Multiple sequence alignment - TraesCS5B01G086700

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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 TraesCS5B01G086700 chr5B 100.000 2237 0 0 1 2237 110118653 110120889 0.000000e+00 4132.0
1 TraesCS5B01G086700 chr5B 93.408 804 50 3 1436 2237 669499975 669500777 0.000000e+00 1188.0
2 TraesCS5B01G086700 chr5B 92.611 812 54 6 1427 2237 477522346 477521540 0.000000e+00 1162.0
3 TraesCS5B01G086700 chr4B 93.061 807 51 5 1433 2237 497418967 497419770 0.000000e+00 1175.0
4 TraesCS5B01G086700 chr4B 92.910 804 53 4 1436 2237 608622227 608621426 0.000000e+00 1166.0
5 TraesCS5B01G086700 chr7D 93.035 804 53 3 1436 2237 34031472 34032274 0.000000e+00 1171.0
6 TraesCS5B01G086700 chr1A 93.035 804 52 4 1435 2237 267351949 267351149 0.000000e+00 1171.0
7 TraesCS5B01G086700 chr1A 93.035 804 53 3 1436 2237 556720061 556720863 0.000000e+00 1171.0
8 TraesCS5B01G086700 chr2B 92.937 807 50 5 1436 2237 545364622 545363818 0.000000e+00 1168.0
9 TraesCS5B01G086700 chr6D 92.902 803 56 1 1436 2237 402562048 402561246 0.000000e+00 1166.0
10 TraesCS5B01G086700 chr5D 92.535 710 28 15 743 1435 101705359 101706060 0.000000e+00 994.0
11 TraesCS5B01G086700 chr5D 85.538 650 74 15 1 632 101703676 101704323 0.000000e+00 662.0
12 TraesCS5B01G086700 chr5A 89.636 714 50 15 702 1398 98444960 98444254 0.000000e+00 887.0
13 TraesCS5B01G086700 chr5A 83.081 727 85 24 1 696 98445972 98445253 5.240000e-176 627.0
14 TraesCS5B01G086700 chr5A 100.000 33 0 0 600 632 566209315 566209283 6.670000e-06 62.1
15 TraesCS5B01G086700 chr5A 94.737 38 1 1 600 636 439874818 439874781 8.630000e-05 58.4


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 TraesCS5B01G086700 chr5B 110118653 110120889 2236 False 4132 4132 100.0000 1 2237 1 chr5B.!!$F1 2236
1 TraesCS5B01G086700 chr5B 669499975 669500777 802 False 1188 1188 93.4080 1436 2237 1 chr5B.!!$F2 801
2 TraesCS5B01G086700 chr5B 477521540 477522346 806 True 1162 1162 92.6110 1427 2237 1 chr5B.!!$R1 810
3 TraesCS5B01G086700 chr4B 497418967 497419770 803 False 1175 1175 93.0610 1433 2237 1 chr4B.!!$F1 804
4 TraesCS5B01G086700 chr4B 608621426 608622227 801 True 1166 1166 92.9100 1436 2237 1 chr4B.!!$R1 801
5 TraesCS5B01G086700 chr7D 34031472 34032274 802 False 1171 1171 93.0350 1436 2237 1 chr7D.!!$F1 801
6 TraesCS5B01G086700 chr1A 267351149 267351949 800 True 1171 1171 93.0350 1435 2237 1 chr1A.!!$R1 802
7 TraesCS5B01G086700 chr1A 556720061 556720863 802 False 1171 1171 93.0350 1436 2237 1 chr1A.!!$F1 801
8 TraesCS5B01G086700 chr2B 545363818 545364622 804 True 1168 1168 92.9370 1436 2237 1 chr2B.!!$R1 801
9 TraesCS5B01G086700 chr6D 402561246 402562048 802 True 1166 1166 92.9020 1436 2237 1 chr6D.!!$R1 801
10 TraesCS5B01G086700 chr5D 101703676 101706060 2384 False 828 994 89.0365 1 1435 2 chr5D.!!$F1 1434
11 TraesCS5B01G086700 chr5A 98444254 98445972 1718 True 757 887 86.3585 1 1398 2 chr5A.!!$R3 1397

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
91 92 0.108186 CCTGCTTGCCATCGTCACTA 60.108 55.0 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2026 3005 0.248949 GGCGTTGGACGGATACTCTC 60.249 60.0 2.48 0.0 42.82 3.2 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
85 86 2.842256 GCATCCCTGCTTGCCATCG 61.842 63.158 0.00 0.00 45.32 3.84
91 92 0.108186 CCTGCTTGCCATCGTCACTA 60.108 55.000 0.00 0.00 0.00 2.74
106 107 2.630098 GTCACTAGAGATGGCTATGGCA 59.370 50.000 2.58 0.00 43.52 4.92
110 111 1.303155 GAGATGGCTATGGCAGGGC 60.303 63.158 2.58 9.29 42.43 5.19
112 115 4.275508 ATGGCTATGGCAGGGCGG 62.276 66.667 2.58 0.00 42.43 6.13
126 129 3.749064 GCGGTCGCACAGAGGAGA 61.749 66.667 10.67 0.00 41.49 3.71
129 132 1.009389 CGGTCGCACAGAGGAGAAAC 61.009 60.000 0.00 0.00 0.00 2.78
165 168 3.555795 CCTTGTGGACGCTATGCTCATAT 60.556 47.826 0.00 0.00 34.57 1.78
167 170 4.864704 TGTGGACGCTATGCTCATATAA 57.135 40.909 0.00 0.00 0.00 0.98
177 180 6.529829 CGCTATGCTCATATAAAGGAAGAGTC 59.470 42.308 0.00 0.00 0.00 3.36
187 190 1.376466 GGAAGAGTCCAAGCAGCCA 59.624 57.895 0.00 0.00 44.26 4.75
201 204 4.670896 AGCAGCCAAAAACATTACAACT 57.329 36.364 0.00 0.00 0.00 3.16
210 213 8.247562 GCCAAAAACATTACAACTCCATACATA 58.752 33.333 0.00 0.00 0.00 2.29
224 227 6.068461 TCCATACATAAAAGGCTAACCACA 57.932 37.500 0.00 0.00 39.06 4.17
235 238 2.226437 GGCTAACCACATCAACACACAG 59.774 50.000 0.00 0.00 35.26 3.66
238 241 4.554723 GCTAACCACATCAACACACAGAAC 60.555 45.833 0.00 0.00 0.00 3.01
239 242 2.997980 ACCACATCAACACACAGAACA 58.002 42.857 0.00 0.00 0.00 3.18
240 243 2.682856 ACCACATCAACACACAGAACAC 59.317 45.455 0.00 0.00 0.00 3.32
241 244 2.682352 CCACATCAACACACAGAACACA 59.318 45.455 0.00 0.00 0.00 3.72
242 245 3.316029 CCACATCAACACACAGAACACAT 59.684 43.478 0.00 0.00 0.00 3.21
251 255 1.302431 CAGAACACATGCCGACCCA 60.302 57.895 0.00 0.00 0.00 4.51
252 256 0.888736 CAGAACACATGCCGACCCAA 60.889 55.000 0.00 0.00 0.00 4.12
254 258 1.152860 AACACATGCCGACCCAACA 60.153 52.632 0.00 0.00 0.00 3.33
265 269 1.653151 GACCCAACATCTAAGGCGAC 58.347 55.000 0.00 0.00 0.00 5.19
272 276 2.641305 ACATCTAAGGCGACTACTCGT 58.359 47.619 0.00 0.00 42.68 4.18
274 278 2.391616 TCTAAGGCGACTACTCGTGA 57.608 50.000 0.00 0.00 42.68 4.35
282 286 2.282290 GCGACTACTCGTGACTCTCTAC 59.718 54.545 0.00 0.00 42.33 2.59
283 287 2.859538 CGACTACTCGTGACTCTCTACC 59.140 54.545 0.00 0.00 35.00 3.18
284 288 2.859538 GACTACTCGTGACTCTCTACCG 59.140 54.545 0.00 0.00 0.00 4.02
287 295 1.001746 ACTCGTGACTCTCTACCGACA 59.998 52.381 0.00 0.00 0.00 4.35
322 331 4.028131 ACGGATCTACCCTAATCAACACA 58.972 43.478 0.00 0.00 34.64 3.72
323 332 4.468510 ACGGATCTACCCTAATCAACACAA 59.531 41.667 0.00 0.00 34.64 3.33
327 336 6.351881 GGATCTACCCTAATCAACACAACAGA 60.352 42.308 0.00 0.00 0.00 3.41
347 356 3.636764 AGATCACCAAAACACAAACTCCC 59.363 43.478 0.00 0.00 0.00 4.30
369 379 0.179045 CCAATGAGCCTAAGGACCGG 60.179 60.000 0.00 0.00 0.00 5.28
376 386 2.060980 CCTAAGGACCGGCTGAGCT 61.061 63.158 3.72 0.00 0.00 4.09
377 387 0.755698 CCTAAGGACCGGCTGAGCTA 60.756 60.000 3.72 0.00 0.00 3.32
381 391 0.912486 AGGACCGGCTGAGCTAAAAT 59.088 50.000 3.72 0.00 0.00 1.82
387 397 3.905900 GCTGAGCTAAAATCGGCAC 57.094 52.632 0.00 0.00 46.31 5.01
404 414 1.080298 ACGTCGTCGAAATCCACCC 60.080 57.895 9.47 0.00 40.62 4.61
410 420 1.389555 GTCGAAATCCACCCCATTCC 58.610 55.000 0.00 0.00 0.00 3.01
412 422 2.171870 GTCGAAATCCACCCCATTCCTA 59.828 50.000 0.00 0.00 0.00 2.94
428 438 3.737559 TCCTATGGTGCCAAAAGACAT 57.262 42.857 0.00 0.00 0.00 3.06
477 488 1.153289 CATTGGCCACTCTCGAGGG 60.153 63.158 11.78 11.78 0.00 4.30
491 505 1.515954 GAGGGCGGACGAAATGAGA 59.484 57.895 0.00 0.00 0.00 3.27
499 513 3.243101 GCGGACGAAATGAGATCTAGTGA 60.243 47.826 0.00 0.00 0.00 3.41
537 562 6.951198 TGGACTTGTCTTTTATCTCTCTCTCT 59.049 38.462 0.61 0.00 0.00 3.10
538 563 7.122055 TGGACTTGTCTTTTATCTCTCTCTCTC 59.878 40.741 0.61 0.00 0.00 3.20
539 564 7.339466 GGACTTGTCTTTTATCTCTCTCTCTCT 59.661 40.741 0.61 0.00 0.00 3.10
540 565 9.391006 GACTTGTCTTTTATCTCTCTCTCTCTA 57.609 37.037 0.00 0.00 0.00 2.43
541 566 9.920946 ACTTGTCTTTTATCTCTCTCTCTCTAT 57.079 33.333 0.00 0.00 0.00 1.98
552 577 9.925545 ATCTCTCTCTCTCTATATATGTGCATT 57.074 33.333 0.00 0.00 0.00 3.56
701 1099 9.807649 ACAAATCTGCATTTTAAAGGTGATATC 57.192 29.630 0.00 0.00 28.97 1.63
702 1100 9.806203 CAAATCTGCATTTTAAAGGTGATATCA 57.194 29.630 0.00 0.00 28.97 2.15
704 1102 9.976511 AATCTGCATTTTAAAGGTGATATCATG 57.023 29.630 9.02 0.80 0.00 3.07
705 1103 7.944061 TCTGCATTTTAAAGGTGATATCATGG 58.056 34.615 9.02 0.00 0.00 3.66
733 1399 3.277416 AGAAGTCTTGGTACCCCTCTT 57.723 47.619 10.07 8.75 0.00 2.85
734 1400 3.174779 AGAAGTCTTGGTACCCCTCTTC 58.825 50.000 10.07 16.34 0.00 2.87
746 1701 1.480683 CCCCTCTTCGATACCCAGCTA 60.481 57.143 0.00 0.00 0.00 3.32
747 1702 2.530701 CCCTCTTCGATACCCAGCTAT 58.469 52.381 0.00 0.00 0.00 2.97
754 1709 1.002087 CGATACCCAGCTATGTTCCCC 59.998 57.143 0.00 0.00 0.00 4.81
758 1713 0.918983 CCCAGCTATGTTCCCCTTGA 59.081 55.000 0.00 0.00 0.00 3.02
759 1714 1.496429 CCCAGCTATGTTCCCCTTGAT 59.504 52.381 0.00 0.00 0.00 2.57
760 1715 2.711009 CCCAGCTATGTTCCCCTTGATA 59.289 50.000 0.00 0.00 0.00 2.15
761 1716 3.496870 CCCAGCTATGTTCCCCTTGATAC 60.497 52.174 0.00 0.00 0.00 2.24
764 1719 2.441750 GCTATGTTCCCCTTGATACCCA 59.558 50.000 0.00 0.00 0.00 4.51
765 1720 3.747708 GCTATGTTCCCCTTGATACCCAC 60.748 52.174 0.00 0.00 0.00 4.61
769 1724 1.308746 CCCCTTGATACCCACCCCT 60.309 63.158 0.00 0.00 0.00 4.79
816 1785 3.606662 AGGCTCACACGCGTCACT 61.607 61.111 9.86 0.00 0.00 3.41
827 1796 3.150895 CGTCACTCGCAGCAGTTC 58.849 61.111 0.00 0.00 0.00 3.01
873 1842 1.751924 ACAATCTAGACGAGCCAGTCC 59.248 52.381 0.00 0.00 41.83 3.85
891 1860 2.537214 GTCCCGCGTATACTTAAGCAAC 59.463 50.000 4.92 0.00 33.03 4.17
907 1876 0.321210 CAACCATAGCGTGTCCCACA 60.321 55.000 0.00 0.00 33.40 4.17
930 1899 6.710744 ACAAAATACTCGATTCACCTCACTTT 59.289 34.615 0.00 0.00 0.00 2.66
1255 2224 2.222027 AGCTTCGCTAGTTTGTGCTTT 58.778 42.857 0.00 0.00 36.99 3.51
1256 2225 3.399330 AGCTTCGCTAGTTTGTGCTTTA 58.601 40.909 0.00 0.00 36.99 1.85
1259 2228 4.387862 GCTTCGCTAGTTTGTGCTTTAGTA 59.612 41.667 0.00 0.00 0.00 1.82
1260 2229 5.063564 GCTTCGCTAGTTTGTGCTTTAGTAT 59.936 40.000 0.00 0.00 0.00 2.12
1269 2239 2.232696 TGTGCTTTAGTATCCACGCTCA 59.767 45.455 0.00 0.00 0.00 4.26
1278 2249 0.250467 ATCCACGCTCACTTGCTTGT 60.250 50.000 0.00 0.00 31.43 3.16
1279 2250 0.391228 TCCACGCTCACTTGCTTGTA 59.609 50.000 0.00 0.00 31.43 2.41
1318 2289 3.181520 CGCTCGACAGTTTATTTCCCTTG 60.182 47.826 0.00 0.00 0.00 3.61
1323 2294 5.008217 TCGACAGTTTATTTCCCTTGTTGTG 59.992 40.000 0.00 0.00 0.00 3.33
1326 2297 5.221244 ACAGTTTATTTCCCTTGTTGTGAGC 60.221 40.000 0.00 0.00 0.00 4.26
1358 2332 3.064545 CCTCATTCGCATCCTTGTCTTTC 59.935 47.826 0.00 0.00 0.00 2.62
1359 2333 3.009723 TCATTCGCATCCTTGTCTTTCC 58.990 45.455 0.00 0.00 0.00 3.13
1414 2388 8.437360 TGCTAATTAATAATGGGATATCTGCG 57.563 34.615 2.05 0.00 0.00 5.18
1453 2427 7.621796 ACTTCCTTGTTAGAATAAATCCGAGT 58.378 34.615 0.00 0.00 0.00 4.18
1471 2445 0.738975 GTCACTCCGTCGATCATCCA 59.261 55.000 0.00 0.00 0.00 3.41
1539 2517 2.987149 GTTCACCGATATGGCTACATCG 59.013 50.000 3.45 3.45 43.94 3.84
1575 2553 3.461773 CGCTCCTCCCCGTGACAT 61.462 66.667 0.00 0.00 0.00 3.06
1644 2622 4.077184 CCCCCTTGCGCGTCTGTA 62.077 66.667 8.43 0.00 0.00 2.74
1653 2631 2.390938 TGCGCGTCTGTACTATTATGC 58.609 47.619 8.43 0.00 0.00 3.14
1656 2634 3.852205 GCGCGTCTGTACTATTATGCTGA 60.852 47.826 8.43 0.00 0.00 4.26
1696 2674 3.952967 GTCTACCCCCGCTATATAAGAGG 59.047 52.174 0.00 0.00 44.40 3.69
1779 2758 7.180408 ACAACTCATAGTCCAACTGTAACCTAT 59.820 37.037 0.00 0.00 0.00 2.57
1850 2829 7.310423 CGAATATACTCCATCACCCTGGATTTA 60.310 40.741 0.00 0.00 44.23 1.40
1965 2944 6.842676 ACTTGTAGTCCCTTCTTTTCTTGAT 58.157 36.000 0.00 0.00 0.00 2.57
2025 3004 4.347000 ACTCTAGTTTGTGCTCCCAACTTA 59.653 41.667 5.95 0.00 0.00 2.24
2026 3005 4.894784 TCTAGTTTGTGCTCCCAACTTAG 58.105 43.478 5.95 3.58 0.00 2.18
2038 3018 4.205587 TCCCAACTTAGAGAGTATCCGTC 58.794 47.826 0.00 0.00 37.72 4.79
2160 3141 3.777106 TCTTGACTGCCTGTCTGAAAT 57.223 42.857 3.32 0.00 45.54 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 2.751436 GCCCAAGCAAGATCGGCA 60.751 61.111 13.69 0.00 39.50 5.69
63 64 1.077501 GGCAAGCAGGGATGCACTA 60.078 57.895 2.73 0.00 44.32 2.74
74 75 0.894835 TCTAGTGACGATGGCAAGCA 59.105 50.000 0.00 0.00 0.00 3.91
85 86 2.630098 TGCCATAGCCATCTCTAGTGAC 59.370 50.000 0.00 0.00 38.69 3.67
91 92 1.776975 GCCCTGCCATAGCCATCTCT 61.777 60.000 0.00 0.00 38.69 3.10
110 111 1.009389 GTTTCTCCTCTGTGCGACCG 61.009 60.000 0.00 0.00 0.00 4.79
112 115 0.318762 AGGTTTCTCCTCTGTGCGAC 59.681 55.000 0.00 0.00 44.42 5.19
126 129 5.301805 CCACAAGGACAAAGATACAAGGTTT 59.698 40.000 0.00 0.00 36.89 3.27
129 132 4.651778 TCCACAAGGACAAAGATACAAGG 58.348 43.478 0.00 0.00 39.61 3.61
142 145 0.175760 GAGCATAGCGTCCACAAGGA 59.824 55.000 0.00 0.00 43.21 3.36
157 160 6.560003 TTGGACTCTTCCTTTATATGAGCA 57.440 37.500 0.00 0.00 43.31 4.26
165 168 2.290323 GGCTGCTTGGACTCTTCCTTTA 60.290 50.000 0.00 0.00 43.31 1.85
167 170 0.037447 GGCTGCTTGGACTCTTCCTT 59.963 55.000 0.00 0.00 43.31 3.36
177 180 3.726607 TGTAATGTTTTTGGCTGCTTGG 58.273 40.909 0.00 0.00 0.00 3.61
183 186 5.806654 ATGGAGTTGTAATGTTTTTGGCT 57.193 34.783 0.00 0.00 0.00 4.75
201 204 6.068461 TGTGGTTAGCCTTTTATGTATGGA 57.932 37.500 0.00 0.00 35.27 3.41
210 213 3.957497 TGTGTTGATGTGGTTAGCCTTTT 59.043 39.130 0.00 0.00 35.27 2.27
224 227 2.294233 GGCATGTGTTCTGTGTGTTGAT 59.706 45.455 0.00 0.00 0.00 2.57
235 238 1.169661 TGTTGGGTCGGCATGTGTTC 61.170 55.000 0.00 0.00 0.00 3.18
238 241 0.677731 AGATGTTGGGTCGGCATGTG 60.678 55.000 0.00 0.00 0.00 3.21
239 242 0.908910 TAGATGTTGGGTCGGCATGT 59.091 50.000 0.00 0.00 0.00 3.21
240 243 1.942657 CTTAGATGTTGGGTCGGCATG 59.057 52.381 0.00 0.00 0.00 4.06
241 244 1.134098 CCTTAGATGTTGGGTCGGCAT 60.134 52.381 0.00 0.00 0.00 4.40
242 245 0.251916 CCTTAGATGTTGGGTCGGCA 59.748 55.000 0.00 0.00 0.00 5.69
251 255 3.694535 CGAGTAGTCGCCTTAGATGTT 57.305 47.619 7.09 0.00 39.88 2.71
265 269 2.859538 GTCGGTAGAGAGTCACGAGTAG 59.140 54.545 0.00 0.00 33.92 2.57
272 276 1.202964 TGGGTTGTCGGTAGAGAGTCA 60.203 52.381 0.00 0.00 0.00 3.41
274 278 1.254954 GTGGGTTGTCGGTAGAGAGT 58.745 55.000 0.00 0.00 0.00 3.24
301 309 4.665833 TGTGTTGATTAGGGTAGATCCG 57.334 45.455 0.00 0.00 37.00 4.18
322 331 5.394115 GGAGTTTGTGTTTTGGTGATCTGTT 60.394 40.000 0.00 0.00 0.00 3.16
323 332 4.097892 GGAGTTTGTGTTTTGGTGATCTGT 59.902 41.667 0.00 0.00 0.00 3.41
327 336 2.360801 CGGGAGTTTGTGTTTTGGTGAT 59.639 45.455 0.00 0.00 0.00 3.06
347 356 0.815615 GTCCTTAGGCTCATTGGGCG 60.816 60.000 1.68 0.00 36.85 6.13
369 379 0.026803 CGTGCCGATTTTAGCTCAGC 59.973 55.000 0.00 0.00 0.00 4.26
376 386 0.109827 TCGACGACGTGCCGATTTTA 60.110 50.000 4.58 0.00 40.69 1.52
377 387 0.940519 TTCGACGACGTGCCGATTTT 60.941 50.000 4.58 0.00 40.69 1.82
381 391 1.798725 GATTTCGACGACGTGCCGA 60.799 57.895 4.58 6.44 40.69 5.54
387 397 1.808390 GGGGTGGATTTCGACGACG 60.808 63.158 0.00 0.00 41.26 5.12
410 420 4.264253 TCTGATGTCTTTTGGCACCATAG 58.736 43.478 0.00 0.00 36.59 2.23
412 422 3.159213 TCTGATGTCTTTTGGCACCAT 57.841 42.857 0.00 0.00 36.59 3.55
423 433 4.758674 CCATTGTCTTGTGTTCTGATGTCT 59.241 41.667 0.00 0.00 0.00 3.41
428 438 3.136443 ACCTCCATTGTCTTGTGTTCTGA 59.864 43.478 0.00 0.00 0.00 3.27
477 488 3.046390 CACTAGATCTCATTTCGTCCGC 58.954 50.000 0.00 0.00 0.00 5.54
480 491 5.885881 AGTGTCACTAGATCTCATTTCGTC 58.114 41.667 2.87 0.00 0.00 4.20
491 505 8.982723 AGTCCAACATAAATAGTGTCACTAGAT 58.017 33.333 17.43 11.13 33.66 1.98
499 513 8.691661 AAAGACAAGTCCAACATAAATAGTGT 57.308 30.769 0.00 0.00 0.00 3.55
526 550 9.925545 AATGCACATATATAGAGAGAGAGAGAT 57.074 33.333 0.00 0.00 0.00 2.75
584 609 5.180680 CCATGTGGTACAAGATATGCATCTG 59.819 44.000 0.19 0.00 44.16 2.90
683 1081 9.846248 GATACCATGATATCACCTTTAAAATGC 57.154 33.333 7.78 0.00 32.64 3.56
700 1098 7.496346 ACCAAGACTTCTAAAGATACCATGA 57.504 36.000 0.00 0.00 0.00 3.07
701 1099 7.711339 GGTACCAAGACTTCTAAAGATACCATG 59.289 40.741 7.15 0.00 0.00 3.66
702 1100 7.793036 GGTACCAAGACTTCTAAAGATACCAT 58.207 38.462 7.15 0.00 0.00 3.55
733 1399 1.968493 GGGAACATAGCTGGGTATCGA 59.032 52.381 0.00 0.00 0.00 3.59
734 1400 1.002087 GGGGAACATAGCTGGGTATCG 59.998 57.143 0.00 0.00 0.00 2.92
746 1701 1.569072 GGTGGGTATCAAGGGGAACAT 59.431 52.381 0.00 0.00 0.00 2.71
747 1702 0.996583 GGTGGGTATCAAGGGGAACA 59.003 55.000 0.00 0.00 0.00 3.18
754 1709 3.739401 AAGAAAGGGGTGGGTATCAAG 57.261 47.619 0.00 0.00 0.00 3.02
781 1736 1.306141 TGAGGTCTCGGGCCATTCT 60.306 57.895 4.39 0.00 0.00 2.40
782 1737 1.144936 CTGAGGTCTCGGGCCATTC 59.855 63.158 4.39 0.00 32.43 2.67
791 1756 1.214062 CGTGTGAGCCTGAGGTCTC 59.786 63.158 13.69 13.69 41.26 3.36
816 1785 1.139989 CTTCTTTCGAACTGCTGCGA 58.860 50.000 0.00 0.00 34.32 5.10
827 1796 1.730176 CAACACGTGTGCTTCTTTCG 58.270 50.000 24.16 0.00 0.00 3.46
873 1842 2.542597 TGGTTGCTTAAGTATACGCGG 58.457 47.619 12.47 0.00 0.00 6.46
907 1876 7.444183 TGAAAAGTGAGGTGAATCGAGTATTTT 59.556 33.333 0.00 0.00 0.00 1.82
930 1899 2.664851 CCGCAGTCGCAAGGTGAA 60.665 61.111 0.00 0.00 38.40 3.18
1056 2025 2.650116 GGGAGACTGCTGCTTCGGA 61.650 63.158 0.00 0.00 32.36 4.55
1255 2224 2.100197 AGCAAGTGAGCGTGGATACTA 58.900 47.619 0.00 0.00 40.15 1.82
1256 2225 0.898320 AGCAAGTGAGCGTGGATACT 59.102 50.000 0.00 0.00 40.15 2.12
1259 2228 0.250467 ACAAGCAAGTGAGCGTGGAT 60.250 50.000 6.79 0.00 46.17 3.41
1260 2229 0.391228 TACAAGCAAGTGAGCGTGGA 59.609 50.000 6.79 0.00 46.17 4.02
1269 2239 9.874205 TTTTATTACTACGGTATACAAGCAAGT 57.126 29.630 5.01 7.95 0.00 3.16
1278 2249 7.069569 GTCGAGCGTTTTATTACTACGGTATA 58.930 38.462 0.00 0.00 44.75 1.47
1279 2250 5.909610 GTCGAGCGTTTTATTACTACGGTAT 59.090 40.000 0.00 0.00 44.75 2.73
1318 2289 0.308993 GGTGTTCTGCAGCTCACAAC 59.691 55.000 28.42 21.00 41.99 3.32
1326 2297 0.445436 GCGAATGAGGTGTTCTGCAG 59.555 55.000 7.63 7.63 0.00 4.41
1400 2374 2.050144 ACTCACCGCAGATATCCCATT 58.950 47.619 0.00 0.00 0.00 3.16
1471 2445 0.729116 CGTGCGATTGCTTGATCCTT 59.271 50.000 6.47 0.00 43.34 3.36
1575 2553 1.635844 GGTGTGCGATATTGTGACGA 58.364 50.000 0.00 0.00 0.00 4.20
1644 2622 9.358872 CGATGTAACATATGTCAGCATAATAGT 57.641 33.333 9.23 0.00 40.55 2.12
1653 2631 6.036470 AGACACACGATGTAACATATGTCAG 58.964 40.000 9.23 0.32 43.56 3.51
1656 2634 6.270815 GGTAGACACACGATGTAACATATGT 58.729 40.000 1.41 1.41 43.56 2.29
1696 2674 3.644335 AGGACACTTGTATCCTAGACCC 58.356 50.000 0.00 0.00 43.85 4.46
1779 2758 7.823665 AGTTGTGTCGAATATAGTGTACAAGA 58.176 34.615 0.00 0.00 0.00 3.02
1850 2829 0.611618 TGGAAGTTTGGCGCATGGAT 60.612 50.000 10.83 0.00 0.00 3.41
1965 2944 0.744281 TGCTCGAGTGTTGACTGTGA 59.256 50.000 15.13 0.00 30.16 3.58
2025 3004 0.739561 GCGTTGGACGGATACTCTCT 59.260 55.000 2.48 0.00 42.82 3.10
2026 3005 0.248949 GGCGTTGGACGGATACTCTC 60.249 60.000 2.48 0.00 42.82 3.20
2038 3018 0.884259 TCAGTGTGTGATGGCGTTGG 60.884 55.000 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.