Multiple sequence alignment - TraesCS1B01G334700

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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 TraesCS1B01G334700 chr1B 100.000 3587 0 0 1 3587 561710771 561714357 0.000000e+00 6625.0
1 TraesCS1B01G334700 chr1A 93.371 3002 140 36 609 3587 512884394 512887359 0.000000e+00 4386.0
2 TraesCS1B01G334700 chr1A 85.603 514 30 15 1 481 512883700 512884202 1.920000e-137 499.0
3 TraesCS1B01G334700 chr1D 92.749 2110 101 29 609 2684 415421838 415423929 0.000000e+00 3001.0
4 TraesCS1B01G334700 chr1D 90.176 397 17 8 18 407 415421135 415421516 6.920000e-137 497.0
5 TraesCS1B01G334700 chr3D 84.615 65 9 1 3353 3417 495247918 495247855 2.990000e-06 63.9
6 TraesCS1B01G334700 chr3B 96.970 33 1 0 3354 3386 110231724 110231756 5.000000e-04 56.5


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 TraesCS1B01G334700 chr1B 561710771 561714357 3586 False 6625.0 6625 100.0000 1 3587 1 chr1B.!!$F1 3586
1 TraesCS1B01G334700 chr1A 512883700 512887359 3659 False 2442.5 4386 89.4870 1 3587 2 chr1A.!!$F1 3586
2 TraesCS1B01G334700 chr1D 415421135 415423929 2794 False 1749.0 3001 91.4625 18 2684 2 chr1D.!!$F1 2666

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
952 1143 0.684805 TGCCCCCTCAACGTGTTTTT 60.685 50.0 0.0 0.0 0.0 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2594 2785 0.545646 ATCCCCAGCAGAAGAGCTTC 59.454 55.0 2.03 2.03 43.7 3.86 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
37 38 7.038302 TGACAAGAAGTGGATAAGATAAGTGGT 60.038 37.037 0.00 0.00 0.00 4.16
79 84 6.069440 TCCATACCATCTTTGGAAGTGAAGAT 60.069 38.462 0.00 0.00 46.92 2.40
116 121 2.872858 GCTGGGTATCTTGACGAATTCC 59.127 50.000 0.00 0.00 0.00 3.01
258 263 4.233789 GCTGTGTAGTCAGTCAAAGAGAG 58.766 47.826 0.00 0.00 37.70 3.20
259 264 4.022762 GCTGTGTAGTCAGTCAAAGAGAGA 60.023 45.833 0.00 0.00 37.70 3.10
260 265 5.336372 GCTGTGTAGTCAGTCAAAGAGAGAT 60.336 44.000 0.00 0.00 37.70 2.75
261 266 6.656632 TGTGTAGTCAGTCAAAGAGAGATT 57.343 37.500 0.00 0.00 0.00 2.40
262 267 7.575909 GCTGTGTAGTCAGTCAAAGAGAGATTA 60.576 40.741 0.00 0.00 37.70 1.75
270 275 6.936900 TCAGTCAAAGAGAGATTAAAACCAGG 59.063 38.462 0.00 0.00 0.00 4.45
276 281 5.810095 AGAGAGATTAAAACCAGGTGGAAG 58.190 41.667 2.10 0.00 38.94 3.46
300 309 2.685100 CTACAGAACCCTGAACCGAAC 58.315 52.381 0.00 0.00 43.02 3.95
351 365 4.673968 AGTGGGTCACTATCAGTCAAGTA 58.326 43.478 0.00 0.00 43.46 2.24
377 392 7.636150 AAAAATTAGCATCTCTACTGCATGT 57.364 32.000 0.00 0.00 42.15 3.21
398 413 7.013274 GCATGTAGAGTTAATTTCCAAGGCATA 59.987 37.037 0.00 0.00 0.00 3.14
481 516 2.043801 TGGTTTAGGCCCCTATTGCTTT 59.956 45.455 0.00 0.00 0.00 3.51
482 517 3.269906 TGGTTTAGGCCCCTATTGCTTTA 59.730 43.478 0.00 0.00 0.00 1.85
483 518 4.264442 TGGTTTAGGCCCCTATTGCTTTAA 60.264 41.667 0.00 0.00 0.00 1.52
485 520 6.072649 GGTTTAGGCCCCTATTGCTTTAATA 58.927 40.000 0.00 0.00 0.00 0.98
486 521 6.551975 GGTTTAGGCCCCTATTGCTTTAATAA 59.448 38.462 0.00 0.00 31.12 1.40
489 524 8.873186 TTAGGCCCCTATTGCTTTAATAATAC 57.127 34.615 0.00 0.00 31.12 1.89
491 526 7.175797 AGGCCCCTATTGCTTTAATAATACTC 58.824 38.462 0.00 0.00 31.12 2.59
492 527 7.018650 AGGCCCCTATTGCTTTAATAATACTCT 59.981 37.037 0.00 0.00 31.12 3.24
493 528 7.121315 GGCCCCTATTGCTTTAATAATACTCTG 59.879 40.741 0.00 0.00 31.12 3.35
495 530 9.442047 CCCCTATTGCTTTAATAATACTCTGAG 57.558 37.037 2.45 2.45 31.12 3.35
496 531 8.940952 CCCTATTGCTTTAATAATACTCTGAGC 58.059 37.037 4.19 0.00 31.12 4.26
497 532 8.940952 CCTATTGCTTTAATAATACTCTGAGCC 58.059 37.037 4.19 0.00 31.12 4.70
552 621 0.689623 AGAGCAAGTTGAGGACTGGG 59.310 55.000 7.16 0.00 39.00 4.45
649 802 1.531423 ACTGCATCCAAGACAGCAAG 58.469 50.000 0.00 0.00 36.44 4.01
656 809 4.791974 CATCCAAGACAGCAAGAGAAAAC 58.208 43.478 0.00 0.00 0.00 2.43
691 850 2.203998 CACCTCACCCTGACCCCT 60.204 66.667 0.00 0.00 0.00 4.79
693 852 2.689034 CCTCACCCTGACCCCTCC 60.689 72.222 0.00 0.00 0.00 4.30
694 853 3.077556 CTCACCCTGACCCCTCCG 61.078 72.222 0.00 0.00 0.00 4.63
766 930 3.382832 ACGAACAGAGGAGGCCCG 61.383 66.667 0.00 0.00 37.58 6.13
808 975 3.775654 GACGGGGCAGGAGGAGTG 61.776 72.222 0.00 0.00 0.00 3.51
896 1087 8.770828 TCGTCTGGCTGCTATTTTATTATTTAC 58.229 33.333 0.00 0.00 0.00 2.01
902 1093 9.169592 GGCTGCTATTTTATTATTTACCCGATA 57.830 33.333 0.00 0.00 0.00 2.92
951 1142 1.076632 TGCCCCCTCAACGTGTTTT 60.077 52.632 0.00 0.00 0.00 2.43
952 1143 0.684805 TGCCCCCTCAACGTGTTTTT 60.685 50.000 0.00 0.00 0.00 1.94
974 1165 3.814005 ACAGTAGTTATTACGGGGCTG 57.186 47.619 0.00 0.00 37.35 4.85
1354 1545 4.514585 ACAACGTTGCCCTGGCCA 62.515 61.111 27.61 4.71 41.09 5.36
1388 1579 3.991051 CCACTCTCGCACGGTGGT 61.991 66.667 10.60 0.00 43.72 4.16
1432 1623 3.743636 TCGTCGTCAGCGGCATCA 61.744 61.111 1.45 0.00 43.91 3.07
1611 1802 1.473434 GCGTACCAGCTATTCCTTGCT 60.473 52.381 0.00 0.00 40.54 3.91
1727 1918 2.121538 TGTCTCCATCCTCGAGCCG 61.122 63.158 6.99 0.00 0.00 5.52
1770 1961 1.600916 GTCCACTGTCCTTGGTGCC 60.601 63.158 0.00 0.00 35.42 5.01
1815 2006 1.001503 TGGGATTTGGGTCCATGCC 59.998 57.895 0.00 0.00 40.17 4.40
1830 2021 5.239525 GGTCCATGCCTATATTGACAAGAAC 59.760 44.000 0.00 0.00 0.00 3.01
1848 2039 2.057137 ACCGGATGAATCACAATGGG 57.943 50.000 9.46 0.00 0.00 4.00
1906 2097 2.700773 GGAAGCATTGACACGGCCC 61.701 63.158 0.00 0.00 0.00 5.80
1968 2159 3.254166 ACTCATGGACAACAGTGATTTGC 59.746 43.478 0.00 0.00 0.00 3.68
1977 2168 1.073025 AGTGATTTGCGGACTGGCA 59.927 52.632 0.00 0.00 42.12 4.92
2023 2214 1.744522 TGCGGATGTTTCACATGATGG 59.255 47.619 0.00 0.00 39.27 3.51
2046 2237 2.513897 GGTGGTATGCGCCCTGAC 60.514 66.667 4.18 0.00 0.00 3.51
2052 2243 1.067416 TATGCGCCCTGACGATGTC 59.933 57.895 4.18 0.00 34.06 3.06
2169 2360 4.202567 ACACCCAAGATTGAACACTATGGT 60.203 41.667 0.00 0.00 0.00 3.55
2187 2378 2.290260 TGGTTGCATGGTCGATCTTCTT 60.290 45.455 0.00 0.00 0.00 2.52
2438 2629 4.171234 AGAGAGAGGAGGGAAATGAACAA 58.829 43.478 0.00 0.00 0.00 2.83
2546 2737 3.943381 CCTCTGCATGCTGAGATTTGTAA 59.057 43.478 40.37 14.36 42.28 2.41
2594 2785 1.447838 ATACAGGTTGAGGCACGCG 60.448 57.895 3.53 3.53 0.00 6.01
2612 2803 1.892819 CGAAGCTCTTCTGCTGGGGA 61.893 60.000 7.88 0.00 43.24 4.81
2613 2804 0.545646 GAAGCTCTTCTGCTGGGGAT 59.454 55.000 2.55 0.00 43.24 3.85
2614 2805 0.998145 AAGCTCTTCTGCTGGGGATT 59.002 50.000 0.00 0.00 43.24 3.01
2648 2839 3.198853 AGGAGCTGAGGGTGAAGATTTAC 59.801 47.826 0.00 0.00 0.00 2.01
2684 2877 1.227823 GTAGGTGGTGTGCTGTGCA 60.228 57.895 0.00 0.00 35.60 4.57
2687 2880 2.195567 GGTGGTGTGCTGTGCATGT 61.196 57.895 0.00 0.00 41.91 3.21
2692 2885 2.263021 TGTGCTGTGCATGTGCTCC 61.263 57.895 6.55 0.00 41.91 4.70
2703 2896 1.068055 CATGTGCTCCTTCCTTTGTGC 60.068 52.381 0.00 0.00 0.00 4.57
2719 2912 2.590007 GCGCCAGCATACAGAGGG 60.590 66.667 0.00 0.00 44.35 4.30
2720 2913 2.590007 CGCCAGCATACAGAGGGC 60.590 66.667 0.00 0.00 41.20 5.19
2721 2914 2.203266 GCCAGCATACAGAGGGCC 60.203 66.667 0.00 0.00 38.70 5.80
2722 2915 2.750657 GCCAGCATACAGAGGGCCT 61.751 63.158 5.25 5.25 38.70 5.19
2724 2917 1.340399 CCAGCATACAGAGGGCCTGA 61.340 60.000 12.95 0.00 45.78 3.86
2725 2918 0.106335 CAGCATACAGAGGGCCTGAG 59.894 60.000 12.95 5.33 45.78 3.35
2803 3000 2.484264 ACCGAGTAAATGTTGAAGCTGC 59.516 45.455 0.00 0.00 0.00 5.25
2807 3004 4.388773 CGAGTAAATGTTGAAGCTGCTGTA 59.611 41.667 1.35 0.00 0.00 2.74
2840 3037 3.758554 ACTTCAATTCAGAATCCCGTTGG 59.241 43.478 0.00 0.00 0.00 3.77
2846 3043 1.626321 TCAGAATCCCGTTGGTAAGCA 59.374 47.619 0.00 0.00 0.00 3.91
2848 3045 2.420022 CAGAATCCCGTTGGTAAGCAAG 59.580 50.000 0.00 0.00 0.00 4.01
2849 3046 2.039879 AGAATCCCGTTGGTAAGCAAGT 59.960 45.455 0.00 0.00 0.00 3.16
2906 3107 4.218200 TCCTACATTCTTGCACCAATGTTG 59.782 41.667 21.72 19.44 39.69 3.33
2941 3142 1.275291 CCGTGGTACTGTCAGTGGATT 59.725 52.381 16.03 0.00 0.00 3.01
2944 3145 3.306088 CGTGGTACTGTCAGTGGATTTCT 60.306 47.826 16.03 0.00 0.00 2.52
2963 3164 2.025981 TCTCCAACCAATCATCCCTGTG 60.026 50.000 0.00 0.00 0.00 3.66
3003 3204 0.656495 ACTGTATATCGCGACGCACG 60.656 55.000 21.35 4.34 45.66 5.34
3018 3219 1.717937 CACGCTCATGGCTTAGTGC 59.282 57.895 0.00 0.00 39.13 4.40
3047 3248 3.531207 CGAGATGGAGAGGGCGCA 61.531 66.667 10.83 0.00 0.00 6.09
3054 3255 1.078143 GGAGAGGGCGCAACAATCT 60.078 57.895 10.83 4.09 0.00 2.40
3055 3256 1.092345 GGAGAGGGCGCAACAATCTC 61.092 60.000 10.83 13.22 36.50 2.75
3057 3258 0.254178 AGAGGGCGCAACAATCTCAT 59.746 50.000 10.83 0.00 0.00 2.90
3058 3259 1.098050 GAGGGCGCAACAATCTCATT 58.902 50.000 10.83 0.00 0.00 2.57
3059 3260 1.474077 GAGGGCGCAACAATCTCATTT 59.526 47.619 10.83 0.00 0.00 2.32
3071 3272 4.142534 ACAATCTCATTTGTCGCAGGAATG 60.143 41.667 0.00 0.00 34.83 2.67
3140 3341 5.008331 ACTGTCTAGTGGATACTGACGAAA 58.992 41.667 0.00 0.00 37.57 3.46
3162 3363 7.966753 CGAAATTATATGGATTCTGAGCATTGG 59.033 37.037 0.00 0.00 0.00 3.16
3164 3365 8.716674 AATTATATGGATTCTGAGCATTGGTT 57.283 30.769 0.00 0.00 0.00 3.67
3198 3399 8.615211 GCATATTGTCATCTATCAAACAGTCAA 58.385 33.333 0.00 0.00 0.00 3.18
3224 3425 1.018752 TGTCCAATCGTGATGTGGCG 61.019 55.000 6.32 0.00 32.10 5.69
3226 3427 2.397754 CCAATCGTGATGTGGCGCA 61.398 57.895 10.83 1.92 0.00 6.09
3231 3432 2.679934 CGTGATGTGGCGCATGTGT 61.680 57.895 19.78 0.00 38.06 3.72
3270 3471 3.691342 CGCCCCCTCGTCTGTTCA 61.691 66.667 0.00 0.00 0.00 3.18
3481 3683 6.926280 TCACGCAATTCAACAAATATGTTC 57.074 33.333 0.00 0.00 46.78 3.18
3496 3698 9.187455 ACAAATATGTTCGTGACATTTAAAACC 57.813 29.630 11.30 0.00 46.80 3.27
3509 3712 7.974501 TGACATTTAAAACCAATTGTACAACGT 59.025 29.630 11.22 4.74 0.00 3.99
3530 3733 6.915349 ACGTAAAAATTGCTAGCATGGTTTA 58.085 32.000 20.13 18.06 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 7.797062 TGGTATGGACTGTTATTGCTACATAA 58.203 34.615 0.00 0.00 0.00 1.90
79 84 3.379880 GCATTGGCAAGGCTTGGA 58.620 55.556 27.72 0.00 40.72 3.53
116 121 1.521450 CCCAGTCCAAGCTGTTGCAG 61.521 60.000 0.00 0.00 42.74 4.41
258 263 3.056821 GCCACTTCCACCTGGTTTTAATC 60.057 47.826 0.00 0.00 36.34 1.75
259 264 2.897326 GCCACTTCCACCTGGTTTTAAT 59.103 45.455 0.00 0.00 36.34 1.40
260 265 2.091555 AGCCACTTCCACCTGGTTTTAA 60.092 45.455 0.00 0.00 36.34 1.52
261 266 1.497286 AGCCACTTCCACCTGGTTTTA 59.503 47.619 0.00 0.00 36.34 1.52
262 267 0.261696 AGCCACTTCCACCTGGTTTT 59.738 50.000 0.00 0.00 36.34 2.43
270 275 1.610886 GGGTTCTGTAGCCACTTCCAC 60.611 57.143 0.00 0.00 44.15 4.02
300 309 2.690497 TCTCTGCCTCGTCTTATTCCTG 59.310 50.000 0.00 0.00 0.00 3.86
311 323 0.953727 CTCAGGATCTCTCTGCCTCG 59.046 60.000 0.00 0.00 32.63 4.63
377 392 7.987458 CAGTCTATGCCTTGGAAATTAACTCTA 59.013 37.037 0.00 0.00 0.00 2.43
379 394 6.599638 ACAGTCTATGCCTTGGAAATTAACTC 59.400 38.462 0.00 0.00 0.00 3.01
432 467 7.978975 TGAAATAATCCTTTTGGCCGATAAAAG 59.021 33.333 16.30 16.30 42.13 2.27
453 488 3.490060 AGGGGCCTAAACCAATGAAAT 57.510 42.857 0.84 0.00 0.00 2.17
454 489 4.618378 ATAGGGGCCTAAACCAATGAAA 57.382 40.909 0.84 0.00 31.73 2.69
455 490 4.285863 CAATAGGGGCCTAAACCAATGAA 58.714 43.478 0.84 0.00 31.73 2.57
456 491 3.909732 CAATAGGGGCCTAAACCAATGA 58.090 45.455 0.84 0.00 31.73 2.57
481 516 4.149598 TGCCTCGGCTCAGAGTATTATTA 58.850 43.478 9.65 0.00 42.51 0.98
482 517 2.965831 TGCCTCGGCTCAGAGTATTATT 59.034 45.455 9.65 0.00 42.51 1.40
483 518 2.598565 TGCCTCGGCTCAGAGTATTAT 58.401 47.619 9.65 0.00 42.51 1.28
485 520 1.195115 TTGCCTCGGCTCAGAGTATT 58.805 50.000 9.65 0.00 42.51 1.89
486 521 1.137872 CTTTGCCTCGGCTCAGAGTAT 59.862 52.381 9.65 0.00 42.51 2.12
489 524 0.177604 ATCTTTGCCTCGGCTCAGAG 59.822 55.000 9.65 0.00 42.51 3.35
491 526 0.177604 AGATCTTTGCCTCGGCTCAG 59.822 55.000 9.65 5.19 42.51 3.35
492 527 1.137086 GTAGATCTTTGCCTCGGCTCA 59.863 52.381 9.65 0.00 42.51 4.26
493 528 1.137086 TGTAGATCTTTGCCTCGGCTC 59.863 52.381 9.65 0.00 42.51 4.70
495 530 1.291132 GTGTAGATCTTTGCCTCGGC 58.709 55.000 0.00 0.00 42.35 5.54
496 531 2.672961 TGTGTAGATCTTTGCCTCGG 57.327 50.000 0.00 0.00 0.00 4.63
497 532 3.849911 TCTTGTGTAGATCTTTGCCTCG 58.150 45.455 0.00 0.00 0.00 4.63
552 621 4.166011 GGGCATCGCAGTCGCAAC 62.166 66.667 0.00 0.00 38.40 4.17
564 662 6.613699 TGATTCTGTCAAATTATAGGGGCAT 58.386 36.000 0.00 0.00 32.78 4.40
691 850 5.221641 TGACTCCAAGAATCTTCTTTTCGGA 60.222 40.000 2.45 6.32 44.70 4.55
693 852 5.106908 GGTGACTCCAAGAATCTTCTTTTCG 60.107 44.000 2.45 0.00 44.70 3.46
694 853 6.000840 AGGTGACTCCAAGAATCTTCTTTTC 58.999 40.000 2.45 0.00 39.83 2.29
726 887 3.121030 CGCTCCCACCTCTTTGCG 61.121 66.667 0.00 0.00 37.57 4.85
728 889 3.121030 CGCGCTCCCACCTCTTTG 61.121 66.667 5.56 0.00 0.00 2.77
750 914 4.148825 CCGGGCCTCCTCTGTTCG 62.149 72.222 0.84 0.00 0.00 3.95
751 915 2.683933 TCCGGGCCTCCTCTGTTC 60.684 66.667 0.84 0.00 0.00 3.18
752 916 2.685380 CTCCGGGCCTCCTCTGTT 60.685 66.667 0.84 0.00 0.00 3.16
753 917 4.787280 CCTCCGGGCCTCCTCTGT 62.787 72.222 0.84 0.00 0.00 3.41
754 918 3.849836 TATTCCTCCGGGCCTCCTCTG 62.850 61.905 0.84 0.00 0.00 3.35
755 919 1.665948 TATTCCTCCGGGCCTCCTCT 61.666 60.000 0.84 0.00 0.00 3.69
766 930 1.009389 CGCCGCGAATCTATTCCTCC 61.009 60.000 8.23 0.00 33.28 4.30
896 1087 0.531974 CACATCGGGGTGTTATCGGG 60.532 60.000 0.00 0.00 34.09 5.14
932 1123 1.106944 AAAACACGTTGAGGGGGCAG 61.107 55.000 0.00 0.00 0.00 4.85
951 1142 5.395546 CCAGCCCCGTAATAACTACTGTAAA 60.396 44.000 0.00 0.00 0.00 2.01
952 1143 4.099881 CCAGCCCCGTAATAACTACTGTAA 59.900 45.833 0.00 0.00 0.00 2.41
953 1144 3.638160 CCAGCCCCGTAATAACTACTGTA 59.362 47.826 0.00 0.00 0.00 2.74
1205 1396 1.463674 GGGCATTTCATCGAACAGGT 58.536 50.000 0.00 0.00 0.00 4.00
1206 1397 0.378257 CGGGCATTTCATCGAACAGG 59.622 55.000 0.00 0.00 0.00 4.00
1388 1579 3.467226 GGACCATCCTTCCCGCGA 61.467 66.667 8.23 0.00 32.53 5.87
1432 1623 0.389948 GAGACGAACATGTCCGGCTT 60.390 55.000 16.15 0.00 45.23 4.35
1495 1686 0.612174 TCGAACACCCTCCTGGAGAG 60.612 60.000 25.18 14.87 42.83 3.20
1602 1793 1.071385 CTCCTCGGCATAGCAAGGAAT 59.929 52.381 11.77 0.00 40.02 3.01
1611 1802 1.121407 CCACATCCCTCCTCGGCATA 61.121 60.000 0.00 0.00 0.00 3.14
1815 2006 7.657354 TGATTCATCCGGTTCTTGTCAATATAG 59.343 37.037 0.00 0.00 0.00 1.31
1830 2021 1.949525 GTCCCATTGTGATTCATCCGG 59.050 52.381 0.00 0.00 0.00 5.14
1848 2039 6.155827 GTCTATCAAGCATCTATCCAGTGTC 58.844 44.000 0.00 0.00 0.00 3.67
1906 2097 0.595095 GCCTTCTCAAACACCTGCAG 59.405 55.000 6.78 6.78 0.00 4.41
1968 2159 1.996786 GACCATGCATTGCCAGTCCG 61.997 60.000 6.12 0.00 0.00 4.79
2023 2214 1.166531 GGGCGCATACCACCATCTTC 61.167 60.000 10.83 0.00 0.00 2.87
2082 2273 1.147153 GTCCACTAGCCCTCCATGC 59.853 63.158 0.00 0.00 0.00 4.06
2169 2360 2.358957 CCAAGAAGATCGACCATGCAA 58.641 47.619 0.00 0.00 0.00 4.08
2208 2399 5.185249 TGTCTTTATCATCCTATACGCCTCC 59.815 44.000 0.00 0.00 0.00 4.30
2214 2405 8.621532 TTGGCATTGTCTTTATCATCCTATAC 57.378 34.615 0.00 0.00 0.00 1.47
2280 2471 1.080298 GCTGCCATGGACTTTGCAC 60.080 57.895 18.40 0.00 0.00 4.57
2415 2606 4.947883 TGTTCATTTCCCTCCTCTCTCTA 58.052 43.478 0.00 0.00 0.00 2.43
2418 2609 3.009584 GGTTGTTCATTTCCCTCCTCTCT 59.990 47.826 0.00 0.00 0.00 3.10
2438 2629 2.235898 GGAGTCTTCTTCATCTGCAGGT 59.764 50.000 15.13 2.68 0.00 4.00
2546 2737 1.609061 CCTCGACAAACTCCAGCACAT 60.609 52.381 0.00 0.00 0.00 3.21
2594 2785 0.545646 ATCCCCAGCAGAAGAGCTTC 59.454 55.000 2.03 2.03 43.70 3.86
2624 2815 0.967887 TCTTCACCCTCAGCTCCTCG 60.968 60.000 0.00 0.00 0.00 4.63
2626 2817 1.963985 AATCTTCACCCTCAGCTCCT 58.036 50.000 0.00 0.00 0.00 3.69
2633 2824 3.198853 AGGCTCAGTAAATCTTCACCCTC 59.801 47.826 0.00 0.00 0.00 4.30
2648 2839 1.613836 ACTGAAAGGCAAAGGCTCAG 58.386 50.000 7.85 7.85 42.44 3.35
2684 2877 1.251251 GCACAAAGGAAGGAGCACAT 58.749 50.000 0.00 0.00 0.00 3.21
2687 2880 2.260869 GCGCACAAAGGAAGGAGCA 61.261 57.895 0.30 0.00 0.00 4.26
2692 2885 2.256461 GCTGGCGCACAAAGGAAG 59.744 61.111 10.83 0.00 35.78 3.46
2703 2896 2.590007 GCCCTCTGTATGCTGGCG 60.590 66.667 0.00 0.00 31.55 5.69
2719 2912 4.279420 ACCAACTGATTTTTCTTCTCAGGC 59.721 41.667 4.06 0.00 40.55 4.85
2720 2913 5.532406 TGACCAACTGATTTTTCTTCTCAGG 59.468 40.000 4.06 0.00 40.55 3.86
2721 2914 6.624352 TGACCAACTGATTTTTCTTCTCAG 57.376 37.500 0.00 0.00 41.69 3.35
2722 2915 8.690203 TTATGACCAACTGATTTTTCTTCTCA 57.310 30.769 0.00 0.00 0.00 3.27
2725 2918 9.065871 CGAATTATGACCAACTGATTTTTCTTC 57.934 33.333 0.00 0.00 0.00 2.87
2749 2946 8.035394 AGCTTATTAACTTCATGAGTTCTTCGA 58.965 33.333 12.05 0.00 45.40 3.71
2803 3000 2.153645 TGAAGTGCACAATGGCTACAG 58.846 47.619 21.04 0.00 34.04 2.74
2807 3004 2.629137 TGAATTGAAGTGCACAATGGCT 59.371 40.909 21.04 0.00 37.89 4.75
2848 3045 1.239968 CCAGTTCCAGCTCAGGCAAC 61.240 60.000 0.00 0.00 41.70 4.17
2849 3046 1.073722 CCAGTTCCAGCTCAGGCAA 59.926 57.895 0.00 0.00 41.70 4.52
2906 3107 2.180017 CGGCTTGGCTGATGCAAC 59.820 61.111 0.00 0.00 41.91 4.17
2929 3130 3.077359 GGTTGGAGAAATCCACTGACAG 58.923 50.000 0.00 0.00 39.90 3.51
2941 3142 2.649312 ACAGGGATGATTGGTTGGAGAA 59.351 45.455 0.00 0.00 0.00 2.87
2944 3145 1.991813 TCACAGGGATGATTGGTTGGA 59.008 47.619 0.00 0.00 0.00 3.53
2963 3164 5.977129 CAGTTAGGTTGTGTTTGGTTTGATC 59.023 40.000 0.00 0.00 0.00 2.92
3003 3204 0.740868 TGACGCACTAAGCCATGAGC 60.741 55.000 0.00 0.00 41.38 4.26
3010 3211 2.218759 CGATAACCATGACGCACTAAGC 59.781 50.000 0.00 0.00 40.87 3.09
3018 3219 3.253432 TCTCCATCTCGATAACCATGACG 59.747 47.826 0.00 0.00 0.00 4.35
3047 3248 3.411446 TCCTGCGACAAATGAGATTGTT 58.589 40.909 0.00 0.00 43.31 2.83
3054 3255 4.735985 CAAATCATTCCTGCGACAAATGA 58.264 39.130 8.41 8.41 41.99 2.57
3055 3256 3.305094 GCAAATCATTCCTGCGACAAATG 59.695 43.478 0.00 0.00 0.00 2.32
3057 3258 2.557924 AGCAAATCATTCCTGCGACAAA 59.442 40.909 0.00 0.00 41.05 2.83
3058 3259 2.161855 AGCAAATCATTCCTGCGACAA 58.838 42.857 0.00 0.00 41.05 3.18
3059 3260 1.825090 AGCAAATCATTCCTGCGACA 58.175 45.000 0.00 0.00 41.05 4.35
3071 3272 5.310720 ACTTTTCCGGTTCATAGCAAATC 57.689 39.130 0.00 0.00 0.00 2.17
3113 3314 6.097412 TCGTCAGTATCCACTAGACAGTACTA 59.903 42.308 0.00 0.00 34.85 1.82
3114 3315 5.105023 TCGTCAGTATCCACTAGACAGTACT 60.105 44.000 0.00 0.00 34.85 2.73
3115 3316 5.114780 TCGTCAGTATCCACTAGACAGTAC 58.885 45.833 0.00 0.00 34.85 2.73
3140 3341 8.118976 CAACCAATGCTCAGAATCCATATAAT 57.881 34.615 0.00 0.00 0.00 1.28
3198 3399 6.563422 CCACATCACGATTGGACAAAATATT 58.437 36.000 0.00 0.00 31.39 1.28
3334 3536 5.736813 TGCCACGTAGATTAGGTTTTACAT 58.263 37.500 0.00 0.00 0.00 2.29
3341 3543 6.229936 TCTAAAATGCCACGTAGATTAGGT 57.770 37.500 0.00 0.00 0.00 3.08
3342 3544 7.548196 TTTCTAAAATGCCACGTAGATTAGG 57.452 36.000 0.00 0.00 0.00 2.69
3453 3655 7.384660 ACATATTTGTTGAATTGCGTGAACAAT 59.615 29.630 0.00 0.00 37.94 2.71
3454 3656 6.699204 ACATATTTGTTGAATTGCGTGAACAA 59.301 30.769 0.00 0.00 36.71 2.83
3481 3683 7.916128 TGTACAATTGGTTTTAAATGTCACG 57.084 32.000 10.83 0.00 0.00 4.35
3495 3697 7.401484 AGCAATTTTTACGTTGTACAATTGG 57.599 32.000 12.26 7.11 33.89 3.16
3496 3698 8.153411 GCTAGCAATTTTTACGTTGTACAATTG 58.847 33.333 12.26 10.31 35.58 2.32


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

AutoCloner maintained by Alex Coulton.