Multiple sequence alignment - TraesCS4B01G203100

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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 TraesCS4B01G203100 chr4B 100.000 3458 0 0 1 3458 434471038 434467581 0.000000e+00 6386.0
1 TraesCS4B01G203100 chr4A 92.943 2565 108 26 1 2508 113852263 113854811 0.000000e+00 3666.0
2 TraesCS4B01G203100 chr4A 93.146 963 52 10 2504 3458 113854855 113855811 0.000000e+00 1400.0
3 TraesCS4B01G203100 chr4A 88.106 454 35 9 310 753 120453618 120453174 3.950000e-144 521.0
4 TraesCS4B01G203100 chr4A 96.992 133 4 0 774 906 120413656 120413524 1.250000e-54 224.0
5 TraesCS4B01G203100 chr4A 93.548 62 4 0 916 977 120389676 120389615 3.670000e-15 93.5
6 TraesCS4B01G203100 chr4A 100.000 39 0 0 1608 1646 581149226 581149188 4.790000e-09 73.1
7 TraesCS4B01G203100 chr4A 100.000 39 0 0 1607 1645 590908020 590907982 4.790000e-09 73.1
8 TraesCS4B01G203100 chr4D 91.847 969 47 14 2504 3458 351465904 351464954 0.000000e+00 1323.0
9 TraesCS4B01G203100 chr4D 92.865 869 36 11 1654 2508 351466806 351465950 0.000000e+00 1238.0
10 TraesCS4B01G203100 chr4D 92.882 857 24 6 774 1609 351467647 351466807 0.000000e+00 1210.0
11 TraesCS4B01G203100 chr4D 93.582 670 25 9 1 658 351468330 351467667 0.000000e+00 983.0
12 TraesCS4B01G203100 chr4D 100.000 39 0 0 1607 1645 11567902 11567940 4.790000e-09 73.1
13 TraesCS4B01G203100 chr7A 100.000 41 0 0 1605 1645 82204215 82204175 3.700000e-10 76.8
14 TraesCS4B01G203100 chr1D 97.561 41 1 0 1605 1645 6139947 6139907 1.720000e-08 71.3
15 TraesCS4B01G203100 chr1D 94.872 39 2 0 731 769 201495069 201495031 1.040000e-05 62.1
16 TraesCS4B01G203100 chr2B 93.617 47 2 1 1599 1645 552427025 552427070 6.190000e-08 69.4
17 TraesCS4B01G203100 chr6A 91.837 49 1 1 1597 1645 572166270 572166225 8.010000e-07 65.8
18 TraesCS4B01G203100 chr6A 95.000 40 2 0 730 769 237755309 237755270 2.880000e-06 63.9
19 TraesCS4B01G203100 chr6A 95.000 40 2 0 730 769 237756338 237756299 2.880000e-06 63.9
20 TraesCS4B01G203100 chr6A 95.000 40 2 0 730 769 237757364 237757325 2.880000e-06 63.9
21 TraesCS4B01G203100 chr5B 97.368 38 1 0 1608 1645 673768000 673767963 8.010000e-07 65.8
22 TraesCS4B01G203100 chr3D 95.122 41 2 0 730 770 373324972 373325012 8.010000e-07 65.8
23 TraesCS4B01G203100 chr3D 93.023 43 2 1 723 764 261571948 261571990 1.040000e-05 62.1
24 TraesCS4B01G203100 chr3B 95.000 40 2 0 730 769 487045480 487045519 2.880000e-06 63.9


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 TraesCS4B01G203100 chr4B 434467581 434471038 3457 True 6386.0 6386 100.0000 1 3458 1 chr4B.!!$R1 3457
1 TraesCS4B01G203100 chr4A 113852263 113855811 3548 False 2533.0 3666 93.0445 1 3458 2 chr4A.!!$F1 3457
2 TraesCS4B01G203100 chr4D 351464954 351468330 3376 True 1188.5 1323 92.7940 1 3458 4 chr4D.!!$R1 3457

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
990 1009 0.678950 GCTAGGATCAGAGCTCCACC 59.321 60.0 10.93 8.91 35.73 4.61 F
2132 2198 0.108851 TGCTACGCTGCAAAGATCGA 60.109 50.0 0.00 0.00 40.29 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2441 2512 0.179250 CAATCACGCGTTCAAGTCCG 60.179 55.0 10.22 0.0 0.0 4.79 R
3399 3535 0.316841 TGGTTTTGAAGAATGCGCCC 59.683 50.0 4.18 0.0 0.0 6.13 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 47 1.765597 AAGGAGGAACGGGTTTCGCT 61.766 55.000 0.00 0.00 43.89 4.93
103 104 2.026262 GCATTTAGGGAGTGGTTCTGGA 60.026 50.000 0.00 0.00 0.00 3.86
176 185 6.147821 ACTGTTGTTGTATAATGCTGTCAGTC 59.852 38.462 0.93 0.00 0.00 3.51
420 432 3.624861 AGAGCAGATATTCGTTTGCCTTG 59.375 43.478 0.00 0.00 37.26 3.61
421 433 3.347216 AGCAGATATTCGTTTGCCTTGT 58.653 40.909 0.00 0.00 37.26 3.16
422 434 4.513442 AGCAGATATTCGTTTGCCTTGTA 58.487 39.130 0.00 0.00 37.26 2.41
600 612 4.142730 GCAAATTCTGTGGTGAGATGACTC 60.143 45.833 0.00 0.00 42.88 3.36
621 633 6.222389 ACTCTTGCATCTCTACAGATTATGC 58.778 40.000 14.98 14.98 37.25 3.14
671 683 1.440145 GGAGAATGCGTTAGGCCTGC 61.440 60.000 17.99 11.60 42.61 4.85
674 686 1.076777 AATGCGTTAGGCCTGCCAT 60.077 52.632 17.99 9.39 42.61 4.40
675 687 1.386525 AATGCGTTAGGCCTGCCATG 61.387 55.000 17.99 5.87 42.61 3.66
682 694 2.370189 GTTAGGCCTGCCATGTATCTCT 59.630 50.000 17.99 0.00 38.92 3.10
702 714 6.361433 TCTCTACAAAATCACCACAGGAAAA 58.639 36.000 0.00 0.00 0.00 2.29
714 726 4.041075 ACCACAGGAAAACAAACCAAAACT 59.959 37.500 0.00 0.00 0.00 2.66
769 781 9.781834 CCAAAATATAAGACGATTTTGCTGTTA 57.218 29.630 12.44 0.00 45.44 2.41
776 788 6.351327 AGACGATTTTGCTGTTATTCTAGC 57.649 37.500 0.00 0.00 40.29 3.42
803 815 2.626743 CCATCAGAAGGGAATGAATGGC 59.373 50.000 0.00 0.00 0.00 4.40
990 1009 0.678950 GCTAGGATCAGAGCTCCACC 59.321 60.000 10.93 8.91 35.73 4.61
1036 1055 5.416952 CAGAGCTTGATTTCCAAACAGGTAT 59.583 40.000 0.00 0.00 39.02 2.73
1086 1109 4.826274 TCTCTTGATTTCGTTCCTGGAT 57.174 40.909 0.00 0.00 0.00 3.41
1091 1114 6.707290 TCTTGATTTCGTTCCTGGATTTAGA 58.293 36.000 0.00 0.00 0.00 2.10
1254 1286 5.422214 TTTAAAGGTTGGCACAGGAAAAA 57.578 34.783 0.00 0.00 42.39 1.94
1349 1381 2.054799 GGGGCATTATCCACTGTCCTA 58.945 52.381 0.00 0.00 37.31 2.94
1389 1421 3.882102 ATGCTGAAGGTATGCCCATTA 57.118 42.857 0.00 0.00 34.66 1.90
1529 1572 8.429641 AGATTTCAGAAGTACCAAAGAACTACA 58.570 33.333 0.00 0.00 0.00 2.74
1561 1604 2.538037 CGATGCAAACGACGGATATTCA 59.462 45.455 10.41 0.00 31.90 2.57
1620 1663 3.567478 TTACTAGTACTCCCTCCGTCC 57.433 52.381 0.91 0.00 0.00 4.79
1624 1667 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
1693 1739 4.834496 AGAAGGACAATTCAGATGCCAAAA 59.166 37.500 0.00 0.00 0.00 2.44
1716 1768 6.809630 AAAGTTTCTAAGTCATTGGCTCTC 57.190 37.500 0.00 0.00 0.00 3.20
1733 1789 3.309954 GCTCTCGTGGATTTCACATAACC 59.690 47.826 0.00 0.00 46.36 2.85
1749 1805 1.657072 AACCCTTTTGTTCCCCCGGA 61.657 55.000 0.73 0.00 0.00 5.14
1838 1894 2.738521 CTGTCCGTGTGGCCTTCG 60.739 66.667 3.32 6.04 34.14 3.79
2075 2141 5.595885 TGCTTGCATTGCAGTTTTTAAGTA 58.404 33.333 11.76 1.33 40.61 2.24
2082 2148 6.635239 GCATTGCAGTTTTTAAGTAGTCGAAA 59.365 34.615 3.15 0.00 0.00 3.46
2083 2149 7.166804 GCATTGCAGTTTTTAAGTAGTCGAAAA 59.833 33.333 3.15 0.00 0.00 2.29
2084 2150 9.015577 CATTGCAGTTTTTAAGTAGTCGAAAAA 57.984 29.630 0.00 0.00 31.42 1.94
2132 2198 0.108851 TGCTACGCTGCAAAGATCGA 60.109 50.000 0.00 0.00 40.29 3.59
2306 2377 5.222213 GGGATTCTGATCATATGTTTCCCCT 60.222 44.000 1.90 0.00 35.30 4.79
2441 2512 1.535015 CGCCGACTCCTTCAAGATCTC 60.535 57.143 0.00 0.00 0.00 2.75
2442 2513 1.535015 GCCGACTCCTTCAAGATCTCG 60.535 57.143 0.00 0.00 0.00 4.04
2454 2525 0.179161 AGATCTCGGACTTGAACGCG 60.179 55.000 3.53 3.53 0.00 6.01
2461 2532 1.144969 GGACTTGAACGCGTGATTGA 58.855 50.000 14.98 0.00 0.00 2.57
2469 2540 1.225936 CGCGTGATTGAGCAAGCTG 60.226 57.895 0.00 0.00 40.40 4.24
2470 2541 1.513586 GCGTGATTGAGCAAGCTGC 60.514 57.895 0.00 0.00 45.46 5.25
2489 2560 3.118454 CATGTCCGTCGGCACCAC 61.118 66.667 6.34 0.00 0.00 4.16
2492 2563 4.388499 GTCCGTCGGCACCACCAT 62.388 66.667 6.34 0.00 39.03 3.55
2493 2564 4.077184 TCCGTCGGCACCACCATC 62.077 66.667 6.34 0.00 39.03 3.51
2496 2567 4.028490 GTCGGCACCACCATCCCA 62.028 66.667 0.00 0.00 39.03 4.37
2497 2568 4.028490 TCGGCACCACCATCCCAC 62.028 66.667 0.00 0.00 39.03 4.61
2501 2572 3.646715 CACCACCATCCCACCGGT 61.647 66.667 0.00 0.00 35.27 5.28
2514 2633 1.070786 ACCGGTGCAACGAATCTGT 59.929 52.632 28.95 11.97 38.12 3.41
2518 2637 3.191669 CCGGTGCAACGAATCTGTATTA 58.808 45.455 28.95 0.00 38.12 0.98
2529 2648 9.684448 CAACGAATCTGTATTACTCATACATCT 57.316 33.333 0.00 0.00 45.61 2.90
2545 2664 6.592994 TCATACATCTAGCTATTCATGCTTGC 59.407 38.462 0.00 0.00 41.46 4.01
2645 2765 4.901849 CAGGGAGTATGATTCCTAGGACAA 59.098 45.833 12.22 0.00 35.01 3.18
2671 2791 1.403679 CACGGCTGTTCTTGTTTCCAA 59.596 47.619 0.00 0.00 0.00 3.53
2678 2798 3.558033 TGTTCTTGTTTCCAAGGGGTAC 58.442 45.455 2.88 0.00 46.65 3.34
2681 2801 2.038033 TCTTGTTTCCAAGGGGTACTCG 59.962 50.000 2.88 0.00 46.65 4.18
2685 2805 1.263356 TTCCAAGGGGTACTCGACAG 58.737 55.000 0.00 0.00 34.93 3.51
2687 2807 1.616187 TCCAAGGGGTACTCGACAGAG 60.616 57.143 0.00 0.00 41.96 3.35
2718 2841 5.009510 TGAATGAACAAACGACAATCCACAT 59.990 36.000 0.00 0.00 0.00 3.21
2734 2857 4.707105 TCCACATGATCATCGCTAAACAT 58.293 39.130 4.86 0.00 0.00 2.71
2767 2893 7.454380 TCAAATCACCAGGAATTCAACCTATTT 59.546 33.333 7.93 3.46 35.84 1.40
2768 2894 8.748412 CAAATCACCAGGAATTCAACCTATTTA 58.252 33.333 7.93 0.00 35.84 1.40
2769 2895 9.492730 AAATCACCAGGAATTCAACCTATTTAT 57.507 29.630 7.93 0.00 35.84 1.40
2793 2923 6.927294 AAGACTTTTCTTTACACACCTGAG 57.073 37.500 0.00 0.00 39.17 3.35
2835 2965 5.063204 ACAAAGGTGAAATGAATCGAGTGA 58.937 37.500 0.00 0.00 0.00 3.41
2908 3039 1.203001 CCCTCCCACCAAACTTGCTAA 60.203 52.381 0.00 0.00 0.00 3.09
2923 3054 8.616076 CAAACTTGCTAACTATTTCCAGGATAG 58.384 37.037 0.00 0.00 34.11 2.08
2991 3122 4.642885 TCGAAAATTTTGTCAAGACCAGGT 59.357 37.500 8.47 0.00 0.00 4.00
2996 3127 1.507140 TTGTCAAGACCAGGTCACCT 58.493 50.000 22.31 0.00 34.60 4.00
3009 3140 0.874390 GTCACCTTTCTGCGCATTCA 59.126 50.000 12.24 0.00 0.00 2.57
3010 3141 0.874390 TCACCTTTCTGCGCATTCAC 59.126 50.000 12.24 0.00 0.00 3.18
3068 3199 2.681778 ACAGAGAGCGACAGGGGG 60.682 66.667 0.00 0.00 0.00 5.40
3087 3218 2.487986 GGGGACTTGATCATGCCCTAAG 60.488 54.545 25.97 11.91 38.84 2.18
3102 3233 8.154856 TCATGCCCTAAGATAATTTACACCTAC 58.845 37.037 0.00 0.00 0.00 3.18
3183 3319 3.503748 GGGGCTGCATCAATCTAACATAC 59.496 47.826 0.50 0.00 0.00 2.39
3399 3535 1.331756 GCCTCGTCCAACAGCAATATG 59.668 52.381 0.00 0.00 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 0.246360 CTAGGTGGTCATCGTGTGCA 59.754 55.000 0.00 0.00 0.00 4.57
103 104 1.065126 GCAGGCTTCACCAATCCTAGT 60.065 52.381 0.00 0.00 43.14 2.57
237 247 6.873997 AGTATCGTTTGTTCCAGATCATACA 58.126 36.000 0.00 0.00 0.00 2.29
317 328 1.269448 GTCAAGCGCCAAAGAAATCCA 59.731 47.619 2.29 0.00 0.00 3.41
415 427 3.199880 AGCATGATGGTACTACAAGGC 57.800 47.619 0.00 0.00 0.00 4.35
420 432 5.411361 TGTGAACAAAGCATGATGGTACTAC 59.589 40.000 0.00 0.00 0.00 2.73
421 433 5.555966 TGTGAACAAAGCATGATGGTACTA 58.444 37.500 0.00 0.00 0.00 1.82
422 434 4.397420 TGTGAACAAAGCATGATGGTACT 58.603 39.130 0.00 0.00 0.00 2.73
492 504 4.721776 ACTAGGGACTCTTTGGATTGCATA 59.278 41.667 0.00 0.00 41.75 3.14
493 505 3.525199 ACTAGGGACTCTTTGGATTGCAT 59.475 43.478 0.00 0.00 41.75 3.96
600 612 5.549347 AGGCATAATCTGTAGAGATGCAAG 58.451 41.667 22.58 2.98 43.54 4.01
621 633 6.884832 TGTGGTTTAACTACATAGATGGAGG 58.115 40.000 10.17 0.00 43.20 4.30
667 679 6.017605 GTGATTTTGTAGAGATACATGGCAGG 60.018 42.308 0.00 0.00 0.00 4.85
669 681 5.822519 GGTGATTTTGTAGAGATACATGGCA 59.177 40.000 0.00 0.00 0.00 4.92
671 683 6.823182 TGTGGTGATTTTGTAGAGATACATGG 59.177 38.462 0.00 0.00 0.00 3.66
674 686 6.212589 TCCTGTGGTGATTTTGTAGAGATACA 59.787 38.462 0.00 0.00 0.00 2.29
675 687 6.640518 TCCTGTGGTGATTTTGTAGAGATAC 58.359 40.000 0.00 0.00 0.00 2.24
682 694 6.531503 TTGTTTTCCTGTGGTGATTTTGTA 57.468 33.333 0.00 0.00 0.00 2.41
702 714 4.882842 AACTTGGTCAGTTTTGGTTTGT 57.117 36.364 0.00 0.00 43.89 2.83
714 726 5.269991 AGGTAGTAGCTCATAACTTGGTCA 58.730 41.667 0.00 0.00 0.00 4.02
728 740 1.188863 TTTGGGACGGAGGTAGTAGC 58.811 55.000 0.00 0.00 0.00 3.58
733 745 5.221303 CGTCTTATATTTTGGGACGGAGGTA 60.221 44.000 0.00 0.00 43.69 3.08
769 781 5.248020 CCCTTCTGATGGATAGTGCTAGAAT 59.752 44.000 10.93 0.00 0.00 2.40
776 788 5.557576 TCATTCCCTTCTGATGGATAGTG 57.442 43.478 10.93 6.23 0.00 2.74
803 815 2.676471 CCGGCTGACAAAAGGGGG 60.676 66.667 0.00 0.00 0.00 5.40
990 1009 0.109132 GGCTTGCCATTTCACCTTCG 60.109 55.000 6.79 0.00 0.00 3.79
1036 1055 2.363306 ACAGGGTTCATTCAAGCACA 57.637 45.000 0.00 0.00 33.79 4.57
1086 1109 5.421277 TGAAGACAACACCGAGTTTCTAAA 58.579 37.500 0.00 0.00 38.74 1.85
1091 1114 3.261981 ACTGAAGACAACACCGAGTTT 57.738 42.857 0.00 0.00 38.74 2.66
1136 1159 2.757099 CCCCATTCAGCCTGGCAC 60.757 66.667 22.65 0.00 32.08 5.01
1254 1286 9.525826 AGGAAGAGTGATTCTATCAACAATTTT 57.474 29.630 0.00 0.00 41.69 1.82
1255 1287 8.954350 CAGGAAGAGTGATTCTATCAACAATTT 58.046 33.333 0.00 0.00 41.69 1.82
1256 1288 8.324306 TCAGGAAGAGTGATTCTATCAACAATT 58.676 33.333 0.00 0.00 41.69 2.32
1272 1304 7.597327 ACCTCTATAATAAGGTCAGGAAGAGT 58.403 38.462 0.00 0.00 42.28 3.24
1455 1487 5.277683 GCTCACACAATCCTACATGCTAATG 60.278 44.000 0.00 0.00 39.89 1.90
1495 1538 6.936279 TGGTACTTCTGAAATCTAGGAACAG 58.064 40.000 0.00 0.00 0.00 3.16
1529 1572 1.993370 GTTTGCATCGACGTAAGAGCT 59.007 47.619 0.00 0.00 43.62 4.09
1561 1604 2.975489 CCAATCAGCTGGGTAGAGGTAT 59.025 50.000 15.13 0.00 32.32 2.73
1645 1688 5.184479 TGCACACTAATTTACTACTCCGTCT 59.816 40.000 0.00 0.00 0.00 4.18
1646 1689 5.404946 TGCACACTAATTTACTACTCCGTC 58.595 41.667 0.00 0.00 0.00 4.79
1648 1691 6.097356 TCTTGCACACTAATTTACTACTCCG 58.903 40.000 0.00 0.00 0.00 4.63
1649 1692 7.064728 CCTTCTTGCACACTAATTTACTACTCC 59.935 40.741 0.00 0.00 0.00 3.85
1693 1739 5.409826 CGAGAGCCAATGACTTAGAAACTTT 59.590 40.000 0.00 0.00 0.00 2.66
1700 1746 2.166459 TCCACGAGAGCCAATGACTTAG 59.834 50.000 0.00 0.00 0.00 2.18
1702 1748 0.976641 TCCACGAGAGCCAATGACTT 59.023 50.000 0.00 0.00 0.00 3.01
1733 1789 1.604147 GCATCCGGGGGAACAAAAGG 61.604 60.000 0.00 0.00 34.34 3.11
1749 1805 3.624861 GTCGAAATCCTGACATGAAGCAT 59.375 43.478 0.00 0.00 35.20 3.79
1838 1894 6.128795 CGAATGTCTGTTTTCTGAGTAGGAAC 60.129 42.308 0.00 0.00 0.00 3.62
1920 1986 3.181454 TGGTCAGAAGAAAGGGAAGACAC 60.181 47.826 0.00 0.00 0.00 3.67
2040 2106 1.985473 TGCAAGCAGTGGATGAAACT 58.015 45.000 0.00 0.00 0.00 2.66
2084 2150 5.414765 GGGAATTCTATGTCTGGTCGTTTTT 59.585 40.000 5.23 0.00 0.00 1.94
2085 2151 4.941873 GGGAATTCTATGTCTGGTCGTTTT 59.058 41.667 5.23 0.00 0.00 2.43
2087 2153 3.430374 CGGGAATTCTATGTCTGGTCGTT 60.430 47.826 5.23 0.00 0.00 3.85
2088 2154 2.100916 CGGGAATTCTATGTCTGGTCGT 59.899 50.000 5.23 0.00 0.00 4.34
2096 2162 4.321304 CGTAGCAGATCGGGAATTCTATGT 60.321 45.833 5.23 0.00 0.00 2.29
2306 2377 2.029964 GCTTCGTGTCCACCGGAA 59.970 61.111 9.46 0.00 31.38 4.30
2441 2512 0.179250 CAATCACGCGTTCAAGTCCG 60.179 55.000 10.22 0.00 0.00 4.79
2442 2513 1.126846 CTCAATCACGCGTTCAAGTCC 59.873 52.381 10.22 0.00 0.00 3.85
2469 2540 3.188786 GTGCCGACGGACATGAGC 61.189 66.667 20.50 0.00 0.00 4.26
2470 2541 2.509336 GGTGCCGACGGACATGAG 60.509 66.667 20.50 0.00 0.00 2.90
2472 2543 3.118454 GTGGTGCCGACGGACATG 61.118 66.667 20.50 0.00 0.00 3.21
2489 2560 3.061848 GTTGCACCGGTGGGATGG 61.062 66.667 34.58 10.02 36.97 3.51
2491 2562 2.478335 ATTCGTTGCACCGGTGGGAT 62.478 55.000 34.58 16.08 36.97 3.85
2492 2563 3.185299 ATTCGTTGCACCGGTGGGA 62.185 57.895 34.58 14.36 36.97 4.37
2493 2564 2.671619 ATTCGTTGCACCGGTGGG 60.672 61.111 34.58 12.47 40.11 4.61
2496 2567 0.319083 TACAGATTCGTTGCACCGGT 59.681 50.000 0.00 0.00 0.00 5.28
2497 2568 1.651987 ATACAGATTCGTTGCACCGG 58.348 50.000 3.08 0.00 0.00 5.28
2498 2569 3.863424 AGTAATACAGATTCGTTGCACCG 59.137 43.478 0.00 0.00 0.00 4.94
2500 2571 6.589830 ATGAGTAATACAGATTCGTTGCAC 57.410 37.500 0.00 0.00 0.00 4.57
2501 2572 7.262048 TGTATGAGTAATACAGATTCGTTGCA 58.738 34.615 0.00 0.00 45.02 4.08
2502 2573 7.694388 TGTATGAGTAATACAGATTCGTTGC 57.306 36.000 0.00 0.00 45.02 4.17
2518 2637 7.479352 AGCATGAATAGCTAGATGTATGAGT 57.521 36.000 0.00 0.00 41.32 3.41
2529 2648 3.177997 TCGTGCAAGCATGAATAGCTA 57.822 42.857 14.12 0.00 42.53 3.32
2545 2664 9.181805 CATGTATACTGGTTCTACTAATTCGTG 57.818 37.037 4.17 0.00 0.00 4.35
2605 2725 5.672194 ACTCCCTGTGGTTCCTCAATATATT 59.328 40.000 0.00 0.00 0.00 1.28
2606 2726 5.227593 ACTCCCTGTGGTTCCTCAATATAT 58.772 41.667 0.00 0.00 0.00 0.86
2607 2727 4.631234 ACTCCCTGTGGTTCCTCAATATA 58.369 43.478 0.00 0.00 0.00 0.86
2622 2742 4.483950 TGTCCTAGGAATCATACTCCCTG 58.516 47.826 14.65 0.00 32.95 4.45
2645 2765 1.148310 CAAGAACAGCCGTGACGAAT 58.852 50.000 6.54 0.00 0.00 3.34
2678 2798 4.550422 TCATTCAAACAGACTCTGTCGAG 58.450 43.478 12.22 5.79 44.62 4.04
2681 2801 5.991328 TGTTCATTCAAACAGACTCTGTC 57.009 39.130 12.22 0.00 44.62 3.51
2692 2812 5.746245 GTGGATTGTCGTTTGTTCATTCAAA 59.254 36.000 0.00 0.00 35.36 2.69
2718 2841 6.427547 TGATTATGCATGTTTAGCGATGATCA 59.572 34.615 10.16 0.00 30.83 2.92
2734 2857 6.380560 TGAATTCCTGGTGATTTGATTATGCA 59.619 34.615 2.27 0.00 0.00 3.96
2767 2893 9.706691 CTCAGGTGTGTAAAGAAAAGTCTTATA 57.293 33.333 0.00 0.00 43.59 0.98
2768 2894 8.211629 ACTCAGGTGTGTAAAGAAAAGTCTTAT 58.788 33.333 0.00 0.00 43.59 1.73
2769 2895 7.562135 ACTCAGGTGTGTAAAGAAAAGTCTTA 58.438 34.615 0.00 0.00 43.59 2.10
2793 2923 2.031560 TGTAATGCGCCGATTTGATGAC 59.968 45.455 4.18 0.00 0.00 3.06
2835 2965 0.998145 ATTCTTTGGGAGGCTCTGCT 59.002 50.000 15.23 0.00 0.00 4.24
2908 3039 6.213525 AGGGAACTTCTATCCTGGAAATAGT 58.786 40.000 0.00 0.00 37.44 2.12
2923 3054 5.305585 TGTGTTGAATCTGTAGGGAACTTC 58.694 41.667 0.00 0.00 43.67 3.01
2991 3122 0.874390 GTGAATGCGCAGAAAGGTGA 59.126 50.000 18.32 0.00 0.00 4.02
2996 3127 2.665245 CGATGTTGTGAATGCGCAGAAA 60.665 45.455 18.32 0.00 35.67 2.52
3039 3170 0.888619 CTCTCTGTCCAGCCACGTAA 59.111 55.000 0.00 0.00 0.00 3.18
3068 3199 3.845781 TCTTAGGGCATGATCAAGTCC 57.154 47.619 13.71 13.71 0.00 3.85
3069 3200 7.992754 AATTATCTTAGGGCATGATCAAGTC 57.007 36.000 0.00 0.00 0.00 3.01
3075 3206 7.759607 AGGTGTAAATTATCTTAGGGCATGAT 58.240 34.615 0.00 0.00 0.00 2.45
3087 3218 7.177041 TGTTGGGTTTGGTAGGTGTAAATTATC 59.823 37.037 0.00 0.00 0.00 1.75
3102 3233 7.494298 GGCTAATGTAATTAATGTTGGGTTTGG 59.506 37.037 0.00 0.00 38.53 3.28
3300 3436 1.002087 GTCATGGGGAACAAGACGACT 59.998 52.381 0.00 0.00 37.95 4.18
3399 3535 0.316841 TGGTTTTGAAGAATGCGCCC 59.683 50.000 4.18 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.