Multiple sequence alignment - TraesCS6A01G001400

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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 TraesCS6A01G001400 chr6A 100.000 4127 0 0 552 4678 775081 770955 0.000000e+00 7622.0
1 TraesCS6A01G001400 chr6A 81.538 1690 234 36 627 2261 587890305 587891971 0.000000e+00 1321.0
2 TraesCS6A01G001400 chr6A 80.403 1689 235 47 626 2261 587972165 587970520 0.000000e+00 1197.0
3 TraesCS6A01G001400 chr6A 95.680 625 23 4 4056 4678 613601712 613602334 0.000000e+00 1002.0
4 TraesCS6A01G001400 chr6A 100.000 166 0 0 1 166 775632 775467 1.640000e-79 307.0
5 TraesCS6A01G001400 chr6D 93.169 2357 101 19 552 2865 2133903 2136242 0.000000e+00 3406.0
6 TraesCS6A01G001400 chr6D 96.837 1328 31 6 1540 2865 4209039 4210357 0.000000e+00 2209.0
7 TraesCS6A01G001400 chr6D 97.029 1178 29 3 2885 4060 4210610 4211783 0.000000e+00 1977.0
8 TraesCS6A01G001400 chr6D 94.562 1177 59 3 2885 4060 2136495 2137667 0.000000e+00 1814.0
9 TraesCS6A01G001400 chr6D 96.928 944 28 1 552 1495 4208101 4209043 0.000000e+00 1581.0
10 TraesCS6A01G001400 chr6D 81.936 1694 222 37 626 2261 439616067 439617734 0.000000e+00 1356.0
11 TraesCS6A01G001400 chr6D 94.712 624 32 1 4056 4678 402561088 402561711 0.000000e+00 968.0
12 TraesCS6A01G001400 chr6D 93.976 166 10 0 1 166 4207904 4208069 7.770000e-63 252.0
13 TraesCS6A01G001400 chr6D 84.242 165 23 3 1 165 178628394 178628233 1.740000e-34 158.0
14 TraesCS6A01G001400 chr6B 92.411 2227 124 20 552 2740 3799560 3801779 0.000000e+00 3134.0
15 TraesCS6A01G001400 chr6B 93.537 1176 68 3 2885 4060 4376341 4375174 0.000000e+00 1744.0
16 TraesCS6A01G001400 chr6B 93.458 1177 68 4 2885 4060 3837152 3838320 0.000000e+00 1738.0
17 TraesCS6A01G001400 chr6B 95.059 1012 47 2 552 1560 3835062 3836073 0.000000e+00 1589.0
18 TraesCS6A01G001400 chr6B 94.071 1012 57 2 552 1560 4379028 4378017 0.000000e+00 1533.0
19 TraesCS6A01G001400 chr6B 81.457 1688 236 34 626 2261 664477321 664478983 0.000000e+00 1312.0
20 TraesCS6A01G001400 chr6B 77.664 1858 301 57 1087 2863 664506689 664504865 0.000000e+00 1027.0
21 TraesCS6A01G001400 chr6B 92.022 727 41 10 1558 2272 4377935 4377214 0.000000e+00 1005.0
22 TraesCS6A01G001400 chr6B 79.335 1534 225 40 626 2110 664525157 664523667 0.000000e+00 992.0
23 TraesCS6A01G001400 chr6B 95.270 592 24 3 2276 2865 4377183 4376594 0.000000e+00 935.0
24 TraesCS6A01G001400 chr6B 95.992 524 16 3 2344 2865 3836379 3836899 0.000000e+00 846.0
25 TraesCS6A01G001400 chr6B 95.690 232 10 0 1558 1789 3836155 3836386 1.590000e-99 374.0
26 TraesCS6A01G001400 chrUn 93.622 1176 66 4 2885 4060 355128969 355127803 0.000000e+00 1748.0
27 TraesCS6A01G001400 chrUn 94.836 1007 49 2 552 1555 255513865 255514871 0.000000e+00 1568.0
28 TraesCS6A01G001400 chrUn 93.100 884 53 3 3177 4060 355695289 355694414 0.000000e+00 1288.0
29 TraesCS6A01G001400 chrUn 95.301 681 30 1 552 1230 380680165 380680845 0.000000e+00 1079.0
30 TraesCS6A01G001400 chrUn 92.033 728 39 12 1558 2272 255514958 255515679 0.000000e+00 1005.0
31 TraesCS6A01G001400 chrUn 95.032 624 30 1 4056 4678 47641666 47641043 0.000000e+00 979.0
32 TraesCS6A01G001400 chrUn 94.541 403 22 0 3177 3579 478404781 478405183 1.430000e-174 623.0
33 TraesCS6A01G001400 chrUn 96.284 296 11 0 2885 3180 475068658 475068363 1.960000e-133 486.0
34 TraesCS6A01G001400 chrUn 94.792 96 5 0 2273 2368 255515707 255515802 2.920000e-32 150.0
35 TraesCS6A01G001400 chr2D 95.513 624 27 1 4056 4678 566284327 566283704 0.000000e+00 996.0
36 TraesCS6A01G001400 chr2D 94.872 624 30 2 4056 4678 635193547 635194169 0.000000e+00 974.0
37 TraesCS6A01G001400 chr2D 77.778 162 34 2 1 162 326154297 326154138 1.070000e-16 99.0
38 TraesCS6A01G001400 chr3D 95.032 624 29 2 4056 4678 610533239 610533861 0.000000e+00 979.0
39 TraesCS6A01G001400 chr1D 94.745 628 31 2 4052 4678 440060113 440060739 0.000000e+00 976.0
40 TraesCS6A01G001400 chr7D 94.864 623 32 0 4056 4678 555164764 555165386 0.000000e+00 974.0
41 TraesCS6A01G001400 chr4A 94.712 624 32 1 4056 4678 574717820 574717197 0.000000e+00 968.0
42 TraesCS6A01G001400 chr7A 86.503 163 19 2 1 163 469153838 469153679 4.810000e-40 176.0
43 TraesCS6A01G001400 chr7A 75.758 165 34 5 1 163 313677983 313677823 1.400000e-10 78.7
44 TraesCS6A01G001400 chr5B 78.607 201 36 6 3820 4016 711837867 711837670 4.910000e-25 126.0
45 TraesCS6A01G001400 chr3B 79.878 164 23 10 3 162 71806420 71806263 1.380000e-20 111.0
46 TraesCS6A01G001400 chr5A 83.051 118 19 1 3869 3986 555306645 555306529 6.400000e-19 106.0
47 TraesCS6A01G001400 chr1B 78.125 160 34 1 6 165 452305096 452304938 2.980000e-17 100.0
48 TraesCS6A01G001400 chr3A 76.970 165 36 2 1 165 454995660 454995498 4.980000e-15 93.5
49 TraesCS6A01G001400 chr1A 77.108 166 34 4 1 165 363638434 363638596 4.980000e-15 93.5


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 TraesCS6A01G001400 chr6A 770955 775632 4677 True 3964.500000 7622 100.00000 1 4678 2 chr6A.!!$R2 4677
1 TraesCS6A01G001400 chr6A 587890305 587891971 1666 False 1321.000000 1321 81.53800 627 2261 1 chr6A.!!$F1 1634
2 TraesCS6A01G001400 chr6A 587970520 587972165 1645 True 1197.000000 1197 80.40300 626 2261 1 chr6A.!!$R1 1635
3 TraesCS6A01G001400 chr6A 613601712 613602334 622 False 1002.000000 1002 95.68000 4056 4678 1 chr6A.!!$F2 622
4 TraesCS6A01G001400 chr6D 2133903 2137667 3764 False 2610.000000 3406 93.86550 552 4060 2 chr6D.!!$F3 3508
5 TraesCS6A01G001400 chr6D 4207904 4211783 3879 False 1504.750000 2209 96.19250 1 4060 4 chr6D.!!$F4 4059
6 TraesCS6A01G001400 chr6D 439616067 439617734 1667 False 1356.000000 1356 81.93600 626 2261 1 chr6D.!!$F2 1635
7 TraesCS6A01G001400 chr6D 402561088 402561711 623 False 968.000000 968 94.71200 4056 4678 1 chr6D.!!$F1 622
8 TraesCS6A01G001400 chr6B 3799560 3801779 2219 False 3134.000000 3134 92.41100 552 2740 1 chr6B.!!$F1 2188
9 TraesCS6A01G001400 chr6B 664477321 664478983 1662 False 1312.000000 1312 81.45700 626 2261 1 chr6B.!!$F2 1635
10 TraesCS6A01G001400 chr6B 4375174 4379028 3854 True 1304.250000 1744 93.72500 552 4060 4 chr6B.!!$R3 3508
11 TraesCS6A01G001400 chr6B 3835062 3838320 3258 False 1136.750000 1738 95.04975 552 4060 4 chr6B.!!$F3 3508
12 TraesCS6A01G001400 chr6B 664504865 664506689 1824 True 1027.000000 1027 77.66400 1087 2863 1 chr6B.!!$R1 1776
13 TraesCS6A01G001400 chr6B 664523667 664525157 1490 True 992.000000 992 79.33500 626 2110 1 chr6B.!!$R2 1484
14 TraesCS6A01G001400 chrUn 355127803 355128969 1166 True 1748.000000 1748 93.62200 2885 4060 1 chrUn.!!$R2 1175
15 TraesCS6A01G001400 chrUn 355694414 355695289 875 True 1288.000000 1288 93.10000 3177 4060 1 chrUn.!!$R3 883
16 TraesCS6A01G001400 chrUn 380680165 380680845 680 False 1079.000000 1079 95.30100 552 1230 1 chrUn.!!$F1 678
17 TraesCS6A01G001400 chrUn 47641043 47641666 623 True 979.000000 979 95.03200 4056 4678 1 chrUn.!!$R1 622
18 TraesCS6A01G001400 chrUn 255513865 255515802 1937 False 907.666667 1568 93.88700 552 2368 3 chrUn.!!$F3 1816
19 TraesCS6A01G001400 chr2D 566283704 566284327 623 True 996.000000 996 95.51300 4056 4678 1 chr2D.!!$R2 622
20 TraesCS6A01G001400 chr2D 635193547 635194169 622 False 974.000000 974 94.87200 4056 4678 1 chr2D.!!$F1 622
21 TraesCS6A01G001400 chr3D 610533239 610533861 622 False 979.000000 979 95.03200 4056 4678 1 chr3D.!!$F1 622
22 TraesCS6A01G001400 chr1D 440060113 440060739 626 False 976.000000 976 94.74500 4052 4678 1 chr1D.!!$F1 626
23 TraesCS6A01G001400 chr7D 555164764 555165386 622 False 974.000000 974 94.86400 4056 4678 1 chr7D.!!$F1 622
24 TraesCS6A01G001400 chr4A 574717197 574717820 623 True 968.000000 968 94.71200 4056 4678 1 chr4A.!!$R1 622

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
162 163 4.218312 TCTCTGGCAAGCTATGATAGACA 58.782 43.478 3.13 0.00 0.00 3.41 F
1008 1024 6.603940 TTCCCTATTTTCACAATGAAAGGG 57.396 37.500 16.13 16.13 46.32 3.95 F
1198 1214 4.466015 AGCATATGTTTTGGGGGTTAACAG 59.534 41.667 8.10 0.00 35.48 3.16 F
1862 2016 4.499040 GCGTGTAATTGTGGCATTTGATAC 59.501 41.667 0.00 0.00 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1008 1024 2.165030 AGTTGCACTAATGGCTTGCATC 59.835 45.455 0.0 0.0 45.35 3.91 R
2590 2801 2.978978 CACCCCATATACATCACCCTGA 59.021 50.000 0.0 0.0 0.00 3.86 R
2865 3079 3.486383 TCACTCAATGTTGGAAAGACCC 58.514 45.455 0.0 0.0 38.00 4.46 R
3772 4221 1.131638 CCCCAATACTGCTGCTAGGA 58.868 55.000 0.0 0.0 0.00 2.94 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
28 29 6.857964 CCGAGGACACATAAATGCATATTTTC 59.142 38.462 0.00 0.00 37.64 2.29
30 31 8.077991 CGAGGACACATAAATGCATATTTTCAT 58.922 33.333 0.00 0.00 37.64 2.57
62 63 7.539710 CACAGTTGGATCATCTTTGTTACATTG 59.460 37.037 0.00 0.00 0.00 2.82
125 126 6.461640 ACATTTACACCGTAAGAAGCTTAGT 58.538 36.000 0.00 0.00 43.02 2.24
137 138 7.328737 CGTAAGAAGCTTAGTGAGTGTTAACAT 59.671 37.037 12.26 0.85 43.02 2.71
143 144 6.647067 AGCTTAGTGAGTGTTAACATGTTCTC 59.353 38.462 15.85 15.26 0.00 2.87
162 163 4.218312 TCTCTGGCAAGCTATGATAGACA 58.782 43.478 3.13 0.00 0.00 3.41
1008 1024 6.603940 TTCCCTATTTTCACAATGAAAGGG 57.396 37.500 16.13 16.13 46.32 3.95
1128 1144 5.277825 CAGATTCTCACTTATCACCGAGTC 58.722 45.833 0.00 0.00 0.00 3.36
1192 1208 8.007742 TGTATATTTAGCATATGTTTTGGGGGT 58.992 33.333 4.29 0.00 0.00 4.95
1198 1214 4.466015 AGCATATGTTTTGGGGGTTAACAG 59.534 41.667 8.10 0.00 35.48 3.16
1397 1415 8.999220 TTAATTGCATAAATGTTGATTCAGCA 57.001 26.923 5.63 5.63 0.00 4.41
1843 1997 6.173339 AGGGTTGATTATGGATATTAGCGTG 58.827 40.000 0.00 0.00 0.00 5.34
1862 2016 4.499040 GCGTGTAATTGTGGCATTTGATAC 59.501 41.667 0.00 0.00 0.00 2.24
1989 2150 8.429237 TGGTAATGGTTAATTTTCCATCAAGT 57.571 30.769 12.40 3.10 42.73 3.16
2079 2244 5.708736 TTTATAGTGAATGAAGGGCCTCA 57.291 39.130 6.46 7.38 0.00 3.86
2182 2353 5.255687 TGAACATTATGTCTGCATGAAGGT 58.744 37.500 0.00 0.00 36.58 3.50
2384 2591 9.502145 TGATACATTTGAAATGCTTTCGAATAC 57.498 29.630 17.19 0.00 46.80 1.89
2555 2766 7.730364 TTCATTCTTCTCACTTAAAGGTGTC 57.270 36.000 0.00 0.00 38.28 3.67
2807 3019 9.533253 CTTGGGTAATGCTTAATTTTATTCAGG 57.467 33.333 0.00 0.00 0.00 3.86
2877 3091 7.881775 ATAAGTTCATATGGGTCTTTCCAAC 57.118 36.000 2.13 0.00 40.62 3.77
2878 3092 5.255397 AGTTCATATGGGTCTTTCCAACA 57.745 39.130 2.13 0.00 40.62 3.33
2879 3093 5.831103 AGTTCATATGGGTCTTTCCAACAT 58.169 37.500 2.13 0.00 40.62 2.71
2880 3094 6.256053 AGTTCATATGGGTCTTTCCAACATT 58.744 36.000 2.13 0.00 40.62 2.71
2881 3095 6.153340 AGTTCATATGGGTCTTTCCAACATTG 59.847 38.462 2.13 0.00 40.62 2.82
2883 3097 5.887598 TCATATGGGTCTTTCCAACATTGAG 59.112 40.000 2.13 0.00 40.62 3.02
3287 3734 6.072508 ACGGCATCTAACCTGCAATAAATATG 60.073 38.462 0.00 0.00 41.47 1.78
3451 3898 2.276743 CTCGTCGAACTCTCCGCG 60.277 66.667 0.00 0.00 0.00 6.46
3536 3984 5.997746 CCAGATTGCGAATAATAAGAAGGGA 59.002 40.000 0.00 0.00 0.00 4.20
3559 4007 8.429641 GGGATATTTTGACACTCCAGATAAGTA 58.570 37.037 0.00 0.00 0.00 2.24
3569 4017 4.402793 ACTCCAGATAAGTATCAAGTGCGT 59.597 41.667 1.35 0.00 35.17 5.24
3772 4221 5.762179 TCTGTTCATGATAGAAGTTGGGT 57.238 39.130 0.00 0.00 0.00 4.51
3781 4230 0.615850 AGAAGTTGGGTCCTAGCAGC 59.384 55.000 0.00 0.00 0.00 5.25
3785 4234 0.902531 GTTGGGTCCTAGCAGCAGTA 59.097 55.000 0.00 0.00 0.00 2.74
3941 4390 1.686325 CTACTGCCCCGCACCACTAT 61.686 60.000 0.00 0.00 33.79 2.12
3949 4398 1.806542 CCCGCACCACTATTATGCATC 59.193 52.381 0.19 0.00 39.39 3.91
4025 4476 8.991243 TGTTATACCGTAGCAATGATATAACC 57.009 34.615 13.29 2.83 35.82 2.85
4028 4479 5.546621 ACCGTAGCAATGATATAACCACT 57.453 39.130 0.00 0.00 0.00 4.00
4029 4480 5.539048 ACCGTAGCAATGATATAACCACTC 58.461 41.667 0.00 0.00 0.00 3.51
4030 4481 5.069914 ACCGTAGCAATGATATAACCACTCA 59.930 40.000 0.00 0.00 0.00 3.41
4060 4511 6.555812 TCATCGTAGCGATATAACAACTCT 57.444 37.500 3.64 0.00 45.19 3.24
4061 4512 6.371389 TCATCGTAGCGATATAACAACTCTG 58.629 40.000 3.64 0.00 45.19 3.35
4174 4626 1.440476 GCGGTAATAGTGGCGAGGT 59.560 57.895 0.00 0.00 0.00 3.85
4204 4656 3.075005 CGGGACATGGAGACGGGT 61.075 66.667 0.00 0.00 0.00 5.28
4281 4733 8.196771 GGATGATTACAAGCAATGGTGAAATTA 58.803 33.333 0.00 0.00 0.00 1.40
4404 4856 3.306294 GGTCAGTGATCAGTGTGTGATGA 60.306 47.826 26.03 6.14 46.64 2.92
4405 4857 4.502016 GTCAGTGATCAGTGTGTGATGAT 58.498 43.478 26.03 0.00 46.64 2.45
4434 4886 3.772025 CTGATACTCTGGAAGTTGGGAGT 59.228 47.826 0.00 0.00 39.55 3.85
4555 5007 1.763968 AGTAGCAGCGGTACTCATGA 58.236 50.000 12.51 0.00 42.16 3.07
4580 5032 8.023021 AGATAAGCTCAAGTCCAATGTACATA 57.977 34.615 9.21 0.00 0.00 2.29
4617 5069 1.271379 ACGAATTCAAGGTGGTGGAGG 60.271 52.381 6.22 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 7.563888 AAGATGATCCAACTGTGTGATTATG 57.436 36.000 0.00 0.00 0.00 1.90
30 31 6.942005 ACAAAGATGATCCAACTGTGTGATTA 59.058 34.615 6.10 0.00 34.25 1.75
39 40 7.765695 ACAATGTAACAAAGATGATCCAACT 57.234 32.000 0.00 0.00 0.00 3.16
99 100 6.628919 AAGCTTCTTACGGTGTAAATGTTT 57.371 33.333 0.00 0.00 0.00 2.83
125 126 4.065088 GCCAGAGAACATGTTAACACTCA 58.935 43.478 20.82 0.00 0.00 3.41
137 138 3.920231 ATCATAGCTTGCCAGAGAACA 57.080 42.857 0.00 0.00 0.00 3.18
143 144 3.806521 GTGTGTCTATCATAGCTTGCCAG 59.193 47.826 0.00 0.00 0.00 4.85
556 557 2.040412 CTCCTCTTTACCACCTTGCCTT 59.960 50.000 0.00 0.00 0.00 4.35
566 567 1.208293 CTGGGTCTGCTCCTCTTTACC 59.792 57.143 0.00 0.00 0.00 2.85
958 974 7.514721 TGTTAGTTTTGGAGTTCTTAGACCAT 58.485 34.615 0.00 0.00 32.31 3.55
1008 1024 2.165030 AGTTGCACTAATGGCTTGCATC 59.835 45.455 0.00 0.00 45.35 3.91
1192 1208 8.934023 ATTTTGATGTTTCCTCTACCTGTTAA 57.066 30.769 0.00 0.00 0.00 2.01
1198 1214 8.964476 TCATCTATTTTGATGTTTCCTCTACC 57.036 34.615 0.00 0.00 43.03 3.18
1397 1415 6.126863 TGAAACATGAAGGGAGTAGAACAT 57.873 37.500 0.00 0.00 0.00 2.71
1809 1961 8.837099 ATCCATAATCAACCCTACAAAAATCA 57.163 30.769 0.00 0.00 0.00 2.57
1843 1997 4.667262 TGCGTATCAAATGCCACAATTAC 58.333 39.130 0.00 0.00 39.57 1.89
1862 2016 6.363088 ACTCAACATTGTAAATTTGACATGCG 59.637 34.615 0.00 0.00 0.00 4.73
1989 2150 5.357878 ACCTAGACCGTTCATTATTACGACA 59.642 40.000 0.00 0.00 40.03 4.35
2555 2766 4.614284 CGCTGACTGCAAGAATTAAAAGTG 59.386 41.667 5.11 0.00 43.06 3.16
2590 2801 2.978978 CACCCCATATACATCACCCTGA 59.021 50.000 0.00 0.00 0.00 3.86
2865 3079 3.486383 TCACTCAATGTTGGAAAGACCC 58.514 45.455 0.00 0.00 38.00 4.46
2866 3080 5.712152 AATCACTCAATGTTGGAAAGACC 57.288 39.130 0.00 0.00 39.54 3.85
2867 3081 9.696917 AATAAAATCACTCAATGTTGGAAAGAC 57.303 29.630 0.00 0.00 0.00 3.01
2874 3088 8.419435 CACACGAAATAAAATCACTCAATGTTG 58.581 33.333 0.00 0.00 0.00 3.33
2875 3089 7.114811 GCACACGAAATAAAATCACTCAATGTT 59.885 33.333 0.00 0.00 0.00 2.71
2876 3090 6.582295 GCACACGAAATAAAATCACTCAATGT 59.418 34.615 0.00 0.00 0.00 2.71
2877 3091 6.581919 TGCACACGAAATAAAATCACTCAATG 59.418 34.615 0.00 0.00 0.00 2.82
2878 3092 6.676950 TGCACACGAAATAAAATCACTCAAT 58.323 32.000 0.00 0.00 0.00 2.57
2879 3093 6.066054 TGCACACGAAATAAAATCACTCAA 57.934 33.333 0.00 0.00 0.00 3.02
2880 3094 5.681337 TGCACACGAAATAAAATCACTCA 57.319 34.783 0.00 0.00 0.00 3.41
2881 3095 7.218204 GGTTATGCACACGAAATAAAATCACTC 59.782 37.037 0.00 0.00 0.00 3.51
2883 3097 6.804295 TGGTTATGCACACGAAATAAAATCAC 59.196 34.615 0.00 0.00 0.00 3.06
3287 3734 6.184789 TGACACAGGGTCCTAAAATAAATCC 58.815 40.000 0.00 0.00 46.38 3.01
3390 3837 1.376424 CCCAGAATGCTGCGTCACT 60.376 57.895 0.00 0.00 40.91 3.41
3440 3887 2.174319 GCCCATTCGCGGAGAGTTC 61.174 63.158 6.13 0.00 0.00 3.01
3451 3898 2.932187 GCAAAATGTCCACTGCCCATTC 60.932 50.000 0.00 0.00 0.00 2.67
3511 3959 5.182001 CCCTTCTTATTATTCGCAATCTGGG 59.818 44.000 0.00 0.00 0.00 4.45
3528 3976 6.012508 TCTGGAGTGTCAAAATATCCCTTCTT 60.013 38.462 0.00 0.00 0.00 2.52
3559 4007 2.768253 TGATTCAGGACGCACTTGAT 57.232 45.000 0.00 0.00 34.68 2.57
3569 4017 5.034852 TGGATTTATCGCTTGATTCAGGA 57.965 39.130 0.00 0.00 33.40 3.86
3746 4195 6.656693 CCCAACTTCTATCATGAACAGAACTT 59.343 38.462 15.55 11.63 0.00 2.66
3752 4201 4.536090 AGGACCCAACTTCTATCATGAACA 59.464 41.667 0.00 0.00 0.00 3.18
3772 4221 1.131638 CCCCAATACTGCTGCTAGGA 58.868 55.000 0.00 0.00 0.00 2.94
3818 4267 4.698304 GCCCACACTACTGCTAAATGTTAA 59.302 41.667 0.00 0.00 0.00 2.01
3941 4390 6.039159 TGCTGAAATGAAATACGGATGCATAA 59.961 34.615 0.00 0.00 0.00 1.90
3976 4425 8.999431 ACAATTCTATAAGGGTGTATAAATGCG 58.001 33.333 0.00 0.00 0.00 4.73
4025 4476 3.607209 CGCTACGATGATGATGATGAGTG 59.393 47.826 0.00 0.00 0.00 3.51
4028 4479 4.708726 ATCGCTACGATGATGATGATGA 57.291 40.909 1.02 0.00 45.24 2.92
4029 4480 7.645340 TGTTATATCGCTACGATGATGATGATG 59.355 37.037 12.45 0.00 46.43 3.07
4030 4481 7.707104 TGTTATATCGCTACGATGATGATGAT 58.293 34.615 12.45 0.00 46.43 2.45
4060 4511 0.249447 GATCATCACCGACCGATGCA 60.249 55.000 0.00 0.00 40.11 3.96
4061 4512 1.278172 CGATCATCACCGACCGATGC 61.278 60.000 0.00 0.00 40.11 3.91
4204 4656 2.024369 TGTATGACCACTAGAGCCCTGA 60.024 50.000 0.00 0.00 0.00 3.86
4281 4733 3.118738 ACCGTCTGTCTGAAACTTGAAGT 60.119 43.478 0.00 0.00 0.00 3.01
4404 4856 4.780021 ACTTCCAGAGTATCAGTCCAACAT 59.220 41.667 0.00 0.00 36.65 2.71
4405 4857 4.160329 ACTTCCAGAGTATCAGTCCAACA 58.840 43.478 0.00 0.00 36.65 3.33
4555 5007 6.299805 TGTACATTGGACTTGAGCTTATCT 57.700 37.500 0.00 0.00 0.00 1.98
4580 5032 5.607119 ATTCGTTAATGCGTCAAACTTCT 57.393 34.783 0.00 0.00 0.00 2.85
4617 5069 2.622064 ACTCCACCTTGGCGAATATC 57.378 50.000 0.00 0.00 37.47 1.63


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

AutoCloner maintained by Alex Coulton.