Multiple sequence alignment - TraesCS7D01G434700

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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 TraesCS7D01G434700 chr7D 100.000 2663 0 0 1 2663 554354897 554352235 0.000000e+00 4918.0
1 TraesCS7D01G434700 chr7D 88.500 600 55 3 835 1431 588848596 588849184 0.000000e+00 713.0
2 TraesCS7D01G434700 chr7D 84.578 616 74 15 810 1419 554226101 554225501 2.280000e-165 592.0
3 TraesCS7D01G434700 chr7D 84.124 611 85 6 810 1419 554184097 554183498 4.940000e-162 580.0
4 TraesCS7D01G434700 chr7D 81.884 414 42 14 192 601 503285336 503284952 4.280000e-83 318.0
5 TraesCS7D01G434700 chr7D 82.474 194 15 15 1 190 588848305 588848483 4.590000e-33 152.0
6 TraesCS7D01G434700 chr7D 81.865 193 18 14 1 190 588668246 588668068 2.140000e-31 147.0
7 TraesCS7D01G434700 chr7D 76.174 298 52 16 208 497 588790368 588790654 3.570000e-29 139.0
8 TraesCS7D01G434700 chr7D 95.588 68 2 1 610 676 588668062 588667995 1.010000e-19 108.0
9 TraesCS7D01G434700 chr7D 92.424 66 4 1 610 674 588848489 588848554 2.820000e-15 93.5
10 TraesCS7D01G434700 chr7B 91.984 1784 91 27 150 1917 600478425 600480172 0.000000e+00 2455.0
11 TraesCS7D01G434700 chr7B 90.217 552 54 0 880 1431 663257998 663258549 0.000000e+00 721.0
12 TraesCS7D01G434700 chr7B 85.197 635 77 13 798 1431 600752368 600752986 1.040000e-178 636.0
13 TraesCS7D01G434700 chr7B 84.051 627 79 13 810 1431 600801859 600802469 3.820000e-163 584.0
14 TraesCS7D01G434700 chr7B 84.706 595 76 10 840 1431 600719867 600720449 4.940000e-162 580.0
15 TraesCS7D01G434700 chr7B 82.903 310 30 6 192 499 531799992 531799704 9.460000e-65 257.0
16 TraesCS7D01G434700 chr7B 79.352 247 30 9 253 498 362440177 362439951 1.280000e-33 154.0
17 TraesCS7D01G434700 chr7B 89.000 100 7 4 1898 1997 600483136 600483231 1.290000e-23 121.0
18 TraesCS7D01G434700 chr7B 82.963 135 17 1 1542 1670 600364662 600364796 1.670000e-22 117.0
19 TraesCS7D01G434700 chr7B 91.935 62 4 1 609 669 663257882 663257943 4.720000e-13 86.1
20 TraesCS7D01G434700 chr2B 89.387 669 68 3 1996 2663 229331216 229331882 0.000000e+00 839.0
21 TraesCS7D01G434700 chr3B 89.371 668 62 8 1997 2663 187491379 187492038 0.000000e+00 832.0
22 TraesCS7D01G434700 chr3B 88.789 669 70 5 1997 2663 64306303 64305638 0.000000e+00 815.0
23 TraesCS7D01G434700 chr5A 88.806 670 63 9 1996 2663 648358716 648359375 0.000000e+00 811.0
24 TraesCS7D01G434700 chr3D 88.314 676 67 11 1996 2663 557049609 557050280 0.000000e+00 800.0
25 TraesCS7D01G434700 chr3D 80.328 183 29 6 424 600 27251291 27251472 5.980000e-27 132.0
26 TraesCS7D01G434700 chr2D 88.024 668 67 11 1998 2663 365371944 365372600 0.000000e+00 778.0
27 TraesCS7D01G434700 chr4B 87.892 669 70 9 1996 2663 542189086 542188428 0.000000e+00 776.0
28 TraesCS7D01G434700 chr6B 87.481 671 78 6 1996 2663 245140182 245139515 0.000000e+00 769.0
29 TraesCS7D01G434700 chr6B 79.898 393 60 13 211 600 19777252 19776876 1.210000e-68 270.0
30 TraesCS7D01G434700 chr6B 83.278 299 35 8 193 488 40726107 40726393 7.310000e-66 261.0
31 TraesCS7D01G434700 chr7A 88.686 601 64 1 835 1431 680419563 680420163 0.000000e+00 730.0
32 TraesCS7D01G434700 chr7A 87.083 480 42 10 1441 1917 639781532 639781994 2.350000e-145 525.0
33 TraesCS7D01G434700 chr7A 88.430 242 23 4 126 363 639780986 639781226 1.210000e-73 287.0
34 TraesCS7D01G434700 chr7A 92.941 85 5 1 1913 1997 639783872 639783955 3.600000e-24 122.0
35 TraesCS7D01G434700 chr7A 92.045 88 6 1 104 190 680419354 680419441 3.600000e-24 122.0
36 TraesCS7D01G434700 chr7A 92.308 52 4 0 445 496 617916387 617916336 1.020000e-09 75.0
37 TraesCS7D01G434700 chr4A 86.418 670 82 8 1996 2663 722002756 722002094 0.000000e+00 725.0
38 TraesCS7D01G434700 chr6D 80.208 384 62 10 208 588 463861627 463861999 2.610000e-70 276.0
39 TraesCS7D01G434700 chr6D 80.719 306 42 9 192 495 24617638 24617348 3.450000e-54 222.0
40 TraesCS7D01G434700 chr6D 85.149 202 20 7 287 488 25001577 25001768 5.810000e-47 198.0
41 TraesCS7D01G434700 chr1D 80.838 167 27 5 423 588 484578080 484577918 2.780000e-25 126.0
42 TraesCS7D01G434700 chr1B 80.000 165 25 6 423 583 674829247 674829087 6.020000e-22 115.0


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 TraesCS7D01G434700 chr7D 554352235 554354897 2662 True 4918.000000 4918 100.000000 1 2663 1 chr7D.!!$R4 2662
1 TraesCS7D01G434700 chr7D 554225501 554226101 600 True 592.000000 592 84.578000 810 1419 1 chr7D.!!$R3 609
2 TraesCS7D01G434700 chr7D 554183498 554184097 599 True 580.000000 580 84.124000 810 1419 1 chr7D.!!$R2 609
3 TraesCS7D01G434700 chr7D 588848305 588849184 879 False 319.500000 713 87.799333 1 1431 3 chr7D.!!$F2 1430
4 TraesCS7D01G434700 chr7B 600478425 600483231 4806 False 1288.000000 2455 90.492000 150 1997 2 chr7B.!!$F5 1847
5 TraesCS7D01G434700 chr7B 600752368 600752986 618 False 636.000000 636 85.197000 798 1431 1 chr7B.!!$F3 633
6 TraesCS7D01G434700 chr7B 600801859 600802469 610 False 584.000000 584 84.051000 810 1431 1 chr7B.!!$F4 621
7 TraesCS7D01G434700 chr7B 600719867 600720449 582 False 580.000000 580 84.706000 840 1431 1 chr7B.!!$F2 591
8 TraesCS7D01G434700 chr7B 663257882 663258549 667 False 403.550000 721 91.076000 609 1431 2 chr7B.!!$F6 822
9 TraesCS7D01G434700 chr2B 229331216 229331882 666 False 839.000000 839 89.387000 1996 2663 1 chr2B.!!$F1 667
10 TraesCS7D01G434700 chr3B 187491379 187492038 659 False 832.000000 832 89.371000 1997 2663 1 chr3B.!!$F1 666
11 TraesCS7D01G434700 chr3B 64305638 64306303 665 True 815.000000 815 88.789000 1997 2663 1 chr3B.!!$R1 666
12 TraesCS7D01G434700 chr5A 648358716 648359375 659 False 811.000000 811 88.806000 1996 2663 1 chr5A.!!$F1 667
13 TraesCS7D01G434700 chr3D 557049609 557050280 671 False 800.000000 800 88.314000 1996 2663 1 chr3D.!!$F2 667
14 TraesCS7D01G434700 chr2D 365371944 365372600 656 False 778.000000 778 88.024000 1998 2663 1 chr2D.!!$F1 665
15 TraesCS7D01G434700 chr4B 542188428 542189086 658 True 776.000000 776 87.892000 1996 2663 1 chr4B.!!$R1 667
16 TraesCS7D01G434700 chr6B 245139515 245140182 667 True 769.000000 769 87.481000 1996 2663 1 chr6B.!!$R2 667
17 TraesCS7D01G434700 chr7A 680419354 680420163 809 False 426.000000 730 90.365500 104 1431 2 chr7A.!!$F2 1327
18 TraesCS7D01G434700 chr7A 639780986 639783955 2969 False 311.333333 525 89.484667 126 1997 3 chr7A.!!$F1 1871
19 TraesCS7D01G434700 chr4A 722002094 722002756 662 True 725.000000 725 86.418000 1996 2663 1 chr4A.!!$R1 667

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
102 104 0.250684 TTGGCTCTTCGGTTGCATCA 60.251 50.0 0.00 0.0 0.00 3.07 F
448 487 0.251354 TGTGAGAGCTCAAGGGATGC 59.749 55.0 17.77 0.0 41.85 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1454 1532 0.315251 CTTCACGTCCAGAGACTGCA 59.685 55.0 0.0 0.0 41.16 4.41 R
1859 1940 0.539986 ATGGCTATTTCACGGACGGT 59.460 50.0 0.0 0.0 0.00 4.83 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
33 34 4.715523 GGCGGGTGGCTACTGCAA 62.716 66.667 16.78 0.00 42.94 4.08
50 51 1.474077 GCAACCAGTGAAGCCAATAGG 59.526 52.381 0.00 0.00 38.23 2.57
53 54 0.918983 CCAGTGAAGCCAATAGGGGA 59.081 55.000 0.00 0.00 37.04 4.81
57 58 1.141053 GTGAAGCCAATAGGGGACGAT 59.859 52.381 0.00 0.00 37.04 3.73
59 60 1.141053 GAAGCCAATAGGGGACGATGT 59.859 52.381 0.00 0.00 37.04 3.06
61 62 1.564348 AGCCAATAGGGGACGATGTTT 59.436 47.619 0.00 0.00 37.04 2.83
95 97 0.620556 ATGATGGTTGGCTCTTCGGT 59.379 50.000 0.00 0.00 0.00 4.69
102 104 0.250684 TTGGCTCTTCGGTTGCATCA 60.251 50.000 0.00 0.00 0.00 3.07
123 125 6.525578 TCATTACTTCAACGATACTGGAGT 57.474 37.500 0.00 0.00 36.56 3.85
142 144 4.039730 GGAGTATGCATGATGGTAGTCAGT 59.960 45.833 10.16 0.00 0.00 3.41
143 145 4.953667 AGTATGCATGATGGTAGTCAGTG 58.046 43.478 10.16 0.00 0.00 3.66
144 146 4.651045 AGTATGCATGATGGTAGTCAGTGA 59.349 41.667 10.16 0.00 0.00 3.41
145 147 3.251479 TGCATGATGGTAGTCAGTGAC 57.749 47.619 15.78 15.78 0.00 3.67
148 150 2.319025 TGATGGTAGTCAGTGACCCA 57.681 50.000 19.71 19.68 34.58 4.51
190 194 5.588648 AGGTATCCGTGGATGTTTATGTTTG 59.411 40.000 11.68 0.00 36.17 2.93
217 223 6.875972 AGTGGATTTTCTACTCAGGTGTAT 57.124 37.500 0.00 0.00 32.42 2.29
363 369 0.969149 CTGAGTAGCTCCCACACACA 59.031 55.000 0.00 0.00 0.00 3.72
364 370 0.679505 TGAGTAGCTCCCACACACAC 59.320 55.000 0.00 0.00 0.00 3.82
411 450 3.374745 CACAAAACTTTGAGCAGCGATT 58.625 40.909 9.12 0.00 40.55 3.34
413 452 4.975502 CACAAAACTTTGAGCAGCGATTTA 59.024 37.500 9.12 0.00 40.55 1.40
414 453 5.630680 CACAAAACTTTGAGCAGCGATTTAT 59.369 36.000 9.12 0.00 40.55 1.40
415 454 6.144402 CACAAAACTTTGAGCAGCGATTTATT 59.856 34.615 9.12 0.00 40.55 1.40
416 455 6.701400 ACAAAACTTTGAGCAGCGATTTATTT 59.299 30.769 9.12 0.00 40.55 1.40
417 456 7.224557 ACAAAACTTTGAGCAGCGATTTATTTT 59.775 29.630 9.12 0.00 40.55 1.82
418 457 7.713764 AAACTTTGAGCAGCGATTTATTTTT 57.286 28.000 0.00 0.00 0.00 1.94
444 483 2.847327 TTTCTGTGAGAGCTCAAGGG 57.153 50.000 17.77 2.02 41.85 3.95
445 484 2.015456 TTCTGTGAGAGCTCAAGGGA 57.985 50.000 17.77 4.49 41.85 4.20
446 485 2.244486 TCTGTGAGAGCTCAAGGGAT 57.756 50.000 17.77 0.00 41.85 3.85
447 486 1.829849 TCTGTGAGAGCTCAAGGGATG 59.170 52.381 17.77 0.00 41.85 3.51
448 487 0.251354 TGTGAGAGCTCAAGGGATGC 59.749 55.000 17.77 0.00 41.85 3.91
449 488 0.540923 GTGAGAGCTCAAGGGATGCT 59.459 55.000 17.77 0.00 41.85 3.79
450 489 1.759445 GTGAGAGCTCAAGGGATGCTA 59.241 52.381 17.77 0.00 41.85 3.49
468 507 8.400186 GGGATGCTATTTTTGGATGAAATTTTG 58.600 33.333 0.00 0.00 0.00 2.44
479 518 5.070180 TGGATGAAATTTTGCAAGAACCTCA 59.930 36.000 0.00 0.57 0.00 3.86
481 520 6.482973 GGATGAAATTTTGCAAGAACCTCAAA 59.517 34.615 0.00 0.00 0.00 2.69
482 521 6.660887 TGAAATTTTGCAAGAACCTCAAAC 57.339 33.333 0.00 0.00 30.45 2.93
483 522 6.169094 TGAAATTTTGCAAGAACCTCAAACA 58.831 32.000 0.00 0.00 30.45 2.83
570 613 2.131776 TTTTGGACAAACTCGGGTGT 57.868 45.000 0.00 0.00 0.00 4.16
573 616 0.682852 TGGACAAACTCGGGTGTAGG 59.317 55.000 0.00 0.00 0.00 3.18
594 637 1.755380 ACACCCGAGAATAGCCACTAC 59.245 52.381 0.00 0.00 0.00 2.73
651 694 2.076863 GTGTATGTTGGTGGAGTCAGC 58.923 52.381 0.00 0.00 41.42 4.26
656 699 1.070134 TGTTGGTGGAGTCAGCTGTAC 59.930 52.381 14.67 10.66 41.59 2.90
661 704 2.163509 GTGGAGTCAGCTGTACTCTCA 58.836 52.381 29.14 24.45 42.48 3.27
695 744 9.431887 GGTCAGTGTTTATACTCATCTTTGTAA 57.568 33.333 0.00 0.00 0.00 2.41
730 779 1.968493 GTAGCATAGATGTCCCCGGAA 59.032 52.381 0.73 0.00 0.00 4.30
731 780 1.507140 AGCATAGATGTCCCCGGAAA 58.493 50.000 0.73 0.00 0.00 3.13
754 803 3.543680 AAGGCATAGATGTGTACGCTT 57.456 42.857 8.10 0.59 0.00 4.68
765 814 2.222213 TGTGTACGCTTGGACGAATTTG 59.778 45.455 8.10 0.00 36.70 2.32
767 816 0.800012 TACGCTTGGACGAATTTGCC 59.200 50.000 0.00 0.00 36.70 4.52
770 819 1.531739 GCTTGGACGAATTTGCCCCA 61.532 55.000 0.00 0.00 0.00 4.96
776 825 2.741517 GGACGAATTTGCCCCAAAATTG 59.258 45.455 0.00 0.00 39.31 2.32
807 856 7.193377 TGCTCGATAATGTATAACGTACTGA 57.807 36.000 0.00 0.00 0.00 3.41
849 904 7.824779 GTCCGAGCCTTATCCTAATTTGAATAT 59.175 37.037 0.00 0.00 0.00 1.28
850 905 8.383175 TCCGAGCCTTATCCTAATTTGAATATT 58.617 33.333 0.00 0.00 0.00 1.28
1394 1469 2.125512 CCAGGGTTTCGCTCTCGG 60.126 66.667 0.00 0.00 36.13 4.63
1427 1502 1.228490 ACACGAAGGAGGAGGACGT 60.228 57.895 0.00 0.00 37.68 4.34
1436 1514 0.966920 GAGGAGGACGTTGAGTTCCA 59.033 55.000 0.00 0.00 33.22 3.53
1454 1532 2.035632 CCAGGGTTTATCTCTCGCTCT 58.964 52.381 0.00 0.00 0.00 4.09
1493 1574 0.658829 GAGGACGCTGATGACGATCG 60.659 60.000 14.88 14.88 0.00 3.69
1507 1588 0.665835 CGATCGTGAGGAGGAGAAGG 59.334 60.000 7.03 0.00 0.00 3.46
1714 1795 0.397254 TTTTGGCCCGGTTTCCTTCA 60.397 50.000 0.00 0.00 0.00 3.02
1749 1830 6.038825 TCAACTTGTTTAGCTTTTCAATCCGA 59.961 34.615 0.00 0.00 0.00 4.55
1757 1838 8.639428 GTTTAGCTTTTCAATCCGATTTTCTTC 58.361 33.333 0.00 0.00 0.00 2.87
1821 1902 2.193248 GATTTCTCCCCTGGGCGG 59.807 66.667 7.39 1.72 34.68 6.13
1856 1937 8.449251 AAACTATGTGTTTTTGCCATCATTTT 57.551 26.923 0.00 0.00 45.69 1.82
1859 1940 9.553064 ACTATGTGTTTTTGCCATCATTTTAAA 57.447 25.926 0.00 0.00 0.00 1.52
1873 1954 6.798315 TCATTTTAAACCGTCCGTGAAATA 57.202 33.333 0.00 0.00 0.00 1.40
1882 1963 2.365582 GTCCGTGAAATAGCCATGGTT 58.634 47.619 14.67 10.52 40.63 3.67
1905 1986 1.740025 GCCACTATTGTTGCTGGAGTC 59.260 52.381 0.00 0.00 32.77 3.36
1908 1989 2.926200 CACTATTGTTGCTGGAGTCTCG 59.074 50.000 0.00 0.00 0.00 4.04
1909 1990 2.093973 ACTATTGTTGCTGGAGTCTCGG 60.094 50.000 0.00 0.00 0.00 4.63
1910 1991 0.687354 ATTGTTGCTGGAGTCTCGGT 59.313 50.000 0.00 0.00 0.00 4.69
1934 5785 2.254152 AGCTATGGAACCCTGAGTGA 57.746 50.000 0.00 0.00 0.00 3.41
1935 5786 2.551270 AGCTATGGAACCCTGAGTGAA 58.449 47.619 0.00 0.00 0.00 3.18
1990 5841 7.867909 CCAAATTCTGAAGAAACCTCCTTAAAC 59.132 37.037 0.00 0.00 37.61 2.01
1992 5843 7.751768 ATTCTGAAGAAACCTCCTTAAACTG 57.248 36.000 0.00 0.00 37.61 3.16
2059 5914 4.457834 TTTTTGAGAAGCAACGGGAAAA 57.542 36.364 0.00 0.00 35.91 2.29
2233 6097 0.468214 CTCCGGGTCTGCCTCTATCA 60.468 60.000 0.00 0.00 34.45 2.15
2252 6116 0.907704 ATCGGGTTGTGCCTACCTCA 60.908 55.000 5.97 0.00 35.92 3.86
2268 6132 1.179152 CTCATCATTTGGTGGCTGCA 58.821 50.000 0.50 0.00 0.00 4.41
2287 6151 3.998672 GGCGACCTTCGGGACACA 61.999 66.667 0.00 0.00 40.84 3.72
2299 6163 1.805120 CGGGACACAGTTGTTTCGACT 60.805 52.381 0.00 0.00 35.47 4.18
2311 6175 7.556996 ACAGTTGTTTCGACTACTCTATCCTAT 59.443 37.037 0.00 0.00 0.00 2.57
2318 6182 4.325119 GACTACTCTATCCTATGACGGCA 58.675 47.826 0.00 0.00 0.00 5.69
2322 6186 7.120051 ACTACTCTATCCTATGACGGCATAAT 58.880 38.462 13.03 6.56 36.60 1.28
2323 6187 6.859112 ACTCTATCCTATGACGGCATAATT 57.141 37.500 13.03 2.61 36.60 1.40
2364 6229 3.507103 TGCATCAATCCCGTTTCATTG 57.493 42.857 0.00 0.00 0.00 2.82
2469 6335 8.580720 TGCTCTAATTAAAGCCAAACAACATAA 58.419 29.630 8.30 0.00 37.73 1.90
2543 6411 2.586079 CCGACCATGCACCGCTAG 60.586 66.667 0.00 0.00 0.00 3.42
2574 6442 7.064016 TGGCCAATGCGAAATATTTAAGAAAAC 59.936 33.333 0.61 0.00 38.85 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.125912 CACCCGCCTCTGAAGACG 60.126 66.667 0.00 0.00 0.00 4.18
33 34 0.625849 CCCCTATTGGCTTCACTGGT 59.374 55.000 0.00 0.00 0.00 4.00
36 37 0.541863 CGTCCCCTATTGGCTTCACT 59.458 55.000 0.00 0.00 0.00 3.41
61 62 6.482641 CCAACCATCATCAACAACATCAAAAA 59.517 34.615 0.00 0.00 0.00 1.94
66 67 3.194116 AGCCAACCATCATCAACAACATC 59.806 43.478 0.00 0.00 0.00 3.06
67 68 3.167485 AGCCAACCATCATCAACAACAT 58.833 40.909 0.00 0.00 0.00 2.71
68 69 2.557924 GAGCCAACCATCATCAACAACA 59.442 45.455 0.00 0.00 0.00 3.33
69 70 2.821969 AGAGCCAACCATCATCAACAAC 59.178 45.455 0.00 0.00 0.00 3.32
71 72 2.885135 AGAGCCAACCATCATCAACA 57.115 45.000 0.00 0.00 0.00 3.33
72 73 2.096496 CGAAGAGCCAACCATCATCAAC 59.904 50.000 0.00 0.00 0.00 3.18
74 75 1.407299 CCGAAGAGCCAACCATCATCA 60.407 52.381 0.00 0.00 0.00 3.07
95 97 6.037062 CCAGTATCGTTGAAGTAATGATGCAA 59.963 38.462 10.89 0.00 44.84 4.08
102 104 6.924060 GCATACTCCAGTATCGTTGAAGTAAT 59.076 38.462 0.00 0.00 39.06 1.89
123 125 4.202253 GGTCACTGACTACCATCATGCATA 60.202 45.833 9.08 0.00 35.73 3.14
143 145 4.410400 CTTCCGGCCTGGTGGGTC 62.410 72.222 12.46 0.00 39.52 4.46
148 150 0.394352 CTTTATGCTTCCGGCCTGGT 60.394 55.000 12.46 0.00 40.92 4.00
190 194 4.468153 ACCTGAGTAGAAAATCCACTCTCC 59.532 45.833 7.31 0.00 39.54 3.71
217 223 6.766944 TCAATTTTTAGACAACTCGGGTGTAA 59.233 34.615 0.00 0.00 0.00 2.41
273 279 7.738847 AGAGTTTGATGTCCCAAAATTTCAAT 58.261 30.769 0.00 0.00 37.72 2.57
274 280 7.123355 AGAGTTTGATGTCCCAAAATTTCAA 57.877 32.000 0.00 0.00 37.72 2.69
280 286 7.831691 TTTGATAGAGTTTGATGTCCCAAAA 57.168 32.000 0.00 0.00 37.72 2.44
345 351 0.679505 GTGTGTGTGGGAGCTACTCA 59.320 55.000 0.00 0.00 31.08 3.41
349 355 2.719531 TTTTGTGTGTGTGGGAGCTA 57.280 45.000 0.00 0.00 0.00 3.32
374 413 1.031029 TGTGCACTGTTTGAGCAGCA 61.031 50.000 19.41 0.00 42.56 4.41
375 414 0.101040 TTGTGCACTGTTTGAGCAGC 59.899 50.000 19.41 0.00 42.56 5.25
430 469 0.540923 AGCATCCCTTGAGCTCTCAC 59.459 55.000 16.19 0.00 39.66 3.51
444 483 8.452534 TGCAAAATTTCATCCAAAAATAGCATC 58.547 29.630 0.00 0.00 30.47 3.91
445 484 8.338072 TGCAAAATTTCATCCAAAAATAGCAT 57.662 26.923 0.00 0.00 30.47 3.79
446 485 7.741027 TGCAAAATTTCATCCAAAAATAGCA 57.259 28.000 0.00 0.00 31.74 3.49
447 486 8.505625 TCTTGCAAAATTTCATCCAAAAATAGC 58.494 29.630 0.00 0.00 0.00 2.97
450 489 8.136800 GGTTCTTGCAAAATTTCATCCAAAAAT 58.863 29.630 0.00 0.00 0.00 1.82
468 507 4.058721 ACCAAATGTTTGAGGTTCTTGC 57.941 40.909 7.04 0.00 40.55 4.01
570 613 1.063492 TGGCTATTCTCGGGTGTCCTA 60.063 52.381 0.00 0.00 0.00 2.94
573 616 0.824759 AGTGGCTATTCTCGGGTGTC 59.175 55.000 0.00 0.00 0.00 3.67
651 694 7.067615 ACACTGACCTATACAATGAGAGTACAG 59.932 40.741 0.00 0.00 0.00 2.74
695 744 6.636705 TCTATGCTACGGTGTACAGAAAAAT 58.363 36.000 0.00 0.00 0.00 1.82
703 752 3.305199 GGGACATCTATGCTACGGTGTAC 60.305 52.174 0.00 0.00 0.00 2.90
704 753 2.889045 GGGACATCTATGCTACGGTGTA 59.111 50.000 0.00 0.00 0.00 2.90
731 780 4.261801 AGCGTACACATCTATGCCTTTTT 58.738 39.130 0.00 0.00 30.00 1.94
754 803 1.414158 TTTTGGGGCAAATTCGTCCA 58.586 45.000 0.00 0.00 33.19 4.02
765 814 3.613030 AGCAATCAATCAATTTTGGGGC 58.387 40.909 0.00 0.00 0.00 5.80
767 816 4.746729 TCGAGCAATCAATCAATTTTGGG 58.253 39.130 0.00 0.00 0.00 4.12
776 825 8.648097 ACGTTATACATTATCGAGCAATCAATC 58.352 33.333 0.00 0.00 0.00 2.67
797 846 1.999735 GCAGCAGCATTCAGTACGTTA 59.000 47.619 0.00 0.00 41.58 3.18
798 847 0.798776 GCAGCAGCATTCAGTACGTT 59.201 50.000 0.00 0.00 41.58 3.99
807 856 3.984193 GACCCGGAGCAGCAGCATT 62.984 63.158 0.73 0.00 45.49 3.56
829 884 9.626045 CCGAAAATATTCAAATTAGGATAAGGC 57.374 33.333 0.00 0.00 35.15 4.35
833 888 9.073475 CCCACCGAAAATATTCAAATTAGGATA 57.927 33.333 4.37 0.00 35.15 2.59
1237 1312 2.328099 GCTTCACGCAGGGGTTCTG 61.328 63.158 0.00 0.00 46.03 3.02
1365 1440 2.138656 AACCCTGGAACTCGACGACG 62.139 60.000 0.00 0.00 41.26 5.12
1394 1469 3.371063 TGTCCAGAGACGGCGGAC 61.371 66.667 13.24 6.86 46.74 4.79
1427 1502 4.081642 CGAGAGATAAACCCTGGAACTCAA 60.082 45.833 0.00 0.00 0.00 3.02
1436 1514 1.410882 GCAGAGCGAGAGATAAACCCT 59.589 52.381 0.00 0.00 0.00 4.34
1454 1532 0.315251 CTTCACGTCCAGAGACTGCA 59.685 55.000 0.00 0.00 41.16 4.41
1493 1574 1.286553 TCTCCTCCTTCTCCTCCTCAC 59.713 57.143 0.00 0.00 0.00 3.51
1507 1588 2.732597 CGTCAACCTCGTCAATCTCCTC 60.733 54.545 0.00 0.00 0.00 3.71
1714 1795 5.067283 AGCTAAACAAGTTGAATCCGTTTGT 59.933 36.000 10.54 0.00 33.73 2.83
1757 1838 8.673711 TCAAGGAAAATATTGATCCAGTTTACG 58.326 33.333 18.12 0.00 35.62 3.18
1840 1921 6.293713 ACGGTTTAAAATGATGGCAAAAAC 57.706 33.333 0.00 0.00 0.00 2.43
1856 1937 2.028294 TGGCTATTTCACGGACGGTTTA 60.028 45.455 0.00 0.00 0.00 2.01
1859 1940 0.539986 ATGGCTATTTCACGGACGGT 59.460 50.000 0.00 0.00 0.00 4.83
1905 1986 2.474816 GTTCCATAGCTTAGCACCGAG 58.525 52.381 7.07 0.00 0.00 4.63
1908 1989 1.490910 AGGGTTCCATAGCTTAGCACC 59.509 52.381 7.07 3.66 0.00 5.01
1909 1990 2.170607 TCAGGGTTCCATAGCTTAGCAC 59.829 50.000 7.07 0.00 0.00 4.40
1910 1991 2.435805 CTCAGGGTTCCATAGCTTAGCA 59.564 50.000 7.07 0.00 0.00 3.49
2041 5893 5.776173 TTATTTTTCCCGTTGCTTCTCAA 57.224 34.783 0.00 0.00 0.00 3.02
2233 6097 0.907704 TGAGGTAGGCACAACCCGAT 60.908 55.000 0.64 0.00 40.58 4.18
2252 6116 1.597797 CCGTGCAGCCACCAAATGAT 61.598 55.000 0.00 0.00 38.79 2.45
2287 6151 7.774157 TCATAGGATAGAGTAGTCGAAACAACT 59.226 37.037 0.00 0.00 0.00 3.16
2299 6163 7.956328 AATTATGCCGTCATAGGATAGAGTA 57.044 36.000 0.00 0.00 36.60 2.59
2311 6175 4.431416 AATCCACCTAATTATGCCGTCA 57.569 40.909 0.00 0.00 0.00 4.35
2322 6186 8.016301 TGCATTGCAATTAATAATCCACCTAA 57.984 30.769 9.83 0.00 34.76 2.69
2323 6187 7.594351 TGCATTGCAATTAATAATCCACCTA 57.406 32.000 9.83 0.00 34.76 3.08
2420 6286 1.825090 TTATGGGCACTTGAGCACTG 58.175 50.000 0.00 0.00 39.15 3.66
2526 6394 2.586079 CTAGCGGTGCATGGTCGG 60.586 66.667 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.