Multiple sequence alignment - TraesCS7A01G290300

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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 TraesCS7A01G290300 chr7A 100.000 2211 0 0 1 2211 352622165 352619955 0.000000e+00 4084
1 TraesCS7A01G290300 chr7A 95.548 876 35 4 1338 2211 334443532 334442659 0.000000e+00 1399
2 TraesCS7A01G290300 chr7A 95.320 876 32 7 1338 2211 339554701 339553833 0.000000e+00 1382
3 TraesCS7A01G290300 chr7A 94.191 878 40 9 1338 2208 240998977 240999850 0.000000e+00 1328
4 TraesCS7A01G290300 chr6A 95.108 879 36 6 1338 2211 577918675 577917799 0.000000e+00 1378
5 TraesCS7A01G290300 chr6A 96.204 764 29 0 513 1276 53807846 53807083 0.000000e+00 1251
6 TraesCS7A01G290300 chr2A 94.413 877 40 5 1339 2208 702450496 702451370 0.000000e+00 1339
7 TraesCS7A01G290300 chr2A 93.919 888 38 13 1338 2211 733375337 733374452 0.000000e+00 1327
8 TraesCS7A01G290300 chr2A 98.810 84 1 0 1265 1348 119554925 119555008 1.370000e-32 150
9 TraesCS7A01G290300 chr2A 92.708 96 7 0 1253 1348 524095620 524095525 2.960000e-29 139
10 TraesCS7A01G290300 chr4A 94.312 879 36 9 1338 2208 595035464 595036336 0.000000e+00 1334
11 TraesCS7A01G290300 chr4A 94.191 878 41 5 1344 2211 12796725 12795848 0.000000e+00 1330
12 TraesCS7A01G290300 chr4A 94.091 880 38 11 1338 2208 84312901 84313775 0.000000e+00 1325
13 TraesCS7A01G290300 chr4A 92.857 98 4 3 1251 1348 491341050 491340956 2.960000e-29 139
14 TraesCS7A01G290300 chr3B 96.466 764 27 0 513 1276 101915550 101914787 0.000000e+00 1262
15 TraesCS7A01G290300 chr3B 93.678 522 22 2 6 516 101916124 101915603 0.000000e+00 771
16 TraesCS7A01G290300 chr3B 93.678 522 22 3 6 516 201531972 201531451 0.000000e+00 771
17 TraesCS7A01G290300 chr3B 93.487 522 22 3 6 516 6002669 6002149 0.000000e+00 765
18 TraesCS7A01G290300 chr3A 96.452 761 27 0 513 1273 66013251 66014011 0.000000e+00 1256
19 TraesCS7A01G290300 chr3A 96.321 761 28 0 513 1273 164859691 164860451 0.000000e+00 1251
20 TraesCS7A01G290300 chr6D 96.443 759 27 0 513 1271 168262040 168261282 0.000000e+00 1253
21 TraesCS7A01G290300 chr6D 93.678 522 22 2 6 516 168262614 168262093 0.000000e+00 771
22 TraesCS7A01G290300 chr6D 92.952 525 26 3 3 516 135459499 135460023 0.000000e+00 754
23 TraesCS7A01G290300 chr6D 92.912 522 26 3 6 516 458920260 458919739 0.000000e+00 749
24 TraesCS7A01G290300 chr5D 96.204 764 29 0 513 1276 446178668 446177905 0.000000e+00 1251
25 TraesCS7A01G290300 chr5D 93.487 522 23 2 6 516 503223164 503222643 0.000000e+00 765
26 TraesCS7A01G290300 chr5D 93.143 525 25 2 3 516 503273924 503274448 0.000000e+00 760
27 TraesCS7A01G290300 chr5D 92.992 528 24 4 1 516 6193889 6193363 0.000000e+00 758
28 TraesCS7A01G290300 chr5D 91.919 99 6 1 1250 1348 433473247 433473151 1.060000e-28 137
29 TraesCS7A01G290300 chr1B 96.321 761 28 0 513 1273 633749524 633750284 0.000000e+00 1251
30 TraesCS7A01G290300 chr1B 93.359 527 24 2 1 516 619187239 619186713 0.000000e+00 769
31 TraesCS7A01G290300 chr1B 94.565 92 3 2 1258 1348 432335356 432335446 8.230000e-30 141
32 TraesCS7A01G290300 chr1B 92.000 100 3 5 1250 1348 168099817 168099722 3.830000e-28 135
33 TraesCS7A01G290300 chr1A 96.204 764 29 0 513 1276 554516622 554515859 0.000000e+00 1251
34 TraesCS7A01G290300 chr1A 89.720 107 5 6 1243 1348 261284959 261285060 4.950000e-27 132
35 TraesCS7A01G290300 chr1D 96.189 761 29 0 513 1273 254393742 254394502 0.000000e+00 1245
36 TraesCS7A01G290300 chr2B 93.359 527 24 3 1 516 234533068 234532542 0.000000e+00 769
37 TraesCS7A01G290300 chrUn 93.333 525 23 3 3 516 379971431 379971954 0.000000e+00 765
38 TraesCS7A01G290300 chr7D 93.333 525 24 2 3 516 231578115 231578639 0.000000e+00 765
39 TraesCS7A01G290300 chr4D 93.169 527 25 2 1 516 177444490 177445016 0.000000e+00 763
40 TraesCS7A01G290300 chr4D 90.857 525 37 3 3 516 207365319 207365843 0.000000e+00 693
41 TraesCS7A01G290300 chr5A 91.099 191 7 2 1 181 505899255 505899445 1.310000e-62 250
42 TraesCS7A01G290300 chr5A 94.565 92 4 1 1257 1348 550200853 550200763 8.230000e-30 141
43 TraesCS7A01G290300 chr5A 93.684 95 3 3 1256 1348 191476290 191476197 2.960000e-29 139


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 TraesCS7A01G290300 chr7A 352619955 352622165 2210 True 4084.0 4084 100.0000 1 2211 1 chr7A.!!$R3 2210
1 TraesCS7A01G290300 chr7A 334442659 334443532 873 True 1399.0 1399 95.5480 1338 2211 1 chr7A.!!$R1 873
2 TraesCS7A01G290300 chr7A 339553833 339554701 868 True 1382.0 1382 95.3200 1338 2211 1 chr7A.!!$R2 873
3 TraesCS7A01G290300 chr7A 240998977 240999850 873 False 1328.0 1328 94.1910 1338 2208 1 chr7A.!!$F1 870
4 TraesCS7A01G290300 chr6A 577917799 577918675 876 True 1378.0 1378 95.1080 1338 2211 1 chr6A.!!$R2 873
5 TraesCS7A01G290300 chr6A 53807083 53807846 763 True 1251.0 1251 96.2040 513 1276 1 chr6A.!!$R1 763
6 TraesCS7A01G290300 chr2A 702450496 702451370 874 False 1339.0 1339 94.4130 1339 2208 1 chr2A.!!$F2 869
7 TraesCS7A01G290300 chr2A 733374452 733375337 885 True 1327.0 1327 93.9190 1338 2211 1 chr2A.!!$R2 873
8 TraesCS7A01G290300 chr4A 595035464 595036336 872 False 1334.0 1334 94.3120 1338 2208 1 chr4A.!!$F2 870
9 TraesCS7A01G290300 chr4A 12795848 12796725 877 True 1330.0 1330 94.1910 1344 2211 1 chr4A.!!$R1 867
10 TraesCS7A01G290300 chr4A 84312901 84313775 874 False 1325.0 1325 94.0910 1338 2208 1 chr4A.!!$F1 870
11 TraesCS7A01G290300 chr3B 101914787 101916124 1337 True 1016.5 1262 95.0720 6 1276 2 chr3B.!!$R3 1270
12 TraesCS7A01G290300 chr3B 201531451 201531972 521 True 771.0 771 93.6780 6 516 1 chr3B.!!$R2 510
13 TraesCS7A01G290300 chr3B 6002149 6002669 520 True 765.0 765 93.4870 6 516 1 chr3B.!!$R1 510
14 TraesCS7A01G290300 chr3A 66013251 66014011 760 False 1256.0 1256 96.4520 513 1273 1 chr3A.!!$F1 760
15 TraesCS7A01G290300 chr3A 164859691 164860451 760 False 1251.0 1251 96.3210 513 1273 1 chr3A.!!$F2 760
16 TraesCS7A01G290300 chr6D 168261282 168262614 1332 True 1012.0 1253 95.0605 6 1271 2 chr6D.!!$R2 1265
17 TraesCS7A01G290300 chr6D 135459499 135460023 524 False 754.0 754 92.9520 3 516 1 chr6D.!!$F1 513
18 TraesCS7A01G290300 chr6D 458919739 458920260 521 True 749.0 749 92.9120 6 516 1 chr6D.!!$R1 510
19 TraesCS7A01G290300 chr5D 446177905 446178668 763 True 1251.0 1251 96.2040 513 1276 1 chr5D.!!$R3 763
20 TraesCS7A01G290300 chr5D 503222643 503223164 521 True 765.0 765 93.4870 6 516 1 chr5D.!!$R4 510
21 TraesCS7A01G290300 chr5D 503273924 503274448 524 False 760.0 760 93.1430 3 516 1 chr5D.!!$F1 513
22 TraesCS7A01G290300 chr5D 6193363 6193889 526 True 758.0 758 92.9920 1 516 1 chr5D.!!$R1 515
23 TraesCS7A01G290300 chr1B 633749524 633750284 760 False 1251.0 1251 96.3210 513 1273 1 chr1B.!!$F2 760
24 TraesCS7A01G290300 chr1B 619186713 619187239 526 True 769.0 769 93.3590 1 516 1 chr1B.!!$R2 515
25 TraesCS7A01G290300 chr1A 554515859 554516622 763 True 1251.0 1251 96.2040 513 1276 1 chr1A.!!$R1 763
26 TraesCS7A01G290300 chr1D 254393742 254394502 760 False 1245.0 1245 96.1890 513 1273 1 chr1D.!!$F1 760
27 TraesCS7A01G290300 chr2B 234532542 234533068 526 True 769.0 769 93.3590 1 516 1 chr2B.!!$R1 515
28 TraesCS7A01G290300 chrUn 379971431 379971954 523 False 765.0 765 93.3330 3 516 1 chrUn.!!$F1 513
29 TraesCS7A01G290300 chr7D 231578115 231578639 524 False 765.0 765 93.3330 3 516 1 chr7D.!!$F1 513
30 TraesCS7A01G290300 chr4D 177444490 177445016 526 False 763.0 763 93.1690 1 516 1 chr4D.!!$F1 515
31 TraesCS7A01G290300 chr4D 207365319 207365843 524 False 693.0 693 90.8570 3 516 1 chr4D.!!$F2 513

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
435 449 0.978146 GGCCTTCCTCCACTAGCAGA 60.978 60.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1304 1430 0.188342 ACTTGGAGGCCCAACAACAT 59.812 50.0 0.0 0.0 46.94 2.71 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
49 50 3.993535 CTGCTTCAGCTTCACCCC 58.006 61.111 0.00 0.00 42.66 4.95
115 126 9.213777 TCTTCTGGAAATCCTAGCTATTCTTAA 57.786 33.333 0.00 0.00 36.82 1.85
206 217 8.046708 TCCATAGGGAAAATCGGATATGTAATG 58.953 37.037 0.00 0.00 41.32 1.90
298 309 7.257790 TCTCCATGATTCTAGGAACTTTTGA 57.742 36.000 0.00 0.00 41.75 2.69
307 318 5.713025 TCTAGGAACTTTTGATTGCATTGC 58.287 37.500 0.46 0.46 41.75 3.56
322 333 4.919206 TGCATTGCATTATTTGGTCTACG 58.081 39.130 7.38 0.00 31.71 3.51
325 336 5.455525 GCATTGCATTATTTGGTCTACGTTC 59.544 40.000 3.15 0.00 0.00 3.95
349 361 5.050769 CCGGAACTGATAACATTCGAGATTG 60.051 44.000 0.00 0.00 0.00 2.67
362 374 6.648310 ACATTCGAGATTGTGCAGGATTATAG 59.352 38.462 0.00 0.00 0.00 1.31
376 389 7.500227 TGCAGGATTATAGACAAAAGATCCTTG 59.500 37.037 0.15 4.06 40.94 3.61
380 394 9.178758 GGATTATAGACAAAAGATCCTTGTTGT 57.821 33.333 11.08 6.46 37.14 3.32
435 449 0.978146 GGCCTTCCTCCACTAGCAGA 60.978 60.000 0.00 0.00 0.00 4.26
495 509 3.366052 AGCGGGCCTATATTTATTGGG 57.634 47.619 0.84 0.00 0.00 4.12
580 706 6.437162 TCCCCTTTAAGATCAAACAATTCCAG 59.563 38.462 0.00 0.00 0.00 3.86
582 708 6.295236 CCCTTTAAGATCAAACAATTCCAGCA 60.295 38.462 0.00 0.00 0.00 4.41
595 721 7.414222 ACAATTCCAGCAAATTGAGTATGAT 57.586 32.000 19.72 0.70 45.40 2.45
611 737 7.154656 TGAGTATGATTGTATGTGTGATAGCC 58.845 38.462 0.00 0.00 0.00 3.93
623 749 5.001874 TGTGTGATAGCCTCTACTATACCG 58.998 45.833 0.00 0.00 32.95 4.02
677 803 4.589374 GCTCAGGATACCCTCTTTTAGCTA 59.411 45.833 0.00 0.00 42.02 3.32
714 840 9.716556 TTCTTAGTTCAAGATCCCTCTTACTAT 57.283 33.333 0.00 0.00 42.88 2.12
813 939 5.797934 GGAATCGACTCGATCATCAGATTAC 59.202 44.000 14.25 0.00 46.30 1.89
829 955 9.334947 CATCAGATTACAAGTTCATTCCATACT 57.665 33.333 0.00 0.00 0.00 2.12
864 990 6.073548 CGTGGACATTCTTATTATGAGAAGGC 60.074 42.308 10.53 4.87 38.19 4.35
865 991 6.767902 GTGGACATTCTTATTATGAGAAGGCA 59.232 38.462 10.53 0.83 38.19 4.75
866 992 6.767902 TGGACATTCTTATTATGAGAAGGCAC 59.232 38.462 10.53 5.49 38.19 5.01
1015 1141 1.410083 GCCATATGCACCTCTTTGGGA 60.410 52.381 0.00 0.00 41.11 4.37
1102 1228 8.405418 TGATACATATAAGGTGTCCTACTGAC 57.595 38.462 3.37 0.00 44.72 3.51
1141 1267 0.900421 TGATGTCTGACTCAGGCCTG 59.100 55.000 27.87 27.87 34.88 4.85
1153 1279 0.752658 CAGGCCTGTATGACCGATCA 59.247 55.000 25.53 0.00 39.83 2.92
1157 1283 2.417719 GCCTGTATGACCGATCAATCC 58.582 52.381 0.00 0.00 38.69 3.01
1273 1399 3.007506 TGATGGTGAAATGGTAGACACGT 59.992 43.478 0.00 0.00 34.59 4.49
1276 1402 3.007506 TGGTGAAATGGTAGACACGTGAT 59.992 43.478 25.01 12.89 34.59 3.06
1277 1403 3.370978 GGTGAAATGGTAGACACGTGATG 59.629 47.826 25.01 0.00 34.59 3.07
1289 1415 4.841443 ACACGTGATGTCTACTACACAA 57.159 40.909 25.01 0.00 42.09 3.33
1290 1416 4.543692 ACACGTGATGTCTACTACACAAC 58.456 43.478 25.01 0.00 42.09 3.32
1291 1417 3.918591 CACGTGATGTCTACTACACAACC 59.081 47.826 10.90 0.00 42.09 3.77
1292 1418 3.825014 ACGTGATGTCTACTACACAACCT 59.175 43.478 0.00 0.00 42.09 3.50
1293 1419 4.280174 ACGTGATGTCTACTACACAACCTT 59.720 41.667 0.00 0.00 42.09 3.50
1294 1420 4.857588 CGTGATGTCTACTACACAACCTTC 59.142 45.833 0.00 0.00 42.09 3.46
1295 1421 5.335740 CGTGATGTCTACTACACAACCTTCT 60.336 44.000 0.00 0.00 42.09 2.85
1296 1422 6.456501 GTGATGTCTACTACACAACCTTCTT 58.543 40.000 0.00 0.00 42.09 2.52
1297 1423 6.586844 GTGATGTCTACTACACAACCTTCTTC 59.413 42.308 0.00 0.00 42.09 2.87
1298 1424 6.493802 TGATGTCTACTACACAACCTTCTTCT 59.506 38.462 0.00 0.00 42.09 2.85
1299 1425 6.726490 TGTCTACTACACAACCTTCTTCTT 57.274 37.500 0.00 0.00 31.43 2.52
1300 1426 6.513180 TGTCTACTACACAACCTTCTTCTTG 58.487 40.000 0.00 0.00 31.43 3.02
1301 1427 6.097839 TGTCTACTACACAACCTTCTTCTTGT 59.902 38.462 0.00 0.00 31.43 3.16
1302 1428 7.286087 TGTCTACTACACAACCTTCTTCTTGTA 59.714 37.037 0.00 0.00 31.43 2.41
1303 1429 7.808856 GTCTACTACACAACCTTCTTCTTGTAG 59.191 40.741 5.27 5.27 41.37 2.74
1304 1430 6.726490 ACTACACAACCTTCTTCTTGTAGA 57.274 37.500 12.31 0.00 39.06 2.59
1305 1431 7.304497 ACTACACAACCTTCTTCTTGTAGAT 57.696 36.000 12.31 0.00 39.06 1.98
1306 1432 7.155328 ACTACACAACCTTCTTCTTGTAGATG 58.845 38.462 12.31 0.00 39.06 2.90
1307 1433 5.930135 ACACAACCTTCTTCTTGTAGATGT 58.070 37.500 0.00 0.00 0.00 3.06
1308 1434 6.357367 ACACAACCTTCTTCTTGTAGATGTT 58.643 36.000 0.00 0.00 0.00 2.71
1309 1435 6.260936 ACACAACCTTCTTCTTGTAGATGTTG 59.739 38.462 13.30 13.30 40.02 3.33
1310 1436 6.260936 CACAACCTTCTTCTTGTAGATGTTGT 59.739 38.462 14.10 14.10 43.62 3.32
1311 1437 6.828785 ACAACCTTCTTCTTGTAGATGTTGTT 59.171 34.615 14.10 0.00 42.06 2.83
1312 1438 6.867662 ACCTTCTTCTTGTAGATGTTGTTG 57.132 37.500 0.00 0.00 0.00 3.33
1313 1439 5.765182 ACCTTCTTCTTGTAGATGTTGTTGG 59.235 40.000 0.00 0.00 0.00 3.77
1314 1440 5.182001 CCTTCTTCTTGTAGATGTTGTTGGG 59.818 44.000 0.00 0.00 0.00 4.12
1315 1441 4.072131 TCTTCTTGTAGATGTTGTTGGGC 58.928 43.478 0.00 0.00 0.00 5.36
1316 1442 2.790433 TCTTGTAGATGTTGTTGGGCC 58.210 47.619 0.00 0.00 0.00 5.80
1317 1443 2.375174 TCTTGTAGATGTTGTTGGGCCT 59.625 45.455 4.53 0.00 0.00 5.19
1318 1444 2.489938 TGTAGATGTTGTTGGGCCTC 57.510 50.000 4.53 0.00 0.00 4.70
1319 1445 1.004277 TGTAGATGTTGTTGGGCCTCC 59.996 52.381 4.53 0.00 0.00 4.30
1320 1446 1.004277 GTAGATGTTGTTGGGCCTCCA 59.996 52.381 4.53 0.00 42.25 3.86
1328 1454 2.853542 TGGGCCTCCAAGTGCAGA 60.854 61.111 4.53 0.00 40.73 4.26
1329 1455 2.045536 GGGCCTCCAAGTGCAGAG 60.046 66.667 0.84 0.00 0.00 3.35
1333 1459 3.733709 CCTCCAAGTGCAGAGGTTT 57.266 52.632 10.81 0.00 44.01 3.27
1334 1460 1.242076 CCTCCAAGTGCAGAGGTTTG 58.758 55.000 10.81 0.88 44.01 2.93
1335 1461 1.477558 CCTCCAAGTGCAGAGGTTTGT 60.478 52.381 10.81 0.00 44.01 2.83
1336 1462 2.224523 CCTCCAAGTGCAGAGGTTTGTA 60.225 50.000 10.81 0.00 44.01 2.41
1337 1463 3.070018 CTCCAAGTGCAGAGGTTTGTAG 58.930 50.000 0.00 0.00 0.00 2.74
1338 1464 2.154462 CCAAGTGCAGAGGTTTGTAGG 58.846 52.381 0.00 0.00 0.00 3.18
1339 1465 2.224523 CCAAGTGCAGAGGTTTGTAGGA 60.225 50.000 0.00 0.00 0.00 2.94
1340 1466 2.808543 CAAGTGCAGAGGTTTGTAGGAC 59.191 50.000 0.00 0.00 0.00 3.85
1341 1467 2.047061 AGTGCAGAGGTTTGTAGGACA 58.953 47.619 0.00 0.00 0.00 4.02
1342 1468 2.037772 AGTGCAGAGGTTTGTAGGACAG 59.962 50.000 0.00 0.00 0.00 3.51
1433 1560 5.208890 ACTAGGTGTATCAACAGGCTATGA 58.791 41.667 4.83 4.83 35.91 2.15
1548 1675 1.003580 ACTAGTGGGTGTGCATCCAAG 59.996 52.381 5.65 3.86 44.47 3.61
1561 1688 1.610038 CATCCAAGTTGCTTGCTCACA 59.390 47.619 0.00 0.00 39.85 3.58
1606 1734 5.074929 AGGCCCATCATTGGAATATACAAGA 59.925 40.000 0.00 0.00 46.92 3.02
1955 2109 7.121974 ACAACTCAAGAATTACAACTCGATG 57.878 36.000 0.00 0.00 0.00 3.84
1960 2114 7.276658 ACTCAAGAATTACAACTCGATGCTTAG 59.723 37.037 0.00 0.00 0.00 2.18
1968 2124 4.691216 ACAACTCGATGCTTAGGAAAAGAC 59.309 41.667 0.00 0.00 0.00 3.01
2082 2238 5.106869 GCCACAAATACGATGTCAACTACAA 60.107 40.000 0.00 0.00 42.70 2.41
2117 2273 5.759763 AGCAATATGACAATGATGAAGCGTA 59.240 36.000 0.00 0.00 0.00 4.42
2168 2324 8.362639 GTTGCATGGAAATATATCTTGGAATGT 58.637 33.333 0.00 0.00 0.00 2.71
2208 2364 2.238898 AGGTAGGTATGGTGGCTGTTTC 59.761 50.000 0.00 0.00 0.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.822026 AGCAGCTACTTTCGAAGTAACAT 58.178 39.130 0.00 0.00 42.99 2.71
46 47 3.402628 AATATCGAGAATTCGTGGGGG 57.597 47.619 0.00 0.00 46.72 5.40
49 50 8.520835 TGATTAGAAATATCGAGAATTCGTGG 57.479 34.615 2.39 0.00 46.72 4.94
70 81 5.416952 AGAAGAAGATGCCATTCGTTTGATT 59.583 36.000 0.00 0.00 0.00 2.57
115 126 4.614967 AGGAGATTCCCCAAAATCATGT 57.385 40.909 0.00 0.00 37.19 3.21
206 217 7.630242 TGAGTCTCCAACAATTATTCCAATC 57.370 36.000 0.00 0.00 0.00 2.67
283 294 6.158598 GCAATGCAATCAAAAGTTCCTAGAA 58.841 36.000 0.00 0.00 0.00 2.10
298 309 5.978919 CGTAGACCAAATAATGCAATGCAAT 59.021 36.000 13.45 6.50 43.62 3.56
322 333 4.178540 TCGAATGTTATCAGTTCCGGAAC 58.821 43.478 35.28 35.28 41.45 3.62
325 336 4.041740 TCTCGAATGTTATCAGTTCCGG 57.958 45.455 0.00 0.00 0.00 5.14
349 361 6.995091 AGGATCTTTTGTCTATAATCCTGCAC 59.005 38.462 1.06 0.00 41.05 4.57
362 374 5.994668 AGAGAGACAACAAGGATCTTTTGTC 59.005 40.000 12.26 12.26 45.42 3.18
376 389 5.128008 ACATAGGGCTAAAGAGAGAGACAAC 59.872 44.000 0.00 0.00 0.00 3.32
380 394 5.133660 AGAGACATAGGGCTAAAGAGAGAGA 59.866 44.000 0.00 0.00 0.00 3.10
490 504 5.396436 CGTAAGGAGTCCTATTGAACCCAAT 60.396 44.000 13.43 0.00 44.56 3.16
495 509 5.579904 GGTTTCGTAAGGAGTCCTATTGAAC 59.420 44.000 13.43 13.20 31.13 3.18
580 706 8.183536 TCACACATACAATCATACTCAATTTGC 58.816 33.333 0.00 0.00 0.00 3.68
595 721 9.011095 GTATAGTAGAGGCTATCACACATACAA 57.989 37.037 0.00 0.00 34.00 2.41
611 737 8.521170 TCATTGATATTCCCGGTATAGTAGAG 57.479 38.462 0.00 0.00 0.00 2.43
623 749 5.397360 AGAATGGGGTTCATTGATATTCCC 58.603 41.667 0.00 0.00 45.36 3.97
763 889 9.725019 CATGATTATAAGTTCATAACCCTAGCA 57.275 33.333 2.05 0.00 31.50 3.49
829 955 0.762418 AATGTCCACGGTCTGGTTCA 59.238 50.000 0.00 0.00 41.52 3.18
843 969 6.767902 TGGTGCCTTCTCATAATAAGAATGTC 59.232 38.462 0.00 0.00 32.56 3.06
864 990 2.620251 TTCCATAGGCTCGAATGGTG 57.380 50.000 13.19 0.00 42.77 4.17
865 991 3.864789 ATTTCCATAGGCTCGAATGGT 57.135 42.857 13.19 0.00 42.77 3.55
866 992 4.256920 CCTATTTCCATAGGCTCGAATGG 58.743 47.826 8.26 8.26 44.71 3.16
946 1072 5.997129 TGTCAAAAGCAGATCTGATTACACA 59.003 36.000 25.44 22.28 38.36 3.72
958 1084 9.935241 GAATAGGATAGATATGTCAAAAGCAGA 57.065 33.333 0.00 0.00 0.00 4.26
995 1121 1.035139 CCCAAAGAGGTGCATATGGC 58.965 55.000 4.56 0.00 37.56 4.40
1099 1225 5.565592 AATAGCTTCGATTTGCATTGTCA 57.434 34.783 0.00 0.00 0.00 3.58
1102 1228 6.474427 ACATCAAATAGCTTCGATTTGCATTG 59.526 34.615 13.39 12.52 41.86 2.82
1141 1267 6.369065 GGAGTATTTGGATTGATCGGTCATAC 59.631 42.308 0.00 0.00 33.56 2.39
1153 1279 5.501156 GTGGAGTCTTGGAGTATTTGGATT 58.499 41.667 0.00 0.00 0.00 3.01
1157 1283 4.559862 AGGTGGAGTCTTGGAGTATTTG 57.440 45.455 0.00 0.00 0.00 2.32
1273 1399 6.493802 AGAAGAAGGTTGTGTAGTAGACATCA 59.506 38.462 0.29 0.00 41.14 3.07
1276 1402 6.097839 ACAAGAAGAAGGTTGTGTAGTAGACA 59.902 38.462 0.00 0.00 35.55 3.41
1277 1403 6.514063 ACAAGAAGAAGGTTGTGTAGTAGAC 58.486 40.000 0.00 0.00 35.55 2.59
1278 1404 6.726490 ACAAGAAGAAGGTTGTGTAGTAGA 57.274 37.500 0.00 0.00 35.55 2.59
1279 1405 7.883217 TCTACAAGAAGAAGGTTGTGTAGTAG 58.117 38.462 8.12 0.00 39.49 2.57
1280 1406 7.828508 TCTACAAGAAGAAGGTTGTGTAGTA 57.171 36.000 8.12 0.00 39.49 1.82
1281 1407 6.726490 TCTACAAGAAGAAGGTTGTGTAGT 57.274 37.500 8.12 0.00 39.49 2.73
1282 1408 7.155328 ACATCTACAAGAAGAAGGTTGTGTAG 58.845 38.462 0.00 0.00 39.72 2.74
1283 1409 7.062749 ACATCTACAAGAAGAAGGTTGTGTA 57.937 36.000 0.00 0.00 37.46 2.90
1284 1410 5.930135 ACATCTACAAGAAGAAGGTTGTGT 58.070 37.500 0.00 0.00 37.46 3.72
1285 1411 6.260936 ACAACATCTACAAGAAGAAGGTTGTG 59.739 38.462 18.48 4.23 45.86 3.33
1286 1412 6.357367 ACAACATCTACAAGAAGAAGGTTGT 58.643 36.000 15.66 15.66 44.51 3.32
1287 1413 6.867662 ACAACATCTACAAGAAGAAGGTTG 57.132 37.500 14.80 14.80 43.41 3.77
1288 1414 6.263168 CCAACAACATCTACAAGAAGAAGGTT 59.737 38.462 0.00 0.00 31.23 3.50
1289 1415 5.765182 CCAACAACATCTACAAGAAGAAGGT 59.235 40.000 0.00 0.00 0.00 3.50
1290 1416 5.182001 CCCAACAACATCTACAAGAAGAAGG 59.818 44.000 0.00 0.00 0.00 3.46
1291 1417 5.335191 GCCCAACAACATCTACAAGAAGAAG 60.335 44.000 0.00 0.00 0.00 2.85
1292 1418 4.518970 GCCCAACAACATCTACAAGAAGAA 59.481 41.667 0.00 0.00 0.00 2.52
1293 1419 4.072131 GCCCAACAACATCTACAAGAAGA 58.928 43.478 0.00 0.00 0.00 2.87
1294 1420 3.191371 GGCCCAACAACATCTACAAGAAG 59.809 47.826 0.00 0.00 0.00 2.85
1295 1421 3.153919 GGCCCAACAACATCTACAAGAA 58.846 45.455 0.00 0.00 0.00 2.52
1296 1422 2.375174 AGGCCCAACAACATCTACAAGA 59.625 45.455 0.00 0.00 0.00 3.02
1297 1423 2.749621 GAGGCCCAACAACATCTACAAG 59.250 50.000 0.00 0.00 0.00 3.16
1298 1424 2.554344 GGAGGCCCAACAACATCTACAA 60.554 50.000 0.00 0.00 0.00 2.41
1299 1425 1.004277 GGAGGCCCAACAACATCTACA 59.996 52.381 0.00 0.00 0.00 2.74
1300 1426 1.004277 TGGAGGCCCAACAACATCTAC 59.996 52.381 0.00 0.00 40.09 2.59
1301 1427 1.367346 TGGAGGCCCAACAACATCTA 58.633 50.000 0.00 0.00 40.09 1.98
1302 1428 0.482446 TTGGAGGCCCAACAACATCT 59.518 50.000 0.00 0.00 46.94 2.90
1303 1429 0.890683 CTTGGAGGCCCAACAACATC 59.109 55.000 0.00 0.00 46.94 3.06
1304 1430 0.188342 ACTTGGAGGCCCAACAACAT 59.812 50.000 0.00 0.00 46.94 2.71
1305 1431 0.754957 CACTTGGAGGCCCAACAACA 60.755 55.000 0.00 0.00 46.94 3.33
1306 1432 2.041153 CACTTGGAGGCCCAACAAC 58.959 57.895 0.00 0.00 46.94 3.32
1307 1433 1.832167 GCACTTGGAGGCCCAACAA 60.832 57.895 0.00 1.03 46.94 2.83
1308 1434 2.203480 GCACTTGGAGGCCCAACA 60.203 61.111 0.00 0.00 46.94 3.33
1309 1435 2.203480 TGCACTTGGAGGCCCAAC 60.203 61.111 0.00 0.00 46.94 3.77
1311 1437 2.853542 TCTGCACTTGGAGGCCCA 60.854 61.111 0.00 0.00 41.64 5.36
1312 1438 2.045536 CTCTGCACTTGGAGGCCC 60.046 66.667 0.00 0.00 34.00 5.80
1313 1439 2.045536 CCTCTGCACTTGGAGGCC 60.046 66.667 6.78 0.00 41.92 5.19
1316 1442 1.972872 ACAAACCTCTGCACTTGGAG 58.027 50.000 2.33 0.00 34.56 3.86
1317 1443 2.224523 CCTACAAACCTCTGCACTTGGA 60.225 50.000 2.33 0.00 0.00 3.53
1318 1444 2.154462 CCTACAAACCTCTGCACTTGG 58.846 52.381 0.00 0.00 0.00 3.61
1319 1445 2.808543 GTCCTACAAACCTCTGCACTTG 59.191 50.000 0.00 0.00 0.00 3.16
1320 1446 2.438021 TGTCCTACAAACCTCTGCACTT 59.562 45.455 0.00 0.00 0.00 3.16
1321 1447 2.037772 CTGTCCTACAAACCTCTGCACT 59.962 50.000 0.00 0.00 0.00 4.40
1322 1448 2.224305 ACTGTCCTACAAACCTCTGCAC 60.224 50.000 0.00 0.00 0.00 4.57
1323 1449 2.047061 ACTGTCCTACAAACCTCTGCA 58.953 47.619 0.00 0.00 0.00 4.41
1324 1450 2.841442 ACTGTCCTACAAACCTCTGC 57.159 50.000 0.00 0.00 0.00 4.26
1325 1451 3.258372 TGCTACTGTCCTACAAACCTCTG 59.742 47.826 0.00 0.00 0.00 3.35
1326 1452 3.258622 GTGCTACTGTCCTACAAACCTCT 59.741 47.826 0.00 0.00 0.00 3.69
1327 1453 3.258622 AGTGCTACTGTCCTACAAACCTC 59.741 47.826 0.00 0.00 0.00 3.85
1328 1454 3.240302 AGTGCTACTGTCCTACAAACCT 58.760 45.455 0.00 0.00 0.00 3.50
1329 1455 3.679824 AGTGCTACTGTCCTACAAACC 57.320 47.619 0.00 0.00 0.00 3.27
1330 1456 6.096564 ACCTATAGTGCTACTGTCCTACAAAC 59.903 42.308 0.00 0.00 0.00 2.93
1331 1457 6.096423 CACCTATAGTGCTACTGTCCTACAAA 59.904 42.308 0.00 0.00 40.28 2.83
1332 1458 5.593095 CACCTATAGTGCTACTGTCCTACAA 59.407 44.000 0.00 0.00 40.28 2.41
1333 1459 5.131067 CACCTATAGTGCTACTGTCCTACA 58.869 45.833 0.00 0.00 40.28 2.74
1334 1460 4.519730 CCACCTATAGTGCTACTGTCCTAC 59.480 50.000 0.00 0.00 45.83 3.18
1335 1461 4.414514 TCCACCTATAGTGCTACTGTCCTA 59.585 45.833 0.00 0.00 45.83 2.94
1336 1462 3.204606 TCCACCTATAGTGCTACTGTCCT 59.795 47.826 0.00 0.00 45.83 3.85
1337 1463 3.563223 TCCACCTATAGTGCTACTGTCC 58.437 50.000 0.00 0.00 45.83 4.02
1338 1464 5.793030 ATTCCACCTATAGTGCTACTGTC 57.207 43.478 0.00 0.00 45.83 3.51
1339 1465 6.611785 TCTATTCCACCTATAGTGCTACTGT 58.388 40.000 0.00 0.00 45.83 3.55
1340 1466 7.526142 TTCTATTCCACCTATAGTGCTACTG 57.474 40.000 0.00 0.00 45.83 2.74
1341 1467 7.179338 CCATTCTATTCCACCTATAGTGCTACT 59.821 40.741 0.00 0.00 45.83 2.57
1342 1468 7.038941 ACCATTCTATTCCACCTATAGTGCTAC 60.039 40.741 0.00 0.00 45.83 3.58
1433 1560 8.114102 ACATTGATATCTATTGATGGGCATCTT 58.886 33.333 3.98 0.00 38.60 2.40
1526 1653 2.261729 TGGATGCACACCCACTAGTTA 58.738 47.619 8.94 0.00 0.00 2.24
1548 1675 1.678101 AGGTCTTTGTGAGCAAGCAAC 59.322 47.619 0.00 0.00 44.98 4.17
1561 1688 2.919602 TCCTCAAATGCCCTAGGTCTTT 59.080 45.455 8.29 0.00 0.00 2.52
1606 1734 9.178758 GTGGGAATCTTTCATTATAGAACTTGT 57.821 33.333 0.00 0.00 0.00 3.16
1955 2109 9.202273 CATATAGAGTCATGTCTTTTCCTAAGC 57.798 37.037 0.00 0.00 0.00 3.09
2082 2238 6.459670 TTGTCATATTGCTTTGCATGATCT 57.540 33.333 0.00 0.00 38.76 2.75
2117 2273 5.947663 TCCCACCGTTCCATTTATTATGAT 58.052 37.500 0.00 0.00 0.00 2.45


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

AutoCloner maintained by Alex Coulton.