Multiple sequence alignment - TraesCS2A01G107400

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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 TraesCS2A01G107400 chr2A 100.000 3621 0 0 1 3621 59740125 59743745 0.000000e+00 6687
1 TraesCS2A01G107400 chr2A 85.779 1329 118 28 1381 2653 197558058 197559371 0.000000e+00 1341
2 TraesCS2A01G107400 chr2A 88.757 169 15 4 2727 2893 197559543 197559709 1.700000e-48 204
3 TraesCS2A01G107400 chr2A 83.041 171 7 6 2892 3062 70935954 70936102 6.310000e-28 135
4 TraesCS2A01G107400 chr4A 94.024 1389 72 6 2 1384 555570859 555572242 0.000000e+00 2095
5 TraesCS2A01G107400 chr4A 90.257 739 61 3 1804 2540 353109765 353109036 0.000000e+00 955
6 TraesCS2A01G107400 chr4A 93.211 383 24 1 2160 2540 207387375 207387757 2.440000e-156 562
7 TraesCS2A01G107400 chr5D 88.855 1328 84 18 1381 2653 298136773 298138091 0.000000e+00 1574
8 TraesCS2A01G107400 chr5D 89.091 165 16 2 2728 2892 298138276 298138438 1.700000e-48 204
9 TraesCS2A01G107400 chr5A 87.216 1189 109 21 1381 2540 671546564 671547738 0.000000e+00 1314
10 TraesCS2A01G107400 chr5A 83.943 1339 187 17 66 1384 450465367 450464037 0.000000e+00 1256
11 TraesCS2A01G107400 chr5A 89.179 536 52 2 1457 1991 450225363 450224833 0.000000e+00 664
12 TraesCS2A01G107400 chr5A 86.441 590 49 24 3043 3621 706477981 706478550 5.140000e-173 617
13 TraesCS2A01G107400 chr5A 87.199 539 55 6 2129 2653 601238349 601238887 5.170000e-168 601
14 TraesCS2A01G107400 chr5A 88.670 203 21 1 2021 2221 450224418 450224216 2.790000e-61 246
15 TraesCS2A01G107400 chr5A 93.220 118 8 0 2536 2653 54761115 54761232 1.340000e-39 174
16 TraesCS2A01G107400 chr5A 96.154 78 3 0 1381 1458 450225522 450225445 1.060000e-25 128
17 TraesCS2A01G107400 chr5A 90.698 86 6 2 2892 2977 706477726 706477809 2.950000e-21 113
18 TraesCS2A01G107400 chr3D 82.777 1318 215 8 72 1384 552720973 552719663 0.000000e+00 1166
19 TraesCS2A01G107400 chr3D 83.565 791 86 17 1381 2130 552717485 552716698 0.000000e+00 701
20 TraesCS2A01G107400 chr7A 90.257 739 61 3 1804 2540 269088314 269087585 0.000000e+00 955
21 TraesCS2A01G107400 chr7A 97.628 253 4 2 3370 3621 502009406 502009657 2.000000e-117 433
22 TraesCS2A01G107400 chr7A 89.744 312 18 8 3311 3621 82214755 82214457 1.580000e-103 387
23 TraesCS2A01G107400 chr7A 91.549 142 10 2 2975 3114 502009017 502009158 1.030000e-45 195
24 TraesCS2A01G107400 chr7A 94.915 118 6 0 2536 2653 114356048 114356165 6.170000e-43 185
25 TraesCS2A01G107400 chr7A 92.063 126 10 0 1381 1506 114354992 114355117 1.030000e-40 178
26 TraesCS2A01G107400 chr7A 92.063 126 4 5 2883 3007 502008903 502009023 4.810000e-39 172
27 TraesCS2A01G107400 chr7A 82.456 171 6 8 2892 3062 82215368 82215222 1.060000e-25 128
28 TraesCS2A01G107400 chr6B 87.139 762 70 11 1381 2116 101740894 101740135 0.000000e+00 839
29 TraesCS2A01G107400 chr6B 90.865 416 31 2 2129 2540 42818896 42818484 5.280000e-153 551
30 TraesCS2A01G107400 chr6B 87.151 179 18 5 2727 2903 42818160 42817985 7.930000e-47 198
31 TraesCS2A01G107400 chr6B 95.690 116 5 0 2538 2653 42818456 42818341 1.720000e-43 187
32 TraesCS2A01G107400 chr6D 95.455 528 12 9 3097 3621 216846962 216846444 0.000000e+00 832
33 TraesCS2A01G107400 chr6D 92.718 412 27 1 2129 2540 336836173 336835765 3.110000e-165 592
34 TraesCS2A01G107400 chr6D 92.818 362 23 3 1 360 438533253 438532893 4.140000e-144 521
35 TraesCS2A01G107400 chr6D 92.889 225 9 5 2892 3114 216847215 216846996 1.620000e-83 320
36 TraesCS2A01G107400 chr6D 87.952 166 17 3 2727 2892 336835472 336835310 3.690000e-45 193
37 TraesCS2A01G107400 chr2D 94.382 534 14 12 3097 3621 626873034 626872508 0.000000e+00 806
38 TraesCS2A01G107400 chr2D 93.333 195 8 4 2901 3092 626873484 626873292 2.130000e-72 283
39 TraesCS2A01G107400 chr2D 80.103 387 50 12 1381 1741 463920103 463920488 2.770000e-66 263
40 TraesCS2A01G107400 chr2D 89.308 159 13 4 2735 2892 80230386 80230231 2.850000e-46 196
41 TraesCS2A01G107400 chr2D 84.375 224 7 9 2892 3109 584598259 584598058 1.030000e-45 195
42 TraesCS2A01G107400 chr2D 88.571 140 14 2 2536 2673 80230644 80230505 6.220000e-38 169
43 TraesCS2A01G107400 chr2D 92.308 78 5 1 1957 2033 463920555 463920632 3.820000e-20 110
44 TraesCS2A01G107400 chr6A 85.255 746 51 37 2891 3621 597036188 597036889 0.000000e+00 713
45 TraesCS2A01G107400 chr6A 92.950 383 25 1 2160 2540 599216514 599216132 1.140000e-154 556
46 TraesCS2A01G107400 chr6A 85.714 539 54 8 2129 2653 555580746 555581275 6.840000e-152 547
47 TraesCS2A01G107400 chr6A 96.562 320 10 1 3301 3620 59812786 59812468 2.480000e-146 529
48 TraesCS2A01G107400 chr6A 91.234 308 3 4 2892 3178 59813498 59813194 7.280000e-107 398
49 TraesCS2A01G107400 chr6A 89.720 214 22 0 1804 2017 599216730 599216517 1.280000e-69 274
50 TraesCS2A01G107400 chr6A 88.889 162 15 3 2735 2895 599215800 599215641 2.850000e-46 196
51 TraesCS2A01G107400 chr1A 83.792 691 100 8 1 685 12998587 12999271 0.000000e+00 645
52 TraesCS2A01G107400 chr1A 87.954 523 38 19 3104 3621 300926577 300926075 8.660000e-166 593
53 TraesCS2A01G107400 chr1A 77.778 378 54 11 1381 1741 9752029 9751665 4.740000e-49 206
54 TraesCS2A01G107400 chr1D 87.569 547 50 5 2019 2548 421660371 421660916 5.140000e-173 617
55 TraesCS2A01G107400 chr3A 91.283 413 35 1 2129 2540 46216211 46215799 2.440000e-156 562
56 TraesCS2A01G107400 chr3A 91.971 137 9 2 2536 2670 17531973 17531837 1.330000e-44 191
57 TraesCS2A01G107400 chr3A 91.971 137 9 2 2536 2670 17534067 17533931 1.330000e-44 191
58 TraesCS2A01G107400 chr3A 92.800 125 9 0 1381 1505 17532597 17532473 7.990000e-42 182
59 TraesCS2A01G107400 chr3A 92.800 125 9 0 1381 1505 17534691 17534567 7.990000e-42 182
60 TraesCS2A01G107400 chr2B 91.019 412 34 1 2129 2540 789011488 789011896 1.470000e-153 553
61 TraesCS2A01G107400 chr2B 88.889 162 14 4 2732 2892 789012179 789012337 2.850000e-46 196
62 TraesCS2A01G107400 chr5B 89.355 310 23 8 3317 3621 525424560 525424256 7.340000e-102 381
63 TraesCS2A01G107400 chr1B 88.690 168 14 5 2727 2893 338884465 338884302 2.200000e-47 200
64 TraesCS2A01G107400 chr1B 87.500 168 16 5 2727 2893 339077618 339077455 4.770000e-44 189
65 TraesCS2A01G107400 chr3B 89.773 88 9 0 1149 1236 18199627 18199714 2.950000e-21 113


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 TraesCS2A01G107400 chr2A 59740125 59743745 3620 False 6687.000000 6687 100.000000 1 3621 1 chr2A.!!$F1 3620
1 TraesCS2A01G107400 chr2A 197558058 197559709 1651 False 772.500000 1341 87.268000 1381 2893 2 chr2A.!!$F3 1512
2 TraesCS2A01G107400 chr4A 555570859 555572242 1383 False 2095.000000 2095 94.024000 2 1384 1 chr4A.!!$F2 1382
3 TraesCS2A01G107400 chr4A 353109036 353109765 729 True 955.000000 955 90.257000 1804 2540 1 chr4A.!!$R1 736
4 TraesCS2A01G107400 chr5D 298136773 298138438 1665 False 889.000000 1574 88.973000 1381 2892 2 chr5D.!!$F1 1511
5 TraesCS2A01G107400 chr5A 671546564 671547738 1174 False 1314.000000 1314 87.216000 1381 2540 1 chr5A.!!$F3 1159
6 TraesCS2A01G107400 chr5A 450464037 450465367 1330 True 1256.000000 1256 83.943000 66 1384 1 chr5A.!!$R1 1318
7 TraesCS2A01G107400 chr5A 601238349 601238887 538 False 601.000000 601 87.199000 2129 2653 1 chr5A.!!$F2 524
8 TraesCS2A01G107400 chr5A 706477726 706478550 824 False 365.000000 617 88.569500 2892 3621 2 chr5A.!!$F4 729
9 TraesCS2A01G107400 chr5A 450224216 450225522 1306 True 346.000000 664 91.334333 1381 2221 3 chr5A.!!$R2 840
10 TraesCS2A01G107400 chr3D 552716698 552720973 4275 True 933.500000 1166 83.171000 72 2130 2 chr3D.!!$R1 2058
11 TraesCS2A01G107400 chr7A 269087585 269088314 729 True 955.000000 955 90.257000 1804 2540 1 chr7A.!!$R1 736
12 TraesCS2A01G107400 chr7A 502008903 502009657 754 False 266.666667 433 93.746667 2883 3621 3 chr7A.!!$F2 738
13 TraesCS2A01G107400 chr7A 82214457 82215368 911 True 257.500000 387 86.100000 2892 3621 2 chr7A.!!$R2 729
14 TraesCS2A01G107400 chr6B 101740135 101740894 759 True 839.000000 839 87.139000 1381 2116 1 chr6B.!!$R1 735
15 TraesCS2A01G107400 chr6B 42817985 42818896 911 True 312.000000 551 91.235333 2129 2903 3 chr6B.!!$R2 774
16 TraesCS2A01G107400 chr6D 216846444 216847215 771 True 576.000000 832 94.172000 2892 3621 2 chr6D.!!$R2 729
17 TraesCS2A01G107400 chr6D 336835310 336836173 863 True 392.500000 592 90.335000 2129 2892 2 chr6D.!!$R3 763
18 TraesCS2A01G107400 chr2D 626872508 626873484 976 True 544.500000 806 93.857500 2901 3621 2 chr2D.!!$R3 720
19 TraesCS2A01G107400 chr6A 597036188 597036889 701 False 713.000000 713 85.255000 2891 3621 1 chr6A.!!$F2 730
20 TraesCS2A01G107400 chr6A 555580746 555581275 529 False 547.000000 547 85.714000 2129 2653 1 chr6A.!!$F1 524
21 TraesCS2A01G107400 chr6A 59812468 59813498 1030 True 463.500000 529 93.898000 2892 3620 2 chr6A.!!$R1 728
22 TraesCS2A01G107400 chr6A 599215641 599216730 1089 True 342.000000 556 90.519667 1804 2895 3 chr6A.!!$R2 1091
23 TraesCS2A01G107400 chr1A 12998587 12999271 684 False 645.000000 645 83.792000 1 685 1 chr1A.!!$F1 684
24 TraesCS2A01G107400 chr1A 300926075 300926577 502 True 593.000000 593 87.954000 3104 3621 1 chr1A.!!$R2 517
25 TraesCS2A01G107400 chr1D 421660371 421660916 545 False 617.000000 617 87.569000 2019 2548 1 chr1D.!!$F1 529
26 TraesCS2A01G107400 chr2B 789011488 789012337 849 False 374.500000 553 89.954000 2129 2892 2 chr2B.!!$F1 763

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
902 922 1.064017 TGCTTTCAGAAACCCACCACT 60.064 47.619 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2895 6300 0.034896 CACGCCCTCCTACTTGTGTT 59.965 55.0 0.0 0.0 0.0 3.32 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
131 134 1.682854 ACGTAGTCGAACTGTTTCCCA 59.317 47.619 0.00 0.00 29.74 4.37
181 184 2.851195 CCCTATTCCAAAGTGCGCTAT 58.149 47.619 9.73 0.00 0.00 2.97
255 258 6.088483 GTGTGATGTGAACTTATGTGCAAATG 59.912 38.462 0.00 0.00 29.81 2.32
293 296 4.771114 TGAATTCTGTACCCGGATCATT 57.229 40.909 0.73 0.00 0.00 2.57
294 297 4.450976 TGAATTCTGTACCCGGATCATTG 58.549 43.478 0.73 0.00 0.00 2.82
376 379 6.204108 CCTATTATGGTAGTGCCCTTTTAACG 59.796 42.308 0.00 0.00 36.04 3.18
428 445 3.381045 CGGTTGTCTCGCATACATACAT 58.619 45.455 0.00 0.00 0.00 2.29
429 446 4.542735 CGGTTGTCTCGCATACATACATA 58.457 43.478 0.00 0.00 0.00 2.29
430 447 4.381863 CGGTTGTCTCGCATACATACATAC 59.618 45.833 0.00 0.00 0.00 2.39
431 448 5.286438 GGTTGTCTCGCATACATACATACA 58.714 41.667 0.00 0.00 0.00 2.29
434 451 4.278419 TGTCTCGCATACATACATACAGCT 59.722 41.667 0.00 0.00 0.00 4.24
573 590 7.347508 TCGAACTGTGCTAAATTAGTTCTTC 57.652 36.000 12.42 0.00 44.12 2.87
586 603 8.989653 AAATTAGTTCTTCCGTTTGTTTGAAA 57.010 26.923 0.00 0.00 0.00 2.69
776 796 3.195610 CCTGAGTACACATGCCAGTTCTA 59.804 47.826 0.00 0.00 0.00 2.10
890 910 1.884579 AGTGTCAATGCCTGCTTTCAG 59.115 47.619 0.00 0.00 40.02 3.02
902 922 1.064017 TGCTTTCAGAAACCCACCACT 60.064 47.619 0.00 0.00 0.00 4.00
1110 1130 1.667724 CTTCTGCCAAATAGAGGTGCG 59.332 52.381 0.00 0.00 0.00 5.34
1271 1291 7.464710 GCTTGATGAGTTTAATCCTCTTGTACG 60.465 40.741 4.78 0.00 0.00 3.67
1294 1314 6.183361 ACGGACATTTAGAATGGCTAGAGATT 60.183 38.462 6.48 0.00 0.00 2.40
1401 3604 4.884458 TGCACAATCAACAAGACGTTTA 57.116 36.364 0.00 0.00 34.86 2.01
1450 3653 5.221106 GCTCAAATGCACAGCCTATTCAATA 60.221 40.000 0.00 0.00 0.00 1.90
1459 3745 9.056005 TGCACAGCCTATTCAATATTTACTAAG 57.944 33.333 0.00 0.00 0.00 2.18
1497 3783 8.830580 CCAAATTGTATCTCCATACTGTACAAG 58.169 37.037 0.00 0.00 38.28 3.16
1514 3800 7.012989 ACTGTACAAGTCCCACTTTTTATTGTC 59.987 37.037 0.00 0.00 36.03 3.18
1543 3831 5.464030 ACAGAAAAGATGCTGCTTGATTT 57.536 34.783 0.00 0.00 35.57 2.17
1552 3840 2.095263 TGCTGCTTGATTTTAACCGAGC 60.095 45.455 0.00 0.00 39.61 5.03
1557 3845 4.094887 TGCTTGATTTTAACCGAGCATCTC 59.905 41.667 8.69 0.00 42.91 2.75
1606 3894 6.436843 ACACTACTAATGCTTTAATGGCAC 57.563 37.500 5.90 0.00 42.69 5.01
1820 4146 5.766670 TCTTCACTCTTTTCATGTGCTTCAT 59.233 36.000 0.00 0.00 37.22 2.57
1843 4169 9.276590 TCATCAGCCATTTTACAGAATATACAG 57.723 33.333 0.00 0.00 0.00 2.74
1999 4329 6.866770 TGTTCATACTACTTAACAGTCAGCAC 59.133 38.462 0.00 0.00 34.06 4.40
2033 4762 8.528044 TCTTACAAATACCAATTATGTTCCCC 57.472 34.615 0.00 0.00 0.00 4.81
2047 4776 7.931015 TTATGTTCCCCTTCTCACTGTATAT 57.069 36.000 0.00 0.00 0.00 0.86
2090 4819 4.522789 TCTGTTGTTATTTTTCTCCTGCCC 59.477 41.667 0.00 0.00 0.00 5.36
2138 5360 9.358872 CTTTTCTAGCTTACCATTTTTCATTCC 57.641 33.333 0.00 0.00 0.00 3.01
2252 5484 8.545420 GCCATTTTACTTGAGCATTCATAAATG 58.455 33.333 0.00 0.00 44.31 2.32
2272 5504 5.552870 ATGTGGGTCCTCAAGATATGTAC 57.447 43.478 0.00 0.00 0.00 2.90
2276 5508 4.649674 TGGGTCCTCAAGATATGTACTCAC 59.350 45.833 0.00 0.00 0.00 3.51
2281 5513 7.133513 GTCCTCAAGATATGTACTCACTAACG 58.866 42.308 0.00 0.00 0.00 3.18
2282 5514 7.012138 GTCCTCAAGATATGTACTCACTAACGA 59.988 40.741 0.00 0.00 0.00 3.85
2330 5562 7.097192 TCATTAATATCCATAGAACACGCTCC 58.903 38.462 0.00 0.00 0.00 4.70
2383 5615 8.637986 TGTCCATGTAAATAACTTGCTTTCTTT 58.362 29.630 0.00 0.00 33.06 2.52
2425 5657 5.845391 ACTATACTGAAGAGAACCTGCTC 57.155 43.478 0.00 0.00 35.11 4.26
2529 5780 0.977395 ACTGACAAGAGGGCCACTAC 59.023 55.000 6.18 1.02 0.00 2.73
2588 5869 4.065088 TCGTTTCAGGATCACTTCAAAGG 58.935 43.478 0.00 0.00 0.00 3.11
2653 5934 4.111016 CGCTGCAGCCCATGTGTG 62.111 66.667 32.07 12.26 37.91 3.82
2654 5935 2.674033 GCTGCAGCCCATGTGTGA 60.674 61.111 28.76 0.00 34.31 3.58
2655 5936 2.986306 GCTGCAGCCCATGTGTGAC 61.986 63.158 28.76 0.00 34.31 3.67
2656 5937 1.303074 CTGCAGCCCATGTGTGACT 60.303 57.895 0.00 0.00 0.00 3.41
2657 5938 1.583495 CTGCAGCCCATGTGTGACTG 61.583 60.000 0.00 0.00 34.42 3.51
2658 5939 1.601759 GCAGCCCATGTGTGACTGT 60.602 57.895 0.00 0.00 34.05 3.55
2659 5940 1.859427 GCAGCCCATGTGTGACTGTG 61.859 60.000 0.00 0.00 34.05 3.66
2660 5941 0.535780 CAGCCCATGTGTGACTGTGT 60.536 55.000 0.00 0.00 0.00 3.72
2670 5951 7.714813 CCCATGTGTGACTGTGTCAATATAATA 59.285 37.037 1.73 0.00 44.49 0.98
2710 6023 1.173043 CTATGGTTCGCTTTTGGGCA 58.827 50.000 0.00 0.00 0.00 5.36
2713 6026 0.825425 TGGTTCGCTTTTGGGCATCA 60.825 50.000 0.00 0.00 0.00 3.07
2716 6029 0.531657 TTCGCTTTTGGGCATCATGG 59.468 50.000 0.00 0.00 0.00 3.66
2717 6030 0.611618 TCGCTTTTGGGCATCATGGT 60.612 50.000 0.00 0.00 0.00 3.55
2718 6031 0.247185 CGCTTTTGGGCATCATGGTT 59.753 50.000 0.00 0.00 0.00 3.67
2719 6032 1.729284 GCTTTTGGGCATCATGGTTG 58.271 50.000 0.00 0.00 0.00 3.77
2720 6033 1.002315 GCTTTTGGGCATCATGGTTGT 59.998 47.619 0.00 0.00 0.00 3.32
2730 6087 4.641989 GGCATCATGGTTGTCACTATTCTT 59.358 41.667 0.00 0.00 0.00 2.52
2733 6132 7.013655 GGCATCATGGTTGTCACTATTCTTTAT 59.986 37.037 0.00 0.00 0.00 1.40
2797 6201 1.732405 GCAAGCATCCCAAACGCTAAC 60.732 52.381 0.00 0.00 34.11 2.34
2895 6300 0.322322 CGCCCCAACACCTAGTGTAA 59.678 55.000 0.00 0.00 46.79 2.41
2896 6301 1.270947 CGCCCCAACACCTAGTGTAAA 60.271 52.381 0.00 0.00 46.79 2.01
2897 6302 2.156917 GCCCCAACACCTAGTGTAAAC 58.843 52.381 0.00 0.00 46.79 2.01
3037 6498 3.508402 TGTCTATAACAGAACGTGCTCCA 59.492 43.478 0.00 0.00 34.17 3.86
3486 7602 7.991460 TCAGACTGCAGATTCTCAAATGAATAT 59.009 33.333 23.35 0.00 36.86 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 71 5.045359 TCAGGATCAGTGGAATTCATGTTCT 60.045 40.000 7.93 0.00 0.00 3.01
131 134 0.466543 TGCCACTCTGTTACGGTGTT 59.533 50.000 0.00 0.00 0.00 3.32
165 168 2.128771 ACCATAGCGCACTTTGGAAT 57.871 45.000 16.85 0.00 45.17 3.01
181 184 8.274322 AGAATAACCTATGATCATGTCAAACCA 58.726 33.333 18.72 0.00 40.97 3.67
216 219 8.865978 GTTCACATCACACAGAACGTAATATTA 58.134 33.333 0.00 0.00 32.17 0.98
233 236 6.207221 AGTCATTTGCACATAAGTTCACATCA 59.793 34.615 0.00 0.00 0.00 3.07
255 258 1.519408 TCAAGGCGCCTAAACAAGTC 58.481 50.000 33.07 0.00 0.00 3.01
293 296 0.478072 ACCATTTGCACCAGAGGACA 59.522 50.000 0.00 0.00 0.00 4.02
294 297 0.883833 CACCATTTGCACCAGAGGAC 59.116 55.000 0.00 0.00 0.00 3.85
376 379 4.465305 ACCACCTCCTATGGCGTAATATAC 59.535 45.833 0.00 0.00 41.31 1.47
428 445 0.101759 CGGCGCCTTAACTAGCTGTA 59.898 55.000 26.68 0.00 0.00 2.74
429 446 1.153628 CGGCGCCTTAACTAGCTGT 60.154 57.895 26.68 0.00 0.00 4.40
430 447 1.146358 GACGGCGCCTTAACTAGCTG 61.146 60.000 26.68 7.01 41.40 4.24
431 448 1.141234 GACGGCGCCTTAACTAGCT 59.859 57.895 26.68 0.00 0.00 3.32
434 451 1.153706 GCTGACGGCGCCTTAACTA 60.154 57.895 26.68 3.67 0.00 2.24
497 514 1.597854 CAAGGCGACACAAGCAGGA 60.598 57.895 0.00 0.00 36.08 3.86
523 540 7.648039 AATGACCTAGGTGTTGTTTTTACAA 57.352 32.000 22.10 0.00 0.00 2.41
573 590 3.382227 AGGGGTAACTTTCAAACAAACGG 59.618 43.478 0.00 0.00 0.00 4.44
586 603 4.232354 AGATGTAGTCTGGTAGGGGTAACT 59.768 45.833 0.00 0.00 35.31 2.24
686 706 9.415544 GAATGCATTAGATGTTTTCAGAAAGTT 57.584 29.630 12.97 0.00 0.00 2.66
776 796 2.414840 GAACCAAAACACGGCGCCAT 62.415 55.000 28.98 8.91 0.00 4.40
783 803 1.083015 CTCGCGGAACCAAAACACG 60.083 57.895 6.13 0.00 0.00 4.49
833 853 8.860088 TGCAGCATAGGTTATATATGATACGAT 58.140 33.333 0.00 0.00 33.30 3.73
890 910 3.445805 TGACAGAAAAAGTGGTGGGTTTC 59.554 43.478 0.00 0.00 0.00 2.78
902 922 8.889717 CAAACCTAAGTAGTTCTGACAGAAAAA 58.110 33.333 19.32 7.93 35.75 1.94
1110 1130 1.541588 AGCTCGGCAAATTTTGGAGTC 59.458 47.619 10.96 6.53 0.00 3.36
1271 1291 7.172361 GTCAATCTCTAGCCATTCTAAATGTCC 59.828 40.741 0.00 0.00 0.00 4.02
1358 1380 3.754965 TGCAGGGAGATTATATTGCACC 58.245 45.455 0.00 0.00 36.71 5.01
1466 3752 9.998106 ACAGTATGGAGATACAATTTGGTATAC 57.002 33.333 0.78 0.00 43.62 1.47
1471 3757 8.731275 TTGTACAGTATGGAGATACAATTTGG 57.269 34.615 0.78 0.00 43.62 3.28
1497 3783 9.589111 TGTTAAAAAGACAATAAAAAGTGGGAC 57.411 29.630 0.00 0.00 0.00 4.46
1514 3800 7.436080 TCAAGCAGCATCTTTTCTGTTAAAAAG 59.564 33.333 0.00 3.32 44.16 2.27
1536 3824 5.728898 GCAGAGATGCTCGGTTAAAATCAAG 60.729 44.000 0.00 0.00 35.36 3.02
1543 3831 3.334583 AAAGCAGAGATGCTCGGTTAA 57.665 42.857 2.79 0.00 45.54 2.01
1583 3871 5.064707 CGTGCCATTAAAGCATTAGTAGTGT 59.935 40.000 6.80 0.00 43.29 3.55
1606 3894 3.649870 TTTTCATATACAGTGTGCGCG 57.350 42.857 5.88 0.00 0.00 6.86
1727 4026 8.692710 TGAATGGTCGACTACAGAGTAATATTT 58.307 33.333 16.46 0.00 35.45 1.40
1796 4122 5.125356 TGAAGCACATGAAAAGAGTGAAGA 58.875 37.500 0.00 0.00 35.33 2.87
1820 4146 8.046708 ACACTGTATATTCTGTAAAATGGCTGA 58.953 33.333 0.00 0.00 0.00 4.26
1877 4203 8.349245 CCTTTGTATCATCACAAACTTACAACA 58.651 33.333 0.00 0.00 42.08 3.33
1879 4205 7.721842 TCCCTTTGTATCATCACAAACTTACAA 59.278 33.333 0.00 0.00 42.08 2.41
2047 4776 4.403752 CAGACCAGGTGTTGATCTATCTGA 59.596 45.833 0.00 0.00 34.32 3.27
2138 5360 9.988815 AGCCTAGTGTATGAATAGATAACAAAG 57.011 33.333 0.00 0.00 0.00 2.77
2252 5484 4.649674 TGAGTACATATCTTGAGGACCCAC 59.350 45.833 0.00 0.00 0.00 4.61
2272 5504 7.140048 GGTGATAGGAAAGTATCGTTAGTGAG 58.860 42.308 0.00 0.00 32.79 3.51
2276 5508 9.976511 TTAATGGTGATAGGAAAGTATCGTTAG 57.023 33.333 0.00 0.00 32.79 2.34
2330 5562 9.941664 GAAATTGTTGTGTGATATGGAAGATAG 57.058 33.333 0.00 0.00 0.00 2.08
2425 5657 6.421377 TCATTGTTTGGATCAATGTAGTCG 57.579 37.500 15.09 0.00 46.76 4.18
2529 5780 2.287547 CCTTCACGAATGTTGGTGGTTG 60.288 50.000 7.82 0.51 37.47 3.77
2683 5995 5.299279 CCAAAAGCGAACCATAGGTTATCAT 59.701 40.000 0.67 0.00 46.95 2.45
2699 6011 0.247185 AACCATGATGCCCAAAAGCG 59.753 50.000 0.00 0.00 34.65 4.68
2762 6166 6.704050 GGGATGCTTGCTTTAGTTAACAAAAA 59.296 34.615 8.61 7.12 0.00 1.94
2763 6167 6.183360 TGGGATGCTTGCTTTAGTTAACAAAA 60.183 34.615 8.61 0.00 0.00 2.44
2767 6171 5.385509 TTGGGATGCTTGCTTTAGTTAAC 57.614 39.130 0.00 0.00 0.00 2.01
2781 6185 2.901249 TCTAGTTAGCGTTTGGGATGC 58.099 47.619 0.00 0.00 40.73 3.91
2797 6201 9.384764 CCCCTTTAACACTCTTTTCTATTCTAG 57.615 37.037 0.00 0.00 0.00 2.43
2895 6300 0.034896 CACGCCCTCCTACTTGTGTT 59.965 55.000 0.00 0.00 0.00 3.32
2896 6301 1.671742 CACGCCCTCCTACTTGTGT 59.328 57.895 0.00 0.00 0.00 3.72
2897 6302 1.741770 GCACGCCCTCCTACTTGTG 60.742 63.158 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.