Multiple sequence alignment - TraesCS1D01G076900

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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 TraesCS1D01G076900 chr1D 100.000 5141 0 0 1 5141 58871020 58865880 0.000000e+00 9494.0
1 TraesCS1D01G076900 chr1D 79.602 3162 519 81 1112 4219 58628637 58625548 0.000000e+00 2150.0
2 TraesCS1D01G076900 chr1D 82.214 2322 355 38 1166 3446 58764093 58761789 0.000000e+00 1947.0
3 TraesCS1D01G076900 chr1D 79.932 1465 264 17 1932 3373 38559351 38557894 0.000000e+00 1050.0
4 TraesCS1D01G076900 chr1D 79.768 1463 267 23 1933 3373 36623655 36622200 0.000000e+00 1035.0
5 TraesCS1D01G076900 chr1D 79.209 1467 271 22 1932 3373 36617245 36615788 0.000000e+00 989.0
6 TraesCS1D01G076900 chr1D 78.484 818 153 17 1116 1917 36618175 36617365 9.870000e-142 514.0
7 TraesCS1D01G076900 chr1D 76.842 190 31 10 1713 1893 13309559 13309744 1.520000e-15 95.3
8 TraesCS1D01G076900 chr1D 80.682 88 9 6 4680 4765 349294740 349294821 1.550000e-05 62.1
9 TraesCS1D01G076900 chr1B 92.510 4820 222 41 379 5136 94327946 94323204 0.000000e+00 6772.0
10 TraesCS1D01G076900 chr1B 81.860 2365 373 33 1122 3446 94233226 94230878 0.000000e+00 1940.0
11 TraesCS1D01G076900 chr1B 79.021 1430 272 18 1966 3373 57016881 57018304 0.000000e+00 953.0
12 TraesCS1D01G076900 chr1B 78.313 1494 279 33 1932 3396 70170762 70172239 0.000000e+00 922.0
13 TraesCS1D01G076900 chr1B 78.566 1395 269 24 1932 3303 57137999 57139386 0.000000e+00 893.0
14 TraesCS1D01G076900 chr1B 78.082 1460 270 41 1933 3359 70186441 70187883 0.000000e+00 878.0
15 TraesCS1D01G076900 chr1B 77.228 1111 215 24 2290 3374 69365245 69364147 2.630000e-172 616.0
16 TraesCS1D01G076900 chr1B 77.903 801 163 9 1153 1942 56620466 56619669 2.150000e-133 486.0
17 TraesCS1D01G076900 chr1B 76.914 862 180 15 1096 1942 56493617 56492760 6.030000e-129 472.0
18 TraesCS1D01G076900 chr1B 78.189 729 143 9 1203 1921 69260373 69259651 7.850000e-123 451.0
19 TraesCS1D01G076900 chr1B 89.222 167 16 1 4235 4401 67537603 67537439 1.880000e-49 207.0
20 TraesCS1D01G076900 chr1B 88.415 164 18 1 4236 4398 533863063 533863226 4.060000e-46 196.0
21 TraesCS1D01G076900 chr1B 75.862 261 57 6 1112 1369 17966178 17965921 1.500000e-25 128.0
22 TraesCS1D01G076900 chr1A 79.282 3094 520 79 1181 4219 57405747 57402720 0.000000e+00 2050.0
23 TraesCS1D01G076900 chr1A 82.150 1535 240 25 1134 2647 57640146 57638625 0.000000e+00 1286.0
24 TraesCS1D01G076900 chr1A 80.068 1465 262 16 1932 3373 37504384 37502927 0.000000e+00 1061.0
25 TraesCS1D01G076900 chr1A 79.618 1467 265 26 1932 3373 36605794 36607251 0.000000e+00 1022.0
26 TraesCS1D01G076900 chr1A 79.528 1397 248 25 1932 3301 36187370 36185985 0.000000e+00 961.0
27 TraesCS1D01G076900 chr1A 78.008 1496 280 37 1932 3396 49246150 49247627 0.000000e+00 894.0
28 TraesCS1D01G076900 chr1A 90.494 263 23 2 119 380 573508415 573508154 3.810000e-91 346.0
29 TraesCS1D01G076900 chr1A 84.066 182 28 1 4920 5101 494886902 494887082 1.900000e-39 174.0
30 TraesCS1D01G076900 chr4A 91.667 264 20 2 118 380 674616793 674617055 1.050000e-96 364.0
31 TraesCS1D01G076900 chr2D 92.549 255 18 1 113 367 25334116 25334369 1.050000e-96 364.0
32 TraesCS1D01G076900 chr2D 90.943 265 20 3 117 380 608922452 608922191 2.280000e-93 353.0
33 TraesCS1D01G076900 chr2D 81.752 137 17 4 4615 4744 539004693 539004558 1.960000e-19 108.0
34 TraesCS1D01G076900 chr2A 89.531 277 26 3 113 387 606519330 606519055 1.060000e-91 348.0
35 TraesCS1D01G076900 chr2A 84.831 178 21 4 4917 5088 25378824 25379001 1.900000e-39 174.0
36 TraesCS1D01G076900 chr2B 90.262 267 23 3 116 380 65225214 65224949 3.810000e-91 346.0
37 TraesCS1D01G076900 chr2B 89.668 271 25 3 116 385 723031949 723031681 4.930000e-90 342.0
38 TraesCS1D01G076900 chr4B 89.668 271 25 3 113 381 22857624 22857355 4.930000e-90 342.0
39 TraesCS1D01G076900 chr4B 100.000 28 0 0 4738 4765 651809380 651809353 9.000000e-03 52.8
40 TraesCS1D01G076900 chr4B 100.000 28 0 0 4738 4765 651871617 651871590 9.000000e-03 52.8
41 TraesCS1D01G076900 chr7D 89.377 273 26 3 110 381 629317051 629316781 1.770000e-89 340.0
42 TraesCS1D01G076900 chr6A 89.881 168 17 0 4232 4399 108947868 108947701 3.120000e-52 217.0
43 TraesCS1D01G076900 chr6A 85.207 169 21 3 4920 5088 64662254 64662418 2.460000e-38 171.0
44 TraesCS1D01G076900 chr3D 89.024 164 18 0 4236 4399 365521019 365520856 2.430000e-48 204.0
45 TraesCS1D01G076900 chr3D 85.629 167 22 2 4920 5086 591606833 591606669 1.900000e-39 174.0
46 TraesCS1D01G076900 chr3B 89.024 164 18 0 4236 4399 112325137 112325300 2.430000e-48 204.0
47 TraesCS1D01G076900 chr3B 88.344 163 19 0 4236 4398 474144065 474143903 4.060000e-46 196.0
48 TraesCS1D01G076900 chr3B 78.947 133 25 2 4616 4746 53590569 53590438 2.550000e-13 87.9
49 TraesCS1D01G076900 chr5B 88.344 163 19 0 4235 4397 576799914 576799752 4.060000e-46 196.0
50 TraesCS1D01G076900 chr4D 87.500 168 20 1 4236 4403 310479280 310479446 5.250000e-45 193.0
51 TraesCS1D01G076900 chr4D 100.000 29 0 0 504 532 464083521 464083549 3.000000e-03 54.7
52 TraesCS1D01G076900 chr4D 100.000 28 0 0 4738 4765 505241432 505241459 9.000000e-03 52.8
53 TraesCS1D01G076900 chr3A 85.465 172 25 0 4917 5088 561038551 561038722 4.090000e-41 180.0
54 TraesCS1D01G076900 chr3A 85.380 171 23 1 4920 5088 37308956 37308786 5.290000e-40 176.0
55 TraesCS1D01G076900 chr3A 85.057 174 20 5 4920 5088 628192088 628191916 6.840000e-39 172.0
56 TraesCS1D01G076900 chr3A 86.667 75 9 1 4752 4826 449269138 449269211 1.190000e-11 82.4
57 TraesCS1D01G076900 chr3A 92.453 53 2 2 4753 4805 449268750 449268800 1.990000e-09 75.0
58 TraesCS1D01G076900 chr7B 84.884 172 23 2 4920 5088 277651823 277651652 2.460000e-38 171.0
59 TraesCS1D01G076900 chr6D 88.235 68 7 1 4739 4806 9536415 9536349 4.270000e-11 80.5
60 TraesCS1D01G076900 chr6B 86.957 69 6 3 4739 4806 17489686 17489620 1.990000e-09 75.0
61 TraesCS1D01G076900 chr5A 100.000 30 0 0 4752 4781 475715895 475715866 7.190000e-04 56.5


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 TraesCS1D01G076900 chr1D 58865880 58871020 5140 True 9494.0 9494 100.0000 1 5141 1 chr1D.!!$R5 5140
1 TraesCS1D01G076900 chr1D 58625548 58628637 3089 True 2150.0 2150 79.6020 1112 4219 1 chr1D.!!$R3 3107
2 TraesCS1D01G076900 chr1D 58761789 58764093 2304 True 1947.0 1947 82.2140 1166 3446 1 chr1D.!!$R4 2280
3 TraesCS1D01G076900 chr1D 38557894 38559351 1457 True 1050.0 1050 79.9320 1932 3373 1 chr1D.!!$R2 1441
4 TraesCS1D01G076900 chr1D 36622200 36623655 1455 True 1035.0 1035 79.7680 1933 3373 1 chr1D.!!$R1 1440
5 TraesCS1D01G076900 chr1D 36615788 36618175 2387 True 751.5 989 78.8465 1116 3373 2 chr1D.!!$R6 2257
6 TraesCS1D01G076900 chr1B 94323204 94327946 4742 True 6772.0 6772 92.5100 379 5136 1 chr1B.!!$R8 4757
7 TraesCS1D01G076900 chr1B 94230878 94233226 2348 True 1940.0 1940 81.8600 1122 3446 1 chr1B.!!$R7 2324
8 TraesCS1D01G076900 chr1B 57016881 57018304 1423 False 953.0 953 79.0210 1966 3373 1 chr1B.!!$F1 1407
9 TraesCS1D01G076900 chr1B 70170762 70172239 1477 False 922.0 922 78.3130 1932 3396 1 chr1B.!!$F3 1464
10 TraesCS1D01G076900 chr1B 57137999 57139386 1387 False 893.0 893 78.5660 1932 3303 1 chr1B.!!$F2 1371
11 TraesCS1D01G076900 chr1B 70186441 70187883 1442 False 878.0 878 78.0820 1933 3359 1 chr1B.!!$F4 1426
12 TraesCS1D01G076900 chr1B 69364147 69365245 1098 True 616.0 616 77.2280 2290 3374 1 chr1B.!!$R6 1084
13 TraesCS1D01G076900 chr1B 56619669 56620466 797 True 486.0 486 77.9030 1153 1942 1 chr1B.!!$R3 789
14 TraesCS1D01G076900 chr1B 56492760 56493617 857 True 472.0 472 76.9140 1096 1942 1 chr1B.!!$R2 846
15 TraesCS1D01G076900 chr1B 69259651 69260373 722 True 451.0 451 78.1890 1203 1921 1 chr1B.!!$R5 718
16 TraesCS1D01G076900 chr1A 57402720 57405747 3027 True 2050.0 2050 79.2820 1181 4219 1 chr1A.!!$R3 3038
17 TraesCS1D01G076900 chr1A 57638625 57640146 1521 True 1286.0 1286 82.1500 1134 2647 1 chr1A.!!$R4 1513
18 TraesCS1D01G076900 chr1A 37502927 37504384 1457 True 1061.0 1061 80.0680 1932 3373 1 chr1A.!!$R2 1441
19 TraesCS1D01G076900 chr1A 36605794 36607251 1457 False 1022.0 1022 79.6180 1932 3373 1 chr1A.!!$F1 1441
20 TraesCS1D01G076900 chr1A 36185985 36187370 1385 True 961.0 961 79.5280 1932 3301 1 chr1A.!!$R1 1369
21 TraesCS1D01G076900 chr1A 49246150 49247627 1477 False 894.0 894 78.0080 1932 3396 1 chr1A.!!$F2 1464

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
631 648 0.252057 AGGTGGGTTTTATGGGTGGC 60.252 55.0 0.00 0.0 0.0 5.01 F
942 966 0.613292 ACAGCCACTCGATCCACTCT 60.613 55.0 0.00 0.0 0.0 3.24 F
1412 1442 0.901114 TGTGTAGAGCCGCCCACTTA 60.901 55.0 0.00 0.0 0.0 2.24 F
2925 3089 1.098869 TGGAAAAACTTGCGCTGACA 58.901 45.0 9.73 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1963 2112 0.176680 TCCCTGCTTGCGAAGAGATC 59.823 55.0 0.00 0.0 0.00 2.75 R
2495 2644 0.600057 CCCTTCCTTCTTTGCACAGC 59.400 55.0 0.00 0.0 0.00 4.40 R
3173 3338 1.930251 TGAGAGCTAGGAGCACAACT 58.070 50.0 0.64 0.0 45.56 3.16 R
4178 4371 0.037590 TCCATTCCTCCCAAACCACG 59.962 55.0 0.00 0.0 0.00 4.94 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
23 24 6.671614 ACATTTTTCGTACACAGAGAAACA 57.328 33.333 0.00 0.00 34.14 2.83
24 25 7.259290 ACATTTTTCGTACACAGAGAAACAT 57.741 32.000 0.00 0.00 34.14 2.71
25 26 7.703328 ACATTTTTCGTACACAGAGAAACATT 58.297 30.769 0.00 0.00 34.14 2.71
26 27 8.188139 ACATTTTTCGTACACAGAGAAACATTT 58.812 29.630 0.00 0.00 34.14 2.32
27 28 9.019764 CATTTTTCGTACACAGAGAAACATTTT 57.980 29.630 0.00 0.00 34.14 1.82
28 29 8.609478 TTTTTCGTACACAGAGAAACATTTTC 57.391 30.769 0.00 0.00 34.14 2.29
29 30 7.548196 TTTCGTACACAGAGAAACATTTTCT 57.452 32.000 0.72 0.72 0.00 2.52
30 31 7.548196 TTCGTACACAGAGAAACATTTTCTT 57.452 32.000 2.79 0.00 0.00 2.52
31 32 7.548196 TCGTACACAGAGAAACATTTTCTTT 57.452 32.000 2.79 0.00 0.00 2.52
32 33 8.651391 TCGTACACAGAGAAACATTTTCTTTA 57.349 30.769 2.79 0.00 0.00 1.85
33 34 9.268268 TCGTACACAGAGAAACATTTTCTTTAT 57.732 29.630 2.79 0.00 0.00 1.40
34 35 9.318041 CGTACACAGAGAAACATTTTCTTTATG 57.682 33.333 2.79 0.13 0.00 1.90
68 69 9.941325 AAAATATGTCAAATGATTGGTTAGCAA 57.059 25.926 0.00 0.00 37.15 3.91
72 73 8.851541 ATGTCAAATGATTGGTTAGCAATTTT 57.148 26.923 11.06 6.11 37.15 1.82
73 74 8.674263 TGTCAAATGATTGGTTAGCAATTTTT 57.326 26.923 11.06 10.93 37.15 1.94
164 165 9.236006 ACTTTGCATATTAGATTTGACTGAAGT 57.764 29.630 0.00 0.00 0.00 3.01
165 166 9.713740 CTTTGCATATTAGATTTGACTGAAGTC 57.286 33.333 3.41 3.41 44.97 3.01
331 332 8.840833 AAACATTGTCAAAGTTTACAAACCTT 57.159 26.923 15.37 0.00 38.95 3.50
332 333 7.826260 ACATTGTCAAAGTTTACAAACCTTG 57.174 32.000 9.06 9.06 40.15 3.61
333 334 7.607250 ACATTGTCAAAGTTTACAAACCTTGA 58.393 30.769 12.61 12.61 43.35 3.02
334 335 8.257306 ACATTGTCAAAGTTTACAAACCTTGAT 58.743 29.630 17.40 4.40 45.61 2.57
335 336 9.097257 CATTGTCAAAGTTTACAAACCTTGATT 57.903 29.630 17.40 7.38 45.61 2.57
336 337 9.665719 ATTGTCAAAGTTTACAAACCTTGATTT 57.334 25.926 17.40 7.13 45.61 2.17
337 338 9.495572 TTGTCAAAGTTTACAAACCTTGATTTT 57.504 25.926 17.40 3.10 45.61 1.82
338 339 8.930760 TGTCAAAGTTTACAAACCTTGATTTTG 58.069 29.630 17.40 12.42 45.61 2.44
339 340 9.145865 GTCAAAGTTTACAAACCTTGATTTTGA 57.854 29.630 17.40 13.95 45.61 2.69
340 341 9.145865 TCAAAGTTTACAAACCTTGATTTTGAC 57.854 29.630 12.61 0.00 41.73 3.18
341 342 8.387354 CAAAGTTTACAAACCTTGATTTTGACC 58.613 33.333 9.57 0.00 40.87 4.02
342 343 7.176589 AGTTTACAAACCTTGATTTTGACCA 57.823 32.000 1.27 0.00 39.71 4.02
343 344 7.616313 AGTTTACAAACCTTGATTTTGACCAA 58.384 30.769 1.27 0.00 39.71 3.67
344 345 8.097662 AGTTTACAAACCTTGATTTTGACCAAA 58.902 29.630 1.27 0.00 39.71 3.28
345 346 8.387354 GTTTACAAACCTTGATTTTGACCAAAG 58.613 33.333 1.97 0.00 37.39 2.77
346 347 4.875536 ACAAACCTTGATTTTGACCAAAGC 59.124 37.500 1.97 0.00 37.39 3.51
347 348 5.118286 CAAACCTTGATTTTGACCAAAGCT 58.882 37.500 0.00 0.00 36.24 3.74
348 349 6.127196 ACAAACCTTGATTTTGACCAAAGCTA 60.127 34.615 1.97 0.00 37.39 3.32
349 350 6.478512 AACCTTGATTTTGACCAAAGCTAA 57.521 33.333 0.00 0.00 31.55 3.09
350 351 6.670695 ACCTTGATTTTGACCAAAGCTAAT 57.329 33.333 0.00 0.00 31.55 1.73
351 352 7.775053 ACCTTGATTTTGACCAAAGCTAATA 57.225 32.000 0.00 0.00 31.55 0.98
352 353 7.602753 ACCTTGATTTTGACCAAAGCTAATAC 58.397 34.615 0.00 0.00 31.55 1.89
353 354 7.232534 ACCTTGATTTTGACCAAAGCTAATACA 59.767 33.333 0.00 0.00 31.55 2.29
354 355 8.253113 CCTTGATTTTGACCAAAGCTAATACAT 58.747 33.333 0.00 0.00 31.55 2.29
355 356 8.984891 TTGATTTTGACCAAAGCTAATACATG 57.015 30.769 0.00 0.00 31.55 3.21
356 357 7.546358 TGATTTTGACCAAAGCTAATACATGG 58.454 34.615 0.00 0.00 37.19 3.66
357 358 7.395772 TGATTTTGACCAAAGCTAATACATGGA 59.604 33.333 0.00 0.00 35.16 3.41
358 359 6.757897 TTTGACCAAAGCTAATACATGGAG 57.242 37.500 0.00 0.00 35.16 3.86
359 360 5.435686 TGACCAAAGCTAATACATGGAGT 57.564 39.130 0.00 0.00 35.16 3.85
360 361 5.815581 TGACCAAAGCTAATACATGGAGTT 58.184 37.500 0.00 0.00 35.16 3.01
361 362 6.953101 TGACCAAAGCTAATACATGGAGTTA 58.047 36.000 0.00 0.00 35.16 2.24
362 363 7.398829 TGACCAAAGCTAATACATGGAGTTAA 58.601 34.615 0.00 0.00 35.16 2.01
363 364 8.052748 TGACCAAAGCTAATACATGGAGTTAAT 58.947 33.333 0.00 0.00 35.16 1.40
364 365 9.555727 GACCAAAGCTAATACATGGAGTTAATA 57.444 33.333 0.00 0.00 35.16 0.98
365 366 9.914834 ACCAAAGCTAATACATGGAGTTAATAA 57.085 29.630 0.00 0.00 35.16 1.40
374 375 6.806668 ACATGGAGTTAATAAAAATGGGGG 57.193 37.500 0.00 0.00 0.00 5.40
375 376 6.507568 ACATGGAGTTAATAAAAATGGGGGA 58.492 36.000 0.00 0.00 0.00 4.81
376 377 6.611236 ACATGGAGTTAATAAAAATGGGGGAG 59.389 38.462 0.00 0.00 0.00 4.30
377 378 6.160483 TGGAGTTAATAAAAATGGGGGAGT 57.840 37.500 0.00 0.00 0.00 3.85
378 379 7.286667 TGGAGTTAATAAAAATGGGGGAGTA 57.713 36.000 0.00 0.00 0.00 2.59
379 380 7.889178 TGGAGTTAATAAAAATGGGGGAGTAT 58.111 34.615 0.00 0.00 0.00 2.12
380 381 9.016243 TGGAGTTAATAAAAATGGGGGAGTATA 57.984 33.333 0.00 0.00 0.00 1.47
492 495 2.089349 GGCGTGACTTCAGCGAGTC 61.089 63.158 9.95 9.95 44.97 3.36
499 502 0.894184 ACTTCAGCGAGTCGGAAGGA 60.894 55.000 25.45 0.71 46.74 3.36
506 509 1.667154 CGAGTCGGAAGGATGCCTCA 61.667 60.000 4.10 0.00 30.89 3.86
515 518 3.321497 GAAGGATGCCTCACTATAAGCG 58.679 50.000 0.00 0.00 30.89 4.68
524 527 4.439016 GCCTCACTATAAGCGAGGTATAGC 60.439 50.000 11.55 0.00 44.42 2.97
525 528 4.096682 CCTCACTATAAGCGAGGTATAGCC 59.903 50.000 0.00 0.00 39.21 3.93
526 529 4.659115 TCACTATAAGCGAGGTATAGCCA 58.341 43.478 0.00 0.00 40.61 4.75
540 543 1.746157 TAGCCATGCCCCATGTATCT 58.254 50.000 4.69 2.16 39.94 1.98
549 552 3.774766 TGCCCCATGTATCTCGCTATAAT 59.225 43.478 0.00 0.00 0.00 1.28
551 554 4.141937 GCCCCATGTATCTCGCTATAATGA 60.142 45.833 0.00 0.00 0.00 2.57
568 571 6.893958 ATAATGAAAATATAGCTCTCGCGG 57.106 37.500 6.13 0.00 42.32 6.46
569 572 2.404215 TGAAAATATAGCTCTCGCGGC 58.596 47.619 6.13 0.89 42.32 6.53
619 636 1.535687 ACGTAGGCTTCAGGTGGGT 60.536 57.895 0.00 0.00 0.00 4.51
623 640 2.289819 CGTAGGCTTCAGGTGGGTTTTA 60.290 50.000 0.00 0.00 0.00 1.52
627 644 1.824852 GCTTCAGGTGGGTTTTATGGG 59.175 52.381 0.00 0.00 0.00 4.00
631 648 0.252057 AGGTGGGTTTTATGGGTGGC 60.252 55.000 0.00 0.00 0.00 5.01
633 650 1.304547 TGGGTTTTATGGGTGGCCG 60.305 57.895 0.00 0.00 0.00 6.13
635 652 2.055633 GGTTTTATGGGTGGCCGGG 61.056 63.158 2.18 0.00 0.00 5.73
636 653 1.304630 GTTTTATGGGTGGCCGGGT 60.305 57.895 2.18 0.00 0.00 5.28
637 654 1.304547 TTTTATGGGTGGCCGGGTG 60.305 57.895 2.18 0.00 0.00 4.61
638 655 2.082836 TTTTATGGGTGGCCGGGTGT 62.083 55.000 2.18 0.00 0.00 4.16
664 682 2.952978 GAGTCCGACATGACATAGGTCT 59.047 50.000 9.22 4.51 44.61 3.85
668 686 3.960755 TCCGACATGACATAGGTCTGAAT 59.039 43.478 9.22 0.00 44.61 2.57
671 689 3.812053 GACATGACATAGGTCTGAATGCC 59.188 47.826 9.22 0.00 44.61 4.40
673 691 1.138859 TGACATAGGTCTGAATGCCCG 59.861 52.381 9.22 0.00 44.61 6.13
685 703 4.986708 TGCCCGCAAACCTTCCCC 62.987 66.667 0.00 0.00 0.00 4.81
686 704 4.678743 GCCCGCAAACCTTCCCCT 62.679 66.667 0.00 0.00 0.00 4.79
687 705 3.083386 CCCGCAAACCTTCCCCTA 58.917 61.111 0.00 0.00 0.00 3.53
688 706 1.378119 CCCGCAAACCTTCCCCTAC 60.378 63.158 0.00 0.00 0.00 3.18
689 707 1.743995 CCGCAAACCTTCCCCTACG 60.744 63.158 0.00 0.00 0.00 3.51
702 720 3.941573 TCCCCTACGTTTGTTTATGGTC 58.058 45.455 0.00 0.00 0.00 4.02
720 741 3.009033 TGGTCTGTGGATTTTGGACTAGG 59.991 47.826 0.00 0.00 0.00 3.02
731 752 1.684734 GGACTAGGCCGGTCCTGAA 60.685 63.158 30.70 7.30 46.98 3.02
744 765 3.483574 CGGTCCTGAAAAATTCGATGACG 60.484 47.826 0.00 0.00 41.26 4.35
748 769 2.155279 TGAAAAATTCGATGACGGGCA 58.845 42.857 0.00 0.00 40.21 5.36
754 775 3.778619 TCGATGACGGGCATTGAAT 57.221 47.368 11.46 0.00 43.00 2.57
760 783 4.035091 CGATGACGGGCATTGAATAGAAAA 59.965 41.667 4.99 0.00 40.29 2.29
784 807 8.659925 AAAAATAAAATGCACAGTGACATTGA 57.340 26.923 18.25 12.50 36.64 2.57
785 808 7.878477 AAATAAAATGCACAGTGACATTGAG 57.122 32.000 18.25 0.00 36.64 3.02
786 809 4.924305 AAAATGCACAGTGACATTGAGT 57.076 36.364 18.25 8.75 36.64 3.41
787 810 4.924305 AAATGCACAGTGACATTGAGTT 57.076 36.364 18.25 5.77 36.64 3.01
788 811 4.924305 AATGCACAGTGACATTGAGTTT 57.076 36.364 17.33 0.00 35.24 2.66
789 812 4.924305 ATGCACAGTGACATTGAGTTTT 57.076 36.364 4.15 0.00 0.00 2.43
790 813 4.717233 TGCACAGTGACATTGAGTTTTT 57.283 36.364 4.15 0.00 0.00 1.94
820 843 1.406477 GGGTACCGGACATTGAGGTTC 60.406 57.143 9.46 4.49 40.86 3.62
821 844 1.636988 GTACCGGACATTGAGGTTCG 58.363 55.000 9.46 0.00 39.50 3.95
849 872 1.110442 TGTTTGAGTTGCCCCAAGTG 58.890 50.000 0.00 0.00 0.00 3.16
865 889 1.001641 GTGCAAGTCAGATGCCCCT 60.002 57.895 0.00 0.00 43.16 4.79
870 894 2.879756 GCAAGTCAGATGCCCCTAACAA 60.880 50.000 0.00 0.00 37.85 2.83
873 897 2.846206 AGTCAGATGCCCCTAACAATGA 59.154 45.455 0.00 0.00 0.00 2.57
874 898 3.118112 AGTCAGATGCCCCTAACAATGAG 60.118 47.826 0.00 0.00 0.00 2.90
875 899 2.173356 TCAGATGCCCCTAACAATGAGG 59.827 50.000 0.00 0.00 0.00 3.86
878 902 2.806945 TGCCCCTAACAATGAGGAAG 57.193 50.000 0.00 0.00 35.99 3.46
879 903 1.284785 TGCCCCTAACAATGAGGAAGG 59.715 52.381 0.00 0.00 35.99 3.46
880 904 1.410224 GCCCCTAACAATGAGGAAGGG 60.410 57.143 0.00 0.00 45.57 3.95
886 910 6.253946 CCTAACAATGAGGAAGGGAATACT 57.746 41.667 0.00 0.00 35.99 2.12
887 911 6.058183 CCTAACAATGAGGAAGGGAATACTG 58.942 44.000 0.00 0.00 35.99 2.74
888 912 5.520748 AACAATGAGGAAGGGAATACTGT 57.479 39.130 0.00 0.00 0.00 3.55
889 913 5.104259 ACAATGAGGAAGGGAATACTGTC 57.896 43.478 0.00 0.00 0.00 3.51
892 916 4.061131 TGAGGAAGGGAATACTGTCAGA 57.939 45.455 6.91 0.00 0.00 3.27
894 918 4.264397 TGAGGAAGGGAATACTGTCAGAGA 60.264 45.833 6.91 0.00 0.00 3.10
897 921 5.548056 AGGAAGGGAATACTGTCAGAGAAAA 59.452 40.000 6.91 0.00 0.00 2.29
900 924 6.187727 AGGGAATACTGTCAGAGAAAAACA 57.812 37.500 6.91 0.00 0.00 2.83
901 925 6.601332 AGGGAATACTGTCAGAGAAAAACAA 58.399 36.000 6.91 0.00 0.00 2.83
904 928 7.201785 GGGAATACTGTCAGAGAAAAACAACAA 60.202 37.037 6.91 0.00 0.00 2.83
906 930 4.969816 ACTGTCAGAGAAAAACAACAACG 58.030 39.130 6.91 0.00 0.00 4.10
907 931 4.693566 ACTGTCAGAGAAAAACAACAACGA 59.306 37.500 6.91 0.00 0.00 3.85
908 932 5.163854 ACTGTCAGAGAAAAACAACAACGAG 60.164 40.000 6.91 0.00 0.00 4.18
942 966 0.613292 ACAGCCACTCGATCCACTCT 60.613 55.000 0.00 0.00 0.00 3.24
946 970 1.066303 GCCACTCGATCCACTCTACTG 59.934 57.143 0.00 0.00 0.00 2.74
964 988 3.782244 GCAGGAAGCACGCGACTG 61.782 66.667 15.93 11.76 44.79 3.51
965 989 3.114616 CAGGAAGCACGCGACTGG 61.115 66.667 15.93 0.00 0.00 4.00
972 996 3.733960 CACGCGACTGGACTCGGA 61.734 66.667 15.93 0.00 34.06 4.55
981 1005 2.343163 CTGGACTCGGACGCTCCATC 62.343 65.000 10.19 0.24 35.91 3.51
1004 1028 1.119574 AGGAACCACACGCCTACACT 61.120 55.000 0.00 0.00 0.00 3.55
1089 1113 3.449227 CCGCTGTCCGTGCTCCTA 61.449 66.667 0.00 0.00 34.38 2.94
1259 1286 1.668419 GAATTGCTACGCCAGTCCAT 58.332 50.000 0.00 0.00 0.00 3.41
1400 1430 2.180159 GAAGCCGGCCCTTGTGTAGA 62.180 60.000 26.15 0.00 0.00 2.59
1411 1441 1.764571 TTGTGTAGAGCCGCCCACTT 61.765 55.000 0.00 0.00 0.00 3.16
1412 1442 0.901114 TGTGTAGAGCCGCCCACTTA 60.901 55.000 0.00 0.00 0.00 2.24
1500 1530 2.978824 GGCCGCCTACTCAAGTCA 59.021 61.111 0.71 0.00 0.00 3.41
1758 1791 6.274001 GTGTCATATAACACCGTCATTCAG 57.726 41.667 0.00 0.00 43.01 3.02
1776 1809 3.898482 TCAGGGCTTATTTAAGGAAGGC 58.102 45.455 13.51 13.51 45.06 4.35
1801 1834 4.183686 GCATGGCGCGCACATTCT 62.184 61.111 34.42 10.69 0.00 2.40
1802 1835 2.486504 CATGGCGCGCACATTCTT 59.513 55.556 34.42 10.21 0.00 2.52
1803 1836 1.584483 CATGGCGCGCACATTCTTC 60.584 57.895 34.42 13.35 0.00 2.87
1854 1894 4.707105 TGTGGTGACATATAGCTTGATGG 58.293 43.478 11.12 0.00 46.14 3.51
1861 1901 4.464008 ACATATAGCTTGATGGTTGGTGG 58.536 43.478 11.12 0.00 0.00 4.61
1882 1922 3.365265 GTGCAAGGTCGGGGCAAG 61.365 66.667 0.00 0.00 39.57 4.01
1923 1963 4.348461 TCCTTCGGCATATGGTTGGTAATA 59.652 41.667 4.56 0.00 0.00 0.98
1963 2112 6.356556 TGTATACTTGGAACTCATTCATGGG 58.643 40.000 4.17 0.00 36.46 4.00
1971 2120 5.062528 GGAACTCATTCATGGGATCTCTTC 58.937 45.833 0.00 0.00 36.46 2.87
2110 2259 7.548427 AGGATGCTTCACTGATATGATTAATCG 59.452 37.037 10.80 0.00 0.00 3.34
2495 2644 3.132289 TCTTCAACTCGGTAATAGCCAGG 59.868 47.826 0.00 0.00 0.00 4.45
2698 2847 8.731326 CGATGTTGTTACTTATACTACACTTCG 58.269 37.037 0.00 0.00 34.89 3.79
2746 2910 5.125097 GGTGATTGTTCAGAGAATTGATGCT 59.875 40.000 0.00 0.00 30.85 3.79
2766 2930 6.801539 TGCTTGACAGAATTTAACCTACAG 57.198 37.500 0.00 0.00 0.00 2.74
2802 2966 4.426416 CATCATACTGCATGGGTTGTTTG 58.574 43.478 0.00 0.00 35.16 2.93
2914 3078 5.105513 TCCTTGGAGAACTTTGTGGAAAAAC 60.106 40.000 0.00 0.00 0.00 2.43
2925 3089 1.098869 TGGAAAAACTTGCGCTGACA 58.901 45.000 9.73 0.00 0.00 3.58
2958 3122 4.837860 TCCTGTTTGGAAAATTAGGTGCAT 59.162 37.500 0.00 0.00 42.94 3.96
3173 3338 9.952030 TGTTTTCATCAATGGACAATACTAGTA 57.048 29.630 4.77 4.77 0.00 1.82
3334 3502 5.703130 GCTGTATGTCTTTTCAAGAGAAGGT 59.297 40.000 1.17 0.00 38.41 3.50
3489 3665 4.803452 CCCTTTTGCTGGGATAGGAAATA 58.197 43.478 0.00 0.00 44.66 1.40
3537 3713 3.616219 CCCGTCATTCCTTGGTTGATTA 58.384 45.455 0.00 0.00 0.00 1.75
3584 3767 2.654749 TAGAGTTGCACAGTCATCGG 57.345 50.000 0.00 0.00 0.00 4.18
3616 3799 6.715347 AACTTCTTATTCAACTGCAAACCT 57.285 33.333 0.00 0.00 0.00 3.50
3830 4013 8.918202 ACCAGTGAGTGTTTATTCTTTATTGA 57.082 30.769 0.00 0.00 0.00 2.57
3831 4014 9.520515 ACCAGTGAGTGTTTATTCTTTATTGAT 57.479 29.630 0.00 0.00 0.00 2.57
4062 4255 6.740110 AGTATCTTTTATCTGAGTAGCACCG 58.260 40.000 0.00 0.00 0.00 4.94
4178 4371 3.131046 CCTTGCTCATAAATTGGTGACCC 59.869 47.826 0.00 0.00 0.00 4.46
4240 4433 4.574828 TCAGTTTGTTCTGCTTTGTACTCC 59.425 41.667 0.00 0.00 35.63 3.85
4248 4441 1.418637 TGCTTTGTACTCCCTCCGTTT 59.581 47.619 0.00 0.00 0.00 3.60
4251 4444 3.326747 CTTTGTACTCCCTCCGTTTCTG 58.673 50.000 0.00 0.00 0.00 3.02
4297 4490 4.384846 CCAATACGAACTACATACGGATGC 59.615 45.833 7.78 0.00 36.43 3.91
4401 4594 2.472029 AGGAGTGGAGGGAGTACAATG 58.528 52.381 0.00 0.00 0.00 2.82
4415 4608 5.870978 GGAGTACAATGCTTGCAATTGAAAT 59.129 36.000 16.18 3.36 38.21 2.17
4460 4653 8.094798 TGTTAACATGTTATGAAGACTTGACC 57.905 34.615 18.69 0.00 0.00 4.02
4479 4672 2.558359 ACCTGTGCAGACCTAAAATTGC 59.442 45.455 0.02 0.00 37.09 3.56
4550 4757 4.528206 TGGCCAGTACATAGGTGATGATAG 59.472 45.833 0.00 0.00 39.06 2.08
4602 4809 4.072131 TGCTGGTCATACACTCCTTTTTC 58.928 43.478 0.00 0.00 0.00 2.29
4666 4876 8.291191 TCAAATATGTATCAAATTGTGGAGCA 57.709 30.769 0.00 0.00 0.00 4.26
4668 4878 7.886629 AATATGTATCAAATTGTGGAGCAGT 57.113 32.000 0.00 0.00 0.00 4.40
4693 4903 4.269183 CCATGTGGCTGGTCTATTTTACA 58.731 43.478 0.00 0.00 0.00 2.41
4699 4909 5.239525 GTGGCTGGTCTATTTTACATCATCC 59.760 44.000 0.00 0.00 0.00 3.51
4762 4972 3.550030 GGAGTTGGACGTTTTTGGTGATG 60.550 47.826 0.00 0.00 0.00 3.07
4767 4977 6.657541 AGTTGGACGTTTTTGGTGATGTATAT 59.342 34.615 0.00 0.00 0.00 0.86
4769 4979 7.455641 TGGACGTTTTTGGTGATGTATATTT 57.544 32.000 0.00 0.00 0.00 1.40
4770 4980 7.887381 TGGACGTTTTTGGTGATGTATATTTT 58.113 30.769 0.00 0.00 0.00 1.82
4771 4981 9.011095 TGGACGTTTTTGGTGATGTATATTTTA 57.989 29.630 0.00 0.00 0.00 1.52
4772 4982 9.281075 GGACGTTTTTGGTGATGTATATTTTAC 57.719 33.333 0.00 0.00 0.00 2.01
4779 4989 8.500753 TTGGTGATGTATATTTTACTCACACC 57.499 34.615 0.00 0.00 42.61 4.16
4781 4991 7.551262 TGGTGATGTATATTTTACTCACACCAC 59.449 37.037 0.00 3.74 45.44 4.16
4782 4992 7.551262 GGTGATGTATATTTTACTCACACCACA 59.449 37.037 0.00 0.00 42.10 4.17
4783 4993 8.941977 GTGATGTATATTTTACTCACACCACAA 58.058 33.333 0.00 0.00 34.57 3.33
4784 4994 9.679661 TGATGTATATTTTACTCACACCACAAT 57.320 29.630 0.00 0.00 0.00 2.71
4787 4997 9.290988 TGTATATTTTACTCACACCACAATTGT 57.709 29.630 4.92 4.92 0.00 2.71
4788 4998 9.554724 GTATATTTTACTCACACCACAATTGTG 57.445 33.333 28.18 28.18 44.89 3.33
4876 5086 1.139947 GACTAGCCGCACTGGAGTC 59.860 63.158 0.00 0.00 42.00 3.36
4885 5095 0.951040 GCACTGGAGTCCTTGTTCGG 60.951 60.000 11.33 0.00 0.00 4.30
4886 5096 0.679505 CACTGGAGTCCTTGTTCGGA 59.320 55.000 11.33 0.00 0.00 4.55
4887 5097 1.276421 CACTGGAGTCCTTGTTCGGAT 59.724 52.381 11.33 0.00 35.11 4.18
4908 5118 3.505835 TTTTTGAAGCCCAGACCGT 57.494 47.368 0.00 0.00 0.00 4.83
4909 5119 2.642154 TTTTTGAAGCCCAGACCGTA 57.358 45.000 0.00 0.00 0.00 4.02
4910 5120 2.178912 TTTTGAAGCCCAGACCGTAG 57.821 50.000 0.00 0.00 0.00 3.51
4911 5121 1.344065 TTTGAAGCCCAGACCGTAGA 58.656 50.000 0.00 0.00 0.00 2.59
4932 5142 3.250040 GAACTCTCGGTTTTGCTAAAGCA 59.750 43.478 19.87 0.00 43.25 3.91
4974 5184 6.889198 AGTATTGCACACCTAAGTCATATGT 58.111 36.000 1.90 0.00 0.00 2.29
5064 5285 9.470399 TCACTTAGATGTACAATAACTAGACCA 57.530 33.333 0.00 0.00 0.00 4.02
5117 5338 1.604604 TTCTTTTGAAGCCCTGGTCG 58.395 50.000 0.00 0.00 33.92 4.79
5136 5357 1.080501 CGCTGGAGTTCTTGCTCGA 60.081 57.895 0.00 0.00 36.41 4.04
5137 5358 0.667487 CGCTGGAGTTCTTGCTCGAA 60.667 55.000 0.00 0.00 36.41 3.71
5138 5359 0.793250 GCTGGAGTTCTTGCTCGAAC 59.207 55.000 9.70 9.70 42.73 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.981142 AGAAAATGTTTCTCTGTGTACGAAAA 58.019 30.769 0.00 0.00 0.00 2.29
5 6 7.548196 AGAAAATGTTTCTCTGTGTACGAAA 57.452 32.000 0.00 0.00 0.00 3.46
6 7 7.548196 AAGAAAATGTTTCTCTGTGTACGAA 57.452 32.000 3.82 0.00 0.00 3.85
7 8 7.548196 AAAGAAAATGTTTCTCTGTGTACGA 57.452 32.000 3.82 0.00 0.00 3.43
8 9 9.318041 CATAAAGAAAATGTTTCTCTGTGTACG 57.682 33.333 3.82 0.00 0.00 3.67
42 43 9.941325 TTGCTAACCAATCATTTGACATATTTT 57.059 25.926 0.00 0.00 34.60 1.82
46 47 9.941325 AAAATTGCTAACCAATCATTTGACATA 57.059 25.926 0.00 0.00 43.22 2.29
47 48 8.851541 AAAATTGCTAACCAATCATTTGACAT 57.148 26.923 0.00 0.00 43.22 3.06
48 49 8.674263 AAAAATTGCTAACCAATCATTTGACA 57.326 26.923 0.00 0.00 43.22 3.58
138 139 9.236006 ACTTCAGTCAAATCTAATATGCAAAGT 57.764 29.630 0.00 0.00 0.00 2.66
139 140 9.713740 GACTTCAGTCAAATCTAATATGCAAAG 57.286 33.333 1.86 0.00 44.18 2.77
305 306 9.930693 AAGGTTTGTAAACTTTGACAATGTTTA 57.069 25.926 24.58 24.58 36.92 2.01
306 307 8.840833 AAGGTTTGTAAACTTTGACAATGTTT 57.159 26.923 26.11 26.11 36.92 2.83
316 317 8.097662 TGGTCAAAATCAAGGTTTGTAAACTTT 58.902 29.630 7.36 3.58 38.53 2.66
317 318 7.616313 TGGTCAAAATCAAGGTTTGTAAACTT 58.384 30.769 7.36 0.00 38.89 2.66
318 319 7.176589 TGGTCAAAATCAAGGTTTGTAAACT 57.823 32.000 7.36 0.00 38.89 2.66
319 320 7.835634 TTGGTCAAAATCAAGGTTTGTAAAC 57.164 32.000 0.00 0.00 37.28 2.01
320 321 7.065204 GCTTTGGTCAAAATCAAGGTTTGTAAA 59.935 33.333 0.00 0.00 37.28 2.01
321 322 6.536941 GCTTTGGTCAAAATCAAGGTTTGTAA 59.463 34.615 0.00 0.00 37.28 2.41
322 323 6.045955 GCTTTGGTCAAAATCAAGGTTTGTA 58.954 36.000 0.00 0.00 37.28 2.41
323 324 4.875536 GCTTTGGTCAAAATCAAGGTTTGT 59.124 37.500 0.00 0.00 37.28 2.83
324 325 5.118286 AGCTTTGGTCAAAATCAAGGTTTG 58.882 37.500 0.00 0.00 37.32 2.93
325 326 5.357742 AGCTTTGGTCAAAATCAAGGTTT 57.642 34.783 0.00 0.00 0.00 3.27
326 327 6.478512 TTAGCTTTGGTCAAAATCAAGGTT 57.521 33.333 0.00 0.00 0.00 3.50
327 328 6.670695 ATTAGCTTTGGTCAAAATCAAGGT 57.329 33.333 0.00 0.00 0.00 3.50
328 329 7.601856 TGTATTAGCTTTGGTCAAAATCAAGG 58.398 34.615 0.00 0.00 0.00 3.61
329 330 9.079833 CATGTATTAGCTTTGGTCAAAATCAAG 57.920 33.333 0.00 0.00 0.00 3.02
330 331 8.034215 CCATGTATTAGCTTTGGTCAAAATCAA 58.966 33.333 0.00 0.00 0.00 2.57
331 332 7.395772 TCCATGTATTAGCTTTGGTCAAAATCA 59.604 33.333 0.00 0.00 0.00 2.57
332 333 7.771183 TCCATGTATTAGCTTTGGTCAAAATC 58.229 34.615 0.00 0.00 0.00 2.17
333 334 7.397192 ACTCCATGTATTAGCTTTGGTCAAAAT 59.603 33.333 0.00 0.00 0.00 1.82
334 335 6.719370 ACTCCATGTATTAGCTTTGGTCAAAA 59.281 34.615 0.00 0.00 0.00 2.44
335 336 6.245408 ACTCCATGTATTAGCTTTGGTCAAA 58.755 36.000 0.00 0.00 0.00 2.69
336 337 5.815581 ACTCCATGTATTAGCTTTGGTCAA 58.184 37.500 0.00 0.00 0.00 3.18
337 338 5.435686 ACTCCATGTATTAGCTTTGGTCA 57.564 39.130 0.00 0.00 0.00 4.02
338 339 7.859325 TTAACTCCATGTATTAGCTTTGGTC 57.141 36.000 0.00 0.00 0.00 4.02
339 340 9.914834 TTATTAACTCCATGTATTAGCTTTGGT 57.085 29.630 0.00 0.00 0.00 3.67
348 349 8.933653 CCCCCATTTTTATTAACTCCATGTATT 58.066 33.333 0.00 0.00 0.00 1.89
349 350 8.293216 TCCCCCATTTTTATTAACTCCATGTAT 58.707 33.333 0.00 0.00 0.00 2.29
350 351 7.653503 TCCCCCATTTTTATTAACTCCATGTA 58.346 34.615 0.00 0.00 0.00 2.29
351 352 6.507568 TCCCCCATTTTTATTAACTCCATGT 58.492 36.000 0.00 0.00 0.00 3.21
352 353 6.611236 ACTCCCCCATTTTTATTAACTCCATG 59.389 38.462 0.00 0.00 0.00 3.66
353 354 6.752091 ACTCCCCCATTTTTATTAACTCCAT 58.248 36.000 0.00 0.00 0.00 3.41
354 355 6.160483 ACTCCCCCATTTTTATTAACTCCA 57.840 37.500 0.00 0.00 0.00 3.86
421 422 4.938080 TGCCTCGCTTTTTCATGTTTTTA 58.062 34.783 0.00 0.00 0.00 1.52
428 431 0.798776 CGACTGCCTCGCTTTTTCAT 59.201 50.000 0.00 0.00 35.06 2.57
466 469 1.596260 CTGAAGTCACGCCAGCATATG 59.404 52.381 0.00 0.00 0.00 1.78
467 470 1.945387 CTGAAGTCACGCCAGCATAT 58.055 50.000 0.00 0.00 0.00 1.78
469 472 4.291047 CTGAAGTCACGCCAGCAT 57.709 55.556 0.00 0.00 0.00 3.79
476 479 1.797933 CCGACTCGCTGAAGTCACG 60.798 63.158 10.24 0.00 44.88 4.35
478 481 0.241213 CTTCCGACTCGCTGAAGTCA 59.759 55.000 10.24 0.00 44.88 3.41
492 495 3.862642 GCTTATAGTGAGGCATCCTTCCG 60.863 52.174 0.00 0.00 31.76 4.30
506 509 4.142138 GCATGGCTATACCTCGCTTATAGT 60.142 45.833 0.00 0.00 40.22 2.12
515 518 0.995024 ATGGGGCATGGCTATACCTC 59.005 55.000 19.78 0.00 40.22 3.85
524 527 0.957395 GCGAGATACATGGGGCATGG 60.957 60.000 0.00 0.00 45.16 3.66
525 528 0.035881 AGCGAGATACATGGGGCATG 59.964 55.000 0.00 0.00 46.18 4.06
526 529 1.644509 TAGCGAGATACATGGGGCAT 58.355 50.000 0.00 0.00 0.00 4.40
568 571 1.673923 GCCAAAGCCCATCTTTTCTGC 60.674 52.381 0.00 0.00 42.82 4.26
569 572 1.619827 TGCCAAAGCCCATCTTTTCTG 59.380 47.619 0.00 0.00 42.82 3.02
603 620 2.287977 AAAACCCACCTGAAGCCTAC 57.712 50.000 0.00 0.00 0.00 3.18
604 621 3.308832 CCATAAAACCCACCTGAAGCCTA 60.309 47.826 0.00 0.00 0.00 3.93
605 622 2.557452 CCATAAAACCCACCTGAAGCCT 60.557 50.000 0.00 0.00 0.00 4.58
619 636 1.304547 CACCCGGCCACCCATAAAA 60.305 57.895 2.24 0.00 0.00 1.52
658 676 0.326595 TTTGCGGGCATTCAGACCTA 59.673 50.000 0.00 0.00 46.64 3.08
664 682 1.531739 GGAAGGTTTGCGGGCATTCA 61.532 55.000 0.00 0.00 0.00 2.57
668 686 4.986708 GGGGAAGGTTTGCGGGCA 62.987 66.667 0.00 0.00 0.00 5.36
671 689 1.743995 CGTAGGGGAAGGTTTGCGG 60.744 63.158 0.00 0.00 0.00 5.69
673 691 1.268625 CAAACGTAGGGGAAGGTTTGC 59.731 52.381 8.62 0.00 43.83 3.68
685 703 4.992319 TCCACAGACCATAAACAAACGTAG 59.008 41.667 0.00 0.00 0.00 3.51
686 704 4.958509 TCCACAGACCATAAACAAACGTA 58.041 39.130 0.00 0.00 0.00 3.57
687 705 3.811083 TCCACAGACCATAAACAAACGT 58.189 40.909 0.00 0.00 0.00 3.99
688 706 5.371115 AATCCACAGACCATAAACAAACG 57.629 39.130 0.00 0.00 0.00 3.60
689 707 6.423604 CCAAAATCCACAGACCATAAACAAAC 59.576 38.462 0.00 0.00 0.00 2.93
702 720 2.369394 GGCCTAGTCCAAAATCCACAG 58.631 52.381 0.00 0.00 0.00 3.66
720 741 1.161843 TCGAATTTTTCAGGACCGGC 58.838 50.000 0.00 0.00 0.00 6.13
728 749 2.155279 TGCCCGTCATCGAATTTTTCA 58.845 42.857 0.00 0.00 39.71 2.69
731 752 2.752354 TCAATGCCCGTCATCGAATTTT 59.248 40.909 0.00 0.00 39.71 1.82
760 783 7.927629 ACTCAATGTCACTGTGCATTTTATTTT 59.072 29.630 20.22 4.42 33.55 1.82
765 788 4.924305 ACTCAATGTCACTGTGCATTTT 57.076 36.364 20.22 10.36 33.55 1.82
791 814 1.493871 TGTCCGGTACCCCTTCAAAAA 59.506 47.619 6.25 0.00 0.00 1.94
792 815 1.138568 TGTCCGGTACCCCTTCAAAA 58.861 50.000 6.25 0.00 0.00 2.44
793 816 1.364269 ATGTCCGGTACCCCTTCAAA 58.636 50.000 6.25 0.00 0.00 2.69
794 817 1.003812 CAATGTCCGGTACCCCTTCAA 59.996 52.381 6.25 0.00 0.00 2.69
795 818 0.616371 CAATGTCCGGTACCCCTTCA 59.384 55.000 6.25 1.28 0.00 3.02
796 819 0.906775 TCAATGTCCGGTACCCCTTC 59.093 55.000 6.25 0.00 0.00 3.46
797 820 0.909623 CTCAATGTCCGGTACCCCTT 59.090 55.000 6.25 0.00 0.00 3.95
798 821 0.981277 CCTCAATGTCCGGTACCCCT 60.981 60.000 6.25 0.00 0.00 4.79
799 822 1.269703 ACCTCAATGTCCGGTACCCC 61.270 60.000 6.25 0.00 0.00 4.95
800 823 0.616891 AACCTCAATGTCCGGTACCC 59.383 55.000 6.25 0.00 0.00 3.69
801 824 1.738030 CGAACCTCAATGTCCGGTACC 60.738 57.143 0.16 0.16 0.00 3.34
802 825 1.636988 CGAACCTCAATGTCCGGTAC 58.363 55.000 0.00 0.00 0.00 3.34
803 826 0.533491 CCGAACCTCAATGTCCGGTA 59.467 55.000 0.00 0.00 33.02 4.02
804 827 1.295423 CCGAACCTCAATGTCCGGT 59.705 57.895 0.00 0.00 33.02 5.28
821 844 1.533129 GCAACTCAAACACGGTTCACC 60.533 52.381 0.00 0.00 0.00 4.02
849 872 1.340017 TGTTAGGGGCATCTGACTTGC 60.340 52.381 0.00 0.00 39.41 4.01
865 889 6.214615 TGACAGTATTCCCTTCCTCATTGTTA 59.785 38.462 0.00 0.00 0.00 2.41
870 894 4.624913 TCTGACAGTATTCCCTTCCTCAT 58.375 43.478 1.59 0.00 0.00 2.90
873 897 4.338795 TCTCTGACAGTATTCCCTTCCT 57.661 45.455 1.59 0.00 0.00 3.36
874 898 5.422214 TTTCTCTGACAGTATTCCCTTCC 57.578 43.478 1.59 0.00 0.00 3.46
875 899 6.710744 TGTTTTTCTCTGACAGTATTCCCTTC 59.289 38.462 1.59 0.00 0.00 3.46
878 902 6.262273 TGTTGTTTTTCTCTGACAGTATTCCC 59.738 38.462 1.59 0.00 0.00 3.97
879 903 7.259290 TGTTGTTTTTCTCTGACAGTATTCC 57.741 36.000 1.59 0.00 0.00 3.01
880 904 7.373441 CGTTGTTGTTTTTCTCTGACAGTATTC 59.627 37.037 1.59 0.00 0.00 1.75
882 906 6.537301 TCGTTGTTGTTTTTCTCTGACAGTAT 59.463 34.615 1.59 0.00 0.00 2.12
883 907 5.870433 TCGTTGTTGTTTTTCTCTGACAGTA 59.130 36.000 1.59 0.00 0.00 2.74
884 908 4.693566 TCGTTGTTGTTTTTCTCTGACAGT 59.306 37.500 1.59 0.00 0.00 3.55
885 909 5.163854 ACTCGTTGTTGTTTTTCTCTGACAG 60.164 40.000 0.00 0.00 0.00 3.51
886 910 4.693566 ACTCGTTGTTGTTTTTCTCTGACA 59.306 37.500 0.00 0.00 0.00 3.58
887 911 5.022021 CACTCGTTGTTGTTTTTCTCTGAC 58.978 41.667 0.00 0.00 0.00 3.51
888 912 4.094294 CCACTCGTTGTTGTTTTTCTCTGA 59.906 41.667 0.00 0.00 0.00 3.27
889 913 4.342772 CCACTCGTTGTTGTTTTTCTCTG 58.657 43.478 0.00 0.00 0.00 3.35
892 916 2.159296 GCCCACTCGTTGTTGTTTTTCT 60.159 45.455 0.00 0.00 0.00 2.52
894 918 1.822371 AGCCCACTCGTTGTTGTTTTT 59.178 42.857 0.00 0.00 0.00 1.94
897 921 1.134340 TGTAGCCCACTCGTTGTTGTT 60.134 47.619 0.00 0.00 0.00 2.83
900 924 0.034896 CCTGTAGCCCACTCGTTGTT 59.965 55.000 0.00 0.00 0.00 2.83
901 925 1.671742 CCTGTAGCCCACTCGTTGT 59.328 57.895 0.00 0.00 0.00 3.32
934 958 2.114616 CTTCCTGCCAGTAGAGTGGAT 58.885 52.381 7.62 0.00 40.44 3.41
942 966 2.047274 GCGTGCTTCCTGCCAGTA 60.047 61.111 0.00 0.00 42.00 2.74
963 987 2.362503 ATGGAGCGTCCGAGTCCA 60.363 61.111 11.98 11.98 44.48 4.02
964 988 2.413765 GATGGAGCGTCCGAGTCC 59.586 66.667 0.00 0.00 40.17 3.85
965 989 2.024871 CGATGGAGCGTCCGAGTC 59.975 66.667 0.00 0.00 40.17 3.36
972 996 1.215647 GTTCCTGTCGATGGAGCGT 59.784 57.895 9.53 0.00 34.76 5.07
981 1005 2.149803 TAGGCGTGTGGTTCCTGTCG 62.150 60.000 0.00 0.00 0.00 4.35
1004 1028 1.562008 TGTTCCTGTTGGAGTGGTTCA 59.438 47.619 0.00 0.00 44.24 3.18
1089 1113 2.989824 CGGTGGAGGTGGTCGAGT 60.990 66.667 0.00 0.00 0.00 4.18
1400 1430 1.046204 GGTATAGTAAGTGGGCGGCT 58.954 55.000 9.56 0.00 0.00 5.52
1411 1441 9.021807 GTCCATTAGAATGCTGTAGGTATAGTA 57.978 37.037 0.00 0.00 35.08 1.82
1412 1442 7.509318 TGTCCATTAGAATGCTGTAGGTATAGT 59.491 37.037 0.00 0.00 35.08 2.12
1461 1491 0.890996 AGAAAGCAAGCCCAAGGTCG 60.891 55.000 0.00 0.00 0.00 4.79
1715 1748 1.386533 CACATTAGGGGAGCAGCAAG 58.613 55.000 0.00 0.00 0.00 4.01
1758 1791 3.026707 TGGCCTTCCTTAAATAAGCCC 57.973 47.619 3.32 0.00 32.02 5.19
1776 1809 2.404789 CGCGCCATGCTTACTTGG 59.595 61.111 0.00 0.00 43.27 3.61
1777 1810 2.277501 GCGCGCCATGCTTACTTG 60.278 61.111 23.24 0.00 43.27 3.16
1792 1825 7.008440 TCATTTCATAGAAGAAGAATGTGCG 57.992 36.000 0.00 0.00 0.00 5.34
1800 1833 8.790718 CATAACCCCATCATTTCATAGAAGAAG 58.209 37.037 0.00 0.00 0.00 2.85
1801 1834 7.231317 GCATAACCCCATCATTTCATAGAAGAA 59.769 37.037 0.00 0.00 0.00 2.52
1802 1835 6.716628 GCATAACCCCATCATTTCATAGAAGA 59.283 38.462 0.00 0.00 0.00 2.87
1803 1836 6.071728 GGCATAACCCCATCATTTCATAGAAG 60.072 42.308 0.00 0.00 0.00 2.85
1854 1894 1.326951 ACCTTGCACAACCCACCAAC 61.327 55.000 0.00 0.00 0.00 3.77
1861 1901 2.983592 CCCCGACCTTGCACAACC 60.984 66.667 0.00 0.00 0.00 3.77
1882 1922 1.527433 GACCAGCTTTGCCTTGTCCC 61.527 60.000 0.00 0.00 0.00 4.46
1923 1963 7.426410 CAAGTATACATATCTGGTCGAACACT 58.574 38.462 0.00 0.00 0.00 3.55
1963 2112 0.176680 TCCCTGCTTGCGAAGAGATC 59.823 55.000 0.00 0.00 0.00 2.75
1971 2120 1.518056 TTGCTTCTTCCCTGCTTGCG 61.518 55.000 0.00 0.00 0.00 4.85
2110 2259 4.327087 CGTTGCCTTCCATTGAATTAAAGC 59.673 41.667 0.00 0.00 0.00 3.51
2495 2644 0.600057 CCCTTCCTTCTTTGCACAGC 59.400 55.000 0.00 0.00 0.00 4.40
2630 2779 3.605634 CATGTCATCAAGTACCCCGAAA 58.394 45.455 0.00 0.00 0.00 3.46
2698 2847 8.371699 ACCTTCTATTTCTAGAATAGCCATGAC 58.628 37.037 5.89 0.00 41.87 3.06
2746 2910 6.296026 ACAGCTGTAGGTTAAATTCTGTCAA 58.704 36.000 20.16 0.00 0.00 3.18
2766 2930 4.153655 CAGTATGATGCCATATGTGACAGC 59.846 45.833 1.24 0.76 39.69 4.40
2899 3063 2.670905 GCGCAAGTTTTTCCACAAAGTT 59.329 40.909 0.30 0.00 41.68 2.66
2925 3089 5.549742 TTTCCAAACAGGATGATTGCTTT 57.450 34.783 0.00 0.00 46.10 3.51
2958 3122 6.493449 TGCAATATCGAACTTCACATTCAA 57.507 33.333 0.00 0.00 0.00 2.69
2999 3163 5.357878 TCTCCTAACCATGTGCATTGAATTC 59.642 40.000 0.00 0.00 0.00 2.17
3173 3338 1.930251 TGAGAGCTAGGAGCACAACT 58.070 50.000 0.64 0.00 45.56 3.16
3584 3767 7.357287 GCAGTTGAATAAGAAGTTAACAAACGC 60.357 37.037 8.61 0.00 0.00 4.84
3925 4111 3.201487 TCCTTTCAGATGCATCCAGTCAT 59.799 43.478 23.06 0.04 0.00 3.06
4062 4255 2.421424 GAGCATCACACCCTTTCATGAC 59.579 50.000 0.00 0.00 33.17 3.06
4085 4278 5.041191 ACCTACAATTCAGATAAGGGCTG 57.959 43.478 0.00 0.00 34.71 4.85
4178 4371 0.037590 TCCATTCCTCCCAAACCACG 59.962 55.000 0.00 0.00 0.00 4.94
4240 4433 6.867662 AATGCTTATATTCAGAAACGGAGG 57.132 37.500 0.00 0.00 0.00 4.30
4278 4471 4.841443 ATGCATCCGTATGTAGTTCGTA 57.159 40.909 0.00 0.00 35.38 3.43
4386 4579 2.787473 CAAGCATTGTACTCCCTCCA 57.213 50.000 0.00 0.00 42.34 3.86
4401 4594 5.406767 TGTTCAACATTTCAATTGCAAGC 57.593 34.783 4.94 0.00 0.00 4.01
4415 4608 9.509855 GTTAACATGTTTCTACAATGTTCAACA 57.490 29.630 17.78 0.00 37.29 3.33
4460 4653 5.824904 ATAGCAATTTTAGGTCTGCACAG 57.175 39.130 0.00 0.00 37.26 3.66
4501 4694 7.665559 AGTTCAATTTGTGCTCTATTCCTGTTA 59.334 33.333 0.00 0.00 0.00 2.41
4550 4757 0.382873 TTGCATTGCCATCAGCGATC 59.617 50.000 6.12 0.00 44.35 3.69
4602 4809 8.492748 CAAAATCATCTCAAACCAACAAATGAG 58.507 33.333 0.00 0.00 40.46 2.90
4679 4889 6.017934 CCAACGGATGATGTAAAATAGACCAG 60.018 42.308 0.00 0.00 0.00 4.00
4699 4909 1.745320 ATAGGGTAGCCGCTCCAACG 61.745 60.000 5.06 0.00 35.22 4.10
4712 4922 9.936329 ACTCCAACAAATGATATAAAATAGGGT 57.064 29.630 0.00 0.00 0.00 4.34
4779 4989 6.089476 TGTATTTTACATCGCCACAATTGTG 58.911 36.000 28.18 28.18 38.56 3.33
4780 4990 6.260870 TGTATTTTACATCGCCACAATTGT 57.739 33.333 4.92 4.92 32.89 2.71
4811 5021 5.683876 TCCCCTCTTTAGAACATCTTCAG 57.316 43.478 0.00 0.00 0.00 3.02
4820 5030 1.282382 CCCCGTTCCCCTCTTTAGAA 58.718 55.000 0.00 0.00 0.00 2.10
4906 5116 2.673833 AGCAAAACCGAGAGTTCTACG 58.326 47.619 0.00 0.00 37.88 3.51
4907 5117 5.389620 GCTTTAGCAAAACCGAGAGTTCTAC 60.390 44.000 0.00 0.00 38.28 2.59
4908 5118 4.689345 GCTTTAGCAAAACCGAGAGTTCTA 59.311 41.667 0.00 0.00 38.28 2.10
4909 5119 3.498777 GCTTTAGCAAAACCGAGAGTTCT 59.501 43.478 0.00 0.00 38.28 3.01
4910 5120 3.811514 GCTTTAGCAAAACCGAGAGTTC 58.188 45.455 0.00 0.00 38.28 3.01
4911 5121 3.898517 GCTTTAGCAAAACCGAGAGTT 57.101 42.857 0.00 0.00 39.97 3.01
4947 5157 5.222079 TGACTTAGGTGTGCAATACTTGA 57.778 39.130 0.00 0.00 0.00 3.02
4948 5158 7.280876 ACATATGACTTAGGTGTGCAATACTTG 59.719 37.037 10.38 0.00 0.00 3.16
4974 5184 6.316140 CACGAATCTCCACCTAAAATCAATGA 59.684 38.462 0.00 0.00 0.00 2.57
5016 5226 9.396022 AGTGACTCAATGAGACTTAAAAAGAAA 57.604 29.630 18.20 0.00 33.32 2.52
5061 5282 0.614979 AGGGCACGTCTAGATGTGGT 60.615 55.000 35.01 13.32 45.81 4.16
5064 5285 2.299521 GTCTAGGGCACGTCTAGATGT 58.700 52.381 11.99 11.99 43.25 3.06
5117 5338 2.734673 CGAGCAAGAACTCCAGCGC 61.735 63.158 0.00 0.00 32.79 5.92


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

AutoCloner maintained by Alex Coulton.