Multiple sequence alignment - TraesCS2B01G546100

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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 TraesCS2B01G546100 chr2B 100.000 3966 0 0 1 3966 742895575 742891610 0.000000e+00 7324
1 TraesCS2B01G546100 chr2B 77.860 271 58 2 1 270 163562278 163562547 2.450000e-37 167
2 TraesCS2B01G546100 chr2A 92.740 3113 145 29 1 3066 740876445 740873367 0.000000e+00 4421
3 TraesCS2B01G546100 chr2A 93.281 893 55 4 3077 3966 740873312 740872422 0.000000e+00 1312
4 TraesCS2B01G546100 chr2D 94.172 1287 54 11 1787 3062 608980232 608978956 0.000000e+00 1941
5 TraesCS2B01G546100 chr2D 91.749 909 67 7 3061 3966 608978902 608977999 0.000000e+00 1256
6 TraesCS2B01G546100 chr2D 90.550 836 55 11 975 1791 608981163 608980333 0.000000e+00 1085
7 TraesCS2B01G546100 chr2D 96.996 566 13 3 319 884 608982083 608981522 0.000000e+00 948
8 TraesCS2B01G546100 chr2D 92.476 319 16 4 1 317 608982438 608982126 2.170000e-122 449
9 TraesCS2B01G546100 chr2D 79.104 268 55 1 1 268 451693873 451694139 2.430000e-42 183
10 TraesCS2B01G546100 chr6A 82.222 270 45 3 1 269 56069015 56069282 3.080000e-56 230
11 TraesCS2B01G546100 chr4A 81.111 270 46 4 1 267 537549176 537548909 1.120000e-50 211
12 TraesCS2B01G546100 chr4D 80.597 268 51 1 1 268 19338750 19339016 5.200000e-49 206
13 TraesCS2B01G546100 chr6D 80.408 245 42 5 7 245 461815778 461815534 8.750000e-42 182
14 TraesCS2B01G546100 chr5D 78.810 269 52 5 1 267 56807027 56807292 4.070000e-40 176


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 TraesCS2B01G546100 chr2B 742891610 742895575 3965 True 7324.0 7324 100.0000 1 3966 1 chr2B.!!$R1 3965
1 TraesCS2B01G546100 chr2A 740872422 740876445 4023 True 2866.5 4421 93.0105 1 3966 2 chr2A.!!$R1 3965
2 TraesCS2B01G546100 chr2D 608977999 608982438 4439 True 1135.8 1941 93.1886 1 3966 5 chr2D.!!$R1 3965

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
953 1299 0.178990 GCCTCCCTCTCTCTCTCTCC 60.179 65.000 0.0 0.0 0.0 3.71 F
1879 2366 1.000274 GCCACCAGTGCTACAAAAAGG 60.000 52.381 0.0 0.0 0.0 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2547 3041 0.179062 CTCCTCTTCCCTGATTGCCG 60.179 60.0 0.0 0.0 0.00 5.69 R
3689 4246 0.031721 ACCACACGAAGACGAAGGTC 59.968 55.0 0.0 0.0 43.76 3.85 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
69 70 2.886124 GAGTCTTAGCACGGCGGC 60.886 66.667 13.24 12.27 0.00 6.53
130 131 2.124278 GGGAGGGGAAATGACGGC 60.124 66.667 0.00 0.00 0.00 5.68
131 132 2.680370 GGGAGGGGAAATGACGGCT 61.680 63.158 0.00 0.00 0.00 5.52
151 152 2.433318 GCGCCTTCGTCTTGCTCT 60.433 61.111 0.00 0.00 38.14 4.09
171 172 6.147985 TGCTCTAGTACTTATAGTCATCGCTG 59.852 42.308 0.00 0.00 0.00 5.18
172 173 6.369340 GCTCTAGTACTTATAGTCATCGCTGA 59.631 42.308 0.00 0.00 0.00 4.26
176 178 9.373603 CTAGTACTTATAGTCATCGCTGAGTAT 57.626 37.037 17.96 17.96 45.69 2.12
227 229 6.294361 TCTGCTATTCTTTGTGCTACCTTA 57.706 37.500 0.00 0.00 0.00 2.69
237 239 4.948341 TGTGCTACCTTAACAGTTGAGA 57.052 40.909 6.65 0.00 0.00 3.27
365 408 3.720494 TGGCATGGGCGAGAACTA 58.280 55.556 0.00 0.00 42.47 2.24
381 424 6.617741 GCGAGAACTATGAATTTTCACGTCAA 60.618 38.462 7.95 0.00 40.49 3.18
403 446 3.449018 ACTCCTGATACTTCACAGCGATT 59.551 43.478 0.00 0.00 33.40 3.34
410 453 8.244113 CCTGATACTTCACAGCGATTATACATA 58.756 37.037 0.00 0.00 33.40 2.29
412 455 9.573133 TGATACTTCACAGCGATTATACATATG 57.427 33.333 0.00 0.00 0.00 1.78
413 456 9.574458 GATACTTCACAGCGATTATACATATGT 57.426 33.333 13.93 13.93 0.00 2.29
414 457 9.929180 ATACTTCACAGCGATTATACATATGTT 57.071 29.630 14.77 4.83 0.00 2.71
415 458 8.299262 ACTTCACAGCGATTATACATATGTTC 57.701 34.615 14.77 4.41 0.00 3.18
416 459 7.385205 ACTTCACAGCGATTATACATATGTTCC 59.615 37.037 14.77 0.42 0.00 3.62
417 460 6.754193 TCACAGCGATTATACATATGTTCCA 58.246 36.000 14.77 0.00 0.00 3.53
491 534 2.221906 TAGTTCCCAGCGCGACTTCC 62.222 60.000 12.10 0.00 0.00 3.46
589 632 4.922206 TCAATGGCATCAGGACTAAAAGT 58.078 39.130 0.00 0.00 0.00 2.66
837 882 1.658596 CACGGTGTCATATCAACCACG 59.341 52.381 0.00 0.00 0.00 4.94
898 948 1.820519 CTCTCTCTCTCTGCAGTTGCT 59.179 52.381 14.67 0.00 42.66 3.91
909 959 4.697514 TCTGCAGTTGCTTACATATCTCC 58.302 43.478 14.67 0.00 42.66 3.71
939 1285 4.168291 CTCTTCCCCTGCGCCTCC 62.168 72.222 4.18 0.00 0.00 4.30
952 1298 0.535102 CGCCTCCCTCTCTCTCTCTC 60.535 65.000 0.00 0.00 0.00 3.20
953 1299 0.178990 GCCTCCCTCTCTCTCTCTCC 60.179 65.000 0.00 0.00 0.00 3.71
954 1300 1.522900 CCTCCCTCTCTCTCTCTCCT 58.477 60.000 0.00 0.00 0.00 3.69
960 1324 3.434167 CCCTCTCTCTCTCTCCTTCTCTG 60.434 56.522 0.00 0.00 0.00 3.35
963 1327 3.587061 TCTCTCTCTCTCCTTCTCTGTGT 59.413 47.826 0.00 0.00 0.00 3.72
1172 1538 8.666129 TCTATGGAGAAAAAGAAAGTAGGAGA 57.334 34.615 0.00 0.00 0.00 3.71
1194 1560 8.032451 GGAGATACAAGTTTCTATCTATGCCTC 58.968 40.741 1.36 0.00 31.13 4.70
1201 1578 7.430760 AGTTTCTATCTATGCCTCACTTCTT 57.569 36.000 0.00 0.00 0.00 2.52
1209 1586 6.042777 TCTATGCCTCACTTCTTGTAATTCG 58.957 40.000 0.00 0.00 0.00 3.34
1225 1602 2.577606 TTCGAAACCCATGTGTCCAT 57.422 45.000 0.00 0.00 0.00 3.41
1319 1698 3.921119 TTTGCATGATTTCTGCTCGTT 57.079 38.095 0.00 0.00 40.34 3.85
1341 1720 6.200097 CGTTGGAAATTTGTTTTTAGGGTCAG 59.800 38.462 0.00 0.00 0.00 3.51
1357 1736 4.079253 GGGTCAGTTGGATAAAAGAAGCA 58.921 43.478 0.00 0.00 0.00 3.91
1360 1739 5.335976 GGTCAGTTGGATAAAAGAAGCAAGG 60.336 44.000 0.00 0.00 0.00 3.61
1362 1741 4.022068 CAGTTGGATAAAAGAAGCAAGGCA 60.022 41.667 0.00 0.00 0.00 4.75
1418 1797 9.708222 CACAATTTCATAGGATTTCTAAGAACG 57.292 33.333 0.00 0.00 35.98 3.95
1427 1806 6.536447 AGGATTTCTAAGAACGGGTTAAACA 58.464 36.000 0.00 0.00 0.00 2.83
1480 1859 5.011943 ACATGGAAATGTGTATTTGTGCCTT 59.988 36.000 0.00 0.00 36.66 4.35
1547 1928 8.345724 AGCATCAAATGAGTCAAGTAAATTCT 57.654 30.769 0.00 0.00 0.00 2.40
1609 1991 9.030452 ACATCTTAACCATACATTTTTGCCTAA 57.970 29.630 0.00 0.00 0.00 2.69
1617 1999 8.143835 ACCATACATTTTTGCCTAATCATAAGC 58.856 33.333 0.00 0.00 0.00 3.09
1649 2031 2.490903 CTGAGTTCCAAAGATGCCCTTG 59.509 50.000 0.00 0.00 34.79 3.61
1656 2038 4.415596 TCCAAAGATGCCCTTGTTATTGT 58.584 39.130 0.00 0.00 34.79 2.71
1666 2048 5.472137 TGCCCTTGTTATTGTTCAAGTAGTC 59.528 40.000 0.00 0.00 39.25 2.59
1667 2049 5.390567 GCCCTTGTTATTGTTCAAGTAGTCG 60.391 44.000 0.00 0.00 39.25 4.18
1879 2366 1.000274 GCCACCAGTGCTACAAAAAGG 60.000 52.381 0.00 0.00 0.00 3.11
1940 2428 5.047021 ACATCTGACTGTACTGCACTAATGT 60.047 40.000 0.00 2.03 0.00 2.71
1944 2432 7.258441 TCTGACTGTACTGCACTAATGTTATC 58.742 38.462 0.00 0.00 0.00 1.75
1958 2446 6.818644 ACTAATGTTATCTGTTCGTTCATGCT 59.181 34.615 0.00 0.00 0.00 3.79
2186 2674 1.304381 GGCAAGGTGATCAAGGGCA 60.304 57.895 0.00 0.00 0.00 5.36
2293 2781 4.097361 GGGAAGGAGTCACCGCCC 62.097 72.222 4.92 4.92 45.58 6.13
2332 2820 2.440627 ACAAGCATATCATCCTCAGCCA 59.559 45.455 0.00 0.00 0.00 4.75
2365 2856 1.837439 CCACAGGCATACTACCCTCAA 59.163 52.381 0.00 0.00 0.00 3.02
2374 2865 3.324108 TACCCTCAACCGCCCACC 61.324 66.667 0.00 0.00 0.00 4.61
2547 3041 0.601311 GAGGTATCAGCGACCATGCC 60.601 60.000 0.00 0.00 39.65 4.40
2560 3054 1.753848 CATGCCGGCAATCAGGGAA 60.754 57.895 36.33 6.47 0.00 3.97
2581 3075 2.498726 GAGAGGCCGCAAGAGAGG 59.501 66.667 9.88 0.00 43.02 3.69
2633 3127 1.004745 AGGTCCATTTCGTGCCAGAAT 59.995 47.619 0.00 0.00 0.00 2.40
2639 3133 0.322456 TTTCGTGCCAGAATCAGGGG 60.322 55.000 0.00 0.00 0.00 4.79
2672 3166 0.637743 GAACCCTAGGGAGAGGAGGT 59.362 60.000 35.38 6.09 39.15 3.85
2967 3461 3.631686 GGTGCTTGCACCATAATGTGATA 59.368 43.478 32.37 0.00 44.39 2.15
2984 3478 4.661993 TGATATGTTCACTGTTTCGTGC 57.338 40.909 0.00 0.00 34.92 5.34
2987 3481 1.087202 TGTTCACTGTTTCGTGCGCT 61.087 50.000 9.73 0.00 34.92 5.92
3004 3498 0.454957 GCTACAACCATTGTGCTGCG 60.455 55.000 4.46 0.00 45.03 5.18
3006 3500 1.266718 CTACAACCATTGTGCTGCGTT 59.733 47.619 4.46 0.00 45.03 4.84
3008 3502 0.030504 CAACCATTGTGCTGCGTTGA 59.969 50.000 9.32 0.00 36.72 3.18
3009 3503 0.961019 AACCATTGTGCTGCGTTGAT 59.039 45.000 0.00 0.00 0.00 2.57
3010 3504 0.523072 ACCATTGTGCTGCGTTGATC 59.477 50.000 0.00 0.00 0.00 2.92
3012 3506 1.133598 CCATTGTGCTGCGTTGATCAT 59.866 47.619 0.00 0.00 0.00 2.45
3013 3507 2.355444 CCATTGTGCTGCGTTGATCATA 59.645 45.455 0.00 0.00 0.00 2.15
3014 3508 3.547413 CCATTGTGCTGCGTTGATCATAG 60.547 47.826 0.00 0.00 0.00 2.23
3015 3509 1.655484 TGTGCTGCGTTGATCATAGG 58.345 50.000 0.00 0.00 0.00 2.57
3016 3510 0.305922 GTGCTGCGTTGATCATAGGC 59.694 55.000 0.00 5.98 0.00 3.93
3017 3511 0.107752 TGCTGCGTTGATCATAGGCA 60.108 50.000 17.88 17.88 35.38 4.75
3019 3513 1.003116 GCTGCGTTGATCATAGGCAAG 60.003 52.381 18.81 15.15 36.15 4.01
3020 3514 2.283298 CTGCGTTGATCATAGGCAAGT 58.717 47.619 18.81 0.00 36.15 3.16
3023 3517 2.792542 GCGTTGATCATAGGCAAGTTGC 60.793 50.000 19.87 19.87 44.08 4.17
3047 3546 6.587226 GCATCTTTTTGCATGTCTTGATTACA 59.413 34.615 0.00 0.00 42.31 2.41
3326 3882 9.944663 AAATTCGTACGATTAAATGCAATACAT 57.055 25.926 20.27 0.93 42.30 2.29
3363 3919 9.612620 CTCAGATTTGTTAATAAGGTTCAACAC 57.387 33.333 0.00 0.00 31.00 3.32
3380 3936 2.632377 ACACAAATGCCTACATCCTCG 58.368 47.619 0.00 0.00 34.62 4.63
3386 3942 1.681538 TGCCTACATCCTCGACTCTC 58.318 55.000 0.00 0.00 0.00 3.20
3449 4005 4.792066 CCGGTCTGGTTACCCCTA 57.208 61.111 0.00 0.00 36.03 3.53
3484 4040 2.675371 GGCCAGTCTGGTTACCCC 59.325 66.667 20.24 8.62 40.46 4.95
3496 4052 2.132996 TTACCCCCGTGTCGTGTGT 61.133 57.895 0.00 0.00 0.00 3.72
3497 4053 1.684386 TTACCCCCGTGTCGTGTGTT 61.684 55.000 0.00 0.00 0.00 3.32
3499 4055 2.970324 CCCCGTGTCGTGTGTTGG 60.970 66.667 0.00 0.00 0.00 3.77
3560 4116 4.082354 ACTTTGTCTAGTCTATTTCGCGGT 60.082 41.667 6.13 0.00 0.00 5.68
3618 4175 5.530543 TGAAAATTCACACACTGCATCACTA 59.469 36.000 0.00 0.00 31.01 2.74
3629 4186 4.081972 CACTGCATCACTACTACTGTCCTT 60.082 45.833 0.00 0.00 0.00 3.36
3632 4189 3.447586 GCATCACTACTACTGTCCTTCCA 59.552 47.826 0.00 0.00 0.00 3.53
3665 4222 8.665685 CCAAATACACTTAGTAGAAACCATGTC 58.334 37.037 0.00 0.00 35.85 3.06
3689 4246 5.296748 CACCAAGTAAAATCCAACCCAAAG 58.703 41.667 0.00 0.00 0.00 2.77
3740 4297 0.398381 TGGCTTGGCTGAACCCTTTT 60.398 50.000 0.00 0.00 37.83 2.27
3741 4298 0.758734 GGCTTGGCTGAACCCTTTTT 59.241 50.000 0.00 0.00 37.83 1.94
3753 4310 7.064609 GGCTGAACCCTTTTTATGCTATTTTTC 59.935 37.037 0.00 0.00 0.00 2.29
3756 4313 6.308015 ACCCTTTTTATGCTATTTTTCCCC 57.692 37.500 0.00 0.00 0.00 4.81
3817 4374 6.033966 CCTCCCAAAACGTCTTATATTTTGC 58.966 40.000 0.00 0.00 40.43 3.68
3887 4444 0.391130 CCACCATGACAGGTACGGTG 60.391 60.000 6.81 6.81 45.46 4.94
3888 4445 3.060828 ACCATGACAGGTACGGTGA 57.939 52.632 0.00 0.00 40.98 4.02
3889 4446 1.568504 ACCATGACAGGTACGGTGAT 58.431 50.000 0.00 0.00 40.98 3.06
3948 4505 2.479560 GCAAACTTTGAGTGCCTCGTTT 60.480 45.455 5.65 0.00 32.35 3.60
3963 4520 3.556423 CCTCGTTTTGCCACTAAGTAGGT 60.556 47.826 0.00 0.00 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 5.624344 TCTTGTAGTAGACAGTCGGAAAG 57.376 43.478 0.00 0.00 39.88 2.62
130 131 4.139420 CAAGACGAAGGCGCGCAG 62.139 66.667 34.42 22.00 42.48 5.18
143 144 7.095144 GCGATGACTATAAGTACTAGAGCAAGA 60.095 40.741 0.00 0.00 0.00 3.02
151 152 9.722184 AATACTCAGCGATGACTATAAGTACTA 57.278 33.333 0.00 0.00 0.00 1.82
272 274 2.851534 CTACACTTAAAAAGGCAGCGC 58.148 47.619 0.00 0.00 0.00 5.92
363 406 6.368791 TCAGGAGTTGACGTGAAAATTCATAG 59.631 38.462 0.00 0.34 39.73 2.23
365 408 5.063204 TCAGGAGTTGACGTGAAAATTCAT 58.937 37.500 0.00 0.00 39.73 2.57
381 424 2.447443 TCGCTGTGAAGTATCAGGAGT 58.553 47.619 0.00 0.00 35.88 3.85
410 453 8.635765 TTTGAATAGCTAGAAAACTGGAACAT 57.364 30.769 0.00 0.00 38.20 2.71
412 455 8.324163 TCTTTGAATAGCTAGAAAACTGGAAC 57.676 34.615 0.00 0.00 0.00 3.62
413 456 8.918202 TTCTTTGAATAGCTAGAAAACTGGAA 57.082 30.769 0.00 0.00 0.00 3.53
449 492 1.858458 CGTACATGTCCGCGAATCAAT 59.142 47.619 8.23 0.00 0.00 2.57
491 534 1.065854 ACAAAGGAATCCTCGAGCAGG 60.066 52.381 6.99 0.00 45.15 4.85
589 632 6.916360 ATCTGGTTCTTGCCATTAAAGAAA 57.084 33.333 0.46 0.00 43.37 2.52
898 948 1.640917 GGCGGGAGGGAGATATGTAA 58.359 55.000 0.00 0.00 0.00 2.41
909 959 4.806339 AAGAGAGGGGGCGGGAGG 62.806 72.222 0.00 0.00 0.00 4.30
939 1285 3.200825 ACAGAGAAGGAGAGAGAGAGAGG 59.799 52.174 0.00 0.00 0.00 3.69
952 1298 2.917933 TGGTTTGTCACACAGAGAAGG 58.082 47.619 0.00 0.00 30.41 3.46
953 1299 3.941483 AGTTGGTTTGTCACACAGAGAAG 59.059 43.478 0.00 0.00 30.41 2.85
954 1300 3.950397 AGTTGGTTTGTCACACAGAGAA 58.050 40.909 0.00 0.00 0.00 2.87
1026 1390 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1172 1538 8.256356 AGTGAGGCATAGATAGAAACTTGTAT 57.744 34.615 0.00 0.00 0.00 2.29
1194 1560 5.682943 TGGGTTTCGAATTACAAGAAGTG 57.317 39.130 0.00 0.00 0.00 3.16
1201 1578 3.754323 GGACACATGGGTTTCGAATTACA 59.246 43.478 0.00 0.00 0.00 2.41
1209 1586 3.023119 TGCATATGGACACATGGGTTTC 58.977 45.455 0.00 0.00 37.97 2.78
1288 1667 9.042008 GCAGAAATCATGCAAAAATCTTATGAT 57.958 29.630 0.00 0.00 43.31 2.45
1319 1698 6.800072 ACTGACCCTAAAAACAAATTTCCA 57.200 33.333 0.00 0.00 0.00 3.53
1341 1720 4.519540 TGCCTTGCTTCTTTTATCCAAC 57.480 40.909 0.00 0.00 0.00 3.77
1357 1736 7.427989 ACAATCCATAGAAATTGATTGCCTT 57.572 32.000 11.73 0.00 43.86 4.35
1360 1739 9.374838 AGAAAACAATCCATAGAAATTGATTGC 57.625 29.630 11.73 0.00 43.86 3.56
1427 1806 5.578157 ACCACTATTTTTCACTAGGTGGT 57.422 39.130 8.76 8.76 37.79 4.16
1456 1835 4.527816 AGGCACAAATACACATTTCCATGT 59.472 37.500 0.00 0.00 45.18 3.21
1466 1845 3.146066 TGTCTGGAAGGCACAAATACAC 58.854 45.455 0.00 0.00 44.24 2.90
1480 1859 7.429374 AATATGAAGTGAGAAGATGTCTGGA 57.571 36.000 0.00 0.00 36.41 3.86
1547 1928 5.782331 TGGTCCATGGGAAACAAAAATATGA 59.218 36.000 13.02 0.00 31.38 2.15
1556 1937 2.490718 CCTCTTTGGTCCATGGGAAACA 60.491 50.000 13.02 0.00 31.38 2.83
1609 1991 8.870075 AACTCAGGTTTCTAAAAGCTTATGAT 57.130 30.769 0.00 0.00 30.55 2.45
1617 1999 7.568199 TCTTTGGAACTCAGGTTTCTAAAAG 57.432 36.000 0.00 0.00 35.58 2.27
1649 2031 7.829378 ATTCCTCGACTACTTGAACAATAAC 57.171 36.000 0.00 0.00 0.00 1.89
1656 2038 4.245660 CTGCAATTCCTCGACTACTTGAA 58.754 43.478 0.00 0.00 0.00 2.69
1666 2048 3.705604 ACACAAAAACTGCAATTCCTCG 58.294 40.909 0.00 0.00 0.00 4.63
1667 2049 4.051237 GGACACAAAAACTGCAATTCCTC 58.949 43.478 0.00 0.00 0.00 3.71
1802 2289 3.544684 TGTGTTGACAGAAGCATCAGTT 58.455 40.909 0.00 0.00 0.00 3.16
1940 2428 5.478407 TGAGAAGCATGAACGAACAGATAA 58.522 37.500 0.00 0.00 0.00 1.75
1944 2432 3.062763 ACTGAGAAGCATGAACGAACAG 58.937 45.455 0.00 0.92 0.00 3.16
1958 2446 5.104941 TGGAGAGTTTCTTTGTGACTGAGAA 60.105 40.000 0.00 0.00 0.00 2.87
2089 2577 2.546368 GACTGCGTTATTGTTGGTGTCA 59.454 45.455 0.00 0.00 0.00 3.58
2461 2952 4.162690 GGCGGCTGAGGGTGGTAG 62.163 72.222 0.00 0.00 0.00 3.18
2531 3025 1.956170 CCGGCATGGTCGCTGATAC 60.956 63.158 0.00 0.00 41.00 2.24
2547 3041 0.179062 CTCCTCTTCCCTGATTGCCG 60.179 60.000 0.00 0.00 0.00 5.69
2551 3045 1.506025 GCCTCTCCTCTTCCCTGATT 58.494 55.000 0.00 0.00 0.00 2.57
2552 3046 0.399806 GGCCTCTCCTCTTCCCTGAT 60.400 60.000 0.00 0.00 0.00 2.90
2560 3054 2.038007 TCTTGCGGCCTCTCCTCT 59.962 61.111 0.00 0.00 0.00 3.69
2581 3075 4.760047 TTCTCAAGCTCGGCCGGC 62.760 66.667 27.83 26.36 0.00 6.13
2639 3133 2.617274 GGTTCTTGTGGCACTCCGC 61.617 63.158 19.83 5.33 43.16 5.54
2672 3166 0.832135 GGCATCTCTCCCATCGGGTA 60.832 60.000 0.00 0.00 44.74 3.69
2967 3461 0.041312 GCGCACGAAACAGTGAACAT 60.041 50.000 0.30 0.00 44.43 2.71
2984 3478 0.454957 GCAGCACAATGGTTGTAGCG 60.455 55.000 0.00 0.00 43.23 4.26
2987 3481 1.001924 CAACGCAGCACAATGGTTGTA 60.002 47.619 0.00 0.00 43.23 2.41
3004 3498 4.337555 AGATGCAACTTGCCTATGATCAAC 59.662 41.667 11.29 0.00 44.23 3.18
3006 3500 4.160642 AGATGCAACTTGCCTATGATCA 57.839 40.909 11.29 0.00 44.23 2.92
3008 3502 5.927281 AAAAGATGCAACTTGCCTATGAT 57.073 34.783 10.27 0.00 44.23 2.45
3009 3503 5.472148 CAAAAAGATGCAACTTGCCTATGA 58.528 37.500 10.27 0.00 44.23 2.15
3010 3504 4.092383 GCAAAAAGATGCAACTTGCCTATG 59.908 41.667 10.27 6.56 44.23 2.23
3012 3506 3.652274 GCAAAAAGATGCAACTTGCCTA 58.348 40.909 10.27 0.00 44.23 3.93
3013 3507 2.486918 GCAAAAAGATGCAACTTGCCT 58.513 42.857 10.27 0.92 44.23 4.75
3014 3508 2.955607 GCAAAAAGATGCAACTTGCC 57.044 45.000 10.27 0.00 44.23 4.52
3023 3517 8.523523 TTGTAATCAAGACATGCAAAAAGATG 57.476 30.769 0.00 0.00 0.00 2.90
3024 3518 9.715121 ATTTGTAATCAAGACATGCAAAAAGAT 57.285 25.926 0.00 0.00 34.88 2.40
3025 3519 8.980610 CATTTGTAATCAAGACATGCAAAAAGA 58.019 29.630 0.00 0.00 34.88 2.52
3026 3520 8.980610 TCATTTGTAATCAAGACATGCAAAAAG 58.019 29.630 0.00 0.00 34.88 2.27
3027 3521 8.883954 TCATTTGTAATCAAGACATGCAAAAA 57.116 26.923 0.00 0.00 34.88 1.94
3034 3528 8.044060 ACACGAATCATTTGTAATCAAGACAT 57.956 30.769 0.00 0.00 34.88 3.06
3047 3546 4.126437 TGGCGATGATACACGAATCATTT 58.874 39.130 11.84 0.00 44.69 2.32
3326 3882 8.771920 ATTAACAAATCTGAGTGTCGTATTGA 57.228 30.769 0.00 0.00 0.00 2.57
3363 3919 3.126831 GAGTCGAGGATGTAGGCATTTG 58.873 50.000 0.00 0.00 35.07 2.32
3380 3936 3.560896 AGGAGCGTTTATAGTCGAGAGTC 59.439 47.826 0.00 0.00 0.00 3.36
3386 3942 3.766151 TGTTGAGGAGCGTTTATAGTCG 58.234 45.455 0.00 0.00 0.00 4.18
3448 4004 2.435234 GTTGTCGCACCCCGCATA 60.435 61.111 0.00 0.00 42.60 3.14
3484 4040 2.107343 TCCCAACACACGACACGG 59.893 61.111 0.00 0.00 0.00 4.94
3499 4055 2.355818 GGATTGTAAGAGTGGGTGGTCC 60.356 54.545 0.00 0.00 0.00 4.46
3560 4116 4.346709 TGAAGATTGTGGAGTTGACTGGTA 59.653 41.667 0.00 0.00 0.00 3.25
3607 4164 3.702792 AGGACAGTAGTAGTGATGCAGT 58.297 45.455 12.05 0.00 0.00 4.40
3610 4167 3.447586 TGGAAGGACAGTAGTAGTGATGC 59.552 47.826 12.05 2.15 0.00 3.91
3613 4170 4.108501 TGTGGAAGGACAGTAGTAGTGA 57.891 45.455 12.05 0.00 0.00 3.41
3618 4175 2.290323 GGCATTGTGGAAGGACAGTAGT 60.290 50.000 0.00 0.00 0.00 2.73
3629 4186 3.168035 AGTGTATTTGGGCATTGTGGA 57.832 42.857 0.00 0.00 0.00 4.02
3632 4189 6.717289 TCTACTAAGTGTATTTGGGCATTGT 58.283 36.000 0.00 0.00 0.00 2.71
3665 4222 3.235200 TGGGTTGGATTTTACTTGGTGG 58.765 45.455 0.00 0.00 0.00 4.61
3689 4246 0.031721 ACCACACGAAGACGAAGGTC 59.968 55.000 0.00 0.00 43.76 3.85
3740 4297 7.684529 ACAAAATGTGGGGAAAAATAGCATAA 58.315 30.769 0.00 0.00 0.00 1.90
3741 4298 7.251321 ACAAAATGTGGGGAAAAATAGCATA 57.749 32.000 0.00 0.00 0.00 3.14
3753 4310 3.194116 CCATCAGAGAACAAAATGTGGGG 59.806 47.826 0.00 0.00 0.00 4.96
3817 4374 8.585189 AAAGAAACAAACTACTACTTCCGTAG 57.415 34.615 0.00 0.00 46.82 3.51
3887 4444 2.431057 AGACGGTCCACTGGATAACATC 59.569 50.000 4.14 0.00 32.73 3.06
3888 4445 2.431057 GAGACGGTCCACTGGATAACAT 59.569 50.000 4.14 0.00 32.73 2.71
3889 4446 1.822990 GAGACGGTCCACTGGATAACA 59.177 52.381 4.14 0.00 32.73 2.41


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

AutoCloner maintained by Alex Coulton.