Multiple sequence alignment - TraesCS3B01G597400

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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 TraesCS3B01G597400 chr3B 100.000 4256 0 0 1 4256 819788755 819784500 0.000000e+00 7860.0
1 TraesCS3B01G597400 chr3D 93.387 3221 162 23 79 3259 609085633 609082424 0.000000e+00 4721.0
2 TraesCS3B01G597400 chr3D 94.091 440 16 3 3291 3729 609082119 609081689 0.000000e+00 660.0
3 TraesCS3B01G597400 chr3D 95.652 115 5 0 4141 4255 609081694 609081580 7.270000e-43 185.0
4 TraesCS3B01G597400 chr3D 97.143 35 1 0 3260 3294 609082403 609082369 4.600000e-05 60.2
5 TraesCS3B01G597400 chr3D 100.000 31 0 0 2 32 609085682 609085652 1.650000e-04 58.4
6 TraesCS3B01G597400 chr3A 92.064 3314 182 36 1 3261 742440312 742437027 0.000000e+00 4588.0
7 TraesCS3B01G597400 chr3A 93.422 973 35 11 3291 4256 742436721 742435771 0.000000e+00 1415.0
8 TraesCS3B01G597400 chr3A 94.845 97 5 0 4160 4256 742434830 742434734 7.370000e-33 152.0
9 TraesCS3B01G597400 chr3A 93.939 66 4 0 4184 4249 742435377 742435312 2.710000e-17 100.0
10 TraesCS3B01G597400 chr3A 100.000 44 0 0 4160 4203 742435295 742435252 9.810000e-12 82.4
11 TraesCS3B01G597400 chr3A 90.566 53 5 0 4197 4249 742434899 742434847 2.120000e-08 71.3
12 TraesCS3B01G597400 chr3A 100.000 35 0 0 3260 3294 742437006 742436972 9.880000e-07 65.8
13 TraesCS3B01G597400 chr2D 86.381 257 20 9 978 1222 623474985 623474732 2.520000e-67 267.0
14 TraesCS3B01G597400 chr2D 90.370 135 13 0 1496 1630 623474735 623474601 1.220000e-40 178.0
15 TraesCS3B01G597400 chr2D 74.022 358 59 26 1016 1361 642203691 642203356 9.670000e-22 115.0
16 TraesCS3B01G597400 chr2D 76.682 223 37 10 1149 1361 598308983 598308766 4.500000e-20 110.0
17 TraesCS3B01G597400 chr2D 91.667 60 3 1 8 65 623496184 623496125 9.810000e-12 82.4
18 TraesCS3B01G597400 chr2B 85.981 214 17 7 291 502 765484586 765484384 2.580000e-52 217.0
19 TraesCS3B01G597400 chr2B 77.401 354 58 15 1016 1361 799614132 799614471 1.560000e-44 191.0
20 TraesCS3B01G597400 chr7D 81.855 248 27 11 3433 3678 303039488 303039257 4.340000e-45 193.0
21 TraesCS3B01G597400 chr7B 81.452 248 28 11 3433 3678 285468713 285468944 2.020000e-43 187.0
22 TraesCS3B01G597400 chr7A 81.452 248 28 11 3433 3678 367259187 367259418 2.020000e-43 187.0
23 TraesCS3B01G597400 chr2A 78.205 234 40 7 1103 1328 766919347 766919117 5.740000e-29 139.0
24 TraesCS3B01G597400 chr2A 93.333 60 2 1 8 65 754707971 754707912 2.110000e-13 87.9
25 TraesCS3B01G597400 chr2A 74.089 247 39 14 976 1217 766973925 766973699 1.270000e-10 78.7


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 TraesCS3B01G597400 chr3B 819784500 819788755 4255 True 7860.000000 7860 100.000000 1 4256 1 chr3B.!!$R1 4255
1 TraesCS3B01G597400 chr3D 609081580 609085682 4102 True 1136.920000 4721 96.054600 2 4255 5 chr3D.!!$R1 4253
2 TraesCS3B01G597400 chr3A 742434734 742440312 5578 True 924.928571 4588 94.976571 1 4256 7 chr3A.!!$R1 4255

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
331 342 0.035881 CTCCAGCTGCTGAAGGAACA 59.964 55.0 30.1 4.63 32.44 3.18 F
1596 1655 0.039618 TGTTTGGGAAGATGGGGCTC 59.960 55.0 0.0 0.00 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1966 2025 0.034089 ACCTGCCTTCCTTGCCATAC 60.034 55.0 0.00 0.0 0.00 2.39 R
3425 3760 0.750546 ATGGCTATGTGCAGTGCCTG 60.751 55.0 13.72 0.0 45.11 4.85 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
65 66 2.971660 TGCTATTGCATTGCATTGCT 57.028 40.000 28.14 15.45 45.31 3.91
67 68 3.601435 TGCTATTGCATTGCATTGCTTT 58.399 36.364 28.14 19.38 45.31 3.51
68 69 4.004314 TGCTATTGCATTGCATTGCTTTT 58.996 34.783 28.14 17.41 45.31 2.27
69 70 5.176592 TGCTATTGCATTGCATTGCTTTTA 58.823 33.333 28.14 17.55 45.31 1.52
70 71 5.642491 TGCTATTGCATTGCATTGCTTTTAA 59.358 32.000 28.14 17.38 45.31 1.52
71 72 6.148976 TGCTATTGCATTGCATTGCTTTTAAA 59.851 30.769 28.14 17.08 45.31 1.52
72 73 7.022384 GCTATTGCATTGCATTGCTTTTAAAA 58.978 30.769 28.14 16.48 43.18 1.52
73 74 7.537991 GCTATTGCATTGCATTGCTTTTAAAAA 59.462 29.630 28.14 15.89 43.18 1.94
136 137 9.777297 AGGATTTTTAAATGTGCTAAAATGTGT 57.223 25.926 0.00 0.00 32.14 3.72
137 138 9.810231 GGATTTTTAAATGTGCTAAAATGTGTG 57.190 29.630 0.00 0.00 32.14 3.82
280 291 3.949980 AGCAGCAGCAGCAGGTGA 61.950 61.111 20.16 0.00 45.95 4.02
330 341 0.676151 CCTCCAGCTGCTGAAGGAAC 60.676 60.000 28.80 0.00 32.44 3.62
331 342 0.035881 CTCCAGCTGCTGAAGGAACA 59.964 55.000 30.10 4.63 32.44 3.18
333 344 0.535780 CCAGCTGCTGAAGGAACACA 60.536 55.000 30.10 0.00 32.44 3.72
335 346 1.467734 CAGCTGCTGAAGGAACACATC 59.532 52.381 24.88 0.00 32.44 3.06
336 347 1.350351 AGCTGCTGAAGGAACACATCT 59.650 47.619 0.00 0.00 0.00 2.90
349 362 1.228644 ACATCTTGCCTTGCCTGCA 60.229 52.632 0.00 0.00 36.84 4.41
450 464 7.454260 ACTCACAGGTCATTTTATTTTCCTC 57.546 36.000 0.00 0.00 0.00 3.71
451 465 7.234355 ACTCACAGGTCATTTTATTTTCCTCT 58.766 34.615 0.00 0.00 0.00 3.69
452 466 7.725844 ACTCACAGGTCATTTTATTTTCCTCTT 59.274 33.333 0.00 0.00 0.00 2.85
453 467 8.110860 TCACAGGTCATTTTATTTTCCTCTTC 57.889 34.615 0.00 0.00 0.00 2.87
517 531 6.205101 TCCTCTGTCGGTTAATAAGAGAAC 57.795 41.667 0.00 0.00 37.20 3.01
613 627 9.559958 CCAGATGTTCATATAAAAACAGTTCAC 57.440 33.333 8.65 0.00 38.66 3.18
643 657 8.366401 TCCAATTCTTGCACATTTTCTCATTAA 58.634 29.630 0.00 0.00 0.00 1.40
644 658 8.991026 CCAATTCTTGCACATTTTCTCATTAAA 58.009 29.630 0.00 0.00 0.00 1.52
747 774 9.540538 TTGGATTATTATTTTTCCTTGAGTGGA 57.459 29.630 0.00 0.00 0.00 4.02
752 779 6.834168 TTATTTTTCCTTGAGTGGATGGAC 57.166 37.500 0.00 0.00 35.83 4.02
773 800 8.654485 TGGACTTGGTAATTTCTACTAGTACA 57.346 34.615 0.00 0.00 0.00 2.90
895 935 3.372060 GCGAGGGCTATATTTTTGTTGC 58.628 45.455 0.00 0.00 35.83 4.17
911 951 2.749441 GCTGAGGCCAGGCTGAAC 60.749 66.667 17.94 8.24 40.72 3.18
928 968 3.556999 TGAACTAGCTAGCCCAGTAGAG 58.443 50.000 20.91 4.94 0.00 2.43
951 991 0.246360 GCCCATTAGCCCAACAACAC 59.754 55.000 0.00 0.00 0.00 3.32
965 1012 1.238439 CAACACCCAGCAGTTACCAG 58.762 55.000 0.00 0.00 0.00 4.00
976 1023 0.117340 AGTTACCAGTCCTCTGCCCT 59.883 55.000 0.00 0.00 40.09 5.19
1134 1181 1.381327 CCTCGCCAACCTCCTCCTA 60.381 63.158 0.00 0.00 0.00 2.94
1596 1655 0.039618 TGTTTGGGAAGATGGGGCTC 59.960 55.000 0.00 0.00 0.00 4.70
1688 1747 3.264897 CGGCAGGCAGATACACGC 61.265 66.667 0.00 0.00 0.00 5.34
1704 1763 3.814268 GCCTACGCGTACCGGACA 61.814 66.667 24.26 2.12 42.52 4.02
1729 1788 1.506718 GAGTCAGATGCGTCGGTGA 59.493 57.895 5.95 0.00 0.00 4.02
1730 1789 0.798771 GAGTCAGATGCGTCGGTGAC 60.799 60.000 16.67 16.67 39.74 3.67
1734 1793 1.374252 AGATGCGTCGGTGACCAAC 60.374 57.895 1.11 0.00 0.00 3.77
1821 1880 1.126846 GAGAACCGCAATCTTGTGTCG 59.873 52.381 3.09 0.00 36.98 4.35
1958 2017 1.795286 CTTGAACTCGTGTGGCTCTTC 59.205 52.381 0.00 0.00 0.00 2.87
2019 2078 5.146010 CCATAAAGGCTGATCTAGAGTCC 57.854 47.826 0.00 0.00 0.00 3.85
2025 2084 2.887783 GGCTGATCTAGAGTCCGATGAA 59.112 50.000 0.00 0.00 0.00 2.57
2148 2207 5.679734 ACAATGCAATGATCGAAGGATAC 57.320 39.130 9.20 0.00 31.51 2.24
2253 2312 4.680237 TCGCTGCTTGGGGTGTCG 62.680 66.667 0.00 0.00 0.00 4.35
2256 2315 2.738521 CTGCTTGGGGTGTCGTCG 60.739 66.667 0.00 0.00 0.00 5.12
2265 2324 2.323580 GGTGTCGTCGTCTCGGTCT 61.324 63.158 0.00 0.00 0.00 3.85
2292 2351 2.810274 TGAACTGAGCAAGCAGATTCAC 59.190 45.455 8.04 0.00 39.20 3.18
2293 2352 2.556144 ACTGAGCAAGCAGATTCACA 57.444 45.000 8.04 0.00 39.20 3.58
2319 2378 3.926527 TCATCGTCAAATCAGGAACTTCG 59.073 43.478 0.00 0.00 34.60 3.79
2385 2444 0.608035 TTTCCCTTGTGGACGATGCC 60.608 55.000 0.00 0.00 45.11 4.40
2394 2453 0.950836 TGGACGATGCCAAAGTTGTG 59.049 50.000 0.00 0.00 34.31 3.33
2454 2513 2.195922 GCTATGATTTTTGGCCTTGCG 58.804 47.619 3.32 0.00 0.00 4.85
2503 2562 1.696832 GCTCTTTACCCAGCTTCGCG 61.697 60.000 0.00 0.00 32.48 5.87
2508 2567 2.221906 TTACCCAGCTTCGCGTCTCC 62.222 60.000 5.77 0.00 0.00 3.71
2652 2711 4.430007 CCCATGTTTCAAATGCTCTCATG 58.570 43.478 0.00 0.00 32.23 3.07
2693 2752 0.606096 TTCATCGAAGAAGGACGGCA 59.394 50.000 0.00 0.00 43.58 5.69
2789 2848 1.807573 CCGAGGAAGCTCTTCGTGC 60.808 63.158 9.25 2.10 43.28 5.34
2878 2937 1.751927 GCTCATGGAGGCCTTGTGG 60.752 63.158 6.77 0.00 31.64 4.17
2913 2972 7.448748 ACAGTATTTTAACTCCATGAACACC 57.551 36.000 0.00 0.00 0.00 4.16
2920 2979 7.825331 TTTAACTCCATGAACACCAAATACA 57.175 32.000 0.00 0.00 0.00 2.29
3006 3065 2.223665 GCATGCTGCCAAGGAGTTTATC 60.224 50.000 11.37 0.00 37.42 1.75
3156 3215 1.473434 GGCCCCTCTGTTCTTATGTCG 60.473 57.143 0.00 0.00 0.00 4.35
3184 3243 1.729586 TGCCTCTAAAGGACTGTGGT 58.270 50.000 0.00 0.00 46.67 4.16
3230 3289 2.591715 GGACTGTGCTGGCGTTGT 60.592 61.111 0.00 0.00 0.00 3.32
3308 3643 4.456911 AGTGATACAACAGCTTGTCCAATG 59.543 41.667 0.00 0.00 41.15 2.82
3309 3644 4.455533 GTGATACAACAGCTTGTCCAATGA 59.544 41.667 0.00 0.00 41.15 2.57
3310 3645 4.455533 TGATACAACAGCTTGTCCAATGAC 59.544 41.667 0.00 0.00 41.15 3.06
3311 3646 2.936202 ACAACAGCTTGTCCAATGACT 58.064 42.857 0.00 0.00 42.28 3.41
3384 3719 6.527423 ACTTGATCAGGTCAAATGCAAAATT 58.473 32.000 4.34 0.00 45.74 1.82
3424 3759 0.319813 GTGGGCTTGACAAATGCACC 60.320 55.000 0.00 1.09 0.00 5.01
3425 3760 1.293179 GGGCTTGACAAATGCACCC 59.707 57.895 0.00 0.00 0.00 4.61
3426 3761 1.470996 GGGCTTGACAAATGCACCCA 61.471 55.000 0.00 0.00 35.84 4.51
3427 3762 0.037975 GGCTTGACAAATGCACCCAG 60.038 55.000 0.00 0.00 0.00 4.45
3428 3763 0.037975 GCTTGACAAATGCACCCAGG 60.038 55.000 0.00 0.00 0.00 4.45
3646 3982 1.726853 ACTGGAACATTAGCGTGCTC 58.273 50.000 0.00 0.00 38.20 4.26
3678 4014 5.336451 GGTGAACTTGTTCCTGAAAAAGTGT 60.336 40.000 14.55 6.74 45.44 3.55
3758 4095 3.192844 TGGTCCTTTTCTACTAGACTGCG 59.807 47.826 0.00 0.00 0.00 5.18
3790 4127 2.643272 GAGTGCCACGTCGTCTGA 59.357 61.111 0.00 0.00 0.00 3.27
3843 4180 1.396653 GATGGCTGGATGGACTTTGG 58.603 55.000 0.00 0.00 0.00 3.28
3869 4206 3.507009 GCCTCGTCGACGGCTACT 61.507 66.667 35.05 0.00 42.98 2.57
3878 4215 1.069258 GACGGCTACTACATGCCCC 59.931 63.158 0.00 0.00 45.90 5.80
3887 4224 0.820891 CTACATGCCCCTGCCATGTC 60.821 60.000 9.96 0.00 38.89 3.06
3889 4226 3.410628 ATGCCCCTGCCATGTCGA 61.411 61.111 0.00 0.00 36.33 4.20
3891 4228 2.592861 GCCCCTGCCATGTCGATC 60.593 66.667 0.00 0.00 0.00 3.69
3892 4229 2.910360 CCCCTGCCATGTCGATCA 59.090 61.111 0.00 0.00 0.00 2.92
3893 4230 1.524621 CCCCTGCCATGTCGATCAC 60.525 63.158 0.00 0.00 0.00 3.06
3894 4231 1.221566 CCCTGCCATGTCGATCACA 59.778 57.895 0.00 0.00 40.18 3.58
3895 4232 0.392863 CCCTGCCATGTCGATCACAA 60.393 55.000 0.00 0.00 38.97 3.33
3896 4233 1.671979 CCTGCCATGTCGATCACAAT 58.328 50.000 0.00 0.00 38.97 2.71
3948 4285 1.139734 CGAGGACACCATCTCCACG 59.860 63.158 0.00 0.00 35.90 4.94
3993 4330 0.682209 GCATGACCTTCTGCCCACAT 60.682 55.000 0.00 0.00 32.15 3.21
4053 4393 5.716703 TGACAAGTAGAGTCCTTCATCATCA 59.283 40.000 0.00 0.00 35.15 3.07
4070 4410 8.095937 TCATCATCATGCTGTAAATCTCATTC 57.904 34.615 0.00 0.00 0.00 2.67
4089 4429 6.001460 TCATTCAACTCAACGGGTATCTTTT 58.999 36.000 0.00 0.00 0.00 2.27
4150 4490 4.526438 ATGTAAAATGGGGAAGGAGAGG 57.474 45.455 0.00 0.00 0.00 3.69
4159 4499 1.691163 GGGAAGGAGAGGGGAAGAGAG 60.691 61.905 0.00 0.00 0.00 3.20
4216 5587 4.630644 TGAGTTGCTCTTTCTTGGATCT 57.369 40.909 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 119 9.190858 GTTCATTCACACATTTTAGCACATTTA 57.809 29.630 0.00 0.00 0.00 1.40
131 132 3.507162 TGTCCTGGTTCATTCACACAT 57.493 42.857 0.00 0.00 0.00 3.21
136 137 2.441375 TCCACTTGTCCTGGTTCATTCA 59.559 45.455 0.00 0.00 0.00 2.57
137 138 3.140325 TCCACTTGTCCTGGTTCATTC 57.860 47.619 0.00 0.00 0.00 2.67
280 291 2.130193 TCCTGAAGCCTTGCCTGATAT 58.870 47.619 0.00 0.00 0.00 1.63
330 341 1.214589 GCAGGCAAGGCAAGATGTG 59.785 57.895 0.00 0.00 0.00 3.21
331 342 0.613853 ATGCAGGCAAGGCAAGATGT 60.614 50.000 0.00 0.00 45.60 3.06
333 344 1.213678 TCTATGCAGGCAAGGCAAGAT 59.786 47.619 0.00 0.00 45.60 2.40
335 346 1.022735 CTCTATGCAGGCAAGGCAAG 58.977 55.000 0.00 3.20 45.60 4.01
336 347 0.620030 TCTCTATGCAGGCAAGGCAA 59.380 50.000 0.00 0.00 45.60 4.52
450 464 5.560567 GCAGCAAACAGAGAAGAAGAAGAAG 60.561 44.000 0.00 0.00 0.00 2.85
451 465 4.274459 GCAGCAAACAGAGAAGAAGAAGAA 59.726 41.667 0.00 0.00 0.00 2.52
452 466 3.812053 GCAGCAAACAGAGAAGAAGAAGA 59.188 43.478 0.00 0.00 0.00 2.87
453 467 3.814283 AGCAGCAAACAGAGAAGAAGAAG 59.186 43.478 0.00 0.00 0.00 2.85
485 499 0.179150 CCGACAGAGGAAAGAGAGCG 60.179 60.000 0.00 0.00 0.00 5.03
517 531 0.458025 GTCGAGACCAGGCGTTTAGG 60.458 60.000 0.00 0.00 0.00 2.69
565 579 9.921637 TCTGGTAAATATTGAAACATTCCAAAC 57.078 29.630 0.00 0.00 0.00 2.93
742 769 5.520748 AGAAATTACCAAGTCCATCCACT 57.479 39.130 0.00 0.00 0.00 4.00
743 770 6.415573 AGTAGAAATTACCAAGTCCATCCAC 58.584 40.000 0.00 0.00 0.00 4.02
747 774 9.263446 TGTACTAGTAGAAATTACCAAGTCCAT 57.737 33.333 1.87 0.00 0.00 3.41
773 800 9.178758 CTAGCAACTACCATTTCCTAAGAAAAT 57.821 33.333 0.00 0.00 44.91 1.82
778 805 9.444600 TTTTACTAGCAACTACCATTTCCTAAG 57.555 33.333 0.00 0.00 0.00 2.18
871 911 3.477530 ACAAAAATATAGCCCTCGCTCC 58.522 45.455 0.00 0.00 43.95 4.70
895 935 0.177604 CTAGTTCAGCCTGGCCTCAG 59.822 60.000 16.57 3.25 40.59 3.35
911 951 2.554344 CCTCCTCTACTGGGCTAGCTAG 60.554 59.091 16.84 16.84 0.00 3.42
951 991 0.250513 GAGGACTGGTAACTGCTGGG 59.749 60.000 0.00 0.00 39.52 4.45
965 1012 1.760480 GGGAGAGAGGGCAGAGGAC 60.760 68.421 0.00 0.00 0.00 3.85
1134 1181 3.358076 GAGCTTGGAGTAGCCGCGT 62.358 63.158 4.92 0.00 42.20 6.01
1200 1247 3.020237 GCCCCAGGAGACGAGGTTC 62.020 68.421 0.00 0.00 0.00 3.62
1502 1561 2.203182 AGGTGACCGGGTTCCTCA 59.797 61.111 15.86 0.00 0.00 3.86
1560 1619 0.896940 ACAGCTCCAATGCAACCCTG 60.897 55.000 0.00 0.00 34.99 4.45
1561 1620 0.178953 AACAGCTCCAATGCAACCCT 60.179 50.000 0.00 0.00 34.99 4.34
1569 1628 2.978156 TCTTCCCAAACAGCTCCAAT 57.022 45.000 0.00 0.00 0.00 3.16
1615 1674 4.389576 GCTCGCCAGCACAAACCG 62.390 66.667 0.00 0.00 46.06 4.44
1701 1760 3.069980 ATCTGACTCCGCCGCTGTC 62.070 63.158 1.67 1.67 0.00 3.51
1704 1763 4.521062 GCATCTGACTCCGCCGCT 62.521 66.667 0.00 0.00 0.00 5.52
1729 1788 1.878522 GATCGATCAGCGCGTTGGT 60.879 57.895 22.99 16.96 40.61 3.67
1730 1789 1.589993 AGATCGATCAGCGCGTTGG 60.590 57.895 26.47 7.23 40.61 3.77
1734 1793 0.040870 AGTACAGATCGATCAGCGCG 60.041 55.000 26.47 0.00 40.61 6.86
1740 1799 5.176407 AGCACTTACAGTACAGATCGATC 57.824 43.478 17.91 17.91 0.00 3.69
1783 1842 1.402968 CTCCATGGAATCAAACAGCCG 59.597 52.381 17.00 0.00 0.00 5.52
1821 1880 1.064296 AGCGATCATCGTCGTCCAC 59.936 57.895 9.23 0.00 42.81 4.02
1907 1966 2.976840 GCGAAAACATCCGGCTGCA 61.977 57.895 4.91 0.00 0.00 4.41
1958 2017 3.576356 CTTGCCATACCGCTGCCG 61.576 66.667 0.00 0.00 0.00 5.69
1966 2025 0.034089 ACCTGCCTTCCTTGCCATAC 60.034 55.000 0.00 0.00 0.00 2.39
2019 2078 6.423001 TCAGAGCATTCTTGACATATTCATCG 59.577 38.462 0.00 0.00 32.84 3.84
2025 2084 7.052248 TGTCAATCAGAGCATTCTTGACATAT 58.948 34.615 11.23 0.00 40.86 1.78
2074 2133 1.857837 GAATACTGCTCTCGCTTCTGC 59.142 52.381 0.00 0.00 36.97 4.26
2082 2141 2.863137 CAAGGCTTCGAATACTGCTCTC 59.137 50.000 0.00 0.00 0.00 3.20
2088 2147 1.555075 TCTGCCAAGGCTTCGAATACT 59.445 47.619 12.96 0.00 42.51 2.12
2094 2153 0.731417 CATCTTCTGCCAAGGCTTCG 59.269 55.000 12.96 0.00 42.51 3.79
2148 2207 2.463589 TAAGGTCACCCAGCCTTGCG 62.464 60.000 6.13 0.00 44.11 4.85
2253 2312 0.109689 CAAGGTCAGACCGAGACGAC 60.110 60.000 14.32 0.00 44.90 4.34
2256 2315 1.614413 AGTTCAAGGTCAGACCGAGAC 59.386 52.381 14.32 11.28 44.90 3.36
2265 2324 1.134128 TGCTTGCTCAGTTCAAGGTCA 60.134 47.619 5.10 0.00 40.79 4.02
2292 2351 4.115401 TCCTGATTTGACGATGAGACTG 57.885 45.455 0.00 0.00 0.00 3.51
2293 2352 4.221703 AGTTCCTGATTTGACGATGAGACT 59.778 41.667 0.00 0.00 0.00 3.24
2319 2378 2.706190 ACTCCCTGCATATAGGTCCAAC 59.294 50.000 0.00 0.00 36.02 3.77
2385 2444 3.635331 CATCAGGCTGAACACAACTTTG 58.365 45.455 22.84 7.93 0.00 2.77
2394 2453 0.953727 TGTTGTGCATCAGGCTGAAC 59.046 50.000 22.84 15.72 45.15 3.18
2454 2513 0.813210 CTTCCCCTCGCTCATTCTGC 60.813 60.000 0.00 0.00 0.00 4.26
2503 2562 1.188863 TTAGGTGTTAGCCCGGAGAC 58.811 55.000 0.73 0.00 0.00 3.36
2508 2567 2.981859 ACTCATTAGGTGTTAGCCCG 57.018 50.000 0.00 0.00 0.00 6.13
2652 2711 2.415893 GCCACACTTTGCATACATGTCC 60.416 50.000 0.00 0.00 0.00 4.02
2693 2752 2.878406 CCCGATGTTGACTCAAACAACT 59.122 45.455 0.00 0.00 45.08 3.16
2772 2831 3.773974 GCACGAAGAGCTTCCTCG 58.226 61.111 10.42 10.42 41.95 4.63
2789 2848 1.412074 CCCCTCCCATCATCCCAAAAG 60.412 57.143 0.00 0.00 0.00 2.27
2867 2926 3.181526 CCTTCATCCACAAGGCCTC 57.818 57.895 5.23 0.00 34.21 4.70
2878 2937 8.613482 GGAGTTAAAATACTGTAAGCCTTCATC 58.387 37.037 0.00 0.00 37.60 2.92
2931 2990 2.897350 GCATAGTGCTCGGTGCCC 60.897 66.667 0.00 0.00 40.96 5.36
3006 3065 1.064060 GGTTCAATCGGCATCCTTTCG 59.936 52.381 0.00 0.00 0.00 3.46
3156 3215 8.778358 CACAGTCCTTTAGAGGCATAAATATTC 58.222 37.037 0.00 0.00 43.21 1.75
3230 3289 3.326006 CCAGCTATATCCTGCTTCCTTCA 59.674 47.826 0.00 0.00 37.44 3.02
3308 3643 4.721132 AGTACCTAGCCAGATAGTCAGTC 58.279 47.826 0.00 0.00 0.00 3.51
3309 3644 4.799715 AGTACCTAGCCAGATAGTCAGT 57.200 45.455 0.00 0.00 0.00 3.41
3310 3645 5.871834 AGTAGTACCTAGCCAGATAGTCAG 58.128 45.833 0.00 0.00 0.00 3.51
3311 3646 5.908562 AGTAGTACCTAGCCAGATAGTCA 57.091 43.478 0.00 0.00 0.00 3.41
3384 3719 3.115892 GAACATGCGCGGTCGGAA 61.116 61.111 8.83 0.00 40.05 4.30
3424 3759 2.117156 GGCTATGTGCAGTGCCTGG 61.117 63.158 13.72 0.45 45.15 4.45
3425 3760 0.750546 ATGGCTATGTGCAGTGCCTG 60.751 55.000 13.72 0.00 45.11 4.85
3426 3761 0.750546 CATGGCTATGTGCAGTGCCT 60.751 55.000 13.72 0.00 45.11 4.75
3427 3762 1.731700 CATGGCTATGTGCAGTGCC 59.268 57.895 13.72 10.98 45.15 5.01
3428 3763 1.065273 GCATGGCTATGTGCAGTGC 59.935 57.895 8.58 8.58 45.15 4.40
3528 3863 7.502561 TCCCTTTTTCTCTTAGAAACAAGAAGG 59.497 37.037 16.66 16.66 43.25 3.46
3646 3982 4.392940 AGGAACAAGTTCACCTGAATCAG 58.607 43.478 14.25 2.68 41.20 2.90
3732 4068 6.102663 CAGTCTAGTAGAAAAGGACCATGTG 58.897 44.000 0.17 0.00 0.00 3.21
3741 4077 3.440228 GAGCCGCAGTCTAGTAGAAAAG 58.560 50.000 0.17 0.00 0.00 2.27
3758 4095 4.200283 CTCGACCTCGCTGGAGCC 62.200 72.222 1.32 0.00 39.06 4.70
3843 4180 2.951745 CGACGAGGCTGACATCGC 60.952 66.667 0.00 0.00 42.61 4.58
3878 4215 3.303593 GCTTATTGTGATCGACATGGCAG 60.304 47.826 0.00 0.00 33.40 4.85
3887 4224 0.041839 GGCAGCGCTTATTGTGATCG 60.042 55.000 7.50 0.00 0.00 3.69
3889 4226 1.103398 GGGGCAGCGCTTATTGTGAT 61.103 55.000 7.50 0.00 0.00 3.06
3891 4228 2.774799 GGGGGCAGCGCTTATTGTG 61.775 63.158 7.50 0.00 0.00 3.33
3892 4229 2.440247 GGGGGCAGCGCTTATTGT 60.440 61.111 7.50 0.00 0.00 2.71
3893 4230 2.124151 AGGGGGCAGCGCTTATTG 60.124 61.111 7.50 0.00 0.00 1.90
3894 4231 2.124151 CAGGGGGCAGCGCTTATT 60.124 61.111 7.50 0.00 0.00 1.40
3895 4232 3.411517 ACAGGGGGCAGCGCTTAT 61.412 61.111 7.50 0.00 0.00 1.73
3896 4233 4.408821 CACAGGGGGCAGCGCTTA 62.409 66.667 7.50 0.00 0.00 3.09
3948 4285 1.299089 GGTGTGGTTGCAAGCGAAC 60.299 57.895 22.55 20.90 0.00 3.95
3993 4330 5.701224 AGAAAGTACCTGTTTGGATTGGAA 58.299 37.500 0.00 0.00 39.71 3.53
4053 4393 7.533426 GTTGAGTTGAATGAGATTTACAGCAT 58.467 34.615 0.00 0.00 0.00 3.79
4070 4410 4.994852 TCAGAAAAGATACCCGTTGAGTTG 59.005 41.667 0.00 0.00 0.00 3.16
4216 5587 0.981183 AGACCAACATACAAGGCGGA 59.019 50.000 0.00 0.00 0.00 5.54


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

AutoCloner maintained by Alex Coulton.