Multiple sequence alignment - TraesCS7B01G123400

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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 TraesCS7B01G123400 chr7B 100.000 4219 0 0 1 4219 144664711 144660493 0.000000e+00 7792.0
1 TraesCS7B01G123400 chr7A 93.454 3712 168 35 1 3675 182619310 182615637 0.000000e+00 5439.0
2 TraesCS7B01G123400 chr7A 91.652 563 29 10 3671 4219 182615610 182615052 0.000000e+00 763.0
3 TraesCS7B01G123400 chr7D 93.092 3706 186 37 1 3675 178612219 178608553 0.000000e+00 5361.0
4 TraesCS7B01G123400 chr7D 90.909 462 35 7 3759 4219 178608413 178607958 7.750000e-172 614.0
5 TraesCS7B01G123400 chr7D 91.892 74 5 1 3671 3744 178608528 178608456 7.460000e-18 102.0
6 TraesCS7B01G123400 chr2D 96.875 32 1 0 1712 1743 335132018 335131987 2.000000e-03 54.7
7 TraesCS7B01G123400 chr2B 96.875 32 1 0 1712 1743 403106518 403106487 2.000000e-03 54.7
8 TraesCS7B01G123400 chr2A 96.875 32 1 0 1712 1743 445758740 445758709 2.000000e-03 54.7


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 TraesCS7B01G123400 chr7B 144660493 144664711 4218 True 7792.000000 7792 100.000000 1 4219 1 chr7B.!!$R1 4218
1 TraesCS7B01G123400 chr7A 182615052 182619310 4258 True 3101.000000 5439 92.553000 1 4219 2 chr7A.!!$R1 4218
2 TraesCS7B01G123400 chr7D 178607958 178612219 4261 True 2025.666667 5361 91.964333 1 4219 3 chr7D.!!$R1 4218

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
247 249 0.111253 CAACCCCTGCTTTCTCCAGT 59.889 55.0 0.0 0.0 0.0 4.00 F
1037 1048 0.684535 CCCCAAACCATCCCAACAAC 59.315 55.0 0.0 0.0 0.0 3.32 F
1976 1989 0.037697 TCCGATTCTGTGTGTTCCCG 60.038 55.0 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1569 1580 1.004560 ACTGCCGATGTCACCACAG 60.005 57.895 0.00 0.0 35.41 3.66 R
2714 2739 0.249489 ATCGCGCATCACTAGGTTCC 60.249 55.000 8.75 0.0 0.00 3.62 R
3378 3406 0.310854 GCGACTTCAAAACTGGTGGG 59.689 55.000 0.00 0.0 0.00 4.61 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
19 20 2.472695 TTCCGGTGAGATTTCCTGTG 57.527 50.000 0.00 0.00 0.00 3.66
88 89 1.000486 CTCGTCCCTCTTCCTCCCA 60.000 63.158 0.00 0.00 0.00 4.37
109 110 1.636988 CGTTACCGGACTGTGATTCC 58.363 55.000 9.46 0.00 0.00 3.01
133 134 1.521681 GTTTAGATCTGCGCCGCCT 60.522 57.895 6.63 0.00 0.00 5.52
134 135 1.521457 TTTAGATCTGCGCCGCCTG 60.521 57.895 6.63 0.00 0.00 4.85
135 136 2.923426 TTTAGATCTGCGCCGCCTGG 62.923 60.000 6.63 0.00 38.77 4.45
137 138 4.615815 GATCTGCGCCGCCTGGAT 62.616 66.667 6.63 7.84 37.49 3.41
138 139 3.226429 GATCTGCGCCGCCTGGATA 62.226 63.158 6.63 0.00 37.49 2.59
139 140 3.521529 ATCTGCGCCGCCTGGATAC 62.522 63.158 6.63 0.00 37.49 2.24
152 153 2.607892 GGATACTTCATGCGCGCCC 61.608 63.158 30.77 15.34 0.00 6.13
153 154 2.943345 GATACTTCATGCGCGCCCG 61.943 63.158 30.77 19.85 37.57 6.13
167 168 1.813337 GCCCGCTGCTTTCTCTCTC 60.813 63.158 0.00 0.00 36.87 3.20
172 173 3.431486 CCCGCTGCTTTCTCTCTCTTTAT 60.431 47.826 0.00 0.00 0.00 1.40
173 175 3.801594 CCGCTGCTTTCTCTCTCTTTATC 59.198 47.826 0.00 0.00 0.00 1.75
176 178 5.181748 GCTGCTTTCTCTCTCTTTATCCAA 58.818 41.667 0.00 0.00 0.00 3.53
180 182 5.869888 GCTTTCTCTCTCTTTATCCAACGAA 59.130 40.000 0.00 0.00 0.00 3.85
199 201 2.496817 GCGAGATTCCGTGCCTCT 59.503 61.111 0.00 0.00 0.00 3.69
229 231 2.096268 CAGATCAAAAGACGAAAGCGCA 60.096 45.455 11.47 0.00 42.48 6.09
230 232 2.548057 AGATCAAAAGACGAAAGCGCAA 59.452 40.909 11.47 0.00 42.48 4.85
231 233 2.099633 TCAAAAGACGAAAGCGCAAC 57.900 45.000 11.47 0.00 42.48 4.17
232 234 1.120437 CAAAAGACGAAAGCGCAACC 58.880 50.000 11.47 0.00 42.48 3.77
234 236 1.792118 AAAGACGAAAGCGCAACCCC 61.792 55.000 11.47 0.00 42.48 4.95
235 237 2.668550 GACGAAAGCGCAACCCCT 60.669 61.111 11.47 0.00 42.48 4.79
236 238 2.966309 GACGAAAGCGCAACCCCTG 61.966 63.158 11.47 0.00 42.48 4.45
247 249 0.111253 CAACCCCTGCTTTCTCCAGT 59.889 55.000 0.00 0.00 0.00 4.00
253 255 3.160269 CCCTGCTTTCTCCAGTTTCATT 58.840 45.455 0.00 0.00 0.00 2.57
262 271 8.465201 GCTTTCTCCAGTTTCATTATGATTTCT 58.535 33.333 0.00 0.00 0.00 2.52
281 290 3.222603 TCTTGCTTTCCCTCAGTTTTCC 58.777 45.455 0.00 0.00 0.00 3.13
380 391 5.209977 CAGTATCGTTTCCAATCGATCGTA 58.790 41.667 15.94 2.15 44.01 3.43
381 392 5.115171 CAGTATCGTTTCCAATCGATCGTAC 59.885 44.000 15.94 5.57 44.01 3.67
382 393 2.443387 TCGTTTCCAATCGATCGTACG 58.557 47.619 15.94 9.53 0.00 3.67
383 394 2.159531 TCGTTTCCAATCGATCGTACGT 60.160 45.455 15.94 2.33 34.70 3.57
654 665 1.228925 ACTAGGATAGGAGGGGCGC 60.229 63.158 0.00 0.00 44.97 6.53
695 706 7.771361 TGATAACTTTGTTAAGTCCAGTTGTGA 59.229 33.333 0.00 0.00 43.74 3.58
757 768 3.118112 GGTTGATGGATCTGAGTGGTGAT 60.118 47.826 0.00 0.00 0.00 3.06
831 842 6.906659 TGATCTTTTGCTCTTTGAGTTGATC 58.093 36.000 0.00 0.00 31.39 2.92
832 843 6.487668 TGATCTTTTGCTCTTTGAGTTGATCA 59.512 34.615 0.00 0.00 35.66 2.92
1037 1048 0.684535 CCCCAAACCATCCCAACAAC 59.315 55.000 0.00 0.00 0.00 3.32
1064 1075 5.296780 CCAACACTGAAGAAAAGAAGCAGTA 59.703 40.000 0.00 0.00 37.69 2.74
1070 1081 6.652900 ACTGAAGAAAAGAAGCAGTATTCTCC 59.347 38.462 0.00 0.00 38.59 3.71
1080 1091 5.543507 AGCAGTATTCTCCGAATGATTCT 57.456 39.130 3.43 0.00 0.00 2.40
1081 1092 5.537188 AGCAGTATTCTCCGAATGATTCTC 58.463 41.667 3.43 0.00 0.00 2.87
1152 1163 2.663196 CCCGAATCGGCTATCCCC 59.337 66.667 17.50 0.00 46.86 4.81
1306 1317 2.412089 GGAAACGTGAAATCAGACTCGG 59.588 50.000 0.00 0.00 0.00 4.63
1773 1784 5.669477 GAGACTGATAAGTTCTCATGCCTT 58.331 41.667 5.32 0.00 0.00 4.35
1893 1904 9.203421 TCCATCTTTTACGCTGTACATAATATG 57.797 33.333 0.00 0.00 0.00 1.78
1923 1934 7.740805 ACTGTCTTCTTGACTTTTAGGATTCT 58.259 34.615 0.00 0.00 45.54 2.40
1976 1989 0.037697 TCCGATTCTGTGTGTTCCCG 60.038 55.000 0.00 0.00 0.00 5.14
1982 1995 2.448926 TCTGTGTGTTCCCGTGTATG 57.551 50.000 0.00 0.00 0.00 2.39
2051 2064 9.643693 CAAGTTAGCTGAATGTATGGAAAATTT 57.356 29.630 0.00 0.00 0.00 1.82
2072 2085 8.823220 AATTTCCAGTAATGTAGCTAATTGGT 57.177 30.769 0.00 0.00 0.00 3.67
2085 2098 8.261522 TGTAGCTAATTGGTGACATATTGTGTA 58.738 33.333 0.00 0.00 42.36 2.90
2094 2107 6.128035 TGGTGACATATTGTGTAATCTTGTGC 60.128 38.462 0.00 0.00 42.36 4.57
2095 2108 5.959527 GTGACATATTGTGTAATCTTGTGCG 59.040 40.000 0.00 0.00 42.36 5.34
2131 2154 8.720562 ACATTTGCAAATTTAATTTCCTGCTAC 58.279 29.630 21.95 0.00 0.00 3.58
2136 2160 9.282569 TGCAAATTTAATTTCCTGCTACAAAAT 57.717 25.926 12.22 0.00 0.00 1.82
2144 2168 7.814264 ATTTCCTGCTACAAAATCCATCTAG 57.186 36.000 0.00 0.00 0.00 2.43
2146 2170 5.918608 TCCTGCTACAAAATCCATCTAGTC 58.081 41.667 0.00 0.00 0.00 2.59
2211 2235 8.500837 TCAAATTAAATGAAGCAAGTACAACG 57.499 30.769 0.00 0.00 0.00 4.10
2345 2370 7.796197 GCATTTCTTCTTAATCGCAGATTCTAC 59.204 37.037 6.99 0.00 45.12 2.59
2480 2505 2.185608 GACCTCTCCCTTCGCTGC 59.814 66.667 0.00 0.00 0.00 5.25
2505 2530 1.329256 TAGCCCGACTCTAATCAGGC 58.671 55.000 0.00 0.00 41.77 4.85
2594 2619 2.173143 TGAGCCATCCTGCATGATACAA 59.827 45.455 4.01 0.00 33.80 2.41
2648 2673 1.540267 CCTCGGTTCTTCTCGAAGTCA 59.460 52.381 6.56 0.00 39.38 3.41
2834 2859 5.505780 TGGTGGACCTTTGGTATATTCTTG 58.494 41.667 0.00 0.00 35.25 3.02
2936 2961 2.629051 CGTTTCCCAGAATACCCAGTC 58.371 52.381 0.00 0.00 0.00 3.51
2945 2970 2.567615 AGAATACCCAGTCGTGAGCTTT 59.432 45.455 0.00 0.00 0.00 3.51
3104 3129 0.390472 CAGAGGTTCCGAAGCCTGTC 60.390 60.000 15.25 5.67 34.81 3.51
3281 3309 1.200020 AGTTGTAGGCTTTTCGCATGC 59.800 47.619 7.91 7.91 41.67 4.06
3338 3366 4.214119 TGTGTCTGTCAAGCTATTTTCTGC 59.786 41.667 0.00 0.00 0.00 4.26
3383 3411 7.189079 TGTTTCAAATTTATATTCCCCCACC 57.811 36.000 0.00 0.00 0.00 4.61
3413 3444 5.635280 TGAAGTCGCTAATCTTTGTGAGAAG 59.365 40.000 0.00 0.00 38.06 2.85
3420 3451 4.999751 AATCTTTGTGAGAAGTCTTCGC 57.000 40.909 9.21 9.21 38.06 4.70
3422 3453 2.128035 CTTTGTGAGAAGTCTTCGCGT 58.872 47.619 5.77 0.00 31.63 6.01
3423 3454 1.487482 TTGTGAGAAGTCTTCGCGTG 58.513 50.000 5.77 0.00 31.63 5.34
3424 3455 0.666374 TGTGAGAAGTCTTCGCGTGA 59.334 50.000 5.77 2.87 31.63 4.35
3438 3469 2.739379 TCGCGTGATGTGCAGAATTAAA 59.261 40.909 5.77 0.00 0.00 1.52
3451 3482 8.462811 TGTGCAGAATTAAACTCAGTTTTGTAA 58.537 29.630 8.41 0.00 37.01 2.41
3505 3536 2.742589 GTCAGCAACTAAGGCACCTTAC 59.257 50.000 5.00 0.00 37.47 2.34
3518 3549 1.886542 CACCTTACAGGGCCTTGTTTC 59.113 52.381 27.05 0.00 40.58 2.78
3524 3555 0.821711 CAGGGCCTTGTTTCGTTGGA 60.822 55.000 1.32 0.00 0.00 3.53
3551 3583 1.601914 CGGTGTTTTTACCTGCTTGGC 60.602 52.381 0.00 0.00 38.62 4.52
3575 3607 1.202675 TGCTGTTGCTCACACTGATGA 60.203 47.619 0.00 0.00 40.48 2.92
3618 3666 3.994392 TCCGACAAGTCTTGCTGAAATAC 59.006 43.478 12.66 0.00 0.00 1.89
3628 3676 8.621532 AGTCTTGCTGAAATACTGTTTGATTA 57.378 30.769 0.00 0.00 0.00 1.75
3669 3717 1.021390 GTCAGCTTGCACTACGGCAT 61.021 55.000 0.00 0.00 44.48 4.40
3744 3822 7.979444 TTATGCTACTAATTGATTGGCTACC 57.021 36.000 0.00 0.00 0.00 3.18
3755 3833 4.832248 TGATTGGCTACCACTTCTACTTG 58.168 43.478 0.00 0.00 30.78 3.16
3757 3835 5.189736 TGATTGGCTACCACTTCTACTTGAT 59.810 40.000 0.00 0.00 30.78 2.57
3773 3879 5.571784 ACTTGATCAGTTATGCATGTTGG 57.428 39.130 10.16 0.00 27.32 3.77
3814 3920 4.530553 TCTTAAGACCACAGGTGCATCTAA 59.469 41.667 0.00 0.00 35.25 2.10
3816 3922 3.059352 AGACCACAGGTGCATCTAAAC 57.941 47.619 0.00 0.00 35.25 2.01
3823 3929 2.357009 CAGGTGCATCTAAACCATCTGC 59.643 50.000 0.00 0.00 39.05 4.26
3872 3978 1.674441 CATGCAGCTCCATAACCACTG 59.326 52.381 0.00 0.00 0.00 3.66
3877 3983 2.357009 CAGCTCCATAACCACTGCAATC 59.643 50.000 0.00 0.00 0.00 2.67
3988 4094 9.425248 AATTATCTCATTTGTACACCATGGATT 57.575 29.630 21.47 6.94 0.00 3.01
3989 4095 8.821686 TTATCTCATTTGTACACCATGGATTT 57.178 30.769 21.47 4.11 0.00 2.17
4046 4153 9.660180 TTTTAATCACAAACTTTTTGCTACCTT 57.340 25.926 0.00 0.00 0.00 3.50
4086 4193 1.202687 TCCAGCTGTGAAAGTGACTGG 60.203 52.381 13.81 0.00 44.87 4.00
4113 4220 2.777536 TCAGGATGACAGGCACCTT 58.222 52.632 0.00 0.00 42.56 3.50
4184 4291 4.649692 CCATCAACTGCCTCTATGCTATT 58.350 43.478 0.00 0.00 0.00 1.73
4186 4293 4.760530 TCAACTGCCTCTATGCTATTGT 57.239 40.909 0.00 0.00 32.28 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.381272 TGGAAGAACAAGAAAAGGCACAG 59.619 43.478 0.00 0.00 0.00 3.66
16 17 3.360867 TGGAAGAACAAGAAAAGGCACA 58.639 40.909 0.00 0.00 0.00 4.57
18 19 3.321682 CCATGGAAGAACAAGAAAAGGCA 59.678 43.478 5.56 0.00 0.00 4.75
19 20 3.862264 GCCATGGAAGAACAAGAAAAGGC 60.862 47.826 18.40 0.00 0.00 4.35
101 102 3.342377 TCTAAACATGGCGGAATCACA 57.658 42.857 0.00 0.00 0.00 3.58
109 110 0.041839 GCGCAGATCTAAACATGGCG 60.042 55.000 14.85 14.85 45.15 5.69
133 134 1.887242 GGCGCGCATGAAGTATCCA 60.887 57.895 34.42 0.00 0.00 3.41
134 135 2.607892 GGGCGCGCATGAAGTATCC 61.608 63.158 34.42 17.52 0.00 2.59
135 136 2.939022 GGGCGCGCATGAAGTATC 59.061 61.111 34.42 11.78 0.00 2.24
136 137 2.967076 CGGGCGCGCATGAAGTAT 60.967 61.111 34.42 0.00 0.00 2.12
152 153 3.801594 GGATAAAGAGAGAGAAAGCAGCG 59.198 47.826 0.00 0.00 0.00 5.18
153 154 4.764172 TGGATAAAGAGAGAGAAAGCAGC 58.236 43.478 0.00 0.00 0.00 5.25
155 156 5.047306 TCGTTGGATAAAGAGAGAGAAAGCA 60.047 40.000 0.00 0.00 0.00 3.91
156 157 5.411781 TCGTTGGATAAAGAGAGAGAAAGC 58.588 41.667 0.00 0.00 0.00 3.51
157 158 6.034044 CGTTCGTTGGATAAAGAGAGAGAAAG 59.966 42.308 0.00 0.00 0.00 2.62
159 160 5.399858 CGTTCGTTGGATAAAGAGAGAGAA 58.600 41.667 0.00 0.00 0.00 2.87
160 161 4.674623 GCGTTCGTTGGATAAAGAGAGAGA 60.675 45.833 0.00 0.00 0.00 3.10
161 162 3.548268 GCGTTCGTTGGATAAAGAGAGAG 59.452 47.826 0.00 0.00 0.00 3.20
162 163 3.508762 GCGTTCGTTGGATAAAGAGAGA 58.491 45.455 0.00 0.00 0.00 3.10
167 168 2.256174 TCTCGCGTTCGTTGGATAAAG 58.744 47.619 5.77 0.00 36.96 1.85
172 173 0.734942 GGAATCTCGCGTTCGTTGGA 60.735 55.000 5.77 0.00 36.96 3.53
173 175 1.708027 GGAATCTCGCGTTCGTTGG 59.292 57.895 5.77 0.00 36.96 3.77
176 178 1.800315 CACGGAATCTCGCGTTCGT 60.800 57.895 5.77 0.00 36.96 3.85
180 182 3.701604 GAGGCACGGAATCTCGCGT 62.702 63.158 5.77 0.00 0.00 6.01
204 206 1.438651 TTCGTCTTTTGATCTGCGGG 58.561 50.000 0.00 0.00 0.00 6.13
229 231 0.853530 AACTGGAGAAAGCAGGGGTT 59.146 50.000 0.00 0.00 0.00 4.11
230 232 0.853530 AAACTGGAGAAAGCAGGGGT 59.146 50.000 0.00 0.00 0.00 4.95
231 233 1.202927 TGAAACTGGAGAAAGCAGGGG 60.203 52.381 0.00 0.00 0.00 4.79
232 234 2.276732 TGAAACTGGAGAAAGCAGGG 57.723 50.000 0.00 0.00 0.00 4.45
234 236 6.748333 TCATAATGAAACTGGAGAAAGCAG 57.252 37.500 0.00 0.00 0.00 4.24
235 237 7.707624 AATCATAATGAAACTGGAGAAAGCA 57.292 32.000 0.00 0.00 0.00 3.91
236 238 8.465201 AGAAATCATAATGAAACTGGAGAAAGC 58.535 33.333 0.00 0.00 0.00 3.51
239 241 8.246180 GCAAGAAATCATAATGAAACTGGAGAA 58.754 33.333 0.00 0.00 0.00 2.87
241 243 7.769220 AGCAAGAAATCATAATGAAACTGGAG 58.231 34.615 0.00 0.00 0.00 3.86
242 244 7.707624 AGCAAGAAATCATAATGAAACTGGA 57.292 32.000 0.00 0.00 0.00 3.86
245 247 8.037166 GGGAAAGCAAGAAATCATAATGAAACT 58.963 33.333 0.00 0.00 0.00 2.66
247 249 8.137745 AGGGAAAGCAAGAAATCATAATGAAA 57.862 30.769 0.00 0.00 0.00 2.69
253 255 5.819991 ACTGAGGGAAAGCAAGAAATCATA 58.180 37.500 0.00 0.00 0.00 2.15
262 271 1.953686 CGGAAAACTGAGGGAAAGCAA 59.046 47.619 0.00 0.00 0.00 3.91
263 272 1.604604 CGGAAAACTGAGGGAAAGCA 58.395 50.000 0.00 0.00 0.00 3.91
281 290 1.663494 GAAACGCAGACTTTCTTGCG 58.337 50.000 16.16 16.16 43.94 4.85
380 391 0.725117 GCAGGCGCATTTTACTACGT 59.275 50.000 10.83 0.00 38.36 3.57
381 392 0.315059 CGCAGGCGCATTTTACTACG 60.315 55.000 10.83 0.00 38.40 3.51
382 393 1.003851 TCGCAGGCGCATTTTACTAC 58.996 50.000 10.83 0.00 38.40 2.73
383 394 1.286501 CTCGCAGGCGCATTTTACTA 58.713 50.000 10.83 0.00 38.40 1.82
439 450 1.177401 AAGAAAAGCGGCTCCCAATC 58.823 50.000 1.45 0.00 0.00 2.67
539 550 1.007721 AGATGTAGCACTCCCCACTCT 59.992 52.381 0.00 0.00 0.00 3.24
654 665 7.173907 ACAAAGTTATCACTTGAGAGTTCATGG 59.826 37.037 0.00 0.00 42.89 3.66
757 768 5.310409 AGATCAAGAAAGAACCTCCACAA 57.690 39.130 0.00 0.00 0.00 3.33
1037 1048 2.944129 TCTTTTCTTCAGTGTTGGGGG 58.056 47.619 0.00 0.00 0.00 5.40
1064 1075 4.040217 CCAGAGGAGAATCATTCGGAGAAT 59.960 45.833 0.00 0.00 38.64 2.40
1070 1081 4.280425 TGAGATCCAGAGGAGAATCATTCG 59.720 45.833 0.00 0.00 36.25 3.34
1100 1111 2.616524 AGGCTGTACTGGGTTTACTCA 58.383 47.619 1.65 0.00 0.00 3.41
1152 1163 3.243201 GGACTTCTTTGTTTGGACTGCTG 60.243 47.826 0.00 0.00 0.00 4.41
1266 1277 6.036517 CGTTTCCATTTGTGTTTCCATTTTCA 59.963 34.615 0.00 0.00 0.00 2.69
1282 1293 4.152402 CGAGTCTGATTTCACGTTTCCATT 59.848 41.667 0.00 0.00 0.00 3.16
1306 1317 3.589988 CACCATGATCCTTATCTACCGC 58.410 50.000 0.00 0.00 32.93 5.68
1569 1580 1.004560 ACTGCCGATGTCACCACAG 60.005 57.895 0.00 0.00 35.41 3.66
1773 1784 1.281867 CCAGGGCAGAACTCCATAACA 59.718 52.381 0.00 0.00 0.00 2.41
1948 1961 4.690748 ACACACAGAATCGGATAAACACTG 59.309 41.667 0.00 0.00 0.00 3.66
1951 1964 4.693566 GGAACACACAGAATCGGATAAACA 59.306 41.667 0.00 0.00 0.00 2.83
1976 1989 2.621055 TCACTTTGTTGCCACCATACAC 59.379 45.455 0.00 0.00 0.00 2.90
1982 1995 3.733443 ATTCTTCACTTTGTTGCCACC 57.267 42.857 0.00 0.00 0.00 4.61
2005 2018 7.989416 ACTTGAAACGGATAATAACTTTCCA 57.011 32.000 0.00 0.00 0.00 3.53
2051 2064 6.070481 TGTCACCAATTAGCTACATTACTGGA 60.070 38.462 0.00 0.00 0.00 3.86
2072 2085 5.872070 TCGCACAAGATTACACAATATGTCA 59.128 36.000 0.00 0.00 42.09 3.58
2080 2093 5.180304 TGCTTAATTCGCACAAGATTACACA 59.820 36.000 0.00 0.00 31.40 3.72
2085 2098 5.119931 TGTTGCTTAATTCGCACAAGATT 57.880 34.783 2.16 0.00 37.07 2.40
2124 2147 5.757320 CAGACTAGATGGATTTTGTAGCAGG 59.243 44.000 0.00 0.00 0.00 4.85
2131 2154 6.111382 TCTGAAGCAGACTAGATGGATTTTG 58.889 40.000 0.00 0.00 35.39 2.44
2136 2160 5.893824 TGTAATCTGAAGCAGACTAGATGGA 59.106 40.000 0.00 0.00 43.63 3.41
2144 2168 4.024218 GCATGGATGTAATCTGAAGCAGAC 60.024 45.833 0.00 0.00 43.63 3.51
2146 2170 3.881089 TGCATGGATGTAATCTGAAGCAG 59.119 43.478 0.00 0.00 44.71 4.24
2204 2228 8.792538 GGATATTTATGTCGCTATACGTTGTAC 58.207 37.037 0.00 0.00 44.19 2.90
2345 2370 1.936547 GCAAGGAGGATTTCTGCTACG 59.063 52.381 0.00 0.00 43.70 3.51
2480 2505 3.130516 TGATTAGAGTCGGGCTAACTGTG 59.869 47.826 0.00 0.00 31.27 3.66
2505 2530 3.129988 GCTTCTGTTTCAGGATTGGATGG 59.870 47.826 0.00 0.00 31.51 3.51
2573 2598 1.770061 TGTATCATGCAGGATGGCTCA 59.230 47.619 23.44 13.51 35.86 4.26
2594 2619 4.722700 GGGGCTGTGCACGATGGT 62.723 66.667 13.13 0.00 29.41 3.55
2648 2673 4.550422 GCTTTGGCTTTCGATCTTTCTTT 58.450 39.130 0.00 0.00 35.22 2.52
2714 2739 0.249489 ATCGCGCATCACTAGGTTCC 60.249 55.000 8.75 0.00 0.00 3.62
2834 2859 0.388134 TGCCGAACAGAAGCTCGTAC 60.388 55.000 0.00 0.00 31.66 3.67
2936 2961 2.138320 TCTCTTGCTGAAAAGCTCACG 58.862 47.619 0.00 0.00 35.49 4.35
2945 2970 5.594317 GCCCCTTATTAAATCTCTTGCTGAA 59.406 40.000 0.00 0.00 0.00 3.02
3104 3129 2.685388 TGTAGTCTGCCTCTCAATCTCG 59.315 50.000 0.00 0.00 0.00 4.04
3281 3309 3.177487 CGACTCATCTGTCAGACACATG 58.823 50.000 11.59 11.59 36.82 3.21
3338 3366 6.241207 ACATCCAATTCGTTCACTACAAAG 57.759 37.500 0.00 0.00 0.00 2.77
3378 3406 0.310854 GCGACTTCAAAACTGGTGGG 59.689 55.000 0.00 0.00 0.00 4.61
3383 3411 6.358030 CACAAAGATTAGCGACTTCAAAACTG 59.642 38.462 0.00 0.00 0.00 3.16
3413 3444 1.008875 TCTGCACATCACGCGAAGAC 61.009 55.000 15.93 0.00 0.00 3.01
3420 3451 5.106948 ACTGAGTTTAATTCTGCACATCACG 60.107 40.000 0.00 0.00 0.00 4.35
3422 3453 6.882610 AACTGAGTTTAATTCTGCACATCA 57.117 33.333 0.00 0.00 0.00 3.07
3423 3454 7.649306 ACAAAACTGAGTTTAATTCTGCACATC 59.351 33.333 11.43 0.00 34.43 3.06
3424 3455 7.491682 ACAAAACTGAGTTTAATTCTGCACAT 58.508 30.769 11.43 0.00 34.43 3.21
3438 3469 6.002062 GCATAAGCTGTTACAAAACTGAGT 57.998 37.500 0.00 0.00 36.85 3.41
3505 3536 0.821711 TCCAACGAAACAAGGCCCTG 60.822 55.000 0.00 0.00 0.00 4.45
3518 3549 4.428615 AAAACACCGGATAATTCCAACG 57.571 40.909 9.46 0.00 42.74 4.10
3524 3555 5.014202 AGCAGGTAAAAACACCGGATAATT 58.986 37.500 9.46 0.00 43.84 1.40
3551 3583 0.956633 AGTGTGAGCAACAGCAATGG 59.043 50.000 0.00 0.00 40.26 3.16
3628 3676 9.342308 CTGACATACACATGATTACCCTATTTT 57.658 33.333 0.00 0.00 35.96 1.82
3631 3679 6.270927 AGCTGACATACACATGATTACCCTAT 59.729 38.462 0.00 0.00 35.96 2.57
3713 3791 9.467258 CCAATCAATTAGTAGCATAATTGTTGG 57.533 33.333 24.54 24.54 46.34 3.77
3744 3822 7.279536 ACATGCATAACTGATCAAGTAGAAGTG 59.720 37.037 0.00 0.00 38.56 3.16
3755 3833 2.689471 TGCCCAACATGCATAACTGATC 59.311 45.455 0.00 0.00 32.85 2.92
3757 3835 2.212812 TGCCCAACATGCATAACTGA 57.787 45.000 0.00 0.00 32.85 3.41
3773 3879 9.129209 GTCTTAAGACTTCATAAACATTTTGCC 57.871 33.333 25.30 0.00 41.65 4.52
3814 3920 4.571919 CAATTGGAAACATGCAGATGGTT 58.428 39.130 0.00 0.00 42.53 3.67
3816 3922 2.933906 GCAATTGGAAACATGCAGATGG 59.066 45.455 7.72 0.00 40.54 3.51
3856 3962 1.825090 TTGCAGTGGTTATGGAGCTG 58.175 50.000 0.00 0.00 0.00 4.24
3872 3978 4.708726 ATGAAGCCTTGTACTTGATTGC 57.291 40.909 0.00 0.00 0.00 3.56
3877 3983 9.906660 TTATTTTGTAATGAAGCCTTGTACTTG 57.093 29.630 0.00 0.00 0.00 3.16
4046 4153 2.549064 ATGCTGTATGCGCCATCTTA 57.451 45.000 4.18 0.00 46.63 2.10
4086 4193 2.681848 CCTGTCATCCTGATTGCTGTTC 59.318 50.000 0.00 0.00 0.00 3.18
4184 4291 3.205338 CCATCATCTACGCCAAATCACA 58.795 45.455 0.00 0.00 0.00 3.58
4186 4293 2.221169 GCCATCATCTACGCCAAATCA 58.779 47.619 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.