Multiple sequence alignment - TraesCS1D01G166600

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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 TraesCS1D01G166600 chr1D 100.000 4821 0 0 1 4821 237807529 237802709 0.000000e+00 8903.0
1 TraesCS1D01G166600 chr1B 90.451 2817 132 45 313 3070 336645767 336648505 0.000000e+00 3585.0
2 TraesCS1D01G166600 chr1B 92.705 987 41 13 3205 4184 336648583 336649545 0.000000e+00 1395.0
3 TraesCS1D01G166600 chr1B 92.834 628 29 8 930 1544 434763927 434764551 0.000000e+00 896.0
4 TraesCS1D01G166600 chr1B 91.083 314 15 6 1 311 336645335 336645638 3.470000e-111 412.0
5 TraesCS1D01G166600 chr1B 92.941 255 11 3 4262 4515 336649705 336649953 9.860000e-97 364.0
6 TraesCS1D01G166600 chr1B 90.805 87 6 2 4183 4267 336649573 336649659 1.100000e-21 115.0
7 TraesCS1D01G166600 chr1B 91.011 89 0 1 4682 4770 336650215 336650295 3.940000e-21 113.0
8 TraesCS1D01G166600 chr1A 92.952 1433 42 21 730 2136 301200165 301198766 0.000000e+00 2032.0
9 TraesCS1D01G166600 chr1A 92.540 1126 44 23 3088 4184 301197767 301196653 0.000000e+00 1578.0
10 TraesCS1D01G166600 chr1A 93.008 944 41 11 2135 3076 301198733 301197813 0.000000e+00 1354.0
11 TraesCS1D01G166600 chr1A 83.431 513 43 25 4283 4770 301196486 301195991 5.730000e-119 438.0
12 TraesCS1D01G166600 chr1A 91.279 172 13 2 460 630 301200504 301200334 2.900000e-57 233.0
13 TraesCS1D01G166600 chr1A 89.189 185 8 2 3 187 301201770 301201598 2.260000e-53 220.0
14 TraesCS1D01G166600 chr1A 94.318 88 4 1 4181 4267 301196627 301196540 3.030000e-27 134.0
15 TraesCS1D01G166600 chr1A 93.056 72 5 0 313 384 301200784 301200713 6.600000e-19 106.0
16 TraesCS1D01G166600 chr1A 95.082 61 0 1 672 732 301200325 301200268 5.140000e-15 93.5
17 TraesCS1D01G166600 chr1A 85.000 100 1 3 184 280 301201325 301201237 6.650000e-14 89.8
18 TraesCS1D01G166600 chr1A 97.727 44 1 0 4778 4821 301195953 301195910 5.170000e-10 76.8
19 TraesCS1D01G166600 chr3D 89.465 617 45 7 2128 2736 20623353 20622749 0.000000e+00 761.0
20 TraesCS1D01G166600 chr5B 93.037 517 26 6 1031 1544 13200678 13200169 0.000000e+00 747.0
21 TraesCS1D01G166600 chr5B 84.382 429 46 8 2392 2819 342860356 342860764 7.520000e-108 401.0
22 TraesCS1D01G166600 chr5B 93.023 43 3 0 2305 2347 503730713 503730671 4.030000e-06 63.9
23 TraesCS1D01G166600 chr6B 92.731 454 20 8 1109 1552 720461104 720460654 1.130000e-180 643.0
24 TraesCS1D01G166600 chrUn 87.697 317 26 4 2421 2736 70269693 70269389 1.650000e-94 357.0
25 TraesCS1D01G166600 chrUn 86.250 160 12 3 2660 2819 367340376 367340227 1.070000e-36 165.0
26 TraesCS1D01G166600 chr2A 87.342 316 29 2 2421 2736 610249835 610250139 7.680000e-93 351.0
27 TraesCS1D01G166600 chr5A 87.138 311 26 4 2427 2736 70977795 70977498 1.660000e-89 340.0
28 TraesCS1D01G166600 chr5A 86.174 311 30 4 2427 2736 291396566 291396864 1.670000e-84 324.0


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 TraesCS1D01G166600 chr1D 237802709 237807529 4820 True 8903.000000 8903 100.000000 1 4821 1 chr1D.!!$R1 4820
1 TraesCS1D01G166600 chr1B 336645335 336650295 4960 False 997.333333 3585 91.499333 1 4770 6 chr1B.!!$F2 4769
2 TraesCS1D01G166600 chr1B 434763927 434764551 624 False 896.000000 896 92.834000 930 1544 1 chr1B.!!$F1 614
3 TraesCS1D01G166600 chr1A 301195910 301201770 5860 True 577.736364 2032 91.598364 3 4821 11 chr1A.!!$R1 4818
4 TraesCS1D01G166600 chr3D 20622749 20623353 604 True 761.000000 761 89.465000 2128 2736 1 chr3D.!!$R1 608
5 TraesCS1D01G166600 chr5B 13200169 13200678 509 True 747.000000 747 93.037000 1031 1544 1 chr5B.!!$R1 513

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
224 501 0.040336 CGATGGACGTATGGGAGACG 60.040 60.000 0.00 0.0 45.75 4.18 F
395 1127 0.784778 GAACTGCTCGTCAAACGGAG 59.215 55.000 0.00 0.0 42.81 4.63 F
398 1130 1.544691 ACTGCTCGTCAAACGGAGTAT 59.455 47.619 0.00 0.0 45.00 2.12 F
1593 2583 0.966179 ATCCGTCCCAACCTTTTTGC 59.034 50.000 0.00 0.0 0.00 3.68 F
3014 4090 0.031178 CCTTGCAAGTTGTGGCTGTC 59.969 55.000 24.35 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1517 2507 2.117156 CAGCGAAATGGGAGGCAGG 61.117 63.158 0.0 0.0 0.00 4.85 R
1519 2509 2.751436 GCAGCGAAATGGGAGGCA 60.751 61.111 0.0 0.0 0.00 4.75 R
2096 3117 2.916702 AGCCATTATCATCAGCGTGA 57.083 45.000 0.0 0.0 0.00 4.35 R
3086 4162 0.037697 TCGACTGCACGCCTTAACAT 60.038 50.000 0.0 0.0 0.00 2.71 R
4262 5437 0.108585 AGCGAGAAAAAGGACAGCCA 59.891 50.000 0.0 0.0 36.29 4.75 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 2.620242 GGTACGAAAATAGGAACGCCA 58.380 47.619 0.00 0.00 36.29 5.69
79 80 1.935933 AGGAACGCCATAACGACATC 58.064 50.000 0.00 0.00 36.29 3.06
135 136 2.725723 CCATACACGTTTTTGCTTGCTG 59.274 45.455 0.00 0.00 0.00 4.41
136 137 2.483583 TACACGTTTTTGCTTGCTGG 57.516 45.000 0.00 0.00 0.00 4.85
137 138 0.805711 ACACGTTTTTGCTTGCTGGC 60.806 50.000 0.00 0.00 0.00 4.85
138 139 0.805322 CACGTTTTTGCTTGCTGGCA 60.805 50.000 0.33 0.33 40.74 4.92
139 140 0.528249 ACGTTTTTGCTTGCTGGCAG 60.528 50.000 10.94 10.94 43.39 4.85
224 501 0.040336 CGATGGACGTATGGGAGACG 60.040 60.000 0.00 0.00 45.75 4.18
287 866 5.634896 TCGTAGTAACTACTTTGTGCTAGC 58.365 41.667 8.10 8.10 37.73 3.42
311 890 7.764443 AGCTAGTAAACTGCTCGATTTAATGAA 59.236 33.333 0.00 0.00 30.41 2.57
373 1079 2.434359 GTGGTGGCTGCTACCGTC 60.434 66.667 26.86 19.22 41.18 4.79
393 1125 1.487231 CGAACTGCTCGTCAAACGG 59.513 57.895 0.00 0.00 42.81 4.44
395 1127 0.784778 GAACTGCTCGTCAAACGGAG 59.215 55.000 0.00 0.00 42.81 4.63
398 1130 1.544691 ACTGCTCGTCAAACGGAGTAT 59.455 47.619 0.00 0.00 45.00 2.12
452 1185 7.278646 TCGACCAATGAAATGAAGAGTCTAATG 59.721 37.037 0.00 0.00 0.00 1.90
453 1186 7.093322 ACCAATGAAATGAAGAGTCTAATGC 57.907 36.000 0.00 0.00 0.00 3.56
457 1297 8.886719 CAATGAAATGAAGAGTCTAATGCTACA 58.113 33.333 0.00 0.00 0.00 2.74
458 1298 9.624373 AATGAAATGAAGAGTCTAATGCTACAT 57.376 29.630 0.00 0.00 0.00 2.29
556 1396 2.288763 GGTGTCATTTTCCAAATGCCGT 60.289 45.455 4.59 0.00 0.00 5.68
634 1475 3.223157 CAACGCGTGAAGTTAAATGACC 58.777 45.455 14.98 0.00 0.00 4.02
643 1484 6.579292 CGTGAAGTTAAATGACCGCAAAATAA 59.421 34.615 0.00 0.00 0.00 1.40
885 1853 2.360726 AAATCAACCGCCCCGTCC 60.361 61.111 0.00 0.00 0.00 4.79
886 1854 4.770874 AATCAACCGCCCCGTCCG 62.771 66.667 0.00 0.00 0.00 4.79
1170 2148 3.214123 CGGATCCGCGACCACCTA 61.214 66.667 23.37 0.00 0.00 3.08
1501 2488 2.893404 CCGAAATGGTACGGCCCG 60.893 66.667 0.00 0.00 42.55 6.13
1518 2508 4.890306 GCCCCTCCTCCTCCTCCC 62.890 77.778 0.00 0.00 0.00 4.30
1519 2509 3.039526 CCCCTCCTCCTCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
1593 2583 0.966179 ATCCGTCCCAACCTTTTTGC 59.034 50.000 0.00 0.00 0.00 3.68
2096 3117 3.704566 TCAGATTGGTTGGCGTCTAGTAT 59.295 43.478 0.00 0.00 0.00 2.12
2116 3137 3.198409 TCACGCTGATGATAATGGCTT 57.802 42.857 0.00 0.00 0.00 4.35
2209 3264 4.566987 ACTGAAGTACTTCACCGGATTTC 58.433 43.478 30.07 5.64 43.90 2.17
2219 3274 6.942976 ACTTCACCGGATTTCTTACTATTCA 58.057 36.000 9.46 0.00 0.00 2.57
2470 3537 7.046033 ACTACTACCACTACCATTTGCATAAC 58.954 38.462 0.00 0.00 0.00 1.89
2592 3659 9.223099 GTTTGTTAGGGTGAAAGCTATTTACTA 57.777 33.333 0.00 0.00 0.00 1.82
2597 3664 9.969001 TTAGGGTGAAAGCTATTTACTAACATT 57.031 29.630 0.00 0.00 0.00 2.71
2634 3701 8.561738 TGTTTAGAGAATTCAATCTGTTACCC 57.438 34.615 8.44 0.00 0.00 3.69
2647 3714 3.259876 TCTGTTACCCGCATCTTAACTGT 59.740 43.478 0.00 0.00 0.00 3.55
2654 3721 3.370978 CCCGCATCTTAACTGTAACAGTG 59.629 47.826 0.00 0.00 44.62 3.66
2907 3982 4.037222 TGCCATCTGGTTCTGATTAGGTA 58.963 43.478 0.00 0.00 37.57 3.08
2912 3987 7.473511 GCCATCTGGTTCTGATTAGGTAATAGT 60.474 40.741 0.00 0.00 37.57 2.12
2942 4018 4.876107 AGGCAAGATAAGTGGTACGATTTG 59.124 41.667 0.00 0.00 0.00 2.32
3014 4090 0.031178 CCTTGCAAGTTGTGGCTGTC 59.969 55.000 24.35 0.00 0.00 3.51
3078 4154 9.628500 TGATTTAGTCTTGTAGCTGTATCTAGA 57.372 33.333 0.00 0.00 0.00 2.43
3104 4214 0.370273 GATGTTAAGGCGTGCAGTCG 59.630 55.000 0.00 0.00 0.00 4.18
3111 4221 0.528466 AGGCGTGCAGTCGATATGTG 60.528 55.000 0.24 0.00 0.00 3.21
3112 4222 0.806102 GGCGTGCAGTCGATATGTGT 60.806 55.000 0.24 0.00 0.00 3.72
3118 4228 5.190342 CGTGCAGTCGATATGTGTTTAATG 58.810 41.667 0.00 0.00 0.00 1.90
3128 4238 7.041440 TCGATATGTGTTTAATGCCCAATACTG 60.041 37.037 0.00 0.00 0.00 2.74
3133 4243 6.092748 GTGTTTAATGCCCAATACTGACTTG 58.907 40.000 0.00 0.00 0.00 3.16
3188 4300 2.964209 TCCATGTGGAGGATAGAGACC 58.036 52.381 0.00 0.00 39.78 3.85
3233 4369 5.598417 AGCTAAATGTTTTTGTCCTTCCAGT 59.402 36.000 0.00 0.00 0.00 4.00
3292 4428 4.774200 AGAGCAGCCAAGTAAAATTTGGAT 59.226 37.500 8.13 0.00 46.42 3.41
3660 4797 2.222027 CTTCTTCCAGAGCCGTTTTGT 58.778 47.619 0.00 0.00 0.00 2.83
3700 4837 1.253100 TGAAAGCCCGGGATTTTGAC 58.747 50.000 35.58 23.72 33.61 3.18
3796 4933 2.048603 GGAGAGCCACCACCATTGC 61.049 63.158 0.00 0.00 0.00 3.56
3798 4935 2.283101 GAGCCACCACCATTGCCA 60.283 61.111 0.00 0.00 0.00 4.92
3928 5065 4.605968 ACTCATTGACGAGATCAGATTCG 58.394 43.478 11.27 11.27 38.99 3.34
3958 5096 0.684535 TCGAAATGCCTGTGTCCTGA 59.315 50.000 0.00 0.00 0.00 3.86
3959 5097 1.278985 TCGAAATGCCTGTGTCCTGAT 59.721 47.619 0.00 0.00 0.00 2.90
3960 5098 1.399440 CGAAATGCCTGTGTCCTGATG 59.601 52.381 0.00 0.00 0.00 3.07
3961 5099 1.747355 GAAATGCCTGTGTCCTGATGG 59.253 52.381 0.00 0.00 0.00 3.51
3962 5100 0.994247 AATGCCTGTGTCCTGATGGA 59.006 50.000 0.00 0.00 40.69 3.41
3963 5101 1.219773 ATGCCTGTGTCCTGATGGAT 58.780 50.000 0.00 0.00 45.29 3.41
3964 5102 0.253894 TGCCTGTGTCCTGATGGATG 59.746 55.000 0.00 0.00 45.29 3.51
3965 5103 0.465097 GCCTGTGTCCTGATGGATGG 60.465 60.000 0.00 0.00 45.29 3.51
3985 5123 2.488528 GGATGGATGGATGCATGTGAGT 60.489 50.000 2.46 0.00 39.04 3.41
4069 5210 7.147958 TGGGAAGAAAAATGGAAAGGAAAAT 57.852 32.000 0.00 0.00 0.00 1.82
4277 5505 4.473444 TCTTCAATGGCTGTCCTTTTTCT 58.527 39.130 0.00 0.00 0.00 2.52
4285 5513 1.801178 CTGTCCTTTTTCTCGCTGTCC 59.199 52.381 0.00 0.00 0.00 4.02
4309 5537 6.250819 CGTTTTTGGACTATGTCATGTCATC 58.749 40.000 8.77 0.00 35.11 2.92
4367 5595 6.226052 GGTTTCTTTCATTTGATGCCTTCTT 58.774 36.000 0.00 0.00 0.00 2.52
4391 5619 2.034179 CGTGACCGTCCATTGCTATCTA 59.966 50.000 0.00 0.00 0.00 1.98
4397 5625 2.755650 GTCCATTGCTATCTACACCCG 58.244 52.381 0.00 0.00 0.00 5.28
4497 5757 0.036483 TTAACTCGCCATGCAGCAGA 60.036 50.000 0.00 0.00 0.00 4.26
4498 5758 0.178767 TAACTCGCCATGCAGCAGAT 59.821 50.000 0.00 0.00 0.00 2.90
4499 5759 1.374343 AACTCGCCATGCAGCAGATG 61.374 55.000 0.00 0.00 0.00 2.90
4510 5770 2.687700 CAGCAGATGCAGGAACTAGT 57.312 50.000 7.68 0.00 45.16 2.57
4511 5771 2.277969 CAGCAGATGCAGGAACTAGTG 58.722 52.381 7.68 0.00 45.16 2.74
4512 5772 1.209019 AGCAGATGCAGGAACTAGTGG 59.791 52.381 7.68 0.00 45.16 4.00
4513 5773 1.208052 GCAGATGCAGGAACTAGTGGA 59.792 52.381 0.00 0.00 41.59 4.02
4514 5774 2.158842 GCAGATGCAGGAACTAGTGGAT 60.159 50.000 0.00 0.00 41.59 3.41
4515 5775 3.683847 GCAGATGCAGGAACTAGTGGATT 60.684 47.826 0.00 0.00 41.59 3.01
4516 5776 4.521146 CAGATGCAGGAACTAGTGGATTT 58.479 43.478 0.00 0.00 36.02 2.17
4517 5777 4.946157 CAGATGCAGGAACTAGTGGATTTT 59.054 41.667 0.00 0.00 36.02 1.82
4518 5778 5.416952 CAGATGCAGGAACTAGTGGATTTTT 59.583 40.000 0.00 0.00 36.02 1.94
4541 5801 0.898320 TGAGAGGTGCTGGAACTAGC 59.102 55.000 3.29 3.29 43.95 3.42
4593 5853 1.597663 GTTTTACACGCACAGCTGTCT 59.402 47.619 18.64 0.00 0.00 3.41
4594 5854 1.217001 TTTACACGCACAGCTGTCTG 58.783 50.000 18.64 14.81 45.71 3.51
4595 5855 1.221466 TTACACGCACAGCTGTCTGC 61.221 55.000 18.64 17.72 44.10 4.26
4596 5856 2.362329 TACACGCACAGCTGTCTGCA 62.362 55.000 24.12 7.19 44.10 4.41
4597 5857 2.969238 ACGCACAGCTGTCTGCAC 60.969 61.111 24.12 9.44 44.10 4.57
4598 5858 3.720193 CGCACAGCTGTCTGCACC 61.720 66.667 24.12 6.99 44.10 5.01
4599 5859 2.592574 GCACAGCTGTCTGCACCA 60.593 61.111 18.64 0.00 44.10 4.17
4600 5860 2.614446 GCACAGCTGTCTGCACCAG 61.614 63.158 18.64 4.10 44.10 4.00
4601 5861 1.227764 CACAGCTGTCTGCACCAGT 60.228 57.895 18.64 0.00 44.10 4.00
4603 5863 1.964891 CAGCTGTCTGCACCAGTGG 60.965 63.158 7.91 7.91 45.94 4.00
4604 5864 3.360340 GCTGTCTGCACCAGTGGC 61.360 66.667 9.78 0.00 42.31 5.01
4605 5865 3.046087 CTGTCTGCACCAGTGGCG 61.046 66.667 9.78 0.00 32.61 5.69
4624 5884 1.333791 CGCCCGTCAACAAAAGAAGAC 60.334 52.381 0.00 0.00 0.00 3.01
4660 5920 0.453390 GTTGCAATCTAGCACTGCCC 59.547 55.000 0.59 0.00 45.61 5.36
4724 6136 1.070108 GGAAAGGAACAGCGAACGAAC 60.070 52.381 0.00 0.00 0.00 3.95
4725 6137 0.580104 AAAGGAACAGCGAACGAACG 59.420 50.000 0.00 0.00 0.00 3.95
4726 6138 0.249155 AAGGAACAGCGAACGAACGA 60.249 50.000 9.67 0.00 35.09 3.85
4727 6139 0.249155 AGGAACAGCGAACGAACGAA 60.249 50.000 9.67 0.00 35.09 3.85
4728 6140 0.111398 GGAACAGCGAACGAACGAAC 60.111 55.000 9.67 0.00 35.09 3.95
4729 6141 0.446784 GAACAGCGAACGAACGAACG 60.447 55.000 9.67 7.22 39.31 3.95
4730 6142 0.866906 AACAGCGAACGAACGAACGA 60.867 50.000 16.66 0.00 37.03 3.85
4731 6143 1.266786 ACAGCGAACGAACGAACGAG 61.267 55.000 16.66 11.97 37.03 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 5.555069 CGTTATGGCGTTCCTATTTTCGTAC 60.555 44.000 0.00 0.00 0.00 3.67
109 110 1.338655 GCAAAAACGTGTATGGGGTGT 59.661 47.619 0.00 0.00 0.00 4.16
110 111 1.611491 AGCAAAAACGTGTATGGGGTG 59.389 47.619 0.00 0.00 0.00 4.61
137 138 2.031919 TACAACGGCCTGCCACTG 59.968 61.111 9.17 6.94 35.37 3.66
138 139 1.764571 TTCTACAACGGCCTGCCACT 61.765 55.000 9.17 0.00 35.37 4.00
139 140 1.302192 TTCTACAACGGCCTGCCAC 60.302 57.895 9.17 0.00 35.37 5.01
215 492 0.540830 CCTAGCTAGGCGTCTCCCAT 60.541 60.000 26.62 0.00 36.53 4.00
216 493 1.152735 CCTAGCTAGGCGTCTCCCA 60.153 63.158 26.62 0.00 36.53 4.37
385 1117 6.317857 ACTAACGAGTAATACTCCGTTTGAC 58.682 40.000 26.71 4.80 42.12 3.18
393 1125 4.809815 AGCGGACTAACGAGTAATACTC 57.190 45.455 10.26 10.26 41.71 2.59
395 1127 4.025647 ACGTAGCGGACTAACGAGTAATAC 60.026 45.833 0.63 0.00 35.45 1.89
398 1130 2.094258 CACGTAGCGGACTAACGAGTAA 59.906 50.000 0.63 0.00 35.45 2.24
506 1346 0.963225 TCGACACACCATCTCCGAAA 59.037 50.000 0.00 0.00 0.00 3.46
509 1349 0.458543 CCTTCGACACACCATCTCCG 60.459 60.000 0.00 0.00 0.00 4.63
556 1396 0.820226 CATCACTTCTGCCTCTCCGA 59.180 55.000 0.00 0.00 0.00 4.55
665 1515 9.762933 AGCTTTGATTTTCTTTAAAATGTAGCA 57.237 25.926 15.73 3.20 43.69 3.49
668 1518 9.762933 AGCAGCTTTGATTTTCTTTAAAATGTA 57.237 25.926 1.06 0.00 43.69 2.29
669 1519 8.553696 CAGCAGCTTTGATTTTCTTTAAAATGT 58.446 29.630 0.00 0.00 43.69 2.71
670 1520 7.532884 GCAGCAGCTTTGATTTTCTTTAAAATG 59.467 33.333 0.00 0.00 40.23 2.32
671 1521 7.578852 GCAGCAGCTTTGATTTTCTTTAAAAT 58.421 30.769 0.00 0.00 41.51 1.82
672 1522 6.947258 GCAGCAGCTTTGATTTTCTTTAAAA 58.053 32.000 0.00 0.00 37.08 1.52
978 1956 1.490693 CTATGATGTGCGTCGGTGGC 61.491 60.000 0.00 0.00 0.00 5.01
981 1959 0.108377 TTGCTATGATGTGCGTCGGT 60.108 50.000 0.00 0.00 0.00 4.69
982 1960 1.070376 CATTGCTATGATGTGCGTCGG 60.070 52.381 1.51 0.00 33.37 4.79
983 1961 1.070376 CCATTGCTATGATGTGCGTCG 60.070 52.381 9.87 0.00 33.37 5.12
984 1962 1.334419 GCCATTGCTATGATGTGCGTC 60.334 52.381 9.87 0.00 33.37 5.19
1501 2488 4.890306 GGGAGGAGGAGGAGGGGC 62.890 77.778 0.00 0.00 0.00 5.80
1515 2505 2.998097 CGAAATGGGAGGCAGGGA 59.002 61.111 0.00 0.00 0.00 4.20
1517 2507 2.117156 CAGCGAAATGGGAGGCAGG 61.117 63.158 0.00 0.00 0.00 4.85
1518 2508 2.768492 GCAGCGAAATGGGAGGCAG 61.768 63.158 0.00 0.00 0.00 4.85
1519 2509 2.751436 GCAGCGAAATGGGAGGCA 60.751 61.111 0.00 0.00 0.00 4.75
1593 2583 4.378874 GCTAACTGCAAGGCAAAACTAGAG 60.379 45.833 0.00 0.00 38.41 2.43
2096 3117 2.916702 AGCCATTATCATCAGCGTGA 57.083 45.000 0.00 0.00 0.00 4.35
2116 3137 4.462483 GTGCTCCAATTCCCAAAATAGTGA 59.538 41.667 0.00 0.00 0.00 3.41
2413 3474 9.975218 ATCTTCCACTATGTAACCAACTAAATT 57.025 29.630 0.00 0.00 0.00 1.82
2454 3521 6.128007 GCACTACTTGTTATGCAAATGGTAGT 60.128 38.462 11.82 11.82 42.35 2.73
2455 3522 6.258160 GCACTACTTGTTATGCAAATGGTAG 58.742 40.000 0.00 2.09 38.38 3.18
2456 3523 5.124776 GGCACTACTTGTTATGCAAATGGTA 59.875 40.000 0.00 0.00 39.92 3.25
2457 3524 4.082245 GGCACTACTTGTTATGCAAATGGT 60.082 41.667 0.00 0.00 39.92 3.55
2458 3525 4.158394 AGGCACTACTTGTTATGCAAATGG 59.842 41.667 0.00 0.00 39.92 3.16
2459 3526 5.097529 CAGGCACTACTTGTTATGCAAATG 58.902 41.667 0.00 3.89 39.92 2.32
2603 3670 9.415544 ACAGATTGAATTCTCTAAACAAAATGC 57.584 29.630 7.05 0.00 0.00 3.56
2634 3701 6.090783 TCTACACTGTTACAGTTAAGATGCG 58.909 40.000 16.06 4.55 42.59 4.73
2880 3955 1.352017 TCAGAACCAGATGGCATGTGT 59.648 47.619 21.47 5.70 39.32 3.72
2907 3982 8.589338 CCACTTATCTTGCCTATGAGTACTATT 58.411 37.037 0.00 0.00 0.00 1.73
2912 3987 6.016527 CGTACCACTTATCTTGCCTATGAGTA 60.017 42.308 0.00 0.00 0.00 2.59
2942 4018 3.126171 GGGACCAAGCAAAAACAAACAAC 59.874 43.478 0.00 0.00 0.00 3.32
3014 4090 2.580589 CAAATAGTTTTGTCACCGCCG 58.419 47.619 0.00 0.00 37.92 6.46
3076 4152 5.414454 TGCACGCCTTAACATCTAAAATTCT 59.586 36.000 0.00 0.00 0.00 2.40
3077 4153 5.636837 TGCACGCCTTAACATCTAAAATTC 58.363 37.500 0.00 0.00 0.00 2.17
3078 4154 5.183140 ACTGCACGCCTTAACATCTAAAATT 59.817 36.000 0.00 0.00 0.00 1.82
3079 4155 4.700213 ACTGCACGCCTTAACATCTAAAAT 59.300 37.500 0.00 0.00 0.00 1.82
3082 4158 3.259064 GACTGCACGCCTTAACATCTAA 58.741 45.455 0.00 0.00 0.00 2.10
3086 4162 0.037697 TCGACTGCACGCCTTAACAT 60.038 50.000 0.00 0.00 0.00 2.71
3104 4214 8.076178 GTCAGTATTGGGCATTAAACACATATC 58.924 37.037 0.00 0.00 0.00 1.63
3111 4221 6.072175 TGTCAAGTCAGTATTGGGCATTAAAC 60.072 38.462 0.00 0.00 0.00 2.01
3112 4222 6.007076 TGTCAAGTCAGTATTGGGCATTAAA 58.993 36.000 0.00 0.00 0.00 1.52
3118 4228 4.846779 TTTTGTCAAGTCAGTATTGGGC 57.153 40.909 0.00 0.00 0.00 5.36
3185 4297 5.544136 AAACAAGTGCAAAATGTTTGGTC 57.456 34.783 19.17 0.00 43.50 4.02
3233 4369 6.769822 GGAGATCCATCAAAGAAAGAGCAATA 59.230 38.462 0.00 0.00 35.64 1.90
3660 4797 0.601046 CAGACGCTTCTGCTTCACCA 60.601 55.000 7.34 0.00 42.99 4.17
3796 4933 2.439409 TGACAATGGCAGTGAGAATGG 58.561 47.619 23.05 0.00 0.00 3.16
3798 4935 4.338012 TCAATGACAATGGCAGTGAGAAT 58.662 39.130 23.05 8.76 35.70 2.40
3928 5065 5.572896 CACAGGCATTTCGAGTTTAAAATCC 59.427 40.000 9.88 0.00 0.00 3.01
3958 5096 1.714217 TGCATCCATCCATCCATCCAT 59.286 47.619 0.00 0.00 0.00 3.41
3959 5097 1.150872 TGCATCCATCCATCCATCCA 58.849 50.000 0.00 0.00 0.00 3.41
3960 5098 2.100197 CATGCATCCATCCATCCATCC 58.900 52.381 0.00 0.00 0.00 3.51
3961 5099 2.492088 CACATGCATCCATCCATCCATC 59.508 50.000 0.00 0.00 0.00 3.51
3962 5100 2.109304 TCACATGCATCCATCCATCCAT 59.891 45.455 0.00 0.00 0.00 3.41
3963 5101 1.495574 TCACATGCATCCATCCATCCA 59.504 47.619 0.00 0.00 0.00 3.41
3964 5102 2.160205 CTCACATGCATCCATCCATCC 58.840 52.381 0.00 0.00 0.00 3.51
3965 5103 2.860009 ACTCACATGCATCCATCCATC 58.140 47.619 0.00 0.00 0.00 3.51
3985 5123 4.001652 CTCGTCTACTACCTCAGTCACAA 58.998 47.826 0.00 0.00 38.80 3.33
4075 5216 8.831715 ATGACAATTCCTTGGTTTTTGTAATC 57.168 30.769 0.00 0.00 36.64 1.75
4076 5217 7.877612 GGATGACAATTCCTTGGTTTTTGTAAT 59.122 33.333 0.00 0.00 36.64 1.89
4077 5218 7.147655 TGGATGACAATTCCTTGGTTTTTGTAA 60.148 33.333 0.00 0.00 36.64 2.41
4078 5219 6.325028 TGGATGACAATTCCTTGGTTTTTGTA 59.675 34.615 0.00 0.00 36.64 2.41
4079 5220 5.130145 TGGATGACAATTCCTTGGTTTTTGT 59.870 36.000 0.00 0.00 36.64 2.83
4082 5226 4.262592 GCTGGATGACAATTCCTTGGTTTT 60.263 41.667 0.00 0.00 36.64 2.43
4151 5295 5.347364 GCCTATGTGAAGAGAATAATCGCTC 59.653 44.000 0.00 0.00 34.31 5.03
4246 5421 3.325716 ACAGCCATTGAAGATGCCTTTTT 59.674 39.130 0.00 0.00 31.62 1.94
4259 5434 2.669391 GCGAGAAAAAGGACAGCCATTG 60.669 50.000 0.00 0.00 36.29 2.82
4260 5435 1.541588 GCGAGAAAAAGGACAGCCATT 59.458 47.619 0.00 0.00 36.29 3.16
4262 5437 0.108585 AGCGAGAAAAAGGACAGCCA 59.891 50.000 0.00 0.00 36.29 4.75
4263 5438 0.519077 CAGCGAGAAAAAGGACAGCC 59.481 55.000 0.00 0.00 0.00 4.85
4277 5505 4.859400 TCCAAAAACGGACAGCGA 57.141 50.000 0.00 0.00 0.00 4.93
4285 5513 5.605564 TGACATGACATAGTCCAAAAACG 57.394 39.130 0.00 0.00 33.89 3.60
4367 5595 1.080093 GCAATGGACGGTCACGAGA 60.080 57.895 10.76 0.00 44.60 4.04
4397 5625 2.676839 GAGTTAAAAACTAGAGCCGGGC 59.323 50.000 12.11 12.11 43.03 6.13
4518 5778 3.297134 AGTTCCAGCACCTCTCAAAAA 57.703 42.857 0.00 0.00 0.00 1.94
4519 5779 3.807209 GCTAGTTCCAGCACCTCTCAAAA 60.807 47.826 0.00 0.00 41.40 2.44
4520 5780 2.289694 GCTAGTTCCAGCACCTCTCAAA 60.290 50.000 0.00 0.00 41.40 2.69
4521 5781 1.276421 GCTAGTTCCAGCACCTCTCAA 59.724 52.381 0.00 0.00 41.40 3.02
4522 5782 0.898320 GCTAGTTCCAGCACCTCTCA 59.102 55.000 0.00 0.00 41.40 3.27
4523 5783 0.179124 CGCTAGTTCCAGCACCTCTC 60.179 60.000 0.00 0.00 41.88 3.20
4524 5784 1.608717 CCGCTAGTTCCAGCACCTCT 61.609 60.000 0.00 0.00 41.88 3.69
4525 5785 1.153549 CCGCTAGTTCCAGCACCTC 60.154 63.158 0.00 0.00 41.88 3.85
4526 5786 0.978146 ATCCGCTAGTTCCAGCACCT 60.978 55.000 0.00 0.00 41.88 4.00
4527 5787 0.811616 CATCCGCTAGTTCCAGCACC 60.812 60.000 0.00 0.00 41.88 5.01
4532 5792 1.220749 GTGCCATCCGCTAGTTCCA 59.779 57.895 0.00 0.00 38.78 3.53
4563 5823 2.044135 GCGTGTAAAACTTGCTTCTGC 58.956 47.619 0.00 0.00 40.20 4.26
4565 5825 2.680841 TGTGCGTGTAAAACTTGCTTCT 59.319 40.909 0.00 0.00 0.00 2.85
4573 5833 1.597663 AGACAGCTGTGCGTGTAAAAC 59.402 47.619 27.27 5.33 0.00 2.43
4599 5859 4.555709 TTGTTGACGGGCGCCACT 62.556 61.111 30.85 12.56 0.00 4.00
4600 5860 2.999363 CTTTTGTTGACGGGCGCCAC 62.999 60.000 30.85 18.15 0.00 5.01
4601 5861 2.829003 TTTTGTTGACGGGCGCCA 60.829 55.556 30.85 3.84 0.00 5.69
4603 5863 0.660300 CTTCTTTTGTTGACGGGCGC 60.660 55.000 0.00 0.00 0.00 6.53
4604 5864 0.941542 TCTTCTTTTGTTGACGGGCG 59.058 50.000 0.00 0.00 0.00 6.13
4605 5865 1.673920 TGTCTTCTTTTGTTGACGGGC 59.326 47.619 0.00 0.00 32.64 6.13
4606 5866 4.364415 TTTGTCTTCTTTTGTTGACGGG 57.636 40.909 0.00 0.00 32.64 5.28
4643 5903 1.077501 GGGGCAGTGCTAGATTGCA 60.078 57.895 16.11 0.00 39.05 4.08
4776 6196 4.444838 TCGTCACCGCCCATTCCG 62.445 66.667 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.