Multiple sequence alignment - TraesCS5D01G075500

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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 TraesCS5D01G075500 chr5D 100.000 1720 0 0 1 1720 74733854 74735573 0.000000e+00 3177.0
1 TraesCS5D01G075500 chr5D 100.000 1683 0 0 2155 3837 74736008 74737690 0.000000e+00 3109.0
2 TraesCS5D01G075500 chr5D 96.721 183 6 0 2155 2337 418290619 418290437 4.820000e-79 305.0
3 TraesCS5D01G075500 chr5D 76.852 540 110 14 1187 1720 560008608 560008078 1.350000e-74 291.0
4 TraesCS5D01G075500 chr5B 95.821 1364 50 3 357 1720 77671487 77670131 0.000000e+00 2196.0
5 TraesCS5D01G075500 chr5B 90.593 1265 98 16 2394 3644 77670106 77668849 0.000000e+00 1657.0
6 TraesCS5D01G075500 chr5B 89.014 355 36 3 1 355 77703385 77703034 1.640000e-118 436.0
7 TraesCS5D01G075500 chr5B 83.237 173 16 7 3676 3837 77668889 77668719 3.090000e-31 147.0
8 TraesCS5D01G075500 chr5A 91.190 1487 84 14 2392 3834 70000118 70001601 0.000000e+00 1977.0
9 TraesCS5D01G075500 chr5A 96.885 899 27 1 823 1720 69999195 70000093 0.000000e+00 1504.0
10 TraesCS5D01G075500 chr5A 90.962 520 28 6 1 518 69971486 69971988 0.000000e+00 682.0
11 TraesCS5D01G075500 chr5A 95.819 287 9 1 509 795 69998913 69999196 9.710000e-126 460.0
12 TraesCS5D01G075500 chr5A 93.684 95 6 0 2517 2611 14272888 14272794 4.000000e-30 143.0
13 TraesCS5D01G075500 chr5A 84.507 142 15 7 2396 2536 14288447 14288312 2.400000e-27 134.0
14 TraesCS5D01G075500 chr3B 80.445 629 117 4 1095 1720 786139087 786139712 3.470000e-130 475.0
15 TraesCS5D01G075500 chr3A 81.784 538 90 7 1187 1720 717901264 717901797 9.780000e-121 444.0
16 TraesCS5D01G075500 chr3A 94.022 184 10 1 2155 2337 536524131 536524314 1.050000e-70 278.0
17 TraesCS5D01G075500 chr4A 77.920 548 108 12 1178 1720 604209557 604209018 2.860000e-86 329.0
18 TraesCS5D01G075500 chr4D 94.009 217 9 4 2155 2367 5573776 5573992 3.700000e-85 326.0
19 TraesCS5D01G075500 chrUn 77.574 544 102 15 1184 1720 287474427 287474957 1.040000e-80 311.0
20 TraesCS5D01G075500 chrUn 77.634 541 101 15 1187 1720 296159289 296158762 1.040000e-80 311.0
21 TraesCS5D01G075500 chr6D 77.603 509 105 9 1215 1720 469069240 469069742 2.240000e-77 300.0
22 TraesCS5D01G075500 chr7D 91.031 223 16 2 2156 2374 390209373 390209151 8.060000e-77 298.0
23 TraesCS5D01G075500 chr7D 94.536 183 10 0 2155 2337 630438883 630439065 2.260000e-72 283.0
24 TraesCS5D01G075500 chr2A 92.019 213 15 2 2155 2365 490636061 490635849 8.060000e-77 298.0
25 TraesCS5D01G075500 chr2A 94.737 38 2 0 3567 3604 722067757 722067794 4.140000e-05 60.2
26 TraesCS5D01G075500 chr3D 88.142 253 24 4 2155 2403 47750912 47751162 2.900000e-76 296.0
27 TraesCS5D01G075500 chr3D 81.944 144 25 1 1155 1298 588015253 588015395 1.870000e-23 121.0
28 TraesCS5D01G075500 chr7A 94.022 184 10 1 2155 2337 15849069 15848886 1.050000e-70 278.0
29 TraesCS5D01G075500 chr2D 93.989 183 11 0 2155 2337 277049505 277049323 1.050000e-70 278.0
30 TraesCS5D01G075500 chr2D 95.000 40 2 0 3567 3606 598007939 598007900 3.200000e-06 63.9
31 TraesCS5D01G075500 chr2B 94.737 38 2 0 3513 3550 31586792 31586829 4.140000e-05 60.2
32 TraesCS5D01G075500 chr1B 96.774 31 1 0 3520 3550 364821032 364821062 7.000000e-03 52.8


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 TraesCS5D01G075500 chr5D 74733854 74737690 3836 False 3143.000000 3177 100.000000 1 3837 2 chr5D.!!$F1 3836
1 TraesCS5D01G075500 chr5D 560008078 560008608 530 True 291.000000 291 76.852000 1187 1720 1 chr5D.!!$R2 533
2 TraesCS5D01G075500 chr5B 77668719 77671487 2768 True 1333.333333 2196 89.883667 357 3837 3 chr5B.!!$R2 3480
3 TraesCS5D01G075500 chr5A 69998913 70001601 2688 False 1313.666667 1977 94.631333 509 3834 3 chr5A.!!$F2 3325
4 TraesCS5D01G075500 chr5A 69971486 69971988 502 False 682.000000 682 90.962000 1 518 1 chr5A.!!$F1 517
5 TraesCS5D01G075500 chr3B 786139087 786139712 625 False 475.000000 475 80.445000 1095 1720 1 chr3B.!!$F1 625
6 TraesCS5D01G075500 chr3A 717901264 717901797 533 False 444.000000 444 81.784000 1187 1720 1 chr3A.!!$F2 533
7 TraesCS5D01G075500 chr4A 604209018 604209557 539 True 329.000000 329 77.920000 1178 1720 1 chr4A.!!$R1 542
8 TraesCS5D01G075500 chrUn 287474427 287474957 530 False 311.000000 311 77.574000 1184 1720 1 chrUn.!!$F1 536
9 TraesCS5D01G075500 chrUn 296158762 296159289 527 True 311.000000 311 77.634000 1187 1720 1 chrUn.!!$R1 533
10 TraesCS5D01G075500 chr6D 469069240 469069742 502 False 300.000000 300 77.603000 1215 1720 1 chr6D.!!$F1 505

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
130 132 0.036010 CCATCTCTGGGTTGAAGCGT 60.036 55.000 0.00 0.0 39.04 5.07 F
199 201 0.235926 GTTGTCGGTTGCAGCTTCTC 59.764 55.000 0.00 0.0 0.00 2.87 F
355 358 0.388907 GGAGTTAGCCGCAACACGTA 60.389 55.000 0.00 0.0 41.42 3.57 F
363 366 0.876777 CCGCAACACGTAACACCTCA 60.877 55.000 0.00 0.0 41.42 3.86 F
364 367 1.144969 CGCAACACGTAACACCTCAT 58.855 50.000 0.00 0.0 36.87 2.90 F
714 721 1.170442 CCGGCCGTTCCTAAACATTT 58.830 50.000 26.12 0.0 34.93 2.32 F
1086 1096 1.270839 TGCTTCTACACTTGGTGCCTC 60.271 52.381 0.00 0.0 36.98 4.70 F
2629 2639 0.617413 CCTCAGAGCTGACCCATGTT 59.383 55.000 0.00 0.0 35.46 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1075 1085 0.036010 CCGATTGAGAGGCACCAAGT 60.036 55.000 0.0 0.0 0.00 3.16 R
1623 1633 0.387622 CAATGCCAAAGTCTGCCACG 60.388 55.000 0.0 0.0 0.00 4.94 R
2242 2252 3.947910 TCCGACATAAAAAGAGACCGT 57.052 42.857 0.0 0.0 0.00 4.83 R
2243 2253 5.796350 ATTTCCGACATAAAAAGAGACCG 57.204 39.130 0.0 0.0 0.00 4.79 R
2302 2312 6.672218 TCTTCACCTCCTCTATTTTACCATCA 59.328 38.462 0.0 0.0 0.00 3.07 R
2612 2622 1.059098 ACAACATGGGTCAGCTCTGA 58.941 50.000 0.0 0.0 37.24 3.27 R
2716 2726 0.036732 AAGGCGAGTCATTGGAGCAA 59.963 50.000 0.0 0.0 0.00 3.91 R
3802 3938 0.810031 GGCATCGTCGGCACTACAAT 60.810 55.000 0.0 0.0 0.00 2.71 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
43 45 5.065474 CACTAGGTTGAAACTTTTTCCGTCA 59.935 40.000 0.00 0.00 0.00 4.35
45 47 5.592104 AGGTTGAAACTTTTTCCGTCAAT 57.408 34.783 0.00 0.00 31.38 2.57
91 93 1.268999 TGCAGCTTTTAAGGTTGTGCG 60.269 47.619 0.00 0.00 33.87 5.34
130 132 0.036010 CCATCTCTGGGTTGAAGCGT 60.036 55.000 0.00 0.00 39.04 5.07
133 135 1.593196 TCTCTGGGTTGAAGCGTTTG 58.407 50.000 0.00 0.00 0.00 2.93
141 143 2.870411 GGTTGAAGCGTTTGTAGTCAGT 59.130 45.455 0.00 0.00 0.00 3.41
144 146 2.159014 TGAAGCGTTTGTAGTCAGTGGT 60.159 45.455 0.00 0.00 0.00 4.16
145 147 2.150397 AGCGTTTGTAGTCAGTGGTC 57.850 50.000 0.00 0.00 0.00 4.02
199 201 0.235926 GTTGTCGGTTGCAGCTTCTC 59.764 55.000 0.00 0.00 0.00 2.87
200 202 0.884704 TTGTCGGTTGCAGCTTCTCC 60.885 55.000 0.00 0.00 0.00 3.71
208 210 1.378250 GCAGCTTCTCCATGCACCT 60.378 57.895 0.00 0.00 39.75 4.00
317 319 3.695606 TCGCAGCCCTCGCTTTCT 61.696 61.111 0.00 0.00 45.55 2.52
321 323 1.642952 GCAGCCCTCGCTTTCTTCTG 61.643 60.000 0.00 0.00 45.55 3.02
352 355 3.165498 CGGAGTTAGCCGCAACAC 58.835 61.111 0.00 0.00 45.38 3.32
353 356 2.726691 CGGAGTTAGCCGCAACACG 61.727 63.158 0.00 1.65 45.38 4.49
354 357 1.666872 GGAGTTAGCCGCAACACGT 60.667 57.895 0.00 0.00 41.42 4.49
355 358 0.388907 GGAGTTAGCCGCAACACGTA 60.389 55.000 0.00 0.00 41.42 3.57
363 366 0.876777 CCGCAACACGTAACACCTCA 60.877 55.000 0.00 0.00 41.42 3.86
364 367 1.144969 CGCAACACGTAACACCTCAT 58.855 50.000 0.00 0.00 36.87 2.90
498 503 1.942657 GACGATAGCCACAATGTGCAT 59.057 47.619 8.05 0.76 42.67 3.96
650 655 2.700897 CCTGAGGACCGATGGATTAAGT 59.299 50.000 0.00 0.00 0.00 2.24
714 721 1.170442 CCGGCCGTTCCTAAACATTT 58.830 50.000 26.12 0.00 34.93 2.32
715 722 2.358015 CCGGCCGTTCCTAAACATTTA 58.642 47.619 26.12 0.00 34.93 1.40
716 723 2.096335 CCGGCCGTTCCTAAACATTTAC 59.904 50.000 26.12 0.00 34.93 2.01
756 763 2.279784 GCGAAGGGGCTCATCGAG 60.280 66.667 17.16 0.00 38.82 4.04
778 785 6.128982 CGAGAGAACGAAGCTACGTATGTATA 60.129 42.308 0.00 0.00 45.83 1.47
779 786 6.886307 AGAGAACGAAGCTACGTATGTATAC 58.114 40.000 0.00 0.00 45.83 1.47
793 802 5.401376 CGTATGTATACACACTGCCACATAC 59.599 44.000 12.25 10.99 42.39 2.39
967 976 2.095768 CCAACACTCCAGCAAATACGTG 60.096 50.000 0.00 0.00 0.00 4.49
968 977 2.543777 ACACTCCAGCAAATACGTGT 57.456 45.000 0.00 0.00 0.00 4.49
1075 1085 4.024048 GTGCTACTGCTTTTTGCTTCTACA 60.024 41.667 0.00 0.00 43.37 2.74
1086 1096 1.270839 TGCTTCTACACTTGGTGCCTC 60.271 52.381 0.00 0.00 36.98 4.70
1152 1162 3.780307 TCTGGAAGACCCGGTAAGT 57.220 52.632 0.00 0.00 38.67 2.24
1299 1309 4.379394 GCAATAAAGGTTCTTGACATGCGA 60.379 41.667 0.00 0.00 0.00 5.10
1327 1337 3.854809 GCACAGCGTTAAAAGTTTTGACA 59.145 39.130 19.61 0.00 0.00 3.58
1578 1588 2.035704 TGAAGTGGTTTTGCATTGCGAT 59.964 40.909 3.84 0.00 0.00 4.58
1623 1633 2.005451 GATGAGGACATGACTGCACAC 58.995 52.381 0.00 0.00 36.82 3.82
2261 2271 7.760131 TTATTACGGTCTCTTTTTATGTCGG 57.240 36.000 0.00 0.00 0.00 4.79
2262 2272 3.947910 ACGGTCTCTTTTTATGTCGGA 57.052 42.857 0.00 0.00 0.00 4.55
2263 2273 4.261578 ACGGTCTCTTTTTATGTCGGAA 57.738 40.909 0.00 0.00 0.00 4.30
2264 2274 4.634199 ACGGTCTCTTTTTATGTCGGAAA 58.366 39.130 0.00 0.00 0.00 3.13
2265 2275 5.243207 ACGGTCTCTTTTTATGTCGGAAAT 58.757 37.500 0.00 0.00 0.00 2.17
2266 2276 6.400568 ACGGTCTCTTTTTATGTCGGAAATA 58.599 36.000 0.00 0.00 0.00 1.40
2267 2277 6.875195 ACGGTCTCTTTTTATGTCGGAAATAA 59.125 34.615 0.00 0.00 0.00 1.40
2268 2278 7.064253 ACGGTCTCTTTTTATGTCGGAAATAAG 59.936 37.037 1.16 0.00 0.00 1.73
2269 2279 7.277098 CGGTCTCTTTTTATGTCGGAAATAAGA 59.723 37.037 1.16 0.00 0.00 2.10
2270 2280 8.388853 GGTCTCTTTTTATGTCGGAAATAAGAC 58.611 37.037 7.84 7.84 37.85 3.01
2280 2290 6.879962 TGTCGGAAATAAGACAAAACTTACG 58.120 36.000 0.00 0.00 43.47 3.18
2281 2291 6.700960 TGTCGGAAATAAGACAAAACTTACGA 59.299 34.615 0.00 0.00 43.47 3.43
2282 2292 7.224362 TGTCGGAAATAAGACAAAACTTACGAA 59.776 33.333 0.00 0.00 43.47 3.85
2283 2293 8.063630 GTCGGAAATAAGACAAAACTTACGAAA 58.936 33.333 0.00 0.00 35.60 3.46
2284 2294 8.063630 TCGGAAATAAGACAAAACTTACGAAAC 58.936 33.333 0.00 0.00 35.60 2.78
2285 2295 7.057566 CGGAAATAAGACAAAACTTACGAAACG 59.942 37.037 0.00 0.00 35.60 3.60
2286 2296 7.852454 GGAAATAAGACAAAACTTACGAAACGT 59.148 33.333 1.91 1.91 44.35 3.99
2287 2297 9.848172 GAAATAAGACAAAACTTACGAAACGTA 57.152 29.630 0.00 0.00 41.54 3.57
2322 2332 6.605119 CCATTGATGGTAAAATAGAGGAGGT 58.395 40.000 1.73 0.00 43.05 3.85
2323 2333 6.488006 CCATTGATGGTAAAATAGAGGAGGTG 59.512 42.308 1.73 0.00 43.05 4.00
2324 2334 6.884472 TTGATGGTAAAATAGAGGAGGTGA 57.116 37.500 0.00 0.00 0.00 4.02
2325 2335 6.884472 TGATGGTAAAATAGAGGAGGTGAA 57.116 37.500 0.00 0.00 0.00 3.18
2326 2336 6.889198 TGATGGTAAAATAGAGGAGGTGAAG 58.111 40.000 0.00 0.00 0.00 3.02
2327 2337 6.672218 TGATGGTAAAATAGAGGAGGTGAAGA 59.328 38.462 0.00 0.00 0.00 2.87
2328 2338 6.945636 TGGTAAAATAGAGGAGGTGAAGAA 57.054 37.500 0.00 0.00 0.00 2.52
2329 2339 7.510675 TGGTAAAATAGAGGAGGTGAAGAAT 57.489 36.000 0.00 0.00 0.00 2.40
2330 2340 8.618240 TGGTAAAATAGAGGAGGTGAAGAATA 57.382 34.615 0.00 0.00 0.00 1.75
2331 2341 9.053472 TGGTAAAATAGAGGAGGTGAAGAATAA 57.947 33.333 0.00 0.00 0.00 1.40
2332 2342 9.327628 GGTAAAATAGAGGAGGTGAAGAATAAC 57.672 37.037 0.00 0.00 0.00 1.89
2448 2458 4.977963 GTCATGTTGAAACCTGTGTTCATG 59.022 41.667 0.00 0.00 35.71 3.07
2454 2464 5.651387 TGAAACCTGTGTTCATGTTTTGA 57.349 34.783 0.00 0.00 40.53 2.69
2612 2622 2.719705 TGGGTTTACCAGTCATTTCCCT 59.280 45.455 0.69 0.00 46.80 4.20
2629 2639 0.617413 CCTCAGAGCTGACCCATGTT 59.383 55.000 0.00 0.00 35.46 2.71
2652 2662 2.593468 GATGCCCGGCTACTGCAAGA 62.593 60.000 11.61 0.00 41.91 3.02
2716 2726 3.005367 CGGTATTGGAAGTTGGTTTGCTT 59.995 43.478 0.00 0.00 0.00 3.91
2738 2748 0.674581 CTCCAATGACTCGCCTTGCA 60.675 55.000 0.00 0.00 0.00 4.08
2779 2789 5.163893 CGATGTGGTCGTTATGCTAAAAAGT 60.164 40.000 0.00 0.00 45.19 2.66
2806 2816 0.692476 TGAAGTACACTGCATGGGCT 59.308 50.000 0.00 0.00 41.91 5.19
2807 2817 1.089920 GAAGTACACTGCATGGGCTG 58.910 55.000 0.00 0.00 43.82 4.85
2824 2834 2.028658 GGCTGTTGAGACATCACAGAGA 60.029 50.000 2.72 0.00 37.04 3.10
2936 2948 9.733556 ACCAATTTGTGTATACTAGTCATCAAA 57.266 29.630 0.00 6.40 0.00 2.69
2969 2981 3.119495 GCACGGGCTAGTGATTTTGAAAT 60.119 43.478 0.00 0.00 44.43 2.17
2972 2984 5.925969 CACGGGCTAGTGATTTTGAAATTTT 59.074 36.000 7.67 0.00 44.43 1.82
2996 3010 5.756833 TGAAAGTAGAAAGGAAACCGAAGAC 59.243 40.000 0.00 0.00 0.00 3.01
3003 3017 3.314357 AAAGGAAACCGAAGACCTTTTCG 59.686 43.478 0.00 1.46 46.32 3.46
3005 3019 2.615447 GGAAACCGAAGACCTTTTCGTT 59.385 45.455 7.29 0.00 46.31 3.85
3276 3295 4.882671 ACATGGAATCGAGCATTGTTAC 57.117 40.909 0.00 0.00 0.00 2.50
3366 3386 9.739276 AAACTATGGTTCTGAATCAAGTAATCA 57.261 29.630 7.53 0.00 34.14 2.57
3367 3387 8.723942 ACTATGGTTCTGAATCAAGTAATCAC 57.276 34.615 7.53 0.00 0.00 3.06
3503 3538 6.161381 CACCTGGGATGAAAAAGAAATCAAG 58.839 40.000 0.00 0.00 0.00 3.02
3647 3683 9.927081 AATAATAAAGATGAGTGATGAGGGTTT 57.073 29.630 0.00 0.00 0.00 3.27
3648 3684 9.927081 ATAATAAAGATGAGTGATGAGGGTTTT 57.073 29.630 0.00 0.00 0.00 2.43
3649 3685 8.655935 AATAAAGATGAGTGATGAGGGTTTTT 57.344 30.769 0.00 0.00 0.00 1.94
3671 3707 5.990120 TTTTAGGCTCTTCTACGGTAACT 57.010 39.130 0.00 0.00 0.00 2.24
3672 3708 5.990120 TTTAGGCTCTTCTACGGTAACTT 57.010 39.130 0.00 0.00 0.00 2.66
3673 3709 5.990120 TTAGGCTCTTCTACGGTAACTTT 57.010 39.130 0.00 0.00 0.00 2.66
3674 3710 4.453177 AGGCTCTTCTACGGTAACTTTC 57.547 45.455 0.00 0.00 0.00 2.62
3675 3711 4.087907 AGGCTCTTCTACGGTAACTTTCT 58.912 43.478 0.00 0.00 0.00 2.52
3676 3712 5.259632 AGGCTCTTCTACGGTAACTTTCTA 58.740 41.667 0.00 0.00 0.00 2.10
3677 3713 5.892686 AGGCTCTTCTACGGTAACTTTCTAT 59.107 40.000 0.00 0.00 0.00 1.98
3678 3714 6.380560 AGGCTCTTCTACGGTAACTTTCTATT 59.619 38.462 0.00 0.00 0.00 1.73
3679 3715 7.559170 AGGCTCTTCTACGGTAACTTTCTATTA 59.441 37.037 0.00 0.00 0.00 0.98
3680 3716 8.193438 GGCTCTTCTACGGTAACTTTCTATTAA 58.807 37.037 0.00 0.00 0.00 1.40
3681 3717 9.578439 GCTCTTCTACGGTAACTTTCTATTAAA 57.422 33.333 0.00 0.00 0.00 1.52
3762 3897 4.982295 TGAAGTAACAACAGAGACATCACG 59.018 41.667 0.00 0.00 0.00 4.35
3802 3938 0.389025 TCACTCTTGCAGCTTCGTCA 59.611 50.000 0.00 0.00 0.00 4.35
3818 3954 1.922570 GTCATTGTAGTGCCGACGAT 58.077 50.000 0.00 0.00 0.00 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 14 4.602340 AGTTTCAACCTAGTGACATCGT 57.398 40.909 0.00 0.00 0.00 3.73
28 30 5.106442 ACAACCATTGACGGAAAAAGTTTC 58.894 37.500 0.00 0.00 0.00 2.78
29 31 5.079689 ACAACCATTGACGGAAAAAGTTT 57.920 34.783 0.00 0.00 0.00 2.66
43 45 4.828829 CGGTAGAGAAAGGTACAACCATT 58.171 43.478 0.00 0.00 41.95 3.16
45 47 2.028748 GCGGTAGAGAAAGGTACAACCA 60.029 50.000 0.00 0.00 41.95 3.67
106 108 0.329261 TCAACCCAGAGATGGCCAAG 59.671 55.000 10.96 0.00 0.00 3.61
130 132 2.889045 AGCTACGACCACTGACTACAAA 59.111 45.455 0.00 0.00 0.00 2.83
133 135 3.190953 AGAAAGCTACGACCACTGACTAC 59.809 47.826 0.00 0.00 0.00 2.73
141 143 0.321298 GGCCAAGAAAGCTACGACCA 60.321 55.000 0.00 0.00 0.00 4.02
144 146 0.685097 AGTGGCCAAGAAAGCTACGA 59.315 50.000 7.24 0.00 45.44 3.43
145 147 0.798776 CAGTGGCCAAGAAAGCTACG 59.201 55.000 7.24 0.00 45.44 3.51
225 227 3.535280 TTTTTGCTGGAACCAAAGACC 57.465 42.857 0.00 0.00 34.10 3.85
251 253 2.025156 CCAATTGCTGCGATCGCC 59.975 61.111 35.12 21.99 41.09 5.54
336 339 0.388907 TACGTGTTGCGGCTAACTCC 60.389 55.000 0.00 0.00 46.52 3.85
498 503 3.146066 GAGACAAAACCACAGCCATGTA 58.854 45.455 0.00 0.00 37.65 2.29
650 655 2.202690 CGCGTCCTACGAATGGCA 60.203 61.111 0.00 0.00 46.05 4.92
672 679 2.717485 CAGCAATTGGGCCGATCG 59.283 61.111 8.51 8.51 0.00 3.69
673 680 3.122850 CCAGCAATTGGGCCGATC 58.877 61.111 6.76 0.00 43.75 3.69
714 721 7.335924 GCAGATGGTCTTTGTAAATTGGTAGTA 59.664 37.037 0.00 0.00 0.00 1.82
715 722 6.151144 GCAGATGGTCTTTGTAAATTGGTAGT 59.849 38.462 0.00 0.00 0.00 2.73
716 723 6.555315 GCAGATGGTCTTTGTAAATTGGTAG 58.445 40.000 0.00 0.00 0.00 3.18
756 763 6.572989 GTGTATACATACGTAGCTTCGTTCTC 59.427 42.308 23.51 8.35 43.80 2.87
778 785 3.550820 TGAAAAGTATGTGGCAGTGTGT 58.449 40.909 0.00 0.00 0.00 3.72
779 786 3.610114 GCTGAAAAGTATGTGGCAGTGTG 60.610 47.826 0.00 0.00 0.00 3.82
793 802 1.401931 CGGTCAATGCTGGCTGAAAAG 60.402 52.381 0.00 0.00 35.36 2.27
967 976 8.534333 TCACTTTGTTTGATCTATGTGTCTAC 57.466 34.615 0.00 0.00 0.00 2.59
968 977 9.554395 TTTCACTTTGTTTGATCTATGTGTCTA 57.446 29.630 0.00 0.00 0.00 2.59
1075 1085 0.036010 CCGATTGAGAGGCACCAAGT 60.036 55.000 0.00 0.00 0.00 3.16
1086 1096 6.545504 TTCTCAAGTTTCTTTCCGATTGAG 57.454 37.500 6.44 6.44 43.07 3.02
1152 1162 6.699575 TCGACATGAGAGATTAACTGATGA 57.300 37.500 0.00 0.00 34.21 2.92
1223 1233 1.886422 AACTTTTCCAAAGCCCCCAA 58.114 45.000 0.00 0.00 0.00 4.12
1299 1309 2.884639 ACTTTTAACGCTGTGCTTGGAT 59.115 40.909 0.00 0.00 0.00 3.41
1327 1337 2.908817 GGAACACACGACATTCCGT 58.091 52.632 0.00 0.00 44.43 4.69
1578 1588 6.588719 AACAATACATTGCTAGGCTTCAAA 57.411 33.333 0.00 0.00 41.38 2.69
1623 1633 0.387622 CAATGCCAAAGTCTGCCACG 60.388 55.000 0.00 0.00 0.00 4.94
2235 2245 9.467258 CCGACATAAAAAGAGACCGTAATAATA 57.533 33.333 0.00 0.00 0.00 0.98
2236 2246 8.199449 TCCGACATAAAAAGAGACCGTAATAAT 58.801 33.333 0.00 0.00 0.00 1.28
2237 2247 7.546358 TCCGACATAAAAAGAGACCGTAATAA 58.454 34.615 0.00 0.00 0.00 1.40
2238 2248 7.099266 TCCGACATAAAAAGAGACCGTAATA 57.901 36.000 0.00 0.00 0.00 0.98
2239 2249 5.969423 TCCGACATAAAAAGAGACCGTAAT 58.031 37.500 0.00 0.00 0.00 1.89
2240 2250 5.389859 TCCGACATAAAAAGAGACCGTAA 57.610 39.130 0.00 0.00 0.00 3.18
2241 2251 5.389859 TTCCGACATAAAAAGAGACCGTA 57.610 39.130 0.00 0.00 0.00 4.02
2242 2252 3.947910 TCCGACATAAAAAGAGACCGT 57.052 42.857 0.00 0.00 0.00 4.83
2243 2253 5.796350 ATTTCCGACATAAAAAGAGACCG 57.204 39.130 0.00 0.00 0.00 4.79
2244 2254 8.388853 GTCTTATTTCCGACATAAAAAGAGACC 58.611 37.037 0.00 0.00 31.30 3.85
2245 2255 8.932791 TGTCTTATTTCCGACATAAAAAGAGAC 58.067 33.333 0.00 0.00 35.40 3.36
2246 2256 9.496873 TTGTCTTATTTCCGACATAAAAAGAGA 57.503 29.630 0.00 0.00 39.63 3.10
2254 2264 8.649841 CGTAAGTTTTGTCTTATTTCCGACATA 58.350 33.333 0.00 0.00 39.63 2.29
2255 2265 7.385752 TCGTAAGTTTTGTCTTATTTCCGACAT 59.614 33.333 0.00 0.00 38.11 3.06
2256 2266 6.700960 TCGTAAGTTTTGTCTTATTTCCGACA 59.299 34.615 0.00 0.00 37.19 4.35
2257 2267 7.109006 TCGTAAGTTTTGTCTTATTTCCGAC 57.891 36.000 0.00 0.00 39.48 4.79
2258 2268 7.712264 TTCGTAAGTTTTGTCTTATTTCCGA 57.288 32.000 0.00 0.00 39.48 4.55
2259 2269 7.057566 CGTTTCGTAAGTTTTGTCTTATTTCCG 59.942 37.037 0.00 0.00 39.48 4.30
2260 2270 7.852454 ACGTTTCGTAAGTTTTGTCTTATTTCC 59.148 33.333 0.00 0.00 38.73 3.13
2261 2271 8.757817 ACGTTTCGTAAGTTTTGTCTTATTTC 57.242 30.769 0.00 0.00 38.73 2.17
2299 2309 7.282585 TCACCTCCTCTATTTTACCATCAATG 58.717 38.462 0.00 0.00 0.00 2.82
2300 2310 7.451731 TCACCTCCTCTATTTTACCATCAAT 57.548 36.000 0.00 0.00 0.00 2.57
2301 2311 6.884472 TCACCTCCTCTATTTTACCATCAA 57.116 37.500 0.00 0.00 0.00 2.57
2302 2312 6.672218 TCTTCACCTCCTCTATTTTACCATCA 59.328 38.462 0.00 0.00 0.00 3.07
2303 2313 7.125792 TCTTCACCTCCTCTATTTTACCATC 57.874 40.000 0.00 0.00 0.00 3.51
2304 2314 7.510675 TTCTTCACCTCCTCTATTTTACCAT 57.489 36.000 0.00 0.00 0.00 3.55
2305 2315 6.945636 TTCTTCACCTCCTCTATTTTACCA 57.054 37.500 0.00 0.00 0.00 3.25
2306 2316 9.327628 GTTATTCTTCACCTCCTCTATTTTACC 57.672 37.037 0.00 0.00 0.00 2.85
2437 2447 5.350633 ACACAATCAAAACATGAACACAGG 58.649 37.500 0.00 0.00 42.54 4.00
2448 2458 8.492673 TGATCCATACTCTACACAATCAAAAC 57.507 34.615 0.00 0.00 0.00 2.43
2454 2464 8.670521 TCCATATGATCCATACTCTACACAAT 57.329 34.615 3.65 0.00 0.00 2.71
2612 2622 1.059098 ACAACATGGGTCAGCTCTGA 58.941 50.000 0.00 0.00 37.24 3.27
2629 2639 1.078497 CAGTAGCCGGGCATCAACA 60.078 57.895 23.09 0.00 0.00 3.33
2652 2662 3.567478 AGTTGCAACTTGAAGAGGAGT 57.433 42.857 26.36 0.00 35.21 3.85
2716 2726 0.036732 AAGGCGAGTCATTGGAGCAA 59.963 50.000 0.00 0.00 0.00 3.91
2738 2748 6.169094 CCACATCGCTCATCTTTATCCTATT 58.831 40.000 0.00 0.00 0.00 1.73
2779 2789 6.095300 CCCATGCAGTGTACTTCATTTGAATA 59.905 38.462 0.00 0.00 33.01 1.75
2806 2816 2.629617 TGCTCTCTGTGATGTCTCAACA 59.370 45.455 0.00 0.00 40.38 3.33
2807 2817 3.309961 TGCTCTCTGTGATGTCTCAAC 57.690 47.619 0.00 0.00 31.85 3.18
2808 2818 3.070015 TGTTGCTCTCTGTGATGTCTCAA 59.930 43.478 0.00 0.00 31.85 3.02
2809 2819 2.629617 TGTTGCTCTCTGTGATGTCTCA 59.370 45.455 0.00 0.00 0.00 3.27
2824 2834 3.693085 GAGTGATCAATCATGGTGTTGCT 59.307 43.478 17.87 0.00 39.30 3.91
2969 2981 7.337436 TCTTCGGTTTCCTTTCTACTTTCAAAA 59.663 33.333 0.00 0.00 0.00 2.44
2972 2984 5.756833 GTCTTCGGTTTCCTTTCTACTTTCA 59.243 40.000 0.00 0.00 0.00 2.69
2979 2991 3.859061 AAGGTCTTCGGTTTCCTTTCT 57.141 42.857 0.00 0.00 37.01 2.52
2980 2992 4.554134 CGAAAAGGTCTTCGGTTTCCTTTC 60.554 45.833 12.95 8.18 45.69 2.62
2981 2993 6.608183 AACGAAAAGGTCTTCGGTTTCCTTT 61.608 40.000 10.16 0.00 46.24 3.11
3648 3684 6.350629 AGTTACCGTAGAAGAGCCTAAAAA 57.649 37.500 0.00 0.00 0.00 1.94
3649 3685 5.990120 AGTTACCGTAGAAGAGCCTAAAA 57.010 39.130 0.00 0.00 0.00 1.52
3650 3686 5.990120 AAGTTACCGTAGAAGAGCCTAAA 57.010 39.130 0.00 0.00 0.00 1.85
3651 3687 5.713861 AGAAAGTTACCGTAGAAGAGCCTAA 59.286 40.000 0.00 0.00 0.00 2.69
3652 3688 5.259632 AGAAAGTTACCGTAGAAGAGCCTA 58.740 41.667 0.00 0.00 0.00 3.93
3653 3689 4.087907 AGAAAGTTACCGTAGAAGAGCCT 58.912 43.478 0.00 0.00 0.00 4.58
3654 3690 4.453177 AGAAAGTTACCGTAGAAGAGCC 57.547 45.455 0.00 0.00 0.00 4.70
3655 3691 9.578439 TTTAATAGAAAGTTACCGTAGAAGAGC 57.422 33.333 0.00 0.00 0.00 4.09
3692 3728 9.988815 ACCTCATCACTCATCTTTGTATATAAC 57.011 33.333 0.00 0.00 0.00 1.89
3694 3730 9.987272 CAACCTCATCACTCATCTTTGTATATA 57.013 33.333 0.00 0.00 0.00 0.86
3695 3731 8.489489 ACAACCTCATCACTCATCTTTGTATAT 58.511 33.333 0.00 0.00 0.00 0.86
3696 3732 7.851228 ACAACCTCATCACTCATCTTTGTATA 58.149 34.615 0.00 0.00 0.00 1.47
3697 3733 6.715280 ACAACCTCATCACTCATCTTTGTAT 58.285 36.000 0.00 0.00 0.00 2.29
3698 3734 6.114187 ACAACCTCATCACTCATCTTTGTA 57.886 37.500 0.00 0.00 0.00 2.41
3699 3735 4.978099 ACAACCTCATCACTCATCTTTGT 58.022 39.130 0.00 0.00 0.00 2.83
3700 3736 5.954296 AACAACCTCATCACTCATCTTTG 57.046 39.130 0.00 0.00 0.00 2.77
3701 3737 6.094603 GCATAACAACCTCATCACTCATCTTT 59.905 38.462 0.00 0.00 0.00 2.52
3702 3738 5.587844 GCATAACAACCTCATCACTCATCTT 59.412 40.000 0.00 0.00 0.00 2.40
3703 3739 5.104610 AGCATAACAACCTCATCACTCATCT 60.105 40.000 0.00 0.00 0.00 2.90
3704 3740 5.121811 AGCATAACAACCTCATCACTCATC 58.878 41.667 0.00 0.00 0.00 2.92
3705 3741 5.108187 AGCATAACAACCTCATCACTCAT 57.892 39.130 0.00 0.00 0.00 2.90
3706 3742 4.558226 AGCATAACAACCTCATCACTCA 57.442 40.909 0.00 0.00 0.00 3.41
3707 3743 6.985188 TTTAGCATAACAACCTCATCACTC 57.015 37.500 0.00 0.00 0.00 3.51
3762 3897 2.161855 TCATTCATGGTGTTGCACTCC 58.838 47.619 0.00 0.00 34.40 3.85
3779 3914 2.277969 CGAAGCTGCAAGAGTGATCAT 58.722 47.619 0.00 0.00 34.07 2.45
3802 3938 0.810031 GGCATCGTCGGCACTACAAT 60.810 55.000 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.