Multiple sequence alignment - TraesCS2A01G348800

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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 TraesCS2A01G348800 chr2A 100.000 2853 0 0 1 2853 587735050 587737902 0.000000e+00 5269
1 TraesCS2A01G348800 chr2A 89.087 1347 76 27 738 2042 610660338 610661655 0.000000e+00 1607
2 TraesCS2A01G348800 chr2A 91.198 693 39 5 60 751 610645746 610646417 0.000000e+00 922
3 TraesCS2A01G348800 chr2A 85.758 660 62 16 2041 2676 610662158 610662809 0.000000e+00 669
4 TraesCS2A01G348800 chr2A 75.379 264 53 8 2522 2779 105681649 105681392 1.800000e-22 117
5 TraesCS2A01G348800 chr2D 90.690 2202 110 42 330 2468 445387173 445389342 0.000000e+00 2843
6 TraesCS2A01G348800 chr2D 84.232 482 66 5 2382 2853 445389829 445390310 7.200000e-126 460
7 TraesCS2A01G348800 chr2B 87.395 2499 199 54 420 2853 523525075 523527522 0.000000e+00 2763
8 TraesCS2A01G348800 chr2B 88.657 335 16 5 27 360 523524738 523525051 3.450000e-104 388
9 TraesCS2A01G348800 chr6B 83.523 352 35 12 1592 1935 145901039 145900703 9.930000e-80 307


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 TraesCS2A01G348800 chr2A 587735050 587737902 2852 False 5269.0 5269 100.0000 1 2853 1 chr2A.!!$F1 2852
1 TraesCS2A01G348800 chr2A 610660338 610662809 2471 False 1138.0 1607 87.4225 738 2676 2 chr2A.!!$F3 1938
2 TraesCS2A01G348800 chr2A 610645746 610646417 671 False 922.0 922 91.1980 60 751 1 chr2A.!!$F2 691
3 TraesCS2A01G348800 chr2D 445387173 445390310 3137 False 1651.5 2843 87.4610 330 2853 2 chr2D.!!$F1 2523
4 TraesCS2A01G348800 chr2B 523524738 523527522 2784 False 1575.5 2763 88.0260 27 2853 2 chr2B.!!$F1 2826

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
533 536 0.179189 CGAATCGGCAGCCAAAGAAC 60.179 55.0 13.3 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2097 2669 0.317938 AGTCACTGACGCAACGACTC 60.318 55.0 3.46 0.0 37.67 3.36 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
25 26 7.509546 TCTAAGGGCTATTTCTAACAAGATGG 58.490 38.462 0.00 0.00 0.00 3.51
45 46 8.991783 AGATGGACATCATATTGAGTTTCATT 57.008 30.769 14.16 0.00 40.22 2.57
48 49 7.988737 TGGACATCATATTGAGTTTCATTCAC 58.011 34.615 0.00 0.00 0.00 3.18
55 56 5.597813 ATTGAGTTTCATTCACGAGACAC 57.402 39.130 0.00 0.00 0.00 3.67
89 90 5.120053 CGTGTACTGTGCACAATATTCTTCA 59.880 40.000 24.93 6.23 36.71 3.02
118 119 4.330894 CAGTACACATGCATCTGTAACCAG 59.669 45.833 15.32 3.90 40.25 4.00
143 144 3.746751 GCTCATGATATCCCTGCAAGTGT 60.747 47.826 0.00 0.00 0.00 3.55
144 145 4.063689 CTCATGATATCCCTGCAAGTGTC 58.936 47.826 0.00 0.00 0.00 3.67
145 146 3.144506 CATGATATCCCTGCAAGTGTCC 58.855 50.000 0.00 0.00 0.00 4.02
146 147 2.481441 TGATATCCCTGCAAGTGTCCT 58.519 47.619 0.00 0.00 0.00 3.85
147 148 2.846206 TGATATCCCTGCAAGTGTCCTT 59.154 45.455 0.00 0.00 0.00 3.36
175 176 1.717194 TTTGGACTCGCACGTTATCC 58.283 50.000 0.00 0.00 0.00 2.59
196 197 3.194329 CCAGCGCTGATAGATAAGGATCA 59.806 47.826 38.06 0.00 34.17 2.92
198 199 3.446873 AGCGCTGATAGATAAGGATCAGG 59.553 47.826 10.39 5.43 46.13 3.86
199 200 3.445450 GCGCTGATAGATAAGGATCAGGA 59.555 47.826 0.00 0.00 46.13 3.86
200 201 4.099266 GCGCTGATAGATAAGGATCAGGAT 59.901 45.833 0.00 0.00 46.13 3.24
201 202 5.735922 GCGCTGATAGATAAGGATCAGGATC 60.736 48.000 0.00 0.55 46.13 3.36
205 206 7.765360 GCTGATAGATAAGGATCAGGATCAAAG 59.235 40.741 11.12 0.00 46.13 2.77
252 253 1.618343 TCTGCTTCCTGATGACGTTCA 59.382 47.619 0.00 0.00 0.00 3.18
302 303 4.040376 CGTAACCTCGTGATAAGGTAAGC 58.960 47.826 0.00 0.00 46.54 3.09
335 337 6.369005 CACGAATAGTGGAATAGTAGTACCG 58.631 44.000 0.00 0.00 46.77 4.02
371 373 4.240881 ACCCCTCTGTGTATACTACGAA 57.759 45.455 4.17 0.00 0.00 3.85
391 393 3.369242 ACAGGAGACTAGGAGTACCAC 57.631 52.381 0.00 0.00 40.21 4.16
533 536 0.179189 CGAATCGGCAGCCAAAGAAC 60.179 55.000 13.30 0.00 0.00 3.01
581 584 0.322008 GGAGGGAACTTGAGCACCAG 60.322 60.000 0.00 0.00 44.43 4.00
602 605 6.126911 ACCAGTCTAGAGATTCCATTTTCCTC 60.127 42.308 0.00 0.00 0.00 3.71
629 632 6.630071 CACTGTTTGGGTTATAATTTCCAGG 58.370 40.000 0.00 0.00 0.00 4.45
644 647 2.316108 TCCAGGAGGGAAACAAAAAGC 58.684 47.619 0.00 0.00 44.80 3.51
810 825 0.679505 TGAGACTGAAACCAGACCCG 59.320 55.000 0.00 0.00 35.67 5.28
814 829 0.535102 ACTGAAACCAGACCCGCTTG 60.535 55.000 0.00 0.00 35.67 4.01
818 833 0.535102 AAACCAGACCCGCTTGTGAG 60.535 55.000 0.00 0.00 0.00 3.51
861 876 2.289694 CCATGAAACCGACCTCTGAACT 60.290 50.000 0.00 0.00 0.00 3.01
926 943 4.458295 GGGCTAGCTCGTATAGTCATACAA 59.542 45.833 15.72 0.00 37.47 2.41
1048 1065 0.944311 CAAGAGGAACCACACCGACG 60.944 60.000 0.00 0.00 0.00 5.12
1131 1148 4.516195 GGCTCGGAGGAGTTCGGC 62.516 72.222 7.20 0.00 42.53 5.54
1132 1149 4.516195 GCTCGGAGGAGTTCGGCC 62.516 72.222 7.20 0.00 42.53 6.13
1157 1174 1.219393 GGTCCAAGAAGCCGAGGAG 59.781 63.158 0.00 0.00 0.00 3.69
1220 1246 0.092351 CGTACGGCTAAGTTTGCACG 59.908 55.000 7.57 13.33 0.00 5.34
1227 1253 1.779569 CTAAGTTTGCACGTCGACCT 58.220 50.000 10.58 0.00 0.00 3.85
1270 1305 5.300034 TGCTGAAGTGATTTTGTTGTGATCT 59.700 36.000 0.00 0.00 0.00 2.75
1271 1306 5.855395 GCTGAAGTGATTTTGTTGTGATCTC 59.145 40.000 0.00 0.00 0.00 2.75
1349 1384 2.495669 CGCCATTTGGGAAGGTATTTGT 59.504 45.455 0.00 0.00 40.01 2.83
1359 1414 4.000988 GGAAGGTATTTGTTCGCTTCTCA 58.999 43.478 0.00 0.00 0.00 3.27
1387 1443 2.796651 GCAGCTCGCTTGGAATGG 59.203 61.111 1.48 0.00 37.77 3.16
1389 1445 1.308069 GCAGCTCGCTTGGAATGGAA 61.308 55.000 1.48 0.00 37.77 3.53
1396 1452 2.749076 TCGCTTGGAATGGAAGATTGTG 59.251 45.455 0.00 0.00 0.00 3.33
1397 1453 2.733227 CGCTTGGAATGGAAGATTGTGC 60.733 50.000 0.00 0.00 0.00 4.57
1401 1458 5.484715 CTTGGAATGGAAGATTGTGCATTT 58.515 37.500 0.00 0.00 39.37 2.32
1402 1459 5.486735 TGGAATGGAAGATTGTGCATTTT 57.513 34.783 0.00 0.00 39.37 1.82
1403 1460 5.867330 TGGAATGGAAGATTGTGCATTTTT 58.133 33.333 0.00 0.00 39.37 1.94
1404 1461 5.701750 TGGAATGGAAGATTGTGCATTTTTG 59.298 36.000 0.00 0.00 39.37 2.44
1405 1462 5.122711 GGAATGGAAGATTGTGCATTTTTGG 59.877 40.000 0.00 0.00 39.37 3.28
1407 1464 4.630111 TGGAAGATTGTGCATTTTTGGTC 58.370 39.130 0.00 0.00 0.00 4.02
1408 1465 3.674753 GGAAGATTGTGCATTTTTGGTCG 59.325 43.478 0.00 0.00 0.00 4.79
1410 1467 3.641648 AGATTGTGCATTTTTGGTCGTG 58.358 40.909 0.00 0.00 0.00 4.35
1411 1468 2.949451 TTGTGCATTTTTGGTCGTGT 57.051 40.000 0.00 0.00 0.00 4.49
1412 1469 2.483583 TGTGCATTTTTGGTCGTGTC 57.516 45.000 0.00 0.00 0.00 3.67
1413 1470 1.066303 TGTGCATTTTTGGTCGTGTCC 59.934 47.619 0.00 0.00 0.00 4.02
1414 1471 0.671251 TGCATTTTTGGTCGTGTCCC 59.329 50.000 0.00 0.00 0.00 4.46
1415 1472 0.958822 GCATTTTTGGTCGTGTCCCT 59.041 50.000 0.00 0.00 0.00 4.20
1416 1473 2.156098 GCATTTTTGGTCGTGTCCCTA 58.844 47.619 0.00 0.00 0.00 3.53
1417 1474 2.554893 GCATTTTTGGTCGTGTCCCTAA 59.445 45.455 0.00 0.00 0.00 2.69
1418 1475 3.610821 GCATTTTTGGTCGTGTCCCTAAC 60.611 47.826 0.00 0.00 0.00 2.34
1419 1476 2.259266 TTTTGGTCGTGTCCCTAACC 57.741 50.000 0.00 0.00 0.00 2.85
1421 1478 0.971386 TTGGTCGTGTCCCTAACCTC 59.029 55.000 0.00 0.00 32.82 3.85
1422 1479 1.246056 TGGTCGTGTCCCTAACCTCG 61.246 60.000 0.00 0.00 32.82 4.63
1423 1480 1.509923 GTCGTGTCCCTAACCTCGG 59.490 63.158 0.00 0.00 0.00 4.63
1424 1481 2.183555 CGTGTCCCTAACCTCGGC 59.816 66.667 0.00 0.00 0.00 5.54
1425 1482 2.183555 GTGTCCCTAACCTCGGCG 59.816 66.667 0.00 0.00 0.00 6.46
1426 1483 3.766691 TGTCCCTAACCTCGGCGC 61.767 66.667 0.00 0.00 0.00 6.53
1427 1484 4.867599 GTCCCTAACCTCGGCGCG 62.868 72.222 0.00 0.00 0.00 6.86
1429 1486 4.446413 CCCTAACCTCGGCGCGTT 62.446 66.667 8.43 14.87 0.00 4.84
1430 1487 2.433664 CCTAACCTCGGCGCGTTT 60.434 61.111 15.53 1.14 0.00 3.60
1431 1488 2.736682 CCTAACCTCGGCGCGTTTG 61.737 63.158 15.53 13.49 0.00 2.93
1465 1522 1.719600 CTTCTGTTCTTCAGGAGGCG 58.280 55.000 0.00 0.00 44.03 5.52
1560 1617 4.069232 CGCCGAGCCTGAGGTGAA 62.069 66.667 0.00 0.00 40.26 3.18
1565 1622 0.108424 CGAGCCTGAGGTGAAAGAGG 60.108 60.000 0.00 0.00 0.00 3.69
1634 1691 5.573219 TCCCTGAACATTCTGAACATGATT 58.427 37.500 0.00 0.00 0.00 2.57
1691 1749 6.783892 TTTTTATTTGTGCTGAAGGAATGC 57.216 33.333 0.00 0.00 0.00 3.56
1692 1750 5.465532 TTTATTTGTGCTGAAGGAATGCA 57.534 34.783 0.00 0.00 0.00 3.96
1693 1751 5.664294 TTATTTGTGCTGAAGGAATGCAT 57.336 34.783 0.00 0.00 39.00 3.96
1698 1756 1.944709 TGCTGAAGGAATGCATCATCG 59.055 47.619 0.00 0.00 0.00 3.84
2005 2073 1.935199 GTTTCGTTTCCGTGAACCTCA 59.065 47.619 0.00 0.00 35.01 3.86
2006 2074 2.312722 TTCGTTTCCGTGAACCTCAA 57.687 45.000 0.00 0.00 35.01 3.02
2109 2687 2.050714 TGGTCGAGTCGTTGCGTC 60.051 61.111 13.12 0.00 0.00 5.19
2110 2688 2.050714 GGTCGAGTCGTTGCGTCA 60.051 61.111 13.12 0.00 0.00 4.35
2117 2695 0.949397 AGTCGTTGCGTCAGTGACTA 59.051 50.000 20.64 7.30 38.09 2.59
2122 2700 1.126846 GTTGCGTCAGTGACTATGTGC 59.873 52.381 20.64 15.82 0.00 4.57
2123 2701 0.316841 TGCGTCAGTGACTATGTGCA 59.683 50.000 20.64 18.07 0.00 4.57
2125 2703 1.325640 GCGTCAGTGACTATGTGCATG 59.674 52.381 20.64 3.43 0.00 4.06
2126 2704 2.610433 CGTCAGTGACTATGTGCATGT 58.390 47.619 20.64 0.00 0.00 3.21
2127 2705 2.346545 CGTCAGTGACTATGTGCATGTG 59.653 50.000 20.64 0.00 0.00 3.21
2128 2706 2.674852 GTCAGTGACTATGTGCATGTGG 59.325 50.000 16.26 0.00 0.00 4.17
2129 2707 2.302733 TCAGTGACTATGTGCATGTGGT 59.697 45.455 0.00 0.00 0.00 4.16
2235 2813 7.281841 ACCCTTGTAGTACTAGAGAGTATCAC 58.718 42.308 12.62 0.00 40.32 3.06
2236 2814 7.127647 ACCCTTGTAGTACTAGAGAGTATCACT 59.872 40.741 12.62 0.00 40.32 3.41
2246 2824 1.001268 AGAGTATCACTATGCGGTGCG 60.001 52.381 0.33 0.00 37.82 5.34
2257 2835 2.331098 CGGTGCGTGCATTTGTGT 59.669 55.556 0.00 0.00 0.00 3.72
2360 2938 1.135199 TCTTGTGTCGGCGGATAGTTC 60.135 52.381 7.21 0.00 0.00 3.01
2371 2949 3.498777 GGCGGATAGTTCCTTAAATCAGC 59.501 47.826 0.00 0.00 40.17 4.26
2374 2952 5.047847 CGGATAGTTCCTTAAATCAGCGAA 58.952 41.667 0.00 0.00 40.17 4.70
2398 2990 2.811307 CCATTAGGGCACATGTGGG 58.189 57.895 26.55 13.58 0.00 4.61
2442 3034 2.513753 CTGCATTTGGGTAGTTGGTCA 58.486 47.619 0.00 0.00 0.00 4.02
2502 3677 5.010213 GTGTTTTTAGGGTAGTGGCATGAAA 59.990 40.000 0.00 0.00 0.00 2.69
2509 3684 3.307762 GGGTAGTGGCATGAAAGAAGACT 60.308 47.826 0.00 0.00 0.00 3.24
2528 3713 2.225650 ACTGGACCCAAGTAGATCCACT 60.226 50.000 0.00 0.00 36.30 4.00
2537 3723 1.834263 AGTAGATCCACTGAAGGCCAC 59.166 52.381 5.01 0.00 0.00 5.01
2552 3738 0.674534 GCCACTACCGATCGAATCCT 59.325 55.000 18.66 0.00 0.00 3.24
2553 3739 1.884579 GCCACTACCGATCGAATCCTA 59.115 52.381 18.66 0.00 0.00 2.94
2562 3748 3.696548 CCGATCGAATCCTATGAGATCCA 59.303 47.826 18.66 0.00 35.56 3.41
2563 3749 4.439426 CCGATCGAATCCTATGAGATCCAC 60.439 50.000 18.66 0.00 35.56 4.02
2580 3766 2.283529 ACCGGAGACACGCCTTCAT 61.284 57.895 9.46 0.00 0.00 2.57
2594 3780 4.202161 ACGCCTTCATATGTCCTTCTACAG 60.202 45.833 1.90 0.00 31.70 2.74
2600 3786 4.767409 TCATATGTCCTTCTACAGCGCTAT 59.233 41.667 10.99 0.00 31.70 2.97
2621 3807 1.377987 GCATTACCAGAACGGGGCA 60.378 57.895 0.00 0.00 40.22 5.36
2634 3820 2.680370 GGGGCAAGACGGGGAGAAT 61.680 63.158 0.00 0.00 0.00 2.40
2641 3827 4.200092 GCAAGACGGGGAGAATCTTATTT 58.800 43.478 0.00 0.00 31.47 1.40
2651 3837 7.283127 CGGGGAGAATCTTATTTCATTTTCTGA 59.717 37.037 0.00 0.00 33.73 3.27
2658 3844 3.772060 ATTTCATTTTCTGAGAGCCGC 57.228 42.857 0.00 0.00 34.68 6.53
2678 3864 2.121786 CCGTCGTCTCGTCTTTTTGAA 58.878 47.619 0.00 0.00 0.00 2.69
2681 3867 3.181774 CGTCGTCTCGTCTTTTTGAACAT 59.818 43.478 0.00 0.00 0.00 2.71
2684 3870 4.988540 TCGTCTCGTCTTTTTGAACATGAT 59.011 37.500 0.00 0.00 0.00 2.45
2686 3872 6.643360 TCGTCTCGTCTTTTTGAACATGATAA 59.357 34.615 0.00 0.00 0.00 1.75
2689 3875 8.892905 GTCTCGTCTTTTTGAACATGATAAAAC 58.107 33.333 0.00 0.00 0.00 2.43
2698 3884 7.841282 TTGAACATGATAAAACCCCTAAACA 57.159 32.000 0.00 0.00 0.00 2.83
2725 3913 4.722361 AAAAACACCTAAAACGGAGCAA 57.278 36.364 0.00 0.00 0.00 3.91
2735 3923 1.961180 AACGGAGCAAGATCCTCCCG 61.961 60.000 10.02 8.83 44.86 5.14
2744 3932 2.683933 ATCCTCCCGTCGGCAAGT 60.684 61.111 5.50 0.00 0.00 3.16
2746 3934 4.003788 CCTCCCGTCGGCAAGTGT 62.004 66.667 5.50 0.00 0.00 3.55
2775 3963 1.447643 CGTTCCTCCATGGCCCTAG 59.552 63.158 6.96 0.00 35.26 3.02
2786 3974 3.942439 GCCCTAGGCCCATCGGAC 61.942 72.222 2.05 0.00 44.06 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.347222 TCCATCTTGTTAGAAATAGCCCTTAGA 59.653 37.037 0.00 0.00 33.20 2.10
1 2 7.442666 GTCCATCTTGTTAGAAATAGCCCTTAG 59.557 40.741 0.00 0.00 33.20 2.18
2 3 7.092623 TGTCCATCTTGTTAGAAATAGCCCTTA 60.093 37.037 0.00 0.00 33.20 2.69
3 4 6.122964 GTCCATCTTGTTAGAAATAGCCCTT 58.877 40.000 0.00 0.00 33.20 3.95
4 5 5.191722 TGTCCATCTTGTTAGAAATAGCCCT 59.808 40.000 0.00 0.00 33.20 5.19
5 6 5.437060 TGTCCATCTTGTTAGAAATAGCCC 58.563 41.667 0.00 0.00 33.20 5.19
6 7 6.767902 TGATGTCCATCTTGTTAGAAATAGCC 59.232 38.462 8.61 0.00 38.60 3.93
7 8 7.792374 TGATGTCCATCTTGTTAGAAATAGC 57.208 36.000 8.61 0.00 38.60 2.97
11 12 9.904198 TCAATATGATGTCCATCTTGTTAGAAA 57.096 29.630 8.61 0.00 39.20 2.52
12 13 9.551734 CTCAATATGATGTCCATCTTGTTAGAA 57.448 33.333 8.61 0.00 39.20 2.10
13 14 8.708378 ACTCAATATGATGTCCATCTTGTTAGA 58.292 33.333 8.61 6.69 39.20 2.10
14 15 8.899427 ACTCAATATGATGTCCATCTTGTTAG 57.101 34.615 8.61 7.64 39.20 2.34
15 16 9.685276 AAACTCAATATGATGTCCATCTTGTTA 57.315 29.630 8.61 0.00 39.20 2.41
16 17 8.585471 AAACTCAATATGATGTCCATCTTGTT 57.415 30.769 8.61 4.53 39.20 2.83
17 18 7.830697 TGAAACTCAATATGATGTCCATCTTGT 59.169 33.333 8.61 0.00 39.20 3.16
18 19 8.217131 TGAAACTCAATATGATGTCCATCTTG 57.783 34.615 8.61 5.41 39.39 3.02
19 20 8.991783 ATGAAACTCAATATGATGTCCATCTT 57.008 30.769 8.61 5.11 38.60 2.40
20 21 8.991783 AATGAAACTCAATATGATGTCCATCT 57.008 30.769 8.61 0.00 38.60 2.90
21 22 8.843262 TGAATGAAACTCAATATGATGTCCATC 58.157 33.333 0.22 0.22 36.71 3.51
22 23 8.627403 GTGAATGAAACTCAATATGATGTCCAT 58.373 33.333 0.00 0.00 39.25 3.41
23 24 7.201635 CGTGAATGAAACTCAATATGATGTCCA 60.202 37.037 0.00 0.00 0.00 4.02
24 25 7.011389 TCGTGAATGAAACTCAATATGATGTCC 59.989 37.037 0.00 0.00 0.00 4.02
25 26 7.909267 TCGTGAATGAAACTCAATATGATGTC 58.091 34.615 0.00 0.00 0.00 3.06
45 46 4.860352 CACGGTTATAATTGTGTCTCGTGA 59.140 41.667 0.00 0.00 45.25 4.35
48 49 6.020916 CAGTACACGGTTATAATTGTGTCTCG 60.021 42.308 21.71 11.91 43.91 4.04
55 56 5.120986 TGTGCACAGTACACGGTTATAATTG 59.879 40.000 17.42 0.00 41.03 2.32
89 90 5.922053 ACAGATGCATGTGTACTGTGATAT 58.078 37.500 26.55 0.00 39.76 1.63
118 119 1.072806 TGCAGGGATATCATGAGCACC 59.927 52.381 4.83 4.01 0.00 5.01
143 144 2.687935 GAGTCCAAAACACTTGCAAGGA 59.312 45.455 29.18 13.84 0.00 3.36
144 145 2.541588 CGAGTCCAAAACACTTGCAAGG 60.542 50.000 29.18 19.84 0.00 3.61
145 146 2.719798 CGAGTCCAAAACACTTGCAAG 58.280 47.619 24.84 24.84 0.00 4.01
146 147 1.202245 GCGAGTCCAAAACACTTGCAA 60.202 47.619 0.00 0.00 46.71 4.08
147 148 0.380378 GCGAGTCCAAAACACTTGCA 59.620 50.000 7.11 0.00 46.71 4.08
148 149 3.164028 GCGAGTCCAAAACACTTGC 57.836 52.632 0.00 0.00 42.68 4.01
149 150 1.594518 CGTGCGAGTCCAAAACACTTG 60.595 52.381 0.00 0.00 0.00 3.16
150 151 0.655733 CGTGCGAGTCCAAAACACTT 59.344 50.000 0.00 0.00 0.00 3.16
151 152 0.461339 ACGTGCGAGTCCAAAACACT 60.461 50.000 0.00 0.00 0.00 3.55
152 153 0.375803 AACGTGCGAGTCCAAAACAC 59.624 50.000 0.00 0.00 0.00 3.32
153 154 1.937278 TAACGTGCGAGTCCAAAACA 58.063 45.000 0.00 0.00 0.00 2.83
175 176 4.422840 CTGATCCTTATCTATCAGCGCTG 58.577 47.826 31.53 31.53 41.80 5.18
205 206 8.718734 CCGGGTCAAAGCTAATTAATAATCTAC 58.281 37.037 0.00 0.00 0.00 2.59
325 327 4.996758 GGGCAAAGAAAAACGGTACTACTA 59.003 41.667 0.00 0.00 0.00 1.82
326 328 3.817084 GGGCAAAGAAAAACGGTACTACT 59.183 43.478 0.00 0.00 0.00 2.57
327 329 3.817084 AGGGCAAAGAAAAACGGTACTAC 59.183 43.478 0.00 0.00 0.00 2.73
335 337 2.561419 GAGGGGTAGGGCAAAGAAAAAC 59.439 50.000 0.00 0.00 0.00 2.43
371 373 2.648304 TGTGGTACTCCTAGTCTCCTGT 59.352 50.000 0.00 0.00 34.23 4.00
391 393 7.496920 TCTTCATTGTGAGGCAGTAGAATAATG 59.503 37.037 0.00 0.00 40.12 1.90
533 536 1.220206 CTGGAGTGCTGGCCTAGTG 59.780 63.158 3.32 0.00 0.00 2.74
581 584 5.293560 CCGAGGAAAATGGAATCTCTAGAC 58.706 45.833 0.00 0.00 0.00 2.59
602 605 4.712122 AATTATAACCCAAACAGTGCCG 57.288 40.909 0.00 0.00 0.00 5.69
629 632 3.800261 GCCAGAAGCTTTTTGTTTCCCTC 60.800 47.826 0.00 0.00 36.69 4.30
661 664 6.341316 CGTCAAGAATCCTTCTTCTATTCCA 58.659 40.000 0.00 0.00 46.62 3.53
662 665 5.235401 GCGTCAAGAATCCTTCTTCTATTCC 59.765 44.000 0.00 0.00 46.62 3.01
720 723 4.980590 TGCGCAAGTAACAATAATGGAAG 58.019 39.130 8.16 0.00 41.68 3.46
788 803 2.569404 GGGTCTGGTTTCAGTCTCAGAT 59.431 50.000 0.00 0.00 41.59 2.90
810 825 5.069781 ACTCTCCCATTATCTACTCACAAGC 59.930 44.000 0.00 0.00 0.00 4.01
814 829 6.909550 ATCACTCTCCCATTATCTACTCAC 57.090 41.667 0.00 0.00 0.00 3.51
818 833 7.067496 TGGAAATCACTCTCCCATTATCTAC 57.933 40.000 0.00 0.00 0.00 2.59
861 876 5.826586 TGACTTTTACAACCGTAGTCGTTA 58.173 37.500 0.00 0.00 35.01 3.18
926 943 1.067060 GCTGAAAACCAGGAGCGTTTT 59.933 47.619 0.00 0.00 44.09 2.43
983 1000 1.459730 ATCTTCCTCCCCCGCTACC 60.460 63.158 0.00 0.00 0.00 3.18
1131 1148 1.750399 CTTCTTGGACCCCATGCGG 60.750 63.158 0.00 0.00 31.53 5.69
1132 1149 2.409870 GCTTCTTGGACCCCATGCG 61.410 63.158 0.00 0.00 31.53 4.73
1220 1246 2.380084 TTACAGGCATGAAGGTCGAC 57.620 50.000 4.84 7.13 0.00 4.20
1227 1253 4.096833 CAGCAGCTAATTTACAGGCATGAA 59.903 41.667 4.84 0.00 0.00 2.57
1270 1305 1.273606 CTTGTCCTTCTTCTCCTGCGA 59.726 52.381 0.00 0.00 0.00 5.10
1271 1306 1.674221 CCTTGTCCTTCTTCTCCTGCG 60.674 57.143 0.00 0.00 0.00 5.18
1349 1384 2.749280 TTGCAGAGATGAGAAGCGAA 57.251 45.000 0.00 0.00 0.00 4.70
1387 1443 4.148696 CACGACCAAAAATGCACAATCTTC 59.851 41.667 0.00 0.00 0.00 2.87
1389 1445 3.068024 ACACGACCAAAAATGCACAATCT 59.932 39.130 0.00 0.00 0.00 2.40
1396 1452 0.958822 AGGGACACGACCAAAAATGC 59.041 50.000 0.00 0.00 0.00 3.56
1397 1453 3.057806 GGTTAGGGACACGACCAAAAATG 60.058 47.826 0.00 0.00 32.51 2.32
1401 1458 1.345415 GAGGTTAGGGACACGACCAAA 59.655 52.381 6.15 0.00 34.03 3.28
1402 1459 0.971386 GAGGTTAGGGACACGACCAA 59.029 55.000 6.15 0.00 34.03 3.67
1403 1460 1.246056 CGAGGTTAGGGACACGACCA 61.246 60.000 6.15 0.00 34.03 4.02
1404 1461 1.509923 CGAGGTTAGGGACACGACC 59.490 63.158 0.00 0.00 33.60 4.79
1405 1462 1.509923 CCGAGGTTAGGGACACGAC 59.490 63.158 0.00 0.00 33.60 4.34
1407 1464 2.183555 GCCGAGGTTAGGGACACG 59.816 66.667 0.00 0.00 0.00 4.49
1408 1465 2.183555 CGCCGAGGTTAGGGACAC 59.816 66.667 0.00 0.00 0.00 3.67
1410 1467 4.867599 CGCGCCGAGGTTAGGGAC 62.868 72.222 0.00 0.00 0.00 4.46
1412 1469 3.945304 AAACGCGCCGAGGTTAGGG 62.945 63.158 5.73 0.00 0.00 3.53
1413 1470 2.433664 AAACGCGCCGAGGTTAGG 60.434 61.111 5.73 0.00 0.00 2.69
1414 1471 2.736682 CCAAACGCGCCGAGGTTAG 61.737 63.158 5.73 0.00 0.00 2.34
1415 1472 2.739287 CCAAACGCGCCGAGGTTA 60.739 61.111 5.73 0.00 0.00 2.85
1424 1481 4.072088 GTCCGTCTGCCAAACGCG 62.072 66.667 3.53 3.53 42.08 6.01
1425 1482 2.970324 TGTCCGTCTGCCAAACGC 60.970 61.111 0.00 0.00 38.77 4.84
1426 1483 2.935955 GTGTCCGTCTGCCAAACG 59.064 61.111 0.00 0.00 39.78 3.60
1427 1484 2.604174 CCGTGTCCGTCTGCCAAAC 61.604 63.158 0.00 0.00 0.00 2.93
1428 1485 2.280524 CCGTGTCCGTCTGCCAAA 60.281 61.111 0.00 0.00 0.00 3.28
1429 1486 4.980805 GCCGTGTCCGTCTGCCAA 62.981 66.667 0.00 0.00 0.00 4.52
1431 1488 4.681978 AAGCCGTGTCCGTCTGCC 62.682 66.667 0.00 0.00 0.00 4.85
1465 1522 1.207329 AGGAACTTGATGTAGCCCGAC 59.793 52.381 0.00 0.00 27.25 4.79
1634 1691 6.457355 TGCGGTTTATACTTCTGTCAAGTTA 58.543 36.000 0.00 0.00 0.00 2.24
1679 1737 1.945394 ACGATGATGCATTCCTTCAGC 59.055 47.619 0.00 0.00 31.96 4.26
1686 1744 7.148918 GCAAAACCATTATACGATGATGCATTC 60.149 37.037 0.00 0.00 0.00 2.67
1691 1749 6.070897 TGGCAAAACCATTATACGATGATG 57.929 37.500 0.00 0.00 46.36 3.07
2005 2073 2.073232 AGCACAGGGTCTGCTGATT 58.927 52.632 0.00 0.00 43.54 2.57
2006 2074 3.817508 AGCACAGGGTCTGCTGAT 58.182 55.556 0.00 0.00 43.54 2.90
2092 2664 2.050714 GACGCAACGACTCGACCA 60.051 61.111 5.20 0.00 0.00 4.02
2093 2665 2.050714 TGACGCAACGACTCGACC 60.051 61.111 5.20 0.00 0.00 4.79
2094 2666 1.370172 ACTGACGCAACGACTCGAC 60.370 57.895 5.20 0.00 0.00 4.20
2095 2667 1.370051 CACTGACGCAACGACTCGA 60.370 57.895 5.20 0.00 0.00 4.04
2096 2668 1.370051 TCACTGACGCAACGACTCG 60.370 57.895 0.00 0.00 0.00 4.18
2097 2669 0.317938 AGTCACTGACGCAACGACTC 60.318 55.000 3.46 0.00 37.67 3.36
2098 2670 0.949397 TAGTCACTGACGCAACGACT 59.051 50.000 3.46 12.21 40.03 4.18
2109 2687 2.703416 ACCACATGCACATAGTCACTG 58.297 47.619 0.00 0.00 0.00 3.66
2110 2688 3.423539 AACCACATGCACATAGTCACT 57.576 42.857 0.00 0.00 0.00 3.41
2123 2701 3.687698 GTCGCTACCATGTTAAACCACAT 59.312 43.478 0.00 0.00 37.93 3.21
2125 2703 2.417586 GGTCGCTACCATGTTAAACCAC 59.582 50.000 1.78 0.00 45.98 4.16
2126 2704 2.702261 GGTCGCTACCATGTTAAACCA 58.298 47.619 1.78 0.00 45.98 3.67
2246 2824 0.733566 CGCATCCCACACAAATGCAC 60.734 55.000 7.27 0.00 44.71 4.57
2257 2835 2.807107 CCCGGAGAATCGCATCCCA 61.807 63.158 0.73 0.00 34.37 4.37
2360 2938 1.401905 GCCCTGTTCGCTGATTTAAGG 59.598 52.381 0.00 0.00 0.00 2.69
2371 2949 4.559502 CCCTAATGGCCCTGTTCG 57.440 61.111 0.00 0.00 0.00 3.95
2398 2990 6.098266 AGGTTTTAGCATTAATCCCCAATCAC 59.902 38.462 0.00 0.00 0.00 3.06
2430 3022 1.674817 CCGACACATGACCAACTACCC 60.675 57.143 0.00 0.00 0.00 3.69
2442 3034 1.134220 ACAAACTGTCCACCGACACAT 60.134 47.619 0.00 0.00 44.20 3.21
2502 3677 3.544698 TCTACTTGGGTCCAGTCTTCT 57.455 47.619 0.00 0.00 0.00 2.85
2509 3684 2.187958 CAGTGGATCTACTTGGGTCCA 58.812 52.381 9.32 0.00 38.37 4.02
2528 3713 0.681887 TCGATCGGTAGTGGCCTTCA 60.682 55.000 16.41 0.00 0.00 3.02
2537 3723 5.008217 GGATCTCATAGGATTCGATCGGTAG 59.992 48.000 16.41 0.00 33.15 3.18
2552 3738 2.307768 GTGTCTCCGGTGGATCTCATA 58.692 52.381 0.00 0.00 0.00 2.15
2553 3739 1.115467 GTGTCTCCGGTGGATCTCAT 58.885 55.000 0.00 0.00 0.00 2.90
2562 3748 0.968901 TATGAAGGCGTGTCTCCGGT 60.969 55.000 0.00 0.00 0.00 5.28
2563 3749 0.389391 ATATGAAGGCGTGTCTCCGG 59.611 55.000 0.00 0.00 0.00 5.14
2580 3766 4.153655 CGTATAGCGCTGTAGAAGGACATA 59.846 45.833 22.90 2.29 0.00 2.29
2600 3786 0.176219 CCCCGTTCTGGTAATGCGTA 59.824 55.000 0.00 0.00 35.15 4.42
2607 3793 1.675219 GTCTTGCCCCGTTCTGGTA 59.325 57.895 0.00 0.00 35.15 3.25
2621 3807 5.693769 TGAAATAAGATTCTCCCCGTCTT 57.306 39.130 0.00 0.00 36.30 3.01
2634 3820 5.065218 GCGGCTCTCAGAAAATGAAATAAGA 59.935 40.000 0.00 0.00 37.52 2.10
2641 3827 0.740868 CGGCGGCTCTCAGAAAATGA 60.741 55.000 7.61 0.00 36.21 2.57
2658 3844 1.762419 TCAAAAAGACGAGACGACGG 58.238 50.000 0.00 0.00 37.61 4.79
2678 3864 7.849322 AGTTTGTTTAGGGGTTTTATCATGT 57.151 32.000 0.00 0.00 0.00 3.21
2709 3895 2.678336 GGATCTTGCTCCGTTTTAGGTG 59.322 50.000 0.00 0.00 0.00 4.00
2725 3913 2.363795 TTGCCGACGGGAGGATCT 60.364 61.111 17.22 0.00 34.06 2.75
2735 3923 2.280592 AACCCGACACTTGCCGAC 60.281 61.111 0.00 0.00 0.00 4.79
2775 3963 4.530857 CCTCGTGTCCGATGGGCC 62.531 72.222 0.00 0.00 43.27 5.80
2805 3993 2.440409 TCCTCTACCTTTAGTCGCGTT 58.560 47.619 5.77 0.00 0.00 4.84
2810 3998 7.421087 ACTTATGGTTCCTCTACCTTTAGTC 57.579 40.000 0.00 0.00 39.04 2.59


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

AutoCloner maintained by Alex Coulton.