Multiple sequence alignment - TraesCS3A01G388200

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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 TraesCS3A01G388200 chr3A 100.000 4571 0 0 1 4571 637116569 637111999 0.000000e+00 8442.0
1 TraesCS3A01G388200 chr3B 93.655 4586 221 30 1 4570 657645205 657649736 0.000000e+00 6793.0
2 TraesCS3A01G388200 chr3B 85.211 284 29 5 4062 4340 727505352 727505627 3.480000e-71 279.0
3 TraesCS3A01G388200 chr3B 86.538 260 24 7 4022 4276 798486597 798486850 4.500000e-70 276.0
4 TraesCS3A01G388200 chr3D 92.811 4632 206 51 1 4570 497597683 497602249 0.000000e+00 6591.0
5 TraesCS3A01G388200 chr3D 84.158 404 35 15 3947 4344 40809159 40808779 9.350000e-97 364.0
6 TraesCS3A01G388200 chr3D 84.586 266 31 6 4022 4282 595029868 595030128 5.870000e-64 255.0
7 TraesCS3A01G388200 chr2B 88.447 528 61 0 2229 2756 34038450 34038977 4.990000e-179 638.0
8 TraesCS3A01G388200 chr2B 85.855 304 31 7 2799 3100 34038985 34039278 3.430000e-81 313.0
9 TraesCS3A01G388200 chr1D 86.551 461 43 9 3681 4128 348125156 348124702 1.480000e-134 490.0
10 TraesCS3A01G388200 chr1D 84.116 277 29 10 4118 4383 348124645 348124373 2.110000e-63 254.0
11 TraesCS3A01G388200 chr6B 84.454 476 54 12 3669 4130 570080281 570079812 6.970000e-123 451.0
12 TraesCS3A01G388200 chr6B 83.403 476 55 14 3669 4130 308977826 308977361 1.970000e-113 420.0
13 TraesCS3A01G388200 chr5B 84.848 462 52 8 3681 4130 176793093 176793548 2.510000e-122 449.0
14 TraesCS3A01G388200 chr1B 84.648 469 52 11 3669 4123 177159289 177158827 2.510000e-122 449.0
15 TraesCS3A01G388200 chr1B 82.563 476 53 14 3669 4130 192674573 192674114 4.290000e-105 392.0
16 TraesCS3A01G388200 chr5A 84.698 464 53 12 3683 4134 73841751 73841294 9.020000e-122 448.0
17 TraesCS3A01G388200 chr5A 85.932 263 25 9 4131 4383 73841253 73840993 2.100000e-68 270.0
18 TraesCS3A01G388200 chr6D 84.110 472 51 13 3681 4138 77328580 77328119 7.020000e-118 435.0
19 TraesCS3A01G388200 chr7D 82.661 248 31 5 4097 4340 180843505 180843744 4.630000e-50 209.0
20 TraesCS3A01G388200 chr6A 88.961 154 13 4 4233 4383 568178565 568178717 2.170000e-43 187.0
21 TraesCS3A01G388200 chr6A 87.209 86 8 3 4118 4201 568178479 568178563 1.350000e-15 95.3
22 TraesCS3A01G388200 chrUn 91.743 109 7 1 4234 4340 291226107 291226215 2.850000e-32 150.0
23 TraesCS3A01G388200 chrUn 91.743 109 7 1 4234 4340 299189972 299190080 2.850000e-32 150.0


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 TraesCS3A01G388200 chr3A 637111999 637116569 4570 True 8442.0 8442 100.0000 1 4571 1 chr3A.!!$R1 4570
1 TraesCS3A01G388200 chr3B 657645205 657649736 4531 False 6793.0 6793 93.6550 1 4570 1 chr3B.!!$F1 4569
2 TraesCS3A01G388200 chr3D 497597683 497602249 4566 False 6591.0 6591 92.8110 1 4570 1 chr3D.!!$F1 4569
3 TraesCS3A01G388200 chr2B 34038450 34039278 828 False 475.5 638 87.1510 2229 3100 2 chr2B.!!$F1 871
4 TraesCS3A01G388200 chr1D 348124373 348125156 783 True 372.0 490 85.3335 3681 4383 2 chr1D.!!$R1 702
5 TraesCS3A01G388200 chr5A 73840993 73841751 758 True 359.0 448 85.3150 3683 4383 2 chr5A.!!$R1 700

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
384 443 0.110056 GTGCGACCACTTGCTGAATG 60.110 55.0 0.0 0.0 38.93 2.67 F
385 444 0.250252 TGCGACCACTTGCTGAATGA 60.250 50.0 0.0 0.0 0.00 2.57 F
1176 1245 0.960364 ACTCGCCGTGCCAATTTCAT 60.960 50.0 0.0 0.0 0.00 2.57 F
2220 2289 1.322442 GGGGATTGCCTAATGCTGTC 58.678 55.0 0.0 0.0 42.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 2115 0.040067 CGCTTTGGCACAGGAACTTC 60.040 55.0 2.39 0.00 42.39 3.01 R
2058 2127 0.381801 ACTGCAGTTTGTCGCTTTGG 59.618 50.0 15.25 0.00 0.00 3.28 R
2756 2825 0.035630 CCTCCAGCCTTCTGAAGTGG 60.036 60.0 16.86 16.86 42.95 4.00 R
4007 4098 0.471971 ACCACAGAGGCCACTACACT 60.472 55.0 5.01 0.00 43.14 3.55 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 0.371301 CATGGTTCATGTCGCTGACG 59.629 55.000 0.00 0.00 37.12 4.35
27 28 2.740714 GGTTCATGTCGCTGACGGC 61.741 63.158 0.00 0.00 46.48 5.68
119 153 2.254350 GGAACTTCGCCCGTTTGC 59.746 61.111 0.00 0.00 0.00 3.68
120 154 2.548295 GGAACTTCGCCCGTTTGCA 61.548 57.895 0.00 0.00 0.00 4.08
121 155 1.082104 GAACTTCGCCCGTTTGCAG 60.082 57.895 0.00 0.00 0.00 4.41
122 156 1.503818 GAACTTCGCCCGTTTGCAGA 61.504 55.000 0.00 0.00 0.00 4.26
123 157 0.889186 AACTTCGCCCGTTTGCAGAT 60.889 50.000 0.00 0.00 0.00 2.90
147 181 4.456535 AGATCATGTAGTAGAGTGTCGCT 58.543 43.478 0.00 0.00 0.00 4.93
152 186 1.989966 TAGTAGAGTGTCGCTGCGCC 61.990 60.000 18.65 6.66 0.00 6.53
199 234 1.863454 GGCAACGATCTGCTGTAGATG 59.137 52.381 13.12 8.02 46.12 2.90
269 304 8.766994 ATACTAGACAATGGCCATATGTTTTT 57.233 30.769 21.15 15.46 0.00 1.94
270 305 7.100458 ACTAGACAATGGCCATATGTTTTTC 57.900 36.000 21.15 12.58 0.00 2.29
276 317 7.452562 ACAATGGCCATATGTTTTTCTTTTCT 58.547 30.769 21.15 0.00 0.00 2.52
347 388 4.917906 ATAAGGACCTTTGTTCTGCTCT 57.082 40.909 13.11 0.00 27.82 4.09
353 412 2.108952 ACCTTTGTTCTGCTCTGGGAAT 59.891 45.455 0.00 0.00 0.00 3.01
356 415 3.507162 TTGTTCTGCTCTGGGAATCAA 57.493 42.857 0.00 0.00 0.00 2.57
357 416 3.507162 TGTTCTGCTCTGGGAATCAAA 57.493 42.857 0.00 0.00 0.00 2.69
358 417 4.038271 TGTTCTGCTCTGGGAATCAAAT 57.962 40.909 0.00 0.00 0.00 2.32
359 418 4.410099 TGTTCTGCTCTGGGAATCAAATT 58.590 39.130 0.00 0.00 0.00 1.82
360 419 4.219070 TGTTCTGCTCTGGGAATCAAATTG 59.781 41.667 0.00 0.00 0.00 2.32
361 420 4.038271 TCTGCTCTGGGAATCAAATTGT 57.962 40.909 0.00 0.00 0.00 2.71
362 421 4.410099 TCTGCTCTGGGAATCAAATTGTT 58.590 39.130 0.00 0.00 0.00 2.83
363 422 4.460382 TCTGCTCTGGGAATCAAATTGTTC 59.540 41.667 0.00 0.00 0.00 3.18
364 423 4.410099 TGCTCTGGGAATCAAATTGTTCT 58.590 39.130 0.00 0.00 0.00 3.01
365 424 4.219070 TGCTCTGGGAATCAAATTGTTCTG 59.781 41.667 0.00 0.00 0.00 3.02
366 425 4.219288 GCTCTGGGAATCAAATTGTTCTGT 59.781 41.667 0.00 0.00 0.00 3.41
367 426 5.706916 CTCTGGGAATCAAATTGTTCTGTG 58.293 41.667 0.00 0.00 0.00 3.66
368 427 4.022068 TCTGGGAATCAAATTGTTCTGTGC 60.022 41.667 0.00 0.00 0.00 4.57
369 428 3.244976 GGGAATCAAATTGTTCTGTGCG 58.755 45.455 0.00 0.00 0.00 5.34
370 429 3.057596 GGGAATCAAATTGTTCTGTGCGA 60.058 43.478 0.00 0.00 0.00 5.10
371 430 3.914364 GGAATCAAATTGTTCTGTGCGAC 59.086 43.478 0.00 0.00 0.00 5.19
372 431 3.559238 ATCAAATTGTTCTGTGCGACC 57.441 42.857 0.00 0.00 0.00 4.79
373 432 2.293170 TCAAATTGTTCTGTGCGACCA 58.707 42.857 0.00 0.00 0.00 4.02
384 443 0.110056 GTGCGACCACTTGCTGAATG 60.110 55.000 0.00 0.00 38.93 2.67
385 444 0.250252 TGCGACCACTTGCTGAATGA 60.250 50.000 0.00 0.00 0.00 2.57
386 445 1.089920 GCGACCACTTGCTGAATGAT 58.910 50.000 0.00 0.00 0.00 2.45
387 446 1.063174 GCGACCACTTGCTGAATGATC 59.937 52.381 0.00 0.00 0.00 2.92
468 528 3.104843 CGAGAGGCTGGGAAAAGATAG 57.895 52.381 0.00 0.00 0.00 2.08
492 552 8.520119 AGGGGTATATCCAATTAATGTACAGT 57.480 34.615 3.96 0.07 38.11 3.55
494 554 9.662947 GGGGTATATCCAATTAATGTACAGTAC 57.337 37.037 3.96 3.49 38.11 2.73
556 618 6.816140 GCAGTGCTTAGAAACTTAGAAGAGAT 59.184 38.462 8.18 0.00 0.00 2.75
615 677 8.476064 AGAATTAGAGCATGAGAAGACTGATA 57.524 34.615 0.00 0.00 0.00 2.15
616 678 8.359642 AGAATTAGAGCATGAGAAGACTGATAC 58.640 37.037 0.00 0.00 0.00 2.24
617 679 7.838079 ATTAGAGCATGAGAAGACTGATACT 57.162 36.000 0.00 0.00 0.00 2.12
618 680 5.518848 AGAGCATGAGAAGACTGATACTG 57.481 43.478 0.00 0.00 0.00 2.74
619 681 4.341806 AGAGCATGAGAAGACTGATACTGG 59.658 45.833 0.00 0.00 0.00 4.00
620 682 4.029520 AGCATGAGAAGACTGATACTGGT 58.970 43.478 0.00 0.00 0.00 4.00
689 751 1.134220 TGGTCCCCACGATTATTCAGC 60.134 52.381 0.00 0.00 0.00 4.26
694 756 2.364632 CCCACGATTATTCAGCACCAA 58.635 47.619 0.00 0.00 0.00 3.67
700 762 5.740569 CACGATTATTCAGCACCAAGATTTG 59.259 40.000 0.00 0.00 0.00 2.32
711 773 3.947910 CCAAGATTTGGCACAGTGATT 57.052 42.857 4.15 0.00 45.17 2.57
715 777 4.510038 AGATTTGGCACAGTGATTTGTC 57.490 40.909 4.15 0.00 42.39 3.18
752 814 3.916172 CACTTCAATTTCCATCAACTGCG 59.084 43.478 0.00 0.00 0.00 5.18
761 823 5.957842 TTCCATCAACTGCGATAAAAGTT 57.042 34.783 0.00 0.00 37.09 2.66
765 827 4.903638 TCAACTGCGATAAAAGTTCGAG 57.096 40.909 0.00 0.00 38.88 4.04
802 864 1.471327 GCCAACTGCAAACTGCTTTCA 60.471 47.619 0.00 0.00 45.31 2.69
826 888 7.389330 TCATTCGTTTCTGGAATTTAAGCAGTA 59.611 33.333 0.00 0.00 31.98 2.74
829 891 6.315393 TCGTTTCTGGAATTTAAGCAGTATCC 59.685 38.462 0.00 0.00 0.00 2.59
834 896 6.823689 TCTGGAATTTAAGCAGTATCCACTTC 59.176 38.462 0.00 0.00 33.61 3.01
862 924 8.870879 GTGGAAATATCGTCTAGGCATTTATAC 58.129 37.037 0.00 0.00 0.00 1.47
863 925 8.038944 TGGAAATATCGTCTAGGCATTTATACC 58.961 37.037 0.00 0.00 0.00 2.73
874 936 8.535335 TCTAGGCATTTATACCTTCATCAGATC 58.465 37.037 0.00 0.00 37.50 2.75
879 941 7.094890 GCATTTATACCTTCATCAGATCCAGTG 60.095 40.741 0.00 0.00 0.00 3.66
880 942 7.437713 TTTATACCTTCATCAGATCCAGTGT 57.562 36.000 0.00 0.00 0.00 3.55
881 943 3.623906 ACCTTCATCAGATCCAGTGTG 57.376 47.619 0.00 0.00 0.00 3.82
882 944 2.909006 ACCTTCATCAGATCCAGTGTGT 59.091 45.455 0.00 0.00 0.00 3.72
883 945 3.055530 ACCTTCATCAGATCCAGTGTGTC 60.056 47.826 0.00 0.00 0.00 3.67
884 946 3.529533 CTTCATCAGATCCAGTGTGTCC 58.470 50.000 0.00 0.00 0.00 4.02
885 947 2.539302 TCATCAGATCCAGTGTGTCCA 58.461 47.619 0.00 0.00 0.00 4.02
887 949 1.715785 TCAGATCCAGTGTGTCCACA 58.284 50.000 0.00 0.00 44.39 4.17
927 996 6.929606 CCCTTATTTCTAGGTACACAGTATGC 59.070 42.308 0.00 0.00 42.53 3.14
928 997 7.418597 CCCTTATTTCTAGGTACACAGTATGCA 60.419 40.741 0.00 0.00 42.53 3.96
929 998 7.653713 CCTTATTTCTAGGTACACAGTATGCAG 59.346 40.741 0.00 0.00 42.53 4.41
930 999 5.339008 TTTCTAGGTACACAGTATGCAGG 57.661 43.478 0.00 0.00 42.53 4.85
944 1013 1.003233 GCAGGTCAACCTCACCTCC 60.003 63.158 0.00 0.00 46.65 4.30
1027 1096 5.540337 TCAACCTCGCCTCTTCAGATATATT 59.460 40.000 0.00 0.00 0.00 1.28
1031 1100 6.268847 ACCTCGCCTCTTCAGATATATTTCTT 59.731 38.462 0.00 0.00 0.00 2.52
1117 1186 5.401550 TCCTCGACATCAAAATTCATTTGC 58.598 37.500 0.00 0.00 46.53 3.68
1135 1204 3.998913 TGCAGGATCCACAGAATTACA 57.001 42.857 15.82 0.00 0.00 2.41
1161 1230 3.193263 CAACTGGGATGAATCTCACTCG 58.807 50.000 0.00 0.00 32.90 4.18
1170 1239 2.449031 AATCTCACTCGCCGTGCCAA 62.449 55.000 0.47 0.00 43.46 4.52
1176 1245 0.960364 ACTCGCCGTGCCAATTTCAT 60.960 50.000 0.00 0.00 0.00 2.57
1189 1258 3.241701 CAATTTCATGGTGTAACGTGCC 58.758 45.455 0.00 0.00 38.12 5.01
1319 1388 2.429610 GTGCAAATTCCATCTCAGGCAT 59.570 45.455 0.00 0.00 32.16 4.40
1420 1489 6.683110 GCCTGATCTTTCATCATTGCTCAAAT 60.683 38.462 0.00 0.00 0.00 2.32
1449 1518 9.881529 CAAGTTTTTGATTTATCAACAAATGGG 57.118 29.630 4.70 0.00 45.63 4.00
1464 1533 4.136051 CAAATGGGTTTTCTGGTGCATTT 58.864 39.130 0.00 0.00 0.00 2.32
1525 1594 2.567615 GGCCTAGGAGAGAACAGTTTCA 59.432 50.000 14.75 0.00 33.72 2.69
1566 1635 4.313020 AAGCATTGGACTCCTGAAGAAT 57.687 40.909 0.00 0.00 0.00 2.40
1627 1696 5.083533 AGAGATACCAGCTTCAGTCTTTG 57.916 43.478 0.00 0.00 0.00 2.77
1734 1803 3.196469 TGTGGAAGATTGAGCTCTACCAG 59.804 47.826 16.19 0.00 0.00 4.00
1740 1809 4.826556 AGATTGAGCTCTACCAGAACAAC 58.173 43.478 16.19 0.00 0.00 3.32
1746 1815 2.300437 GCTCTACCAGAACAACCTGACT 59.700 50.000 0.00 0.00 36.29 3.41
1769 1838 3.416156 GTGAAATTCCTCCTGAGCTTGT 58.584 45.455 0.00 0.00 0.00 3.16
1785 1854 4.968259 AGCTTGTACACCTGACATTGTTA 58.032 39.130 0.00 0.00 0.00 2.41
1845 1914 2.041620 ACTGCCCAAGGAAATTGCTAGA 59.958 45.455 0.00 0.00 37.60 2.43
1869 1938 8.257306 AGACTGAAGAATCTTAAGATCTTCCAC 58.743 37.037 30.04 24.59 37.60 4.02
1870 1939 7.038659 ACTGAAGAATCTTAAGATCTTCCACG 58.961 38.462 30.04 24.64 37.60 4.94
2046 2115 7.477494 AGAATTATTTTACCGGTGAATTTCCG 58.523 34.615 19.93 13.64 46.49 4.30
2058 2127 2.552315 TGAATTTCCGAAGTTCCTGTGC 59.448 45.455 12.39 0.00 0.00 4.57
2220 2289 1.322442 GGGGATTGCCTAATGCTGTC 58.678 55.000 0.00 0.00 42.00 3.51
2353 2422 2.305009 CAATGGAGCTGGGAAATCTCC 58.695 52.381 0.00 0.00 45.02 3.71
2412 2481 1.880819 CTGGCCAAATCCCTGCACAC 61.881 60.000 7.01 0.00 0.00 3.82
2547 2616 5.184671 AGAGAATTCTTTGTCTGGCCAAATC 59.815 40.000 7.01 0.15 34.39 2.17
2574 2643 2.629617 CACAGTTGGCTCCCTTTTGATT 59.370 45.455 0.00 0.00 0.00 2.57
2756 2825 2.232452 ACTCTGACCTATGTGTCACTGC 59.768 50.000 4.27 0.00 40.22 4.40
3055 3126 3.389983 GGTACCCATGGTTACATAGCTCA 59.610 47.826 19.89 0.00 37.09 4.26
3153 3227 5.438117 GGTTTAACGTTTAGTCTTCTGTGC 58.562 41.667 5.91 0.00 0.00 4.57
3536 3612 2.032528 TGAACTGCAGGGCTTCCG 59.967 61.111 19.93 0.00 35.17 4.30
3550 3626 2.168728 GGCTTCCGTATTCTCTCAAGGT 59.831 50.000 0.00 0.00 0.00 3.50
3565 3641 0.605589 AAGGTGCGAGAAGAGAGTGG 59.394 55.000 0.00 0.00 0.00 4.00
3569 3645 0.958876 TGCGAGAAGAGAGTGGCGTA 60.959 55.000 0.00 0.00 0.00 4.42
3719 3797 7.451429 GCAACTATGCGTCAGAAGATATAATG 58.549 38.462 0.00 0.00 43.83 1.90
3808 3888 8.196771 AGAAGTTGTGAAAATGCTTATTGACAA 58.803 29.630 0.00 0.00 0.00 3.18
3843 3923 1.826385 ATTCGGAGGGCAAAGAACAG 58.174 50.000 0.00 0.00 0.00 3.16
3864 3944 7.334844 ACAGGAATAATAAGTAAAAGCAGGC 57.665 36.000 0.00 0.00 0.00 4.85
4007 4098 8.090788 AGAAGGCTGTTAATAATACTCTGGAA 57.909 34.615 0.00 0.00 0.00 3.53
4018 4109 0.977395 ACTCTGGAAGTGTAGTGGCC 59.023 55.000 0.00 0.00 39.18 5.36
4019 4110 1.270907 CTCTGGAAGTGTAGTGGCCT 58.729 55.000 3.32 0.00 33.76 5.19
4022 4113 0.976641 TGGAAGTGTAGTGGCCTCTG 59.023 55.000 17.65 0.00 0.00 3.35
4058 4149 4.080919 AGGTCATGTATCTGCAGCAGTTTA 60.081 41.667 22.10 12.21 32.61 2.01
4108 4200 6.749118 GCAGTTTCTGTAAAAATGCTAGATGG 59.251 38.462 13.73 0.00 36.95 3.51
4124 4216 6.379988 TGCTAGATGGTGATTTACTGTACTGA 59.620 38.462 6.77 0.00 0.00 3.41
4145 4305 8.394971 ACTGAACTGTGATAATGATGAAACAA 57.605 30.769 0.00 0.00 0.00 2.83
4151 4311 7.040201 ACTGTGATAATGATGAAACAAAGCAGT 60.040 33.333 0.00 0.00 0.00 4.40
4477 4649 1.064825 TGAAAGGGGTGGAGACCTTC 58.935 55.000 0.00 0.00 45.98 3.46
4495 4667 0.668535 TCAGGCTATCCACGATGTCG 59.331 55.000 0.11 0.11 46.33 4.35
4570 4742 2.026822 ACCTTGCAGGAGATACCACTTG 60.027 50.000 8.91 0.00 37.67 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.308069 ATGAACACCAGCACATCGCC 61.308 55.000 0.00 0.00 44.04 5.54
27 28 1.395954 CTGATGAACACCAGCACATCG 59.604 52.381 0.00 0.00 41.04 3.84
34 35 4.631131 TGTCAAGTACTGATGAACACCAG 58.369 43.478 0.00 0.00 36.14 4.00
119 153 7.509141 ACACTCTACTACATGATCTCATCTG 57.491 40.000 0.00 0.00 33.61 2.90
120 154 6.426633 CGACACTCTACTACATGATCTCATCT 59.573 42.308 0.00 0.00 33.61 2.90
121 155 6.598525 CGACACTCTACTACATGATCTCATC 58.401 44.000 0.00 0.00 33.61 2.92
122 156 5.049060 GCGACACTCTACTACATGATCTCAT 60.049 44.000 0.00 0.00 36.96 2.90
123 157 4.273724 GCGACACTCTACTACATGATCTCA 59.726 45.833 0.00 0.00 0.00 3.27
161 196 2.297912 CGACCACACACGACCGAAC 61.298 63.158 0.00 0.00 0.00 3.95
166 201 2.586635 TTGCCGACCACACACGAC 60.587 61.111 0.00 0.00 0.00 4.34
195 230 1.001641 GGTGCCTGCAGTTCCATCT 60.002 57.895 13.81 0.00 0.00 2.90
199 234 1.228245 TTCTGGTGCCTGCAGTTCC 60.228 57.895 13.81 11.98 0.00 3.62
347 388 3.305267 CGCACAGAACAATTTGATTCCCA 60.305 43.478 2.79 0.00 0.00 4.37
353 412 2.293170 TGGTCGCACAGAACAATTTGA 58.707 42.857 2.79 0.00 44.92 2.69
359 418 1.436195 GCAAGTGGTCGCACAGAACA 61.436 55.000 0.00 0.00 45.88 3.18
360 419 1.160329 AGCAAGTGGTCGCACAGAAC 61.160 55.000 0.00 0.00 37.00 3.01
361 420 1.146041 AGCAAGTGGTCGCACAGAA 59.854 52.632 0.00 0.00 0.00 3.02
362 421 1.595109 CAGCAAGTGGTCGCACAGA 60.595 57.895 0.00 0.00 0.00 3.41
363 422 1.159713 TTCAGCAAGTGGTCGCACAG 61.160 55.000 0.00 0.00 0.00 3.66
364 423 0.534877 ATTCAGCAAGTGGTCGCACA 60.535 50.000 0.00 0.00 0.00 4.57
365 424 0.110056 CATTCAGCAAGTGGTCGCAC 60.110 55.000 0.00 0.00 0.00 5.34
366 425 0.250252 TCATTCAGCAAGTGGTCGCA 60.250 50.000 0.00 0.00 0.00 5.10
367 426 1.063174 GATCATTCAGCAAGTGGTCGC 59.937 52.381 0.00 0.00 0.00 5.19
368 427 1.325640 CGATCATTCAGCAAGTGGTCG 59.674 52.381 3.56 3.56 39.69 4.79
369 428 2.606725 CTCGATCATTCAGCAAGTGGTC 59.393 50.000 0.00 0.00 0.00 4.02
370 429 2.027745 ACTCGATCATTCAGCAAGTGGT 60.028 45.455 0.00 0.00 0.00 4.16
371 430 2.606725 GACTCGATCATTCAGCAAGTGG 59.393 50.000 0.00 0.00 0.00 4.00
372 431 2.280971 CGACTCGATCATTCAGCAAGTG 59.719 50.000 0.00 0.00 0.00 3.16
373 432 2.164422 TCGACTCGATCATTCAGCAAGT 59.836 45.455 0.00 0.00 0.00 3.16
467 527 8.520119 ACTGTACATTAATTGGATATACCCCT 57.480 34.615 0.00 0.00 38.00 4.79
468 528 9.662947 GTACTGTACATTAATTGGATATACCCC 57.337 37.037 12.89 0.00 38.00 4.95
490 550 8.432805 ACTTATGCAGATATTTTAGCAGGTACT 58.567 33.333 0.00 0.00 40.71 2.73
491 551 8.608844 ACTTATGCAGATATTTTAGCAGGTAC 57.391 34.615 0.00 0.00 40.71 3.34
492 552 9.627123 AAACTTATGCAGATATTTTAGCAGGTA 57.373 29.630 0.00 0.00 40.71 3.08
524 586 6.396829 AAGTTTCTAAGCACTGCAGATTTT 57.603 33.333 23.35 13.00 0.00 1.82
556 618 9.219603 CAGAAATGTACTCTCTGAATACCAAAA 57.780 33.333 11.68 0.00 39.15 2.44
615 677 2.482494 AGGCTCCTAGCAAATACCAGT 58.518 47.619 0.78 0.00 44.75 4.00
616 678 3.007398 CCTAGGCTCCTAGCAAATACCAG 59.993 52.174 15.80 0.00 44.75 4.00
617 679 2.972713 CCTAGGCTCCTAGCAAATACCA 59.027 50.000 15.80 0.00 44.75 3.25
618 680 2.289756 GCCTAGGCTCCTAGCAAATACC 60.290 54.545 27.17 0.00 44.75 2.73
619 681 3.046968 GCCTAGGCTCCTAGCAAATAC 57.953 52.381 27.17 0.00 44.75 1.89
650 712 6.776603 GGGACCAAGCTACTAAAGAGATACTA 59.223 42.308 0.00 0.00 0.00 1.82
651 713 5.599242 GGGACCAAGCTACTAAAGAGATACT 59.401 44.000 0.00 0.00 0.00 2.12
652 714 5.845103 GGGACCAAGCTACTAAAGAGATAC 58.155 45.833 0.00 0.00 0.00 2.24
694 756 4.147321 AGACAAATCACTGTGCCAAATCT 58.853 39.130 2.12 0.79 0.00 2.40
700 762 3.316308 ACTTCAAGACAAATCACTGTGCC 59.684 43.478 2.12 0.00 0.00 5.01
702 764 5.998454 AGACTTCAAGACAAATCACTGTG 57.002 39.130 0.17 0.17 0.00 3.66
706 768 7.218963 GTGTGAAAAGACTTCAAGACAAATCAC 59.781 37.037 0.00 2.10 34.44 3.06
711 773 6.817765 AAGTGTGAAAAGACTTCAAGACAA 57.182 33.333 0.00 0.00 0.00 3.18
752 814 8.592998 CACCATAGTTGTACTCGAACTTTTATC 58.407 37.037 2.75 0.00 35.30 1.75
761 823 4.277672 GGCTATCACCATAGTTGTACTCGA 59.722 45.833 0.00 0.00 35.28 4.04
765 827 5.523916 CAGTTGGCTATCACCATAGTTGTAC 59.476 44.000 0.00 0.00 40.13 2.90
802 864 6.575162 ACTGCTTAAATTCCAGAAACGAAT 57.425 33.333 0.00 0.00 0.00 3.34
829 891 5.980116 CCTAGACGATATTTCCACAGAAGTG 59.020 44.000 0.00 0.00 45.47 3.16
834 896 4.322080 TGCCTAGACGATATTTCCACAG 57.678 45.455 0.00 0.00 0.00 3.66
862 924 3.529533 GACACACTGGATCTGATGAAGG 58.470 50.000 0.00 0.00 0.00 3.46
863 925 3.055602 TGGACACACTGGATCTGATGAAG 60.056 47.826 0.00 0.00 0.00 3.02
879 941 6.095021 GGGATCCTAAAAATTAGTGTGGACAC 59.905 42.308 12.58 1.42 46.77 3.67
880 942 6.011981 AGGGATCCTAAAAATTAGTGTGGACA 60.012 38.462 12.58 0.00 28.47 4.02
881 943 6.424032 AGGGATCCTAAAAATTAGTGTGGAC 58.576 40.000 12.58 0.00 28.47 4.02
882 944 6.652205 AGGGATCCTAAAAATTAGTGTGGA 57.348 37.500 12.58 0.00 28.47 4.02
883 945 8.996651 ATAAGGGATCCTAAAAATTAGTGTGG 57.003 34.615 12.58 0.00 31.13 4.17
911 975 3.699538 TGACCTGCATACTGTGTACCTAG 59.300 47.826 0.00 0.00 0.00 3.02
929 998 0.610687 CTGAGGAGGTGAGGTTGACC 59.389 60.000 0.00 0.00 0.00 4.02
930 999 1.633774 TCTGAGGAGGTGAGGTTGAC 58.366 55.000 0.00 0.00 0.00 3.18
1011 1080 6.484643 TGCACAAGAAATATATCTGAAGAGGC 59.515 38.462 0.00 0.00 0.00 4.70
1027 1096 5.709631 TGGCAAATAGTAGAATGCACAAGAA 59.290 36.000 0.00 0.00 40.51 2.52
1031 1100 5.418524 ACATTGGCAAATAGTAGAATGCACA 59.581 36.000 3.01 0.00 40.51 4.57
1076 1145 1.531578 GGAGTGCGTCTTTTTCCAGAC 59.468 52.381 0.00 0.00 40.02 3.51
1117 1186 4.514441 GCTCATGTAATTCTGTGGATCCTG 59.486 45.833 14.23 3.49 0.00 3.86
1135 1204 3.201487 TGAGATTCATCCCAGTTGCTCAT 59.799 43.478 0.00 0.00 0.00 2.90
1161 1230 0.737019 CACCATGAAATTGGCACGGC 60.737 55.000 0.00 0.00 40.68 5.68
1170 1239 2.509569 TGGCACGTTACACCATGAAAT 58.490 42.857 0.00 0.00 0.00 2.17
1176 1245 1.968704 TTTCATGGCACGTTACACCA 58.031 45.000 0.00 0.00 37.99 4.17
1189 1258 4.520111 TGTGACCTCACCAGAAATTTCATG 59.480 41.667 19.99 14.16 45.88 3.07
1319 1388 0.253044 GGTCAGTGCAGCAGGGATAA 59.747 55.000 0.00 0.00 0.00 1.75
1449 1518 3.181476 ACACAGGAAATGCACCAGAAAAC 60.181 43.478 0.00 0.00 0.00 2.43
1525 1594 3.593442 TTCAGGAACACCACCTTCATT 57.407 42.857 0.00 0.00 35.35 2.57
1566 1635 2.173356 CCCCAAGAATAGCCATGTCAGA 59.827 50.000 0.00 0.00 0.00 3.27
1627 1696 1.694696 AGTCCCAAGTGACTCCAAGTC 59.305 52.381 0.08 0.08 41.75 3.01
1647 1716 0.458543 GATTGCGCGAGAAGTCCAGA 60.459 55.000 12.10 0.00 0.00 3.86
1740 1809 2.307098 AGGAGGAATTTCACCAGTCAGG 59.693 50.000 2.77 0.00 45.67 3.86
1746 1815 1.988107 AGCTCAGGAGGAATTTCACCA 59.012 47.619 2.77 0.00 0.00 4.17
1769 1838 8.729756 CAAATTCAGATAACAATGTCAGGTGTA 58.270 33.333 0.00 0.00 0.00 2.90
1785 1854 9.623000 TGATTATGAGACACATCAAATTCAGAT 57.377 29.630 0.00 0.00 40.07 2.90
1845 1914 7.038659 CGTGGAAGATCTTAAGATTCTTCAGT 58.961 38.462 31.72 15.96 38.70 3.41
1869 1938 5.103000 CCATAGAAGTTGTTCCTGTAGACG 58.897 45.833 0.00 0.00 32.48 4.18
1870 1939 5.869888 CACCATAGAAGTTGTTCCTGTAGAC 59.130 44.000 0.00 0.00 32.48 2.59
2046 2115 0.040067 CGCTTTGGCACAGGAACTTC 60.040 55.000 2.39 0.00 42.39 3.01
2058 2127 0.381801 ACTGCAGTTTGTCGCTTTGG 59.618 50.000 15.25 0.00 0.00 3.28
2124 2193 6.597672 TCTCTAGAGTCTTGCAAGAAGAGTAG 59.402 42.308 34.03 27.34 37.47 2.57
2163 2232 2.229784 GCTCCCACTGAACTGATTTTGG 59.770 50.000 0.00 0.00 0.00 3.28
2220 2289 4.803613 CCATTGTCAGCAACATCAATGATG 59.196 41.667 20.58 20.58 45.40 3.07
2412 2481 5.138125 ACAATTGCTTCAGGTTACCAATG 57.862 39.130 5.05 0.00 0.00 2.82
2461 2530 4.431378 TCTGGTGGTATTGACCCTTCTAA 58.569 43.478 0.00 0.00 46.32 2.10
2542 2611 1.270550 GCCAACTGTGTCAGGGATTTG 59.729 52.381 1.90 0.00 35.51 2.32
2547 2616 1.302832 GGAGCCAACTGTGTCAGGG 60.303 63.158 1.90 0.00 35.51 4.45
2574 2643 5.218959 TGGGATAGATTGAGTGAATCCAGA 58.781 41.667 0.00 0.00 41.47 3.86
2703 2772 1.199327 GCATCATCTCCGGCAATCATG 59.801 52.381 0.00 0.00 0.00 3.07
2756 2825 0.035630 CCTCCAGCCTTCTGAAGTGG 60.036 60.000 16.86 16.86 42.95 4.00
3153 3227 9.559958 CTGGCAAAATATTTTCTACAGTACTTG 57.440 33.333 10.53 0.00 0.00 3.16
3322 3396 4.518970 AGACAAACTGCGTCCATTTAACAT 59.481 37.500 0.00 0.00 33.70 2.71
3334 3408 7.678194 TGAAGAAATTAAAAGACAAACTGCG 57.322 32.000 0.00 0.00 0.00 5.18
3487 3563 7.324178 AGCTGACGTAAGACTTAAATCTTCAT 58.676 34.615 3.33 0.00 39.65 2.57
3550 3626 0.958876 TACGCCACTCTCTTCTCGCA 60.959 55.000 0.00 0.00 0.00 5.10
3565 3641 1.389106 CGGCACAAGACTAGTTTACGC 59.611 52.381 0.00 0.00 0.00 4.42
3569 3645 2.364324 TCTGACGGCACAAGACTAGTTT 59.636 45.455 0.00 0.00 0.00 2.66
3719 3797 4.280929 ACAAGGGCAATGTTAAAGACCTTC 59.719 41.667 0.00 0.00 34.83 3.46
3843 3923 7.720074 AGGTAGCCTGCTTTTACTTATTATTCC 59.280 37.037 0.00 0.00 29.57 3.01
3864 3944 6.349363 GGTGGCATCTTACAAAGAAAAGGTAG 60.349 42.308 0.00 0.00 41.63 3.18
3984 4075 7.770897 CACTTCCAGAGTATTATTAACAGCCTT 59.229 37.037 0.00 0.00 36.65 4.35
4000 4091 1.205893 GAGGCCACTACACTTCCAGAG 59.794 57.143 5.01 0.00 0.00 3.35
4007 4098 0.471971 ACCACAGAGGCCACTACACT 60.472 55.000 5.01 0.00 43.14 3.55
4015 4106 1.341156 ATGAGGCTACCACAGAGGCC 61.341 60.000 0.00 0.00 43.14 5.19
4018 4109 2.625790 GACCTATGAGGCTACCACAGAG 59.374 54.545 0.00 0.00 39.63 3.35
4019 4110 2.024369 TGACCTATGAGGCTACCACAGA 60.024 50.000 0.00 0.00 39.63 3.41
4022 4113 2.700897 ACATGACCTATGAGGCTACCAC 59.299 50.000 0.00 0.00 39.63 4.16
4108 4200 7.891183 ATCACAGTTCAGTACAGTAAATCAC 57.109 36.000 0.00 0.00 0.00 3.06
4124 4216 7.660112 TGCTTTGTTTCATCATTATCACAGTT 58.340 30.769 0.00 0.00 0.00 3.16
4145 4305 3.746492 GTCGAAATTGGACTACACTGCTT 59.254 43.478 0.77 0.00 0.00 3.91
4477 4649 0.941463 GCGACATCGTGGATAGCCTG 60.941 60.000 0.00 0.00 42.22 4.85


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

AutoCloner maintained by Alex Coulton.