Multiple sequence alignment - TraesCS7D01G536400

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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 TraesCS7D01G536400 chr7D 100.000 3001 0 0 1 3001 628210408 628213408 0.000000e+00 5542.0
1 TraesCS7D01G536400 chr7D 95.000 40 2 0 2541 2580 418919026 418918987 2.500000e-06 63.9
2 TraesCS7D01G536400 chr7B 88.739 2291 127 61 166 2412 730818871 730816668 0.000000e+00 2680.0
3 TraesCS7D01G536400 chr7B 96.949 590 17 1 2412 3001 730816238 730815650 0.000000e+00 989.0
4 TraesCS7D01G536400 chr7A 92.886 1462 86 9 585 2032 724967796 724966339 0.000000e+00 2108.0
5 TraesCS7D01G536400 chr7A 95.517 870 26 5 2138 3001 724966164 724965302 0.000000e+00 1378.0
6 TraesCS7D01G536400 chr7A 84.400 500 40 15 72 551 724968275 724967794 9.810000e-125 457.0
7 TraesCS7D01G536400 chr7A 100.000 28 0 0 2075 2102 724966263 724966236 5.000000e-03 52.8
8 TraesCS7D01G536400 chr3D 92.449 874 52 9 2138 3001 29706116 29706985 0.000000e+00 1236.0
9 TraesCS7D01G536400 chr3D 86.559 930 120 4 1107 2032 29704998 29705926 0.000000e+00 1020.0
10 TraesCS7D01G536400 chr3D 83.750 80 6 4 2031 2110 29705970 29706042 5.370000e-08 69.4
11 TraesCS7D01G536400 chr3B 90.068 876 55 18 2138 3001 50937430 50938285 0.000000e+00 1107.0
12 TraesCS7D01G536400 chr3B 86.845 935 113 5 1107 2032 50932416 50933349 0.000000e+00 1037.0
13 TraesCS7D01G536400 chr3B 84.959 492 39 22 2138 2617 50933490 50933958 1.630000e-127 466.0
14 TraesCS7D01G536400 chr3B 86.563 387 30 3 2615 3001 50936662 50937026 1.000000e-109 407.0
15 TraesCS7D01G536400 chr3B 91.121 214 16 2 1822 2032 50937038 50937251 1.360000e-73 287.0
16 TraesCS7D01G536400 chr3B 100.000 37 0 0 2075 2111 50937327 50937363 5.370000e-08 69.4
17 TraesCS7D01G536400 chr3A 86.882 930 114 5 1109 2032 40362749 40363676 0.000000e+00 1035.0
18 TraesCS7D01G536400 chr3A 87.486 879 66 19 2138 3001 40363855 40364704 0.000000e+00 974.0


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 TraesCS7D01G536400 chr7D 628210408 628213408 3000 False 5542.000000 5542 100.00000 1 3001 1 chr7D.!!$F1 3000
1 TraesCS7D01G536400 chr7B 730815650 730818871 3221 True 1834.500000 2680 92.84400 166 3001 2 chr7B.!!$R1 2835
2 TraesCS7D01G536400 chr7A 724965302 724968275 2973 True 998.950000 2108 93.20075 72 3001 4 chr7A.!!$R1 2929
3 TraesCS7D01G536400 chr3D 29704998 29706985 1987 False 775.133333 1236 87.58600 1107 3001 3 chr3D.!!$F1 1894
4 TraesCS7D01G536400 chr3B 50932416 50938285 5869 False 562.233333 1107 89.92600 1107 3001 6 chr3B.!!$F1 1894
5 TraesCS7D01G536400 chr3A 40362749 40364704 1955 False 1004.500000 1035 87.18400 1109 3001 2 chr3A.!!$F1 1892

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
515 535 0.036858 GCTGGGTCTGTTCCTCACTC 60.037 60.0 0.00 0.0 0.00 3.51 F
562 582 0.108662 TAGTCGCACTCACATGGCTG 60.109 55.0 0.00 0.0 0.00 4.85 F
596 616 0.539438 GGTCAGGCCATGAACACCAA 60.539 55.0 5.01 0.0 45.69 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1316 1381 0.951558 CAAAGGCAGCACGGTTAAGT 59.048 50.000 0.00 0.00 0.00 2.24 R
1363 1428 0.954452 CAGCTGGAACCACTGTTTCC 59.046 55.000 5.57 4.62 33.97 3.13 R
2053 6071 3.380954 TGTGGCTATGTATGCACCATTTG 59.619 43.478 6.06 2.46 31.99 2.32 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
26 27 8.645814 TTGTCTGTGAAAATACCTCTAGTAGA 57.354 34.615 0.00 0.00 33.42 2.59
27 28 8.645814 TGTCTGTGAAAATACCTCTAGTAGAA 57.354 34.615 0.64 0.00 33.42 2.10
28 29 9.085645 TGTCTGTGAAAATACCTCTAGTAGAAA 57.914 33.333 0.64 0.00 33.42 2.52
29 30 9.924650 GTCTGTGAAAATACCTCTAGTAGAAAA 57.075 33.333 0.64 0.00 33.42 2.29
30 31 9.924650 TCTGTGAAAATACCTCTAGTAGAAAAC 57.075 33.333 0.64 0.00 33.42 2.43
31 32 9.706691 CTGTGAAAATACCTCTAGTAGAAAACA 57.293 33.333 0.64 0.00 33.42 2.83
59 60 9.965902 AAACAATATAGGATTCAACTTCACTCT 57.034 29.630 0.00 0.00 0.00 3.24
60 61 9.965902 AACAATATAGGATTCAACTTCACTCTT 57.034 29.630 0.00 0.00 0.00 2.85
61 62 9.965902 ACAATATAGGATTCAACTTCACTCTTT 57.034 29.630 0.00 0.00 0.00 2.52
65 66 6.179906 AGGATTCAACTTCACTCTTTCTCA 57.820 37.500 0.00 0.00 0.00 3.27
66 67 6.777782 AGGATTCAACTTCACTCTTTCTCAT 58.222 36.000 0.00 0.00 0.00 2.90
67 68 6.654161 AGGATTCAACTTCACTCTTTCTCATG 59.346 38.462 0.00 0.00 0.00 3.07
68 69 5.679734 TTCAACTTCACTCTTTCTCATGC 57.320 39.130 0.00 0.00 0.00 4.06
69 70 4.067896 TCAACTTCACTCTTTCTCATGCC 58.932 43.478 0.00 0.00 0.00 4.40
70 71 3.777106 ACTTCACTCTTTCTCATGCCA 57.223 42.857 0.00 0.00 0.00 4.92
71 72 4.090761 ACTTCACTCTTTCTCATGCCAA 57.909 40.909 0.00 0.00 0.00 4.52
72 73 4.464008 ACTTCACTCTTTCTCATGCCAAA 58.536 39.130 0.00 0.00 0.00 3.28
73 74 4.889409 ACTTCACTCTTTCTCATGCCAAAA 59.111 37.500 0.00 0.00 0.00 2.44
74 75 5.537674 ACTTCACTCTTTCTCATGCCAAAAT 59.462 36.000 0.00 0.00 0.00 1.82
75 76 6.716628 ACTTCACTCTTTCTCATGCCAAAATA 59.283 34.615 0.00 0.00 0.00 1.40
79 80 8.084073 TCACTCTTTCTCATGCCAAAATAAAAG 58.916 33.333 0.00 0.00 0.00 2.27
95 96 9.039870 CAAAATAAAAGACAAAGTGCCAACATA 57.960 29.630 0.00 0.00 0.00 2.29
106 107 2.862541 TGCCAACATAGCACTCAACTT 58.137 42.857 0.00 0.00 34.69 2.66
116 117 9.502091 AACATAGCACTCAACTTTCAGTTATTA 57.498 29.630 0.00 0.00 36.03 0.98
135 136 8.832735 AGTTATTACTGAATTACCCTTCTTCCA 58.167 33.333 0.00 0.00 31.99 3.53
138 143 7.996098 TTACTGAATTACCCTTCTTCCAAAG 57.004 36.000 0.00 0.00 0.00 2.77
141 146 7.066781 ACTGAATTACCCTTCTTCCAAAGAAA 58.933 34.615 3.92 0.00 46.13 2.52
156 161 9.423061 CTTCCAAAGAAAACAAATATACCCTTG 57.577 33.333 0.00 0.00 0.00 3.61
158 163 9.589461 TCCAAAGAAAACAAATATACCCTTGTA 57.411 29.630 0.00 0.00 34.71 2.41
159 164 9.634163 CCAAAGAAAACAAATATACCCTTGTAC 57.366 33.333 0.00 0.00 34.71 2.90
160 165 9.337091 CAAAGAAAACAAATATACCCTTGTACG 57.663 33.333 0.00 0.00 34.71 3.67
161 166 8.625786 AAGAAAACAAATATACCCTTGTACGT 57.374 30.769 0.00 0.00 34.71 3.57
162 167 9.723601 AAGAAAACAAATATACCCTTGTACGTA 57.276 29.630 0.00 0.00 34.71 3.57
163 168 9.723601 AGAAAACAAATATACCCTTGTACGTAA 57.276 29.630 0.00 0.00 34.71 3.18
209 214 1.066908 CACGCATCTCTCCTTCCTCTC 59.933 57.143 0.00 0.00 0.00 3.20
217 222 0.686112 CTCCTTCCTCTCCTTCCGCT 60.686 60.000 0.00 0.00 0.00 5.52
224 229 2.010582 CTCTCCTTCCGCTTCCCGAG 62.011 65.000 0.00 0.00 40.02 4.63
282 287 1.622607 CCCATTGACCTCCGCCTGTA 61.623 60.000 0.00 0.00 0.00 2.74
290 295 4.753662 TCCGCCTGTACTCCCGCT 62.754 66.667 0.00 0.00 0.00 5.52
292 297 3.141488 CGCCTGTACTCCCGCTCT 61.141 66.667 0.00 0.00 0.00 4.09
294 299 2.052690 GCCTGTACTCCCGCTCTCA 61.053 63.158 0.00 0.00 0.00 3.27
307 322 1.737355 GCTCTCATCTCCGCTGCTCT 61.737 60.000 0.00 0.00 0.00 4.09
368 388 1.815421 CGCCTATCGCCTGCAAGTT 60.815 57.895 0.00 0.00 0.00 2.66
369 389 1.723870 GCCTATCGCCTGCAAGTTG 59.276 57.895 0.00 0.00 0.00 3.16
438 458 4.176851 GCGACCTCGACCTCGACC 62.177 72.222 10.46 0.00 44.22 4.79
449 469 3.764466 CTCGACCGCCCTTGCTCT 61.764 66.667 0.00 0.00 34.43 4.09
515 535 0.036858 GCTGGGTCTGTTCCTCACTC 60.037 60.000 0.00 0.00 0.00 3.51
548 568 2.356382 CTGCTGTCTCCTTACCTAGTCG 59.644 54.545 0.00 0.00 0.00 4.18
560 580 0.807667 CCTAGTCGCACTCACATGGC 60.808 60.000 0.00 0.00 0.00 4.40
561 581 0.174389 CTAGTCGCACTCACATGGCT 59.826 55.000 0.00 0.00 0.00 4.75
562 582 0.108662 TAGTCGCACTCACATGGCTG 60.109 55.000 0.00 0.00 0.00 4.85
563 583 2.743538 TCGCACTCACATGGCTGC 60.744 61.111 0.00 0.00 0.00 5.25
564 584 3.051479 CGCACTCACATGGCTGCA 61.051 61.111 0.50 0.00 0.00 4.41
565 585 2.875485 GCACTCACATGGCTGCAG 59.125 61.111 10.11 10.11 0.00 4.41
566 586 1.970114 GCACTCACATGGCTGCAGT 60.970 57.895 16.64 0.00 0.00 4.40
582 602 1.793258 CAGTCTGCAGAAGTGGTCAG 58.207 55.000 20.19 0.00 0.00 3.51
583 603 0.683973 AGTCTGCAGAAGTGGTCAGG 59.316 55.000 20.19 0.00 0.00 3.86
584 604 0.952984 GTCTGCAGAAGTGGTCAGGC 60.953 60.000 20.19 0.00 0.00 4.85
585 605 1.673665 CTGCAGAAGTGGTCAGGCC 60.674 63.158 8.42 0.00 37.90 5.19
586 606 2.401699 CTGCAGAAGTGGTCAGGCCA 62.402 60.000 8.42 0.00 46.95 5.36
594 614 4.002797 GGTCAGGCCATGAACACC 57.997 61.111 5.01 0.75 45.69 4.16
595 615 1.074775 GGTCAGGCCATGAACACCA 59.925 57.895 5.01 0.00 45.69 4.17
596 616 0.539438 GGTCAGGCCATGAACACCAA 60.539 55.000 5.01 0.00 45.69 3.67
597 617 1.549203 GTCAGGCCATGAACACCAAT 58.451 50.000 5.01 0.00 40.43 3.16
598 618 1.203052 GTCAGGCCATGAACACCAATG 59.797 52.381 5.01 0.00 40.43 2.82
599 619 1.203038 TCAGGCCATGAACACCAATGT 60.203 47.619 5.01 0.00 42.46 2.71
600 620 3.401637 TCAGGCCATGAACACCAATGTG 61.402 50.000 5.01 0.00 39.71 3.21
619 639 1.332195 GGGGTTGCTTTCTTTCAGCT 58.668 50.000 0.00 0.00 38.19 4.24
728 750 6.311690 GCAATGAAGAGAACTACAGGAACTAC 59.688 42.308 0.00 0.00 36.02 2.73
777 827 4.858850 TCCAGTGTCAATGCCAATAATCT 58.141 39.130 0.00 0.00 0.00 2.40
808 858 1.604378 CTGATTTCGCCCTCCCAGT 59.396 57.895 0.00 0.00 0.00 4.00
828 878 7.040961 TCCCAGTAACCTAAAAATGAAAGTTCG 60.041 37.037 0.00 0.00 0.00 3.95
884 944 9.905171 CGGTTACATCATCTATATCCAGATATG 57.095 37.037 9.90 0.00 35.71 1.78
916 976 1.532868 GCAAGTTGAGCTGTGTACTGG 59.467 52.381 7.16 0.00 0.00 4.00
918 978 1.051812 AGTTGAGCTGTGTACTGGCT 58.948 50.000 0.00 7.33 39.16 4.75
1016 1081 6.348704 CCCAAATCAATGGCAAGAAATTTGAC 60.349 38.462 20.26 0.00 39.26 3.18
1017 1082 6.348704 CCAAATCAATGGCAAGAAATTTGACC 60.349 38.462 20.26 0.00 36.62 4.02
1029 1094 5.127491 AGAAATTTGACCACTCGTAAACCA 58.873 37.500 0.00 0.00 0.00 3.67
1079 1144 4.023365 GTGCTTCTGCTTCATCTGTCTTTT 60.023 41.667 0.00 0.00 40.48 2.27
1132 1197 5.227569 TCTGTTTCTCAGCTTATGGACAA 57.772 39.130 0.00 0.00 43.32 3.18
1267 1332 6.483974 TCGAAACTTGTGGCAACTTTATCTAA 59.516 34.615 0.00 0.00 37.61 2.10
1270 1335 7.759489 AACTTGTGGCAACTTTATCTAATCA 57.241 32.000 0.00 0.00 37.61 2.57
1311 1376 2.079158 GTGTGAATCTGCAGCAAGCTA 58.921 47.619 9.47 0.00 45.94 3.32
1316 1381 3.055891 TGAATCTGCAGCAAGCTACACTA 60.056 43.478 9.47 0.00 45.94 2.74
1601 1669 6.258727 CAGATTTTGTAGCTTACCGTCATCAT 59.741 38.462 0.00 0.00 0.00 2.45
1889 1960 4.093556 CCGTCCAGAGAAGAAGCAAATAAC 59.906 45.833 0.00 0.00 0.00 1.89
2040 6058 5.414454 TGTACTCCTATTGGTGTGCATTTTC 59.586 40.000 13.32 0.00 43.73 2.29
2053 6071 6.305638 GGTGTGCATTTTCGAAAGATTTCTAC 59.694 38.462 10.98 6.64 41.60 2.59
2062 6085 5.938322 TCGAAAGATTTCTACAAATGGTGC 58.062 37.500 3.98 0.00 31.94 5.01
2063 6086 5.471797 TCGAAAGATTTCTACAAATGGTGCA 59.528 36.000 3.98 0.00 31.94 4.57
2064 6087 6.150976 TCGAAAGATTTCTACAAATGGTGCAT 59.849 34.615 0.00 0.00 31.94 3.96
2065 6088 7.335673 TCGAAAGATTTCTACAAATGGTGCATA 59.664 33.333 0.00 0.00 31.94 3.14
2066 6089 7.429340 CGAAAGATTTCTACAAATGGTGCATAC 59.571 37.037 0.00 0.00 31.94 2.39
2067 6090 7.701539 AAGATTTCTACAAATGGTGCATACA 57.298 32.000 0.00 0.00 31.94 2.29
2068 6091 7.886629 AGATTTCTACAAATGGTGCATACAT 57.113 32.000 0.00 0.00 31.94 2.29
2069 6092 8.978874 AGATTTCTACAAATGGTGCATACATA 57.021 30.769 7.20 0.00 31.94 2.29
2070 6093 9.060347 AGATTTCTACAAATGGTGCATACATAG 57.940 33.333 7.20 6.32 31.94 2.23
2071 6094 6.618287 TTCTACAAATGGTGCATACATAGC 57.382 37.500 7.20 0.00 0.00 2.97
2072 6095 5.063204 TCTACAAATGGTGCATACATAGCC 58.937 41.667 7.20 0.00 0.00 3.93
2073 6096 3.630168 ACAAATGGTGCATACATAGCCA 58.370 40.909 7.20 0.00 0.00 4.75
2157 6226 6.183347 CCTTTAGAAACCTCTGAATGACCAT 58.817 40.000 0.00 0.00 32.70 3.55
2191 6260 6.935208 AGTGTATTGAAGAAAAGAGGTACACC 59.065 38.462 8.26 0.00 40.71 4.16
2216 6290 8.680903 CCAGATACATTTTCTTATTTGCAGACT 58.319 33.333 0.00 0.00 0.00 3.24
2280 6359 9.914834 ACATTCAGGCCTTAAGTATACATTTAA 57.085 29.630 0.00 1.81 0.00 1.52
2339 6421 6.231211 ACTGAAGGTACAATGTCTGTAAAGG 58.769 40.000 0.00 0.00 42.23 3.11
2618 7132 6.515531 CGCATTGGCAATTCTATCTGGTAATT 60.516 38.462 10.65 0.00 41.24 1.40
2791 7309 4.437239 AGCATTGCAGTATCGATATAGGC 58.563 43.478 11.91 12.66 0.00 3.93
2807 7325 7.718314 TCGATATAGGCTTCTGTACTAGAACAA 59.282 37.037 0.00 0.00 40.43 2.83
2818 7336 7.576236 TCTGTACTAGAACAACTACGTGTTAC 58.424 38.462 0.00 0.00 41.78 2.50
2831 7349 8.482429 CAACTACGTGTTACTTTAGTGGTTAAG 58.518 37.037 0.00 0.00 35.35 1.85
2834 7352 5.693555 ACGTGTTACTTTAGTGGTTAAGAGC 59.306 40.000 0.00 0.00 0.00 4.09
2835 7353 5.924825 CGTGTTACTTTAGTGGTTAAGAGCT 59.075 40.000 0.00 0.00 0.00 4.09
2993 7511 3.876914 TGTTTGGCAGCCTATCTTTATCG 59.123 43.478 14.15 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.924650 TTTTCTACTAGAGGTATTTTCACAGAC 57.075 33.333 0.00 0.00 0.00 3.51
5 6 9.706691 TGTTTTCTACTAGAGGTATTTTCACAG 57.293 33.333 0.00 0.00 0.00 3.66
33 34 9.965902 AGAGTGAAGTTGAATCCTATATTGTTT 57.034 29.630 0.00 0.00 0.00 2.83
34 35 9.965902 AAGAGTGAAGTTGAATCCTATATTGTT 57.034 29.630 0.00 0.00 0.00 2.83
35 36 9.965902 AAAGAGTGAAGTTGAATCCTATATTGT 57.034 29.630 0.00 0.00 0.00 2.71
39 40 9.035890 TGAGAAAGAGTGAAGTTGAATCCTATA 57.964 33.333 0.00 0.00 0.00 1.31
40 41 7.911651 TGAGAAAGAGTGAAGTTGAATCCTAT 58.088 34.615 0.00 0.00 0.00 2.57
41 42 7.303182 TGAGAAAGAGTGAAGTTGAATCCTA 57.697 36.000 0.00 0.00 0.00 2.94
42 43 6.179906 TGAGAAAGAGTGAAGTTGAATCCT 57.820 37.500 0.00 0.00 0.00 3.24
43 44 6.622462 GCATGAGAAAGAGTGAAGTTGAATCC 60.622 42.308 0.00 0.00 0.00 3.01
44 45 6.313252 GCATGAGAAAGAGTGAAGTTGAATC 58.687 40.000 0.00 0.00 0.00 2.52
45 46 5.182760 GGCATGAGAAAGAGTGAAGTTGAAT 59.817 40.000 0.00 0.00 0.00 2.57
46 47 4.516698 GGCATGAGAAAGAGTGAAGTTGAA 59.483 41.667 0.00 0.00 0.00 2.69
47 48 4.067896 GGCATGAGAAAGAGTGAAGTTGA 58.932 43.478 0.00 0.00 0.00 3.18
48 49 3.817084 TGGCATGAGAAAGAGTGAAGTTG 59.183 43.478 0.00 0.00 0.00 3.16
49 50 4.090761 TGGCATGAGAAAGAGTGAAGTT 57.909 40.909 0.00 0.00 0.00 2.66
50 51 3.777106 TGGCATGAGAAAGAGTGAAGT 57.223 42.857 0.00 0.00 0.00 3.01
51 52 5.443185 TTTTGGCATGAGAAAGAGTGAAG 57.557 39.130 0.00 0.00 0.00 3.02
52 53 7.523293 TTATTTTGGCATGAGAAAGAGTGAA 57.477 32.000 0.00 0.00 0.00 3.18
53 54 7.523293 TTTATTTTGGCATGAGAAAGAGTGA 57.477 32.000 0.00 0.00 0.00 3.41
54 55 8.084073 TCTTTTATTTTGGCATGAGAAAGAGTG 58.916 33.333 0.00 0.00 30.84 3.51
55 56 8.084684 GTCTTTTATTTTGGCATGAGAAAGAGT 58.915 33.333 0.00 0.00 33.92 3.24
56 57 8.084073 TGTCTTTTATTTTGGCATGAGAAAGAG 58.916 33.333 0.00 4.82 33.92 2.85
57 58 7.950512 TGTCTTTTATTTTGGCATGAGAAAGA 58.049 30.769 0.00 0.00 31.61 2.52
58 59 8.592105 TTGTCTTTTATTTTGGCATGAGAAAG 57.408 30.769 0.00 0.00 0.00 2.62
59 60 8.954950 TTTGTCTTTTATTTTGGCATGAGAAA 57.045 26.923 0.00 0.00 0.00 2.52
60 61 8.203485 ACTTTGTCTTTTATTTTGGCATGAGAA 58.797 29.630 0.00 0.00 0.00 2.87
61 62 7.652909 CACTTTGTCTTTTATTTTGGCATGAGA 59.347 33.333 0.00 0.00 0.00 3.27
62 63 7.569957 GCACTTTGTCTTTTATTTTGGCATGAG 60.570 37.037 0.00 0.00 0.00 2.90
63 64 6.202570 GCACTTTGTCTTTTATTTTGGCATGA 59.797 34.615 0.00 0.00 0.00 3.07
64 65 6.365050 GCACTTTGTCTTTTATTTTGGCATG 58.635 36.000 0.00 0.00 0.00 4.06
65 66 5.469760 GGCACTTTGTCTTTTATTTTGGCAT 59.530 36.000 0.00 0.00 0.00 4.40
66 67 4.813697 GGCACTTTGTCTTTTATTTTGGCA 59.186 37.500 0.00 0.00 0.00 4.92
67 68 4.813697 TGGCACTTTGTCTTTTATTTTGGC 59.186 37.500 0.00 0.00 0.00 4.52
68 69 6.314896 TGTTGGCACTTTGTCTTTTATTTTGG 59.685 34.615 0.00 0.00 0.00 3.28
69 70 7.301068 TGTTGGCACTTTGTCTTTTATTTTG 57.699 32.000 0.00 0.00 0.00 2.44
70 71 9.260002 CTATGTTGGCACTTTGTCTTTTATTTT 57.740 29.630 0.00 0.00 0.00 1.82
71 72 7.384932 GCTATGTTGGCACTTTGTCTTTTATTT 59.615 33.333 0.00 0.00 0.00 1.40
72 73 6.868339 GCTATGTTGGCACTTTGTCTTTTATT 59.132 34.615 0.00 0.00 0.00 1.40
73 74 6.015519 TGCTATGTTGGCACTTTGTCTTTTAT 60.016 34.615 0.00 0.00 34.56 1.40
74 75 5.300539 TGCTATGTTGGCACTTTGTCTTTTA 59.699 36.000 0.00 0.00 34.56 1.52
75 76 4.099266 TGCTATGTTGGCACTTTGTCTTTT 59.901 37.500 0.00 0.00 34.56 2.27
116 117 6.200878 TCTTTGGAAGAAGGGTAATTCAGT 57.799 37.500 0.00 0.00 33.83 3.41
128 129 9.374711 AGGGTATATTTGTTTTCTTTGGAAGAA 57.625 29.630 0.00 0.00 45.30 2.52
129 130 8.950007 AGGGTATATTTGTTTTCTTTGGAAGA 57.050 30.769 0.00 0.00 35.26 2.87
130 131 9.423061 CAAGGGTATATTTGTTTTCTTTGGAAG 57.577 33.333 0.00 0.00 32.61 3.46
134 135 9.337091 CGTACAAGGGTATATTTGTTTTCTTTG 57.663 33.333 0.00 0.00 38.41 2.77
135 136 9.070179 ACGTACAAGGGTATATTTGTTTTCTTT 57.930 29.630 0.00 0.00 38.41 2.52
167 172 3.150767 CGTGGTGATAGGGTTGGAAAAA 58.849 45.455 0.00 0.00 0.00 1.94
168 173 2.785562 CGTGGTGATAGGGTTGGAAAA 58.214 47.619 0.00 0.00 0.00 2.29
169 174 1.612199 GCGTGGTGATAGGGTTGGAAA 60.612 52.381 0.00 0.00 0.00 3.13
173 178 1.358725 CGTGCGTGGTGATAGGGTTG 61.359 60.000 0.00 0.00 0.00 3.77
258 263 1.815421 CGGAGGTCAATGGGAAGCG 60.815 63.158 0.00 0.00 0.00 4.68
268 273 1.681327 GGAGTACAGGCGGAGGTCA 60.681 63.158 0.00 0.00 0.00 4.02
282 287 1.826054 CGGAGATGAGAGCGGGAGT 60.826 63.158 0.00 0.00 0.00 3.85
294 299 2.841988 GGGGAGAGCAGCGGAGAT 60.842 66.667 0.00 0.00 0.00 2.75
321 336 1.821332 GAGCAGAAGATTGGGGCGG 60.821 63.158 0.00 0.00 0.00 6.13
322 337 2.176273 CGAGCAGAAGATTGGGGCG 61.176 63.158 0.00 0.00 0.00 6.13
323 338 2.476320 GCGAGCAGAAGATTGGGGC 61.476 63.158 0.00 0.00 0.00 5.80
324 339 1.821332 GGCGAGCAGAAGATTGGGG 60.821 63.158 0.00 0.00 0.00 4.96
486 506 1.910772 AGACCCAGCAAGAGACGCT 60.911 57.895 0.00 0.00 41.47 5.07
515 535 3.333804 GAGACAGCAGGAAAGAAAGGAG 58.666 50.000 0.00 0.00 0.00 3.69
548 568 1.919956 GACTGCAGCCATGTGAGTGC 61.920 60.000 15.27 0.00 36.42 4.40
562 582 0.250038 TGACCACTTCTGCAGACTGC 60.250 55.000 18.03 20.86 45.29 4.40
563 583 1.607509 CCTGACCACTTCTGCAGACTG 60.608 57.143 18.03 14.38 0.00 3.51
564 584 0.683973 CCTGACCACTTCTGCAGACT 59.316 55.000 18.03 0.82 0.00 3.24
565 585 0.952984 GCCTGACCACTTCTGCAGAC 60.953 60.000 18.03 4.16 0.00 3.51
566 586 1.372683 GCCTGACCACTTCTGCAGA 59.627 57.895 13.74 13.74 0.00 4.26
582 602 0.247185 CCACATTGGTGTTCATGGCC 59.753 55.000 0.00 0.00 43.71 5.36
583 603 0.247185 CCCACATTGGTGTTCATGGC 59.753 55.000 0.00 0.00 43.71 4.40
584 604 0.896923 CCCCACATTGGTGTTCATGG 59.103 55.000 0.00 0.00 43.71 3.66
585 605 1.631405 ACCCCACATTGGTGTTCATG 58.369 50.000 0.00 0.00 43.71 3.07
586 606 1.969923 CAACCCCACATTGGTGTTCAT 59.030 47.619 0.00 0.00 43.71 2.57
587 607 1.407936 CAACCCCACATTGGTGTTCA 58.592 50.000 0.00 0.00 43.71 3.18
588 608 0.033366 GCAACCCCACATTGGTGTTC 59.967 55.000 0.00 0.00 43.71 3.18
589 609 0.398381 AGCAACCCCACATTGGTGTT 60.398 50.000 0.00 0.00 43.71 3.32
590 610 0.398381 AAGCAACCCCACATTGGTGT 60.398 50.000 0.00 0.00 43.71 4.16
591 611 0.758123 AAAGCAACCCCACATTGGTG 59.242 50.000 0.00 0.00 44.85 4.17
592 612 1.047801 GAAAGCAACCCCACATTGGT 58.952 50.000 0.00 0.00 39.38 3.67
593 613 1.341080 AGAAAGCAACCCCACATTGG 58.659 50.000 0.00 0.00 37.25 3.16
594 614 3.181467 TGAAAGAAAGCAACCCCACATTG 60.181 43.478 0.00 0.00 0.00 2.82
595 615 3.037549 TGAAAGAAAGCAACCCCACATT 58.962 40.909 0.00 0.00 0.00 2.71
596 616 2.629617 CTGAAAGAAAGCAACCCCACAT 59.370 45.455 0.00 0.00 34.07 3.21
597 617 2.031120 CTGAAAGAAAGCAACCCCACA 58.969 47.619 0.00 0.00 34.07 4.17
598 618 1.269778 GCTGAAAGAAAGCAACCCCAC 60.270 52.381 0.00 0.00 40.52 4.61
599 619 1.039856 GCTGAAAGAAAGCAACCCCA 58.960 50.000 0.00 0.00 40.52 4.96
600 620 1.332195 AGCTGAAAGAAAGCAACCCC 58.668 50.000 0.00 0.00 43.37 4.95
619 639 5.176590 GCCGCATGATTTCTTTTGTACAAAA 59.823 36.000 27.42 27.42 37.90 2.44
728 750 7.253983 GCAATGAGTTTGATGTTGCTATGATTG 60.254 37.037 0.00 0.00 41.30 2.67
756 805 4.641541 TCAGATTATTGGCATTGACACTGG 59.358 41.667 7.10 0.00 0.00 4.00
808 858 8.398878 ACATCCGAACTTTCATTTTTAGGTTA 57.601 30.769 0.00 0.00 0.00 2.85
828 878 4.574599 AAGTGAGCTTTGTTTGACATCC 57.425 40.909 0.00 0.00 0.00 3.51
884 944 4.035675 AGCTCAACTTGCAGTGAGTAAAAC 59.964 41.667 19.38 7.73 30.96 2.43
910 970 1.734163 AACATTGCGGTAGCCAGTAC 58.266 50.000 0.00 0.00 44.33 2.73
911 971 2.419021 GGTAACATTGCGGTAGCCAGTA 60.419 50.000 0.00 0.00 44.33 2.74
916 976 1.014352 CAGGGTAACATTGCGGTAGC 58.986 55.000 0.00 0.00 41.37 3.58
918 978 3.162448 GCAGGGTAACATTGCGGTA 57.838 52.632 0.00 0.00 38.63 4.02
985 1050 5.456779 TCTTGCCATTGATTTGGGATCATA 58.543 37.500 0.00 0.00 36.93 2.15
990 1055 5.502089 AATTTCTTGCCATTGATTTGGGA 57.498 34.783 0.00 0.00 37.24 4.37
991 1056 5.706369 TCAAATTTCTTGCCATTGATTTGGG 59.294 36.000 0.00 0.00 37.24 4.12
1016 1081 4.985538 ACTCTATCTGGTTTACGAGTGG 57.014 45.455 0.00 0.00 31.19 4.00
1017 1082 6.432607 TGTACTCTATCTGGTTTACGAGTG 57.567 41.667 0.00 0.00 34.06 3.51
1029 1094 9.570488 GTCGAATTGTTAACTTGTACTCTATCT 57.430 33.333 7.22 0.00 0.00 1.98
1051 1116 0.038251 ATGAAGCAGAAGCACGTCGA 60.038 50.000 0.00 0.00 45.49 4.20
1132 1197 2.285368 TCCATCTTGGACCCGCCT 60.285 61.111 0.00 0.00 42.67 5.52
1267 1332 2.769621 TCGCATCCCTGCCCTGAT 60.770 61.111 0.00 0.00 46.07 2.90
1311 1376 1.607251 GGCAGCACGGTTAAGTAGTGT 60.607 52.381 0.00 0.00 38.10 3.55
1316 1381 0.951558 CAAAGGCAGCACGGTTAAGT 59.048 50.000 0.00 0.00 0.00 2.24
1363 1428 0.954452 CAGCTGGAACCACTGTTTCC 59.046 55.000 5.57 4.62 33.97 3.13
1601 1669 3.749064 GAGTGGACGAGCGCTGGA 61.749 66.667 26.95 0.00 0.00 3.86
1889 1960 3.653344 TCTTGTGTGATCCTGTTCTTCG 58.347 45.455 0.00 0.00 0.00 3.79
1928 1999 6.387513 TGAAGCCTAGTATTACACCCCAATAA 59.612 38.462 0.00 0.00 0.00 1.40
2040 6058 5.698832 TGCACCATTTGTAGAAATCTTTCG 58.301 37.500 0.00 0.00 41.92 3.46
2053 6071 3.380954 TGTGGCTATGTATGCACCATTTG 59.619 43.478 6.06 2.46 31.99 2.32
2065 6088 9.212593 TGTATGGATATATGTATGTGGCTATGT 57.787 33.333 0.00 0.00 0.00 2.29
2068 6091 9.267071 AGTTGTATGGATATATGTATGTGGCTA 57.733 33.333 0.00 0.00 0.00 3.93
2069 6092 8.043113 CAGTTGTATGGATATATGTATGTGGCT 58.957 37.037 0.00 0.00 0.00 4.75
2070 6093 7.824289 ACAGTTGTATGGATATATGTATGTGGC 59.176 37.037 0.00 0.00 0.00 5.01
2169 6238 7.159372 TCTGGTGTACCTCTTTTCTTCAATAC 58.841 38.462 2.32 0.00 36.82 1.89
2280 6359 9.290988 ACAGTAGATATCGACTCTGATGTTTAT 57.709 33.333 14.81 0.00 29.21 1.40
2339 6421 6.629128 CCACCTCTGTCTATGATCATACATC 58.371 44.000 11.49 5.86 0.00 3.06
2516 7030 4.559300 GCATGCTGTTATTTCCACAGTTGT 60.559 41.667 11.37 0.00 43.21 3.32
2764 7282 8.140628 CCTATATCGATACTGCAATGCTAGATT 58.859 37.037 7.41 0.00 0.00 2.40
2765 7283 7.656412 CCTATATCGATACTGCAATGCTAGAT 58.344 38.462 7.41 0.00 0.00 1.98
2766 7284 6.460261 GCCTATATCGATACTGCAATGCTAGA 60.460 42.308 7.41 0.00 0.00 2.43
2767 7285 5.689514 GCCTATATCGATACTGCAATGCTAG 59.310 44.000 7.41 4.98 0.00 3.42
2791 7309 6.666417 ACACGTAGTTGTTCTAGTACAGAAG 58.334 40.000 2.27 0.00 41.43 2.85


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

AutoCloner maintained by Alex Coulton.