Multiple sequence alignment - TraesCS4B01G251800

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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 TraesCS4B01G251800 chr4B 100.000 3284 0 0 1 3284 517953577 517956860 0.000000e+00 6065.0
1 TraesCS4B01G251800 chr4B 76.715 481 55 33 1507 1948 517955017 517955479 7.140000e-52 215.0
2 TraesCS4B01G251800 chr4B 76.715 481 55 33 1441 1903 517955083 517955524 7.140000e-52 215.0
3 TraesCS4B01G251800 chr4D 91.085 3107 171 42 42 3102 420147093 420144047 0.000000e+00 4106.0
4 TraesCS4B01G251800 chr4D 76.098 569 67 36 1410 1948 420145782 420145253 1.970000e-57 233.0
5 TraesCS4B01G251800 chr4D 75.773 582 63 46 1349 1903 420145738 420145208 4.270000e-54 222.0
6 TraesCS4B01G251800 chr4D 94.231 104 5 1 3181 3284 420143879 420143777 1.220000e-34 158.0
7 TraesCS4B01G251800 chr4D 84.314 153 17 3 200 352 346475314 346475459 3.420000e-30 143.0
8 TraesCS4B01G251800 chr4D 85.185 108 13 3 557 663 112229955 112230060 1.250000e-19 108.0
9 TraesCS4B01G251800 chr4A 94.001 1567 70 12 352 1903 43369857 43368300 0.000000e+00 2351.0
10 TraesCS4B01G251800 chr4A 89.583 1824 121 40 1507 3284 43368762 43366962 0.000000e+00 2252.0
11 TraesCS4B01G251800 chr4A 75.059 425 54 30 1568 1948 43368761 43368345 2.040000e-32 150.0
12 TraesCS4B01G251800 chr4A 73.715 506 70 31 1349 1824 43368752 43368280 4.420000e-29 139.0
13 TraesCS4B01G251800 chr4A 84.397 141 19 3 214 352 139530086 139530225 5.720000e-28 135.0
14 TraesCS4B01G251800 chr5A 84.817 191 22 6 551 736 338221461 338221649 5.600000e-43 185.0
15 TraesCS4B01G251800 chr5A 86.250 80 9 2 3099 3177 321667486 321667564 5.840000e-13 86.1
16 TraesCS4B01G251800 chr7D 81.281 203 29 5 549 742 578730395 578730597 4.390000e-34 156.0
17 TraesCS4B01G251800 chr3A 84.375 160 17 5 198 352 7473451 7473607 2.040000e-32 150.0
18 TraesCS4B01G251800 chr3A 81.529 157 26 3 556 710 716381117 716380962 3.440000e-25 126.0
19 TraesCS4B01G251800 chr3A 86.047 86 7 3 3094 3175 469414721 469414637 1.620000e-13 87.9
20 TraesCS4B01G251800 chr1B 87.050 139 11 3 214 352 325812557 325812688 2.040000e-32 150.0
21 TraesCS4B01G251800 chr1D 84.277 159 18 3 194 352 225704776 225704927 7.340000e-32 148.0
22 TraesCS4B01G251800 chr5B 84.892 139 19 1 214 352 682068668 682068804 4.420000e-29 139.0
23 TraesCS4B01G251800 chr5B 87.013 77 6 3 3100 3176 647891110 647891182 2.100000e-12 84.2
24 TraesCS4B01G251800 chr6D 82.895 152 21 3 201 352 33677555 33677409 7.390000e-27 132.0
25 TraesCS4B01G251800 chr6D 83.212 137 16 4 556 689 429612306 429612174 5.760000e-23 119.0
26 TraesCS4B01G251800 chr6D 84.167 120 17 2 3 122 127483798 127483915 7.450000e-22 115.0
27 TraesCS4B01G251800 chr2A 84.286 140 14 5 214 352 703708414 703708282 2.660000e-26 130.0
28 TraesCS4B01G251800 chr2B 90.244 82 6 2 3095 3175 656942020 656941940 4.480000e-19 106.0
29 TraesCS4B01G251800 chr6A 82.500 120 20 1 3 122 150852553 150852435 1.610000e-18 104.0
30 TraesCS4B01G251800 chr5D 81.034 116 21 1 548 663 220707779 220707665 1.250000e-14 91.6
31 TraesCS4B01G251800 chr2D 87.654 81 7 3 3100 3179 416856717 416856639 1.250000e-14 91.6
32 TraesCS4B01G251800 chr3B 85.882 85 7 4 3096 3176 707431400 707431483 5.840000e-13 86.1
33 TraesCS4B01G251800 chr3B 86.585 82 6 4 3099 3176 707431484 707431404 5.840000e-13 86.1
34 TraesCS4B01G251800 chr6B 82.955 88 11 4 3093 3180 647951619 647951536 3.510000e-10 76.8


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 TraesCS4B01G251800 chr4B 517953577 517956860 3283 False 2165.00 6065 84.476667 1 3284 3 chr4B.!!$F1 3283
1 TraesCS4B01G251800 chr4D 420143777 420147093 3316 True 1179.75 4106 84.296750 42 3284 4 chr4D.!!$R1 3242
2 TraesCS4B01G251800 chr4A 43366962 43369857 2895 True 1223.00 2351 83.089500 352 3284 4 chr4A.!!$R1 2932

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
54 55 0.250513 GAGGACGAGGGCTTCATTGT 59.749 55.000 0.00 0.0 0.00 2.71 F
529 563 1.001268 TCGGCGATGCTCTTACATCTC 60.001 52.381 4.99 0.0 43.54 2.75 F
944 990 1.104577 ATCGAAGCCCCGTCTCTCTC 61.105 60.000 0.00 0.0 0.00 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1598 1644 0.413832 ACCACTAGGAGGCCTCTTGA 59.586 55.0 31.36 15.94 38.69 3.02 R
2127 2176 0.321671 CTTTTCCACTCTCAGGGCGA 59.678 55.0 0.00 0.00 0.00 5.54 R
2867 2923 2.499289 ACAAGATCAGAGCCAGTAGGTG 59.501 50.0 0.00 0.00 37.19 4.00 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
38 39 9.682465 ATGATTATGATAATCTCAACATGGAGG 57.318 33.333 21.81 0.00 37.44 4.30
39 40 8.883302 TGATTATGATAATCTCAACATGGAGGA 58.117 33.333 21.81 0.00 37.44 3.71
40 41 9.160496 GATTATGATAATCTCAACATGGAGGAC 57.840 37.037 15.99 0.00 37.44 3.85
54 55 0.250513 GAGGACGAGGGCTTCATTGT 59.749 55.000 0.00 0.00 0.00 2.71
60 61 1.467920 GAGGGCTTCATTGTCAAGGG 58.532 55.000 0.00 0.00 0.00 3.95
78 79 6.039382 GTCAAGGGAAGAACCGCAAATTATAT 59.961 38.462 0.00 0.00 40.11 0.86
105 106 3.908382 GTCGAAGATGTGTTGATTTGCAC 59.092 43.478 0.00 0.00 40.67 4.57
121 122 1.237285 GCACCGCATGGAAGTTGAGT 61.237 55.000 0.00 0.00 39.21 3.41
175 176 4.801624 CTGTAGGCTGCTGCGCGA 62.802 66.667 12.10 0.00 40.82 5.87
205 206 7.927048 AGGCGTTTTACATCTTCAAATATACC 58.073 34.615 0.00 0.00 0.00 2.73
207 208 7.012989 GGCGTTTTACATCTTCAAATATACCCT 59.987 37.037 0.00 0.00 0.00 4.34
495 519 8.918202 ACAATGTCTATGTTTACTTCTCCAAA 57.082 30.769 0.00 0.00 0.00 3.28
496 520 9.520515 ACAATGTCTATGTTTACTTCTCCAAAT 57.479 29.630 0.00 0.00 0.00 2.32
529 563 1.001268 TCGGCGATGCTCTTACATCTC 60.001 52.381 4.99 0.00 43.54 2.75
539 573 6.798427 TGCTCTTACATCTCTAATGAAGGT 57.202 37.500 0.00 0.00 0.00 3.50
543 578 7.930865 GCTCTTACATCTCTAATGAAGGTGATT 59.069 37.037 0.00 0.00 0.00 2.57
545 580 8.424918 TCTTACATCTCTAATGAAGGTGATTCC 58.575 37.037 0.00 0.00 37.08 3.01
569 604 7.396055 TCCAAAAATAAAGACCCTGATAAGTGG 59.604 37.037 0.00 0.00 0.00 4.00
570 605 7.178451 CCAAAAATAAAGACCCTGATAAGTGGT 59.822 37.037 0.00 0.00 34.33 4.16
600 635 2.546368 GGCACGAACACATGACAACTTA 59.454 45.455 0.00 0.00 0.00 2.24
633 668 6.656314 TTATGACAAGTTTAATGACGCGAT 57.344 33.333 15.93 0.00 0.00 4.58
696 739 8.977505 CGGATGACATGTTTCAGTTTTAATTTT 58.022 29.630 0.00 0.00 0.00 1.82
725 768 7.437748 TCTTTCTTTCCGAATGGCAATTTTAA 58.562 30.769 0.00 0.00 34.14 1.52
794 838 2.515057 AGCAAAACGTGTGCCCGA 60.515 55.556 18.14 0.00 43.27 5.14
850 894 4.069232 CTCCGACGGCAGCTGGAA 62.069 66.667 17.12 0.00 0.00 3.53
873 917 1.468914 GAGGGAGGTTCGCATCAAAAC 59.531 52.381 0.00 0.00 0.00 2.43
944 990 1.104577 ATCGAAGCCCCGTCTCTCTC 61.105 60.000 0.00 0.00 0.00 3.20
945 991 1.751162 CGAAGCCCCGTCTCTCTCT 60.751 63.158 0.00 0.00 0.00 3.10
1011 1057 1.367840 GACGCGAATGGCCTCCTAT 59.632 57.895 15.93 0.00 38.94 2.57
1417 1463 2.224066 GGGAGGTACGAACAGGATGATG 60.224 54.545 0.00 0.00 39.69 3.07
1418 1464 2.693591 GGAGGTACGAACAGGATGATGA 59.306 50.000 0.00 0.00 39.69 2.92
1419 1465 3.322254 GGAGGTACGAACAGGATGATGAT 59.678 47.826 0.00 0.00 39.69 2.45
1445 1491 1.768684 AAGAAGAAGCCCAGCGGTGA 61.769 55.000 17.83 0.00 0.00 4.02
1489 1535 3.764434 TGAGTACAGGAAGAAGCCTACTG 59.236 47.826 0.00 0.00 36.22 2.74
1502 1548 1.125093 CCTACTGGTGGTGGTGGTGA 61.125 60.000 0.00 0.00 0.00 4.02
1598 1644 5.396213 GGAGGTATGAGCAAGAAGATGACTT 60.396 44.000 0.00 0.00 39.24 3.01
1629 1678 2.748058 CTAGTGGTGGTGGTGGTGGC 62.748 65.000 0.00 0.00 0.00 5.01
1656 1705 1.212195 GGTGGGGGAAGGTATGAAGAC 59.788 57.143 0.00 0.00 0.00 3.01
1866 1915 2.960104 GCCTAGTGGTGGAGGAAGGTAT 60.960 54.545 0.00 0.00 34.46 2.73
1875 1924 4.141824 GGTGGAGGAAGGTATGAAGAAGAG 60.142 50.000 0.00 0.00 0.00 2.85
1890 1939 6.987386 TGAAGAAGAGGACTACAAGAAGAAG 58.013 40.000 0.00 0.00 0.00 2.85
2010 2059 6.058833 TGGAGACTACATTAAACTTGCACAA 58.941 36.000 0.00 0.00 0.00 3.33
2033 2082 4.012374 GGTTTCATGAAGAAGCAGGATGA 58.988 43.478 8.41 0.00 39.01 2.92
2061 2110 1.623811 GGGCACAAGAAGACTAGTGGA 59.376 52.381 0.00 0.00 32.80 4.02
2103 2152 4.702612 GGAAAGGAGGAAAATGAAGAGGAC 59.297 45.833 0.00 0.00 0.00 3.85
2127 2176 1.963515 GGCAAGAAGAAACATGGTGGT 59.036 47.619 0.00 0.00 0.00 4.16
2390 2439 4.460263 TGTGGGATTTCCTATGATTTCCG 58.540 43.478 0.00 0.00 36.20 4.30
2495 2547 7.523219 TGGATGAATAAACGTGTGTTATTCAC 58.477 34.615 25.22 20.01 46.31 3.18
2511 2563 9.389570 GTGTTATTCACGCTTTGTAAATAGTTT 57.610 29.630 0.00 0.00 37.31 2.66
2515 2567 7.901874 TTCACGCTTTGTAAATAGTTTTGAC 57.098 32.000 0.00 0.00 0.00 3.18
2570 2623 7.484035 AGAAGTGTTGAATAGAACTTGTGTC 57.516 36.000 0.00 0.00 33.14 3.67
2610 2663 4.635223 TGAATGTAGCTATGCTGGTGATC 58.365 43.478 0.00 0.00 40.10 2.92
2775 2830 7.113658 TCAGTTAAAGAGACACTCTGTTTCT 57.886 36.000 1.97 0.00 42.72 2.52
2811 2866 1.879380 TGACTTTGCCCTGTGAAATCG 59.121 47.619 0.00 0.00 0.00 3.34
2867 2923 4.579869 TCTGCATCTTACTTTCCTGTTCC 58.420 43.478 0.00 0.00 0.00 3.62
2873 2929 5.479124 TCTTACTTTCCTGTTCCACCTAC 57.521 43.478 0.00 0.00 0.00 3.18
2884 2940 1.781786 TCCACCTACTGGCTCTGATC 58.218 55.000 0.00 0.00 40.39 2.92
2939 2996 4.524714 TGTTTTGAGGACACCTTTTCAACA 59.475 37.500 0.00 0.00 31.76 3.33
2960 3017 8.739039 TCAACAGATGGTAGTTTTGGATATTTG 58.261 33.333 0.00 0.00 0.00 2.32
3001 3074 3.007074 TCCGGCATCTGTGTACAGTTAAA 59.993 43.478 11.44 0.00 44.12 1.52
3004 3077 4.629634 CGGCATCTGTGTACAGTTAAATGA 59.370 41.667 10.35 0.00 44.12 2.57
3008 3081 7.017645 GCATCTGTGTACAGTTAAATGACAAG 58.982 38.462 10.35 9.41 44.12 3.16
3010 3083 6.052360 TCTGTGTACAGTTAAATGACAAGCA 58.948 36.000 10.35 4.78 44.12 3.91
3017 3090 6.096695 ACAGTTAAATGACAAGCAAACGTTT 58.903 32.000 10.35 7.96 0.00 3.60
3021 3094 9.308318 AGTTAAATGACAAGCAAACGTTTTAAT 57.692 25.926 11.66 0.00 0.00 1.40
3032 3105 8.056710 AGCAAACGTTTTAATGTAAACATCAC 57.943 30.769 11.66 0.00 37.77 3.06
3033 3106 7.168469 AGCAAACGTTTTAATGTAAACATCACC 59.832 33.333 11.66 0.00 37.77 4.02
3086 3159 5.182001 GGTGTCATGTTATCAGCTTGAACTT 59.818 40.000 0.00 0.00 0.00 2.66
3146 3227 8.418597 AGTGTCCTGATTTAGTACAAAGTAGA 57.581 34.615 0.00 0.00 0.00 2.59
3153 3234 9.915629 CTGATTTAGTACAAAGTAGACACTTCT 57.084 33.333 0.00 0.00 44.41 2.85
3196 3365 8.433421 AGTATGTTATACCAGTTATTGCACAC 57.567 34.615 0.00 0.00 0.00 3.82
3199 3368 7.753309 TGTTATACCAGTTATTGCACACTTT 57.247 32.000 0.00 0.00 0.00 2.66
3280 3449 5.248477 AGCTGTTCTTTCTTCCACTATGGTA 59.752 40.000 0.00 0.00 39.03 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.682465 CCTCCATGTTGAGATTATCATAATCAT 57.318 33.333 17.94 4.96 37.89 2.45
13 14 8.883302 TCCTCCATGTTGAGATTATCATAATCA 58.117 33.333 17.94 0.00 37.89 2.57
14 15 9.160496 GTCCTCCATGTTGAGATTATCATAATC 57.840 37.037 9.15 9.15 37.89 1.75
15 16 7.821359 CGTCCTCCATGTTGAGATTATCATAAT 59.179 37.037 0.93 0.00 37.89 1.28
16 17 7.015195 TCGTCCTCCATGTTGAGATTATCATAA 59.985 37.037 0.93 0.00 37.89 1.90
17 18 6.493458 TCGTCCTCCATGTTGAGATTATCATA 59.507 38.462 0.93 0.00 37.89 2.15
18 19 5.305386 TCGTCCTCCATGTTGAGATTATCAT 59.695 40.000 0.93 0.00 37.89 2.45
19 20 4.649218 TCGTCCTCCATGTTGAGATTATCA 59.351 41.667 0.93 0.00 34.11 2.15
20 21 5.201713 TCGTCCTCCATGTTGAGATTATC 57.798 43.478 0.93 0.00 34.11 1.75
21 22 4.039730 CCTCGTCCTCCATGTTGAGATTAT 59.960 45.833 0.93 0.00 34.11 1.28
22 23 3.384789 CCTCGTCCTCCATGTTGAGATTA 59.615 47.826 0.93 0.00 34.11 1.75
23 24 2.169352 CCTCGTCCTCCATGTTGAGATT 59.831 50.000 0.93 0.00 34.11 2.40
24 25 1.759445 CCTCGTCCTCCATGTTGAGAT 59.241 52.381 0.93 0.00 34.11 2.75
25 26 1.186200 CCTCGTCCTCCATGTTGAGA 58.814 55.000 0.93 0.00 34.11 3.27
26 27 0.176680 CCCTCGTCCTCCATGTTGAG 59.823 60.000 0.00 0.00 0.00 3.02
27 28 1.899437 GCCCTCGTCCTCCATGTTGA 61.899 60.000 0.00 0.00 0.00 3.18
28 29 1.450312 GCCCTCGTCCTCCATGTTG 60.450 63.158 0.00 0.00 0.00 3.33
29 30 1.201429 AAGCCCTCGTCCTCCATGTT 61.201 55.000 0.00 0.00 0.00 2.71
30 31 1.613630 AAGCCCTCGTCCTCCATGT 60.614 57.895 0.00 0.00 0.00 3.21
31 32 1.144936 GAAGCCCTCGTCCTCCATG 59.855 63.158 0.00 0.00 0.00 3.66
32 33 0.692419 ATGAAGCCCTCGTCCTCCAT 60.692 55.000 0.00 0.00 0.00 3.41
33 34 0.909610 AATGAAGCCCTCGTCCTCCA 60.910 55.000 0.00 0.00 0.00 3.86
34 35 0.462759 CAATGAAGCCCTCGTCCTCC 60.463 60.000 0.00 0.00 0.00 4.30
35 36 0.250513 ACAATGAAGCCCTCGTCCTC 59.749 55.000 0.00 0.00 0.00 3.71
36 37 0.250513 GACAATGAAGCCCTCGTCCT 59.749 55.000 0.00 0.00 0.00 3.85
37 38 0.036388 TGACAATGAAGCCCTCGTCC 60.036 55.000 0.00 0.00 0.00 4.79
38 39 1.734465 CTTGACAATGAAGCCCTCGTC 59.266 52.381 0.00 0.00 0.00 4.20
39 40 1.611673 CCTTGACAATGAAGCCCTCGT 60.612 52.381 0.00 0.00 0.00 4.18
40 41 1.089920 CCTTGACAATGAAGCCCTCG 58.910 55.000 0.00 0.00 0.00 4.63
54 55 2.286365 ATTTGCGGTTCTTCCCTTGA 57.714 45.000 0.00 0.00 0.00 3.02
60 61 6.888430 ACGATCATATAATTTGCGGTTCTTC 58.112 36.000 0.00 0.00 0.00 2.87
78 79 3.569250 TCAACACATCTTCGACGATCA 57.431 42.857 0.66 0.00 0.00 2.92
105 106 0.443869 CGAACTCAACTTCCATGCGG 59.556 55.000 0.00 0.00 0.00 5.69
134 135 1.128200 ACTCCAGCCACTGTACAACA 58.872 50.000 0.00 0.00 0.00 3.33
151 152 4.767255 GCAGCCTACAGCCGCACT 62.767 66.667 0.00 0.00 44.77 4.40
175 176 3.256558 GAAGATGTAAAACGCCTACGGT 58.743 45.455 0.00 0.00 45.01 4.83
296 300 9.182214 AGTACATATGAAGCAAAATGAGTGAAT 57.818 29.630 10.38 0.00 0.00 2.57
337 341 7.110043 ACTCCCTCCGTATAAGTCTTTTTAG 57.890 40.000 0.00 0.00 0.00 1.85
344 348 5.068636 TGATGTACTCCCTCCGTATAAGTC 58.931 45.833 0.00 0.00 0.00 3.01
345 349 5.057843 TGATGTACTCCCTCCGTATAAGT 57.942 43.478 0.00 0.00 0.00 2.24
346 350 7.339721 ACATATGATGTACTCCCTCCGTATAAG 59.660 40.741 10.38 0.00 42.78 1.73
347 351 7.179966 ACATATGATGTACTCCCTCCGTATAA 58.820 38.462 10.38 0.00 42.78 0.98
349 353 5.580998 ACATATGATGTACTCCCTCCGTAT 58.419 41.667 10.38 0.00 42.78 3.06
350 354 4.994282 ACATATGATGTACTCCCTCCGTA 58.006 43.478 10.38 0.00 42.78 4.02
487 511 8.035394 GCCGATAGAAGATGTATATTTGGAGAA 58.965 37.037 0.00 0.00 39.76 2.87
488 512 7.548097 GCCGATAGAAGATGTATATTTGGAGA 58.452 38.462 0.00 0.00 39.76 3.71
489 513 6.473778 CGCCGATAGAAGATGTATATTTGGAG 59.526 42.308 0.00 0.00 39.76 3.86
490 514 6.152154 TCGCCGATAGAAGATGTATATTTGGA 59.848 38.462 0.00 0.00 39.76 3.53
491 515 6.330278 TCGCCGATAGAAGATGTATATTTGG 58.670 40.000 0.00 0.00 39.76 3.28
492 516 7.515841 GCATCGCCGATAGAAGATGTATATTTG 60.516 40.741 0.00 0.00 45.15 2.32
493 517 6.477033 GCATCGCCGATAGAAGATGTATATTT 59.523 38.462 0.00 0.00 45.15 1.40
494 518 5.980116 GCATCGCCGATAGAAGATGTATATT 59.020 40.000 0.00 0.00 45.15 1.28
495 519 5.300539 AGCATCGCCGATAGAAGATGTATAT 59.699 40.000 0.00 0.00 45.15 0.86
496 520 4.640647 AGCATCGCCGATAGAAGATGTATA 59.359 41.667 0.00 0.00 45.15 1.47
539 573 9.540538 TTATCAGGGTCTTTATTTTTGGAATCA 57.459 29.630 0.00 0.00 0.00 2.57
543 578 7.396055 CCACTTATCAGGGTCTTTATTTTTGGA 59.604 37.037 0.00 0.00 0.00 3.53
545 580 8.122472 ACCACTTATCAGGGTCTTTATTTTTG 57.878 34.615 0.00 0.00 0.00 2.44
611 646 5.808030 TCATCGCGTCATTAAACTTGTCATA 59.192 36.000 5.77 0.00 0.00 2.15
696 739 4.141287 TGCCATTCGGAAAGAAAGAAAGA 58.859 39.130 0.00 0.00 42.91 2.52
697 740 4.503741 TGCCATTCGGAAAGAAAGAAAG 57.496 40.909 0.00 0.00 42.91 2.62
794 838 0.031994 GTTGGACACGGCTTGCATTT 59.968 50.000 0.00 0.00 0.00 2.32
850 894 2.683933 ATGCGAACCTCCCTCGGT 60.684 61.111 0.00 0.00 39.48 4.69
905 951 3.660111 GACAACACGGCACAGGGC 61.660 66.667 0.00 0.00 43.74 5.19
944 990 0.457035 GAGGAGACAGAGCAGAGCAG 59.543 60.000 0.00 0.00 0.00 4.24
945 991 0.039472 AGAGGAGACAGAGCAGAGCA 59.961 55.000 0.00 0.00 0.00 4.26
1011 1057 3.429141 GAGTCGTCCTCGCCGTCA 61.429 66.667 0.00 0.00 36.96 4.35
1317 1363 4.704833 CCGTGACCACTGGGCTGG 62.705 72.222 1.57 0.08 37.90 4.85
1417 1463 4.187694 CTGGGCTTCTTCTTGTACTCATC 58.812 47.826 0.00 0.00 0.00 2.92
1418 1464 3.620966 GCTGGGCTTCTTCTTGTACTCAT 60.621 47.826 0.00 0.00 0.00 2.90
1419 1465 2.289694 GCTGGGCTTCTTCTTGTACTCA 60.290 50.000 0.00 0.00 0.00 3.41
1445 1491 4.219392 TCATCCTCTTCATACCTCCCAT 57.781 45.455 0.00 0.00 0.00 4.00
1489 1535 1.005394 CGTAGTCACCACCACCACC 60.005 63.158 0.00 0.00 0.00 4.61
1502 1548 2.024655 TCATACCTTCCACCTCCGTAGT 60.025 50.000 0.00 0.00 0.00 2.73
1598 1644 0.413832 ACCACTAGGAGGCCTCTTGA 59.586 55.000 31.36 15.94 38.69 3.02
1629 1678 2.510906 CTTCCCCCACCATAGCCG 59.489 66.667 0.00 0.00 0.00 5.52
1656 1705 4.505922 GGCTTCTTCTTGTACTCATCATCG 59.494 45.833 0.00 0.00 0.00 3.84
1686 1735 1.695664 CCTCCACCTCCATATCCACCA 60.696 57.143 0.00 0.00 0.00 4.17
1866 1915 6.517529 GCTTCTTCTTGTAGTCCTCTTCTTCA 60.518 42.308 0.00 0.00 0.00 3.02
1875 1924 4.382147 CCACTAGGCTTCTTCTTGTAGTCC 60.382 50.000 0.00 0.00 0.00 3.85
1890 1939 0.910088 ACCTTCCTCCACCACTAGGC 60.910 60.000 0.00 0.00 39.06 3.93
2010 2059 3.795688 TCCTGCTTCTTCATGAAACCT 57.204 42.857 9.88 0.00 33.79 3.50
2033 2082 2.397413 CTTCTTGTGCCCACCCTCGT 62.397 60.000 0.00 0.00 0.00 4.18
2061 2110 1.415126 CCATACCCTCCTCCTCCATGT 60.415 57.143 0.00 0.00 0.00 3.21
2103 2152 1.401931 CCATGTTTCTTCTTGCCGCTG 60.402 52.381 0.00 0.00 0.00 5.18
2127 2176 0.321671 CTTTTCCACTCTCAGGGCGA 59.678 55.000 0.00 0.00 0.00 5.54
2373 2422 3.186613 GTCGGCGGAAATCATAGGAAATC 59.813 47.826 7.21 0.00 0.00 2.17
2495 2547 8.555166 TTCAAGTCAAAACTATTTACAAAGCG 57.445 30.769 0.00 0.00 33.48 4.68
2547 2599 7.484035 AGACACAAGTTCTATTCAACACTTC 57.516 36.000 0.00 0.00 0.00 3.01
2775 2830 5.107143 GCAAAGTCAAAACACTTGCTGAAAA 60.107 36.000 0.00 0.00 40.55 2.29
2811 2866 3.764237 TCAACCAACCCACTTAGAGAC 57.236 47.619 0.00 0.00 0.00 3.36
2867 2923 2.499289 ACAAGATCAGAGCCAGTAGGTG 59.501 50.000 0.00 0.00 37.19 4.00
2873 2929 4.662468 TTAGCTACAAGATCAGAGCCAG 57.338 45.455 0.00 0.00 35.45 4.85
2939 2996 7.888021 TGACACAAATATCCAAAACTACCATCT 59.112 33.333 0.00 0.00 0.00 2.90
2960 3017 4.533222 CGGAAACTACCAACATTTGACAC 58.467 43.478 0.00 0.00 0.00 3.67
3001 3074 8.536407 GTTTACATTAAAACGTTTGCTTGTCAT 58.464 29.630 15.46 0.00 30.30 3.06
3004 3077 7.813852 TGTTTACATTAAAACGTTTGCTTGT 57.186 28.000 15.46 18.42 41.33 3.16
3008 3081 7.277917 GGTGATGTTTACATTAAAACGTTTGC 58.722 34.615 15.46 0.00 41.33 3.68
3010 3083 7.490000 TGGGTGATGTTTACATTAAAACGTTT 58.510 30.769 7.96 7.96 41.33 3.60
3017 3090 6.015856 CAGGTGTTGGGTGATGTTTACATTAA 60.016 38.462 0.00 0.00 36.57 1.40
3021 3094 3.218453 CAGGTGTTGGGTGATGTTTACA 58.782 45.455 0.00 0.00 0.00 2.41
3032 3105 3.359002 GCTTCAGCAGGTGTTGGG 58.641 61.111 0.00 0.00 41.59 4.12
3086 3159 4.347000 GGAGGGAGTATATGTTTGCAGGTA 59.653 45.833 0.00 0.00 0.00 3.08
3196 3365 1.597742 CCGCCATGGTATCTGGAAAG 58.402 55.000 14.67 0.00 35.70 2.62
3199 3368 2.818169 GCCCGCCATGGTATCTGGA 61.818 63.158 14.67 0.00 35.70 3.86


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

AutoCloner maintained by Alex Coulton.