Multiple sequence alignment - TraesCS5A01G192000

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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 TraesCS5A01G192000 chr5A 100.000 5614 0 0 1 5614 395874085 395868472 0.000000e+00 10368.0
1 TraesCS5A01G192000 chr5A 96.471 85 0 3 805 887 395873245 395873162 2.730000e-28 137.0
2 TraesCS5A01G192000 chr5A 96.471 85 0 3 841 924 395873281 395873199 2.730000e-28 137.0
3 TraesCS5A01G192000 chr5B 94.418 4228 151 24 876 5043 344934979 344939181 0.000000e+00 6421.0
4 TraesCS5A01G192000 chr5B 86.935 597 50 9 5027 5614 344939197 344939774 0.000000e+00 645.0
5 TraesCS5A01G192000 chr5B 93.074 231 15 1 463 693 344897060 344897289 2.510000e-88 337.0
6 TraesCS5A01G192000 chr5B 94.702 151 5 3 708 856 344934883 344935032 1.220000e-56 231.0
7 TraesCS5A01G192000 chr5B 76.142 197 37 9 425 617 684601253 684601063 1.670000e-15 95.3
8 TraesCS5A01G192000 chr5B 76.129 155 32 5 465 617 296110088 296109937 6.030000e-10 76.8
9 TraesCS5A01G192000 chr5D 94.836 3486 115 20 882 4317 301986505 301989975 0.000000e+00 5380.0
10 TraesCS5A01G192000 chr5D 95.409 697 17 4 4355 5043 301990118 301990807 0.000000e+00 1096.0
11 TraesCS5A01G192000 chr5D 87.779 851 59 22 46 887 301985735 301986549 0.000000e+00 953.0
12 TraesCS5A01G192000 chr5D 79.518 166 26 8 463 624 359047313 359047152 1.650000e-20 111.0
13 TraesCS5A01G192000 chr5D 77.222 180 32 8 475 649 545284577 545284752 4.630000e-16 97.1
14 TraesCS5A01G192000 chr5D 91.228 57 3 2 4303 4358 301989994 301990049 6.030000e-10 76.8
15 TraesCS5A01G192000 chr5D 100.000 32 0 0 5027 5058 301990824 301990855 6.070000e-05 60.2
16 TraesCS5A01G192000 chr7A 85.083 181 24 3 5435 5614 731748009 731748187 1.240000e-41 182.0
17 TraesCS5A01G192000 chr3A 77.358 212 37 9 464 670 485992552 485992347 1.280000e-21 115.0
18 TraesCS5A01G192000 chr6B 78.667 150 27 5 475 622 62151230 62151376 1.670000e-15 95.3
19 TraesCS5A01G192000 chr7D 76.042 192 37 7 463 649 599716175 599715988 2.150000e-14 91.6


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 TraesCS5A01G192000 chr5A 395868472 395874085 5613 True 3547.333333 10368 97.647333 1 5614 3 chr5A.!!$R1 5613
1 TraesCS5A01G192000 chr5B 344934883 344939774 4891 False 2432.333333 6421 92.018333 708 5614 3 chr5B.!!$F2 4906
2 TraesCS5A01G192000 chr5D 301985735 301990855 5120 False 1513.200000 5380 93.850400 46 5058 5 chr5D.!!$F2 5012

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
840 869 0.108138 CACGGGGAGATGACCTGAAC 60.108 60.0 0.00 0.00 37.80 3.18 F
914 943 0.176680 CTGGGAGATGACCTGAACCG 59.823 60.0 0.00 0.00 0.00 4.44 F
1120 1149 0.394352 CGCTCCCTAACCTGGCATTT 60.394 55.0 0.00 0.00 0.00 2.32 F
1964 1998 0.413832 AGGTGCCTCCTCAGGTCTTA 59.586 55.0 0.00 0.00 44.42 2.10 F
2006 2040 0.749649 TTGTTGCCGAATTGGTTGCT 59.250 45.0 0.00 0.00 41.21 3.91 F
3274 3334 0.883370 GACCACTTGTTCCGGACCAC 60.883 60.0 1.83 0.06 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2060 2094 0.391793 AGTTTCAAGGAGGCGCTAGC 60.392 55.000 7.64 4.06 44.18 3.42 R
2911 2951 1.339055 TGTTCCCTGGCTTCTTCATCG 60.339 52.381 0.00 0.00 0.00 3.84 R
3064 3104 4.594920 AGAGAGAGAGAGAGAGATTCGGAT 59.405 45.833 0.00 0.00 0.00 4.18 R
3809 3870 1.134175 ACAATAAGAAAATGCCGCCCG 59.866 47.619 0.00 0.00 0.00 6.13 R
3972 4055 6.648879 ACAAGCTGAAAAGGCTATTTACAA 57.351 33.333 0.00 0.00 39.30 2.41 R
4737 4926 0.179189 CGAATCCGCAGCAGGTTTTC 60.179 55.000 0.00 3.19 0.00 2.29 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
22 23 3.348236 GCAGTCAGTGGCTTGGTG 58.652 61.111 0.00 0.00 0.00 4.17
23 24 2.912624 GCAGTCAGTGGCTTGGTGC 61.913 63.158 0.00 0.00 41.94 5.01
32 33 3.723348 GCTTGGTGCCGACGAACC 61.723 66.667 11.49 11.49 36.96 3.62
33 34 3.047877 CTTGGTGCCGACGAACCC 61.048 66.667 14.67 4.00 35.44 4.11
34 35 4.629523 TTGGTGCCGACGAACCCC 62.630 66.667 14.67 0.73 35.44 4.95
36 37 4.754667 GGTGCCGACGAACCCCTC 62.755 72.222 8.11 0.00 0.00 4.30
37 38 4.754667 GTGCCGACGAACCCCTCC 62.755 72.222 0.00 0.00 0.00 4.30
41 42 4.125695 CGACGAACCCCTCCCGTC 62.126 72.222 0.00 0.00 46.27 4.79
43 44 2.524887 ACGAACCCCTCCCGTCAA 60.525 61.111 0.00 0.00 29.82 3.18
44 45 2.142104 ACGAACCCCTCCCGTCAAA 61.142 57.895 0.00 0.00 29.82 2.69
69 70 1.610886 CCCAACTTCTTCCTTCCGACC 60.611 57.143 0.00 0.00 0.00 4.79
74 75 2.037381 ACTTCTTCCTTCCGACCACTTC 59.963 50.000 0.00 0.00 0.00 3.01
88 89 2.251818 CCACTTCCTCTTCACCTCTCA 58.748 52.381 0.00 0.00 0.00 3.27
99 100 3.169512 TCACCTCTCATGTGGTCACTA 57.830 47.619 2.66 0.00 37.92 2.74
103 104 4.081476 CACCTCTCATGTGGTCACTATCAA 60.081 45.833 2.66 0.00 37.92 2.57
113 114 3.010420 GGTCACTATCAACTTCAAGGGC 58.990 50.000 0.00 0.00 0.00 5.19
122 123 3.260884 TCAACTTCAAGGGCGTTAGATCT 59.739 43.478 0.00 0.00 0.00 2.75
130 131 1.599542 GGGCGTTAGATCTGTCATTGC 59.400 52.381 5.18 0.76 0.00 3.56
142 143 3.519107 TCTGTCATTGCCTATCCAAGTGA 59.481 43.478 0.00 0.00 0.00 3.41
148 149 1.134007 TGCCTATCCAAGTGATGCTGG 60.134 52.381 0.00 0.00 34.76 4.85
152 153 0.622136 ATCCAAGTGATGCTGGCAGA 59.378 50.000 20.86 3.68 30.54 4.26
162 163 1.644509 TGCTGGCAGAGAGGAAGTTA 58.355 50.000 20.86 0.00 0.00 2.24
168 169 3.009473 TGGCAGAGAGGAAGTTAGCAATT 59.991 43.478 0.00 0.00 0.00 2.32
169 170 3.376546 GGCAGAGAGGAAGTTAGCAATTG 59.623 47.826 0.00 0.00 0.00 2.32
173 174 4.880696 AGAGAGGAAGTTAGCAATTGCATC 59.119 41.667 30.89 19.45 45.16 3.91
178 179 4.036144 GGAAGTTAGCAATTGCATCCTCTC 59.964 45.833 30.89 18.42 45.16 3.20
199 200 0.315251 AAAAGCTTTCTTGCCTCCGC 59.685 50.000 13.10 0.00 31.78 5.54
208 209 3.151958 TTGCCTCCGCGAGATAGCC 62.152 63.158 8.23 0.00 38.08 3.93
251 258 2.935201 CAATCTTGGCTTCTTCTCTCGG 59.065 50.000 0.00 0.00 0.00 4.63
255 262 1.267574 TGGCTTCTTCTCTCGGGCAT 61.268 55.000 0.00 0.00 0.00 4.40
256 263 0.753262 GGCTTCTTCTCTCGGGCATA 59.247 55.000 0.00 0.00 0.00 3.14
257 264 1.346068 GGCTTCTTCTCTCGGGCATAT 59.654 52.381 0.00 0.00 0.00 1.78
259 266 2.869636 GCTTCTTCTCTCGGGCATATGG 60.870 54.545 4.56 0.00 0.00 2.74
260 267 2.088104 TCTTCTCTCGGGCATATGGT 57.912 50.000 4.56 0.00 0.00 3.55
261 268 1.688735 TCTTCTCTCGGGCATATGGTG 59.311 52.381 4.56 0.00 0.00 4.17
262 269 1.414181 CTTCTCTCGGGCATATGGTGT 59.586 52.381 4.56 0.00 0.00 4.16
263 270 0.752658 TCTCTCGGGCATATGGTGTG 59.247 55.000 4.56 0.00 0.00 3.82
264 271 0.752658 CTCTCGGGCATATGGTGTGA 59.247 55.000 4.56 0.00 0.00 3.58
265 272 0.752658 TCTCGGGCATATGGTGTGAG 59.247 55.000 4.56 0.00 0.00 3.51
266 273 0.250038 CTCGGGCATATGGTGTGAGG 60.250 60.000 4.56 0.00 0.00 3.86
267 274 0.980754 TCGGGCATATGGTGTGAGGT 60.981 55.000 4.56 0.00 0.00 3.85
268 275 0.532862 CGGGCATATGGTGTGAGGTC 60.533 60.000 4.56 0.00 0.00 3.85
269 276 0.546122 GGGCATATGGTGTGAGGTCA 59.454 55.000 4.56 0.00 0.00 4.02
270 277 1.475751 GGGCATATGGTGTGAGGTCAG 60.476 57.143 4.56 0.00 0.00 3.51
271 278 1.303309 GCATATGGTGTGAGGTCAGC 58.697 55.000 4.56 0.00 36.52 4.26
272 279 1.134280 GCATATGGTGTGAGGTCAGCT 60.134 52.381 4.56 0.00 36.85 4.24
273 280 2.103094 GCATATGGTGTGAGGTCAGCTA 59.897 50.000 4.56 0.00 36.85 3.32
276 283 2.238084 TGGTGTGAGGTCAGCTAGAT 57.762 50.000 0.00 0.00 36.85 1.98
307 314 3.250762 CGAGTCACCATTGATTTGTGTGT 59.749 43.478 0.00 0.00 33.11 3.72
313 320 5.703130 TCACCATTGATTTGTGTGTCGATTA 59.297 36.000 0.00 0.00 0.00 1.75
315 322 7.550906 TCACCATTGATTTGTGTGTCGATTATA 59.449 33.333 0.00 0.00 0.00 0.98
328 335 9.638300 GTGTGTCGATTATAATGTTCATTTCTC 57.362 33.333 1.78 0.00 0.00 2.87
361 368 7.363431 CCTTGTTGTCTCTAAAAAGTGGATTC 58.637 38.462 0.00 0.00 0.00 2.52
395 402 8.514594 ACATGTTGTATCGATTTTCATCTGTTT 58.485 29.630 1.71 0.00 0.00 2.83
396 403 9.345517 CATGTTGTATCGATTTTCATCTGTTTT 57.654 29.630 1.71 0.00 0.00 2.43
397 404 8.948853 TGTTGTATCGATTTTCATCTGTTTTC 57.051 30.769 1.71 0.00 0.00 2.29
398 405 8.783093 TGTTGTATCGATTTTCATCTGTTTTCT 58.217 29.630 1.71 0.00 0.00 2.52
399 406 9.267096 GTTGTATCGATTTTCATCTGTTTTCTC 57.733 33.333 1.71 0.00 0.00 2.87
400 407 8.777865 TGTATCGATTTTCATCTGTTTTCTCT 57.222 30.769 1.71 0.00 0.00 3.10
401 408 9.869757 TGTATCGATTTTCATCTGTTTTCTCTA 57.130 29.630 1.71 0.00 0.00 2.43
444 451 2.685850 AATTACTTTCTCCGTCCGGG 57.314 50.000 0.00 0.00 35.59 5.73
477 484 6.998673 GCACCCCTCATATTTTGTATCTAAGT 59.001 38.462 0.00 0.00 0.00 2.24
536 543 9.689976 TGTATCTCACAAAAATTGTATTGTTGG 57.310 29.630 7.12 0.00 43.23 3.77
617 625 9.696917 ATTTTGCTTGTTAAATCTAAGGTCAAG 57.303 29.630 0.00 0.00 35.43 3.02
631 639 4.937201 AGGTCAAGGTTTGATCCAAAAC 57.063 40.909 0.00 0.00 41.78 2.43
634 642 5.049828 GGTCAAGGTTTGATCCAAAACAAG 58.950 41.667 9.73 2.53 42.78 3.16
637 645 5.890985 TCAAGGTTTGATCCAAAACAAGAGA 59.109 36.000 9.73 0.41 42.78 3.10
639 647 4.829492 AGGTTTGATCCAAAACAAGAGAGG 59.171 41.667 9.73 0.00 42.78 3.69
718 728 3.756963 GACACCCAAAGGATCTTGGTAAC 59.243 47.826 11.63 0.00 43.84 2.50
730 740 5.475564 GGATCTTGGTAACTGTTTTGCCTTA 59.524 40.000 0.00 0.00 37.61 2.69
760 770 6.266786 TGAAGGAAAAGGAAATTACCAAGTCC 59.733 38.462 0.00 0.00 0.00 3.85
822 851 4.690719 CGTAACGGGCCAGCCACA 62.691 66.667 11.50 0.00 37.98 4.17
823 852 3.053896 GTAACGGGCCAGCCACAC 61.054 66.667 11.50 0.00 37.98 3.82
824 853 4.690719 TAACGGGCCAGCCACACG 62.691 66.667 11.50 7.62 37.98 4.49
831 860 3.402681 CCAGCCACACGGGGAGAT 61.403 66.667 0.00 0.00 37.04 2.75
832 861 2.124983 CAGCCACACGGGGAGATG 60.125 66.667 0.00 0.00 37.04 2.90
833 862 2.284625 AGCCACACGGGGAGATGA 60.285 61.111 0.00 0.00 37.04 2.92
834 863 2.125106 GCCACACGGGGAGATGAC 60.125 66.667 0.00 0.00 37.04 3.06
835 864 2.584608 CCACACGGGGAGATGACC 59.415 66.667 0.00 0.00 0.00 4.02
836 865 1.990060 CCACACGGGGAGATGACCT 60.990 63.158 0.00 0.00 0.00 3.85
837 866 1.219124 CACACGGGGAGATGACCTG 59.781 63.158 0.00 0.00 40.32 4.00
838 867 1.078528 ACACGGGGAGATGACCTGA 59.921 57.895 0.00 0.00 37.80 3.86
839 868 0.544357 ACACGGGGAGATGACCTGAA 60.544 55.000 0.00 0.00 37.80 3.02
840 869 0.108138 CACGGGGAGATGACCTGAAC 60.108 60.000 0.00 0.00 37.80 3.18
841 870 1.265454 ACGGGGAGATGACCTGAACC 61.265 60.000 0.00 0.00 37.80 3.62
842 871 1.522569 GGGGAGATGACCTGAACCG 59.477 63.158 0.00 0.00 0.00 4.44
843 872 1.265454 GGGGAGATGACCTGAACCGT 61.265 60.000 0.00 0.00 0.00 4.83
844 873 1.481871 GGGAGATGACCTGAACCGTA 58.518 55.000 0.00 0.00 0.00 4.02
845 874 1.829222 GGGAGATGACCTGAACCGTAA 59.171 52.381 0.00 0.00 0.00 3.18
846 875 2.418334 GGGAGATGACCTGAACCGTAAC 60.418 54.545 0.00 0.00 0.00 2.50
847 876 2.527100 GAGATGACCTGAACCGTAACG 58.473 52.381 0.00 0.00 0.00 3.18
869 898 1.448540 CAGCCACACGGGAGATGAC 60.449 63.158 0.00 0.00 40.01 3.06
903 932 3.408229 CAGGCCACACTGGGAGAT 58.592 61.111 5.01 0.00 38.19 2.75
904 933 1.077930 CAGGCCACACTGGGAGATG 60.078 63.158 5.01 0.00 38.19 2.90
905 934 1.229625 AGGCCACACTGGGAGATGA 60.230 57.895 5.01 0.00 38.19 2.92
906 935 1.078143 GGCCACACTGGGAGATGAC 60.078 63.158 0.00 0.00 38.19 3.06
907 936 1.078143 GCCACACTGGGAGATGACC 60.078 63.158 0.00 0.00 38.19 4.02
908 937 1.557269 GCCACACTGGGAGATGACCT 61.557 60.000 0.00 0.00 38.19 3.85
909 938 0.251354 CCACACTGGGAGATGACCTG 59.749 60.000 0.00 0.00 32.67 4.00
910 939 1.269958 CACACTGGGAGATGACCTGA 58.730 55.000 0.00 0.00 0.00 3.86
911 940 1.625315 CACACTGGGAGATGACCTGAA 59.375 52.381 0.00 0.00 0.00 3.02
912 941 1.625818 ACACTGGGAGATGACCTGAAC 59.374 52.381 0.00 0.00 0.00 3.18
913 942 1.065854 CACTGGGAGATGACCTGAACC 60.066 57.143 0.00 0.00 0.00 3.62
914 943 0.176680 CTGGGAGATGACCTGAACCG 59.823 60.000 0.00 0.00 0.00 4.44
915 944 0.544357 TGGGAGATGACCTGAACCGT 60.544 55.000 0.00 0.00 0.00 4.83
916 945 1.272816 TGGGAGATGACCTGAACCGTA 60.273 52.381 0.00 0.00 0.00 4.02
917 946 1.829222 GGGAGATGACCTGAACCGTAA 59.171 52.381 0.00 0.00 0.00 3.18
918 947 2.418334 GGGAGATGACCTGAACCGTAAC 60.418 54.545 0.00 0.00 0.00 2.50
919 948 2.527100 GAGATGACCTGAACCGTAACG 58.473 52.381 0.00 0.00 0.00 3.18
963 992 0.408309 TCGAGAAGTCTCTTCCCCCA 59.592 55.000 6.75 0.00 40.75 4.96
1114 1143 0.760945 ATCCTCCGCTCCCTAACCTG 60.761 60.000 0.00 0.00 0.00 4.00
1120 1149 0.394352 CGCTCCCTAACCTGGCATTT 60.394 55.000 0.00 0.00 0.00 2.32
1351 1380 3.144193 CGCCTCCTCTCGAAGGCT 61.144 66.667 20.61 0.00 45.78 4.58
1416 1445 1.284785 CCCCAACCTATTCTGGCTCAA 59.715 52.381 0.00 0.00 0.00 3.02
1453 1482 1.212934 ACCTCCACGGTCTCTCCCTA 61.213 60.000 0.00 0.00 44.93 3.53
1463 1496 3.689649 CGGTCTCTCCCTAATTTGTTTGG 59.310 47.826 0.00 0.00 0.00 3.28
1472 1505 5.474189 TCCCTAATTTGTTTGGTTAACCGAG 59.526 40.000 19.65 3.61 39.43 4.63
1475 1508 6.149807 CCTAATTTGTTTGGTTAACCGAGCTA 59.850 38.462 24.41 16.91 39.43 3.32
1479 1512 4.250464 TGTTTGGTTAACCGAGCTATCAG 58.750 43.478 24.41 0.00 39.43 2.90
1490 1523 6.563222 ACCGAGCTATCAGTAGATTACTTC 57.437 41.667 0.00 0.00 36.76 3.01
1492 1525 6.205853 ACCGAGCTATCAGTAGATTACTTCAG 59.794 42.308 0.00 0.00 36.76 3.02
1501 1534 5.741510 CAGTAGATTACTTCAGCAAGAGTCG 59.258 44.000 0.00 0.00 36.76 4.18
1504 1537 2.065993 TACTTCAGCAAGAGTCGTGC 57.934 50.000 21.64 21.64 42.55 5.34
1524 1557 5.559991 CGTGCTCACTTGCTACATTTTTGTA 60.560 40.000 0.00 0.00 0.00 2.41
1525 1558 5.625311 GTGCTCACTTGCTACATTTTTGTAC 59.375 40.000 0.00 0.00 0.00 2.90
1526 1559 5.530915 TGCTCACTTGCTACATTTTTGTACT 59.469 36.000 0.00 0.00 0.00 2.73
1527 1560 6.080406 GCTCACTTGCTACATTTTTGTACTC 58.920 40.000 0.00 0.00 0.00 2.59
1528 1561 6.554334 TCACTTGCTACATTTTTGTACTCC 57.446 37.500 0.00 0.00 0.00 3.85
1529 1562 6.296026 TCACTTGCTACATTTTTGTACTCCT 58.704 36.000 0.00 0.00 0.00 3.69
1578 1611 4.065088 TGTGAGCTGATTTACCTGACAAC 58.935 43.478 0.00 0.00 0.00 3.32
1630 1663 5.796437 GCTTGTTTTAATTGCCATTGATTGC 59.204 36.000 0.00 0.00 0.00 3.56
1645 1678 3.157087 TGATTGCTTTCCCCTTCTGTTC 58.843 45.455 0.00 0.00 0.00 3.18
1646 1679 2.746279 TTGCTTTCCCCTTCTGTTCA 57.254 45.000 0.00 0.00 0.00 3.18
1964 1998 0.413832 AGGTGCCTCCTCAGGTCTTA 59.586 55.000 0.00 0.00 44.42 2.10
2006 2040 0.749649 TTGTTGCCGAATTGGTTGCT 59.250 45.000 0.00 0.00 41.21 3.91
2060 2094 9.988815 ACTCATATAGTAGCTTAATTGTTGAGG 57.011 33.333 0.00 0.00 36.36 3.86
2066 2100 2.939103 AGCTTAATTGTTGAGGCTAGCG 59.061 45.455 9.00 0.00 32.89 4.26
2067 2101 2.539750 GCTTAATTGTTGAGGCTAGCGC 60.540 50.000 9.00 0.00 0.00 5.92
2126 2163 9.866798 TTGATATCATACACTGAGATTCTATGC 57.133 33.333 6.17 0.00 35.95 3.14
2127 2164 8.473219 TGATATCATACACTGAGATTCTATGCC 58.527 37.037 0.00 0.00 35.95 4.40
2137 2174 5.096521 TGAGATTCTATGCCACCATCCTAT 58.903 41.667 0.00 0.00 32.85 2.57
2186 2226 3.733443 AACAGAAGTGTGCCAAATTCC 57.267 42.857 0.00 0.00 36.84 3.01
2243 2283 4.323417 TCACATTGCAGGTACTAAAGGTG 58.677 43.478 0.00 1.41 43.01 4.00
2299 2339 1.279846 TCTCCCCATGTTACCCGTTTC 59.720 52.381 0.00 0.00 0.00 2.78
2320 2360 2.969821 TTGGACTTGCTAATGTGGGT 57.030 45.000 0.00 0.00 0.00 4.51
2345 2385 9.819267 GTAACAAAGAGAAGCAGGTATACTTAT 57.181 33.333 2.25 0.00 0.00 1.73
2369 2409 6.436843 ACTTAACAAAGTCAACTTGTCCTG 57.563 37.500 0.00 0.00 36.12 3.86
2381 2421 7.013369 AGTCAACTTGTCCTGAAATACTTTTCC 59.987 37.037 0.00 0.00 40.49 3.13
2512 2552 5.692204 ACATATATCTCGTGCTGCTGTTAAC 59.308 40.000 0.00 0.00 0.00 2.01
2515 2555 3.653539 TCTCGTGCTGCTGTTAACTTA 57.346 42.857 7.22 0.00 0.00 2.24
2751 2791 3.508762 CTCCAGCAAAATCTGTTCATGC 58.491 45.455 0.00 0.00 37.28 4.06
2758 2798 5.185249 AGCAAAATCTGTTCATGCTGAAGAT 59.815 36.000 0.00 0.00 45.03 2.40
2911 2951 3.366374 GGAGTAAATGCAACTTCAGGCAC 60.366 47.826 0.00 0.00 43.75 5.01
2960 3000 9.305925 GTCAGAGAAATGTCTGTTTTGATTTTT 57.694 29.630 7.36 0.00 43.89 1.94
3274 3334 0.883370 GACCACTTGTTCCGGACCAC 60.883 60.000 1.83 0.06 0.00 4.16
3390 3450 6.080406 GCAAGTATTTTGAGAAACGAGGAAG 58.920 40.000 0.00 0.00 0.00 3.46
3540 3600 8.358729 CAAATTTCTTTGTGAAGGCTGTCCCT 62.359 42.308 0.00 0.00 40.39 4.20
3598 3658 1.741770 CACCTAGCAGCCCAACGAC 60.742 63.158 0.00 0.00 0.00 4.34
3717 3778 4.020928 ACATTCTTTCAATCCATGCAGCAA 60.021 37.500 0.00 0.00 0.00 3.91
3727 3788 1.000607 CCATGCAGCAAGATACATGCC 60.001 52.381 0.00 0.00 44.91 4.40
3732 3793 2.223433 GCAGCAAGATACATGCCTTGTC 60.223 50.000 18.32 13.00 44.91 3.18
3759 3820 6.381994 TGGTTACCTACTCGTCATTATTTCCT 59.618 38.462 2.07 0.00 0.00 3.36
3802 3863 9.657419 GAAACATATTGATCTTTCCACCAATTT 57.343 29.630 0.00 0.00 32.28 1.82
3809 3870 7.645058 TGATCTTTCCACCAATTTTCCTATC 57.355 36.000 0.00 0.00 0.00 2.08
3922 3983 3.511540 TCTCGGTCTCATGTCAAGTCATT 59.488 43.478 0.00 0.00 0.00 2.57
3923 3984 3.588955 TCGGTCTCATGTCAAGTCATTG 58.411 45.455 0.00 0.00 37.80 2.82
3925 3986 3.748048 CGGTCTCATGTCAAGTCATTGTT 59.252 43.478 0.00 0.00 37.68 2.83
3954 4037 9.025041 GGGGATTAGATAACTGAAATTAATGGG 57.975 37.037 0.00 0.00 0.00 4.00
3972 4055 2.971330 TGGGTTGCAAATCATTGTCCTT 59.029 40.909 0.00 0.00 38.85 3.36
3975 4058 4.379652 GGTTGCAAATCATTGTCCTTTGT 58.620 39.130 0.00 0.00 38.85 2.83
4013 4096 7.224753 TCAGCTTGTTCTATCGATTAAATGGTC 59.775 37.037 1.71 0.00 0.00 4.02
4200 4284 4.518249 GCTTGTTTTATGTAGAGCTCCCT 58.482 43.478 10.93 0.00 0.00 4.20
4283 4367 4.646945 ACGTGAGGTATGTCAGAGATGATT 59.353 41.667 0.00 0.00 0.00 2.57
4380 4569 8.843885 ACTTCAGTAACTTACTTGGTTAATCC 57.156 34.615 0.00 0.00 36.76 3.01
4591 4780 4.466015 GGATGATTTTAAGCAAGGGTTCCA 59.534 41.667 0.00 0.00 0.00 3.53
4666 4855 2.227194 TGATGATGCATGCCTGATGTC 58.773 47.619 16.68 6.59 34.14 3.06
4682 4871 5.426504 CTGATGTCCATGACTTCTTAAGCT 58.573 41.667 0.00 0.00 37.53 3.74
4737 4926 4.240103 TGAGCCGGGCCATGATCG 62.240 66.667 17.02 0.00 0.00 3.69
4946 5144 7.910683 CCTTCTTTGTTTGAACTCTAGAACAAC 59.089 37.037 5.17 0.25 40.49 3.32
5022 5221 2.149578 CTCCATCATGATCCGGCTTTC 58.850 52.381 4.86 0.00 0.00 2.62
5058 5290 5.614324 AATAGATGTTCATCTGGGACGAA 57.386 39.130 21.15 4.17 32.36 3.85
5082 5314 5.567138 AACTGCTTATACATGTTGAAGGC 57.433 39.130 2.30 2.78 0.00 4.35
5124 5356 5.677567 AGTGGGAACTAATACCATTAACCG 58.322 41.667 0.00 0.00 36.54 4.44
5125 5357 4.818005 GTGGGAACTAATACCATTAACCGG 59.182 45.833 0.00 0.00 36.54 5.28
5129 5361 5.882000 GGAACTAATACCATTAACCGGTGTT 59.118 40.000 8.52 2.50 40.51 3.32
5179 5411 4.987408 TTGCATGGAAATGTCTACATGG 57.013 40.909 0.00 0.00 40.66 3.66
5191 5427 4.037222 TGTCTACATGGGATCCTTGCTTA 58.963 43.478 12.58 0.00 32.73 3.09
5249 5485 1.274728 CGAGAAGCCCATCATAGGAGG 59.725 57.143 0.00 0.00 0.00 4.30
5256 5492 2.575279 GCCCATCATAGGAGGACATCAT 59.425 50.000 0.00 0.00 0.00 2.45
5268 5504 1.477553 GACATCATTGGCCATGTGGT 58.522 50.000 14.36 6.52 33.22 4.16
5269 5505 2.653726 GACATCATTGGCCATGTGGTA 58.346 47.619 14.36 0.00 33.22 3.25
5270 5506 2.358898 GACATCATTGGCCATGTGGTAC 59.641 50.000 14.36 4.03 33.22 3.34
5282 5519 4.618460 GCCATGTGGTACGTCTATCATAGG 60.618 50.000 0.00 0.53 37.57 2.57
5290 5527 6.322969 TGGTACGTCTATCATAGGTTGTGAAT 59.677 38.462 0.00 0.00 0.00 2.57
5291 5528 7.147794 TGGTACGTCTATCATAGGTTGTGAATT 60.148 37.037 0.00 0.00 0.00 2.17
5295 5532 7.147897 ACGTCTATCATAGGTTGTGAATTGAGA 60.148 37.037 0.00 0.00 0.00 3.27
5315 5552 2.034066 ACCTCAATGGCCACGTGG 59.966 61.111 30.66 30.66 40.22 4.94
5325 5562 4.659172 CCACGTGGCCACATGGGT 62.659 66.667 37.81 23.58 40.69 4.51
5327 5564 2.038269 CACGTGGCCACATGGGTAC 61.038 63.158 34.16 6.15 39.65 3.34
5339 5576 4.765339 CCACATGGGTACGTCTATCATAGA 59.235 45.833 0.00 0.00 0.00 1.98
5353 5590 7.509546 GTCTATCATAGATTTTGAAGGGGTGA 58.490 38.462 0.00 0.00 37.13 4.02
5362 5599 0.918983 TGAAGGGGTGAATAGGGCTG 59.081 55.000 0.00 0.00 0.00 4.85
5365 5602 1.227383 GGGGTGAATAGGGCTGTGG 59.773 63.158 0.00 0.00 0.00 4.17
5369 5606 2.640184 GGTGAATAGGGCTGTGGTTAC 58.360 52.381 0.00 0.00 0.00 2.50
5371 5608 2.093869 GTGAATAGGGCTGTGGTTACGA 60.094 50.000 0.00 0.00 0.00 3.43
5372 5609 2.568062 TGAATAGGGCTGTGGTTACGAA 59.432 45.455 0.00 0.00 0.00 3.85
5391 5628 2.503895 AAGCATGAACCAAGGAGAGG 57.496 50.000 0.00 0.00 0.00 3.69
5397 5634 0.321996 GAACCAAGGAGAGGACGCTT 59.678 55.000 0.00 0.00 0.00 4.68
5410 5650 2.832129 AGGACGCTTCTAAATCTCACCA 59.168 45.455 0.00 0.00 0.00 4.17
5450 5690 2.485814 GTGAGAAGGCCAAAGTGTGATC 59.514 50.000 5.01 0.00 0.00 2.92
5468 5708 0.684535 TCGGATGCTTGGTTGAGACA 59.315 50.000 0.00 0.00 0.00 3.41
5481 5721 3.437049 GGTTGAGACAAAGACATGGCTAC 59.563 47.826 0.00 0.00 39.31 3.58
5482 5722 4.065088 GTTGAGACAAAGACATGGCTACA 58.935 43.478 0.00 0.00 39.31 2.74
5485 5725 6.048732 TGAGACAAAGACATGGCTACATTA 57.951 37.500 0.00 0.00 39.31 1.90
5520 5760 0.237235 CGGGTTTTGATGTGGACACG 59.763 55.000 0.00 0.00 32.23 4.49
5531 5771 3.083997 GGACACGCTCCAGGGGAT 61.084 66.667 0.00 0.00 39.21 3.85
5543 5783 1.542375 AGGGGATGGTTGGAGCAGT 60.542 57.895 0.00 0.00 0.00 4.40
5544 5784 1.077429 GGGGATGGTTGGAGCAGTC 60.077 63.158 0.00 0.00 0.00 3.51
5545 5785 1.685224 GGGATGGTTGGAGCAGTCA 59.315 57.895 0.00 0.00 0.00 3.41
5546 5786 0.257039 GGGATGGTTGGAGCAGTCAT 59.743 55.000 0.00 0.00 0.00 3.06
5547 5787 1.341383 GGGATGGTTGGAGCAGTCATT 60.341 52.381 0.00 0.00 0.00 2.57
5548 5788 2.019984 GGATGGTTGGAGCAGTCATTC 58.980 52.381 0.00 0.00 0.00 2.67
5549 5789 1.667724 GATGGTTGGAGCAGTCATTCG 59.332 52.381 0.00 0.00 0.00 3.34
5550 5790 0.684535 TGGTTGGAGCAGTCATTCGA 59.315 50.000 0.00 0.00 0.00 3.71
5551 5791 1.338105 TGGTTGGAGCAGTCATTCGAG 60.338 52.381 0.00 0.00 0.00 4.04
5552 5792 1.066858 GGTTGGAGCAGTCATTCGAGA 60.067 52.381 0.00 0.00 0.00 4.04
5572 5812 6.259387 TCGAGATCATCATGGAAAGTTCATTG 59.741 38.462 0.00 0.00 0.00 2.82
5573 5813 6.037940 CGAGATCATCATGGAAAGTTCATTGT 59.962 38.462 0.00 0.00 0.00 2.71
5575 5815 8.447924 AGATCATCATGGAAAGTTCATTGTAG 57.552 34.615 0.00 0.00 0.00 2.74
5581 5822 4.072131 TGGAAAGTTCATTGTAGCCTCAC 58.928 43.478 0.00 0.00 0.00 3.51
5593 5834 5.227569 TGTAGCCTCACTGAAAAGATTGA 57.772 39.130 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.303888 AAGCCACTGACTGCCATGG 60.304 57.895 7.63 7.63 35.17 3.66
1 2 1.592400 CCAAGCCACTGACTGCCATG 61.592 60.000 0.00 0.00 0.00 3.66
2 3 1.303888 CCAAGCCACTGACTGCCAT 60.304 57.895 0.00 0.00 0.00 4.40
3 4 2.113774 CCAAGCCACTGACTGCCA 59.886 61.111 0.00 0.00 0.00 4.92
4 5 2.113986 ACCAAGCCACTGACTGCC 59.886 61.111 0.00 0.00 0.00 4.85
5 6 2.912624 GCACCAAGCCACTGACTGC 61.913 63.158 0.00 0.00 37.23 4.40
6 7 3.348236 GCACCAAGCCACTGACTG 58.652 61.111 0.00 0.00 37.23 3.51
15 16 3.723348 GGTTCGTCGGCACCAAGC 61.723 66.667 9.05 0.00 44.65 4.01
16 17 3.047877 GGGTTCGTCGGCACCAAG 61.048 66.667 14.28 0.00 34.36 3.61
17 18 4.629523 GGGGTTCGTCGGCACCAA 62.630 66.667 14.28 0.00 34.36 3.67
19 20 4.754667 GAGGGGTTCGTCGGCACC 62.755 72.222 6.08 6.08 0.00 5.01
20 21 4.754667 GGAGGGGTTCGTCGGCAC 62.755 72.222 0.00 0.00 0.00 5.01
24 25 4.125695 GACGGGAGGGGTTCGTCG 62.126 72.222 0.00 0.00 42.60 5.12
26 27 2.142104 TTTGACGGGAGGGGTTCGT 61.142 57.895 0.00 0.00 39.99 3.85
27 28 1.670083 GTTTGACGGGAGGGGTTCG 60.670 63.158 0.00 0.00 0.00 3.95
28 29 1.303074 GGTTTGACGGGAGGGGTTC 60.303 63.158 0.00 0.00 0.00 3.62
29 30 2.837326 GGGTTTGACGGGAGGGGTT 61.837 63.158 0.00 0.00 0.00 4.11
30 31 3.254617 GGGTTTGACGGGAGGGGT 61.255 66.667 0.00 0.00 0.00 4.95
31 32 2.933834 AGGGTTTGACGGGAGGGG 60.934 66.667 0.00 0.00 0.00 4.79
32 33 2.669240 GAGGGTTTGACGGGAGGG 59.331 66.667 0.00 0.00 0.00 4.30
33 34 2.669240 GGAGGGTTTGACGGGAGG 59.331 66.667 0.00 0.00 0.00 4.30
34 35 1.774894 TTGGGAGGGTTTGACGGGAG 61.775 60.000 0.00 0.00 0.00 4.30
35 36 1.770927 TTGGGAGGGTTTGACGGGA 60.771 57.895 0.00 0.00 0.00 5.14
36 37 1.602605 GTTGGGAGGGTTTGACGGG 60.603 63.158 0.00 0.00 0.00 5.28
37 38 0.179001 AAGTTGGGAGGGTTTGACGG 60.179 55.000 0.00 0.00 0.00 4.79
38 39 1.202770 AGAAGTTGGGAGGGTTTGACG 60.203 52.381 0.00 0.00 0.00 4.35
39 40 2.658807 AGAAGTTGGGAGGGTTTGAC 57.341 50.000 0.00 0.00 0.00 3.18
40 41 2.158519 GGAAGAAGTTGGGAGGGTTTGA 60.159 50.000 0.00 0.00 0.00 2.69
41 42 2.158460 AGGAAGAAGTTGGGAGGGTTTG 60.158 50.000 0.00 0.00 0.00 2.93
42 43 2.144450 AGGAAGAAGTTGGGAGGGTTT 58.856 47.619 0.00 0.00 0.00 3.27
43 44 1.834540 AGGAAGAAGTTGGGAGGGTT 58.165 50.000 0.00 0.00 0.00 4.11
44 45 1.705745 GAAGGAAGAAGTTGGGAGGGT 59.294 52.381 0.00 0.00 0.00 4.34
69 70 3.260380 ACATGAGAGGTGAAGAGGAAGTG 59.740 47.826 0.00 0.00 0.00 3.16
74 75 1.905215 ACCACATGAGAGGTGAAGAGG 59.095 52.381 0.00 0.00 37.33 3.69
88 89 5.248640 CCTTGAAGTTGATAGTGACCACAT 58.751 41.667 2.78 0.00 0.00 3.21
99 100 3.695830 TCTAACGCCCTTGAAGTTGAT 57.304 42.857 0.00 0.00 0.00 2.57
103 104 2.567615 ACAGATCTAACGCCCTTGAAGT 59.432 45.455 0.00 0.00 0.00 3.01
113 114 4.926238 GGATAGGCAATGACAGATCTAACG 59.074 45.833 0.00 0.00 0.00 3.18
122 123 3.998913 TCACTTGGATAGGCAATGACA 57.001 42.857 0.00 0.00 0.00 3.58
130 131 1.134007 TGCCAGCATCACTTGGATAGG 60.134 52.381 0.00 0.00 33.95 2.57
142 143 0.990374 AACTTCCTCTCTGCCAGCAT 59.010 50.000 0.00 0.00 0.00 3.79
148 149 3.181502 GCAATTGCTAACTTCCTCTCTGC 60.182 47.826 23.21 0.00 38.21 4.26
152 153 3.950395 GGATGCAATTGCTAACTTCCTCT 59.050 43.478 29.37 3.26 42.66 3.69
162 163 2.519771 TTGGAGAGGATGCAATTGCT 57.480 45.000 29.37 15.95 42.66 3.91
168 169 2.592102 AAGCTTTTGGAGAGGATGCA 57.408 45.000 0.00 0.00 0.00 3.96
169 170 3.087781 AGAAAGCTTTTGGAGAGGATGC 58.912 45.455 14.05 0.00 0.00 3.91
173 174 2.029560 GGCAAGAAAGCTTTTGGAGAGG 60.030 50.000 14.05 0.90 30.14 3.69
178 179 1.336240 CGGAGGCAAGAAAGCTTTTGG 60.336 52.381 14.05 7.20 30.14 3.28
199 200 1.096416 GTAGATCCGGGGCTATCTCG 58.904 60.000 6.65 0.00 34.36 4.04
251 258 1.959042 CTGACCTCACACCATATGCC 58.041 55.000 0.00 0.00 0.00 4.40
255 262 3.382083 TCTAGCTGACCTCACACCATA 57.618 47.619 0.00 0.00 0.00 2.74
256 263 2.238084 TCTAGCTGACCTCACACCAT 57.762 50.000 0.00 0.00 0.00 3.55
257 264 2.234661 CAATCTAGCTGACCTCACACCA 59.765 50.000 0.00 0.00 0.00 4.17
259 266 2.898705 CCAATCTAGCTGACCTCACAC 58.101 52.381 0.00 0.00 0.00 3.82
260 267 1.208052 GCCAATCTAGCTGACCTCACA 59.792 52.381 0.00 0.00 0.00 3.58
261 268 1.804372 CGCCAATCTAGCTGACCTCAC 60.804 57.143 0.00 0.00 0.00 3.51
262 269 0.461548 CGCCAATCTAGCTGACCTCA 59.538 55.000 0.00 0.00 0.00 3.86
263 270 0.249657 CCGCCAATCTAGCTGACCTC 60.250 60.000 0.00 0.00 0.00 3.85
264 271 0.687757 TCCGCCAATCTAGCTGACCT 60.688 55.000 0.00 0.00 0.00 3.85
265 272 0.249657 CTCCGCCAATCTAGCTGACC 60.250 60.000 0.00 0.00 0.00 4.02
266 273 0.878086 GCTCCGCCAATCTAGCTGAC 60.878 60.000 0.00 0.00 32.18 3.51
267 274 1.443407 GCTCCGCCAATCTAGCTGA 59.557 57.895 0.00 0.00 32.18 4.26
268 275 1.953138 CGCTCCGCCAATCTAGCTG 60.953 63.158 0.00 0.00 32.73 4.24
269 276 2.081425 CTCGCTCCGCCAATCTAGCT 62.081 60.000 0.00 0.00 32.73 3.32
270 277 1.663074 CTCGCTCCGCCAATCTAGC 60.663 63.158 0.00 0.00 0.00 3.42
271 278 0.318275 GACTCGCTCCGCCAATCTAG 60.318 60.000 0.00 0.00 0.00 2.43
272 279 1.035385 TGACTCGCTCCGCCAATCTA 61.035 55.000 0.00 0.00 0.00 1.98
273 280 2.351244 TGACTCGCTCCGCCAATCT 61.351 57.895 0.00 0.00 0.00 2.40
276 283 4.373116 GGTGACTCGCTCCGCCAA 62.373 66.667 0.00 0.00 33.37 4.52
290 297 3.894782 TCGACACACAAATCAATGGTG 57.105 42.857 0.00 0.00 38.47 4.17
307 314 8.642908 ACACGAGAAATGAACATTATAATCGA 57.357 30.769 19.63 0.00 31.71 3.59
313 320 6.071952 AGGCAAACACGAGAAATGAACATTAT 60.072 34.615 0.37 0.00 0.00 1.28
315 322 4.037923 AGGCAAACACGAGAAATGAACATT 59.962 37.500 0.00 0.00 0.00 2.71
328 335 1.670811 AGAGACAACAAGGCAAACACG 59.329 47.619 0.00 0.00 0.00 4.49
361 368 2.666022 TCGATACAACATGTGCAAGTCG 59.334 45.455 0.00 6.83 0.00 4.18
423 430 3.708121 ACCCGGACGGAGAAAGTAATTAT 59.292 43.478 13.13 0.00 37.50 1.28
444 451 5.869649 AAATATGAGGGGTGCCAATAAAC 57.130 39.130 0.00 0.00 0.00 2.01
599 607 8.934023 ATCAAACCTTGACCTTAGATTTAACA 57.066 30.769 0.00 0.00 43.48 2.41
617 625 4.584743 ACCTCTCTTGTTTTGGATCAAACC 59.415 41.667 6.28 0.00 32.79 3.27
631 639 6.407525 CCTCTGGGTTTATTAGACCTCTCTTG 60.408 46.154 3.62 0.00 37.34 3.02
634 642 5.209659 TCCTCTGGGTTTATTAGACCTCTC 58.790 45.833 3.62 0.00 37.34 3.20
637 645 4.722279 CCTTCCTCTGGGTTTATTAGACCT 59.278 45.833 3.62 0.00 37.34 3.85
639 647 4.720273 TCCCTTCCTCTGGGTTTATTAGAC 59.280 45.833 0.00 0.00 44.84 2.59
687 695 3.173965 TCCTTTGGGTGTCTCTCTTAGG 58.826 50.000 0.00 0.00 0.00 2.69
692 700 3.604582 CAAGATCCTTTGGGTGTCTCTC 58.395 50.000 0.00 0.00 31.82 3.20
718 728 5.901552 TCCTTCAAAACTAAGGCAAAACAG 58.098 37.500 0.00 0.00 42.79 3.16
730 740 8.084985 TGGTAATTTCCTTTTCCTTCAAAACT 57.915 30.769 2.53 0.00 30.42 2.66
760 770 8.422973 TTGACTTCTGAAAAATTCACCATTTG 57.577 30.769 0.00 0.00 35.09 2.32
818 847 1.990060 AGGTCATCTCCCCGTGTGG 60.990 63.158 0.00 0.00 0.00 4.17
820 849 0.544357 TTCAGGTCATCTCCCCGTGT 60.544 55.000 0.00 0.00 0.00 4.49
821 850 0.108138 GTTCAGGTCATCTCCCCGTG 60.108 60.000 0.00 0.00 0.00 4.94
822 851 1.265454 GGTTCAGGTCATCTCCCCGT 61.265 60.000 0.00 0.00 0.00 5.28
823 852 1.522569 GGTTCAGGTCATCTCCCCG 59.477 63.158 0.00 0.00 0.00 5.73
824 853 1.265454 ACGGTTCAGGTCATCTCCCC 61.265 60.000 0.00 0.00 0.00 4.81
825 854 1.481871 TACGGTTCAGGTCATCTCCC 58.518 55.000 0.00 0.00 0.00 4.30
826 855 2.734492 CGTTACGGTTCAGGTCATCTCC 60.734 54.545 0.00 0.00 0.00 3.71
827 856 2.527100 CGTTACGGTTCAGGTCATCTC 58.473 52.381 0.00 0.00 0.00 2.75
828 857 1.203994 CCGTTACGGTTCAGGTCATCT 59.796 52.381 16.53 0.00 42.73 2.90
829 858 1.636988 CCGTTACGGTTCAGGTCATC 58.363 55.000 16.53 0.00 42.73 2.92
830 859 0.248289 CCCGTTACGGTTCAGGTCAT 59.752 55.000 22.78 0.00 46.80 3.06
831 860 1.667151 CCCGTTACGGTTCAGGTCA 59.333 57.895 22.78 0.00 46.80 4.02
832 861 1.739196 GCCCGTTACGGTTCAGGTC 60.739 63.158 22.78 0.11 46.80 3.85
833 862 2.344872 GCCCGTTACGGTTCAGGT 59.655 61.111 22.78 0.00 46.80 4.00
834 863 2.435410 GGCCCGTTACGGTTCAGG 60.435 66.667 22.78 7.82 46.80 3.86
835 864 1.740296 CTGGCCCGTTACGGTTCAG 60.740 63.158 22.78 22.22 46.80 3.02
836 865 2.344500 CTGGCCCGTTACGGTTCA 59.656 61.111 22.78 17.57 46.80 3.18
837 866 3.122971 GCTGGCCCGTTACGGTTC 61.123 66.667 22.78 13.98 46.80 3.62
838 867 4.710167 GGCTGGCCCGTTACGGTT 62.710 66.667 22.78 0.00 46.80 4.44
841 870 4.690719 TGTGGCTGGCCCGTTACG 62.691 66.667 9.28 0.00 35.87 3.18
842 871 3.053896 GTGTGGCTGGCCCGTTAC 61.054 66.667 9.28 1.21 35.87 2.50
843 872 4.690719 CGTGTGGCTGGCCCGTTA 62.691 66.667 9.28 0.00 35.87 3.18
849 878 4.101448 ATCTCCCGTGTGGCTGGC 62.101 66.667 0.00 0.00 0.00 4.85
850 879 2.124983 CATCTCCCGTGTGGCTGG 60.125 66.667 0.00 0.00 0.00 4.85
851 880 1.448540 GTCATCTCCCGTGTGGCTG 60.449 63.158 0.00 0.00 0.00 4.85
852 881 2.660064 GGTCATCTCCCGTGTGGCT 61.660 63.158 0.00 0.00 0.00 4.75
853 882 2.125106 GGTCATCTCCCGTGTGGC 60.125 66.667 0.00 0.00 0.00 5.01
869 898 2.435410 GGCCCGTTACGGTTCAGG 60.435 66.667 22.78 7.82 46.80 3.86
887 916 1.229625 TCATCTCCCAGTGTGGCCT 60.230 57.895 3.32 0.00 35.79 5.19
888 917 1.078143 GTCATCTCCCAGTGTGGCC 60.078 63.158 0.00 0.00 35.79 5.36
889 918 1.078143 GGTCATCTCCCAGTGTGGC 60.078 63.158 0.00 0.00 35.79 5.01
890 919 0.251354 CAGGTCATCTCCCAGTGTGG 59.749 60.000 0.00 0.00 37.25 4.17
891 920 1.269958 TCAGGTCATCTCCCAGTGTG 58.730 55.000 0.00 0.00 0.00 3.82
892 921 1.625818 GTTCAGGTCATCTCCCAGTGT 59.374 52.381 0.00 0.00 0.00 3.55
893 922 1.065854 GGTTCAGGTCATCTCCCAGTG 60.066 57.143 0.00 0.00 0.00 3.66
894 923 1.280457 GGTTCAGGTCATCTCCCAGT 58.720 55.000 0.00 0.00 0.00 4.00
895 924 0.176680 CGGTTCAGGTCATCTCCCAG 59.823 60.000 0.00 0.00 0.00 4.45
896 925 0.544357 ACGGTTCAGGTCATCTCCCA 60.544 55.000 0.00 0.00 0.00 4.37
897 926 1.481871 TACGGTTCAGGTCATCTCCC 58.518 55.000 0.00 0.00 0.00 4.30
898 927 2.734492 CGTTACGGTTCAGGTCATCTCC 60.734 54.545 0.00 0.00 0.00 3.71
899 928 2.527100 CGTTACGGTTCAGGTCATCTC 58.473 52.381 0.00 0.00 0.00 2.75
900 929 1.203994 CCGTTACGGTTCAGGTCATCT 59.796 52.381 16.53 0.00 42.73 2.90
901 930 1.636988 CCGTTACGGTTCAGGTCATC 58.363 55.000 16.53 0.00 42.73 2.92
902 931 0.248289 CCCGTTACGGTTCAGGTCAT 59.752 55.000 22.78 0.00 46.80 3.06
903 932 1.667151 CCCGTTACGGTTCAGGTCA 59.333 57.895 22.78 0.00 46.80 4.02
904 933 1.739196 GCCCGTTACGGTTCAGGTC 60.739 63.158 22.78 0.11 46.80 3.85
905 934 2.344872 GCCCGTTACGGTTCAGGT 59.655 61.111 22.78 0.00 46.80 4.00
906 935 1.606885 TAGGCCCGTTACGGTTCAGG 61.607 60.000 22.78 7.82 46.80 3.86
907 936 0.179119 CTAGGCCCGTTACGGTTCAG 60.179 60.000 22.78 8.21 46.80 3.02
908 937 1.892338 CTAGGCCCGTTACGGTTCA 59.108 57.895 22.78 3.91 46.80 3.18
909 938 1.520120 GCTAGGCCCGTTACGGTTC 60.520 63.158 22.78 13.57 46.80 3.62
910 939 1.953231 GAGCTAGGCCCGTTACGGTT 61.953 60.000 22.78 10.16 46.80 4.44
911 940 2.363406 AGCTAGGCCCGTTACGGT 60.363 61.111 22.78 6.84 46.80 4.83
913 942 1.996786 TTCGAGCTAGGCCCGTTACG 61.997 60.000 0.00 0.00 0.00 3.18
914 943 0.248949 CTTCGAGCTAGGCCCGTTAC 60.249 60.000 0.00 0.00 0.00 2.50
915 944 2.012902 GCTTCGAGCTAGGCCCGTTA 62.013 60.000 0.00 0.00 38.45 3.18
916 945 2.893398 CTTCGAGCTAGGCCCGTT 59.107 61.111 0.00 0.00 0.00 4.44
917 946 3.839432 GCTTCGAGCTAGGCCCGT 61.839 66.667 0.00 0.00 38.45 5.28
918 947 4.933064 CGCTTCGAGCTAGGCCCG 62.933 72.222 0.00 0.00 39.60 6.13
919 948 4.593864 CCGCTTCGAGCTAGGCCC 62.594 72.222 0.00 0.00 39.60 5.80
922 951 3.838271 TGGCCGCTTCGAGCTAGG 61.838 66.667 0.00 0.65 39.60 3.02
923 952 2.583593 GTGGCCGCTTCGAGCTAG 60.584 66.667 9.68 0.00 39.60 3.42
928 957 2.184322 GATCTGTGGCCGCTTCGA 59.816 61.111 18.96 11.59 0.00 3.71
934 963 0.526524 GACTTCTCGATCTGTGGCCG 60.527 60.000 0.00 0.00 0.00 6.13
963 992 2.351924 TTTTCCTTGCAGCGGAGGGT 62.352 55.000 13.24 0.00 33.73 4.34
1114 1143 2.488153 AGACGAAACCAGCTAAAATGCC 59.512 45.455 0.00 0.00 0.00 4.40
1120 1149 4.537135 ATGAGAAGACGAAACCAGCTAA 57.463 40.909 0.00 0.00 0.00 3.09
1357 1386 2.165301 GTTGAATCCTCGGGCGTCG 61.165 63.158 0.00 0.00 40.90 5.12
1453 1482 4.929819 AGCTCGGTTAACCAAACAAATT 57.070 36.364 24.14 0.00 40.08 1.82
1463 1496 7.873910 AGTAATCTACTGATAGCTCGGTTAAC 58.126 38.462 0.00 0.00 41.36 2.01
1472 1505 7.429633 TCTTGCTGAAGTAATCTACTGATAGC 58.570 38.462 0.00 0.00 39.39 2.97
1475 1508 7.416964 ACTCTTGCTGAAGTAATCTACTGAT 57.583 36.000 0.00 0.00 39.39 2.90
1479 1512 5.513495 CACGACTCTTGCTGAAGTAATCTAC 59.487 44.000 0.00 0.00 0.00 2.59
1492 1525 0.510359 CAAGTGAGCACGACTCTTGC 59.490 55.000 10.68 0.00 46.41 4.01
1501 1534 4.610945 ACAAAAATGTAGCAAGTGAGCAC 58.389 39.130 0.00 0.00 36.85 4.40
1504 1537 6.428159 AGGAGTACAAAAATGTAGCAAGTGAG 59.572 38.462 0.00 0.00 0.00 3.51
1508 1541 6.595716 AGCTAGGAGTACAAAAATGTAGCAAG 59.404 38.462 0.00 0.00 35.21 4.01
1524 1557 6.313519 TGAAATGGTTTATCAGCTAGGAGT 57.686 37.500 0.00 0.00 0.00 3.85
1525 1558 7.199541 CATGAAATGGTTTATCAGCTAGGAG 57.800 40.000 0.00 0.00 41.79 3.69
1578 1611 6.456584 GCCATACAAATGATCTCATATGCTCG 60.457 42.308 0.00 0.00 35.10 5.03
1630 1663 4.576330 ACCTATGAACAGAAGGGGAAAG 57.424 45.455 9.66 0.00 34.52 2.62
1645 1678 4.957296 AGTAAGCCACCGATAAACCTATG 58.043 43.478 0.00 0.00 0.00 2.23
1646 1679 5.104652 ACAAGTAAGCCACCGATAAACCTAT 60.105 40.000 0.00 0.00 0.00 2.57
1964 1998 2.732507 AGGATCATACCCCTGAGGATCT 59.267 50.000 0.00 0.00 39.89 2.75
2060 2094 0.391793 AGTTTCAAGGAGGCGCTAGC 60.392 55.000 7.64 4.06 44.18 3.42
2066 2100 8.607441 AAAATTCAAATTAGTTTCAAGGAGGC 57.393 30.769 0.00 0.00 0.00 4.70
2126 2163 4.526438 AAGGGAAAAGATAGGATGGTGG 57.474 45.455 0.00 0.00 0.00 4.61
2127 2164 6.857437 AAAAAGGGAAAAGATAGGATGGTG 57.143 37.500 0.00 0.00 0.00 4.17
2155 2195 5.393678 GGCACACTTCTGTTTTCTGGTTTAA 60.394 40.000 0.00 0.00 0.00 1.52
2186 2226 7.594758 AGAAACAAATCATGTCACGTATTTTGG 59.405 33.333 8.11 0.00 42.99 3.28
2243 2283 7.920682 CACATAAGGTTCCCTTGCATAAAATAC 59.079 37.037 5.78 0.00 44.44 1.89
2299 2339 3.091545 ACCCACATTAGCAAGTCCAATG 58.908 45.455 0.00 0.00 36.07 2.82
2345 2385 7.332557 TCAGGACAAGTTGACTTTGTTAAGTA 58.667 34.615 10.54 0.00 44.51 2.24
2369 2409 9.148104 ACAGAAGTATACACGGAAAAGTATTTC 57.852 33.333 5.50 0.00 43.46 2.17
2381 2421 5.348986 AGTGGCATAACAGAAGTATACACG 58.651 41.667 5.50 0.00 0.00 4.49
2751 2791 3.118956 AGGACGCTTTGGAGTATCTTCAG 60.119 47.826 0.00 0.00 33.73 3.02
2785 2825 5.527951 TCATAACGCCAATATTGCAAATCC 58.472 37.500 10.11 0.00 0.00 3.01
2911 2951 1.339055 TGTTCCCTGGCTTCTTCATCG 60.339 52.381 0.00 0.00 0.00 3.84
2960 3000 5.538433 CCCTCTCACATTTTCCCTTGTTTAA 59.462 40.000 0.00 0.00 0.00 1.52
3064 3104 4.594920 AGAGAGAGAGAGAGAGATTCGGAT 59.405 45.833 0.00 0.00 0.00 4.18
3068 3108 6.041409 TGAGAGAGAGAGAGAGAGAGAGATTC 59.959 46.154 0.00 0.00 0.00 2.52
3274 3334 3.770263 TCAACCGGTATCACTAGAACG 57.230 47.619 8.00 0.00 0.00 3.95
3390 3450 4.274459 CCCACTCAAAATATACTGCTGCTC 59.726 45.833 0.00 0.00 0.00 4.26
3512 3572 4.746611 CAGCCTTCACAAAGAAATTTGGTC 59.253 41.667 0.00 0.00 35.40 4.02
3598 3658 6.514947 TCACAACAGAAAATTCAAATCCCAG 58.485 36.000 0.00 0.00 0.00 4.45
3691 3752 3.192466 GCATGGATTGAAAGAATGTGCC 58.808 45.455 0.00 0.00 0.00 5.01
3717 3778 2.200081 ACCAGGACAAGGCATGTATCT 58.800 47.619 0.00 0.00 44.12 1.98
3727 3788 2.824341 ACGAGTAGGTAACCAGGACAAG 59.176 50.000 0.00 0.00 37.17 3.16
3732 3793 5.786264 ATAATGACGAGTAGGTAACCAGG 57.214 43.478 0.00 0.00 37.17 4.45
3809 3870 1.134175 ACAATAAGAAAATGCCGCCCG 59.866 47.619 0.00 0.00 0.00 6.13
3922 3983 6.884472 TTCAGTTATCTAATCCCCAGAACA 57.116 37.500 0.00 0.00 0.00 3.18
3923 3984 8.753497 AATTTCAGTTATCTAATCCCCAGAAC 57.247 34.615 0.00 0.00 0.00 3.01
3954 4037 7.475771 TTTACAAAGGACAATGATTTGCAAC 57.524 32.000 0.00 0.00 37.42 4.17
3972 4055 6.648879 ACAAGCTGAAAAGGCTATTTACAA 57.351 33.333 0.00 0.00 39.30 2.41
3975 4058 8.807948 ATAGAACAAGCTGAAAAGGCTATTTA 57.192 30.769 0.00 0.00 39.30 1.40
4200 4284 1.347378 TGCAAGAGTAGTGTGCCATCA 59.653 47.619 0.00 0.00 37.48 3.07
4591 4780 2.839486 TTCAGCAGGATCAAACTCGT 57.161 45.000 0.00 0.00 0.00 4.18
4666 4855 4.333926 GTGGCTTAGCTTAAGAAGTCATGG 59.666 45.833 12.71 0.00 39.34 3.66
4682 4871 2.609747 AGGACTTGTCTCAGTGGCTTA 58.390 47.619 0.61 0.00 0.00 3.09
4737 4926 0.179189 CGAATCCGCAGCAGGTTTTC 60.179 55.000 0.00 3.19 0.00 2.29
4884 5082 2.158623 ACAGACTCAAATGGCAGGTTGA 60.159 45.455 13.80 13.80 32.91 3.18
4885 5083 2.233271 ACAGACTCAAATGGCAGGTTG 58.767 47.619 7.24 7.24 0.00 3.77
4993 5192 1.221566 CATGATGGAGGGTGCGTCA 59.778 57.895 0.00 0.00 38.10 4.35
5058 5290 6.389906 GCCTTCAACATGTATAAGCAGTTTT 58.610 36.000 0.00 0.00 0.00 2.43
5082 5314 3.849911 ACTCCATGTGATGTCACTTACG 58.150 45.455 13.71 2.87 46.55 3.18
5172 5404 4.696479 AGTAAGCAAGGATCCCATGTAG 57.304 45.455 8.55 0.00 0.00 2.74
5179 5411 3.956744 ACTCCAAAGTAAGCAAGGATCC 58.043 45.455 2.48 2.48 32.59 3.36
5191 5427 3.492482 CCGATTTGCCAAAACTCCAAAGT 60.492 43.478 0.00 0.00 37.32 2.66
5239 5475 3.009916 GGCCAATGATGTCCTCCTATGAT 59.990 47.826 0.00 0.00 0.00 2.45
5249 5485 1.477553 ACCACATGGCCAATGATGTC 58.522 50.000 19.46 0.00 38.72 3.06
5256 5492 1.268066 TAGACGTACCACATGGCCAA 58.732 50.000 10.96 0.00 39.32 4.52
5263 5499 4.951715 ACAACCTATGATAGACGTACCACA 59.048 41.667 0.00 0.00 0.00 4.17
5268 5504 8.002984 TCAATTCACAACCTATGATAGACGTA 57.997 34.615 0.00 0.00 0.00 3.57
5269 5505 6.873997 TCAATTCACAACCTATGATAGACGT 58.126 36.000 0.00 0.00 0.00 4.34
5270 5506 7.203218 TCTCAATTCACAACCTATGATAGACG 58.797 38.462 0.00 0.00 0.00 4.18
5295 5532 0.606401 CACGTGGCCATTGAGGTCTT 60.606 55.000 9.72 0.00 44.59 3.01
5315 5552 1.411246 TGATAGACGTACCCATGTGGC 59.589 52.381 0.00 0.00 37.83 5.01
5316 5553 4.765339 TCTATGATAGACGTACCCATGTGG 59.235 45.833 0.00 0.00 41.37 4.17
5317 5554 5.959618 TCTATGATAGACGTACCCATGTG 57.040 43.478 0.00 0.00 0.00 3.21
5318 5555 7.540474 AAATCTATGATAGACGTACCCATGT 57.460 36.000 3.96 0.00 37.69 3.21
5319 5556 8.088365 TCAAAATCTATGATAGACGTACCCATG 58.912 37.037 3.96 0.00 37.69 3.66
5320 5557 8.190326 TCAAAATCTATGATAGACGTACCCAT 57.810 34.615 3.96 0.00 37.69 4.00
5321 5558 7.591421 TCAAAATCTATGATAGACGTACCCA 57.409 36.000 3.96 0.00 37.69 4.51
5325 5562 7.289317 ACCCCTTCAAAATCTATGATAGACGTA 59.711 37.037 3.96 0.00 37.69 3.57
5327 5564 6.425114 CACCCCTTCAAAATCTATGATAGACG 59.575 42.308 3.96 0.00 37.69 4.18
5339 5576 3.012844 AGCCCTATTCACCCCTTCAAAAT 59.987 43.478 0.00 0.00 0.00 1.82
5353 5590 3.606687 CTTTCGTAACCACAGCCCTATT 58.393 45.455 0.00 0.00 0.00 1.73
5362 5599 2.550606 TGGTTCATGCTTTCGTAACCAC 59.449 45.455 8.43 0.00 43.44 4.16
5365 5602 3.500680 TCCTTGGTTCATGCTTTCGTAAC 59.499 43.478 0.00 0.00 0.00 2.50
5369 5606 2.417933 CTCTCCTTGGTTCATGCTTTCG 59.582 50.000 0.00 0.00 0.00 3.46
5371 5608 2.376518 TCCTCTCCTTGGTTCATGCTTT 59.623 45.455 0.00 0.00 0.00 3.51
5372 5609 1.988107 TCCTCTCCTTGGTTCATGCTT 59.012 47.619 0.00 0.00 0.00 3.91
5391 5628 2.605366 GCTGGTGAGATTTAGAAGCGTC 59.395 50.000 0.00 0.00 0.00 5.19
5423 5663 6.382859 TCACACTTTGGCCTTCTCACTATATA 59.617 38.462 3.32 0.00 0.00 0.86
5427 5667 2.703536 TCACACTTTGGCCTTCTCACTA 59.296 45.455 3.32 0.00 0.00 2.74
5429 5669 1.967319 TCACACTTTGGCCTTCTCAC 58.033 50.000 3.32 0.00 0.00 3.51
5430 5670 2.783135 GATCACACTTTGGCCTTCTCA 58.217 47.619 3.32 0.00 0.00 3.27
5435 5675 0.620556 ATCCGATCACACTTTGGCCT 59.379 50.000 3.32 0.00 0.00 5.19
5450 5690 1.522668 TTGTCTCAACCAAGCATCCG 58.477 50.000 0.00 0.00 0.00 4.18
5481 5721 6.279882 ACCCGCATCCATGTTTAATTTAATG 58.720 36.000 0.00 0.00 0.00 1.90
5482 5722 6.478512 ACCCGCATCCATGTTTAATTTAAT 57.521 33.333 0.00 0.00 0.00 1.40
5485 5725 4.817318 AACCCGCATCCATGTTTAATTT 57.183 36.364 0.00 0.00 0.00 1.82
5495 5735 0.887247 CACATCAAAACCCGCATCCA 59.113 50.000 0.00 0.00 0.00 3.41
5525 5765 1.542375 ACTGCTCCAACCATCCCCT 60.542 57.895 0.00 0.00 0.00 4.79
5531 5771 0.684535 TCGAATGACTGCTCCAACCA 59.315 50.000 0.00 0.00 0.00 3.67
5543 5783 5.922053 ACTTTCCATGATGATCTCGAATGA 58.078 37.500 0.00 0.00 0.00 2.57
5544 5784 6.259387 TGAACTTTCCATGATGATCTCGAATG 59.741 38.462 0.00 0.00 0.00 2.67
5545 5785 6.351711 TGAACTTTCCATGATGATCTCGAAT 58.648 36.000 0.00 0.00 0.00 3.34
5546 5786 5.733676 TGAACTTTCCATGATGATCTCGAA 58.266 37.500 0.00 0.00 0.00 3.71
5547 5787 5.343307 TGAACTTTCCATGATGATCTCGA 57.657 39.130 0.00 0.00 0.00 4.04
5548 5788 6.037940 ACAATGAACTTTCCATGATGATCTCG 59.962 38.462 0.00 0.00 0.00 4.04
5549 5789 7.330900 ACAATGAACTTTCCATGATGATCTC 57.669 36.000 0.00 0.00 0.00 2.75
5550 5790 7.013083 GCTACAATGAACTTTCCATGATGATCT 59.987 37.037 0.00 0.00 0.00 2.75
5551 5791 7.137426 GCTACAATGAACTTTCCATGATGATC 58.863 38.462 0.00 0.00 0.00 2.92
5552 5792 6.040166 GGCTACAATGAACTTTCCATGATGAT 59.960 38.462 0.00 0.00 0.00 2.45
5572 5812 7.044798 ACTATCAATCTTTTCAGTGAGGCTAC 58.955 38.462 0.00 0.00 0.00 3.58
5573 5813 7.187824 ACTATCAATCTTTTCAGTGAGGCTA 57.812 36.000 0.00 0.00 0.00 3.93
5575 5815 6.549952 CAACTATCAATCTTTTCAGTGAGGC 58.450 40.000 0.00 0.00 0.00 4.70
5581 5822 8.295288 AGTCAAAGCAACTATCAATCTTTTCAG 58.705 33.333 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.