Multiple sequence alignment - TraesCS1B01G213400

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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 TraesCS1B01G213400 chr1B 100.000 3455 0 0 1 3455 387309083 387305629 0.000000e+00 6381
1 TraesCS1B01G213400 chr1D 93.596 2842 117 28 1 2822 285058203 285055407 0.000000e+00 4180
2 TraesCS1B01G213400 chr1D 95.622 571 22 2 2886 3455 285055391 285054823 0.000000e+00 913
3 TraesCS1B01G213400 chr1D 83.333 114 15 3 2847 2957 285055578 285055466 6.100000e-18 102
4 TraesCS1B01G213400 chr1A 92.021 3008 153 44 1 2987 356476949 356474008 0.000000e+00 4145
5 TraesCS1B01G213400 chr1A 96.970 429 12 1 3028 3455 356474004 356473576 0.000000e+00 719


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 TraesCS1B01G213400 chr1B 387305629 387309083 3454 True 6381.000000 6381 100.000000 1 3455 1 chr1B.!!$R1 3454
1 TraesCS1B01G213400 chr1D 285054823 285058203 3380 True 1731.666667 4180 90.850333 1 3455 3 chr1D.!!$R1 3454
2 TraesCS1B01G213400 chr1A 356473576 356476949 3373 True 2432.000000 4145 94.495500 1 3455 2 chr1A.!!$R1 3454

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
989 1018 0.322975 CTCACAGGCTAGGTTGCTGT 59.677 55.0 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2629 2663 0.319297 GCCAACCTTGCTGCAAAGAG 60.319 55.0 17.27 10.87 0.0 2.85 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
157 164 3.372554 GAGTAGCCTCCCACACCGC 62.373 68.421 0.00 0.00 0.00 5.68
213 223 0.811915 CCACACGACCACACCAAAAA 59.188 50.000 0.00 0.00 0.00 1.94
297 310 4.405756 TTCCAGGTTACTCTCTCTCCTT 57.594 45.455 0.00 0.00 0.00 3.36
298 311 3.970842 TCCAGGTTACTCTCTCTCCTTC 58.029 50.000 0.00 0.00 0.00 3.46
397 411 0.667792 GATTAGCATCGCCCTCGTCC 60.668 60.000 0.00 0.00 36.96 4.79
412 426 3.802685 CCTCGTCCAATTCGATTTAGGAC 59.197 47.826 20.17 20.17 44.05 3.85
415 429 3.528532 GTCCAATTCGATTTAGGACGGT 58.471 45.455 17.69 0.00 39.33 4.83
416 430 3.308866 GTCCAATTCGATTTAGGACGGTG 59.691 47.826 17.69 0.00 39.33 4.94
417 431 3.055675 TCCAATTCGATTTAGGACGGTGT 60.056 43.478 0.00 0.00 0.00 4.16
419 433 3.604875 ATTCGATTTAGGACGGTGTGT 57.395 42.857 0.00 0.00 0.00 3.72
420 434 2.357327 TCGATTTAGGACGGTGTGTG 57.643 50.000 0.00 0.00 0.00 3.82
421 435 1.614903 TCGATTTAGGACGGTGTGTGT 59.385 47.619 0.00 0.00 0.00 3.72
422 436 1.990563 CGATTTAGGACGGTGTGTGTC 59.009 52.381 0.00 0.00 35.60 3.67
423 437 2.352421 CGATTTAGGACGGTGTGTGTCT 60.352 50.000 0.00 0.00 36.58 3.41
432 448 3.157949 TGTGTGTCTGGCCGGTCA 61.158 61.111 9.26 9.26 0.00 4.02
439 455 1.079405 TCTGGCCGGTCAATTCGTC 60.079 57.895 11.40 0.00 0.00 4.20
445 461 0.524816 CCGGTCAATTCGTCGATCGT 60.525 55.000 15.94 0.00 40.80 3.73
505 526 2.135933 GATTCCGAGCAAATCTACCGG 58.864 52.381 0.00 0.00 41.36 5.28
535 556 3.771216 CCCCTATCATTTCCCCTGATTG 58.229 50.000 0.00 0.00 35.12 2.67
587 608 8.266392 TGGAATGAAATTAATTTTGCACCATC 57.734 30.769 14.45 8.39 36.07 3.51
645 673 7.820578 AGAGCCGATACTAATTAGTAACAGT 57.179 36.000 25.21 11.84 41.64 3.55
646 674 7.873910 AGAGCCGATACTAATTAGTAACAGTC 58.126 38.462 25.21 17.72 41.64 3.51
685 713 0.679505 GTGGGTCTCTGTGTAGTGCA 59.320 55.000 0.00 0.00 0.00 4.57
697 725 8.311109 TCTCTGTGTAGTGCATGTTTTTATAGA 58.689 33.333 0.00 0.00 0.00 1.98
703 731 9.448438 TGTAGTGCATGTTTTTATAGATGAGTT 57.552 29.630 0.00 0.00 0.00 3.01
805 833 9.956720 GGATGAAATTTAATCAGACTGTATTGG 57.043 33.333 16.02 0.00 0.00 3.16
824 852 4.665833 TGGGTTAATCTGTCTATCCACG 57.334 45.455 0.00 0.00 0.00 4.94
825 853 4.283337 TGGGTTAATCTGTCTATCCACGA 58.717 43.478 0.00 0.00 0.00 4.35
836 864 5.842907 TGTCTATCCACGACCTATCAATTG 58.157 41.667 0.00 0.00 0.00 2.32
863 891 7.389330 TGTCGGTGCTAAAGAAGATTGAATTTA 59.611 33.333 0.00 0.00 0.00 1.40
922 951 2.056481 GACGATTGGCAGCTGCATCC 62.056 60.000 37.63 22.24 44.36 3.51
964 993 4.411540 ACCATCTCCTGACTCATATTGCTT 59.588 41.667 0.00 0.00 0.00 3.91
965 994 4.996122 CCATCTCCTGACTCATATTGCTTC 59.004 45.833 0.00 0.00 0.00 3.86
967 996 4.293494 TCTCCTGACTCATATTGCTTCCT 58.707 43.478 0.00 0.00 0.00 3.36
989 1018 0.322975 CTCACAGGCTAGGTTGCTGT 59.677 55.000 0.00 0.00 0.00 4.40
1166 1195 3.231818 CTCCGGTATGTCCTTACCATCT 58.768 50.000 0.00 0.00 41.53 2.90
1183 1212 5.538877 ACCATCTACCCCTCTTTATCTGAA 58.461 41.667 0.00 0.00 0.00 3.02
1184 1213 6.153924 ACCATCTACCCCTCTTTATCTGAAT 58.846 40.000 0.00 0.00 0.00 2.57
1185 1214 7.313731 ACCATCTACCCCTCTTTATCTGAATA 58.686 38.462 0.00 0.00 0.00 1.75
1186 1215 7.964293 ACCATCTACCCCTCTTTATCTGAATAT 59.036 37.037 0.00 0.00 0.00 1.28
1299 1332 2.637025 CCCAACTTTGACACGGCG 59.363 61.111 4.80 4.80 0.00 6.46
1314 1347 0.515564 CGGCGTTTCGAGTTTTCCAT 59.484 50.000 0.00 0.00 0.00 3.41
1537 1570 3.206639 CCTCCCCCAGGTAATTATGGTTT 59.793 47.826 4.74 0.00 37.53 3.27
1559 1592 3.250762 TCTCTTTTCCTCGTGCATTTGTG 59.749 43.478 0.00 0.00 0.00 3.33
1560 1593 2.948979 TCTTTTCCTCGTGCATTTGTGT 59.051 40.909 0.00 0.00 0.00 3.72
1563 1596 4.481930 TTTCCTCGTGCATTTGTGTTAG 57.518 40.909 0.00 0.00 0.00 2.34
1564 1597 3.394674 TCCTCGTGCATTTGTGTTAGA 57.605 42.857 0.00 0.00 0.00 2.10
1565 1598 3.734463 TCCTCGTGCATTTGTGTTAGAA 58.266 40.909 0.00 0.00 0.00 2.10
1566 1599 4.323417 TCCTCGTGCATTTGTGTTAGAAT 58.677 39.130 0.00 0.00 0.00 2.40
1567 1600 4.154015 TCCTCGTGCATTTGTGTTAGAATG 59.846 41.667 0.00 0.00 36.56 2.67
1568 1601 4.083324 CCTCGTGCATTTGTGTTAGAATGT 60.083 41.667 0.00 0.00 36.03 2.71
1569 1602 5.431420 TCGTGCATTTGTGTTAGAATGTT 57.569 34.783 0.00 0.00 36.03 2.71
1570 1603 5.826586 TCGTGCATTTGTGTTAGAATGTTT 58.173 33.333 0.00 0.00 36.03 2.83
1571 1604 6.960468 TCGTGCATTTGTGTTAGAATGTTTA 58.040 32.000 0.00 0.00 36.03 2.01
1572 1605 7.075121 TCGTGCATTTGTGTTAGAATGTTTAG 58.925 34.615 0.00 0.00 36.03 1.85
1606 1639 6.086222 CCATCCTTTGTGTTAGAATGTTTCG 58.914 40.000 0.00 0.00 34.02 3.46
1612 1645 7.749126 CCTTTGTGTTAGAATGTTTCGTTATCC 59.251 37.037 0.00 0.00 34.02 2.59
1625 1658 1.466866 CGTTATCCTGTCGAACGAGCA 60.467 52.381 0.28 0.00 46.78 4.26
1705 1738 8.644619 CAAGCTTCACATGATATTTTTGAACTG 58.355 33.333 0.00 0.00 0.00 3.16
1800 1833 6.269769 TCATTTACCTGATTTTGCTTTCCCTT 59.730 34.615 0.00 0.00 0.00 3.95
2118 2151 0.114364 TCTGGAGGGAGCACACTACA 59.886 55.000 0.00 0.00 38.17 2.74
2133 2166 5.030295 CACACTACAAAGTTTTCAGTGCAG 58.970 41.667 19.41 12.29 40.17 4.41
2232 2265 0.034059 CCCTTACCATAGCTGCCTCG 59.966 60.000 0.00 0.00 0.00 4.63
2345 2378 3.551259 GGATTGAAGCTCCGGTGAA 57.449 52.632 7.92 0.00 0.00 3.18
2364 2397 1.439543 ACCTGAAAACTGGGAGCTCT 58.560 50.000 14.64 0.00 0.00 4.09
2439 2472 2.047179 GCCCTGGTTCCGACTGTC 60.047 66.667 0.00 0.00 0.00 3.51
2465 2498 4.933400 TGCCATGTATTGATGAGATGATCG 59.067 41.667 0.00 0.00 0.00 3.69
2482 2515 3.737172 GTGCTTCATTGCGGCGGT 61.737 61.111 9.78 0.00 35.36 5.68
2580 2614 2.922283 ACATTGGATTCTTCTCCCCACT 59.078 45.455 0.00 0.00 34.12 4.00
2581 2615 4.111577 ACATTGGATTCTTCTCCCCACTA 58.888 43.478 0.00 0.00 34.12 2.74
2582 2616 4.728860 ACATTGGATTCTTCTCCCCACTAT 59.271 41.667 0.00 0.00 34.12 2.12
2583 2617 5.163152 ACATTGGATTCTTCTCCCCACTATC 60.163 44.000 0.00 0.00 34.12 2.08
2584 2618 4.007581 TGGATTCTTCTCCCCACTATCA 57.992 45.455 0.00 0.00 34.12 2.15
2586 2620 4.349048 TGGATTCTTCTCCCCACTATCATG 59.651 45.833 0.00 0.00 34.12 3.07
2587 2621 4.594920 GGATTCTTCTCCCCACTATCATGA 59.405 45.833 0.00 0.00 0.00 3.07
2588 2622 5.279910 GGATTCTTCTCCCCACTATCATGAG 60.280 48.000 0.09 0.00 0.00 2.90
2598 2632 2.941064 CACTATCATGAGTTGGGTGCAG 59.059 50.000 0.09 0.00 0.00 4.41
2618 2652 6.646240 GTGCAGTCAATAAATTTCACCATGTT 59.354 34.615 0.00 0.00 0.00 2.71
2629 2663 4.664150 TTCACCATGTTCTTTGGTTTCC 57.336 40.909 0.00 0.00 45.19 3.13
2656 2690 0.964358 AGCAAGGTTGGCTGATGAGC 60.964 55.000 0.00 0.00 45.40 4.26
2671 2705 5.994054 GCTGATGAGCCTATTTCTATGTTCA 59.006 40.000 0.00 0.00 39.57 3.18
2672 2706 6.147492 GCTGATGAGCCTATTTCTATGTTCAG 59.853 42.308 0.00 0.00 39.57 3.02
2673 2707 7.365497 TGATGAGCCTATTTCTATGTTCAGA 57.635 36.000 0.00 0.00 0.00 3.27
2675 2709 7.712639 TGATGAGCCTATTTCTATGTTCAGAAC 59.287 37.037 6.32 6.32 34.31 3.01
2676 2710 6.946340 TGAGCCTATTTCTATGTTCAGAACA 58.054 36.000 18.42 18.42 46.94 3.18
2677 2711 6.818644 TGAGCCTATTTCTATGTTCAGAACAC 59.181 38.462 18.49 1.89 45.50 3.32
2678 2712 6.711277 AGCCTATTTCTATGTTCAGAACACA 58.289 36.000 18.49 6.07 45.50 3.72
2679 2713 7.168219 AGCCTATTTCTATGTTCAGAACACAA 58.832 34.615 18.49 8.84 45.50 3.33
2680 2714 7.831193 AGCCTATTTCTATGTTCAGAACACAAT 59.169 33.333 18.49 14.96 45.50 2.71
2681 2715 8.462016 GCCTATTTCTATGTTCAGAACACAATT 58.538 33.333 18.49 5.28 45.50 2.32
2712 2746 2.036346 GCTTGGTCAAAAGCCAGAACAT 59.964 45.455 0.00 0.00 45.60 2.71
2715 2749 5.567423 GCTTGGTCAAAAGCCAGAACATAAT 60.567 40.000 0.00 0.00 45.60 1.28
2721 2755 6.317391 GTCAAAAGCCAGAACATAATAGCTCT 59.683 38.462 0.00 0.00 0.00 4.09
2765 2801 5.048013 GGCCAACAAAGTCTACTGCTAAAAT 60.048 40.000 0.00 0.00 0.00 1.82
2766 2802 6.447162 GCCAACAAAGTCTACTGCTAAAATT 58.553 36.000 0.00 0.00 0.00 1.82
2771 2807 7.807680 ACAAAGTCTACTGCTAAAATTAGTGC 58.192 34.615 2.42 0.00 33.32 4.40
2822 2858 4.618489 GCAGTTGCTTGCTGTGTAAAATAG 59.382 41.667 0.00 0.00 40.89 1.73
2823 2859 5.762045 CAGTTGCTTGCTGTGTAAAATAGT 58.238 37.500 0.00 0.00 0.00 2.12
2824 2860 6.567701 GCAGTTGCTTGCTGTGTAAAATAGTA 60.568 38.462 0.00 0.00 40.89 1.82
2825 2861 6.797033 CAGTTGCTTGCTGTGTAAAATAGTAC 59.203 38.462 0.00 0.00 0.00 2.73
2826 2862 6.710744 AGTTGCTTGCTGTGTAAAATAGTACT 59.289 34.615 0.00 0.00 0.00 2.73
2827 2863 7.876068 AGTTGCTTGCTGTGTAAAATAGTACTA 59.124 33.333 4.77 4.77 0.00 1.82
2828 2864 7.827819 TGCTTGCTGTGTAAAATAGTACTAG 57.172 36.000 8.85 0.00 0.00 2.57
2829 2865 7.383687 TGCTTGCTGTGTAAAATAGTACTAGT 58.616 34.615 8.85 2.42 0.00 2.57
2830 2866 8.525316 TGCTTGCTGTGTAAAATAGTACTAGTA 58.475 33.333 8.85 0.00 0.00 1.82
2920 2957 0.874390 AACACAACAGCTACGCCATG 59.126 50.000 0.00 0.00 0.00 3.66
2987 3024 6.204688 ACATCATCTTTGTTTGACGAAAGCTA 59.795 34.615 0.00 0.00 0.00 3.32
3006 3043 2.111878 AGCGACTGCCTGCTGTTT 59.888 55.556 3.12 0.00 44.31 2.83
3023 3060 5.530543 TGCTGTTTGAAATACATGTGACTGA 59.469 36.000 9.11 0.00 0.00 3.41
3144 3181 2.359975 GGAACCGGCTCAAGTGGG 60.360 66.667 7.26 0.00 0.00 4.61
3147 3184 0.539986 GAACCGGCTCAAGTGGGATA 59.460 55.000 0.00 0.00 0.00 2.59
3168 3205 0.596082 TGCTGTCTTCGTCGATCACA 59.404 50.000 0.00 1.11 0.00 3.58
3171 3208 0.955905 TGTCTTCGTCGATCACACCA 59.044 50.000 0.00 0.00 0.00 4.17
3189 3226 4.279922 ACACCATCGATGATACCGTAATCA 59.720 41.667 26.86 0.01 40.07 2.57
3252 3289 3.451402 TTCTCTACCTGCTCCAGTGTA 57.549 47.619 0.00 0.00 0.00 2.90
3261 3298 2.035469 TCCAGTGTACGCCCCGTA 59.965 61.111 1.98 0.00 41.54 4.02
3270 3307 1.952102 TACGCCCCGTAAAGCCTGAG 61.952 60.000 0.00 0.00 39.44 3.35
3324 3361 0.112412 TTTCCTTGGCTTGGACCTCC 59.888 55.000 0.00 0.00 32.65 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.485346 GACCTGTGACCCGGCCAAA 62.485 63.158 2.24 0.00 0.00 3.28
165 175 1.288439 CGAGATGAGGATGGCCGAG 59.712 63.158 0.00 0.00 39.96 4.63
168 178 2.031768 GGCGAGATGAGGATGGCC 59.968 66.667 0.00 0.00 0.00 5.36
169 179 1.301558 CAGGCGAGATGAGGATGGC 60.302 63.158 0.00 0.00 0.00 4.40
170 180 0.249784 CACAGGCGAGATGAGGATGG 60.250 60.000 0.00 0.00 0.00 3.51
171 181 0.879400 GCACAGGCGAGATGAGGATG 60.879 60.000 0.00 0.00 0.00 3.51
172 182 1.445095 GCACAGGCGAGATGAGGAT 59.555 57.895 0.00 0.00 0.00 3.24
213 223 4.115199 GGCGGGCAGGTCTGGATT 62.115 66.667 0.00 0.00 0.00 3.01
242 252 3.844090 GGAGGCAGACGAGGAGGC 61.844 72.222 0.00 0.00 0.00 4.70
243 253 2.043450 AGGAGGCAGACGAGGAGG 60.043 66.667 0.00 0.00 0.00 4.30
244 254 1.077068 AGAGGAGGCAGACGAGGAG 60.077 63.158 0.00 0.00 0.00 3.69
245 255 1.077357 GAGAGGAGGCAGACGAGGA 60.077 63.158 0.00 0.00 0.00 3.71
246 256 2.124693 GGAGAGGAGGCAGACGAGG 61.125 68.421 0.00 0.00 0.00 4.63
297 310 2.648613 GATGAGAGGAGGCGGGAGGA 62.649 65.000 0.00 0.00 0.00 3.71
298 311 2.123077 ATGAGAGGAGGCGGGAGG 60.123 66.667 0.00 0.00 0.00 4.30
397 411 3.682858 ACACACCGTCCTAAATCGAATTG 59.317 43.478 0.00 0.00 0.00 2.32
415 429 2.050836 ATTGACCGGCCAGACACACA 62.051 55.000 0.00 0.00 0.00 3.72
416 430 0.889186 AATTGACCGGCCAGACACAC 60.889 55.000 0.00 0.00 0.00 3.82
417 431 0.605319 GAATTGACCGGCCAGACACA 60.605 55.000 0.00 0.00 0.00 3.72
419 433 1.375396 CGAATTGACCGGCCAGACA 60.375 57.895 0.00 0.00 0.00 3.41
420 434 1.359459 GACGAATTGACCGGCCAGAC 61.359 60.000 0.00 0.00 0.00 3.51
421 435 1.079405 GACGAATTGACCGGCCAGA 60.079 57.895 0.00 0.00 0.00 3.86
422 436 2.452813 CGACGAATTGACCGGCCAG 61.453 63.158 0.00 0.00 0.00 4.85
423 437 2.233605 ATCGACGAATTGACCGGCCA 62.234 55.000 0.00 0.00 0.00 5.36
432 448 2.959275 GCAGGACGATCGACGAATT 58.041 52.632 24.34 0.00 45.77 2.17
445 461 1.550072 TGTGATGTTCATCTCGCAGGA 59.450 47.619 12.94 0.00 0.00 3.86
505 526 3.425659 GAAATGATAGGGGCAAGGATCC 58.574 50.000 2.48 2.48 0.00 3.36
645 673 2.203280 CCAACCCAGCAACCACGA 60.203 61.111 0.00 0.00 0.00 4.35
646 674 2.124693 AACCAACCCAGCAACCACG 61.125 57.895 0.00 0.00 0.00 4.94
697 725 5.349817 GTGATTGAGTCATCGAACAACTCAT 59.650 40.000 21.31 14.40 46.31 2.90
703 731 3.676291 TGGTGATTGAGTCATCGAACA 57.324 42.857 0.00 0.00 41.06 3.18
750 778 3.808728 CATATGGTCGGATTGGTTGACT 58.191 45.455 0.00 0.00 33.21 3.41
805 833 4.341520 AGGTCGTGGATAGACAGATTAACC 59.658 45.833 0.00 0.00 40.20 2.85
824 852 2.351726 GCACCGACACAATTGATAGGTC 59.648 50.000 13.59 12.23 0.00 3.85
825 853 2.027192 AGCACCGACACAATTGATAGGT 60.027 45.455 13.59 12.26 0.00 3.08
836 864 3.994392 TCAATCTTCTTTAGCACCGACAC 59.006 43.478 0.00 0.00 0.00 3.67
863 891 7.095060 CCATGATCGGAACTTATGAAATCGATT 60.095 37.037 4.39 4.39 36.26 3.34
899 928 2.437359 AGCTGCCAATCGTCCTGC 60.437 61.111 0.00 0.00 0.00 4.85
904 933 2.117156 GGATGCAGCTGCCAATCGT 61.117 57.895 34.64 14.09 41.18 3.73
949 978 5.021033 AGTGAGGAAGCAATATGAGTCAG 57.979 43.478 0.00 0.00 0.00 3.51
964 993 0.409876 ACCTAGCCTGTGAGTGAGGA 59.590 55.000 0.00 0.00 31.48 3.71
965 994 1.066573 CAACCTAGCCTGTGAGTGAGG 60.067 57.143 0.00 0.00 0.00 3.86
967 996 0.321671 GCAACCTAGCCTGTGAGTGA 59.678 55.000 0.00 0.00 0.00 3.41
989 1018 5.867903 AAAGGAATCCATGTGAACAACAA 57.132 34.783 0.61 0.00 43.61 2.83
1299 1332 2.552315 TCTGCCATGGAAAACTCGAAAC 59.448 45.455 18.40 0.00 0.00 2.78
1314 1347 2.391724 GAACAACCCCGTCTCTGCCA 62.392 60.000 0.00 0.00 0.00 4.92
1537 1570 3.250762 CACAAATGCACGAGGAAAAGAGA 59.749 43.478 0.00 0.00 0.00 3.10
1565 1598 9.927668 CAAAGGATGGTAATTTGAACTAAACAT 57.072 29.630 0.00 0.00 36.28 2.71
1566 1599 8.919145 ACAAAGGATGGTAATTTGAACTAAACA 58.081 29.630 4.08 0.00 37.37 2.83
1567 1600 9.191995 CACAAAGGATGGTAATTTGAACTAAAC 57.808 33.333 4.08 0.00 37.37 2.01
1568 1601 8.919145 ACACAAAGGATGGTAATTTGAACTAAA 58.081 29.630 4.08 0.00 37.37 1.85
1569 1602 8.472007 ACACAAAGGATGGTAATTTGAACTAA 57.528 30.769 4.08 0.00 37.37 2.24
1570 1603 8.472007 AACACAAAGGATGGTAATTTGAACTA 57.528 30.769 4.08 0.00 37.37 2.24
1571 1604 6.976934 ACACAAAGGATGGTAATTTGAACT 57.023 33.333 4.08 0.00 37.37 3.01
1572 1605 8.573035 TCTAACACAAAGGATGGTAATTTGAAC 58.427 33.333 4.08 0.00 37.37 3.18
1590 1623 6.932400 ACAGGATAACGAAACATTCTAACACA 59.068 34.615 0.00 0.00 0.00 3.72
1606 1639 2.273370 TGCTCGTTCGACAGGATAAC 57.727 50.000 0.00 0.00 0.00 1.89
1612 1645 4.105486 TCATCTAAATGCTCGTTCGACAG 58.895 43.478 0.00 0.00 32.58 3.51
1800 1833 6.248433 AGACTGGCCTTTATTCTGAAATGAA 58.752 36.000 3.32 0.00 0.00 2.57
2118 2151 4.244862 CAAACCACTGCACTGAAAACTTT 58.755 39.130 0.00 0.00 0.00 2.66
2232 2265 5.652014 TGAACCAATTGTCTGACCCAATATC 59.348 40.000 5.17 0.00 32.40 1.63
2345 2378 1.072965 CAGAGCTCCCAGTTTTCAGGT 59.927 52.381 10.93 0.00 0.00 4.00
2439 2472 2.837498 TCTCATCAATACATGGCACCG 58.163 47.619 0.00 0.00 0.00 4.94
2465 2498 3.267597 AACCGCCGCAATGAAGCAC 62.268 57.895 0.00 0.00 0.00 4.40
2482 2515 6.768483 TGGAACTCTGATACAATTCTCACAA 58.232 36.000 0.00 0.00 0.00 3.33
2532 2566 6.567891 GCCAGTAATCCTTTACAAGACACAAC 60.568 42.308 0.00 0.00 40.20 3.32
2580 2614 2.571202 TGACTGCACCCAACTCATGATA 59.429 45.455 0.00 0.00 0.00 2.15
2581 2615 1.352017 TGACTGCACCCAACTCATGAT 59.648 47.619 0.00 0.00 0.00 2.45
2582 2616 0.764271 TGACTGCACCCAACTCATGA 59.236 50.000 0.00 0.00 0.00 3.07
2583 2617 1.608055 TTGACTGCACCCAACTCATG 58.392 50.000 0.00 0.00 0.00 3.07
2584 2618 2.592102 ATTGACTGCACCCAACTCAT 57.408 45.000 0.00 0.00 0.00 2.90
2586 2620 5.391312 AATTTATTGACTGCACCCAACTC 57.609 39.130 0.00 0.00 0.00 3.01
2587 2621 5.304101 TGAAATTTATTGACTGCACCCAACT 59.696 36.000 0.00 0.00 0.00 3.16
2588 2622 5.405269 GTGAAATTTATTGACTGCACCCAAC 59.595 40.000 0.00 0.00 0.00 3.77
2598 2632 8.711457 CCAAAGAACATGGTGAAATTTATTGAC 58.289 33.333 0.00 0.00 33.08 3.18
2618 2652 2.362077 GCTGCAAAGAGGAAACCAAAGA 59.638 45.455 0.00 0.00 0.00 2.52
2629 2663 0.319297 GCCAACCTTGCTGCAAAGAG 60.319 55.000 17.27 10.87 0.00 2.85
2653 2687 6.818644 TGTGTTCTGAACATAGAAATAGGCTC 59.181 38.462 24.44 8.81 44.35 4.70
2656 2690 9.994432 GAATTGTGTTCTGAACATAGAAATAGG 57.006 33.333 24.44 0.00 44.35 2.57
2671 2705 6.480981 CCAAGCAAATGAAAGAATTGTGTTCT 59.519 34.615 0.00 0.00 0.00 3.01
2672 2706 6.258507 ACCAAGCAAATGAAAGAATTGTGTTC 59.741 34.615 0.00 0.00 0.00 3.18
2673 2707 6.114767 ACCAAGCAAATGAAAGAATTGTGTT 58.885 32.000 0.00 0.00 0.00 3.32
2675 2709 5.754406 TGACCAAGCAAATGAAAGAATTGTG 59.246 36.000 0.00 0.00 0.00 3.33
2676 2710 5.916318 TGACCAAGCAAATGAAAGAATTGT 58.084 33.333 0.00 0.00 0.00 2.71
2677 2711 6.847956 TTGACCAAGCAAATGAAAGAATTG 57.152 33.333 0.00 0.00 0.00 2.32
2678 2712 7.862512 TTTTGACCAAGCAAATGAAAGAATT 57.137 28.000 0.00 0.00 37.57 2.17
2679 2713 7.486802 CTTTTGACCAAGCAAATGAAAGAAT 57.513 32.000 0.00 0.00 37.57 2.40
2680 2714 6.907206 CTTTTGACCAAGCAAATGAAAGAA 57.093 33.333 0.00 0.00 37.57 2.52
2712 2746 7.938490 TGCATTTGGTATGATTGAGAGCTATTA 59.062 33.333 0.00 0.00 0.00 0.98
2715 2749 5.683681 TGCATTTGGTATGATTGAGAGCTA 58.316 37.500 0.00 0.00 0.00 3.32
2721 2755 3.428725 GCCGTTGCATTTGGTATGATTGA 60.429 43.478 0.00 0.00 37.47 2.57
2765 2801 7.147143 TGTCAAAACAAAGTTGTAGCACTAA 57.853 32.000 0.00 0.00 41.31 2.24
2766 2802 6.745159 TGTCAAAACAAAGTTGTAGCACTA 57.255 33.333 0.00 0.00 41.31 2.74
2815 2851 8.141835 TCGTCGCATGTACTAGTACTATTTTA 57.858 34.615 28.56 11.85 37.00 1.52
2822 2858 2.601741 GCCTCGTCGCATGTACTAGTAC 60.602 54.545 23.58 23.58 36.63 2.73
2823 2859 1.600957 GCCTCGTCGCATGTACTAGTA 59.399 52.381 0.00 0.00 0.00 1.82
2824 2860 0.381089 GCCTCGTCGCATGTACTAGT 59.619 55.000 0.00 0.00 0.00 2.57
2825 2861 0.663688 AGCCTCGTCGCATGTACTAG 59.336 55.000 0.00 0.00 0.00 2.57
2826 2862 1.871676 CTAGCCTCGTCGCATGTACTA 59.128 52.381 0.00 0.00 0.00 1.82
2827 2863 0.663688 CTAGCCTCGTCGCATGTACT 59.336 55.000 0.00 0.00 0.00 2.73
2828 2864 0.935366 GCTAGCCTCGTCGCATGTAC 60.935 60.000 2.29 0.00 0.00 2.90
2829 2865 1.101635 AGCTAGCCTCGTCGCATGTA 61.102 55.000 12.13 0.00 0.00 2.29
2830 2866 2.105128 GCTAGCCTCGTCGCATGT 59.895 61.111 2.29 0.00 0.00 3.21
2920 2957 2.147958 TCTGCCGTTACATTTGGTGTC 58.852 47.619 0.00 0.00 42.29 3.67
2931 2968 4.679662 GCAGTAGACTTTATCTGCCGTTA 58.320 43.478 4.90 0.00 44.84 3.18
2954 2991 7.482743 CGTCAAACAAAGATGATGTAATCCTTG 59.517 37.037 0.00 0.00 44.73 3.61
3006 3043 4.002982 GCCTGTCAGTCACATGTATTTCA 58.997 43.478 0.00 0.00 33.23 2.69
3023 3060 6.317642 CGATGAGATATACTAAGCTAGCCTGT 59.682 42.308 12.13 10.40 0.00 4.00
3144 3181 4.147306 GTGATCGACGAAGACAGCATTATC 59.853 45.833 0.00 0.00 0.00 1.75
3147 3184 2.263077 GTGATCGACGAAGACAGCATT 58.737 47.619 0.00 0.00 0.00 3.56
3168 3205 5.221362 TGTTGATTACGGTATCATCGATGGT 60.221 40.000 24.61 20.86 34.67 3.55
3171 3208 4.923871 GCTGTTGATTACGGTATCATCGAT 59.076 41.667 0.00 0.00 34.67 3.59
3180 3217 2.301870 TCTTGAGGCTGTTGATTACGGT 59.698 45.455 0.00 0.00 35.43 4.83
3189 3226 0.768221 TGGGTCCTCTTGAGGCTGTT 60.768 55.000 11.61 0.00 0.00 3.16
3252 3289 3.310860 CTCAGGCTTTACGGGGCGT 62.311 63.158 0.00 0.00 44.35 5.68
3270 3307 1.071385 AGGAATGTCATCCGGCTGATC 59.929 52.381 11.82 5.08 44.60 2.92


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

AutoCloner maintained by Alex Coulton.