Multiple sequence alignment - TraesCS2B01G625300

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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 TraesCS2B01G625300 chr2B 100.000 6500 0 0 1 6500 798140344 798133845 0.000000e+00 12004.0
1 TraesCS2B01G625300 chr2B 100.000 45 0 0 2807 2851 798137492 798137448 4.180000e-12 84.2
2 TraesCS2B01G625300 chr2B 100.000 45 0 0 2853 2897 798137538 798137494 4.180000e-12 84.2
3 TraesCS2B01G625300 chr2B 100.000 36 0 0 5731 5766 798134580 798134545 4.210000e-07 67.6
4 TraesCS2B01G625300 chr2B 100.000 36 0 0 5765 5800 798134614 798134579 4.210000e-07 67.6
5 TraesCS2B01G625300 chr2A 90.668 5583 360 88 1 5495 764327152 764321643 0.000000e+00 7275.0
6 TraesCS2B01G625300 chr2A 88.877 944 69 13 4726 5661 764319581 764318666 0.000000e+00 1129.0
7 TraesCS2B01G625300 chr2A 89.258 633 43 9 3495 4119 764299819 764299204 0.000000e+00 769.0
8 TraesCS2B01G625300 chr2A 86.882 526 49 14 4149 4661 764298907 764298389 7.310000e-159 571.0
9 TraesCS2B01G625300 chr2A 86.047 301 29 5 6134 6426 764320443 764320148 1.760000e-80 311.0
10 TraesCS2B01G625300 chr2A 79.009 343 36 22 5317 5645 764298298 764297978 1.110000e-47 202.0
11 TraesCS2B01G625300 chr2A 85.632 174 22 3 511 684 764326477 764326307 5.180000e-41 180.0
12 TraesCS2B01G625300 chr2A 93.902 82 5 0 127 208 764331713 764331632 2.460000e-24 124.0
13 TraesCS2B01G625300 chr2A 100.000 46 0 0 2806 2851 764324296 764324251 1.160000e-12 86.1
14 TraesCS2B01G625300 chr2A 97.872 47 1 0 2853 2899 764324341 764324295 1.500000e-11 82.4
15 TraesCS2B01G625300 chr2A 100.000 36 0 0 4117 4152 764298959 764298924 4.210000e-07 67.6
16 TraesCS2B01G625300 chr2A 92.308 39 3 0 526 564 30936087 30936049 1.000000e-03 56.5
17 TraesCS2B01G625300 chr2D 88.766 2172 149 45 696 2810 638815471 638813338 0.000000e+00 2571.0
18 TraesCS2B01G625300 chr2D 92.828 1464 91 10 4309 5764 638811564 638810107 0.000000e+00 2109.0
19 TraesCS2B01G625300 chr2D 92.511 1362 64 17 2807 4134 638813181 638811824 0.000000e+00 1916.0
20 TraesCS2B01G625300 chr2D 92.459 1220 83 6 4548 5764 638731205 638729992 0.000000e+00 1735.0
21 TraesCS2B01G625300 chr2D 87.537 682 47 17 1 676 638815972 638815323 0.000000e+00 754.0
22 TraesCS2B01G625300 chr2D 86.538 520 32 12 4056 4553 638749766 638749263 7.420000e-149 538.0
23 TraesCS2B01G625300 chr2D 87.309 457 36 6 5765 6219 638730025 638729589 2.710000e-138 503.0
24 TraesCS2B01G625300 chr2D 91.776 304 23 2 3346 3649 638750352 638750051 7.790000e-114 422.0
25 TraesCS2B01G625300 chr2D 88.561 271 24 5 5950 6219 638809995 638809731 8.130000e-84 322.0
26 TraesCS2B01G625300 chr2D 87.645 259 25 6 3807 4059 638750052 638749795 1.770000e-75 294.0
27 TraesCS2B01G625300 chr2D 84.211 285 23 11 6216 6500 638809678 638809416 2.330000e-64 257.0
28 TraesCS2B01G625300 chr2D 93.151 146 8 1 5765 5908 638810140 638809995 5.110000e-51 213.0
29 TraesCS2B01G625300 chr2D 84.103 195 27 3 5881 6072 17617099 17617292 1.110000e-42 185.0
30 TraesCS2B01G625300 chr2D 83.854 192 30 1 5881 6071 287890326 287890517 1.440000e-41 182.0
31 TraesCS2B01G625300 chr2D 83.756 197 24 6 5881 6072 17644883 17645076 5.180000e-41 180.0
32 TraesCS2B01G625300 chr2D 100.000 45 0 0 2807 2851 638813127 638813083 4.180000e-12 84.2
33 TraesCS2B01G625300 chr7B 85.492 193 25 3 5881 6071 697289201 697289010 1.430000e-46 198.0
34 TraesCS2B01G625300 chr3D 84.184 196 29 2 5877 6071 436020075 436020269 8.600000e-44 189.0
35 TraesCS2B01G625300 chr5B 84.456 193 27 3 5881 6071 483951060 483951251 3.090000e-43 187.0
36 TraesCS2B01G625300 chr1B 84.211 190 29 1 5881 6069 242744591 242744402 4.000000e-42 183.0
37 TraesCS2B01G625300 chr7D 92.222 90 7 0 4972 5061 41269205 41269116 1.900000e-25 128.0
38 TraesCS2B01G625300 chr7A 100.000 33 0 0 521 553 611489544 611489576 1.960000e-05 62.1


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 TraesCS2B01G625300 chr2B 798133845 798140344 6499 True 12004.000000 12004 100.000000 1 6500 1 chr2B.!!$R1 6499
1 TraesCS2B01G625300 chr2A 764318666 764327152 8486 True 1510.583333 7275 91.516000 1 6426 6 chr2A.!!$R4 6425
2 TraesCS2B01G625300 chr2A 764297978 764299819 1841 True 402.400000 769 88.787250 3495 5645 4 chr2A.!!$R3 2150
3 TraesCS2B01G625300 chr2D 638729589 638731205 1616 True 1119.000000 1735 89.884000 4548 6219 2 chr2D.!!$R1 1671
4 TraesCS2B01G625300 chr2D 638809416 638815972 6556 True 1028.275000 2571 90.945625 1 6500 8 chr2D.!!$R3 6499
5 TraesCS2B01G625300 chr2D 638749263 638750352 1089 True 418.000000 538 88.653000 3346 4553 3 chr2D.!!$R2 1207

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
348 359 1.021390 GCGTCAAGATCACACCCCAG 61.021 60.000 0.0 0.0 0.0 4.45 F
406 417 1.071385 CCACCCTCAGAGCATATCCAC 59.929 57.143 0.0 0.0 0.0 4.02 F
1330 1376 0.645868 GCTGACTATTTGACGGACGC 59.354 55.000 0.0 0.0 0.0 5.19 F
2207 2276 0.179094 TGTCGTCTTTCGTTGCAGGT 60.179 50.000 0.0 0.0 40.8 4.00 F
2953 3211 0.739813 CTCCGGCAGTAAAAGGGTCG 60.740 60.000 0.0 0.0 0.0 4.79 F
4470 5189 0.676782 CGGAGACCACCCCATTGTTC 60.677 60.000 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1213 1250 0.250295 TCTTTGACAGGGCTTGACCG 60.250 55.000 2.65 0.0 40.62 4.79 R
1366 1416 0.458025 CTGGAAACCTAGCGACGGAC 60.458 60.000 0.00 0.0 0.00 4.79 R
2588 2659 1.078989 AGCAGTAGGTAGGGAACAGGT 59.921 52.381 0.00 0.0 0.00 4.00 R
3566 3842 1.205655 CCAGGCTGAGTTCTCGAATGA 59.794 52.381 17.94 0.0 0.00 2.57 R
4653 5372 0.804156 GGTCTGCGCTACTTCTGCTC 60.804 60.000 9.73 0.0 0.00 4.26 R
5928 7430 0.107456 ATGAGACAGGCGGCTTATGG 59.893 55.000 9.66 0.0 0.00 2.74 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
53 54 5.008619 ACAAACAATGAACAAGCACATGA 57.991 34.783 0.00 0.00 0.00 3.07
54 55 5.045215 ACAAACAATGAACAAGCACATGAG 58.955 37.500 0.00 0.00 0.00 2.90
55 56 5.163530 ACAAACAATGAACAAGCACATGAGA 60.164 36.000 0.00 0.00 0.00 3.27
56 57 4.761235 ACAATGAACAAGCACATGAGAG 57.239 40.909 0.00 0.00 0.00 3.20
57 58 4.392047 ACAATGAACAAGCACATGAGAGA 58.608 39.130 0.00 0.00 0.00 3.10
58 59 4.454847 ACAATGAACAAGCACATGAGAGAG 59.545 41.667 0.00 0.00 0.00 3.20
97 102 3.387397 AGTACTACAAACAACAGCCGAC 58.613 45.455 0.00 0.00 0.00 4.79
102 107 1.528309 AAACAACAGCCGACCTGGG 60.528 57.895 0.00 0.00 46.14 4.45
174 183 4.020485 AGGTATCACTAACACCAGTCCAAC 60.020 45.833 0.00 0.00 34.62 3.77
191 200 9.354673 CCAGTCCAACCATCACTTAATAATAAT 57.645 33.333 0.00 0.00 0.00 1.28
220 229 5.242434 CACACCAAGCTACAAATACAGGTA 58.758 41.667 0.00 0.00 0.00 3.08
221 230 5.351465 CACACCAAGCTACAAATACAGGTAG 59.649 44.000 0.00 0.00 39.92 3.18
222 231 5.012768 ACACCAAGCTACAAATACAGGTAGT 59.987 40.000 0.00 0.00 39.30 2.73
223 232 6.211986 ACACCAAGCTACAAATACAGGTAGTA 59.788 38.462 0.00 0.00 39.30 1.82
296 305 3.585990 CATGCCCATTCGACGGCC 61.586 66.667 13.33 0.00 45.07 6.13
346 357 1.745489 GGCGTCAAGATCACACCCC 60.745 63.158 0.00 0.00 0.00 4.95
348 359 1.021390 GCGTCAAGATCACACCCCAG 61.021 60.000 0.00 0.00 0.00 4.45
389 400 3.648067 TGATAGATTGATGTCCCCTCCAC 59.352 47.826 0.00 0.00 0.00 4.02
406 417 1.071385 CCACCCTCAGAGCATATCCAC 59.929 57.143 0.00 0.00 0.00 4.02
437 448 3.554692 CGCATCCGTCCGCTTCAC 61.555 66.667 0.00 0.00 0.00 3.18
438 449 3.195698 GCATCCGTCCGCTTCACC 61.196 66.667 0.00 0.00 0.00 4.02
562 578 3.621715 GCTTCAACTAATTTCGGACGGAT 59.378 43.478 0.00 0.00 0.00 4.18
605 621 6.668323 CATCGTAAATGGTGTTTCTGTCTTT 58.332 36.000 0.00 0.00 0.00 2.52
606 622 6.055231 TCGTAAATGGTGTTTCTGTCTTTG 57.945 37.500 0.00 0.00 0.00 2.77
614 630 5.104444 TGGTGTTTCTGTCTTTGTTAGGGTA 60.104 40.000 0.00 0.00 0.00 3.69
626 642 3.781808 TGTTAGGGTACTACTCCAGCAA 58.218 45.455 0.00 0.00 0.00 3.91
638 654 4.326504 ACTCCAGCAAAAACAATTCTGG 57.673 40.909 0.00 0.00 44.18 3.86
642 658 3.803778 CCAGCAAAAACAATTCTGGTGTC 59.196 43.478 0.00 0.00 39.45 3.67
652 668 5.835257 ACAATTCTGGTGTCATTTTCTGTG 58.165 37.500 0.00 0.00 0.00 3.66
671 687 3.057174 TGTGGGAGAAACAAAACACACAC 60.057 43.478 0.00 0.00 34.31 3.82
700 716 8.635765 TTTTCTAAACACTTTCTGCTGGATAT 57.364 30.769 0.00 0.00 0.00 1.63
703 719 9.547753 TTCTAAACACTTTCTGCTGGATATATC 57.452 33.333 3.96 3.96 0.00 1.63
725 741 7.923414 ATCCGTCTGAGCTTTAACTAATTTT 57.077 32.000 0.00 0.00 0.00 1.82
726 742 7.129109 TCCGTCTGAGCTTTAACTAATTTTG 57.871 36.000 0.00 0.00 0.00 2.44
729 745 7.015877 CGTCTGAGCTTTAACTAATTTTGGAC 58.984 38.462 0.00 0.00 0.00 4.02
730 746 7.015877 GTCTGAGCTTTAACTAATTTTGGACG 58.984 38.462 0.00 0.00 0.00 4.79
745 761 2.176889 TGGACGGAGGGAGTAGAAAAG 58.823 52.381 0.00 0.00 0.00 2.27
746 762 2.225192 TGGACGGAGGGAGTAGAAAAGA 60.225 50.000 0.00 0.00 0.00 2.52
747 763 2.427812 GGACGGAGGGAGTAGAAAAGAG 59.572 54.545 0.00 0.00 0.00 2.85
752 768 4.098155 GGAGGGAGTAGAAAAGAGGAAGT 58.902 47.826 0.00 0.00 0.00 3.01
754 770 5.900699 GGAGGGAGTAGAAAAGAGGAAGTAT 59.099 44.000 0.00 0.00 0.00 2.12
784 800 6.126863 TGATGTTTCTGTCTTGATTAGGGT 57.873 37.500 0.00 0.00 0.00 4.34
785 801 7.252612 TGATGTTTCTGTCTTGATTAGGGTA 57.747 36.000 0.00 0.00 0.00 3.69
797 813 4.816126 TGATTAGGGTACTACTCCAGCAT 58.184 43.478 0.00 0.00 30.19 3.79
798 814 5.960704 TGATTAGGGTACTACTCCAGCATA 58.039 41.667 0.00 0.00 30.19 3.14
799 815 6.378745 TGATTAGGGTACTACTCCAGCATAA 58.621 40.000 0.00 0.00 30.19 1.90
800 816 6.493802 TGATTAGGGTACTACTCCAGCATAAG 59.506 42.308 0.00 0.00 30.19 1.73
801 817 2.966516 AGGGTACTACTCCAGCATAAGC 59.033 50.000 0.00 0.00 42.56 3.09
804 820 4.120589 GGTACTACTCCAGCATAAGCAAC 58.879 47.826 0.00 0.00 45.49 4.17
828 844 5.916883 CACAATTCTGGTGTCATTTTCTGTC 59.083 40.000 0.00 0.00 0.00 3.51
833 849 2.367241 TGGTGTCATTTTCTGTCGGAGA 59.633 45.455 0.00 0.00 0.00 3.71
842 858 4.609691 TTTCTGTCGGAGAAACAAACAC 57.390 40.909 6.48 0.00 44.32 3.32
843 859 3.254470 TCTGTCGGAGAAACAAACACA 57.746 42.857 0.00 0.00 39.69 3.72
844 860 2.933906 TCTGTCGGAGAAACAAACACAC 59.066 45.455 0.00 0.00 39.69 3.82
845 861 2.675844 CTGTCGGAGAAACAAACACACA 59.324 45.455 0.00 0.00 39.69 3.72
923 956 1.472878 GAAGAGGGTCGCCATTTTTCC 59.527 52.381 0.00 0.00 0.00 3.13
951 984 1.340568 GGTCAAGTACGGATAGGCTCC 59.659 57.143 0.00 0.00 41.07 4.70
961 994 3.120493 ATAGGCTCCCCCTCCCCTG 62.120 68.421 0.00 0.00 44.96 4.45
974 1010 3.721706 CCCTGCCCTGTCCACCTC 61.722 72.222 0.00 0.00 0.00 3.85
975 1011 3.721706 CCTGCCCTGTCCACCTCC 61.722 72.222 0.00 0.00 0.00 4.30
976 1012 3.721706 CTGCCCTGTCCACCTCCC 61.722 72.222 0.00 0.00 0.00 4.30
1016 1052 3.299190 CCTCGGCTCGATCCCCTC 61.299 72.222 0.00 0.00 34.61 4.30
1135 1172 1.121407 CGCCCTCAGGTATCCCATCA 61.121 60.000 0.00 0.00 34.57 3.07
1213 1250 2.960384 TCGTTCCCCTTTTTCCTTTTCC 59.040 45.455 0.00 0.00 0.00 3.13
1241 1279 1.614317 CCCTGTCAAAGATTCGGCCTT 60.614 52.381 0.00 0.00 0.00 4.35
1330 1376 0.645868 GCTGACTATTTGACGGACGC 59.354 55.000 0.00 0.00 0.00 5.19
1361 1407 3.593247 CGAAAGGCAGATTCGCTTG 57.407 52.632 7.07 0.00 42.52 4.01
1366 1416 2.705826 GCAGATTCGCTTGCTCCG 59.294 61.111 0.00 0.00 0.00 4.63
1376 1430 3.047718 CTTGCTCCGTCCGTCGCTA 62.048 63.158 0.00 0.00 38.35 4.26
1432 1486 2.627945 GTGGTGATTTAGATGCCGACA 58.372 47.619 0.00 0.00 0.00 4.35
1439 1493 2.515926 TTAGATGCCGACATGAGAGC 57.484 50.000 0.00 0.00 36.35 4.09
1454 1508 3.008157 ATGAGAGCATATCCAGCTTCTGG 59.992 47.826 6.53 6.53 43.58 3.86
1497 1551 3.636300 CCCGATTTGATTTGCCTATCCAA 59.364 43.478 0.00 0.00 0.00 3.53
1538 1592 5.757320 GGATGTATATGCCAGCATCATACTC 59.243 44.000 8.71 12.41 39.39 2.59
1572 1626 0.955428 GCTGGTGATTCGGTTCTGCA 60.955 55.000 0.00 0.00 0.00 4.41
1626 1681 3.354948 TGGAATGAACCAGACAGGATG 57.645 47.619 0.00 0.00 41.22 3.51
1669 1724 2.088423 AGGTGGAATTATGCGCGAAAA 58.912 42.857 12.10 0.00 0.00 2.29
1670 1725 2.490115 AGGTGGAATTATGCGCGAAAAA 59.510 40.909 12.10 0.00 0.00 1.94
1731 1786 2.369203 TGGTGATGAAAAGTACCGGTCA 59.631 45.455 12.40 0.86 35.98 4.02
1773 1834 4.717280 AGCCTGGTTGCTAGTACTAATCTT 59.283 41.667 3.76 0.00 40.56 2.40
1781 1842 7.804129 GGTTGCTAGTACTAATCTTACTCATCG 59.196 40.741 3.76 0.00 31.99 3.84
1850 1912 7.385752 CACCGTTACTTATTCCTGACTTGTTTA 59.614 37.037 0.00 0.00 0.00 2.01
1851 1913 7.601508 ACCGTTACTTATTCCTGACTTGTTTAG 59.398 37.037 0.00 0.00 0.00 1.85
1871 1936 9.017509 TGTTTAGAAACGTTAGAGAGGATCTTA 57.982 33.333 0.00 0.00 43.82 2.10
1935 2000 5.593968 ACCGTGTTTATGGAAAAGGAAAAC 58.406 37.500 0.00 0.00 36.75 2.43
1961 2030 6.183361 ACCTGATTCCTTAAAGGTCTTCACTT 60.183 38.462 0.00 0.00 38.73 3.16
2029 2098 7.730364 ACTTGTGATTTAGTTTGGACTACAG 57.270 36.000 0.00 0.00 38.07 2.74
2031 2100 5.556915 TGTGATTTAGTTTGGACTACAGGG 58.443 41.667 0.00 0.00 38.07 4.45
2036 2105 0.331616 GTTTGGACTACAGGGCCCAT 59.668 55.000 27.56 14.91 44.39 4.00
2040 2109 1.272425 TGGACTACAGGGCCCATTTTG 60.272 52.381 27.56 16.54 44.39 2.44
2097 2166 9.747898 AGTATGTAATTATTTGAAACCTGTGGA 57.252 29.630 0.00 0.00 0.00 4.02
2197 2266 6.808008 ATGAATCTCAACATTGTCGTCTTT 57.192 33.333 0.00 0.00 0.00 2.52
2207 2276 0.179094 TGTCGTCTTTCGTTGCAGGT 60.179 50.000 0.00 0.00 40.80 4.00
2210 2279 2.735134 GTCGTCTTTCGTTGCAGGTATT 59.265 45.455 0.00 0.00 40.80 1.89
2300 2369 3.303461 CGTGGTTTTGACGCATTGAAGTA 60.303 43.478 0.00 0.00 0.00 2.24
2354 2423 6.167685 ACCTGTAAAAACAAGTTGGGTTTTC 58.832 36.000 17.75 10.96 45.02 2.29
2356 2425 4.626172 TGTAAAAACAAGTTGGGTTTTCGC 59.374 37.500 17.75 13.86 45.02 4.70
2380 2449 5.754406 CCAAGAGCTGATAAGATGAAGAGTG 59.246 44.000 0.00 0.00 0.00 3.51
2382 2451 4.405036 AGAGCTGATAAGATGAAGAGTGCA 59.595 41.667 0.00 0.00 0.00 4.57
2424 2493 1.889170 CTCTGTCTCTGTGCAGTGGTA 59.111 52.381 0.00 0.00 34.57 3.25
2490 2559 6.943718 TGGGGAATAATCTTACTTTGTCGTTT 59.056 34.615 0.00 0.00 0.00 3.60
2493 2562 8.674607 GGGAATAATCTTACTTTGTCGTTTGAT 58.325 33.333 0.00 0.00 0.00 2.57
2542 2611 8.428063 AGTTCTGGATTTCTTACCATCATCTAG 58.572 37.037 0.00 0.00 35.54 2.43
2553 2622 5.283457 ACCATCATCTAGCAACTTCTACC 57.717 43.478 0.00 0.00 0.00 3.18
2574 2643 4.022068 ACCATTTGGCTGTCACTACATTTG 60.022 41.667 0.00 0.00 39.32 2.32
2588 2659 5.462729 CACTACATTTGTTTGCATGCTTTCA 59.537 36.000 20.33 11.73 0.00 2.69
2596 2667 0.961019 TGCATGCTTTCACCTGTTCC 59.039 50.000 20.33 0.00 0.00 3.62
2598 2669 1.915141 CATGCTTTCACCTGTTCCCT 58.085 50.000 0.00 0.00 0.00 4.20
2662 2733 1.160137 ACTTCTTGGCTGCGATGTTC 58.840 50.000 0.00 0.00 0.00 3.18
2677 2748 4.539870 CGATGTTCATTTATGGTGGCATC 58.460 43.478 0.00 0.00 0.00 3.91
2690 2761 3.197265 GGTGGCATCCAAAATATGTTGC 58.803 45.455 0.00 0.00 34.18 4.17
2714 2803 9.161629 TGCAATAATCCTATTATGTTATGTCCG 57.838 33.333 0.00 0.00 0.00 4.79
2730 2819 1.275573 GTCCGGCCAACTCTCTTAACT 59.724 52.381 2.24 0.00 0.00 2.24
2755 2844 9.438291 CTACATTAAGCTTGATTTGTTATTCCG 57.562 33.333 9.86 0.00 0.00 4.30
2953 3211 0.739813 CTCCGGCAGTAAAAGGGTCG 60.740 60.000 0.00 0.00 0.00 4.79
3149 3407 5.913137 TGACAATGAAAACAGTGGAGTTT 57.087 34.783 0.00 0.00 43.13 2.66
3257 3533 1.973515 TGGAACAGACTGAGATGCACT 59.026 47.619 10.08 0.00 0.00 4.40
3362 3638 5.537188 TGTTGATATGTTTTTGGGAACTGC 58.463 37.500 0.00 0.00 0.00 4.40
3370 3646 2.561478 TTTGGGAACTGCTCCTACAC 57.439 50.000 0.00 0.00 44.68 2.90
3387 3663 7.068470 GCTCCTACACCTATAGTTTTCACTAGT 59.932 40.741 0.00 0.00 38.96 2.57
3428 3704 6.625362 TCGGATCATATATTCTCTGCACTTC 58.375 40.000 0.00 0.00 0.00 3.01
3565 3841 3.455849 TGTGGAGGTGTGGATAATACCA 58.544 45.455 0.00 0.00 36.94 3.25
3566 3842 4.044308 TGTGGAGGTGTGGATAATACCAT 58.956 43.478 0.00 0.00 42.17 3.55
3679 3959 1.971357 AGACATCGAATAAGGCGGGAT 59.029 47.619 0.00 0.00 0.00 3.85
3881 4178 6.529829 CAGTATGTCTAGCAAACTCTGTCTTC 59.470 42.308 0.00 0.00 0.00 2.87
3968 4270 5.808030 GTCACCTCTATTTGCTGTACTTCTC 59.192 44.000 0.00 0.00 0.00 2.87
3974 4276 2.561478 TTGCTGTACTTCTCCAACCC 57.439 50.000 0.00 0.00 0.00 4.11
4017 4319 9.683069 AAATAATGTTCTGTGCTAGTTTTTGAG 57.317 29.630 0.00 0.00 0.00 3.02
4025 4327 4.941263 TGTGCTAGTTTTTGAGTCTGTTGT 59.059 37.500 0.00 0.00 0.00 3.32
4046 4352 3.565482 GTCATGATGACTGTTGGTGTGTT 59.435 43.478 17.84 0.00 43.73 3.32
4052 4358 4.955925 TGACTGTTGGTGTGTTGTAAAG 57.044 40.909 0.00 0.00 0.00 1.85
4062 4400 9.281075 GTTGGTGTGTTGTAAAGTTTACTTAAG 57.719 33.333 22.87 0.00 34.61 1.85
4153 4774 2.429971 TGGTGCTGCACTTGAAATTTCA 59.570 40.909 29.54 16.91 34.40 2.69
4181 4803 9.110502 TGTAACAGTGTGTGTGTAATTCATTTA 57.889 29.630 0.00 0.00 40.26 1.40
4261 4919 7.227049 AGTACTACAAATTGAACCAATTGGG 57.773 36.000 27.89 10.20 42.32 4.12
4470 5189 0.676782 CGGAGACCACCCCATTGTTC 60.677 60.000 0.00 0.00 0.00 3.18
4523 5242 4.814294 ATTCCGGTCGAGCGTGGC 62.814 66.667 32.11 0.00 0.00 5.01
4550 5269 1.923148 CCCTCCCAGACCAATAAACCT 59.077 52.381 0.00 0.00 0.00 3.50
4593 5312 1.282447 TCTCGGGTCTACTCTGCTTCT 59.718 52.381 0.00 0.00 0.00 2.85
4662 5381 2.017623 GCCATGAGCATGAGCAGAAGT 61.018 52.381 11.84 0.00 45.49 3.01
4716 5435 3.374402 CGCACCTCACTCCTCCGT 61.374 66.667 0.00 0.00 0.00 4.69
4778 5497 5.496556 TCCACCAGTCAACATAAGTTATGG 58.503 41.667 23.49 10.56 40.47 2.74
5077 5802 1.355043 AGTCCTTCCGTCAGTCCTACT 59.645 52.381 0.00 0.00 0.00 2.57
5153 5878 2.976903 GCTGCCGGGATGCTGATC 60.977 66.667 2.18 0.00 32.50 2.92
5159 5884 1.072678 CGGGATGCTGATCATGGCT 59.927 57.895 8.27 0.00 35.05 4.75
5188 5914 2.094752 GCTCGCTCTGAACTCTTCTTCT 60.095 50.000 0.00 0.00 0.00 2.85
5189 5915 3.613910 GCTCGCTCTGAACTCTTCTTCTT 60.614 47.826 0.00 0.00 0.00 2.52
5190 5916 4.555262 CTCGCTCTGAACTCTTCTTCTTT 58.445 43.478 0.00 0.00 0.00 2.52
5207 5933 2.709629 TTTGTTGCGCGCGAAAGAGG 62.710 55.000 37.18 2.07 0.00 3.69
5230 5956 3.127548 CAGTGTGGCTTGTGAATACATCC 59.872 47.826 0.00 0.00 36.53 3.51
5287 6014 2.676463 GCCTGAGGAGTGAGTCAATGAC 60.676 54.545 0.65 5.02 0.00 3.06
5295 6024 3.157881 AGTGAGTCAATGACGGAGAGAA 58.842 45.455 7.83 0.00 37.67 2.87
5296 6025 3.057174 AGTGAGTCAATGACGGAGAGAAC 60.057 47.826 7.83 0.79 37.67 3.01
5313 6044 6.183360 GGAGAGAACTGCATAGATTTTGTTCC 60.183 42.308 7.38 1.50 35.71 3.62
5464 6198 9.185680 GTTATGGAAGTGGAAGTAATGGTAAAT 57.814 33.333 0.00 0.00 0.00 1.40
5496 6531 0.179073 GCATCAGTCCTGGCGTATGT 60.179 55.000 0.00 0.00 0.00 2.29
5514 6549 8.847196 GGCGTATGTTATATATGATCCTGTCTA 58.153 37.037 0.00 0.00 0.00 2.59
5560 6602 3.134458 GGGGCTCATTTATCTCGTCTTG 58.866 50.000 0.00 0.00 0.00 3.02
5706 6753 5.163513 CAGTGTTTTCATTAGGGATTGTGC 58.836 41.667 0.00 0.00 0.00 4.57
5751 6798 5.220912 GCTGCATCAAGTATATGTGAAGCAA 60.221 40.000 15.16 4.92 44.90 3.91
5752 6799 6.367686 TGCATCAAGTATATGTGAAGCAAG 57.632 37.500 13.11 0.00 43.29 4.01
5754 6801 6.375174 TGCATCAAGTATATGTGAAGCAAGTT 59.625 34.615 13.11 0.00 43.29 2.66
5755 6802 7.094248 TGCATCAAGTATATGTGAAGCAAGTTT 60.094 33.333 13.11 0.00 43.29 2.66
5756 6803 7.219535 GCATCAAGTATATGTGAAGCAAGTTTG 59.780 37.037 9.62 0.00 38.14 2.93
5757 6804 7.144722 TCAAGTATATGTGAAGCAAGTTTGG 57.855 36.000 0.00 0.00 0.00 3.28
5758 6805 6.150976 TCAAGTATATGTGAAGCAAGTTTGGG 59.849 38.462 0.00 0.00 0.00 4.12
5759 6806 5.570320 AGTATATGTGAAGCAAGTTTGGGT 58.430 37.500 0.00 0.00 0.00 4.51
5760 6807 6.010219 AGTATATGTGAAGCAAGTTTGGGTT 58.990 36.000 0.00 0.00 0.00 4.11
5761 6808 7.172342 AGTATATGTGAAGCAAGTTTGGGTTA 58.828 34.615 0.00 0.00 0.00 2.85
5762 6809 4.853924 ATGTGAAGCAAGTTTGGGTTAG 57.146 40.909 0.00 0.00 0.00 2.34
5763 6810 3.892284 TGTGAAGCAAGTTTGGGTTAGA 58.108 40.909 0.00 0.00 0.00 2.10
5764 6811 3.882888 TGTGAAGCAAGTTTGGGTTAGAG 59.117 43.478 0.00 0.00 0.00 2.43
5765 6812 2.884639 TGAAGCAAGTTTGGGTTAGAGC 59.115 45.455 0.00 0.00 0.00 4.09
5766 6813 2.656947 AGCAAGTTTGGGTTAGAGCA 57.343 45.000 0.00 0.00 0.00 4.26
5767 6814 3.160679 AGCAAGTTTGGGTTAGAGCAT 57.839 42.857 0.00 0.00 0.00 3.79
5768 6815 3.084786 AGCAAGTTTGGGTTAGAGCATC 58.915 45.455 0.00 0.00 0.00 3.91
5769 6816 2.819608 GCAAGTTTGGGTTAGAGCATCA 59.180 45.455 0.00 0.00 37.82 3.07
5775 7274 7.195374 AGTTTGGGTTAGAGCATCAAGTATA 57.805 36.000 0.00 0.00 37.82 1.47
5778 7277 6.747414 TGGGTTAGAGCATCAAGTATATGT 57.253 37.500 0.00 0.00 37.82 2.29
5779 7278 6.524734 TGGGTTAGAGCATCAAGTATATGTG 58.475 40.000 0.00 0.00 37.82 3.21
5794 7293 6.010219 AGTATATGTGAAGCAAGTTTGGGTT 58.990 36.000 0.00 0.00 0.00 4.11
5808 7307 1.681229 TGGGTTAGAGCCTGGGAATT 58.319 50.000 0.00 0.00 36.53 2.17
5839 7340 8.293699 ACCTCAAAAACATATAATCTCCCAAC 57.706 34.615 0.00 0.00 0.00 3.77
5928 7430 2.589014 CGCCTCATTCACAGCTTTTTC 58.411 47.619 0.00 0.00 0.00 2.29
5939 7441 3.345737 GCTTTTTCCATAAGCCGCC 57.654 52.632 0.00 0.00 41.62 6.13
5940 7442 0.817654 GCTTTTTCCATAAGCCGCCT 59.182 50.000 0.00 0.00 41.62 5.52
5941 7443 1.469767 GCTTTTTCCATAAGCCGCCTG 60.470 52.381 0.00 0.00 41.62 4.85
5942 7444 1.818674 CTTTTTCCATAAGCCGCCTGT 59.181 47.619 0.00 0.00 0.00 4.00
5943 7445 1.459450 TTTTCCATAAGCCGCCTGTC 58.541 50.000 0.00 0.00 0.00 3.51
5944 7446 0.618458 TTTCCATAAGCCGCCTGTCT 59.382 50.000 0.00 0.00 0.00 3.41
5945 7447 0.178068 TTCCATAAGCCGCCTGTCTC 59.822 55.000 0.00 0.00 0.00 3.36
5946 7448 0.975556 TCCATAAGCCGCCTGTCTCA 60.976 55.000 0.00 0.00 0.00 3.27
5947 7449 0.107456 CCATAAGCCGCCTGTCTCAT 59.893 55.000 0.00 0.00 0.00 2.90
5948 7450 1.475751 CCATAAGCCGCCTGTCTCATT 60.476 52.381 0.00 0.00 0.00 2.57
5949 7451 1.869767 CATAAGCCGCCTGTCTCATTC 59.130 52.381 0.00 0.00 0.00 2.67
6011 7513 2.628178 AGGCTTAACAAGTTTTGGGAGC 59.372 45.455 0.00 0.00 34.99 4.70
6016 7518 1.172812 ACAAGTTTTGGGAGCGGCTC 61.173 55.000 21.57 21.57 34.12 4.70
6059 7562 5.009210 AGACAACTTAATTTTAAGCCGCACA 59.991 36.000 9.45 0.00 42.98 4.57
6077 7580 1.480545 ACAAAAGAACTGGCACAACCC 59.519 47.619 0.00 0.00 38.70 4.11
6078 7581 1.480137 CAAAAGAACTGGCACAACCCA 59.520 47.619 0.00 0.00 38.70 4.51
6137 7640 6.136541 ACTTTGAAAGAAAGGTTGCTAGTG 57.863 37.500 12.53 0.00 0.00 2.74
6152 7655 6.459298 GGTTGCTAGTGAAAATCTGATGATGG 60.459 42.308 0.00 0.00 32.44 3.51
6189 7699 7.266922 TGTTTGTACTACAGAACAAATTCCC 57.733 36.000 4.18 0.00 44.73 3.97
6192 7702 5.556915 TGTACTACAGAACAAATTCCCCTG 58.443 41.667 0.00 0.00 35.18 4.45
6264 7830 9.849166 GTTTACGGAAAATATCAGAATTTTGGA 57.151 29.630 0.00 0.00 38.77 3.53
6288 7854 7.041030 GGATTATGTGACTGATAACGAGAGAGA 60.041 40.741 0.00 0.00 0.00 3.10
6289 7855 5.749596 ATGTGACTGATAACGAGAGAGAG 57.250 43.478 0.00 0.00 0.00 3.20
6290 7856 4.580868 TGTGACTGATAACGAGAGAGAGT 58.419 43.478 0.00 0.00 0.00 3.24
6302 7868 3.066064 CGAGAGAGAGTAGTCATGGTTGG 59.934 52.174 0.00 0.00 0.00 3.77
6308 7874 3.515901 AGAGTAGTCATGGTTGGAGGTTC 59.484 47.826 0.00 0.00 0.00 3.62
6392 7958 1.893786 GTGCCTGACGAGGAGATGT 59.106 57.895 0.00 0.00 42.93 3.06
6401 7967 4.498520 AGGAGATGTGACGCCGCG 62.499 66.667 12.14 12.14 35.00 6.46
6424 7990 0.881118 GGTCATGGCATCAACAACGT 59.119 50.000 0.00 0.00 0.00 3.99
6425 7991 1.401409 GGTCATGGCATCAACAACGTG 60.401 52.381 0.00 0.00 0.00 4.49
6426 7992 1.535028 GTCATGGCATCAACAACGTGA 59.465 47.619 0.00 0.00 0.00 4.35
6427 7993 1.535028 TCATGGCATCAACAACGTGAC 59.465 47.619 0.00 0.00 0.00 3.67
6428 7994 1.536766 CATGGCATCAACAACGTGACT 59.463 47.619 0.00 0.00 0.00 3.41
6429 7995 2.535012 TGGCATCAACAACGTGACTA 57.465 45.000 0.00 0.00 0.00 2.59
6430 7996 2.412870 TGGCATCAACAACGTGACTAG 58.587 47.619 0.00 0.00 0.00 2.57
6431 7997 2.036604 TGGCATCAACAACGTGACTAGA 59.963 45.455 0.00 0.00 0.00 2.43
6432 7998 2.412089 GGCATCAACAACGTGACTAGAC 59.588 50.000 0.00 0.00 0.00 2.59
6433 7999 2.090658 GCATCAACAACGTGACTAGACG 59.909 50.000 0.00 0.00 45.09 4.18
6434 8000 1.762419 TCAACAACGTGACTAGACGC 58.238 50.000 0.00 0.00 43.33 5.19
6435 8001 0.429736 CAACAACGTGACTAGACGCG 59.570 55.000 23.07 23.07 43.33 6.01
6436 8002 0.662374 AACAACGTGACTAGACGCGG 60.662 55.000 26.83 15.33 46.02 6.46
6437 8003 2.126580 AACGTGACTAGACGCGGC 60.127 61.111 26.83 7.86 46.02 6.53
6438 8004 2.911484 AACGTGACTAGACGCGGCA 61.911 57.895 26.83 0.00 46.02 5.69
6446 8012 3.751401 TAGACGCGGCATGTCGAGC 62.751 63.158 26.38 16.21 41.24 5.03
6475 8052 3.268103 ATGGGTTCGAGTGTGGGCC 62.268 63.158 0.00 0.00 0.00 5.80
6497 8074 3.308053 CACGAAATCATGGCTGTAGAGTG 59.692 47.826 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 5.826601 TGTGCTTGTTCATTGTTTGTCTA 57.173 34.783 0.00 0.00 0.00 2.59
30 31 5.042593 TCATGTGCTTGTTCATTGTTTGTC 58.957 37.500 0.00 0.00 0.00 3.18
35 36 4.392047 TCTCTCATGTGCTTGTTCATTGT 58.608 39.130 0.00 0.00 0.00 2.71
53 54 4.040047 TGAGTCCATCTCTCTCTCTCTCT 58.960 47.826 0.00 0.00 43.13 3.10
54 55 4.422073 TGAGTCCATCTCTCTCTCTCTC 57.578 50.000 0.00 0.00 43.13 3.20
55 56 4.228210 ACTTGAGTCCATCTCTCTCTCTCT 59.772 45.833 0.00 0.00 43.13 3.10
56 57 4.526970 ACTTGAGTCCATCTCTCTCTCTC 58.473 47.826 0.00 0.00 43.13 3.20
57 58 4.591321 ACTTGAGTCCATCTCTCTCTCT 57.409 45.455 0.00 0.00 43.13 3.10
58 59 5.437060 AGTACTTGAGTCCATCTCTCTCTC 58.563 45.833 0.00 0.00 43.13 3.20
77 82 2.477754 GGTCGGCTGTTGTTTGTAGTAC 59.522 50.000 0.00 0.00 0.00 2.73
102 107 2.347114 GTTTTGGTGCATGGGGGC 59.653 61.111 0.00 0.00 0.00 5.80
107 112 1.274167 AGCATCTGGTTTTGGTGCATG 59.726 47.619 0.00 0.00 38.23 4.06
108 113 1.636148 AGCATCTGGTTTTGGTGCAT 58.364 45.000 0.00 0.00 38.23 3.96
109 114 2.284754 TAGCATCTGGTTTTGGTGCA 57.715 45.000 1.84 0.00 38.23 4.57
110 115 2.352715 GGTTAGCATCTGGTTTTGGTGC 60.353 50.000 0.00 0.00 36.11 5.01
111 116 2.890311 TGGTTAGCATCTGGTTTTGGTG 59.110 45.455 0.00 0.00 0.00 4.17
112 117 3.237268 TGGTTAGCATCTGGTTTTGGT 57.763 42.857 0.00 0.00 0.00 3.67
113 118 3.119029 CCATGGTTAGCATCTGGTTTTGG 60.119 47.826 2.57 0.00 0.00 3.28
114 119 3.511146 ACCATGGTTAGCATCTGGTTTTG 59.489 43.478 13.00 0.00 36.86 2.44
115 120 3.778265 ACCATGGTTAGCATCTGGTTTT 58.222 40.909 13.00 0.00 36.86 2.43
174 183 7.014134 TGTGGTGGCATTATTATTAAGTGATGG 59.986 37.037 0.00 0.00 0.00 3.51
191 200 1.228124 GTAGCTTGGTGTGGTGGCA 60.228 57.895 0.00 0.00 0.00 4.92
220 229 3.323775 TGAAAGGGACAAGGAACCTACT 58.676 45.455 0.00 0.00 33.37 2.57
221 230 3.782656 TGAAAGGGACAAGGAACCTAC 57.217 47.619 0.00 0.00 33.37 3.18
222 231 4.263771 GGAATGAAAGGGACAAGGAACCTA 60.264 45.833 0.00 0.00 33.37 3.08
223 232 3.500471 GGAATGAAAGGGACAAGGAACCT 60.500 47.826 0.00 0.00 35.78 3.50
321 330 1.461127 GTGATCTTGACGCCTTGTGAC 59.539 52.381 0.00 0.00 0.00 3.67
346 357 4.095334 TCATTCATTCATTGAGTTCGGCTG 59.905 41.667 0.00 0.00 35.27 4.85
348 359 4.621068 TCATTCATTCATTGAGTTCGGC 57.379 40.909 0.00 0.00 35.27 5.54
389 400 1.271934 CGAGTGGATATGCTCTGAGGG 59.728 57.143 6.83 0.00 0.00 4.30
406 417 1.493950 GATGCGGAGAATGGTGCGAG 61.494 60.000 0.00 0.00 32.11 5.03
462 473 8.805145 ATTATCTTCTTTTCTGATAGGAGGGA 57.195 34.615 0.00 0.00 0.00 4.20
579 595 3.190535 ACAGAAACACCATTTACGATGCC 59.809 43.478 0.00 0.00 0.00 4.40
581 597 5.862924 AGACAGAAACACCATTTACGATG 57.137 39.130 0.00 0.00 0.00 3.84
583 599 5.587043 ACAAAGACAGAAACACCATTTACGA 59.413 36.000 0.00 0.00 0.00 3.43
605 621 3.461378 TGCTGGAGTAGTACCCTAACA 57.539 47.619 0.00 0.00 0.00 2.41
606 622 4.813750 TTTGCTGGAGTAGTACCCTAAC 57.186 45.455 0.00 0.00 0.00 2.34
614 630 6.076981 CAGAATTGTTTTTGCTGGAGTAGT 57.923 37.500 0.00 0.00 0.00 2.73
626 642 7.278424 CACAGAAAATGACACCAGAATTGTTTT 59.722 33.333 0.00 0.00 0.00 2.43
652 668 4.450082 AAGTGTGTGTTTTGTTTCTCCC 57.550 40.909 0.00 0.00 0.00 4.30
700 716 8.879759 CAAAATTAGTTAAAGCTCAGACGGATA 58.120 33.333 0.00 0.00 0.00 2.59
703 719 6.148811 TCCAAAATTAGTTAAAGCTCAGACGG 59.851 38.462 0.00 0.00 0.00 4.79
705 721 7.015877 CGTCCAAAATTAGTTAAAGCTCAGAC 58.984 38.462 0.00 0.00 0.00 3.51
707 723 6.148811 TCCGTCCAAAATTAGTTAAAGCTCAG 59.851 38.462 0.00 0.00 0.00 3.35
715 731 4.533311 ACTCCCTCCGTCCAAAATTAGTTA 59.467 41.667 0.00 0.00 0.00 2.24
725 741 2.176889 CTTTTCTACTCCCTCCGTCCA 58.823 52.381 0.00 0.00 0.00 4.02
726 742 2.427812 CTCTTTTCTACTCCCTCCGTCC 59.572 54.545 0.00 0.00 0.00 4.79
729 745 2.736347 TCCTCTTTTCTACTCCCTCCG 58.264 52.381 0.00 0.00 0.00 4.63
730 746 4.098155 ACTTCCTCTTTTCTACTCCCTCC 58.902 47.826 0.00 0.00 0.00 4.30
745 761 9.994432 CAGAAACATCATTTACAATACTTCCTC 57.006 33.333 0.00 0.00 0.00 3.71
746 762 9.520515 ACAGAAACATCATTTACAATACTTCCT 57.479 29.630 0.00 0.00 0.00 3.36
747 763 9.774742 GACAGAAACATCATTTACAATACTTCC 57.225 33.333 0.00 0.00 0.00 3.46
763 779 7.259088 AGTACCCTAATCAAGACAGAAACAT 57.741 36.000 0.00 0.00 0.00 2.71
764 780 6.681729 AGTACCCTAATCAAGACAGAAACA 57.318 37.500 0.00 0.00 0.00 2.83
784 800 4.221924 TGTGTTGCTTATGCTGGAGTAGTA 59.778 41.667 1.96 0.00 40.48 1.82
785 801 3.007940 TGTGTTGCTTATGCTGGAGTAGT 59.992 43.478 1.96 0.00 40.48 2.73
797 813 4.203226 TGACACCAGAATTGTGTTGCTTA 58.797 39.130 0.00 0.00 46.43 3.09
798 814 3.023119 TGACACCAGAATTGTGTTGCTT 58.977 40.909 0.00 0.00 46.43 3.91
799 815 2.653726 TGACACCAGAATTGTGTTGCT 58.346 42.857 0.00 0.00 46.43 3.91
800 816 3.648339 ATGACACCAGAATTGTGTTGC 57.352 42.857 0.00 0.00 46.43 4.17
801 817 6.199531 CAGAAAATGACACCAGAATTGTGTTG 59.800 38.462 1.49 0.00 46.43 3.33
804 820 5.835257 ACAGAAAATGACACCAGAATTGTG 58.165 37.500 0.00 0.00 39.63 3.33
923 956 2.094659 CGTACTTGACCAGCCTGCG 61.095 63.158 0.00 0.00 0.00 5.18
1135 1172 1.054406 ACGGGATGGATGGGAATCGT 61.054 55.000 0.00 0.00 0.00 3.73
1213 1250 0.250295 TCTTTGACAGGGCTTGACCG 60.250 55.000 2.65 0.00 40.62 4.79
1241 1279 1.602237 GGAGGGAATTGACGAGGCA 59.398 57.895 0.00 0.00 0.00 4.75
1345 1391 0.807496 GAGCAAGCGAATCTGCCTTT 59.193 50.000 0.00 0.00 34.65 3.11
1361 1407 4.253257 CCTAGCGACGGACGGAGC 62.253 72.222 1.66 5.73 42.83 4.70
1366 1416 0.458025 CTGGAAACCTAGCGACGGAC 60.458 60.000 0.00 0.00 0.00 4.79
1374 1428 1.156736 CAACGCCACTGGAAACCTAG 58.843 55.000 0.00 0.00 0.00 3.02
1376 1430 0.535102 CTCAACGCCACTGGAAACCT 60.535 55.000 0.00 0.00 0.00 3.50
1432 1486 4.274602 CAGAAGCTGGATATGCTCTCAT 57.725 45.455 0.00 0.00 40.22 2.90
1454 1508 3.126000 GGACACAGCACTAAAAGATCAGC 59.874 47.826 0.00 0.00 0.00 4.26
1497 1551 1.742308 TCCAGCAGGTTTCTTAGGGT 58.258 50.000 0.00 0.00 35.89 4.34
1538 1592 1.148310 CCAGCATACCGGATTTAGCG 58.852 55.000 9.46 1.75 0.00 4.26
1591 1645 1.768684 TTCCAAGCTTCCGGCACTCT 61.769 55.000 0.00 0.00 44.79 3.24
1626 1681 8.695456 ACCTGTTTCATTCAAATGGAATATACC 58.305 33.333 0.00 0.00 44.41 2.73
1637 1692 6.873076 GCATAATTCCACCTGTTTCATTCAAA 59.127 34.615 0.00 0.00 0.00 2.69
1678 1733 2.858839 GGAATAAAAGTTCCGCCAACG 58.141 47.619 0.00 0.00 40.32 4.10
1731 1786 2.880890 GCTTATCACATTCCGCCAGAAT 59.119 45.455 0.00 0.00 46.54 2.40
1773 1834 7.230712 TCTCCTAAACTTATCATGCGATGAGTA 59.769 37.037 0.91 0.00 45.14 2.59
1781 1842 6.484643 TCAGCAATCTCCTAAACTTATCATGC 59.515 38.462 0.00 0.00 0.00 4.06
1850 1912 9.945904 AAAAATAAGATCCTCTCTAACGTTTCT 57.054 29.630 5.91 0.00 32.41 2.52
1851 1913 9.974750 CAAAAATAAGATCCTCTCTAACGTTTC 57.025 33.333 5.91 0.00 32.41 2.78
1879 1944 1.068895 TGGACAGCCAGCAACAAATTG 59.931 47.619 0.00 0.00 39.92 2.32
1935 2000 5.412904 GTGAAGACCTTTAAGGAATCAGGTG 59.587 44.000 18.97 0.00 39.90 4.00
1961 2030 2.091610 TCCAACCTTGTTCCCATCACAA 60.092 45.455 0.00 0.00 33.09 3.33
2029 2098 1.249407 TACGACAACAAAATGGGCCC 58.751 50.000 17.59 17.59 0.00 5.80
2031 2100 4.149747 CACAAATACGACAACAAAATGGGC 59.850 41.667 0.00 0.00 0.00 5.36
2036 2105 5.007823 ACGGATCACAAATACGACAACAAAA 59.992 36.000 0.00 0.00 0.00 2.44
2040 2109 4.657075 AACGGATCACAAATACGACAAC 57.343 40.909 0.00 0.00 0.00 3.32
2116 2185 5.180680 AGCAGGACTTTTACACGGAAAATAC 59.819 40.000 0.00 0.00 0.00 1.89
2197 2266 2.232696 TCAGCTACAATACCTGCAACGA 59.767 45.455 0.00 0.00 0.00 3.85
2207 2276 5.237127 CGAAAGCATCCAATCAGCTACAATA 59.763 40.000 0.00 0.00 37.70 1.90
2210 2279 2.938451 CGAAAGCATCCAATCAGCTACA 59.062 45.455 0.00 0.00 37.70 2.74
2283 2352 6.348950 CCACCTAATACTTCAATGCGTCAAAA 60.349 38.462 0.00 0.00 0.00 2.44
2289 2358 3.206150 AGCCACCTAATACTTCAATGCG 58.794 45.455 0.00 0.00 0.00 4.73
2300 2369 3.258123 ACGCAATGAAAAAGCCACCTAAT 59.742 39.130 0.00 0.00 0.00 1.73
2356 2425 5.754406 CACTCTTCATCTTATCAGCTCTTGG 59.246 44.000 0.00 0.00 0.00 3.61
2380 2449 2.541762 GAGATAACATTGCTCCTCGTGC 59.458 50.000 0.00 0.00 0.00 5.34
2382 2451 3.460857 GGAGATAACATTGCTCCTCGT 57.539 47.619 0.00 0.00 43.79 4.18
2490 2559 5.163426 ACAAAAGTTTGCCTCAACATCATCA 60.163 36.000 3.68 0.00 41.79 3.07
2493 2562 4.734398 ACAAAAGTTTGCCTCAACATCA 57.266 36.364 3.68 0.00 41.79 3.07
2525 2594 7.624549 AGAAGTTGCTAGATGATGGTAAGAAA 58.375 34.615 0.00 0.00 0.00 2.52
2526 2595 7.187824 AGAAGTTGCTAGATGATGGTAAGAA 57.812 36.000 0.00 0.00 0.00 2.52
2542 2611 2.558359 ACAGCCAAATGGTAGAAGTTGC 59.442 45.455 0.71 0.00 37.57 4.17
2553 2622 5.125100 ACAAATGTAGTGACAGCCAAATG 57.875 39.130 0.00 0.00 39.50 2.32
2574 2643 2.514205 ACAGGTGAAAGCATGCAAAC 57.486 45.000 21.98 11.62 36.26 2.93
2588 2659 1.078989 AGCAGTAGGTAGGGAACAGGT 59.921 52.381 0.00 0.00 0.00 4.00
2662 2733 7.218614 ACATATTTTGGATGCCACCATAAATG 58.781 34.615 17.98 16.08 39.82 2.32
2690 2761 8.612619 GCCGGACATAACATAATAGGATTATTG 58.387 37.037 5.05 0.00 31.97 1.90
2730 2819 8.952278 ACGGAATAACAAATCAAGCTTAATGTA 58.048 29.630 0.00 0.00 0.00 2.29
2744 2833 4.038042 TGGCACAATCAACGGAATAACAAA 59.962 37.500 0.00 0.00 31.92 2.83
2794 2884 8.689251 AAAAGTGCAAAGTAGAAGAGAAAAAC 57.311 30.769 0.00 0.00 0.00 2.43
2795 2885 8.739972 AGAAAAGTGCAAAGTAGAAGAGAAAAA 58.260 29.630 0.00 0.00 0.00 1.94
2953 3211 7.468220 GCAGTATAAACTAAGCCATTAACACCC 60.468 40.741 0.00 0.00 33.48 4.61
3149 3407 6.263617 GGACAAGGTACATTACTTGAAACCAA 59.736 38.462 14.22 0.00 45.22 3.67
3362 3638 8.522542 ACTAGTGAAAACTATAGGTGTAGGAG 57.477 38.462 4.43 0.00 0.00 3.69
3387 3663 7.655236 TGATCCGAACAATACTAAAACGAAA 57.345 32.000 0.00 0.00 0.00 3.46
3565 3841 2.158986 CCAGGCTGAGTTCTCGAATGAT 60.159 50.000 17.94 0.00 0.00 2.45
3566 3842 1.205655 CCAGGCTGAGTTCTCGAATGA 59.794 52.381 17.94 0.00 0.00 2.57
3679 3959 3.833070 GGGAATCTAGATTTCTAGGCCGA 59.167 47.826 20.84 0.00 44.60 5.54
3866 4146 7.988028 ACTAGTTTTTAGAAGACAGAGTTTGCT 59.012 33.333 0.00 0.00 0.00 3.91
3869 4149 9.761504 GGTACTAGTTTTTAGAAGACAGAGTTT 57.238 33.333 0.00 0.00 0.00 2.66
3968 4270 6.518208 TTTAATACCAAATTCGAGGGTTGG 57.482 37.500 17.55 17.55 46.05 3.77
4025 4327 3.490439 ACACACCAACAGTCATCATGA 57.510 42.857 0.00 0.00 0.00 3.07
4038 4342 8.564509 ACTTAAGTAAACTTTACAACACACCA 57.435 30.769 6.26 0.00 37.40 4.17
4153 4774 7.561021 TGAATTACACACACACTGTTACAAT 57.439 32.000 0.00 0.00 0.00 2.71
4261 4919 5.293079 GCTGATTGTATGAAAGGAGAGTCAC 59.707 44.000 0.00 0.00 0.00 3.67
4301 5017 4.516698 CAGAGTGCTGCCTTAGAAAGAAAA 59.483 41.667 0.00 0.00 34.95 2.29
4305 5021 3.325293 TCAGAGTGCTGCCTTAGAAAG 57.675 47.619 0.00 0.00 42.01 2.62
4523 5242 2.750657 GGTCTGGGAGGGGATGCTG 61.751 68.421 0.00 0.00 0.00 4.41
4653 5372 0.804156 GGTCTGCGCTACTTCTGCTC 60.804 60.000 9.73 0.00 0.00 4.26
4716 5435 2.217038 GGAGTGTGTGGAGCCTCCA 61.217 63.158 10.05 10.05 45.98 3.86
4778 5497 1.152963 ATCTGCGGTGGGGCATAAC 60.153 57.895 0.00 0.00 42.99 1.89
5153 5878 0.654683 GCGAGCTTTGACTAGCCATG 59.345 55.000 0.00 0.00 42.20 3.66
5159 5884 2.558795 AGTTCAGAGCGAGCTTTGACTA 59.441 45.455 16.38 2.39 36.99 2.59
5188 5914 1.368731 CTCTTTCGCGCGCAACAAA 60.369 52.632 32.61 23.11 0.00 2.83
5189 5915 2.248140 CTCTTTCGCGCGCAACAA 59.752 55.556 32.61 17.35 0.00 2.83
5190 5916 3.711842 CCTCTTTCGCGCGCAACA 61.712 61.111 32.61 11.52 0.00 3.33
5207 5933 1.879380 TGTATTCACAAGCCACACTGC 59.121 47.619 0.00 0.00 0.00 4.40
5209 5935 3.244875 TGGATGTATTCACAAGCCACACT 60.245 43.478 0.00 0.00 37.91 3.55
5211 5937 3.346315 CTGGATGTATTCACAAGCCACA 58.654 45.455 0.00 0.00 37.91 4.17
5230 5956 2.495366 TACAGTTACACGCCGCCCTG 62.495 60.000 0.00 0.00 0.00 4.45
5272 5999 1.819288 TCTCCGTCATTGACTCACTCC 59.181 52.381 14.54 0.00 0.00 3.85
5287 6014 4.872691 ACAAAATCTATGCAGTTCTCTCCG 59.127 41.667 0.00 0.00 0.00 4.63
5295 6024 6.655078 AAACAGGAACAAAATCTATGCAGT 57.345 33.333 0.00 0.00 0.00 4.40
5296 6025 6.925165 ACAAAACAGGAACAAAATCTATGCAG 59.075 34.615 0.00 0.00 0.00 4.41
5416 6149 4.646492 ACCATGAAGACAAAGCTCAAAAGT 59.354 37.500 0.00 0.00 0.00 2.66
5417 6150 5.192327 ACCATGAAGACAAAGCTCAAAAG 57.808 39.130 0.00 0.00 0.00 2.27
5464 6198 5.183713 CAGGACTGATGCATCTAAAACCAAA 59.816 40.000 26.32 2.94 0.00 3.28
5514 6549 0.534412 CCGGACAGAGAGCAGTGATT 59.466 55.000 0.00 0.00 0.00 2.57
5573 6615 8.475331 TTCTCGATAAATCTGGTCAAACTTAC 57.525 34.615 0.00 0.00 0.00 2.34
5670 6717 1.473258 AACACTGCAACAAAGGAGCA 58.527 45.000 0.00 0.00 36.72 4.26
5751 6798 4.373156 ACTTGATGCTCTAACCCAAACT 57.627 40.909 0.00 0.00 0.00 2.66
5752 6799 7.499232 ACATATACTTGATGCTCTAACCCAAAC 59.501 37.037 0.00 0.00 0.00 2.93
5754 6801 6.992123 CACATATACTTGATGCTCTAACCCAA 59.008 38.462 0.00 0.00 0.00 4.12
5755 6802 6.326323 TCACATATACTTGATGCTCTAACCCA 59.674 38.462 0.00 0.00 0.00 4.51
5756 6803 6.759272 TCACATATACTTGATGCTCTAACCC 58.241 40.000 0.00 0.00 0.00 4.11
5757 6804 7.095439 GCTTCACATATACTTGATGCTCTAACC 60.095 40.741 12.63 0.00 38.96 2.85
5758 6805 7.439356 TGCTTCACATATACTTGATGCTCTAAC 59.561 37.037 17.45 0.00 41.30 2.34
5759 6806 7.500141 TGCTTCACATATACTTGATGCTCTAA 58.500 34.615 17.45 2.92 41.30 2.10
5760 6807 7.054491 TGCTTCACATATACTTGATGCTCTA 57.946 36.000 17.45 3.16 41.30 2.43
5761 6808 5.922053 TGCTTCACATATACTTGATGCTCT 58.078 37.500 17.45 0.00 41.30 4.09
5762 6809 6.259608 ACTTGCTTCACATATACTTGATGCTC 59.740 38.462 17.45 0.00 41.30 4.26
5763 6810 6.118170 ACTTGCTTCACATATACTTGATGCT 58.882 36.000 17.45 3.16 41.30 3.79
5764 6811 6.369059 ACTTGCTTCACATATACTTGATGC 57.631 37.500 12.86 12.86 41.17 3.91
5765 6812 7.699391 CCAAACTTGCTTCACATATACTTGATG 59.301 37.037 0.00 0.00 0.00 3.07
5766 6813 7.148018 CCCAAACTTGCTTCACATATACTTGAT 60.148 37.037 0.00 0.00 0.00 2.57
5767 6814 6.150976 CCCAAACTTGCTTCACATATACTTGA 59.849 38.462 0.00 0.00 0.00 3.02
5768 6815 6.071952 ACCCAAACTTGCTTCACATATACTTG 60.072 38.462 0.00 0.00 0.00 3.16
5769 6816 6.010219 ACCCAAACTTGCTTCACATATACTT 58.990 36.000 0.00 0.00 0.00 2.24
5775 7274 4.469657 TCTAACCCAAACTTGCTTCACAT 58.530 39.130 0.00 0.00 0.00 3.21
5778 7277 2.884639 GCTCTAACCCAAACTTGCTTCA 59.115 45.455 0.00 0.00 0.00 3.02
5779 7278 2.229062 GGCTCTAACCCAAACTTGCTTC 59.771 50.000 0.00 0.00 0.00 3.86
5794 7293 3.046374 GTTCCCTAATTCCCAGGCTCTA 58.954 50.000 0.00 0.00 0.00 2.43
5808 7307 9.847224 GAGATTATATGTTTTTGAGGTTCCCTA 57.153 33.333 0.00 0.00 31.76 3.53
5839 7340 3.516981 TCAACACAAAACATGGTGTGG 57.483 42.857 22.60 13.58 46.82 4.17
5914 7416 4.380867 CGGCTTATGGAAAAAGCTGTGAAT 60.381 41.667 8.19 0.00 46.62 2.57
5928 7430 0.107456 ATGAGACAGGCGGCTTATGG 59.893 55.000 9.66 0.00 0.00 2.74
5944 7446 7.378966 ACTAGTTCGAAAGTCTCATTGAATGA 58.621 34.615 7.73 7.73 37.76 2.57
5945 7447 7.588143 ACTAGTTCGAAAGTCTCATTGAATG 57.412 36.000 0.00 0.00 0.00 2.67
5946 7448 9.877178 ATAACTAGTTCGAAAGTCTCATTGAAT 57.123 29.630 12.39 0.00 0.00 2.57
5949 7451 9.239002 CCTATAACTAGTTCGAAAGTCTCATTG 57.761 37.037 12.39 0.00 0.00 2.82
5988 7490 4.279922 GCTCCCAAAACTTGTTAAGCCTTA 59.720 41.667 0.00 0.00 0.00 2.69
5995 7497 0.955905 GCCGCTCCCAAAACTTGTTA 59.044 50.000 0.00 0.00 0.00 2.41
6001 7503 0.603065 AAATGAGCCGCTCCCAAAAC 59.397 50.000 17.81 0.00 0.00 2.43
6026 7528 9.495572 CTTAAAATTAAGTTGTCTCTCCTCAGT 57.504 33.333 5.02 0.00 36.31 3.41
6030 7532 6.371825 CGGCTTAAAATTAAGTTGTCTCTCCT 59.628 38.462 12.99 0.00 41.63 3.69
6034 7536 5.567915 GTGCGGCTTAAAATTAAGTTGTCTC 59.432 40.000 12.99 0.00 41.63 3.36
6059 7562 1.859302 TGGGTTGTGCCAGTTCTTTT 58.141 45.000 0.00 0.00 39.65 2.27
6103 7606 7.390162 ACCTTTCTTTCAAAGTTTCAAATTGCA 59.610 29.630 0.00 0.00 0.00 4.08
6108 7611 6.934083 AGCAACCTTTCTTTCAAAGTTTCAAA 59.066 30.769 0.00 0.00 0.00 2.69
6115 7618 6.377327 TCACTAGCAACCTTTCTTTCAAAG 57.623 37.500 0.00 0.00 0.00 2.77
6116 7619 6.767524 TTCACTAGCAACCTTTCTTTCAAA 57.232 33.333 0.00 0.00 0.00 2.69
6123 7626 6.560253 TCAGATTTTCACTAGCAACCTTTC 57.440 37.500 0.00 0.00 0.00 2.62
6137 7640 1.952296 AGCGCCCATCATCAGATTTTC 59.048 47.619 2.29 0.00 30.20 2.29
6152 7655 3.871594 AGTACAAACATAAGATGAGCGCC 59.128 43.478 2.29 0.00 0.00 6.53
6264 7830 7.500892 ACTCTCTCTCGTTATCAGTCACATAAT 59.499 37.037 0.00 0.00 0.00 1.28
6288 7854 2.572104 GGAACCTCCAACCATGACTACT 59.428 50.000 0.00 0.00 36.28 2.57
6289 7855 2.304761 TGGAACCTCCAACCATGACTAC 59.695 50.000 0.00 0.00 45.00 2.73
6290 7856 2.626785 TGGAACCTCCAACCATGACTA 58.373 47.619 0.00 0.00 45.00 2.59
6302 7868 7.812669 CAGTTAACCATTTTGTTATGGAACCTC 59.187 37.037 9.49 0.00 46.63 3.85
6374 7940 0.459237 CACATCTCCTCGTCAGGCAC 60.459 60.000 0.00 0.00 40.12 5.01
6375 7941 0.611896 TCACATCTCCTCGTCAGGCA 60.612 55.000 0.00 0.00 40.12 4.75
6379 7945 1.506718 GCGTCACATCTCCTCGTCA 59.493 57.895 0.00 0.00 0.00 4.35
6382 7948 2.278206 CGGCGTCACATCTCCTCG 60.278 66.667 0.00 0.00 0.00 4.63
6407 7973 1.535028 GTCACGTTGTTGATGCCATGA 59.465 47.619 0.00 0.00 0.00 3.07
6416 7982 0.429736 CGCGTCTAGTCACGTTGTTG 59.570 55.000 0.00 0.00 42.04 3.33
6424 7990 1.138883 GACATGCCGCGTCTAGTCA 59.861 57.895 4.92 0.00 0.00 3.41
6425 7991 1.939785 CGACATGCCGCGTCTAGTC 60.940 63.158 4.92 7.14 0.00 2.59
6426 7992 2.102357 CGACATGCCGCGTCTAGT 59.898 61.111 4.92 0.00 0.00 2.57
6427 7993 1.655654 CTCGACATGCCGCGTCTAG 60.656 63.158 4.92 0.00 0.00 2.43
6428 7994 2.407616 CTCGACATGCCGCGTCTA 59.592 61.111 4.92 0.00 0.00 2.59
6446 8012 1.883021 GAACCCATCAAAGCACCGG 59.117 57.895 0.00 0.00 0.00 5.28
6455 8021 1.676968 CCCACACTCGAACCCATCA 59.323 57.895 0.00 0.00 0.00 3.07
6475 8052 3.308053 CACTCTACAGCCATGATTTCGTG 59.692 47.826 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.