Multiple sequence alignment - TraesCS2A01G100600

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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 TraesCS2A01G100600 chr2A 100.000 3919 0 0 1 3919 53607944 53611862 0.000000e+00 7238
1 TraesCS2A01G100600 chr2B 90.188 3873 208 80 2 3771 81337086 81340889 0.000000e+00 4889
2 TraesCS2A01G100600 chr2B 86.578 678 51 13 3123 3771 81345227 81345893 0.000000e+00 712
3 TraesCS2A01G100600 chr2B 85.251 678 57 12 3123 3771 81344182 81344845 0.000000e+00 658
4 TraesCS2A01G100600 chr2B 89.015 528 45 8 3152 3670 81346293 81346816 3.300000e-180 641
5 TraesCS2A01G100600 chr2B 91.503 153 12 1 3767 3919 81341311 81341462 3.970000e-50 209
6 TraesCS2A01G100600 chr2D 92.133 2377 125 33 1 2350 52062182 52064523 0.000000e+00 3297
7 TraesCS2A01G100600 chr2D 92.446 887 41 13 2379 3260 52064516 52065381 0.000000e+00 1243
8 TraesCS2A01G100600 chr2D 94.156 154 6 3 3767 3919 52069194 52069345 8.470000e-57 231
9 TraesCS2A01G100600 chr2D 92.308 91 7 0 3262 3352 52065667 52065757 3.180000e-26 130
10 TraesCS2A01G100600 chr1B 92.053 151 11 1 3622 3771 259022762 259022912 1.100000e-50 211


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 TraesCS2A01G100600 chr2A 53607944 53611862 3918 False 7238.00 7238 100.00000 1 3919 1 chr2A.!!$F1 3918
1 TraesCS2A01G100600 chr2B 81337086 81346816 9730 False 1421.80 4889 88.50700 2 3919 5 chr2B.!!$F1 3917
2 TraesCS2A01G100600 chr2D 52062182 52069345 7163 False 1225.25 3297 92.76075 1 3919 4 chr2D.!!$F1 3918

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
242 243 0.247460 GGATCGATCGCATGGATGGA 59.753 55.000 18.81 9.93 42.95 3.41 F
895 918 0.398318 AGGCCAAGGTTGTCTCACTC 59.602 55.000 5.01 0.00 0.00 3.51 F
1262 1303 0.399806 GGCAGGAGGAGGAGGAGATT 60.400 60.000 0.00 0.00 0.00 2.40 F
2018 2092 1.080434 GGTCCAGAGACGACTGCAC 60.080 63.158 0.00 0.00 44.54 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1807 1879 0.733150 GCCCTTCACACGCTTTATCC 59.267 55.000 0.00 0.00 0.00 2.59 R
2586 2667 0.524862 GAGCCGTCGTTCTGGAGTAA 59.475 55.000 0.00 0.00 0.00 2.24 R
2603 2684 2.584418 CAGCTGTCATCGGCCGAG 60.584 66.667 33.87 23.75 46.23 4.63 R
3290 3660 0.320771 CACGGGTATAGGCTCCATGC 60.321 60.000 0.00 0.00 41.94 4.06 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
99 100 1.999634 ATTCCCCTTCTGGATGCCCG 62.000 60.000 0.00 0.00 35.39 6.13
103 104 3.801997 CTTCTGGATGCCCGCCCT 61.802 66.667 0.00 0.00 34.29 5.19
239 240 4.898002 CGGATCGATCGCATGGAT 57.102 55.556 18.81 0.00 38.35 3.41
240 241 2.366833 CGGATCGATCGCATGGATG 58.633 57.895 18.81 0.00 34.82 3.51
242 243 0.247460 GGATCGATCGCATGGATGGA 59.753 55.000 18.81 9.93 42.95 3.41
243 244 1.338105 GGATCGATCGCATGGATGGAA 60.338 52.381 18.81 0.00 42.21 3.53
244 245 2.625737 GATCGATCGCATGGATGGAAT 58.374 47.619 11.09 0.00 42.21 3.01
245 246 3.430790 GGATCGATCGCATGGATGGAATA 60.431 47.826 18.81 0.00 42.21 1.75
247 248 2.562738 TCGATCGCATGGATGGAATACT 59.437 45.455 11.09 0.00 37.00 2.12
280 285 1.729131 GACCACAAATGTTGCCGCG 60.729 57.895 0.00 0.00 0.00 6.46
282 287 3.460278 CACAAATGTTGCCGCGCG 61.460 61.111 25.67 25.67 0.00 6.86
294 299 3.891834 CGCGCGCTCTCTCGTTTC 61.892 66.667 30.48 0.00 0.00 2.78
295 300 2.805353 GCGCGCTCTCTCGTTTCA 60.805 61.111 26.67 0.00 0.00 2.69
296 301 2.783064 GCGCGCTCTCTCGTTTCAG 61.783 63.158 26.67 0.00 0.00 3.02
299 304 1.284982 GCGCTCTCTCGTTTCAGCAA 61.285 55.000 0.00 0.00 0.00 3.91
300 305 1.354040 CGCTCTCTCGTTTCAGCAAT 58.646 50.000 0.00 0.00 0.00 3.56
301 306 1.322936 CGCTCTCTCGTTTCAGCAATC 59.677 52.381 0.00 0.00 0.00 2.67
302 307 2.341257 GCTCTCTCGTTTCAGCAATCA 58.659 47.619 0.00 0.00 0.00 2.57
303 308 2.738846 GCTCTCTCGTTTCAGCAATCAA 59.261 45.455 0.00 0.00 0.00 2.57
393 401 4.821260 AGTTCTCATGCAACACATACAACA 59.179 37.500 9.31 0.00 36.64 3.33
394 402 5.049198 AGTTCTCATGCAACACATACAACAG 60.049 40.000 9.31 0.00 36.64 3.16
415 423 2.288152 GCTCGAGGAATCTAAGAGCAGG 60.288 54.545 15.58 0.00 45.25 4.85
565 573 2.349590 GTACGTAACTTCCGGCCAAAT 58.650 47.619 2.24 0.00 0.00 2.32
634 649 1.680735 TGTTGTTGTAGCTGCAAAGGG 59.319 47.619 19.29 0.00 0.00 3.95
653 668 1.616628 AGAAAGATCGGCCAGGGGT 60.617 57.895 2.24 0.00 0.00 4.95
760 783 1.129437 GTTGAGCTTGCTCCAACGATC 59.871 52.381 18.48 0.00 32.19 3.69
783 806 2.993038 GATTCCCTCCCTCCCTCCCC 62.993 70.000 0.00 0.00 0.00 4.81
895 918 0.398318 AGGCCAAGGTTGTCTCACTC 59.602 55.000 5.01 0.00 0.00 3.51
982 1005 1.900351 CAGCGGGGATCTTGTCTGA 59.100 57.895 0.00 0.00 0.00 3.27
1067 1094 2.158608 AGCAGGTAAAAGAGTTGCACCT 60.159 45.455 0.00 0.00 40.25 4.00
1088 1116 4.488879 CTGCAAGGAAGAATTACCTTTGC 58.511 43.478 11.51 11.51 43.54 3.68
1262 1303 0.399806 GGCAGGAGGAGGAGGAGATT 60.400 60.000 0.00 0.00 0.00 2.40
1381 1422 5.986135 GCCTGACAGTAAGTAAATGATCGAT 59.014 40.000 0.00 0.00 0.00 3.59
1382 1423 6.480320 GCCTGACAGTAAGTAAATGATCGATT 59.520 38.462 0.00 0.00 0.00 3.34
1421 1462 2.754552 TGGCAGAAATGCATAGGTGAAC 59.245 45.455 0.00 0.00 36.33 3.18
1519 1560 4.101119 CCGGGATTAACTCTGTACCATCTT 59.899 45.833 0.00 0.00 0.00 2.40
1528 1569 4.160626 ACTCTGTACCATCTTAAGAGCCAC 59.839 45.833 11.53 6.80 38.33 5.01
1614 1679 4.640201 TGTTTGAGCAAGAAACTTAGCTGT 59.360 37.500 0.00 0.00 37.48 4.40
1710 1779 9.889128 AAAAATGGTGAGTAAATCATAAATGGG 57.111 29.630 0.00 0.00 40.92 4.00
1719 1788 4.524802 AATCATAAATGGGTCTGAGGCA 57.475 40.909 0.00 0.00 0.00 4.75
1770 1842 5.527214 TGATGTATCATTAACCCTGCTTTCG 59.473 40.000 0.00 0.00 0.00 3.46
1807 1879 4.389576 GGCTTTGGCACAGCGACG 62.390 66.667 18.52 0.00 42.39 5.12
1816 1888 1.631072 CACAGCGACGGATAAAGCG 59.369 57.895 0.00 0.00 34.34 4.68
1835 1907 1.748244 CGTGTGAAGGGCATGGATCAT 60.748 52.381 0.00 0.00 0.00 2.45
1839 1911 1.144298 TGAAGGGCATGGATCATCAGG 59.856 52.381 0.00 0.00 0.00 3.86
1893 1966 6.553476 AGCAGGTAAGAAGTAATTTGGGTTTT 59.447 34.615 0.00 0.00 0.00 2.43
1894 1967 7.070696 AGCAGGTAAGAAGTAATTTGGGTTTTT 59.929 33.333 0.00 0.00 0.00 1.94
1927 2000 1.281899 GCACTCGACTTGCATCCTAC 58.718 55.000 9.01 0.00 39.93 3.18
1982 2056 2.034001 GTCTATGCACATAAACGACGCC 60.034 50.000 0.00 0.00 0.00 5.68
2018 2092 1.080434 GGTCCAGAGACGACTGCAC 60.080 63.158 0.00 0.00 44.54 4.57
2036 2110 2.479049 GCACGAGCAAATAGAGGTACGA 60.479 50.000 0.00 0.00 41.58 3.43
2063 2137 2.175878 AACAGCGCAGTCTCAATCTT 57.824 45.000 11.47 0.00 0.00 2.40
2068 2142 2.233431 AGCGCAGTCTCAATCTTCTTCT 59.767 45.455 11.47 0.00 0.00 2.85
2072 2146 4.560819 CGCAGTCTCAATCTTCTTCTGTAC 59.439 45.833 0.00 0.00 0.00 2.90
2152 2226 5.049167 TCATTCAACATGACTGGTTTTTGC 58.951 37.500 0.00 0.00 29.31 3.68
2172 2246 3.118408 TGCTATCCATGTCACCTGTAACC 60.118 47.826 0.00 0.00 0.00 2.85
2176 2250 2.039746 TCCATGTCACCTGTAACCTTGG 59.960 50.000 0.00 0.00 0.00 3.61
2330 2411 7.095017 GCTGTTTCTGAAACTGATAAACTAGCT 60.095 37.037 31.50 0.00 41.24 3.32
2331 2412 9.424319 CTGTTTCTGAAACTGATAAACTAGCTA 57.576 33.333 27.75 7.24 41.24 3.32
2332 2413 9.204570 TGTTTCTGAAACTGATAAACTAGCTAC 57.795 33.333 27.75 3.06 41.90 3.58
2375 2456 5.723672 TTCTCGAATACCAAGTCTGAAGT 57.276 39.130 0.00 0.00 0.00 3.01
2376 2457 5.723672 TCTCGAATACCAAGTCTGAAGTT 57.276 39.130 0.00 0.00 0.00 2.66
2377 2458 6.829229 TCTCGAATACCAAGTCTGAAGTTA 57.171 37.500 0.00 0.00 0.00 2.24
2378 2459 7.406031 TCTCGAATACCAAGTCTGAAGTTAT 57.594 36.000 0.00 0.00 0.00 1.89
2379 2460 7.258441 TCTCGAATACCAAGTCTGAAGTTATG 58.742 38.462 0.00 0.00 0.00 1.90
2380 2461 7.122204 TCTCGAATACCAAGTCTGAAGTTATGA 59.878 37.037 0.00 0.00 0.00 2.15
2381 2462 7.033791 TCGAATACCAAGTCTGAAGTTATGAC 58.966 38.462 0.00 0.86 0.00 3.06
2603 2684 1.557651 GATTACTCCAGAACGACGGC 58.442 55.000 0.00 0.00 0.00 5.68
2702 2783 3.785499 GGCGCTCCGTTCGAAACC 61.785 66.667 7.64 0.00 0.00 3.27
2946 3028 1.471287 GAGCAAGTGAGATGCATGCAA 59.529 47.619 26.68 4.80 46.22 4.08
3007 3089 0.520847 GCAGAGTTTCAGAAGCAGGC 59.479 55.000 0.00 0.00 0.00 4.85
3045 3127 0.671781 CCAGAACGGCAGGACAAGAG 60.672 60.000 0.00 0.00 0.00 2.85
3149 3234 2.033801 GCTCTTGTGTCATGCTTGTGTT 59.966 45.455 0.00 0.00 0.00 3.32
3150 3235 3.250762 GCTCTTGTGTCATGCTTGTGTTA 59.749 43.478 0.00 0.00 0.00 2.41
3151 3236 4.083110 GCTCTTGTGTCATGCTTGTGTTAT 60.083 41.667 0.00 0.00 0.00 1.89
3152 3237 5.563475 GCTCTTGTGTCATGCTTGTGTTATT 60.563 40.000 0.00 0.00 0.00 1.40
3153 3238 5.761003 TCTTGTGTCATGCTTGTGTTATTG 58.239 37.500 0.00 0.00 0.00 1.90
3154 3239 5.299028 TCTTGTGTCATGCTTGTGTTATTGT 59.701 36.000 0.00 0.00 0.00 2.71
3155 3240 4.857799 TGTGTCATGCTTGTGTTATTGTG 58.142 39.130 0.00 0.00 0.00 3.33
3156 3241 3.670055 GTGTCATGCTTGTGTTATTGTGC 59.330 43.478 0.00 0.00 0.00 4.57
3199 3285 1.340017 GCAAATGTAGGAGCTCCACCA 60.340 52.381 33.90 27.44 38.89 4.17
3212 3298 5.091261 AGCTCCACCACTTTATCAAGTAG 57.909 43.478 0.00 0.00 41.69 2.57
3286 3656 4.099380 AGCTCAACTCGTCTAGCTAAAC 57.901 45.455 0.00 0.00 43.29 2.01
3290 3660 9.521534 GAGCTCAACTCGTCTAGCTAAACTAGG 62.522 48.148 9.40 0.00 45.04 3.02
3329 3699 2.616376 TGTTGACAAGACGGTGAAATGG 59.384 45.455 0.00 0.00 0.00 3.16
3341 3711 3.611530 CGGTGAAATGGGCTACAAAACAG 60.612 47.826 0.00 0.00 0.00 3.16
3380 3753 6.500684 AAACAACATACATCAGACCATGAC 57.499 37.500 0.00 0.00 41.91 3.06
3395 3768 3.057019 CCATGACGAAGAGAAACAACGA 58.943 45.455 0.00 0.00 0.00 3.85
3396 3769 3.679980 CCATGACGAAGAGAAACAACGAT 59.320 43.478 0.00 0.00 0.00 3.73
3397 3770 4.201628 CCATGACGAAGAGAAACAACGATC 60.202 45.833 0.00 0.00 0.00 3.69
3398 3771 4.238761 TGACGAAGAGAAACAACGATCT 57.761 40.909 0.00 0.00 0.00 2.75
3399 3772 4.227538 TGACGAAGAGAAACAACGATCTC 58.772 43.478 0.00 0.00 41.92 2.75
3445 3819 4.325119 TGCATCGGGTACTAGACTAGATC 58.675 47.826 16.55 8.05 0.00 2.75
3455 3829 4.909001 ACTAGACTAGATCCGGTATGACC 58.091 47.826 16.55 0.00 34.05 4.02
3457 3831 3.757270 AGACTAGATCCGGTATGACCTG 58.243 50.000 0.00 0.00 35.66 4.00
3462 3836 1.940613 GATCCGGTATGACCTGCAAAC 59.059 52.381 0.00 0.00 35.66 2.93
3517 3892 2.080693 TGTGCAAGATACCGCGAAAAT 58.919 42.857 8.23 0.00 0.00 1.82
3526 3901 4.565564 AGATACCGCGAAAATGAAGTACAC 59.434 41.667 8.23 0.00 0.00 2.90
3528 3903 2.222445 ACCGCGAAAATGAAGTACACAC 59.778 45.455 8.23 0.00 0.00 3.82
3541 3916 5.518847 TGAAGTACACACGAAAGAAACTCTG 59.481 40.000 0.00 0.00 0.00 3.35
3551 3926 1.308998 AGAAACTCTGGTTGTTGCCG 58.691 50.000 0.00 0.00 35.63 5.69
3566 3941 0.106918 TGCCGACAACCAAGAAACCT 60.107 50.000 0.00 0.00 0.00 3.50
3581 3956 7.177392 ACCAAGAAACCTCTCCATCAAAATAAG 59.823 37.037 0.00 0.00 0.00 1.73
3584 3959 9.539194 AAGAAACCTCTCCATCAAAATAAGAAT 57.461 29.630 0.00 0.00 0.00 2.40
3588 3963 6.543831 ACCTCTCCATCAAAATAAGAATTCCG 59.456 38.462 0.65 0.00 0.00 4.30
3686 4064 2.790433 TGTGCAGACAGTAATTTCCCC 58.210 47.619 0.00 0.00 0.00 4.81
3687 4065 2.375174 TGTGCAGACAGTAATTTCCCCT 59.625 45.455 0.00 0.00 0.00 4.79
3688 4066 3.181434 TGTGCAGACAGTAATTTCCCCTT 60.181 43.478 0.00 0.00 0.00 3.95
3689 4067 3.191371 GTGCAGACAGTAATTTCCCCTTG 59.809 47.826 0.00 0.00 0.00 3.61
3773 7810 6.266558 GGAAGTTGCATCTAGAAGAGGATAGA 59.733 42.308 0.00 0.00 32.79 1.98
3779 7816 7.851228 TGCATCTAGAAGAGGATAGACAAAAA 58.149 34.615 0.00 0.00 31.09 1.94
3804 7841 0.685097 TTGGAGCGCTACTGGAGTTT 59.315 50.000 22.67 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 0.449388 CGATCTTTTGACTGCAGGGC 59.551 55.000 19.93 10.32 0.00 5.19
103 104 1.739466 GCCATCGATCTTTTGACTGCA 59.261 47.619 0.00 0.00 0.00 4.41
239 240 6.318648 GTCAATCAGCATTGGTTAGTATTCCA 59.681 38.462 0.00 0.00 40.08 3.53
240 241 6.238759 GGTCAATCAGCATTGGTTAGTATTCC 60.239 42.308 0.00 0.00 40.08 3.01
242 243 6.095440 GTGGTCAATCAGCATTGGTTAGTATT 59.905 38.462 0.00 0.00 40.08 1.89
243 244 5.590259 GTGGTCAATCAGCATTGGTTAGTAT 59.410 40.000 0.00 0.00 40.08 2.12
244 245 4.941263 GTGGTCAATCAGCATTGGTTAGTA 59.059 41.667 0.00 0.00 40.08 1.82
245 246 3.758554 GTGGTCAATCAGCATTGGTTAGT 59.241 43.478 0.00 0.00 40.08 2.24
247 248 3.760738 TGTGGTCAATCAGCATTGGTTA 58.239 40.909 0.00 0.00 40.08 2.85
280 285 1.284982 TTGCTGAAACGAGAGAGCGC 61.285 55.000 0.00 0.00 33.97 5.92
282 287 2.341257 TGATTGCTGAAACGAGAGAGC 58.659 47.619 0.00 0.00 0.00 4.09
286 291 3.748048 CCTCTTTGATTGCTGAAACGAGA 59.252 43.478 0.00 0.00 0.00 4.04
287 292 3.669023 GCCTCTTTGATTGCTGAAACGAG 60.669 47.826 0.00 0.00 0.00 4.18
289 294 2.589014 GCCTCTTTGATTGCTGAAACG 58.411 47.619 0.00 0.00 0.00 3.60
291 296 1.895131 GGGCCTCTTTGATTGCTGAAA 59.105 47.619 0.84 0.00 0.00 2.69
292 297 1.549203 GGGCCTCTTTGATTGCTGAA 58.451 50.000 0.84 0.00 0.00 3.02
293 298 0.677731 CGGGCCTCTTTGATTGCTGA 60.678 55.000 0.84 0.00 0.00 4.26
294 299 1.660560 CCGGGCCTCTTTGATTGCTG 61.661 60.000 0.84 0.00 0.00 4.41
295 300 1.379044 CCGGGCCTCTTTGATTGCT 60.379 57.895 0.84 0.00 0.00 3.91
296 301 0.965363 TTCCGGGCCTCTTTGATTGC 60.965 55.000 0.84 0.00 0.00 3.56
299 304 1.284785 TCATTTCCGGGCCTCTTTGAT 59.715 47.619 0.84 0.00 0.00 2.57
300 305 0.695924 TCATTTCCGGGCCTCTTTGA 59.304 50.000 0.84 0.00 0.00 2.69
301 306 0.811281 GTCATTTCCGGGCCTCTTTG 59.189 55.000 0.84 0.00 0.00 2.77
302 307 0.404040 TGTCATTTCCGGGCCTCTTT 59.596 50.000 0.84 0.00 0.00 2.52
303 308 0.322546 GTGTCATTTCCGGGCCTCTT 60.323 55.000 0.84 0.00 0.00 2.85
337 345 3.845781 TGGATAGATTCCTTGAGTGCC 57.154 47.619 0.00 0.00 45.68 5.01
393 401 2.622942 CTGCTCTTAGATTCCTCGAGCT 59.377 50.000 6.99 0.75 42.12 4.09
394 402 2.288152 CCTGCTCTTAGATTCCTCGAGC 60.288 54.545 6.99 10.17 42.03 5.03
415 423 0.392327 GAGAACTTGCAGGCCTCTCC 60.392 60.000 0.00 0.00 0.00 3.71
565 573 3.198409 AGATGATACATTTGCGCCTGA 57.802 42.857 4.18 0.00 0.00 3.86
634 649 1.147153 CCCCTGGCCGATCTTTCTC 59.853 63.158 0.00 0.00 0.00 2.87
671 686 1.129058 TCCTTATTCCTTCCGAGGGC 58.871 55.000 0.00 0.00 43.72 5.19
760 783 1.839296 GGGAGGGAGGGAATCTCGG 60.839 68.421 0.00 0.00 43.34 4.63
783 806 2.842058 GGATGGATGAGGCAGGGG 59.158 66.667 0.00 0.00 0.00 4.79
857 880 3.747708 GCCTATGACTATGGAACCCAACC 60.748 52.174 0.00 0.00 36.95 3.77
968 991 1.153349 GCCGTCAGACAAGATCCCC 60.153 63.158 0.41 0.00 0.00 4.81
993 1016 1.813859 CATGCTGCACATTCCTGGG 59.186 57.895 3.57 0.00 36.64 4.45
1067 1094 4.151883 AGCAAAGGTAATTCTTCCTTGCA 58.848 39.130 19.68 0.00 42.38 4.08
1068 1095 4.672801 CGAGCAAAGGTAATTCTTCCTTGC 60.673 45.833 9.30 12.73 42.38 4.01
1078 1105 4.452455 CAGAACAAGTCGAGCAAAGGTAAT 59.548 41.667 0.00 0.00 0.00 1.89
1079 1106 3.807622 CAGAACAAGTCGAGCAAAGGTAA 59.192 43.478 0.00 0.00 0.00 2.85
1080 1107 3.069016 TCAGAACAAGTCGAGCAAAGGTA 59.931 43.478 0.00 0.00 0.00 3.08
1088 1116 3.448686 ACACAAGTCAGAACAAGTCGAG 58.551 45.455 0.00 0.00 0.00 4.04
1262 1303 3.147595 CGACAGGATGAGCCCCGA 61.148 66.667 0.00 0.00 39.69 5.14
1300 1341 0.898320 GCAGCTCAGGAGTCCACTTA 59.102 55.000 12.86 0.00 0.00 2.24
1388 1429 4.297510 CATTTCTGCCATGAACAACGAAA 58.702 39.130 0.00 0.42 0.00 3.46
1391 1432 1.987770 GCATTTCTGCCATGAACAACG 59.012 47.619 0.00 0.00 42.88 4.10
1421 1462 3.853355 AATGTAGCCATCAGAAGGAGG 57.147 47.619 0.00 0.00 0.00 4.30
1528 1569 4.219115 ACTCTGTATCATGTACCTGGAGG 58.781 47.826 0.00 0.00 42.17 4.30
1705 1774 2.683211 AACTTTGCCTCAGACCCATT 57.317 45.000 0.00 0.00 0.00 3.16
1754 1826 8.702163 AATAAAAATCGAAAGCAGGGTTAATG 57.298 30.769 0.00 0.00 0.00 1.90
1795 1867 0.739462 CTTTATCCGTCGCTGTGCCA 60.739 55.000 0.00 0.00 0.00 4.92
1807 1879 0.733150 GCCCTTCACACGCTTTATCC 59.267 55.000 0.00 0.00 0.00 2.59
1816 1888 1.952296 GATGATCCATGCCCTTCACAC 59.048 52.381 0.00 0.00 0.00 3.82
1839 1911 1.819288 TCTCTCGGTTCAGGTGATCAC 59.181 52.381 17.91 17.91 0.00 3.06
1893 1966 7.158099 AGTCGAGTGCATATATATGTAGCAA 57.842 36.000 21.10 3.60 36.91 3.91
1894 1967 6.759497 AGTCGAGTGCATATATATGTAGCA 57.241 37.500 21.10 12.14 36.11 3.49
1938 2012 6.569780 ACCTAACCAAAATATGCCGAATTTC 58.430 36.000 0.00 0.00 0.00 2.17
1944 2018 5.334879 GCATAGACCTAACCAAAATATGCCG 60.335 44.000 0.00 0.00 38.57 5.69
1982 2056 3.368739 GGACCTCAATTTGCATTTGGAGG 60.369 47.826 18.22 18.22 32.40 4.30
2018 2092 7.639162 ATTTTATCGTACCTCTATTTGCTCG 57.361 36.000 0.00 0.00 0.00 5.03
2036 2110 6.494893 TTGAGACTGCGCTGTTTATTTTAT 57.505 33.333 21.36 0.00 0.00 1.40
2063 2137 5.834460 TGTAGGTTCCATAGGTACAGAAGA 58.166 41.667 0.00 0.00 0.00 2.87
2068 2142 7.620491 TGATAAACTGTAGGTTCCATAGGTACA 59.380 37.037 0.00 0.00 37.12 2.90
2072 2146 7.125792 AGTGATAAACTGTAGGTTCCATAGG 57.874 40.000 0.00 0.00 37.88 2.57
2142 2216 4.380867 GGTGACATGGATAGCAAAAACCAG 60.381 45.833 0.00 0.00 35.84 4.00
2144 2218 3.763897 AGGTGACATGGATAGCAAAAACC 59.236 43.478 0.00 0.00 0.00 3.27
2152 2226 5.118990 CAAGGTTACAGGTGACATGGATAG 58.881 45.833 1.27 0.00 0.00 2.08
2189 2263 4.074970 ACAAGACTACCATTTGCTTCCAG 58.925 43.478 0.00 0.00 0.00 3.86
2332 2413 9.746711 CGAGAAAAATAACTTCAGACATTGTAG 57.253 33.333 0.00 0.00 0.00 2.74
2375 2456 6.071391 TGCACTGTCTCACTCATAAGTCATAA 60.071 38.462 0.00 0.00 31.71 1.90
2376 2457 5.418840 TGCACTGTCTCACTCATAAGTCATA 59.581 40.000 0.00 0.00 31.71 2.15
2377 2458 4.221482 TGCACTGTCTCACTCATAAGTCAT 59.779 41.667 0.00 0.00 31.71 3.06
2378 2459 3.573967 TGCACTGTCTCACTCATAAGTCA 59.426 43.478 0.00 0.00 31.71 3.41
2379 2460 4.179926 TGCACTGTCTCACTCATAAGTC 57.820 45.455 0.00 0.00 31.71 3.01
2380 2461 4.221482 TCATGCACTGTCTCACTCATAAGT 59.779 41.667 0.00 0.00 35.60 2.24
2381 2462 4.752146 TCATGCACTGTCTCACTCATAAG 58.248 43.478 0.00 0.00 0.00 1.73
2585 2666 1.134560 GAGCCGTCGTTCTGGAGTAAT 59.865 52.381 0.00 0.00 0.00 1.89
2586 2667 0.524862 GAGCCGTCGTTCTGGAGTAA 59.475 55.000 0.00 0.00 0.00 2.24
2588 2669 2.963371 GAGCCGTCGTTCTGGAGT 59.037 61.111 0.00 0.00 0.00 3.85
2603 2684 2.584418 CAGCTGTCATCGGCCGAG 60.584 66.667 33.87 23.75 46.23 4.63
2663 2744 2.893398 CCTCTACGGGTGGCAGAC 59.107 66.667 0.00 0.00 0.00 3.51
2729 2810 3.190874 GAGAAACAGGTAGCATTCCTCG 58.809 50.000 0.00 0.00 32.37 4.63
3045 3127 3.626924 AGGAGGCCACCACGTCAC 61.627 66.667 22.29 0.00 0.00 3.67
3242 3328 9.048446 AGCTCGTTGTATAAGTTTTTCAGTTAA 57.952 29.630 0.00 0.00 0.00 2.01
3247 3333 7.225931 AGTTGAGCTCGTTGTATAAGTTTTTCA 59.774 33.333 9.64 0.00 0.00 2.69
3264 3634 4.099824 GTTTAGCTAGACGAGTTGAGCTC 58.900 47.826 6.82 6.82 44.05 4.09
3290 3660 0.320771 CACGGGTATAGGCTCCATGC 60.321 60.000 0.00 0.00 41.94 4.06
3341 3711 0.858583 GTTTTGTGGTTGATTGGCGC 59.141 50.000 0.00 0.00 0.00 6.53
3380 3753 4.476862 TGAGAGATCGTTGTTTCTCTTCG 58.523 43.478 4.13 0.00 46.67 3.79
3396 3769 9.383519 GTGATGATATTTTTGGTAGTTGAGAGA 57.616 33.333 0.00 0.00 0.00 3.10
3397 3770 9.388506 AGTGATGATATTTTTGGTAGTTGAGAG 57.611 33.333 0.00 0.00 0.00 3.20
3398 3771 9.166173 CAGTGATGATATTTTTGGTAGTTGAGA 57.834 33.333 0.00 0.00 0.00 3.27
3399 3772 7.912250 GCAGTGATGATATTTTTGGTAGTTGAG 59.088 37.037 0.00 0.00 0.00 3.02
3400 3773 7.392953 TGCAGTGATGATATTTTTGGTAGTTGA 59.607 33.333 0.00 0.00 0.00 3.18
3401 3774 7.537715 TGCAGTGATGATATTTTTGGTAGTTG 58.462 34.615 0.00 0.00 0.00 3.16
3403 3776 7.254898 CGATGCAGTGATGATATTTTTGGTAGT 60.255 37.037 0.00 0.00 0.00 2.73
3404 3777 7.073883 CGATGCAGTGATGATATTTTTGGTAG 58.926 38.462 0.00 0.00 0.00 3.18
3445 3819 2.477880 GGTTTGCAGGTCATACCGG 58.522 57.895 0.00 0.00 44.90 5.28
3455 3829 2.249309 CGTGTGCTCGGTTTGCAG 59.751 61.111 0.00 0.00 41.41 4.41
3496 3870 0.793861 TTTCGCGGTATCTTGCACAC 59.206 50.000 6.13 0.00 0.00 3.82
3497 3871 1.514003 TTTTCGCGGTATCTTGCACA 58.486 45.000 6.13 0.00 0.00 4.57
3498 3872 2.095213 TCATTTTCGCGGTATCTTGCAC 59.905 45.455 6.13 0.00 0.00 4.57
3499 3873 2.351455 TCATTTTCGCGGTATCTTGCA 58.649 42.857 6.13 0.00 0.00 4.08
3509 3884 2.154198 TCGTGTGTACTTCATTTTCGCG 59.846 45.455 0.00 0.00 0.00 5.87
3517 3892 5.518847 CAGAGTTTCTTTCGTGTGTACTTCA 59.481 40.000 0.00 0.00 0.00 3.02
3526 3901 4.342772 CAACAACCAGAGTTTCTTTCGTG 58.657 43.478 0.00 0.00 32.45 4.35
3528 3903 3.363178 GCAACAACCAGAGTTTCTTTCG 58.637 45.455 0.00 0.00 32.45 3.46
3551 3926 3.208747 TGGAGAGGTTTCTTGGTTGTC 57.791 47.619 0.00 0.00 32.53 3.18
3566 3941 6.122277 AGCGGAATTCTTATTTTGATGGAGA 58.878 36.000 5.23 0.00 0.00 3.71
3651 4029 2.749076 CTGCACATTGCCTTAGTTGCTA 59.251 45.455 0.00 0.00 44.23 3.49
3658 4036 2.566833 ACTGTCTGCACATTGCCTTA 57.433 45.000 0.00 0.00 44.23 2.69
3686 4064 3.812053 CGGAGGCAATCTATTTCCTCAAG 59.188 47.826 18.90 10.87 45.21 3.02
3687 4065 3.454447 TCGGAGGCAATCTATTTCCTCAA 59.546 43.478 18.90 7.38 45.21 3.02
3688 4066 3.038280 TCGGAGGCAATCTATTTCCTCA 58.962 45.455 18.90 1.78 45.21 3.86
3689 4067 3.556004 CCTCGGAGGCAATCTATTTCCTC 60.556 52.174 11.83 11.58 43.27 3.71
3708 4107 6.455360 TGAATGTAATTTCAGATTGGCCTC 57.545 37.500 3.32 0.00 36.07 4.70
3773 7810 2.884639 AGCGCTCCAAGTACATTTTTGT 59.115 40.909 2.64 0.00 0.00 2.83
3779 7816 1.137086 CCAGTAGCGCTCCAAGTACAT 59.863 52.381 16.34 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.