Multiple sequence alignment - TraesCS5A01G151900

Loading Multiple Alignment...

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 TraesCS5A01G151900 chr5A 100.000 3254 0 0 1 3254 328943369 328946622 0.000000e+00 6010
1 TraesCS5A01G151900 chr5B 91.698 2373 122 28 1 2334 278227454 278229790 0.000000e+00 3221
2 TraesCS5A01G151900 chr5B 96.065 864 31 2 2392 3254 278229790 278230651 0.000000e+00 1404
3 TraesCS5A01G151900 chr5D 94.475 1647 68 12 1619 3254 244705836 244707470 0.000000e+00 2516
4 TraesCS5A01G151900 chr5D 92.780 1205 45 14 1 1176 244704123 244705314 0.000000e+00 1705
5 TraesCS5A01G151900 chr5D 91.772 474 31 4 1130 1601 244705310 244705777 0.000000e+00 652
6 TraesCS5A01G151900 chr4D 93.506 154 9 1 2359 2511 74079351 74079504 9.080000e-56 228
7 TraesCS5A01G151900 chr3D 93.506 154 8 2 2359 2510 315480425 315480578 9.080000e-56 228
8 TraesCS5A01G151900 chr2D 93.464 153 10 0 2359 2511 79056167 79056319 9.080000e-56 228
9 TraesCS5A01G151900 chr4A 92.857 154 11 0 2358 2511 460230648 460230801 1.170000e-54 224
10 TraesCS5A01G151900 chr1D 92.405 158 10 2 2359 2514 156133492 156133335 1.170000e-54 224
11 TraesCS5A01G151900 chr4B 92.810 153 11 0 2359 2511 106227409 106227561 4.230000e-54 222
12 TraesCS5A01G151900 chr2A 92.810 153 11 0 2359 2511 79316005 79316157 4.230000e-54 222


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 TraesCS5A01G151900 chr5A 328943369 328946622 3253 False 6010.000000 6010 100.0000 1 3254 1 chr5A.!!$F1 3253
1 TraesCS5A01G151900 chr5B 278227454 278230651 3197 False 2312.500000 3221 93.8815 1 3254 2 chr5B.!!$F1 3253
2 TraesCS5A01G151900 chr5D 244704123 244707470 3347 False 1624.333333 2516 93.0090 1 3254 3 chr5D.!!$F1 3253

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
508 536 1.270732 CCATAGTCCAGAGGCATCAGC 60.271 57.143 0.0 0.0 41.1 4.26 F
1180 1256 0.404812 TACCGGCTATCTCTCCCCTC 59.595 60.000 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1820 1945 0.174389 TCTCCTGCTCATCACGCTTC 59.826 55.0 0.0 0.0 0.0 3.86 R
2354 2488 1.915141 ACGAACGGAGGGAGTAAGAA 58.085 50.0 0.0 0.0 0.0 2.52 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
223 225 4.009675 TCAAGGGATCAACAATCTTTCCG 58.990 43.478 0.00 0.00 34.56 4.30
232 234 5.344884 TCAACAATCTTTCCGGTTCAAAAC 58.655 37.500 0.00 0.00 0.00 2.43
242 244 8.186821 TCTTTCCGGTTCAAAACGTAAATTTAA 58.813 29.630 0.00 0.00 0.00 1.52
329 357 5.247862 TGCAGATTGACTACACATGAATGT 58.752 37.500 0.00 0.00 42.84 2.71
340 368 2.743664 CACATGAATGTCAAAGGCTCGA 59.256 45.455 0.00 0.00 39.39 4.04
362 390 9.185192 CTCGAAATTTCTAGCACAAAATCTTTT 57.815 29.630 15.92 0.00 0.00 2.27
506 534 2.180946 ACCATAGTCCAGAGGCATCA 57.819 50.000 0.00 0.00 0.00 3.07
508 536 1.270732 CCATAGTCCAGAGGCATCAGC 60.271 57.143 0.00 0.00 41.10 4.26
542 571 4.651045 GGATGGCAAGAAAGAACCCATATT 59.349 41.667 0.00 0.00 36.48 1.28
655 684 1.671054 ATCCCAACCGTGTCAAGCG 60.671 57.895 0.00 0.00 0.00 4.68
702 734 1.759445 GCAGTCATAGCTTCCTCCTCA 59.241 52.381 0.00 0.00 0.00 3.86
717 749 1.561542 TCCTCATTCCTTTCAGGCTCC 59.438 52.381 0.00 0.00 34.61 4.70
720 752 1.839994 TCATTCCTTTCAGGCTCCGAT 59.160 47.619 0.00 0.00 34.61 4.18
931 963 3.068064 TCGCCGCCATGAGTCTGA 61.068 61.111 0.00 0.00 0.00 3.27
932 964 2.584418 CGCCGCCATGAGTCTGAG 60.584 66.667 0.00 0.00 0.00 3.35
933 965 2.894387 GCCGCCATGAGTCTGAGC 60.894 66.667 0.00 0.00 0.00 4.26
934 966 2.584418 CCGCCATGAGTCTGAGCG 60.584 66.667 12.37 12.37 46.04 5.03
1002 1034 2.319844 TCAGTCTTCAGTGGCAGAGAA 58.680 47.619 0.00 0.00 0.00 2.87
1026 1058 1.365999 CCGGTTTTGTTGGGCCTTC 59.634 57.895 4.53 0.00 0.00 3.46
1069 1101 0.747852 CTACCTCTTCTTCGCCCTCC 59.252 60.000 0.00 0.00 0.00 4.30
1180 1256 0.404812 TACCGGCTATCTCTCCCCTC 59.595 60.000 0.00 0.00 0.00 4.30
1186 1262 3.247162 GGCTATCTCTCCCCTCTCATTT 58.753 50.000 0.00 0.00 0.00 2.32
1187 1263 3.007831 GGCTATCTCTCCCCTCTCATTTG 59.992 52.174 0.00 0.00 0.00 2.32
1218 1294 1.079503 GCTGATCGGACTTTGTGGAC 58.920 55.000 5.48 0.00 0.00 4.02
1223 1299 1.300620 CGGACTTTGTGGACGCAGA 60.301 57.895 0.00 0.00 0.00 4.26
1349 1425 1.599576 GCTTCTGTGAGTCCCTCCC 59.400 63.158 0.00 0.00 0.00 4.30
1372 1448 2.102578 CTCCATTCAACATCCAACCCC 58.897 52.381 0.00 0.00 0.00 4.95
1380 1456 4.746466 TCAACATCCAACCCCTTGTAATT 58.254 39.130 0.00 0.00 0.00 1.40
1388 1464 4.086457 CAACCCCTTGTAATTAGCTGGTT 58.914 43.478 0.00 0.00 35.33 3.67
1389 1465 3.964411 ACCCCTTGTAATTAGCTGGTTC 58.036 45.455 0.00 0.00 0.00 3.62
1390 1466 3.332485 ACCCCTTGTAATTAGCTGGTTCA 59.668 43.478 0.00 0.00 0.00 3.18
1391 1467 4.202631 ACCCCTTGTAATTAGCTGGTTCAA 60.203 41.667 0.00 0.00 0.00 2.69
1392 1468 4.770010 CCCCTTGTAATTAGCTGGTTCAAA 59.230 41.667 0.00 0.00 0.00 2.69
1417 1493 3.735237 ATCGTTAGGGTAGATGCACTG 57.265 47.619 0.00 0.00 0.00 3.66
1461 1537 4.261197 GCGTGTCAAGTCTCCTCAAAATTT 60.261 41.667 0.00 0.00 0.00 1.82
1467 1543 7.556275 TGTCAAGTCTCCTCAAAATTTTACACT 59.444 33.333 2.44 0.00 0.00 3.55
1507 1583 3.693578 TGTCAGTTGTTGCTGTGAAATCA 59.306 39.130 0.00 0.00 37.70 2.57
1530 1606 3.242867 TGGGGCCTCTAGACATCATTAG 58.757 50.000 3.07 0.00 0.00 1.73
1533 1609 2.353208 GGCCTCTAGACATCATTAGCCG 60.353 54.545 0.00 0.00 0.00 5.52
1536 1612 3.192422 CCTCTAGACATCATTAGCCGAGG 59.808 52.174 0.00 0.00 0.00 4.63
1540 1616 3.505386 AGACATCATTAGCCGAGGATCT 58.495 45.455 0.00 0.00 0.00 2.75
1564 1640 3.117738 AGCATCCCCTCCTGAAGTAATTG 60.118 47.826 0.00 0.00 0.00 2.32
1572 1648 5.514834 CCCTCCTGAAGTAATTGAACTGGAA 60.515 44.000 0.00 0.00 0.00 3.53
1579 1655 6.775142 TGAAGTAATTGAACTGGAATGGTGAA 59.225 34.615 0.00 0.00 0.00 3.18
1585 1661 8.421249 AATTGAACTGGAATGGTGAAGAAATA 57.579 30.769 0.00 0.00 0.00 1.40
1588 1664 8.421249 TGAACTGGAATGGTGAAGAAATATTT 57.579 30.769 0.00 0.00 0.00 1.40
1590 1666 7.410120 ACTGGAATGGTGAAGAAATATTTCC 57.590 36.000 21.86 9.71 37.92 3.13
1591 1667 6.953520 ACTGGAATGGTGAAGAAATATTTCCA 59.046 34.615 21.86 14.58 37.92 3.53
1592 1668 7.620888 ACTGGAATGGTGAAGAAATATTTCCAT 59.379 33.333 21.86 16.00 37.92 3.41
1593 1669 8.010733 TGGAATGGTGAAGAAATATTTCCATC 57.989 34.615 21.86 19.76 37.92 3.51
1594 1670 7.840716 TGGAATGGTGAAGAAATATTTCCATCT 59.159 33.333 21.86 10.66 37.92 2.90
1595 1671 8.139989 GGAATGGTGAAGAAATATTTCCATCTG 58.860 37.037 21.86 0.00 37.92 2.90
1596 1672 8.599624 AATGGTGAAGAAATATTTCCATCTGT 57.400 30.769 21.86 2.46 37.92 3.41
1597 1673 9.699410 AATGGTGAAGAAATATTTCCATCTGTA 57.301 29.630 21.86 11.99 37.92 2.74
1598 1674 9.699410 ATGGTGAAGAAATATTTCCATCTGTAA 57.301 29.630 21.86 10.21 37.92 2.41
1599 1675 8.956426 TGGTGAAGAAATATTTCCATCTGTAAC 58.044 33.333 21.86 14.29 37.92 2.50
1600 1676 8.956426 GGTGAAGAAATATTTCCATCTGTAACA 58.044 33.333 21.86 8.43 37.92 2.41
1618 1694 8.018520 TCTGTAACAACTAACAACACAAACTTG 58.981 33.333 0.00 0.00 0.00 3.16
1636 1761 4.079253 ACTTGTACTTTTAGGTGCCCATG 58.921 43.478 0.00 0.00 0.00 3.66
1644 1769 5.073008 ACTTTTAGGTGCCCATGGAAATTTT 59.927 36.000 15.22 0.00 0.00 1.82
1653 1778 5.248020 TGCCCATGGAAATTTTCATTGTACT 59.752 36.000 15.22 0.00 0.00 2.73
1656 1781 7.653311 GCCCATGGAAATTTTCATTGTACTATC 59.347 37.037 15.22 0.00 0.00 2.08
1682 1807 7.555087 TCATTCATTTTGTCAAGTTCTTTGGT 58.445 30.769 0.00 0.00 37.39 3.67
1684 1809 7.826260 TTCATTTTGTCAAGTTCTTTGGTTC 57.174 32.000 0.00 0.00 37.39 3.62
1700 1825 2.688446 TGGTTCGTTTGGTGCATAACAA 59.312 40.909 0.00 0.00 0.00 2.83
1984 2109 1.194781 TCTCTCTGGGGTTGCTGGAC 61.195 60.000 0.00 0.00 0.00 4.02
2019 2144 7.362401 CCAGCAATGTTCTAAAAGAGTTATGCT 60.362 37.037 0.00 0.00 35.14 3.79
2033 2158 9.664332 AAAGAGTTATGCTCATATCATATCCAC 57.336 33.333 0.00 0.00 46.47 4.02
2035 2160 8.819845 AGAGTTATGCTCATATCATATCCACAA 58.180 33.333 0.00 0.00 46.47 3.33
2095 2220 3.182972 GCATATGCGTCCATTTTGAATGC 59.817 43.478 12.82 0.00 33.68 3.56
2171 2296 8.375493 ACTTGTAGAGGTCAAACCAATCTATA 57.625 34.615 0.00 0.00 41.95 1.31
2269 2402 9.545105 CAGCTTGCCCATTAATTCAAATTATAA 57.455 29.630 0.00 0.00 31.47 0.98
2333 2467 4.344359 TGTTTGCTGTGTCATGTAGGTA 57.656 40.909 0.00 0.00 0.00 3.08
2334 2468 4.709250 TGTTTGCTGTGTCATGTAGGTAA 58.291 39.130 0.00 0.00 0.00 2.85
2335 2469 5.126779 TGTTTGCTGTGTCATGTAGGTAAA 58.873 37.500 0.00 0.00 0.00 2.01
2336 2470 5.767665 TGTTTGCTGTGTCATGTAGGTAAAT 59.232 36.000 0.00 0.00 0.00 1.40
2337 2471 6.937465 TGTTTGCTGTGTCATGTAGGTAAATA 59.063 34.615 0.00 0.00 0.00 1.40
2338 2472 7.445707 TGTTTGCTGTGTCATGTAGGTAAATAA 59.554 33.333 0.00 0.00 0.00 1.40
2339 2473 6.978343 TGCTGTGTCATGTAGGTAAATAAC 57.022 37.500 0.00 0.00 0.00 1.89
2340 2474 6.707290 TGCTGTGTCATGTAGGTAAATAACT 58.293 36.000 0.00 0.00 0.00 2.24
2341 2475 6.593770 TGCTGTGTCATGTAGGTAAATAACTG 59.406 38.462 0.00 0.00 0.00 3.16
2342 2476 6.816640 GCTGTGTCATGTAGGTAAATAACTGA 59.183 38.462 0.00 0.00 0.00 3.41
2343 2477 7.333423 GCTGTGTCATGTAGGTAAATAACTGAA 59.667 37.037 0.00 0.00 0.00 3.02
2344 2478 9.214957 CTGTGTCATGTAGGTAAATAACTGAAA 57.785 33.333 0.00 0.00 0.00 2.69
2345 2479 9.214957 TGTGTCATGTAGGTAAATAACTGAAAG 57.785 33.333 0.00 0.00 42.29 2.62
2346 2480 9.431887 GTGTCATGTAGGTAAATAACTGAAAGA 57.568 33.333 0.00 0.00 37.43 2.52
2367 2501 6.608539 AGAAACTACTTTCTTACTCCCTCC 57.391 41.667 0.00 0.00 43.10 4.30
2368 2502 5.185442 AGAAACTACTTTCTTACTCCCTCCG 59.815 44.000 0.00 0.00 43.10 4.63
2369 2503 4.044946 ACTACTTTCTTACTCCCTCCGT 57.955 45.455 0.00 0.00 0.00 4.69
2370 2504 4.414677 ACTACTTTCTTACTCCCTCCGTT 58.585 43.478 0.00 0.00 0.00 4.44
2371 2505 3.957591 ACTTTCTTACTCCCTCCGTTC 57.042 47.619 0.00 0.00 0.00 3.95
2372 2506 2.230750 ACTTTCTTACTCCCTCCGTTCG 59.769 50.000 0.00 0.00 0.00 3.95
2373 2507 1.915141 TTCTTACTCCCTCCGTTCGT 58.085 50.000 0.00 0.00 0.00 3.85
2374 2508 2.787473 TCTTACTCCCTCCGTTCGTA 57.213 50.000 0.00 0.00 0.00 3.43
2375 2509 3.071874 TCTTACTCCCTCCGTTCGTAA 57.928 47.619 0.00 0.00 0.00 3.18
2376 2510 3.420893 TCTTACTCCCTCCGTTCGTAAA 58.579 45.455 0.00 0.00 0.00 2.01
2377 2511 4.019174 TCTTACTCCCTCCGTTCGTAAAT 58.981 43.478 0.00 0.00 0.00 1.40
2378 2512 5.192927 TCTTACTCCCTCCGTTCGTAAATA 58.807 41.667 0.00 0.00 0.00 1.40
2379 2513 5.829924 TCTTACTCCCTCCGTTCGTAAATAT 59.170 40.000 0.00 0.00 0.00 1.28
2380 2514 6.998074 TCTTACTCCCTCCGTTCGTAAATATA 59.002 38.462 0.00 0.00 0.00 0.86
2381 2515 7.502226 TCTTACTCCCTCCGTTCGTAAATATAA 59.498 37.037 0.00 0.00 0.00 0.98
2382 2516 6.081872 ACTCCCTCCGTTCGTAAATATAAG 57.918 41.667 0.00 0.00 0.00 1.73
2383 2517 5.829924 ACTCCCTCCGTTCGTAAATATAAGA 59.170 40.000 0.00 0.00 0.00 2.10
2384 2518 6.492772 ACTCCCTCCGTTCGTAAATATAAGAT 59.507 38.462 0.00 0.00 0.00 2.40
2385 2519 6.684686 TCCCTCCGTTCGTAAATATAAGATG 58.315 40.000 0.00 0.00 0.00 2.90
2386 2520 6.266103 TCCCTCCGTTCGTAAATATAAGATGT 59.734 38.462 0.00 0.00 0.00 3.06
2387 2521 6.927381 CCCTCCGTTCGTAAATATAAGATGTT 59.073 38.462 0.00 0.00 0.00 2.71
2388 2522 7.115947 CCCTCCGTTCGTAAATATAAGATGTTC 59.884 40.741 0.00 0.00 0.00 3.18
2389 2523 7.866393 CCTCCGTTCGTAAATATAAGATGTTCT 59.134 37.037 0.00 0.00 0.00 3.01
2390 2524 9.888878 CTCCGTTCGTAAATATAAGATGTTCTA 57.111 33.333 0.00 0.00 0.00 2.10
2538 2731 4.333926 CCAAGCCTAGCATTTTAGACAGAC 59.666 45.833 0.00 0.00 0.00 3.51
2563 2756 6.127730 CCCAATTTCAACTCCACCATACTTAC 60.128 42.308 0.00 0.00 0.00 2.34
2626 2819 7.148557 GGTCAGAAAGAAACATCAGTAGTAAGC 60.149 40.741 0.00 0.00 0.00 3.09
2769 2962 9.256477 CGTGATGGTAGTAATTACATGTATTGT 57.744 33.333 17.65 0.00 42.62 2.71
2917 3111 1.137675 TGACCAGCAGCAGTAGCATAG 59.862 52.381 0.00 0.00 45.49 2.23
3074 3268 4.233005 GTTGTCCAGTACCGTACTCTTTC 58.767 47.826 8.31 1.52 36.76 2.62
3100 3294 3.591695 TTTGCATCATATACCAGGGCA 57.408 42.857 0.00 0.00 0.00 5.36
3136 3330 0.179936 GGAGTGAGCCAAGAGGGATG 59.820 60.000 0.00 0.00 40.01 3.51
3181 3375 0.937304 CACCGATGCTATTTGGTCCG 59.063 55.000 0.00 0.00 30.72 4.79
3199 3393 0.453793 CGAAGAGCTCGGATGTCACT 59.546 55.000 8.37 0.00 44.20 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 111 9.535878 TTCAATTTGGTGTCCAAGTTATTTAAC 57.464 29.630 8.50 0.00 44.84 2.01
158 159 0.663153 GTTCAACCGAACTTGCTGCT 59.337 50.000 0.00 0.00 46.72 4.24
206 208 3.756434 TGAACCGGAAAGATTGTTGATCC 59.244 43.478 9.46 0.00 35.21 3.36
216 218 5.754543 ATTTACGTTTTGAACCGGAAAGA 57.245 34.783 9.46 0.00 39.96 2.52
284 286 6.650807 TGCAGAAGTTTCTCGAATGTAATCTT 59.349 34.615 0.00 0.00 34.74 2.40
329 357 4.946784 GCTAGAAATTTCGAGCCTTTGA 57.053 40.909 31.59 4.91 46.14 2.69
362 390 2.557924 CAGCATTGCAACCCAGAAACTA 59.442 45.455 11.91 0.00 0.00 2.24
363 391 1.342174 CAGCATTGCAACCCAGAAACT 59.658 47.619 11.91 0.00 0.00 2.66
407 435 8.320617 ACCAACAATATTCACAGCCAAATTATT 58.679 29.630 0.00 0.00 0.00 1.40
417 445 7.370383 AGCAACTTAACCAACAATATTCACAG 58.630 34.615 0.00 0.00 0.00 3.66
506 534 1.379443 CCATCCTGCACACATGGCT 60.379 57.895 0.00 0.00 30.94 4.75
508 536 1.252215 TTGCCATCCTGCACACATGG 61.252 55.000 8.81 8.81 41.88 3.66
510 538 0.038599 TCTTGCCATCCTGCACACAT 59.961 50.000 0.00 0.00 41.88 3.21
542 571 2.165167 CCTTCGTCGGCCATATAGGTA 58.835 52.381 2.24 0.00 40.61 3.08
675 704 2.907897 AAGCTATGACTGCGACGGGC 62.908 60.000 0.00 0.00 43.96 6.13
717 749 2.585247 GACGCTTCCCGGGAATCG 60.585 66.667 42.62 42.62 45.50 3.34
720 752 3.387947 GAGGACGCTTCCCGGGAA 61.388 66.667 33.52 33.52 44.10 3.97
954 986 2.211410 CCGTACTCCCACCCACACA 61.211 63.158 0.00 0.00 0.00 3.72
1002 1034 1.960417 CCCAACAAAACCGGCAAATT 58.040 45.000 0.00 0.00 0.00 1.82
1076 1108 4.803426 GAGGCACGAGCTGACCGG 62.803 72.222 0.00 0.00 41.70 5.28
1078 1110 3.749064 TCGAGGCACGAGCTGACC 61.749 66.667 2.07 0.00 46.45 4.02
1092 1124 0.699577 AGGAGGAGGAGGAGGATCGA 60.700 60.000 0.00 0.00 34.37 3.59
1097 1129 2.197324 CGGAGGAGGAGGAGGAGG 59.803 72.222 0.00 0.00 0.00 4.30
1098 1130 2.520741 GCGGAGGAGGAGGAGGAG 60.521 72.222 0.00 0.00 0.00 3.69
1099 1131 4.144727 GGCGGAGGAGGAGGAGGA 62.145 72.222 0.00 0.00 0.00 3.71
1141 1173 1.181786 CCTGTCAGGAGTCAGAGGAC 58.818 60.000 14.26 0.00 44.66 3.85
1180 1256 4.571984 TCAGCCGTACATCAATCAAATGAG 59.428 41.667 0.00 0.00 31.76 2.90
1186 1262 2.545742 CCGATCAGCCGTACATCAATCA 60.546 50.000 0.00 0.00 0.00 2.57
1187 1263 2.061773 CCGATCAGCCGTACATCAATC 58.938 52.381 0.00 0.00 0.00 2.67
1349 1425 3.019564 GGTTGGATGTTGAATGGAGGAG 58.980 50.000 0.00 0.00 0.00 3.69
1372 1448 9.643693 ATTTCATTTGAACCAGCTAATTACAAG 57.356 29.630 0.00 0.00 33.13 3.16
1380 1456 5.957842 AACGATTTCATTTGAACCAGCTA 57.042 34.783 0.00 0.00 33.13 3.32
1388 1464 6.260050 GCATCTACCCTAACGATTTCATTTGA 59.740 38.462 0.00 0.00 0.00 2.69
1389 1465 6.038161 TGCATCTACCCTAACGATTTCATTTG 59.962 38.462 0.00 0.00 0.00 2.32
1390 1466 6.038271 GTGCATCTACCCTAACGATTTCATTT 59.962 38.462 0.00 0.00 0.00 2.32
1391 1467 5.527582 GTGCATCTACCCTAACGATTTCATT 59.472 40.000 0.00 0.00 0.00 2.57
1392 1468 5.057149 GTGCATCTACCCTAACGATTTCAT 58.943 41.667 0.00 0.00 0.00 2.57
1417 1493 4.582459 GCGCAGAGATGAAATTTGTCTAC 58.418 43.478 0.30 0.00 0.00 2.59
1461 1537 6.506500 ACTTAACGCTAGAGCTAAGTGTAA 57.493 37.500 17.97 8.57 39.21 2.41
1467 1543 5.048224 ACTGACAACTTAACGCTAGAGCTAA 60.048 40.000 0.00 0.00 39.32 3.09
1507 1583 2.196742 TGATGTCTAGAGGCCCCATT 57.803 50.000 0.00 0.00 0.00 3.16
1533 1609 0.975887 GAGGGGATGCTGAGATCCTC 59.024 60.000 9.66 6.75 42.75 3.71
1536 1612 3.162394 AGGAGGGGATGCTGAGATC 57.838 57.895 0.00 0.00 0.00 2.75
1564 1640 7.976175 GGAAATATTTCTTCACCATTCCAGTTC 59.024 37.037 23.85 1.78 37.35 3.01
1572 1648 9.699410 TTACAGATGGAAATATTTCTTCACCAT 57.301 29.630 23.85 19.16 39.00 3.55
1585 1661 8.349983 GTGTTGTTAGTTGTTACAGATGGAAAT 58.650 33.333 0.00 0.00 0.00 2.17
1588 1664 6.350103 TGTGTTGTTAGTTGTTACAGATGGA 58.650 36.000 0.00 0.00 0.00 3.41
1590 1666 8.181573 AGTTTGTGTTGTTAGTTGTTACAGATG 58.818 33.333 0.00 0.00 0.00 2.90
1591 1667 8.276252 AGTTTGTGTTGTTAGTTGTTACAGAT 57.724 30.769 0.00 0.00 0.00 2.90
1592 1668 7.675962 AGTTTGTGTTGTTAGTTGTTACAGA 57.324 32.000 0.00 0.00 0.00 3.41
1593 1669 7.806014 ACAAGTTTGTGTTGTTAGTTGTTACAG 59.194 33.333 0.00 0.00 40.49 2.74
1594 1670 7.649973 ACAAGTTTGTGTTGTTAGTTGTTACA 58.350 30.769 0.00 0.00 40.49 2.41
1595 1671 9.054191 GTACAAGTTTGTGTTGTTAGTTGTTAC 57.946 33.333 7.73 0.00 42.31 2.50
1596 1672 9.001542 AGTACAAGTTTGTGTTGTTAGTTGTTA 57.998 29.630 7.73 0.00 42.31 2.41
1597 1673 7.878036 AGTACAAGTTTGTGTTGTTAGTTGTT 58.122 30.769 7.73 0.00 42.31 2.83
1598 1674 7.443259 AGTACAAGTTTGTGTTGTTAGTTGT 57.557 32.000 7.73 0.00 42.31 3.32
1599 1675 8.736751 AAAGTACAAGTTTGTGTTGTTAGTTG 57.263 30.769 7.73 0.00 42.31 3.16
1602 1678 9.498307 CCTAAAAGTACAAGTTTGTGTTGTTAG 57.502 33.333 7.73 9.47 42.31 2.34
1608 1684 5.163591 GGCACCTAAAAGTACAAGTTTGTGT 60.164 40.000 7.73 0.00 42.31 3.72
1656 1781 7.707893 ACCAAAGAACTTGACAAAATGAATGAG 59.292 33.333 0.00 0.00 37.17 2.90
1682 1807 2.355132 ACGTTGTTATGCACCAAACGAA 59.645 40.909 24.00 9.51 0.00 3.85
1684 1809 2.392933 ACGTTGTTATGCACCAAACG 57.607 45.000 18.58 18.58 0.00 3.60
1700 1825 7.435068 AGTAAACAGAAAGCATCATTAACGT 57.565 32.000 0.00 0.00 0.00 3.99
1820 1945 0.174389 TCTCCTGCTCATCACGCTTC 59.826 55.000 0.00 0.00 0.00 3.86
2044 2169 7.808381 GGAAACAGTAAAAGAATCCTTGTTAGC 59.192 37.037 0.00 0.00 31.91 3.09
2095 2220 4.134379 AGCAGATACTGAGTGTGAATGG 57.866 45.455 0.00 0.00 32.44 3.16
2102 2227 6.276091 TGCTAAACATAGCAGATACTGAGTG 58.724 40.000 6.45 1.08 46.94 3.51
2151 2276 8.871125 GGAAGATATAGATTGGTTTGACCTCTA 58.129 37.037 0.00 0.00 39.58 2.43
2171 2296 5.511386 AAGACAGTCCTTGAATGGAAGAT 57.489 39.130 0.00 0.00 37.93 2.40
2248 2381 9.877178 AACGTTTATAATTTGAATTAATGGGCA 57.123 25.926 0.00 0.00 34.79 5.36
2345 2479 5.047448 ACGGAGGGAGTAAGAAAGTAGTTTC 60.047 44.000 14.15 14.15 42.25 2.78
2346 2480 4.837298 ACGGAGGGAGTAAGAAAGTAGTTT 59.163 41.667 0.00 0.00 0.00 2.66
2347 2481 4.414677 ACGGAGGGAGTAAGAAAGTAGTT 58.585 43.478 0.00 0.00 0.00 2.24
2348 2482 4.044946 ACGGAGGGAGTAAGAAAGTAGT 57.955 45.455 0.00 0.00 0.00 2.73
2349 2483 4.438472 CGAACGGAGGGAGTAAGAAAGTAG 60.438 50.000 0.00 0.00 0.00 2.57
2350 2484 3.441572 CGAACGGAGGGAGTAAGAAAGTA 59.558 47.826 0.00 0.00 0.00 2.24
2351 2485 2.230750 CGAACGGAGGGAGTAAGAAAGT 59.769 50.000 0.00 0.00 0.00 2.66
2352 2486 2.230750 ACGAACGGAGGGAGTAAGAAAG 59.769 50.000 0.00 0.00 0.00 2.62
2353 2487 2.242043 ACGAACGGAGGGAGTAAGAAA 58.758 47.619 0.00 0.00 0.00 2.52
2354 2488 1.915141 ACGAACGGAGGGAGTAAGAA 58.085 50.000 0.00 0.00 0.00 2.52
2355 2489 2.787473 TACGAACGGAGGGAGTAAGA 57.213 50.000 0.00 0.00 0.00 2.10
2356 2490 3.855689 TTTACGAACGGAGGGAGTAAG 57.144 47.619 0.00 0.00 0.00 2.34
2357 2491 7.502226 TCTTATATTTACGAACGGAGGGAGTAA 59.498 37.037 0.00 0.00 0.00 2.24
2358 2492 6.998074 TCTTATATTTACGAACGGAGGGAGTA 59.002 38.462 0.00 0.00 0.00 2.59
2359 2493 5.829924 TCTTATATTTACGAACGGAGGGAGT 59.170 40.000 0.00 0.00 0.00 3.85
2360 2494 6.323203 TCTTATATTTACGAACGGAGGGAG 57.677 41.667 0.00 0.00 0.00 4.30
2361 2495 6.266103 ACATCTTATATTTACGAACGGAGGGA 59.734 38.462 0.00 0.00 0.00 4.20
2362 2496 6.453092 ACATCTTATATTTACGAACGGAGGG 58.547 40.000 0.00 0.00 0.00 4.30
2363 2497 7.866393 AGAACATCTTATATTTACGAACGGAGG 59.134 37.037 0.00 0.00 0.00 4.30
2364 2498 8.798748 AGAACATCTTATATTTACGAACGGAG 57.201 34.615 0.00 0.00 0.00 4.63
2538 2731 4.344104 AGTATGGTGGAGTTGAAATTGGG 58.656 43.478 0.00 0.00 0.00 4.12
2563 2756 5.771469 TCAATTTGTCCATGTTTGCTACTG 58.229 37.500 0.00 0.00 0.00 2.74
2731 2924 5.171476 ACTACCATCACGAGATTCAACAAG 58.829 41.667 0.00 0.00 30.20 3.16
2769 2962 2.316677 TCTGGGTGGACTGGGTTAGATA 59.683 50.000 0.00 0.00 0.00 1.98
3029 3223 2.515057 TGGCACGGTTGACACCAC 60.515 61.111 0.00 0.00 44.53 4.16
3074 3268 2.819019 TGGTATATGATGCAAATGGCCG 59.181 45.455 0.00 0.00 43.89 6.13
3100 3294 2.028130 CTCCTCTACGGACAGATTGCT 58.972 52.381 0.00 0.00 36.69 3.91
3136 3330 2.489329 CCACAACATCCTCATCACCAAC 59.511 50.000 0.00 0.00 0.00 3.77
3181 3375 1.474478 TCAGTGACATCCGAGCTCTTC 59.526 52.381 12.85 1.02 0.00 2.87
3199 3393 4.600576 TTCGCTGCGGCAGTGTCA 62.601 61.111 34.59 23.26 41.99 3.58


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

AutoCloner maintained by Alex Coulton.