Multiple sequence alignment - TraesCS4A01G326700

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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 TraesCS4A01G326700 chr4A 100.000 3514 0 0 1 3514 613583994 613580481 0.000000e+00 6490.0
1 TraesCS4A01G326700 chr4A 88.931 786 52 14 1911 2688 613675510 613676268 0.000000e+00 937.0
2 TraesCS4A01G326700 chr4A 90.221 542 38 5 1352 1888 613674891 613675422 0.000000e+00 693.0
3 TraesCS4A01G326700 chr5B 95.567 1015 41 2 2016 3030 694315233 694314223 0.000000e+00 1622.0
4 TraesCS4A01G326700 chr5B 93.366 829 52 2 1055 1883 694692608 694693433 0.000000e+00 1223.0
5 TraesCS4A01G326700 chr5B 95.484 620 28 0 1911 2530 694693532 694694151 0.000000e+00 990.0
6 TraesCS4A01G326700 chr5B 94.309 492 19 5 3030 3514 694314169 694313680 0.000000e+00 745.0
7 TraesCS4A01G326700 chr5B 84.698 745 92 17 1932 2672 222355961 222356687 0.000000e+00 725.0
8 TraesCS4A01G326700 chr5B 84.960 625 70 8 1 612 694691320 694691933 2.320000e-171 612.0
9 TraesCS4A01G326700 chr5B 86.538 468 61 2 1286 1752 222355333 222355799 6.730000e-142 514.0
10 TraesCS4A01G326700 chr5B 92.733 344 22 1 715 1058 694692086 694692426 8.760000e-136 494.0
11 TraesCS4A01G326700 chr5B 100.000 28 0 0 3077 3104 21599725 21599752 6.000000e-03 52.8
12 TraesCS4A01G326700 chr5B 100.000 28 0 0 3077 3104 483796822 483796795 6.000000e-03 52.8
13 TraesCS4A01G326700 chr5D 94.125 834 46 2 1055 1888 556141767 556140937 0.000000e+00 1266.0
14 TraesCS4A01G326700 chr5D 87.593 1072 110 15 1 1058 556143011 556141949 0.000000e+00 1221.0
15 TraesCS4A01G326700 chr5D 92.278 790 36 9 1911 2694 556140842 556140072 0.000000e+00 1098.0
16 TraesCS4A01G326700 chr5D 84.564 745 93 17 1932 2672 209303295 209304021 0.000000e+00 719.0
17 TraesCS4A01G326700 chr5D 85.487 503 60 10 1272 1765 209302653 209303151 2.420000e-141 512.0
18 TraesCS4A01G326700 chr5D 88.235 51 6 0 34 84 363978539 363978489 1.050000e-05 62.1
19 TraesCS4A01G326700 chr5A 86.475 732 80 14 1944 2672 270155041 270155756 0.000000e+00 785.0
20 TraesCS4A01G326700 chr5A 87.832 452 53 2 1303 1753 270154312 270154762 2.400000e-146 529.0
21 TraesCS4A01G326700 chr5A 79.470 151 20 6 871 1021 270151774 270151913 2.890000e-16 97.1
22 TraesCS4A01G326700 chr5A 94.286 35 2 0 3070 3104 169818494 169818460 2.000000e-03 54.7
23 TraesCS4A01G326700 chrUn 91.525 177 13 1 1712 1888 396811652 396811478 3.500000e-60 243.0
24 TraesCS4A01G326700 chrUn 91.525 177 13 1 1712 1888 428824225 428824051 3.500000e-60 243.0
25 TraesCS4A01G326700 chr6B 82.081 173 31 0 26 198 708590914 708590742 7.860000e-32 148.0
26 TraesCS4A01G326700 chr6B 94.286 35 2 0 3071 3105 472496382 472496416 2.000000e-03 54.7
27 TraesCS4A01G326700 chr3D 78.534 191 41 0 10 200 39904689 39904879 3.680000e-25 126.0
28 TraesCS4A01G326700 chr3D 96.875 32 1 0 3079 3110 477784794 477784763 2.000000e-03 54.7
29 TraesCS4A01G326700 chr7D 87.273 110 11 3 11 118 604503484 604503592 4.760000e-24 122.0
30 TraesCS4A01G326700 chr1B 79.290 169 33 2 32 200 357226972 357227138 2.220000e-22 117.0
31 TraesCS4A01G326700 chr3A 80.000 150 28 1 49 198 51441945 51442092 3.710000e-20 110.0
32 TraesCS4A01G326700 chr6D 78.344 157 33 1 49 205 29776294 29776449 2.230000e-17 100.0
33 TraesCS4A01G326700 chr6D 78.344 157 33 1 49 205 29839258 29839413 2.230000e-17 100.0
34 TraesCS4A01G326700 chr2B 90.698 43 3 1 3065 3107 769918448 769918489 4.900000e-04 56.5
35 TraesCS4A01G326700 chr3B 100.000 28 0 0 3077 3104 762017145 762017118 6.000000e-03 52.8
36 TraesCS4A01G326700 chr2A 94.118 34 2 0 3071 3104 621486752 621486785 6.000000e-03 52.8


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 TraesCS4A01G326700 chr4A 613580481 613583994 3513 True 6490.000000 6490 100.000000 1 3514 1 chr4A.!!$R1 3513
1 TraesCS4A01G326700 chr4A 613674891 613676268 1377 False 815.000000 937 89.576000 1352 2688 2 chr4A.!!$F1 1336
2 TraesCS4A01G326700 chr5B 694313680 694315233 1553 True 1183.500000 1622 94.938000 2016 3514 2 chr5B.!!$R2 1498
3 TraesCS4A01G326700 chr5B 694691320 694694151 2831 False 829.750000 1223 91.635750 1 2530 4 chr5B.!!$F3 2529
4 TraesCS4A01G326700 chr5B 222355333 222356687 1354 False 619.500000 725 85.618000 1286 2672 2 chr5B.!!$F2 1386
5 TraesCS4A01G326700 chr5D 556140072 556143011 2939 True 1195.000000 1266 91.332000 1 2694 3 chr5D.!!$R2 2693
6 TraesCS4A01G326700 chr5D 209302653 209304021 1368 False 615.500000 719 85.025500 1272 2672 2 chr5D.!!$F1 1400
7 TraesCS4A01G326700 chr5A 270151774 270155756 3982 False 470.366667 785 84.592333 871 2672 3 chr5A.!!$F1 1801

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
619 707 0.033109 ATGGCTTTCCTACTTGCCCC 60.033 55.0 0.00 0.00 44.32 5.80 F
677 765 0.178990 TAGCTATGCTCAGGCCGAGA 60.179 55.0 23.26 13.53 45.45 4.04 F
1032 1129 0.592637 TTTCAGTGTGCAAGCATCCG 59.407 50.0 0.00 0.00 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1690 3938 0.763652 CCACCTGCCTCATATCAGCT 59.236 55.000 0.0 0.0 0.00 4.24 R
1889 4146 1.006922 GCTGCTGAAGGTTGCCAAC 60.007 57.895 0.0 0.0 0.00 3.77 R
2753 5123 0.878523 CACCAACGAAGAGAACGGCA 60.879 55.000 0.0 0.0 34.93 5.69 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
40 42 7.805083 ACCTCTTCATAAGGCATAGTATCAT 57.195 36.000 0.00 0.00 37.42 2.45
161 163 7.972832 TCTATTTCCTCGTTTAATTGTGTGT 57.027 32.000 0.00 0.00 0.00 3.72
166 168 3.363575 CCTCGTTTAATTGTGTGTCACCG 60.364 47.826 0.00 0.00 32.73 4.94
167 169 2.544686 TCGTTTAATTGTGTGTCACCGG 59.455 45.455 0.00 0.00 32.73 5.28
201 203 7.564793 TGTCTAGTTGGTATGCATGATACTTT 58.435 34.615 10.16 0.00 37.64 2.66
213 227 5.476254 TGCATGATACTTTCATTGTGACCAA 59.524 36.000 0.00 0.00 42.62 3.67
229 243 2.598467 AACCTTGGCGTGGGTTGA 59.402 55.556 7.58 0.00 43.28 3.18
242 256 0.108041 GGGTTGACGGCGATCCTTTA 60.108 55.000 16.62 0.00 0.00 1.85
301 315 5.497464 TTCCGATGATAATCATGGCCTTA 57.503 39.130 3.32 0.00 37.20 2.69
304 318 3.308053 CGATGATAATCATGGCCTTAGCG 59.692 47.826 3.32 0.00 37.20 4.26
307 321 0.400213 TAATCATGGCCTTAGCGGGG 59.600 55.000 3.32 0.00 41.24 5.73
321 335 2.280457 GGGGCACTGATAGCTCGC 60.280 66.667 0.00 0.00 31.73 5.03
332 346 5.306394 ACTGATAGCTCGCAGTGTAGTATA 58.694 41.667 17.64 0.00 43.26 1.47
344 358 5.454187 GCAGTGTAGTATATTGGGTGCCTAA 60.454 44.000 0.00 0.00 0.00 2.69
367 381 0.319555 TGCCACTAACAGACACTCGC 60.320 55.000 0.00 0.00 0.00 5.03
377 391 1.446099 GACACTCGCGATGGAAGCA 60.446 57.895 10.36 0.00 34.19 3.91
385 399 0.595095 GCGATGGAAGCATGGGATTC 59.405 55.000 0.00 0.00 38.69 2.52
411 425 0.967887 TGGCGTCTTCTCTCCCTCTG 60.968 60.000 0.00 0.00 0.00 3.35
426 440 1.143305 CTCTGCGATTAATGGCTCCG 58.857 55.000 21.06 10.98 32.36 4.63
432 446 2.545113 GCGATTAATGGCTCCGTGACTA 60.545 50.000 14.51 0.00 0.00 2.59
439 453 1.681793 TGGCTCCGTGACTAGCTATTC 59.318 52.381 4.20 4.20 38.80 1.75
444 458 2.693591 TCCGTGACTAGCTATTCCTTGG 59.306 50.000 8.48 7.58 0.00 3.61
450 464 4.081642 TGACTAGCTATTCCTTGGTGTGTC 60.082 45.833 8.48 2.21 0.00 3.67
465 479 3.821033 GGTGTGTCTATGGTTTTCAGCTT 59.179 43.478 0.00 0.00 0.00 3.74
470 484 2.742053 TCTATGGTTTTCAGCTTGCGTC 59.258 45.455 0.00 0.00 0.00 5.19
472 486 1.092921 TGGTTTTCAGCTTGCGTCGT 61.093 50.000 0.00 0.00 0.00 4.34
486 500 4.316205 TGCGTCGTTATTATGTCTGGAT 57.684 40.909 0.00 0.00 0.00 3.41
488 502 4.037565 TGCGTCGTTATTATGTCTGGATCT 59.962 41.667 0.00 0.00 0.00 2.75
493 507 7.808381 CGTCGTTATTATGTCTGGATCTTATGT 59.192 37.037 0.00 0.00 0.00 2.29
505 519 7.443575 GTCTGGATCTTATGTGCTTACATCATT 59.556 37.037 0.00 0.00 0.00 2.57
509 523 8.623903 GGATCTTATGTGCTTACATCATTTTCA 58.376 33.333 0.00 0.00 0.00 2.69
513 527 6.822667 ATGTGCTTACATCATTTTCAGTGA 57.177 33.333 0.00 0.00 0.00 3.41
524 538 4.038282 TCATTTTCAGTGATTGCAACTGCT 59.962 37.500 11.44 2.85 42.66 4.24
526 540 2.259266 TCAGTGATTGCAACTGCTCA 57.741 45.000 11.44 4.40 42.66 4.26
529 543 2.033675 CAGTGATTGCAACTGCTCAACA 59.966 45.455 0.00 0.00 42.66 3.33
531 545 3.047796 GTGATTGCAACTGCTCAACAAG 58.952 45.455 0.00 0.00 42.66 3.16
608 622 3.119708 AGCGTTGATCTTTCATGGCTTTC 60.120 43.478 0.00 0.00 37.43 2.62
618 706 1.106285 CATGGCTTTCCTACTTGCCC 58.894 55.000 0.00 0.00 44.32 5.36
619 707 0.033109 ATGGCTTTCCTACTTGCCCC 60.033 55.000 0.00 0.00 44.32 5.80
620 708 1.379977 GGCTTTCCTACTTGCCCCC 60.380 63.158 0.00 0.00 39.49 5.40
641 729 3.362295 CGTGATTCTTTGTGTGTTGGTG 58.638 45.455 0.00 0.00 0.00 4.17
645 733 3.584406 TTCTTTGTGTGTTGGTGTTGG 57.416 42.857 0.00 0.00 0.00 3.77
646 734 2.520069 TCTTTGTGTGTTGGTGTTGGT 58.480 42.857 0.00 0.00 0.00 3.67
647 735 2.894126 TCTTTGTGTGTTGGTGTTGGTT 59.106 40.909 0.00 0.00 0.00 3.67
648 736 2.732412 TTGTGTGTTGGTGTTGGTTG 57.268 45.000 0.00 0.00 0.00 3.77
649 737 1.621992 TGTGTGTTGGTGTTGGTTGT 58.378 45.000 0.00 0.00 0.00 3.32
650 738 1.270826 TGTGTGTTGGTGTTGGTTGTG 59.729 47.619 0.00 0.00 0.00 3.33
651 739 1.271102 GTGTGTTGGTGTTGGTTGTGT 59.729 47.619 0.00 0.00 0.00 3.72
652 740 1.542030 TGTGTTGGTGTTGGTTGTGTC 59.458 47.619 0.00 0.00 0.00 3.67
670 758 4.202192 TGTGTCCATTCTAGCTATGCTCAG 60.202 45.833 0.00 0.00 40.44 3.35
677 765 0.178990 TAGCTATGCTCAGGCCGAGA 60.179 55.000 23.26 13.53 45.45 4.04
679 767 1.743321 GCTATGCTCAGGCCGAGACT 61.743 60.000 23.26 13.62 45.45 3.24
695 783 5.163509 GCCGAGACTGGATATATGCTCATTA 60.164 44.000 5.77 0.00 0.00 1.90
697 785 7.144661 CCGAGACTGGATATATGCTCATTATC 58.855 42.308 5.77 0.00 0.00 1.75
713 801 7.147320 TGCTCATTATCTTTTCTATCCCCTTCA 60.147 37.037 0.00 0.00 0.00 3.02
787 875 6.304445 ACAATTACACAAATTATGCGTTGACG 59.696 34.615 0.00 0.00 35.54 4.35
964 1053 0.865769 GTTGTTGCGTACTGAGGTGG 59.134 55.000 0.00 0.00 0.00 4.61
990 1079 1.000506 TGTAGCTTCTGAACCACGGAC 59.999 52.381 0.00 0.00 33.15 4.79
1001 1090 2.360350 CACGGACCCTGCAAGCAT 60.360 61.111 0.00 0.00 0.00 3.79
1032 1129 0.592637 TTTCAGTGTGCAAGCATCCG 59.407 50.000 0.00 0.00 0.00 4.18
1039 1136 2.030946 GTGTGCAAGCATCCGAGTAATC 59.969 50.000 0.00 0.00 0.00 1.75
1104 2401 2.629656 CGCCTCCCAAGCACCTTTG 61.630 63.158 0.00 0.00 0.00 2.77
1145 2442 1.477700 CAAAATCACGGTGATGGCCAT 59.522 47.619 20.96 20.96 37.15 4.40
1154 2451 1.380246 TGATGGCCATGGCTTCCAC 60.380 57.895 34.70 19.00 41.60 4.02
1177 2474 2.291741 GCCAAGTGAGTTCTGAACCAAG 59.708 50.000 16.48 8.08 0.00 3.61
1206 2503 9.294614 AGATTCATATGCCTATCTTTTCCTTTC 57.705 33.333 0.00 0.00 0.00 2.62
1228 3471 6.633500 TCATTGACCTTTACTTTGTCTTGG 57.367 37.500 0.00 0.00 0.00 3.61
1233 3476 8.561738 TTGACCTTTACTTTGTCTTGGATATC 57.438 34.615 0.00 0.00 0.00 1.63
1297 3540 2.179517 CACAGAGACCGAGTCGCC 59.820 66.667 7.12 0.68 37.67 5.54
1369 3612 1.808945 GCAGAGGACAACATTCTGGTG 59.191 52.381 3.26 0.00 41.80 4.17
1489 3737 0.827925 CCGAGGAGATCCCCGATGAA 60.828 60.000 4.15 0.00 36.42 2.57
1570 3818 6.837568 AGAAAATGCTCAATATCCTTGATGGT 59.162 34.615 0.00 0.00 37.07 3.55
1768 4021 2.042104 GCACTTGTGTCTGATTGTGC 57.958 50.000 0.00 0.00 42.69 4.57
1784 4041 0.954452 GTGCCACCCTTCTTTGTCAG 59.046 55.000 0.00 0.00 0.00 3.51
1797 4054 5.695851 TCTTTGTCAGAGCTTCCATTTTC 57.304 39.130 0.00 0.00 0.00 2.29
1802 4059 4.074970 GTCAGAGCTTCCATTTTCCTTGA 58.925 43.478 0.00 0.00 0.00 3.02
1823 4080 7.816031 CCTTGATTGATTGTTTTATTGCTCACT 59.184 33.333 0.00 0.00 0.00 3.41
1824 4081 9.199982 CTTGATTGATTGTTTTATTGCTCACTT 57.800 29.630 0.00 0.00 0.00 3.16
1844 4101 6.717997 TCACTTAAATAAAGGGAAGGGAACAC 59.282 38.462 0.00 0.00 44.85 3.32
1889 4146 6.705825 TGATATTACTTCGTTCATCCCATGTG 59.294 38.462 0.00 0.00 0.00 3.21
1973 4331 1.824852 GATCCAAAAACCGAGGCCAAT 59.175 47.619 5.01 0.00 0.00 3.16
2540 4902 9.517609 GTAAGATTTCAAGACACGAGTGTATAT 57.482 33.333 9.03 0.00 45.05 0.86
2674 5044 9.256477 TGACATAATTATACGAACACATCCTTC 57.744 33.333 0.00 0.00 0.00 3.46
2726 5096 4.019860 TGAGCTCCTTGATAGTTTTCTGCT 60.020 41.667 12.15 0.00 0.00 4.24
2753 5123 1.936203 GCAGCCGTCAATGTTGCATTT 60.936 47.619 0.00 0.00 34.99 2.32
2847 5217 1.697432 ACTTCATCTTCCCCAACGTCA 59.303 47.619 0.00 0.00 0.00 4.35
2852 5222 4.148838 TCATCTTCCCCAACGTCAAAATT 58.851 39.130 0.00 0.00 0.00 1.82
2869 5239 8.028938 CGTCAAAATTCCCTTGTTATTCTGATT 58.971 33.333 0.00 0.00 0.00 2.57
2885 5255 9.816354 TTATTCTGATTGATATTGTCTCGAACA 57.184 29.630 0.00 0.00 35.59 3.18
2932 5302 6.235664 AGACAAATCTTAGCGGTAAAAAGGA 58.764 36.000 8.61 2.68 0.00 3.36
2936 5306 7.393515 ACAAATCTTAGCGGTAAAAAGGAAGAT 59.606 33.333 8.61 4.76 34.47 2.40
2954 5324 9.614792 AAGGAAGATATGTACAAGACAATTACC 57.385 33.333 0.00 0.00 42.78 2.85
2965 5335 7.982761 ACAAGACAATTACCGTGGTTATTAA 57.017 32.000 3.19 0.00 0.00 1.40
2998 5368 8.159447 AGGCAAGACTATTCTCAATATGCATTA 58.841 33.333 3.54 0.00 30.83 1.90
3096 5520 6.330778 ACTTTCCCCGTCCCATAATATAAGAA 59.669 38.462 0.00 0.00 0.00 2.52
3097 5521 6.963117 TTCCCCGTCCCATAATATAAGAAT 57.037 37.500 0.00 0.00 0.00 2.40
3098 5522 6.308015 TCCCCGTCCCATAATATAAGAATG 57.692 41.667 0.00 0.00 0.00 2.67
3148 5572 1.999735 ACCTTATCACAATGACGCACG 59.000 47.619 0.00 0.00 0.00 5.34
3206 5631 4.785453 CCCCTCTGCCGTTGCTCC 62.785 72.222 0.00 0.00 38.71 4.70
3237 5666 2.104859 CCGCGAGAGGTACGAGACA 61.105 63.158 8.23 0.00 32.88 3.41
3290 5719 2.224719 GGTGATGGGGATCAAGGAGATG 60.225 54.545 0.00 0.00 37.00 2.90
3300 5729 1.774254 TCAAGGAGATGGGTGTGTTGT 59.226 47.619 0.00 0.00 0.00 3.32
3305 5734 2.487265 GGAGATGGGTGTGTTGTGAAGT 60.487 50.000 0.00 0.00 0.00 3.01
3317 5746 1.298014 GTGAAGTCAGGGGAGGCAG 59.702 63.158 0.00 0.00 0.00 4.85
3413 5844 1.395635 AGGGTTGGGTTTCGTTGTTC 58.604 50.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 5.773176 TGCCTTATGAAGAGGTATCATACGA 59.227 40.000 0.00 0.00 38.99 3.43
19 20 8.349568 ACGTATGATACTATGCCTTATGAAGA 57.650 34.615 0.66 0.00 0.00 2.87
120 122 9.902684 AGGAAATAGATGATTGGATATCATGAC 57.097 33.333 4.83 0.00 38.73 3.06
129 131 9.627123 AATTAAACGAGGAAATAGATGATTGGA 57.373 29.630 0.00 0.00 0.00 3.53
144 146 3.363575 CGGTGACACACAATTAAACGAGG 60.364 47.826 8.08 0.00 35.86 4.63
161 163 4.710324 ACTAGACATTTTTGTTCCGGTGA 58.290 39.130 0.00 0.00 0.00 4.02
166 168 6.806739 GCATACCAACTAGACATTTTTGTTCC 59.193 38.462 0.00 0.00 0.00 3.62
167 169 7.367285 TGCATACCAACTAGACATTTTTGTTC 58.633 34.615 0.00 0.00 0.00 3.18
213 227 2.203294 GTCAACCCACGCCAAGGT 60.203 61.111 0.00 0.00 38.27 3.50
223 237 0.108041 TAAAGGATCGCCGTCAACCC 60.108 55.000 0.00 0.00 39.96 4.11
242 256 8.755941 CATTATCTTCTTAACGTGATGTTCGAT 58.244 33.333 0.00 0.00 42.09 3.59
254 268 9.783256 AAAATTACCACGCATTATCTTCTTAAC 57.217 29.630 0.00 0.00 0.00 2.01
301 315 2.765807 AGCTATCAGTGCCCCGCT 60.766 61.111 0.00 0.00 0.00 5.52
304 318 2.280457 GCGAGCTATCAGTGCCCC 60.280 66.667 0.00 0.00 0.00 5.80
307 321 4.823276 ACTGCGAGCTATCAGTGC 57.177 55.556 16.76 2.33 41.53 4.40
321 335 4.689612 AGGCACCCAATATACTACACTG 57.310 45.455 0.00 0.00 0.00 3.66
332 346 1.266178 GGCAAGTTTAGGCACCCAAT 58.734 50.000 0.00 0.00 0.00 3.16
344 358 3.467803 GAGTGTCTGTTAGTGGCAAGTT 58.532 45.455 0.00 0.00 0.00 2.66
367 381 1.878088 CTGAATCCCATGCTTCCATCG 59.122 52.381 0.00 0.00 0.00 3.84
377 391 1.307647 GCCACCACCTGAATCCCAT 59.692 57.895 0.00 0.00 0.00 4.00
385 399 1.374758 GAGAAGACGCCACCACCTG 60.375 63.158 0.00 0.00 0.00 4.00
411 425 0.582005 GTCACGGAGCCATTAATCGC 59.418 55.000 0.00 0.00 0.00 4.58
426 440 4.184629 CACACCAAGGAATAGCTAGTCAC 58.815 47.826 21.66 11.59 0.00 3.67
432 446 4.141620 CCATAGACACACCAAGGAATAGCT 60.142 45.833 0.00 0.00 0.00 3.32
439 453 4.141287 TGAAAACCATAGACACACCAAGG 58.859 43.478 0.00 0.00 0.00 3.61
444 458 4.787598 CAAGCTGAAAACCATAGACACAC 58.212 43.478 0.00 0.00 0.00 3.82
450 464 2.474526 CGACGCAAGCTGAAAACCATAG 60.475 50.000 0.00 0.00 45.62 2.23
465 479 3.786516 TCCAGACATAATAACGACGCA 57.213 42.857 0.00 0.00 0.00 5.24
470 484 7.600375 AGCACATAAGATCCAGACATAATAACG 59.400 37.037 0.00 0.00 0.00 3.18
486 500 8.453320 CACTGAAAATGATGTAAGCACATAAGA 58.547 33.333 0.00 0.00 45.58 2.10
488 502 8.334263 TCACTGAAAATGATGTAAGCACATAA 57.666 30.769 0.00 0.00 45.58 1.90
493 507 6.094719 GCAATCACTGAAAATGATGTAAGCA 58.905 36.000 0.00 0.00 36.89 3.91
505 519 2.950975 TGAGCAGTTGCAATCACTGAAA 59.049 40.909 18.94 2.74 45.16 2.69
509 523 2.300433 TGTTGAGCAGTTGCAATCACT 58.700 42.857 0.59 0.00 45.16 3.41
513 527 2.309613 TCCTTGTTGAGCAGTTGCAAT 58.690 42.857 0.59 0.00 45.16 3.56
526 540 4.942761 AACAGCAACATTGATCCTTGTT 57.057 36.364 4.91 4.91 36.53 2.83
608 622 0.463833 GAATCACGGGGGCAAGTAGG 60.464 60.000 0.00 0.00 0.00 3.18
618 706 2.287547 CCAACACACAAAGAATCACGGG 60.288 50.000 0.00 0.00 0.00 5.28
619 707 2.357637 ACCAACACACAAAGAATCACGG 59.642 45.455 0.00 0.00 0.00 4.94
620 708 3.181501 ACACCAACACACAAAGAATCACG 60.182 43.478 0.00 0.00 0.00 4.35
641 729 3.412386 AGCTAGAATGGACACAACCAAC 58.588 45.455 0.00 0.00 43.47 3.77
645 733 4.446371 AGCATAGCTAGAATGGACACAAC 58.554 43.478 0.00 0.00 36.99 3.32
646 734 4.162131 TGAGCATAGCTAGAATGGACACAA 59.838 41.667 0.00 0.00 39.88 3.33
647 735 3.706086 TGAGCATAGCTAGAATGGACACA 59.294 43.478 0.00 0.00 39.88 3.72
648 736 4.305769 CTGAGCATAGCTAGAATGGACAC 58.694 47.826 0.00 0.00 39.88 3.67
649 737 3.323115 CCTGAGCATAGCTAGAATGGACA 59.677 47.826 0.00 0.00 39.88 4.02
650 738 3.864160 GCCTGAGCATAGCTAGAATGGAC 60.864 52.174 0.00 0.00 39.88 4.02
651 739 2.301296 GCCTGAGCATAGCTAGAATGGA 59.699 50.000 0.00 0.00 39.88 3.41
652 740 2.614987 GGCCTGAGCATAGCTAGAATGG 60.615 54.545 0.00 0.00 39.88 3.16
670 758 1.827969 AGCATATATCCAGTCTCGGCC 59.172 52.381 0.00 0.00 0.00 6.13
695 783 8.953665 ACTCATAATGAAGGGGATAGAAAAGAT 58.046 33.333 0.00 0.00 0.00 2.40
697 785 8.986929 AACTCATAATGAAGGGGATAGAAAAG 57.013 34.615 0.00 0.00 0.00 2.27
769 857 3.804688 TCACGTCAACGCATAATTTGTG 58.195 40.909 1.81 0.00 44.43 3.33
787 875 6.743575 ACAAGCCACTTATCATAGTTTCAC 57.256 37.500 0.00 0.00 0.00 3.18
930 1019 5.067674 ACGCAACAACATATCCATGCTTATT 59.932 36.000 0.00 0.00 35.39 1.40
990 1079 1.180456 TGTGGTTCATGCTTGCAGGG 61.180 55.000 7.41 0.00 0.00 4.45
1023 1120 4.578601 GTTTTCGATTACTCGGATGCTTG 58.421 43.478 2.41 0.00 45.10 4.01
1154 2451 0.868406 GTTCAGAACTCACTTGGCCG 59.132 55.000 6.00 0.00 0.00 6.13
1177 2474 7.887495 AGGAAAAGATAGGCATATGAATCTTCC 59.113 37.037 19.97 18.25 37.63 3.46
1206 2503 6.633500 TCCAAGACAAAGTAAAGGTCAATG 57.367 37.500 0.00 0.00 34.04 2.82
1282 3525 3.062466 TGGGCGACTCGGTCTCTG 61.062 66.667 0.00 0.00 0.00 3.35
1297 3540 1.619654 TTTCAGGTGGCAATGAGTGG 58.380 50.000 4.13 0.00 0.00 4.00
1489 3737 5.030147 TCTCCAACCAGACATACCAAGTAT 58.970 41.667 0.00 0.00 0.00 2.12
1570 3818 4.034258 GTCTCGTCGCGGACACCA 62.034 66.667 6.13 0.00 32.09 4.17
1690 3938 0.763652 CCACCTGCCTCATATCAGCT 59.236 55.000 0.00 0.00 0.00 4.24
1768 4021 1.072965 AGCTCTGACAAAGAAGGGTGG 59.927 52.381 0.00 0.00 33.37 4.61
1784 4041 5.649782 TCAATCAAGGAAAATGGAAGCTC 57.350 39.130 0.00 0.00 0.00 4.09
1797 4054 7.816031 AGTGAGCAATAAAACAATCAATCAAGG 59.184 33.333 0.00 0.00 0.00 3.61
1823 4080 7.916077 TTTGTGTTCCCTTCCCTTTATTTAA 57.084 32.000 0.00 0.00 0.00 1.52
1824 4081 8.499288 AATTTGTGTTCCCTTCCCTTTATTTA 57.501 30.769 0.00 0.00 0.00 1.40
1828 4085 5.663556 ACAAATTTGTGTTCCCTTCCCTTTA 59.336 36.000 22.71 0.00 40.49 1.85
1829 4086 4.473196 ACAAATTTGTGTTCCCTTCCCTTT 59.527 37.500 22.71 0.00 40.49 3.11
1889 4146 1.006922 GCTGCTGAAGGTTGCCAAC 60.007 57.895 0.00 0.00 0.00 3.77
1973 4331 6.938030 ACGTGTAAATGAAAAACTCATAGGGA 59.062 34.615 0.00 0.00 44.43 4.20
2068 4426 2.381911 CACATATCTGGGCCAGCTTTT 58.618 47.619 29.02 14.88 0.00 2.27
2069 4427 1.410648 CCACATATCTGGGCCAGCTTT 60.411 52.381 29.02 17.32 0.00 3.51
2625 4992 8.981647 GTCATTTTAAGCTTATTTGGCATATGG 58.018 33.333 7.08 0.00 0.00 2.74
2701 5071 5.163774 GCAGAAAACTATCAAGGAGCTCAAG 60.164 44.000 17.19 4.44 0.00 3.02
2753 5123 0.878523 CACCAACGAAGAGAACGGCA 60.879 55.000 0.00 0.00 34.93 5.69
2819 5189 2.103941 GGGGAAGATGAAGTAGAGCAGG 59.896 54.545 0.00 0.00 0.00 4.85
2852 5222 9.342308 GACAATATCAATCAGAATAACAAGGGA 57.658 33.333 0.00 0.00 0.00 4.20
2875 5245 4.186856 TGCACTCATATTGTTCGAGACA 57.813 40.909 0.00 0.00 36.19 3.41
2932 5302 7.494625 CCACGGTAATTGTCTTGTACATATCTT 59.505 37.037 0.00 0.00 38.10 2.40
2936 5306 6.040209 ACCACGGTAATTGTCTTGTACATA 57.960 37.500 0.00 0.00 38.10 2.29
2998 5368 3.281727 TTCTCAAGTTCACCTGCTGTT 57.718 42.857 0.00 0.00 0.00 3.16
3064 5488 2.767960 TGGGACGGGGAAAGTAGTATTC 59.232 50.000 0.00 0.00 0.00 1.75
3075 5499 5.788533 ACATTCTTATATTATGGGACGGGGA 59.211 40.000 0.00 0.00 0.00 4.81
3077 5501 7.996098 AAACATTCTTATATTATGGGACGGG 57.004 36.000 0.00 0.00 0.00 5.28
3109 5533 2.056577 GTACGTGGTCGAGAAAACAGG 58.943 52.381 0.00 0.00 40.62 4.00
3148 5572 2.506438 GGCAGAGGCGACGTACAC 60.506 66.667 0.00 0.00 42.47 2.90
3206 5631 2.105128 CGCGGTAGCAGGAGGAAG 59.895 66.667 0.00 0.00 45.49 3.46
3237 5666 4.049817 ACCTCCTCTCTCGGGCGT 62.050 66.667 0.00 0.00 0.00 5.68
3290 5719 1.308998 CCTGACTTCACAACACACCC 58.691 55.000 0.00 0.00 0.00 4.61
3300 5729 0.473694 TTCTGCCTCCCCTGACTTCA 60.474 55.000 0.00 0.00 0.00 3.02
3305 5734 3.706373 GCGTTCTGCCTCCCCTGA 61.706 66.667 0.00 0.00 37.76 3.86
3413 5844 0.379669 CAAAAGAGCAGCCGCCATAG 59.620 55.000 0.00 0.00 39.83 2.23
3470 5901 8.990163 AGTTTTTGGTCCAATAGAAAAGTAGA 57.010 30.769 4.80 0.00 0.00 2.59
3471 5902 9.463443 CAAGTTTTTGGTCCAATAGAAAAGTAG 57.537 33.333 4.80 0.00 0.00 2.57
3472 5903 9.191479 TCAAGTTTTTGGTCCAATAGAAAAGTA 57.809 29.630 4.80 0.00 34.97 2.24
3473 5904 8.073467 TCAAGTTTTTGGTCCAATAGAAAAGT 57.927 30.769 4.80 3.25 34.97 2.66
3474 5905 8.940768 TTCAAGTTTTTGGTCCAATAGAAAAG 57.059 30.769 4.80 0.00 34.97 2.27
3481 5912 7.797121 AGGATATTCAAGTTTTTGGTCCAAT 57.203 32.000 4.80 0.00 34.97 3.16
3483 5914 7.610580 AAAGGATATTCAAGTTTTTGGTCCA 57.389 32.000 0.00 0.00 34.97 4.02


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

AutoCloner maintained by Alex Coulton.