Multiple sequence alignment - TraesCS7B01G460000

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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 TraesCS7B01G460000 chr7B 100.000 3326 0 0 1 3326 717751688 717748363 0.000000e+00 6143
1 TraesCS7B01G460000 chr7B 89.467 2383 135 28 1027 3318 719720382 719722739 0.000000e+00 2904
2 TraesCS7B01G460000 chr7B 77.108 747 123 26 1893 2605 719083055 719082323 4.020000e-104 388
3 TraesCS7B01G460000 chr7A 91.299 2333 131 21 1063 3326 717744315 717746644 0.000000e+00 3118
4 TraesCS7B01G460000 chr7A 77.984 754 124 28 1884 2605 716246941 716247684 5.100000e-118 435
5 TraesCS7B01G460000 chr7A 83.005 406 32 12 268 645 717743556 717743952 1.910000e-87 333
6 TraesCS7B01G460000 chr7A 84.307 274 43 0 1830 2103 716403687 716403960 5.470000e-68 268
7 TraesCS7B01G460000 chr7D 89.839 1614 83 20 1773 3318 622002808 622004408 0.000000e+00 1997
8 TraesCS7B01G460000 chr7D 83.064 1051 85 37 1 996 622000945 622001957 0.000000e+00 869
9 TraesCS7B01G460000 chr7D 85.480 854 97 16 982 1823 622001982 622002820 0.000000e+00 865
10 TraesCS7B01G460000 chr7D 78.062 743 123 27 1893 2605 620985567 620984835 1.830000e-117 433
11 TraesCS7B01G460000 chr6A 87.218 266 31 3 1283 1547 34707134 34707397 1.940000e-77 300
12 TraesCS7B01G460000 chrUn 86.617 269 33 3 1280 1547 378460233 378459967 9.020000e-76 294
13 TraesCS7B01G460000 chr4B 86.617 269 33 3 1280 1547 624391323 624391589 9.020000e-76 294
14 TraesCS7B01G460000 chr2A 86.617 269 33 3 1280 1547 775613145 775612879 9.020000e-76 294
15 TraesCS7B01G460000 chr2A 71.003 738 170 33 1893 2599 11910327 11909603 1.610000e-28 137
16 TraesCS7B01G460000 chr6D 86.517 267 33 3 1282 1547 460581385 460581121 1.170000e-74 291
17 TraesCS7B01G460000 chr6B 86.245 269 34 3 1280 1547 103159573 103159307 4.200000e-74 289
18 TraesCS7B01G460000 chr2D 73.558 416 83 20 1893 2290 11046073 11046479 2.080000e-27 134
19 TraesCS7B01G460000 chr2B 72.414 464 93 26 1893 2334 17365526 17365076 7.540000e-22 115


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 TraesCS7B01G460000 chr7B 717748363 717751688 3325 True 6143.000000 6143 100.000000 1 3326 1 chr7B.!!$R1 3325
1 TraesCS7B01G460000 chr7B 719720382 719722739 2357 False 2904.000000 2904 89.467000 1027 3318 1 chr7B.!!$F1 2291
2 TraesCS7B01G460000 chr7B 719082323 719083055 732 True 388.000000 388 77.108000 1893 2605 1 chr7B.!!$R2 712
3 TraesCS7B01G460000 chr7A 717743556 717746644 3088 False 1725.500000 3118 87.152000 268 3326 2 chr7A.!!$F3 3058
4 TraesCS7B01G460000 chr7A 716246941 716247684 743 False 435.000000 435 77.984000 1884 2605 1 chr7A.!!$F1 721
5 TraesCS7B01G460000 chr7D 622000945 622004408 3463 False 1243.666667 1997 86.127667 1 3318 3 chr7D.!!$F1 3317
6 TraesCS7B01G460000 chr7D 620984835 620985567 732 True 433.000000 433 78.062000 1893 2605 1 chr7D.!!$R1 712

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
260 276 0.038310 TCTCGCTCTTGGACCTCTCA 59.962 55.0 0.00 0.00 0.00 3.27 F
399 441 0.106708 TCAGTCCACAGCTTGTGTCC 59.893 55.0 13.06 5.45 46.45 4.02 F
400 442 0.107456 CAGTCCACAGCTTGTGTCCT 59.893 55.0 13.06 7.11 46.45 3.85 F
1119 1229 0.244721 GTTCTGTGCAATGGCCCTTC 59.755 55.0 0.00 0.00 40.13 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1604 1742 0.961019 TTCCATTGAACTGCACCAGC 59.039 50.000 0.00 0.00 42.57 4.85 R
1856 2037 1.001860 GCAGGTTCAGCTGAAGAGACT 59.998 52.381 29.13 20.22 34.27 3.24 R
2168 2410 1.357420 TGTACCCACTGGATGCCATTT 59.643 47.619 0.00 0.00 30.82 2.32 R
2485 2729 1.661463 ACTTGATGGAGGCCTTCTGA 58.339 50.000 13.68 0.00 0.00 3.27 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 6.962686 TGTTGAAAGAAATGTCATGAGTCAG 58.037 36.000 0.00 0.00 0.00 3.51
77 78 4.493049 GCGTTTGCCCGGGGGATA 62.493 66.667 25.28 4.01 37.50 2.59
78 79 2.513895 CGTTTGCCCGGGGGATAT 59.486 61.111 25.28 0.00 37.50 1.63
79 80 1.599797 CGTTTGCCCGGGGGATATC 60.600 63.158 25.28 4.28 37.50 1.63
80 81 1.599797 GTTTGCCCGGGGGATATCG 60.600 63.158 25.28 0.00 37.50 2.92
81 82 1.766864 TTTGCCCGGGGGATATCGA 60.767 57.895 25.28 0.00 37.50 3.59
82 83 2.047213 TTTGCCCGGGGGATATCGAC 62.047 60.000 25.28 1.66 37.50 4.20
83 84 2.920912 GCCCGGGGGATATCGACA 60.921 66.667 25.28 0.00 37.50 4.35
102 103 2.652179 CGACATCGACGCGCATCT 60.652 61.111 5.73 0.00 43.02 2.90
110 111 1.078759 CGACGCGCATCTCTTTTCCT 61.079 55.000 5.73 0.00 0.00 3.36
115 116 2.729156 CGCGCATCTCTTTTCCTTTTCC 60.729 50.000 8.75 0.00 0.00 3.13
122 123 5.835113 TCTCTTTTCCTTTTCCACAGTTG 57.165 39.130 0.00 0.00 0.00 3.16
151 167 2.977178 CCGTTGCTCCTCTGCTCT 59.023 61.111 0.00 0.00 0.00 4.09
152 168 1.447489 CCGTTGCTCCTCTGCTCTG 60.447 63.158 0.00 0.00 0.00 3.35
153 169 2.099431 CGTTGCTCCTCTGCTCTGC 61.099 63.158 0.00 0.00 0.00 4.26
154 170 1.004080 GTTGCTCCTCTGCTCTGCA 60.004 57.895 0.00 0.00 36.92 4.41
156 172 0.107800 TTGCTCCTCTGCTCTGCATC 60.108 55.000 0.00 0.00 38.13 3.91
157 173 1.592131 GCTCCTCTGCTCTGCATCG 60.592 63.158 0.00 0.00 38.13 3.84
174 190 4.339530 TGCATCGATATATACTCTGCTCCC 59.660 45.833 0.00 0.00 0.00 4.30
176 192 4.586306 TCGATATATACTCTGCTCCCCA 57.414 45.455 0.00 0.00 0.00 4.96
188 204 3.618780 CTCCCCACACCTGCAGCTC 62.619 68.421 8.66 0.00 0.00 4.09
194 210 0.807667 CACACCTGCAGCTCGTATCC 60.808 60.000 8.66 0.00 0.00 2.59
206 222 2.184830 CGTATCCACTCCGCCTCGA 61.185 63.158 0.00 0.00 0.00 4.04
217 233 1.079819 CGCCTCGAAAGCAAGGAGA 60.080 57.895 7.76 0.00 34.70 3.71
232 248 1.080434 GAGACCGCCACTCACTCAC 60.080 63.158 0.00 0.00 34.87 3.51
233 249 1.528292 GAGACCGCCACTCACTCACT 61.528 60.000 0.00 0.00 34.87 3.41
235 251 1.806461 GACCGCCACTCACTCACTCA 61.806 60.000 0.00 0.00 0.00 3.41
236 252 1.373497 CCGCCACTCACTCACTCAC 60.373 63.158 0.00 0.00 0.00 3.51
237 253 1.373497 CGCCACTCACTCACTCACC 60.373 63.158 0.00 0.00 0.00 4.02
238 254 1.810606 CGCCACTCACTCACTCACCT 61.811 60.000 0.00 0.00 0.00 4.00
258 274 1.309499 CGTCTCGCTCTTGGACCTCT 61.309 60.000 0.00 0.00 0.00 3.69
260 276 0.038310 TCTCGCTCTTGGACCTCTCA 59.962 55.000 0.00 0.00 0.00 3.27
261 277 0.455410 CTCGCTCTTGGACCTCTCAG 59.545 60.000 0.00 0.00 0.00 3.35
262 278 1.153667 CGCTCTTGGACCTCTCAGC 60.154 63.158 0.00 0.00 0.00 4.26
263 279 1.881903 CGCTCTTGGACCTCTCAGCA 61.882 60.000 0.00 0.00 0.00 4.41
264 280 0.108233 GCTCTTGGACCTCTCAGCAG 60.108 60.000 0.00 0.00 0.00 4.24
265 281 0.108233 CTCTTGGACCTCTCAGCAGC 60.108 60.000 0.00 0.00 0.00 5.25
266 282 1.447489 CTTGGACCTCTCAGCAGCG 60.447 63.158 0.00 0.00 0.00 5.18
267 283 2.164865 CTTGGACCTCTCAGCAGCGT 62.165 60.000 0.00 0.00 0.00 5.07
273 289 1.226267 CTCTCAGCAGCGTCGTCTC 60.226 63.158 0.00 0.00 0.00 3.36
316 332 0.401356 TCTCAAGTGCTCCATGGCAA 59.599 50.000 6.96 0.00 44.18 4.52
342 358 0.462581 TCCAAGCTCCGCATCATGTC 60.463 55.000 0.00 0.00 0.00 3.06
365 407 3.303791 GCTCTGTCGTGGTTTGGTAAAAG 60.304 47.826 0.00 0.00 0.00 2.27
367 409 1.677052 TGTCGTGGTTTGGTAAAAGGC 59.323 47.619 0.00 0.00 0.00 4.35
392 434 2.341543 CAGCGTCAGTCCACAGCT 59.658 61.111 0.00 0.00 38.90 4.24
395 437 1.595382 GCGTCAGTCCACAGCTTGT 60.595 57.895 0.00 0.00 0.00 3.16
399 441 0.106708 TCAGTCCACAGCTTGTGTCC 59.893 55.000 13.06 5.45 46.45 4.02
400 442 0.107456 CAGTCCACAGCTTGTGTCCT 59.893 55.000 13.06 7.11 46.45 3.85
417 459 2.756207 GTCCTCTCAGTCCCTAGTTCAC 59.244 54.545 0.00 0.00 0.00 3.18
418 460 2.650322 TCCTCTCAGTCCCTAGTTCACT 59.350 50.000 0.00 0.00 0.00 3.41
419 461 3.850774 TCCTCTCAGTCCCTAGTTCACTA 59.149 47.826 0.00 0.00 0.00 2.74
420 462 4.080243 TCCTCTCAGTCCCTAGTTCACTAG 60.080 50.000 6.98 6.98 44.22 2.57
485 527 3.281787 AGAGGAACGGGAGGGGGA 61.282 66.667 0.00 0.00 0.00 4.81
582 632 4.778143 GGCCGTCGTCCCATTGCT 62.778 66.667 0.00 0.00 0.00 3.91
583 633 3.499737 GCCGTCGTCCCATTGCTG 61.500 66.667 0.00 0.00 0.00 4.41
615 670 1.146774 CTCCCCCAGATCTAGAGCTGA 59.853 57.143 34.02 16.52 46.99 4.26
629 684 2.467826 GCTGATGGTCTTCGCTGCC 61.468 63.158 0.00 0.00 0.00 4.85
631 686 2.125512 GATGGTCTTCGCTGCCGT 60.126 61.111 0.00 0.00 35.54 5.68
634 689 1.320344 ATGGTCTTCGCTGCCGTCTA 61.320 55.000 0.00 0.00 35.54 2.59
647 702 2.760385 GTCTAGCCTCCAGCCGGT 60.760 66.667 1.90 0.00 45.47 5.28
684 740 4.154347 GGAGCTGGCCAGTCCGAG 62.154 72.222 32.81 8.97 37.80 4.63
699 755 2.756207 GTCCGAGGCTCTCCTATAATCC 59.244 54.545 13.50 0.00 44.46 3.01
725 781 2.032528 TGCTCTGCAGTTTCCCCG 59.967 61.111 14.67 0.00 33.32 5.73
747 803 1.599047 CAGTTCGTGCCATCCCTCT 59.401 57.895 0.00 0.00 0.00 3.69
748 804 0.824109 CAGTTCGTGCCATCCCTCTA 59.176 55.000 0.00 0.00 0.00 2.43
749 805 1.115467 AGTTCGTGCCATCCCTCTAG 58.885 55.000 0.00 0.00 0.00 2.43
753 809 1.112315 CGTGCCATCCCTCTAGCTCT 61.112 60.000 0.00 0.00 0.00 4.09
773 829 2.043852 ATCTGACCGCTCGAGGGT 60.044 61.111 25.69 23.33 41.48 4.34
816 872 3.120025 GCCTTTTACTCTGCTTCTTCTGC 60.120 47.826 0.00 0.00 0.00 4.26
833 896 0.391228 TGCTGCTCTTCACGGTGTAA 59.609 50.000 8.17 0.89 0.00 2.41
872 935 2.264480 CGAAGATGGCCGTCCACA 59.736 61.111 21.73 0.00 46.92 4.17
935 1007 2.259439 GCACTGCTTCTGCTGCTGT 61.259 57.895 0.00 0.00 41.94 4.40
996 1106 1.571919 GCACCATACCGTCTAGCTTG 58.428 55.000 0.00 0.00 0.00 4.01
1001 1111 3.451178 ACCATACCGTCTAGCTTGTGAAT 59.549 43.478 0.00 0.00 0.00 2.57
1006 1116 1.662629 CGTCTAGCTTGTGAATGCCTG 59.337 52.381 0.00 0.00 0.00 4.85
1013 1123 0.770499 TTGTGAATGCCTGGAGGTGA 59.230 50.000 0.00 0.00 37.57 4.02
1034 1144 1.825090 TTATGTGCTGAGCCCTTGTG 58.175 50.000 0.23 0.00 0.00 3.33
1068 1178 1.520342 CAGCGTTAGAGGCAGGCTC 60.520 63.158 16.35 16.35 33.09 4.70
1081 1191 2.470196 CAGGCTCTGCAATCAATTCG 57.530 50.000 0.00 0.00 0.00 3.34
1119 1229 0.244721 GTTCTGTGCAATGGCCCTTC 59.755 55.000 0.00 0.00 40.13 3.46
1167 1296 0.590195 GAACACTTGTGGCAGCTCAG 59.410 55.000 5.72 0.00 0.00 3.35
1173 1302 1.102809 TTGTGGCAGCTCAGTTGTGG 61.103 55.000 0.00 0.00 0.00 4.17
1180 1309 2.775890 CAGCTCAGTTGTGGACTCATT 58.224 47.619 0.00 0.00 36.10 2.57
1212 1346 0.542467 ATGAACAGCAATGGCCACCA 60.542 50.000 8.16 0.00 42.56 4.17
1236 1370 6.708054 CAGAAGTAATAGCCAAGACATTAGGG 59.292 42.308 0.00 0.00 0.00 3.53
1265 1399 3.890674 CTACCGAAGCAACTGCCC 58.109 61.111 0.00 0.00 43.38 5.36
1266 1400 1.003839 CTACCGAAGCAACTGCCCA 60.004 57.895 0.00 0.00 43.38 5.36
1384 1518 7.518188 TCCCATTAACATCTTCTATCCTTTCC 58.482 38.462 0.00 0.00 0.00 3.13
1391 1525 4.222124 TCTTCTATCCTTTCCACCAAGC 57.778 45.455 0.00 0.00 0.00 4.01
1413 1547 8.881743 CAAGCTTGATAAGAGATGCTAATATCC 58.118 37.037 22.31 0.00 0.00 2.59
1419 1557 9.547279 TGATAAGAGATGCTAATATCCCTGTAA 57.453 33.333 0.00 0.00 0.00 2.41
1580 1718 2.762535 ACATAGTCGAGTTGGTTGGG 57.237 50.000 0.00 0.00 0.00 4.12
1604 1742 2.551459 CTGCTGGGAAACACAGAAGAAG 59.449 50.000 3.08 0.00 43.10 2.85
1617 1755 1.141657 AGAAGAAGCTGGTGCAGTTCA 59.858 47.619 0.00 0.00 42.74 3.18
1636 1774 7.056635 CAGTTCAATGGAAGGTATATTCAGGT 58.943 38.462 0.00 0.00 32.62 4.00
1856 2037 1.408702 GGAACAAAAACAGCTGAGGCA 59.591 47.619 23.35 0.00 41.70 4.75
2120 2301 8.752005 AAGCTCATTACAAGCCTTGATAATAA 57.248 30.769 12.25 0.00 40.75 1.40
2247 2489 6.534634 GGCCCAGTCAGACATATATAGTTTT 58.465 40.000 2.66 0.00 0.00 2.43
2413 2657 8.978874 AGTTTGCATACTATAACCAATGATCA 57.021 30.769 8.15 0.00 0.00 2.92
2416 2660 7.926674 TGCATACTATAACCAATGATCATGG 57.073 36.000 9.46 14.63 43.84 3.66
2484 2728 4.515191 GCGTCCAAATATGCATCCTTAGAA 59.485 41.667 0.19 0.00 0.00 2.10
2485 2729 5.182001 GCGTCCAAATATGCATCCTTAGAAT 59.818 40.000 0.19 0.00 0.00 2.40
2520 2765 9.459640 CTCCATCAAGTTAAATATGCATTGAAG 57.540 33.333 3.54 0.00 31.14 3.02
2620 2865 2.543430 GTGCAAATGAAATGGCAAACGT 59.457 40.909 0.00 0.00 38.84 3.99
2645 2890 6.679303 TGGTAAATAACAGGGGATAAAGAGGA 59.321 38.462 0.00 0.00 0.00 3.71
2646 2891 7.184936 TGGTAAATAACAGGGGATAAAGAGGAA 59.815 37.037 0.00 0.00 0.00 3.36
2721 2966 9.663904 TTTAGTTTTTCTTCGAATGACTGATTG 57.336 29.630 0.00 0.00 0.00 2.67
2864 3111 0.098552 TGCAACTGTGAAGCAACACG 59.901 50.000 8.34 6.32 42.86 4.49
2881 3128 7.027161 AGCAACACGTTATAGCCATTTTTAAG 58.973 34.615 0.00 0.00 0.00 1.85
2895 3142 6.811665 GCCATTTTTAAGTAGGTTGAATGACC 59.188 38.462 0.00 0.00 40.11 4.02
2898 3145 9.927668 CATTTTTAAGTAGGTTGAATGACCATT 57.072 29.630 0.00 0.00 42.35 3.16
2922 3169 5.670792 TTCTTAATTAAGAGGCGACCTGA 57.329 39.130 23.41 7.08 42.66 3.86
3057 3321 8.439971 ACATTCCAGATGGTTCTAATTAGCATA 58.560 33.333 7.67 0.00 34.15 3.14
3060 3324 7.445121 TCCAGATGGTTCTAATTAGCATACTG 58.555 38.462 7.67 12.69 34.15 2.74
3097 3361 1.070445 GGTCCCTCATGCATCTCCG 59.930 63.158 0.00 0.00 0.00 4.63
3124 3388 4.289672 AGCAAGAAGATGGGTTTTCTAGGA 59.710 41.667 0.00 0.00 33.49 2.94
3198 3484 8.552083 AATTTGCTTTGGAAATAAGACCATTC 57.448 30.769 0.00 0.00 36.02 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.965147 TGACTTGACCTGACTCATGACA 59.035 45.455 0.00 0.00 0.00 3.58
34 35 4.696479 AAGTTGACTTGACCTGACTCAT 57.304 40.909 0.00 0.00 34.38 2.90
89 90 0.924090 GAAAAGAGATGCGCGTCGAT 59.076 50.000 23.15 13.37 0.00 3.59
115 116 1.938814 CAACAACGCGCCAACTGTG 60.939 57.895 5.73 0.00 0.00 3.66
151 167 4.339530 GGGAGCAGAGTATATATCGATGCA 59.660 45.833 8.54 0.00 34.71 3.96
152 168 4.261825 GGGGAGCAGAGTATATATCGATGC 60.262 50.000 8.54 0.31 0.00 3.91
153 169 4.889995 TGGGGAGCAGAGTATATATCGATG 59.110 45.833 8.54 0.00 0.00 3.84
154 170 4.890581 GTGGGGAGCAGAGTATATATCGAT 59.109 45.833 2.16 2.16 0.00 3.59
156 172 4.017126 TGTGGGGAGCAGAGTATATATCG 58.983 47.826 0.00 0.00 0.00 2.92
157 173 4.160626 GGTGTGGGGAGCAGAGTATATATC 59.839 50.000 0.00 0.00 0.00 1.63
174 190 0.807667 GATACGAGCTGCAGGTGTGG 60.808 60.000 25.60 14.42 0.00 4.17
176 192 1.257750 TGGATACGAGCTGCAGGTGT 61.258 55.000 25.60 21.87 42.51 4.16
188 204 1.721664 TTCGAGGCGGAGTGGATACG 61.722 60.000 0.00 0.00 38.74 3.06
194 210 1.630244 CTTGCTTTCGAGGCGGAGTG 61.630 60.000 7.71 0.00 0.00 3.51
206 222 1.600916 GTGGCGGTCTCCTTGCTTT 60.601 57.895 0.00 0.00 0.00 3.51
217 233 1.832608 TGAGTGAGTGAGTGGCGGT 60.833 57.895 0.00 0.00 0.00 5.68
232 248 0.179176 CAAGAGCGAGACGAGGTGAG 60.179 60.000 0.00 0.00 0.00 3.51
233 249 1.587043 CCAAGAGCGAGACGAGGTGA 61.587 60.000 0.00 0.00 0.00 4.02
235 251 1.303398 TCCAAGAGCGAGACGAGGT 60.303 57.895 0.00 0.00 0.00 3.85
236 252 1.137825 GTCCAAGAGCGAGACGAGG 59.862 63.158 0.00 0.00 0.00 4.63
237 253 1.137825 GGTCCAAGAGCGAGACGAG 59.862 63.158 0.00 0.00 0.00 4.18
238 254 1.303398 AGGTCCAAGAGCGAGACGA 60.303 57.895 0.00 0.00 35.00 4.20
258 274 3.749064 GGGAGACGACGCTGCTGA 61.749 66.667 9.72 0.00 0.00 4.26
288 304 1.206849 GAGCACTTGAGAAGGGAGAGG 59.793 57.143 0.00 0.00 32.08 3.69
295 311 1.093159 GCCATGGAGCACTTGAGAAG 58.907 55.000 18.40 0.00 0.00 2.85
316 332 4.598257 CGGAGCTTGGAACGATGT 57.402 55.556 0.00 0.00 0.00 3.06
342 358 0.319211 TACCAAACCACGACAGAGCG 60.319 55.000 0.00 0.00 37.29 5.03
367 409 0.040958 GGACTGACGCTGCAACTTTG 60.041 55.000 0.00 0.00 0.00 2.77
392 434 2.110188 ACTAGGGACTGAGAGGACACAA 59.890 50.000 0.00 0.00 41.52 3.33
395 437 2.378886 TGAACTAGGGACTGAGAGGACA 59.621 50.000 0.00 0.00 41.52 4.02
399 441 3.630312 GCTAGTGAACTAGGGACTGAGAG 59.370 52.174 17.10 0.00 44.63 3.20
400 442 3.267291 AGCTAGTGAACTAGGGACTGAGA 59.733 47.826 17.10 0.00 44.63 3.27
498 540 1.683917 CGGACATACAGAGGAAGAGGG 59.316 57.143 0.00 0.00 0.00 4.30
615 670 1.320344 TAGACGGCAGCGAAGACCAT 61.320 55.000 0.00 0.00 0.00 3.55
624 679 3.438017 CTGGAGGCTAGACGGCAGC 62.438 68.421 4.33 4.33 41.46 5.25
629 684 3.905678 CCGGCTGGAGGCTAGACG 61.906 72.222 5.28 5.54 46.01 4.18
631 686 2.759973 CACCGGCTGGAGGCTAGA 60.760 66.667 21.41 0.00 41.46 2.43
658 714 4.228567 GCCAGCTCCTACGCTCCC 62.229 72.222 0.00 0.00 38.41 4.30
684 740 1.557371 GCAGGGGATTATAGGAGAGCC 59.443 57.143 0.00 0.00 0.00 4.70
692 748 3.326006 CAGAGCAGAAGCAGGGGATTATA 59.674 47.826 0.00 0.00 45.49 0.98
699 755 2.350134 TGCAGAGCAGAAGCAGGG 59.650 61.111 0.00 0.00 45.49 4.45
742 798 3.686016 GGTCAGATCTAGAGCTAGAGGG 58.314 54.545 10.79 0.00 44.47 4.30
747 803 2.773487 GAGCGGTCAGATCTAGAGCTA 58.227 52.381 10.79 0.00 33.26 3.32
748 804 1.604604 GAGCGGTCAGATCTAGAGCT 58.395 55.000 10.30 4.23 36.06 4.09
749 805 0.237235 CGAGCGGTCAGATCTAGAGC 59.763 60.000 15.89 0.00 32.02 4.09
753 809 0.535328 CCCTCGAGCGGTCAGATCTA 60.535 60.000 15.89 0.00 32.02 1.98
773 829 2.832129 CAGTGAGCAACCTAGGGTTAGA 59.168 50.000 14.81 0.00 45.01 2.10
816 872 2.926200 CAGATTACACCGTGAAGAGCAG 59.074 50.000 5.28 0.00 0.00 4.24
833 896 1.815003 CCGGCAAAGAAAGAAGCAGAT 59.185 47.619 0.00 0.00 0.00 2.90
896 959 2.417924 CCTCCTGAATCAACAGAGACCG 60.418 54.545 6.27 0.00 39.94 4.79
900 963 2.027377 AGTGCCTCCTGAATCAACAGAG 60.027 50.000 0.00 0.00 39.94 3.35
925 988 1.669115 GCTTCGGAACAGCAGCAGA 60.669 57.895 0.00 0.00 37.22 4.26
976 1048 0.464452 AAGCTAGACGGTATGGTGCC 59.536 55.000 0.00 0.00 0.00 5.01
979 1051 2.453521 TCACAAGCTAGACGGTATGGT 58.546 47.619 0.00 0.00 0.00 3.55
996 1106 2.134789 ATTCACCTCCAGGCATTCAC 57.865 50.000 0.00 0.00 39.32 3.18
1001 1111 2.945440 GCACATAATTCACCTCCAGGCA 60.945 50.000 0.00 0.00 39.32 4.75
1006 1116 2.615912 GCTCAGCACATAATTCACCTCC 59.384 50.000 0.00 0.00 0.00 4.30
1013 1123 2.756760 CACAAGGGCTCAGCACATAATT 59.243 45.455 0.00 0.00 32.33 1.40
1034 1144 1.394917 CGCTGTGTGTCCTAAAGCATC 59.605 52.381 0.00 0.00 33.41 3.91
1068 1178 4.466567 TTATACGGCGAATTGATTGCAG 57.533 40.909 16.62 0.00 0.00 4.41
1075 1185 6.578545 CCAATTCTGAATTATACGGCGAATTG 59.421 38.462 16.62 14.32 42.51 2.32
1081 1191 6.619801 AGAACCAATTCTGAATTATACGGC 57.380 37.500 14.78 4.18 43.86 5.68
1119 1229 3.675228 GCATTTTCATTGCAGAGGACCAG 60.675 47.826 0.00 0.00 39.90 4.00
1167 1296 8.696410 TCAAAAAGTTTTAATGAGTCCACAAC 57.304 30.769 0.24 0.00 0.00 3.32
1180 1309 8.610896 CCATTGCTGTTCATTCAAAAAGTTTTA 58.389 29.630 0.24 0.00 0.00 1.52
1212 1346 6.689177 GCCCTAATGTCTTGGCTATTACTTCT 60.689 42.308 0.00 0.00 40.77 2.85
1265 1399 9.663904 TTTGTAATTTTCTTCAGAAAGTCGATG 57.336 29.630 2.35 0.00 43.90 3.84
1266 1400 9.665264 GTTTGTAATTTTCTTCAGAAAGTCGAT 57.335 29.630 2.35 0.00 43.90 3.59
1384 1518 4.197750 AGCATCTCTTATCAAGCTTGGTG 58.802 43.478 25.73 8.65 0.00 4.17
1391 1525 8.538701 ACAGGGATATTAGCATCTCTTATCAAG 58.461 37.037 0.00 0.00 33.26 3.02
1413 1547 6.432783 TGTTTAATCAATCCCACAGTTACAGG 59.567 38.462 0.00 0.00 0.00 4.00
1419 1557 4.044065 TCCCTGTTTAATCAATCCCACAGT 59.956 41.667 0.00 0.00 31.52 3.55
1580 1718 1.967319 TCTGTGTTTCCCAGCAGAAC 58.033 50.000 0.00 0.00 35.36 3.01
1604 1742 0.961019 TTCCATTGAACTGCACCAGC 59.039 50.000 0.00 0.00 42.57 4.85
1617 1755 7.931015 TGTCTACCTGAATATACCTTCCATT 57.069 36.000 0.00 0.00 0.00 3.16
1636 1774 6.868864 GCAGAGTAAACTTTCAGTGATGTCTA 59.131 38.462 0.00 0.00 0.00 2.59
1679 1817 3.601443 AGATTCTGTTGAAGACTCCCG 57.399 47.619 0.00 0.00 35.65 5.14
1685 1823 7.014134 TGCATACCAAAAAGATTCTGTTGAAGA 59.986 33.333 10.49 0.00 35.44 2.87
1761 1902 3.567478 AAGCTAAAGGTGATGCCCTAG 57.433 47.619 0.00 0.00 38.26 3.02
1803 1945 4.644685 ACGCAAAATGCTAAAGGGTCATAT 59.355 37.500 0.43 0.00 42.25 1.78
1804 1946 4.013728 ACGCAAAATGCTAAAGGGTCATA 58.986 39.130 0.43 0.00 42.25 2.15
1805 1947 2.825532 ACGCAAAATGCTAAAGGGTCAT 59.174 40.909 0.43 0.00 42.25 3.06
1856 2037 1.001860 GCAGGTTCAGCTGAAGAGACT 59.998 52.381 29.13 20.22 34.27 3.24
2002 2183 5.841957 ATCAGCAATCTTTGGAACCATAC 57.158 39.130 0.00 0.00 0.00 2.39
2134 2374 8.034313 AGTTTATTAGGCAATACTGGAGATGA 57.966 34.615 0.00 0.00 0.00 2.92
2168 2410 1.357420 TGTACCCACTGGATGCCATTT 59.643 47.619 0.00 0.00 30.82 2.32
2247 2489 7.526142 ACTGATCTCGAGTATTAATAAGCCA 57.474 36.000 13.13 0.00 0.00 4.75
2413 2657 4.157105 GCGTACCTAAACAAATGGAACCAT 59.843 41.667 0.00 0.00 38.46 3.55
2416 2660 3.432933 TCGCGTACCTAAACAAATGGAAC 59.567 43.478 5.77 0.00 0.00 3.62
2425 2669 3.305361 GTCCAATCTTCGCGTACCTAAAC 59.695 47.826 5.77 0.00 0.00 2.01
2463 2707 7.663081 TCTGATTCTAAGGATGCATATTTGGAC 59.337 37.037 0.00 0.00 0.00 4.02
2484 2728 2.203584 ACTTGATGGAGGCCTTCTGAT 58.796 47.619 13.68 0.00 0.00 2.90
2485 2729 1.661463 ACTTGATGGAGGCCTTCTGA 58.339 50.000 13.68 0.00 0.00 3.27
2520 2765 2.819608 TCTCAGCACATTTTAGCCCAAC 59.180 45.455 0.00 0.00 0.00 3.77
2620 2865 6.679303 TCCTCTTTATCCCCTGTTATTTACCA 59.321 38.462 0.00 0.00 0.00 3.25
2645 2890 9.141400 GTGAAATTAAATCGTCTCAGTAGAGTT 57.859 33.333 0.00 0.00 42.66 3.01
2646 2891 8.304596 TGTGAAATTAAATCGTCTCAGTAGAGT 58.695 33.333 0.00 0.00 42.66 3.24
2720 2965 4.908601 ACCTAGGACACACATGAAATCA 57.091 40.909 17.98 0.00 0.00 2.57
2721 2966 6.575162 AAAACCTAGGACACACATGAAATC 57.425 37.500 17.98 0.00 0.00 2.17
2895 3142 7.698130 CAGGTCGCCTCTTAATTAAGAAAAATG 59.302 37.037 24.41 14.41 41.37 2.32
2898 3145 6.469410 TCAGGTCGCCTCTTAATTAAGAAAA 58.531 36.000 24.41 10.56 41.37 2.29
2922 3169 7.886970 AGGCTATGCAGATTGTATGAATGTTAT 59.113 33.333 0.00 0.00 0.00 1.89
3027 3291 9.613428 CTAATTAGAACCATCTGGAATGTGTAA 57.387 33.333 6.64 0.00 37.10 2.41
3097 3361 4.767409 AGAAAACCCATCTTCTTGCTAACC 59.233 41.667 0.00 0.00 0.00 2.85
3124 3388 7.700656 CACACGTTTTATTTCTTCTTGAAACCT 59.299 33.333 0.00 0.00 46.08 3.50
3198 3484 4.098501 TCCAGACTGGCATATATAGCATCG 59.901 45.833 17.33 0.00 37.47 3.84
3281 3567 7.783090 TTATTGCTTCAATTTCTTGTTGCAA 57.217 28.000 16.22 16.22 45.43 4.08


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

AutoCloner maintained by Alex Coulton.