Multiple sequence alignment - TraesCS7A01G287800

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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 TraesCS7A01G287800 chr7A 100.000 6278 0 0 1 6278 344674059 344680336 0.000000e+00 11594.0
1 TraesCS7A01G287800 chr7D 96.707 5435 108 24 891 6278 339119696 339114286 0.000000e+00 8979.0
2 TraesCS7A01G287800 chr7D 81.250 256 44 4 3230 3485 215789976 215789725 2.970000e-48 204.0
3 TraesCS7A01G287800 chr7D 79.167 168 27 5 259 426 330354900 330355059 6.650000e-20 110.0
4 TraesCS7A01G287800 chr7B 96.550 2435 69 7 3519 5941 284147065 284144634 0.000000e+00 4017.0
5 TraesCS7A01G287800 chr7B 94.087 2672 76 30 925 3529 284150065 284147409 0.000000e+00 3984.0
6 TraesCS7A01G287800 chr7B 86.332 578 54 14 299 861 329859701 329859134 1.940000e-169 606.0
7 TraesCS7A01G287800 chr7B 93.593 359 12 5 5926 6278 284144621 284144268 5.580000e-145 525.0
8 TraesCS7A01G287800 chr7B 89.617 183 13 6 17 194 329859979 329859798 1.760000e-55 228.0
9 TraesCS7A01G287800 chr2B 77.178 574 89 25 296 862 397267687 397268225 4.760000e-76 296.0
10 TraesCS7A01G287800 chr2B 89.216 204 22 0 1768 1971 636775409 636775612 8.080000e-64 255.0
11 TraesCS7A01G287800 chr2B 85.185 81 8 3 3689 3766 576693534 576693455 5.220000e-11 80.5
12 TraesCS7A01G287800 chr6D 85.385 260 33 4 3229 3488 172118063 172117809 1.340000e-66 265.0
13 TraesCS7A01G287800 chr6A 85.603 257 32 3 3229 3485 242203956 242204207 1.340000e-66 265.0
14 TraesCS7A01G287800 chr6A 88.018 217 23 2 1768 1984 522421013 522421226 2.900000e-63 254.0
15 TraesCS7A01G287800 chr4D 89.573 211 18 4 1768 1975 51076132 51076341 1.340000e-66 265.0
16 TraesCS7A01G287800 chr3B 89.100 211 21 2 1768 1978 519399115 519399323 1.740000e-65 261.0
17 TraesCS7A01G287800 chr3A 89.423 208 19 2 1768 1975 501225845 501225641 6.240000e-65 259.0
18 TraesCS7A01G287800 chr3A 87.615 218 24 3 1768 1984 24786319 24786534 3.760000e-62 250.0
19 TraesCS7A01G287800 chr3A 83.529 255 40 2 3229 3482 566132242 566132495 2.930000e-58 237.0
20 TraesCS7A01G287800 chr3A 80.784 255 46 3 3230 3483 453671035 453670783 4.970000e-46 196.0
21 TraesCS7A01G287800 chr4A 88.670 203 23 0 1768 1970 674523600 674523398 1.350000e-61 248.0
22 TraesCS7A01G287800 chr3D 84.314 255 38 2 3229 3482 422738343 422738090 1.350000e-61 248.0
23 TraesCS7A01G287800 chr1B 90.260 154 14 1 3701 3853 546684913 546684760 3.840000e-47 200.0
24 TraesCS7A01G287800 chr1D 89.744 156 15 1 3701 3855 406557852 406557697 1.380000e-46 198.0
25 TraesCS7A01G287800 chr5A 80.620 258 47 3 3229 3485 653289618 653289873 4.970000e-46 196.0
26 TraesCS7A01G287800 chr2A 88.750 80 5 3 3689 3765 637194552 637194474 1.860000e-15 95.3


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 TraesCS7A01G287800 chr7A 344674059 344680336 6277 False 11594 11594 100.000000 1 6278 1 chr7A.!!$F1 6277
1 TraesCS7A01G287800 chr7D 339114286 339119696 5410 True 8979 8979 96.707000 891 6278 1 chr7D.!!$R2 5387
2 TraesCS7A01G287800 chr7B 284144268 284150065 5797 True 2842 4017 94.743333 925 6278 3 chr7B.!!$R1 5353
3 TraesCS7A01G287800 chr7B 329859134 329859979 845 True 417 606 87.974500 17 861 2 chr7B.!!$R2 844
4 TraesCS7A01G287800 chr2B 397267687 397268225 538 False 296 296 77.178000 296 862 1 chr2B.!!$F1 566

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
828 878 0.319555 GGCAGCGTGTGTCTGTAAGA 60.320 55.000 0.00 0.00 43.69 2.10 F
1896 1985 0.835941 TTGCCATGTTTGCCAACCTT 59.164 45.000 0.00 0.00 31.02 3.50 F
2216 2309 0.743701 CTCACACAGCCAGGATCAGC 60.744 60.000 0.00 0.00 0.00 4.26 F
2217 2310 1.002990 CACACAGCCAGGATCAGCA 60.003 57.895 0.00 0.00 0.00 4.41 F
3010 3133 1.184970 ACCATGGGCAAGGAAAACCG 61.185 55.000 18.09 0.00 0.00 4.44 F
3017 3140 1.362355 CAAGGAAAACCGTGGCCAC 59.638 57.895 26.78 26.78 0.00 5.01 F
4457 4939 1.557371 TGCCACATGGGATAAACGAGA 59.443 47.619 0.00 0.00 40.01 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2169 2259 0.036732 TCCATGAACTGTCAGCACCC 59.963 55.000 0.00 0.0 37.14 4.61 R
3602 4080 1.402720 GCCTTGCATTGCGCTTTAAGA 60.403 47.619 9.73 0.0 43.06 2.10 R
4164 4646 4.439057 GTCACGGCAAGATATAAGACCAA 58.561 43.478 0.00 0.0 0.00 3.67 R
4214 4696 6.085555 TGTAGGTGACAAAGAAGACACTAG 57.914 41.667 0.00 0.0 34.15 2.57 R
4426 4908 1.224075 CATGTGGCATCTCGTCCATC 58.776 55.000 0.00 0.0 34.47 3.51 R
4958 5450 1.895707 GGTGCACAGCAGAAGCAGT 60.896 57.895 20.43 0.0 45.49 4.40 R
5742 6235 4.261801 GCCTACTTTTGTGCTCCTTCATA 58.738 43.478 0.00 0.0 0.00 2.15 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
41 43 3.331889 AGGTTCACAGATCTCCAACCAAT 59.668 43.478 21.29 6.43 39.26 3.16
46 48 3.446161 CACAGATCTCCAACCAATTGCAT 59.554 43.478 0.00 0.00 34.17 3.96
68 70 3.207549 TGATAACATCTCCCTCCCTCTCA 59.792 47.826 0.00 0.00 0.00 3.27
76 78 0.326048 CCCTCCCTCTCACTCCACAT 60.326 60.000 0.00 0.00 0.00 3.21
77 79 0.829333 CCTCCCTCTCACTCCACATG 59.171 60.000 0.00 0.00 0.00 3.21
86 91 1.073722 ACTCCACATGCCACACCTG 59.926 57.895 0.00 0.00 0.00 4.00
88 93 2.598099 CCACATGCCACACCTGCA 60.598 61.111 0.00 0.00 43.97 4.41
120 125 1.988293 TTTGGCAACCCTTCGAATCA 58.012 45.000 0.00 0.00 0.00 2.57
123 128 2.917933 TGGCAACCCTTCGAATCATAG 58.082 47.619 0.00 0.00 0.00 2.23
145 151 3.025262 TCACCAGTACCCAAACCAAAAC 58.975 45.455 0.00 0.00 0.00 2.43
174 180 7.615365 ACAAGTGCTTAATCCATTCCTAATCAA 59.385 33.333 0.00 0.00 0.00 2.57
191 197 8.605947 TCCTAATCAATTAACCTATCCATCAGG 58.394 37.037 0.00 0.00 39.25 3.86
196 202 9.965902 ATCAATTAACCTATCCATCAGGTAATC 57.034 33.333 0.00 0.00 45.90 1.75
198 204 9.442047 CAATTAACCTATCCATCAGGTAATCTC 57.558 37.037 0.00 0.00 45.90 2.75
199 205 8.980832 ATTAACCTATCCATCAGGTAATCTCT 57.019 34.615 0.00 0.00 45.90 3.10
201 207 7.784470 AACCTATCCATCAGGTAATCTCTAC 57.216 40.000 0.00 0.00 45.90 2.59
202 208 6.864421 ACCTATCCATCAGGTAATCTCTACA 58.136 40.000 0.00 0.00 44.77 2.74
203 209 7.306013 ACCTATCCATCAGGTAATCTCTACAA 58.694 38.462 0.00 0.00 44.77 2.41
204 210 7.453126 ACCTATCCATCAGGTAATCTCTACAAG 59.547 40.741 0.00 0.00 44.77 3.16
205 211 6.678568 ATCCATCAGGTAATCTCTACAAGG 57.321 41.667 0.00 0.00 35.89 3.61
206 212 5.777449 TCCATCAGGTAATCTCTACAAGGA 58.223 41.667 0.00 0.00 35.89 3.36
207 213 6.385443 TCCATCAGGTAATCTCTACAAGGAT 58.615 40.000 0.00 0.00 35.89 3.24
208 214 7.535738 TCCATCAGGTAATCTCTACAAGGATA 58.464 38.462 0.00 0.00 35.89 2.59
209 215 8.010697 TCCATCAGGTAATCTCTACAAGGATAA 58.989 37.037 0.00 0.00 35.89 1.75
210 216 8.091449 CCATCAGGTAATCTCTACAAGGATAAC 58.909 40.741 0.00 0.00 0.00 1.89
211 217 8.642432 CATCAGGTAATCTCTACAAGGATAACA 58.358 37.037 0.00 0.00 0.00 2.41
212 218 8.239038 TCAGGTAATCTCTACAAGGATAACAG 57.761 38.462 0.00 0.00 0.00 3.16
213 219 7.839705 TCAGGTAATCTCTACAAGGATAACAGT 59.160 37.037 0.00 0.00 0.00 3.55
214 220 9.132923 CAGGTAATCTCTACAAGGATAACAGTA 57.867 37.037 0.00 0.00 0.00 2.74
215 221 9.134055 AGGTAATCTCTACAAGGATAACAGTAC 57.866 37.037 0.00 0.00 0.00 2.73
216 222 9.134055 GGTAATCTCTACAAGGATAACAGTACT 57.866 37.037 0.00 0.00 0.00 2.73
218 224 8.824756 AATCTCTACAAGGATAACAGTACTCA 57.175 34.615 0.00 0.00 0.00 3.41
219 225 9.427821 AATCTCTACAAGGATAACAGTACTCAT 57.572 33.333 0.00 0.00 0.00 2.90
220 226 8.453238 TCTCTACAAGGATAACAGTACTCATC 57.547 38.462 0.00 0.00 0.00 2.92
221 227 7.226918 TCTCTACAAGGATAACAGTACTCATCG 59.773 40.741 0.00 0.00 0.00 3.84
222 228 7.052248 TCTACAAGGATAACAGTACTCATCGA 58.948 38.462 0.00 0.00 0.00 3.59
223 229 6.716934 ACAAGGATAACAGTACTCATCGAT 57.283 37.500 0.00 0.00 0.00 3.59
224 230 7.113658 ACAAGGATAACAGTACTCATCGATT 57.886 36.000 0.00 0.00 0.00 3.34
225 231 7.556844 ACAAGGATAACAGTACTCATCGATTT 58.443 34.615 0.00 0.00 0.00 2.17
226 232 7.707035 ACAAGGATAACAGTACTCATCGATTTC 59.293 37.037 0.00 0.00 0.00 2.17
227 233 6.439599 AGGATAACAGTACTCATCGATTTCG 58.560 40.000 0.00 0.00 41.45 3.46
228 234 5.117287 GGATAACAGTACTCATCGATTTCGC 59.883 44.000 0.00 0.00 39.60 4.70
229 235 2.810650 ACAGTACTCATCGATTTCGCC 58.189 47.619 0.00 0.00 39.60 5.54
230 236 2.128035 CAGTACTCATCGATTTCGCCC 58.872 52.381 0.00 0.00 39.60 6.13
231 237 1.754803 AGTACTCATCGATTTCGCCCA 59.245 47.619 0.00 0.00 39.60 5.36
232 238 2.167693 AGTACTCATCGATTTCGCCCAA 59.832 45.455 0.00 0.00 39.60 4.12
233 239 2.107950 ACTCATCGATTTCGCCCAAA 57.892 45.000 0.00 0.00 39.60 3.28
234 240 2.432444 ACTCATCGATTTCGCCCAAAA 58.568 42.857 0.00 0.00 39.60 2.44
235 241 3.016736 ACTCATCGATTTCGCCCAAAAT 58.983 40.909 0.00 0.00 39.60 1.82
236 242 3.181497 ACTCATCGATTTCGCCCAAAATG 60.181 43.478 0.00 0.00 39.60 2.32
246 252 0.532115 GCCCAAAATGCGGTGAATCT 59.468 50.000 0.00 0.00 0.00 2.40
268 274 4.415596 TGACAAGCCTACAAAATGGGATT 58.584 39.130 0.00 0.00 38.24 3.01
279 285 6.862469 ACAAAATGGGATTGATGAACTCAT 57.138 33.333 0.00 0.00 39.70 2.90
316 352 4.162690 GCGATTCTGCCCCTCCGT 62.163 66.667 0.00 0.00 0.00 4.69
324 360 4.966787 GCCCCTCCGTGCCAACAA 62.967 66.667 0.00 0.00 0.00 2.83
412 448 0.891373 GACTGCTGCTACCACAGAGA 59.109 55.000 0.00 0.00 40.25 3.10
416 452 1.153745 CTGCTACCACAGAGACCGC 60.154 63.158 0.00 0.00 40.25 5.68
515 551 2.602676 GCACAGGCTACCCCCTTCA 61.603 63.158 0.00 0.00 36.96 3.02
526 562 2.131709 CCCCTTCATACTCCGGCGA 61.132 63.158 9.30 0.00 0.00 5.54
645 693 1.591158 GTTTCGAAATGCGCCGAGATA 59.409 47.619 14.69 0.00 40.61 1.98
657 705 0.676736 CCGAGATAGAAGTGGGGAGC 59.323 60.000 0.00 0.00 0.00 4.70
680 728 1.203492 AGAAGAAGTGGAGGGACCCAT 60.203 52.381 14.60 0.00 38.66 4.00
702 750 1.078708 CGCCTAATCACCCAACGGT 60.079 57.895 0.00 0.00 46.31 4.83
735 783 4.436998 CACGACCAGGCGACTCCC 62.437 72.222 0.00 0.00 40.21 4.30
751 799 4.892379 CCGGCGCACGCATCAATG 62.892 66.667 17.69 0.00 44.11 2.82
753 801 2.023741 GGCGCACGCATCAATGAG 59.976 61.111 17.69 0.00 44.11 2.90
765 813 2.044946 AATGAGGGGCAGCGGTTC 60.045 61.111 0.00 0.00 0.00 3.62
824 874 2.588877 GTGGCAGCGTGTGTCTGT 60.589 61.111 0.00 0.00 34.21 3.41
825 875 1.300620 GTGGCAGCGTGTGTCTGTA 60.301 57.895 0.00 0.00 34.21 2.74
826 876 0.878523 GTGGCAGCGTGTGTCTGTAA 60.879 55.000 0.00 0.00 34.21 2.41
828 878 0.319555 GGCAGCGTGTGTCTGTAAGA 60.320 55.000 0.00 0.00 43.69 2.10
842 896 4.776349 TCTGTAAGACAAAAGGAGCACAA 58.224 39.130 0.00 0.00 38.67 3.33
848 902 2.034124 ACAAAAGGAGCACAACTGCAT 58.966 42.857 0.00 0.00 46.97 3.96
879 933 7.452630 GGTTTTATGTAAAAACTTTGCGTCA 57.547 32.000 11.78 0.00 39.23 4.35
880 934 7.896894 GGTTTTATGTAAAAACTTTGCGTCAA 58.103 30.769 11.78 0.00 39.23 3.18
881 935 8.544597 GGTTTTATGTAAAAACTTTGCGTCAAT 58.455 29.630 11.78 0.00 39.23 2.57
882 936 9.909043 GTTTTATGTAAAAACTTTGCGTCAATT 57.091 25.926 6.19 0.00 36.97 2.32
948 1005 2.513204 CCCATCTCAGCACTGCCG 60.513 66.667 0.00 0.00 0.00 5.69
994 1051 1.373435 CCTGTTAGGGTTCGTGCCA 59.627 57.895 1.03 0.00 0.00 4.92
1532 1590 5.408204 TGTTGCATAATGTGTCGATCATC 57.592 39.130 6.54 0.00 0.00 2.92
1533 1591 5.118286 TGTTGCATAATGTGTCGATCATCT 58.882 37.500 6.54 2.00 0.00 2.90
1648 1712 0.887247 ATGCTTTGCGTGTTGGCATA 59.113 45.000 0.00 0.00 43.52 3.14
1707 1771 1.065199 TCTGCCCATCATCTGTGAACC 60.065 52.381 0.00 0.00 38.01 3.62
1710 1774 1.474077 GCCCATCATCTGTGAACCAAC 59.526 52.381 0.00 0.00 38.01 3.77
1788 1876 2.292267 AGCATGTCATCCCGAACATTC 58.708 47.619 0.00 0.00 0.00 2.67
1801 1890 4.023279 CCCGAACATTCTTTCATGTCAACA 60.023 41.667 0.00 0.00 36.30 3.33
1896 1985 0.835941 TTGCCATGTTTGCCAACCTT 59.164 45.000 0.00 0.00 31.02 3.50
1948 2037 2.166254 CGGGTTGCCATGCTTAAAATCT 59.834 45.455 0.00 0.00 0.00 2.40
1949 2038 3.524541 GGGTTGCCATGCTTAAAATCTG 58.475 45.455 0.00 0.00 0.00 2.90
2107 2197 1.078567 CCTCTTGCTGCTGAGTCCC 60.079 63.158 17.13 0.00 0.00 4.46
2169 2259 6.580963 GCAAGAGCGATATAATGTAGGATG 57.419 41.667 0.00 0.00 0.00 3.51
2216 2309 0.743701 CTCACACAGCCAGGATCAGC 60.744 60.000 0.00 0.00 0.00 4.26
2217 2310 1.002990 CACACAGCCAGGATCAGCA 60.003 57.895 0.00 0.00 0.00 4.41
2540 2660 6.912426 ACTGGTGGAGACTATACTCATTCTA 58.088 40.000 0.00 0.00 38.51 2.10
2546 2666 8.658609 GTGGAGACTATACTCATTCTACGTATC 58.341 40.741 0.00 0.00 38.51 2.24
2958 3081 2.365901 CCATGCCCCTTTGCCCAT 60.366 61.111 0.00 0.00 0.00 4.00
3010 3133 1.184970 ACCATGGGCAAGGAAAACCG 61.185 55.000 18.09 0.00 0.00 4.44
3017 3140 1.362355 CAAGGAAAACCGTGGCCAC 59.638 57.895 26.78 26.78 0.00 5.01
3155 3278 6.049790 GTCACCATATCCTGAAAAGGTCTAC 58.950 44.000 0.00 0.00 0.00 2.59
3197 3320 5.580022 ACCCTGACCTAATAATTTTGCTGT 58.420 37.500 0.00 0.00 0.00 4.40
3348 3471 6.959311 GTGATTAGCGTTGACGTTGATATTTT 59.041 34.615 5.36 0.00 42.22 1.82
3394 3517 2.816087 ACATGTTGAGTGCTCACCATTC 59.184 45.455 9.10 0.00 39.25 2.67
3602 4080 7.625828 ACTAAACAACACTCACTTTTAAGCT 57.374 32.000 0.00 0.00 0.00 3.74
3654 4132 3.754850 GACATGGCAGAGCATATGCATAA 59.245 43.478 28.62 8.93 45.68 1.90
3927 4409 7.568325 CAATGCACTTGAGTACCTTCCTAAGG 61.568 46.154 4.13 4.13 45.03 2.69
4135 4617 3.787634 GTCTCGCACGTTATCGACATTTA 59.212 43.478 0.00 0.00 40.62 1.40
4164 4646 7.604927 TGGTGAATTTAACGTATTGCTACTCTT 59.395 33.333 0.00 0.00 0.00 2.85
4214 4696 7.661127 TTTATATGTGTGCCGTGGTATATTC 57.339 36.000 0.00 0.00 0.00 1.75
4233 4715 9.303537 GTATATTCTAGTGTCTTCTTTGTCACC 57.696 37.037 0.00 0.00 0.00 4.02
4253 4735 8.526147 TGTCACCTACAAGTTATTTAGGTCTAC 58.474 37.037 6.94 8.62 43.16 2.59
4381 4863 3.245016 TGTCTCTGGTGAATGCCAATCTT 60.245 43.478 0.00 0.00 38.18 2.40
4426 4908 8.824159 AATCAAGATCGTTAGATACTTGATGG 57.176 34.615 21.85 4.68 46.32 3.51
4457 4939 1.557371 TGCCACATGGGATAAACGAGA 59.443 47.619 0.00 0.00 40.01 4.04
4458 4940 2.026729 TGCCACATGGGATAAACGAGAA 60.027 45.455 0.00 0.00 40.01 2.87
4958 5450 1.814394 GTGATTTGCAGGATGTGAGCA 59.186 47.619 0.00 0.00 39.31 4.26
5199 5692 5.904941 TCTGTAGTCCTTAACGTTTGAACA 58.095 37.500 5.91 3.25 0.00 3.18
5650 6143 4.392047 TGCCACATTATGATCTGGACATC 58.608 43.478 0.00 0.00 0.00 3.06
5756 6249 3.825585 TGCATGTTTATGAAGGAGCACAA 59.174 39.130 0.00 0.00 36.36 3.33
5757 6250 4.280425 TGCATGTTTATGAAGGAGCACAAA 59.720 37.500 0.00 0.00 36.36 2.83
5835 6331 0.323999 AAGAAGCATGCAGGCATCCA 60.324 50.000 26.87 0.00 33.90 3.41
6138 6683 9.241919 TCTATTATTTGTCCATGTGTGATTTGT 57.758 29.630 0.00 0.00 0.00 2.83
6139 6684 9.859427 CTATTATTTGTCCATGTGTGATTTGTT 57.141 29.630 0.00 0.00 0.00 2.83
6140 6685 8.761575 ATTATTTGTCCATGTGTGATTTGTTC 57.238 30.769 0.00 0.00 0.00 3.18
6141 6686 5.588958 TTTGTCCATGTGTGATTTGTTCA 57.411 34.783 0.00 0.00 0.00 3.18
6142 6687 5.787953 TTGTCCATGTGTGATTTGTTCAT 57.212 34.783 0.00 0.00 36.54 2.57
6192 6737 3.744660 TGTTTGCTTGGTTTTGTTGGTT 58.255 36.364 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 6.187727 TGGAGATCTGTGAACCTACTTTTT 57.812 37.500 0.00 0.00 0.00 1.94
13 14 5.825593 TGGAGATCTGTGAACCTACTTTT 57.174 39.130 0.00 0.00 0.00 2.27
14 15 5.513267 GGTTGGAGATCTGTGAACCTACTTT 60.513 44.000 15.44 0.00 34.43 2.66
15 16 4.020128 GGTTGGAGATCTGTGAACCTACTT 60.020 45.833 15.44 0.00 34.43 2.24
33 35 5.909477 AGATGTTATCATGCAATTGGTTGG 58.091 37.500 7.72 0.00 33.66 3.77
41 43 3.181440 GGGAGGGAGATGTTATCATGCAA 60.181 47.826 0.00 0.00 34.06 4.08
46 48 3.207549 TGAGAGGGAGGGAGATGTTATCA 59.792 47.826 0.00 0.00 0.00 2.15
68 70 1.073722 CAGGTGTGGCATGTGGAGT 59.926 57.895 0.00 0.00 0.00 3.85
76 78 3.200329 ATGCTCTGCAGGTGTGGCA 62.200 57.895 15.13 15.98 43.65 4.92
77 79 2.360852 ATGCTCTGCAGGTGTGGC 60.361 61.111 15.13 11.07 43.65 5.01
86 91 2.094390 TGCCAAATTGAAGATGCTCTGC 60.094 45.455 0.00 0.00 0.00 4.26
88 93 3.056322 GGTTGCCAAATTGAAGATGCTCT 60.056 43.478 0.00 0.00 0.00 4.09
120 125 3.253220 TGGTTTGGGTACTGGTGACTAT 58.747 45.455 0.00 0.00 0.00 2.12
123 128 2.351706 TTGGTTTGGGTACTGGTGAC 57.648 50.000 0.00 0.00 0.00 3.67
145 151 8.506168 TTAGGAATGGATTAAGCACTTGTTAG 57.494 34.615 0.00 0.00 0.00 2.34
174 180 8.980832 AGAGATTACCTGATGGATAGGTTAAT 57.019 34.615 1.59 1.42 46.13 1.40
184 190 6.678568 ATCCTTGTAGAGATTACCTGATGG 57.321 41.667 0.00 0.00 39.83 3.51
194 200 9.073475 GATGAGTACTGTTATCCTTGTAGAGAT 57.927 37.037 0.00 0.00 0.00 2.75
195 201 7.226918 CGATGAGTACTGTTATCCTTGTAGAGA 59.773 40.741 0.00 0.00 0.00 3.10
196 202 7.226918 TCGATGAGTACTGTTATCCTTGTAGAG 59.773 40.741 0.00 0.00 0.00 2.43
198 204 7.260558 TCGATGAGTACTGTTATCCTTGTAG 57.739 40.000 0.00 0.00 0.00 2.74
199 205 7.818997 ATCGATGAGTACTGTTATCCTTGTA 57.181 36.000 0.00 0.00 0.00 2.41
200 206 6.716934 ATCGATGAGTACTGTTATCCTTGT 57.283 37.500 0.00 0.00 0.00 3.16
201 207 7.096436 CGAAATCGATGAGTACTGTTATCCTTG 60.096 40.741 0.00 0.00 43.02 3.61
202 208 6.918569 CGAAATCGATGAGTACTGTTATCCTT 59.081 38.462 0.00 0.00 43.02 3.36
203 209 6.439599 CGAAATCGATGAGTACTGTTATCCT 58.560 40.000 0.00 0.00 43.02 3.24
204 210 5.117287 GCGAAATCGATGAGTACTGTTATCC 59.883 44.000 0.00 0.00 43.02 2.59
205 211 5.117287 GGCGAAATCGATGAGTACTGTTATC 59.883 44.000 0.00 0.67 43.02 1.75
206 212 4.982916 GGCGAAATCGATGAGTACTGTTAT 59.017 41.667 0.00 0.00 43.02 1.89
207 213 4.357142 GGCGAAATCGATGAGTACTGTTA 58.643 43.478 0.00 0.00 43.02 2.41
208 214 3.187700 GGCGAAATCGATGAGTACTGTT 58.812 45.455 0.00 0.00 43.02 3.16
209 215 2.481449 GGGCGAAATCGATGAGTACTGT 60.481 50.000 0.00 0.00 43.02 3.55
210 216 2.128035 GGGCGAAATCGATGAGTACTG 58.872 52.381 0.00 0.00 43.02 2.74
211 217 1.754803 TGGGCGAAATCGATGAGTACT 59.245 47.619 7.06 0.00 43.02 2.73
212 218 2.218953 TGGGCGAAATCGATGAGTAC 57.781 50.000 7.06 0.00 43.02 2.73
213 219 2.971660 TTGGGCGAAATCGATGAGTA 57.028 45.000 7.06 0.00 43.02 2.59
214 220 2.107950 TTTGGGCGAAATCGATGAGT 57.892 45.000 7.06 0.00 43.02 3.41
215 221 3.365832 CATTTTGGGCGAAATCGATGAG 58.634 45.455 7.06 0.00 43.02 2.90
216 222 2.479389 GCATTTTGGGCGAAATCGATGA 60.479 45.455 7.06 0.00 43.02 2.92
217 223 1.854126 GCATTTTGGGCGAAATCGATG 59.146 47.619 7.06 1.63 43.02 3.84
218 224 2.208326 GCATTTTGGGCGAAATCGAT 57.792 45.000 7.06 0.00 43.02 3.59
219 225 3.712020 GCATTTTGGGCGAAATCGA 57.288 47.368 7.06 0.00 43.02 3.59
227 233 0.532115 AGATTCACCGCATTTTGGGC 59.468 50.000 0.00 0.00 0.00 5.36
228 234 1.818060 TCAGATTCACCGCATTTTGGG 59.182 47.619 0.00 0.00 0.00 4.12
229 235 2.228582 TGTCAGATTCACCGCATTTTGG 59.771 45.455 0.00 0.00 0.00 3.28
230 236 3.557577 TGTCAGATTCACCGCATTTTG 57.442 42.857 0.00 0.00 0.00 2.44
231 237 3.612479 GCTTGTCAGATTCACCGCATTTT 60.612 43.478 0.00 0.00 0.00 1.82
232 238 2.095059 GCTTGTCAGATTCACCGCATTT 60.095 45.455 0.00 0.00 0.00 2.32
233 239 1.470098 GCTTGTCAGATTCACCGCATT 59.530 47.619 0.00 0.00 0.00 3.56
234 240 1.089920 GCTTGTCAGATTCACCGCAT 58.910 50.000 0.00 0.00 0.00 4.73
235 241 0.955428 GGCTTGTCAGATTCACCGCA 60.955 55.000 0.00 0.00 0.00 5.69
236 242 0.674895 AGGCTTGTCAGATTCACCGC 60.675 55.000 0.00 0.00 0.00 5.68
242 248 4.463891 CCCATTTTGTAGGCTTGTCAGATT 59.536 41.667 0.00 0.00 0.00 2.40
246 252 3.517296 TCCCATTTTGTAGGCTTGTCA 57.483 42.857 0.00 0.00 0.00 3.58
279 285 0.250295 CGTGAGCAAAACCTCCCAGA 60.250 55.000 0.00 0.00 0.00 3.86
282 288 2.626780 GCCGTGAGCAAAACCTCCC 61.627 63.158 0.00 0.00 42.97 4.30
288 294 0.516877 CAGAATCGCCGTGAGCAAAA 59.483 50.000 0.00 0.00 44.04 2.44
339 375 4.099170 CGAGGAGGAACGACGCGT 62.099 66.667 13.85 13.85 43.97 6.01
392 428 0.457509 CTCTGTGGTAGCAGCAGTCG 60.458 60.000 17.88 10.63 36.49 4.18
393 429 0.891373 TCTCTGTGGTAGCAGCAGTC 59.109 55.000 17.88 0.00 36.49 3.51
416 452 1.568612 CTACAACCGCAGCACACCAG 61.569 60.000 0.00 0.00 0.00 4.00
468 504 1.262640 GGAGGGGTTAAGCGACCAGA 61.263 60.000 8.80 0.00 41.65 3.86
511 547 2.194271 GTCTTTCGCCGGAGTATGAAG 58.806 52.381 5.05 6.35 0.00 3.02
620 668 1.801512 GCGCATTTCGAAACTGCCC 60.802 57.895 25.66 18.93 41.67 5.36
624 672 0.669318 TCTCGGCGCATTTCGAAACT 60.669 50.000 13.81 0.00 41.67 2.66
645 693 1.229209 TTCTCCGCTCCCCACTTCT 60.229 57.895 0.00 0.00 0.00 2.85
657 705 0.533032 GTCCCTCCACTTCTTCTCCG 59.467 60.000 0.00 0.00 0.00 4.63
680 728 0.035820 GTTGGGTGATTAGGCGGTCA 60.036 55.000 0.00 0.00 0.00 4.02
735 783 3.778609 CTCATTGATGCGTGCGCCG 62.779 63.158 14.16 9.69 41.09 6.46
806 856 3.705638 CAGACACACGCTGCCACG 61.706 66.667 0.00 0.00 39.50 4.94
808 858 0.599991 CTTACAGACACACGCTGCCA 60.600 55.000 0.00 0.00 36.86 4.92
821 871 4.576463 AGTTGTGCTCCTTTTGTCTTACAG 59.424 41.667 0.00 0.00 0.00 2.74
871 925 9.884465 CCCAAAATTAATTAAAATTGACGCAAA 57.116 25.926 19.86 0.00 0.00 3.68
872 926 9.273016 TCCCAAAATTAATTAAAATTGACGCAA 57.727 25.926 19.86 0.00 0.00 4.85
873 927 8.833231 TCCCAAAATTAATTAAAATTGACGCA 57.167 26.923 19.86 5.72 0.00 5.24
874 928 8.387354 CCTCCCAAAATTAATTAAAATTGACGC 58.613 33.333 19.86 0.00 0.00 5.19
875 929 8.878769 CCCTCCCAAAATTAATTAAAATTGACG 58.121 33.333 19.86 12.95 0.00 4.35
876 930 9.952030 TCCCTCCCAAAATTAATTAAAATTGAC 57.048 29.630 19.86 0.00 0.00 3.18
877 931 9.952030 GTCCCTCCCAAAATTAATTAAAATTGA 57.048 29.630 19.86 7.32 0.00 2.57
878 932 9.173021 GGTCCCTCCCAAAATTAATTAAAATTG 57.827 33.333 14.70 14.70 0.00 2.32
948 1005 0.106967 GAGATTGGGTTCTGGGGCTC 60.107 60.000 0.00 0.00 0.00 4.70
1532 1590 5.642063 TCTGACCCAAAAAGCGTATTTCTAG 59.358 40.000 0.00 0.00 0.00 2.43
1533 1591 5.553123 TCTGACCCAAAAAGCGTATTTCTA 58.447 37.500 0.00 0.00 0.00 2.10
1648 1712 3.623060 CAGCCGTAGCACATAATTCTTGT 59.377 43.478 0.00 0.00 43.56 3.16
1707 1771 7.409697 CCATAATTCCTCATTAGTTCACGTTG 58.590 38.462 0.00 0.00 30.48 4.10
1710 1774 5.049405 GGCCATAATTCCTCATTAGTTCACG 60.049 44.000 0.00 0.00 30.48 4.35
1801 1890 4.330944 TTGTCACCTCGTGTCAACTAAT 57.669 40.909 1.21 0.00 36.87 1.73
1862 1951 5.613329 ACATGGCAATGTTCTGACAAAAAT 58.387 33.333 0.00 0.00 44.94 1.82
1896 1985 4.203226 TCATGGCAACTTTAGTTCACACA 58.797 39.130 0.00 0.00 35.83 3.72
1948 2037 5.675071 GCAAATGATAAATCCCGAACGTTCA 60.675 40.000 26.71 9.14 0.00 3.18
1949 2038 4.733405 GCAAATGATAAATCCCGAACGTTC 59.267 41.667 18.47 18.47 0.00 3.95
2055 2145 3.825160 GAGCACGGTGGTCAAGCCA 62.825 63.158 29.56 0.00 43.79 4.75
2107 2197 1.965754 CTCTGGGCCGAGGAGAAAGG 61.966 65.000 15.52 0.00 0.00 3.11
2169 2259 0.036732 TCCATGAACTGTCAGCACCC 59.963 55.000 0.00 0.00 37.14 4.61
2217 2310 5.834742 TGGTATAATGCATTGAAGCTCCAAT 59.165 36.000 22.27 6.49 37.24 3.16
2540 2660 2.599677 GAATGGAGGAGGAGGATACGT 58.400 52.381 0.00 0.00 46.39 3.57
2546 2666 1.348775 GGGTGGAATGGAGGAGGAGG 61.349 65.000 0.00 0.00 0.00 4.30
2851 2974 8.490355 GGTAAACTATATTTTGAATACGGACCG 58.510 37.037 13.61 13.61 0.00 4.79
2958 3081 7.346751 AGTTGGCAAGAAAAATGAACTAGAA 57.653 32.000 0.00 0.00 0.00 2.10
3176 3299 7.830739 AGAAACAGCAAAATTATTAGGTCAGG 58.169 34.615 0.00 0.00 0.00 3.86
3197 3320 8.405531 CAAGAAAACAAGTGTAATGAGGAGAAA 58.594 33.333 0.00 0.00 0.00 2.52
3296 3419 7.766219 AATTAACGCGCGAATAATATCCTAT 57.234 32.000 39.36 18.77 0.00 2.57
3394 3517 7.041167 TGCCAATCCAATGATCTAAATTACTCG 60.041 37.037 0.00 0.00 0.00 4.18
3602 4080 1.402720 GCCTTGCATTGCGCTTTAAGA 60.403 47.619 9.73 0.00 43.06 2.10
3654 4132 5.649395 AGTGCTATGCTGTGATTTATTGTGT 59.351 36.000 0.00 0.00 0.00 3.72
4135 4617 8.736244 AGTAGCAATACGTTAAATTCACCAAAT 58.264 29.630 0.00 0.00 0.00 2.32
4164 4646 4.439057 GTCACGGCAAGATATAAGACCAA 58.561 43.478 0.00 0.00 0.00 3.67
4214 4696 6.085555 TGTAGGTGACAAAGAAGACACTAG 57.914 41.667 0.00 0.00 34.15 2.57
4239 4721 9.654663 ACTGTCATTTCAGTAGACCTAAATAAC 57.345 33.333 0.00 0.00 45.31 1.89
4253 4735 6.176183 AGTCTTATCCCAACTGTCATTTCAG 58.824 40.000 0.00 0.00 40.80 3.02
4381 4863 5.424573 TGATTTGGAATTTCATATGCCCACA 59.575 36.000 0.00 0.00 0.00 4.17
4426 4908 1.224075 CATGTGGCATCTCGTCCATC 58.776 55.000 0.00 0.00 34.47 3.51
4457 4939 5.939883 TCTATTCAAGTACTGCAGCACATTT 59.060 36.000 19.16 2.89 0.00 2.32
4458 4940 5.491070 TCTATTCAAGTACTGCAGCACATT 58.509 37.500 19.16 7.73 0.00 2.71
4958 5450 1.895707 GGTGCACAGCAGAAGCAGT 60.896 57.895 20.43 0.00 45.49 4.40
5177 5670 6.780706 ATGTTCAAACGTTAAGGACTACAG 57.219 37.500 0.00 0.00 0.00 2.74
5607 6100 5.599732 GCAATGCCATTACCACATGAAATA 58.400 37.500 0.00 0.00 0.00 1.40
5742 6235 4.261801 GCCTACTTTTGTGCTCCTTCATA 58.738 43.478 0.00 0.00 0.00 2.15
5756 6249 4.847198 TGTCATGTCATGATGCCTACTTT 58.153 39.130 18.32 0.00 42.04 2.66
5757 6250 4.492494 TGTCATGTCATGATGCCTACTT 57.508 40.909 18.32 0.00 42.04 2.24
6124 6669 6.319405 TCTCCATATGAACAAATCACACATGG 59.681 38.462 3.65 0.00 41.93 3.66
6128 6673 6.595326 TCAGTCTCCATATGAACAAATCACAC 59.405 38.462 3.65 0.00 41.93 3.82
6129 6674 6.710278 TCAGTCTCCATATGAACAAATCACA 58.290 36.000 3.65 0.00 41.93 3.58
6130 6675 7.615582 TTCAGTCTCCATATGAACAAATCAC 57.384 36.000 3.65 0.00 41.93 3.06
6131 6676 8.270030 AGATTCAGTCTCCATATGAACAAATCA 58.730 33.333 3.65 0.00 35.70 2.57
6132 6677 8.674263 AGATTCAGTCTCCATATGAACAAATC 57.326 34.615 3.65 11.54 35.89 2.17
6133 6678 9.118300 GAAGATTCAGTCTCCATATGAACAAAT 57.882 33.333 3.65 4.32 35.67 2.32
6134 6679 8.324306 AGAAGATTCAGTCTCCATATGAACAAA 58.676 33.333 3.65 0.00 35.67 2.83
6135 6680 7.855375 AGAAGATTCAGTCTCCATATGAACAA 58.145 34.615 3.65 0.00 35.67 2.83
6136 6681 7.429374 AGAAGATTCAGTCTCCATATGAACA 57.571 36.000 3.65 0.00 35.67 3.18
6142 6687 9.661954 AGGTTTATAGAAGATTCAGTCTCCATA 57.338 33.333 0.00 0.00 35.67 2.74
6192 6737 9.114952 TCCGCATAAAACTAATATTCATGACAA 57.885 29.630 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.