Multiple sequence alignment - TraesCS3A01G379200

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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 TraesCS3A01G379200 chr3A 100.000 2959 0 0 1 2959 628876106 628873148 0.000000e+00 5465.0
1 TraesCS3A01G379200 chr3A 97.347 1244 31 2 1 1244 696169155 696167914 0.000000e+00 2113.0
2 TraesCS3A01G379200 chr3A 96.599 588 15 2 1531 2117 696167920 696167337 0.000000e+00 970.0
3 TraesCS3A01G379200 chr3A 97.861 374 8 0 2494 2867 696139337 696138964 0.000000e+00 647.0
4 TraesCS3A01G379200 chr3A 97.861 374 8 0 2494 2867 696151555 696151182 0.000000e+00 647.0
5 TraesCS3A01G379200 chr3A 99.588 243 1 0 2264 2506 696141598 696141356 7.530000e-121 444.0
6 TraesCS3A01G379200 chr3A 98.354 243 4 0 2264 2506 696153813 696153571 7.580000e-116 427.0
7 TraesCS3A01G379200 chr3A 92.364 275 20 1 559 833 225919827 225920100 9.940000e-105 390.0
8 TraesCS3A01G379200 chr3A 98.058 103 2 0 2164 2266 696167035 696166933 2.340000e-41 180.0
9 TraesCS3A01G379200 chr3A 94.393 107 5 1 2853 2959 696150582 696150477 2.360000e-36 163.0
10 TraesCS3A01G379200 chr3A 95.181 83 4 0 2877 2959 696138484 696138402 6.650000e-27 132.0
11 TraesCS3A01G379200 chr3D 89.708 651 41 8 1531 2180 559916390 559915765 0.000000e+00 808.0
12 TraesCS3A01G379200 chr3D 92.224 553 34 6 1531 2082 559937192 559936648 0.000000e+00 774.0
13 TraesCS3A01G379200 chr3D 85.962 634 81 7 2332 2959 559936451 559935820 0.000000e+00 671.0
14 TraesCS3A01G379200 chr3D 87.589 564 49 5 1 563 559917352 559916809 4.160000e-178 634.0
15 TraesCS3A01G379200 chr3D 84.046 608 83 9 2328 2931 559911100 559910503 9.200000e-160 573.0
16 TraesCS3A01G379200 chr3D 85.404 507 35 9 7 513 559938046 559937579 9.530000e-135 490.0
17 TraesCS3A01G379200 chr3D 87.298 433 38 9 820 1242 559916811 559916386 2.060000e-131 479.0
18 TraesCS3A01G379200 chr3D 93.548 279 18 0 966 1244 559937464 559937186 1.640000e-112 416.0
19 TraesCS3A01G379200 chr3D 79.498 239 22 12 1015 1244 582817146 582816926 8.550000e-31 145.0
20 TraesCS3A01G379200 chr3D 80.447 179 35 0 1011 1189 582162726 582162548 1.430000e-28 137.0
21 TraesCS3A01G379200 chr3D 76.847 203 32 12 1042 1244 582056815 582056628 1.880000e-17 100.0
22 TraesCS3A01G379200 chr3D 75.369 203 38 9 1042 1244 582116214 582116024 1.460000e-13 87.9
23 TraesCS3A01G379200 chr3B 93.214 501 29 4 1531 2029 743813693 743813196 0.000000e+00 732.0
24 TraesCS3A01G379200 chr3B 90.376 426 33 4 820 1244 743814105 743813687 1.200000e-153 553.0
25 TraesCS3A01G379200 chr3B 95.486 288 12 1 1244 1531 4310876 4310590 2.690000e-125 459.0
26 TraesCS3A01G379200 chr3B 86.275 306 40 2 2629 2932 743810613 743810308 6.110000e-87 331.0
27 TraesCS3A01G379200 chr3B 89.299 271 20 2 207 476 743814435 743814173 6.110000e-87 331.0
28 TraesCS3A01G379200 chr3B 100.000 28 0 0 2269 2296 262841594 262841621 5.000000e-03 52.8
29 TraesCS3A01G379200 chr3B 100.000 28 0 0 1217 1244 720263278 720263305 5.000000e-03 52.8
30 TraesCS3A01G379200 chr1B 99.313 291 1 1 1242 1531 670905109 670904819 2.610000e-145 525.0
31 TraesCS3A01G379200 chr6D 96.864 287 8 1 1245 1531 36066708 36066993 2.060000e-131 479.0
32 TraesCS3A01G379200 chr4A 96.516 287 10 0 1245 1531 667224997 667225283 2.670000e-130 475.0
33 TraesCS3A01G379200 chr4A 95.533 291 10 3 1241 1531 602736033 602736320 2.080000e-126 462.0
34 TraesCS3A01G379200 chr6A 96.167 287 10 1 1245 1531 575466011 575465726 4.470000e-128 468.0
35 TraesCS3A01G379200 chr6A 93.561 264 17 0 559 822 511119006 511118743 7.690000e-106 394.0
36 TraesCS3A01G379200 chr6A 93.561 264 17 0 559 822 511149907 511149644 7.690000e-106 394.0
37 TraesCS3A01G379200 chr2D 95.833 288 10 2 1244 1531 645315143 645314858 5.780000e-127 464.0
38 TraesCS3A01G379200 chr7A 95.470 287 12 1 1245 1531 11381142 11380857 9.670000e-125 457.0
39 TraesCS3A01G379200 chr7A 93.870 261 16 0 562 822 193563497 193563757 7.690000e-106 394.0
40 TraesCS3A01G379200 chr7A 92.279 272 21 0 562 833 9210710 9210439 1.290000e-103 387.0
41 TraesCS3A01G379200 chr2B 95.470 287 12 1 1245 1531 685568688 685568973 9.670000e-125 457.0
42 TraesCS3A01G379200 chr4B 94.318 264 15 0 559 822 382819782 382819519 3.550000e-109 405.0
43 TraesCS3A01G379200 chr4B 92.674 273 20 0 552 824 400363439 400363167 7.690000e-106 394.0
44 TraesCS3A01G379200 chr5B 93.939 264 16 0 559 822 445601248 445600985 1.650000e-107 399.0


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 TraesCS3A01G379200 chr3A 628873148 628876106 2958 True 5465.000000 5465 100.000000 1 2959 1 chr3A.!!$R1 2958
1 TraesCS3A01G379200 chr3A 696166933 696169155 2222 True 1087.666667 2113 97.334667 1 2266 3 chr3A.!!$R4 2265
2 TraesCS3A01G379200 chr3A 696150477 696153813 3336 True 412.333333 647 96.869333 2264 2959 3 chr3A.!!$R3 695
3 TraesCS3A01G379200 chr3A 696138402 696141598 3196 True 407.666667 647 97.543333 2264 2959 3 chr3A.!!$R2 695
4 TraesCS3A01G379200 chr3D 559915765 559917352 1587 True 640.333333 808 88.198333 1 2180 3 chr3D.!!$R6 2179
5 TraesCS3A01G379200 chr3D 559935820 559938046 2226 True 587.750000 774 89.284500 7 2959 4 chr3D.!!$R7 2952
6 TraesCS3A01G379200 chr3D 559910503 559911100 597 True 573.000000 573 84.046000 2328 2931 1 chr3D.!!$R1 603
7 TraesCS3A01G379200 chr3B 743810308 743814435 4127 True 486.750000 732 89.791000 207 2932 4 chr3B.!!$R2 2725

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
602 632 0.031857 TCTGCACATTGGTTTTGCCG 59.968 50.000 0.0 0.0 41.21 5.69 F
1253 1317 1.058695 CGAGTACGTCGCATGGTTTTC 59.941 52.381 0.0 0.0 43.03 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1847 1911 0.343372 AGGCAGGGTAATCCTCCTCA 59.657 55.0 0.00 0.0 46.12 3.86 R
2140 2329 1.165270 GGGATCGTTGGTCCAAGTTG 58.835 55.0 3.96 0.0 37.49 3.16 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 34 3.573772 CTCCGTCGTGCTCAGCCAA 62.574 63.158 0.00 0.00 0.00 4.52
135 137 1.572085 CTTCACGCCACAAGCTCTGG 61.572 60.000 6.09 6.09 40.39 3.86
204 206 3.392947 TGACCTCTGTTACAACATGGGAA 59.607 43.478 15.65 4.76 38.41 3.97
454 478 1.683938 CCTTTGGCATCAGCATCTCCA 60.684 52.381 0.00 0.00 44.61 3.86
567 597 1.065998 TGCCCAACGTAATGTACTCCC 60.066 52.381 0.00 0.00 0.00 4.30
570 600 2.159000 CCCAACGTAATGTACTCCCTCC 60.159 54.545 0.00 0.00 0.00 4.30
571 601 2.498481 CCAACGTAATGTACTCCCTCCA 59.502 50.000 0.00 0.00 0.00 3.86
602 632 0.031857 TCTGCACATTGGTTTTGCCG 59.968 50.000 0.00 0.00 41.21 5.69
616 646 5.336531 TGGTTTTGCCGAAAGTCAAACTTTA 60.337 36.000 5.13 0.00 42.54 1.85
787 817 5.476599 TGGATGAAATTGACTTCGGACAAAT 59.523 36.000 0.00 0.00 33.90 2.32
942 1004 1.553248 GTAGACACCACACCTGCCATA 59.447 52.381 0.00 0.00 0.00 2.74
1250 1314 4.470876 CGAGTACGTCGCATGGTT 57.529 55.556 0.00 0.00 43.03 3.67
1251 1315 2.733127 CGAGTACGTCGCATGGTTT 58.267 52.632 0.00 0.00 43.03 3.27
1252 1316 1.065358 CGAGTACGTCGCATGGTTTT 58.935 50.000 0.00 0.00 43.03 2.43
1253 1317 1.058695 CGAGTACGTCGCATGGTTTTC 59.941 52.381 0.00 0.00 43.03 2.29
1254 1318 2.063266 GAGTACGTCGCATGGTTTTCA 58.937 47.619 0.00 0.00 0.00 2.69
1255 1319 1.796459 AGTACGTCGCATGGTTTTCAC 59.204 47.619 0.00 0.00 0.00 3.18
1256 1320 1.796459 GTACGTCGCATGGTTTTCACT 59.204 47.619 0.00 0.00 0.00 3.41
1257 1321 1.305201 ACGTCGCATGGTTTTCACTT 58.695 45.000 0.00 0.00 0.00 3.16
1258 1322 1.673920 ACGTCGCATGGTTTTCACTTT 59.326 42.857 0.00 0.00 0.00 2.66
1259 1323 2.286772 ACGTCGCATGGTTTTCACTTTC 60.287 45.455 0.00 0.00 0.00 2.62
1260 1324 2.286713 CGTCGCATGGTTTTCACTTTCA 60.287 45.455 0.00 0.00 0.00 2.69
1261 1325 3.300009 GTCGCATGGTTTTCACTTTCAG 58.700 45.455 0.00 0.00 0.00 3.02
1262 1326 2.948979 TCGCATGGTTTTCACTTTCAGT 59.051 40.909 0.00 0.00 0.00 3.41
1275 1339 4.336889 ACTTTCAGTGAGATTTCGGTGA 57.663 40.909 0.00 0.00 0.00 4.02
1276 1340 4.703897 ACTTTCAGTGAGATTTCGGTGAA 58.296 39.130 0.00 0.00 0.00 3.18
1277 1341 5.123227 ACTTTCAGTGAGATTTCGGTGAAA 58.877 37.500 10.55 10.55 36.26 2.69
1278 1342 5.765182 ACTTTCAGTGAGATTTCGGTGAAAT 59.235 36.000 11.13 4.54 43.77 2.17
1279 1343 6.263168 ACTTTCAGTGAGATTTCGGTGAAATT 59.737 34.615 11.13 5.67 41.56 1.82
1280 1344 5.862924 TCAGTGAGATTTCGGTGAAATTC 57.137 39.130 6.26 6.79 41.56 2.17
1281 1345 5.304778 TCAGTGAGATTTCGGTGAAATTCA 58.695 37.500 6.26 8.76 41.56 2.57
1282 1346 5.179368 TCAGTGAGATTTCGGTGAAATTCAC 59.821 40.000 17.16 17.16 46.23 3.18
1283 1347 5.180117 CAGTGAGATTTCGGTGAAATTCACT 59.820 40.000 23.30 24.62 46.05 3.41
1307 1371 6.602179 TGAATTTCAGTAATTTCAGCAGACG 58.398 36.000 0.00 0.00 36.59 4.18
1308 1372 4.404507 TTTCAGTAATTTCAGCAGACGC 57.595 40.909 0.00 0.00 38.99 5.19
1309 1373 5.182001 AATTTCAGTAATTTCAGCAGACGCT 59.818 36.000 0.00 0.00 40.50 5.07
1322 1386 4.516092 GCAGACGCTGAAATATTACGTT 57.484 40.909 10.46 0.00 37.05 3.99
1323 1387 4.893795 GCAGACGCTGAAATATTACGTTT 58.106 39.130 10.46 0.76 37.05 3.60
1324 1388 4.956184 GCAGACGCTGAAATATTACGTTTC 59.044 41.667 10.46 0.00 37.05 2.78
1325 1389 5.181084 CAGACGCTGAAATATTACGTTTCG 58.819 41.667 0.00 0.00 38.18 3.46
1326 1390 4.266976 AGACGCTGAAATATTACGTTTCGG 59.733 41.667 0.00 0.00 42.25 4.30
1329 1393 4.868450 CTGAAATATTACGTTTCGGCCA 57.132 40.909 2.24 0.00 38.18 5.36
1330 1394 5.224562 CTGAAATATTACGTTTCGGCCAA 57.775 39.130 2.24 0.00 38.18 4.52
1331 1395 5.624344 TGAAATATTACGTTTCGGCCAAA 57.376 34.783 2.24 0.00 38.18 3.28
1332 1396 6.010294 TGAAATATTACGTTTCGGCCAAAA 57.990 33.333 2.24 0.00 38.18 2.44
1333 1397 6.622549 TGAAATATTACGTTTCGGCCAAAAT 58.377 32.000 2.24 0.00 38.18 1.82
1334 1398 7.759465 TGAAATATTACGTTTCGGCCAAAATA 58.241 30.769 2.24 0.00 38.18 1.40
1335 1399 8.407064 TGAAATATTACGTTTCGGCCAAAATAT 58.593 29.630 2.24 1.02 38.18 1.28
1336 1400 9.240159 GAAATATTACGTTTCGGCCAAAATATT 57.760 29.630 2.24 6.54 32.32 1.28
1337 1401 9.589111 AAATATTACGTTTCGGCCAAAATATTT 57.411 25.926 2.24 11.26 35.11 1.40
1338 1402 8.791355 ATATTACGTTTCGGCCAAAATATTTC 57.209 30.769 2.24 0.00 0.00 2.17
1339 1403 4.506886 ACGTTTCGGCCAAAATATTTCA 57.493 36.364 2.24 0.00 0.00 2.69
1340 1404 4.481463 ACGTTTCGGCCAAAATATTTCAG 58.519 39.130 2.24 0.00 0.00 3.02
1341 1405 3.303229 CGTTTCGGCCAAAATATTTCAGC 59.697 43.478 2.24 11.95 0.00 4.26
1342 1406 4.241681 GTTTCGGCCAAAATATTTCAGCA 58.758 39.130 18.73 2.88 0.00 4.41
1343 1407 4.527509 TTCGGCCAAAATATTTCAGCAA 57.472 36.364 18.73 7.49 0.00 3.91
1344 1408 4.734398 TCGGCCAAAATATTTCAGCAAT 57.266 36.364 18.73 0.00 0.00 3.56
1345 1409 5.083533 TCGGCCAAAATATTTCAGCAATT 57.916 34.783 18.73 0.00 0.00 2.32
1346 1410 5.486526 TCGGCCAAAATATTTCAGCAATTT 58.513 33.333 18.73 0.00 0.00 1.82
1347 1411 5.580297 TCGGCCAAAATATTTCAGCAATTTC 59.420 36.000 18.73 5.61 0.00 2.17
1348 1412 5.350914 CGGCCAAAATATTTCAGCAATTTCA 59.649 36.000 18.73 0.00 0.00 2.69
1349 1413 6.545508 GGCCAAAATATTTCAGCAATTTCAC 58.454 36.000 18.73 2.53 0.00 3.18
1350 1414 6.372381 GGCCAAAATATTTCAGCAATTTCACT 59.628 34.615 18.73 0.00 0.00 3.41
1351 1415 7.548780 GGCCAAAATATTTCAGCAATTTCACTA 59.451 33.333 18.73 0.00 0.00 2.74
1352 1416 9.101655 GCCAAAATATTTCAGCAATTTCACTAT 57.898 29.630 14.39 0.00 0.00 2.12
1357 1421 9.956720 AATATTTCAGCAATTTCACTATAGCAC 57.043 29.630 0.00 0.00 0.00 4.40
1358 1422 7.636150 ATTTCAGCAATTTCACTATAGCACT 57.364 32.000 0.00 0.00 0.00 4.40
1359 1423 8.737168 ATTTCAGCAATTTCACTATAGCACTA 57.263 30.769 0.00 0.00 0.00 2.74
1360 1424 7.539712 TTCAGCAATTTCACTATAGCACTAC 57.460 36.000 0.00 0.00 0.00 2.73
1361 1425 6.639563 TCAGCAATTTCACTATAGCACTACA 58.360 36.000 0.00 0.00 0.00 2.74
1362 1426 7.102993 TCAGCAATTTCACTATAGCACTACAA 58.897 34.615 0.00 0.00 0.00 2.41
1363 1427 7.770433 TCAGCAATTTCACTATAGCACTACAAT 59.230 33.333 0.00 0.00 0.00 2.71
1364 1428 8.400947 CAGCAATTTCACTATAGCACTACAATT 58.599 33.333 0.00 0.00 0.00 2.32
1365 1429 8.616076 AGCAATTTCACTATAGCACTACAATTC 58.384 33.333 0.00 0.00 0.00 2.17
1366 1430 7.857885 GCAATTTCACTATAGCACTACAATTCC 59.142 37.037 0.00 0.00 0.00 3.01
1367 1431 8.892723 CAATTTCACTATAGCACTACAATTCCA 58.107 33.333 0.00 0.00 0.00 3.53
1368 1432 9.461312 AATTTCACTATAGCACTACAATTCCAA 57.539 29.630 0.00 0.00 0.00 3.53
1369 1433 9.632638 ATTTCACTATAGCACTACAATTCCAAT 57.367 29.630 0.00 0.00 0.00 3.16
1379 1443 9.995003 AGCACTACAATTCCAATATTTTTCAAA 57.005 25.926 0.00 0.00 0.00 2.69
1433 1497 9.573133 AATTGAATTCAAGTGAATATTTCGGTC 57.427 29.630 24.17 0.85 43.41 4.79
1434 1498 7.680442 TGAATTCAAGTGAATATTTCGGTCA 57.320 32.000 5.45 3.23 43.41 4.02
1435 1499 8.279970 TGAATTCAAGTGAATATTTCGGTCAT 57.720 30.769 5.45 0.00 43.41 3.06
1436 1500 8.739039 TGAATTCAAGTGAATATTTCGGTCATT 58.261 29.630 5.45 0.00 43.41 2.57
1437 1501 9.573133 GAATTCAAGTGAATATTTCGGTCATTT 57.427 29.630 6.95 0.00 43.41 2.32
1438 1502 8.915871 ATTCAAGTGAATATTTCGGTCATTTG 57.084 30.769 4.71 4.16 42.48 2.32
1439 1503 7.680442 TCAAGTGAATATTTCGGTCATTTGA 57.320 32.000 7.72 7.72 42.30 2.69
1440 1504 7.526608 TCAAGTGAATATTTCGGTCATTTGAC 58.473 34.615 7.72 1.99 40.75 3.18
1441 1505 7.390440 TCAAGTGAATATTTCGGTCATTTGACT 59.610 33.333 10.32 0.00 40.75 3.41
1460 1524 9.820725 ATTTGACTGAAATGAAAACTGAAATCA 57.179 25.926 0.00 0.00 32.69 2.57
1461 1525 8.633075 TTGACTGAAATGAAAACTGAAATCAC 57.367 30.769 0.00 0.00 0.00 3.06
1462 1526 7.999679 TGACTGAAATGAAAACTGAAATCACT 58.000 30.769 0.00 0.00 0.00 3.41
1463 1527 7.916977 TGACTGAAATGAAAACTGAAATCACTG 59.083 33.333 0.00 0.00 0.00 3.66
1464 1528 7.999679 ACTGAAATGAAAACTGAAATCACTGA 58.000 30.769 0.00 0.00 0.00 3.41
1465 1529 8.469200 ACTGAAATGAAAACTGAAATCACTGAA 58.531 29.630 0.00 0.00 0.00 3.02
1466 1530 9.304731 CTGAAATGAAAACTGAAATCACTGAAA 57.695 29.630 0.00 0.00 0.00 2.69
1467 1531 9.820725 TGAAATGAAAACTGAAATCACTGAAAT 57.179 25.926 0.00 0.00 0.00 2.17
1470 1534 9.820725 AATGAAAACTGAAATCACTGAAATTCA 57.179 25.926 0.00 0.00 0.00 2.57
1471 1535 8.633075 TGAAAACTGAAATCACTGAAATTCAC 57.367 30.769 0.00 0.46 0.00 3.18
1472 1536 8.469200 TGAAAACTGAAATCACTGAAATTCACT 58.531 29.630 0.00 0.00 0.00 3.41
1473 1537 8.638685 AAAACTGAAATCACTGAAATTCACTG 57.361 30.769 0.00 0.00 0.00 3.66
1474 1538 7.572523 AACTGAAATCACTGAAATTCACTGA 57.427 32.000 7.57 7.57 0.00 3.41
1475 1539 7.572523 ACTGAAATCACTGAAATTCACTGAA 57.427 32.000 8.87 0.00 0.00 3.02
1476 1540 8.174733 ACTGAAATCACTGAAATTCACTGAAT 57.825 30.769 8.87 0.00 33.25 2.57
1477 1541 8.636213 ACTGAAATCACTGAAATTCACTGAATT 58.364 29.630 10.71 10.71 43.07 2.17
1495 1559 6.573664 TGAATTTCAGTGATTTCGATTGGT 57.426 33.333 0.00 0.00 0.00 3.67
1496 1560 6.380995 TGAATTTCAGTGATTTCGATTGGTG 58.619 36.000 0.00 0.00 0.00 4.17
1497 1561 3.829886 TTCAGTGATTTCGATTGGTGC 57.170 42.857 0.00 0.00 0.00 5.01
1498 1562 3.057969 TCAGTGATTTCGATTGGTGCT 57.942 42.857 0.00 0.00 0.00 4.40
1499 1563 2.743664 TCAGTGATTTCGATTGGTGCTG 59.256 45.455 0.00 0.00 0.00 4.41
1500 1564 2.743664 CAGTGATTTCGATTGGTGCTGA 59.256 45.455 0.00 0.00 0.00 4.26
1501 1565 3.189080 CAGTGATTTCGATTGGTGCTGAA 59.811 43.478 0.00 0.00 0.00 3.02
1502 1566 3.820467 AGTGATTTCGATTGGTGCTGAAA 59.180 39.130 0.00 0.00 35.09 2.69
1503 1567 4.460382 AGTGATTTCGATTGGTGCTGAAAT 59.540 37.500 0.00 0.00 42.12 2.17
1504 1568 5.047802 AGTGATTTCGATTGGTGCTGAAATT 60.048 36.000 1.15 0.00 40.18 1.82
1505 1569 5.634859 GTGATTTCGATTGGTGCTGAAATTT 59.365 36.000 0.00 0.00 40.18 1.82
1506 1570 6.146021 GTGATTTCGATTGGTGCTGAAATTTT 59.854 34.615 0.00 0.00 40.18 1.82
1507 1571 6.705381 TGATTTCGATTGGTGCTGAAATTTTT 59.295 30.769 0.00 0.00 40.18 1.94
1508 1572 6.523676 TTTCGATTGGTGCTGAAATTTTTC 57.476 33.333 0.00 0.00 37.69 2.29
1509 1573 5.452078 TCGATTGGTGCTGAAATTTTTCT 57.548 34.783 4.80 0.00 38.02 2.52
1510 1574 5.221880 TCGATTGGTGCTGAAATTTTTCTG 58.778 37.500 4.80 5.32 38.02 3.02
1511 1575 5.009510 TCGATTGGTGCTGAAATTTTTCTGA 59.990 36.000 12.42 0.00 38.07 3.27
1512 1576 5.691305 CGATTGGTGCTGAAATTTTTCTGAA 59.309 36.000 12.42 1.18 38.07 3.02
1513 1577 6.200665 CGATTGGTGCTGAAATTTTTCTGAAA 59.799 34.615 12.42 0.00 38.07 2.69
1514 1578 6.660887 TTGGTGCTGAAATTTTTCTGAAAC 57.339 33.333 12.42 6.57 38.07 2.78
1515 1579 5.976458 TGGTGCTGAAATTTTTCTGAAACT 58.024 33.333 12.42 0.00 38.07 2.66
1516 1580 5.811613 TGGTGCTGAAATTTTTCTGAAACTG 59.188 36.000 12.42 0.00 38.07 3.16
1517 1581 6.042143 GGTGCTGAAATTTTTCTGAAACTGA 58.958 36.000 12.42 0.00 38.07 3.41
1518 1582 6.534793 GGTGCTGAAATTTTTCTGAAACTGAA 59.465 34.615 12.42 0.00 38.07 3.02
1519 1583 7.064490 GGTGCTGAAATTTTTCTGAAACTGAAA 59.936 33.333 12.42 0.00 38.07 2.69
1520 1584 8.606602 GTGCTGAAATTTTTCTGAAACTGAAAT 58.393 29.630 12.42 0.00 38.07 2.17
1521 1585 9.165035 TGCTGAAATTTTTCTGAAACTGAAATT 57.835 25.926 12.42 3.83 38.07 1.82
1522 1586 9.429600 GCTGAAATTTTTCTGAAACTGAAATTG 57.570 29.630 12.42 0.00 38.07 2.32
1529 1593 8.839310 TTTTCTGAAACTGAAATTGAAAACCA 57.161 26.923 1.58 0.00 32.91 3.67
1530 1594 9.447157 TTTTCTGAAACTGAAATTGAAAACCAT 57.553 25.926 1.58 0.00 32.91 3.55
1532 1596 9.528018 TTCTGAAACTGAAATTGAAAACCATAC 57.472 29.630 0.00 0.00 0.00 2.39
1533 1597 7.860373 TCTGAAACTGAAATTGAAAACCATACG 59.140 33.333 0.00 0.00 0.00 3.06
1534 1598 7.484975 TGAAACTGAAATTGAAAACCATACGT 58.515 30.769 0.00 0.00 0.00 3.57
1535 1599 7.646130 TGAAACTGAAATTGAAAACCATACGTC 59.354 33.333 0.00 0.00 0.00 4.34
1536 1600 5.685841 ACTGAAATTGAAAACCATACGTCG 58.314 37.500 0.00 0.00 0.00 5.12
1624 1688 2.357034 GCAGTTCGCCTCCGACAA 60.357 61.111 0.00 0.00 44.30 3.18
1701 1765 1.535444 TTCGTGGAGGAGGCCAAGA 60.535 57.895 5.01 0.00 43.21 3.02
1754 1818 2.997897 AGGCGCTTCTTCGGAGGT 60.998 61.111 7.64 0.00 0.00 3.85
1847 1911 2.738643 CGTGGAAACTAGCATGATCCGT 60.739 50.000 0.00 0.00 32.72 4.69
1950 2014 1.595466 CGAGATGGTCGCCTACTACT 58.405 55.000 0.00 0.00 43.03 2.57
2017 2082 8.901748 CACAAGAAATAAGACCAAAATTGTACG 58.098 33.333 0.00 0.00 0.00 3.67
2018 2083 8.626526 ACAAGAAATAAGACCAAAATTGTACGT 58.373 29.630 0.00 0.00 0.00 3.57
2025 2202 5.055812 AGACCAAAATTGTACGTACCGAAA 58.944 37.500 22.43 11.00 0.00 3.46
2146 2335 8.736751 AAATATTTAGCCGTTACAACAACTTG 57.263 30.769 0.00 0.00 0.00 3.16
2157 2346 2.616842 ACAACAACTTGGACCAACGATC 59.383 45.455 1.69 0.00 0.00 3.69
2161 2350 1.077716 CTTGGACCAACGATCCCCC 60.078 63.158 1.69 0.00 35.12 5.40
2192 4270 3.560068 ACTTTGACCAACGCTCAGTTTAG 59.440 43.478 0.00 0.00 42.02 1.85
2446 4563 7.433708 ACGTGTCATCAATTTTGTATCTTGA 57.566 32.000 0.00 0.00 33.75 3.02
2660 6814 5.116983 CGTCATTCAAACTTTAATTGCGCTT 59.883 36.000 9.73 0.00 0.00 4.68
2743 6897 4.481930 TGCAACGGCTTACATAATATGC 57.518 40.909 0.00 0.00 41.91 3.14
2827 6981 0.762418 TCATGTCACGTCCTTTGGGT 59.238 50.000 0.00 0.00 0.00 4.51
2858 7012 1.133809 AACCTCAAGCCTACCTGCCA 61.134 55.000 0.00 0.00 0.00 4.92
2922 8159 1.690352 GGTTAGGGCCTGCTATTACGA 59.310 52.381 18.53 0.00 0.00 3.43
2946 8183 4.752101 GCCACTTGATCGAAAGCTATGTAT 59.248 41.667 0.00 0.00 0.00 2.29
2953 8190 5.293324 TGATCGAAAGCTATGTATGCGTTTT 59.707 36.000 0.00 0.00 32.78 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 34 2.579201 CGGAGGTGTTGGATCGCT 59.421 61.111 0.00 0.00 0.00 4.93
135 137 7.125755 GCAGAAACCTTTTCTTTTTATTGCAC 58.874 34.615 0.00 0.00 0.00 4.57
454 478 3.382546 AGTTTGCTGAAGTTTGCAGTGAT 59.617 39.130 0.00 0.00 40.46 3.06
567 597 3.748568 GTGCAGAGTAAAAAGGACTGGAG 59.251 47.826 0.00 0.00 30.52 3.86
570 600 5.455392 CAATGTGCAGAGTAAAAAGGACTG 58.545 41.667 0.00 0.00 0.00 3.51
571 601 4.520492 CCAATGTGCAGAGTAAAAAGGACT 59.480 41.667 0.00 0.00 0.00 3.85
765 795 6.846350 AGATTTGTCCGAAGTCAATTTCATC 58.154 36.000 0.00 0.00 0.00 2.92
796 826 5.103643 ACTCCCTCAGGTTCTTTTTACCTTT 60.104 40.000 0.00 0.00 43.45 3.11
798 828 3.981375 ACTCCCTCAGGTTCTTTTTACCT 59.019 43.478 0.00 0.00 46.87 3.08
799 829 4.368565 ACTCCCTCAGGTTCTTTTTACC 57.631 45.455 0.00 0.00 35.85 2.85
807 837 2.742204 GCGGAATTACTCCCTCAGGTTC 60.742 54.545 0.00 0.00 41.87 3.62
808 838 1.209747 GCGGAATTACTCCCTCAGGTT 59.790 52.381 0.00 0.00 41.87 3.50
812 842 1.475034 GCATGCGGAATTACTCCCTCA 60.475 52.381 0.00 0.00 41.87 3.86
942 1004 1.408702 ACAAGCAACACGGCTGAAATT 59.591 42.857 0.00 0.00 45.07 1.82
1071 1134 2.208349 ACCCCCTTCAGCCTGAGT 59.792 61.111 0.00 0.00 0.00 3.41
1254 1318 5.765182 ATTTCACCGAAATCTCACTGAAAGT 59.235 36.000 0.00 0.00 42.81 2.66
1255 1319 5.673337 TTTCACCGAAATCTCACTGAAAG 57.327 39.130 0.00 0.00 42.29 2.62
1256 1320 6.262049 TGAATTTCACCGAAATCTCACTGAAA 59.738 34.615 2.62 0.00 40.77 2.69
1257 1321 5.762711 TGAATTTCACCGAAATCTCACTGAA 59.237 36.000 2.62 0.00 40.77 3.02
1258 1322 5.179368 GTGAATTTCACCGAAATCTCACTGA 59.821 40.000 17.07 0.00 40.77 3.41
1259 1323 5.385617 GTGAATTTCACCGAAATCTCACTG 58.614 41.667 17.07 0.00 40.77 3.66
1260 1324 5.613358 GTGAATTTCACCGAAATCTCACT 57.387 39.130 17.07 4.84 40.77 3.41
1282 1346 8.558063 GCGTCTGCTGAAATTACTGAAATTCAG 61.558 40.741 20.35 20.35 43.44 3.02
1283 1347 6.602179 CGTCTGCTGAAATTACTGAAATTCA 58.398 36.000 0.00 0.00 36.76 2.57
1284 1348 5.509622 GCGTCTGCTGAAATTACTGAAATTC 59.490 40.000 0.00 0.00 35.96 2.17
1285 1349 5.393962 GCGTCTGCTGAAATTACTGAAATT 58.606 37.500 0.00 0.00 37.49 1.82
1286 1350 4.974591 GCGTCTGCTGAAATTACTGAAAT 58.025 39.130 0.00 0.00 38.39 2.17
1287 1351 4.404507 GCGTCTGCTGAAATTACTGAAA 57.595 40.909 0.00 0.00 38.39 2.69
1301 1365 4.516092 AACGTAATATTTCAGCGTCTGC 57.484 40.909 0.00 0.00 43.24 4.26
1302 1366 5.181084 CGAAACGTAATATTTCAGCGTCTG 58.819 41.667 0.00 1.02 36.09 3.51
1303 1367 4.266976 CCGAAACGTAATATTTCAGCGTCT 59.733 41.667 0.00 0.00 36.09 4.18
1304 1368 4.502558 CCGAAACGTAATATTTCAGCGTC 58.497 43.478 0.00 0.00 36.09 5.19
1305 1369 3.242188 GCCGAAACGTAATATTTCAGCGT 60.242 43.478 0.00 0.00 36.09 5.07
1306 1370 3.277481 GCCGAAACGTAATATTTCAGCG 58.723 45.455 0.00 0.00 36.09 5.18
1307 1371 3.064271 TGGCCGAAACGTAATATTTCAGC 59.936 43.478 0.00 0.00 38.29 4.26
1308 1372 4.868450 TGGCCGAAACGTAATATTTCAG 57.132 40.909 0.00 0.00 36.09 3.02
1309 1373 5.624344 TTTGGCCGAAACGTAATATTTCA 57.376 34.783 1.75 0.00 36.09 2.69
1310 1374 8.791355 ATATTTTGGCCGAAACGTAATATTTC 57.209 30.769 20.75 0.00 33.52 2.17
1311 1375 9.589111 AAATATTTTGGCCGAAACGTAATATTT 57.411 25.926 20.75 19.98 34.43 1.40
1312 1376 9.240159 GAAATATTTTGGCCGAAACGTAATATT 57.760 29.630 20.75 15.83 31.57 1.28
1313 1377 8.407064 TGAAATATTTTGGCCGAAACGTAATAT 58.593 29.630 20.75 10.96 0.00 1.28
1314 1378 7.759465 TGAAATATTTTGGCCGAAACGTAATA 58.241 30.769 20.75 9.08 0.00 0.98
1315 1379 6.622549 TGAAATATTTTGGCCGAAACGTAAT 58.377 32.000 20.75 7.01 0.00 1.89
1316 1380 6.010294 TGAAATATTTTGGCCGAAACGTAA 57.990 33.333 20.75 7.15 0.00 3.18
1317 1381 5.624344 TGAAATATTTTGGCCGAAACGTA 57.376 34.783 20.75 10.53 0.00 3.57
1318 1382 4.481463 CTGAAATATTTTGGCCGAAACGT 58.519 39.130 20.75 8.51 0.00 3.99
1319 1383 3.303229 GCTGAAATATTTTGGCCGAAACG 59.697 43.478 20.75 5.63 0.00 3.60
1320 1384 4.241681 TGCTGAAATATTTTGGCCGAAAC 58.758 39.130 20.75 8.10 0.00 2.78
1321 1385 4.527509 TGCTGAAATATTTTGGCCGAAA 57.472 36.364 20.60 20.60 0.00 3.46
1322 1386 4.527509 TTGCTGAAATATTTTGGCCGAA 57.472 36.364 17.58 0.00 0.00 4.30
1323 1387 4.734398 ATTGCTGAAATATTTTGGCCGA 57.266 36.364 17.58 0.00 0.00 5.54
1324 1388 5.350914 TGAAATTGCTGAAATATTTTGGCCG 59.649 36.000 17.58 0.24 0.00 6.13
1325 1389 6.372381 AGTGAAATTGCTGAAATATTTTGGCC 59.628 34.615 17.58 0.00 0.00 5.36
1326 1390 7.368480 AGTGAAATTGCTGAAATATTTTGGC 57.632 32.000 15.06 15.06 0.00 4.52
1331 1395 9.956720 GTGCTATAGTGAAATTGCTGAAATATT 57.043 29.630 0.84 0.00 0.00 1.28
1332 1396 9.347240 AGTGCTATAGTGAAATTGCTGAAATAT 57.653 29.630 0.84 0.00 0.00 1.28
1333 1397 8.737168 AGTGCTATAGTGAAATTGCTGAAATA 57.263 30.769 0.84 0.00 0.00 1.40
1334 1398 7.636150 AGTGCTATAGTGAAATTGCTGAAAT 57.364 32.000 0.84 0.00 0.00 2.17
1335 1399 7.606073 TGTAGTGCTATAGTGAAATTGCTGAAA 59.394 33.333 0.84 0.00 0.00 2.69
1336 1400 7.102993 TGTAGTGCTATAGTGAAATTGCTGAA 58.897 34.615 0.84 0.00 0.00 3.02
1337 1401 6.639563 TGTAGTGCTATAGTGAAATTGCTGA 58.360 36.000 0.84 0.00 0.00 4.26
1338 1402 6.908870 TGTAGTGCTATAGTGAAATTGCTG 57.091 37.500 0.84 0.00 0.00 4.41
1339 1403 8.511604 AATTGTAGTGCTATAGTGAAATTGCT 57.488 30.769 0.84 0.00 0.00 3.91
1340 1404 7.857885 GGAATTGTAGTGCTATAGTGAAATTGC 59.142 37.037 0.84 2.49 0.00 3.56
1341 1405 8.892723 TGGAATTGTAGTGCTATAGTGAAATTG 58.107 33.333 0.84 0.00 0.00 2.32
1342 1406 9.461312 TTGGAATTGTAGTGCTATAGTGAAATT 57.539 29.630 0.84 0.73 0.00 1.82
1343 1407 9.632638 ATTGGAATTGTAGTGCTATAGTGAAAT 57.367 29.630 0.84 0.00 0.00 2.17
1353 1417 9.995003 TTTGAAAAATATTGGAATTGTAGTGCT 57.005 25.926 0.00 0.00 0.00 4.40
1407 1471 9.573133 GACCGAAATATTCACTTGAATTCAATT 57.427 29.630 20.76 13.01 41.64 2.32
1408 1472 8.739039 TGACCGAAATATTCACTTGAATTCAAT 58.261 29.630 20.76 8.72 41.64 2.57
1409 1473 8.105097 TGACCGAAATATTCACTTGAATTCAA 57.895 30.769 19.45 19.45 41.64 2.69
1410 1474 7.680442 TGACCGAAATATTCACTTGAATTCA 57.320 32.000 9.68 3.38 41.64 2.57
1411 1475 9.573133 AAATGACCGAAATATTCACTTGAATTC 57.427 29.630 9.68 0.00 41.64 2.17
1412 1476 9.357652 CAAATGACCGAAATATTCACTTGAATT 57.642 29.630 9.68 0.00 41.64 2.17
1413 1477 8.739039 TCAAATGACCGAAATATTCACTTGAAT 58.261 29.630 9.37 9.37 45.77 2.57
1414 1478 8.020819 GTCAAATGACCGAAATATTCACTTGAA 58.979 33.333 2.04 0.00 37.27 2.69
1415 1479 7.390440 AGTCAAATGACCGAAATATTCACTTGA 59.610 33.333 9.84 0.00 45.85 3.02
1416 1480 7.482743 CAGTCAAATGACCGAAATATTCACTTG 59.517 37.037 9.84 0.00 45.85 3.16
1417 1481 7.390440 TCAGTCAAATGACCGAAATATTCACTT 59.610 33.333 9.84 0.00 45.85 3.16
1418 1482 6.878923 TCAGTCAAATGACCGAAATATTCACT 59.121 34.615 9.84 0.00 45.85 3.41
1419 1483 7.072177 TCAGTCAAATGACCGAAATATTCAC 57.928 36.000 9.84 0.00 45.85 3.18
1420 1484 7.680442 TTCAGTCAAATGACCGAAATATTCA 57.320 32.000 9.84 0.00 45.85 2.57
1434 1498 9.820725 TGATTTCAGTTTTCATTTCAGTCAAAT 57.179 25.926 0.00 0.00 34.79 2.32
1435 1499 9.086336 GTGATTTCAGTTTTCATTTCAGTCAAA 57.914 29.630 0.00 0.00 0.00 2.69
1436 1500 8.469200 AGTGATTTCAGTTTTCATTTCAGTCAA 58.531 29.630 0.00 0.00 0.00 3.18
1437 1501 7.916977 CAGTGATTTCAGTTTTCATTTCAGTCA 59.083 33.333 0.00 0.00 0.00 3.41
1438 1502 8.131100 TCAGTGATTTCAGTTTTCATTTCAGTC 58.869 33.333 0.00 0.00 0.00 3.51
1439 1503 7.999679 TCAGTGATTTCAGTTTTCATTTCAGT 58.000 30.769 0.00 0.00 0.00 3.41
1440 1504 8.861033 TTCAGTGATTTCAGTTTTCATTTCAG 57.139 30.769 0.00 0.00 0.00 3.02
1441 1505 9.820725 ATTTCAGTGATTTCAGTTTTCATTTCA 57.179 25.926 0.00 0.00 0.00 2.69
1444 1508 9.820725 TGAATTTCAGTGATTTCAGTTTTCATT 57.179 25.926 12.59 0.00 0.00 2.57
1445 1509 9.252962 GTGAATTTCAGTGATTTCAGTTTTCAT 57.747 29.630 15.60 0.00 0.00 2.57
1446 1510 8.469200 AGTGAATTTCAGTGATTTCAGTTTTCA 58.531 29.630 15.60 5.41 0.00 2.69
1447 1511 8.862550 AGTGAATTTCAGTGATTTCAGTTTTC 57.137 30.769 15.60 7.22 0.00 2.29
1472 1536 6.380995 CACCAATCGAAATCACTGAAATTCA 58.619 36.000 0.00 0.00 0.00 2.57
1473 1537 5.287035 GCACCAATCGAAATCACTGAAATTC 59.713 40.000 0.00 0.00 0.00 2.17
1474 1538 5.047802 AGCACCAATCGAAATCACTGAAATT 60.048 36.000 0.00 0.00 0.00 1.82
1475 1539 4.460382 AGCACCAATCGAAATCACTGAAAT 59.540 37.500 0.00 0.00 0.00 2.17
1476 1540 3.820467 AGCACCAATCGAAATCACTGAAA 59.180 39.130 0.00 0.00 0.00 2.69
1477 1541 3.189080 CAGCACCAATCGAAATCACTGAA 59.811 43.478 0.00 0.00 0.00 3.02
1478 1542 2.743664 CAGCACCAATCGAAATCACTGA 59.256 45.455 0.00 0.00 0.00 3.41
1479 1543 2.743664 TCAGCACCAATCGAAATCACTG 59.256 45.455 0.00 0.00 0.00 3.66
1480 1544 3.057969 TCAGCACCAATCGAAATCACT 57.942 42.857 0.00 0.00 0.00 3.41
1481 1545 3.829886 TTCAGCACCAATCGAAATCAC 57.170 42.857 0.00 0.00 0.00 3.06
1482 1546 5.389859 AATTTCAGCACCAATCGAAATCA 57.610 34.783 0.00 0.00 37.15 2.57
1483 1547 6.710692 AAAATTTCAGCACCAATCGAAATC 57.289 33.333 0.00 0.00 37.15 2.17
1484 1548 6.930722 AGAAAAATTTCAGCACCAATCGAAAT 59.069 30.769 8.47 0.00 39.20 2.17
1485 1549 6.200665 CAGAAAAATTTCAGCACCAATCGAAA 59.799 34.615 8.47 0.00 39.61 3.46
1486 1550 5.691305 CAGAAAAATTTCAGCACCAATCGAA 59.309 36.000 8.47 0.00 39.61 3.71
1487 1551 5.009510 TCAGAAAAATTTCAGCACCAATCGA 59.990 36.000 8.47 0.00 39.61 3.59
1488 1552 5.221880 TCAGAAAAATTTCAGCACCAATCG 58.778 37.500 8.47 0.00 39.61 3.34
1489 1553 7.225341 AGTTTCAGAAAAATTTCAGCACCAATC 59.775 33.333 8.47 0.00 39.61 2.67
1490 1554 7.011669 CAGTTTCAGAAAAATTTCAGCACCAAT 59.988 33.333 8.47 0.00 39.61 3.16
1491 1555 6.313411 CAGTTTCAGAAAAATTTCAGCACCAA 59.687 34.615 8.47 0.00 39.61 3.67
1492 1556 5.811613 CAGTTTCAGAAAAATTTCAGCACCA 59.188 36.000 8.47 0.00 39.61 4.17
1493 1557 6.042143 TCAGTTTCAGAAAAATTTCAGCACC 58.958 36.000 8.47 0.00 39.61 5.01
1494 1558 7.524294 TTCAGTTTCAGAAAAATTTCAGCAC 57.476 32.000 8.47 1.84 39.61 4.40
1495 1559 8.721019 ATTTCAGTTTCAGAAAAATTTCAGCA 57.279 26.923 8.47 0.00 38.36 4.41
1496 1560 9.429600 CAATTTCAGTTTCAGAAAAATTTCAGC 57.570 29.630 8.47 0.00 38.36 4.26
1503 1567 9.277783 TGGTTTTCAATTTCAGTTTCAGAAAAA 57.722 25.926 0.00 0.00 38.36 1.94
1504 1568 8.839310 TGGTTTTCAATTTCAGTTTCAGAAAA 57.161 26.923 0.00 0.00 38.36 2.29
1506 1570 9.528018 GTATGGTTTTCAATTTCAGTTTCAGAA 57.472 29.630 0.00 0.00 0.00 3.02
1507 1571 7.860373 CGTATGGTTTTCAATTTCAGTTTCAGA 59.140 33.333 0.00 0.00 0.00 3.27
1508 1572 7.647715 ACGTATGGTTTTCAATTTCAGTTTCAG 59.352 33.333 0.00 0.00 0.00 3.02
1509 1573 7.484975 ACGTATGGTTTTCAATTTCAGTTTCA 58.515 30.769 0.00 0.00 0.00 2.69
1510 1574 7.149192 CGACGTATGGTTTTCAATTTCAGTTTC 60.149 37.037 0.00 0.00 0.00 2.78
1511 1575 6.635239 CGACGTATGGTTTTCAATTTCAGTTT 59.365 34.615 0.00 0.00 0.00 2.66
1512 1576 6.017770 TCGACGTATGGTTTTCAATTTCAGTT 60.018 34.615 0.00 0.00 0.00 3.16
1513 1577 5.467399 TCGACGTATGGTTTTCAATTTCAGT 59.533 36.000 0.00 0.00 0.00 3.41
1514 1578 5.788531 GTCGACGTATGGTTTTCAATTTCAG 59.211 40.000 0.00 0.00 0.00 3.02
1515 1579 5.612925 CGTCGACGTATGGTTTTCAATTTCA 60.613 40.000 29.08 0.00 34.11 2.69
1516 1580 4.779523 CGTCGACGTATGGTTTTCAATTTC 59.220 41.667 29.08 0.00 34.11 2.17
1517 1581 4.448395 TCGTCGACGTATGGTTTTCAATTT 59.552 37.500 34.40 0.00 40.80 1.82
1518 1582 3.989167 TCGTCGACGTATGGTTTTCAATT 59.011 39.130 34.40 0.00 40.80 2.32
1519 1583 3.577667 TCGTCGACGTATGGTTTTCAAT 58.422 40.909 34.40 0.00 40.80 2.57
1520 1584 2.981805 CTCGTCGACGTATGGTTTTCAA 59.018 45.455 34.40 12.16 40.80 2.69
1521 1585 2.587956 CTCGTCGACGTATGGTTTTCA 58.412 47.619 34.40 12.68 40.80 2.69
1522 1586 1.916000 CCTCGTCGACGTATGGTTTTC 59.084 52.381 34.40 0.00 40.80 2.29
1523 1587 1.986698 CCTCGTCGACGTATGGTTTT 58.013 50.000 34.40 0.00 40.80 2.43
1524 1588 0.457337 GCCTCGTCGACGTATGGTTT 60.457 55.000 34.40 0.00 40.80 3.27
1525 1589 1.138247 GCCTCGTCGACGTATGGTT 59.862 57.895 34.40 0.00 40.80 3.67
1526 1590 2.768492 GGCCTCGTCGACGTATGGT 61.768 63.158 34.40 0.00 40.80 3.55
1527 1591 2.001361 AAGGCCTCGTCGACGTATGG 62.001 60.000 34.40 30.94 40.80 2.74
1528 1592 0.591741 GAAGGCCTCGTCGACGTATG 60.592 60.000 34.40 24.13 40.80 2.39
1529 1593 1.726265 GAAGGCCTCGTCGACGTAT 59.274 57.895 34.40 16.65 40.80 3.06
1530 1594 2.743752 CGAAGGCCTCGTCGACGTA 61.744 63.158 34.40 21.01 45.29 3.57
1531 1595 4.099170 CGAAGGCCTCGTCGACGT 62.099 66.667 34.40 16.81 45.29 4.34
1532 1596 3.720106 CTCGAAGGCCTCGTCGACG 62.720 68.421 31.30 31.30 45.82 5.12
1533 1597 2.100603 CTCGAAGGCCTCGTCGAC 59.899 66.667 22.65 5.18 45.82 4.20
1624 1688 2.479412 GAACAGCGTCCTCGAGCACT 62.479 60.000 6.99 0.00 39.71 4.40
1701 1765 1.377725 CCATGAGCGCCAGGTTCTT 60.378 57.895 2.29 0.00 0.00 2.52
1754 1818 1.395045 CGAGCAGCCCTATGGAGTCA 61.395 60.000 0.00 0.00 0.00 3.41
1847 1911 0.343372 AGGCAGGGTAATCCTCCTCA 59.657 55.000 0.00 0.00 46.12 3.86
1950 2014 2.905996 AAGCGGTCCTTCATGGCCA 61.906 57.895 8.56 8.56 33.44 5.36
2017 2082 2.717011 CACACGCAACAATTTTCGGTAC 59.283 45.455 0.00 0.00 0.00 3.34
2018 2083 2.355132 ACACACGCAACAATTTTCGGTA 59.645 40.909 0.00 0.00 0.00 4.02
2019 2084 1.133407 ACACACGCAACAATTTTCGGT 59.867 42.857 0.00 0.00 0.00 4.69
2025 2202 1.065401 CTCACCACACACGCAACAATT 59.935 47.619 0.00 0.00 0.00 2.32
2129 2318 1.944709 GTCCAAGTTGTTGTAACGGCT 59.055 47.619 1.45 0.00 30.95 5.52
2136 2325 2.116827 TCGTTGGTCCAAGTTGTTGT 57.883 45.000 3.96 0.00 30.95 3.32
2140 2329 1.165270 GGGATCGTTGGTCCAAGTTG 58.835 55.000 3.96 0.00 37.49 3.16
2446 4563 8.296713 AGAATTTGTTCAGCAATACGTAATGTT 58.703 29.630 12.06 3.30 36.89 2.71
2660 6814 5.007626 GCGAACAGAAATACAATGCTATGGA 59.992 40.000 0.00 0.00 0.00 3.41
2743 6897 2.864343 GGACCCAACGATCGTAAAGATG 59.136 50.000 23.04 15.27 40.26 2.90
2827 6981 2.297033 GCTTGAGGTTGCTCATTCCAAA 59.703 45.455 0.00 0.00 32.91 3.28
2922 8159 3.201290 CATAGCTTTCGATCAAGTGGCT 58.799 45.455 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.