Multiple sequence alignment - TraesCS7D01G009100

Loading Multiple Alignment...

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 TraesCS7D01G009100 chr7D 100.000 4706 0 0 1 4706 4415889 4411184 0.000000e+00 8691
1 TraesCS7D01G009100 chr7D 79.200 2024 366 37 1783 3773 4503405 4501404 0.000000e+00 1354
2 TraesCS7D01G009100 chr7D 80.380 948 166 18 1756 2695 4291496 4290561 0.000000e+00 702
3 TraesCS7D01G009100 chr7D 77.040 858 179 15 1784 2635 4794077 4794922 1.180000e-130 477
4 TraesCS7D01G009100 chr7D 79.256 699 131 12 3021 3715 4424232 4423544 4.260000e-130 475
5 TraesCS7D01G009100 chr7D 78.234 657 126 13 1756 2406 29581912 29582557 5.670000e-109 405
6 TraesCS7D01G009100 chr7D 78.550 331 54 11 4354 4676 4388880 4388559 7.990000e-48 202
7 TraesCS7D01G009100 chr7D 83.981 206 6 17 3921 4118 4389283 4389097 6.260000e-39 172
8 TraesCS7D01G009100 chr4A 94.324 2114 92 11 1742 3835 739152604 739154709 0.000000e+00 3214
9 TraesCS7D01G009100 chr4A 89.547 861 51 14 910 1748 739151599 739152442 0.000000e+00 1055
10 TraesCS7D01G009100 chr4A 94.280 472 24 1 4235 4703 739155637 739156108 0.000000e+00 719
11 TraesCS7D01G009100 chr4A 79.831 947 175 14 1756 2695 739273603 739274540 0.000000e+00 676
12 TraesCS7D01G009100 chr4A 87.897 504 33 11 1 476 739150688 739151191 6.830000e-158 568
13 TraesCS7D01G009100 chr4A 79.597 794 153 7 2988 3773 739080543 739081335 1.140000e-155 560
14 TraesCS7D01G009100 chr4A 79.542 699 129 12 3018 3712 739131523 739132211 1.970000e-133 486
15 TraesCS7D01G009100 chr4A 85.714 357 39 8 4353 4703 739160317 739160667 2.680000e-97 366
16 TraesCS7D01G009100 chr4A 76.399 661 147 5 3018 3672 739275475 739276132 9.690000e-92 348
17 TraesCS7D01G009100 chr4A 93.860 114 4 2 504 614 739151184 739151297 8.100000e-38 169
18 TraesCS7D01G009100 chr4A 95.000 80 4 0 3918 3997 739159259 739159338 4.940000e-25 126
19 TraesCS7D01G009100 chr7A 93.592 2169 90 26 1733 3891 4208219 4206090 0.000000e+00 3190
20 TraesCS7D01G009100 chr7A 86.252 1833 97 57 37 1759 4210028 4208241 0.000000e+00 1845
21 TraesCS7D01G009100 chr7A 92.194 743 39 10 3977 4706 4203023 4202287 0.000000e+00 1033
22 TraesCS7D01G009100 chr7A 81.110 937 158 14 1783 2708 4329851 4328923 0.000000e+00 732
23 TraesCS7D01G009100 chr7A 80.696 948 170 10 1783 2723 4254334 4253393 0.000000e+00 725
24 TraesCS7D01G009100 chr7A 79.262 921 176 11 1783 2695 4069961 4069048 3.090000e-176 628
25 TraesCS7D01G009100 chr7A 77.326 1107 205 30 2700 3773 4328899 4327806 3.110000e-171 612
26 TraesCS7D01G009100 chr7A 79.286 700 129 13 3021 3715 4252806 4252118 4.260000e-130 475
27 TraesCS7D01G009100 chr7A 76.779 857 183 13 1784 2635 4626562 4627407 2.560000e-127 466
28 TraesCS7D01G009100 chr7A 88.889 378 25 11 3923 4289 4203710 4203339 2.580000e-122 449
29 TraesCS7D01G009100 chr7A 82.095 296 26 11 3921 4208 4196228 4195952 1.320000e-55 228


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 TraesCS7D01G009100 chr7D 4411184 4415889 4705 True 8691.000000 8691 100.000000 1 4706 1 chr7D.!!$R2 4705
1 TraesCS7D01G009100 chr7D 4501404 4503405 2001 True 1354.000000 1354 79.200000 1783 3773 1 chr7D.!!$R4 1990
2 TraesCS7D01G009100 chr7D 4290561 4291496 935 True 702.000000 702 80.380000 1756 2695 1 chr7D.!!$R1 939
3 TraesCS7D01G009100 chr7D 4794077 4794922 845 False 477.000000 477 77.040000 1784 2635 1 chr7D.!!$F1 851
4 TraesCS7D01G009100 chr7D 4423544 4424232 688 True 475.000000 475 79.256000 3021 3715 1 chr7D.!!$R3 694
5 TraesCS7D01G009100 chr7D 29581912 29582557 645 False 405.000000 405 78.234000 1756 2406 1 chr7D.!!$F2 650
6 TraesCS7D01G009100 chr4A 739150688 739160667 9979 False 888.142857 3214 91.517429 1 4703 7 chr4A.!!$F3 4702
7 TraesCS7D01G009100 chr4A 739080543 739081335 792 False 560.000000 560 79.597000 2988 3773 1 chr4A.!!$F1 785
8 TraesCS7D01G009100 chr4A 739273603 739276132 2529 False 512.000000 676 78.115000 1756 3672 2 chr4A.!!$F4 1916
9 TraesCS7D01G009100 chr4A 739131523 739132211 688 False 486.000000 486 79.542000 3018 3712 1 chr4A.!!$F2 694
10 TraesCS7D01G009100 chr7A 4202287 4210028 7741 True 1629.250000 3190 90.231750 37 4706 4 chr7A.!!$R3 4669
11 TraesCS7D01G009100 chr7A 4327806 4329851 2045 True 672.000000 732 79.218000 1783 3773 2 chr7A.!!$R5 1990
12 TraesCS7D01G009100 chr7A 4069048 4069961 913 True 628.000000 628 79.262000 1783 2695 1 chr7A.!!$R1 912
13 TraesCS7D01G009100 chr7A 4252118 4254334 2216 True 600.000000 725 79.991000 1783 3715 2 chr7A.!!$R4 1932
14 TraesCS7D01G009100 chr7A 4626562 4627407 845 False 466.000000 466 76.779000 1784 2635 1 chr7A.!!$F1 851

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
719 784 0.109532 CCCCCACACACACACACATA 59.890 55.0 0.0 0.0 0.00 2.29 F
2081 2406 0.105607 GAAGACCCCCTCCTCCGTAT 60.106 60.0 0.0 0.0 0.00 3.06 F
2424 2749 0.460311 AGTGGCATGACTACTACGCC 59.540 55.0 0.0 0.0 38.52 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2424 2749 0.682209 CTGCATCAAACCTCCCCAGG 60.682 60.0 0.0 0.0 46.87 4.45 R
3235 4487 0.384309 TAGCTAACATCGGCCTCGTG 59.616 55.0 0.0 0.0 37.69 4.35 R
4073 8724 0.394488 TCGGTTGTTGCCTTGTTGGA 60.394 50.0 0.0 0.0 38.35 3.53 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
23 24 3.664107 TCCATTAGATAAGCATGACCGC 58.336 45.455 0.00 0.00 0.00 5.68
55 56 6.775594 AATAAAAGGACCCAATAGAACTGC 57.224 37.500 0.00 0.00 0.00 4.40
126 137 6.350110 GGTGTTTCCATTTGTATAGTGCACAT 60.350 38.462 21.04 12.77 35.97 3.21
168 180 5.611374 AGTTTGTGCTCTGTGTGTATAAGT 58.389 37.500 0.00 0.00 0.00 2.24
187 219 5.340439 AAGTGTTGTGGCCTAGTCTATAC 57.660 43.478 3.32 0.00 0.00 1.47
249 281 5.348724 GCGTCTATTGTGAAGTCTCATTTCA 59.651 40.000 0.00 0.00 33.05 2.69
292 325 0.326264 GAGGCTGGAACCACTCATGT 59.674 55.000 0.00 0.00 0.00 3.21
355 416 5.702670 TCTCTCTACTTTGTTTGCATCCTTG 59.297 40.000 0.00 0.00 0.00 3.61
434 495 0.528017 CTCACTAGTCTTGAGCGGCA 59.472 55.000 1.45 0.00 34.41 5.69
450 511 1.539065 CGGCAAGGCTGGTACTCTATG 60.539 57.143 0.00 0.00 0.00 2.23
475 536 6.539649 TGTTTTCTTCTATGTAGTGCACAC 57.460 37.500 21.04 15.19 40.86 3.82
481 542 6.230472 TCTTCTATGTAGTGCACACAACATT 58.770 36.000 26.92 16.32 40.86 2.71
561 623 5.647658 GGAGTGTTGGATGTTGTGATCAATA 59.352 40.000 0.00 0.00 35.92 1.90
609 671 1.682740 GGCGAGGCTAGTACTCTCTT 58.317 55.000 0.00 0.00 32.83 2.85
610 672 1.335496 GGCGAGGCTAGTACTCTCTTG 59.665 57.143 0.00 0.92 32.83 3.02
612 674 2.424246 GCGAGGCTAGTACTCTCTTGTT 59.576 50.000 0.00 0.00 32.83 2.83
614 676 4.416620 CGAGGCTAGTACTCTCTTGTTTG 58.583 47.826 0.00 0.00 32.83 2.93
618 680 4.621886 GGCTAGTACTCTCTTGTTTGTTCG 59.378 45.833 0.00 0.00 0.00 3.95
622 687 4.686554 AGTACTCTCTTGTTTGTTCGATGC 59.313 41.667 0.00 0.00 0.00 3.91
627 692 2.553602 TCTTGTTTGTTCGATGCTGCAT 59.446 40.909 16.20 16.20 0.00 3.96
650 715 9.159364 GCATGCATCATCTTCATAACTCTATTA 57.841 33.333 14.21 0.00 0.00 0.98
662 727 9.451002 TTCATAACTCTATTATCTCCCTCTACG 57.549 37.037 0.00 0.00 0.00 3.51
663 728 8.604184 TCATAACTCTATTATCTCCCTCTACGT 58.396 37.037 0.00 0.00 0.00 3.57
664 729 9.887629 CATAACTCTATTATCTCCCTCTACGTA 57.112 37.037 0.00 0.00 0.00 3.57
665 730 9.889128 ATAACTCTATTATCTCCCTCTACGTAC 57.111 37.037 0.00 0.00 0.00 3.67
666 731 6.710278 ACTCTATTATCTCCCTCTACGTACC 58.290 44.000 0.00 0.00 0.00 3.34
667 732 6.059787 TCTATTATCTCCCTCTACGTACCC 57.940 45.833 0.00 0.00 0.00 3.69
668 733 3.515602 TTATCTCCCTCTACGTACCCC 57.484 52.381 0.00 0.00 0.00 4.95
669 734 0.482006 ATCTCCCTCTACGTACCCCC 59.518 60.000 0.00 0.00 0.00 5.40
714 779 2.518349 CCACCCCCACACACACAC 60.518 66.667 0.00 0.00 0.00 3.82
717 782 2.273776 CCCCCACACACACACACA 59.726 61.111 0.00 0.00 0.00 3.72
718 783 1.152777 CCCCCACACACACACACAT 60.153 57.895 0.00 0.00 0.00 3.21
719 784 0.109532 CCCCCACACACACACACATA 59.890 55.000 0.00 0.00 0.00 2.29
720 785 1.234821 CCCCACACACACACACATAC 58.765 55.000 0.00 0.00 0.00 2.39
721 786 1.202758 CCCCACACACACACACATACT 60.203 52.381 0.00 0.00 0.00 2.12
722 787 2.571212 CCCACACACACACACATACTT 58.429 47.619 0.00 0.00 0.00 2.24
723 788 2.948979 CCCACACACACACACATACTTT 59.051 45.455 0.00 0.00 0.00 2.66
743 808 2.623878 TTTTCAACACGAGTAGGGCA 57.376 45.000 0.00 0.00 0.00 5.36
758 824 2.641197 GGCACGACCCAAAATCTGT 58.359 52.632 0.00 0.00 0.00 3.41
760 826 0.521735 GCACGACCCAAAATCTGTCC 59.478 55.000 0.00 0.00 0.00 4.02
761 827 1.882352 GCACGACCCAAAATCTGTCCT 60.882 52.381 0.00 0.00 0.00 3.85
763 829 3.670625 CACGACCCAAAATCTGTCCTAA 58.329 45.455 0.00 0.00 0.00 2.69
764 830 3.435671 CACGACCCAAAATCTGTCCTAAC 59.564 47.826 0.00 0.00 0.00 2.34
766 832 4.261801 CGACCCAAAATCTGTCCTAACAT 58.738 43.478 0.00 0.00 34.13 2.71
768 834 5.183140 CGACCCAAAATCTGTCCTAACATTT 59.817 40.000 0.00 0.00 34.13 2.32
770 836 7.094549 CGACCCAAAATCTGTCCTAACATTTTA 60.095 37.037 0.00 0.00 34.13 1.52
771 837 8.664669 ACCCAAAATCTGTCCTAACATTTTAT 57.335 30.769 0.00 0.00 34.13 1.40
807 885 5.519722 ACAAAACTAGAAATTGCAACTCGG 58.480 37.500 0.00 3.42 0.00 4.63
814 892 3.751698 AGAAATTGCAACTCGGTCCTAAC 59.248 43.478 0.00 0.00 0.00 2.34
896 991 2.559698 TCGCCAAGATCCAAGACAAA 57.440 45.000 0.00 0.00 0.00 2.83
948 1044 6.072230 GGAAGTAGTAGTAACGTTCCTCTTGT 60.072 42.308 2.82 0.00 34.51 3.16
965 1061 1.295792 TGTGAACAGAAGGAACACGC 58.704 50.000 0.00 0.00 34.72 5.34
1063 1163 1.497722 CTTTCCAGTTCCGAAGCGC 59.502 57.895 0.00 0.00 0.00 5.92
1064 1164 1.227704 TTTCCAGTTCCGAAGCGCA 60.228 52.632 11.47 0.00 0.00 6.09
1233 1342 2.506438 GCGCTAGTCGTCACCCAC 60.506 66.667 0.00 0.00 41.07 4.61
1263 1381 3.782042 GTGGGCGACGATCTCAAC 58.218 61.111 0.00 0.00 0.00 3.18
1264 1382 2.158959 GTGGGCGACGATCTCAACG 61.159 63.158 0.00 0.00 0.00 4.10
1265 1383 2.337246 TGGGCGACGATCTCAACGA 61.337 57.895 0.00 0.00 34.70 3.85
1487 1609 3.526534 TGAACGGTATGCAATCGATTCA 58.473 40.909 7.92 9.91 0.00 2.57
1489 1611 4.574421 TGAACGGTATGCAATCGATTCATT 59.426 37.500 20.54 7.95 0.00 2.57
1490 1612 5.065859 TGAACGGTATGCAATCGATTCATTT 59.934 36.000 20.54 12.84 0.00 2.32
1491 1613 6.258947 TGAACGGTATGCAATCGATTCATTTA 59.741 34.615 20.54 7.98 0.00 1.40
1492 1614 6.228273 ACGGTATGCAATCGATTCATTTAG 57.772 37.500 20.54 15.68 0.00 1.85
1493 1615 5.758296 ACGGTATGCAATCGATTCATTTAGT 59.242 36.000 20.54 16.08 0.00 2.24
1571 1700 8.158169 TGCATTACATGGTTTGATCTATCTTC 57.842 34.615 0.00 0.00 0.00 2.87
1586 1715 1.865865 TCTTCCACACTTTCGCTGTC 58.134 50.000 0.00 0.00 0.00 3.51
1743 1889 2.210116 CGTACCAGCTGTCTGTTTGTT 58.790 47.619 13.81 0.00 38.66 2.83
1977 2302 2.903855 GGATCCGCCACCATGCTG 60.904 66.667 0.00 0.00 36.34 4.41
2081 2406 0.105607 GAAGACCCCCTCCTCCGTAT 60.106 60.000 0.00 0.00 0.00 3.06
2151 2476 2.893398 GACAGGGACTTCCGCGAT 59.107 61.111 8.23 0.00 41.52 4.58
2338 2663 1.834263 GGGAGTGCATTGACCTCTACT 59.166 52.381 0.00 0.00 0.00 2.57
2339 2664 2.419297 GGGAGTGCATTGACCTCTACTG 60.419 54.545 0.00 0.00 0.00 2.74
2424 2749 0.460311 AGTGGCATGACTACTACGCC 59.540 55.000 0.00 0.00 38.52 5.68
2490 2815 0.758734 CGGAAGCTGATGTGGGGATA 59.241 55.000 0.00 0.00 0.00 2.59
2695 3024 8.233868 TGTGTTTACCATCTATCATTTGTTTCG 58.766 33.333 0.00 0.00 0.00 3.46
2851 3660 4.399004 TTTTGTGCTTTGCTAACCACAT 57.601 36.364 9.35 0.00 37.94 3.21
3120 4372 2.677003 CCGCTACAACGCCACCAAG 61.677 63.158 0.00 0.00 0.00 3.61
3468 4723 2.141448 TGTGGTGGGAAGCACCGTA 61.141 57.895 5.68 0.00 45.31 4.02
3585 4840 1.400530 GCGTGTACCCTATGGAGGCT 61.401 60.000 0.00 0.00 42.21 4.58
3672 4927 3.490759 GTGGTGCACGAGATGGCG 61.491 66.667 11.45 0.00 37.29 5.69
3715 4970 8.720562 CATACCGTGATGCATGAGATTAATTTA 58.279 33.333 2.46 0.00 0.00 1.40
3742 5004 9.340695 TGTATTTTTCATGTTCGATGTCAAATC 57.659 29.630 0.00 0.00 0.00 2.17
3745 5007 5.550232 TTCATGTTCGATGTCAAATCTGG 57.450 39.130 0.00 0.00 0.00 3.86
3779 5041 9.258826 CTTTCAGATGGATCTAGTTAATCAGTG 57.741 37.037 0.00 0.00 34.85 3.66
3793 5063 8.862325 AGTTAATCAGTGGACATACATGAAAA 57.138 30.769 0.00 0.00 0.00 2.29
3794 5064 8.950210 AGTTAATCAGTGGACATACATGAAAAG 58.050 33.333 0.00 0.00 0.00 2.27
3841 5382 8.696043 ACCTTTATGCAGCAGATTTGATTATA 57.304 30.769 0.00 0.00 0.00 0.98
3924 7802 0.913934 TGCTGGGTGCTCTATTGGGA 60.914 55.000 0.00 0.00 43.37 4.37
3998 7891 0.250338 ACAGAAAACGTGCCTCCTCC 60.250 55.000 0.00 0.00 0.00 4.30
4017 8663 6.878317 TCCTCCTGCAAGCATATATACATAC 58.122 40.000 0.00 0.00 0.00 2.39
4062 8713 2.156446 CCGCACGCGTACAACTAGG 61.156 63.158 13.44 0.00 37.81 3.02
4072 8723 2.671396 CGTACAACTAGGCAAAGCGATT 59.329 45.455 0.00 0.00 0.00 3.34
4073 8724 3.124636 CGTACAACTAGGCAAAGCGATTT 59.875 43.478 0.00 0.00 0.00 2.17
4157 8808 2.980233 GCTGGTGCAGGTGGTGAC 60.980 66.667 0.00 0.00 39.41 3.67
4158 8809 2.510411 CTGGTGCAGGTGGTGACA 59.490 61.111 0.00 0.00 38.70 3.58
4180 8834 1.728490 GCTTGGCAATCGCTTAGGGG 61.728 60.000 0.00 0.00 38.60 4.79
4185 8839 0.536006 GCAATCGCTTAGGGGCATCT 60.536 55.000 0.00 0.00 34.30 2.90
4212 8868 2.237643 ACTACTTCCTCTCTCTCGCTCA 59.762 50.000 0.00 0.00 0.00 4.26
4227 8883 4.101585 TCTCGCTCATACCTTTGGATCAAT 59.898 41.667 0.00 0.00 0.00 2.57
4257 9024 7.231925 TCGTATGTATGTAGAGCAATTTCCCTA 59.768 37.037 0.00 0.00 0.00 3.53
4258 9025 7.870954 CGTATGTATGTAGAGCAATTTCCCTAA 59.129 37.037 0.00 0.00 0.00 2.69
4306 9073 0.035439 TGCCTTTGTTCCCGGATCTC 60.035 55.000 0.73 0.00 0.00 2.75
4307 9074 0.253327 GCCTTTGTTCCCGGATCTCT 59.747 55.000 0.73 0.00 0.00 3.10
4446 9213 0.976073 CGGAGGTCCAGGCTTTCCTA 60.976 60.000 0.00 0.00 41.93 2.94
4502 9269 0.389687 GAGGCTGCGAGGATCTATGC 60.390 60.000 0.00 0.00 0.00 3.14
4504 9271 1.287191 GCTGCGAGGATCTATGCGA 59.713 57.895 0.00 0.00 0.00 5.10
4579 9346 1.873572 TCAGCGCGTGACATCATCG 60.874 57.895 8.43 3.18 0.00 3.84
4644 9414 8.106247 TCTTGCTTAATTTGTAAGGTCGAATT 57.894 30.769 0.00 0.00 36.04 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 7.945664 TGGGTCCTTTTATTAAATATATGCGGT 59.054 33.333 0.00 0.00 0.00 5.68
36 37 3.806949 TGCAGTTCTATTGGGTCCTTT 57.193 42.857 0.00 0.00 0.00 3.11
39 40 5.047377 TGAAATTTGCAGTTCTATTGGGTCC 60.047 40.000 0.00 0.00 0.00 4.46
52 53 4.696455 ACTCAAGGGTTTGAAATTTGCAG 58.304 39.130 0.00 0.00 42.48 4.41
55 56 5.291971 CAGGACTCAAGGGTTTGAAATTTG 58.708 41.667 0.00 0.00 42.48 2.32
155 167 3.188460 GGCCACAACACTTATACACACAG 59.812 47.826 0.00 0.00 0.00 3.66
168 180 5.950544 AATGTATAGACTAGGCCACAACA 57.049 39.130 5.01 0.00 0.00 3.33
187 219 8.393366 GCCACTGATATATAGTGCAACATAATG 58.607 37.037 12.09 0.00 43.19 1.90
249 281 4.443034 GCGGACCATGGAGTAAAGTTCTAT 60.443 45.833 21.47 0.00 0.00 1.98
292 325 1.004511 GTAGGCTCGCCCTCTAGGATA 59.995 57.143 3.92 0.00 44.96 2.59
355 416 5.048713 CCCATTGAAGAGTACAACAAAGTCC 60.049 44.000 0.00 0.00 0.00 3.85
434 495 4.910458 AACAACATAGAGTACCAGCCTT 57.090 40.909 0.00 0.00 0.00 4.35
450 511 6.851330 GTGTGCACTACATAGAAGAAAACAAC 59.149 38.462 19.41 0.00 42.24 3.32
491 552 4.090761 AGGTGTGAACATGAGACAACAT 57.909 40.909 0.00 0.00 29.16 2.71
492 553 3.558931 AGGTGTGAACATGAGACAACA 57.441 42.857 0.00 0.00 29.16 3.33
609 671 1.666599 GCATGCAGCATCGAACAAACA 60.667 47.619 14.21 0.00 44.79 2.83
610 672 0.986992 GCATGCAGCATCGAACAAAC 59.013 50.000 14.21 0.00 44.79 2.93
622 687 5.470437 AGAGTTATGAAGATGATGCATGCAG 59.530 40.000 26.69 0.00 0.00 4.41
650 715 0.482006 GGGGGTACGTAGAGGGAGAT 59.518 60.000 0.00 0.00 0.00 2.75
671 736 4.410400 GTGGGGGAGGCGGTTGAG 62.410 72.222 0.00 0.00 0.00 3.02
695 760 3.816090 GTGTGTGTGGGGGTGGGT 61.816 66.667 0.00 0.00 0.00 4.51
698 763 2.118404 GTGTGTGTGTGTGGGGGTG 61.118 63.158 0.00 0.00 0.00 4.61
723 788 2.614983 GTGCCCTACTCGTGTTGAAAAA 59.385 45.455 0.00 0.00 0.00 1.94
730 795 2.633509 GGTCGTGCCCTACTCGTGT 61.634 63.158 0.00 0.00 36.65 4.49
742 807 2.185004 AGGACAGATTTTGGGTCGTG 57.815 50.000 0.00 0.00 32.39 4.35
743 808 3.071892 TGTTAGGACAGATTTTGGGTCGT 59.928 43.478 0.00 0.00 34.45 4.34
756 822 8.050930 GGGTCCTTTCTATAAAATGTTAGGACA 58.949 37.037 16.94 0.00 42.56 4.02
757 823 8.050930 TGGGTCCTTTCTATAAAATGTTAGGAC 58.949 37.037 0.00 0.00 40.74 3.85
758 824 8.165267 TGGGTCCTTTCTATAAAATGTTAGGA 57.835 34.615 0.00 0.00 0.00 2.94
760 826 9.238368 TGTTGGGTCCTTTCTATAAAATGTTAG 57.762 33.333 0.00 0.00 0.00 2.34
761 827 9.589461 TTGTTGGGTCCTTTCTATAAAATGTTA 57.411 29.630 0.00 0.00 0.00 2.41
763 829 8.485578 TTTGTTGGGTCCTTTCTATAAAATGT 57.514 30.769 0.00 0.00 0.00 2.71
764 830 9.203421 GTTTTGTTGGGTCCTTTCTATAAAATG 57.797 33.333 0.00 0.00 0.00 2.32
766 832 8.541899 AGTTTTGTTGGGTCCTTTCTATAAAA 57.458 30.769 0.00 0.00 0.00 1.52
768 834 8.662255 TCTAGTTTTGTTGGGTCCTTTCTATAA 58.338 33.333 0.00 0.00 0.00 0.98
770 836 7.086685 TCTAGTTTTGTTGGGTCCTTTCTAT 57.913 36.000 0.00 0.00 0.00 1.98
771 837 6.503560 TCTAGTTTTGTTGGGTCCTTTCTA 57.496 37.500 0.00 0.00 0.00 2.10
773 839 6.459670 TTTCTAGTTTTGTTGGGTCCTTTC 57.540 37.500 0.00 0.00 0.00 2.62
807 885 7.226128 CGGGTCCTTTCTATAAAATGTTAGGAC 59.774 40.741 0.00 0.00 40.74 3.85
814 892 8.129211 GTGATTTCGGGTCCTTTCTATAAAATG 58.871 37.037 0.00 0.00 0.00 2.32
896 991 2.181021 GGTTCGTCCATCGCGAGT 59.819 61.111 16.66 0.00 39.61 4.18
948 1044 0.103390 TCGCGTGTTCCTTCTGTTCA 59.897 50.000 5.77 0.00 0.00 3.18
1011 1111 3.461773 CTCATCCTGCGGTCCCGT 61.462 66.667 7.66 0.00 42.09 5.28
1063 1163 1.078759 GACTTCATCGTCACGGCCTG 61.079 60.000 0.00 0.00 34.11 4.85
1064 1164 1.215647 GACTTCATCGTCACGGCCT 59.784 57.895 0.00 0.00 34.11 5.19
1072 1172 2.809601 GCCGCGTGACTTCATCGT 60.810 61.111 4.92 0.00 0.00 3.73
1257 1375 1.007734 GTCAGCCACGTCGTTGAGA 60.008 57.895 0.00 0.00 0.00 3.27
1258 1376 2.022129 GGTCAGCCACGTCGTTGAG 61.022 63.158 0.00 0.00 34.09 3.02
1259 1377 2.028484 GGTCAGCCACGTCGTTGA 59.972 61.111 0.00 0.00 34.09 3.18
1260 1378 3.041940 GGGTCAGCCACGTCGTTG 61.042 66.667 0.00 0.00 36.17 4.10
1261 1379 4.657824 CGGGTCAGCCACGTCGTT 62.658 66.667 0.00 0.00 36.17 3.85
1264 1382 3.352338 CTACCGGGTCAGCCACGTC 62.352 68.421 6.32 0.00 36.17 4.34
1265 1383 3.379445 CTACCGGGTCAGCCACGT 61.379 66.667 6.32 0.00 36.17 4.49
1421 1539 3.468326 TAACCAGTGCGCTGCCACA 62.468 57.895 22.03 3.49 41.26 4.17
1458 1576 4.418013 TTGCATACCGTTCATGAAGTTG 57.582 40.909 8.80 2.85 0.00 3.16
1571 1700 3.108144 CAAAAAGACAGCGAAAGTGTGG 58.892 45.455 0.00 0.00 0.00 4.17
1586 1715 4.321480 GCAAGCAAGCAAACAAACAAAAAG 59.679 37.500 0.00 0.00 0.00 2.27
1743 1889 5.352846 ACGTAAGCAACATGCATACATACAA 59.647 36.000 15.34 0.00 44.88 2.41
2081 2406 3.160585 CAGGGTGCTTGGTCCAGA 58.839 61.111 0.00 0.00 0.00 3.86
2163 2488 3.810941 TGTTGTCGGACTTATCAAACCAC 59.189 43.478 9.88 0.00 0.00 4.16
2338 2663 3.133464 GCTGCCACCGCTAATGCA 61.133 61.111 0.00 0.00 39.64 3.96
2339 2664 2.699768 TTGCTGCCACCGCTAATGC 61.700 57.895 0.00 0.00 35.36 3.56
2424 2749 0.682209 CTGCATCAAACCTCCCCAGG 60.682 60.000 0.00 0.00 46.87 4.45
2490 2815 1.528824 CCAATCGACCCTCATGCCT 59.471 57.895 0.00 0.00 0.00 4.75
2695 3024 1.502231 ATCGAGCATGCATAACGGAC 58.498 50.000 21.98 0.00 0.00 4.79
3120 4372 1.723870 GATGGTGATGCCGCTGAAC 59.276 57.895 0.00 0.00 41.21 3.18
3235 4487 0.384309 TAGCTAACATCGGCCTCGTG 59.616 55.000 0.00 0.00 37.69 4.35
3585 4840 1.480212 CCCTACCAGCCGCATGGATA 61.480 60.000 13.75 4.46 43.57 2.59
3672 4927 3.377172 GGTATGGTTGTATTGGTGCTGAC 59.623 47.826 0.00 0.00 0.00 3.51
3715 4970 9.859427 ATTTGACATCGAACATGAAAAATACAT 57.141 25.926 0.00 0.00 0.00 2.29
3725 4980 4.633126 AGACCAGATTTGACATCGAACATG 59.367 41.667 0.00 0.00 0.00 3.21
3727 4982 4.271696 AGACCAGATTTGACATCGAACA 57.728 40.909 0.00 0.00 0.00 3.18
3728 4983 5.411781 ACTAGACCAGATTTGACATCGAAC 58.588 41.667 0.00 0.00 0.00 3.95
3731 4986 5.655488 AGAACTAGACCAGATTTGACATCG 58.345 41.667 0.00 0.00 0.00 3.84
3732 4987 7.604164 TGAAAGAACTAGACCAGATTTGACATC 59.396 37.037 0.00 0.00 0.00 3.06
3733 4988 7.453393 TGAAAGAACTAGACCAGATTTGACAT 58.547 34.615 0.00 0.00 0.00 3.06
3779 5041 5.041951 TGCGAAACTTTTCATGTATGTCC 57.958 39.130 2.77 0.00 37.01 4.02
3841 5382 5.538433 TCATGATGATGGACATGCATGAAAT 59.462 36.000 32.75 20.71 42.71 2.17
3924 7802 2.452600 GACTCCTCTCTCCAGTCCAT 57.547 55.000 0.00 0.00 31.93 3.41
4062 8713 2.061028 CCTTGTTGGAAATCGCTTTGC 58.939 47.619 0.00 0.00 38.35 3.68
4072 8723 0.457851 CGGTTGTTGCCTTGTTGGAA 59.542 50.000 0.00 0.00 38.35 3.53
4073 8724 0.394488 TCGGTTGTTGCCTTGTTGGA 60.394 50.000 0.00 0.00 38.35 3.53
4122 8773 3.672255 CTGCGCCGCCATTGTCTTG 62.672 63.158 6.63 0.00 0.00 3.02
4157 8808 0.810648 TAAGCGATTGCCAAGCCTTG 59.189 50.000 0.00 0.00 44.31 3.61
4158 8809 1.098050 CTAAGCGATTGCCAAGCCTT 58.902 50.000 0.00 2.81 44.31 4.35
4168 8819 1.000955 CGTAGATGCCCCTAAGCGATT 59.999 52.381 0.00 0.00 34.65 3.34
4180 8834 4.136051 AGAGGAAGTAGTACCGTAGATGC 58.864 47.826 0.00 0.00 0.00 3.91
4185 8839 4.202101 CGAGAGAGAGGAAGTAGTACCGTA 60.202 50.000 0.00 0.00 0.00 4.02
4212 8868 4.766375 ACGACGAATTGATCCAAAGGTAT 58.234 39.130 0.00 0.00 0.00 2.73
4227 8883 5.488645 TTGCTCTACATACATACGACGAA 57.511 39.130 0.00 0.00 0.00 3.85
4257 9024 1.079438 AGGGAGAGGGCGAGAACTT 59.921 57.895 0.00 0.00 0.00 2.66
4258 9025 1.684049 CAGGGAGAGGGCGAGAACT 60.684 63.158 0.00 0.00 0.00 3.01
4289 9056 2.789409 AAGAGATCCGGGAACAAAGG 57.211 50.000 0.00 0.00 0.00 3.11
4306 9073 1.386533 CTGTGCCATGGAAGCCTAAG 58.613 55.000 18.40 0.00 0.00 2.18
4307 9074 0.680921 GCTGTGCCATGGAAGCCTAA 60.681 55.000 18.40 0.00 0.00 2.69
4340 9107 4.884164 GTCAAGTTTCAAGGATATGGAGGG 59.116 45.833 0.00 0.00 0.00 4.30
4446 9213 5.339008 TGTAGTCAATAGGAAGCGATTGT 57.661 39.130 0.00 0.00 35.10 2.71
4502 9269 2.094442 GGACCTTTCCTCTTGAGACTCG 60.094 54.545 0.00 0.00 39.13 4.18
4504 9271 2.903135 CTGGACCTTTCCTCTTGAGACT 59.097 50.000 0.00 0.00 43.31 3.24
4579 9346 5.368256 AGATCCAAATATCATTTGCTCGC 57.632 39.130 6.17 0.00 0.00 5.03
4644 9414 9.832445 GTCAGGTATTTCTAAATATGGAGAACA 57.168 33.333 0.00 0.00 33.79 3.18


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

AutoCloner maintained by Alex Coulton.