Multiple sequence alignment - TraesCS7D01G308400

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 TraesCS7D01G308400 chr7D 100.000 4553 0 0 1 4553 390903913 390908465 0.000000e+00 8408.0
1 TraesCS7D01G308400 chr7B 96.849 2761 79 5 849 3608 387642233 387644986 0.000000e+00 4610.0
2 TraesCS7D01G308400 chr7B 92.647 952 36 10 3614 4553 387645038 387645967 0.000000e+00 1339.0
3 TraesCS7D01G308400 chr7B 82.158 241 36 6 63 298 631067340 631067578 2.780000e-47 200.0
4 TraesCS7D01G308400 chr7A 95.489 2793 96 6 820 3606 442948647 442951415 0.000000e+00 4433.0
5 TraesCS7D01G308400 chr7A 91.049 972 43 14 3614 4553 442951469 442952428 0.000000e+00 1273.0
6 TraesCS7D01G308400 chr7A 89.662 474 32 6 940 1408 442947699 442948160 5.070000e-164 588.0
7 TraesCS7D01G308400 chr3B 81.450 814 99 33 1 775 222141959 222142759 1.800000e-173 619.0
8 TraesCS7D01G308400 chr2D 86.646 322 36 7 1 317 469887873 469888192 2.610000e-92 350.0
9 TraesCS7D01G308400 chr2D 75.513 731 122 46 78 768 141106540 141107253 5.720000e-79 305.0
10 TraesCS7D01G308400 chr2D 73.740 377 54 22 61 409 639612261 639612620 6.230000e-19 106.0
11 TraesCS7D01G308400 chrUn 74.452 775 142 49 13 752 63256133 63256886 2.680000e-72 283.0
12 TraesCS7D01G308400 chr5A 74.452 775 142 49 13 752 547372386 547373139 2.680000e-72 283.0
13 TraesCS7D01G308400 chr5A 88.506 87 8 1 284 370 491704217 491704133 2.240000e-18 104.0
14 TraesCS7D01G308400 chr4A 87.391 230 20 9 30 253 709710350 709710124 5.850000e-64 255.0
15 TraesCS7D01G308400 chr2A 77.604 384 71 13 26 403 160043023 160042649 7.670000e-53 219.0
16 TraesCS7D01G308400 chr4D 80.695 259 38 9 79 332 105221506 105221757 1.670000e-44 191.0
17 TraesCS7D01G308400 chr5B 77.358 212 36 10 232 436 596682373 596682167 1.040000e-21 115.0
18 TraesCS7D01G308400 chr6B 73.720 293 58 14 284 561 560667154 560667442 3.750000e-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 TraesCS7D01G308400 chr7D 390903913 390908465 4552 False 8408.0 8408 100.000000 1 4553 1 chr7D.!!$F1 4552
1 TraesCS7D01G308400 chr7B 387642233 387645967 3734 False 2974.5 4610 94.748000 849 4553 2 chr7B.!!$F2 3704
2 TraesCS7D01G308400 chr7A 442947699 442952428 4729 False 2098.0 4433 92.066667 820 4553 3 chr7A.!!$F1 3733
3 TraesCS7D01G308400 chr3B 222141959 222142759 800 False 619.0 619 81.450000 1 775 1 chr3B.!!$F1 774
4 TraesCS7D01G308400 chr2D 141106540 141107253 713 False 305.0 305 75.513000 78 768 1 chr2D.!!$F1 690
5 TraesCS7D01G308400 chrUn 63256133 63256886 753 False 283.0 283 74.452000 13 752 1 chrUn.!!$F1 739
6 TraesCS7D01G308400 chr5A 547372386 547373139 753 False 283.0 283 74.452000 13 752 1 chr5A.!!$F1 739

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
779 888 0.110509 TACACGTTCACGAGCTCGAC 60.111 55.0 40.58 26.73 43.02 4.20 F
1835 1967 0.034477 GTTGGTGGGGTCTGTATGGG 60.034 60.0 0.00 0.00 0.00 4.00 F
2632 2764 0.182775 GTGGTTGACAGGAGGGTTGT 59.817 55.0 0.00 0.00 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2483 2615 0.037697 AATCCGCGTGCTGAAGTACA 60.038 50.0 4.92 0.00 0.00 2.90 R
3437 3574 0.837691 TTGCTTCCTGCTGGAGAGGA 60.838 55.0 12.54 11.17 44.24 3.71 R
4205 4400 1.295357 TACTGGATTGTGTTGCCGCG 61.295 55.0 0.00 0.00 0.00 6.46 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
47 49 7.588854 TCCGAATATTTACTAAGATCACGAACG 59.411 37.037 0.00 0.00 0.00 3.95
55 57 8.624701 TTACTAAGATCACGAACGGATTTAAG 57.375 34.615 0.00 1.79 0.00 1.85
60 63 5.805994 AGATCACGAACGGATTTAAGTTCTC 59.194 40.000 0.00 0.00 43.15 2.87
191 199 6.399880 CGATCAAAATTTGAAACATGGGAACG 60.400 38.462 12.75 3.21 43.95 3.95
205 214 4.720649 TGGGAACGTTTGTTGAAATTGA 57.279 36.364 0.46 0.00 38.78 2.57
224 233 8.961294 AAATTGAGAACAAAATGATGAAACCA 57.039 26.923 0.00 0.00 39.54 3.67
225 234 9.563748 AAATTGAGAACAAAATGATGAAACCAT 57.436 25.926 0.00 0.00 39.54 3.55
270 280 8.558973 ACATTTTTCTGAAATGGTGAAAACAA 57.441 26.923 13.98 0.00 40.84 2.83
378 440 4.609691 TCTTGAACTGTTTCGAAACACC 57.390 40.909 33.86 25.19 43.45 4.16
382 444 6.316640 TCTTGAACTGTTTCGAAACACCAATA 59.683 34.615 33.86 24.77 43.45 1.90
383 445 6.438259 TGAACTGTTTCGAAACACCAATAA 57.562 33.333 33.86 17.51 43.45 1.40
388 450 8.710835 ACTGTTTCGAAACACCAATAATTTTT 57.289 26.923 33.86 8.50 43.45 1.94
453 515 7.689299 TGAATTTCGAACAAATTTTGGAAACC 58.311 30.769 13.42 9.11 36.43 3.27
456 518 5.331876 TCGAACAAATTTTGGAAACCAGT 57.668 34.783 13.42 0.00 33.81 4.00
457 519 5.725362 TCGAACAAATTTTGGAAACCAGTT 58.275 33.333 13.42 0.00 33.81 3.16
649 758 8.504812 AACGTAAACAGAAAAAGAAAAACGAA 57.495 26.923 0.00 0.00 0.00 3.85
650 759 8.153724 ACGTAAACAGAAAAAGAAAAACGAAG 57.846 30.769 0.00 0.00 0.00 3.79
651 760 8.016801 ACGTAAACAGAAAAAGAAAAACGAAGA 58.983 29.630 0.00 0.00 0.00 2.87
656 765 9.471084 AACAGAAAAAGAAAAACGAAGAAGAAA 57.529 25.926 0.00 0.00 0.00 2.52
657 766 8.912658 ACAGAAAAAGAAAAACGAAGAAGAAAC 58.087 29.630 0.00 0.00 0.00 2.78
658 767 8.911662 CAGAAAAAGAAAAACGAAGAAGAAACA 58.088 29.630 0.00 0.00 0.00 2.83
659 768 9.471084 AGAAAAAGAAAAACGAAGAAGAAACAA 57.529 25.926 0.00 0.00 0.00 2.83
711 820 3.572642 AGAAGGTTCCCAAAACCGAATT 58.427 40.909 1.52 0.00 44.82 2.17
756 865 2.145536 GGTTCCTAAAACCGAAAGCGA 58.854 47.619 0.00 0.00 40.82 4.93
775 884 2.325761 GATGTTACACGTTCACGAGCT 58.674 47.619 6.30 0.00 43.02 4.09
776 885 1.762419 TGTTACACGTTCACGAGCTC 58.238 50.000 6.30 2.73 43.02 4.09
777 886 0.701303 GTTACACGTTCACGAGCTCG 59.299 55.000 33.45 33.45 43.02 5.03
778 887 0.587768 TTACACGTTCACGAGCTCGA 59.412 50.000 40.58 18.63 43.02 4.04
779 888 0.110509 TACACGTTCACGAGCTCGAC 60.111 55.000 40.58 26.73 43.02 4.20
780 889 1.370051 CACGTTCACGAGCTCGACA 60.370 57.895 40.58 23.54 43.02 4.35
781 890 1.082038 ACGTTCACGAGCTCGACAG 60.082 57.895 40.58 27.51 43.02 3.51
782 891 1.082038 CGTTCACGAGCTCGACAGT 60.082 57.895 40.58 17.41 43.02 3.55
783 892 0.660595 CGTTCACGAGCTCGACAGTT 60.661 55.000 40.58 17.00 43.02 3.16
784 893 1.488527 GTTCACGAGCTCGACAGTTT 58.511 50.000 40.58 16.19 43.02 2.66
785 894 1.190323 GTTCACGAGCTCGACAGTTTG 59.810 52.381 40.58 26.45 43.02 2.93
786 895 0.666374 TCACGAGCTCGACAGTTTGA 59.334 50.000 40.58 28.19 43.02 2.69
787 896 0.778815 CACGAGCTCGACAGTTTGAC 59.221 55.000 40.58 0.00 43.02 3.18
788 897 0.660595 ACGAGCTCGACAGTTTGACG 60.661 55.000 40.58 12.33 43.02 4.35
790 899 0.939577 GAGCTCGACAGTTTGACGCA 60.940 55.000 0.00 0.00 35.65 5.24
791 900 0.529773 AGCTCGACAGTTTGACGCAA 60.530 50.000 0.00 0.00 35.65 4.85
792 901 0.303493 GCTCGACAGTTTGACGCAAA 59.697 50.000 1.63 1.63 35.65 3.68
793 902 1.267832 GCTCGACAGTTTGACGCAAAA 60.268 47.619 6.59 0.00 35.03 2.44
794 903 2.602217 GCTCGACAGTTTGACGCAAAAT 60.602 45.455 6.59 3.58 35.03 1.82
809 918 3.632189 GCAAAATGCGTCAGGATATTCC 58.368 45.455 0.00 0.00 32.39 3.01
810 919 3.550842 GCAAAATGCGTCAGGATATTCCC 60.551 47.826 0.00 0.00 32.57 3.97
811 920 3.864789 AAATGCGTCAGGATATTCCCT 57.135 42.857 0.00 0.00 37.19 4.20
813 922 2.088104 TGCGTCAGGATATTCCCTCT 57.912 50.000 0.00 0.00 37.19 3.69
814 923 1.964223 TGCGTCAGGATATTCCCTCTC 59.036 52.381 0.00 0.00 37.19 3.20
815 924 1.068194 GCGTCAGGATATTCCCTCTCG 60.068 57.143 0.00 0.00 37.19 4.04
816 925 1.068194 CGTCAGGATATTCCCTCTCGC 60.068 57.143 0.00 0.00 37.19 5.03
817 926 2.243810 GTCAGGATATTCCCTCTCGCT 58.756 52.381 0.00 0.00 37.19 4.93
818 927 2.029470 GTCAGGATATTCCCTCTCGCTG 60.029 54.545 0.00 0.00 37.19 5.18
819 928 0.972883 AGGATATTCCCTCTCGCTGC 59.027 55.000 0.00 0.00 37.19 5.25
821 930 1.070758 GGATATTCCCTCTCGCTGCAA 59.929 52.381 0.00 0.00 0.00 4.08
822 931 2.411904 GATATTCCCTCTCGCTGCAAG 58.588 52.381 0.00 0.00 0.00 4.01
842 972 1.098050 CTTTCATCCGGCCTTTCCAG 58.902 55.000 0.00 0.00 34.01 3.86
855 985 3.446516 GCCTTTCCAGCTCATGAAATTCT 59.553 43.478 0.00 0.00 30.67 2.40
865 995 2.026356 TCATGAAATTCTCTTGGGCCGA 60.026 45.455 0.00 0.00 31.55 5.54
866 996 2.806945 TGAAATTCTCTTGGGCCGAT 57.193 45.000 0.00 0.00 0.00 4.18
875 1005 2.689983 CTCTTGGGCCGATTTATTGCTT 59.310 45.455 0.00 0.00 0.00 3.91
910 1040 2.192175 CATCCCCTAACGGCCCAC 59.808 66.667 0.00 0.00 0.00 4.61
928 1058 4.566907 GCCCACTAATACCCTCAGAAACAA 60.567 45.833 0.00 0.00 0.00 2.83
976 1106 3.211045 CTTCTTCGTCTTCCCCAAAACA 58.789 45.455 0.00 0.00 0.00 2.83
980 1110 2.846193 TCGTCTTCCCCAAAACAAGAG 58.154 47.619 0.00 0.00 0.00 2.85
997 1128 1.222936 AGCAGAGCTCCAAATCCCG 59.777 57.895 10.93 0.00 30.62 5.14
1129 1260 2.544686 CGTCTCCGAACGATCTGTAGAT 59.455 50.000 0.00 0.00 45.37 1.98
1130 1261 3.002451 CGTCTCCGAACGATCTGTAGATT 59.998 47.826 0.00 0.00 45.37 2.40
1176 1308 1.526455 AAACGGCGTTAGGGTTGCA 60.526 52.632 27.05 0.00 0.00 4.08
1209 1341 2.225041 ACCTTTTGCTTTCCTCCCTACC 60.225 50.000 0.00 0.00 0.00 3.18
1380 1512 5.980698 CGATAGGATGTTCATATGATGGC 57.019 43.478 6.17 1.16 0.00 4.40
1408 1540 2.090153 CCCTCCTCCCCCTAACAGATTA 60.090 54.545 0.00 0.00 0.00 1.75
1678 1810 2.665603 GGAGAAAGCCGACTGCCT 59.334 61.111 0.00 0.00 42.71 4.75
1699 1831 1.826720 GCATTTCCAAGAGGCCATGAA 59.173 47.619 5.01 0.00 33.74 2.57
1719 1851 3.518634 AATTGACGCAACAACTTGGTT 57.481 38.095 0.00 0.00 32.50 3.67
1825 1957 1.266178 GAATGGAAAGGTTGGTGGGG 58.734 55.000 0.00 0.00 0.00 4.96
1835 1967 0.034477 GTTGGTGGGGTCTGTATGGG 60.034 60.000 0.00 0.00 0.00 4.00
1961 2093 1.202580 ACCGGAAGCATGCAGAGTATC 60.203 52.381 21.98 7.67 0.00 2.24
2408 2540 4.660303 AGGGAGGCAGATTATGATTACACA 59.340 41.667 0.00 0.00 0.00 3.72
2483 2615 3.914426 AGAATCCGACCACTTTATGCT 57.086 42.857 0.00 0.00 0.00 3.79
2484 2616 3.535561 AGAATCCGACCACTTTATGCTG 58.464 45.455 0.00 0.00 0.00 4.41
2632 2764 0.182775 GTGGTTGACAGGAGGGTTGT 59.817 55.000 0.00 0.00 0.00 3.32
2686 2818 6.740681 GCAGGTAAGGACTAAGTTACTGTGTT 60.741 42.308 0.00 0.00 31.07 3.32
2689 2821 7.289549 AGGTAAGGACTAAGTTACTGTGTTTCT 59.710 37.037 0.00 0.00 31.07 2.52
2690 2822 7.930325 GGTAAGGACTAAGTTACTGTGTTTCTT 59.070 37.037 0.00 0.53 31.07 2.52
2693 2825 8.803397 AGGACTAAGTTACTGTGTTTCTTTTT 57.197 30.769 0.00 0.00 0.00 1.94
3170 3307 4.142687 CCTGCGGTTCGAACAATCTAAAAT 60.143 41.667 28.24 0.00 0.00 1.82
3192 3329 9.426534 AAAATAGATAAGGAAGAAAAGGATGGG 57.573 33.333 0.00 0.00 0.00 4.00
3281 3418 4.038402 CCCTATCATGGATTGGCTGAAAAC 59.962 45.833 0.00 0.00 34.49 2.43
3288 3425 2.087857 ATTGGCTGAAAACCCCCGGA 62.088 55.000 0.73 0.00 0.00 5.14
3304 3441 1.207089 CCGGAAGTGCATCCTTGACTA 59.793 52.381 0.00 0.00 37.34 2.59
3381 3518 5.473162 TGGTATGATATGCAAAGGGAAATCG 59.527 40.000 0.00 0.00 0.00 3.34
3437 3574 6.409524 TTTGGAATTGAAGAAGAACTGCAT 57.590 33.333 0.00 0.00 33.64 3.96
3527 3664 7.042335 CACGGAATGTCTACTAGGAAAAAGAT 58.958 38.462 0.00 0.00 0.00 2.40
3547 3684 1.047801 GAAGGATCTCTCCAGCCTCC 58.952 60.000 0.00 0.00 44.79 4.30
3548 3685 0.341258 AAGGATCTCTCCAGCCTCCA 59.659 55.000 0.00 0.00 44.79 3.86
3549 3686 0.398381 AGGATCTCTCCAGCCTCCAC 60.398 60.000 0.00 0.00 44.79 4.02
3599 3736 1.795170 GAAGTTGCCAGCAAAGCGGA 61.795 55.000 6.64 0.00 37.70 5.54
3628 3811 8.006590 GCTACTAAATGATCTAAATCAAGTGCG 58.993 37.037 0.00 0.00 44.85 5.34
3641 3824 1.798813 CAAGTGCGAACCTAACACTCC 59.201 52.381 0.00 0.00 43.63 3.85
3647 3834 2.353803 GCGAACCTAACACTCCTGACAT 60.354 50.000 0.00 0.00 0.00 3.06
3657 3844 6.469782 AACACTCCTGACATTTTTGTTGAT 57.530 33.333 0.00 0.00 0.00 2.57
3701 3888 4.955450 TCATGGATAACCTTTGGATGTTGG 59.045 41.667 0.00 0.00 37.04 3.77
3821 4015 6.478512 AGATCTTAGGGTTGTGATCTCTTC 57.521 41.667 0.00 0.00 40.90 2.87
3837 4031 5.730296 TCTCTTCCTGATTTCGAACTCTT 57.270 39.130 15.49 0.00 0.00 2.85
3845 4039 4.568956 TGATTTCGAACTCTTGATGCTGA 58.431 39.130 15.49 0.00 0.00 4.26
4017 4211 1.327303 TTGTGCGCCTTTGGAATCTT 58.673 45.000 4.18 0.00 0.00 2.40
4146 4341 3.034635 TGCCCCTAAAGTTTGCTTCAAA 58.965 40.909 0.00 0.00 33.01 2.69
4150 4345 6.183361 TGCCCCTAAAGTTTGCTTCAAATAAA 60.183 34.615 0.00 0.00 35.74 1.40
4205 4400 4.512571 TCCACTTTACGCCAAGAAAAGTAC 59.487 41.667 1.32 0.00 40.52 2.73
4208 4403 1.062258 TACGCCAAGAAAAGTACGCG 58.938 50.000 3.53 3.53 44.78 6.01
4271 4466 8.649973 AAAGAATTTGTCCTCGTAGATATCAC 57.350 34.615 5.32 0.69 36.60 3.06
4336 4555 1.681264 CTGGCTTCGGTCCAAAAACTT 59.319 47.619 0.00 0.00 32.41 2.66
4354 4573 3.864243 ACTTTACACAACACAACCGAGA 58.136 40.909 0.00 0.00 0.00 4.04
4367 4586 0.815734 ACCGAGACCAACATCCTACG 59.184 55.000 0.00 0.00 0.00 3.51
4510 4729 2.023673 CACCAACCTTGCTGTTCTCAA 58.976 47.619 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 37 6.164176 AGAACTTAAATCCGTTCGTGATCTT 58.836 36.000 0.00 0.00 43.15 2.40
169 177 5.665459 ACGTTCCCATGTTTCAAATTTTGA 58.335 33.333 7.74 7.74 38.04 2.69
205 214 7.499292 TGTTCATGGTTTCATCATTTTGTTCT 58.501 30.769 0.00 0.00 0.00 3.01
239 249 6.424509 TCACCATTTCAGAAAAATGTTCATGC 59.575 34.615 0.00 0.00 36.24 4.06
349 394 8.807581 GTTTCGAAACAGTTCAAGAATTTCAAT 58.192 29.630 30.99 0.00 38.74 2.57
427 489 8.341903 GGTTTCCAAAATTTGTTCGAAATTCAT 58.658 29.630 0.00 0.00 0.00 2.57
507 574 8.771920 TGCTCTCGTCTTAATTTCTTTTCATA 57.228 30.769 0.00 0.00 0.00 2.15
508 575 7.672983 TGCTCTCGTCTTAATTTCTTTTCAT 57.327 32.000 0.00 0.00 0.00 2.57
510 577 8.956617 AAATGCTCTCGTCTTAATTTCTTTTC 57.043 30.769 0.00 0.00 0.00 2.29
622 731 8.629132 TCGTTTTTCTTTTTCTGTTTACGTTTC 58.371 29.630 0.00 0.00 0.00 2.78
632 741 8.911662 TGTTTCTTCTTCGTTTTTCTTTTTCTG 58.088 29.630 0.00 0.00 0.00 3.02
674 783 5.048846 ACCTTCTAAAAAGCTCCTGAACA 57.951 39.130 0.00 0.00 0.00 3.18
711 820 2.093869 CAGAGATTCCCGACCGGTTTTA 60.094 50.000 9.42 0.00 0.00 1.52
721 830 2.237392 AGGAACCTTTCAGAGATTCCCG 59.763 50.000 0.00 0.00 39.80 5.14
756 865 2.325761 GAGCTCGTGAACGTGTAACAT 58.674 47.619 0.00 0.00 40.80 2.71
775 884 2.852901 GCATTTTGCGTCAAACTGTCGA 60.853 45.455 17.23 0.00 36.71 4.20
776 885 1.447938 GCATTTTGCGTCAAACTGTCG 59.552 47.619 17.23 0.00 36.71 4.35
788 897 3.550842 GGGAATATCCTGACGCATTTTGC 60.551 47.826 0.00 0.00 37.01 3.68
790 899 4.137543 GAGGGAATATCCTGACGCATTTT 58.862 43.478 0.00 0.00 37.25 1.82
791 900 3.392616 AGAGGGAATATCCTGACGCATTT 59.607 43.478 0.00 0.00 37.25 2.32
792 901 2.975489 AGAGGGAATATCCTGACGCATT 59.025 45.455 0.00 0.00 37.25 3.56
793 902 2.564947 GAGAGGGAATATCCTGACGCAT 59.435 50.000 0.00 0.00 37.25 4.73
794 903 1.964223 GAGAGGGAATATCCTGACGCA 59.036 52.381 0.00 0.00 37.25 5.24
796 905 1.068194 GCGAGAGGGAATATCCTGACG 60.068 57.143 0.00 0.00 37.25 4.35
797 906 2.029470 CAGCGAGAGGGAATATCCTGAC 60.029 54.545 0.00 0.00 37.25 3.51
800 909 0.972883 GCAGCGAGAGGGAATATCCT 59.027 55.000 0.00 0.00 40.43 3.24
801 910 0.681733 TGCAGCGAGAGGGAATATCC 59.318 55.000 0.00 0.00 35.23 2.59
802 911 2.411904 CTTGCAGCGAGAGGGAATATC 58.588 52.381 3.08 0.00 0.00 1.63
803 912 1.542108 GCTTGCAGCGAGAGGGAATAT 60.542 52.381 14.52 0.00 0.00 1.28
804 913 0.179073 GCTTGCAGCGAGAGGGAATA 60.179 55.000 14.52 0.00 0.00 1.75
805 914 1.451028 GCTTGCAGCGAGAGGGAAT 60.451 57.895 14.52 0.00 0.00 3.01
806 915 2.046892 GCTTGCAGCGAGAGGGAA 60.047 61.111 14.52 0.00 0.00 3.97
815 924 1.138247 CCGGATGAAAGCTTGCAGC 59.862 57.895 14.65 14.65 42.84 5.25
816 925 1.138247 GCCGGATGAAAGCTTGCAG 59.862 57.895 13.80 0.00 0.00 4.41
817 926 2.342650 GGCCGGATGAAAGCTTGCA 61.343 57.895 10.26 10.26 0.00 4.08
818 927 1.598701 AAGGCCGGATGAAAGCTTGC 61.599 55.000 5.05 0.00 0.00 4.01
819 928 0.890683 AAAGGCCGGATGAAAGCTTG 59.109 50.000 5.05 0.00 0.00 4.01
821 930 0.681243 GGAAAGGCCGGATGAAAGCT 60.681 55.000 5.05 0.00 0.00 3.74
822 931 0.965363 TGGAAAGGCCGGATGAAAGC 60.965 55.000 5.05 0.00 40.66 3.51
823 932 1.098050 CTGGAAAGGCCGGATGAAAG 58.902 55.000 5.05 0.00 46.81 2.62
824 933 0.965363 GCTGGAAAGGCCGGATGAAA 60.965 55.000 5.05 0.00 46.81 2.69
830 960 2.117156 CATGAGCTGGAAAGGCCGG 61.117 63.158 0.00 0.00 46.56 6.13
832 962 1.549203 TTTCATGAGCTGGAAAGGCC 58.451 50.000 0.00 0.00 37.10 5.19
842 972 2.100418 GGCCCAAGAGAATTTCATGAGC 59.900 50.000 0.00 0.00 28.71 4.26
855 985 2.435372 AGCAATAAATCGGCCCAAGA 57.565 45.000 0.00 0.00 0.00 3.02
910 1040 7.148069 GGGATGTTTTGTTTCTGAGGGTATTAG 60.148 40.741 0.00 0.00 0.00 1.73
928 1058 1.555967 CGGATTGTTGGGGGATGTTT 58.444 50.000 0.00 0.00 0.00 2.83
980 1110 1.821332 CCGGGATTTGGAGCTCTGC 60.821 63.158 14.64 0.00 0.00 4.26
990 1121 1.153168 CGACTCCATGCCGGGATTT 60.153 57.895 5.36 0.00 36.09 2.17
1082 1213 9.396938 GAGTTCGAGTAGAAGGCTATTAATTAC 57.603 37.037 0.00 0.00 39.95 1.89
1129 1260 3.420893 GACCCACAACAGATGGATGAAA 58.579 45.455 0.00 0.00 39.87 2.69
1130 1261 2.615240 CGACCCACAACAGATGGATGAA 60.615 50.000 0.00 0.00 39.87 2.57
1176 1308 0.461135 CAAAAGGTGTTGGCACTGCT 59.539 50.000 0.00 0.00 44.65 4.24
1209 1341 0.318784 GCGGCGATCTACAAGTAGGG 60.319 60.000 12.98 0.00 34.06 3.53
1380 1512 0.800239 AGGGGGAGGAGGGGTATATG 59.200 60.000 0.00 0.00 0.00 1.78
1408 1540 2.504367 GCCGTATTCCACCATAGCAAT 58.496 47.619 0.00 0.00 0.00 3.56
1678 1810 1.187974 CATGGCCTCTTGGAAATGCA 58.812 50.000 3.32 0.00 34.57 3.96
1699 1831 3.443976 GAACCAAGTTGTTGCGTCAATT 58.556 40.909 1.45 0.00 31.64 2.32
1719 1851 1.364901 GAACGTCCTGAACCACCGA 59.635 57.895 0.00 0.00 0.00 4.69
1825 1957 4.081087 ACATCACAGTAACCCCATACAGAC 60.081 45.833 0.00 0.00 0.00 3.51
1835 1967 3.990092 TGAGTCACACATCACAGTAACC 58.010 45.455 0.00 0.00 0.00 2.85
1961 2093 8.067751 TCCTAATCAATTCATAGAGATACGGG 57.932 38.462 0.00 0.00 0.00 5.28
2447 2579 7.314393 GTCGGATTCTATCTAGTACCCATTTC 58.686 42.308 0.00 0.00 0.00 2.17
2483 2615 0.037697 AATCCGCGTGCTGAAGTACA 60.038 50.000 4.92 0.00 0.00 2.90
2484 2616 0.645868 GAATCCGCGTGCTGAAGTAC 59.354 55.000 4.92 0.00 0.00 2.73
2632 2764 9.927081 TCATAAGAGTGCCATCATATAGATCTA 57.073 33.333 4.57 4.57 33.72 1.98
2967 3104 8.809468 GGAGTTTTACTTCTCCTCCAAAATAT 57.191 34.615 0.00 0.00 44.68 1.28
3170 3307 7.147302 CCTTCCCATCCTTTTCTTCCTTATCTA 60.147 40.741 0.00 0.00 0.00 1.98
3215 3352 5.281727 CAACATCCATCATCAATCTGCAAG 58.718 41.667 0.00 0.00 0.00 4.01
3281 3418 2.983879 AAGGATGCACTTCCGGGGG 61.984 63.158 0.00 0.00 40.94 5.40
3288 3425 3.557898 CCAGTGTAGTCAAGGATGCACTT 60.558 47.826 0.00 0.00 35.34 3.16
3304 3441 4.821805 ACATTCATCTTTTTCGTCCAGTGT 59.178 37.500 0.00 0.00 0.00 3.55
3437 3574 0.837691 TTGCTTCCTGCTGGAGAGGA 60.838 55.000 12.54 11.17 44.24 3.71
3527 3664 1.690845 GGAGGCTGGAGAGATCCTTCA 60.691 57.143 0.00 0.00 0.00 3.02
3608 3745 6.375455 AGGTTCGCACTTGATTTAGATCATTT 59.625 34.615 0.00 0.00 41.71 2.32
3610 3747 5.431765 AGGTTCGCACTTGATTTAGATCAT 58.568 37.500 0.00 0.00 41.71 2.45
3611 3748 4.832248 AGGTTCGCACTTGATTTAGATCA 58.168 39.130 0.00 0.00 40.46 2.92
3612 3749 6.312918 TGTTAGGTTCGCACTTGATTTAGATC 59.687 38.462 0.00 0.00 0.00 2.75
3628 3811 6.039382 ACAAAAATGTCAGGAGTGTTAGGTTC 59.961 38.462 0.00 0.00 0.00 3.62
3657 3844 9.231297 CCATGACAGATTAACCTAAAGAAGAAA 57.769 33.333 0.00 0.00 0.00 2.52
3680 3867 4.016666 TCCCAACATCCAAAGGTTATCCAT 60.017 41.667 0.00 0.00 35.89 3.41
3701 3888 3.152341 CCATCTGAATAGCCACCATTCC 58.848 50.000 0.00 0.00 32.46 3.01
3821 4015 3.937706 AGCATCAAGAGTTCGAAATCAGG 59.062 43.478 25.61 17.02 0.00 3.86
3845 4039 7.173047 GGTCATTAAAAATCACAAGTTGGCATT 59.827 33.333 7.96 1.94 0.00 3.56
3926 4120 5.581085 AGATAACCAGCGAACATTAGAACAC 59.419 40.000 0.00 0.00 0.00 3.32
4048 4242 7.320443 TGATGAAACATTTATGCCTACAGAC 57.680 36.000 0.00 0.00 0.00 3.51
4175 4370 4.158025 TCTTGGCGTAAAGTGGAAAACAAA 59.842 37.500 0.18 0.00 0.00 2.83
4205 4400 1.295357 TACTGGATTGTGTTGCCGCG 61.295 55.000 0.00 0.00 0.00 6.46
4208 4403 1.533625 TGCTACTGGATTGTGTTGCC 58.466 50.000 0.00 0.00 34.89 4.52
4271 4466 3.932710 ACATGTGCTCTTGTATTACCACG 59.067 43.478 0.00 0.00 31.62 4.94
4336 4555 2.093606 TGGTCTCGGTTGTGTTGTGTAA 60.094 45.455 0.00 0.00 0.00 2.41
4354 4573 2.494870 GGACTGTACGTAGGATGTTGGT 59.505 50.000 0.00 0.00 0.00 3.67
4367 4586 3.260884 TCCCTTTGATCACTGGACTGTAC 59.739 47.826 13.20 0.00 0.00 2.90
4510 4729 5.566469 TGAAGACTAAAATGAACCCGGATT 58.434 37.500 0.73 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.