Multiple sequence alignment - TraesCS7D01G152200

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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 TraesCS7D01G152200 chr7D 100.000 4382 0 0 1 4382 101050005 101045624 0.000000e+00 8093
1 TraesCS7D01G152200 chr7D 98.583 635 6 1 3751 4382 538351084 538350450 0.000000e+00 1120
2 TraesCS7D01G152200 chr7D 98.084 522 6 2 3751 4269 513314735 513315255 0.000000e+00 905
3 TraesCS7D01G152200 chr7D 97.893 522 7 2 3751 4269 23859425 23858905 0.000000e+00 900
4 TraesCS7D01G152200 chr7D 86.096 561 73 4 177 734 521890204 521890762 2.260000e-167 599
5 TraesCS7D01G152200 chr7D 97.628 253 2 4 3496 3745 32671687 32671436 8.710000e-117 431
6 TraesCS7D01G152200 chr7D 97.177 248 6 1 3501 3748 141955656 141955410 6.780000e-113 418
7 TraesCS7D01G152200 chr7D 78.702 601 93 25 211 787 600494397 600494986 6.920000e-98 368
8 TraesCS7D01G152200 chr7A 96.253 2669 93 5 834 3501 103146554 103143892 0.000000e+00 4368
9 TraesCS7D01G152200 chr7B 95.894 2630 105 3 873 3501 57462856 57460229 0.000000e+00 4255
10 TraesCS7D01G152200 chr7B 87.365 649 60 13 177 813 57463499 57462861 0.000000e+00 725
11 TraesCS7D01G152200 chr7B 93.182 176 12 0 1 176 57463760 57463585 4.350000e-65 259
12 TraesCS7D01G152200 chr2D 98.268 635 8 1 3751 4382 533855179 533854545 0.000000e+00 1109
13 TraesCS7D01G152200 chr2D 94.992 659 6 10 3751 4382 174569822 174569164 0.000000e+00 1009
14 TraesCS7D01G152200 chr2D 98.084 522 6 2 3751 4269 367576899 367577419 0.000000e+00 905
15 TraesCS7D01G152200 chr2D 96.386 249 7 2 3504 3750 174570333 174570085 4.080000e-110 409
16 TraesCS7D01G152200 chr2D 94.253 261 13 2 3490 3750 112951013 112950755 8.830000e-107 398
17 TraesCS7D01G152200 chr2D 100.000 176 0 0 4207 4382 174568191 174568016 4.230000e-85 326
18 TraesCS7D01G152200 chr5D 98.276 522 5 2 3751 4269 459895779 459895259 0.000000e+00 911
19 TraesCS7D01G152200 chr5D 98.084 522 6 2 3751 4269 305205271 305204751 0.000000e+00 905
20 TraesCS7D01G152200 chr5D 98.883 179 2 0 4204 4382 77870354 77870532 1.970000e-83 320
21 TraesCS7D01G152200 chr6D 97.893 522 7 2 3751 4269 469717143 469717663 0.000000e+00 900
22 TraesCS7D01G152200 chr4D 97.893 522 7 2 3751 4269 476665654 476665134 0.000000e+00 900
23 TraesCS7D01G152200 chr4D 98.800 250 3 0 3501 3750 138174049 138174298 3.110000e-121 446
24 TraesCS7D01G152200 chr3B 86.212 631 72 9 177 795 603826041 603826668 0.000000e+00 669
25 TraesCS7D01G152200 chr3B 78.505 428 73 15 210 627 377709228 377708810 3.360000e-66 263
26 TraesCS7D01G152200 chr5B 86.196 623 72 8 177 795 710169880 710169268 0.000000e+00 662
27 TraesCS7D01G152200 chr2B 87.250 549 63 6 177 720 87333198 87332652 1.730000e-173 619
28 TraesCS7D01G152200 chr2B 78.967 271 39 7 180 438 713864488 713864224 7.540000e-38 169
29 TraesCS7D01G152200 chr1B 84.006 619 79 10 180 795 684732964 684732363 1.060000e-160 577
30 TraesCS7D01G152200 chr1B 78.503 628 102 24 184 787 529388467 529387849 8.890000e-102 381
31 TraesCS7D01G152200 chr1A 88.067 419 46 3 177 592 588668040 588668457 1.090000e-135 494
32 TraesCS7D01G152200 chr6A 79.841 630 100 20 180 786 546985446 546984821 6.730000e-118 435
33 TraesCS7D01G152200 chr3D 96.887 257 6 2 3495 3750 550452423 550452168 3.130000e-116 429
34 TraesCS7D01G152200 chr3D 96.414 251 8 1 3501 3750 555026122 555025872 3.150000e-111 412
35 TraesCS7D01G152200 chr1D 96.400 250 9 0 3501 3750 205074382 205074631 3.150000e-111 412
36 TraesCS7D01G152200 chr1D 96.400 250 8 1 3501 3750 421383596 421383844 1.130000e-110 411
37 TraesCS7D01G152200 chr1D 98.883 179 2 0 4204 4382 3331840 3332018 1.970000e-83 320
38 TraesCS7D01G152200 chr1D 98.883 179 2 0 4204 4382 70573185 70573363 1.970000e-83 320
39 TraesCS7D01G152200 chr1D 98.883 179 2 0 4204 4382 421385717 421385895 1.970000e-83 320
40 TraesCS7D01G152200 chr1D 99.432 176 1 0 4207 4382 465810592 465810417 1.970000e-83 320
41 TraesCS7D01G152200 chrUn 80.420 429 62 18 210 627 75414471 75414888 1.530000e-79 307
42 TraesCS7D01G152200 chr5A 77.632 380 72 10 255 627 404627857 404628230 7.380000e-53 219


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 TraesCS7D01G152200 chr7D 101045624 101050005 4381 True 8093.000000 8093 100.0000 1 4382 1 chr7D.!!$R3 4381
1 TraesCS7D01G152200 chr7D 538350450 538351084 634 True 1120.000000 1120 98.5830 3751 4382 1 chr7D.!!$R5 631
2 TraesCS7D01G152200 chr7D 513314735 513315255 520 False 905.000000 905 98.0840 3751 4269 1 chr7D.!!$F1 518
3 TraesCS7D01G152200 chr7D 23858905 23859425 520 True 900.000000 900 97.8930 3751 4269 1 chr7D.!!$R1 518
4 TraesCS7D01G152200 chr7D 521890204 521890762 558 False 599.000000 599 86.0960 177 734 1 chr7D.!!$F2 557
5 TraesCS7D01G152200 chr7D 600494397 600494986 589 False 368.000000 368 78.7020 211 787 1 chr7D.!!$F3 576
6 TraesCS7D01G152200 chr7A 103143892 103146554 2662 True 4368.000000 4368 96.2530 834 3501 1 chr7A.!!$R1 2667
7 TraesCS7D01G152200 chr7B 57460229 57463760 3531 True 1746.333333 4255 92.1470 1 3501 3 chr7B.!!$R1 3500
8 TraesCS7D01G152200 chr2D 533854545 533855179 634 True 1109.000000 1109 98.2680 3751 4382 1 chr2D.!!$R2 631
9 TraesCS7D01G152200 chr2D 367576899 367577419 520 False 905.000000 905 98.0840 3751 4269 1 chr2D.!!$F1 518
10 TraesCS7D01G152200 chr2D 174568016 174570333 2317 True 581.333333 1009 97.1260 3504 4382 3 chr2D.!!$R3 878
11 TraesCS7D01G152200 chr5D 459895259 459895779 520 True 911.000000 911 98.2760 3751 4269 1 chr5D.!!$R2 518
12 TraesCS7D01G152200 chr5D 305204751 305205271 520 True 905.000000 905 98.0840 3751 4269 1 chr5D.!!$R1 518
13 TraesCS7D01G152200 chr6D 469717143 469717663 520 False 900.000000 900 97.8930 3751 4269 1 chr6D.!!$F1 518
14 TraesCS7D01G152200 chr4D 476665134 476665654 520 True 900.000000 900 97.8930 3751 4269 1 chr4D.!!$R1 518
15 TraesCS7D01G152200 chr3B 603826041 603826668 627 False 669.000000 669 86.2120 177 795 1 chr3B.!!$F1 618
16 TraesCS7D01G152200 chr5B 710169268 710169880 612 True 662.000000 662 86.1960 177 795 1 chr5B.!!$R1 618
17 TraesCS7D01G152200 chr2B 87332652 87333198 546 True 619.000000 619 87.2500 177 720 1 chr2B.!!$R1 543
18 TraesCS7D01G152200 chr1B 684732363 684732964 601 True 577.000000 577 84.0060 180 795 1 chr1B.!!$R2 615
19 TraesCS7D01G152200 chr1B 529387849 529388467 618 True 381.000000 381 78.5030 184 787 1 chr1B.!!$R1 603
20 TraesCS7D01G152200 chr6A 546984821 546985446 625 True 435.000000 435 79.8410 180 786 1 chr6A.!!$R1 606
21 TraesCS7D01G152200 chr1D 421383596 421385895 2299 False 365.500000 411 97.6415 3501 4382 2 chr1D.!!$F4 881

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
170 171 0.036388 ATCACCCCGTGCAGTACAAG 60.036 55.0 0.0 0.0 32.98 3.16 F
374 473 0.320771 GGACACATGAGCCAAGACGT 60.321 55.0 0.0 0.0 0.00 4.34 F
531 633 0.521735 GGCACAATCGAAAGGTCACC 59.478 55.0 0.0 0.0 0.00 4.02 F
2088 2220 0.798771 CGACAGCGCTTACCACTCTC 60.799 60.0 7.5 0.0 0.00 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1686 1818 1.079819 CGTCACATCCGCAACCTCT 60.080 57.895 0.0 0.0 0.00 3.69 R
2106 2238 2.356125 GGCTTTCCTTGCAGACTCCATA 60.356 50.000 0.0 0.0 0.00 2.74 R
2493 2625 0.524862 CTTCAGCACCTTGACCATGC 59.475 55.000 0.0 0.0 39.74 4.06 R
3748 3982 1.675720 GGAAATGGGTGGCGGGAATG 61.676 60.000 0.0 0.0 0.00 2.67 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
27 28 1.105167 TATGCCGTCGGACCGAGATT 61.105 55.000 18.98 3.46 36.23 2.40
47 48 9.490663 CGAGATTGGAAAATGTATTGAACTAAC 57.509 33.333 0.00 0.00 0.00 2.34
68 69 3.815401 ACATAAAGAACAGTGACACCTGC 59.185 43.478 0.84 0.00 35.83 4.85
79 80 1.926511 GACACCTGCAAATGCCCTCG 61.927 60.000 2.46 0.00 41.18 4.63
142 143 6.481644 ACTTGAAATGAGATCTAGAAATCGCC 59.518 38.462 0.00 0.00 0.00 5.54
159 160 1.815421 CCGAAGAAGCATCACCCCG 60.815 63.158 0.00 0.00 0.00 5.73
170 171 0.036388 ATCACCCCGTGCAGTACAAG 60.036 55.000 0.00 0.00 32.98 3.16
204 290 5.129320 AGAAACAAAGAGGGAAAGCACAAAT 59.871 36.000 0.00 0.00 0.00 2.32
208 296 6.458210 ACAAAGAGGGAAAGCACAAATAATG 58.542 36.000 0.00 0.00 0.00 1.90
239 334 1.073177 CCGCCAAAGTAATCGAACGT 58.927 50.000 0.00 0.00 0.00 3.99
349 446 1.228003 CTGTGCCGTGGGGTGTAAA 60.228 57.895 0.00 0.00 34.97 2.01
374 473 0.320771 GGACACATGAGCCAAGACGT 60.321 55.000 0.00 0.00 0.00 4.34
438 539 4.323562 GCCTAGTAGACCAAACCAAGACAT 60.324 45.833 0.00 0.00 0.00 3.06
473 574 4.817063 CGAAAGGCACCGCGCATG 62.817 66.667 8.75 6.20 45.17 4.06
531 633 0.521735 GGCACAATCGAAAGGTCACC 59.478 55.000 0.00 0.00 0.00 4.02
605 708 4.731612 CGCCGCAGCAGAGACACT 62.732 66.667 0.00 0.00 39.83 3.55
642 756 1.730064 CACGAACCATAAGAACACCGG 59.270 52.381 0.00 0.00 0.00 5.28
648 762 2.014128 CCATAAGAACACCGGCGAAAT 58.986 47.619 9.30 0.00 0.00 2.17
666 796 1.550130 ATCGAGGGAAGACGGCCAAA 61.550 55.000 2.24 0.00 0.00 3.28
670 800 2.114411 GGAAGACGGCCAAACCCA 59.886 61.111 2.24 0.00 33.26 4.51
741 872 2.517875 GCCATGGAGCTCGCCAAT 60.518 61.111 18.40 0.00 42.16 3.16
806 938 2.147150 GCTCTTCCACTCTTTGACACC 58.853 52.381 0.00 0.00 0.00 4.16
807 939 2.485479 GCTCTTCCACTCTTTGACACCA 60.485 50.000 0.00 0.00 0.00 4.17
812 944 4.916983 TCCACTCTTTGACACCATTTTG 57.083 40.909 0.00 0.00 0.00 2.44
813 945 3.068024 TCCACTCTTTGACACCATTTTGC 59.932 43.478 0.00 0.00 0.00 3.68
815 947 4.501915 CCACTCTTTGACACCATTTTGCAT 60.502 41.667 0.00 0.00 0.00 3.96
817 949 5.860182 CACTCTTTGACACCATTTTGCATAG 59.140 40.000 0.00 0.00 0.00 2.23
818 950 5.769662 ACTCTTTGACACCATTTTGCATAGA 59.230 36.000 0.00 0.00 0.00 1.98
819 951 6.012658 TCTTTGACACCATTTTGCATAGAC 57.987 37.500 0.00 0.00 0.00 2.59
820 952 5.534278 TCTTTGACACCATTTTGCATAGACA 59.466 36.000 0.00 0.00 0.00 3.41
821 953 5.981088 TTGACACCATTTTGCATAGACAT 57.019 34.783 0.00 0.00 0.00 3.06
822 954 5.313520 TGACACCATTTTGCATAGACATG 57.686 39.130 0.00 0.00 35.07 3.21
823 955 4.766373 TGACACCATTTTGCATAGACATGT 59.234 37.500 0.00 0.00 34.40 3.21
824 956 5.106197 TGACACCATTTTGCATAGACATGTC 60.106 40.000 18.47 18.47 34.40 3.06
825 957 4.142622 ACACCATTTTGCATAGACATGTCG 60.143 41.667 19.85 7.49 34.40 4.35
826 958 4.009675 ACCATTTTGCATAGACATGTCGT 58.990 39.130 19.85 10.34 34.40 4.34
827 959 5.064579 CACCATTTTGCATAGACATGTCGTA 59.935 40.000 19.85 12.72 34.40 3.43
828 960 5.822519 ACCATTTTGCATAGACATGTCGTAT 59.177 36.000 19.85 14.26 34.40 3.06
829 961 6.318648 ACCATTTTGCATAGACATGTCGTATT 59.681 34.615 19.85 5.40 34.40 1.89
830 962 7.148086 ACCATTTTGCATAGACATGTCGTATTT 60.148 33.333 19.85 5.01 34.40 1.40
831 963 7.701924 CCATTTTGCATAGACATGTCGTATTTT 59.298 33.333 19.85 4.27 34.40 1.82
832 964 9.715123 CATTTTGCATAGACATGTCGTATTTTA 57.285 29.630 19.85 6.46 34.40 1.52
886 1018 5.387113 TGCCCATTCTAGGACAAATATGT 57.613 39.130 0.00 0.00 44.25 2.29
911 1043 6.358558 TCATTTCGTTAGCAAATTGAAACGTC 59.641 34.615 23.32 0.00 43.74 4.34
952 1084 1.326548 GCGATCGAACGGCTACATTTT 59.673 47.619 21.57 0.00 0.00 1.82
953 1085 2.596807 GCGATCGAACGGCTACATTTTC 60.597 50.000 21.57 0.00 0.00 2.29
954 1086 2.858344 CGATCGAACGGCTACATTTTCT 59.142 45.455 10.26 0.00 0.00 2.52
955 1087 3.061139 CGATCGAACGGCTACATTTTCTC 60.061 47.826 10.26 0.00 0.00 2.87
1350 1482 1.226435 CGACTCCTTCTCCTTCGCG 60.226 63.158 0.00 0.00 0.00 5.87
1372 1504 4.680237 CCGCCACCTCGCTCAACA 62.680 66.667 0.00 0.00 0.00 3.33
1410 1542 1.361993 CATCGCTTCTAGCTCCGCT 59.638 57.895 0.00 0.00 39.60 5.52
1626 1758 2.507547 GCGTTCGTGCGGATGGTA 60.508 61.111 0.00 0.00 0.00 3.25
1627 1759 2.514013 GCGTTCGTGCGGATGGTAG 61.514 63.158 0.00 0.00 0.00 3.18
1630 1762 1.683025 TTCGTGCGGATGGTAGGGA 60.683 57.895 0.00 0.00 0.00 4.20
1638 1770 1.481428 CGGATGGTAGGGACAGGATCT 60.481 57.143 0.00 0.00 0.00 2.75
1668 1800 1.930188 CTCGTCGACGCTGTCATCG 60.930 63.158 32.19 6.51 39.60 3.84
1677 1809 3.023949 GCTGTCATCGGTCCTGCCT 62.024 63.158 0.00 0.00 34.25 4.75
1680 1812 4.147449 TCATCGGTCCTGCCTGCG 62.147 66.667 0.00 0.00 34.25 5.18
1764 1896 0.950555 TGGCACAAGACGAGCATGTC 60.951 55.000 0.00 0.41 39.21 3.06
2028 2160 2.616960 CTTACTCGGTGCTTACATGCA 58.383 47.619 0.00 0.00 41.05 3.96
2088 2220 0.798771 CGACAGCGCTTACCACTCTC 60.799 60.000 7.50 0.00 0.00 3.20
2094 2226 1.799548 GCGCTTACCACTCTCTACTGC 60.800 57.143 0.00 0.00 0.00 4.40
2106 2238 4.463186 ACTCTCTACTGCAGGTTAAACGAT 59.537 41.667 19.93 0.00 0.00 3.73
2112 2244 4.442706 ACTGCAGGTTAAACGATATGGAG 58.557 43.478 19.93 0.00 33.02 3.86
2158 2290 2.517959 TGCCTGAAAAGACCATGGAAG 58.482 47.619 21.47 3.87 0.00 3.46
2258 2390 1.273048 GCTCAATGTGCCACCAAATCA 59.727 47.619 0.00 0.00 0.00 2.57
2283 2415 0.813821 CCATCTCGAGCACTCTGTCA 59.186 55.000 7.81 0.00 0.00 3.58
2493 2625 3.518303 TGATGATCTCTGGATATGGCCTG 59.482 47.826 3.32 0.00 31.46 4.85
2645 2777 1.207329 AGCCTTCCGGTCAATGACTAC 59.793 52.381 13.53 0.00 32.47 2.73
2667 2799 0.252197 ATTACGGGTTCACTCCAGGC 59.748 55.000 0.00 0.00 0.00 4.85
2813 2945 2.756760 CTGCTTGCATGGTTCATAAGGT 59.243 45.455 1.34 0.00 0.00 3.50
2839 2971 0.390209 CCTTGCAAAATTGGCCTCCG 60.390 55.000 3.32 0.00 0.00 4.63
3003 3135 6.655848 GGTGTACTCTAATCGAGATAGGTGAT 59.344 42.308 7.86 0.00 42.62 3.06
3035 3167 0.324614 TTCATGGCTGGTGATCGTGT 59.675 50.000 0.00 0.00 0.00 4.49
3093 3225 7.268586 TGGAGAAGCTAACTACAAAGATGATC 58.731 38.462 3.64 0.00 0.00 2.92
3264 3396 0.550147 ACCTTAGGGTGTGCCTGGAT 60.550 55.000 2.32 0.00 45.43 3.41
3300 3432 5.476599 CACCAAGATTATTTCCAAGGTGACA 59.523 40.000 0.00 0.00 40.66 3.58
3488 3620 5.572252 TCAAATAATTTGTAACCCTCGGGT 58.428 37.500 0.65 0.65 44.89 5.28
3498 3630 3.274601 CCCTCGGGTGCCAATTTTA 57.725 52.632 0.00 0.00 0.00 1.52
3501 3633 1.202405 CCTCGGGTGCCAATTTTATGC 60.202 52.381 0.00 0.00 0.00 3.14
3502 3634 1.750778 CTCGGGTGCCAATTTTATGCT 59.249 47.619 0.00 0.00 0.00 3.79
3622 3756 2.108362 GGACCTAATCGGCCCACG 59.892 66.667 0.00 0.00 46.11 4.94
3793 4189 1.301401 CCGCAGTCGTTCTTTCCCA 60.301 57.895 0.00 0.00 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 5.588648 TCAATACATTTTCCAATCTCGGTCC 59.411 40.000 0.00 0.00 0.00 4.46
47 48 3.814842 TGCAGGTGTCACTGTTCTTTATG 59.185 43.478 2.35 0.00 40.59 1.90
54 55 1.067516 GCATTTGCAGGTGTCACTGTT 59.932 47.619 2.35 0.00 40.59 3.16
56 57 0.038892 GGCATTTGCAGGTGTCACTG 60.039 55.000 4.74 0.84 44.36 3.66
59 60 0.895100 GAGGGCATTTGCAGGTGTCA 60.895 55.000 4.74 0.00 44.36 3.58
62 63 1.926511 GACGAGGGCATTTGCAGGTG 61.927 60.000 4.74 0.00 44.36 4.00
68 69 0.958091 TGGTTTGACGAGGGCATTTG 59.042 50.000 0.00 0.00 0.00 2.32
79 80 6.508777 TGTGTTATTTAAAGCCTGGTTTGAC 58.491 36.000 0.00 0.00 0.00 3.18
142 143 1.079127 ACGGGGTGATGCTTCTTCG 60.079 57.895 0.88 2.89 0.00 3.79
159 160 1.207593 CCGCAAGCTTGTACTGCAC 59.792 57.895 26.55 8.01 0.00 4.57
170 171 0.039165 CTTTGTTTCTCCCCGCAAGC 60.039 55.000 0.00 0.00 0.00 4.01
204 290 0.521291 GCGGTGCTCTTGTTGCATTA 59.479 50.000 0.00 0.00 42.69 1.90
208 296 2.348605 TTTGGCGGTGCTCTTGTTGC 62.349 55.000 0.00 0.00 0.00 4.17
349 446 0.396435 TGGCTCATGTGTCCTTTCGT 59.604 50.000 0.00 0.00 0.00 3.85
374 473 1.596752 GGCACATGTGACGTGGTGA 60.597 57.895 29.80 0.00 34.85 4.02
382 481 0.884259 CTTGTCGGTGGCACATGTGA 60.884 55.000 29.80 6.58 44.52 3.58
473 574 3.050275 GGCGTTGGGCAGACTCAC 61.050 66.667 0.00 0.00 46.16 3.51
511 613 1.234821 GTGACCTTTCGATTGTGCCA 58.765 50.000 0.00 0.00 0.00 4.92
605 708 0.250467 GTGCTCAGGTGCTCCTTCAA 60.250 55.000 4.10 0.00 43.07 2.69
642 756 1.146358 CCGTCTTCCCTCGATTTCGC 61.146 60.000 0.00 0.00 39.60 4.70
648 762 2.211410 TTTGGCCGTCTTCCCTCGA 61.211 57.895 0.00 0.00 0.00 4.04
806 938 8.619146 AAAATACGACATGTCTATGCAAAATG 57.381 30.769 22.95 6.41 37.85 2.32
859 991 9.685276 CATATTTGTCCTAGAATGGGCATTATA 57.315 33.333 0.00 0.00 41.79 0.98
860 992 8.172741 ACATATTTGTCCTAGAATGGGCATTAT 58.827 33.333 0.00 0.00 41.79 1.28
861 993 7.526041 ACATATTTGTCCTAGAATGGGCATTA 58.474 34.615 0.00 0.00 41.79 1.90
862 994 6.376248 ACATATTTGTCCTAGAATGGGCATT 58.624 36.000 0.00 0.00 41.79 3.56
886 1018 6.202937 ACGTTTCAATTTGCTAACGAAATGA 58.797 32.000 27.67 6.17 44.32 2.57
911 1043 0.941463 GATAGACGGCCGACATGCAG 60.941 60.000 35.90 0.00 0.00 4.41
952 1084 6.951062 TGTTATGTGGTTTTTGATGTGAGA 57.049 33.333 0.00 0.00 0.00 3.27
953 1085 7.042791 GGTTTGTTATGTGGTTTTTGATGTGAG 60.043 37.037 0.00 0.00 0.00 3.51
954 1086 6.758886 GGTTTGTTATGTGGTTTTTGATGTGA 59.241 34.615 0.00 0.00 0.00 3.58
955 1087 6.018343 GGGTTTGTTATGTGGTTTTTGATGTG 60.018 38.462 0.00 0.00 0.00 3.21
1001 1133 1.602237 GGAGAAGGCATCGGTTCCA 59.398 57.895 0.00 0.00 0.00 3.53
1306 1438 2.683933 GAAGAGGAGGTCCGGGCA 60.684 66.667 9.07 0.00 42.08 5.36
1311 1443 2.371259 GCAGGGGAAGAGGAGGTCC 61.371 68.421 0.00 0.00 0.00 4.46
1626 1758 2.685017 TGCGCAGATCCTGTCCCT 60.685 61.111 5.66 0.00 33.43 4.20
1627 1759 2.202987 CTGCGCAGATCCTGTCCC 60.203 66.667 33.66 0.00 33.43 4.46
1630 1762 3.397439 AGGCTGCGCAGATCCTGT 61.397 61.111 40.21 15.12 33.43 4.00
1638 1770 4.724602 GACGAGTCAGGCTGCGCA 62.725 66.667 10.98 10.98 0.00 6.09
1686 1818 1.079819 CGTCACATCCGCAACCTCT 60.080 57.895 0.00 0.00 0.00 3.69
1764 1896 2.951745 GAGATCAGCGCCGTCACG 60.952 66.667 2.29 0.00 0.00 4.35
1804 1936 2.669569 ATGCCGTGCACACTCCAC 60.670 61.111 18.64 0.00 43.04 4.02
2028 2160 5.132502 TCAAATCCAGACTTGACAACATGT 58.867 37.500 0.00 0.00 37.16 3.21
2029 2161 5.694231 TCAAATCCAGACTTGACAACATG 57.306 39.130 0.00 0.00 0.00 3.21
2041 2173 2.691526 GAGCATTGGCATCAAATCCAGA 59.308 45.455 0.00 0.00 44.61 3.86
2088 2220 5.597806 TCCATATCGTTTAACCTGCAGTAG 58.402 41.667 13.81 0.00 0.00 2.57
2094 2226 4.508124 GCAGACTCCATATCGTTTAACCTG 59.492 45.833 0.00 0.00 0.00 4.00
2106 2238 2.356125 GGCTTTCCTTGCAGACTCCATA 60.356 50.000 0.00 0.00 0.00 2.74
2283 2415 2.596631 CCAAGCTGTGCACAGGCT 60.597 61.111 39.92 33.16 43.94 4.58
2493 2625 0.524862 CTTCAGCACCTTGACCATGC 59.475 55.000 0.00 0.00 39.74 4.06
2667 2799 1.134075 GCAAGTGCAGTGCTCGATG 59.866 57.895 17.60 17.02 41.59 3.84
2740 2872 1.078848 CGCTCTTGGGGAACTCTGG 60.079 63.158 0.00 0.00 0.00 3.86
2839 2971 6.761714 TCAGGTTCTAGTTCAAACAACTTCTC 59.238 38.462 0.00 0.00 0.00 2.87
2976 3108 4.701171 CCTATCTCGATTAGAGTACACCCC 59.299 50.000 0.00 0.00 46.86 4.95
3035 3167 2.867855 GCGTCTGACTGTGGGTGGA 61.868 63.158 6.21 0.00 0.00 4.02
3093 3225 3.834799 GGTCGGTACCCAGCCTCG 61.835 72.222 6.25 0.00 40.21 4.63
3300 3432 2.026822 CCTAACCACAATCAGCCTCTGT 60.027 50.000 0.00 0.00 32.61 3.41
3369 3501 3.118775 TCCCAGTGAATCACCAGTAATCG 60.119 47.826 10.12 0.00 34.49 3.34
3748 3982 1.675720 GGAAATGGGTGGCGGGAATG 61.676 60.000 0.00 0.00 0.00 2.67
3793 4189 8.855804 TTTATAGGTAGAGAGGAGAAAATGGT 57.144 34.615 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.