Multiple sequence alignment - TraesCS6A01G108800

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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 TraesCS6A01G108800 chr6A 100.000 4045 0 0 1 4045 77540002 77535958 0.000000e+00 7470.0
1 TraesCS6A01G108800 chr6D 91.503 3460 180 51 660 4045 60548758 60545339 0.000000e+00 4656.0
2 TraesCS6A01G108800 chr6D 96.200 500 15 2 1 496 60549689 60549190 0.000000e+00 815.0
3 TraesCS6A01G108800 chr6D 95.604 182 6 1 479 660 60549178 60548999 1.420000e-74 291.0
4 TraesCS6A01G108800 chr6B 89.187 3320 260 54 104 3349 134827600 134824306 0.000000e+00 4050.0
5 TraesCS6A01G108800 chr6B 86.511 556 46 18 3513 4045 134824222 134823673 5.830000e-163 584.0
6 TraesCS6A01G108800 chr6B 81.385 693 54 33 160 795 134828273 134827599 2.810000e-136 496.0
7 TraesCS6A01G108800 chr6B 90.647 139 8 1 1 139 134828386 134828253 3.210000e-41 180.0
8 TraesCS6A01G108800 chr3D 91.820 868 56 11 1499 2358 135040702 135041562 0.000000e+00 1195.0
9 TraesCS6A01G108800 chr3D 86.901 626 70 9 852 1467 135018798 135019421 0.000000e+00 691.0
10 TraesCS6A01G108800 chr3A 90.658 760 50 15 1606 2358 149982968 149983713 0.000000e+00 990.0
11 TraesCS6A01G108800 chr3A 86.458 768 92 9 852 1609 149962018 149962783 0.000000e+00 832.0
12 TraesCS6A01G108800 chr4D 79.204 226 38 8 351 571 380282174 380281953 9.060000e-32 148.0
13 TraesCS6A01G108800 chr4B 78.855 227 39 8 351 571 467460719 467460496 1.170000e-30 145.0
14 TraesCS6A01G108800 chr4B 83.721 86 13 1 1993 2078 377800200 377800116 3.350000e-11 80.5
15 TraesCS6A01G108800 chr2D 78.673 211 42 3 356 565 62063153 62062945 1.960000e-28 137.0
16 TraesCS6A01G108800 chr1D 77.934 213 44 2 356 565 338927369 338927157 3.280000e-26 130.0
17 TraesCS6A01G108800 chr2A 77.725 211 45 2 356 565 62388251 62388042 1.180000e-25 128.0
18 TraesCS6A01G108800 chr2A 76.754 228 44 5 343 565 15610831 15611054 7.100000e-23 119.0
19 TraesCS6A01G108800 chr7D 96.774 62 2 0 2554 2615 528026736 528026675 1.990000e-18 104.0
20 TraesCS6A01G108800 chr7B 95.161 62 3 0 2554 2615 565054729 565054668 9.250000e-17 99.0
21 TraesCS6A01G108800 chr7A 93.548 62 4 0 2554 2615 608204629 608204568 4.300000e-15 93.5
22 TraesCS6A01G108800 chr4A 83.146 89 14 1 1990 2078 176539244 176539331 3.350000e-11 80.5


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 TraesCS6A01G108800 chr6A 77535958 77540002 4044 True 7470.000000 7470 100.000000 1 4045 1 chr6A.!!$R1 4044
1 TraesCS6A01G108800 chr6D 60545339 60549689 4350 True 1920.666667 4656 94.435667 1 4045 3 chr6D.!!$R1 4044
2 TraesCS6A01G108800 chr6B 134823673 134828386 4713 True 1327.500000 4050 86.932500 1 4045 4 chr6B.!!$R1 4044
3 TraesCS6A01G108800 chr3D 135040702 135041562 860 False 1195.000000 1195 91.820000 1499 2358 1 chr3D.!!$F2 859
4 TraesCS6A01G108800 chr3D 135018798 135019421 623 False 691.000000 691 86.901000 852 1467 1 chr3D.!!$F1 615
5 TraesCS6A01G108800 chr3A 149982968 149983713 745 False 990.000000 990 90.658000 1606 2358 1 chr3A.!!$F2 752
6 TraesCS6A01G108800 chr3A 149962018 149962783 765 False 832.000000 832 86.458000 852 1609 1 chr3A.!!$F1 757


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
967 1951 0.779997 AGGGTTGGATTGGAGCAAGT 59.220 50.0 0.00 0.00 0.00 3.16 F
1070 2054 0.251474 ATGGCTCACACCTGCAATGT 60.251 50.0 0.00 0.00 0.00 2.71 F
1213 2197 0.723414 CTGTGCAAGCATGTACTCGG 59.277 55.0 11.38 0.00 42.06 4.63 F
1218 2202 0.735978 CAAGCATGTACTCGGCGTCA 60.736 55.0 6.85 3.05 0.00 4.35 F
1219 2203 0.736325 AAGCATGTACTCGGCGTCAC 60.736 55.0 6.85 4.02 0.00 3.67 F
1366 2350 1.021390 CAGCGATGGTGGTCAAGGTC 61.021 60.0 0.00 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2828 3861 0.249784 CATGCTCCTCTATGCGCAGT 60.250 55.000 18.32 6.92 35.66 4.40 R
2896 3929 1.203087 TCTCCTCTGGTTTCGGTACCA 60.203 52.381 13.54 8.87 45.73 3.25 R
2926 3959 1.673665 GGAGCTGAAGTGGTGCTGG 60.674 63.158 0.00 0.00 37.16 4.85 R
2989 4023 2.026641 GCCTTCTGCTATCCATTTGCA 58.973 47.619 0.00 0.00 36.87 4.08 R
2993 4027 2.106166 CTCTGGCCTTCTGCTATCCATT 59.894 50.000 3.32 0.00 40.92 3.16 R
3255 4313 0.694771 TGAGCATGAACAGGGAGCTT 59.305 50.000 0.00 0.00 35.36 3.74 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
190 880 2.239654 TCCTGCTTATGGGAAGGAACTG 59.760 50.000 0.00 0.00 38.06 3.16
213 903 6.228258 TGTCATCAAGTTTTGGTAGGAGTAC 58.772 40.000 0.00 0.00 0.00 2.73
371 1074 9.419297 GTCCCAAGTGAAAATTTATAAAGTTCC 57.581 33.333 11.01 0.00 0.00 3.62
577 1310 3.702045 CGGAGGGAGTGTCTATTTTCTCT 59.298 47.826 0.00 0.00 0.00 3.10
640 1373 2.236146 TCCAGACATGACCGTAGCAATT 59.764 45.455 0.00 0.00 0.00 2.32
727 1701 6.841601 TCTGGGAATATTCTTATGTCCCTTG 58.158 40.000 14.95 4.95 36.90 3.61
734 1708 9.561069 GAATATTCTTATGTCCCTTGTGTACAT 57.439 33.333 8.27 0.00 37.58 2.29
781 1755 6.709397 TCAATCTGGATCATTCTATTGACAGC 59.291 38.462 0.00 0.00 30.59 4.40
795 1769 3.116096 TGACAGCCTAGTACTCCCAAT 57.884 47.619 0.00 0.00 0.00 3.16
802 1776 5.297776 CAGCCTAGTACTCCCAATTCAAATG 59.702 44.000 0.00 0.00 0.00 2.32
803 1777 5.044846 AGCCTAGTACTCCCAATTCAAATGT 60.045 40.000 0.00 0.00 0.00 2.71
821 1796 9.985318 TTCAAATGTAATGCTTTGTTTTTCTTG 57.015 25.926 0.00 0.00 34.66 3.02
822 1797 8.121708 TCAAATGTAATGCTTTGTTTTTCTTGC 58.878 29.630 0.00 0.00 34.66 4.01
823 1798 7.551035 AATGTAATGCTTTGTTTTTCTTGCA 57.449 28.000 0.00 0.00 34.88 4.08
824 1799 7.733402 ATGTAATGCTTTGTTTTTCTTGCAT 57.267 28.000 0.00 0.00 42.01 3.96
922 1905 6.633500 TTGAAAGGACTTGGAACTTGTATG 57.367 37.500 0.00 0.00 0.00 2.39
923 1906 4.518970 TGAAAGGACTTGGAACTTGTATGC 59.481 41.667 0.00 0.00 0.00 3.14
967 1951 0.779997 AGGGTTGGATTGGAGCAAGT 59.220 50.000 0.00 0.00 0.00 3.16
978 1962 2.426522 TGGAGCAAGTTTTCCATCTCG 58.573 47.619 2.39 0.00 38.53 4.04
982 1966 4.876107 GGAGCAAGTTTTCCATCTCGATTA 59.124 41.667 0.00 0.00 33.55 1.75
988 1972 7.589221 GCAAGTTTTCCATCTCGATTATCATTC 59.411 37.037 0.00 0.00 0.00 2.67
991 1975 8.206867 AGTTTTCCATCTCGATTATCATTCTCA 58.793 33.333 0.00 0.00 0.00 3.27
993 1977 8.599055 TTTCCATCTCGATTATCATTCTCAAG 57.401 34.615 0.00 0.00 0.00 3.02
1030 2014 4.950050 ACAGAGTGTACTTCCTGTGAAAG 58.050 43.478 11.75 0.00 38.32 2.62
1070 2054 0.251474 ATGGCTCACACCTGCAATGT 60.251 50.000 0.00 0.00 0.00 2.71
1085 2069 2.863704 GCAATGTTCCACAACCTTCAGC 60.864 50.000 0.00 0.00 0.00 4.26
1113 2097 9.361315 CATCAAATGTTCAATGCTAAATCTGAA 57.639 29.630 0.00 0.00 0.00 3.02
1133 2117 4.155826 TGAAATTTACAGTTCGGCAGATGG 59.844 41.667 0.00 0.00 29.01 3.51
1149 2133 0.828022 ATGGTATTTCCCGCGTCTCA 59.172 50.000 4.92 0.00 34.77 3.27
1212 2196 1.713597 TCTGTGCAAGCATGTACTCG 58.286 50.000 11.38 3.26 42.06 4.18
1213 2197 0.723414 CTGTGCAAGCATGTACTCGG 59.277 55.000 11.38 0.00 42.06 4.63
1218 2202 0.735978 CAAGCATGTACTCGGCGTCA 60.736 55.000 6.85 3.05 0.00 4.35
1219 2203 0.736325 AAGCATGTACTCGGCGTCAC 60.736 55.000 6.85 4.02 0.00 3.67
1247 2231 5.422145 GAACTCCAAATTATGCTGGCAAAT 58.578 37.500 0.00 0.00 32.33 2.32
1311 2295 4.528002 CAGTTTTCAGCTGCGCAG 57.472 55.556 32.83 32.83 0.00 5.18
1346 2330 2.551032 CTCTGTTGTTTGCTGCTGATCA 59.449 45.455 0.00 0.00 0.00 2.92
1366 2350 1.021390 CAGCGATGGTGGTCAAGGTC 61.021 60.000 0.00 0.00 0.00 3.85
1450 2434 2.203788 TCCGTGGAGGAGGCAGTT 60.204 61.111 0.00 0.00 45.98 3.16
1485 2469 2.368548 TGAGCAGCTGGAGTTTCAGTTA 59.631 45.455 17.12 0.00 37.12 2.24
1663 2647 9.569122 TTGGCTAAGTTCAGATTTTAACTAGTT 57.431 29.630 13.68 13.68 34.91 2.24
1704 2691 7.989170 TCATTGCTTAGGACATATATGGCATAG 59.011 37.037 20.24 13.61 37.62 2.23
1728 2715 2.464865 CGCAATGCTCACCTAGTCTAC 58.535 52.381 2.94 0.00 0.00 2.59
1817 2807 2.259917 TCACCTTCTTCATCTGGAGCA 58.740 47.619 0.00 0.00 0.00 4.26
1818 2808 2.639347 TCACCTTCTTCATCTGGAGCAA 59.361 45.455 0.00 0.00 0.00 3.91
1819 2809 2.746362 CACCTTCTTCATCTGGAGCAAC 59.254 50.000 0.00 0.00 0.00 4.17
1900 2892 1.971357 TCTGAAAAAGCTCGGAGGACT 59.029 47.619 7.20 0.00 0.00 3.85
1936 2929 6.366061 GTGATCACTCTGTTAAATTTTTGGGC 59.634 38.462 18.83 0.00 0.00 5.36
2048 3041 2.743636 TGAAGGTAGAAGGCTTGACG 57.256 50.000 3.46 0.00 0.00 4.35
2132 3126 8.495148 TCACAAACATATATCACATTACGATGC 58.505 33.333 0.00 0.00 36.72 3.91
2415 3417 7.523293 TCAGAAGATAACAAGGCAAAATCAA 57.477 32.000 0.00 0.00 0.00 2.57
2452 3454 5.505181 TCTGGCAAAAAGAAGTATCTCCT 57.495 39.130 0.00 0.00 33.77 3.69
2504 3506 3.070115 ATGAGGGGCATGCACAAAA 57.930 47.368 23.88 6.18 35.42 2.44
2505 3507 1.350071 ATGAGGGGCATGCACAAAAA 58.650 45.000 23.88 4.12 35.42 1.94
2526 3528 6.698008 AAAGTGTCATCAAAACTCACATCA 57.302 33.333 0.00 0.00 0.00 3.07
2538 3540 7.381948 TCAAAACTCACATCAATTTCCATTTCG 59.618 33.333 0.00 0.00 0.00 3.46
2557 3559 4.015872 TCGTAGGAGTTTTCAAATGGCT 57.984 40.909 0.00 0.00 0.00 4.75
2658 3663 6.419484 TGATAGGTTCAGAAACAGTTCTCA 57.581 37.500 0.00 0.00 42.45 3.27
2659 3664 7.009179 TGATAGGTTCAGAAACAGTTCTCAT 57.991 36.000 0.00 0.00 42.45 2.90
2660 3665 6.875726 TGATAGGTTCAGAAACAGTTCTCATG 59.124 38.462 0.00 0.00 42.45 3.07
2661 3666 5.296151 AGGTTCAGAAACAGTTCTCATGA 57.704 39.130 0.00 0.00 42.45 3.07
2663 3668 5.762218 AGGTTCAGAAACAGTTCTCATGAAG 59.238 40.000 0.00 0.00 42.45 3.02
2665 3670 6.038714 GGTTCAGAAACAGTTCTCATGAAGTT 59.961 38.462 0.00 0.00 42.45 2.66
2666 3671 6.851222 TCAGAAACAGTTCTCATGAAGTTC 57.149 37.500 0.00 0.00 42.45 3.01
2668 3673 6.481313 TCAGAAACAGTTCTCATGAAGTTCAG 59.519 38.462 11.91 4.09 42.45 3.02
2828 3861 5.279406 CCATCAGGTGCAAAGGAAATTACAA 60.279 40.000 0.00 0.00 0.00 2.41
2896 3929 4.077822 CAACAGAAGGCCAGAAAATCTCT 58.922 43.478 5.01 0.00 33.23 3.10
2926 3959 1.349357 ACCAGAGGAGAAAACAGAGGC 59.651 52.381 0.00 0.00 0.00 4.70
2929 3962 1.627834 AGAGGAGAAAACAGAGGCCAG 59.372 52.381 5.01 0.00 0.00 4.85
2966 3999 4.148891 CGTCGCTGAAGTGTAAAATTTCC 58.851 43.478 0.00 0.00 0.00 3.13
2976 4010 4.575645 AGTGTAAAATTTCCGACACCGAAA 59.424 37.500 19.49 0.00 42.55 3.46
2984 4018 3.226346 TCCGACACCGAAATAGAACAG 57.774 47.619 0.00 0.00 38.22 3.16
2989 4023 4.684703 CGACACCGAAATAGAACAGAACTT 59.315 41.667 0.00 0.00 38.22 2.66
2993 4027 4.819630 ACCGAAATAGAACAGAACTTGCAA 59.180 37.500 0.00 0.00 0.00 4.08
3041 4075 5.207768 CAACTTGATCTTGAAAGTGAACCG 58.792 41.667 0.00 0.00 36.75 4.44
3043 4077 5.607477 ACTTGATCTTGAAAGTGAACCGTA 58.393 37.500 0.00 0.00 35.34 4.02
3070 4104 3.633525 ACGATCATGGTGCATGCTTTAAT 59.366 39.130 20.33 4.63 41.18 1.40
3072 4106 4.023450 CGATCATGGTGCATGCTTTAATCT 60.023 41.667 20.33 0.00 41.18 2.40
3159 4217 3.055819 TGACAAGGTTCTAGCTAAGCCAG 60.056 47.826 9.62 5.32 0.00 4.85
3169 4227 8.030106 GGTTCTAGCTAAGCCAGTGTATATAAG 58.970 40.741 0.00 0.00 0.00 1.73
3191 4249 1.952296 AGTTCTGCTGCTTGTTTCCAG 59.048 47.619 0.00 0.00 0.00 3.86
3195 4253 1.891150 CTGCTGCTTGTTTCCAGGAAT 59.109 47.619 1.58 0.00 0.00 3.01
3213 4271 9.784531 TCCAGGAATAAACAAGATATTCTCATC 57.215 33.333 6.32 0.00 38.96 2.92
3233 4291 8.830580 TCTCATCTGTAATTAAACTAGCATTGC 58.169 33.333 0.00 0.00 0.00 3.56
3235 4293 8.615211 TCATCTGTAATTAAACTAGCATTGCAG 58.385 33.333 11.91 8.74 40.21 4.41
3252 4310 6.614160 CATTGCAGTTCAAACATAGATGTCA 58.386 36.000 0.00 0.00 40.80 3.58
3255 4313 5.530543 TGCAGTTCAAACATAGATGTCACAA 59.469 36.000 0.00 0.00 40.80 3.33
3256 4314 6.039159 TGCAGTTCAAACATAGATGTCACAAA 59.961 34.615 0.00 0.00 40.80 2.83
3313 4371 8.474577 GCATGCAAGATAAACTGAATTAAATCG 58.525 33.333 14.21 0.00 0.00 3.34
3358 4417 2.231478 CCTACATATGGGAGTACTGCGG 59.769 54.545 8.41 0.00 0.00 5.69
3441 4500 0.320374 CGTCCTGAGCACCCTAAACA 59.680 55.000 0.00 0.00 0.00 2.83
3487 4551 0.914417 CCAAGGTAGCCAGGAGGGAA 60.914 60.000 0.00 0.00 40.01 3.97
3489 4553 1.065126 CAAGGTAGCCAGGAGGGAAAG 60.065 57.143 0.00 0.00 40.01 2.62
3508 4573 2.745968 AGAGGAATCAGGTGGTCTCTC 58.254 52.381 0.00 0.00 0.00 3.20
3533 4598 8.225416 TCAGAAGTATACCATCTAAGCCTCTAA 58.775 37.037 8.12 0.00 0.00 2.10
3534 4599 8.519526 CAGAAGTATACCATCTAAGCCTCTAAG 58.480 40.741 8.12 0.00 0.00 2.18
3593 4659 8.336235 TGATGGAATGGAATAAGTTAAGAACCT 58.664 33.333 0.00 0.00 0.00 3.50
3647 4714 0.250038 TGAGACCTCACTTGCTGCAC 60.250 55.000 0.00 0.00 34.14 4.57
3707 4780 5.596836 TCAACTTTCATTCTTTGCTGGTT 57.403 34.783 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
190 880 5.642491 GGTACTCCTACCAAAACTTGATGAC 59.358 44.000 0.00 0.00 42.16 3.06
282 976 0.670162 CCCAGTGCCAAACTTGACTG 59.330 55.000 0.00 0.00 36.83 3.51
415 1119 7.443272 TCACTGGCTATATTTTGACATCAGATG 59.557 37.037 9.03 9.03 0.00 2.90
434 1138 2.906354 ACCGTTAGATTCATCACTGGC 58.094 47.619 0.00 0.00 0.00 4.85
577 1310 4.202274 TGAAATCAAACTCACGTACAGGGA 60.202 41.667 0.00 0.00 0.00 4.20
640 1373 9.381038 AGAGGTAATGATAGTTTGCTTCCTATA 57.619 33.333 0.00 0.00 0.00 1.31
679 1653 8.552296 AGATGATTTAGACCCTTCAACAATAGT 58.448 33.333 0.00 0.00 0.00 2.12
781 1755 8.840321 CATTACATTTGAATTGGGAGTACTAGG 58.160 37.037 0.00 0.00 0.00 3.02
795 1769 9.985318 CAAGAAAAACAAAGCATTACATTTGAA 57.015 25.926 4.79 0.00 38.42 2.69
802 1776 9.532697 CATTATGCAAGAAAAACAAAGCATTAC 57.467 29.630 0.00 0.00 42.16 1.89
803 1777 9.486497 TCATTATGCAAGAAAAACAAAGCATTA 57.514 25.926 0.00 0.00 42.16 1.90
887 1863 9.312904 TCCAAGTCCTTTCAAATTTCAATATCT 57.687 29.630 0.00 0.00 0.00 1.98
888 1864 9.927668 TTCCAAGTCCTTTCAAATTTCAATATC 57.072 29.630 0.00 0.00 0.00 1.63
903 1886 4.074970 CAGCATACAAGTTCCAAGTCCTT 58.925 43.478 0.00 0.00 0.00 3.36
907 1890 3.146104 AGCAGCATACAAGTTCCAAGT 57.854 42.857 0.00 0.00 0.00 3.16
922 1905 4.578105 AGCTTAAATATCCAGTCAAGCAGC 59.422 41.667 6.86 0.00 40.58 5.25
923 1906 5.505324 GCAGCTTAAATATCCAGTCAAGCAG 60.505 44.000 6.86 0.25 40.58 4.24
967 1951 8.962884 TTGAGAATGATAATCGAGATGGAAAA 57.037 30.769 0.00 0.00 0.00 2.29
978 1962 6.263842 TCATTGTGCCCTTGAGAATGATAATC 59.736 38.462 0.00 0.00 30.05 1.75
982 1966 3.952323 CTCATTGTGCCCTTGAGAATGAT 59.048 43.478 0.00 0.00 39.36 2.45
988 1972 0.524862 GTGCTCATTGTGCCCTTGAG 59.475 55.000 8.14 0.00 39.87 3.02
991 1975 0.467844 TGTGTGCTCATTGTGCCCTT 60.468 50.000 8.14 0.00 0.00 3.95
993 1977 0.890542 TCTGTGTGCTCATTGTGCCC 60.891 55.000 8.14 0.00 0.00 5.36
1030 2014 3.736720 TGCTGTCAGGAGCAATGATATC 58.263 45.455 1.14 0.00 46.05 1.63
1070 2054 0.482446 ATGGGCTGAAGGTTGTGGAA 59.518 50.000 0.00 0.00 0.00 3.53
1085 2069 7.223971 CAGATTTAGCATTGAACATTTGATGGG 59.776 37.037 0.00 0.00 33.60 4.00
1113 2097 3.686016 ACCATCTGCCGAACTGTAAATT 58.314 40.909 0.00 0.00 0.00 1.82
1133 2117 2.412089 GCATATGAGACGCGGGAAATAC 59.588 50.000 12.47 0.00 0.00 1.89
1218 2202 2.676342 GCATAATTTGGAGTTCGTCGGT 59.324 45.455 0.00 0.00 0.00 4.69
1219 2203 2.936498 AGCATAATTTGGAGTTCGTCGG 59.064 45.455 0.00 0.00 0.00 4.79
1247 2231 1.150536 AGGAAAGGCAAACCGCTGA 59.849 52.632 0.00 0.00 42.76 4.26
1311 2295 3.114809 CAACAGAGCAGAGATCGATGAC 58.885 50.000 0.54 0.00 0.00 3.06
1346 2330 1.003355 CCTTGACCACCATCGCTGT 60.003 57.895 0.00 0.00 0.00 4.40
1351 2335 2.787473 TCATGACCTTGACCACCATC 57.213 50.000 0.00 0.00 0.00 3.51
1366 2350 7.259290 TGAGATCATGTGAATGTTCATCATG 57.741 36.000 20.20 20.20 41.99 3.07
1448 2432 3.084039 TGCTCACTGAAATCCATGGAAC 58.916 45.455 20.67 13.65 0.00 3.62
1450 2434 2.942752 GCTGCTCACTGAAATCCATGGA 60.943 50.000 18.88 18.88 0.00 3.41
1485 2469 4.262164 GCAATCCCAAGTTGTTCAGACAAT 60.262 41.667 1.45 0.00 46.63 2.71
1677 2661 6.175471 TGCCATATATGTCCTAAGCAATGAG 58.825 40.000 11.73 0.00 0.00 2.90
1728 2715 2.478872 TGGTCAGAGGAAGGGGATAG 57.521 55.000 0.00 0.00 0.00 2.08
1817 2807 5.493133 TTCTCGTTTTGCTACATGTTGTT 57.507 34.783 2.30 0.00 0.00 2.83
1818 2808 5.238432 TCATTCTCGTTTTGCTACATGTTGT 59.762 36.000 2.30 0.00 0.00 3.32
1819 2809 5.688823 TCATTCTCGTTTTGCTACATGTTG 58.311 37.500 2.30 2.50 0.00 3.33
1900 2892 3.515502 CAGAGTGATCACCCTACTTTCCA 59.484 47.826 22.21 0.00 0.00 3.53
2210 3205 8.483758 TGTATAGATTTTCCCTTCACCTTAGTC 58.516 37.037 0.00 0.00 0.00 2.59
2368 3370 7.776107 TGAACATGGTCTCTTCACTAGATTAG 58.224 38.462 12.94 0.00 30.92 1.73
2369 3371 7.615757 TCTGAACATGGTCTCTTCACTAGATTA 59.384 37.037 12.94 0.00 30.92 1.75
2415 3417 3.972133 TGCCAGAATCAATTCCAGATGT 58.028 40.909 0.00 0.00 37.51 3.06
2452 3454 6.365970 AAAGAGATAGCAAGTTCTGGAGAA 57.634 37.500 0.00 0.00 0.00 2.87
2504 3506 6.698008 TTGATGTGAGTTTTGATGACACTT 57.302 33.333 0.00 0.00 33.41 3.16
2505 3507 6.889301 ATTGATGTGAGTTTTGATGACACT 57.111 33.333 0.00 0.00 33.41 3.55
2518 3520 6.316140 TCCTACGAAATGGAAATTGATGTGAG 59.684 38.462 0.00 0.00 0.00 3.51
2526 3528 7.519032 TGAAAACTCCTACGAAATGGAAATT 57.481 32.000 0.00 0.00 31.23 1.82
2538 3540 5.703876 CTTCAGCCATTTGAAAACTCCTAC 58.296 41.667 0.00 0.00 36.69 3.18
2557 3559 2.760634 TTTGCATCCGTAGAGCTTCA 57.239 45.000 0.00 0.00 0.00 3.02
2657 3662 4.276678 TGACAAAGGCTTCTGAACTTCATG 59.723 41.667 0.00 0.00 0.00 3.07
2658 3663 4.464008 TGACAAAGGCTTCTGAACTTCAT 58.536 39.130 0.00 0.00 0.00 2.57
2659 3664 3.879295 CTGACAAAGGCTTCTGAACTTCA 59.121 43.478 0.00 1.22 0.00 3.02
2660 3665 3.304324 GCTGACAAAGGCTTCTGAACTTC 60.304 47.826 0.00 0.00 0.00 3.01
2661 3666 2.620585 GCTGACAAAGGCTTCTGAACTT 59.379 45.455 0.00 0.00 0.00 2.66
2663 3668 1.949525 TGCTGACAAAGGCTTCTGAAC 59.050 47.619 0.00 3.15 0.00 3.18
2665 3670 2.574006 ATGCTGACAAAGGCTTCTGA 57.426 45.000 0.00 0.00 0.00 3.27
2666 3671 2.818432 AGAATGCTGACAAAGGCTTCTG 59.182 45.455 0.00 4.08 30.79 3.02
2668 3673 3.572584 CAAGAATGCTGACAAAGGCTTC 58.427 45.455 0.00 0.00 0.00 3.86
2828 3861 0.249784 CATGCTCCTCTATGCGCAGT 60.250 55.000 18.32 6.92 35.66 4.40
2863 3896 4.081087 TGGCCTTCTGTTGTTCTAGTATCC 60.081 45.833 3.32 0.00 0.00 2.59
2896 3929 1.203087 TCTCCTCTGGTTTCGGTACCA 60.203 52.381 13.54 8.87 45.73 3.25
2926 3959 1.673665 GGAGCTGAAGTGGTGCTGG 60.674 63.158 0.00 0.00 37.16 4.85
2929 3962 2.029844 GACGGAGCTGAAGTGGTGC 61.030 63.158 0.00 0.00 0.00 5.01
2955 3988 5.692613 ATTTCGGTGTCGGAAATTTTACA 57.307 34.783 8.67 0.00 37.43 2.41
2966 3999 4.235360 AGTTCTGTTCTATTTCGGTGTCG 58.765 43.478 0.00 0.00 37.82 4.35
2976 4010 7.201767 GCTATCCATTTGCAAGTTCTGTTCTAT 60.202 37.037 0.00 0.00 0.00 1.98
2984 4018 4.970662 TCTGCTATCCATTTGCAAGTTC 57.029 40.909 0.00 0.00 36.22 3.01
2989 4023 2.026641 GCCTTCTGCTATCCATTTGCA 58.973 47.619 0.00 0.00 36.87 4.08
2993 4027 2.106166 CTCTGGCCTTCTGCTATCCATT 59.894 50.000 3.32 0.00 40.92 3.16
3041 4075 4.530388 CATGCACCATGATCGTTCATTAC 58.470 43.478 6.24 0.00 43.81 1.89
3043 4077 2.223641 GCATGCACCATGATCGTTCATT 60.224 45.455 14.21 0.00 43.81 2.57
3070 4104 5.717178 ACTAGAACTCTACATGGCAAGAAGA 59.283 40.000 0.00 0.00 0.00 2.87
3072 4106 5.724328 CACTAGAACTCTACATGGCAAGAA 58.276 41.667 0.00 0.00 0.00 2.52
3159 4217 7.707035 ACAAGCAGCAGAACTACTTATATACAC 59.293 37.037 0.00 0.00 29.67 2.90
3169 4227 2.878406 TGGAAACAAGCAGCAGAACTAC 59.122 45.455 0.00 0.00 37.44 2.73
3213 4271 8.236586 TGAACTGCAATGCTAGTTTAATTACAG 58.763 33.333 18.70 2.58 37.27 2.74
3229 4287 6.207221 TGTGACATCTATGTTTGAACTGCAAT 59.793 34.615 0.00 0.00 41.95 3.56
3233 4291 6.580041 GCTTTGTGACATCTATGTTTGAACTG 59.420 38.462 0.00 0.00 41.95 3.16
3235 4293 6.672147 AGCTTTGTGACATCTATGTTTGAAC 58.328 36.000 0.00 0.00 41.95 3.18
3252 4310 1.202976 AGCATGAACAGGGAGCTTTGT 60.203 47.619 0.00 0.00 29.98 2.83
3255 4313 0.694771 TGAGCATGAACAGGGAGCTT 59.305 50.000 0.00 0.00 35.36 3.74
3256 4314 0.917533 ATGAGCATGAACAGGGAGCT 59.082 50.000 0.00 0.00 38.43 4.09
3278 4336 5.643777 AGTTTATCTTGCATGCTTAAGACGT 59.356 36.000 19.43 9.88 35.91 4.34
3313 4371 2.548057 TCACATCGCAACCTCAAACTTC 59.452 45.455 0.00 0.00 0.00 3.01
3358 4417 3.993234 CCACGCGCATCATCTCGC 61.993 66.667 5.73 0.00 46.98 5.03
3384 4443 2.505557 CGCCAGGACGTCCGTAAC 60.506 66.667 28.26 17.64 42.08 2.50
3441 4500 0.962356 CCTTCGCAATCCAAGCAGGT 60.962 55.000 0.00 0.00 39.02 4.00
3469 4533 0.991920 TTTCCCTCCTGGCTACCTTG 59.008 55.000 0.00 0.00 0.00 3.61
3487 4551 3.103742 GAGAGACCACCTGATTCCTCTT 58.896 50.000 0.00 0.00 31.86 2.85
3489 4553 2.430332 CTGAGAGACCACCTGATTCCTC 59.570 54.545 0.00 0.00 0.00 3.71
3508 4573 6.909550 AGAGGCTTAGATGGTATACTTCTG 57.090 41.667 15.06 5.01 35.44 3.02
3533 4598 3.942829 TCGAAATTGCATCAACTCCTCT 58.057 40.909 0.00 0.00 0.00 3.69
3534 4599 4.497006 CCATCGAAATTGCATCAACTCCTC 60.497 45.833 0.00 0.00 0.00 3.71
3544 4609 4.533919 ATTCAAACCCATCGAAATTGCA 57.466 36.364 0.00 0.00 0.00 4.08
3586 4652 7.771927 AGATCAATCAAAACATCAGGTTCTT 57.228 32.000 0.00 0.00 39.29 2.52
3707 4780 5.425217 TGTAGGCAGATTCTCTTGTTATGGA 59.575 40.000 0.00 0.00 0.00 3.41
3805 4884 3.350833 AGGTCTTTCAAGTGCATCCATC 58.649 45.455 0.00 0.00 0.00 3.51



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

AutoCloner maintained by Alex Coulton.