Multiple sequence alignment - TraesCS3B01G288300

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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 TraesCS3B01G288300 chr3B 100.000 3154 0 0 1 3154 462889522 462892675 0.000000e+00 5825.0
1 TraesCS3B01G288300 chr3B 79.734 977 165 25 1018 1977 462866369 462867329 0.000000e+00 676.0
2 TraesCS3B01G288300 chr3B 80.896 670 118 6 1035 1699 464505183 464504519 1.300000e-143 520.0
3 TraesCS3B01G288300 chr3B 88.372 129 8 2 2437 2558 773662916 773662788 7.050000e-32 148.0
4 TraesCS3B01G288300 chr3A 94.469 2893 73 28 319 3154 477429854 477432716 0.000000e+00 4375.0
5 TraesCS3B01G288300 chr3A 80.000 990 166 23 1001 1972 477427517 477428492 0.000000e+00 702.0
6 TraesCS3B01G288300 chr3A 78.964 965 166 27 1035 1977 478169478 478168529 9.610000e-175 623.0
7 TraesCS3B01G288300 chr3A 98.387 62 1 0 230 291 477429800 477429861 3.330000e-20 110.0
8 TraesCS3B01G288300 chr3D 93.326 1828 77 23 545 2334 358187583 358189403 0.000000e+00 2658.0
9 TraesCS3B01G288300 chr3D 80.103 975 163 22 1019 1977 358176877 358177836 0.000000e+00 697.0
10 TraesCS3B01G288300 chr3D 91.915 470 19 3 68 537 358187036 358187486 9.540000e-180 640.0
11 TraesCS3B01G288300 chr3D 78.415 959 176 26 1035 1977 358504478 358503535 2.090000e-166 595.0
12 TraesCS3B01G288300 chr3D 88.413 397 42 3 2757 3152 313081727 313081334 2.850000e-130 475.0
13 TraesCS3B01G288300 chr3D 93.333 120 8 0 2317 2436 358189420 358189539 8.990000e-41 178.0
14 TraesCS3B01G288300 chr3D 90.099 101 9 1 2593 2692 358193863 358193963 2.550000e-26 130.0
15 TraesCS3B01G288300 chr3D 97.297 74 2 0 2678 2751 358193977 358194050 3.300000e-25 126.0
16 TraesCS3B01G288300 chr5B 90.148 406 30 8 2757 3154 18588778 18589181 1.300000e-143 520.0
17 TraesCS3B01G288300 chr5B 90.051 392 27 7 2767 3151 164393583 164393969 6.080000e-137 497.0
18 TraesCS3B01G288300 chr1B 76.636 963 193 27 1035 1976 617968615 617967664 1.310000e-138 503.0
19 TraesCS3B01G288300 chr1B 91.057 123 10 1 2437 2558 164667316 164667194 7.000000e-37 165.0
20 TraesCS3B01G288300 chr5D 89.109 404 35 8 2758 3154 142870398 142870799 7.860000e-136 494.0
21 TraesCS3B01G288300 chr5D 86.849 403 42 9 2758 3152 237603207 237602808 1.040000e-119 440.0
22 TraesCS3B01G288300 chr4D 89.027 401 38 5 2757 3152 40116797 40117196 2.830000e-135 492.0
23 TraesCS3B01G288300 chr4D 87.500 128 9 2 2437 2557 462840863 462840990 1.180000e-29 141.0
24 TraesCS3B01G288300 chr5A 88.834 403 36 6 2758 3152 180303303 180303704 1.320000e-133 486.0
25 TraesCS3B01G288300 chr1D 87.000 400 46 4 2758 3152 42981846 42982244 2.230000e-121 446.0
26 TraesCS3B01G288300 chr1D 97.000 100 2 1 952 1051 246507055 246507153 1.950000e-37 167.0
27 TraesCS3B01G288300 chr2D 88.636 132 8 2 2436 2560 286778364 286778233 1.510000e-33 154.0
28 TraesCS3B01G288300 chr2D 88.372 129 8 2 2436 2557 484873942 484873814 7.050000e-32 148.0
29 TraesCS3B01G288300 chr7B 86.765 136 9 6 2429 2557 574210760 574210893 3.280000e-30 143.0
30 TraesCS3B01G288300 chr7D 87.500 128 9 2 2437 2557 635616355 635616482 1.180000e-29 141.0
31 TraesCS3B01G288300 chr6D 87.500 128 9 2 2437 2557 464487032 464487159 1.180000e-29 141.0
32 TraesCS3B01G288300 chr7A 100.000 29 0 0 2553 2581 113529515 113529487 2.000000e-03 54.7


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 TraesCS3B01G288300 chr3B 462889522 462892675 3153 False 5825.000000 5825 100.000 1 3154 1 chr3B.!!$F2 3153
1 TraesCS3B01G288300 chr3B 462866369 462867329 960 False 676.000000 676 79.734 1018 1977 1 chr3B.!!$F1 959
2 TraesCS3B01G288300 chr3B 464504519 464505183 664 True 520.000000 520 80.896 1035 1699 1 chr3B.!!$R1 664
3 TraesCS3B01G288300 chr3A 477427517 477432716 5199 False 1729.000000 4375 90.952 230 3154 3 chr3A.!!$F1 2924
4 TraesCS3B01G288300 chr3A 478168529 478169478 949 True 623.000000 623 78.964 1035 1977 1 chr3A.!!$R1 942
5 TraesCS3B01G288300 chr3D 358187036 358189539 2503 False 1158.666667 2658 92.858 68 2436 3 chr3D.!!$F2 2368
6 TraesCS3B01G288300 chr3D 358176877 358177836 959 False 697.000000 697 80.103 1019 1977 1 chr3D.!!$F1 958
7 TraesCS3B01G288300 chr3D 358503535 358504478 943 True 595.000000 595 78.415 1035 1977 1 chr3D.!!$R2 942
8 TraesCS3B01G288300 chr1B 617967664 617968615 951 True 503.000000 503 76.636 1035 1976 1 chr1B.!!$R2 941

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
300 301 0.034337 TGGACGTGTCTTGCCCTTAC 59.966 55.0 0.0 0.0 0.0 2.34 F
304 305 0.244450 CGTGTCTTGCCCTTACGGTA 59.756 55.0 0.0 0.0 0.0 4.02 F
306 307 0.248289 TGTCTTGCCCTTACGGTAGC 59.752 55.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1227 1328 1.004394 TCGAGGAAGAGCTGGTACTCA 59.996 52.381 0.0 0.0 39.26 3.41 R
1386 1487 2.280592 ACGTTCCGTGCCTTCACC 60.281 61.111 0.0 0.0 39.18 4.02 R
2525 5735 5.365605 TCCGTTCCATAATACATGTCTTCCT 59.634 40.000 0.0 0.0 0.00 3.36 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
33 34 2.982470 GCTCAAACAGCTCAAAAATCGG 59.018 45.455 0.00 0.00 45.83 4.18
34 35 2.982470 CTCAAACAGCTCAAAAATCGGC 59.018 45.455 0.00 0.00 0.00 5.54
35 36 2.061028 CAAACAGCTCAAAAATCGGCC 58.939 47.619 0.00 0.00 0.00 6.13
36 37 1.327303 AACAGCTCAAAAATCGGCCA 58.673 45.000 2.24 0.00 0.00 5.36
37 38 0.598065 ACAGCTCAAAAATCGGCCAC 59.402 50.000 2.24 0.00 0.00 5.01
38 39 0.454957 CAGCTCAAAAATCGGCCACG 60.455 55.000 2.24 0.00 42.74 4.94
39 40 0.889186 AGCTCAAAAATCGGCCACGT 60.889 50.000 2.24 0.00 41.85 4.49
40 41 0.729140 GCTCAAAAATCGGCCACGTG 60.729 55.000 9.08 9.08 41.85 4.49
41 42 0.591170 CTCAAAAATCGGCCACGTGT 59.409 50.000 15.65 0.00 41.85 4.49
42 43 1.801771 CTCAAAAATCGGCCACGTGTA 59.198 47.619 15.65 0.00 41.85 2.90
43 44 1.532007 TCAAAAATCGGCCACGTGTAC 59.468 47.619 15.65 6.01 41.85 2.90
44 45 0.513820 AAAAATCGGCCACGTGTACG 59.486 50.000 19.21 19.21 46.33 3.67
45 46 1.903783 AAAATCGGCCACGTGTACGC 61.904 55.000 20.12 14.04 44.43 4.42
46 47 3.576932 AATCGGCCACGTGTACGCA 62.577 57.895 20.12 11.87 44.43 5.24
49 50 2.740826 GGCCACGTGTACGCACAT 60.741 61.111 15.65 0.00 45.50 3.21
50 51 2.474266 GCCACGTGTACGCACATG 59.526 61.111 15.65 6.44 45.50 3.21
51 52 2.474266 CCACGTGTACGCACATGC 59.526 61.111 15.65 0.00 44.22 4.06
52 53 2.027073 CCACGTGTACGCACATGCT 61.027 57.895 15.65 0.00 44.22 3.79
53 54 1.565156 CCACGTGTACGCACATGCTT 61.565 55.000 15.65 0.00 44.22 3.91
54 55 0.450972 CACGTGTACGCACATGCTTG 60.451 55.000 7.58 0.00 44.22 4.01
55 56 0.598942 ACGTGTACGCACATGCTTGA 60.599 50.000 7.93 0.00 44.22 3.02
56 57 0.093535 CGTGTACGCACATGCTTGAG 59.906 55.000 6.60 0.00 45.50 3.02
57 58 1.428448 GTGTACGCACATGCTTGAGA 58.572 50.000 6.60 0.00 44.64 3.27
58 59 1.126846 GTGTACGCACATGCTTGAGAC 59.873 52.381 6.60 0.00 44.64 3.36
59 60 1.000843 TGTACGCACATGCTTGAGACT 59.999 47.619 6.60 0.00 39.32 3.24
60 61 2.230266 TGTACGCACATGCTTGAGACTA 59.770 45.455 6.60 0.00 39.32 2.59
61 62 2.001812 ACGCACATGCTTGAGACTAG 57.998 50.000 6.60 0.00 39.32 2.57
62 63 1.273606 ACGCACATGCTTGAGACTAGT 59.726 47.619 6.60 0.00 39.32 2.57
63 64 2.492088 ACGCACATGCTTGAGACTAGTA 59.508 45.455 6.60 0.00 39.32 1.82
64 65 3.131223 ACGCACATGCTTGAGACTAGTAT 59.869 43.478 6.60 0.00 39.32 2.12
65 66 4.338400 ACGCACATGCTTGAGACTAGTATA 59.662 41.667 6.60 0.00 39.32 1.47
66 67 5.010112 ACGCACATGCTTGAGACTAGTATAT 59.990 40.000 6.60 0.00 39.32 0.86
67 68 5.570973 CGCACATGCTTGAGACTAGTATATC 59.429 44.000 6.60 0.00 39.32 1.63
68 69 5.866633 GCACATGCTTGAGACTAGTATATCC 59.133 44.000 6.60 0.00 38.21 2.59
69 70 6.393990 CACATGCTTGAGACTAGTATATCCC 58.606 44.000 6.60 0.00 0.00 3.85
124 125 6.106673 CAGGAACGATGGACAAGTAACTAAT 58.893 40.000 0.00 0.00 0.00 1.73
150 151 2.097038 CAGCTTCAGCCGAACTCCG 61.097 63.158 0.00 0.00 43.38 4.63
163 164 0.320771 AACTCCGTCACATGGCTGTC 60.321 55.000 0.00 0.00 31.62 3.51
177 178 1.363744 GCTGTCCTGTCCAAAGATCG 58.636 55.000 0.00 0.00 0.00 3.69
188 189 1.089920 CAAAGATCGGTCAGGGCTTG 58.910 55.000 0.00 0.00 0.00 4.01
256 257 0.714439 GAACGAAACGTGCCTCTAGC 59.286 55.000 0.00 0.00 39.99 3.42
295 296 1.009829 GATGATGGACGTGTCTTGCC 58.990 55.000 0.00 0.00 0.00 4.52
299 300 0.981183 ATGGACGTGTCTTGCCCTTA 59.019 50.000 0.00 0.00 0.00 2.69
300 301 0.034337 TGGACGTGTCTTGCCCTTAC 59.966 55.000 0.00 0.00 0.00 2.34
301 302 1.012486 GGACGTGTCTTGCCCTTACG 61.012 60.000 0.00 0.00 40.30 3.18
302 303 1.005394 ACGTGTCTTGCCCTTACGG 60.005 57.895 0.00 0.00 38.92 4.02
303 304 1.005394 CGTGTCTTGCCCTTACGGT 60.005 57.895 0.00 0.00 0.00 4.83
304 305 0.244450 CGTGTCTTGCCCTTACGGTA 59.756 55.000 0.00 0.00 0.00 4.02
305 306 1.734707 CGTGTCTTGCCCTTACGGTAG 60.735 57.143 0.00 0.00 0.00 3.18
306 307 0.248289 TGTCTTGCCCTTACGGTAGC 59.752 55.000 0.00 0.00 0.00 3.58
307 308 0.535797 GTCTTGCCCTTACGGTAGCT 59.464 55.000 0.00 0.00 0.00 3.32
308 309 0.822164 TCTTGCCCTTACGGTAGCTC 59.178 55.000 0.00 0.00 0.00 4.09
309 310 0.824759 CTTGCCCTTACGGTAGCTCT 59.175 55.000 0.00 0.00 0.00 4.09
310 311 1.207329 CTTGCCCTTACGGTAGCTCTT 59.793 52.381 0.00 0.00 0.00 2.85
355 356 1.996191 CTGCAAAGCCTAACGAGAGAC 59.004 52.381 0.00 0.00 0.00 3.36
384 385 1.136147 CGAGACTGGGACGTAACCG 59.864 63.158 4.50 2.66 40.83 4.44
409 410 1.266211 GCACATAACTAACACGACGCG 60.266 52.381 3.53 3.53 0.00 6.01
438 439 2.884894 CCTTATCGGTTAGGCTCGTT 57.115 50.000 0.00 0.00 0.00 3.85
484 485 3.424703 CAAAATGACAGTCCACCCAGAT 58.575 45.455 0.00 0.00 0.00 2.90
485 486 4.567537 CCAAAATGACAGTCCACCCAGATA 60.568 45.833 0.00 0.00 0.00 1.98
486 487 3.914426 AATGACAGTCCACCCAGATAC 57.086 47.619 0.00 0.00 0.00 2.24
512 513 1.873591 ACTGAAGCAAGTAAGCAACCG 59.126 47.619 0.00 0.00 36.85 4.44
513 514 2.143122 CTGAAGCAAGTAAGCAACCGA 58.857 47.619 0.00 0.00 36.85 4.69
514 515 1.871039 TGAAGCAAGTAAGCAACCGAC 59.129 47.619 0.00 0.00 36.85 4.79
537 538 9.784680 CGACGCTAGTATATATCCACTATTTTT 57.215 33.333 0.00 0.00 0.00 1.94
574 664 5.763204 AGTTATTATCCATTGGGTTACTGCG 59.237 40.000 2.09 0.00 34.93 5.18
576 666 1.750193 ATCCATTGGGTTACTGCGTG 58.250 50.000 2.09 0.00 34.93 5.34
631 721 1.014044 GCATCACGTGACGTCCACAT 61.014 55.000 22.71 0.00 45.98 3.21
679 769 0.319383 CTGAAGCCGATCCAGATCCG 60.319 60.000 2.11 0.00 34.40 4.18
712 802 0.941542 CAGCAGAAAAACGACGGGAA 59.058 50.000 0.00 0.00 0.00 3.97
714 804 2.031157 CAGCAGAAAAACGACGGGAAAT 60.031 45.455 0.00 0.00 0.00 2.17
716 806 2.315901 CAGAAAAACGACGGGAAATGC 58.684 47.619 0.00 0.00 0.00 3.56
718 808 1.001158 GAAAAACGACGGGAAATGCCA 60.001 47.619 0.00 0.00 38.95 4.92
781 872 3.064324 CCTTCCTTTGCAGCCGGG 61.064 66.667 2.18 0.00 0.00 5.73
856 947 1.635663 CCATTCTCGCACGTGTTCCC 61.636 60.000 18.38 0.00 0.00 3.97
915 1010 3.435671 GCCACTCCGCACATATAAATACC 59.564 47.826 0.00 0.00 0.00 2.73
924 1019 1.924524 CATATAAATACCCCTCGCGCG 59.075 52.381 26.76 26.76 0.00 6.86
941 1036 3.866582 GCCACCCCTCCATCCTCG 61.867 72.222 0.00 0.00 0.00 4.63
945 1040 1.121407 CACCCCTCCATCCTCGCATA 61.121 60.000 0.00 0.00 0.00 3.14
946 1041 1.122019 ACCCCTCCATCCTCGCATAC 61.122 60.000 0.00 0.00 0.00 2.39
947 1042 1.121407 CCCCTCCATCCTCGCATACA 61.121 60.000 0.00 0.00 0.00 2.29
949 1044 1.140852 CCCTCCATCCTCGCATACAAA 59.859 52.381 0.00 0.00 0.00 2.83
950 1045 2.224621 CCCTCCATCCTCGCATACAAAT 60.225 50.000 0.00 0.00 0.00 2.32
969 1064 7.516198 ACAAATTACAAAGTCAGCTCAGAAT 57.484 32.000 0.00 0.00 0.00 2.40
977 1072 4.564782 AGTCAGCTCAGAATCAATCCAA 57.435 40.909 0.00 0.00 0.00 3.53
1016 1111 2.186903 GATGGATGTCGCCGTGGT 59.813 61.111 0.00 0.00 0.00 4.16
1883 5027 2.175322 GACACCGACGACGAGGAC 59.825 66.667 18.00 0.00 42.66 3.85
2566 5776 1.202782 CGGAGGGAGTAGTAGCTAGCA 60.203 57.143 18.83 0.00 0.00 3.49
2606 5816 2.098770 CCCTTCGGTAAAGTAGTCGGAG 59.901 54.545 0.00 0.00 32.69 4.63
2652 5862 8.737168 TTGAGGACAGAATAGTGGAATATTTG 57.263 34.615 0.00 0.00 0.00 2.32
2720 5930 2.819595 GCGGTGCATCGTCATGGT 60.820 61.111 22.24 0.00 0.00 3.55
2785 5995 2.477176 TTGGACGCGCTTTGCTGTT 61.477 52.632 5.73 0.00 43.27 3.16
2810 6020 6.652900 TCCATCGATGTTGTTGTGATTCTTAA 59.347 34.615 23.27 0.00 0.00 1.85
2815 6025 9.743057 TCGATGTTGTTGTGATTCTTAAATTTT 57.257 25.926 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.288152 GGCCGATTTTTGAGCTGTTTGA 60.288 45.455 0.00 0.00 0.00 2.69
15 16 2.061028 GGCCGATTTTTGAGCTGTTTG 58.939 47.619 0.00 0.00 0.00 2.93
16 17 1.686052 TGGCCGATTTTTGAGCTGTTT 59.314 42.857 0.00 0.00 0.00 2.83
17 18 1.000274 GTGGCCGATTTTTGAGCTGTT 60.000 47.619 0.00 0.00 0.00 3.16
18 19 0.598065 GTGGCCGATTTTTGAGCTGT 59.402 50.000 0.00 0.00 0.00 4.40
19 20 0.454957 CGTGGCCGATTTTTGAGCTG 60.455 55.000 0.00 0.00 35.63 4.24
20 21 0.889186 ACGTGGCCGATTTTTGAGCT 60.889 50.000 0.00 0.00 37.88 4.09
21 22 0.729140 CACGTGGCCGATTTTTGAGC 60.729 55.000 7.95 0.00 37.88 4.26
22 23 0.591170 ACACGTGGCCGATTTTTGAG 59.409 50.000 21.57 0.00 37.88 3.02
23 24 1.532007 GTACACGTGGCCGATTTTTGA 59.468 47.619 21.57 0.00 37.88 2.69
24 25 1.723384 CGTACACGTGGCCGATTTTTG 60.723 52.381 21.57 0.00 37.88 2.44
25 26 0.513820 CGTACACGTGGCCGATTTTT 59.486 50.000 21.57 0.00 37.88 1.94
26 27 1.903783 GCGTACACGTGGCCGATTTT 61.904 55.000 26.48 4.95 42.22 1.82
27 28 2.385091 GCGTACACGTGGCCGATTT 61.385 57.895 26.48 5.65 42.22 2.17
28 29 2.812178 GCGTACACGTGGCCGATT 60.812 61.111 26.48 6.34 42.22 3.34
29 30 4.058732 TGCGTACACGTGGCCGAT 62.059 61.111 26.48 7.04 42.22 4.18
44 45 5.866633 GGATATACTAGTCTCAAGCATGTGC 59.133 44.000 0.00 0.00 42.49 4.57
45 46 6.393990 GGGATATACTAGTCTCAAGCATGTG 58.606 44.000 0.00 0.00 0.00 3.21
46 47 5.482175 GGGGATATACTAGTCTCAAGCATGT 59.518 44.000 0.00 0.00 0.00 3.21
47 48 5.719085 AGGGGATATACTAGTCTCAAGCATG 59.281 44.000 0.00 0.00 0.00 4.06
48 49 5.719085 CAGGGGATATACTAGTCTCAAGCAT 59.281 44.000 0.00 0.00 0.00 3.79
49 50 5.080337 CAGGGGATATACTAGTCTCAAGCA 58.920 45.833 0.00 0.00 0.00 3.91
50 51 4.081917 GCAGGGGATATACTAGTCTCAAGC 60.082 50.000 0.00 0.00 0.00 4.01
51 52 5.080337 TGCAGGGGATATACTAGTCTCAAG 58.920 45.833 0.00 0.00 0.00 3.02
52 53 5.074746 TGCAGGGGATATACTAGTCTCAA 57.925 43.478 0.00 0.00 0.00 3.02
53 54 4.741928 TGCAGGGGATATACTAGTCTCA 57.258 45.455 0.00 0.00 0.00 3.27
54 55 5.020132 ACATGCAGGGGATATACTAGTCTC 58.980 45.833 2.31 0.00 0.00 3.36
55 56 4.774726 CACATGCAGGGGATATACTAGTCT 59.225 45.833 2.31 0.00 0.00 3.24
56 57 4.621747 GCACATGCAGGGGATATACTAGTC 60.622 50.000 3.93 0.00 41.59 2.59
57 58 3.261897 GCACATGCAGGGGATATACTAGT 59.738 47.826 3.93 0.00 41.59 2.57
58 59 3.517100 AGCACATGCAGGGGATATACTAG 59.483 47.826 3.93 0.00 45.16 2.57
59 60 3.520696 AGCACATGCAGGGGATATACTA 58.479 45.455 3.93 0.00 45.16 1.82
60 61 2.342659 AGCACATGCAGGGGATATACT 58.657 47.619 3.93 0.00 45.16 2.12
61 62 2.816087 CAAGCACATGCAGGGGATATAC 59.184 50.000 3.93 0.00 45.16 1.47
62 63 2.815215 GCAAGCACATGCAGGGGATATA 60.815 50.000 3.93 0.00 45.70 0.86
63 64 1.991121 CAAGCACATGCAGGGGATAT 58.009 50.000 3.93 0.00 45.16 1.63
64 65 0.752743 GCAAGCACATGCAGGGGATA 60.753 55.000 3.93 0.00 45.70 2.59
65 66 2.056223 GCAAGCACATGCAGGGGAT 61.056 57.895 3.93 0.00 45.70 3.85
66 67 2.677524 GCAAGCACATGCAGGGGA 60.678 61.111 3.93 0.00 45.70 4.81
99 100 3.000727 GTTACTTGTCCATCGTTCCTGG 58.999 50.000 0.00 0.00 34.93 4.45
124 125 1.910722 GGCTGAAGCTGATGGAGGA 59.089 57.895 1.74 0.00 41.70 3.71
150 151 0.674895 GGACAGGACAGCCATGTGAC 60.675 60.000 0.00 0.00 40.68 3.67
163 164 2.015736 CTGACCGATCTTTGGACAGG 57.984 55.000 8.87 0.00 42.90 4.00
256 257 2.930385 ATCCAGTCCATCGCCGCTTG 62.930 60.000 0.00 0.00 0.00 4.01
259 260 2.721971 ATCATCCAGTCCATCGCCGC 62.722 60.000 0.00 0.00 0.00 6.53
299 300 2.750712 GTCTCAGAAGAAGAGCTACCGT 59.249 50.000 0.00 0.00 31.93 4.83
300 301 2.750166 TGTCTCAGAAGAAGAGCTACCG 59.250 50.000 0.00 0.00 31.93 4.02
301 302 4.644685 AGATGTCTCAGAAGAAGAGCTACC 59.355 45.833 0.00 0.00 31.93 3.18
302 303 5.221048 GGAGATGTCTCAGAAGAAGAGCTAC 60.221 48.000 11.78 0.00 44.60 3.58
303 304 4.887071 GGAGATGTCTCAGAAGAAGAGCTA 59.113 45.833 11.78 0.00 44.60 3.32
304 305 3.701040 GGAGATGTCTCAGAAGAAGAGCT 59.299 47.826 11.78 0.00 44.60 4.09
305 306 3.446873 TGGAGATGTCTCAGAAGAAGAGC 59.553 47.826 11.78 0.00 44.60 4.09
306 307 4.438608 CGTGGAGATGTCTCAGAAGAAGAG 60.439 50.000 11.78 0.00 44.60 2.85
307 308 3.441922 CGTGGAGATGTCTCAGAAGAAGA 59.558 47.826 11.78 0.00 44.60 2.87
308 309 3.192422 ACGTGGAGATGTCTCAGAAGAAG 59.808 47.826 11.78 0.00 44.60 2.85
309 310 3.157881 ACGTGGAGATGTCTCAGAAGAA 58.842 45.455 11.78 0.00 44.60 2.52
310 311 2.796557 ACGTGGAGATGTCTCAGAAGA 58.203 47.619 11.78 0.00 44.60 2.87
355 356 0.742281 CCAGTCTCGCCTTGGACATG 60.742 60.000 0.00 0.00 35.18 3.21
384 385 1.323534 CGTGTTAGTTATGTGCCTCGC 59.676 52.381 0.00 0.00 0.00 5.03
409 410 0.745468 ACCGATAAGGCTTCCTCGAC 59.255 55.000 25.06 4.99 46.52 4.20
412 413 3.388345 CCTAACCGATAAGGCTTCCTC 57.612 52.381 1.30 0.98 46.52 3.71
437 438 2.355363 CGTGACGTGCTCCGGAAA 60.355 61.111 5.23 0.00 42.24 3.13
438 439 3.598715 ACGTGACGTGCTCCGGAA 61.599 61.111 10.91 0.00 39.18 4.30
511 512 9.784680 AAAAATAGTGGATATATACTAGCGTCG 57.215 33.333 0.00 0.00 33.32 5.12
538 539 9.408648 CAATGGATAATAACTACTCCCACTTTT 57.591 33.333 0.00 0.00 0.00 2.27
539 540 7.998964 CCAATGGATAATAACTACTCCCACTTT 59.001 37.037 0.00 0.00 0.00 2.66
540 541 7.421382 CCCAATGGATAATAACTACTCCCACTT 60.421 40.741 0.00 0.00 0.00 3.16
541 542 6.044404 CCCAATGGATAATAACTACTCCCACT 59.956 42.308 0.00 0.00 0.00 4.00
542 543 6.183361 ACCCAATGGATAATAACTACTCCCAC 60.183 42.308 0.00 0.00 34.81 4.61
574 664 4.201400 CGACGTATACGATGATCATTGCAC 60.201 45.833 30.77 15.11 43.02 4.57
576 666 4.029198 GTCGACGTATACGATGATCATTGC 59.971 45.833 30.77 10.86 43.02 3.56
631 721 0.451383 CATCGGCGCCTGAATTGAAA 59.549 50.000 26.68 0.43 0.00 2.69
679 769 0.940991 CTGCTGCCTTTTCGTTTGGC 60.941 55.000 0.00 0.00 46.26 4.52
712 802 1.620819 TGGTATTTTTGGCGTGGCATT 59.379 42.857 0.00 0.00 0.00 3.56
714 804 1.067283 CATGGTATTTTTGGCGTGGCA 60.067 47.619 0.00 0.00 0.00 4.92
716 806 2.416701 GGTCATGGTATTTTTGGCGTGG 60.417 50.000 0.00 0.00 0.00 4.94
718 808 2.520069 TGGTCATGGTATTTTTGGCGT 58.480 42.857 0.00 0.00 0.00 5.68
781 872 4.769488 AGAAATGAAAAAGCCTTCTCCTCC 59.231 41.667 0.00 0.00 0.00 4.30
793 884 3.366273 CGGCTGCTGCTAGAAATGAAAAA 60.366 43.478 15.64 0.00 39.59 1.94
924 1019 3.866582 CGAGGATGGAGGGGTGGC 61.867 72.222 0.00 0.00 0.00 5.01
928 1023 1.121407 TGTATGCGAGGATGGAGGGG 61.121 60.000 0.00 0.00 0.00 4.79
941 1036 6.611381 TGAGCTGACTTTGTAATTTGTATGC 58.389 36.000 0.00 0.00 0.00 3.14
945 1040 6.942532 TTCTGAGCTGACTTTGTAATTTGT 57.057 33.333 0.00 0.00 0.00 2.83
946 1041 7.587629 TGATTCTGAGCTGACTTTGTAATTTG 58.412 34.615 0.00 0.00 0.00 2.32
947 1042 7.750229 TGATTCTGAGCTGACTTTGTAATTT 57.250 32.000 0.00 0.00 0.00 1.82
949 1044 7.066766 GGATTGATTCTGAGCTGACTTTGTAAT 59.933 37.037 0.00 0.00 0.00 1.89
950 1045 6.372659 GGATTGATTCTGAGCTGACTTTGTAA 59.627 38.462 0.00 0.00 0.00 2.41
969 1064 1.611519 GGTGTTTCCGGTTGGATTGA 58.388 50.000 0.00 0.00 45.91 2.57
984 1079 1.372499 CATCGTTGGTCGTCGGTGT 60.372 57.895 0.00 0.00 40.80 4.16
985 1080 2.092291 CCATCGTTGGTCGTCGGTG 61.092 63.158 4.23 0.00 38.30 4.94
986 1081 1.601419 ATCCATCGTTGGTCGTCGGT 61.601 55.000 12.19 0.00 44.06 4.69
1016 1111 0.391661 GATCCGCCTGAGTTGCTTCA 60.392 55.000 0.00 0.00 0.00 3.02
1158 1259 4.452733 AGCCCGGTTAGCACGCTC 62.453 66.667 0.00 0.00 0.00 5.03
1227 1328 1.004394 TCGAGGAAGAGCTGGTACTCA 59.996 52.381 0.00 0.00 39.26 3.41
1386 1487 2.280592 ACGTTCCGTGCCTTCACC 60.281 61.111 0.00 0.00 39.18 4.02
2525 5735 5.365605 TCCGTTCCATAATACATGTCTTCCT 59.634 40.000 0.00 0.00 0.00 3.36
2527 5737 5.696724 CCTCCGTTCCATAATACATGTCTTC 59.303 44.000 0.00 0.00 0.00 2.87
2566 5776 2.487986 GGGAGATGGATTTCGCTGGATT 60.488 50.000 0.00 0.00 0.00 3.01
2606 5816 1.578206 GCTGGCCGGAGAGAAACAAC 61.578 60.000 18.31 0.00 0.00 3.32
2652 5862 3.621715 AGAAACTGACACTTGGAAACGAC 59.378 43.478 0.00 0.00 0.00 4.34
2720 5930 1.586028 GCTCGGCTTCAAAATGGCA 59.414 52.632 0.00 0.00 0.00 4.92
2785 5995 4.578871 AGAATCACAACAACATCGATGGA 58.421 39.130 28.09 14.45 0.00 3.41
2921 6138 9.112725 CACTTCATGATGAATCTAATAACACCA 57.887 33.333 15.03 0.00 35.59 4.17


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

AutoCloner maintained by Alex Coulton.