Multiple sequence alignment - TraesCS3B01G044000

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 TraesCS3B01G044000 chr3B 100.000 5225 0 0 1 5225 22462465 22457241 0.000000e+00 9649.0
1 TraesCS3B01G044000 chr3B 91.578 1496 114 5 2925 4410 22321651 22320158 0.000000e+00 2054.0
2 TraesCS3B01G044000 chr3B 82.661 1090 160 15 3297 4358 22518370 22519458 0.000000e+00 939.0
3 TraesCS3B01G044000 chr3B 81.243 837 124 13 1001 1810 22516645 22517475 0.000000e+00 645.0
4 TraesCS3B01G044000 chr3B 86.042 523 48 9 1959 2478 22322202 22321702 5.950000e-149 538.0
5 TraesCS3B01G044000 chr3B 86.241 407 40 9 2524 2922 14460239 14460637 1.340000e-115 427.0
6 TraesCS3B01G044000 chr3B 88.172 279 29 2 2975 3253 22518092 22518366 3.900000e-86 329.0
7 TraesCS3B01G044000 chr3B 100.000 29 0 0 1823 1851 22517470 22517498 3.000000e-03 54.7
8 TraesCS3B01G044000 chr3A 95.024 2311 104 6 2925 5225 20938290 20940599 0.000000e+00 3620.0
9 TraesCS3B01G044000 chr3A 93.716 1639 64 12 854 2488 20936671 20938274 0.000000e+00 2420.0
10 TraesCS3B01G044000 chr3A 83.695 1245 174 19 3007 4230 20843262 20844498 0.000000e+00 1147.0
11 TraesCS3B01G044000 chr3A 89.376 753 70 9 1 745 20935356 20936106 0.000000e+00 939.0
12 TraesCS3B01G044000 chr3A 83.854 960 120 20 3297 4230 20915798 20916748 0.000000e+00 881.0
13 TraesCS3B01G044000 chr3A 81.004 837 123 21 1001 1803 20841799 20842633 2.650000e-177 632.0
14 TraesCS3B01G044000 chr3A 80.023 881 127 17 1001 1851 20914070 20914931 1.610000e-169 606.0
15 TraesCS3B01G044000 chr3A 89.919 248 24 1 3007 3253 20915547 20915794 8.440000e-83 318.0
16 TraesCS3B01G044000 chr3A 87.742 155 18 1 1968 2122 20842725 20842878 4.160000e-41 180.0
17 TraesCS3B01G044000 chr3D 95.220 1548 58 7 2401 3946 15342933 15341400 0.000000e+00 2435.0
18 TraesCS3B01G044000 chr3D 92.295 1194 53 15 737 1896 15345317 15344129 0.000000e+00 1659.0
19 TraesCS3B01G044000 chr3D 95.044 1029 47 4 4139 5164 15341404 15340377 0.000000e+00 1615.0
20 TraesCS3B01G044000 chr3D 85.301 1245 152 19 3007 4230 15388166 15386932 0.000000e+00 1256.0
21 TraesCS3B01G044000 chr3D 81.793 1093 164 22 3296 4358 15366315 15365228 0.000000e+00 883.0
22 TraesCS3B01G044000 chr3D 86.533 750 71 8 1 744 15347373 15346648 0.000000e+00 798.0
23 TraesCS3B01G044000 chr3D 81.272 865 120 16 1011 1851 15368033 15367187 0.000000e+00 662.0
24 TraesCS3B01G044000 chr3D 80.817 881 124 17 1001 1851 15389619 15388754 0.000000e+00 649.0
25 TraesCS3B01G044000 chr3D 95.902 244 9 1 2161 2403 15343336 15343093 1.360000e-105 394.0
26 TraesCS3B01G044000 chr3D 97.129 209 5 1 1921 2129 15344045 15343838 8.320000e-93 351.0
27 TraesCS3B01G044000 chr3D 88.889 279 28 2 2975 3253 15366594 15366319 1.800000e-89 340.0
28 TraesCS3B01G044000 chr3D 88.462 156 17 1 1970 2125 15367124 15366970 2.480000e-43 187.0
29 TraesCS3B01G044000 chr3D 93.103 58 4 0 1581 1638 15396666 15396609 9.320000e-13 86.1
30 TraesCS3B01G044000 chr5B 83.087 946 139 18 3346 4275 704311985 704312925 0.000000e+00 841.0
31 TraesCS3B01G044000 chr5B 83.026 813 124 7 1001 1803 704310158 704310966 0.000000e+00 725.0
32 TraesCS3B01G044000 chr4A 83.479 914 127 17 3346 4240 611265077 611264169 0.000000e+00 830.0
33 TraesCS3B01G044000 chr5D 82.371 970 146 17 3346 4296 558340407 558339444 0.000000e+00 821.0
34 TraesCS3B01G044000 chr5D 83.701 816 119 8 1001 1806 558342291 558341480 0.000000e+00 758.0
35 TraesCS3B01G044000 chr5D 85.784 408 46 10 2520 2919 324595269 324595672 6.260000e-114 422.0
36 TraesCS3B01G044000 chr5D 85.680 412 46 10 2520 2922 554517370 554516963 6.260000e-114 422.0
37 TraesCS3B01G044000 chr5D 89.412 255 23 3 2975 3228 558340718 558340467 8.440000e-83 318.0
38 TraesCS3B01G044000 chr5D 96.875 32 1 0 1784 1815 379839738 379839769 3.000000e-03 54.7
39 TraesCS3B01G044000 chr6B 87.379 412 37 12 2520 2922 135947872 135947467 4.770000e-125 459.0
40 TraesCS3B01G044000 chr6B 86.765 408 40 11 2524 2921 173576565 173576968 4.800000e-120 442.0
41 TraesCS3B01G044000 chr6B 87.000 400 40 10 2520 2912 420919887 420919493 1.730000e-119 440.0
42 TraesCS3B01G044000 chr7D 85.472 413 44 12 2529 2931 54198116 54198522 2.910000e-112 416.0
43 TraesCS3B01G044000 chr7A 85.000 420 48 10 2520 2928 655373117 655372702 3.770000e-111 412.0
44 TraesCS3B01G044000 chr2D 89.937 159 10 4 701 857 373610129 373610283 3.190000e-47 200.0


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 TraesCS3B01G044000 chr3B 22457241 22462465 5224 True 9649.000000 9649 100.000000 1 5225 1 chr3B.!!$R1 5224
1 TraesCS3B01G044000 chr3B 22320158 22322202 2044 True 1296.000000 2054 88.810000 1959 4410 2 chr3B.!!$R2 2451
2 TraesCS3B01G044000 chr3B 22516645 22519458 2813 False 491.925000 939 88.019000 1001 4358 4 chr3B.!!$F2 3357
3 TraesCS3B01G044000 chr3A 20935356 20940599 5243 False 2326.333333 3620 92.705333 1 5225 3 chr3A.!!$F3 5224
4 TraesCS3B01G044000 chr3A 20841799 20844498 2699 False 653.000000 1147 84.147000 1001 4230 3 chr3A.!!$F1 3229
5 TraesCS3B01G044000 chr3A 20914070 20916748 2678 False 601.666667 881 84.598667 1001 4230 3 chr3A.!!$F2 3229
6 TraesCS3B01G044000 chr3D 15340377 15347373 6996 True 1208.666667 2435 93.687167 1 5164 6 chr3D.!!$R2 5163
7 TraesCS3B01G044000 chr3D 15386932 15389619 2687 True 952.500000 1256 83.059000 1001 4230 2 chr3D.!!$R4 3229
8 TraesCS3B01G044000 chr3D 15365228 15368033 2805 True 518.000000 883 85.104000 1011 4358 4 chr3D.!!$R3 3347
9 TraesCS3B01G044000 chr5B 704310158 704312925 2767 False 783.000000 841 83.056500 1001 4275 2 chr5B.!!$F1 3274
10 TraesCS3B01G044000 chr4A 611264169 611265077 908 True 830.000000 830 83.479000 3346 4240 1 chr4A.!!$R1 894
11 TraesCS3B01G044000 chr5D 558339444 558342291 2847 True 632.333333 821 85.161333 1001 4296 3 chr5D.!!$R2 3295

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
364 371 0.111446 TGGATCTAGAGCTCGGGGAG 59.889 60.0 8.37 4.93 0.00 4.30 F
624 632 0.246635 GCCTCCACTGCGAAGACTTA 59.753 55.0 0.00 0.00 0.00 2.24 F
789 2143 0.251787 AGATTTTCAGGTGGGTGGGC 60.252 55.0 0.00 0.00 0.00 5.36 F
1406 3156 0.325671 AGTCCGGGATCCAGTGTCAT 60.326 55.0 15.23 0.00 0.00 3.06 F
2527 5164 0.035725 TCTTCTACTCAGGACGCGGA 60.036 55.0 12.47 0.00 0.00 5.54 F
2909 5548 0.326048 AGTAGATGAGCCTGGGCACT 60.326 55.0 14.39 4.44 44.88 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1389 3139 0.032117 AGATGACACTGGATCCCGGA 60.032 55.000 9.90 0.0 33.36 5.14 R
2508 5145 0.035725 TCCGCGTCCTGAGTAGAAGA 60.036 55.000 4.92 0.0 0.00 2.87 R
2527 5164 1.130054 TGAGCCAGGGAGCAGAAACT 61.130 55.000 0.00 0.0 34.23 2.66 R
2892 5531 0.325577 TCAGTGCCCAGGCTCATCTA 60.326 55.000 10.58 0.0 42.51 1.98 R
4160 6843 0.316204 CGACCGAGTTGTAGTGGGTT 59.684 55.000 0.00 0.0 29.22 4.11 R
4399 7088 1.409521 CCCATGCCCTAAAACCATCGA 60.410 52.381 0.00 0.0 0.00 3.59 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 4.418013 TGCATGACAACGTAGAAAATGG 57.582 40.909 0.00 0.00 0.00 3.16
54 55 1.969208 TGAATGGTTGCATGGCAGAAA 59.031 42.857 0.00 0.00 40.61 2.52
123 124 0.321996 GTGGGAGGAGTGGAGTGTTC 59.678 60.000 0.00 0.00 0.00 3.18
233 234 0.325272 GAAGAAGGGGAAGAAGCGGT 59.675 55.000 0.00 0.00 0.00 5.68
277 278 1.599518 GGAACATGGTCGTGTGGCA 60.600 57.895 4.29 0.00 31.49 4.92
283 284 2.672996 GGTCGTGTGGCAAGGCAT 60.673 61.111 0.00 0.00 0.00 4.40
302 307 3.274288 CATGCAGGGTTAGGAGTCTTTC 58.726 50.000 0.00 0.00 0.00 2.62
312 317 0.246910 GGAGTCTTTCCTCGGGTGAC 59.753 60.000 0.00 0.00 43.16 3.67
341 348 1.651240 ATGCATGCAAGGTGCTCGAC 61.651 55.000 26.68 0.00 45.31 4.20
364 371 0.111446 TGGATCTAGAGCTCGGGGAG 59.889 60.000 8.37 4.93 0.00 4.30
404 411 7.068103 TGTGGCCGATTTTCTCATATAATTTGT 59.932 33.333 0.00 0.00 0.00 2.83
452 459 8.470002 GCTTTGAAACATGAGGGACTAAATATT 58.530 33.333 0.00 0.00 41.55 1.28
455 462 6.321181 TGAAACATGAGGGACTAAATATTGCC 59.679 38.462 0.00 0.00 41.55 4.52
493 500 3.432252 GGACCAGATGTAGACGTTTGTTG 59.568 47.826 0.00 0.00 0.00 3.33
497 504 4.509970 CCAGATGTAGACGTTTGTTGAACA 59.490 41.667 0.00 0.00 38.18 3.18
499 506 6.367695 CCAGATGTAGACGTTTGTTGAACATA 59.632 38.462 0.00 0.00 38.18 2.29
510 517 6.143758 CGTTTGTTGAACATATGGGACAAAAG 59.856 38.462 20.00 18.66 39.34 2.27
541 549 6.539649 TTCTCAAAAATTAGAGTGACACCG 57.460 37.500 0.84 0.00 33.63 4.94
568 576 1.217882 CAACGGTCAACAGACTGGTC 58.782 55.000 7.51 0.00 41.87 4.02
572 580 2.022129 GTCAACAGACTGGTCGGCG 61.022 63.158 7.51 0.00 34.09 6.46
573 581 3.414700 CAACAGACTGGTCGGCGC 61.415 66.667 7.51 0.00 34.09 6.53
607 615 0.818040 AGTCAACAAACTGGTCGGCC 60.818 55.000 0.00 0.00 0.00 6.13
624 632 0.246635 GCCTCCACTGCGAAGACTTA 59.753 55.000 0.00 0.00 0.00 2.24
652 660 5.181811 TGCATTCTTACAAGTCAATCCACTG 59.818 40.000 0.00 0.00 0.00 3.66
723 732 2.134346 GCTAGACGTACGGAGTCCTAG 58.866 57.143 21.06 19.09 43.93 3.02
730 739 2.031930 CGTACGGAGTCCTAGAAGCTTC 59.968 54.545 19.11 19.11 43.93 3.86
756 2106 4.080299 CAGGCTCCTTCCTAACCAACTAAT 60.080 45.833 0.00 0.00 33.95 1.73
761 2111 6.636454 TCCTTCCTAACCAACTAATCATGT 57.364 37.500 0.00 0.00 0.00 3.21
764 2118 6.353082 CCTTCCTAACCAACTAATCATGTCCT 60.353 42.308 0.00 0.00 0.00 3.85
770 2124 5.529289 ACCAACTAATCATGTCCTCCTCTA 58.471 41.667 0.00 0.00 0.00 2.43
777 2131 8.646900 ACTAATCATGTCCTCCTCTAGATTTTC 58.353 37.037 0.00 0.00 0.00 2.29
780 2134 5.365025 TCATGTCCTCCTCTAGATTTTCAGG 59.635 44.000 0.00 0.00 0.00 3.86
789 2143 0.251787 AGATTTTCAGGTGGGTGGGC 60.252 55.000 0.00 0.00 0.00 5.36
809 2164 1.708551 CCCCAACCTCCTTTAGTCCAA 59.291 52.381 0.00 0.00 0.00 3.53
834 2189 8.970691 ATCATAATTTGACAGCTTAAACACAC 57.029 30.769 0.00 0.00 37.11 3.82
846 2201 4.500205 GCTTAAACACACCCTGTAAAACCC 60.500 45.833 0.00 0.00 30.51 4.11
851 2493 3.245122 ACACACCCTGTAAAACCCCATAG 60.245 47.826 0.00 0.00 0.00 2.23
857 2499 4.166144 CCCTGTAAAACCCCATAGATGTCT 59.834 45.833 0.00 0.00 0.00 3.41
858 2500 5.340027 CCCTGTAAAACCCCATAGATGTCTT 60.340 44.000 0.00 0.00 0.00 3.01
859 2501 5.590259 CCTGTAAAACCCCATAGATGTCTTG 59.410 44.000 0.00 0.00 0.00 3.02
861 2503 3.737559 AAACCCCATAGATGTCTTGCA 57.262 42.857 0.00 0.00 0.00 4.08
865 2534 3.461085 ACCCCATAGATGTCTTGCATTCT 59.539 43.478 0.00 0.00 38.06 2.40
898 2567 0.515717 GCGCGAAACACACGTACATC 60.516 55.000 12.10 0.00 0.00 3.06
908 2577 0.992072 CACGTACATCTCCAAGTGCG 59.008 55.000 0.00 0.00 46.76 5.34
974 2643 1.711060 AACCAACACAAGCACGGACG 61.711 55.000 0.00 0.00 0.00 4.79
992 2661 1.377202 GATCAGAAACCCTGCCGCA 60.377 57.895 0.00 0.00 42.62 5.69
994 2663 2.410322 ATCAGAAACCCTGCCGCACA 62.410 55.000 0.00 0.00 42.62 4.57
995 2664 2.192861 CAGAAACCCTGCCGCACAA 61.193 57.895 0.00 0.00 35.89 3.33
996 2665 1.454847 AGAAACCCTGCCGCACAAA 60.455 52.632 0.00 0.00 0.00 2.83
1034 2706 0.633921 CTCCTCCTCCTCCTCCTCAA 59.366 60.000 0.00 0.00 0.00 3.02
1305 3055 3.283684 CCGAAACACAAGGCCGCA 61.284 61.111 0.00 0.00 0.00 5.69
1389 3139 4.070552 GACGGCGGCTTCCTCAGT 62.071 66.667 13.24 0.00 0.00 3.41
1406 3156 0.325671 AGTCCGGGATCCAGTGTCAT 60.326 55.000 15.23 0.00 0.00 3.06
1719 3475 2.049156 CTCCGCTGCAACGTGAGA 60.049 61.111 17.63 4.87 34.38 3.27
1722 3478 1.133253 CCGCTGCAACGTGAGATTG 59.867 57.895 8.91 0.00 0.00 2.67
1872 3671 2.793790 TCACGCATGCAACAATTCAAAC 59.206 40.909 19.57 0.00 0.00 2.93
2117 4009 9.841295 GGTGGGTATATTAGTTACTGAAAATGA 57.159 33.333 0.00 0.00 0.00 2.57
2178 4580 8.905660 AAGACTCATAATTGAAGAGATCCATG 57.094 34.615 9.66 0.00 33.69 3.66
2508 5145 8.919145 TCCAAATTCCAAAGTAGTGTAAATGTT 58.081 29.630 0.00 0.00 0.00 2.71
2527 5164 0.035725 TCTTCTACTCAGGACGCGGA 60.036 55.000 12.47 0.00 0.00 5.54
2557 5194 2.284625 TGGCTCATCTCCACCCGT 60.285 61.111 0.00 0.00 0.00 5.28
2639 5276 3.918258 TGTAGATAATTTGACGCGTGC 57.082 42.857 20.70 9.34 0.00 5.34
2644 5281 0.668096 TAATTTGACGCGTGCGGTCT 60.668 50.000 20.70 0.00 44.69 3.85
2677 5314 4.005650 TCAACTCATTTGGACATCTGAGC 58.994 43.478 10.00 0.00 38.94 4.26
2751 5388 2.224523 TGCACTCTTCTGACCCGATTTT 60.225 45.455 0.00 0.00 0.00 1.82
2754 5391 2.907042 ACTCTTCTGACCCGATTTTCCT 59.093 45.455 0.00 0.00 0.00 3.36
2755 5392 3.328050 ACTCTTCTGACCCGATTTTCCTT 59.672 43.478 0.00 0.00 0.00 3.36
2796 5433 6.791887 CTCAGCTGTCTAAATGAGTTGAAA 57.208 37.500 14.67 0.00 35.52 2.69
2799 5436 8.169977 TCAGCTGTCTAAATGAGTTGAAATTT 57.830 30.769 14.67 0.00 0.00 1.82
2801 5438 7.327761 CAGCTGTCTAAATGAGTTGAAATTTGG 59.672 37.037 5.25 0.00 0.00 3.28
2802 5439 7.231317 AGCTGTCTAAATGAGTTGAAATTTGGA 59.769 33.333 0.00 0.00 32.77 3.53
2803 5440 7.540055 GCTGTCTAAATGAGTTGAAATTTGGAG 59.460 37.037 0.00 0.00 34.98 3.86
2804 5441 7.370383 TGTCTAAATGAGTTGAAATTTGGAGC 58.630 34.615 0.00 0.00 34.98 4.70
2805 5442 6.524586 GTCTAAATGAGTTGAAATTTGGAGCG 59.475 38.462 0.00 0.00 34.98 5.03
2829 5466 5.135508 ACCTCACGCATATTATCTACCAC 57.864 43.478 0.00 0.00 0.00 4.16
2909 5548 0.326048 AGTAGATGAGCCTGGGCACT 60.326 55.000 14.39 4.44 44.88 4.40
3229 5879 6.494893 TTGGATTTCTTCATCTTTGGTACG 57.505 37.500 0.00 0.00 0.00 3.67
3325 5977 6.566197 AGGTTCTCAGCTTTAGATTGTTTG 57.434 37.500 0.00 0.00 0.00 2.93
3665 6324 8.677148 ACTTAAATTGCAACTCGACCATATAT 57.323 30.769 0.00 0.00 0.00 0.86
4103 6774 1.069296 TGTCGCAATGCTAAGCAACAC 60.069 47.619 2.94 0.00 43.62 3.32
4113 6784 3.194861 GCTAAGCAACACGACCATGATA 58.805 45.455 0.00 0.00 0.00 2.15
4160 6843 1.724545 TTCACGGGGGAGAAAGAAGA 58.275 50.000 0.00 0.00 0.00 2.87
4175 6858 3.662247 AGAAGAACCCACTACAACTCG 57.338 47.619 0.00 0.00 0.00 4.18
4275 6959 6.707290 ACTTAGATGGTGTGTAGTGCATAAA 58.293 36.000 0.00 0.00 0.00 1.40
4435 7124 2.544844 TGGGACTACTTCGAGGGATT 57.455 50.000 0.00 0.00 0.00 3.01
4510 7199 4.949238 TGGTCTTGGACATGATACATTTGG 59.051 41.667 0.00 0.00 33.68 3.28
4654 7344 3.033764 TCACGCGAGTTTGACGGC 61.034 61.111 15.93 0.00 46.40 5.68
4656 7346 3.335534 ACGCGAGTTTGACGGCAC 61.336 61.111 15.93 0.00 46.40 5.01
4683 7373 3.598693 TGGGATGGCATGTATCAATGT 57.401 42.857 3.81 0.00 0.00 2.71
5174 7867 5.766590 TCTTGATGAGACATCCCTACTACA 58.233 41.667 8.87 0.00 0.00 2.74
5189 7882 5.509840 CCCTACTACATACAGTTGCATCCTC 60.510 48.000 0.00 0.00 0.00 3.71
5206 7899 2.753043 CAGCCCACATGACCAGGC 60.753 66.667 0.00 5.81 46.13 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 7.095523 GCCATGCAACCATTCATAATTGTATTC 60.096 37.037 0.00 0.00 0.00 1.75
70 71 1.373570 CGGGCACAAGAGAATTCCTC 58.626 55.000 0.65 0.00 42.28 3.71
123 124 0.745486 TTCTCCGCATGCCATGACAG 60.745 55.000 13.15 0.29 0.00 3.51
158 159 1.341187 ACAACCTCCTCTACTCCTCCG 60.341 57.143 0.00 0.00 0.00 4.63
233 234 2.997315 CAGGAGCCCGTGGTGAGA 60.997 66.667 0.00 0.00 0.00 3.27
277 278 0.257039 CTCCTAACCCTGCATGCCTT 59.743 55.000 16.68 3.81 0.00 4.35
283 284 1.628846 GGAAAGACTCCTAACCCTGCA 59.371 52.381 0.00 0.00 41.61 4.41
309 314 1.533965 GCATGCATCGAGTAGTCGTCA 60.534 52.381 18.99 14.99 46.85 4.35
314 319 1.208052 ACCTTGCATGCATCGAGTAGT 59.792 47.619 23.37 7.52 0.00 2.73
316 321 1.655484 CACCTTGCATGCATCGAGTA 58.345 50.000 23.37 3.98 0.00 2.59
341 348 1.519751 CCGAGCTCTAGATCCACCCG 61.520 65.000 12.85 0.00 0.00 5.28
392 399 9.549509 CTTTCGTCCGAAAAACAAATTATATGA 57.450 29.630 14.88 0.00 42.61 2.15
404 411 4.611130 GCCGAATAACTTTCGTCCGAAAAA 60.611 41.667 14.88 5.44 42.61 1.94
423 430 1.073125 TCCCTCATGTTTCAAAGCCGA 59.927 47.619 0.00 0.00 0.00 5.54
427 434 9.793252 CAATATTTAGTCCCTCATGTTTCAAAG 57.207 33.333 0.00 0.00 0.00 2.77
452 459 4.086457 GTCCCTTAAGATTTTTCTGGGCA 58.914 43.478 3.36 0.00 33.56 5.36
455 462 5.570320 TCTGGTCCCTTAAGATTTTTCTGG 58.430 41.667 3.36 0.00 0.00 3.86
493 500 8.947055 AAAATATGCTTTTGTCCCATATGTTC 57.053 30.769 1.24 0.00 33.68 3.18
497 504 8.980596 TGAGAAAAATATGCTTTTGTCCCATAT 58.019 29.630 7.10 0.00 37.63 1.78
499 506 7.243604 TGAGAAAAATATGCTTTTGTCCCAT 57.756 32.000 7.10 0.00 37.63 4.00
515 522 7.913297 CGGTGTCACTCTAATTTTTGAGAAAAA 59.087 33.333 2.35 0.00 43.76 1.94
538 546 2.188469 ACCGTTGCTTGACACGGT 59.812 55.556 10.52 10.52 45.31 4.83
541 549 0.730265 TGTTGACCGTTGCTTGACAC 59.270 50.000 0.00 0.00 0.00 3.67
552 560 1.372997 CCGACCAGTCTGTTGACCG 60.373 63.158 0.00 0.00 43.91 4.79
568 576 3.350612 TTTTCGAAGTGGGCGCCG 61.351 61.111 22.54 7.88 0.00 6.46
572 580 2.762745 TGACTAGTTTTCGAAGTGGGC 58.237 47.619 0.00 0.00 0.00 5.36
573 581 4.124238 TGTTGACTAGTTTTCGAAGTGGG 58.876 43.478 0.00 0.00 0.00 4.61
579 587 5.180271 ACCAGTTTGTTGACTAGTTTTCGA 58.820 37.500 0.00 0.00 0.00 3.71
580 588 5.479716 ACCAGTTTGTTGACTAGTTTTCG 57.520 39.130 0.00 0.00 0.00 3.46
607 615 3.305398 AAGTAAGTCTTCGCAGTGGAG 57.695 47.619 0.00 0.00 0.00 3.86
624 632 6.265196 TGGATTGACTTGTAAGAATGCAAAGT 59.735 34.615 0.00 0.00 30.44 2.66
673 681 3.327757 AGCAAGTTGATCCAGTGAACCTA 59.672 43.478 7.16 0.00 0.00 3.08
674 682 2.107204 AGCAAGTTGATCCAGTGAACCT 59.893 45.455 7.16 0.00 0.00 3.50
676 684 3.141398 TGAGCAAGTTGATCCAGTGAAC 58.859 45.455 17.99 0.00 30.48 3.18
677 685 3.490439 TGAGCAAGTTGATCCAGTGAA 57.510 42.857 17.99 0.00 30.48 3.18
681 690 4.387862 GCATTTTTGAGCAAGTTGATCCAG 59.612 41.667 17.99 3.52 30.48 3.86
684 693 6.525976 GTCTAGCATTTTTGAGCAAGTTGATC 59.474 38.462 14.20 14.20 32.56 2.92
723 732 2.419436 GGAAGGAGCCTGTAGAAGCTTC 60.419 54.545 19.11 19.11 40.11 3.86
730 739 2.467880 TGGTTAGGAAGGAGCCTGTAG 58.532 52.381 0.00 0.00 39.08 2.74
756 2106 5.365025 CCTGAAAATCTAGAGGAGGACATGA 59.635 44.000 0.00 0.00 0.00 3.07
761 2111 4.033709 CCACCTGAAAATCTAGAGGAGGA 58.966 47.826 0.00 0.00 38.30 3.71
764 2118 3.519510 CACCCACCTGAAAATCTAGAGGA 59.480 47.826 0.00 0.00 0.00 3.71
770 2124 0.251787 GCCCACCCACCTGAAAATCT 60.252 55.000 0.00 0.00 0.00 2.40
789 2143 1.368374 TGGACTAAAGGAGGTTGGGG 58.632 55.000 0.00 0.00 0.00 4.96
792 2146 8.525290 AATTATGATTGGACTAAAGGAGGTTG 57.475 34.615 0.00 0.00 0.00 3.77
809 2164 8.028938 GGTGTGTTTAAGCTGTCAAATTATGAT 58.971 33.333 0.00 0.00 40.97 2.45
834 2189 4.166144 AGACATCTATGGGGTTTTACAGGG 59.834 45.833 0.00 0.00 0.00 4.45
846 2201 6.988580 TGACTTAGAATGCAAGACATCTATGG 59.011 38.462 0.00 0.00 38.34 2.74
851 2493 6.094603 ACCATTGACTTAGAATGCAAGACATC 59.905 38.462 0.00 0.00 38.34 3.06
857 2499 3.763360 CCCACCATTGACTTAGAATGCAA 59.237 43.478 0.00 0.00 30.66 4.08
858 2500 3.355378 CCCACCATTGACTTAGAATGCA 58.645 45.455 0.00 0.00 30.66 3.96
859 2501 2.099756 GCCCACCATTGACTTAGAATGC 59.900 50.000 0.00 0.00 30.66 3.56
861 2503 2.643551 CGCCCACCATTGACTTAGAAT 58.356 47.619 0.00 0.00 0.00 2.40
865 2534 1.743623 CGCGCCCACCATTGACTTA 60.744 57.895 0.00 0.00 0.00 2.24
898 2567 3.414700 GCACGGACGCACTTGGAG 61.415 66.667 0.00 0.00 0.00 3.86
908 2577 1.011574 GTGTTTGACACGCACGGAC 60.012 57.895 0.00 0.00 39.53 4.79
974 2643 1.377202 TGCGGCAGGGTTTCTGATC 60.377 57.895 0.00 0.00 46.18 2.92
992 2661 0.103937 CACGCCCACCATTGTTTTGT 59.896 50.000 0.00 0.00 0.00 2.83
994 2663 1.068921 GCACGCCCACCATTGTTTT 59.931 52.632 0.00 0.00 0.00 2.43
995 2664 1.832167 AGCACGCCCACCATTGTTT 60.832 52.632 0.00 0.00 0.00 2.83
996 2665 2.203480 AGCACGCCCACCATTGTT 60.203 55.556 0.00 0.00 0.00 2.83
1389 3139 0.032117 AGATGACACTGGATCCCGGA 60.032 55.000 9.90 0.00 33.36 5.14
1581 3337 2.125512 CACTGCGCCAGGGAGTAC 60.126 66.667 4.18 0.00 46.67 2.73
1719 3475 4.415596 TGTGGAACATAAAAGGCTCCAAT 58.584 39.130 0.00 0.00 45.67 3.16
1872 3671 5.784750 TTTATCAAGAGTCTTGTCGCATG 57.215 39.130 27.83 6.12 0.00 4.06
2157 4049 8.672823 TCAACATGGATCTCTTCAATTATGAG 57.327 34.615 0.00 0.00 36.78 2.90
2178 4580 3.485947 TTATGAACCAGCGCAATCAAC 57.514 42.857 11.47 0.00 0.00 3.18
2487 5124 9.574516 AGAAGAACATTTACACTACTTTGGAAT 57.425 29.630 0.00 0.00 0.00 3.01
2488 5125 8.974060 AGAAGAACATTTACACTACTTTGGAA 57.026 30.769 0.00 0.00 0.00 3.53
2489 5126 9.485206 GTAGAAGAACATTTACACTACTTTGGA 57.515 33.333 0.00 0.00 0.00 3.53
2490 5127 9.490379 AGTAGAAGAACATTTACACTACTTTGG 57.510 33.333 0.00 0.00 36.67 3.28
2493 5130 9.915629 CTGAGTAGAAGAACATTTACACTACTT 57.084 33.333 0.00 0.00 38.98 2.24
2508 5145 0.035725 TCCGCGTCCTGAGTAGAAGA 60.036 55.000 4.92 0.00 0.00 2.87
2514 5151 1.179814 AGAAACTCCGCGTCCTGAGT 61.180 55.000 4.92 7.72 43.47 3.41
2518 5155 2.048127 GCAGAAACTCCGCGTCCT 60.048 61.111 4.92 0.00 0.00 3.85
2527 5164 1.130054 TGAGCCAGGGAGCAGAAACT 61.130 55.000 0.00 0.00 34.23 2.66
2639 5276 2.554032 AGTTGAAATTTGGAGCAGACCG 59.446 45.455 0.00 0.00 0.00 4.79
2649 5286 7.868922 TCAGATGTCCAAATGAGTTGAAATTTG 59.131 33.333 0.00 0.00 41.41 2.32
2669 5306 1.592131 GCCGAGAGCTGCTCAGATG 60.592 63.158 29.49 16.14 44.15 2.90
2778 5415 7.540055 GCTCCAAATTTCAACTCATTTAGACAG 59.460 37.037 0.00 0.00 0.00 3.51
2783 5420 5.475220 TCCGCTCCAAATTTCAACTCATTTA 59.525 36.000 0.00 0.00 0.00 1.40
2790 5427 1.886542 AGGTCCGCTCCAAATTTCAAC 59.113 47.619 0.00 0.00 0.00 3.18
2796 5433 1.079127 CGTGAGGTCCGCTCCAAAT 60.079 57.895 0.00 0.00 0.00 2.32
2804 5441 3.577649 AGATAATATGCGTGAGGTCCG 57.422 47.619 0.00 0.00 0.00 4.79
2805 5442 4.219944 TGGTAGATAATATGCGTGAGGTCC 59.780 45.833 0.00 0.00 0.00 4.46
2878 5517 2.690497 CTCATCTACTCCCGCTCAGAAA 59.310 50.000 0.00 0.00 0.00 2.52
2888 5527 1.050988 TGCCCAGGCTCATCTACTCC 61.051 60.000 10.58 0.00 42.51 3.85
2892 5531 0.325577 TCAGTGCCCAGGCTCATCTA 60.326 55.000 10.58 0.00 42.51 1.98
2909 5548 6.017109 GCTGAGTAAAACAGAAATCCAACTCA 60.017 38.462 0.00 0.00 39.65 3.41
3037 5683 6.035866 GTGAATCAAGTCTCTTCACTGCTATG 59.964 42.308 12.35 0.00 43.35 2.23
3682 6341 7.264221 CCATGTAGCCACTAAAATTATGCAAA 58.736 34.615 0.00 0.00 0.00 3.68
4103 6774 5.906113 AGGCTTATCTACTATCATGGTCG 57.094 43.478 0.00 0.00 0.00 4.79
4113 6784 2.628657 CGGGTGCTTAGGCTTATCTACT 59.371 50.000 0.00 0.00 39.59 2.57
4160 6843 0.316204 CGACCGAGTTGTAGTGGGTT 59.684 55.000 0.00 0.00 29.22 4.11
4175 6858 5.061808 GTCACATCATTAACACTACACGACC 59.938 44.000 0.00 0.00 0.00 4.79
4275 6959 9.836864 TCATGCACTTCATATAGTACTTCAATT 57.163 29.630 0.00 0.00 33.19 2.32
4399 7088 1.409521 CCCATGCCCTAAAACCATCGA 60.410 52.381 0.00 0.00 0.00 3.59
4551 7241 9.060347 TGCCATGAAAATTGCAAATTTTAGTTA 57.940 25.926 13.49 0.46 32.03 2.24
4654 7344 4.675976 ACATGCCATCCCAAATATTGTG 57.324 40.909 0.00 0.00 0.00 3.33
4656 7346 6.593268 TGATACATGCCATCCCAAATATTG 57.407 37.500 0.00 0.00 0.00 1.90
4770 7461 5.643379 ATATAAACAAACCACACTGCTGG 57.357 39.130 0.00 0.00 37.33 4.85
4931 7624 8.696043 TTCAGAAAAATTTCTCCTCAATCTGA 57.304 30.769 5.45 3.08 45.23 3.27
5061 7754 4.543590 AGAGAAGTACACAAGGACATGG 57.456 45.455 0.00 0.00 0.00 3.66
5089 7782 6.883217 ACTGGATATGCATATCAAGACCAATC 59.117 38.462 40.00 23.89 41.39 2.67
5091 7784 6.191657 ACTGGATATGCATATCAAGACCAA 57.808 37.500 40.00 20.14 41.39 3.67
5129 7822 2.415168 ACTATGTTTCGATGTGGCAACG 59.585 45.455 0.00 0.00 42.51 4.10
5174 7867 1.133976 GGGCTGAGGATGCAACTGTAT 60.134 52.381 0.00 0.00 0.00 2.29
5189 7882 2.753043 GCCTGGTCATGTGGGCTG 60.753 66.667 11.50 0.00 41.20 4.85


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

AutoCloner maintained by Alex Coulton.