Multiple sequence alignment - TraesCS4A01G101500

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 TraesCS4A01G101500 chr4A 100.000 3500 0 0 1 3500 113852265 113855764 0.000000e+00 6464.0
1 TraesCS4A01G101500 chr4A 86.696 451 40 9 310 746 120453618 120453174 1.890000e-132 483.0
2 TraesCS4A01G101500 chr4A 96.732 153 5 0 767 919 120413656 120413504 4.480000e-64 255.0
3 TraesCS4A01G101500 chr4A 93.548 62 4 0 916 977 120389676 120389615 3.720000e-15 93.5
4 TraesCS4A01G101500 chr4B 92.938 2563 108 26 1 2547 434471036 434468531 0.000000e+00 3663.0
5 TraesCS4A01G101500 chr4B 92.795 916 52 10 2591 3500 434468535 434467628 0.000000e+00 1314.0
6 TraesCS4A01G101500 chr4B 96.154 52 1 1 1627 1677 21371137 21371188 2.240000e-12 84.2
7 TraesCS4A01G101500 chr4D 93.757 1842 62 28 1676 3500 351466806 351465001 0.000000e+00 2715.0
8 TraesCS4A01G101500 chr4D 93.163 863 37 5 767 1629 351467647 351466807 0.000000e+00 1247.0
9 TraesCS4A01G101500 chr4D 93.213 663 35 3 1 654 351468328 351467667 0.000000e+00 966.0
10 TraesCS4A01G101500 chr2D 94.444 54 2 1 1625 1677 420169489 420169436 8.050000e-12 82.4
11 TraesCS4A01G101500 chr7D 95.652 46 1 1 1628 1672 468940473 468940428 4.850000e-09 73.1
12 TraesCS4A01G101500 chrUn 92.157 51 2 2 1628 1677 356424642 356424593 1.740000e-08 71.3
13 TraesCS4A01G101500 chr3B 95.455 44 2 0 719 762 108816065 108816108 1.740000e-08 71.3
14 TraesCS4A01G101500 chr3B 95.556 45 1 1 1634 1677 802617417 802617373 1.740000e-08 71.3
15 TraesCS4A01G101500 chr2B 92.157 51 3 1 1628 1677 508006136 508006186 1.740000e-08 71.3
16 TraesCS4A01G101500 chr3D 97.500 40 1 0 719 758 65310221 65310260 6.270000e-08 69.4
17 TraesCS4A01G101500 chr7A 91.837 49 3 1 1628 1675 711827740 711827692 2.250000e-07 67.6
18 TraesCS4A01G101500 chr6A 91.667 48 3 1 1631 1677 585483184 585483137 8.110000e-07 65.8
19 TraesCS4A01G101500 chr3A 88.636 44 5 0 713 756 746216570 746216527 2.000000e-03 54.7


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 TraesCS4A01G101500 chr4A 113852265 113855764 3499 False 6464.000000 6464 100.000000 1 3500 1 chr4A.!!$F1 3499
1 TraesCS4A01G101500 chr4B 434467628 434471036 3408 True 2488.500000 3663 92.866500 1 3500 2 chr4B.!!$R1 3499
2 TraesCS4A01G101500 chr4D 351465001 351468328 3327 True 1642.666667 2715 93.377667 1 3500 3 chr4D.!!$R1 3499

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
303 312 0.381801 CGTGCTTGTGGTTTTGCTCT 59.618 50.0 0.0 0.0 0.00 4.09 F
1428 1458 0.038744 AGTTTCACCTCCATGGCAGG 59.961 55.0 21.9 21.9 40.22 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1930 1966 0.035056 AGTCCAGAAAATCCAGGCGG 60.035 55.0 0.00 0.0 0.00 6.13 R
2908 2965 0.369931 TGCGCACTCGATTCATTTCG 59.630 50.0 5.66 0.0 40.46 3.46 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
206 215 5.163290 TGGCACGAATATATGTAACCTGGAA 60.163 40.000 0.00 0.00 0.00 3.53
283 292 7.177878 ACTCAGGTTTTTCATCCAAGTGATAT 58.822 34.615 0.00 0.00 30.56 1.63
284 293 7.337942 ACTCAGGTTTTTCATCCAAGTGATATC 59.662 37.037 0.00 0.00 30.56 1.63
292 301 3.610040 TCCAAGTGATATCGTGCTTGT 57.390 42.857 21.95 0.00 37.28 3.16
303 312 0.381801 CGTGCTTGTGGTTTTGCTCT 59.618 50.000 0.00 0.00 0.00 4.09
317 326 5.586243 GGTTTTGCTCTGATGCAGTATCTAA 59.414 40.000 0.00 0.00 44.27 2.10
346 356 0.679505 TGGCGCTTGACTGTCTTACT 59.320 50.000 7.64 0.00 0.00 2.24
437 450 4.009675 TCCTTGTACCATCATGCTTTGTC 58.990 43.478 0.00 0.00 0.00 3.18
452 465 5.129634 TGCTTTGTCCACATTCAGAACTTA 58.870 37.500 0.00 0.00 0.00 2.24
536 550 8.344098 GTGGTAAGCAGTACTATAAGTCTGTAG 58.656 40.741 0.00 0.00 32.80 2.74
565 579 3.572584 CTTTGCAGTGAGATGGCTTTTC 58.427 45.455 0.00 0.00 0.00 2.29
647 661 9.396022 CATCTATGTAGTTAAACCACAGGAAAT 57.604 33.333 0.00 0.00 0.00 2.17
663 677 3.054361 AGGAAATGGAGAATGCGTTAGGT 60.054 43.478 0.00 0.00 33.19 3.08
665 679 3.627395 AATGGAGAATGCGTTAGGTCA 57.373 42.857 0.00 0.00 32.28 4.02
667 681 2.176045 TGGAGAATGCGTTAGGTCAGA 58.824 47.619 0.00 0.00 0.00 3.27
676 692 3.003378 TGCGTTAGGTCAGACATATCTCG 59.997 47.826 2.17 6.73 30.42 4.04
707 724 3.266636 CCACAGGAAACAAACCAAAACC 58.733 45.455 0.00 0.00 0.00 3.27
721 738 4.208746 ACCAAAACCGACCAAGTTATGAA 58.791 39.130 0.00 0.00 0.00 2.57
726 743 4.877378 ACCGACCAAGTTATGAACTACA 57.123 40.909 0.00 0.00 41.91 2.74
762 779 9.139174 CCAAAATATAAGACGATTTTGCTGTTT 57.861 29.630 12.44 0.00 45.44 2.83
813 830 1.072505 GTCCCCTTTTGTCAGCCGA 59.927 57.895 0.00 0.00 0.00 5.54
831 848 1.537776 CGATGGCCAGCACAAAACAAA 60.538 47.619 22.95 0.00 0.00 2.83
991 1008 1.613437 GCTAGGATCAGAGCTCCACTC 59.387 57.143 10.93 4.27 46.66 3.51
1011 1028 2.170166 CAAGGTGAAATGGCAAGCCTA 58.830 47.619 12.96 0.00 36.94 3.93
1036 1053 5.525378 CAGAGCTTGATATCCAAACAGGTAC 59.475 44.000 0.00 0.00 39.02 3.34
1037 1054 4.442706 AGCTTGATATCCAAACAGGTACG 58.557 43.478 0.00 0.00 39.02 3.67
1038 1055 4.081087 AGCTTGATATCCAAACAGGTACGT 60.081 41.667 0.00 0.00 39.02 3.57
1039 1056 5.128171 AGCTTGATATCCAAACAGGTACGTA 59.872 40.000 0.00 0.00 39.02 3.57
1047 1064 3.500680 CCAAACAGGTACGTATGTGCTTT 59.499 43.478 0.00 1.30 0.00 3.51
1092 1109 3.926616 TCTTGATTTCGTTCCTGGACTC 58.073 45.455 0.00 0.00 0.00 3.36
1098 1116 0.966920 TCGTTCCTGGACTCAGAACC 59.033 55.000 0.00 0.00 43.49 3.62
1131 1149 1.797537 GTTGATTGCGCCGAACTGC 60.798 57.895 4.18 0.00 0.00 4.40
1226 1244 4.739195 GAGAAGAGTAATTCTCGTGTGCT 58.261 43.478 1.08 0.00 44.13 4.40
1227 1245 4.489810 AGAAGAGTAATTCTCGTGTGCTG 58.510 43.478 0.00 0.00 46.86 4.41
1228 1246 3.944055 AGAGTAATTCTCGTGTGCTGT 57.056 42.857 0.00 0.00 46.86 4.40
1229 1247 4.258702 AGAGTAATTCTCGTGTGCTGTT 57.741 40.909 0.00 0.00 46.86 3.16
1230 1248 4.238514 AGAGTAATTCTCGTGTGCTGTTC 58.761 43.478 0.00 0.00 46.86 3.18
1231 1249 3.987868 GAGTAATTCTCGTGTGCTGTTCA 59.012 43.478 0.00 0.00 33.25 3.18
1283 1313 8.743714 ACAGGAAAAATTGTTGATAGAATCTCC 58.256 33.333 0.00 0.00 0.00 3.71
1297 1327 4.034410 AGAATCTCCCTTCCTGACCTTAC 58.966 47.826 0.00 0.00 0.00 2.34
1417 1447 6.423604 CCCATTGTTAATTGTTCAGTTTCACC 59.576 38.462 0.00 0.00 0.00 4.02
1428 1458 0.038744 AGTTTCACCTCCATGGCAGG 59.961 55.000 21.90 21.90 40.22 4.85
1475 1510 7.510549 TCAGCTTGTTAAATATTAGCATCCC 57.489 36.000 9.29 0.00 34.37 3.85
1476 1511 6.490040 TCAGCTTGTTAAATATTAGCATCCCC 59.510 38.462 9.29 0.00 34.37 4.81
1477 1512 6.265196 CAGCTTGTTAAATATTAGCATCCCCA 59.735 38.462 9.29 0.00 34.37 4.96
1478 1513 7.012607 AGCTTGTTAAATATTAGCATCCCCAT 58.987 34.615 9.29 0.00 34.37 4.00
1479 1514 7.039504 AGCTTGTTAAATATTAGCATCCCCATG 60.040 37.037 9.29 0.00 34.37 3.66
1480 1515 7.255942 GCTTGTTAAATATTAGCATCCCCATGT 60.256 37.037 2.87 0.00 31.86 3.21
1481 1516 9.295825 CTTGTTAAATATTAGCATCCCCATGTA 57.704 33.333 0.00 0.00 31.86 2.29
1482 1517 8.630054 TGTTAAATATTAGCATCCCCATGTAC 57.370 34.615 0.00 0.00 31.86 2.90
1483 1518 8.221251 TGTTAAATATTAGCATCCCCATGTACA 58.779 33.333 0.00 0.00 31.86 2.90
1545 1580 8.826765 TCCTAGATTTCAGAAGTACCAAAGAAT 58.173 33.333 0.00 0.00 0.00 2.40
1640 1675 4.018960 TGTTTACTAGTACTCCCTCCGTCT 60.019 45.833 0.91 0.00 0.00 4.18
1718 1754 7.343833 AGAAGGACAATTCAGATGCCAAATAAT 59.656 33.333 0.00 0.00 0.00 1.28
1720 1756 8.537728 AGGACAATTCAGATGCCAAATAATTA 57.462 30.769 0.00 0.00 0.00 1.40
1774 1810 7.763172 TTTCATTCACATAACGCTTTTGTTT 57.237 28.000 0.00 0.00 33.32 2.83
1780 1816 0.311477 TAACGCTTTTGTTTCCCCGC 59.689 50.000 0.00 0.00 33.32 6.13
1783 1819 1.843734 CGCTTTTGTTTCCCCGCGTA 61.844 55.000 4.92 0.00 36.28 4.42
1930 1966 2.679082 TGGATGAGGTAGGTAGCCTTC 58.321 52.381 0.00 0.00 36.29 3.46
2039 2075 0.599558 TAACCGAAGTGTACGCTGCT 59.400 50.000 10.25 0.00 0.00 4.24
2101 2137 0.453282 CGTTTCATCCACTGCTTGCG 60.453 55.000 0.00 0.00 0.00 4.85
2177 2214 0.798776 ACGCTGCAAAGATCGGAAAG 59.201 50.000 0.00 0.00 0.00 2.62
2184 2221 2.286067 GCAAAGATCGGAAAGATGAGCG 60.286 50.000 0.00 0.00 40.26 5.03
2242 2283 0.537188 ATGGCAGGAACTACTGGACG 59.463 55.000 0.00 0.00 38.90 4.79
2333 2374 1.745087 CACGTTTCATGGGGATTCTGG 59.255 52.381 0.00 0.00 0.00 3.86
2338 2379 3.301794 TTCATGGGGATTCTGGTCATG 57.698 47.619 0.00 0.00 37.23 3.07
2344 2385 2.755103 GGGGATTCTGGTCATGTGTTTC 59.245 50.000 0.00 0.00 0.00 2.78
2352 2394 0.698818 GTCATGTGTTTCCCCCTCCT 59.301 55.000 0.00 0.00 0.00 3.69
2610 2658 2.477357 CCAACGAATCTGCATTGCTCAG 60.477 50.000 10.49 0.00 0.00 3.35
2617 2665 0.027716 CTGCATTGCTCAGACATCGC 59.972 55.000 10.49 0.00 33.54 4.58
2622 2670 0.802222 TTGCTCAGACATCGCGCTAC 60.802 55.000 5.56 0.00 0.00 3.58
2644 2692 5.344066 ACTCATGCTTGTACGAATCTAGTG 58.656 41.667 0.00 0.00 0.00 2.74
2725 2777 3.513515 CCAGAGGGAGTATGATTCCTAGC 59.486 52.174 0.00 0.00 35.59 3.42
2743 2795 2.031163 ACAGTTCGTCAGGGCTGC 59.969 61.111 0.00 0.00 32.65 5.25
2744 2796 2.743928 CAGTTCGTCAGGGCTGCC 60.744 66.667 11.05 11.05 0.00 4.85
2756 2808 2.203480 GCTGCCCTGGTTTCCACA 60.203 61.111 0.00 0.00 0.00 4.17
2762 2814 3.261354 CTGGTTTCCACAGGGGGT 58.739 61.111 0.00 0.00 37.22 4.95
2763 2815 2.470311 CTGGTTTCCACAGGGGGTA 58.530 57.895 0.00 0.00 37.22 3.69
2764 2816 0.774908 CTGGTTTCCACAGGGGGTAA 59.225 55.000 0.00 0.00 37.22 2.85
2765 2817 1.357761 CTGGTTTCCACAGGGGGTAAT 59.642 52.381 0.00 0.00 37.22 1.89
2766 2818 1.356398 TGGTTTCCACAGGGGGTAATC 59.644 52.381 0.00 0.00 37.22 1.75
2767 2819 1.680860 GGTTTCCACAGGGGGTAATCG 60.681 57.143 0.00 0.00 37.22 3.34
2772 2824 0.611200 CACAGGGGGTAATCGACACA 59.389 55.000 0.00 0.00 30.38 3.72
2774 2826 0.611200 CAGGGGGTAATCGACACACA 59.389 55.000 3.85 0.00 37.31 3.72
2776 2828 0.899720 GGGGGTAATCGACACACAGA 59.100 55.000 3.85 0.00 33.63 3.41
2777 2829 1.405121 GGGGGTAATCGACACACAGAC 60.405 57.143 3.85 0.00 33.63 3.51
2778 2830 1.549170 GGGGTAATCGACACACAGACT 59.451 52.381 3.85 0.00 30.38 3.24
2779 2831 2.607187 GGGTAATCGACACACAGACTG 58.393 52.381 0.00 0.00 0.00 3.51
2908 2965 0.100503 AATCGGCGCATTACAAAGGC 59.899 50.000 10.83 0.00 0.00 4.35
3017 3074 6.062095 TGCTACCTATTTCCAGGATAAAAGC 58.938 40.000 0.00 0.00 39.18 3.51
3116 3173 3.512516 GGAACATCGCCAGCAGCC 61.513 66.667 0.00 0.00 38.78 4.85
3136 3193 3.677648 AACCGTGGAGCTACGCGT 61.678 61.111 28.86 19.17 42.44 6.01
3201 3259 9.095700 ACATAATTTACACCTAACAAACCCAAT 57.904 29.630 0.00 0.00 0.00 3.16
3392 3455 1.153628 GTGCGCTATCAGGACCGTT 60.154 57.895 9.73 0.00 0.00 4.44
3481 3544 2.281484 GCTGGCCTCGTCCAACAA 60.281 61.111 3.32 0.00 35.36 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.601166 CGAAACCCGTTCCTCCTTTT 58.399 50.000 0.00 0.00 31.99 2.27
283 292 0.380378 GAGCAAAACCACAAGCACGA 59.620 50.000 0.00 0.00 0.00 4.35
284 293 0.381801 AGAGCAAAACCACAAGCACG 59.618 50.000 0.00 0.00 0.00 5.34
292 301 1.985473 ACTGCATCAGAGCAAAACCA 58.015 45.000 0.29 0.00 45.13 3.67
303 312 7.500227 CCAAAGAAATCCTTAGATACTGCATCA 59.500 37.037 0.00 0.00 33.06 3.07
317 326 1.541588 GTCAAGCGCCAAAGAAATCCT 59.458 47.619 2.29 0.00 0.00 3.24
346 356 8.590204 TCTCCAGTGTGACAACATATAAAACTA 58.410 33.333 0.00 0.00 38.92 2.24
437 450 2.025887 AGGCCCTAAGTTCTGAATGTGG 60.026 50.000 0.00 0.00 0.00 4.17
452 465 1.074566 CAGAAGTTCCAAAGAGGCCCT 59.925 52.381 0.00 0.00 37.29 5.19
488 501 1.988107 AGGGACTCTTTGGATTGCAGA 59.012 47.619 0.00 0.00 0.00 4.26
536 550 2.923121 TCTCACTGCAAAGGGATATGC 58.077 47.619 0.00 0.00 42.86 3.14
565 579 3.991773 CACCACAGAATTTGCAGAAATGG 59.008 43.478 0.00 0.00 31.83 3.16
647 661 2.094182 GTCTGACCTAACGCATTCTCCA 60.094 50.000 0.00 0.00 0.00 3.86
663 677 6.042777 GGTGATTTTGTCGAGATATGTCTGA 58.957 40.000 0.00 0.00 33.97 3.27
665 679 5.812642 GTGGTGATTTTGTCGAGATATGTCT 59.187 40.000 0.00 0.00 37.42 3.41
667 681 5.487433 TGTGGTGATTTTGTCGAGATATGT 58.513 37.500 0.00 0.00 0.00 2.29
676 692 4.647424 TGTTTCCTGTGGTGATTTTGTC 57.353 40.909 0.00 0.00 0.00 3.18
707 724 5.235516 AGGTTGTAGTTCATAACTTGGTCG 58.764 41.667 0.00 0.00 42.81 4.79
721 738 1.426751 TTTGGGACGGAGGTTGTAGT 58.573 50.000 0.00 0.00 0.00 2.73
726 743 5.434408 GTCTTATATTTTGGGACGGAGGTT 58.566 41.667 0.00 0.00 0.00 3.50
762 779 7.592736 TCCCTTCTGATGGATAGTACTAGAAA 58.407 38.462 8.85 0.00 0.00 2.52
813 830 1.761784 TCTTTGTTTTGTGCTGGCCAT 59.238 42.857 5.51 0.00 0.00 4.40
821 838 8.741278 CAAAACCTTTTGTTTCTTTGTTTTGTG 58.259 29.630 13.77 0.00 46.39 3.33
831 848 9.952030 TTATCCTTTTCAAAACCTTTTGTTTCT 57.048 25.926 9.72 0.00 46.39 2.52
991 1008 0.971386 AGGCTTGCCATTTCACCTTG 59.029 50.000 14.54 0.00 0.00 3.61
1011 1028 4.018960 ACCTGTTTGGATATCAAGCTCTGT 60.019 41.667 4.83 0.00 37.45 3.41
1023 1040 3.055385 AGCACATACGTACCTGTTTGGAT 60.055 43.478 0.00 0.00 39.71 3.41
1036 1053 4.394920 ACAGGGTTCATTAAAGCACATACG 59.605 41.667 0.00 0.00 37.09 3.06
1037 1054 5.897377 ACAGGGTTCATTAAAGCACATAC 57.103 39.130 0.00 0.00 37.09 2.39
1038 1055 7.831690 TGATAACAGGGTTCATTAAAGCACATA 59.168 33.333 0.00 0.00 37.09 2.29
1039 1056 6.663093 TGATAACAGGGTTCATTAAAGCACAT 59.337 34.615 0.00 0.00 37.09 3.21
1047 1064 7.348274 AGAGAAGGATGATAACAGGGTTCATTA 59.652 37.037 0.00 0.00 30.48 1.90
1092 1109 1.226746 GAAGACAACACCGGGTTCTG 58.773 55.000 6.32 0.00 37.72 3.02
1098 1116 1.948104 TCAACTGAAGACAACACCGG 58.052 50.000 0.00 0.00 0.00 5.28
1137 1155 3.052082 CCGTTCAGCCTGGCAGTG 61.052 66.667 22.65 11.66 0.00 3.66
1222 1240 4.494350 AACACATTGAGATGAACAGCAC 57.506 40.909 0.00 0.00 36.73 4.40
1223 1241 5.518848 AAAACACATTGAGATGAACAGCA 57.481 34.783 0.00 0.00 36.73 4.41
1224 1242 7.928908 TTAAAAACACATTGAGATGAACAGC 57.071 32.000 0.00 0.00 36.73 4.40
1225 1243 8.971321 CCTTTAAAAACACATTGAGATGAACAG 58.029 33.333 0.00 0.00 36.73 3.16
1226 1244 8.474025 ACCTTTAAAAACACATTGAGATGAACA 58.526 29.630 0.00 0.00 36.73 3.18
1227 1245 8.871686 ACCTTTAAAAACACATTGAGATGAAC 57.128 30.769 0.00 0.00 36.73 3.18
1228 1246 9.311916 CAACCTTTAAAAACACATTGAGATGAA 57.688 29.630 0.00 0.00 36.73 2.57
1229 1247 7.925483 CCAACCTTTAAAAACACATTGAGATGA 59.075 33.333 0.00 0.00 36.73 2.92
1230 1248 7.307337 GCCAACCTTTAAAAACACATTGAGATG 60.307 37.037 0.00 0.00 39.25 2.90
1231 1249 6.705825 GCCAACCTTTAAAAACACATTGAGAT 59.294 34.615 0.00 0.00 0.00 2.75
1283 1313 5.707495 ACCTCTATAGTAAGGTCAGGAAGG 58.293 45.833 7.21 1.64 42.28 3.46
1297 1327 7.497249 CCAATCTCCTTTTTGTGACCTCTATAG 59.503 40.741 0.00 0.00 0.00 1.31
1377 1407 2.283145 ATGGGCATACCTTCAGCATC 57.717 50.000 0.00 0.00 41.11 3.91
1417 1447 1.303799 GCATATCGCCTGCCATGGAG 61.304 60.000 18.40 10.04 33.44 3.86
1454 1484 6.648879 TGGGGATGCTAATATTTAACAAGC 57.351 37.500 0.00 0.00 0.00 4.01
1473 1508 3.199946 ACACAATCCTACTGTACATGGGG 59.800 47.826 0.00 0.00 0.00 4.96
1474 1509 4.081142 TCACACAATCCTACTGTACATGGG 60.081 45.833 0.00 0.00 0.00 4.00
1475 1510 5.084818 TCACACAATCCTACTGTACATGG 57.915 43.478 0.00 0.00 0.00 3.66
1476 1511 4.568359 GCTCACACAATCCTACTGTACATG 59.432 45.833 0.00 0.00 0.00 3.21
1477 1512 4.467795 AGCTCACACAATCCTACTGTACAT 59.532 41.667 0.00 0.00 0.00 2.29
1478 1513 3.832490 AGCTCACACAATCCTACTGTACA 59.168 43.478 0.00 0.00 0.00 2.90
1479 1514 4.457834 AGCTCACACAATCCTACTGTAC 57.542 45.455 0.00 0.00 0.00 2.90
1480 1515 6.573434 CATTAGCTCACACAATCCTACTGTA 58.427 40.000 0.00 0.00 0.00 2.74
1481 1516 5.423015 CATTAGCTCACACAATCCTACTGT 58.577 41.667 0.00 0.00 0.00 3.55
1482 1517 4.272018 GCATTAGCTCACACAATCCTACTG 59.728 45.833 0.00 0.00 37.91 2.74
1483 1518 4.446371 GCATTAGCTCACACAATCCTACT 58.554 43.478 0.00 0.00 37.91 2.57
1545 1580 1.532505 GCATCGACGTAAGAGCGGTAA 60.533 52.381 0.00 0.00 43.62 2.85
1665 1701 9.884636 TGCACACTAATTTACTACTCACATATT 57.115 29.630 0.00 0.00 0.00 1.28
1667 1703 9.366216 CTTGCACACTAATTTACTACTCACATA 57.634 33.333 0.00 0.00 0.00 2.29
1668 1704 8.094548 TCTTGCACACTAATTTACTACTCACAT 58.905 33.333 0.00 0.00 0.00 3.21
1669 1705 7.438564 TCTTGCACACTAATTTACTACTCACA 58.561 34.615 0.00 0.00 0.00 3.58
1670 1706 7.884816 TCTTGCACACTAATTTACTACTCAC 57.115 36.000 0.00 0.00 0.00 3.51
1671 1707 7.602644 CCTTCTTGCACACTAATTTACTACTCA 59.397 37.037 0.00 0.00 0.00 3.41
1726 1762 1.895798 ACAAGAGCCAATGACTCGAGA 59.104 47.619 21.68 0.00 39.23 4.04
1728 1764 1.338105 CCACAAGAGCCAATGACTCGA 60.338 52.381 0.00 0.00 39.23 4.04
1729 1765 1.081892 CCACAAGAGCCAATGACTCG 58.918 55.000 0.00 0.00 39.23 4.18
1730 1766 2.479566 TCCACAAGAGCCAATGACTC 57.520 50.000 0.00 0.00 0.00 3.36
1774 1810 1.252215 TGACATGAAGTACGCGGGGA 61.252 55.000 12.47 0.00 0.00 4.81
1780 1816 4.265556 GTCGAAATCCTGACATGAAGTACG 59.734 45.833 0.00 0.00 35.20 3.67
1783 1819 4.543590 AGTCGAAATCCTGACATGAAGT 57.456 40.909 0.00 0.00 37.58 3.01
1930 1966 0.035056 AGTCCAGAAAATCCAGGCGG 60.035 55.000 0.00 0.00 0.00 6.13
1963 1999 2.037251 TGGTCAGAAGAAAGGGAAGACG 59.963 50.000 0.00 0.00 0.00 4.18
2039 2075 1.548081 TCGTTGGTATCTGGTTCGGA 58.452 50.000 0.00 0.00 0.00 4.55
2101 2137 8.061125 AGATTCGACAACTTAAAAATTGCAAC 57.939 30.769 0.00 0.00 0.00 4.17
2177 2214 3.810373 CACAACAAAGTAACCGCTCATC 58.190 45.455 0.00 0.00 0.00 2.92
2184 2221 6.200097 CCAATTTACAGCACAACAAAGTAACC 59.800 38.462 0.00 0.00 0.00 2.85
2242 2283 2.541556 GCCTCCAGATCGTACTCAAAC 58.458 52.381 0.00 0.00 0.00 2.93
2319 2360 2.092267 CACATGACCAGAATCCCCATGA 60.092 50.000 0.00 0.00 38.29 3.07
2333 2374 0.698818 AGGAGGGGGAAACACATGAC 59.301 55.000 0.00 0.00 32.66 3.06
2338 2379 1.074951 CCACAGGAGGGGGAAACAC 59.925 63.158 0.00 0.00 0.00 3.32
2344 2385 3.706373 CGTGTCCACAGGAGGGGG 61.706 72.222 0.00 0.00 33.92 5.40
2352 2394 0.464036 AACTCAGCTTCGTGTCCACA 59.536 50.000 0.00 0.00 0.00 4.17
2576 2624 1.057851 TCGTTGGGTTGGGTTCCTCT 61.058 55.000 0.00 0.00 0.00 3.69
2589 2637 1.469703 TGAGCAATGCAGATTCGTTGG 59.530 47.619 8.35 0.00 34.44 3.77
2610 2658 0.596083 AGCATGAGTAGCGCGATGTC 60.596 55.000 12.10 5.85 37.01 3.06
2617 2665 2.188837 TCGTACAAGCATGAGTAGCG 57.811 50.000 0.00 3.58 37.01 4.26
2622 2670 4.742167 CCACTAGATTCGTACAAGCATGAG 59.258 45.833 0.00 0.00 0.00 2.90
2644 2692 7.280356 ACCACTAATTCATGTATACTGGTTCC 58.720 38.462 4.17 0.00 0.00 3.62
2725 2777 2.320587 GCAGCCCTGACGAACTGTG 61.321 63.158 0.00 0.00 32.65 3.66
2744 2796 1.137594 TACCCCCTGTGGAAACCAGG 61.138 60.000 0.00 0.00 44.06 4.45
2747 2799 1.680860 CGATTACCCCCTGTGGAAACC 60.681 57.143 0.00 0.00 35.39 3.27
2756 2808 0.902531 CTGTGTGTCGATTACCCCCT 59.097 55.000 0.00 0.00 0.00 4.79
2760 2812 3.299340 ACAGTCTGTGTGTCGATTACC 57.701 47.619 4.21 0.00 38.28 2.85
2761 2813 4.295870 TCAACAGTCTGTGTGTCGATTAC 58.704 43.478 6.18 0.00 40.26 1.89
2762 2814 4.577834 TCAACAGTCTGTGTGTCGATTA 57.422 40.909 6.18 0.00 40.26 1.75
2763 2815 3.452755 TCAACAGTCTGTGTGTCGATT 57.547 42.857 6.18 0.00 40.26 3.34
2764 2816 3.452755 TTCAACAGTCTGTGTGTCGAT 57.547 42.857 6.18 0.00 40.26 3.59
2765 2817 2.951457 TTCAACAGTCTGTGTGTCGA 57.049 45.000 6.18 0.00 40.26 4.20
2766 2818 3.123050 TCATTCAACAGTCTGTGTGTCG 58.877 45.455 6.18 0.00 40.26 4.35
2767 2819 4.332543 TGTTCATTCAACAGTCTGTGTGTC 59.667 41.667 6.18 3.62 40.29 3.67
2772 2824 4.634004 TCGTTTGTTCATTCAACAGTCTGT 59.366 37.500 0.00 0.00 45.98 3.41
2774 2826 4.634004 TGTCGTTTGTTCATTCAACAGTCT 59.366 37.500 0.00 0.00 45.98 3.24
2776 2828 4.955925 TGTCGTTTGTTCATTCAACAGT 57.044 36.364 0.00 0.00 45.98 3.55
2777 2829 5.399301 GGATTGTCGTTTGTTCATTCAACAG 59.601 40.000 0.00 0.00 45.98 3.16
2778 2830 5.163612 TGGATTGTCGTTTGTTCATTCAACA 60.164 36.000 0.00 0.00 43.68 3.33
2779 2831 5.173131 GTGGATTGTCGTTTGTTCATTCAAC 59.827 40.000 0.00 0.00 35.28 3.18
2824 2876 7.035612 GGTTGAATTCCTGGTGATTTGATTAC 58.964 38.462 2.27 0.00 0.00 1.89
2908 2965 0.369931 TGCGCACTCGATTCATTTCG 59.630 50.000 5.66 0.00 40.46 3.46
2964 3021 3.260632 GTGGGAGGGCATTGTAATTGTTT 59.739 43.478 0.00 0.00 0.00 2.83
3017 3074 4.899502 AGTTGTGTTGAATCTGTAGGGAG 58.100 43.478 0.00 0.00 0.00 4.30
3116 3173 2.125673 CGTAGCTCCACGGTTGGG 60.126 66.667 0.92 0.00 44.11 4.12
3134 3191 1.135731 GTCGCTCTCTGTCCAGACG 59.864 63.158 0.00 0.00 33.22 4.18
3136 3193 0.962855 CCTGTCGCTCTCTGTCCAGA 60.963 60.000 0.00 0.00 35.85 3.86
3201 3259 7.494625 GCATCGGCTAGGCTAATGTAATTAATA 59.505 37.037 21.63 0.00 36.18 0.98
3392 3455 1.144691 TGGTCATGGGGAACAAGACA 58.855 50.000 5.30 0.00 46.73 3.41


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

AutoCloner maintained by Alex Coulton.