Multiple sequence alignment - TraesCS7D01G190700

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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 TraesCS7D01G190700 chr7D 100.000 4108 0 0 1 4108 146103669 146107776 0.000000e+00 7587.0
1 TraesCS7D01G190700 chr7D 82.703 185 26 5 215 394 582123505 582123322 4.250000e-35 159.0
2 TraesCS7D01G190700 chr7D 76.218 349 46 17 2759 3082 40705428 40705092 2.560000e-32 150.0
3 TraesCS7D01G190700 chr7B 93.739 1693 82 17 1746 3424 108284890 108286572 0.000000e+00 2518.0
4 TraesCS7D01G190700 chr7B 94.737 1159 48 7 586 1734 108283667 108284822 0.000000e+00 1790.0
5 TraesCS7D01G190700 chr7B 90.417 480 41 3 1 480 108283032 108283506 9.690000e-176 627.0
6 TraesCS7D01G190700 chr7B 79.605 608 76 29 3426 3992 108286641 108287241 3.850000e-105 392.0
7 TraesCS7D01G190700 chr7B 93.805 113 7 0 3995 4107 108287278 108287390 1.960000e-38 171.0
8 TraesCS7D01G190700 chr7A 92.564 1708 85 24 1747 3424 146950218 146951913 0.000000e+00 2412.0
9 TraesCS7D01G190700 chr7A 93.492 922 40 8 716 1626 146949252 146950164 0.000000e+00 1352.0
10 TraesCS7D01G190700 chr7A 90.909 517 42 5 1 516 146948511 146949023 0.000000e+00 689.0
11 TraesCS7D01G190700 chr7A 83.784 259 15 11 3835 4066 146952729 146952987 1.920000e-53 220.0
12 TraesCS7D01G190700 chr7A 100.000 41 0 0 4065 4105 146953091 146953131 4.400000e-10 76.8
13 TraesCS7D01G190700 chr7A 97.561 41 1 0 1643 1683 146950159 146950199 2.050000e-08 71.3
14 TraesCS7D01G190700 chr5A 81.818 198 32 3 201 394 657774216 657774019 3.290000e-36 163.0
15 TraesCS7D01G190700 chr5A 76.791 349 43 21 2759 3082 4131067 4130732 1.180000e-35 161.0
16 TraesCS7D01G190700 chr2D 82.796 186 29 3 212 394 546411997 546412182 3.290000e-36 163.0
17 TraesCS7D01G190700 chr3A 81.818 187 30 4 212 394 703807047 703806861 1.980000e-33 154.0
18 TraesCS7D01G190700 chr3A 81.250 192 31 4 210 396 100863850 100863659 2.560000e-32 150.0
19 TraesCS7D01G190700 chr3A 85.882 85 12 0 2897 2981 725842932 725843016 1.570000e-14 91.6
20 TraesCS7D01G190700 chr3A 85.882 85 12 0 2897 2981 725905356 725905440 1.570000e-14 91.6
21 TraesCS7D01G190700 chr4B 81.250 192 32 4 200 387 595717883 595718074 7.110000e-33 152.0
22 TraesCS7D01G190700 chr1B 82.222 180 28 4 212 387 651902884 651903063 7.110000e-33 152.0
23 TraesCS7D01G190700 chr3B 87.059 85 11 0 2897 2981 798397812 798397896 3.380000e-16 97.1
24 TraesCS7D01G190700 chr3B 85.882 85 12 0 2897 2981 798404347 798404431 1.570000e-14 91.6
25 TraesCS7D01G190700 chr5B 90.278 72 7 0 1800 1871 678908854 678908783 1.220000e-15 95.3
26 TraesCS7D01G190700 chr3D 85.882 85 12 0 2897 2981 594955817 594955901 1.570000e-14 91.6


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 TraesCS7D01G190700 chr7D 146103669 146107776 4107 False 7587.000000 7587 100.000000 1 4108 1 chr7D.!!$F1 4107
1 TraesCS7D01G190700 chr7B 108283032 108287390 4358 False 1099.600000 2518 90.460600 1 4107 5 chr7B.!!$F1 4106
2 TraesCS7D01G190700 chr7A 146948511 146953131 4620 False 803.516667 2412 93.051667 1 4105 6 chr7A.!!$F1 4104

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
165 166 0.541063 TGGTTGGACGTAGCTCCTCA 60.541 55.0 0.00 0.0 0.0 3.86 F
1450 1528 0.605589 GGGCAAGGCGAACAGTAAGT 60.606 55.0 0.00 0.0 0.0 2.24 F
2594 2755 0.748005 GTTATGTCATGCGCCCCACT 60.748 55.0 4.18 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1970 2123 0.750249 CTCGGTTTTGGGGCAGTTTT 59.250 50.0 0.0 0.0 0.00 2.43 R
2888 3053 0.387622 CGCTGGTCAAACTGCAATGG 60.388 55.0 0.0 0.0 35.35 3.16 R
3595 3841 0.530744 TTCGAACAGAGGACCCATCG 59.469 55.0 0.0 0.0 0.00 3.84 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
18 19 2.300967 GGCCCCACATGTGAGGAGA 61.301 63.158 28.92 0.00 0.00 3.71
36 37 5.583932 AGGAGAATTTTATGAAGCCAACCT 58.416 37.500 0.00 0.00 0.00 3.50
127 128 7.200455 ACTTTTATAGTTTGTTGAGTGGTTGC 58.800 34.615 0.00 0.00 31.29 4.17
154 155 3.430929 CCTGATAGCTAGTGTGGTTGGAC 60.431 52.174 0.00 0.00 0.00 4.02
165 166 0.541063 TGGTTGGACGTAGCTCCTCA 60.541 55.000 0.00 0.00 0.00 3.86
179 180 3.077359 GCTCCTCATTGCTAGTGTTTGT 58.923 45.455 0.00 0.00 0.00 2.83
185 186 5.181690 TCATTGCTAGTGTTTGTTGTTCC 57.818 39.130 0.00 0.00 0.00 3.62
193 194 3.250040 AGTGTTTGTTGTTCCTGATACGC 59.750 43.478 0.00 0.00 0.00 4.42
219 220 8.683615 CCAAGTTCCTTTTCTAGTTAGTTTTGT 58.316 33.333 0.00 0.00 0.00 2.83
258 259 9.790297 ATCCTGGTATGGTAATATAGATCAGTT 57.210 33.333 0.00 0.00 0.00 3.16
318 319 7.200455 TGATGTGGTTATAGATTAGTGACGTG 58.800 38.462 0.00 0.00 0.00 4.49
319 320 5.345702 TGTGGTTATAGATTAGTGACGTGC 58.654 41.667 0.00 0.00 0.00 5.34
416 418 3.892588 CTGATCTACCACCCTCTTAGACC 59.107 52.174 0.00 0.00 0.00 3.85
480 482 5.239525 CGTGATGTCTAGGATGAGTGATACA 59.760 44.000 0.00 0.00 0.00 2.29
521 523 9.777575 ACTATAGTACAACACAAACAAACAAAC 57.222 29.630 2.75 0.00 0.00 2.93
522 524 9.997482 CTATAGTACAACACAAACAAACAAACT 57.003 29.630 0.00 0.00 0.00 2.66
523 525 8.905103 ATAGTACAACACAAACAAACAAACTC 57.095 30.769 0.00 0.00 0.00 3.01
525 527 7.375053 AGTACAACACAAACAAACAAACTCAT 58.625 30.769 0.00 0.00 0.00 2.90
526 528 7.870445 AGTACAACACAAACAAACAAACTCATT 59.130 29.630 0.00 0.00 0.00 2.57
527 529 7.489574 ACAACACAAACAAACAAACTCATTT 57.510 28.000 0.00 0.00 0.00 2.32
528 530 7.924940 ACAACACAAACAAACAAACTCATTTT 58.075 26.923 0.00 0.00 0.00 1.82
529 531 8.401709 ACAACACAAACAAACAAACTCATTTTT 58.598 25.926 0.00 0.00 0.00 1.94
553 555 9.723601 TTTTAAACTATACATAAACTGGACCGT 57.276 29.630 0.00 0.00 0.00 4.83
554 556 8.706492 TTAAACTATACATAAACTGGACCGTG 57.294 34.615 0.00 0.00 0.00 4.94
555 557 6.534475 AACTATACATAAACTGGACCGTGA 57.466 37.500 0.00 0.00 0.00 4.35
557 559 6.513180 ACTATACATAAACTGGACCGTGATG 58.487 40.000 0.00 0.00 0.00 3.07
559 561 3.596214 ACATAAACTGGACCGTGATGTC 58.404 45.455 9.48 0.00 34.42 3.06
676 741 9.406828 TCAAAAGAGACCATTCGAATATATACG 57.593 33.333 10.97 0.00 0.00 3.06
677 742 7.813852 AAAGAGACCATTCGAATATATACGC 57.186 36.000 10.97 3.47 0.00 4.42
732 800 7.993183 CCTAATACCAGTGGAAGTGAATACAAT 59.007 37.037 18.40 0.00 40.62 2.71
780 848 4.981806 TTTGGGAACTCAAAAGACACAG 57.018 40.909 0.00 0.00 34.17 3.66
791 859 5.520632 TCAAAAGACACAGTTCGAGTAGAG 58.479 41.667 0.00 0.00 0.00 2.43
917 985 0.669318 TCGTCAACCCATTCGTCTGC 60.669 55.000 0.00 0.00 0.00 4.26
956 1028 1.743321 CTGAGATCCCCTCACGAGCC 61.743 65.000 0.00 0.00 46.38 4.70
990 1062 3.633418 GAAACCCTAGAGTAGAGCAGGA 58.367 50.000 0.00 0.00 0.00 3.86
1373 1451 3.760035 CTCGGTGGTGACGGAGGG 61.760 72.222 0.00 0.00 42.87 4.30
1450 1528 0.605589 GGGCAAGGCGAACAGTAAGT 60.606 55.000 0.00 0.00 0.00 2.24
1470 1549 4.152647 AGTCCCTGTTTTCATTTCCCTTC 58.847 43.478 0.00 0.00 0.00 3.46
1472 1551 2.231235 CCCTGTTTTCATTTCCCTTCGG 59.769 50.000 0.00 0.00 0.00 4.30
1642 1721 2.710377 TGCGTGATAGCTTGGTTGATT 58.290 42.857 0.00 0.00 38.13 2.57
1678 1757 8.489489 AGATACTGGATGAGTTTATGTTGATGT 58.511 33.333 0.00 0.00 35.96 3.06
1699 1778 5.291178 TGTTTTGACAAATCATGAGCAAGG 58.709 37.500 0.09 0.00 33.85 3.61
1722 1801 4.398044 GGGAAGTTGTCTGTTTCAGTCAAA 59.602 41.667 9.94 0.00 40.02 2.69
1726 1805 6.515272 AGTTGTCTGTTTCAGTCAAATTGT 57.485 33.333 9.94 0.00 40.02 2.71
1734 1813 8.087750 TCTGTTTCAGTCAAATTGTTTTCTGTT 58.912 29.630 0.00 0.00 32.61 3.16
1735 1814 8.238481 TGTTTCAGTCAAATTGTTTTCTGTTC 57.762 30.769 0.00 0.00 0.00 3.18
1736 1815 7.330700 TGTTTCAGTCAAATTGTTTTCTGTTCC 59.669 33.333 0.00 0.00 0.00 3.62
1737 1816 6.522625 TCAGTCAAATTGTTTTCTGTTCCA 57.477 33.333 0.00 0.00 0.00 3.53
1739 1818 6.152661 TCAGTCAAATTGTTTTCTGTTCCAGT 59.847 34.615 0.00 0.00 32.61 4.00
1740 1819 6.473455 CAGTCAAATTGTTTTCTGTTCCAGTC 59.527 38.462 0.00 0.00 32.61 3.51
1741 1820 6.152661 AGTCAAATTGTTTTCTGTTCCAGTCA 59.847 34.615 0.00 0.00 32.61 3.41
1742 1821 6.811170 GTCAAATTGTTTTCTGTTCCAGTCAA 59.189 34.615 0.00 0.00 32.61 3.18
1933 2072 7.311364 TCAGTTTCTTAAACACCACACTTAC 57.689 36.000 5.42 0.00 43.79 2.34
1948 2101 7.170489 CACCACACTTACTATCTGCTTATGATG 59.830 40.741 0.00 0.00 0.00 3.07
2040 2194 4.022589 CAGAAGTCATGGTTCATTGCAGTT 60.023 41.667 10.28 0.00 0.00 3.16
2240 2394 2.467880 ACTAACGGTGACCCATCTCAT 58.532 47.619 0.00 0.00 0.00 2.90
2324 2478 6.879458 AGTTACCAGAGGTTAATGTCAATGTC 59.121 38.462 0.00 0.00 37.09 3.06
2411 2565 4.033776 TTGAAGGGCCAGCCTCCG 62.034 66.667 6.18 0.00 36.10 4.63
2434 2588 6.805760 CCGATCATTGATGTGAGTAGTATCAG 59.194 42.308 3.32 0.00 32.92 2.90
2581 2742 4.013728 ACCACATGCCATTTACGTTATGT 58.986 39.130 0.00 0.00 0.00 2.29
2582 2743 4.095782 ACCACATGCCATTTACGTTATGTC 59.904 41.667 0.00 0.00 0.00 3.06
2594 2755 0.748005 GTTATGTCATGCGCCCCACT 60.748 55.000 4.18 0.00 0.00 4.00
2671 2832 5.304614 GGATGGGAAAGCACTGTCTATACTA 59.695 44.000 0.00 0.00 0.00 1.82
2797 2958 2.158885 GGATCCTGAGACTAGGCAAACC 60.159 54.545 3.84 0.00 37.76 3.27
2888 3053 7.745620 TTCTTCAGACCCTAATTTTTGTCTC 57.254 36.000 0.00 0.00 35.97 3.36
2947 3112 3.181468 TGCCAACAAGTGATGAAATGCAA 60.181 39.130 0.00 0.00 0.00 4.08
2977 3142 3.755378 ACATGCTCAAGAAGTTCATGTCC 59.245 43.478 5.50 0.45 42.63 4.02
2991 3156 3.384168 TCATGTCCCAGGTAAGTAGCAT 58.616 45.455 0.00 0.00 0.00 3.79
3018 3183 3.551846 TCATCCTAGTGTATGCGTCTCA 58.448 45.455 0.00 0.00 0.00 3.27
3033 3198 0.108585 TCTCAGGTTGACTTGGCACC 59.891 55.000 0.00 0.00 0.00 5.01
3094 3259 2.192263 GGAGATGGACTTCTCAAGGGT 58.808 52.381 14.65 0.00 43.28 4.34
3278 3444 5.175127 ACAATGTTTTCTGTTGTTGGAACC 58.825 37.500 0.00 0.00 32.53 3.62
3292 3458 1.160329 GGAACCGATCGATTGCCCAG 61.160 60.000 18.66 0.00 0.00 4.45
3332 3498 1.268692 CGTTCATGTGCTGTGTGCTTT 60.269 47.619 0.00 0.00 43.37 3.51
3398 3566 8.325477 AGCTGTTTATCTTCTCTTACCCTATT 57.675 34.615 0.00 0.00 0.00 1.73
3432 3669 0.811281 GGACATGCAACACTAAGGGC 59.189 55.000 0.00 0.00 0.00 5.19
3457 3694 6.528321 TGAAGAAATCTGATCTTGTCACAGT 58.472 36.000 0.00 0.00 37.26 3.55
3475 3721 4.623167 CACAGTATGAAGAGGTCAAAGTCG 59.377 45.833 0.00 0.00 40.50 4.18
3496 3742 3.302935 CGCTGTGCTAATGATCACACATC 60.303 47.826 14.99 11.12 41.80 3.06
3517 3763 0.035458 GGAGTGGCCGGAGATATTGG 59.965 60.000 5.05 0.00 0.00 3.16
3553 3799 6.757897 TGCTGACATTGTTAGGGAAATAAG 57.242 37.500 10.25 0.00 0.00 1.73
3570 3816 7.387673 GGGAAATAAGAACCAAAGGAAAACATG 59.612 37.037 0.00 0.00 0.00 3.21
3608 3862 0.178767 TGAATGCGATGGGTCCTCTG 59.821 55.000 0.00 0.00 0.00 3.35
3626 4204 2.171840 CTGTTCGAAAGAGAGGAGGGA 58.828 52.381 0.00 0.00 43.69 4.20
3661 4239 0.118346 TGGAAGAACCCTAGGAGGCA 59.882 55.000 11.48 0.00 38.00 4.75
3674 4252 1.078143 GAGGCAACGGCTTGGAGAT 60.078 57.895 0.00 0.00 46.39 2.75
3678 4256 2.024414 GGCAACGGCTTGGAGATAAAT 58.976 47.619 0.00 0.00 40.87 1.40
3713 4291 2.489938 TTTGGTGTCTATCTGTGGCC 57.510 50.000 0.00 0.00 0.00 5.36
3714 4292 1.656587 TTGGTGTCTATCTGTGGCCT 58.343 50.000 3.32 0.00 0.00 5.19
3715 4293 1.656587 TGGTGTCTATCTGTGGCCTT 58.343 50.000 3.32 0.00 0.00 4.35
3730 4313 1.119684 GCCTTGGGGTGTCTTGTTTT 58.880 50.000 0.00 0.00 34.45 2.43
3733 4316 1.480137 CTTGGGGTGTCTTGTTTTGCA 59.520 47.619 0.00 0.00 0.00 4.08
3749 4332 5.931146 TGTTTTGCAAGTGTGATCTTGTTTT 59.069 32.000 0.00 0.00 44.41 2.43
3757 4340 6.369059 AGTGTGATCTTGTTTTGTGAAGAG 57.631 37.500 0.00 0.00 31.83 2.85
3758 4341 4.972440 GTGTGATCTTGTTTTGTGAAGAGC 59.028 41.667 0.00 0.00 35.59 4.09
3777 4360 6.552445 AGAGCTTCCTAGAAGCAATTCTTA 57.448 37.500 26.23 0.00 45.30 2.10
3780 4363 7.071071 AGAGCTTCCTAGAAGCAATTCTTAGAT 59.929 37.037 26.23 6.18 45.30 1.98
3781 4364 8.256356 AGCTTCCTAGAAGCAATTCTTAGATA 57.744 34.615 26.23 0.00 45.30 1.98
3901 4528 3.118038 TGGTGCCAATTATAGAGGACCAC 60.118 47.826 0.00 0.00 31.90 4.16
3914 4541 2.814336 GAGGACCACCAATTCTGAACAC 59.186 50.000 0.00 0.00 38.94 3.32
3951 4578 6.080682 AGATTAGATGGGAGTGCATTCTCTA 58.919 40.000 10.76 6.61 35.11 2.43
3952 4579 6.556495 AGATTAGATGGGAGTGCATTCTCTAA 59.444 38.462 16.53 16.53 35.11 2.10
3953 4580 4.686191 AGATGGGAGTGCATTCTCTAAG 57.314 45.455 10.76 0.00 35.11 2.18
3964 4591 7.769220 AGTGCATTCTCTAAGGAATTTTCATG 58.231 34.615 0.00 0.00 34.15 3.07
3976 4603 3.837213 ATTTTCATGGCAGAAGACACG 57.163 42.857 0.00 0.00 33.89 4.49
3981 4608 2.169144 TCATGGCAGAAGACACGATCAT 59.831 45.455 0.00 0.00 33.89 2.45
3984 4611 2.101415 TGGCAGAAGACACGATCATAGG 59.899 50.000 0.00 0.00 0.00 2.57
3992 4619 5.815233 AGACACGATCATAGGATTCCAAT 57.185 39.130 5.29 0.00 32.67 3.16
3993 4620 6.918067 AGACACGATCATAGGATTCCAATA 57.082 37.500 5.29 0.00 32.67 1.90
4025 4686 5.304686 TGGAGTAGAAGCCAGAAGAAAAA 57.695 39.130 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 6.916360 TTCAGAGGTTGGCTTCATAAAATT 57.084 33.333 0.00 0.00 0.00 1.82
36 37 0.251474 AGGCCAGCAAGCATTTCAGA 60.251 50.000 5.01 0.00 0.00 3.27
66 67 3.749088 AGGCACGACATCGAAATTAACAA 59.251 39.130 8.54 0.00 43.02 2.83
127 128 3.894427 ACCACACTAGCTATCAGGATCAG 59.106 47.826 0.00 0.00 0.00 2.90
154 155 2.099921 ACACTAGCAATGAGGAGCTACG 59.900 50.000 0.00 0.00 42.05 3.51
165 166 4.887071 TCAGGAACAACAAACACTAGCAAT 59.113 37.500 0.00 0.00 0.00 3.56
179 180 2.851263 ACTTGGCGTATCAGGAACAA 57.149 45.000 0.00 0.00 0.00 2.83
219 220 5.456619 CCATACCAGGATGCTCCAATCTAAA 60.457 44.000 0.00 0.00 39.61 1.85
226 227 2.487746 TACCATACCAGGATGCTCCA 57.512 50.000 0.00 0.00 39.61 3.86
258 259 5.172934 CCTAGCAAATCTAACCGTTACACA 58.827 41.667 0.00 0.00 0.00 3.72
318 319 1.602605 AGGGCAACTAACCAACCGC 60.603 57.895 0.00 0.00 0.00 5.68
319 320 0.536460 ACAGGGCAACTAACCAACCG 60.536 55.000 0.00 0.00 0.00 4.44
370 372 1.022451 TTTATCGAAGGGCCACACGC 61.022 55.000 6.18 0.00 0.00 5.34
444 446 8.637196 TCCTAGACATCACGATCTATTATGTT 57.363 34.615 0.00 0.00 31.19 2.71
527 529 9.723601 ACGGTCCAGTTTATGTATAGTTTAAAA 57.276 29.630 0.00 0.00 0.00 1.52
528 530 9.153721 CACGGTCCAGTTTATGTATAGTTTAAA 57.846 33.333 0.00 0.00 0.00 1.52
529 531 8.530311 TCACGGTCCAGTTTATGTATAGTTTAA 58.470 33.333 0.00 0.00 0.00 1.52
531 533 6.938507 TCACGGTCCAGTTTATGTATAGTTT 58.061 36.000 0.00 0.00 0.00 2.66
532 534 6.534475 TCACGGTCCAGTTTATGTATAGTT 57.466 37.500 0.00 0.00 0.00 2.24
533 535 6.097839 ACATCACGGTCCAGTTTATGTATAGT 59.902 38.462 8.55 0.00 30.72 2.12
534 536 6.513180 ACATCACGGTCCAGTTTATGTATAG 58.487 40.000 8.55 0.00 30.72 1.31
536 538 5.353394 ACATCACGGTCCAGTTTATGTAT 57.647 39.130 8.55 0.00 30.72 2.29
537 539 4.751060 GACATCACGGTCCAGTTTATGTA 58.249 43.478 9.56 0.00 31.89 2.29
538 540 3.596214 GACATCACGGTCCAGTTTATGT 58.404 45.455 9.44 9.44 33.43 2.29
548 550 2.163818 TGAAACTGGACATCACGGTC 57.836 50.000 0.00 0.00 37.06 4.79
549 551 2.616842 GTTTGAAACTGGACATCACGGT 59.383 45.455 0.00 0.00 0.00 4.83
550 552 2.878406 AGTTTGAAACTGGACATCACGG 59.122 45.455 10.18 0.00 41.01 4.94
551 553 3.559655 TGAGTTTGAAACTGGACATCACG 59.440 43.478 16.25 0.00 43.03 4.35
553 555 6.713762 AAATGAGTTTGAAACTGGACATCA 57.286 33.333 16.25 6.60 43.03 3.07
554 556 7.492344 ACAAAAATGAGTTTGAAACTGGACATC 59.508 33.333 16.25 0.51 43.03 3.06
555 557 7.330262 ACAAAAATGAGTTTGAAACTGGACAT 58.670 30.769 16.25 9.84 43.03 3.06
557 559 7.595311 AACAAAAATGAGTTTGAAACTGGAC 57.405 32.000 16.25 1.72 43.03 4.02
559 561 7.463544 GGAAACAAAAATGAGTTTGAAACTGG 58.536 34.615 16.25 0.00 43.03 4.00
565 602 6.443934 TCTCGGAAACAAAAATGAGTTTGA 57.556 33.333 4.76 0.00 40.29 2.69
624 689 5.295431 TCCAACATATGAGCGAGTTTTTG 57.705 39.130 10.38 0.00 0.00 2.44
702 770 8.792830 ATTCACTTCCACTGGTATTAGGTATA 57.207 34.615 0.00 0.00 0.00 1.47
710 778 6.357367 GGATTGTATTCACTTCCACTGGTAT 58.643 40.000 0.00 0.00 31.60 2.73
714 782 4.848357 AGGGATTGTATTCACTTCCACTG 58.152 43.478 3.76 0.00 32.40 3.66
780 848 4.867608 AGTTACTACGGTCTCTACTCGAAC 59.132 45.833 0.00 0.00 0.00 3.95
791 859 1.470098 TCCGCTTCAGTTACTACGGTC 59.530 52.381 12.59 0.00 41.33 4.79
917 985 2.536997 ATTGGAGAGGGGTTTCGGCG 62.537 60.000 0.00 0.00 0.00 6.46
1450 1528 3.153919 CGAAGGGAAATGAAAACAGGGA 58.846 45.455 0.00 0.00 0.00 4.20
1470 1549 9.630098 ATTAAGCATCAATATCAATTAAAGCCG 57.370 29.630 0.00 0.00 0.00 5.52
1642 1721 4.086457 TCATCCAGTATCTATGGCGCTAA 58.914 43.478 7.64 0.00 37.76 3.09
1678 1757 4.262549 CCCCTTGCTCATGATTTGTCAAAA 60.263 41.667 1.31 0.00 0.00 2.44
1691 1770 1.140312 AGACAACTTCCCCTTGCTCA 58.860 50.000 0.00 0.00 0.00 4.26
1699 1778 3.541632 TGACTGAAACAGACAACTTCCC 58.458 45.455 5.76 0.00 33.83 3.97
1810 1945 7.164230 TGTCCAACAAATAAATCACCCATAC 57.836 36.000 0.00 0.00 0.00 2.39
1859 1994 7.792032 AGAGTAATTAACCATGCTGCTAGTTA 58.208 34.615 0.00 3.61 0.00 2.24
1860 1995 6.653989 AGAGTAATTAACCATGCTGCTAGTT 58.346 36.000 0.00 4.59 0.00 2.24
1887 2024 9.349713 ACTGAACAAGTGTAATTTCATCCTAAA 57.650 29.630 0.00 0.00 37.88 1.85
1922 2060 6.573434 TCATAAGCAGATAGTAAGTGTGGTG 58.427 40.000 0.00 0.00 0.00 4.17
1948 2101 8.592155 GTTTTTACAGGTGACAATGAAAACTTC 58.408 33.333 0.00 0.00 35.20 3.01
1957 2110 3.320826 GGGCAGTTTTTACAGGTGACAAT 59.679 43.478 0.00 0.00 0.00 2.71
1964 2117 3.462982 GTTTTGGGGCAGTTTTTACAGG 58.537 45.455 0.00 0.00 0.00 4.00
1970 2123 0.750249 CTCGGTTTTGGGGCAGTTTT 59.250 50.000 0.00 0.00 0.00 2.43
2063 2217 3.059800 GCAGACTCGGTTGTAGAACAAAC 60.060 47.826 5.00 0.00 42.17 2.93
2240 2394 3.731652 CCAGCATTTGGTTCTGTTCAA 57.268 42.857 0.00 0.00 42.41 2.69
2411 2565 7.377398 AGCTGATACTACTCACATCAATGATC 58.623 38.462 0.00 0.00 0.00 2.92
2434 2588 3.365364 GGCAAGATGAACTGTTGTGTAGC 60.365 47.826 0.00 0.00 30.91 3.58
2581 2742 1.077787 CCTAAAGTGGGGCGCATGA 60.078 57.895 10.83 0.00 0.00 3.07
2582 2743 0.466189 ATCCTAAAGTGGGGCGCATG 60.466 55.000 10.83 0.00 0.00 4.06
2640 2801 2.376518 AGTGCTTTCCCATCCTCTGAAA 59.623 45.455 0.00 0.00 0.00 2.69
2671 2832 4.341806 TCCATTTGATTGTGCTTTGTCAGT 59.658 37.500 0.00 0.00 0.00 3.41
2797 2958 4.115516 CACTTACCATCATCTTCTCCACG 58.884 47.826 0.00 0.00 0.00 4.94
2830 2991 3.708631 CCTAGTCAGTCCATCAATCAGGT 59.291 47.826 0.00 0.00 0.00 4.00
2884 3046 2.227388 CTGGTCAAACTGCAATGGAGAC 59.773 50.000 9.20 0.00 0.00 3.36
2888 3053 0.387622 CGCTGGTCAAACTGCAATGG 60.388 55.000 0.00 0.00 35.35 3.16
2977 3142 4.769688 TGAACATGATGCTACTTACCTGG 58.230 43.478 0.00 0.00 0.00 4.45
2991 3156 4.099419 ACGCATACACTAGGATGAACATGA 59.901 41.667 0.00 0.00 0.00 3.07
3018 3183 1.152756 GGTGGTGCCAAGTCAACCT 60.153 57.895 0.00 0.00 37.17 3.50
3094 3259 5.045651 TCCAACCAATCTCAAGCTATCTTCA 60.046 40.000 0.00 0.00 0.00 3.02
3278 3444 2.009774 AGAAAACTGGGCAATCGATCG 58.990 47.619 9.36 9.36 0.00 3.69
3292 3458 8.555166 TGAACGATACACAAATTTCAGAAAAC 57.445 30.769 0.00 0.00 0.00 2.43
3302 3468 4.455533 ACAGCACATGAACGATACACAAAT 59.544 37.500 0.00 0.00 0.00 2.32
3332 3498 3.863424 GCTAGAAAGCGCACAACATAGTA 59.137 43.478 11.47 0.00 39.39 1.82
3398 3566 2.583024 TGTCCATTGCAGATGAACCA 57.417 45.000 9.56 2.55 0.00 3.67
3424 3592 5.428131 AGATCAGATTTCTTCAGCCCTTAGT 59.572 40.000 0.00 0.00 0.00 2.24
3432 3669 6.649973 ACTGTGACAAGATCAGATTTCTTCAG 59.350 38.462 0.00 0.00 38.28 3.02
3457 3694 3.258372 ACAGCGACTTTGACCTCTTCATA 59.742 43.478 0.00 0.00 32.84 2.15
3517 3763 1.228245 TCAGCAAGGTGAAGGTGGC 60.228 57.895 0.00 0.00 34.23 5.01
3553 3799 7.687941 TCTAGATCATGTTTTCCTTTGGTTC 57.312 36.000 0.00 0.00 0.00 3.62
3585 3831 1.004745 AGGACCCATCGCATTCACTTT 59.995 47.619 0.00 0.00 0.00 2.66
3595 3841 0.530744 TTCGAACAGAGGACCCATCG 59.469 55.000 0.00 0.00 0.00 3.84
3608 3862 2.353903 GGTTCCCTCCTCTCTTTCGAAC 60.354 54.545 0.00 0.00 0.00 3.95
3661 4239 5.722021 ACAAAATTTATCTCCAAGCCGTT 57.278 34.783 0.00 0.00 0.00 4.44
3706 4284 2.282462 GACACCCCAAGGCCACAG 60.282 66.667 5.01 0.00 36.11 3.66
3707 4285 2.391130 AAGACACCCCAAGGCCACA 61.391 57.895 5.01 0.00 36.11 4.17
3712 4290 1.202521 GCAAAACAAGACACCCCAAGG 60.203 52.381 0.00 0.00 40.04 3.61
3713 4291 1.480137 TGCAAAACAAGACACCCCAAG 59.520 47.619 0.00 0.00 0.00 3.61
3714 4292 1.561643 TGCAAAACAAGACACCCCAA 58.438 45.000 0.00 0.00 0.00 4.12
3715 4293 1.561643 TTGCAAAACAAGACACCCCA 58.438 45.000 0.00 0.00 33.24 4.96
3733 4316 6.678900 GCTCTTCACAAAACAAGATCACACTT 60.679 38.462 0.00 0.00 0.00 3.16
3749 4332 2.899900 TGCTTCTAGGAAGCTCTTCACA 59.100 45.455 25.69 7.65 43.38 3.58
3757 4340 8.894768 TTATCTAAGAATTGCTTCTAGGAAGC 57.105 34.615 21.01 21.01 40.93 3.86
3817 4420 8.774890 TTATTTAACATGACAATGCAAGCAAT 57.225 26.923 0.00 0.00 37.29 3.56
3821 4424 9.791820 TGAGATTATTTAACATGACAATGCAAG 57.208 29.630 0.00 0.00 37.29 4.01
3868 4495 2.452600 TTGGCACCAAGAAAAGAGGT 57.547 45.000 0.00 0.00 35.65 3.85
3872 4499 6.603201 TCCTCTATAATTGGCACCAAGAAAAG 59.397 38.462 8.30 3.76 39.47 2.27
3901 4528 5.043248 GGTTGTTCTTGTGTTCAGAATTGG 58.957 41.667 0.00 0.00 0.00 3.16
3914 4541 6.058183 CCCATCTAATCTAGGGTTGTTCTTG 58.942 44.000 0.00 0.00 36.52 3.02
3951 4578 4.834496 TGTCTTCTGCCATGAAAATTCCTT 59.166 37.500 0.00 0.00 0.00 3.36
3952 4579 4.219288 GTGTCTTCTGCCATGAAAATTCCT 59.781 41.667 0.00 0.00 0.00 3.36
3953 4580 4.488879 GTGTCTTCTGCCATGAAAATTCC 58.511 43.478 0.00 0.00 0.00 3.01
3964 4591 2.362397 TCCTATGATCGTGTCTTCTGCC 59.638 50.000 0.00 0.00 0.00 4.85
3976 4603 8.370940 TGACAGACTTATTGGAATCCTATGATC 58.629 37.037 6.48 1.95 0.00 2.92
3981 4608 6.615316 TCCATGACAGACTTATTGGAATCCTA 59.385 38.462 0.00 0.00 0.00 2.94
3984 4611 6.352516 ACTCCATGACAGACTTATTGGAATC 58.647 40.000 0.00 0.00 0.00 2.52
3992 4619 4.402793 GGCTTCTACTCCATGACAGACTTA 59.597 45.833 0.00 0.00 0.00 2.24
3993 4620 3.196685 GGCTTCTACTCCATGACAGACTT 59.803 47.826 0.00 0.00 0.00 3.01
4025 4686 2.558359 GCTTGCAGGTTTAGACACCAAT 59.442 45.455 0.00 0.00 39.62 3.16


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

AutoCloner maintained by Alex Coulton.