Multiple sequence alignment - TraesCS3B01G555500

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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 TraesCS3B01G555500 chr3B 100.000 7035 0 0 1 7035 789174882 789181916 0.000000e+00 12992.0
1 TraesCS3B01G555500 chr3B 85.929 1798 173 42 4330 6098 789220647 789222393 0.000000e+00 1845.0
2 TraesCS3B01G555500 chr3B 88.699 1407 117 19 4761 6145 789229001 789230387 0.000000e+00 1679.0
3 TraesCS3B01G555500 chr3B 83.363 1659 209 40 565 2196 789217342 789218960 0.000000e+00 1472.0
4 TraesCS3B01G555500 chr3B 86.462 1012 111 14 1136 2129 789226921 789227924 0.000000e+00 1086.0
5 TraesCS3B01G555500 chr3B 88.868 530 51 5 2718 3243 789220096 789220621 0.000000e+00 645.0
6 TraesCS3B01G555500 chr3B 87.347 245 23 5 2479 2722 789219484 789219721 2.500000e-69 274.0
7 TraesCS3B01G555500 chr3B 80.791 354 49 16 4323 4663 789228608 789228955 7.000000e-65 259.0
8 TraesCS3B01G555500 chr3B 83.333 294 34 8 2 286 789216604 789216891 2.520000e-64 257.0
9 TraesCS3B01G555500 chr3B 77.124 306 54 12 357 652 789217043 789217342 5.650000e-36 163.0
10 TraesCS3B01G555500 chr3A 96.498 1856 61 3 4292 6145 719935524 719937377 0.000000e+00 3064.0
11 TraesCS3B01G555500 chr3A 85.103 1893 186 44 4292 6143 719995668 719997505 0.000000e+00 1845.0
12 TraesCS3B01G555500 chr3A 89.392 1414 114 20 977 2365 719932825 719934227 0.000000e+00 1748.0
13 TraesCS3B01G555500 chr3A 89.397 1377 108 19 4785 6145 720077497 720078851 0.000000e+00 1700.0
14 TraesCS3B01G555500 chr3A 88.897 1396 117 21 4764 6145 720230799 720232170 0.000000e+00 1685.0
15 TraesCS3B01G555500 chr3A 88.453 1325 113 19 4853 6143 720221841 720223159 0.000000e+00 1563.0
16 TraesCS3B01G555500 chr3A 96.284 888 32 1 2356 3243 719934638 719935524 0.000000e+00 1456.0
17 TraesCS3B01G555500 chr3A 84.397 1301 166 17 908 2191 719991537 719992817 0.000000e+00 1243.0
18 TraesCS3B01G555500 chr3A 84.161 1168 162 14 1136 2286 720075336 720076497 0.000000e+00 1110.0
19 TraesCS3B01G555500 chr3A 87.150 965 113 6 1040 2001 720228116 720229072 0.000000e+00 1085.0
20 TraesCS3B01G555500 chr3A 84.819 718 76 22 2548 3243 720229665 720230371 0.000000e+00 691.0
21 TraesCS3B01G555500 chr3A 82.656 738 94 21 2528 3243 720215925 720216650 2.150000e-174 623.0
22 TraesCS3B01G555500 chr3A 87.086 573 39 12 6467 7035 720079298 720079839 3.610000e-172 616.0
23 TraesCS3B01G555500 chr3A 87.403 516 55 6 2722 3233 719995151 719995660 1.020000e-162 584.0
24 TraesCS3B01G555500 chr3A 86.948 521 57 8 2724 3239 720076526 720077040 6.120000e-160 575.0
25 TraesCS3B01G555500 chr3A 76.881 1103 195 39 1021 2109 719942595 719941539 2.850000e-158 569.0
26 TraesCS3B01G555500 chr3A 91.443 409 30 4 6467 6875 719937656 719938059 2.220000e-154 556.0
27 TraesCS3B01G555500 chr3A 88.583 254 20 4 39 286 719990515 719990765 4.120000e-77 300.0
28 TraesCS3B01G555500 chr3A 84.932 292 33 7 2 286 719931621 719931908 1.150000e-72 285.0
29 TraesCS3B01G555500 chr3A 79.856 417 52 15 2067 2471 720229105 720229501 6.950000e-70 276.0
30 TraesCS3B01G555500 chr3A 90.816 196 13 3 6142 6332 719937410 719937605 2.520000e-64 257.0
31 TraesCS3B01G555500 chr3A 79.241 395 54 19 4289 4663 720077050 720077436 4.210000e-62 250.0
32 TraesCS3B01G555500 chr3A 86.341 205 18 5 6157 6351 720223259 720223463 1.540000e-51 215.0
33 TraesCS3B01G555500 chr3A 83.077 260 19 10 6220 6465 720079020 720079268 5.530000e-51 213.0
34 TraesCS3B01G555500 chr3A 86.525 141 19 0 6220 6360 720232419 720232559 9.450000e-34 156.0
35 TraesCS3B01G555500 chr3A 87.218 133 15 2 566 696 719991218 719991350 4.400000e-32 150.0
36 TraesCS3B01G555500 chr3A 75.641 312 49 18 357 652 719990872 719991172 5.730000e-26 130.0
37 TraesCS3B01G555500 chr3A 75.235 319 43 19 4289 4598 720216656 720216947 1.240000e-22 119.0
38 TraesCS3B01G555500 chr3A 85.593 118 7 5 6158 6265 720232268 720232385 1.600000e-21 115.0
39 TraesCS3B01G555500 chr3A 95.556 45 2 0 6221 6265 720078942 720078986 9.790000e-09 73.1
40 TraesCS3B01G555500 chr3D 95.535 1859 78 2 4292 6145 590203573 590205431 0.000000e+00 2968.0
41 TraesCS3B01G555500 chr3D 86.298 2715 268 55 565 3243 590237866 590240512 0.000000e+00 2857.0
42 TraesCS3B01G555500 chr3D 84.932 1898 208 37 600 2474 590200061 590201903 0.000000e+00 1849.0
43 TraesCS3B01G555500 chr3D 89.635 1399 106 21 4761 6145 590308337 590309710 0.000000e+00 1744.0
44 TraesCS3B01G555500 chr3D 90.337 1128 87 11 4292 5411 590240512 590241625 0.000000e+00 1459.0
45 TraesCS3B01G555500 chr3D 83.360 1268 166 23 1054 2286 590306095 590307352 0.000000e+00 1131.0
46 TraesCS3B01G555500 chr3D 84.503 1097 133 20 4554 5630 588977858 588976779 0.000000e+00 1050.0
47 TraesCS3B01G555500 chr3D 92.661 654 45 3 2591 3243 590202922 590203573 0.000000e+00 939.0
48 TraesCS3B01G555500 chr3D 92.579 539 28 5 6142 6669 590205464 590206001 0.000000e+00 763.0
49 TraesCS3B01G555500 chr3D 86.389 529 58 11 2724 3243 590307381 590307904 3.680000e-157 566.0
50 TraesCS3B01G555500 chr3D 94.006 317 19 0 5810 6126 590241623 590241939 1.370000e-131 481.0
51 TraesCS3B01G555500 chr3D 92.226 283 15 3 1 283 590199396 590199671 1.840000e-105 394.0
52 TraesCS3B01G555500 chr3D 79.310 551 81 17 2695 3221 590222606 590222065 8.680000e-94 355.0
53 TraesCS3B01G555500 chr3D 86.486 296 24 9 2 286 590237223 590237513 1.910000e-80 311.0
54 TraesCS3B01G555500 chr3D 92.308 130 10 0 2476 2605 590201961 590202090 1.210000e-42 185.0
55 TraesCS3B01G555500 chr3D 78.802 217 26 15 6158 6360 590309805 590310015 2.060000e-25 128.0
56 TraesCS3B01G555500 chr1B 94.402 1054 44 11 3242 4293 575894197 575893157 0.000000e+00 1605.0
57 TraesCS3B01G555500 chr1B 93.441 1052 58 9 3242 4293 153427039 153425999 0.000000e+00 1550.0
58 TraesCS3B01G555500 chr1B 93.377 1057 55 8 3242 4296 302038583 302037540 0.000000e+00 1550.0
59 TraesCS3B01G555500 chr5B 94.202 1052 48 12 3241 4292 57022301 57021263 0.000000e+00 1592.0
60 TraesCS3B01G555500 chr5B 92.897 1070 67 7 3240 4305 232702620 232703684 0.000000e+00 1546.0
61 TraesCS3B01G555500 chr4A 92.589 1093 64 15 3239 4327 665793437 665792358 0.000000e+00 1554.0
62 TraesCS3B01G555500 chr7B 93.078 1069 60 9 3236 4302 733422909 733421853 0.000000e+00 1552.0
63 TraesCS3B01G555500 chr7B 93.084 1070 55 15 3236 4303 639271689 639272741 0.000000e+00 1548.0
64 TraesCS3B01G555500 chr7B 93.524 1050 51 13 3247 4295 656997712 656996679 0.000000e+00 1546.0
65 TraesCS3B01G555500 chr2D 83.784 111 13 4 796 906 617630042 617629937 4.490000e-17 100.0
66 TraesCS3B01G555500 chr2D 91.803 61 5 0 285 345 116795331 116795391 1.260000e-12 86.1


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 TraesCS3B01G555500 chr3B 789174882 789181916 7034 False 12992.000000 12992 100.000000 1 7035 1 chr3B.!!$F1 7034
1 TraesCS3B01G555500 chr3B 789226921 789230387 3466 False 1008.000000 1679 85.317333 1136 6145 3 chr3B.!!$F3 5009
2 TraesCS3B01G555500 chr3B 789216604 789222393 5789 False 776.000000 1845 84.327333 2 6098 6 chr3B.!!$F2 6096
3 TraesCS3B01G555500 chr3A 719931621 719938059 6438 False 1227.666667 3064 91.560833 2 6875 6 chr3A.!!$F1 6873
4 TraesCS3B01G555500 chr3A 720221841 720223463 1622 False 889.000000 1563 87.397000 4853 6351 2 chr3A.!!$F5 1498
5 TraesCS3B01G555500 chr3A 719990515 719997505 6990 False 708.666667 1845 84.724167 39 6143 6 chr3A.!!$F2 6104
6 TraesCS3B01G555500 chr3A 720228116 720232559 4443 False 668.000000 1685 85.473333 1040 6360 6 chr3A.!!$F6 5320
7 TraesCS3B01G555500 chr3A 720075336 720079839 4503 False 648.157143 1700 86.495143 1136 7035 7 chr3A.!!$F3 5899
8 TraesCS3B01G555500 chr3A 719941539 719942595 1056 True 569.000000 569 76.881000 1021 2109 1 chr3A.!!$R1 1088
9 TraesCS3B01G555500 chr3A 720215925 720216947 1022 False 371.000000 623 78.945500 2528 4598 2 chr3A.!!$F4 2070
10 TraesCS3B01G555500 chr3D 590237223 590241939 4716 False 1277.000000 2857 89.281750 2 6126 4 chr3D.!!$F2 6124
11 TraesCS3B01G555500 chr3D 590199396 590206001 6605 False 1183.000000 2968 91.706833 1 6669 6 chr3D.!!$F1 6668
12 TraesCS3B01G555500 chr3D 588976779 588977858 1079 True 1050.000000 1050 84.503000 4554 5630 1 chr3D.!!$R1 1076
13 TraesCS3B01G555500 chr3D 590306095 590310015 3920 False 892.250000 1744 84.546500 1054 6360 4 chr3D.!!$F3 5306
14 TraesCS3B01G555500 chr3D 590222065 590222606 541 True 355.000000 355 79.310000 2695 3221 1 chr3D.!!$R2 526
15 TraesCS3B01G555500 chr1B 575893157 575894197 1040 True 1605.000000 1605 94.402000 3242 4293 1 chr1B.!!$R3 1051
16 TraesCS3B01G555500 chr1B 153425999 153427039 1040 True 1550.000000 1550 93.441000 3242 4293 1 chr1B.!!$R1 1051
17 TraesCS3B01G555500 chr1B 302037540 302038583 1043 True 1550.000000 1550 93.377000 3242 4296 1 chr1B.!!$R2 1054
18 TraesCS3B01G555500 chr5B 57021263 57022301 1038 True 1592.000000 1592 94.202000 3241 4292 1 chr5B.!!$R1 1051
19 TraesCS3B01G555500 chr5B 232702620 232703684 1064 False 1546.000000 1546 92.897000 3240 4305 1 chr5B.!!$F1 1065
20 TraesCS3B01G555500 chr4A 665792358 665793437 1079 True 1554.000000 1554 92.589000 3239 4327 1 chr4A.!!$R1 1088
21 TraesCS3B01G555500 chr7B 733421853 733422909 1056 True 1552.000000 1552 93.078000 3236 4302 1 chr7B.!!$R2 1066
22 TraesCS3B01G555500 chr7B 639271689 639272741 1052 False 1548.000000 1548 93.084000 3236 4303 1 chr7B.!!$F1 1067
23 TraesCS3B01G555500 chr7B 656996679 656997712 1033 True 1546.000000 1546 93.524000 3247 4295 1 chr7B.!!$R1 1048

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
100 115 0.028902 GAAAAACAAGCGCACTCCGT 59.971 50.000 11.47 0.0 39.71 4.69 F
360 478 0.037605 GTGCCCCTATCCGTAATCCG 60.038 60.000 0.00 0.0 0.00 4.18 F
996 1601 0.097674 GCTTGGTGTGCTATCGCTTG 59.902 55.000 0.00 0.0 36.97 4.01 F
1481 2108 0.179015 TGCGAGGGCTGTTTGGTTAA 60.179 50.000 0.00 0.0 40.82 2.01 F
1710 2343 0.955428 TGAACAGCACGGCTCAATCC 60.955 55.000 0.00 0.0 36.40 3.01 F
2142 2806 1.380785 CCTTGGCTGGACATGGCAT 60.381 57.895 0.00 0.0 39.67 4.40 F
3419 7330 0.610785 AAATCAACCCGCCGTCCATT 60.611 50.000 0.00 0.0 0.00 3.16 F
4044 7983 2.408565 GGAGAGAGAGAGAGGGAGAGA 58.591 57.143 0.00 0.0 0.00 3.10 F
4864 8852 0.828022 TGTACATACTTCCAGGGCCG 59.172 55.000 0.00 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1329 1956 0.105453 GGGTGGATGAGAGGAGCCTA 60.105 60.000 0.00 0.0 0.00 3.93 R
1443 2070 0.116143 AGGCAGAGGAGTTGGAGTCT 59.884 55.000 0.00 0.0 0.00 3.24 R
2103 2761 1.144936 CTGCCGGGAAGGATGAGAC 59.855 63.158 2.18 0.0 45.00 3.36 R
3019 6915 0.871722 TCCAAACCAATGCGTCTTCG 59.128 50.000 0.00 0.0 40.37 3.79 R
3082 6978 1.548719 TGTGTAGCACGCAATACCTCT 59.451 47.619 0.89 0.0 35.42 3.69 R
4058 7997 1.841277 TCCTAAGGCGTCTCTCTCTCT 59.159 52.381 0.00 0.0 0.00 3.10 R
4264 8203 3.959975 GAGCCCGTGCGTTGCAAA 61.960 61.111 0.00 0.0 41.47 3.68 R
5753 9779 3.452264 TGGATCTCCTCAACAATCGATGT 59.548 43.478 0.00 0.0 39.67 3.06 R
6360 10622 1.177401 GGCCTCAAGGTTTCCATGAC 58.823 55.000 0.00 0.0 37.57 3.06 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 71 0.467804 GCCAGTCATTCTCCTCCTCC 59.532 60.000 0.00 0.00 0.00 4.30
66 75 1.062505 AGTCATTCTCCTCCTCCTCCC 60.063 57.143 0.00 0.00 0.00 4.30
68 77 1.118356 CATTCTCCTCCTCCTCCCCG 61.118 65.000 0.00 0.00 0.00 5.73
74 83 3.273654 TCCTCCTCCCCGTCCACT 61.274 66.667 0.00 0.00 0.00 4.00
100 115 0.028902 GAAAAACAAGCGCACTCCGT 59.971 50.000 11.47 0.00 39.71 4.69
152 170 2.203998 CCCCACTCCCCACTCTGT 60.204 66.667 0.00 0.00 0.00 3.41
157 175 0.896019 CACTCCCCACTCTGTCGACT 60.896 60.000 17.92 0.00 0.00 4.18
259 279 3.842923 CGTGCCGGAGAGGAGCAT 61.843 66.667 5.05 0.00 45.00 3.79
261 281 2.685017 TGCCGGAGAGGAGCATGT 60.685 61.111 5.05 0.00 45.00 3.21
300 330 1.209504 GCCATCCTACAGTGGTAAGCA 59.790 52.381 0.00 0.00 37.81 3.91
302 332 2.501723 CCATCCTACAGTGGTAAGCACT 59.498 50.000 0.00 0.00 0.00 4.40
357 475 1.692519 GACAGTGCCCCTATCCGTAAT 59.307 52.381 0.00 0.00 0.00 1.89
360 478 0.037605 GTGCCCCTATCCGTAATCCG 60.038 60.000 0.00 0.00 0.00 4.18
361 479 0.470456 TGCCCCTATCCGTAATCCGT 60.470 55.000 0.00 0.00 33.66 4.69
370 488 1.688269 CCGTAATCCGTAAGCCCCCA 61.688 60.000 0.00 0.00 33.66 4.96
371 489 0.178533 CGTAATCCGTAAGCCCCCAA 59.821 55.000 0.00 0.00 0.00 4.12
372 490 1.808891 CGTAATCCGTAAGCCCCCAAG 60.809 57.143 0.00 0.00 0.00 3.61
373 491 1.211212 GTAATCCGTAAGCCCCCAAGT 59.789 52.381 0.00 0.00 0.00 3.16
374 492 1.587066 AATCCGTAAGCCCCCAAGTA 58.413 50.000 0.00 0.00 0.00 2.24
375 493 1.587066 ATCCGTAAGCCCCCAAGTAA 58.413 50.000 0.00 0.00 0.00 2.24
376 494 0.614812 TCCGTAAGCCCCCAAGTAAC 59.385 55.000 0.00 0.00 0.00 2.50
377 495 0.616891 CCGTAAGCCCCCAAGTAACT 59.383 55.000 0.00 0.00 0.00 2.24
392 514 5.877012 CCAAGTAACTATCTGCAGTGTCAAT 59.123 40.000 14.67 1.49 0.00 2.57
462 586 4.319177 CGGGGCTAGATTCTTTATTCAGG 58.681 47.826 0.00 0.00 0.00 3.86
468 592 7.201741 GGGCTAGATTCTTTATTCAGGTTGAAC 60.202 40.741 0.00 0.00 39.45 3.18
480 605 7.790823 ATTCAGGTTGAACAGAAAATTTTGG 57.209 32.000 8.47 2.95 39.45 3.28
488 613 7.621428 TGAACAGAAAATTTTGGATTTTGCA 57.379 28.000 8.47 0.00 32.03 4.08
489 614 8.223177 TGAACAGAAAATTTTGGATTTTGCAT 57.777 26.923 8.47 0.00 32.03 3.96
490 615 8.129840 TGAACAGAAAATTTTGGATTTTGCATG 58.870 29.630 8.47 0.00 32.03 4.06
491 616 7.571080 ACAGAAAATTTTGGATTTTGCATGT 57.429 28.000 8.47 2.43 32.03 3.21
492 617 7.998580 ACAGAAAATTTTGGATTTTGCATGTT 58.001 26.923 8.47 0.00 32.03 2.71
494 619 8.129840 CAGAAAATTTTGGATTTTGCATGTTGA 58.870 29.630 8.47 0.00 32.03 3.18
495 620 8.347035 AGAAAATTTTGGATTTTGCATGTTGAG 58.653 29.630 8.47 0.00 32.03 3.02
496 621 7.571080 AAATTTTGGATTTTGCATGTTGAGT 57.429 28.000 0.00 0.00 0.00 3.41
497 622 7.571080 AATTTTGGATTTTGCATGTTGAGTT 57.429 28.000 0.00 0.00 0.00 3.01
498 623 5.987777 TTTGGATTTTGCATGTTGAGTTG 57.012 34.783 0.00 0.00 0.00 3.16
519 652 6.265422 AGTTGAGAATTGAGAATTTTCGGGTT 59.735 34.615 0.00 0.00 35.41 4.11
528 661 2.200373 ATTTTCGGGTTCCTGTCCAG 57.800 50.000 0.00 0.00 0.00 3.86
530 663 1.133363 TTTCGGGTTCCTGTCCAGAA 58.867 50.000 0.00 0.00 37.37 3.02
533 666 2.542550 TCGGGTTCCTGTCCAGAATAA 58.457 47.619 0.00 0.00 0.00 1.40
535 668 3.521937 TCGGGTTCCTGTCCAGAATAAAT 59.478 43.478 0.00 0.00 0.00 1.40
536 669 4.717778 TCGGGTTCCTGTCCAGAATAAATA 59.282 41.667 0.00 0.00 0.00 1.40
538 671 5.883673 CGGGTTCCTGTCCAGAATAAATAAA 59.116 40.000 0.00 0.00 0.00 1.40
539 672 6.546034 CGGGTTCCTGTCCAGAATAAATAAAT 59.454 38.462 0.00 0.00 0.00 1.40
573 716 1.821336 TTTTGAGCGCGTTTTGACTG 58.179 45.000 8.43 0.00 0.00 3.51
579 722 1.782028 GCGCGTTTTGACTGGGAGTT 61.782 55.000 8.43 0.00 0.00 3.01
592 735 3.714798 ACTGGGAGTTGACTTCCTAAACA 59.285 43.478 9.79 0.00 42.41 2.83
598 741 5.280011 GGAGTTGACTTCCTAAACATCCAGA 60.280 44.000 0.00 0.00 0.00 3.86
604 747 8.737168 TGACTTCCTAAACATCCAGATTAATG 57.263 34.615 0.00 0.00 0.00 1.90
623 904 7.575414 TTAATGCTGTTTTGACTTGGAGTAA 57.425 32.000 0.00 0.00 0.00 2.24
670 996 6.322931 TCCCTGATATCTGAATGGCTACTTA 58.677 40.000 10.93 0.00 0.00 2.24
673 999 7.046652 CCTGATATCTGAATGGCTACTTATGG 58.953 42.308 10.93 0.00 0.00 2.74
690 1016 9.774742 CTACTTATGGCATCTGAACTTTTAAAC 57.225 33.333 1.65 0.00 0.00 2.01
732 1267 8.851960 TCTTATTAATAACTGTCTAGCACACG 57.148 34.615 3.71 0.00 0.00 4.49
733 1268 8.464404 TCTTATTAATAACTGTCTAGCACACGT 58.536 33.333 3.71 0.00 0.00 4.49
739 1274 5.840940 AACTGTCTAGCACACGTTATTTC 57.159 39.130 0.00 0.00 29.66 2.17
740 1275 5.135508 ACTGTCTAGCACACGTTATTTCT 57.864 39.130 0.00 0.00 0.00 2.52
741 1276 5.162075 ACTGTCTAGCACACGTTATTTCTC 58.838 41.667 0.00 0.00 0.00 2.87
744 1279 5.048294 TGTCTAGCACACGTTATTTCTCTGA 60.048 40.000 0.00 0.00 0.00 3.27
745 1280 6.037098 GTCTAGCACACGTTATTTCTCTGAT 58.963 40.000 0.00 0.00 0.00 2.90
746 1281 6.020281 GTCTAGCACACGTTATTTCTCTGATG 60.020 42.308 0.00 0.00 0.00 3.07
747 1282 3.372206 AGCACACGTTATTTCTCTGATGC 59.628 43.478 0.00 0.00 0.00 3.91
748 1283 3.372206 GCACACGTTATTTCTCTGATGCT 59.628 43.478 0.00 0.00 0.00 3.79
749 1284 4.142816 GCACACGTTATTTCTCTGATGCTT 60.143 41.667 0.00 0.00 0.00 3.91
750 1285 5.063438 GCACACGTTATTTCTCTGATGCTTA 59.937 40.000 0.00 0.00 0.00 3.09
751 1286 6.470160 CACACGTTATTTCTCTGATGCTTAC 58.530 40.000 0.00 0.00 0.00 2.34
752 1287 6.090763 CACACGTTATTTCTCTGATGCTTACA 59.909 38.462 0.00 0.00 0.00 2.41
762 1297 4.779696 TCTGATGCTTACATTACATGCCA 58.220 39.130 0.00 0.00 36.35 4.92
773 1308 5.736813 ACATTACATGCCATCAATTTTGCT 58.263 33.333 0.00 0.00 0.00 3.91
774 1309 6.174760 ACATTACATGCCATCAATTTTGCTT 58.825 32.000 0.00 0.00 0.00 3.91
775 1310 6.655848 ACATTACATGCCATCAATTTTGCTTT 59.344 30.769 0.00 0.00 0.00 3.51
776 1311 7.175293 ACATTACATGCCATCAATTTTGCTTTT 59.825 29.630 0.00 0.00 0.00 2.27
777 1312 5.616488 ACATGCCATCAATTTTGCTTTTC 57.384 34.783 0.00 0.00 0.00 2.29
784 1329 6.565247 GCCATCAATTTTGCTTTTCAGAACAG 60.565 38.462 0.00 0.00 0.00 3.16
788 1333 7.950512 TCAATTTTGCTTTTCAGAACAGGATA 58.049 30.769 0.00 0.00 0.00 2.59
790 1335 9.044150 CAATTTTGCTTTTCAGAACAGGATAAA 57.956 29.630 0.00 1.15 0.00 1.40
817 1362 0.174162 GCTCAAATGGATGGTGGTGC 59.826 55.000 0.00 0.00 0.00 5.01
826 1371 2.876368 GATGGTGGTGCTCCCTTCCG 62.876 65.000 1.59 0.00 32.88 4.30
827 1372 3.319198 GGTGGTGCTCCCTTCCGA 61.319 66.667 1.59 0.00 0.00 4.55
851 1404 3.473647 CAGCTCCTGATGGCCCGA 61.474 66.667 0.00 0.00 32.44 5.14
888 1454 5.467035 GAGCATATTCTTCTAGCTCCACT 57.533 43.478 0.00 0.00 44.37 4.00
893 1459 4.917906 ATTCTTCTAGCTCCACTGGTTT 57.082 40.909 0.00 0.00 0.00 3.27
898 1464 2.029290 TCTAGCTCCACTGGTTTCGAAC 60.029 50.000 0.00 0.00 0.00 3.95
916 1493 3.748048 CGAACTCTGAGAATTCTTGCCAA 59.252 43.478 12.44 0.00 0.00 4.52
926 1503 5.899299 AGAATTCTTGCCAACAATAGCATC 58.101 37.500 0.88 0.00 39.11 3.91
928 1505 6.830324 AGAATTCTTGCCAACAATAGCATCTA 59.170 34.615 0.88 0.00 39.11 1.98
931 1508 5.500234 TCTTGCCAACAATAGCATCTAGTT 58.500 37.500 0.00 0.00 39.11 2.24
932 1509 5.945784 TCTTGCCAACAATAGCATCTAGTTT 59.054 36.000 0.00 0.00 39.11 2.66
939 1516 6.764308 ACAATAGCATCTAGTTTGTTGCAT 57.236 33.333 0.00 0.00 35.71 3.96
948 1553 3.004024 AGTTTGTTGCATTTCTGAGCG 57.996 42.857 0.00 0.00 0.00 5.03
951 1556 0.874390 TGTTGCATTTCTGAGCGGAC 59.126 50.000 0.00 0.00 0.00 4.79
957 1562 0.389948 ATTTCTGAGCGGACGGACAC 60.390 55.000 0.00 0.00 0.00 3.67
978 1583 4.688413 CACTTCTCCTCTGTGTTCTTTAGC 59.312 45.833 0.00 0.00 0.00 3.09
988 1593 2.618709 GTGTTCTTTAGCTTGGTGTGCT 59.381 45.455 0.00 0.00 43.79 4.40
996 1601 0.097674 GCTTGGTGTGCTATCGCTTG 59.902 55.000 0.00 0.00 36.97 4.01
998 1603 2.616960 CTTGGTGTGCTATCGCTTGTA 58.383 47.619 0.00 0.00 36.97 2.41
1019 1624 7.809546 TGTAGATGATCCAGAGTTACTACAG 57.190 40.000 0.00 0.00 35.61 2.74
1031 1636 3.646637 AGTTACTACAGCTTGTGGAGGTT 59.353 43.478 6.65 0.00 42.30 3.50
1049 1654 2.100916 GGTTGAGCTTCGAGGTATGCTA 59.899 50.000 0.00 0.00 35.76 3.49
1052 1659 1.338337 GAGCTTCGAGGTATGCTAGCA 59.662 52.381 21.85 21.85 35.76 3.49
1124 1737 7.102847 TCTAACGAATTTTGTTGTTTCCCTT 57.897 32.000 11.56 0.00 0.00 3.95
1131 1744 7.691877 CGAATTTTGTTGTTTCCCTTCTTTTTG 59.308 33.333 0.00 0.00 0.00 2.44
1132 1745 5.871465 TTTGTTGTTTCCCTTCTTTTTGC 57.129 34.783 0.00 0.00 0.00 3.68
1134 1747 4.502962 TGTTGTTTCCCTTCTTTTTGCAG 58.497 39.130 0.00 0.00 0.00 4.41
1142 1755 2.035576 CCTTCTTTTTGCAGCAGAGCTT 59.964 45.455 0.00 0.00 36.40 3.74
1147 1760 1.971481 TTTGCAGCAGAGCTTCTCAA 58.029 45.000 0.00 0.00 36.40 3.02
1159 1772 6.591834 GCAGAGCTTCTCAATTTCTACAAGTA 59.408 38.462 0.00 0.00 32.06 2.24
1177 1795 1.906574 GTACCCTGGTGATGAGGTTCA 59.093 52.381 0.00 0.00 33.70 3.18
1197 1815 5.883685 TCATATCATCCATAGATCTGCCC 57.116 43.478 5.18 0.00 0.00 5.36
1206 1824 2.783379 TAGATCTGCCCTGTCATCCT 57.217 50.000 5.18 0.00 0.00 3.24
1314 1941 4.094294 GGCGACTACAAATCAAATAGCACA 59.906 41.667 0.00 0.00 0.00 4.57
1329 1956 1.165270 GCACATACGAAGCCAACCTT 58.835 50.000 0.00 0.00 36.19 3.50
1395 2022 2.651361 CTCTTCGCCACCGACACT 59.349 61.111 0.00 0.00 44.30 3.55
1443 2070 4.056125 CTCGCACTCTGCCGTGGA 62.056 66.667 0.00 0.00 41.12 4.02
1481 2108 0.179015 TGCGAGGGCTGTTTGGTTAA 60.179 50.000 0.00 0.00 40.82 2.01
1710 2343 0.955428 TGAACAGCACGGCTCAATCC 60.955 55.000 0.00 0.00 36.40 3.01
1996 2635 2.474266 CGGCGATCAACAACACCG 59.526 61.111 0.00 0.00 0.00 4.94
2086 2743 1.452145 GCAAGCGACCACCCAAGAAA 61.452 55.000 0.00 0.00 0.00 2.52
2103 2761 8.531146 ACCCAAGAAATTCATGGTATGTAAAAG 58.469 33.333 15.06 0.78 33.63 2.27
2130 2788 3.344137 TTCCCGGCAGATCCTTGGC 62.344 63.158 0.00 0.00 40.00 4.52
2142 2806 1.380785 CCTTGGCTGGACATGGCAT 60.381 57.895 0.00 0.00 39.67 4.40
2170 2835 8.612619 TCGGCTTCAGTTAGATTGATTAATTTC 58.387 33.333 0.00 0.00 0.00 2.17
2428 3732 6.294731 GCAATGTCCACTTACAAGGAAAATCT 60.295 38.462 0.00 0.00 35.29 2.40
2430 3734 7.923414 ATGTCCACTTACAAGGAAAATCTAC 57.077 36.000 0.00 0.00 35.29 2.59
2434 3738 8.092687 GTCCACTTACAAGGAAAATCTACACTA 58.907 37.037 0.00 0.00 35.29 2.74
2498 5088 7.429636 TGTGGTAGCATTTTTAGACAAGTAC 57.570 36.000 0.00 0.00 0.00 2.73
2499 5089 6.146510 TGTGGTAGCATTTTTAGACAAGTACG 59.853 38.462 0.00 0.00 0.00 3.67
2963 6853 7.011576 TGTCAATCTTAACGTTGTATGTGTGTT 59.988 33.333 11.99 0.00 0.00 3.32
2964 6854 7.853929 GTCAATCTTAACGTTGTATGTGTGTTT 59.146 33.333 11.99 0.00 0.00 2.83
3019 6915 4.065110 GCCATGAATAGGCCGGAC 57.935 61.111 5.05 0.00 46.50 4.79
3332 7243 6.049955 TCTATTTCAGAGAATTCAACCCGT 57.950 37.500 8.44 0.00 0.00 5.28
3418 7329 1.001393 AAATCAACCCGCCGTCCAT 60.001 52.632 0.00 0.00 0.00 3.41
3419 7330 0.610785 AAATCAACCCGCCGTCCATT 60.611 50.000 0.00 0.00 0.00 3.16
3447 7358 2.548904 TCACACCCGAACCGTTATTTTG 59.451 45.455 0.00 0.00 0.00 2.44
3966 7889 6.355747 TCTGAAAAATGTTGCAAGGGAAAAT 58.644 32.000 0.00 0.00 0.00 1.82
4044 7983 2.408565 GGAGAGAGAGAGAGGGAGAGA 58.591 57.143 0.00 0.00 0.00 3.10
4048 7987 3.051803 AGAGAGAGAGAGGGAGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
4049 7988 3.312890 AGAGAGAGAGGGAGAGAGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
4050 7989 3.051803 AGAGAGAGAGGGAGAGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
4058 7997 3.051803 AGGGAGAGAGAGAGAGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
4097 8036 9.354673 CCTTAGGATTAACCATATTCAACACAT 57.645 33.333 0.00 0.00 42.04 3.21
4214 8153 3.464828 AGGAGATGGACCTATTGTGGTT 58.535 45.455 0.00 0.00 41.00 3.67
4264 8203 5.473504 GTGTGTGTTATGTTTTCTCTCCCAT 59.526 40.000 0.00 0.00 0.00 4.00
4496 8458 8.715998 CATTATATTATCGATGCCCTAGAATGC 58.284 37.037 8.54 0.00 0.00 3.56
4621 8598 6.541934 AACGTAGCCCTAAACTAGAAAGAT 57.458 37.500 0.00 0.00 0.00 2.40
4622 8599 6.541934 ACGTAGCCCTAAACTAGAAAGATT 57.458 37.500 0.00 0.00 0.00 2.40
4623 8600 6.944096 ACGTAGCCCTAAACTAGAAAGATTT 58.056 36.000 0.00 0.00 0.00 2.17
4624 8601 7.392418 ACGTAGCCCTAAACTAGAAAGATTTT 58.608 34.615 0.00 0.00 0.00 1.82
4864 8852 0.828022 TGTACATACTTCCAGGGCCG 59.172 55.000 0.00 0.00 0.00 6.13
4962 8950 8.816640 AAATGAAGTTGAACTTATTGCGAAAT 57.183 26.923 11.01 0.00 38.80 2.17
5597 9612 8.557215 GGAATTCTGGTTTCCATCAGCATGAC 62.557 46.154 5.23 0.00 40.68 3.06
5753 9779 5.105146 GGGAGATGTCTTGAGCTTCTAGAAA 60.105 44.000 6.63 0.00 30.60 2.52
5782 9808 0.913924 TTGAGGAGATCCATGCAGCA 59.086 50.000 0.00 0.00 38.89 4.41
5837 9863 1.733041 GTACAAGAGCGCGCAGACA 60.733 57.895 35.10 10.08 0.00 3.41
5877 9903 4.987832 ACTGTCGTTGCAATGTTAAACAA 58.012 34.783 17.94 0.00 0.00 2.83
6116 10154 1.625818 CAGGTCAAGTGAACTAGGGCT 59.374 52.381 0.00 0.00 40.79 5.19
6164 10291 5.046159 TGGTTGTTCGGTCCTCAGTTAATAT 60.046 40.000 0.00 0.00 0.00 1.28
6215 10347 0.182537 TTTACACTGGTGGCTGCTGT 59.817 50.000 0.00 0.00 34.19 4.40
6351 10593 4.555709 TCCGTTGGCGTGCAAGGT 62.556 61.111 0.79 0.00 36.15 3.50
6354 10596 1.206578 CGTTGGCGTGCAAGGTTAG 59.793 57.895 0.79 0.00 0.00 2.34
6360 10622 1.281899 GCGTGCAAGGTTAGCTAGAG 58.718 55.000 0.79 0.00 0.00 2.43
6400 10662 4.202284 GCCATAACTGATAAGGTTCCGGTA 60.202 45.833 0.00 0.00 0.00 4.02
6465 10755 4.925068 ACGAAAAGATGCATTTCCATAGC 58.075 39.130 0.00 0.00 34.10 2.97
6470 10760 4.011966 AGATGCATTTCCATAGCGATCA 57.988 40.909 0.00 0.00 0.00 2.92
6505 10795 2.936498 CCTGCTAACGGTCCATAAGTTG 59.064 50.000 0.00 0.00 0.00 3.16
6724 11014 3.391296 ACCTGCTAGTTCTTTCCAACAGA 59.609 43.478 0.00 0.00 0.00 3.41
6741 11031 8.006298 TCCAACAGAACATTGTGTTTTTCTAT 57.994 30.769 4.51 0.00 41.21 1.98
6749 11039 9.986833 GAACATTGTGTTTTTCTATTGCTTTTT 57.013 25.926 0.00 0.00 41.28 1.94
6793 11087 4.201940 TGTCTTGATATGCGCAATTCTTGG 60.202 41.667 17.11 8.73 0.00 3.61
6794 11088 3.316029 TCTTGATATGCGCAATTCTTGGG 59.684 43.478 17.11 0.99 45.41 4.12
6795 11089 2.653726 TGATATGCGCAATTCTTGGGT 58.346 42.857 17.11 0.00 44.56 4.51
6861 11155 8.822855 TGTATTGTAGTTATTTAGGACGCAATG 58.177 33.333 0.00 0.00 32.71 2.82
6879 11173 2.579207 TGTAGCGTCTCAACTATGGC 57.421 50.000 0.00 0.00 0.00 4.40
6882 11176 1.186200 AGCGTCTCAACTATGGCAGA 58.814 50.000 0.00 0.00 0.00 4.26
6883 11177 1.759445 AGCGTCTCAACTATGGCAGAT 59.241 47.619 0.00 0.00 0.00 2.90
6884 11178 2.959030 AGCGTCTCAACTATGGCAGATA 59.041 45.455 0.00 0.00 0.00 1.98
6885 11179 3.053455 GCGTCTCAACTATGGCAGATAC 58.947 50.000 0.00 0.00 0.00 2.24
6886 11180 3.490933 GCGTCTCAACTATGGCAGATACA 60.491 47.826 0.00 0.00 0.00 2.29
6887 11181 4.682787 CGTCTCAACTATGGCAGATACAA 58.317 43.478 0.00 0.00 0.00 2.41
6888 11182 5.292765 CGTCTCAACTATGGCAGATACAAT 58.707 41.667 0.00 0.00 0.00 2.71
6889 11183 5.176406 CGTCTCAACTATGGCAGATACAATG 59.824 44.000 0.00 0.00 0.00 2.82
6890 11184 6.283694 GTCTCAACTATGGCAGATACAATGA 58.716 40.000 0.00 0.00 0.00 2.57
6891 11185 6.423302 GTCTCAACTATGGCAGATACAATGAG 59.577 42.308 0.00 0.96 0.00 2.90
6892 11186 6.098838 TCTCAACTATGGCAGATACAATGAGT 59.901 38.462 0.00 0.00 0.00 3.41
6893 11187 7.287696 TCTCAACTATGGCAGATACAATGAGTA 59.712 37.037 0.00 0.00 37.06 2.59
6894 11188 7.791029 TCAACTATGGCAGATACAATGAGTAA 58.209 34.615 0.00 0.00 36.05 2.24
6895 11189 8.432013 TCAACTATGGCAGATACAATGAGTAAT 58.568 33.333 0.00 0.00 36.05 1.89
6896 11190 8.501580 CAACTATGGCAGATACAATGAGTAATG 58.498 37.037 0.00 0.00 36.05 1.90
6897 11191 7.966812 ACTATGGCAGATACAATGAGTAATGA 58.033 34.615 0.00 0.00 36.05 2.57
6898 11192 7.875041 ACTATGGCAGATACAATGAGTAATGAC 59.125 37.037 0.00 0.00 36.05 3.06
6899 11193 5.988287 TGGCAGATACAATGAGTAATGACA 58.012 37.500 0.00 0.00 38.47 3.58
6900 11194 6.594744 TGGCAGATACAATGAGTAATGACAT 58.405 36.000 0.00 0.00 36.88 3.06
6901 11195 6.707608 TGGCAGATACAATGAGTAATGACATC 59.292 38.462 0.00 0.00 36.88 3.06
6902 11196 6.128715 GGCAGATACAATGAGTAATGACATCG 60.129 42.308 0.00 0.00 36.05 3.84
6903 11197 6.642540 GCAGATACAATGAGTAATGACATCGA 59.357 38.462 0.00 0.00 36.05 3.59
6904 11198 7.358765 GCAGATACAATGAGTAATGACATCGAC 60.359 40.741 0.00 0.00 36.05 4.20
6905 11199 7.115520 CAGATACAATGAGTAATGACATCGACC 59.884 40.741 0.00 0.00 36.05 4.79
6906 11200 5.084818 ACAATGAGTAATGACATCGACCA 57.915 39.130 0.00 0.00 0.00 4.02
6907 11201 5.487433 ACAATGAGTAATGACATCGACCAA 58.513 37.500 0.00 0.00 0.00 3.67
6940 11234 3.040147 ACGACATCGACCAAAACATCT 57.960 42.857 8.54 0.00 43.02 2.90
6943 11237 4.566759 ACGACATCGACCAAAACATCTATG 59.433 41.667 8.54 0.00 43.02 2.23
6945 11239 3.309682 ACATCGACCAAAACATCTATGCG 59.690 43.478 0.00 0.00 0.00 4.73
6946 11240 3.239587 TCGACCAAAACATCTATGCGA 57.760 42.857 0.00 0.00 0.00 5.10
6962 11256 8.678199 CATCTATGCGAGGATAGATACACTTTA 58.322 37.037 21.22 0.00 41.71 1.85
6963 11257 8.041829 TCTATGCGAGGATAGATACACTTTAC 57.958 38.462 9.75 0.00 31.26 2.01
6967 11261 6.978659 TGCGAGGATAGATACACTTTACAAAG 59.021 38.462 0.13 0.13 41.73 2.77
6981 11275 9.220767 ACACTTTACAAAGGTCTCAATATCTTC 57.779 33.333 6.66 0.00 40.31 2.87
6988 11282 8.986991 ACAAAGGTCTCAATATCTTCTAGACAT 58.013 33.333 0.00 0.00 38.63 3.06
7017 11311 2.346803 TGCGCCTCTATGAGTTTTGAC 58.653 47.619 4.18 0.00 0.00 3.18
7020 11314 2.345641 CGCCTCTATGAGTTTTGACACG 59.654 50.000 0.00 0.00 0.00 4.49
7026 11320 0.730265 TGAGTTTTGACACGGTGCAC 59.270 50.000 8.80 8.80 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 71 0.818296 CAACTAGAGTGGACGGGGAG 59.182 60.000 0.00 0.00 0.00 4.30
66 75 4.124238 TGTTTTTCAACTAGAGTGGACGG 58.876 43.478 0.00 0.00 33.58 4.79
68 77 5.511571 GCTTGTTTTTCAACTAGAGTGGAC 58.488 41.667 0.00 0.00 37.81 4.02
74 83 3.625764 AGTGCGCTTGTTTTTCAACTAGA 59.374 39.130 9.73 0.00 37.81 2.43
100 115 1.945354 GATTCAGTGGAGGACGGCGA 61.945 60.000 16.62 0.00 0.00 5.54
152 170 1.076559 TGGGCCGGAGATAAGTCGA 60.077 57.895 5.05 0.00 0.00 4.20
332 375 2.224066 CGGATAGGGGCACTGTCTAAAG 60.224 54.545 13.47 0.00 37.47 1.85
335 378 0.260816 ACGGATAGGGGCACTGTCTA 59.739 55.000 13.47 0.00 37.47 2.59
357 475 0.614812 GTTACTTGGGGGCTTACGGA 59.385 55.000 0.00 0.00 0.00 4.69
360 478 4.704965 CAGATAGTTACTTGGGGGCTTAC 58.295 47.826 0.00 0.00 0.00 2.34
361 479 3.135895 GCAGATAGTTACTTGGGGGCTTA 59.864 47.826 0.00 0.00 0.00 3.09
370 488 6.109359 GGATTGACACTGCAGATAGTTACTT 58.891 40.000 23.35 3.27 0.00 2.24
371 489 5.187772 TGGATTGACACTGCAGATAGTTACT 59.812 40.000 23.35 6.86 0.00 2.24
372 490 5.419542 TGGATTGACACTGCAGATAGTTAC 58.580 41.667 23.35 6.65 0.00 2.50
373 491 5.675684 TGGATTGACACTGCAGATAGTTA 57.324 39.130 23.35 9.73 0.00 2.24
374 492 4.558226 TGGATTGACACTGCAGATAGTT 57.442 40.909 23.35 0.00 0.00 2.24
375 493 4.767578 ATGGATTGACACTGCAGATAGT 57.232 40.909 23.35 15.55 0.00 2.12
376 494 6.370994 GGATTATGGATTGACACTGCAGATAG 59.629 42.308 23.35 12.22 0.00 2.08
377 495 6.183361 TGGATTATGGATTGACACTGCAGATA 60.183 38.462 23.35 0.94 0.00 1.98
392 514 1.071699 GGCTTACCGCTGGATTATGGA 59.928 52.381 1.50 0.00 39.13 3.41
462 586 7.967303 TGCAAAATCCAAAATTTTCTGTTCAAC 59.033 29.630 0.00 0.00 0.00 3.18
468 592 8.129840 TCAACATGCAAAATCCAAAATTTTCTG 58.870 29.630 0.00 0.00 0.00 3.02
475 600 6.111382 TCAACTCAACATGCAAAATCCAAAA 58.889 32.000 0.00 0.00 0.00 2.44
476 601 5.668471 TCAACTCAACATGCAAAATCCAAA 58.332 33.333 0.00 0.00 0.00 3.28
480 605 7.383029 TCAATTCTCAACTCAACATGCAAAATC 59.617 33.333 0.00 0.00 0.00 2.17
488 613 9.688592 GAAAATTCTCAATTCTCAACTCAACAT 57.311 29.630 0.00 0.00 0.00 2.71
489 614 7.857389 CGAAAATTCTCAATTCTCAACTCAACA 59.143 33.333 0.00 0.00 0.00 3.33
490 615 7.324616 CCGAAAATTCTCAATTCTCAACTCAAC 59.675 37.037 0.00 0.00 0.00 3.18
491 616 7.362662 CCGAAAATTCTCAATTCTCAACTCAA 58.637 34.615 0.00 0.00 0.00 3.02
492 617 6.072508 CCCGAAAATTCTCAATTCTCAACTCA 60.073 38.462 0.00 0.00 0.00 3.41
494 619 5.770162 ACCCGAAAATTCTCAATTCTCAACT 59.230 36.000 0.00 0.00 0.00 3.16
495 620 6.013842 ACCCGAAAATTCTCAATTCTCAAC 57.986 37.500 0.00 0.00 0.00 3.18
496 621 6.294508 GGAACCCGAAAATTCTCAATTCTCAA 60.295 38.462 0.00 0.00 0.00 3.02
497 622 5.183140 GGAACCCGAAAATTCTCAATTCTCA 59.817 40.000 0.00 0.00 0.00 3.27
498 623 5.416013 AGGAACCCGAAAATTCTCAATTCTC 59.584 40.000 0.00 0.00 0.00 2.87
549 682 0.852136 AAAACGCGCTCAAAATGTGC 59.148 45.000 5.73 0.00 37.55 4.57
554 687 1.532921 CCAGTCAAAACGCGCTCAAAA 60.533 47.619 5.73 0.00 0.00 2.44
555 688 0.028770 CCAGTCAAAACGCGCTCAAA 59.971 50.000 5.73 0.00 0.00 2.69
556 689 1.646540 CCAGTCAAAACGCGCTCAA 59.353 52.632 5.73 0.00 0.00 3.02
558 691 1.901650 CTCCCAGTCAAAACGCGCTC 61.902 60.000 5.73 0.00 0.00 5.03
573 716 4.262617 GGATGTTTAGGAAGTCAACTCCC 58.737 47.826 0.00 0.00 0.00 4.30
579 722 7.283127 GCATTAATCTGGATGTTTAGGAAGTCA 59.717 37.037 0.00 0.00 0.00 3.41
592 735 7.318141 CAAGTCAAAACAGCATTAATCTGGAT 58.682 34.615 15.06 5.41 35.94 3.41
598 741 6.655078 ACTCCAAGTCAAAACAGCATTAAT 57.345 33.333 0.00 0.00 0.00 1.40
604 747 5.500645 AGTTTACTCCAAGTCAAAACAGC 57.499 39.130 7.74 0.00 32.08 4.40
670 996 8.635765 TCTAAGTTTAAAAGTTCAGATGCCAT 57.364 30.769 0.00 0.00 0.00 4.40
673 999 7.584987 TGCTCTAAGTTTAAAAGTTCAGATGC 58.415 34.615 0.00 0.00 0.00 3.91
705 1211 9.250624 GTGTGCTAGACAGTTATTAATAAGAGG 57.749 37.037 8.18 4.12 34.28 3.69
712 1247 8.991243 AATAACGTGTGCTAGACAGTTATTAA 57.009 30.769 21.36 0.00 41.26 1.40
713 1248 8.991243 AAATAACGTGTGCTAGACAGTTATTA 57.009 30.769 22.00 11.49 41.64 0.98
715 1250 7.321153 AGAAATAACGTGTGCTAGACAGTTAT 58.679 34.615 0.00 8.45 38.80 1.89
719 1254 5.287274 CAGAGAAATAACGTGTGCTAGACAG 59.713 44.000 0.00 0.00 34.28 3.51
752 1287 7.390996 TGAAAAGCAAAATTGATGGCATGTAAT 59.609 29.630 3.81 2.51 0.00 1.89
762 1297 6.819284 TCCTGTTCTGAAAAGCAAAATTGAT 58.181 32.000 1.85 0.00 0.00 2.57
773 1308 6.205464 CAGCTCTGTTTATCCTGTTCTGAAAA 59.795 38.462 0.00 0.00 0.00 2.29
774 1309 5.702670 CAGCTCTGTTTATCCTGTTCTGAAA 59.297 40.000 0.00 0.00 0.00 2.69
775 1310 5.240891 CAGCTCTGTTTATCCTGTTCTGAA 58.759 41.667 0.00 0.00 0.00 3.02
776 1311 4.825422 CAGCTCTGTTTATCCTGTTCTGA 58.175 43.478 0.00 0.00 0.00 3.27
777 1312 3.373439 GCAGCTCTGTTTATCCTGTTCTG 59.627 47.826 0.00 0.00 0.00 3.02
784 1329 4.201990 CCATTTGAGCAGCTCTGTTTATCC 60.202 45.833 23.15 0.00 0.00 2.59
788 1333 2.867624 TCCATTTGAGCAGCTCTGTTT 58.132 42.857 23.15 3.17 0.00 2.83
790 1335 2.366533 CATCCATTTGAGCAGCTCTGT 58.633 47.619 23.15 6.47 0.00 3.41
817 1362 1.067821 GCTGATACACTCGGAAGGGAG 59.932 57.143 0.00 0.00 39.97 4.30
851 1404 0.111061 TGCTCCTCTGTTTGTGGCAT 59.889 50.000 0.00 0.00 0.00 4.40
856 1409 6.059787 AGAAGAATATGCTCCTCTGTTTGT 57.940 37.500 0.00 0.00 0.00 2.83
888 1454 5.215252 AGAATTCTCAGAGTTCGAAACCA 57.785 39.130 0.88 0.00 34.27 3.67
893 1459 3.006859 TGGCAAGAATTCTCAGAGTTCGA 59.993 43.478 8.78 0.00 34.27 3.71
898 1464 5.640189 ATTGTTGGCAAGAATTCTCAGAG 57.360 39.130 16.07 0.86 38.10 3.35
916 1493 6.764308 ATGCAACAAACTAGATGCTATTGT 57.236 33.333 0.00 0.00 38.05 2.71
926 1503 4.153986 CGCTCAGAAATGCAACAAACTAG 58.846 43.478 0.00 0.00 0.00 2.57
928 1505 2.287788 CCGCTCAGAAATGCAACAAACT 60.288 45.455 0.00 0.00 0.00 2.66
931 1508 1.266718 GTCCGCTCAGAAATGCAACAA 59.733 47.619 0.00 0.00 0.00 2.83
932 1509 0.874390 GTCCGCTCAGAAATGCAACA 59.126 50.000 0.00 0.00 0.00 3.33
939 1516 1.006571 GTGTCCGTCCGCTCAGAAA 60.007 57.895 0.00 0.00 0.00 2.52
948 1553 0.528470 CAGAGGAGAAGTGTCCGTCC 59.472 60.000 0.00 0.00 42.05 4.79
951 1556 0.962489 ACACAGAGGAGAAGTGTCCG 59.038 55.000 0.00 0.00 42.36 4.79
957 1562 5.146010 AGCTAAAGAACACAGAGGAGAAG 57.854 43.478 0.00 0.00 0.00 2.85
988 1593 5.073428 ACTCTGGATCATCTACAAGCGATA 58.927 41.667 0.00 0.00 0.00 2.92
996 1601 6.488683 AGCTGTAGTAACTCTGGATCATCTAC 59.511 42.308 0.00 0.00 0.00 2.59
998 1603 5.454062 AGCTGTAGTAACTCTGGATCATCT 58.546 41.667 0.00 0.00 0.00 2.90
1019 1624 0.877743 GAAGCTCAACCTCCACAAGC 59.122 55.000 0.00 0.00 0.00 4.01
1031 1636 1.338337 GCTAGCATACCTCGAAGCTCA 59.662 52.381 10.63 0.00 38.47 4.26
1049 1654 6.006449 ACAATGTAGAGAACTGGAAAATGCT 58.994 36.000 0.00 0.00 0.00 3.79
1052 1659 9.533253 CAAAAACAATGTAGAGAACTGGAAAAT 57.467 29.630 0.00 0.00 0.00 1.82
1107 1720 7.040132 TGCAAAAAGAAGGGAAACAACAAAATT 60.040 29.630 0.00 0.00 0.00 1.82
1113 1726 3.309682 GCTGCAAAAAGAAGGGAAACAAC 59.690 43.478 0.00 0.00 0.00 3.32
1124 1737 2.551459 GAGAAGCTCTGCTGCAAAAAGA 59.449 45.455 3.02 0.00 39.62 2.52
1131 1744 2.748532 AGAAATTGAGAAGCTCTGCTGC 59.251 45.455 0.00 0.00 39.62 5.25
1132 1745 4.934001 TGTAGAAATTGAGAAGCTCTGCTG 59.066 41.667 0.00 0.00 39.62 4.41
1134 1747 5.411053 ACTTGTAGAAATTGAGAAGCTCTGC 59.589 40.000 0.00 0.00 0.00 4.26
1142 1755 5.546499 ACCAGGGTACTTGTAGAAATTGAGA 59.454 40.000 0.00 0.00 0.00 3.27
1147 1760 5.487488 TCATCACCAGGGTACTTGTAGAAAT 59.513 40.000 0.00 0.00 0.00 2.17
1159 1772 1.673767 ATGAACCTCATCACCAGGGT 58.326 50.000 0.00 0.00 29.59 4.34
1177 1795 5.287042 ACAGGGCAGATCTATGGATGATAT 58.713 41.667 0.00 0.00 31.46 1.63
1188 1806 1.489649 CAAGGATGACAGGGCAGATCT 59.510 52.381 0.00 0.00 0.00 2.75
1284 1911 0.530744 ATTTGTAGTCGCCGCTCTCA 59.469 50.000 0.00 0.00 0.00 3.27
1314 1941 2.327200 GCCTAAGGTTGGCTTCGTAT 57.673 50.000 0.00 0.00 46.38 3.06
1329 1956 0.105453 GGGTGGATGAGAGGAGCCTA 60.105 60.000 0.00 0.00 0.00 3.93
1374 2001 3.379445 TCGGTGGCGAAGAGGGTC 61.379 66.667 0.00 0.00 0.00 4.46
1395 2022 1.959985 ACATTCGGAACATTGCCAACA 59.040 42.857 0.00 0.00 0.00 3.33
1443 2070 0.116143 AGGCAGAGGAGTTGGAGTCT 59.884 55.000 0.00 0.00 0.00 3.24
1520 2147 1.603171 TAGTACACGGTGGCGTCCA 60.603 57.895 13.48 0.00 0.00 4.02
1544 2171 3.186345 CTGAGCATGCAGGGATTGT 57.814 52.632 21.98 0.00 32.26 2.71
1648 2281 1.878656 AAGGAGTCGGCTCTTGTCGG 61.879 60.000 17.97 0.00 42.24 4.79
1996 2635 1.463444 GTTCACGGTAATCAGTGGCAC 59.537 52.381 10.29 10.29 39.53 5.01
2086 2743 8.497745 AGGATGAGACTTTTACATACCATGAAT 58.502 33.333 0.00 0.00 0.00 2.57
2103 2761 1.144936 CTGCCGGGAAGGATGAGAC 59.855 63.158 2.18 0.00 45.00 3.36
2130 2788 1.890979 GCCGAGATGCCATGTCCAG 60.891 63.158 0.00 0.00 0.00 3.86
2142 2806 5.344743 AATCAATCTAACTGAAGCCGAGA 57.655 39.130 0.00 0.00 0.00 4.04
2170 2835 1.737838 AGATGTGTGGCATGTTACCG 58.262 50.000 0.00 0.00 38.06 4.02
2588 5178 7.372260 ACCATTCTGACTATAGCATCTTTCT 57.628 36.000 0.00 0.00 0.00 2.52
2600 5190 5.560722 TGACCTTTGAACCATTCTGACTA 57.439 39.130 0.00 0.00 0.00 2.59
2746 6594 9.166126 CGTCCTAAGAAAAACAAAAAGTCATAC 57.834 33.333 0.00 0.00 0.00 2.39
2964 6854 9.387257 GTAAGATTTCCGTTCCTAAATTAAGGA 57.613 33.333 0.00 0.00 44.12 3.36
3019 6915 0.871722 TCCAAACCAATGCGTCTTCG 59.128 50.000 0.00 0.00 40.37 3.79
3082 6978 1.548719 TGTGTAGCACGCAATACCTCT 59.451 47.619 0.89 0.00 35.42 3.69
3418 7329 2.613133 CGGTTCGGGTGTGACTTAAAAA 59.387 45.455 0.00 0.00 0.00 1.94
3419 7330 2.211806 CGGTTCGGGTGTGACTTAAAA 58.788 47.619 0.00 0.00 0.00 1.52
3852 7775 2.910479 ATCGCCGCCGGTATGAGA 60.910 61.111 4.45 0.00 34.56 3.27
3853 7776 2.430921 GATCGCCGCCGGTATGAG 60.431 66.667 4.45 0.00 34.56 2.90
3921 7844 4.643334 AGAGGTATGCACGTGTAGTTATCA 59.357 41.667 18.38 4.75 0.00 2.15
4024 7961 2.370189 CTCTCTCCCTCTCTCTCTCTCC 59.630 59.091 0.00 0.00 0.00 3.71
4044 7983 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4048 7987 3.634448 CGTCTCTCTCTCTCTCTCTCTCT 59.366 52.174 0.00 0.00 0.00 3.10
4049 7988 3.797184 GCGTCTCTCTCTCTCTCTCTCTC 60.797 56.522 0.00 0.00 0.00 3.20
4050 7989 2.101582 GCGTCTCTCTCTCTCTCTCTCT 59.898 54.545 0.00 0.00 0.00 3.10
4058 7997 1.841277 TCCTAAGGCGTCTCTCTCTCT 59.159 52.381 0.00 0.00 0.00 3.10
4214 8153 8.275015 TCTTAACTCAACAAACATCACTCAAA 57.725 30.769 0.00 0.00 0.00 2.69
4264 8203 3.959975 GAGCCCGTGCGTTGCAAA 61.960 61.111 0.00 0.00 41.47 3.68
4464 8426 7.633789 AGGGCATCGATAATATAATGGAAAGT 58.366 34.615 0.00 0.00 0.00 2.66
4864 8852 5.622233 GCAATTTCTGTTCCATCTGGTAACC 60.622 44.000 0.00 0.00 36.34 2.85
4962 8950 5.123820 GCTTGACCAGATTATTGTGCTGTAA 59.876 40.000 0.00 0.00 0.00 2.41
5115 9104 8.478066 ACATGAGAGAGTGCATTTTATAGTACA 58.522 33.333 0.00 0.00 0.00 2.90
5170 9159 9.438291 CGATTATCACACATCTTTTATTCCAAC 57.562 33.333 0.00 0.00 0.00 3.77
5597 9612 4.267349 TCCAAGGAGGTTAAGAAAGTCG 57.733 45.455 0.00 0.00 39.02 4.18
5679 9694 9.630098 GCAGAGAATTTATCAACATGAAAAAGA 57.370 29.630 0.00 0.00 0.00 2.52
5753 9779 3.452264 TGGATCTCCTCAACAATCGATGT 59.548 43.478 0.00 0.00 39.67 3.06
5782 9808 7.687103 GCAATGTTAATGTACCTACTAGCCTCT 60.687 40.741 0.00 0.00 0.00 3.69
5877 9903 5.586643 GGCTCTGGAAGAATAAAATTCTCGT 59.413 40.000 2.79 0.00 46.34 4.18
6116 10154 7.502226 CCAAAATATGATAGGCTTACTTGGTCA 59.498 37.037 0.00 0.00 0.00 4.02
6164 10291 4.541779 CGGTGCACAAAAGCTAAATACAA 58.458 39.130 20.43 0.00 34.99 2.41
6215 10347 5.932303 CCTTTGGATTTCAAGTCTTCTACGA 59.068 40.000 0.00 0.00 36.62 3.43
6351 10593 5.483937 TCAAGGTTTCCATGACTCTAGCTAA 59.516 40.000 0.00 0.00 0.00 3.09
6354 10596 4.187694 CTCAAGGTTTCCATGACTCTAGC 58.812 47.826 0.00 0.00 27.96 3.42
6360 10622 1.177401 GGCCTCAAGGTTTCCATGAC 58.823 55.000 0.00 0.00 37.57 3.06
6465 10755 7.206981 AGCAGGATAAATACCAAAATGATCG 57.793 36.000 0.00 0.00 0.00 3.69
6470 10760 6.831868 ACCGTTAGCAGGATAAATACCAAAAT 59.168 34.615 0.00 0.00 0.00 1.82
6505 10795 7.727181 AGTACCAATGAGTAGTATGGTTGATC 58.273 38.462 1.16 0.00 43.47 2.92
6561 10851 2.749776 ACTTGCCACGTAAATTTTGCC 58.250 42.857 0.00 0.00 0.00 4.52
6678 10968 4.343814 TGCGAGGTCATCATATTTGGTCTA 59.656 41.667 0.00 0.00 0.00 2.59
6782 11076 2.616842 GGTATACCACCCAAGAATTGCG 59.383 50.000 17.44 0.00 42.07 4.85
6795 11089 8.887264 ATTTCACCTTATTGTTTGGTATACCA 57.113 30.769 21.05 21.05 45.94 3.25
6861 11155 2.099263 TCTGCCATAGTTGAGACGCTAC 59.901 50.000 0.00 0.00 0.00 3.58
6866 11160 6.283694 TCATTGTATCTGCCATAGTTGAGAC 58.716 40.000 0.00 0.00 0.00 3.36
6876 11170 5.988287 TGTCATTACTCATTGTATCTGCCA 58.012 37.500 0.00 0.00 0.00 4.92
6879 11173 7.115520 GGTCGATGTCATTACTCATTGTATCTG 59.884 40.741 0.00 0.00 0.00 2.90
6882 11176 6.816136 TGGTCGATGTCATTACTCATTGTAT 58.184 36.000 0.00 0.00 0.00 2.29
6883 11177 6.215495 TGGTCGATGTCATTACTCATTGTA 57.785 37.500 0.00 0.00 0.00 2.41
6884 11178 5.084818 TGGTCGATGTCATTACTCATTGT 57.915 39.130 0.00 0.00 0.00 2.71
6885 11179 6.421377 TTTGGTCGATGTCATTACTCATTG 57.579 37.500 0.00 0.00 0.00 2.82
6886 11180 7.768582 TGTATTTGGTCGATGTCATTACTCATT 59.231 33.333 0.00 0.00 0.00 2.57
6887 11181 7.272244 TGTATTTGGTCGATGTCATTACTCAT 58.728 34.615 0.00 0.00 0.00 2.90
6888 11182 6.635755 TGTATTTGGTCGATGTCATTACTCA 58.364 36.000 0.00 0.00 0.00 3.41
6889 11183 7.534085 TTGTATTTGGTCGATGTCATTACTC 57.466 36.000 0.00 0.00 0.00 2.59
6890 11184 7.768582 TCATTGTATTTGGTCGATGTCATTACT 59.231 33.333 0.00 0.00 0.00 2.24
6891 11185 7.915508 TCATTGTATTTGGTCGATGTCATTAC 58.084 34.615 0.00 0.00 0.00 1.89
6892 11186 7.768582 ACTCATTGTATTTGGTCGATGTCATTA 59.231 33.333 0.00 0.00 0.00 1.90
6893 11187 6.599244 ACTCATTGTATTTGGTCGATGTCATT 59.401 34.615 0.00 0.00 0.00 2.57
6894 11188 6.115446 ACTCATTGTATTTGGTCGATGTCAT 58.885 36.000 0.00 0.00 0.00 3.06
6895 11189 5.487433 ACTCATTGTATTTGGTCGATGTCA 58.513 37.500 0.00 0.00 0.00 3.58
6896 11190 7.399523 GTTACTCATTGTATTTGGTCGATGTC 58.600 38.462 0.00 0.00 0.00 3.06
6897 11191 6.035650 CGTTACTCATTGTATTTGGTCGATGT 59.964 38.462 0.00 0.00 0.00 3.06
6898 11192 6.254804 TCGTTACTCATTGTATTTGGTCGATG 59.745 38.462 0.00 0.00 0.00 3.84
6899 11193 6.255020 GTCGTTACTCATTGTATTTGGTCGAT 59.745 38.462 0.00 0.00 0.00 3.59
6900 11194 5.574055 GTCGTTACTCATTGTATTTGGTCGA 59.426 40.000 0.00 0.00 0.00 4.20
6901 11195 5.346551 TGTCGTTACTCATTGTATTTGGTCG 59.653 40.000 0.00 0.00 0.00 4.79
6902 11196 6.715344 TGTCGTTACTCATTGTATTTGGTC 57.285 37.500 0.00 0.00 0.00 4.02
6903 11197 6.035650 CGATGTCGTTACTCATTGTATTTGGT 59.964 38.462 0.00 0.00 34.11 3.67
6904 11198 6.254804 TCGATGTCGTTACTCATTGTATTTGG 59.745 38.462 2.04 0.00 40.80 3.28
6905 11199 7.111139 GTCGATGTCGTTACTCATTGTATTTG 58.889 38.462 2.04 0.00 40.80 2.32
6906 11200 6.255020 GGTCGATGTCGTTACTCATTGTATTT 59.745 38.462 2.04 0.00 40.80 1.40
6907 11201 5.747197 GGTCGATGTCGTTACTCATTGTATT 59.253 40.000 2.04 0.00 40.80 1.89
6940 11234 7.754851 TGTAAAGTGTATCTATCCTCGCATA 57.245 36.000 0.00 0.00 0.00 3.14
6943 11237 6.421202 CCTTTGTAAAGTGTATCTATCCTCGC 59.579 42.308 3.90 0.00 34.20 5.03
6945 11239 8.697292 AGACCTTTGTAAAGTGTATCTATCCTC 58.303 37.037 3.90 0.00 34.20 3.71
6946 11240 8.611051 AGACCTTTGTAAAGTGTATCTATCCT 57.389 34.615 3.90 0.00 34.20 3.24
6962 11256 8.367660 TGTCTAGAAGATATTGAGACCTTTGT 57.632 34.615 0.00 0.00 36.52 2.83
6963 11257 9.258826 CATGTCTAGAAGATATTGAGACCTTTG 57.741 37.037 0.00 2.70 36.52 2.77
6967 11261 6.991938 AGCATGTCTAGAAGATATTGAGACC 58.008 40.000 0.00 0.00 36.52 3.85
6976 11270 4.806247 GCAACGTAAGCATGTCTAGAAGAT 59.194 41.667 7.92 0.00 45.62 2.40
6981 11275 1.005975 GCGCAACGTAAGCATGTCTAG 60.006 52.381 0.30 0.00 45.62 2.43
6988 11282 0.174845 ATAGAGGCGCAACGTAAGCA 59.825 50.000 10.83 0.00 45.62 3.91


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

AutoCloner maintained by Alex Coulton.