Multiple sequence alignment - TraesCS2B01G197800

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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 TraesCS2B01G197800 chr2B 100.000 4114 0 0 1 4114 175455899 175460012 0.000000e+00 7598.0
1 TraesCS2B01G197800 chr2A 94.346 4139 179 21 1 4114 126992671 126996779 0.000000e+00 6296.0
2 TraesCS2B01G197800 chr6D 89.542 306 29 2 14 319 454889538 454889236 6.450000e-103 385.0
3 TraesCS2B01G197800 chr6D 89.216 306 30 2 14 319 454923093 454922791 3.000000e-101 379.0
4 TraesCS2B01G197800 chr6D 91.549 71 5 1 394 463 62497433 62497363 3.380000e-16 97.1
5 TraesCS2B01G197800 chr3D 89.474 304 29 2 16 319 79555400 79555100 8.350000e-102 381.0
6 TraesCS2B01G197800 chr3D 89.180 305 29 3 16 319 527520241 527520542 1.080000e-100 377.0
7 TraesCS2B01G197800 chr3D 90.541 74 6 1 394 466 474550389 474550316 3.380000e-16 97.1
8 TraesCS2B01G197800 chr6A 88.925 307 32 1 13 319 422775945 422776249 1.080000e-100 377.0
9 TraesCS2B01G197800 chr3A 89.180 305 30 2 16 319 111839796 111840098 1.080000e-100 377.0
10 TraesCS2B01G197800 chr3A 88.889 306 30 3 15 319 55840501 55840199 1.400000e-99 374.0
11 TraesCS2B01G197800 chr4A 86.866 335 30 12 2 328 615099541 615099213 3.020000e-96 363.0
12 TraesCS2B01G197800 chr4A 92.857 70 5 0 394 463 648377589 648377658 7.280000e-18 102.0
13 TraesCS2B01G197800 chr1B 93.151 73 5 0 394 466 23597202 23597130 1.560000e-19 108.0
14 TraesCS2B01G197800 chr1B 93.151 73 5 0 394 466 23895978 23895906 1.560000e-19 108.0
15 TraesCS2B01G197800 chr2D 92.958 71 4 1 394 463 629978282 629978352 7.280000e-18 102.0
16 TraesCS2B01G197800 chr7A 92.754 69 5 0 395 463 12904330 12904398 2.620000e-17 100.0
17 TraesCS2B01G197800 chr7D 91.549 71 5 1 394 463 396381199 396381269 3.380000e-16 97.1


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 TraesCS2B01G197800 chr2B 175455899 175460012 4113 False 7598 7598 100.000 1 4114 1 chr2B.!!$F1 4113
1 TraesCS2B01G197800 chr2A 126992671 126996779 4108 False 6296 6296 94.346 1 4114 1 chr2A.!!$F1 4113

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
218 219 0.322975 ATGATATGCCGGCTCAGTCC 59.677 55.000 29.7 12.19 0.00 3.85 F
260 261 1.131826 GGTGTGCGTGTATGCGTTC 59.868 57.895 0.0 0.00 37.81 3.95 F
1053 1055 0.684479 TCGTCACATCCCCTCCTCTG 60.684 60.000 0.0 0.00 0.00 3.35 F
2852 2876 0.034337 GACGTCTTGGGCCTTACACA 59.966 55.000 8.7 0.00 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1049 1051 0.108709 GAGGTCAGTCAGCAGCAGAG 60.109 60.0 0.0 0.00 0.0 3.35 R
1078 1080 0.539438 ACATTGTGCGGTGGTGGATT 60.539 50.0 0.0 0.00 0.0 3.01 R
2918 2942 0.976641 TATGGCGATGGATCCCTGAC 59.023 55.0 9.9 1.09 0.0 3.51 R
3719 3743 1.634702 CTGAGCGAAGAAGGTAGCAC 58.365 55.0 0.0 0.00 0.0 4.40 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
25 26 1.808411 ATCAATCACGCGAACCAACT 58.192 45.000 15.93 0.00 0.00 3.16
51 52 1.285280 TGGGATGGTTAGGTGGACAG 58.715 55.000 0.00 0.00 0.00 3.51
60 61 3.105283 GTTAGGTGGACAGTGGTATCCT 58.895 50.000 0.00 0.00 35.86 3.24
63 64 1.482593 GGTGGACAGTGGTATCCTCAG 59.517 57.143 0.00 0.00 35.86 3.35
68 69 1.135094 CAGTGGTATCCTCAGCCCAT 58.865 55.000 0.00 0.00 0.00 4.00
90 91 3.366052 AGGGTTTAATTCCTGATGCGT 57.634 42.857 0.00 0.00 31.11 5.24
92 93 2.479560 GGGTTTAATTCCTGATGCGTGC 60.480 50.000 0.00 0.00 0.00 5.34
102 103 3.947196 TCCTGATGCGTGCATTTATTCTT 59.053 39.130 8.98 0.00 36.70 2.52
122 123 8.986477 ATTCTTGATTTATTTCAGGTTTTCCG 57.014 30.769 0.00 0.00 46.35 4.30
126 127 2.476126 TATTTCAGGTTTTCCGGCGA 57.524 45.000 9.30 0.00 46.35 5.54
130 131 0.458889 TCAGGTTTTCCGGCGATACG 60.459 55.000 9.30 0.00 46.35 3.06
142 143 2.006772 CGATACGCTTTCAGTGGGC 58.993 57.895 0.00 0.00 0.00 5.36
176 177 3.379372 AGTCAACTATACGAAGCGCCTAA 59.621 43.478 2.29 0.00 0.00 2.69
218 219 0.322975 ATGATATGCCGGCTCAGTCC 59.677 55.000 29.70 12.19 0.00 3.85
238 239 1.457643 TCGGAGGTGCTCATAGGGG 60.458 63.158 0.00 0.00 31.08 4.79
241 242 1.343069 GGAGGTGCTCATAGGGGTAG 58.657 60.000 0.00 0.00 31.08 3.18
253 254 2.285024 GGGGTAGGGTGTGCGTGTA 61.285 63.158 0.00 0.00 0.00 2.90
260 261 1.131826 GGTGTGCGTGTATGCGTTC 59.868 57.895 0.00 0.00 37.81 3.95
264 265 2.092995 GTGTGCGTGTATGCGTTCATAA 59.907 45.455 0.00 0.00 36.96 1.90
278 279 3.555956 CGTTCATAAGGGTGAGTGTATGC 59.444 47.826 0.00 0.00 0.00 3.14
280 281 1.867233 CATAAGGGTGAGTGTATGCGC 59.133 52.381 0.00 0.00 0.00 6.09
339 340 3.656559 AGCAAAATCAATCACAACTGGC 58.343 40.909 0.00 0.00 0.00 4.85
433 434 9.606631 AGACTTTATTTCTCATAGAATGGTCAC 57.393 33.333 0.00 0.00 33.67 3.67
552 553 8.043710 CACAGGGGGATAATTGAATAGAGATAC 58.956 40.741 0.00 0.00 0.00 2.24
571 572 8.325046 AGAGATACTAAAGATCCAAAAGCAAGT 58.675 33.333 0.00 0.00 0.00 3.16
572 573 8.273780 AGATACTAAAGATCCAAAAGCAAGTG 57.726 34.615 0.00 0.00 0.00 3.16
595 596 6.038714 GTGTATCTGCTCCCAATAAAAAGAGG 59.961 42.308 0.00 0.00 0.00 3.69
647 648 3.270027 GCACATAGCACAGTTGTATGGA 58.730 45.455 4.57 0.00 44.79 3.41
648 649 3.879295 GCACATAGCACAGTTGTATGGAT 59.121 43.478 4.57 0.00 44.79 3.41
658 659 2.628657 AGTTGTATGGATCCGTAGAGGC 59.371 50.000 14.27 9.68 40.77 4.70
677 678 2.835764 GGCCCCGTATATTGAGGACATA 59.164 50.000 0.00 0.00 0.00 2.29
763 765 6.915349 AGAGACGTGCCATAATTATCTCTAC 58.085 40.000 9.68 1.46 39.64 2.59
791 793 4.135306 AGATTATCATCACTTGGCAGCAG 58.865 43.478 0.00 0.00 0.00 4.24
842 844 7.715657 TCATGGTTGTTCATCATTAAATAGGC 58.284 34.615 0.00 0.00 0.00 3.93
861 863 1.468054 GCAACATCAGCGACCAAATCC 60.468 52.381 0.00 0.00 0.00 3.01
905 907 9.991906 ATTTTCAGACATCATTTGTGAGAATTT 57.008 25.926 0.00 0.00 39.18 1.82
951 953 4.697756 TTCCGCTTGAGGCCACCG 62.698 66.667 5.01 0.00 37.74 4.94
973 975 4.819761 TGCACTCATCTCCGGCGC 62.820 66.667 0.00 0.00 0.00 6.53
1011 1013 2.451294 ATCCCCATGCTCCTCCCC 60.451 66.667 0.00 0.00 0.00 4.81
1012 1014 4.843331 TCCCCATGCTCCTCCCCC 62.843 72.222 0.00 0.00 0.00 5.40
1016 1018 3.801997 CATGCTCCTCCCCCGCTT 61.802 66.667 0.00 0.00 0.00 4.68
1017 1019 2.040884 ATGCTCCTCCCCCGCTTA 60.041 61.111 0.00 0.00 0.00 3.09
1018 1020 2.444256 ATGCTCCTCCCCCGCTTAC 61.444 63.158 0.00 0.00 0.00 2.34
1019 1021 4.222847 GCTCCTCCCCCGCTTACG 62.223 72.222 0.00 0.00 39.67 3.18
1049 1051 1.258445 ACAGTCGTCACATCCCCTCC 61.258 60.000 0.00 0.00 0.00 4.30
1053 1055 0.684479 TCGTCACATCCCCTCCTCTG 60.684 60.000 0.00 0.00 0.00 3.35
1078 1080 0.452184 GACTGACCTCGAGCGAATCA 59.548 55.000 6.99 6.81 0.00 2.57
1089 1091 0.744414 AGCGAATCAATCCACCACCG 60.744 55.000 0.00 0.00 0.00 4.94
1091 1093 1.024046 CGAATCAATCCACCACCGCA 61.024 55.000 0.00 0.00 0.00 5.69
1145 1147 1.270893 GGAGAAGAAGGTTGCCTCGTT 60.271 52.381 0.00 0.00 30.89 3.85
1152 1154 1.538047 AGGTTGCCTCGTTAGTCGTA 58.462 50.000 0.00 0.00 40.80 3.43
1153 1155 1.471684 AGGTTGCCTCGTTAGTCGTAG 59.528 52.381 0.00 0.00 40.80 3.51
1160 1162 2.008329 CTCGTTAGTCGTAGGAGCAGT 58.992 52.381 0.00 0.00 40.80 4.40
1191 1193 0.912486 AGATTTTGGGGAGGAGACGG 59.088 55.000 0.00 0.00 0.00 4.79
1196 1198 1.596006 TTGGGGAGGAGACGGGGATA 61.596 60.000 0.00 0.00 0.00 2.59
1198 1200 1.909287 GGGAGGAGACGGGGATAGC 60.909 68.421 0.00 0.00 0.00 2.97
1235 1237 5.592688 CCAACAACGGGAAAACCTATATGAT 59.407 40.000 0.00 0.00 36.97 2.45
1261 1263 1.124116 GCGTCAAATTTTCGCGCAAAT 59.876 42.857 10.98 10.98 46.23 2.32
1265 1267 2.097007 TCAAATTTTCGCGCAAATGCAC 60.097 40.909 17.16 0.00 42.21 4.57
1273 1275 3.846754 GCAAATGCACAGGCGAAC 58.153 55.556 0.00 0.00 45.35 3.95
1331 1333 2.282180 GAGGCAGCCGGTTTTGGA 60.282 61.111 5.55 0.00 0.00 3.53
1343 1345 2.035449 CGGTTTTGGAAAGAAGGTTCCC 59.965 50.000 1.65 0.00 45.67 3.97
1667 1671 2.898705 ACATTTTCCAAAAAGTGCGCA 58.101 38.095 5.66 5.66 35.99 6.09
1679 1683 2.977405 AGTGCGCAGAAGATGAAAAC 57.023 45.000 12.22 0.00 0.00 2.43
1785 1789 3.486383 TCCAAATTTTGCTCGGAGTTCT 58.514 40.909 6.90 0.00 0.00 3.01
1795 1799 4.062991 TGCTCGGAGTTCTAAAAAGTTCC 58.937 43.478 6.90 0.00 0.00 3.62
1923 1927 0.181350 GGGCTCCCGAATCTGTCATT 59.819 55.000 0.00 0.00 0.00 2.57
1926 1930 2.356069 GGCTCCCGAATCTGTCATTTTC 59.644 50.000 0.00 0.00 0.00 2.29
1948 1954 9.899661 TTTTCGGGAGAGAATAGAAAAATATGA 57.100 29.630 0.00 0.00 41.75 2.15
1961 1967 7.016361 AGAAAAATATGAATACGCTGTGGTC 57.984 36.000 0.00 0.00 0.00 4.02
2203 2209 4.555709 TGCGGCAGTTTCGTGGGT 62.556 61.111 0.00 0.00 0.00 4.51
2328 2334 0.596082 CGCAGGTTTGGTTCGGAAAT 59.404 50.000 0.00 0.00 0.00 2.17
2443 2467 1.271982 ACCTCTAACTGCTCCGAGACA 60.272 52.381 0.00 0.00 0.00 3.41
2475 2499 2.177016 AGCCAACCTTTTCCTGGTAACT 59.823 45.455 0.00 0.00 36.69 2.24
2580 2604 6.940298 TCGGAGAAACAATATCTTCTTTTGGT 59.060 34.615 0.00 0.00 32.01 3.67
2594 2618 7.083858 TCTTCTTTTGGTAAATGCTTCGATTG 58.916 34.615 0.00 0.00 0.00 2.67
2621 2645 6.757947 ACCATGAATTTGCTGCAATTACATAC 59.242 34.615 16.77 4.90 0.00 2.39
2622 2646 6.982141 CCATGAATTTGCTGCAATTACATACT 59.018 34.615 16.77 0.00 0.00 2.12
2623 2647 8.136800 CCATGAATTTGCTGCAATTACATACTA 58.863 33.333 16.77 0.00 0.00 1.82
2680 2704 9.431887 GTTGTTGACAAAGATCATACTACCTTA 57.568 33.333 0.00 0.00 37.63 2.69
2852 2876 0.034337 GACGTCTTGGGCCTTACACA 59.966 55.000 8.70 0.00 0.00 3.72
2873 2897 2.429610 ACCATGGCTTCAGATTGCATTC 59.570 45.455 13.04 0.16 0.00 2.67
2918 2942 7.810658 ACTATCTGTTGCTGTAAAGAAATGTG 58.189 34.615 0.00 0.00 0.00 3.21
2922 2946 5.820131 TGTTGCTGTAAAGAAATGTGTCAG 58.180 37.500 0.00 0.00 0.00 3.51
2971 2995 1.069432 GCGGCATATTCATGTGCTCTG 60.069 52.381 8.25 1.42 43.38 3.35
3045 3069 6.218019 CAACTTCCTTCTCATTTTGCATTGA 58.782 36.000 0.00 0.00 0.00 2.57
3095 3119 6.582636 CCTTCCAATGTTACTGCAGATAGTA 58.417 40.000 23.35 0.00 32.19 1.82
3184 3208 1.520342 GACTCCAGCCGATGCAGTC 60.520 63.158 0.00 0.00 41.13 3.51
3244 3268 1.736681 GCTGCTGTCTTCAATCAGTCC 59.263 52.381 0.00 0.00 34.57 3.85
3247 3271 2.009042 GCTGTCTTCAATCAGTCCCCG 61.009 57.143 0.00 0.00 34.57 5.73
3249 3273 0.744771 GTCTTCAATCAGTCCCCGCC 60.745 60.000 0.00 0.00 0.00 6.13
3318 3342 5.114780 CACTCATCTTCTACCCTGTTCATG 58.885 45.833 0.00 0.00 0.00 3.07
3325 3349 6.250711 TCTTCTACCCTGTTCATGTACTACA 58.749 40.000 4.01 0.00 0.00 2.74
3415 3439 2.093890 TGCACCATAATGTTGCTCCAG 58.906 47.619 3.64 0.00 0.00 3.86
3510 3534 0.098376 GCTTGCTTCCAGATGCTTCG 59.902 55.000 7.02 0.00 33.23 3.79
3527 3551 2.736144 TCGTAGTTCATCACCCACAC 57.264 50.000 0.00 0.00 0.00 3.82
3530 3554 2.699954 GTAGTTCATCACCCACACAGG 58.300 52.381 0.00 0.00 37.03 4.00
3598 3622 6.427150 CAATTACCTCGATCCATTTTTACCG 58.573 40.000 0.00 0.00 0.00 4.02
3631 3655 5.574891 TGGCTTATGCATACGAAATGTTT 57.425 34.783 14.00 0.00 41.91 2.83
3748 3772 2.437413 TCTTCGCTCAGCTCTTGTCTA 58.563 47.619 0.00 0.00 0.00 2.59
3773 3797 7.920160 TTGTGATGTGCTCAGTTCAATTATA 57.080 32.000 0.00 0.00 33.51 0.98
3892 3916 4.226168 CCTTACTTCCCTCCACATTCTTCT 59.774 45.833 0.00 0.00 0.00 2.85
3935 3959 6.904626 ACCTGCAAAAGAGAACATATAGGAT 58.095 36.000 0.00 0.00 0.00 3.24
4057 4081 6.611613 TGATATTTATTGGGCCACAACAAA 57.388 33.333 5.23 8.94 42.94 2.83
4081 4105 8.893563 AAATCCAAAAGTAATCTATCCACCAA 57.106 30.769 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.010125 CCACAAGTTGGTTCGCGTG 60.010 57.895 5.77 0.00 41.10 5.34
25 26 1.783979 ACCTAACCATCCCAACCACAA 59.216 47.619 0.00 0.00 0.00 3.33
39 40 3.105283 AGGATACCACTGTCCACCTAAC 58.895 50.000 0.00 0.00 36.96 2.34
51 52 1.071385 CTGATGGGCTGAGGATACCAC 59.929 57.143 0.00 0.00 35.52 4.16
79 80 3.947196 AGAATAAATGCACGCATCAGGAA 59.053 39.130 4.73 0.00 35.31 3.36
85 86 8.876275 AATAAATCAAGAATAAATGCACGCAT 57.124 26.923 0.00 0.00 38.46 4.73
102 103 4.380023 CGCCGGAAAACCTGAAATAAATCA 60.380 41.667 5.05 0.00 0.00 2.57
126 127 4.201951 CGCCCACTGAAAGCGTAT 57.798 55.556 0.00 0.00 44.65 3.06
130 131 2.035442 GTCTCCGCCCACTGAAAGC 61.035 63.158 0.00 0.00 37.60 3.51
142 143 2.135664 AGTTGACTGAAACGTCTCCG 57.864 50.000 0.00 0.00 40.83 4.63
152 153 2.479049 GGCGCTTCGTATAGTTGACTGA 60.479 50.000 7.64 0.00 0.00 3.41
165 166 0.389948 AAGTCACCTTAGGCGCTTCG 60.390 55.000 7.64 0.00 0.00 3.79
176 177 4.041198 TCTTGGGATTTTACGAAGTCACCT 59.959 41.667 0.00 0.00 43.93 4.00
194 195 1.271001 TGAGCCGGCATATCATCTTGG 60.271 52.381 31.54 0.00 0.00 3.61
218 219 1.467678 CCCTATGAGCACCTCCGAGG 61.468 65.000 13.31 13.31 42.49 4.63
238 239 1.418342 CGCATACACGCACACCCTAC 61.418 60.000 0.00 0.00 0.00 3.18
241 242 2.235536 GAACGCATACACGCACACCC 62.236 60.000 0.00 0.00 36.19 4.61
253 254 2.027192 ACACTCACCCTTATGAACGCAT 60.027 45.455 0.00 0.00 38.54 4.73
260 261 1.867233 GCGCATACACTCACCCTTATG 59.133 52.381 0.30 0.00 0.00 1.90
264 265 2.167398 AACGCGCATACACTCACCCT 62.167 55.000 5.73 0.00 0.00 4.34
280 281 0.447260 CGCACGCGCTCATATAAACG 60.447 55.000 5.73 0.00 35.30 3.60
295 296 4.782252 TTTTAACACAGTACAGACGCAC 57.218 40.909 0.00 0.00 0.00 5.34
319 320 3.391965 TGCCAGTTGTGATTGATTTTGC 58.608 40.909 0.00 0.00 0.00 3.68
320 321 5.987777 TTTGCCAGTTGTGATTGATTTTG 57.012 34.783 0.00 0.00 0.00 2.44
321 322 6.373774 TGTTTTTGCCAGTTGTGATTGATTTT 59.626 30.769 0.00 0.00 0.00 1.82
356 357 0.460987 AAGATGCCGCTTTCCTCTCG 60.461 55.000 0.00 0.00 0.00 4.04
414 415 8.991783 AATGATGTGACCATTCTATGAGAAAT 57.008 30.769 0.00 0.00 37.82 2.17
463 464 9.757227 AATAGAATGAAGTGTAATAGAGAGCAC 57.243 33.333 0.00 0.00 0.00 4.40
518 519 1.006813 TATCCCCCTGTGGTTGCATT 58.993 50.000 0.00 0.00 0.00 3.56
519 520 1.006813 TTATCCCCCTGTGGTTGCAT 58.993 50.000 0.00 0.00 0.00 3.96
552 553 8.180267 CAGATACACTTGCTTTTGGATCTTTAG 58.820 37.037 4.52 0.00 39.99 1.85
571 572 6.122277 CCTCTTTTTATTGGGAGCAGATACA 58.878 40.000 0.00 0.00 0.00 2.29
572 573 6.038714 CACCTCTTTTTATTGGGAGCAGATAC 59.961 42.308 0.00 0.00 0.00 2.24
595 596 8.331022 CAATCTGCTACATTTAGTATGACACAC 58.669 37.037 0.00 0.00 30.93 3.82
610 611 2.580962 TGTGCCAAACAATCTGCTACA 58.419 42.857 0.00 0.00 35.24 2.74
639 640 1.968493 GGCCTCTACGGATCCATACAA 59.032 52.381 13.41 0.00 33.16 2.41
647 648 0.700564 TATACGGGGCCTCTACGGAT 59.299 55.000 0.00 6.84 35.07 4.18
648 649 0.700564 ATATACGGGGCCTCTACGGA 59.299 55.000 0.00 0.00 33.16 4.69
658 659 4.876107 GCAATATGTCCTCAATATACGGGG 59.124 45.833 0.00 0.00 0.00 5.73
730 731 1.141254 TGGCACGTCTCTTTTTGGGTA 59.859 47.619 0.00 0.00 0.00 3.69
731 732 0.106918 TGGCACGTCTCTTTTTGGGT 60.107 50.000 0.00 0.00 0.00 4.51
734 735 7.697691 AGATAATTATGGCACGTCTCTTTTTG 58.302 34.615 1.78 0.00 0.00 2.44
740 741 6.915349 AGTAGAGATAATTATGGCACGTCTC 58.085 40.000 1.78 2.50 0.00 3.36
741 742 6.717540 AGAGTAGAGATAATTATGGCACGTCT 59.282 38.462 1.78 0.00 0.00 4.18
742 743 6.915349 AGAGTAGAGATAATTATGGCACGTC 58.085 40.000 1.78 0.00 0.00 4.34
743 744 6.490381 TGAGAGTAGAGATAATTATGGCACGT 59.510 38.462 1.78 0.00 0.00 4.49
763 765 6.053650 TGCCAAGTGATGATAATCTTGAGAG 58.946 40.000 0.00 0.00 39.39 3.20
842 844 1.811965 TGGATTTGGTCGCTGATGTTG 59.188 47.619 0.00 0.00 0.00 3.33
905 907 7.433131 CGCGGTAGAGTGTGATAAAAGTTAATA 59.567 37.037 0.00 0.00 0.00 0.98
906 908 6.255020 CGCGGTAGAGTGTGATAAAAGTTAAT 59.745 38.462 0.00 0.00 0.00 1.40
909 911 3.924686 CGCGGTAGAGTGTGATAAAAGTT 59.075 43.478 0.00 0.00 0.00 2.66
951 953 1.812922 CGGAGATGAGTGCAGTGGC 60.813 63.158 0.00 0.00 41.68 5.01
973 975 0.250038 ACGCATCAGATTGATCCCCG 60.250 55.000 0.00 0.00 34.28 5.73
1012 1014 4.728102 TGGCGACCACCGTAAGCG 62.728 66.667 0.00 0.00 41.15 4.68
1013 1015 2.357760 TTGGCGACCACCGTAAGC 60.358 61.111 0.00 0.00 41.15 3.09
1014 1016 1.289109 CTGTTGGCGACCACCGTAAG 61.289 60.000 1.61 0.00 41.15 2.34
1015 1017 1.301087 CTGTTGGCGACCACCGTAA 60.301 57.895 1.61 0.00 41.15 3.18
1016 1018 2.340809 CTGTTGGCGACCACCGTA 59.659 61.111 1.61 0.00 41.15 4.02
1017 1019 3.802418 GACTGTTGGCGACCACCGT 62.802 63.158 1.61 0.00 41.15 4.83
1018 1020 3.041940 GACTGTTGGCGACCACCG 61.042 66.667 1.61 0.00 42.21 4.94
1019 1021 3.041940 CGACTGTTGGCGACCACC 61.042 66.667 1.61 0.00 30.78 4.61
1020 1022 2.279918 ACGACTGTTGGCGACCAC 60.280 61.111 1.61 0.00 30.78 4.16
1049 1051 0.108709 GAGGTCAGTCAGCAGCAGAG 60.109 60.000 0.00 0.00 0.00 3.35
1053 1055 1.153862 CTCGAGGTCAGTCAGCAGC 60.154 63.158 3.91 0.00 0.00 5.25
1078 1080 0.539438 ACATTGTGCGGTGGTGGATT 60.539 50.000 0.00 0.00 0.00 3.01
1114 1116 0.836400 TTCTTCTCCCCCTTCGCACT 60.836 55.000 0.00 0.00 0.00 4.40
1145 1147 2.228059 GGCATACTGCTCCTACGACTA 58.772 52.381 0.00 0.00 44.28 2.59
1152 1154 1.961180 GACACCGGCATACTGCTCCT 61.961 60.000 0.00 0.00 44.28 3.69
1153 1155 1.521681 GACACCGGCATACTGCTCC 60.522 63.158 0.00 0.00 44.28 4.70
1160 1162 2.364632 CCAAAATCTGACACCGGCATA 58.635 47.619 0.00 0.00 0.00 3.14
1167 1169 2.305927 TCTCCTCCCCAAAATCTGACAC 59.694 50.000 0.00 0.00 0.00 3.67
1168 1170 2.305927 GTCTCCTCCCCAAAATCTGACA 59.694 50.000 0.00 0.00 0.00 3.58
1218 1220 5.560183 GCAACGAATCATATAGGTTTTCCCG 60.560 44.000 0.00 0.00 41.86 5.14
1279 1281 1.077089 GCCGACCTAAAGTCTCGCAC 61.077 60.000 0.00 0.00 43.91 5.34
1287 1289 2.036862 GGTATAGTGGGCCGACCTAAAG 59.963 54.545 15.08 0.00 41.11 1.85
1291 1293 1.458967 GGGTATAGTGGGCCGACCT 60.459 63.158 15.08 5.03 41.11 3.85
1654 1658 2.030893 TCATCTTCTGCGCACTTTTTGG 60.031 45.455 5.66 0.00 0.00 3.28
1655 1659 3.272439 TCATCTTCTGCGCACTTTTTG 57.728 42.857 5.66 1.90 0.00 2.44
1679 1683 8.745837 GTGAACAAATAGTGAAAACATGAACAG 58.254 33.333 0.00 0.00 0.00 3.16
1753 1757 6.293027 CGAGCAAAATTTGGAGAAAAGCAAAT 60.293 34.615 7.89 0.00 0.00 2.32
1891 1895 1.683319 GGGAGCCCCTCTTGACAATTC 60.683 57.143 3.16 0.00 41.34 2.17
1914 1918 4.826274 TTCTCTCCCGAAAATGACAGAT 57.174 40.909 0.00 0.00 0.00 2.90
1923 1927 9.899661 TTCATATTTTTCTATTCTCTCCCGAAA 57.100 29.630 0.00 0.00 0.00 3.46
1948 1954 2.125269 GCCGGACCACAGCGTATT 60.125 61.111 5.05 0.00 0.00 1.89
1961 1967 2.624169 CGGTATTTACATGGGCCGG 58.376 57.895 0.00 0.00 36.05 6.13
2069 2075 4.377760 AAGAGGTCGGCGAGGGGA 62.378 66.667 11.20 0.00 0.00 4.81
2090 2096 3.889044 GAGCGGATCTCGACGGCA 61.889 66.667 7.64 0.00 42.43 5.69
2092 2098 2.899044 GAGGAGCGGATCTCGACGG 61.899 68.421 7.64 0.00 42.82 4.79
2093 2099 2.634777 GAGGAGCGGATCTCGACG 59.365 66.667 7.64 0.00 42.82 5.12
2203 2209 4.833495 TCCCCATCCGCCCCATCA 62.833 66.667 0.00 0.00 0.00 3.07
2328 2334 1.056660 AAGAGACGAAAGCAGGGGAA 58.943 50.000 0.00 0.00 0.00 3.97
2389 2395 2.046285 CCGCCCCATTCTTGACCAC 61.046 63.158 0.00 0.00 0.00 4.16
2414 2420 3.688235 AGCAGTTAGAGGTAGACGAACT 58.312 45.455 0.00 0.00 34.58 3.01
2416 2422 3.015327 GGAGCAGTTAGAGGTAGACGAA 58.985 50.000 0.00 0.00 0.00 3.85
2443 2467 2.048127 GTTGGCTCGCTTCTCCGT 60.048 61.111 0.00 0.00 0.00 4.69
2475 2499 1.112113 GATTACTCCGACCTGGCTCA 58.888 55.000 0.00 0.00 37.80 4.26
2594 2618 5.638657 TGTAATTGCAGCAAATTCATGGTTC 59.361 36.000 12.97 0.00 32.16 3.62
2622 2646 7.692460 AGAATCTCTGTTTGCATGTCAAATA 57.308 32.000 15.20 12.54 45.43 1.40
2623 2647 6.585695 AGAATCTCTGTTTGCATGTCAAAT 57.414 33.333 15.20 2.06 45.43 2.32
2680 2704 6.552445 ACTAGTTGCAGGATTCAGACTTAT 57.448 37.500 0.00 0.00 0.00 1.73
2852 2876 2.154567 ATGCAATCTGAAGCCATGGT 57.845 45.000 14.67 0.00 0.00 3.55
2918 2942 0.976641 TATGGCGATGGATCCCTGAC 59.023 55.000 9.90 1.09 0.00 3.51
2922 2946 2.496899 AACATATGGCGATGGATCCC 57.503 50.000 9.90 0.00 0.00 3.85
2971 2995 1.609208 TTCCTCTGGAAGCAAGTTGC 58.391 50.000 20.44 20.44 45.46 4.17
3045 3069 2.172082 AGATGCACATAGTGTCCAGCAT 59.828 45.455 6.20 6.20 39.30 3.79
3184 3208 2.136196 GATCTAGAGGCAGGGTCGCG 62.136 65.000 0.00 0.00 0.00 5.87
3247 3271 2.124695 GAGGTTGTCGGGGATGGC 60.125 66.667 0.00 0.00 0.00 4.40
3249 3273 2.186903 CGGAGGTTGTCGGGGATG 59.813 66.667 0.00 0.00 0.00 3.51
3318 3342 3.800506 GTGTATGGCGGACATTGTAGTAC 59.199 47.826 0.00 0.00 41.03 2.73
3325 3349 0.908910 TGAGGTGTATGGCGGACATT 59.091 50.000 0.00 0.00 41.03 2.71
3432 3456 7.798596 ACTCAATCCACTGCTTTAATATCAG 57.201 36.000 0.00 0.00 0.00 2.90
3450 3474 2.898729 CCATCGAGGCTGTACTCAAT 57.101 50.000 0.00 0.00 37.34 2.57
3510 3534 2.038557 ACCTGTGTGGGTGATGAACTAC 59.961 50.000 0.00 0.00 41.11 2.73
3527 3551 0.835941 AGCTTCATGGGAGCTACCTG 59.164 55.000 18.18 12.16 37.11 4.00
3530 3554 3.323403 AGTCATAGCTTCATGGGAGCTAC 59.677 47.826 24.51 18.06 42.87 3.58
3598 3622 6.197096 CGTATGCATAAGCCAAATCAAAAGAC 59.803 38.462 8.28 0.00 41.13 3.01
3631 3655 2.505650 TTCCTTCGGCCATTTCATCA 57.494 45.000 2.24 0.00 0.00 3.07
3719 3743 1.634702 CTGAGCGAAGAAGGTAGCAC 58.365 55.000 0.00 0.00 0.00 4.40
3748 3772 5.717078 AATTGAACTGAGCACATCACAAT 57.283 34.783 0.00 0.00 33.22 2.71
3823 3847 7.874940 TCAAACACATGACTCCTAAAATTCAG 58.125 34.615 0.00 0.00 0.00 3.02
3892 3916 6.782494 TGCAGGTCCTATATGTTCTCATAGAA 59.218 38.462 0.00 0.00 39.49 2.10
4057 4081 8.893563 TTTGGTGGATAGATTACTTTTGGATT 57.106 30.769 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.