Multiple sequence alignment - TraesCS4A01G095600

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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 TraesCS4A01G095600 chr4A 100.000 4563 0 0 1 4563 103726324 103730886 0.000000e+00 8427
1 TraesCS4A01G095600 chr4A 96.141 1736 49 1 1403 3120 600517019 600515284 0.000000e+00 2819
2 TraesCS4A01G095600 chr4A 98.381 1112 16 2 2214 3325 612509759 612508650 0.000000e+00 1953
3 TraesCS4A01G095600 chr4A 96.186 839 14 1 1401 2221 612515571 612514733 0.000000e+00 1356
4 TraesCS4A01G095600 chr4A 93.782 193 12 0 3112 3304 600470035 600469843 1.610000e-74 291
5 TraesCS4A01G095600 chr1A 98.880 1696 17 2 1627 3321 561379435 561377741 0.000000e+00 3025
6 TraesCS4A01G095600 chr6D 95.221 1716 64 4 1405 3102 157373588 157371873 0.000000e+00 2699
7 TraesCS4A01G095600 chr5B 91.723 1933 140 8 1406 3324 605858181 605856255 0.000000e+00 2665
8 TraesCS4A01G095600 chr4B 91.576 1935 136 12 1409 3325 469471324 469469399 0.000000e+00 2645
9 TraesCS4A01G095600 chr4B 92.635 1385 50 13 1 1356 446334367 446335728 0.000000e+00 1945
10 TraesCS4A01G095600 chr4B 88.610 518 55 3 4047 4563 446336654 446337168 1.080000e-175 627
11 TraesCS4A01G095600 chr4B 89.286 420 33 8 3324 3742 446335718 446336126 2.430000e-142 516
12 TraesCS4A01G095600 chr4B 88.406 207 22 2 3726 3931 446336272 446336477 9.800000e-62 248
13 TraesCS4A01G095600 chr4D 91.456 1346 53 27 50 1348 360953814 360952484 0.000000e+00 1792
14 TraesCS4A01G095600 chr4D 96.178 968 34 3 3328 4294 360952489 360951524 0.000000e+00 1580
15 TraesCS4A01G095600 chr4D 96.215 502 18 1 4063 4563 360951523 360951022 0.000000e+00 821
16 TraesCS4A01G095600 chr2A 98.272 810 11 2 2514 3321 778334780 778335588 0.000000e+00 1415
17 TraesCS4A01G095600 chr7D 87.097 372 45 3 2957 3327 622289986 622290355 7.060000e-113 418
18 TraesCS4A01G095600 chr7D 86.472 377 39 10 2960 3330 622282254 622282624 1.980000e-108 403
19 TraesCS4A01G095600 chr7D 85.908 369 49 3 2960 3327 622281395 622281761 1.540000e-104 390
20 TraesCS4A01G095600 chr3A 79.263 217 41 4 1597 1811 614686642 614686856 1.020000e-31 148
21 TraesCS4A01G095600 chr1B 79.263 217 41 4 1597 1811 645298850 645299064 1.020000e-31 148
22 TraesCS4A01G095600 chr7B 75.342 365 59 24 1473 1811 480852456 480852815 3.680000e-31 147


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 TraesCS4A01G095600 chr4A 103726324 103730886 4562 False 8427.000000 8427 100.000000 1 4563 1 chr4A.!!$F1 4562
1 TraesCS4A01G095600 chr4A 600515284 600517019 1735 True 2819.000000 2819 96.141000 1403 3120 1 chr4A.!!$R2 1717
2 TraesCS4A01G095600 chr4A 612508650 612509759 1109 True 1953.000000 1953 98.381000 2214 3325 1 chr4A.!!$R3 1111
3 TraesCS4A01G095600 chr4A 612514733 612515571 838 True 1356.000000 1356 96.186000 1401 2221 1 chr4A.!!$R4 820
4 TraesCS4A01G095600 chr1A 561377741 561379435 1694 True 3025.000000 3025 98.880000 1627 3321 1 chr1A.!!$R1 1694
5 TraesCS4A01G095600 chr6D 157371873 157373588 1715 True 2699.000000 2699 95.221000 1405 3102 1 chr6D.!!$R1 1697
6 TraesCS4A01G095600 chr5B 605856255 605858181 1926 True 2665.000000 2665 91.723000 1406 3324 1 chr5B.!!$R1 1918
7 TraesCS4A01G095600 chr4B 469469399 469471324 1925 True 2645.000000 2645 91.576000 1409 3325 1 chr4B.!!$R1 1916
8 TraesCS4A01G095600 chr4B 446334367 446337168 2801 False 834.000000 1945 89.734250 1 4563 4 chr4B.!!$F1 4562
9 TraesCS4A01G095600 chr4D 360951022 360953814 2792 True 1397.666667 1792 94.616333 50 4563 3 chr4D.!!$R1 4513
10 TraesCS4A01G095600 chr2A 778334780 778335588 808 False 1415.000000 1415 98.272000 2514 3321 1 chr2A.!!$F1 807
11 TraesCS4A01G095600 chr7D 622281395 622282624 1229 False 396.500000 403 86.190000 2960 3330 2 chr7D.!!$F2 370

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
433 462 0.179166 CACAACACAGCACACCACAC 60.179 55.000 0.0 0.0 0.00 3.82 F
753 798 0.318441 TCAGAGACAAACTGGCGAGG 59.682 55.000 0.0 0.0 36.22 4.63 F
1370 1431 0.322187 AATGGTGGGAACTACGTGGC 60.322 55.000 0.0 0.0 0.00 5.01 F
1376 1437 0.392060 GGGAACTACGTGGCCGAATT 60.392 55.000 0.0 0.0 37.88 2.17 F
1377 1438 1.004595 GGAACTACGTGGCCGAATTC 58.995 55.000 0.0 0.0 37.88 2.17 F
1378 1439 1.405121 GGAACTACGTGGCCGAATTCT 60.405 52.381 0.0 0.0 37.88 2.40 F
3387 4341 1.737793 GGATTTCGGTGCTGATTTCGT 59.262 47.619 0.0 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1357 1418 0.392060 AATTCGGCCACGTAGTTCCC 60.392 55.000 2.24 0.00 41.61 3.97 R
2280 2359 1.577328 CCAAGCAGCGGAAACATCGT 61.577 55.000 0.00 0.00 0.00 3.73 R
3332 4277 0.798009 CATCAACGCAATTCGCCACC 60.798 55.000 0.00 0.00 43.23 4.61 R
3392 4346 5.123661 CCAGCAAAAACACAAACCAGAAAAT 59.876 36.000 0.00 0.00 0.00 1.82 R
3403 4357 4.081198 ACCTGAATTTCCAGCAAAAACACA 60.081 37.500 0.00 0.00 32.97 3.72 R
3404 4358 4.270808 CACCTGAATTTCCAGCAAAAACAC 59.729 41.667 0.00 0.00 32.97 3.32 R
4263 5463 1.270550 CTGAACCATGGGTCAGCAAAC 59.729 52.381 39.79 11.12 33.12 2.93 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
47 48 4.014847 ACGAATACCAATCGCAATGTTG 57.985 40.909 0.00 0.00 43.88 3.33
121 126 6.573664 TCACCTAAATTGTTCAGAACCATG 57.426 37.500 10.93 0.00 0.00 3.66
153 158 2.368221 TCTTTTCAAGGGTGGGCAAATG 59.632 45.455 0.00 0.00 0.00 2.32
192 197 4.102210 CCACACATCCATCATCCTTACTCT 59.898 45.833 0.00 0.00 0.00 3.24
215 220 9.605275 CTCTATCATCAAAACTCTACAATCCAA 57.395 33.333 0.00 0.00 0.00 3.53
242 247 1.067354 ACTACCAATCGACCACCGTTC 60.067 52.381 0.00 0.00 39.75 3.95
344 373 2.124109 AGCGCGATCTCCCTCAGA 60.124 61.111 12.10 0.00 34.78 3.27
433 462 0.179166 CACAACACAGCACACCACAC 60.179 55.000 0.00 0.00 0.00 3.82
473 502 4.301628 CCCAAATGAAAACAGCAGAAGAC 58.698 43.478 0.00 0.00 0.00 3.01
486 517 3.201708 AGCAGAAGACATAAAGCCTCCAT 59.798 43.478 0.00 0.00 0.00 3.41
688 733 2.126580 GCGGTTAGTCGAGTGCGT 60.127 61.111 2.10 0.00 38.98 5.24
722 767 1.194772 CGTTCGTTGGCTTTCTCTTCC 59.805 52.381 0.00 0.00 0.00 3.46
737 782 0.730834 CTTCCTCGAGTGCGTGTCAG 60.731 60.000 12.31 0.00 38.98 3.51
751 796 0.750249 TGTCAGAGACAAACTGGCGA 59.250 50.000 0.00 0.00 42.06 5.54
752 797 1.269778 TGTCAGAGACAAACTGGCGAG 60.270 52.381 0.00 0.00 42.06 5.03
753 798 0.318441 TCAGAGACAAACTGGCGAGG 59.682 55.000 0.00 0.00 36.22 4.63
754 799 1.004440 AGAGACAAACTGGCGAGGC 60.004 57.895 0.00 0.00 0.00 4.70
755 800 2.357517 AGACAAACTGGCGAGGCG 60.358 61.111 0.00 0.00 0.00 5.52
816 862 2.263077 CTCATCGGTTTCCTTCGTCTG 58.737 52.381 0.00 0.00 0.00 3.51
1023 1084 3.768922 GCAGCGTGCTCCCTCTCT 61.769 66.667 0.00 0.00 40.96 3.10
1112 1173 3.804329 TGGTAGGAATGCCGGGGC 61.804 66.667 2.18 1.86 39.96 5.80
1329 1390 5.006649 TGTTCTTTGTTGTCTGTCGAATCAG 59.993 40.000 0.00 0.00 36.85 2.90
1348 1409 1.913419 AGTTCGCTCCCCCTTGAATAA 59.087 47.619 0.00 0.00 0.00 1.40
1350 1411 2.618709 GTTCGCTCCCCCTTGAATAATG 59.381 50.000 0.00 0.00 0.00 1.90
1352 1413 2.507886 TCGCTCCCCCTTGAATAATGAA 59.492 45.455 0.00 0.00 0.00 2.57
1353 1414 3.138283 TCGCTCCCCCTTGAATAATGAAT 59.862 43.478 0.00 0.00 0.00 2.57
1354 1415 3.254166 CGCTCCCCCTTGAATAATGAATG 59.746 47.826 0.00 0.00 0.00 2.67
1355 1416 3.575687 GCTCCCCCTTGAATAATGAATGG 59.424 47.826 0.00 0.00 0.00 3.16
1356 1417 4.808042 CTCCCCCTTGAATAATGAATGGT 58.192 43.478 0.00 0.00 0.00 3.55
1357 1418 4.545678 TCCCCCTTGAATAATGAATGGTG 58.454 43.478 0.00 0.00 0.00 4.17
1358 1419 3.642848 CCCCCTTGAATAATGAATGGTGG 59.357 47.826 0.00 0.00 0.00 4.61
1359 1420 3.642848 CCCCTTGAATAATGAATGGTGGG 59.357 47.826 0.00 0.00 0.00 4.61
1360 1421 4.545678 CCCTTGAATAATGAATGGTGGGA 58.454 43.478 0.00 0.00 33.14 4.37
1361 1422 4.961730 CCCTTGAATAATGAATGGTGGGAA 59.038 41.667 0.00 0.00 33.14 3.97
1362 1423 5.163416 CCCTTGAATAATGAATGGTGGGAAC 60.163 44.000 0.00 0.00 33.14 3.62
1363 1424 5.658190 CCTTGAATAATGAATGGTGGGAACT 59.342 40.000 0.00 0.00 0.00 3.01
1364 1425 6.833416 CCTTGAATAATGAATGGTGGGAACTA 59.167 38.462 0.00 0.00 0.00 2.24
1365 1426 7.201821 CCTTGAATAATGAATGGTGGGAACTAC 60.202 40.741 0.00 0.00 0.00 2.73
1366 1427 5.820423 TGAATAATGAATGGTGGGAACTACG 59.180 40.000 0.00 0.00 0.00 3.51
1367 1428 3.713826 AATGAATGGTGGGAACTACGT 57.286 42.857 0.00 0.00 0.00 3.57
1368 1429 2.465860 TGAATGGTGGGAACTACGTG 57.534 50.000 0.00 0.00 0.00 4.49
1369 1430 1.002659 TGAATGGTGGGAACTACGTGG 59.997 52.381 0.00 0.00 0.00 4.94
1370 1431 0.322187 AATGGTGGGAACTACGTGGC 60.322 55.000 0.00 0.00 0.00 5.01
1371 1432 2.046604 GGTGGGAACTACGTGGCC 60.047 66.667 0.00 0.00 0.00 5.36
1372 1433 2.433664 GTGGGAACTACGTGGCCG 60.434 66.667 0.00 0.00 40.83 6.13
1373 1434 2.601067 TGGGAACTACGTGGCCGA 60.601 61.111 0.00 0.00 37.88 5.54
1374 1435 2.208619 TGGGAACTACGTGGCCGAA 61.209 57.895 0.00 0.00 37.88 4.30
1375 1436 1.219935 GGGAACTACGTGGCCGAAT 59.780 57.895 0.00 0.00 37.88 3.34
1376 1437 0.392060 GGGAACTACGTGGCCGAATT 60.392 55.000 0.00 0.00 37.88 2.17
1377 1438 1.004595 GGAACTACGTGGCCGAATTC 58.995 55.000 0.00 0.00 37.88 2.17
1378 1439 1.405121 GGAACTACGTGGCCGAATTCT 60.405 52.381 0.00 0.00 37.88 2.40
1379 1440 2.344025 GAACTACGTGGCCGAATTCTT 58.656 47.619 0.00 0.00 37.88 2.52
1380 1441 2.467566 ACTACGTGGCCGAATTCTTT 57.532 45.000 0.00 0.00 37.88 2.52
1381 1442 2.774687 ACTACGTGGCCGAATTCTTTT 58.225 42.857 0.00 0.00 37.88 2.27
1382 1443 3.143728 ACTACGTGGCCGAATTCTTTTT 58.856 40.909 0.00 0.00 37.88 1.94
1383 1444 2.415697 ACGTGGCCGAATTCTTTTTG 57.584 45.000 3.52 0.00 37.88 2.44
1384 1445 1.950909 ACGTGGCCGAATTCTTTTTGA 59.049 42.857 3.52 0.00 37.88 2.69
1385 1446 2.556622 ACGTGGCCGAATTCTTTTTGAT 59.443 40.909 3.52 0.00 37.88 2.57
1386 1447 3.754323 ACGTGGCCGAATTCTTTTTGATA 59.246 39.130 3.52 0.00 37.88 2.15
1387 1448 4.216687 ACGTGGCCGAATTCTTTTTGATAA 59.783 37.500 3.52 0.00 37.88 1.75
1388 1449 5.157781 CGTGGCCGAATTCTTTTTGATAAA 58.842 37.500 3.52 0.00 35.63 1.40
1389 1450 5.060446 CGTGGCCGAATTCTTTTTGATAAAC 59.940 40.000 3.52 0.00 35.63 2.01
1390 1451 5.347635 GTGGCCGAATTCTTTTTGATAAACC 59.652 40.000 3.52 0.00 0.00 3.27
1391 1452 5.011125 TGGCCGAATTCTTTTTGATAAACCA 59.989 36.000 3.52 0.00 0.00 3.67
1392 1453 5.347635 GGCCGAATTCTTTTTGATAAACCAC 59.652 40.000 3.52 0.00 0.00 4.16
1393 1454 5.060446 GCCGAATTCTTTTTGATAAACCACG 59.940 40.000 3.52 0.00 0.00 4.94
1394 1455 6.375377 CCGAATTCTTTTTGATAAACCACGA 58.625 36.000 3.52 0.00 0.00 4.35
1395 1456 6.304683 CCGAATTCTTTTTGATAAACCACGAC 59.695 38.462 3.52 0.00 0.00 4.34
1396 1457 6.031003 CGAATTCTTTTTGATAAACCACGACG 59.969 38.462 3.52 0.00 0.00 5.12
1397 1458 5.738118 TTCTTTTTGATAAACCACGACGT 57.262 34.783 0.00 0.00 0.00 4.34
1398 1459 5.333046 TCTTTTTGATAAACCACGACGTC 57.667 39.130 5.18 5.18 0.00 4.34
1399 1460 3.774282 TTTTGATAAACCACGACGTCG 57.226 42.857 34.58 34.58 46.33 5.12
2280 2359 2.820728 TCAGACGGAGAACCTATGGA 57.179 50.000 0.00 0.00 0.00 3.41
3151 4095 1.862602 GCATGAGGTTTCGCGGGTTT 61.863 55.000 6.13 0.00 0.00 3.27
3387 4341 1.737793 GGATTTCGGTGCTGATTTCGT 59.262 47.619 0.00 0.00 0.00 3.85
3392 4346 2.093890 TCGGTGCTGATTTCGTAGGTA 58.906 47.619 0.00 0.00 0.00 3.08
3403 4357 7.361799 GCTGATTTCGTAGGTATTTTCTGGTTT 60.362 37.037 0.00 0.00 0.00 3.27
3404 4358 7.812648 TGATTTCGTAGGTATTTTCTGGTTTG 58.187 34.615 0.00 0.00 0.00 2.93
3407 4361 5.613329 TCGTAGGTATTTTCTGGTTTGTGT 58.387 37.500 0.00 0.00 0.00 3.72
3421 4375 5.006386 TGGTTTGTGTTTTTGCTGGAAATT 58.994 33.333 0.00 0.00 0.00 1.82
3499 4453 1.457455 GAGGGAGGAGGCTGAGAGG 60.457 68.421 0.00 0.00 0.00 3.69
3923 5041 6.057533 AGAAACATCTCACACTCACATTTGA 58.942 36.000 0.00 0.00 0.00 2.69
3976 5094 6.877611 AACATGTTTTTAGATGGAAGACGT 57.122 33.333 4.92 0.00 0.00 4.34
3995 5117 2.545526 CGTGCCCAGCTTTACAGATATG 59.454 50.000 0.00 0.00 0.00 1.78
3999 5121 4.080356 TGCCCAGCTTTACAGATATGAAGT 60.080 41.667 0.00 0.00 0.00 3.01
4102 5302 9.477484 GAAAACTCTAGACAGAAGACAAATACA 57.523 33.333 0.00 0.00 0.00 2.29
4166 5366 2.138320 CCATGACACTCGCATATGGAC 58.862 52.381 4.56 0.00 40.52 4.02
4183 5383 1.933853 GGACGTATTCATGCACACCTC 59.066 52.381 0.00 0.00 0.00 3.85
4240 5440 5.689383 TCAGAAATTTGTACTTCAGCCAC 57.311 39.130 0.00 0.00 0.00 5.01
4260 5460 3.439476 CACAGAGCAGAAAAATGGAGAGG 59.561 47.826 0.00 0.00 0.00 3.69
4263 5463 1.006400 AGCAGAAAAATGGAGAGGGGG 59.994 52.381 0.00 0.00 0.00 5.40
4305 5737 3.654414 CTGGTCCATATCTCTAAACCGC 58.346 50.000 0.00 0.00 0.00 5.68
4345 5777 4.248691 TCTCGAGATCCATACAGCATTG 57.751 45.455 12.08 0.00 0.00 2.82
4347 5779 3.721035 TCGAGATCCATACAGCATTGTG 58.279 45.455 0.00 0.00 38.23 3.33
4470 5902 5.127519 CCCAGAGCACAAAATGGATCATTTA 59.872 40.000 6.34 0.00 42.32 1.40
4501 5933 2.093306 TTGCACCCATACAGAAGACG 57.907 50.000 0.00 0.00 0.00 4.18
4522 5954 5.507077 ACGTGAACACATACAATGTCAAAC 58.493 37.500 5.80 0.00 42.70 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.434555 TTCGTAATCCACACTTGCCG 58.565 50.000 0.00 0.00 0.00 5.69
47 48 7.533222 CAGCATTCTGAATATTCTGTAATTCGC 59.467 37.037 16.24 14.61 42.95 4.70
192 197 8.049117 AGCTTGGATTGTAGAGTTTTGATGATA 58.951 33.333 0.00 0.00 0.00 2.15
208 213 6.929049 TCGATTGGTAGTATTAGCTTGGATTG 59.071 38.462 0.00 0.00 0.00 2.67
215 220 4.038883 GGTGGTCGATTGGTAGTATTAGCT 59.961 45.833 0.00 0.00 0.00 3.32
242 247 0.040870 CGGATCAGTCGTCGAGGATG 60.041 60.000 11.48 10.40 0.00 3.51
396 425 2.650116 GCAGTGAGGAGGAGCGGAA 61.650 63.158 0.00 0.00 0.00 4.30
473 502 4.202050 CGAAGGGAAAATGGAGGCTTTATG 60.202 45.833 0.00 0.00 0.00 1.90
486 517 2.116556 GGTGGGGCGAAGGGAAAA 59.883 61.111 0.00 0.00 0.00 2.29
722 767 0.453615 GTCTCTGACACGCACTCGAG 60.454 60.000 11.84 11.84 39.41 4.04
737 782 2.383527 CGCCTCGCCAGTTTGTCTC 61.384 63.158 0.00 0.00 0.00 3.36
816 862 2.224967 CCAGAGAAATCCATCCCCATCC 60.225 54.545 0.00 0.00 0.00 3.51
995 1056 1.889105 CACGCTGCCGCCATTATCT 60.889 57.895 0.00 0.00 38.22 1.98
996 1057 2.633657 CACGCTGCCGCCATTATC 59.366 61.111 0.00 0.00 38.22 1.75
997 1058 3.585990 GCACGCTGCCGCCATTAT 61.586 61.111 0.00 0.00 37.42 1.28
1304 1365 4.857871 TTCGACAGACAACAAAGAACAG 57.142 40.909 0.00 0.00 0.00 3.16
1329 1390 2.413310 TTATTCAAGGGGGAGCGAAC 57.587 50.000 0.00 0.00 0.00 3.95
1338 1399 4.545678 TCCCACCATTCATTATTCAAGGG 58.454 43.478 0.00 0.00 0.00 3.95
1348 1409 2.355716 CCACGTAGTTCCCACCATTCAT 60.356 50.000 0.00 0.00 41.61 2.57
1350 1411 1.734163 CCACGTAGTTCCCACCATTC 58.266 55.000 0.00 0.00 41.61 2.67
1352 1413 1.298667 GCCACGTAGTTCCCACCAT 59.701 57.895 0.00 0.00 41.61 3.55
1353 1414 2.745037 GCCACGTAGTTCCCACCA 59.255 61.111 0.00 0.00 41.61 4.17
1354 1415 2.046604 GGCCACGTAGTTCCCACC 60.047 66.667 0.00 0.00 41.61 4.61
1355 1416 2.433664 CGGCCACGTAGTTCCCAC 60.434 66.667 2.24 0.00 41.61 4.61
1356 1417 1.546589 ATTCGGCCACGTAGTTCCCA 61.547 55.000 2.24 0.00 41.61 4.37
1357 1418 0.392060 AATTCGGCCACGTAGTTCCC 60.392 55.000 2.24 0.00 41.61 3.97
1358 1419 1.004595 GAATTCGGCCACGTAGTTCC 58.995 55.000 2.24 0.00 41.61 3.62
1359 1420 2.005971 AGAATTCGGCCACGTAGTTC 57.994 50.000 2.24 0.00 41.61 3.01
1360 1421 2.467566 AAGAATTCGGCCACGTAGTT 57.532 45.000 2.24 0.00 41.61 2.24
1362 1423 3.187637 TCAAAAAGAATTCGGCCACGTAG 59.812 43.478 2.24 0.00 41.85 3.51
1363 1424 3.139850 TCAAAAAGAATTCGGCCACGTA 58.860 40.909 2.24 0.00 41.85 3.57
1364 1425 1.950909 TCAAAAAGAATTCGGCCACGT 59.049 42.857 2.24 0.00 41.85 4.49
1365 1426 2.697431 TCAAAAAGAATTCGGCCACG 57.303 45.000 2.24 0.00 42.74 4.94
1366 1427 5.347635 GGTTTATCAAAAAGAATTCGGCCAC 59.652 40.000 2.24 0.00 0.00 5.01
1367 1428 5.011125 TGGTTTATCAAAAAGAATTCGGCCA 59.989 36.000 2.24 0.00 0.00 5.36
1368 1429 5.347635 GTGGTTTATCAAAAAGAATTCGGCC 59.652 40.000 0.00 0.00 0.00 6.13
1369 1430 5.060446 CGTGGTTTATCAAAAAGAATTCGGC 59.940 40.000 0.00 0.00 0.00 5.54
1370 1431 6.304683 GTCGTGGTTTATCAAAAAGAATTCGG 59.695 38.462 0.00 0.00 0.00 4.30
1371 1432 6.031003 CGTCGTGGTTTATCAAAAAGAATTCG 59.969 38.462 0.00 0.00 0.00 3.34
1372 1433 6.854381 ACGTCGTGGTTTATCAAAAAGAATTC 59.146 34.615 0.00 0.00 0.00 2.17
1373 1434 6.731164 ACGTCGTGGTTTATCAAAAAGAATT 58.269 32.000 0.00 0.00 0.00 2.17
1374 1435 6.308371 ACGTCGTGGTTTATCAAAAAGAAT 57.692 33.333 0.00 0.00 0.00 2.40
1375 1436 5.556758 CGACGTCGTGGTTTATCAAAAAGAA 60.557 40.000 29.08 0.00 34.11 2.52
1376 1437 4.084952 CGACGTCGTGGTTTATCAAAAAGA 60.085 41.667 29.08 0.00 34.11 2.52
1377 1438 4.084952 TCGACGTCGTGGTTTATCAAAAAG 60.085 41.667 34.40 3.39 40.80 2.27
1378 1439 3.801050 TCGACGTCGTGGTTTATCAAAAA 59.199 39.130 34.40 9.89 40.80 1.94
1379 1440 3.379240 TCGACGTCGTGGTTTATCAAAA 58.621 40.909 34.40 10.34 40.80 2.44
1380 1441 2.981805 CTCGACGTCGTGGTTTATCAAA 59.018 45.455 34.40 12.16 40.80 2.69
1381 1442 2.587956 CTCGACGTCGTGGTTTATCAA 58.412 47.619 34.40 12.68 40.80 2.57
1382 1443 1.135603 CCTCGACGTCGTGGTTTATCA 60.136 52.381 37.87 17.93 45.02 2.15
1383 1444 1.542544 CCTCGACGTCGTGGTTTATC 58.457 55.000 37.87 2.35 45.02 1.75
1384 1445 3.708195 CCTCGACGTCGTGGTTTAT 57.292 52.632 37.87 0.00 45.02 1.40
1390 1451 1.649171 CATCTTTTCCTCGACGTCGTG 59.351 52.381 34.40 31.02 40.80 4.35
1391 1452 1.402456 CCATCTTTTCCTCGACGTCGT 60.402 52.381 34.40 11.86 40.80 4.34
1392 1453 1.269166 CCATCTTTTCCTCGACGTCG 58.731 55.000 31.30 31.30 41.45 5.12
1393 1454 1.203994 TCCCATCTTTTCCTCGACGTC 59.796 52.381 5.18 5.18 0.00 4.34
1394 1455 1.204941 CTCCCATCTTTTCCTCGACGT 59.795 52.381 0.00 0.00 0.00 4.34
1395 1456 1.927895 CTCCCATCTTTTCCTCGACG 58.072 55.000 0.00 0.00 0.00 5.12
1396 1457 1.066143 TGCTCCCATCTTTTCCTCGAC 60.066 52.381 0.00 0.00 0.00 4.20
1397 1458 1.208052 CTGCTCCCATCTTTTCCTCGA 59.792 52.381 0.00 0.00 0.00 4.04
1398 1459 1.661341 CTGCTCCCATCTTTTCCTCG 58.339 55.000 0.00 0.00 0.00 4.63
1399 1460 1.340405 TGCTGCTCCCATCTTTTCCTC 60.340 52.381 0.00 0.00 0.00 3.71
2024 2103 3.899981 ATTGCAGCGCCGGAAGTGA 62.900 57.895 5.05 0.00 0.00 3.41
2280 2359 1.577328 CCAAGCAGCGGAAACATCGT 61.577 55.000 0.00 0.00 0.00 3.73
3151 4095 3.345808 GACGCCTCGCAACAAGCA 61.346 61.111 0.00 0.00 46.13 3.91
3321 4266 5.527951 GCAATTCGCCACCATTCATTATTA 58.472 37.500 0.00 0.00 32.94 0.98
3323 4268 3.550639 CGCAATTCGCCACCATTCATTAT 60.551 43.478 0.00 0.00 37.30 1.28
3324 4269 2.223456 CGCAATTCGCCACCATTCATTA 60.223 45.455 0.00 0.00 37.30 1.90
3330 4275 1.212490 CAACGCAATTCGCCACCAT 59.788 52.632 0.00 0.00 43.23 3.55
3331 4276 1.240641 ATCAACGCAATTCGCCACCA 61.241 50.000 0.00 0.00 43.23 4.17
3332 4277 0.798009 CATCAACGCAATTCGCCACC 60.798 55.000 0.00 0.00 43.23 4.61
3333 4278 0.798009 CCATCAACGCAATTCGCCAC 60.798 55.000 0.00 0.00 43.23 5.01
3387 4341 7.492994 GCAAAAACACAAACCAGAAAATACCTA 59.507 33.333 0.00 0.00 0.00 3.08
3392 4346 5.123661 CCAGCAAAAACACAAACCAGAAAAT 59.876 36.000 0.00 0.00 0.00 1.82
3403 4357 4.081198 ACCTGAATTTCCAGCAAAAACACA 60.081 37.500 0.00 0.00 32.97 3.72
3404 4358 4.270808 CACCTGAATTTCCAGCAAAAACAC 59.729 41.667 0.00 0.00 32.97 3.32
3407 4361 5.305128 AGATCACCTGAATTTCCAGCAAAAA 59.695 36.000 0.00 0.00 32.97 1.94
3421 4375 1.332195 CCGCCAGATAGATCACCTGA 58.668 55.000 9.64 0.00 0.00 3.86
3499 4453 1.153469 CCTCGCCTCCTCTTTCTGC 60.153 63.158 0.00 0.00 0.00 4.26
3772 4889 4.020218 AGCATATACGGTGGCTGAATACAT 60.020 41.667 0.00 0.00 34.83 2.29
3774 4891 3.926616 AGCATATACGGTGGCTGAATAC 58.073 45.455 0.00 0.00 34.83 1.89
3806 4923 1.339342 ACCCGCGGCTAAAGTACAAAT 60.339 47.619 22.85 0.00 0.00 2.32
3951 5069 7.323656 CACGTCTTCCATCTAAAAACATGTTTC 59.676 37.037 23.47 6.08 31.45 2.78
3976 5094 4.080356 ACTTCATATCTGTAAAGCTGGGCA 60.080 41.667 0.00 0.00 0.00 5.36
3995 5117 1.304134 ATGGCCGGTTTGGGACTTC 60.304 57.895 1.90 0.00 35.49 3.01
3999 5121 1.304052 CTTGATGGCCGGTTTGGGA 60.304 57.895 1.90 0.00 38.63 4.37
4045 5167 8.922058 AAAATGATGAACTCATAGAACATTGC 57.078 30.769 0.00 0.00 44.03 3.56
4102 5302 6.816140 ACAAAATTCGATGTGTTGGTTCTTTT 59.184 30.769 6.29 0.00 0.00 2.27
4149 5349 0.815095 ACGTCCATATGCGAGTGTCA 59.185 50.000 9.34 0.00 0.00 3.58
4166 5366 4.418013 TTTTGAGGTGTGCATGAATACG 57.582 40.909 0.00 0.00 0.00 3.06
4240 5440 3.015327 CCCTCTCCATTTTTCTGCTCTG 58.985 50.000 0.00 0.00 0.00 3.35
4263 5463 1.270550 CTGAACCATGGGTCAGCAAAC 59.729 52.381 39.79 11.12 33.12 2.93
4305 5737 3.480470 AGATACCAAAATCCGCATCCTG 58.520 45.455 0.00 0.00 0.00 3.86
4313 5745 5.215252 TGGATCTCGAGATACCAAAATCC 57.785 43.478 30.48 23.30 34.43 3.01
4345 5777 5.869344 TGTGCACTATACTCATTGAGTTCAC 59.131 40.000 23.53 18.85 40.28 3.18
4347 5779 6.968131 TTGTGCACTATACTCATTGAGTTC 57.032 37.500 23.53 7.90 40.28 3.01
4357 5789 7.796054 AGACTTTGGATATTGTGCACTATACT 58.204 34.615 20.77 11.55 0.00 2.12
4470 5902 8.538701 TCTGTATGGGTGCAAAATTTTATGAAT 58.461 29.630 2.44 0.00 0.00 2.57
4501 5933 7.748031 TTTGTTTGACATTGTATGTGTTCAC 57.252 32.000 0.00 0.00 45.03 3.18


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

AutoCloner maintained by Alex Coulton.