Multiple sequence alignment - TraesCS7D01G241000

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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 TraesCS7D01G241000 chr7D 100.000 3713 0 0 1 3713 205537529 205541241 0.000000e+00 6857
1 TraesCS7D01G241000 chr7D 90.364 851 75 6 5 850 446355031 446355879 0.000000e+00 1110
2 TraesCS7D01G241000 chr7D 90.675 815 69 6 1 811 19571981 19572792 0.000000e+00 1077
3 TraesCS7D01G241000 chr7A 96.269 2305 80 3 871 3170 217551888 217554191 0.000000e+00 3775
4 TraesCS7D01G241000 chr7A 89.744 858 70 16 5 854 47703729 47704576 0.000000e+00 1081
5 TraesCS7D01G241000 chr7A 95.103 388 13 4 3327 3713 217554189 217554571 1.140000e-169 606
6 TraesCS7D01G241000 chr7A 81.173 324 33 10 2638 2960 217555080 217555376 6.200000e-58 235
7 TraesCS7D01G241000 chr7B 97.023 1881 50 3 861 2739 196913202 196911326 0.000000e+00 3158
8 TraesCS7D01G241000 chr7B 90.727 399 19 4 2735 3115 196911013 196910615 1.980000e-142 516
9 TraesCS7D01G241000 chr7B 87.404 389 11 14 3327 3713 196910594 196910242 2.670000e-111 412
10 TraesCS7D01G241000 chr3D 91.588 844 67 4 5 846 9326972 9326131 0.000000e+00 1162
11 TraesCS7D01G241000 chr3D 91.469 844 63 7 5 846 553244054 553243218 0.000000e+00 1151
12 TraesCS7D01G241000 chr3D 91.698 807 65 2 5 810 537630534 537631339 0.000000e+00 1118
13 TraesCS7D01G241000 chr3D 89.385 179 17 2 3159 3336 457652460 457652637 1.340000e-54 224
14 TraesCS7D01G241000 chr4D 90.577 849 71 8 5 848 405710203 405709359 0.000000e+00 1116
15 TraesCS7D01G241000 chr5D 90.071 846 78 6 5 846 565334947 565335790 0.000000e+00 1092
16 TraesCS7D01G241000 chr5D 89.055 868 79 15 1 859 324409623 324410483 0.000000e+00 1062
17 TraesCS7D01G241000 chr3B 95.062 162 5 3 3169 3329 169656562 169656403 6.160000e-63 252
18 TraesCS7D01G241000 chr4B 92.308 169 11 2 3169 3336 532435162 532434995 4.790000e-59 239
19 TraesCS7D01G241000 chr4B 93.210 162 9 2 3169 3329 499224502 499224662 1.720000e-58 237
20 TraesCS7D01G241000 chr4B 93.210 162 9 2 3169 3329 549841756 549841916 1.720000e-58 237
21 TraesCS7D01G241000 chr4B 92.727 165 9 3 3168 3330 406389295 406389458 6.200000e-58 235
22 TraesCS7D01G241000 chr5B 93.210 162 9 2 3169 3329 411971866 411972026 1.720000e-58 237
23 TraesCS7D01G241000 chr6D 90.000 180 15 3 3151 3329 438321911 438321734 2.880000e-56 230
24 TraesCS7D01G241000 chr2D 91.176 170 13 2 3162 3330 296364042 296364210 2.880000e-56 230


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 TraesCS7D01G241000 chr7D 205537529 205541241 3712 False 6857.000000 6857 100.000000 1 3713 1 chr7D.!!$F2 3712
1 TraesCS7D01G241000 chr7D 446355031 446355879 848 False 1110.000000 1110 90.364000 5 850 1 chr7D.!!$F3 845
2 TraesCS7D01G241000 chr7D 19571981 19572792 811 False 1077.000000 1077 90.675000 1 811 1 chr7D.!!$F1 810
3 TraesCS7D01G241000 chr7A 217551888 217555376 3488 False 1538.666667 3775 90.848333 871 3713 3 chr7A.!!$F2 2842
4 TraesCS7D01G241000 chr7A 47703729 47704576 847 False 1081.000000 1081 89.744000 5 854 1 chr7A.!!$F1 849
5 TraesCS7D01G241000 chr7B 196910242 196913202 2960 True 1362.000000 3158 91.718000 861 3713 3 chr7B.!!$R1 2852
6 TraesCS7D01G241000 chr3D 9326131 9326972 841 True 1162.000000 1162 91.588000 5 846 1 chr3D.!!$R1 841
7 TraesCS7D01G241000 chr3D 553243218 553244054 836 True 1151.000000 1151 91.469000 5 846 1 chr3D.!!$R2 841
8 TraesCS7D01G241000 chr3D 537630534 537631339 805 False 1118.000000 1118 91.698000 5 810 1 chr3D.!!$F2 805
9 TraesCS7D01G241000 chr4D 405709359 405710203 844 True 1116.000000 1116 90.577000 5 848 1 chr4D.!!$R1 843
10 TraesCS7D01G241000 chr5D 565334947 565335790 843 False 1092.000000 1092 90.071000 5 846 1 chr5D.!!$F2 841
11 TraesCS7D01G241000 chr5D 324409623 324410483 860 False 1062.000000 1062 89.055000 1 859 1 chr5D.!!$F1 858

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
927 950 0.10412 CAGCCGTCGGATACCAATCA 59.896 55.0 17.49 0.0 33.41 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2834 3197 0.677731 TATGAAGCACACAGGGCAGC 60.678 55.0 0.0 0.0 0.0 5.25 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
42 43 1.884075 TATCAGTTCGCCCACACGCT 61.884 55.000 0.00 0.00 0.00 5.07
83 84 2.567497 GCTGCCAGTTGCCATGTGT 61.567 57.895 0.00 0.00 40.16 3.72
91 92 2.676839 CAGTTGCCATGTGTTTTTGCAA 59.323 40.909 0.00 0.00 39.42 4.08
146 147 4.287067 ACCAGATGGCAACTCTCTCTTTTA 59.713 41.667 0.00 0.00 39.32 1.52
147 148 5.045286 ACCAGATGGCAACTCTCTCTTTTAT 60.045 40.000 0.00 0.00 39.32 1.40
158 160 9.319143 CAACTCTCTCTTTTATCCGAACATATT 57.681 33.333 0.00 0.00 0.00 1.28
265 271 6.215121 TGTTATTTTGCCATGTCTCTTTGTG 58.785 36.000 0.00 0.00 0.00 3.33
312 318 5.993441 TGTTAGTAGGTGGCAACTCTTAAAC 59.007 40.000 9.14 10.44 37.61 2.01
326 332 9.248291 GCAACTCTTAAACTTTTCAAATCATGA 57.752 29.630 0.00 0.00 35.85 3.07
355 363 5.909456 TGTAGTAAACAGACCATACATGGCG 60.909 44.000 8.20 0.33 41.60 5.69
380 391 5.361285 ACTTCCTAGTGTTAGTAGATGGCAG 59.639 44.000 0.00 0.00 31.99 4.85
386 397 1.131638 TTAGTAGATGGCAGCCCCTG 58.868 55.000 9.64 0.00 34.12 4.45
450 461 1.659233 CAACAATTGCGGCTGTCCA 59.341 52.632 5.05 0.00 0.00 4.02
537 550 2.094390 GTCCGACATGGCACTGTAGTTA 60.094 50.000 0.00 0.00 37.80 2.24
541 554 3.334691 GACATGGCACTGTAGTTAAGCA 58.665 45.455 0.00 0.00 0.00 3.91
579 595 5.826208 AGTTAAACGAACATGAAAGAGGGTT 59.174 36.000 0.00 0.00 40.86 4.11
661 678 1.760875 GGAGGCCTGACGTATGGGA 60.761 63.158 12.00 0.00 0.00 4.37
682 700 5.362263 GGAGTGTGGGCGTTATCTATTTTA 58.638 41.667 0.00 0.00 0.00 1.52
698 717 3.977134 TTTTACCCACACGTAGGCATA 57.023 42.857 0.78 0.00 0.00 3.14
760 783 4.010667 ACTTATTTTGCCCACACGTAGA 57.989 40.909 0.00 0.00 0.00 2.59
795 818 6.549364 TGATCCTCTTAAACACCACACAAAAT 59.451 34.615 0.00 0.00 0.00 1.82
798 821 6.829298 TCCTCTTAAACACCACACAAAATGTA 59.171 34.615 0.00 0.00 40.64 2.29
850 873 4.873827 TGGCAGTTATCATCGTCCTAAAAC 59.126 41.667 0.00 0.00 0.00 2.43
855 878 7.241376 CAGTTATCATCGTCCTAAAACAAACC 58.759 38.462 0.00 0.00 0.00 3.27
858 881 6.894339 ATCATCGTCCTAAAACAAACCTTT 57.106 33.333 0.00 0.00 0.00 3.11
859 882 6.702716 TCATCGTCCTAAAACAAACCTTTT 57.297 33.333 0.00 0.00 0.00 2.27
867 890 8.609176 GTCCTAAAACAAACCTTTTCCAAATTC 58.391 33.333 0.00 0.00 0.00 2.17
905 928 4.068257 CCCCCTTCCAGACCTACC 57.932 66.667 0.00 0.00 0.00 3.18
916 939 2.754658 ACCTACCCTCAGCCGTCG 60.755 66.667 0.00 0.00 0.00 5.12
920 943 0.536687 CTACCCTCAGCCGTCGGATA 60.537 60.000 17.49 0.00 0.00 2.59
927 950 0.104120 CAGCCGTCGGATACCAATCA 59.896 55.000 17.49 0.00 33.41 2.57
1563 1588 0.109532 TGGTGTTCGAGGAAATGCCA 59.890 50.000 0.00 0.00 40.02 4.92
1743 1768 2.911484 CCACTGGCTAGGAAGATGTTC 58.089 52.381 0.85 0.00 0.00 3.18
1857 1882 1.936547 GATGTGATGCCGGAGAAAGAC 59.063 52.381 5.05 0.00 0.00 3.01
1911 1936 4.435436 CAGGCTGGACGCTACGCA 62.435 66.667 6.61 0.00 39.13 5.24
1929 1954 1.683385 GCAGAAACCCTTGAGCTGTTT 59.317 47.619 0.00 0.00 35.06 2.83
1989 2014 1.672356 GACCATGGTGAGCGTGCTT 60.672 57.895 25.52 0.00 0.00 3.91
2127 2152 2.510664 TGCCAAGTGTGGGAAAACC 58.489 52.632 0.00 0.00 43.30 3.27
2154 2179 4.245660 TGGCTGTCAAAATCTTCTACTCG 58.754 43.478 0.00 0.00 0.00 4.18
2366 2391 6.347270 CTTTCAGAGCATGTCATCTACTTG 57.653 41.667 0.00 0.00 36.55 3.16
2464 2492 2.703007 GAGGAGCTGATAAGGACCATGT 59.297 50.000 0.00 0.00 0.00 3.21
2485 2513 0.538977 GATGGCCCCAGATGTCATGG 60.539 60.000 0.00 0.00 37.58 3.66
2493 2521 2.557229 CCCAGATGTCATGGTTTTGGGA 60.557 50.000 14.29 0.00 45.24 4.37
2784 3129 6.721318 TCTCTAGCATTAAATGGTGTCCTTT 58.279 36.000 0.00 0.00 41.73 3.11
2876 3239 9.932699 CATATCTGAATTTGAGATGAAACAGAC 57.067 33.333 8.43 0.00 35.79 3.51
2879 3242 6.205464 TCTGAATTTGAGATGAAACAGACCAC 59.795 38.462 0.00 0.00 0.00 4.16
2898 3261 1.202976 ACATGCTTGTCCCTTCTTGCT 60.203 47.619 0.00 0.00 0.00 3.91
2917 3280 4.385825 TGCTGATAACCGTTTCTCTGTTT 58.614 39.130 0.00 0.00 0.00 2.83
2986 3349 5.665916 ACCAAATTTCACTGATGGGATTC 57.334 39.130 2.22 0.00 35.44 2.52
3051 3414 7.388500 ACAATAACATTTCCAAATTTCAGCTGG 59.612 33.333 15.13 0.00 0.00 4.85
3063 3426 4.829064 TTTCAGCTGGTGTTAATGTGAC 57.171 40.909 15.13 0.00 0.00 3.67
3085 3448 7.278868 GTGACTATGATCTGGTTCTTTTCGATT 59.721 37.037 0.00 0.00 0.00 3.34
3146 3509 4.268884 GCTGACGCCAGAAGAAATAGTAAG 59.731 45.833 1.66 0.00 43.02 2.34
3170 3533 4.148696 GCTGCAAACACAAATGTCATGTAC 59.851 41.667 0.00 0.00 38.45 2.90
3171 3534 5.512753 TGCAAACACAAATGTCATGTACT 57.487 34.783 0.00 0.00 38.45 2.73
3172 3535 5.518812 TGCAAACACAAATGTCATGTACTC 58.481 37.500 0.00 0.00 38.45 2.59
3173 3536 4.917415 GCAAACACAAATGTCATGTACTCC 59.083 41.667 0.00 0.00 38.45 3.85
3174 3537 5.460646 CAAACACAAATGTCATGTACTCCC 58.539 41.667 0.00 0.00 38.45 4.30
3175 3538 4.640771 ACACAAATGTCATGTACTCCCT 57.359 40.909 0.00 0.00 31.55 4.20
3176 3539 4.579869 ACACAAATGTCATGTACTCCCTC 58.420 43.478 0.00 0.00 31.55 4.30
3177 3540 3.941483 CACAAATGTCATGTACTCCCTCC 59.059 47.826 0.00 0.00 0.00 4.30
3178 3541 3.198068 CAAATGTCATGTACTCCCTCCG 58.802 50.000 0.00 0.00 0.00 4.63
3179 3542 2.160721 ATGTCATGTACTCCCTCCGT 57.839 50.000 0.00 0.00 0.00 4.69
3180 3543 1.933021 TGTCATGTACTCCCTCCGTT 58.067 50.000 0.00 0.00 0.00 4.44
3181 3544 1.822990 TGTCATGTACTCCCTCCGTTC 59.177 52.381 0.00 0.00 0.00 3.95
3182 3545 1.136500 GTCATGTACTCCCTCCGTTCC 59.864 57.143 0.00 0.00 0.00 3.62
3183 3546 1.006758 TCATGTACTCCCTCCGTTCCT 59.993 52.381 0.00 0.00 0.00 3.36
3184 3547 2.242965 TCATGTACTCCCTCCGTTCCTA 59.757 50.000 0.00 0.00 0.00 2.94
3185 3548 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
3186 3549 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
3187 3550 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
3188 3551 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
3189 3552 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
3190 3553 6.613699 TGTACTCCCTCCGTTCCTAAATATA 58.386 40.000 0.00 0.00 0.00 0.86
3191 3554 7.068702 TGTACTCCCTCCGTTCCTAAATATAA 58.931 38.462 0.00 0.00 0.00 0.98
3192 3555 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
3193 3556 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
3194 3557 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
3195 3558 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
3196 3559 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
3197 3560 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
3198 3561 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
3199 3562 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
3226 3589 9.698309 AGAGATTTCAATATTGACTACATACGG 57.302 33.333 17.76 0.00 36.83 4.02
3227 3590 9.692749 GAGATTTCAATATTGACTACATACGGA 57.307 33.333 17.76 0.00 36.83 4.69
3230 3593 9.778741 ATTTCAATATTGACTACATACGGATGT 57.221 29.630 19.12 19.12 42.14 3.06
3239 3602 9.729281 TTGACTACATACGGATGTATATAGACA 57.271 33.333 20.64 13.92 45.42 3.41
3240 3603 9.901172 TGACTACATACGGATGTATATAGACAT 57.099 33.333 20.64 12.70 45.42 3.06
3262 3625 9.303537 GACATAGTTTAGAGTGTTGATTACTCC 57.696 37.037 0.00 0.00 44.35 3.85
3263 3626 9.036980 ACATAGTTTAGAGTGTTGATTACTCCT 57.963 33.333 0.00 0.00 44.35 3.69
3264 3627 9.877178 CATAGTTTAGAGTGTTGATTACTCCTT 57.123 33.333 0.00 0.00 44.35 3.36
3267 3630 9.628500 AGTTTAGAGTGTTGATTACTCCTTTTT 57.372 29.630 0.00 0.00 44.35 1.94
3295 3658 9.692749 TTCGTATGTAGTCCATATTGAAATCTC 57.307 33.333 0.00 0.00 38.29 2.75
3296 3659 8.304596 TCGTATGTAGTCCATATTGAAATCTCC 58.695 37.037 0.00 0.00 38.29 3.71
3297 3660 8.088365 CGTATGTAGTCCATATTGAAATCTCCA 58.912 37.037 0.00 0.00 38.29 3.86
3298 3661 9.778741 GTATGTAGTCCATATTGAAATCTCCAA 57.221 33.333 0.00 0.00 38.29 3.53
3300 3663 9.699410 ATGTAGTCCATATTGAAATCTCCAAAA 57.301 29.630 0.00 0.00 29.82 2.44
3301 3664 9.527157 TGTAGTCCATATTGAAATCTCCAAAAA 57.473 29.630 0.00 0.00 0.00 1.94
3303 3666 8.884124 AGTCCATATTGAAATCTCCAAAAAGA 57.116 30.769 0.00 0.00 0.00 2.52
3304 3667 8.743714 AGTCCATATTGAAATCTCCAAAAAGAC 58.256 33.333 0.00 0.00 0.00 3.01
3305 3668 8.743714 GTCCATATTGAAATCTCCAAAAAGACT 58.256 33.333 0.00 0.00 0.00 3.24
3306 3669 9.312904 TCCATATTGAAATCTCCAAAAAGACTT 57.687 29.630 0.00 0.00 0.00 3.01
3320 3683 9.169592 TCCAAAAAGACTTATATTTAGGAACGG 57.830 33.333 0.00 0.00 0.00 4.44
3321 3684 9.169592 CCAAAAAGACTTATATTTAGGAACGGA 57.830 33.333 0.00 0.00 0.00 4.69
3323 3686 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
3324 3687 7.909485 AAGACTTATATTTAGGAACGGAGGA 57.091 36.000 0.00 0.00 0.00 3.71
3325 3688 7.909485 AGACTTATATTTAGGAACGGAGGAA 57.091 36.000 0.00 0.00 0.00 3.36
3326 3689 7.953752 AGACTTATATTTAGGAACGGAGGAAG 58.046 38.462 0.00 0.00 0.00 3.46
3327 3690 7.564292 AGACTTATATTTAGGAACGGAGGAAGT 59.436 37.037 0.00 0.00 0.00 3.01
3328 3691 8.773033 ACTTATATTTAGGAACGGAGGAAGTA 57.227 34.615 0.00 0.00 0.00 2.24
3372 3735 1.556911 AGGATCATGCCAAGACGTCTT 59.443 47.619 24.93 24.93 36.45 3.01
3380 3743 6.869695 TCATGCCAAGACGTCTTAGTAATAA 58.130 36.000 29.28 11.93 34.28 1.40
3381 3744 7.497595 TCATGCCAAGACGTCTTAGTAATAAT 58.502 34.615 29.28 13.49 34.28 1.28
3382 3745 8.635328 TCATGCCAAGACGTCTTAGTAATAATA 58.365 33.333 29.28 9.63 34.28 0.98
3394 3757 9.188588 GTCTTAGTAATAATATACGCAAGCACA 57.811 33.333 0.00 0.00 45.62 4.57
3395 3758 9.923143 TCTTAGTAATAATATACGCAAGCACAT 57.077 29.630 0.00 0.00 45.62 3.21
3413 3776 9.657419 CAAGCACATATATATACTCATGTGGAA 57.343 33.333 22.79 0.00 45.34 3.53
3561 3926 8.787852 AGAATTGTACTTTCCAACTGAGAAATC 58.212 33.333 0.00 0.00 33.01 2.17
3623 3988 8.854614 AACTGTATAAACTGCAGATTCTTCTT 57.145 30.769 23.35 0.00 39.75 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.378112 CGAACTGATAAATGCCCACACAT 59.622 43.478 0.00 0.00 0.00 3.21
42 43 2.276116 GGTGTGGGAGAGCAGACGA 61.276 63.158 0.00 0.00 0.00 4.20
48 49 1.973812 GCTTTGGGTGTGGGAGAGC 60.974 63.158 0.00 0.00 0.00 4.09
83 84 3.133721 AGTTGCCATGTACCTTGCAAAAA 59.866 39.130 10.50 0.00 44.44 1.94
146 147 5.239306 CACATGGCAACTAATATGTTCGGAT 59.761 40.000 0.00 0.00 31.84 4.18
147 148 4.574421 CACATGGCAACTAATATGTTCGGA 59.426 41.667 0.00 0.00 31.84 4.55
158 160 2.035704 CCTGCAAAACACATGGCAACTA 59.964 45.455 0.00 0.00 35.59 2.24
265 271 1.860078 GCAGTTGTCGTGTAGTGCC 59.140 57.895 0.00 0.00 35.23 5.01
268 274 2.030185 CACTAGGCAGTTGTCGTGTAGT 60.030 50.000 0.00 0.00 30.46 2.73
355 363 5.360144 TGCCATCTACTAACACTAGGAAGTC 59.640 44.000 0.00 0.00 31.97 3.01
359 367 3.637229 GCTGCCATCTACTAACACTAGGA 59.363 47.826 0.00 0.00 0.00 2.94
380 391 4.248058 CATGATTTGAAAACTTCAGGGGC 58.752 43.478 0.00 0.00 41.38 5.80
386 397 9.294030 CTATAGTTGCCATGATTTGAAAACTTC 57.706 33.333 0.00 0.00 34.56 3.01
438 449 0.033228 CCATTTTTGGACAGCCGCAA 59.967 50.000 0.00 0.00 36.79 4.85
442 453 1.551883 AGATGCCATTTTTGGACAGCC 59.448 47.619 0.00 0.00 0.00 4.85
450 461 2.633967 TCAAGTGCCAGATGCCATTTTT 59.366 40.909 0.00 0.00 40.16 1.94
537 550 2.586425 ACTGTAGTTGCCATGTTGCTT 58.414 42.857 0.00 0.00 0.00 3.91
541 554 4.817464 TCGTTTAACTGTAGTTGCCATGTT 59.183 37.500 7.50 0.00 38.90 2.71
579 595 2.359850 GCAGTTGCCATGGTCCGA 60.360 61.111 14.67 0.00 34.31 4.55
661 678 5.121105 GGTAAAATAGATAACGCCCACACT 58.879 41.667 0.00 0.00 0.00 3.55
682 700 1.412710 CTCATATGCCTACGTGTGGGT 59.587 52.381 0.00 0.00 33.26 4.51
698 717 0.970937 TTTCTCGCGGTCCCTCTCAT 60.971 55.000 6.13 0.00 0.00 2.90
728 750 5.719085 TGGGCAAAATAAGTAATGACCACAT 59.281 36.000 0.00 0.00 45.90 3.21
734 756 4.762765 ACGTGTGGGCAAAATAAGTAATGA 59.237 37.500 0.00 0.00 0.00 2.57
760 783 1.261480 AAGAGGATCAGCTCACACGT 58.739 50.000 0.00 0.00 37.82 4.49
767 790 3.327757 TGTGGTGTTTAAGAGGATCAGCT 59.672 43.478 0.00 0.00 37.82 4.24
810 833 1.153842 CACGCGTGTGCCATCTAGA 60.154 57.895 30.50 0.00 39.67 2.43
811 834 2.167219 CCACGCGTGTGCCATCTAG 61.167 63.158 34.81 14.58 45.04 2.43
818 841 2.563086 GATAACTGCCACGCGTGTGC 62.563 60.000 34.81 33.35 45.04 4.57
825 848 1.202417 AGGACGATGATAACTGCCACG 60.202 52.381 0.00 0.00 0.00 4.94
850 873 9.657419 ATTGCTATAGAATTTGGAAAAGGTTTG 57.343 29.630 3.21 0.00 0.00 2.93
855 878 6.638468 GCCGATTGCTATAGAATTTGGAAAAG 59.362 38.462 11.78 0.00 36.87 2.27
858 881 5.689383 GCCGATTGCTATAGAATTTGGAA 57.311 39.130 11.78 0.00 36.87 3.53
905 928 1.672854 TTGGTATCCGACGGCTGAGG 61.673 60.000 9.66 2.00 0.00 3.86
951 976 5.460748 GGGAGTTTTTGTACCACGAAAAATG 59.539 40.000 8.88 0.00 41.57 2.32
986 1011 2.607038 GGTGCCATTCCGTTTTGAGTTC 60.607 50.000 0.00 0.00 0.00 3.01
1267 1292 2.202892 GGTGAATCGGTCGGGAGC 60.203 66.667 0.00 0.00 0.00 4.70
1436 1461 1.077501 AACACCTCCCGCATGGATG 60.078 57.895 0.00 0.00 44.07 3.51
1437 1462 1.224592 GAACACCTCCCGCATGGAT 59.775 57.895 0.00 0.00 44.07 3.41
1563 1588 0.178861 AGGACACCCCATTCCTCTGT 60.179 55.000 0.00 0.00 37.77 3.41
1743 1768 1.371758 CCGTACCGGCATCTCATCG 60.372 63.158 0.00 0.00 41.17 3.84
1857 1882 2.604174 GCACGTCCAGGAAACCACG 61.604 63.158 0.00 0.00 38.24 4.94
1911 1936 3.498661 CCCTAAACAGCTCAAGGGTTTCT 60.499 47.826 9.98 0.00 43.26 2.52
1929 1954 1.410517 CTCTCGCTCTGCATTTCCCTA 59.589 52.381 0.00 0.00 0.00 3.53
1989 2014 4.548494 CTGTTAAATGTGCACATGCTGAA 58.452 39.130 31.98 19.49 42.66 3.02
2149 2174 3.576982 ACATTCTTCTGGTCCAACGAGTA 59.423 43.478 0.00 0.00 0.00 2.59
2154 2179 3.339141 GGAGACATTCTTCTGGTCCAAC 58.661 50.000 0.00 0.00 31.99 3.77
2366 2391 2.436292 CCTCTGGCTGCACTCTGC 60.436 66.667 0.50 0.00 45.29 4.26
2367 2392 2.436292 GCCTCTGGCTGCACTCTG 60.436 66.667 0.50 0.00 46.69 3.35
2464 2492 1.056125 ATGACATCTGGGGCCATCGA 61.056 55.000 4.39 0.00 0.00 3.59
2485 2513 3.335579 CACCTAGTAGTGCTCCCAAAAC 58.664 50.000 0.00 0.00 0.00 2.43
2784 3129 7.888514 ATGGTCTAATCCCAATACCAATAGA 57.111 36.000 0.00 0.00 43.10 1.98
2811 3156 9.515020 CAGCTGAACACTTTTAACAGAAATTTA 57.485 29.630 8.42 0.00 0.00 1.40
2834 3197 0.677731 TATGAAGCACACAGGGCAGC 60.678 55.000 0.00 0.00 0.00 5.25
2876 3239 1.542915 CAAGAAGGGACAAGCATGTGG 59.457 52.381 0.00 0.00 40.74 4.17
2879 3242 1.201647 CAGCAAGAAGGGACAAGCATG 59.798 52.381 0.00 0.00 0.00 4.06
2898 3261 5.369833 TCCAAAACAGAGAAACGGTTATCA 58.630 37.500 10.92 0.00 36.02 2.15
2917 3280 5.623956 ATTACGGATGACCAATACTCCAA 57.376 39.130 0.00 0.00 35.59 3.53
2986 3349 6.148948 TGATACAACCAAATTTTGAGAAGCG 58.851 36.000 10.72 0.00 0.00 4.68
3051 3414 7.766278 AGAACCAGATCATAGTCACATTAACAC 59.234 37.037 0.00 0.00 0.00 3.32
3063 3426 7.518052 GCAGAATCGAAAAGAACCAGATCATAG 60.518 40.741 0.00 0.00 0.00 2.23
3107 3470 1.203187 TCAGCCAGGGTTACTCACTCT 60.203 52.381 0.00 0.00 36.14 3.24
3108 3471 1.066787 GTCAGCCAGGGTTACTCACTC 60.067 57.143 0.00 0.00 0.00 3.51
3146 3509 2.222007 TGACATTTGTGTTTGCAGCC 57.778 45.000 0.00 0.00 0.00 4.85
3170 3533 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
3171 3534 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
3172 3535 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
3173 3536 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
3200 3563 9.698309 CCGTATGTAGTCAATATTGAAATCTCT 57.302 33.333 19.55 13.86 39.21 3.10
3201 3564 9.692749 TCCGTATGTAGTCAATATTGAAATCTC 57.307 33.333 19.55 7.25 39.21 2.75
3204 3567 9.778741 ACATCCGTATGTAGTCAATATTGAAAT 57.221 29.630 19.55 13.50 44.66 2.17
3236 3599 9.303537 GGAGTAATCAACACTCTAAACTATGTC 57.696 37.037 2.81 0.00 41.78 3.06
3237 3600 9.036980 AGGAGTAATCAACACTCTAAACTATGT 57.963 33.333 2.81 0.00 41.78 2.29
3238 3601 9.877178 AAGGAGTAATCAACACTCTAAACTATG 57.123 33.333 2.81 0.00 41.78 2.23
3241 3604 9.628500 AAAAAGGAGTAATCAACACTCTAAACT 57.372 29.630 2.81 0.00 41.78 2.66
3269 3632 9.692749 GAGATTTCAATATGGACTACATACGAA 57.307 33.333 0.00 0.00 44.41 3.85
3270 3633 8.304596 GGAGATTTCAATATGGACTACATACGA 58.695 37.037 0.00 0.00 44.41 3.43
3271 3634 8.088365 TGGAGATTTCAATATGGACTACATACG 58.912 37.037 0.00 0.00 44.41 3.06
3272 3635 9.778741 TTGGAGATTTCAATATGGACTACATAC 57.221 33.333 0.00 0.00 44.41 2.39
3274 3637 9.699410 TTTTGGAGATTTCAATATGGACTACAT 57.301 29.630 0.00 0.00 43.68 2.29
3275 3638 9.527157 TTTTTGGAGATTTCAATATGGACTACA 57.473 29.630 0.00 0.00 0.00 2.74
3277 3640 9.973661 TCTTTTTGGAGATTTCAATATGGACTA 57.026 29.630 0.00 0.00 0.00 2.59
3278 3641 8.743714 GTCTTTTTGGAGATTTCAATATGGACT 58.256 33.333 0.00 0.00 0.00 3.85
3279 3642 8.743714 AGTCTTTTTGGAGATTTCAATATGGAC 58.256 33.333 0.00 0.00 0.00 4.02
3280 3643 8.884124 AGTCTTTTTGGAGATTTCAATATGGA 57.116 30.769 0.00 0.00 0.00 3.41
3294 3657 9.169592 CCGTTCCTAAATATAAGTCTTTTTGGA 57.830 33.333 0.00 0.00 34.13 3.53
3295 3658 9.169592 TCCGTTCCTAAATATAAGTCTTTTTGG 57.830 33.333 0.00 0.00 0.00 3.28
3297 3660 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
3298 3661 8.765517 TCCTCCGTTCCTAAATATAAGTCTTTT 58.234 33.333 0.00 0.00 0.00 2.27
3299 3662 8.315220 TCCTCCGTTCCTAAATATAAGTCTTT 57.685 34.615 0.00 0.00 0.00 2.52
3300 3663 7.909485 TCCTCCGTTCCTAAATATAAGTCTT 57.091 36.000 0.00 0.00 0.00 3.01
3301 3664 7.564292 ACTTCCTCCGTTCCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
3302 3665 7.724287 ACTTCCTCCGTTCCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
3303 3666 7.672122 ACTTCCTCCGTTCCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
3304 3667 9.857957 GATACTTCCTCCGTTCCTAAATATAAG 57.142 37.037 0.00 0.00 0.00 1.73
3305 3668 9.597681 AGATACTTCCTCCGTTCCTAAATATAA 57.402 33.333 0.00 0.00 0.00 0.98
3306 3669 9.597681 AAGATACTTCCTCCGTTCCTAAATATA 57.402 33.333 0.00 0.00 0.00 0.86
3307 3670 8.493787 AAGATACTTCCTCCGTTCCTAAATAT 57.506 34.615 0.00 0.00 0.00 1.28
3308 3671 7.909485 AAGATACTTCCTCCGTTCCTAAATA 57.091 36.000 0.00 0.00 0.00 1.40
3309 3672 6.809976 AAGATACTTCCTCCGTTCCTAAAT 57.190 37.500 0.00 0.00 0.00 1.40
3310 3673 6.616237 AAAGATACTTCCTCCGTTCCTAAA 57.384 37.500 0.00 0.00 0.00 1.85
3311 3674 6.616237 AAAAGATACTTCCTCCGTTCCTAA 57.384 37.500 0.00 0.00 0.00 2.69
3312 3675 6.616237 AAAAAGATACTTCCTCCGTTCCTA 57.384 37.500 0.00 0.00 0.00 2.94
3313 3676 5.500546 AAAAAGATACTTCCTCCGTTCCT 57.499 39.130 0.00 0.00 0.00 3.36
3382 3745 9.468532 CATGAGTATATATATGTGCTTGCGTAT 57.531 33.333 5.44 0.00 0.00 3.06
3395 3758 9.467796 CCTCAGACTTCCACATGAGTATATATA 57.532 37.037 0.00 0.00 37.97 0.86
3413 3776 6.983906 AAAATCAATGTTTTCCCTCAGACT 57.016 33.333 0.00 0.00 0.00 3.24
3461 3826 3.379452 AGTCCATCTCCCCTCAAAGTAG 58.621 50.000 0.00 0.00 0.00 2.57
3561 3926 1.008538 GCTGTTGAACGTTGCAGGG 60.009 57.895 5.00 0.00 0.00 4.45
3623 3988 5.483937 TGGGAGTTCTGCTAGAAGAAATACA 59.516 40.000 22.00 16.49 36.93 2.29


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

AutoCloner maintained by Alex Coulton.