Multiple sequence alignment - TraesCS1B01G186600

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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 TraesCS1B01G186600 chr1B 100.000 3239 0 0 1 3239 333600534 333603772 0.000000e+00 5982
1 TraesCS1B01G186600 chr1B 89.937 159 15 1 1149 1306 333625816 333625974 1.520000e-48 204
2 TraesCS1B01G186600 chr1D 93.670 2338 83 30 155 2449 240600301 240597986 0.000000e+00 3437
3 TraesCS1B01G186600 chr1D 90.062 161 15 1 1146 1306 240595812 240595653 1.180000e-49 207
4 TraesCS1B01G186600 chr1A 93.303 1314 45 14 1138 2433 305328865 305327577 0.000000e+00 1899
5 TraesCS1B01G186600 chr1A 84.394 487 39 19 671 1136 305329373 305328903 8.250000e-121 444
6 TraesCS1B01G186600 chr1A 87.129 303 16 6 361 644 305329668 305329370 4.030000e-84 322
7 TraesCS1B01G186600 chr1A 90.062 161 15 1 1146 1306 305006155 305005996 1.180000e-49 207
8 TraesCS1B01G186600 chr6A 99.226 775 6 0 2465 3239 44982910 44982136 0.000000e+00 1399
9 TraesCS1B01G186600 chr6A 98.198 777 12 1 2463 3239 604312944 604313718 0.000000e+00 1356
10 TraesCS1B01G186600 chrUn 98.839 775 9 0 2465 3239 264011142 264011916 0.000000e+00 1382
11 TraesCS1B01G186600 chrUn 98.839 775 9 0 2465 3239 294197616 294198390 0.000000e+00 1382
12 TraesCS1B01G186600 chr7A 98.716 779 8 2 2463 3239 22018753 22019531 0.000000e+00 1382
13 TraesCS1B01G186600 chr2A 98.327 777 13 0 2463 3239 736252474 736253250 0.000000e+00 1363
14 TraesCS1B01G186600 chr2A 98.067 776 15 0 2464 3239 532084808 532084033 0.000000e+00 1351
15 TraesCS1B01G186600 chr2A 80.368 489 69 20 1167 1637 746775471 746775950 2.390000e-91 346
16 TraesCS1B01G186600 chr2B 98.323 775 13 0 2465 3239 473768680 473767906 0.000000e+00 1360
17 TraesCS1B01G186600 chr2B 85.714 378 51 1 1478 1852 751571750 751572127 2.340000e-106 396
18 TraesCS1B01G186600 chr2B 91.228 228 20 0 1154 1381 751571424 751571651 8.730000e-81 311
19 TraesCS1B01G186600 chr7B 98.069 777 15 0 2463 3239 57199086 57199862 0.000000e+00 1352
20 TraesCS1B01G186600 chr2D 93.043 230 16 0 1152 1381 616599096 616599325 1.440000e-88 337


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 TraesCS1B01G186600 chr1B 333600534 333603772 3238 False 5982.000000 5982 100.000000 1 3239 1 chr1B.!!$F1 3238
1 TraesCS1B01G186600 chr1D 240595653 240600301 4648 True 1822.000000 3437 91.866000 155 2449 2 chr1D.!!$R1 2294
2 TraesCS1B01G186600 chr1A 305327577 305329668 2091 True 888.333333 1899 88.275333 361 2433 3 chr1A.!!$R2 2072
3 TraesCS1B01G186600 chr6A 44982136 44982910 774 True 1399.000000 1399 99.226000 2465 3239 1 chr6A.!!$R1 774
4 TraesCS1B01G186600 chr6A 604312944 604313718 774 False 1356.000000 1356 98.198000 2463 3239 1 chr6A.!!$F1 776
5 TraesCS1B01G186600 chrUn 264011142 264011916 774 False 1382.000000 1382 98.839000 2465 3239 1 chrUn.!!$F1 774
6 TraesCS1B01G186600 chrUn 294197616 294198390 774 False 1382.000000 1382 98.839000 2465 3239 1 chrUn.!!$F2 774
7 TraesCS1B01G186600 chr7A 22018753 22019531 778 False 1382.000000 1382 98.716000 2463 3239 1 chr7A.!!$F1 776
8 TraesCS1B01G186600 chr2A 736252474 736253250 776 False 1363.000000 1363 98.327000 2463 3239 1 chr2A.!!$F1 776
9 TraesCS1B01G186600 chr2A 532084033 532084808 775 True 1351.000000 1351 98.067000 2464 3239 1 chr2A.!!$R1 775
10 TraesCS1B01G186600 chr2B 473767906 473768680 774 True 1360.000000 1360 98.323000 2465 3239 1 chr2B.!!$R1 774
11 TraesCS1B01G186600 chr2B 751571424 751572127 703 False 353.500000 396 88.471000 1154 1852 2 chr2B.!!$F1 698
12 TraesCS1B01G186600 chr7B 57199086 57199862 776 False 1352.000000 1352 98.069000 2463 3239 1 chr7B.!!$F1 776

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
87 88 0.168128 CCGTTGATGGCGAACTTTCC 59.832 55.0 0.0 0.0 0.0 3.13 F
642 666 0.606401 ATGCTGTTCCGGGTGAGTTG 60.606 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1888 2027 1.070134 TGAGGACACAAAGAACCTCCG 59.930 52.381 0.0 0.0 45.61 4.63 R
2296 2452 0.108945 GGTTCAAGCAGAGCAATGGC 60.109 55.000 0.0 0.0 41.61 4.40 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
28 29 4.033776 GGGGCTGCTGCTGGTGTA 62.034 66.667 15.64 0.00 39.59 2.90
29 30 2.034066 GGGCTGCTGCTGGTGTAA 59.966 61.111 15.64 0.00 39.59 2.41
30 31 2.335712 GGGCTGCTGCTGGTGTAAC 61.336 63.158 15.64 0.00 39.59 2.50
31 32 1.600636 GGCTGCTGCTGGTGTAACA 60.601 57.895 15.64 0.00 37.82 2.41
32 33 1.172180 GGCTGCTGCTGGTGTAACAA 61.172 55.000 15.64 0.00 37.82 2.83
33 34 0.239347 GCTGCTGCTGGTGTAACAAG 59.761 55.000 8.53 0.00 42.31 3.16
42 43 4.410492 CTGGTGTAACAAGCATCACTTC 57.590 45.455 0.00 0.00 39.98 3.01
43 44 3.814625 TGGTGTAACAAGCATCACTTCA 58.185 40.909 0.00 0.00 39.98 3.02
44 45 3.563808 TGGTGTAACAAGCATCACTTCAC 59.436 43.478 0.00 0.00 39.98 3.18
45 46 3.815401 GGTGTAACAAGCATCACTTCACT 59.185 43.478 0.00 0.00 39.98 3.41
46 47 4.319766 GGTGTAACAAGCATCACTTCACTG 60.320 45.833 0.00 0.00 39.98 3.66
47 48 3.814842 TGTAACAAGCATCACTTCACTGG 59.185 43.478 0.00 0.00 36.04 4.00
48 49 2.936919 ACAAGCATCACTTCACTGGA 57.063 45.000 0.00 0.00 36.04 3.86
49 50 3.430042 ACAAGCATCACTTCACTGGAT 57.570 42.857 0.00 0.00 36.04 3.41
50 51 3.079578 ACAAGCATCACTTCACTGGATG 58.920 45.455 0.00 0.00 40.99 3.51
51 52 3.079578 CAAGCATCACTTCACTGGATGT 58.920 45.455 0.00 0.00 40.35 3.06
52 53 2.708051 AGCATCACTTCACTGGATGTG 58.292 47.619 0.00 4.82 45.62 3.21
64 65 4.162040 ACTGGATGTGAGATGGGAAATC 57.838 45.455 0.00 0.00 0.00 2.17
65 66 3.524789 ACTGGATGTGAGATGGGAAATCA 59.475 43.478 0.00 0.00 0.00 2.57
66 67 4.135306 CTGGATGTGAGATGGGAAATCAG 58.865 47.826 0.00 0.00 0.00 2.90
67 68 3.117776 TGGATGTGAGATGGGAAATCAGG 60.118 47.826 0.00 0.00 0.00 3.86
68 69 2.425143 TGTGAGATGGGAAATCAGGC 57.575 50.000 0.00 0.00 0.00 4.85
69 70 1.064463 TGTGAGATGGGAAATCAGGCC 60.064 52.381 0.00 0.00 0.00 5.19
70 71 0.181114 TGAGATGGGAAATCAGGCCG 59.819 55.000 0.00 0.00 0.00 6.13
71 72 0.181350 GAGATGGGAAATCAGGCCGT 59.819 55.000 0.00 0.00 0.00 5.68
72 73 0.625849 AGATGGGAAATCAGGCCGTT 59.374 50.000 0.00 0.00 0.00 4.44
73 74 0.740737 GATGGGAAATCAGGCCGTTG 59.259 55.000 0.00 0.00 0.00 4.10
74 75 0.331278 ATGGGAAATCAGGCCGTTGA 59.669 50.000 0.00 0.00 0.00 3.18
75 76 0.331278 TGGGAAATCAGGCCGTTGAT 59.669 50.000 1.64 1.64 39.42 2.57
76 77 0.740737 GGGAAATCAGGCCGTTGATG 59.259 55.000 8.18 0.00 37.83 3.07
77 78 0.740737 GGAAATCAGGCCGTTGATGG 59.259 55.000 8.18 0.00 37.83 3.51
84 85 3.263941 GCCGTTGATGGCGAACTT 58.736 55.556 0.00 0.00 46.75 2.66
85 86 1.579429 GCCGTTGATGGCGAACTTT 59.421 52.632 0.00 0.00 46.75 2.66
86 87 0.454452 GCCGTTGATGGCGAACTTTC 60.454 55.000 0.00 0.00 46.75 2.62
87 88 0.168128 CCGTTGATGGCGAACTTTCC 59.832 55.000 0.00 0.00 0.00 3.13
88 89 0.168128 CGTTGATGGCGAACTTTCCC 59.832 55.000 0.00 0.00 0.00 3.97
89 90 1.534729 GTTGATGGCGAACTTTCCCT 58.465 50.000 0.00 0.00 0.00 4.20
90 91 1.468914 GTTGATGGCGAACTTTCCCTC 59.531 52.381 0.00 0.00 0.00 4.30
91 92 0.984230 TGATGGCGAACTTTCCCTCT 59.016 50.000 0.00 0.00 0.00 3.69
92 93 2.184533 TGATGGCGAACTTTCCCTCTA 58.815 47.619 0.00 0.00 0.00 2.43
93 94 2.093658 TGATGGCGAACTTTCCCTCTAC 60.094 50.000 0.00 0.00 0.00 2.59
94 95 1.640917 TGGCGAACTTTCCCTCTACT 58.359 50.000 0.00 0.00 0.00 2.57
95 96 2.811410 TGGCGAACTTTCCCTCTACTA 58.189 47.619 0.00 0.00 0.00 1.82
96 97 3.371965 TGGCGAACTTTCCCTCTACTAT 58.628 45.455 0.00 0.00 0.00 2.12
97 98 3.773119 TGGCGAACTTTCCCTCTACTATT 59.227 43.478 0.00 0.00 0.00 1.73
98 99 4.120589 GGCGAACTTTCCCTCTACTATTG 58.879 47.826 0.00 0.00 0.00 1.90
99 100 3.556365 GCGAACTTTCCCTCTACTATTGC 59.444 47.826 0.00 0.00 0.00 3.56
100 101 4.120589 CGAACTTTCCCTCTACTATTGCC 58.879 47.826 0.00 0.00 0.00 4.52
101 102 4.452825 GAACTTTCCCTCTACTATTGCCC 58.547 47.826 0.00 0.00 0.00 5.36
102 103 3.460825 ACTTTCCCTCTACTATTGCCCA 58.539 45.455 0.00 0.00 0.00 5.36
103 104 3.200165 ACTTTCCCTCTACTATTGCCCAC 59.800 47.826 0.00 0.00 0.00 4.61
104 105 2.561209 TCCCTCTACTATTGCCCACA 57.439 50.000 0.00 0.00 0.00 4.17
105 106 3.060479 TCCCTCTACTATTGCCCACAT 57.940 47.619 0.00 0.00 0.00 3.21
106 107 2.705658 TCCCTCTACTATTGCCCACATG 59.294 50.000 0.00 0.00 0.00 3.21
107 108 2.705658 CCCTCTACTATTGCCCACATGA 59.294 50.000 0.00 0.00 0.00 3.07
108 109 3.136443 CCCTCTACTATTGCCCACATGAA 59.864 47.826 0.00 0.00 0.00 2.57
109 110 4.130118 CCTCTACTATTGCCCACATGAAC 58.870 47.826 0.00 0.00 0.00 3.18
110 111 4.141620 CCTCTACTATTGCCCACATGAACT 60.142 45.833 0.00 0.00 0.00 3.01
111 112 5.023533 TCTACTATTGCCCACATGAACTC 57.976 43.478 0.00 0.00 0.00 3.01
112 113 4.716784 TCTACTATTGCCCACATGAACTCT 59.283 41.667 0.00 0.00 0.00 3.24
113 114 4.307032 ACTATTGCCCACATGAACTCTT 57.693 40.909 0.00 0.00 0.00 2.85
114 115 4.265073 ACTATTGCCCACATGAACTCTTC 58.735 43.478 0.00 0.00 0.00 2.87
115 116 1.909700 TTGCCCACATGAACTCTTCC 58.090 50.000 0.00 0.00 0.00 3.46
116 117 0.770499 TGCCCACATGAACTCTTCCA 59.230 50.000 0.00 0.00 0.00 3.53
117 118 1.355381 TGCCCACATGAACTCTTCCAT 59.645 47.619 0.00 0.00 0.00 3.41
118 119 1.747355 GCCCACATGAACTCTTCCATG 59.253 52.381 0.00 0.00 44.12 3.66
128 129 8.455903 CATGAACTCTTCCATGTACCAATATT 57.544 34.615 0.00 0.00 36.36 1.28
129 130 8.906867 CATGAACTCTTCCATGTACCAATATTT 58.093 33.333 0.00 0.00 36.36 1.40
130 131 8.506168 TGAACTCTTCCATGTACCAATATTTC 57.494 34.615 0.00 0.00 0.00 2.17
131 132 8.328758 TGAACTCTTCCATGTACCAATATTTCT 58.671 33.333 0.00 0.00 0.00 2.52
132 133 9.832445 GAACTCTTCCATGTACCAATATTTCTA 57.168 33.333 0.00 0.00 0.00 2.10
164 165 1.453155 ACAATAGTGAAGCCCGCAAG 58.547 50.000 0.00 0.00 0.00 4.01
198 199 4.261405 CGGCTCTGAGTTCTTATAGTGAGG 60.261 50.000 6.53 0.00 0.00 3.86
250 251 3.254903 GGAATAGCCGTTGTCTGGTTTTT 59.745 43.478 0.00 0.00 0.00 1.94
255 256 3.049912 GCCGTTGTCTGGTTTTTCATTC 58.950 45.455 0.00 0.00 0.00 2.67
318 319 6.673154 TGTGCTCTGTATTTGATCTGAATG 57.327 37.500 0.00 0.00 0.00 2.67
349 350 5.049818 TGGCGCCATTTCTTTTGTTAAAATG 60.050 36.000 29.03 0.00 39.16 2.32
351 352 6.128309 GGCGCCATTTCTTTTGTTAAAATGAT 60.128 34.615 24.80 0.00 40.97 2.45
352 353 7.064016 GGCGCCATTTCTTTTGTTAAAATGATA 59.936 33.333 24.80 0.00 40.97 2.15
353 354 8.439286 GCGCCATTTCTTTTGTTAAAATGATAA 58.561 29.630 0.00 0.00 40.97 1.75
508 510 1.275291 CTAAAGCCCTCGTGGTTCAGA 59.725 52.381 2.33 0.00 36.04 3.27
524 527 6.316390 GTGGTTCAGACCTGGACTATTTTATG 59.684 42.308 0.00 0.00 46.66 1.90
551 571 1.528292 GGAGCCACGAGTCACTCACT 61.528 60.000 5.45 0.00 38.45 3.41
592 612 4.926238 CAGGTAAACAGCACAAACAAACAA 59.074 37.500 0.00 0.00 0.00 2.83
642 666 0.606401 ATGCTGTTCCGGGTGAGTTG 60.606 55.000 0.00 0.00 0.00 3.16
708 732 1.592400 CCCTGGTGCAGTGCTGATTG 61.592 60.000 17.60 2.20 0.00 2.67
717 741 2.749076 GCAGTGCTGATTGTTATCCACA 59.251 45.455 8.18 0.00 30.07 4.17
724 748 5.048083 TGCTGATTGTTATCCACAGGAAAAC 60.048 40.000 0.00 0.00 36.48 2.43
912 937 5.333566 TTCCCCACTACCAAAAGATTTCT 57.666 39.130 0.00 0.00 0.00 2.52
941 973 9.538508 CTATCCTTTCATTTTGGGAATCAATTC 57.461 33.333 0.00 0.00 34.98 2.17
989 1026 2.115911 ACGCACTAGAGCTCCGGAG 61.116 63.158 27.83 27.83 0.00 4.63
1099 1144 2.438021 GGCTTGTTTCCCCCTTCTTTTT 59.562 45.455 0.00 0.00 0.00 1.94
1101 1146 3.133901 GCTTGTTTCCCCCTTCTTTTTGA 59.866 43.478 0.00 0.00 0.00 2.69
1109 1154 1.885887 CCCTTCTTTTTGACATCGGCA 59.114 47.619 0.00 0.00 0.00 5.69
1113 1158 1.130373 TCTTTTTGACATCGGCATCGC 59.870 47.619 0.00 0.00 36.13 4.58
1142 1246 2.095364 GCTTGAGCTTGATGGTTCTGTG 60.095 50.000 0.00 0.00 38.21 3.66
1209 1313 2.188817 GGCTTCCCGGAGATATGGTAT 58.811 52.381 0.73 0.00 0.00 2.73
1391 1495 3.195293 TCCAGAAGGTACGTAGTCACGG 61.195 54.545 0.00 0.00 43.93 4.94
1534 1670 2.202260 CGTACGACTTCGCGCTGA 60.202 61.111 10.44 1.08 44.43 4.26
1535 1671 1.794785 CGTACGACTTCGCGCTGAA 60.795 57.895 10.44 10.12 44.43 3.02
1890 2029 3.464111 CCATACAGGTAGGTTAACCGG 57.536 52.381 18.91 0.00 44.77 5.28
1911 2050 1.202818 AGGTTCTTTGTGTCCTCAGCC 60.203 52.381 0.00 0.00 0.00 4.85
1912 2051 1.476833 GGTTCTTTGTGTCCTCAGCCA 60.477 52.381 0.00 0.00 0.00 4.75
1913 2052 2.508526 GTTCTTTGTGTCCTCAGCCAT 58.491 47.619 0.00 0.00 0.00 4.40
1914 2053 2.189594 TCTTTGTGTCCTCAGCCATG 57.810 50.000 0.00 0.00 0.00 3.66
1915 2054 1.171308 CTTTGTGTCCTCAGCCATGG 58.829 55.000 7.63 7.63 0.00 3.66
1916 2055 0.895100 TTTGTGTCCTCAGCCATGGC 60.895 55.000 30.12 30.12 42.33 4.40
1917 2056 2.439156 GTGTCCTCAGCCATGGCC 60.439 66.667 33.14 16.93 43.17 5.36
1918 2057 3.731728 TGTCCTCAGCCATGGCCC 61.732 66.667 33.14 14.17 43.17 5.80
1919 2058 3.731728 GTCCTCAGCCATGGCCCA 61.732 66.667 33.14 18.67 43.17 5.36
1920 2059 2.697263 TCCTCAGCCATGGCCCAT 60.697 61.111 33.14 12.66 43.17 4.00
1921 2060 2.203451 CCTCAGCCATGGCCCATC 60.203 66.667 33.14 5.56 43.17 3.51
1922 2061 2.593725 CTCAGCCATGGCCCATCG 60.594 66.667 33.14 16.26 43.17 3.84
1923 2062 4.881440 TCAGCCATGGCCCATCGC 62.881 66.667 33.14 5.02 43.17 4.58
1972 2121 4.681942 AGAAGAAACAGATTGACGAACTCG 59.318 41.667 0.00 0.00 46.33 4.18
2032 2185 1.147376 CACGTGGACCCCAAGTTCA 59.853 57.895 7.95 0.00 43.15 3.18
2242 2395 2.104451 CTCAAGGACCATCCCTGATCTG 59.896 54.545 0.00 0.00 36.48 2.90
2252 2405 4.287845 CCATCCCTGATCTGTAATCCATCA 59.712 45.833 0.00 0.00 0.00 3.07
2279 2435 3.959991 GAGTGAGCTCCGGGCCAAC 62.960 68.421 12.15 5.60 43.05 3.77
2294 2450 1.202143 GCCAACGAATAAAGCTTCCGG 60.202 52.381 0.00 0.00 0.00 5.14
2373 2529 6.097129 TGGATAGTGTAATGTAATCGTGTCCA 59.903 38.462 0.00 0.00 0.00 4.02
2678 2929 6.875076 TCTCACCTAAGCCTAACATCTAAAC 58.125 40.000 0.00 0.00 0.00 2.01
2960 3212 1.795170 GCCAAACACCTCACACGCAT 61.795 55.000 0.00 0.00 0.00 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.567579 TTACACCAGCAGCAGCCCC 62.568 63.158 0.00 0.00 43.56 5.80
12 13 2.034066 TTACACCAGCAGCAGCCC 59.966 61.111 0.00 0.00 43.56 5.19
13 14 1.172180 TTGTTACACCAGCAGCAGCC 61.172 55.000 0.00 0.00 43.56 4.85
14 15 0.239347 CTTGTTACACCAGCAGCAGC 59.761 55.000 0.00 0.00 42.56 5.25
15 16 0.239347 GCTTGTTACACCAGCAGCAG 59.761 55.000 4.36 0.00 0.00 4.24
16 17 0.465278 TGCTTGTTACACCAGCAGCA 60.465 50.000 7.55 6.15 0.00 4.41
17 18 0.883833 ATGCTTGTTACACCAGCAGC 59.116 50.000 15.52 8.18 38.95 5.25
18 19 2.095567 GTGATGCTTGTTACACCAGCAG 60.096 50.000 15.52 0.00 38.95 4.24
19 20 1.879380 GTGATGCTTGTTACACCAGCA 59.121 47.619 13.18 13.18 39.91 4.41
20 21 2.154462 AGTGATGCTTGTTACACCAGC 58.846 47.619 2.37 2.37 34.33 4.85
21 22 3.814842 TGAAGTGATGCTTGTTACACCAG 59.185 43.478 0.00 0.00 37.59 4.00
22 23 3.563808 GTGAAGTGATGCTTGTTACACCA 59.436 43.478 0.00 0.00 37.59 4.17
23 24 3.815401 AGTGAAGTGATGCTTGTTACACC 59.185 43.478 0.00 0.00 37.59 4.16
24 25 4.319766 CCAGTGAAGTGATGCTTGTTACAC 60.320 45.833 0.00 0.00 37.59 2.90
25 26 3.814842 CCAGTGAAGTGATGCTTGTTACA 59.185 43.478 0.00 0.00 37.59 2.41
26 27 4.065088 TCCAGTGAAGTGATGCTTGTTAC 58.935 43.478 0.00 0.00 37.59 2.50
27 28 4.350368 TCCAGTGAAGTGATGCTTGTTA 57.650 40.909 0.00 0.00 37.59 2.41
28 29 3.213206 TCCAGTGAAGTGATGCTTGTT 57.787 42.857 0.00 0.00 37.59 2.83
29 30 2.936919 TCCAGTGAAGTGATGCTTGT 57.063 45.000 0.00 0.00 37.59 3.16
30 31 3.079578 ACATCCAGTGAAGTGATGCTTG 58.920 45.455 6.93 0.00 39.55 4.01
31 32 3.430042 ACATCCAGTGAAGTGATGCTT 57.570 42.857 6.93 0.00 39.55 3.91
43 44 3.524789 TGATTTCCCATCTCACATCCAGT 59.475 43.478 0.00 0.00 0.00 4.00
44 45 4.135306 CTGATTTCCCATCTCACATCCAG 58.865 47.826 0.00 0.00 0.00 3.86
45 46 3.117776 CCTGATTTCCCATCTCACATCCA 60.118 47.826 0.00 0.00 0.00 3.41
46 47 3.484407 CCTGATTTCCCATCTCACATCC 58.516 50.000 0.00 0.00 0.00 3.51
47 48 2.883386 GCCTGATTTCCCATCTCACATC 59.117 50.000 0.00 0.00 0.00 3.06
48 49 2.423947 GGCCTGATTTCCCATCTCACAT 60.424 50.000 0.00 0.00 0.00 3.21
49 50 1.064463 GGCCTGATTTCCCATCTCACA 60.064 52.381 0.00 0.00 0.00 3.58
50 51 1.685148 GGCCTGATTTCCCATCTCAC 58.315 55.000 0.00 0.00 0.00 3.51
51 52 0.181114 CGGCCTGATTTCCCATCTCA 59.819 55.000 0.00 0.00 0.00 3.27
52 53 0.181350 ACGGCCTGATTTCCCATCTC 59.819 55.000 0.00 0.00 0.00 2.75
53 54 0.625849 AACGGCCTGATTTCCCATCT 59.374 50.000 0.00 0.00 0.00 2.90
54 55 0.740737 CAACGGCCTGATTTCCCATC 59.259 55.000 0.00 0.00 0.00 3.51
55 56 0.331278 TCAACGGCCTGATTTCCCAT 59.669 50.000 0.00 0.00 0.00 4.00
56 57 0.331278 ATCAACGGCCTGATTTCCCA 59.669 50.000 0.00 0.00 31.84 4.37
57 58 0.740737 CATCAACGGCCTGATTTCCC 59.259 55.000 4.76 0.00 33.66 3.97
58 59 0.740737 CCATCAACGGCCTGATTTCC 59.259 55.000 4.76 0.00 33.66 3.13
68 69 0.168128 GGAAAGTTCGCCATCAACGG 59.832 55.000 0.00 0.00 0.00 4.44
69 70 0.168128 GGGAAAGTTCGCCATCAACG 59.832 55.000 0.00 0.00 34.41 4.10
70 71 1.468914 GAGGGAAAGTTCGCCATCAAC 59.531 52.381 4.63 0.00 40.63 3.18
71 72 1.351017 AGAGGGAAAGTTCGCCATCAA 59.649 47.619 10.73 0.00 40.63 2.57
72 73 0.984230 AGAGGGAAAGTTCGCCATCA 59.016 50.000 10.73 0.00 40.63 3.07
73 74 2.168728 AGTAGAGGGAAAGTTCGCCATC 59.831 50.000 4.63 2.19 40.63 3.51
74 75 2.188817 AGTAGAGGGAAAGTTCGCCAT 58.811 47.619 4.63 0.00 40.63 4.40
75 76 1.640917 AGTAGAGGGAAAGTTCGCCA 58.359 50.000 4.63 0.00 40.63 5.69
76 77 4.120589 CAATAGTAGAGGGAAAGTTCGCC 58.879 47.826 4.63 0.00 40.63 5.54
77 78 3.556365 GCAATAGTAGAGGGAAAGTTCGC 59.444 47.826 0.05 0.05 40.10 4.70
78 79 4.120589 GGCAATAGTAGAGGGAAAGTTCG 58.879 47.826 0.00 0.00 0.00 3.95
79 80 4.080526 TGGGCAATAGTAGAGGGAAAGTTC 60.081 45.833 0.00 0.00 0.00 3.01
80 81 3.850173 TGGGCAATAGTAGAGGGAAAGTT 59.150 43.478 0.00 0.00 0.00 2.66
81 82 3.200165 GTGGGCAATAGTAGAGGGAAAGT 59.800 47.826 0.00 0.00 0.00 2.66
82 83 3.199946 TGTGGGCAATAGTAGAGGGAAAG 59.800 47.826 0.00 0.00 0.00 2.62
83 84 3.186283 TGTGGGCAATAGTAGAGGGAAA 58.814 45.455 0.00 0.00 0.00 3.13
84 85 2.840511 TGTGGGCAATAGTAGAGGGAA 58.159 47.619 0.00 0.00 0.00 3.97
85 86 2.561209 TGTGGGCAATAGTAGAGGGA 57.439 50.000 0.00 0.00 0.00 4.20
86 87 2.705658 TCATGTGGGCAATAGTAGAGGG 59.294 50.000 0.00 0.00 0.00 4.30
87 88 4.130118 GTTCATGTGGGCAATAGTAGAGG 58.870 47.826 0.00 0.00 0.00 3.69
88 89 5.028549 AGTTCATGTGGGCAATAGTAGAG 57.971 43.478 0.00 0.00 0.00 2.43
89 90 4.716784 AGAGTTCATGTGGGCAATAGTAGA 59.283 41.667 0.00 0.00 0.00 2.59
90 91 5.028549 AGAGTTCATGTGGGCAATAGTAG 57.971 43.478 0.00 0.00 0.00 2.57
91 92 5.428253 GAAGAGTTCATGTGGGCAATAGTA 58.572 41.667 0.00 0.00 0.00 1.82
92 93 4.265073 GAAGAGTTCATGTGGGCAATAGT 58.735 43.478 0.00 0.00 0.00 2.12
93 94 3.629398 GGAAGAGTTCATGTGGGCAATAG 59.371 47.826 0.00 0.00 0.00 1.73
94 95 3.010027 TGGAAGAGTTCATGTGGGCAATA 59.990 43.478 0.00 0.00 0.00 1.90
95 96 2.225091 TGGAAGAGTTCATGTGGGCAAT 60.225 45.455 0.00 0.00 0.00 3.56
96 97 1.144708 TGGAAGAGTTCATGTGGGCAA 59.855 47.619 0.00 0.00 0.00 4.52
97 98 0.770499 TGGAAGAGTTCATGTGGGCA 59.230 50.000 0.00 0.00 0.00 5.36
98 99 1.747355 CATGGAAGAGTTCATGTGGGC 59.253 52.381 0.00 0.00 36.82 5.36
103 104 8.455903 AATATTGGTACATGGAAGAGTTCATG 57.544 34.615 0.00 0.00 44.42 3.07
104 105 9.125026 GAAATATTGGTACATGGAAGAGTTCAT 57.875 33.333 0.00 0.00 39.30 2.57
105 106 8.328758 AGAAATATTGGTACATGGAAGAGTTCA 58.671 33.333 0.00 0.00 39.30 3.18
106 107 8.738645 AGAAATATTGGTACATGGAAGAGTTC 57.261 34.615 0.00 0.00 39.30 3.01
132 133 7.988028 GGCTTCACTATTGTACTCCTAGAAAAT 59.012 37.037 0.00 0.00 0.00 1.82
133 134 7.328737 GGCTTCACTATTGTACTCCTAGAAAA 58.671 38.462 0.00 0.00 0.00 2.29
134 135 6.127140 GGGCTTCACTATTGTACTCCTAGAAA 60.127 42.308 0.00 0.00 0.00 2.52
135 136 5.363005 GGGCTTCACTATTGTACTCCTAGAA 59.637 44.000 0.00 0.00 0.00 2.10
136 137 4.894114 GGGCTTCACTATTGTACTCCTAGA 59.106 45.833 0.00 0.00 0.00 2.43
137 138 4.261656 CGGGCTTCACTATTGTACTCCTAG 60.262 50.000 0.00 0.00 0.00 3.02
138 139 3.635373 CGGGCTTCACTATTGTACTCCTA 59.365 47.826 0.00 0.00 0.00 2.94
139 140 2.431057 CGGGCTTCACTATTGTACTCCT 59.569 50.000 0.00 0.00 0.00 3.69
140 141 2.822764 CGGGCTTCACTATTGTACTCC 58.177 52.381 0.00 0.00 0.00 3.85
141 142 2.202566 GCGGGCTTCACTATTGTACTC 58.797 52.381 0.00 0.00 0.00 2.59
142 143 1.553248 TGCGGGCTTCACTATTGTACT 59.447 47.619 0.00 0.00 0.00 2.73
143 144 2.018542 TGCGGGCTTCACTATTGTAC 57.981 50.000 0.00 0.00 0.00 2.90
144 145 2.027561 ACTTGCGGGCTTCACTATTGTA 60.028 45.455 0.00 0.00 0.00 2.41
145 146 1.271379 ACTTGCGGGCTTCACTATTGT 60.271 47.619 0.00 0.00 0.00 2.71
146 147 1.453155 ACTTGCGGGCTTCACTATTG 58.547 50.000 0.00 0.00 0.00 1.90
147 148 2.200373 AACTTGCGGGCTTCACTATT 57.800 45.000 0.00 0.00 0.00 1.73
148 149 1.812571 CAAACTTGCGGGCTTCACTAT 59.187 47.619 0.00 0.00 0.00 2.12
149 150 1.234821 CAAACTTGCGGGCTTCACTA 58.765 50.000 0.00 0.00 0.00 2.74
150 151 2.032981 CAAACTTGCGGGCTTCACT 58.967 52.632 0.00 0.00 0.00 3.41
151 152 1.661509 GCAAACTTGCGGGCTTCAC 60.662 57.895 0.00 0.00 45.11 3.18
152 153 2.727544 GCAAACTTGCGGGCTTCA 59.272 55.556 0.00 0.00 45.11 3.02
164 165 0.391661 TCAGAGCCGGATGAGCAAAC 60.392 55.000 5.05 0.00 0.00 2.93
198 199 3.536570 GGGTGAGAGCTCTGAAAATACC 58.463 50.000 23.91 17.38 0.00 2.73
229 230 4.023536 TGAAAAACCAGACAACGGCTATTC 60.024 41.667 0.00 0.00 0.00 1.75
237 238 5.154222 GGATCGAATGAAAAACCAGACAAC 58.846 41.667 0.00 0.00 0.00 3.32
250 251 8.955388 TGATAAGTTTCATTTTGGATCGAATGA 58.045 29.630 11.49 11.49 39.71 2.57
255 256 6.974622 CCCTTGATAAGTTTCATTTTGGATCG 59.025 38.462 0.00 0.00 0.00 3.69
318 319 4.747540 AAAGAAATGGCGCCAAATTTTC 57.252 36.364 32.46 32.46 0.00 2.29
349 350 8.306680 TGTTAGCGATGCTACCTTTATTTATC 57.693 34.615 0.00 0.00 41.12 1.75
351 352 7.307751 GCATGTTAGCGATGCTACCTTTATTTA 60.308 37.037 0.00 0.00 41.12 1.40
352 353 6.513393 GCATGTTAGCGATGCTACCTTTATTT 60.513 38.462 0.00 0.00 41.12 1.40
353 354 5.049405 GCATGTTAGCGATGCTACCTTTATT 60.049 40.000 0.00 0.00 41.12 1.40
354 355 4.452455 GCATGTTAGCGATGCTACCTTTAT 59.548 41.667 0.00 0.00 41.12 1.40
355 356 3.807622 GCATGTTAGCGATGCTACCTTTA 59.192 43.478 0.00 0.00 41.12 1.85
356 357 2.614057 GCATGTTAGCGATGCTACCTTT 59.386 45.455 0.00 0.00 41.12 3.11
396 397 5.649557 TGTTTGTCAACTGTTCTTGGATTG 58.350 37.500 0.00 0.00 33.58 2.67
443 444 3.871594 GCCGGCCTATGCTACTAATAATG 59.128 47.826 18.11 0.00 37.74 1.90
457 458 2.041922 AGATGTCAGGCCGGCCTA 60.042 61.111 46.42 32.62 46.28 3.93
508 510 3.877508 GCGCTTCATAAAATAGTCCAGGT 59.122 43.478 0.00 0.00 0.00 4.00
524 527 4.742201 TCGTGGCTCCTGCGCTTC 62.742 66.667 9.73 0.00 40.82 3.86
551 571 3.133362 ACCTGAACAAAGACAGTTACGGA 59.867 43.478 0.00 0.00 32.93 4.69
592 612 0.604243 TCTGCACCGCGGTAATTGTT 60.604 50.000 33.70 2.52 36.18 2.83
642 666 5.078411 TGCTCAGATCTGTTTAACCTCTC 57.922 43.478 21.92 2.17 0.00 3.20
724 748 8.469309 ACCCTGAAATCCTACAATGATTTATG 57.531 34.615 0.00 0.00 41.29 1.90
847 872 5.118357 CACTCTCTTTGTCGTCTCTTTGATG 59.882 44.000 0.00 0.00 0.00 3.07
912 937 7.181361 TGATTCCCAAAATGAAAGGATAGTGA 58.819 34.615 0.00 0.00 0.00 3.41
930 962 5.901232 GCCAGGAGGAGGAATTGATTCCC 62.901 56.522 17.05 9.89 45.53 3.97
941 973 5.087323 TCACTTTATATAGCCAGGAGGAGG 58.913 45.833 0.00 0.00 36.89 4.30
1099 1144 2.278792 CTCGCGATGCCGATGTCA 60.279 61.111 10.36 0.00 36.54 3.58
1101 1146 2.167219 CAACTCGCGATGCCGATGT 61.167 57.895 10.36 0.00 36.54 3.06
1109 1154 1.080995 GCTCAAGCTCAACTCGCGAT 61.081 55.000 10.36 0.00 38.21 4.58
1142 1246 1.790623 CATCTGCAAGCAACACAAAGC 59.209 47.619 0.00 0.00 0.00 3.51
1884 2023 2.224354 GGACACAAAGAACCTCCGGTTA 60.224 50.000 0.00 0.00 46.95 2.85
1888 2027 1.070134 TGAGGACACAAAGAACCTCCG 59.930 52.381 0.00 0.00 45.61 4.63
1890 2029 2.147150 GCTGAGGACACAAAGAACCTC 58.853 52.381 0.00 0.00 46.16 3.85
1893 2032 1.967319 TGGCTGAGGACACAAAGAAC 58.033 50.000 0.00 0.00 0.00 3.01
1899 2038 2.352422 GCCATGGCTGAGGACACA 59.648 61.111 29.98 0.00 38.26 3.72
1903 2042 2.697263 ATGGGCCATGGCTGAGGA 60.697 61.111 34.70 15.27 41.60 3.71
1906 2045 4.881440 GCGATGGGCCATGGCTGA 62.881 66.667 36.90 22.04 41.25 4.26
1923 2062 5.390461 CGTTGTAATATAATCGTGCCATGGG 60.390 44.000 15.13 0.00 0.00 4.00
1924 2063 5.407084 TCGTTGTAATATAATCGTGCCATGG 59.593 40.000 7.63 7.63 0.00 3.66
1972 2121 3.070076 TGCGATCATGGAAGCAGTC 57.930 52.632 5.94 0.00 34.39 3.51
2032 2185 1.378762 CCATGAACACCGGGACCTT 59.621 57.895 6.32 0.00 0.00 3.50
2242 2395 3.181489 ACTCTCGTCCGTTGATGGATTAC 60.181 47.826 0.00 0.00 40.91 1.89
2252 2405 1.587933 GGAGCTCACTCTCGTCCGTT 61.588 60.000 17.19 0.00 42.98 4.44
2271 2424 0.808755 AAGCTTTATTCGTTGGCCCG 59.191 50.000 0.00 0.00 0.00 6.13
2279 2435 1.011131 GCGCCGGAAGCTTTATTCG 60.011 57.895 5.05 4.13 40.39 3.34
2296 2452 0.108945 GGTTCAAGCAGAGCAATGGC 60.109 55.000 0.00 0.00 41.61 4.40
2367 2523 4.918810 AACTGAAAAACCAGATGGACAC 57.081 40.909 5.72 0.00 37.59 3.67
2519 2770 9.057089 GTCCTCGAGAATAATCAATAAAATGGT 57.943 33.333 15.71 0.00 0.00 3.55
2910 3162 2.739913 GTGTGCAGCGTTTCACCTATTA 59.260 45.455 0.00 0.00 32.51 0.98


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

AutoCloner maintained by Alex Coulton.