Multiple sequence alignment - TraesCS1B01G020800

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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 TraesCS1B01G020800 chr1B 100.000 3905 0 0 1 3905 9646370 9650274 0.000000e+00 7212
1 TraesCS1B01G020800 chr1B 78.866 1869 333 52 969 2813 592367267 592365437 0.000000e+00 1206
2 TraesCS1B01G020800 chr1B 97.260 73 2 0 3448 3520 9516087 9516159 1.470000e-24 124
3 TraesCS1B01G020800 chr1A 94.125 3166 146 23 1 3160 9534047 9530916 0.000000e+00 4780
4 TraesCS1B01G020800 chr1A 78.627 1806 323 51 1030 2813 534275261 534277025 0.000000e+00 1138
5 TraesCS1B01G020800 chr1A 88.696 690 41 13 3210 3887 9530916 9530252 0.000000e+00 808
6 TraesCS1B01G020800 chr1D 94.148 3110 145 23 1 3094 7371029 7374117 0.000000e+00 4700
7 TraesCS1B01G020800 chr1D 77.860 2019 366 67 969 2953 437293040 437291069 0.000000e+00 1177
8 TraesCS1B01G020800 chr1D 91.875 320 10 5 3202 3520 7374124 7374428 2.160000e-117 433
9 TraesCS1B01G020800 chr2B 82.979 517 75 9 989 1503 785984566 785984061 4.600000e-124 455
10 TraesCS1B01G020800 chr2B 80.418 526 85 12 1002 1519 775385749 775386264 6.120000e-103 385
11 TraesCS1B01G020800 chr5D 80.897 513 84 11 1017 1519 41878429 41877921 3.660000e-105 392
12 TraesCS1B01G020800 chr2D 79.808 520 89 11 1008 1519 631983066 631983577 7.970000e-97 364
13 TraesCS1B01G020800 chr3D 76.993 552 98 18 1015 1543 514681196 514680651 4.940000e-74 289
14 TraesCS1B01G020800 chr3A 85.171 263 39 0 1246 1508 709070302 709070040 1.790000e-68 270


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 TraesCS1B01G020800 chr1B 9646370 9650274 3904 False 7212.0 7212 100.0000 1 3905 1 chr1B.!!$F2 3904
1 TraesCS1B01G020800 chr1B 592365437 592367267 1830 True 1206.0 1206 78.8660 969 2813 1 chr1B.!!$R1 1844
2 TraesCS1B01G020800 chr1A 9530252 9534047 3795 True 2794.0 4780 91.4105 1 3887 2 chr1A.!!$R1 3886
3 TraesCS1B01G020800 chr1A 534275261 534277025 1764 False 1138.0 1138 78.6270 1030 2813 1 chr1A.!!$F1 1783
4 TraesCS1B01G020800 chr1D 7371029 7374428 3399 False 2566.5 4700 93.0115 1 3520 2 chr1D.!!$F1 3519
5 TraesCS1B01G020800 chr1D 437291069 437293040 1971 True 1177.0 1177 77.8600 969 2953 1 chr1D.!!$R1 1984
6 TraesCS1B01G020800 chr2B 785984061 785984566 505 True 455.0 455 82.9790 989 1503 1 chr2B.!!$R1 514
7 TraesCS1B01G020800 chr2B 775385749 775386264 515 False 385.0 385 80.4180 1002 1519 1 chr2B.!!$F1 517
8 TraesCS1B01G020800 chr5D 41877921 41878429 508 True 392.0 392 80.8970 1017 1519 1 chr5D.!!$R1 502
9 TraesCS1B01G020800 chr2D 631983066 631983577 511 False 364.0 364 79.8080 1008 1519 1 chr2D.!!$F1 511
10 TraesCS1B01G020800 chr3D 514680651 514681196 545 True 289.0 289 76.9930 1015 1543 1 chr3D.!!$R1 528

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
262 264 0.958091 GCCAAACTGTGTGCACCATA 59.042 50.0 15.69 0.0 0.0 2.74 F
445 451 1.048601 CATACGGCTATGTCCCCTGT 58.951 55.0 0.00 0.0 0.0 4.00 F
1644 1686 1.086696 CCGAGTGTAGCATGTTTGGG 58.913 55.0 0.00 0.0 0.0 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1426 1468 1.394618 AACACAAAGCTACCCGCAAA 58.605 45.0 0.0 0.0 42.61 3.68 R
2279 2330 0.461339 TCCTTGGGCTTTATCGTCGC 60.461 55.0 0.0 0.0 0.00 5.19 R
3196 3256 0.165944 GCACATGCGGACACTTACAC 59.834 55.0 0.0 0.0 0.00 2.90 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 6.795098 CTTGGCAGTATTTATTATACGCCA 57.205 37.500 19.59 19.59 44.25 5.69
28 29 7.283580 TGGCAGTATTTATTATACGCCAAAACT 59.716 33.333 20.45 0.00 43.67 2.66
33 34 7.648039 ATTTATTATACGCCAAAACTGGGAA 57.352 32.000 0.00 0.00 0.00 3.97
126 127 1.538419 GGTCGTTCGATCCCAAGATCC 60.538 57.143 0.00 0.00 45.32 3.36
130 131 2.737359 CGTTCGATCCCAAGATCCGAAA 60.737 50.000 0.00 0.00 45.32 3.46
147 148 2.677037 CGAAACCTTTATCCCACGAGCT 60.677 50.000 0.00 0.00 0.00 4.09
153 154 0.975556 TTATCCCACGAGCTGAGCCA 60.976 55.000 0.00 0.00 0.00 4.75
220 222 3.118775 TGAGTATATGCCGTGTCAAGCTT 60.119 43.478 0.00 0.00 0.00 3.74
221 223 3.198068 AGTATATGCCGTGTCAAGCTTG 58.802 45.455 20.81 20.81 0.00 4.01
243 245 3.067106 ACACAATGCTACTTCGGAAGTG 58.933 45.455 28.81 19.99 42.84 3.16
260 262 1.680314 TGCCAAACTGTGTGCACCA 60.680 52.632 15.69 10.97 31.10 4.17
262 264 0.958091 GCCAAACTGTGTGCACCATA 59.042 50.000 15.69 0.00 0.00 2.74
285 290 3.773119 ACCCTTTAAATCTGAGGCGTCTA 59.227 43.478 8.06 0.00 0.00 2.59
336 341 6.465894 GGTTCTACCATCCCTTTATGCTATGT 60.466 42.308 0.00 0.00 38.42 2.29
340 345 3.828451 CCATCCCTTTATGCTATGTTGGG 59.172 47.826 0.00 0.00 34.76 4.12
363 368 7.039363 TGGGTTTTTAGTTTGTCTATGAATGGG 60.039 37.037 0.00 0.00 0.00 4.00
400 406 6.798482 ACTCACATGCAAATTACCATACATG 58.202 36.000 0.00 0.00 40.48 3.21
436 442 6.664714 AGTAGGAGACATATCATACGGCTAT 58.335 40.000 0.00 0.00 40.48 2.97
437 443 5.843673 AGGAGACATATCATACGGCTATG 57.156 43.478 0.00 0.00 0.00 2.23
443 449 2.327325 ATCATACGGCTATGTCCCCT 57.673 50.000 0.00 0.00 32.76 4.79
445 451 1.048601 CATACGGCTATGTCCCCTGT 58.951 55.000 0.00 0.00 0.00 4.00
578 594 3.055312 GGGTTTTAGGACCTACAGGAGTG 60.055 52.174 0.00 0.00 39.71 3.51
586 602 3.181464 GGACCTACAGGAGTGATTAAGCC 60.181 52.174 1.29 0.00 38.94 4.35
597 613 2.093658 GTGATTAAGCCGGAGTCTTCCA 60.094 50.000 5.05 0.00 44.26 3.53
605 621 1.192146 CGGAGTCTTCCAAGGTCCCA 61.192 60.000 0.00 0.00 44.26 4.37
636 652 4.074970 AGCTAGACAATCACTTGGTTTGG 58.925 43.478 0.00 0.00 36.64 3.28
715 731 7.775397 AATTCCTCTTGTTTGTTCATTTGTG 57.225 32.000 0.00 0.00 0.00 3.33
848 865 4.754322 TCCAGTTTTTCTTGAGCCAAAAC 58.246 39.130 8.92 8.92 39.63 2.43
854 871 7.323416 CAGTTTTTCTTGAGCCAAAACAAAAAC 59.677 33.333 19.25 19.25 41.09 2.43
855 872 6.867662 TTTTCTTGAGCCAAAACAAAAACA 57.132 29.167 0.00 0.00 0.00 2.83
856 873 7.446001 TTTTCTTGAGCCAAAACAAAAACAT 57.554 28.000 0.00 0.00 0.00 2.71
858 875 6.419980 TCTTGAGCCAAAACAAAAACATTG 57.580 33.333 0.00 0.00 0.00 2.82
861 878 5.435291 TGAGCCAAAACAAAAACATTGGAT 58.565 33.333 7.53 0.49 43.69 3.41
862 879 6.586344 TGAGCCAAAACAAAAACATTGGATA 58.414 32.000 7.53 0.00 41.29 2.59
863 880 7.222872 TGAGCCAAAACAAAAACATTGGATAT 58.777 30.769 7.53 0.00 41.29 1.63
882 899 9.820725 TTGGATATTATTTCCTCATTGCAAAAG 57.179 29.630 1.71 4.08 34.17 2.27
1426 1468 5.221244 GGAAAACACAGTGCAAACCTTCTAT 60.221 40.000 0.00 0.00 0.00 1.98
1470 1512 5.593909 TGTTGCTGGAATTATCAAGTATGGG 59.406 40.000 0.00 0.00 0.00 4.00
1593 1635 1.166531 GGTTTGTCCGTGCTGCTCTT 61.167 55.000 0.00 0.00 0.00 2.85
1630 1672 8.595362 TCATACCATTGATATCTTATCCGAGT 57.405 34.615 3.98 0.00 0.00 4.18
1644 1686 1.086696 CCGAGTGTAGCATGTTTGGG 58.913 55.000 0.00 0.00 0.00 4.12
1879 1921 8.200024 AGCTGACACTATCATTACCTATTCAT 57.800 34.615 0.00 0.00 36.48 2.57
1960 2002 2.374839 TGGACATGGACATGGTTGAAGA 59.625 45.455 15.94 0.00 42.91 2.87
2340 2391 5.276963 CCATGTGAAAACAGCAATGAACAAC 60.277 40.000 0.00 0.00 0.00 3.32
2351 2402 4.342092 AGCAATGAACAACTGCCTTAAAGT 59.658 37.500 8.07 0.00 36.73 2.66
2401 2452 6.073331 GCATCTATTAACTGAGGCACATCTTC 60.073 42.308 10.13 0.00 39.42 2.87
2461 2512 0.911769 TCCAAGGGCAGATGTACCTG 59.088 55.000 0.00 0.00 34.17 4.00
2512 2566 8.100791 AGCTTTCAAACTACATGATGTACCTTA 58.899 33.333 0.23 0.00 0.00 2.69
2685 2739 1.234615 GGCTCCTTGTTTACGCTGCA 61.235 55.000 0.00 0.00 0.00 4.41
2766 2820 2.591753 GCCTGGCTACTCATGGCA 59.408 61.111 12.43 0.00 42.79 4.92
2823 2877 8.057623 AGATTCCATCTTACCACTGATGATTTT 58.942 33.333 0.00 0.00 41.69 1.82
2844 2904 2.948979 TCATGCGGAAACAAACTTGACT 59.051 40.909 0.00 0.00 0.00 3.41
2848 2908 4.854399 TGCGGAAACAAACTTGACTAATG 58.146 39.130 0.00 0.00 0.00 1.90
2877 2937 5.163457 CCTCTTCTATGTTCCCTCAGAAGAC 60.163 48.000 8.43 0.00 44.92 3.01
2895 2955 3.378512 AGACCAGATATCAGGTGCTGAA 58.621 45.455 23.28 0.00 44.04 3.02
3128 3188 1.200716 TGTCGACCTTCCATACGTGTC 59.799 52.381 14.12 0.00 0.00 3.67
3129 3189 2.939782 CGACCTTCCATACGTGTCG 58.060 57.895 7.76 7.76 42.13 4.35
3140 3200 2.424705 TACGTGTCGGGGTGTGCTTC 62.425 60.000 0.00 0.00 0.00 3.86
3159 3219 3.004752 TCAGCCTTTCCATTAAGCCTC 57.995 47.619 0.00 0.00 0.00 4.70
3160 3220 2.027385 CAGCCTTTCCATTAAGCCTCC 58.973 52.381 0.00 0.00 0.00 4.30
3161 3221 1.925959 AGCCTTTCCATTAAGCCTCCT 59.074 47.619 0.00 0.00 0.00 3.69
3162 3222 3.117888 CAGCCTTTCCATTAAGCCTCCTA 60.118 47.826 0.00 0.00 0.00 2.94
3163 3223 3.724209 AGCCTTTCCATTAAGCCTCCTAT 59.276 43.478 0.00 0.00 0.00 2.57
3164 3224 3.823304 GCCTTTCCATTAAGCCTCCTATG 59.177 47.826 0.00 0.00 0.00 2.23
3165 3225 4.446311 GCCTTTCCATTAAGCCTCCTATGA 60.446 45.833 0.00 0.00 0.00 2.15
3166 3226 5.694995 CCTTTCCATTAAGCCTCCTATGAA 58.305 41.667 0.00 0.00 0.00 2.57
3167 3227 6.310149 CCTTTCCATTAAGCCTCCTATGAAT 58.690 40.000 0.00 0.00 0.00 2.57
3168 3228 6.432472 CCTTTCCATTAAGCCTCCTATGAATC 59.568 42.308 0.00 0.00 0.00 2.52
3169 3229 6.514012 TTCCATTAAGCCTCCTATGAATCA 57.486 37.500 0.00 0.00 0.00 2.57
3170 3230 6.708885 TCCATTAAGCCTCCTATGAATCAT 57.291 37.500 0.00 0.00 0.00 2.45
3171 3231 7.813087 TCCATTAAGCCTCCTATGAATCATA 57.187 36.000 2.68 2.68 0.00 2.15
3172 3232 7.855375 TCCATTAAGCCTCCTATGAATCATAG 58.145 38.462 20.37 20.37 42.28 2.23
3289 3349 2.584835 AAGGCACCACATCTTTGCTA 57.415 45.000 0.00 0.00 36.46 3.49
3409 3470 3.394606 TCAAGAGGTATTATTCCCTGCCC 59.605 47.826 0.00 0.00 0.00 5.36
3444 3505 9.730705 ATAATCAACAGGTATTATGATGTCTGG 57.269 33.333 0.00 0.00 33.06 3.86
3446 3507 7.379059 TCAACAGGTATTATGATGTCTGGAT 57.621 36.000 0.00 0.00 0.00 3.41
3530 3591 2.554032 CCTTTCGAGATTGGCAAGTTGT 59.446 45.455 5.96 0.00 0.00 3.32
3531 3592 3.751175 CCTTTCGAGATTGGCAAGTTGTA 59.249 43.478 5.96 0.00 0.00 2.41
3533 3594 5.106157 CCTTTCGAGATTGGCAAGTTGTATT 60.106 40.000 5.96 0.00 0.00 1.89
3534 3595 5.545658 TTCGAGATTGGCAAGTTGTATTC 57.454 39.130 5.96 0.00 0.00 1.75
3535 3596 3.616821 TCGAGATTGGCAAGTTGTATTCG 59.383 43.478 5.96 7.15 0.00 3.34
3551 3612 3.616284 TCGGTTTTCGATCAGCCAA 57.384 47.368 0.00 0.00 43.74 4.52
3563 3624 4.160439 TCGATCAGCCAACAGTATCTTCTT 59.840 41.667 0.00 0.00 0.00 2.52
3569 3630 5.879223 CAGCCAACAGTATCTTCTTCATCTT 59.121 40.000 0.00 0.00 0.00 2.40
3626 3687 2.046892 CCCCACCAAGCGTCTCAG 60.047 66.667 0.00 0.00 0.00 3.35
3634 3695 4.876107 CCACCAAGCGTCTCAGTATTAATT 59.124 41.667 0.00 0.00 0.00 1.40
3638 3699 5.163764 CCAAGCGTCTCAGTATTAATTTGCA 60.164 40.000 0.00 0.00 0.00 4.08
3734 3796 5.275494 ACGGAGTTGTTTTTGTTTTATCGG 58.725 37.500 0.00 0.00 37.78 4.18
3735 3797 4.147479 CGGAGTTGTTTTTGTTTTATCGGC 59.853 41.667 0.00 0.00 0.00 5.54
3736 3798 5.286438 GGAGTTGTTTTTGTTTTATCGGCT 58.714 37.500 0.00 0.00 0.00 5.52
3737 3799 5.174943 GGAGTTGTTTTTGTTTTATCGGCTG 59.825 40.000 0.00 0.00 0.00 4.85
3738 3800 5.047188 AGTTGTTTTTGTTTTATCGGCTGG 58.953 37.500 0.00 0.00 0.00 4.85
3739 3801 3.385577 TGTTTTTGTTTTATCGGCTGGC 58.614 40.909 0.00 0.00 0.00 4.85
3740 3802 2.734276 TTTTGTTTTATCGGCTGGCC 57.266 45.000 0.00 0.00 0.00 5.36
3741 3803 1.621992 TTTGTTTTATCGGCTGGCCA 58.378 45.000 4.71 4.71 35.37 5.36
3742 3804 1.173043 TTGTTTTATCGGCTGGCCAG 58.827 50.000 29.34 29.34 35.37 4.85
3760 3822 9.132923 GCTGGCCAGATTATATATAGTAGTACA 57.867 37.037 37.21 0.00 0.00 2.90
3800 3862 6.266103 TCCAATCTTTTCATTGCAGTTCTTCT 59.734 34.615 0.00 0.00 33.08 2.85
3813 3875 7.346751 TGCAGTTCTTCTTCAAAAGGTTAAT 57.653 32.000 0.00 0.00 0.00 1.40
3824 3896 8.736244 TCTTCAAAAGGTTAATAGTTGGCATAC 58.264 33.333 0.00 0.00 0.00 2.39
3863 3935 2.765807 AGAGATGTGGGAGGCCGG 60.766 66.667 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 5.301045 GGCTTAACAACTAGTTCCCAGTTTT 59.699 40.000 4.77 0.00 41.64 2.43
28 29 2.712087 TGGGCTTAACAACTAGTTCCCA 59.288 45.455 21.02 21.02 44.92 4.37
33 34 5.451381 GCAAAACTTGGGCTTAACAACTAGT 60.451 40.000 0.00 0.00 0.00 2.57
126 127 1.664151 GCTCGTGGGATAAAGGTTTCG 59.336 52.381 0.00 0.00 0.00 3.46
130 131 1.482593 CTCAGCTCGTGGGATAAAGGT 59.517 52.381 0.00 0.00 0.00 3.50
195 197 1.066454 TGACACGGCATATACTCACGG 59.934 52.381 0.00 0.00 0.00 4.94
220 222 3.244078 ACTTCCGAAGTAGCATTGTGTCA 60.244 43.478 12.24 0.00 40.69 3.58
221 223 3.123621 CACTTCCGAAGTAGCATTGTGTC 59.876 47.826 13.47 0.00 40.46 3.67
243 245 0.958091 TATGGTGCACACAGTTTGGC 59.042 50.000 20.43 0.00 0.00 4.52
260 262 5.104485 AGACGCCTCAGATTTAAAGGGTTAT 60.104 40.000 0.00 0.00 0.00 1.89
262 264 3.009143 AGACGCCTCAGATTTAAAGGGTT 59.991 43.478 0.00 0.00 0.00 4.11
285 290 2.825532 GGCCACACTTAAATCACATGGT 59.174 45.455 0.00 0.00 0.00 3.55
336 341 8.364142 CCATTCATAGACAAACTAAAAACCCAA 58.636 33.333 0.00 0.00 34.56 4.12
340 345 9.758651 AAACCCATTCATAGACAAACTAAAAAC 57.241 29.630 0.00 0.00 34.56 2.43
372 377 7.555914 TGTATGGTAATTTGCATGTGAGTATGT 59.444 33.333 0.00 0.00 0.00 2.29
427 433 1.048601 CACAGGGGACATAGCCGTAT 58.951 55.000 0.00 0.00 0.00 3.06
430 436 2.203070 GCACAGGGGACATAGCCG 60.203 66.667 0.00 0.00 0.00 5.52
436 442 1.476845 ATGTACACGCACAGGGGACA 61.477 55.000 0.00 0.00 0.00 4.02
437 443 0.533491 TATGTACACGCACAGGGGAC 59.467 55.000 0.00 0.00 0.00 4.46
465 471 5.130477 GGTGGTAGAAGTAGGAATCCATTCA 59.870 44.000 0.61 0.00 38.53 2.57
467 473 5.036916 TGGTGGTAGAAGTAGGAATCCATT 58.963 41.667 0.61 0.00 0.00 3.16
468 474 4.631234 TGGTGGTAGAAGTAGGAATCCAT 58.369 43.478 0.61 0.00 0.00 3.41
470 476 5.011840 GGTATGGTGGTAGAAGTAGGAATCC 59.988 48.000 0.00 0.00 0.00 3.01
471 477 5.839606 AGGTATGGTGGTAGAAGTAGGAATC 59.160 44.000 0.00 0.00 0.00 2.52
472 478 5.602978 CAGGTATGGTGGTAGAAGTAGGAAT 59.397 44.000 0.00 0.00 0.00 3.01
473 479 4.960469 CAGGTATGGTGGTAGAAGTAGGAA 59.040 45.833 0.00 0.00 0.00 3.36
578 594 2.981859 TGGAAGACTCCGGCTTAATC 57.018 50.000 0.00 0.00 45.85 1.75
586 602 1.192146 TGGGACCTTGGAAGACTCCG 61.192 60.000 0.00 0.00 45.85 4.63
597 613 2.203584 AGCTCTGATTCATGGGACCTT 58.796 47.619 0.00 0.00 0.00 3.50
605 621 6.482898 AGTGATTGTCTAGCTCTGATTCAT 57.517 37.500 0.00 0.00 0.00 2.57
699 715 8.467402 ACGAAAATACACAAATGAACAAACAA 57.533 26.923 0.00 0.00 0.00 2.83
715 731 6.513991 CGCGCCAGTTTATATAACGAAAATAC 59.486 38.462 0.00 0.00 0.00 1.89
854 871 9.767228 TTTGCAATGAGGAAATAATATCCAATG 57.233 29.630 0.00 0.00 39.55 2.82
856 873 9.820725 CTTTTGCAATGAGGAAATAATATCCAA 57.179 29.630 0.00 0.00 37.40 3.53
955 972 4.066490 CGGACCACCTAAAACATACAACA 58.934 43.478 0.00 0.00 0.00 3.33
963 980 0.035739 TGCCTCGGACCACCTAAAAC 59.964 55.000 0.00 0.00 0.00 2.43
1426 1468 1.394618 AACACAAAGCTACCCGCAAA 58.605 45.000 0.00 0.00 42.61 3.68
1470 1512 4.453819 CACTTGAGAGACCATGTTCTTTCC 59.546 45.833 8.12 0.00 0.00 3.13
1593 1635 5.386924 TCAATGGTATGATGCATGGAATCA 58.613 37.500 2.46 0.00 38.37 2.57
1630 1672 2.666272 TTGGACCCAAACATGCTACA 57.334 45.000 0.00 0.00 32.44 2.74
1644 1686 4.935808 TCCGCTAATTCTTCTCTTTTGGAC 59.064 41.667 0.00 0.00 0.00 4.02
2278 2329 0.462047 CCTTGGGCTTTATCGTCGCT 60.462 55.000 0.00 0.00 0.00 4.93
2279 2330 0.461339 TCCTTGGGCTTTATCGTCGC 60.461 55.000 0.00 0.00 0.00 5.19
2318 2369 5.521010 CAGTTGTTCATTGCTGTTTTCACAT 59.479 36.000 0.00 0.00 30.39 3.21
2319 2370 4.863689 CAGTTGTTCATTGCTGTTTTCACA 59.136 37.500 0.00 0.00 0.00 3.58
2351 2402 8.178964 GCATCACGACAATACTATAACCAAAAA 58.821 33.333 0.00 0.00 0.00 1.94
2385 2436 3.213206 TGTTGAAGATGTGCCTCAGTT 57.787 42.857 0.00 0.00 0.00 3.16
2401 2452 4.396166 AGAACGGGAAGAAGCATATTGTTG 59.604 41.667 0.00 0.00 0.00 3.33
2461 2512 2.565841 GCATACCTCCATCAGACCAAC 58.434 52.381 0.00 0.00 0.00 3.77
2727 2781 0.323816 ACGTGATGAGCTCTCCTCCA 60.324 55.000 16.19 2.86 39.98 3.86
2766 2820 2.057922 GTATCCCCCATCTCCATGTGT 58.942 52.381 0.00 0.00 0.00 3.72
2823 2877 2.948979 AGTCAAGTTTGTTTCCGCATGA 59.051 40.909 0.00 0.00 0.00 3.07
2844 2904 9.310449 GAGGGAACATAGAAGAGGTATACATTA 57.690 37.037 5.01 0.00 0.00 1.90
2848 2908 7.005296 TCTGAGGGAACATAGAAGAGGTATAC 58.995 42.308 0.00 0.00 0.00 1.47
2877 2937 4.212847 CGATTTTCAGCACCTGATATCTGG 59.787 45.833 23.19 23.19 40.39 3.86
2895 2955 4.704540 TGATGGAATTGCAGTTACCGATTT 59.295 37.500 5.69 0.00 0.00 2.17
3106 3166 1.471287 CACGTATGGAAGGTCGACAGA 59.529 52.381 18.91 0.00 0.00 3.41
3128 3188 3.850098 AAGGCTGAAGCACACCCCG 62.850 63.158 4.43 0.00 44.36 5.73
3129 3189 1.527433 GAAAGGCTGAAGCACACCCC 61.527 60.000 4.43 0.00 44.36 4.95
3179 3239 9.582648 ACACTTACACCTTACAAAAATCCTATT 57.417 29.630 0.00 0.00 0.00 1.73
3180 3240 9.227777 GACACTTACACCTTACAAAAATCCTAT 57.772 33.333 0.00 0.00 0.00 2.57
3181 3241 7.662669 GGACACTTACACCTTACAAAAATCCTA 59.337 37.037 0.00 0.00 0.00 2.94
3182 3242 6.489022 GGACACTTACACCTTACAAAAATCCT 59.511 38.462 0.00 0.00 0.00 3.24
3183 3243 6.567132 CGGACACTTACACCTTACAAAAATCC 60.567 42.308 0.00 0.00 0.00 3.01
3184 3244 6.368213 CGGACACTTACACCTTACAAAAATC 58.632 40.000 0.00 0.00 0.00 2.17
3185 3245 5.278120 GCGGACACTTACACCTTACAAAAAT 60.278 40.000 0.00 0.00 0.00 1.82
3186 3246 4.035441 GCGGACACTTACACCTTACAAAAA 59.965 41.667 0.00 0.00 0.00 1.94
3187 3247 3.560896 GCGGACACTTACACCTTACAAAA 59.439 43.478 0.00 0.00 0.00 2.44
3188 3248 3.132925 GCGGACACTTACACCTTACAAA 58.867 45.455 0.00 0.00 0.00 2.83
3189 3249 2.102757 TGCGGACACTTACACCTTACAA 59.897 45.455 0.00 0.00 0.00 2.41
3190 3250 1.687660 TGCGGACACTTACACCTTACA 59.312 47.619 0.00 0.00 0.00 2.41
3191 3251 2.443887 TGCGGACACTTACACCTTAC 57.556 50.000 0.00 0.00 0.00 2.34
3192 3252 2.300723 ACATGCGGACACTTACACCTTA 59.699 45.455 0.00 0.00 0.00 2.69
3193 3253 1.071699 ACATGCGGACACTTACACCTT 59.928 47.619 0.00 0.00 0.00 3.50
3194 3254 0.685097 ACATGCGGACACTTACACCT 59.315 50.000 0.00 0.00 0.00 4.00
3195 3255 0.796312 CACATGCGGACACTTACACC 59.204 55.000 0.00 0.00 0.00 4.16
3196 3256 0.165944 GCACATGCGGACACTTACAC 59.834 55.000 0.00 0.00 0.00 2.90
3197 3257 2.539003 GCACATGCGGACACTTACA 58.461 52.632 0.00 0.00 0.00 2.41
3289 3349 1.614317 GCAGGAAATAGCACCACACCT 60.614 52.381 0.00 0.00 0.00 4.00
3418 3479 9.730705 CCAGACATCATAATACCTGTTGATTAT 57.269 33.333 0.00 0.00 0.00 1.28
3419 3480 8.933653 TCCAGACATCATAATACCTGTTGATTA 58.066 33.333 0.00 0.00 0.00 1.75
3444 3505 6.318648 TGCAGGTCAAGTTAAATCATACCATC 59.681 38.462 0.00 0.00 0.00 3.51
3446 3507 5.565509 TGCAGGTCAAGTTAAATCATACCA 58.434 37.500 0.00 0.00 0.00 3.25
3534 3595 0.871722 TGTTGGCTGATCGAAAACCG 59.128 50.000 0.00 0.00 40.25 4.44
3535 3596 1.880027 ACTGTTGGCTGATCGAAAACC 59.120 47.619 0.00 0.00 0.00 3.27
3546 3607 5.690464 AGATGAAGAAGATACTGTTGGCT 57.310 39.130 0.00 0.00 0.00 4.75
3563 3624 5.077564 AGTGAGGCCGTATACATAAGATGA 58.922 41.667 3.32 0.00 0.00 2.92
3569 3630 3.154710 CCTGAGTGAGGCCGTATACATA 58.845 50.000 3.32 0.00 34.01 2.29
3718 3780 3.385577 GCCAGCCGATAAAACAAAAACA 58.614 40.909 0.00 0.00 0.00 2.83
3719 3781 2.734606 GGCCAGCCGATAAAACAAAAAC 59.265 45.455 0.00 0.00 0.00 2.43
3720 3782 2.365617 TGGCCAGCCGATAAAACAAAAA 59.634 40.909 0.00 0.00 39.42 1.94
3722 3784 1.543802 CTGGCCAGCCGATAAAACAAA 59.456 47.619 22.33 0.00 39.42 2.83
3723 3785 1.173043 CTGGCCAGCCGATAAAACAA 58.827 50.000 22.33 0.00 39.42 2.83
3724 3786 0.326595 TCTGGCCAGCCGATAAAACA 59.673 50.000 28.91 3.28 39.42 2.83
3725 3787 1.680338 ATCTGGCCAGCCGATAAAAC 58.320 50.000 28.91 0.00 39.42 2.43
3726 3788 2.435372 AATCTGGCCAGCCGATAAAA 57.565 45.000 28.91 8.57 39.42 1.52
3727 3789 3.788227 ATAATCTGGCCAGCCGATAAA 57.212 42.857 28.91 9.41 39.42 1.40
3728 3790 6.747414 ATATATAATCTGGCCAGCCGATAA 57.253 37.500 28.91 10.24 39.42 1.75
3729 3791 7.010771 ACTATATATAATCTGGCCAGCCGATA 58.989 38.462 28.91 21.93 39.42 2.92
3730 3792 5.841237 ACTATATATAATCTGGCCAGCCGAT 59.159 40.000 28.91 20.57 39.42 4.18
3731 3793 5.208890 ACTATATATAATCTGGCCAGCCGA 58.791 41.667 28.91 12.20 39.42 5.54
3732 3794 5.537300 ACTATATATAATCTGGCCAGCCG 57.463 43.478 28.91 5.92 39.42 5.52
3733 3795 7.604657 ACTACTATATATAATCTGGCCAGCC 57.395 40.000 28.91 0.38 0.00 4.85
3734 3796 9.132923 TGTACTACTATATATAATCTGGCCAGC 57.867 37.037 28.91 7.60 0.00 4.85
3736 3798 9.984590 TGTGTACTACTATATATAATCTGGCCA 57.015 33.333 4.71 4.71 0.00 5.36
3760 3822 8.655935 AAAAGATTGGATAAACTCCTTGATGT 57.344 30.769 0.00 0.00 45.21 3.06
3772 3834 8.125978 AGAACTGCAATGAAAAGATTGGATAA 57.874 30.769 0.00 0.00 33.73 1.75
3800 3862 8.410673 TGTATGCCAACTATTAACCTTTTGAA 57.589 30.769 0.00 0.00 0.00 2.69
3863 3935 2.743928 CTTCGGTGTGCAGGCCTC 60.744 66.667 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.