Multiple sequence alignment - TraesCS5D01G206900

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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 TraesCS5D01G206900 chr5D 100.000 3302 0 0 1 3302 313150876 313154177 0.000000e+00 6098
1 TraesCS5D01G206900 chr5D 87.668 1265 86 28 883 2133 313333179 313331971 0.000000e+00 1408
2 TraesCS5D01G206900 chr5D 87.548 779 90 4 4 781 313334011 313333239 0.000000e+00 894
3 TraesCS5D01G206900 chr5D 87.097 186 22 1 2401 2584 537693295 537693110 3.340000e-50 209
4 TraesCS5D01G206900 chr5A 92.749 1710 81 21 1088 2770 407125323 407127016 0.000000e+00 2431
5 TraesCS5D01G206900 chr5A 91.113 1024 80 7 1124 2136 407154549 407153526 0.000000e+00 1376
6 TraesCS5D01G206900 chr5A 89.196 759 79 3 2 758 407124338 407125095 0.000000e+00 944
7 TraesCS5D01G206900 chr5A 85.114 833 105 10 1 823 407157428 407156605 0.000000e+00 833
8 TraesCS5D01G206900 chr5A 85.311 531 56 13 2792 3302 407126980 407127508 2.260000e-146 529
9 TraesCS5D01G206900 chr5B 91.110 1676 94 30 1090 2732 360861365 360863018 0.000000e+00 2218
10 TraesCS5D01G206900 chr5B 88.818 787 82 5 1 784 360860351 360861134 0.000000e+00 961
11 TraesCS5D01G206900 chr5B 90.894 604 28 6 2716 3302 360863034 360863627 0.000000e+00 785
12 TraesCS5D01G206900 chr5B 90.023 431 36 4 1709 2137 360922577 360922152 4.820000e-153 551
13 TraesCS5D01G206900 chr3B 79.803 812 113 34 2400 3168 67376596 67375793 8.060000e-151 544
14 TraesCS5D01G206900 chr3A 78.822 798 117 31 2417 3168 55213493 55212702 1.060000e-134 490
15 TraesCS5D01G206900 chr3D 78.064 816 126 28 2400 3168 43242185 43241376 1.790000e-127 466
16 TraesCS5D01G206900 chr7D 80.921 608 84 22 2585 3168 13710583 13711182 5.020000e-123 451
17 TraesCS5D01G206900 chr7D 87.031 293 33 4 2880 3168 14922109 14922400 3.180000e-85 326
18 TraesCS5D01G206900 chr7D 89.119 193 19 1 2396 2586 14921848 14922040 4.260000e-59 239
19 TraesCS5D01G206900 chr7D 87.831 189 21 1 2400 2586 78118191 78118379 1.540000e-53 220
20 TraesCS5D01G206900 chr4A 81.736 553 76 12 2645 3174 279548081 279547531 3.910000e-119 438
21 TraesCS5D01G206900 chr4A 88.770 187 19 1 2401 2585 279617838 279617652 9.220000e-56 228
22 TraesCS5D01G206900 chr4B 81.562 461 59 12 2732 3168 458983730 458984188 1.130000e-94 357
23 TraesCS5D01G206900 chr4D 87.889 289 29 6 2884 3168 508332682 508332396 5.280000e-88 335
24 TraesCS5D01G206900 chr4D 88.298 188 20 1 2401 2586 28559134 28559321 1.190000e-54 224
25 TraesCS5D01G206900 chr4D 88.356 146 16 1 2585 2729 52771425 52771280 1.220000e-39 174
26 TraesCS5D01G206900 chr4D 84.058 138 14 5 2633 2769 42096833 42096703 3.460000e-25 126
27 TraesCS5D01G206900 chr1B 89.011 273 25 4 2878 3146 304385512 304385241 1.900000e-87 333
28 TraesCS5D01G206900 chr1B 88.298 188 20 1 2401 2586 304385159 304385346 1.190000e-54 224
29 TraesCS5D01G206900 chr2D 87.372 293 32 4 2880 3168 617417980 617418271 6.830000e-87 331
30 TraesCS5D01G206900 chr2D 88.889 189 18 2 2400 2586 617417724 617417911 2.560000e-56 230
31 TraesCS5D01G206900 chr2D 84.138 145 23 0 2585 2729 484078296 484078152 1.240000e-29 141
32 TraesCS5D01G206900 chr6A 75.534 609 105 24 2583 3169 188352778 188352192 3.270000e-65 259
33 TraesCS5D01G206900 chr7A 81.712 257 40 4 485 739 581039996 581040247 1.200000e-49 207
34 TraesCS5D01G206900 chr7B 85.950 121 17 0 619 739 538574875 538574995 2.670000e-26 130


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 TraesCS5D01G206900 chr5D 313150876 313154177 3301 False 6098.000000 6098 100.000000 1 3302 1 chr5D.!!$F1 3301
1 TraesCS5D01G206900 chr5D 313331971 313334011 2040 True 1151.000000 1408 87.608000 4 2133 2 chr5D.!!$R2 2129
2 TraesCS5D01G206900 chr5A 407124338 407127508 3170 False 1301.333333 2431 89.085333 2 3302 3 chr5A.!!$F1 3300
3 TraesCS5D01G206900 chr5A 407153526 407157428 3902 True 1104.500000 1376 88.113500 1 2136 2 chr5A.!!$R1 2135
4 TraesCS5D01G206900 chr5B 360860351 360863627 3276 False 1321.333333 2218 90.274000 1 3302 3 chr5B.!!$F1 3301
5 TraesCS5D01G206900 chr3B 67375793 67376596 803 True 544.000000 544 79.803000 2400 3168 1 chr3B.!!$R1 768
6 TraesCS5D01G206900 chr3A 55212702 55213493 791 True 490.000000 490 78.822000 2417 3168 1 chr3A.!!$R1 751
7 TraesCS5D01G206900 chr3D 43241376 43242185 809 True 466.000000 466 78.064000 2400 3168 1 chr3D.!!$R1 768
8 TraesCS5D01G206900 chr7D 13710583 13711182 599 False 451.000000 451 80.921000 2585 3168 1 chr7D.!!$F1 583
9 TraesCS5D01G206900 chr7D 14921848 14922400 552 False 282.500000 326 88.075000 2396 3168 2 chr7D.!!$F3 772
10 TraesCS5D01G206900 chr4A 279547531 279548081 550 True 438.000000 438 81.736000 2645 3174 1 chr4A.!!$R1 529
11 TraesCS5D01G206900 chr2D 617417724 617418271 547 False 280.500000 331 88.130500 2400 3168 2 chr2D.!!$F1 768
12 TraesCS5D01G206900 chr6A 188352192 188352778 586 True 259.000000 259 75.534000 2583 3169 1 chr6A.!!$R1 586

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
364 365 0.027979 CAACCATCTTGCGCATACCG 59.972 55.0 12.75 0.0 40.75 4.02 F
775 786 0.108472 TCGCGACGTCTCTCCTCTAA 60.108 55.0 14.70 0.0 0.00 2.10 F
1075 2672 0.249363 GGGAAAGGTACGGATCTCGC 60.249 60.0 3.85 0.0 43.89 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1477 3348 0.323451 TGAGCGAGAGAAGGCACCTA 60.323 55.000 0.00 0.00 0.00 3.08 R
2175 4057 1.374758 CCTGCCTCACGTCAAGGAC 60.375 63.158 16.07 8.69 35.83 3.85 R
2798 4764 1.355381 AGCCATTCAACATGGAGGACA 59.645 47.619 4.98 0.00 41.64 4.02 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
65 66 0.532573 GAGGACGACCATCAGCTCAA 59.467 55.000 6.71 0.00 38.94 3.02
79 80 1.816863 GCTCAACCTGGTCGGACTCA 61.817 60.000 8.23 3.83 36.31 3.41
115 116 5.406477 GTCTTCGTATACAAACCCGAAACTT 59.594 40.000 3.32 0.00 38.66 2.66
116 117 5.990996 TCTTCGTATACAAACCCGAAACTTT 59.009 36.000 3.32 0.00 38.66 2.66
118 119 4.451774 TCGTATACAAACCCGAAACTTTGG 59.548 41.667 3.32 0.00 32.57 3.28
124 125 1.665442 CCCGAAACTTTGGGGCTTG 59.335 57.895 8.55 0.00 46.55 4.01
187 188 1.478137 CGGCTAATCTTCCGTCTTCG 58.522 55.000 0.00 0.00 40.72 3.79
202 203 6.157904 TCCGTCTTCGAGTAGTAGATAGATG 58.842 44.000 0.00 0.00 39.71 2.90
207 208 7.386848 GTCTTCGAGTAGTAGATAGATGAAGCT 59.613 40.741 0.00 0.00 32.47 3.74
230 231 2.312323 TGGAACACAGGGTTGGACA 58.688 52.632 0.00 0.00 40.63 4.02
259 260 2.215196 GCCGTAAACTTTGTCCTGTCA 58.785 47.619 0.00 0.00 0.00 3.58
266 267 1.348036 ACTTTGTCCTGTCAGGGTAGC 59.652 52.381 19.11 7.70 35.59 3.58
271 272 2.292257 TGTCCTGTCAGGGTAGCAGTAT 60.292 50.000 19.11 0.00 35.59 2.12
290 291 2.513895 CCCAACGTTCCCACACCT 59.486 61.111 0.00 0.00 0.00 4.00
325 326 2.798976 TGCAACAACCAATCTCTTGC 57.201 45.000 0.00 0.00 38.16 4.01
327 328 2.034939 TGCAACAACCAATCTCTTGCAG 59.965 45.455 0.00 0.00 41.67 4.41
329 330 1.251251 ACAACCAATCTCTTGCAGGC 58.749 50.000 0.00 0.00 0.00 4.85
330 331 1.250328 CAACCAATCTCTTGCAGGCA 58.750 50.000 0.00 0.00 0.00 4.75
333 334 1.615392 ACCAATCTCTTGCAGGCAAAC 59.385 47.619 8.20 0.00 35.33 2.93
346 347 1.361993 GCAAACCGTGTCAATGCCA 59.638 52.632 0.00 0.00 0.00 4.92
348 349 1.486439 CAAACCGTGTCAATGCCAAC 58.514 50.000 0.00 0.00 0.00 3.77
357 358 0.527113 TCAATGCCAACCATCTTGCG 59.473 50.000 0.00 0.00 31.43 4.85
364 365 0.027979 CAACCATCTTGCGCATACCG 59.972 55.000 12.75 0.00 40.75 4.02
387 391 2.719556 CGTAGACGATATGCTCAAACCG 59.280 50.000 0.00 0.00 43.02 4.44
388 392 2.225068 AGACGATATGCTCAAACCGG 57.775 50.000 0.00 0.00 0.00 5.28
397 401 1.347707 TGCTCAAACCGGAACTGAGAT 59.652 47.619 25.89 0.00 39.15 2.75
401 405 4.680708 GCTCAAACCGGAACTGAGATATCA 60.681 45.833 25.89 0.00 39.15 2.15
414 418 5.953183 CTGAGATATCAGTGGCAGATAGTC 58.047 45.833 9.26 0.00 32.00 2.59
416 420 4.402829 AGATATCAGTGGCAGATAGTCGT 58.597 43.478 5.32 0.00 32.00 4.34
417 421 4.830046 AGATATCAGTGGCAGATAGTCGTT 59.170 41.667 5.32 0.00 32.00 3.85
423 427 2.086094 TGGCAGATAGTCGTTGTCGTA 58.914 47.619 0.00 0.00 38.33 3.43
425 429 2.110226 GCAGATAGTCGTTGTCGTAGC 58.890 52.381 0.00 0.00 38.33 3.58
429 433 3.688185 AGATAGTCGTTGTCGTAGCTCAA 59.312 43.478 0.00 0.00 38.33 3.02
445 449 4.210331 AGCTCAAAAGGTCAACATTGAGT 58.790 39.130 13.87 1.60 46.56 3.41
448 452 6.150140 AGCTCAAAAGGTCAACATTGAGTATC 59.850 38.462 13.87 0.98 46.56 2.24
456 460 5.392380 GGTCAACATTGAGTATCTGCTTTGG 60.392 44.000 0.00 0.00 37.98 3.28
469 473 1.473677 TGCTTTGGCATGCATAGTGTC 59.526 47.619 21.36 0.00 44.28 3.67
471 475 2.733227 GCTTTGGCATGCATAGTGTCAC 60.733 50.000 21.36 0.00 38.54 3.67
482 486 0.523072 TAGTGTCACGTACCTTCCGC 59.477 55.000 0.00 0.00 0.00 5.54
508 512 3.207669 CAGATCTTGGCGCCAGGC 61.208 66.667 32.14 19.72 44.11 4.85
567 571 2.442502 AGTAGGGACTGTAGTAGCGGAT 59.557 50.000 0.00 0.00 41.52 4.18
568 572 1.693627 AGGGACTGTAGTAGCGGATG 58.306 55.000 0.00 0.00 37.18 3.51
682 686 2.668550 GCGAAACTCGGGTGGCTT 60.669 61.111 0.00 0.00 40.84 4.35
772 783 1.010574 CATCGCGACGTCTCTCCTC 60.011 63.158 12.93 0.00 0.00 3.71
775 786 0.108472 TCGCGACGTCTCTCCTCTAA 60.108 55.000 14.70 0.00 0.00 2.10
786 804 1.352156 CTCCTCTAACCGCACAACGC 61.352 60.000 0.00 0.00 41.76 4.84
852 881 9.925865 CGTTTCAAAAATAAATAAATAACGCGT 57.074 25.926 5.58 5.58 0.00 6.01
867 896 2.954868 CGTACGTGCGGCTGGATC 60.955 66.667 18.81 0.00 0.00 3.36
870 899 3.120979 TACGTGCGGCTGGATCTCG 62.121 63.158 0.00 0.00 0.00 4.04
871 900 4.193334 CGTGCGGCTGGATCTCGA 62.193 66.667 0.00 0.00 0.00 4.04
904 960 9.520515 TTTATGCTAAAATTTCTCTCTTGGAGT 57.479 29.630 0.00 0.00 42.40 3.85
905 961 9.520515 TTATGCTAAAATTTCTCTCTTGGAGTT 57.479 29.630 0.00 0.00 42.40 3.01
943 1005 1.406898 CGAGTAGGAAGCAGCAGATGA 59.593 52.381 0.00 0.00 0.00 2.92
945 1007 2.167281 GAGTAGGAAGCAGCAGATGACA 59.833 50.000 0.00 0.00 0.00 3.58
946 1008 2.093764 AGTAGGAAGCAGCAGATGACAC 60.094 50.000 0.00 0.00 0.00 3.67
947 1009 0.390866 AGGAAGCAGCAGATGACACG 60.391 55.000 0.00 0.00 0.00 4.49
948 1010 0.671781 GGAAGCAGCAGATGACACGT 60.672 55.000 0.00 0.00 0.00 4.49
986 1053 4.604114 CGACCCGGAACCTAAACC 57.396 61.111 0.73 0.00 0.00 3.27
987 1054 1.977685 CGACCCGGAACCTAAACCT 59.022 57.895 0.73 0.00 0.00 3.50
996 1063 2.884207 CCTAAACCTCGCGTCCGC 60.884 66.667 5.77 0.68 37.85 5.54
1031 1105 3.043340 GCAAACGGCAACACAAACT 57.957 47.368 0.00 0.00 43.97 2.66
1035 1109 3.364465 GCAAACGGCAACACAAACTTTTT 60.364 39.130 0.00 0.00 43.97 1.94
1067 2664 9.774413 ATACATAAAATAGAAGGGAAAGGTACG 57.226 33.333 0.00 0.00 0.00 3.67
1068 2665 7.052248 ACATAAAATAGAAGGGAAAGGTACGG 58.948 38.462 0.00 0.00 0.00 4.02
1071 2668 5.548181 AATAGAAGGGAAAGGTACGGATC 57.452 43.478 0.00 0.00 0.00 3.36
1072 2669 3.117552 AGAAGGGAAAGGTACGGATCT 57.882 47.619 0.00 0.00 0.00 2.75
1073 2670 3.032459 AGAAGGGAAAGGTACGGATCTC 58.968 50.000 0.00 0.00 0.00 2.75
1074 2671 1.400737 AGGGAAAGGTACGGATCTCG 58.599 55.000 0.00 0.00 45.88 4.04
1075 2672 0.249363 GGGAAAGGTACGGATCTCGC 60.249 60.000 3.85 0.00 43.89 5.03
1076 2673 0.458669 GGAAAGGTACGGATCTCGCA 59.541 55.000 3.85 0.00 43.89 5.10
1077 2674 1.068741 GGAAAGGTACGGATCTCGCAT 59.931 52.381 3.85 0.00 43.89 4.73
1078 2675 2.295349 GGAAAGGTACGGATCTCGCATA 59.705 50.000 3.85 0.00 43.89 3.14
1080 2677 2.563261 AGGTACGGATCTCGCATAGA 57.437 50.000 3.85 0.00 43.89 1.98
1082 2679 3.422796 AGGTACGGATCTCGCATAGATT 58.577 45.455 3.85 0.00 45.35 2.40
1083 2680 3.191581 AGGTACGGATCTCGCATAGATTG 59.808 47.826 3.85 0.45 45.35 2.67
1115 2986 6.423905 GGAAATTAAGAAAACTTTGCAGGGAC 59.576 38.462 0.00 0.00 0.00 4.46
1116 2987 6.478512 AATTAAGAAAACTTTGCAGGGACA 57.521 33.333 0.00 0.00 0.00 4.02
1117 2988 3.801114 AAGAAAACTTTGCAGGGACAC 57.199 42.857 0.00 0.00 0.00 3.67
1118 2989 1.676006 AGAAAACTTTGCAGGGACACG 59.324 47.619 0.00 0.00 0.00 4.49
1119 2990 1.673920 GAAAACTTTGCAGGGACACGA 59.326 47.619 0.00 0.00 0.00 4.35
1120 2991 1.021968 AAACTTTGCAGGGACACGAC 58.978 50.000 0.00 0.00 0.00 4.34
1121 2992 1.157870 AACTTTGCAGGGACACGACG 61.158 55.000 0.00 0.00 0.00 5.12
1122 2993 1.594293 CTTTGCAGGGACACGACGT 60.594 57.895 0.00 0.00 0.00 4.34
1127 2998 2.592574 AGGGACACGACGTGACGA 60.593 61.111 33.12 0.00 36.96 4.20
1266 3137 4.753877 CGAGGCAAGCGACGACGA 62.754 66.667 12.29 0.00 42.66 4.20
1477 3348 2.723746 CAAGCCGCACAAAGCAGT 59.276 55.556 0.00 0.00 46.13 4.40
1665 3538 1.135721 GTTCTACGCATACGACCCCTT 59.864 52.381 0.00 0.00 43.93 3.95
1682 3564 3.124636 CCCCTTTAAACGTCAGATTGTCG 59.875 47.826 0.00 0.00 35.19 4.35
1687 3569 1.139989 AACGTCAGATTGTCGCACTG 58.860 50.000 0.00 0.00 32.42 3.66
1706 3588 2.571653 CTGGAGTTCTCACCATACCCAA 59.428 50.000 2.24 0.00 34.11 4.12
1942 3824 1.922189 CGATAGTTGCCGCGGTTAC 59.078 57.895 28.70 23.53 0.00 2.50
1982 3864 2.003301 GCCAGCTCGGTCTAAGAAAAG 58.997 52.381 4.45 0.00 36.97 2.27
2160 4042 4.813161 CAGCACAACCATCTATTCGAGATT 59.187 41.667 0.00 0.00 42.70 2.40
2175 4057 6.486253 TTCGAGATTCAATTCAGACTTTGG 57.514 37.500 0.00 0.00 0.00 3.28
2201 4083 0.608640 ACGTGAGGCAGGTCTTTAGG 59.391 55.000 0.00 0.00 0.00 2.69
2202 4084 0.741221 CGTGAGGCAGGTCTTTAGGC 60.741 60.000 0.00 0.00 0.00 3.93
2206 4088 2.568003 GGCAGGTCTTTAGGCCAAC 58.432 57.895 5.01 0.00 45.70 3.77
2224 4106 5.187772 GGCCAACCTATTCCATTTCTCTTTT 59.812 40.000 0.00 0.00 0.00 2.27
2307 4190 5.841957 AAAGCAAGTATCCAACATCCATC 57.158 39.130 0.00 0.00 0.00 3.51
2308 4191 4.508551 AGCAAGTATCCAACATCCATCA 57.491 40.909 0.00 0.00 0.00 3.07
2310 4193 4.641989 AGCAAGTATCCAACATCCATCAAC 59.358 41.667 0.00 0.00 0.00 3.18
2311 4194 4.202050 GCAAGTATCCAACATCCATCAACC 60.202 45.833 0.00 0.00 0.00 3.77
2313 4196 5.456921 AGTATCCAACATCCATCAACCTT 57.543 39.130 0.00 0.00 0.00 3.50
2315 4198 6.256053 AGTATCCAACATCCATCAACCTTTT 58.744 36.000 0.00 0.00 0.00 2.27
2316 4199 7.410174 AGTATCCAACATCCATCAACCTTTTA 58.590 34.615 0.00 0.00 0.00 1.52
2318 4201 6.985653 TCCAACATCCATCAACCTTTTAAA 57.014 33.333 0.00 0.00 0.00 1.52
2319 4202 6.991938 TCCAACATCCATCAACCTTTTAAAG 58.008 36.000 0.00 0.00 0.00 1.85
2570 4482 3.035363 TGGAGGTGTGTCAGTTTAGTCA 58.965 45.455 0.00 0.00 0.00 3.41
2618 4548 1.081376 CACTCCTTCGCGTCGTCTT 60.081 57.895 5.77 0.00 0.00 3.01
2624 4554 3.841379 TTCGCGTCGTCTTGCAGCT 62.841 57.895 5.77 0.00 0.00 4.24
2761 4726 1.213430 TCATGCATCCTGATTGGCTCA 59.787 47.619 0.00 0.00 35.26 4.26
2770 4735 1.280133 CTGATTGGCTCAGGTTCTCCA 59.720 52.381 0.00 0.00 46.52 3.86
2798 4764 1.392710 CGCCGAGGTAGAGGGATGTT 61.393 60.000 0.00 0.00 0.00 2.71
2922 4904 1.906574 ACGTGGAAGTGTATGGACCAT 59.093 47.619 12.67 12.67 33.19 3.55
2950 4932 5.889289 TGGGGAAGTAAACACATATAAAGGC 59.111 40.000 0.00 0.00 0.00 4.35
3135 5126 6.875972 ATAGGACTAAATTGACACACCTCT 57.124 37.500 0.00 0.00 0.00 3.69
3258 5249 1.182385 TCGTTGTTGGCCCCAAATCC 61.182 55.000 0.00 0.00 37.70 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 3.468063 GGTTGAGTCCGACCAGGT 58.532 61.111 0.00 0.00 44.71 4.00
79 80 4.803098 ATACGAAGACAGCTACTTGGTT 57.197 40.909 19.32 9.52 37.46 3.67
115 116 3.303938 TGAAATTCTTGACAAGCCCCAA 58.696 40.909 10.50 0.00 0.00 4.12
116 117 2.956132 TGAAATTCTTGACAAGCCCCA 58.044 42.857 10.50 1.68 0.00 4.96
118 119 4.931601 GGATTTGAAATTCTTGACAAGCCC 59.068 41.667 10.50 0.00 0.00 5.19
124 125 7.324616 CACGAAGAAGGATTTGAAATTCTTGAC 59.675 37.037 15.80 3.21 40.97 3.18
187 188 5.391523 CCGCAGCTTCATCTATCTACTACTC 60.392 48.000 0.00 0.00 0.00 2.59
202 203 1.845809 CTGTGTTCCACCGCAGCTTC 61.846 60.000 0.00 0.00 36.29 3.86
207 208 3.050354 AACCCTGTGTTCCACCGCA 62.050 57.895 0.00 0.00 32.73 5.69
230 231 0.105408 AAGTTTACGGCGTCACCAGT 59.895 50.000 19.21 0.00 39.03 4.00
259 260 0.546598 GTTGGGCATACTGCTACCCT 59.453 55.000 0.00 0.00 44.28 4.34
266 267 0.322098 TGGGAACGTTGGGCATACTG 60.322 55.000 5.00 0.00 0.00 2.74
271 272 2.517402 GTGTGGGAACGTTGGGCA 60.517 61.111 5.00 0.00 0.00 5.36
290 291 1.082169 GCATGCAAAACAGCGACGA 60.082 52.632 14.21 0.00 37.31 4.20
325 326 0.664166 GCATTGACACGGTTTGCCTG 60.664 55.000 0.00 0.00 0.00 4.85
327 328 1.372872 GGCATTGACACGGTTTGCC 60.373 57.895 0.00 0.00 45.31 4.52
329 330 1.486439 GTTGGCATTGACACGGTTTG 58.514 50.000 0.00 0.00 0.00 2.93
330 331 0.387565 GGTTGGCATTGACACGGTTT 59.612 50.000 0.00 0.00 0.00 3.27
333 334 0.171007 GATGGTTGGCATTGACACGG 59.829 55.000 0.00 0.00 0.00 4.94
346 347 0.392461 ACGGTATGCGCAAGATGGTT 60.392 50.000 17.11 0.00 43.02 3.67
348 349 1.821241 CGACGGTATGCGCAAGATGG 61.821 60.000 17.11 5.67 43.02 3.51
379 383 5.011090 TGATATCTCAGTTCCGGTTTGAG 57.989 43.478 19.60 19.60 39.69 3.02
397 401 3.699538 ACAACGACTATCTGCCACTGATA 59.300 43.478 0.00 0.00 0.00 2.15
401 405 1.135373 CGACAACGACTATCTGCCACT 60.135 52.381 0.00 0.00 42.66 4.00
406 410 3.063588 TGAGCTACGACAACGACTATCTG 59.936 47.826 0.00 0.00 42.66 2.90
410 414 3.902261 TTTGAGCTACGACAACGACTA 57.098 42.857 0.00 0.00 42.66 2.59
411 415 2.787601 TTTGAGCTACGACAACGACT 57.212 45.000 0.00 0.00 42.66 4.18
414 418 2.132762 ACCTTTTGAGCTACGACAACG 58.867 47.619 0.00 0.00 45.75 4.10
416 420 3.462483 TGACCTTTTGAGCTACGACAA 57.538 42.857 0.00 0.00 0.00 3.18
417 421 3.128349 GTTGACCTTTTGAGCTACGACA 58.872 45.455 0.00 0.00 0.00 4.35
423 427 4.210331 ACTCAATGTTGACCTTTTGAGCT 58.790 39.130 10.53 0.00 45.66 4.09
425 429 7.524912 CAGATACTCAATGTTGACCTTTTGAG 58.475 38.462 9.34 9.34 46.63 3.02
429 433 5.564550 AGCAGATACTCAATGTTGACCTTT 58.435 37.500 0.00 0.00 32.90 3.11
456 460 1.593006 GGTACGTGACACTATGCATGC 59.407 52.381 11.82 11.82 0.00 4.06
469 473 2.813908 GCCAGCGGAAGGTACGTG 60.814 66.667 0.00 0.00 41.81 4.49
482 486 1.798735 CCAAGATCTGTTGCGCCAG 59.201 57.895 4.18 6.07 0.00 4.85
517 521 1.965083 ACTTCGAGATTGACGACACG 58.035 50.000 0.00 0.00 39.46 4.49
524 528 6.055588 ACTTCCAGAAAAACTTCGAGATTGA 58.944 36.000 0.00 0.00 0.00 2.57
691 695 1.475403 TCCTGATCCTCAACCGTCTC 58.525 55.000 0.00 0.00 0.00 3.36
697 701 3.135530 ACCTGCTTATCCTGATCCTCAAC 59.864 47.826 0.00 0.00 0.00 3.18
700 704 2.301583 GGACCTGCTTATCCTGATCCTC 59.698 54.545 0.00 0.00 0.00 3.71
760 771 0.377905 GCGGTTAGAGGAGAGACGTC 59.622 60.000 7.70 7.70 0.00 4.34
761 772 0.322277 TGCGGTTAGAGGAGAGACGT 60.322 55.000 0.00 0.00 0.00 4.34
763 774 1.174783 TGTGCGGTTAGAGGAGAGAC 58.825 55.000 0.00 0.00 0.00 3.36
786 804 4.778415 CCTCGGTGCACGGACTCG 62.778 72.222 21.83 13.91 44.45 4.18
787 805 3.681835 ACCTCGGTGCACGGACTC 61.682 66.667 21.83 1.36 44.45 3.36
800 818 2.111756 CGTACGCGTTATTACCACCTC 58.888 52.381 20.78 0.00 0.00 3.85
826 855 9.925865 ACGCGTTATTTATTTATTTTTGAAACG 57.074 25.926 5.58 0.00 39.04 3.60
850 879 2.954868 GATCCAGCCGCACGTACG 60.955 66.667 15.01 15.01 0.00 3.67
851 880 1.589196 GAGATCCAGCCGCACGTAC 60.589 63.158 0.00 0.00 0.00 3.67
852 881 2.805546 GAGATCCAGCCGCACGTA 59.194 61.111 0.00 0.00 0.00 3.57
853 882 4.498520 CGAGATCCAGCCGCACGT 62.499 66.667 0.00 0.00 0.00 4.49
854 883 3.490793 ATCGAGATCCAGCCGCACG 62.491 63.158 0.00 0.00 0.00 5.34
855 884 1.663074 GATCGAGATCCAGCCGCAC 60.663 63.158 1.77 0.00 31.76 5.34
856 885 2.730733 GATCGAGATCCAGCCGCA 59.269 61.111 1.77 0.00 31.76 5.69
857 886 2.429907 CGATCGAGATCCAGCCGC 60.430 66.667 10.26 0.00 34.40 6.53
904 960 4.019321 ACTCGGGATGGAATTCTTCTTGAA 60.019 41.667 5.23 0.00 39.24 2.69
905 961 3.519510 ACTCGGGATGGAATTCTTCTTGA 59.480 43.478 5.23 4.96 0.00 3.02
948 1010 1.668751 GACCGGGATTGTACGTACGTA 59.331 52.381 23.60 23.60 0.00 3.57
976 1043 1.074872 CGGACGCGAGGTTTAGGTTC 61.075 60.000 15.93 0.00 0.00 3.62
1048 2645 5.666265 AGATCCGTACCTTTCCCTTCTATTT 59.334 40.000 0.00 0.00 0.00 1.40
1049 2646 5.217400 AGATCCGTACCTTTCCCTTCTATT 58.783 41.667 0.00 0.00 0.00 1.73
1050 2647 4.817286 AGATCCGTACCTTTCCCTTCTAT 58.183 43.478 0.00 0.00 0.00 1.98
1051 2648 4.213513 GAGATCCGTACCTTTCCCTTCTA 58.786 47.826 0.00 0.00 0.00 2.10
1052 2649 3.032459 GAGATCCGTACCTTTCCCTTCT 58.968 50.000 0.00 0.00 0.00 2.85
1053 2650 2.223758 CGAGATCCGTACCTTTCCCTTC 60.224 54.545 0.00 0.00 0.00 3.46
1056 2653 0.249363 GCGAGATCCGTACCTTTCCC 60.249 60.000 5.66 0.00 41.15 3.97
1057 2654 0.458669 TGCGAGATCCGTACCTTTCC 59.541 55.000 5.66 0.00 41.15 3.13
1058 2655 2.510768 ATGCGAGATCCGTACCTTTC 57.489 50.000 5.66 0.00 41.15 2.62
1059 2656 3.220110 TCTATGCGAGATCCGTACCTTT 58.780 45.455 5.66 0.00 41.15 3.11
1060 2657 2.860009 TCTATGCGAGATCCGTACCTT 58.140 47.619 5.66 0.00 41.15 3.50
1061 2658 2.563261 TCTATGCGAGATCCGTACCT 57.437 50.000 5.66 0.00 41.15 3.08
1062 2659 3.502920 CAATCTATGCGAGATCCGTACC 58.497 50.000 1.68 0.00 44.68 3.34
1063 2660 3.502920 CCAATCTATGCGAGATCCGTAC 58.497 50.000 1.68 0.00 44.68 3.67
1065 2662 1.273606 CCCAATCTATGCGAGATCCGT 59.726 52.381 1.68 0.00 44.68 4.69
1066 2663 2.001812 CCCAATCTATGCGAGATCCG 57.998 55.000 1.68 0.00 44.68 4.18
1067 2664 1.731720 GCCCAATCTATGCGAGATCC 58.268 55.000 1.68 0.00 44.68 3.36
1074 2671 0.819259 TTCCTGCGCCCAATCTATGC 60.819 55.000 4.18 0.00 0.00 3.14
1075 2672 1.679139 TTTCCTGCGCCCAATCTATG 58.321 50.000 4.18 0.00 0.00 2.23
1076 2673 2.664402 ATTTCCTGCGCCCAATCTAT 57.336 45.000 4.18 0.00 0.00 1.98
1077 2674 2.435372 AATTTCCTGCGCCCAATCTA 57.565 45.000 4.18 0.00 0.00 1.98
1078 2675 2.435372 TAATTTCCTGCGCCCAATCT 57.565 45.000 4.18 0.00 0.00 2.40
1080 2677 2.733956 TCTTAATTTCCTGCGCCCAAT 58.266 42.857 4.18 0.00 0.00 3.16
1081 2678 2.208132 TCTTAATTTCCTGCGCCCAA 57.792 45.000 4.18 0.00 0.00 4.12
1082 2679 2.208132 TTCTTAATTTCCTGCGCCCA 57.792 45.000 4.18 0.00 0.00 5.36
1083 2680 3.056821 AGTTTTCTTAATTTCCTGCGCCC 60.057 43.478 4.18 0.00 0.00 6.13
1115 2986 2.794166 GTCCGTCGTCACGTCGTG 60.794 66.667 19.38 19.38 45.17 4.35
1116 2987 4.360027 CGTCCGTCGTCACGTCGT 62.360 66.667 15.43 0.00 45.17 4.34
1127 2998 1.527611 TATCCATCTCGCCGTCCGT 60.528 57.895 0.00 0.00 38.35 4.69
1134 3005 2.049985 AGCGCGTATCCATCTCGC 60.050 61.111 8.43 0.00 45.34 5.03
1260 3131 1.822990 ACAGGAATATGGTGTCGTCGT 59.177 47.619 0.00 0.00 0.00 4.34
1266 3137 5.045578 GGGATGCTATACAGGAATATGGTGT 60.046 44.000 0.00 0.00 0.00 4.16
1477 3348 0.323451 TGAGCGAGAGAAGGCACCTA 60.323 55.000 0.00 0.00 0.00 3.08
1665 3538 3.183574 CAGTGCGACAATCTGACGTTTAA 59.816 43.478 0.00 0.00 37.80 1.52
1682 3564 2.622436 GTATGGTGAGAACTCCAGTGC 58.378 52.381 0.00 0.00 41.88 4.40
1687 3569 3.009143 ACTTTGGGTATGGTGAGAACTCC 59.991 47.826 0.00 0.00 0.00 3.85
1706 3588 3.649986 GCCGCGTGTGCTGAACTT 61.650 61.111 4.92 0.00 39.65 2.66
1942 3824 3.017323 GCATGGAACGATGCTCCG 58.983 61.111 13.00 0.00 44.57 4.63
1962 3844 2.003301 CTTTTCTTAGACCGAGCTGGC 58.997 52.381 0.00 0.00 43.94 4.85
1982 3864 5.594317 ACATCAAAAAGTATATGCAGTCCCC 59.406 40.000 0.00 0.00 0.00 4.81
2160 4042 4.821805 GTCAAGGACCAAAGTCTGAATTGA 59.178 41.667 0.00 0.00 43.05 2.57
2175 4057 1.374758 CCTGCCTCACGTCAAGGAC 60.375 63.158 16.07 8.69 35.83 3.85
2201 4083 5.921962 AAAGAGAAATGGAATAGGTTGGC 57.078 39.130 0.00 0.00 0.00 4.52
2202 4084 7.466746 TGAAAAGAGAAATGGAATAGGTTGG 57.533 36.000 0.00 0.00 0.00 3.77
2311 4194 5.047590 AGGCAAAATACGACCCCTTTAAAAG 60.048 40.000 0.00 0.00 0.00 2.27
2313 4196 4.409187 AGGCAAAATACGACCCCTTTAAA 58.591 39.130 0.00 0.00 0.00 1.52
2315 4198 3.724732 AGGCAAAATACGACCCCTTTA 57.275 42.857 0.00 0.00 0.00 1.85
2316 4199 2.597578 AGGCAAAATACGACCCCTTT 57.402 45.000 0.00 0.00 0.00 3.11
2318 4201 1.633945 AGAAGGCAAAATACGACCCCT 59.366 47.619 0.00 0.00 0.00 4.79
2319 4202 2.014857 GAGAAGGCAAAATACGACCCC 58.985 52.381 0.00 0.00 0.00 4.95
2320 4203 2.937149 GAGAGAAGGCAAAATACGACCC 59.063 50.000 0.00 0.00 0.00 4.46
2321 4204 2.937149 GGAGAGAAGGCAAAATACGACC 59.063 50.000 0.00 0.00 0.00 4.79
2322 4205 2.603560 CGGAGAGAAGGCAAAATACGAC 59.396 50.000 0.00 0.00 0.00 4.34
2324 4207 2.348666 CACGGAGAGAAGGCAAAATACG 59.651 50.000 0.00 0.00 0.00 3.06
2618 4548 2.679934 CGGAATTGTCGCAGCTGCA 61.680 57.895 36.03 21.33 42.21 4.41
2761 4726 2.679716 GGCTGCCATGGAGAACCT 59.320 61.111 18.40 0.00 37.04 3.50
2798 4764 1.355381 AGCCATTCAACATGGAGGACA 59.645 47.619 4.98 0.00 41.64 4.02
3225 5216 5.345702 CCAACAACGAAGGAGAACGATATA 58.654 41.667 0.00 0.00 0.00 0.86
3258 5249 1.800586 CAAGACAACCAGTGTGGATCG 59.199 52.381 0.00 0.00 41.96 3.69


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

AutoCloner maintained by Alex Coulton.