Multiple sequence alignment - TraesCS2B01G390800

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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 TraesCS2B01G390800 chr2B 100.000 3365 0 0 1 3365 555383383 555386747 0.000000e+00 6215
1 TraesCS2B01G390800 chr2D 92.299 3350 205 25 1 3309 474510808 474514145 0.000000e+00 4708
2 TraesCS2B01G390800 chr2A 92.690 2859 117 33 548 3361 616991693 616994504 0.000000e+00 4037
3 TraesCS2B01G390800 chr6D 86.944 337 38 5 1501 1834 307517590 307517257 1.140000e-99 374
4 TraesCS2B01G390800 chr6D 83.333 174 27 2 1610 1782 388951399 388951227 3.480000e-35 159
5 TraesCS2B01G390800 chr6A 86.350 337 40 5 1501 1834 444674675 444674342 2.470000e-96 363
6 TraesCS2B01G390800 chr6B 86.053 337 41 5 1501 1834 474749569 474749236 1.150000e-94 357
7 TraesCS2B01G390800 chr7A 83.333 186 30 1 1598 1783 135689654 135689470 1.610000e-38 171
8 TraesCS2B01G390800 chr7B 83.146 178 30 0 1606 1783 99089375 99089198 2.690000e-36 163
9 TraesCS2B01G390800 chr7D 81.726 197 33 2 1587 1783 136204701 136204508 9.660000e-36 161


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 TraesCS2B01G390800 chr2B 555383383 555386747 3364 False 6215 6215 100.000 1 3365 1 chr2B.!!$F1 3364
1 TraesCS2B01G390800 chr2D 474510808 474514145 3337 False 4708 4708 92.299 1 3309 1 chr2D.!!$F1 3308
2 TraesCS2B01G390800 chr2A 616991693 616994504 2811 False 4037 4037 92.690 548 3361 1 chr2A.!!$F1 2813

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
152 153 0.033504 CGCACCTCCACACTAACAGT 59.966 55.0 0.0 0.0 0.00 3.55 F
663 668 0.034896 AGAAACTGTCGTGCCCGATT 59.965 50.0 0.0 0.0 46.30 3.34 F
857 868 0.039617 CCCATCGCAACGAAGCAAAA 60.040 50.0 0.0 0.0 39.99 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1960 2004 0.745845 ATGGACCATTCTGCGTGCTC 60.746 55.0 0.00 0.00 0.00 4.26 R
2338 2385 1.109323 AAGTTTGGAGCCTGGTGTGC 61.109 55.0 0.00 0.00 0.00 4.57 R
2408 2455 1.174783 ATCCTAACCGGGATCGATCG 58.825 55.0 18.81 9.36 41.84 3.69 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 40 4.543590 CTGTAAGGGCCGAATCATATCT 57.456 45.455 0.00 0.00 0.00 1.98
47 48 2.934364 GCCGAATCATATCTGGCCTCAG 60.934 54.545 3.32 0.00 39.83 3.35
50 51 0.612229 ATCATATCTGGCCTCAGCGG 59.388 55.000 3.32 0.00 40.69 5.52
83 84 3.844090 GCGAGGGAGAGGAGCACC 61.844 72.222 0.00 0.00 0.00 5.01
94 95 3.050275 GAGCACCGCTTCACCCAC 61.050 66.667 0.00 0.00 39.88 4.61
96 97 2.672996 GCACCGCTTCACCCACAT 60.673 61.111 0.00 0.00 0.00 3.21
105 106 1.782201 TTCACCCACATGCTCCAGCT 61.782 55.000 0.00 0.00 42.66 4.24
148 149 2.214216 AGGCGCACCTCCACACTAA 61.214 57.895 10.83 0.00 46.34 2.24
151 152 1.291877 GCGCACCTCCACACTAACAG 61.292 60.000 0.30 0.00 0.00 3.16
152 153 0.033504 CGCACCTCCACACTAACAGT 59.966 55.000 0.00 0.00 0.00 3.55
155 156 1.873591 CACCTCCACACTAACAGTTGC 59.126 52.381 0.00 0.00 0.00 4.17
157 158 2.092646 ACCTCCACACTAACAGTTGCAA 60.093 45.455 0.00 0.00 0.00 4.08
161 162 2.375110 CACACTAACAGTTGCAAAGCG 58.625 47.619 0.00 0.00 0.00 4.68
179 180 1.668294 GCACCAGATCCCGATCGAT 59.332 57.895 18.66 2.16 42.48 3.59
181 182 0.668706 CACCAGATCCCGATCGATGC 60.669 60.000 18.66 2.84 42.48 3.91
189 190 4.957684 CGATCGATGCGCAGGGCT 62.958 66.667 18.32 0.00 44.05 5.19
212 213 2.923426 GATCCGCGTGCCCTCATCAA 62.923 60.000 4.92 0.00 0.00 2.57
221 222 1.203038 TGCCCTCATCAACACACCATT 60.203 47.619 0.00 0.00 0.00 3.16
222 223 1.203052 GCCCTCATCAACACACCATTG 59.797 52.381 0.00 0.00 0.00 2.82
224 225 2.751259 CCCTCATCAACACACCATTGAG 59.249 50.000 0.00 0.00 39.36 3.02
234 235 2.865551 CACACCATTGAGCAAAAACCAC 59.134 45.455 0.00 0.00 0.00 4.16
236 237 1.068434 ACCATTGAGCAAAAACCACCG 59.932 47.619 0.00 0.00 0.00 4.94
238 239 2.482839 CCATTGAGCAAAAACCACCGTT 60.483 45.455 0.00 0.00 0.00 4.44
240 241 1.178276 TGAGCAAAAACCACCGTTGT 58.822 45.000 0.00 0.00 30.72 3.32
242 243 2.190161 GAGCAAAAACCACCGTTGTTC 58.810 47.619 0.00 0.00 25.96 3.18
245 246 1.204941 CAAAAACCACCGTTGTTCCCA 59.795 47.619 0.00 0.00 25.96 4.37
248 249 1.324383 AACCACCGTTGTTCCCAATC 58.676 50.000 0.00 0.00 32.11 2.67
251 252 0.596082 CACCGTTGTTCCCAATCACC 59.404 55.000 0.00 0.00 32.11 4.02
253 254 1.582610 CCGTTGTTCCCAATCACCGG 61.583 60.000 0.00 0.00 32.43 5.28
254 255 0.604243 CGTTGTTCCCAATCACCGGA 60.604 55.000 9.46 0.00 32.11 5.14
262 263 1.740296 CAATCACCGGACCGACCAC 60.740 63.158 17.49 0.00 38.90 4.16
263 264 1.911766 AATCACCGGACCGACCACT 60.912 57.895 17.49 0.00 38.90 4.00
279 280 4.082733 CGACCACTGTATCAACAAGAGAGA 60.083 45.833 0.00 0.00 34.49 3.10
286 287 6.881602 ACTGTATCAACAAGAGAGAAAATCCC 59.118 38.462 0.00 0.00 34.49 3.85
296 297 4.352298 AGAGAGAAAATCCCTGACACCTTT 59.648 41.667 0.00 0.00 0.00 3.11
297 298 5.066913 AGAGAAAATCCCTGACACCTTTT 57.933 39.130 0.00 0.00 0.00 2.27
310 311 0.965363 ACCTTTTAGTGCATGGCCCG 60.965 55.000 0.00 0.00 0.00 6.13
311 312 1.139520 CTTTTAGTGCATGGCCCGC 59.860 57.895 0.00 3.18 0.00 6.13
333 334 1.200020 GTCATAACAGTGTTGGCTGGC 59.800 52.381 18.90 10.68 40.59 4.85
341 342 2.345991 GTTGGCTGGCGGTAGTGA 59.654 61.111 0.00 0.00 0.00 3.41
345 346 1.521681 GGCTGGCGGTAGTGATGAC 60.522 63.158 0.00 0.00 0.00 3.06
355 358 1.950909 GTAGTGATGACGAGGGAGAGG 59.049 57.143 0.00 0.00 0.00 3.69
359 362 0.825840 GATGACGAGGGAGAGGGGAG 60.826 65.000 0.00 0.00 0.00 4.30
365 368 1.869452 AGGGAGAGGGGAGGAAGGT 60.869 63.158 0.00 0.00 0.00 3.50
367 370 1.275421 GGGAGAGGGGAGGAAGGTTG 61.275 65.000 0.00 0.00 0.00 3.77
373 376 4.344865 GGAGGAAGGTTGGCGGCA 62.345 66.667 7.97 7.97 0.00 5.69
398 401 1.848895 TTCCCCCTTGTACCGCCTT 60.849 57.895 0.00 0.00 0.00 4.35
404 407 1.481871 CCTTGTACCGCCTTAGAGGA 58.518 55.000 0.00 0.00 37.67 3.71
407 410 3.118371 CCTTGTACCGCCTTAGAGGAAAT 60.118 47.826 0.00 0.00 37.67 2.17
421 424 1.067212 AGGAAATACTAGCGCCGTCTG 59.933 52.381 2.29 0.00 0.00 3.51
434 437 1.918800 CGTCTGGAAGGAGGGGGTT 60.919 63.158 0.00 0.00 0.00 4.11
435 438 1.685820 GTCTGGAAGGAGGGGGTTG 59.314 63.158 0.00 0.00 0.00 3.77
437 440 0.547712 TCTGGAAGGAGGGGGTTGAG 60.548 60.000 0.00 0.00 0.00 3.02
447 450 0.955919 GGGGGTTGAGTCGAGCTTTG 60.956 60.000 9.41 0.00 0.00 2.77
491 494 2.648593 TTTTTGGGACCGCCTTAGC 58.351 52.632 0.00 0.00 0.00 3.09
492 495 0.111639 TTTTTGGGACCGCCTTAGCT 59.888 50.000 0.00 0.00 36.60 3.32
493 496 0.608035 TTTTGGGACCGCCTTAGCTG 60.608 55.000 0.00 0.00 36.60 4.24
538 542 2.723658 GCATTTGCGAACGTTTTCATGA 59.276 40.909 0.46 0.00 0.00 3.07
539 543 3.364621 GCATTTGCGAACGTTTTCATGAT 59.635 39.130 0.46 0.00 0.00 2.45
542 546 6.413526 GCATTTGCGAACGTTTTCATGATATA 59.586 34.615 0.46 0.00 0.00 0.86
545 549 8.903570 TTTGCGAACGTTTTCATGATATATTT 57.096 26.923 0.46 0.00 0.00 1.40
546 550 9.989869 TTTGCGAACGTTTTCATGATATATTTA 57.010 25.926 0.46 0.00 0.00 1.40
563 568 8.815565 ATATATTTAATTGTGTGTGGGTGACA 57.184 30.769 0.00 0.00 0.00 3.58
576 581 4.137543 GTGGGTGACAGTTTCTTCAGAAT 58.862 43.478 0.00 0.00 33.54 2.40
581 586 6.262273 GGGTGACAGTTTCTTCAGAATAACAA 59.738 38.462 9.69 0.00 33.54 2.83
611 616 8.862325 TTTTCTCATATGAAGCCTCAAAACTA 57.138 30.769 6.90 0.00 34.49 2.24
612 617 7.849804 TTCTCATATGAAGCCTCAAAACTAC 57.150 36.000 6.90 0.00 34.49 2.73
623 628 4.566907 GCCTCAAAACTACCATCCTACCAA 60.567 45.833 0.00 0.00 0.00 3.67
624 629 4.941873 CCTCAAAACTACCATCCTACCAAC 59.058 45.833 0.00 0.00 0.00 3.77
643 648 2.771089 ACAAATGTCATGTCGCTCTGT 58.229 42.857 0.00 0.00 0.00 3.41
653 658 3.284323 TGTCGCTCTGTAGAAACTGTC 57.716 47.619 0.00 0.00 0.00 3.51
654 659 2.243407 GTCGCTCTGTAGAAACTGTCG 58.757 52.381 0.00 0.00 0.00 4.35
655 660 1.878088 TCGCTCTGTAGAAACTGTCGT 59.122 47.619 0.00 0.00 0.00 4.34
656 661 1.979469 CGCTCTGTAGAAACTGTCGTG 59.021 52.381 0.00 0.00 0.00 4.35
662 667 0.892755 TAGAAACTGTCGTGCCCGAT 59.107 50.000 0.00 0.00 46.30 4.18
663 668 0.034896 AGAAACTGTCGTGCCCGATT 59.965 50.000 0.00 0.00 46.30 3.34
675 682 3.869246 CGTGCCCGATTCATAAAACTACT 59.131 43.478 0.00 0.00 35.63 2.57
688 697 8.129161 TCATAAAACTACTCGAAAAACGTTCA 57.871 30.769 0.00 0.00 43.13 3.18
706 715 0.251742 CAAAATGCCACCCTCTCCCA 60.252 55.000 0.00 0.00 0.00 4.37
707 716 0.486879 AAAATGCCACCCTCTCCCAA 59.513 50.000 0.00 0.00 0.00 4.12
709 718 1.434513 AATGCCACCCTCTCCCAACA 61.435 55.000 0.00 0.00 0.00 3.33
713 722 0.539669 CCACCCTCTCCCAACAAACC 60.540 60.000 0.00 0.00 0.00 3.27
734 743 3.188460 CCGCAACCAGATATAATTTCCGG 59.812 47.826 0.00 0.00 0.00 5.14
814 825 1.304134 ACCACGATCTTTTGCCCCC 60.304 57.895 0.00 0.00 0.00 5.40
857 868 0.039617 CCCATCGCAACGAAGCAAAA 60.040 50.000 0.00 0.00 39.99 2.44
858 869 1.052287 CCATCGCAACGAAGCAAAAC 58.948 50.000 0.00 0.00 39.99 2.43
859 870 1.599171 CCATCGCAACGAAGCAAAACA 60.599 47.619 0.00 0.00 39.99 2.83
860 871 1.447938 CATCGCAACGAAGCAAAACAC 59.552 47.619 0.00 0.00 39.99 3.32
862 873 1.131504 TCGCAACGAAGCAAAACACTT 59.868 42.857 0.00 0.00 31.06 3.16
863 874 1.512771 CGCAACGAAGCAAAACACTTC 59.487 47.619 0.00 0.00 40.13 3.01
905 921 3.735029 GGTCGCACTCGTCTCGGT 61.735 66.667 0.00 0.00 36.96 4.69
995 1028 2.202623 CCGCGAAGTCTTCTCCGG 60.203 66.667 20.19 20.19 36.43 5.14
1068 1101 1.761174 GACTGGCAGGAGGTGGAAA 59.239 57.895 20.34 0.00 0.00 3.13
1074 1107 0.112412 GCAGGAGGTGGAAAGGGAAA 59.888 55.000 0.00 0.00 0.00 3.13
1434 1478 1.065928 GATGATCTCGTTCGGCGGT 59.934 57.895 7.21 0.00 41.72 5.68
1437 1481 1.139095 GATCTCGTTCGGCGGTTCT 59.861 57.895 7.21 0.00 41.72 3.01
1472 1516 1.609061 CCAGTCGTTCTTCATGCCAGT 60.609 52.381 0.00 0.00 0.00 4.00
1522 1566 3.450115 GGTACTGGAGCGAGGCGT 61.450 66.667 0.00 0.00 0.00 5.68
1624 1668 3.502990 AAACTGTACCGCGGCGTGA 62.503 57.895 28.58 5.08 0.00 4.35
1755 1799 2.821810 GAGGCCTTCAAGCTCCGC 60.822 66.667 6.77 0.00 0.00 5.54
1881 1925 4.704833 GGCACCGCTTCCTGCTCA 62.705 66.667 0.00 0.00 40.11 4.26
1893 1937 0.596083 CCTGCTCATCGTCATCGTCC 60.596 60.000 0.00 0.00 38.33 4.79
1921 1965 1.901650 GCAAACTTCTGACGAGGCGG 61.902 60.000 0.00 0.00 0.00 6.13
1979 2023 0.745845 GAGCACGCAGAATGGTCCAT 60.746 55.000 0.00 0.00 38.39 3.41
2087 2131 3.033764 GTTTCACTCGTCGGCGCA 61.034 61.111 10.83 0.00 38.14 6.09
2131 2175 1.604438 CCGACGAGTCATGGTTCAACA 60.604 52.381 0.00 0.00 0.00 3.33
2202 2246 1.760192 GCAGCCTCTTCATTCACCAT 58.240 50.000 0.00 0.00 0.00 3.55
2338 2385 3.701040 CTCTTCTTCTCCTCCTCCAGAAG 59.299 52.174 2.79 2.79 44.87 2.85
2408 2455 3.518634 TCAAAGTTTGAACACCTTGGC 57.481 42.857 15.92 0.00 36.59 4.52
2420 2467 2.356313 CTTGGCGATCGATCCCGG 60.356 66.667 21.57 13.30 36.24 5.73
2421 2468 3.151710 TTGGCGATCGATCCCGGT 61.152 61.111 21.57 0.00 36.24 5.28
2611 2661 2.772077 TTTGGCCAGCTTGACGTATA 57.228 45.000 5.11 0.00 0.00 1.47
2684 2734 9.093970 TGAATGTCTTAGATATTTGTTGTACGG 57.906 33.333 5.71 0.00 0.00 4.02
2685 2735 9.309516 GAATGTCTTAGATATTTGTTGTACGGA 57.690 33.333 5.71 0.00 0.00 4.69
2686 2736 9.661563 AATGTCTTAGATATTTGTTGTACGGAA 57.338 29.630 0.00 0.00 0.00 4.30
2687 2737 9.832445 ATGTCTTAGATATTTGTTGTACGGAAT 57.168 29.630 0.00 0.00 0.00 3.01
2698 2748 8.789881 TTTGTTGTACGGAATAGTTTTCAATG 57.210 30.769 0.00 0.00 0.00 2.82
2755 2805 7.682628 TCTATGTGATGGCTCATATGATTTGA 58.317 34.615 5.72 0.00 34.49 2.69
2805 2858 4.751767 ACCTTGCTTTGAAACATTCCAA 57.248 36.364 0.00 0.00 0.00 3.53
2851 2904 8.273643 CTACTTGTAAGTTGCTTGTTCATTTG 57.726 34.615 2.20 0.00 40.37 2.32
2854 2907 4.803088 TGTAAGTTGCTTGTTCATTTGCAC 59.197 37.500 0.00 0.00 35.01 4.57
2856 2909 2.431782 AGTTGCTTGTTCATTTGCACCT 59.568 40.909 0.00 0.00 35.01 4.00
2880 2933 4.219115 TGGGTACATTTTCTTGGCTTTCA 58.781 39.130 0.00 0.00 0.00 2.69
3057 3112 2.563179 AGTCGATTGTGCTACTTCTGGT 59.437 45.455 0.00 0.00 0.00 4.00
3066 3121 2.497675 TGCTACTTCTGGTCTGATCCAC 59.502 50.000 0.00 0.00 33.55 4.02
3084 3139 3.009253 TCCACCGTTTGCCTATTTCCTAA 59.991 43.478 0.00 0.00 0.00 2.69
3118 3173 4.196193 TGTTTTATAGCCCACTTCATCGG 58.804 43.478 0.00 0.00 0.00 4.18
3153 3208 4.477780 GCTAGTGATAAGTATCGAGGTGC 58.522 47.826 0.00 0.00 35.48 5.01
3169 3224 1.620822 GTGCCCTCATCTTTTGGTGT 58.379 50.000 0.00 0.00 0.00 4.16
3182 3237 3.678056 TTTGGTGTGAGCGATAACTCT 57.322 42.857 0.00 0.00 37.58 3.24
3197 3253 6.701841 GCGATAACTCTGATTTGGTGAAGATA 59.298 38.462 0.00 0.00 0.00 1.98
3210 3266 3.585862 GTGAAGATAGCTTTGACGACCA 58.414 45.455 0.00 0.00 33.61 4.02
3243 3299 8.567285 AACATGTGACAAATTTTGGGTTTTAA 57.433 26.923 13.42 0.00 34.12 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.397535 CCCTTACAGGCCATGGCATT 60.398 55.000 36.56 22.08 44.11 3.56
33 34 4.689484 CCGCTGAGGCCAGATATG 57.311 61.111 5.01 0.00 43.02 1.78
83 84 2.401766 GGAGCATGTGGGTGAAGCG 61.402 63.158 0.00 0.00 0.00 4.68
94 95 1.091771 CACGGGTAAGCTGGAGCATG 61.092 60.000 0.65 0.00 45.16 4.06
96 97 2.662596 CACGGGTAAGCTGGAGCA 59.337 61.111 0.65 0.00 45.16 4.26
105 106 0.906066 TAGCTCAATGCCACGGGTAA 59.094 50.000 0.00 0.00 44.23 2.85
155 156 2.753966 CGGGATCTGGTGCGCTTTG 61.754 63.158 9.73 0.00 0.00 2.77
157 158 2.650813 GATCGGGATCTGGTGCGCTT 62.651 60.000 9.73 0.00 35.04 4.68
161 162 0.668706 CATCGATCGGGATCTGGTGC 60.669 60.000 16.41 0.00 35.72 5.01
166 167 2.259818 GCGCATCGATCGGGATCT 59.740 61.111 16.41 0.00 35.72 2.75
169 170 4.284860 CCTGCGCATCGATCGGGA 62.285 66.667 12.24 0.00 0.00 5.14
179 180 4.838152 GATCCGAAGCCCTGCGCA 62.838 66.667 10.98 10.98 41.38 6.09
204 205 2.163010 GCTCAATGGTGTGTTGATGAGG 59.837 50.000 0.00 0.00 35.26 3.86
212 213 2.499289 TGGTTTTTGCTCAATGGTGTGT 59.501 40.909 0.00 0.00 0.00 3.72
221 222 1.178276 ACAACGGTGGTTTTTGCTCA 58.822 45.000 4.97 0.00 32.98 4.26
222 223 2.190161 GAACAACGGTGGTTTTTGCTC 58.810 47.619 4.97 0.00 32.98 4.26
224 225 1.282817 GGAACAACGGTGGTTTTTGC 58.717 50.000 4.97 0.00 32.98 3.68
238 239 1.377229 GGTCCGGTGATTGGGAACA 59.623 57.895 0.00 0.00 39.89 3.18
240 241 1.914263 TCGGTCCGGTGATTGGGAA 60.914 57.895 12.29 0.00 33.27 3.97
242 243 2.125269 GTCGGTCCGGTGATTGGG 60.125 66.667 12.29 0.00 0.00 4.12
245 246 1.911766 AGTGGTCGGTCCGGTGATT 60.912 57.895 12.29 0.00 39.52 2.57
248 249 1.601419 ATACAGTGGTCGGTCCGGTG 61.601 60.000 12.29 4.38 39.52 4.94
251 252 0.528924 TTGATACAGTGGTCGGTCCG 59.471 55.000 4.39 4.39 39.52 4.79
253 254 2.736144 TGTTGATACAGTGGTCGGTC 57.264 50.000 0.00 0.00 0.00 4.79
254 255 2.631062 TCTTGTTGATACAGTGGTCGGT 59.369 45.455 0.00 0.00 35.28 4.69
262 263 7.065563 CAGGGATTTTCTCTCTTGTTGATACAG 59.934 40.741 0.00 0.00 29.65 2.74
263 264 6.881065 CAGGGATTTTCTCTCTTGTTGATACA 59.119 38.462 0.00 0.00 29.65 2.29
279 280 4.280929 GCACTAAAAGGTGTCAGGGATTTT 59.719 41.667 0.00 0.00 39.21 1.82
286 287 2.095059 GCCATGCACTAAAAGGTGTCAG 60.095 50.000 0.00 0.00 39.21 3.51
296 297 2.438254 CAGCGGGCCATGCACTAA 60.438 61.111 19.93 0.00 33.85 2.24
297 298 3.680620 GACAGCGGGCCATGCACTA 62.681 63.158 19.93 0.00 33.85 2.74
325 326 1.078497 CATCACTACCGCCAGCCAA 60.078 57.895 0.00 0.00 0.00 4.52
327 328 1.521681 GTCATCACTACCGCCAGCC 60.522 63.158 0.00 0.00 0.00 4.85
330 331 1.663379 CCTCGTCATCACTACCGCCA 61.663 60.000 0.00 0.00 0.00 5.69
333 334 0.663688 CTCCCTCGTCATCACTACCG 59.336 60.000 0.00 0.00 0.00 4.02
341 342 1.231641 CTCCCCTCTCCCTCGTCAT 59.768 63.158 0.00 0.00 0.00 3.06
345 346 1.456705 CTTCCTCCCCTCTCCCTCG 60.457 68.421 0.00 0.00 0.00 4.63
359 362 1.745489 CTAGTGCCGCCAACCTTCC 60.745 63.158 0.00 0.00 0.00 3.46
365 368 2.349755 GAACCCTAGTGCCGCCAA 59.650 61.111 0.00 0.00 0.00 4.52
367 370 4.484872 GGGAACCCTAGTGCCGCC 62.485 72.222 2.17 0.00 43.81 6.13
390 393 4.522022 GCTAGTATTTCCTCTAAGGCGGTA 59.478 45.833 0.00 0.00 34.61 4.02
392 395 3.612004 CGCTAGTATTTCCTCTAAGGCGG 60.612 52.174 0.00 0.00 34.61 6.13
398 401 2.551459 GACGGCGCTAGTATTTCCTCTA 59.449 50.000 6.90 0.00 0.00 2.43
404 407 1.108776 TCCAGACGGCGCTAGTATTT 58.891 50.000 6.90 0.00 0.00 1.40
407 410 1.381928 CCTTCCAGACGGCGCTAGTA 61.382 60.000 6.90 0.00 0.00 1.82
421 424 1.900545 CGACTCAACCCCCTCCTTCC 61.901 65.000 0.00 0.00 0.00 3.46
447 450 1.216710 CTCCACTCCCGTGAAGAGC 59.783 63.158 0.00 0.00 43.97 4.09
452 455 2.662309 GGTAACTCCACTCCCGTGA 58.338 57.895 0.00 0.00 43.97 4.35
476 479 2.668632 CAGCTAAGGCGGTCCCAA 59.331 61.111 0.00 0.00 44.37 4.12
478 481 4.858680 GCCAGCTAAGGCGGTCCC 62.859 72.222 0.00 0.00 46.12 4.46
487 490 4.590487 CGAAGGTTCGCCAGCTAA 57.410 55.556 0.00 0.00 44.26 3.09
507 511 1.153978 CGCAAATGCCACGCTTCAT 60.154 52.632 0.00 0.00 37.91 2.57
508 512 1.790090 TTCGCAAATGCCACGCTTCA 61.790 50.000 0.00 0.00 37.91 3.02
513 517 0.932585 AAACGTTCGCAAATGCCACG 60.933 50.000 18.18 18.18 44.84 4.94
538 542 8.815565 TGTCACCCACACACAATTAAATATAT 57.184 30.769 0.00 0.00 0.00 0.86
539 543 7.885922 ACTGTCACCCACACACAATTAAATATA 59.114 33.333 0.00 0.00 0.00 0.86
542 546 4.892934 ACTGTCACCCACACACAATTAAAT 59.107 37.500 0.00 0.00 0.00 1.40
545 549 3.569194 ACTGTCACCCACACACAATTA 57.431 42.857 0.00 0.00 0.00 1.40
546 550 2.435372 ACTGTCACCCACACACAATT 57.565 45.000 0.00 0.00 0.00 2.32
581 586 9.857656 TTTGAGGCTTCATATGAGAAAATATCT 57.142 29.630 5.39 0.00 35.40 1.98
594 599 5.191722 AGGATGGTAGTTTTGAGGCTTCATA 59.808 40.000 0.00 0.00 32.27 2.15
600 605 3.054655 TGGTAGGATGGTAGTTTTGAGGC 60.055 47.826 0.00 0.00 0.00 4.70
611 616 4.380843 TGACATTTGTTGGTAGGATGGT 57.619 40.909 0.00 0.00 0.00 3.55
612 617 4.706476 ACATGACATTTGTTGGTAGGATGG 59.294 41.667 0.00 0.00 0.00 3.51
623 628 2.771089 ACAGAGCGACATGACATTTGT 58.229 42.857 0.00 0.00 0.00 2.83
624 629 4.176271 TCTACAGAGCGACATGACATTTG 58.824 43.478 0.00 0.00 0.00 2.32
643 648 2.343506 TCGGGCACGACAGTTTCTA 58.656 52.632 7.15 0.00 45.59 2.10
653 658 3.869246 AGTAGTTTTATGAATCGGGCACG 59.131 43.478 0.00 0.00 42.74 5.34
654 659 4.025979 CGAGTAGTTTTATGAATCGGGCAC 60.026 45.833 0.00 0.00 0.00 5.01
655 660 4.116961 CGAGTAGTTTTATGAATCGGGCA 58.883 43.478 0.00 0.00 0.00 5.36
656 661 4.365723 TCGAGTAGTTTTATGAATCGGGC 58.634 43.478 0.00 0.00 0.00 6.13
662 667 8.602328 TGAACGTTTTTCGAGTAGTTTTATGAA 58.398 29.630 0.46 0.00 42.86 2.57
663 668 8.129161 TGAACGTTTTTCGAGTAGTTTTATGA 57.871 30.769 0.46 0.00 42.86 2.15
675 682 3.548268 GTGGCATTTTGAACGTTTTTCGA 59.452 39.130 0.46 0.00 42.86 3.71
688 697 0.486879 TTGGGAGAGGGTGGCATTTT 59.513 50.000 0.00 0.00 0.00 1.82
706 715 6.524101 AATTATATCTGGTTGCGGTTTGTT 57.476 33.333 0.00 0.00 0.00 2.83
707 716 6.405397 GGAAATTATATCTGGTTGCGGTTTGT 60.405 38.462 0.00 0.00 0.00 2.83
709 718 5.220970 CGGAAATTATATCTGGTTGCGGTTT 60.221 40.000 0.00 0.00 30.60 3.27
713 722 4.404507 CCGGAAATTATATCTGGTTGCG 57.595 45.455 0.00 0.00 38.34 4.85
787 797 1.183030 AAGATCGTGGTCGGTGGTCA 61.183 55.000 0.00 0.00 37.69 4.02
857 868 3.715315 GCTTATAAGGGTAGGGGAAGTGT 59.285 47.826 14.28 0.00 0.00 3.55
858 869 3.244112 CGCTTATAAGGGTAGGGGAAGTG 60.244 52.174 18.81 0.00 34.59 3.16
859 870 2.970640 CGCTTATAAGGGTAGGGGAAGT 59.029 50.000 18.81 0.00 34.59 3.01
860 871 3.679824 CGCTTATAAGGGTAGGGGAAG 57.320 52.381 18.81 0.00 34.59 3.46
905 921 2.447429 TGGTGGGGTTTTGGTTCTGATA 59.553 45.455 0.00 0.00 0.00 2.15
1068 1101 3.647771 GGCGTCACCCCTTTCCCT 61.648 66.667 0.00 0.00 0.00 4.20
1074 1107 2.363276 TGTATCGGCGTCACCCCT 60.363 61.111 6.85 0.00 33.26 4.79
1410 1454 1.066152 CCGAACGAGATCATCTGCTGA 59.934 52.381 0.00 0.00 38.53 4.26
1522 1566 4.344865 GCGGGGGCTCAGGTTCAA 62.345 66.667 0.00 0.00 0.00 2.69
1734 1778 3.649277 GAGCTTGAAGGCCTCGCGA 62.649 63.158 5.23 9.26 0.00 5.87
1881 1925 1.787057 GAGGCGAGGACGATGACGAT 61.787 60.000 0.00 0.00 42.66 3.73
1893 1937 1.374758 AGAAGTTTGCGGAGGCGAG 60.375 57.895 0.00 0.00 44.10 5.03
1960 2004 0.745845 ATGGACCATTCTGCGTGCTC 60.746 55.000 0.00 0.00 0.00 4.26
2202 2246 2.035155 TCACCGGAGAAGCGAGGA 59.965 61.111 9.46 0.00 0.00 3.71
2338 2385 1.109323 AAGTTTGGAGCCTGGTGTGC 61.109 55.000 0.00 0.00 0.00 4.57
2408 2455 1.174783 ATCCTAACCGGGATCGATCG 58.825 55.000 18.81 9.36 41.84 3.69
2420 2467 5.293560 GTGCATCTCTGTCCTAATCCTAAC 58.706 45.833 0.00 0.00 0.00 2.34
2421 2468 4.038042 CGTGCATCTCTGTCCTAATCCTAA 59.962 45.833 0.00 0.00 0.00 2.69
2487 2535 1.787989 CGAAACGATGCTGTGATGTGC 60.788 52.381 0.00 0.00 0.00 4.57
2611 2661 2.183679 GAGAGATTGACTGGTCACCCT 58.816 52.381 2.65 3.75 39.66 4.34
2682 2732 6.420604 AGCAAACAACATTGAAAACTATTCCG 59.579 34.615 0.00 0.00 31.84 4.30
2683 2733 7.566709 CAGCAAACAACATTGAAAACTATTCC 58.433 34.615 0.00 0.00 31.84 3.01
2684 2734 7.065283 GCAGCAAACAACATTGAAAACTATTC 58.935 34.615 0.00 0.00 31.84 1.75
2685 2735 6.538021 TGCAGCAAACAACATTGAAAACTATT 59.462 30.769 0.00 0.00 31.84 1.73
2686 2736 6.047870 TGCAGCAAACAACATTGAAAACTAT 58.952 32.000 0.00 0.00 31.84 2.12
2687 2737 5.414360 TGCAGCAAACAACATTGAAAACTA 58.586 33.333 0.00 0.00 31.84 2.24
2689 2739 4.596801 TGCAGCAAACAACATTGAAAAC 57.403 36.364 0.00 0.00 31.84 2.43
2690 2740 5.618056 TTTGCAGCAAACAACATTGAAAA 57.382 30.435 16.93 0.00 31.84 2.29
2786 2839 7.951530 AATAGTTGGAATGTTTCAAAGCAAG 57.048 32.000 0.00 0.00 0.00 4.01
2805 2858 9.838339 AAGTAGCATAGCTGAACAATTAATAGT 57.162 29.630 0.00 0.00 40.10 2.12
2854 2907 3.578282 AGCCAAGAAAATGTACCCAAAGG 59.422 43.478 0.00 0.00 40.04 3.11
2856 2909 5.129485 TGAAAGCCAAGAAAATGTACCCAAA 59.871 36.000 0.00 0.00 0.00 3.28
2880 2933 1.712869 AGGGCCTGATACTGACCCT 59.287 57.895 4.50 0.00 46.35 4.34
2959 3014 9.644993 GTTGTTTTAAGGTAATTTGTGATTTGC 57.355 29.630 0.00 0.00 0.00 3.68
2987 3042 8.928733 GTCATTTGCATGATTCAATTACAAACT 58.071 29.630 0.00 0.08 41.64 2.66
3023 3078 6.017933 GCACAATCGACTTGAGAATTTAGTG 58.982 40.000 12.53 0.00 38.29 2.74
3057 3112 1.271856 TAGGCAAACGGTGGATCAGA 58.728 50.000 0.00 0.00 0.00 3.27
3066 3121 3.626217 GGACTTAGGAAATAGGCAAACGG 59.374 47.826 0.00 0.00 0.00 4.44
3084 3139 6.157994 TGGGCTATAAAACAGTGATAAGGACT 59.842 38.462 0.00 0.00 0.00 3.85
3153 3208 1.815003 GCTCACACCAAAAGATGAGGG 59.185 52.381 2.56 0.00 39.20 4.30
3169 3224 4.081697 TCACCAAATCAGAGTTATCGCTCA 60.082 41.667 0.00 0.00 37.94 4.26
3182 3237 5.122239 CGTCAAAGCTATCTTCACCAAATCA 59.878 40.000 0.00 0.00 0.00 2.57
3197 3253 1.160137 GCAGAATGGTCGTCAAAGCT 58.840 50.000 0.00 0.00 35.86 3.74
3210 3266 7.411274 CAAAATTTGTCACATGTTTGCAGAAT 58.589 30.769 0.00 0.00 0.00 2.40
3243 3299 8.164070 ACCCTCTTGAGTTTGAATAACTATTGT 58.836 33.333 0.00 0.00 0.00 2.71
3256 3312 4.202430 ACCGTCAATAACCCTCTTGAGTTT 60.202 41.667 0.00 0.00 32.33 2.66


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

AutoCloner maintained by Alex Coulton.