Multiple sequence alignment - TraesCS4A01G197400

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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 TraesCS4A01G197400 chr4A 100.000 3431 0 0 1 3431 481065905 481062475 0.000000e+00 6336
1 TraesCS4A01G197400 chr4A 91.931 2330 156 14 390 2688 479625496 479623168 0.000000e+00 3232
2 TraesCS4A01G197400 chr4A 89.026 2588 224 35 373 2927 479904300 479901740 0.000000e+00 3151
3 TraesCS4A01G197400 chr4A 92.119 1954 134 7 755 2688 480558132 480556179 0.000000e+00 2737
4 TraesCS4A01G197400 chr4A 91.627 1899 140 6 755 2634 479431440 479429542 0.000000e+00 2608
5 TraesCS4A01G197400 chr4A 92.836 684 45 2 373 1053 479647835 479647153 0.000000e+00 989
6 TraesCS4A01G197400 chr4A 88.645 546 52 8 2145 2687 479620978 479620440 0.000000e+00 656
7 TraesCS4A01G197400 chr4A 92.571 350 23 3 373 722 480558476 480558130 1.840000e-137 499
8 TraesCS4A01G197400 chr4A 92.286 350 24 3 373 722 479431784 479431438 8.550000e-136 494
9 TraesCS4A01G197400 chr4A 81.566 396 49 13 2712 3104 479615155 479614781 4.300000e-79 305
10 TraesCS4A01G197400 chr4A 85.586 111 4 5 2915 3025 479901321 479901223 4.680000e-19 106
11 TraesCS4A01G197400 chr4D 96.050 2810 77 9 370 3158 96891691 96894487 0.000000e+00 4543
12 TraesCS4A01G197400 chr4D 92.166 2336 158 10 374 2688 96711356 96713687 0.000000e+00 3277
13 TraesCS4A01G197400 chr4B 88.075 2281 190 30 370 2618 137701675 137703905 0.000000e+00 2630
14 TraesCS4A01G197400 chr4B 90.338 1480 123 9 1171 2634 138276147 138277622 0.000000e+00 1923
15 TraesCS4A01G197400 chr4B 90.024 421 22 11 768 1175 138275810 138276223 8.430000e-146 527
16 TraesCS4A01G197400 chr4B 84.511 368 47 8 2795 3157 138277797 138278159 4.210000e-94 355
17 TraesCS4A01G197400 chr4B 83.764 271 37 6 370 636 138275473 138275740 2.040000e-62 250
18 TraesCS4A01G197400 chr7A 86.148 1285 150 18 1171 2435 79335044 79333768 0.000000e+00 1362
19 TraesCS4A01G197400 chr1A 96.866 351 10 1 4 354 235063409 235063060 1.370000e-163 586
20 TraesCS4A01G197400 chr7B 96.246 293 11 0 56 348 641877020 641877312 6.660000e-132 481
21 TraesCS4A01G197400 chr7B 84.594 357 34 6 12 348 645598170 645597815 5.490000e-88 335
22 TraesCS4A01G197400 chr1B 94.915 295 14 1 56 350 504509957 504509664 8.680000e-126 460
23 TraesCS4A01G197400 chr1B 91.304 299 26 0 56 354 668027439 668027737 3.190000e-110 409
24 TraesCS4A01G197400 chr2A 93.919 296 18 0 56 351 14404233 14403938 6.750000e-122 448
25 TraesCS4A01G197400 chr2B 91.304 299 26 0 56 354 553610001 553610299 3.190000e-110 409
26 TraesCS4A01G197400 chr5B 90.635 299 27 1 56 354 471314869 471314572 2.480000e-106 396
27 TraesCS4A01G197400 chr3B 96.203 237 9 0 118 354 798313161 798312925 4.150000e-104 388
28 TraesCS4A01G197400 chr2D 84.906 371 30 14 4 350 14839860 14839492 5.450000e-93 351
29 TraesCS4A01G197400 chr1D 84.324 370 34 11 10 355 361211603 361211234 1.180000e-89 340


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 TraesCS4A01G197400 chr4A 481062475 481065905 3430 True 6336.00 6336 100.00000 1 3431 1 chr4A.!!$R3 3430
1 TraesCS4A01G197400 chr4A 479620440 479625496 5056 True 1944.00 3232 90.28800 390 2688 2 chr4A.!!$R5 2298
2 TraesCS4A01G197400 chr4A 479901223 479904300 3077 True 1628.50 3151 87.30600 373 3025 2 chr4A.!!$R6 2652
3 TraesCS4A01G197400 chr4A 480556179 480558476 2297 True 1618.00 2737 92.34500 373 2688 2 chr4A.!!$R7 2315
4 TraesCS4A01G197400 chr4A 479429542 479431784 2242 True 1551.00 2608 91.95650 373 2634 2 chr4A.!!$R4 2261
5 TraesCS4A01G197400 chr4A 479647153 479647835 682 True 989.00 989 92.83600 373 1053 1 chr4A.!!$R2 680
6 TraesCS4A01G197400 chr4D 96891691 96894487 2796 False 4543.00 4543 96.05000 370 3158 1 chr4D.!!$F2 2788
7 TraesCS4A01G197400 chr4D 96711356 96713687 2331 False 3277.00 3277 92.16600 374 2688 1 chr4D.!!$F1 2314
8 TraesCS4A01G197400 chr4B 137701675 137703905 2230 False 2630.00 2630 88.07500 370 2618 1 chr4B.!!$F1 2248
9 TraesCS4A01G197400 chr4B 138275473 138278159 2686 False 763.75 1923 87.15925 370 3157 4 chr4B.!!$F2 2787
10 TraesCS4A01G197400 chr7A 79333768 79335044 1276 True 1362.00 1362 86.14800 1171 2435 1 chr7A.!!$R1 1264

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
718 762 0.041238 TCTCCCTCTCCCATCGTTGT 59.959 55.000 0.0 0.0 0.0 3.32 F
1449 1517 1.135333 GCGGAGAAGAGGGTCTACAAG 59.865 57.143 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1665 1733 1.152525 GGGCTCTAGGTCCGGATCA 60.153 63.158 19.03 1.81 0.00 2.92 R
3353 4023 0.251922 AACCAAGACATGCCCATGCT 60.252 50.000 8.11 4.23 42.39 3.79 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
76 77 3.749064 GCCACTCCGCTCAGACGA 61.749 66.667 0.00 0.00 34.06 4.20
77 78 2.487428 CCACTCCGCTCAGACGAG 59.513 66.667 0.00 0.00 42.66 4.18
78 79 2.041115 CCACTCCGCTCAGACGAGA 61.041 63.158 0.00 0.00 42.34 4.04
79 80 1.427419 CACTCCGCTCAGACGAGAG 59.573 63.158 0.00 0.00 42.34 3.20
85 86 2.487428 CTCAGACGAGAGCCACGG 59.513 66.667 0.00 0.00 42.34 4.94
86 87 3.057547 CTCAGACGAGAGCCACGGG 62.058 68.421 0.00 0.00 42.34 5.28
110 111 3.368571 GTGCCTTGCCAGAGCCAC 61.369 66.667 0.00 0.00 38.69 5.01
111 112 4.666253 TGCCTTGCCAGAGCCACC 62.666 66.667 0.00 0.00 38.69 4.61
113 114 4.748144 CCTTGCCAGAGCCACCCC 62.748 72.222 0.00 0.00 38.69 4.95
114 115 4.748144 CTTGCCAGAGCCACCCCC 62.748 72.222 0.00 0.00 38.69 5.40
148 149 4.812476 CGAACCATGCCGGCGAGA 62.812 66.667 23.90 4.21 39.03 4.04
149 150 2.892425 GAACCATGCCGGCGAGAG 60.892 66.667 23.90 13.05 39.03 3.20
150 151 4.473520 AACCATGCCGGCGAGAGG 62.474 66.667 23.90 21.83 39.03 3.69
152 153 4.899239 CCATGCCGGCGAGAGGAC 62.899 72.222 23.90 0.00 0.00 3.85
153 154 4.899239 CATGCCGGCGAGAGGACC 62.899 72.222 23.90 0.00 0.00 4.46
166 167 4.593864 GGACCTCCGCGCCAGATC 62.594 72.222 0.00 0.00 0.00 2.75
167 168 3.532155 GACCTCCGCGCCAGATCT 61.532 66.667 0.00 0.00 0.00 2.75
168 169 3.781770 GACCTCCGCGCCAGATCTG 62.782 68.421 16.24 16.24 0.00 2.90
202 203 0.540923 CAAGAGCTTGGAGAGGAGGG 59.459 60.000 2.30 0.00 36.95 4.30
203 204 0.620121 AAGAGCTTGGAGAGGAGGGG 60.620 60.000 0.00 0.00 0.00 4.79
204 205 1.002274 GAGCTTGGAGAGGAGGGGA 59.998 63.158 0.00 0.00 0.00 4.81
205 206 1.002792 AGCTTGGAGAGGAGGGGAG 59.997 63.158 0.00 0.00 0.00 4.30
206 207 1.002274 GCTTGGAGAGGAGGGGAGA 59.998 63.158 0.00 0.00 0.00 3.71
207 208 0.618968 GCTTGGAGAGGAGGGGAGAA 60.619 60.000 0.00 0.00 0.00 2.87
208 209 1.958288 CTTGGAGAGGAGGGGAGAAA 58.042 55.000 0.00 0.00 0.00 2.52
209 210 1.557371 CTTGGAGAGGAGGGGAGAAAC 59.443 57.143 0.00 0.00 0.00 2.78
210 211 0.252742 TGGAGAGGAGGGGAGAAACC 60.253 60.000 0.00 0.00 38.08 3.27
250 251 3.774702 GCTTTGCCCGACGTCGTC 61.775 66.667 33.49 24.71 37.74 4.20
251 252 3.110178 CTTTGCCCGACGTCGTCC 61.110 66.667 33.49 23.91 37.74 4.79
252 253 4.668118 TTTGCCCGACGTCGTCCC 62.668 66.667 33.49 21.59 37.74 4.46
256 257 4.430765 CCCGACGTCGTCCCTTGG 62.431 72.222 33.49 23.00 37.74 3.61
315 316 3.199891 GCGGCGCGATTTAGGGTT 61.200 61.111 19.09 0.00 0.00 4.11
316 317 3.011583 CGGCGCGATTTAGGGTTC 58.988 61.111 12.10 0.00 0.00 3.62
317 318 2.531376 CGGCGCGATTTAGGGTTCC 61.531 63.158 12.10 0.00 0.00 3.62
318 319 1.153229 GGCGCGATTTAGGGTTCCT 60.153 57.895 12.10 0.00 37.71 3.36
319 320 1.158484 GGCGCGATTTAGGGTTCCTC 61.158 60.000 12.10 0.00 34.61 3.71
320 321 1.158484 GCGCGATTTAGGGTTCCTCC 61.158 60.000 12.10 0.00 34.61 4.30
365 366 3.311110 GACGGGTCCAGCCAGACA 61.311 66.667 6.11 0.00 38.59 3.41
366 367 2.847234 ACGGGTCCAGCCAGACAA 60.847 61.111 6.11 0.00 38.59 3.18
367 368 2.391724 GACGGGTCCAGCCAGACAAA 62.392 60.000 6.11 0.00 38.59 2.83
368 369 1.672356 CGGGTCCAGCCAGACAAAG 60.672 63.158 6.11 0.00 38.59 2.77
371 372 0.606673 GGTCCAGCCAGACAAAGTCC 60.607 60.000 6.11 0.00 38.59 3.85
399 400 5.389428 GCGCGAAAGTTTTCAAATCAAAAAG 59.611 36.000 12.10 0.00 37.01 2.27
460 468 0.459899 TGCTCGGTCGCATAACTGAT 59.540 50.000 0.00 0.00 34.14 2.90
462 470 1.802880 GCTCGGTCGCATAACTGATGT 60.803 52.381 0.00 0.00 37.90 3.06
485 493 0.951040 CTCCGGTCACCTCTGCAAAC 60.951 60.000 0.00 0.00 0.00 2.93
487 495 1.300620 CGGTCACCTCTGCAAACGA 60.301 57.895 0.00 0.00 0.00 3.85
581 589 1.972660 GCTAATCCCACCACGCCTCT 61.973 60.000 0.00 0.00 0.00 3.69
602 610 4.085204 ATCCCGTTTACCGCCGCA 62.085 61.111 0.00 0.00 34.38 5.69
718 762 0.041238 TCTCCCTCTCCCATCGTTGT 59.959 55.000 0.00 0.00 0.00 3.32
860 916 4.714802 TCCCTTCTTCTAATCGGATCACAA 59.285 41.667 0.00 0.00 0.00 3.33
901 957 2.575532 GATATAAAGTGCAGCCAGCCA 58.424 47.619 0.00 0.00 44.83 4.75
974 1042 3.745723 GAAGCAACTCTTCCCCCAA 57.254 52.632 0.00 0.00 44.22 4.12
1404 1472 1.980765 ACCTCTGAATCTGCTGGTGAA 59.019 47.619 4.54 0.00 0.00 3.18
1449 1517 1.135333 GCGGAGAAGAGGGTCTACAAG 59.865 57.143 0.00 0.00 0.00 3.16
1665 1733 4.380843 TGAATTGTGGGACCAACTGTAT 57.619 40.909 0.00 0.00 0.00 2.29
1675 1743 1.485066 ACCAACTGTATGATCCGGACC 59.515 52.381 6.12 0.00 0.00 4.46
1752 1835 4.526970 TCAGGGCATTTATCTTTCCAGAC 58.473 43.478 0.00 0.00 0.00 3.51
1821 1904 2.036217 TCAGCTTTCATTTGCAAGGGTG 59.964 45.455 0.00 0.64 0.00 4.61
2347 2433 7.182026 TGGAAGATGACAGTAGGGAAGAAATTA 59.818 37.037 0.00 0.00 0.00 1.40
2444 2530 5.414454 TGTGCAAATAGGTAGCCTTTTGTAG 59.586 40.000 14.81 4.42 35.80 2.74
2554 2642 9.739276 TCTATCTCCTTTTCATATGTTGTTTGT 57.261 29.630 1.90 0.00 0.00 2.83
2567 2655 9.712359 CATATGTTGTTTGTTGTATCTGATGAG 57.288 33.333 0.00 0.00 0.00 2.90
2668 2759 6.829849 TCCTATTCACATGCATATTCTGACA 58.170 36.000 0.00 0.00 0.00 3.58
2799 3013 7.400599 ACTGTATTTCTGATTGCATTGATGT 57.599 32.000 0.00 0.00 0.00 3.06
2921 3566 2.162681 GTGCAGTTGCTAATCCCTGTT 58.837 47.619 5.62 0.00 42.66 3.16
2994 3643 1.003580 CTTGCTCCTGGGCTACTTCAA 59.996 52.381 8.32 0.00 0.00 2.69
3040 3689 3.181516 GCATTTCTGCTCAGTTACCTTCG 60.182 47.826 0.00 0.00 45.32 3.79
3153 3802 0.589223 ACATGTAACGGTGGCGTTTG 59.411 50.000 0.00 0.00 33.80 2.93
3157 3806 0.041047 GTAACGGTGGCGTTTGTTCC 60.041 55.000 0.00 0.00 33.80 3.62
3158 3807 0.179051 TAACGGTGGCGTTTGTTCCT 60.179 50.000 0.00 0.00 33.80 3.36
3159 3808 1.033202 AACGGTGGCGTTTGTTCCTT 61.033 50.000 0.00 0.00 0.00 3.36
3160 3809 1.008995 CGGTGGCGTTTGTTCCTTG 60.009 57.895 0.00 0.00 0.00 3.61
3161 3810 1.440938 CGGTGGCGTTTGTTCCTTGA 61.441 55.000 0.00 0.00 0.00 3.02
3162 3811 0.958822 GGTGGCGTTTGTTCCTTGAT 59.041 50.000 0.00 0.00 0.00 2.57
3163 3812 1.339929 GGTGGCGTTTGTTCCTTGATT 59.660 47.619 0.00 0.00 0.00 2.57
3164 3813 2.554893 GGTGGCGTTTGTTCCTTGATTA 59.445 45.455 0.00 0.00 0.00 1.75
3165 3814 3.004944 GGTGGCGTTTGTTCCTTGATTAA 59.995 43.478 0.00 0.00 0.00 1.40
3166 3815 4.321675 GGTGGCGTTTGTTCCTTGATTAAT 60.322 41.667 0.00 0.00 0.00 1.40
3167 3816 5.227152 GTGGCGTTTGTTCCTTGATTAATT 58.773 37.500 0.00 0.00 0.00 1.40
3168 3817 5.118510 GTGGCGTTTGTTCCTTGATTAATTG 59.881 40.000 0.00 0.00 0.00 2.32
3169 3818 4.625311 GGCGTTTGTTCCTTGATTAATTGG 59.375 41.667 0.00 0.00 0.00 3.16
3170 3819 5.227152 GCGTTTGTTCCTTGATTAATTGGT 58.773 37.500 0.00 0.00 0.00 3.67
3171 3820 5.694458 GCGTTTGTTCCTTGATTAATTGGTT 59.306 36.000 0.00 0.00 0.00 3.67
3172 3821 6.864165 GCGTTTGTTCCTTGATTAATTGGTTA 59.136 34.615 0.00 0.00 0.00 2.85
3173 3822 7.544217 GCGTTTGTTCCTTGATTAATTGGTTAT 59.456 33.333 0.00 0.00 0.00 1.89
3174 3823 8.859156 CGTTTGTTCCTTGATTAATTGGTTATG 58.141 33.333 0.00 0.00 0.00 1.90
3175 3824 8.655970 GTTTGTTCCTTGATTAATTGGTTATGC 58.344 33.333 0.00 0.00 0.00 3.14
3176 3825 7.716799 TGTTCCTTGATTAATTGGTTATGCT 57.283 32.000 0.00 0.00 0.00 3.79
3177 3826 8.133024 TGTTCCTTGATTAATTGGTTATGCTT 57.867 30.769 0.00 0.00 0.00 3.91
3178 3827 8.592809 TGTTCCTTGATTAATTGGTTATGCTTT 58.407 29.630 0.00 0.00 0.00 3.51
3179 3828 9.087424 GTTCCTTGATTAATTGGTTATGCTTTC 57.913 33.333 0.00 0.00 0.00 2.62
3180 3829 8.359875 TCCTTGATTAATTGGTTATGCTTTCA 57.640 30.769 0.00 0.00 0.00 2.69
3181 3830 8.980596 TCCTTGATTAATTGGTTATGCTTTCAT 58.019 29.630 0.00 0.00 36.73 2.57
3193 3842 2.151202 TGCTTTCATCACGGTTTCCTC 58.849 47.619 0.00 0.00 0.00 3.71
3196 3845 3.191371 GCTTTCATCACGGTTTCCTCATT 59.809 43.478 0.00 0.00 0.00 2.57
3223 3872 4.031636 AGGAAGTCCTTAGTCGTACAGT 57.968 45.455 0.00 0.00 46.09 3.55
3224 3873 3.757493 AGGAAGTCCTTAGTCGTACAGTG 59.243 47.826 0.00 0.00 46.09 3.66
3240 3889 2.903784 ACAGTGTGCCTCTGGTATGTAA 59.096 45.455 0.00 0.00 37.25 2.41
3241 3890 3.326588 ACAGTGTGCCTCTGGTATGTAAA 59.673 43.478 0.00 0.00 37.25 2.01
3242 3891 4.019321 ACAGTGTGCCTCTGGTATGTAAAT 60.019 41.667 0.00 0.00 37.25 1.40
3243 3892 4.572389 CAGTGTGCCTCTGGTATGTAAATC 59.428 45.833 0.00 0.00 0.00 2.17
3273 3922 0.104409 AACCCCCTCTGAACTCCACT 60.104 55.000 0.00 0.00 0.00 4.00
3292 3941 4.752101 CCACTGCTTCTTATGTAGGTATGC 59.248 45.833 0.00 0.00 0.00 3.14
3296 3945 7.383572 CACTGCTTCTTATGTAGGTATGCTTAG 59.616 40.741 0.00 0.00 0.00 2.18
3298 3947 6.042093 TGCTTCTTATGTAGGTATGCTTAGCT 59.958 38.462 14.80 14.80 39.44 3.32
3299 3948 7.232737 TGCTTCTTATGTAGGTATGCTTAGCTA 59.767 37.037 12.97 12.97 37.37 3.32
3319 3968 7.374975 AGCTATGCTAATAAAACTCCCTGTA 57.625 36.000 0.00 0.00 36.99 2.74
3320 3969 7.978925 AGCTATGCTAATAAAACTCCCTGTAT 58.021 34.615 0.00 0.00 36.99 2.29
3321 3970 9.101325 AGCTATGCTAATAAAACTCCCTGTATA 57.899 33.333 0.00 0.00 36.99 1.47
3335 4005 6.767902 ACTCCCTGTATACAAATACAATGCAG 59.232 38.462 7.06 0.00 45.64 4.41
3353 4023 4.402829 TGCAGTTTTATGCTCCCTGTAAA 58.597 39.130 0.00 0.00 46.63 2.01
3359 4029 3.575506 TGCTCCCTGTAAAGCATGG 57.424 52.632 0.00 0.00 43.30 3.66
3366 4036 1.406539 CCTGTAAAGCATGGGCATGTC 59.593 52.381 0.00 0.00 44.61 3.06
3379 4049 4.892433 TGGGCATGTCTTGGTTAAAAATG 58.108 39.130 0.00 0.00 0.00 2.32
3383 4053 6.484977 GGGCATGTCTTGGTTAAAAATGAAAA 59.515 34.615 0.00 0.00 0.00 2.29
3384 4054 7.012799 GGGCATGTCTTGGTTAAAAATGAAAAA 59.987 33.333 0.00 0.00 0.00 1.94
3385 4055 8.567104 GGCATGTCTTGGTTAAAAATGAAAAAT 58.433 29.630 0.00 0.00 0.00 1.82
3418 4091 5.323371 TGGCAAAATTACAGCATAGAACC 57.677 39.130 0.00 0.00 0.00 3.62
3419 4092 4.159506 TGGCAAAATTACAGCATAGAACCC 59.840 41.667 0.00 0.00 0.00 4.11
3420 4093 4.351192 GCAAAATTACAGCATAGAACCCG 58.649 43.478 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 3.691744 CTCGTCTGAGCGGAGTGGC 62.692 68.421 0.00 0.00 34.96 5.01
60 61 1.987704 CTCTCGTCTGAGCGGAGTGG 61.988 65.000 0.73 0.00 42.26 4.00
61 62 1.427419 CTCTCGTCTGAGCGGAGTG 59.573 63.158 0.73 0.00 42.26 3.51
62 63 3.897936 CTCTCGTCTGAGCGGAGT 58.102 61.111 0.73 0.00 42.26 3.85
68 69 2.487428 CCGTGGCTCTCGTCTGAG 59.513 66.667 0.00 0.00 43.99 3.35
69 70 3.062466 CCCGTGGCTCTCGTCTGA 61.062 66.667 0.00 0.00 0.00 3.27
70 71 4.803426 GCCCGTGGCTCTCGTCTG 62.803 72.222 7.58 0.00 46.69 3.51
96 97 4.748144 GGGGTGGCTCTGGCAAGG 62.748 72.222 0.00 0.00 40.46 3.61
97 98 4.748144 GGGGGTGGCTCTGGCAAG 62.748 72.222 0.00 0.00 40.46 4.01
131 132 4.812476 TCTCGCCGGCATGGTTCG 62.812 66.667 28.98 8.23 41.21 3.95
132 133 2.892425 CTCTCGCCGGCATGGTTC 60.892 66.667 28.98 0.00 41.21 3.62
133 134 4.473520 CCTCTCGCCGGCATGGTT 62.474 66.667 28.98 0.00 41.21 3.67
135 136 4.899239 GTCCTCTCGCCGGCATGG 62.899 72.222 28.98 20.97 42.50 3.66
136 137 4.899239 GGTCCTCTCGCCGGCATG 62.899 72.222 28.98 18.32 0.00 4.06
149 150 4.593864 GATCTGGCGCGGAGGTCC 62.594 72.222 8.83 0.00 0.00 4.46
150 151 3.532155 AGATCTGGCGCGGAGGTC 61.532 66.667 8.83 9.71 0.00 3.85
151 152 3.842923 CAGATCTGGCGCGGAGGT 61.843 66.667 15.38 0.00 0.00 3.85
152 153 4.598894 CCAGATCTGGCGCGGAGG 62.599 72.222 28.45 2.73 44.73 4.30
183 184 0.540923 CCCTCCTCTCCAAGCTCTTG 59.459 60.000 2.74 2.74 40.13 3.02
184 185 0.620121 CCCCTCCTCTCCAAGCTCTT 60.620 60.000 0.00 0.00 0.00 2.85
185 186 1.002792 CCCCTCCTCTCCAAGCTCT 59.997 63.158 0.00 0.00 0.00 4.09
186 187 1.002274 TCCCCTCCTCTCCAAGCTC 59.998 63.158 0.00 0.00 0.00 4.09
187 188 1.002792 CTCCCCTCCTCTCCAAGCT 59.997 63.158 0.00 0.00 0.00 3.74
188 189 0.618968 TTCTCCCCTCCTCTCCAAGC 60.619 60.000 0.00 0.00 0.00 4.01
189 190 1.557371 GTTTCTCCCCTCCTCTCCAAG 59.443 57.143 0.00 0.00 0.00 3.61
190 191 1.657804 GTTTCTCCCCTCCTCTCCAA 58.342 55.000 0.00 0.00 0.00 3.53
191 192 0.252742 GGTTTCTCCCCTCCTCTCCA 60.253 60.000 0.00 0.00 0.00 3.86
192 193 2.610282 GGTTTCTCCCCTCCTCTCC 58.390 63.158 0.00 0.00 0.00 3.71
233 234 3.774702 GACGACGTCGGGCAAAGC 61.775 66.667 37.89 16.10 44.95 3.51
234 235 3.110178 GGACGACGTCGGGCAAAG 61.110 66.667 37.89 12.57 44.95 2.77
235 236 4.668118 GGGACGACGTCGGGCAAA 62.668 66.667 37.89 0.00 44.95 3.68
239 240 4.430765 CCAAGGGACGACGTCGGG 62.431 72.222 37.89 25.27 44.95 5.14
298 299 3.164390 GAACCCTAAATCGCGCCGC 62.164 63.158 0.00 0.00 0.00 6.53
299 300 2.531376 GGAACCCTAAATCGCGCCG 61.531 63.158 0.00 0.00 0.00 6.46
300 301 1.153229 AGGAACCCTAAATCGCGCC 60.153 57.895 0.00 0.00 28.47 6.53
301 302 1.158484 GGAGGAACCCTAAATCGCGC 61.158 60.000 0.00 0.00 31.76 6.86
302 303 2.987752 GGAGGAACCCTAAATCGCG 58.012 57.895 0.00 0.00 31.76 5.87
348 349 2.391724 TTTGTCTGGCTGGACCCGTC 62.392 60.000 8.26 0.00 37.83 4.79
349 350 2.397413 CTTTGTCTGGCTGGACCCGT 62.397 60.000 8.26 0.00 37.83 5.28
350 351 1.672356 CTTTGTCTGGCTGGACCCG 60.672 63.158 8.26 0.00 37.83 5.28
351 352 0.606673 GACTTTGTCTGGCTGGACCC 60.607 60.000 8.26 0.00 37.83 4.46
352 353 0.606673 GGACTTTGTCTGGCTGGACC 60.607 60.000 8.26 0.00 35.54 4.46
353 354 0.606673 GGGACTTTGTCTGGCTGGAC 60.607 60.000 4.67 4.67 36.81 4.02
354 355 0.768221 AGGGACTTTGTCTGGCTGGA 60.768 55.000 0.00 0.00 27.25 3.86
355 356 0.322008 GAGGGACTTTGTCTGGCTGG 60.322 60.000 0.00 0.00 41.55 4.85
356 357 0.671781 CGAGGGACTTTGTCTGGCTG 60.672 60.000 0.00 0.00 41.55 4.85
357 358 1.674057 CGAGGGACTTTGTCTGGCT 59.326 57.895 0.00 0.00 41.55 4.75
358 359 2.035442 GCGAGGGACTTTGTCTGGC 61.035 63.158 0.00 0.00 41.55 4.85
359 360 1.738099 CGCGAGGGACTTTGTCTGG 60.738 63.158 0.00 0.00 41.55 3.86
360 361 2.383527 GCGCGAGGGACTTTGTCTG 61.384 63.158 12.10 0.00 41.55 3.51
361 362 2.048127 GCGCGAGGGACTTTGTCT 60.048 61.111 12.10 0.00 41.55 3.41
371 372 0.041663 TTGAAAACTTTCGCGCGAGG 60.042 50.000 32.74 28.47 40.01 4.63
399 400 5.164090 GCGAACGATTCCTTTTTCATTTTCC 60.164 40.000 0.00 0.00 0.00 3.13
460 468 1.304217 GAGGTGACCGGAGAGGACA 60.304 63.158 9.46 0.00 45.00 4.02
462 470 1.000771 CAGAGGTGACCGGAGAGGA 60.001 63.158 9.46 0.00 45.00 3.71
485 493 3.636231 TTGTGGGGGCAGGTCTCG 61.636 66.667 0.00 0.00 0.00 4.04
487 495 3.953775 CGTTGTGGGGGCAGGTCT 61.954 66.667 0.00 0.00 0.00 3.85
555 563 1.212935 GTGGTGGGATTAGCAGTGGAT 59.787 52.381 0.00 0.00 0.00 3.41
581 589 2.041686 GGCGGTAAACGGGATGCAA 61.042 57.895 0.00 0.00 44.51 4.08
718 762 3.089874 CCTCGGAAGGATGCCCCA 61.090 66.667 0.00 0.00 46.67 4.96
832 888 2.365941 CCGATTAGAAGAAGGGAGTCCC 59.634 54.545 21.81 21.81 45.90 4.46
860 916 4.742649 TCGAGCCGAGGCCTCACT 62.743 66.667 31.67 26.67 43.17 3.41
901 957 1.895798 TCTGAGAAGAAGCACACCGAT 59.104 47.619 0.00 0.00 0.00 4.18
974 1042 2.874086 GCAATTGCAAAAGCAGGTCTTT 59.126 40.909 25.36 0.00 46.42 2.52
1177 1245 0.909610 TCCATGGGTGGTGAGACCTC 60.910 60.000 13.02 0.00 46.16 3.85
1293 1361 1.548357 GCCAGGAGGAGCTGACAGAA 61.548 60.000 6.65 0.00 36.89 3.02
1404 1472 3.576648 GCTGTAGAGACAAGCTACGTTT 58.423 45.455 0.00 0.00 40.79 3.60
1449 1517 1.138464 GGTGGATCCGGGAGAGTTAAC 59.862 57.143 7.39 0.00 0.00 2.01
1665 1733 1.152525 GGGCTCTAGGTCCGGATCA 60.153 63.158 19.03 1.81 0.00 2.92
1675 1743 3.798202 AGCTTAACATTTCGGGCTCTAG 58.202 45.455 0.00 0.00 0.00 2.43
1752 1835 1.218316 GTAGCTTCCTGTGGACGGG 59.782 63.158 0.00 0.00 43.86 5.28
1821 1904 1.212195 GGGGTCCACTTACAATCTCCC 59.788 57.143 0.00 0.00 0.00 4.30
2347 2433 2.700897 AGCTACACCAAAGCGGAGATAT 59.299 45.455 0.00 0.00 44.87 1.63
2444 2530 5.104235 AGACCCCATAACCAAGGTACATAAC 60.104 44.000 0.00 0.00 31.10 1.89
2554 2642 6.062095 TCGGTCATAGTCTCATCAGATACAA 58.938 40.000 0.00 0.00 0.00 2.41
2592 2680 5.534278 TGTTGTAGAGCACCATTTTCATTCA 59.466 36.000 0.00 0.00 0.00 2.57
2618 2709 7.178712 AGAAATGTGAGAACAGAAAACGTAG 57.821 36.000 0.00 0.00 0.00 3.51
2921 3566 8.868522 AAATCTTCAGTTATCTTCAACCATGA 57.131 30.769 0.00 0.00 0.00 3.07
2968 3616 1.673665 GCCCAGGAGCAAGAGTGTG 60.674 63.158 0.00 0.00 0.00 3.82
2994 3643 2.545742 GCCAAAGCATGAAAGAACCGTT 60.546 45.455 0.00 0.00 39.53 4.44
3029 3678 2.409975 TCCGCTTTTCGAAGGTAACTG 58.590 47.619 0.00 0.00 44.42 3.16
3036 3685 2.143925 AGAACCTTCCGCTTTTCGAAG 58.856 47.619 0.00 0.00 41.67 3.79
3040 3689 2.495084 AGTGAGAACCTTCCGCTTTTC 58.505 47.619 0.00 0.00 0.00 2.29
3153 3802 9.087424 GAAAGCATAACCAATTAATCAAGGAAC 57.913 33.333 8.14 0.00 0.00 3.62
3157 3806 9.806203 TGATGAAAGCATAACCAATTAATCAAG 57.194 29.630 0.00 0.00 34.11 3.02
3158 3807 9.585099 GTGATGAAAGCATAACCAATTAATCAA 57.415 29.630 0.00 0.00 30.84 2.57
3159 3808 7.914871 CGTGATGAAAGCATAACCAATTAATCA 59.085 33.333 0.00 0.00 30.84 2.57
3160 3809 7.379529 CCGTGATGAAAGCATAACCAATTAATC 59.620 37.037 0.00 0.00 30.84 1.75
3161 3810 7.147915 ACCGTGATGAAAGCATAACCAATTAAT 60.148 33.333 0.00 0.00 30.84 1.40
3162 3811 6.151985 ACCGTGATGAAAGCATAACCAATTAA 59.848 34.615 0.00 0.00 30.84 1.40
3163 3812 5.650266 ACCGTGATGAAAGCATAACCAATTA 59.350 36.000 0.00 0.00 30.84 1.40
3164 3813 4.462483 ACCGTGATGAAAGCATAACCAATT 59.538 37.500 0.00 0.00 30.84 2.32
3165 3814 4.016444 ACCGTGATGAAAGCATAACCAAT 58.984 39.130 0.00 0.00 30.84 3.16
3166 3815 3.417101 ACCGTGATGAAAGCATAACCAA 58.583 40.909 0.00 0.00 30.84 3.67
3167 3816 3.066291 ACCGTGATGAAAGCATAACCA 57.934 42.857 0.00 0.00 30.84 3.67
3168 3817 4.412207 GAAACCGTGATGAAAGCATAACC 58.588 43.478 0.00 0.00 30.84 2.85
3169 3818 4.156008 AGGAAACCGTGATGAAAGCATAAC 59.844 41.667 0.00 0.00 30.84 1.89
3170 3819 4.331968 AGGAAACCGTGATGAAAGCATAA 58.668 39.130 0.00 0.00 30.84 1.90
3171 3820 3.938963 GAGGAAACCGTGATGAAAGCATA 59.061 43.478 0.00 0.00 30.84 3.14
3172 3821 2.749621 GAGGAAACCGTGATGAAAGCAT 59.250 45.455 0.00 0.00 30.84 3.79
3173 3822 2.151202 GAGGAAACCGTGATGAAAGCA 58.849 47.619 0.00 0.00 0.00 3.91
3174 3823 2.151202 TGAGGAAACCGTGATGAAAGC 58.849 47.619 0.00 0.00 0.00 3.51
3175 3824 6.111768 CTAATGAGGAAACCGTGATGAAAG 57.888 41.667 0.00 0.00 0.00 2.62
3203 3852 3.505293 ACACTGTACGACTAAGGACTTCC 59.495 47.826 0.00 0.00 0.00 3.46
3206 3855 2.228343 GCACACTGTACGACTAAGGACT 59.772 50.000 0.00 0.00 0.00 3.85
3209 3858 1.544691 AGGCACACTGTACGACTAAGG 59.455 52.381 0.00 0.00 0.00 2.69
3210 3859 2.488545 AGAGGCACACTGTACGACTAAG 59.511 50.000 0.00 0.00 0.00 2.18
3215 3864 0.826256 ACCAGAGGCACACTGTACGA 60.826 55.000 0.00 0.00 45.47 3.43
3223 3872 3.118038 GGGATTTACATACCAGAGGCACA 60.118 47.826 0.00 0.00 32.59 4.57
3224 3873 3.477530 GGGATTTACATACCAGAGGCAC 58.522 50.000 0.00 0.00 32.59 5.01
3249 3898 2.206036 TTCAGAGGGGGTTCGGGT 59.794 61.111 0.00 0.00 0.00 5.28
3257 3906 1.197430 AGCAGTGGAGTTCAGAGGGG 61.197 60.000 0.00 0.00 0.00 4.79
3258 3907 0.689623 AAGCAGTGGAGTTCAGAGGG 59.310 55.000 0.00 0.00 0.00 4.30
3260 3909 3.399440 AAGAAGCAGTGGAGTTCAGAG 57.601 47.619 0.00 0.00 0.00 3.35
3261 3910 4.284490 ACATAAGAAGCAGTGGAGTTCAGA 59.716 41.667 0.00 0.00 0.00 3.27
3273 3922 6.042093 AGCTAAGCATACCTACATAAGAAGCA 59.958 38.462 0.00 0.00 0.00 3.91
3296 3945 9.152595 GTATACAGGGAGTTTTATTAGCATAGC 57.847 37.037 0.00 0.00 0.00 2.97
3299 3948 9.914834 TTTGTATACAGGGAGTTTTATTAGCAT 57.085 29.630 5.56 0.00 0.00 3.79
3307 3956 8.466798 GCATTGTATTTGTATACAGGGAGTTTT 58.533 33.333 5.56 0.00 45.40 2.43
3308 3957 7.613801 TGCATTGTATTTGTATACAGGGAGTTT 59.386 33.333 5.56 0.00 45.40 2.66
3310 3959 6.658849 TGCATTGTATTTGTATACAGGGAGT 58.341 36.000 5.56 0.00 45.40 3.85
3311 3960 6.767902 ACTGCATTGTATTTGTATACAGGGAG 59.232 38.462 5.56 13.61 45.40 4.30
3312 3961 6.658849 ACTGCATTGTATTTGTATACAGGGA 58.341 36.000 5.56 0.00 45.40 4.20
3313 3962 6.942532 ACTGCATTGTATTTGTATACAGGG 57.057 37.500 5.56 0.00 45.40 4.45
3319 3968 9.520204 GAGCATAAAACTGCATTGTATTTGTAT 57.480 29.630 0.00 0.00 44.77 2.29
3320 3969 7.973388 GGAGCATAAAACTGCATTGTATTTGTA 59.027 33.333 0.00 0.00 44.77 2.41
3321 3970 6.813152 GGAGCATAAAACTGCATTGTATTTGT 59.187 34.615 0.00 0.00 44.77 2.83
3323 3972 6.155049 AGGGAGCATAAAACTGCATTGTATTT 59.845 34.615 0.00 0.00 44.77 1.40
3324 3973 5.658190 AGGGAGCATAAAACTGCATTGTATT 59.342 36.000 0.00 0.00 44.77 1.89
3328 3998 3.194116 ACAGGGAGCATAAAACTGCATTG 59.806 43.478 0.00 0.00 44.77 2.82
3353 4023 0.251922 AACCAAGACATGCCCATGCT 60.252 50.000 8.11 4.23 42.39 3.79
3359 4029 7.489574 TTTTCATTTTTAACCAAGACATGCC 57.510 32.000 0.00 0.00 0.00 4.40
3379 4049 5.859521 TTGCCAACATGCATACATTTTTC 57.140 34.783 0.00 0.00 41.70 2.29
3383 4053 6.877855 TGTAATTTTGCCAACATGCATACATT 59.122 30.769 0.00 0.00 41.70 2.71
3384 4054 6.404708 TGTAATTTTGCCAACATGCATACAT 58.595 32.000 0.00 0.00 41.70 2.29
3385 4055 5.787380 TGTAATTTTGCCAACATGCATACA 58.213 33.333 0.00 0.00 41.70 2.29
3396 4069 4.159506 GGGTTCTATGCTGTAATTTTGCCA 59.840 41.667 0.00 0.00 0.00 4.92
3406 4079 0.833287 ATGCTCGGGTTCTATGCTGT 59.167 50.000 0.00 0.00 0.00 4.40
3407 4080 2.820059 TATGCTCGGGTTCTATGCTG 57.180 50.000 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.