Multiple sequence alignment - TraesCS2A01G569000

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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 TraesCS2A01G569000 chr2A 100.000 2627 0 0 1 2627 766980547 766983173 0.000000e+00 4852.0
1 TraesCS2A01G569000 chr2A 86.041 831 80 14 932 1739 767018623 767019440 0.000000e+00 859.0
2 TraesCS2A01G569000 chr2A 94.585 277 13 1 815 1091 767147315 767147041 6.720000e-116 427.0
3 TraesCS2A01G569000 chr2A 92.115 279 12 5 660 937 767017969 767018238 4.100000e-103 385.0
4 TraesCS2A01G569000 chr2A 88.506 261 16 5 1771 2021 767019731 767019987 1.180000e-78 303.0
5 TraesCS2A01G569000 chr2A 94.595 185 7 2 27 208 767015522 767015706 1.540000e-72 283.0
6 TraesCS2A01G569000 chr2A 85.892 241 15 9 1775 2006 767146754 767146524 3.380000e-59 239.0
7 TraesCS2A01G569000 chr2A 83.920 199 17 7 251 442 767015707 767015897 2.690000e-40 176.0
8 TraesCS2A01G569000 chr2A 82.075 212 15 13 443 651 767017718 767017909 2.710000e-35 159.0
9 TraesCS2A01G569000 chr2A 87.500 80 5 3 2541 2620 47512293 47512219 1.300000e-13 87.9
10 TraesCS2A01G569000 chr2A 80.412 97 7 6 2524 2620 12176008 12176092 2.180000e-06 63.9
11 TraesCS2A01G569000 chr2D 85.978 813 83 12 945 1739 598329357 598330156 0.000000e+00 841.0
12 TraesCS2A01G569000 chr2D 85.080 811 81 13 945 1739 642100911 642101697 0.000000e+00 791.0
13 TraesCS2A01G569000 chr2D 82.626 495 31 25 443 902 642100013 642100487 1.140000e-103 387.0
14 TraesCS2A01G569000 chr2D 94.262 244 12 2 660 902 598328690 598328932 3.190000e-99 372.0
15 TraesCS2A01G569000 chr2D 88.845 251 28 0 1771 2021 642212901 642213151 2.540000e-80 309.0
16 TraesCS2A01G569000 chr2D 89.270 233 16 6 1775 2006 642101770 642101994 1.540000e-72 283.0
17 TraesCS2A01G569000 chr2D 88.841 233 17 6 1775 2006 598330229 598330453 7.160000e-71 278.0
18 TraesCS2A01G569000 chr2D 78.926 242 16 17 443 669 598328433 598328654 5.900000e-27 132.0
19 TraesCS2A01G569000 chr2D 95.890 73 2 1 27 98 598326335 598326407 1.650000e-22 117.0
20 TraesCS2A01G569000 chr2D 94.521 73 3 1 27 98 642097996 642098068 7.690000e-21 111.0
21 TraesCS2A01G569000 chr2B 83.836 829 79 16 932 1739 799576561 799575767 0.000000e+00 737.0
22 TraesCS2A01G569000 chr2B 84.291 522 33 22 443 944 799577430 799576938 5.120000e-127 464.0
23 TraesCS2A01G569000 chr2B 91.429 245 20 1 1775 2019 799575696 799575453 4.190000e-88 335.0
24 TraesCS2A01G569000 chr2B 90.476 231 22 0 1791 2021 799595660 799595430 3.280000e-79 305.0
25 TraesCS2A01G569000 chr2B 88.800 125 14 0 1791 1915 799597536 799597412 1.260000e-33 154.0
26 TraesCS2A01G569000 chr2B 87.097 93 8 3 2413 2504 72176939 72177028 4.630000e-18 102.0
27 TraesCS2A01G569000 chr2B 90.909 77 4 2 2428 2504 71876134 71876207 1.660000e-17 100.0
28 TraesCS2A01G569000 chr1A 86.740 543 54 11 2027 2560 471480242 471479709 2.910000e-164 588.0
29 TraesCS2A01G569000 chr4B 84.916 179 14 10 272 444 483796950 483796779 4.500000e-38 169.0
30 TraesCS2A01G569000 chr4B 82.990 194 15 15 257 441 401385519 401385703 2.710000e-35 159.0
31 TraesCS2A01G569000 chr3B 85.000 180 12 12 272 444 442060979 442061150 4.500000e-38 169.0
32 TraesCS2A01G569000 chr3B 86.170 94 7 4 2524 2617 450357106 450357019 2.150000e-16 97.1
33 TraesCS2A01G569000 chr7B 83.163 196 18 10 257 444 585206323 585206511 5.820000e-37 165.0
34 TraesCS2A01G569000 chr6B 84.916 179 10 11 273 444 478423970 478423802 5.820000e-37 165.0
35 TraesCS2A01G569000 chr7D 84.153 183 14 10 268 444 453975854 453976027 2.090000e-36 163.0
36 TraesCS2A01G569000 chr7D 100.000 29 0 0 1 29 495108610 495108638 1.000000e-03 54.7
37 TraesCS2A01G569000 chr4D 84.444 180 13 11 272 444 348932628 348932799 2.090000e-36 163.0
38 TraesCS2A01G569000 chr4D 84.444 180 13 10 272 444 348934029 348933858 2.090000e-36 163.0
39 TraesCS2A01G569000 chr4D 86.735 98 7 4 2524 2620 307812996 307813088 1.290000e-18 104.0
40 TraesCS2A01G569000 chr5A 86.598 97 7 4 2524 2620 293862867 293862957 4.630000e-18 102.0
41 TraesCS2A01G569000 chr6A 88.312 77 6 3 2524 2600 607385053 607385126 3.600000e-14 89.8
42 TraesCS2A01G569000 chr6A 100.000 32 0 0 1 32 9478233 9478264 2.820000e-05 60.2
43 TraesCS2A01G569000 chr6A 100.000 29 0 0 1 29 504214557 504214585 1.000000e-03 54.7
44 TraesCS2A01G569000 chr7A 100.000 28 0 0 2228 2255 91533112 91533139 5.000000e-03 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 TraesCS2A01G569000 chr2A 766980547 766983173 2626 False 4852.000000 4852 100.000000 1 2627 1 chr2A.!!$F2 2626
1 TraesCS2A01G569000 chr2A 767015522 767019987 4465 False 360.833333 859 87.875333 27 2021 6 chr2A.!!$F3 1994
2 TraesCS2A01G569000 chr2A 767146524 767147315 791 True 333.000000 427 90.238500 815 2006 2 chr2A.!!$R2 1191
3 TraesCS2A01G569000 chr2D 642097996 642101994 3998 False 393.000000 791 87.874250 27 2006 4 chr2D.!!$F3 1979
4 TraesCS2A01G569000 chr2D 598326335 598330453 4118 False 348.000000 841 88.779400 27 2006 5 chr2D.!!$F2 1979
5 TraesCS2A01G569000 chr2B 799575453 799577430 1977 True 512.000000 737 86.518667 443 2019 3 chr2B.!!$R1 1576
6 TraesCS2A01G569000 chr2B 799595430 799597536 2106 True 229.500000 305 89.638000 1791 2021 2 chr2B.!!$R2 230
7 TraesCS2A01G569000 chr1A 471479709 471480242 533 True 588.000000 588 86.740000 2027 2560 1 chr1A.!!$R1 533

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
663 3894 0.179084 CGTACGCCCCTTGACATGAT 60.179 55.0 0.52 0.0 0.0 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2563 8284 0.10104 CGCCCCAAAGTACATGCATG 59.899 55.0 25.09 25.09 0.0 4.06 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 3.859278 GGGGACGGGATTAAACGAA 57.141 52.632 0.00 0.00 0.00 3.85
21 22 1.372582 GGGGACGGGATTAAACGAAC 58.627 55.000 0.00 0.12 0.00 3.95
22 23 1.338960 GGGGACGGGATTAAACGAACA 60.339 52.381 0.00 0.00 0.00 3.18
24 25 2.417586 GGGACGGGATTAAACGAACAAG 59.582 50.000 0.00 0.00 0.00 3.16
25 26 2.417586 GGACGGGATTAAACGAACAAGG 59.582 50.000 0.00 0.00 0.00 3.61
26 27 1.808343 ACGGGATTAAACGAACAAGGC 59.192 47.619 0.00 0.00 0.00 4.35
27 28 1.131693 CGGGATTAAACGAACAAGGCC 59.868 52.381 0.00 0.00 0.00 5.19
28 29 2.443416 GGGATTAAACGAACAAGGCCT 58.557 47.619 0.00 0.00 0.00 5.19
110 111 1.002468 CTCCCAGTTTTTGCAGTCACG 60.002 52.381 0.00 0.00 0.00 4.35
202 205 2.950309 CCATGGAAATCTCAGCTCCAAG 59.050 50.000 5.56 0.00 42.41 3.61
208 211 1.202330 ATCTCAGCTCCAAGACAGGG 58.798 55.000 0.00 0.00 0.00 4.45
210 213 1.077169 TCTCAGCTCCAAGACAGGGTA 59.923 52.381 0.00 0.00 0.00 3.69
211 214 2.114616 CTCAGCTCCAAGACAGGGTAT 58.885 52.381 0.00 0.00 0.00 2.73
215 218 2.503356 AGCTCCAAGACAGGGTATTGAG 59.497 50.000 5.38 3.11 36.96 3.02
216 219 2.420687 GCTCCAAGACAGGGTATTGAGG 60.421 54.545 5.38 0.04 36.96 3.86
218 221 2.838202 TCCAAGACAGGGTATTGAGGTC 59.162 50.000 5.38 0.00 36.96 3.85
219 222 2.840651 CCAAGACAGGGTATTGAGGTCT 59.159 50.000 5.38 0.00 36.96 3.85
292 295 9.601810 TTGAGGTAGGATTTTCTATCATAGCTA 57.398 33.333 10.06 0.00 41.31 3.32
293 296 9.249053 TGAGGTAGGATTTTCTATCATAGCTAG 57.751 37.037 10.06 0.00 41.31 3.42
294 297 8.073467 AGGTAGGATTTTCTATCATAGCTAGC 57.927 38.462 6.62 6.62 40.06 3.42
295 298 7.898636 AGGTAGGATTTTCTATCATAGCTAGCT 59.101 37.037 23.12 23.12 40.06 3.32
320 323 8.667076 TTACCACAGAACTAGTTAAGGTTTTC 57.333 34.615 19.51 3.19 0.00 2.29
323 326 6.073927 CCACAGAACTAGTTAAGGTTTTCGAC 60.074 42.308 8.42 0.00 0.00 4.20
336 339 4.395854 AGGTTTTCGACGGTGTAAAAGTTT 59.604 37.500 0.00 0.00 0.00 2.66
337 340 4.730042 GGTTTTCGACGGTGTAAAAGTTTC 59.270 41.667 0.00 0.00 0.00 2.78
339 342 6.238076 GGTTTTCGACGGTGTAAAAGTTTCTA 60.238 38.462 0.00 0.00 0.00 2.10
344 347 7.918643 TCGACGGTGTAAAAGTTTCTAAAAAT 58.081 30.769 0.00 0.00 0.00 1.82
345 348 8.397148 TCGACGGTGTAAAAGTTTCTAAAAATT 58.603 29.630 0.00 0.00 0.00 1.82
346 349 8.675888 CGACGGTGTAAAAGTTTCTAAAAATTC 58.324 33.333 0.00 0.00 0.00 2.17
347 350 9.505995 GACGGTGTAAAAGTTTCTAAAAATTCA 57.494 29.630 0.00 0.00 0.00 2.57
348 351 9.511144 ACGGTGTAAAAGTTTCTAAAAATTCAG 57.489 29.630 0.00 0.00 0.00 3.02
349 352 9.511144 CGGTGTAAAAGTTTCTAAAAATTCAGT 57.489 29.630 0.00 0.00 0.00 3.41
481 3697 2.615869 CTCTAGGCAGTTGACTTGCTC 58.384 52.381 0.00 0.00 33.72 4.26
520 3736 1.080025 GCCACTGAGTACACGGACC 60.080 63.158 6.10 0.00 0.00 4.46
530 3746 1.070309 GTACACGGACCGATAGCTACG 60.070 57.143 23.38 2.00 0.00 3.51
584 3806 7.894376 AATAACGAGGTCGATTTTAGAAACA 57.106 32.000 6.35 0.00 43.02 2.83
585 3807 5.840940 AACGAGGTCGATTTTAGAAACAG 57.159 39.130 6.35 0.00 43.02 3.16
586 3808 4.879598 ACGAGGTCGATTTTAGAAACAGT 58.120 39.130 6.35 0.00 43.02 3.55
587 3809 4.922103 ACGAGGTCGATTTTAGAAACAGTC 59.078 41.667 6.35 0.00 43.02 3.51
588 3810 5.162075 CGAGGTCGATTTTAGAAACAGTCT 58.838 41.667 0.00 0.00 43.02 3.24
594 3816 7.597743 GGTCGATTTTAGAAACAGTCTAACAGA 59.402 37.037 0.00 0.00 46.40 3.41
617 3839 0.600557 AGAGACGACTGACTTGCTGG 59.399 55.000 0.00 0.00 0.00 4.85
643 3874 1.745768 GACACGGCAATACGCGTACC 61.746 60.000 23.19 17.28 43.84 3.34
659 3890 3.697747 CCCGTACGCCCCTTGACA 61.698 66.667 10.49 0.00 0.00 3.58
663 3894 0.179084 CGTACGCCCCTTGACATGAT 60.179 55.000 0.52 0.00 0.00 2.45
755 4030 2.159382 CCTCGATCTAGCCCTCTTCTC 58.841 57.143 0.00 0.00 0.00 2.87
770 4045 4.227073 CCTCTTCTCCCCTTTTCATCTCTT 59.773 45.833 0.00 0.00 0.00 2.85
792 4067 5.929697 TGCATCAAAGTCTTACTGAGTTG 57.070 39.130 0.00 0.00 38.27 3.16
797 4072 6.235231 TCAAAGTCTTACTGAGTTGGAGTT 57.765 37.500 0.00 0.00 38.27 3.01
902 4184 1.745653 CAGCGAGGTATGTGTCTCTCA 59.254 52.381 0.00 0.00 0.00 3.27
903 4185 1.746220 AGCGAGGTATGTGTCTCTCAC 59.254 52.381 0.00 0.00 46.31 3.51
904 4186 1.746220 GCGAGGTATGTGTCTCTCACT 59.254 52.381 0.00 0.00 46.27 3.41
905 4187 2.223386 GCGAGGTATGTGTCTCTCACTC 60.223 54.545 0.00 0.00 46.27 3.51
906 4188 3.275143 CGAGGTATGTGTCTCTCACTCT 58.725 50.000 0.00 0.00 46.27 3.24
907 4189 3.311322 CGAGGTATGTGTCTCTCACTCTC 59.689 52.174 0.00 0.00 46.27 3.20
908 4190 4.523083 GAGGTATGTGTCTCTCACTCTCT 58.477 47.826 0.00 0.00 46.27 3.10
909 4191 4.523083 AGGTATGTGTCTCTCACTCTCTC 58.477 47.826 0.00 0.00 46.27 3.20
924 4206 5.301551 TCACTCTCTCTGCTTATCATCCTTC 59.698 44.000 0.00 0.00 0.00 3.46
978 4660 4.515567 GTCTTGCTAACCTAAAGTTGTGCT 59.484 41.667 0.00 0.00 39.67 4.40
979 4661 5.699458 GTCTTGCTAACCTAAAGTTGTGCTA 59.301 40.000 0.00 0.00 39.67 3.49
980 4662 5.932303 TCTTGCTAACCTAAAGTTGTGCTAG 59.068 40.000 0.00 0.00 40.12 3.42
981 4663 4.000988 TGCTAACCTAAAGTTGTGCTAGC 58.999 43.478 8.10 8.10 39.67 3.42
999 4681 0.662970 GCTAGCTTGATCGCCTCGAG 60.663 60.000 7.70 5.13 39.91 4.04
1000 4682 0.947960 CTAGCTTGATCGCCTCGAGA 59.052 55.000 15.71 0.00 39.91 4.04
1001 4683 1.539388 CTAGCTTGATCGCCTCGAGAT 59.461 52.381 15.71 0.00 39.91 2.75
1008 4690 1.000283 GATCGCCTCGAGATGATGGTT 60.000 52.381 15.71 0.00 39.91 3.67
1049 4734 2.146342 CATGATCCTAACGATGGTGCC 58.854 52.381 0.00 0.00 0.00 5.01
1099 4784 2.031333 CAGCAGAACAAGAAGAAGTGCC 60.031 50.000 0.00 0.00 0.00 5.01
1156 4841 2.380084 ACTGCCCAACTACACATACG 57.620 50.000 0.00 0.00 0.00 3.06
1164 4849 4.876828 TACACATACGCGGCGGCC 62.877 66.667 27.37 9.54 35.02 6.13
1181 4866 3.041940 CAACGACCAGGACACGGC 61.042 66.667 0.00 0.00 0.00 5.68
1184 4869 4.778415 CGACCAGGACACGGCGAG 62.778 72.222 16.62 8.85 0.00 5.03
1189 4874 4.057428 AGGACACGGCGAGAGTGC 62.057 66.667 16.62 14.33 42.94 4.40
1207 4892 2.031012 TGCACACGCTCAAGGAGG 59.969 61.111 0.00 0.00 39.64 4.30
1212 4897 3.710722 ACGCTCAAGGAGGCCCTG 61.711 66.667 0.00 0.00 43.48 4.45
1245 4930 1.300963 GCTCATCCACTCCTGCCAA 59.699 57.895 0.00 0.00 0.00 4.52
1249 4934 2.237143 CTCATCCACTCCTGCCAAACTA 59.763 50.000 0.00 0.00 0.00 2.24
1250 4935 2.237143 TCATCCACTCCTGCCAAACTAG 59.763 50.000 0.00 0.00 0.00 2.57
1275 4975 1.300481 GGAAGGCCGCTGAATTAGAC 58.700 55.000 0.00 0.00 0.00 2.59
1285 4985 3.861834 GCTGAATTAGACGGCGTTAATG 58.138 45.455 16.19 9.45 0.00 1.90
1286 4986 3.844943 GCTGAATTAGACGGCGTTAATGC 60.845 47.826 16.19 17.56 0.00 3.56
1297 4997 3.179048 GGCGTTAATGCAAAGATCAACC 58.821 45.455 20.80 0.00 36.28 3.77
1299 4999 3.853671 GCGTTAATGCAAAGATCAACCAG 59.146 43.478 14.86 0.00 34.15 4.00
1307 5007 3.305539 GCAAAGATCAACCAGTGCATCAA 60.306 43.478 0.00 0.00 32.29 2.57
1308 5008 4.232221 CAAAGATCAACCAGTGCATCAAC 58.768 43.478 0.00 0.00 0.00 3.18
1327 5027 5.304778 TCAACGACCTCAATTTCATCAGAA 58.695 37.500 0.00 0.00 0.00 3.02
1329 5029 5.613358 ACGACCTCAATTTCATCAGAAAC 57.387 39.130 0.00 0.00 45.79 2.78
1331 5031 4.436050 CGACCTCAATTTCATCAGAAACGG 60.436 45.833 0.00 0.00 45.79 4.44
1354 5060 1.464687 GCACAAATCACGTAGCAGCAG 60.465 52.381 0.00 0.00 0.00 4.24
1424 5130 1.208052 TCAGTATCAGGCACAAGGAGC 59.792 52.381 0.00 0.00 0.00 4.70
1523 5232 0.179073 CCGTCTCCCTACCATGCTTG 60.179 60.000 0.00 0.00 0.00 4.01
1556 5265 2.230750 CCTCGACCTCGGGTTATAATCC 59.769 54.545 4.51 4.51 38.37 3.01
1567 5276 5.012768 TCGGGTTATAATCCATCTTCCCTTC 59.987 44.000 15.16 0.00 0.00 3.46
1568 5277 5.246307 GGGTTATAATCCATCTTCCCTTCG 58.754 45.833 10.07 0.00 0.00 3.79
1569 5278 5.246307 GGTTATAATCCATCTTCCCTTCGG 58.754 45.833 0.00 0.00 0.00 4.30
1573 5282 0.042731 TCCATCTTCCCTTCGGACCT 59.957 55.000 0.00 0.00 38.14 3.85
1574 5283 0.912486 CCATCTTCCCTTCGGACCTT 59.088 55.000 0.00 0.00 38.14 3.50
1575 5284 2.116238 CCATCTTCCCTTCGGACCTTA 58.884 52.381 0.00 0.00 38.14 2.69
1576 5285 2.706190 CCATCTTCCCTTCGGACCTTAT 59.294 50.000 0.00 0.00 38.14 1.73
1589 5298 3.007635 GGACCTTATTTCCAACCGTCAG 58.992 50.000 0.00 0.00 32.82 3.51
1594 5304 1.247567 ATTTCCAACCGTCAGCAAGG 58.752 50.000 0.00 0.00 0.00 3.61
1739 5452 2.404265 TCATTTGTTCGCAGCAAGTG 57.596 45.000 0.00 0.00 35.69 3.16
1741 5454 1.782569 CATTTGTTCGCAGCAAGTGTG 59.217 47.619 0.00 0.00 38.09 3.82
1743 5456 0.098552 TTGTTCGCAGCAAGTGTGTG 59.901 50.000 0.00 0.00 37.93 3.82
1744 5457 1.655350 GTTCGCAGCAAGTGTGTGC 60.655 57.895 0.00 0.00 45.28 4.57
1745 5458 2.833533 TTCGCAGCAAGTGTGTGCC 61.834 57.895 0.00 0.00 46.14 5.01
1747 5460 3.279116 GCAGCAAGTGTGTGCCGA 61.279 61.111 0.00 0.00 46.14 5.54
1748 5461 2.620112 GCAGCAAGTGTGTGCCGAT 61.620 57.895 0.00 0.00 46.14 4.18
1749 5462 1.499056 CAGCAAGTGTGTGCCGATC 59.501 57.895 0.00 0.00 46.14 3.69
1750 5463 1.672356 AGCAAGTGTGTGCCGATCC 60.672 57.895 0.00 0.00 46.14 3.36
1751 5464 1.965930 GCAAGTGTGTGCCGATCCA 60.966 57.895 0.00 0.00 38.66 3.41
1770 5715 2.160615 CCATGCAACGAAACGATTGGTA 59.839 45.455 0.00 0.00 0.00 3.25
1771 5716 3.365465 CCATGCAACGAAACGATTGGTAA 60.365 43.478 0.00 0.00 0.00 2.85
1772 5717 3.529634 TGCAACGAAACGATTGGTAAG 57.470 42.857 0.00 0.00 0.00 2.34
1773 5718 2.224549 TGCAACGAAACGATTGGTAAGG 59.775 45.455 0.00 0.00 0.00 2.69
1776 5721 4.555116 GCAACGAAACGATTGGTAAGGAAA 60.555 41.667 0.00 0.00 0.00 3.13
1778 5723 5.754543 ACGAAACGATTGGTAAGGAAAAA 57.245 34.783 0.00 0.00 0.00 1.94
1883 7578 7.279615 AGGTATTTCGTATGTTTCCATCATCA 58.720 34.615 0.00 0.00 32.29 3.07
1924 7619 6.970043 CAGTTTTCGGATGTGTTTCAACTTTA 59.030 34.615 0.00 0.00 0.00 1.85
1969 7681 4.394610 ACACCAATGTTTTTCCTGCAAAAC 59.605 37.500 5.03 5.03 43.96 2.43
1974 7686 1.849829 GTTTTTCCTGCAAAACGGACG 59.150 47.619 0.00 0.00 37.01 4.79
2021 7733 0.391597 GGATCAAGCAATGGCATGGG 59.608 55.000 0.00 0.00 44.61 4.00
2022 7734 1.405872 GATCAAGCAATGGCATGGGA 58.594 50.000 0.00 0.00 44.61 4.37
2023 7735 1.068127 GATCAAGCAATGGCATGGGAC 59.932 52.381 0.00 0.00 44.61 4.46
2024 7736 1.140161 CAAGCAATGGCATGGGACG 59.860 57.895 0.00 0.00 44.61 4.79
2025 7737 1.304381 AAGCAATGGCATGGGACGT 60.304 52.632 0.00 0.00 44.61 4.34
2033 7745 1.299541 GGCATGGGACGTAATCACTG 58.700 55.000 0.00 0.00 0.00 3.66
2048 7760 6.089551 CGTAATCACTGTTCTGACCTTGTTAG 59.910 42.308 0.00 0.00 0.00 2.34
2053 7765 6.538742 TCACTGTTCTGACCTTGTTAGAAAAG 59.461 38.462 14.15 14.15 44.17 2.27
2117 7829 4.786507 TGATTCTTTTCGCAACATCACAG 58.213 39.130 0.00 0.00 0.00 3.66
2129 7841 1.070786 ATCACAGACCGTGGCGTTT 59.929 52.632 0.00 0.00 46.36 3.60
2132 7844 1.594293 ACAGACCGTGGCGTTTCTG 60.594 57.895 12.71 12.71 39.44 3.02
2140 7852 0.517316 GTGGCGTTTCTGATGACCAC 59.483 55.000 0.00 0.00 40.64 4.16
2142 7854 1.635663 GGCGTTTCTGATGACCACCG 61.636 60.000 0.00 0.00 0.00 4.94
2147 7859 2.178912 TTCTGATGACCACCGAAACC 57.821 50.000 0.00 0.00 0.00 3.27
2157 7869 0.753848 CACCGAAACCCCAAACCAGT 60.754 55.000 0.00 0.00 0.00 4.00
2161 7873 1.749286 CGAAACCCCAAACCAGTCAGT 60.749 52.381 0.00 0.00 0.00 3.41
2173 7885 0.035317 CAGTCAGTGTTGCTGCCCTA 59.965 55.000 0.00 0.00 44.66 3.53
2174 7886 0.322975 AGTCAGTGTTGCTGCCCTAG 59.677 55.000 0.00 0.00 44.66 3.02
2188 7909 1.147824 CCTAGCCAGGCTGATGTGG 59.852 63.158 25.59 13.57 40.10 4.17
2226 7947 1.202405 GGGCCATGGCGTTTCTAAATG 60.202 52.381 29.90 0.00 43.06 2.32
2227 7948 1.202405 GGCCATGGCGTTTCTAAATGG 60.202 52.381 29.90 0.00 43.06 3.16
2299 8020 5.701290 GGATACAATGAGTATTGGTAGCACC 59.299 44.000 0.00 0.00 46.33 5.01
2302 8023 0.177141 TGAGTATTGGTAGCACCGCC 59.823 55.000 0.00 0.00 42.58 6.13
2305 8026 0.814010 GTATTGGTAGCACCGCCCTG 60.814 60.000 0.00 0.00 42.58 4.45
2311 8032 0.463833 GTAGCACCGCCCTGCTTAAT 60.464 55.000 8.01 0.00 45.64 1.40
2317 8038 1.488812 ACCGCCCTGCTTAATGTGATA 59.511 47.619 0.00 0.00 0.00 2.15
2319 8040 2.290641 CCGCCCTGCTTAATGTGATAAC 59.709 50.000 0.00 0.00 0.00 1.89
2324 8045 3.623060 CCTGCTTAATGTGATAACTGCGT 59.377 43.478 0.00 0.00 0.00 5.24
2330 8051 1.295357 TGTGATAACTGCGTTGCCCG 61.295 55.000 4.52 0.00 40.40 6.13
2332 8053 3.108357 GATAACTGCGTTGCCCGGC 62.108 63.158 1.04 1.04 36.94 6.13
2381 8102 2.238646 AGTGTCCATGGCCGAAAAGATA 59.761 45.455 6.96 0.00 0.00 1.98
2423 8144 1.160137 CTGCTAAACAGTGGGTGCTC 58.840 55.000 0.00 0.00 41.86 4.26
2426 8147 0.320771 CTAAACAGTGGGTGCTCGCT 60.321 55.000 4.41 0.00 0.00 4.93
2429 8150 3.730761 CAGTGGGTGCTCGCTTGC 61.731 66.667 4.41 0.00 0.00 4.01
2435 8156 1.354506 GGTGCTCGCTTGCATGATC 59.645 57.895 3.33 0.00 45.23 2.92
2478 8199 2.678934 CAAGGCCATGCTGCTGGT 60.679 61.111 5.01 0.00 38.63 4.00
2479 8200 1.378911 CAAGGCCATGCTGCTGGTA 60.379 57.895 5.01 0.00 38.63 3.25
2503 8224 3.009723 TGTTTAGCAGCTAATCAGTGGC 58.990 45.455 18.33 4.90 0.00 5.01
2524 8245 3.041940 GTGACGAACCCAGCCGTG 61.042 66.667 0.00 0.00 39.30 4.94
2541 8262 1.683365 TGGTACGTAGCACTCCCCC 60.683 63.158 22.78 5.54 0.00 5.40
2557 8278 1.143813 CCCCTAGTCCAAGGCATCAT 58.856 55.000 0.00 0.00 35.09 2.45
2579 8300 2.816689 CATGCATGCATGTACTTTGGG 58.183 47.619 40.30 20.25 46.20 4.12
2580 8301 1.184431 TGCATGCATGTACTTTGGGG 58.816 50.000 26.79 0.00 0.00 4.96
2581 8302 0.179103 GCATGCATGTACTTTGGGGC 60.179 55.000 26.79 5.57 0.00 5.80
2582 8303 0.101040 CATGCATGTACTTTGGGGCG 59.899 55.000 18.91 0.00 0.00 6.13
2583 8304 1.666209 ATGCATGTACTTTGGGGCGC 61.666 55.000 0.00 0.00 0.00 6.53
2584 8305 2.791256 CATGTACTTTGGGGCGCG 59.209 61.111 0.00 0.00 0.00 6.86
2585 8306 1.743623 CATGTACTTTGGGGCGCGA 60.744 57.895 12.10 0.00 0.00 5.87
2586 8307 1.095228 CATGTACTTTGGGGCGCGAT 61.095 55.000 12.10 0.00 0.00 4.58
2587 8308 0.814010 ATGTACTTTGGGGCGCGATC 60.814 55.000 12.10 0.00 0.00 3.69
2588 8309 2.178235 GTACTTTGGGGCGCGATCC 61.178 63.158 12.10 11.18 0.00 3.36
2589 8310 2.661066 TACTTTGGGGCGCGATCCA 61.661 57.895 12.10 14.14 0.00 3.41
2590 8311 1.978455 TACTTTGGGGCGCGATCCAT 61.978 55.000 12.10 4.11 32.48 3.41
2591 8312 2.515991 TTTGGGGCGCGATCCATC 60.516 61.111 12.10 0.00 32.48 3.51
2592 8313 2.947938 CTTTGGGGCGCGATCCATCT 62.948 60.000 12.10 0.00 32.48 2.90
2593 8314 2.550699 TTTGGGGCGCGATCCATCTT 62.551 55.000 12.10 0.00 32.48 2.40
2594 8315 2.203209 GGGGCGCGATCCATCTTT 60.203 61.111 12.10 0.00 0.00 2.52
2595 8316 1.070786 GGGGCGCGATCCATCTTTA 59.929 57.895 12.10 0.00 0.00 1.85
2596 8317 0.534203 GGGGCGCGATCCATCTTTAA 60.534 55.000 12.10 0.00 0.00 1.52
2597 8318 1.523758 GGGCGCGATCCATCTTTAAT 58.476 50.000 12.10 0.00 0.00 1.40
2598 8319 1.880027 GGGCGCGATCCATCTTTAATT 59.120 47.619 12.10 0.00 0.00 1.40
2599 8320 2.293399 GGGCGCGATCCATCTTTAATTT 59.707 45.455 12.10 0.00 0.00 1.82
2600 8321 3.300009 GGCGCGATCCATCTTTAATTTG 58.700 45.455 12.10 0.00 0.00 2.32
2601 8322 3.243068 GGCGCGATCCATCTTTAATTTGT 60.243 43.478 12.10 0.00 0.00 2.83
2602 8323 4.024387 GGCGCGATCCATCTTTAATTTGTA 60.024 41.667 12.10 0.00 0.00 2.41
2603 8324 5.140177 GCGCGATCCATCTTTAATTTGTAG 58.860 41.667 12.10 0.00 0.00 2.74
2604 8325 5.277345 GCGCGATCCATCTTTAATTTGTAGT 60.277 40.000 12.10 0.00 0.00 2.73
2605 8326 6.073980 GCGCGATCCATCTTTAATTTGTAGTA 60.074 38.462 12.10 0.00 0.00 1.82
2606 8327 7.281484 CGCGATCCATCTTTAATTTGTAGTAC 58.719 38.462 0.00 0.00 0.00 2.73
2607 8328 7.169308 CGCGATCCATCTTTAATTTGTAGTACT 59.831 37.037 0.00 0.00 0.00 2.73
2608 8329 9.472361 GCGATCCATCTTTAATTTGTAGTACTA 57.528 33.333 0.00 0.00 0.00 1.82
2618 8339 6.903883 AATTTGTAGTACTAGTGGAATGCG 57.096 37.500 5.39 0.00 0.00 4.73
2619 8340 5.395682 TTTGTAGTACTAGTGGAATGCGT 57.604 39.130 5.39 0.00 0.00 5.24
2620 8341 4.365899 TGTAGTACTAGTGGAATGCGTG 57.634 45.455 5.39 0.00 0.00 5.34
2621 8342 2.295253 AGTACTAGTGGAATGCGTGC 57.705 50.000 5.39 0.00 0.00 5.34
2622 8343 1.134788 AGTACTAGTGGAATGCGTGCC 60.135 52.381 5.39 0.00 0.00 5.01
2623 8344 0.179121 TACTAGTGGAATGCGTGCCG 60.179 55.000 5.39 0.00 0.00 5.69
2624 8345 1.447838 CTAGTGGAATGCGTGCCGT 60.448 57.895 0.00 0.00 0.00 5.68
2625 8346 1.695893 CTAGTGGAATGCGTGCCGTG 61.696 60.000 0.00 0.00 0.00 4.94
2626 8347 4.759096 GTGGAATGCGTGCCGTGC 62.759 66.667 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.175621 CGTTTAATCCCGTCCCCGC 61.176 63.158 0.00 0.00 0.00 6.13
2 3 1.338960 TGTTCGTTTAATCCCGTCCCC 60.339 52.381 0.00 0.00 0.00 4.81
3 4 2.097680 TGTTCGTTTAATCCCGTCCC 57.902 50.000 0.00 0.00 0.00 4.46
5 6 2.159612 GCCTTGTTCGTTTAATCCCGTC 60.160 50.000 0.00 0.00 0.00 4.79
6 7 1.808343 GCCTTGTTCGTTTAATCCCGT 59.192 47.619 0.00 0.00 0.00 5.28
7 8 1.131693 GGCCTTGTTCGTTTAATCCCG 59.868 52.381 0.00 0.00 0.00 5.14
8 9 2.443416 AGGCCTTGTTCGTTTAATCCC 58.557 47.619 0.00 0.00 0.00 3.85
9 10 5.632244 TTAAGGCCTTGTTCGTTTAATCC 57.368 39.130 28.77 0.00 0.00 3.01
10 11 7.364970 TCTTTTAAGGCCTTGTTCGTTTAATC 58.635 34.615 28.77 0.00 0.00 1.75
11 12 7.279750 TCTTTTAAGGCCTTGTTCGTTTAAT 57.720 32.000 28.77 0.00 0.00 1.40
12 13 6.696441 TCTTTTAAGGCCTTGTTCGTTTAA 57.304 33.333 28.77 8.67 0.00 1.52
13 14 6.696441 TTCTTTTAAGGCCTTGTTCGTTTA 57.304 33.333 28.77 1.62 0.00 2.01
15 16 5.585820 TTTCTTTTAAGGCCTTGTTCGTT 57.414 34.783 28.77 1.45 0.00 3.85
16 17 5.784578 ATTTCTTTTAAGGCCTTGTTCGT 57.215 34.783 28.77 2.32 0.00 3.85
17 18 8.647226 CAATTATTTCTTTTAAGGCCTTGTTCG 58.353 33.333 28.77 13.54 0.00 3.95
18 19 8.443160 GCAATTATTTCTTTTAAGGCCTTGTTC 58.557 33.333 28.77 0.00 0.00 3.18
19 20 7.936301 TGCAATTATTTCTTTTAAGGCCTTGTT 59.064 29.630 28.77 4.09 0.00 2.83
20 21 7.449247 TGCAATTATTTCTTTTAAGGCCTTGT 58.551 30.769 28.77 4.97 0.00 3.16
21 22 7.903995 TGCAATTATTTCTTTTAAGGCCTTG 57.096 32.000 28.77 11.38 0.00 3.61
22 23 8.102676 ACATGCAATTATTTCTTTTAAGGCCTT 58.897 29.630 24.18 24.18 0.00 4.35
24 25 7.848223 ACATGCAATTATTTCTTTTAAGGCC 57.152 32.000 0.00 0.00 0.00 5.19
110 111 4.202398 TGGAATAGACAGCATCATCCTTCC 60.202 45.833 0.00 0.00 31.44 3.46
184 187 2.639347 TGTCTTGGAGCTGAGATTTCCA 59.361 45.455 0.00 0.00 39.16 3.53
202 205 3.769844 TCAAGAGACCTCAATACCCTGTC 59.230 47.826 0.00 0.00 0.00 3.51
246 249 9.778741 ACCTCAACAACATATATCGTAAATCAT 57.221 29.630 0.00 0.00 0.00 2.45
249 252 9.706691 CCTACCTCAACAACATATATCGTAAAT 57.293 33.333 0.00 0.00 0.00 1.40
250 253 8.916062 TCCTACCTCAACAACATATATCGTAAA 58.084 33.333 0.00 0.00 0.00 2.01
251 254 8.467963 TCCTACCTCAACAACATATATCGTAA 57.532 34.615 0.00 0.00 0.00 3.18
252 255 8.645814 ATCCTACCTCAACAACATATATCGTA 57.354 34.615 0.00 0.00 0.00 3.43
253 256 6.971726 TCCTACCTCAACAACATATATCGT 57.028 37.500 0.00 0.00 0.00 3.73
254 257 8.833231 AAATCCTACCTCAACAACATATATCG 57.167 34.615 0.00 0.00 0.00 2.92
259 262 9.832445 GATAGAAAATCCTACCTCAACAACATA 57.168 33.333 0.00 0.00 0.00 2.29
260 263 8.328758 TGATAGAAAATCCTACCTCAACAACAT 58.671 33.333 0.00 0.00 0.00 2.71
261 264 7.685481 TGATAGAAAATCCTACCTCAACAACA 58.315 34.615 0.00 0.00 0.00 3.33
262 265 8.738645 ATGATAGAAAATCCTACCTCAACAAC 57.261 34.615 0.00 0.00 0.00 3.32
270 273 8.073467 AGCTAGCTATGATAGAAAATCCTACC 57.927 38.462 17.69 0.00 0.00 3.18
284 287 4.956700 AGTTCTGTGGTAAGCTAGCTATGA 59.043 41.667 19.70 3.51 0.00 2.15
292 295 5.543020 ACCTTAACTAGTTCTGTGGTAAGCT 59.457 40.000 12.39 0.00 0.00 3.74
293 296 5.791666 ACCTTAACTAGTTCTGTGGTAAGC 58.208 41.667 12.39 0.00 0.00 3.09
294 297 8.672823 AAAACCTTAACTAGTTCTGTGGTAAG 57.327 34.615 12.39 8.12 0.00 2.34
295 298 7.439056 CGAAAACCTTAACTAGTTCTGTGGTAA 59.561 37.037 12.39 0.00 0.00 2.85
320 323 8.551122 AATTTTTAGAAACTTTTACACCGTCG 57.449 30.769 0.00 0.00 0.00 5.12
323 326 9.511144 ACTGAATTTTTAGAAACTTTTACACCG 57.489 29.630 0.00 0.00 0.00 4.94
392 396 8.786898 CACATACAGTTTTATAATCCCTCCATG 58.213 37.037 0.00 0.00 0.00 3.66
394 398 7.867921 ACACATACAGTTTTATAATCCCTCCA 58.132 34.615 0.00 0.00 0.00 3.86
395 399 7.444487 GGACACATACAGTTTTATAATCCCTCC 59.556 40.741 0.00 0.00 0.00 4.30
399 403 7.990886 TCCAGGACACATACAGTTTTATAATCC 59.009 37.037 0.00 0.00 0.00 3.01
404 408 6.121776 TGTCCAGGACACATACAGTTTTAT 57.878 37.500 19.21 0.00 37.67 1.40
405 409 5.554437 TGTCCAGGACACATACAGTTTTA 57.446 39.130 19.21 0.00 37.67 1.52
435 445 4.202010 GCCCATAAATCACGTACATTTGCT 60.202 41.667 12.71 1.15 0.00 3.91
436 446 4.041723 GCCCATAAATCACGTACATTTGC 58.958 43.478 12.71 5.94 0.00 3.68
437 447 5.273170 CAGCCCATAAATCACGTACATTTG 58.727 41.667 12.71 1.27 0.00 2.32
440 450 2.878406 GCAGCCCATAAATCACGTACAT 59.122 45.455 0.00 0.00 0.00 2.29
441 451 2.093181 AGCAGCCCATAAATCACGTACA 60.093 45.455 0.00 0.00 0.00 2.90
499 3715 1.374252 CCGTGTACTCAGTGGCCAC 60.374 63.158 29.22 29.22 0.00 5.01
508 3724 1.307097 AGCTATCGGTCCGTGTACTC 58.693 55.000 11.88 0.00 0.00 2.59
513 3729 1.194098 CTACGTAGCTATCGGTCCGTG 59.806 57.143 10.14 4.35 0.00 4.94
520 3736 3.808726 ACTCCTTGTCTACGTAGCTATCG 59.191 47.826 18.00 12.26 0.00 2.92
530 3746 8.099364 TGAAAAATTGATCACTCCTTGTCTAC 57.901 34.615 0.00 0.00 0.00 2.59
562 3784 6.449698 ACTGTTTCTAAAATCGACCTCGTTA 58.550 36.000 0.00 0.00 40.80 3.18
563 3785 5.295152 ACTGTTTCTAAAATCGACCTCGTT 58.705 37.500 0.00 0.00 40.80 3.85
564 3786 4.879598 ACTGTTTCTAAAATCGACCTCGT 58.120 39.130 0.00 0.00 40.80 4.18
565 3787 5.162075 AGACTGTTTCTAAAATCGACCTCG 58.838 41.667 0.00 0.00 34.76 4.63
566 3788 7.597743 TGTTAGACTGTTTCTAAAATCGACCTC 59.402 37.037 0.00 0.00 46.40 3.85
567 3789 7.439381 TGTTAGACTGTTTCTAAAATCGACCT 58.561 34.615 0.00 0.00 46.40 3.85
568 3790 7.597743 TCTGTTAGACTGTTTCTAAAATCGACC 59.402 37.037 0.00 0.00 46.40 4.79
571 3793 8.294341 TGTCTGTTAGACTGTTTCTAAAATCG 57.706 34.615 10.03 0.00 46.40 3.34
581 3803 4.214545 CGTCTCTCTGTCTGTTAGACTGTT 59.785 45.833 10.03 0.00 45.27 3.16
582 3804 3.749088 CGTCTCTCTGTCTGTTAGACTGT 59.251 47.826 10.03 0.00 45.27 3.55
583 3805 3.997681 TCGTCTCTCTGTCTGTTAGACTG 59.002 47.826 10.03 9.44 45.27 3.51
584 3806 3.998341 GTCGTCTCTCTGTCTGTTAGACT 59.002 47.826 10.03 0.00 45.27 3.24
585 3807 3.998341 AGTCGTCTCTCTGTCTGTTAGAC 59.002 47.826 2.11 2.11 45.26 2.59
586 3808 3.997681 CAGTCGTCTCTCTGTCTGTTAGA 59.002 47.826 0.00 0.00 0.00 2.10
587 3809 3.997681 TCAGTCGTCTCTCTGTCTGTTAG 59.002 47.826 0.00 0.00 33.89 2.34
588 3810 3.747010 GTCAGTCGTCTCTCTGTCTGTTA 59.253 47.826 0.00 0.00 33.89 2.41
594 3816 1.268352 GCAAGTCAGTCGTCTCTCTGT 59.732 52.381 0.00 0.00 33.89 3.41
630 3852 2.207177 GTACGGGTACGCGTATTGC 58.793 57.895 37.07 25.12 46.04 3.56
643 3874 1.813753 CATGTCAAGGGGCGTACGG 60.814 63.158 18.39 0.00 0.00 4.02
695 3970 3.058639 GGTGACTACTGCTTTGCTTGAAG 60.059 47.826 0.00 0.00 0.00 3.02
755 4030 3.359033 TGATGCAAGAGATGAAAAGGGG 58.641 45.455 0.00 0.00 0.00 4.79
770 4045 4.756642 CCAACTCAGTAAGACTTTGATGCA 59.243 41.667 0.00 0.00 0.00 3.96
902 4184 4.588528 GGAAGGATGATAAGCAGAGAGAGT 59.411 45.833 0.00 0.00 0.00 3.24
903 4185 4.021192 GGGAAGGATGATAAGCAGAGAGAG 60.021 50.000 0.00 0.00 0.00 3.20
904 4186 3.900601 GGGAAGGATGATAAGCAGAGAGA 59.099 47.826 0.00 0.00 0.00 3.10
905 4187 3.645212 TGGGAAGGATGATAAGCAGAGAG 59.355 47.826 0.00 0.00 0.00 3.20
906 4188 3.657610 TGGGAAGGATGATAAGCAGAGA 58.342 45.455 0.00 0.00 0.00 3.10
907 4189 4.637387 ATGGGAAGGATGATAAGCAGAG 57.363 45.455 0.00 0.00 0.00 3.35
908 4190 4.446745 CCAATGGGAAGGATGATAAGCAGA 60.447 45.833 0.00 0.00 35.59 4.26
909 4191 3.825014 CCAATGGGAAGGATGATAAGCAG 59.175 47.826 0.00 0.00 35.59 4.24
978 4660 0.593618 CGAGGCGATCAAGCTAGCTA 59.406 55.000 19.70 3.08 37.29 3.32
979 4661 1.103987 TCGAGGCGATCAAGCTAGCT 61.104 55.000 12.68 12.68 37.29 3.32
980 4662 0.662970 CTCGAGGCGATCAAGCTAGC 60.663 60.000 6.62 6.62 34.61 3.42
981 4663 0.947960 TCTCGAGGCGATCAAGCTAG 59.052 55.000 13.56 0.00 34.61 3.42
1049 4734 3.197790 CGGCCCTTGCGATCAGTG 61.198 66.667 0.00 0.00 38.85 3.66
1071 4756 1.159713 TCTTGTTCTGCTGTGCCGTG 61.160 55.000 0.00 0.00 0.00 4.94
1164 4849 3.041940 GCCGTGTCCTGGTCGTTG 61.042 66.667 0.00 0.00 0.00 4.10
1181 4866 3.771491 GCGTGTGCAGCACTCTCG 61.771 66.667 25.83 24.43 45.57 4.04
1184 4869 2.167808 CTTGAGCGTGTGCAGCACTC 62.168 60.000 25.83 20.89 45.57 3.51
1189 4874 2.031516 CCTCCTTGAGCGTGTGCAG 61.032 63.158 0.00 0.00 46.23 4.41
1192 4877 2.743928 GGCCTCCTTGAGCGTGTG 60.744 66.667 0.00 0.00 0.00 3.82
1193 4878 4.021925 GGGCCTCCTTGAGCGTGT 62.022 66.667 0.84 0.00 0.00 4.49
1194 4879 3.710722 AGGGCCTCCTTGAGCGTG 61.711 66.667 0.00 0.00 41.56 5.34
1196 4881 4.479993 CCAGGGCCTCCTTGAGCG 62.480 72.222 0.95 0.00 42.67 5.03
1222 4907 2.887568 GGAGTGGATGAGCGTGCG 60.888 66.667 0.00 0.00 0.00 5.34
1223 4908 1.812922 CAGGAGTGGATGAGCGTGC 60.813 63.158 0.00 0.00 0.00 5.34
1224 4909 1.812922 GCAGGAGTGGATGAGCGTG 60.813 63.158 0.00 0.00 0.00 5.34
1236 4921 1.743996 GGCTTCTAGTTTGGCAGGAG 58.256 55.000 0.00 0.00 0.00 3.69
1266 4966 3.263261 TGCATTAACGCCGTCTAATTCA 58.737 40.909 0.00 0.00 0.00 2.57
1275 4975 2.823196 TGATCTTTGCATTAACGCCG 57.177 45.000 0.00 0.00 0.00 6.46
1278 4978 4.853196 CACTGGTTGATCTTTGCATTAACG 59.147 41.667 0.00 0.00 0.00 3.18
1285 4985 2.229543 TGATGCACTGGTTGATCTTTGC 59.770 45.455 0.00 0.00 0.00 3.68
1286 4986 4.232221 GTTGATGCACTGGTTGATCTTTG 58.768 43.478 0.00 0.00 0.00 2.77
1297 4997 1.511850 TTGAGGTCGTTGATGCACTG 58.488 50.000 0.00 0.00 0.00 3.66
1299 4999 3.058293 TGAAATTGAGGTCGTTGATGCAC 60.058 43.478 0.00 0.00 0.00 4.57
1307 5007 4.152402 CGTTTCTGATGAAATTGAGGTCGT 59.848 41.667 0.00 0.00 43.14 4.34
1308 5008 4.436050 CCGTTTCTGATGAAATTGAGGTCG 60.436 45.833 0.00 0.00 43.14 4.79
1327 5027 1.155424 ACGTGATTTGTGCGACCGTT 61.155 50.000 0.00 0.00 0.00 4.44
1329 5029 0.365523 CTACGTGATTTGTGCGACCG 59.634 55.000 0.00 0.00 0.00 4.79
1331 5031 0.787787 TGCTACGTGATTTGTGCGAC 59.212 50.000 0.00 0.00 0.00 5.19
1354 5060 4.416738 GAGTGGGACTGGGCCAGC 62.417 72.222 33.04 23.85 34.37 4.85
1360 5066 2.608988 AGCTGGGAGTGGGACTGG 60.609 66.667 0.00 0.00 0.00 4.00
1540 5249 4.286291 GGAAGATGGATTATAACCCGAGGT 59.714 45.833 0.00 0.00 37.65 3.85
1567 5276 2.004733 GACGGTTGGAAATAAGGTCCG 58.995 52.381 0.00 0.00 38.06 4.79
1568 5277 3.007635 CTGACGGTTGGAAATAAGGTCC 58.992 50.000 0.00 0.00 35.55 4.46
1569 5278 2.418976 GCTGACGGTTGGAAATAAGGTC 59.581 50.000 0.00 0.00 0.00 3.85
1573 5282 2.817258 CCTTGCTGACGGTTGGAAATAA 59.183 45.455 0.00 0.00 0.00 1.40
1574 5283 2.224670 ACCTTGCTGACGGTTGGAAATA 60.225 45.455 0.00 0.00 0.00 1.40
1575 5284 1.247567 CCTTGCTGACGGTTGGAAAT 58.752 50.000 0.00 0.00 0.00 2.17
1576 5285 0.106918 ACCTTGCTGACGGTTGGAAA 60.107 50.000 0.00 0.00 0.00 3.13
1589 5298 3.815401 ACACATACTGTCAAAGACCTTGC 59.185 43.478 0.00 0.00 34.76 4.01
1594 5304 7.849804 ATCCATTACACATACTGTCAAAGAC 57.150 36.000 0.00 0.00 33.91 3.01
1739 5452 1.137404 GTTGCATGGATCGGCACAC 59.863 57.895 5.01 4.37 40.23 3.82
1741 5454 1.643868 TTCGTTGCATGGATCGGCAC 61.644 55.000 16.25 0.00 40.23 5.01
1743 5456 0.523335 GTTTCGTTGCATGGATCGGC 60.523 55.000 16.25 5.30 0.00 5.54
1744 5457 0.247655 CGTTTCGTTGCATGGATCGG 60.248 55.000 16.25 0.00 0.00 4.18
1745 5458 0.718904 TCGTTTCGTTGCATGGATCG 59.281 50.000 11.03 11.03 0.00 3.69
1747 5460 2.159393 CCAATCGTTTCGTTGCATGGAT 60.159 45.455 0.00 0.00 0.00 3.41
1748 5461 1.198867 CCAATCGTTTCGTTGCATGGA 59.801 47.619 0.00 0.00 0.00 3.41
1749 5462 1.068610 ACCAATCGTTTCGTTGCATGG 60.069 47.619 0.00 0.00 0.00 3.66
1750 5463 2.330231 ACCAATCGTTTCGTTGCATG 57.670 45.000 0.00 0.00 0.00 4.06
1751 5464 3.119990 CCTTACCAATCGTTTCGTTGCAT 60.120 43.478 0.00 0.00 0.00 3.96
1778 5723 8.801882 TGATATTAAAATGAAAGGGACGACTT 57.198 30.769 0.00 0.00 0.00 3.01
1779 5724 8.801882 TTGATATTAAAATGAAAGGGACGACT 57.198 30.769 0.00 0.00 0.00 4.18
1781 5726 8.801882 ACTTGATATTAAAATGAAAGGGACGA 57.198 30.769 0.00 0.00 0.00 4.20
1883 7578 5.685511 CGAAAACTGACAAATTCACGGAAAT 59.314 36.000 0.00 0.00 0.00 2.17
1952 7664 3.453424 GTCCGTTTTGCAGGAAAAACAT 58.547 40.909 14.28 0.00 45.98 2.71
1969 7681 0.667487 ATGAGTTGCAGTCACGTCCG 60.667 55.000 3.13 0.00 29.04 4.79
1974 7686 1.875514 TGCTTGATGAGTTGCAGTCAC 59.124 47.619 3.13 0.00 29.04 3.67
2021 7733 4.175787 AGGTCAGAACAGTGATTACGTC 57.824 45.455 0.00 0.00 0.00 4.34
2022 7734 4.202223 ACAAGGTCAGAACAGTGATTACGT 60.202 41.667 0.00 0.00 0.00 3.57
2023 7735 4.307432 ACAAGGTCAGAACAGTGATTACG 58.693 43.478 0.00 0.00 0.00 3.18
2024 7736 7.152645 TCTAACAAGGTCAGAACAGTGATTAC 58.847 38.462 0.00 0.00 0.00 1.89
2025 7737 7.297936 TCTAACAAGGTCAGAACAGTGATTA 57.702 36.000 0.00 0.00 0.00 1.75
2053 7765 9.678941 TCGTGAAGAGTTCATTATGTGATATAC 57.321 33.333 0.00 0.00 42.47 1.47
2058 7770 6.929049 ACTTTCGTGAAGAGTTCATTATGTGA 59.071 34.615 8.00 0.00 42.47 3.58
2090 7802 6.250104 GTGATGTTGCGAAAAGAATCAGATTC 59.750 38.462 14.56 14.56 39.56 2.52
2099 7811 2.548057 GGTCTGTGATGTTGCGAAAAGA 59.452 45.455 0.00 0.00 0.00 2.52
2117 7829 0.669318 TCATCAGAAACGCCACGGTC 60.669 55.000 0.00 0.00 0.00 4.79
2129 7841 0.323629 GGGTTTCGGTGGTCATCAGA 59.676 55.000 0.00 0.00 0.00 3.27
2132 7844 0.250989 TTGGGGTTTCGGTGGTCATC 60.251 55.000 0.00 0.00 0.00 2.92
2140 7852 0.466555 TGACTGGTTTGGGGTTTCGG 60.467 55.000 0.00 0.00 0.00 4.30
2142 7854 1.681264 CACTGACTGGTTTGGGGTTTC 59.319 52.381 0.00 0.00 0.00 2.78
2147 7859 0.385390 GCAACACTGACTGGTTTGGG 59.615 55.000 0.00 0.00 0.00 4.12
2178 7890 0.680921 TTTAGCCTGCCACATCAGCC 60.681 55.000 0.00 0.00 32.87 4.85
2179 7891 1.176527 TTTTAGCCTGCCACATCAGC 58.823 50.000 0.00 0.00 32.87 4.26
2233 7954 2.262292 CAACGCCATGGCCTTTGG 59.738 61.111 30.79 18.45 37.98 3.28
2275 7996 5.701290 GGTGCTACCAATACTCATTGTATCC 59.299 44.000 1.01 0.00 40.69 2.59
2276 7997 5.405571 CGGTGCTACCAATACTCATTGTATC 59.594 44.000 6.21 0.00 40.04 2.24
2280 8001 2.287915 GCGGTGCTACCAATACTCATTG 59.712 50.000 6.21 0.00 38.47 2.82
2289 8010 4.715523 GCAGGGCGGTGCTACCAA 62.716 66.667 3.38 0.00 38.47 3.67
2299 8020 3.002656 CAGTTATCACATTAAGCAGGGCG 59.997 47.826 0.00 0.00 0.00 6.13
2302 8023 3.623060 ACGCAGTTATCACATTAAGCAGG 59.377 43.478 0.00 0.00 37.78 4.85
2330 8051 4.643387 ACCACTCAAGTGCCGGCC 62.643 66.667 26.77 15.80 44.34 6.13
2332 8053 2.738521 CGACCACTCAAGTGCCGG 60.739 66.667 0.00 0.00 44.34 6.13
2337 8058 0.742505 TGTTCGTCGACCACTCAAGT 59.257 50.000 10.58 0.00 0.00 3.16
2362 8083 3.054728 TCTTATCTTTTCGGCCATGGACA 60.055 43.478 20.22 1.33 0.00 4.02
2363 8084 3.541632 TCTTATCTTTTCGGCCATGGAC 58.458 45.455 18.40 13.35 0.00 4.02
2381 8102 2.832129 TCCACAGCTCGTTATTCCTCTT 59.168 45.455 0.00 0.00 0.00 2.85
2423 8144 2.222752 GCTCATATCGATCATGCAAGCG 60.223 50.000 0.00 0.00 0.00 4.68
2426 8147 4.571919 TCATGCTCATATCGATCATGCAA 58.428 39.130 15.61 1.78 44.44 4.08
2429 8150 5.744819 GTCTCTCATGCTCATATCGATCATG 59.255 44.000 14.69 14.69 45.60 3.07
2435 8156 3.487536 GTCGTCTCTCATGCTCATATCG 58.512 50.000 0.00 0.00 0.00 2.92
2478 8199 6.650807 GCCACTGATTAGCTGCTAAACATATA 59.349 38.462 25.93 9.24 30.58 0.86
2479 8200 5.471456 GCCACTGATTAGCTGCTAAACATAT 59.529 40.000 25.93 17.28 30.58 1.78
2493 8214 0.389296 CGTCACCGTGCCACTGATTA 60.389 55.000 0.00 0.00 0.00 1.75
2524 8245 0.106519 TAGGGGGAGTGCTACGTACC 60.107 60.000 0.00 0.00 0.00 3.34
2535 8256 0.695803 ATGCCTTGGACTAGGGGGAG 60.696 60.000 0.00 0.00 35.74 4.30
2536 8257 0.694444 GATGCCTTGGACTAGGGGGA 60.694 60.000 0.00 0.00 35.74 4.81
2537 8258 0.988145 TGATGCCTTGGACTAGGGGG 60.988 60.000 0.00 0.00 35.74 5.40
2539 8260 1.816961 GCATGATGCCTTGGACTAGGG 60.817 57.143 6.04 0.00 37.42 3.53
2541 8262 2.336945 TGCATGATGCCTTGGACTAG 57.663 50.000 15.70 0.00 44.23 2.57
2560 8281 1.758280 CCCCAAAGTACATGCATGCAT 59.242 47.619 27.46 27.46 37.08 3.96
2561 8282 1.184431 CCCCAAAGTACATGCATGCA 58.816 50.000 26.53 25.04 0.00 3.96
2562 8283 0.179103 GCCCCAAAGTACATGCATGC 60.179 55.000 26.53 11.82 0.00 4.06
2563 8284 0.101040 CGCCCCAAAGTACATGCATG 59.899 55.000 25.09 25.09 0.00 4.06
2564 8285 1.666209 GCGCCCCAAAGTACATGCAT 61.666 55.000 0.00 0.00 0.00 3.96
2565 8286 2.339556 GCGCCCCAAAGTACATGCA 61.340 57.895 0.00 0.00 0.00 3.96
2566 8287 2.489751 GCGCCCCAAAGTACATGC 59.510 61.111 0.00 0.00 0.00 4.06
2567 8288 1.095228 ATCGCGCCCCAAAGTACATG 61.095 55.000 0.00 0.00 0.00 3.21
2568 8289 0.814010 GATCGCGCCCCAAAGTACAT 60.814 55.000 0.00 0.00 0.00 2.29
2569 8290 1.448893 GATCGCGCCCCAAAGTACA 60.449 57.895 0.00 0.00 0.00 2.90
2570 8291 2.178235 GGATCGCGCCCCAAAGTAC 61.178 63.158 0.00 0.00 0.00 2.73
2571 8292 1.978455 ATGGATCGCGCCCCAAAGTA 61.978 55.000 20.11 0.65 35.85 2.24
2572 8293 3.344137 ATGGATCGCGCCCCAAAGT 62.344 57.895 20.11 4.74 35.85 2.66
2573 8294 2.516930 ATGGATCGCGCCCCAAAG 60.517 61.111 20.11 0.00 35.85 2.77
2574 8295 2.515991 GATGGATCGCGCCCCAAA 60.516 61.111 20.11 1.95 35.85 3.28
2575 8296 2.550699 AAAGATGGATCGCGCCCCAA 62.551 55.000 20.11 7.14 35.85 4.12
2576 8297 1.691195 TAAAGATGGATCGCGCCCCA 61.691 55.000 18.89 18.89 36.79 4.96
2577 8298 0.534203 TTAAAGATGGATCGCGCCCC 60.534 55.000 0.00 5.30 0.00 5.80
2578 8299 1.523758 ATTAAAGATGGATCGCGCCC 58.476 50.000 0.00 5.73 0.00 6.13
2579 8300 3.243068 ACAAATTAAAGATGGATCGCGCC 60.243 43.478 0.00 0.00 0.00 6.53
2580 8301 3.952535 ACAAATTAAAGATGGATCGCGC 58.047 40.909 0.00 0.00 0.00 6.86
2581 8302 6.287107 ACTACAAATTAAAGATGGATCGCG 57.713 37.500 0.00 0.00 0.00 5.87
2582 8303 8.366671 AGTACTACAAATTAAAGATGGATCGC 57.633 34.615 0.00 0.00 0.00 4.58
2592 8313 8.875803 CGCATTCCACTAGTACTACAAATTAAA 58.124 33.333 0.00 0.00 0.00 1.52
2593 8314 8.036575 ACGCATTCCACTAGTACTACAAATTAA 58.963 33.333 0.00 0.00 0.00 1.40
2594 8315 7.490079 CACGCATTCCACTAGTACTACAAATTA 59.510 37.037 0.00 0.00 0.00 1.40
2595 8316 6.312918 CACGCATTCCACTAGTACTACAAATT 59.687 38.462 0.00 0.00 0.00 1.82
2596 8317 5.810587 CACGCATTCCACTAGTACTACAAAT 59.189 40.000 0.00 0.00 0.00 2.32
2597 8318 5.165676 CACGCATTCCACTAGTACTACAAA 58.834 41.667 0.00 0.00 0.00 2.83
2598 8319 4.740268 CACGCATTCCACTAGTACTACAA 58.260 43.478 0.00 0.00 0.00 2.41
2599 8320 3.428452 GCACGCATTCCACTAGTACTACA 60.428 47.826 0.00 0.00 0.00 2.74
2600 8321 3.114065 GCACGCATTCCACTAGTACTAC 58.886 50.000 0.00 0.00 0.00 2.73
2601 8322 2.100252 GGCACGCATTCCACTAGTACTA 59.900 50.000 1.89 1.89 0.00 1.82
2602 8323 1.134788 GGCACGCATTCCACTAGTACT 60.135 52.381 0.00 0.00 0.00 2.73
2603 8324 1.287425 GGCACGCATTCCACTAGTAC 58.713 55.000 0.00 0.00 0.00 2.73
2604 8325 3.752796 GGCACGCATTCCACTAGTA 57.247 52.632 0.00 0.00 0.00 1.82
2605 8326 4.617875 GGCACGCATTCCACTAGT 57.382 55.556 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.