Multiple sequence alignment - TraesCS2A01G067300

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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 TraesCS2A01G067300 chr2A 100.000 3565 0 0 1 3565 30128344 30124780 0.000000e+00 6584.0
1 TraesCS2A01G067300 chr2A 89.045 1780 149 25 1320 3081 30086432 30084681 0.000000e+00 2165.0
2 TraesCS2A01G067300 chr2A 88.973 1723 149 28 1452 3152 30091205 30089502 0.000000e+00 2091.0
3 TraesCS2A01G067300 chr2A 87.827 879 77 21 2122 2979 30076494 30075625 0.000000e+00 1003.0
4 TraesCS2A01G067300 chr2A 92.932 665 31 11 1452 2108 30080139 30079483 0.000000e+00 953.0
5 TraesCS2A01G067300 chr2A 89.333 375 17 6 876 1241 30091876 30091516 1.950000e-122 449.0
6 TraesCS2A01G067300 chr2A 89.722 360 22 6 895 1241 30087003 30086646 2.530000e-121 446.0
7 TraesCS2A01G067300 chr2A 87.240 384 43 3 436 819 30092276 30091899 1.970000e-117 433.0
8 TraesCS2A01G067300 chr2A 88.301 359 25 8 895 1239 30080826 30080471 7.120000e-112 414.0
9 TraesCS2A01G067300 chr2A 92.647 136 10 0 268 403 30092415 30092280 2.810000e-46 196.0
10 TraesCS2A01G067300 chr2A 90.909 77 7 0 674 750 30092365 30092289 1.750000e-18 104.0
11 TraesCS2A01G067300 chr2A 89.362 47 5 0 1251 1297 150913991 150914037 3.840000e-05 60.2
12 TraesCS2A01G067300 chr2B 92.410 2846 134 34 791 3565 44362121 44359287 0.000000e+00 3984.0
13 TraesCS2A01G067300 chr2B 90.050 1608 130 21 1452 3038 44352365 44350767 0.000000e+00 2056.0
14 TraesCS2A01G067300 chr2B 89.757 1562 116 25 1538 3083 44347062 44345529 0.000000e+00 1958.0
15 TraesCS2A01G067300 chr2B 90.032 632 50 6 108 737 44362745 44362125 0.000000e+00 806.0
16 TraesCS2A01G067300 chr2B 85.366 697 58 23 558 1239 44353367 44352700 0.000000e+00 682.0
17 TraesCS2A01G067300 chr2B 89.722 360 22 6 895 1241 44347951 44347594 2.530000e-121 446.0
18 TraesCS2A01G067300 chr2B 82.895 228 26 7 1320 1539 44347388 44347166 3.630000e-45 193.0
19 TraesCS2A01G067300 chr2B 92.208 77 6 0 674 750 44362543 44362467 3.760000e-20 110.0
20 TraesCS2A01G067300 chr2D 93.345 2284 105 21 727 2979 27902906 27900639 0.000000e+00 3332.0
21 TraesCS2A01G067300 chr2D 90.187 1549 106 30 1452 2979 27888548 27887025 0.000000e+00 1977.0
22 TraesCS2A01G067300 chr2D 89.212 1548 120 32 1320 2847 27891907 27890387 0.000000e+00 1890.0
23 TraesCS2A01G067300 chr2D 89.913 575 36 7 155 728 27903985 27903432 0.000000e+00 721.0
24 TraesCS2A01G067300 chr2D 91.029 379 19 7 876 1241 27892492 27892116 6.870000e-137 497.0
25 TraesCS2A01G067300 chr2D 88.806 402 32 11 430 825 27892903 27892509 6.920000e-132 481.0
26 TraesCS2A01G067300 chr2D 89.385 358 22 7 896 1239 27889234 27888879 1.520000e-118 436.0
27 TraesCS2A01G067300 chr2D 91.463 164 14 0 1 164 27904305 27904142 3.580000e-55 226.0
28 TraesCS2A01G067300 chr2D 89.610 77 5 1 674 750 27903831 27903758 1.050000e-15 95.3
29 TraesCS2A01G067300 chr3D 93.617 47 3 0 1251 1297 608238759 608238805 1.780000e-08 71.3
30 TraesCS2A01G067300 chr3A 88.889 54 4 2 1249 1300 95018397 95018344 8.260000e-07 65.8
31 TraesCS2A01G067300 chr4D 86.441 59 6 2 1249 1306 30221540 30221483 2.970000e-06 63.9
32 TraesCS2A01G067300 chr3B 89.583 48 5 0 1250 1297 125576558 125576605 1.070000e-05 62.1
33 TraesCS2A01G067300 chr3B 90.909 44 4 0 1255 1298 152833032 152832989 3.840000e-05 60.2
34 TraesCS2A01G067300 chrUn 89.130 46 5 0 1252 1297 478962443 478962488 1.380000e-04 58.4


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 TraesCS2A01G067300 chr2A 30124780 30128344 3564 True 6584.000000 6584 100.00000 1 3565 1 chr2A.!!$R1 3564
1 TraesCS2A01G067300 chr2A 30075625 30092415 16790 True 825.400000 2165 89.69290 268 3152 10 chr2A.!!$R2 2884
2 TraesCS2A01G067300 chr2B 44359287 44362745 3458 True 1633.333333 3984 91.55000 108 3565 3 chr2B.!!$R2 3457
3 TraesCS2A01G067300 chr2B 44345529 44353367 7838 True 1067.000000 2056 87.55800 558 3083 5 chr2B.!!$R1 2525
4 TraesCS2A01G067300 chr2D 27900639 27904305 3666 True 1093.575000 3332 91.08275 1 2979 4 chr2D.!!$R2 2978
5 TraesCS2A01G067300 chr2D 27887025 27892903 5878 True 1056.200000 1977 89.72380 430 2979 5 chr2D.!!$R1 2549

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
104 105 0.466543 GCCACCCGTGTATCCATGTA 59.533 55.0 0.0 0.0 0.00 2.29 F
219 386 0.729116 CATTCATTTGTCGCTCCGCT 59.271 50.0 0.0 0.0 0.00 5.52 F
1039 1762 1.133809 TGAGGGGTGTAGCCAAGCTT 61.134 55.0 0.0 0.0 40.44 3.74 F
2155 13147 0.725784 GTTCACATTTGTCGGCAGCG 60.726 55.0 0.0 0.0 0.00 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1018 1728 0.837272 GCTTGGCTACACCCCTCATA 59.163 55.000 0.00 0.0 37.83 2.15 R
1301 2155 1.270625 TGTTGGTCCTACCTCGCAAAG 60.271 52.381 0.72 0.0 39.58 2.77 R
2510 16728 2.762887 TCAATTTCCAACTGTTGCCACA 59.237 40.909 14.94 0.0 0.00 4.17 R
3252 26670 0.670546 AGTCAGGTTCCGACATTGCG 60.671 55.000 13.09 0.0 35.77 4.85 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
42 43 3.760580 CAGAGGACTGTTATGATCCCC 57.239 52.381 0.00 0.00 39.11 4.81
50 51 7.956357 AGGACTGTTATGATCCCCTATACTAT 58.044 38.462 0.00 0.00 32.47 2.12
56 57 7.561722 TGTTATGATCCCCTATACTATCAGAGC 59.438 40.741 0.00 0.00 32.25 4.09
60 61 1.402259 CCCTATACTATCAGAGCGCGG 59.598 57.143 8.83 0.00 0.00 6.46
78 79 1.745232 GGCCATTATGTGTTGGTCGA 58.255 50.000 0.00 0.00 35.34 4.20
84 85 5.708948 CCATTATGTGTTGGTCGATGTTTT 58.291 37.500 0.00 0.00 0.00 2.43
86 87 2.483583 TGTGTTGGTCGATGTTTTGC 57.516 45.000 0.00 0.00 0.00 3.68
91 92 1.175983 TGGTCGATGTTTTGCCACCC 61.176 55.000 0.00 0.00 0.00 4.61
104 105 0.466543 GCCACCCGTGTATCCATGTA 59.533 55.000 0.00 0.00 0.00 2.29
111 112 3.007506 CCCGTGTATCCATGTATTAGGCA 59.992 47.826 0.00 0.00 0.00 4.75
127 128 1.224592 GCACCAGGTGGATGGGTAG 59.775 63.158 21.77 0.00 45.25 3.18
144 145 4.079154 TGGGTAGACCTCATCAGATAGTGT 60.079 45.833 0.00 0.00 41.11 3.55
201 368 2.745308 CCGGGGTGCATCTCCATCA 61.745 63.158 0.00 0.00 36.19 3.07
219 386 0.729116 CATTCATTTGTCGCTCCGCT 59.271 50.000 0.00 0.00 0.00 5.52
332 502 5.116180 AGACACAAACACAAATCTTCGAGA 58.884 37.500 0.00 0.00 0.00 4.04
333 503 5.584649 AGACACAAACACAAATCTTCGAGAA 59.415 36.000 0.00 0.00 0.00 2.87
334 504 5.810525 ACACAAACACAAATCTTCGAGAAG 58.189 37.500 6.51 6.51 39.71 2.85
343 513 8.836413 ACACAAATCTTCGAGAAGTAATTTTCA 58.164 29.630 12.01 0.00 39.38 2.69
360 530 7.833285 AATTTTCAGGAGCAGTAACCTTTTA 57.167 32.000 0.00 0.00 33.91 1.52
365 535 5.995897 TCAGGAGCAGTAACCTTTTAGAAAC 59.004 40.000 0.00 0.00 33.91 2.78
459 631 2.484062 CCCGATTGCCATGGAGTGC 61.484 63.158 18.40 0.00 0.00 4.40
583 755 3.988379 TTTGAACAAGAGTGCCATGTC 57.012 42.857 0.00 0.00 0.00 3.06
599 771 6.425114 GTGCCATGTCTATATAACCAGTTCAG 59.575 42.308 0.00 0.00 0.00 3.02
612 784 5.508200 ACCAGTTCAGCGTATTTTTCAAA 57.492 34.783 0.00 0.00 0.00 2.69
617 789 6.577055 CAGTTCAGCGTATTTTTCAAATTCGA 59.423 34.615 11.10 0.00 0.00 3.71
758 1460 3.922171 AGTGGGAGCCTTAGATGAAAG 57.078 47.619 0.00 0.00 0.00 2.62
780 1482 2.649531 ACGGTAGATGAGGAGAGAGG 57.350 55.000 0.00 0.00 0.00 3.69
953 1657 1.597027 AACAGGCAAAGGACGACCG 60.597 57.895 0.00 0.00 41.83 4.79
1018 1728 4.276183 CGCTGATATATATACTGGAGCGGT 59.724 45.833 19.25 0.00 43.23 5.68
1039 1762 1.133809 TGAGGGGTGTAGCCAAGCTT 61.134 55.000 0.00 0.00 40.44 3.74
1230 1953 2.265589 TCAGATGCATGCAGGTATGG 57.734 50.000 26.69 11.73 0.00 2.74
1249 1972 7.125356 AGGTATGGAAACTAATTACTTCCTCGT 59.875 37.037 17.00 9.52 39.54 4.18
1317 2171 3.814005 TTATCTTTGCGAGGTAGGACC 57.186 47.619 0.00 0.00 38.99 4.46
1327 2181 2.165845 CGAGGTAGGACCAACACTAAGG 59.834 54.545 0.00 0.00 41.95 2.69
1364 2218 4.678509 TGTCGGCACAGTTGATTAATTC 57.321 40.909 0.00 0.00 0.00 2.17
1526 2392 6.729391 TGTGAACGGAAATCGATTTTATCA 57.271 33.333 23.49 19.79 42.43 2.15
1530 2396 7.007099 GTGAACGGAAATCGATTTTATCACAAC 59.993 37.037 29.67 19.58 42.43 3.32
1645 2523 0.911769 TGGGCAGACCATAAGGAGTG 59.088 55.000 0.00 0.00 46.80 3.51
1659 2537 8.058847 ACCATAAGGAGTGATTTTTGCCTTATA 58.941 33.333 10.97 0.00 45.39 0.98
1701 2579 4.977963 CACCAAGTGTTGATCAATTGTGTC 59.022 41.667 12.12 6.05 46.49 3.67
1702 2580 4.221342 CCAAGTGTTGATCAATTGTGTCG 58.779 43.478 12.12 0.00 46.49 4.35
1704 2582 4.732285 AGTGTTGATCAATTGTGTCGAC 57.268 40.909 12.12 9.11 0.00 4.20
1780 2658 2.121963 TTGCCACCCCTCTCCACT 60.122 61.111 0.00 0.00 0.00 4.00
2155 13147 0.725784 GTTCACATTTGTCGGCAGCG 60.726 55.000 0.00 0.00 0.00 5.18
2395 16611 7.532884 GCATTGTTTTCTTCTCATGCATTTTTC 59.467 33.333 0.00 0.00 34.31 2.29
2400 16617 5.892160 TCTTCTCATGCATTTTTCCTCAG 57.108 39.130 0.00 0.00 0.00 3.35
2402 16619 5.771666 TCTTCTCATGCATTTTTCCTCAGTT 59.228 36.000 0.00 0.00 0.00 3.16
2491 16709 5.774690 TGGAGAAACACATAAAAAGATGGCT 59.225 36.000 0.00 0.00 0.00 4.75
2492 16710 6.945435 TGGAGAAACACATAAAAAGATGGCTA 59.055 34.615 0.00 0.00 0.00 3.93
2510 16728 3.895656 GGCTAAGAACCCCTTGAAAACTT 59.104 43.478 0.00 0.00 36.34 2.66
2676 16930 5.746307 ACATCGATTCATCAAAGACATGG 57.254 39.130 0.00 0.00 0.00 3.66
2793 17051 9.970395 ACAAATATGTGCAAATTACATATCCAG 57.030 29.630 11.13 7.93 45.91 3.86
2897 17159 1.275666 ACATCGGTCCTTCCATGACA 58.724 50.000 0.00 0.00 34.36 3.58
2986 26403 9.793259 TCCATATCCAGTCATAAAATTAGGAAC 57.207 33.333 0.00 0.00 0.00 3.62
3097 26514 2.141011 TTGGGGTGGATGGCTGTGAG 62.141 60.000 0.00 0.00 0.00 3.51
3121 26538 1.226018 GGCTAATTCACGCGCACAC 60.226 57.895 5.73 0.00 0.00 3.82
3141 26559 1.351707 CCCACGCGATCAATTTCCG 59.648 57.895 15.93 0.00 0.00 4.30
3145 26563 2.190161 CACGCGATCAATTTCCGACTA 58.810 47.619 15.93 0.00 0.00 2.59
3154 26572 3.006430 TCAATTTCCGACTAGCTGTCACA 59.994 43.478 14.09 0.00 45.60 3.58
3173 26591 1.472480 CAAAGGGTTAGGGAATGCGTG 59.528 52.381 0.00 0.00 0.00 5.34
3176 26594 1.910671 AGGGTTAGGGAATGCGTGTAA 59.089 47.619 0.00 0.00 0.00 2.41
3185 26603 2.218603 GAATGCGTGTAATAGGTGGGG 58.781 52.381 0.00 0.00 0.00 4.96
3197 26615 2.723530 AGGTGGGGCTGCTATACTAT 57.276 50.000 0.00 0.00 0.00 2.12
3217 26635 2.276740 GGGGCCACCATTCTCAGG 59.723 66.667 4.39 0.00 39.85 3.86
3227 26645 4.023193 CCACCATTCTCAGGTAAACAACAC 60.023 45.833 0.00 0.00 37.23 3.32
3228 26646 4.578516 CACCATTCTCAGGTAAACAACACA 59.421 41.667 0.00 0.00 37.23 3.72
3230 26648 4.578516 CCATTCTCAGGTAAACAACACACA 59.421 41.667 0.00 0.00 0.00 3.72
3252 26670 7.277760 ACACAAAAGTTTGAAAAGGAACATAGC 59.722 33.333 10.66 0.00 40.55 2.97
3253 26671 6.475402 ACAAAAGTTTGAAAAGGAACATAGCG 59.525 34.615 10.66 0.00 40.55 4.26
3254 26672 4.160736 AGTTTGAAAAGGAACATAGCGC 57.839 40.909 0.00 0.00 0.00 5.92
3255 26673 3.568007 AGTTTGAAAAGGAACATAGCGCA 59.432 39.130 11.47 0.00 0.00 6.09
3256 26674 4.037446 AGTTTGAAAAGGAACATAGCGCAA 59.963 37.500 11.47 0.00 0.00 4.85
3259 26677 3.505680 TGAAAAGGAACATAGCGCAATGT 59.494 39.130 11.47 0.00 41.87 2.71
3260 26678 3.764885 AAAGGAACATAGCGCAATGTC 57.235 42.857 11.47 0.00 39.16 3.06
3261 26679 1.290203 AGGAACATAGCGCAATGTCG 58.710 50.000 11.47 0.00 39.16 4.35
3262 26680 0.304705 GGAACATAGCGCAATGTCGG 59.695 55.000 11.47 0.00 39.16 4.79
3279 26699 2.166664 GTCGGAACCTGACTGCTTCTAT 59.833 50.000 0.00 0.00 33.54 1.98
3329 26749 3.366374 GGCGAAGGAGTCTTTTTGGATTG 60.366 47.826 0.00 0.00 32.52 2.67
3390 26811 7.857734 AAAATGATGATACCACATTGTCGTA 57.142 32.000 0.00 0.00 35.00 3.43
3408 26829 3.709653 TCGTAGGAAAGGCCACATCTAAT 59.290 43.478 5.01 0.00 40.02 1.73
3414 26835 4.439057 GAAAGGCCACATCTAATACACGA 58.561 43.478 5.01 0.00 0.00 4.35
3416 26837 3.995199 AGGCCACATCTAATACACGATG 58.005 45.455 5.01 0.00 42.03 3.84
3420 26841 4.501571 GCCACATCTAATACACGATGGAGT 60.502 45.833 0.00 0.00 40.93 3.85
3495 26921 5.783111 ACTTCATGAATTTTAGTGTTGGCC 58.217 37.500 8.96 0.00 0.00 5.36
3505 26931 2.271944 AGTGTTGGCCTGGTTTACTC 57.728 50.000 3.32 0.00 0.00 2.59
3517 26943 4.326826 CTGGTTTACTCTCATGGCAAAGA 58.673 43.478 0.00 0.00 0.00 2.52
3530 26956 8.974238 TCTCATGGCAAAGAATTTCTTCATAAT 58.026 29.630 11.92 2.68 35.03 1.28
3557 26983 5.139727 TGAGGTGGCCTTATATTTTGATGG 58.860 41.667 3.32 0.00 31.76 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.010696 TCTGTCTGATGAGGTCACCTACT 59.989 47.826 0.00 0.00 31.76 2.57
42 43 1.202200 GGCCGCGCTCTGATAGTATAG 60.202 57.143 5.56 0.00 0.00 1.31
50 51 1.595109 CATAATGGCCGCGCTCTGA 60.595 57.895 5.56 0.00 0.00 3.27
56 57 1.063972 CCAACACATAATGGCCGCG 59.936 57.895 0.00 0.00 0.00 6.46
60 61 2.682856 ACATCGACCAACACATAATGGC 59.317 45.455 0.00 0.00 40.51 4.40
78 79 1.816224 GATACACGGGTGGCAAAACAT 59.184 47.619 0.00 0.00 34.19 2.71
104 105 0.552848 CCATCCACCTGGTGCCTAAT 59.447 55.000 21.47 8.59 36.34 1.73
111 112 0.620700 GGTCTACCCATCCACCTGGT 60.621 60.000 0.00 0.00 34.23 4.00
127 128 2.544694 CCGCACACTATCTGATGAGGTC 60.545 54.545 0.00 0.00 0.00 3.85
160 161 4.163649 GGCCAGTATAAGTAGAAGGTTGGT 59.836 45.833 0.00 0.00 0.00 3.67
219 386 3.962530 AAGGGGGAAGGGATGCGGA 62.963 63.158 0.00 0.00 0.00 5.54
332 502 6.543735 AGGTTACTGCTCCTGAAAATTACTT 58.456 36.000 0.00 0.00 32.29 2.24
333 503 6.128138 AGGTTACTGCTCCTGAAAATTACT 57.872 37.500 0.00 0.00 32.29 2.24
334 504 6.819397 AAGGTTACTGCTCCTGAAAATTAC 57.181 37.500 0.00 0.00 33.97 1.89
343 513 5.937111 TGTTTCTAAAAGGTTACTGCTCCT 58.063 37.500 0.00 0.00 35.34 3.69
365 535 7.254421 GGCTCCCGCTAATTTTGATTTATTTTG 60.254 37.037 0.00 0.00 36.09 2.44
384 554 1.966451 GTGGTTGTCAAGGCTCCCG 60.966 63.158 0.00 0.00 0.00 5.14
420 592 1.203038 TCCCACATGTCAAGGCACAAT 60.203 47.619 0.00 0.00 0.00 2.71
428 600 0.695924 AATCGGGTCCCACATGTCAA 59.304 50.000 9.12 0.00 0.00 3.18
476 648 1.069765 CTTGCAGTGTCGGGACAGT 59.930 57.895 0.94 2.24 45.21 3.55
599 771 5.932021 ATGCTCGAATTTGAAAAATACGC 57.068 34.783 0.00 0.00 0.00 4.42
612 784 5.580691 TCGATGTTCACTTTAATGCTCGAAT 59.419 36.000 0.00 0.00 30.59 3.34
617 789 4.201950 GCCATCGATGTTCACTTTAATGCT 60.202 41.667 23.27 0.00 0.00 3.79
758 1460 3.071479 CTCTCTCCTCATCTACCGTAGC 58.929 54.545 0.18 0.00 0.00 3.58
903 1607 3.133437 TCCCTCTGGATAAGCGGAG 57.867 57.895 0.00 0.00 35.03 4.63
953 1657 1.276138 CCAACAAGATTTCCAAGGGGC 59.724 52.381 0.00 0.00 0.00 5.80
997 1707 8.622948 TCATACCGCTCCAGTATATATATCAG 57.377 38.462 0.00 0.00 0.00 2.90
1018 1728 0.837272 GCTTGGCTACACCCCTCATA 59.163 55.000 0.00 0.00 37.83 2.15
1200 1923 1.958205 GCATCTGATCCTTCCGCCG 60.958 63.158 0.00 0.00 0.00 6.46
1249 1972 8.682710 AGTGTTGCAGTTTTGAACTAAGATTAA 58.317 29.630 0.00 0.00 40.46 1.40
1301 2155 1.270625 TGTTGGTCCTACCTCGCAAAG 60.271 52.381 0.72 0.00 39.58 2.77
1327 2181 7.192913 TGTGCCGACAAAAATATTCATATGAC 58.807 34.615 4.48 0.00 0.00 3.06
1331 2185 6.751514 ACTGTGCCGACAAAAATATTCATA 57.248 33.333 0.00 0.00 0.00 2.15
1364 2218 6.774656 AGGATAGCTTTGGAAAATACCTGATG 59.225 38.462 0.00 0.00 0.00 3.07
1590 2466 2.551459 CTCCACAAGCAAGAAGGTCAAG 59.449 50.000 0.00 0.00 0.00 3.02
1659 2537 3.149981 GTGCTTAAAGAAAGACCTGGCT 58.850 45.455 0.00 0.00 37.38 4.75
1701 2579 3.491619 CCACACCTGAATAGATGGAGTCG 60.492 52.174 0.00 0.00 0.00 4.18
1702 2580 3.742640 GCCACACCTGAATAGATGGAGTC 60.743 52.174 0.00 0.00 0.00 3.36
1704 2582 2.486191 GGCCACACCTGAATAGATGGAG 60.486 54.545 0.00 0.00 34.51 3.86
1780 2658 2.300996 CTGCTTTAGGAGGGCCTCA 58.699 57.895 33.27 12.89 45.54 3.86
2155 13147 3.498777 AGAAGTAAAACCGAGAAAGCAGC 59.501 43.478 0.00 0.00 0.00 5.25
2205 13197 7.954835 ACGTTGGTAGGTGCTTACATAATATA 58.045 34.615 0.00 0.00 0.00 0.86
2491 16709 4.647399 CCACAAGTTTTCAAGGGGTTCTTA 59.353 41.667 0.00 0.00 33.68 2.10
2492 16710 3.450817 CCACAAGTTTTCAAGGGGTTCTT 59.549 43.478 0.00 0.00 35.79 2.52
2510 16728 2.762887 TCAATTTCCAACTGTTGCCACA 59.237 40.909 14.94 0.00 0.00 4.17
2522 16769 5.818887 TCATCTGGTTCTCATCAATTTCCA 58.181 37.500 0.00 0.00 0.00 3.53
2589 16841 6.099341 GTCCTTGTCTTGTTTTGACACATTT 58.901 36.000 0.00 0.00 43.13 2.32
2592 16844 4.075682 TGTCCTTGTCTTGTTTTGACACA 58.924 39.130 0.00 0.00 43.13 3.72
2676 16930 5.277297 GGTGCAAAATGGTTAGAAAAAGTGC 60.277 40.000 0.00 0.00 0.00 4.40
2733 16990 9.747898 ACACATTCTATGGTTTACTGGAATTTA 57.252 29.630 0.00 0.00 33.60 1.40
2793 17051 4.657436 AGATATCTTGGGACTCGTCAAC 57.343 45.455 0.00 0.00 0.00 3.18
2822 17080 6.677781 TCATCGTAGAAGGCCAAAATTTAG 57.322 37.500 5.01 0.00 43.58 1.85
3012 26429 5.000591 TGTGTGTACCTCCACAATGTAATG 58.999 41.667 7.43 0.00 46.22 1.90
3079 26496 2.531428 TCACAGCCATCCACCCCA 60.531 61.111 0.00 0.00 0.00 4.96
3090 26507 1.348775 ATTAGCCTCCCCCTCACAGC 61.349 60.000 0.00 0.00 0.00 4.40
3097 26514 1.526225 GCGTGAATTAGCCTCCCCC 60.526 63.158 0.00 0.00 0.00 5.40
3145 26563 1.073923 CCCTAACCCTTTGTGACAGCT 59.926 52.381 0.00 0.00 0.00 4.24
3154 26572 1.074889 ACACGCATTCCCTAACCCTTT 59.925 47.619 0.00 0.00 0.00 3.11
3173 26591 3.838903 AGTATAGCAGCCCCACCTATTAC 59.161 47.826 0.00 0.00 0.00 1.89
3176 26594 2.723530 AGTATAGCAGCCCCACCTAT 57.276 50.000 0.00 0.00 0.00 2.57
3185 26603 1.339151 GGCCCCACATAGTATAGCAGC 60.339 57.143 0.00 0.00 0.00 5.25
3212 26630 5.949735 ACTTTTGTGTGTTGTTTACCTGAG 58.050 37.500 0.00 0.00 0.00 3.35
3217 26635 9.364110 CTTTTCAAACTTTTGTGTGTTGTTTAC 57.636 29.630 1.75 0.00 38.74 2.01
3227 26645 7.515059 CGCTATGTTCCTTTTCAAACTTTTGTG 60.515 37.037 1.75 0.00 39.18 3.33
3228 26646 6.475402 CGCTATGTTCCTTTTCAAACTTTTGT 59.525 34.615 1.75 0.00 39.18 2.83
3230 26648 5.462068 GCGCTATGTTCCTTTTCAAACTTTT 59.538 36.000 0.00 0.00 0.00 2.27
3252 26670 0.670546 AGTCAGGTTCCGACATTGCG 60.671 55.000 13.09 0.00 35.77 4.85
3253 26671 0.798776 CAGTCAGGTTCCGACATTGC 59.201 55.000 13.09 0.00 35.77 3.56
3254 26672 0.798776 GCAGTCAGGTTCCGACATTG 59.201 55.000 13.09 7.26 35.77 2.82
3255 26673 0.687354 AGCAGTCAGGTTCCGACATT 59.313 50.000 13.09 0.88 35.77 2.71
3256 26674 0.687354 AAGCAGTCAGGTTCCGACAT 59.313 50.000 13.09 1.31 35.77 3.06
3306 26726 0.881796 CCAAAAAGACTCCTTCGCCC 59.118 55.000 0.00 0.00 0.00 6.13
3308 26728 3.253432 ACAATCCAAAAAGACTCCTTCGC 59.747 43.478 0.00 0.00 0.00 4.70
3309 26729 4.515191 TCACAATCCAAAAAGACTCCTTCG 59.485 41.667 0.00 0.00 0.00 3.79
3329 26749 9.836076 GTAAAAGGTCTTACATATTGGTTTCAC 57.164 33.333 0.00 0.00 32.91 3.18
3384 26805 0.981183 ATGTGGCCTTTCCTACGACA 59.019 50.000 3.32 0.00 35.26 4.35
3390 26811 4.683400 CGTGTATTAGATGTGGCCTTTCCT 60.683 45.833 3.32 0.00 35.26 3.36
3414 26835 5.965033 AGAAAGTGATGGTATGACTCCAT 57.035 39.130 0.00 0.00 46.78 3.41
3416 26837 6.173339 TGAAAGAAAGTGATGGTATGACTCC 58.827 40.000 0.00 0.00 0.00 3.85
3420 26841 9.685276 ATTACATGAAAGAAAGTGATGGTATGA 57.315 29.630 0.00 0.00 0.00 2.15
3492 26918 2.019156 GCCATGAGAGTAAACCAGGCC 61.019 57.143 0.00 0.00 34.94 5.19
3495 26921 4.326826 TCTTTGCCATGAGAGTAAACCAG 58.673 43.478 0.00 0.00 0.00 4.00
3505 26931 9.031360 CATTATGAAGAAATTCTTTGCCATGAG 57.969 33.333 9.84 1.27 36.73 2.90
3517 26943 7.418254 GGCCACCTCATTCATTATGAAGAAATT 60.418 37.037 13.29 0.00 42.56 1.82
3530 26956 6.430864 TCAAAATATAAGGCCACCTCATTCA 58.569 36.000 5.01 0.00 30.89 2.57


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

AutoCloner maintained by Alex Coulton.