Multiple sequence alignment - TraesCS4D01G352700

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 TraesCS4D01G352700 chr4D 100.000 5232 0 0 1 5232 503784960 503790191 0.000000e+00 9662.0
1 TraesCS4D01G352700 chr4B 93.895 4324 120 60 491 4707 649577320 649581606 0.000000e+00 6390.0
2 TraesCS4D01G352700 chr4B 84.390 205 10 5 5029 5232 649581661 649581844 1.160000e-41 182.0
3 TraesCS4D01G352700 chr4B 98.039 51 1 0 4822 4872 649581663 649581613 7.220000e-14 89.8
4 TraesCS4D01G352700 chr5A 95.584 3940 94 35 581 4471 688291605 688295513 0.000000e+00 6239.0
5 TraesCS4D01G352700 chr5A 92.026 765 29 5 4468 5232 688295798 688296530 0.000000e+00 1046.0
6 TraesCS4D01G352700 chr5D 96.825 252 7 1 239 489 389931999 389931748 2.250000e-113 420.0
7 TraesCS4D01G352700 chr5D 97.925 241 2 2 1 239 389932329 389932090 1.050000e-111 414.0
8 TraesCS4D01G352700 chr7D 95.238 252 10 2 239 489 17387801 17388051 1.060000e-106 398.0
9 TraesCS4D01G352700 chr7D 94.531 256 12 2 239 492 9940102 9940357 1.370000e-105 394.0
10 TraesCS4D01G352700 chr7D 93.004 243 13 3 1 239 9939769 9940011 8.340000e-93 351.0
11 TraesCS4D01G352700 chr7D 92.116 241 17 1 1 239 17387471 17387711 6.490000e-89 339.0
12 TraesCS4D01G352700 chr7D 89.583 240 21 3 3 239 25026170 25026408 8.510000e-78 302.0
13 TraesCS4D01G352700 chr3A 95.238 252 10 2 239 489 700297503 700297253 1.060000e-106 398.0
14 TraesCS4D01G352700 chr3A 94.355 248 10 3 1 246 700297833 700297588 1.380000e-100 377.0
15 TraesCS4D01G352700 chr3B 96.250 240 6 2 1 237 793354935 793354696 1.770000e-104 390.0
16 TraesCS4D01G352700 chr3B 91.093 247 21 1 244 489 30454731 30454485 3.020000e-87 333.0
17 TraesCS4D01G352700 chr3D 93.200 250 16 1 239 487 29371393 29371642 2.980000e-97 366.0
18 TraesCS4D01G352700 chr3D 93.802 242 11 3 1 239 29371062 29371302 1.390000e-95 361.0
19 TraesCS4D01G352700 chr2B 94.239 243 9 3 1 239 756159350 756159109 2.980000e-97 366.0
20 TraesCS4D01G352700 chr2A 93.860 228 12 2 270 496 3258079 3258305 5.020000e-90 342.0
21 TraesCS4D01G352700 chr5B 90.873 252 22 1 239 489 642792631 642792380 2.330000e-88 337.0
22 TraesCS4D01G352700 chr5B 89.958 239 19 3 3 239 642792957 642792722 2.370000e-78 303.0
23 TraesCS4D01G352700 chr4A 90.476 252 23 1 239 489 670936326 670936075 1.090000e-86 331.0
24 TraesCS4D01G352700 chr1B 76.765 340 69 8 1130 1461 677526498 677526835 1.160000e-41 182.0


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 TraesCS4D01G352700 chr4D 503784960 503790191 5231 False 9662.0 9662 100.0000 1 5232 1 chr4D.!!$F1 5231
1 TraesCS4D01G352700 chr4B 649577320 649581844 4524 False 3286.0 6390 89.1425 491 5232 2 chr4B.!!$F1 4741
2 TraesCS4D01G352700 chr5A 688291605 688296530 4925 False 3642.5 6239 93.8050 581 5232 2 chr5A.!!$F1 4651
3 TraesCS4D01G352700 chr5D 389931748 389932329 581 True 417.0 420 97.3750 1 489 2 chr5D.!!$R1 488
4 TraesCS4D01G352700 chr7D 9939769 9940357 588 False 372.5 394 93.7675 1 492 2 chr7D.!!$F2 491
5 TraesCS4D01G352700 chr7D 17387471 17388051 580 False 368.5 398 93.6770 1 489 2 chr7D.!!$F3 488
6 TraesCS4D01G352700 chr3A 700297253 700297833 580 True 387.5 398 94.7965 1 489 2 chr3A.!!$R1 488
7 TraesCS4D01G352700 chr3D 29371062 29371642 580 False 363.5 366 93.5010 1 487 2 chr3D.!!$F1 486
8 TraesCS4D01G352700 chr5B 642792380 642792957 577 True 320.0 337 90.4155 3 489 2 chr5B.!!$R1 486

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
992 1171 0.040351 AGCTGGCTAGTCCTCACAGA 59.960 55.000 0.00 0.0 35.26 3.41 F
1980 2183 1.450312 CAGTGGCATCGTTCCTCCC 60.450 63.158 0.00 0.0 0.00 4.30 F
2090 2293 3.129638 ACCACGTTAACAAATTGCACAGT 59.870 39.130 6.39 0.0 0.00 3.55 F
2799 3003 3.391296 TGTCAGGCCAGATACCTAAATCC 59.609 47.826 5.01 0.0 35.10 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2851 3055 0.038166 GTGATTGGCACTTCCCCAGA 59.962 55.0 0.00 0.00 44.27 3.86 R
3095 3299 0.530870 TTGCATGGACGTTGTCGACA 60.531 50.0 15.76 15.76 40.62 4.35 R
3099 3303 0.951558 AACCTTGCATGGACGTTGTC 59.048 50.0 24.48 0.00 0.00 3.18 R
4557 5058 0.317770 CAAACAAAGACGCGCCACAT 60.318 50.0 5.73 0.00 0.00 3.21 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
28 29 7.945033 TTGACACTTAGAAAATGGAAATTGC 57.055 32.000 0.00 0.00 0.00 3.56
318 416 1.739049 CAAAGCCCTGTTTGCCGAA 59.261 52.632 0.00 0.00 30.94 4.30
345 443 8.983307 TTTGTTATTTTACCGAGTGTTTTGTT 57.017 26.923 0.00 0.00 0.00 2.83
508 607 3.768799 GCCATCAGGGGACGAGAGTTG 62.769 61.905 0.00 0.00 40.80 3.16
535 634 2.816689 CGTATACCATGTTGAAGCCGA 58.183 47.619 0.00 0.00 0.00 5.54
555 654 1.072678 TCCTCGGTCAGTCTCGTGT 59.927 57.895 0.00 0.00 0.00 4.49
556 655 0.954449 TCCTCGGTCAGTCTCGTGTC 60.954 60.000 0.00 0.00 0.00 3.67
557 656 0.956410 CCTCGGTCAGTCTCGTGTCT 60.956 60.000 0.00 0.00 0.00 3.41
558 657 0.167033 CTCGGTCAGTCTCGTGTCTG 59.833 60.000 5.53 5.53 0.00 3.51
559 658 1.210413 CGGTCAGTCTCGTGTCTGG 59.790 63.158 10.93 0.00 31.79 3.86
560 659 1.516365 CGGTCAGTCTCGTGTCTGGT 61.516 60.000 10.93 0.00 31.79 4.00
578 677 0.180406 GTCTGGTGTTGGGTCACAGT 59.820 55.000 0.00 0.00 39.76 3.55
653 758 1.690893 ACCATCCGGAGTCATCATCAG 59.309 52.381 11.34 0.00 35.59 2.90
659 764 2.093500 CCGGAGTCATCATCAGAAACCA 60.093 50.000 0.00 0.00 0.00 3.67
660 765 2.932614 CGGAGTCATCATCAGAAACCAC 59.067 50.000 0.00 0.00 0.00 4.16
661 766 3.274288 GGAGTCATCATCAGAAACCACC 58.726 50.000 0.00 0.00 0.00 4.61
662 767 3.054802 GGAGTCATCATCAGAAACCACCT 60.055 47.826 0.00 0.00 0.00 4.00
663 768 4.566488 GGAGTCATCATCAGAAACCACCTT 60.566 45.833 0.00 0.00 0.00 3.50
664 769 5.338381 GGAGTCATCATCAGAAACCACCTTA 60.338 44.000 0.00 0.00 0.00 2.69
665 770 5.491982 AGTCATCATCAGAAACCACCTTAC 58.508 41.667 0.00 0.00 0.00 2.34
666 771 5.249393 AGTCATCATCAGAAACCACCTTACT 59.751 40.000 0.00 0.00 0.00 2.24
667 772 5.352569 GTCATCATCAGAAACCACCTTACTG 59.647 44.000 0.00 0.00 0.00 2.74
668 773 3.674997 TCATCAGAAACCACCTTACTGC 58.325 45.455 0.00 0.00 0.00 4.40
737 842 2.175530 CGACGACGCCAGATATATCC 57.824 55.000 9.18 0.00 0.00 2.59
743 848 0.109272 CGCCAGATATATCCACGCGT 60.109 55.000 21.54 5.58 33.88 6.01
770 875 3.061848 GGTCCCACAACCATGGCG 61.062 66.667 13.04 5.85 39.27 5.69
912 1055 1.927931 GCTGATTTAGCGACGAGGC 59.072 57.895 0.00 0.00 43.63 4.70
914 1057 0.924090 CTGATTTAGCGACGAGGCAC 59.076 55.000 0.00 0.00 34.64 5.01
915 1058 0.459585 TGATTTAGCGACGAGGCACC 60.460 55.000 0.00 0.00 34.64 5.01
916 1059 0.459585 GATTTAGCGACGAGGCACCA 60.460 55.000 0.00 0.00 34.64 4.17
925 1068 4.648626 GAGGCACCAGCACCAGCA 62.649 66.667 0.00 0.00 45.49 4.41
966 1129 0.316841 TGTATGCACAGACACGCTCA 59.683 50.000 0.00 0.00 0.00 4.26
977 1140 1.446792 CACGCTCACCACCTAGCTG 60.447 63.158 0.00 0.00 36.56 4.24
989 1168 1.036707 CCTAGCTGGCTAGTCCTCAC 58.963 60.000 22.85 0.00 43.22 3.51
992 1171 0.040351 AGCTGGCTAGTCCTCACAGA 59.960 55.000 0.00 0.00 35.26 3.41
1023 1202 3.501062 TGACATTGCTCAGCTTCTTCTTG 59.499 43.478 0.00 0.00 0.00 3.02
1653 1856 6.054295 CCTCTCCAACCTCAAATATCTTCAG 58.946 44.000 0.00 0.00 0.00 3.02
1980 2183 1.450312 CAGTGGCATCGTTCCTCCC 60.450 63.158 0.00 0.00 0.00 4.30
2089 2292 3.701241 ACCACGTTAACAAATTGCACAG 58.299 40.909 6.39 0.00 0.00 3.66
2090 2293 3.129638 ACCACGTTAACAAATTGCACAGT 59.870 39.130 6.39 0.00 0.00 3.55
2209 2413 6.375455 TCAAGAGAACAAAATATCAGGAAGCC 59.625 38.462 0.00 0.00 0.00 4.35
2625 2829 5.893824 TCTAGTAGAATTCCATGCAGAGTCA 59.106 40.000 0.65 0.00 0.00 3.41
2630 2834 5.014858 AGAATTCCATGCAGAGTCAAACAT 58.985 37.500 0.65 0.00 0.00 2.71
2631 2835 5.479375 AGAATTCCATGCAGAGTCAAACATT 59.521 36.000 0.65 0.00 0.00 2.71
2649 2853 5.835113 ACATTTTATCAGGTGAAATCCCG 57.165 39.130 0.00 0.00 0.00 5.14
2725 2929 3.931907 TTGAAGGTACCATCCCATCAG 57.068 47.619 15.94 0.00 0.00 2.90
2799 3003 3.391296 TGTCAGGCCAGATACCTAAATCC 59.609 47.826 5.01 0.00 35.10 3.01
2851 3055 6.721208 TCTCAACCTTTCATTCAATAGCCTTT 59.279 34.615 0.00 0.00 0.00 3.11
3095 3299 7.041848 GCAAAATAAAAGACAAGCAACAATCCT 60.042 33.333 0.00 0.00 0.00 3.24
3099 3303 2.146342 AGACAAGCAACAATCCTGTCG 58.854 47.619 0.00 0.00 33.45 4.35
3417 3621 9.661563 AATGAATTCAAAGCAATTGTGTATGAT 57.338 25.926 13.09 0.00 40.11 2.45
3689 3894 3.176552 CTCATTTCTCGAGCAGTCCAT 57.823 47.619 7.81 0.00 0.00 3.41
3753 3958 4.223953 CAGGTTAGCCCACCTCTTCTATA 58.776 47.826 1.21 0.00 44.63 1.31
3793 3998 9.452287 TTCCGTGCCTAGTTATATAAAGTTTTT 57.548 29.630 0.00 0.00 0.00 1.94
4381 4586 8.760569 GTTAACATGGAAGTACAACCAATTTTG 58.239 33.333 13.49 10.22 39.69 2.44
4416 4621 6.320926 TGCAGCTATTTCCTAATGTTTGCATA 59.679 34.615 0.00 0.00 34.39 3.14
4623 5124 8.635877 ATGTTCAGAACAGAATTACGATACTC 57.364 34.615 20.55 0.00 45.95 2.59
4672 5173 8.239038 TGATGGTTAATAGTTTTGTCAAACCA 57.761 30.769 6.50 6.50 46.29 3.67
4778 5279 4.521256 TGGTAATTTGCAGGTTAGTCCAAC 59.479 41.667 0.00 0.00 39.02 3.77
4788 5289 4.092968 CAGGTTAGTCCAACGTTTATGCTC 59.907 45.833 0.00 0.00 38.09 4.26
4793 5294 1.001068 TCCAACGTTTATGCTCGTCCA 59.999 47.619 0.00 0.00 39.39 4.02
4812 5313 2.233676 CCACCCATCTTAAACCAAAGCC 59.766 50.000 0.00 0.00 0.00 4.35
4832 5333 1.822990 CGTGTAACCCTCAAGGCTCTA 59.177 52.381 0.00 0.00 40.58 2.43
4833 5334 2.416972 CGTGTAACCCTCAAGGCTCTAC 60.417 54.545 0.00 0.00 40.58 2.59
4834 5335 2.832733 GTGTAACCCTCAAGGCTCTACT 59.167 50.000 0.00 0.00 40.58 2.57
4875 5376 5.445964 GGATACTAAGGCCTCCAAATTCAA 58.554 41.667 5.23 0.00 0.00 2.69
4908 5409 6.455513 GCAAACTTTGTTCCAATTGACAAGAC 60.456 38.462 7.12 0.00 37.12 3.01
4918 5419 5.242838 TCCAATTGACAAGACATTTACCACC 59.757 40.000 7.12 0.00 0.00 4.61
4955 5456 4.551671 AGCTAGCCCAAAGAGAAGATCTA 58.448 43.478 12.13 0.00 37.23 1.98
4980 5481 7.908458 ACAAAGCTTGTTCATCTGAGCATCAA 61.908 38.462 0.00 0.00 43.63 2.57
4992 5493 4.025040 TGAGCATCAACTCACTTGGATT 57.975 40.909 0.00 0.00 45.97 3.01
5004 5505 0.831288 CTTGGATTGGTTGGTGGCCA 60.831 55.000 0.00 0.00 0.00 5.36
5008 5509 0.532115 GATTGGTTGGTGGCCATCAC 59.468 55.000 21.13 13.98 45.34 3.06
5032 5533 3.074390 TGAAAAGAGGGGATTGCAGAGAA 59.926 43.478 0.00 0.00 0.00 2.87
5039 5540 2.417787 GGGGATTGCAGAGAAAACATGC 60.418 50.000 0.00 0.00 40.40 4.06
5085 5587 5.741964 GCATTTGAGATGAATTGCCCATGAT 60.742 40.000 0.00 0.00 0.00 2.45
5089 5591 4.105217 TGAGATGAATTGCCCATGATACCT 59.895 41.667 0.00 0.00 0.00 3.08
5106 5608 3.942130 ACCTTGATAACTTGGCAAAGC 57.058 42.857 0.00 0.00 36.84 3.51
5110 5612 4.458989 CCTTGATAACTTGGCAAAGCTGTA 59.541 41.667 0.00 0.00 36.84 2.74
5139 5641 9.160496 GGATAGCTTGATAGTCATTATTTCTGG 57.840 37.037 0.00 0.00 0.00 3.86
5140 5642 9.935241 GATAGCTTGATAGTCATTATTTCTGGA 57.065 33.333 0.00 0.00 0.00 3.86
5141 5643 9.941325 ATAGCTTGATAGTCATTATTTCTGGAG 57.059 33.333 0.00 0.00 0.00 3.86
5142 5644 8.027524 AGCTTGATAGTCATTATTTCTGGAGA 57.972 34.615 0.00 0.00 0.00 3.71
5143 5645 7.930865 AGCTTGATAGTCATTATTTCTGGAGAC 59.069 37.037 0.00 0.00 0.00 3.36
5144 5646 7.172361 GCTTGATAGTCATTATTTCTGGAGACC 59.828 40.741 0.00 0.00 0.00 3.85
5145 5647 7.921041 TGATAGTCATTATTTCTGGAGACCT 57.079 36.000 0.00 0.00 0.00 3.85
5146 5648 7.957002 TGATAGTCATTATTTCTGGAGACCTC 58.043 38.462 0.00 0.00 0.00 3.85
5147 5649 7.786943 TGATAGTCATTATTTCTGGAGACCTCT 59.213 37.037 0.00 0.00 0.00 3.69
5148 5650 6.882768 AGTCATTATTTCTGGAGACCTCTT 57.117 37.500 0.00 0.00 0.00 2.85
5149 5651 7.979786 AGTCATTATTTCTGGAGACCTCTTA 57.020 36.000 0.00 0.00 0.00 2.10
5150 5652 8.560124 AGTCATTATTTCTGGAGACCTCTTAT 57.440 34.615 0.00 0.00 0.00 1.73
5151 5653 8.997734 AGTCATTATTTCTGGAGACCTCTTATT 58.002 33.333 0.00 0.00 0.00 1.40
5152 5654 9.620259 GTCATTATTTCTGGAGACCTCTTATTT 57.380 33.333 0.00 0.00 0.00 1.40
5153 5655 9.838339 TCATTATTTCTGGAGACCTCTTATTTC 57.162 33.333 0.00 0.00 0.00 2.17
5154 5656 9.844257 CATTATTTCTGGAGACCTCTTATTTCT 57.156 33.333 0.00 0.00 0.00 2.52
5155 5657 9.844257 ATTATTTCTGGAGACCTCTTATTTCTG 57.156 33.333 0.00 0.00 0.00 3.02
5174 5676 2.032071 GGTGGTGAACGGACAGGG 59.968 66.667 0.00 0.00 0.00 4.45
5207 5709 3.134262 GGTAGGTACAGGGAAATGAGGAC 59.866 52.174 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
318 416 9.589111 ACAAAACACTCGGTAAAATAACAAAAT 57.411 25.926 0.00 0.00 0.00 1.82
345 443 0.874175 CACTTTGCCGAGTGTCGTGA 60.874 55.000 8.07 0.00 41.62 4.35
489 588 0.176680 CAACTCTCGTCCCCTGATGG 59.823 60.000 0.00 0.00 0.00 3.51
508 607 1.330521 CAACATGGTATACGCCAGCAC 59.669 52.381 0.00 0.00 42.47 4.40
511 610 2.287915 GCTTCAACATGGTATACGCCAG 59.712 50.000 0.00 0.00 42.47 4.85
513 612 1.602377 GGCTTCAACATGGTATACGCC 59.398 52.381 0.00 0.00 0.00 5.68
535 634 0.956410 CACGAGACTGACCGAGGACT 60.956 60.000 0.00 0.00 0.00 3.85
543 642 1.068885 CAGACCAGACACGAGACTGAC 60.069 57.143 13.16 7.41 39.43 3.51
546 645 0.178987 ACCAGACCAGACACGAGACT 60.179 55.000 0.00 0.00 0.00 3.24
555 654 0.692756 TGACCCAACACCAGACCAGA 60.693 55.000 0.00 0.00 0.00 3.86
556 655 0.535102 GTGACCCAACACCAGACCAG 60.535 60.000 0.00 0.00 35.07 4.00
557 656 1.275421 TGTGACCCAACACCAGACCA 61.275 55.000 0.00 0.00 39.69 4.02
558 657 0.535102 CTGTGACCCAACACCAGACC 60.535 60.000 0.00 0.00 39.69 3.85
559 658 0.180406 ACTGTGACCCAACACCAGAC 59.820 55.000 0.00 0.00 39.69 3.51
560 659 1.691976 CTACTGTGACCCAACACCAGA 59.308 52.381 0.00 0.00 39.69 3.86
578 677 3.755628 GGGTCGCCGTGTGCTCTA 61.756 66.667 0.00 0.00 38.05 2.43
637 742 2.168521 GGTTTCTGATGATGACTCCGGA 59.831 50.000 2.93 2.93 0.00 5.14
653 758 1.244816 GTGGGCAGTAAGGTGGTTTC 58.755 55.000 0.00 0.00 0.00 2.78
659 764 0.770557 TGGAAGGTGGGCAGTAAGGT 60.771 55.000 0.00 0.00 0.00 3.50
660 765 0.322546 GTGGAAGGTGGGCAGTAAGG 60.323 60.000 0.00 0.00 0.00 2.69
661 766 0.322546 GGTGGAAGGTGGGCAGTAAG 60.323 60.000 0.00 0.00 0.00 2.34
662 767 1.765074 GGTGGAAGGTGGGCAGTAA 59.235 57.895 0.00 0.00 0.00 2.24
663 768 2.589157 CGGTGGAAGGTGGGCAGTA 61.589 63.158 0.00 0.00 0.00 2.74
664 769 3.953775 CGGTGGAAGGTGGGCAGT 61.954 66.667 0.00 0.00 0.00 4.40
665 770 4.722700 CCGGTGGAAGGTGGGCAG 62.723 72.222 0.00 0.00 0.00 4.85
668 773 4.029809 GTCCCGGTGGAAGGTGGG 62.030 72.222 0.00 0.00 44.07 4.61
719 824 2.728225 CGTGGATATATCTGGCGTCGTC 60.728 54.545 12.42 0.00 0.00 4.20
720 825 1.199327 CGTGGATATATCTGGCGTCGT 59.801 52.381 12.42 0.00 0.00 4.34
722 827 1.630148 GCGTGGATATATCTGGCGTC 58.370 55.000 12.42 7.40 0.00 5.19
723 828 0.109272 CGCGTGGATATATCTGGCGT 60.109 55.000 24.26 0.00 36.12 5.68
725 830 2.527100 GTACGCGTGGATATATCTGGC 58.473 52.381 24.59 11.56 0.00 4.85
727 832 3.759418 CTGGTACGCGTGGATATATCTG 58.241 50.000 24.59 0.55 0.00 2.90
728 833 2.163815 GCTGGTACGCGTGGATATATCT 59.836 50.000 24.59 0.00 0.00 1.98
729 834 2.163815 AGCTGGTACGCGTGGATATATC 59.836 50.000 24.59 3.96 33.54 1.63
730 835 2.168496 AGCTGGTACGCGTGGATATAT 58.832 47.619 24.59 0.00 33.54 0.86
731 836 1.612676 AGCTGGTACGCGTGGATATA 58.387 50.000 24.59 0.00 33.54 0.86
733 838 0.949397 CTAGCTGGTACGCGTGGATA 59.051 55.000 24.59 11.07 33.54 2.59
734 839 1.734137 CTAGCTGGTACGCGTGGAT 59.266 57.895 24.59 10.48 33.54 3.41
735 840 2.412323 CCTAGCTGGTACGCGTGGA 61.412 63.158 24.59 0.00 33.54 4.02
736 841 2.104331 CCTAGCTGGTACGCGTGG 59.896 66.667 24.59 7.93 33.54 4.94
737 842 2.104331 CCCTAGCTGGTACGCGTG 59.896 66.667 24.59 5.87 33.54 5.34
743 848 0.117541 TTGTGGGACCCTAGCTGGTA 59.882 55.000 13.00 0.00 39.24 3.25
912 1055 2.981909 CTGGTGCTGGTGCTGGTG 60.982 66.667 0.00 0.00 40.48 4.17
925 1068 6.382925 ACACTAGAGGGTTTATATAGCTGGT 58.617 40.000 0.00 0.00 0.00 4.00
957 1120 1.446272 GCTAGGTGGTGAGCGTGTC 60.446 63.158 0.00 0.00 0.00 3.67
960 1123 2.650116 CCAGCTAGGTGGTGAGCGT 61.650 63.158 29.24 0.00 46.27 5.07
961 1124 2.185350 CCAGCTAGGTGGTGAGCG 59.815 66.667 29.24 6.05 46.27 5.03
962 1125 1.330655 TAGCCAGCTAGGTGGTGAGC 61.331 60.000 35.00 23.32 46.27 4.26
977 1140 1.754226 CTCCTTCTGTGAGGACTAGCC 59.246 57.143 0.00 0.00 40.87 3.93
1023 1202 2.107953 GCGTGGGAGCAGAGGATC 59.892 66.667 0.00 0.00 37.05 3.36
1206 1401 2.279517 GCCATGCGTAGGGAGACG 60.280 66.667 8.85 0.00 45.70 4.18
1212 1407 1.227674 GAAGGAGGCCATGCGTAGG 60.228 63.158 5.01 0.00 0.00 3.18
1215 1410 1.675641 GTTGAAGGAGGCCATGCGT 60.676 57.895 5.01 0.00 0.00 5.24
1365 1564 1.211457 CCCTGGAGAGAATTCACCCTG 59.789 57.143 8.44 8.96 33.55 4.45
2089 2292 3.431068 CCCAACCCCAAAACTTGTAACAC 60.431 47.826 0.00 0.00 0.00 3.32
2090 2293 2.766828 CCCAACCCCAAAACTTGTAACA 59.233 45.455 0.00 0.00 0.00 2.41
2209 2413 8.903059 ATGAGGTTACCTATATCTTTAGGGAG 57.097 38.462 2.88 0.00 42.68 4.30
2571 2775 6.120507 AGATTCCCTATTTCATGAGGTAGC 57.879 41.667 9.71 0.00 0.00 3.58
2625 2829 6.435904 TCGGGATTTCACCTGATAAAATGTTT 59.564 34.615 0.00 0.00 40.00 2.83
2630 2834 3.945285 GCTCGGGATTTCACCTGATAAAA 59.055 43.478 0.00 0.00 43.32 1.52
2631 2835 3.054728 TGCTCGGGATTTCACCTGATAAA 60.055 43.478 0.00 0.00 43.32 1.40
2725 2929 7.159372 TGTAGACCTTTCATTTGACTAAGGAC 58.841 38.462 14.93 10.22 39.60 3.85
2799 3003 2.808543 GAGTGTGGTAAGGTCTGCAAAG 59.191 50.000 0.00 0.00 0.00 2.77
2851 3055 0.038166 GTGATTGGCACTTCCCCAGA 59.962 55.000 0.00 0.00 44.27 3.86
2979 3183 3.175929 CGCAACCGGGAATTTATGTTTC 58.824 45.455 6.32 0.00 0.00 2.78
3095 3299 0.530870 TTGCATGGACGTTGTCGACA 60.531 50.000 15.76 15.76 40.62 4.35
3099 3303 0.951558 AACCTTGCATGGACGTTGTC 59.048 50.000 24.48 0.00 0.00 3.18
3157 3361 1.281419 TTCCCTGCCGAGAAACCATA 58.719 50.000 0.00 0.00 0.00 2.74
3417 3621 7.419057 CCTTCTAGACTACCATTAGGCATGAAA 60.419 40.741 0.00 0.00 35.47 2.69
3689 3894 2.420547 CCTCGAAATCCCATTGAGCTCA 60.421 50.000 13.74 13.74 0.00 4.26
3753 3958 6.481434 AGGCACGGAATAAGTAGAGTAAAT 57.519 37.500 0.00 0.00 0.00 1.40
4416 4621 6.883217 TGAAACATAGTAGAGACCGTACTCTT 59.117 38.462 12.51 1.19 43.62 2.85
4557 5058 0.317770 CAAACAAAGACGCGCCACAT 60.318 50.000 5.73 0.00 0.00 3.21
4623 5124 5.345702 TCGGTTTACAATATTCTCGACAGG 58.654 41.667 0.00 0.00 0.00 4.00
4747 5248 3.891366 ACCTGCAAATTACCATGGATAGC 59.109 43.478 21.47 13.31 0.00 2.97
4778 5279 0.390603 TGGGTGGACGAGCATAAACG 60.391 55.000 0.00 0.00 0.00 3.60
4788 5289 2.483014 TGGTTTAAGATGGGTGGACG 57.517 50.000 0.00 0.00 0.00 4.79
4793 5294 2.167662 CGGCTTTGGTTTAAGATGGGT 58.832 47.619 0.00 0.00 0.00 4.51
4834 5335 5.667626 AGTATCCCTAATCCTGAAGCTTTCA 59.332 40.000 0.00 0.00 38.17 2.69
4853 5354 6.073003 CGATTGAATTTGGAGGCCTTAGTATC 60.073 42.308 6.77 2.41 0.00 2.24
4875 5376 1.886542 GAACAAAGTTTGCTCCCCGAT 59.113 47.619 15.59 0.00 0.00 4.18
4901 5402 4.213482 GTGTCAGGTGGTAAATGTCTTGTC 59.787 45.833 0.00 0.00 0.00 3.18
4908 5409 6.878923 TCTGATAAAGTGTCAGGTGGTAAATG 59.121 38.462 3.58 0.00 42.58 2.32
4918 5419 4.367450 GGCTAGCTCTGATAAAGTGTCAG 58.633 47.826 15.72 0.00 43.46 3.51
4980 5481 2.586425 CACCAACCAATCCAAGTGAGT 58.414 47.619 0.00 0.00 0.00 3.41
5004 5505 3.879321 GCAATCCCCTCTTTTCAGGTGAT 60.879 47.826 0.00 0.00 32.38 3.06
5008 5509 2.097825 CTGCAATCCCCTCTTTTCAGG 58.902 52.381 0.00 0.00 0.00 3.86
5032 5533 0.387565 GGTGTTGGTTCGGCATGTTT 59.612 50.000 0.00 0.00 0.00 2.83
5039 5540 0.248866 GCAAAGTGGTGTTGGTTCGG 60.249 55.000 0.00 0.00 0.00 4.30
5085 5587 4.458989 CAGCTTTGCCAAGTTATCAAGGTA 59.541 41.667 0.00 0.00 31.86 3.08
5089 5591 5.312895 TCTACAGCTTTGCCAAGTTATCAA 58.687 37.500 0.00 0.00 31.86 2.57
5106 5608 7.701539 ATGACTATCAAGCTATCCTCTACAG 57.298 40.000 0.00 0.00 0.00 2.74
5139 5641 4.020128 ACCACCACAGAAATAAGAGGTCTC 60.020 45.833 0.00 0.00 0.00 3.36
5140 5642 3.910627 ACCACCACAGAAATAAGAGGTCT 59.089 43.478 0.00 0.00 0.00 3.85
5141 5643 4.003648 CACCACCACAGAAATAAGAGGTC 58.996 47.826 0.00 0.00 0.00 3.85
5142 5644 3.650942 TCACCACCACAGAAATAAGAGGT 59.349 43.478 0.00 0.00 0.00 3.85
5143 5645 4.286297 TCACCACCACAGAAATAAGAGG 57.714 45.455 0.00 0.00 0.00 3.69
5144 5646 4.152402 CGTTCACCACCACAGAAATAAGAG 59.848 45.833 0.00 0.00 0.00 2.85
5145 5647 4.062293 CGTTCACCACCACAGAAATAAGA 58.938 43.478 0.00 0.00 0.00 2.10
5146 5648 3.188460 CCGTTCACCACCACAGAAATAAG 59.812 47.826 0.00 0.00 0.00 1.73
5147 5649 3.142951 CCGTTCACCACCACAGAAATAA 58.857 45.455 0.00 0.00 0.00 1.40
5148 5650 2.369203 TCCGTTCACCACCACAGAAATA 59.631 45.455 0.00 0.00 0.00 1.40
5149 5651 1.142060 TCCGTTCACCACCACAGAAAT 59.858 47.619 0.00 0.00 0.00 2.17
5150 5652 0.542333 TCCGTTCACCACCACAGAAA 59.458 50.000 0.00 0.00 0.00 2.52
5151 5653 0.179067 GTCCGTTCACCACCACAGAA 60.179 55.000 0.00 0.00 0.00 3.02
5152 5654 1.331399 TGTCCGTTCACCACCACAGA 61.331 55.000 0.00 0.00 0.00 3.41
5153 5655 0.880278 CTGTCCGTTCACCACCACAG 60.880 60.000 0.00 0.00 0.00 3.66
5154 5656 1.145156 CTGTCCGTTCACCACCACA 59.855 57.895 0.00 0.00 0.00 4.17
5155 5657 1.597027 CCTGTCCGTTCACCACCAC 60.597 63.158 0.00 0.00 0.00 4.16
5174 5676 1.557832 TGTACCTACCTTGGCATGTCC 59.442 52.381 0.00 0.00 0.00 4.02
5207 5709 2.514592 AATCTCCCGCGCACCATG 60.515 61.111 8.75 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.