Multiple sequence alignment - TraesCS3B01G226000

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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 TraesCS3B01G226000 chr3B 100.000 2114 0 0 1 2114 312892745 312894858 0.000000e+00 3904
1 TraesCS3B01G226000 chr3B 94.804 1405 58 11 397 1798 201506396 201507788 0.000000e+00 2176
2 TraesCS3B01G226000 chr3B 86.453 406 51 4 1 402 590560560 590560965 1.930000e-120 442
3 TraesCS3B01G226000 chr2A 94.377 1405 67 9 397 1798 335826096 335827491 0.000000e+00 2146
4 TraesCS3B01G226000 chr2A 94.494 563 29 2 397 958 276441256 276440695 0.000000e+00 867
5 TraesCS3B01G226000 chr1D 94.113 1410 66 12 397 1798 394178727 394180127 0.000000e+00 2128
6 TraesCS3B01G226000 chr1D 93.808 1405 70 10 397 1798 254489518 254490908 0.000000e+00 2097
7 TraesCS3B01G226000 chr1D 95.726 819 29 4 982 1798 483922562 483921748 0.000000e+00 1314
8 TraesCS3B01G226000 chr1D 91.275 298 24 2 1818 2114 214760044 214759748 2.530000e-109 405
9 TraesCS3B01G226000 chrUn 93.688 1410 69 12 397 1798 317473373 317471976 0.000000e+00 2093
10 TraesCS3B01G226000 chrUn 94.470 1085 41 11 397 1473 404958051 404959124 0.000000e+00 1653
11 TraesCS3B01G226000 chrUn 93.525 695 29 7 397 1089 53261820 53261140 0.000000e+00 1020
12 TraesCS3B01G226000 chr2D 93.737 1405 65 11 397 1798 334225742 334227126 0.000000e+00 2085
13 TraesCS3B01G226000 chr6D 93.599 1406 70 12 397 1798 431399847 431401236 0.000000e+00 2080
14 TraesCS3B01G226000 chr6D 90.461 304 27 2 1812 2114 218532675 218532373 1.180000e-107 399
15 TraesCS3B01G226000 chr5D 93.305 1404 73 11 397 1798 6207997 6206613 0.000000e+00 2052
16 TraesCS3B01G226000 chr5D 94.381 1050 45 10 755 1798 554200515 554201556 0.000000e+00 1600
17 TraesCS3B01G226000 chr5D 91.246 297 26 0 1818 2114 451731668 451731372 2.530000e-109 405
18 TraesCS3B01G226000 chr5D 91.275 298 23 2 1818 2113 52706204 52706500 9.080000e-109 403
19 TraesCS3B01G226000 chr1A 93.333 675 29 7 397 1068 256026350 256025689 0.000000e+00 983
20 TraesCS3B01G226000 chr5A 95.390 564 25 1 397 959 684325405 684325968 0.000000e+00 896
21 TraesCS3B01G226000 chr4A 93.805 565 25 5 397 958 677309936 677309379 0.000000e+00 841
22 TraesCS3B01G226000 chr1B 86.700 406 49 5 1 402 553884928 553884524 1.490000e-121 446
23 TraesCS3B01G226000 chr7D 86.856 388 47 4 1 384 276684622 276684235 4.170000e-117 431
24 TraesCS3B01G226000 chr7D 85.995 407 52 5 1 402 392804625 392804219 4.170000e-117 431
25 TraesCS3B01G226000 chr7D 85.749 407 52 6 1 402 404131960 404131555 1.940000e-115 425
26 TraesCS3B01G226000 chr7D 91.275 298 23 3 1818 2114 276684138 276683843 9.080000e-109 403
27 TraesCS3B01G226000 chr2B 86.632 389 47 5 1 384 21524055 21524443 1.940000e-115 425
28 TraesCS3B01G226000 chr2B 85.468 406 55 3 1 402 21524778 21525183 9.020000e-114 420
29 TraesCS3B01G226000 chr2B 85.468 406 55 3 1 402 369046794 369046389 9.020000e-114 420
30 TraesCS3B01G226000 chr7B 85.504 407 53 4 1 402 289227245 289227650 9.020000e-114 420
31 TraesCS3B01G226000 chr3D 91.246 297 25 1 1818 2114 385687888 385687593 9.080000e-109 403
32 TraesCS3B01G226000 chr4D 90.970 299 24 2 1818 2114 344803356 344803653 1.180000e-107 399
33 TraesCS3B01G226000 chr4D 90.909 297 25 2 1818 2114 250545235 250545529 4.230000e-107 398
34 TraesCS3B01G226000 chr4D 90.909 297 26 1 1818 2114 335481669 335481374 4.230000e-107 398


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 TraesCS3B01G226000 chr3B 312892745 312894858 2113 False 3904.0 3904 100.0000 1 2114 1 chr3B.!!$F2 2113
1 TraesCS3B01G226000 chr3B 201506396 201507788 1392 False 2176.0 2176 94.8040 397 1798 1 chr3B.!!$F1 1401
2 TraesCS3B01G226000 chr2A 335826096 335827491 1395 False 2146.0 2146 94.3770 397 1798 1 chr2A.!!$F1 1401
3 TraesCS3B01G226000 chr2A 276440695 276441256 561 True 867.0 867 94.4940 397 958 1 chr2A.!!$R1 561
4 TraesCS3B01G226000 chr1D 394178727 394180127 1400 False 2128.0 2128 94.1130 397 1798 1 chr1D.!!$F2 1401
5 TraesCS3B01G226000 chr1D 254489518 254490908 1390 False 2097.0 2097 93.8080 397 1798 1 chr1D.!!$F1 1401
6 TraesCS3B01G226000 chr1D 483921748 483922562 814 True 1314.0 1314 95.7260 982 1798 1 chr1D.!!$R2 816
7 TraesCS3B01G226000 chrUn 317471976 317473373 1397 True 2093.0 2093 93.6880 397 1798 1 chrUn.!!$R2 1401
8 TraesCS3B01G226000 chrUn 404958051 404959124 1073 False 1653.0 1653 94.4700 397 1473 1 chrUn.!!$F1 1076
9 TraesCS3B01G226000 chrUn 53261140 53261820 680 True 1020.0 1020 93.5250 397 1089 1 chrUn.!!$R1 692
10 TraesCS3B01G226000 chr2D 334225742 334227126 1384 False 2085.0 2085 93.7370 397 1798 1 chr2D.!!$F1 1401
11 TraesCS3B01G226000 chr6D 431399847 431401236 1389 False 2080.0 2080 93.5990 397 1798 1 chr6D.!!$F1 1401
12 TraesCS3B01G226000 chr5D 6206613 6207997 1384 True 2052.0 2052 93.3050 397 1798 1 chr5D.!!$R1 1401
13 TraesCS3B01G226000 chr5D 554200515 554201556 1041 False 1600.0 1600 94.3810 755 1798 1 chr5D.!!$F2 1043
14 TraesCS3B01G226000 chr1A 256025689 256026350 661 True 983.0 983 93.3330 397 1068 1 chr1A.!!$R1 671
15 TraesCS3B01G226000 chr5A 684325405 684325968 563 False 896.0 896 95.3900 397 959 1 chr5A.!!$F1 562
16 TraesCS3B01G226000 chr4A 677309379 677309936 557 True 841.0 841 93.8050 397 958 1 chr4A.!!$R1 561
17 TraesCS3B01G226000 chr7D 276683843 276684622 779 True 417.0 431 89.0655 1 2114 2 chr7D.!!$R3 2113
18 TraesCS3B01G226000 chr2B 21524055 21525183 1128 False 422.5 425 86.0500 1 402 2 chr2B.!!$F1 401

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
269 275 0.179048 CTCCGCATGGGCATCAACTA 60.179 55.0 3.8 0.0 41.24 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1880 1911 0.17576 GCGAAGATGTAGCTGGTGGA 59.824 55.0 0.0 0.0 0.0 4.02 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
22 23 1.760613 ACCGTACGATGTCCATCCAAT 59.239 47.619 18.76 0.00 34.40 3.16
24 25 2.223947 CCGTACGATGTCCATCCAATGA 60.224 50.000 18.76 0.00 34.40 2.57
27 28 4.261447 CGTACGATGTCCATCCAATGACTA 60.261 45.833 10.44 0.00 34.40 2.59
46 47 5.000012 ACTATAGTGCTTCTTCAACCTCG 58.000 43.478 4.10 0.00 0.00 4.63
60 61 0.543174 ACCTCGGGTCTTCTTGCTCT 60.543 55.000 0.00 0.00 0.00 4.09
63 64 2.096248 CTCGGGTCTTCTTGCTCTAGT 58.904 52.381 0.00 0.00 0.00 2.57
72 73 4.287067 TCTTCTTGCTCTAGTCACCCAAAT 59.713 41.667 0.00 0.00 0.00 2.32
78 79 1.899814 TCTAGTCACCCAAATCAGCGT 59.100 47.619 0.00 0.00 0.00 5.07
82 83 1.375396 CACCCAAATCAGCGTCGGA 60.375 57.895 0.00 0.00 0.00 4.55
191 193 1.348064 CCTCTACTCACCCACAACCA 58.652 55.000 0.00 0.00 0.00 3.67
201 204 4.331968 TCACCCACAACCATGTTATTCTC 58.668 43.478 0.00 0.00 37.82 2.87
202 205 4.078537 CACCCACAACCATGTTATTCTCA 58.921 43.478 0.00 0.00 37.82 3.27
203 206 4.079253 ACCCACAACCATGTTATTCTCAC 58.921 43.478 0.00 0.00 37.82 3.51
204 207 4.078537 CCCACAACCATGTTATTCTCACA 58.921 43.478 0.00 0.00 37.82 3.58
206 209 4.082787 CCACAACCATGTTATTCTCACACC 60.083 45.833 0.00 0.00 37.82 4.16
207 210 3.751175 ACAACCATGTTATTCTCACACCG 59.249 43.478 0.00 0.00 35.91 4.94
220 226 2.126071 CACCGTAGCCTCACACCG 60.126 66.667 0.00 0.00 0.00 4.94
221 227 2.599578 ACCGTAGCCTCACACCGT 60.600 61.111 0.00 0.00 0.00 4.83
232 238 1.079405 CACACCGTAGCCGAACCAT 60.079 57.895 0.00 0.00 35.63 3.55
256 262 0.468214 CCCTCATACTCCTCTCCGCA 60.468 60.000 0.00 0.00 0.00 5.69
265 271 2.507452 CTCTCCGCATGGGCATCA 59.493 61.111 3.80 0.00 41.24 3.07
269 275 0.179048 CTCCGCATGGGCATCAACTA 60.179 55.000 3.80 0.00 41.24 2.24
274 280 0.747644 CATGGGCATCAACTACCGCA 60.748 55.000 0.00 0.00 0.00 5.69
289 295 3.001514 GCATCTTCCCTGGCTCCA 58.998 61.111 0.00 0.00 0.00 3.86
290 296 1.535685 GCATCTTCCCTGGCTCCAT 59.464 57.895 0.00 0.00 0.00 3.41
292 298 0.841961 CATCTTCCCTGGCTCCATGA 59.158 55.000 0.00 0.00 0.00 3.07
309 315 1.684734 GACGTCCCCTTCCTAGGCA 60.685 63.158 3.51 0.00 40.50 4.75
312 318 1.048724 CGTCCCCTTCCTAGGCATCA 61.049 60.000 2.96 0.00 40.50 3.07
317 323 0.541863 CCTTCCTAGGCATCACCGTT 59.458 55.000 2.96 0.00 46.52 4.44
325 331 1.599518 GCATCACCGTTGTCCACCA 60.600 57.895 0.00 0.00 0.00 4.17
363 369 2.097036 CAGCATGGTCAATGTGGTCAT 58.903 47.619 0.00 0.00 38.65 3.06
394 400 5.943349 TTCCATCGGAAGTTTACTATCCA 57.057 39.130 0.00 1.83 36.71 3.41
476 482 5.223449 TCTACTTTGGTTGGAGTTCGAAT 57.777 39.130 0.00 0.00 0.00 3.34
477 483 5.617252 TCTACTTTGGTTGGAGTTCGAATT 58.383 37.500 0.00 0.00 0.00 2.17
553 565 1.648467 GGCAGGTCGTGGAATGCTTC 61.648 60.000 0.00 0.00 38.71 3.86
637 649 4.373527 TCGATCGTTCACTCCAAAAAGAA 58.626 39.130 15.94 0.00 0.00 2.52
746 764 8.574196 TCCTTGAAAATCGAACTTCATTTTTC 57.426 30.769 11.91 10.90 37.01 2.29
771 789 7.233632 CCATTCAATGGGGTTAGATGATCTAA 58.766 38.462 8.78 10.70 46.86 2.10
899 918 9.944663 CACTTCTGTATCTTACTCTATCTTGTC 57.055 37.037 0.00 0.00 0.00 3.18
963 982 7.956420 TCCATAACTTAGGTAAATGTATGCG 57.044 36.000 0.00 0.00 0.00 4.73
964 983 6.932400 TCCATAACTTAGGTAAATGTATGCGG 59.068 38.462 0.00 0.00 0.00 5.69
966 985 7.117812 CCATAACTTAGGTAAATGTATGCGGAG 59.882 40.741 0.00 0.00 0.00 4.63
967 986 5.609533 ACTTAGGTAAATGTATGCGGAGT 57.390 39.130 0.00 0.00 0.00 3.85
969 988 7.116075 ACTTAGGTAAATGTATGCGGAGTAA 57.884 36.000 0.00 0.00 0.00 2.24
970 989 7.558604 ACTTAGGTAAATGTATGCGGAGTAAA 58.441 34.615 0.00 0.00 0.00 2.01
971 990 7.493645 ACTTAGGTAAATGTATGCGGAGTAAAC 59.506 37.037 0.00 0.00 0.00 2.01
972 991 5.985911 AGGTAAATGTATGCGGAGTAAACT 58.014 37.500 0.00 0.00 0.00 2.66
973 992 6.047231 AGGTAAATGTATGCGGAGTAAACTC 58.953 40.000 1.30 1.30 42.14 3.01
974 993 6.047231 GGTAAATGTATGCGGAGTAAACTCT 58.953 40.000 9.84 0.00 42.48 3.24
975 994 6.537660 GGTAAATGTATGCGGAGTAAACTCTT 59.462 38.462 9.84 0.00 42.48 2.85
976 995 7.065443 GGTAAATGTATGCGGAGTAAACTCTTT 59.935 37.037 9.84 3.31 42.48 2.52
977 996 6.663944 AATGTATGCGGAGTAAACTCTTTC 57.336 37.500 9.84 1.17 42.48 2.62
980 999 6.869695 TGTATGCGGAGTAAACTCTTTCATA 58.130 36.000 9.84 10.95 42.48 2.15
1055 1081 9.636789 AACTAGTTATTTTGGTTTTCTACTGGT 57.363 29.630 6.26 0.00 0.00 4.00
1075 1101 5.642165 TGGTTGCTTTAACTATAACCCCAA 58.358 37.500 0.00 0.00 39.95 4.12
1082 1108 8.208903 TGCTTTAACTATAACCCCAACTCTATC 58.791 37.037 0.00 0.00 0.00 2.08
1089 1115 8.239478 ACTATAACCCCAACTCTATCTATTGGA 58.761 37.037 3.80 0.00 44.84 3.53
1308 1335 8.764287 ACAAATCGAAATGATTGAAGTTTTTCC 58.236 29.630 7.70 0.00 46.65 3.13
1358 1385 8.197592 TCCTATTACTTTAGCGGGATTATTCA 57.802 34.615 0.00 0.00 0.00 2.57
1364 1391 7.062749 ACTTTAGCGGGATTATTCATGACTA 57.937 36.000 0.00 0.00 0.00 2.59
1414 1441 6.169094 TCAGTTGGATCTTTGATTGAGTCTC 58.831 40.000 0.00 0.00 0.00 3.36
1580 1610 2.345760 GGAGACCCGCGTTCTACCA 61.346 63.158 4.92 0.00 0.00 3.25
1675 1705 7.331193 ACGTATAGTCTCCACAAATTCAAGTTC 59.669 37.037 0.00 0.00 0.00 3.01
1691 1721 8.762481 ATTCAAGTTCTACCCACTTTACTTTT 57.238 30.769 0.00 0.00 31.83 2.27
1708 1738 8.867112 TTTACTTTTATTGATCTCGTCGCTAT 57.133 30.769 0.00 0.00 0.00 2.97
1746 1776 9.453830 AAGAAAGAAGTAATAGGTAGGGATGAT 57.546 33.333 0.00 0.00 0.00 2.45
1760 1790 5.574970 AGGGATGATAGGATTTGAACCTC 57.425 43.478 0.00 0.00 38.76 3.85
1762 1792 6.393897 AGGGATGATAGGATTTGAACCTCTA 58.606 40.000 0.00 0.00 38.76 2.43
1787 1817 3.870633 TTTGTACCCAAAACAAACGCT 57.129 38.095 0.00 0.00 40.83 5.07
1798 1828 3.396260 AACAAACGCTCTACCAAGCTA 57.604 42.857 0.00 0.00 40.23 3.32
1799 1829 3.611766 ACAAACGCTCTACCAAGCTAT 57.388 42.857 0.00 0.00 40.23 2.97
1800 1830 3.262420 ACAAACGCTCTACCAAGCTATG 58.738 45.455 0.00 0.00 40.23 2.23
1801 1831 3.056107 ACAAACGCTCTACCAAGCTATGA 60.056 43.478 0.00 0.00 40.23 2.15
1802 1832 4.122776 CAAACGCTCTACCAAGCTATGAT 58.877 43.478 0.00 0.00 40.23 2.45
1803 1833 3.377346 ACGCTCTACCAAGCTATGATG 57.623 47.619 0.00 0.00 40.23 3.07
1804 1834 2.036475 ACGCTCTACCAAGCTATGATGG 59.964 50.000 0.37 0.37 40.23 3.51
1805 1835 2.297315 CGCTCTACCAAGCTATGATGGA 59.703 50.000 9.19 0.00 40.23 3.41
1806 1836 3.243873 CGCTCTACCAAGCTATGATGGAA 60.244 47.826 9.19 0.00 40.23 3.53
1807 1837 4.562347 CGCTCTACCAAGCTATGATGGAAT 60.562 45.833 9.19 0.00 40.23 3.01
1808 1838 5.336770 CGCTCTACCAAGCTATGATGGAATA 60.337 44.000 9.19 0.00 40.23 1.75
1809 1839 6.105333 GCTCTACCAAGCTATGATGGAATAG 58.895 44.000 9.19 2.00 39.12 1.73
1810 1840 6.611613 TCTACCAAGCTATGATGGAATAGG 57.388 41.667 9.19 0.00 39.12 2.57
1811 1841 4.647564 ACCAAGCTATGATGGAATAGGG 57.352 45.455 9.19 0.00 39.12 3.53
1812 1842 4.242811 ACCAAGCTATGATGGAATAGGGA 58.757 43.478 9.19 0.00 39.12 4.20
1813 1843 4.665009 ACCAAGCTATGATGGAATAGGGAA 59.335 41.667 9.19 0.00 39.12 3.97
1814 1844 5.134339 ACCAAGCTATGATGGAATAGGGAAA 59.866 40.000 9.19 0.00 39.12 3.13
1815 1845 5.709164 CCAAGCTATGATGGAATAGGGAAAG 59.291 44.000 0.00 0.00 39.12 2.62
1816 1846 6.466326 CCAAGCTATGATGGAATAGGGAAAGA 60.466 42.308 0.00 0.00 39.12 2.52
1832 1862 3.703127 GACAGGGACCCACCGGAC 61.703 72.222 14.60 0.00 40.11 4.79
1848 1878 0.179067 GGACGGGCCATCGTATTTCA 60.179 55.000 4.39 0.00 43.96 2.69
1880 1911 0.722676 TCCCCCTTGACTACTGGGAT 59.277 55.000 0.00 0.00 43.47 3.85
1902 1933 0.608130 ACCAGCTACATCTTCGCACA 59.392 50.000 0.00 0.00 0.00 4.57
1904 1935 1.404717 CCAGCTACATCTTCGCACACT 60.405 52.381 0.00 0.00 0.00 3.55
1924 1955 4.982916 CACTAGGAAGTGCGTCCATATTAC 59.017 45.833 6.90 0.00 46.28 1.89
1933 1964 2.540157 GCGTCCATATTACGGGCAAAAC 60.540 50.000 8.90 0.00 40.64 2.43
1948 1979 4.218312 GGCAAAACATATGATTCTCCCCT 58.782 43.478 10.38 0.00 0.00 4.79
1952 1983 6.041296 GCAAAACATATGATTCTCCCCTTGAT 59.959 38.462 10.38 0.00 0.00 2.57
1966 1997 1.207791 CTTGATAGCTGGGACCCACT 58.792 55.000 9.95 14.37 0.00 4.00
1975 2006 3.336997 AGCTGGGACCCACTAGCTATATA 59.663 47.826 21.25 0.00 44.10 0.86
2007 2059 1.574263 GAAGTGCCTCCTTACCTCCT 58.426 55.000 0.00 0.00 0.00 3.69
2025 2077 1.770110 TTGACAGCTGGGACCCACT 60.770 57.895 19.93 9.47 0.00 4.00
2056 2137 3.682858 CCGTACATAGGGTTGTTTGTCTG 59.317 47.826 0.00 0.00 0.00 3.51
2061 2142 0.544697 AGGGTTGTTTGTCTGGTCGT 59.455 50.000 0.00 0.00 0.00 4.34
2064 2145 2.011222 GGTTGTTTGTCTGGTCGTGAA 58.989 47.619 0.00 0.00 0.00 3.18
2065 2146 2.616842 GGTTGTTTGTCTGGTCGTGAAT 59.383 45.455 0.00 0.00 0.00 2.57
2080 2241 5.327091 GTCGTGAATGTGTACGTACATACT 58.673 41.667 29.58 18.60 40.24 2.12
2098 2259 1.065636 ACTGGTCGATCGGTCTGTCTA 60.066 52.381 16.41 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 5.393135 CGAGGTTGAAGAAGCACTATAGTCA 60.393 44.000 1.26 0.00 31.56 3.41
24 25 4.142138 CCGAGGTTGAAGAAGCACTATAGT 60.142 45.833 0.00 0.00 31.56 2.12
27 28 2.093447 CCCGAGGTTGAAGAAGCACTAT 60.093 50.000 0.00 0.00 31.56 2.12
46 47 2.093921 GGTGACTAGAGCAAGAAGACCC 60.094 54.545 0.00 0.00 0.00 4.46
60 61 1.403647 CGACGCTGATTTGGGTGACTA 60.404 52.381 0.00 0.00 33.20 2.59
63 64 1.375396 CCGACGCTGATTTGGGTGA 60.375 57.895 0.00 0.00 33.20 4.02
91 92 4.020617 CACGGGAGGCAGGAGCAA 62.021 66.667 0.00 0.00 44.61 3.91
191 193 3.451178 AGGCTACGGTGTGAGAATAACAT 59.549 43.478 0.00 0.00 27.65 2.71
201 204 1.374252 GGTGTGAGGCTACGGTGTG 60.374 63.158 0.00 0.00 0.00 3.82
202 205 2.927580 CGGTGTGAGGCTACGGTGT 61.928 63.158 0.00 0.00 0.00 4.16
203 206 1.588824 TACGGTGTGAGGCTACGGTG 61.589 60.000 8.78 0.00 33.32 4.94
204 207 1.303561 TACGGTGTGAGGCTACGGT 60.304 57.895 4.78 4.78 35.10 4.83
206 209 1.226603 GCTACGGTGTGAGGCTACG 60.227 63.158 0.00 0.00 0.00 3.51
207 210 1.141234 GGCTACGGTGTGAGGCTAC 59.859 63.158 0.00 0.00 35.45 3.58
220 226 1.092348 GGGTTGAATGGTTCGGCTAC 58.908 55.000 0.00 0.00 0.00 3.58
221 227 0.988832 AGGGTTGAATGGTTCGGCTA 59.011 50.000 0.00 0.00 0.00 3.93
232 238 3.375699 GGAGAGGAGTATGAGGGTTGAA 58.624 50.000 0.00 0.00 0.00 2.69
256 262 0.183492 ATGCGGTAGTTGATGCCCAT 59.817 50.000 0.00 0.00 0.00 4.00
265 271 0.541863 CCAGGGAAGATGCGGTAGTT 59.458 55.000 0.00 0.00 0.00 2.24
269 275 3.011517 AGCCAGGGAAGATGCGGT 61.012 61.111 0.00 0.00 0.00 5.68
274 280 0.842635 GTCATGGAGCCAGGGAAGAT 59.157 55.000 0.92 0.00 0.00 2.40
289 295 1.049289 GCCTAGGAAGGGGACGTCAT 61.049 60.000 18.91 0.00 43.87 3.06
290 296 1.684734 GCCTAGGAAGGGGACGTCA 60.685 63.158 18.91 0.00 43.87 4.35
292 298 1.003051 ATGCCTAGGAAGGGGACGT 59.997 57.895 14.75 0.00 43.87 4.34
309 315 1.072505 GGTGGTGGACAACGGTGAT 59.927 57.895 7.88 0.00 0.00 3.06
312 318 1.153046 CAAGGTGGTGGACAACGGT 60.153 57.895 0.00 0.00 43.31 4.83
325 331 4.379243 CGCCGAGAGCACCAAGGT 62.379 66.667 0.00 0.00 44.04 3.50
347 353 3.091545 GTTCCATGACCACATTGACCAT 58.908 45.455 0.00 0.00 34.15 3.55
384 390 7.126061 TCTTCTGTCTCTCCATGGATAGTAAA 58.874 38.462 22.67 13.31 0.00 2.01
385 391 6.673583 TCTTCTGTCTCTCCATGGATAGTAA 58.326 40.000 22.67 13.28 0.00 2.24
390 396 5.963092 TCTATCTTCTGTCTCTCCATGGAT 58.037 41.667 16.63 0.00 0.00 3.41
392 398 6.669125 ATTCTATCTTCTGTCTCTCCATGG 57.331 41.667 4.97 4.97 0.00 3.66
393 399 8.634335 TCTATTCTATCTTCTGTCTCTCCATG 57.366 38.462 0.00 0.00 0.00 3.66
394 400 9.077885 GTTCTATTCTATCTTCTGTCTCTCCAT 57.922 37.037 0.00 0.00 0.00 3.41
553 565 7.308450 TCCATATGGAATAAGAGGAGAACAG 57.692 40.000 22.52 0.00 42.18 3.16
637 649 9.768215 TGGATAATTTCTTTTTCAATAGGACCT 57.232 29.630 0.00 0.00 0.00 3.85
746 764 7.233632 TTAGATCATCTAACCCCATTGAATGG 58.766 38.462 17.22 17.22 40.67 3.16
797 815 8.971321 CAAGAGATTTGTTGTGGAATTTGTTAG 58.029 33.333 0.00 0.00 0.00 2.34
799 817 7.555087 TCAAGAGATTTGTTGTGGAATTTGTT 58.445 30.769 0.00 0.00 0.00 2.83
836 854 9.043548 TGGATTCATCAGATGATACATGAGTAT 57.956 33.333 14.11 1.28 43.49 2.12
837 855 8.309656 GTGGATTCATCAGATGATACATGAGTA 58.690 37.037 14.11 0.00 39.39 2.59
959 978 7.653713 CACTATATGAAAGAGTTTACTCCGCAT 59.346 37.037 6.28 9.63 43.88 4.73
961 980 6.979238 ACACTATATGAAAGAGTTTACTCCGC 59.021 38.462 6.28 0.00 43.88 5.54
962 981 9.666626 CTACACTATATGAAAGAGTTTACTCCG 57.333 37.037 6.28 0.00 43.88 4.63
1055 1081 6.786122 AGAGTTGGGGTTATAGTTAAAGCAA 58.214 36.000 0.00 0.00 0.00 3.91
1082 1108 8.511604 AAGGTGTATCTTGTTCAATCCAATAG 57.488 34.615 0.00 0.00 0.00 1.73
1142 1168 6.652062 CCAGGAATCCCAAAGAAAGATTTTTG 59.348 38.462 0.00 0.00 34.79 2.44
1308 1335 3.545703 AGGCCTAAGACGATTCCAAATG 58.454 45.455 1.29 0.00 0.00 2.32
1358 1385 5.236478 GCCTGTATTGCAAATACGTAGTCAT 59.764 40.000 1.71 0.00 43.93 3.06
1364 1391 2.095213 CACGCCTGTATTGCAAATACGT 59.905 45.455 1.71 5.37 0.00 3.57
1421 1451 2.314852 TCTGGTCTGGAGGAGGTCAATA 59.685 50.000 0.00 0.00 0.00 1.90
1498 1528 8.985315 ATTCCATCTATCTTATGTTGAAGCAA 57.015 30.769 0.00 0.00 0.00 3.91
1505 1535 7.015682 AGACCGTGATTCCATCTATCTTATGTT 59.984 37.037 0.00 0.00 0.00 2.71
1580 1610 4.127171 TGAAAGCGCTCTTAGTTCAGTTT 58.873 39.130 12.06 0.00 31.02 2.66
1639 1669 4.748600 TGGAGACTATACGTACGTGAGATG 59.251 45.833 30.25 16.79 0.00 2.90
1675 1705 8.818057 CGAGATCAATAAAAGTAAAGTGGGTAG 58.182 37.037 0.00 0.00 0.00 3.18
1691 1721 3.255888 AGGCAATAGCGACGAGATCAATA 59.744 43.478 0.00 0.00 43.41 1.90
1746 1776 8.934023 ACAAAATGTTAGAGGTTCAAATCCTA 57.066 30.769 0.00 0.00 35.20 2.94
1787 1817 5.485353 CCCTATTCCATCATAGCTTGGTAGA 59.515 44.000 0.00 0.00 34.48 2.59
1798 1828 4.105377 CCCTGTCTTTCCCTATTCCATCAT 59.895 45.833 0.00 0.00 0.00 2.45
1799 1829 3.459598 CCCTGTCTTTCCCTATTCCATCA 59.540 47.826 0.00 0.00 0.00 3.07
1800 1830 3.716872 TCCCTGTCTTTCCCTATTCCATC 59.283 47.826 0.00 0.00 0.00 3.51
1801 1831 3.459969 GTCCCTGTCTTTCCCTATTCCAT 59.540 47.826 0.00 0.00 0.00 3.41
1802 1832 2.844348 GTCCCTGTCTTTCCCTATTCCA 59.156 50.000 0.00 0.00 0.00 3.53
1803 1833 2.172930 GGTCCCTGTCTTTCCCTATTCC 59.827 54.545 0.00 0.00 0.00 3.01
1804 1834 2.172930 GGGTCCCTGTCTTTCCCTATTC 59.827 54.545 0.00 0.00 35.63 1.75
1805 1835 2.206223 GGGTCCCTGTCTTTCCCTATT 58.794 52.381 0.00 0.00 35.63 1.73
1806 1836 1.082194 TGGGTCCCTGTCTTTCCCTAT 59.918 52.381 10.00 0.00 38.95 2.57
1807 1837 0.494551 TGGGTCCCTGTCTTTCCCTA 59.505 55.000 10.00 0.00 38.95 3.53
1808 1838 1.134438 GTGGGTCCCTGTCTTTCCCT 61.134 60.000 10.00 0.00 38.95 4.20
1809 1839 1.379146 GTGGGTCCCTGTCTTTCCC 59.621 63.158 10.00 0.00 38.68 3.97
1810 1840 1.379146 GGTGGGTCCCTGTCTTTCC 59.621 63.158 10.00 0.00 0.00 3.13
1811 1841 1.003718 CGGTGGGTCCCTGTCTTTC 60.004 63.158 10.00 0.00 0.00 2.62
1812 1842 2.526046 CCGGTGGGTCCCTGTCTTT 61.526 63.158 10.00 0.00 0.00 2.52
1813 1843 2.928396 CCGGTGGGTCCCTGTCTT 60.928 66.667 10.00 0.00 0.00 3.01
1814 1844 3.923645 TCCGGTGGGTCCCTGTCT 61.924 66.667 10.00 0.00 33.83 3.41
1815 1845 3.703127 GTCCGGTGGGTCCCTGTC 61.703 72.222 10.00 0.00 33.83 3.51
1832 1862 1.374560 TTGTGAAATACGATGGCCCG 58.625 50.000 0.00 0.00 0.00 6.13
1867 1898 2.187958 CTGGTGGATCCCAGTAGTCAA 58.812 52.381 9.90 0.00 45.81 3.18
1880 1911 0.175760 GCGAAGATGTAGCTGGTGGA 59.824 55.000 0.00 0.00 0.00 4.02
1902 1933 4.261489 CGTAATATGGACGCACTTCCTAGT 60.261 45.833 0.00 0.00 36.51 2.57
1904 1935 3.005050 CCGTAATATGGACGCACTTCCTA 59.995 47.826 5.16 0.00 38.99 2.94
1924 1955 3.004734 GGGAGAATCATATGTTTTGCCCG 59.995 47.826 15.93 0.00 36.25 6.13
1933 1964 6.114089 CAGCTATCAAGGGGAGAATCATATG 58.886 44.000 0.00 0.00 36.25 1.78
1948 1979 2.398588 CTAGTGGGTCCCAGCTATCAA 58.601 52.381 12.21 0.00 32.34 2.57
1952 1983 0.931468 TAGCTAGTGGGTCCCAGCTA 59.069 55.000 21.13 21.13 34.94 3.32
1966 1997 4.157105 TCCTTGCGTGCGAATATATAGCTA 59.843 41.667 12.47 0.00 0.00 3.32
1975 2006 1.868997 CACTTCCTTGCGTGCGAAT 59.131 52.632 0.00 0.00 0.00 3.34
2007 2059 1.768684 GAGTGGGTCCCAGCTGTCAA 61.769 60.000 12.21 0.00 32.34 3.18
2050 2131 2.613026 ACACATTCACGACCAGACAA 57.387 45.000 0.00 0.00 0.00 3.18
2056 2137 2.932498 TGTACGTACACATTCACGACC 58.068 47.619 24.10 0.00 40.56 4.79
2061 2142 5.643664 GACCAGTATGTACGTACACATTCA 58.356 41.667 29.54 7.17 39.77 2.57
2064 2145 3.940852 TCGACCAGTATGTACGTACACAT 59.059 43.478 29.54 18.75 41.88 3.21
2065 2146 3.333804 TCGACCAGTATGTACGTACACA 58.666 45.455 29.54 17.26 39.30 3.72
2080 2241 1.339342 TGTAGACAGACCGATCGACCA 60.339 52.381 18.66 0.20 0.00 4.02


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

AutoCloner maintained by Alex Coulton.