Multiple sequence alignment - TraesCS3A01G270000

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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 TraesCS3A01G270000 chr3A 100.000 4808 0 0 1 4808 496708384 496703577 0.000000e+00 8879.0
1 TraesCS3A01G270000 chr3A 98.148 54 1 0 2936 2989 496705396 496705343 1.420000e-15 95.3
2 TraesCS3A01G270000 chr3A 98.148 54 1 0 2989 3042 496705449 496705396 1.420000e-15 95.3
3 TraesCS3A01G270000 chr3D 94.129 2487 89 23 2370 4808 374209586 374207109 0.000000e+00 3731.0
4 TraesCS3A01G270000 chr3D 89.719 2169 76 55 1 2110 374212227 374210147 0.000000e+00 2634.0
5 TraesCS3A01G270000 chr3D 87.786 131 15 1 2112 2241 374210024 374209894 8.330000e-33 152.0
6 TraesCS3A01G270000 chr3D 98.182 55 1 0 2694 2748 374210049 374210103 3.960000e-16 97.1
7 TraesCS3A01G270000 chr3D 96.296 54 2 0 2936 2989 374208963 374208910 6.630000e-14 89.8
8 TraesCS3A01G270000 chr3D 89.583 48 1 4 4750 4795 339252958 339253003 1.870000e-04 58.4
9 TraesCS3A01G270000 chr3B 94.455 2038 81 15 2788 4808 487909227 487907205 0.000000e+00 3109.0
10 TraesCS3A01G270000 chr3B 88.630 2190 103 59 1 2108 487912372 487910247 0.000000e+00 2531.0
11 TraesCS3A01G270000 chr3B 87.101 690 38 30 2118 2761 487910108 487909424 0.000000e+00 734.0
12 TraesCS3A01G270000 chr3B 96.491 57 2 0 2694 2750 487910150 487910206 1.420000e-15 95.3
13 TraesCS3A01G270000 chr3B 96.296 54 2 0 2936 2989 487909027 487908974 6.630000e-14 89.8
14 TraesCS3A01G270000 chr3B 96.296 54 1 1 2989 3042 487909079 487909027 2.380000e-13 87.9
15 TraesCS3A01G270000 chr4A 82.133 750 107 20 3073 3807 658262252 658261515 6.840000e-173 617.0
16 TraesCS3A01G270000 chr7B 82.013 745 105 16 3080 3807 164157811 164158543 1.480000e-169 606.0
17 TraesCS3A01G270000 chr2B 81.004 737 111 19 3079 3807 785240832 785240117 4.200000e-155 558.0
18 TraesCS3A01G270000 chr2B 79.892 741 119 20 3079 3807 793488129 793487407 2.570000e-142 516.0
19 TraesCS3A01G270000 chr6B 80.641 749 119 20 3066 3807 351224235 351224964 1.510000e-154 556.0
20 TraesCS3A01G270000 chr4B 80.707 736 117 18 3080 3807 16557433 16558151 2.530000e-152 549.0
21 TraesCS3A01G270000 chr2A 82.629 639 94 11 3181 3807 778619716 778620349 2.530000e-152 549.0
22 TraesCS3A01G270000 chr1B 77.686 242 40 10 1427 1655 642392312 642392072 8.390000e-28 135.0
23 TraesCS3A01G270000 chr1D 77.273 242 41 10 1427 1655 465522431 465522191 3.910000e-26 130.0
24 TraesCS3A01G270000 chr1A 84.375 128 20 0 1528 1655 557935723 557935596 5.050000e-25 126.0
25 TraesCS3A01G270000 chr7D 82.308 130 20 2 1528 1654 632756271 632756400 5.090000e-20 110.0
26 TraesCS3A01G270000 chr6A 80.916 131 22 2 1528 1655 575589572 575589702 3.060000e-17 100.0
27 TraesCS3A01G270000 chr5A 84.615 65 9 1 2655 2719 403876069 403876132 4.020000e-06 63.9


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 TraesCS3A01G270000 chr3A 496703577 496708384 4807 True 3023.20 8879 98.765333 1 4808 3 chr3A.!!$R1 4807
1 TraesCS3A01G270000 chr3D 374207109 374212227 5118 True 1651.70 3731 91.982500 1 4808 4 chr3D.!!$R1 4807
2 TraesCS3A01G270000 chr3B 487907205 487912372 5167 True 1310.34 3109 92.555600 1 4808 5 chr3B.!!$R1 4807
3 TraesCS3A01G270000 chr4A 658261515 658262252 737 True 617.00 617 82.133000 3073 3807 1 chr4A.!!$R1 734
4 TraesCS3A01G270000 chr7B 164157811 164158543 732 False 606.00 606 82.013000 3080 3807 1 chr7B.!!$F1 727
5 TraesCS3A01G270000 chr2B 785240117 785240832 715 True 558.00 558 81.004000 3079 3807 1 chr2B.!!$R1 728
6 TraesCS3A01G270000 chr2B 793487407 793488129 722 True 516.00 516 79.892000 3079 3807 1 chr2B.!!$R2 728
7 TraesCS3A01G270000 chr6B 351224235 351224964 729 False 556.00 556 80.641000 3066 3807 1 chr6B.!!$F1 741
8 TraesCS3A01G270000 chr4B 16557433 16558151 718 False 549.00 549 80.707000 3080 3807 1 chr4B.!!$F1 727
9 TraesCS3A01G270000 chr2A 778619716 778620349 633 False 549.00 549 82.629000 3181 3807 1 chr2A.!!$F1 626

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
586 631 0.227234 CGCGTGTGATTAGTCGATGC 59.773 55.0 0.00 0.0 0.0 3.91 F
1890 2000 0.461961 AGGACAGGCTCACTAATCGC 59.538 55.0 0.00 0.0 0.0 4.58 F
2385 2886 0.957395 CAACGAATCTGCCAGGCTGT 60.957 55.0 14.15 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2351 2657 0.598065 CGTTGCTTTCTTTCAGGGGG 59.402 55.000 0.0 0.0 0.00 5.40 R
3646 4365 2.038952 TGCAGTGCTTCCTCACATAAGT 59.961 45.455 17.6 0.0 39.35 2.24 R
4188 4912 0.611062 ATCTTGACGAGGACGACCCA 60.611 55.000 0.0 0.0 42.66 4.51 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
101 102 2.125753 GAGCACGAGAGCCCTGTG 60.126 66.667 0.00 0.00 36.70 3.66
311 337 2.922335 GCTGAACTTGCGGGTGATTTTC 60.922 50.000 0.00 0.00 0.00 2.29
321 347 0.243636 GGTGATTTTCGGCCCAACAG 59.756 55.000 0.00 0.00 0.00 3.16
425 458 5.704217 ACATCGCGTTTTATCTTCTTCTC 57.296 39.130 5.77 0.00 0.00 2.87
437 470 2.300152 TCTTCTTCTCGCTGGTTGTCAT 59.700 45.455 0.00 0.00 0.00 3.06
522 560 1.106285 CCATTAGCAGACAAAGCCCC 58.894 55.000 0.00 0.00 0.00 5.80
539 583 1.898574 CCTTGTGACACCCAGTGGC 60.899 63.158 2.61 0.00 42.82 5.01
575 620 4.476410 CTAGCTCCGCGCGTGTGA 62.476 66.667 29.95 17.83 45.59 3.58
576 621 3.758088 CTAGCTCCGCGCGTGTGAT 62.758 63.158 29.95 20.33 45.59 3.06
586 631 0.227234 CGCGTGTGATTAGTCGATGC 59.773 55.000 0.00 0.00 0.00 3.91
591 636 3.487544 CGTGTGATTAGTCGATGCTGAGA 60.488 47.826 0.00 0.00 0.00 3.27
598 643 5.638596 TTAGTCGATGCTGAGACAGTTAA 57.361 39.130 0.00 0.00 39.67 2.01
606 651 3.134458 GCTGAGACAGTTAACAAGCAGT 58.866 45.455 8.61 0.00 33.43 4.40
608 653 4.122776 CTGAGACAGTTAACAAGCAGTGT 58.877 43.478 8.61 1.85 44.64 3.55
618 663 2.165167 ACAAGCAGTGTCATCCAATGG 58.835 47.619 0.00 0.00 39.51 3.16
620 665 1.028330 AGCAGTGTCATCCAATGGCG 61.028 55.000 0.00 0.00 39.51 5.69
622 667 1.750399 AGTGTCATCCAATGGCGGC 60.750 57.895 0.00 0.00 37.81 6.53
629 674 2.361757 TCATCCAATGGCGGCAATTTAG 59.638 45.455 18.31 5.01 0.00 1.85
632 677 2.426738 TCCAATGGCGGCAATTTAGAAG 59.573 45.455 18.31 0.00 0.00 2.85
636 681 1.816224 TGGCGGCAATTTAGAAGAACC 59.184 47.619 10.22 0.00 0.00 3.62
688 744 4.760204 GTCACAGCAGTACCCAACTAAAAT 59.240 41.667 0.00 0.00 35.76 1.82
749 810 0.721718 GCTCCGAACAATGGTCGAAG 59.278 55.000 23.41 13.28 0.00 3.79
792 853 1.588667 GCACACAAACAAGGTGGCG 60.589 57.895 0.00 0.00 40.54 5.69
793 854 1.588667 CACACAAACAAGGTGGCGC 60.589 57.895 0.00 0.00 40.54 6.53
936 1002 0.900647 CAAGTCGTCTCCCACTCCCT 60.901 60.000 0.00 0.00 0.00 4.20
938 1004 0.612453 AGTCGTCTCCCACTCCCTTC 60.612 60.000 0.00 0.00 0.00 3.46
939 1005 1.305046 TCGTCTCCCACTCCCTTCC 60.305 63.158 0.00 0.00 0.00 3.46
940 1006 2.359967 CGTCTCCCACTCCCTTCCC 61.360 68.421 0.00 0.00 0.00 3.97
941 1007 1.081277 GTCTCCCACTCCCTTCCCT 59.919 63.158 0.00 0.00 0.00 4.20
974 1050 3.708631 CTCCCTCCAAAGCATAGAGAAGA 59.291 47.826 0.00 0.00 0.00 2.87
989 1065 2.007636 AGAAGAGAACCTCTCCTCCCT 58.992 52.381 0.00 0.00 44.42 4.20
1160 1254 3.225061 GATCCGAGTCCCCCGACC 61.225 72.222 0.00 0.00 40.12 4.79
1350 1444 2.544267 CCGCCAAGTAAGATTCGATTCC 59.456 50.000 3.75 0.00 0.00 3.01
1355 1449 5.278022 GCCAAGTAAGATTCGATTCCATTCC 60.278 44.000 3.75 0.00 0.00 3.01
1370 1464 2.098117 CCATTCCATTCGCCTCTGAAAC 59.902 50.000 0.00 0.00 0.00 2.78
1414 1510 3.447025 CTGATCGACGGGGCCTTCC 62.447 68.421 0.84 0.00 0.00 3.46
1415 1511 3.155167 GATCGACGGGGCCTTCCT 61.155 66.667 0.84 0.00 35.33 3.36
1416 1512 3.153270 GATCGACGGGGCCTTCCTC 62.153 68.421 0.84 0.00 35.33 3.71
1614 1710 1.288439 CGAGGATCTCTCCATGGCG 59.712 63.158 6.96 0.00 44.79 5.69
1711 1807 1.435577 GTTTGAACGTATCCAGCGGT 58.564 50.000 0.00 0.00 0.00 5.68
1712 1808 2.609350 GTTTGAACGTATCCAGCGGTA 58.391 47.619 0.00 0.00 0.00 4.02
1713 1809 2.282701 TTGAACGTATCCAGCGGTAC 57.717 50.000 0.00 0.00 0.00 3.34
1722 1818 4.379186 CGTATCCAGCGGTACTATTACCTG 60.379 50.000 7.60 0.60 45.32 4.00
1735 1831 2.943036 TTACCTGGGTGTTCAGTTCC 57.057 50.000 2.07 0.00 33.14 3.62
1788 1884 0.472471 AAAGCCTGGACGTTGGAAGA 59.528 50.000 0.00 0.00 0.00 2.87
1794 1890 3.868754 GCCTGGACGTTGGAAGAGTAAAT 60.869 47.826 0.00 0.00 0.00 1.40
1800 1896 7.669427 TGGACGTTGGAAGAGTAAATTTACTA 58.331 34.615 26.80 11.44 43.64 1.82
1801 1897 7.599998 TGGACGTTGGAAGAGTAAATTTACTAC 59.400 37.037 26.80 19.29 43.64 2.73
1802 1898 7.816513 GGACGTTGGAAGAGTAAATTTACTACT 59.183 37.037 26.80 21.40 43.64 2.57
1803 1899 8.754230 ACGTTGGAAGAGTAAATTTACTACTC 57.246 34.615 26.80 23.34 43.64 2.59
1804 1900 7.816513 ACGTTGGAAGAGTAAATTTACTACTCC 59.183 37.037 30.33 30.33 44.26 3.85
1805 1901 7.816031 CGTTGGAAGAGTAAATTTACTACTCCA 59.184 37.037 32.96 32.96 44.55 3.86
1806 1902 9.668497 GTTGGAAGAGTAAATTTACTACTCCAT 57.332 33.333 34.74 19.35 45.01 3.41
1807 1903 9.886132 TTGGAAGAGTAAATTTACTACTCCATC 57.114 33.333 34.74 23.62 45.01 3.51
1808 1904 9.268282 TGGAAGAGTAAATTTACTACTCCATCT 57.732 33.333 32.96 22.27 44.26 2.90
1809 1905 9.752961 GGAAGAGTAAATTTACTACTCCATCTC 57.247 37.037 31.14 21.58 44.26 2.75
1890 2000 0.461961 AGGACAGGCTCACTAATCGC 59.538 55.000 0.00 0.00 0.00 4.58
1923 2033 5.129485 TGATTCCCTCCAAGATCAAGAGTAC 59.871 44.000 0.00 0.00 0.00 2.73
1988 2098 3.471680 GTGATCTTCCATGGGAGTAAGC 58.528 50.000 20.09 4.95 31.21 3.09
1991 2101 3.121929 TCTTCCATGGGAGTAAGCTCT 57.878 47.619 20.09 0.00 41.38 4.09
2020 2136 6.614694 TTGCTACTCCTATTTACTGTGGAA 57.385 37.500 0.00 0.00 0.00 3.53
2055 2171 7.740805 AGGAGTAATCCCAGAATATCTTTGAC 58.259 38.462 5.39 0.00 0.00 3.18
2084 2200 8.857216 TCTTAAATACAAATCTCGTCGAACTTC 58.143 33.333 0.00 0.00 0.00 3.01
2110 2226 8.363390 CAATCTCTATTGCAGATGGAACTACTA 58.637 37.037 0.00 0.00 36.35 1.82
2114 2351 5.543507 ATTGCAGATGGAACTACTAGGAG 57.456 43.478 0.00 0.00 0.00 3.69
2135 2383 6.651225 AGGAGTACTTAAGATTCACTTGTTGC 59.349 38.462 10.09 0.00 39.38 4.17
2194 2443 9.682465 ATGATCATGATTGATTTACTATCTGGG 57.318 33.333 10.14 0.00 42.73 4.45
2255 2504 3.309961 TGCCTCATAATCTCTGATCGC 57.690 47.619 0.00 0.00 0.00 4.58
2268 2517 2.943690 TCTGATCGCACTAGTAGTCACC 59.056 50.000 0.00 0.00 0.00 4.02
2269 2518 2.683362 CTGATCGCACTAGTAGTCACCA 59.317 50.000 0.00 0.00 0.00 4.17
2270 2519 3.086282 TGATCGCACTAGTAGTCACCAA 58.914 45.455 0.00 0.00 0.00 3.67
2272 2521 2.511659 TCGCACTAGTAGTCACCAACT 58.488 47.619 0.00 0.00 42.33 3.16
2294 2577 7.213178 ACTCTCCCCATACTGAAAATTGTAT 57.787 36.000 0.00 0.00 0.00 2.29
2302 2585 7.506938 CCCATACTGAAAATTGTATCCATCCTT 59.493 37.037 0.00 0.00 0.00 3.36
2321 2604 5.866207 TCCTTGAGGAAAAGAAGACTAACC 58.134 41.667 0.00 0.00 42.18 2.85
2322 2605 4.691216 CCTTGAGGAAAAGAAGACTAACCG 59.309 45.833 0.00 0.00 37.39 4.44
2323 2606 4.950205 TGAGGAAAAGAAGACTAACCGT 57.050 40.909 0.00 0.00 0.00 4.83
2335 2641 4.807443 AGACTAACCGTAGAACAAGCTTC 58.193 43.478 0.00 0.00 0.00 3.86
2336 2642 3.922910 ACTAACCGTAGAACAAGCTTCC 58.077 45.455 0.00 0.00 0.00 3.46
2350 2656 7.393515 AGAACAAGCTTCCGTTATATTTCCTTT 59.606 33.333 0.00 0.00 0.00 3.11
2351 2657 7.085052 ACAAGCTTCCGTTATATTTCCTTTC 57.915 36.000 0.00 0.00 0.00 2.62
2355 2661 4.442401 TCCGTTATATTTCCTTTCCCCC 57.558 45.455 0.00 0.00 0.00 5.40
2385 2886 0.957395 CAACGAATCTGCCAGGCTGT 60.957 55.000 14.15 0.00 0.00 4.40
2540 3046 2.171448 ACATGGATCTTCACTGGCCTAC 59.829 50.000 3.32 0.00 0.00 3.18
2669 3176 4.737855 ATAGATTTATATGCGCCGACCT 57.262 40.909 4.18 0.00 0.00 3.85
2769 3278 8.547069 TGTTGGTGAATTTTCGAAATTGATTTC 58.453 29.630 12.12 10.29 42.00 2.17
2771 3280 7.212976 TGGTGAATTTTCGAAATTGATTTCCA 58.787 30.769 12.12 15.90 42.34 3.53
2801 3480 5.565592 TTGCCTTAGCTTTCATACATGTG 57.434 39.130 9.11 0.00 40.80 3.21
2836 3515 7.013369 GGAAGTCAAGTTCTAACAGTTCCAATT 59.987 37.037 10.93 0.00 34.51 2.32
2980 3659 6.723298 ACTTGTATTTGTGTTTCCCATTGA 57.277 33.333 0.00 0.00 0.00 2.57
3071 3750 6.620877 ATTTCCACTAGTGTCAATCCTGTA 57.379 37.500 21.18 0.00 0.00 2.74
3248 3941 5.629133 GCTGACAGAAACCTGGGATATGTTA 60.629 44.000 6.65 0.00 36.01 2.41
3321 4016 7.387948 ACACAGACTGTTGAACATTTATACCTC 59.612 37.037 5.04 0.00 0.00 3.85
3580 4297 2.800544 CACGTGTTTCTTAGACCTGTGG 59.199 50.000 7.58 0.00 0.00 4.17
3600 4317 4.078537 TGGGTCAAATGTCTGTAATGTGG 58.921 43.478 0.00 0.00 0.00 4.17
3606 4323 5.700832 TCAAATGTCTGTAATGTGGTCTGTC 59.299 40.000 0.00 0.00 0.00 3.51
3626 4345 3.006940 TCGAGGTATTGCAATTGTGGTC 58.993 45.455 18.75 7.01 0.00 4.02
3646 4365 3.058777 GTCGCCGTATTTTCACTTGGAAA 60.059 43.478 0.00 0.00 43.59 3.13
3662 4381 4.365514 TGGAAACTTATGTGAGGAAGCA 57.634 40.909 0.00 0.00 0.00 3.91
3691 4414 1.614903 CCTGAATGCAAGCTTTCCACA 59.385 47.619 15.34 0.00 31.57 4.17
3829 4552 5.525745 TCGAAGAAAACTGCTACATTGTTGA 59.474 36.000 2.29 0.00 0.00 3.18
3869 4592 9.495754 GATTGAGAAAACTGCTAATGTACAATC 57.504 33.333 0.00 0.00 34.48 2.67
3896 4619 6.612247 TCAAGTTGCTGAACGATTTCTTTA 57.388 33.333 0.00 0.00 37.15 1.85
3926 4649 7.064016 GCCAAGAAGTACAACAATTTGACAAAA 59.936 33.333 4.41 0.00 36.48 2.44
3928 4651 8.379902 CAAGAAGTACAACAATTTGACAAAACC 58.620 33.333 4.41 0.00 36.48 3.27
4133 4857 2.879462 GTAGAACGGTCTGGCGCG 60.879 66.667 14.77 0.00 35.12 6.86
4170 4894 1.756408 CTTTGTGGCAATGGGGTGCA 61.756 55.000 0.00 0.00 46.81 4.57
4218 4942 0.028242 CGTCAAGATCCGTCTCCGAG 59.972 60.000 0.00 0.00 35.63 4.63
4294 5018 4.819761 TCCCACAGCGAGCGCATC 62.820 66.667 17.68 3.18 44.88 3.91
4314 5047 2.664851 TCCGCGCTGGTGTTCTTG 60.665 61.111 16.00 0.00 39.52 3.02
4457 5190 1.095807 GTAGAATTCCTGGCACCGGC 61.096 60.000 0.00 0.00 40.13 6.13
4716 5449 0.108615 AGAAGAACTGTCGCCATCCG 60.109 55.000 0.00 0.00 38.61 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 2.355126 CACGCCGATCGGATGAGG 60.355 66.667 37.64 20.59 43.86 3.86
101 102 1.217244 CCCCACCACTACGTACAGC 59.783 63.158 0.00 0.00 0.00 4.40
311 337 1.672356 CTTCTGACCTGTTGGGCCG 60.672 63.158 0.00 0.00 42.00 6.13
321 347 3.003793 GGCAAGTTTGTTCTCTTCTGACC 59.996 47.826 0.00 0.00 0.00 4.02
425 458 0.110056 GTTGCAGATGACAACCAGCG 60.110 55.000 8.17 0.00 41.22 5.18
517 555 2.776526 TGGGTGTCACAAGGGGCT 60.777 61.111 5.12 0.00 0.00 5.19
518 556 2.282462 CTGGGTGTCACAAGGGGC 60.282 66.667 5.12 0.00 0.00 5.80
522 560 2.253758 CGCCACTGGGTGTCACAAG 61.254 63.158 5.12 4.43 39.94 3.16
562 607 1.472276 GACTAATCACACGCGCGGAG 61.472 60.000 35.22 27.20 0.00 4.63
563 608 1.515519 GACTAATCACACGCGCGGA 60.516 57.895 35.22 22.09 0.00 5.54
564 609 2.845739 CGACTAATCACACGCGCGG 61.846 63.158 35.22 24.36 0.00 6.46
565 610 1.200474 ATCGACTAATCACACGCGCG 61.200 55.000 30.96 30.96 0.00 6.86
566 611 0.227234 CATCGACTAATCACACGCGC 59.773 55.000 5.73 0.00 0.00 6.86
567 612 0.227234 GCATCGACTAATCACACGCG 59.773 55.000 3.53 3.53 0.00 6.01
568 613 1.256376 CAGCATCGACTAATCACACGC 59.744 52.381 0.00 0.00 0.00 5.34
569 614 2.786027 CTCAGCATCGACTAATCACACG 59.214 50.000 0.00 0.00 0.00 4.49
570 615 3.794028 GTCTCAGCATCGACTAATCACAC 59.206 47.826 0.00 0.00 0.00 3.82
571 616 3.443681 TGTCTCAGCATCGACTAATCACA 59.556 43.478 0.00 0.00 0.00 3.58
572 617 4.033990 TGTCTCAGCATCGACTAATCAC 57.966 45.455 0.00 0.00 0.00 3.06
573 618 3.696548 ACTGTCTCAGCATCGACTAATCA 59.303 43.478 0.00 0.00 34.37 2.57
574 619 4.300189 ACTGTCTCAGCATCGACTAATC 57.700 45.455 0.00 0.00 34.37 1.75
575 620 4.727507 AACTGTCTCAGCATCGACTAAT 57.272 40.909 0.00 0.00 34.37 1.73
576 621 5.048294 TGTTAACTGTCTCAGCATCGACTAA 60.048 40.000 7.22 0.00 34.37 2.24
586 631 4.122776 ACACTGCTTGTTAACTGTCTCAG 58.877 43.478 7.22 9.13 33.09 3.35
591 636 3.815401 GGATGACACTGCTTGTTAACTGT 59.185 43.478 7.22 1.27 39.17 3.55
598 643 2.165167 CCATTGGATGACACTGCTTGT 58.835 47.619 0.00 0.00 43.10 3.16
606 651 0.683828 ATTGCCGCCATTGGATGACA 60.684 50.000 6.95 0.00 0.00 3.58
608 653 1.193323 AAATTGCCGCCATTGGATGA 58.807 45.000 6.95 0.00 0.00 2.92
618 663 3.190535 TCTTGGTTCTTCTAAATTGCCGC 59.809 43.478 0.00 0.00 0.00 6.53
620 665 6.575162 TTCTCTTGGTTCTTCTAAATTGCC 57.425 37.500 0.00 0.00 0.00 4.52
649 694 7.726291 ACTGCTGTGACTATAATACTGGAGTAT 59.274 37.037 0.00 0.00 40.89 2.12
652 697 6.398234 ACTGCTGTGACTATAATACTGGAG 57.602 41.667 0.00 0.00 37.60 3.86
653 698 6.264744 GGTACTGCTGTGACTATAATACTGGA 59.735 42.308 6.48 0.00 0.00 3.86
654 699 6.448006 GGTACTGCTGTGACTATAATACTGG 58.552 44.000 6.48 0.00 0.00 4.00
655 700 6.040504 TGGGTACTGCTGTGACTATAATACTG 59.959 42.308 6.48 0.00 0.00 2.74
657 702 6.401047 TGGGTACTGCTGTGACTATAATAC 57.599 41.667 6.48 0.00 0.00 1.89
658 703 6.610020 AGTTGGGTACTGCTGTGACTATAATA 59.390 38.462 6.48 0.00 35.19 0.98
659 704 5.425539 AGTTGGGTACTGCTGTGACTATAAT 59.574 40.000 6.48 0.00 35.19 1.28
660 705 4.775780 AGTTGGGTACTGCTGTGACTATAA 59.224 41.667 6.48 0.00 35.19 0.98
661 706 4.350245 AGTTGGGTACTGCTGTGACTATA 58.650 43.478 6.48 0.00 35.19 1.31
662 707 3.173965 AGTTGGGTACTGCTGTGACTAT 58.826 45.455 6.48 0.00 35.19 2.12
663 708 2.605257 AGTTGGGTACTGCTGTGACTA 58.395 47.619 6.48 0.00 35.19 2.59
664 709 1.424638 AGTTGGGTACTGCTGTGACT 58.575 50.000 6.48 0.51 35.19 3.41
665 710 3.396260 TTAGTTGGGTACTGCTGTGAC 57.604 47.619 6.48 0.00 37.73 3.67
666 711 4.425180 TTTTAGTTGGGTACTGCTGTGA 57.575 40.909 6.48 0.00 37.73 3.58
667 712 6.811253 TTATTTTAGTTGGGTACTGCTGTG 57.189 37.500 6.48 0.00 37.73 3.66
711 772 2.122564 GCAACAAGTCAAAGCAAGAGC 58.877 47.619 0.00 0.00 42.56 4.09
749 810 3.905339 GTCTCGACGAGTAGAGTACAC 57.095 52.381 23.41 8.81 34.54 2.90
772 833 1.588667 CCACCTTGTTTGTGTGCGC 60.589 57.895 0.00 0.00 31.71 6.09
861 922 1.431845 CGGGGGTTTCTTTATGCGC 59.568 57.895 0.00 0.00 0.00 6.09
936 1002 4.332543 AGGCGAGTGGGGAGGGAA 62.333 66.667 0.00 0.00 0.00 3.97
940 1006 4.787280 AGGGAGGCGAGTGGGGAG 62.787 72.222 0.00 0.00 0.00 4.30
941 1007 4.779733 GAGGGAGGCGAGTGGGGA 62.780 72.222 0.00 0.00 0.00 4.81
974 1050 1.707200 GGGAGGGAGGAGAGGTTCT 59.293 63.158 0.00 0.00 0.00 3.01
1350 1444 3.012518 AGTTTCAGAGGCGAATGGAATG 58.987 45.455 0.00 0.00 0.00 2.67
1355 1449 1.734465 GTCCAGTTTCAGAGGCGAATG 59.266 52.381 0.00 0.00 0.00 2.67
1524 1620 3.603532 CATGCTCACCTTGACATAGTGT 58.396 45.455 5.54 0.00 33.21 3.55
1614 1710 2.159544 GCAGCTGAACATCTTCTGAAGC 60.160 50.000 20.43 0.00 32.89 3.86
1678 1774 3.179599 CGTTCAAACGCAAAGATGGAAAC 59.820 43.478 1.95 0.00 46.06 2.78
1711 1807 5.188359 GGAACTGAACACCCAGGTAATAGTA 59.812 44.000 0.00 0.00 38.44 1.82
1712 1808 4.019591 GGAACTGAACACCCAGGTAATAGT 60.020 45.833 0.00 0.00 38.44 2.12
1713 1809 4.019681 TGGAACTGAACACCCAGGTAATAG 60.020 45.833 0.00 0.00 38.44 1.73
1735 1831 6.535508 GGCAAAGATGGAAACTACTACTAGTG 59.464 42.308 5.39 0.00 33.14 2.74
1788 1884 9.482175 ACTCAGAGATGGAGTAGTAAATTTACT 57.518 33.333 28.78 28.78 43.50 2.24
1800 1896 6.841229 TGGATGTTATTACTCAGAGATGGAGT 59.159 38.462 3.79 0.00 46.71 3.85
1801 1897 7.295322 TGGATGTTATTACTCAGAGATGGAG 57.705 40.000 3.79 0.00 38.36 3.86
1802 1898 7.732140 AGATGGATGTTATTACTCAGAGATGGA 59.268 37.037 3.79 0.00 0.00 3.41
1803 1899 7.905265 AGATGGATGTTATTACTCAGAGATGG 58.095 38.462 3.79 0.00 0.00 3.51
1804 1900 8.805175 AGAGATGGATGTTATTACTCAGAGATG 58.195 37.037 3.79 0.00 0.00 2.90
1805 1901 8.805175 CAGAGATGGATGTTATTACTCAGAGAT 58.195 37.037 3.79 0.00 0.00 2.75
1806 1902 8.001292 TCAGAGATGGATGTTATTACTCAGAGA 58.999 37.037 3.79 0.00 0.00 3.10
1807 1903 8.175925 TCAGAGATGGATGTTATTACTCAGAG 57.824 38.462 0.00 0.00 0.00 3.35
1808 1904 8.718158 ATCAGAGATGGATGTTATTACTCAGA 57.282 34.615 0.00 0.00 0.00 3.27
1809 1905 9.421806 GAATCAGAGATGGATGTTATTACTCAG 57.578 37.037 0.00 0.00 0.00 3.35
1810 1906 9.152327 AGAATCAGAGATGGATGTTATTACTCA 57.848 33.333 0.00 0.00 0.00 3.41
1890 2000 5.012239 TCTTGGAGGGAATCAACATTTGAG 58.988 41.667 0.00 0.00 43.98 3.02
1923 2033 4.103357 CCTTGTCTTCGTATGTAAGGACG 58.897 47.826 0.00 0.00 37.46 4.79
2020 2136 2.239907 GGGATTACTCCTTGAACTGGCT 59.760 50.000 0.00 0.00 41.74 4.75
2055 2171 7.736031 TCGACGAGATTTGTATTTAAGACAG 57.264 36.000 0.00 0.00 0.00 3.51
2084 2200 7.215789 AGTAGTTCCATCTGCAATAGAGATTG 58.784 38.462 0.00 0.00 44.62 2.67
2110 2226 6.651225 GCAACAAGTGAATCTTAAGTACTCCT 59.349 38.462 1.63 0.00 34.66 3.69
2114 2351 7.603024 ACCTAGCAACAAGTGAATCTTAAGTAC 59.397 37.037 1.63 0.00 34.66 2.73
2128 2376 3.070018 CTCAGACCAACCTAGCAACAAG 58.930 50.000 0.00 0.00 0.00 3.16
2135 2383 1.561643 TGAGCCTCAGACCAACCTAG 58.438 55.000 0.00 0.00 0.00 3.02
2172 2420 8.496534 TCTCCCAGATAGTAAATCAATCATGA 57.503 34.615 0.00 0.00 40.57 3.07
2179 2427 9.494055 CCCTAATATCTCCCAGATAGTAAATCA 57.506 37.037 3.15 0.00 40.23 2.57
2180 2428 8.425703 GCCCTAATATCTCCCAGATAGTAAATC 58.574 40.741 3.15 0.00 40.23 2.17
2194 2443 4.965200 AACAGTGGAGCCCTAATATCTC 57.035 45.455 0.00 0.00 0.00 2.75
2219 2468 3.973305 TGAGGCAATACATGTAGATGGGA 59.027 43.478 11.91 0.00 33.39 4.37
2220 2469 4.356405 TGAGGCAATACATGTAGATGGG 57.644 45.455 11.91 0.36 33.39 4.00
2233 2482 4.252073 GCGATCAGAGATTATGAGGCAAT 58.748 43.478 0.00 0.00 32.99 3.56
2255 2504 3.444388 GGGAGAGTTGGTGACTACTAGTG 59.556 52.174 5.39 0.00 46.54 2.74
2268 2517 5.711976 ACAATTTTCAGTATGGGGAGAGTTG 59.288 40.000 0.00 0.00 36.16 3.16
2269 2518 5.892348 ACAATTTTCAGTATGGGGAGAGTT 58.108 37.500 0.00 0.00 36.16 3.01
2270 2519 5.520748 ACAATTTTCAGTATGGGGAGAGT 57.479 39.130 0.00 0.00 36.16 3.24
2272 2521 6.601332 GGATACAATTTTCAGTATGGGGAGA 58.399 40.000 0.00 0.00 36.16 3.71
2294 2577 4.599241 AGTCTTCTTTTCCTCAAGGATGGA 59.401 41.667 0.00 0.00 44.98 3.41
2302 2585 4.950205 ACGGTTAGTCTTCTTTTCCTCA 57.050 40.909 0.00 0.00 0.00 3.86
2318 2601 1.069668 ACGGAAGCTTGTTCTACGGTT 59.930 47.619 2.10 0.00 0.00 4.44
2319 2602 0.677842 ACGGAAGCTTGTTCTACGGT 59.322 50.000 2.10 0.00 0.00 4.83
2320 2603 1.792006 AACGGAAGCTTGTTCTACGG 58.208 50.000 2.10 0.00 0.00 4.02
2321 2604 6.823678 AATATAACGGAAGCTTGTTCTACG 57.176 37.500 2.10 0.00 0.00 3.51
2322 2605 7.494952 AGGAAATATAACGGAAGCTTGTTCTAC 59.505 37.037 2.10 0.00 0.00 2.59
2323 2606 7.562135 AGGAAATATAACGGAAGCTTGTTCTA 58.438 34.615 2.10 0.36 0.00 2.10
2335 2641 4.141344 TCAGGGGGAAAGGAAATATAACGG 60.141 45.833 0.00 0.00 0.00 4.44
2336 2642 5.043737 TCAGGGGGAAAGGAAATATAACG 57.956 43.478 0.00 0.00 0.00 3.18
2350 2656 1.817740 CGTTGCTTTCTTTCAGGGGGA 60.818 52.381 0.00 0.00 0.00 4.81
2351 2657 0.598065 CGTTGCTTTCTTTCAGGGGG 59.402 55.000 0.00 0.00 0.00 5.40
2355 2661 3.910767 GCAGATTCGTTGCTTTCTTTCAG 59.089 43.478 0.00 0.00 38.51 3.02
2540 3046 5.423015 TCTAAGCTTTCTATCCAGTGCTTG 58.577 41.667 3.20 0.18 40.36 4.01
2642 3148 7.139392 GTCGGCGCATATAAATCTATATCTCA 58.861 38.462 10.83 0.00 29.67 3.27
2651 3157 2.960819 AGAGGTCGGCGCATATAAATC 58.039 47.619 10.83 0.00 0.00 2.17
2769 3278 5.300034 TGAAAGCTAAGGCAATATGACATGG 59.700 40.000 0.00 0.00 41.70 3.66
2771 3280 7.720957 TGTATGAAAGCTAAGGCAATATGACAT 59.279 33.333 0.00 0.00 41.70 3.06
2801 3480 4.327680 AGAACTTGACTTCCATAGCCAAC 58.672 43.478 0.00 0.00 0.00 3.77
2836 3515 7.339466 GCAAGGAAGAATTTAAGGTCAGGAATA 59.661 37.037 0.00 0.00 0.00 1.75
2980 3659 8.466798 GTTCCATATGGTAAAAACTATGCAACT 58.533 33.333 21.28 0.00 36.34 3.16
3122 3801 8.466798 ACAAGTGTTTTACCAGCCATAATATTC 58.533 33.333 0.00 0.00 0.00 1.75
3131 3810 3.254657 TGCATACAAGTGTTTTACCAGCC 59.745 43.478 0.00 0.00 0.00 4.85
3248 3941 9.574516 ACATTATAAGTTGAAGTTTCAGGTTCT 57.425 29.630 0.00 0.00 38.61 3.01
3364 4075 7.386059 TCTCAGTTCAGAGCATGTTTGTAATA 58.614 34.615 0.00 0.00 35.59 0.98
3526 4243 8.621286 CACTAACATTTGGGATATTTGAGGTAC 58.379 37.037 0.00 0.00 0.00 3.34
3527 4244 8.333235 ACACTAACATTTGGGATATTTGAGGTA 58.667 33.333 0.00 0.00 0.00 3.08
3528 4245 7.182060 ACACTAACATTTGGGATATTTGAGGT 58.818 34.615 0.00 0.00 0.00 3.85
3580 4297 5.003804 AGACCACATTACAGACATTTGACC 58.996 41.667 0.00 0.00 0.00 4.02
3600 4317 3.684788 ACAATTGCAATACCTCGACAGAC 59.315 43.478 13.39 0.00 0.00 3.51
3606 4323 2.223021 CGACCACAATTGCAATACCTCG 60.223 50.000 13.39 10.73 0.00 4.63
3626 4345 3.058501 AGTTTCCAAGTGAAAATACGGCG 60.059 43.478 4.80 4.80 44.30 6.46
3646 4365 2.038952 TGCAGTGCTTCCTCACATAAGT 59.961 45.455 17.60 0.00 39.35 2.24
3662 4381 3.731716 TGCATTCAGGAAGTGCAGT 57.268 47.368 12.09 0.00 43.30 4.40
3829 4552 9.260002 AGTTTTCTCAATCGCAAATAAATTGTT 57.740 25.926 0.00 0.00 41.32 2.83
3869 4592 4.675190 AATCGTTCAGCAACTTGATCAG 57.325 40.909 0.00 0.00 0.00 2.90
3896 4619 6.205853 TCAAATTGTTGTACTTCTTGGCGTAT 59.794 34.615 0.00 0.00 36.07 3.06
3926 4649 7.888546 GGATTAGGTACATATAGGCATTTTGGT 59.111 37.037 0.00 0.00 0.00 3.67
3928 4651 7.822334 TCGGATTAGGTACATATAGGCATTTTG 59.178 37.037 0.00 0.00 0.00 2.44
4133 4857 2.777832 AGCAGGTGAATCTTCAGGAC 57.222 50.000 0.00 0.00 37.98 3.85
4188 4912 0.611062 ATCTTGACGAGGACGACCCA 60.611 55.000 0.00 0.00 42.66 4.51
4296 5020 2.665185 AAGAACACCAGCGCGGAC 60.665 61.111 22.10 11.36 38.63 4.79
4314 5047 3.712881 GTGACGTCTGGGCGCAAC 61.713 66.667 17.92 1.07 34.88 4.17
4364 5097 2.997315 CCAGTCCCGTGCTGAGGA 60.997 66.667 0.00 0.00 36.12 3.71
4379 5112 1.768684 GACCCACAGCAGGAACTCCA 61.769 60.000 0.00 0.00 34.60 3.86
4427 5160 4.564116 ATTCTACGGCGGCGTCGG 62.564 66.667 40.80 30.93 33.75 4.79
4490 5223 1.448013 GGCGACAACTACTCTGGCC 60.448 63.158 0.00 0.00 0.00 5.36
4605 5338 2.426522 CTCGACCATGGCAAAGAAGAA 58.573 47.619 13.04 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.