Multiple sequence alignment - TraesCS6A01G128100

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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 TraesCS6A01G128100 chr6A 100.000 4136 0 0 1 4136 100737230 100741365 0.000000e+00 7638
1 TraesCS6A01G128100 chr6A 84.866 2491 341 25 847 3310 100229053 100226572 0.000000e+00 2479
2 TraesCS6A01G128100 chr6A 83.503 2449 374 21 971 3394 100797485 100799928 0.000000e+00 2257
3 TraesCS6A01G128100 chr6A 82.491 2553 396 27 971 3489 100755377 100757912 0.000000e+00 2191
4 TraesCS6A01G128100 chr6A 74.471 2503 535 79 698 3135 100363760 100361297 0.000000e+00 987
5 TraesCS6A01G128100 chr6A 86.644 292 30 4 417 700 100364091 100363801 8.630000e-82 315
6 TraesCS6A01G128100 chr6B 93.836 3861 157 25 310 4136 159377283 159381096 0.000000e+00 5736
7 TraesCS6A01G128100 chr6B 85.209 2515 335 26 866 3362 158163177 158160682 0.000000e+00 2549
8 TraesCS6A01G128100 chr6B 83.587 2297 339 27 1025 3295 159395974 159398258 0.000000e+00 2119
9 TraesCS6A01G128100 chr6B 83.121 1961 322 5 1058 3013 156375930 156373974 0.000000e+00 1779
10 TraesCS6A01G128100 chr6B 89.141 396 35 6 310 700 158190666 158190274 1.730000e-133 486
11 TraesCS6A01G128100 chr6B 91.638 287 23 1 1 286 159376917 159377203 3.000000e-106 396
12 TraesCS6A01G128100 chr6B 84.321 287 32 6 1 286 158191012 158190738 6.820000e-68 268
13 TraesCS6A01G128100 chr6D 85.250 2644 345 27 866 3492 83160567 83157952 0.000000e+00 2680
14 TraesCS6A01G128100 chr6D 82.635 1981 327 12 1043 3013 81673805 81671832 0.000000e+00 1736
15 TraesCS6A01G128100 chr6D 89.114 395 36 6 310 700 83205995 83205604 6.220000e-133 484
16 TraesCS6A01G128100 chr6D 83.916 286 32 5 1 286 83206338 83206067 1.140000e-65 261
17 TraesCS6A01G128100 chr3B 76.891 476 59 30 3041 3492 680860903 680860455 5.380000e-54 222
18 TraesCS6A01G128100 chr5B 84.496 129 9 3 3202 3319 22096633 22096761 2.610000e-22 117


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 TraesCS6A01G128100 chr6A 100737230 100741365 4135 False 7638.0 7638 100.0000 1 4136 1 chr6A.!!$F1 4135
1 TraesCS6A01G128100 chr6A 100226572 100229053 2481 True 2479.0 2479 84.8660 847 3310 1 chr6A.!!$R1 2463
2 TraesCS6A01G128100 chr6A 100797485 100799928 2443 False 2257.0 2257 83.5030 971 3394 1 chr6A.!!$F3 2423
3 TraesCS6A01G128100 chr6A 100755377 100757912 2535 False 2191.0 2191 82.4910 971 3489 1 chr6A.!!$F2 2518
4 TraesCS6A01G128100 chr6A 100361297 100364091 2794 True 651.0 987 80.5575 417 3135 2 chr6A.!!$R2 2718
5 TraesCS6A01G128100 chr6B 159376917 159381096 4179 False 3066.0 5736 92.7370 1 4136 2 chr6B.!!$F2 4135
6 TraesCS6A01G128100 chr6B 158160682 158163177 2495 True 2549.0 2549 85.2090 866 3362 1 chr6B.!!$R2 2496
7 TraesCS6A01G128100 chr6B 159395974 159398258 2284 False 2119.0 2119 83.5870 1025 3295 1 chr6B.!!$F1 2270
8 TraesCS6A01G128100 chr6B 156373974 156375930 1956 True 1779.0 1779 83.1210 1058 3013 1 chr6B.!!$R1 1955
9 TraesCS6A01G128100 chr6B 158190274 158191012 738 True 377.0 486 86.7310 1 700 2 chr6B.!!$R3 699
10 TraesCS6A01G128100 chr6D 83157952 83160567 2615 True 2680.0 2680 85.2500 866 3492 1 chr6D.!!$R2 2626
11 TraesCS6A01G128100 chr6D 81671832 81673805 1973 True 1736.0 1736 82.6350 1043 3013 1 chr6D.!!$R1 1970
12 TraesCS6A01G128100 chr6D 83205604 83206338 734 True 372.5 484 86.5150 1 700 2 chr6D.!!$R3 699

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
749 865 1.499007 ACCCCTTCACATCAAACTGGT 59.501 47.619 0.0 0.0 0.0 4.00 F
1539 1710 0.391661 TGATGAAGAGCCTCGTTGCC 60.392 55.000 0.0 0.0 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1911 2089 0.250858 CCCCTGACATGCTGTTGTGA 60.251 55.0 0.00 0.0 0.00 3.58 R
3173 3374 0.031314 CTGATGACCACCGGAGATCG 59.969 60.0 9.46 0.0 38.88 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
34 35 2.643551 ACCAGAACTTATGGATTGGCG 58.356 47.619 9.50 0.00 40.51 5.69
51 52 2.004733 GGCGTATCAAGTTACCACACC 58.995 52.381 0.00 0.00 0.00 4.16
58 59 7.515643 CGTATCAAGTTACCACACCTAAAAAG 58.484 38.462 0.00 0.00 0.00 2.27
61 62 7.324354 TCAAGTTACCACACCTAAAAAGAAC 57.676 36.000 0.00 0.00 0.00 3.01
126 128 4.058124 CAAAGAATGTCTCGGACAGTTCA 58.942 43.478 18.89 3.98 46.04 3.18
139 141 3.798337 GGACAGTTCACAACAGCAAAATG 59.202 43.478 0.00 0.00 0.00 2.32
143 145 3.701040 AGTTCACAACAGCAAAATGGACT 59.299 39.130 0.00 0.00 0.00 3.85
144 146 3.713858 TCACAACAGCAAAATGGACTG 57.286 42.857 0.00 0.00 37.45 3.51
166 168 4.118410 GCTCTACACTGATCAATGACAGG 58.882 47.826 11.80 3.65 38.30 4.00
169 171 6.550938 TCTACACTGATCAATGACAGGAAT 57.449 37.500 11.80 0.00 38.30 3.01
233 235 4.180377 AGCATTCAATGACAGGATCCAT 57.820 40.909 15.82 0.36 0.00 3.41
503 567 8.738645 AATAAATCTTGACTATGGGTGAGAAC 57.261 34.615 0.00 0.00 0.00 3.01
651 722 9.816787 AGTGGGTGTATTTTTATTAAGAAAGGA 57.183 29.630 0.00 0.00 0.00 3.36
747 863 1.806542 CGACCCCTTCACATCAAACTG 59.193 52.381 0.00 0.00 0.00 3.16
748 864 2.162681 GACCCCTTCACATCAAACTGG 58.837 52.381 0.00 0.00 0.00 4.00
749 865 1.499007 ACCCCTTCACATCAAACTGGT 59.501 47.619 0.00 0.00 0.00 4.00
750 866 2.714250 ACCCCTTCACATCAAACTGGTA 59.286 45.455 0.00 0.00 0.00 3.25
751 867 3.139397 ACCCCTTCACATCAAACTGGTAA 59.861 43.478 0.00 0.00 0.00 2.85
752 868 3.758554 CCCCTTCACATCAAACTGGTAAG 59.241 47.826 0.00 0.00 0.00 2.34
753 869 3.191371 CCCTTCACATCAAACTGGTAAGC 59.809 47.826 0.00 0.00 0.00 3.09
754 870 3.120199 CCTTCACATCAAACTGGTAAGCG 60.120 47.826 0.00 0.00 0.00 4.68
755 871 3.394674 TCACATCAAACTGGTAAGCGA 57.605 42.857 0.00 0.00 0.00 4.93
756 872 3.734463 TCACATCAAACTGGTAAGCGAA 58.266 40.909 0.00 0.00 0.00 4.70
757 873 4.130857 TCACATCAAACTGGTAAGCGAAA 58.869 39.130 0.00 0.00 0.00 3.46
758 874 4.024387 TCACATCAAACTGGTAAGCGAAAC 60.024 41.667 0.00 0.00 0.00 2.78
759 875 3.880490 ACATCAAACTGGTAAGCGAAACA 59.120 39.130 0.00 0.00 0.00 2.83
760 876 4.024048 ACATCAAACTGGTAAGCGAAACAG 60.024 41.667 5.00 5.00 37.01 3.16
761 877 3.799366 TCAAACTGGTAAGCGAAACAGA 58.201 40.909 12.61 0.00 35.08 3.41
762 878 3.558418 TCAAACTGGTAAGCGAAACAGAC 59.442 43.478 12.61 0.00 35.08 3.51
763 879 2.902705 ACTGGTAAGCGAAACAGACA 57.097 45.000 12.61 0.00 35.08 3.41
764 880 2.755650 ACTGGTAAGCGAAACAGACAG 58.244 47.619 12.61 0.00 35.08 3.51
765 881 2.364324 ACTGGTAAGCGAAACAGACAGA 59.636 45.455 12.61 0.00 35.08 3.41
766 882 3.006967 ACTGGTAAGCGAAACAGACAGAT 59.993 43.478 12.61 0.00 35.08 2.90
767 883 3.997021 CTGGTAAGCGAAACAGACAGATT 59.003 43.478 0.45 0.00 32.86 2.40
768 884 5.142061 TGGTAAGCGAAACAGACAGATTA 57.858 39.130 0.00 0.00 0.00 1.75
779 917 7.330946 CGAAACAGACAGATTAGGTATCAACAA 59.669 37.037 0.00 0.00 35.59 2.83
806 944 1.620819 TCCTGCTTGGAAGTCAGACTC 59.379 52.381 2.72 0.00 42.94 3.36
818 960 6.269077 TGGAAGTCAGACTCACCAATAAACTA 59.731 38.462 20.53 2.57 33.80 2.24
819 961 6.590677 GGAAGTCAGACTCACCAATAAACTAC 59.409 42.308 17.11 0.00 0.00 2.73
820 962 6.665992 AGTCAGACTCACCAATAAACTACA 57.334 37.500 0.00 0.00 0.00 2.74
824 966 7.755822 GTCAGACTCACCAATAAACTACAGTAG 59.244 40.741 6.00 6.00 0.00 2.57
825 967 7.668469 TCAGACTCACCAATAAACTACAGTAGA 59.332 37.037 14.94 0.00 0.00 2.59
1023 1188 0.457509 AGTCACTCAATCGCTCGCAG 60.458 55.000 0.00 0.00 0.00 5.18
1065 1230 4.340950 CCTTTCTTTGGTTTGGCTCTTGTA 59.659 41.667 0.00 0.00 0.00 2.41
1119 1287 0.607620 GCACAGAGCAGGAGAAGAGT 59.392 55.000 0.00 0.00 44.79 3.24
1214 1382 1.225704 GCAGGTGGGAAGGGATCAG 59.774 63.158 0.00 0.00 0.00 2.90
1256 1427 4.245660 GTCACTGATGTTGTGCTAGCTTA 58.754 43.478 17.23 1.46 35.58 3.09
1263 1434 2.159099 TGTTGTGCTAGCTTATCGAGGG 60.159 50.000 17.23 0.00 0.00 4.30
1323 1494 2.359523 GCTTGTTGCGATTCGATCTC 57.640 50.000 10.88 0.00 0.00 2.75
1448 1619 1.852157 TGCCATCTTCCACCCCTGT 60.852 57.895 0.00 0.00 0.00 4.00
1467 1638 2.423898 GCGGCCTCTGCAGGTACTA 61.424 63.158 15.13 0.00 42.74 1.82
1533 1704 0.467804 GGGAGGTGATGAAGAGCCTC 59.532 60.000 0.00 0.00 44.93 4.70
1539 1710 0.391661 TGATGAAGAGCCTCGTTGCC 60.392 55.000 0.00 0.00 0.00 4.52
1620 1791 2.925306 GCCATCTTTTGCAGTGCTTGAG 60.925 50.000 17.60 10.81 0.00 3.02
1665 1836 0.908198 ACATTCCTCCAGGACTCAGC 59.092 55.000 0.00 0.00 45.39 4.26
1809 1986 3.884091 GAGAGCTCAAAGGCATCATCAAT 59.116 43.478 17.77 0.00 34.17 2.57
1860 2038 3.438434 GGAAGAATGAGTTCAGAGGCAAC 59.562 47.826 0.00 0.00 36.79 4.17
1902 2080 2.551938 GCTGAAGAAGTTGGAGGAGCTT 60.552 50.000 0.00 0.00 0.00 3.74
1911 2089 2.238395 GTTGGAGGAGCTTCTCTTGGAT 59.762 50.000 21.58 0.00 34.39 3.41
2115 2293 0.322008 ACTCCTGCAGCAAGCTAACC 60.322 55.000 8.66 0.00 45.94 2.85
2194 2372 6.677781 ATCTGAAGTCTCTCTCGTTTCTAG 57.322 41.667 0.00 0.00 0.00 2.43
2268 2446 1.152030 TTCCAGGAGCCTCACCACT 60.152 57.895 0.00 0.00 0.00 4.00
2478 2656 2.093288 TGACTGGATCAGCAGCCTAAAG 60.093 50.000 0.00 0.00 34.37 1.85
2497 2675 7.201875 GCCTAAAGTTGCTCTTCTATCTAGACT 60.202 40.741 0.00 0.00 35.02 3.24
2577 2767 1.800805 AATCAGACAAGACTGCACCG 58.199 50.000 0.00 0.00 37.75 4.94
2763 2954 8.112183 AGTTCCAACAAATTATCTGGAGAGATT 58.888 33.333 0.00 0.00 39.76 2.40
3087 3278 1.869774 CCTTTGGTGCTTTCTTTGGC 58.130 50.000 0.00 0.00 0.00 4.52
3154 3347 7.832769 TGGCTAAAACCTTGTAATTGTTATCC 58.167 34.615 0.00 0.00 0.00 2.59
3173 3374 1.901464 ACCACCCAAACCATGACGC 60.901 57.895 0.00 0.00 0.00 5.19
3249 3463 3.873952 CCTGCTAAACCTGCTATCTTGAC 59.126 47.826 0.00 0.00 0.00 3.18
3250 3464 3.521560 TGCTAAACCTGCTATCTTGACG 58.478 45.455 0.00 0.00 0.00 4.35
3252 3466 3.933332 GCTAAACCTGCTATCTTGACGTT 59.067 43.478 0.00 0.00 0.00 3.99
3253 3467 4.392138 GCTAAACCTGCTATCTTGACGTTT 59.608 41.667 0.00 0.00 0.00 3.60
3254 3468 4.749245 AAACCTGCTATCTTGACGTTTG 57.251 40.909 0.00 0.00 0.00 2.93
3257 3481 2.349886 CCTGCTATCTTGACGTTTGCTC 59.650 50.000 0.00 0.00 0.00 4.26
3322 3546 5.107104 ACGTCAACAGTGTGTAAGCATATTG 60.107 40.000 0.00 0.00 31.58 1.90
3394 3620 4.751600 CGCATAGGCTGATGAATGTTTCTA 59.248 41.667 0.00 0.00 38.10 2.10
3395 3621 5.410746 CGCATAGGCTGATGAATGTTTCTAT 59.589 40.000 0.00 0.00 38.10 1.98
3396 3622 6.072838 CGCATAGGCTGATGAATGTTTCTATT 60.073 38.462 0.00 0.00 38.10 1.73
3397 3623 7.521099 CGCATAGGCTGATGAATGTTTCTATTT 60.521 37.037 0.00 0.00 38.10 1.40
3398 3624 7.594015 GCATAGGCTGATGAATGTTTCTATTTG 59.406 37.037 0.00 0.00 36.96 2.32
3399 3625 8.627403 CATAGGCTGATGAATGTTTCTATTTGT 58.373 33.333 0.00 0.00 0.00 2.83
3400 3626 7.472334 AGGCTGATGAATGTTTCTATTTGTT 57.528 32.000 0.00 0.00 0.00 2.83
3401 3627 8.579850 AGGCTGATGAATGTTTCTATTTGTTA 57.420 30.769 0.00 0.00 0.00 2.41
3402 3628 9.023962 AGGCTGATGAATGTTTCTATTTGTTAA 57.976 29.630 0.00 0.00 0.00 2.01
3403 3629 9.294030 GGCTGATGAATGTTTCTATTTGTTAAG 57.706 33.333 0.00 0.00 0.00 1.85
3404 3630 9.846248 GCTGATGAATGTTTCTATTTGTTAAGT 57.154 29.630 0.00 0.00 0.00 2.24
3445 3674 5.696270 TCAGAGTACAACACATAACAAGCAG 59.304 40.000 0.00 0.00 0.00 4.24
3452 3681 2.094258 ACACATAACAAGCAGAATCGCG 59.906 45.455 0.00 0.00 36.85 5.87
3545 3775 1.262640 ACCGATTAAGCCAGACCGGT 61.263 55.000 6.92 6.92 44.37 5.28
3558 3788 0.997196 GACCGGTGCGTTAACAGATC 59.003 55.000 14.63 0.00 0.00 2.75
3574 3804 2.098117 CAGATCGATCAAGGGCAAAACC 59.902 50.000 26.47 0.00 37.93 3.27
3576 3806 0.958382 TCGATCAAGGGCAAAACCGG 60.958 55.000 0.00 0.00 40.62 5.28
3607 3837 1.094073 AGCTCGATGCAGTTGCCATC 61.094 55.000 1.06 4.47 45.94 3.51
3616 3846 1.340889 GCAGTTGCCATCAAACTCCAA 59.659 47.619 0.00 0.00 33.37 3.53
3635 3865 0.181350 ACCCAGGATCGCAATTCTCC 59.819 55.000 0.00 0.00 0.00 3.71
3668 3898 5.847670 ACACACGCTAAGAGAAAGAAATC 57.152 39.130 0.00 0.00 0.00 2.17
3741 3972 4.928601 TCCGTGATTTCTACAATACCTCG 58.071 43.478 0.00 0.00 0.00 4.63
3743 3974 4.202080 CCGTGATTTCTACAATACCTCGGA 60.202 45.833 0.00 0.00 35.94 4.55
3756 3987 1.340795 ACCTCGGATAACGGACTCACT 60.341 52.381 0.00 0.00 44.45 3.41
3757 3988 1.334243 CCTCGGATAACGGACTCACTC 59.666 57.143 0.00 0.00 44.45 3.51
3759 3990 0.029035 CGGATAACGGACTCACTCGG 59.971 60.000 0.00 0.00 39.42 4.63
3760 3991 1.386533 GGATAACGGACTCACTCGGA 58.613 55.000 0.00 0.00 0.00 4.55
3797 4028 2.049627 ATCTTCGATCCCCTGCCTGC 62.050 60.000 0.00 0.00 0.00 4.85
3798 4029 3.764160 CTTCGATCCCCTGCCTGCC 62.764 68.421 0.00 0.00 0.00 4.85
3807 4038 1.566298 CCCTGCCTGCCTAGTTTCCT 61.566 60.000 0.00 0.00 0.00 3.36
3810 4041 0.547712 TGCCTGCCTAGTTTCCTCCT 60.548 55.000 0.00 0.00 0.00 3.69
3817 4048 0.984230 CTAGTTTCCTCCTGCCCACA 59.016 55.000 0.00 0.00 0.00 4.17
3879 4114 2.684843 CGGCCTTGAGCTGCTGAAC 61.685 63.158 7.01 0.00 42.11 3.18
3892 4127 0.755327 GCTGAACCCCTTTGTGTGGT 60.755 55.000 0.00 0.00 0.00 4.16
3893 4128 1.477923 GCTGAACCCCTTTGTGTGGTA 60.478 52.381 0.00 0.00 0.00 3.25
3894 4129 2.227194 CTGAACCCCTTTGTGTGGTAC 58.773 52.381 0.00 0.00 0.00 3.34
3899 4134 1.314730 CCCTTTGTGTGGTACGCTTT 58.685 50.000 0.00 0.00 40.97 3.51
3910 4153 3.799420 GTGGTACGCTTTGATCTCATCTC 59.201 47.826 0.00 0.00 35.02 2.75
3915 4158 2.753296 GCTTTGATCTCATCTCCCTCG 58.247 52.381 0.00 0.00 0.00 4.63
3928 4171 1.815421 CCCTCGACCTGCCAAATCG 60.815 63.158 0.00 0.00 37.20 3.34
3955 4198 1.135527 CATAAAGCCATGCACAGGTGG 59.864 52.381 8.66 4.36 38.55 4.61
3972 4215 8.106247 CACAGGTGGTGTAACTAAATAATGTT 57.894 34.615 0.00 0.00 42.75 2.71
3978 4221 4.726704 GTGTAACTAAATAATGTTGCGGCG 59.273 41.667 0.51 0.51 32.76 6.46
3985 4228 0.952280 TAATGTTGCGGCGTTTGGAA 59.048 45.000 9.37 0.00 0.00 3.53
4001 4244 5.004726 CGTTTGGAAGTTCTTTTGCAGAAAG 59.995 40.000 2.25 12.43 43.52 2.62
4009 4252 6.299141 AGTTCTTTTGCAGAAAGACTGGATA 58.701 36.000 17.88 5.75 45.70 2.59
4026 4269 3.161866 GGATACAAAAAGGGCTGTTCCA 58.838 45.455 0.00 0.00 36.21 3.53
4058 4301 0.593128 CACTTTCTGGGCAAAGACCG 59.407 55.000 3.13 0.00 36.92 4.79
4084 4327 4.007644 CTCCCACGCCACAGCAGA 62.008 66.667 0.00 0.00 39.83 4.26
4121 4364 3.636231 CGCAACCCCTCCACCTCA 61.636 66.667 0.00 0.00 0.00 3.86
4129 4372 3.324930 CTCCACCTCAGCCTGCCA 61.325 66.667 0.00 0.00 0.00 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 8.611654 TCTTTTTAGGTGTGGTAACTTGATAC 57.388 34.615 0.00 0.00 37.61 2.24
51 52 7.707104 AGTTGTGATTCTGTGGTTCTTTTTAG 58.293 34.615 0.00 0.00 0.00 1.85
58 59 5.043248 CCAAAAGTTGTGATTCTGTGGTTC 58.957 41.667 0.00 0.00 0.00 3.62
61 62 3.636300 TCCCAAAAGTTGTGATTCTGTGG 59.364 43.478 0.00 0.00 0.00 4.17
126 128 2.514205 GCAGTCCATTTTGCTGTTGT 57.486 45.000 0.00 0.00 37.35 3.32
139 141 3.876274 TTGATCAGTGTAGAGCAGTCC 57.124 47.619 0.00 0.00 35.10 3.85
143 145 4.382362 CCTGTCATTGATCAGTGTAGAGCA 60.382 45.833 16.80 9.09 31.10 4.26
144 146 4.118410 CCTGTCATTGATCAGTGTAGAGC 58.882 47.826 16.80 5.64 0.00 4.09
166 168 7.993183 TCATGTGGGATTTCTTCCTAGTTATTC 59.007 37.037 0.00 0.00 44.75 1.75
169 171 6.884472 TCATGTGGGATTTCTTCCTAGTTA 57.116 37.500 0.00 0.00 44.75 2.24
195 197 0.665298 GCTTGTGCCCTTAGCTATGC 59.335 55.000 0.00 0.00 44.23 3.14
233 235 1.974875 CTGCAACCTCATGCCAGCA 60.975 57.895 0.00 0.00 45.83 4.41
244 246 5.416083 ACAGGAAAAAGTAAAACTGCAACC 58.584 37.500 0.00 0.00 0.00 3.77
245 247 6.035650 GGAACAGGAAAAAGTAAAACTGCAAC 59.964 38.462 0.00 0.00 0.00 4.17
307 327 4.365723 CAAGCCACAATTCATAGCCAATC 58.634 43.478 0.00 0.00 0.00 2.67
394 454 2.238144 AGCTATTCATGCTGTGTGGACT 59.762 45.455 0.00 0.00 39.56 3.85
397 457 5.762825 ATTAAGCTATTCATGCTGTGTGG 57.237 39.130 0.00 0.00 41.03 4.17
473 533 9.396022 TCACCCATAGTCAAGATTTATTTCTTC 57.604 33.333 0.00 0.00 33.69 2.87
503 567 5.872635 TGAATAAAAAGCAAGCTCATCTCG 58.127 37.500 0.00 0.00 0.00 4.04
747 863 4.567159 CCTAATCTGTCTGTTTCGCTTACC 59.433 45.833 0.00 0.00 0.00 2.85
748 864 5.169295 ACCTAATCTGTCTGTTTCGCTTAC 58.831 41.667 0.00 0.00 0.00 2.34
749 865 5.401531 ACCTAATCTGTCTGTTTCGCTTA 57.598 39.130 0.00 0.00 0.00 3.09
750 866 4.273148 ACCTAATCTGTCTGTTTCGCTT 57.727 40.909 0.00 0.00 0.00 4.68
751 867 3.963428 ACCTAATCTGTCTGTTTCGCT 57.037 42.857 0.00 0.00 0.00 4.93
752 868 5.348986 TGATACCTAATCTGTCTGTTTCGC 58.651 41.667 0.00 0.00 35.45 4.70
753 869 6.811665 TGTTGATACCTAATCTGTCTGTTTCG 59.188 38.462 0.00 0.00 35.45 3.46
754 870 8.547967 TTGTTGATACCTAATCTGTCTGTTTC 57.452 34.615 0.00 0.00 35.45 2.78
755 871 8.375506 TCTTGTTGATACCTAATCTGTCTGTTT 58.624 33.333 0.00 0.00 35.45 2.83
756 872 7.819900 GTCTTGTTGATACCTAATCTGTCTGTT 59.180 37.037 0.00 0.00 35.45 3.16
757 873 7.039011 TGTCTTGTTGATACCTAATCTGTCTGT 60.039 37.037 0.00 0.00 35.45 3.41
758 874 7.323420 TGTCTTGTTGATACCTAATCTGTCTG 58.677 38.462 0.00 0.00 35.45 3.51
759 875 7.482169 TGTCTTGTTGATACCTAATCTGTCT 57.518 36.000 0.00 0.00 35.45 3.41
760 876 8.723942 ATTGTCTTGTTGATACCTAATCTGTC 57.276 34.615 0.00 0.00 35.45 3.51
761 877 9.167311 GAATTGTCTTGTTGATACCTAATCTGT 57.833 33.333 0.00 0.00 35.45 3.41
762 878 8.616076 GGAATTGTCTTGTTGATACCTAATCTG 58.384 37.037 0.00 0.00 35.45 2.90
763 879 8.552296 AGGAATTGTCTTGTTGATACCTAATCT 58.448 33.333 0.00 0.00 35.45 2.40
764 880 8.616076 CAGGAATTGTCTTGTTGATACCTAATC 58.384 37.037 0.00 0.00 34.93 1.75
765 881 7.067494 GCAGGAATTGTCTTGTTGATACCTAAT 59.933 37.037 0.00 0.00 33.46 1.73
766 882 6.374333 GCAGGAATTGTCTTGTTGATACCTAA 59.626 38.462 0.00 0.00 33.46 2.69
767 883 5.880332 GCAGGAATTGTCTTGTTGATACCTA 59.120 40.000 0.00 0.00 33.46 3.08
768 884 4.702131 GCAGGAATTGTCTTGTTGATACCT 59.298 41.667 0.00 0.00 33.46 3.08
806 944 8.262227 TGGGTTATCTACTGTAGTTTATTGGTG 58.738 37.037 14.11 0.00 0.00 4.17
1023 1188 1.270893 GGTATGGGAAATCGGCTCCTC 60.271 57.143 0.00 0.00 33.11 3.71
1065 1230 3.243724 AGAAGCCAAGAAGACCAGTAGT 58.756 45.455 0.00 0.00 0.00 2.73
1119 1287 1.271597 GCAAGAAGCTGGAGAAGGGAA 60.272 52.381 0.00 0.00 41.15 3.97
1214 1382 1.236628 CATCCTATTCAGGCTGCAGC 58.763 55.000 30.88 30.88 42.30 5.25
1263 1434 1.521681 CGAAATGGACCCCTCGAGC 60.522 63.158 6.99 0.00 33.13 5.03
1315 1486 2.612972 GCAAGTTGTGGGAGAGATCGAA 60.613 50.000 4.48 0.00 0.00 3.71
1320 1491 1.070758 GACAGCAAGTTGTGGGAGAGA 59.929 52.381 4.48 0.00 0.00 3.10
1323 1494 1.233019 CAGACAGCAAGTTGTGGGAG 58.767 55.000 4.48 0.00 0.00 4.30
1448 1619 4.082523 GTACCTGCAGAGGCCGCA 62.083 66.667 17.39 6.42 44.33 5.69
1467 1638 4.900635 AAACAAGTTGCTCGAGATGTTT 57.099 36.364 18.75 18.94 36.48 2.83
1533 1704 2.879907 CTGGCATTGAGGGCAACG 59.120 61.111 0.00 0.00 43.25 4.10
1539 1710 1.180456 TGTTGGTGCTGGCATTGAGG 61.180 55.000 0.00 0.00 0.00 3.86
1620 1791 6.503524 TCCACTGAATTTGTTAAAACTGAGC 58.496 36.000 0.00 0.00 0.00 4.26
1860 2038 6.435591 TCAGCTCACCTATAGATTCTGGTATG 59.564 42.308 0.00 0.00 0.00 2.39
1902 2080 3.244665 ACATGCTGTTGTGATCCAAGAGA 60.245 43.478 18.83 9.02 45.02 3.10
1911 2089 0.250858 CCCCTGACATGCTGTTGTGA 60.251 55.000 0.00 0.00 0.00 3.58
2115 2293 2.203800 TGAAAGATAGCCGTAGTGCG 57.796 50.000 0.00 0.00 40.95 5.34
2194 2372 2.861147 AGGGAGAGGTTAACAAGTGC 57.139 50.000 8.10 0.00 0.00 4.40
2497 2675 4.216687 CCCCGTAAAGCTGTTGTTTGATAA 59.783 41.667 0.00 0.00 0.00 1.75
2577 2767 2.431782 AGGCAGCTCAGAGAAGATCTTC 59.568 50.000 25.20 25.20 35.47 2.87
2763 2954 1.656587 AGGTGCCTATCTGTTGTGGA 58.343 50.000 0.00 0.00 0.00 4.02
3013 3204 3.203934 TCTCTGGAGATGATGGACTCTGA 59.796 47.826 0.00 0.00 34.11 3.27
3087 3278 6.262049 CCATCTGATCATATAGGACTCCTACG 59.738 46.154 6.98 0.00 39.10 3.51
3154 3347 1.956043 CGTCATGGTTTGGGTGGTG 59.044 57.895 0.00 0.00 0.00 4.17
3173 3374 0.031314 CTGATGACCACCGGAGATCG 59.969 60.000 9.46 0.00 38.88 3.69
3249 3463 2.688507 ACATGGAGTACAGAGCAAACG 58.311 47.619 0.00 0.00 0.00 3.60
3250 3464 4.994852 TGTTACATGGAGTACAGAGCAAAC 59.005 41.667 0.00 0.00 30.91 2.93
3252 3466 4.322725 CCTGTTACATGGAGTACAGAGCAA 60.323 45.833 10.82 0.00 35.59 3.91
3253 3467 3.195610 CCTGTTACATGGAGTACAGAGCA 59.804 47.826 10.82 0.00 35.59 4.26
3254 3468 3.447586 TCCTGTTACATGGAGTACAGAGC 59.552 47.826 10.82 0.00 35.59 4.09
3257 3481 7.390440 TCATTTTTCCTGTTACATGGAGTACAG 59.610 37.037 3.10 3.10 34.46 2.74
3355 3581 9.025020 CAGCCTATGCGTATGTATAGAATTAAG 57.975 37.037 18.55 4.98 41.70 1.85
3362 3588 6.136541 TCATCAGCCTATGCGTATGTATAG 57.863 41.667 11.89 11.89 44.33 1.31
3395 3621 9.411189 ACCAACTTCCAAATAGTACTTAACAAA 57.589 29.630 0.00 0.00 0.00 2.83
3396 3622 8.983702 ACCAACTTCCAAATAGTACTTAACAA 57.016 30.769 0.00 0.00 0.00 2.83
3397 3623 8.212312 TGACCAACTTCCAAATAGTACTTAACA 58.788 33.333 0.00 0.00 0.00 2.41
3398 3624 8.611654 TGACCAACTTCCAAATAGTACTTAAC 57.388 34.615 0.00 0.00 0.00 2.01
3399 3625 8.653191 TCTGACCAACTTCCAAATAGTACTTAA 58.347 33.333 0.00 0.00 0.00 1.85
3400 3626 8.197592 TCTGACCAACTTCCAAATAGTACTTA 57.802 34.615 0.00 0.00 0.00 2.24
3401 3627 7.074653 TCTGACCAACTTCCAAATAGTACTT 57.925 36.000 0.00 0.00 0.00 2.24
3402 3628 6.270231 ACTCTGACCAACTTCCAAATAGTACT 59.730 38.462 0.00 0.00 0.00 2.73
3403 3629 6.465084 ACTCTGACCAACTTCCAAATAGTAC 58.535 40.000 0.00 0.00 0.00 2.73
3404 3630 6.681729 ACTCTGACCAACTTCCAAATAGTA 57.318 37.500 0.00 0.00 0.00 1.82
3405 3631 5.568620 ACTCTGACCAACTTCCAAATAGT 57.431 39.130 0.00 0.00 0.00 2.12
3406 3632 6.464222 TGTACTCTGACCAACTTCCAAATAG 58.536 40.000 0.00 0.00 0.00 1.73
3407 3633 6.428083 TGTACTCTGACCAACTTCCAAATA 57.572 37.500 0.00 0.00 0.00 1.40
3408 3634 5.304686 TGTACTCTGACCAACTTCCAAAT 57.695 39.130 0.00 0.00 0.00 2.32
3409 3635 4.764050 TGTACTCTGACCAACTTCCAAA 57.236 40.909 0.00 0.00 0.00 3.28
3445 3674 2.860735 ACTTATGTCTGCTTCGCGATTC 59.139 45.455 10.88 5.28 0.00 2.52
3477 3707 2.733552 CAGTGTCATGTGAGTGTGCTAC 59.266 50.000 0.00 0.00 0.00 3.58
3545 3775 3.186909 CCTTGATCGATCTGTTAACGCA 58.813 45.455 25.02 0.17 0.00 5.24
3558 3788 0.958382 TCCGGTTTTGCCCTTGATCG 60.958 55.000 0.00 0.00 0.00 3.69
3574 3804 1.203994 TCGAGCTTTAGGTTCCTTCCG 59.796 52.381 0.00 0.00 0.00 4.30
3576 3806 2.609916 GCATCGAGCTTTAGGTTCCTTC 59.390 50.000 0.00 0.00 41.15 3.46
3607 3837 1.453155 CGATCCTGGGTTGGAGTTTG 58.547 55.000 0.00 0.00 39.78 2.93
3616 3846 0.181350 GGAGAATTGCGATCCTGGGT 59.819 55.000 0.00 0.00 0.00 4.51
3635 3865 2.567151 GCGTGTGTTGTTTGCTGCG 61.567 57.895 0.00 0.00 0.00 5.18
3668 3898 9.953825 GTAGTACTAATTTCGTTGACATTTCTG 57.046 33.333 3.61 0.00 0.00 3.02
3741 3972 1.065251 GTCCGAGTGAGTCCGTTATCC 59.935 57.143 0.00 0.00 0.00 2.59
3743 3974 1.830279 TGTCCGAGTGAGTCCGTTAT 58.170 50.000 0.00 0.00 0.00 1.89
3757 3988 3.163832 TATGCAGGCCCGATGTCCG 62.164 63.158 0.00 0.00 38.18 4.79
3759 3990 1.302033 CCTATGCAGGCCCGATGTC 60.302 63.158 0.00 0.00 34.35 3.06
3760 3991 1.130054 ATCCTATGCAGGCCCGATGT 61.130 55.000 0.00 0.00 42.30 3.06
3797 4028 0.253327 GTGGGCAGGAGGAAACTAGG 59.747 60.000 0.00 0.00 44.43 3.02
3798 4029 0.984230 TGTGGGCAGGAGGAAACTAG 59.016 55.000 0.00 0.00 44.43 2.57
3861 4096 2.359107 TTCAGCAGCTCAAGGCCG 60.359 61.111 0.00 0.00 43.05 6.13
3892 4127 3.300388 AGGGAGATGAGATCAAAGCGTA 58.700 45.455 0.00 0.00 0.00 4.42
3893 4128 2.102252 GAGGGAGATGAGATCAAAGCGT 59.898 50.000 0.00 0.00 0.00 5.07
3894 4129 2.753296 GAGGGAGATGAGATCAAAGCG 58.247 52.381 0.00 0.00 0.00 4.68
3899 4134 1.496857 AGGTCGAGGGAGATGAGATCA 59.503 52.381 0.00 0.00 0.00 2.92
3910 4153 1.815421 CGATTTGGCAGGTCGAGGG 60.815 63.158 15.66 0.00 37.55 4.30
3928 4171 3.673173 CATGGCTTTATGCTTGGGC 57.327 52.632 0.00 0.00 42.39 5.36
3955 4198 4.726704 CGCCGCAACATTATTTAGTTACAC 59.273 41.667 0.00 0.00 0.00 2.90
3961 4204 3.545873 CCAAACGCCGCAACATTATTTAG 59.454 43.478 0.00 0.00 0.00 1.85
3972 4215 1.098712 AAGAACTTCCAAACGCCGCA 61.099 50.000 0.00 0.00 0.00 5.69
3978 4221 6.035005 GTCTTTCTGCAAAAGAACTTCCAAAC 59.965 38.462 19.06 6.84 44.77 2.93
3985 4228 4.526970 TCCAGTCTTTCTGCAAAAGAACT 58.473 39.130 19.06 16.04 44.77 3.01
4001 4244 3.421844 ACAGCCCTTTTTGTATCCAGTC 58.578 45.455 0.00 0.00 0.00 3.51
4009 4252 1.859302 TGTGGAACAGCCCTTTTTGT 58.141 45.000 0.00 0.00 45.67 2.83
4026 4269 4.202010 CCCAGAAAGTGTTTGTCGAAATGT 60.202 41.667 0.00 0.00 0.00 2.71
4079 4322 3.699894 CAGGGGTCTGCGTCTGCT 61.700 66.667 0.00 0.00 43.34 4.24


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

AutoCloner maintained by Alex Coulton.