Multiple sequence alignment - TraesCS4A01G242000

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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 TraesCS4A01G242000 chr4A 100.000 3566 0 0 1 3566 552198461 552194896 0.000000e+00 6586.0
1 TraesCS4A01G242000 chr4A 79.513 493 88 8 3 493 552150731 552150250 4.410000e-89 339.0
2 TraesCS4A01G242000 chr4B 92.661 3134 181 22 385 3507 68360186 68363281 0.000000e+00 4468.0
3 TraesCS4A01G242000 chr4B 92.114 596 35 1 1 596 68359757 68360340 0.000000e+00 830.0
4 TraesCS4A01G242000 chr4B 78.467 613 115 12 3 611 68402687 68403286 5.580000e-103 385.0
5 TraesCS4A01G242000 chr4B 83.462 260 20 5 2787 3042 68404811 68405051 1.670000e-53 220.0
6 TraesCS4A01G242000 chr4B 92.857 84 6 0 3483 3566 68363321 68363404 4.830000e-24 122.0
7 TraesCS4A01G242000 chr4D 92.746 386 28 0 36 421 46647015 46647400 3.110000e-155 558.0
8 TraesCS4A01G242000 chr4D 79.550 489 89 6 3 490 46655458 46655936 4.410000e-89 339.0
9 TraesCS4A01G242000 chr4D 91.837 98 5 1 2786 2880 46657566 46657663 2.230000e-27 134.0
10 TraesCS4A01G242000 chr4D 97.561 41 1 0 1 41 46633971 46634011 1.780000e-08 71.3
11 TraesCS4A01G242000 chr6D 86.705 173 23 0 3136 3308 79728357 79728185 3.630000e-45 193.0
12 TraesCS4A01G242000 chr6D 83.815 173 28 0 3137 3309 446416654 446416482 7.920000e-37 165.0
13 TraesCS4A01G242000 chr1D 82.550 149 22 4 3136 3283 79820635 79820490 1.040000e-25 128.0
14 TraesCS4A01G242000 chr7A 83.761 117 15 4 3136 3249 509957408 509957523 1.350000e-19 108.0
15 TraesCS4A01G242000 chr7A 81.818 88 16 0 2632 2719 83796433 83796520 1.370000e-09 75.0
16 TraesCS4A01G242000 chr2D 95.349 43 2 0 2650 2692 644847437 644847395 6.390000e-08 69.4
17 TraesCS4A01G242000 chr3D 100.000 29 0 0 2648 2676 58596275 58596303 2.000000e-03 54.7
18 TraesCS4A01G242000 chr1A 100.000 29 0 0 2647 2675 447718739 447718767 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 TraesCS4A01G242000 chr4A 552194896 552198461 3565 True 6586.000000 6586 100.0000 1 3566 1 chr4A.!!$R2 3565
1 TraesCS4A01G242000 chr4B 68359757 68363404 3647 False 1806.666667 4468 92.5440 1 3566 3 chr4B.!!$F1 3565
2 TraesCS4A01G242000 chr4B 68402687 68405051 2364 False 302.500000 385 80.9645 3 3042 2 chr4B.!!$F2 3039
3 TraesCS4A01G242000 chr4D 46655458 46657663 2205 False 236.500000 339 85.6935 3 2880 2 chr4D.!!$F3 2877

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
663 826 0.249676 AGCTGACATGTGCTGAGAGG 59.750 55.0 1.15 0.0 38.21 3.69 F
739 902 0.471780 TTCAGGCACTCCCACTCAGA 60.472 55.0 0.00 0.0 34.60 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2454 2661 0.523072 CCACCTCATTGGCTTTCACG 59.477 55.000 0.0 0.0 40.22 4.35 R
2701 2909 2.299521 CTACTACTCCCTCCGTTCCAG 58.700 57.143 0.0 0.0 0.00 3.86 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
61 62 5.738909 TCCCAAAAGAGATCAAGCTAGAAG 58.261 41.667 0.00 0.00 0.00 2.85
138 139 2.676748 CTTAGAGCAGGATGGGAGACT 58.323 52.381 0.00 0.00 35.86 3.24
141 142 2.273619 AGAGCAGGATGGGAGACTTTT 58.726 47.619 0.00 0.00 35.86 2.27
155 156 3.783111 GACTTTTGTCGAAACCTACGG 57.217 47.619 0.00 0.00 39.89 4.02
222 223 6.870965 ACTCTCAGTTCAATGTCATAGTGTTC 59.129 38.462 0.00 0.00 0.00 3.18
249 250 0.250684 TTGGCCGTGAGAAAGCATCA 60.251 50.000 0.00 0.00 0.00 3.07
252 253 0.302890 GCCGTGAGAAAGCATCATCG 59.697 55.000 0.00 0.00 0.00 3.84
268 269 4.729227 TCATCGGTTATTGCAGACAGTA 57.271 40.909 0.00 0.00 0.00 2.74
317 318 1.009829 CACATAGGCGCTCCTGAAAC 58.990 55.000 7.64 0.00 44.08 2.78
323 324 1.172812 GGCGCTCCTGAAACTTTGGT 61.173 55.000 7.64 0.00 0.00 3.67
344 345 3.099905 TCCGTTCTCATGGTCATTCTCT 58.900 45.455 0.00 0.00 0.00 3.10
350 351 0.466922 CATGGTCATTCTCTGCCCCC 60.467 60.000 0.00 0.00 0.00 5.40
353 354 1.225704 GTCATTCTCTGCCCCCTGG 59.774 63.158 0.00 0.00 0.00 4.45
366 367 0.468771 CCCCTGGAATGCAATCTCCC 60.469 60.000 1.01 0.00 0.00 4.30
459 460 1.538047 GTTCTCAAGGGCATGCTCAA 58.462 50.000 22.09 0.97 0.00 3.02
483 484 3.423848 GCAAATGCAACTGCCTACC 57.576 52.632 11.36 0.00 41.18 3.18
501 502 3.160777 ACCGACAATATGAGACGTTCC 57.839 47.619 0.00 0.00 0.00 3.62
532 533 2.696707 CCTCAGCCCATACAAATGCAAT 59.303 45.455 0.00 0.00 0.00 3.56
567 568 4.582701 TGTGGACCATTTTGTTGATGAC 57.417 40.909 0.00 0.00 0.00 3.06
572 630 4.466828 GACCATTTTGTTGATGACAGTCG 58.533 43.478 0.00 0.00 39.94 4.18
624 778 4.872691 ACTCTGAATCGTTCTAATTGCCAG 59.127 41.667 0.00 0.00 0.00 4.85
627 781 1.680338 ATCGTTCTAATTGCCAGCCC 58.320 50.000 0.00 0.00 0.00 5.19
633 787 0.257039 CTAATTGCCAGCCCCAGTCT 59.743 55.000 0.00 0.00 0.00 3.24
663 826 0.249676 AGCTGACATGTGCTGAGAGG 59.750 55.000 1.15 0.00 38.21 3.69
739 902 0.471780 TTCAGGCACTCCCACTCAGA 60.472 55.000 0.00 0.00 34.60 3.27
758 921 7.967854 CACTCAGACTCTAGTTCTTTCATACAG 59.032 40.741 0.00 0.00 0.00 2.74
798 963 3.074412 ACTCCTTGTAAATCGCAACTGG 58.926 45.455 0.00 0.00 0.00 4.00
846 1014 7.639113 TTCAGTAATTGTTCTCCTTTTGTGT 57.361 32.000 0.00 0.00 0.00 3.72
852 1020 3.815809 TGTTCTCCTTTTGTGTACAGGG 58.184 45.455 0.00 0.00 0.00 4.45
866 1034 2.683211 ACAGGGGATTCTTTGTGCTT 57.317 45.000 0.00 0.00 0.00 3.91
867 1035 2.242043 ACAGGGGATTCTTTGTGCTTG 58.758 47.619 0.00 0.00 0.00 4.01
935 1103 2.007608 GAACACCCGTCTAAATCCAGC 58.992 52.381 0.00 0.00 0.00 4.85
943 1111 2.735444 CGTCTAAATCCAGCGCAGAAGA 60.735 50.000 11.47 3.15 0.00 2.87
989 1157 5.380043 ACATATCCCATCTGACAATCCAAC 58.620 41.667 0.00 0.00 0.00 3.77
1077 1247 4.201812 GCTGTTGAATACGCATTCTGCTAA 60.202 41.667 9.69 0.00 42.25 3.09
1151 1326 7.113658 TGAATGCTTTAAGTTGTTAAACCCA 57.886 32.000 0.00 0.00 36.94 4.51
1163 1338 6.780522 AGTTGTTAAACCCACCATGACTAAAT 59.219 34.615 0.00 0.00 36.94 1.40
1252 1427 5.772825 TGCTTGAATGCCATTATCTAACC 57.227 39.130 0.00 0.00 0.00 2.85
1288 1464 5.001232 TCTGTAATTAGAGTGTGCCCAAAC 58.999 41.667 9.28 0.00 0.00 2.93
1339 1515 2.932614 GAGCGCAACATATGTCTTCAGT 59.067 45.455 11.47 0.00 0.00 3.41
1623 1814 2.989422 AGGAAATGCAACTGCGTAAC 57.011 45.000 0.00 0.00 45.83 2.50
1639 1830 3.423123 GCGTAACGAAACAGTGGAAGATG 60.423 47.826 0.00 0.00 0.00 2.90
1656 1847 2.628178 AGATGCTATCGTTCATCCCGAA 59.372 45.455 0.00 0.00 39.79 4.30
1671 1862 1.472480 CCCGAACCCAAGCAAATACAG 59.528 52.381 0.00 0.00 0.00 2.74
1745 1936 2.096713 GCAGCAAGAGTACGACAAGTTG 60.097 50.000 0.00 0.00 0.00 3.16
1891 2098 7.012547 GGAGATTCCTTGTCATCGGAAGATAC 61.013 46.154 9.27 0.26 42.15 2.24
1914 2121 3.192001 TGATCATGAAGAAGGTGCTTTGC 59.808 43.478 0.00 0.00 0.00 3.68
2079 2286 7.612677 TCTAGTGAGTTCCAAACCTTATTCTC 58.387 38.462 0.00 0.00 0.00 2.87
2080 2287 6.441088 AGTGAGTTCCAAACCTTATTCTCT 57.559 37.500 0.00 0.00 0.00 3.10
2081 2288 7.554959 AGTGAGTTCCAAACCTTATTCTCTA 57.445 36.000 0.00 0.00 0.00 2.43
2082 2289 7.974504 AGTGAGTTCCAAACCTTATTCTCTAA 58.025 34.615 0.00 0.00 0.00 2.10
2110 2317 5.874810 TGCTTGTTCCACTAGTGATATTGAC 59.125 40.000 24.68 12.38 0.00 3.18
2119 2326 8.367911 TCCACTAGTGATATTGACCATGTATTC 58.632 37.037 24.68 0.00 0.00 1.75
2120 2327 8.150296 CCACTAGTGATATTGACCATGTATTCA 58.850 37.037 24.68 0.00 0.00 2.57
2201 2408 7.432148 ACCTGGTCATGTGAGTTTACATATA 57.568 36.000 0.00 0.00 39.17 0.86
2202 2409 7.857456 ACCTGGTCATGTGAGTTTACATATAA 58.143 34.615 0.00 0.00 39.17 0.98
2203 2410 8.494433 ACCTGGTCATGTGAGTTTACATATAAT 58.506 33.333 0.00 0.00 39.17 1.28
2204 2411 9.342308 CCTGGTCATGTGAGTTTACATATAATT 57.658 33.333 0.00 0.00 39.17 1.40
2238 2445 7.797062 AGGATTAGTGAAGGATTTAGGAAGTC 58.203 38.462 0.00 0.00 0.00 3.01
2250 2457 9.716556 AGGATTTAGGAAGTCTAGAGTGATTTA 57.283 33.333 0.00 0.00 0.00 1.40
2319 2526 9.959721 TTATTTTGAATCTGTAACTAGAGCCTT 57.040 29.630 0.00 0.00 0.00 4.35
2322 2529 6.605471 TGAATCTGTAACTAGAGCCTTTCA 57.395 37.500 0.00 0.00 0.00 2.69
2360 2567 6.255844 CAAATATTTGGGAGACGAGGTGCG 62.256 50.000 18.72 0.00 39.10 5.34
2400 2607 1.272490 CTTGGCGAGAGGTGTCAAGTA 59.728 52.381 0.00 0.00 32.59 2.24
2414 2621 2.159627 GTCAAGTATGGTTTGGACGCAG 59.840 50.000 0.00 0.00 0.00 5.18
2434 2641 4.446311 GCAGGCCTCAGGATAAAAGGATTA 60.446 45.833 0.00 0.00 31.44 1.75
2454 2661 2.396590 TAGGCGGATGGACAAAGTTC 57.603 50.000 0.00 0.00 0.00 3.01
2481 2688 1.207488 CCAATGAGGTGGAGGTGGGA 61.207 60.000 0.00 0.00 41.65 4.37
2523 2730 2.095059 GCTGAAGCATCGGAAATTGTGT 60.095 45.455 0.99 0.00 41.59 3.72
2550 2757 2.238942 AAGTTCATATCATCCGCGCA 57.761 45.000 8.75 0.00 0.00 6.09
2606 2813 6.774673 TGATTTATCTTGAGGTGGTGTGTAA 58.225 36.000 0.00 0.00 0.00 2.41
2633 2840 5.106555 CCTTTTGTGCTGTTAGGATGTAGTG 60.107 44.000 0.00 0.00 0.00 2.74
2641 2848 4.606210 TGTTAGGATGTAGTGCTACCTCA 58.394 43.478 13.74 0.00 33.97 3.86
2701 2909 9.944663 TTTGAAGTAACATCACAACAAGTATTC 57.055 29.630 0.00 0.00 0.00 1.75
2762 2970 7.229506 GCCTATCTGTCCTTGTTATTTTGCTAT 59.770 37.037 0.00 0.00 0.00 2.97
2764 2972 6.662414 TCTGTCCTTGTTATTTTGCTATCG 57.338 37.500 0.00 0.00 0.00 2.92
2785 2993 1.063642 TGGACACATGTTGGGGAACAA 60.064 47.619 0.00 0.00 36.12 2.83
3159 3377 9.508642 TTGGAGTTGTTTATTTTTCTTTTTGGT 57.491 25.926 0.00 0.00 0.00 3.67
3160 3378 8.940952 TGGAGTTGTTTATTTTTCTTTTTGGTG 58.059 29.630 0.00 0.00 0.00 4.17
3161 3379 8.941977 GGAGTTGTTTATTTTTCTTTTTGGTGT 58.058 29.630 0.00 0.00 0.00 4.16
3162 3380 9.967245 GAGTTGTTTATTTTTCTTTTTGGTGTC 57.033 29.630 0.00 0.00 0.00 3.67
3163 3381 8.652463 AGTTGTTTATTTTTCTTTTTGGTGTCG 58.348 29.630 0.00 0.00 0.00 4.35
3164 3382 8.648968 GTTGTTTATTTTTCTTTTTGGTGTCGA 58.351 29.630 0.00 0.00 0.00 4.20
3165 3383 8.175649 TGTTTATTTTTCTTTTTGGTGTCGAC 57.824 30.769 9.11 9.11 0.00 4.20
3168 3386 6.885735 ATTTTTCTTTTTGGTGTCGACTTG 57.114 33.333 17.92 0.00 0.00 3.16
3169 3387 5.379732 TTTTCTTTTTGGTGTCGACTTGT 57.620 34.783 17.92 0.00 0.00 3.16
3170 3388 6.497785 TTTTCTTTTTGGTGTCGACTTGTA 57.502 33.333 17.92 0.00 0.00 2.41
3176 3394 6.533819 TTTTGGTGTCGACTTGTAACATAG 57.466 37.500 17.92 0.00 0.00 2.23
3192 3410 7.299896 TGTAACATAGGGTTAGTGGCTATCTA 58.700 38.462 0.00 0.00 42.44 1.98
3193 3411 7.785985 TGTAACATAGGGTTAGTGGCTATCTAA 59.214 37.037 0.00 0.00 42.44 2.10
3208 3426 7.171678 GTGGCTATCTAATGGAGTTATTGTCAC 59.828 40.741 0.00 0.00 0.00 3.67
3219 3437 1.655484 TATTGTCACGAGGCATGCAG 58.345 50.000 21.36 12.58 0.00 4.41
3237 3455 2.742774 CAGCCTTGGGTTTTCTTTTCG 58.257 47.619 0.00 0.00 0.00 3.46
3248 3466 5.118050 GGGTTTTCTTTTCGCTTTATTTCCG 59.882 40.000 0.00 0.00 0.00 4.30
3270 3488 0.250945 TTGATGTTGCCCGGTTGCTA 60.251 50.000 0.00 0.00 0.00 3.49
3280 3498 1.463674 CCGGTTGCTAGATTTTGCCT 58.536 50.000 0.00 0.00 0.00 4.75
3307 3525 7.770433 TCCTAATAATATATGGCTGTGTGCATC 59.230 37.037 0.00 0.00 45.15 3.91
3313 3532 3.503363 GCTGTGTGCATCGAGCCC 61.503 66.667 0.00 0.00 44.83 5.19
3373 3592 9.905713 TCATCTAATAAGAGCCTTGTACATTTT 57.094 29.630 0.00 0.00 34.49 1.82
3400 3619 9.606631 CTCTAATAAGAGCCTTGTACATTTTCT 57.393 33.333 0.00 0.00 42.79 2.52
3401 3620 9.601217 TCTAATAAGAGCCTTGTACATTTTCTC 57.399 33.333 0.00 1.84 0.00 2.87
3402 3621 9.606631 CTAATAAGAGCCTTGTACATTTTCTCT 57.393 33.333 0.00 4.18 0.00 3.10
3404 3623 9.959721 AATAAGAGCCTTGTACATTTTCTCTAA 57.040 29.630 13.98 1.40 0.00 2.10
3405 3624 9.959721 ATAAGAGCCTTGTACATTTTCTCTAAA 57.040 29.630 13.98 8.76 0.00 1.85
3406 3625 8.691661 AAGAGCCTTGTACATTTTCTCTAAAA 57.308 30.769 13.98 0.00 38.87 1.52
3407 3626 8.691661 AGAGCCTTGTACATTTTCTCTAAAAA 57.308 30.769 12.72 0.00 38.07 1.94
3408 3627 8.787852 AGAGCCTTGTACATTTTCTCTAAAAAG 58.212 33.333 12.72 0.00 38.07 2.27
3409 3628 8.691661 AGCCTTGTACATTTTCTCTAAAAAGA 57.308 30.769 0.00 0.00 38.07 2.52
3444 3663 0.573279 ATGCCACCCCTAGACCCTAT 59.427 55.000 0.00 0.00 0.00 2.57
3479 3698 4.946157 CCAAGCAACAATGTATCTCTTCCT 59.054 41.667 0.00 0.00 0.00 3.36
3480 3699 5.065731 CCAAGCAACAATGTATCTCTTCCTC 59.934 44.000 0.00 0.00 0.00 3.71
3510 3793 2.025226 TCCTACCCTGAGAATCGACACT 60.025 50.000 0.00 0.00 38.61 3.55
3512 3795 2.223803 ACCCTGAGAATCGACACTCT 57.776 50.000 17.49 7.53 38.61 3.24
3546 3829 4.212214 GGCTACAAACTCCAATCGATGATC 59.788 45.833 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 5.965334 CAGTGTAAATATGACCATTTCGTGC 59.035 40.000 0.00 0.00 30.84 5.34
153 154 1.258458 GAGTCGTCGATCTGTAGACCG 59.742 57.143 0.00 0.00 34.10 4.79
155 156 3.579147 CAGAGTCGTCGATCTGTAGAC 57.421 52.381 18.64 1.96 38.49 2.59
222 223 0.527600 TCTCACGGCCAAATCGATCG 60.528 55.000 9.36 9.36 0.00 3.69
249 250 4.441634 GGAGTACTGTCTGCAATAACCGAT 60.442 45.833 0.00 0.00 0.00 4.18
252 253 4.160626 AGAGGAGTACTGTCTGCAATAACC 59.839 45.833 0.00 0.00 0.00 2.85
268 269 2.763448 GCACATAAGGAGACAGAGGAGT 59.237 50.000 0.00 0.00 0.00 3.85
278 279 2.019984 GCCTTTCCTGCACATAAGGAG 58.980 52.381 16.36 0.00 44.58 3.69
302 303 1.610624 CCAAAGTTTCAGGAGCGCCTA 60.611 52.381 9.34 0.00 44.80 3.93
317 318 2.076863 GACCATGAGAACGGACCAAAG 58.923 52.381 0.00 0.00 0.00 2.77
323 324 3.099905 AGAGAATGACCATGAGAACGGA 58.900 45.455 0.00 0.00 0.00 4.69
344 345 1.381599 GATTGCATTCCAGGGGGCA 60.382 57.895 0.00 0.00 0.00 5.36
350 351 2.022195 CAGTGGGAGATTGCATTCCAG 58.978 52.381 12.73 0.00 35.09 3.86
353 354 4.789012 TTTTCAGTGGGAGATTGCATTC 57.211 40.909 0.16 0.16 0.00 2.67
366 367 9.350357 CCTTGAGAAATATTCACATTTTCAGTG 57.650 33.333 0.00 0.00 38.32 3.66
501 502 2.203126 GGCTGAGGATGCCCTTCG 60.203 66.667 0.00 0.00 44.53 3.79
567 568 1.074319 GCATTTGCATGTGCCGACTG 61.074 55.000 11.60 0.00 41.18 3.51
624 778 1.941999 GCATTTGCAGAGACTGGGGC 61.942 60.000 0.00 0.00 41.59 5.80
663 826 6.992063 TTATTCCTCTGAAGATTTGACTGC 57.008 37.500 0.00 0.00 33.05 4.40
739 902 8.421784 TCACAAACTGTATGAAAGAACTAGAGT 58.578 33.333 0.00 0.00 0.00 3.24
773 936 6.537301 CCAGTTGCGATTTACAAGGAGTTATA 59.463 38.462 0.00 0.00 0.00 0.98
798 963 9.722056 GAATATATCAATTGAAGGTGACAACAC 57.278 33.333 13.09 0.00 45.27 3.32
833 1001 3.050089 TCCCCTGTACACAAAAGGAGAA 58.950 45.455 0.00 0.00 32.43 2.87
846 1014 3.420893 CAAGCACAAAGAATCCCCTGTA 58.579 45.455 0.00 0.00 0.00 2.74
852 1020 4.460382 TCATCTTCCAAGCACAAAGAATCC 59.540 41.667 0.00 0.00 33.10 3.01
891 1059 3.451178 ACCCAAGCGTGTATCTAGATGTT 59.549 43.478 15.79 0.00 0.00 2.71
935 1103 2.872245 TGGTCAACTTTCTTCTTCTGCG 59.128 45.455 0.00 0.00 0.00 5.18
964 1132 5.624159 TGGATTGTCAGATGGGATATGTTC 58.376 41.667 0.00 0.00 0.00 3.18
989 1157 0.458669 GCTCATCATGGCCACAAAGG 59.541 55.000 8.16 0.00 41.84 3.11
1077 1247 1.103398 AAACGGCTTGCTGCAGACTT 61.103 50.000 20.43 0.00 45.15 3.01
1139 1314 6.394025 TTTAGTCATGGTGGGTTTAACAAC 57.606 37.500 0.00 0.00 0.00 3.32
1200 1375 6.753744 GCAGAACAGAATAACATTTCAATCCC 59.246 38.462 0.00 0.00 0.00 3.85
1481 1657 1.374125 TGGACTTCCATCGTGCACG 60.374 57.895 32.76 32.76 42.01 5.34
1623 1814 3.243877 CGATAGCATCTTCCACTGTTTCG 59.756 47.826 0.00 0.00 0.00 3.46
1656 1847 1.256812 GTGGCTGTATTTGCTTGGGT 58.743 50.000 0.00 0.00 0.00 4.51
1661 1852 1.271379 ACGAAGGTGGCTGTATTTGCT 60.271 47.619 0.00 0.00 0.00 3.91
1671 1862 0.591659 GTCTTTCCAACGAAGGTGGC 59.408 55.000 0.00 0.00 0.00 5.01
1745 1936 4.160626 ACCAGATGACTTAGCAGTAGGAAC 59.839 45.833 0.00 0.00 31.22 3.62
1891 2098 4.674623 GCAAAGCACCTTCTTCATGATCAG 60.675 45.833 0.09 0.00 0.00 2.90
2079 2286 8.668510 ATCACTAGTGGAACAAGCATTATTAG 57.331 34.615 22.48 0.00 44.16 1.73
2081 2288 9.632638 AATATCACTAGTGGAACAAGCATTATT 57.367 29.630 22.48 7.88 44.16 1.40
2082 2289 9.060347 CAATATCACTAGTGGAACAAGCATTAT 57.940 33.333 22.48 6.76 44.16 1.28
2110 2317 8.843885 AGAACACATGATAGATGAATACATGG 57.156 34.615 0.00 0.00 41.41 3.66
2119 2326 7.854557 TCCAAGAAAGAACACATGATAGATG 57.145 36.000 0.00 0.00 0.00 2.90
2120 2327 8.270030 TGATCCAAGAAAGAACACATGATAGAT 58.730 33.333 0.00 0.00 0.00 1.98
2201 2408 7.569111 TCCTTCACTAATCCTAGGAAGCTAATT 59.431 37.037 17.30 6.93 34.43 1.40
2202 2409 7.076446 TCCTTCACTAATCCTAGGAAGCTAAT 58.924 38.462 17.30 0.00 34.43 1.73
2203 2410 6.441222 TCCTTCACTAATCCTAGGAAGCTAA 58.559 40.000 17.30 6.72 34.43 3.09
2204 2411 6.027025 TCCTTCACTAATCCTAGGAAGCTA 57.973 41.667 17.30 6.98 34.43 3.32
2205 2412 4.884961 TCCTTCACTAATCCTAGGAAGCT 58.115 43.478 17.30 6.09 34.43 3.74
2206 2413 5.816955 ATCCTTCACTAATCCTAGGAAGC 57.183 43.478 17.30 0.00 38.42 3.86
2207 2414 8.371699 CCTAAATCCTTCACTAATCCTAGGAAG 58.628 40.741 17.30 12.37 38.42 3.46
2293 2500 9.959721 AAGGCTCTAGTTACAGATTCAAAATAA 57.040 29.630 0.00 0.00 0.00 1.40
2334 2541 5.878116 CACCTCGTCTCCCAAATATTTGTTA 59.122 40.000 23.24 11.98 36.45 2.41
2340 2547 1.202533 CGCACCTCGTCTCCCAAATAT 60.203 52.381 0.00 0.00 0.00 1.28
2352 2559 2.584418 CAGATGCTCCGCACCTCG 60.584 66.667 0.00 0.00 43.04 4.63
2360 2567 2.178890 CGCTCAAGGCAGATGCTCC 61.179 63.158 4.59 0.00 41.91 4.70
2370 2577 2.048222 TCGCCAAGTCGCTCAAGG 60.048 61.111 0.00 0.00 0.00 3.61
2400 2607 2.676471 GGCCTGCGTCCAAACCAT 60.676 61.111 0.00 0.00 0.00 3.55
2414 2621 6.418946 CCTATAATCCTTTTATCCTGAGGCC 58.581 44.000 0.00 0.00 0.00 5.19
2434 2641 2.741878 CGAACTTTGTCCATCCGCCTAT 60.742 50.000 0.00 0.00 0.00 2.57
2454 2661 0.523072 CCACCTCATTGGCTTTCACG 59.477 55.000 0.00 0.00 40.22 4.35
2523 2730 4.516321 CGGATGATATGAACTTTCATGGCA 59.484 41.667 13.67 11.34 46.68 4.92
2550 2757 6.218746 GCATTTTGATCAACTGAAGTCCTTT 58.781 36.000 17.39 0.00 0.00 3.11
2606 2813 3.806949 TCCTAACAGCACAAAAGGGAT 57.193 42.857 0.00 0.00 0.00 3.85
2633 2840 7.411588 CGACAAGTATTTTGTTACTGAGGTAGC 60.412 40.741 0.00 0.00 32.78 3.58
2687 2895 4.062293 CCGTTCCAGAATACTTGTTGTGA 58.938 43.478 0.00 0.00 0.00 3.58
2701 2909 2.299521 CTACTACTCCCTCCGTTCCAG 58.700 57.143 0.00 0.00 0.00 3.86
2711 2919 7.683945 GCATAAACAGAGTAACCTACTACTCCC 60.684 44.444 7.06 0.00 46.10 4.30
2762 2970 1.072332 CCCCAACATGTGTCCACGA 59.928 57.895 0.00 0.00 0.00 4.35
2764 2972 0.958822 GTTCCCCAACATGTGTCCAC 59.041 55.000 0.00 0.00 32.14 4.02
2938 3152 8.978472 AGATAACAAATGCACTACCTAGTTCTA 58.022 33.333 0.00 0.00 33.46 2.10
3021 3239 2.615912 GCTGCCTGCTCCTAAATAGTTG 59.384 50.000 0.00 0.00 38.95 3.16
3023 3241 1.839994 TGCTGCCTGCTCCTAAATAGT 59.160 47.619 0.00 0.00 43.37 2.12
3046 3264 4.286032 ACATGGTTAGACAACTAGGCAGAA 59.714 41.667 0.00 0.00 30.89 3.02
3158 3376 4.184079 ACCCTATGTTACAAGTCGACAC 57.816 45.455 19.50 7.19 0.00 3.67
3159 3377 4.877378 AACCCTATGTTACAAGTCGACA 57.123 40.909 19.50 0.00 34.69 4.35
3160 3378 5.803967 CACTAACCCTATGTTACAAGTCGAC 59.196 44.000 7.70 7.70 38.42 4.20
3161 3379 5.105635 CCACTAACCCTATGTTACAAGTCGA 60.106 44.000 0.00 0.00 38.42 4.20
3162 3380 5.107133 CCACTAACCCTATGTTACAAGTCG 58.893 45.833 0.00 0.00 38.42 4.18
3163 3381 4.874396 GCCACTAACCCTATGTTACAAGTC 59.126 45.833 0.00 0.00 38.42 3.01
3164 3382 4.534897 AGCCACTAACCCTATGTTACAAGT 59.465 41.667 0.00 0.00 38.42 3.16
3165 3383 5.099042 AGCCACTAACCCTATGTTACAAG 57.901 43.478 0.00 0.00 38.42 3.16
3168 3386 6.667558 AGATAGCCACTAACCCTATGTTAC 57.332 41.667 0.00 0.00 38.42 2.50
3169 3387 8.812972 CATTAGATAGCCACTAACCCTATGTTA 58.187 37.037 0.00 0.00 38.42 2.41
3170 3388 7.256691 CCATTAGATAGCCACTAACCCTATGTT 60.257 40.741 0.00 0.00 41.11 2.71
3176 3394 4.593634 ACTCCATTAGATAGCCACTAACCC 59.406 45.833 0.00 0.00 33.58 4.11
3192 3410 3.270877 GCCTCGTGACAATAACTCCATT 58.729 45.455 0.00 0.00 0.00 3.16
3193 3411 2.236146 TGCCTCGTGACAATAACTCCAT 59.764 45.455 0.00 0.00 0.00 3.41
3219 3437 1.068588 AGCGAAAAGAAAACCCAAGGC 59.931 47.619 0.00 0.00 0.00 4.35
3223 3441 5.986741 GGAAATAAAGCGAAAAGAAAACCCA 59.013 36.000 0.00 0.00 0.00 4.51
3237 3455 4.173256 CAACATCAACCCGGAAATAAAGC 58.827 43.478 0.73 0.00 0.00 3.51
3248 3466 1.906333 AACCGGGCAACATCAACCC 60.906 57.895 6.32 0.00 40.51 4.11
3280 3498 7.457561 TGCACACAGCCATATATTATTAGGAA 58.542 34.615 0.00 0.00 44.83 3.36
3341 3560 7.406104 ACAAGGCTCTTATTAGATGAAACCTT 58.594 34.615 0.00 0.00 32.29 3.50
3342 3561 6.963322 ACAAGGCTCTTATTAGATGAAACCT 58.037 36.000 0.00 0.00 0.00 3.50
3380 3599 9.787435 TTTTAGAGAAAATGTACAAGGCTCTTA 57.213 29.630 19.28 11.87 33.69 2.10
3395 3614 9.998106 ACAGCTATGTACTCTTTTTAGAGAAAA 57.002 29.630 9.03 0.00 38.09 2.29
3402 3621 9.261180 GCATCATACAGCTATGTACTCTTTTTA 57.739 33.333 0.00 0.00 44.51 1.52
3403 3622 7.227512 GGCATCATACAGCTATGTACTCTTTTT 59.772 37.037 0.00 0.00 44.51 1.94
3404 3623 6.708054 GGCATCATACAGCTATGTACTCTTTT 59.292 38.462 0.00 0.00 44.51 2.27
3405 3624 6.183361 TGGCATCATACAGCTATGTACTCTTT 60.183 38.462 0.00 0.00 44.51 2.52
3406 3625 5.305386 TGGCATCATACAGCTATGTACTCTT 59.695 40.000 0.00 0.00 44.51 2.85
3407 3626 4.835056 TGGCATCATACAGCTATGTACTCT 59.165 41.667 0.00 0.00 44.51 3.24
3408 3627 4.926238 GTGGCATCATACAGCTATGTACTC 59.074 45.833 0.00 0.00 44.51 2.59
3409 3628 4.262635 GGTGGCATCATACAGCTATGTACT 60.263 45.833 0.00 0.00 44.51 2.73
3413 3632 2.430465 GGGTGGCATCATACAGCTATG 58.570 52.381 0.00 0.00 35.56 2.23
3420 3639 1.348036 GGTCTAGGGGTGGCATCATAC 59.652 57.143 0.00 0.00 0.00 2.39
3444 3663 7.215789 ACATTGTTGCTTGGTTGATAATGAAA 58.784 30.769 0.00 0.00 0.00 2.69
3479 3698 3.715315 TCTCAGGGTAGGAGAATAGACGA 59.285 47.826 0.00 0.00 38.40 4.20
3480 3699 4.088056 TCTCAGGGTAGGAGAATAGACG 57.912 50.000 0.00 0.00 38.40 4.18
3510 3793 1.324383 TGTAGCCACGACACTCAAGA 58.676 50.000 0.00 0.00 0.00 3.02
3512 3795 2.159014 AGTTTGTAGCCACGACACTCAA 60.159 45.455 0.00 0.00 0.00 3.02
3519 3802 2.695359 GATTGGAGTTTGTAGCCACGA 58.305 47.619 0.00 0.00 0.00 4.35
3521 3804 2.695359 TCGATTGGAGTTTGTAGCCAC 58.305 47.619 0.00 0.00 0.00 5.01
3546 3829 4.727725 CGTCTCGCGGATCTATCG 57.272 61.111 6.13 0.00 36.85 2.92


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

AutoCloner maintained by Alex Coulton.