Multiple sequence alignment - TraesCS7A01G179700

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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 TraesCS7A01G179700 chr7A 100.000 3618 0 0 1 3618 134185123 134188740 0.000000e+00 6682.0
1 TraesCS7A01G179700 chr7A 90.039 1024 92 7 869 1887 518139417 518140435 0.000000e+00 1317.0
2 TraesCS7A01G179700 chr7A 98.246 57 1 0 2324 2380 191267661 191267605 2.300000e-17 100.0
3 TraesCS7A01G179700 chr4A 93.734 1532 88 6 879 2405 522457338 522455810 0.000000e+00 2290.0
4 TraesCS7A01G179700 chr4A 86.335 805 70 16 2847 3617 200167046 200167844 0.000000e+00 841.0
5 TraesCS7A01G179700 chr4A 100.000 36 0 0 2246 2281 662459572 662459537 2.330000e-07 67.6
6 TraesCS7A01G179700 chr4A 94.595 37 2 0 2287 2323 662459515 662459479 1.400000e-04 58.4
7 TraesCS7A01G179700 chr5B 90.395 1239 80 10 2415 3617 166710322 166711557 0.000000e+00 1592.0
8 TraesCS7A01G179700 chr5A 90.226 1238 87 15 2410 3617 687335679 687336912 0.000000e+00 1585.0
9 TraesCS7A01G179700 chr5A 92.424 330 22 1 1919 2245 608811460 608811789 5.470000e-128 468.0
10 TraesCS7A01G179700 chr5A 100.000 36 0 0 2246 2281 599649420 599649455 2.330000e-07 67.6
11 TraesCS7A01G179700 chr5A 94.595 37 2 0 2287 2323 599649477 599649513 1.400000e-04 58.4
12 TraesCS7A01G179700 chr4B 95.824 934 38 1 1473 2405 349105910 349106843 0.000000e+00 1507.0
13 TraesCS7A01G179700 chr4B 100.000 34 0 0 2248 2281 158102163 158102196 3.020000e-06 63.9
14 TraesCS7A01G179700 chr7B 87.551 1237 118 8 2410 3617 341976520 341977749 0.000000e+00 1399.0
15 TraesCS7A01G179700 chr7B 89.844 1024 93 8 870 1887 723883277 723884295 0.000000e+00 1304.0
16 TraesCS7A01G179700 chr7B 93.258 178 9 1 2071 2245 729820854 729820677 3.580000e-65 259.0
17 TraesCS7A01G179700 chr1A 87.601 1234 85 24 2410 3613 568054915 568056110 0.000000e+00 1369.0
18 TraesCS7A01G179700 chr1A 93.915 871 53 0 1 871 373563793 373564663 0.000000e+00 1315.0
19 TraesCS7A01G179700 chr1A 87.163 1114 95 12 2410 3491 19515908 19514811 0.000000e+00 1221.0
20 TraesCS7A01G179700 chr3B 90.625 1024 85 8 870 1887 728284793 728285811 0.000000e+00 1349.0
21 TraesCS7A01G179700 chr3B 96.970 33 0 1 2246 2278 462597193 462597162 2.000000e-03 54.7
22 TraesCS7A01G179700 chr5D 94.374 871 49 0 1 871 167056366 167057236 0.000000e+00 1338.0
23 TraesCS7A01G179700 chr5D 94.131 869 51 0 3 871 242049922 242050790 0.000000e+00 1323.0
24 TraesCS7A01G179700 chr2A 94.266 872 49 1 1 871 498874553 498875424 0.000000e+00 1332.0
25 TraesCS7A01G179700 chr2A 90.323 1023 88 7 871 1887 177891332 177892349 0.000000e+00 1330.0
26 TraesCS7A01G179700 chr2A 90.225 1023 88 9 871 1887 279478628 279477612 0.000000e+00 1325.0
27 TraesCS7A01G179700 chr2A 92.438 767 54 4 2410 3175 82187310 82186547 0.000000e+00 1092.0
28 TraesCS7A01G179700 chr2A 93.784 370 21 2 3180 3547 82186503 82186134 4.080000e-154 555.0
29 TraesCS7A01G179700 chr2A 93.258 178 9 1 2071 2245 279476701 279476524 3.580000e-65 259.0
30 TraesCS7A01G179700 chrUn 90.323 1023 88 8 871 1887 13805909 13806926 0.000000e+00 1330.0
31 TraesCS7A01G179700 chrUn 92.697 178 10 1 2071 2245 13807837 13808014 1.670000e-63 254.0
32 TraesCS7A01G179700 chrUn 97.222 36 1 0 2246 2281 29319631 29319666 1.080000e-05 62.1
33 TraesCS7A01G179700 chr6D 94.030 871 52 0 1 871 379198566 379197696 0.000000e+00 1321.0
34 TraesCS7A01G179700 chr6D 85.650 446 44 9 2410 2851 448692330 448692759 5.510000e-123 451.0
35 TraesCS7A01G179700 chr6D 97.222 36 1 0 2246 2281 291652629 291652664 1.080000e-05 62.1
36 TraesCS7A01G179700 chr4D 94.030 871 51 1 1 871 71285855 71284986 0.000000e+00 1319.0
37 TraesCS7A01G179700 chr4D 93.929 873 51 1 1 871 465977623 465978495 0.000000e+00 1317.0
38 TraesCS7A01G179700 chr4D 86.921 367 34 3 1886 2245 398294012 398294371 2.020000e-107 399.0
39 TraesCS7A01G179700 chr7D 93.915 871 53 0 1 871 58527354 58528224 0.000000e+00 1315.0
40 TraesCS7A01G179700 chr7D 92.073 328 24 2 1925 2251 471209886 471209560 9.150000e-126 460.0
41 TraesCS7A01G179700 chr7D 97.222 36 1 0 2246 2281 636678030 636678065 1.080000e-05 62.1
42 TraesCS7A01G179700 chr1D 93.915 871 53 0 1 871 194573195 194574065 0.000000e+00 1315.0
43 TraesCS7A01G179700 chr2B 89.922 1032 86 13 868 1887 710990899 710991924 0.000000e+00 1314.0
44 TraesCS7A01G179700 chr2B 84.395 801 66 17 2847 3617 106717042 106716271 0.000000e+00 732.0
45 TraesCS7A01G179700 chr2B 93.258 178 9 1 2071 2245 357158594 357158771 3.580000e-65 259.0
46 TraesCS7A01G179700 chr3A 89.766 1026 89 11 871 1887 645796964 645797982 0.000000e+00 1299.0
47 TraesCS7A01G179700 chr2D 87.383 959 66 15 2702 3617 21420586 21421532 0.000000e+00 1050.0
48 TraesCS7A01G179700 chr2D 87.594 266 33 0 2410 2675 21420327 21420592 3.510000e-80 309.0
49 TraesCS7A01G179700 chr6B 89.509 448 40 4 2410 2851 680081167 680081613 8.770000e-156 560.0
50 TraesCS7A01G179700 chr6B 85.301 449 51 12 2408 2851 679758862 679759300 1.980000e-122 449.0
51 TraesCS7A01G179700 chr6A 88.196 449 30 12 2410 2851 594729453 594729885 6.930000e-142 514.0
52 TraesCS7A01G179700 chr6A 95.833 120 4 1 2287 2405 128224636 128224517 3.690000e-45 193.0
53 TraesCS7A01G179700 chr1B 100.000 36 0 0 2246 2281 588477982 588477947 2.330000e-07 67.6
54 TraesCS7A01G179700 chr1B 94.595 37 2 0 2287 2323 588477925 588477889 1.400000e-04 58.4


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 TraesCS7A01G179700 chr7A 134185123 134188740 3617 False 6682.0 6682 100.0000 1 3618 1 chr7A.!!$F1 3617
1 TraesCS7A01G179700 chr7A 518139417 518140435 1018 False 1317.0 1317 90.0390 869 1887 1 chr7A.!!$F2 1018
2 TraesCS7A01G179700 chr4A 522455810 522457338 1528 True 2290.0 2290 93.7340 879 2405 1 chr4A.!!$R1 1526
3 TraesCS7A01G179700 chr4A 200167046 200167844 798 False 841.0 841 86.3350 2847 3617 1 chr4A.!!$F1 770
4 TraesCS7A01G179700 chr5B 166710322 166711557 1235 False 1592.0 1592 90.3950 2415 3617 1 chr5B.!!$F1 1202
5 TraesCS7A01G179700 chr5A 687335679 687336912 1233 False 1585.0 1585 90.2260 2410 3617 1 chr5A.!!$F2 1207
6 TraesCS7A01G179700 chr4B 349105910 349106843 933 False 1507.0 1507 95.8240 1473 2405 1 chr4B.!!$F2 932
7 TraesCS7A01G179700 chr7B 341976520 341977749 1229 False 1399.0 1399 87.5510 2410 3617 1 chr7B.!!$F1 1207
8 TraesCS7A01G179700 chr7B 723883277 723884295 1018 False 1304.0 1304 89.8440 870 1887 1 chr7B.!!$F2 1017
9 TraesCS7A01G179700 chr1A 568054915 568056110 1195 False 1369.0 1369 87.6010 2410 3613 1 chr1A.!!$F2 1203
10 TraesCS7A01G179700 chr1A 373563793 373564663 870 False 1315.0 1315 93.9150 1 871 1 chr1A.!!$F1 870
11 TraesCS7A01G179700 chr1A 19514811 19515908 1097 True 1221.0 1221 87.1630 2410 3491 1 chr1A.!!$R1 1081
12 TraesCS7A01G179700 chr3B 728284793 728285811 1018 False 1349.0 1349 90.6250 870 1887 1 chr3B.!!$F1 1017
13 TraesCS7A01G179700 chr5D 167056366 167057236 870 False 1338.0 1338 94.3740 1 871 1 chr5D.!!$F1 870
14 TraesCS7A01G179700 chr5D 242049922 242050790 868 False 1323.0 1323 94.1310 3 871 1 chr5D.!!$F2 868
15 TraesCS7A01G179700 chr2A 498874553 498875424 871 False 1332.0 1332 94.2660 1 871 1 chr2A.!!$F2 870
16 TraesCS7A01G179700 chr2A 177891332 177892349 1017 False 1330.0 1330 90.3230 871 1887 1 chr2A.!!$F1 1016
17 TraesCS7A01G179700 chr2A 82186134 82187310 1176 True 823.5 1092 93.1110 2410 3547 2 chr2A.!!$R1 1137
18 TraesCS7A01G179700 chr2A 279476524 279478628 2104 True 792.0 1325 91.7415 871 2245 2 chr2A.!!$R2 1374
19 TraesCS7A01G179700 chrUn 13805909 13808014 2105 False 792.0 1330 91.5100 871 2245 2 chrUn.!!$F2 1374
20 TraesCS7A01G179700 chr6D 379197696 379198566 870 True 1321.0 1321 94.0300 1 871 1 chr6D.!!$R1 870
21 TraesCS7A01G179700 chr4D 71284986 71285855 869 True 1319.0 1319 94.0300 1 871 1 chr4D.!!$R1 870
22 TraesCS7A01G179700 chr4D 465977623 465978495 872 False 1317.0 1317 93.9290 1 871 1 chr4D.!!$F2 870
23 TraesCS7A01G179700 chr7D 58527354 58528224 870 False 1315.0 1315 93.9150 1 871 1 chr7D.!!$F1 870
24 TraesCS7A01G179700 chr1D 194573195 194574065 870 False 1315.0 1315 93.9150 1 871 1 chr1D.!!$F1 870
25 TraesCS7A01G179700 chr2B 710990899 710991924 1025 False 1314.0 1314 89.9220 868 1887 1 chr2B.!!$F2 1019
26 TraesCS7A01G179700 chr2B 106716271 106717042 771 True 732.0 732 84.3950 2847 3617 1 chr2B.!!$R1 770
27 TraesCS7A01G179700 chr3A 645796964 645797982 1018 False 1299.0 1299 89.7660 871 1887 1 chr3A.!!$F1 1016
28 TraesCS7A01G179700 chr2D 21420327 21421532 1205 False 679.5 1050 87.4885 2410 3617 2 chr2D.!!$F1 1207

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
976 982 0.251916 CAACCCGCACTCCTTATGGA 59.748 55.0 0.0 0.0 40.69 3.41 F
1138 1150 0.035458 CTCACCTCCCGTTGCTTTCT 59.965 55.0 0.0 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2177 2932 0.036010 CTGTTCATCCTGCCGAACCT 60.036 55.0 0.0 0.0 40.65 3.50 R
3037 3825 0.175531 GCAGAGAGAGCAAGGGAGAC 59.824 60.0 0.0 0.0 0.00 3.36 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
82 83 1.202698 ACTCTTGCTCCTGGTTGTGTC 60.203 52.381 0.00 0.00 0.00 3.67
203 206 6.688073 TTAAAGAAGAGAGTCTCCCACAAT 57.312 37.500 16.74 2.27 0.00 2.71
446 450 2.347731 CTAAACCCACTCCGAAGAAGC 58.652 52.381 0.00 0.00 0.00 3.86
470 474 6.134055 CGGGGTATATTATATCTCAGTCCCA 58.866 44.000 0.00 0.00 33.55 4.37
511 515 8.820933 GCAAAGAAATATATGAAGGAAAAAGGC 58.179 33.333 0.00 0.00 0.00 4.35
631 635 5.912528 ACGAAGTTCAATGATAACGACAAC 58.087 37.500 3.32 0.00 37.78 3.32
641 645 4.000325 TGATAACGACAACCCTCACAATG 59.000 43.478 0.00 0.00 0.00 2.82
664 668 4.035675 GTGCATCCTAGTCAATGCCTTTAC 59.964 45.833 15.41 6.85 46.10 2.01
818 822 4.854173 TGGAAAGCATGCTTCTATGGTTA 58.146 39.130 32.01 10.87 45.13 2.85
848 852 8.677148 TCAGTTAGAACAAGTTGCTAAATCTT 57.323 30.769 1.81 0.00 0.00 2.40
902 906 8.989980 CCTAATAATAAAGAACGGATTGAGTCC 58.010 37.037 0.00 0.00 44.10 3.85
970 976 1.299976 GGAATCAACCCGCACTCCT 59.700 57.895 0.00 0.00 0.00 3.69
976 982 0.251916 CAACCCGCACTCCTTATGGA 59.748 55.000 0.00 0.00 40.69 3.41
987 993 2.047061 TCCTTATGGAGATCAACCGGG 58.953 52.381 6.32 0.00 37.46 5.73
988 994 2.047061 CCTTATGGAGATCAACCGGGA 58.953 52.381 6.32 0.00 34.57 5.14
992 1003 1.271840 TGGAGATCAACCGGGAAGGG 61.272 60.000 6.32 0.00 46.96 3.95
1003 1015 0.246360 CGGGAAGGGGAAAAACATGC 59.754 55.000 0.00 0.00 0.00 4.06
1058 1070 0.528901 TCCAACACGAACACGAGTGG 60.529 55.000 8.19 0.00 42.25 4.00
1138 1150 0.035458 CTCACCTCCCGTTGCTTTCT 59.965 55.000 0.00 0.00 0.00 2.52
1142 1154 1.600636 CTCCCGTTGCTTTCTGCCA 60.601 57.895 0.00 0.00 42.00 4.92
1246 1267 2.710902 CGTCCTCGCTCCACCATCA 61.711 63.158 0.00 0.00 0.00 3.07
1249 1270 2.362369 CCTCGCTCCACCATCACCT 61.362 63.158 0.00 0.00 0.00 4.00
1435 1456 4.815108 TCGAGGGCGAGGCAGCTA 62.815 66.667 5.04 0.00 42.51 3.32
1491 1512 4.530857 GCAGAGGCCGCGTATGGT 62.531 66.667 4.92 0.00 0.00 3.55
1518 1539 2.824341 GGAGTTCCTGTTCGACTTCCTA 59.176 50.000 0.00 0.00 0.00 2.94
1606 1630 0.538057 CTGCTTCTTCCCTGTGCCAA 60.538 55.000 0.00 0.00 0.00 4.52
1680 1704 1.381872 CGGGGTGGATGAGAGGTCT 60.382 63.158 0.00 0.00 0.00 3.85
1681 1705 0.106167 CGGGGTGGATGAGAGGTCTA 60.106 60.000 0.00 0.00 0.00 2.59
1682 1706 1.710816 GGGGTGGATGAGAGGTCTAG 58.289 60.000 0.00 0.00 0.00 2.43
1724 1748 2.708325 AGTCCTCAATCCAGCCTAATCC 59.292 50.000 0.00 0.00 0.00 3.01
1821 1845 3.689872 TGTACTGCTATCTCCTCCCTT 57.310 47.619 0.00 0.00 0.00 3.95
1962 2117 4.458642 AGACGGACAAGTTCTACTAGGTTC 59.541 45.833 0.00 0.00 0.00 3.62
2405 3161 7.860872 GGATCAGACGTATTTTGTTTGAAGTTT 59.139 33.333 0.00 0.00 34.61 2.66
2406 3162 9.233232 GATCAGACGTATTTTGTTTGAAGTTTT 57.767 29.630 0.00 0.00 34.61 2.43
2407 3163 8.973835 TCAGACGTATTTTGTTTGAAGTTTTT 57.026 26.923 0.00 0.00 28.71 1.94
2455 3211 4.147322 CAACATGGACGGCGTCGC 62.147 66.667 31.02 23.81 40.63 5.19
2531 3295 3.161450 GAGCAGGGATGGGCCGTA 61.161 66.667 0.00 0.00 37.63 4.02
2572 3336 0.390472 CCGTGCTTCTCCTCTGTTCC 60.390 60.000 0.00 0.00 0.00 3.62
2581 3345 4.884668 TCTCCTCTGTTCCATTACGTTT 57.115 40.909 0.00 0.00 0.00 3.60
2596 3360 1.206831 GTTTCGCCCTGCTTTCGTC 59.793 57.895 0.00 0.00 0.00 4.20
2611 3375 2.954684 CGTCCTTGCCTGCCTGGTA 61.955 63.158 0.00 0.00 38.35 3.25
2661 3425 7.812669 CCAAATGTTTTTCTTACCTGGTATGAC 59.187 37.037 18.87 10.72 0.00 3.06
2695 3459 2.307686 AGGGCGAGGAATTTTTAGGACA 59.692 45.455 0.00 0.00 0.00 4.02
2759 3523 6.020678 GTCCGTGAATTATGCTTTTGTATTGC 60.021 38.462 0.00 0.00 0.00 3.56
2765 3529 6.885735 ATTATGCTTTTGTATTGCGGTTTC 57.114 33.333 0.00 0.00 0.00 2.78
2874 3646 1.140312 AGGAGAAAAGTCAGCCACCA 58.860 50.000 0.00 0.00 0.00 4.17
2893 3665 1.372872 CTGTGGTGACATGTCGCGA 60.373 57.895 28.09 23.66 46.14 5.87
2922 3701 2.523168 TGTGGACGGGCTGACTGA 60.523 61.111 0.00 0.00 0.00 3.41
3036 3824 2.972348 ACTGGTTCTACAGGTTCCTCA 58.028 47.619 0.00 0.00 42.75 3.86
3037 3825 2.900546 ACTGGTTCTACAGGTTCCTCAG 59.099 50.000 0.00 0.00 42.75 3.35
3123 3919 1.831736 AGAACGACTGGTTATGGAGGG 59.168 52.381 0.00 0.00 39.50 4.30
3129 3925 0.181350 CTGGTTATGGAGGGGAGTGC 59.819 60.000 0.00 0.00 0.00 4.40
3130 3926 0.253160 TGGTTATGGAGGGGAGTGCT 60.253 55.000 0.00 0.00 0.00 4.40
3131 3927 0.470341 GGTTATGGAGGGGAGTGCTC 59.530 60.000 0.00 0.00 0.00 4.26
3263 4106 5.475564 TGGTTAAATAAGCACAACCCTCTTC 59.524 40.000 1.16 0.00 39.79 2.87
3290 4133 5.944007 ACAAGGTTAAGTTCAACTTGACACT 59.056 36.000 22.70 15.50 43.83 3.55
3425 4269 6.812879 TTGAATCGACAACACTCTAGAGTA 57.187 37.500 24.75 8.37 40.20 2.59
3428 4272 7.473366 TGAATCGACAACACTCTAGAGTATTC 58.527 38.462 24.75 23.98 40.20 1.75
3528 4374 6.971726 TCAGAGAGGTAAACACTAGACAAA 57.028 37.500 0.00 0.00 0.00 2.83
3530 4376 7.434492 TCAGAGAGGTAAACACTAGACAAAAG 58.566 38.462 0.00 0.00 0.00 2.27
3591 4440 3.310774 CGATGTGGATTCCAGCTTACTTG 59.689 47.826 5.39 0.00 32.34 3.16
3617 4466 8.956426 GGATGTTTACATGAGACTATTTTCCAA 58.044 33.333 0.00 0.00 36.57 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 5.951747 AGCTTTAGCATCACCCTTTAATGAA 59.048 36.000 4.33 0.00 45.16 2.57
82 83 5.832539 AAATCATATCCTGGGGACTACAG 57.167 43.478 0.00 0.00 32.98 2.74
203 206 2.440599 GCAAAGCCTCCCCCAAGA 59.559 61.111 0.00 0.00 0.00 3.02
234 237 5.569355 TCTTAAGTGGATGATCAGGCAAAA 58.431 37.500 0.09 0.00 0.00 2.44
446 450 6.134055 TGGGACTGAGATATAATATACCCCG 58.866 44.000 0.00 0.00 33.46 5.73
625 629 0.238289 GCACATTGTGAGGGTTGTCG 59.762 55.000 20.77 0.00 35.23 4.35
631 635 2.092753 ACTAGGATGCACATTGTGAGGG 60.093 50.000 20.77 5.20 35.23 4.30
684 688 3.376859 TGCGTTGAAGTGATCTTGTTTGT 59.623 39.130 0.00 0.00 33.64 2.83
685 689 3.951306 TGCGTTGAAGTGATCTTGTTTG 58.049 40.909 0.00 0.00 33.64 2.93
730 734 7.259882 TCAAGCGAGCAATCATATCAAAATTT 58.740 30.769 0.00 0.00 0.00 1.82
785 789 3.445096 GCATGCTTTCCAACACCTCTAAT 59.555 43.478 11.37 0.00 0.00 1.73
818 822 6.759497 AGCAACTTGTTCTAACTGAGTTTT 57.241 33.333 1.97 0.00 35.43 2.43
848 852 9.458727 AGAGATTTCATCAAGCAATTCTCTTTA 57.541 29.630 0.00 0.00 36.57 1.85
919 923 5.163733 TGAGGGACTTTTGTGTAAAAACGTC 60.164 40.000 0.00 0.00 41.55 4.34
920 924 4.701171 TGAGGGACTTTTGTGTAAAAACGT 59.299 37.500 0.00 0.00 41.55 3.99
970 976 2.438021 CCTTCCCGGTTGATCTCCATAA 59.562 50.000 0.00 0.00 0.00 1.90
976 982 0.549169 TTCCCCTTCCCGGTTGATCT 60.549 55.000 0.00 0.00 0.00 2.75
982 988 0.485543 ATGTTTTTCCCCTTCCCGGT 59.514 50.000 0.00 0.00 0.00 5.28
984 990 0.246360 GCATGTTTTTCCCCTTCCCG 59.754 55.000 0.00 0.00 0.00 5.14
985 991 0.613260 GGCATGTTTTTCCCCTTCCC 59.387 55.000 0.00 0.00 0.00 3.97
986 992 0.246360 CGGCATGTTTTTCCCCTTCC 59.754 55.000 0.00 0.00 0.00 3.46
987 993 0.966179 ACGGCATGTTTTTCCCCTTC 59.034 50.000 0.00 0.00 0.00 3.46
988 994 0.966179 GACGGCATGTTTTTCCCCTT 59.034 50.000 0.00 0.00 0.00 3.95
992 1003 0.109919 GGACGACGGCATGTTTTTCC 60.110 55.000 1.63 0.00 0.00 3.13
1058 1070 3.939592 CCAGATCGACCTTTTTAGTTCCC 59.060 47.826 0.00 0.00 0.00 3.97
1138 1150 2.106131 CGGAATCGGTCGATGGCA 59.894 61.111 6.63 0.00 34.70 4.92
1142 1154 1.429148 GCTTTGCGGAATCGGTCGAT 61.429 55.000 0.00 0.00 36.79 3.59
1202 1223 4.843331 GGAGAGGGGATGGGGGCA 62.843 72.222 0.00 0.00 0.00 5.36
1208 1229 3.164269 CACCGGGGAGAGGGGATG 61.164 72.222 6.32 0.00 32.83 3.51
1243 1264 2.359981 TCTCGTCCGGATTAGGTGAT 57.640 50.000 7.81 0.00 0.00 3.06
1246 1267 1.236628 CGATCTCGTCCGGATTAGGT 58.763 55.000 7.81 4.10 34.11 3.08
1431 1452 1.115930 CCCGGTGTAGAGGCATAGCT 61.116 60.000 0.00 0.00 0.00 3.32
1445 1466 4.096003 CATCCAGGAACGCCCGGT 62.096 66.667 0.00 0.00 40.87 5.28
1461 1482 2.525629 TCTGCGAACACCCTCCCA 60.526 61.111 0.00 0.00 0.00 4.37
1518 1539 1.889105 GTCGATGCGCACCATCCAT 60.889 57.895 14.90 0.00 46.17 3.41
1606 1630 0.252284 TTCCTCTTCCTCCCGCTCTT 60.252 55.000 0.00 0.00 0.00 2.85
1680 1704 2.485582 GTGTCGCTGCTCTCGCTA 59.514 61.111 0.00 0.00 36.97 4.26
1681 1705 4.767841 CGTGTCGCTGCTCTCGCT 62.768 66.667 0.00 0.00 36.97 4.93
1724 1748 1.078567 GTGCTTGAGAGAGGCAGGG 60.079 63.158 0.00 0.00 36.62 4.45
1821 1845 3.054802 GGAAGAGGCAAATCAGGAGAGAA 60.055 47.826 0.00 0.00 0.00 2.87
1923 1947 3.465403 CTCCTCCAGCCTCACCGG 61.465 72.222 0.00 0.00 0.00 5.28
1962 2117 5.546526 AGGAAGAGCTTCTTGACAAGTAAG 58.453 41.667 14.75 15.90 36.73 2.34
2061 2789 1.379916 CCCTGCATCTGGAACACCA 59.620 57.895 0.00 0.00 0.00 4.17
2105 2857 4.778143 GGCATTGCCCTCGTCGGT 62.778 66.667 17.28 0.00 44.06 4.69
2177 2932 0.036010 CTGTTCATCCTGCCGAACCT 60.036 55.000 0.00 0.00 40.65 3.50
2231 2986 1.613630 AACCAGGCGAGAGGTGGAT 60.614 57.895 0.00 0.00 38.37 3.41
2405 3161 1.298157 CGGCATCCTCGCACTCAAAA 61.298 55.000 0.00 0.00 0.00 2.44
2406 3162 1.741401 CGGCATCCTCGCACTCAAA 60.741 57.895 0.00 0.00 0.00 2.69
2407 3163 2.125552 CGGCATCCTCGCACTCAA 60.126 61.111 0.00 0.00 0.00 3.02
2432 3188 0.461163 CGCCGTCCATGTTGTCCATA 60.461 55.000 0.00 0.00 30.71 2.74
2455 3211 3.479269 GGACGCAGCCGAAGAACG 61.479 66.667 0.00 0.00 42.18 3.95
2530 3294 0.830648 GCCTGACATACCTGGCTGTA 59.169 55.000 2.79 0.00 44.61 2.74
2531 3295 1.604378 GCCTGACATACCTGGCTGT 59.396 57.895 2.43 2.43 44.61 4.40
2572 3336 0.802494 AAGCAGGGCGAAACGTAATG 59.198 50.000 0.00 0.00 0.00 1.90
2581 3345 2.879233 AAGGACGAAAGCAGGGCGA 61.879 57.895 0.00 0.00 0.00 5.54
2596 3360 2.439156 GCTACCAGGCAGGCAAGG 60.439 66.667 0.00 0.00 43.14 3.61
2611 3375 2.188817 CCCTAACCCTAGTGTCAAGCT 58.811 52.381 0.00 0.00 0.00 3.74
2661 3425 1.933853 CTCGCCCTTAATCTTCCAACG 59.066 52.381 0.00 0.00 0.00 4.10
2805 3569 8.137745 ACATGGACAATTCATTTTTCTACCAT 57.862 30.769 0.00 0.00 35.24 3.55
2874 3646 1.664649 CGCGACATGTCACCACAGT 60.665 57.895 24.93 0.00 35.41 3.55
2881 3653 2.158330 GCACGATCGCGACATGTCA 61.158 57.895 24.93 6.74 41.64 3.58
2893 3665 1.372997 GTCCACACACTCGCACGAT 60.373 57.895 0.00 0.00 0.00 3.73
2922 3701 1.381867 TGTTCCCCAAGTCCCATCAT 58.618 50.000 0.00 0.00 0.00 2.45
3000 3788 1.452651 AGTAGGCGCCGCTACACTA 60.453 57.895 23.20 2.40 0.00 2.74
3036 3824 1.851304 CAGAGAGAGCAAGGGAGACT 58.149 55.000 0.00 0.00 0.00 3.24
3037 3825 0.175531 GCAGAGAGAGCAAGGGAGAC 59.824 60.000 0.00 0.00 0.00 3.36
3102 3896 2.159085 CCCTCCATAACCAGTCGTTCTC 60.159 54.545 0.00 0.00 35.79 2.87
3129 3925 0.256752 TGCTTGTCATGGATGGGGAG 59.743 55.000 0.00 0.00 0.00 4.30
3130 3926 0.928505 ATGCTTGTCATGGATGGGGA 59.071 50.000 0.00 0.00 33.26 4.81
3131 3927 2.107031 TCTATGCTTGTCATGGATGGGG 59.893 50.000 3.34 0.00 37.69 4.96
3222 4065 7.809226 TTTAACCAACACTCGGTTTAAAAAC 57.191 32.000 0.00 0.00 44.46 2.43
3263 4106 7.908601 GTGTCAAGTTGAACTTAACCTTGTAAG 59.091 37.037 10.63 0.00 36.03 2.34
3425 4269 6.088016 TCAAAGCAACAGTTAAGCATGAAT 57.912 33.333 0.00 0.00 0.00 2.57
3428 4272 6.774354 ATTTCAAAGCAACAGTTAAGCATG 57.226 33.333 0.00 0.00 0.00 4.06
3528 4374 2.365293 GGTTTGCATCAAAGTGACCCTT 59.635 45.455 0.00 0.00 33.82 3.95
3530 4376 1.000843 GGGTTTGCATCAAAGTGACCC 59.999 52.381 0.00 0.00 34.75 4.46
3547 4393 1.349688 TGAAGCCTCATGTAAACGGGT 59.650 47.619 0.00 0.00 0.00 5.28
3591 4440 8.506168 TGGAAAATAGTCTCATGTAAACATCC 57.494 34.615 0.00 0.00 33.61 3.51


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

AutoCloner maintained by Alex Coulton.