Multiple sequence alignment - TraesCS7D01G036000

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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 TraesCS7D01G036000 chr7D 100.000 3023 0 0 1 3023 18427255 18424233 0.000000e+00 5583.0
1 TraesCS7D01G036000 chr7D 84.384 365 43 11 1933 2291 18409964 18409608 2.230000e-91 346.0
2 TraesCS7D01G036000 chr7D 91.228 57 4 1 2790 2845 18393358 18393302 3.230000e-10 76.8
3 TraesCS7D01G036000 chr7D 88.889 63 6 1 2425 2486 18393444 18393382 3.230000e-10 76.8
4 TraesCS7D01G036000 chr7A 91.287 1274 61 12 662 1915 18875527 18874284 0.000000e+00 1692.0
5 TraesCS7D01G036000 chr7A 81.796 824 85 28 1933 2697 18874223 18873406 5.500000e-177 630.0
6 TraesCS7D01G036000 chr7A 92.638 163 11 1 1 162 18876207 18876045 1.810000e-57 233.0
7 TraesCS7D01G036000 chr7A 91.200 125 11 0 361 485 18875814 18875690 1.440000e-38 171.0
8 TraesCS7D01G036000 chr7A 80.342 234 36 6 2425 2648 18800016 18799783 5.180000e-38 169.0
9 TraesCS7D01G036000 chr7A 82.123 179 11 5 185 363 18876055 18875898 1.890000e-27 134.0
10 TraesCS7D01G036000 chrUn 89.824 1307 70 13 642 1915 50833967 50832691 0.000000e+00 1618.0
11 TraesCS7D01G036000 chrUn 92.321 1120 52 13 1937 3023 50832627 50831509 0.000000e+00 1561.0
12 TraesCS7D01G036000 chrUn 93.664 363 20 2 1 363 50835062 50834703 9.530000e-150 540.0
13 TraesCS7D01G036000 chrUn 84.507 355 36 10 1933 2275 50797706 50797359 1.740000e-87 333.0
14 TraesCS7D01G036000 chrUn 84.507 355 36 10 1933 2275 355087574 355087227 1.740000e-87 333.0
15 TraesCS7D01G036000 chrUn 84.507 355 36 10 1933 2275 413652532 413652185 1.740000e-87 333.0
16 TraesCS7D01G036000 chrUn 88.757 169 12 5 361 528 50834583 50834421 1.840000e-47 200.0
17 TraesCS7D01G036000 chrUn 83.636 220 27 4 2438 2648 50924578 50924359 6.610000e-47 198.0
18 TraesCS7D01G036000 chrUn 82.500 120 11 3 2735 2845 50924250 50924132 2.480000e-16 97.1


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 TraesCS7D01G036000 chr7D 18424233 18427255 3022 True 5583.00 5583 100.0000 1 3023 1 chr7D.!!$R2 3022
1 TraesCS7D01G036000 chr7A 18873406 18876207 2801 True 572.00 1692 87.8088 1 2697 5 chr7A.!!$R2 2696
2 TraesCS7D01G036000 chrUn 50831509 50835062 3553 True 979.75 1618 91.1415 1 3023 4 chrUn.!!$R4 3022

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
510 637 0.107831 CCCACCGAAGTTCAAGTCCA 59.892 55.0 3.32 0.0 0.0 4.02 F
690 1170 0.517316 AGCTCAAAAACGGTCGATGC 59.483 50.0 0.00 0.0 0.0 3.91 F
852 1347 0.963355 TACCAAATTCAGGCCACCGC 60.963 55.0 5.01 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1538 2051 0.321564 CTCAACCTCATCCACCGCAA 60.322 55.0 0.00 0.00 0.00 4.85 R
1655 2168 0.323178 CTTGCCAGCACCATTCTCCT 60.323 55.0 0.00 0.00 0.00 3.69 R
2057 2617 0.749454 GCATCACCGGCAGGAAAGAT 60.749 55.0 10.86 7.13 41.02 2.40 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
259 261 1.063469 GTTCGTTATCCGGCAACATGG 59.937 52.381 16.10 3.67 37.11 3.66
327 329 1.344191 GGGAGGAGCTGGCTTCATCT 61.344 60.000 3.56 0.00 0.00 2.90
377 504 2.307392 TCAGCATACTAGTTGCCCCAAA 59.693 45.455 19.73 5.48 41.06 3.28
381 508 3.761752 GCATACTAGTTGCCCCAAAAGAA 59.238 43.478 15.14 0.00 33.95 2.52
473 600 1.061546 TGGGTGGTTAGGAGGACAAC 58.938 55.000 0.00 0.00 0.00 3.32
481 608 3.006644 GGTTAGGAGGACAACGATATCCC 59.993 52.174 0.00 0.00 35.38 3.85
484 611 1.344763 GGAGGACAACGATATCCCCAG 59.655 57.143 0.00 0.00 35.38 4.45
485 612 2.040178 GAGGACAACGATATCCCCAGT 58.960 52.381 0.00 0.00 35.38 4.00
486 613 2.036089 GAGGACAACGATATCCCCAGTC 59.964 54.545 0.00 0.99 35.38 3.51
487 614 1.070289 GGACAACGATATCCCCAGTCC 59.930 57.143 12.64 12.64 37.50 3.85
488 615 1.760613 GACAACGATATCCCCAGTCCA 59.239 52.381 0.00 0.00 0.00 4.02
489 616 1.485066 ACAACGATATCCCCAGTCCAC 59.515 52.381 0.00 0.00 0.00 4.02
510 637 0.107831 CCCACCGAAGTTCAAGTCCA 59.892 55.000 3.32 0.00 0.00 4.02
511 638 1.226746 CCACCGAAGTTCAAGTCCAC 58.773 55.000 3.32 0.00 0.00 4.02
526 653 3.262420 AGTCCACGACTTACATTGATGC 58.738 45.455 0.00 0.00 40.28 3.91
527 654 3.055819 AGTCCACGACTTACATTGATGCT 60.056 43.478 0.00 0.00 40.28 3.79
530 657 3.063997 CCACGACTTACATTGATGCTTCC 59.936 47.826 0.00 0.00 0.00 3.46
531 658 3.063997 CACGACTTACATTGATGCTTCCC 59.936 47.826 0.00 0.00 0.00 3.97
533 660 3.689161 CGACTTACATTGATGCTTCCCAA 59.311 43.478 0.00 0.00 0.00 4.12
542 696 2.756207 TGATGCTTCCCAATGATGTGTG 59.244 45.455 0.00 0.00 0.00 3.82
545 699 2.964464 TGCTTCCCAATGATGTGTGTTT 59.036 40.909 0.00 0.00 0.00 2.83
547 701 4.586421 TGCTTCCCAATGATGTGTGTTTAA 59.414 37.500 0.00 0.00 0.00 1.52
551 705 6.907853 TCCCAATGATGTGTGTTTAATGAA 57.092 33.333 0.00 0.00 0.00 2.57
553 707 7.377398 TCCCAATGATGTGTGTTTAATGAAAG 58.623 34.615 0.00 0.00 0.00 2.62
557 711 7.765695 ATGATGTGTGTTTAATGAAAGGAGT 57.234 32.000 0.00 0.00 0.00 3.85
558 712 7.581213 TGATGTGTGTTTAATGAAAGGAGTT 57.419 32.000 0.00 0.00 0.00 3.01
585 741 0.646381 TGACAACGAAAACGTCACCG 59.354 50.000 0.00 0.00 34.83 4.94
588 744 0.646381 CAACGAAAACGTCACCGACA 59.354 50.000 9.77 0.00 37.88 4.35
600 756 3.131396 GTCACCGACAACTTCATCAAGT 58.869 45.455 0.00 0.00 45.43 3.16
617 773 8.593492 TCATCAAGTTCAAGATAATATGTCGG 57.407 34.615 0.00 0.00 0.00 4.79
625 781 6.582636 TCAAGATAATATGTCGGCTCAGTTT 58.417 36.000 0.00 0.00 0.00 2.66
626 782 6.479990 TCAAGATAATATGTCGGCTCAGTTTG 59.520 38.462 0.00 0.00 0.00 2.93
633 789 1.176619 TCGGCTCAGTTTGTCGGAGA 61.177 55.000 0.00 0.00 40.01 3.71
651 1131 2.297315 GAGACGGATGCATAGGATGTGA 59.703 50.000 0.00 0.00 0.00 3.58
654 1134 3.405831 ACGGATGCATAGGATGTGAATG 58.594 45.455 0.00 0.00 0.00 2.67
661 1141 5.798015 GCATAGGATGTGAATGCATAGAG 57.202 43.478 0.00 0.00 44.27 2.43
664 1144 3.051581 AGGATGTGAATGCATAGAGGGT 58.948 45.455 0.00 0.00 0.00 4.34
670 1150 7.665559 GGATGTGAATGCATAGAGGGTTTTATA 59.334 37.037 0.00 0.00 0.00 0.98
671 1151 8.995027 ATGTGAATGCATAGAGGGTTTTATAA 57.005 30.769 0.00 0.00 0.00 0.98
672 1152 8.450578 TGTGAATGCATAGAGGGTTTTATAAG 57.549 34.615 0.00 0.00 0.00 1.73
673 1153 7.013274 TGTGAATGCATAGAGGGTTTTATAAGC 59.987 37.037 0.00 0.00 0.00 3.09
674 1154 7.229506 GTGAATGCATAGAGGGTTTTATAAGCT 59.770 37.037 0.00 0.00 32.40 3.74
675 1155 7.445402 TGAATGCATAGAGGGTTTTATAAGCTC 59.555 37.037 0.00 0.00 32.40 4.09
677 1157 6.658849 TGCATAGAGGGTTTTATAAGCTCAA 58.341 36.000 0.00 0.00 32.40 3.02
678 1158 7.116075 TGCATAGAGGGTTTTATAAGCTCAAA 58.884 34.615 0.00 0.00 32.40 2.69
679 1159 7.613801 TGCATAGAGGGTTTTATAAGCTCAAAA 59.386 33.333 0.00 0.00 32.40 2.44
680 1160 8.466798 GCATAGAGGGTTTTATAAGCTCAAAAA 58.533 33.333 0.00 0.00 32.40 1.94
682 1162 6.909909 AGAGGGTTTTATAAGCTCAAAAACG 58.090 36.000 17.79 0.00 41.70 3.60
684 1164 5.537295 AGGGTTTTATAAGCTCAAAAACGGT 59.463 36.000 17.79 9.69 41.70 4.83
687 1167 6.365050 GTTTTATAAGCTCAAAAACGGTCGA 58.635 36.000 12.62 0.00 34.51 4.20
688 1168 6.730960 TTTATAAGCTCAAAAACGGTCGAT 57.269 33.333 0.00 0.00 0.00 3.59
689 1169 2.969443 AAGCTCAAAAACGGTCGATG 57.031 45.000 0.00 0.00 0.00 3.84
690 1170 0.517316 AGCTCAAAAACGGTCGATGC 59.483 50.000 0.00 0.00 0.00 3.91
778 1258 2.023015 GGGGAAGGGAAGGGAAATCAAT 60.023 50.000 0.00 0.00 0.00 2.57
779 1259 3.300388 GGGAAGGGAAGGGAAATCAATC 58.700 50.000 0.00 0.00 0.00 2.67
780 1260 3.300388 GGAAGGGAAGGGAAATCAATCC 58.700 50.000 0.00 0.00 38.86 3.01
781 1261 3.309848 GGAAGGGAAGGGAAATCAATCCA 60.310 47.826 0.00 0.00 41.55 3.41
782 1262 4.550669 GAAGGGAAGGGAAATCAATCCAT 58.449 43.478 0.00 0.00 41.55 3.41
851 1346 1.094785 CTACCAAATTCAGGCCACCG 58.905 55.000 5.01 0.00 0.00 4.94
852 1347 0.963355 TACCAAATTCAGGCCACCGC 60.963 55.000 5.01 0.00 0.00 5.68
853 1348 2.179018 CAAATTCAGGCCACCGCG 59.821 61.111 5.01 0.00 35.02 6.46
854 1349 3.061848 AAATTCAGGCCACCGCGG 61.062 61.111 26.86 26.86 35.02 6.46
961 1468 4.028490 CCGCAACCCTAGCACCCA 62.028 66.667 0.00 0.00 0.00 4.51
963 1470 2.332654 CGCAACCCTAGCACCCAAC 61.333 63.158 0.00 0.00 0.00 3.77
1210 1720 2.805353 CCAACGAGCTCGACGTGG 60.805 66.667 40.58 34.01 43.16 4.94
1346 1856 3.974835 ATGCCGATGACAAGCCGCA 62.975 57.895 0.00 0.00 0.00 5.69
1347 1857 3.430862 GCCGATGACAAGCCGCAA 61.431 61.111 0.00 0.00 0.00 4.85
1499 2009 2.890474 GCCCCACACGTATGCGAG 60.890 66.667 11.07 4.30 42.00 5.03
1500 2010 2.890474 CCCCACACGTATGCGAGC 60.890 66.667 11.07 0.00 42.00 5.03
1506 2019 4.266070 ACGTATGCGAGCGCCGAT 62.266 61.111 20.06 12.93 41.76 4.18
1534 2047 3.075005 AGATGGTCGGTGGGTCGG 61.075 66.667 0.00 0.00 0.00 4.79
1660 2173 3.147595 CGGCGATGGTGGAGGAGA 61.148 66.667 0.00 0.00 0.00 3.71
1662 2175 1.832912 GGCGATGGTGGAGGAGAAT 59.167 57.895 0.00 0.00 0.00 2.40
1713 2226 1.883638 GCTGTGGTCAAGAGCAATCCA 60.884 52.381 3.23 0.00 40.82 3.41
1717 2230 3.507233 TGTGGTCAAGAGCAATCCATTTC 59.493 43.478 3.23 0.00 40.82 2.17
1736 2249 3.038788 TCTTCAGTCAGCATTGCGTTA 57.961 42.857 2.38 0.00 0.00 3.18
1740 2253 2.009051 CAGTCAGCATTGCGTTATGGA 58.991 47.619 2.38 0.00 0.00 3.41
1743 2256 2.030946 GTCAGCATTGCGTTATGGAGAC 59.969 50.000 2.38 0.02 0.00 3.36
1763 2276 1.059913 AAGGAGGTGTCAGAGGTTGG 58.940 55.000 0.00 0.00 0.00 3.77
1929 2475 0.171007 CGGTGGTGATGGCATTGAAC 59.829 55.000 0.00 0.74 0.00 3.18
1995 2550 1.688772 GGAGGGCACTGTCGATACTA 58.311 55.000 0.00 0.00 0.00 1.82
2007 2562 4.933330 TGTCGATACTAGCAGAACCAATC 58.067 43.478 0.00 0.00 0.00 2.67
2019 2574 3.100671 AGAACCAATCGAGAAGCCTAGT 58.899 45.455 0.00 0.00 0.00 2.57
2082 2642 3.746949 CTGCCGGTGATGCTCTCCC 62.747 68.421 1.90 0.00 0.00 4.30
2083 2643 3.785859 GCCGGTGATGCTCTCCCA 61.786 66.667 1.90 0.00 0.00 4.37
2092 2664 4.518211 GGTGATGCTCTCCCATTTCTTATG 59.482 45.833 0.00 0.00 0.00 1.90
2128 2700 1.604378 CTTGGAGATCCTTGCCGGT 59.396 57.895 1.90 0.00 36.82 5.28
2157 2743 7.763985 TCGAAACATATTGTTGATAGAAGCAGA 59.236 33.333 0.00 0.00 40.14 4.26
2186 2772 1.612950 TGCATGGTTAGTTGCTTGTGG 59.387 47.619 0.00 0.00 39.60 4.17
2199 2785 5.408299 AGTTGCTTGTGGAAACAAGTTTTTC 59.592 36.000 17.31 4.07 46.36 2.29
2312 2899 7.612065 TTGGTTCCTACATATGTAGCTATGT 57.388 36.000 29.91 0.27 44.97 2.29
2385 2972 3.427909 GCCAATTGCTGATTCGAATGTCA 60.428 43.478 16.96 8.38 36.87 3.58
2389 2976 6.974048 CCAATTGCTGATTCGAATGTCAATTA 59.026 34.615 25.21 8.86 33.15 1.40
2406 2993 2.579410 TTACTTTCAGGGAACAGGCC 57.421 50.000 0.00 0.00 0.00 5.19
2433 3020 5.300969 TGCTTCATTATCTTGTTCTGTGC 57.699 39.130 0.00 0.00 0.00 4.57
2452 3039 2.156117 TGCGACGAGAACAAATTTACCG 59.844 45.455 0.00 0.00 0.00 4.02
2523 3132 9.897744 CTTCTTGACAATTAGAATGCTGTTTAA 57.102 29.630 0.00 0.00 30.57 1.52
2681 3311 2.032799 CGGCGTATTATGCACATTTGGT 59.967 45.455 9.96 0.00 0.00 3.67
3001 3632 8.475639 ACCATCTATCTTTGTATTAAGTGACGT 58.524 33.333 0.00 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.136500 CCTACTGGGTAAGCGGTTCTC 59.864 57.143 1.59 0.00 0.00 2.87
26 27 2.814805 ATTGAGGGCTGCACTTATGT 57.185 45.000 5.59 0.00 0.00 2.29
214 216 5.205821 TGTTCCATAGCTAGTGTTAGGCTA 58.794 41.667 0.00 0.00 41.77 3.93
259 261 4.035102 GCCACCCCACCTGTCTCC 62.035 72.222 0.00 0.00 0.00 3.71
349 351 3.034635 CAACTAGTATGCTGACCCCTCT 58.965 50.000 0.00 0.00 0.00 3.69
359 486 3.352648 TCTTTTGGGGCAACTAGTATGC 58.647 45.455 16.84 16.84 43.08 3.14
451 578 2.354328 TGTCCTCCTAACCACCCAAAT 58.646 47.619 0.00 0.00 0.00 2.32
473 600 1.006102 GCGTGGACTGGGGATATCG 60.006 63.158 0.00 0.00 0.00 2.92
484 611 3.819877 AACTTCGGTGGGCGTGGAC 62.820 63.158 0.00 0.00 0.00 4.02
485 612 3.524648 GAACTTCGGTGGGCGTGGA 62.525 63.158 0.00 0.00 0.00 4.02
486 613 3.047877 GAACTTCGGTGGGCGTGG 61.048 66.667 0.00 0.00 0.00 4.94
487 614 1.841663 CTTGAACTTCGGTGGGCGTG 61.842 60.000 0.00 0.00 0.00 5.34
488 615 1.597027 CTTGAACTTCGGTGGGCGT 60.597 57.895 0.00 0.00 0.00 5.68
489 616 1.566018 GACTTGAACTTCGGTGGGCG 61.566 60.000 0.00 0.00 0.00 6.13
510 637 3.270877 GGGAAGCATCAATGTAAGTCGT 58.729 45.455 0.00 0.00 0.00 4.34
511 638 3.270027 TGGGAAGCATCAATGTAAGTCG 58.730 45.455 0.00 0.00 0.00 4.18
517 644 4.028131 ACATCATTGGGAAGCATCAATGT 58.972 39.130 13.45 0.00 46.01 2.71
518 645 4.142026 ACACATCATTGGGAAGCATCAATG 60.142 41.667 9.08 9.08 46.77 2.82
519 646 4.028131 ACACATCATTGGGAAGCATCAAT 58.972 39.130 0.00 0.00 34.31 2.57
520 647 3.193903 CACACATCATTGGGAAGCATCAA 59.806 43.478 0.00 0.00 0.00 2.57
522 649 2.756760 ACACACATCATTGGGAAGCATC 59.243 45.455 0.00 0.00 0.00 3.91
523 650 2.811410 ACACACATCATTGGGAAGCAT 58.189 42.857 0.00 0.00 0.00 3.79
524 651 2.291209 ACACACATCATTGGGAAGCA 57.709 45.000 0.00 0.00 0.00 3.91
525 652 3.665745 AAACACACATCATTGGGAAGC 57.334 42.857 0.00 0.00 0.00 3.86
526 653 6.923012 TCATTAAACACACATCATTGGGAAG 58.077 36.000 0.00 0.00 0.00 3.46
527 654 6.907853 TCATTAAACACACATCATTGGGAA 57.092 33.333 0.00 0.00 0.00 3.97
530 657 7.377398 TCCTTTCATTAAACACACATCATTGG 58.623 34.615 0.00 0.00 0.00 3.16
531 658 8.084073 ACTCCTTTCATTAAACACACATCATTG 58.916 33.333 0.00 0.00 0.00 2.82
533 660 7.765695 ACTCCTTTCATTAAACACACATCAT 57.234 32.000 0.00 0.00 0.00 2.45
542 696 6.068473 ACGGAACAACTCCTTTCATTAAAC 57.932 37.500 0.00 0.00 42.85 2.01
545 699 5.237779 GTCAACGGAACAACTCCTTTCATTA 59.762 40.000 0.00 0.00 42.85 1.90
547 701 3.564225 GTCAACGGAACAACTCCTTTCAT 59.436 43.478 0.00 0.00 42.85 2.57
551 705 2.681344 GTTGTCAACGGAACAACTCCTT 59.319 45.455 17.46 0.00 42.85 3.36
553 707 2.750301 GTTGTCAACGGAACAACTCC 57.250 50.000 17.46 0.00 40.17 3.85
600 756 6.161855 ACTGAGCCGACATATTATCTTGAA 57.838 37.500 0.00 0.00 0.00 2.69
604 760 5.918608 ACAAACTGAGCCGACATATTATCT 58.081 37.500 0.00 0.00 0.00 1.98
606 762 4.745125 CGACAAACTGAGCCGACATATTAT 59.255 41.667 0.00 0.00 0.00 1.28
607 763 4.109766 CGACAAACTGAGCCGACATATTA 58.890 43.478 0.00 0.00 0.00 0.98
608 764 2.930040 CGACAAACTGAGCCGACATATT 59.070 45.455 0.00 0.00 0.00 1.28
609 765 2.540515 CGACAAACTGAGCCGACATAT 58.459 47.619 0.00 0.00 0.00 1.78
610 766 1.403647 CCGACAAACTGAGCCGACATA 60.404 52.381 0.00 0.00 0.00 2.29
611 767 0.670546 CCGACAAACTGAGCCGACAT 60.671 55.000 0.00 0.00 0.00 3.06
612 768 1.300620 CCGACAAACTGAGCCGACA 60.301 57.895 0.00 0.00 0.00 4.35
613 769 1.006571 TCCGACAAACTGAGCCGAC 60.007 57.895 0.00 0.00 0.00 4.79
614 770 1.176619 TCTCCGACAAACTGAGCCGA 61.177 55.000 0.00 0.00 31.43 5.54
615 771 1.009389 GTCTCCGACAAACTGAGCCG 61.009 60.000 0.00 0.00 32.09 5.52
616 772 1.009389 CGTCTCCGACAAACTGAGCC 61.009 60.000 0.00 0.00 35.63 4.70
617 773 1.009389 CCGTCTCCGACAAACTGAGC 61.009 60.000 0.00 0.00 35.63 4.26
625 781 0.668535 CTATGCATCCGTCTCCGACA 59.331 55.000 0.19 0.00 35.63 4.35
626 782 0.039074 CCTATGCATCCGTCTCCGAC 60.039 60.000 0.19 0.00 35.63 4.79
633 789 3.405831 CATTCACATCCTATGCATCCGT 58.594 45.455 0.19 0.00 0.00 4.69
634 790 2.161012 GCATTCACATCCTATGCATCCG 59.839 50.000 0.19 0.00 43.13 4.18
640 796 5.183969 CCCTCTATGCATTCACATCCTATG 58.816 45.833 3.54 0.00 0.00 2.23
651 1131 7.290061 TGAGCTTATAAAACCCTCTATGCATT 58.710 34.615 3.54 0.00 0.00 3.56
654 1134 7.568199 TTTGAGCTTATAAAACCCTCTATGC 57.432 36.000 0.00 0.00 0.00 3.14
656 1136 8.674607 CGTTTTTGAGCTTATAAAACCCTCTAT 58.325 33.333 18.35 0.00 38.09 1.98
659 1139 6.090783 CCGTTTTTGAGCTTATAAAACCCTC 58.909 40.000 18.35 0.00 38.09 4.30
661 1141 5.775686 ACCGTTTTTGAGCTTATAAAACCC 58.224 37.500 18.35 7.75 38.09 4.11
664 1144 6.542574 TCGACCGTTTTTGAGCTTATAAAA 57.457 33.333 0.00 0.00 0.00 1.52
670 1150 1.069227 GCATCGACCGTTTTTGAGCTT 60.069 47.619 0.00 0.00 0.00 3.74
671 1151 0.517316 GCATCGACCGTTTTTGAGCT 59.483 50.000 0.00 0.00 0.00 4.09
672 1152 0.454452 GGCATCGACCGTTTTTGAGC 60.454 55.000 0.00 0.00 0.00 4.26
673 1153 0.871722 TGGCATCGACCGTTTTTGAG 59.128 50.000 0.00 0.00 0.00 3.02
674 1154 0.871722 CTGGCATCGACCGTTTTTGA 59.128 50.000 0.00 0.00 0.00 2.69
675 1155 0.729140 GCTGGCATCGACCGTTTTTG 60.729 55.000 0.00 0.00 0.00 2.44
677 1157 1.577328 CTGCTGGCATCGACCGTTTT 61.577 55.000 0.00 0.00 0.00 2.43
678 1158 2.031919 TGCTGGCATCGACCGTTT 59.968 55.556 0.00 0.00 0.00 3.60
679 1159 2.434884 CTGCTGGCATCGACCGTT 60.435 61.111 0.00 0.00 0.00 4.44
680 1160 4.457496 CCTGCTGGCATCGACCGT 62.457 66.667 0.00 0.00 0.00 4.83
682 1162 2.512515 GACCTGCTGGCATCGACC 60.513 66.667 9.95 0.00 36.63 4.79
684 1164 4.147449 CCGACCTGCTGGCATCGA 62.147 66.667 19.87 0.00 34.85 3.59
778 1258 1.427895 TTTGGACCGTTGGGGATGGA 61.428 55.000 0.00 0.00 39.97 3.41
779 1259 1.075836 TTTGGACCGTTGGGGATGG 59.924 57.895 0.00 0.00 39.97 3.51
780 1260 1.248101 GGTTTGGACCGTTGGGGATG 61.248 60.000 0.00 0.00 39.97 3.51
781 1261 1.076014 GGTTTGGACCGTTGGGGAT 59.924 57.895 0.00 0.00 39.97 3.85
782 1262 2.516909 GGTTTGGACCGTTGGGGA 59.483 61.111 0.00 0.00 39.97 4.81
854 1349 4.193334 GGATTTGAAGGCGGCCGC 62.193 66.667 41.63 41.63 41.06 6.53
855 1350 3.518068 GGGATTTGAAGGCGGCCG 61.518 66.667 24.05 24.05 0.00 6.13
856 1351 3.147595 GGGGATTTGAAGGCGGCC 61.148 66.667 12.11 12.11 0.00 6.13
857 1352 3.147595 GGGGGATTTGAAGGCGGC 61.148 66.667 0.00 0.00 0.00 6.53
943 1450 4.796495 GGGTGCTAGGGTTGCGGG 62.796 72.222 0.00 0.00 0.00 6.13
1210 1720 4.900154 CTCCTCGAGGAACTGCAC 57.100 61.111 32.94 0.00 44.91 4.57
1277 1787 2.279120 CGGAGCTGACGAGGCATC 60.279 66.667 0.00 0.00 0.00 3.91
1278 1788 3.842923 CCGGAGCTGACGAGGCAT 61.843 66.667 0.00 0.00 0.00 4.40
1288 1798 4.421479 CTTGACGACGCCGGAGCT 62.421 66.667 5.05 0.00 40.78 4.09
1362 1872 2.852075 ACCGGAAACCTGGGCAGA 60.852 61.111 9.46 0.00 0.00 4.26
1398 1908 3.823421 CTAACACACGACCGCGCG 61.823 66.667 25.67 25.67 42.48 6.86
1399 1909 4.130281 GCTAACACACGACCGCGC 62.130 66.667 0.00 0.00 42.48 6.86
1506 2019 2.362503 ACCATCTCGCCCGACTCA 60.363 61.111 0.00 0.00 0.00 3.41
1534 2047 3.499737 CTCATCCACCGCAACCGC 61.500 66.667 0.00 0.00 0.00 5.68
1538 2051 0.321564 CTCAACCTCATCCACCGCAA 60.322 55.000 0.00 0.00 0.00 4.85
1655 2168 0.323178 CTTGCCAGCACCATTCTCCT 60.323 55.000 0.00 0.00 0.00 3.69
1660 2173 2.284112 CCCCTTGCCAGCACCATT 60.284 61.111 0.00 0.00 0.00 3.16
1662 2175 3.506743 TTCCCCTTGCCAGCACCA 61.507 61.111 0.00 0.00 0.00 4.17
1713 2226 2.816087 ACGCAATGCTGACTGAAGAAAT 59.184 40.909 2.94 0.00 0.00 2.17
1717 2230 3.486375 CCATAACGCAATGCTGACTGAAG 60.486 47.826 2.94 0.00 0.00 3.02
1736 2249 1.905215 CTGACACCTCCTTGTCTCCAT 59.095 52.381 4.97 0.00 45.34 3.41
1740 2253 1.133009 ACCTCTGACACCTCCTTGTCT 60.133 52.381 4.97 0.00 45.34 3.41
1743 2256 1.271054 CCAACCTCTGACACCTCCTTG 60.271 57.143 0.00 0.00 0.00 3.61
1873 2386 3.181474 GGAACTATCCTCTTCCGACCTTG 60.181 52.174 0.00 0.00 42.93 3.61
1874 2387 3.032459 GGAACTATCCTCTTCCGACCTT 58.968 50.000 0.00 0.00 42.93 3.50
1929 2475 1.726533 GGCCCTTACGGTCTCTCGAG 61.727 65.000 5.93 5.93 31.28 4.04
1995 2550 1.677217 GGCTTCTCGATTGGTTCTGCT 60.677 52.381 0.00 0.00 0.00 4.24
2007 2562 2.100584 AGCAGATCAACTAGGCTTCTCG 59.899 50.000 0.00 0.00 0.00 4.04
2019 2574 4.882842 TGGTAAGTGTACAGCAGATCAA 57.117 40.909 0.00 0.00 31.21 2.57
2057 2617 0.749454 GCATCACCGGCAGGAAAGAT 60.749 55.000 10.86 7.13 41.02 2.40
2082 2642 3.313526 CACCGGGAAGAGCATAAGAAATG 59.686 47.826 6.32 0.00 0.00 2.32
2083 2643 3.545703 CACCGGGAAGAGCATAAGAAAT 58.454 45.455 6.32 0.00 0.00 2.17
2128 2700 9.554724 GCTTCTATCAACAATATGTTTCGAAAA 57.445 29.630 13.10 3.75 38.77 2.29
2157 2743 5.243730 AGCAACTAACCATGCAGTATGTTTT 59.756 36.000 0.00 0.00 44.95 2.43
2169 2755 3.957497 TGTTTCCACAAGCAACTAACCAT 59.043 39.130 0.00 0.00 0.00 3.55
2186 2772 9.445786 TTGAGATGAATACGAAAAACTTGTTTC 57.554 29.630 0.00 0.00 34.71 2.78
2199 2785 7.693951 GTCAGGTTCAAAATTGAGATGAATACG 59.306 37.037 7.93 0.00 38.61 3.06
2312 2899 3.790223 GGCCAACCTGAATGCCAA 58.210 55.556 0.00 0.00 43.46 4.52
2385 2972 3.431415 GGCCTGTTCCCTGAAAGTAATT 58.569 45.455 0.00 0.00 0.00 1.40
2389 2976 1.073199 CGGCCTGTTCCCTGAAAGT 59.927 57.895 0.00 0.00 0.00 2.66
2406 2993 2.292267 ACAAGATAATGAAGCAGGCCG 58.708 47.619 0.00 0.00 0.00 6.13
2433 3020 2.410730 AGCGGTAAATTTGTTCTCGTCG 59.589 45.455 0.00 0.00 0.00 5.12
2505 3109 5.807011 GGCCAGTTAAACAGCATTCTAATTG 59.193 40.000 0.00 0.00 0.00 2.32
2611 3224 5.426833 ACCTAGCATGAGAAACTAACAGGAT 59.573 40.000 0.00 0.00 0.00 3.24
2616 3229 6.401153 CGTTCAACCTAGCATGAGAAACTAAC 60.401 42.308 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.