Multiple sequence alignment - TraesCS1A01G235300

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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 TraesCS1A01G235300 chr1A 100.000 2420 0 0 1 2420 415641009 415643428 0.000000e+00 4470.0
1 TraesCS1A01G235300 chr1B 89.433 1306 69 26 483 1746 439448107 439449385 0.000000e+00 1583.0
2 TraesCS1A01G235300 chr1B 84.064 684 96 9 1745 2420 439449533 439450211 0.000000e+00 647.0
3 TraesCS1A01G235300 chr1B 91.102 472 28 5 1 463 439447655 439448121 5.680000e-176 627.0
4 TraesCS1A01G235300 chr1D 91.537 898 42 20 592 1485 326167909 326168776 0.000000e+00 1206.0
5 TraesCS1A01G235300 chr1D 93.564 404 22 2 6 409 326167494 326167893 1.240000e-167 599.0
6 TraesCS1A01G235300 chr1D 83.908 522 76 6 1745 2262 326169036 326169553 2.160000e-135 492.0
7 TraesCS1A01G235300 chr1D 90.909 220 17 3 1508 1727 326168766 326168982 2.350000e-75 292.0
8 TraesCS1A01G235300 chr2D 80.511 313 58 3 1942 2254 596984029 596983720 1.120000e-58 237.0
9 TraesCS1A01G235300 chr5A 81.429 280 49 3 1956 2235 654123138 654122862 2.420000e-55 226.0
10 TraesCS1A01G235300 chr5A 74.229 454 100 13 1975 2420 668903415 668902971 8.890000e-40 174.0
11 TraesCS1A01G235300 chr4A 72.356 662 139 29 1761 2413 136752929 136752303 4.140000e-38 169.0
12 TraesCS1A01G235300 chr4B 75.815 368 64 18 2043 2405 414866438 414866785 1.930000e-36 163.0
13 TraesCS1A01G235300 chr4B 83.077 65 10 1 2186 2249 148134456 148134520 9.350000e-05 58.4
14 TraesCS1A01G235300 chr4B 83.077 65 10 1 2186 2249 148167519 148167583 9.350000e-05 58.4
15 TraesCS1A01G235300 chr3A 89.000 100 7 4 2140 2236 693344405 693344307 1.180000e-23 121.0


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 TraesCS1A01G235300 chr1A 415641009 415643428 2419 False 4470.000000 4470 100.000000 1 2420 1 chr1A.!!$F1 2419
1 TraesCS1A01G235300 chr1B 439447655 439450211 2556 False 952.333333 1583 88.199667 1 2420 3 chr1B.!!$F1 2419
2 TraesCS1A01G235300 chr1D 326167494 326169553 2059 False 647.250000 1206 89.979500 6 2262 4 chr1D.!!$F1 2256

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
686 715 0.02811 GGCTACGTGCTTTGCTATGC 59.972 55.0 0.0 0.0 42.39 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1499 1555 0.036164 TGTGTTGAACTCATCCCCCG 59.964 55.0 0.0 0.0 0.0 5.73 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
111 112 6.955963 CACTGTTGTCGATAAAAGCATTAGTC 59.044 38.462 11.67 0.00 0.00 2.59
157 158 2.775911 ATATGTGGATGGATGGCTCG 57.224 50.000 0.00 0.00 0.00 5.03
171 172 1.136305 TGGCTCGTACTATTGCAGGTC 59.864 52.381 0.00 0.00 0.00 3.85
173 174 2.464865 GCTCGTACTATTGCAGGTCAG 58.535 52.381 0.00 0.00 0.00 3.51
181 182 2.116983 ATTGCAGGTCAGCGTCAGGT 62.117 55.000 0.00 0.00 37.31 4.00
195 196 2.166459 CGTCAGGTTGAGAGATAAGCCA 59.834 50.000 0.00 0.00 0.00 4.75
199 200 4.718774 TCAGGTTGAGAGATAAGCCAGAAT 59.281 41.667 0.00 0.00 0.00 2.40
203 204 6.069731 AGGTTGAGAGATAAGCCAGAATTCTT 60.070 38.462 4.86 0.00 0.00 2.52
205 206 5.923204 TGAGAGATAAGCCAGAATTCTTCC 58.077 41.667 4.86 0.00 0.00 3.46
207 208 4.061596 GAGATAAGCCAGAATTCTTCCCG 58.938 47.826 4.86 0.00 0.00 5.14
219 220 1.101635 TCTTCCCGATGAGCGTCGAT 61.102 55.000 13.22 0.00 44.06 3.59
403 407 4.948004 TGACGTACTACATGACTTGAGGAT 59.052 41.667 0.00 0.00 0.00 3.24
444 448 3.118629 CCCTATGTCTATGTGTGCAGTGT 60.119 47.826 0.00 0.00 0.00 3.55
445 449 3.867493 CCTATGTCTATGTGTGCAGTGTG 59.133 47.826 0.00 0.00 0.00 3.82
446 450 2.908688 TGTCTATGTGTGCAGTGTGT 57.091 45.000 0.00 0.00 0.00 3.72
447 451 2.482864 TGTCTATGTGTGCAGTGTGTG 58.517 47.619 0.00 0.00 0.00 3.82
448 452 2.102252 TGTCTATGTGTGCAGTGTGTGA 59.898 45.455 0.00 0.00 0.00 3.58
452 456 1.748950 TGTGTGCAGTGTGTGATGTT 58.251 45.000 0.00 0.00 0.00 2.71
453 457 2.090760 TGTGTGCAGTGTGTGATGTTT 58.909 42.857 0.00 0.00 0.00 2.83
454 458 2.159407 TGTGTGCAGTGTGTGATGTTTG 60.159 45.455 0.00 0.00 0.00 2.93
455 459 1.404748 TGTGCAGTGTGTGATGTTTGG 59.595 47.619 0.00 0.00 0.00 3.28
456 460 1.405105 GTGCAGTGTGTGATGTTTGGT 59.595 47.619 0.00 0.00 0.00 3.67
457 461 1.404748 TGCAGTGTGTGATGTTTGGTG 59.595 47.619 0.00 0.00 0.00 4.17
458 462 1.865248 GCAGTGTGTGATGTTTGGTGC 60.865 52.381 0.00 0.00 0.00 5.01
459 463 1.032014 AGTGTGTGATGTTTGGTGCC 58.968 50.000 0.00 0.00 0.00 5.01
460 464 0.743688 GTGTGTGATGTTTGGTGCCA 59.256 50.000 0.00 0.00 0.00 4.92
461 465 1.031235 TGTGTGATGTTTGGTGCCAG 58.969 50.000 0.00 0.00 0.00 4.85
462 466 1.032014 GTGTGATGTTTGGTGCCAGT 58.968 50.000 0.00 0.00 0.00 4.00
463 467 1.408702 GTGTGATGTTTGGTGCCAGTT 59.591 47.619 0.00 0.00 0.00 3.16
464 468 1.680735 TGTGATGTTTGGTGCCAGTTC 59.319 47.619 0.00 0.00 0.00 3.01
465 469 1.956477 GTGATGTTTGGTGCCAGTTCT 59.044 47.619 0.00 0.00 0.00 3.01
466 470 1.955778 TGATGTTTGGTGCCAGTTCTG 59.044 47.619 0.00 0.00 0.00 3.02
467 471 1.956477 GATGTTTGGTGCCAGTTCTGT 59.044 47.619 0.00 0.00 0.00 3.41
468 472 1.388547 TGTTTGGTGCCAGTTCTGTC 58.611 50.000 0.00 0.00 0.00 3.51
469 473 1.340502 TGTTTGGTGCCAGTTCTGTCA 60.341 47.619 0.00 0.00 0.00 3.58
470 474 1.748493 GTTTGGTGCCAGTTCTGTCAA 59.252 47.619 0.00 0.00 0.00 3.18
471 475 2.136298 TTGGTGCCAGTTCTGTCAAA 57.864 45.000 0.00 0.00 0.00 2.69
472 476 2.136298 TGGTGCCAGTTCTGTCAAAA 57.864 45.000 0.00 0.00 0.00 2.44
473 477 2.451490 TGGTGCCAGTTCTGTCAAAAA 58.549 42.857 0.00 0.00 0.00 1.94
501 505 1.032014 ATGTTTGGTGCCAGTGTCAC 58.968 50.000 0.00 0.00 0.00 3.67
525 529 5.422331 CCTATAGGTTCAGGTTCAGTCAAGA 59.578 44.000 10.96 0.00 0.00 3.02
585 589 2.284552 ATGGGCCGGGCAATGTTT 60.285 55.556 30.95 0.00 0.00 2.83
631 660 9.388506 AGATGATTCGAGTATGAAAGAACAAAT 57.611 29.630 0.00 0.00 0.00 2.32
641 670 4.196193 TGAAAGAACAAATCGTGTCCTGT 58.804 39.130 0.00 0.00 40.60 4.00
642 671 4.638421 TGAAAGAACAAATCGTGTCCTGTT 59.362 37.500 0.00 0.00 40.60 3.16
646 675 6.687081 AGAACAAATCGTGTCCTGTTTTTA 57.313 33.333 0.00 0.00 40.60 1.52
683 712 0.391130 CTGGGCTACGTGCTTTGCTA 60.391 55.000 0.00 0.00 42.39 3.49
684 713 0.251916 TGGGCTACGTGCTTTGCTAT 59.748 50.000 0.00 0.00 42.39 2.97
685 714 0.657840 GGGCTACGTGCTTTGCTATG 59.342 55.000 0.00 0.00 42.39 2.23
686 715 0.028110 GGCTACGTGCTTTGCTATGC 59.972 55.000 0.00 0.00 42.39 3.14
687 716 1.009829 GCTACGTGCTTTGCTATGCT 58.990 50.000 0.00 0.00 38.95 3.79
690 719 1.297158 CGTGCTTTGCTATGCTCGC 60.297 57.895 14.86 2.95 38.84 5.03
729 768 4.072088 GCGCCCGCGTATGTATGC 62.072 66.667 11.18 0.00 42.09 3.14
731 770 2.657757 CGCCCGCGTATGTATGCAG 61.658 63.158 4.92 0.00 38.09 4.41
732 771 1.594293 GCCCGCGTATGTATGCAGT 60.594 57.895 4.92 0.00 38.09 4.40
733 772 0.319211 GCCCGCGTATGTATGCAGTA 60.319 55.000 4.92 0.00 38.09 2.74
734 773 1.671850 GCCCGCGTATGTATGCAGTAT 60.672 52.381 4.92 0.00 38.09 2.12
735 774 1.992667 CCCGCGTATGTATGCAGTATG 59.007 52.381 4.92 0.00 38.09 2.39
755 794 2.180086 TGCTGGTAGATGAGATAGGGGT 59.820 50.000 0.00 0.00 0.00 4.95
776 818 4.522789 GGTTTTCACCTGAAATAGAAGGCA 59.477 41.667 1.35 0.00 42.83 4.75
860 905 6.490381 GTGATTCCCTTTTACTTTTCTGGACT 59.510 38.462 0.00 0.00 0.00 3.85
863 908 4.102054 TCCCTTTTACTTTTCTGGACTCGT 59.898 41.667 0.00 0.00 0.00 4.18
940 985 3.964875 CCGCGCAGGTTTGTTGCT 61.965 61.111 8.75 0.00 39.38 3.91
980 1025 1.135333 CTCCCTCCTCTGTCTAAACGC 59.865 57.143 0.00 0.00 0.00 4.84
981 1026 0.895530 CCCTCCTCTGTCTAAACGCA 59.104 55.000 0.00 0.00 0.00 5.24
1020 1067 4.560108 GCAATGCCTCAGAAGACACATTTT 60.560 41.667 0.00 0.00 0.00 1.82
1035 1082 7.260603 AGACACATTTTCCTTTCTTCACTTTG 58.739 34.615 0.00 0.00 0.00 2.77
1063 1110 6.582295 GCTCTTTCAGATTCAGATAGATCGAC 59.418 42.308 0.00 0.00 0.00 4.20
1086 1133 3.883549 GGAGCCATGCCTCTCCCC 61.884 72.222 3.38 0.00 42.30 4.81
1230 1279 0.396435 AGAACGACAGGTGCCATCAA 59.604 50.000 0.00 0.00 0.00 2.57
1239 1288 5.567423 CGACAGGTGCCATCAATGATATCTA 60.567 44.000 3.98 0.00 0.00 1.98
1243 1292 5.545335 AGGTGCCATCAATGATATCTACTCA 59.455 40.000 3.98 0.00 0.00 3.41
1260 1309 0.114364 TCACCTCACCTGGAGCACTA 59.886 55.000 0.00 0.00 42.62 2.74
1261 1310 0.534412 CACCTCACCTGGAGCACTAG 59.466 60.000 0.00 0.00 42.62 2.57
1262 1311 0.115349 ACCTCACCTGGAGCACTAGT 59.885 55.000 0.00 0.00 42.62 2.57
1263 1312 1.358103 ACCTCACCTGGAGCACTAGTA 59.642 52.381 0.00 0.00 42.62 1.82
1268 1317 2.826128 CACCTGGAGCACTAGTACTTCA 59.174 50.000 0.00 3.96 0.00 3.02
1356 1405 2.113139 CTTGTGCCCCTGACGGTT 59.887 61.111 0.00 0.00 0.00 4.44
1359 1408 3.637273 GTGCCCCTGACGGTTCCT 61.637 66.667 0.00 0.00 0.00 3.36
1485 1541 2.558378 AGGCATCATGAGTTCATCACG 58.442 47.619 0.09 0.00 41.91 4.35
1486 1542 1.600957 GGCATCATGAGTTCATCACGG 59.399 52.381 0.09 0.00 41.91 4.94
1489 1545 3.127548 GCATCATGAGTTCATCACGGTTT 59.872 43.478 0.09 0.00 41.91 3.27
1514 1570 0.111446 TTTGCGGGGGATGAGTTCAA 59.889 50.000 0.00 0.00 0.00 2.69
1522 1578 2.554032 GGGGATGAGTTCAACACACTTG 59.446 50.000 0.00 0.00 0.00 3.16
1538 1594 8.767085 CAACACACTTGAGATTGCAATATTTTT 58.233 29.630 12.97 0.00 0.00 1.94
1539 1595 8.524870 ACACACTTGAGATTGCAATATTTTTC 57.475 30.769 12.97 0.00 0.00 2.29
1596 1654 1.883926 CTTTGGGGAAAACTACGGTGG 59.116 52.381 0.00 0.00 0.00 4.61
1599 1657 1.279846 TGGGGAAAACTACGGTGGATC 59.720 52.381 0.00 0.00 0.00 3.36
1681 1740 6.649557 AGCCGATTCCTTATAATTTAACTCCG 59.350 38.462 0.00 0.00 0.00 4.63
1716 1775 9.413048 CTCTAACCGATCTTGTATAATCCTTTC 57.587 37.037 0.00 0.00 0.00 2.62
1732 1791 4.553678 TCCTTTCGTGGAGGATAATAGGT 58.446 43.478 1.05 0.00 38.37 3.08
1754 1962 1.070289 GCTAATTGGACCCCTACTCGG 59.930 57.143 0.00 0.00 0.00 4.63
1759 1967 3.766691 GACCCCTACTCGGCGCAA 61.767 66.667 10.83 0.00 0.00 4.85
1763 1971 2.813908 CCTACTCGGCGCAACCAC 60.814 66.667 10.83 0.00 39.03 4.16
1775 1983 3.575247 AACCACCACCGATGCCCA 61.575 61.111 0.00 0.00 0.00 5.36
1776 1984 3.860930 AACCACCACCGATGCCCAC 62.861 63.158 0.00 0.00 0.00 4.61
1783 1991 2.367202 ACCGATGCCCACGATTCCT 61.367 57.895 0.00 0.00 0.00 3.36
1785 1993 1.153369 CGATGCCCACGATTCCTGT 60.153 57.895 0.00 0.00 0.00 4.00
1793 2001 1.065491 CCACGATTCCTGTTGGGATGA 60.065 52.381 0.00 0.00 44.66 2.92
1809 2017 2.291217 GGATGAAGAGGCAAGACCCTTT 60.291 50.000 0.00 0.00 40.58 3.11
1811 2019 1.270839 TGAAGAGGCAAGACCCTTTCG 60.271 52.381 0.00 0.00 40.58 3.46
1862 2073 1.658994 GTTGTCAGAAACGACCACCA 58.341 50.000 0.00 0.00 36.41 4.17
1863 2074 2.011222 GTTGTCAGAAACGACCACCAA 58.989 47.619 0.00 0.00 36.41 3.67
1879 2090 4.794648 AAGCCGCCGCCTGCATTA 62.795 61.111 0.00 0.00 41.33 1.90
1999 2210 4.681978 GCTGCTCCAACCGTCGGT 62.682 66.667 12.23 12.23 37.65 4.69
2016 2227 1.377333 GTAAGCGGGCAAGGAAGCT 60.377 57.895 0.00 0.00 42.35 3.74
2056 2267 4.162690 GCCGAGGAGGTGGCGAAT 62.163 66.667 0.00 0.00 42.22 3.34
2117 2328 3.441290 CGCCTCGGACCTCGTCTT 61.441 66.667 0.00 0.00 40.32 3.01
2132 2343 0.962356 GTCTTCGACCACCCCTACGA 60.962 60.000 0.00 0.00 0.00 3.43
2141 2352 1.000107 ACCCCTACGACCACTCCTC 60.000 63.158 0.00 0.00 0.00 3.71
2147 2358 2.759641 TACGACCACTCCTCTGGCGT 62.760 60.000 10.84 10.84 42.65 5.68
2153 2364 3.374402 CTCCTCTGGCGTGTCCGT 61.374 66.667 0.00 0.00 37.80 4.69
2254 2465 0.878416 TAGTCGGTGCATTGTTTGGC 59.122 50.000 0.00 0.00 0.00 4.52
2258 2469 1.069823 TCGGTGCATTGTTTGGCATTT 59.930 42.857 0.00 0.00 42.75 2.32
2262 2473 4.314121 GGTGCATTGTTTGGCATTTCTTA 58.686 39.130 0.00 0.00 42.75 2.10
2264 2475 4.749099 GTGCATTGTTTGGCATTTCTTACA 59.251 37.500 0.00 0.00 42.75 2.41
2265 2476 5.236047 GTGCATTGTTTGGCATTTCTTACAA 59.764 36.000 0.00 0.00 42.75 2.41
2297 2511 7.116233 GGGTGATGAATATTGTTGTTGTTGTTC 59.884 37.037 0.00 0.00 0.00 3.18
2311 2525 0.741574 TTGTTCTTGTCGTGGTGCGT 60.742 50.000 0.00 0.00 42.13 5.24
2319 2533 0.989890 GTCGTGGTGCGTAGATGAAC 59.010 55.000 0.00 0.00 42.13 3.18
2320 2534 0.599060 TCGTGGTGCGTAGATGAACA 59.401 50.000 0.00 0.00 42.13 3.18
2324 2538 1.693083 GGTGCGTAGATGAACACGGC 61.693 60.000 0.00 0.00 38.57 5.68
2327 2541 0.457853 GCGTAGATGAACACGGCTGA 60.458 55.000 0.00 0.00 38.57 4.26
2332 2546 4.565166 CGTAGATGAACACGGCTGAAATTA 59.435 41.667 0.00 0.00 34.57 1.40
2337 2551 5.446143 TGAACACGGCTGAAATTATTGTT 57.554 34.783 0.00 0.00 0.00 2.83
2388 2602 5.293079 GGCTTGACAATCTCAACTATGACTC 59.707 44.000 0.00 0.00 33.65 3.36
2389 2603 5.005203 GCTTGACAATCTCAACTATGACTCG 59.995 44.000 0.00 0.00 33.65 4.18
2390 2604 5.897377 TGACAATCTCAACTATGACTCGA 57.103 39.130 0.00 0.00 0.00 4.04
2391 2605 6.456795 TGACAATCTCAACTATGACTCGAT 57.543 37.500 0.00 0.00 0.00 3.59
2396 2610 5.897377 TCTCAACTATGACTCGATGTTCA 57.103 39.130 0.00 0.00 0.00 3.18
2409 2623 4.445453 TCGATGTTCAATCATCAAGAGGG 58.555 43.478 7.32 0.00 42.82 4.30
2415 2629 2.237143 TCAATCATCAAGAGGGCGAAGT 59.763 45.455 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 3.960571 ACCATTTCAGATTCCACCTCTG 58.039 45.455 0.00 0.00 41.23 3.35
111 112 9.976511 ATAATTCAGAATTTCATACAAGGCATG 57.023 29.630 13.71 0.00 32.38 4.06
157 158 2.194271 GACGCTGACCTGCAATAGTAC 58.806 52.381 0.00 0.00 0.00 2.73
171 172 3.443037 CTTATCTCTCAACCTGACGCTG 58.557 50.000 0.00 0.00 0.00 5.18
173 174 2.197577 GCTTATCTCTCAACCTGACGC 58.802 52.381 0.00 0.00 0.00 5.19
181 182 6.352516 GGAAGAATTCTGGCTTATCTCTCAA 58.647 40.000 9.17 0.00 46.56 3.02
195 196 1.482593 ACGCTCATCGGGAAGAATTCT 59.517 47.619 0.88 0.88 42.91 2.40
199 200 1.138883 CGACGCTCATCGGGAAGAA 59.861 57.895 0.00 0.00 43.86 2.52
203 204 1.172812 ATCATCGACGCTCATCGGGA 61.173 55.000 0.00 2.20 42.50 5.14
205 206 0.239613 AGATCATCGACGCTCATCGG 59.760 55.000 0.00 0.00 42.50 4.18
207 208 2.695613 TGAGATCATCGACGCTCATC 57.304 50.000 0.00 0.00 32.85 2.92
219 220 5.596361 GTCCCTAAACAGAGAGATGAGATCA 59.404 44.000 0.00 0.00 0.00 2.92
237 238 2.123428 GGCCGCTACTTCGTCCCTA 61.123 63.158 0.00 0.00 0.00 3.53
357 358 1.523095 GCTCAGACGTTCAAGACACAC 59.477 52.381 0.00 0.00 0.00 3.82
403 407 1.545428 GGGAGCACACCACAGAAATGA 60.545 52.381 0.00 0.00 0.00 2.57
444 448 1.680735 GAACTGGCACCAAACATCACA 59.319 47.619 0.00 0.00 0.00 3.58
445 449 1.956477 AGAACTGGCACCAAACATCAC 59.044 47.619 0.00 0.00 0.00 3.06
446 450 1.955778 CAGAACTGGCACCAAACATCA 59.044 47.619 0.00 0.00 0.00 3.07
447 451 1.956477 ACAGAACTGGCACCAAACATC 59.044 47.619 6.76 0.00 34.19 3.06
448 452 1.956477 GACAGAACTGGCACCAAACAT 59.044 47.619 2.50 0.00 38.82 2.71
471 475 7.972832 CACTGGCACCAAACATTTTTAATTTTT 59.027 29.630 0.00 0.00 0.00 1.94
472 476 7.121907 ACACTGGCACCAAACATTTTTAATTTT 59.878 29.630 0.00 0.00 0.00 1.82
473 477 6.601217 ACACTGGCACCAAACATTTTTAATTT 59.399 30.769 0.00 0.00 0.00 1.82
474 478 6.118852 ACACTGGCACCAAACATTTTTAATT 58.881 32.000 0.00 0.00 0.00 1.40
475 479 5.679601 ACACTGGCACCAAACATTTTTAAT 58.320 33.333 0.00 0.00 0.00 1.40
476 480 5.091261 ACACTGGCACCAAACATTTTTAA 57.909 34.783 0.00 0.00 0.00 1.52
477 481 4.160439 TGACACTGGCACCAAACATTTTTA 59.840 37.500 0.00 0.00 0.00 1.52
478 482 3.055530 TGACACTGGCACCAAACATTTTT 60.056 39.130 0.00 0.00 0.00 1.94
479 483 2.499289 TGACACTGGCACCAAACATTTT 59.501 40.909 0.00 0.00 0.00 1.82
480 484 2.106566 TGACACTGGCACCAAACATTT 58.893 42.857 0.00 0.00 0.00 2.32
481 485 1.408702 GTGACACTGGCACCAAACATT 59.591 47.619 3.28 0.00 0.00 2.71
501 505 5.422331 TCTTGACTGAACCTGAACCTATAGG 59.578 44.000 17.73 17.73 40.01 2.57
525 529 1.001974 TGTAGAAACACCGCAGCTCAT 59.998 47.619 0.00 0.00 0.00 2.90
585 589 1.349357 TGTGCATAGGCCAACACAGTA 59.651 47.619 5.01 0.00 38.07 2.74
631 660 5.613329 ACTTGGTATAAAAACAGGACACGA 58.387 37.500 0.00 0.00 0.00 4.35
642 671 9.238368 CCCAGTTTTCATAGACTTGGTATAAAA 57.762 33.333 0.00 0.00 0.00 1.52
646 675 5.044846 AGCCCAGTTTTCATAGACTTGGTAT 60.045 40.000 0.00 0.00 32.72 2.73
683 712 1.144936 GCCTAGGACAAGCGAGCAT 59.855 57.895 14.75 0.00 0.00 3.79
684 713 1.617018 ATGCCTAGGACAAGCGAGCA 61.617 55.000 14.75 0.00 0.00 4.26
685 714 0.878086 GATGCCTAGGACAAGCGAGC 60.878 60.000 14.75 0.00 0.00 5.03
686 715 0.596083 CGATGCCTAGGACAAGCGAG 60.596 60.000 14.75 0.00 0.00 5.03
687 716 1.320344 ACGATGCCTAGGACAAGCGA 61.320 55.000 24.28 2.44 0.00 4.93
690 719 4.686554 GCTATAAACGATGCCTAGGACAAG 59.313 45.833 14.75 10.93 0.00 3.16
729 768 5.126869 CCCTATCTCATCTACCAGCATACTG 59.873 48.000 0.00 0.00 44.05 2.74
731 770 4.404073 CCCCTATCTCATCTACCAGCATAC 59.596 50.000 0.00 0.00 0.00 2.39
732 771 4.045974 ACCCCTATCTCATCTACCAGCATA 59.954 45.833 0.00 0.00 0.00 3.14
733 772 3.181402 ACCCCTATCTCATCTACCAGCAT 60.181 47.826 0.00 0.00 0.00 3.79
734 773 2.180086 ACCCCTATCTCATCTACCAGCA 59.820 50.000 0.00 0.00 0.00 4.41
735 774 2.896039 ACCCCTATCTCATCTACCAGC 58.104 52.381 0.00 0.00 0.00 4.85
736 775 5.366768 TGAAAACCCCTATCTCATCTACCAG 59.633 44.000 0.00 0.00 0.00 4.00
737 776 5.130477 GTGAAAACCCCTATCTCATCTACCA 59.870 44.000 0.00 0.00 0.00 3.25
738 777 5.454897 GGTGAAAACCCCTATCTCATCTACC 60.455 48.000 0.00 0.00 0.00 3.18
751 790 4.462834 CCTTCTATTTCAGGTGAAAACCCC 59.537 45.833 9.13 0.00 45.81 4.95
755 794 4.218417 GCTGCCTTCTATTTCAGGTGAAAA 59.782 41.667 9.13 0.00 45.81 2.29
882 927 2.505777 CAGCAGCTCGTCGGTCTG 60.506 66.667 0.00 9.36 0.00 3.51
968 1013 1.864711 GCTTGTGTGCGTTTAGACAGA 59.135 47.619 0.00 0.00 0.00 3.41
980 1025 2.249309 CGCCGAACAGCTTGTGTG 59.751 61.111 0.00 0.00 40.26 3.82
981 1026 3.649986 GCGCCGAACAGCTTGTGT 61.650 61.111 0.00 0.00 43.24 3.72
1020 1067 4.526970 AGAGCAACAAAGTGAAGAAAGGA 58.473 39.130 0.00 0.00 0.00 3.36
1086 1133 0.675522 ACCCCATTACAAGGTTCGCG 60.676 55.000 0.00 0.00 0.00 5.87
1223 1270 6.047511 AGGTGAGTAGATATCATTGATGGC 57.952 41.667 9.46 1.45 0.00 4.40
1230 1279 5.083122 CCAGGTGAGGTGAGTAGATATCAT 58.917 45.833 5.32 0.00 0.00 2.45
1239 1288 1.152247 TGCTCCAGGTGAGGTGAGT 60.152 57.895 0.00 0.00 41.73 3.41
1243 1292 0.115349 ACTAGTGCTCCAGGTGAGGT 59.885 55.000 0.00 0.00 41.73 3.85
1356 1405 1.831106 ACAGCCACGATTATGACAGGA 59.169 47.619 0.00 0.00 0.00 3.86
1359 1408 2.760634 ACACAGCCACGATTATGACA 57.239 45.000 0.00 0.00 0.00 3.58
1497 1553 1.002624 GTTGAACTCATCCCCCGCA 60.003 57.895 0.00 0.00 0.00 5.69
1498 1554 1.002624 TGTTGAACTCATCCCCCGC 60.003 57.895 0.00 0.00 0.00 6.13
1499 1555 0.036164 TGTGTTGAACTCATCCCCCG 59.964 55.000 0.00 0.00 0.00 5.73
1500 1556 1.073923 AGTGTGTTGAACTCATCCCCC 59.926 52.381 3.25 0.00 0.00 5.40
1501 1557 2.554032 CAAGTGTGTTGAACTCATCCCC 59.446 50.000 3.25 0.00 0.00 4.81
1514 1570 8.362639 AGAAAAATATTGCAATCTCAAGTGTGT 58.637 29.630 16.86 0.00 0.00 3.72
1617 1675 9.770097 ACACCTCAGTTATAATATGATCAAGTG 57.230 33.333 0.00 10.32 0.00 3.16
1618 1676 9.770097 CACACCTCAGTTATAATATGATCAAGT 57.230 33.333 0.00 0.00 0.00 3.16
1663 1722 7.788026 TGCTCTTCGGAGTTAAATTATAAGGA 58.212 34.615 0.00 0.00 43.59 3.36
1681 1740 4.846779 AGATCGGTTAGAGATGCTCTTC 57.153 45.455 1.88 0.00 41.50 2.87
1716 1775 1.971357 AGCCACCTATTATCCTCCACG 59.029 52.381 0.00 0.00 0.00 4.94
1730 1789 1.133884 GTAGGGGTCCAATTAGCCACC 60.134 57.143 0.00 0.00 38.85 4.61
1732 1791 2.124411 GAGTAGGGGTCCAATTAGCCA 58.876 52.381 0.00 0.00 38.85 4.75
1754 1962 4.101790 CATCGGTGGTGGTTGCGC 62.102 66.667 0.00 0.00 0.00 6.09
1759 1967 4.344865 GTGGGCATCGGTGGTGGT 62.345 66.667 0.00 0.00 0.00 4.16
1763 1971 2.124736 AATCGTGGGCATCGGTGG 60.125 61.111 0.00 0.00 0.00 4.61
1783 1991 1.704628 TCTTGCCTCTTCATCCCAACA 59.295 47.619 0.00 0.00 0.00 3.33
1785 1993 1.004745 GGTCTTGCCTCTTCATCCCAA 59.995 52.381 0.00 0.00 0.00 4.12
1793 2001 0.606673 GCGAAAGGGTCTTGCCTCTT 60.607 55.000 0.00 0.00 37.43 2.85
1847 2058 0.534203 GGCTTGGTGGTCGTTTCTGA 60.534 55.000 0.00 0.00 0.00 3.27
1898 2109 1.704641 GTGGCTCCAAGGAGGTTTTT 58.295 50.000 17.34 0.00 42.19 1.94
1906 2117 2.352805 GGTGAGGTGGCTCCAAGG 59.647 66.667 8.51 0.00 39.02 3.61
1930 2141 1.292223 GACCTTGCTGTCAGCGGTA 59.708 57.895 20.49 8.69 46.26 4.02
1999 2210 1.377202 CAGCTTCCTTGCCCGCTTA 60.377 57.895 0.00 0.00 0.00 3.09
2056 2267 2.979678 AGCCACCTTCTTGTCCTTCTTA 59.020 45.455 0.00 0.00 0.00 2.10
2117 2328 2.361610 GGTCGTAGGGGTGGTCGA 60.362 66.667 0.00 0.00 0.00 4.20
2235 2446 0.878416 GCCAAACAATGCACCGACTA 59.122 50.000 0.00 0.00 0.00 2.59
2236 2447 1.106351 TGCCAAACAATGCACCGACT 61.106 50.000 0.00 0.00 31.31 4.18
2254 2465 6.828273 TCATCACCCTATGGTTGTAAGAAATG 59.172 38.462 0.00 0.00 44.75 2.32
2258 2469 6.575244 ATTCATCACCCTATGGTTGTAAGA 57.425 37.500 0.00 0.00 44.75 2.10
2262 2473 6.672593 ACAATATTCATCACCCTATGGTTGT 58.327 36.000 0.00 0.00 44.75 3.32
2264 2475 7.125391 ACAACAATATTCATCACCCTATGGTT 58.875 34.615 0.00 0.00 44.75 3.67
2281 2492 6.024664 CACGACAAGAACAACAACAACAATA 58.975 36.000 0.00 0.00 0.00 1.90
2311 2525 6.597672 ACAATAATTTCAGCCGTGTTCATCTA 59.402 34.615 0.00 0.00 0.00 1.98
2319 2533 5.046910 AGACAACAATAATTTCAGCCGTG 57.953 39.130 0.00 0.00 0.00 4.94
2320 2534 5.705609 AAGACAACAATAATTTCAGCCGT 57.294 34.783 0.00 0.00 0.00 5.68
2324 2538 7.885297 TCCTCCAAAGACAACAATAATTTCAG 58.115 34.615 0.00 0.00 0.00 3.02
2327 2541 7.308589 CGACTCCTCCAAAGACAACAATAATTT 60.309 37.037 0.00 0.00 0.00 1.82
2332 2546 3.071023 TCGACTCCTCCAAAGACAACAAT 59.929 43.478 0.00 0.00 0.00 2.71
2337 2551 4.680708 GCATATTCGACTCCTCCAAAGACA 60.681 45.833 0.00 0.00 0.00 3.41
2388 2602 3.003068 GCCCTCTTGATGATTGAACATCG 59.997 47.826 0.00 0.00 46.49 3.84
2389 2603 3.003068 CGCCCTCTTGATGATTGAACATC 59.997 47.826 0.00 0.00 44.58 3.06
2390 2604 2.947652 CGCCCTCTTGATGATTGAACAT 59.052 45.455 0.00 0.00 0.00 2.71
2391 2605 2.027285 TCGCCCTCTTGATGATTGAACA 60.027 45.455 0.00 0.00 0.00 3.18
2396 2610 2.636830 CACTTCGCCCTCTTGATGATT 58.363 47.619 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.