Multiple sequence alignment - TraesCS5A01G328100

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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 TraesCS5A01G328100 chr5A 100.000 3701 0 0 1 3701 537260969 537257269 0.000000e+00 6835.0
1 TraesCS5A01G328100 chr5A 85.657 2001 241 33 1241 3213 653861825 653859843 0.000000e+00 2063.0
2 TraesCS5A01G328100 chr5D 91.387 3007 176 31 719 3701 423841207 423838260 0.000000e+00 4041.0
3 TraesCS5A01G328100 chr5D 80.769 390 58 12 89 476 423841888 423841514 4.680000e-74 289.0
4 TraesCS5A01G328100 chr5B 89.425 2676 192 29 719 3340 511613770 511611132 0.000000e+00 3290.0
5 TraesCS5A01G328100 chr5B 88.571 350 27 5 3354 3701 511610734 511610396 2.660000e-111 412.0
6 TraesCS5A01G328100 chr5B 77.295 207 31 10 38 235 511655046 511654847 1.410000e-19 108.0
7 TraesCS5A01G328100 chr5B 95.122 41 2 0 436 476 511614129 511614089 8.580000e-07 65.8
8 TraesCS5A01G328100 chr5B 95.122 41 2 0 436 476 511614222 511614182 8.580000e-07 65.8
9 TraesCS5A01G328100 chr4A 85.800 2000 234 38 1241 3210 323097225 323099204 0.000000e+00 2074.0
10 TraesCS5A01G328100 chr4A 87.023 1757 203 18 1241 2976 533561474 533559722 0.000000e+00 1958.0
11 TraesCS5A01G328100 chr3A 86.878 1768 209 16 1241 2989 646609805 646611568 0.000000e+00 1958.0
12 TraesCS5A01G328100 chr2D 86.708 1768 213 15 1241 2989 646623052 646624816 0.000000e+00 1943.0
13 TraesCS5A01G328100 chr2D 80.315 127 19 5 2864 2986 628990194 628990070 1.420000e-14 91.6
14 TraesCS5A01G328100 chr7A 86.674 1771 212 16 1241 2992 713554480 713552715 0.000000e+00 1941.0
15 TraesCS5A01G328100 chr7A 86.554 1770 216 14 1241 2992 713606042 713604277 0.000000e+00 1930.0
16 TraesCS5A01G328100 chr7A 86.561 1771 213 17 1241 2992 713520872 713519108 0.000000e+00 1929.0
17 TraesCS5A01G328100 chr7B 81.860 1075 132 36 2209 3261 115366643 115367676 0.000000e+00 846.0
18 TraesCS5A01G328100 chr3D 75.255 687 118 24 2471 3131 592907613 592908273 2.810000e-71 279.0
19 TraesCS5A01G328100 chr6A 79.330 179 29 6 3024 3200 536585425 536585253 6.490000e-23 119.0
20 TraesCS5A01G328100 chr1D 90.909 44 4 0 3298 3341 257356476 257356433 3.990000e-05 60.2


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 TraesCS5A01G328100 chr5A 537257269 537260969 3700 True 6835.0 6835 100.000 1 3701 1 chr5A.!!$R1 3700
1 TraesCS5A01G328100 chr5A 653859843 653861825 1982 True 2063.0 2063 85.657 1241 3213 1 chr5A.!!$R2 1972
2 TraesCS5A01G328100 chr5D 423838260 423841888 3628 True 2165.0 4041 86.078 89 3701 2 chr5D.!!$R1 3612
3 TraesCS5A01G328100 chr5B 511610396 511614222 3826 True 958.4 3290 92.060 436 3701 4 chr5B.!!$R2 3265
4 TraesCS5A01G328100 chr4A 323097225 323099204 1979 False 2074.0 2074 85.800 1241 3210 1 chr4A.!!$F1 1969
5 TraesCS5A01G328100 chr4A 533559722 533561474 1752 True 1958.0 1958 87.023 1241 2976 1 chr4A.!!$R1 1735
6 TraesCS5A01G328100 chr3A 646609805 646611568 1763 False 1958.0 1958 86.878 1241 2989 1 chr3A.!!$F1 1748
7 TraesCS5A01G328100 chr2D 646623052 646624816 1764 False 1943.0 1943 86.708 1241 2989 1 chr2D.!!$F1 1748
8 TraesCS5A01G328100 chr7A 713552715 713554480 1765 True 1941.0 1941 86.674 1241 2992 1 chr7A.!!$R2 1751
9 TraesCS5A01G328100 chr7A 713604277 713606042 1765 True 1930.0 1930 86.554 1241 2992 1 chr7A.!!$R3 1751
10 TraesCS5A01G328100 chr7A 713519108 713520872 1764 True 1929.0 1929 86.561 1241 2992 1 chr7A.!!$R1 1751
11 TraesCS5A01G328100 chr7B 115366643 115367676 1033 False 846.0 846 81.860 2209 3261 1 chr7B.!!$F1 1052
12 TraesCS5A01G328100 chr3D 592907613 592908273 660 False 279.0 279 75.255 2471 3131 1 chr3D.!!$F1 660

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
506 658 0.038310 TCTCGCTCCTCTTCCACTCA 59.962 55.0 0.00 0.0 0.0 3.41 F
1361 1581 0.038709 TGCATGCCGTTTTTAGTGCC 60.039 50.0 16.68 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2166 2387 1.221635 CCCACCCATTGTCCCTCATA 58.778 55.0 0.0 0.0 0.0 2.15 R
3348 3914 0.324614 CCCACACTGTAGACATGCCA 59.675 55.0 0.0 0.0 0.0 4.92 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
55 56 6.651755 AATATTTTTCATCGGCTGCTTTTG 57.348 33.333 0.00 0.00 0.00 2.44
56 57 2.437200 TTTTCATCGGCTGCTTTTGG 57.563 45.000 0.00 0.00 0.00 3.28
57 58 1.327303 TTTCATCGGCTGCTTTTGGT 58.673 45.000 0.00 0.00 0.00 3.67
58 59 1.327303 TTCATCGGCTGCTTTTGGTT 58.673 45.000 0.00 0.00 0.00 3.67
59 60 1.327303 TCATCGGCTGCTTTTGGTTT 58.673 45.000 0.00 0.00 0.00 3.27
60 61 1.686052 TCATCGGCTGCTTTTGGTTTT 59.314 42.857 0.00 0.00 0.00 2.43
61 62 1.794116 CATCGGCTGCTTTTGGTTTTG 59.206 47.619 0.00 0.00 0.00 2.44
62 63 0.820871 TCGGCTGCTTTTGGTTTTGT 59.179 45.000 0.00 0.00 0.00 2.83
63 64 2.025155 TCGGCTGCTTTTGGTTTTGTA 58.975 42.857 0.00 0.00 0.00 2.41
64 65 2.124122 CGGCTGCTTTTGGTTTTGTAC 58.876 47.619 0.00 0.00 0.00 2.90
65 66 2.223711 CGGCTGCTTTTGGTTTTGTACT 60.224 45.455 0.00 0.00 0.00 2.73
66 67 3.123050 GGCTGCTTTTGGTTTTGTACTG 58.877 45.455 0.00 0.00 0.00 2.74
67 68 3.181480 GGCTGCTTTTGGTTTTGTACTGA 60.181 43.478 0.00 0.00 0.00 3.41
68 69 4.501400 GGCTGCTTTTGGTTTTGTACTGAT 60.501 41.667 0.00 0.00 0.00 2.90
69 70 4.445385 GCTGCTTTTGGTTTTGTACTGATG 59.555 41.667 0.00 0.00 0.00 3.07
70 71 4.367450 TGCTTTTGGTTTTGTACTGATGC 58.633 39.130 0.00 0.00 0.00 3.91
71 72 4.142071 TGCTTTTGGTTTTGTACTGATGCA 60.142 37.500 0.00 0.00 0.00 3.96
72 73 4.990426 GCTTTTGGTTTTGTACTGATGCAT 59.010 37.500 0.00 0.00 0.00 3.96
73 74 5.466393 GCTTTTGGTTTTGTACTGATGCATT 59.534 36.000 0.00 0.00 0.00 3.56
74 75 6.346838 GCTTTTGGTTTTGTACTGATGCATTC 60.347 38.462 0.00 0.00 0.00 2.67
75 76 4.782019 TGGTTTTGTACTGATGCATTCC 57.218 40.909 0.00 0.00 0.00 3.01
76 77 4.406456 TGGTTTTGTACTGATGCATTCCT 58.594 39.130 0.00 0.00 0.00 3.36
77 78 4.832266 TGGTTTTGTACTGATGCATTCCTT 59.168 37.500 0.00 0.00 0.00 3.36
78 79 5.163513 GGTTTTGTACTGATGCATTCCTTG 58.836 41.667 0.00 0.00 0.00 3.61
79 80 5.278957 GGTTTTGTACTGATGCATTCCTTGT 60.279 40.000 0.00 0.00 0.00 3.16
80 81 5.375417 TTTGTACTGATGCATTCCTTGTG 57.625 39.130 0.00 0.00 0.00 3.33
81 82 3.346315 TGTACTGATGCATTCCTTGTGG 58.654 45.455 0.00 0.00 0.00 4.17
82 83 2.592102 ACTGATGCATTCCTTGTGGT 57.408 45.000 0.00 0.00 34.23 4.16
83 84 3.719268 ACTGATGCATTCCTTGTGGTA 57.281 42.857 0.00 0.00 34.23 3.25
84 85 3.614092 ACTGATGCATTCCTTGTGGTAG 58.386 45.455 0.00 0.00 34.23 3.18
85 86 3.264193 ACTGATGCATTCCTTGTGGTAGA 59.736 43.478 0.00 0.00 34.23 2.59
86 87 3.609853 TGATGCATTCCTTGTGGTAGAC 58.390 45.455 0.00 0.00 34.23 2.59
87 88 2.093306 TGCATTCCTTGTGGTAGACG 57.907 50.000 0.00 0.00 34.23 4.18
101 102 5.750067 TGTGGTAGACGTTTTTGTCTTCTAC 59.250 40.000 1.31 5.99 46.85 2.59
108 109 4.089065 ACGTTTTTGTCTTCTACGCGATAC 59.911 41.667 15.93 1.56 35.77 2.24
109 110 8.771433 GACGTTTTTGTCTTCTACGCGATACG 62.771 46.154 15.93 5.82 40.88 3.06
144 145 5.884792 AGTCATTCTGAATTCTTCATCCCAC 59.115 40.000 7.05 0.00 39.30 4.61
154 155 4.220693 TCTTCATCCCACATTGTCGATT 57.779 40.909 0.00 0.00 0.00 3.34
200 201 8.918961 TTGTTGATAAATTTAACTATTGCGGG 57.081 30.769 1.21 0.00 0.00 6.13
204 205 6.320164 TGATAAATTTAACTATTGCGGGTGCT 59.680 34.615 1.21 0.00 43.34 4.40
235 236 2.239402 TCTGGGTAGCATCAGCATTTGA 59.761 45.455 0.00 0.00 45.49 2.69
241 242 4.635765 GGTAGCATCAGCATTTGACAGTAA 59.364 41.667 0.00 0.00 45.49 2.24
265 266 5.218139 CAGCTGAAAGAAAGTGAAACCATC 58.782 41.667 8.42 0.00 32.83 3.51
266 267 5.009410 CAGCTGAAAGAAAGTGAAACCATCT 59.991 40.000 8.42 0.00 32.83 2.90
267 268 5.595952 AGCTGAAAGAAAGTGAAACCATCTT 59.404 36.000 0.00 0.00 42.04 2.40
269 270 6.758416 GCTGAAAGAAAGTGAAACCATCTTTT 59.242 34.615 8.52 0.00 46.04 2.27
270 271 7.278646 GCTGAAAGAAAGTGAAACCATCTTTTT 59.721 33.333 8.52 0.00 46.04 1.94
314 315 9.728100 ATAAGAATGGGGGATTTTATTCTTGAA 57.272 29.630 16.86 3.50 44.83 2.69
315 316 8.448068 AAGAATGGGGGATTTTATTCTTGAAA 57.552 30.769 9.50 0.00 44.04 2.69
316 317 7.851228 AGAATGGGGGATTTTATTCTTGAAAC 58.149 34.615 0.00 0.00 36.72 2.78
317 318 5.652994 TGGGGGATTTTATTCTTGAAACG 57.347 39.130 0.00 0.00 0.00 3.60
318 319 4.081917 TGGGGGATTTTATTCTTGAAACGC 60.082 41.667 0.00 0.00 0.00 4.84
319 320 4.430007 GGGGATTTTATTCTTGAAACGCC 58.570 43.478 0.00 0.00 0.00 5.68
322 323 5.028375 GGATTTTATTCTTGAAACGCCGAG 58.972 41.667 0.00 0.00 0.00 4.63
323 324 4.413495 TTTTATTCTTGAAACGCCGAGG 57.587 40.909 0.00 0.00 0.00 4.63
324 325 3.322211 TTATTCTTGAAACGCCGAGGA 57.678 42.857 0.00 0.00 0.00 3.71
325 326 2.178912 ATTCTTGAAACGCCGAGGAA 57.821 45.000 0.00 0.00 0.00 3.36
326 327 1.508632 TTCTTGAAACGCCGAGGAAG 58.491 50.000 0.00 0.00 0.00 3.46
327 328 0.320421 TCTTGAAACGCCGAGGAAGG 60.320 55.000 0.00 0.00 0.00 3.46
328 329 0.602905 CTTGAAACGCCGAGGAAGGT 60.603 55.000 0.00 0.00 0.00 3.50
329 330 0.601841 TTGAAACGCCGAGGAAGGTC 60.602 55.000 0.00 0.00 0.00 3.85
330 331 1.292541 GAAACGCCGAGGAAGGTCT 59.707 57.895 0.00 0.00 0.00 3.85
331 332 0.320508 GAAACGCCGAGGAAGGTCTT 60.321 55.000 0.00 0.00 0.00 3.01
332 333 0.108019 AAACGCCGAGGAAGGTCTTT 59.892 50.000 0.00 0.00 0.00 2.52
336 337 1.374947 CCGAGGAAGGTCTTTGGCA 59.625 57.895 0.00 0.00 0.00 4.92
351 352 7.992608 AGGTCTTTGGCAAAATAACAAGATTTT 59.007 29.630 14.43 0.00 39.13 1.82
352 353 8.620416 GGTCTTTGGCAAAATAACAAGATTTTT 58.380 29.630 14.43 0.00 36.99 1.94
353 354 9.437045 GTCTTTGGCAAAATAACAAGATTTTTG 57.563 29.630 14.43 0.00 41.19 2.44
354 355 9.171877 TCTTTGGCAAAATAACAAGATTTTTGT 57.828 25.926 14.43 0.00 40.65 2.83
407 413 5.248640 TGAGAGAAGGCAAATAACAAGAGG 58.751 41.667 0.00 0.00 0.00 3.69
427 433 3.384789 AGGCGAGCTGTTCATTACTATGA 59.615 43.478 0.00 0.00 39.00 2.15
428 434 4.119862 GGCGAGCTGTTCATTACTATGAA 58.880 43.478 0.00 0.00 45.99 2.57
470 476 0.691078 TCTCCAGCCCACCTATGACC 60.691 60.000 0.00 0.00 0.00 4.02
476 575 2.000701 CCCACCTATGACCCAGCCA 61.001 63.158 0.00 0.00 0.00 4.75
477 576 1.528824 CCACCTATGACCCAGCCAG 59.471 63.158 0.00 0.00 0.00 4.85
478 577 1.153086 CACCTATGACCCAGCCAGC 60.153 63.158 0.00 0.00 0.00 4.85
479 578 1.616327 ACCTATGACCCAGCCAGCA 60.616 57.895 0.00 0.00 0.00 4.41
480 579 1.153086 CCTATGACCCAGCCAGCAC 60.153 63.158 0.00 0.00 0.00 4.40
481 580 1.603842 CTATGACCCAGCCAGCACA 59.396 57.895 0.00 0.00 0.00 4.57
483 582 1.487850 TATGACCCAGCCAGCACACA 61.488 55.000 0.00 0.00 0.00 3.72
484 583 2.670934 GACCCAGCCAGCACACAG 60.671 66.667 0.00 0.00 0.00 3.66
485 584 3.482232 GACCCAGCCAGCACACAGT 62.482 63.158 0.00 0.00 0.00 3.55
486 585 2.670934 CCCAGCCAGCACACAGTC 60.671 66.667 0.00 0.00 0.00 3.51
502 654 0.329931 AGTCTCTCGCTCCTCTTCCA 59.670 55.000 0.00 0.00 0.00 3.53
504 656 0.329931 TCTCTCGCTCCTCTTCCACT 59.670 55.000 0.00 0.00 0.00 4.00
505 657 0.738389 CTCTCGCTCCTCTTCCACTC 59.262 60.000 0.00 0.00 0.00 3.51
506 658 0.038310 TCTCGCTCCTCTTCCACTCA 59.962 55.000 0.00 0.00 0.00 3.41
507 659 0.891373 CTCGCTCCTCTTCCACTCAA 59.109 55.000 0.00 0.00 0.00 3.02
510 662 2.072298 CGCTCCTCTTCCACTCAAAAG 58.928 52.381 0.00 0.00 0.00 2.27
533 685 0.899019 AAAAGGTCTCGCTCCTCTCC 59.101 55.000 0.00 0.00 33.76 3.71
556 708 0.664767 GTTCAGAGCTCGTTCGCAGT 60.665 55.000 8.37 0.00 0.00 4.40
558 710 2.148982 CAGAGCTCGTTCGCAGTCG 61.149 63.158 8.37 0.00 0.00 4.18
561 713 3.832171 GCTCGTTCGCAGTCGCAG 61.832 66.667 0.00 0.00 38.40 5.18
562 714 3.832171 CTCGTTCGCAGTCGCAGC 61.832 66.667 0.00 0.00 38.40 5.25
609 771 3.804329 GCCCCGCCAACCCTATCA 61.804 66.667 0.00 0.00 0.00 2.15
616 778 1.878102 CGCCAACCCTATCATAGGCAC 60.878 57.143 4.99 0.00 44.86 5.01
622 784 0.320771 CCTATCATAGGCACCGGCAC 60.321 60.000 0.00 0.00 43.71 5.01
624 786 0.762842 TATCATAGGCACCGGCACCT 60.763 55.000 19.07 19.07 43.71 4.00
625 787 2.044806 ATCATAGGCACCGGCACCTC 62.045 60.000 18.69 0.00 43.71 3.85
688 867 1.605058 GACGCCAGCCTTCAGGAGTA 61.605 60.000 0.00 0.00 38.08 2.59
739 947 4.400961 GCTGGCAGAAGCGGAGGT 62.401 66.667 20.86 0.00 43.41 3.85
773 985 3.257561 CAGGATTCGGCTCGCACG 61.258 66.667 0.00 0.00 0.00 5.34
775 987 4.814294 GGATTCGGCTCGCACGGT 62.814 66.667 0.00 0.00 0.00 4.83
813 1027 0.324091 TTACCGGAGTGAGGAGGTCC 60.324 60.000 9.46 0.00 38.12 4.46
851 1065 3.197790 CGCATCGGCTGTTGGAGG 61.198 66.667 5.76 0.00 38.10 4.30
852 1066 2.825836 GCATCGGCTGTTGGAGGG 60.826 66.667 5.76 0.00 36.96 4.30
853 1067 2.825836 CATCGGCTGTTGGAGGGC 60.826 66.667 0.00 0.00 0.00 5.19
854 1068 3.329889 ATCGGCTGTTGGAGGGCA 61.330 61.111 0.00 0.00 0.00 5.36
855 1069 2.905996 ATCGGCTGTTGGAGGGCAA 61.906 57.895 0.00 0.00 0.00 4.52
856 1070 2.424842 ATCGGCTGTTGGAGGGCAAA 62.425 55.000 0.00 0.00 0.00 3.68
871 1088 2.331809 GCAAAGACGCCAAGGTTTAG 57.668 50.000 0.00 0.00 0.00 1.85
996 1214 5.112220 TCTACAGTTTGCTTGCAGATTTG 57.888 39.130 0.00 0.00 0.00 2.32
1012 1230 6.098017 GCAGATTTGGAAATGAAGAGAAAGG 58.902 40.000 0.00 0.00 0.00 3.11
1057 1275 3.142174 GCAAGCAGTTCAGTTACTCCTT 58.858 45.455 0.00 0.00 0.00 3.36
1071 1289 2.190578 CCTTCCCCTGCCGATGTC 59.809 66.667 0.00 0.00 0.00 3.06
1111 1329 3.019564 GCTAATGTGACTGCAAATCCCT 58.980 45.455 0.00 0.00 0.00 4.20
1120 1338 4.086457 GACTGCAAATCCCTTTCCCTTAA 58.914 43.478 0.00 0.00 0.00 1.85
1124 1342 4.843516 TGCAAATCCCTTTCCCTTAATTGT 59.156 37.500 0.00 0.00 0.00 2.71
1135 1353 3.820467 TCCCTTAATTGTTGTGAGCACAG 59.180 43.478 3.32 0.00 42.94 3.66
1187 1405 2.092753 AGGAGAGCAATGGTACCACATG 60.093 50.000 19.09 19.85 0.00 3.21
1226 1444 0.882042 CCAAGGCAGCGCATACTAGG 60.882 60.000 11.47 0.00 0.00 3.02
1229 1447 0.605589 AGGCAGCGCATACTAGGATC 59.394 55.000 11.47 0.00 0.00 3.36
1350 1568 0.659427 CTGTGAGGTAATGCATGCCG 59.341 55.000 16.68 0.00 39.12 5.69
1361 1581 0.038709 TGCATGCCGTTTTTAGTGCC 60.039 50.000 16.68 0.00 0.00 5.01
1369 1589 4.142859 TGCCGTTTTTAGTGCCGTTTATAG 60.143 41.667 0.00 0.00 0.00 1.31
1379 1599 8.861033 TTAGTGCCGTTTATAGTGTACTAATG 57.139 34.615 0.00 0.00 31.39 1.90
1382 1602 8.202137 AGTGCCGTTTATAGTGTACTAATGATT 58.798 33.333 0.00 0.00 31.39 2.57
1512 1732 8.303876 GGAATTAAAGAAGCTTTGGTTGATGTA 58.696 33.333 0.00 0.00 0.00 2.29
1555 1775 2.502142 TTCTAGGCTACGTGGACAGA 57.498 50.000 7.78 5.16 0.00 3.41
1644 1864 6.742109 AGCTCCATATGCATTTTATGTTCAC 58.258 36.000 3.54 0.00 0.00 3.18
1666 1886 0.313043 CTTTGCTCACCAGTTGCAGG 59.687 55.000 0.00 0.00 38.01 4.85
1676 1896 2.127232 AGTTGCAGGTGGTGGTTGC 61.127 57.895 0.00 0.00 38.30 4.17
1699 1919 4.322725 CCACTGTTGCTCAATGTAGTCCTA 60.323 45.833 0.00 0.00 0.00 2.94
1721 1941 7.550551 TCCTACTATTGCTGATTTCTTCAACTG 59.449 37.037 0.00 0.00 32.78 3.16
1762 1982 3.047796 CAAGTGTGTTCATCTTGCAAGC 58.952 45.455 21.99 7.80 33.51 4.01
1804 2024 5.342259 GCCAAACATCAAGACGAATTGTTAC 59.658 40.000 0.00 0.00 28.81 2.50
1823 2043 7.395190 TGTTACATTTGATGGAGAATGGAAG 57.605 36.000 0.00 0.00 36.90 3.46
2037 2257 9.813446 ATTAAGATGGAATGCTTTGAATTTCTC 57.187 29.630 0.00 0.00 0.00 2.87
2068 2288 7.920151 TCATGTTGTTCTCAATAAACTTGTTGG 59.080 33.333 0.00 0.00 35.92 3.77
2117 2338 8.768019 AGCTTTGCAAAGAAAGAATCAAAATAC 58.232 29.630 37.14 16.43 38.28 1.89
2121 2342 8.801715 TGCAAAGAAAGAATCAAAATACTGTC 57.198 30.769 0.00 0.00 0.00 3.51
2166 2387 4.924305 TGTGAAAGAAAGCTTGCAAGAT 57.076 36.364 30.39 22.23 41.32 2.40
2284 2505 1.860950 CTATGGGTCAATCTGTTCGCG 59.139 52.381 0.00 0.00 0.00 5.87
2301 2522 1.859080 CGCGCTAAGAATAAGGTGACC 59.141 52.381 5.56 0.00 0.00 4.02
2391 2612 5.939883 TCATCGATTCAATGAAGTTTCCACT 59.060 36.000 1.10 0.00 30.37 4.00
2519 2741 0.237498 GCTGACCGGTTGTTGCTAAC 59.763 55.000 9.42 0.00 0.00 2.34
2532 2754 3.252215 TGTTGCTAACATTTGACCTTCCG 59.748 43.478 0.00 0.00 36.25 4.30
2579 2801 4.870636 AGTGAGGAATTTAATGGATGCCA 58.129 39.130 0.00 0.00 38.19 4.92
2619 2843 5.163513 GCTCGATTGATGGTTCAAACAAAT 58.836 37.500 0.00 0.00 44.70 2.32
2723 2964 5.998454 ATATTTTCGGCAAGAGACAGATG 57.002 39.130 0.00 0.00 0.00 2.90
2750 2991 5.008911 CGCAATGAGGTATCAAATGAATGGA 59.991 40.000 0.00 0.00 39.39 3.41
2774 3015 8.352201 GGATAAATGATTTAATGCTGTGCTACA 58.648 33.333 1.27 0.00 0.00 2.74
2788 3029 4.676546 TGTGCTACATCGAGAAAGAGATG 58.323 43.478 4.15 4.15 46.95 2.90
2994 3258 2.345760 GGCTGGTCACTTGGGCATG 61.346 63.158 0.00 0.00 0.00 4.06
3085 3357 4.689612 TGGTCTTCTAGTTGTTGCTTCT 57.310 40.909 0.00 0.00 0.00 2.85
3086 3358 4.632153 TGGTCTTCTAGTTGTTGCTTCTC 58.368 43.478 0.00 0.00 0.00 2.87
3087 3359 3.997681 GGTCTTCTAGTTGTTGCTTCTCC 59.002 47.826 0.00 0.00 0.00 3.71
3088 3360 4.503296 GGTCTTCTAGTTGTTGCTTCTCCA 60.503 45.833 0.00 0.00 0.00 3.86
3089 3361 4.688413 GTCTTCTAGTTGTTGCTTCTCCAG 59.312 45.833 0.00 0.00 0.00 3.86
3200 3473 5.826601 TGTTACTTTGAGCACATGTTTGA 57.173 34.783 0.00 0.00 0.00 2.69
3224 3497 7.178274 TGACAGATATTGGCTGTTTAAATTGGT 59.822 33.333 0.00 0.00 45.94 3.67
3281 3560 2.751806 ACTCTAGCAAATTCCAGCAAGC 59.248 45.455 0.00 0.00 0.00 4.01
3291 3570 2.408271 TCCAGCAAGCTTCCATAGTG 57.592 50.000 0.00 0.00 0.00 2.74
3343 3909 7.442656 ACAATAGGATTAGGAGGTAATGAACG 58.557 38.462 0.00 0.00 30.93 3.95
3348 3914 4.895668 TTAGGAGGTAATGAACGGTGTT 57.104 40.909 0.00 0.00 0.00 3.32
3444 4109 1.279271 GGCCCAGCTGTTAGAGAAGAA 59.721 52.381 13.81 0.00 0.00 2.52
3455 4120 6.252655 GCTGTTAGAGAAGAAGACGAAGAATC 59.747 42.308 0.00 0.00 0.00 2.52
3457 4122 4.364415 AGAGAAGAAGACGAAGAATCCG 57.636 45.455 0.00 0.00 0.00 4.18
3472 4137 5.161943 AGAATCCGTTGGTTTAAGCTACT 57.838 39.130 7.08 0.00 0.00 2.57
3473 4138 6.290294 AGAATCCGTTGGTTTAAGCTACTA 57.710 37.500 7.08 0.00 0.00 1.82
3474 4139 6.104665 AGAATCCGTTGGTTTAAGCTACTAC 58.895 40.000 7.08 0.00 0.00 2.73
3475 4140 3.836949 TCCGTTGGTTTAAGCTACTACG 58.163 45.455 7.08 6.11 0.00 3.51
3513 4178 2.354704 GCAGGTACTTATGCACACCTCA 60.355 50.000 11.64 0.00 39.40 3.86
3545 4210 8.954834 ATAGTTCTGATTCCTCATCTGTAGAT 57.045 34.615 0.00 0.00 33.52 1.98
3571 4236 6.126409 TGGAAATCACACCATATCCTTTACC 58.874 40.000 0.00 0.00 0.00 2.85
3607 4272 7.226720 AGTTTCCATCTTTATAATAGCCACACG 59.773 37.037 0.00 0.00 0.00 4.49
3630 4295 5.341617 GCTTACACATGTAGTAGACTCCAC 58.658 45.833 0.00 0.00 0.00 4.02
3690 4355 0.597568 TTTTTGATGCAGTGAGGGCG 59.402 50.000 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 9.462174 CAAAAGCAGCCGATGAAAAATATTATA 57.538 29.630 0.00 0.00 0.00 0.98
30 31 7.439056 CCAAAAGCAGCCGATGAAAAATATTAT 59.561 33.333 0.00 0.00 0.00 1.28
31 32 6.756074 CCAAAAGCAGCCGATGAAAAATATTA 59.244 34.615 0.00 0.00 0.00 0.98
32 33 5.581874 CCAAAAGCAGCCGATGAAAAATATT 59.418 36.000 0.00 0.00 0.00 1.28
33 34 5.111293 CCAAAAGCAGCCGATGAAAAATAT 58.889 37.500 0.00 0.00 0.00 1.28
34 35 4.021544 ACCAAAAGCAGCCGATGAAAAATA 60.022 37.500 0.00 0.00 0.00 1.40
35 36 3.244181 ACCAAAAGCAGCCGATGAAAAAT 60.244 39.130 0.00 0.00 0.00 1.82
36 37 2.102252 ACCAAAAGCAGCCGATGAAAAA 59.898 40.909 0.00 0.00 0.00 1.94
37 38 1.686052 ACCAAAAGCAGCCGATGAAAA 59.314 42.857 0.00 0.00 0.00 2.29
38 39 1.327303 ACCAAAAGCAGCCGATGAAA 58.673 45.000 0.00 0.00 0.00 2.69
39 40 1.327303 AACCAAAAGCAGCCGATGAA 58.673 45.000 0.00 0.00 0.00 2.57
40 41 1.327303 AAACCAAAAGCAGCCGATGA 58.673 45.000 0.00 0.00 0.00 2.92
41 42 1.794116 CAAAACCAAAAGCAGCCGATG 59.206 47.619 0.00 0.00 0.00 3.84
42 43 1.412343 ACAAAACCAAAAGCAGCCGAT 59.588 42.857 0.00 0.00 0.00 4.18
43 44 0.820871 ACAAAACCAAAAGCAGCCGA 59.179 45.000 0.00 0.00 0.00 5.54
44 45 2.124122 GTACAAAACCAAAAGCAGCCG 58.876 47.619 0.00 0.00 0.00 5.52
45 46 3.123050 CAGTACAAAACCAAAAGCAGCC 58.877 45.455 0.00 0.00 0.00 4.85
46 47 4.040445 TCAGTACAAAACCAAAAGCAGC 57.960 40.909 0.00 0.00 0.00 5.25
47 48 4.445385 GCATCAGTACAAAACCAAAAGCAG 59.555 41.667 0.00 0.00 0.00 4.24
48 49 4.142071 TGCATCAGTACAAAACCAAAAGCA 60.142 37.500 0.00 0.00 0.00 3.91
49 50 4.367450 TGCATCAGTACAAAACCAAAAGC 58.633 39.130 0.00 0.00 0.00 3.51
50 51 6.146021 GGAATGCATCAGTACAAAACCAAAAG 59.854 38.462 0.00 0.00 0.00 2.27
51 52 5.988561 GGAATGCATCAGTACAAAACCAAAA 59.011 36.000 0.00 0.00 0.00 2.44
52 53 5.304101 AGGAATGCATCAGTACAAAACCAAA 59.696 36.000 0.00 0.00 0.00 3.28
53 54 4.832266 AGGAATGCATCAGTACAAAACCAA 59.168 37.500 0.00 0.00 0.00 3.67
54 55 4.406456 AGGAATGCATCAGTACAAAACCA 58.594 39.130 0.00 0.00 0.00 3.67
55 56 5.163513 CAAGGAATGCATCAGTACAAAACC 58.836 41.667 0.00 0.00 0.00 3.27
56 57 5.630680 CACAAGGAATGCATCAGTACAAAAC 59.369 40.000 0.00 0.00 0.00 2.43
57 58 5.278907 CCACAAGGAATGCATCAGTACAAAA 60.279 40.000 0.00 0.00 36.89 2.44
58 59 4.218200 CCACAAGGAATGCATCAGTACAAA 59.782 41.667 0.00 0.00 36.89 2.83
59 60 3.758023 CCACAAGGAATGCATCAGTACAA 59.242 43.478 0.00 0.00 36.89 2.41
60 61 3.244875 ACCACAAGGAATGCATCAGTACA 60.245 43.478 0.00 0.00 38.69 2.90
61 62 3.347216 ACCACAAGGAATGCATCAGTAC 58.653 45.455 0.00 0.00 38.69 2.73
62 63 3.719268 ACCACAAGGAATGCATCAGTA 57.281 42.857 0.00 0.00 38.69 2.74
63 64 2.592102 ACCACAAGGAATGCATCAGT 57.408 45.000 0.00 0.00 38.69 3.41
64 65 3.624861 GTCTACCACAAGGAATGCATCAG 59.375 47.826 0.00 0.00 38.69 2.90
65 66 3.609853 GTCTACCACAAGGAATGCATCA 58.390 45.455 0.00 0.00 38.69 3.07
66 67 2.609459 CGTCTACCACAAGGAATGCATC 59.391 50.000 0.00 0.00 38.69 3.91
67 68 2.027192 ACGTCTACCACAAGGAATGCAT 60.027 45.455 0.00 0.00 38.69 3.96
68 69 1.346395 ACGTCTACCACAAGGAATGCA 59.654 47.619 0.00 0.00 38.69 3.96
69 70 2.094762 ACGTCTACCACAAGGAATGC 57.905 50.000 0.00 0.00 38.69 3.56
70 71 5.212194 CAAAAACGTCTACCACAAGGAATG 58.788 41.667 0.00 0.00 38.69 2.67
71 72 4.885325 ACAAAAACGTCTACCACAAGGAAT 59.115 37.500 0.00 0.00 38.69 3.01
72 73 4.263435 ACAAAAACGTCTACCACAAGGAA 58.737 39.130 0.00 0.00 38.69 3.36
73 74 3.872771 GACAAAAACGTCTACCACAAGGA 59.127 43.478 0.00 0.00 34.21 3.36
74 75 3.875134 AGACAAAAACGTCTACCACAAGG 59.125 43.478 0.00 0.00 44.46 3.61
75 76 5.293569 AGAAGACAAAAACGTCTACCACAAG 59.706 40.000 0.00 0.00 45.56 3.16
76 77 5.180271 AGAAGACAAAAACGTCTACCACAA 58.820 37.500 0.00 0.00 45.56 3.33
77 78 4.761975 AGAAGACAAAAACGTCTACCACA 58.238 39.130 0.00 0.00 45.56 4.17
78 79 5.108103 CGTAGAAGACAAAAACGTCTACCAC 60.108 44.000 0.00 0.00 45.56 4.16
79 80 4.977963 CGTAGAAGACAAAAACGTCTACCA 59.022 41.667 0.00 0.00 45.56 3.25
80 81 4.143452 GCGTAGAAGACAAAAACGTCTACC 60.143 45.833 0.00 0.00 45.56 3.18
81 82 4.430830 CGCGTAGAAGACAAAAACGTCTAC 60.431 45.833 0.00 0.00 45.56 2.59
82 83 3.665409 CGCGTAGAAGACAAAAACGTCTA 59.335 43.478 0.00 0.00 45.56 2.59
84 85 2.468777 TCGCGTAGAAGACAAAAACGTC 59.531 45.455 5.77 0.00 36.03 4.34
85 86 2.462889 TCGCGTAGAAGACAAAAACGT 58.537 42.857 5.77 0.00 36.03 3.99
86 87 3.700130 ATCGCGTAGAAGACAAAAACG 57.300 42.857 5.77 0.00 36.67 3.60
87 88 4.489841 CCGTATCGCGTAGAAGACAAAAAC 60.490 45.833 5.77 0.00 39.32 2.43
108 109 2.285220 CAGAATGACTTAATCCGCACCG 59.715 50.000 0.00 0.00 39.69 4.94
109 110 3.531538 TCAGAATGACTTAATCCGCACC 58.468 45.455 0.00 0.00 42.56 5.01
176 177 7.971168 CACCCGCAATAGTTAAATTTATCAACA 59.029 33.333 8.59 0.00 0.00 3.33
179 180 6.320164 AGCACCCGCAATAGTTAAATTTATCA 59.680 34.615 8.59 0.00 42.27 2.15
191 192 0.881118 AAACACAGCACCCGCAATAG 59.119 50.000 0.00 0.00 42.27 1.73
192 193 1.323412 AAAACACAGCACCCGCAATA 58.677 45.000 0.00 0.00 42.27 1.90
195 196 3.609703 AAAAACACAGCACCCGCA 58.390 50.000 0.00 0.00 42.27 5.69
216 217 2.290832 TGTCAAATGCTGATGCTACCCA 60.291 45.455 0.00 0.00 40.48 4.51
219 220 5.122239 TGTTACTGTCAAATGCTGATGCTAC 59.878 40.000 0.00 0.00 40.48 3.58
220 221 5.244755 TGTTACTGTCAAATGCTGATGCTA 58.755 37.500 0.00 0.00 40.48 3.49
221 222 4.074259 TGTTACTGTCAAATGCTGATGCT 58.926 39.130 0.00 0.00 40.48 3.79
222 223 4.409570 CTGTTACTGTCAAATGCTGATGC 58.590 43.478 0.00 0.00 36.14 3.91
223 224 4.155462 AGCTGTTACTGTCAAATGCTGATG 59.845 41.667 0.00 0.00 36.14 3.07
224 225 4.155462 CAGCTGTTACTGTCAAATGCTGAT 59.845 41.667 5.25 0.00 46.40 2.90
225 226 3.499537 CAGCTGTTACTGTCAAATGCTGA 59.500 43.478 5.25 0.00 46.40 4.26
226 227 3.499537 TCAGCTGTTACTGTCAAATGCTG 59.500 43.478 14.67 0.00 45.31 4.41
227 228 3.743521 TCAGCTGTTACTGTCAAATGCT 58.256 40.909 14.67 0.00 38.84 3.79
228 229 4.488126 TTCAGCTGTTACTGTCAAATGC 57.512 40.909 14.67 0.00 38.84 3.56
229 230 6.304356 TCTTTCAGCTGTTACTGTCAAATG 57.696 37.500 14.67 0.00 38.84 2.32
235 236 5.428253 TCACTTTCTTTCAGCTGTTACTGT 58.572 37.500 14.67 2.95 38.84 3.55
241 242 4.016444 TGGTTTCACTTTCTTTCAGCTGT 58.984 39.130 14.67 0.00 0.00 4.40
288 289 9.728100 TTCAAGAATAAAATCCCCCATTCTTAT 57.272 29.630 7.80 0.00 42.79 1.73
290 291 8.321353 GTTTCAAGAATAAAATCCCCCATTCTT 58.679 33.333 3.25 3.25 44.53 2.52
292 293 6.756542 CGTTTCAAGAATAAAATCCCCCATTC 59.243 38.462 0.00 0.00 0.00 2.67
296 297 4.430007 GCGTTTCAAGAATAAAATCCCCC 58.570 43.478 0.00 0.00 0.00 5.40
306 307 2.076863 CTTCCTCGGCGTTTCAAGAAT 58.923 47.619 6.85 0.00 0.00 2.40
309 310 0.602905 ACCTTCCTCGGCGTTTCAAG 60.603 55.000 6.85 5.30 0.00 3.02
311 312 1.005394 GACCTTCCTCGGCGTTTCA 60.005 57.895 6.85 0.00 0.00 2.69
312 313 0.320508 AAGACCTTCCTCGGCGTTTC 60.321 55.000 6.85 0.00 0.00 2.78
313 314 0.108019 AAAGACCTTCCTCGGCGTTT 59.892 50.000 6.85 0.00 0.00 3.60
314 315 0.602905 CAAAGACCTTCCTCGGCGTT 60.603 55.000 6.85 0.00 0.00 4.84
315 316 1.004918 CAAAGACCTTCCTCGGCGT 60.005 57.895 6.85 0.00 0.00 5.68
316 317 1.741770 CCAAAGACCTTCCTCGGCG 60.742 63.158 0.00 0.00 0.00 6.46
317 318 2.041115 GCCAAAGACCTTCCTCGGC 61.041 63.158 0.00 0.00 0.00 5.54
318 319 0.250727 TTGCCAAAGACCTTCCTCGG 60.251 55.000 0.00 0.00 0.00 4.63
319 320 1.604604 TTTGCCAAAGACCTTCCTCG 58.395 50.000 0.00 0.00 0.00 4.63
322 323 5.208463 TGTTATTTTGCCAAAGACCTTCC 57.792 39.130 0.00 0.00 0.00 3.46
323 324 6.512297 TCTTGTTATTTTGCCAAAGACCTTC 58.488 36.000 0.00 0.00 0.00 3.46
324 325 6.478512 TCTTGTTATTTTGCCAAAGACCTT 57.521 33.333 0.00 0.00 0.00 3.50
325 326 6.670695 ATCTTGTTATTTTGCCAAAGACCT 57.329 33.333 0.00 0.00 0.00 3.85
326 327 7.728847 AAATCTTGTTATTTTGCCAAAGACC 57.271 32.000 0.00 0.00 0.00 3.85
327 328 9.437045 CAAAAATCTTGTTATTTTGCCAAAGAC 57.563 29.630 0.00 0.00 38.68 3.01
328 329 9.171877 ACAAAAATCTTGTTATTTTGCCAAAGA 57.828 25.926 9.42 0.00 44.08 2.52
329 330 9.786105 AACAAAAATCTTGTTATTTTGCCAAAG 57.214 25.926 9.42 0.00 44.08 2.77
433 439 0.253327 GACTGGGAAGTTGGGCTAGG 59.747 60.000 0.00 0.00 0.00 3.02
470 476 1.670406 GAGACTGTGTGCTGGCTGG 60.670 63.158 0.00 0.00 31.64 4.85
476 575 1.583986 GAGCGAGAGACTGTGTGCT 59.416 57.895 0.00 0.00 34.96 4.40
477 576 1.445238 GGAGCGAGAGACTGTGTGC 60.445 63.158 0.00 0.00 0.00 4.57
478 577 0.170116 GAGGAGCGAGAGACTGTGTG 59.830 60.000 0.00 0.00 0.00 3.82
479 578 0.037590 AGAGGAGCGAGAGACTGTGT 59.962 55.000 0.00 0.00 0.00 3.72
480 579 1.132262 GAAGAGGAGCGAGAGACTGTG 59.868 57.143 0.00 0.00 0.00 3.66
481 580 1.459450 GAAGAGGAGCGAGAGACTGT 58.541 55.000 0.00 0.00 0.00 3.55
483 582 0.329931 TGGAAGAGGAGCGAGAGACT 59.670 55.000 0.00 0.00 0.00 3.24
484 583 0.454196 GTGGAAGAGGAGCGAGAGAC 59.546 60.000 0.00 0.00 0.00 3.36
485 584 0.329931 AGTGGAAGAGGAGCGAGAGA 59.670 55.000 0.00 0.00 0.00 3.10
486 585 0.738389 GAGTGGAAGAGGAGCGAGAG 59.262 60.000 0.00 0.00 0.00 3.20
517 669 1.226262 GAGGAGAGGAGCGAGACCT 59.774 63.158 0.00 0.00 40.80 3.85
533 685 1.612156 CGAACGAGCTCTGAACTGAG 58.388 55.000 12.85 4.71 37.16 3.35
568 720 1.572447 CGCGTCTCCTAGCTCTAGC 59.428 63.158 0.00 0.00 42.49 3.42
569 721 1.572447 GCGCGTCTCCTAGCTCTAG 59.428 63.158 8.43 0.00 0.00 2.43
570 722 1.892862 GGCGCGTCTCCTAGCTCTA 60.893 63.158 8.43 0.00 0.00 2.43
571 723 3.213402 GGCGCGTCTCCTAGCTCT 61.213 66.667 8.43 0.00 0.00 4.09
572 724 4.615834 CGGCGCGTCTCCTAGCTC 62.616 72.222 9.90 0.00 0.00 4.09
607 769 2.687200 AGGTGCCGGTGCCTATGA 60.687 61.111 15.76 0.00 36.33 2.15
609 771 3.480133 GGAGGTGCCGGTGCCTAT 61.480 66.667 17.00 0.00 34.81 2.57
673 852 1.142748 CGCTACTCCTGAAGGCTGG 59.857 63.158 0.00 0.00 34.44 4.85
680 859 1.439228 GATGCTGCGCTACTCCTGA 59.561 57.895 9.73 0.00 0.00 3.86
711 890 1.893808 CTGCCAGCCAACGACTGTT 60.894 57.895 0.00 0.00 39.43 3.16
713 892 1.572085 CTTCTGCCAGCCAACGACTG 61.572 60.000 0.00 0.00 34.82 3.51
714 893 1.302033 CTTCTGCCAGCCAACGACT 60.302 57.895 0.00 0.00 0.00 4.18
715 894 2.970974 GCTTCTGCCAGCCAACGAC 61.971 63.158 0.00 0.00 33.21 4.34
716 895 2.669569 GCTTCTGCCAGCCAACGA 60.670 61.111 0.00 0.00 33.21 3.85
748 956 1.522580 GCCGAATCCTGACTCCAGC 60.523 63.158 0.00 0.00 39.07 4.85
750 958 1.667154 CGAGCCGAATCCTGACTCCA 61.667 60.000 0.00 0.00 0.00 3.86
755 963 2.184322 GTGCGAGCCGAATCCTGA 59.816 61.111 0.00 0.00 0.00 3.86
756 964 3.257561 CGTGCGAGCCGAATCCTG 61.258 66.667 0.00 0.00 0.00 3.86
793 1007 0.816373 GACCTCCTCACTCCGGTAAC 59.184 60.000 0.00 0.00 0.00 2.50
794 1008 0.324091 GGACCTCCTCACTCCGGTAA 60.324 60.000 0.00 0.00 0.00 2.85
796 1010 2.037527 GGACCTCCTCACTCCGGT 59.962 66.667 0.00 0.00 0.00 5.28
843 1057 1.896660 GCGTCTTTGCCCTCCAACA 60.897 57.895 0.00 0.00 31.97 3.33
852 1066 1.607148 ACTAAACCTTGGCGTCTTTGC 59.393 47.619 0.00 0.00 0.00 3.68
853 1067 3.304458 GGAACTAAACCTTGGCGTCTTTG 60.304 47.826 0.00 0.00 0.00 2.77
854 1068 2.882761 GGAACTAAACCTTGGCGTCTTT 59.117 45.455 0.00 0.00 0.00 2.52
855 1069 2.501261 GGAACTAAACCTTGGCGTCTT 58.499 47.619 0.00 0.00 0.00 3.01
856 1070 1.271217 GGGAACTAAACCTTGGCGTCT 60.271 52.381 0.00 0.00 0.00 4.18
863 1080 7.973402 AGCAAATAATTTGGGAACTAAACCTT 58.027 30.769 0.00 0.00 40.94 3.50
871 1088 7.765819 AGCAATAGAAGCAAATAATTTGGGAAC 59.234 33.333 0.00 0.00 40.94 3.62
906 1124 7.320399 TGTAATCGACACTGAATCAACTACAT 58.680 34.615 0.00 0.00 31.20 2.29
907 1125 6.683715 TGTAATCGACACTGAATCAACTACA 58.316 36.000 0.00 0.00 31.20 2.74
968 1186 4.074259 TGCAAGCAAACTGTAGATGACAT 58.926 39.130 0.00 0.00 37.45 3.06
974 1192 4.022935 CCAAATCTGCAAGCAAACTGTAGA 60.023 41.667 0.00 0.00 0.00 2.59
996 1214 4.504858 TCGTAGCCTTTCTCTTCATTTCC 58.495 43.478 0.00 0.00 0.00 3.13
1012 1230 6.521133 GCATAAAAATCATGCATACTCGTAGC 59.479 38.462 0.00 0.00 46.47 3.58
1057 1275 3.147595 CTCGACATCGGCAGGGGA 61.148 66.667 0.73 0.00 40.29 4.81
1071 1289 2.747855 GGGGCAAGTTCAGGCTCG 60.748 66.667 0.00 0.00 0.00 5.03
1111 1329 4.646945 TGTGCTCACAACAATTAAGGGAAA 59.353 37.500 0.00 0.00 38.56 3.13
1120 1338 0.670162 GGCACTGTGCTCACAACAAT 59.330 50.000 29.54 0.00 44.28 2.71
1124 1342 1.227943 GGAGGCACTGTGCTCACAA 60.228 57.895 29.54 0.00 44.28 3.33
1187 1405 3.251571 GGTCGGTTTGTACTCTCATCAC 58.748 50.000 0.00 0.00 0.00 3.06
1248 1466 4.582869 TCTTGTCTCCAATGTCATCCTTG 58.417 43.478 0.00 0.00 0.00 3.61
1252 1470 5.936956 AGAAGTTCTTGTCTCCAATGTCATC 59.063 40.000 0.00 0.00 0.00 2.92
1350 1568 8.021955 AGTACACTATAAACGGCACTAAAAAC 57.978 34.615 0.00 0.00 0.00 2.43
1382 1602 8.339344 TGCATCAAGAAATTAGATCAGTGAAA 57.661 30.769 0.00 0.00 0.00 2.69
1394 1614 9.582431 CAAGAAATCTACATGCATCAAGAAATT 57.418 29.630 10.70 9.21 0.00 1.82
1512 1732 6.989155 ATCTGCAAACCATGATAATCCAAT 57.011 33.333 0.00 0.00 0.00 3.16
1555 1775 6.613699 TCATATTTGAAGCCCCATCATAACT 58.386 36.000 0.00 0.00 0.00 2.24
1676 1896 2.744202 GGACTACATTGAGCAACAGTGG 59.256 50.000 10.08 0.00 39.93 4.00
1699 1919 8.798859 ATACAGTTGAAGAAATCAGCAATAGT 57.201 30.769 0.00 0.00 41.36 2.12
1762 1982 1.334869 GGCCAGTAATGCATCTTTCCG 59.665 52.381 0.00 0.00 0.00 4.30
1804 2024 6.726490 AATCCTTCCATTCTCCATCAAATG 57.274 37.500 0.00 0.00 33.57 2.32
2035 2255 9.552114 GTTTATTGAGAACAACATGATGAAGAG 57.448 33.333 10.29 0.00 38.90 2.85
2037 2257 9.903682 AAGTTTATTGAGAACAACATGATGAAG 57.096 29.630 10.29 0.00 38.90 3.02
2068 2288 6.449635 TTGTGATAGATAATTTGTGGTGCC 57.550 37.500 0.00 0.00 0.00 5.01
2117 2338 1.469703 TCAAATGCATGGCTTCGACAG 59.530 47.619 0.00 0.00 0.00 3.51
2121 2342 3.431922 AAGATCAAATGCATGGCTTCG 57.568 42.857 0.00 0.00 0.00 3.79
2166 2387 1.221635 CCCACCCATTGTCCCTCATA 58.778 55.000 0.00 0.00 0.00 2.15
2284 2505 3.132467 AGTCGGGTCACCTTATTCTTAGC 59.868 47.826 0.00 0.00 33.28 3.09
2301 2522 5.519206 GCTAACCTTGTAATAGTGAAGTCGG 59.481 44.000 0.00 0.00 0.00 4.79
2391 2612 9.739276 AGACAAGAAATACAATCCAATAACTCA 57.261 29.630 0.00 0.00 0.00 3.41
2519 2741 3.878778 AGGAATCTCGGAAGGTCAAATG 58.121 45.455 0.00 0.00 0.00 2.32
2532 2754 9.487790 CTTCTCCTAATGTTCATAAGGAATCTC 57.512 37.037 0.00 0.00 37.67 2.75
2619 2843 5.197451 ACCAACTGGAAAGATGTGTGTTTA 58.803 37.500 1.86 0.00 38.94 2.01
2723 2964 3.065233 TCATTTGATACCTCATTGCGCAC 59.935 43.478 11.12 0.00 0.00 5.34
2750 2991 9.903682 GATGTAGCACAGCATTAAATCATTTAT 57.096 29.630 0.00 0.00 34.10 1.40
2765 3006 4.362932 TCTCTTTCTCGATGTAGCACAG 57.637 45.455 0.00 0.00 0.00 3.66
2774 3015 6.634805 TGCTTCTAAACATCTCTTTCTCGAT 58.365 36.000 0.00 0.00 0.00 3.59
2788 3029 9.745880 ATTTGATCATCATGAATGCTTCTAAAC 57.254 29.630 0.00 0.00 35.17 2.01
2821 3071 4.157656 TCACGCCTTAATTTCTGGAATTGG 59.842 41.667 4.13 0.00 38.40 3.16
2994 3258 7.492344 CACCTCCAAACCAAAATATAGAAATGC 59.508 37.037 0.00 0.00 0.00 3.56
3085 3357 6.895756 ACCAATACATCAAGTACTAGACTGGA 59.104 38.462 0.00 0.00 42.62 3.86
3086 3358 6.980978 CACCAATACATCAAGTACTAGACTGG 59.019 42.308 0.00 0.00 38.87 4.00
3087 3359 7.489435 CACACCAATACATCAAGTACTAGACTG 59.511 40.741 0.00 0.00 38.87 3.51
3088 3360 7.178628 ACACACCAATACATCAAGTACTAGACT 59.821 37.037 0.00 0.00 41.56 3.24
3089 3361 7.275779 CACACACCAATACATCAAGTACTAGAC 59.724 40.741 0.00 0.00 35.05 2.59
3181 3454 5.122519 TCTGTCAAACATGTGCTCAAAGTA 58.877 37.500 0.00 0.00 0.00 2.24
3183 3456 4.556942 TCTGTCAAACATGTGCTCAAAG 57.443 40.909 0.00 0.00 0.00 2.77
3200 3473 7.480760 ACCAATTTAAACAGCCAATATCTGT 57.519 32.000 0.00 0.00 45.83 3.41
3256 3533 5.789643 TGCTGGAATTTGCTAGAGTTTTT 57.210 34.783 0.00 0.00 0.00 1.94
3261 3538 3.015327 AGCTTGCTGGAATTTGCTAGAG 58.985 45.455 11.96 4.95 34.83 2.43
3265 3542 1.274447 GGAAGCTTGCTGGAATTTGCT 59.726 47.619 11.19 0.00 0.00 3.91
3266 3543 1.001181 TGGAAGCTTGCTGGAATTTGC 59.999 47.619 19.34 0.00 0.00 3.68
3267 3544 3.604875 ATGGAAGCTTGCTGGAATTTG 57.395 42.857 19.34 0.00 0.00 2.32
3291 3570 9.264719 CCAAATAAGCTCAAAATTTCCCATATC 57.735 33.333 0.00 0.00 0.00 1.63
3343 3909 1.806542 CACTGTAGACATGCCAACACC 59.193 52.381 0.00 0.00 0.00 4.16
3348 3914 0.324614 CCCACACTGTAGACATGCCA 59.675 55.000 0.00 0.00 0.00 4.92
3444 4109 2.833631 AACCAACGGATTCTTCGTCT 57.166 45.000 0.00 0.00 40.18 4.18
3455 4120 3.578688 ACGTAGTAGCTTAAACCAACGG 58.421 45.455 12.52 0.00 41.94 4.44
3472 4137 7.101054 ACCTGCAAGATCTTGTAAAATACGTA 58.899 34.615 30.88 0.00 42.31 3.57
3473 4138 5.938125 ACCTGCAAGATCTTGTAAAATACGT 59.062 36.000 30.88 15.26 42.31 3.57
3474 4139 6.422776 ACCTGCAAGATCTTGTAAAATACG 57.577 37.500 30.88 16.45 42.31 3.06
3475 4140 8.494016 AGTACCTGCAAGATCTTGTAAAATAC 57.506 34.615 30.88 25.28 42.31 1.89
3513 4178 9.875708 AGATGAGGAATCAGAACTATAGTAAGT 57.124 33.333 5.65 0.00 37.81 2.24
3545 4210 7.942341 GGTAAAGGATATGGTGTGATTTCCATA 59.058 37.037 6.40 6.40 46.37 2.74
3607 4272 5.341617 GTGGAGTCTACTACATGTGTAAGC 58.658 45.833 9.11 5.09 39.36 3.09
3630 4295 5.025986 ACGGTGTTAGCAAGTAATTTTCG 57.974 39.130 0.00 0.00 0.00 3.46
3676 4341 0.533755 ATAAGCGCCCTCACTGCATC 60.534 55.000 2.29 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.