Multiple sequence alignment - TraesCS4B01G128000

Loading Multiple Alignment...

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 TraesCS4B01G128000 chr4B 100.000 3142 0 0 1 3142 167586036 167589177 0.000000e+00 5803.0
1 TraesCS4B01G128000 chr4D 92.884 1602 58 22 738 2312 109073667 109072095 0.000000e+00 2276.0
2 TraesCS4B01G128000 chr4D 86.339 366 19 12 304 665 109074144 109073806 1.380000e-98 370.0
3 TraesCS4B01G128000 chr4D 95.455 88 4 0 1 88 109074412 109074325 1.170000e-29 141.0
4 TraesCS4B01G128000 chr4D 98.413 63 1 0 209 271 109074208 109074146 9.210000e-21 111.0
5 TraesCS4B01G128000 chrUn 92.927 1541 71 18 787 2312 47069145 47067628 0.000000e+00 2207.0
6 TraesCS4B01G128000 chrUn 92.927 1541 71 18 787 2312 288708375 288709892 0.000000e+00 2207.0
7 TraesCS4B01G128000 chrUn 95.455 88 4 0 1 88 47069725 47069638 1.170000e-29 141.0
8 TraesCS4B01G128000 chrUn 95.455 88 4 0 1 88 288707795 288707882 1.170000e-29 141.0
9 TraesCS4B01G128000 chrUn 91.489 94 5 2 2223 2316 47066261 47066171 3.290000e-25 126.0
10 TraesCS4B01G128000 chrUn 92.308 91 4 2 2223 2313 288711259 288711346 3.290000e-25 126.0
11 TraesCS4B01G128000 chrUn 91.489 94 5 2 2223 2316 409127584 409127494 3.290000e-25 126.0
12 TraesCS4B01G128000 chrUn 100.000 67 0 0 205 271 47069503 47069437 1.180000e-24 124.0
13 TraesCS4B01G128000 chrUn 100.000 67 0 0 205 271 288708017 288708083 1.180000e-24 124.0
14 TraesCS4B01G128000 chrUn 83.333 144 8 8 308 442 47069431 47069295 5.500000e-23 119.0
15 TraesCS4B01G128000 chrUn 83.333 144 8 8 308 442 288708089 288708225 5.500000e-23 119.0
16 TraesCS4B01G128000 chr2A 89.277 1259 66 26 734 1967 723236646 723237860 0.000000e+00 1513.0
17 TraesCS4B01G128000 chr2A 90.659 1017 51 14 958 1967 723225859 723226838 0.000000e+00 1312.0
18 TraesCS4B01G128000 chr2A 80.085 472 36 28 456 893 723225397 723225844 6.590000e-77 298.0
19 TraesCS4B01G128000 chr2A 91.453 117 6 3 150 266 723234764 723234876 1.170000e-34 158.0
20 TraesCS4B01G128000 chr2A 90.833 120 6 3 152 271 723224929 723225043 4.200000e-34 156.0
21 TraesCS4B01G128000 chr2A 89.552 67 3 2 2038 2101 723237860 723237925 7.220000e-12 82.4
22 TraesCS4B01G128000 chr1D 94.539 824 44 1 2320 3142 481876339 481877162 0.000000e+00 1271.0
23 TraesCS4B01G128000 chr7D 94.539 824 40 4 2320 3142 182408019 182407200 0.000000e+00 1267.0
24 TraesCS4B01G128000 chr7D 94.053 824 48 1 2320 3142 8159265 8158442 0.000000e+00 1249.0
25 TraesCS4B01G128000 chr7D 93.932 824 49 1 2320 3142 391146563 391147386 0.000000e+00 1243.0
26 TraesCS4B01G128000 chr5D 94.417 824 44 2 2320 3142 31217543 31216721 0.000000e+00 1266.0
27 TraesCS4B01G128000 chr5D 76.688 785 137 32 1158 1911 240502982 240502213 8.170000e-106 394.0
28 TraesCS4B01G128000 chr1B 94.296 824 46 1 2320 3142 438214706 438215529 0.000000e+00 1260.0
29 TraesCS4B01G128000 chr6D 93.932 824 49 1 2320 3142 150633631 150632808 0.000000e+00 1243.0
30 TraesCS4B01G128000 chr3D 94.053 824 42 2 2320 3142 252759665 252760482 0.000000e+00 1243.0
31 TraesCS4B01G128000 chr3D 93.932 824 49 1 2320 3142 447298291 447297468 0.000000e+00 1243.0
32 TraesCS4B01G128000 chr5A 77.635 778 131 31 1163 1911 313314005 313314768 1.730000e-117 433.0
33 TraesCS4B01G128000 chr5B 76.783 771 141 30 1163 1911 263220962 263221716 6.310000e-107 398.0


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 TraesCS4B01G128000 chr4B 167586036 167589177 3141 False 5803.000000 5803 100.000000 1 3142 1 chr4B.!!$F1 3141
1 TraesCS4B01G128000 chr4D 109072095 109074412 2317 True 724.500000 2276 93.272750 1 2312 4 chr4D.!!$R1 2311
2 TraesCS4B01G128000 chrUn 47066171 47069725 3554 True 543.400000 2207 92.640800 1 2316 5 chrUn.!!$R2 2315
3 TraesCS4B01G128000 chrUn 288707795 288711346 3551 False 543.400000 2207 92.804600 1 2313 5 chrUn.!!$F1 2312
4 TraesCS4B01G128000 chr2A 723224929 723226838 1909 False 588.666667 1312 87.192333 152 1967 3 chr2A.!!$F1 1815
5 TraesCS4B01G128000 chr2A 723234764 723237925 3161 False 584.466667 1513 90.094000 150 2101 3 chr2A.!!$F2 1951
6 TraesCS4B01G128000 chr1D 481876339 481877162 823 False 1271.000000 1271 94.539000 2320 3142 1 chr1D.!!$F1 822
7 TraesCS4B01G128000 chr7D 182407200 182408019 819 True 1267.000000 1267 94.539000 2320 3142 1 chr7D.!!$R2 822
8 TraesCS4B01G128000 chr7D 8158442 8159265 823 True 1249.000000 1249 94.053000 2320 3142 1 chr7D.!!$R1 822
9 TraesCS4B01G128000 chr7D 391146563 391147386 823 False 1243.000000 1243 93.932000 2320 3142 1 chr7D.!!$F1 822
10 TraesCS4B01G128000 chr5D 31216721 31217543 822 True 1266.000000 1266 94.417000 2320 3142 1 chr5D.!!$R1 822
11 TraesCS4B01G128000 chr5D 240502213 240502982 769 True 394.000000 394 76.688000 1158 1911 1 chr5D.!!$R2 753
12 TraesCS4B01G128000 chr1B 438214706 438215529 823 False 1260.000000 1260 94.296000 2320 3142 1 chr1B.!!$F1 822
13 TraesCS4B01G128000 chr6D 150632808 150633631 823 True 1243.000000 1243 93.932000 2320 3142 1 chr6D.!!$R1 822
14 TraesCS4B01G128000 chr3D 252759665 252760482 817 False 1243.000000 1243 94.053000 2320 3142 1 chr3D.!!$F1 822
15 TraesCS4B01G128000 chr3D 447297468 447298291 823 True 1243.000000 1243 93.932000 2320 3142 1 chr3D.!!$R1 822
16 TraesCS4B01G128000 chr5A 313314005 313314768 763 False 433.000000 433 77.635000 1163 1911 1 chr5A.!!$F1 748
17 TraesCS4B01G128000 chr5B 263220962 263221716 754 False 398.000000 398 76.783000 1163 1911 1 chr5B.!!$F1 748

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
142 148 0.17895 TTTGGTGCAATGCTACCCCA 60.179 50.0 19.02 11.69 36.1 4.96 F
1017 2571 0.16923 CACACTCTTCTCCCGTCTCG 59.831 60.0 0.00 0.00 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2036 3626 0.106519 ACTACTTGCATGCATCCCCC 60.107 55.0 23.37 0.0 0.0 5.40 R
2282 5346 0.104487 TCGCGTTGTTGGTGAGGTTA 59.896 50.0 5.77 0.0 0.0 2.85 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
20 21 1.608025 CGTCTCAAGGCAGGCTAAACA 60.608 52.381 0.00 0.00 0.00 2.83
34 35 6.516693 GCAGGCTAAACAAGGACTTTAACATT 60.517 38.462 0.00 0.00 0.00 2.71
75 76 6.436261 GCGTGTGTATGTACTACTCATATGT 58.564 40.000 1.90 0.00 36.51 2.29
76 77 7.569957 CGCGTGTGTATGTACTACTCATATGTA 60.570 40.741 0.00 0.00 36.51 2.29
77 78 7.745155 GCGTGTGTATGTACTACTCATATGTAG 59.255 40.741 1.90 0.82 43.88 2.74
78 79 8.228464 CGTGTGTATGTACTACTCATATGTAGG 58.772 40.741 1.90 0.00 42.92 3.18
79 80 9.281371 GTGTGTATGTACTACTCATATGTAGGA 57.719 37.037 1.90 0.00 42.92 2.94
84 85 6.821031 GTACTACTCATATGTAGGACCTGG 57.179 45.833 3.53 0.00 44.51 4.45
85 86 5.405063 ACTACTCATATGTAGGACCTGGT 57.595 43.478 3.53 0.00 42.92 4.00
86 87 5.141182 ACTACTCATATGTAGGACCTGGTG 58.859 45.833 2.82 0.00 42.92 4.17
87 88 3.995636 ACTCATATGTAGGACCTGGTGT 58.004 45.455 2.82 0.00 0.00 4.16
88 89 3.706594 ACTCATATGTAGGACCTGGTGTG 59.293 47.826 2.82 0.00 0.00 3.82
89 90 3.706594 CTCATATGTAGGACCTGGTGTGT 59.293 47.826 2.82 0.00 0.00 3.72
90 91 3.450817 TCATATGTAGGACCTGGTGTGTG 59.549 47.826 2.82 0.00 0.00 3.82
91 92 1.729586 ATGTAGGACCTGGTGTGTGT 58.270 50.000 2.82 0.00 0.00 3.72
92 93 1.502690 TGTAGGACCTGGTGTGTGTT 58.497 50.000 2.82 0.00 0.00 3.32
93 94 2.680251 TGTAGGACCTGGTGTGTGTTA 58.320 47.619 2.82 0.00 0.00 2.41
94 95 3.039743 TGTAGGACCTGGTGTGTGTTAA 58.960 45.455 2.82 0.00 0.00 2.01
95 96 3.455177 TGTAGGACCTGGTGTGTGTTAAA 59.545 43.478 2.82 0.00 0.00 1.52
96 97 3.655615 AGGACCTGGTGTGTGTTAAAA 57.344 42.857 2.82 0.00 0.00 1.52
97 98 3.970842 AGGACCTGGTGTGTGTTAAAAA 58.029 40.909 2.82 0.00 0.00 1.94
136 142 0.829333 TGTTGGTTTGGTGCAATGCT 59.171 45.000 6.82 0.00 0.00 3.79
142 148 0.178950 TTTGGTGCAATGCTACCCCA 60.179 50.000 19.02 11.69 36.10 4.96
167 173 1.638467 CAGATAGTCAAAGCCGCGC 59.362 57.895 0.00 0.00 0.00 6.86
200 206 5.819825 TCGATCATCATCCTATTCCTACG 57.180 43.478 0.00 0.00 0.00 3.51
202 208 6.412214 TCGATCATCATCCTATTCCTACGTA 58.588 40.000 0.00 0.00 0.00 3.57
203 209 6.539103 TCGATCATCATCCTATTCCTACGTAG 59.461 42.308 15.92 15.92 0.00 3.51
271 324 4.307259 TCCTACTTTCATAGATGGCCCTT 58.693 43.478 0.00 0.00 0.00 3.95
274 327 5.893824 CCTACTTTCATAGATGGCCCTTTTT 59.106 40.000 0.00 0.00 0.00 1.94
275 328 7.060421 CCTACTTTCATAGATGGCCCTTTTTA 58.940 38.462 0.00 0.00 0.00 1.52
276 329 7.725844 CCTACTTTCATAGATGGCCCTTTTTAT 59.274 37.037 0.00 0.00 0.00 1.40
277 330 7.978099 ACTTTCATAGATGGCCCTTTTTATT 57.022 32.000 0.00 0.00 0.00 1.40
278 331 8.379428 ACTTTCATAGATGGCCCTTTTTATTT 57.621 30.769 0.00 0.00 0.00 1.40
279 332 8.825774 ACTTTCATAGATGGCCCTTTTTATTTT 58.174 29.630 0.00 0.00 0.00 1.82
280 333 9.671279 CTTTCATAGATGGCCCTTTTTATTTTT 57.329 29.630 0.00 0.00 0.00 1.94
306 359 4.513442 TCTATTTTGGAAGTGATGTCCCG 58.487 43.478 0.00 0.00 33.89 5.14
358 416 6.094603 ACAAGGACCTACTAACTACGTACATG 59.905 42.308 0.00 0.00 0.00 3.21
408 477 1.862827 GTTGCGTTTCCTTGTCTACGT 59.137 47.619 0.00 0.00 36.45 3.57
442 716 1.297598 GGTGCACATACGCGCATTC 60.298 57.895 20.43 0.00 44.30 2.67
443 717 1.297598 GTGCACATACGCGCATTCC 60.298 57.895 13.17 0.00 42.07 3.01
444 718 2.327940 GCACATACGCGCATTCCC 59.672 61.111 5.73 0.00 0.00 3.97
445 719 2.180204 GCACATACGCGCATTCCCT 61.180 57.895 5.73 0.00 0.00 4.20
446 720 1.714899 GCACATACGCGCATTCCCTT 61.715 55.000 5.73 0.00 0.00 3.95
502 776 1.532868 AGCATTGCAAGACAAGACGAC 59.467 47.619 11.91 0.00 42.87 4.34
508 782 0.944311 CAAGACAAGACGACACCGGG 60.944 60.000 6.32 0.00 40.78 5.73
509 783 1.111116 AAGACAAGACGACACCGGGA 61.111 55.000 6.32 0.00 40.78 5.14
510 784 1.372623 GACAAGACGACACCGGGAC 60.373 63.158 6.32 0.00 40.78 4.46
511 785 2.048503 CAAGACGACACCGGGACC 60.049 66.667 6.32 0.00 40.78 4.46
512 786 3.677648 AAGACGACACCGGGACCG 61.678 66.667 6.32 8.33 40.78 4.79
534 808 0.324285 AGGGAAAGCAGAGCAGAGTG 59.676 55.000 0.00 0.00 0.00 3.51
617 892 1.738099 CCTTCTGGAACCGCGAGTG 60.738 63.158 8.23 0.00 34.57 3.51
653 928 2.533916 TCAGGTCTCTGTCAAGCTCAT 58.466 47.619 0.00 0.00 41.59 2.90
654 929 2.233186 TCAGGTCTCTGTCAAGCTCATG 59.767 50.000 0.00 0.00 41.59 3.07
690 987 2.365617 TGTTCTCTGACGCTTTCTTCCT 59.634 45.455 0.00 0.00 0.00 3.36
691 988 3.181465 TGTTCTCTGACGCTTTCTTCCTT 60.181 43.478 0.00 0.00 0.00 3.36
692 989 3.753294 TCTCTGACGCTTTCTTCCTTT 57.247 42.857 0.00 0.00 0.00 3.11
693 990 3.654414 TCTCTGACGCTTTCTTCCTTTC 58.346 45.455 0.00 0.00 0.00 2.62
694 991 3.069586 TCTCTGACGCTTTCTTCCTTTCA 59.930 43.478 0.00 0.00 0.00 2.69
695 992 3.804036 TCTGACGCTTTCTTCCTTTCAA 58.196 40.909 0.00 0.00 0.00 2.69
757 2270 4.036027 AGCTTAATCGATCAAATGGTGCAG 59.964 41.667 0.00 0.00 0.00 4.41
771 2289 7.655328 TCAAATGGTGCAGGTTATGTTAAAAAG 59.345 33.333 0.00 0.00 0.00 2.27
778 2296 6.093404 GCAGGTTATGTTAAAAAGGAGAAGC 58.907 40.000 0.00 0.00 0.00 3.86
889 2423 3.964688 CCAAAAAGAAGTACCCCAGGTTT 59.035 43.478 0.00 0.00 37.09 3.27
890 2424 4.202212 CCAAAAAGAAGTACCCCAGGTTTG 60.202 45.833 0.00 0.00 37.09 2.93
891 2425 4.529716 AAAAGAAGTACCCCAGGTTTGA 57.470 40.909 0.00 0.00 37.09 2.69
892 2426 4.529716 AAAGAAGTACCCCAGGTTTGAA 57.470 40.909 0.00 0.00 37.09 2.69
893 2427 4.741928 AAGAAGTACCCCAGGTTTGAAT 57.258 40.909 0.00 0.00 37.09 2.57
935 2469 2.424302 CCACGTGTCCCTTTCGGT 59.576 61.111 15.65 0.00 0.00 4.69
1016 2570 1.470890 CTCACACTCTTCTCCCGTCTC 59.529 57.143 0.00 0.00 0.00 3.36
1017 2571 0.169230 CACACTCTTCTCCCGTCTCG 59.831 60.000 0.00 0.00 0.00 4.04
1018 2572 0.250814 ACACTCTTCTCCCGTCTCGT 60.251 55.000 0.00 0.00 0.00 4.18
1019 2573 0.448593 CACTCTTCTCCCGTCTCGTC 59.551 60.000 0.00 0.00 0.00 4.20
1020 2574 0.325602 ACTCTTCTCCCGTCTCGTCT 59.674 55.000 0.00 0.00 0.00 4.18
1041 2595 0.248825 CCCGATCGAGCTTCAGTCAG 60.249 60.000 18.66 0.00 0.00 3.51
1042 2596 0.735471 CCGATCGAGCTTCAGTCAGA 59.265 55.000 18.66 0.00 0.00 3.27
1043 2597 1.532921 CCGATCGAGCTTCAGTCAGAC 60.533 57.143 18.66 0.00 0.00 3.51
1044 2598 1.821336 GATCGAGCTTCAGTCAGACG 58.179 55.000 0.00 0.00 0.00 4.18
1055 2609 1.109920 AGTCAGACGCACACCTCACT 61.110 55.000 0.00 0.00 0.00 3.41
1585 3169 3.138798 GCGTCTCCTACTCCGGCA 61.139 66.667 0.00 0.00 0.00 5.69
1602 3186 4.501285 ATCCTCCTCGCGACGGGA 62.501 66.667 15.50 15.50 0.00 5.14
1785 3375 2.579738 GTGAGGCTCGGGAAGGTC 59.420 66.667 10.42 0.00 0.00 3.85
1881 3471 4.579384 AACAGGGGGTGCACGGTG 62.579 66.667 11.45 3.15 0.00 4.94
1968 3558 3.133721 AGGCTCTTTGATAAGATCACGCT 59.866 43.478 0.00 0.00 39.58 5.07
1971 3561 5.043903 GCTCTTTGATAAGATCACGCTACA 58.956 41.667 0.00 0.00 39.58 2.74
1984 3574 3.366724 TCACGCTACACAATCAATTCGAC 59.633 43.478 0.00 0.00 0.00 4.20
2027 3617 6.183361 TGGATTAATTCGTGTGATCTGGAGAT 60.183 38.462 0.00 0.00 37.51 2.75
2101 3694 8.181904 TCTGATCAGTTGTAGATGCATGTATA 57.818 34.615 21.92 0.00 0.00 1.47
2102 3695 8.810041 TCTGATCAGTTGTAGATGCATGTATAT 58.190 33.333 21.92 0.00 0.00 0.86
2146 3754 3.973206 AACTACATGTCGATGAACCCA 57.027 42.857 0.00 0.00 33.36 4.51
2190 3804 7.982761 TTATCATTTTACAGTTACGGTTGGT 57.017 32.000 0.00 0.00 0.00 3.67
2277 5341 2.479219 CGAAAGCCTCCTTCGTAGTACC 60.479 54.545 0.00 0.00 0.00 3.34
2282 5346 2.233186 GCCTCCTTCGTAGTACCACTTT 59.767 50.000 0.00 0.00 0.00 2.66
2313 5377 5.174216 ACCAACAACGCGAAAATTGATTAAC 59.826 36.000 15.93 0.00 0.00 2.01
2316 5380 5.151389 ACAACGCGAAAATTGATTAACCTC 58.849 37.500 15.93 0.00 0.00 3.85
2317 5381 5.150683 CAACGCGAAAATTGATTAACCTCA 58.849 37.500 15.93 0.00 0.00 3.86
2318 5382 4.719040 ACGCGAAAATTGATTAACCTCAC 58.281 39.130 15.93 0.00 0.00 3.51
2355 5419 2.093658 GTGGGATGAATACGGTGTGAGT 60.094 50.000 0.00 0.00 0.00 3.41
2362 5426 4.329392 TGAATACGGTGTGAGTAGAGACA 58.671 43.478 0.00 0.00 0.00 3.41
2513 5577 0.469144 ACGAACCCATGGCCAAGTTT 60.469 50.000 10.96 0.00 0.00 2.66
2566 5630 3.309582 GGAACCAGATCCGAGGCA 58.690 61.111 0.00 0.00 0.00 4.75
2583 5648 3.367743 AGCGAACGACGGGTAGCA 61.368 61.111 0.00 0.00 42.83 3.49
2601 5666 0.737367 CAGGAACAGCTTCGATGCGA 60.737 55.000 16.59 0.00 38.13 5.10
2671 5736 0.250858 TCGGAGTGGTTCTGGTACGA 60.251 55.000 0.00 0.00 32.69 3.43
2742 5813 1.002087 CTAAGTCCTTGAGGGCGTTGT 59.998 52.381 0.00 0.00 46.49 3.32
2767 5838 1.358725 CGGTTGCGTTGGATGACGAT 61.359 55.000 1.15 0.00 45.47 3.73
2774 5845 0.174845 GTTGGATGACGATGTCGGGA 59.825 55.000 7.38 0.00 44.95 5.14
2893 5964 4.910585 GGCGCCCACGGAGTATGG 62.911 72.222 18.11 0.00 41.61 2.74
3057 6128 0.850100 TCAGGTGTCCCAAATGTGGT 59.150 50.000 0.00 0.00 44.30 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 6.514376 CGTGCTTGGTTAATGTTAAAGTCCTT 60.514 38.462 0.00 0.00 0.00 3.36
75 76 4.774660 TTTTAACACACACCAGGTCCTA 57.225 40.909 0.00 0.00 0.00 2.94
76 77 3.655615 TTTTAACACACACCAGGTCCT 57.344 42.857 0.00 0.00 0.00 3.85
102 103 4.193240 ACCAACACCAGGTCCTATTTTT 57.807 40.909 0.00 0.00 32.90 1.94
103 104 3.895704 ACCAACACCAGGTCCTATTTT 57.104 42.857 0.00 0.00 32.90 1.82
104 105 3.895041 CAAACCAACACCAGGTCCTATTT 59.105 43.478 0.00 0.00 38.76 1.40
105 106 3.496331 CAAACCAACACCAGGTCCTATT 58.504 45.455 0.00 0.00 38.76 1.73
106 107 2.225017 CCAAACCAACACCAGGTCCTAT 60.225 50.000 0.00 0.00 38.76 2.57
136 142 3.401342 TGACTATCTGCCTATCTGGGGTA 59.599 47.826 0.00 0.00 36.00 3.69
142 148 3.006323 CGGCTTTGACTATCTGCCTATCT 59.994 47.826 0.00 0.00 41.25 1.98
177 183 5.888724 ACGTAGGAATAGGATGATGATCGAT 59.111 40.000 0.00 0.00 0.00 3.59
178 184 5.254115 ACGTAGGAATAGGATGATGATCGA 58.746 41.667 0.00 0.00 0.00 3.59
195 201 6.370718 ACAATTGTTTTTAGCTCCTACGTAGG 59.629 38.462 32.05 32.05 45.02 3.18
196 202 7.360575 ACAATTGTTTTTAGCTCCTACGTAG 57.639 36.000 15.92 15.92 0.00 3.51
200 206 7.141100 TGCTACAATTGTTTTTAGCTCCTAC 57.859 36.000 24.31 3.50 40.32 3.18
202 208 6.624423 CATGCTACAATTGTTTTTAGCTCCT 58.376 36.000 24.31 11.67 40.32 3.69
203 209 5.289434 GCATGCTACAATTGTTTTTAGCTCC 59.711 40.000 24.31 13.11 40.32 4.70
279 332 8.966868 GGGACATCACTTCCAAAATAGAAATAA 58.033 33.333 0.00 0.00 34.45 1.40
280 333 7.282224 CGGGACATCACTTCCAAAATAGAAATA 59.718 37.037 0.00 0.00 34.45 1.40
281 334 6.095440 CGGGACATCACTTCCAAAATAGAAAT 59.905 38.462 0.00 0.00 34.45 2.17
282 335 5.414454 CGGGACATCACTTCCAAAATAGAAA 59.586 40.000 0.00 0.00 34.45 2.52
283 336 4.941263 CGGGACATCACTTCCAAAATAGAA 59.059 41.667 0.00 0.00 34.45 2.10
284 337 4.019681 ACGGGACATCACTTCCAAAATAGA 60.020 41.667 0.00 0.00 34.45 1.98
285 338 4.261801 ACGGGACATCACTTCCAAAATAG 58.738 43.478 0.00 0.00 34.45 1.73
286 339 4.295141 ACGGGACATCACTTCCAAAATA 57.705 40.909 0.00 0.00 34.45 1.40
287 340 3.154827 ACGGGACATCACTTCCAAAAT 57.845 42.857 0.00 0.00 34.45 1.82
288 341 2.649531 ACGGGACATCACTTCCAAAA 57.350 45.000 0.00 0.00 34.45 2.44
289 342 2.621055 CAAACGGGACATCACTTCCAAA 59.379 45.455 0.00 0.00 34.45 3.28
290 343 2.158740 TCAAACGGGACATCACTTCCAA 60.159 45.455 0.00 0.00 34.45 3.53
291 344 1.418264 TCAAACGGGACATCACTTCCA 59.582 47.619 0.00 0.00 34.45 3.53
292 345 2.178912 TCAAACGGGACATCACTTCC 57.821 50.000 0.00 0.00 0.00 3.46
293 346 4.475944 CAAATCAAACGGGACATCACTTC 58.524 43.478 0.00 0.00 0.00 3.01
294 347 3.255642 CCAAATCAAACGGGACATCACTT 59.744 43.478 0.00 0.00 0.00 3.16
295 348 2.819608 CCAAATCAAACGGGACATCACT 59.180 45.455 0.00 0.00 0.00 3.41
296 349 2.817258 TCCAAATCAAACGGGACATCAC 59.183 45.455 0.00 0.00 0.00 3.06
297 350 3.147553 TCCAAATCAAACGGGACATCA 57.852 42.857 0.00 0.00 0.00 3.07
298 351 3.669557 CGTTCCAAATCAAACGGGACATC 60.670 47.826 0.00 0.00 43.31 3.06
299 352 2.227865 CGTTCCAAATCAAACGGGACAT 59.772 45.455 0.00 0.00 43.31 3.06
300 353 1.604755 CGTTCCAAATCAAACGGGACA 59.395 47.619 0.00 0.00 43.31 4.02
301 354 1.664874 GCGTTCCAAATCAAACGGGAC 60.665 52.381 9.34 0.00 46.20 4.46
302 355 0.594110 GCGTTCCAAATCAAACGGGA 59.406 50.000 9.34 0.00 46.20 5.14
306 359 2.223377 AGTCTCGCGTTCCAAATCAAAC 59.777 45.455 5.77 0.00 0.00 2.93
358 416 7.147983 CCTGACTATGACTAGATTACATAGGCC 60.148 44.444 21.33 0.00 46.17 5.19
366 424 6.027025 ACCACCCTGACTATGACTAGATTA 57.973 41.667 0.00 0.00 0.00 1.75
408 477 4.019411 TGTGCACCAGATGAGGATTTTCTA 60.019 41.667 15.69 0.00 0.00 2.10
442 716 2.490509 GTTCGGGATGGTTTGTAAAGGG 59.509 50.000 0.00 0.00 0.00 3.95
443 717 3.190535 CAGTTCGGGATGGTTTGTAAAGG 59.809 47.826 0.00 0.00 0.00 3.11
444 718 4.069304 TCAGTTCGGGATGGTTTGTAAAG 58.931 43.478 0.00 0.00 0.00 1.85
445 719 4.088056 TCAGTTCGGGATGGTTTGTAAA 57.912 40.909 0.00 0.00 0.00 2.01
446 720 3.773418 TCAGTTCGGGATGGTTTGTAA 57.227 42.857 0.00 0.00 0.00 2.41
508 782 2.245438 CTCTGCTTTCCCTCCCGGTC 62.245 65.000 0.00 0.00 0.00 4.79
509 783 2.203938 TCTGCTTTCCCTCCCGGT 60.204 61.111 0.00 0.00 0.00 5.28
510 784 2.586792 CTCTGCTTTCCCTCCCGG 59.413 66.667 0.00 0.00 0.00 5.73
511 785 2.124942 GCTCTGCTTTCCCTCCCG 60.125 66.667 0.00 0.00 0.00 5.14
512 786 1.077858 CTGCTCTGCTTTCCCTCCC 60.078 63.158 0.00 0.00 0.00 4.30
513 787 0.107752 CTCTGCTCTGCTTTCCCTCC 60.108 60.000 0.00 0.00 0.00 4.30
514 788 0.612744 ACTCTGCTCTGCTTTCCCTC 59.387 55.000 0.00 0.00 0.00 4.30
515 789 0.324285 CACTCTGCTCTGCTTTCCCT 59.676 55.000 0.00 0.00 0.00 4.20
516 790 0.676151 CCACTCTGCTCTGCTTTCCC 60.676 60.000 0.00 0.00 0.00 3.97
517 791 0.322975 TCCACTCTGCTCTGCTTTCC 59.677 55.000 0.00 0.00 0.00 3.13
518 792 1.001860 ACTCCACTCTGCTCTGCTTTC 59.998 52.381 0.00 0.00 0.00 2.62
519 793 1.055040 ACTCCACTCTGCTCTGCTTT 58.945 50.000 0.00 0.00 0.00 3.51
520 794 1.824230 CTACTCCACTCTGCTCTGCTT 59.176 52.381 0.00 0.00 0.00 3.91
521 795 1.005332 TCTACTCCACTCTGCTCTGCT 59.995 52.381 0.00 0.00 0.00 4.24
522 796 1.405105 CTCTACTCCACTCTGCTCTGC 59.595 57.143 0.00 0.00 0.00 4.26
523 797 2.023673 CCTCTACTCCACTCTGCTCTG 58.976 57.143 0.00 0.00 0.00 3.35
524 798 1.684869 GCCTCTACTCCACTCTGCTCT 60.685 57.143 0.00 0.00 0.00 4.09
534 808 0.320697 AACAACGGTGCCTCTACTCC 59.679 55.000 0.00 0.00 0.00 3.85
574 848 9.710900 GGAAAGTGATTTTTCTGTGGAATAATT 57.289 29.630 0.00 0.00 37.26 1.40
599 874 1.738099 CACTCGCGGTTCCAGAAGG 60.738 63.158 6.13 0.00 0.00 3.46
617 892 2.907042 ACCTGAATATTCGGAGGGGATC 59.093 50.000 23.36 0.00 35.56 3.36
653 928 2.622942 AGAACACGTACGGGTTAACTCA 59.377 45.455 33.95 0.00 42.45 3.41
654 929 3.057946 AGAGAACACGTACGGGTTAACTC 60.058 47.826 33.95 31.78 42.45 3.01
694 991 2.223735 TGTCTCGAAAGCAAGTCGTCTT 60.224 45.455 4.03 0.00 39.52 3.01
695 992 1.337071 TGTCTCGAAAGCAAGTCGTCT 59.663 47.619 4.03 0.00 39.52 4.18
757 2270 7.215719 ACAGCTTCTCCTTTTTAACATAACC 57.784 36.000 0.00 0.00 0.00 2.85
848 2372 0.514691 GTGCTGCTTTTGAGACGAGG 59.485 55.000 0.00 0.00 0.00 4.63
889 2423 0.310543 GCCACACGCTGTTCAATTCA 59.689 50.000 0.00 0.00 0.00 2.57
890 2424 0.725784 CGCCACACGCTGTTCAATTC 60.726 55.000 0.00 0.00 34.21 2.17
891 2425 1.163420 TCGCCACACGCTGTTCAATT 61.163 50.000 0.00 0.00 43.23 2.32
892 2426 1.596752 TCGCCACACGCTGTTCAAT 60.597 52.632 0.00 0.00 43.23 2.57
893 2427 2.202946 TCGCCACACGCTGTTCAA 60.203 55.556 0.00 0.00 43.23 2.69
1016 2570 2.395367 GAAGCTCGATCGGGGAGACG 62.395 65.000 18.35 0.00 33.27 4.18
1017 2571 1.360911 GAAGCTCGATCGGGGAGAC 59.639 63.158 18.35 0.00 33.27 3.36
1018 2572 1.076995 TGAAGCTCGATCGGGGAGA 60.077 57.895 18.35 0.00 33.27 3.71
1019 2573 1.361993 CTGAAGCTCGATCGGGGAG 59.638 63.158 18.35 7.56 34.62 4.30
1020 2574 1.379977 ACTGAAGCTCGATCGGGGA 60.380 57.895 18.35 0.00 0.00 4.81
1041 2595 3.044305 GCCAGTGAGGTGTGCGTC 61.044 66.667 0.00 0.00 40.61 5.19
1042 2596 4.969196 CGCCAGTGAGGTGTGCGT 62.969 66.667 0.00 0.00 43.15 5.24
1441 3007 2.675772 GGAGAGGGACGTGACGGT 60.676 66.667 10.66 0.00 0.00 4.83
1585 3169 4.501285 TCCCGTCGCGAGGAGGAT 62.501 66.667 28.85 0.00 32.22 3.24
1617 3201 3.766691 TTCCTCGGCGCCTGGTAC 61.767 66.667 26.68 0.00 0.00 3.34
1968 3558 7.223971 GGCAGTAATAGTCGAATTGATTGTGTA 59.776 37.037 0.00 0.00 0.00 2.90
1971 3561 5.234329 CGGCAGTAATAGTCGAATTGATTGT 59.766 40.000 0.00 0.00 35.87 2.71
1984 3574 2.167693 TCCACTTCACCGGCAGTAATAG 59.832 50.000 0.00 0.00 0.00 1.73
2036 3626 0.106519 ACTACTTGCATGCATCCCCC 60.107 55.000 23.37 0.00 0.00 5.40
2051 3641 5.111989 TGCTCTGCTGATTGATTGTACTAC 58.888 41.667 0.00 0.00 0.00 2.73
2104 3697 8.340618 AGTTTATTTCTATGCAAGAAGAAGCA 57.659 30.769 8.84 0.00 44.95 3.91
2120 3713 7.065324 TGGGTTCATCGACATGTAGTTTATTTC 59.935 37.037 0.00 0.00 0.00 2.17
2143 3751 3.226777 TGACTGGTTTTTGTACCATGGG 58.773 45.455 18.09 0.00 46.63 4.00
2146 3754 8.415950 TGATAAATGACTGGTTTTTGTACCAT 57.584 30.769 0.00 0.00 46.63 3.55
2168 3776 5.335348 GCACCAACCGTAACTGTAAAATGAT 60.335 40.000 0.00 0.00 0.00 2.45
2179 3793 0.533308 TGGACAGCACCAACCGTAAC 60.533 55.000 0.00 0.00 36.96 2.50
2190 3804 2.139917 GTTACATGAACGTGGACAGCA 58.860 47.619 0.00 0.00 0.00 4.41
2277 5341 3.790789 GCGTTGTTGGTGAGGTTAAAGTG 60.791 47.826 0.00 0.00 0.00 3.16
2282 5346 0.104487 TCGCGTTGTTGGTGAGGTTA 59.896 50.000 5.77 0.00 0.00 2.85
2313 5377 4.211374 CACGAAAGAAACTAGTTGGTGAGG 59.789 45.833 9.34 0.92 34.14 3.86
2316 5380 3.250040 CCCACGAAAGAAACTAGTTGGTG 59.750 47.826 9.34 10.19 32.64 4.17
2317 5381 3.135167 TCCCACGAAAGAAACTAGTTGGT 59.865 43.478 9.34 0.00 0.00 3.67
2318 5382 3.735591 TCCCACGAAAGAAACTAGTTGG 58.264 45.455 9.34 3.88 0.00 3.77
2355 5419 9.249457 CTTATTCGTGCAAATCTTATGTCTCTA 57.751 33.333 0.00 0.00 0.00 2.43
2362 5426 7.054124 TCTTCCCTTATTCGTGCAAATCTTAT 58.946 34.615 0.00 0.00 0.00 1.73
2513 5577 1.821759 CCACCGCACCACACTCAAA 60.822 57.895 0.00 0.00 0.00 2.69
2538 5602 1.076777 CTGGTTCCCCATTGCCGAT 60.077 57.895 0.00 0.00 40.90 4.18
2544 5608 0.839946 CTCGGATCTGGTTCCCCATT 59.160 55.000 0.62 0.00 40.90 3.16
2545 5609 1.056700 CCTCGGATCTGGTTCCCCAT 61.057 60.000 0.62 0.00 40.90 4.00
2546 5610 1.689233 CCTCGGATCTGGTTCCCCA 60.689 63.158 0.62 0.00 38.87 4.96
2566 5630 3.338126 CTGCTACCCGTCGTTCGCT 62.338 63.158 0.00 0.00 38.35 4.93
2583 5648 0.176680 ATCGCATCGAAGCTGTTCCT 59.823 50.000 11.27 0.00 39.99 3.36
2601 5666 1.667830 CACTGTCGCAACCGTCCAT 60.668 57.895 0.00 0.00 35.54 3.41
2742 5813 0.604243 ATCCAACGCAACCGCAACTA 60.604 50.000 0.00 0.00 38.40 2.24
2774 5845 1.270305 CCATCATGTCGAAGCCGGTAT 60.270 52.381 1.90 0.00 36.24 2.73
2786 5857 2.446848 CCGCCCTCCTCCATCATGT 61.447 63.158 0.00 0.00 0.00 3.21
2893 5964 1.527370 CTCCCTCCGTTTCCCCATC 59.473 63.158 0.00 0.00 0.00 3.51
3057 6128 0.824595 TCGGCCGAAATCTATCCCGA 60.825 55.000 28.99 0.00 41.94 5.14
3084 6155 2.666862 TGTGGGCGCCTAAACACG 60.667 61.111 28.56 0.00 36.67 4.49


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

AutoCloner maintained by Alex Coulton.