0.00 39.83 1.94
6569 8563 5.944599 TGGGTTTTACCGATAGCACATAAAA 59.055 36.000 0.00 0.00 39.83 1.52
6573 8567 3.637911 TGGGTTTTACCGATAGCACAT 57.362 42.857 0.00 0.00 39.83 3.21
6641 8635 5.478407 AGGGTTTGATTTAAAATTCTGCGG 58.522 37.500 0.00 0.00 0.00 5.69
6643 8637 7.378181 TGAGAGGGTTTGATTTAAAATTCTGC 58.622 34.615 0.00 0.00 0.00 4.26
6717 8711 5.466728 GCATCGAGATGGTAAGCTAAAATGA 59.533 40.000 14.13 0.00 39.16 2.57
6814 8808 0.964358 ACCCGAAGTACCTCCTCACG 60.964 60.000 0.00 0.00 0.00 4.35
6816 8810 0.406750 TGACCCGAAGTACCTCCTCA 59.593 55.000 0.00 0.00 0.00 3.86
6969 8963 4.776322 TCGCCGCCACCCTTGATG 62.776 66.667 0.00 0.00 0.00 3.07
7880 9887 4.838152 TGGATCTTCTGCGCCGCC 62.838 66.667 6.63 0.00 0.00 6.13
7881 9888 3.267860 CTGGATCTTCTGCGCCGC 61.268 66.667 4.18 0.00 0.00 6.53
7882 9889 3.267860 GCTGGATCTTCTGCGCCG 61.268 66.667 4.18 0.00 0.00 6.46
7883 9890 2.899339 GGCTGGATCTTCTGCGCC 60.899 66.667 4.18 0.00 33.27 6.53
7884 9891 3.267860 CGGCTGGATCTTCTGCGC 61.268 66.667 0.00 0.00 33.27 6.09
7885 9892 3.267860 GCGGCTGGATCTTCTGCG 61.268 66.667 0.00 0.00 33.27 5.18
7886 9893 2.899339 GGCGGCTGGATCTTCTGC 60.899 66.667 0.00 0.00 0.00 4.26
7887 9894 1.523258 CAGGCGGCTGGATCTTCTG 60.523 63.158 30.03 2.63 0.00 3.02
7888 9895 2.906458 CAGGCGGCTGGATCTTCT 59.094 61.111 30.03 0.00 0.00 2.85
7889 9896 2.899339 GCAGGCGGCTGGATCTTC 60.899 66.667 36.25 17.52 40.25 2.87
7910 9917 4.176752 GACGACAGGGGCCCATCC 62.177 72.222 27.72 9.91 0.00 3.51
7911 9918 3.083997 AGACGACAGGGGCCCATC 61.084 66.667 27.72 20.58 0.00 3.51
7912 9919 3.083997 GAGACGACAGGGGCCCAT 61.084 66.667 27.72 16.07 0.00 4.00
7925 9932 0.592754 GTCTATGCCAGACGCGAGAC 60.593 60.000 15.93 9.03 44.19 3.36
7926 9933 1.728069 GTCTATGCCAGACGCGAGA 59.272 57.895 15.93 0.00 44.19 4.04
7927 9934 4.310672 GTCTATGCCAGACGCGAG 57.689 61.111 15.93 1.33 44.19 5.03
7933 9940 3.536917 CCGCGGGTCTATGCCAGA 61.537 66.667 20.10 0.00 0.00 3.86
7934 9941 3.849951 ACCGCGGGTCTATGCCAG 61.850 66.667 31.76 0.00 0.00 4.85
7935 9942 4.155733 CACCGCGGGTCTATGCCA 62.156 66.667 31.76 0.00 31.02 4.92
7936 9943 4.157120 ACACCGCGGGTCTATGCC 62.157 66.667 31.76 0.00 31.02 4.40
7937 9944 2.585247 GACACCGCGGGTCTATGC 60.585 66.667 31.76 10.38 31.02 3.14
7938 9945 1.226974 CTGACACCGCGGGTCTATG 60.227 63.158 32.51 23.84 36.26 2.23
7939 9946 2.423898 CCTGACACCGCGGGTCTAT 61.424 63.158 32.51 15.92 36.26 1.98
7940 9947 3.066190 CCTGACACCGCGGGTCTA 61.066 66.667 32.51 22.75 36.26 2.59
7946 9953 4.025401 GTTTGGCCTGACACCGCG 62.025 66.667 3.32 0.00 0.00 6.46
7947 9954 3.670377 GGTTTGGCCTGACACCGC 61.670 66.667 3.32 0.00 0.00 5.68
7948 9955 3.353836 CGGTTTGGCCTGACACCG 61.354 66.667 17.36 17.36 45.75 4.94
7949 9956 3.670377 GCGGTTTGGCCTGACACC 61.670 66.667 3.32 3.61 34.25 4.16
7950 9957 4.025401 CGCGGTTTGGCCTGACAC 62.025 66.667 3.32 0.00 34.25 3.67
7951 9958 4.555709 ACGCGGTTTGGCCTGACA 62.556 61.111 12.47 0.00 34.25 3.58
7952 9959 3.723348 GACGCGGTTTGGCCTGAC 61.723 66.667 12.47 1.89 34.25 3.51
7991 9998 3.706373 CACGTCTCCACCTGGGGG 61.706 72.222 9.31 9.31 39.19 5.40
7992 9999 2.923035 ACACGTCTCCACCTGGGG 60.923 66.667 0.00 0.00 37.22 4.96
7993 10000 2.657237 GACACGTCTCCACCTGGG 59.343 66.667 0.00 0.00 35.41 4.45
7994 10001 2.201436 CTCGACACGTCTCCACCTGG 62.201 65.000 0.00 0.00 0.00 4.45
7995 10002 1.210413 CTCGACACGTCTCCACCTG 59.790 63.158 0.00 0.00 0.00 4.00
7996 10003 2.627737 GCTCGACACGTCTCCACCT 61.628 63.158 0.00 0.00 0.00 4.00
7997 10004 2.126424 GCTCGACACGTCTCCACC 60.126 66.667 0.00 0.00 0.00 4.61
7998 10005 2.502080 CGCTCGACACGTCTCCAC 60.502 66.667 0.00 0.00 0.00 4.02
7999 10006 2.667199 TCGCTCGACACGTCTCCA 60.667 61.111 3.30 0.00 0.00 3.86
8000 10007 2.098680 CTCGCTCGACACGTCTCC 59.901 66.667 3.30 0.00 0.00 3.71
8001 10008 2.098680 CCTCGCTCGACACGTCTC 59.901 66.667 3.30 0.00 0.00 3.36
8002 10009 2.358369 TCCTCGCTCGACACGTCT 60.358 61.111 3.30 0.00 0.00 4.18
8003 10010 2.098680 CTCCTCGCTCGACACGTC 59.901 66.667 3.30 0.00 0.00 4.34
8004 10011 3.432588 CCTCCTCGCTCGACACGT 61.433 66.667 3.30 0.00 0.00 4.49
8005 10012 4.180946 CCCTCCTCGCTCGACACG 62.181 72.222 0.00 0.00 0.00 4.49
8006 10013 3.827898 CCCCTCCTCGCTCGACAC 61.828 72.222 0.00 0.00 0.00 3.67
8030 10037 1.126846 CGAATCTTCACGAGGCAACAC 59.873 52.381 0.00 0.00 41.41 3.32
8031 10038 1.428448 CGAATCTTCACGAGGCAACA 58.572 50.000 0.00 0.00 41.41 3.33
8032 10039 0.721718 CCGAATCTTCACGAGGCAAC 59.278 55.000 0.00 0.00 0.00 4.17
8033 10040 0.320374 ACCGAATCTTCACGAGGCAA 59.680 50.000 0.00 0.00 0.00 4.52
8034 10041 0.389817 CACCGAATCTTCACGAGGCA 60.390 55.000 0.00 0.00 0.00 4.75
8035 10042 1.084370 CCACCGAATCTTCACGAGGC 61.084 60.000 0.00 0.00 0.00 4.70
8036 10043 1.084370 GCCACCGAATCTTCACGAGG 61.084 60.000 0.00 0.00 0.00 4.63
8037 10044 1.413767 CGCCACCGAATCTTCACGAG 61.414 60.000 0.00 0.00 36.29 4.18
8038 10045 1.445410 CGCCACCGAATCTTCACGA 60.445 57.895 0.00 0.00 36.29 4.35
8039 10046 3.081133 CGCCACCGAATCTTCACG 58.919 61.111 0.00 0.00 36.29 4.35
8040 10047 1.970917 CTGCGCCACCGAATCTTCAC 61.971 60.000 4.18 0.00 36.29 3.18
8041 10048 1.741401 CTGCGCCACCGAATCTTCA 60.741 57.895 4.18 0.00 36.29 3.02
8042 10049 3.093278 CTGCGCCACCGAATCTTC 58.907 61.111 4.18 0.00 36.29 2.87
8043 10050 3.127533 GCTGCGCCACCGAATCTT 61.128 61.111 4.18 0.00 36.29 2.40


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

AutoCloner maintained by Alex Coulton.