Multiple sequence alignment - TraesCS5B01G515000

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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 TraesCS5B01G515000 chr5B 100.000 3546 0 0 1 3546 679671214 679674759 0.000000e+00 6549.0
1 TraesCS5B01G515000 chr5B 79.539 1476 177 57 876 2270 679405435 679404004 0.000000e+00 937.0
2 TraesCS5B01G515000 chr5B 81.588 1222 143 43 865 2054 679559949 679558778 0.000000e+00 935.0
3 TraesCS5B01G515000 chr5B 88.764 356 39 1 2209 2563 679558579 679558224 5.440000e-118 435.0
4 TraesCS5B01G515000 chr5B 81.305 567 55 13 973 1506 679379451 679378903 2.550000e-111 412.0
5 TraesCS5B01G515000 chr5B 76.590 393 58 21 3103 3471 679401876 679401494 6.050000e-43 185.0
6 TraesCS5B01G515000 chr4A 91.564 2039 137 18 1533 3546 630877586 630875558 0.000000e+00 2780.0
7 TraesCS5B01G515000 chr4A 92.377 1325 86 10 1633 2945 631501051 631502372 0.000000e+00 1873.0
8 TraesCS5B01G515000 chr4A 81.109 2001 232 79 865 2791 631475857 631477785 0.000000e+00 1467.0
9 TraesCS5B01G515000 chr4A 79.455 1908 257 84 948 2782 631494188 631496033 0.000000e+00 1227.0
10 TraesCS5B01G515000 chr4A 84.089 1345 128 34 2148 3460 630898305 630897015 0.000000e+00 1219.0
11 TraesCS5B01G515000 chr4A 85.994 971 78 27 972 1914 630899255 630898315 0.000000e+00 987.0
12 TraesCS5B01G515000 chr4A 90.767 704 30 10 804 1476 630878296 630877597 0.000000e+00 907.0
13 TraesCS5B01G515000 chr4A 79.560 910 88 55 972 1848 631507180 631508024 8.600000e-156 560.0
14 TraesCS5B01G515000 chr4A 90.634 331 26 4 1 329 630881554 630881227 5.440000e-118 435.0
15 TraesCS5B01G515000 chr4A 83.065 496 45 22 325 789 630879243 630878756 7.080000e-112 414.0
16 TraesCS5B01G515000 chr4A 87.266 267 21 2 3057 3323 631502373 631502626 3.460000e-75 292.0
17 TraesCS5B01G515000 chr4A 77.079 445 75 17 3047 3471 631498431 631498868 7.660000e-57 231.0
18 TraesCS5B01G515000 chr4A 90.805 174 10 2 3371 3544 631502619 631502786 9.900000e-56 228.0
19 TraesCS5B01G515000 chr4A 86.228 167 22 1 624 789 688646361 688646527 2.810000e-41 180.0
20 TraesCS5B01G515000 chr4A 100.000 28 0 0 3519 3546 630875633 630875606 6.000000e-03 52.8
21 TraesCS5B01G515000 chr5D 81.689 2037 252 68 865 2857 538442377 538440418 0.000000e+00 1583.0
22 TraesCS5B01G515000 chr5D 87.510 1281 111 15 2193 3460 538622736 538623980 0.000000e+00 1434.0
23 TraesCS5B01G515000 chr5D 81.490 1718 209 48 967 2613 538425269 538423590 0.000000e+00 1310.0
24 TraesCS5B01G515000 chr5D 86.586 1163 100 30 964 2093 538621531 538622670 0.000000e+00 1232.0
25 TraesCS5B01G515000 chr5D 86.747 1162 84 20 796 1914 538655281 538656415 0.000000e+00 1229.0
26 TraesCS5B01G515000 chr5D 90.606 809 56 8 2148 2945 538656425 538657224 0.000000e+00 1055.0
27 TraesCS5B01G515000 chr5D 81.889 900 106 34 969 1829 538417306 538416425 0.000000e+00 706.0
28 TraesCS5B01G515000 chr5D 92.525 495 24 6 3052 3546 538657222 538657703 0.000000e+00 697.0
29 TraesCS5B01G515000 chr5D 83.885 453 39 15 363 785 538654667 538655115 5.510000e-108 401.0
30 TraesCS5B01G515000 chr5D 86.726 226 29 1 148 373 538648282 538648506 2.110000e-62 250.0
31 TraesCS5B01G515000 chr5D 92.810 153 9 2 1 152 538647297 538647448 1.660000e-53 220.0
32 TraesCS5B01G515000 chr5D 100.000 28 0 0 3519 3546 538657630 538657657 6.000000e-03 52.8
33 TraesCS5B01G515000 chrUn 86.564 1429 142 19 2058 3460 67362340 67360936 0.000000e+00 1530.0
34 TraesCS5B01G515000 chrUn 86.937 1087 110 19 972 2031 67363417 67362336 0.000000e+00 1192.0
35 TraesCS5B01G515000 chr1D 77.014 1266 175 54 2218 3454 6386263 6385085 1.400000e-173 619.0
36 TraesCS5B01G515000 chr1D 100.000 28 0 0 790 817 269856694 269856667 6.000000e-03 52.8
37 TraesCS5B01G515000 chr6B 91.071 168 14 1 623 789 288654707 288654874 3.560000e-55 226.0
38 TraesCS5B01G515000 chr2B 87.349 166 20 1 623 787 593683177 593683342 4.670000e-44 189.0
39 TraesCS5B01G515000 chr2B 83.688 141 22 1 624 763 57025262 57025122 7.990000e-27 132.0
40 TraesCS5B01G515000 chr3B 86.826 167 21 1 624 789 750357301 750357467 6.050000e-43 185.0
41 TraesCS5B01G515000 chr3B 86.228 167 22 1 624 789 494072317 494072483 2.810000e-41 180.0
42 TraesCS5B01G515000 chr3B 96.875 32 0 1 790 820 5697053 5697022 6.000000e-03 52.8
43 TraesCS5B01G515000 chr7B 86.228 167 22 1 624 789 106108271 106108105 2.810000e-41 180.0
44 TraesCS5B01G515000 chr7B 100.000 30 0 0 790 819 106108334 106108363 4.950000e-04 56.5
45 TraesCS5B01G515000 chr2D 86.228 167 22 1 624 789 476763869 476764035 2.810000e-41 180.0
46 TraesCS5B01G515000 chr1A 83.688 141 22 1 624 763 19518088 19518228 7.990000e-27 132.0
47 TraesCS5B01G515000 chr6D 79.167 144 23 6 623 760 292373929 292374071 3.770000e-15 93.5
48 TraesCS5B01G515000 chr1B 80.769 104 14 5 34 135 596391982 596391883 3.800000e-10 76.8
49 TraesCS5B01G515000 chr3D 100.000 28 0 0 790 817 297466808 297466835 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 TraesCS5B01G515000 chr5B 679671214 679674759 3545 False 6549.00 6549 100.0000 1 3546 1 chr5B.!!$F1 3545
1 TraesCS5B01G515000 chr5B 679558224 679559949 1725 True 685.00 935 85.1760 865 2563 2 chr5B.!!$R3 1698
2 TraesCS5B01G515000 chr5B 679401494 679405435 3941 True 561.00 937 78.0645 876 3471 2 chr5B.!!$R2 2595
3 TraesCS5B01G515000 chr5B 679378903 679379451 548 True 412.00 412 81.3050 973 1506 1 chr5B.!!$R1 533
4 TraesCS5B01G515000 chr4A 631475857 631477785 1928 False 1467.00 1467 81.1090 865 2791 1 chr4A.!!$F1 1926
5 TraesCS5B01G515000 chr4A 630897015 630899255 2240 True 1103.00 1219 85.0415 972 3460 2 chr4A.!!$R2 2488
6 TraesCS5B01G515000 chr4A 630875558 630881554 5996 True 917.76 2780 91.2060 1 3546 5 chr4A.!!$R1 3545
7 TraesCS5B01G515000 chr4A 631494188 631502786 8598 False 770.20 1873 85.3964 948 3544 5 chr4A.!!$F4 2596
8 TraesCS5B01G515000 chr4A 631507180 631508024 844 False 560.00 560 79.5600 972 1848 1 chr4A.!!$F2 876
9 TraesCS5B01G515000 chr5D 538440418 538442377 1959 True 1583.00 1583 81.6890 865 2857 1 chr5D.!!$R3 1992
10 TraesCS5B01G515000 chr5D 538621531 538623980 2449 False 1333.00 1434 87.0480 964 3460 2 chr5D.!!$F1 2496
11 TraesCS5B01G515000 chr5D 538423590 538425269 1679 True 1310.00 1310 81.4900 967 2613 1 chr5D.!!$R2 1646
12 TraesCS5B01G515000 chr5D 538416425 538417306 881 True 706.00 706 81.8890 969 1829 1 chr5D.!!$R1 860
13 TraesCS5B01G515000 chr5D 538654667 538657703 3036 False 686.96 1229 90.7526 363 3546 5 chr5D.!!$F3 3183
14 TraesCS5B01G515000 chr5D 538647297 538648506 1209 False 235.00 250 89.7680 1 373 2 chr5D.!!$F2 372
15 TraesCS5B01G515000 chrUn 67360936 67363417 2481 True 1361.00 1530 86.7505 972 3460 2 chrUn.!!$R1 2488
16 TraesCS5B01G515000 chr1D 6385085 6386263 1178 True 619.00 619 77.0140 2218 3454 1 chr1D.!!$R1 1236

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
92 94 0.397254 GGACCTCCTCCGGATTCTCA 60.397 60.000 3.57 0.0 0.0 3.27 F
427 3257 0.958822 ACCATGGGCGTCTTCAAAAC 59.041 50.000 18.09 0.0 0.0 2.43 F
1201 4573 1.004277 TCCGGTCTCCCATTTCCTTTG 59.996 52.381 0.00 0.0 0.0 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1979 11632 0.740737 ACCACACAGCAACTTTCAGC 59.259 50.000 0.0 0.0 0.00 4.26 R
2173 11966 4.093743 TGAATAAGTAGACACAGCTCCCA 58.906 43.478 0.0 0.0 0.00 4.37 R
2906 12803 0.887387 TAAACTGCAGTTCCCCGTGC 60.887 55.000 31.2 0.0 37.25 5.34 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
81 83 4.787534 AGAATCTTGAGAATTGGACCTCCT 59.212 41.667 0.00 0.00 36.82 3.69
92 94 0.397254 GGACCTCCTCCGGATTCTCA 60.397 60.000 3.57 0.00 0.00 3.27
112 114 5.129485 TCTCATAGAATCTTGAACCCACCTC 59.871 44.000 0.00 0.00 0.00 3.85
159 1001 8.710749 TCAAGATTCTGGAAAAATATATGGGG 57.289 34.615 0.00 0.00 0.00 4.96
165 1007 5.074515 TCTGGAAAAATATATGGGGAGGTCC 59.925 44.000 0.00 0.00 0.00 4.46
180 1022 3.493524 GGAGGTCCGATTCTCAAGATTCC 60.494 52.174 0.00 0.00 0.00 3.01
194 1036 1.146263 ATTCCGTGAGAATCGGCCC 59.854 57.895 0.00 0.00 41.60 5.80
214 1056 3.270877 CCAAAGAGTTGTCCCTTATCGG 58.729 50.000 0.00 0.00 32.40 4.18
219 1061 4.576879 AGAGTTGTCCCTTATCGGAAAAC 58.423 43.478 2.93 2.93 46.66 2.43
256 1098 7.691213 TCCTATAAACTTGTGGGTTATCAACA 58.309 34.615 0.00 0.00 38.59 3.33
272 1114 2.443016 CACCCCGCTAGCTCCTCT 60.443 66.667 13.93 0.00 0.00 3.69
276 1118 2.430610 CCCGCTAGCTCCTCTTGCT 61.431 63.158 13.93 0.00 40.62 3.91
345 3175 3.197790 CATCAAGCCGCCCGACAG 61.198 66.667 0.00 0.00 0.00 3.51
355 3185 1.490693 CGCCCGACAGACATATGCAC 61.491 60.000 1.58 0.00 0.00 4.57
357 3187 1.490693 CCCGACAGACATATGCACGC 61.491 60.000 1.58 0.00 0.00 5.34
385 3215 4.632688 GCAAAACATTGCAGAAATATGGCT 59.367 37.500 8.56 0.00 46.60 4.75
415 3245 4.802051 CGGTCCAGCCACCATGGG 62.802 72.222 18.09 4.89 38.19 4.00
427 3257 0.958822 ACCATGGGCGTCTTCAAAAC 59.041 50.000 18.09 0.00 0.00 2.43
436 3266 2.290641 GCGTCTTCAAAACACACATCCT 59.709 45.455 0.00 0.00 0.00 3.24
452 3282 2.118313 TCCTGTGCACAGATTGGATG 57.882 50.000 41.50 25.29 46.59 3.51
544 3404 3.315470 ACACATACGTCACTATGCGATCT 59.685 43.478 0.00 0.00 0.00 2.75
546 3406 5.082723 CACATACGTCACTATGCGATCTAG 58.917 45.833 0.00 0.00 0.00 2.43
549 3409 1.266989 CGTCACTATGCGATCTAGCCA 59.733 52.381 0.00 0.00 36.02 4.75
550 3410 2.287608 CGTCACTATGCGATCTAGCCAA 60.288 50.000 0.00 0.00 36.02 4.52
567 3427 2.355756 GCCAAGCATGTGTATGACGAAT 59.644 45.455 0.00 0.00 36.36 3.34
568 3428 3.546815 GCCAAGCATGTGTATGACGAATC 60.547 47.826 0.00 0.00 36.36 2.52
605 3465 4.161001 AGGATAAAGTATCGTCCAACGGTT 59.839 41.667 0.00 0.00 42.81 4.44
623 3483 2.139917 GTTGTGCACCAAGTATCGTCA 58.860 47.619 15.69 0.00 32.51 4.35
649 3509 8.165239 TGGACTAAACATGTATAAATGGCATC 57.835 34.615 7.81 0.00 31.46 3.91
664 3524 5.679734 ATGGCATCATCGTATTTGTCTTC 57.320 39.130 0.00 0.00 0.00 2.87
665 3525 3.876914 TGGCATCATCGTATTTGTCTTCC 59.123 43.478 0.00 0.00 0.00 3.46
745 3606 9.462174 GAAAATCATAATCAAAGTTGTGTGACA 57.538 29.630 0.00 0.00 0.00 3.58
753 3614 4.083003 TCAAAGTTGTGTGACAAAGACCAC 60.083 41.667 0.00 0.00 40.15 4.16
764 3625 5.516339 GTGACAAAGACCACAAAAGTCAATG 59.484 40.000 0.00 0.00 36.43 2.82
789 3650 4.215109 TGCCTTATATTTTGGGAAGGAGC 58.785 43.478 3.71 0.00 40.88 4.70
791 3652 4.895889 GCCTTATATTTTGGGAAGGAGCTT 59.104 41.667 3.71 0.00 40.88 3.74
827 4133 2.778270 AGGGAGTAGTAATTTGGAGGGC 59.222 50.000 0.00 0.00 0.00 5.19
944 4270 1.133823 TCCCAAACAGAGCAAGAGCAA 60.134 47.619 0.00 0.00 45.49 3.91
1007 4360 3.880846 CGAGAAGGCAATGGCGGC 61.881 66.667 0.00 0.00 42.47 6.53
1050 4403 1.742768 CCGTAGGCAGATGGAGGAC 59.257 63.158 0.00 0.00 46.14 3.85
1201 4573 1.004277 TCCGGTCTCCCATTTCCTTTG 59.996 52.381 0.00 0.00 0.00 2.77
1471 4896 1.372087 GCCTTCGTCAAGCCCATGAG 61.372 60.000 0.00 0.00 0.00 2.90
1478 4903 1.675310 CAAGCCCATGAGCCACGAA 60.675 57.895 0.00 0.00 0.00 3.85
1486 4911 4.166011 GAGCCACGAATGCGCCAC 62.166 66.667 4.18 0.00 42.48 5.01
1491 4916 4.329545 ACGAATGCGCCACCAGGT 62.330 61.111 4.18 0.00 42.48 4.00
1511 4946 5.990668 AGGTCAATCCTGATGGTAAAGTAC 58.009 41.667 0.00 0.00 46.19 2.73
1524 4959 7.602644 TGATGGTAAAGTACTGTAGCAAGAAAG 59.397 37.037 24.84 0.00 31.97 2.62
1602 5068 8.820933 GTTATATATATGCATCGTGACAGCAAT 58.179 33.333 0.19 0.00 42.15 3.56
1628 5094 5.396772 CCCCAAGCACTTCATCAAGTATCTA 60.397 44.000 0.00 0.00 41.24 1.98
1653 11284 4.148825 ACGATGAGGCAGCCGTCC 62.149 66.667 5.55 0.00 0.00 4.79
1718 11358 1.750778 CACAGAAAGGGCAAACACTGT 59.249 47.619 0.00 0.00 38.79 3.55
1719 11359 2.024414 ACAGAAAGGGCAAACACTGTC 58.976 47.619 0.00 0.00 34.21 3.51
1720 11360 2.023673 CAGAAAGGGCAAACACTGTCA 58.976 47.619 0.00 0.00 0.00 3.58
1721 11361 2.024414 AGAAAGGGCAAACACTGTCAC 58.976 47.619 0.00 0.00 0.00 3.67
1722 11362 2.024414 GAAAGGGCAAACACTGTCACT 58.976 47.619 0.00 0.00 0.00 3.41
1723 11363 3.118038 AGAAAGGGCAAACACTGTCACTA 60.118 43.478 0.00 0.00 0.00 2.74
1803 11443 3.779759 TGCTTGGTTTTTCACATGACAC 58.220 40.909 0.00 0.00 0.00 3.67
1891 11534 9.463443 CTTTTTACTTTAAGGAACTCCACATTG 57.537 33.333 0.00 0.00 38.49 2.82
1979 11632 3.859386 GGCCTTGCGATTCTAAAACATTG 59.141 43.478 0.00 0.00 0.00 2.82
1992 11646 5.978919 TCTAAAACATTGCTGAAAGTTGCTG 59.021 36.000 0.00 0.00 35.30 4.41
1993 11647 3.806625 AACATTGCTGAAAGTTGCTGT 57.193 38.095 0.00 0.00 35.30 4.40
2087 11802 7.735326 ACCTGGTATGTCTACTGAATAACTT 57.265 36.000 0.00 0.00 0.00 2.66
2138 11930 9.515226 TGTCTTAGCTTCAAATTATAAAGTGGT 57.485 29.630 0.00 0.00 0.00 4.16
2224 12050 7.011499 TGAGTAATTAGGCTTGTTTGGACTA 57.989 36.000 0.00 0.00 0.00 2.59
2332 12166 6.741724 TGAAAGGGCCTCTAGGAATTATTTT 58.258 36.000 6.46 0.00 37.39 1.82
2359 12204 2.171003 AGGCCTTTAATTGTCCACAGC 58.829 47.619 0.00 0.00 0.00 4.40
2429 12281 4.911390 AGGAGGTTGTTTTATCTCACTGG 58.089 43.478 0.00 0.00 0.00 4.00
2464 12326 5.808540 TCGTGCAACCTCATTAGTTATGTAC 59.191 40.000 0.00 0.00 35.64 2.90
2551 12413 6.477053 TCTGAGGATGAAGAGTAATGAAGG 57.523 41.667 0.00 0.00 0.00 3.46
2565 12427 0.257328 TGAAGGTGTGTGCTTCCCAA 59.743 50.000 0.00 0.00 0.00 4.12
2604 12484 6.489022 AGGTACTTTGTTACCATTGTTTCCTC 59.511 38.462 2.29 0.00 38.78 3.71
2745 12641 9.483916 AAAATAAATACAAACCCACTTGCTTAC 57.516 29.630 0.00 0.00 0.00 2.34
2756 12652 3.262420 CACTTGCTTACGAGTTATGGCT 58.738 45.455 0.00 0.00 38.57 4.75
2834 12731 5.528600 TGTTTCTCCCATTTCCCTATTGA 57.471 39.130 0.00 0.00 0.00 2.57
2903 12800 1.651987 TGCTTATGCTAGCCGTGAAC 58.348 50.000 13.29 0.00 40.49 3.18
2906 12803 2.032549 GCTTATGCTAGCCGTGAACATG 60.033 50.000 13.29 0.00 35.06 3.21
2962 12860 2.158623 ACTTCTCATCAGTGGCCAAACA 60.159 45.455 7.24 0.00 0.00 2.83
2969 12867 1.120795 CAGTGGCCAAACACCCCAAT 61.121 55.000 7.24 0.00 42.28 3.16
3022 12922 5.506708 AGAAAGTAAAAACTGCCGGGATAT 58.493 37.500 2.18 0.00 0.00 1.63
3216 14504 5.363101 TGCCAAATATGTCTTTTGTTGCAA 58.637 33.333 0.00 0.00 32.24 4.08
3244 14537 3.923563 GAAGCACGCTCTCCGCTGT 62.924 63.158 0.00 0.00 41.76 4.40
3246 14539 2.126071 GCACGCTCTCCGCTGTTA 60.126 61.111 0.00 0.00 41.76 2.41
3259 14554 1.009829 GCTGTTATTGGAGTCGGCTG 58.990 55.000 0.00 0.00 0.00 4.85
3362 14661 2.320681 TGGGAGTAGCAGGTAACAGT 57.679 50.000 0.00 0.00 41.41 3.55
3364 14663 1.900486 GGGAGTAGCAGGTAACAGTGT 59.100 52.381 0.00 0.00 41.41 3.55
3372 14671 0.837272 AGGTAACAGTGTGTGGTGCT 59.163 50.000 0.00 0.00 41.41 4.40
3388 14687 2.488153 GGTGCTGACCTTGTATTGGTTC 59.512 50.000 0.00 0.00 39.47 3.62
3463 14774 2.875933 TCCTGTTTGTTTTCGGCTACTG 59.124 45.455 0.00 0.00 0.00 2.74
3505 14816 1.416401 TGAGTTCTTGGACACTGACCC 59.584 52.381 0.00 0.00 0.00 4.46
3506 14817 0.765510 AGTTCTTGGACACTGACCCC 59.234 55.000 0.00 0.00 0.00 4.95
3507 14818 0.765510 GTTCTTGGACACTGACCCCT 59.234 55.000 0.00 0.00 0.00 4.79
3508 14819 0.764890 TTCTTGGACACTGACCCCTG 59.235 55.000 0.00 0.00 0.00 4.45
3509 14820 1.127567 TCTTGGACACTGACCCCTGG 61.128 60.000 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 0.107848 TGGGCCTAAAGTAAGAGCGC 60.108 55.000 4.53 0.00 36.97 5.92
19 20 5.661056 AAAATTGGGCCTAAAGTAAGAGC 57.339 39.130 5.31 0.00 0.00 4.09
92 94 6.394345 AAAGAGGTGGGTTCAAGATTCTAT 57.606 37.500 0.00 0.00 0.00 1.98
112 114 6.100004 TGAACTAGCTAGGATTGTCGAAAAG 58.900 40.000 24.35 0.00 0.00 2.27
159 1001 3.723260 GGAATCTTGAGAATCGGACCTC 58.277 50.000 0.00 3.15 38.61 3.85
165 1007 4.033990 TCTCACGGAATCTTGAGAATCG 57.966 45.455 11.07 0.00 42.75 3.34
180 1022 0.391130 TCTTTGGGCCGATTCTCACG 60.391 55.000 0.00 0.00 0.00 4.35
194 1036 4.202245 TCCGATAAGGGACAACTCTTTG 57.798 45.455 0.00 0.00 37.97 2.77
252 1094 2.125106 GGAGCTAGCGGGGTGTTG 60.125 66.667 9.55 0.00 0.00 3.33
256 1098 2.060980 CAAGAGGAGCTAGCGGGGT 61.061 63.158 9.55 0.00 0.00 4.95
260 1102 1.299014 CGAGCAAGAGGAGCTAGCG 60.299 63.158 9.55 0.00 43.58 4.26
272 1114 1.964608 CTCTCTGCCCATCCGAGCAA 61.965 60.000 0.00 0.00 38.82 3.91
276 1118 1.758514 GGACTCTCTGCCCATCCGA 60.759 63.158 0.00 0.00 0.00 4.55
345 3175 2.598632 GCCCGAGCGTGCATATGTC 61.599 63.158 4.29 0.00 0.00 3.06
355 3185 4.151417 CAATGTTTTGCCCGAGCG 57.849 55.556 0.00 0.00 44.31 5.03
415 3245 2.290641 AGGATGTGTGTTTTGAAGACGC 59.709 45.455 0.00 0.00 35.90 5.19
436 3266 1.536940 CACCATCCAATCTGTGCACA 58.463 50.000 20.37 20.37 0.00 4.57
441 3271 0.608856 TTGCGCACCATCCAATCTGT 60.609 50.000 11.12 0.00 0.00 3.41
514 3345 6.293790 GCATAGTGACGTATGTGTAGACCATA 60.294 42.308 0.00 0.00 33.56 2.74
515 3346 5.507482 GCATAGTGACGTATGTGTAGACCAT 60.507 44.000 0.00 0.00 33.56 3.55
516 3347 4.201980 GCATAGTGACGTATGTGTAGACCA 60.202 45.833 0.00 0.00 33.56 4.02
518 3349 3.966844 CGCATAGTGACGTATGTGTAGAC 59.033 47.826 0.00 0.00 36.54 2.59
519 3350 3.872771 TCGCATAGTGACGTATGTGTAGA 59.127 43.478 8.90 0.83 40.40 2.59
527 3363 2.483106 GGCTAGATCGCATAGTGACGTA 59.517 50.000 0.00 0.00 0.00 3.57
544 3404 2.167487 TCGTCATACACATGCTTGGCTA 59.833 45.455 4.44 0.00 31.73 3.93
546 3406 1.368641 TCGTCATACACATGCTTGGC 58.631 50.000 4.44 0.00 31.73 4.52
549 3409 2.866156 CCGATTCGTCATACACATGCTT 59.134 45.455 5.20 0.00 31.73 3.91
550 3410 2.100749 TCCGATTCGTCATACACATGCT 59.899 45.455 5.20 0.00 31.73 3.79
605 3465 2.345876 CATGACGATACTTGGTGCACA 58.654 47.619 20.43 1.62 0.00 4.57
623 3483 8.710749 ATGCCATTTATACATGTTTAGTCCAT 57.289 30.769 2.30 0.00 0.00 3.41
729 3590 4.704540 TGGTCTTTGTCACACAACTTTGAT 59.295 37.500 0.00 0.00 37.90 2.57
735 3596 3.840890 TTGTGGTCTTTGTCACACAAC 57.159 42.857 5.11 0.00 45.62 3.32
745 3606 5.739935 GCATCCATTGACTTTTGTGGTCTTT 60.740 40.000 0.00 0.00 35.04 2.52
764 3625 5.393866 TCCTTCCCAAAATATAAGGCATCC 58.606 41.667 0.00 0.00 38.70 3.51
789 3650 6.267492 ACTCCCTCCTTCCCAAAATATAAG 57.733 41.667 0.00 0.00 0.00 1.73
791 3652 6.458784 ACTACTCCCTCCTTCCCAAAATATA 58.541 40.000 0.00 0.00 0.00 0.86
827 4133 3.628017 CGACCACACCTTTGCTTTTTAG 58.372 45.455 0.00 0.00 0.00 1.85
944 4270 3.292159 GTTTTCCAGCCGCCCGTT 61.292 61.111 0.00 0.00 0.00 4.44
1007 4360 1.595003 GCTCCTCGTACGAGTTCGATG 60.595 57.143 35.85 22.93 43.02 3.84
1035 4388 1.204146 GGTTGTCCTCCATCTGCCTA 58.796 55.000 0.00 0.00 0.00 3.93
1201 4573 2.050077 GTATACGGGTACGGGCGC 60.050 66.667 0.00 0.00 46.48 6.53
1478 4903 1.750399 GATTGACCTGGTGGCGCAT 60.750 57.895 10.83 0.00 36.63 4.73
1491 4916 6.620877 ACAGTACTTTACCATCAGGATTGA 57.379 37.500 0.00 0.00 38.69 2.57
1499 4934 7.413109 GCTTTCTTGCTACAGTACTTTACCATC 60.413 40.741 0.00 0.00 0.00 3.51
1506 4941 5.931441 CAAGCTTTCTTGCTACAGTACTT 57.069 39.130 0.00 0.00 43.24 2.24
1524 4959 2.164827 TCACATCACATCCAATGCAAGC 59.835 45.455 0.00 0.00 0.00 4.01
1531 4966 2.583024 TTGCCTCACATCACATCCAA 57.417 45.000 0.00 0.00 0.00 3.53
1602 5068 2.158475 ACTTGATGAAGTGCTTGGGGAA 60.158 45.455 0.00 0.00 41.12 3.97
1653 11284 3.461773 ATCCGCCTCGTCCACCAG 61.462 66.667 0.00 0.00 0.00 4.00
1718 11358 3.053842 ACCCCTTGTCGAGATAGTAGTGA 60.054 47.826 0.00 0.00 0.00 3.41
1719 11359 3.066900 CACCCCTTGTCGAGATAGTAGTG 59.933 52.174 0.00 0.00 0.00 2.74
1720 11360 3.288964 CACCCCTTGTCGAGATAGTAGT 58.711 50.000 0.00 0.00 0.00 2.73
1721 11361 2.623889 CCACCCCTTGTCGAGATAGTAG 59.376 54.545 0.00 0.00 0.00 2.57
1722 11362 2.242965 TCCACCCCTTGTCGAGATAGTA 59.757 50.000 0.00 0.00 0.00 1.82
1723 11363 1.006758 TCCACCCCTTGTCGAGATAGT 59.993 52.381 0.00 0.00 0.00 2.12
1803 11443 1.610522 CACCTTGAACTTTGCCCTCTG 59.389 52.381 0.00 0.00 0.00 3.35
1928 11580 2.774439 ACACAGCGATTCCACAAAAC 57.226 45.000 0.00 0.00 0.00 2.43
1979 11632 0.740737 ACCACACAGCAACTTTCAGC 59.259 50.000 0.00 0.00 0.00 4.26
1992 11646 4.330074 GCATTAGTGAGTATGACACCACAC 59.670 45.833 0.00 0.00 36.10 3.82
1993 11647 4.503910 GCATTAGTGAGTATGACACCACA 58.496 43.478 0.00 0.00 33.32 4.17
2173 11966 4.093743 TGAATAAGTAGACACAGCTCCCA 58.906 43.478 0.00 0.00 0.00 4.37
2175 11968 9.579768 CATATATGAATAAGTAGACACAGCTCC 57.420 37.037 6.92 0.00 0.00 4.70
2204 12022 6.129414 TGGTAGTCCAAACAAGCCTAATTA 57.871 37.500 0.00 0.00 41.25 1.40
2224 12050 8.100791 TGCAAACTCTATGTAGAATTAACTGGT 58.899 33.333 0.00 0.00 0.00 4.00
2228 12054 8.718102 TCCTGCAAACTCTATGTAGAATTAAC 57.282 34.615 0.00 0.00 32.96 2.01
2332 12166 7.350382 TGTGGACAATTAAAGGCCTATGAATA 58.650 34.615 5.16 0.00 0.00 1.75
2359 12204 8.660435 TCCCTTCCACTATCTAAAAAGATATGG 58.340 37.037 12.70 12.70 34.49 2.74
2464 12326 7.558161 TCTAAAAATGTAGACCTGCATCATG 57.442 36.000 1.24 0.00 34.83 3.07
2604 12484 6.020678 GCGAATGATGGAAAGAAATTTAACCG 60.021 38.462 0.00 0.00 0.00 4.44
2683 12571 5.188359 ACTGAGCTTGGCCAATTATGAAATT 59.812 36.000 20.85 0.00 35.65 1.82
2723 12615 5.996513 TCGTAAGCAAGTGGGTTTGTATTTA 59.003 36.000 0.00 0.00 38.39 1.40
2724 12616 4.822896 TCGTAAGCAAGTGGGTTTGTATTT 59.177 37.500 0.00 0.00 38.39 1.40
2725 12617 4.391155 TCGTAAGCAAGTGGGTTTGTATT 58.609 39.130 0.00 0.00 38.39 1.89
2756 12652 4.709250 TGCAGGACACACAGTTATGTTTA 58.291 39.130 0.00 0.00 37.65 2.01
2834 12731 3.942829 TGTCAGGCTCGAAATCTCAAAT 58.057 40.909 0.00 0.00 0.00 2.32
2903 12800 2.672651 TGCAGTTCCCCGTGCATG 60.673 61.111 0.00 0.00 44.70 4.06
2906 12803 0.887387 TAAACTGCAGTTCCCCGTGC 60.887 55.000 31.20 0.00 37.25 5.34
2962 12860 3.992943 TGTCGATCAGTTAATTGGGGT 57.007 42.857 0.00 0.00 0.00 4.95
2969 12867 6.308041 GCGCATCTAATATGTCGATCAGTTAA 59.692 38.462 0.30 0.00 0.00 2.01
3022 12922 4.637276 TGCTCCTACGAATCAAGAAACAA 58.363 39.130 0.00 0.00 0.00 2.83
3216 14504 2.234908 AGAGCGTGCTTCTCCTACAAAT 59.765 45.455 0.00 0.00 0.00 2.32
3244 14537 4.954933 GGCAGCCGACTCCAATAA 57.045 55.556 0.00 0.00 0.00 1.40
3259 14554 0.031994 AACCAGCACAAAATCACGGC 59.968 50.000 0.00 0.00 0.00 5.68
3263 14558 0.743688 ACGCAACCAGCACAAAATCA 59.256 45.000 0.00 0.00 46.13 2.57
3362 14661 0.833949 TACAAGGTCAGCACCACACA 59.166 50.000 0.00 0.00 46.68 3.72
3364 14663 2.503331 CAATACAAGGTCAGCACCACA 58.497 47.619 0.00 0.00 46.68 4.17
3372 14671 9.083422 TCATTTAATTGAACCAATACAAGGTCA 57.917 29.630 0.00 0.00 38.76 4.02
3388 14687 9.642312 CATCGTCAGACTACAATCATTTAATTG 57.358 33.333 0.00 0.00 41.46 2.32
3483 14794 2.872858 GGTCAGTGTCCAAGAACTCAAC 59.127 50.000 1.10 0.00 0.00 3.18
3505 14816 1.706866 TGATCATTATCCAGGGCCAGG 59.293 52.381 9.04 9.04 0.00 4.45
3506 14817 3.618351 GATGATCATTATCCAGGGCCAG 58.382 50.000 10.14 0.00 0.00 4.85
3507 14818 2.309755 GGATGATCATTATCCAGGGCCA 59.690 50.000 10.14 0.00 42.93 5.36
3508 14819 2.579860 AGGATGATCATTATCCAGGGCC 59.420 50.000 10.14 0.00 45.28 5.80
3509 14820 3.522750 AGAGGATGATCATTATCCAGGGC 59.477 47.826 10.14 0.00 45.28 5.19


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

AutoCloner maintained by Alex Coulton.