Multiple sequence alignment - TraesCS5D01G359500

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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 TraesCS5D01G359500 chr5D 100.000 5173 0 0 1 5173 438725674 438720502 0.000000e+00 9553.0
1 TraesCS5D01G359500 chr5D 95.297 3423 110 15 837 4255 438660926 438657551 0.000000e+00 5382.0
2 TraesCS5D01G359500 chr5D 82.869 1868 261 38 3153 4995 438569614 438567781 0.000000e+00 1622.0
3 TraesCS5D01G359500 chr5D 82.552 1771 262 34 3149 4895 438589794 438588047 0.000000e+00 1515.0
4 TraesCS5D01G359500 chr5D 81.113 1509 239 33 3294 4785 438559078 438557599 0.000000e+00 1166.0
5 TraesCS5D01G359500 chr5D 80.787 1499 249 28 3301 4784 438545170 438543696 0.000000e+00 1136.0
6 TraesCS5D01G359500 chr5D 89.399 849 70 13 1 844 438661782 438660949 0.000000e+00 1051.0
7 TraesCS5D01G359500 chr5D 78.633 1507 299 16 964 2457 438592048 438590552 0.000000e+00 977.0
8 TraesCS5D01G359500 chr5D 90.663 739 63 5 4245 4979 438624318 438623582 0.000000e+00 977.0
9 TraesCS5D01G359500 chr5D 87.931 580 69 1 956 1535 437568876 437568298 0.000000e+00 682.0
10 TraesCS5D01G359500 chr5D 100.000 350 0 0 5431 5780 438720244 438719895 0.000000e+00 647.0
11 TraesCS5D01G359500 chr5D 78.140 860 139 25 2151 2982 438570686 438569848 8.650000e-138 501.0
12 TraesCS5D01G359500 chr5D 94.000 50 3 0 4997 5046 542387378 542387329 6.210000e-10 76.8
13 TraesCS5D01G359500 chr5A 93.776 4997 225 33 63 5029 554239378 554234438 0.000000e+00 7426.0
14 TraesCS5D01G359500 chr5A 96.473 1361 46 2 3142 4502 554218854 554217496 0.000000e+00 2246.0
15 TraesCS5D01G359500 chr5A 90.790 1303 106 3 981 2283 554221266 554219978 0.000000e+00 1729.0
16 TraesCS5D01G359500 chr5A 83.411 1724 232 36 3290 4995 554182807 554181120 0.000000e+00 1550.0
17 TraesCS5D01G359500 chr5A 82.626 1767 259 36 3164 4902 554201452 554199706 0.000000e+00 1519.0
18 TraesCS5D01G359500 chr5A 79.031 1960 326 49 954 2892 554185100 554183205 0.000000e+00 1264.0
19 TraesCS5D01G359500 chr5A 80.637 1508 248 36 3308 4797 554083182 554081701 0.000000e+00 1127.0
20 TraesCS5D01G359500 chr5A 91.568 676 38 11 4497 5168 554212318 554211658 0.000000e+00 915.0
21 TraesCS5D01G359500 chr5A 78.531 1430 264 28 964 2365 554203810 554202396 0.000000e+00 900.0
22 TraesCS5D01G359500 chr5A 86.585 820 64 19 2315 3109 554219646 554218848 0.000000e+00 863.0
23 TraesCS5D01G359500 chr5A 92.614 352 17 5 5431 5780 554211497 554211153 1.120000e-136 497.0
24 TraesCS5D01G359500 chr5A 73.465 1368 316 31 998 2343 553499040 553497698 6.780000e-129 472.0
25 TraesCS5D01G359500 chr5B 94.696 4110 163 21 837 4933 533575507 533571440 0.000000e+00 6331.0
26 TraesCS5D01G359500 chr5B 93.390 1649 93 9 3290 4924 533515387 533513741 0.000000e+00 2427.0
27 TraesCS5D01G359500 chr5B 88.483 1971 183 23 837 2798 533525463 533523528 0.000000e+00 2342.0
28 TraesCS5D01G359500 chr5B 90.523 1414 105 13 3532 4936 533565266 533563873 0.000000e+00 1842.0
29 TraesCS5D01G359500 chr5B 83.630 1796 237 39 3219 4994 533451460 533449702 0.000000e+00 1635.0
30 TraesCS5D01G359500 chr5B 85.668 1542 191 16 936 2462 533567931 533566405 0.000000e+00 1596.0
31 TraesCS5D01G359500 chr5B 81.808 1814 272 43 3149 4937 533494384 533492604 0.000000e+00 1469.0
32 TraesCS5D01G359500 chr5B 91.142 858 61 8 1 847 533576380 533575527 0.000000e+00 1149.0
33 TraesCS5D01G359500 chr5B 79.900 1398 244 26 1565 2949 533473898 533472525 0.000000e+00 990.0
34 TraesCS5D01G359500 chr5B 79.462 1412 264 19 964 2361 533496635 533495236 0.000000e+00 977.0
35 TraesCS5D01G359500 chr5B 87.440 629 42 16 222 844 533526083 533525486 0.000000e+00 689.0
36 TraesCS5D01G359500 chr5B 91.729 399 33 0 3149 3547 533565679 533565281 6.540000e-154 555.0
37 TraesCS5D01G359500 chr5B 81.142 578 66 20 2531 3102 533566370 533565830 1.930000e-114 424.0
38 TraesCS5D01G359500 chr5B 92.019 213 12 3 1 211 533526345 533526136 1.580000e-75 294.0
39 TraesCS5D01G359500 chr5B 90.152 132 10 3 3154 3285 533519163 533519035 9.960000e-38 169.0
40 TraesCS5D01G359500 chr5B 77.219 338 39 20 2851 3152 533519590 533519255 4.630000e-36 163.0
41 TraesCS5D01G359500 chrUn 80.751 1491 225 34 3312 4785 63291953 63290508 0.000000e+00 1107.0
42 TraesCS5D01G359500 chrUn 82.171 875 126 13 3916 4785 299954525 299953676 0.000000e+00 725.0
43 TraesCS5D01G359500 chrUn 78.125 256 41 12 5499 5752 48607199 48606957 1.300000e-31 148.0
44 TraesCS5D01G359500 chrUn 77.455 275 45 14 5480 5752 478393271 478393530 1.300000e-31 148.0
45 TraesCS5D01G359500 chr2B 82.407 324 47 10 5431 5751 794363838 794364154 2.050000e-69 274.0
46 TraesCS5D01G359500 chr2B 94.000 50 3 0 4997 5046 342500053 342500004 6.210000e-10 76.8
47 TraesCS5D01G359500 chr7A 78.286 350 63 10 5438 5780 206586953 206586610 4.540000e-51 213.0
48 TraesCS5D01G359500 chr7A 96.154 52 2 0 4995 5046 50004311 50004260 1.030000e-12 86.1
49 TraesCS5D01G359500 chr7B 77.874 348 55 19 5442 5780 243277395 243277061 4.570000e-46 196.0
50 TraesCS5D01G359500 chr4A 83.732 209 25 9 5495 5701 38726249 38726048 7.650000e-44 189.0
51 TraesCS5D01G359500 chr4A 77.186 263 38 16 5495 5752 689545880 689546125 3.630000e-27 134.0
52 TraesCS5D01G359500 chr6B 81.373 204 26 12 5431 5629 46976692 46976496 7.750000e-34 156.0
53 TraesCS5D01G359500 chr2D 89.474 76 5 2 712 784 12635028 12634953 6.170000e-15 93.5
54 TraesCS5D01G359500 chr2D 91.228 57 3 1 4992 5046 512165833 512165889 6.210000e-10 76.8
55 TraesCS5D01G359500 chr7D 92.157 51 4 0 4996 5046 221683567 221683517 8.030000e-09 73.1
56 TraesCS5D01G359500 chr1A 90.741 54 5 0 4993 5046 517104434 517104487 8.030000e-09 73.1
57 TraesCS5D01G359500 chr4B 89.474 57 5 1 4991 5046 182632507 182632563 2.890000e-08 71.3


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 TraesCS5D01G359500 chr5D 438719895 438725674 5779 True 5100.000000 9553 100.000000 1 5780 2 chr5D.!!$R9 5779
1 TraesCS5D01G359500 chr5D 438657551 438661782 4231 True 3216.500000 5382 92.348000 1 4255 2 chr5D.!!$R8 4254
2 TraesCS5D01G359500 chr5D 438588047 438592048 4001 True 1246.000000 1515 80.592500 964 4895 2 chr5D.!!$R7 3931
3 TraesCS5D01G359500 chr5D 438557599 438559078 1479 True 1166.000000 1166 81.113000 3294 4785 1 chr5D.!!$R3 1491
4 TraesCS5D01G359500 chr5D 438543696 438545170 1474 True 1136.000000 1136 80.787000 3301 4784 1 chr5D.!!$R2 1483
5 TraesCS5D01G359500 chr5D 438567781 438570686 2905 True 1061.500000 1622 80.504500 2151 4995 2 chr5D.!!$R6 2844
6 TraesCS5D01G359500 chr5D 438623582 438624318 736 True 977.000000 977 90.663000 4245 4979 1 chr5D.!!$R4 734
7 TraesCS5D01G359500 chr5D 437568298 437568876 578 True 682.000000 682 87.931000 956 1535 1 chr5D.!!$R1 579
8 TraesCS5D01G359500 chr5A 554234438 554239378 4940 True 7426.000000 7426 93.776000 63 5029 1 chr5A.!!$R3 4966
9 TraesCS5D01G359500 chr5A 554217496 554221266 3770 True 1612.666667 2246 91.282667 981 4502 3 chr5A.!!$R7 3521
10 TraesCS5D01G359500 chr5A 554181120 554185100 3980 True 1407.000000 1550 81.221000 954 4995 2 chr5A.!!$R4 4041
11 TraesCS5D01G359500 chr5A 554199706 554203810 4104 True 1209.500000 1519 80.578500 964 4902 2 chr5A.!!$R5 3938
12 TraesCS5D01G359500 chr5A 554081701 554083182 1481 True 1127.000000 1127 80.637000 3308 4797 1 chr5A.!!$R2 1489
13 TraesCS5D01G359500 chr5A 554211153 554212318 1165 True 706.000000 915 92.091000 4497 5780 2 chr5A.!!$R6 1283
14 TraesCS5D01G359500 chr5A 553497698 553499040 1342 True 472.000000 472 73.465000 998 2343 1 chr5A.!!$R1 1345
15 TraesCS5D01G359500 chr5B 533563873 533576380 12507 True 1982.833333 6331 89.150000 1 4936 6 chr5B.!!$R5 4935
16 TraesCS5D01G359500 chr5B 533449702 533451460 1758 True 1635.000000 1635 83.630000 3219 4994 1 chr5B.!!$R1 1775
17 TraesCS5D01G359500 chr5B 533492604 533496635 4031 True 1223.000000 1469 80.635000 964 4937 2 chr5B.!!$R3 3973
18 TraesCS5D01G359500 chr5B 533513741 533526345 12604 True 1014.000000 2427 88.117167 1 4924 6 chr5B.!!$R4 4923
19 TraesCS5D01G359500 chr5B 533472525 533473898 1373 True 990.000000 990 79.900000 1565 2949 1 chr5B.!!$R2 1384
20 TraesCS5D01G359500 chrUn 63290508 63291953 1445 True 1107.000000 1107 80.751000 3312 4785 1 chrUn.!!$R2 1473
21 TraesCS5D01G359500 chrUn 299953676 299954525 849 True 725.000000 725 82.171000 3916 4785 1 chrUn.!!$R3 869

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
394 451 0.250684 TGCTTGATCCGGTCAGCAAA 60.251 50.000 18.74 3.77 37.74 3.68 F
1608 1725 1.299850 CAGCGACACGAACAGGTCA 60.300 57.895 0.00 0.00 33.66 4.02 F
2201 2343 0.620030 TGCTCCTGTGTGGCATATGT 59.380 50.000 4.29 0.00 35.26 2.29 F
3090 7746 0.620556 ATCGTGGGGCTGAGAAACAT 59.379 50.000 0.00 0.00 0.00 2.71 F
3092 7748 1.066430 TCGTGGGGCTGAGAAACATAC 60.066 52.381 0.00 0.00 0.00 2.39 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1883 2018 1.438651 TTCAGCGGATGGAAACTTCG 58.561 50.000 0.00 0.0 35.43 3.79 R
3008 7519 1.148310 CACGAAGCGAATGTGGTCTT 58.852 50.000 0.00 0.0 0.00 3.01 R
3092 7748 1.339438 CCCTCAGTCCACAGATGTTGG 60.339 57.143 0.00 0.0 0.00 3.77 R
4507 13013 3.512516 GTCCGGCAGCTCATTGGC 61.513 66.667 0.00 0.0 40.00 4.52 R
5000 21111 3.698040 GTCTTACATTGTAGGACGGAGGA 59.302 47.826 19.41 0.0 0.00 3.71 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
21 22 4.052159 AGCTGACAGTGATATGTACAGC 57.948 45.455 16.50 16.50 45.02 4.40
22 23 4.052159 GCTGACAGTGATATGTACAGCT 57.948 45.455 16.75 0.00 43.39 4.24
33 34 1.374947 GTACAGCTGGGTTGGCAGA 59.625 57.895 19.93 0.00 0.00 4.26
41 42 0.824109 TGGGTTGGCAGATAGACTCG 59.176 55.000 0.00 0.00 0.00 4.18
111 121 1.845809 GCTCACAAGTGCGTCCAAGG 61.846 60.000 0.00 0.00 0.00 3.61
121 131 1.480954 TGCGTCCAAGGTCTCCTTATC 59.519 52.381 0.50 0.00 42.67 1.75
240 297 1.978580 ACCAGCTAGTTTACACCAGCT 59.021 47.619 0.00 0.00 45.01 4.24
273 330 5.059404 TGTAAGCTGTTAAGTACCGTACC 57.941 43.478 5.02 0.00 0.00 3.34
288 345 2.167693 CCGTACCTGGACAGCTGAAATA 59.832 50.000 23.35 2.59 0.00 1.40
303 360 7.044181 CAGCTGAAATATCAACTCCAAGACTA 58.956 38.462 8.42 0.00 34.49 2.59
317 374 4.099120 CCAAGACTATCTCAACTCGAACG 58.901 47.826 0.00 0.00 0.00 3.95
339 396 5.403466 ACGAGAATTCAAAGCTTTGCATTTC 59.597 36.000 29.34 27.03 34.89 2.17
341 398 4.687483 AGAATTCAAAGCTTTGCATTTCCG 59.313 37.500 29.34 9.88 34.89 4.30
369 426 4.780815 TCCGCTTTCATTATCAACCTGAT 58.219 39.130 0.00 0.00 40.72 2.90
373 430 5.585390 GCTTTCATTATCAACCTGATGTGG 58.415 41.667 0.00 0.00 37.70 4.17
379 436 0.478072 TCAACCTGATGTGGGTGCTT 59.522 50.000 0.00 0.00 44.14 3.91
394 451 0.250684 TGCTTGATCCGGTCAGCAAA 60.251 50.000 18.74 3.77 37.74 3.68
542 600 3.329929 AGGGTGAACTTGTACGGATTC 57.670 47.619 0.00 0.00 0.00 2.52
574 633 6.715718 AGAGACTCTATACAATTAGGCGCTTA 59.284 38.462 7.64 0.00 0.00 3.09
601 660 1.451936 AGGCTGACACTTCGCCTTT 59.548 52.632 0.18 0.00 44.39 3.11
671 730 3.058016 GCATTTGCACAAGAAGCAGTCTA 60.058 43.478 0.00 0.00 43.75 2.59
674 733 3.475566 TGCACAAGAAGCAGTCTAACT 57.524 42.857 0.00 0.00 37.02 2.24
729 796 9.982651 TCTATATAGCTTAATGTTTCAGTCACC 57.017 33.333 4.75 0.00 0.00 4.02
738 805 2.158957 TGTTTCAGTCACCAGTCTGACC 60.159 50.000 3.76 0.00 41.44 4.02
773 840 2.577059 GCATCCCAACTCCGACGA 59.423 61.111 0.00 0.00 0.00 4.20
1284 1401 3.567478 ACTTCCTCAACACTGAAGCTT 57.433 42.857 0.00 0.00 39.23 3.74
1312 1429 4.841813 TCACCAACACCTCTAATCTGGTTA 59.158 41.667 0.00 0.00 34.97 2.85
1360 1477 4.782019 GTCATTTGGACAACAGCCATAA 57.218 40.909 0.00 0.00 46.19 1.90
1608 1725 1.299850 CAGCGACACGAACAGGTCA 60.300 57.895 0.00 0.00 33.66 4.02
1749 1872 8.053963 GGTCTTATCATCTACCTAGCCTATGTA 58.946 40.741 0.00 0.00 0.00 2.29
1927 2062 2.999331 ACCATTACAGTTATTGCGGCT 58.001 42.857 0.00 0.00 0.00 5.52
2148 2283 2.038863 TTGCTGGAGGGAGGAGTAAA 57.961 50.000 0.00 0.00 0.00 2.01
2149 2284 2.038863 TGCTGGAGGGAGGAGTAAAA 57.961 50.000 0.00 0.00 0.00 1.52
2201 2343 0.620030 TGCTCCTGTGTGGCATATGT 59.380 50.000 4.29 0.00 35.26 2.29
2423 2867 7.065803 TCTCTCTTTCTACCAGTTGTTTTGTTG 59.934 37.037 0.00 0.00 0.00 3.33
2472 2944 2.238646 TCATTTGGGACCATCGCTTAGT 59.761 45.455 0.00 0.00 0.00 2.24
2473 2945 2.396590 TTTGGGACCATCGCTTAGTC 57.603 50.000 0.00 0.00 0.00 2.59
2732 3245 4.081420 CAGTTGTAGGCTCTGGTGTTCTAT 60.081 45.833 0.00 0.00 0.00 1.98
2949 7439 6.481954 AATTTTGTAGACGGTTTAGAGCAG 57.518 37.500 0.00 0.00 0.00 4.24
3090 7746 0.620556 ATCGTGGGGCTGAGAAACAT 59.379 50.000 0.00 0.00 0.00 2.71
3092 7748 1.066430 TCGTGGGGCTGAGAAACATAC 60.066 52.381 0.00 0.00 0.00 2.39
3677 12126 6.874288 AGAGATTCTCAACAAGGAACAAAG 57.126 37.500 15.83 0.00 32.06 2.77
3759 12210 1.451028 GGATGCTGCAGTGAGGGAC 60.451 63.158 16.64 0.00 0.00 4.46
4090 12549 1.884926 GGCGAGGATCTTTGGCGAG 60.885 63.158 2.68 0.00 0.00 5.03
4141 12600 6.100004 CGTTGTTGGAACATAGTGAGTATCT 58.900 40.000 0.00 0.00 39.30 1.98
4507 13013 5.310594 TGGAATATGTGGAAGGAAGATAGGG 59.689 44.000 0.00 0.00 0.00 3.53
4940 21044 7.043986 CGTGTGTTGCTTAGTAGTCATTATCTC 60.044 40.741 0.00 0.00 0.00 2.75
5062 21173 6.597280 TGTTAGCTTTTTCATTGCTTTTTGGT 59.403 30.769 0.00 0.00 38.15 3.67
5100 21211 8.742188 TCTTTGTTTTTCATCGATTTTTCTTCG 58.258 29.630 0.00 0.00 37.94 3.79
5101 21212 6.432802 TGTTTTTCATCGATTTTTCTTCGC 57.567 33.333 0.00 0.00 36.56 4.70
5107 21218 6.241207 TCATCGATTTTTCTTCGCTTCTTT 57.759 33.333 0.00 0.00 36.56 2.52
5110 21221 5.916969 TCGATTTTTCTTCGCTTCTTTCTC 58.083 37.500 0.00 0.00 36.56 2.87
5111 21222 5.465390 TCGATTTTTCTTCGCTTCTTTCTCA 59.535 36.000 0.00 0.00 36.56 3.27
5112 21223 6.018262 TCGATTTTTCTTCGCTTCTTTCTCAA 60.018 34.615 0.00 0.00 36.56 3.02
5170 21281 9.438228 TTTATTCGGGTTGTTTTTCTTTTTCTT 57.562 25.926 0.00 0.00 0.00 2.52
5171 21282 7.915293 ATTCGGGTTGTTTTTCTTTTTCTTT 57.085 28.000 0.00 0.00 0.00 2.52
5763 21874 8.892887 TTTTCAAATGCTTGTTCAATGTTTTC 57.107 26.923 0.00 0.00 33.94 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.827008 ACCCAGCTGTACATATCACTG 57.173 47.619 13.81 0.00 0.00 3.66
20 21 0.543749 AGTCTATCTGCCAACCCAGC 59.456 55.000 0.00 0.00 32.87 4.85
21 22 1.202463 CGAGTCTATCTGCCAACCCAG 60.202 57.143 0.00 0.00 0.00 4.45
22 23 0.824109 CGAGTCTATCTGCCAACCCA 59.176 55.000 0.00 0.00 0.00 4.51
33 34 5.014858 TGTACTTGAAGGAACCGAGTCTAT 58.985 41.667 0.00 0.00 31.22 1.98
41 42 8.092687 TGAAAGTATAGTGTACTTGAAGGAACC 58.907 37.037 12.47 0.00 37.77 3.62
82 91 2.415893 GCACTTGTGAGCCGCAATATTT 60.416 45.455 4.79 0.00 33.31 1.40
111 121 3.982475 TGCATGTGATCGATAAGGAGAC 58.018 45.455 0.00 0.00 0.00 3.36
121 131 1.322637 CACGAGAACTGCATGTGATCG 59.677 52.381 15.34 15.34 40.81 3.69
240 297 6.432783 ACTTAACAGCTTACAATGGCAATGTA 59.567 34.615 11.26 11.26 32.27 2.29
273 330 4.574013 GGAGTTGATATTTCAGCTGTCCAG 59.426 45.833 14.67 0.00 42.72 3.86
288 345 6.405286 CGAGTTGAGATAGTCTTGGAGTTGAT 60.405 42.308 0.00 0.00 0.00 2.57
303 360 5.060662 TGAATTCTCGTTCGAGTTGAGAT 57.939 39.130 19.26 6.92 38.46 2.75
317 374 5.164022 CGGAAATGCAAAGCTTTGAATTCTC 60.164 40.000 35.11 30.30 43.82 2.87
339 396 1.656652 AATGAAAGCGGATGACTCGG 58.343 50.000 0.00 0.00 0.00 4.63
341 398 5.277538 GGTTGATAATGAAAGCGGATGACTC 60.278 44.000 0.00 0.00 0.00 3.36
369 426 2.350895 CCGGATCAAGCACCCACA 59.649 61.111 0.00 0.00 0.00 4.17
373 430 2.109126 GCTGACCGGATCAAGCACC 61.109 63.158 9.46 0.00 36.69 5.01
379 436 2.083774 GACAATTTGCTGACCGGATCA 58.916 47.619 9.46 7.57 35.45 2.92
394 451 6.970484 AGAACAGCGTTAATTTCTTGACAAT 58.030 32.000 0.00 0.00 0.00 2.71
534 592 6.591750 AGAGTCTCTTTTCAAGAATCCGTA 57.408 37.500 0.00 0.00 38.33 4.02
554 612 7.145985 TCTGTTAAGCGCCTAATTGTATAGAG 58.854 38.462 2.29 0.00 0.00 2.43
574 633 3.553096 CGAAGTGTCAGCCTTACTCTGTT 60.553 47.826 0.00 0.00 33.48 3.16
671 730 9.726438 AGCTTTTGTATATCAACACTTCTAGTT 57.274 29.630 0.00 0.00 35.61 2.24
729 796 3.681897 GTCATTGCTTACTGGTCAGACTG 59.318 47.826 4.84 0.00 0.00 3.51
738 805 0.447801 GCCACCGTCATTGCTTACTG 59.552 55.000 0.00 0.00 0.00 2.74
773 840 3.072184 AGACTTCACAAATCAGCTGTCCT 59.928 43.478 14.67 0.00 0.00 3.85
1284 1401 2.409064 TAGAGGTGTTGGTGAGGGAA 57.591 50.000 0.00 0.00 0.00 3.97
1312 1429 1.524002 CGCCACCACCATCAGAGAT 59.476 57.895 0.00 0.00 0.00 2.75
1358 1475 2.994699 CCAGGCCGGTGGTCATTA 59.005 61.111 1.90 0.00 32.32 1.90
1608 1725 3.255642 CGTCCCACAAGAATGTTTGGAAT 59.744 43.478 0.00 0.00 38.80 3.01
1724 1847 7.948034 ACATAGGCTAGGTAGATGATAAGAC 57.052 40.000 10.55 0.00 0.00 3.01
1749 1872 3.309682 CGTATGCCTCATCGTCATTGTTT 59.690 43.478 0.00 0.00 0.00 2.83
1883 2018 1.438651 TTCAGCGGATGGAAACTTCG 58.561 50.000 0.00 0.00 35.43 3.79
1927 2062 1.669265 CTCGTCACAGTAGCCATACGA 59.331 52.381 0.00 0.00 36.97 3.43
2148 2283 2.034879 CGCCGCACACTCCTCAATT 61.035 57.895 0.00 0.00 0.00 2.32
2149 2284 2.434884 CGCCGCACACTCCTCAAT 60.435 61.111 0.00 0.00 0.00 2.57
2201 2343 1.597854 CTGCTCAGGTTGGCGAACA 60.598 57.895 13.86 0.00 33.27 3.18
2396 2840 6.763610 ACAAAACAACTGGTAGAAAGAGAGAG 59.236 38.462 0.00 0.00 0.00 3.20
2732 3245 4.645535 GCAAGGGAGATGCATATGAGTAA 58.354 43.478 6.97 0.00 43.29 2.24
2949 7439 7.499232 ACATCACCACAAATAGTAGCTAAATCC 59.501 37.037 0.00 0.00 0.00 3.01
3008 7519 1.148310 CACGAAGCGAATGTGGTCTT 58.852 50.000 0.00 0.00 0.00 3.01
3090 7746 2.567169 CCTCAGTCCACAGATGTTGGTA 59.433 50.000 0.00 0.00 0.00 3.25
3092 7748 1.339438 CCCTCAGTCCACAGATGTTGG 60.339 57.143 0.00 0.00 0.00 3.77
3759 12210 6.219473 ACTCGTATATCAGGAGCTTTTCATG 58.781 40.000 0.00 0.00 41.90 3.07
4090 12549 4.082463 TGGGTATTCGCATTTTCCAAGTTC 60.082 41.667 0.00 0.00 0.00 3.01
4379 12858 9.574458 TTCGTAACAAAATTTGACAGAATTCAA 57.426 25.926 13.19 0.00 33.55 2.69
4507 13013 3.512516 GTCCGGCAGCTCATTGGC 61.513 66.667 0.00 0.00 40.00 4.52
5000 21111 3.698040 GTCTTACATTGTAGGACGGAGGA 59.302 47.826 19.41 0.00 0.00 3.71
5078 21189 6.205784 AGCGAAGAAAAATCGATGAAAAACA 58.794 32.000 0.00 0.00 42.76 2.83
5085 21196 6.310197 AGAAAGAAGCGAAGAAAAATCGATG 58.690 36.000 0.00 0.00 42.76 3.84
5090 21201 8.877808 AAATTGAGAAAGAAGCGAAGAAAAAT 57.122 26.923 0.00 0.00 0.00 1.82
5137 21248 9.908152 AGAAAAACAACCCGAATAAAATAGAAG 57.092 29.630 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.