Multiple sequence alignment - TraesCS7B01G233300

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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 TraesCS7B01G233300 chr7B 100.000 3338 0 0 1 3338 436788905 436785568 0.000000e+00 6165.0
1 TraesCS7B01G233300 chr7D 91.975 3240 153 46 1 3215 420743927 420740770 0.000000e+00 4444.0
2 TraesCS7B01G233300 chr7D 81.992 261 45 2 1291 1550 33754878 33755137 1.560000e-53 220.0
3 TraesCS7B01G233300 chr7D 81.132 265 48 2 1287 1550 34011514 34011251 9.380000e-51 211.0
4 TraesCS7B01G233300 chr7D 81.132 265 48 2 1287 1550 34445249 34445512 9.380000e-51 211.0
5 TraesCS7B01G233300 chr7D 80.392 153 28 2 1027 1178 34011747 34011596 7.570000e-22 115.0
6 TraesCS7B01G233300 chr7D 80.690 145 28 0 1027 1171 34444996 34445140 2.720000e-21 113.0
7 TraesCS7B01G233300 chr7D 80.000 145 29 0 1027 1171 33754651 33754795 1.270000e-19 108.0
8 TraesCS7B01G233300 chr7D 80.000 145 29 0 1027 1171 34077143 34076999 1.270000e-19 108.0
9 TraesCS7B01G233300 chr7D 87.356 87 5 2 2284 2364 484370718 484370804 9.860000e-16 95.3
10 TraesCS7B01G233300 chr7A 90.246 3127 163 61 1 3069 512327618 512330660 0.000000e+00 3954.0
11 TraesCS7B01G233300 chr7A 81.887 265 46 2 1287 1550 34519329 34519066 4.330000e-54 222.0
12 TraesCS7B01G233300 chr7A 100.000 38 0 0 3107 3144 512330662 512330699 1.660000e-08 71.3
13 TraesCS7B01G233300 chr4A 83.333 264 42 2 1287 1549 691324117 691324379 3.330000e-60 243.0
14 TraesCS7B01G233300 chr4A 82.558 258 45 0 1287 1544 691247024 691247281 9.320000e-56 228.0
15 TraesCS7B01G233300 chr4A 81.569 255 45 2 1291 1544 691150892 691151145 3.370000e-50 209.0
16 TraesCS7B01G233300 chr4A 82.069 145 26 0 1027 1171 691150665 691150809 1.260000e-24 124.0
17 TraesCS7B01G233300 chr4A 84.800 125 16 2 3211 3335 609091964 609092085 4.520000e-24 122.0
18 TraesCS7B01G233300 chr4A 80.690 145 28 0 1027 1171 691166529 691166673 2.720000e-21 113.0
19 TraesCS7B01G233300 chr4A 79.470 151 31 0 1027 1177 690886942 690886792 1.270000e-19 108.0
20 TraesCS7B01G233300 chr2B 89.552 134 11 1 3208 3338 250964278 250964411 2.060000e-37 167.0
21 TraesCS7B01G233300 chr4D 87.705 122 15 0 3214 3335 213841746 213841867 3.470000e-30 143.0
22 TraesCS7B01G233300 chr4D 84.496 129 15 3 3211 3338 439873911 439873787 4.520000e-24 122.0
23 TraesCS7B01G233300 chr1A 86.719 128 14 2 3208 3335 527886911 527887035 4.490000e-29 139.0
24 TraesCS7B01G233300 chr1A 86.719 128 14 2 3208 3335 527887654 527887778 4.490000e-29 139.0
25 TraesCS7B01G233300 chr3D 84.252 127 14 5 3210 3335 5799059 5798938 5.850000e-23 119.0
26 TraesCS7B01G233300 chr2D 85.470 117 14 2 3211 3327 89280417 89280530 5.850000e-23 119.0
27 TraesCS7B01G233300 chr6B 83.077 130 17 3 3209 3338 520241286 520241162 2.720000e-21 113.0


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 TraesCS7B01G233300 chr7B 436785568 436788905 3337 True 6165.00 6165 100.000 1 3338 1 chr7B.!!$R1 3337
1 TraesCS7B01G233300 chr7D 420740770 420743927 3157 True 4444.00 4444 91.975 1 3215 1 chr7D.!!$R2 3214
2 TraesCS7B01G233300 chr7A 512327618 512330699 3081 False 2012.65 3954 95.123 1 3144 2 chr7A.!!$F1 3143

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
592 600 0.323725 AATCGCCAGCTCAAACCCAT 60.324 50.0 0.00 0.0 0.00 4.00 F
1098 1154 0.543174 ACCTGAGGAAGAAGGTCGCT 60.543 55.0 4.99 0.0 43.52 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1645 1711 0.111446 TCCTGCATTCCGGACCAAAA 59.889 50.0 1.83 0.00 0.0 2.44 R
2700 2774 0.392193 CAACCAGGCTAGCTCCACAG 60.392 60.0 15.72 0.64 0.0 3.66 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
39 41 2.833794 AGGCATTAATCTAAAGCGCGA 58.166 42.857 12.10 0.00 33.51 5.87
40 42 2.802816 AGGCATTAATCTAAAGCGCGAG 59.197 45.455 12.10 0.00 33.51 5.03
101 103 5.939447 AGAAGAATGGAGAGATTGGGATTC 58.061 41.667 0.00 0.00 0.00 2.52
104 106 2.174685 TGGAGAGATTGGGATTCGGA 57.825 50.000 0.00 0.00 0.00 4.55
105 107 2.477245 TGGAGAGATTGGGATTCGGAA 58.523 47.619 0.00 0.00 0.00 4.30
155 157 2.047844 CCTGACTCCCACGTGCAG 60.048 66.667 10.91 11.42 0.00 4.41
193 195 3.457380 ACGGATAGTCTACCACTCTACCA 59.543 47.826 0.00 0.00 36.43 3.25
322 329 4.175337 GTGGCAGGGGCGCATCTA 62.175 66.667 10.83 0.00 42.47 1.98
342 349 7.280876 GCATCTACAAAAGATCACACAGGAATA 59.719 37.037 0.00 0.00 43.42 1.75
484 492 3.219176 AGACATGCCTGGTCCATATTG 57.781 47.619 0.00 0.00 35.89 1.90
501 509 2.495155 TTGCTACATGTGCATGGACT 57.505 45.000 18.75 0.64 42.91 3.85
515 523 4.711846 TGCATGGACTCTAGTACTGTGATT 59.288 41.667 5.39 0.00 0.00 2.57
523 531 7.308348 GGACTCTAGTACTGTGATTCTATCAGC 60.308 44.444 5.39 0.00 40.53 4.26
576 584 9.357161 AGCTACCTATATAGTATAGCACCAATC 57.643 37.037 28.22 10.88 38.01 2.67
590 598 1.508088 CAATCGCCAGCTCAAACCC 59.492 57.895 0.00 0.00 0.00 4.11
591 599 1.074775 AATCGCCAGCTCAAACCCA 59.925 52.632 0.00 0.00 0.00 4.51
592 600 0.323725 AATCGCCAGCTCAAACCCAT 60.324 50.000 0.00 0.00 0.00 4.00
593 601 1.033746 ATCGCCAGCTCAAACCCATG 61.034 55.000 0.00 0.00 0.00 3.66
650 658 8.612145 ACATTTTATAGACCTAGGGTTTGTCTT 58.388 33.333 14.81 0.92 39.84 3.01
668 676 1.815003 CTTTGGTGAGCATCTTGGACC 59.185 52.381 0.00 0.00 34.92 4.46
671 679 1.296715 GTGAGCATCTTGGACCGGT 59.703 57.895 6.92 6.92 34.92 5.28
714 722 3.990933 TGCCCCTTTCCATATAACCCATA 59.009 43.478 0.00 0.00 0.00 2.74
776 784 5.511202 CCTGTTTCTCTTGCTTCTCTCTCTT 60.511 44.000 0.00 0.00 0.00 2.85
778 790 5.757320 TGTTTCTCTTGCTTCTCTCTCTTTG 59.243 40.000 0.00 0.00 0.00 2.77
781 793 6.019779 TCTCTTGCTTCTCTCTCTTTGTAC 57.980 41.667 0.00 0.00 0.00 2.90
790 804 2.029290 TCTCTCTTTGTACCTCGTTGCC 60.029 50.000 0.00 0.00 0.00 4.52
816 830 4.335647 CAACCAGGCGGCCAGACT 62.336 66.667 23.09 0.00 40.36 3.24
817 831 4.021925 AACCAGGCGGCCAGACTC 62.022 66.667 23.09 0.00 34.57 3.36
820 834 3.842923 CAGGCGGCCAGACTCGAT 61.843 66.667 23.09 0.00 34.57 3.59
868 883 3.691049 TTGTGCTCTTCCTTTTGTTCG 57.309 42.857 0.00 0.00 0.00 3.95
875 896 4.035909 GCTCTTCCTTTTGTTCGTTTACCA 59.964 41.667 0.00 0.00 0.00 3.25
881 902 5.470777 TCCTTTTGTTCGTTTACCACTATGG 59.529 40.000 0.00 0.00 45.02 2.74
897 918 5.279708 CCACTATGGATGATGAGGAAGGTAC 60.280 48.000 0.00 0.00 40.96 3.34
908 929 6.325028 TGATGAGGAAGGTACATAGAGGAAAG 59.675 42.308 0.00 0.00 0.00 2.62
910 931 6.261435 TGAGGAAGGTACATAGAGGAAAGAA 58.739 40.000 0.00 0.00 0.00 2.52
933 954 4.006319 GCTGTTAATGTGAGAGGAGCTTT 58.994 43.478 0.00 0.00 0.00 3.51
943 964 3.822735 TGAGAGGAGCTTTTGATTTGGTG 59.177 43.478 0.00 0.00 0.00 4.17
974 1026 4.402829 TCTTCTCAGATCGATCTTAGGGG 58.597 47.826 28.01 21.65 34.22 4.79
975 1027 3.162147 TCTCAGATCGATCTTAGGGGG 57.838 52.381 28.01 17.35 34.22 5.40
1098 1154 0.543174 ACCTGAGGAAGAAGGTCGCT 60.543 55.000 4.99 0.00 43.52 4.93
1187 1243 3.618171 GTAGGTGACCAAAAGCCGA 57.382 52.632 3.63 0.00 0.00 5.54
1188 1244 2.109425 GTAGGTGACCAAAAGCCGAT 57.891 50.000 3.63 0.00 0.00 4.18
1193 1249 1.019278 TGACCAAAAGCCGATCGAGC 61.019 55.000 18.66 17.93 0.00 5.03
1214 1271 0.687354 CCCCGTATTCAGGCAGCTAT 59.313 55.000 0.00 0.00 0.00 2.97
1215 1272 1.899814 CCCCGTATTCAGGCAGCTATA 59.100 52.381 0.00 0.00 0.00 1.31
1216 1273 2.093973 CCCCGTATTCAGGCAGCTATAG 60.094 54.545 0.00 0.00 0.00 1.31
1217 1274 2.563179 CCCGTATTCAGGCAGCTATAGT 59.437 50.000 0.84 0.00 0.00 2.12
1232 1289 8.696374 GGCAGCTATAGTTAATATACTGATGGA 58.304 37.037 0.84 0.00 32.70 3.41
1269 1327 4.740205 CGATCGTGCTGACAAACTATATGT 59.260 41.667 7.03 0.00 0.00 2.29
1270 1328 5.331830 CGATCGTGCTGACAAACTATATGTG 60.332 44.000 7.03 0.00 0.00 3.21
1271 1329 3.616821 TCGTGCTGACAAACTATATGTGC 59.383 43.478 0.00 0.00 0.00 4.57
1559 1622 1.665161 CGCCTAGACGAAGACAACGTT 60.665 52.381 0.00 0.00 43.97 3.99
1578 1641 1.440618 TGAGGTCCAGGTAGGCAAAA 58.559 50.000 0.00 0.00 37.29 2.44
1579 1642 1.351017 TGAGGTCCAGGTAGGCAAAAG 59.649 52.381 0.00 0.00 37.29 2.27
1587 1650 3.313526 CCAGGTAGGCAAAAGATTCATCG 59.686 47.826 0.00 0.00 0.00 3.84
1589 1652 2.033424 GGTAGGCAAAAGATTCATCGGC 59.967 50.000 0.00 0.00 0.00 5.54
1600 1663 2.198827 TTCATCGGCCACAAACTGAT 57.801 45.000 2.24 0.00 33.31 2.90
1602 1665 3.558931 TCATCGGCCACAAACTGATAT 57.441 42.857 2.24 0.00 31.84 1.63
1604 1667 1.934589 TCGGCCACAAACTGATATCG 58.065 50.000 2.24 0.00 0.00 2.92
1605 1668 0.937304 CGGCCACAAACTGATATCGG 59.063 55.000 10.14 10.14 0.00 4.18
1606 1669 1.742411 CGGCCACAAACTGATATCGGT 60.742 52.381 11.61 11.61 36.96 4.69
1618 1681 6.732531 ACTGATATCGGTTTCATGCATATG 57.267 37.500 11.61 0.00 31.54 1.78
1620 1683 6.369890 ACTGATATCGGTTTCATGCATATGTC 59.630 38.462 11.61 0.00 31.96 3.06
1621 1684 5.643348 TGATATCGGTTTCATGCATATGTCC 59.357 40.000 0.00 0.00 35.73 4.02
1622 1685 3.274095 TCGGTTTCATGCATATGTCCA 57.726 42.857 0.00 0.00 35.73 4.02
1639 1705 9.046296 CATATGTCCATCTTTTCTTACCAGTAC 57.954 37.037 0.00 0.00 0.00 2.73
1640 1706 6.428083 TGTCCATCTTTTCTTACCAGTACA 57.572 37.500 0.00 0.00 0.00 2.90
1641 1707 7.016153 TGTCCATCTTTTCTTACCAGTACAT 57.984 36.000 0.00 0.00 0.00 2.29
1642 1708 8.141298 TGTCCATCTTTTCTTACCAGTACATA 57.859 34.615 0.00 0.00 0.00 2.29
1655 1721 5.617252 ACCAGTACATATATTTTGGTCCGG 58.383 41.667 0.00 0.00 33.92 5.14
2031 2097 2.636893 ACAGAACCTGATGAAGCTCACT 59.363 45.455 0.45 0.00 35.18 3.41
2217 2286 1.337703 GCATCAATGGCGCCTTATCAA 59.662 47.619 29.70 6.08 0.00 2.57
2257 2326 3.694058 ATGGAGCAGCTTGGAGGCG 62.694 63.158 0.00 0.00 37.29 5.52
2280 2349 1.620739 GCACCTCCTCCATGCAGAGA 61.621 60.000 4.59 0.00 39.23 3.10
2465 2536 1.280710 ACCTTGGTACGGAATGCATCA 59.719 47.619 0.00 0.00 0.00 3.07
2484 2555 9.941325 ATGCATCAAAATGTGTATAAAGGAAAA 57.059 25.926 0.00 0.00 35.18 2.29
2529 2600 8.134202 AGTTTGCCTTAATTTGCTTAACCTAT 57.866 30.769 0.00 0.00 0.00 2.57
2534 2605 9.863845 TGCCTTAATTTGCTTAACCTATAAAAC 57.136 29.630 0.00 0.00 0.00 2.43
2601 2672 2.171003 GGGCAGTTAATTTGCTCCACT 58.829 47.619 12.74 0.00 41.27 4.00
2602 2673 3.010138 AGGGCAGTTAATTTGCTCCACTA 59.990 43.478 10.22 0.00 43.12 2.74
2603 2674 3.761752 GGGCAGTTAATTTGCTCCACTAA 59.238 43.478 12.74 0.00 41.27 2.24
2604 2675 4.402474 GGGCAGTTAATTTGCTCCACTAAT 59.598 41.667 12.74 0.00 41.27 1.73
2682 2753 8.306038 ACAAAGAAAAATCTAGCAATGCATACA 58.694 29.630 8.35 0.00 0.00 2.29
2683 2754 9.142515 CAAAGAAAAATCTAGCAATGCATACAA 57.857 29.630 8.35 0.00 0.00 2.41
2700 2774 1.334054 CAATGTCTTTTGCGCTCTGC 58.666 50.000 9.73 0.00 46.70 4.26
2786 2860 2.223479 GCTTCGAAGGTTTGCTTGTTGA 60.223 45.455 25.77 0.00 0.00 3.18
3186 3262 4.702131 GGCAATTGTATGTTGAGAGAACCT 59.298 41.667 7.40 0.00 0.00 3.50
3188 3264 5.634896 CAATTGTATGTTGAGAGAACCTGC 58.365 41.667 0.00 0.00 0.00 4.85
3211 3288 5.118203 GCAAGAAAATGCATGTTGAGAGAAC 59.882 40.000 6.90 0.00 45.70 3.01
3215 3292 6.373774 AGAAAATGCATGTTGAGAGAACTAGG 59.626 38.462 6.90 0.00 0.00 3.02
3216 3293 4.833478 ATGCATGTTGAGAGAACTAGGT 57.167 40.909 0.00 0.00 0.00 3.08
3217 3294 3.930336 TGCATGTTGAGAGAACTAGGTG 58.070 45.455 0.00 0.00 0.00 4.00
3218 3295 3.578282 TGCATGTTGAGAGAACTAGGTGA 59.422 43.478 0.00 0.00 0.00 4.02
3219 3296 4.223700 TGCATGTTGAGAGAACTAGGTGAT 59.776 41.667 0.00 0.00 0.00 3.06
3220 3297 4.569966 GCATGTTGAGAGAACTAGGTGATG 59.430 45.833 0.00 0.00 0.00 3.07
3221 3298 4.193826 TGTTGAGAGAACTAGGTGATGC 57.806 45.455 0.00 0.00 0.00 3.91
3222 3299 3.055819 TGTTGAGAGAACTAGGTGATGCC 60.056 47.826 0.00 0.00 37.58 4.40
3223 3300 2.111384 TGAGAGAACTAGGTGATGCCC 58.889 52.381 0.00 0.00 38.26 5.36
3224 3301 2.292521 TGAGAGAACTAGGTGATGCCCT 60.293 50.000 0.00 0.00 38.26 5.19
3225 3302 2.102252 GAGAGAACTAGGTGATGCCCTG 59.898 54.545 0.00 0.00 38.26 4.45
3226 3303 0.543749 AGAACTAGGTGATGCCCTGC 59.456 55.000 0.00 0.00 38.26 4.85
3227 3304 0.253044 GAACTAGGTGATGCCCTGCA 59.747 55.000 0.00 0.00 44.86 4.41
3228 3305 0.035056 AACTAGGTGATGCCCTGCAC 60.035 55.000 0.00 0.00 43.04 4.57
3229 3306 1.200760 ACTAGGTGATGCCCTGCACA 61.201 55.000 0.00 0.00 43.04 4.57
3230 3307 0.182061 CTAGGTGATGCCCTGCACAT 59.818 55.000 0.00 0.00 43.04 3.21
3231 3308 0.625316 TAGGTGATGCCCTGCACATT 59.375 50.000 0.00 0.00 43.04 2.71
3232 3309 0.625316 AGGTGATGCCCTGCACATTA 59.375 50.000 0.00 0.00 43.04 1.90
3233 3310 1.216175 AGGTGATGCCCTGCACATTAT 59.784 47.619 0.00 0.00 43.04 1.28
3234 3311 2.034124 GGTGATGCCCTGCACATTATT 58.966 47.619 0.00 0.00 43.04 1.40
3235 3312 2.223876 GGTGATGCCCTGCACATTATTG 60.224 50.000 0.00 0.00 43.04 1.90
3236 3313 1.409790 TGATGCCCTGCACATTATTGC 59.590 47.619 0.00 0.00 43.04 3.56
3248 3325 5.802064 GCACATTATTGCATGGATGTTTTG 58.198 37.500 6.61 0.00 42.49 2.44
3249 3326 5.728344 GCACATTATTGCATGGATGTTTTGC 60.728 40.000 6.61 4.99 42.49 3.68
3250 3327 5.351740 CACATTATTGCATGGATGTTTTGCA 59.648 36.000 6.61 0.00 44.12 4.08
3259 3336 8.734218 TGCATGGATGTTTTGCAATATATTTT 57.266 26.923 0.00 0.00 42.95 1.82
3260 3337 9.828039 TGCATGGATGTTTTGCAATATATTTTA 57.172 25.926 0.00 0.00 42.95 1.52
3302 3379 9.640952 ATGGAAAAATAGGAATATTCGGAGAAA 57.359 29.630 9.32 0.00 45.90 2.52
3303 3380 9.640952 TGGAAAAATAGGAATATTCGGAGAAAT 57.359 29.630 9.32 0.00 45.90 2.17
3320 3397 9.477484 TCGGAGAAATAATATGAGAGCTAAAAC 57.523 33.333 0.00 0.00 0.00 2.43
3321 3398 9.482627 CGGAGAAATAATATGAGAGCTAAAACT 57.517 33.333 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 41 2.163613 GCCTTACTTTATTTGCACCGCT 59.836 45.455 0.00 0.00 0.00 5.52
40 42 2.526077 GCCTTACTTTATTTGCACCGC 58.474 47.619 0.00 0.00 0.00 5.68
41 43 2.417239 TCGCCTTACTTTATTTGCACCG 59.583 45.455 0.00 0.00 0.00 4.94
42 44 4.632538 ATCGCCTTACTTTATTTGCACC 57.367 40.909 0.00 0.00 0.00 5.01
43 45 6.317910 CAAATCGCCTTACTTTATTTGCAC 57.682 37.500 0.00 0.00 32.61 4.57
101 103 3.454371 ACCTCTAATTCCATCGTTCCG 57.546 47.619 0.00 0.00 0.00 4.30
132 134 2.663196 GTGGGAGTCAGGGGAACG 59.337 66.667 0.00 0.00 0.00 3.95
155 157 0.951040 CCGTGCTCCAGTTTGGACTC 60.951 60.000 0.00 0.00 42.67 3.36
173 175 4.789807 TGTGGTAGAGTGGTAGACTATCC 58.210 47.826 0.00 0.00 33.83 2.59
322 329 8.862325 TGTATTATTCCTGTGTGATCTTTTGT 57.138 30.769 0.00 0.00 0.00 2.83
484 492 2.322355 AGAGTCCATGCACATGTAGC 57.678 50.000 9.63 5.65 37.11 3.58
501 509 7.040132 CCATGCTGATAGAATCACAGTACTAGA 60.040 40.741 0.00 0.00 35.06 2.43
523 531 4.183865 TCTTTACGAGAGCATTGACCATG 58.816 43.478 0.00 0.00 35.73 3.66
576 584 2.879907 CATGGGTTTGAGCTGGCG 59.120 61.111 0.00 0.00 0.00 5.69
650 658 0.321564 CGGTCCAAGATGCTCACCAA 60.322 55.000 0.00 0.00 0.00 3.67
668 676 2.750237 GGGCAGCAGGGTTAACCG 60.750 66.667 18.39 6.86 46.96 4.44
671 679 4.733542 GCGGGGCAGCAGGGTTAA 62.734 66.667 0.00 0.00 37.05 2.01
714 722 2.625639 AGGGAAGTGAAGAGGATGTGT 58.374 47.619 0.00 0.00 0.00 3.72
776 784 0.250553 CCCAAGGCAACGAGGTACAA 60.251 55.000 0.00 0.00 46.39 2.41
778 790 1.376812 CCCCAAGGCAACGAGGTAC 60.377 63.158 0.00 0.00 46.39 3.34
781 793 2.045926 CTCCCCAAGGCAACGAGG 60.046 66.667 0.00 0.00 46.39 4.63
790 804 2.677875 GCCTGGTTGCTCCCCAAG 60.678 66.667 0.00 0.00 33.21 3.61
812 826 1.002430 TGCTGCCTTTTGATCGAGTCT 59.998 47.619 0.00 0.00 0.00 3.24
814 828 1.446907 CTGCTGCCTTTTGATCGAGT 58.553 50.000 0.00 0.00 0.00 4.18
816 830 0.324614 TCCTGCTGCCTTTTGATCGA 59.675 50.000 0.00 0.00 0.00 3.59
817 831 0.731417 CTCCTGCTGCCTTTTGATCG 59.269 55.000 0.00 0.00 0.00 3.69
818 832 2.119801 TCTCCTGCTGCCTTTTGATC 57.880 50.000 0.00 0.00 0.00 2.92
819 833 2.822707 ATCTCCTGCTGCCTTTTGAT 57.177 45.000 0.00 0.00 0.00 2.57
820 834 2.592102 AATCTCCTGCTGCCTTTTGA 57.408 45.000 0.00 0.00 0.00 2.69
868 883 6.174720 TCCTCATCATCCATAGTGGTAAAC 57.825 41.667 0.00 0.00 39.03 2.01
875 896 5.467738 TGTACCTTCCTCATCATCCATAGT 58.532 41.667 0.00 0.00 0.00 2.12
881 902 6.013379 TCCTCTATGTACCTTCCTCATCATC 58.987 44.000 0.00 0.00 0.00 2.92
897 918 7.550551 TCACATTAACAGCTTCTTTCCTCTATG 59.449 37.037 0.00 0.00 0.00 2.23
908 929 3.620821 GCTCCTCTCACATTAACAGCTTC 59.379 47.826 0.00 0.00 0.00 3.86
910 931 2.836981 AGCTCCTCTCACATTAACAGCT 59.163 45.455 0.00 0.00 0.00 4.24
933 954 5.360714 AGAAGAAGAAGCAACACCAAATCAA 59.639 36.000 0.00 0.00 0.00 2.57
943 964 4.489810 TCGATCTGAGAAGAAGAAGCAAC 58.510 43.478 0.00 0.00 0.00 4.17
996 1052 1.227645 GCCACTCGGATGCATGCTA 60.228 57.895 20.33 4.29 0.00 3.49
1098 1154 4.588951 ACGTCAAGATCTATGGCCTCATAA 59.411 41.667 3.32 0.00 35.64 1.90
1224 1281 9.915629 GATCGAGTTAATTAATACTCCATCAGT 57.084 33.333 15.54 0.00 38.26 3.41
1225 1282 9.066939 CGATCGAGTTAATTAATACTCCATCAG 57.933 37.037 10.26 11.40 38.27 2.90
1232 1289 7.378995 GTCAGCACGATCGAGTTAATTAATACT 59.621 37.037 24.34 0.00 0.00 2.12
1269 1327 0.322008 TGCCATTACATGACACCGCA 60.322 50.000 0.00 0.00 0.00 5.69
1270 1328 1.024271 ATGCCATTACATGACACCGC 58.976 50.000 0.00 0.00 0.00 5.68
1313 1376 4.379243 CACTCGTTCTGCGGCCCT 62.379 66.667 0.00 0.00 41.72 5.19
1559 1622 1.351017 CTTTTGCCTACCTGGACCTCA 59.649 52.381 0.00 0.00 38.35 3.86
1578 1641 2.086869 CAGTTTGTGGCCGATGAATCT 58.913 47.619 0.00 0.00 0.00 2.40
1579 1642 2.083774 TCAGTTTGTGGCCGATGAATC 58.916 47.619 0.00 0.00 0.00 2.52
1587 1650 2.038387 ACCGATATCAGTTTGTGGCC 57.962 50.000 3.12 0.00 0.00 5.36
1589 1652 5.572211 CATGAAACCGATATCAGTTTGTGG 58.428 41.667 19.36 5.54 36.36 4.17
1600 1663 4.967036 TGGACATATGCATGAAACCGATA 58.033 39.130 10.16 0.00 35.96 2.92
1602 1665 3.274095 TGGACATATGCATGAAACCGA 57.726 42.857 10.16 0.00 35.96 4.69
1604 1667 5.779529 AAGATGGACATATGCATGAAACC 57.220 39.130 10.16 8.50 36.94 3.27
1605 1668 7.486647 AGAAAAGATGGACATATGCATGAAAC 58.513 34.615 10.16 0.00 36.94 2.78
1606 1669 7.649533 AGAAAAGATGGACATATGCATGAAA 57.350 32.000 10.16 0.00 36.94 2.69
1608 1671 7.229306 GGTAAGAAAAGATGGACATATGCATGA 59.771 37.037 10.16 0.00 36.94 3.07
1610 1673 7.062322 TGGTAAGAAAAGATGGACATATGCAT 58.938 34.615 3.79 3.79 40.05 3.96
1611 1674 6.422333 TGGTAAGAAAAGATGGACATATGCA 58.578 36.000 1.58 0.00 0.00 3.96
1612 1675 6.543831 ACTGGTAAGAAAAGATGGACATATGC 59.456 38.462 1.58 0.00 0.00 3.14
1613 1676 9.046296 GTACTGGTAAGAAAAGATGGACATATG 57.954 37.037 0.00 0.00 0.00 1.78
1614 1677 8.768397 TGTACTGGTAAGAAAAGATGGACATAT 58.232 33.333 0.00 0.00 0.00 1.78
1615 1678 8.141298 TGTACTGGTAAGAAAAGATGGACATA 57.859 34.615 0.00 0.00 0.00 2.29
1616 1679 7.016153 TGTACTGGTAAGAAAAGATGGACAT 57.984 36.000 0.00 0.00 0.00 3.06
1617 1680 6.428083 TGTACTGGTAAGAAAAGATGGACA 57.572 37.500 0.00 0.00 0.00 4.02
1639 1705 5.335897 CCTGCATTCCGGACCAAAATATATG 60.336 44.000 1.83 2.70 0.00 1.78
1640 1706 4.766891 CCTGCATTCCGGACCAAAATATAT 59.233 41.667 1.83 0.00 0.00 0.86
1641 1707 4.141287 CCTGCATTCCGGACCAAAATATA 58.859 43.478 1.83 0.00 0.00 0.86
1642 1708 2.958355 CCTGCATTCCGGACCAAAATAT 59.042 45.455 1.83 0.00 0.00 1.28
1645 1711 0.111446 TCCTGCATTCCGGACCAAAA 59.889 50.000 1.83 0.00 0.00 2.44
1655 1721 1.030457 CCAGCCATCTTCCTGCATTC 58.970 55.000 0.00 0.00 0.00 2.67
1730 1796 4.580551 CGTCGTACCCCGCCATCC 62.581 72.222 0.00 0.00 36.19 3.51
1869 1935 0.896226 AGGAAGGGAAGTCGTAGTGC 59.104 55.000 0.00 0.00 0.00 4.40
1870 1936 2.415625 CGAAGGAAGGGAAGTCGTAGTG 60.416 54.545 0.00 0.00 0.00 2.74
1871 1937 1.817447 CGAAGGAAGGGAAGTCGTAGT 59.183 52.381 0.00 0.00 0.00 2.73
1974 2040 2.747460 GAGCTCATGGCAACGGCA 60.747 61.111 9.40 0.00 44.79 5.69
1980 2046 3.995219 CTCGTGCGAGCTCATGGCA 62.995 63.158 15.40 12.59 44.79 4.92
2187 2256 1.586303 CATTGATGCTGCTGCTGCG 60.586 57.895 23.38 7.14 43.34 5.18
2188 2257 1.226974 CCATTGATGCTGCTGCTGC 60.227 57.895 22.51 22.51 40.48 5.25
2189 2258 1.226974 GCCATTGATGCTGCTGCTG 60.227 57.895 17.00 6.00 40.48 4.41
2257 2326 2.124403 CATGGAGGAGGTGCTGCC 60.124 66.667 0.00 0.00 37.58 4.85
2484 2555 7.250569 CAAACTCGAAGCCACATATACAAAAT 58.749 34.615 0.00 0.00 0.00 1.82
2529 2600 8.943002 GCTAAACAATACTAGCTCCAAGTTTTA 58.057 33.333 0.00 0.00 38.01 1.52
2534 2605 7.265673 TGTAGCTAAACAATACTAGCTCCAAG 58.734 38.462 6.86 0.00 46.21 3.61
2560 2631 5.956563 GCCCTACCTGCTCTAATAGGTATAA 59.043 44.000 3.82 0.00 45.70 0.98
2682 2753 1.068748 CAGCAGAGCGCAAAAGACATT 60.069 47.619 11.47 0.00 46.13 2.71
2683 2754 0.520404 CAGCAGAGCGCAAAAGACAT 59.480 50.000 11.47 0.00 46.13 3.06
2700 2774 0.392193 CAACCAGGCTAGCTCCACAG 60.392 60.000 15.72 0.64 0.00 3.66
2786 2860 8.995027 ACTCTCTCTTCACACTCATATATCTT 57.005 34.615 0.00 0.00 0.00 2.40
3095 3171 4.010667 TCATGCATGCTGCTCATATGTA 57.989 40.909 22.25 0.00 45.31 2.29
3096 3172 2.858745 TCATGCATGCTGCTCATATGT 58.141 42.857 22.25 0.00 45.31 2.29
3097 3173 3.762779 CATCATGCATGCTGCTCATATG 58.237 45.455 22.25 13.22 45.31 1.78
3188 3264 6.444633 AGTTCTCTCAACATGCATTTTCTTG 58.555 36.000 0.00 0.00 0.00 3.02
3211 3288 0.182061 ATGTGCAGGGCATCACCTAG 59.818 55.000 0.00 0.00 41.91 3.02
3215 3292 2.800629 GCAATAATGTGCAGGGCATCAC 60.801 50.000 0.00 0.00 44.29 3.06
3216 3293 1.409790 GCAATAATGTGCAGGGCATCA 59.590 47.619 0.00 0.00 44.29 3.07
3217 3294 2.144482 GCAATAATGTGCAGGGCATC 57.856 50.000 0.00 0.00 44.29 3.91
3225 3302 5.728344 GCAAAACATCCATGCAATAATGTGC 60.728 40.000 10.75 7.53 45.15 4.57
3226 3303 5.351740 TGCAAAACATCCATGCAATAATGTG 59.648 36.000 10.75 0.00 46.23 3.21
3227 3304 5.489249 TGCAAAACATCCATGCAATAATGT 58.511 33.333 0.00 0.00 46.23 2.71
3276 3353 9.640952 TTTCTCCGAATATTCCTATTTTTCCAT 57.359 29.630 9.87 0.00 0.00 3.41
3277 3354 9.640952 ATTTCTCCGAATATTCCTATTTTTCCA 57.359 29.630 9.87 0.00 0.00 3.53
3294 3371 9.477484 GTTTTAGCTCTCATATTATTTCTCCGA 57.523 33.333 0.00 0.00 0.00 4.55
3295 3372 9.482627 AGTTTTAGCTCTCATATTATTTCTCCG 57.517 33.333 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.