Multiple sequence alignment - TraesCS2B01G342900

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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 TraesCS2B01G342900 chr2B 100.000 3698 0 0 1 3698 488993699 488997396 0.000000e+00 6830.0
1 TraesCS2B01G342900 chr2B 97.214 718 19 1 2981 3697 513355035 513354318 0.000000e+00 1214.0
2 TraesCS2B01G342900 chr2B 81.658 1532 209 45 1078 2579 489015653 489017142 0.000000e+00 1206.0
3 TraesCS2B01G342900 chr2B 81.366 161 28 2 2083 2242 419503000 419502841 3.000000e-26 130.0
4 TraesCS2B01G342900 chr2D 91.849 2245 121 34 761 2964 417086084 417088307 0.000000e+00 3075.0
5 TraesCS2B01G342900 chr2D 83.428 1412 184 27 1078 2458 417183569 417184961 0.000000e+00 1266.0
6 TraesCS2B01G342900 chr2D 92.318 755 46 6 1 753 417085178 417085922 0.000000e+00 1062.0
7 TraesCS2B01G342900 chr2D 81.366 161 28 2 2083 2242 352913400 352913241 3.000000e-26 130.0
8 TraesCS2B01G342900 chr2A 92.554 1934 84 22 993 2873 572842376 572840450 0.000000e+00 2719.0
9 TraesCS2B01G342900 chr2A 84.329 887 127 7 1078 1956 572748354 572747472 0.000000e+00 857.0
10 TraesCS2B01G342900 chr2A 92.718 412 28 2 341 751 572847196 572846786 8.840000e-166 593.0
11 TraesCS2B01G342900 chr2A 83.423 555 80 3 2036 2590 572747417 572746875 4.260000e-139 505.0
12 TraesCS2B01G342900 chr2A 90.058 342 13 2 20 361 572847689 572847369 1.230000e-114 424.0
13 TraesCS2B01G342900 chr2A 78.836 189 38 2 2055 2242 471013223 471013036 3.880000e-25 126.0
14 TraesCS2B01G342900 chr2A 94.545 55 3 0 2910 2964 572840453 572840399 6.580000e-13 86.1
15 TraesCS2B01G342900 chr2A 82.353 85 6 7 659 735 752918334 752918417 8.570000e-07 65.8
16 TraesCS2B01G342900 chr1B 96.936 718 21 1 2981 3697 279615953 279615236 0.000000e+00 1203.0
17 TraesCS2B01G342900 chr1B 95.652 46 2 0 701 746 632065219 632065174 1.420000e-09 75.0
18 TraesCS2B01G342900 chr3B 96.657 718 23 1 2981 3697 147467626 147466909 0.000000e+00 1192.0
19 TraesCS2B01G342900 chr3B 85.569 589 54 8 2981 3538 404584511 404583923 4.110000e-164 588.0
20 TraesCS2B01G342900 chr3B 92.857 42 3 0 895 936 2304382 2304341 1.110000e-05 62.1
21 TraesCS2B01G342900 chr4A 95.978 721 23 5 2981 3697 712587963 712587245 0.000000e+00 1166.0
22 TraesCS2B01G342900 chr4A 95.404 718 27 6 2981 3697 94984967 94984255 0.000000e+00 1138.0
23 TraesCS2B01G342900 chr4A 75.333 750 100 43 2981 3695 691289524 691290223 7.820000e-72 281.0
24 TraesCS2B01G342900 chr5B 80.692 347 48 10 2981 3314 503715869 503716209 6.130000e-63 252.0
25 TraesCS2B01G342900 chr5B 88.000 50 5 1 3566 3614 503716534 503716583 1.430000e-04 58.4
26 TraesCS2B01G342900 chr4B 79.944 354 45 17 2981 3328 510190841 510191174 1.720000e-58 237.0
27 TraesCS2B01G342900 chr3A 77.852 149 22 5 659 796 684872403 684872255 8.510000e-12 82.4
28 TraesCS2B01G342900 chr3A 81.000 100 15 4 701 796 684871609 684871510 3.960000e-10 76.8
29 TraesCS2B01G342900 chr6B 91.228 57 5 0 2186 2242 508149868 508149812 1.100000e-10 78.7
30 TraesCS2B01G342900 chr5A 95.745 47 2 0 701 747 441096784 441096830 3.960000e-10 76.8
31 TraesCS2B01G342900 chr6D 73.191 235 50 10 701 935 407183191 407182970 5.120000e-09 73.1
32 TraesCS2B01G342900 chr5D 93.617 47 3 0 701 747 339960953 339960999 1.840000e-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 TraesCS2B01G342900 chr2B 488993699 488997396 3697 False 6830.00 6830 100.0000 1 3698 1 chr2B.!!$F1 3697
1 TraesCS2B01G342900 chr2B 513354318 513355035 717 True 1214.00 1214 97.2140 2981 3697 1 chr2B.!!$R2 716
2 TraesCS2B01G342900 chr2B 489015653 489017142 1489 False 1206.00 1206 81.6580 1078 2579 1 chr2B.!!$F2 1501
3 TraesCS2B01G342900 chr2D 417085178 417088307 3129 False 2068.50 3075 92.0835 1 2964 2 chr2D.!!$F2 2963
4 TraesCS2B01G342900 chr2D 417183569 417184961 1392 False 1266.00 1266 83.4280 1078 2458 1 chr2D.!!$F1 1380
5 TraesCS2B01G342900 chr2A 572840399 572842376 1977 True 1402.55 2719 93.5495 993 2964 2 chr2A.!!$R3 1971
6 TraesCS2B01G342900 chr2A 572746875 572748354 1479 True 681.00 857 83.8760 1078 2590 2 chr2A.!!$R2 1512
7 TraesCS2B01G342900 chr2A 572846786 572847689 903 True 508.50 593 91.3880 20 751 2 chr2A.!!$R4 731
8 TraesCS2B01G342900 chr1B 279615236 279615953 717 True 1203.00 1203 96.9360 2981 3697 1 chr1B.!!$R1 716
9 TraesCS2B01G342900 chr3B 147466909 147467626 717 True 1192.00 1192 96.6570 2981 3697 1 chr3B.!!$R2 716
10 TraesCS2B01G342900 chr3B 404583923 404584511 588 True 588.00 588 85.5690 2981 3538 1 chr3B.!!$R3 557
11 TraesCS2B01G342900 chr4A 712587245 712587963 718 True 1166.00 1166 95.9780 2981 3697 1 chr4A.!!$R2 716
12 TraesCS2B01G342900 chr4A 94984255 94984967 712 True 1138.00 1138 95.4040 2981 3697 1 chr4A.!!$R1 716
13 TraesCS2B01G342900 chr4A 691289524 691290223 699 False 281.00 281 75.3330 2981 3695 1 chr4A.!!$F1 714

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
500 697 0.232816 TCGCGAGTTTTTGTTACGCC 59.767 50.0 3.71 0.00 45.15 5.68 F
803 1154 0.599204 CGTTATGGCCGCGACCTTAT 60.599 55.0 14.09 0.61 0.00 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2254 2645 0.034380 TCCTCTCCTCGATGACCGTT 60.034 55.0 0.0 0.0 39.75 4.44 R
2745 3158 0.468029 AGACCTTGCCACACCTTTGG 60.468 55.0 0.0 0.0 39.98 3.28 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
46 48 5.807520 TGCAAATTGAGATCGAGAACTCTAC 59.192 40.000 10.87 0.00 34.65 2.59
109 111 7.594758 TCAAGAAACATGCTCTTTAATTTTCGG 59.405 33.333 7.71 0.19 30.58 4.30
115 117 4.247258 TGCTCTTTAATTTTCGGCGAGTA 58.753 39.130 10.46 2.15 0.00 2.59
191 193 5.903764 TGCAAATTGTTTCGAAAATCCAG 57.096 34.783 13.10 2.89 0.00 3.86
304 306 9.793259 TTTAGGTCTTCAATTTGACTAATGTCT 57.207 29.630 0.00 0.00 43.29 3.41
306 308 7.453393 AGGTCTTCAATTTGACTAATGTCTCA 58.547 34.615 0.00 0.00 43.29 3.27
416 613 6.575162 AATCAATGCCCGATTATAGTTTCC 57.425 37.500 0.00 0.00 31.33 3.13
440 637 3.721021 TGAAGGGAGGGAGTACTAAAGG 58.279 50.000 0.00 0.00 0.00 3.11
441 638 3.078612 TGAAGGGAGGGAGTACTAAAGGT 59.921 47.826 0.00 0.00 0.00 3.50
443 640 1.485480 GGGAGGGAGTACTAAAGGTGC 59.515 57.143 0.00 0.00 0.00 5.01
470 667 1.202806 CCGGTCAATGAGCCATATGGT 60.203 52.381 22.79 9.86 37.57 3.55
499 696 1.699892 GTTCGCGAGTTTTTGTTACGC 59.300 47.619 9.59 0.00 44.64 4.42
500 697 0.232816 TCGCGAGTTTTTGTTACGCC 59.767 50.000 3.71 0.00 45.15 5.68
501 698 1.050670 CGCGAGTTTTTGTTACGCCG 61.051 55.000 0.00 0.00 45.15 6.46
535 732 4.550577 TGCTCGCATTGTTACCATTATG 57.449 40.909 0.00 0.00 0.00 1.90
546 743 4.704057 TGTTACCATTATGCACATGCTTCA 59.296 37.500 5.31 0.00 42.66 3.02
616 813 1.572895 TGGTAATCCCCATGCATCCAA 59.427 47.619 0.00 0.00 0.00 3.53
632 829 2.053244 TCCAATGTTTTGTGGGCCAAT 58.947 42.857 8.40 0.00 35.46 3.16
639 836 5.296151 TGTTTTGTGGGCCAATCATTTTA 57.704 34.783 8.40 0.00 31.81 1.52
647 844 3.305335 GGGCCAATCATTTTAGTATGCCG 60.305 47.826 4.39 0.00 37.23 5.69
648 845 3.568007 GGCCAATCATTTTAGTATGCCGA 59.432 43.478 0.00 0.00 0.00 5.54
753 950 4.040339 TGAGATTTCAAGACCACTACTGCA 59.960 41.667 0.00 0.00 0.00 4.41
755 952 3.838244 TTTCAAGACCACTACTGCAGT 57.162 42.857 25.12 25.12 38.32 4.40
756 953 3.386768 TTCAAGACCACTACTGCAGTC 57.613 47.619 25.56 8.14 34.26 3.51
757 954 2.598565 TCAAGACCACTACTGCAGTCT 58.401 47.619 25.56 10.66 41.25 3.24
803 1154 0.599204 CGTTATGGCCGCGACCTTAT 60.599 55.000 14.09 0.61 0.00 1.73
825 1176 2.039216 TGAAGCCGGTTTGACCTTATCA 59.961 45.455 8.82 0.00 35.66 2.15
829 1180 2.752903 GCCGGTTTGACCTTATCAATGT 59.247 45.455 1.90 0.00 46.80 2.71
836 1187 3.605634 TGACCTTATCAATGTCAACCGG 58.394 45.455 0.00 0.00 36.16 5.28
837 1188 3.262151 TGACCTTATCAATGTCAACCGGA 59.738 43.478 9.46 0.00 36.16 5.14
846 1197 4.036262 TCAATGTCAACCGGAAAGTCTTTG 59.964 41.667 9.46 9.68 0.00 2.77
849 1200 1.673920 TCAACCGGAAAGTCTTTGTGC 59.326 47.619 9.46 0.00 0.00 4.57
851 1202 1.981256 ACCGGAAAGTCTTTGTGCAT 58.019 45.000 9.46 0.00 0.00 3.96
856 1207 2.397549 GAAAGTCTTTGTGCATGTGCC 58.602 47.619 1.60 0.00 41.18 5.01
863 1214 5.476599 AGTCTTTGTGCATGTGCCTATAAAA 59.523 36.000 2.07 0.00 41.18 1.52
869 1220 4.157656 GTGCATGTGCCTATAAAAGACCAA 59.842 41.667 2.07 0.00 41.18 3.67
885 1236 2.047560 AACGCCCTGAAGCCGTAC 60.048 61.111 0.00 0.00 34.41 3.67
887 1238 2.108278 AACGCCCTGAAGCCGTACTT 62.108 55.000 0.00 0.00 42.98 2.24
888 1239 1.252904 ACGCCCTGAAGCCGTACTTA 61.253 55.000 0.00 0.00 39.29 2.24
901 1252 4.110482 GCCGTACTTATCATCGTTGAACT 58.890 43.478 0.00 0.00 34.96 3.01
905 1256 7.191551 CCGTACTTATCATCGTTGAACTCTTA 58.808 38.462 0.00 0.00 34.96 2.10
922 1273 9.982651 TGAACTCTTACATATATCTAAAGCACC 57.017 33.333 0.00 0.00 0.00 5.01
941 1292 5.046807 AGCACCTAACACTAAATCTTACCGT 60.047 40.000 0.00 0.00 0.00 4.83
946 1297 8.193438 ACCTAACACTAAATCTTACCGTATGAC 58.807 37.037 0.00 0.00 0.00 3.06
949 1300 8.475331 AACACTAAATCTTACCGTATGACAAG 57.525 34.615 0.00 0.00 0.00 3.16
951 1302 8.475639 ACACTAAATCTTACCGTATGACAAGAT 58.524 33.333 5.58 5.58 38.95 2.40
952 1303 9.314321 CACTAAATCTTACCGTATGACAAGATT 57.686 33.333 13.66 13.66 45.20 2.40
955 1306 7.464830 AATCTTACCGTATGACAAGATTTCG 57.535 36.000 13.66 0.00 42.30 3.46
956 1307 4.802039 TCTTACCGTATGACAAGATTTCGC 59.198 41.667 0.00 0.00 0.00 4.70
957 1308 3.247006 ACCGTATGACAAGATTTCGCT 57.753 42.857 0.00 0.00 0.00 4.93
959 1310 4.751060 ACCGTATGACAAGATTTCGCTAA 58.249 39.130 0.00 0.00 0.00 3.09
961 1312 4.025979 CCGTATGACAAGATTTCGCTAACC 60.026 45.833 0.00 0.00 0.00 2.85
962 1313 4.804139 CGTATGACAAGATTTCGCTAACCT 59.196 41.667 0.00 0.00 0.00 3.50
963 1314 5.051641 CGTATGACAAGATTTCGCTAACCTC 60.052 44.000 0.00 0.00 0.00 3.85
964 1315 3.250744 TGACAAGATTTCGCTAACCTCG 58.749 45.455 0.00 0.00 0.00 4.63
965 1316 2.603560 GACAAGATTTCGCTAACCTCGG 59.396 50.000 0.00 0.00 0.00 4.63
970 1321 1.259609 TTTCGCTAACCTCGGAAGGA 58.740 50.000 0.00 0.00 46.67 3.36
991 1342 4.385754 GGAAACTTCAGGAATCTATGCCCT 60.386 45.833 0.00 0.00 0.00 5.19
1026 1383 6.747280 ACTTGCATAAACAAAGCATTATCGTC 59.253 34.615 0.00 0.00 38.19 4.20
1032 1389 3.071479 ACAAAGCATTATCGTCGTTGGT 58.929 40.909 0.00 0.00 0.00 3.67
1038 1395 2.665649 TTATCGTCGTTGGTGCTCAT 57.334 45.000 0.00 0.00 0.00 2.90
1293 1657 1.434555 TCCGTTGGTTTCGCATGTAG 58.565 50.000 0.00 0.00 0.00 2.74
1294 1658 1.153353 CCGTTGGTTTCGCATGTAGT 58.847 50.000 0.00 0.00 0.00 2.73
1295 1659 2.029200 TCCGTTGGTTTCGCATGTAGTA 60.029 45.455 0.00 0.00 0.00 1.82
1340 1705 1.299468 CGCTCCGATGAGTGTAGGC 60.299 63.158 0.00 0.00 42.87 3.93
1553 1918 1.546923 TCATCTTTCCTGTACGCCGAA 59.453 47.619 0.00 0.00 0.00 4.30
1626 1991 2.683933 TCTTCCCGGACTCCAGCC 60.684 66.667 0.73 0.00 0.00 4.85
1972 2355 1.198178 GGTACTCGCCTCATCGATCTC 59.802 57.143 0.00 0.00 37.87 2.75
1974 2357 1.208870 CTCGCCTCATCGATCTCCG 59.791 63.158 0.00 0.00 37.87 4.63
1986 2369 0.820871 GATCTCCGGCTGAAGAGTGT 59.179 55.000 0.00 0.00 0.00 3.55
1987 2370 0.820871 ATCTCCGGCTGAAGAGTGTC 59.179 55.000 0.00 0.00 0.00 3.67
1988 2371 1.216710 CTCCGGCTGAAGAGTGTCC 59.783 63.158 0.00 0.00 0.00 4.02
1989 2372 2.125912 CCGGCTGAAGAGTGTCCG 60.126 66.667 0.00 0.00 39.79 4.79
1991 2374 2.636412 CGGCTGAAGAGTGTCCGGA 61.636 63.158 0.00 0.00 36.73 5.14
1992 2375 1.901085 GGCTGAAGAGTGTCCGGAT 59.099 57.895 7.81 0.00 0.00 4.18
1993 2376 1.112113 GGCTGAAGAGTGTCCGGATA 58.888 55.000 7.81 0.10 0.00 2.59
1996 2379 3.432326 GGCTGAAGAGTGTCCGGATAATT 60.432 47.826 7.81 0.19 0.00 1.40
2075 2466 2.095869 CAGATGCTGGCGATATGCTTTC 60.096 50.000 0.00 0.00 45.43 2.62
2242 2633 1.019278 CCAAGTACGCGCTCATGGTT 61.019 55.000 5.73 0.00 0.00 3.67
2254 2645 1.880796 CATGGTTACGCCGATCGCA 60.881 57.895 10.32 0.08 43.23 5.10
2461 2852 2.066393 CCTCAGGATCTTCGGGGCA 61.066 63.158 0.00 0.00 0.00 5.36
2479 2870 1.593196 CACCGTCCATCAAGTGTTGT 58.407 50.000 0.00 0.00 0.00 3.32
2627 3018 1.439679 ATGCTCGGTCTTTCGTTTCC 58.560 50.000 0.00 0.00 0.00 3.13
2664 3077 9.411801 GGAAATCAAATTGTAGTTTCTTCTTCC 57.588 33.333 15.01 0.00 0.00 3.46
2725 3138 4.450976 TGCCGCACTTTGTTCTGATATAT 58.549 39.130 0.00 0.00 0.00 0.86
2758 3183 5.559148 ATTTTTATTCCAAAGGTGTGGCA 57.441 34.783 0.00 0.00 38.68 4.92
2765 3190 0.954452 CAAAGGTGTGGCAAGGTCTC 59.046 55.000 0.00 0.00 0.00 3.36
2908 3342 5.514274 AAGAGACTAGATGTAGCAAGAGC 57.486 43.478 0.00 0.00 42.56 4.09
2918 3352 2.175322 GCAAGAGCGCAAGACTGC 59.825 61.111 11.47 7.21 45.75 4.40
2964 3398 1.904287 TCGCAAGCAAACAGGGTATT 58.096 45.000 0.00 0.00 37.18 1.89
2965 3399 3.060736 TCGCAAGCAAACAGGGTATTA 57.939 42.857 0.00 0.00 37.18 0.98
2966 3400 3.413327 TCGCAAGCAAACAGGGTATTAA 58.587 40.909 0.00 0.00 37.18 1.40
2967 3401 3.821600 TCGCAAGCAAACAGGGTATTAAA 59.178 39.130 0.00 0.00 37.18 1.52
2968 3402 4.083003 TCGCAAGCAAACAGGGTATTAAAG 60.083 41.667 0.00 0.00 37.18 1.85
2969 3403 4.083003 CGCAAGCAAACAGGGTATTAAAGA 60.083 41.667 0.00 0.00 0.00 2.52
2970 3404 5.161358 GCAAGCAAACAGGGTATTAAAGAC 58.839 41.667 0.00 0.00 0.00 3.01
2971 3405 5.709966 CAAGCAAACAGGGTATTAAAGACC 58.290 41.667 1.98 1.98 36.12 3.85
2972 3406 4.007659 AGCAAACAGGGTATTAAAGACCG 58.992 43.478 4.33 0.00 37.90 4.79
2973 3407 4.004982 GCAAACAGGGTATTAAAGACCGA 58.995 43.478 4.33 0.00 37.90 4.69
2974 3408 4.456566 GCAAACAGGGTATTAAAGACCGAA 59.543 41.667 4.33 0.00 37.90 4.30
2975 3409 5.391629 GCAAACAGGGTATTAAAGACCGAAG 60.392 44.000 4.33 0.66 37.90 3.79
2976 3410 5.750352 AACAGGGTATTAAAGACCGAAGA 57.250 39.130 4.33 0.00 37.90 2.87
2977 3411 5.082251 ACAGGGTATTAAAGACCGAAGAC 57.918 43.478 4.33 0.00 37.90 3.01
2978 3412 4.081254 ACAGGGTATTAAAGACCGAAGACC 60.081 45.833 4.33 0.00 37.90 3.85
2979 3413 3.131755 AGGGTATTAAAGACCGAAGACCG 59.868 47.826 4.33 0.00 37.73 4.79
2989 3423 0.509929 CCGAAGACCGAAAACCGAAC 59.490 55.000 0.00 0.00 41.76 3.95
3217 3654 0.374063 AGTCACGAGCGAGATACACG 59.626 55.000 0.00 0.00 0.00 4.49
3303 3773 4.867599 GCGACGAACCCTAGCCGG 62.868 72.222 0.00 0.00 0.00 6.13
3643 4132 1.918262 TGTCCTCTTCCCATGCTTCAT 59.082 47.619 0.00 0.00 0.00 2.57
3697 4186 6.279123 TCTGATCTCTCTATGTGCATCAAAC 58.721 40.000 0.00 0.00 0.00 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 34 6.673316 GCAAATTGGTTGTAGAGTTCTCGATC 60.673 42.308 0.00 0.00 39.63 3.69
46 48 6.376581 AGGAGAGAAATAGAGCAAATTGGTTG 59.623 38.462 0.00 0.00 40.50 3.77
109 111 9.502145 CTCTTCATGATTATCTAAGATACTCGC 57.498 37.037 0.00 0.00 0.00 5.03
191 193 1.092345 GCTGATTTGAGAGGGCGGTC 61.092 60.000 0.00 0.00 0.00 4.79
267 269 6.834168 TTGAAGACCTAAAATTCCATGTCC 57.166 37.500 0.00 0.00 0.00 4.02
397 594 6.126409 TCAAAGGAAACTATAATCGGGCATT 58.874 36.000 0.00 0.00 42.68 3.56
416 613 5.338463 CCTTTAGTACTCCCTCCCTTCAAAG 60.338 48.000 0.00 0.00 0.00 2.77
440 637 1.741770 ATTGACCGGCTTCTCGCAC 60.742 57.895 0.00 0.00 41.67 5.34
441 638 1.741401 CATTGACCGGCTTCTCGCA 60.741 57.895 0.00 0.00 41.67 5.10
443 640 1.424493 GCTCATTGACCGGCTTCTCG 61.424 60.000 0.00 0.00 0.00 4.04
470 667 1.647346 AACTCGCGAACTCACACAAA 58.353 45.000 11.33 0.00 0.00 2.83
499 696 1.458445 CGAGCATTGCATCATAGTCGG 59.542 52.381 11.91 0.00 0.00 4.79
500 697 2.850441 CGAGCATTGCATCATAGTCG 57.150 50.000 11.91 5.64 0.00 4.18
546 743 1.397945 CGTTAACGAAAGCATGCACGT 60.398 47.619 23.35 23.19 43.02 4.49
616 813 4.370094 AAATGATTGGCCCACAAAACAT 57.630 36.364 0.00 0.00 43.46 2.71
632 829 6.767524 AAATTGGTCGGCATACTAAAATGA 57.232 33.333 0.00 0.00 0.00 2.57
639 836 5.476945 AGAAAAGAAAATTGGTCGGCATACT 59.523 36.000 0.00 0.00 0.00 2.12
647 844 9.277565 GCTTTTTGAAAGAAAAGAAAATTGGTC 57.722 29.630 12.75 0.00 45.20 4.02
648 845 8.791675 TGCTTTTTGAAAGAAAAGAAAATTGGT 58.208 25.926 12.75 0.00 45.20 3.67
691 888 2.315925 TGAGATGCTTTCGGTGATCC 57.684 50.000 0.00 0.00 0.00 3.36
737 934 2.297315 CAGACTGCAGTAGTGGTCTTGA 59.703 50.000 21.73 0.00 40.53 3.02
753 950 0.601311 GCTCGTTCTTGCCACAGACT 60.601 55.000 0.00 0.00 0.00 3.24
755 952 4.361253 GCTCGTTCTTGCCACAGA 57.639 55.556 0.00 0.00 0.00 3.41
774 1125 2.657296 CCATAACGGCGCGTCGAT 60.657 61.111 41.68 31.64 39.99 3.59
788 1139 0.107410 TTCAATAAGGTCGCGGCCAT 60.107 50.000 34.17 24.46 0.00 4.40
794 1145 0.743345 ACCGGCTTCAATAAGGTCGC 60.743 55.000 0.00 0.00 32.98 5.19
795 1146 1.734163 AACCGGCTTCAATAAGGTCG 58.266 50.000 0.00 0.00 33.50 4.79
796 1147 3.078837 TCAAACCGGCTTCAATAAGGTC 58.921 45.455 0.00 0.00 33.50 3.85
797 1148 2.817844 GTCAAACCGGCTTCAATAAGGT 59.182 45.455 0.00 0.00 36.66 3.50
798 1149 2.163613 GGTCAAACCGGCTTCAATAAGG 59.836 50.000 0.00 0.00 32.98 2.69
803 1154 2.642154 TAAGGTCAAACCGGCTTCAA 57.358 45.000 0.00 0.00 44.90 2.69
825 1176 3.951680 ACAAAGACTTTCCGGTTGACATT 59.048 39.130 0.00 0.00 0.00 2.71
829 1180 1.673920 GCACAAAGACTTTCCGGTTGA 59.326 47.619 0.00 0.00 0.00 3.18
836 1187 2.035066 AGGCACATGCACAAAGACTTTC 59.965 45.455 6.15 0.00 44.36 2.62
837 1188 2.034124 AGGCACATGCACAAAGACTTT 58.966 42.857 6.15 0.00 44.36 2.66
846 1197 3.694072 TGGTCTTTTATAGGCACATGCAC 59.306 43.478 6.15 0.00 44.36 4.57
849 1200 4.730613 GCGTTGGTCTTTTATAGGCACATG 60.731 45.833 0.00 0.00 0.00 3.21
851 1202 2.745281 GCGTTGGTCTTTTATAGGCACA 59.255 45.455 0.00 0.00 0.00 4.57
856 1207 3.869065 TCAGGGCGTTGGTCTTTTATAG 58.131 45.455 0.00 0.00 0.00 1.31
863 1214 2.032681 GCTTCAGGGCGTTGGTCT 59.967 61.111 0.00 0.00 0.00 3.85
882 1233 8.906636 TGTAAGAGTTCAACGATGATAAGTAC 57.093 34.615 0.00 0.00 34.96 2.73
922 1273 9.577110 TTGTCATACGGTAAGATTTAGTGTTAG 57.423 33.333 0.00 0.00 0.00 2.34
924 1275 8.308931 TCTTGTCATACGGTAAGATTTAGTGTT 58.691 33.333 0.00 0.00 0.00 3.32
941 1292 5.041287 CGAGGTTAGCGAAATCTTGTCATA 58.959 41.667 0.00 0.00 0.00 2.15
946 1297 2.888594 TCCGAGGTTAGCGAAATCTTG 58.111 47.619 0.00 0.00 30.30 3.02
949 1300 2.159142 TCCTTCCGAGGTTAGCGAAATC 60.159 50.000 0.00 0.00 43.97 2.17
951 1302 1.259609 TCCTTCCGAGGTTAGCGAAA 58.740 50.000 0.00 0.00 43.97 3.46
952 1303 1.259609 TTCCTTCCGAGGTTAGCGAA 58.740 50.000 0.00 0.00 43.97 4.70
953 1304 1.067354 GTTTCCTTCCGAGGTTAGCGA 60.067 52.381 0.00 0.00 43.97 4.93
954 1305 1.067071 AGTTTCCTTCCGAGGTTAGCG 60.067 52.381 0.00 0.00 43.97 4.26
955 1306 2.764439 AGTTTCCTTCCGAGGTTAGC 57.236 50.000 0.00 0.00 43.97 3.09
956 1307 4.246458 CTGAAGTTTCCTTCCGAGGTTAG 58.754 47.826 0.38 0.00 45.45 2.34
957 1308 3.007614 CCTGAAGTTTCCTTCCGAGGTTA 59.992 47.826 0.38 0.00 45.45 2.85
959 1310 1.348036 CCTGAAGTTTCCTTCCGAGGT 59.652 52.381 0.38 0.00 45.45 3.85
961 1312 3.402628 TTCCTGAAGTTTCCTTCCGAG 57.597 47.619 0.38 0.00 45.45 4.63
962 1313 3.583086 AGATTCCTGAAGTTTCCTTCCGA 59.417 43.478 0.38 0.00 45.45 4.55
963 1314 3.944087 AGATTCCTGAAGTTTCCTTCCG 58.056 45.455 0.38 0.00 45.45 4.30
964 1315 5.298026 GCATAGATTCCTGAAGTTTCCTTCC 59.702 44.000 0.38 0.00 45.45 3.46
965 1316 5.298026 GGCATAGATTCCTGAAGTTTCCTTC 59.702 44.000 0.00 0.00 46.09 3.46
970 1321 4.870021 AGGGCATAGATTCCTGAAGTTT 57.130 40.909 0.00 0.00 0.00 2.66
991 1342 0.326595 TTATGCAAGTGGGCGGAGAA 59.673 50.000 0.00 0.00 36.28 2.87
1026 1383 1.503542 GCTGGAATGAGCACCAACG 59.496 57.895 0.00 0.00 38.95 4.10
1032 1389 2.046023 CCCACGCTGGAATGAGCA 60.046 61.111 5.71 0.00 40.96 4.26
1038 1395 1.180029 GTACTACTCCCACGCTGGAA 58.820 55.000 5.71 0.00 40.96 3.53
1293 1657 6.427150 ACAGTGTCAATCAAACGAAATGTAC 58.573 36.000 0.00 0.00 0.00 2.90
1294 1658 6.612247 ACAGTGTCAATCAAACGAAATGTA 57.388 33.333 0.00 0.00 0.00 2.29
1295 1659 5.499139 ACAGTGTCAATCAAACGAAATGT 57.501 34.783 0.00 0.00 0.00 2.71
1340 1705 4.619227 ACCGACAGCACCCCAACG 62.619 66.667 0.00 0.00 0.00 4.10
1535 1900 1.549170 ACTTCGGCGTACAGGAAAGAT 59.451 47.619 6.85 0.00 0.00 2.40
1972 2355 2.125912 CGGACACTCTTCAGCCGG 60.126 66.667 0.00 0.00 38.40 6.13
1974 2357 1.112113 TATCCGGACACTCTTCAGCC 58.888 55.000 6.12 0.00 0.00 4.85
2012 2399 4.734917 AGATCTCACGTTTGCTACAGTAC 58.265 43.478 0.00 0.00 0.00 2.73
2020 2407 4.739195 AGAGAAGTAGATCTCACGTTTGC 58.261 43.478 0.00 0.00 46.73 3.68
2075 2466 0.945743 TAGTTGAGCGTGCACAGCAG 60.946 55.000 27.05 10.15 40.08 4.24
2254 2645 0.034380 TCCTCTCCTCGATGACCGTT 60.034 55.000 0.00 0.00 39.75 4.44
2461 2852 1.872237 CGACAACACTTGATGGACGGT 60.872 52.381 0.00 0.00 0.00 4.83
2468 2859 1.841663 GCGGTGCGACAACACTTGAT 61.842 55.000 0.00 0.00 40.52 2.57
2533 2924 4.996434 GTGCCTGTCACAGCCGCT 62.996 66.667 0.00 0.00 44.98 5.52
2627 3018 2.829741 TTGATTTCCCCCGCAAAAAG 57.170 45.000 0.00 0.00 0.00 2.27
2664 3077 8.460428 ACTACGGTTTATACTCAGAAAGAAGAG 58.540 37.037 0.00 0.00 37.87 2.85
2725 3138 8.802267 CCTTTGGAATAAAAATTAGACCACTCA 58.198 33.333 0.00 0.00 0.00 3.41
2745 3158 0.468029 AGACCTTGCCACACCTTTGG 60.468 55.000 0.00 0.00 39.98 3.28
2758 3183 5.070446 TGTTATGTCACTTGACTGAGACCTT 59.930 40.000 10.63 0.00 44.99 3.50
2837 3265 9.363763 CTAGTCTCGGTTGATACTATATTCGTA 57.636 37.037 0.00 0.00 34.45 3.43
2888 3322 3.851838 GCGCTCTTGCTACATCTAGTCTC 60.852 52.174 0.00 0.00 36.97 3.36
2910 3344 2.294512 GGGGTTTTCAGAAGCAGTCTTG 59.705 50.000 0.00 0.00 32.70 3.02
2911 3345 2.175715 AGGGGTTTTCAGAAGCAGTCTT 59.824 45.455 0.00 0.00 32.70 3.01
2912 3346 1.777272 AGGGGTTTTCAGAAGCAGTCT 59.223 47.619 0.00 0.00 36.88 3.24
2918 3352 1.740025 GCGATGAGGGGTTTTCAGAAG 59.260 52.381 0.00 0.00 0.00 2.85
2964 3398 3.392882 GGTTTTCGGTCTTCGGTCTTTA 58.607 45.455 0.00 0.00 39.77 1.85
2965 3399 2.216046 GGTTTTCGGTCTTCGGTCTTT 58.784 47.619 0.00 0.00 39.77 2.52
2966 3400 1.870993 CGGTTTTCGGTCTTCGGTCTT 60.871 52.381 0.00 0.00 39.77 3.01
2967 3401 0.319297 CGGTTTTCGGTCTTCGGTCT 60.319 55.000 0.00 0.00 39.77 3.85
2968 3402 0.318955 TCGGTTTTCGGTCTTCGGTC 60.319 55.000 0.00 0.00 39.77 4.79
2969 3403 0.104671 TTCGGTTTTCGGTCTTCGGT 59.895 50.000 0.00 0.00 39.77 4.69
2970 3404 0.509929 GTTCGGTTTTCGGTCTTCGG 59.490 55.000 0.00 0.00 39.77 4.30
2971 3405 0.509929 GGTTCGGTTTTCGGTCTTCG 59.490 55.000 0.00 0.00 39.77 3.79
2972 3406 0.870393 GGGTTCGGTTTTCGGTCTTC 59.130 55.000 0.00 0.00 39.77 2.87
2973 3407 0.881600 CGGGTTCGGTTTTCGGTCTT 60.882 55.000 0.00 0.00 39.77 3.01
2974 3408 1.301165 CGGGTTCGGTTTTCGGTCT 60.301 57.895 0.00 0.00 39.77 3.85
2975 3409 0.879839 TTCGGGTTCGGTTTTCGGTC 60.880 55.000 0.00 0.00 39.77 4.79
2976 3410 0.463474 TTTCGGGTTCGGTTTTCGGT 60.463 50.000 0.00 0.00 39.77 4.69
2977 3411 0.662085 TTTTCGGGTTCGGTTTTCGG 59.338 50.000 0.00 0.00 39.77 4.30
2978 3412 1.597690 GGTTTTCGGGTTCGGTTTTCG 60.598 52.381 0.00 0.00 40.90 3.46
2979 3413 1.597690 CGGTTTTCGGGTTCGGTTTTC 60.598 52.381 0.00 0.00 36.95 2.29
2989 3423 1.165284 TTTCGGGTTCGGTTTTCGGG 61.165 55.000 0.00 0.00 39.77 5.14
3643 4132 2.703536 TGGCTTACCTTCAGTTGTGAGA 59.296 45.455 0.00 0.00 36.63 3.27


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

AutoCloner maintained by Alex Coulton.