Multiple sequence alignment - TraesCS6D01G034100

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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 TraesCS6D01G034100 chr6D 100.000 2547 0 0 1 2547 14242033 14244579 0.000000e+00 4704.0
1 TraesCS6D01G034100 chr6D 88.112 143 11 3 5 141 14201261 14201119 5.640000e-37 165.0
2 TraesCS6D01G034100 chr2D 90.631 1964 120 25 626 2547 590929778 590927837 0.000000e+00 2549.0
3 TraesCS6D01G034100 chr2D 89.949 1970 128 16 626 2547 12544080 12542133 0.000000e+00 2477.0
4 TraesCS6D01G034100 chr2D 90.970 1794 117 14 626 2381 614811141 614809355 0.000000e+00 2374.0
5 TraesCS6D01G034100 chr2D 90.316 1487 94 19 1085 2547 551247278 551248738 0.000000e+00 1903.0
6 TraesCS6D01G034100 chr5B 90.298 1948 158 11 626 2547 548479668 548477726 0.000000e+00 2521.0
7 TraesCS6D01G034100 chr1B 90.137 1967 137 24 623 2545 577793151 577791198 0.000000e+00 2505.0
8 TraesCS6D01G034100 chr7B 89.969 1964 151 16 627 2547 27463312 27465272 0.000000e+00 2494.0
9 TraesCS6D01G034100 chr4B 89.558 1944 154 22 630 2547 94513666 94515586 0.000000e+00 2420.0
10 TraesCS6D01G034100 chr4B 90.358 1649 121 18 923 2547 35634871 35636505 0.000000e+00 2130.0
11 TraesCS6D01G034100 chr5D 90.261 1879 117 22 626 2462 257136381 257138235 0.000000e+00 2396.0
12 TraesCS6D01G034100 chr5D 89.688 1600 112 16 972 2547 386170230 386171800 0.000000e+00 1991.0
13 TraesCS6D01G034100 chr1D 89.141 1943 141 24 626 2547 347252940 347251047 0.000000e+00 2355.0
14 TraesCS6D01G034100 chr1D 87.691 1901 137 37 626 2506 464037617 464039440 0.000000e+00 2124.0
15 TraesCS6D01G034100 chr1D 87.974 1871 132 37 626 2466 25464343 25466150 0.000000e+00 2122.0
16 TraesCS6D01G034100 chr7D 88.940 1962 130 26 626 2547 565949594 565947680 0.000000e+00 2340.0
17 TraesCS6D01G034100 chr7D 86.734 1877 147 38 626 2466 63995414 63997224 0.000000e+00 1993.0
18 TraesCS6D01G034100 chr3B 88.045 1974 162 38 626 2547 778875506 778873555 0.000000e+00 2270.0
19 TraesCS6D01G034100 chr3B 87.647 1959 182 30 626 2547 778932232 778930297 0.000000e+00 2222.0
20 TraesCS6D01G034100 chrUn 92.109 1356 79 8 1215 2547 110637310 110638660 0.000000e+00 1886.0
21 TraesCS6D01G034100 chr6B 88.723 603 47 15 6 599 26120249 26119659 0.000000e+00 717.0
22 TraesCS6D01G034100 chr6B 88.284 606 49 15 3 599 26005385 26005977 0.000000e+00 706.0
23 TraesCS6D01G034100 chr6A 86.822 129 7 7 5 124 15456707 15456580 4.420000e-28 135.0
24 TraesCS6D01G034100 chr6A 100.000 51 0 0 423 473 15548937 15548987 7.500000e-16 95.3
25 TraesCS6D01G034100 chr6A 90.625 64 2 1 363 426 15547053 15547112 5.840000e-12 82.4


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 TraesCS6D01G034100 chr6D 14242033 14244579 2546 False 4704 4704 100.000 1 2547 1 chr6D.!!$F1 2546
1 TraesCS6D01G034100 chr2D 590927837 590929778 1941 True 2549 2549 90.631 626 2547 1 chr2D.!!$R2 1921
2 TraesCS6D01G034100 chr2D 12542133 12544080 1947 True 2477 2477 89.949 626 2547 1 chr2D.!!$R1 1921
3 TraesCS6D01G034100 chr2D 614809355 614811141 1786 True 2374 2374 90.970 626 2381 1 chr2D.!!$R3 1755
4 TraesCS6D01G034100 chr2D 551247278 551248738 1460 False 1903 1903 90.316 1085 2547 1 chr2D.!!$F1 1462
5 TraesCS6D01G034100 chr5B 548477726 548479668 1942 True 2521 2521 90.298 626 2547 1 chr5B.!!$R1 1921
6 TraesCS6D01G034100 chr1B 577791198 577793151 1953 True 2505 2505 90.137 623 2545 1 chr1B.!!$R1 1922
7 TraesCS6D01G034100 chr7B 27463312 27465272 1960 False 2494 2494 89.969 627 2547 1 chr7B.!!$F1 1920
8 TraesCS6D01G034100 chr4B 94513666 94515586 1920 False 2420 2420 89.558 630 2547 1 chr4B.!!$F2 1917
9 TraesCS6D01G034100 chr4B 35634871 35636505 1634 False 2130 2130 90.358 923 2547 1 chr4B.!!$F1 1624
10 TraesCS6D01G034100 chr5D 257136381 257138235 1854 False 2396 2396 90.261 626 2462 1 chr5D.!!$F1 1836
11 TraesCS6D01G034100 chr5D 386170230 386171800 1570 False 1991 1991 89.688 972 2547 1 chr5D.!!$F2 1575
12 TraesCS6D01G034100 chr1D 347251047 347252940 1893 True 2355 2355 89.141 626 2547 1 chr1D.!!$R1 1921
13 TraesCS6D01G034100 chr1D 464037617 464039440 1823 False 2124 2124 87.691 626 2506 1 chr1D.!!$F2 1880
14 TraesCS6D01G034100 chr1D 25464343 25466150 1807 False 2122 2122 87.974 626 2466 1 chr1D.!!$F1 1840
15 TraesCS6D01G034100 chr7D 565947680 565949594 1914 True 2340 2340 88.940 626 2547 1 chr7D.!!$R1 1921
16 TraesCS6D01G034100 chr7D 63995414 63997224 1810 False 1993 1993 86.734 626 2466 1 chr7D.!!$F1 1840
17 TraesCS6D01G034100 chr3B 778873555 778875506 1951 True 2270 2270 88.045 626 2547 1 chr3B.!!$R1 1921
18 TraesCS6D01G034100 chr3B 778930297 778932232 1935 True 2222 2222 87.647 626 2547 1 chr3B.!!$R2 1921
19 TraesCS6D01G034100 chrUn 110637310 110638660 1350 False 1886 1886 92.109 1215 2547 1 chrUn.!!$F1 1332
20 TraesCS6D01G034100 chr6B 26119659 26120249 590 True 717 717 88.723 6 599 1 chr6B.!!$R1 593
21 TraesCS6D01G034100 chr6B 26005385 26005977 592 False 706 706 88.284 3 599 1 chr6B.!!$F1 596

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
350 370 0.112606 TTCCTCCCCTAGCGATCGAT 59.887 55.0 21.57 16.78 0.0 3.59 F
351 371 0.112606 TCCTCCCCTAGCGATCGATT 59.887 55.0 21.57 8.62 0.0 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1364 1463 0.321671 TTGCCCTCCGTCTCTTCTTG 59.678 55.000 0.0 0.0 0.0 3.02 R
2267 2481 1.470098 CAAAGTCTTTCCATCTGCCCG 59.530 52.381 0.0 0.0 0.0 6.13 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
68 69 2.279851 GCCGGCCGCAAAAACTTT 60.280 55.556 22.85 0.00 37.47 2.66
73 74 2.918600 CCGGCCGCAAAAACTTTATAAC 59.081 45.455 22.85 0.00 0.00 1.89
74 75 3.366577 CCGGCCGCAAAAACTTTATAACT 60.367 43.478 22.85 0.00 0.00 2.24
79 80 6.307077 GGCCGCAAAAACTTTATAACTAAGTG 59.693 38.462 0.00 0.00 36.06 3.16
124 125 6.840789 GCATGAATTCGTTTTGTTTTCTGTTC 59.159 34.615 0.00 0.00 0.00 3.18
125 126 6.879188 TGAATTCGTTTTGTTTTCTGTTCC 57.121 33.333 0.04 0.00 0.00 3.62
150 151 3.863396 TTTGTTGTTGTCGTACATCGG 57.137 42.857 0.00 0.00 40.32 4.18
161 162 1.799181 CGTACATCGGTCAAGCCTCTG 60.799 57.143 0.00 0.00 35.71 3.35
198 200 2.033049 GCAGGAGCAAAGATAGCATGTG 59.967 50.000 0.00 0.00 41.58 3.21
199 201 3.276857 CAGGAGCAAAGATAGCATGTGT 58.723 45.455 0.00 0.00 0.00 3.72
200 202 3.693085 CAGGAGCAAAGATAGCATGTGTT 59.307 43.478 0.00 0.00 0.00 3.32
201 203 3.693085 AGGAGCAAAGATAGCATGTGTTG 59.307 43.478 0.00 0.00 0.00 3.33
202 204 3.441572 GGAGCAAAGATAGCATGTGTTGT 59.558 43.478 0.00 0.00 0.00 3.32
203 205 4.409570 GAGCAAAGATAGCATGTGTTGTG 58.590 43.478 0.00 0.00 0.00 3.33
204 206 3.822735 AGCAAAGATAGCATGTGTTGTGT 59.177 39.130 0.00 0.00 0.00 3.72
205 207 4.279169 AGCAAAGATAGCATGTGTTGTGTT 59.721 37.500 0.00 0.00 0.00 3.32
206 208 4.984161 GCAAAGATAGCATGTGTTGTGTTT 59.016 37.500 0.00 0.00 0.00 2.83
207 209 5.107760 GCAAAGATAGCATGTGTTGTGTTTG 60.108 40.000 10.20 10.20 35.24 2.93
208 210 5.772825 AAGATAGCATGTGTTGTGTTTGT 57.227 34.783 0.00 0.00 0.00 2.83
209 211 5.112220 AGATAGCATGTGTTGTGTTTGTG 57.888 39.130 0.00 0.00 0.00 3.33
210 212 4.821260 AGATAGCATGTGTTGTGTTTGTGA 59.179 37.500 0.00 0.00 0.00 3.58
211 213 3.149436 AGCATGTGTTGTGTTTGTGAC 57.851 42.857 0.00 0.00 0.00 3.67
212 214 2.754552 AGCATGTGTTGTGTTTGTGACT 59.245 40.909 0.00 0.00 0.00 3.41
213 215 3.193267 AGCATGTGTTGTGTTTGTGACTT 59.807 39.130 0.00 0.00 0.00 3.01
214 216 3.925913 GCATGTGTTGTGTTTGTGACTTT 59.074 39.130 0.00 0.00 0.00 2.66
215 217 4.201608 GCATGTGTTGTGTTTGTGACTTTG 60.202 41.667 0.00 0.00 0.00 2.77
216 218 4.576216 TGTGTTGTGTTTGTGACTTTGT 57.424 36.364 0.00 0.00 0.00 2.83
257 259 3.188254 TGTTGCGTTCGTCATGATTCAAT 59.812 39.130 0.00 0.00 0.00 2.57
266 268 8.245777 CGTTCGTCATGATTCAATTTATTTTCG 58.754 33.333 0.00 0.00 0.00 3.46
347 367 1.633774 TCATTCCTCCCCTAGCGATC 58.366 55.000 0.00 0.00 0.00 3.69
348 368 0.244994 CATTCCTCCCCTAGCGATCG 59.755 60.000 11.69 11.69 0.00 3.69
350 370 0.112606 TTCCTCCCCTAGCGATCGAT 59.887 55.000 21.57 16.78 0.00 3.59
351 371 0.112606 TCCTCCCCTAGCGATCGATT 59.887 55.000 21.57 8.62 0.00 3.34
352 372 1.353358 TCCTCCCCTAGCGATCGATTA 59.647 52.381 21.57 9.38 0.00 1.75
353 373 2.168496 CCTCCCCTAGCGATCGATTAA 58.832 52.381 21.57 0.00 0.00 1.40
354 374 2.164624 CCTCCCCTAGCGATCGATTAAG 59.835 54.545 21.57 7.84 0.00 1.85
396 416 3.297830 TCTGACGTTCGACATTCATGT 57.702 42.857 0.00 0.00 45.16 3.21
398 418 4.993905 TCTGACGTTCGACATTCATGTAT 58.006 39.130 0.00 0.00 41.95 2.29
410 433 6.513884 CGACATTCATGTATTGGGATCCTTTG 60.514 42.308 12.58 0.00 41.95 2.77
509 532 1.506493 GCTGATGATCATGGGACGTC 58.494 55.000 14.30 7.13 0.00 4.34
523 546 1.352156 GACGTCATTGACCGGCTGAC 61.352 60.000 11.55 9.14 36.72 3.51
577 600 1.399714 CTCCACCGTGGCACTATCTA 58.600 55.000 16.72 0.00 37.47 1.98
589 612 6.473778 CGTGGCACTATCTATATGCAATACTC 59.526 42.308 16.72 0.00 41.27 2.59
606 629 9.685828 TGCAATACTCCTTTTGTTTTTGTATAC 57.314 29.630 0.00 0.00 0.00 1.47
607 630 9.685828 GCAATACTCCTTTTGTTTTTGTATACA 57.314 29.630 0.08 0.08 0.00 2.29
610 633 7.284919 ACTCCTTTTGTTTTTGTATACAGGG 57.715 36.000 5.56 0.00 0.00 4.45
611 634 6.091718 TCCTTTTGTTTTTGTATACAGGGC 57.908 37.500 5.56 0.00 0.00 5.19
612 635 5.011227 TCCTTTTGTTTTTGTATACAGGGCC 59.989 40.000 5.56 0.00 0.00 5.80
613 636 5.221541 CCTTTTGTTTTTGTATACAGGGCCA 60.222 40.000 6.18 0.02 0.00 5.36
614 637 6.426646 TTTTGTTTTTGTATACAGGGCCAT 57.573 33.333 6.18 0.00 0.00 4.40
615 638 6.426646 TTTGTTTTTGTATACAGGGCCATT 57.573 33.333 6.18 0.00 0.00 3.16
616 639 6.426646 TTGTTTTTGTATACAGGGCCATTT 57.573 33.333 6.18 0.00 0.00 2.32
617 640 6.031751 TGTTTTTGTATACAGGGCCATTTC 57.968 37.500 6.18 0.00 0.00 2.17
618 641 5.540337 TGTTTTTGTATACAGGGCCATTTCA 59.460 36.000 6.18 0.00 0.00 2.69
619 642 6.212388 TGTTTTTGTATACAGGGCCATTTCAT 59.788 34.615 6.18 0.00 0.00 2.57
620 643 6.865834 TTTTGTATACAGGGCCATTTCATT 57.134 33.333 6.18 0.00 0.00 2.57
621 644 6.865834 TTTGTATACAGGGCCATTTCATTT 57.134 33.333 6.18 0.00 0.00 2.32
622 645 6.865834 TTGTATACAGGGCCATTTCATTTT 57.134 33.333 6.18 0.00 0.00 1.82
623 646 6.865834 TGTATACAGGGCCATTTCATTTTT 57.134 33.333 6.18 0.00 0.00 1.94
624 647 6.872920 TGTATACAGGGCCATTTCATTTTTC 58.127 36.000 6.18 0.00 0.00 2.29
638 661 4.390264 TCATTTTTCGTGGTGTCCATGTA 58.610 39.130 7.70 0.00 41.03 2.29
696 719 1.076014 TCCCTAGTCTGTCCGCACA 59.924 57.895 0.00 0.00 0.00 4.57
882 923 1.038130 ATAAGCGGGCGACAGAGAGT 61.038 55.000 0.00 0.00 0.00 3.24
910 970 2.986413 ACGGCGACAGAGAGCACT 60.986 61.111 16.62 0.00 34.54 4.40
920 996 2.919856 AGAGCACTGCGGTGACCT 60.920 61.111 29.83 20.17 45.61 3.85
1071 1165 2.552743 CGTGGAGATGCCTATCTTCGTA 59.447 50.000 0.00 0.00 43.63 3.43
1244 1341 2.419057 TTTGGCGTTCATGCAGGTGC 62.419 55.000 0.00 1.18 42.50 5.01
1287 1386 0.877743 GCTCTGGCCAAGACTTTGAC 59.122 55.000 7.01 0.00 36.36 3.18
1409 1508 1.066908 GCGATGACAGAGAGCTAGCTT 59.933 52.381 20.42 8.93 0.00 3.74
1515 1631 1.202651 AGGTATGGTAATCGCACTGGC 60.203 52.381 0.00 0.00 0.00 4.85
1543 1673 5.798125 TGTTGAAATTGTATGGAAAGGCA 57.202 34.783 0.00 0.00 0.00 4.75
1544 1674 6.357579 TGTTGAAATTGTATGGAAAGGCAT 57.642 33.333 0.00 0.00 0.00 4.40
1545 1675 6.164876 TGTTGAAATTGTATGGAAAGGCATG 58.835 36.000 0.00 0.00 0.00 4.06
1546 1676 6.014755 TGTTGAAATTGTATGGAAAGGCATGA 60.015 34.615 0.00 0.00 0.00 3.07
1547 1677 6.602410 TGAAATTGTATGGAAAGGCATGAA 57.398 33.333 0.00 0.00 0.00 2.57
1548 1678 7.185318 TGAAATTGTATGGAAAGGCATGAAT 57.815 32.000 0.00 0.00 0.00 2.57
1549 1679 7.622713 TGAAATTGTATGGAAAGGCATGAATT 58.377 30.769 0.00 0.00 0.00 2.17
1550 1680 8.756927 TGAAATTGTATGGAAAGGCATGAATTA 58.243 29.630 0.00 0.00 0.00 1.40
1551 1681 9.252962 GAAATTGTATGGAAAGGCATGAATTAG 57.747 33.333 0.00 0.00 0.00 1.73
1552 1682 6.713762 TTGTATGGAAAGGCATGAATTAGG 57.286 37.500 0.00 0.00 0.00 2.69
1553 1683 6.012337 TGTATGGAAAGGCATGAATTAGGA 57.988 37.500 0.00 0.00 0.00 2.94
1554 1684 5.827797 TGTATGGAAAGGCATGAATTAGGAC 59.172 40.000 0.00 0.00 0.00 3.85
1555 1685 3.631250 TGGAAAGGCATGAATTAGGACC 58.369 45.455 0.00 0.00 0.00 4.46
1556 1686 2.959030 GGAAAGGCATGAATTAGGACCC 59.041 50.000 0.00 0.00 0.00 4.46
1557 1687 2.755952 AAGGCATGAATTAGGACCCC 57.244 50.000 0.00 0.00 0.00 4.95
1888 2078 5.974751 TGCGTGTTTTTCTGTTTTCTATTCC 59.025 36.000 0.00 0.00 0.00 3.01
1894 2084 9.243637 TGTTTTTCTGTTTTCTATTCCGATTTG 57.756 29.630 0.00 0.00 0.00 2.32
1911 2101 5.263185 CGATTTGGTTTAGGCAGTAAATCG 58.737 41.667 13.21 13.21 45.36 3.34
2219 2433 4.097361 GGGGCTGGGACTCGAACC 62.097 72.222 0.28 0.28 0.00 3.62
2252 2466 1.525941 GTTTGTGGCGTTTAGGGCTA 58.474 50.000 0.00 0.00 0.00 3.93
2267 2481 1.877165 GCTACGCTGGTAACCGCTC 60.877 63.158 0.00 0.00 0.00 5.03
2291 2505 3.057946 GGCAGATGGAAAGACTTTGACAC 60.058 47.826 4.85 0.78 0.00 3.67
2296 2510 3.869065 TGGAAAGACTTTGACACGACTT 58.131 40.909 4.85 0.00 0.00 3.01
2430 2706 1.533625 ACGTATGTTTGCACTGCCAT 58.466 45.000 0.00 0.00 0.00 4.40
2437 2713 6.293353 CGTATGTTTGCACTGCCATATGATTA 60.293 38.462 3.65 0.00 31.45 1.75
2440 2716 5.360429 TGTTTGCACTGCCATATGATTATGT 59.640 36.000 3.65 0.00 34.54 2.29
2523 2800 7.780271 ACTTGGTTTAGGGAAGAAATGATATCC 59.220 37.037 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.121407 TAGGAGATGGTGCCGATGGG 61.121 60.000 0.00 0.00 0.00 4.00
68 69 5.128205 TCGAGTAGCAGGCACTTAGTTATA 58.872 41.667 0.00 0.00 34.60 0.98
73 74 2.621055 AGATCGAGTAGCAGGCACTTAG 59.379 50.000 0.00 0.00 34.60 2.18
74 75 2.656002 AGATCGAGTAGCAGGCACTTA 58.344 47.619 0.00 0.00 34.60 2.24
79 80 0.103937 AGCAAGATCGAGTAGCAGGC 59.896 55.000 0.00 0.00 0.00 4.85
124 125 2.931512 ACGACAACAACAAAACCTGG 57.068 45.000 0.00 0.00 0.00 4.45
125 126 4.343811 TGTACGACAACAACAAAACCTG 57.656 40.909 0.00 0.00 0.00 4.00
150 151 2.911484 CAGATAACCCAGAGGCTTGAC 58.089 52.381 0.00 0.00 36.11 3.18
184 186 5.978919 ACAAACACAACACATGCTATCTTTG 59.021 36.000 0.00 0.00 0.00 2.77
185 187 5.978919 CACAAACACAACACATGCTATCTTT 59.021 36.000 0.00 0.00 0.00 2.52
198 200 4.742659 ACAACACAAAGTCACAAACACAAC 59.257 37.500 0.00 0.00 0.00 3.32
199 201 4.742167 CACAACACAAAGTCACAAACACAA 59.258 37.500 0.00 0.00 0.00 3.33
200 202 4.202060 ACACAACACAAAGTCACAAACACA 60.202 37.500 0.00 0.00 0.00 3.72
201 203 4.295051 ACACAACACAAAGTCACAAACAC 58.705 39.130 0.00 0.00 0.00 3.32
202 204 4.576216 ACACAACACAAAGTCACAAACA 57.424 36.364 0.00 0.00 0.00 2.83
203 205 5.233263 ACAAACACAACACAAAGTCACAAAC 59.767 36.000 0.00 0.00 0.00 2.93
204 206 5.233050 CACAAACACAACACAAAGTCACAAA 59.767 36.000 0.00 0.00 0.00 2.83
205 207 4.742167 CACAAACACAACACAAAGTCACAA 59.258 37.500 0.00 0.00 0.00 3.33
206 208 4.036852 TCACAAACACAACACAAAGTCACA 59.963 37.500 0.00 0.00 0.00 3.58
207 209 4.381566 GTCACAAACACAACACAAAGTCAC 59.618 41.667 0.00 0.00 0.00 3.67
208 210 4.277174 AGTCACAAACACAACACAAAGTCA 59.723 37.500 0.00 0.00 0.00 3.41
209 211 4.794169 AGTCACAAACACAACACAAAGTC 58.206 39.130 0.00 0.00 0.00 3.01
210 212 4.846779 AGTCACAAACACAACACAAAGT 57.153 36.364 0.00 0.00 0.00 2.66
211 213 5.461737 ACAAAGTCACAAACACAACACAAAG 59.538 36.000 0.00 0.00 0.00 2.77
212 214 5.233050 CACAAAGTCACAAACACAACACAAA 59.767 36.000 0.00 0.00 0.00 2.83
213 215 4.742167 CACAAAGTCACAAACACAACACAA 59.258 37.500 0.00 0.00 0.00 3.33
214 216 4.202060 ACACAAAGTCACAAACACAACACA 60.202 37.500 0.00 0.00 0.00 3.72
215 217 4.295051 ACACAAAGTCACAAACACAACAC 58.705 39.130 0.00 0.00 0.00 3.32
216 218 4.576216 ACACAAAGTCACAAACACAACA 57.424 36.364 0.00 0.00 0.00 3.33
257 259 9.249457 TGTTTCATGTACAATTGCGAAAATAAA 57.751 25.926 5.05 0.00 0.00 1.40
266 268 3.896122 ACCGTGTTTCATGTACAATTGC 58.104 40.909 5.05 0.00 0.00 3.56
306 326 2.708861 TCCATTGGTCATAGGGCGTAAT 59.291 45.455 1.86 0.00 0.00 1.89
347 367 0.177141 TCCCCTGGCGAACTTAATCG 59.823 55.000 0.00 0.00 45.41 3.34
348 368 2.014857 GTTCCCCTGGCGAACTTAATC 58.985 52.381 15.33 0.00 37.28 1.75
350 370 0.037160 GGTTCCCCTGGCGAACTTAA 59.963 55.000 20.32 0.00 39.65 1.85
351 371 0.838987 AGGTTCCCCTGGCGAACTTA 60.839 55.000 20.32 0.00 40.58 2.24
352 372 2.125766 GAGGTTCCCCTGGCGAACTT 62.126 60.000 20.32 14.87 42.86 2.66
353 373 2.529389 AGGTTCCCCTGGCGAACT 60.529 61.111 20.32 7.13 40.58 3.01
354 374 2.046217 GAGGTTCCCCTGGCGAAC 60.046 66.667 14.47 14.47 42.86 3.95
396 416 4.079787 AGCAGCTTACAAAGGATCCCAATA 60.080 41.667 8.55 0.00 0.00 1.90
398 418 2.041620 AGCAGCTTACAAAGGATCCCAA 59.958 45.455 8.55 0.00 0.00 4.12
523 546 4.565564 GTCTTATTAGCCAACACTACACCG 59.434 45.833 0.00 0.00 0.00 4.94
525 548 4.565564 CGGTCTTATTAGCCAACACTACAC 59.434 45.833 0.00 0.00 0.00 2.90
589 612 5.221541 TGGCCCTGTATACAAAAACAAAAGG 60.222 40.000 7.06 1.27 0.00 3.11
599 622 6.865834 AAAATGAAATGGCCCTGTATACAA 57.134 33.333 7.06 0.00 0.00 2.41
600 623 6.405286 CGAAAAATGAAATGGCCCTGTATACA 60.405 38.462 5.25 5.25 0.00 2.29
601 624 5.977129 CGAAAAATGAAATGGCCCTGTATAC 59.023 40.000 0.00 0.00 0.00 1.47
602 625 5.654650 ACGAAAAATGAAATGGCCCTGTATA 59.345 36.000 0.00 0.00 0.00 1.47
603 626 4.466015 ACGAAAAATGAAATGGCCCTGTAT 59.534 37.500 0.00 0.00 0.00 2.29
604 627 3.829601 ACGAAAAATGAAATGGCCCTGTA 59.170 39.130 0.00 0.00 0.00 2.74
605 628 2.632512 ACGAAAAATGAAATGGCCCTGT 59.367 40.909 0.00 0.00 0.00 4.00
606 629 2.995258 CACGAAAAATGAAATGGCCCTG 59.005 45.455 0.00 0.00 0.00 4.45
607 630 2.028203 CCACGAAAAATGAAATGGCCCT 60.028 45.455 0.00 0.00 0.00 5.19
608 631 2.289382 ACCACGAAAAATGAAATGGCCC 60.289 45.455 0.00 0.00 0.00 5.80
609 632 2.736192 CACCACGAAAAATGAAATGGCC 59.264 45.455 0.00 0.00 0.00 5.36
610 633 3.389221 ACACCACGAAAAATGAAATGGC 58.611 40.909 0.00 0.00 0.00 4.40
611 634 3.987220 GGACACCACGAAAAATGAAATGG 59.013 43.478 0.00 0.00 0.00 3.16
612 635 4.615949 TGGACACCACGAAAAATGAAATG 58.384 39.130 0.00 0.00 0.00 2.32
613 636 4.927978 TGGACACCACGAAAAATGAAAT 57.072 36.364 0.00 0.00 0.00 2.17
614 637 4.098654 ACATGGACACCACGAAAAATGAAA 59.901 37.500 0.00 0.00 35.80 2.69
615 638 3.634448 ACATGGACACCACGAAAAATGAA 59.366 39.130 0.00 0.00 35.80 2.57
616 639 3.218453 ACATGGACACCACGAAAAATGA 58.782 40.909 0.00 0.00 35.80 2.57
617 640 3.641437 ACATGGACACCACGAAAAATG 57.359 42.857 0.00 0.00 35.80 2.32
618 641 4.394729 AGTACATGGACACCACGAAAAAT 58.605 39.130 11.55 0.00 35.80 1.82
619 642 3.810941 GAGTACATGGACACCACGAAAAA 59.189 43.478 11.55 0.00 35.80 1.94
620 643 3.181464 TGAGTACATGGACACCACGAAAA 60.181 43.478 11.55 0.00 35.80 2.29
621 644 2.365941 TGAGTACATGGACACCACGAAA 59.634 45.455 11.55 0.00 35.80 3.46
622 645 1.964933 TGAGTACATGGACACCACGAA 59.035 47.619 11.55 0.00 35.80 3.85
623 646 1.544246 CTGAGTACATGGACACCACGA 59.456 52.381 11.55 0.00 35.80 4.35
624 647 1.272490 ACTGAGTACATGGACACCACG 59.728 52.381 11.55 4.97 35.80 4.94
638 661 2.301346 CAACTGAGGGCAAAACTGAGT 58.699 47.619 0.00 0.00 33.77 3.41
775 798 0.248134 GTCTGATCGTCTAGCGCGTT 60.248 55.000 8.43 3.54 41.07 4.84
920 996 3.500642 CGCTCTCTCTGTCGCCGA 61.501 66.667 0.00 0.00 0.00 5.54
1100 1194 0.393077 CGGTGTGTGAGAAACCCTCT 59.607 55.000 0.00 0.00 42.44 3.69
1200 1296 5.591472 CAGATCAACCCATTGCTCAAAGATA 59.409 40.000 0.00 0.00 34.09 1.98
1244 1341 3.568007 TCGACCCAAAGGAAGAAACATTG 59.432 43.478 0.00 0.00 36.73 2.82
1287 1386 2.481568 TGCTCTTCTTGCAGTTCATTCG 59.518 45.455 0.00 0.00 35.31 3.34
1364 1463 0.321671 TTGCCCTCCGTCTCTTCTTG 59.678 55.000 0.00 0.00 0.00 3.02
1391 1490 4.753233 TCAAAAGCTAGCTCTCTGTCATC 58.247 43.478 19.65 0.00 0.00 2.92
1409 1508 6.533730 TCTTCTTCAACATCCTAAGCTCAAA 58.466 36.000 0.00 0.00 0.00 2.69
1462 1564 7.560368 CCCAAAAGTAATTGCAAATGGGTATA 58.440 34.615 16.95 0.00 41.08 1.47
1515 1631 9.357652 CCTTTCCATACAATTTCAACATTACAG 57.642 33.333 0.00 0.00 0.00 2.74
1557 1687 8.636213 AGCTTACAAATTCCTCCATAATTCATG 58.364 33.333 0.00 0.00 0.00 3.07
1888 2078 5.263185 CGATTTACTGCCTAAACCAAATCG 58.737 41.667 11.38 11.38 44.38 3.34
1894 2084 8.975410 AAATAAAACGATTTACTGCCTAAACC 57.025 30.769 0.00 0.00 33.98 3.27
1939 2131 8.870075 AGCTCTGGAATAACTCAATTAGTTTT 57.130 30.769 0.00 0.00 46.61 2.43
1942 2134 9.959721 TTTTAGCTCTGGAATAACTCAATTAGT 57.040 29.630 0.00 0.00 41.49 2.24
2035 2234 8.481974 TTTGGTCTTCGATTTAAATCACGATA 57.518 30.769 24.23 9.02 35.11 2.92
2051 2252 6.930722 ACATTTTCCATGACATTTTGGTCTTC 59.069 34.615 0.00 0.00 38.61 2.87
2203 2415 4.097361 GGGTTCGAGTCCCAGCCC 62.097 72.222 18.83 0.00 44.05 5.19
2219 2433 2.035626 AAACCCATGCAGTCCCGG 59.964 61.111 0.00 0.00 0.00 5.73
2221 2435 1.535204 CCACAAACCCATGCAGTCCC 61.535 60.000 0.00 0.00 0.00 4.46
2252 2466 4.430765 CCGAGCGGTTACCAGCGT 62.431 66.667 1.13 0.00 45.98 5.07
2267 2481 1.470098 CAAAGTCTTTCCATCTGCCCG 59.530 52.381 0.00 0.00 0.00 6.13
2291 2505 2.990066 ATAGCTTCCTTCCCAAGTCG 57.010 50.000 0.00 0.00 0.00 4.18
2296 2510 3.130734 ACCAGTATAGCTTCCTTCCCA 57.869 47.619 0.00 0.00 0.00 4.37
2349 2609 3.365832 CACTCTCATGTGTGTGCAAAAC 58.634 45.455 14.75 0.00 34.20 2.43
2430 2706 7.498900 CCAAGTGCCACTCTAAACATAATCATA 59.501 37.037 0.00 0.00 0.00 2.15
2437 2713 3.508845 ACCAAGTGCCACTCTAAACAT 57.491 42.857 0.00 0.00 0.00 2.71
2440 2716 4.394729 CCTAAACCAAGTGCCACTCTAAA 58.605 43.478 0.00 0.00 0.00 1.85
2523 2800 1.339610 TCAAAAATGTCCGTGCCCAAG 59.660 47.619 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.