Multiple sequence alignment - TraesCS4D01G268000

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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 TraesCS4D01G268000 chr4D 100.000 3609 0 0 1 3609 439294378 439290770 0.000000e+00 6665.0
1 TraesCS4D01G268000 chr4B 90.626 3563 179 63 110 3609 543401613 543398143 0.000000e+00 4586.0
2 TraesCS4D01G268000 chr4B 94.595 37 2 0 77 113 543402485 543402449 1.400000e-04 58.4
3 TraesCS4D01G268000 chr4A 88.957 2608 152 56 630 3183 28602646 28600121 0.000000e+00 3096.0
4 TraesCS4D01G268000 chr4A 95.960 99 4 0 3180 3278 28600086 28599988 1.040000e-35 161.0
5 TraesCS4D01G268000 chr4A 81.481 135 13 10 433 560 28602778 28602649 2.290000e-17 100.0
6 TraesCS4D01G268000 chr5D 97.143 35 1 0 2563 2597 562062906 562062872 3.890000e-05 60.2
7 TraesCS4D01G268000 chr5B 97.143 35 1 0 2563 2597 712436665 712436631 3.890000e-05 60.2
8 TraesCS4D01G268000 chr7B 100.000 29 0 0 2563 2591 642448 642476 2.000000e-03 54.7


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 TraesCS4D01G268000 chr4D 439290770 439294378 3608 True 6665.0 6665 100.000000 1 3609 1 chr4D.!!$R1 3608
1 TraesCS4D01G268000 chr4B 543398143 543402485 4342 True 2322.2 4586 92.610500 77 3609 2 chr4B.!!$R1 3532
2 TraesCS4D01G268000 chr4A 28599988 28602778 2790 True 1119.0 3096 88.799333 433 3278 3 chr4A.!!$R1 2845

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
238 1078 0.321564 CCAGGCATGTCCGAAACTCA 60.322 55.0 0.0 0.0 40.77 3.41 F
1447 2357 0.108329 GGCGACAAGAAGAATCCCGA 60.108 55.0 0.0 0.0 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1462 2372 0.106894 CTTATCCCCCTTGTCGGCTC 59.893 60.0 0.0 0.0 0.0 4.70 R
3028 3975 0.169230 GCTCTCACATCGACGACAGT 59.831 55.0 0.0 0.0 0.0 3.55 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
24 25 3.430333 AACTTGTAAACTGTTTGCGGG 57.570 42.857 15.69 12.37 0.00 6.13
25 26 1.679153 ACTTGTAAACTGTTTGCGGGG 59.321 47.619 15.69 10.24 0.00 5.73
26 27 0.386113 TTGTAAACTGTTTGCGGGGC 59.614 50.000 15.69 0.75 0.00 5.80
27 28 1.287815 GTAAACTGTTTGCGGGGCC 59.712 57.895 15.69 0.00 0.00 5.80
28 29 1.152735 TAAACTGTTTGCGGGGCCA 60.153 52.632 15.69 0.00 0.00 5.36
29 30 0.540830 TAAACTGTTTGCGGGGCCAT 60.541 50.000 15.69 0.00 0.00 4.40
30 31 2.098426 AAACTGTTTGCGGGGCCATG 62.098 55.000 4.39 0.00 0.00 3.66
31 32 2.676121 CTGTTTGCGGGGCCATGA 60.676 61.111 4.39 0.00 0.00 3.07
32 33 2.988684 TGTTTGCGGGGCCATGAC 60.989 61.111 4.39 0.00 0.00 3.06
33 34 3.758931 GTTTGCGGGGCCATGACC 61.759 66.667 4.39 0.00 0.00 4.02
43 44 3.560251 CCATGACCCCGCCCCTAG 61.560 72.222 0.00 0.00 0.00 3.02
44 45 2.445845 CATGACCCCGCCCCTAGA 60.446 66.667 0.00 0.00 0.00 2.43
45 46 1.843376 CATGACCCCGCCCCTAGAT 60.843 63.158 0.00 0.00 0.00 1.98
46 47 1.536662 ATGACCCCGCCCCTAGATC 60.537 63.158 0.00 0.00 0.00 2.75
47 48 2.923568 GACCCCGCCCCTAGATCC 60.924 72.222 0.00 0.00 0.00 3.36
48 49 4.936081 ACCCCGCCCCTAGATCCG 62.936 72.222 0.00 0.00 0.00 4.18
52 53 4.301027 CGCCCCTAGATCCGCCAC 62.301 72.222 0.00 0.00 0.00 5.01
53 54 2.844839 GCCCCTAGATCCGCCACT 60.845 66.667 0.00 0.00 0.00 4.00
54 55 3.142393 CCCCTAGATCCGCCACTG 58.858 66.667 0.00 0.00 0.00 3.66
55 56 2.423446 CCCTAGATCCGCCACTGC 59.577 66.667 0.00 0.00 0.00 4.40
56 57 2.136878 CCCTAGATCCGCCACTGCT 61.137 63.158 0.00 0.00 34.43 4.24
57 58 1.365633 CCTAGATCCGCCACTGCTC 59.634 63.158 0.00 0.00 34.43 4.26
58 59 1.007964 CTAGATCCGCCACTGCTCG 60.008 63.158 0.00 0.00 34.43 5.03
59 60 2.413437 CTAGATCCGCCACTGCTCGG 62.413 65.000 0.00 0.00 46.52 4.63
66 67 4.680237 CCACTGCTCGGCCGTTGA 62.680 66.667 27.15 4.62 0.00 3.18
67 68 3.114616 CACTGCTCGGCCGTTGAG 61.115 66.667 27.15 20.10 36.53 3.02
68 69 3.303135 ACTGCTCGGCCGTTGAGA 61.303 61.111 27.15 3.71 35.43 3.27
69 70 2.811317 CTGCTCGGCCGTTGAGAC 60.811 66.667 27.15 11.79 35.43 3.36
70 71 4.373116 TGCTCGGCCGTTGAGACC 62.373 66.667 27.15 4.03 35.43 3.85
71 72 4.070552 GCTCGGCCGTTGAGACCT 62.071 66.667 27.15 0.00 35.43 3.85
72 73 2.182030 CTCGGCCGTTGAGACCTC 59.818 66.667 27.15 0.00 35.43 3.85
73 74 3.685214 CTCGGCCGTTGAGACCTCG 62.685 68.421 27.15 0.00 35.43 4.63
74 75 4.052229 CGGCCGTTGAGACCTCGT 62.052 66.667 19.50 0.00 0.00 4.18
75 76 2.693762 CGGCCGTTGAGACCTCGTA 61.694 63.158 19.50 0.00 0.00 3.43
82 83 2.724228 CGTTGAGACCTCGTAGAACGAC 60.724 54.545 12.19 0.00 46.73 4.34
83 84 2.469274 TGAGACCTCGTAGAACGACT 57.531 50.000 0.00 0.00 46.73 4.18
113 114 5.194432 AGAGAGACGGCTAGAACAAGATAA 58.806 41.667 0.00 0.00 0.00 1.75
114 115 5.066764 AGAGAGACGGCTAGAACAAGATAAC 59.933 44.000 0.00 0.00 0.00 1.89
115 116 4.705507 AGAGACGGCTAGAACAAGATAACA 59.294 41.667 0.00 0.00 0.00 2.41
116 117 4.745649 AGACGGCTAGAACAAGATAACAC 58.254 43.478 0.00 0.00 0.00 3.32
117 118 4.463186 AGACGGCTAGAACAAGATAACACT 59.537 41.667 0.00 0.00 0.00 3.55
118 119 4.745649 ACGGCTAGAACAAGATAACACTC 58.254 43.478 0.00 0.00 0.00 3.51
119 120 4.113354 CGGCTAGAACAAGATAACACTCC 58.887 47.826 0.00 0.00 0.00 3.85
120 121 4.381612 CGGCTAGAACAAGATAACACTCCA 60.382 45.833 0.00 0.00 0.00 3.86
149 989 4.589216 TCATTGCTGGTTTCAAGAAAGG 57.411 40.909 0.00 0.00 0.00 3.11
238 1078 0.321564 CCAGGCATGTCCGAAACTCA 60.322 55.000 0.00 0.00 40.77 3.41
243 1083 1.999735 GCATGTCCGAAACTCAATCGA 59.000 47.619 0.00 0.00 42.76 3.59
244 1084 2.029728 GCATGTCCGAAACTCAATCGAG 59.970 50.000 0.00 0.00 42.76 4.04
245 1085 3.511699 CATGTCCGAAACTCAATCGAGA 58.488 45.455 0.00 0.00 42.34 4.04
246 1086 3.653539 TGTCCGAAACTCAATCGAGAA 57.346 42.857 0.00 0.00 42.34 2.87
294 1134 0.725117 CCGCAAACACCTATCGTTCC 59.275 55.000 0.00 0.00 0.00 3.62
295 1135 1.434555 CGCAAACACCTATCGTTCCA 58.565 50.000 0.00 0.00 0.00 3.53
310 1150 2.158645 CGTTCCATGACACGCAAACATA 59.841 45.455 0.00 0.00 0.00 2.29
311 1151 3.488489 GTTCCATGACACGCAAACATAC 58.512 45.455 0.00 0.00 0.00 2.39
313 1153 3.342719 TCCATGACACGCAAACATACAT 58.657 40.909 0.00 0.00 0.00 2.29
314 1154 3.126686 TCCATGACACGCAAACATACATG 59.873 43.478 0.00 0.00 35.11 3.21
367 1209 4.443063 TGTCATGACGTCTACGAAAACAAG 59.557 41.667 20.54 2.09 43.02 3.16
378 1220 2.621526 ACGAAAACAAGGTAAAGGCCAG 59.378 45.455 5.01 0.00 0.00 4.85
417 1259 6.557110 CCGTGTTTTAGACTTTGGAAAAAGA 58.443 36.000 5.27 0.00 34.06 2.52
418 1260 7.030768 CCGTGTTTTAGACTTTGGAAAAAGAA 58.969 34.615 5.27 0.00 34.06 2.52
419 1261 7.542824 CCGTGTTTTAGACTTTGGAAAAAGAAA 59.457 33.333 5.27 0.00 34.06 2.52
430 1272 9.778741 ACTTTGGAAAAAGAAAGAAAGAAAACT 57.221 25.926 5.27 0.00 34.02 2.66
523 1370 1.198759 CCGGTGGAGGAAAAGGGAGA 61.199 60.000 0.00 0.00 0.00 3.71
529 1380 2.291153 TGGAGGAAAAGGGAGAGCAATG 60.291 50.000 0.00 0.00 0.00 2.82
530 1381 2.025887 GGAGGAAAAGGGAGAGCAATGA 60.026 50.000 0.00 0.00 0.00 2.57
531 1382 3.013219 GAGGAAAAGGGAGAGCAATGAC 58.987 50.000 0.00 0.00 0.00 3.06
547 1398 0.531090 TGACGACGGGTTCACCTTTG 60.531 55.000 0.00 0.00 36.97 2.77
561 1412 3.191791 TCACCTTTGCATGACATGACATG 59.808 43.478 27.06 27.06 46.96 3.21
591 1442 3.116531 GCGGCGACAGTAACACCC 61.117 66.667 12.98 0.00 0.00 4.61
592 1443 2.340809 CGGCGACAGTAACACCCA 59.659 61.111 0.00 0.00 0.00 4.51
655 1506 2.125673 CGTAACCAGCACTCCCCG 60.126 66.667 0.00 0.00 0.00 5.73
777 1653 2.344592 TGCCTTCTACCTTTCCTTCCA 58.655 47.619 0.00 0.00 0.00 3.53
786 1662 2.821679 CTTTCCTTCCACCCGCTCCC 62.822 65.000 0.00 0.00 0.00 4.30
842 1719 0.578211 GCCGTTTTGTTTCGTCTCGA 59.422 50.000 0.00 0.00 0.00 4.04
844 1721 2.349155 GCCGTTTTGTTTCGTCTCGATT 60.349 45.455 0.00 0.00 35.23 3.34
894 1772 4.280019 AAACACCCACGCTCCCCC 62.280 66.667 0.00 0.00 0.00 5.40
933 1811 0.997363 TGTAGGAGACCCGGAGAAGA 59.003 55.000 0.73 0.00 37.58 2.87
934 1812 1.064611 TGTAGGAGACCCGGAGAAGAG 60.065 57.143 0.73 0.00 37.58 2.85
935 1813 0.551879 TAGGAGACCCGGAGAAGAGG 59.448 60.000 0.73 0.00 37.58 3.69
961 1839 4.649218 GGCAGAGAGGAAGAGTCTAGAAAT 59.351 45.833 0.00 0.00 0.00 2.17
965 1847 7.056635 CAGAGAGGAAGAGTCTAGAAATCTCT 58.943 42.308 13.43 13.43 41.13 3.10
966 1848 7.227512 CAGAGAGGAAGAGTCTAGAAATCTCTC 59.772 44.444 18.72 18.72 42.72 3.20
967 1849 6.055588 AGAGGAAGAGTCTAGAAATCTCTCG 58.944 44.000 10.81 0.00 37.54 4.04
1110 1998 4.697756 TGCGCCAAGAAGGTCCGG 62.698 66.667 4.18 0.00 40.61 5.14
1189 2086 2.297033 TGCCCTTCTCTGCATTTTGTTC 59.703 45.455 0.00 0.00 31.31 3.18
1214 2112 1.639298 GGTGGCTGATTCGTGTGCTC 61.639 60.000 0.00 0.00 0.00 4.26
1218 2119 1.811266 CTGATTCGTGTGCTCCGGG 60.811 63.158 0.00 0.00 0.00 5.73
1440 2341 0.321671 CAAGGAGGGCGACAAGAAGA 59.678 55.000 0.00 0.00 0.00 2.87
1446 2356 1.090052 GGGCGACAAGAAGAATCCCG 61.090 60.000 0.00 0.00 0.00 5.14
1447 2357 0.108329 GGCGACAAGAAGAATCCCGA 60.108 55.000 0.00 0.00 0.00 5.14
1448 2358 1.000145 GCGACAAGAAGAATCCCGAC 59.000 55.000 0.00 0.00 0.00 4.79
1449 2359 1.671850 GCGACAAGAAGAATCCCGACA 60.672 52.381 0.00 0.00 0.00 4.35
1450 2360 2.893637 CGACAAGAAGAATCCCGACAT 58.106 47.619 0.00 0.00 0.00 3.06
1451 2361 2.604914 CGACAAGAAGAATCCCGACATG 59.395 50.000 0.00 0.00 0.00 3.21
1452 2362 2.939103 GACAAGAAGAATCCCGACATGG 59.061 50.000 0.00 0.00 37.55 3.66
1526 2436 2.047179 AAAGAGGAAGACGCGGCC 60.047 61.111 9.25 4.67 0.00 6.13
1613 2523 0.311790 AACACACGCAGCAAATCCTG 59.688 50.000 0.00 0.00 35.93 3.86
1797 2707 0.033366 ATCAAAGGTGCGGTTTTGCC 59.967 50.000 2.75 0.00 34.96 4.52
1811 2721 1.544724 TTTGCCGGGATTCTTCTTGG 58.455 50.000 2.18 0.00 0.00 3.61
1822 2732 5.065346 GGGATTCTTCTTGGTTCTTCGAATC 59.935 44.000 0.00 0.00 36.31 2.52
1827 2739 2.000447 CTTGGTTCTTCGAATCCGGTC 59.000 52.381 0.00 0.00 36.24 4.79
1851 2763 5.587289 TGTTCTGCTGTTAATTTTGTGTCC 58.413 37.500 0.00 0.00 0.00 4.02
1903 2815 1.814429 TGTCTCTTCCAGGGGTCAAA 58.186 50.000 0.00 0.00 0.00 2.69
2094 3006 1.443872 GCGACGGCGAGAAGAAGAA 60.444 57.895 18.90 0.00 40.82 2.52
2109 3021 2.126850 GAAAGACAAAGCGGCGGC 60.127 61.111 9.78 8.43 40.37 6.53
2356 3280 2.873472 CGGCTACTACCAACAACAACAA 59.127 45.455 0.00 0.00 0.00 2.83
2447 3371 3.249189 AACCAAGAGAGGCCGGCA 61.249 61.111 30.85 0.00 0.00 5.69
2469 3393 2.244117 TACTACCAGCAGCAGCAGCC 62.244 60.000 6.10 0.00 45.49 4.85
2476 3400 4.717313 CAGCAGCAGCCCAGCTCA 62.717 66.667 0.00 0.00 44.54 4.26
2633 3560 2.202427 CGCCGCCCGAAAATTCAC 60.202 61.111 0.00 0.00 40.02 3.18
2681 3616 2.840102 CCGGCCGGGAGAGAAGAT 60.840 66.667 37.42 0.00 38.47 2.40
2817 3755 0.030603 TTTGGTTCCCCCTGCCTTTT 60.031 50.000 0.00 0.00 0.00 2.27
2821 3759 0.405973 GTTCCCCCTGCCTTTTCTCT 59.594 55.000 0.00 0.00 0.00 3.10
2833 3771 2.075338 CTTTTCTCTGCTGTCTCTGCC 58.925 52.381 0.00 0.00 0.00 4.85
2883 3821 5.448632 CCACGAGCTCCATTGGTTAATTAAC 60.449 44.000 18.30 18.30 35.50 2.01
2890 3828 8.470002 AGCTCCATTGGTTAATTAACTTGATTC 58.530 33.333 23.89 9.86 36.47 2.52
2892 3830 9.793252 CTCCATTGGTTAATTAACTTGATTCTG 57.207 33.333 23.89 13.22 36.47 3.02
2898 3838 6.183360 GGTTAATTAACTTGATTCTGACCCCG 60.183 42.308 23.89 0.00 36.47 5.73
2917 3857 4.541085 CCGGTGGTTCGGTTAAATTATC 57.459 45.455 0.00 0.00 44.60 1.75
2926 3866 9.184523 TGGTTCGGTTAAATTATCAGATGAATT 57.815 29.630 0.00 0.00 0.00 2.17
3108 4055 5.332707 GGCGAAGATTTCCACATTAAGAAC 58.667 41.667 0.00 0.00 0.00 3.01
3109 4056 5.123979 GGCGAAGATTTCCACATTAAGAACT 59.876 40.000 0.00 0.00 0.00 3.01
3119 4066 9.567776 TTTCCACATTAAGAACTGATTAACTGA 57.432 29.630 0.00 0.00 0.00 3.41
3303 4289 3.195002 CGGCATGGCGTACACCTG 61.195 66.667 31.39 2.69 0.00 4.00
3377 4364 7.012894 TGGATATTTTCGGAATTATTCTGCGTT 59.987 33.333 8.80 0.00 35.98 4.84
3378 4365 7.323656 GGATATTTTCGGAATTATTCTGCGTTG 59.676 37.037 8.80 0.00 35.98 4.10
3379 4366 4.349663 TTTCGGAATTATTCTGCGTTGG 57.650 40.909 8.80 0.00 35.98 3.77
3380 4367 2.980568 TCGGAATTATTCTGCGTTGGT 58.019 42.857 8.80 0.00 35.98 3.67
3381 4368 2.675844 TCGGAATTATTCTGCGTTGGTG 59.324 45.455 8.80 0.00 35.98 4.17
3382 4369 2.418628 CGGAATTATTCTGCGTTGGTGT 59.581 45.455 4.87 0.00 0.00 4.16
3383 4370 3.485216 CGGAATTATTCTGCGTTGGTGTC 60.485 47.826 4.87 0.00 0.00 3.67
3384 4371 3.438781 GGAATTATTCTGCGTTGGTGTCA 59.561 43.478 4.87 0.00 0.00 3.58
3385 4372 4.096382 GGAATTATTCTGCGTTGGTGTCAT 59.904 41.667 4.87 0.00 0.00 3.06
3391 4378 0.950836 TGCGTTGGTGTCATCTTTGG 59.049 50.000 0.00 0.00 0.00 3.28
3402 4389 6.496565 TGGTGTCATCTTTGGATATTTTTGGT 59.503 34.615 0.00 0.00 0.00 3.67
3403 4390 7.671819 TGGTGTCATCTTTGGATATTTTTGGTA 59.328 33.333 0.00 0.00 0.00 3.25
3404 4391 8.190784 GGTGTCATCTTTGGATATTTTTGGTAG 58.809 37.037 0.00 0.00 0.00 3.18
3405 4392 8.739972 GTGTCATCTTTGGATATTTTTGGTAGT 58.260 33.333 0.00 0.00 0.00 2.73
3406 4393 9.967451 TGTCATCTTTGGATATTTTTGGTAGTA 57.033 29.630 0.00 0.00 0.00 1.82
3410 4397 9.975218 ATCTTTGGATATTTTTGGTAGTACTGT 57.025 29.630 5.39 0.00 0.00 3.55
3423 4410 9.647797 TTTGGTAGTACTGTATTATTCTGTGTG 57.352 33.333 5.39 0.00 0.00 3.82
3438 4425 6.394025 TTCTGTGTGTGTATGTGTGTACTA 57.606 37.500 0.00 0.00 0.00 1.82
3459 4446 0.249741 GTGTGTTGGACGGCAGTAGT 60.250 55.000 0.00 0.00 0.00 2.73
3480 4467 4.851558 AGTTTTTGATATTTTCGTCTGCGC 59.148 37.500 0.00 0.00 38.14 6.09
3530 4517 1.522355 CTGCGGCCTGATGTACTGG 60.522 63.158 0.00 0.00 40.02 4.00
3532 4519 0.973496 TGCGGCCTGATGTACTGGTA 60.973 55.000 0.00 0.00 39.38 3.25
3577 4571 4.143009 CGATGACATACTCGATCGTGATCT 60.143 45.833 22.80 4.26 37.05 2.75
3578 4572 4.474226 TGACATACTCGATCGTGATCTG 57.526 45.455 22.80 16.90 35.72 2.90
3581 4575 2.632987 TACTCGATCGTGATCTGGGA 57.367 50.000 22.80 0.00 35.72 4.37
3592 4586 6.001449 TCGTGATCTGGGAAAAAGGATTAT 57.999 37.500 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.127842 CCCCGCAAACAGTTTACAAGTTATAT 60.128 38.462 0.00 0.00 0.00 0.86
2 3 4.022676 CCCCGCAAACAGTTTACAAGTTAT 60.023 41.667 0.00 0.00 0.00 1.89
4 5 2.100087 CCCCGCAAACAGTTTACAAGTT 59.900 45.455 0.00 0.00 0.00 2.66
5 6 1.679153 CCCCGCAAACAGTTTACAAGT 59.321 47.619 0.00 0.00 0.00 3.16
6 7 1.601914 GCCCCGCAAACAGTTTACAAG 60.602 52.381 0.00 0.00 0.00 3.16
7 8 0.386113 GCCCCGCAAACAGTTTACAA 59.614 50.000 0.00 0.00 0.00 2.41
8 9 1.457009 GGCCCCGCAAACAGTTTACA 61.457 55.000 0.00 0.00 0.00 2.41
9 10 1.287815 GGCCCCGCAAACAGTTTAC 59.712 57.895 0.00 0.00 0.00 2.01
10 11 0.540830 ATGGCCCCGCAAACAGTTTA 60.541 50.000 0.00 0.00 0.00 2.01
12 13 2.203625 ATGGCCCCGCAAACAGTT 60.204 55.556 0.00 0.00 0.00 3.16
13 14 2.990967 CATGGCCCCGCAAACAGT 60.991 61.111 0.00 0.00 0.00 3.55
14 15 2.676121 TCATGGCCCCGCAAACAG 60.676 61.111 0.00 0.00 0.00 3.16
15 16 2.988684 GTCATGGCCCCGCAAACA 60.989 61.111 0.00 0.00 0.00 2.83
16 17 3.758931 GGTCATGGCCCCGCAAAC 61.759 66.667 4.49 0.00 0.00 2.93
26 27 3.560251 CTAGGGGCGGGGTCATGG 61.560 72.222 0.00 0.00 0.00 3.66
27 28 1.831652 GATCTAGGGGCGGGGTCATG 61.832 65.000 0.00 0.00 0.00 3.07
28 29 1.536662 GATCTAGGGGCGGGGTCAT 60.537 63.158 0.00 0.00 0.00 3.06
29 30 2.122989 GATCTAGGGGCGGGGTCA 60.123 66.667 0.00 0.00 0.00 4.02
30 31 2.923568 GGATCTAGGGGCGGGGTC 60.924 72.222 0.00 0.00 0.00 4.46
31 32 4.936081 CGGATCTAGGGGCGGGGT 62.936 72.222 0.00 0.00 0.00 4.95
35 36 4.301027 GTGGCGGATCTAGGGGCG 62.301 72.222 0.00 0.00 0.00 6.13
36 37 2.844839 AGTGGCGGATCTAGGGGC 60.845 66.667 0.00 0.00 0.00 5.80
37 38 3.142393 CAGTGGCGGATCTAGGGG 58.858 66.667 0.00 0.00 0.00 4.79
38 39 2.423446 GCAGTGGCGGATCTAGGG 59.577 66.667 0.00 0.00 0.00 3.53
49 50 4.680237 TCAACGGCCGAGCAGTGG 62.680 66.667 35.90 6.41 37.01 4.00
50 51 3.114616 CTCAACGGCCGAGCAGTG 61.115 66.667 35.90 20.04 37.01 3.66
51 52 3.303135 TCTCAACGGCCGAGCAGT 61.303 61.111 35.90 5.52 38.82 4.40
52 53 2.811317 GTCTCAACGGCCGAGCAG 60.811 66.667 35.90 22.55 0.00 4.24
53 54 4.373116 GGTCTCAACGGCCGAGCA 62.373 66.667 35.90 13.52 0.00 4.26
54 55 3.991536 GAGGTCTCAACGGCCGAGC 62.992 68.421 35.90 19.08 0.00 5.03
55 56 2.182030 GAGGTCTCAACGGCCGAG 59.818 66.667 35.90 23.74 0.00 4.63
56 57 3.744719 CGAGGTCTCAACGGCCGA 61.745 66.667 35.90 8.90 0.00 5.54
57 58 2.594119 CTACGAGGTCTCAACGGCCG 62.594 65.000 26.86 26.86 0.00 6.13
58 59 1.139095 CTACGAGGTCTCAACGGCC 59.861 63.158 0.00 0.00 0.00 6.13
59 60 0.524862 TTCTACGAGGTCTCAACGGC 59.475 55.000 0.00 0.00 0.00 5.68
60 61 1.465354 CGTTCTACGAGGTCTCAACGG 60.465 57.143 11.16 0.00 46.05 4.44
61 62 1.462283 TCGTTCTACGAGGTCTCAACG 59.538 52.381 12.21 12.21 46.73 4.10
72 73 4.437239 TCTCTAACCCTAGTCGTTCTACG 58.563 47.826 0.00 0.00 44.19 3.51
73 74 5.523552 GTCTCTCTAACCCTAGTCGTTCTAC 59.476 48.000 0.00 0.00 0.00 2.59
74 75 5.669477 GTCTCTCTAACCCTAGTCGTTCTA 58.331 45.833 0.00 0.00 0.00 2.10
75 76 4.516323 GTCTCTCTAACCCTAGTCGTTCT 58.484 47.826 0.00 0.00 0.00 3.01
82 83 2.351706 AGCCGTCTCTCTAACCCTAG 57.648 55.000 0.00 0.00 0.00 3.02
83 84 3.044156 TCTAGCCGTCTCTCTAACCCTA 58.956 50.000 0.00 0.00 0.00 3.53
142 982 3.135167 TGTCGTTAAGTCACCCCTTTCTT 59.865 43.478 0.00 0.00 0.00 2.52
149 989 2.858344 CGATGATGTCGTTAAGTCACCC 59.142 50.000 0.00 0.00 45.19 4.61
170 1010 1.403679 CAGTCGACCTCATCTCTGGTC 59.596 57.143 13.01 0.00 46.69 4.02
172 1012 1.468985 ACAGTCGACCTCATCTCTGG 58.531 55.000 13.01 0.00 33.80 3.86
219 1059 0.321564 TGAGTTTCGGACATGCCTGG 60.322 55.000 0.00 0.00 0.00 4.45
257 1097 2.028930 GCGGTATAGTGGCAGCTCTATT 60.029 50.000 13.12 2.74 0.00 1.73
268 1108 3.734231 CGATAGGTGTTTGCGGTATAGTG 59.266 47.826 0.00 0.00 0.00 2.74
294 1134 4.082274 ACATGTATGTTTGCGTGTCATG 57.918 40.909 0.00 0.00 37.90 3.07
295 1135 5.175127 TCTACATGTATGTTTGCGTGTCAT 58.825 37.500 5.91 0.00 41.97 3.06
367 1209 1.950954 GCTGTCCTTCTGGCCTTTACC 60.951 57.143 3.32 0.00 0.00 2.85
430 1272 5.473504 GGAGTGGCTTTCTGATTACAAAAGA 59.526 40.000 0.00 0.00 32.89 2.52
483 1325 2.663188 GATTGCCCGGCTCGCTAG 60.663 66.667 11.61 0.00 0.00 3.42
484 1326 4.235762 GGATTGCCCGGCTCGCTA 62.236 66.667 11.61 0.00 0.00 4.26
523 1370 0.949105 GTGAACCCGTCGTCATTGCT 60.949 55.000 0.00 0.00 0.00 3.91
529 1380 1.838568 GCAAAGGTGAACCCGTCGTC 61.839 60.000 0.00 0.00 38.74 4.20
530 1381 1.890510 GCAAAGGTGAACCCGTCGT 60.891 57.895 0.00 0.00 38.74 4.34
531 1382 1.234615 ATGCAAAGGTGAACCCGTCG 61.235 55.000 0.00 0.00 38.74 5.12
547 1398 1.063027 CCGTGTCATGTCATGTCATGC 59.937 52.381 23.09 18.65 43.18 4.06
582 1433 3.399330 CGTTGAGTTGATGGGTGTTACT 58.601 45.455 0.00 0.00 0.00 2.24
591 1442 1.078709 ATCACCGCGTTGAGTTGATG 58.921 50.000 13.02 0.00 0.00 3.07
592 1443 1.078709 CATCACCGCGTTGAGTTGAT 58.921 50.000 13.02 3.90 0.00 2.57
634 1485 2.813908 GAGTGCTGGTTACGCCCG 60.814 66.667 0.00 0.00 36.04 6.13
635 1486 2.436115 GGAGTGCTGGTTACGCCC 60.436 66.667 0.00 0.00 36.04 6.13
671 1522 3.174788 CGGTAAGTTTCTGCCGCC 58.825 61.111 0.00 0.00 37.69 6.13
704 1565 2.504032 GCCCGATCCGATCCACAA 59.496 61.111 2.69 0.00 0.00 3.33
842 1719 1.606668 TGCGAGAAAAACCAAGCGAAT 59.393 42.857 0.00 0.00 0.00 3.34
844 1721 0.586319 CTGCGAGAAAAACCAAGCGA 59.414 50.000 0.00 0.00 0.00 4.93
933 1811 0.032217 CTCTTCCTCTCTGCCTCCCT 60.032 60.000 0.00 0.00 0.00 4.20
934 1812 0.325203 ACTCTTCCTCTCTGCCTCCC 60.325 60.000 0.00 0.00 0.00 4.30
935 1813 1.111277 GACTCTTCCTCTCTGCCTCC 58.889 60.000 0.00 0.00 0.00 4.30
940 1818 7.056635 AGAGATTTCTAGACTCTTCCTCTCTG 58.943 42.308 5.71 0.00 37.69 3.35
961 1839 0.751452 TAGCTACGCTCTCCGAGAGA 59.249 55.000 26.64 9.14 45.07 3.10
965 1847 1.892862 GGCTAGCTACGCTCTCCGA 60.893 63.158 15.72 0.00 40.44 4.55
966 1848 2.123988 CTGGCTAGCTACGCTCTCCG 62.124 65.000 15.72 0.00 40.44 4.63
967 1849 1.657556 CTGGCTAGCTACGCTCTCC 59.342 63.158 15.72 0.00 40.44 3.71
1110 1998 1.202268 GGCATGCTCTTGATGCTGTTC 60.202 52.381 18.92 0.00 44.75 3.18
1189 2086 1.811266 CGAATCAGCCACCAGACCG 60.811 63.158 0.00 0.00 0.00 4.79
1218 2119 4.374702 CACACCTGCGCGACAAGC 62.375 66.667 12.10 0.00 43.95 4.01
1461 2371 1.342672 TTATCCCCCTTGTCGGCTCC 61.343 60.000 0.00 0.00 0.00 4.70
1462 2372 0.106894 CTTATCCCCCTTGTCGGCTC 59.893 60.000 0.00 0.00 0.00 4.70
1463 2373 1.345715 CCTTATCCCCCTTGTCGGCT 61.346 60.000 0.00 0.00 0.00 5.52
1464 2374 1.148498 CCTTATCCCCCTTGTCGGC 59.852 63.158 0.00 0.00 0.00 5.54
1465 2375 1.148498 GCCTTATCCCCCTTGTCGG 59.852 63.158 0.00 0.00 0.00 4.79
1466 2376 1.148498 GGCCTTATCCCCCTTGTCG 59.852 63.158 0.00 0.00 0.00 4.35
1526 2436 2.644992 GTGGGCGGTTGCTTCTTG 59.355 61.111 0.00 0.00 42.25 3.02
1550 2460 1.901085 CTTCTTCTCCTCGGTGGGG 59.099 63.158 0.00 0.00 37.77 4.96
1551 2461 1.219393 GCTTCTTCTCCTCGGTGGG 59.781 63.158 0.00 0.00 36.20 4.61
1552 2462 1.219393 GGCTTCTTCTCCTCGGTGG 59.781 63.158 0.00 0.00 37.10 4.61
1613 2523 1.819632 CAGAGTATTGCGTGGGGGC 60.820 63.158 0.00 0.00 0.00 5.80
1667 2577 0.171455 GAAGCGGAGACATCGTGAGT 59.829 55.000 0.00 0.00 0.00 3.41
1797 2707 2.673368 CGAAGAACCAAGAAGAATCCCG 59.327 50.000 0.00 0.00 0.00 5.14
1811 2721 2.365408 ACAGACCGGATTCGAAGAAC 57.635 50.000 9.46 0.00 45.90 3.01
1822 2732 2.163818 TTAACAGCAGAACAGACCGG 57.836 50.000 0.00 0.00 0.00 5.28
1827 2739 5.687285 GGACACAAAATTAACAGCAGAACAG 59.313 40.000 0.00 0.00 0.00 3.16
1851 2763 2.666508 ACATCGTCAATTTCGAACGGAG 59.333 45.455 0.00 0.00 40.61 4.63
1903 2815 2.976490 GCCCTCCAGCTCCACATGT 61.976 63.158 0.00 0.00 0.00 3.21
1987 2899 2.433318 GCGCGGTTGAGCTTCTCT 60.433 61.111 8.83 0.00 37.97 3.10
2417 3341 2.234908 CTCTTGGTTGCTGGTAGTAGCT 59.765 50.000 0.35 0.00 44.01 3.32
2469 3393 2.127869 TAGTAGCCGCCTGAGCTGG 61.128 63.158 0.00 0.00 41.71 4.85
2471 3395 2.128507 GGTAGTAGCCGCCTGAGCT 61.129 63.158 0.00 0.00 44.49 4.09
2472 3396 2.356818 CTGGTAGTAGCCGCCTGAGC 62.357 65.000 0.00 0.00 0.00 4.26
2474 3398 2.423898 GCTGGTAGTAGCCGCCTGA 61.424 63.158 4.57 0.00 37.73 3.86
2475 3399 2.107141 GCTGGTAGTAGCCGCCTG 59.893 66.667 4.57 0.00 37.73 4.85
2476 3400 2.363795 TGCTGGTAGTAGCCGCCT 60.364 61.111 12.40 0.00 43.02 5.52
2629 3556 1.446099 GTCGGCGCTGATGAGTGAA 60.446 57.895 24.03 0.00 0.00 3.18
2633 3560 2.951745 GTCGTCGGCGCTGATGAG 60.952 66.667 35.54 23.07 34.68 2.90
2674 3609 6.365789 GCTACTATGTCAGCATTGATCTTCTC 59.634 42.308 0.00 0.00 37.73 2.87
2675 3610 6.183360 TGCTACTATGTCAGCATTGATCTTCT 60.183 38.462 0.00 0.00 42.68 2.85
2681 3616 4.160252 TGTCTGCTACTATGTCAGCATTGA 59.840 41.667 0.00 0.00 46.15 2.57
2762 3700 0.947244 GCATCGGTTCATGGATGGAC 59.053 55.000 10.48 0.00 40.25 4.02
2817 3755 1.986757 GGGGCAGAGACAGCAGAGA 60.987 63.158 0.00 0.00 0.00 3.10
2821 3759 1.614525 ATCAGGGGCAGAGACAGCA 60.615 57.895 0.00 0.00 0.00 4.41
2833 3771 1.290203 CGAACAATGGTCGATCAGGG 58.710 55.000 16.60 0.72 0.00 4.45
2883 3821 0.392998 CCACCGGGGTCAGAATCAAG 60.393 60.000 6.32 0.00 0.00 3.02
2898 3838 6.540914 TCATCTGATAATTTAACCGAACCACC 59.459 38.462 0.00 0.00 0.00 4.61
2916 3856 6.642540 CCATTCGTCGATCTTAATTCATCTGA 59.357 38.462 0.00 0.00 0.00 3.27
2917 3857 6.128715 CCCATTCGTCGATCTTAATTCATCTG 60.129 42.308 0.00 0.00 0.00 2.90
3028 3975 0.169230 GCTCTCACATCGACGACAGT 59.831 55.000 0.00 0.00 0.00 3.55
3119 4066 0.904649 TCAACGATGATCACTGCCCT 59.095 50.000 0.00 0.00 0.00 5.19
3131 4079 1.275291 ACTCACGGTCCAATCAACGAT 59.725 47.619 0.00 0.00 0.00 3.73
3377 4364 6.496565 ACCAAAAATATCCAAAGATGACACCA 59.503 34.615 0.00 0.00 33.67 4.17
3378 4365 6.935167 ACCAAAAATATCCAAAGATGACACC 58.065 36.000 0.00 0.00 33.67 4.16
3379 4366 8.739972 ACTACCAAAAATATCCAAAGATGACAC 58.260 33.333 0.00 0.00 33.67 3.67
3380 4367 8.877864 ACTACCAAAAATATCCAAAGATGACA 57.122 30.769 0.00 0.00 33.67 3.58
3384 4371 9.975218 ACAGTACTACCAAAAATATCCAAAGAT 57.025 29.630 0.00 0.00 36.44 2.40
3403 4390 9.803315 CATACACACACAGAATAATACAGTACT 57.197 33.333 0.00 0.00 0.00 2.73
3404 4391 9.582431 ACATACACACACAGAATAATACAGTAC 57.418 33.333 0.00 0.00 0.00 2.73
3405 4392 9.581099 CACATACACACACAGAATAATACAGTA 57.419 33.333 0.00 0.00 0.00 2.74
3406 4393 8.094548 ACACATACACACACAGAATAATACAGT 58.905 33.333 0.00 0.00 0.00 3.55
3407 4394 8.382875 CACACATACACACACAGAATAATACAG 58.617 37.037 0.00 0.00 0.00 2.74
3408 4395 7.875554 ACACACATACACACACAGAATAATACA 59.124 33.333 0.00 0.00 0.00 2.29
3409 4396 8.251750 ACACACATACACACACAGAATAATAC 57.748 34.615 0.00 0.00 0.00 1.89
3410 4397 9.361315 GTACACACATACACACACAGAATAATA 57.639 33.333 0.00 0.00 0.00 0.98
3423 4410 6.128661 CCAACACACATAGTACACACATACAC 60.129 42.308 0.00 0.00 0.00 2.90
3427 4414 4.994852 GTCCAACACACATAGTACACACAT 59.005 41.667 0.00 0.00 0.00 3.21
3438 4425 0.394938 TACTGCCGTCCAACACACAT 59.605 50.000 0.00 0.00 0.00 3.21
3459 4446 3.843541 CGCGCAGACGAAAATATCAAAAA 59.156 39.130 8.75 0.00 43.93 1.94
3516 4503 4.455877 GCATTATTACCAGTACATCAGGCC 59.544 45.833 0.00 0.00 0.00 5.19
3532 4519 9.630098 CATCGAAAGCCTTAATAATGCATTATT 57.370 29.630 35.04 35.04 43.32 1.40
3577 4571 7.673641 ATGCAATACATAATCCTTTTTCCCA 57.326 32.000 0.00 0.00 37.17 4.37
3578 4572 8.203485 TGAATGCAATACATAATCCTTTTTCCC 58.797 33.333 0.00 0.00 38.34 3.97


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

AutoCloner maintained by Alex Coulton.