Multiple sequence alignment - TraesCS3B01G093300

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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 TraesCS3B01G093300 chr3B 100.000 4008 0 0 1 4008 62316365 62312358 0.000000e+00 7402.0
1 TraesCS3B01G093300 chr3B 94.166 737 38 2 3277 4008 62300770 62300034 0.000000e+00 1118.0
2 TraesCS3B01G093300 chr3D 91.828 1860 85 39 2191 4008 39325249 39323415 0.000000e+00 2531.0
3 TraesCS3B01G093300 chr3D 94.291 1489 62 11 71 1548 39326848 39325372 0.000000e+00 2257.0
4 TraesCS3B01G093300 chr3A 87.189 1889 126 70 2191 3994 50727349 50725492 0.000000e+00 2041.0
5 TraesCS3B01G093300 chr3A 90.262 1602 83 31 1 1548 50729063 50727481 0.000000e+00 2026.0
6 TraesCS3B01G093300 chr3A 89.300 243 24 2 1607 1848 727762722 727762963 1.810000e-78 303.0
7 TraesCS3B01G093300 chr3A 100.000 35 0 0 1572 1606 727762698 727762732 9.300000e-07 65.8
8 TraesCS3B01G093300 chr1B 97.505 481 9 2 1568 2046 657280853 657281332 0.000000e+00 819.0
9 TraesCS3B01G093300 chr1B 86.891 534 48 10 1572 2099 66940822 66941339 2.690000e-161 579.0
10 TraesCS3B01G093300 chr1B 92.174 230 6 3 1888 2105 657281359 657281588 8.360000e-82 315.0
11 TraesCS3B01G093300 chr1B 100.000 30 0 0 2036 2065 657281331 657281360 5.600000e-04 56.5
12 TraesCS3B01G093300 chr6B 92.351 536 22 6 1568 2099 699608920 699609440 0.000000e+00 745.0
13 TraesCS3B01G093300 chr7D 89.442 502 50 3 1601 2101 53314089 53314588 7.310000e-177 630.0
14 TraesCS3B01G093300 chr4A 86.778 537 57 6 1572 2097 515271709 515271176 1.600000e-163 586.0
15 TraesCS3B01G093300 chr4A 76.538 439 67 27 1072 1497 521919878 521919463 1.460000e-49 207.0
16 TraesCS3B01G093300 chr4A 85.030 167 11 5 1967 2121 716510211 716510047 1.490000e-34 158.0
17 TraesCS3B01G093300 chr5D 79.417 515 75 19 1607 2099 487506943 487507448 6.420000e-88 335.0
18 TraesCS3B01G093300 chr7A 87.500 232 22 5 1872 2099 696738654 696738882 1.100000e-65 261.0
19 TraesCS3B01G093300 chr2D 85.433 254 26 8 1243 1492 54487722 54487476 1.850000e-63 254.0
20 TraesCS3B01G093300 chr2D 85.837 233 30 3 1244 1476 175331641 175331870 1.110000e-60 244.0
21 TraesCS3B01G093300 chr2B 85.039 254 27 8 1243 1492 85177655 85177409 8.600000e-62 248.0
22 TraesCS3B01G093300 chr2B 84.646 254 28 8 1243 1492 85074277 85074523 4.000000e-60 243.0
23 TraesCS3B01G093300 chr2A 84.585 253 30 6 1243 1492 54882637 54882883 4.000000e-60 243.0
24 TraesCS3B01G093300 chr5A 77.412 425 68 22 1073 1489 645726285 645726689 1.120000e-55 228.0
25 TraesCS3B01G093300 chr4B 82.129 263 38 8 1244 1506 380653800 380654053 2.430000e-52 217.0
26 TraesCS3B01G093300 chr4B 76.136 440 67 30 1072 1497 103056376 103055961 3.160000e-46 196.0
27 TraesCS3B01G093300 chr4D 76.136 440 67 29 1072 1497 69680130 69679715 3.160000e-46 196.0
28 TraesCS3B01G093300 chr6A 91.379 58 3 2 1072 1128 599259563 599259619 1.190000e-10 78.7
29 TraesCS3B01G093300 chr5B 100.000 35 0 0 1572 1606 70556534 70556500 9.300000e-07 65.8


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 TraesCS3B01G093300 chr3B 62312358 62316365 4007 True 7402.000000 7402 100.000000 1 4008 1 chr3B.!!$R2 4007
1 TraesCS3B01G093300 chr3B 62300034 62300770 736 True 1118.000000 1118 94.166000 3277 4008 1 chr3B.!!$R1 731
2 TraesCS3B01G093300 chr3D 39323415 39326848 3433 True 2394.000000 2531 93.059500 71 4008 2 chr3D.!!$R1 3937
3 TraesCS3B01G093300 chr3A 50725492 50729063 3571 True 2033.500000 2041 88.725500 1 3994 2 chr3A.!!$R1 3993
4 TraesCS3B01G093300 chr1B 66940822 66941339 517 False 579.000000 579 86.891000 1572 2099 1 chr1B.!!$F1 527
5 TraesCS3B01G093300 chr1B 657280853 657281588 735 False 396.833333 819 96.559667 1568 2105 3 chr1B.!!$F2 537
6 TraesCS3B01G093300 chr6B 699608920 699609440 520 False 745.000000 745 92.351000 1568 2099 1 chr6B.!!$F1 531
7 TraesCS3B01G093300 chr4A 515271176 515271709 533 True 586.000000 586 86.778000 1572 2097 1 chr4A.!!$R1 525
8 TraesCS3B01G093300 chr5D 487506943 487507448 505 False 335.000000 335 79.417000 1607 2099 1 chr5D.!!$F1 492

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
983 1031 0.108898 CTTGCCCTGAGTCTCTGACG 60.109 60.0 8.24 0.00 37.67 4.35 F
1018 1073 0.248825 GATGACGATCGAGCTGCAGT 60.249 55.0 24.34 1.59 0.00 4.40 F
2481 2836 0.386352 CCTTCTTGTGTGCGTGCATG 60.386 55.0 0.09 0.09 0.00 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2410 2751 0.038159 ACAGTCGCTTGACAGGTAGC 60.038 55.000 0.0 0.00 45.40 3.58 R
2634 2998 1.004080 TCCTCTTGCTGCTGCTGTC 60.004 57.895 17.0 1.84 40.48 3.51 R
3712 4113 1.630148 CCTCTTTTAGGCGAGACACG 58.370 55.000 0.0 0.00 38.97 4.49 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
52 54 8.929827 TTTGAAACTTGAACCATATGCATATG 57.070 30.769 31.52 31.52 39.80 1.78
54 56 7.706159 TGAAACTTGAACCATATGCATATGAC 58.294 34.615 37.19 27.89 42.05 3.06
57 59 5.766670 ACTTGAACCATATGCATATGACAGG 59.233 40.000 37.19 31.20 42.05 4.00
63 65 4.395231 CCATATGCATATGACAGGCTCAAG 59.605 45.833 37.19 18.77 42.05 3.02
66 68 2.239402 TGCATATGACAGGCTCAAGGAA 59.761 45.455 6.97 0.00 34.20 3.36
80 83 9.472361 CAGGCTCAAGGAATATTTTCATAAATG 57.528 33.333 0.00 0.00 35.61 2.32
156 160 9.691362 AAACTTGCATTTTAAAGATCGTGTTAT 57.309 25.926 0.00 0.00 0.00 1.89
182 186 4.261114 CCAAAAATGCGCCTTTTTGTGAAT 60.261 37.500 37.96 18.43 46.98 2.57
186 190 1.410517 TGCGCCTTTTTGTGAATTGGA 59.589 42.857 4.18 0.00 0.00 3.53
190 194 2.289631 GCCTTTTTGTGAATTGGAGGGG 60.290 50.000 0.00 0.00 0.00 4.79
208 212 3.596500 AGGGGGTAGCTACCTGAAATTTT 59.403 43.478 35.80 14.63 45.72 1.82
218 222 4.937201 ACCTGAAATTTTTGTGGACTCC 57.063 40.909 0.00 0.00 0.00 3.85
289 301 5.359576 TGTGAACCTTATTGCACTTTTGAGT 59.640 36.000 0.00 0.00 32.69 3.41
297 309 2.203401 TGCACTTTTGAGTTTGCATGC 58.797 42.857 11.82 11.82 40.01 4.06
298 310 2.159071 TGCACTTTTGAGTTTGCATGCT 60.159 40.909 20.33 0.00 40.01 3.79
310 322 7.219322 TGAGTTTGCATGCTATATAGTGACAT 58.781 34.615 20.33 3.94 0.00 3.06
311 323 8.367156 TGAGTTTGCATGCTATATAGTGACATA 58.633 33.333 20.33 0.00 0.00 2.29
312 324 8.539770 AGTTTGCATGCTATATAGTGACATAC 57.460 34.615 20.33 9.50 0.00 2.39
313 325 7.329471 AGTTTGCATGCTATATAGTGACATACG 59.671 37.037 20.33 0.00 0.00 3.06
314 326 5.650543 TGCATGCTATATAGTGACATACGG 58.349 41.667 20.33 0.00 0.00 4.02
315 327 5.417580 TGCATGCTATATAGTGACATACGGA 59.582 40.000 20.33 0.00 0.00 4.69
316 328 5.974158 GCATGCTATATAGTGACATACGGAG 59.026 44.000 11.37 0.00 0.00 4.63
515 557 7.201679 GCATGTATAGGAATATGGAGTCAATGC 60.202 40.741 0.00 0.00 0.00 3.56
545 587 9.950680 CATACATAAAAACACCTGGTATTCATC 57.049 33.333 0.00 0.00 0.00 2.92
594 636 1.303317 ACCATCAACACTTCCCGGC 60.303 57.895 0.00 0.00 0.00 6.13
615 657 3.248602 GCCCTACAACATCGAGCTTAATG 59.751 47.826 7.51 7.51 0.00 1.90
641 684 7.116805 GTCCATCTTTTCCAATCATTTGACAAC 59.883 37.037 0.00 0.00 34.60 3.32
648 691 8.961294 TTTCCAATCATTTGACAACTGATTTT 57.039 26.923 23.72 9.03 37.48 1.82
649 692 8.961294 TTCCAATCATTTGACAACTGATTTTT 57.039 26.923 23.72 8.45 37.48 1.94
691 734 6.367149 GCTCATGTCTTTTTCAGATTTTTCCC 59.633 38.462 0.00 0.00 32.60 3.97
692 735 7.358770 TCATGTCTTTTTCAGATTTTTCCCA 57.641 32.000 0.00 0.00 32.60 4.37
766 812 0.610174 TCTAGCCAAGTGAGCACTGG 59.390 55.000 3.57 8.88 41.58 4.00
777 823 1.215655 GAGCACTGGTGACGTGACAC 61.216 60.000 7.63 2.92 37.13 3.67
909 957 4.227134 CCCATCGGCTCCACCTCG 62.227 72.222 0.00 0.00 35.61 4.63
958 1006 1.140134 CACCTTCCCTTCCCTTCCCA 61.140 60.000 0.00 0.00 0.00 4.37
965 1013 0.842467 CCTTCCCTTCCCACTCACCT 60.842 60.000 0.00 0.00 0.00 4.00
966 1014 1.068121 CTTCCCTTCCCACTCACCTT 58.932 55.000 0.00 0.00 0.00 3.50
983 1031 0.108898 CTTGCCCTGAGTCTCTGACG 60.109 60.000 8.24 0.00 37.67 4.35
1018 1073 0.248825 GATGACGATCGAGCTGCAGT 60.249 55.000 24.34 1.59 0.00 4.40
1192 1247 1.825474 CGGAGGTGGACATCTACAAGT 59.175 52.381 0.00 0.00 0.00 3.16
1200 1255 2.618053 GACATCTACAAGTTGGACCCG 58.382 52.381 7.96 0.00 0.00 5.28
1937 2015 1.274447 AGCCACTACGGTAGAACAACC 59.726 52.381 21.39 4.11 36.97 3.77
2108 2391 1.470098 CCAAAACCTTGCTCTCCATCG 59.530 52.381 0.00 0.00 0.00 3.84
2114 2425 4.222124 ACCTTGCTCTCCATCGTAATTT 57.778 40.909 0.00 0.00 0.00 1.82
2119 2430 3.561310 TGCTCTCCATCGTAATTTCATGC 59.439 43.478 0.00 0.00 0.00 4.06
2124 2435 7.308229 GCTCTCCATCGTAATTTCATGCTTTAT 60.308 37.037 0.00 0.00 0.00 1.40
2126 2437 9.554395 TCTCCATCGTAATTTCATGCTTTATTA 57.446 29.630 0.00 0.00 0.00 0.98
2148 2459 5.970317 ATTTCTTCTTGATCACACATGCA 57.030 34.783 0.00 0.00 0.00 3.96
2149 2460 5.771153 TTTCTTCTTGATCACACATGCAA 57.229 34.783 0.00 0.00 0.00 4.08
2150 2461 5.366829 TTCTTCTTGATCACACATGCAAG 57.633 39.130 0.00 0.00 39.17 4.01
2151 2462 3.189910 TCTTCTTGATCACACATGCAAGC 59.810 43.478 0.00 0.00 38.05 4.01
2167 2478 1.788308 CAAGCATGTTTTCTGCGGTTG 59.212 47.619 0.00 0.00 44.38 3.77
2181 2492 1.334599 GCGGTTGCAAATGAACGAAGA 60.335 47.619 0.00 0.00 42.15 2.87
2182 2493 2.856720 GCGGTTGCAAATGAACGAAGAA 60.857 45.455 0.00 0.00 42.15 2.52
2183 2494 2.973224 CGGTTGCAAATGAACGAAGAAG 59.027 45.455 0.00 0.00 0.00 2.85
2184 2495 3.308530 GGTTGCAAATGAACGAAGAAGG 58.691 45.455 0.00 0.00 0.00 3.46
2185 2496 2.704725 TGCAAATGAACGAAGAAGGC 57.295 45.000 0.00 0.00 0.00 4.35
2186 2497 1.952990 TGCAAATGAACGAAGAAGGCA 59.047 42.857 0.00 0.00 0.00 4.75
2187 2498 2.557924 TGCAAATGAACGAAGAAGGCAT 59.442 40.909 0.00 0.00 0.00 4.40
2188 2499 3.174375 GCAAATGAACGAAGAAGGCATC 58.826 45.455 0.00 0.00 0.00 3.91
2189 2500 3.119708 GCAAATGAACGAAGAAGGCATCT 60.120 43.478 0.00 0.00 41.32 2.90
2194 2505 1.714794 ACGAAGAAGGCATCTCGTTG 58.285 50.000 10.05 0.00 38.13 4.10
2281 2605 0.948141 AGCTCGAGCAAGCAACTCAC 60.948 55.000 36.87 5.17 45.00 3.51
2282 2606 1.905922 GCTCGAGCAAGCAACTCACC 61.906 60.000 31.91 0.00 42.05 4.02
2283 2607 1.294659 CTCGAGCAAGCAACTCACCC 61.295 60.000 0.00 0.00 33.58 4.61
2284 2608 1.302033 CGAGCAAGCAACTCACCCT 60.302 57.895 0.00 0.00 33.58 4.34
2285 2609 1.572085 CGAGCAAGCAACTCACCCTG 61.572 60.000 0.00 0.00 33.58 4.45
2286 2610 1.228367 AGCAAGCAACTCACCCTGG 60.228 57.895 0.00 0.00 0.00 4.45
2287 2611 2.270986 GCAAGCAACTCACCCTGGG 61.271 63.158 12.28 12.28 0.00 4.45
2288 2612 1.151450 CAAGCAACTCACCCTGGGT 59.849 57.895 14.05 14.05 35.62 4.51
2306 2630 1.534729 GTCCCTGGTCAATGAACCAC 58.465 55.000 0.00 0.00 44.40 4.16
2307 2631 1.073923 GTCCCTGGTCAATGAACCACT 59.926 52.381 0.00 0.00 44.40 4.00
2351 2688 5.796502 TTTACCCATGGGATCTTCTTTCT 57.203 39.130 38.07 13.18 38.96 2.52
2384 2725 4.702131 AGACTTGCATTATCACCCTTCAAC 59.298 41.667 0.00 0.00 0.00 3.18
2390 2731 4.947388 GCATTATCACCCTTCAACCTACAA 59.053 41.667 0.00 0.00 0.00 2.41
2451 2806 1.268285 TGTTGCAACATACACGTGTGC 60.268 47.619 30.83 23.88 33.17 4.57
2453 2808 1.304254 TGCAACATACACGTGTGCTT 58.696 45.000 30.83 15.34 31.49 3.91
2479 2834 0.746204 TTCCTTCTTGTGTGCGTGCA 60.746 50.000 0.00 0.00 0.00 4.57
2480 2835 0.534877 TCCTTCTTGTGTGCGTGCAT 60.535 50.000 0.00 0.00 0.00 3.96
2481 2836 0.386352 CCTTCTTGTGTGCGTGCATG 60.386 55.000 0.09 0.09 0.00 4.06
2482 2837 1.000233 CTTCTTGTGTGCGTGCATGC 61.000 55.000 24.20 24.20 0.00 4.06
2689 3056 1.449353 GATGCTGCCGAGGAATCCT 59.551 57.895 0.00 0.00 36.03 3.24
2782 3152 1.446966 GGAGACGACTGCAAGCTCC 60.447 63.158 0.96 0.00 37.60 4.70
2810 3180 0.606604 GTTCTTCCTCGGCACCACTA 59.393 55.000 0.00 0.00 0.00 2.74
2813 3183 1.005097 TCTTCCTCGGCACCACTACTA 59.995 52.381 0.00 0.00 0.00 1.82
2814 3184 1.134560 CTTCCTCGGCACCACTACTAC 59.865 57.143 0.00 0.00 0.00 2.73
2815 3185 0.330604 TCCTCGGCACCACTACTACT 59.669 55.000 0.00 0.00 0.00 2.57
2938 3308 1.071471 GGGTAGCGATGGGTCCATG 59.929 63.158 7.29 1.73 36.70 3.66
2939 3309 1.407656 GGGTAGCGATGGGTCCATGA 61.408 60.000 7.29 0.00 36.70 3.07
2940 3310 0.249911 GGTAGCGATGGGTCCATGAC 60.250 60.000 7.29 0.00 36.70 3.06
2998 3368 2.687610 CCAGCCTTCCCAGCAGGAT 61.688 63.158 0.00 0.00 46.94 3.24
3063 3433 4.363999 AGCAAGCTAGCGACTTAACTATG 58.636 43.478 9.55 0.00 40.15 2.23
3151 3531 7.199541 ACTCATGCATAATTTGTAGATCAGC 57.800 36.000 0.00 0.00 0.00 4.26
3202 3586 9.485206 AAAGTTAGTGTAACATATTATAGGCCG 57.515 33.333 0.00 0.00 41.43 6.13
3206 3602 5.778750 AGTGTAACATATTATAGGCCGGAGT 59.221 40.000 5.05 0.00 41.43 3.85
3223 3619 5.006746 GCCGGAGTAGAAGAACACAATTATG 59.993 44.000 5.05 0.00 0.00 1.90
3225 3621 6.255887 CCGGAGTAGAAGAACACAATTATGTC 59.744 42.308 0.00 0.00 37.82 3.06
3226 3622 6.811665 CGGAGTAGAAGAACACAATTATGTCA 59.188 38.462 0.00 0.00 37.82 3.58
3303 3699 4.091549 TGTAGGGTGAACTAGGGTGTAAG 58.908 47.826 0.00 0.00 0.00 2.34
3380 3777 6.500684 TTATTGCAATCAAGTCTTGGACTC 57.499 37.500 16.86 1.66 42.59 3.36
3486 3883 8.573035 TGAAGTGCAGGTACTTTAAAATAAAGG 58.427 33.333 12.91 0.00 40.78 3.11
3712 4113 2.045926 ACCGATGGAAGCCAGTGC 60.046 61.111 0.00 0.00 36.75 4.40
3718 4119 2.031163 GGAAGCCAGTGCGTGTCT 59.969 61.111 0.00 0.00 44.33 3.41
3720 4121 2.356313 AAGCCAGTGCGTGTCTCG 60.356 61.111 0.00 0.00 44.33 4.04
3876 4307 9.958234 TTGAATCGATTTCAGAATTTTACACAA 57.042 25.926 12.81 3.79 44.90 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 54 6.705863 ATGAAAATATTCCTTGAGCCTGTC 57.294 37.500 0.00 0.00 34.49 3.51
54 56 9.472361 CATTTATGAAAATATTCCTTGAGCCTG 57.528 33.333 0.00 0.00 33.45 4.85
124 128 8.702438 CGATCTTTAAAATGCAAGTTTGACAAT 58.298 29.630 8.57 0.00 33.75 2.71
148 152 3.816091 CGCATTTTTGGACATAACACGA 58.184 40.909 0.00 0.00 0.00 4.35
156 160 2.611225 AAAAGGCGCATTTTTGGACA 57.389 40.000 25.53 0.00 0.00 4.02
182 186 4.822734 GGTAGCTACCCCCTCCAA 57.177 61.111 29.68 0.00 40.53 3.53
190 194 5.475564 TCCACAAAAATTTCAGGTAGCTACC 59.524 40.000 32.07 32.07 46.82 3.18
208 212 6.513720 GCAATTTTTAGTAACGGAGTCCACAA 60.514 38.462 10.49 0.00 45.00 3.33
218 222 6.660722 TGGTAGTGTGCAATTTTTAGTAACG 58.339 36.000 0.00 0.00 0.00 3.18
289 301 6.589907 CCGTATGTCACTATATAGCATGCAAA 59.410 38.462 21.98 7.96 0.00 3.68
297 309 9.819267 TCATCTACTCCGTATGTCACTATATAG 57.181 37.037 8.27 8.27 0.00 1.31
298 310 9.819267 CTCATCTACTCCGTATGTCACTATATA 57.181 37.037 0.00 0.00 0.00 0.86
311 323 8.865090 AGATTTAATCATTCTCATCTACTCCGT 58.135 33.333 7.74 0.00 0.00 4.69
312 324 9.703892 AAGATTTAATCATTCTCATCTACTCCG 57.296 33.333 7.74 0.00 0.00 4.63
360 372 7.502120 TGAGAATTGCTTAAATATCTCCAGC 57.498 36.000 0.00 0.00 34.68 4.85
410 433 5.630415 ACCTCGGAAAATCATTGGAGATA 57.370 39.130 0.00 0.00 0.00 1.98
515 557 6.249035 ACCAGGTGTTTTTATGTATGTTCG 57.751 37.500 0.00 0.00 0.00 3.95
594 636 4.442706 ACATTAAGCTCGATGTTGTAGGG 58.557 43.478 8.63 0.00 32.85 3.53
615 657 6.690530 TGTCAAATGATTGGAAAAGATGGAC 58.309 36.000 0.00 0.00 37.15 4.02
648 691 7.162761 ACATGAGCAAAATGAATGGATGAAAA 58.837 30.769 0.00 0.00 0.00 2.29
649 692 6.703319 ACATGAGCAAAATGAATGGATGAAA 58.297 32.000 0.00 0.00 0.00 2.69
653 696 6.540438 AAGACATGAGCAAAATGAATGGAT 57.460 33.333 0.00 0.00 0.00 3.41
691 734 0.792640 GTGCCACATGAGAACGAGTG 59.207 55.000 0.00 0.00 0.00 3.51
692 735 0.392706 TGTGCCACATGAGAACGAGT 59.607 50.000 0.00 0.00 0.00 4.18
766 812 1.007336 GTCCATCCGTGTCACGTCAC 61.007 60.000 23.01 8.71 40.58 3.67
777 823 2.156446 GTACGTGCGTGTCCATCCG 61.156 63.158 7.55 0.00 0.00 4.18
909 957 4.072839 ACGGAGGAGAACTGAAATTTTCC 58.927 43.478 6.68 0.00 33.87 3.13
958 1006 4.320844 ACTCAGGGCAAGGTGAGT 57.679 55.556 0.00 0.00 46.91 3.41
965 1013 1.536073 CCGTCAGAGACTCAGGGCAA 61.536 60.000 5.02 0.00 0.00 4.52
966 1014 1.979155 CCGTCAGAGACTCAGGGCA 60.979 63.158 5.02 0.00 0.00 5.36
983 1031 1.375523 ATCACAACCCGAACGCTCC 60.376 57.895 0.00 0.00 0.00 4.70
1098 1153 1.357334 GATCAGCTCCTCGTCCGTC 59.643 63.158 0.00 0.00 0.00 4.79
1192 1247 3.319198 GAGCTCCCACGGGTCCAA 61.319 66.667 0.87 0.00 36.47 3.53
1317 1372 2.267961 CCGGTGGCCTTCCAGTAC 59.732 66.667 3.32 0.00 44.48 2.73
1422 1477 2.356667 GTCTTGAGCCCCTTGGGG 59.643 66.667 20.18 20.18 44.57 4.96
1670 1736 8.582930 GCGATCGTTTGAATTCAAATATTTCAA 58.417 29.630 30.63 14.73 46.12 2.69
2124 2435 7.451501 TGCATGTGTGATCAAGAAGAAATAA 57.548 32.000 0.00 0.00 0.00 1.40
2126 2437 5.970317 TGCATGTGTGATCAAGAAGAAAT 57.030 34.783 0.00 0.00 0.00 2.17
2127 2438 5.765176 CTTGCATGTGTGATCAAGAAGAAA 58.235 37.500 0.00 0.00 38.45 2.52
2129 2440 3.189910 GCTTGCATGTGTGATCAAGAAGA 59.810 43.478 11.31 0.00 38.45 2.87
2130 2441 3.057806 TGCTTGCATGTGTGATCAAGAAG 60.058 43.478 11.31 0.00 38.45 2.85
2132 2443 2.506444 TGCTTGCATGTGTGATCAAGA 58.494 42.857 11.31 0.00 38.45 3.02
2133 2444 3.179048 CATGCTTGCATGTGTGATCAAG 58.821 45.455 23.00 0.00 39.00 3.02
2134 2445 2.559231 ACATGCTTGCATGTGTGATCAA 59.441 40.909 32.10 0.00 43.42 2.57
2135 2446 2.164338 ACATGCTTGCATGTGTGATCA 58.836 42.857 32.10 0.00 43.42 2.92
2136 2447 2.933495 ACATGCTTGCATGTGTGATC 57.067 45.000 32.10 0.00 43.42 2.92
2137 2448 3.671008 AAACATGCTTGCATGTGTGAT 57.329 38.095 32.91 19.44 44.19 3.06
2139 2450 3.183574 CAGAAAACATGCTTGCATGTGTG 59.816 43.478 32.91 24.33 44.19 3.82
2140 2451 3.386486 CAGAAAACATGCTTGCATGTGT 58.614 40.909 32.91 27.48 44.19 3.72
2141 2452 2.156891 GCAGAAAACATGCTTGCATGTG 59.843 45.455 32.91 23.24 44.19 3.21
2143 2454 1.388768 CGCAGAAAACATGCTTGCATG 59.611 47.619 27.64 27.64 41.61 4.06
2144 2455 1.670674 CCGCAGAAAACATGCTTGCAT 60.671 47.619 1.81 1.81 41.61 3.96
2145 2456 0.318869 CCGCAGAAAACATGCTTGCA 60.319 50.000 0.00 0.00 41.61 4.08
2146 2457 0.318955 ACCGCAGAAAACATGCTTGC 60.319 50.000 0.00 0.00 41.61 4.01
2147 2458 1.788308 CAACCGCAGAAAACATGCTTG 59.212 47.619 0.00 0.00 41.61 4.01
2148 2459 1.869342 GCAACCGCAGAAAACATGCTT 60.869 47.619 0.00 0.00 41.61 3.91
2149 2460 0.318955 GCAACCGCAGAAAACATGCT 60.319 50.000 0.00 0.00 41.61 3.79
2150 2461 0.597118 TGCAACCGCAGAAAACATGC 60.597 50.000 0.00 0.00 45.36 4.06
2151 2462 3.566273 TGCAACCGCAGAAAACATG 57.434 47.368 0.00 0.00 45.36 3.21
2167 2478 2.704725 TGCCTTCTTCGTTCATTTGC 57.295 45.000 0.00 0.00 0.00 3.68
2175 2486 1.673033 CCAACGAGATGCCTTCTTCGT 60.673 52.381 0.00 0.00 38.78 3.85
2181 2492 1.137872 CTAGCTCCAACGAGATGCCTT 59.862 52.381 0.00 0.00 38.52 4.35
2182 2493 0.749649 CTAGCTCCAACGAGATGCCT 59.250 55.000 0.00 0.00 38.52 4.75
2183 2494 0.878086 GCTAGCTCCAACGAGATGCC 60.878 60.000 7.70 0.00 38.52 4.40
2184 2495 0.103937 AGCTAGCTCCAACGAGATGC 59.896 55.000 12.68 0.00 38.52 3.91
2185 2496 2.030363 CCTAGCTAGCTCCAACGAGATG 60.030 54.545 23.26 0.00 38.52 2.90
2186 2497 2.158593 TCCTAGCTAGCTCCAACGAGAT 60.159 50.000 23.26 0.00 38.52 2.75
2187 2498 1.212195 TCCTAGCTAGCTCCAACGAGA 59.788 52.381 23.26 5.86 38.52 4.04
2188 2499 1.681538 TCCTAGCTAGCTCCAACGAG 58.318 55.000 23.26 11.84 39.33 4.18
2189 2500 2.139323 TTCCTAGCTAGCTCCAACGA 57.861 50.000 23.26 7.73 0.00 3.85
2194 2505 3.812609 GCAAAAGATTCCTAGCTAGCTCC 59.187 47.826 23.26 4.88 0.00 4.70
2281 2605 1.930656 ATTGACCAGGGACCCAGGG 60.931 63.158 25.02 21.09 34.22 4.45
2282 2606 1.207488 TCATTGACCAGGGACCCAGG 61.207 60.000 20.31 20.31 36.18 4.45
2283 2607 0.698238 TTCATTGACCAGGGACCCAG 59.302 55.000 14.60 4.17 0.00 4.45
2284 2608 0.404040 GTTCATTGACCAGGGACCCA 59.596 55.000 14.60 0.00 0.00 4.51
2285 2609 0.323451 GGTTCATTGACCAGGGACCC 60.323 60.000 0.59 0.59 39.57 4.46
2286 2610 0.404040 TGGTTCATTGACCAGGGACC 59.596 55.000 0.00 1.09 44.53 4.46
2351 2688 6.372659 GTGATAATGCAAGTCTCTTTCTTGGA 59.627 38.462 0.00 5.29 44.50 3.53
2384 2725 6.880942 CTAGGTTAGCTAGTAGGTTGTAGG 57.119 45.833 7.27 0.00 0.00 3.18
2409 2750 0.244994 CAGTCGCTTGACAGGTAGCT 59.755 55.000 0.00 0.00 45.40 3.32
2410 2751 0.038159 ACAGTCGCTTGACAGGTAGC 60.038 55.000 0.00 0.00 45.40 3.58
2412 2753 2.159014 ACAAACAGTCGCTTGACAGGTA 60.159 45.455 0.00 0.00 45.40 3.08
2413 2754 1.299541 CAAACAGTCGCTTGACAGGT 58.700 50.000 0.00 0.00 45.40 4.00
2414 2755 1.299541 ACAAACAGTCGCTTGACAGG 58.700 50.000 0.00 0.00 45.40 4.00
2415 2756 2.708514 CAACAAACAGTCGCTTGACAG 58.291 47.619 0.00 0.00 45.40 3.51
2416 2757 1.202132 GCAACAAACAGTCGCTTGACA 60.202 47.619 0.00 0.00 45.40 3.58
2417 2758 1.202132 TGCAACAAACAGTCGCTTGAC 60.202 47.619 0.00 0.00 43.21 3.18
2418 2759 1.090728 TGCAACAAACAGTCGCTTGA 58.909 45.000 0.00 0.00 0.00 3.02
2451 2806 5.218139 GCACACAAGAAGGAAAATCAGAAG 58.782 41.667 0.00 0.00 0.00 2.85
2453 2808 3.250762 CGCACACAAGAAGGAAAATCAGA 59.749 43.478 0.00 0.00 0.00 3.27
2479 2834 3.706563 ATCGTCGAGCTGCACGCAT 62.707 57.895 14.59 3.93 42.61 4.73
2480 2835 3.914605 AATCGTCGAGCTGCACGCA 62.915 57.895 14.59 1.68 42.61 5.24
2481 2836 3.181967 AATCGTCGAGCTGCACGC 61.182 61.111 14.59 8.87 35.93 5.34
2482 2837 2.691522 CAATCGTCGAGCTGCACG 59.308 61.111 13.28 13.28 37.36 5.34
2634 2998 1.004080 TCCTCTTGCTGCTGCTGTC 60.004 57.895 17.00 1.84 40.48 3.51
2635 2999 1.302351 GTCCTCTTGCTGCTGCTGT 60.302 57.895 17.00 0.00 40.48 4.40
2689 3056 1.676746 CGAGGTAGTCGGAGATGGAA 58.323 55.000 0.00 0.00 45.58 3.53
2752 3119 4.394712 GTCTCCGGCTGTGGTGGG 62.395 72.222 0.00 0.00 0.00 4.61
2782 3152 4.394712 AGGAAGAACTGGCCGGCG 62.395 66.667 22.54 10.51 0.00 6.46
2847 3217 4.379243 CCGTCGCCTGCCTCTTGT 62.379 66.667 0.00 0.00 0.00 3.16
2938 3308 1.798368 CGCCGTTCATCATCGTCGTC 61.798 60.000 0.00 0.00 0.00 4.20
2939 3309 1.872234 CGCCGTTCATCATCGTCGT 60.872 57.895 0.00 0.00 0.00 4.34
2940 3310 2.576893 CCGCCGTTCATCATCGTCG 61.577 63.158 0.00 0.00 0.00 5.12
2974 3344 2.121963 TGGGAAGGCTGGTCTGGT 60.122 61.111 0.00 0.00 0.00 4.00
3063 3433 5.186198 AGTGAATAATCAACTAGTGTGGCC 58.814 41.667 0.00 0.00 37.30 5.36
3193 3577 4.340381 GTGTTCTTCTACTCCGGCCTATAA 59.660 45.833 0.00 0.00 0.00 0.98
3197 3581 0.896226 GTGTTCTTCTACTCCGGCCT 59.104 55.000 0.00 0.00 0.00 5.19
3198 3582 0.606604 TGTGTTCTTCTACTCCGGCC 59.393 55.000 0.00 0.00 0.00 6.13
3199 3583 2.450609 TTGTGTTCTTCTACTCCGGC 57.549 50.000 0.00 0.00 0.00 6.13
3200 3584 6.106673 ACATAATTGTGTTCTTCTACTCCGG 58.893 40.000 1.42 0.00 33.85 5.14
3201 3585 6.811665 TGACATAATTGTGTTCTTCTACTCCG 59.188 38.462 9.37 0.00 35.79 4.63
3202 3586 7.819900 AGTGACATAATTGTGTTCTTCTACTCC 59.180 37.037 9.37 0.00 35.79 3.85
3223 3619 7.936584 ACAATCAGTTCTAGCTATCTAGTGAC 58.063 38.462 0.00 2.27 42.28 3.67
3225 3621 9.278978 TCTACAATCAGTTCTAGCTATCTAGTG 57.721 37.037 0.00 0.00 42.28 2.74
3354 3751 7.899973 AGTCCAAGACTTGATTGCAATAAATT 58.100 30.769 16.99 5.40 40.28 1.82
3363 3760 4.645535 TCCAAGAGTCCAAGACTTGATTG 58.354 43.478 16.99 11.77 43.53 2.67
3366 3763 3.903714 TCATCCAAGAGTCCAAGACTTGA 59.096 43.478 16.99 0.20 43.53 3.02
3380 3777 5.271625 CAAGCTCGAATTGATTCATCCAAG 58.728 41.667 4.41 0.00 36.61 3.61
3439 3836 5.245531 TCAATTATGCACGTCTCTTTTCCT 58.754 37.500 0.00 0.00 0.00 3.36
3442 3839 6.373779 CACTTCAATTATGCACGTCTCTTTT 58.626 36.000 0.00 0.00 0.00 2.27
3712 4113 1.630148 CCTCTTTTAGGCGAGACACG 58.370 55.000 0.00 0.00 38.97 4.49
3839 4270 6.566141 TGAAATCGATTCAACCTACGTATGA 58.434 36.000 11.83 0.00 44.94 2.15
3934 4365 2.427812 TGCCAATGCACAATATCACCAG 59.572 45.455 0.00 0.00 44.23 4.00


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

AutoCloner maintained by Alex Coulton.