Multiple sequence alignment - TraesCS4D01G117500

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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 TraesCS4D01G117500 chr4D 100.000 3734 0 0 1 3734 98016759 98013026 0.000000e+00 6896.0
1 TraesCS4D01G117500 chr4D 87.928 1226 107 12 1548 2772 374041175 374039990 0.000000e+00 1406.0
2 TraesCS4D01G117500 chr4D 81.510 1709 247 36 1162 2856 435198935 435197282 0.000000e+00 1341.0
3 TraesCS4D01G117500 chr4D 79.760 1418 251 25 1342 2740 97962020 97960620 0.000000e+00 996.0
4 TraesCS4D01G117500 chr4D 86.982 676 68 13 899 1557 374049670 374048998 0.000000e+00 743.0
5 TraesCS4D01G117500 chr4A 94.947 2909 107 20 852 3734 478190929 478193823 0.000000e+00 4521.0
6 TraesCS4D01G117500 chr4A 85.513 1912 215 30 875 2767 90438989 90440857 0.000000e+00 1940.0
7 TraesCS4D01G117500 chr4A 86.813 273 34 2 3459 3730 678136105 678136376 1.690000e-78 303.0
8 TraesCS4D01G117500 chr4B 92.020 3020 167 29 1 2987 139594984 139592006 0.000000e+00 4174.0
9 TraesCS4D01G117500 chr4B 88.954 1358 133 10 912 2261 460157053 460155705 0.000000e+00 1661.0
10 TraesCS4D01G117500 chr4B 80.682 1760 265 46 1113 2856 535331731 535330031 0.000000e+00 1297.0
11 TraesCS4D01G117500 chr4B 89.418 567 38 7 3170 3734 139574477 139573931 0.000000e+00 695.0
12 TraesCS4D01G117500 chr4B 86.538 572 54 5 2307 2855 460155696 460155125 3.190000e-170 608.0
13 TraesCS4D01G117500 chr4B 100.000 44 0 0 3093 3136 139574517 139574474 8.600000e-12 82.4
14 TraesCS4D01G117500 chr4B 90.323 62 3 2 2998 3057 139574578 139574518 1.110000e-10 78.7
15 TraesCS4D01G117500 chr3B 83.104 1456 205 26 1117 2554 706028935 706027503 0.000000e+00 1288.0
16 TraesCS4D01G117500 chr3B 82.794 1174 171 24 1117 2270 706182854 706184016 0.000000e+00 1020.0
17 TraesCS4D01G117500 chr3D 82.716 1458 204 33 1117 2554 533960133 533958704 0.000000e+00 1253.0
18 TraesCS4D01G117500 chr3D 81.415 1512 243 28 1143 2635 535399957 535401449 0.000000e+00 1201.0
19 TraesCS4D01G117500 chr3D 81.370 1460 219 38 1117 2554 534115582 534117010 0.000000e+00 1140.0
20 TraesCS4D01G117500 chr3D 84.906 424 61 1 2308 2728 134963080 134962657 3.450000e-115 425.0
21 TraesCS4D01G117500 chr3D 73.256 430 73 34 437 838 382779085 382779500 6.550000e-23 119.0
22 TraesCS4D01G117500 chr7D 79.709 1513 242 35 1113 2594 63462316 63463794 0.000000e+00 1033.0
23 TraesCS4D01G117500 chr3A 80.618 939 146 22 1634 2558 670545603 670546519 0.000000e+00 693.0
24 TraesCS4D01G117500 chr2A 86.245 269 31 5 3463 3730 565374362 565374099 1.700000e-73 287.0
25 TraesCS4D01G117500 chr7B 77.283 427 61 21 446 851 43669207 43668796 6.280000e-53 219.0
26 TraesCS4D01G117500 chr5D 77.030 431 66 25 434 845 466490542 466490126 2.260000e-52 217.0
27 TraesCS4D01G117500 chr5A 75.198 379 65 18 436 798 689159226 689159591 6.460000e-33 152.0
28 TraesCS4D01G117500 chr6D 76.151 239 45 10 619 851 267730226 267729994 8.470000e-22 115.0
29 TraesCS4D01G117500 chr1B 76.033 242 40 13 437 662 45482276 45482515 3.940000e-20 110.0
30 TraesCS4D01G117500 chr1B 76.033 242 40 13 437 662 45542646 45542885 3.940000e-20 110.0
31 TraesCS4D01G117500 chr1B 76.033 242 40 13 437 662 45599925 45600164 3.940000e-20 110.0
32 TraesCS4D01G117500 chr1B 76.033 242 40 13 437 662 45624623 45624862 3.940000e-20 110.0
33 TraesCS4D01G117500 chr2D 97.059 34 1 0 3566 3599 198631224 198631257 1.450000e-04 58.4
34 TraesCS4D01G117500 chr2B 87.755 49 5 1 700 748 506219136 506219089 5.210000e-04 56.5


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 TraesCS4D01G117500 chr4D 98013026 98016759 3733 True 6896.000000 6896 100.000 1 3734 1 chr4D.!!$R2 3733
1 TraesCS4D01G117500 chr4D 374039990 374041175 1185 True 1406.000000 1406 87.928 1548 2772 1 chr4D.!!$R3 1224
2 TraesCS4D01G117500 chr4D 435197282 435198935 1653 True 1341.000000 1341 81.510 1162 2856 1 chr4D.!!$R5 1694
3 TraesCS4D01G117500 chr4D 97960620 97962020 1400 True 996.000000 996 79.760 1342 2740 1 chr4D.!!$R1 1398
4 TraesCS4D01G117500 chr4D 374048998 374049670 672 True 743.000000 743 86.982 899 1557 1 chr4D.!!$R4 658
5 TraesCS4D01G117500 chr4A 478190929 478193823 2894 False 4521.000000 4521 94.947 852 3734 1 chr4A.!!$F2 2882
6 TraesCS4D01G117500 chr4A 90438989 90440857 1868 False 1940.000000 1940 85.513 875 2767 1 chr4A.!!$F1 1892
7 TraesCS4D01G117500 chr4B 139592006 139594984 2978 True 4174.000000 4174 92.020 1 2987 1 chr4B.!!$R1 2986
8 TraesCS4D01G117500 chr4B 535330031 535331731 1700 True 1297.000000 1297 80.682 1113 2856 1 chr4B.!!$R2 1743
9 TraesCS4D01G117500 chr4B 460155125 460157053 1928 True 1134.500000 1661 87.746 912 2855 2 chr4B.!!$R4 1943
10 TraesCS4D01G117500 chr4B 139573931 139574578 647 True 285.366667 695 93.247 2998 3734 3 chr4B.!!$R3 736
11 TraesCS4D01G117500 chr3B 706027503 706028935 1432 True 1288.000000 1288 83.104 1117 2554 1 chr3B.!!$R1 1437
12 TraesCS4D01G117500 chr3B 706182854 706184016 1162 False 1020.000000 1020 82.794 1117 2270 1 chr3B.!!$F1 1153
13 TraesCS4D01G117500 chr3D 533958704 533960133 1429 True 1253.000000 1253 82.716 1117 2554 1 chr3D.!!$R2 1437
14 TraesCS4D01G117500 chr3D 535399957 535401449 1492 False 1201.000000 1201 81.415 1143 2635 1 chr3D.!!$F3 1492
15 TraesCS4D01G117500 chr3D 534115582 534117010 1428 False 1140.000000 1140 81.370 1117 2554 1 chr3D.!!$F2 1437
16 TraesCS4D01G117500 chr7D 63462316 63463794 1478 False 1033.000000 1033 79.709 1113 2594 1 chr7D.!!$F1 1481
17 TraesCS4D01G117500 chr3A 670545603 670546519 916 False 693.000000 693 80.618 1634 2558 1 chr3A.!!$F1 924

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
319 327 0.188342 ATGTCCCAGGTGGTTGCTTT 59.812 50.0 0.0 0.0 34.77 3.51 F
483 493 0.606673 GAAGCTCCCCTGACACCAAC 60.607 60.0 0.0 0.0 0.00 3.77 F
938 970 0.612229 CTGCTCCAGTCCACAGACAT 59.388 55.0 0.0 0.0 46.15 3.06 F
2148 2250 0.179015 TGGCTTTGGAGGTGCGTTTA 60.179 50.0 0.0 0.0 0.00 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1653 1704 0.622665 CCAAGTCCCTGCTCTCCATT 59.377 55.000 0.00 0.0 0.0 3.16 R
2127 2229 2.032528 CGCACCTCCAAAGCCAGA 59.967 61.111 0.00 0.0 0.0 3.86 R
2248 2350 4.131649 ACATGATGGTGCAAATGAATGG 57.868 40.909 0.00 0.0 0.0 3.16 R
3261 3439 0.594602 CTTCGGTTCCGGTTTTTCCC 59.405 55.000 11.37 0.0 0.0 3.97 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
42 43 6.109156 TGCATAGATAATATTGTCCGTGGT 57.891 37.500 8.45 0.00 0.00 4.16
47 48 5.548406 AGATAATATTGTCCGTGGTTAGCC 58.452 41.667 8.45 0.00 0.00 3.93
61 62 5.067954 GTGGTTAGCCTTCTAGGAACAAAA 58.932 41.667 0.00 0.00 37.67 2.44
67 68 4.822350 AGCCTTCTAGGAACAAAAGTTGAC 59.178 41.667 0.00 0.00 37.67 3.18
89 90 2.029918 TGTTCCACAGAGATGACGTCAG 60.030 50.000 24.41 12.12 0.00 3.51
95 96 0.534412 AGAGATGACGTCAGGCAAGG 59.466 55.000 24.41 0.00 39.91 3.61
105 106 2.079925 GTCAGGCAAGGTGAGCTTTAG 58.920 52.381 0.00 0.00 0.00 1.85
107 108 2.079925 CAGGCAAGGTGAGCTTTAGTC 58.920 52.381 0.00 0.00 0.00 2.59
115 116 5.036117 AGGTGAGCTTTAGTCTGTTGAAA 57.964 39.130 0.00 0.00 0.00 2.69
128 129 9.567776 TTAGTCTGTTGAAAATCACTTTGGATA 57.432 29.630 0.00 0.00 0.00 2.59
166 167 5.283717 CACATTGCACAAACTTATAAGTCGC 59.716 40.000 18.28 17.14 38.57 5.19
169 170 4.778904 TGCACAAACTTATAAGTCGCAAC 58.221 39.130 18.28 9.21 38.57 4.17
172 173 5.333798 GCACAAACTTATAAGTCGCAACTGA 60.334 40.000 18.28 0.00 38.57 3.41
177 178 4.929808 ACTTATAAGTCGCAACTGACCAAG 59.070 41.667 12.50 0.00 39.77 3.61
190 191 3.458487 ACTGACCAAGAAGTGTAGGGTTT 59.542 43.478 0.00 0.00 30.55 3.27
191 192 3.815401 CTGACCAAGAAGTGTAGGGTTTG 59.185 47.826 0.00 0.00 30.55 2.93
200 201 4.094830 AGTGTAGGGTTTGTTACCTTGG 57.905 45.455 0.00 0.00 46.86 3.61
207 208 5.718039 AGGGTTTGTTACCTTGGGAATTAA 58.282 37.500 0.00 0.00 46.86 1.40
208 209 5.541101 AGGGTTTGTTACCTTGGGAATTAAC 59.459 40.000 0.00 0.00 46.86 2.01
216 219 5.327737 ACCTTGGGAATTAACCAACACTA 57.672 39.130 9.41 0.00 42.75 2.74
234 237 7.533900 CCAACACTACTTCATTAATGTGTTTCG 59.466 37.037 14.97 6.55 43.27 3.46
262 265 8.257306 ACTCTCTTCTCCTTTCATAATCTTGAC 58.743 37.037 0.00 0.00 0.00 3.18
271 274 2.425668 TCATAATCTTGACGACAGCCGA 59.574 45.455 0.00 0.00 41.76 5.54
307 315 2.247372 TCTCCTCTCCACATATGTCCCA 59.753 50.000 5.07 0.00 0.00 4.37
319 327 0.188342 ATGTCCCAGGTGGTTGCTTT 59.812 50.000 0.00 0.00 34.77 3.51
351 359 8.710835 TTCCAATTAACAACTTGTCCTTTTTC 57.289 30.769 0.00 0.00 0.00 2.29
352 360 7.841956 TCCAATTAACAACTTGTCCTTTTTCA 58.158 30.769 0.00 0.00 0.00 2.69
383 393 8.922931 AATTGCTTGTCCTTTTTATTGGATTT 57.077 26.923 0.00 0.00 34.58 2.17
401 411 8.634335 TTGGATTTCAATCAATAACTGACTGA 57.366 30.769 2.04 0.00 38.50 3.41
402 412 8.044060 TGGATTTCAATCAATAACTGACTGAC 57.956 34.615 2.04 0.00 39.92 3.51
426 436 1.128200 TTAGTGGGCCACGAGCATAT 58.872 50.000 29.76 13.94 46.50 1.78
472 482 5.297029 GTGATACCAACATTTAGAAGCTCCC 59.703 44.000 0.00 0.00 0.00 4.30
473 483 3.087370 ACCAACATTTAGAAGCTCCCC 57.913 47.619 0.00 0.00 0.00 4.81
474 484 2.649816 ACCAACATTTAGAAGCTCCCCT 59.350 45.455 0.00 0.00 0.00 4.79
477 487 3.636153 ACATTTAGAAGCTCCCCTGAC 57.364 47.619 0.00 0.00 0.00 3.51
483 493 0.606673 GAAGCTCCCCTGACACCAAC 60.607 60.000 0.00 0.00 0.00 3.77
486 496 1.768684 GCTCCCCTGACACCAACTCA 61.769 60.000 0.00 0.00 0.00 3.41
489 499 1.566703 TCCCCTGACACCAACTCAAAA 59.433 47.619 0.00 0.00 0.00 2.44
564 574 9.344772 ACAACATATGTGTCTACAAAACCTAAA 57.655 29.630 9.63 0.00 41.93 1.85
611 628 1.972872 AAGAGACAAACCTGCTGTGG 58.027 50.000 0.00 0.00 0.00 4.17
616 633 2.906389 AGACAAACCTGCTGTGGATAGA 59.094 45.455 0.00 0.00 0.00 1.98
617 634 3.327757 AGACAAACCTGCTGTGGATAGAA 59.672 43.478 0.00 0.00 0.00 2.10
618 635 4.018960 AGACAAACCTGCTGTGGATAGAAT 60.019 41.667 0.00 0.00 0.00 2.40
626 643 6.599638 ACCTGCTGTGGATAGAATAGTTTTTC 59.400 38.462 0.00 0.00 0.00 2.29
653 670 9.630098 ACACTATTCATGCTTTTGTCTTTATTG 57.370 29.630 0.00 0.00 0.00 1.90
703 721 4.891627 TTTTTCTCTGTGCGTGATTTGA 57.108 36.364 0.00 0.00 0.00 2.69
768 786 7.647907 GTGAGCTTCACAAATTTTCATGAAT 57.352 32.000 9.40 0.00 46.22 2.57
769 787 8.080083 GTGAGCTTCACAAATTTTCATGAATT 57.920 30.769 9.40 0.00 46.22 2.17
770 788 8.553696 GTGAGCTTCACAAATTTTCATGAATTT 58.446 29.630 9.40 5.09 46.22 1.82
771 789 9.111613 TGAGCTTCACAAATTTTCATGAATTTT 57.888 25.926 9.40 9.65 37.17 1.82
772 790 9.940166 GAGCTTCACAAATTTTCATGAATTTTT 57.060 25.926 9.40 9.31 37.17 1.94
824 843 3.057174 CGAGTTGGTATCCTAGGAGCATC 60.057 52.174 18.34 8.49 0.00 3.91
831 850 4.464597 GGTATCCTAGGAGCATCTAAGTGG 59.535 50.000 18.34 0.00 33.73 4.00
838 860 3.643792 AGGAGCATCTAAGTGGTGTATCC 59.356 47.826 0.00 0.00 33.73 2.59
938 970 0.612229 CTGCTCCAGTCCACAGACAT 59.388 55.000 0.00 0.00 46.15 3.06
1653 1704 1.153647 CGGGCTCTGCAACGTCATA 60.154 57.895 0.00 0.00 0.00 2.15
1782 1833 1.227234 CCGGTGCGTGCAGATCATA 60.227 57.895 0.00 0.00 0.00 2.15
1874 1928 1.231068 CCCCTAATGGCACCTGCAT 59.769 57.895 0.00 0.00 44.36 3.96
1996 2071 3.432890 GCCTCATCTCCCCTTTAGTTCAG 60.433 52.174 0.00 0.00 0.00 3.02
2099 2201 2.951813 TGGGACAGGGGTGAGTCT 59.048 61.111 0.00 0.00 0.00 3.24
2148 2250 0.179015 TGGCTTTGGAGGTGCGTTTA 60.179 50.000 0.00 0.00 0.00 2.01
2239 2341 1.464198 AAGGTGAGGCCCCTGAAGT 60.464 57.895 0.00 0.00 38.26 3.01
2248 2350 1.751351 GGCCCCTGAAGTTTCTATTGC 59.249 52.381 0.00 0.00 0.00 3.56
2273 2378 4.968812 TCATTTGCACCATCATGTACTG 57.031 40.909 0.00 0.00 0.00 2.74
2868 3033 6.567050 AGCATGATTAGCCATTACAAGTTTG 58.433 36.000 0.00 0.00 0.00 2.93
2917 3082 5.988561 GGTTAGAATGCAAATTTTCACACCA 59.011 36.000 11.04 0.00 0.00 4.17
3015 3184 4.023450 TCGATAGATAGCCAAGGTGTAACG 60.023 45.833 0.00 0.00 42.67 3.18
3298 3476 4.287720 CGAAGCCTTGTCCAGTTTTTAAC 58.712 43.478 0.00 0.00 0.00 2.01
3307 3485 4.454847 TGTCCAGTTTTTAACGTGTGTTGA 59.545 37.500 0.00 0.00 39.12 3.18
3318 3496 5.493133 AACGTGTGTTGATCTTTTAGCAA 57.507 34.783 0.00 0.00 36.81 3.91
3374 3552 9.545105 TGTAAACTAGAAATCGAACCTTTAACA 57.455 29.630 0.00 0.00 0.00 2.41
3539 3718 6.296026 GTGGTAGTAATGGAGCCATTATCAA 58.704 40.000 21.22 9.94 46.44 2.57
3540 3719 6.942576 GTGGTAGTAATGGAGCCATTATCAAT 59.057 38.462 21.22 12.28 46.44 2.57
3604 3783 3.961477 TTGAAGGTCGTGTTGTCAATG 57.039 42.857 0.00 0.00 0.00 2.82
3631 3810 2.159881 GCACGTAGTTTAGCCAAGTTCG 60.160 50.000 0.00 0.30 41.61 3.95
3686 3866 1.613255 CGCCAACCCTACAACCAGAAT 60.613 52.381 0.00 0.00 0.00 2.40
3709 3889 7.722949 ATTGTATCCCACATTCTGTTGATTT 57.277 32.000 0.00 0.00 36.90 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 7.764443 ACCACGGACAATATTATCTATGCATAC 59.236 37.037 1.16 0.00 0.00 2.39
23 24 6.495872 AGGCTAACCACGGACAATATTATCTA 59.504 38.462 0.00 0.00 39.06 1.98
25 26 5.548406 AGGCTAACCACGGACAATATTATC 58.452 41.667 0.00 0.00 39.06 1.75
31 32 1.628846 AGAAGGCTAACCACGGACAAT 59.371 47.619 0.00 0.00 39.06 2.71
42 43 6.485648 GTCAACTTTTGTTCCTAGAAGGCTAA 59.514 38.462 0.00 0.00 41.35 3.09
47 48 6.927294 ACAGTCAACTTTTGTTCCTAGAAG 57.073 37.500 0.00 0.00 41.35 2.85
84 85 0.886490 AAAGCTCACCTTGCCTGACG 60.886 55.000 0.00 0.00 33.01 4.35
89 90 2.079925 CAGACTAAAGCTCACCTTGCC 58.920 52.381 0.00 0.00 33.01 4.52
95 96 6.853362 GTGATTTTCAACAGACTAAAGCTCAC 59.147 38.462 0.00 0.00 0.00 3.51
105 106 7.875971 AGTATCCAAAGTGATTTTCAACAGAC 58.124 34.615 0.00 0.00 0.00 3.51
107 108 9.533253 AAAAGTATCCAAAGTGATTTTCAACAG 57.467 29.630 0.00 0.00 0.00 3.16
136 137 8.514136 TTATAAGTTTGTGCAATGTGCTTTAC 57.486 30.769 1.43 0.00 45.31 2.01
137 138 8.356657 ACTTATAAGTTTGTGCAATGTGCTTTA 58.643 29.630 12.50 0.00 39.28 1.85
138 139 7.209475 ACTTATAAGTTTGTGCAATGTGCTTT 58.791 30.769 12.50 0.00 39.28 3.51
139 140 6.748132 ACTTATAAGTTTGTGCAATGTGCTT 58.252 32.000 12.50 0.00 39.28 3.91
140 141 6.331369 ACTTATAAGTTTGTGCAATGTGCT 57.669 33.333 12.50 0.00 39.28 4.40
141 142 5.283717 CGACTTATAAGTTTGTGCAATGTGC 59.716 40.000 18.96 1.44 41.02 4.57
142 143 5.283717 GCGACTTATAAGTTTGTGCAATGTG 59.716 40.000 18.96 0.75 39.88 3.21
143 144 5.049060 TGCGACTTATAAGTTTGTGCAATGT 60.049 36.000 18.96 0.00 39.88 2.71
144 145 5.389778 TGCGACTTATAAGTTTGTGCAATG 58.610 37.500 18.96 3.39 39.88 2.82
145 146 5.621197 TGCGACTTATAAGTTTGTGCAAT 57.379 34.783 18.96 0.00 39.88 3.56
146 147 5.008217 AGTTGCGACTTATAAGTTTGTGCAA 59.992 36.000 26.83 26.83 39.88 4.08
147 148 4.513692 AGTTGCGACTTATAAGTTTGTGCA 59.486 37.500 18.96 20.56 39.88 4.57
156 157 5.142061 TCTTGGTCAGTTGCGACTTATAA 57.858 39.130 3.02 0.00 36.12 0.98
161 162 1.139058 ACTTCTTGGTCAGTTGCGACT 59.861 47.619 0.00 0.00 36.12 4.18
166 167 3.181454 ACCCTACACTTCTTGGTCAGTTG 60.181 47.826 0.00 0.00 0.00 3.16
169 170 3.771577 AACCCTACACTTCTTGGTCAG 57.228 47.619 0.00 0.00 0.00 3.51
172 173 3.945640 ACAAACCCTACACTTCTTGGT 57.054 42.857 0.00 0.00 0.00 3.67
190 191 5.302313 GTGTTGGTTAATTCCCAAGGTAACA 59.698 40.000 9.21 3.10 42.44 2.41
191 192 5.537295 AGTGTTGGTTAATTCCCAAGGTAAC 59.463 40.000 9.21 6.71 42.44 2.50
207 208 7.817418 AACACATTAATGAAGTAGTGTTGGT 57.183 32.000 22.16 2.17 45.28 3.67
208 209 7.533900 CGAAACACATTAATGAAGTAGTGTTGG 59.466 37.037 22.16 11.58 45.99 3.77
228 231 1.964223 AGGAGAAGAGAGTGCGAAACA 59.036 47.619 0.00 0.00 0.00 2.83
234 237 6.581712 AGATTATGAAAGGAGAAGAGAGTGC 58.418 40.000 0.00 0.00 0.00 4.40
241 244 6.813649 TGTCGTCAAGATTATGAAAGGAGAAG 59.186 38.462 0.00 0.00 0.00 2.85
271 274 1.007721 AGGAGATCACTAGGGCTGTGT 59.992 52.381 0.00 0.00 36.83 3.72
307 315 6.926630 TGGAATTTATAAAAGCAACCACCT 57.073 33.333 1.21 0.00 0.00 4.00
360 370 7.504403 TGAAATCCAATAAAAAGGACAAGCAA 58.496 30.769 0.00 0.00 36.60 3.91
362 372 7.961325 TTGAAATCCAATAAAAAGGACAAGC 57.039 32.000 0.00 0.00 36.60 4.01
375 385 9.246670 TCAGTCAGTTATTGATTGAAATCCAAT 57.753 29.630 0.83 0.00 45.96 3.16
376 386 8.634335 TCAGTCAGTTATTGATTGAAATCCAA 57.366 30.769 0.83 0.00 45.96 3.53
392 402 5.246307 GCCCACTAAATTAGTCAGTCAGTT 58.754 41.667 2.14 0.00 36.76 3.16
394 404 4.192317 GGCCCACTAAATTAGTCAGTCAG 58.808 47.826 2.14 0.00 36.76 3.51
401 411 2.679930 GCTCGTGGCCCACTAAATTAGT 60.680 50.000 12.94 0.00 35.49 2.24
402 412 1.940613 GCTCGTGGCCCACTAAATTAG 59.059 52.381 12.94 0.00 34.27 1.73
434 444 3.655777 TGGTATCACCTGATATTTCCCCC 59.344 47.826 0.00 0.00 39.58 5.40
448 458 5.297029 GGGAGCTTCTAAATGTTGGTATCAC 59.703 44.000 0.00 0.00 0.00 3.06
466 476 1.462238 AGTTGGTGTCAGGGGAGCT 60.462 57.895 0.00 0.00 0.00 4.09
513 523 6.705381 TGAACATCCATGCTTTTTCGATTTTT 59.295 30.769 0.00 0.00 0.00 1.94
514 524 6.146021 GTGAACATCCATGCTTTTTCGATTTT 59.854 34.615 0.00 0.00 0.00 1.82
515 525 5.634859 GTGAACATCCATGCTTTTTCGATTT 59.365 36.000 0.00 0.00 0.00 2.17
516 526 5.163513 GTGAACATCCATGCTTTTTCGATT 58.836 37.500 0.00 0.00 0.00 3.34
517 527 4.218200 TGTGAACATCCATGCTTTTTCGAT 59.782 37.500 0.00 0.00 0.00 3.59
518 528 3.567585 TGTGAACATCCATGCTTTTTCGA 59.432 39.130 0.00 0.00 0.00 3.71
519 529 3.899734 TGTGAACATCCATGCTTTTTCG 58.100 40.909 0.00 0.00 0.00 3.46
520 530 5.049167 TGTTGTGAACATCCATGCTTTTTC 58.951 37.500 0.00 0.00 36.25 2.29
594 611 2.191128 ATCCACAGCAGGTTTGTCTC 57.809 50.000 0.00 0.00 0.00 3.36
601 618 5.700402 AAACTATTCTATCCACAGCAGGT 57.300 39.130 0.00 0.00 0.00 4.00
602 619 6.599244 TGAAAAACTATTCTATCCACAGCAGG 59.401 38.462 0.00 0.00 0.00 4.85
606 623 8.553459 AGTGTGAAAAACTATTCTATCCACAG 57.447 34.615 0.00 0.00 27.55 3.66
618 635 9.462174 CAAAAGCATGAATAGTGTGAAAAACTA 57.538 29.630 0.00 0.00 41.80 2.24
626 643 9.630098 AATAAAGACAAAAGCATGAATAGTGTG 57.370 29.630 0.00 0.00 0.00 3.82
694 712 8.470040 AAATTCAGATCCAAATTCAAATCACG 57.530 30.769 4.00 0.00 0.00 4.35
703 721 8.034804 CGAACCCTAAAAATTCAGATCCAAATT 58.965 33.333 0.00 0.00 0.00 1.82
802 821 2.307768 TGCTCCTAGGATACCAACTCG 58.692 52.381 13.12 0.00 37.17 4.18
803 822 4.156477 AGATGCTCCTAGGATACCAACTC 58.844 47.826 13.12 5.94 37.17 3.01
805 824 5.540719 ACTTAGATGCTCCTAGGATACCAAC 59.459 44.000 13.12 8.86 37.17 3.77
812 831 3.300388 CACCACTTAGATGCTCCTAGGA 58.700 50.000 11.98 11.98 0.00 2.94
814 833 5.047660 GGATACACCACTTAGATGCTCCTAG 60.048 48.000 0.00 0.00 38.79 3.02
824 843 7.310113 GGGAGAATATCAGGATACACCACTTAG 60.310 44.444 0.00 0.00 42.04 2.18
831 850 5.394663 CCGATGGGAGAATATCAGGATACAC 60.395 48.000 0.00 0.00 34.58 2.90
838 860 1.065854 GGGCCGATGGGAGAATATCAG 60.066 57.143 0.00 0.00 34.06 2.90
1513 1564 1.550976 GAAAGTGTCGGGGAGAGTGAT 59.449 52.381 0.00 0.00 0.00 3.06
1653 1704 0.622665 CCAAGTCCCTGCTCTCCATT 59.377 55.000 0.00 0.00 0.00 3.16
1782 1833 3.075134 AGATTTCTTCAAGGAAGCACCCT 59.925 43.478 0.00 0.00 39.29 4.34
1874 1928 2.449464 CATGCCCAATCTTCACCTTGA 58.551 47.619 0.00 0.00 0.00 3.02
2127 2229 2.032528 CGCACCTCCAAAGCCAGA 59.967 61.111 0.00 0.00 0.00 3.86
2239 2341 5.177326 GGTGCAAATGAATGGCAATAGAAA 58.823 37.500 0.00 0.00 39.57 2.52
2248 2350 4.131649 ACATGATGGTGCAAATGAATGG 57.868 40.909 0.00 0.00 0.00 3.16
2673 2817 8.274322 TCAGATCCTATTTTGAAGCTCCAAATA 58.726 33.333 0.00 2.34 36.12 1.40
2868 3033 5.211174 AGTTGGTTAGACCTGACAACTAC 57.789 43.478 6.58 0.00 46.88 2.73
2905 3070 6.669154 ACCATTCCATATCTGGTGTGAAAATT 59.331 34.615 0.00 0.00 41.65 1.82
2917 3082 7.946219 TGATGATTAAAGCACCATTCCATATCT 59.054 33.333 0.00 0.00 0.00 1.98
3091 3261 7.977293 CACCATTTCAAGATTAAAGCATGATGA 59.023 33.333 0.00 0.00 0.00 2.92
3254 3432 0.781278 TCCGGTTTTTCCCCCTTCAT 59.219 50.000 0.00 0.00 0.00 2.57
3261 3439 0.594602 CTTCGGTTCCGGTTTTTCCC 59.405 55.000 11.37 0.00 0.00 3.97
3298 3476 6.804534 TTTTTGCTAAAAGATCAACACACG 57.195 33.333 1.76 0.00 0.00 4.49
3363 3541 3.572255 TGGTGGCTCAATGTTAAAGGTTC 59.428 43.478 0.00 0.00 0.00 3.62
3374 3552 2.672996 GGCGTGTGGTGGCTCAAT 60.673 61.111 0.00 0.00 0.00 2.57
3461 3639 1.210155 GCATCCGAAGCAACCACAC 59.790 57.895 0.00 0.00 0.00 3.82
3569 3748 8.953990 CACGACCTTCAAAAGTAAAATTACAAG 58.046 33.333 6.13 1.07 36.12 3.16
3604 3783 2.803956 TGGCTAAACTACGTGCTTCAAC 59.196 45.455 0.00 0.00 0.00 3.18
3709 3889 5.471797 TCACAACCAAGCTTTATTCATCGAA 59.528 36.000 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.