Multiple sequence alignment - TraesCS6D01G271700

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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 TraesCS6D01G271700 chr6D 100.000 3048 0 0 1 3048 380578054 380575007 0.000000e+00 5629.0
1 TraesCS6D01G271700 chr6D 84.717 1734 208 24 988 2684 380594322 380592609 0.000000e+00 1681.0
2 TraesCS6D01G271700 chr6D 79.571 1493 209 49 876 2300 380565378 380566842 0.000000e+00 979.0
3 TraesCS6D01G271700 chr6D 80.544 992 137 26 933 1877 380495461 380496443 0.000000e+00 712.0
4 TraesCS6D01G271700 chr6D 83.983 718 85 19 2179 2883 380566846 380567546 0.000000e+00 662.0
5 TraesCS6D01G271700 chr6D 82.065 184 25 7 2725 2907 380592365 380592189 1.890000e-32 150.0
6 TraesCS6D01G271700 chr6A 93.910 1330 61 12 1721 3044 522061298 522059983 0.000000e+00 1989.0
7 TraesCS6D01G271700 chr6A 84.426 854 125 5 1 851 553060525 553061373 0.000000e+00 833.0
8 TraesCS6D01G271700 chr6A 93.418 471 21 2 1045 1505 522061966 522061496 0.000000e+00 689.0
9 TraesCS6D01G271700 chr6A 84.867 641 76 13 2208 2841 522046160 522046786 7.170000e-176 627.0
10 TraesCS6D01G271700 chr6A 78.304 908 149 33 1415 2300 522044884 522045765 2.670000e-150 542.0
11 TraesCS6D01G271700 chr6A 86.177 463 64 0 947 1409 522044387 522044849 4.540000e-138 501.0
12 TraesCS6D01G271700 chr6A 94.149 188 11 0 1491 1678 522061468 522061281 1.380000e-73 287.0
13 TraesCS6D01G271700 chr6A 82.787 122 18 2 2179 2300 522045769 522045887 4.160000e-19 106.0
14 TraesCS6D01G271700 chr6A 89.130 46 5 0 2007 2052 19830076 19830121 1.180000e-04 58.4
15 TraesCS6D01G271700 chr6B 79.651 1892 286 58 933 2764 567764823 567766675 0.000000e+00 1269.0
16 TraesCS6D01G271700 chr6B 94.411 662 35 2 2358 3017 567854136 567853475 0.000000e+00 1016.0
17 TraesCS6D01G271700 chr6B 93.014 501 24 5 1875 2375 567856112 567855623 0.000000e+00 721.0
18 TraesCS6D01G271700 chr6B 85.163 674 81 11 2179 2847 567845717 567846376 0.000000e+00 673.0
19 TraesCS6D01G271700 chr6B 83.900 559 64 9 876 1409 567844016 567844573 7.540000e-141 510.0
20 TraesCS6D01G271700 chr6B 89.130 46 5 0 2007 2052 35377485 35377440 1.180000e-04 58.4
21 TraesCS6D01G271700 chr6B 100.000 30 0 0 3019 3048 567853368 567853339 4.250000e-04 56.5
22 TraesCS6D01G271700 chr7A 87.207 852 105 4 1 851 287886132 287885284 0.000000e+00 966.0
23 TraesCS6D01G271700 chr7A 93.023 43 3 0 2604 2646 554501171 554501129 2.540000e-06 63.9
24 TraesCS6D01G271700 chr5A 86.215 856 112 4 1 851 568038976 568039830 0.000000e+00 922.0
25 TraesCS6D01G271700 chr2D 86.401 853 101 10 1 851 647815598 647816437 0.000000e+00 918.0
26 TraesCS6D01G271700 chr3D 86.066 854 113 6 1 851 54384739 54385589 0.000000e+00 913.0
27 TraesCS6D01G271700 chr5D 85.915 852 109 10 1 851 217287520 217286679 0.000000e+00 898.0
28 TraesCS6D01G271700 chr4A 85.874 807 101 10 1 803 7178879 7178082 0.000000e+00 846.0
29 TraesCS6D01G271700 chr4B 86.898 748 92 6 101 846 397889534 397890277 0.000000e+00 833.0
30 TraesCS6D01G271700 chr7B 84.390 852 119 7 1 850 685213709 685212870 0.000000e+00 824.0
31 TraesCS6D01G271700 chr1B 91.014 345 28 1 2497 2838 56615148 56615492 2.140000e-126 462.0
32 TraesCS6D01G271700 chr3B 79.358 436 48 17 1091 1484 139222334 139222769 5.010000e-68 268.0
33 TraesCS6D01G271700 chr1A 91.045 201 7 3 2310 2499 36185288 36185488 8.380000e-66 261.0
34 TraesCS6D01G271700 chr3A 78.091 461 59 17 1068 1486 106401559 106402019 1.400000e-63 254.0


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 TraesCS6D01G271700 chr6D 380575007 380578054 3047 True 5629.000000 5629 100.000000 1 3048 1 chr6D.!!$R1 3047
1 TraesCS6D01G271700 chr6D 380592189 380594322 2133 True 915.500000 1681 83.391000 988 2907 2 chr6D.!!$R2 1919
2 TraesCS6D01G271700 chr6D 380565378 380567546 2168 False 820.500000 979 81.777000 876 2883 2 chr6D.!!$F2 2007
3 TraesCS6D01G271700 chr6D 380495461 380496443 982 False 712.000000 712 80.544000 933 1877 1 chr6D.!!$F1 944
4 TraesCS6D01G271700 chr6A 522059983 522061966 1983 True 988.333333 1989 93.825667 1045 3044 3 chr6A.!!$R1 1999
5 TraesCS6D01G271700 chr6A 553060525 553061373 848 False 833.000000 833 84.426000 1 851 1 chr6A.!!$F2 850
6 TraesCS6D01G271700 chr6A 522044387 522046786 2399 False 444.000000 627 83.033750 947 2841 4 chr6A.!!$F3 1894
7 TraesCS6D01G271700 chr6B 567764823 567766675 1852 False 1269.000000 1269 79.651000 933 2764 1 chr6B.!!$F1 1831
8 TraesCS6D01G271700 chr6B 567853339 567856112 2773 True 597.833333 1016 95.808333 1875 3048 3 chr6B.!!$R2 1173
9 TraesCS6D01G271700 chr6B 567844016 567846376 2360 False 591.500000 673 84.531500 876 2847 2 chr6B.!!$F2 1971
10 TraesCS6D01G271700 chr7A 287885284 287886132 848 True 966.000000 966 87.207000 1 851 1 chr7A.!!$R1 850
11 TraesCS6D01G271700 chr5A 568038976 568039830 854 False 922.000000 922 86.215000 1 851 1 chr5A.!!$F1 850
12 TraesCS6D01G271700 chr2D 647815598 647816437 839 False 918.000000 918 86.401000 1 851 1 chr2D.!!$F1 850
13 TraesCS6D01G271700 chr3D 54384739 54385589 850 False 913.000000 913 86.066000 1 851 1 chr3D.!!$F1 850
14 TraesCS6D01G271700 chr5D 217286679 217287520 841 True 898.000000 898 85.915000 1 851 1 chr5D.!!$R1 850
15 TraesCS6D01G271700 chr4A 7178082 7178879 797 True 846.000000 846 85.874000 1 803 1 chr4A.!!$R1 802
16 TraesCS6D01G271700 chr4B 397889534 397890277 743 False 833.000000 833 86.898000 101 846 1 chr4B.!!$F1 745
17 TraesCS6D01G271700 chr7B 685212870 685213709 839 True 824.000000 824 84.390000 1 850 1 chr7B.!!$R1 849

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
263 278 0.844661 TAGGTGGTGGAAGGGTGCAT 60.845 55.0 0.00 0.0 0.0 3.96 F
1541 1666 0.179062 ATTCAGGAGCTCGGCATGTC 60.179 55.0 7.83 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1696 1829 0.029035 GCGTCCGTCACATCGACTAT 59.971 55.0 0.0 0.0 42.98 2.12 R
2509 4692 0.813821 GAGAGAGCCACCAATTTGCC 59.186 55.0 0.0 0.0 0.00 4.52 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
94 101 1.474677 GCAGGGAGATGATGGAGTGTG 60.475 57.143 0.00 0.00 0.00 3.82
158 165 8.774586 GTGATTCTGTGTTATCCGCTAATAAAT 58.225 33.333 0.00 0.00 0.00 1.40
191 198 1.200020 GGGGAAATTTCTGCGTCAGTG 59.800 52.381 17.42 0.00 32.61 3.66
192 199 2.151202 GGGAAATTTCTGCGTCAGTGA 58.849 47.619 17.42 0.00 32.61 3.41
195 202 3.994392 GGAAATTTCTGCGTCAGTGACTA 59.006 43.478 20.64 9.01 32.61 2.59
199 206 3.660501 TTCTGCGTCAGTGACTACATT 57.339 42.857 20.64 0.00 32.61 2.71
263 278 0.844661 TAGGTGGTGGAAGGGTGCAT 60.845 55.000 0.00 0.00 0.00 3.96
265 280 1.978617 GTGGTGGAAGGGTGCATGG 60.979 63.158 0.00 0.00 0.00 3.66
383 398 4.954092 ATCGAATGAAAGAGCTCCAAAC 57.046 40.909 10.93 0.38 0.00 2.93
425 440 7.747809 TTAAAATAATTGAATGGGGGAGCTT 57.252 32.000 0.00 0.00 0.00 3.74
477 493 6.414732 TCGAGTGACCCAATTCTAAATTGAT 58.585 36.000 12.73 2.40 0.00 2.57
519 535 8.976353 TGATGCCTTAAAAATTAGGAAGCATAA 58.024 29.630 0.00 0.00 30.53 1.90
578 600 5.593968 AGAAATTGTTAACCCGGTCAAAAC 58.406 37.500 0.00 0.00 0.00 2.43
636 658 6.723977 TGATTGTGAGGCCTTAAAAATTAGGT 59.276 34.615 6.77 0.00 33.91 3.08
806 829 5.954335 GTCAAAATCGAATGACCCAATCTT 58.046 37.500 14.87 0.00 40.00 2.40
852 875 4.527816 TGGGCTCTTTAAAACTACGGAGTA 59.472 41.667 0.00 0.00 45.11 2.59
866 889 4.868314 ACGGAGTAGAAAGCTTAGTGTT 57.132 40.909 0.00 0.00 41.94 3.32
867 890 5.972107 ACGGAGTAGAAAGCTTAGTGTTA 57.028 39.130 0.00 0.00 41.94 2.41
868 891 5.707931 ACGGAGTAGAAAGCTTAGTGTTAC 58.292 41.667 0.00 0.00 41.94 2.50
869 892 5.100943 CGGAGTAGAAAGCTTAGTGTTACC 58.899 45.833 0.00 0.00 0.00 2.85
870 893 5.105837 CGGAGTAGAAAGCTTAGTGTTACCT 60.106 44.000 0.00 0.00 0.00 3.08
871 894 6.094603 CGGAGTAGAAAGCTTAGTGTTACCTA 59.905 42.308 0.00 0.00 0.00 3.08
872 895 7.482474 GGAGTAGAAAGCTTAGTGTTACCTAG 58.518 42.308 0.00 0.00 0.00 3.02
873 896 7.407393 AGTAGAAAGCTTAGTGTTACCTAGG 57.593 40.000 7.41 7.41 0.00 3.02
874 897 7.180663 AGTAGAAAGCTTAGTGTTACCTAGGA 58.819 38.462 17.98 0.00 0.00 2.94
878 901 7.840210 AGAAAGCTTAGTGTTACCTAGGATAGT 59.160 37.037 17.98 4.01 36.82 2.12
888 915 1.417890 CCTAGGATAGTTGGCCCAGTG 59.582 57.143 1.05 0.00 36.82 3.66
905 932 4.141688 CCCAGTGAAAACCCTATCCTACTC 60.142 50.000 0.00 0.00 0.00 2.59
912 939 1.790157 ACCCTATCCTACTCTCCCCTG 59.210 57.143 0.00 0.00 0.00 4.45
913 940 2.074579 CCCTATCCTACTCTCCCCTGA 58.925 57.143 0.00 0.00 0.00 3.86
914 941 2.657459 CCCTATCCTACTCTCCCCTGAT 59.343 54.545 0.00 0.00 0.00 2.90
928 955 3.263425 TCCCCTGATTACTTTCACTCCAC 59.737 47.826 0.00 0.00 0.00 4.02
931 958 4.223923 CCCTGATTACTTTCACTCCACTCT 59.776 45.833 0.00 0.00 0.00 3.24
984 1026 3.712907 GCCGCCACCCTTCCACTA 61.713 66.667 0.00 0.00 0.00 2.74
985 1027 3.074281 CCGCCACCCTTCCACTAA 58.926 61.111 0.00 0.00 0.00 2.24
986 1028 1.078426 CCGCCACCCTTCCACTAAG 60.078 63.158 0.00 0.00 34.73 2.18
1334 1382 3.197790 CTGCAGGTTCGCATCCCG 61.198 66.667 5.57 0.00 42.06 5.14
1417 1465 1.153997 GTCAACGACGAGGAGCTCC 60.154 63.158 26.22 26.22 0.00 4.70
1486 1569 0.319405 CTTTACGTTCCCGGACACCT 59.681 55.000 0.73 0.00 38.78 4.00
1490 1573 2.273179 CGTTCCCGGACACCTCTGA 61.273 63.158 0.73 0.00 0.00 3.27
1499 1582 1.063266 GGACACCTCTGATCTCTCCCT 60.063 57.143 0.00 0.00 0.00 4.20
1506 1631 0.754957 CTGATCTCTCCCTCCGTGCT 60.755 60.000 0.00 0.00 0.00 4.40
1541 1666 0.179062 ATTCAGGAGCTCGGCATGTC 60.179 55.000 7.83 0.00 0.00 3.06
1663 1796 3.306595 CTCCGCTGCAAGAGCCTCA 62.307 63.158 0.00 0.00 46.01 3.86
1682 1815 2.357517 GTGCGTGGTCCTCTGGTG 60.358 66.667 0.00 0.00 0.00 4.17
1686 1819 0.818040 GCGTGGTCCTCTGGTGTTTT 60.818 55.000 0.00 0.00 0.00 2.43
1693 1826 1.526575 CCTCTGGTGTTTTGCGGCAT 61.527 55.000 2.28 0.00 0.00 4.40
1694 1827 0.314935 CTCTGGTGTTTTGCGGCATT 59.685 50.000 2.28 0.00 0.00 3.56
1696 1829 0.031857 CTGGTGTTTTGCGGCATTCA 59.968 50.000 2.28 0.64 0.00 2.57
1697 1830 0.678395 TGGTGTTTTGCGGCATTCAT 59.322 45.000 2.28 0.00 0.00 2.57
1698 1831 1.889170 TGGTGTTTTGCGGCATTCATA 59.111 42.857 2.28 0.00 0.00 2.15
1703 1836 2.017138 TTTGCGGCATTCATAGTCGA 57.983 45.000 2.28 0.00 0.00 4.20
1708 1841 2.742774 CGGCATTCATAGTCGATGTGA 58.257 47.619 0.00 0.00 36.84 3.58
1718 1851 4.129737 CGATGTGACGGACGCCCT 62.130 66.667 0.00 0.00 0.00 5.19
1767 1912 4.436998 CCCCGCAGAGGTGACGAC 62.437 72.222 0.00 0.00 38.74 4.34
1768 1913 3.374402 CCCGCAGAGGTGACGACT 61.374 66.667 0.00 0.00 38.74 4.18
1849 1994 0.960364 GCCAAGATTTCACCGGCTGA 60.960 55.000 0.00 1.26 39.73 4.26
2064 2237 5.820423 GGCTTTGAAGGTTAATTTTGGTGTT 59.180 36.000 0.00 0.00 0.00 3.32
2103 2276 2.064581 GGTGGCCTACCTCGGATGT 61.065 63.158 14.93 0.00 46.51 3.06
2139 2312 2.375766 GCTGCACGTCGAGGTGAAG 61.376 63.158 35.27 33.93 44.94 3.02
2142 2315 1.286260 GCACGTCGAGGTGAAGTCT 59.714 57.895 35.27 0.00 40.38 3.24
2145 2318 2.606308 GCACGTCGAGGTGAAGTCTTTA 60.606 50.000 35.27 0.00 40.38 1.85
2146 2319 3.635331 CACGTCGAGGTGAAGTCTTTAA 58.365 45.455 29.41 0.00 40.38 1.52
2147 2320 3.424529 CACGTCGAGGTGAAGTCTTTAAC 59.575 47.826 29.41 0.00 40.38 2.01
2149 2322 3.669122 CGTCGAGGTGAAGTCTTTAACTG 59.331 47.826 0.00 0.00 38.58 3.16
2150 2323 4.556104 CGTCGAGGTGAAGTCTTTAACTGA 60.556 45.833 0.00 0.00 38.58 3.41
2151 2324 5.287226 GTCGAGGTGAAGTCTTTAACTGAA 58.713 41.667 0.00 0.00 38.58 3.02
2152 2325 5.175308 GTCGAGGTGAAGTCTTTAACTGAAC 59.825 44.000 0.00 0.00 38.58 3.18
2153 2326 4.448060 CGAGGTGAAGTCTTTAACTGAACC 59.552 45.833 0.00 0.00 41.50 3.62
2154 2327 4.715713 AGGTGAAGTCTTTAACTGAACCC 58.284 43.478 0.00 0.00 41.86 4.11
2155 2328 4.165372 AGGTGAAGTCTTTAACTGAACCCA 59.835 41.667 0.00 0.00 41.86 4.51
2156 2329 4.275196 GGTGAAGTCTTTAACTGAACCCAC 59.725 45.833 0.00 0.00 37.92 4.61
2157 2330 5.123936 GTGAAGTCTTTAACTGAACCCACT 58.876 41.667 0.00 0.00 38.58 4.00
2158 2331 5.007724 GTGAAGTCTTTAACTGAACCCACTG 59.992 44.000 0.00 0.00 38.58 3.66
2159 2332 5.104693 TGAAGTCTTTAACTGAACCCACTGA 60.105 40.000 0.00 0.00 38.58 3.41
2160 2333 5.367945 AGTCTTTAACTGAACCCACTGAA 57.632 39.130 0.00 0.00 36.65 3.02
2161 2334 5.751586 AGTCTTTAACTGAACCCACTGAAA 58.248 37.500 0.00 0.00 36.65 2.69
2162 2335 5.823045 AGTCTTTAACTGAACCCACTGAAAG 59.177 40.000 0.00 0.00 36.65 2.62
2163 2336 5.820947 GTCTTTAACTGAACCCACTGAAAGA 59.179 40.000 0.00 0.00 37.43 2.52
2164 2337 6.486993 GTCTTTAACTGAACCCACTGAAAGAT 59.513 38.462 0.00 0.00 35.01 2.40
2165 2338 6.710744 TCTTTAACTGAACCCACTGAAAGATC 59.289 38.462 0.00 0.00 37.43 2.75
2220 2414 9.289782 ACCACTATTTATTAGCAATGGAAGATC 57.710 33.333 0.00 0.00 30.00 2.75
2221 2415 8.446273 CCACTATTTATTAGCAATGGAAGATCG 58.554 37.037 0.00 0.00 0.00 3.69
2222 2416 7.959651 CACTATTTATTAGCAATGGAAGATCGC 59.040 37.037 0.00 0.00 0.00 4.58
2223 2417 7.880195 ACTATTTATTAGCAATGGAAGATCGCT 59.120 33.333 0.00 0.00 36.72 4.93
2224 2418 9.371136 CTATTTATTAGCAATGGAAGATCGCTA 57.629 33.333 0.00 0.00 34.18 4.26
2225 2419 7.421530 TTTATTAGCAATGGAAGATCGCTAC 57.578 36.000 0.00 0.00 35.04 3.58
2226 2420 2.246719 AGCAATGGAAGATCGCTACC 57.753 50.000 0.00 0.00 0.00 3.18
2235 2429 2.522836 AGATCGCTACCTCTTGCATG 57.477 50.000 0.00 0.00 0.00 4.06
2244 2684 3.947612 ACCTCTTGCATGATCCATCTT 57.052 42.857 2.33 0.00 0.00 2.40
2252 2819 5.700722 TGCATGATCCATCTTTCTAATGC 57.299 39.130 0.00 0.00 39.61 3.56
2269 2948 8.978874 TTCTAATGCACCATTTACTGATATGT 57.021 30.769 0.00 0.00 35.54 2.29
2400 4583 9.197694 CATAAATATAGAGGGAAACGAAGTGAG 57.802 37.037 0.00 0.00 45.00 3.51
2509 4692 2.619147 CCAAGCAGACAGAGATGACAG 58.381 52.381 0.00 0.00 0.00 3.51
2670 4857 2.544486 GGCTGGCTATACATTTGCTTGC 60.544 50.000 0.00 0.00 0.00 4.01
2743 5133 3.430236 GCAAGGGCACTGTTTAGTTTGTT 60.430 43.478 0.00 0.00 40.72 2.83
2757 5151 7.499563 TGTTTAGTTTGTTGGCAAGTATGTCTA 59.500 33.333 0.00 0.00 35.82 2.59
2856 5252 6.853720 TCATTCAGAGTGTACTAGTAACTGC 58.146 40.000 17.16 11.25 0.00 4.40
2916 5326 3.009033 TGATCCTCCTTCCGAACATGTTT 59.991 43.478 13.36 0.00 0.00 2.83
2961 5371 4.880886 TGATGGCGTCTATGTCAATTTG 57.119 40.909 8.40 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 101 6.363896 CCACCAAATCACCGTGTTATAAAAAC 59.636 38.462 0.00 0.00 0.00 2.43
131 138 2.540515 AGCGGATAACACAGAATCACG 58.459 47.619 0.00 0.00 0.00 4.35
158 165 6.015918 AGAAATTTCCCCACACACATATGAA 58.984 36.000 14.61 0.00 0.00 2.57
165 172 1.335872 CGCAGAAATTTCCCCACACAC 60.336 52.381 14.61 0.00 0.00 3.82
167 174 0.958822 ACGCAGAAATTTCCCCACAC 59.041 50.000 14.61 0.00 0.00 3.82
191 198 9.976511 TGTAGCACCAATATAGTAAATGTAGTC 57.023 33.333 0.00 0.00 0.00 2.59
192 199 9.982651 CTGTAGCACCAATATAGTAAATGTAGT 57.017 33.333 0.00 0.00 0.00 2.73
199 206 9.582648 TCTGATACTGTAGCACCAATATAGTAA 57.417 33.333 0.93 0.00 32.70 2.24
263 278 7.754624 TGGCTTATAGAAACATATCAATCCCA 58.245 34.615 0.00 0.00 0.00 4.37
265 280 8.854614 ACTGGCTTATAGAAACATATCAATCC 57.145 34.615 0.00 0.00 0.00 3.01
316 331 4.157840 GGTTTACTATTTTGACCAGGCCAG 59.842 45.833 5.01 0.00 0.00 4.85
449 465 8.673711 CAATTTAGAATTGGGTCACTCGATTTA 58.326 33.333 0.00 0.00 0.00 1.40
549 569 6.041069 TGACCGGGTTAACAATTTCTCAAATT 59.959 34.615 6.32 0.00 41.57 1.82
550 571 5.536916 TGACCGGGTTAACAATTTCTCAAAT 59.463 36.000 6.32 0.00 0.00 2.32
578 600 3.324993 CAATTGAAATTGGTTCACCCGG 58.675 45.455 0.00 0.00 46.09 5.73
636 658 5.361571 TGACCGGATCAACAATACTAAGCTA 59.638 40.000 9.46 0.00 33.02 3.32
653 676 3.316868 GGTTCAACTTGATTTTGACCGGA 59.683 43.478 9.46 0.00 32.65 5.14
666 689 8.290325 GTCTTCAATTTAGAATCGGTTCAACTT 58.710 33.333 11.72 1.45 36.79 2.66
700 723 8.871629 TCCTTAACTTTTAAGGCATCACAATA 57.128 30.769 16.79 0.00 42.83 1.90
766 789 6.478512 TTTTGACCTAGCCAACAATTTCTT 57.521 33.333 0.00 0.00 0.00 2.52
824 847 7.114095 TCCGTAGTTTTAAAGAGCCCATATTT 58.886 34.615 0.00 0.00 0.00 1.40
846 869 5.100943 GGTAACACTAAGCTTTCTACTCCG 58.899 45.833 3.20 0.00 0.00 4.63
851 874 9.352191 CTATCCTAGGTAACACTAAGCTTTCTA 57.648 37.037 3.20 0.00 41.41 2.10
852 875 7.840210 ACTATCCTAGGTAACACTAAGCTTTCT 59.160 37.037 3.20 0.00 41.41 2.52
853 876 8.009622 ACTATCCTAGGTAACACTAAGCTTTC 57.990 38.462 3.20 0.00 41.41 2.62
854 877 7.974730 ACTATCCTAGGTAACACTAAGCTTT 57.025 36.000 3.20 0.00 41.41 3.51
855 878 7.147707 CCAACTATCCTAGGTAACACTAAGCTT 60.148 40.741 9.08 3.48 41.41 3.74
856 879 6.324254 CCAACTATCCTAGGTAACACTAAGCT 59.676 42.308 9.08 0.00 41.41 3.74
857 880 6.514063 CCAACTATCCTAGGTAACACTAAGC 58.486 44.000 9.08 0.00 41.41 3.09
858 881 6.462628 GGCCAACTATCCTAGGTAACACTAAG 60.463 46.154 9.08 0.00 41.41 2.18
859 882 5.364735 GGCCAACTATCCTAGGTAACACTAA 59.635 44.000 9.08 0.00 41.41 2.24
860 883 4.897670 GGCCAACTATCCTAGGTAACACTA 59.102 45.833 9.08 0.00 41.41 2.74
861 884 3.710165 GGCCAACTATCCTAGGTAACACT 59.290 47.826 9.08 0.00 41.41 3.55
862 885 3.181457 GGGCCAACTATCCTAGGTAACAC 60.181 52.174 9.08 0.00 41.41 3.32
863 886 3.043418 GGGCCAACTATCCTAGGTAACA 58.957 50.000 9.08 0.00 41.41 2.41
864 887 3.043418 TGGGCCAACTATCCTAGGTAAC 58.957 50.000 2.13 0.00 0.00 2.50
865 888 3.311103 ACTGGGCCAACTATCCTAGGTAA 60.311 47.826 8.04 0.00 35.53 2.85
866 889 2.249214 ACTGGGCCAACTATCCTAGGTA 59.751 50.000 8.04 0.00 35.53 3.08
867 890 1.009675 ACTGGGCCAACTATCCTAGGT 59.990 52.381 8.04 0.00 35.53 3.08
868 891 1.417890 CACTGGGCCAACTATCCTAGG 59.582 57.143 8.04 0.82 35.53 3.02
869 892 2.398588 TCACTGGGCCAACTATCCTAG 58.601 52.381 8.04 0.00 37.04 3.02
870 893 2.561209 TCACTGGGCCAACTATCCTA 57.439 50.000 8.04 0.00 0.00 2.94
871 894 1.668826 TTCACTGGGCCAACTATCCT 58.331 50.000 8.04 0.00 0.00 3.24
872 895 2.492088 GTTTTCACTGGGCCAACTATCC 59.508 50.000 8.04 0.00 0.00 2.59
873 896 2.492088 GGTTTTCACTGGGCCAACTATC 59.508 50.000 8.04 0.00 0.00 2.08
874 897 2.525368 GGTTTTCACTGGGCCAACTAT 58.475 47.619 8.04 0.00 0.00 2.12
878 901 0.854218 TAGGGTTTTCACTGGGCCAA 59.146 50.000 8.04 0.00 34.26 4.52
888 915 3.647113 GGGGAGAGTAGGATAGGGTTTTC 59.353 52.174 0.00 0.00 0.00 2.29
905 932 3.519510 TGGAGTGAAAGTAATCAGGGGAG 59.480 47.826 0.00 0.00 0.00 4.30
912 939 4.425520 CGGAGAGTGGAGTGAAAGTAATC 58.574 47.826 0.00 0.00 0.00 1.75
913 940 3.368531 GCGGAGAGTGGAGTGAAAGTAAT 60.369 47.826 0.00 0.00 0.00 1.89
914 941 2.029290 GCGGAGAGTGGAGTGAAAGTAA 60.029 50.000 0.00 0.00 0.00 2.24
973 1015 1.972588 ATGGAGCTTAGTGGAAGGGT 58.027 50.000 0.00 0.00 35.49 4.34
975 1017 2.743183 CGGAATGGAGCTTAGTGGAAGG 60.743 54.545 0.00 0.00 35.49 3.46
976 1018 2.555199 CGGAATGGAGCTTAGTGGAAG 58.445 52.381 0.00 0.00 38.30 3.46
977 1019 1.209504 CCGGAATGGAGCTTAGTGGAA 59.790 52.381 0.00 0.00 42.00 3.53
984 1026 1.454479 CATGGCCGGAATGGAGCTT 60.454 57.895 5.05 0.00 42.00 3.74
985 1027 2.194056 CATGGCCGGAATGGAGCT 59.806 61.111 5.05 0.00 42.00 4.09
986 1028 2.908940 CCATGGCCGGAATGGAGC 60.909 66.667 25.21 0.00 46.44 4.70
1009 1056 2.006888 GCCCATGATTTTCTCGACGAA 58.993 47.619 0.00 0.00 0.00 3.85
1413 1461 3.083997 AGGATGTCGGTGGGGAGC 61.084 66.667 0.00 0.00 0.00 4.70
1417 1465 4.530857 GCGGAGGATGTCGGTGGG 62.531 72.222 0.00 0.00 0.00 4.61
1486 1569 0.753479 GCACGGAGGGAGAGATCAGA 60.753 60.000 0.00 0.00 0.00 3.27
1490 1573 1.040339 GTCAGCACGGAGGGAGAGAT 61.040 60.000 0.00 0.00 0.00 2.75
1522 1647 0.179062 GACATGCCGAGCTCCTGAAT 60.179 55.000 8.47 0.00 0.00 2.57
1663 1796 3.314331 CCAGAGGACCACGCACCT 61.314 66.667 0.00 0.00 39.41 4.00
1682 1815 2.095213 TCGACTATGAATGCCGCAAAAC 59.905 45.455 0.00 0.00 0.00 2.43
1686 1819 1.202521 ACATCGACTATGAATGCCGCA 60.203 47.619 0.00 0.00 39.07 5.69
1693 1826 2.223180 CGTCCGTCACATCGACTATGAA 60.223 50.000 0.00 0.00 42.98 2.57
1694 1827 1.329599 CGTCCGTCACATCGACTATGA 59.670 52.381 0.00 0.00 42.98 2.15
1696 1829 0.029035 GCGTCCGTCACATCGACTAT 59.971 55.000 0.00 0.00 42.98 2.12
1697 1830 1.426621 GCGTCCGTCACATCGACTA 59.573 57.895 0.00 0.00 42.98 2.59
1698 1831 2.178521 GCGTCCGTCACATCGACT 59.821 61.111 0.00 0.00 42.98 4.18
1703 1836 4.760047 GCAGGGCGTCCGTCACAT 62.760 66.667 0.00 0.00 38.33 3.21
1767 1912 7.520131 GCAATCTTGATCATCACAATACTCCAG 60.520 40.741 0.00 0.00 0.00 3.86
1768 1913 6.261603 GCAATCTTGATCATCACAATACTCCA 59.738 38.462 0.00 0.00 0.00 3.86
1849 1994 2.205074 GATGTCATTGTCGCCGATCTT 58.795 47.619 0.00 0.00 0.00 2.40
1997 2170 2.033194 GTACTTGGGCTCGGCACAC 61.033 63.158 0.00 0.00 43.74 3.82
1998 2171 2.345991 GTACTTGGGCTCGGCACA 59.654 61.111 0.00 0.00 41.67 4.57
2064 2237 5.887598 CACCATCATCTTGACATCCCTTAAA 59.112 40.000 0.00 0.00 0.00 1.52
2103 2276 2.028130 AGCGTGTCAATGTTGGGAAAA 58.972 42.857 0.00 0.00 0.00 2.29
2128 2301 4.868067 TCAGTTAAAGACTTCACCTCGAC 58.132 43.478 0.00 0.00 36.10 4.20
2139 2312 5.820947 TCTTTCAGTGGGTTCAGTTAAAGAC 59.179 40.000 6.52 0.00 39.60 3.01
2142 2315 6.361433 TGATCTTTCAGTGGGTTCAGTTAAA 58.639 36.000 0.00 0.00 0.00 1.52
2145 2318 4.437682 TGATCTTTCAGTGGGTTCAGTT 57.562 40.909 0.00 0.00 0.00 3.16
2146 2319 4.647564 ATGATCTTTCAGTGGGTTCAGT 57.352 40.909 0.00 0.00 34.73 3.41
2147 2320 7.337689 TGAATAATGATCTTTCAGTGGGTTCAG 59.662 37.037 0.00 0.00 34.73 3.02
2149 2322 7.630242 TGAATAATGATCTTTCAGTGGGTTC 57.370 36.000 0.00 0.00 34.73 3.62
2150 2323 8.599624 ATTGAATAATGATCTTTCAGTGGGTT 57.400 30.769 0.00 0.00 34.73 4.11
2151 2324 7.835682 TGATTGAATAATGATCTTTCAGTGGGT 59.164 33.333 0.00 0.00 34.73 4.51
2152 2325 8.229253 TGATTGAATAATGATCTTTCAGTGGG 57.771 34.615 0.00 0.00 34.73 4.61
2153 2326 8.900781 ACTGATTGAATAATGATCTTTCAGTGG 58.099 33.333 8.32 2.86 37.83 4.00
2164 2337 9.699410 AGGGTCAAATAACTGATTGAATAATGA 57.301 29.630 0.00 0.00 37.31 2.57
2165 2338 9.956720 GAGGGTCAAATAACTGATTGAATAATG 57.043 33.333 0.00 0.00 37.31 1.90
2186 2380 7.626999 TGCTAATAAATAGTGGTATGAGGGT 57.373 36.000 0.00 0.00 33.87 4.34
2188 2382 8.950210 CCATTGCTAATAAATAGTGGTATGAGG 58.050 37.037 0.00 0.00 33.87 3.86
2220 2414 1.202568 TGGATCATGCAAGAGGTAGCG 60.203 52.381 0.00 0.00 0.00 4.26
2221 2415 2.627515 TGGATCATGCAAGAGGTAGC 57.372 50.000 0.00 0.00 0.00 3.58
2222 2416 4.620589 AGATGGATCATGCAAGAGGTAG 57.379 45.455 0.00 0.00 0.00 3.18
2223 2417 5.131642 AGAAAGATGGATCATGCAAGAGGTA 59.868 40.000 0.00 0.00 0.00 3.08
2224 2418 3.947612 AAGATGGATCATGCAAGAGGT 57.052 42.857 0.00 0.00 0.00 3.85
2225 2419 4.462133 AGAAAGATGGATCATGCAAGAGG 58.538 43.478 0.00 0.00 0.00 3.69
2226 2420 7.585867 CATTAGAAAGATGGATCATGCAAGAG 58.414 38.462 0.00 0.00 0.00 2.85
2235 2429 6.645790 AATGGTGCATTAGAAAGATGGATC 57.354 37.500 0.00 0.00 31.77 3.36
2244 2684 8.978874 ACATATCAGTAAATGGTGCATTAGAA 57.021 30.769 0.00 0.00 32.43 2.10
2252 2819 8.900511 CTGAAACAACATATCAGTAAATGGTG 57.099 34.615 0.00 0.00 44.64 4.17
2400 4583 7.378181 TGGAAATGAACTTAAGGAATTCAAGC 58.622 34.615 7.93 2.69 36.03 4.01
2509 4692 0.813821 GAGAGAGCCACCAATTTGCC 59.186 55.000 0.00 0.00 0.00 4.52
2547 4730 3.976793 AGCACCATTATCTTGCAATCG 57.023 42.857 0.00 0.00 38.81 3.34
2743 5133 6.048732 TGTCAAGAATAGACATACTTGCCA 57.951 37.500 0.00 0.00 40.80 4.92
2856 5252 7.551585 ACATCAGGAACAAACAGAGTAGATAG 58.448 38.462 0.00 0.00 0.00 2.08


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

AutoCloner maintained by Alex Coulton.