Multiple sequence alignment - TraesCS1D01G208500

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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 TraesCS1D01G208500 chr1D 100.000 7565 0 0 1 7565 294470962 294463398 0.000000e+00 13971.0
1 TraesCS1D01G208500 chr1B 95.549 5392 183 32 1514 6869 396150291 396144921 0.000000e+00 8575.0
2 TraesCS1D01G208500 chr1B 91.579 1235 70 18 1 1224 396160496 396159285 0.000000e+00 1674.0
3 TraesCS1D01G208500 chr1B 84.091 704 75 19 6890 7563 396144928 396144232 0.000000e+00 645.0
4 TraesCS1D01G208500 chr1B 88.344 326 11 5 1225 1525 396159221 396158898 4.310000e-97 366.0
5 TraesCS1D01G208500 chr1A 94.123 2348 106 16 1464 3792 367436786 367434452 0.000000e+00 3542.0
6 TraesCS1D01G208500 chr1A 96.282 1533 50 6 4202 5730 367434174 367432645 0.000000e+00 2508.0
7 TraesCS1D01G208500 chr1A 89.666 987 57 22 5732 6703 367432608 367431652 0.000000e+00 1216.0
8 TraesCS1D01G208500 chr1A 84.392 897 79 27 6721 7563 367431664 367430775 0.000000e+00 824.0
9 TraesCS1D01G208500 chr1A 87.676 568 27 14 668 1225 367438229 367437695 8.340000e-174 621.0
10 TraesCS1D01G208500 chr1A 96.390 277 9 1 3893 4168 367434451 367434175 8.950000e-124 455.0
11 TraesCS1D01G208500 chr1A 91.322 242 14 2 1225 1459 367437468 367437227 2.630000e-84 324.0
12 TraesCS1D01G208500 chr7A 77.076 855 133 44 1499 2308 30810944 30811780 1.170000e-117 435.0
13 TraesCS1D01G208500 chr7A 80.576 556 84 15 2992 3542 183715151 183714615 2.540000e-109 407.0
14 TraesCS1D01G208500 chr7A 89.474 247 25 1 2987 3233 30812608 30812853 2.050000e-80 311.0
15 TraesCS1D01G208500 chr7A 82.286 350 42 13 4452 4783 30814039 30814386 1.240000e-72 285.0
16 TraesCS1D01G208500 chr7A 82.203 354 41 12 4450 4783 183713733 183713382 1.240000e-72 285.0
17 TraesCS1D01G208500 chr7A 91.736 121 9 1 3914 4034 183714215 183714096 4.700000e-37 167.0
18 TraesCS1D01G208500 chr7A 93.694 111 6 1 3432 3542 30813065 30813174 1.690000e-36 165.0
19 TraesCS1D01G208500 chr7A 83.436 163 20 5 3870 4031 30813532 30813688 2.200000e-30 145.0
20 TraesCS1D01G208500 chr7A 87.500 64 8 0 6088 6151 90295579 90295642 2.930000e-09 75.0
21 TraesCS1D01G208500 chr7A 87.500 64 8 0 6088 6151 90305259 90305322 2.930000e-09 75.0
22 TraesCS1D01G208500 chr7D 81.149 557 78 14 2992 3542 179185817 179185282 9.080000e-114 422.0
23 TraesCS1D01G208500 chr7D 75.924 839 155 37 1499 2308 179187445 179186625 3.310000e-103 387.0
24 TraesCS1D01G208500 chr7D 89.879 247 24 1 2987 3233 30306488 30306733 4.410000e-82 316.0
25 TraesCS1D01G208500 chr7D 82.571 350 41 13 4452 4783 30307921 30308268 2.670000e-74 291.0
26 TraesCS1D01G208500 chr7D 81.918 365 43 14 4450 4794 179184410 179184049 3.450000e-73 287.0
27 TraesCS1D01G208500 chr7D 89.630 135 11 2 3408 3542 30306924 30307055 1.310000e-37 169.0
28 TraesCS1D01G208500 chr7D 85.366 164 17 6 3878 4034 179184925 179184762 6.070000e-36 163.0
29 TraesCS1D01G208500 chr7D 82.822 163 21 5 3870 4031 30307413 30307569 1.020000e-28 139.0
30 TraesCS1D01G208500 chr7D 89.062 64 7 0 6088 6151 88892275 88892338 6.290000e-11 80.5
31 TraesCS1D01G208500 chr7B 80.357 560 80 18 2992 3542 145374455 145373917 1.530000e-106 398.0
32 TraesCS1D01G208500 chr7B 81.769 373 46 15 4450 4802 145373044 145372674 7.420000e-75 292.0
33 TraesCS1D01G208500 chr7B 93.333 105 7 0 3930 4034 145373505 145373401 1.020000e-33 156.0
34 TraesCS1D01G208500 chr7B 87.500 64 8 0 6088 6151 39635896 39635833 2.930000e-09 75.0
35 TraesCS1D01G208500 chr4A 89.879 247 24 1 2987 3233 698429252 698429497 4.410000e-82 316.0
36 TraesCS1D01G208500 chr4A 82.808 349 41 11 4452 4783 698430682 698431028 2.060000e-75 294.0
37 TraesCS1D01G208500 chr4A 95.192 104 5 0 3432 3535 698429710 698429813 1.690000e-36 165.0
38 TraesCS1D01G208500 chr4A 84.049 163 19 5 3870 4031 698430177 698430333 4.730000e-32 150.0
39 TraesCS1D01G208500 chr5D 86.047 86 11 1 7457 7542 17504705 17504789 2.910000e-14 91.6
40 TraesCS1D01G208500 chr5B 91.228 57 5 0 7483 7539 36187501 36187557 2.260000e-10 78.7


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 TraesCS1D01G208500 chr1D 294463398 294470962 7564 True 13971.000000 13971 100.000000 1 7565 1 chr1D.!!$R1 7564
1 TraesCS1D01G208500 chr1B 396144232 396150291 6059 True 4610.000000 8575 89.820000 1514 7563 2 chr1B.!!$R1 6049
2 TraesCS1D01G208500 chr1B 396158898 396160496 1598 True 1020.000000 1674 89.961500 1 1525 2 chr1B.!!$R2 1524
3 TraesCS1D01G208500 chr1A 367430775 367438229 7454 True 1355.714286 3542 91.407286 668 7563 7 chr1A.!!$R1 6895
4 TraesCS1D01G208500 chr7A 183713382 183715151 1769 True 286.333333 407 84.838333 2992 4783 3 chr7A.!!$R1 1791
5 TraesCS1D01G208500 chr7A 30810944 30814386 3442 False 268.200000 435 85.193200 1499 4783 5 chr7A.!!$F3 3284
6 TraesCS1D01G208500 chr7D 179184049 179187445 3396 True 314.750000 422 81.089250 1499 4794 4 chr7D.!!$R1 3295
7 TraesCS1D01G208500 chr7D 30306488 30308268 1780 False 228.750000 316 86.225500 2987 4783 4 chr7D.!!$F2 1796
8 TraesCS1D01G208500 chr7B 145372674 145374455 1781 True 282.000000 398 85.153000 2992 4802 3 chr7B.!!$R2 1810
9 TraesCS1D01G208500 chr4A 698429252 698431028 1776 False 231.250000 316 87.982000 2987 4783 4 chr4A.!!$F1 1796

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
120 121 0.107945 AGCTCGTGGGAAATCTGCTC 60.108 55.000 0.00 0.0 0.00 4.26 F
157 158 0.322456 TCTGAAATTGCTGGTCGGGG 60.322 55.000 0.00 0.0 0.00 5.73 F
225 226 0.400213 TTCAACTGATCGGTGGCCTT 59.600 50.000 8.25 0.0 0.00 4.35 F
981 993 0.613292 GCCTCAGTCCTCAGTCCTCA 60.613 60.000 0.00 0.0 0.00 3.86 F
1118 1130 0.938637 CGACTCATCAGCGCCAGATC 60.939 60.000 2.29 0.0 0.00 2.75 F
2107 2827 1.251251 GCCTGCTGAACAAATGACCT 58.749 50.000 0.00 0.0 0.00 3.85 F
2490 3231 1.470098 CCAGTGCTATGGTTTGCTGTC 59.530 52.381 0.02 0.0 35.47 3.51 F
2536 3287 2.507407 TCCCTGGAGCCAAATGTTAC 57.493 50.000 0.00 0.0 0.00 2.50 F
2575 3327 3.253677 CGTTAACATTGCCCCAAACTACA 59.746 43.478 6.39 0.0 0.00 2.74 F
3714 4821 3.426787 TTAAGGTCGGGCATCAAGAAA 57.573 42.857 0.00 0.0 0.00 2.52 F
4121 5285 5.139435 TCATGACTTGTTGACTTCGATCT 57.861 39.130 0.00 0.0 0.00 2.75 F
5814 7131 1.588674 TGTAAACTTCTGTGGGTGCG 58.411 50.000 0.00 0.0 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1100 1112 0.599728 GGATCTGGCGCTGATGAGTC 60.600 60.000 18.09 7.25 0.00 3.36 R
2104 2824 0.829333 ATCGAGCAGCAAGATGAGGT 59.171 50.000 0.00 0.00 0.00 3.85 R
2107 2827 2.678471 TGAATCGAGCAGCAAGATGA 57.322 45.000 0.00 0.00 0.00 2.92 R
2536 3287 0.038526 ACGTAAAGACAGCTGGACCG 60.039 55.000 19.93 12.92 0.00 4.79 R
2807 3817 0.608130 TGTGCCTACAGTGCCTACAG 59.392 55.000 0.00 0.00 31.91 2.74 R
3822 4948 4.690748 TCATCAGTTCGATTCGCTCTTTTT 59.309 37.500 0.00 0.00 29.21 1.94 R
4150 5314 2.996621 AGCACAGATCGCTCAACTTTAC 59.003 45.455 0.00 0.00 33.35 2.01 R
4160 5358 5.176590 CCTTAATCTCTTAAGCACAGATCGC 59.823 44.000 5.81 0.00 41.63 4.58 R
4198 5396 5.357878 GTGAAGGCATTTGGTTCAGATGATA 59.642 40.000 3.11 0.00 30.94 2.15 R
5330 6603 2.860735 AGACGATGATAAACTTCTGCGC 59.139 45.455 0.00 0.00 0.00 6.09 R
5897 7217 5.827797 ACATGCAAAGAAGTAAGAGAAACCA 59.172 36.000 0.00 0.00 0.00 3.67 R
7477 8891 0.445436 CTCGTGCTTGATGCTTGACC 59.555 55.000 0.00 0.00 43.37 4.02 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
32 33 2.165641 ACAACAGCTGCATGATCAATGG 59.834 45.455 22.77 0.00 36.71 3.16
48 49 0.178909 ATGGTTGGGGTGGATTTGCA 60.179 50.000 0.00 0.00 0.00 4.08
55 56 1.523154 GGGTGGATTTGCACGCTTCA 61.523 55.000 11.18 0.00 0.00 3.02
58 59 0.447406 TGGATTTGCACGCTTCATCG 59.553 50.000 0.00 0.00 0.00 3.84
59 60 0.726827 GGATTTGCACGCTTCATCGA 59.273 50.000 0.00 0.00 0.00 3.59
83 84 0.831307 GGCTTGGGTAAGGTCGATCT 59.169 55.000 0.00 0.00 34.40 2.75
87 88 3.118884 GCTTGGGTAAGGTCGATCTGTTA 60.119 47.826 0.00 0.00 34.40 2.41
114 115 2.859165 TTCTTGAGCTCGTGGGAAAT 57.141 45.000 9.64 0.00 0.00 2.17
120 121 0.107945 AGCTCGTGGGAAATCTGCTC 60.108 55.000 0.00 0.00 0.00 4.26
130 131 2.222819 GGAAATCTGCTCGTTGTAAGCG 60.223 50.000 0.00 0.00 42.83 4.68
141 142 1.912110 GTTGTAAGCGAGCTACGTCTG 59.088 52.381 0.00 0.00 44.60 3.51
156 157 0.804989 GTCTGAAATTGCTGGTCGGG 59.195 55.000 0.00 0.00 0.00 5.14
157 158 0.322456 TCTGAAATTGCTGGTCGGGG 60.322 55.000 0.00 0.00 0.00 5.73
170 171 2.358247 CGGGGGTGACTTGGTTCG 60.358 66.667 0.00 0.00 0.00 3.95
174 175 2.315386 GGGTGACTTGGTTCGCGTC 61.315 63.158 5.77 0.09 0.00 5.19
225 226 0.400213 TTCAACTGATCGGTGGCCTT 59.600 50.000 8.25 0.00 0.00 4.35
299 300 3.109612 ATCGTCTCGCTCCGAACCG 62.110 63.158 0.00 0.00 36.57 4.44
316 317 2.668632 GGATCTCACCCCGTGCAA 59.331 61.111 0.00 0.00 32.98 4.08
323 324 0.953471 TCACCCCGTGCAAGATTTCG 60.953 55.000 0.00 0.00 32.98 3.46
327 328 1.298157 CCCGTGCAAGATTTCGAGCA 61.298 55.000 0.00 0.00 34.10 4.26
334 335 3.174375 GCAAGATTTCGAGCAATTCACC 58.826 45.455 0.00 0.00 0.00 4.02
357 358 1.399744 ATGAATCGCCCCTAGCACGA 61.400 55.000 0.00 3.02 44.04 4.35
367 368 3.810743 GCCCCTAGCACGATGGATTTTAT 60.811 47.826 0.00 0.00 42.97 1.40
369 370 5.178797 CCCCTAGCACGATGGATTTTATAG 58.821 45.833 0.00 0.00 0.00 1.31
372 373 6.758886 CCCTAGCACGATGGATTTTATAGATC 59.241 42.308 0.00 0.00 0.00 2.75
373 374 7.323420 CCTAGCACGATGGATTTTATAGATCA 58.677 38.462 0.00 0.00 0.00 2.92
378 379 8.128582 GCACGATGGATTTTATAGATCAACAAA 58.871 33.333 0.00 0.00 0.00 2.83
394 395 9.381033 AGATCAACAAAGAAAGTATGAGATCAG 57.619 33.333 0.00 0.00 34.62 2.90
415 416 1.406341 CGGATTGTAATGTCCCGTGGT 60.406 52.381 0.00 0.00 35.83 4.16
460 462 2.840651 GTGAGAGGAGAAAGGGGATCAA 59.159 50.000 0.00 0.00 0.00 2.57
473 475 4.629122 AGGGGATCAATTGAGAAGAGAGA 58.371 43.478 14.54 0.00 0.00 3.10
579 589 5.882557 GGTGAGGATTTGCTTCTCAATTCTA 59.117 40.000 0.00 0.00 38.97 2.10
581 591 7.094205 GGTGAGGATTTGCTTCTCAATTCTAAA 60.094 37.037 0.00 0.00 38.97 1.85
608 619 8.908786 TTTTTAGAAGAGCTTCTCAATTCTGA 57.091 30.769 15.47 0.00 46.13 3.27
615 626 3.937706 AGCTTCTCAATTCTGATCAACGG 59.062 43.478 0.00 0.00 0.00 4.44
623 634 6.414732 TCAATTCTGATCAACGGTAAATCCT 58.585 36.000 0.00 0.00 0.00 3.24
655 666 6.257193 AGGCGTTTAACGATAAATCCTAACAG 59.743 38.462 22.15 0.00 46.05 3.16
663 674 6.281405 ACGATAAATCCTAACAGTGGCTTAG 58.719 40.000 0.00 0.00 0.00 2.18
665 676 6.642950 CGATAAATCCTAACAGTGGCTTAGAG 59.357 42.308 0.00 0.00 0.00 2.43
666 677 3.828875 ATCCTAACAGTGGCTTAGAGC 57.171 47.619 0.00 0.00 41.46 4.09
786 798 5.337169 GCTGGACTCTAGTTCATCTTCAGTT 60.337 44.000 0.00 0.00 32.18 3.16
810 822 3.311871 GCTGCATGTTCAGGTTCAGATAG 59.688 47.826 0.00 0.00 34.74 2.08
811 823 4.511527 CTGCATGTTCAGGTTCAGATAGT 58.488 43.478 0.00 0.00 0.00 2.12
812 824 5.664457 CTGCATGTTCAGGTTCAGATAGTA 58.336 41.667 0.00 0.00 0.00 1.82
889 901 1.548719 GTTGAACCCTAACCCCATTGC 59.451 52.381 0.00 0.00 0.00 3.56
962 974 4.335647 AACCCTCCAGTGCTGCCG 62.336 66.667 0.00 0.00 0.00 5.69
975 987 3.368190 CTGCCGCCTCAGTCCTCAG 62.368 68.421 0.00 0.00 0.00 3.35
976 988 3.386237 GCCGCCTCAGTCCTCAGT 61.386 66.667 0.00 0.00 0.00 3.41
977 989 2.888863 CCGCCTCAGTCCTCAGTC 59.111 66.667 0.00 0.00 0.00 3.51
978 990 2.716017 CCGCCTCAGTCCTCAGTCC 61.716 68.421 0.00 0.00 0.00 3.85
979 991 1.680651 CGCCTCAGTCCTCAGTCCT 60.681 63.158 0.00 0.00 0.00 3.85
980 992 1.662438 CGCCTCAGTCCTCAGTCCTC 61.662 65.000 0.00 0.00 0.00 3.71
981 993 0.613292 GCCTCAGTCCTCAGTCCTCA 60.613 60.000 0.00 0.00 0.00 3.86
1022 1034 2.982130 GATCACGGCACAGACCCT 59.018 61.111 0.00 0.00 0.00 4.34
1039 1051 2.362503 TCGACATCCTGGGCGAGT 60.363 61.111 0.00 0.00 0.00 4.18
1085 1097 2.358267 CGCAGAACGGTAATACTCCTCT 59.642 50.000 0.00 0.00 38.44 3.69
1100 1112 1.431440 CTCTTCTCCTGCTCGTCCG 59.569 63.158 0.00 0.00 0.00 4.79
1118 1130 0.938637 CGACTCATCAGCGCCAGATC 60.939 60.000 2.29 0.00 0.00 2.75
1205 1227 6.083630 GTGTTTAATTGTGCTTCTGCGATTA 58.916 36.000 0.00 0.00 43.34 1.75
1211 1233 2.288763 TGTGCTTCTGCGATTACAGTGA 60.289 45.455 0.00 0.00 43.34 3.41
1341 1597 1.349688 GGTGTGGATGTAGTTCACCCA 59.650 52.381 0.00 0.00 41.58 4.51
1408 1667 8.906636 TCTGTAATCTAATAACGAACAGTGAC 57.093 34.615 0.00 0.00 35.51 3.67
1430 1689 3.430236 CGTTAGATGGTAGTGCATCCACA 60.430 47.826 9.73 0.00 44.53 4.17
1447 1706 9.770097 TGCATCCACAGTAATTTTGAAAATAAA 57.230 25.926 3.26 0.00 0.00 1.40
1495 2190 7.724305 TGGAATGAACTAATTTAGCGTATCC 57.276 36.000 3.28 6.24 0.00 2.59
1527 2222 4.888823 TGGTGGATGATATTGGTGATGTTG 59.111 41.667 0.00 0.00 0.00 3.33
1674 2374 3.131478 CGGGGGTCCATTCGTTGC 61.131 66.667 0.00 0.00 0.00 4.17
1735 2435 4.042809 AGGTTGGTGATGGAACAACATCTA 59.957 41.667 5.06 0.00 44.42 1.98
1756 2456 2.149973 TGTCCTCATAGCTGCAGAGA 57.850 50.000 20.43 3.79 0.00 3.10
1818 2521 5.118990 TCTTCTCTATGAATTTCCCAAGCG 58.881 41.667 0.00 0.00 33.71 4.68
1842 2545 9.227490 GCGTTATGCATACAAATTTACAATGTA 57.773 29.630 5.74 0.00 45.45 2.29
1874 2578 1.992557 ACCAGGGAGCCAATGAACTTA 59.007 47.619 0.00 0.00 0.00 2.24
2104 2824 2.030371 TGTTGCCTGCTGAACAAATGA 58.970 42.857 0.00 0.00 0.00 2.57
2107 2827 1.251251 GCCTGCTGAACAAATGACCT 58.749 50.000 0.00 0.00 0.00 3.85
2126 2846 2.547826 CTCATCTTGCTGCTCGATTCA 58.452 47.619 0.00 0.00 0.00 2.57
2245 2977 3.059884 TCACAGCGACAGTGATTTCTTC 58.940 45.455 0.00 0.00 40.80 2.87
2263 2995 4.637276 TCTTCGCAAATCTGGTAAGTTCA 58.363 39.130 0.00 0.00 0.00 3.18
2301 3033 5.649831 ACTTCAGGTTTCTTAATCATGCCTC 59.350 40.000 0.00 0.00 0.00 4.70
2312 3045 8.055279 TCTTAATCATGCCTCCTTTTTACTTG 57.945 34.615 0.00 0.00 0.00 3.16
2406 3147 6.929049 TGATCAGTGGTGTTTGTTAACTCTAG 59.071 38.462 7.22 0.00 35.24 2.43
2473 3214 5.063204 TGTATTTTGAGGTGTTCTGTCCAG 58.937 41.667 0.00 0.00 0.00 3.86
2490 3231 1.470098 CCAGTGCTATGGTTTGCTGTC 59.530 52.381 0.02 0.00 35.47 3.51
2510 3252 9.031360 TGCTGTCGTCTGATATTTTTATCTAAC 57.969 33.333 0.00 0.00 0.00 2.34
2536 3287 2.507407 TCCCTGGAGCCAAATGTTAC 57.493 50.000 0.00 0.00 0.00 2.50
2575 3327 3.253677 CGTTAACATTGCCCCAAACTACA 59.746 43.478 6.39 0.00 0.00 2.74
2674 3427 5.295540 GGAGAAGTGAAGTATCCAATCAAGC 59.704 44.000 0.00 0.00 0.00 4.01
2807 3817 8.947115 GTTATCTCCTATATTAATGTTGGGCAC 58.053 37.037 11.61 0.00 0.00 5.01
2944 3954 6.204882 ACATGGTTTTCGAGTCCTCTTTAAAG 59.795 38.462 9.04 9.04 0.00 1.85
3421 4466 4.607239 TCAAGAGGACCGAATACCTTACT 58.393 43.478 0.00 0.00 36.57 2.24
3422 4467 5.021458 TCAAGAGGACCGAATACCTTACTT 58.979 41.667 0.00 0.00 36.57 2.24
3425 4470 7.178983 TCAAGAGGACCGAATACCTTACTTTTA 59.821 37.037 0.00 0.00 36.57 1.52
3503 4548 4.335315 CGGTGCTAATGTTGTATTGACCAT 59.665 41.667 0.00 0.00 0.00 3.55
3714 4821 3.426787 TTAAGGTCGGGCATCAAGAAA 57.573 42.857 0.00 0.00 0.00 2.52
3822 4948 9.642327 CATGGTTAAACTGAATTGATGATTTCA 57.358 29.630 0.00 0.00 0.00 2.69
3839 4965 5.851177 TGATTTCAAAAAGAGCGAATCGAAC 59.149 36.000 6.91 0.00 0.00 3.95
3854 4980 6.021939 GCGAATCGAACTGATGATTTCAAAAG 60.022 38.462 6.91 0.00 37.39 2.27
3876 5002 7.642094 AAGGAGCTAATGTATTATTGGGGTA 57.358 36.000 0.00 0.00 0.00 3.69
4121 5285 5.139435 TCATGACTTGTTGACTTCGATCT 57.861 39.130 0.00 0.00 0.00 2.75
4150 5314 8.075574 TGAACTTACTTGTGATTGCAATTGTAG 58.924 33.333 14.33 11.02 0.00 2.74
4160 5358 8.075574 TGTGATTGCAATTGTAGTAAAGTTGAG 58.924 33.333 14.33 0.00 0.00 3.02
4254 5475 8.731605 TGCTTTACGTTTATATGGTTTTCATCA 58.268 29.630 0.00 0.00 37.30 3.07
4362 5611 7.472334 AACAGAAAATTATTGACTCCAGCAT 57.528 32.000 0.00 0.00 0.00 3.79
4392 5641 7.745620 ATCCGTGTTTTTCTGAGAAATAAGT 57.254 32.000 8.64 0.00 0.00 2.24
4603 5858 5.867716 CACTAGTGCGGTTAGTATTTTCTGT 59.132 40.000 10.54 0.00 30.48 3.41
5268 6541 8.974060 TTAAACTTCTTGGTAGACAGTCAATT 57.026 30.769 2.66 0.00 0.00 2.32
5813 7130 3.857010 GCATTGTAAACTTCTGTGGGTGC 60.857 47.826 0.00 0.00 0.00 5.01
5814 7131 1.588674 TGTAAACTTCTGTGGGTGCG 58.411 50.000 0.00 0.00 0.00 5.34
5845 7163 7.947890 AGATTAACCAACCTCCATAAAAGAACA 59.052 33.333 0.00 0.00 0.00 3.18
5846 7164 7.899648 TTAACCAACCTCCATAAAAGAACAA 57.100 32.000 0.00 0.00 0.00 2.83
5897 7217 5.869649 AAGATGCAAACAGTTACCCTTTT 57.130 34.783 0.00 0.00 0.00 2.27
5925 7245 5.168569 TCTCTTACTTCTTTGCATGTACCG 58.831 41.667 0.00 0.00 0.00 4.02
6165 7486 6.903419 AGTTTGACTTAATGCAAAGCTAGAC 58.097 36.000 0.00 0.00 34.95 2.59
6166 7487 6.486657 AGTTTGACTTAATGCAAAGCTAGACA 59.513 34.615 0.00 0.00 34.95 3.41
6169 7490 5.997746 TGACTTAATGCAAAGCTAGACAACT 59.002 36.000 0.00 0.00 0.00 3.16
6171 7492 7.659799 TGACTTAATGCAAAGCTAGACAACTTA 59.340 33.333 0.00 0.00 0.00 2.24
6172 7493 8.567285 ACTTAATGCAAAGCTAGACAACTTAT 57.433 30.769 0.00 0.00 0.00 1.73
6173 7494 9.667107 ACTTAATGCAAAGCTAGACAACTTATA 57.333 29.630 0.00 0.00 0.00 0.98
6290 7612 5.238432 TGTTGCACATCTTCTGTTCGTAAAT 59.762 36.000 0.00 0.00 35.29 1.40
6364 7690 3.127895 GCAACAACCTTGAATATGGCGTA 59.872 43.478 0.00 0.00 0.00 4.42
6448 7774 4.423913 TGGGATGGGATTGTGATTTTTGA 58.576 39.130 0.00 0.00 0.00 2.69
6484 7811 8.149647 ACCAATTTTCATTTCTATTGCAGTTCA 58.850 29.630 0.00 0.00 0.00 3.18
6506 7833 1.933853 CACTGAAGCGGCCATTACTAC 59.066 52.381 2.24 0.00 0.00 2.73
6537 7864 6.261603 GGATTGATGACATGATCAAGCTTACA 59.738 38.462 19.03 0.25 44.56 2.41
6690 8018 6.433847 TTCATGGATATTCCCGTAGAATGT 57.566 37.500 7.90 2.07 45.11 2.71
6691 8019 6.433847 TCATGGATATTCCCGTAGAATGTT 57.566 37.500 7.90 0.00 45.11 2.71
6692 8020 6.230472 TCATGGATATTCCCGTAGAATGTTG 58.770 40.000 7.90 0.00 45.11 3.33
6693 8021 5.623956 TGGATATTCCCGTAGAATGTTGT 57.376 39.130 7.90 0.00 45.11 3.32
6694 8022 6.734502 TGGATATTCCCGTAGAATGTTGTA 57.265 37.500 7.90 0.00 45.11 2.41
6695 8023 6.518493 TGGATATTCCCGTAGAATGTTGTAC 58.482 40.000 7.90 0.00 45.11 2.90
6696 8024 5.632347 GGATATTCCCGTAGAATGTTGTACG 59.368 44.000 13.52 13.52 45.11 3.67
6697 8025 8.818509 TGGATATTCCCGTAGAATGTTGTACGA 61.819 40.741 19.85 4.87 46.23 3.43
6746 8106 7.737869 TGTACAAAAGTGGACCTTATTCTACA 58.262 34.615 0.00 0.00 37.87 2.74
6755 8115 5.183969 GGACCTTATTCTACAAACACCTCC 58.816 45.833 0.00 0.00 0.00 4.30
6768 8129 1.982958 ACACCTCCGAAACTACCCAAT 59.017 47.619 0.00 0.00 0.00 3.16
6811 8173 2.362736 CAACAGCCTGAGTGCACATAT 58.637 47.619 21.04 0.00 0.00 1.78
6834 8196 3.008704 GCTAACCACTCTGAAACCCCTTA 59.991 47.826 0.00 0.00 0.00 2.69
6839 8201 3.328050 CCACTCTGAAACCCCTTACTCTT 59.672 47.826 0.00 0.00 0.00 2.85
6880 8242 1.073319 TTCCCTCCACCCCTGTGAA 60.073 57.895 0.00 0.00 45.76 3.18
6893 8255 1.545651 CCTGTGAACCACCTTCCTTCC 60.546 57.143 0.00 0.00 32.73 3.46
6895 8257 1.780309 TGTGAACCACCTTCCTTCCAT 59.220 47.619 0.00 0.00 32.73 3.41
6906 8268 1.222936 CCTTCCATTGCGAGCTCCT 59.777 57.895 8.47 0.00 0.00 3.69
6950 8329 0.172803 CCTTCTACCTACGTTGCGCT 59.827 55.000 9.73 0.00 0.00 5.92
7047 8426 2.758737 CGTCGCCCTACCCTTCCT 60.759 66.667 0.00 0.00 0.00 3.36
7048 8427 1.454479 CGTCGCCCTACCCTTCCTA 60.454 63.158 0.00 0.00 0.00 2.94
7094 8473 2.416893 GTGCTTTCTTCCTTGTCGGATC 59.583 50.000 0.00 0.00 42.70 3.36
7095 8474 2.038426 TGCTTTCTTCCTTGTCGGATCA 59.962 45.455 0.00 0.00 42.70 2.92
7096 8475 3.074412 GCTTTCTTCCTTGTCGGATCAA 58.926 45.455 0.00 0.00 42.70 2.57
7185 8590 0.690077 AACTACCCACCCTCGATCCC 60.690 60.000 0.00 0.00 0.00 3.85
7249 8654 0.804933 GAAGGTACATGGTCGTCGGC 60.805 60.000 0.00 0.00 0.00 5.54
7306 8712 0.602106 CCGTAGAGTCGCCGGATCTA 60.602 60.000 5.05 3.66 44.41 1.98
7310 8716 0.463295 AGAGTCGCCGGATCTACGAA 60.463 55.000 5.05 0.00 37.60 3.85
7311 8717 0.041135 GAGTCGCCGGATCTACGAAG 60.041 60.000 5.05 0.00 37.60 3.79
7312 8718 0.463295 AGTCGCCGGATCTACGAAGA 60.463 55.000 5.05 0.00 37.60 2.87
7313 8719 0.316854 GTCGCCGGATCTACGAAGAC 60.317 60.000 5.05 5.53 37.60 3.01
7314 8720 0.745486 TCGCCGGATCTACGAAGACA 60.745 55.000 5.05 0.00 33.57 3.41
7328 8734 1.329599 GAAGACAACGCTTTGTTCCGT 59.670 47.619 10.21 0.00 46.43 4.69
7357 8770 3.028969 GCTCAAGCGCCATGGATC 58.971 61.111 18.40 5.66 0.00 3.36
7440 8854 3.733960 CCACGACGACGCTCTCCA 61.734 66.667 7.30 0.00 43.96 3.86
7441 8855 2.202362 CACGACGACGCTCTCCAG 60.202 66.667 7.30 0.00 43.96 3.86
7473 8887 3.426568 GTGCGCCTCCACTCTTGC 61.427 66.667 4.18 0.00 33.02 4.01
7475 8889 2.282783 TGCGCCTCCACTCTTGCTA 61.283 57.895 4.18 0.00 0.00 3.49
7477 8891 1.517257 CGCCTCCACTCTTGCTACG 60.517 63.158 0.00 0.00 0.00 3.51
7563 8978 2.753043 CCATCAGGCCCAGTGCAC 60.753 66.667 9.40 9.40 43.89 4.57
7564 8979 2.034532 CATCAGGCCCAGTGCACA 59.965 61.111 21.04 0.00 43.89 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.339253 TGATCATGCAGCTGTTGTAGT 57.661 42.857 16.64 5.00 0.00 2.73
14 15 2.139323 ACCATTGATCATGCAGCTGT 57.861 45.000 16.64 0.00 0.00 4.40
32 33 1.288752 CGTGCAAATCCACCCCAAC 59.711 57.895 0.00 0.00 32.10 3.77
48 49 1.878522 GCCGATGTCGATGAAGCGT 60.879 57.895 3.62 0.00 43.02 5.07
55 56 0.828022 TTACCCAAGCCGATGTCGAT 59.172 50.000 3.62 0.00 43.02 3.59
58 59 0.252197 ACCTTACCCAAGCCGATGTC 59.748 55.000 0.00 0.00 0.00 3.06
59 60 0.252197 GACCTTACCCAAGCCGATGT 59.748 55.000 0.00 0.00 0.00 3.06
83 84 2.573462 AGCTCAAGAATCTGGCCTAACA 59.427 45.455 3.32 0.00 0.00 2.41
87 88 0.177604 CGAGCTCAAGAATCTGGCCT 59.822 55.000 15.40 0.00 0.00 5.19
120 121 0.905839 GACGTAGCTCGCTTACAACG 59.094 55.000 9.60 9.60 44.19 4.10
130 131 2.349886 CCAGCAATTTCAGACGTAGCTC 59.650 50.000 0.00 0.00 0.00 4.09
135 136 1.148310 CGACCAGCAATTTCAGACGT 58.852 50.000 0.00 0.00 0.00 4.34
141 142 1.304134 ACCCCCGACCAGCAATTTC 60.304 57.895 0.00 0.00 0.00 2.17
156 157 2.280592 ACGCGAACCAAGTCACCC 60.281 61.111 15.93 0.00 0.00 4.61
157 158 2.654912 CGACGCGAACCAAGTCACC 61.655 63.158 15.93 0.00 34.80 4.02
225 226 3.203086 TTTCTCACCGCCATGGCCA 62.203 57.895 30.79 8.56 43.94 5.36
234 235 2.742372 CCCGCCACTTTCTCACCG 60.742 66.667 0.00 0.00 0.00 4.94
299 300 1.450312 CTTGCACGGGGTGAGATCC 60.450 63.158 0.00 0.00 35.23 3.36
316 317 2.932614 CTCGGTGAATTGCTCGAAATCT 59.067 45.455 0.00 0.00 0.00 2.40
323 324 3.060003 CGATTCATCTCGGTGAATTGCTC 60.060 47.826 6.84 0.00 46.02 4.26
327 328 2.213499 GGCGATTCATCTCGGTGAATT 58.787 47.619 6.84 0.00 46.02 2.17
334 335 0.389166 GCTAGGGGCGATTCATCTCG 60.389 60.000 0.00 0.00 41.54 4.04
369 370 8.121708 GCTGATCTCATACTTTCTTTGTTGATC 58.878 37.037 0.00 0.00 0.00 2.92
372 373 6.246449 CGCTGATCTCATACTTTCTTTGTTG 58.754 40.000 0.00 0.00 0.00 3.33
373 374 5.352569 CCGCTGATCTCATACTTTCTTTGTT 59.647 40.000 0.00 0.00 0.00 2.83
378 379 5.163364 ACAATCCGCTGATCTCATACTTTCT 60.163 40.000 0.00 0.00 0.00 2.52
381 382 4.679373 ACAATCCGCTGATCTCATACTT 57.321 40.909 0.00 0.00 0.00 2.24
394 395 0.655733 CACGGGACATTACAATCCGC 59.344 55.000 0.00 0.00 43.96 5.54
415 416 2.524440 ACTCCCTCTCCTGATTCCCATA 59.476 50.000 0.00 0.00 0.00 2.74
460 462 3.699038 CCCTCTCGTTCTCTCTTCTCAAT 59.301 47.826 0.00 0.00 0.00 2.57
473 475 2.951229 AAAATCCACACCCTCTCGTT 57.049 45.000 0.00 0.00 0.00 3.85
594 605 3.686726 ACCGTTGATCAGAATTGAGAAGC 59.313 43.478 0.00 0.00 36.61 3.86
635 646 7.107542 AGCCACTGTTAGGATTTATCGTTAAA 58.892 34.615 1.36 1.36 0.00 1.52
637 648 6.229936 AGCCACTGTTAGGATTTATCGTTA 57.770 37.500 0.00 0.00 0.00 3.18
665 676 4.744136 AAAACTTAAGCGTGTCTAAGGC 57.256 40.909 1.29 0.00 40.06 4.35
766 777 4.796312 GCGAACTGAAGATGAACTAGAGTC 59.204 45.833 0.00 0.00 0.00 3.36
786 798 0.250252 TGAACCTGAACATGCAGCGA 60.250 50.000 0.00 0.00 34.56 4.93
962 974 0.613292 TGAGGACTGAGGACTGAGGC 60.613 60.000 0.00 0.00 0.00 4.70
967 979 1.005450 GGAGAGTGAGGACTGAGGACT 59.995 57.143 0.00 0.00 30.16 3.85
975 987 2.183046 GCAGCGGAGAGTGAGGAC 59.817 66.667 0.00 0.00 0.00 3.85
976 988 3.071206 GGCAGCGGAGAGTGAGGA 61.071 66.667 0.00 0.00 0.00 3.71
977 989 4.504916 CGGCAGCGGAGAGTGAGG 62.505 72.222 0.00 0.00 0.00 3.86
1022 1034 2.362503 ACTCGCCCAGGATGTCGA 60.363 61.111 0.00 0.00 36.97 4.20
1077 1089 1.282447 ACGAGCAGGAGAAGAGGAGTA 59.718 52.381 0.00 0.00 0.00 2.59
1085 1097 1.303398 AGTCGGACGAGCAGGAGAA 60.303 57.895 1.89 0.00 0.00 2.87
1100 1112 0.599728 GGATCTGGCGCTGATGAGTC 60.600 60.000 18.09 7.25 0.00 3.36
1205 1227 2.759114 CTGGCACCCCATCACTGT 59.241 61.111 0.00 0.00 41.21 3.55
1211 1233 1.691219 CAAGTACCTGGCACCCCAT 59.309 57.895 0.00 0.00 41.21 4.00
1341 1597 1.846007 TCACTGGCAACCAAGTTTGT 58.154 45.000 0.00 0.00 30.80 2.83
1408 1667 3.123804 GTGGATGCACTACCATCTAACG 58.876 50.000 10.51 0.00 41.04 3.18
1495 2190 5.589050 CCAATATCATCCACCAGCATCTATG 59.411 44.000 0.00 0.00 0.00 2.23
1527 2222 3.513680 TGCTCCATCATTTGTGATTGC 57.486 42.857 0.00 0.00 0.00 3.56
1674 2374 2.814336 GGCCAACTCAACAAGAACCTAG 59.186 50.000 0.00 0.00 0.00 3.02
1735 2435 3.036819 TCTCTGCAGCTATGAGGACAAT 58.963 45.455 9.47 0.00 0.00 2.71
1756 2456 3.887716 GCTCCATTTCATACCTTGAGCAT 59.112 43.478 0.00 0.00 42.41 3.79
1791 2492 7.972832 GCTTGGGAAATTCATAGAGAAGAAAAG 59.027 37.037 0.00 0.00 40.15 2.27
1837 2540 7.556635 GCTCCCTGGTAAAGAAAATAGTACATT 59.443 37.037 0.00 0.00 0.00 2.71
1842 2545 4.291249 TGGCTCCCTGGTAAAGAAAATAGT 59.709 41.667 0.00 0.00 0.00 2.12
1874 2578 5.073691 AGGTCGGATGGATTTTATTCCTCAT 59.926 40.000 0.00 0.00 36.68 2.90
1952 2656 9.763465 CAGAATGGTCAATCAAAATTAAAATGC 57.237 29.630 0.00 0.00 0.00 3.56
1971 2675 5.672503 AGAGATGATGTGACTTCAGAATGG 58.327 41.667 7.26 0.00 36.16 3.16
2005 2722 5.996513 AGCAAGCTGATAGAATATGAAGGTG 59.003 40.000 0.00 0.00 0.00 4.00
2104 2824 0.829333 ATCGAGCAGCAAGATGAGGT 59.171 50.000 0.00 0.00 0.00 3.85
2107 2827 2.678471 TGAATCGAGCAGCAAGATGA 57.322 45.000 0.00 0.00 0.00 2.92
2126 2846 2.716217 GTCAGCAAGACAATAGGCCTT 58.284 47.619 12.58 0.00 46.77 4.35
2150 2882 8.754991 TTTCCAAGTTTATCAACCTGAAAGTA 57.245 30.769 0.00 0.00 32.70 2.24
2245 2977 5.296780 ACCATATGAACTTACCAGATTTGCG 59.703 40.000 3.65 0.00 0.00 4.85
2263 2995 5.957771 ACCTGAAGTACACATGACCATAT 57.042 39.130 0.00 0.00 0.00 1.78
2331 3072 9.650539 CATAACAACCATACAATCAAATTCCAA 57.349 29.630 0.00 0.00 0.00 3.53
2386 3127 9.490379 CTTATTCTAGAGTTAACAAACACCACT 57.510 33.333 8.61 0.00 0.00 4.00
2436 3177 9.461312 ACCTCAAAATACATGCATAAACTAAGA 57.539 29.630 0.00 0.00 0.00 2.10
2452 3193 5.063204 CACTGGACAGAACACCTCAAAATA 58.937 41.667 6.29 0.00 0.00 1.40
2473 3214 1.128692 GACGACAGCAAACCATAGCAC 59.871 52.381 0.00 0.00 0.00 4.40
2510 3252 1.500474 TTGGCTCCAGGGATGACTAG 58.500 55.000 0.00 0.00 0.00 2.57
2519 3270 1.094785 CCGTAACATTTGGCTCCAGG 58.905 55.000 0.00 0.00 0.00 4.45
2536 3287 0.038526 ACGTAAAGACAGCTGGACCG 60.039 55.000 19.93 12.92 0.00 4.79
2575 3327 8.469309 ACCATAGCAGTTCATTTAAATAGCAT 57.531 30.769 0.00 0.00 0.00 3.79
2674 3427 6.811253 TGTAACCTAATGCACTTTACTTGG 57.189 37.500 0.00 0.00 0.00 3.61
2730 3483 4.269363 ACCGAGTTAAAGACAGTTTTCACG 59.731 41.667 0.00 0.00 0.00 4.35
2737 3490 3.470645 AGCAACCGAGTTAAAGACAGT 57.529 42.857 0.00 0.00 0.00 3.55
2807 3817 0.608130 TGTGCCTACAGTGCCTACAG 59.392 55.000 0.00 0.00 31.91 2.74
3295 4329 9.740710 AAATATGCTAAAAGGTCAAAGTAGAGT 57.259 29.630 0.00 0.00 0.00 3.24
3421 4466 7.523293 TGTCAGATTCTCTGCCAAAATAAAA 57.477 32.000 0.00 0.00 43.95 1.52
3422 4467 7.707624 ATGTCAGATTCTCTGCCAAAATAAA 57.292 32.000 0.00 0.00 43.95 1.40
3425 4470 6.660521 TGTTATGTCAGATTCTCTGCCAAAAT 59.339 34.615 0.00 0.00 43.95 1.82
3503 4548 8.000127 TCAATGACATATCATCAATTCCCTTGA 59.000 33.333 0.00 0.00 45.26 3.02
3714 4821 7.291411 ACTATCTAATGCGTAGTCCAGAAAT 57.709 36.000 0.00 0.00 0.00 2.17
3822 4948 4.690748 TCATCAGTTCGATTCGCTCTTTTT 59.309 37.500 0.00 0.00 29.21 1.94
3839 4965 7.769220 ACATTAGCTCCTTTTGAAATCATCAG 58.231 34.615 0.00 0.00 39.77 2.90
3854 4980 9.561069 CATATACCCCAATAATACATTAGCTCC 57.439 37.037 0.00 0.00 0.00 4.70
4121 5285 6.631971 TTGCAATCACAAGTAAGTTCATGA 57.368 33.333 0.00 0.00 0.00 3.07
4150 5314 2.996621 AGCACAGATCGCTCAACTTTAC 59.003 45.455 0.00 0.00 33.35 2.01
4160 5358 5.176590 CCTTAATCTCTTAAGCACAGATCGC 59.823 44.000 5.81 0.00 41.63 4.58
4198 5396 5.357878 GTGAAGGCATTTGGTTCAGATGATA 59.642 40.000 3.11 0.00 30.94 2.15
4254 5475 7.108847 AGATTAGCAAAGCATACTCAGAAACT 58.891 34.615 0.00 0.00 0.00 2.66
4283 5504 8.409358 ACAATTTAGCACCTCAAAGTTCTTAT 57.591 30.769 0.00 0.00 0.00 1.73
4603 5858 3.500448 TGACTAGGTCAACATTGGCAA 57.500 42.857 0.68 0.68 39.78 4.52
4972 6245 8.388103 CCAAAACGTCTTATATAGTGAAACAGG 58.612 37.037 0.00 0.00 41.43 4.00
5197 6470 5.404366 TGCTTTAAACAGACATCGTGACTAC 59.596 40.000 0.00 0.00 0.00 2.73
5200 6473 4.725556 TGCTTTAAACAGACATCGTGAC 57.274 40.909 0.00 0.00 0.00 3.67
5330 6603 2.860735 AGACGATGATAAACTTCTGCGC 59.139 45.455 0.00 0.00 0.00 6.09
5813 7130 6.753107 ATGGAGGTTGGTTAATCTAAAACG 57.247 37.500 0.00 0.00 0.00 3.60
5897 7217 5.827797 ACATGCAAAGAAGTAAGAGAAACCA 59.172 36.000 0.00 0.00 0.00 3.67
6290 7612 2.950975 TGCTGCAGAAAGTCAAATCACA 59.049 40.909 20.43 0.00 0.00 3.58
6364 7690 1.552578 TGCTCATTGCTGGCTCAATT 58.447 45.000 3.44 0.00 43.37 2.32
6484 7811 0.676782 GTAATGGCCGCTTCAGTGGT 60.677 55.000 8.22 0.00 46.99 4.16
6506 7833 7.520131 GCTTGATCATGTCATCAATCCTTACAG 60.520 40.741 9.55 0.00 41.06 2.74
6537 7864 2.326428 TCGTTCCCAGACTCTTCCTTT 58.674 47.619 0.00 0.00 0.00 3.11
6593 7920 3.005155 TCACATCATCAGTCGGCTAGATG 59.995 47.826 18.89 18.89 40.29 2.90
6597 7924 2.036346 CCATCACATCATCAGTCGGCTA 59.964 50.000 0.00 0.00 0.00 3.93
6600 7927 1.202615 AGCCATCACATCATCAGTCGG 60.203 52.381 0.00 0.00 0.00 4.79
6601 7928 1.865340 CAGCCATCACATCATCAGTCG 59.135 52.381 0.00 0.00 0.00 4.18
6665 7993 7.461749 ACATTCTACGGGAATATCCATGAATT 58.538 34.615 0.00 0.00 42.20 2.17
6707 8035 9.796120 CCACTTTTGTACAAGATGTAAAAGAAA 57.204 29.630 16.83 2.04 37.78 2.52
6708 8036 9.179909 TCCACTTTTGTACAAGATGTAAAAGAA 57.820 29.630 16.83 2.46 37.78 2.52
6709 8037 8.617809 GTCCACTTTTGTACAAGATGTAAAAGA 58.382 33.333 16.83 5.06 37.78 2.52
6710 8038 7.860872 GGTCCACTTTTGTACAAGATGTAAAAG 59.139 37.037 8.56 9.93 39.75 2.27
6711 8039 7.558444 AGGTCCACTTTTGTACAAGATGTAAAA 59.442 33.333 8.56 0.00 34.21 1.52
6712 8040 7.057894 AGGTCCACTTTTGTACAAGATGTAAA 58.942 34.615 8.56 0.00 34.21 2.01
6713 8041 6.597562 AGGTCCACTTTTGTACAAGATGTAA 58.402 36.000 8.56 0.00 34.21 2.41
6714 8042 6.182507 AGGTCCACTTTTGTACAAGATGTA 57.817 37.500 8.56 0.00 0.00 2.29
6715 8043 5.048846 AGGTCCACTTTTGTACAAGATGT 57.951 39.130 8.56 6.42 0.00 3.06
6716 8044 7.687941 ATAAGGTCCACTTTTGTACAAGATG 57.312 36.000 8.56 8.35 40.64 2.90
6717 8045 8.164070 AGAATAAGGTCCACTTTTGTACAAGAT 58.836 33.333 8.56 0.00 40.64 2.40
6718 8046 7.514721 AGAATAAGGTCCACTTTTGTACAAGA 58.485 34.615 8.56 3.31 40.64 3.02
6719 8047 7.745620 AGAATAAGGTCCACTTTTGTACAAG 57.254 36.000 8.56 0.31 40.64 3.16
6726 8054 7.013942 GGTGTTTGTAGAATAAGGTCCACTTTT 59.986 37.037 0.00 0.00 40.64 2.27
6732 8092 5.183969 GGAGGTGTTTGTAGAATAAGGTCC 58.816 45.833 0.00 0.00 0.00 4.46
6746 8106 1.770061 TGGGTAGTTTCGGAGGTGTTT 59.230 47.619 0.00 0.00 0.00 2.83
6755 8115 0.463116 CGGGGGATTGGGTAGTTTCG 60.463 60.000 0.00 0.00 0.00 3.46
6768 8129 2.848197 TTTGGTCGGTTCGGGGGA 60.848 61.111 0.00 0.00 0.00 4.81
6811 8173 1.073284 GGGGTTTCAGAGTGGTTAGCA 59.927 52.381 0.00 0.00 0.00 3.49
6814 8176 4.237018 AGTAAGGGGTTTCAGAGTGGTTA 58.763 43.478 0.00 0.00 0.00 2.85
6880 8242 0.609131 CGCAATGGAAGGAAGGTGGT 60.609 55.000 0.00 0.00 0.00 4.16
6906 8268 1.852157 AGGCATGGTGAGGTTGGGA 60.852 57.895 0.00 0.00 0.00 4.37
7047 8426 4.849310 GGAGGTGGCCGCGCAATA 62.849 66.667 10.86 0.00 0.00 1.90
7120 8499 0.817654 TCGCAGTCACAGAATCCGAT 59.182 50.000 0.00 0.00 0.00 4.18
7152 8557 2.092484 GGGTAGTTCTACGAGGAGAGGT 60.092 54.545 0.00 0.00 0.00 3.85
7224 8629 1.067425 CGACCATGTACCTTCAACCGA 60.067 52.381 0.00 0.00 0.00 4.69
7259 8664 2.290021 GAAGGGAGGAATGCAGGGGG 62.290 65.000 0.00 0.00 0.00 5.40
7313 8719 1.657181 GGCACGGAACAAAGCGTTG 60.657 57.895 11.02 11.02 38.19 4.10
7314 8720 2.115911 TGGCACGGAACAAAGCGTT 61.116 52.632 0.00 0.00 41.86 4.84
7328 8734 2.853542 TTGAGCTCTGGGGTGGCA 60.854 61.111 16.19 0.00 0.00 4.92
7364 8777 2.018324 GCTGTCAAAAGCTTGCGGC 61.018 57.895 0.00 4.21 40.20 6.53
7383 8796 4.458829 AGGACCTCGGGCGGATCA 62.459 66.667 0.00 0.00 0.00 2.92
7456 8870 2.507110 TAGCAAGAGTGGAGGCGCAC 62.507 60.000 10.83 1.82 0.00 5.34
7473 8887 1.394917 GTGCTTGATGCTTGACCGTAG 59.605 52.381 0.00 0.00 43.37 3.51
7475 8889 1.568612 CGTGCTTGATGCTTGACCGT 61.569 55.000 0.00 0.00 43.37 4.83
7477 8891 0.445436 CTCGTGCTTGATGCTTGACC 59.555 55.000 0.00 0.00 43.37 4.02


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

AutoCloner maintained by Alex Coulton.