Multiple sequence alignment - TraesCS5D01G014200

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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 TraesCS5D01G014200 chr5D 100.000 3779 0 0 1 3779 8019039 8022817 0.000000e+00 6979.0
1 TraesCS5D01G014200 chr5D 78.863 563 100 11 977 1531 8033336 8033887 2.770000e-96 363.0
2 TraesCS5D01G014200 chr5D 81.298 262 39 10 473 731 340742219 340742473 1.780000e-48 204.0
3 TraesCS5D01G014200 chr5B 90.723 2878 167 49 479 3305 8342099 8344927 0.000000e+00 3744.0
4 TraesCS5D01G014200 chr5B 92.075 429 25 3 6 426 8341653 8342080 2.510000e-166 595.0
5 TraesCS5D01G014200 chr5B 79.892 557 89 16 967 1514 8351846 8352388 1.650000e-103 387.0
6 TraesCS5D01G014200 chr5B 81.395 430 37 24 3390 3778 8344943 8345370 1.020000e-80 311.0
7 TraesCS5D01G014200 chr5B 79.276 304 57 5 431 731 107208541 107208241 1.380000e-49 207.0
8 TraesCS5D01G014200 chr5B 81.467 259 43 4 433 690 399775178 399775432 1.380000e-49 207.0
9 TraesCS5D01G014200 chr5A 93.232 2497 143 17 504 2983 6410613 6413100 0.000000e+00 3651.0
10 TraesCS5D01G014200 chr5A 84.943 611 63 19 3176 3779 6413355 6413943 3.250000e-165 592.0
11 TraesCS5D01G014200 chr5A 91.765 340 22 5 55 391 6410140 6410476 5.720000e-128 468.0
12 TraesCS5D01G014200 chr5A 79.218 563 98 11 977 1531 6422144 6422695 1.280000e-99 374.0
13 TraesCS5D01G014200 chr6D 78.105 306 60 7 426 729 42548379 42548679 1.790000e-43 187.0
14 TraesCS5D01G014200 chr3A 77.451 306 61 7 432 732 509854346 509854044 3.880000e-40 176.0
15 TraesCS5D01G014200 chr3D 76.948 308 62 6 433 737 8676724 8676423 2.330000e-37 167.0
16 TraesCS5D01G014200 chr1D 77.170 311 55 15 429 731 420689836 420689534 2.330000e-37 167.0
17 TraesCS5D01G014200 chr1A 75.829 211 41 7 1188 1394 585921793 585921589 8.640000e-17 99.0
18 TraesCS5D01G014200 chr1A 72.906 203 49 5 1328 1527 585844985 585844786 8.760000e-07 65.8
19 TraesCS5D01G014200 chr4A 88.608 79 9 0 22 100 631911270 631911348 3.110000e-16 97.1
20 TraesCS5D01G014200 chr7D 89.831 59 4 2 18 75 330436141 330436084 1.460000e-09 75.0
21 TraesCS5D01G014200 chr1B 100.000 29 0 0 15 43 531376098 531376126 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 TraesCS5D01G014200 chr5D 8019039 8022817 3778 False 6979.000000 6979 100.000000 1 3779 1 chr5D.!!$F1 3778
1 TraesCS5D01G014200 chr5D 8033336 8033887 551 False 363.000000 363 78.863000 977 1531 1 chr5D.!!$F2 554
2 TraesCS5D01G014200 chr5B 8341653 8345370 3717 False 1550.000000 3744 88.064333 6 3778 3 chr5B.!!$F3 3772
3 TraesCS5D01G014200 chr5B 8351846 8352388 542 False 387.000000 387 79.892000 967 1514 1 chr5B.!!$F1 547
4 TraesCS5D01G014200 chr5A 6410140 6413943 3803 False 1570.333333 3651 89.980000 55 3779 3 chr5A.!!$F2 3724
5 TraesCS5D01G014200 chr5A 6422144 6422695 551 False 374.000000 374 79.218000 977 1531 1 chr5A.!!$F1 554

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
57 58 0.032678 AAGTCGCTAGCCCATCGATG 59.967 55.000 18.76 18.76 34.61 3.84 F
499 565 0.101759 TCACCTCTATTACCGCACGC 59.898 55.000 0.00 0.00 0.00 5.34 F
1123 1193 1.289160 AGCATGGGTAAGAGCCTTCA 58.711 50.000 0.00 0.00 36.53 3.02 F
2238 2325 1.210931 CGTCATGGCCAAAGTGCAG 59.789 57.895 10.96 0.00 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 1934 0.179029 AAACCACCCTGAGGAACACG 60.179 55.0 0.00 0.00 36.73 4.49 R
1932 2015 0.788391 CTTCCTTGCCGTGTTCGTAC 59.212 55.0 0.00 0.00 35.01 3.67 R
2710 2797 0.036306 GTCATCCCAAACTGGTCCGT 59.964 55.0 0.00 0.00 35.17 4.69 R
3065 3267 0.519961 GGTTTTCGAACCATGGGACG 59.480 55.0 18.09 20.01 42.38 4.79 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
57 58 0.032678 AAGTCGCTAGCCCATCGATG 59.967 55.000 18.76 18.76 34.61 3.84
110 115 1.202087 GCGGCGCATACACATAAACAA 60.202 47.619 29.21 0.00 0.00 2.83
146 151 2.215196 TGTTCAGGTTTCCGTGCTAAC 58.785 47.619 0.00 0.00 0.00 2.34
172 177 1.329599 GTCTTTGACACGGACAACCAC 59.670 52.381 0.00 0.00 32.15 4.16
205 210 8.988934 TGCTTTTAAGATCGATGGATGTATAAC 58.011 33.333 0.54 0.00 31.51 1.89
340 351 2.340328 GGGCGGACATTTGGTGACC 61.340 63.158 0.00 0.00 38.99 4.02
370 381 2.431419 TCCGCGTTATAGGGACAATTCA 59.569 45.455 4.92 0.00 0.00 2.57
458 524 8.829514 TTTTTAACACAGTACAATCAAAGTCG 57.170 30.769 0.00 0.00 0.00 4.18
469 535 5.423015 ACAATCAAAGTCGCTCACATAGAT 58.577 37.500 0.00 0.00 0.00 1.98
471 537 4.718940 TCAAAGTCGCTCACATAGATGA 57.281 40.909 0.00 0.00 0.00 2.92
492 558 6.392625 TGAGCATACACTCACCTCTATTAC 57.607 41.667 0.00 0.00 41.72 1.89
497 563 2.165845 ACACTCACCTCTATTACCGCAC 59.834 50.000 0.00 0.00 0.00 5.34
499 565 0.101759 TCACCTCTATTACCGCACGC 59.898 55.000 0.00 0.00 0.00 5.34
527 593 6.619852 ACATACCTTATCCCTATGAACACCTT 59.380 38.462 0.00 0.00 0.00 3.50
542 608 2.630580 ACACCTTCAAGAGACAGAGTCC 59.369 50.000 0.00 0.00 32.18 3.85
560 626 2.866762 GTCCGCACATTATCTTGAGGTC 59.133 50.000 0.00 0.00 34.52 3.85
580 646 1.512926 GACAAAGTCGCCACAGATGT 58.487 50.000 0.00 0.00 0.00 3.06
624 690 1.354337 CTCCCACTGAACGCACATCG 61.354 60.000 0.00 0.00 45.38 3.84
627 693 3.112075 ACTGAACGCACATCGCCG 61.112 61.111 0.00 0.00 43.23 6.46
695 761 3.350219 TGGGACTTGAACTCTAATGGC 57.650 47.619 0.00 0.00 0.00 4.40
741 807 5.568620 ACTATCCAACCACAAGTTCTCTT 57.431 39.130 0.00 0.00 36.18 2.85
890 956 9.202273 TGTCAACATAAAGTATTGCCAATTTTC 57.798 29.630 0.00 0.00 0.00 2.29
903 969 5.543714 TGCCAATTTTCTAGACAAGTCGTA 58.456 37.500 0.00 0.00 34.09 3.43
904 970 5.407387 TGCCAATTTTCTAGACAAGTCGTAC 59.593 40.000 0.00 0.00 34.09 3.67
905 971 5.444218 GCCAATTTTCTAGACAAGTCGTACG 60.444 44.000 9.53 9.53 34.09 3.67
906 972 5.632347 CCAATTTTCTAGACAAGTCGTACGT 59.368 40.000 16.05 0.00 34.09 3.57
917 987 1.900016 TCGTACGTGTGGCTGGAGT 60.900 57.895 16.05 0.00 0.00 3.85
1102 1172 2.228582 CTCCTGCTACTCATCATCCGAG 59.771 54.545 0.00 0.00 36.53 4.63
1123 1193 1.289160 AGCATGGGTAAGAGCCTTCA 58.711 50.000 0.00 0.00 36.53 3.02
1140 1210 4.697756 ACCACCACCACCGCATCG 62.698 66.667 0.00 0.00 0.00 3.84
1293 1369 2.880879 CTCGTCCATGTCGGTGCG 60.881 66.667 7.49 0.00 36.21 5.34
1413 1489 1.557099 TCATCCGCTACAACTCCACT 58.443 50.000 0.00 0.00 0.00 4.00
1589 1668 3.540617 ACACAGTACAAACACAGATGCA 58.459 40.909 0.00 0.00 0.00 3.96
1590 1669 3.944650 ACACAGTACAAACACAGATGCAA 59.055 39.130 0.00 0.00 0.00 4.08
1602 1685 2.874701 ACAGATGCAAACACTGACTCAC 59.125 45.455 16.32 0.00 35.85 3.51
1612 1695 2.288702 ACACTGACTCACTGATCACTGC 60.289 50.000 0.00 0.00 0.00 4.40
1639 1722 1.513158 CTCGTGGTCGCCAAGATCT 59.487 57.895 12.97 0.00 40.81 2.75
1956 2039 2.936498 CGAACACGGCAAGGAAGATAAT 59.064 45.455 0.00 0.00 0.00 1.28
1962 2045 2.297701 GGCAAGGAAGATAATGCGGAA 58.702 47.619 0.00 0.00 39.66 4.30
1968 2051 5.104259 AGGAAGATAATGCGGAAGACTTT 57.896 39.130 0.00 0.00 0.00 2.66
1989 2072 8.677148 ACTTTGTACATCTTTTGCTTTCTCTA 57.323 30.769 0.00 0.00 0.00 2.43
2007 2090 6.497785 TCTCTAAAGAAAGAGTACGGTCTG 57.502 41.667 1.15 0.00 43.02 3.51
2013 2096 1.991121 AAGAGTACGGTCTGTCCACA 58.009 50.000 0.00 0.00 35.57 4.17
2044 2127 2.738743 AGGCCATCTTGGTGGTAATTG 58.261 47.619 5.01 0.00 40.46 2.32
2081 2165 2.288334 TGAAGTTGACATGCATGTTGCC 60.288 45.455 31.82 20.04 44.23 4.52
2085 2169 3.057315 AGTTGACATGCATGTTGCCTAAC 60.057 43.478 31.82 26.13 44.23 2.34
2132 2219 6.743575 AGCCAATACTAAGATTTGTGTGAC 57.256 37.500 0.00 0.00 0.00 3.67
2238 2325 1.210931 CGTCATGGCCAAAGTGCAG 59.789 57.895 10.96 0.00 0.00 4.41
2340 2427 2.268920 GCGACCATCAAGGAGGCA 59.731 61.111 0.00 0.00 41.22 4.75
2427 2514 3.114825 ATACACCATTCCCGCGGGG 62.115 63.158 42.36 28.70 46.11 5.73
2710 2797 2.121291 TGGCGCAAAGGTTGATATGA 57.879 45.000 10.83 0.00 0.00 2.15
2712 2799 1.268032 GGCGCAAAGGTTGATATGACG 60.268 52.381 10.83 0.00 0.00 4.35
2863 2954 7.488471 CCGTTATGTTAGCTGCCTATTACTATC 59.512 40.741 0.00 0.00 0.00 2.08
2893 2992 2.217750 TGTAGTCGTGTTGCATGCTTT 58.782 42.857 20.33 0.00 0.00 3.51
2910 3009 2.483538 GCTTTGGGAGTTTGTTGCACAT 60.484 45.455 0.00 0.00 0.00 3.21
2915 3014 2.227388 GGGAGTTTGTTGCACATGAGAG 59.773 50.000 0.00 0.00 0.00 3.20
2917 3016 3.141398 GAGTTTGTTGCACATGAGAGGA 58.859 45.455 0.00 0.00 0.00 3.71
2958 3057 9.425893 CTACAAATGTAACAGCGAATAATGAAG 57.574 33.333 0.00 0.00 0.00 3.02
3005 3207 6.778821 TCAAAGATCATGGGTTCTCAACTAA 58.221 36.000 0.00 0.00 0.00 2.24
3006 3208 7.405292 TCAAAGATCATGGGTTCTCAACTAAT 58.595 34.615 0.00 0.00 0.00 1.73
3007 3209 8.548025 TCAAAGATCATGGGTTCTCAACTAATA 58.452 33.333 0.00 0.00 0.00 0.98
3033 3235 3.370840 ACTCTGCTATTTGGAATGCCA 57.629 42.857 0.00 0.00 44.17 4.92
3065 3267 1.939934 TGCAGCCATATAAACACTCGC 59.060 47.619 0.00 0.00 0.00 5.03
3072 3274 3.390135 CATATAAACACTCGCGTCCCAT 58.610 45.455 5.77 0.00 0.00 4.00
3107 3335 4.038271 ACTCTTCCTGGAATTTCATGCA 57.962 40.909 10.03 0.00 0.00 3.96
3134 3370 6.539173 AGAGATAATACTGTGATCGTCCTCT 58.461 40.000 0.00 0.00 0.00 3.69
3146 3383 5.869888 GTGATCGTCCTCTCACAGTATTTTT 59.130 40.000 0.00 0.00 41.13 1.94
3150 3387 6.618811 TCGTCCTCTCACAGTATTTTTCTAC 58.381 40.000 0.00 0.00 0.00 2.59
3154 3391 4.501071 TCTCACAGTATTTTTCTACGGGC 58.499 43.478 0.00 0.00 0.00 6.13
3155 3392 3.255725 TCACAGTATTTTTCTACGGGCG 58.744 45.455 0.00 0.00 0.00 6.13
3224 3461 5.668471 TGTTGAAAAATCAGCATTCCAACA 58.332 33.333 0.00 0.00 36.01 3.33
3240 3478 9.374838 GCATTCCAACAATGAGAAATAAAGAAT 57.625 29.630 0.00 0.00 0.00 2.40
3280 3521 9.965902 ATATCTCACTACAAAATGAGGAAAAGT 57.034 29.630 1.66 0.00 42.25 2.66
3305 3546 9.988350 GTATAACAATTACTGAACATTCCACTG 57.012 33.333 0.00 0.00 0.00 3.66
3306 3547 6.959639 AACAATTACTGAACATTCCACTGT 57.040 33.333 0.00 0.00 0.00 3.55
3312 3553 3.815401 ACTGAACATTCCACTGTACTTGC 59.185 43.478 0.00 0.00 0.00 4.01
3316 3557 3.412386 ACATTCCACTGTACTTGCCTTC 58.588 45.455 0.00 0.00 0.00 3.46
3321 3562 0.608640 ACTGTACTTGCCTTCGGAGG 59.391 55.000 4.95 4.95 46.50 4.30
3329 3570 3.068881 CCTTCGGAGGCTTCACCA 58.931 61.111 0.00 0.00 43.14 4.17
3333 3574 1.198094 TTCGGAGGCTTCACCATGGA 61.198 55.000 21.47 0.00 43.14 3.41
3334 3575 1.153289 CGGAGGCTTCACCATGGAG 60.153 63.158 21.47 11.61 43.14 3.86
3343 3584 3.366374 GCTTCACCATGGAGCAACTTAAC 60.366 47.826 21.47 0.00 0.00 2.01
3344 3585 2.790433 TCACCATGGAGCAACTTAACC 58.210 47.619 21.47 0.00 0.00 2.85
3345 3586 2.107378 TCACCATGGAGCAACTTAACCA 59.893 45.455 21.47 0.00 36.83 3.67
3346 3587 3.091545 CACCATGGAGCAACTTAACCAT 58.908 45.455 21.47 0.00 42.83 3.55
3347 3588 3.511146 CACCATGGAGCAACTTAACCATT 59.489 43.478 21.47 0.00 40.55 3.16
3348 3589 3.511146 ACCATGGAGCAACTTAACCATTG 59.489 43.478 21.47 0.00 40.55 2.82
3349 3590 3.511146 CCATGGAGCAACTTAACCATTGT 59.489 43.478 5.56 0.00 40.55 2.71
3350 3591 4.021192 CCATGGAGCAACTTAACCATTGTT 60.021 41.667 5.56 0.00 40.55 2.83
3351 3592 5.184864 CCATGGAGCAACTTAACCATTGTTA 59.815 40.000 5.56 0.00 40.55 2.41
3352 3593 6.127366 CCATGGAGCAACTTAACCATTGTTAT 60.127 38.462 5.56 0.00 40.55 1.89
3353 3594 7.068103 CCATGGAGCAACTTAACCATTGTTATA 59.932 37.037 5.56 0.00 40.55 0.98
3354 3595 8.465999 CATGGAGCAACTTAACCATTGTTATAA 58.534 33.333 0.00 0.00 40.55 0.98
3355 3596 8.588290 TGGAGCAACTTAACCATTGTTATAAT 57.412 30.769 0.00 0.00 36.84 1.28
3356 3597 9.030452 TGGAGCAACTTAACCATTGTTATAATT 57.970 29.630 0.00 0.00 36.84 1.40
3425 3667 5.458041 AGTCACAGGTGAAATGGATTTTG 57.542 39.130 3.28 0.00 41.85 2.44
3469 3711 1.002659 TGTGCACCCGTGTAGCTAATT 59.997 47.619 15.69 0.00 0.00 1.40
3473 3715 2.096980 GCACCCGTGTAGCTAATTTTCC 59.903 50.000 0.00 0.00 0.00 3.13
3474 3716 3.340034 CACCCGTGTAGCTAATTTTCCA 58.660 45.455 0.00 0.00 0.00 3.53
3579 3851 9.740239 ATGCACAATTCAGTATTCATATGAAAC 57.260 29.630 21.50 18.49 36.59 2.78
3633 3906 7.328249 GCTACAAGAGAGTATATGTGCAATCTC 59.672 40.741 0.00 0.00 34.69 2.75
3637 3910 9.755804 CAAGAGAGTATATGTGCAATCTCTTTA 57.244 33.333 11.42 0.00 46.61 1.85
3638 3911 9.757227 AAGAGAGTATATGTGCAATCTCTTTAC 57.243 33.333 9.18 0.00 46.61 2.01
3641 3914 7.291182 AGAGTATATGTGCAATCTCTTTACCCT 59.709 37.037 0.00 0.00 0.00 4.34
3642 3915 7.220030 AGTATATGTGCAATCTCTTTACCCTG 58.780 38.462 0.00 0.00 0.00 4.45
3657 3938 7.442656 TCTTTACCCTGTAAAGAGTTCAAGAG 58.557 38.462 20.03 0.00 38.27 2.85
3671 3952 6.216456 AGAGTTCAAGAGATATTGGACCCTTT 59.784 38.462 0.00 0.00 39.17 3.11
3672 3953 6.418946 AGTTCAAGAGATATTGGACCCTTTC 58.581 40.000 0.00 0.00 39.17 2.62
3676 3957 6.158520 TCAAGAGATATTGGACCCTTTCATGA 59.841 38.462 0.00 0.00 0.00 3.07
3689 3970 8.314021 GGACCCTTTCATGACTTCAAATAAAAT 58.686 33.333 0.00 0.00 0.00 1.82
3765 4046 0.482446 AAGGCATCAAAGGTGACCCA 59.518 50.000 0.00 0.00 36.31 4.51
3766 4047 0.706433 AGGCATCAAAGGTGACCCAT 59.294 50.000 0.00 0.00 36.31 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.328382 TCACTTCTTTGTCATACGGGG 57.672 47.619 0.00 0.00 0.00 5.73
1 2 3.871594 GGATCACTTCTTTGTCATACGGG 59.128 47.826 0.00 0.00 0.00 5.28
2 3 4.503910 TGGATCACTTCTTTGTCATACGG 58.496 43.478 0.00 0.00 0.00 4.02
3 4 5.812127 TCATGGATCACTTCTTTGTCATACG 59.188 40.000 0.00 0.00 0.00 3.06
5 6 6.703165 CGATCATGGATCACTTCTTTGTCATA 59.297 38.462 6.98 0.00 38.84 2.15
6 7 5.526479 CGATCATGGATCACTTCTTTGTCAT 59.474 40.000 6.98 0.00 38.84 3.06
7 8 4.872124 CGATCATGGATCACTTCTTTGTCA 59.128 41.667 6.98 0.00 38.84 3.58
8 9 4.260538 GCGATCATGGATCACTTCTTTGTC 60.261 45.833 6.98 0.00 38.84 3.18
9 10 3.624861 GCGATCATGGATCACTTCTTTGT 59.375 43.478 6.98 0.00 38.84 2.83
19 20 3.243301 ACTTTGCATTGCGATCATGGATC 60.243 43.478 3.84 0.00 35.88 3.36
57 58 5.185454 TGACCTCATGTTGAATGGTGTATC 58.815 41.667 0.00 0.00 26.66 2.24
110 115 3.934579 CTGAACAAACCTTGCAGCTTTTT 59.065 39.130 0.00 0.00 0.00 1.94
117 122 2.167487 GGAAACCTGAACAAACCTTGCA 59.833 45.455 0.00 0.00 0.00 4.08
120 125 2.425668 CACGGAAACCTGAACAAACCTT 59.574 45.455 0.00 0.00 0.00 3.50
132 137 1.737793 CCTCATGTTAGCACGGAAACC 59.262 52.381 0.00 0.00 0.00 3.27
146 151 2.069273 GTCCGTGTCAAAGACCTCATG 58.931 52.381 0.00 0.00 0.00 3.07
172 177 5.235186 CCATCGATCTTAAAAGCACCTAGTG 59.765 44.000 0.00 0.00 36.51 2.74
205 210 1.398451 GCAACGGATGTTCGTCAAGTG 60.398 52.381 0.00 0.00 43.07 3.16
306 315 1.611673 CGCCCTTGTCCAGTCTCATTT 60.612 52.381 0.00 0.00 0.00 2.32
340 351 2.404215 CTATAACGCGGATCACTTGGG 58.596 52.381 12.47 0.00 0.00 4.12
370 381 6.476378 CATATATAGGGGCAGTTAAGCTTGT 58.524 40.000 9.86 0.00 34.17 3.16
439 505 3.728845 AGCGACTTTGATTGTACTGTGT 58.271 40.909 0.00 0.00 0.00 3.72
443 509 3.990092 TGTGAGCGACTTTGATTGTACT 58.010 40.909 0.00 0.00 0.00 2.73
445 511 5.961272 TCTATGTGAGCGACTTTGATTGTA 58.039 37.500 0.00 0.00 0.00 2.41
469 535 5.302059 GGTAATAGAGGTGAGTGTATGCTCA 59.698 44.000 0.00 0.00 42.56 4.26
471 537 4.278669 CGGTAATAGAGGTGAGTGTATGCT 59.721 45.833 0.00 0.00 0.00 3.79
479 545 1.864435 GCGTGCGGTAATAGAGGTGAG 60.864 57.143 0.00 0.00 0.00 3.51
480 546 0.101759 GCGTGCGGTAATAGAGGTGA 59.898 55.000 0.00 0.00 0.00 4.02
481 547 1.206745 CGCGTGCGGTAATAGAGGTG 61.207 60.000 6.30 0.00 35.56 4.00
482 548 1.065273 CGCGTGCGGTAATAGAGGT 59.935 57.895 6.30 0.00 35.56 3.85
483 549 2.300787 GCGCGTGCGGTAATAGAGG 61.301 63.158 16.70 0.00 40.19 3.69
484 550 3.221956 GCGCGTGCGGTAATAGAG 58.778 61.111 16.70 0.00 40.19 2.43
497 563 0.033504 AGGGATAAGGTATGTGCGCG 59.966 55.000 0.00 0.00 0.00 6.86
499 565 4.801330 TCATAGGGATAAGGTATGTGCG 57.199 45.455 0.00 0.00 0.00 5.34
527 593 0.598562 GTGCGGACTCTGTCTCTTGA 59.401 55.000 0.00 0.00 32.47 3.02
542 608 2.535984 GTCGACCTCAAGATAATGTGCG 59.464 50.000 3.51 0.00 0.00 5.34
624 690 4.381505 TGAATTTATTCCAAGCCTTTCGGC 60.382 41.667 0.00 0.00 45.19 5.54
627 693 8.831715 TTTCTTGAATTTATTCCAAGCCTTTC 57.168 30.769 0.00 0.00 35.97 2.62
690 756 1.446016 GGTGGTATCCCCTAGCCATT 58.554 55.000 0.00 0.00 33.20 3.16
691 757 0.836400 CGGTGGTATCCCCTAGCCAT 60.836 60.000 0.00 0.00 33.20 4.40
695 761 0.187851 AGGACGGTGGTATCCCCTAG 59.812 60.000 0.00 0.00 35.38 3.02
706 772 2.662866 TGGATAGTTAGGAGGACGGTG 58.337 52.381 0.00 0.00 0.00 4.94
709 775 3.028850 TGGTTGGATAGTTAGGAGGACG 58.971 50.000 0.00 0.00 0.00 4.79
823 889 8.364129 TCTCAATAAAATCCAAAAACAAGTGC 57.636 30.769 0.00 0.00 0.00 4.40
890 956 2.847901 CCACACGTACGACTTGTCTAG 58.152 52.381 24.41 4.46 27.24 2.43
903 969 0.973632 TATTCACTCCAGCCACACGT 59.026 50.000 0.00 0.00 0.00 4.49
904 970 2.093306 TTATTCACTCCAGCCACACG 57.907 50.000 0.00 0.00 0.00 4.49
905 971 2.159627 CGTTTATTCACTCCAGCCACAC 59.840 50.000 0.00 0.00 0.00 3.82
906 972 2.224426 ACGTTTATTCACTCCAGCCACA 60.224 45.455 0.00 0.00 0.00 4.17
917 987 2.479656 GCACACCCGTAACGTTTATTCA 59.520 45.455 5.91 0.00 0.00 2.57
1102 1172 2.170607 TGAAGGCTCTTACCCATGCTAC 59.829 50.000 0.00 0.00 0.00 3.58
1123 1193 4.697756 CGATGCGGTGGTGGTGGT 62.698 66.667 0.00 0.00 0.00 4.16
1524 1600 6.951062 ATACGTCTTTAGTTAGGTACCTCC 57.049 41.667 20.32 10.67 0.00 4.30
1561 1640 8.559536 CATCTGTGTTTGTACTGTGTTTCTATT 58.440 33.333 0.00 0.00 0.00 1.73
1572 1651 4.640201 AGTGTTTGCATCTGTGTTTGTACT 59.360 37.500 0.00 0.00 0.00 2.73
1589 1668 4.375272 CAGTGATCAGTGAGTCAGTGTTT 58.625 43.478 23.74 14.72 39.69 2.83
1590 1669 3.801638 GCAGTGATCAGTGAGTCAGTGTT 60.802 47.826 30.54 17.57 44.06 3.32
1851 1934 0.179029 AAACCACCCTGAGGAACACG 60.179 55.000 0.00 0.00 36.73 4.49
1932 2015 0.788391 CTTCCTTGCCGTGTTCGTAC 59.212 55.000 0.00 0.00 35.01 3.67
1956 2039 3.678056 AGATGTACAAAGTCTTCCGCA 57.322 42.857 0.00 0.00 0.00 5.69
1962 2045 7.500559 AGAGAAAGCAAAAGATGTACAAAGTCT 59.499 33.333 0.00 0.00 0.00 3.24
1968 2051 8.902540 TCTTTAGAGAAAGCAAAAGATGTACA 57.097 30.769 0.00 0.00 41.68 2.90
1989 2072 3.640029 TGGACAGACCGTACTCTTTCTTT 59.360 43.478 0.00 0.00 42.61 2.52
2007 2090 2.000447 GCCTTGACGTTATCTGTGGAC 59.000 52.381 0.00 0.00 0.00 4.02
2013 2096 3.914426 AAGATGGCCTTGACGTTATCT 57.086 42.857 3.32 0.00 32.92 1.98
2068 2152 6.351202 ACATAATTGTTAGGCAACATGCATGT 60.351 34.615 26.61 26.61 44.01 3.21
2091 2175 9.865321 GTATTGGCTATCGATTATTTACCTACA 57.135 33.333 1.71 0.00 0.00 2.74
2105 2189 7.438160 TCACACAAATCTTAGTATTGGCTATCG 59.562 37.037 5.21 0.00 0.00 2.92
2110 2194 5.648092 AGGTCACACAAATCTTAGTATTGGC 59.352 40.000 5.21 0.00 0.00 4.52
2111 2195 7.174946 ACAAGGTCACACAAATCTTAGTATTGG 59.825 37.037 5.21 0.00 0.00 3.16
2238 2325 1.832366 GTGGACTCCCTTACCTCCTTC 59.168 57.143 0.00 0.00 0.00 3.46
2263 2350 1.603739 GGTCCAGCTTTTCGCCCTT 60.604 57.895 0.00 0.00 40.39 3.95
2265 2352 2.034221 AGGTCCAGCTTTTCGCCC 59.966 61.111 0.00 0.00 40.39 6.13
2340 2427 3.209097 GGCGGGTGTATGCGCATT 61.209 61.111 30.42 12.85 0.00 3.56
2361 2448 2.121963 TGTGGGAGCAGGAAGGGT 60.122 61.111 0.00 0.00 0.00 4.34
2427 2514 2.224079 AGCATTCACAATGACACGTGTC 59.776 45.455 36.01 36.01 44.97 3.67
2601 2688 3.999051 GCGATCGCGAAAGTAGCT 58.001 55.556 26.12 0.00 40.82 3.32
2710 2797 0.036306 GTCATCCCAAACTGGTCCGT 59.964 55.000 0.00 0.00 35.17 4.69
2712 2799 1.305930 GCGTCATCCCAAACTGGTCC 61.306 60.000 0.00 0.00 35.17 4.46
2785 2872 6.554334 ACAAATAACACAAAGCTACGATGT 57.446 33.333 0.00 0.00 0.00 3.06
2787 2874 7.254319 CCGATACAAATAACACAAAGCTACGAT 60.254 37.037 0.00 0.00 0.00 3.73
2789 2876 6.182634 CCGATACAAATAACACAAAGCTACG 58.817 40.000 0.00 0.00 0.00 3.51
2829 2916 1.269051 GCTAACATAACGGGCAATGGC 60.269 52.381 0.00 0.00 40.13 4.40
2863 2954 3.604875 ACACGACTACATTAAGGTGGG 57.395 47.619 8.51 1.62 0.00 4.61
2910 3009 1.573108 GATCCCACAGGTTCCTCTCA 58.427 55.000 0.00 0.00 0.00 3.27
2917 3016 2.642171 TGTAGAGGATCCCACAGGTT 57.358 50.000 8.55 0.00 33.66 3.50
2958 3057 8.958119 TGATCTACCATACAACCATACTTTTC 57.042 34.615 0.00 0.00 0.00 2.29
3005 3207 7.229506 GCATTCCAAATAGCAGAGTAAGGTTAT 59.770 37.037 0.00 0.00 0.00 1.89
3006 3208 6.542370 GCATTCCAAATAGCAGAGTAAGGTTA 59.458 38.462 0.00 0.00 0.00 2.85
3007 3209 5.358160 GCATTCCAAATAGCAGAGTAAGGTT 59.642 40.000 0.00 0.00 0.00 3.50
3033 3235 2.703798 GGCTGCACATCGCCACATT 61.704 57.895 9.69 0.00 45.59 2.71
3065 3267 0.519961 GGTTTTCGAACCATGGGACG 59.480 55.000 18.09 20.01 42.38 4.79
3072 3274 3.644738 AGGAAGAGTAGGTTTTCGAACCA 59.355 43.478 8.93 0.00 45.23 3.67
3086 3288 4.038271 TGCATGAAATTCCAGGAAGAGT 57.962 40.909 8.20 0.00 0.00 3.24
3089 3291 6.544931 TCTCTAATGCATGAAATTCCAGGAAG 59.455 38.462 8.20 0.00 0.00 3.46
3090 3292 6.425735 TCTCTAATGCATGAAATTCCAGGAA 58.574 36.000 3.72 3.72 0.00 3.36
3107 3335 8.871629 AGGACGATCACAGTATTATCTCTAAT 57.128 34.615 0.00 0.00 0.00 1.73
3124 3360 6.334202 AGAAAAATACTGTGAGAGGACGATC 58.666 40.000 0.00 0.00 0.00 3.69
3134 3370 3.255725 CGCCCGTAGAAAAATACTGTGA 58.744 45.455 0.00 0.00 0.00 3.58
3146 3383 4.160252 GGGGATAATATTAACGCCCGTAGA 59.840 45.833 21.48 0.00 36.41 2.59
3150 3387 3.337694 TGGGGATAATATTAACGCCCG 57.662 47.619 26.12 0.00 37.62 6.13
3280 3521 9.733556 ACAGTGGAATGTTCAGTAATTGTTATA 57.266 29.630 0.00 0.00 0.00 0.98
3312 3553 0.745845 CATGGTGAAGCCTCCGAAGG 60.746 60.000 0.00 0.00 46.44 3.46
3316 3557 1.153289 CTCCATGGTGAAGCCTCCG 60.153 63.158 12.58 0.00 38.35 4.63
3321 3562 1.251251 AAGTTGCTCCATGGTGAAGC 58.749 50.000 17.98 16.56 0.00 3.86
3322 3563 3.191371 GGTTAAGTTGCTCCATGGTGAAG 59.809 47.826 17.98 6.28 0.00 3.02
3329 3570 8.588290 TTATAACAATGGTTAAGTTGCTCCAT 57.412 30.769 0.00 0.00 42.43 3.41
3383 3624 6.955963 GTGACTTTTCACGCATAAAGTATCAG 59.044 38.462 8.72 0.00 42.82 2.90
3410 3652 4.173036 TCGCTTCAAAATCCATTTCACC 57.827 40.909 0.00 0.00 0.00 4.02
3446 3688 1.671054 GCTACACGGGTGCACACAT 60.671 57.895 21.13 0.00 0.00 3.21
3451 3693 2.483014 AAATTAGCTACACGGGTGCA 57.517 45.000 0.00 0.00 0.00 4.57
3452 3694 2.096980 GGAAAATTAGCTACACGGGTGC 59.903 50.000 0.00 1.66 0.00 5.01
3456 3698 5.360591 AGAGATGGAAAATTAGCTACACGG 58.639 41.667 0.00 0.00 0.00 4.94
3457 3699 6.276847 AGAGAGATGGAAAATTAGCTACACG 58.723 40.000 0.00 0.00 0.00 4.49
3469 3711 8.602424 TGTGAAATAAGGTAAGAGAGATGGAAA 58.398 33.333 0.00 0.00 0.00 3.13
3553 3796 9.740239 GTTTCATATGAATACTGAATTGTGCAT 57.260 29.630 18.61 0.00 33.54 3.96
3579 3851 6.374613 CCATGATGATGAGGACCAATATGAAG 59.625 42.308 0.00 0.00 0.00 3.02
3633 3906 7.442656 TCTCTTGAACTCTTTACAGGGTAAAG 58.557 38.462 18.26 18.26 29.38 1.85
3637 3910 7.741554 ATATCTCTTGAACTCTTTACAGGGT 57.258 36.000 0.00 0.00 33.79 4.34
3638 3911 7.497249 CCAATATCTCTTGAACTCTTTACAGGG 59.503 40.741 0.00 0.00 0.00 4.45
3641 3914 8.041323 GGTCCAATATCTCTTGAACTCTTTACA 58.959 37.037 0.00 0.00 0.00 2.41
3642 3915 7.496263 GGGTCCAATATCTCTTGAACTCTTTAC 59.504 40.741 0.00 0.00 0.00 2.01
3657 3938 6.122277 TGAAGTCATGAAAGGGTCCAATATC 58.878 40.000 0.00 0.00 0.00 1.63


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

AutoCloner maintained by Alex Coulton.