Multiple sequence alignment - TraesCS6B01G076400

Loading Multiple Alignment...

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 TraesCS6B01G076400 chr6B 100.000 5106 0 0 337 5442 52361970 52356865 0.000000e+00 9430.0
1 TraesCS6B01G076400 chr6B 89.291 1905 160 30 994 2877 51912364 51914245 0.000000e+00 2348.0
2 TraesCS6B01G076400 chr6B 78.583 1284 199 41 1044 2289 51577657 51576412 0.000000e+00 778.0
3 TraesCS6B01G076400 chr6B 76.953 1280 217 54 1041 2291 51612004 51613234 0.000000e+00 658.0
4 TraesCS6B01G076400 chr6B 85.548 602 73 8 2320 2919 51576555 51575966 7.740000e-173 617.0
5 TraesCS6B01G076400 chr6B 100.000 161 0 0 1 161 52362306 52362146 1.150000e-76 298.0
6 TraesCS6B01G076400 chr6B 80.456 307 48 10 1009 1312 63364738 63365035 1.970000e-54 224.0
7 TraesCS6B01G076400 chr6B 89.041 146 14 2 3100 3244 51576588 51576444 4.330000e-41 180.0
8 TraesCS6B01G076400 chr6B 75.904 332 65 10 1805 2124 51310796 51310468 7.300000e-34 156.0
9 TraesCS6B01G076400 chr6B 90.526 95 9 0 3310 3404 41404863 41404769 5.720000e-25 126.0
10 TraesCS6B01G076400 chr6B 85.950 121 13 4 3100 3218 51613062 51613180 5.720000e-25 126.0
11 TraesCS6B01G076400 chr6B 81.395 129 19 5 1319 1445 62119418 62119543 3.470000e-17 100.0
12 TraesCS6B01G076400 chr6D 92.425 2495 123 20 855 3302 28305317 28302842 0.000000e+00 3500.0
13 TraesCS6B01G076400 chr6D 89.111 1451 84 15 3393 4836 28302836 28301453 0.000000e+00 1736.0
14 TraesCS6B01G076400 chr6D 83.981 1286 151 31 1034 2283 27860104 27861370 0.000000e+00 1182.0
15 TraesCS6B01G076400 chr6D 77.872 1297 233 36 1045 2320 28411425 28410162 0.000000e+00 756.0
16 TraesCS6B01G076400 chr6D 76.947 1284 215 52 1041 2291 27840341 27841576 0.000000e+00 656.0
17 TraesCS6B01G076400 chr6D 83.792 691 81 18 3393 4071 27861415 27862086 1.290000e-175 627.0
18 TraesCS6B01G076400 chr6D 80.894 492 69 15 1044 1521 27815749 27815269 1.110000e-96 364.0
19 TraesCS6B01G076400 chr6D 88.364 275 29 3 2320 2593 28410335 28410063 1.460000e-85 327.0
20 TraesCS6B01G076400 chr6D 86.239 218 20 10 3100 3311 27861203 27861416 1.520000e-55 228.0
21 TraesCS6B01G076400 chr6D 74.480 529 97 28 3460 3965 27761292 27761805 1.550000e-45 195.0
22 TraesCS6B01G076400 chr6D 90.977 133 10 1 693 825 28305445 28305315 1.560000e-40 178.0
23 TraesCS6B01G076400 chr6D 77.778 315 31 16 5115 5393 27863282 27863593 2.030000e-34 158.0
24 TraesCS6B01G076400 chr6D 75.988 329 64 9 1823 2139 28326642 28326317 7.300000e-34 156.0
25 TraesCS6B01G076400 chr6D 89.524 105 9 1 3310 3414 29232378 29232276 1.230000e-26 132.0
26 TraesCS6B01G076400 chr6D 76.316 266 47 12 1805 2058 36124237 36123976 1.590000e-25 128.0
27 TraesCS6B01G076400 chr6D 92.045 88 7 0 4407 4494 27862269 27862356 2.060000e-24 124.0
28 TraesCS6B01G076400 chr6D 86.667 105 10 3 2320 2421 27761058 27761161 4.460000e-21 113.0
29 TraesCS6B01G076400 chr6A 90.641 1186 69 17 3393 4568 29604107 29605260 0.000000e+00 1537.0
30 TraesCS6B01G076400 chr6A 89.968 937 57 19 4533 5437 29605266 29606197 0.000000e+00 1175.0
31 TraesCS6B01G076400 chr6A 84.138 870 95 20 3393 4248 29887372 29886532 0.000000e+00 802.0
32 TraesCS6B01G076400 chr6A 78.660 1284 198 48 1044 2289 30041684 30040439 0.000000e+00 784.0
33 TraesCS6B01G076400 chr6A 85.904 603 70 12 2320 2919 30040582 30039992 3.580000e-176 628.0
34 TraesCS6B01G076400 chr6A 84.615 520 54 15 2320 2827 596400792 596400287 1.360000e-135 494.0
35 TraesCS6B01G076400 chr6A 82.055 613 70 17 1034 1625 29969422 29968829 2.280000e-133 486.0
36 TraesCS6B01G076400 chr6A 92.038 314 19 4 3003 3311 29603796 29604108 2.330000e-118 436.0
37 TraesCS6B01G076400 chr6A 85.575 409 50 9 1861 2263 29968806 29968401 2.340000e-113 420.0
38 TraesCS6B01G076400 chr6A 76.941 837 122 48 3721 4532 30211741 30210951 1.410000e-110 411.0
39 TraesCS6B01G076400 chr6A 82.198 455 74 6 4089 4537 30033073 30032620 8.550000e-103 385.0
40 TraesCS6B01G076400 chr6A 87.415 294 32 4 2320 2610 29497071 29497362 3.140000e-87 333.0
41 TraesCS6B01G076400 chr6A 83.881 335 50 4 4181 4514 29967663 29967332 3.160000e-82 316.0
42 TraesCS6B01G076400 chr6A 86.813 273 34 2 4243 4514 29886376 29886105 2.460000e-78 303.0
43 TraesCS6B01G076400 chr6A 81.766 351 56 6 4632 4976 29966962 29966614 2.480000e-73 287.0
44 TraesCS6B01G076400 chr6A 79.167 432 66 16 1030 1445 34009363 34009786 1.490000e-70 278.0
45 TraesCS6B01G076400 chr6A 86.634 202 19 7 3114 3311 29968535 29968338 3.300000e-52 217.0
46 TraesCS6B01G076400 chr6A 83.243 185 25 4 3393 3574 29490411 29490592 1.210000e-36 165.0
47 TraesCS6B01G076400 chr6A 77.259 343 39 16 5115 5426 29884591 29884257 1.210000e-36 165.0
48 TraesCS6B01G076400 chr6A 87.075 147 15 4 3100 3244 30040615 30040471 4.360000e-36 163.0
49 TraesCS6B01G076400 chr6A 85.034 147 18 4 3100 3244 30135937 30135793 4.390000e-31 147.0
50 TraesCS6B01G076400 chr6A 94.444 90 5 0 3310 3399 93285704 93285793 7.350000e-29 139.0
51 TraesCS6B01G076400 chr6A 75.568 352 45 17 5115 5429 29960816 29960469 9.510000e-28 135.0
52 TraesCS6B01G076400 chr6A 83.803 142 21 2 1805 1945 39948969 39948829 3.420000e-27 134.0
53 TraesCS6B01G076400 chrUn 77.820 1303 229 41 1045 2320 286651794 286650525 0.000000e+00 750.0
54 TraesCS6B01G076400 chrUn 86.909 275 34 2 2320 2593 286650699 286650426 1.900000e-79 307.0
55 TraesCS6B01G076400 chrUn 88.571 210 21 3 2711 2919 286650345 286650138 9.050000e-63 252.0
56 TraesCS6B01G076400 chrUn 81.230 309 50 6 1007 1314 27364870 27365171 5.450000e-60 243.0
57 TraesCS6B01G076400 chrUn 87.755 147 14 4 3100 3244 286650732 286650588 9.370000e-38 169.0
58 TraesCS6B01G076400 chrUn 72.851 221 50 10 1544 1759 27365416 27365631 3.520000e-07 67.6
59 TraesCS6B01G076400 chr1B 92.023 351 17 4 343 684 525851947 525851599 2.950000e-132 483.0
60 TraesCS6B01G076400 chr1B 87.888 322 20 7 343 646 646858276 646858596 1.440000e-95 361.0
61 TraesCS6B01G076400 chr1B 94.410 161 9 0 1 161 646858114 646858274 1.170000e-61 248.0
62 TraesCS6B01G076400 chr1B 93.293 164 8 2 1 161 207854860 207855023 7.040000e-59 239.0
63 TraesCS6B01G076400 chr1B 93.168 161 11 0 1 161 525852109 525851949 2.530000e-58 237.0
64 TraesCS6B01G076400 chr1B 80.066 301 32 16 421 697 32772666 32772370 1.200000e-46 198.0
65 TraesCS6B01G076400 chr4B 90.909 363 23 6 342 696 172453075 172452715 3.810000e-131 479.0
66 TraesCS6B01G076400 chr4B 90.385 364 26 2 337 692 218788293 218788655 2.290000e-128 470.0
67 TraesCS6B01G076400 chr4B 91.304 161 11 3 2 161 172453236 172453078 3.300000e-52 217.0
68 TraesCS6B01G076400 chr4B 90.741 162 14 1 1 161 218788123 218788284 1.190000e-51 215.0
69 TraesCS6B01G076400 chr7A 90.756 357 23 3 350 697 15631341 15630986 8.250000e-128 468.0
70 TraesCS6B01G076400 chr7A 93.662 142 9 0 2 143 15631994 15631853 4.270000e-51 213.0
71 TraesCS6B01G076400 chr5D 89.189 370 23 12 341 697 64135915 64135550 3.870000e-121 446.0
72 TraesCS6B01G076400 chr5D 95.031 161 8 0 1 161 64136077 64135917 2.520000e-63 254.0
73 TraesCS6B01G076400 chr5D 90.526 95 9 0 3310 3404 541992631 541992537 5.720000e-25 126.0
74 TraesCS6B01G076400 chr3B 89.855 345 21 5 359 695 783883838 783884176 1.080000e-116 431.0
75 TraesCS6B01G076400 chr3B 94.488 127 4 2 1 124 783883589 783883715 5.560000e-45 193.0
76 TraesCS6B01G076400 chr3B 95.349 86 4 0 3309 3394 154213774 154213859 2.640000e-28 137.0
77 TraesCS6B01G076400 chr4A 87.349 332 25 5 369 692 686962581 686962903 1.110000e-96 364.0
78 TraesCS6B01G076400 chr4A 80.000 300 28 17 421 694 625260252 625259959 5.560000e-45 193.0
79 TraesCS6B01G076400 chr4A 82.609 230 23 14 2478 2699 720042534 720042754 2.590000e-43 187.0
80 TraesCS6B01G076400 chr4A 91.954 87 7 0 3305 3391 603447582 603447668 7.400000e-24 122.0
81 TraesCS6B01G076400 chr1A 76.484 455 83 17 1036 1475 536811413 536810968 5.480000e-55 226.0
82 TraesCS6B01G076400 chr7B 81.185 287 28 16 421 684 679615282 679614999 1.990000e-49 207.0
83 TraesCS6B01G076400 chr7B 92.632 95 5 2 3307 3400 348195807 348195900 9.510000e-28 135.0
84 TraesCS6B01G076400 chr5B 95.402 87 4 0 3305 3391 62940318 62940404 7.350000e-29 139.0
85 TraesCS6B01G076400 chr3A 96.341 82 3 0 3310 3391 712187196 712187277 9.510000e-28 135.0
86 TraesCS6B01G076400 chr3A 94.318 88 5 0 3308 3395 712686268 712686181 9.510000e-28 135.0
87 TraesCS6B01G076400 chr3A 90.000 100 8 2 3299 3397 57262247 57262149 1.590000e-25 128.0
88 TraesCS6B01G076400 chr3D 90.816 98 7 2 3305 3401 147277474 147277378 4.420000e-26 130.0
89 TraesCS6B01G076400 chr2D 93.902 82 5 0 3310 3391 302248013 302248094 2.060000e-24 124.0
90 TraesCS6B01G076400 chr2D 89.583 96 10 0 3306 3401 556926425 556926520 7.400000e-24 122.0
91 TraesCS6B01G076400 chr2D 88.350 103 9 2 3303 3404 150380648 150380748 2.660000e-23 121.0
92 TraesCS6B01G076400 chr2B 89.796 98 8 2 3305 3402 494265174 494265079 2.060000e-24 124.0


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 TraesCS6B01G076400 chr6B 52356865 52362306 5441 True 4864.000000 9430 100.000000 1 5442 2 chr6B.!!$R4 5441
1 TraesCS6B01G076400 chr6B 51912364 51914245 1881 False 2348.000000 2348 89.291000 994 2877 1 chr6B.!!$F1 1883
2 TraesCS6B01G076400 chr6B 51575966 51577657 1691 True 525.000000 778 84.390667 1044 3244 3 chr6B.!!$R3 2200
3 TraesCS6B01G076400 chr6B 51612004 51613234 1230 False 392.000000 658 81.451500 1041 3218 2 chr6B.!!$F4 2177
4 TraesCS6B01G076400 chr6D 28301453 28305445 3992 True 1804.666667 3500 90.837667 693 4836 3 chr6D.!!$R5 4143
5 TraesCS6B01G076400 chr6D 27840341 27841576 1235 False 656.000000 656 76.947000 1041 2291 1 chr6D.!!$F1 1250
6 TraesCS6B01G076400 chr6D 28410063 28411425 1362 True 541.500000 756 83.118000 1045 2593 2 chr6D.!!$R6 1548
7 TraesCS6B01G076400 chr6D 27860104 27863593 3489 False 463.800000 1182 84.767000 1034 5393 5 chr6D.!!$F3 4359
8 TraesCS6B01G076400 chr6A 29603796 29606197 2401 False 1049.333333 1537 90.882333 3003 5437 3 chr6A.!!$F5 2434
9 TraesCS6B01G076400 chr6A 30039992 30041684 1692 True 525.000000 784 83.879667 1044 3244 3 chr6A.!!$R9 2200
10 TraesCS6B01G076400 chr6A 596400287 596400792 505 True 494.000000 494 84.615000 2320 2827 1 chr6A.!!$R6 507
11 TraesCS6B01G076400 chr6A 29884257 29887372 3115 True 423.333333 802 82.736667 3393 5426 3 chr6A.!!$R7 2033
12 TraesCS6B01G076400 chr6A 30210951 30211741 790 True 411.000000 411 76.941000 3721 4532 1 chr6A.!!$R4 811
13 TraesCS6B01G076400 chr6A 29966614 29969422 2808 True 345.200000 486 83.982200 1034 4976 5 chr6A.!!$R8 3942
14 TraesCS6B01G076400 chrUn 286650138 286651794 1656 True 369.500000 750 85.263750 1045 3244 4 chrUn.!!$R1 2199
15 TraesCS6B01G076400 chr1B 525851599 525852109 510 True 360.000000 483 92.595500 1 684 2 chr1B.!!$R2 683
16 TraesCS6B01G076400 chr4B 172452715 172453236 521 True 348.000000 479 91.106500 2 696 2 chr4B.!!$R1 694
17 TraesCS6B01G076400 chr4B 218788123 218788655 532 False 342.500000 470 90.563000 1 692 2 chr4B.!!$F1 691
18 TraesCS6B01G076400 chr7A 15630986 15631994 1008 True 340.500000 468 92.209000 2 697 2 chr7A.!!$R1 695
19 TraesCS6B01G076400 chr5D 64135550 64136077 527 True 350.000000 446 92.110000 1 697 2 chr5D.!!$R2 696
20 TraesCS6B01G076400 chr3B 783883589 783884176 587 False 312.000000 431 92.171500 1 695 2 chr3B.!!$F2 694

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
135 140 0.387929 TCGCTCGTGTTCTTCCACTT 59.612 50.0 0.00 0.00 33.07 3.16 F
939 1269 0.460987 GGGATCGCAACCTCACTCAG 60.461 60.0 4.64 0.00 0.00 3.35 F
969 1299 0.669318 TCATTTCGAGTCCACCACGC 60.669 55.0 0.00 0.00 0.00 5.34 F
1010 1340 0.738762 CTGACAGACATGACCAGCCG 60.739 60.0 0.00 0.00 0.00 5.52 F
1806 2230 0.886490 CTGAAGGGCGCTTCACTGTT 60.886 55.0 34.71 5.31 38.30 3.16 F
3698 4373 0.323542 ACTGGGTCACGGTAGGAGAG 60.324 60.0 0.00 0.00 36.76 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2016 2443 0.832135 TGACCGTGAAGAGGCTCCTT 60.832 55.00 11.71 4.88 0.00 3.36 R
2803 3243 0.249911 AGCTCCGACTTGAACCACAC 60.250 55.00 0.00 0.00 0.00 3.82 R
2897 3337 7.202016 TCACAAGCTAGTTTTTCAGGTAATG 57.798 36.00 0.00 0.00 0.00 1.90 R
2903 3343 9.736023 AAATAACTTCACAAGCTAGTTTTTCAG 57.264 29.63 4.24 0.00 34.26 3.02 R
3715 4390 0.467844 TGCCCATGTGTTCAGCAAGT 60.468 50.00 0.00 0.00 0.00 3.16 R
4998 6988 0.323725 GAATGCAGCCAAGGAGGGAA 60.324 55.00 0.00 0.00 38.09 3.97 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
94 96 2.231478 CGTAGAGGAGGTGAAGAAGCAA 59.769 50.000 0.00 0.00 0.00 3.91
135 140 0.387929 TCGCTCGTGTTCTTCCACTT 59.612 50.000 0.00 0.00 33.07 3.16
138 143 1.871080 CTCGTGTTCTTCCACTTGCT 58.129 50.000 0.00 0.00 33.07 3.91
413 723 2.121918 GAGGGGTAGGGGATGGGG 60.122 72.222 0.00 0.00 0.00 4.96
467 777 2.283529 GCCGGTGGTCAAGAGGAGA 61.284 63.158 1.90 0.00 0.00 3.71
496 809 5.454062 TCCATGGAGGAAAAGAAGAAACAA 58.546 37.500 11.44 0.00 45.65 2.83
558 872 9.554395 GAAGAGGATAAGGAAGGAGAAAAATAG 57.446 37.037 0.00 0.00 0.00 1.73
598 912 3.443976 CGTGGACCCAACAAAGAAAAAG 58.556 45.455 0.00 0.00 0.00 2.27
599 913 3.119280 CGTGGACCCAACAAAGAAAAAGT 60.119 43.478 0.00 0.00 0.00 2.66
600 914 4.180817 GTGGACCCAACAAAGAAAAAGTG 58.819 43.478 0.00 0.00 0.00 3.16
601 915 3.194861 GGACCCAACAAAGAAAAAGTGC 58.805 45.455 0.00 0.00 0.00 4.40
605 928 4.162131 ACCCAACAAAGAAAAAGTGCAGAT 59.838 37.500 0.00 0.00 0.00 2.90
607 930 4.025480 CCAACAAAGAAAAAGTGCAGATGC 60.025 41.667 0.00 0.00 42.50 3.91
628 951 4.479993 GCATGCCAGCGAGGACCT 62.480 66.667 6.36 0.00 41.22 3.85
700 1023 7.466050 CGTTGCCAAAATTTTACCTTTTAGCAA 60.466 33.333 2.44 9.26 43.14 3.91
701 1024 8.349245 GTTGCCAAAATTTTACCTTTTAGCAAT 58.651 29.630 14.18 0.00 45.18 3.56
774 1097 9.613428 TTTTTAGATGAACATATAGTCCACCTG 57.387 33.333 0.00 0.00 0.00 4.00
803 1126 9.276590 CAATCTGCATATCACTAATGAACCTTA 57.723 33.333 0.00 0.00 38.69 2.69
804 1127 9.499479 AATCTGCATATCACTAATGAACCTTAG 57.501 33.333 0.00 0.00 38.69 2.18
837 1160 9.793259 TTTGAAGACTAGTGAATTTGGAATAGT 57.207 29.630 0.00 0.00 0.00 2.12
838 1161 9.793259 TTGAAGACTAGTGAATTTGGAATAGTT 57.207 29.630 0.00 0.00 0.00 2.24
839 1162 9.436957 TGAAGACTAGTGAATTTGGAATAGTTC 57.563 33.333 0.00 0.00 0.00 3.01
840 1163 9.660180 GAAGACTAGTGAATTTGGAATAGTTCT 57.340 33.333 0.00 0.00 0.00 3.01
854 1177 8.251750 TGGAATAGTTCTTTTTACAGTCATCG 57.748 34.615 0.00 0.00 0.00 3.84
855 1178 7.876068 TGGAATAGTTCTTTTTACAGTCATCGT 59.124 33.333 0.00 0.00 0.00 3.73
856 1179 8.169268 GGAATAGTTCTTTTTACAGTCATCGTG 58.831 37.037 0.00 0.00 0.00 4.35
902 1225 2.104859 GGCCGGGCTTCGTTTACTC 61.105 63.158 22.87 0.00 37.11 2.59
922 1252 4.080299 ACTCTCCTTTTATAGCCTGTTGGG 60.080 45.833 0.00 0.00 38.36 4.12
923 1253 4.108570 TCTCCTTTTATAGCCTGTTGGGA 58.891 43.478 0.00 0.00 37.23 4.37
924 1254 4.726825 TCTCCTTTTATAGCCTGTTGGGAT 59.273 41.667 0.00 0.00 37.23 3.85
926 1256 3.815401 CCTTTTATAGCCTGTTGGGATCG 59.185 47.826 0.00 0.00 37.23 3.69
929 1259 0.546122 ATAGCCTGTTGGGATCGCAA 59.454 50.000 20.25 20.25 37.23 4.85
931 1261 2.700773 GCCTGTTGGGATCGCAACC 61.701 63.158 37.74 25.41 37.23 3.77
932 1262 1.002134 CCTGTTGGGATCGCAACCT 60.002 57.895 37.74 0.00 37.23 3.50
935 1265 0.605319 TGTTGGGATCGCAACCTCAC 60.605 55.000 37.74 23.02 0.00 3.51
939 1269 0.460987 GGGATCGCAACCTCACTCAG 60.461 60.000 4.64 0.00 0.00 3.35
942 1272 1.830587 ATCGCAACCTCACTCAGCCA 61.831 55.000 0.00 0.00 0.00 4.75
947 1277 0.908198 AACCTCACTCAGCCAGATCC 59.092 55.000 0.00 0.00 0.00 3.36
956 1286 4.036498 CACTCAGCCAGATCCATTCATTTC 59.964 45.833 0.00 0.00 0.00 2.17
964 1294 4.272018 CAGATCCATTCATTTCGAGTCCAC 59.728 45.833 0.00 0.00 0.00 4.02
965 1295 2.985896 TCCATTCATTTCGAGTCCACC 58.014 47.619 0.00 0.00 0.00 4.61
966 1296 2.304470 TCCATTCATTTCGAGTCCACCA 59.696 45.455 0.00 0.00 0.00 4.17
967 1297 2.420022 CCATTCATTTCGAGTCCACCAC 59.580 50.000 0.00 0.00 0.00 4.16
968 1298 1.790755 TTCATTTCGAGTCCACCACG 58.209 50.000 0.00 0.00 0.00 4.94
969 1299 0.669318 TCATTTCGAGTCCACCACGC 60.669 55.000 0.00 0.00 0.00 5.34
1010 1340 0.738762 CTGACAGACATGACCAGCCG 60.739 60.000 0.00 0.00 0.00 5.52
1271 1625 2.170607 TCTGCTTCCAACCTACTATGGC 59.829 50.000 0.00 0.00 36.62 4.40
1291 1645 4.770874 CCCCCAATCGCGTTCCGT 62.771 66.667 5.77 0.00 38.35 4.69
1457 1827 2.428890 AGTTCGATCTAGCCAACTCCTG 59.571 50.000 0.00 0.00 0.00 3.86
1461 1831 2.366916 CGATCTAGCCAACTCCTGGATT 59.633 50.000 0.00 0.00 42.96 3.01
1716 2134 6.377327 TTGTTCAATCTCCTTGAGTTTGAC 57.623 37.500 14.13 11.04 43.53 3.18
1735 2153 2.492484 GACTTGAAGACGGAGAGCCTAA 59.508 50.000 0.00 0.00 0.00 2.69
1806 2230 0.886490 CTGAAGGGCGCTTCACTGTT 60.886 55.000 34.71 5.31 38.30 3.16
2016 2443 2.513259 GGTGTTCCTGTGGACCGGA 61.513 63.158 9.46 0.00 0.00 5.14
2080 2510 6.197364 ACAAACTTTTCGACACCAACAATA 57.803 33.333 0.00 0.00 0.00 1.90
2084 2514 1.816074 TTCGACACCAACAATAGGGC 58.184 50.000 0.00 0.00 0.00 5.19
2104 2534 5.537674 AGGGCTTGCTATTATCCATTTGAAG 59.462 40.000 0.00 0.00 0.00 3.02
2136 2569 6.654959 TGCTACAGGTAATAACATGCCTTTA 58.345 36.000 0.00 0.00 41.08 1.85
2138 2571 6.292703 GCTACAGGTAATAACATGCCTTTACG 60.293 42.308 0.00 0.00 41.08 3.18
2143 2576 1.091537 TAACATGCCTTTACGCTGCC 58.908 50.000 0.00 0.00 0.00 4.85
2194 2628 5.859205 AATTGGTCTATGGAATGCCTTTC 57.141 39.130 0.00 0.00 34.31 2.62
2223 2657 6.437162 TCCTTTCATGTTAGGCTAGCAATTTT 59.563 34.615 18.24 0.00 0.00 1.82
2225 2659 8.250332 CCTTTCATGTTAGGCTAGCAATTTTAA 58.750 33.333 18.24 4.16 0.00 1.52
2226 2660 9.807649 CTTTCATGTTAGGCTAGCAATTTTAAT 57.192 29.630 18.24 0.00 0.00 1.40
2398 2832 8.081633 CCTGTCATGTGAAGCTAACAATTTTAA 58.918 33.333 6.28 0.00 0.00 1.52
2453 2887 7.148606 GCTTGATATGATCTCTTCAGCACATAC 60.149 40.741 0.00 0.00 37.89 2.39
2454 2888 6.695429 TGATATGATCTCTTCAGCACATACC 58.305 40.000 0.00 0.00 37.89 2.73
2464 2898 6.446318 TCTTCAGCACATACCAATTTTGTTC 58.554 36.000 0.00 0.00 0.00 3.18
2477 2911 7.145323 ACCAATTTTGTTCTGTAGTGTTATGC 58.855 34.615 0.00 0.00 0.00 3.14
2480 2914 6.554334 TTTTGTTCTGTAGTGTTATGCCTC 57.446 37.500 0.00 0.00 0.00 4.70
2483 2917 4.159693 TGTTCTGTAGTGTTATGCCTCGAT 59.840 41.667 0.00 0.00 0.00 3.59
2513 2947 7.063898 TGTGTGTTGGTGTTTATGTGATTTTTG 59.936 33.333 0.00 0.00 0.00 2.44
2515 2949 8.251026 TGTGTTGGTGTTTATGTGATTTTTGTA 58.749 29.630 0.00 0.00 0.00 2.41
2517 2951 9.823647 TGTTGGTGTTTATGTGATTTTTGTAAT 57.176 25.926 0.00 0.00 0.00 1.89
2556 2991 6.260936 AGTTTTGATATCCGGTTTAGCTCATG 59.739 38.462 0.00 0.00 0.00 3.07
2581 3016 2.023673 CAGTTCTGTTTCTGTGGCCAA 58.976 47.619 7.24 0.00 0.00 4.52
2638 3078 3.057969 TCATAGTTGTCTGCCTGTTGG 57.942 47.619 0.00 0.00 0.00 3.77
2651 3091 3.155093 CCTGTTGGCATATGCAAGAAC 57.845 47.619 28.07 23.89 44.36 3.01
2670 3110 9.460906 GCAAGAACTGTATAATGGTAGTACTAC 57.539 37.037 22.53 22.53 35.40 2.73
2697 3137 7.024340 CATATAGATGCAGTGCAGTTTTTCT 57.976 36.000 24.20 21.31 43.65 2.52
2803 3243 9.703892 TTTTTCATTAACAATACCATTGGACAG 57.296 29.630 10.37 0.00 0.00 3.51
2858 3298 2.151202 CAGTTTAGTGTGGCGGTGAAT 58.849 47.619 0.00 0.00 0.00 2.57
2897 3337 6.222038 TGAGATACATAACAGTTGGAGACC 57.778 41.667 0.00 0.00 0.00 3.85
2903 3343 5.497474 ACATAACAGTTGGAGACCATTACC 58.503 41.667 0.00 0.00 31.53 2.85
2980 3420 6.912591 GGAGACAACTACATGAAAAACTTGTG 59.087 38.462 0.00 0.00 37.43 3.33
3059 3526 8.974060 AACTTCACAAACTTTTAGGATAGTCA 57.026 30.769 0.00 0.00 0.00 3.41
3079 3546 6.658849 AGTCATGGTGGTGCTTTATGTAATA 58.341 36.000 0.00 0.00 0.00 0.98
3209 3683 9.303116 TCCTTTCATGTTAAGCCAATAACTTTA 57.697 29.630 0.00 0.00 36.84 1.85
3255 3908 3.358707 TGCTGCTTGTTGACTTCAATG 57.641 42.857 0.00 0.00 38.24 2.82
3292 3945 5.239525 GCTCTGTAGTGTTTTCTTCCAATGT 59.760 40.000 0.00 0.00 0.00 2.71
3302 3958 7.332182 GTGTTTTCTTCCAATGTTTGTTTGGTA 59.668 33.333 2.65 0.00 43.41 3.25
3309 3965 9.487790 CTTCCAATGTTTGTTTGGTATTTATGT 57.512 29.630 2.65 0.00 43.41 2.29
3311 3967 9.915629 TCCAATGTTTGTTTGGTATTTATGTAC 57.084 29.630 2.65 0.00 43.41 2.90
3312 3968 9.921637 CCAATGTTTGTTTGGTATTTATGTACT 57.078 29.630 0.00 0.00 39.05 2.73
3315 3971 8.113173 TGTTTGTTTGGTATTTATGTACTCCC 57.887 34.615 0.00 0.00 0.00 4.30
3316 3972 7.945664 TGTTTGTTTGGTATTTATGTACTCCCT 59.054 33.333 0.00 0.00 0.00 4.20
3317 3973 9.452287 GTTTGTTTGGTATTTATGTACTCCCTA 57.548 33.333 0.00 0.00 0.00 3.53
3318 3974 9.452287 TTTGTTTGGTATTTATGTACTCCCTAC 57.548 33.333 0.00 0.00 0.00 3.18
3319 3975 7.267128 TGTTTGGTATTTATGTACTCCCTACG 58.733 38.462 0.00 0.00 0.00 3.51
3320 3976 7.093377 TGTTTGGTATTTATGTACTCCCTACGT 60.093 37.037 0.00 0.00 0.00 3.57
3321 3977 8.413229 GTTTGGTATTTATGTACTCCCTACGTA 58.587 37.037 0.00 0.00 0.00 3.57
3322 3978 8.532186 TTGGTATTTATGTACTCCCTACGTAA 57.468 34.615 0.00 0.00 35.74 3.18
3323 3979 8.532186 TGGTATTTATGTACTCCCTACGTAAA 57.468 34.615 0.00 7.15 45.04 2.01
3324 3980 8.632679 TGGTATTTATGTACTCCCTACGTAAAG 58.367 37.037 0.00 0.00 44.54 1.85
3325 3981 8.850156 GGTATTTATGTACTCCCTACGTAAAGA 58.150 37.037 0.00 0.00 44.54 2.52
3336 3992 8.358895 ACTCCCTACGTAAAGAAATATAAGAGC 58.641 37.037 0.00 0.00 0.00 4.09
3337 3993 7.365741 TCCCTACGTAAAGAAATATAAGAGCG 58.634 38.462 0.00 0.00 0.00 5.03
3338 3994 7.013655 TCCCTACGTAAAGAAATATAAGAGCGT 59.986 37.037 0.00 0.00 0.00 5.07
3339 3995 7.650903 CCCTACGTAAAGAAATATAAGAGCGTT 59.349 37.037 0.00 0.00 0.00 4.84
3340 3996 9.028185 CCTACGTAAAGAAATATAAGAGCGTTT 57.972 33.333 0.00 0.00 0.00 3.60
3343 3999 9.793252 ACGTAAAGAAATATAAGAGCGTTTAGA 57.207 29.630 0.00 0.00 0.00 2.10
3355 4011 9.900710 ATAAGAGCGTTTAGATCACTATGTTAG 57.099 33.333 0.00 0.00 37.82 2.34
3356 4012 7.336161 AGAGCGTTTAGATCACTATGTTAGT 57.664 36.000 0.00 0.00 37.82 2.24
3357 4013 7.773149 AGAGCGTTTAGATCACTATGTTAGTT 58.227 34.615 0.00 0.00 37.82 2.24
3358 4014 8.900781 AGAGCGTTTAGATCACTATGTTAGTTA 58.099 33.333 0.00 0.00 37.82 2.24
3359 4015 9.680315 GAGCGTTTAGATCACTATGTTAGTTAT 57.320 33.333 0.00 0.00 36.76 1.89
3360 4016 9.680315 AGCGTTTAGATCACTATGTTAGTTATC 57.320 33.333 0.00 2.14 38.88 1.75
3361 4017 9.680315 GCGTTTAGATCACTATGTTAGTTATCT 57.320 33.333 13.18 13.18 46.18 1.98
3389 4045 9.892130 AACACTCTTATATTTCTTTACAGAGGG 57.108 33.333 0.00 0.00 36.55 4.30
3390 4046 9.268282 ACACTCTTATATTTCTTTACAGAGGGA 57.732 33.333 2.59 0.00 34.50 4.20
3478 4143 3.133003 GCTCTGCTTCTGTATCCAAGGTA 59.867 47.826 0.00 0.00 0.00 3.08
3492 4157 3.831911 TCCAAGGTAGGCAAATTCTTTGG 59.168 43.478 2.15 0.00 40.94 3.28
3564 4229 5.770417 AGAACGGTATAACTATAGTGCTGC 58.230 41.667 6.06 0.56 0.00 5.25
3567 4232 6.829229 ACGGTATAACTATAGTGCTGCATA 57.171 37.500 5.27 0.00 0.00 3.14
3569 4234 7.088905 ACGGTATAACTATAGTGCTGCATAAC 58.911 38.462 5.27 2.24 0.00 1.89
3571 4236 7.273598 CGGTATAACTATAGTGCTGCATAACTG 59.726 40.741 5.27 0.00 0.00 3.16
3607 4282 9.770097 TTCTCAAGATAGAAATATAACAGCTGG 57.230 33.333 19.93 0.00 32.59 4.85
3620 4295 9.969001 AATATAACAGCTGGAACCTAAAAGTTA 57.031 29.630 19.93 3.11 0.00 2.24
3667 4342 0.591170 GCCATGCGTTGTGTACAGTT 59.409 50.000 0.00 0.00 0.00 3.16
3690 4365 1.961793 TTTCTTCAACTGGGTCACGG 58.038 50.000 0.00 0.00 0.00 4.94
3698 4373 0.323542 ACTGGGTCACGGTAGGAGAG 60.324 60.000 0.00 0.00 36.76 3.20
3705 4380 4.037327 GGGTCACGGTAGGAGAGTTTATAC 59.963 50.000 0.00 0.00 0.00 1.47
3706 4381 4.886489 GGTCACGGTAGGAGAGTTTATACT 59.114 45.833 0.00 0.00 37.31 2.12
3707 4382 5.221009 GGTCACGGTAGGAGAGTTTATACTG 60.221 48.000 0.00 0.00 33.84 2.74
3708 4383 5.587844 GTCACGGTAGGAGAGTTTATACTGA 59.412 44.000 0.00 0.00 33.84 3.41
3709 4384 6.094603 GTCACGGTAGGAGAGTTTATACTGAA 59.905 42.308 0.00 0.00 33.84 3.02
3710 4385 6.094603 TCACGGTAGGAGAGTTTATACTGAAC 59.905 42.308 0.00 0.00 33.84 3.18
3711 4386 5.948162 ACGGTAGGAGAGTTTATACTGAACA 59.052 40.000 0.00 0.00 33.84 3.18
3712 4387 6.127786 ACGGTAGGAGAGTTTATACTGAACAC 60.128 42.308 0.00 0.00 33.84 3.32
3713 4388 6.571605 GGTAGGAGAGTTTATACTGAACACC 58.428 44.000 0.00 0.00 33.84 4.16
3714 4389 6.154021 GGTAGGAGAGTTTATACTGAACACCA 59.846 42.308 0.00 0.00 33.84 4.17
3715 4390 6.681729 AGGAGAGTTTATACTGAACACCAA 57.318 37.500 0.00 0.00 33.84 3.67
3716 4391 6.465084 AGGAGAGTTTATACTGAACACCAAC 58.535 40.000 0.00 0.00 33.84 3.77
3717 4392 6.270231 AGGAGAGTTTATACTGAACACCAACT 59.730 38.462 0.00 0.00 33.84 3.16
3718 4393 6.935208 GGAGAGTTTATACTGAACACCAACTT 59.065 38.462 0.00 0.00 33.84 2.66
3719 4394 7.095187 GGAGAGTTTATACTGAACACCAACTTG 60.095 40.741 0.00 0.00 33.84 3.16
3748 4423 5.415701 ACACATGGGCAAAGTTATAAGACTG 59.584 40.000 0.00 0.00 0.00 3.51
3835 4516 1.055040 AGGAGTGCTCAGAGCTTTGT 58.945 50.000 23.15 5.12 42.97 2.83
3881 4563 6.715347 AAAGATGGCATCTATTTTGTACCC 57.285 37.500 29.02 0.00 39.08 3.69
4020 4706 3.376546 CCTAACCTGATGCTTCTGCTTTC 59.623 47.826 0.88 0.00 40.48 2.62
4021 4707 1.446907 ACCTGATGCTTCTGCTTTCG 58.553 50.000 0.88 0.00 40.48 3.46
4138 4832 7.230747 TCTGAAGTAGGGATTTGAACAATTGA 58.769 34.615 13.59 0.00 0.00 2.57
4177 4871 5.239744 GTGAGAGAAGATGGCGAAGATACTA 59.760 44.000 0.00 0.00 0.00 1.82
4255 5120 9.347240 CCTATTGATAATCTCTGTTTCCATTGT 57.653 33.333 0.00 0.00 0.00 2.71
4257 5122 7.395190 TTGATAATCTCTGTTTCCATTGTGG 57.605 36.000 0.00 0.00 39.43 4.17
4537 5426 4.759782 CGAAGATCAACCCTCTATGTTGT 58.240 43.478 0.00 0.00 42.82 3.32
4664 5919 7.394359 AGCTAATGAATGTTGGAATACACTTGT 59.606 33.333 0.00 0.00 0.00 3.16
4770 6030 9.060347 CAAATGTTCTGTACTGATATATTGGCT 57.940 33.333 3.03 0.00 0.00 4.75
4801 6061 4.723789 AGAGAGGAAAGATAGGGCATTTCA 59.276 41.667 0.00 0.00 35.18 2.69
4883 6871 7.026631 TCACAGTAGTTTGTCCTTCAATTTG 57.973 36.000 0.00 0.00 35.84 2.32
4952 6942 6.040729 TGCTGATCAATTTATGTATGGGTTGG 59.959 38.462 0.00 0.00 0.00 3.77
4961 6951 8.830915 ATTTATGTATGGGTTGGTCAATTGTA 57.169 30.769 5.13 0.00 0.00 2.41
4998 6988 5.392767 AGTGAGTCGTCAACATAATCAGT 57.607 39.130 0.00 0.00 33.27 3.41
5000 6990 5.864474 AGTGAGTCGTCAACATAATCAGTTC 59.136 40.000 0.00 0.00 33.27 3.01
5006 6996 4.383118 CGTCAACATAATCAGTTCCCTCCT 60.383 45.833 0.00 0.00 0.00 3.69
5011 7001 1.376649 AATCAGTTCCCTCCTTGGCT 58.623 50.000 0.00 0.00 0.00 4.75
5019 7009 0.548031 CCCTCCTTGGCTGCATTCTA 59.452 55.000 0.50 0.00 0.00 2.10
5042 7033 2.158449 CACGTCAGGAGATTGCTTTGTC 59.842 50.000 0.00 0.00 0.00 3.18
5156 7205 3.673484 TTTGGCAGCGCTTCAGGC 61.673 61.111 7.50 10.48 37.64 4.85
5173 7228 2.494471 CAGGCCATTCTTTCATGCTTGA 59.506 45.455 5.01 0.00 0.00 3.02
5278 7342 5.020795 TCCAGCATTAGTTACTGACCAGTA 58.979 41.667 5.82 5.82 42.54 2.74
5289 7374 3.009723 ACTGACCAGTAAAATGATGCGG 58.990 45.455 0.03 0.00 40.43 5.69
5412 7505 8.761575 TGGCTGAATTGATTAAAATTTGTCTC 57.238 30.769 0.00 0.00 29.89 3.36
5437 7530 6.699575 AATACATTTGTAACTCTGCCATCC 57.300 37.500 0.00 0.00 33.76 3.51
5438 7531 4.032960 ACATTTGTAACTCTGCCATCCA 57.967 40.909 0.00 0.00 0.00 3.41
5439 7532 4.603131 ACATTTGTAACTCTGCCATCCAT 58.397 39.130 0.00 0.00 0.00 3.41
5440 7533 4.400251 ACATTTGTAACTCTGCCATCCATG 59.600 41.667 0.00 0.00 0.00 3.66
5441 7534 8.606869 ATACATTTGTAACTCTGCCATCCATGG 61.607 40.741 4.97 4.97 41.35 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 140 3.503363 CAGCCACTAAATTTGTGAGAGCA 59.497 43.478 17.13 0.00 37.60 4.26
467 777 5.490357 TCTTCTTTTCCTCCATGGATCTCTT 59.510 40.000 16.63 0.00 45.68 2.85
496 809 0.725133 TCCTCCCCTCATTCCCTCTT 59.275 55.000 0.00 0.00 0.00 2.85
558 872 1.691823 CCTGTCCCTCCCCCTTTTC 59.308 63.158 0.00 0.00 0.00 2.29
582 896 3.513515 TCTGCACTTTTTCTTTGTTGGGT 59.486 39.130 0.00 0.00 0.00 4.51
756 1079 3.517500 TGCACAGGTGGACTATATGTTCA 59.482 43.478 1.10 0.00 0.00 3.18
757 1080 4.137116 TGCACAGGTGGACTATATGTTC 57.863 45.455 1.10 0.00 0.00 3.18
758 1081 4.568072 TTGCACAGGTGGACTATATGTT 57.432 40.909 1.10 0.00 0.00 2.71
759 1082 4.410228 AGATTGCACAGGTGGACTATATGT 59.590 41.667 1.10 0.00 0.00 2.29
774 1097 6.854892 GTTCATTAGTGATATGCAGATTGCAC 59.145 38.462 5.81 5.29 44.84 4.57
828 1151 8.717821 CGATGACTGTAAAAAGAACTATTCCAA 58.282 33.333 0.00 0.00 0.00 3.53
829 1152 7.876068 ACGATGACTGTAAAAAGAACTATTCCA 59.124 33.333 0.00 0.00 0.00 3.53
830 1153 8.169268 CACGATGACTGTAAAAAGAACTATTCC 58.831 37.037 0.00 0.00 0.00 3.01
831 1154 8.169268 CCACGATGACTGTAAAAAGAACTATTC 58.831 37.037 0.00 0.00 0.00 1.75
832 1155 7.119262 CCCACGATGACTGTAAAAAGAACTATT 59.881 37.037 0.00 0.00 0.00 1.73
833 1156 6.594159 CCCACGATGACTGTAAAAAGAACTAT 59.406 38.462 0.00 0.00 0.00 2.12
834 1157 5.929992 CCCACGATGACTGTAAAAAGAACTA 59.070 40.000 0.00 0.00 0.00 2.24
835 1158 4.755123 CCCACGATGACTGTAAAAAGAACT 59.245 41.667 0.00 0.00 0.00 3.01
836 1159 4.612939 GCCCACGATGACTGTAAAAAGAAC 60.613 45.833 0.00 0.00 0.00 3.01
837 1160 3.500680 GCCCACGATGACTGTAAAAAGAA 59.499 43.478 0.00 0.00 0.00 2.52
838 1161 3.071479 GCCCACGATGACTGTAAAAAGA 58.929 45.455 0.00 0.00 0.00 2.52
839 1162 3.074412 AGCCCACGATGACTGTAAAAAG 58.926 45.455 0.00 0.00 0.00 2.27
840 1163 3.134574 AGCCCACGATGACTGTAAAAA 57.865 42.857 0.00 0.00 0.00 1.94
841 1164 2.851263 AGCCCACGATGACTGTAAAA 57.149 45.000 0.00 0.00 0.00 1.52
842 1165 2.037902 TGAAGCCCACGATGACTGTAAA 59.962 45.455 0.00 0.00 0.00 2.01
843 1166 1.621317 TGAAGCCCACGATGACTGTAA 59.379 47.619 0.00 0.00 0.00 2.41
844 1167 1.204704 CTGAAGCCCACGATGACTGTA 59.795 52.381 0.00 0.00 0.00 2.74
845 1168 0.036952 CTGAAGCCCACGATGACTGT 60.037 55.000 0.00 0.00 0.00 3.55
846 1169 0.036952 ACTGAAGCCCACGATGACTG 60.037 55.000 0.00 0.00 0.00 3.51
847 1170 0.036952 CACTGAAGCCCACGATGACT 60.037 55.000 0.00 0.00 0.00 3.41
848 1171 1.021390 CCACTGAAGCCCACGATGAC 61.021 60.000 0.00 0.00 0.00 3.06
849 1172 1.296392 CCACTGAAGCCCACGATGA 59.704 57.895 0.00 0.00 0.00 2.92
850 1173 1.003355 ACCACTGAAGCCCACGATG 60.003 57.895 0.00 0.00 0.00 3.84
851 1174 1.296715 GACCACTGAAGCCCACGAT 59.703 57.895 0.00 0.00 0.00 3.73
852 1175 2.741092 GACCACTGAAGCCCACGA 59.259 61.111 0.00 0.00 0.00 4.35
853 1176 2.358737 GGACCACTGAAGCCCACG 60.359 66.667 0.00 0.00 0.00 4.94
854 1177 0.178990 AAAGGACCACTGAAGCCCAC 60.179 55.000 0.00 0.00 0.00 4.61
855 1178 0.555769 AAAAGGACCACTGAAGCCCA 59.444 50.000 0.00 0.00 0.00 5.36
856 1179 1.202940 AGAAAAGGACCACTGAAGCCC 60.203 52.381 0.00 0.00 0.00 5.19
898 1221 5.130477 CCCAACAGGCTATAAAAGGAGAGTA 59.870 44.000 0.00 0.00 0.00 2.59
902 1225 4.503714 TCCCAACAGGCTATAAAAGGAG 57.496 45.455 0.00 0.00 34.51 3.69
922 1252 1.086634 GGCTGAGTGAGGTTGCGATC 61.087 60.000 0.00 0.00 0.00 3.69
923 1253 1.078848 GGCTGAGTGAGGTTGCGAT 60.079 57.895 0.00 0.00 0.00 4.58
924 1254 2.343758 GGCTGAGTGAGGTTGCGA 59.656 61.111 0.00 0.00 0.00 5.10
926 1256 0.035630 ATCTGGCTGAGTGAGGTTGC 60.036 55.000 0.00 0.00 0.00 4.17
929 1259 0.252421 TGGATCTGGCTGAGTGAGGT 60.252 55.000 0.00 0.00 0.00 3.85
931 1261 2.169978 TGAATGGATCTGGCTGAGTGAG 59.830 50.000 0.00 0.00 0.00 3.51
932 1262 2.190538 TGAATGGATCTGGCTGAGTGA 58.809 47.619 0.00 0.00 0.00 3.41
935 1265 3.250280 CGAAATGAATGGATCTGGCTGAG 59.750 47.826 0.00 0.00 0.00 3.35
939 1269 3.209410 ACTCGAAATGAATGGATCTGGC 58.791 45.455 0.00 0.00 0.00 4.85
942 1272 4.446371 GTGGACTCGAAATGAATGGATCT 58.554 43.478 0.00 0.00 0.00 2.75
947 1277 2.094258 CGTGGTGGACTCGAAATGAATG 59.906 50.000 0.00 0.00 38.27 2.67
969 1299 4.776322 TCACTGATTGGGGCCGCG 62.776 66.667 15.95 0.00 0.00 6.46
970 1300 2.825836 CTCACTGATTGGGGCCGC 60.826 66.667 14.01 14.01 0.00 6.53
971 1301 2.825836 GCTCACTGATTGGGGCCG 60.826 66.667 0.00 0.00 0.00 6.13
972 1302 2.825836 CGCTCACTGATTGGGGCC 60.826 66.667 0.00 0.00 0.00 5.80
973 1303 2.045926 ACGCTCACTGATTGGGGC 60.046 61.111 0.00 0.00 0.00 5.80
974 1304 0.742281 CAGACGCTCACTGATTGGGG 60.742 60.000 0.00 0.00 37.54 4.96
975 1305 0.247460 TCAGACGCTCACTGATTGGG 59.753 55.000 0.00 0.00 39.10 4.12
1434 1801 2.541999 GGAGTTGGCTAGATCGAACTCG 60.542 54.545 14.51 0.00 43.47 4.18
1457 1827 2.516225 GCACCGCCCCACTAATCC 60.516 66.667 0.00 0.00 0.00 3.01
1716 2134 2.417515 GGTTAGGCTCTCCGTCTTCAAG 60.418 54.545 0.00 0.00 37.47 3.02
1735 2153 4.508128 CGGCAGCGGTATCACGGT 62.508 66.667 0.00 0.00 46.53 4.83
1806 2230 4.529219 CCACCCTCTGCGCGCATA 62.529 66.667 36.48 27.04 0.00 3.14
2016 2443 0.832135 TGACCGTGAAGAGGCTCCTT 60.832 55.000 11.71 4.88 0.00 3.36
2058 2488 5.685511 CCTATTGTTGGTGTCGAAAAGTTTG 59.314 40.000 0.00 0.00 0.00 2.93
2080 2510 5.065613 TCAAATGGATAATAGCAAGCCCT 57.934 39.130 0.00 0.00 0.00 5.19
2084 2514 7.013083 AGACAGCTTCAAATGGATAATAGCAAG 59.987 37.037 0.00 0.00 0.00 4.01
2104 2534 6.513180 TGTTATTACCTGTAGCATAGACAGC 58.487 40.000 0.00 0.00 42.52 4.40
2194 2628 2.292267 AGCCTAACATGAAAGGATGCG 58.708 47.619 18.47 0.00 34.58 4.73
2226 2660 8.653338 GCAAAAGAATAACTGATACGACACTAA 58.347 33.333 0.00 0.00 0.00 2.24
2250 2684 6.993902 TGTATTGAATAGATCATCAAGCAGCA 59.006 34.615 12.27 7.21 38.80 4.41
2286 2720 6.617371 ACCATTGGGAGAGAACACTATAGAAT 59.383 38.462 6.78 0.00 38.05 2.40
2291 2725 4.289672 ACAACCATTGGGAGAGAACACTAT 59.710 41.667 7.78 0.00 38.05 2.12
2301 2735 4.594970 TGTTACCATACAACCATTGGGAG 58.405 43.478 7.78 1.28 38.05 4.30
2453 2887 6.586082 GGCATAACACTACAGAACAAAATTGG 59.414 38.462 0.00 0.00 0.00 3.16
2454 2888 7.370383 AGGCATAACACTACAGAACAAAATTG 58.630 34.615 0.00 0.00 0.00 2.32
2464 2898 3.181475 ACCATCGAGGCATAACACTACAG 60.181 47.826 0.00 0.00 43.14 2.74
2477 2911 0.874390 CCAACACACAACCATCGAGG 59.126 55.000 0.00 0.00 45.67 4.63
2480 2914 1.021202 ACACCAACACACAACCATCG 58.979 50.000 0.00 0.00 0.00 3.84
2483 2917 3.764434 ACATAAACACCAACACACAACCA 59.236 39.130 0.00 0.00 0.00 3.67
2529 2963 7.332557 TGAGCTAAACCGGATATCAAAACTAA 58.667 34.615 9.46 0.00 0.00 2.24
2544 2979 1.098050 CTGGTGGCATGAGCTAAACC 58.902 55.000 0.00 0.00 41.70 3.27
2556 2991 1.334869 CACAGAAACAGAACTGGTGGC 59.665 52.381 6.76 0.00 38.30 5.01
2638 3078 7.206981 ACCATTATACAGTTCTTGCATATGC 57.793 36.000 21.09 21.09 42.50 3.14
2648 3088 8.627403 TGCAGTAGTACTACCATTATACAGTTC 58.373 37.037 25.97 2.56 36.75 3.01
2697 3137 3.264998 TCACATCGCCTCATTGATTGA 57.735 42.857 0.00 0.00 0.00 2.57
2735 3175 9.537192 CAACTTGGCATCATATTTATTGACAAT 57.463 29.630 5.87 5.87 36.56 2.71
2790 3230 3.073798 TGAACCACACTGTCCAATGGTAT 59.926 43.478 0.00 0.00 44.80 2.73
2793 3233 1.979855 TGAACCACACTGTCCAATGG 58.020 50.000 0.00 0.00 38.26 3.16
2803 3243 0.249911 AGCTCCGACTTGAACCACAC 60.250 55.000 0.00 0.00 0.00 3.82
2897 3337 7.202016 TCACAAGCTAGTTTTTCAGGTAATG 57.798 36.000 0.00 0.00 0.00 1.90
2903 3343 9.736023 AAATAACTTCACAAGCTAGTTTTTCAG 57.264 29.630 4.24 0.00 34.26 3.02
3059 3526 9.066892 CATAACTATTACATAAAGCACCACCAT 57.933 33.333 0.00 0.00 0.00 3.55
3079 3546 6.071728 CCTGCATCTTTTTCCAGTTCATAACT 60.072 38.462 0.00 0.00 44.06 2.24
3159 3626 2.964464 TGAAAGGCATTCACACAACCAT 59.036 40.909 0.22 0.00 43.08 3.55
3168 3638 4.151121 TGAAAGGATGTGAAAGGCATTCA 58.849 39.130 0.22 0.22 45.71 2.57
3292 3945 9.452287 GTAGGGAGTACATAAATACCAAACAAA 57.548 33.333 0.00 0.00 0.00 2.83
3310 3966 8.358895 GCTCTTATATTTCTTTACGTAGGGAGT 58.641 37.037 0.00 0.00 0.00 3.85
3311 3967 7.537991 CGCTCTTATATTTCTTTACGTAGGGAG 59.462 40.741 0.00 0.00 0.00 4.30
3312 3968 7.013655 ACGCTCTTATATTTCTTTACGTAGGGA 59.986 37.037 0.00 0.00 0.00 4.20
3313 3969 7.144000 ACGCTCTTATATTTCTTTACGTAGGG 58.856 38.462 0.00 0.00 0.00 3.53
3314 3970 8.571461 AACGCTCTTATATTTCTTTACGTAGG 57.429 34.615 0.00 0.00 0.00 3.18
3317 3973 9.793252 TCTAAACGCTCTTATATTTCTTTACGT 57.207 29.630 0.00 0.00 0.00 3.57
3329 3985 9.900710 CTAACATAGTGATCTAAACGCTCTTAT 57.099 33.333 0.00 0.00 0.00 1.73
3330 3986 8.900781 ACTAACATAGTGATCTAAACGCTCTTA 58.099 33.333 0.00 0.00 37.69 2.10
3331 3987 7.773149 ACTAACATAGTGATCTAAACGCTCTT 58.227 34.615 0.00 0.00 37.69 2.85
3332 3988 7.336161 ACTAACATAGTGATCTAAACGCTCT 57.664 36.000 0.00 0.00 37.69 4.09
3333 3989 7.988904 AACTAACATAGTGATCTAAACGCTC 57.011 36.000 0.00 0.00 39.39 5.03
3334 3990 9.680315 GATAACTAACATAGTGATCTAAACGCT 57.320 33.333 7.39 0.00 41.55 5.07
3363 4019 9.892130 CCCTCTGTAAAGAAATATAAGAGTGTT 57.108 33.333 0.00 0.00 0.00 3.32
3364 4020 9.268282 TCCCTCTGTAAAGAAATATAAGAGTGT 57.732 33.333 0.00 0.00 0.00 3.55
3382 4038 7.941238 CCAGATCATAACAATTATTCCCTCTGT 59.059 37.037 0.00 0.00 0.00 3.41
3383 4039 8.159447 TCCAGATCATAACAATTATTCCCTCTG 58.841 37.037 0.00 0.00 0.00 3.35
3384 4040 8.280258 TCCAGATCATAACAATTATTCCCTCT 57.720 34.615 0.00 0.00 0.00 3.69
3385 4041 8.924511 TTCCAGATCATAACAATTATTCCCTC 57.075 34.615 0.00 0.00 0.00 4.30
3386 4042 9.713684 TTTTCCAGATCATAACAATTATTCCCT 57.286 29.630 0.00 0.00 0.00 4.20
3569 4234 6.162079 TCTATCTTGAGAAAGAACTGTGCAG 58.838 40.000 0.00 0.00 31.77 4.41
3571 4236 7.426929 TTTCTATCTTGAGAAAGAACTGTGC 57.573 36.000 0.00 0.00 39.87 4.57
3667 4342 4.517453 CCGTGACCCAGTTGAAGAAATTAA 59.483 41.667 0.00 0.00 0.00 1.40
3690 4365 7.166691 TGGTGTTCAGTATAAACTCTCCTAC 57.833 40.000 0.00 0.00 31.97 3.18
3698 4373 6.017440 TCAGCAAGTTGGTGTTCAGTATAAAC 60.017 38.462 28.86 0.00 45.34 2.01
3705 4380 2.423185 TGTTCAGCAAGTTGGTGTTCAG 59.577 45.455 28.86 8.69 45.34 3.02
3706 4381 2.163412 GTGTTCAGCAAGTTGGTGTTCA 59.837 45.455 28.86 24.45 45.34 3.18
3707 4382 2.163412 TGTGTTCAGCAAGTTGGTGTTC 59.837 45.455 28.86 22.69 45.34 3.18
3708 4383 2.166829 TGTGTTCAGCAAGTTGGTGTT 58.833 42.857 28.86 0.00 45.34 3.32
3709 4384 1.832883 TGTGTTCAGCAAGTTGGTGT 58.167 45.000 28.86 0.00 45.34 4.16
3710 4385 2.544277 CCATGTGTTCAGCAAGTTGGTG 60.544 50.000 25.63 25.63 46.40 4.17
3711 4386 1.682854 CCATGTGTTCAGCAAGTTGGT 59.317 47.619 0.63 0.63 0.00 3.67
3712 4387 1.000060 CCCATGTGTTCAGCAAGTTGG 60.000 52.381 4.75 0.00 0.00 3.77
3713 4388 1.603678 GCCCATGTGTTCAGCAAGTTG 60.604 52.381 0.00 0.00 0.00 3.16
3714 4389 0.675633 GCCCATGTGTTCAGCAAGTT 59.324 50.000 0.00 0.00 0.00 2.66
3715 4390 0.467844 TGCCCATGTGTTCAGCAAGT 60.468 50.000 0.00 0.00 0.00 3.16
3716 4391 0.675083 TTGCCCATGTGTTCAGCAAG 59.325 50.000 0.00 0.00 38.45 4.01
3717 4392 1.068895 CTTTGCCCATGTGTTCAGCAA 59.931 47.619 0.00 0.00 41.39 3.91
3718 4393 0.675083 CTTTGCCCATGTGTTCAGCA 59.325 50.000 0.00 0.00 0.00 4.41
3719 4394 0.675633 ACTTTGCCCATGTGTTCAGC 59.324 50.000 0.00 0.00 0.00 4.26
3796 4477 8.771766 CACTCCTTCAATCATATCATGTTACTG 58.228 37.037 0.00 0.00 0.00 2.74
3903 4585 1.713078 AGAATCCTCAAGCAAGGGGTT 59.287 47.619 0.57 0.00 37.02 4.11
3998 4681 2.706339 AGCAGAAGCATCAGGTTAGG 57.294 50.000 0.00 0.00 45.49 2.69
4020 4706 2.093711 TGATGGGTTCATGTGGAGTACG 60.094 50.000 0.00 0.00 32.98 3.67
4021 4707 3.627395 TGATGGGTTCATGTGGAGTAC 57.373 47.619 0.00 0.00 32.98 2.73
4098 4792 4.401925 ACTTCAGAGGCAAATGCTAAACT 58.598 39.130 5.25 0.00 41.70 2.66
4279 5150 5.351189 AGCAAAAACACCAAAGTTGAATCAC 59.649 36.000 0.00 0.00 0.00 3.06
4375 5247 7.437713 TGTACTATTCATCCATGGAAAGACT 57.562 36.000 20.67 15.73 0.00 3.24
4567 5761 0.831966 AGAGAGAAGAGGCAGGCATG 59.168 55.000 0.00 0.00 0.00 4.06
4568 5762 0.831966 CAGAGAGAAGAGGCAGGCAT 59.168 55.000 0.00 0.00 0.00 4.40
4664 5919 5.245531 CAGTAACAAATAGCACCAGGAAGA 58.754 41.667 0.00 0.00 0.00 2.87
4768 6028 2.037772 TCTTTCCTCTCTGGTGTTCAGC 59.962 50.000 0.00 0.00 43.06 4.26
4770 6030 4.467795 CCTATCTTTCCTCTCTGGTGTTCA 59.532 45.833 0.00 0.00 37.07 3.18
4801 6061 5.178809 GGAGTAAACTCGCAATACTTGTGTT 59.821 40.000 4.13 0.00 43.76 3.32
4940 6930 7.582719 ACTATACAATTGACCAACCCATACAT 58.417 34.615 13.59 0.00 0.00 2.29
4976 6966 5.392767 ACTGATTATGTTGACGACTCACT 57.607 39.130 0.00 0.00 0.00 3.41
4985 6975 5.500234 CAAGGAGGGAACTGATTATGTTGA 58.500 41.667 0.00 0.00 44.43 3.18
4998 6988 0.323725 GAATGCAGCCAAGGAGGGAA 60.324 55.000 0.00 0.00 38.09 3.97
5000 6990 0.548031 TAGAATGCAGCCAAGGAGGG 59.452 55.000 0.00 0.00 38.09 4.30
5006 6996 1.804151 GACGTGTTAGAATGCAGCCAA 59.196 47.619 0.00 0.00 0.00 4.52
5011 7001 2.560981 TCTCCTGACGTGTTAGAATGCA 59.439 45.455 0.00 0.00 0.00 3.96
5019 7009 2.549754 CAAAGCAATCTCCTGACGTGTT 59.450 45.455 0.00 0.00 0.00 3.32
5132 7180 1.468520 GAAGCGCTGCCAAACAAGATA 59.531 47.619 12.58 0.00 0.00 1.98
5156 7205 3.119245 CCAGGTCAAGCATGAAAGAATGG 60.119 47.826 0.00 0.00 37.30 3.16
5173 7228 3.697542 GTCCAAACAAGTTAACACCAGGT 59.302 43.478 8.61 0.00 0.00 4.00
5278 7342 8.506168 TCTTAAATCTTCTACCGCATCATTTT 57.494 30.769 0.00 0.00 0.00 1.82
5279 7343 8.682936 ATCTTAAATCTTCTACCGCATCATTT 57.317 30.769 0.00 0.00 0.00 2.32
5280 7344 7.116948 CGATCTTAAATCTTCTACCGCATCATT 59.883 37.037 0.00 0.00 0.00 2.57
5282 7346 5.920840 CGATCTTAAATCTTCTACCGCATCA 59.079 40.000 0.00 0.00 0.00 3.07
5283 7347 5.346281 CCGATCTTAAATCTTCTACCGCATC 59.654 44.000 0.00 0.00 0.00 3.91
5289 7374 8.404000 TGACTGTACCGATCTTAAATCTTCTAC 58.596 37.037 0.00 0.00 0.00 2.59
5412 7505 7.498900 TGGATGGCAGAGTTACAAATGTATTAG 59.501 37.037 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.