Multiple sequence alignment - TraesCS3B01G575400

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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 TraesCS3B01G575400 chr3B 100.000 4448 0 0 1 4448 805336523 805340970 0.000000e+00 8215.0
1 TraesCS3B01G575400 chr4A 91.523 3716 138 51 3 3629 738513038 738516665 0.000000e+00 4953.0
2 TraesCS3B01G575400 chr4A 94.110 798 24 10 3658 4448 738516660 738517441 0.000000e+00 1192.0
3 TraesCS3B01G575400 chr3A 96.454 2989 83 8 830 3807 678314009 678316985 0.000000e+00 4911.0
4 TraesCS3B01G575400 chr3A 89.655 812 47 18 3 812 678313080 678313856 0.000000e+00 1000.0
5 TraesCS3B01G575400 chr3A 94.057 387 9 4 3847 4230 678316988 678317363 3.860000e-160 575.0
6 TraesCS3B01G575400 chr3A 96.847 222 7 0 4227 4448 678317478 678317699 5.430000e-99 372.0
7 TraesCS3B01G575400 chr2D 79.375 2080 349 48 1399 3417 469984474 469986534 0.000000e+00 1391.0
8 TraesCS3B01G575400 chr2D 77.076 2408 456 63 1070 3420 8348849 8346481 0.000000e+00 1301.0
9 TraesCS3B01G575400 chr2B 77.284 2408 451 64 1070 3420 4754215 4751847 0.000000e+00 1328.0
10 TraesCS3B01G575400 chr2B 78.426 2007 365 46 1460 3417 729767103 729769090 0.000000e+00 1245.0
11 TraesCS3B01G575400 chr2B 77.524 1753 295 62 1108 2786 548609635 548611362 0.000000e+00 963.0
12 TraesCS3B01G575400 chr2A 78.137 2008 369 48 1460 3417 733629413 733631400 0.000000e+00 1212.0
13 TraesCS3B01G575400 chr2A 76.541 1411 237 56 1070 2412 611296244 611297628 0.000000e+00 686.0
14 TraesCS3B01G575400 chr1B 77.989 1999 382 40 1460 3420 548193179 548191201 0.000000e+00 1201.0
15 TraesCS3B01G575400 chr1B 77.253 2075 392 55 1400 3417 8819465 8817414 0.000000e+00 1144.0
16 TraesCS3B01G575400 chr1B 76.778 2011 390 54 1460 3415 9162308 9164296 0.000000e+00 1055.0
17 TraesCS3B01G575400 chr1B 76.755 2009 391 52 1460 3415 8866720 8864735 0.000000e+00 1053.0
18 TraesCS3B01G575400 chr1B 74.340 265 51 12 1070 1327 9161879 9162133 3.660000e-16 97.1
19 TraesCS3B01G575400 chr1D 77.960 2010 378 44 1460 3420 407672038 407670045 0.000000e+00 1197.0
20 TraesCS3B01G575400 chr1D 76.298 2447 460 80 1070 3417 6913247 6915672 0.000000e+00 1195.0
21 TraesCS3B01G575400 chr1D 77.552 2018 380 49 1456 3420 6714096 6712099 0.000000e+00 1149.0
22 TraesCS3B01G575400 chr1D 76.984 2016 380 59 1460 3415 6721084 6719093 0.000000e+00 1075.0
23 TraesCS3B01G575400 chr1D 82.014 139 19 5 13 149 302078616 302078482 3.640000e-21 113.0
24 TraesCS3B01G575400 chr1D 75.641 234 36 14 1103 1327 6721480 6721259 3.660000e-16 97.1
25 TraesCS3B01G575400 chr1A 78.166 1974 351 52 1460 3375 7835189 7837140 0.000000e+00 1184.0
26 TraesCS3B01G575400 chr1A 76.243 2454 448 80 1070 3415 8332035 8334461 0.000000e+00 1177.0
27 TraesCS3B01G575400 chr1A 77.723 2011 359 58 1460 3415 8327657 8329633 0.000000e+00 1149.0
28 TraesCS3B01G575400 chr1A 77.514 2019 379 49 1456 3420 8143988 8141991 0.000000e+00 1144.0
29 TraesCS3B01G575400 chr4B 77.739 2017 374 51 1458 3420 36635344 36633349 0.000000e+00 1168.0
30 TraesCS3B01G575400 chr7A 76.941 1314 273 22 2168 3465 558100951 558099652 0.000000e+00 721.0
31 TraesCS3B01G575400 chr7A 75.694 288 61 7 1070 1354 558082459 558082178 7.760000e-28 135.0
32 TraesCS3B01G575400 chr7B 77.291 1233 253 20 2107 3324 521141721 521140501 0.000000e+00 701.0
33 TraesCS3B01G575400 chr7D 75.694 288 61 7 1070 1354 491790862 491790581 7.760000e-28 135.0
34 TraesCS3B01G575400 chr5D 87.500 80 9 1 1081 1160 447105833 447105911 1.700000e-14 91.6


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 TraesCS3B01G575400 chr3B 805336523 805340970 4447 False 8215.00 8215 100.00000 1 4448 1 chr3B.!!$F1 4447
1 TraesCS3B01G575400 chr4A 738513038 738517441 4403 False 3072.50 4953 92.81650 3 4448 2 chr4A.!!$F1 4445
2 TraesCS3B01G575400 chr3A 678313080 678317699 4619 False 1714.50 4911 94.25325 3 4448 4 chr3A.!!$F1 4445
3 TraesCS3B01G575400 chr2D 469984474 469986534 2060 False 1391.00 1391 79.37500 1399 3417 1 chr2D.!!$F1 2018
4 TraesCS3B01G575400 chr2D 8346481 8348849 2368 True 1301.00 1301 77.07600 1070 3420 1 chr2D.!!$R1 2350
5 TraesCS3B01G575400 chr2B 4751847 4754215 2368 True 1328.00 1328 77.28400 1070 3420 1 chr2B.!!$R1 2350
6 TraesCS3B01G575400 chr2B 729767103 729769090 1987 False 1245.00 1245 78.42600 1460 3417 1 chr2B.!!$F2 1957
7 TraesCS3B01G575400 chr2B 548609635 548611362 1727 False 963.00 963 77.52400 1108 2786 1 chr2B.!!$F1 1678
8 TraesCS3B01G575400 chr2A 733629413 733631400 1987 False 1212.00 1212 78.13700 1460 3417 1 chr2A.!!$F2 1957
9 TraesCS3B01G575400 chr2A 611296244 611297628 1384 False 686.00 686 76.54100 1070 2412 1 chr2A.!!$F1 1342
10 TraesCS3B01G575400 chr1B 548191201 548193179 1978 True 1201.00 1201 77.98900 1460 3420 1 chr1B.!!$R3 1960
11 TraesCS3B01G575400 chr1B 8817414 8819465 2051 True 1144.00 1144 77.25300 1400 3417 1 chr1B.!!$R1 2017
12 TraesCS3B01G575400 chr1B 8864735 8866720 1985 True 1053.00 1053 76.75500 1460 3415 1 chr1B.!!$R2 1955
13 TraesCS3B01G575400 chr1B 9161879 9164296 2417 False 576.05 1055 75.55900 1070 3415 2 chr1B.!!$F1 2345
14 TraesCS3B01G575400 chr1D 407670045 407672038 1993 True 1197.00 1197 77.96000 1460 3420 1 chr1D.!!$R3 1960
15 TraesCS3B01G575400 chr1D 6913247 6915672 2425 False 1195.00 1195 76.29800 1070 3417 1 chr1D.!!$F1 2347
16 TraesCS3B01G575400 chr1D 6712099 6714096 1997 True 1149.00 1149 77.55200 1456 3420 1 chr1D.!!$R1 1964
17 TraesCS3B01G575400 chr1D 6719093 6721480 2387 True 586.05 1075 76.31250 1103 3415 2 chr1D.!!$R4 2312
18 TraesCS3B01G575400 chr1A 7835189 7837140 1951 False 1184.00 1184 78.16600 1460 3375 1 chr1A.!!$F1 1915
19 TraesCS3B01G575400 chr1A 8327657 8334461 6804 False 1163.00 1177 76.98300 1070 3415 2 chr1A.!!$F2 2345
20 TraesCS3B01G575400 chr1A 8141991 8143988 1997 True 1144.00 1144 77.51400 1456 3420 1 chr1A.!!$R1 1964
21 TraesCS3B01G575400 chr4B 36633349 36635344 1995 True 1168.00 1168 77.73900 1458 3420 1 chr4B.!!$R1 1962
22 TraesCS3B01G575400 chr7A 558099652 558100951 1299 True 721.00 721 76.94100 2168 3465 1 chr7A.!!$R2 1297
23 TraesCS3B01G575400 chr7B 521140501 521141721 1220 True 701.00 701 77.29100 2107 3324 1 chr7B.!!$R1 1217

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
688 701 0.035820 TTTTTATCCCTCGTGCGGCT 60.036 50.0 0.0 0.0 0.0 5.52 F
1064 1245 0.107508 ACACCATCATCTTCCGCCAG 60.108 55.0 0.0 0.0 0.0 4.85 F
1992 5440 1.573108 ACTGTGACTGTATGGAGGGG 58.427 55.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1872 5308 0.771127 TACTTTGCCAAGACTGCCCT 59.229 50.0 4.25 0.0 33.72 5.19 R
2035 5483 1.361204 TTTCTGATGCACCCTCCTGA 58.639 50.0 0.00 0.0 0.00 3.86 R
3950 7491 0.108207 ATGCCACTGCCTGCTATCTC 59.892 55.0 0.00 0.0 36.33 2.75 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
33 34 9.842775 AGAATAATCTTTTGCTGACATCATCTA 57.157 29.630 0.00 0.00 29.15 1.98
54 56 7.744087 TCTATTTGTCTTGTAGTTTGCATGT 57.256 32.000 0.00 0.00 0.00 3.21
101 103 3.030168 ATGTCCTTCATCGGCCGCA 62.030 57.895 23.51 10.64 29.76 5.69
112 114 0.394488 TCGGCCGCAAATGGGATTAA 60.394 50.000 23.51 0.00 0.00 1.40
168 170 4.446994 AGCAATTAAGCAAGAGAAAGGC 57.553 40.909 0.00 0.00 36.85 4.35
173 175 1.845809 AAGCAAGAGAAAGGCGCGTG 61.846 55.000 8.43 0.00 0.00 5.34
190 192 1.802880 CGTGCGGATCTGTCCCTAAAG 60.803 57.143 2.89 0.00 41.83 1.85
278 280 7.781056 TGAGATTGTGCTATGTATTCACACTA 58.219 34.615 0.00 0.00 40.04 2.74
462 465 3.947841 GTGCGTGCGTTGCCTTCA 61.948 61.111 0.00 0.00 0.00 3.02
463 466 3.648982 TGCGTGCGTTGCCTTCAG 61.649 61.111 0.00 0.00 0.00 3.02
464 467 4.389576 GCGTGCGTTGCCTTCAGG 62.390 66.667 0.00 0.00 38.53 3.86
688 701 0.035820 TTTTTATCCCTCGTGCGGCT 60.036 50.000 0.00 0.00 0.00 5.52
729 742 3.392616 ACCTGGTCCATGATTAGATGGTC 59.607 47.826 0.54 0.00 43.20 4.02
749 762 3.069158 GTCCGGTGCCACTACTAATACAT 59.931 47.826 0.00 0.00 0.00 2.29
773 790 3.077556 AGACCCAGTGGCGGCTAG 61.078 66.667 11.43 0.00 33.59 3.42
805 912 2.279741 CATGTACCTGGTCCACGATTG 58.720 52.381 0.63 0.00 0.00 2.67
901 1062 2.030562 GCCGGTATCCCCATCGTG 59.969 66.667 1.90 0.00 0.00 4.35
938 1107 0.301687 GTTGCATCGACTACATGCCG 59.698 55.000 5.55 0.00 45.25 5.69
940 1109 2.598632 GCATCGACTACATGCCGGC 61.599 63.158 22.73 22.73 40.79 6.13
941 1110 1.956170 CATCGACTACATGCCGGCC 60.956 63.158 26.77 6.44 0.00 6.13
983 1164 5.509501 GCAGAGTAGCTAGCATTCTCATTCT 60.510 44.000 24.66 11.97 0.00 2.40
1014 1195 1.552337 CACGCCATGCCTCCTATCTAT 59.448 52.381 0.00 0.00 0.00 1.98
1063 1244 0.392863 CACACCATCATCTTCCGCCA 60.393 55.000 0.00 0.00 0.00 5.69
1064 1245 0.107508 ACACCATCATCTTCCGCCAG 60.108 55.000 0.00 0.00 0.00 4.85
1391 4752 6.051717 CCACTCACCTTGTCAATAATAGGAG 58.948 44.000 0.00 0.00 0.00 3.69
1722 5149 4.847198 TGATCAACATGACACTAGGCATT 58.153 39.130 0.00 0.00 0.00 3.56
1872 5308 6.433716 TCATGATAAATGTTTGGTCAGAAGCA 59.566 34.615 0.00 0.00 0.00 3.91
1966 5414 4.281435 TCACGGTCTGTAGTGGTAATTCAA 59.719 41.667 0.00 0.00 38.77 2.69
1992 5440 1.573108 ACTGTGACTGTATGGAGGGG 58.427 55.000 0.00 0.00 0.00 4.79
2035 5483 3.395941 GGGTTGGGACCTTGATGATAGAT 59.604 47.826 0.00 0.00 45.75 1.98
2199 5668 1.004560 TGCAGAAGCTTGTCTCGGG 60.005 57.895 2.10 0.00 42.74 5.14
2897 6409 7.686438 ACTTGCATCATAGTTGTCACAAATA 57.314 32.000 0.00 0.00 0.00 1.40
2898 6410 8.284945 ACTTGCATCATAGTTGTCACAAATAT 57.715 30.769 4.63 4.63 0.00 1.28
2997 6509 0.250295 CAGCAGTTGTCGGAAGGGAA 60.250 55.000 0.00 0.00 0.00 3.97
3228 6755 3.557228 AAGCTTCATGAGGGAGATGTC 57.443 47.619 6.99 0.00 0.00 3.06
3494 7024 6.199937 AGTGTCGGTGTTACTTATATCGTT 57.800 37.500 0.00 0.00 0.00 3.85
3545 7075 0.108774 TGGTGCGTGTGGTTCCAATA 59.891 50.000 0.00 0.00 0.00 1.90
3634 7173 8.128322 TGCTCTATCTAAGAAAAACAGAGTCT 57.872 34.615 0.00 0.00 32.46 3.24
3657 7196 3.157881 ACAGTTAGTGAGCAGAGCACTA 58.842 45.455 0.00 0.00 44.27 2.74
3673 7212 6.016777 CAGAGCACTAAAACAACAAGGATTCT 60.017 38.462 0.00 0.00 0.00 2.40
3767 7306 1.609208 GTCTCCTGAAGGCAAGCAAA 58.391 50.000 0.00 0.00 34.44 3.68
3769 7308 0.243095 CTCCTGAAGGCAAGCAAAGC 59.757 55.000 0.00 0.00 34.44 3.51
3770 7309 0.467844 TCCTGAAGGCAAGCAAAGCA 60.468 50.000 0.00 0.00 34.44 3.91
3771 7310 0.390124 CCTGAAGGCAAGCAAAGCAA 59.610 50.000 0.00 0.00 0.00 3.91
3772 7311 1.001633 CCTGAAGGCAAGCAAAGCAAT 59.998 47.619 0.00 0.00 0.00 3.56
3773 7312 2.066262 CTGAAGGCAAGCAAAGCAATG 58.934 47.619 0.00 0.00 0.00 2.82
3774 7313 1.687660 TGAAGGCAAGCAAAGCAATGA 59.312 42.857 0.00 0.00 0.00 2.57
3775 7314 2.300723 TGAAGGCAAGCAAAGCAATGAT 59.699 40.909 0.00 0.00 0.00 2.45
3840 7381 2.644676 GTTGAGCCCTCTAACCATTCC 58.355 52.381 0.00 0.00 0.00 3.01
3841 7382 1.965414 TGAGCCCTCTAACCATTCCA 58.035 50.000 0.00 0.00 0.00 3.53
3842 7383 2.274542 TGAGCCCTCTAACCATTCCAA 58.725 47.619 0.00 0.00 0.00 3.53
3843 7384 2.852449 TGAGCCCTCTAACCATTCCAAT 59.148 45.455 0.00 0.00 0.00 3.16
3844 7385 3.269381 TGAGCCCTCTAACCATTCCAATT 59.731 43.478 0.00 0.00 0.00 2.32
3845 7386 3.633986 GAGCCCTCTAACCATTCCAATTG 59.366 47.826 0.00 0.00 0.00 2.32
3908 7449 2.744709 GGCCGCAACGCTTTAGGA 60.745 61.111 0.00 0.00 0.00 2.94
3950 7491 1.153549 GGGACTAGACGGCTTGCAG 60.154 63.158 0.00 0.00 0.00 4.41
4060 7601 1.154150 GCACTTCAGCAACATCGGC 60.154 57.895 0.00 0.00 0.00 5.54
4105 7649 2.825836 CAAGGCGGCAGATGGGTC 60.826 66.667 13.08 0.00 0.00 4.46
4106 7650 3.329889 AAGGCGGCAGATGGGTCA 61.330 61.111 13.08 0.00 0.00 4.02
4107 7651 2.683465 AAGGCGGCAGATGGGTCAT 61.683 57.895 13.08 0.00 0.00 3.06
4108 7652 2.898920 AAGGCGGCAGATGGGTCATG 62.899 60.000 13.08 0.00 0.00 3.07
4109 7653 2.903855 GCGGCAGATGGGTCATGG 60.904 66.667 0.00 0.00 0.00 3.66
4110 7654 2.203252 CGGCAGATGGGTCATGGG 60.203 66.667 0.00 0.00 0.00 4.00
4111 7655 3.010144 GGCAGATGGGTCATGGGT 58.990 61.111 0.00 0.00 0.00 4.51
4182 7726 3.689649 GTGCTAATCAACACCTTCCGATT 59.310 43.478 0.00 0.00 32.97 3.34
4208 7752 0.823356 AGCGTGACACCCTGCATTTT 60.823 50.000 0.00 0.00 0.00 1.82
4261 7923 6.016693 TCAGATAAATTCAAACGGTTTGCTCA 60.017 34.615 24.97 13.65 40.43 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 8.749026 AGATGATGTCAGCAAAAGATTATTCT 57.251 30.769 0.00 0.00 34.14 2.40
54 56 7.376615 TGTGTTGATTTGTGATTTCATGCATA 58.623 30.769 0.00 0.00 0.00 3.14
278 280 3.244078 ACGGTTATCGACACATGCCATAT 60.244 43.478 0.00 0.00 42.43 1.78
312 314 4.657013 TGGCATGTGTAGACAATAAACCA 58.343 39.130 0.00 0.00 35.11 3.67
407 410 9.529823 CCCCGTCCTATTCTTATATATATGCTA 57.470 37.037 5.44 0.00 0.00 3.49
414 417 6.065976 TCGACCCCGTCCTATTCTTATATA 57.934 41.667 0.00 0.00 37.05 0.86
416 419 4.371624 TCGACCCCGTCCTATTCTTATA 57.628 45.455 0.00 0.00 37.05 0.98
421 424 1.396653 TCTTCGACCCCGTCCTATTC 58.603 55.000 0.00 0.00 37.05 1.75
458 461 4.749310 AGCCGCGTCTGCCTGAAG 62.749 66.667 4.92 0.00 38.08 3.02
459 462 4.742201 GAGCCGCGTCTGCCTGAA 62.742 66.667 4.92 0.00 38.08 3.02
473 476 2.279784 CAAGGAGGCCGATCGAGC 60.280 66.667 18.66 17.69 0.00 5.03
587 592 5.726397 TCGATTCCGATACTTTCCTTTTCA 58.274 37.500 0.00 0.00 40.30 2.69
688 701 3.054875 AGGTGCATGTTCTTGATGAGCTA 60.055 43.478 0.00 0.00 0.00 3.32
729 742 3.181469 ACATGTATTAGTAGTGGCACCGG 60.181 47.826 15.27 0.00 0.00 5.28
749 762 2.818169 GCCACTGGGTCTGTCCACA 61.818 63.158 0.00 0.00 38.11 4.17
773 790 2.668457 CAGGTACATGTTCTTGACGAGC 59.332 50.000 2.30 0.00 0.00 5.03
805 912 2.629051 GTGTGTTAGTAGGCACCATCC 58.371 52.381 5.01 0.00 34.94 3.51
901 1062 1.549203 ACTTCCATGCATGTTCACCC 58.451 50.000 24.58 0.00 0.00 4.61
938 1107 4.907875 TGCTATATATATGGAGGAAGGGCC 59.092 45.833 10.09 0.00 0.00 5.80
940 1109 7.072562 ACTCTGCTATATATATGGAGGAAGGG 58.927 42.308 10.09 4.22 0.00 3.95
941 1110 9.295825 CTACTCTGCTATATATATGGAGGAAGG 57.704 40.741 10.09 0.00 0.00 3.46
1014 1195 4.901849 ACAAGAGGCCAGAGCAGTAATATA 59.098 41.667 5.01 0.00 42.56 0.86
1063 1244 1.292242 TGCCTTCAGAGTATCCTCCCT 59.708 52.381 0.00 0.00 38.58 4.20
1064 1245 1.691434 CTGCCTTCAGAGTATCCTCCC 59.309 57.143 0.00 0.00 42.95 4.30
1068 1249 0.107643 GGCCTGCCTTCAGAGTATCC 59.892 60.000 0.00 0.00 42.95 2.59
1391 4752 4.416513 GTTCAAGAGAAGGGCACTAGTGC 61.417 52.174 34.99 34.99 44.32 4.40
1722 5149 2.690881 CCTTGGGTCCGGGGATCA 60.691 66.667 0.00 0.00 0.00 2.92
1839 5275 5.449041 CCAAACATTTATCATGACCTGACCG 60.449 44.000 0.00 0.00 36.48 4.79
1872 5308 0.771127 TACTTTGCCAAGACTGCCCT 59.229 50.000 4.25 0.00 33.72 5.19
1992 5440 3.126831 CTGTGGTGACTTGTGAGAGAAC 58.873 50.000 0.00 0.00 0.00 3.01
2035 5483 1.361204 TTTCTGATGCACCCTCCTGA 58.639 50.000 0.00 0.00 0.00 3.86
2081 5544 4.143284 TGTCCGTTGAATTTATCGTGTTCG 60.143 41.667 0.80 0.00 38.55 3.95
2432 5911 7.772292 TGAGTCTCTTCCTCCAAATCATTAATG 59.228 37.037 9.29 9.29 0.00 1.90
2897 6409 9.658799 GTGGCTTAATATCACAGTGTATGATAT 57.341 33.333 9.41 9.41 46.88 1.63
2898 6410 8.646900 TGTGGCTTAATATCACAGTGTATGATA 58.353 33.333 0.00 0.35 41.94 2.15
2997 6509 3.146066 TGCAGTCAAAACTCGGCTAAAT 58.854 40.909 0.00 0.00 31.71 1.40
3228 6755 1.303309 GCGGATCCATCAAAGTCTGG 58.697 55.000 13.41 0.00 0.00 3.86
3438 6968 9.953825 GAAGTATTTATGAATTATTACGCCGAG 57.046 33.333 0.00 0.00 0.00 4.63
3471 7001 5.824904 ACGATATAAGTAACACCGACACT 57.175 39.130 0.00 0.00 0.00 3.55
3494 7024 8.492673 AATACAATTCAGAAATCGCTAGAACA 57.507 30.769 0.00 0.00 0.00 3.18
3545 7075 8.997323 GCATACAATCTTGCTTACATAAGAGAT 58.003 33.333 2.75 0.87 36.47 2.75
3601 7140 8.730680 GTTTTTCTTAGATAGAGCAACCAATCA 58.269 33.333 0.00 0.00 33.51 2.57
3634 7173 1.963515 TGCTCTGCTCACTAACTGTCA 59.036 47.619 0.00 0.00 0.00 3.58
3673 7212 4.811969 TCGCTTAACTGTCATAAAGGGA 57.188 40.909 0.00 0.00 38.22 4.20
3769 7308 4.036027 GGGATGTTACAGACTGCATCATTG 59.964 45.833 17.84 0.00 39.39 2.82
3770 7309 4.202441 GGGATGTTACAGACTGCATCATT 58.798 43.478 17.84 0.00 39.39 2.57
3771 7310 3.434167 GGGGATGTTACAGACTGCATCAT 60.434 47.826 17.84 10.23 39.39 2.45
3772 7311 2.092968 GGGGATGTTACAGACTGCATCA 60.093 50.000 17.84 6.44 39.39 3.07
3773 7312 2.565841 GGGGATGTTACAGACTGCATC 58.434 52.381 1.25 7.59 37.56 3.91
3774 7313 1.212935 GGGGGATGTTACAGACTGCAT 59.787 52.381 1.25 0.00 0.00 3.96
3775 7314 0.618458 GGGGGATGTTACAGACTGCA 59.382 55.000 1.25 0.00 0.00 4.41
3840 7381 6.258287 TCACTTTCAACCTTCAATTGCAATTG 59.742 34.615 35.92 35.92 45.49 2.32
3841 7382 6.347696 TCACTTTCAACCTTCAATTGCAATT 58.652 32.000 18.99 18.99 0.00 2.32
3842 7383 5.916318 TCACTTTCAACCTTCAATTGCAAT 58.084 33.333 5.99 5.99 0.00 3.56
3843 7384 5.336150 TCACTTTCAACCTTCAATTGCAA 57.664 34.783 0.00 0.00 0.00 4.08
3844 7385 4.998671 TCACTTTCAACCTTCAATTGCA 57.001 36.364 0.00 0.00 0.00 4.08
3845 7386 5.984926 TCAATCACTTTCAACCTTCAATTGC 59.015 36.000 0.00 0.00 0.00 3.56
3908 7449 7.759433 CCCTGTTGCTGTATTCGATTTTAATTT 59.241 33.333 0.00 0.00 0.00 1.82
3950 7491 0.108207 ATGCCACTGCCTGCTATCTC 59.892 55.000 0.00 0.00 36.33 2.75
4060 7601 2.470156 TGCCGCTGCAATCTAGTTG 58.530 52.632 0.00 0.00 46.66 3.16
4073 7614 1.294659 CCTTGACAAGACTCTGCCGC 61.295 60.000 16.99 0.00 0.00 6.53
4105 7649 0.527565 GCAGGCACTTTACACCCATG 59.472 55.000 0.00 0.00 34.60 3.66
4106 7650 0.405585 AGCAGGCACTTTACACCCAT 59.594 50.000 0.00 0.00 34.60 4.00
4107 7651 1.003118 CTAGCAGGCACTTTACACCCA 59.997 52.381 0.00 0.00 34.60 4.51
4108 7652 1.278127 TCTAGCAGGCACTTTACACCC 59.722 52.381 0.00 0.00 34.60 4.61
4109 7653 2.347731 GTCTAGCAGGCACTTTACACC 58.652 52.381 0.00 0.00 34.60 4.16
4110 7654 2.028020 AGGTCTAGCAGGCACTTTACAC 60.028 50.000 0.00 0.00 34.60 2.90
4111 7655 2.257207 AGGTCTAGCAGGCACTTTACA 58.743 47.619 0.00 0.00 34.60 2.41
4182 7726 1.045407 AGGGTGTCACGCTAAGACAA 58.955 50.000 20.14 0.00 46.50 3.18
4261 7923 8.923270 TGGTTTCTGGAGATTTGTTCTAAATTT 58.077 29.630 0.00 0.00 33.74 1.82


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

AutoCloner maintained by Alex Coulton.