Multiple sequence alignment - TraesCS7D01G121700

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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 TraesCS7D01G121700 chr7D 100.000 3171 0 0 1 3171 75890881 75887711 0.000000e+00 5856
1 TraesCS7D01G121700 chr7D 80.379 1794 281 42 868 2617 75358358 75356592 0.000000e+00 1297
2 TraesCS7D01G121700 chr7D 79.793 1935 264 80 768 2617 75807085 75805193 0.000000e+00 1290
3 TraesCS7D01G121700 chr7D 96.416 558 11 4 2615 3170 378849654 378849104 0.000000e+00 911
4 TraesCS7D01G121700 chr7D 85.090 389 43 9 868 1244 75400491 75400106 1.780000e-102 383
5 TraesCS7D01G121700 chr7D 79.618 314 50 14 1 309 186791040 186791344 2.480000e-51 213
6 TraesCS7D01G121700 chr7A 89.640 1998 116 32 674 2625 79816950 79814998 0.000000e+00 2459
7 TraesCS7D01G121700 chr7A 90.182 1762 135 16 879 2625 79811383 79809645 0.000000e+00 2261
8 TraesCS7D01G121700 chr7A 80.556 1440 239 28 852 2255 79650072 79648638 0.000000e+00 1070
9 TraesCS7D01G121700 chr7A 96.071 560 14 3 2612 3170 22155651 22155099 0.000000e+00 905
10 TraesCS7D01G121700 chr7A 95.179 560 18 4 2612 3170 21835876 21835325 0.000000e+00 876
11 TraesCS7D01G121700 chr7A 93.381 559 28 4 2612 3169 22162269 22161719 0.000000e+00 819
12 TraesCS7D01G121700 chr7A 80.297 1076 165 31 1580 2622 79645488 79644427 0.000000e+00 769
13 TraesCS7D01G121700 chr7A 91.020 490 39 4 1 489 79818585 79818100 0.000000e+00 656
14 TraesCS7D01G121700 chr7A 83.051 708 86 21 852 1535 79646194 79645497 2.090000e-171 612
15 TraesCS7D01G121700 chr7A 91.935 124 3 3 480 599 79817100 79816980 1.960000e-37 167
16 TraesCS7D01G121700 chr7B 88.429 1642 146 23 734 2350 21936454 21934832 0.000000e+00 1940
17 TraesCS7D01G121700 chr7B 81.681 1725 240 45 852 2529 21722013 21720318 0.000000e+00 1365
18 TraesCS7D01G121700 chr7B 82.859 1406 211 20 855 2238 21821903 21820506 0.000000e+00 1234
19 TraesCS7D01G121700 chr7B 85.800 669 82 10 855 1512 21671741 21671075 0.000000e+00 697
20 TraesCS7D01G121700 chr7B 80.207 965 153 22 1690 2622 21671039 21670081 0.000000e+00 689
21 TraesCS7D01G121700 chr7B 89.062 512 47 5 67 574 21939194 21938688 7.470000e-176 627
22 TraesCS7D01G121700 chr7B 89.273 289 20 6 2346 2625 21934789 21934503 5.030000e-93 351
23 TraesCS7D01G121700 chr7B 79.935 309 39 18 6 303 178391682 178391978 4.150000e-49 206
24 TraesCS7D01G121700 chr7B 96.721 61 1 1 674 734 21938555 21938496 2.010000e-17 100
25 TraesCS7D01G121700 chr5D 95.349 559 23 3 2615 3170 407846352 407845794 0.000000e+00 885
26 TraesCS7D01G121700 chr3D 95.504 556 18 2 2615 3170 610893546 610894094 0.000000e+00 881
27 TraesCS7D01G121700 chr6D 93.705 556 30 2 2615 3170 132362704 132363254 0.000000e+00 828
28 TraesCS7D01G121700 chr5B 93.262 564 30 4 2615 3170 294754015 294754578 0.000000e+00 824
29 TraesCS7D01G121700 chr3B 93.381 559 34 2 2615 3170 181597727 181597169 0.000000e+00 824
30 TraesCS7D01G121700 chr3B 80.805 323 45 10 6 319 456112501 456112187 1.470000e-58 237
31 TraesCS7D01G121700 chr1D 81.646 316 38 15 1 306 445779532 445779837 8.790000e-61 244
32 TraesCS7D01G121700 chr3A 81.056 322 39 16 1 312 474069649 474069340 1.470000e-58 237
33 TraesCS7D01G121700 chr3A 79.310 319 53 11 6 316 714521365 714521678 8.910000e-51 211
34 TraesCS7D01G121700 chr1A 78.662 314 52 8 1 307 484294445 484294140 8.970000e-46 195


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 TraesCS7D01G121700 chr7D 75887711 75890881 3170 True 5856.00 5856 100.000000 1 3171 1 chr7D.!!$R4 3170
1 TraesCS7D01G121700 chr7D 75356592 75358358 1766 True 1297.00 1297 80.379000 868 2617 1 chr7D.!!$R1 1749
2 TraesCS7D01G121700 chr7D 75805193 75807085 1892 True 1290.00 1290 79.793000 768 2617 1 chr7D.!!$R3 1849
3 TraesCS7D01G121700 chr7D 378849104 378849654 550 True 911.00 911 96.416000 2615 3170 1 chr7D.!!$R5 555
4 TraesCS7D01G121700 chr7A 79809645 79818585 8940 True 1385.75 2459 90.694250 1 2625 4 chr7A.!!$R5 2624
5 TraesCS7D01G121700 chr7A 22155099 22155651 552 True 905.00 905 96.071000 2612 3170 1 chr7A.!!$R2 558
6 TraesCS7D01G121700 chr7A 21835325 21835876 551 True 876.00 876 95.179000 2612 3170 1 chr7A.!!$R1 558
7 TraesCS7D01G121700 chr7A 22161719 22162269 550 True 819.00 819 93.381000 2612 3169 1 chr7A.!!$R3 557
8 TraesCS7D01G121700 chr7A 79644427 79650072 5645 True 817.00 1070 81.301333 852 2622 3 chr7A.!!$R4 1770
9 TraesCS7D01G121700 chr7B 21720318 21722013 1695 True 1365.00 1365 81.681000 852 2529 1 chr7B.!!$R1 1677
10 TraesCS7D01G121700 chr7B 21820506 21821903 1397 True 1234.00 1234 82.859000 855 2238 1 chr7B.!!$R2 1383
11 TraesCS7D01G121700 chr7B 21934503 21939194 4691 True 754.50 1940 90.871250 67 2625 4 chr7B.!!$R4 2558
12 TraesCS7D01G121700 chr7B 21670081 21671741 1660 True 693.00 697 83.003500 855 2622 2 chr7B.!!$R3 1767
13 TraesCS7D01G121700 chr5D 407845794 407846352 558 True 885.00 885 95.349000 2615 3170 1 chr5D.!!$R1 555
14 TraesCS7D01G121700 chr3D 610893546 610894094 548 False 881.00 881 95.504000 2615 3170 1 chr3D.!!$F1 555
15 TraesCS7D01G121700 chr6D 132362704 132363254 550 False 828.00 828 93.705000 2615 3170 1 chr6D.!!$F1 555
16 TraesCS7D01G121700 chr5B 294754015 294754578 563 False 824.00 824 93.262000 2615 3170 1 chr5B.!!$F1 555
17 TraesCS7D01G121700 chr3B 181597169 181597727 558 True 824.00 824 93.381000 2615 3170 1 chr3B.!!$R1 555

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
426 428 0.106519 CAGGCGGGAAGAATGGGAAT 60.107 55.0 0.0 0.0 0.0 3.01 F
490 1501 0.463654 TACATGATTGCAGGCGTCCC 60.464 55.0 0.0 0.0 0.0 4.46 F
1447 8505 0.606604 GAAGTGGGTCGTCTTGCCTA 59.393 55.0 0.0 0.0 0.0 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1413 8465 0.250513 ACTTCTCCGTGGCAGGATTC 59.749 55.0 9.09 0.0 39.96 2.52 R
1805 14235 0.302890 CAGATCAATGAACTCGCCGC 59.697 55.0 0.00 0.0 0.00 6.53 R
2995 15532 0.038618 ACTGTGATAACGTCAGCGCA 60.039 50.0 11.47 0.0 42.83 6.09 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
108 110 6.255215 TGTTCGAAATCTAATGAAAATCCGC 58.745 36.000 0.00 0.00 0.00 5.54
109 111 6.093495 TGTTCGAAATCTAATGAAAATCCGCT 59.907 34.615 0.00 0.00 0.00 5.52
111 113 4.672413 CGAAATCTAATGAAAATCCGCTGC 59.328 41.667 0.00 0.00 0.00 5.25
128 130 1.983160 GCGTTTGCATGAATGTCGC 59.017 52.632 0.00 0.00 42.15 5.19
130 132 1.127571 CGTTTGCATGAATGTCGCCG 61.128 55.000 0.00 0.00 0.00 6.46
181 183 5.404968 GCATGAATTTCATTCGGTTTGTTGA 59.595 36.000 9.19 0.00 42.15 3.18
182 184 6.073873 GCATGAATTTCATTCGGTTTGTTGAA 60.074 34.615 9.19 0.00 42.15 2.69
240 242 2.202756 GTCTCCCGCATCCGTGTC 60.203 66.667 0.00 0.00 0.00 3.67
260 262 1.678970 GTGGATTGGTCCCACCTGC 60.679 63.158 0.00 0.00 46.30 4.85
287 289 1.339631 ACGAATGCGGGAGGAAATTCA 60.340 47.619 0.00 0.00 43.17 2.57
324 326 6.318648 TGGAGATGCCTTACATGACATTAAAC 59.681 38.462 0.00 0.00 39.84 2.01
363 365 4.366586 TGCATCGCACAAAATCTCAAAAA 58.633 34.783 0.00 0.00 31.71 1.94
408 410 3.908189 CATGGAATGGCTGCGTCA 58.092 55.556 0.00 0.00 41.79 4.35
410 412 1.452651 ATGGAATGGCTGCGTCAGG 60.453 57.895 8.57 0.00 31.21 3.86
424 426 1.615124 TCAGGCGGGAAGAATGGGA 60.615 57.895 0.00 0.00 0.00 4.37
426 428 0.106519 CAGGCGGGAAGAATGGGAAT 60.107 55.000 0.00 0.00 0.00 3.01
464 466 7.687941 AGTCGAGTCATTTATTTTTGGATGT 57.312 32.000 0.00 0.00 0.00 3.06
484 1495 3.134623 TGTAGGGAGTACATGATTGCAGG 59.865 47.826 0.00 0.00 36.67 4.85
490 1501 0.463654 TACATGATTGCAGGCGTCCC 60.464 55.000 0.00 0.00 0.00 4.46
572 1666 9.187996 GAATGTATCCCTACCCTAGAGTAATAC 57.812 40.741 0.00 0.00 0.00 1.89
573 1667 7.901804 TGTATCCCTACCCTAGAGTAATACT 57.098 40.000 0.00 0.00 0.00 2.12
574 1668 8.995646 TGTATCCCTACCCTAGAGTAATACTA 57.004 38.462 0.00 0.00 0.00 1.82
599 1693 5.584551 ATGTTTTACTCTTGACCCTCCTT 57.415 39.130 0.00 0.00 0.00 3.36
600 1694 5.382664 TGTTTTACTCTTGACCCTCCTTT 57.617 39.130 0.00 0.00 0.00 3.11
601 1695 5.762279 TGTTTTACTCTTGACCCTCCTTTT 58.238 37.500 0.00 0.00 0.00 2.27
627 1721 8.840833 TTTTGAGGGAAAAGGCATTTTATTAC 57.159 30.769 9.37 3.20 38.74 1.89
628 1722 6.538945 TGAGGGAAAAGGCATTTTATTACC 57.461 37.500 9.37 9.53 38.74 2.85
629 1723 5.423931 TGAGGGAAAAGGCATTTTATTACCC 59.576 40.000 18.48 18.48 38.74 3.69
630 1724 5.346270 AGGGAAAAGGCATTTTATTACCCA 58.654 37.500 24.56 0.00 39.52 4.51
631 1725 5.788014 AGGGAAAAGGCATTTTATTACCCAA 59.212 36.000 24.56 0.00 39.52 4.12
632 1726 6.446759 AGGGAAAAGGCATTTTATTACCCAAT 59.553 34.615 24.56 9.35 39.52 3.16
633 1727 7.036935 AGGGAAAAGGCATTTTATTACCCAATT 60.037 33.333 24.56 8.80 39.52 2.32
634 1728 7.613801 GGGAAAAGGCATTTTATTACCCAATTT 59.386 33.333 20.28 0.00 38.07 1.82
635 1729 8.458052 GGAAAAGGCATTTTATTACCCAATTTG 58.542 33.333 9.37 0.00 38.74 2.32
636 1730 8.932434 AAAAGGCATTTTATTACCCAATTTGT 57.068 26.923 7.41 0.00 36.85 2.83
639 1733 9.830975 AAGGCATTTTATTACCCAATTTGTATC 57.169 29.630 0.00 0.00 0.00 2.24
640 1734 8.428852 AGGCATTTTATTACCCAATTTGTATCC 58.571 33.333 0.00 0.00 0.00 2.59
641 1735 8.428852 GGCATTTTATTACCCAATTTGTATCCT 58.571 33.333 0.00 0.00 0.00 3.24
648 1742 8.980481 ATTACCCAATTTGTATCCTACTCTTG 57.020 34.615 0.00 0.00 0.00 3.02
649 1743 6.636454 ACCCAATTTGTATCCTACTCTTGA 57.364 37.500 0.00 0.00 0.00 3.02
650 1744 7.213178 ACCCAATTTGTATCCTACTCTTGAT 57.787 36.000 0.00 0.00 0.00 2.57
651 1745 7.283329 ACCCAATTTGTATCCTACTCTTGATC 58.717 38.462 0.00 0.00 0.00 2.92
652 1746 6.712547 CCCAATTTGTATCCTACTCTTGATCC 59.287 42.308 0.00 0.00 0.00 3.36
653 1747 7.420680 CCCAATTTGTATCCTACTCTTGATCCT 60.421 40.741 0.00 0.00 0.00 3.24
654 1748 7.659390 CCAATTTGTATCCTACTCTTGATCCTC 59.341 40.741 0.00 0.00 0.00 3.71
655 1749 6.732896 TTTGTATCCTACTCTTGATCCTCC 57.267 41.667 0.00 0.00 0.00 4.30
656 1750 5.671463 TGTATCCTACTCTTGATCCTCCT 57.329 43.478 0.00 0.00 0.00 3.69
657 1751 6.781857 TGTATCCTACTCTTGATCCTCCTA 57.218 41.667 0.00 0.00 0.00 2.94
658 1752 7.162973 TGTATCCTACTCTTGATCCTCCTAA 57.837 40.000 0.00 0.00 0.00 2.69
659 1753 7.592736 TGTATCCTACTCTTGATCCTCCTAAA 58.407 38.462 0.00 0.00 0.00 1.85
660 1754 8.065627 TGTATCCTACTCTTGATCCTCCTAAAA 58.934 37.037 0.00 0.00 0.00 1.52
661 1755 7.996758 ATCCTACTCTTGATCCTCCTAAAAA 57.003 36.000 0.00 0.00 0.00 1.94
863 4014 1.112113 GGACAGACTCCCTCGCAATA 58.888 55.000 0.00 0.00 31.83 1.90
934 4098 1.133809 CCTCCCTGTTTCCCTCACCA 61.134 60.000 0.00 0.00 0.00 4.17
936 4100 0.698238 TCCCTGTTTCCCTCACCATG 59.302 55.000 0.00 0.00 0.00 3.66
981 4152 1.001974 CCCTCGTTCACAGATTGACCA 59.998 52.381 0.00 0.00 32.26 4.02
1156 4327 4.129148 GCACCATCTCCCACCCCC 62.129 72.222 0.00 0.00 0.00 5.40
1257 4431 3.863400 GCTGTTTCTTAGGTCGCCACTTA 60.863 47.826 0.00 0.00 0.00 2.24
1413 8465 3.181514 GGGAATTTGATTACGTCGTGTGG 60.182 47.826 8.47 0.00 0.00 4.17
1446 8498 1.122019 AGAAGTGGGTCGTCTTGCCT 61.122 55.000 0.00 0.00 31.22 4.75
1447 8505 0.606604 GAAGTGGGTCGTCTTGCCTA 59.393 55.000 0.00 0.00 0.00 3.93
1461 8519 2.090693 GCCTAGCTTCTTCGGCAAC 58.909 57.895 0.00 0.00 42.06 4.17
1470 8528 1.302033 CTTCGGCAACTGGCAGACT 60.302 57.895 23.66 4.61 46.55 3.24
1512 8570 1.444553 CGTCTCCTCGCACTTCCAC 60.445 63.158 0.00 0.00 0.00 4.02
1669 14089 5.760743 GGCTTCCCAACTAAGATAGTGAATC 59.239 44.000 0.00 0.00 39.39 2.52
1704 14124 5.580297 TGTCTTTTTCAATGGTTTTCTGCAC 59.420 36.000 0.00 0.00 0.00 4.57
1714 14134 2.623416 GGTTTTCTGCACTTGCTTACCT 59.377 45.455 2.33 0.00 42.66 3.08
1717 14137 2.185004 TCTGCACTTGCTTACCTTCC 57.815 50.000 2.33 0.00 42.66 3.46
1760 14183 2.696775 TGTGGAGGGAACTACTTGGAA 58.303 47.619 0.00 0.00 44.03 3.53
1805 14235 2.800250 GGATGCCCCAATAGATCTTGG 58.200 52.381 0.00 3.08 44.45 3.61
1806 14236 2.165998 GATGCCCCAATAGATCTTGGC 58.834 52.381 0.00 6.75 43.66 4.52
1808 14238 0.890996 GCCCCAATAGATCTTGGCGG 60.891 60.000 0.00 8.37 43.66 6.13
1811 14241 0.249868 CCAATAGATCTTGGCGGCGA 60.250 55.000 12.98 0.14 39.32 5.54
1835 14265 2.842496 TCATTGATCTGTCTCAAGGGCT 59.158 45.455 0.00 0.00 38.47 5.19
1849 14279 0.246360 AGGGCTTTTGTATTTGGCGC 59.754 50.000 0.00 0.00 36.37 6.53
1850 14280 0.246360 GGGCTTTTGTATTTGGCGCT 59.754 50.000 7.64 0.00 33.97 5.92
1858 14288 6.676943 GCTTTTGTATTTGGCGCTTACTGATA 60.677 38.462 7.64 0.00 0.00 2.15
1955 14385 9.211485 CAGTGTCACATATATGCATCTATTTCA 57.789 33.333 12.79 0.00 0.00 2.69
1987 14417 2.295349 GCCCATCATGGAAGCAAGTATG 59.705 50.000 4.75 0.00 40.96 2.39
1993 14423 7.148120 CCCATCATGGAAGCAAGTATGATATTC 60.148 40.741 4.75 0.00 40.96 1.75
1994 14424 7.413767 CCATCATGGAAGCAAGTATGATATTCG 60.414 40.741 0.00 0.00 40.96 3.34
1996 14426 4.960938 TGGAAGCAAGTATGATATTCGCT 58.039 39.130 0.00 0.00 0.00 4.93
2016 14448 1.440938 CTCCACCCGCAACGAAACAA 61.441 55.000 0.00 0.00 0.00 2.83
2040 14472 6.332630 AGATTTTCTTTGTTTATGGGCATCG 58.667 36.000 0.00 0.00 0.00 3.84
2041 14473 5.461032 TTTTCTTTGTTTATGGGCATCGT 57.539 34.783 0.00 0.00 0.00 3.73
2083 14515 3.737559 ATGGATAGTGGGAAAGTGCAA 57.262 42.857 0.00 0.00 0.00 4.08
2084 14516 3.071874 TGGATAGTGGGAAAGTGCAAG 57.928 47.619 0.00 0.00 0.00 4.01
2093 14525 0.874390 GAAAGTGCAAGGCATCGACA 59.126 50.000 0.00 0.00 41.91 4.35
2099 14531 2.677836 GTGCAAGGCATCGACAATCTTA 59.322 45.455 0.00 0.00 41.91 2.10
2110 14542 6.423302 GCATCGACAATCTTAGACATGATTCT 59.577 38.462 0.00 0.00 31.35 2.40
2174 14606 5.841957 ATTGGCAGATTGGAACTGATAAC 57.158 39.130 0.00 0.00 37.54 1.89
2212 14644 3.499338 TGCTCCATTGTTGACCTTTCAT 58.501 40.909 0.00 0.00 0.00 2.57
2238 14680 6.715347 AATGTTGAATTATAGGTCCCAAGC 57.285 37.500 0.00 0.00 0.00 4.01
2300 14742 4.342951 TGTTACTTCTCCTTTGGTCTCGAA 59.657 41.667 0.00 0.00 0.00 3.71
2464 14978 6.889301 ATTTATACCATGATTGCTGTCTGG 57.111 37.500 0.00 0.00 0.00 3.86
2558 15083 5.657470 TCTATCGTGCATTCAAACTATGC 57.343 39.130 0.00 0.00 46.63 3.14
2569 15094 8.679288 GCATTCAAACTATGCAATCATATACC 57.321 34.615 0.00 0.00 45.93 2.73
2598 15125 4.714632 ACGTTGGGAGGGAATATATGTTG 58.285 43.478 0.00 0.00 0.00 3.33
2606 15133 6.839134 GGGAGGGAATATATGTTGTTTTCCTT 59.161 38.462 0.00 0.00 36.81 3.36
2627 15155 6.875726 TCCTTTTGTCAATGTAGAGAGATGTG 59.124 38.462 0.00 0.00 0.00 3.21
2710 15241 2.772515 AGGCCTCAACCTCAACTATACC 59.227 50.000 0.00 0.00 33.62 2.73
2995 15532 0.323957 GGTTGGCGGAAAGGTAGACT 59.676 55.000 0.00 0.00 0.00 3.24
3170 15707 4.498241 CTTCGATGACCAAGAGATCAACA 58.502 43.478 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 35 2.526450 AAACCTAACCTACGGCGGCC 62.526 60.000 13.24 9.54 0.00 6.13
36 38 1.202452 CCCTAAACCTAACCTACGGCG 60.202 57.143 4.80 4.80 0.00 6.46
54 56 1.670083 CAAGAAACCGACCCGACCC 60.670 63.158 0.00 0.00 0.00 4.46
55 57 0.533531 AACAAGAAACCGACCCGACC 60.534 55.000 0.00 0.00 0.00 4.79
108 110 1.253116 CGACATTCATGCAAACGCAG 58.747 50.000 0.00 0.00 44.13 5.18
109 111 0.728803 GCGACATTCATGCAAACGCA 60.729 50.000 15.00 0.00 45.23 5.24
111 113 1.127571 CGGCGACATTCATGCAAACG 61.128 55.000 0.00 0.00 0.00 3.60
128 130 3.365969 GGGCAACTTTCATACAAACTCGG 60.366 47.826 0.00 0.00 0.00 4.63
130 132 4.846779 TGGGCAACTTTCATACAAACTC 57.153 40.909 0.00 0.00 0.00 3.01
210 212 1.677552 GGAGACCACCATCCAACGT 59.322 57.895 0.00 0.00 35.54 3.99
268 270 1.378531 TGAATTTCCTCCCGCATTCG 58.621 50.000 0.00 0.00 0.00 3.34
270 272 2.034124 CCATGAATTTCCTCCCGCATT 58.966 47.619 0.00 0.00 0.00 3.56
287 289 0.680921 CATCTCCAACGGCAACCCAT 60.681 55.000 0.00 0.00 0.00 4.00
324 326 1.548269 TGCAAATCCTTTTAAGGCCGG 59.452 47.619 0.00 0.00 46.06 6.13
347 349 3.809279 CCCCACTTTTTGAGATTTTGTGC 59.191 43.478 0.00 0.00 0.00 4.57
363 365 1.551883 GCATTGCATTTTCTCCCCACT 59.448 47.619 3.15 0.00 0.00 4.00
408 410 0.183731 GATTCCCATTCTTCCCGCCT 59.816 55.000 0.00 0.00 0.00 5.52
410 412 0.106719 TGGATTCCCATTCTTCCCGC 60.107 55.000 0.00 0.00 37.58 6.13
424 426 8.234136 TGACTCGACTTTATACTGTATGGATT 57.766 34.615 10.51 0.00 0.00 3.01
426 428 7.818997 ATGACTCGACTTTATACTGTATGGA 57.181 36.000 10.51 0.00 0.00 3.41
443 445 7.282224 TCCCTACATCCAAAAATAAATGACTCG 59.718 37.037 0.00 0.00 0.00 4.18
458 460 4.202357 GCAATCATGTACTCCCTACATCCA 60.202 45.833 0.00 0.00 43.21 3.41
460 462 4.960938 TGCAATCATGTACTCCCTACATC 58.039 43.478 0.00 0.00 43.21 3.06
462 464 3.134623 CCTGCAATCATGTACTCCCTACA 59.865 47.826 0.00 0.00 39.78 2.74
464 466 2.104792 GCCTGCAATCATGTACTCCCTA 59.895 50.000 0.00 0.00 0.00 3.53
484 1495 1.747709 TAGTAGACACTCTGGGACGC 58.252 55.000 0.00 0.00 36.14 5.19
572 1666 7.124448 AGGAGGGTCAAGAGTAAAACATACTAG 59.876 40.741 0.00 0.00 0.00 2.57
573 1667 6.958192 AGGAGGGTCAAGAGTAAAACATACTA 59.042 38.462 0.00 0.00 0.00 1.82
574 1668 5.785940 AGGAGGGTCAAGAGTAAAACATACT 59.214 40.000 0.00 0.00 0.00 2.12
601 1695 9.278978 GTAATAAAATGCCTTTTCCCTCAAAAA 57.721 29.630 2.77 0.00 36.09 1.94
603 1697 7.390823 GGTAATAAAATGCCTTTTCCCTCAAA 58.609 34.615 2.77 0.00 36.09 2.69
604 1698 6.070481 GGGTAATAAAATGCCTTTTCCCTCAA 60.070 38.462 11.93 0.00 34.26 3.02
605 1699 5.423931 GGGTAATAAAATGCCTTTTCCCTCA 59.576 40.000 11.93 0.00 34.26 3.86
606 1700 5.423931 TGGGTAATAAAATGCCTTTTCCCTC 59.576 40.000 17.09 4.57 36.39 4.30
613 1707 9.830975 GATACAAATTGGGTAATAAAATGCCTT 57.169 29.630 0.00 0.00 0.00 4.35
614 1708 8.428852 GGATACAAATTGGGTAATAAAATGCCT 58.571 33.333 0.00 0.00 0.00 4.75
623 1717 8.778059 TCAAGAGTAGGATACAAATTGGGTAAT 58.222 33.333 0.00 0.00 46.26 1.89
624 1718 8.153221 TCAAGAGTAGGATACAAATTGGGTAA 57.847 34.615 0.00 0.00 46.26 2.85
625 1719 7.743116 TCAAGAGTAGGATACAAATTGGGTA 57.257 36.000 0.00 0.00 46.26 3.69
626 1720 6.636454 TCAAGAGTAGGATACAAATTGGGT 57.364 37.500 0.00 0.00 46.26 4.51
627 1721 6.712547 GGATCAAGAGTAGGATACAAATTGGG 59.287 42.308 0.00 0.00 46.26 4.12
628 1722 7.512992 AGGATCAAGAGTAGGATACAAATTGG 58.487 38.462 0.00 0.00 46.26 3.16
629 1723 7.659390 GGAGGATCAAGAGTAGGATACAAATTG 59.341 40.741 0.00 0.00 40.30 2.32
630 1724 7.570607 AGGAGGATCAAGAGTAGGATACAAATT 59.429 37.037 0.00 0.00 40.30 1.82
631 1725 7.079048 AGGAGGATCAAGAGTAGGATACAAAT 58.921 38.462 0.00 0.00 40.30 2.32
632 1726 6.444704 AGGAGGATCAAGAGTAGGATACAAA 58.555 40.000 0.00 0.00 40.30 2.83
633 1727 6.031964 AGGAGGATCAAGAGTAGGATACAA 57.968 41.667 0.00 0.00 40.30 2.41
634 1728 5.671463 AGGAGGATCAAGAGTAGGATACA 57.329 43.478 0.00 0.00 40.30 2.29
635 1729 8.480133 TTTTAGGAGGATCAAGAGTAGGATAC 57.520 38.462 0.00 0.00 38.52 2.24
637 1731 7.996758 TTTTTAGGAGGATCAAGAGTAGGAT 57.003 36.000 0.00 0.00 36.25 3.24
680 1774 2.265904 GGCCTGAAACACCGTTCCC 61.266 63.158 0.00 0.00 0.00 3.97
683 1777 0.536460 AATCGGCCTGAAACACCGTT 60.536 50.000 0.00 0.00 46.92 4.44
848 3984 1.135083 CGTGTTATTGCGAGGGAGTCT 60.135 52.381 0.00 0.00 0.00 3.24
899 4060 3.797269 AGGGAGGAAGAGAGGAATCTACT 59.203 47.826 0.00 0.00 0.00 2.57
934 4098 0.250640 GGAGAGATTGCATCGCCCAT 60.251 55.000 0.00 0.00 31.07 4.00
936 4100 0.602372 GAGGAGAGATTGCATCGCCC 60.602 60.000 5.10 0.00 37.35 6.13
981 4152 3.602030 ACCGTGGGGAGAGGAGGT 61.602 66.667 0.00 0.00 36.97 3.85
1135 4306 4.408821 GTGGGAGATGGTGCCGCA 62.409 66.667 0.00 0.00 46.30 5.69
1142 4313 2.237965 TTGTGGGGGTGGGAGATGG 61.238 63.158 0.00 0.00 0.00 3.51
1413 8465 0.250513 ACTTCTCCGTGGCAGGATTC 59.749 55.000 9.09 0.00 39.96 2.52
1446 8498 0.673644 GCCAGTTGCCGAAGAAGCTA 60.674 55.000 0.00 0.00 0.00 3.32
1447 8505 1.968540 GCCAGTTGCCGAAGAAGCT 60.969 57.895 0.00 0.00 0.00 3.74
1461 8519 2.047465 AAGCGAGCAGTCTGCCAG 60.047 61.111 21.32 15.87 46.52 4.85
1470 8528 3.621805 TCGAACCCCAAGCGAGCA 61.622 61.111 0.00 0.00 0.00 4.26
1512 8570 0.868406 GCTCCAGGAAGTGAAACACG 59.132 55.000 0.00 0.00 41.43 4.49
1576 13996 0.542333 TCAACCCCTTTGACGTGTCA 59.458 50.000 0.00 0.00 39.45 3.58
1669 14089 9.533253 ACCATTGAAAAAGACACTTTTAGAATG 57.467 29.630 19.90 19.90 33.27 2.67
1687 14107 3.132646 AGCAAGTGCAGAAAACCATTGAA 59.867 39.130 6.00 0.00 45.16 2.69
1805 14235 0.302890 CAGATCAATGAACTCGCCGC 59.697 55.000 0.00 0.00 0.00 6.53
1806 14236 1.590238 GACAGATCAATGAACTCGCCG 59.410 52.381 0.00 0.00 0.00 6.46
1808 14238 3.515630 TGAGACAGATCAATGAACTCGC 58.484 45.455 0.00 0.00 33.47 5.03
1811 14241 4.841422 CCCTTGAGACAGATCAATGAACT 58.159 43.478 0.00 0.00 38.47 3.01
1835 14265 5.637006 ATCAGTAAGCGCCAAATACAAAA 57.363 34.783 2.29 0.00 0.00 2.44
1926 14356 5.303165 AGATGCATATATGTGACACTGTGG 58.697 41.667 14.14 0.00 0.00 4.17
1955 14385 3.202818 TCCATGATGGGCATACTTCACTT 59.797 43.478 12.26 0.00 38.32 3.16
1987 14417 0.667792 GCGGGTGGAGAGCGAATATC 60.668 60.000 0.00 0.00 0.00 1.63
1994 14424 3.876589 TTCGTTGCGGGTGGAGAGC 62.877 63.158 0.00 0.00 0.00 4.09
1996 14426 1.595929 GTTTCGTTGCGGGTGGAGA 60.596 57.895 0.00 0.00 0.00 3.71
2016 14448 6.071391 ACGATGCCCATAAACAAAGAAAATCT 60.071 34.615 0.00 0.00 0.00 2.40
2083 14515 4.100035 TCATGTCTAAGATTGTCGATGCCT 59.900 41.667 0.00 0.00 0.00 4.75
2084 14516 4.371786 TCATGTCTAAGATTGTCGATGCC 58.628 43.478 0.00 0.00 0.00 4.40
2093 14525 6.989169 GGTAGCACAGAATCATGTCTAAGATT 59.011 38.462 0.00 0.00 37.19 2.40
2099 14531 3.110705 AGGGTAGCACAGAATCATGTCT 58.889 45.455 0.00 0.00 0.00 3.41
2110 14542 2.337359 AAGGAAGGTAGGGTAGCACA 57.663 50.000 0.00 0.00 0.00 4.57
2174 14606 1.226686 GCAGTGATATGCGAGCCAGG 61.227 60.000 0.00 0.00 36.28 4.45
2212 14644 9.515226 GCTTGGGACCTATAATTCAACATTATA 57.485 33.333 0.00 0.00 0.00 0.98
2238 14680 4.836125 AACCAAATAGCTGCCGATATTG 57.164 40.909 0.00 0.00 32.45 1.90
2300 14742 7.103641 CCATAAAGTGAGGTTACAGTGTACAT 58.896 38.462 1.43 0.00 0.00 2.29
2408 14918 8.539117 AGCTCCATAAAATTAATAGCAAAGGT 57.461 30.769 6.84 0.00 0.00 3.50
2464 14978 5.106157 CCCAACACAACATTCTAGACAATCC 60.106 44.000 0.00 0.00 0.00 3.01
2558 15083 8.625651 TCCCAACGTTTTTATGGTATATGATTG 58.374 33.333 0.00 0.00 32.13 2.67
2569 15094 6.709018 ATATTCCCTCCCAACGTTTTTATG 57.291 37.500 0.00 0.00 0.00 1.90
2598 15125 8.154649 TCTCTCTACATTGACAAAAGGAAAAC 57.845 34.615 0.00 0.00 0.00 2.43
2606 15133 6.073058 GCAACACATCTCTCTACATTGACAAA 60.073 38.462 0.00 0.00 0.00 2.83
2710 15241 1.923395 TGGCCCACCTCCTAGTTGG 60.923 63.158 0.00 0.00 36.63 3.77
2995 15532 0.038618 ACTGTGATAACGTCAGCGCA 60.039 50.000 11.47 0.00 42.83 6.09


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

AutoCloner maintained by Alex Coulton.