Multiple sequence alignment - TraesCS3B01G305300

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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 TraesCS3B01G305300 chr3B 100.000 4834 0 0 1 4834 490594504 490599337 0.000000e+00 8927.0
1 TraesCS3B01G305300 chr3A 92.971 3585 153 44 2 3538 500973230 500976763 0.000000e+00 5132.0
2 TraesCS3B01G305300 chr3A 89.861 937 45 21 3928 4833 500977070 500977987 0.000000e+00 1158.0
3 TraesCS3B01G305300 chr3A 93.930 313 11 1 3568 3880 500976766 500977070 2.630000e-127 466.0
4 TraesCS3B01G305300 chr3D 92.700 2904 104 32 717 3558 376162198 376165055 0.000000e+00 4089.0
5 TraesCS3B01G305300 chr3D 93.025 1104 50 5 3679 4761 376165049 376166146 0.000000e+00 1587.0
6 TraesCS3B01G305300 chr3D 87.316 544 36 17 2 535 376161648 376162168 4.170000e-165 592.0
7 TraesCS3B01G305300 chr3D 86.842 76 8 2 3537 3610 418394817 418394892 3.100000e-12 84.2
8 TraesCS3B01G305300 chrUn 87.654 81 9 1 3528 3607 50872445 50872365 5.150000e-15 93.5
9 TraesCS3B01G305300 chrUn 87.654 81 9 1 3528 3607 50890357 50890277 5.150000e-15 93.5
10 TraesCS3B01G305300 chr6B 89.041 73 6 2 3521 3592 435313270 435313199 6.660000e-14 89.8
11 TraesCS3B01G305300 chr7A 82.353 102 16 2 3510 3609 41436918 41437019 2.400000e-13 87.9
12 TraesCS3B01G305300 chr1A 90.909 66 4 2 3528 3592 21623392 21623328 2.400000e-13 87.9
13 TraesCS3B01G305300 chr1A 100.000 28 0 0 657 684 8124879 8124906 9.000000e-03 52.8
14 TraesCS3B01G305300 chr2A 89.552 67 6 1 3525 3590 34328131 34328197 3.100000e-12 84.2
15 TraesCS3B01G305300 chr2A 92.857 56 3 1 3539 3593 611961475 611961420 4.010000e-11 80.5
16 TraesCS3B01G305300 chr4D 85.185 81 9 3 3528 3606 32768474 32768395 4.010000e-11 80.5


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 TraesCS3B01G305300 chr3B 490594504 490599337 4833 False 8927.000000 8927 100.000000 1 4834 1 chr3B.!!$F1 4833
1 TraesCS3B01G305300 chr3A 500973230 500977987 4757 False 2252.000000 5132 92.254000 2 4833 3 chr3A.!!$F1 4831
2 TraesCS3B01G305300 chr3D 376161648 376166146 4498 False 2089.333333 4089 91.013667 2 4761 3 chr3D.!!$F2 4759

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
944 963 0.041238 TTCCGGATCACTCCCTCAGT 59.959 55.0 4.15 0.0 38.45 3.41 F
1463 1486 0.188342 AAATGTTCTGCAGTGGGGGT 59.812 50.0 14.67 0.0 0.00 4.95 F
2493 2524 0.178767 ATTGCTGCGAGGTATGCTCA 59.821 50.0 0.00 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2435 2466 0.988832 TAAGCAGAAACCACCCCGAT 59.011 50.000 0.0 0.0 0.0 4.18 R
3413 3503 1.304713 CCCCTGCAAGCATTCCAGT 60.305 57.895 0.0 0.0 0.0 4.00 R
3863 3953 0.099791 AACGGCAACAACAACCTTCG 59.900 50.000 0.0 0.0 0.0 3.79 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
89 91 1.648467 GCCATTTCGACACTCCTGGC 61.648 60.000 0.00 0.00 42.00 4.85
95 97 4.148825 GACACTCCTGGCGCCGAT 62.149 66.667 23.90 1.33 0.00 4.18
109 111 0.515564 GCCGATGTGCGTAAACAACT 59.484 50.000 0.00 0.00 38.67 3.16
115 118 4.838642 CGATGTGCGTAAACAACTTTGTAG 59.161 41.667 0.00 0.00 36.30 2.74
243 256 3.550820 ACAGGGCATCGCAAATATTGTA 58.449 40.909 0.00 0.00 0.00 2.41
291 305 3.177228 GGGGAGATGTGTGATATAGCCT 58.823 50.000 0.00 0.00 0.00 4.58
304 318 5.349817 GTGATATAGCCTGATTTCCATGTCG 59.650 44.000 0.00 0.00 0.00 4.35
328 342 1.112950 GGCCCTGTCCTGTAGTAGTC 58.887 60.000 0.00 0.00 0.00 2.59
389 404 1.195115 TCGGTTCTGGGATCCTGAAG 58.805 55.000 12.58 7.47 41.01 3.02
535 551 8.782533 AAATTGTTCAGAATTTCGTGTTACTC 57.217 30.769 0.00 0.00 31.21 2.59
559 575 1.265236 CCTGCCAAGGGTAAATTGCA 58.735 50.000 0.00 0.00 40.27 4.08
607 623 7.498070 GAAGTTATCAATGCTTCGGAAAAAG 57.502 36.000 0.00 0.00 30.94 2.27
613 629 1.289066 GCTTCGGAAAAAGCCCACC 59.711 57.895 0.00 0.00 44.75 4.61
635 651 5.221682 ACCAGAAAACATGCATTTTGATGGA 60.222 36.000 24.90 0.00 37.27 3.41
655 671 4.161333 GGATGTTTGATGACTTTTGCTCG 58.839 43.478 0.00 0.00 0.00 5.03
659 675 6.552859 TGTTTGATGACTTTTGCTCGATTA 57.447 33.333 0.00 0.00 0.00 1.75
662 678 5.739752 TGATGACTTTTGCTCGATTATGG 57.260 39.130 0.00 0.00 0.00 2.74
666 682 3.686016 ACTTTTGCTCGATTATGGTGGT 58.314 40.909 0.00 0.00 0.00 4.16
669 685 3.627395 TTGCTCGATTATGGTGGTCTT 57.373 42.857 0.00 0.00 0.00 3.01
681 697 5.806654 ATGGTGGTCTTTTGCAATTTACT 57.193 34.783 0.00 0.00 0.00 2.24
710 726 2.181975 CCAAGCACATCCCCATTCTTT 58.818 47.619 0.00 0.00 0.00 2.52
767 783 4.463891 AGGCAATGGAGGTGAAAATTACTG 59.536 41.667 0.00 0.00 0.00 2.74
801 819 6.937436 ACTCGGAAATGTATATTTTCCCAC 57.063 37.500 17.78 0.00 36.66 4.61
942 961 1.414158 GATTCCGGATCACTCCCTCA 58.586 55.000 4.15 0.00 38.45 3.86
943 962 1.342819 GATTCCGGATCACTCCCTCAG 59.657 57.143 4.15 0.00 38.45 3.35
944 963 0.041238 TTCCGGATCACTCCCTCAGT 59.959 55.000 4.15 0.00 38.45 3.41
945 964 0.395862 TCCGGATCACTCCCTCAGTC 60.396 60.000 0.00 0.00 38.45 3.51
1367 1386 2.895372 CACGCCGGTAAGCCCATC 60.895 66.667 1.90 0.00 0.00 3.51
1373 1392 3.489513 GGTAAGCCCATCCCCGCT 61.490 66.667 0.00 0.00 36.74 5.52
1415 1438 2.882876 GCGTCTTAGTCCCGCTCA 59.117 61.111 0.00 0.00 43.81 4.26
1442 1465 5.559694 ATTTGTTTCATTTGTTTCGAGCG 57.440 34.783 0.00 0.00 0.00 5.03
1463 1486 0.188342 AAATGTTCTGCAGTGGGGGT 59.812 50.000 14.67 0.00 0.00 4.95
1465 1488 0.251341 ATGTTCTGCAGTGGGGGTTC 60.251 55.000 14.67 0.00 0.00 3.62
1531 1555 2.567615 GAGGACTCAGGGTTTCTAAGCA 59.432 50.000 0.00 0.00 0.00 3.91
1590 1619 1.761198 CACCTCATCTCATCTGCTCCA 59.239 52.381 0.00 0.00 0.00 3.86
1620 1649 2.275812 CGACAATCGTTTCGCGGC 60.276 61.111 6.13 0.00 41.72 6.53
1621 1650 2.857448 GACAATCGTTTCGCGGCA 59.143 55.556 6.13 0.00 41.72 5.69
1804 1833 5.753721 AGTCTTATTCTCTTGCCTCTTGT 57.246 39.130 0.00 0.00 0.00 3.16
1834 1863 5.602145 TCAATGAGTTGGGTTCTTGGAATTT 59.398 36.000 0.00 0.00 35.99 1.82
2047 2076 7.481275 ACAAAAATTTCACCATGTTCACATC 57.519 32.000 0.00 0.00 33.61 3.06
2054 2083 6.990341 TTCACCATGTTCACATCTTCATAG 57.010 37.500 0.00 0.00 33.61 2.23
2101 2132 6.831353 ACCCCTTTTCTAATTTTTGTTTTGGG 59.169 34.615 0.00 0.00 0.00 4.12
2244 2275 8.737168 TTTTAAGTCCATATCAGGATTGAGTG 57.263 34.615 0.00 0.00 40.42 3.51
2260 2291 1.552792 GAGTGCTGCTAGTTTCCTCCT 59.447 52.381 0.00 0.00 0.00 3.69
2265 2296 3.149981 GCTGCTAGTTTCCTCCTTGTTT 58.850 45.455 0.00 0.00 0.00 2.83
2276 2307 5.255397 TCCTCCTTGTTTACCATCAACAT 57.745 39.130 0.00 0.00 34.13 2.71
2282 2313 6.016360 TCCTTGTTTACCATCAACATGAACTG 60.016 38.462 0.00 0.00 34.13 3.16
2288 2319 4.579869 ACCATCAACATGAACTGTACCTC 58.420 43.478 0.00 0.00 36.98 3.85
2306 2337 3.136626 ACCTCTTGGAGTTGTACTTTGCT 59.863 43.478 0.00 0.00 37.04 3.91
2311 2342 6.354130 TCTTGGAGTTGTACTTTGCTAAGTT 58.646 36.000 18.49 0.29 41.85 2.66
2312 2343 7.502696 TCTTGGAGTTGTACTTTGCTAAGTTA 58.497 34.615 18.49 6.27 41.85 2.24
2319 2350 8.154856 AGTTGTACTTTGCTAAGTTATCAAGGA 58.845 33.333 18.49 0.00 41.85 3.36
2326 2357 6.614694 TGCTAAGTTATCAAGGACCAAGTA 57.385 37.500 0.00 0.00 0.00 2.24
2435 2466 4.263550 TGCTTACTTTAGGTATTGGTGGCA 60.264 41.667 0.00 0.00 0.00 4.92
2492 2523 1.303309 AATTGCTGCGAGGTATGCTC 58.697 50.000 0.00 0.00 0.00 4.26
2493 2524 0.178767 ATTGCTGCGAGGTATGCTCA 59.821 50.000 0.00 0.00 0.00 4.26
2495 2526 0.249615 TGCTGCGAGGTATGCTCATC 60.250 55.000 0.00 0.00 0.00 2.92
2496 2527 1.280886 GCTGCGAGGTATGCTCATCG 61.281 60.000 6.77 6.77 38.19 3.84
2497 2528 0.312102 CTGCGAGGTATGCTCATCGA 59.688 55.000 13.08 0.00 37.35 3.59
2498 2529 0.312102 TGCGAGGTATGCTCATCGAG 59.688 55.000 13.08 0.00 37.35 4.04
2499 2530 0.312416 GCGAGGTATGCTCATCGAGT 59.688 55.000 13.08 0.00 37.35 4.18
2500 2531 1.269309 GCGAGGTATGCTCATCGAGTT 60.269 52.381 13.08 0.00 37.35 3.01
2501 2532 2.799917 GCGAGGTATGCTCATCGAGTTT 60.800 50.000 13.08 0.00 37.35 2.66
2503 2534 3.489229 CGAGGTATGCTCATCGAGTTTCA 60.489 47.826 5.58 0.00 37.35 2.69
2504 2535 4.626042 GAGGTATGCTCATCGAGTTTCAT 58.374 43.478 0.00 0.00 31.39 2.57
2505 2536 5.028549 AGGTATGCTCATCGAGTTTCATT 57.971 39.130 0.00 0.00 31.39 2.57
2506 2537 5.053145 AGGTATGCTCATCGAGTTTCATTC 58.947 41.667 0.00 0.00 31.39 2.67
2507 2538 4.811024 GGTATGCTCATCGAGTTTCATTCA 59.189 41.667 0.00 0.00 31.39 2.57
2508 2539 4.871993 ATGCTCATCGAGTTTCATTCAC 57.128 40.909 0.00 0.00 31.39 3.18
2509 2540 3.930336 TGCTCATCGAGTTTCATTCACT 58.070 40.909 0.00 0.00 31.39 3.41
2510 2541 4.318332 TGCTCATCGAGTTTCATTCACTT 58.682 39.130 0.00 0.00 31.39 3.16
2531 2594 8.441608 TCACTTTTGATGTTTGTTCATTTTGTG 58.558 29.630 0.00 0.00 0.00 3.33
2545 2608 9.168451 TGTTCATTTTGTGTCTGAAACTAAGTA 57.832 29.630 0.00 0.00 31.21 2.24
2550 2613 7.900782 TTTGTGTCTGAAACTAAGTATAGGC 57.099 36.000 0.00 0.00 33.15 3.93
2551 2614 6.852420 TGTGTCTGAAACTAAGTATAGGCT 57.148 37.500 0.00 0.00 33.15 4.58
2552 2615 7.949690 TGTGTCTGAAACTAAGTATAGGCTA 57.050 36.000 0.00 0.00 33.15 3.93
2555 2618 9.819267 GTGTCTGAAACTAAGTATAGGCTATTT 57.181 33.333 13.08 4.53 33.15 1.40
2598 2662 2.415491 GGCCTTCTTTGTTACCGATTGC 60.415 50.000 0.00 0.00 0.00 3.56
2630 2694 5.122396 AGTTTGCGTCTTGTTCATTCTATCC 59.878 40.000 0.00 0.00 0.00 2.59
2653 2717 2.126071 GTGCTGCCTTGCATGCTG 60.126 61.111 20.33 11.54 45.23 4.41
2782 2846 5.059833 GCAGCTGCCAAGTATATACTTCTT 58.940 41.667 28.76 2.63 44.19 2.52
2823 2887 6.435430 TTGGATTTGGAATTACACTCGATG 57.565 37.500 0.00 0.00 0.00 3.84
2983 3068 7.962995 TCTGTCAGATAGATAGACAAACCTT 57.037 36.000 0.00 0.00 39.27 3.50
3067 3153 0.465287 CAAAGTTTGCCTGGCCTGTT 59.535 50.000 17.53 1.38 0.00 3.16
3117 3203 2.298610 CACTGGCAGCTCATGATTCAT 58.701 47.619 15.89 0.00 0.00 2.57
3134 3220 8.847196 CATGATTCATGAAGACAAATATGACCT 58.153 33.333 19.84 0.00 43.81 3.85
3158 3244 5.163141 TGTTCAGGTCCTTCCATTCAAGTTA 60.163 40.000 0.00 0.00 39.02 2.24
3273 3361 6.624352 ATGAATTATTCAATGGACACTCCG 57.376 37.500 11.88 0.00 43.95 4.63
3287 3375 5.128008 TGGACACTCCGTTGATTATATGACA 59.872 40.000 0.00 0.00 40.17 3.58
3399 3489 8.926715 TGTCTACTTGCTTGTAATACATGTAG 57.073 34.615 11.91 0.00 40.60 2.74
3548 3638 7.236432 TGCTTCCTCTGCCTCTAAATATAAGAT 59.764 37.037 0.00 0.00 0.00 2.40
3558 3648 9.455847 GCCTCTAAATATAAGATGTTTTTGCAG 57.544 33.333 0.00 0.00 0.00 4.41
3599 3689 9.614792 AAAAACGTCTTATATTTAGAGGCAGAT 57.385 29.630 0.00 0.00 32.26 2.90
3601 3691 6.159988 ACGTCTTATATTTAGAGGCAGATGC 58.840 40.000 0.00 0.00 41.14 3.91
3678 3768 3.310727 GCATGTTTGCCTTTTGCCT 57.689 47.368 0.00 0.00 43.38 4.75
3804 3894 3.942829 ACTCAAGCGATTCAGGAATCAA 58.057 40.909 18.98 1.97 45.60 2.57
3838 3928 0.379316 AACCGCGAAGTTTGAACACC 59.621 50.000 8.23 0.00 0.00 4.16
3863 3953 7.280769 CGTTTTGGCTAATAGAAAAACAAAGC 58.719 34.615 21.05 11.78 40.74 3.51
3880 3970 1.657181 GCGAAGGTTGTTGTTGCCG 60.657 57.895 0.00 0.00 0.00 5.69
3882 3972 0.099791 CGAAGGTTGTTGTTGCCGTT 59.900 50.000 0.00 0.00 0.00 4.44
3903 3993 2.214920 GGGGAGACTGGTCACCGTT 61.215 63.158 10.20 0.00 40.61 4.44
3947 4037 3.782523 AGCCTCATCCTTTCTTCACCATA 59.217 43.478 0.00 0.00 0.00 2.74
3953 4043 7.320443 TCATCCTTTCTTCACCATAATTTCG 57.680 36.000 0.00 0.00 0.00 3.46
3967 4057 2.927553 ATTTCGAAGTTGCCATCAGC 57.072 45.000 0.00 0.00 44.14 4.26
4061 4152 2.751259 CAGGCATGCATGAGTTTACACT 59.249 45.455 30.64 10.57 35.17 3.55
4204 4300 1.521010 CACGCTGAGGCTGAGGATG 60.521 63.158 2.44 0.00 36.09 3.51
4219 4315 4.953667 TGAGGATGCTGTCTGAACATATC 58.046 43.478 0.00 0.00 34.13 1.63
4281 4380 2.955660 TGTACAAAGGGAAGTTGGCAAG 59.044 45.455 0.00 0.00 0.00 4.01
4300 4399 4.791411 GCAAGCACAAATTCAAGTTCCGTA 60.791 41.667 0.00 0.00 0.00 4.02
4384 4483 5.560966 AACATTATTTACGCAAGGAGGTG 57.439 39.130 0.00 0.00 46.39 4.00
4433 4532 2.240493 ATAGTGCGGGCTGTCAATAC 57.760 50.000 0.00 0.00 0.00 1.89
4543 4654 5.006844 TGTGTTGTGTGGTGAGTTTAATACG 59.993 40.000 0.00 0.00 0.00 3.06
4749 4869 2.920724 GGAGTAGATGCCTCCTTTCC 57.079 55.000 0.00 0.00 44.29 3.13
4752 4872 3.034635 GAGTAGATGCCTCCTTTCCTCA 58.965 50.000 0.00 0.00 0.00 3.86
4761 4881 3.370953 GCCTCCTTTCCTCATCTTGCTAA 60.371 47.826 0.00 0.00 0.00 3.09
4762 4882 4.688321 GCCTCCTTTCCTCATCTTGCTAAT 60.688 45.833 0.00 0.00 0.00 1.73
4763 4883 5.455326 GCCTCCTTTCCTCATCTTGCTAATA 60.455 44.000 0.00 0.00 0.00 0.98
4764 4884 6.229733 CCTCCTTTCCTCATCTTGCTAATAG 58.770 44.000 0.00 0.00 0.00 1.73
4765 4885 6.042552 CCTCCTTTCCTCATCTTGCTAATAGA 59.957 42.308 0.00 0.00 0.00 1.98
4766 4886 7.256619 CCTCCTTTCCTCATCTTGCTAATAGAT 60.257 40.741 0.00 0.00 32.66 1.98
4767 4887 7.448420 TCCTTTCCTCATCTTGCTAATAGATG 58.552 38.462 6.53 6.53 46.65 2.90
4781 4901 6.438741 TGCTAATAGATGGTAGATTCCTCTGG 59.561 42.308 0.00 0.00 32.66 3.86
4782 4902 6.439058 GCTAATAGATGGTAGATTCCTCTGGT 59.561 42.308 0.00 0.00 32.66 4.00
4785 4905 3.208692 AGATGGTAGATTCCTCTGGTCCT 59.791 47.826 0.00 0.00 32.66 3.85
4786 4906 2.752030 TGGTAGATTCCTCTGGTCCTG 58.248 52.381 0.00 0.00 32.66 3.86
4787 4907 1.414550 GGTAGATTCCTCTGGTCCTGC 59.585 57.143 0.00 0.00 32.66 4.85
4788 4908 1.067821 GTAGATTCCTCTGGTCCTGCG 59.932 57.143 0.00 0.00 32.66 5.18
4799 4919 2.030412 TCCTGCGTGCGTTGATGT 59.970 55.556 0.00 0.00 0.00 3.06
4806 4926 0.516877 CGTGCGTTGATGTCATTGGT 59.483 50.000 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.747976 GCGGCGCCCTGTCAAAAT 61.748 61.111 23.58 0.00 0.00 1.82
19 20 0.401738 ACAGGTGCTGCAGTTGGTAT 59.598 50.000 16.64 0.00 34.37 2.73
94 96 5.065474 ACACTACAAAGTTGTTTACGCACAT 59.935 36.000 1.35 0.00 42.35 3.21
95 97 4.392445 ACACTACAAAGTTGTTTACGCACA 59.608 37.500 1.35 0.00 42.35 4.57
103 105 4.428615 AACGCAACACTACAAAGTTGTT 57.571 36.364 1.35 0.00 45.16 2.83
189 201 6.716628 AGGCAACAGAAGAGATAGATAGAGAG 59.283 42.308 0.00 0.00 41.41 3.20
190 202 6.489700 CAGGCAACAGAAGAGATAGATAGAGA 59.510 42.308 0.00 0.00 41.41 3.10
191 203 6.680810 CAGGCAACAGAAGAGATAGATAGAG 58.319 44.000 0.00 0.00 41.41 2.43
192 204 5.010516 GCAGGCAACAGAAGAGATAGATAGA 59.989 44.000 0.00 0.00 41.41 1.98
193 205 5.229423 GCAGGCAACAGAAGAGATAGATAG 58.771 45.833 0.00 0.00 41.41 2.08
194 206 4.261783 CGCAGGCAACAGAAGAGATAGATA 60.262 45.833 0.00 0.00 41.41 1.98
243 256 6.267070 CACAAAAATTGCAGCAAAAAGGAAT 58.733 32.000 12.97 0.00 0.00 3.01
291 305 1.819928 CCCACACGACATGGAAATCA 58.180 50.000 0.00 0.00 39.87 2.57
304 318 2.185310 CTACAGGACAGGGCCCACAC 62.185 65.000 27.56 14.10 0.00 3.82
328 342 5.394553 GCAGAATAAACCTTTCATCCCCTTG 60.395 44.000 0.00 0.00 0.00 3.61
420 435 0.813210 GGATGCTTTCAGCTCGAGGG 60.813 60.000 15.58 0.00 42.97 4.30
535 551 0.539438 TTTACCCTTGGCAGGTGCAG 60.539 55.000 8.58 0.00 44.36 4.41
565 581 2.465860 TCGACCCGATTGTGATGTTT 57.534 45.000 0.00 0.00 0.00 2.83
566 582 2.289444 ACTTCGACCCGATTGTGATGTT 60.289 45.455 0.00 0.00 35.23 2.71
567 583 1.275291 ACTTCGACCCGATTGTGATGT 59.725 47.619 0.00 0.00 35.23 3.06
577 593 2.550978 AGCATTGATAACTTCGACCCG 58.449 47.619 0.00 0.00 0.00 5.28
600 616 2.169561 TGTTTTCTGGTGGGCTTTTTCC 59.830 45.455 0.00 0.00 0.00 3.13
607 623 0.609662 ATGCATGTTTTCTGGTGGGC 59.390 50.000 0.00 0.00 0.00 5.36
613 629 6.370442 ACATCCATCAAAATGCATGTTTTCTG 59.630 34.615 0.00 0.00 40.65 3.02
635 651 5.633830 ATCGAGCAAAAGTCATCAAACAT 57.366 34.783 0.00 0.00 0.00 2.71
655 671 8.034804 AGTAAATTGCAAAAGACCACCATAATC 58.965 33.333 1.71 0.00 0.00 1.75
659 675 5.304101 TGAGTAAATTGCAAAAGACCACCAT 59.696 36.000 1.71 0.00 0.00 3.55
662 678 4.982295 GGTGAGTAAATTGCAAAAGACCAC 59.018 41.667 1.71 10.92 0.00 4.16
666 682 5.735922 GCACAGGTGAGTAAATTGCAAAAGA 60.736 40.000 1.71 0.00 0.00 2.52
669 685 3.243704 GGCACAGGTGAGTAAATTGCAAA 60.244 43.478 1.71 0.00 0.00 3.68
767 783 2.024176 TTTCCGAGTTGCATAGGAGC 57.976 50.000 0.00 0.00 33.89 4.70
801 819 1.915614 CTAGTTGCCACTTGCCAGCG 61.916 60.000 0.00 0.00 40.16 5.18
943 962 0.185175 GGAGAGGAGAGGAGAGGGAC 59.815 65.000 0.00 0.00 0.00 4.46
944 963 0.253868 TGGAGAGGAGAGGAGAGGGA 60.254 60.000 0.00 0.00 0.00 4.20
945 964 0.106217 GTGGAGAGGAGAGGAGAGGG 60.106 65.000 0.00 0.00 0.00 4.30
1119 1138 6.017523 GCTTCTTCTTGGGCAGTATTATCTTC 60.018 42.308 0.00 0.00 0.00 2.87
1442 1465 1.818674 CCCCCACTGCAGAACATTTAC 59.181 52.381 23.35 0.00 0.00 2.01
1463 1486 7.048512 GCTTGGTTAGGAGCTTAGAATAAGAA 58.951 38.462 0.76 0.00 36.01 2.52
1465 1488 6.349300 TGCTTGGTTAGGAGCTTAGAATAAG 58.651 40.000 0.00 0.00 39.60 1.73
1531 1555 2.406616 GGTCCATTGCGCGGTTGAT 61.407 57.895 8.83 0.00 0.00 2.57
1620 1649 3.665848 CGCACACCCTACGTTACAAAATG 60.666 47.826 0.00 0.00 0.00 2.32
1621 1650 2.481185 CGCACACCCTACGTTACAAAAT 59.519 45.455 0.00 0.00 0.00 1.82
1804 1833 3.074390 AGAACCCAACTCATTGACATCCA 59.926 43.478 0.00 0.00 38.15 3.41
1834 1863 4.284490 GGATCTATTGACAGCCTACATCCA 59.716 45.833 0.00 0.00 0.00 3.41
1993 2022 1.799994 CTCACATGCACACATCAACGA 59.200 47.619 0.00 0.00 32.87 3.85
2074 2104 9.567776 CCAAAACAAAAATTAGAAAAGGGGTAT 57.432 29.630 0.00 0.00 0.00 2.73
2075 2105 7.993758 CCCAAAACAAAAATTAGAAAAGGGGTA 59.006 33.333 0.00 0.00 0.00 3.69
2228 2259 3.741249 AGCAGCACTCAATCCTGATATG 58.259 45.455 0.00 0.00 0.00 1.78
2239 2270 1.276421 GGAGGAAACTAGCAGCACTCA 59.724 52.381 0.00 0.00 44.43 3.41
2244 2275 2.481289 ACAAGGAGGAAACTAGCAGC 57.519 50.000 0.00 0.00 44.43 5.25
2260 2291 6.707440 ACAGTTCATGTTGATGGTAAACAA 57.293 33.333 0.00 0.00 39.96 2.83
2265 2296 5.483937 AGAGGTACAGTTCATGTTGATGGTA 59.516 40.000 0.00 0.00 39.96 3.25
2276 2307 3.709653 ACAACTCCAAGAGGTACAGTTCA 59.290 43.478 0.00 0.00 29.65 3.18
2282 2313 4.451435 GCAAAGTACAACTCCAAGAGGTAC 59.549 45.833 0.00 0.00 35.68 3.34
2288 2319 6.619801 AACTTAGCAAAGTACAACTCCAAG 57.380 37.500 0.00 0.00 45.37 3.61
2306 2337 9.886132 GAAGAATACTTGGTCCTTGATAACTTA 57.114 33.333 0.00 0.00 36.39 2.24
2311 2342 8.146053 TCTTGAAGAATACTTGGTCCTTGATA 57.854 34.615 0.00 0.00 36.39 2.15
2312 2343 7.020827 TCTTGAAGAATACTTGGTCCTTGAT 57.979 36.000 0.00 0.00 36.39 2.57
2326 2357 9.932207 TTTGTGCATATTTCATTCTTGAAGAAT 57.068 25.926 14.34 14.34 45.23 2.40
2364 2395 7.201617 GCAAAACACCCTCAGTATCAGTAATAC 60.202 40.741 0.00 0.00 40.59 1.89
2435 2466 0.988832 TAAGCAGAAACCACCCCGAT 59.011 50.000 0.00 0.00 0.00 4.18
2492 2523 7.080099 ACATCAAAAGTGAATGAAACTCGATG 58.920 34.615 0.00 0.00 37.30 3.84
2493 2524 7.206981 ACATCAAAAGTGAATGAAACTCGAT 57.793 32.000 0.00 0.00 37.30 3.59
2495 2526 7.220683 ACAAACATCAAAAGTGAATGAAACTCG 59.779 33.333 0.00 0.00 37.30 4.18
2496 2527 8.411318 ACAAACATCAAAAGTGAATGAAACTC 57.589 30.769 0.00 0.00 37.30 3.01
2497 2528 8.776376 AACAAACATCAAAAGTGAATGAAACT 57.224 26.923 0.00 0.00 37.30 2.66
2498 2529 8.655092 TGAACAAACATCAAAAGTGAATGAAAC 58.345 29.630 0.00 0.00 37.30 2.78
2499 2530 8.768957 TGAACAAACATCAAAAGTGAATGAAA 57.231 26.923 0.00 0.00 37.30 2.69
2500 2531 8.945481 ATGAACAAACATCAAAAGTGAATGAA 57.055 26.923 0.00 0.00 37.30 2.57
2501 2532 8.945481 AATGAACAAACATCAAAAGTGAATGA 57.055 26.923 0.00 0.00 37.30 2.57
2503 2534 9.991388 CAAAATGAACAAACATCAAAAGTGAAT 57.009 25.926 0.00 0.00 37.30 2.57
2504 2535 8.997323 ACAAAATGAACAAACATCAAAAGTGAA 58.003 25.926 0.00 0.00 37.30 3.18
2505 2536 8.441608 CACAAAATGAACAAACATCAAAAGTGA 58.558 29.630 0.00 0.00 38.41 3.41
2506 2537 8.229137 ACACAAAATGAACAAACATCAAAAGTG 58.771 29.630 0.00 0.00 0.00 3.16
2507 2538 8.321650 ACACAAAATGAACAAACATCAAAAGT 57.678 26.923 0.00 0.00 0.00 2.66
2508 2539 8.658609 AGACACAAAATGAACAAACATCAAAAG 58.341 29.630 0.00 0.00 0.00 2.27
2509 2540 8.441608 CAGACACAAAATGAACAAACATCAAAA 58.558 29.630 0.00 0.00 0.00 2.44
2510 2541 7.816513 TCAGACACAAAATGAACAAACATCAAA 59.183 29.630 0.00 0.00 0.00 2.69
2547 2610 7.127339 TCCCAAGTTTGTCTAGATAAATAGCCT 59.873 37.037 16.49 7.31 0.00 4.58
2549 2612 8.778358 CATCCCAAGTTTGTCTAGATAAATAGC 58.222 37.037 16.49 5.63 0.00 2.97
2550 2613 9.838339 ACATCCCAAGTTTGTCTAGATAAATAG 57.162 33.333 16.49 9.98 0.00 1.73
2551 2614 9.613428 CACATCCCAAGTTTGTCTAGATAAATA 57.387 33.333 16.49 0.00 0.00 1.40
2552 2615 7.557719 CCACATCCCAAGTTTGTCTAGATAAAT 59.442 37.037 16.49 0.64 0.00 1.40
2555 2618 5.629133 GCCACATCCCAAGTTTGTCTAGATA 60.629 44.000 0.00 0.00 0.00 1.98
2556 2619 4.848357 CCACATCCCAAGTTTGTCTAGAT 58.152 43.478 0.00 0.00 0.00 1.98
2598 2662 3.074412 ACAAGACGCAAACTAATCCTGG 58.926 45.455 0.00 0.00 0.00 4.45
2630 2694 2.341176 GCAAGGCAGCACTTTGGG 59.659 61.111 0.00 0.00 0.00 4.12
2653 2717 7.206687 AGCTGAAGAGTAACTGATATTAGTGC 58.793 38.462 0.16 0.00 0.00 4.40
2782 2846 6.899393 ATCCAATTTGTAAGAGAAACAGCA 57.101 33.333 0.00 0.00 0.00 4.41
2864 2928 4.347000 AGTGTAGCTCTCCCAAACTAAACA 59.653 41.667 0.00 0.00 0.00 2.83
2903 2967 9.270640 GAGACTGCAATGTTATAAATGAGATCT 57.729 33.333 0.00 0.00 0.00 2.75
2925 2989 3.823304 AGCCTTCAATTTTGACCAGAGAC 59.177 43.478 0.00 0.00 36.83 3.36
2926 2990 4.104383 AGCCTTCAATTTTGACCAGAGA 57.896 40.909 0.00 0.00 36.83 3.10
3022 3107 8.092687 GGTGTAAGTCAAGACTAGAATGGTTTA 58.907 37.037 2.72 0.00 41.58 2.01
3067 3153 3.541632 GTGAAAACAGAACCAGGTCTGA 58.458 45.455 19.31 0.00 46.76 3.27
3117 3203 5.939883 CCTGAACAGGTCATATTTGTCTTCA 59.060 40.000 12.21 0.00 43.61 3.02
3134 3220 3.138283 ACTTGAATGGAAGGACCTGAACA 59.862 43.478 0.00 0.00 39.86 3.18
3158 3244 7.094032 GGCTGAAGGCAGATTAGCAATATAAAT 60.094 37.037 0.00 0.00 45.17 1.40
3217 3303 9.227777 GGATCATGATTCAGACAATGATCATTA 57.772 33.333 20.32 4.74 43.49 1.90
3218 3304 7.176865 GGGATCATGATTCAGACAATGATCATT 59.823 37.037 15.36 15.36 43.49 2.57
3219 3305 6.659668 GGGATCATGATTCAGACAATGATCAT 59.340 38.462 20.60 1.18 43.49 2.45
3220 3306 6.002082 GGGATCATGATTCAGACAATGATCA 58.998 40.000 20.60 0.00 43.49 2.92
3221 3307 6.239396 AGGGATCATGATTCAGACAATGATC 58.761 40.000 16.02 14.64 41.95 2.92
3222 3308 6.202202 AGGGATCATGATTCAGACAATGAT 57.798 37.500 16.02 0.44 37.89 2.45
3223 3309 5.641789 AGGGATCATGATTCAGACAATGA 57.358 39.130 16.02 0.00 35.62 2.57
3224 3310 6.996879 ACTTAGGGATCATGATTCAGACAATG 59.003 38.462 16.02 2.00 0.00 2.82
3225 3311 7.146715 ACTTAGGGATCATGATTCAGACAAT 57.853 36.000 16.02 0.00 0.00 2.71
3226 3312 6.566079 ACTTAGGGATCATGATTCAGACAA 57.434 37.500 16.02 3.09 0.00 3.18
3227 3313 7.510343 TCATACTTAGGGATCATGATTCAGACA 59.490 37.037 16.02 0.11 0.00 3.41
3228 3314 7.901029 TCATACTTAGGGATCATGATTCAGAC 58.099 38.462 16.02 0.00 0.00 3.51
3276 3364 9.809096 AAGGTGATCGACATATGTCATATAATC 57.191 33.333 30.15 22.46 44.99 1.75
3304 3392 8.792633 TGCTGCAAGTATGTTTTAGAAATAACT 58.207 29.630 0.00 0.00 35.30 2.24
3325 3415 2.549633 ACGCAGTCAAAATATGCTGC 57.450 45.000 5.42 5.42 46.54 5.25
3399 3489 9.403110 CAAGCATTCCAGTATAAATTTAGATGC 57.597 33.333 3.94 5.12 0.00 3.91
3413 3503 1.304713 CCCCTGCAAGCATTCCAGT 60.305 57.895 0.00 0.00 0.00 4.00
3523 3613 6.998802 TCTTATATTTAGAGGCAGAGGAAGC 58.001 40.000 0.00 0.00 0.00 3.86
3558 3648 7.216920 AGACGTTTTTGCAGTTAATTTGAAC 57.783 32.000 0.00 0.00 0.00 3.18
3601 3691 9.559958 ACGAAAATATTTCAGCAGAAAATACTG 57.440 29.630 8.45 0.00 46.06 2.74
3635 3725 8.836109 GCATGTAAGTTTTTGTTTGTTTGTTTC 58.164 29.630 0.00 0.00 0.00 2.78
3647 3737 5.236911 AGGCAAACATGCATGTAAGTTTTTG 59.763 36.000 31.55 27.73 40.80 2.44
3654 3744 3.497640 GCAAAAGGCAAACATGCATGTAA 59.502 39.130 31.55 0.00 40.70 2.41
3671 3761 9.478244 CTGCATCAGAAAAAGCAAAAGGCAAAA 62.478 37.037 0.00 0.00 38.27 2.44
3672 3762 8.106331 CTGCATCAGAAAAAGCAAAAGGCAAA 62.106 38.462 0.00 0.00 38.27 3.68
3673 3763 6.705287 CTGCATCAGAAAAAGCAAAAGGCAA 61.705 40.000 0.00 0.00 38.27 4.52
3674 3764 5.271549 CTGCATCAGAAAAAGCAAAAGGCA 61.272 41.667 0.00 0.00 38.27 4.75
3675 3765 3.132925 TGCATCAGAAAAAGCAAAAGGC 58.867 40.909 0.00 0.00 45.30 4.35
3676 3766 3.744426 CCTGCATCAGAAAAAGCAAAAGG 59.256 43.478 0.00 0.00 36.44 3.11
3677 3767 4.624015 TCCTGCATCAGAAAAAGCAAAAG 58.376 39.130 0.00 0.00 36.44 2.27
3678 3768 4.669206 TCCTGCATCAGAAAAAGCAAAA 57.331 36.364 0.00 0.00 36.44 2.44
3804 3894 2.365582 GCGGTTTCCAACATCAGGTAT 58.634 47.619 0.00 0.00 0.00 2.73
3838 3928 7.280769 GCTTTGTTTTTCTATTAGCCAAAACG 58.719 34.615 17.41 10.24 40.49 3.60
3863 3953 0.099791 AACGGCAACAACAACCTTCG 59.900 50.000 0.00 0.00 0.00 3.79
3892 3982 5.601662 ACTATATTGATGAACGGTGACCAG 58.398 41.667 1.11 0.00 0.00 4.00
3903 3993 5.997746 GCTTGGCACCTTACTATATTGATGA 59.002 40.000 0.00 0.00 0.00 2.92
3947 4037 2.414559 CGCTGATGGCAACTTCGAAATT 60.415 45.455 0.00 0.00 43.43 1.82
3953 4043 1.580942 TTGCGCTGATGGCAACTTC 59.419 52.632 9.73 0.00 44.79 3.01
3967 4057 4.913924 CCTTCAATTTTCAGAAGAGTTGCG 59.086 41.667 5.13 0.00 42.95 4.85
3999 4090 9.881773 AAAGGGAAGGATGAGCATAAATAAATA 57.118 29.630 0.00 0.00 0.00 1.40
4040 4131 2.751259 AGTGTAAACTCATGCATGCCTG 59.249 45.455 22.25 16.32 0.00 4.85
4132 4223 6.759356 GCTCCAGATTAGACTCTTCTAAAACC 59.241 42.308 0.00 0.00 45.52 3.27
4204 4300 4.033990 TCAGTCGATATGTTCAGACAGC 57.966 45.455 0.00 0.00 39.58 4.40
4219 4315 1.325640 CGGAATGCTGTCAATCAGTCG 59.674 52.381 0.00 0.00 45.23 4.18
4281 4380 6.021596 CACTATACGGAACTTGAATTTGTGC 58.978 40.000 0.00 0.00 0.00 4.57
4300 4399 6.831868 ACCAAAAGTTCAAAGGTGTACACTAT 59.168 34.615 24.55 11.72 0.00 2.12
4384 4483 1.048601 TACTGATCCGAATCCTGCCC 58.951 55.000 0.00 0.00 0.00 5.36
4483 4583 3.367703 GCATTTGAACAGGGTCAATGGAG 60.368 47.826 0.00 0.00 37.36 3.86
4486 4586 2.299582 TGGCATTTGAACAGGGTCAATG 59.700 45.455 0.00 3.47 37.36 2.82
4543 4654 3.855895 GCATTATCATCACATGGTGCAGC 60.856 47.826 9.47 9.47 32.98 5.25
4731 4851 3.034635 TGAGGAAAGGAGGCATCTACTC 58.965 50.000 0.00 0.00 31.62 2.59
4752 4872 8.677870 AGGAATCTACCATCTATTAGCAAGAT 57.322 34.615 0.00 0.00 33.94 2.40
4761 4881 5.077159 AGGACCAGAGGAATCTACCATCTAT 59.923 44.000 0.00 0.00 0.00 1.98
4762 4882 4.420552 AGGACCAGAGGAATCTACCATCTA 59.579 45.833 0.00 0.00 0.00 1.98
4763 4883 3.208692 AGGACCAGAGGAATCTACCATCT 59.791 47.826 0.00 0.00 0.00 2.90
4764 4884 3.323403 CAGGACCAGAGGAATCTACCATC 59.677 52.174 0.00 0.00 0.00 3.51
4765 4885 3.312890 CAGGACCAGAGGAATCTACCAT 58.687 50.000 0.00 0.00 0.00 3.55
4766 4886 2.752030 CAGGACCAGAGGAATCTACCA 58.248 52.381 0.00 0.00 0.00 3.25
4767 4887 1.414550 GCAGGACCAGAGGAATCTACC 59.585 57.143 0.00 0.00 0.00 3.18
4781 4901 2.227968 GACATCAACGCACGCAGGAC 62.228 60.000 0.00 0.00 0.00 3.85
4782 4902 2.027073 GACATCAACGCACGCAGGA 61.027 57.895 0.00 0.00 0.00 3.86
4785 4905 0.110283 CAATGACATCAACGCACGCA 60.110 50.000 0.00 0.00 0.00 5.24
4786 4906 0.794229 CCAATGACATCAACGCACGC 60.794 55.000 0.00 0.00 0.00 5.34
4787 4907 0.516877 ACCAATGACATCAACGCACG 59.483 50.000 0.00 0.00 0.00 5.34
4788 4908 4.142708 TGAATACCAATGACATCAACGCAC 60.143 41.667 0.00 0.00 0.00 5.34
4799 4919 9.747898 AATAAAGTACCACTTGAATACCAATGA 57.252 29.630 0.00 0.00 38.66 2.57


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

AutoCloner maintained by Alex Coulton.