Multiple sequence alignment - TraesCS6A01G191600

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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 TraesCS6A01G191600 chr6A 100.000 2470 0 0 1 2470 259362602 259360133 0.000000e+00 4562
1 TraesCS6A01G191600 chr6A 87.099 1341 135 29 1 1328 266018716 266020031 0.000000e+00 1483
2 TraesCS6A01G191600 chr6A 86.940 1340 140 28 1 1328 266026594 266027910 0.000000e+00 1472
3 TraesCS6A01G191600 chr6A 86.450 1262 137 28 1 1239 430717054 430715804 0.000000e+00 1352
4 TraesCS6A01G191600 chr6A 93.264 772 47 5 1408 2177 266019997 266020765 0.000000e+00 1133
5 TraesCS6A01G191600 chr6A 93.659 757 44 4 1408 2162 266027876 266028630 0.000000e+00 1129
6 TraesCS6A01G191600 chr4A 90.887 2480 186 20 1 2470 205924357 205926806 0.000000e+00 3291
7 TraesCS6A01G191600 chr4A 90.444 2480 202 19 1 2470 205932283 205934737 0.000000e+00 3234
8 TraesCS6A01G191600 chr4A 86.726 1341 147 23 1 1328 197215283 197213961 0.000000e+00 1461
9 TraesCS6A01G191600 chr4A 93.653 772 44 5 1408 2177 197213995 197213227 0.000000e+00 1149
10 TraesCS6A01G191600 chr4A 86.065 775 76 26 1 760 250105401 250104644 0.000000e+00 804
11 TraesCS6A01G191600 chr5A 87.313 1340 141 23 1 1328 176943784 176942462 0.000000e+00 1506
12 TraesCS6A01G191600 chr5A 93.032 775 49 5 1408 2180 176942496 176941725 0.000000e+00 1127
13 TraesCS6A01G191600 chr5A 86.430 759 79 21 1 747 141215556 141214810 0.000000e+00 809
14 TraesCS6A01G191600 chr5A 86.394 757 82 18 1 747 207765837 207766582 0.000000e+00 808
15 TraesCS6A01G191600 chr5A 86.280 758 82 19 1 747 207788004 207788750 0.000000e+00 804
16 TraesCS6A01G191600 chr3A 87.388 1340 133 30 4 1328 347832926 347831608 0.000000e+00 1506
17 TraesCS6A01G191600 chr3A 92.793 777 49 6 1408 2180 347831642 347830869 0.000000e+00 1118
18 TraesCS6A01G191600 chr3A 86.086 769 89 15 1 760 287440244 287439485 0.000000e+00 811
19 TraesCS6A01G191600 chr3A 85.899 773 83 24 1 761 381936648 381937406 0.000000e+00 800
20 TraesCS6A01G191600 chr7A 93.264 772 47 5 1408 2177 420702666 420703434 0.000000e+00 1133
21 TraesCS6A01G191600 chr7A 91.433 677 49 7 652 1328 420702033 420702700 0.000000e+00 920
22 TraesCS6A01G191600 chr7A 87.731 758 72 18 1 748 515668326 515669072 0.000000e+00 865
23 TraesCS6A01G191600 chr7A 91.150 452 39 1 2016 2467 116728665 116729115 1.620000e-171 612
24 TraesCS6A01G191600 chr7A 90.930 441 32 6 1248 1683 324967678 324968115 9.840000e-164 586
25 TraesCS6A01G191600 chr7A 89.421 397 30 9 1604 1999 324976858 324977243 7.940000e-135 490
26 TraesCS6A01G191600 chr2A 86.202 761 85 16 1 750 314293963 314294714 0.000000e+00 806
27 TraesCS6A01G191600 chr2A 90.769 455 40 2 2016 2470 365656960 365657412 7.550000e-170 606
28 TraesCS6A01G191600 chr2A 90.549 455 42 1 2016 2470 69182996 69182543 3.510000e-168 601
29 TraesCS6A01G191600 chr1A 91.209 455 37 3 2016 2469 217151403 217151855 1.260000e-172 616
30 TraesCS6A01G191600 chr1A 90.749 454 40 2 2017 2470 170866220 170865769 2.720000e-169 604
31 TraesCS6A01G191600 chr1A 90.150 467 41 5 2004 2470 170709910 170710371 9.770000e-169 603
32 TraesCS6A01G191600 chr1A 90.351 456 42 2 2016 2470 183678820 183678366 4.550000e-167 597


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 TraesCS6A01G191600 chr6A 259360133 259362602 2469 True 4562.0 4562 100.0000 1 2470 1 chr6A.!!$R1 2469
1 TraesCS6A01G191600 chr6A 430715804 430717054 1250 True 1352.0 1352 86.4500 1 1239 1 chr6A.!!$R2 1238
2 TraesCS6A01G191600 chr6A 266018716 266020765 2049 False 1308.0 1483 90.1815 1 2177 2 chr6A.!!$F1 2176
3 TraesCS6A01G191600 chr6A 266026594 266028630 2036 False 1300.5 1472 90.2995 1 2162 2 chr6A.!!$F2 2161
4 TraesCS6A01G191600 chr4A 205924357 205926806 2449 False 3291.0 3291 90.8870 1 2470 1 chr4A.!!$F1 2469
5 TraesCS6A01G191600 chr4A 205932283 205934737 2454 False 3234.0 3234 90.4440 1 2470 1 chr4A.!!$F2 2469
6 TraesCS6A01G191600 chr4A 197213227 197215283 2056 True 1305.0 1461 90.1895 1 2177 2 chr4A.!!$R2 2176
7 TraesCS6A01G191600 chr4A 250104644 250105401 757 True 804.0 804 86.0650 1 760 1 chr4A.!!$R1 759
8 TraesCS6A01G191600 chr5A 176941725 176943784 2059 True 1316.5 1506 90.1725 1 2180 2 chr5A.!!$R2 2179
9 TraesCS6A01G191600 chr5A 141214810 141215556 746 True 809.0 809 86.4300 1 747 1 chr5A.!!$R1 746
10 TraesCS6A01G191600 chr5A 207765837 207766582 745 False 808.0 808 86.3940 1 747 1 chr5A.!!$F1 746
11 TraesCS6A01G191600 chr5A 207788004 207788750 746 False 804.0 804 86.2800 1 747 1 chr5A.!!$F2 746
12 TraesCS6A01G191600 chr3A 347830869 347832926 2057 True 1312.0 1506 90.0905 4 2180 2 chr3A.!!$R2 2176
13 TraesCS6A01G191600 chr3A 287439485 287440244 759 True 811.0 811 86.0860 1 760 1 chr3A.!!$R1 759
14 TraesCS6A01G191600 chr3A 381936648 381937406 758 False 800.0 800 85.8990 1 761 1 chr3A.!!$F1 760
15 TraesCS6A01G191600 chr7A 420702033 420703434 1401 False 1026.5 1133 92.3485 652 2177 2 chr7A.!!$F5 1525
16 TraesCS6A01G191600 chr7A 515668326 515669072 746 False 865.0 865 87.7310 1 748 1 chr7A.!!$F4 747
17 TraesCS6A01G191600 chr2A 314293963 314294714 751 False 806.0 806 86.2020 1 750 1 chr2A.!!$F1 749

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
940 985 1.206371 AGCGACAGGTAAAATAGCGGT 59.794 47.619 0.0 0.0 37.3 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1751 1909 0.119155 TGATCCCCTTGTCCACCTCT 59.881 55.0 0.0 0.0 0.0 3.69 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
116 120 9.334693 GCAACAGAGTTACATATTGAAGAAAAG 57.665 33.333 0.00 0.00 0.00 2.27
127 133 7.448161 ACATATTGAAGAAAAGACCACATGACA 59.552 33.333 0.00 0.00 0.00 3.58
213 223 7.029563 GGTGAAGCAAATGAAAACTACCTATG 58.970 38.462 0.00 0.00 0.00 2.23
275 288 2.503765 TCCGGAAACTCCTCATATGCAA 59.496 45.455 0.00 0.00 33.30 4.08
277 290 3.885297 CCGGAAACTCCTCATATGCAAAT 59.115 43.478 0.00 0.00 33.30 2.32
281 294 7.390440 CCGGAAACTCCTCATATGCAAATTATA 59.610 37.037 0.00 0.00 33.30 0.98
295 310 8.588290 ATGCAAATTATAAGGTTTGGTACTGA 57.412 30.769 11.61 0.00 36.19 3.41
471 491 8.443953 AGCAAAATTTAACCAAACAGCATTTA 57.556 26.923 0.00 0.00 0.00 1.40
772 817 1.330655 GGAGAGGCTTGTGGATCCGA 61.331 60.000 7.39 0.00 0.00 4.55
834 879 2.685017 AGGAGGATGCAGCGGTCA 60.685 61.111 0.00 0.00 0.00 4.02
917 962 4.214971 GCTGCTCATTTCTGAAGAAGAACA 59.785 41.667 0.00 0.00 44.77 3.18
934 979 2.185004 ACAGCAGCGACAGGTAAAAT 57.815 45.000 0.00 0.00 0.00 1.82
940 985 1.206371 AGCGACAGGTAAAATAGCGGT 59.794 47.619 0.00 0.00 37.30 5.68
945 990 4.189231 GACAGGTAAAATAGCGGTGATGT 58.811 43.478 0.00 0.00 34.86 3.06
1005 1050 2.203056 CGGATCCAGGCGATGCAA 60.203 61.111 13.41 0.00 39.20 4.08
1123 1168 1.154205 CGGGAGGCGTGAACATGATC 61.154 60.000 0.00 0.00 0.00 2.92
1124 1169 1.154205 GGGAGGCGTGAACATGATCG 61.154 60.000 0.00 0.00 0.00 3.69
1332 1377 2.493547 GCCACAGGCTTGGATAACC 58.506 57.895 16.65 0.00 46.69 2.85
1333 1378 1.376609 GCCACAGGCTTGGATAACCG 61.377 60.000 16.65 0.00 46.69 4.44
1334 1379 0.748005 CCACAGGCTTGGATAACCGG 60.748 60.000 0.00 0.00 39.24 5.28
1335 1380 0.251916 CACAGGCTTGGATAACCGGA 59.748 55.000 9.46 0.00 39.42 5.14
1336 1381 0.541863 ACAGGCTTGGATAACCGGAG 59.458 55.000 9.46 0.00 39.42 4.63
1337 1382 0.541863 CAGGCTTGGATAACCGGAGT 59.458 55.000 9.46 0.00 39.42 3.85
1338 1383 1.065418 CAGGCTTGGATAACCGGAGTT 60.065 52.381 9.46 0.00 40.15 3.01
1339 1384 1.633945 AGGCTTGGATAACCGGAGTTT 59.366 47.619 9.46 0.00 37.42 2.66
1340 1385 1.743394 GGCTTGGATAACCGGAGTTTG 59.257 52.381 9.46 0.00 37.42 2.93
1341 1386 1.132453 GCTTGGATAACCGGAGTTTGC 59.868 52.381 9.46 0.00 37.42 3.68
1342 1387 1.743394 CTTGGATAACCGGAGTTTGCC 59.257 52.381 9.46 1.81 37.42 4.52
1350 1395 4.699522 GGAGTTTGCCGGCGACCT 62.700 66.667 23.90 19.30 0.00 3.85
1351 1396 3.423154 GAGTTTGCCGGCGACCTG 61.423 66.667 19.93 0.00 0.00 4.00
1352 1397 3.876589 GAGTTTGCCGGCGACCTGA 62.877 63.158 19.93 0.00 0.00 3.86
1353 1398 3.723348 GTTTGCCGGCGACCTGAC 61.723 66.667 23.90 11.48 0.00 3.51
1360 1405 3.103911 GGCGACCTGACGACGTTG 61.104 66.667 0.13 0.00 35.09 4.10
1361 1406 2.050714 GCGACCTGACGACGTTGA 60.051 61.111 10.51 0.00 35.09 3.18
1362 1407 2.362800 GCGACCTGACGACGTTGAC 61.363 63.158 10.51 3.69 35.09 3.18
1363 1408 2.073220 CGACCTGACGACGTTGACG 61.073 63.158 10.51 0.90 46.33 4.35
1364 1409 1.280746 GACCTGACGACGTTGACGA 59.719 57.895 10.51 0.00 43.02 4.20
1365 1410 0.317269 GACCTGACGACGTTGACGAA 60.317 55.000 10.51 0.00 43.02 3.85
1366 1411 0.317603 ACCTGACGACGTTGACGAAG 60.318 55.000 10.51 6.06 43.02 3.79
1367 1412 1.606350 CCTGACGACGTTGACGAAGC 61.606 60.000 10.51 0.00 43.02 3.86
1368 1413 0.933047 CTGACGACGTTGACGAAGCA 60.933 55.000 10.51 0.57 43.02 3.91
1369 1414 0.933047 TGACGACGTTGACGAAGCAG 60.933 55.000 10.51 0.00 43.02 4.24
1370 1415 1.606350 GACGACGTTGACGAAGCAGG 61.606 60.000 10.51 0.00 43.02 4.85
1371 1416 2.372690 CGACGTTGACGAAGCAGGG 61.373 63.158 10.87 0.00 43.02 4.45
1372 1417 2.027625 GACGTTGACGAAGCAGGGG 61.028 63.158 10.87 0.00 43.02 4.79
1373 1418 2.030562 CGTTGACGAAGCAGGGGT 59.969 61.111 0.00 0.00 43.02 4.95
1374 1419 2.027625 CGTTGACGAAGCAGGGGTC 61.028 63.158 0.00 0.00 43.02 4.46
1375 1420 1.371558 GTTGACGAAGCAGGGGTCT 59.628 57.895 0.00 0.00 0.00 3.85
1376 1421 0.951040 GTTGACGAAGCAGGGGTCTG 60.951 60.000 0.00 0.00 43.64 3.51
1377 1422 1.118965 TTGACGAAGCAGGGGTCTGA 61.119 55.000 0.00 0.00 43.49 3.27
1378 1423 1.079750 GACGAAGCAGGGGTCTGAC 60.080 63.158 0.00 0.00 43.49 3.51
1379 1424 2.125912 CGAAGCAGGGGTCTGACG 60.126 66.667 1.07 0.00 43.49 4.35
1380 1425 2.636412 CGAAGCAGGGGTCTGACGA 61.636 63.158 1.07 0.00 43.49 4.20
1381 1426 1.671742 GAAGCAGGGGTCTGACGAA 59.328 57.895 1.07 0.00 43.49 3.85
1382 1427 0.250513 GAAGCAGGGGTCTGACGAAT 59.749 55.000 1.07 0.00 43.49 3.34
1383 1428 0.250513 AAGCAGGGGTCTGACGAATC 59.749 55.000 1.07 0.00 43.49 2.52
1384 1429 1.153349 GCAGGGGTCTGACGAATCC 60.153 63.158 1.07 1.38 43.49 3.01
1385 1430 1.899437 GCAGGGGTCTGACGAATCCA 61.899 60.000 1.07 0.00 43.49 3.41
1386 1431 0.176680 CAGGGGTCTGACGAATCCAG 59.823 60.000 1.07 0.00 43.49 3.86
1387 1432 0.041238 AGGGGTCTGACGAATCCAGA 59.959 55.000 1.07 0.00 38.24 3.86
1388 1433 1.123928 GGGGTCTGACGAATCCAGAT 58.876 55.000 1.07 0.00 41.98 2.90
1389 1434 1.202580 GGGGTCTGACGAATCCAGATG 60.203 57.143 1.07 0.00 41.98 2.90
1390 1435 1.202580 GGGTCTGACGAATCCAGATGG 60.203 57.143 1.07 0.00 41.98 3.51
1391 1436 1.576356 GTCTGACGAATCCAGATGGC 58.424 55.000 0.00 0.00 41.98 4.40
1392 1437 0.103026 TCTGACGAATCCAGATGGCG 59.897 55.000 0.00 0.00 35.89 5.69
1393 1438 0.877649 CTGACGAATCCAGATGGCGG 60.878 60.000 0.00 0.00 33.65 6.13
1394 1439 2.203070 ACGAATCCAGATGGCGGC 60.203 61.111 0.00 0.00 34.44 6.53
1395 1440 2.109799 CGAATCCAGATGGCGGCT 59.890 61.111 11.43 0.00 34.44 5.52
1396 1441 1.958205 CGAATCCAGATGGCGGCTC 60.958 63.158 11.43 5.40 34.44 4.70
1397 1442 1.958205 GAATCCAGATGGCGGCTCG 60.958 63.158 11.43 2.56 34.44 5.03
1414 1459 3.741476 GCAACAAGGGCGGCAGAG 61.741 66.667 12.47 1.27 0.00 3.35
1415 1460 3.058160 CAACAAGGGCGGCAGAGG 61.058 66.667 12.47 0.00 0.00 3.69
1416 1461 3.249189 AACAAGGGCGGCAGAGGA 61.249 61.111 12.47 0.00 0.00 3.71
1417 1462 3.259633 AACAAGGGCGGCAGAGGAG 62.260 63.158 12.47 0.00 0.00 3.69
1418 1463 4.479993 CAAGGGCGGCAGAGGAGG 62.480 72.222 12.47 0.00 0.00 4.30
1424 1469 4.399395 CGGCAGAGGAGGCAAGCA 62.399 66.667 0.00 0.00 0.00 3.91
1425 1470 2.438075 GGCAGAGGAGGCAAGCAG 60.438 66.667 0.00 0.00 0.00 4.24
1426 1471 3.132801 GCAGAGGAGGCAAGCAGC 61.133 66.667 0.00 0.00 44.65 5.25
1435 1480 4.122515 GCAAGCAGCGACGACGTC 62.123 66.667 18.04 18.04 41.98 4.34
1436 1481 2.429236 CAAGCAGCGACGACGTCT 60.429 61.111 24.36 5.16 41.98 4.18
1439 1484 2.402282 AAGCAGCGACGACGTCTTGA 62.402 55.000 24.36 0.00 41.98 3.02
1452 1610 0.388134 GTCTTGAACGCACGAGGCTA 60.388 55.000 0.00 0.00 41.67 3.93
1467 1625 2.888447 GCTAGAGATGGCGGGGCAT 61.888 63.158 7.51 7.51 0.00 4.40
1515 1673 3.423154 CGAGGAAACTGCCGGTGC 61.423 66.667 1.90 0.00 44.43 5.01
1557 1715 0.537371 CTGGCGTTGGGGAAGAACTT 60.537 55.000 0.00 0.00 0.00 2.66
1659 1817 0.770948 AAACGGGAAGGAGGAAGGGT 60.771 55.000 0.00 0.00 0.00 4.34
1751 1909 1.213275 CATGCGTTCATGGCTGCAA 59.787 52.632 0.50 0.00 44.84 4.08
1824 1982 1.379977 CGAGAGGTGGAGGGCTACA 60.380 63.158 0.00 0.00 0.00 2.74
1836 1994 0.322546 GGGCTACAGTTTGGGTGGAG 60.323 60.000 0.00 0.00 0.00 3.86
1847 2005 1.251527 TGGGTGGAGCGAGAGAAGAC 61.252 60.000 0.00 0.00 0.00 3.01
1901 2059 1.981256 AACTGCCGAACAACAAGGAT 58.019 45.000 0.00 0.00 0.00 3.24
2103 2263 6.369065 CGGAGATGTTTTATAGATGTTAGGGC 59.631 42.308 0.00 0.00 0.00 5.19
2116 2276 1.072331 GTTAGGGCATGATCCGGACAT 59.928 52.381 6.12 10.14 0.00 3.06
2156 2316 1.196104 TCGGGTCCGGGACAGATTTT 61.196 55.000 27.32 0.00 40.25 1.82
2162 2322 0.321298 CCGGGACAGATTTTGGACGT 60.321 55.000 0.00 0.00 0.00 4.34
2165 2325 0.165944 GGACAGATTTTGGACGTGCG 59.834 55.000 1.60 0.00 0.00 5.34
2228 2388 0.622136 TGGCGGTGAGAGGTAGACTA 59.378 55.000 0.00 0.00 0.00 2.59
2318 2478 0.169009 AACGACGTTAGACCGGCTAC 59.831 55.000 12.39 0.00 32.29 3.58
2319 2479 0.674895 ACGACGTTAGACCGGCTACT 60.675 55.000 0.00 0.78 32.29 2.57
2321 2481 1.869767 CGACGTTAGACCGGCTACTAT 59.130 52.381 0.00 0.00 32.29 2.12
2352 2512 3.340928 AGTTTAACGGTTGGGCTATCAC 58.659 45.455 3.07 0.00 0.00 3.06
2361 2521 0.535335 TGGGCTATCACACGAACTCC 59.465 55.000 0.00 0.00 0.00 3.85
2409 2569 9.165035 GCGGTCTATCTACACTATAATAAGACT 57.835 37.037 0.00 0.00 0.00 3.24
2439 2599 4.034285 ACTTTCAACCCATTCCGAGAAT 57.966 40.909 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.677779 GCTTCATTAAACCGGACATGCATT 60.678 41.667 9.46 0.00 0.00 3.56
116 120 8.200792 AGAGAGAACTAAATATGTCATGTGGTC 58.799 37.037 0.00 0.00 0.00 4.02
213 223 4.379082 CCGGCCACATTTAAACTTGACTAC 60.379 45.833 2.24 0.00 0.00 2.73
230 240 1.030488 TTGTTCGTTGTTTCCGGCCA 61.030 50.000 2.24 0.00 0.00 5.36
275 288 7.502561 GGCAGATCAGTACCAAACCTTATAATT 59.497 37.037 0.00 0.00 0.00 1.40
277 290 6.354130 GGCAGATCAGTACCAAACCTTATAA 58.646 40.000 0.00 0.00 0.00 0.98
281 294 2.290960 GGGCAGATCAGTACCAAACCTT 60.291 50.000 0.00 0.00 0.00 3.50
295 310 6.948309 ACTCTAAAATTGTGTTTAGGGCAGAT 59.052 34.615 4.80 0.00 42.87 2.90
481 501 5.798125 TTTGCCACTTTCATCCATGTTTA 57.202 34.783 0.00 0.00 0.00 2.01
881 926 2.048784 GCAGCAGTGACTCGCTCA 60.049 61.111 6.57 0.00 35.96 4.26
917 962 2.280628 GCTATTTTACCTGTCGCTGCT 58.719 47.619 0.00 0.00 0.00 4.24
934 979 2.167693 CCAAGTCCTTACATCACCGCTA 59.832 50.000 0.00 0.00 0.00 4.26
940 985 0.392461 GCCGCCAAGTCCTTACATCA 60.392 55.000 0.00 0.00 0.00 3.07
1005 1050 3.330720 CGCTCCTCCCCAACCCTT 61.331 66.667 0.00 0.00 0.00 3.95
1083 1128 2.123683 CTGAGGCCCGAGCTCCTA 60.124 66.667 8.47 0.00 39.73 2.94
1113 1158 1.123077 CCTCCCCTCGATCATGTTCA 58.877 55.000 4.71 0.00 0.00 3.18
1141 1186 4.003788 CCTGCGTTGACCCGTCCT 62.004 66.667 0.00 0.00 0.00 3.85
1319 1364 1.286248 AACTCCGGTTATCCAAGCCT 58.714 50.000 0.00 0.00 33.39 4.58
1324 1369 0.391927 CGGCAAACTCCGGTTATCCA 60.392 55.000 0.00 0.00 45.38 3.41
1325 1370 2.390427 CGGCAAACTCCGGTTATCC 58.610 57.895 0.00 0.00 45.38 2.59
1333 1378 4.699522 AGGTCGCCGGCAAACTCC 62.700 66.667 28.98 19.18 0.00 3.85
1334 1379 3.423154 CAGGTCGCCGGCAAACTC 61.423 66.667 28.98 16.43 0.00 3.01
1335 1380 3.936203 TCAGGTCGCCGGCAAACT 61.936 61.111 28.98 15.19 0.00 2.66
1336 1381 3.723348 GTCAGGTCGCCGGCAAAC 61.723 66.667 28.98 22.98 0.00 2.93
1342 1387 4.695231 AACGTCGTCAGGTCGCCG 62.695 66.667 0.00 0.00 38.14 6.46
1343 1388 3.103911 CAACGTCGTCAGGTCGCC 61.104 66.667 0.00 0.00 0.00 5.54
1344 1389 2.050714 TCAACGTCGTCAGGTCGC 60.051 61.111 0.00 0.00 0.00 5.19
1345 1390 2.073220 CGTCAACGTCGTCAGGTCG 61.073 63.158 0.00 0.00 34.11 4.79
1346 1391 0.317269 TTCGTCAACGTCGTCAGGTC 60.317 55.000 0.00 0.00 40.80 3.85
1347 1392 0.317603 CTTCGTCAACGTCGTCAGGT 60.318 55.000 0.00 0.00 40.80 4.00
1348 1393 1.606350 GCTTCGTCAACGTCGTCAGG 61.606 60.000 0.00 0.00 40.80 3.86
1349 1394 0.933047 TGCTTCGTCAACGTCGTCAG 60.933 55.000 0.00 0.00 40.80 3.51
1350 1395 0.933047 CTGCTTCGTCAACGTCGTCA 60.933 55.000 0.00 0.00 40.80 4.35
1351 1396 1.606350 CCTGCTTCGTCAACGTCGTC 61.606 60.000 0.00 0.00 40.80 4.20
1352 1397 1.660575 CCTGCTTCGTCAACGTCGT 60.661 57.895 2.09 0.00 40.80 4.34
1353 1398 2.372690 CCCTGCTTCGTCAACGTCG 61.373 63.158 2.09 0.00 40.80 5.12
1354 1399 2.027625 CCCCTGCTTCGTCAACGTC 61.028 63.158 2.09 0.00 40.80 4.34
1355 1400 2.030562 CCCCTGCTTCGTCAACGT 59.969 61.111 2.09 0.00 40.80 3.99
1356 1401 2.027625 GACCCCTGCTTCGTCAACG 61.028 63.158 0.00 0.00 41.45 4.10
1357 1402 0.951040 CAGACCCCTGCTTCGTCAAC 60.951 60.000 0.00 0.00 33.07 3.18
1358 1403 1.118965 TCAGACCCCTGCTTCGTCAA 61.119 55.000 0.00 0.00 40.20 3.18
1359 1404 1.533033 TCAGACCCCTGCTTCGTCA 60.533 57.895 0.00 0.00 40.20 4.35
1360 1405 1.079750 GTCAGACCCCTGCTTCGTC 60.080 63.158 0.00 0.00 40.20 4.20
1361 1406 2.932234 CGTCAGACCCCTGCTTCGT 61.932 63.158 0.00 0.00 40.20 3.85
1362 1407 2.125912 CGTCAGACCCCTGCTTCG 60.126 66.667 0.00 0.00 40.20 3.79
1363 1408 0.250513 ATTCGTCAGACCCCTGCTTC 59.749 55.000 0.00 0.00 40.20 3.86
1364 1409 0.250513 GATTCGTCAGACCCCTGCTT 59.749 55.000 0.00 0.00 40.20 3.91
1365 1410 1.617947 GGATTCGTCAGACCCCTGCT 61.618 60.000 0.00 0.00 40.20 4.24
1366 1411 1.153349 GGATTCGTCAGACCCCTGC 60.153 63.158 0.00 0.00 40.20 4.85
1367 1412 0.176680 CTGGATTCGTCAGACCCCTG 59.823 60.000 0.00 0.00 41.74 4.45
1368 1413 0.041238 TCTGGATTCGTCAGACCCCT 59.959 55.000 0.00 0.00 36.46 4.79
1369 1414 1.123928 ATCTGGATTCGTCAGACCCC 58.876 55.000 0.00 0.00 43.07 4.95
1370 1415 1.202580 CCATCTGGATTCGTCAGACCC 60.203 57.143 0.00 0.00 43.07 4.46
1371 1416 1.808133 GCCATCTGGATTCGTCAGACC 60.808 57.143 0.00 0.00 43.07 3.85
1372 1417 1.576356 GCCATCTGGATTCGTCAGAC 58.424 55.000 0.00 0.00 43.07 3.51
1373 1418 0.103026 CGCCATCTGGATTCGTCAGA 59.897 55.000 0.00 0.00 44.19 3.27
1374 1419 0.877649 CCGCCATCTGGATTCGTCAG 60.878 60.000 0.00 0.00 37.39 3.51
1375 1420 1.143838 CCGCCATCTGGATTCGTCA 59.856 57.895 0.00 0.00 37.39 4.35
1376 1421 2.247437 GCCGCCATCTGGATTCGTC 61.247 63.158 0.00 0.00 37.39 4.20
1377 1422 2.203070 GCCGCCATCTGGATTCGT 60.203 61.111 0.00 0.00 37.39 3.85
1378 1423 1.958205 GAGCCGCCATCTGGATTCG 60.958 63.158 0.00 0.00 37.39 3.34
1379 1424 1.958205 CGAGCCGCCATCTGGATTC 60.958 63.158 0.00 0.00 37.39 2.52
1380 1425 2.109799 CGAGCCGCCATCTGGATT 59.890 61.111 0.00 0.00 37.39 3.01
1397 1442 3.741476 CTCTGCCGCCCTTGTTGC 61.741 66.667 0.00 0.00 0.00 4.17
1398 1443 3.058160 CCTCTGCCGCCCTTGTTG 61.058 66.667 0.00 0.00 0.00 3.33
1399 1444 3.249189 TCCTCTGCCGCCCTTGTT 61.249 61.111 0.00 0.00 0.00 2.83
1400 1445 3.710722 CTCCTCTGCCGCCCTTGT 61.711 66.667 0.00 0.00 0.00 3.16
1401 1446 4.479993 CCTCCTCTGCCGCCCTTG 62.480 72.222 0.00 0.00 0.00 3.61
1407 1452 4.399395 TGCTTGCCTCCTCTGCCG 62.399 66.667 0.00 0.00 0.00 5.69
1408 1453 2.438075 CTGCTTGCCTCCTCTGCC 60.438 66.667 0.00 0.00 0.00 4.85
1409 1454 3.132801 GCTGCTTGCCTCCTCTGC 61.133 66.667 0.00 0.00 35.15 4.26
1410 1455 2.818714 CGCTGCTTGCCTCCTCTG 60.819 66.667 0.00 0.00 38.78 3.35
1411 1456 2.999648 TCGCTGCTTGCCTCCTCT 61.000 61.111 0.00 0.00 38.78 3.69
1412 1457 2.817396 GTCGCTGCTTGCCTCCTC 60.817 66.667 0.00 0.00 38.78 3.71
1413 1458 4.749310 CGTCGCTGCTTGCCTCCT 62.749 66.667 0.00 0.00 38.78 3.69
1414 1459 4.742201 TCGTCGCTGCTTGCCTCC 62.742 66.667 0.00 0.00 38.78 4.30
1415 1460 3.482783 GTCGTCGCTGCTTGCCTC 61.483 66.667 0.00 0.00 38.78 4.70
1418 1463 4.122515 GACGTCGTCGCTGCTTGC 62.123 66.667 10.05 0.00 41.18 4.01
1419 1464 2.016704 AAGACGTCGTCGCTGCTTG 61.017 57.895 19.11 0.00 41.18 4.01
1420 1465 2.016704 CAAGACGTCGTCGCTGCTT 61.017 57.895 19.11 5.42 41.18 3.91
1421 1466 2.402282 TTCAAGACGTCGTCGCTGCT 62.402 55.000 19.11 0.00 41.18 4.24
1422 1467 2.014554 TTCAAGACGTCGTCGCTGC 61.015 57.895 19.11 0.00 41.18 5.25
1423 1468 1.767388 GTTCAAGACGTCGTCGCTG 59.233 57.895 19.11 18.97 41.18 5.18
1424 1469 1.724929 CGTTCAAGACGTCGTCGCT 60.725 57.895 19.11 8.35 46.49 4.93
1425 1470 2.755095 CGTTCAAGACGTCGTCGC 59.245 61.111 19.11 7.99 46.49 5.19
1433 1478 2.853914 GCCTCGTGCGTTCAAGAC 59.146 61.111 0.00 0.00 0.00 3.01
1452 1610 2.152058 ATCATGCCCCGCCATCTCT 61.152 57.895 0.00 0.00 0.00 3.10
1467 1625 1.002990 CAGCAGGTCACCAGCATCA 60.003 57.895 14.59 0.00 38.55 3.07
1515 1673 1.734477 CTCAACCACCTCGCGTCAG 60.734 63.158 5.77 0.00 0.00 3.51
1615 1773 2.916269 TCTCCTCCTCTCTCTCAACTCA 59.084 50.000 0.00 0.00 0.00 3.41
1659 1817 2.883572 GGACCGACCTCTTCTGCTA 58.116 57.895 0.00 0.00 35.41 3.49
1735 1893 1.579964 CTCTTGCAGCCATGAACGCA 61.580 55.000 0.00 0.00 0.00 5.24
1751 1909 0.119155 TGATCCCCTTGTCCACCTCT 59.881 55.000 0.00 0.00 0.00 3.69
1824 1982 0.832135 TCTCTCGCTCCACCCAAACT 60.832 55.000 0.00 0.00 0.00 2.66
1836 1994 0.594110 CTATCGGGGTCTTCTCTCGC 59.406 60.000 0.00 0.00 0.00 5.03
1847 2005 2.175202 CAGATCCCTTCTCTATCGGGG 58.825 57.143 0.00 0.00 38.55 5.73
1886 2044 0.169009 GCTCATCCTTGTTGTTCGGC 59.831 55.000 0.00 0.00 0.00 5.54
2013 2173 0.613853 TTCGATCGGAGGGTCCAACT 60.614 55.000 16.41 0.00 35.91 3.16
2116 2276 0.673333 TCGGACAGTCGTTACCGCTA 60.673 55.000 0.00 0.00 44.19 4.26
2135 2295 2.800159 AATCTGTCCCGGACCCGACT 62.800 60.000 15.24 0.00 42.83 4.18
2181 2341 2.306512 ACCTAACCTCTCTCGTCAGTCT 59.693 50.000 0.00 0.00 0.00 3.24
2228 2388 1.169577 CAGCTCGAGACCGCCTATAT 58.830 55.000 18.75 0.00 35.37 0.86
2299 2459 0.169009 GTAGCCGGTCTAACGTCGTT 59.831 55.000 15.97 15.97 0.00 3.85
2300 2460 0.674895 AGTAGCCGGTCTAACGTCGT 60.675 55.000 1.90 0.00 0.00 4.34
2318 2478 4.986659 ACCGTTAAACTATAGCGGCAATAG 59.013 41.667 13.63 0.00 45.53 1.73
2319 2479 4.947645 ACCGTTAAACTATAGCGGCAATA 58.052 39.130 13.63 0.00 45.53 1.90
2321 2481 3.249986 ACCGTTAAACTATAGCGGCAA 57.750 42.857 13.63 0.00 45.53 4.52
2352 2512 0.298707 CATCGCATTCGGAGTTCGTG 59.701 55.000 0.00 0.00 40.32 4.35
2361 2521 3.410850 CTGTCAAGTTTCATCGCATTCG 58.589 45.455 0.00 0.00 0.00 3.34
2409 2569 1.310904 GGGTTGAAAGTTGGCGTGTA 58.689 50.000 0.00 0.00 0.00 2.90
2410 2570 0.681564 TGGGTTGAAAGTTGGCGTGT 60.682 50.000 0.00 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.