Multiple sequence alignment - TraesCS7A01G199000

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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 TraesCS7A01G199000 chr7A 100.000 3250 0 0 1 3250 161740025 161736776 0.000000e+00 6002
1 TraesCS7A01G199000 chr7A 77.399 323 52 10 207 526 532736094 532735790 4.310000e-39 172
2 TraesCS7A01G199000 chr7A 98.571 70 1 0 730 799 161739228 161739159 1.220000e-24 124
3 TraesCS7A01G199000 chr7A 98.571 70 1 0 798 867 161739296 161739227 1.220000e-24 124
4 TraesCS7A01G199000 chr7D 94.585 1662 51 11 983 2619 160635856 160634209 0.000000e+00 2534
5 TraesCS7A01G199000 chr7D 96.290 566 17 4 2581 3144 160634169 160633606 0.000000e+00 926
6 TraesCS7A01G199000 chr7D 95.745 47 1 1 885 930 160635953 160635907 1.250000e-09 75
7 TraesCS7A01G199000 chr7B 89.555 1752 111 32 798 2505 121891488 121889765 0.000000e+00 2156
8 TraesCS7A01G199000 chr7B 91.304 299 25 1 2951 3248 119293235 119293533 1.090000e-109 407
9 TraesCS7A01G199000 chr7B 81.369 526 74 17 1 512 121892157 121891642 1.090000e-109 407
10 TraesCS7A01G199000 chr7B 93.103 203 12 2 597 798 121891621 121891420 2.450000e-76 296
11 TraesCS7A01G199000 chr7B 79.196 423 39 23 2209 2602 119290325 119290727 6.960000e-62 248
12 TraesCS7A01G199000 chr1D 78.205 624 94 31 1 605 238652311 238651711 8.570000e-96 361
13 TraesCS7A01G199000 chr1B 79.221 539 84 22 1 526 334900606 334901129 1.860000e-92 350
14 TraesCS7A01G199000 chr3B 78.424 533 100 12 5 526 734728391 734728919 1.870000e-87 333
15 TraesCS7A01G199000 chr3B 78.378 518 93 15 19 526 139419311 139418803 5.230000e-83 318
16 TraesCS7A01G199000 chr3B 77.491 542 104 15 3 533 823089614 823089080 3.150000e-80 309
17 TraesCS7A01G199000 chr5A 78.253 538 101 12 1 526 443726177 443725644 6.720000e-87 331
18 TraesCS7A01G199000 chr6D 77.209 645 93 29 1490 2105 414467768 414468387 8.690000e-86 327
19 TraesCS7A01G199000 chr4D 77.419 527 94 20 4 515 75273594 75274110 1.140000e-74 291
20 TraesCS7A01G199000 chr2D 76.796 543 101 22 3 526 357287890 357287354 6.870000e-72 281


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 TraesCS7A01G199000 chr7A 161736776 161740025 3249 True 2083.333333 6002 99.047333 1 3250 3 chr7A.!!$R2 3249
1 TraesCS7A01G199000 chr7D 160633606 160635953 2347 True 1178.333333 2534 95.540000 885 3144 3 chr7D.!!$R1 2259
2 TraesCS7A01G199000 chr7B 121889765 121892157 2392 True 953.000000 2156 88.009000 1 2505 3 chr7B.!!$R1 2504
3 TraesCS7A01G199000 chr7B 119290325 119293533 3208 False 327.500000 407 85.250000 2209 3248 2 chr7B.!!$F1 1039
4 TraesCS7A01G199000 chr1D 238651711 238652311 600 True 361.000000 361 78.205000 1 605 1 chr1D.!!$R1 604
5 TraesCS7A01G199000 chr1B 334900606 334901129 523 False 350.000000 350 79.221000 1 526 1 chr1B.!!$F1 525
6 TraesCS7A01G199000 chr3B 734728391 734728919 528 False 333.000000 333 78.424000 5 526 1 chr3B.!!$F1 521
7 TraesCS7A01G199000 chr3B 139418803 139419311 508 True 318.000000 318 78.378000 19 526 1 chr3B.!!$R1 507
8 TraesCS7A01G199000 chr3B 823089080 823089614 534 True 309.000000 309 77.491000 3 533 1 chr3B.!!$R2 530
9 TraesCS7A01G199000 chr5A 443725644 443726177 533 True 331.000000 331 78.253000 1 526 1 chr5A.!!$R1 525
10 TraesCS7A01G199000 chr6D 414467768 414468387 619 False 327.000000 327 77.209000 1490 2105 1 chr6D.!!$F1 615
11 TraesCS7A01G199000 chr4D 75273594 75274110 516 False 291.000000 291 77.419000 4 515 1 chr4D.!!$F1 511
12 TraesCS7A01G199000 chr2D 357287354 357287890 536 True 281.000000 281 76.796000 3 526 1 chr2D.!!$R1 523

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
542 567 0.172127 GAGACAGATCAGCAGCGACA 59.828 55.0 0.0 0.0 0.00 4.35 F
1041 1082 0.037697 TGACGAAAGGACACCCGATG 60.038 55.0 0.0 0.0 37.58 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1747 1808 1.285578 GATCTTGCAGAGGTCGAAGC 58.714 55.0 0.0 0.0 0.0 3.86 R
2768 3139 1.420430 AAGGGTGACGGAAAGACAGA 58.580 50.0 0.0 0.0 0.0 3.41 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
86 88 1.445095 GCGCTGTCATCATCTCCCT 59.555 57.895 0.00 0.00 0.00 4.20
87 89 0.599728 GCGCTGTCATCATCTCCCTC 60.600 60.000 0.00 0.00 0.00 4.30
90 92 2.039070 GCTGTCATCATCTCCCTCCCT 61.039 57.143 0.00 0.00 0.00 4.20
92 94 1.291939 TGTCATCATCTCCCTCCCTCA 59.708 52.381 0.00 0.00 0.00 3.86
93 95 2.090324 TGTCATCATCTCCCTCCCTCAT 60.090 50.000 0.00 0.00 0.00 2.90
97 99 1.294986 TCATCTCCCTCCCTCATTGGA 59.705 52.381 0.00 0.00 38.35 3.53
154 158 0.396811 ATCGTGCTAAGGCCCCATAC 59.603 55.000 0.00 0.00 37.74 2.39
191 198 4.320608 ACAACAACCACCATCAATGAAC 57.679 40.909 0.00 0.00 0.00 3.18
253 260 1.393539 CGCAAACGAATGAAGACCGAT 59.606 47.619 0.00 0.00 43.93 4.18
285 293 3.797039 TCCACTGAAGACAAACACTGAG 58.203 45.455 0.00 0.00 0.00 3.35
289 297 3.062763 CTGAAGACAAACACTGAGCGAT 58.937 45.455 0.00 0.00 0.00 4.58
340 350 2.993471 GCCCCTCCGACGACGTTAA 61.993 63.158 0.13 0.00 37.88 2.01
368 380 3.728373 GGGACGGGGGCTTCACAT 61.728 66.667 0.00 0.00 0.00 3.21
533 558 2.087646 CACAGGAGACGAGACAGATCA 58.912 52.381 0.00 0.00 0.00 2.92
534 559 2.097304 CACAGGAGACGAGACAGATCAG 59.903 54.545 0.00 0.00 0.00 2.90
536 561 1.098869 GGAGACGAGACAGATCAGCA 58.901 55.000 0.00 0.00 0.00 4.41
537 562 1.065401 GGAGACGAGACAGATCAGCAG 59.935 57.143 0.00 0.00 0.00 4.24
539 564 0.865218 GACGAGACAGATCAGCAGCG 60.865 60.000 0.00 0.00 0.00 5.18
540 565 1.308783 ACGAGACAGATCAGCAGCGA 61.309 55.000 0.00 0.00 0.00 4.93
542 567 0.172127 GAGACAGATCAGCAGCGACA 59.828 55.000 0.00 0.00 0.00 4.35
544 569 1.079543 ACAGATCAGCAGCGACACC 60.080 57.895 0.00 0.00 0.00 4.16
545 570 1.079612 CAGATCAGCAGCGACACCA 60.080 57.895 0.00 0.00 0.00 4.17
546 571 0.461516 CAGATCAGCAGCGACACCAT 60.462 55.000 0.00 0.00 0.00 3.55
558 583 0.969894 GACACCATCGATAGGGAGGG 59.030 60.000 8.68 2.38 43.34 4.30
577 602 3.697619 GGTAAACCCTAGTTGAGCACT 57.302 47.619 0.00 0.00 35.27 4.40
578 603 3.597255 GGTAAACCCTAGTTGAGCACTC 58.403 50.000 0.00 0.00 35.27 3.51
580 605 4.262938 GGTAAACCCTAGTTGAGCACTCTT 60.263 45.833 0.00 0.00 35.27 2.85
584 609 2.039084 CCCTAGTTGAGCACTCTTGGTT 59.961 50.000 0.00 0.00 36.88 3.67
585 610 3.330267 CCTAGTTGAGCACTCTTGGTTC 58.670 50.000 0.00 0.00 36.88 3.62
588 616 0.884704 TTGAGCACTCTTGGTTCGCC 60.885 55.000 0.00 0.00 32.05 5.54
625 653 4.084537 ACGAATCAAACAAAGTACAGAGCG 60.085 41.667 0.00 0.00 0.00 5.03
647 675 0.393537 GCTCTGTTGGCAGGCTATGT 60.394 55.000 0.00 0.00 42.78 2.29
675 703 3.443045 GCTGCCCACCCATGTTCG 61.443 66.667 0.00 0.00 0.00 3.95
733 761 6.245408 TCTCCTATTAAAATATGCCGCCAAT 58.755 36.000 0.00 0.00 0.00 3.16
775 803 7.981789 GTCTTGTTTCTTTTTCTTGGAAGGAAT 59.018 33.333 0.00 0.00 0.00 3.01
804 832 6.633856 ACAGAATTCATCTTAAACCAATGGC 58.366 36.000 8.44 0.00 35.73 4.40
806 834 7.615365 ACAGAATTCATCTTAAACCAATGGCTA 59.385 33.333 8.44 0.00 35.73 3.93
807 835 8.133627 CAGAATTCATCTTAAACCAATGGCTAG 58.866 37.037 8.44 0.00 35.73 3.42
808 836 7.836183 AGAATTCATCTTAAACCAATGGCTAGT 59.164 33.333 8.44 0.00 33.39 2.57
809 837 7.573968 ATTCATCTTAAACCAATGGCTAGTC 57.426 36.000 0.00 0.00 0.00 2.59
810 838 5.437060 TCATCTTAAACCAATGGCTAGTCC 58.563 41.667 0.00 0.00 0.00 3.85
811 839 5.191722 TCATCTTAAACCAATGGCTAGTCCT 59.808 40.000 0.00 0.00 35.26 3.85
812 840 6.385759 TCATCTTAAACCAATGGCTAGTCCTA 59.614 38.462 0.00 0.00 35.26 2.94
813 841 6.235231 TCTTAAACCAATGGCTAGTCCTAG 57.765 41.667 0.00 0.00 36.29 3.02
825 853 4.810191 CTAGTCCTAGCTGGTCTTGTTT 57.190 45.455 0.00 0.00 35.81 2.83
826 854 3.686916 AGTCCTAGCTGGTCTTGTTTC 57.313 47.619 0.00 0.00 37.07 2.78
827 855 3.243724 AGTCCTAGCTGGTCTTGTTTCT 58.756 45.455 0.00 0.00 37.07 2.52
828 856 3.648545 AGTCCTAGCTGGTCTTGTTTCTT 59.351 43.478 0.00 0.00 37.07 2.52
829 857 4.103311 AGTCCTAGCTGGTCTTGTTTCTTT 59.897 41.667 0.00 0.00 37.07 2.52
830 858 4.822350 GTCCTAGCTGGTCTTGTTTCTTTT 59.178 41.667 0.00 0.00 37.07 2.27
831 859 5.299531 GTCCTAGCTGGTCTTGTTTCTTTTT 59.700 40.000 0.00 0.00 37.07 1.94
832 860 5.531287 TCCTAGCTGGTCTTGTTTCTTTTTC 59.469 40.000 0.00 0.00 37.07 2.29
833 861 5.532779 CCTAGCTGGTCTTGTTTCTTTTTCT 59.467 40.000 0.00 0.00 0.00 2.52
834 862 5.921962 AGCTGGTCTTGTTTCTTTTTCTT 57.078 34.783 0.00 0.00 0.00 2.52
835 863 5.654497 AGCTGGTCTTGTTTCTTTTTCTTG 58.346 37.500 0.00 0.00 0.00 3.02
836 864 5.418840 AGCTGGTCTTGTTTCTTTTTCTTGA 59.581 36.000 0.00 0.00 0.00 3.02
837 865 6.071391 AGCTGGTCTTGTTTCTTTTTCTTGAA 60.071 34.615 0.00 0.00 0.00 2.69
838 866 6.589907 GCTGGTCTTGTTTCTTTTTCTTGAAA 59.410 34.615 0.00 0.00 0.00 2.69
839 867 7.201470 GCTGGTCTTGTTTCTTTTTCTTGAAAG 60.201 37.037 0.00 0.00 37.85 2.62
840 868 7.096551 TGGTCTTGTTTCTTTTTCTTGAAAGG 58.903 34.615 0.00 0.00 37.27 3.11
841 869 7.039363 TGGTCTTGTTTCTTTTTCTTGAAAGGA 60.039 33.333 0.00 0.00 37.27 3.36
842 870 7.817478 GGTCTTGTTTCTTTTTCTTGAAAGGAA 59.183 33.333 8.39 8.39 40.34 3.36
843 871 9.371136 GTCTTGTTTCTTTTTCTTGAAAGGAAT 57.629 29.630 11.28 0.00 41.27 3.01
844 872 9.942850 TCTTGTTTCTTTTTCTTGAAAGGAATT 57.057 25.926 11.28 0.00 41.27 2.17
847 875 9.717942 TGTTTCTTTTTCTTGAAAGGAATTTGA 57.282 25.926 11.28 0.00 41.27 2.69
850 878 9.717942 TTCTTTTTCTTGAAAGGAATTTGAACA 57.282 25.926 8.39 0.00 38.11 3.18
851 879 9.369904 TCTTTTTCTTGAAAGGAATTTGAACAG 57.630 29.630 0.00 0.00 37.27 3.16
852 880 9.369904 CTTTTTCTTGAAAGGAATTTGAACAGA 57.630 29.630 0.00 0.00 33.90 3.41
853 881 9.717942 TTTTTCTTGAAAGGAATTTGAACAGAA 57.282 25.926 0.00 0.00 0.00 3.02
854 882 9.889128 TTTTCTTGAAAGGAATTTGAACAGAAT 57.111 25.926 0.00 0.00 0.00 2.40
855 883 9.889128 TTTCTTGAAAGGAATTTGAACAGAATT 57.111 25.926 0.00 0.00 0.00 2.17
856 884 9.533253 TTCTTGAAAGGAATTTGAACAGAATTC 57.467 29.630 0.00 0.00 40.88 2.17
857 885 8.694540 TCTTGAAAGGAATTTGAACAGAATTCA 58.305 29.630 8.44 0.00 42.50 2.57
858 886 9.485206 CTTGAAAGGAATTTGAACAGAATTCAT 57.515 29.630 8.44 2.30 42.50 2.57
859 887 9.480053 TTGAAAGGAATTTGAACAGAATTCATC 57.520 29.630 8.44 3.77 42.50 2.92
860 888 8.863086 TGAAAGGAATTTGAACAGAATTCATCT 58.137 29.630 8.44 0.00 42.50 2.90
861 889 9.702494 GAAAGGAATTTGAACAGAATTCATCTT 57.298 29.630 8.44 0.00 42.50 2.40
955 986 9.533983 GATATAATACTGACACGAAAATGCATG 57.466 33.333 0.00 0.00 0.00 4.06
960 991 6.252967 ACTGACACGAAAATGCATGAATAA 57.747 33.333 0.00 0.00 0.00 1.40
961 992 6.317088 ACTGACACGAAAATGCATGAATAAG 58.683 36.000 0.00 0.00 0.00 1.73
962 993 5.639757 TGACACGAAAATGCATGAATAAGG 58.360 37.500 0.00 0.00 0.00 2.69
964 995 3.798337 CACGAAAATGCATGAATAAGGCC 59.202 43.478 0.00 0.00 0.00 5.19
968 999 1.609208 ATGCATGAATAAGGCCGACC 58.391 50.000 0.00 0.00 0.00 4.79
977 1016 0.325602 TAAGGCCGACCGAAACCAAT 59.674 50.000 0.00 0.00 42.76 3.16
998 1037 0.693049 GAAAGAGGAAGCCCACCTGA 59.307 55.000 0.00 0.00 37.93 3.86
1000 1039 0.178891 AAGAGGAAGCCCACCTGAGA 60.179 55.000 0.00 0.00 37.93 3.27
1009 1048 3.041946 AGCCCACCTGAGACTTATAAGG 58.958 50.000 16.73 0.92 35.82 2.69
1040 1081 0.682852 TTGACGAAAGGACACCCGAT 59.317 50.000 0.00 0.00 37.58 4.18
1041 1082 0.037697 TGACGAAAGGACACCCGATG 60.038 55.000 0.00 0.00 37.58 3.84
1106 1151 1.068121 ACCCACCTCTTCTCCCAAAG 58.932 55.000 0.00 0.00 0.00 2.77
1235 1293 0.173708 ACGAAGAGACCATCGCCTTC 59.826 55.000 0.00 0.00 42.61 3.46
1318 1379 0.914902 TCTGACGAGGAGGAGGAGGA 60.915 60.000 0.00 0.00 0.00 3.71
1319 1380 0.465460 CTGACGAGGAGGAGGAGGAG 60.465 65.000 0.00 0.00 0.00 3.69
1320 1381 1.152839 GACGAGGAGGAGGAGGAGG 60.153 68.421 0.00 0.00 0.00 4.30
1792 1853 2.046314 CGGCCACAAGTACAGGGG 60.046 66.667 2.24 2.42 0.00 4.79
1823 1884 1.447489 CGCTTCTACTGCTGCTGCT 60.447 57.895 17.00 0.00 40.48 4.24
1824 1885 1.694018 CGCTTCTACTGCTGCTGCTG 61.694 60.000 18.66 18.66 42.70 4.41
1827 1888 2.046604 CTACTGCTGCTGCTGCCA 60.047 61.111 25.44 14.14 41.07 4.92
1828 1889 2.359107 TACTGCTGCTGCTGCCAC 60.359 61.111 25.44 5.59 41.07 5.01
1829 1890 2.799814 CTACTGCTGCTGCTGCCACT 62.800 60.000 25.44 12.09 41.07 4.00
1892 1953 2.036346 GTGTGAGTTGTACCCGTACCTT 59.964 50.000 2.66 0.00 35.26 3.50
1895 1956 1.001181 GAGTTGTACCCGTACCTTGCA 59.999 52.381 2.66 0.00 35.26 4.08
2012 2091 1.483827 CAGCAGATGAAGGTGGAGCTA 59.516 52.381 0.00 0.00 0.00 3.32
2048 2127 2.121963 AGGGAGGTGACCAAGGCA 60.122 61.111 3.63 0.00 0.00 4.75
2148 2234 3.805971 GCATCCTAGAATTGGCAAATTGC 59.194 43.478 9.87 9.87 44.08 3.56
2150 2236 3.088532 TCCTAGAATTGGCAAATTGCGT 58.911 40.909 12.15 0.00 46.21 5.24
2152 2238 3.129287 CCTAGAATTGGCAAATTGCGTCT 59.871 43.478 12.15 13.09 46.21 4.18
2194 2282 2.226896 CGGCAAGAGAGCGTGATCG 61.227 63.158 0.00 0.00 40.37 3.69
2358 2446 6.456449 GCGGATTAGATTTCGCTTTTGAGTAA 60.456 38.462 0.00 0.00 44.10 2.24
2394 2483 5.244178 AGACTGGAGTCGTAAGTCTGAATTT 59.756 40.000 16.63 0.00 46.81 1.82
2524 2643 7.772166 TGTTCTGATATCGATGACTGTTAAGT 58.228 34.615 8.54 0.00 40.21 2.24
2601 2971 7.009723 TGCGTTGTTTTTCTTGTCTATTTTTCC 59.990 33.333 0.00 0.00 0.00 3.13
2638 3009 5.096443 AGAGCCTATTTCAGCTATATGGC 57.904 43.478 2.23 2.23 40.11 4.40
2665 3036 1.006922 GCCTTGTTTGTGCTGGAGC 60.007 57.895 0.00 0.00 42.50 4.70
2768 3139 3.228188 TGGTGAATTTTGTGCTCTCCT 57.772 42.857 0.00 0.00 0.00 3.69
2817 3188 3.445096 TCAGCTCTCACGATTGAATCAGA 59.555 43.478 5.95 1.93 0.00 3.27
3067 5443 1.779092 ACATAGCATCCTCCCAGCATT 59.221 47.619 0.00 0.00 0.00 3.56
3069 5445 0.179009 TAGCATCCTCCCAGCATTGC 60.179 55.000 0.00 0.00 0.00 3.56
3146 5523 6.980593 TGTCCATTTAAATCCTGAACAAGTG 58.019 36.000 0.00 0.00 0.00 3.16
3209 5586 6.083098 TGCACATTACAAGTTTGCAACTAT 57.917 33.333 0.00 0.00 41.91 2.12
3210 5587 5.919707 TGCACATTACAAGTTTGCAACTATG 59.080 36.000 0.00 0.36 41.91 2.23
3216 5593 3.228749 CAAGTTTGCAACTATGTCAGCG 58.771 45.455 0.00 0.00 41.91 5.18
3248 5625 8.835467 TGACAATTTTTCTGTTTCTTTAGACG 57.165 30.769 0.00 0.00 0.00 4.18
3249 5626 8.455682 TGACAATTTTTCTGTTTCTTTAGACGT 58.544 29.630 0.00 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 26 1.742268 GTAGTCGTCACTAGGTGGTCC 59.258 57.143 0.00 0.00 35.67 4.46
90 92 1.976474 GGTTTGCCCGCTCCAATGA 60.976 57.895 0.00 0.00 0.00 2.57
92 94 1.228862 AAGGTTTGCCCGCTCCAAT 60.229 52.632 0.00 0.00 38.74 3.16
93 95 2.197324 AAGGTTTGCCCGCTCCAA 59.803 55.556 0.00 0.00 38.74 3.53
97 99 0.466555 TACAACAAGGTTTGCCCGCT 60.467 50.000 0.00 0.00 38.74 5.52
154 158 1.433053 TTGTTCTGGTGCGTTGGTCG 61.433 55.000 0.00 0.00 43.12 4.79
191 198 8.719648 GTTGGATTCTTCATATCTATGCTTCTG 58.280 37.037 0.00 0.00 33.76 3.02
285 293 0.788995 CAGCGAATCTCATGGATCGC 59.211 55.000 20.05 20.05 43.85 4.58
289 297 1.410517 GTCTCCAGCGAATCTCATGGA 59.589 52.381 0.00 0.00 39.50 3.41
340 350 4.636435 CCGTCCCGGTGGTGCTTT 62.636 66.667 0.00 0.00 42.73 3.51
472 497 0.251787 GGTGGATCCCAGCCTTTGTT 60.252 55.000 9.90 0.00 45.22 2.83
539 564 0.969894 CCCTCCCTATCGATGGTGTC 59.030 60.000 8.54 0.00 0.00 3.67
540 565 0.264955 ACCCTCCCTATCGATGGTGT 59.735 55.000 8.54 0.00 30.46 4.16
542 567 2.970640 GTTTACCCTCCCTATCGATGGT 59.029 50.000 8.54 8.13 35.29 3.55
544 569 3.679824 GGTTTACCCTCCCTATCGATG 57.320 52.381 8.54 0.00 0.00 3.84
558 583 4.538746 AGAGTGCTCAACTAGGGTTTAC 57.461 45.455 1.82 0.00 40.07 2.01
559 584 4.262894 CCAAGAGTGCTCAACTAGGGTTTA 60.263 45.833 1.82 0.00 40.07 2.01
572 597 2.032681 GGGCGAACCAAGAGTGCT 59.967 61.111 0.00 0.00 39.85 4.40
575 600 2.657237 CTCGGGCGAACCAAGAGT 59.343 61.111 0.00 0.00 40.22 3.24
588 616 0.179119 ATTCGTACCCTTTCGCTCGG 60.179 55.000 0.00 0.00 0.00 4.63
597 625 5.613329 TGTACTTTGTTTGATTCGTACCCT 58.387 37.500 0.00 0.00 0.00 4.34
631 659 2.679837 CAACTACATAGCCTGCCAACAG 59.320 50.000 0.00 0.00 44.05 3.16
672 700 2.345991 CGAGCCCAAAGTCCCGAA 59.654 61.111 0.00 0.00 0.00 4.30
675 703 1.376037 CTGACGAGCCCAAAGTCCC 60.376 63.158 0.00 0.00 34.24 4.46
680 708 2.429930 CACCCTGACGAGCCCAAA 59.570 61.111 0.00 0.00 0.00 3.28
681 709 4.329545 GCACCCTGACGAGCCCAA 62.330 66.667 0.00 0.00 0.00 4.12
683 711 4.459089 GAGCACCCTGACGAGCCC 62.459 72.222 0.00 0.00 0.00 5.19
684 712 3.655810 CTGAGCACCCTGACGAGCC 62.656 68.421 0.00 0.00 0.00 4.70
744 772 5.394553 CCAAGAAAAAGAAACAAGACCAGCT 60.395 40.000 0.00 0.00 0.00 4.24
804 832 4.464597 AGAAACAAGACCAGCTAGGACTAG 59.535 45.833 8.91 1.98 41.71 2.57
806 834 3.243724 AGAAACAAGACCAGCTAGGACT 58.756 45.455 8.91 5.49 44.54 3.85
807 835 3.686916 AGAAACAAGACCAGCTAGGAC 57.313 47.619 8.91 3.41 41.22 3.85
808 836 4.706842 AAAGAAACAAGACCAGCTAGGA 57.293 40.909 8.91 0.00 41.22 2.94
809 837 5.532779 AGAAAAAGAAACAAGACCAGCTAGG 59.467 40.000 0.00 0.00 45.67 3.02
810 838 6.625873 AGAAAAAGAAACAAGACCAGCTAG 57.374 37.500 0.00 0.00 0.00 3.42
811 839 6.601613 TCAAGAAAAAGAAACAAGACCAGCTA 59.398 34.615 0.00 0.00 0.00 3.32
812 840 5.418840 TCAAGAAAAAGAAACAAGACCAGCT 59.581 36.000 0.00 0.00 0.00 4.24
813 841 5.650543 TCAAGAAAAAGAAACAAGACCAGC 58.349 37.500 0.00 0.00 0.00 4.85
814 842 7.276438 CCTTTCAAGAAAAAGAAACAAGACCAG 59.724 37.037 0.00 0.00 38.30 4.00
815 843 7.039363 TCCTTTCAAGAAAAAGAAACAAGACCA 60.039 33.333 0.00 0.00 38.30 4.02
816 844 7.320399 TCCTTTCAAGAAAAAGAAACAAGACC 58.680 34.615 0.00 0.00 38.30 3.85
817 845 8.757164 TTCCTTTCAAGAAAAAGAAACAAGAC 57.243 30.769 0.00 0.00 38.30 3.01
818 846 9.942850 AATTCCTTTCAAGAAAAAGAAACAAGA 57.057 25.926 10.07 0.00 38.30 3.02
821 849 9.717942 TCAAATTCCTTTCAAGAAAAAGAAACA 57.282 25.926 10.07 0.00 38.30 2.83
824 852 9.717942 TGTTCAAATTCCTTTCAAGAAAAAGAA 57.282 25.926 8.99 8.99 38.30 2.52
825 853 9.369904 CTGTTCAAATTCCTTTCAAGAAAAAGA 57.630 29.630 0.00 0.00 38.30 2.52
826 854 9.369904 TCTGTTCAAATTCCTTTCAAGAAAAAG 57.630 29.630 0.00 0.00 36.26 2.27
827 855 9.717942 TTCTGTTCAAATTCCTTTCAAGAAAAA 57.282 25.926 0.00 0.00 0.00 1.94
828 856 9.889128 ATTCTGTTCAAATTCCTTTCAAGAAAA 57.111 25.926 0.00 0.00 0.00 2.29
829 857 9.889128 AATTCTGTTCAAATTCCTTTCAAGAAA 57.111 25.926 0.00 0.00 0.00 2.52
830 858 9.533253 GAATTCTGTTCAAATTCCTTTCAAGAA 57.467 29.630 0.00 0.00 37.22 2.52
831 859 8.694540 TGAATTCTGTTCAAATTCCTTTCAAGA 58.305 29.630 7.05 0.00 40.72 3.02
832 860 8.876275 TGAATTCTGTTCAAATTCCTTTCAAG 57.124 30.769 7.05 0.00 40.72 3.02
833 861 9.480053 GATGAATTCTGTTCAAATTCCTTTCAA 57.520 29.630 7.05 0.00 40.72 2.69
834 862 8.863086 AGATGAATTCTGTTCAAATTCCTTTCA 58.137 29.630 7.05 0.00 40.72 2.69
835 863 9.702494 AAGATGAATTCTGTTCAAATTCCTTTC 57.298 29.630 7.05 2.42 40.72 2.62
870 898 9.367160 TCCTTTCCAGTTTAAGATCAAGAAAAT 57.633 29.630 0.00 0.00 0.00 1.82
871 899 8.760980 TCCTTTCCAGTTTAAGATCAAGAAAA 57.239 30.769 0.00 0.00 0.00 2.29
872 900 8.217799 TCTCCTTTCCAGTTTAAGATCAAGAAA 58.782 33.333 0.00 0.00 0.00 2.52
873 901 7.745717 TCTCCTTTCCAGTTTAAGATCAAGAA 58.254 34.615 0.00 0.00 0.00 2.52
874 902 7.316393 TCTCCTTTCCAGTTTAAGATCAAGA 57.684 36.000 0.00 0.00 0.00 3.02
875 903 7.986085 TTCTCCTTTCCAGTTTAAGATCAAG 57.014 36.000 0.00 0.00 0.00 3.02
876 904 8.760980 TTTTCTCCTTTCCAGTTTAAGATCAA 57.239 30.769 0.00 0.00 0.00 2.57
877 905 8.796475 CATTTTCTCCTTTCCAGTTTAAGATCA 58.204 33.333 0.00 0.00 0.00 2.92
878 906 8.797438 ACATTTTCTCCTTTCCAGTTTAAGATC 58.203 33.333 0.00 0.00 0.00 2.75
879 907 8.712228 ACATTTTCTCCTTTCCAGTTTAAGAT 57.288 30.769 0.00 0.00 0.00 2.40
955 986 1.012086 GGTTTCGGTCGGCCTTATTC 58.988 55.000 3.66 0.00 0.00 1.75
960 991 0.107848 CTATTGGTTTCGGTCGGCCT 60.108 55.000 3.66 0.00 0.00 5.19
961 992 0.108041 TCTATTGGTTTCGGTCGGCC 60.108 55.000 0.00 0.00 0.00 6.13
962 993 1.729284 TTCTATTGGTTTCGGTCGGC 58.271 50.000 0.00 0.00 0.00 5.54
964 995 3.617263 CCTCTTTCTATTGGTTTCGGTCG 59.383 47.826 0.00 0.00 0.00 4.79
968 999 4.095036 GGCTTCCTCTTTCTATTGGTTTCG 59.905 45.833 0.00 0.00 0.00 3.46
977 1016 1.909302 CAGGTGGGCTTCCTCTTTCTA 59.091 52.381 0.00 0.00 32.37 2.10
998 1037 3.097614 ACACAGTCGGCCTTATAAGTCT 58.902 45.455 11.50 0.00 0.00 3.24
1000 1039 3.097614 AGACACAGTCGGCCTTATAAGT 58.902 45.455 11.50 0.00 37.67 2.24
1009 1048 0.596600 TTCGTCAAGACACAGTCGGC 60.597 55.000 0.72 0.00 37.67 5.54
1040 1081 1.108776 CTTCTTCGGGTATCGGGACA 58.891 55.000 0.00 0.00 39.77 4.02
1041 1082 0.388294 CCTTCTTCGGGTATCGGGAC 59.612 60.000 0.00 0.00 39.77 4.46
1042 1083 0.757935 CCCTTCTTCGGGTATCGGGA 60.758 60.000 0.00 0.00 39.51 5.14
1043 1084 0.757935 TCCCTTCTTCGGGTATCGGG 60.758 60.000 0.00 0.00 44.95 5.14
1044 1085 1.117150 TTCCCTTCTTCGGGTATCGG 58.883 55.000 0.00 0.00 44.95 4.18
1045 1086 2.547826 GTTTCCCTTCTTCGGGTATCG 58.452 52.381 0.00 0.00 44.95 2.92
1046 1087 2.421107 GGGTTTCCCTTCTTCGGGTATC 60.421 54.545 0.00 0.00 44.95 2.24
1047 1088 1.562942 GGGTTTCCCTTCTTCGGGTAT 59.437 52.381 0.00 0.00 44.95 2.73
1048 1089 0.986527 GGGTTTCCCTTCTTCGGGTA 59.013 55.000 0.00 0.00 44.95 3.69
1106 1151 0.683504 TCGGAGAAGTAGGGTGAGCC 60.684 60.000 0.00 0.00 0.00 4.70
1235 1293 3.155167 GGGGCAGGGGTACGAGAG 61.155 72.222 0.00 0.00 0.00 3.20
1747 1808 1.285578 GATCTTGCAGAGGTCGAAGC 58.714 55.000 0.00 0.00 0.00 3.86
1759 1820 1.880340 CCGCTCCAGACGATCTTGC 60.880 63.158 0.00 0.00 0.00 4.01
1824 1885 4.043200 GTTCGCCTTGGCAGTGGC 62.043 66.667 19.45 19.45 45.25 5.01
1827 1888 2.193536 GGTTGTTCGCCTTGGCAGT 61.194 57.895 12.45 0.00 0.00 4.40
1828 1889 2.192861 TGGTTGTTCGCCTTGGCAG 61.193 57.895 12.45 4.96 0.00 4.85
1829 1890 2.124109 TGGTTGTTCGCCTTGGCA 60.124 55.556 12.45 0.00 0.00 4.92
1892 1953 1.898472 CTCTTCTTCACCTCCTCTGCA 59.102 52.381 0.00 0.00 0.00 4.41
1895 1956 2.317371 TGCTCTTCTTCACCTCCTCT 57.683 50.000 0.00 0.00 0.00 3.69
2029 2108 2.352805 CCTTGGTCACCTCCCTGC 59.647 66.667 0.00 0.00 0.00 4.85
2048 2127 5.512060 CCATCAGTCGATCAGGTCCATTATT 60.512 44.000 0.00 0.00 0.00 1.40
2148 2234 5.862924 ACATTCTTACCATCAACAAGACG 57.137 39.130 0.00 0.00 0.00 4.18
2150 2236 7.437862 GCAAAAACATTCTTACCATCAACAAGA 59.562 33.333 0.00 0.00 0.00 3.02
2152 2238 6.199908 CGCAAAAACATTCTTACCATCAACAA 59.800 34.615 0.00 0.00 0.00 2.83
2194 2282 4.946784 AACACTATTTGATCGAACCAGC 57.053 40.909 0.00 0.00 0.00 4.85
2358 2446 5.657302 ACGACTCCAGTCTATACCTTTGAAT 59.343 40.000 5.21 0.00 42.66 2.57
2394 2483 3.181466 CCGGTGATCCATAACAGTCATCA 60.181 47.826 0.00 0.00 0.00 3.07
2524 2643 5.409214 GCAATGCAAAATAAAGCCTGAGAAA 59.591 36.000 0.00 0.00 0.00 2.52
2601 2971 9.704098 GAAATAGGCTCTTCTTGTTAAAATACG 57.296 33.333 0.00 0.00 0.00 3.06
2638 3009 2.602217 GCACAAACAAGGCACGACTAAG 60.602 50.000 0.00 0.00 0.00 2.18
2665 3036 2.354503 CCACTGATCAGGAGTTGGTGAG 60.355 54.545 26.08 5.61 0.00 3.51
2697 3068 2.158475 TCCTTGGTTTGCAGGATTCAGT 60.158 45.455 0.00 0.00 33.99 3.41
2768 3139 1.420430 AAGGGTGACGGAAAGACAGA 58.580 50.000 0.00 0.00 0.00 3.41
2817 3188 8.267894 AGTATTCTATGCCTAATTCACTTGTGT 58.732 33.333 0.46 0.00 0.00 3.72
3067 5443 2.446848 GGGGGCAGATAGAGCAGCA 61.447 63.158 0.00 0.00 0.00 4.41
3069 5445 0.769873 ATTGGGGGCAGATAGAGCAG 59.230 55.000 0.00 0.00 0.00 4.24
3146 5523 5.066893 TGAAATTGTCATGCTCAAGATAGCC 59.933 40.000 8.58 0.00 42.05 3.93
3182 5559 5.715429 TGCAAACTTGTAATGTGCAAAAG 57.285 34.783 0.00 0.00 41.95 2.27
3209 5586 2.671130 TTGTCATGCTATCGCTGACA 57.329 45.000 15.51 15.51 44.63 3.58
3210 5587 4.542662 AAATTGTCATGCTATCGCTGAC 57.457 40.909 12.01 12.01 41.00 3.51
3216 5593 8.976986 AGAAACAGAAAAATTGTCATGCTATC 57.023 30.769 0.00 0.00 0.00 2.08


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

AutoCloner maintained by Alex Coulton.