Multiple sequence alignment - TraesCS1B01G384700

Loading Multiple Alignment...

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 TraesCS1B01G384700 chr1B 100.000 3578 0 0 1 3578 617969688 617966111 0.000000e+00 6608.0
1 TraesCS1B01G384700 chr1D 91.512 3228 139 47 161 3321 450463826 450460667 0.000000e+00 4318.0
2 TraesCS1B01G384700 chr1D 77.606 777 124 33 1274 2022 450739463 450740217 3.300000e-115 425.0
3 TraesCS1B01G384700 chr1D 95.833 48 1 1 3353 3400 450460661 450460615 3.830000e-10 76.8
4 TraesCS1B01G384700 chr1D 92.857 42 3 0 3537 3578 450460323 450460282 1.070000e-05 62.1
5 TraesCS1B01G384700 chr1A 91.064 2876 139 42 564 3356 545649646 545646806 0.000000e+00 3779.0
6 TraesCS1B01G384700 chr1A 87.073 410 33 14 162 561 545652609 545652210 2.530000e-121 446.0
7 TraesCS1B01G384700 chr1A 88.581 289 17 10 262 546 545649912 545649636 1.590000e-88 337.0
8 TraesCS1B01G384700 chr1A 88.764 178 11 5 3407 3578 545646800 545646626 3.620000e-50 209.0
9 TraesCS1B01G384700 chr1A 91.791 134 11 0 25 158 545652782 545652649 1.700000e-43 187.0
10 TraesCS1B01G384700 chr3D 80.040 992 158 32 1050 2025 358504503 358503536 0.000000e+00 699.0
11 TraesCS1B01G384700 chr3D 78.860 965 163 35 1074 2022 358176893 358177832 6.570000e-172 614.0
12 TraesCS1B01G384700 chr3D 76.691 961 197 20 1074 2022 358188074 358189019 3.190000e-140 508.0
13 TraesCS1B01G384700 chr3D 78.283 769 145 18 1066 1825 358564950 358564195 3.230000e-130 475.0
14 TraesCS1B01G384700 chr3A 78.333 960 178 25 1074 2021 477427551 477428492 8.550000e-166 593.0
15 TraesCS1B01G384700 chr3A 76.763 964 191 28 1074 2025 477430563 477431505 3.190000e-140 508.0
16 TraesCS1B01G384700 chr3B 76.660 964 191 28 1074 2025 462890556 462891497 1.480000e-138 503.0


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 TraesCS1B01G384700 chr1B 617966111 617969688 3577 True 6608.000000 6608 100.000000 1 3578 1 chr1B.!!$R1 3577
1 TraesCS1B01G384700 chr1D 450460282 450463826 3544 True 1485.633333 4318 93.400667 161 3578 3 chr1D.!!$R1 3417
2 TraesCS1B01G384700 chr1D 450739463 450740217 754 False 425.000000 425 77.606000 1274 2022 1 chr1D.!!$F1 748
3 TraesCS1B01G384700 chr1A 545646626 545652782 6156 True 991.600000 3779 89.454600 25 3578 5 chr1A.!!$R1 3553
4 TraesCS1B01G384700 chr3D 358503536 358504503 967 True 699.000000 699 80.040000 1050 2025 1 chr3D.!!$R1 975
5 TraesCS1B01G384700 chr3D 358176893 358177832 939 False 614.000000 614 78.860000 1074 2022 1 chr3D.!!$F1 948
6 TraesCS1B01G384700 chr3D 358188074 358189019 945 False 508.000000 508 76.691000 1074 2022 1 chr3D.!!$F2 948
7 TraesCS1B01G384700 chr3D 358564195 358564950 755 True 475.000000 475 78.283000 1066 1825 1 chr3D.!!$R2 759
8 TraesCS1B01G384700 chr3A 477427551 477431505 3954 False 550.500000 593 77.548000 1074 2025 2 chr3A.!!$F1 951
9 TraesCS1B01G384700 chr3B 462890556 462891497 941 False 503.000000 503 76.660000 1074 2025 1 chr3B.!!$F1 951

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
263 302 0.038890 TGTCGGGGCATGGATGAAAA 59.961 50.0 0.0 0.0 0.0 2.29 F
500 3132 0.109532 TCCCTTCGCAAATCCACACA 59.890 50.0 0.0 0.0 0.0 3.72 F
1908 7606 0.322816 ACGCTGCAATGTGGGAATCT 60.323 50.0 0.0 0.0 0.0 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1869 7567 0.682209 CCAATGTGCTCTTGGGGGAG 60.682 60.0 8.33 0.0 39.62 4.30 R
2265 7987 0.514691 CGTCAAACTCTGCTTCCAGC 59.485 55.0 0.00 0.0 42.82 4.85 R
2883 8659 0.311790 TCGGAGGTTCACACACGTAC 59.688 55.0 0.00 0.0 0.00 3.67 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
26 27 5.876612 TTTTTGCAATAAACCATGGATGC 57.123 34.783 21.47 19.04 0.00 3.91
27 28 3.540314 TTGCAATAAACCATGGATGCC 57.460 42.857 21.47 6.31 33.01 4.40
54 55 5.665701 TCCCTCCTCCAAGCTTGTATATAT 58.334 41.667 24.35 0.00 0.00 0.86
56 57 5.485353 CCCTCCTCCAAGCTTGTATATATGA 59.515 44.000 24.35 11.69 0.00 2.15
106 107 2.150397 ACTTCAAAAGACGACCCTCG 57.850 50.000 0.00 0.00 46.93 4.63
154 155 4.584743 AGTTCAAACTTTCCAACTCATCCC 59.415 41.667 0.00 0.00 35.21 3.85
158 159 1.003233 ACTTTCCAACTCATCCCGACC 59.997 52.381 0.00 0.00 0.00 4.79
159 160 1.003118 CTTTCCAACTCATCCCGACCA 59.997 52.381 0.00 0.00 0.00 4.02
164 201 1.949847 AACTCATCCCGACCAGCGAG 61.950 60.000 0.00 0.00 44.57 5.03
179 216 0.452184 GCGAGGAACGATGTCTCTCA 59.548 55.000 0.00 0.00 45.77 3.27
182 219 3.243101 GCGAGGAACGATGTCTCTCAATA 60.243 47.826 0.00 0.00 45.77 1.90
196 233 7.495901 TGTCTCTCAATAGGAAAGCAATAGAG 58.504 38.462 0.00 0.00 0.00 2.43
197 234 7.124901 TGTCTCTCAATAGGAAAGCAATAGAGT 59.875 37.037 0.00 0.00 31.92 3.24
263 302 0.038890 TGTCGGGGCATGGATGAAAA 59.961 50.000 0.00 0.00 0.00 2.29
298 337 1.202313 CCGCACACCGAAAAGGAAAAA 60.202 47.619 0.00 0.00 45.00 1.94
334 373 0.165944 CGGAGTTTTGTCATGCGTCC 59.834 55.000 0.00 0.00 0.00 4.79
343 382 2.124736 CATGCGTCCGGGGTCATT 60.125 61.111 0.00 0.00 0.00 2.57
384 433 2.408565 GAGGAGAGAGAGAGAGAGGGA 58.591 57.143 0.00 0.00 0.00 4.20
412 461 4.687901 AAAAATAGGCACCCCATATTGC 57.312 40.909 0.00 0.00 38.06 3.56
413 462 3.618120 AAATAGGCACCCCATATTGCT 57.382 42.857 0.00 0.00 38.85 3.91
415 464 4.740154 AATAGGCACCCCATATTGCTTA 57.260 40.909 0.00 0.00 38.85 3.09
450 3082 2.359214 GCTTATTTTAGCCACTCCTGCC 59.641 50.000 0.00 0.00 35.06 4.85
488 3120 2.093764 AGAATTCACAGAGCTCCCTTCG 60.094 50.000 10.93 0.00 0.00 3.79
500 3132 0.109532 TCCCTTCGCAAATCCACACA 59.890 50.000 0.00 0.00 0.00 3.72
516 3148 3.573967 CCACACAAGCAAATAGTCCCTTT 59.426 43.478 0.00 0.00 0.00 3.11
534 3166 6.555360 GTCCCTTTCCTTCCTATATTCTCTCA 59.445 42.308 0.00 0.00 0.00 3.27
549 3181 8.848474 ATATTCTCTCAGAAAAAGAAAACGGA 57.152 30.769 0.00 0.00 37.82 4.69
550 3182 6.995511 TTCTCTCAGAAAAAGAAAACGGAA 57.004 33.333 0.00 0.00 29.99 4.30
551 3183 6.995511 TCTCTCAGAAAAAGAAAACGGAAA 57.004 33.333 0.00 0.00 0.00 3.13
552 3184 7.385778 TCTCTCAGAAAAAGAAAACGGAAAA 57.614 32.000 0.00 0.00 0.00 2.29
553 3185 7.472543 TCTCTCAGAAAAAGAAAACGGAAAAG 58.527 34.615 0.00 0.00 0.00 2.27
554 3186 7.335924 TCTCTCAGAAAAAGAAAACGGAAAAGA 59.664 33.333 0.00 0.00 0.00 2.52
555 3187 7.822658 TCTCAGAAAAAGAAAACGGAAAAGAA 58.177 30.769 0.00 0.00 0.00 2.52
556 3188 8.301002 TCTCAGAAAAAGAAAACGGAAAAGAAA 58.699 29.630 0.00 0.00 0.00 2.52
557 3189 8.819643 TCAGAAAAAGAAAACGGAAAAGAAAA 57.180 26.923 0.00 0.00 0.00 2.29
558 3190 9.262358 TCAGAAAAAGAAAACGGAAAAGAAAAA 57.738 25.926 0.00 0.00 0.00 1.94
559 3191 9.528847 CAGAAAAAGAAAACGGAAAAGAAAAAG 57.471 29.630 0.00 0.00 0.00 2.27
560 3192 9.483916 AGAAAAAGAAAACGGAAAAGAAAAAGA 57.516 25.926 0.00 0.00 0.00 2.52
605 3251 0.389948 CTCCCTTCCCGTTTGACTCG 60.390 60.000 0.00 0.00 0.00 4.18
629 3275 2.664436 CCCGTTTTCCACTCGCGTC 61.664 63.158 5.77 0.00 0.00 5.19
652 3298 4.973055 CCGTTCCACGTGGCCGAA 62.973 66.667 33.87 21.48 40.58 4.30
653 3299 3.411351 CGTTCCACGTGGCCGAAG 61.411 66.667 30.68 18.11 36.74 3.79
654 3300 2.280592 GTTCCACGTGGCCGAAGT 60.281 61.111 30.25 0.00 37.88 3.01
655 3301 2.029964 TTCCACGTGGCCGAAGTC 59.970 61.111 30.25 0.00 37.88 3.01
656 3302 3.524648 TTCCACGTGGCCGAAGTCC 62.525 63.158 30.25 0.00 37.88 3.85
657 3303 4.003788 CCACGTGGCCGAAGTCCT 62.004 66.667 24.02 0.00 37.88 3.85
658 3304 2.432628 CACGTGGCCGAAGTCCTC 60.433 66.667 7.95 0.00 37.88 3.71
659 3305 3.692406 ACGTGGCCGAAGTCCTCC 61.692 66.667 0.00 0.00 37.88 4.30
660 3306 3.691342 CGTGGCCGAAGTCCTCCA 61.691 66.667 0.00 0.00 35.63 3.86
678 3324 2.350895 CCGGTCAGCACATTCCCA 59.649 61.111 0.00 0.00 0.00 4.37
860 3509 2.170036 CCGCGCGCCATAAATACG 59.830 61.111 27.36 7.77 0.00 3.06
870 3519 4.253685 CGCCATAAATACGAATCCTCCAT 58.746 43.478 0.00 0.00 0.00 3.41
943 3596 2.088763 CGCGCACAGACTTCGACAT 61.089 57.895 8.75 0.00 0.00 3.06
992 3649 1.135689 CCAATCCTCCAAGAAAACGCG 60.136 52.381 3.53 3.53 0.00 6.01
994 3651 1.305930 ATCCTCCAAGAAAACGCGGC 61.306 55.000 12.47 0.00 0.00 6.53
1022 3679 4.475135 GGAGGAAGGGCTGCGGAC 62.475 72.222 0.00 0.00 0.00 4.79
1556 7244 4.415150 CATGGCGCCTGAGGTGGT 62.415 66.667 29.70 0.07 33.18 4.16
1869 7567 1.973812 GCTGAAGGGCAAGTGGGTC 60.974 63.158 0.00 0.00 0.00 4.46
1893 7591 2.548178 CAAGAGCACATTGGACGCT 58.452 52.632 0.00 0.00 39.12 5.07
1908 7606 0.322816 ACGCTGCAATGTGGGAATCT 60.323 50.000 0.00 0.00 0.00 2.40
2150 7869 7.171337 GGATGATGAAAGAGTAGAAGCAGAATC 59.829 40.741 0.00 0.00 0.00 2.52
2368 8099 2.110901 AGTGAATCAGCAGCAGGAAG 57.889 50.000 0.00 0.00 0.00 3.46
2380 8111 3.525537 CAGCAGGAAGATGTACATTCGT 58.474 45.455 10.30 4.25 0.00 3.85
2425 8159 3.797256 GGCTGTAGTTAGTGTTGATAGCG 59.203 47.826 0.00 0.00 0.00 4.26
2430 8164 4.530710 AGTTAGTGTTGATAGCGGTGAA 57.469 40.909 0.00 0.00 0.00 3.18
2442 8176 7.072177 TGATAGCGGTGAAAAAGAAATACTG 57.928 36.000 0.00 0.00 0.00 2.74
2490 8224 2.941453 TGCTCTATTTCTCGCTTCGT 57.059 45.000 0.00 0.00 0.00 3.85
2502 8246 3.005050 TCTCGCTTCGTTTTCCTCTGTTA 59.995 43.478 0.00 0.00 0.00 2.41
2520 8264 6.432107 TCTGTTACTTTCGCATTTTTACACC 58.568 36.000 0.00 0.00 0.00 4.16
2543 8292 3.578688 TGTCAGATCAGATCACAACGTG 58.421 45.455 13.14 1.28 34.45 4.49
2546 8295 2.093310 CAGATCAGATCACAACGTGCAC 59.907 50.000 13.14 6.82 32.98 4.57
2602 8352 2.148916 TGAGCAGAACGTACCACAAG 57.851 50.000 0.00 0.00 0.00 3.16
2604 8354 0.602905 AGCAGAACGTACCACAAGCC 60.603 55.000 0.00 0.00 0.00 4.35
2605 8355 1.574702 GCAGAACGTACCACAAGCCC 61.575 60.000 0.00 0.00 0.00 5.19
2606 8356 0.953960 CAGAACGTACCACAAGCCCC 60.954 60.000 0.00 0.00 0.00 5.80
2607 8357 1.071814 GAACGTACCACAAGCCCCA 59.928 57.895 0.00 0.00 0.00 4.96
2628 8378 0.819582 CCATCACTGGAAATGCACCC 59.180 55.000 0.00 0.00 46.37 4.61
2642 8395 4.660938 ACCCGCCTTCCAGCAACC 62.661 66.667 0.00 0.00 0.00 3.77
2658 8418 1.018910 AACCGTTGGAGTTGAAACCG 58.981 50.000 0.00 0.00 0.00 4.44
2828 8594 3.370231 CGGAAAAAGGGCCCCGTG 61.370 66.667 21.43 0.00 37.40 4.94
2841 8607 4.221422 CCGTGATCCCGTGGCGAT 62.221 66.667 0.00 0.00 0.00 4.58
2883 8659 3.479370 GCAAGCAGCAGAGGTACG 58.521 61.111 0.00 0.00 44.79 3.67
2911 8693 0.614697 TGAACCTCCGATCAGCTCCA 60.615 55.000 0.00 0.00 0.00 3.86
2955 8737 2.982744 GCCAGCTTTTCGTGAGCCC 61.983 63.158 0.00 0.00 41.03 5.19
2960 8742 1.982073 GCTTTTCGTGAGCCCATCGG 61.982 60.000 0.00 0.00 34.06 4.18
3093 8880 1.665735 GCACGGTGCAGTTGGTTATTG 60.666 52.381 27.10 0.00 44.26 1.90
3136 8923 1.743623 CGGGTTACATCAGCGCCAA 60.744 57.895 2.29 0.00 0.00 4.52
3145 8932 4.607293 ACATCAGCGCCAAGATAGATAA 57.393 40.909 2.29 0.00 0.00 1.75
3155 8942 9.142014 AGCGCCAAGATAGATAAATAGATAGAT 57.858 33.333 2.29 0.00 0.00 1.98
3231 9024 3.519510 CTGGGAAGTTTCTACAGGGATGA 59.480 47.826 8.32 0.00 32.50 2.92
3232 9025 4.111577 TGGGAAGTTTCTACAGGGATGAT 58.888 43.478 0.00 0.00 0.00 2.45
3251 9044 2.676471 CAGGTTTGGGCGGAAGGG 60.676 66.667 0.00 0.00 0.00 3.95
3266 9064 2.124403 GGGTCAGCTGCATCCTGG 60.124 66.667 9.47 0.00 0.00 4.45
3301 9099 4.608445 CGCCTAACTAACTGAATATTGCGC 60.608 45.833 0.00 0.00 0.00 6.09
3403 9391 2.435069 TGGTTTGACCGGTTGAGTTAGA 59.565 45.455 9.42 0.00 42.58 2.10
3405 9393 4.283978 TGGTTTGACCGGTTGAGTTAGATA 59.716 41.667 9.42 0.00 42.58 1.98
3443 9431 8.818622 TGTTCAGTAAGATGTACTGTAGGTAT 57.181 34.615 12.04 0.00 43.84 2.73
3444 9432 8.683615 TGTTCAGTAAGATGTACTGTAGGTATG 58.316 37.037 12.04 0.00 43.84 2.39
3460 9454 8.341892 TGTAGGTATGATCTAGTATCTGCAAG 57.658 38.462 0.00 0.00 0.00 4.01
3484 9478 8.065473 AGATATCTAGTGATGTAATGGCAGAG 57.935 38.462 2.53 0.00 34.32 3.35
3505 9499 1.061546 GTCTAGTGGTGTTTGGGGGA 58.938 55.000 0.00 0.00 0.00 4.81
3519 9513 1.562475 TGGGGGAAGAAAATACCCTCG 59.438 52.381 0.00 0.00 46.53 4.63
3522 9516 2.547826 GGGAAGAAAATACCCTCGACG 58.452 52.381 0.00 0.00 40.39 5.12
3524 9518 2.418334 GGAAGAAAATACCCTCGACGCT 60.418 50.000 0.00 0.00 0.00 5.07
3527 9521 3.259902 AGAAAATACCCTCGACGCTTTC 58.740 45.455 0.00 0.00 0.00 2.62
3528 9522 3.056035 AGAAAATACCCTCGACGCTTTCT 60.056 43.478 0.00 0.00 0.00 2.52
3529 9523 3.329929 AAATACCCTCGACGCTTTCTT 57.670 42.857 0.00 0.00 0.00 2.52
3530 9524 4.460948 AAATACCCTCGACGCTTTCTTA 57.539 40.909 0.00 0.00 0.00 2.10
3531 9525 3.712091 ATACCCTCGACGCTTTCTTAG 57.288 47.619 0.00 0.00 0.00 2.18
3532 9526 1.542492 ACCCTCGACGCTTTCTTAGA 58.458 50.000 0.00 0.00 0.00 2.10
3533 9527 1.473278 ACCCTCGACGCTTTCTTAGAG 59.527 52.381 0.00 0.00 0.00 2.43
3534 9528 1.551145 CCTCGACGCTTTCTTAGAGC 58.449 55.000 0.00 0.00 36.79 4.09
3535 9529 1.135373 CCTCGACGCTTTCTTAGAGCA 60.135 52.381 0.00 0.00 40.13 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.699257 GGCATCCATGGTTTATTGCAAAAA 59.301 37.500 12.58 2.96 0.00 1.94
5 6 4.019501 AGGCATCCATGGTTTATTGCAAAA 60.020 37.500 12.58 0.00 0.00 2.44
6 7 3.518705 AGGCATCCATGGTTTATTGCAAA 59.481 39.130 12.58 0.00 0.00 3.68
7 8 3.106054 AGGCATCCATGGTTTATTGCAA 58.894 40.909 12.58 0.00 0.00 4.08
10 11 4.038402 GGAAGAGGCATCCATGGTTTATTG 59.962 45.833 12.58 4.53 36.92 1.90
11 12 4.218312 GGAAGAGGCATCCATGGTTTATT 58.782 43.478 12.58 0.00 36.92 1.40
12 13 3.437052 GGGAAGAGGCATCCATGGTTTAT 60.437 47.826 12.58 0.00 38.80 1.40
13 14 2.091885 GGGAAGAGGCATCCATGGTTTA 60.092 50.000 12.58 0.00 38.80 2.01
14 15 1.342374 GGGAAGAGGCATCCATGGTTT 60.342 52.381 12.58 0.00 38.80 3.27
15 16 0.259938 GGGAAGAGGCATCCATGGTT 59.740 55.000 12.58 0.00 38.80 3.67
16 17 0.625683 AGGGAAGAGGCATCCATGGT 60.626 55.000 12.58 0.00 38.80 3.55
17 18 0.110104 GAGGGAAGAGGCATCCATGG 59.890 60.000 4.97 4.97 38.80 3.66
18 19 0.110104 GGAGGGAAGAGGCATCCATG 59.890 60.000 0.00 0.00 38.80 3.66
19 20 0.029267 AGGAGGGAAGAGGCATCCAT 60.029 55.000 0.00 0.00 38.80 3.41
20 21 0.692419 GAGGAGGGAAGAGGCATCCA 60.692 60.000 0.00 0.00 38.80 3.41
21 22 1.414866 GGAGGAGGGAAGAGGCATCC 61.415 65.000 0.00 0.00 36.16 3.51
22 23 0.692419 TGGAGGAGGGAAGAGGCATC 60.692 60.000 0.00 0.00 0.00 3.91
23 24 0.253347 TTGGAGGAGGGAAGAGGCAT 60.253 55.000 0.00 0.00 0.00 4.40
24 25 0.911525 CTTGGAGGAGGGAAGAGGCA 60.912 60.000 0.00 0.00 0.00 4.75
25 26 1.911471 CTTGGAGGAGGGAAGAGGC 59.089 63.158 0.00 0.00 0.00 4.70
26 27 0.620121 AGCTTGGAGGAGGGAAGAGG 60.620 60.000 0.00 0.00 0.00 3.69
27 28 1.065564 CAAGCTTGGAGGAGGGAAGAG 60.066 57.143 19.14 0.00 0.00 2.85
77 78 7.245604 GGTCGTCTTTTGAAGTTTTGAAAGTA 58.754 34.615 0.00 0.00 32.43 2.24
82 83 4.266714 AGGGTCGTCTTTTGAAGTTTTGA 58.733 39.130 0.00 0.00 0.00 2.69
96 97 0.815734 TGAAATCCTCGAGGGTCGTC 59.184 55.000 30.80 23.36 41.35 4.20
143 144 1.450312 GCTGGTCGGGATGAGTTGG 60.450 63.158 0.00 0.00 0.00 3.77
151 152 3.379445 GTTCCTCGCTGGTCGGGA 61.379 66.667 0.00 0.00 42.52 5.14
154 155 1.874019 CATCGTTCCTCGCTGGTCG 60.874 63.158 0.00 0.00 39.67 4.79
158 159 0.453793 AGAGACATCGTTCCTCGCTG 59.546 55.000 0.00 0.00 40.80 5.18
159 160 0.736053 GAGAGACATCGTTCCTCGCT 59.264 55.000 0.00 0.00 39.67 4.93
164 201 4.920640 TCCTATTGAGAGACATCGTTCC 57.079 45.455 0.00 0.00 0.00 3.62
179 216 5.882557 CACCACACTCTATTGCTTTCCTATT 59.117 40.000 0.00 0.00 0.00 1.73
182 219 3.327757 TCACCACACTCTATTGCTTTCCT 59.672 43.478 0.00 0.00 0.00 3.36
196 233 0.310543 TCGCATTGCTTTCACCACAC 59.689 50.000 7.12 0.00 0.00 3.82
197 234 0.592637 CTCGCATTGCTTTCACCACA 59.407 50.000 7.12 0.00 0.00 4.17
213 252 6.448053 TTTCATTTTTGTAGAGACGACTCG 57.552 37.500 9.21 0.00 46.64 4.18
263 302 2.756283 CGGCTCTCTTCCTCCCGT 60.756 66.667 0.00 0.00 34.56 5.28
298 337 3.118000 ACTCCGACTTCCCTTTGACTTTT 60.118 43.478 0.00 0.00 0.00 2.27
334 373 2.491152 GCATGTGCAATGACCCCG 59.509 61.111 11.52 0.00 41.59 5.73
364 403 2.408565 TCCCTCTCTCTCTCTCTCCTC 58.591 57.143 0.00 0.00 0.00 3.71
365 404 2.587060 TCCCTCTCTCTCTCTCTCCT 57.413 55.000 0.00 0.00 0.00 3.69
366 405 2.509964 ACTTCCCTCTCTCTCTCTCTCC 59.490 54.545 0.00 0.00 0.00 3.71
450 3082 2.879103 TCTTGGGTGAGCCTAAAAGG 57.121 50.000 1.06 0.00 34.73 3.11
488 3120 4.559153 ACTATTTGCTTGTGTGGATTTGC 58.441 39.130 0.00 0.00 0.00 3.68
500 3132 4.044698 AGGAAGGAAAGGGACTATTTGCTT 59.955 41.667 5.09 5.09 46.74 3.91
516 3148 9.494055 TCTTTTTCTGAGAGAATATAGGAAGGA 57.506 33.333 0.00 0.00 33.67 3.36
534 3166 9.483916 TCTTTTTCTTTTCCGTTTTCTTTTTCT 57.516 25.926 0.00 0.00 0.00 2.52
561 3193 6.352737 GGGACCCTTTTCTCCTTTTTCTTTTT 60.353 38.462 2.09 0.00 0.00 1.94
562 3194 5.130477 GGGACCCTTTTCTCCTTTTTCTTTT 59.870 40.000 2.09 0.00 0.00 2.27
563 3195 4.654262 GGGACCCTTTTCTCCTTTTTCTTT 59.346 41.667 2.09 0.00 0.00 2.52
564 3196 4.078571 AGGGACCCTTTTCTCCTTTTTCTT 60.079 41.667 7.44 0.00 0.00 2.52
565 3197 3.467483 AGGGACCCTTTTCTCCTTTTTCT 59.533 43.478 7.44 0.00 0.00 2.52
566 3198 3.827302 GAGGGACCCTTTTCTCCTTTTTC 59.173 47.826 16.22 0.00 31.76 2.29
567 3199 3.438078 GGAGGGACCCTTTTCTCCTTTTT 60.438 47.826 16.22 0.00 41.76 1.94
568 3200 2.110188 GGAGGGACCCTTTTCTCCTTTT 59.890 50.000 16.22 0.00 41.76 2.27
569 3201 1.711375 GGAGGGACCCTTTTCTCCTTT 59.289 52.381 16.22 0.00 41.76 3.11
570 3202 1.373536 GGAGGGACCCTTTTCTCCTT 58.626 55.000 16.22 0.00 41.76 3.36
571 3203 3.106441 GGAGGGACCCTTTTCTCCT 57.894 57.895 16.22 0.00 41.76 3.69
605 3251 0.949397 GAGTGGAAAACGGGGTCAAC 59.051 55.000 0.00 0.00 0.00 3.18
648 3294 2.995574 ACCGGTGGAGGACTTCGG 60.996 66.667 6.12 0.00 45.42 4.30
649 3295 2.214181 CTGACCGGTGGAGGACTTCG 62.214 65.000 14.63 0.00 34.73 3.79
650 3296 1.592223 CTGACCGGTGGAGGACTTC 59.408 63.158 14.63 0.00 34.73 3.01
651 3297 2.584391 GCTGACCGGTGGAGGACTT 61.584 63.158 14.63 0.00 34.73 3.01
652 3298 2.997897 GCTGACCGGTGGAGGACT 60.998 66.667 14.63 0.00 34.73 3.85
653 3299 3.311110 TGCTGACCGGTGGAGGAC 61.311 66.667 14.63 0.00 34.73 3.85
654 3300 3.311110 GTGCTGACCGGTGGAGGA 61.311 66.667 14.63 5.98 34.73 3.71
655 3301 2.469465 AATGTGCTGACCGGTGGAGG 62.469 60.000 14.63 0.00 37.30 4.30
656 3302 1.003355 AATGTGCTGACCGGTGGAG 60.003 57.895 14.63 9.14 0.00 3.86
657 3303 1.003839 GAATGTGCTGACCGGTGGA 60.004 57.895 14.63 0.00 0.00 4.02
658 3304 2.040544 GGAATGTGCTGACCGGTGG 61.041 63.158 14.63 5.68 0.00 4.61
659 3305 2.040544 GGGAATGTGCTGACCGGTG 61.041 63.158 14.63 0.00 0.00 4.94
660 3306 2.351276 GGGAATGTGCTGACCGGT 59.649 61.111 6.92 6.92 0.00 5.28
860 3509 0.701147 GGATGGGGGATGGAGGATTC 59.299 60.000 0.00 0.00 0.00 2.52
870 3519 3.727258 CTGTTGCGGGATGGGGGA 61.727 66.667 0.00 0.00 0.00 4.81
978 3635 2.173382 CGCCGCGTTTTCTTGGAG 59.827 61.111 4.92 0.00 0.00 3.86
994 3651 2.040884 TTCCTCCCTCATCCCCCG 60.041 66.667 0.00 0.00 0.00 5.73
1548 7236 4.631740 TCCCCTCGCACCACCTCA 62.632 66.667 0.00 0.00 0.00 3.86
1677 7368 2.581409 GCGTCCGTGTACCCGATG 60.581 66.667 0.00 0.00 0.00 3.84
1716 7407 3.649277 CTTGGCCTCCGACGACAGG 62.649 68.421 3.32 8.14 0.00 4.00
1869 7567 0.682209 CCAATGTGCTCTTGGGGGAG 60.682 60.000 8.33 0.00 39.62 4.30
1893 7591 1.452110 CGTCAGATTCCCACATTGCA 58.548 50.000 0.00 0.00 0.00 4.08
1908 7606 2.748647 TCATCCTCGTCGGCGTCA 60.749 61.111 10.18 0.00 39.49 4.35
2150 7869 3.096092 ACTCCAGCTTCTTCTACTCCTG 58.904 50.000 0.00 0.00 0.00 3.86
2208 7930 0.806868 AATCGTACGCCGTCTCTTCA 59.193 50.000 11.24 0.00 37.94 3.02
2252 7974 2.607187 CTTCCAGCAGTAACGACGATT 58.393 47.619 0.00 0.00 0.00 3.34
2265 7987 0.514691 CGTCAAACTCTGCTTCCAGC 59.485 55.000 0.00 0.00 42.82 4.85
2368 8099 3.624900 TCGAATCCGACGAATGTACATC 58.375 45.455 9.23 2.22 40.30 3.06
2380 8111 1.226030 TCGCTAGCGATCGAATCCGA 61.226 55.000 34.66 17.05 44.01 4.55
2425 8159 5.453567 ACTGGCAGTATTTCTTTTTCACC 57.546 39.130 20.61 0.00 0.00 4.02
2430 8164 6.485648 ACGACTTTACTGGCAGTATTTCTTTT 59.514 34.615 26.71 8.36 29.64 2.27
2442 8176 3.424962 GCATCTTCAACGACTTTACTGGC 60.425 47.826 0.00 0.00 0.00 4.85
2490 8224 6.385649 AAATGCGAAAGTAACAGAGGAAAA 57.614 33.333 0.00 0.00 0.00 2.29
2502 8246 5.195001 ACATGGTGTAAAAATGCGAAAGT 57.805 34.783 0.00 0.00 0.00 2.66
2520 8264 4.032558 CACGTTGTGATCTGATCTGACATG 59.967 45.833 17.82 12.08 35.23 3.21
2543 8292 0.962356 CCCAGGTGATCTTGTGGTGC 60.962 60.000 0.00 0.00 0.00 5.01
2546 8295 0.911769 TAGCCCAGGTGATCTTGTGG 59.088 55.000 0.00 0.00 0.00 4.17
2602 8352 0.033208 TTTCCAGTGATGGATGGGGC 60.033 55.000 0.00 0.00 37.87 5.80
2604 8354 1.684983 GCATTTCCAGTGATGGATGGG 59.315 52.381 0.00 0.00 37.87 4.00
2605 8355 2.100252 GTGCATTTCCAGTGATGGATGG 59.900 50.000 0.00 0.00 37.87 3.51
2606 8356 2.100252 GGTGCATTTCCAGTGATGGATG 59.900 50.000 0.00 0.00 37.87 3.51
2607 8357 2.381911 GGTGCATTTCCAGTGATGGAT 58.618 47.619 0.00 0.00 37.87 3.41
2628 8378 2.978010 AACGGTTGCTGGAAGGCG 60.978 61.111 0.00 0.00 34.52 5.52
2642 8395 1.871039 ACATCGGTTTCAACTCCAACG 59.129 47.619 0.00 0.00 0.00 4.10
2658 8418 2.662596 TGGGTCGACCAGCACATC 59.337 61.111 34.40 16.51 46.80 3.06
2685 8445 2.869702 GCCGTCGTTTTCATGCGC 60.870 61.111 0.00 0.00 0.00 6.09
2813 8579 1.320344 GGATCACGGGGCCCTTTTTC 61.320 60.000 24.38 12.36 0.00 2.29
2828 8594 1.595382 CAAGGATCGCCACGGGATC 60.595 63.158 9.53 9.53 46.64 3.36
2841 8607 1.702182 TTGTCAGCAATTGCCAAGGA 58.298 45.000 26.45 15.84 43.38 3.36
2880 8656 1.266718 GGAGGTTCACACACGTACGTA 59.733 52.381 22.34 1.39 0.00 3.57
2883 8659 0.311790 TCGGAGGTTCACACACGTAC 59.688 55.000 0.00 0.00 0.00 3.67
2911 8693 2.611971 CCAGCTGTTTCTGCAATGCAAT 60.612 45.455 13.81 0.00 38.41 3.56
3028 8810 2.011617 AACAACCTTGGCCAGCTCCT 62.012 55.000 5.11 0.00 0.00 3.69
3029 8811 1.531602 AACAACCTTGGCCAGCTCC 60.532 57.895 5.11 0.00 0.00 4.70
3030 8812 1.662044 CAACAACCTTGGCCAGCTC 59.338 57.895 5.11 0.00 0.00 4.09
3093 8880 0.669318 TTTGGACGAGCGTCATGGAC 60.669 55.000 22.49 7.21 46.20 4.02
3155 8942 6.775594 ATCTAGTGTAAGCATGTGTGTCTA 57.224 37.500 0.00 0.00 0.00 2.59
3156 8943 5.667539 ATCTAGTGTAAGCATGTGTGTCT 57.332 39.130 0.00 0.00 0.00 3.41
3157 8944 7.096436 CGAATATCTAGTGTAAGCATGTGTGTC 60.096 40.741 0.00 0.00 0.00 3.67
3158 8945 6.697455 CGAATATCTAGTGTAAGCATGTGTGT 59.303 38.462 0.00 0.00 0.00 3.72
3202 8995 0.695347 AGAAACTTCCCAGAGCCAGG 59.305 55.000 0.00 0.00 0.00 4.45
3231 9024 1.000896 CTTCCGCCCAAACCTGGAT 60.001 57.895 0.00 0.00 46.92 3.41
3232 9025 2.434331 CTTCCGCCCAAACCTGGA 59.566 61.111 0.00 0.00 46.92 3.86
3251 9044 2.627515 TATTCCAGGATGCAGCTGAC 57.372 50.000 20.43 9.67 31.97 3.51
3266 9064 2.572290 AGTTAGGCGCCCACATTATTC 58.428 47.619 26.15 5.15 0.00 1.75
3351 9149 2.200170 GATTTGTGGAGTGGCACGCC 62.200 60.000 30.48 30.48 41.54 5.68
3362 9160 1.156736 AACGGAAGAGCGATTTGTGG 58.843 50.000 0.00 0.00 0.00 4.17
3405 9393 8.896744 CATCTTACTGAACAAACATCATACCAT 58.103 33.333 0.00 0.00 0.00 3.55
3460 9454 7.758980 CACTCTGCCATTACATCACTAGATATC 59.241 40.741 0.00 0.00 31.88 1.63
3471 9465 4.141846 CCACTAGACACTCTGCCATTACAT 60.142 45.833 0.00 0.00 0.00 2.29
3477 9471 0.969149 CACCACTAGACACTCTGCCA 59.031 55.000 0.00 0.00 0.00 4.92
3484 9478 1.544759 CCCCCAAACACCACTAGACAC 60.545 57.143 0.00 0.00 0.00 3.67
3505 9499 3.329929 AAGCGTCGAGGGTATTTTCTT 57.670 42.857 10.56 0.00 0.00 2.52
3519 9513 3.741344 TGAAGTTGCTCTAAGAAAGCGTC 59.259 43.478 0.00 0.00 42.83 5.19
3522 9516 4.275936 TGGTTGAAGTTGCTCTAAGAAAGC 59.724 41.667 0.00 0.00 40.26 3.51
3524 9518 6.299141 AGATGGTTGAAGTTGCTCTAAGAAA 58.701 36.000 0.00 0.00 0.00 2.52
3527 9521 5.486526 AGAGATGGTTGAAGTTGCTCTAAG 58.513 41.667 0.00 0.00 30.17 2.18
3528 9522 5.489792 AGAGATGGTTGAAGTTGCTCTAA 57.510 39.130 0.00 0.00 30.17 2.10
3529 9523 5.247110 AGAAGAGATGGTTGAAGTTGCTCTA 59.753 40.000 0.00 0.00 31.58 2.43
3530 9524 4.041444 AGAAGAGATGGTTGAAGTTGCTCT 59.959 41.667 0.00 0.00 33.05 4.09
3531 9525 4.322567 AGAAGAGATGGTTGAAGTTGCTC 58.677 43.478 0.00 0.00 0.00 4.26
3532 9526 4.363991 AGAAGAGATGGTTGAAGTTGCT 57.636 40.909 0.00 0.00 0.00 3.91
3533 9527 6.560253 TTTAGAAGAGATGGTTGAAGTTGC 57.440 37.500 0.00 0.00 0.00 4.17
3534 9528 9.403110 CAAATTTAGAAGAGATGGTTGAAGTTG 57.597 33.333 0.00 0.00 0.00 3.16
3535 9529 8.084684 GCAAATTTAGAAGAGATGGTTGAAGTT 58.915 33.333 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.