Multiple sequence alignment - TraesCS7A01G526000

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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 TraesCS7A01G526000 chr7A 100.000 4442 0 0 1 4442 708232828 708228387 0.000000e+00 8203
1 TraesCS7A01G526000 chr7A 98.243 797 14 0 1 797 200015570 200014774 0.000000e+00 1395
2 TraesCS7A01G526000 chr7B 92.208 2002 95 25 1958 3913 708417622 708415636 0.000000e+00 2776
3 TraesCS7A01G526000 chr7B 92.089 1125 61 18 801 1911 708418731 708417621 0.000000e+00 1559
4 TraesCS7A01G526000 chr7B 97.992 797 16 0 1 797 742928889 742929685 0.000000e+00 1384
5 TraesCS7A01G526000 chr7B 97.864 796 17 0 1 796 716804404 716803609 0.000000e+00 1376
6 TraesCS7A01G526000 chr7B 91.473 516 33 6 3929 4442 708415652 708415146 0.000000e+00 699
7 TraesCS7A01G526000 chr7D 91.281 1881 97 23 801 2646 615597726 615599574 0.000000e+00 2503
8 TraesCS7A01G526000 chr7D 92.668 1282 58 16 2635 3913 615599591 615600839 0.000000e+00 1814
9 TraesCS7A01G526000 chr7D 90.574 244 21 1 4201 4442 615603246 615603489 5.540000e-84 322
10 TraesCS7A01G526000 chr5B 98.369 797 13 0 1 797 695890673 695891469 0.000000e+00 1400
11 TraesCS7A01G526000 chrUn 98.118 797 15 0 1 797 206792948 206792152 0.000000e+00 1389
12 TraesCS7A01G526000 chrUn 98.118 797 15 0 1 797 246705592 246704796 0.000000e+00 1389
13 TraesCS7A01G526000 chrUn 97.867 797 17 0 1 797 266185749 266184953 0.000000e+00 1378
14 TraesCS7A01G526000 chr5A 97.867 797 17 0 1 797 604994525 604995321 0.000000e+00 1378
15 TraesCS7A01G526000 chr6A 97.742 797 18 0 1 797 597220111 597220907 0.000000e+00 1373
16 TraesCS7A01G526000 chr3B 81.113 683 72 25 2034 2679 684256167 684256829 1.110000e-135 494
17 TraesCS7A01G526000 chr3B 83.618 293 37 7 1686 1969 684255842 684256132 9.470000e-67 265
18 TraesCS7A01G526000 chr3A 81.406 640 70 24 2068 2679 654590006 654590624 1.120000e-130 477
19 TraesCS7A01G526000 chr3A 79.750 400 58 17 1588 1969 654589557 654589951 7.320000e-68 268
20 TraesCS7A01G526000 chr3D 81.046 612 65 27 2085 2668 519668755 519669343 1.470000e-119 440
21 TraesCS7A01G526000 chr3D 79.455 404 49 19 1589 1968 519668229 519668622 5.700000e-64 255


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 TraesCS7A01G526000 chr7A 708228387 708232828 4441 True 8203.000000 8203 100.000000 1 4442 1 chr7A.!!$R2 4441
1 TraesCS7A01G526000 chr7A 200014774 200015570 796 True 1395.000000 1395 98.243000 1 797 1 chr7A.!!$R1 796
2 TraesCS7A01G526000 chr7B 708415146 708418731 3585 True 1678.000000 2776 91.923333 801 4442 3 chr7B.!!$R2 3641
3 TraesCS7A01G526000 chr7B 742928889 742929685 796 False 1384.000000 1384 97.992000 1 797 1 chr7B.!!$F1 796
4 TraesCS7A01G526000 chr7B 716803609 716804404 795 True 1376.000000 1376 97.864000 1 796 1 chr7B.!!$R1 795
5 TraesCS7A01G526000 chr7D 615597726 615603489 5763 False 1546.333333 2503 91.507667 801 4442 3 chr7D.!!$F1 3641
6 TraesCS7A01G526000 chr5B 695890673 695891469 796 False 1400.000000 1400 98.369000 1 797 1 chr5B.!!$F1 796
7 TraesCS7A01G526000 chrUn 206792152 206792948 796 True 1389.000000 1389 98.118000 1 797 1 chrUn.!!$R1 796
8 TraesCS7A01G526000 chrUn 246704796 246705592 796 True 1389.000000 1389 98.118000 1 797 1 chrUn.!!$R2 796
9 TraesCS7A01G526000 chrUn 266184953 266185749 796 True 1378.000000 1378 97.867000 1 797 1 chrUn.!!$R3 796
10 TraesCS7A01G526000 chr5A 604994525 604995321 796 False 1378.000000 1378 97.867000 1 797 1 chr5A.!!$F1 796
11 TraesCS7A01G526000 chr6A 597220111 597220907 796 False 1373.000000 1373 97.742000 1 797 1 chr6A.!!$F1 796
12 TraesCS7A01G526000 chr3B 684255842 684256829 987 False 379.500000 494 82.365500 1686 2679 2 chr3B.!!$F1 993
13 TraesCS7A01G526000 chr3A 654589557 654590624 1067 False 372.500000 477 80.578000 1588 2679 2 chr3A.!!$F1 1091
14 TraesCS7A01G526000 chr3D 519668229 519669343 1114 False 347.500000 440 80.250500 1589 2668 2 chr3D.!!$F1 1079

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
797 798 0.313672 TGAAAATGACAACCGCCTGC 59.686 50.0 0.00 0.00 0.0 4.85 F
799 800 0.314935 AAAATGACAACCGCCTGCAG 59.685 50.0 6.78 6.78 0.0 4.41 F
1564 1584 0.325933 TCTGTCTGGGTCCTGCATTG 59.674 55.0 0.00 0.00 0.0 2.82 F
2934 3096 0.240411 ACGACTTCTAGGCACGACAC 59.760 55.0 0.00 0.00 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2189 2291 1.002468 CAAGCTGAAAGACCCAACACG 60.002 52.381 0.00 0.0 34.07 4.49 R
2385 2487 1.742308 ACCTGACATGGTTACTGGGT 58.258 50.000 0.00 0.0 36.89 4.51 R
3303 3465 0.855349 CTCTCACATATTGCCGCGAC 59.145 55.000 8.23 0.0 0.00 5.19 R
4012 4179 0.098200 GCGCCCACCTTTCGTTAATC 59.902 55.000 0.00 0.0 0.00 1.75 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
333 334 2.695666 GGATGAGACTAAGCAGCTACCA 59.304 50.000 0.00 0.00 0.00 3.25
349 350 4.215742 CATTCCGACGCGCCCCTA 62.216 66.667 5.73 0.00 0.00 3.53
500 501 7.558444 AGAGTTGTAGATTCGTAGAAGAGGATT 59.442 37.037 0.00 0.00 45.90 3.01
602 603 3.905678 CCCGGTTGTTTTGGCGCA 61.906 61.111 10.83 0.00 0.00 6.09
692 693 3.242867 TCTATCGAATCCATGCTTCCCT 58.757 45.455 0.00 0.00 0.00 4.20
726 727 5.221145 GCGAGACTCTATCCAGATCTCAAAA 60.221 44.000 0.03 0.00 36.38 2.44
797 798 0.313672 TGAAAATGACAACCGCCTGC 59.686 50.000 0.00 0.00 0.00 4.85
798 799 0.313672 GAAAATGACAACCGCCTGCA 59.686 50.000 0.00 0.00 0.00 4.41
799 800 0.314935 AAAATGACAACCGCCTGCAG 59.685 50.000 6.78 6.78 0.00 4.41
909 915 4.211164 CGTCCCGGTATATATATACGCGAA 59.789 45.833 27.49 18.97 39.48 4.70
941 951 0.811281 CCCGAAACATTCCAGGCTTC 59.189 55.000 0.00 0.00 0.00 3.86
952 963 1.210478 TCCAGGCTTCTTGTAGCATCC 59.790 52.381 0.00 0.00 43.02 3.51
1035 1049 2.837591 GCCTCCTTCTTCTTCCTTCTCT 59.162 50.000 0.00 0.00 0.00 3.10
1040 1054 1.633774 TCTTCTTCCTTCTCTGGCGT 58.366 50.000 0.00 0.00 0.00 5.68
1226 1242 3.304721 AATGCTTTGCTGCGCCCA 61.305 55.556 4.18 0.00 35.36 5.36
1252 1268 1.662122 CCAATCGTTTGCTACCCGTAC 59.338 52.381 0.47 0.00 0.00 3.67
1253 1269 2.613691 CAATCGTTTGCTACCCGTACT 58.386 47.619 0.00 0.00 0.00 2.73
1359 1375 1.270094 CGGTAGTTGTTGGCACTCTGA 60.270 52.381 0.00 0.00 0.00 3.27
1364 1381 2.684881 AGTTGTTGGCACTCTGAGTTTG 59.315 45.455 7.77 0.00 0.00 2.93
1385 1402 3.171277 GCGTTGTGGTGCATTCTTATTC 58.829 45.455 0.00 0.00 0.00 1.75
1422 1439 5.431765 ACAATTCAATCTCGTAGGCAGAAT 58.568 37.500 0.00 0.00 0.00 2.40
1446 1463 3.222173 TGGAGCTTCTTTGCCACTTTA 57.778 42.857 0.00 0.00 0.00 1.85
1452 1469 3.304726 GCTTCTTTGCCACTTTAGTCACC 60.305 47.826 0.00 0.00 0.00 4.02
1502 1522 7.770801 AAAGCTTCCACTTTTCATTGTTAAC 57.229 32.000 0.00 0.00 36.47 2.01
1561 1581 0.471780 TTCTCTGTCTGGGTCCTGCA 60.472 55.000 0.00 0.00 0.00 4.41
1563 1583 0.617413 CTCTGTCTGGGTCCTGCATT 59.383 55.000 0.00 0.00 0.00 3.56
1564 1584 0.325933 TCTGTCTGGGTCCTGCATTG 59.674 55.000 0.00 0.00 0.00 2.82
1565 1585 1.303561 TGTCTGGGTCCTGCATTGC 60.304 57.895 0.46 0.46 0.00 3.56
1567 1587 0.895100 GTCTGGGTCCTGCATTGCAA 60.895 55.000 13.18 0.00 38.41 4.08
1641 1664 4.815040 TGTTGTGTAAATGGTTGGTACG 57.185 40.909 0.00 0.00 0.00 3.67
1657 1690 7.067251 TGGTTGGTACGTTATCTGAAAGTTTTT 59.933 33.333 0.00 0.00 33.76 1.94
1743 1776 1.131303 TGGGGATGTCCACCGAAAGT 61.131 55.000 0.00 0.00 39.17 2.66
1860 1893 7.439157 TGAATCCGGAAAATATAGCATTCTG 57.561 36.000 9.01 0.00 0.00 3.02
1907 1947 4.275936 CGGTGACCTCTTTTTCTTTCATGT 59.724 41.667 0.00 0.00 0.00 3.21
1912 1952 6.371548 TGACCTCTTTTTCTTTCATGTATCGG 59.628 38.462 0.00 0.00 0.00 4.18
1917 1957 8.348285 TCTTTTTCTTTCATGTATCGGGAAAT 57.652 30.769 0.00 0.00 30.88 2.17
1919 1959 5.499139 TTCTTTCATGTATCGGGAAATGC 57.501 39.130 0.00 0.00 30.88 3.56
1987 2027 2.224378 TGTGATAGGCCTAAGCATGAGC 60.224 50.000 18.42 6.93 42.56 4.26
2032 2079 5.104776 AGGTCATTCATTGAGGAGAAATCGA 60.105 40.000 0.00 0.00 34.17 3.59
2143 2239 6.403866 TTTTTGTGTGAATAGGTGAAGCAT 57.596 33.333 0.00 0.00 0.00 3.79
2147 2243 3.375299 GTGTGAATAGGTGAAGCATCCAC 59.625 47.826 0.00 0.00 0.00 4.02
2189 2291 6.635030 AGGTTTTACTTGTTCTGATGTTCC 57.365 37.500 0.00 0.00 0.00 3.62
2297 2399 4.074970 GCAGTGCAAAGCCAGGTATATAT 58.925 43.478 11.09 0.00 0.00 0.86
2298 2400 5.221823 TGCAGTGCAAAGCCAGGTATATATA 60.222 40.000 17.26 0.00 34.76 0.86
2299 2401 5.882557 GCAGTGCAAAGCCAGGTATATATAT 59.117 40.000 11.09 0.00 0.00 0.86
2300 2402 7.047891 GCAGTGCAAAGCCAGGTATATATATA 58.952 38.462 11.09 0.00 0.00 0.86
2301 2403 7.716998 GCAGTGCAAAGCCAGGTATATATATAT 59.283 37.037 11.09 10.10 0.00 0.86
2364 2466 5.925397 GGTAGTGTGATATCATTGCTCTCTG 59.075 44.000 9.02 0.00 0.00 3.35
2385 2487 7.292356 TCTCTGATGGCTAAAATGGTAGGATAA 59.708 37.037 0.00 0.00 0.00 1.75
2399 2501 4.411212 GGTAGGATAACCCAGTAACCATGT 59.589 45.833 0.00 0.00 37.41 3.21
2471 2581 8.926715 AAACACTTTCAAACCTTACAATTCTC 57.073 30.769 0.00 0.00 0.00 2.87
2550 2682 7.986320 CCATTCTCCTGCATAGAAATATCTAGG 59.014 40.741 13.76 0.00 41.36 3.02
2615 2747 6.072175 TGTCCTTGTTGTGGCATCTAAAATAC 60.072 38.462 0.00 0.00 0.00 1.89
2616 2748 6.007076 TCCTTGTTGTGGCATCTAAAATACA 58.993 36.000 0.00 0.00 0.00 2.29
2617 2749 6.491745 TCCTTGTTGTGGCATCTAAAATACAA 59.508 34.615 0.00 0.00 0.00 2.41
2622 2754 8.028354 TGTTGTGGCATCTAAAATACAATGAAG 58.972 33.333 0.00 0.00 31.68 3.02
2641 2773 9.154847 CAATGAAGTTCTTCAGATATGTGTGTA 57.845 33.333 18.03 0.00 34.02 2.90
2685 2846 9.195411 ACAAACAAACAATCATGCTAAGTAATG 57.805 29.630 0.00 0.00 0.00 1.90
2686 2847 9.409312 CAAACAAACAATCATGCTAAGTAATGA 57.591 29.630 0.00 0.00 37.23 2.57
2737 2898 9.783081 ATGATACTGCTGACATGTATTATTGAA 57.217 29.630 0.00 0.00 0.00 2.69
2757 2918 4.285775 TGAATAGATCCCACATTATCCGCA 59.714 41.667 0.00 0.00 0.00 5.69
2759 2920 2.851195 AGATCCCACATTATCCGCAAC 58.149 47.619 0.00 0.00 0.00 4.17
2886 3048 7.661437 TGCACATACAGTACTCTTTCTGATTTT 59.339 33.333 0.00 0.00 35.84 1.82
2902 3064 9.488762 TTTCTGATTTTATAGGACCAGAGACTA 57.511 33.333 0.00 0.00 33.02 2.59
2911 3073 2.171840 GACCAGAGACTACCAGAAGCA 58.828 52.381 0.00 0.00 0.00 3.91
2934 3096 0.240411 ACGACTTCTAGGCACGACAC 59.760 55.000 0.00 0.00 0.00 3.67
2935 3097 0.456312 CGACTTCTAGGCACGACACC 60.456 60.000 0.00 0.00 0.00 4.16
2947 3109 4.062293 GGCACGACACCTATAATTGCATA 58.938 43.478 0.00 0.00 0.00 3.14
2960 3122 8.579006 CCTATAATTGCATATGGTGTTGATTGT 58.421 33.333 4.56 0.00 0.00 2.71
2992 3154 6.018669 GCAAGGTTCTACTATGTGATTGCTAC 60.019 42.308 0.00 0.00 37.95 3.58
3017 3179 1.098129 TTGCTTGCACACCACGCTAA 61.098 50.000 0.00 0.00 39.29 3.09
3097 3259 1.760613 ACAGTGACCTTTTCGAGACCA 59.239 47.619 0.00 0.00 0.00 4.02
3130 3292 3.058450 GGCATGTCAAGAGATCTGATCG 58.942 50.000 11.73 0.00 0.00 3.69
3157 3319 1.078918 CCAGCGATCAGGTTCAGCA 60.079 57.895 0.00 0.00 0.00 4.41
3229 3391 2.171659 TGCCTTCAGGTTAGTGTGTGAA 59.828 45.455 0.00 0.00 37.57 3.18
3236 3398 3.245284 CAGGTTAGTGTGTGAACTTGACG 59.755 47.826 0.00 0.00 35.32 4.35
3288 3450 6.287525 TGAACTGATGACATGTTGAACTACA 58.712 36.000 0.00 0.00 0.00 2.74
3302 3464 3.500680 TGAACTACAAACCAGGATTTCGC 59.499 43.478 0.00 0.00 0.00 4.70
3303 3465 2.073816 ACTACAAACCAGGATTTCGCG 58.926 47.619 0.00 0.00 0.00 5.87
3537 3703 1.067060 TCTTGTCAGACGTGTGTGAGG 59.933 52.381 12.92 1.45 33.31 3.86
3763 3929 8.528643 AGGAGGTTTTAATAACCATGTTTTAGC 58.471 33.333 16.72 0.00 42.69 3.09
3876 4043 0.396001 GACCCGGCTAGAAGGTCTCT 60.396 60.000 15.39 0.00 45.49 3.10
3908 4075 8.986991 ACAATTGTATTCTCAGTTATCTCTCCT 58.013 33.333 9.97 0.00 0.00 3.69
3911 4078 9.875708 ATTGTATTCTCAGTTATCTCTCCTACT 57.124 33.333 0.00 0.00 0.00 2.57
3912 4079 9.702253 TTGTATTCTCAGTTATCTCTCCTACTT 57.298 33.333 0.00 0.00 0.00 2.24
3913 4080 9.702253 TGTATTCTCAGTTATCTCTCCTACTTT 57.298 33.333 0.00 0.00 0.00 2.66
4012 4179 4.012138 GAACCCCGGTTCCATTGG 57.988 61.111 14.61 0.00 46.21 3.16
4035 4202 3.195698 CGAAAGGTGGGCGCTAGC 61.196 66.667 7.64 4.06 44.18 3.42
4082 4249 4.379499 CGAATAAAAGAACAGTTGCCCTCC 60.379 45.833 0.00 0.00 0.00 4.30
4084 4251 0.555769 AAAGAACAGTTGCCCTCCCA 59.444 50.000 0.00 0.00 0.00 4.37
4085 4252 0.111253 AAGAACAGTTGCCCTCCCAG 59.889 55.000 0.00 0.00 0.00 4.45
4086 4253 1.973812 GAACAGTTGCCCTCCCAGC 60.974 63.158 0.00 0.00 0.00 4.85
4088 4255 3.970410 CAGTTGCCCTCCCAGCCA 61.970 66.667 0.00 0.00 0.00 4.75
4114 4281 7.397221 TCCGATTCATCCTGATATATGCTTTT 58.603 34.615 0.00 0.00 0.00 2.27
4150 4317 1.661617 TCCGACACGTCAACACAAAAG 59.338 47.619 0.00 0.00 0.00 2.27
4295 6635 4.700365 CGGTCGTCGCAGCACTCA 62.700 66.667 0.00 0.00 0.00 3.41
4365 6705 2.741985 TCGCAGCATTCACCACGG 60.742 61.111 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 7.609146 TCACTGATCTGAAATGAAACTTAGCAT 59.391 33.333 6.60 0.00 0.00 3.79
333 334 3.463585 TTAGGGGCGCGTCGGAAT 61.464 61.111 8.43 0.00 0.00 3.01
349 350 5.174037 TCGGTTTGAATCAAGATAGGGTT 57.826 39.130 0.00 0.00 0.00 4.11
458 459 2.645802 ACTCTCTTTACCGAGCGAGAT 58.354 47.619 0.00 0.00 33.72 2.75
467 468 7.983307 TCTACGAATCTACAACTCTCTTTACC 58.017 38.462 0.00 0.00 0.00 2.85
500 501 0.447406 TTTGTAGCGCGCGTACTCTA 59.553 50.000 32.35 20.38 0.00 2.43
560 561 2.554370 CGGAGGGGTCAGTACAAAAA 57.446 50.000 0.00 0.00 0.00 1.94
602 603 1.203225 AGTCTAACGTTGGGGTAGGGT 60.203 52.381 11.99 0.00 0.00 4.34
941 951 0.392998 ACTTGGCGGGATGCTACAAG 60.393 55.000 11.99 11.99 44.00 3.16
971 982 3.245668 AAGCACCCTCGCAGGACAG 62.246 63.158 4.00 0.00 37.67 3.51
1040 1054 0.107703 ATTCGAAGAAGCCGCATCCA 60.108 50.000 3.35 0.00 45.90 3.41
1082 1096 4.147449 TCCCGCATGCTCTCCACG 62.147 66.667 17.13 0.00 0.00 4.94
1226 1242 2.017049 GTAGCAAACGATTGGAGCCAT 58.983 47.619 7.57 0.00 37.02 4.40
1252 1268 6.706055 TTCGTACTAATCAAACAGCAAGAG 57.294 37.500 0.00 0.00 0.00 2.85
1253 1269 7.172532 ACAATTCGTACTAATCAAACAGCAAGA 59.827 33.333 0.00 0.00 0.00 3.02
1332 1348 1.002315 GCCAACAACTACCGGGAAGTA 59.998 52.381 6.32 0.00 0.00 2.24
1359 1375 0.459489 AATGCACCACAACGCAAACT 59.541 45.000 0.00 0.00 42.37 2.66
1364 1381 2.919666 ATAAGAATGCACCACAACGC 57.080 45.000 0.00 0.00 0.00 4.84
1385 1402 1.981254 AATTGTTGCCAATTCGAGCG 58.019 45.000 0.00 0.00 45.92 5.03
1422 1439 2.765699 AGTGGCAAAGAAGCTCCAAAAA 59.234 40.909 0.00 0.00 34.17 1.94
1446 1463 6.893583 AGCATAATTAGAATGTCTGGTGACT 58.106 36.000 0.00 0.00 43.29 3.41
1487 1507 6.930667 ACCTGTACGTTAACAATGAAAAGT 57.069 33.333 6.39 0.00 0.00 2.66
1502 1522 5.391523 CCATGAACCACATAAAACCTGTACG 60.392 44.000 0.00 0.00 37.46 3.67
1835 1868 7.667219 ACAGAATGCTATATTTTCCGGATTCAT 59.333 33.333 4.15 0.00 42.53 2.57
1860 1893 4.156008 AGTTCTTTCACACTCACCACAAAC 59.844 41.667 0.00 0.00 0.00 2.93
1907 1947 3.536570 TGATCGTTTGCATTTCCCGATA 58.463 40.909 0.00 0.00 38.28 2.92
1912 1952 6.455913 CCATGAAAATGATCGTTTGCATTTCC 60.456 38.462 25.44 0.00 42.17 3.13
1917 1957 4.484236 GTCCATGAAAATGATCGTTTGCA 58.516 39.130 20.97 20.97 31.45 4.08
1919 1959 5.314923 AGGTCCATGAAAATGATCGTTTG 57.685 39.130 13.58 2.16 0.00 2.93
1987 2027 5.476945 ACCTTCAAAATAAACCAGCCACTAG 59.523 40.000 0.00 0.00 0.00 2.57
1997 2043 9.143631 CCTCAATGAATGACCTTCAAAATAAAC 57.856 33.333 0.00 0.00 46.62 2.01
2007 2053 5.587844 CGATTTCTCCTCAATGAATGACCTT 59.412 40.000 0.00 0.00 33.47 3.50
2032 2079 6.662755 TCTAGCATATGTTTCCATGGTTTCT 58.337 36.000 12.58 0.00 34.82 2.52
2143 2239 1.132453 CACGATCTGCTTACGAGTGGA 59.868 52.381 0.00 0.00 0.00 4.02
2147 2243 3.181499 ACCTAACACGATCTGCTTACGAG 60.181 47.826 0.00 0.00 0.00 4.18
2189 2291 1.002468 CAAGCTGAAAGACCCAACACG 60.002 52.381 0.00 0.00 34.07 4.49
2316 2418 9.851686 ACCAATCATTATGAATTTACAGCTAGA 57.148 29.630 0.00 0.00 0.00 2.43
2364 2466 5.710567 GGGTTATCCTACCATTTTAGCCATC 59.289 44.000 0.00 0.00 40.09 3.51
2385 2487 1.742308 ACCTGACATGGTTACTGGGT 58.258 50.000 0.00 0.00 36.89 4.51
2470 2580 8.484214 AATGCTAAGAATCTACTACATCAGGA 57.516 34.615 0.00 0.00 0.00 3.86
2512 2626 4.879545 GCAGGAGAATGGGAAACGTTATTA 59.120 41.667 0.00 0.00 0.00 0.98
2550 2682 5.845391 CTAGCCCCATAATCTAGCTAGTC 57.155 47.826 20.10 0.94 45.08 2.59
2563 2695 2.708325 GGTTTGATCTCTCTAGCCCCAT 59.292 50.000 0.00 0.00 0.00 4.00
2622 2754 8.654230 ATCACATACACACATATCTGAAGAAC 57.346 34.615 0.00 0.00 0.00 3.01
2710 2871 9.211485 TCAATAATACATGTCAGCAGTATCATG 57.789 33.333 0.00 0.00 42.00 3.07
2712 2873 9.783081 ATTCAATAATACATGTCAGCAGTATCA 57.217 29.630 0.00 0.00 0.00 2.15
2719 2880 8.887717 GGGATCTATTCAATAATACATGTCAGC 58.112 37.037 0.00 0.00 0.00 4.26
2737 2898 4.041567 TGTTGCGGATAATGTGGGATCTAT 59.958 41.667 0.00 0.00 0.00 1.98
2743 2904 2.036958 TCTGTTGCGGATAATGTGGG 57.963 50.000 0.00 0.00 0.00 4.61
2759 2920 9.551734 TGGATAATGTGTGATCTATTCTTTCTG 57.448 33.333 0.00 0.00 0.00 3.02
2841 3003 2.029649 GCATGTGCATTGAAGGAACACT 60.030 45.455 0.00 0.00 41.59 3.55
2886 3048 5.690632 GCTTCTGGTAGTCTCTGGTCCTATA 60.691 48.000 0.00 0.00 0.00 1.31
2902 3064 4.273148 AGAAGTCGTTATTGCTTCTGGT 57.727 40.909 5.39 0.00 44.82 4.00
2911 3073 3.192001 TGTCGTGCCTAGAAGTCGTTATT 59.808 43.478 0.00 0.00 0.00 1.40
2934 3096 8.579006 ACAATCAACACCATATGCAATTATAGG 58.421 33.333 0.00 0.00 0.00 2.57
2935 3097 9.401873 CACAATCAACACCATATGCAATTATAG 57.598 33.333 0.00 0.00 0.00 1.31
2947 3109 2.297033 GCCAAGTCACAATCAACACCAT 59.703 45.455 0.00 0.00 0.00 3.55
2960 3122 4.286032 ACATAGTAGAACCTTGCCAAGTCA 59.714 41.667 3.37 0.00 0.00 3.41
2992 3154 2.353839 GTGTGCAAGCAACTGCCG 60.354 61.111 0.00 0.00 41.90 5.69
3017 3179 7.596494 CATTACACAAAACATTGGATCAGACT 58.404 34.615 0.00 0.00 0.00 3.24
3097 3259 2.108976 CATGCCATCCGTACCGCT 59.891 61.111 0.00 0.00 0.00 5.52
3157 3319 1.375523 GATCAGAACCGGTTGCGGT 60.376 57.895 27.87 11.76 45.25 5.68
3261 3423 5.240183 AGTTCAACATGTCATCAGTTCAAGG 59.760 40.000 0.00 0.00 0.00 3.61
3266 3428 7.417612 GTTTGTAGTTCAACATGTCATCAGTT 58.582 34.615 0.00 0.00 35.61 3.16
3288 3450 1.908066 GCGACGCGAAATCCTGGTTT 61.908 55.000 15.93 0.00 0.00 3.27
3302 3464 0.869880 TCTCACATATTGCCGCGACG 60.870 55.000 8.23 0.00 0.00 5.12
3303 3465 0.855349 CTCTCACATATTGCCGCGAC 59.145 55.000 8.23 0.00 0.00 5.19
3309 3471 2.686915 AGGCAAAGCTCTCACATATTGC 59.313 45.455 6.90 6.90 41.69 3.56
3314 3476 1.350351 ACTGAGGCAAAGCTCTCACAT 59.650 47.619 0.00 0.00 34.23 3.21
3537 3703 8.909671 GTTCTTGTCATTTCATGTCAGATTTTC 58.090 33.333 0.00 0.00 30.49 2.29
3568 3734 6.183360 GGATTTTCCTCAAGACACATCATGAG 60.183 42.308 0.09 3.18 46.01 2.90
3762 3928 2.352225 CCTCTCCATCAGTACATAGCGC 60.352 54.545 0.00 0.00 0.00 5.92
3763 3929 2.887783 ACCTCTCCATCAGTACATAGCG 59.112 50.000 0.00 0.00 0.00 4.26
3916 4083 7.091533 AGGAGAGATAACTTTCCCTCAAAAA 57.908 36.000 6.01 0.00 45.20 1.94
3917 4084 6.704056 AGGAGAGATAACTTTCCCTCAAAA 57.296 37.500 6.01 0.00 45.20 2.44
3918 4085 6.960542 AGTAGGAGAGATAACTTTCCCTCAAA 59.039 38.462 6.01 0.00 45.20 2.69
3919 4086 6.503944 AGTAGGAGAGATAACTTTCCCTCAA 58.496 40.000 6.01 0.00 45.20 3.02
3920 4087 6.093617 AGTAGGAGAGATAACTTTCCCTCA 57.906 41.667 6.01 0.00 45.20 3.86
3921 4088 8.536340 TTAAGTAGGAGAGATAACTTTCCCTC 57.464 38.462 6.01 0.98 45.20 4.30
3922 4089 8.912614 TTTAAGTAGGAGAGATAACTTTCCCT 57.087 34.615 6.01 1.11 45.20 4.20
4001 4168 4.438200 CCTTTCGTTAATCCAATGGAACCG 60.438 45.833 5.89 6.50 34.34 4.44
4012 4179 0.098200 GCGCCCACCTTTCGTTAATC 59.902 55.000 0.00 0.00 0.00 1.75
4037 4204 1.668419 ACAACCGATTGGCATCTAGC 58.332 50.000 0.00 0.00 40.42 3.42
4038 4205 3.131396 GGTACAACCGATTGGCATCTAG 58.869 50.000 0.00 0.00 40.42 2.43
4039 4206 3.188159 GGTACAACCGATTGGCATCTA 57.812 47.619 0.00 0.00 40.42 1.98
4040 4207 2.038387 GGTACAACCGATTGGCATCT 57.962 50.000 0.00 0.00 40.42 2.90
4082 4249 0.399454 AGGATGAATCGGATGGCTGG 59.601 55.000 0.00 0.00 0.00 4.85
4084 4251 1.427809 TCAGGATGAATCGGATGGCT 58.572 50.000 0.00 0.00 45.97 4.75
4150 4317 5.920273 GCTACTAATGAGATGAAGAGTGCTC 59.080 44.000 0.00 0.00 0.00 4.26
4289 6629 2.546321 CGTGTTGCGAGTGAGTGC 59.454 61.111 0.00 0.00 44.77 4.40
4295 6635 4.539083 TGCCACCGTGTTGCGAGT 62.539 61.111 0.00 0.00 44.77 4.18
4347 6687 2.476051 CGTGGTGAATGCTGCGAC 59.524 61.111 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.