Multiple sequence alignment - TraesCS4A01G347100

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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 TraesCS4A01G347100 chr4A 100.000 2361 0 0 465 2825 625322787 625320427 0.000000e+00 4361.0
1 TraesCS4A01G347100 chr4A 89.889 722 68 4 734 1451 625282403 625281683 0.000000e+00 924.0
2 TraesCS4A01G347100 chr4A 84.859 852 107 10 604 1451 625373109 625372276 0.000000e+00 839.0
3 TraesCS4A01G347100 chr4A 86.701 767 75 12 1449 2210 625281649 625280905 0.000000e+00 826.0
4 TraesCS4A01G347100 chr4A 89.729 516 52 1 1449 1963 625372242 625371727 0.000000e+00 658.0
5 TraesCS4A01G347100 chr4A 84.474 599 93 0 854 1452 625368253 625367655 2.420000e-165 592.0
6 TraesCS4A01G347100 chr4A 100.000 134 0 0 1 134 625323251 625323118 6.040000e-62 248.0
7 TraesCS4A01G347100 chr4A 79.167 336 33 11 1903 2210 625366944 625366618 6.170000e-47 198.0
8 TraesCS4A01G347100 chr5D 94.266 2372 95 11 465 2823 543803099 543805442 0.000000e+00 3589.0
9 TraesCS4A01G347100 chr5D 89.474 722 71 4 734 1451 543816914 543817634 0.000000e+00 907.0
10 TraesCS4A01G347100 chr5D 85.211 852 104 11 604 1451 543771559 543772392 0.000000e+00 856.0
11 TraesCS4A01G347100 chr5D 87.417 755 68 12 1449 2198 543817668 543818400 0.000000e+00 843.0
12 TraesCS4A01G347100 chr5D 90.230 522 51 0 1446 1967 543772423 543772944 0.000000e+00 682.0
13 TraesCS4A01G347100 chr5D 80.755 795 125 6 682 1452 543776270 543777060 1.870000e-166 595.0
14 TraesCS4A01G347100 chr5D 86.933 375 46 1 1449 1820 543777093 543777467 4.350000e-113 418.0
15 TraesCS4A01G347100 chr5D 84.000 125 15 5 10 131 297228501 297228379 6.400000e-22 115.0
16 TraesCS4A01G347100 chr5B 92.382 617 47 0 1453 2069 685691308 685690692 0.000000e+00 880.0
17 TraesCS4A01G347100 chr5B 87.690 723 79 6 734 1451 685692063 685691346 0.000000e+00 833.0
18 TraesCS4A01G347100 chr5B 80.177 792 119 18 686 1451 685658094 685657315 2.460000e-155 558.0
19 TraesCS4A01G347100 chr5B 87.500 232 19 5 805 1036 685607964 685608185 2.790000e-65 259.0
20 TraesCS4A01G347100 chr5B 78.852 331 35 17 2263 2562 685690605 685690279 1.030000e-44 191.0
21 TraesCS4A01G347100 chr5B 79.221 231 48 0 1451 1681 686739669 686739899 8.100000e-36 161.0
22 TraesCS4A01G347100 chr1A 78.509 228 49 0 1454 1681 569680309 569680082 1.750000e-32 150.0
23 TraesCS4A01G347100 chr1A 82.645 121 18 3 7 125 507974985 507974866 1.380000e-18 104.0
24 TraesCS4A01G347100 chr6B 86.614 127 14 3 7 131 449046120 449045995 1.360000e-28 137.0
25 TraesCS4A01G347100 chr1B 84.375 128 15 5 1 125 375253864 375253989 1.370000e-23 121.0
26 TraesCS4A01G347100 chr2B 82.031 128 17 6 7 131 62985953 62985829 1.380000e-18 104.0
27 TraesCS4A01G347100 chr3B 84.694 98 13 2 7 102 148686779 148686876 2.320000e-16 97.1
28 TraesCS4A01G347100 chr3B 79.231 130 20 6 7 131 414388169 414388296 1.800000e-12 84.2
29 TraesCS4A01G347100 chr7B 81.667 120 15 3 7 125 527854023 527853910 3.000000e-15 93.5
30 TraesCS4A01G347100 chr3D 80.315 127 22 3 7 131 98155015 98155140 3.000000e-15 93.5


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 TraesCS4A01G347100 chr4A 625320427 625323251 2824 True 2304.500000 4361 100.00000 1 2825 2 chr4A.!!$R2 2824
1 TraesCS4A01G347100 chr4A 625280905 625282403 1498 True 875.000000 924 88.29500 734 2210 2 chr4A.!!$R1 1476
2 TraesCS4A01G347100 chr4A 625366618 625373109 6491 True 571.750000 839 84.55725 604 2210 4 chr4A.!!$R3 1606
3 TraesCS4A01G347100 chr5D 543803099 543805442 2343 False 3589.000000 3589 94.26600 465 2823 1 chr5D.!!$F1 2358
4 TraesCS4A01G347100 chr5D 543816914 543818400 1486 False 875.000000 907 88.44550 734 2198 2 chr5D.!!$F3 1464
5 TraesCS4A01G347100 chr5D 543771559 543777467 5908 False 637.750000 856 85.78225 604 1967 4 chr5D.!!$F2 1363
6 TraesCS4A01G347100 chr5B 685690279 685692063 1784 True 634.666667 880 86.30800 734 2562 3 chr5B.!!$R2 1828
7 TraesCS4A01G347100 chr5B 685657315 685658094 779 True 558.000000 558 80.17700 686 1451 1 chr5B.!!$R1 765

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
677 683 0.035317 CTACCTGGCAGCTGACAACA 59.965 55.0 25.38 10.44 29.15 3.33 F
682 688 0.179023 TGGCAGCTGACAACATCACA 60.179 50.0 23.06 0.00 32.37 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1605 1679 0.101040 TTACGGTATTGTCGCTCCCG 59.899 55.0 0.0 0.0 44.06 5.14 R
2668 10733 0.249531 TCGCTGCCTTTGTTGTCGTA 60.250 50.0 0.0 0.0 0.00 3.43 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
22 23 4.760047 CGAGTTCCGGCAGGGGTG 62.760 72.222 2.05 0.00 38.33 4.61
23 24 3.637273 GAGTTCCGGCAGGGGTGT 61.637 66.667 2.05 0.00 38.33 4.16
24 25 3.901797 GAGTTCCGGCAGGGGTGTG 62.902 68.421 2.05 0.00 38.33 3.82
54 55 4.767255 GGGTGGTGGAGCTGCGAG 62.767 72.222 0.00 0.00 0.00 5.03
55 56 4.767255 GGTGGTGGAGCTGCGAGG 62.767 72.222 0.00 0.00 0.00 4.63
56 57 3.695606 GTGGTGGAGCTGCGAGGA 61.696 66.667 0.00 0.00 0.00 3.71
57 58 2.685017 TGGTGGAGCTGCGAGGAT 60.685 61.111 0.00 0.00 0.00 3.24
58 59 2.202987 GGTGGAGCTGCGAGGATG 60.203 66.667 0.00 0.00 0.00 3.51
59 60 2.202987 GTGGAGCTGCGAGGATGG 60.203 66.667 0.00 0.00 0.00 3.51
60 61 4.166888 TGGAGCTGCGAGGATGGC 62.167 66.667 0.00 0.00 41.71 4.40
67 68 4.434685 GCGAGGATGGCAAGAGAG 57.565 61.111 0.00 0.00 40.68 3.20
68 69 1.819229 GCGAGGATGGCAAGAGAGA 59.181 57.895 0.00 0.00 40.68 3.10
69 70 0.176680 GCGAGGATGGCAAGAGAGAA 59.823 55.000 0.00 0.00 40.68 2.87
70 71 1.406069 GCGAGGATGGCAAGAGAGAAA 60.406 52.381 0.00 0.00 40.68 2.52
71 72 2.936993 GCGAGGATGGCAAGAGAGAAAA 60.937 50.000 0.00 0.00 40.68 2.29
72 73 3.338249 CGAGGATGGCAAGAGAGAAAAA 58.662 45.455 0.00 0.00 0.00 1.94
73 74 3.944015 CGAGGATGGCAAGAGAGAAAAAT 59.056 43.478 0.00 0.00 0.00 1.82
74 75 4.397417 CGAGGATGGCAAGAGAGAAAAATT 59.603 41.667 0.00 0.00 0.00 1.82
75 76 5.648572 GAGGATGGCAAGAGAGAAAAATTG 58.351 41.667 0.00 0.00 0.00 2.32
76 77 5.327732 AGGATGGCAAGAGAGAAAAATTGA 58.672 37.500 0.00 0.00 0.00 2.57
77 78 5.776716 AGGATGGCAAGAGAGAAAAATTGAA 59.223 36.000 0.00 0.00 0.00 2.69
78 79 6.071503 AGGATGGCAAGAGAGAAAAATTGAAG 60.072 38.462 0.00 0.00 0.00 3.02
79 80 6.071728 GGATGGCAAGAGAGAAAAATTGAAGA 60.072 38.462 0.00 0.00 0.00 2.87
80 81 6.323203 TGGCAAGAGAGAAAAATTGAAGAG 57.677 37.500 0.00 0.00 0.00 2.85
81 82 6.064060 TGGCAAGAGAGAAAAATTGAAGAGA 58.936 36.000 0.00 0.00 0.00 3.10
82 83 6.206243 TGGCAAGAGAGAAAAATTGAAGAGAG 59.794 38.462 0.00 0.00 0.00 3.20
83 84 6.429385 GGCAAGAGAGAAAAATTGAAGAGAGA 59.571 38.462 0.00 0.00 0.00 3.10
84 85 7.040823 GGCAAGAGAGAAAAATTGAAGAGAGAA 60.041 37.037 0.00 0.00 0.00 2.87
85 86 8.348507 GCAAGAGAGAAAAATTGAAGAGAGAAA 58.651 33.333 0.00 0.00 0.00 2.52
96 97 9.924650 AAATTGAAGAGAGAAAATTGAAGGATG 57.075 29.630 0.00 0.00 0.00 3.51
97 98 7.458409 TTGAAGAGAGAAAATTGAAGGATGG 57.542 36.000 0.00 0.00 0.00 3.51
98 99 6.782986 TGAAGAGAGAAAATTGAAGGATGGA 58.217 36.000 0.00 0.00 0.00 3.41
99 100 6.883217 TGAAGAGAGAAAATTGAAGGATGGAG 59.117 38.462 0.00 0.00 0.00 3.86
100 101 5.753716 AGAGAGAAAATTGAAGGATGGAGG 58.246 41.667 0.00 0.00 0.00 4.30
101 102 4.276642 AGAGAAAATTGAAGGATGGAGGC 58.723 43.478 0.00 0.00 0.00 4.70
102 103 3.019564 AGAAAATTGAAGGATGGAGGCG 58.980 45.455 0.00 0.00 0.00 5.52
103 104 1.106285 AAATTGAAGGATGGAGGCGC 58.894 50.000 0.00 0.00 0.00 6.53
104 105 1.097547 AATTGAAGGATGGAGGCGCG 61.098 55.000 0.00 0.00 0.00 6.86
105 106 2.947938 ATTGAAGGATGGAGGCGCGG 62.948 60.000 8.83 0.00 0.00 6.46
120 121 4.692475 CGGCGTTCGAAAGGGGGT 62.692 66.667 13.01 0.00 42.43 4.95
121 122 2.281970 GGCGTTCGAAAGGGGGTT 60.282 61.111 13.01 0.00 0.00 4.11
122 123 1.900016 GGCGTTCGAAAGGGGGTTT 60.900 57.895 13.01 0.00 0.00 3.27
123 124 1.284715 GCGTTCGAAAGGGGGTTTG 59.715 57.895 13.01 0.00 0.00 2.93
124 125 1.953772 CGTTCGAAAGGGGGTTTGG 59.046 57.895 0.00 0.00 0.00 3.28
125 126 0.820482 CGTTCGAAAGGGGGTTTGGT 60.820 55.000 0.00 0.00 0.00 3.67
126 127 0.671796 GTTCGAAAGGGGGTTTGGTG 59.328 55.000 0.00 0.00 0.00 4.17
127 128 0.259356 TTCGAAAGGGGGTTTGGTGT 59.741 50.000 0.00 0.00 0.00 4.16
128 129 0.466555 TCGAAAGGGGGTTTGGTGTG 60.467 55.000 0.00 0.00 0.00 3.82
129 130 1.460273 CGAAAGGGGGTTTGGTGTGG 61.460 60.000 0.00 0.00 0.00 4.17
130 131 1.074850 AAAGGGGGTTTGGTGTGGG 60.075 57.895 0.00 0.00 0.00 4.61
131 132 1.892441 AAAGGGGGTTTGGTGTGGGT 61.892 55.000 0.00 0.00 0.00 4.51
132 133 2.523168 GGGGGTTTGGTGTGGGTG 60.523 66.667 0.00 0.00 0.00 4.61
133 134 2.523168 GGGGTTTGGTGTGGGTGG 60.523 66.667 0.00 0.00 0.00 4.61
495 496 1.597854 CGAACCACTTGGCAGAGCA 60.598 57.895 0.00 0.00 39.32 4.26
496 497 1.572085 CGAACCACTTGGCAGAGCAG 61.572 60.000 0.00 0.00 39.32 4.24
501 502 1.436600 CACTTGGCAGAGCAGTACAG 58.563 55.000 0.00 0.00 0.00 2.74
507 508 1.878656 GCAGAGCAGTACAGGACCGT 61.879 60.000 0.00 0.00 0.00 4.83
519 520 1.548719 CAGGACCGTGTTGGATGACTA 59.451 52.381 0.00 0.00 42.00 2.59
543 544 2.221749 CACATCCAACTCACACAGTTCG 59.778 50.000 0.00 0.00 44.14 3.95
544 545 2.158957 ACATCCAACTCACACAGTTCGT 60.159 45.455 0.00 0.00 44.14 3.85
555 556 2.048877 AGTTCGTACGGTTGCGGG 60.049 61.111 16.52 0.00 0.00 6.13
557 558 2.090524 GTTCGTACGGTTGCGGGAG 61.091 63.158 16.52 0.00 0.00 4.30
565 566 1.072505 GGTTGCGGGAGGTTTGAGA 59.927 57.895 0.00 0.00 0.00 3.27
571 572 1.533469 CGGGAGGTTTGAGAGTCCGT 61.533 60.000 0.00 0.00 0.00 4.69
575 576 3.244318 GGGAGGTTTGAGAGTCCGTTTTA 60.244 47.826 0.00 0.00 0.00 1.52
585 586 2.422479 GAGTCCGTTTTAAAGATGCCCC 59.578 50.000 0.00 0.00 0.00 5.80
586 587 1.475280 GTCCGTTTTAAAGATGCCCCC 59.525 52.381 0.00 0.00 0.00 5.40
662 668 0.762461 AGCTCAGCCCAGATCCTACC 60.762 60.000 0.00 0.00 0.00 3.18
677 683 0.035317 CTACCTGGCAGCTGACAACA 59.965 55.000 25.38 10.44 29.15 3.33
678 684 0.692476 TACCTGGCAGCTGACAACAT 59.308 50.000 25.38 14.18 29.15 2.71
679 685 0.607489 ACCTGGCAGCTGACAACATC 60.607 55.000 25.38 0.00 29.15 3.06
680 686 0.607217 CCTGGCAGCTGACAACATCA 60.607 55.000 25.38 0.00 35.45 3.07
681 687 0.520404 CTGGCAGCTGACAACATCAC 59.480 55.000 25.38 0.00 32.37 3.06
682 688 0.179023 TGGCAGCTGACAACATCACA 60.179 50.000 23.06 0.00 32.37 3.58
683 689 0.953727 GGCAGCTGACAACATCACAA 59.046 50.000 20.43 0.00 32.37 3.33
684 690 1.335324 GGCAGCTGACAACATCACAAC 60.335 52.381 20.43 0.00 32.37 3.32
700 706 6.015180 ACATCACAACAAGCAATAATGGACTT 60.015 34.615 0.00 0.00 0.00 3.01
728 734 3.823304 AGTTTGAATTGACTTGGAGGAGC 59.177 43.478 0.00 0.00 0.00 4.70
762 777 2.188837 TCGATGGATTTCAGTCGACG 57.811 50.000 10.46 5.48 38.09 5.12
797 813 1.273327 CCAAGTTGAATTGGGAGGCAC 59.727 52.381 3.87 0.00 45.07 5.01
849 869 1.823260 CGAACCACTTGCAACGCGTA 61.823 55.000 14.46 0.00 0.00 4.42
1249 1283 2.444256 GGACTTGCGGGGCCTATCT 61.444 63.158 0.84 0.00 0.00 1.98
1317 1351 1.606668 GCCAACAACAAACTGATCGGA 59.393 47.619 9.00 0.00 0.00 4.55
1324 1358 3.703001 ACAAACTGATCGGAACCATCT 57.297 42.857 9.00 0.00 0.00 2.90
1425 1459 1.289160 TGATACAGCTCAAGGGCCTT 58.711 50.000 14.48 14.48 0.00 4.35
1605 1679 3.119495 GGAGCAACAATACCATCACAACC 60.119 47.826 0.00 0.00 0.00 3.77
1626 1700 1.564207 GGAGCGACAATACCGTAACC 58.436 55.000 0.00 0.00 0.00 2.85
1803 1877 0.615331 ATGTCGTGTCTGGGAGCAAT 59.385 50.000 0.00 0.00 0.00 3.56
1910 6827 5.751586 TGGATGTACCATCCTTTTTCTACC 58.248 41.667 20.67 0.00 44.64 3.18
2034 7231 1.400629 GCATCGTGGATGTATGCATGC 60.401 52.381 11.82 11.82 44.27 4.06
2073 7270 4.061596 TGTGATGTGTGATGCTTTCGTAA 58.938 39.130 0.00 0.00 0.00 3.18
2199 8540 3.748048 CACTGTCGAATGTTTGGATGAGT 59.252 43.478 0.00 0.00 0.00 3.41
2237 8585 3.612423 GGCGTGGCAAGCTATTTAAAAAG 59.388 43.478 23.96 0.00 34.52 2.27
2498 10563 0.883833 GGGAGCTGACACAAACCATG 59.116 55.000 0.00 0.00 0.00 3.66
2586 10651 2.203070 CGATCGGCCAAGAAGGGG 60.203 66.667 7.38 0.00 38.09 4.79
2646 10711 5.009610 TCGACCGAGAACAATGATGATGATA 59.990 40.000 0.00 0.00 0.00 2.15
2647 10712 5.866092 CGACCGAGAACAATGATGATGATAT 59.134 40.000 0.00 0.00 0.00 1.63
2648 10713 7.029563 CGACCGAGAACAATGATGATGATATA 58.970 38.462 0.00 0.00 0.00 0.86
2649 10714 7.704047 CGACCGAGAACAATGATGATGATATAT 59.296 37.037 0.00 0.00 0.00 0.86
2652 10717 9.032420 CCGAGAACAATGATGATGATATATGAG 57.968 37.037 0.00 0.00 0.00 2.90
2692 10757 0.592637 CAACAAAGGCAGCGATGACA 59.407 50.000 10.23 0.00 0.00 3.58
2709 10774 4.677673 TGACAATGACGAGGATGATGAT 57.322 40.909 0.00 0.00 0.00 2.45
2710 10775 4.374399 TGACAATGACGAGGATGATGATG 58.626 43.478 0.00 0.00 0.00 3.07
2711 10776 4.099881 TGACAATGACGAGGATGATGATGA 59.900 41.667 0.00 0.00 0.00 2.92
2712 10777 5.221581 TGACAATGACGAGGATGATGATGAT 60.222 40.000 0.00 0.00 0.00 2.45
2713 10778 4.995487 ACAATGACGAGGATGATGATGATG 59.005 41.667 0.00 0.00 0.00 3.07
2714 10779 5.221581 ACAATGACGAGGATGATGATGATGA 60.222 40.000 0.00 0.00 0.00 2.92
2724 10789 7.051000 AGGATGATGATGATGATGATGATGAC 58.949 38.462 0.00 0.00 0.00 3.06
2744 10809 1.983605 CGACTACGTGAAAGCATCGTT 59.016 47.619 0.00 0.00 38.69 3.85
2767 10832 1.134670 CCTTTAAGCTCAGAGACCCCG 60.135 57.143 0.00 0.00 0.00 5.73
2823 10888 0.966179 ATGTCTATGCCGATGCCGTA 59.034 50.000 0.00 0.00 36.33 4.02
2824 10889 0.313987 TGTCTATGCCGATGCCGTAG 59.686 55.000 0.00 0.00 36.33 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.202492 CTGCCGGAACTCGTCGAG 60.202 66.667 20.57 20.57 37.11 4.04
1 2 3.744719 CCTGCCGGAACTCGTCGA 61.745 66.667 5.05 0.00 37.11 4.20
2 3 4.796231 CCCTGCCGGAACTCGTCG 62.796 72.222 5.05 0.00 37.11 5.12
3 4 4.452733 CCCCTGCCGGAACTCGTC 62.453 72.222 5.05 0.00 37.11 4.20
5 6 4.760047 CACCCCTGCCGGAACTCG 62.760 72.222 5.05 0.00 38.88 4.18
6 7 3.637273 ACACCCCTGCCGGAACTC 61.637 66.667 5.05 0.00 0.00 3.01
7 8 3.953775 CACACCCCTGCCGGAACT 61.954 66.667 5.05 0.00 0.00 3.01
37 38 4.767255 CTCGCAGCTCCACCACCC 62.767 72.222 0.00 0.00 0.00 4.61
38 39 4.767255 CCTCGCAGCTCCACCACC 62.767 72.222 0.00 0.00 0.00 4.61
39 40 3.023949 ATCCTCGCAGCTCCACCAC 62.024 63.158 0.00 0.00 0.00 4.16
40 41 2.685017 ATCCTCGCAGCTCCACCA 60.685 61.111 0.00 0.00 0.00 4.17
41 42 2.202987 CATCCTCGCAGCTCCACC 60.203 66.667 0.00 0.00 0.00 4.61
42 43 2.202987 CCATCCTCGCAGCTCCAC 60.203 66.667 0.00 0.00 0.00 4.02
43 44 4.166888 GCCATCCTCGCAGCTCCA 62.167 66.667 0.00 0.00 0.00 3.86
44 45 3.687321 TTGCCATCCTCGCAGCTCC 62.687 63.158 0.00 0.00 37.57 4.70
45 46 2.124983 TTGCCATCCTCGCAGCTC 60.125 61.111 0.00 0.00 37.57 4.09
46 47 2.124819 CTTGCCATCCTCGCAGCT 60.125 61.111 0.00 0.00 37.57 4.24
47 48 2.124983 TCTTGCCATCCTCGCAGC 60.125 61.111 0.00 0.00 37.57 5.25
48 49 0.530211 CTCTCTTGCCATCCTCGCAG 60.530 60.000 0.00 0.00 37.57 5.18
49 50 0.972471 TCTCTCTTGCCATCCTCGCA 60.972 55.000 0.00 0.00 0.00 5.10
50 51 0.176680 TTCTCTCTTGCCATCCTCGC 59.823 55.000 0.00 0.00 0.00 5.03
51 52 2.680312 TTTCTCTCTTGCCATCCTCG 57.320 50.000 0.00 0.00 0.00 4.63
52 53 5.416952 TCAATTTTTCTCTCTTGCCATCCTC 59.583 40.000 0.00 0.00 0.00 3.71
53 54 5.327732 TCAATTTTTCTCTCTTGCCATCCT 58.672 37.500 0.00 0.00 0.00 3.24
54 55 5.649782 TCAATTTTTCTCTCTTGCCATCC 57.350 39.130 0.00 0.00 0.00 3.51
55 56 6.917533 TCTTCAATTTTTCTCTCTTGCCATC 58.082 36.000 0.00 0.00 0.00 3.51
56 57 6.718454 TCTCTTCAATTTTTCTCTCTTGCCAT 59.282 34.615 0.00 0.00 0.00 4.40
57 58 6.064060 TCTCTTCAATTTTTCTCTCTTGCCA 58.936 36.000 0.00 0.00 0.00 4.92
58 59 6.429385 TCTCTCTTCAATTTTTCTCTCTTGCC 59.571 38.462 0.00 0.00 0.00 4.52
59 60 7.432350 TCTCTCTTCAATTTTTCTCTCTTGC 57.568 36.000 0.00 0.00 0.00 4.01
70 71 9.924650 CATCCTTCAATTTTCTCTCTTCAATTT 57.075 29.630 0.00 0.00 0.00 1.82
71 72 8.529476 CCATCCTTCAATTTTCTCTCTTCAATT 58.471 33.333 0.00 0.00 0.00 2.32
72 73 7.892241 TCCATCCTTCAATTTTCTCTCTTCAAT 59.108 33.333 0.00 0.00 0.00 2.57
73 74 7.233632 TCCATCCTTCAATTTTCTCTCTTCAA 58.766 34.615 0.00 0.00 0.00 2.69
74 75 6.782986 TCCATCCTTCAATTTTCTCTCTTCA 58.217 36.000 0.00 0.00 0.00 3.02
75 76 6.318396 CCTCCATCCTTCAATTTTCTCTCTTC 59.682 42.308 0.00 0.00 0.00 2.87
76 77 6.186234 CCTCCATCCTTCAATTTTCTCTCTT 58.814 40.000 0.00 0.00 0.00 2.85
77 78 5.753716 CCTCCATCCTTCAATTTTCTCTCT 58.246 41.667 0.00 0.00 0.00 3.10
78 79 4.337836 GCCTCCATCCTTCAATTTTCTCTC 59.662 45.833 0.00 0.00 0.00 3.20
79 80 4.276642 GCCTCCATCCTTCAATTTTCTCT 58.723 43.478 0.00 0.00 0.00 3.10
80 81 3.065925 CGCCTCCATCCTTCAATTTTCTC 59.934 47.826 0.00 0.00 0.00 2.87
81 82 3.019564 CGCCTCCATCCTTCAATTTTCT 58.980 45.455 0.00 0.00 0.00 2.52
82 83 2.480244 GCGCCTCCATCCTTCAATTTTC 60.480 50.000 0.00 0.00 0.00 2.29
83 84 1.478105 GCGCCTCCATCCTTCAATTTT 59.522 47.619 0.00 0.00 0.00 1.82
84 85 1.106285 GCGCCTCCATCCTTCAATTT 58.894 50.000 0.00 0.00 0.00 1.82
85 86 1.097547 CGCGCCTCCATCCTTCAATT 61.098 55.000 0.00 0.00 0.00 2.32
86 87 1.524621 CGCGCCTCCATCCTTCAAT 60.525 57.895 0.00 0.00 0.00 2.57
87 88 2.125147 CGCGCCTCCATCCTTCAA 60.125 61.111 0.00 0.00 0.00 2.69
88 89 4.161295 CCGCGCCTCCATCCTTCA 62.161 66.667 0.00 0.00 0.00 3.02
103 104 4.692475 ACCCCCTTTCGAACGCCG 62.692 66.667 0.00 0.00 40.25 6.46
104 105 1.900016 AAACCCCCTTTCGAACGCC 60.900 57.895 0.00 0.00 0.00 5.68
105 106 1.284715 CAAACCCCCTTTCGAACGC 59.715 57.895 0.00 0.00 0.00 4.84
106 107 0.820482 ACCAAACCCCCTTTCGAACG 60.820 55.000 0.00 0.00 0.00 3.95
107 108 0.671796 CACCAAACCCCCTTTCGAAC 59.328 55.000 0.00 0.00 0.00 3.95
108 109 0.259356 ACACCAAACCCCCTTTCGAA 59.741 50.000 0.00 0.00 0.00 3.71
109 110 0.466555 CACACCAAACCCCCTTTCGA 60.467 55.000 0.00 0.00 0.00 3.71
110 111 1.460273 CCACACCAAACCCCCTTTCG 61.460 60.000 0.00 0.00 0.00 3.46
111 112 1.118965 CCCACACCAAACCCCCTTTC 61.119 60.000 0.00 0.00 0.00 2.62
112 113 1.074850 CCCACACCAAACCCCCTTT 60.075 57.895 0.00 0.00 0.00 3.11
113 114 2.329399 ACCCACACCAAACCCCCTT 61.329 57.895 0.00 0.00 0.00 3.95
114 115 2.702253 ACCCACACCAAACCCCCT 60.702 61.111 0.00 0.00 0.00 4.79
115 116 2.523168 CACCCACACCAAACCCCC 60.523 66.667 0.00 0.00 0.00 5.40
116 117 2.523168 CCACCCACACCAAACCCC 60.523 66.667 0.00 0.00 0.00 4.95
475 476 1.371183 CTCTGCCAAGTGGTTCGGA 59.629 57.895 0.00 0.00 37.57 4.55
477 478 1.572085 CTGCTCTGCCAAGTGGTTCG 61.572 60.000 0.00 0.00 37.57 3.95
479 480 0.764890 TACTGCTCTGCCAAGTGGTT 59.235 50.000 0.00 0.00 37.57 3.67
495 496 1.275291 CATCCAACACGGTCCTGTACT 59.725 52.381 0.00 0.00 35.57 2.73
496 497 1.274167 TCATCCAACACGGTCCTGTAC 59.726 52.381 0.00 0.00 35.57 2.90
501 502 2.740447 GTTTAGTCATCCAACACGGTCC 59.260 50.000 0.00 0.00 35.57 4.46
519 520 3.620488 ACTGTGTGAGTTGGATGTGTTT 58.380 40.909 0.00 0.00 0.00 2.83
525 526 2.910688 ACGAACTGTGTGAGTTGGAT 57.089 45.000 0.00 0.00 45.48 3.41
541 542 3.751246 CCTCCCGCAACCGTACGA 61.751 66.667 18.76 0.00 0.00 3.43
543 544 1.301953 AAACCTCCCGCAACCGTAC 60.302 57.895 0.00 0.00 0.00 3.67
544 545 1.301874 CAAACCTCCCGCAACCGTA 60.302 57.895 0.00 0.00 0.00 4.02
555 556 5.756833 TCTTTAAAACGGACTCTCAAACCTC 59.243 40.000 0.00 0.00 0.00 3.85
557 558 5.996669 TCTTTAAAACGGACTCTCAAACC 57.003 39.130 0.00 0.00 0.00 3.27
565 566 2.443416 GGGGCATCTTTAAAACGGACT 58.557 47.619 0.00 0.00 0.00 3.85
571 572 4.202409 CCTTTTGTGGGGGCATCTTTAAAA 60.202 41.667 0.00 0.00 0.00 1.52
575 576 1.351076 CCTTTTGTGGGGGCATCTTT 58.649 50.000 0.00 0.00 0.00 2.52
585 586 3.670627 GCAAGAATAGTCGCCTTTTGTGG 60.671 47.826 0.00 0.00 0.00 4.17
586 587 3.058293 TGCAAGAATAGTCGCCTTTTGTG 60.058 43.478 0.00 0.00 0.00 3.33
662 668 0.520404 GTGATGTTGTCAGCTGCCAG 59.480 55.000 9.47 0.00 37.56 4.85
677 683 6.209192 TCAAGTCCATTATTGCTTGTTGTGAT 59.791 34.615 0.00 0.00 39.28 3.06
678 684 5.534278 TCAAGTCCATTATTGCTTGTTGTGA 59.466 36.000 0.00 0.00 39.28 3.58
679 685 5.771469 TCAAGTCCATTATTGCTTGTTGTG 58.229 37.500 0.00 0.00 39.28 3.33
680 686 6.265196 TCTTCAAGTCCATTATTGCTTGTTGT 59.735 34.615 0.00 0.00 39.28 3.32
681 687 6.680810 TCTTCAAGTCCATTATTGCTTGTTG 58.319 36.000 0.00 0.00 39.28 3.33
682 688 6.899393 TCTTCAAGTCCATTATTGCTTGTT 57.101 33.333 0.00 0.00 39.28 2.83
683 689 6.491403 ACTTCTTCAAGTCCATTATTGCTTGT 59.509 34.615 0.00 0.00 38.62 3.16
684 690 6.917533 ACTTCTTCAAGTCCATTATTGCTTG 58.082 36.000 0.00 0.00 38.62 4.01
700 706 6.039717 CCTCCAAGTCAATTCAAACTTCTTCA 59.960 38.462 0.00 0.00 33.53 3.02
745 760 2.194271 GTCCGTCGACTGAAATCCATC 58.806 52.381 14.70 0.00 35.99 3.51
762 777 4.991687 TCAACTTGGTTTTTGTTGTTGTCC 59.008 37.500 0.00 0.00 41.05 4.02
849 869 2.739913 GTGTGTGTGTGTGTGTGTAAGT 59.260 45.455 0.00 0.00 0.00 2.24
1065 1099 3.296709 GAGGTCGTCGGTGTGGCAT 62.297 63.158 0.00 0.00 0.00 4.40
1164 1198 3.160585 CTCACACCTTCCCAGCCA 58.839 61.111 0.00 0.00 0.00 4.75
1245 1279 1.696336 GCCAAGGATGCTCCAGAGATA 59.304 52.381 0.00 0.00 39.61 1.98
1249 1283 2.586245 CGCCAAGGATGCTCCAGA 59.414 61.111 5.21 0.00 39.61 3.86
1317 1351 4.079615 TCACCAATCCATGATGAGATGGTT 60.080 41.667 11.51 0.00 43.20 3.67
1324 1358 3.054213 TCAAGCTCACCAATCCATGATGA 60.054 43.478 0.00 0.00 0.00 2.92
1425 1459 2.137528 TGAACGACCAGTGGAGGCA 61.138 57.895 18.40 9.25 0.00 4.75
1605 1679 0.101040 TTACGGTATTGTCGCTCCCG 59.899 55.000 0.00 0.00 44.06 5.14
1803 1877 5.733620 ATTAACCTCCTGTCACGACTTTA 57.266 39.130 0.00 0.00 0.00 1.85
2034 7231 7.025365 CACATCACAAAGAATAGAACACATGG 58.975 38.462 0.00 0.00 0.00 3.66
2073 7270 2.192605 GCCAAATGCCGAATCAGGT 58.807 52.632 0.00 0.00 0.00 4.00
2199 8540 3.147595 CCCGGTCGCTCCATCTGA 61.148 66.667 0.00 0.00 35.57 3.27
2225 8573 7.538575 TGTTCCATCTGCTCTTTTTAAATAGC 58.461 34.615 9.58 9.58 38.26 2.97
2228 8576 9.783081 ATTTTGTTCCATCTGCTCTTTTTAAAT 57.217 25.926 0.00 0.00 0.00 1.40
2237 8585 2.231964 TGCCATTTTGTTCCATCTGCTC 59.768 45.455 0.00 0.00 0.00 4.26
2278 8626 3.703286 TCAAGACGGATACATGGTACG 57.297 47.619 0.00 0.00 0.00 3.67
2416 9697 2.560981 GAGAGGGCTAGCTCCTTATGAC 59.439 54.545 21.32 11.23 34.21 3.06
2425 10488 0.887387 GTCGATCGAGAGGGCTAGCT 60.887 60.000 20.09 0.00 0.00 3.32
2586 10651 0.389948 CCAGTGTACTCGGCCTTGTC 60.390 60.000 0.00 0.00 0.00 3.18
2646 10711 8.593679 TCGTAATGGTTGTTATCATCCTCATAT 58.406 33.333 3.21 0.00 35.22 1.78
2647 10712 7.870954 GTCGTAATGGTTGTTATCATCCTCATA 59.129 37.037 3.21 0.00 35.22 2.15
2648 10713 6.706270 GTCGTAATGGTTGTTATCATCCTCAT 59.294 38.462 3.21 0.00 35.22 2.90
2649 10714 6.046593 GTCGTAATGGTTGTTATCATCCTCA 58.953 40.000 3.21 0.00 35.22 3.86
2652 10717 6.092944 TGTTGTCGTAATGGTTGTTATCATCC 59.907 38.462 0.00 0.00 34.86 3.51
2667 10732 0.584396 CGCTGCCTTTGTTGTCGTAA 59.416 50.000 0.00 0.00 0.00 3.18
2668 10733 0.249531 TCGCTGCCTTTGTTGTCGTA 60.250 50.000 0.00 0.00 0.00 3.43
2692 10757 5.479124 TCATCATCATCATCCTCGTCATT 57.521 39.130 0.00 0.00 0.00 2.57
2709 10774 4.787598 CGTAGTCGTCATCATCATCATCA 58.212 43.478 0.00 0.00 0.00 3.07
2724 10789 1.614385 ACGATGCTTTCACGTAGTCG 58.386 50.000 0.00 0.00 41.61 4.18


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

AutoCloner maintained by Alex Coulton.