Multiple sequence alignment - TraesCS3B01G420100

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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 TraesCS3B01G420100 chr3B 100.000 3035 0 0 1 3035 656741764 656738730 0.000000e+00 5605.0
1 TraesCS3B01G420100 chr3B 94.962 1171 46 5 927 2087 656917732 656916565 0.000000e+00 1823.0
2 TraesCS3B01G420100 chr3B 91.954 87 7 0 2887 2973 656916496 656916410 4.110000e-24 122.0
3 TraesCS3B01G420100 chr3D 95.118 1823 89 0 265 2087 497016015 497014193 0.000000e+00 2874.0
4 TraesCS3B01G420100 chr3D 94.425 1148 51 4 909 2046 497231897 497230753 0.000000e+00 1753.0
5 TraesCS3B01G420100 chr3D 90.759 303 28 0 1 303 497016316 497016014 3.640000e-109 405.0
6 TraesCS3B01G420100 chr3D 91.954 87 7 0 2887 2973 497156530 497156444 4.110000e-24 122.0
7 TraesCS3B01G420100 chr3D 93.750 48 1 2 2906 2951 497014156 497014109 1.510000e-08 71.3
8 TraesCS3B01G420100 chr3A 90.667 1350 93 17 756 2087 637470955 637472289 0.000000e+00 1764.0
9 TraesCS3B01G420100 chr3A 95.675 948 41 0 1097 2044 637603989 637604936 0.000000e+00 1524.0
10 TraesCS3B01G420100 chr3A 91.107 1102 90 4 1 1102 637588084 637589177 0.000000e+00 1485.0
11 TraesCS3B01G420100 chr3A 92.045 88 7 0 2886 2973 637472713 637472800 1.140000e-24 124.0
12 TraesCS3B01G420100 chr5A 86.220 1045 130 7 994 2031 550656007 550654970 0.000000e+00 1120.0
13 TraesCS3B01G420100 chr2B 92.052 692 51 3 2103 2791 621669122 621669812 0.000000e+00 970.0
14 TraesCS3B01G420100 chr2B 91.667 72 6 0 1226 1297 1749897 1749968 1.930000e-17 100.0
15 TraesCS3B01G420100 chr2B 91.549 71 6 0 1227 1297 1765061 1765131 6.920000e-17 99.0
16 TraesCS3B01G420100 chr1B 87.663 689 69 6 2105 2791 600608805 600608131 0.000000e+00 787.0
17 TraesCS3B01G420100 chr5D 87.262 683 80 1 1352 2027 436207166 436206484 0.000000e+00 773.0
18 TraesCS3B01G420100 chr5D 94.118 272 13 3 2091 2360 457009920 457009650 7.830000e-111 411.0
19 TraesCS3B01G420100 chr5D 85.637 369 40 6 994 1356 436212755 436212394 2.860000e-100 375.0
20 TraesCS3B01G420100 chr5D 76.876 493 87 8 2289 2780 499231718 499232184 1.400000e-63 254.0
21 TraesCS3B01G420100 chr2D 91.067 403 33 3 2336 2737 83852750 83853150 2.660000e-150 542.0
22 TraesCS3B01G420100 chr2D 85.714 84 12 0 1229 1312 7203682 7203599 4.170000e-14 89.8
23 TraesCS3B01G420100 chr2D 78.571 112 16 7 1415 1522 13856602 13856709 1.950000e-07 67.6
24 TraesCS3B01G420100 chr6D 82.416 563 92 6 2234 2792 436264635 436264076 4.550000e-133 484.0
25 TraesCS3B01G420100 chr6D 78.400 500 101 4 1487 1986 324571451 324571943 4.880000e-83 318.0
26 TraesCS3B01G420100 chr1D 81.250 448 70 10 2091 2535 370914436 370914872 1.730000e-92 350.0
27 TraesCS3B01G420100 chr7D 87.747 253 29 2 2306 2557 75079234 75079485 8.230000e-76 294.0
28 TraesCS3B01G420100 chr7D 79.621 211 33 10 159 366 500209670 500209873 3.150000e-30 143.0
29 TraesCS3B01G420100 chr5B 77.246 501 89 10 2284 2782 619856144 619856621 1.390000e-68 270.0


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 TraesCS3B01G420100 chr3B 656738730 656741764 3034 True 5605.000000 5605 100.000 1 3035 1 chr3B.!!$R1 3034
1 TraesCS3B01G420100 chr3B 656916410 656917732 1322 True 972.500000 1823 93.458 927 2973 2 chr3B.!!$R2 2046
2 TraesCS3B01G420100 chr3D 497230753 497231897 1144 True 1753.000000 1753 94.425 909 2046 1 chr3D.!!$R2 1137
3 TraesCS3B01G420100 chr3D 497014109 497016316 2207 True 1116.766667 2874 93.209 1 2951 3 chr3D.!!$R3 2950
4 TraesCS3B01G420100 chr3A 637603989 637604936 947 False 1524.000000 1524 95.675 1097 2044 1 chr3A.!!$F2 947
5 TraesCS3B01G420100 chr3A 637588084 637589177 1093 False 1485.000000 1485 91.107 1 1102 1 chr3A.!!$F1 1101
6 TraesCS3B01G420100 chr3A 637470955 637472800 1845 False 944.000000 1764 91.356 756 2973 2 chr3A.!!$F3 2217
7 TraesCS3B01G420100 chr5A 550654970 550656007 1037 True 1120.000000 1120 86.220 994 2031 1 chr5A.!!$R1 1037
8 TraesCS3B01G420100 chr2B 621669122 621669812 690 False 970.000000 970 92.052 2103 2791 1 chr2B.!!$F3 688
9 TraesCS3B01G420100 chr1B 600608131 600608805 674 True 787.000000 787 87.663 2105 2791 1 chr1B.!!$R1 686
10 TraesCS3B01G420100 chr5D 436206484 436207166 682 True 773.000000 773 87.262 1352 2027 1 chr5D.!!$R1 675
11 TraesCS3B01G420100 chr6D 436264076 436264635 559 True 484.000000 484 82.416 2234 2792 1 chr6D.!!$R1 558

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
817 855 0.322546 GGAGGTGGTGGTTGGATGAC 60.323 60.0 0.0 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2530 2599 0.179129 CTTGGTGCGATGGATTTGGC 60.179 55.0 0.0 0.0 0.0 4.52 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
97 98 0.725784 GTTGCAGCAATTGACGACGG 60.726 55.000 11.96 0.00 0.00 4.79
102 103 2.776072 CAATTGACGACGGCGGTC 59.224 61.111 18.49 14.05 43.17 4.79
160 161 3.964221 CTGGTCGCTAGCGTCGCAA 62.964 63.158 34.10 18.73 40.74 4.85
234 235 0.821711 TGCCCGTTGTAGCTTTGCTT 60.822 50.000 0.00 0.00 40.44 3.91
243 244 3.020274 TGTAGCTTTGCTTGAACACCAA 58.980 40.909 0.00 0.00 40.44 3.67
280 318 4.240096 CGTTGTCGGTTGTAGTATTTCCT 58.760 43.478 0.00 0.00 0.00 3.36
297 335 0.535102 CCTGACAACGGTTCCAGCTT 60.535 55.000 12.02 0.00 0.00 3.74
349 387 1.299926 GTTCCAGCACGACGTCAGT 60.300 57.895 17.16 11.57 0.00 3.41
514 552 1.216444 GGATGTGAGAGCTCGTGCA 59.784 57.895 12.58 8.74 42.74 4.57
516 554 1.649664 GATGTGAGAGCTCGTGCATT 58.350 50.000 12.58 0.00 42.74 3.56
562 600 1.276421 TGCGGGAGAAAGAAGAAGAGG 59.724 52.381 0.00 0.00 0.00 3.69
582 620 4.858850 AGGCATGTGATGGAGAATTGTTA 58.141 39.130 0.00 0.00 0.00 2.41
617 655 5.584551 AGATAAGGACAAGGGAAAAGTGT 57.415 39.130 0.00 0.00 0.00 3.55
625 663 2.265904 GGGAAAAGTGTGGGCCGAC 61.266 63.158 11.57 11.57 0.00 4.79
640 678 1.335597 GCCGACATCCATCGTTCGATA 60.336 52.381 7.38 0.00 40.59 2.92
691 729 2.858158 GAAGTTTCGGCCGGTTCG 59.142 61.111 27.83 8.27 0.00 3.95
694 732 3.785499 GTTTCGGCCGGTTCGCTC 61.785 66.667 27.83 5.50 0.00 5.03
710 748 2.094390 TCGCTCGCTACAAACATTACCT 60.094 45.455 0.00 0.00 0.00 3.08
817 855 0.322546 GGAGGTGGTGGTTGGATGAC 60.323 60.000 0.00 0.00 0.00 3.06
826 864 0.669318 GGTTGGATGACGCGAGACAA 60.669 55.000 15.93 7.75 39.56 3.18
873 911 6.875726 CGCCAATTATAATTGATGAGAGAGGA 59.124 38.462 31.05 0.00 46.72 3.71
890 928 8.200792 TGAGAGAGGAGATATTAGAAAACAAGC 58.799 37.037 0.00 0.00 0.00 4.01
904 942 1.878953 ACAAGCGAAGGAACGACAAT 58.121 45.000 0.00 0.00 35.09 2.71
967 1006 2.866028 CAGAAAGTGGAGCGCTGC 59.134 61.111 23.36 23.36 0.00 5.25
1027 1076 1.623557 CCTCTCCACAATCCTCCTCCA 60.624 57.143 0.00 0.00 0.00 3.86
1031 1080 0.995024 CCACAATCCTCCTCCACCTT 59.005 55.000 0.00 0.00 0.00 3.50
1105 1157 1.911357 TCCTAGAGGTCGTGTCTACCA 59.089 52.381 0.00 0.00 39.64 3.25
1943 2008 1.070786 GGAAGAACCACCTGACGCA 59.929 57.895 0.00 0.00 38.79 5.24
1953 2018 2.202987 CTGACGCAGGAGATGGCC 60.203 66.667 0.00 0.00 0.00 5.36
2040 2105 2.480416 CGCAGATCAGAACTAGTGGGTC 60.480 54.545 0.00 0.00 0.00 4.46
2089 2154 4.503767 CACAACTTGCACAACATTTGTC 57.496 40.909 0.00 0.00 43.23 3.18
2090 2155 4.175516 CACAACTTGCACAACATTTGTCT 58.824 39.130 0.00 0.00 43.23 3.41
2091 2156 4.626604 CACAACTTGCACAACATTTGTCTT 59.373 37.500 0.00 0.00 43.23 3.01
2092 2157 5.120519 CACAACTTGCACAACATTTGTCTTT 59.879 36.000 0.00 0.00 43.23 2.52
2093 2158 5.700373 ACAACTTGCACAACATTTGTCTTTT 59.300 32.000 0.00 0.00 43.23 2.27
2094 2159 6.204495 ACAACTTGCACAACATTTGTCTTTTT 59.796 30.769 0.00 0.00 43.23 1.94
2095 2160 6.407475 ACTTGCACAACATTTGTCTTTTTC 57.593 33.333 0.00 0.00 43.23 2.29
2096 2161 6.165577 ACTTGCACAACATTTGTCTTTTTCT 58.834 32.000 0.00 0.00 43.23 2.52
2097 2162 6.650390 ACTTGCACAACATTTGTCTTTTTCTT 59.350 30.769 0.00 0.00 43.23 2.52
2098 2163 7.173047 ACTTGCACAACATTTGTCTTTTTCTTT 59.827 29.630 0.00 0.00 43.23 2.52
2099 2164 7.432350 TGCACAACATTTGTCTTTTTCTTTT 57.568 28.000 0.00 0.00 43.23 2.27
2100 2165 7.296660 TGCACAACATTTGTCTTTTTCTTTTG 58.703 30.769 0.00 0.00 43.23 2.44
2101 2166 7.172190 TGCACAACATTTGTCTTTTTCTTTTGA 59.828 29.630 0.00 0.00 43.23 2.69
2180 2248 9.503427 GAAAATCACGAGAAAGAAAGAGAAAAA 57.497 29.630 0.00 0.00 0.00 1.94
2213 2281 6.093495 CCCGAGAACATATGCAAGAAAACTTA 59.907 38.462 1.58 0.00 0.00 2.24
2253 2321 1.416401 ACCGTCATCTTCACCACTTGT 59.584 47.619 0.00 0.00 0.00 3.16
2264 2332 0.748450 ACCACTTGTCGTCTTCGGAA 59.252 50.000 0.00 0.00 37.69 4.30
2350 2418 0.738063 ATTATCGTTGTGGCGCGTCA 60.738 50.000 10.57 10.57 0.00 4.35
2473 2541 6.003950 CCTTGTTCTTGGACCTTTATCTTCA 58.996 40.000 0.00 0.00 0.00 3.02
2530 2599 5.872617 TCTTCCATAGACACAATAAACACCG 59.127 40.000 0.00 0.00 0.00 4.94
2554 2623 3.575965 AATCCATCGCACCAAGAAAAC 57.424 42.857 0.00 0.00 0.00 2.43
2594 2663 3.331889 ACAGATCCCTCAATTTCACCACT 59.668 43.478 0.00 0.00 0.00 4.00
2625 2695 1.459455 CGAGATGGGGCTGAGATCGT 61.459 60.000 0.00 0.00 0.00 3.73
2667 2737 1.963855 CGTCACCGCCATCCAAACA 60.964 57.895 0.00 0.00 0.00 2.83
2673 2743 2.405805 CGCCATCCAAACATCGCCA 61.406 57.895 0.00 0.00 0.00 5.69
2676 2746 1.391577 CCATCCAAACATCGCCATGA 58.608 50.000 0.00 0.00 33.72 3.07
2680 2750 0.374758 CCAAACATCGCCATGAGACG 59.625 55.000 0.00 0.00 33.72 4.18
2848 3285 5.304101 AGCAAACATGACAAGGGAAATAACA 59.696 36.000 0.00 0.00 0.00 2.41
2849 3286 5.634859 GCAAACATGACAAGGGAAATAACAG 59.365 40.000 0.00 0.00 0.00 3.16
2850 3287 6.516527 GCAAACATGACAAGGGAAATAACAGA 60.517 38.462 0.00 0.00 0.00 3.41
2851 3288 7.432869 CAAACATGACAAGGGAAATAACAGAA 58.567 34.615 0.00 0.00 0.00 3.02
2852 3289 6.824305 ACATGACAAGGGAAATAACAGAAG 57.176 37.500 0.00 0.00 0.00 2.85
2853 3290 6.306987 ACATGACAAGGGAAATAACAGAAGT 58.693 36.000 0.00 0.00 0.00 3.01
2854 3291 6.207417 ACATGACAAGGGAAATAACAGAAGTG 59.793 38.462 0.00 0.00 0.00 3.16
2855 3292 5.690865 TGACAAGGGAAATAACAGAAGTGT 58.309 37.500 0.00 0.00 39.19 3.55
2903 3340 7.963532 AGAGAGAAAGAAGTGTTACCATACAA 58.036 34.615 0.00 0.00 0.00 2.41
2948 3385 3.004002 CACGTGGTGTCTTCAGTACTGTA 59.996 47.826 21.99 12.28 0.00 2.74
2956 3393 7.614192 TGGTGTCTTCAGTACTGTATCAATAGA 59.386 37.037 21.99 11.21 0.00 1.98
2973 3410 5.814188 TCAATAGATCACAACTTAGCAGCAG 59.186 40.000 0.00 0.00 0.00 4.24
2974 3411 3.969287 AGATCACAACTTAGCAGCAGA 57.031 42.857 0.00 0.00 0.00 4.26
2975 3412 3.859443 AGATCACAACTTAGCAGCAGAG 58.141 45.455 0.00 0.00 0.00 3.35
2976 3413 3.513119 AGATCACAACTTAGCAGCAGAGA 59.487 43.478 0.00 0.00 0.00 3.10
2977 3414 3.309961 TCACAACTTAGCAGCAGAGAG 57.690 47.619 0.00 0.00 0.00 3.20
2978 3415 2.630098 TCACAACTTAGCAGCAGAGAGT 59.370 45.455 0.00 0.00 0.00 3.24
2979 3416 2.735663 CACAACTTAGCAGCAGAGAGTG 59.264 50.000 0.00 3.57 0.00 3.51
2980 3417 2.630098 ACAACTTAGCAGCAGAGAGTGA 59.370 45.455 0.00 0.00 0.00 3.41
2981 3418 3.260380 ACAACTTAGCAGCAGAGAGTGAT 59.740 43.478 0.00 0.00 0.00 3.06
2982 3419 4.252073 CAACTTAGCAGCAGAGAGTGATT 58.748 43.478 0.00 0.00 0.00 2.57
2983 3420 5.047021 ACAACTTAGCAGCAGAGAGTGATTA 60.047 40.000 0.00 0.00 0.00 1.75
2984 3421 5.867903 ACTTAGCAGCAGAGAGTGATTAT 57.132 39.130 0.00 0.00 0.00 1.28
2985 3422 5.841810 ACTTAGCAGCAGAGAGTGATTATC 58.158 41.667 0.00 0.00 0.00 1.75
2986 3423 5.598005 ACTTAGCAGCAGAGAGTGATTATCT 59.402 40.000 0.00 0.00 0.00 1.98
2987 3424 6.098124 ACTTAGCAGCAGAGAGTGATTATCTT 59.902 38.462 0.00 0.00 0.00 2.40
2988 3425 4.695396 AGCAGCAGAGAGTGATTATCTTG 58.305 43.478 0.00 0.00 0.00 3.02
2989 3426 4.161942 AGCAGCAGAGAGTGATTATCTTGT 59.838 41.667 0.00 0.00 0.00 3.16
2990 3427 4.874966 GCAGCAGAGAGTGATTATCTTGTT 59.125 41.667 0.00 0.00 0.00 2.83
2991 3428 5.220624 GCAGCAGAGAGTGATTATCTTGTTG 60.221 44.000 0.00 0.00 0.00 3.33
2992 3429 4.874966 AGCAGAGAGTGATTATCTTGTTGC 59.125 41.667 0.00 0.00 33.12 4.17
2993 3430 4.034975 GCAGAGAGTGATTATCTTGTTGCC 59.965 45.833 0.00 0.00 0.00 4.52
2994 3431 5.426504 CAGAGAGTGATTATCTTGTTGCCT 58.573 41.667 0.00 0.00 0.00 4.75
2995 3432 5.293814 CAGAGAGTGATTATCTTGTTGCCTG 59.706 44.000 0.00 0.00 0.00 4.85
2996 3433 3.944015 AGAGTGATTATCTTGTTGCCTGC 59.056 43.478 0.00 0.00 0.00 4.85
2997 3434 3.019564 AGTGATTATCTTGTTGCCTGCC 58.980 45.455 0.00 0.00 0.00 4.85
2998 3435 2.099756 GTGATTATCTTGTTGCCTGCCC 59.900 50.000 0.00 0.00 0.00 5.36
2999 3436 1.683385 GATTATCTTGTTGCCTGCCCC 59.317 52.381 0.00 0.00 0.00 5.80
3000 3437 0.679640 TTATCTTGTTGCCTGCCCCG 60.680 55.000 0.00 0.00 0.00 5.73
3010 3447 2.978010 CTGCCCCGCGTGAGTTTT 60.978 61.111 4.92 0.00 0.00 2.43
3011 3448 2.966309 CTGCCCCGCGTGAGTTTTC 61.966 63.158 4.92 0.00 0.00 2.29
3012 3449 2.975799 GCCCCGCGTGAGTTTTCA 60.976 61.111 4.92 0.00 0.00 2.69
3013 3450 2.332654 GCCCCGCGTGAGTTTTCAT 61.333 57.895 4.92 0.00 35.39 2.57
3014 3451 1.794222 CCCCGCGTGAGTTTTCATC 59.206 57.895 4.92 0.00 35.39 2.92
3015 3452 1.644786 CCCCGCGTGAGTTTTCATCC 61.645 60.000 4.92 0.00 35.39 3.51
3016 3453 0.673644 CCCGCGTGAGTTTTCATCCT 60.674 55.000 4.92 0.00 35.39 3.24
3017 3454 1.156736 CCGCGTGAGTTTTCATCCTT 58.843 50.000 4.92 0.00 35.39 3.36
3018 3455 1.128692 CCGCGTGAGTTTTCATCCTTC 59.871 52.381 4.92 0.00 35.39 3.46
3019 3456 1.128692 CGCGTGAGTTTTCATCCTTCC 59.871 52.381 0.00 0.00 35.39 3.46
3020 3457 2.151202 GCGTGAGTTTTCATCCTTCCA 58.849 47.619 0.00 0.00 35.39 3.53
3021 3458 2.160417 GCGTGAGTTTTCATCCTTCCAG 59.840 50.000 0.00 0.00 35.39 3.86
3022 3459 3.403038 CGTGAGTTTTCATCCTTCCAGT 58.597 45.455 0.00 0.00 35.39 4.00
3023 3460 3.433615 CGTGAGTTTTCATCCTTCCAGTC 59.566 47.826 0.00 0.00 35.39 3.51
3024 3461 3.433615 GTGAGTTTTCATCCTTCCAGTCG 59.566 47.826 0.00 0.00 35.39 4.18
3025 3462 3.071023 TGAGTTTTCATCCTTCCAGTCGT 59.929 43.478 0.00 0.00 0.00 4.34
3026 3463 3.665190 AGTTTTCATCCTTCCAGTCGTC 58.335 45.455 0.00 0.00 0.00 4.20
3027 3464 3.325135 AGTTTTCATCCTTCCAGTCGTCT 59.675 43.478 0.00 0.00 0.00 4.18
3028 3465 3.594603 TTTCATCCTTCCAGTCGTCTC 57.405 47.619 0.00 0.00 0.00 3.36
3029 3466 2.215942 TCATCCTTCCAGTCGTCTCA 57.784 50.000 0.00 0.00 0.00 3.27
3030 3467 2.739943 TCATCCTTCCAGTCGTCTCAT 58.260 47.619 0.00 0.00 0.00 2.90
3031 3468 2.428530 TCATCCTTCCAGTCGTCTCATG 59.571 50.000 0.00 0.00 0.00 3.07
3032 3469 0.532573 TCCTTCCAGTCGTCTCATGC 59.467 55.000 0.00 0.00 0.00 4.06
3033 3470 0.534412 CCTTCCAGTCGTCTCATGCT 59.466 55.000 0.00 0.00 0.00 3.79
3034 3471 1.470632 CCTTCCAGTCGTCTCATGCTC 60.471 57.143 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 2.878406 TGCTGCAACCAACTCTTAAGAC 59.122 45.455 0.00 0.00 0.00 3.01
72 73 2.397549 GTCAATTGCTGCAACCAACTC 58.602 47.619 18.51 3.10 0.00 3.01
74 75 1.130955 CGTCAATTGCTGCAACCAAC 58.869 50.000 18.51 13.83 0.00 3.77
120 121 0.403655 TGAGGCCAATGCTACAACCA 59.596 50.000 5.01 0.00 37.74 3.67
150 151 4.208460 GCATCTATAAAAGTTGCGACGCTA 59.792 41.667 22.08 11.18 40.22 4.26
191 192 0.609131 CAGAAGTTGGAACCGGCCAT 60.609 55.000 0.00 0.00 37.86 4.40
234 235 2.039818 TTTGCTACGGTTGGTGTTCA 57.960 45.000 0.00 0.00 0.00 3.18
243 244 1.375013 AACGGCGATTTGCTACGGT 60.375 52.632 16.62 0.00 45.43 4.83
280 318 1.021202 CAAAGCTGGAACCGTTGTCA 58.979 50.000 0.00 0.00 0.00 3.58
349 387 0.037326 GACGAGATGCTGGAACCACA 60.037 55.000 0.00 0.00 0.00 4.17
496 534 0.179089 ATGCACGAGCTCTCACATCC 60.179 55.000 12.85 0.00 42.74 3.51
501 539 0.108472 CTCCAATGCACGAGCTCTCA 60.108 55.000 12.85 7.37 42.74 3.27
514 552 1.764723 TCACGCTCCATCATCTCCAAT 59.235 47.619 0.00 0.00 0.00 3.16
516 554 1.069668 CATCACGCTCCATCATCTCCA 59.930 52.381 0.00 0.00 0.00 3.86
540 578 1.071605 CTTCTTCTTTCTCCCGCACG 58.928 55.000 0.00 0.00 0.00 5.34
562 600 6.441093 TCTTAACAATTCTCCATCACATGC 57.559 37.500 0.00 0.00 0.00 4.06
582 620 2.838202 TCCTTATCTTCAACGCCCTCTT 59.162 45.455 0.00 0.00 0.00 2.85
617 655 2.587322 GAACGATGGATGTCGGCCCA 62.587 60.000 0.00 0.00 45.49 5.36
625 663 3.371102 AGTGGTATCGAACGATGGATG 57.629 47.619 18.03 0.00 36.17 3.51
689 727 2.094390 AGGTAATGTTTGTAGCGAGCGA 60.094 45.455 0.00 0.00 0.00 4.93
691 729 4.680171 AAAGGTAATGTTTGTAGCGAGC 57.320 40.909 0.00 0.00 0.00 5.03
817 855 1.083657 CCGTTGTGTTTGTCTCGCG 60.084 57.895 0.00 0.00 0.00 5.87
826 864 2.036862 GGACTCCTTCTACCGTTGTGTT 59.963 50.000 0.00 0.00 0.00 3.32
873 911 7.201530 CGTTCCTTCGCTTGTTTTCTAATATCT 60.202 37.037 0.00 0.00 0.00 1.98
890 928 4.446385 TCTTGTGTTATTGTCGTTCCTTCG 59.554 41.667 0.00 0.00 0.00 3.79
904 942 9.733556 TTTCCTGCTTATAAAGATCTTGTGTTA 57.266 29.630 9.17 0.00 0.00 2.41
967 1006 1.440938 TTCGTGAAGGCCCGTTTGTG 61.441 55.000 0.00 0.00 0.00 3.33
1027 1076 2.498056 CGGCTTTGGGTGCAAAGGT 61.498 57.895 0.00 0.00 41.20 3.50
1031 1080 3.283684 CGTCGGCTTTGGGTGCAA 61.284 61.111 0.00 0.00 0.00 4.08
1943 2008 1.433121 GATCCTTCTGGCCATCTCCT 58.567 55.000 5.51 0.00 0.00 3.69
1953 2018 3.577667 GCTGATCTCATCGATCCTTCTG 58.422 50.000 0.00 0.00 46.52 3.02
2040 2105 4.527509 AATATAGCATCTGTCGTCCTGG 57.472 45.455 0.00 0.00 0.00 4.45
2087 2152 9.877137 GAAATCTCTCTCTCAAAAGAAAAAGAC 57.123 33.333 0.00 0.00 0.00 3.01
2089 2154 7.533561 GCGAAATCTCTCTCTCAAAAGAAAAAG 59.466 37.037 0.00 0.00 0.00 2.27
2090 2155 7.012327 TGCGAAATCTCTCTCTCAAAAGAAAAA 59.988 33.333 0.00 0.00 0.00 1.94
2091 2156 6.483307 TGCGAAATCTCTCTCTCAAAAGAAAA 59.517 34.615 0.00 0.00 0.00 2.29
2092 2157 5.991606 TGCGAAATCTCTCTCTCAAAAGAAA 59.008 36.000 0.00 0.00 0.00 2.52
2093 2158 5.541845 TGCGAAATCTCTCTCTCAAAAGAA 58.458 37.500 0.00 0.00 0.00 2.52
2094 2159 5.139435 TGCGAAATCTCTCTCTCAAAAGA 57.861 39.130 0.00 0.00 0.00 2.52
2095 2160 6.019156 GGTATGCGAAATCTCTCTCTCAAAAG 60.019 42.308 0.00 0.00 0.00 2.27
2096 2161 5.812642 GGTATGCGAAATCTCTCTCTCAAAA 59.187 40.000 0.00 0.00 0.00 2.44
2097 2162 5.105351 TGGTATGCGAAATCTCTCTCTCAAA 60.105 40.000 0.00 0.00 0.00 2.69
2098 2163 4.402474 TGGTATGCGAAATCTCTCTCTCAA 59.598 41.667 0.00 0.00 0.00 3.02
2099 2164 3.954258 TGGTATGCGAAATCTCTCTCTCA 59.046 43.478 0.00 0.00 0.00 3.27
2100 2165 4.576216 TGGTATGCGAAATCTCTCTCTC 57.424 45.455 0.00 0.00 0.00 3.20
2101 2166 5.543507 AATGGTATGCGAAATCTCTCTCT 57.456 39.130 0.00 0.00 0.00 3.10
2184 2252 3.070878 TCTTGCATATGTTCTCGGGCATA 59.929 43.478 4.29 0.00 32.89 3.14
2213 2281 6.048509 ACGGTTGCAAAAATCTTCTTCAATT 58.951 32.000 0.00 0.00 0.00 2.32
2264 2332 1.429463 GACGATGGTGCTTCTTCGTT 58.571 50.000 16.73 6.29 43.99 3.85
2350 2418 1.382695 ACGAGGATGATCCCCGGTT 60.383 57.895 19.53 0.00 37.19 4.44
2414 2482 1.447314 GGCGGTTCCGGTGTTCTAG 60.447 63.158 13.16 0.00 0.00 2.43
2473 2541 1.388837 GGTGTCGCCTTTGTTTGGGT 61.389 55.000 0.00 0.00 0.00 4.51
2530 2599 0.179129 CTTGGTGCGATGGATTTGGC 60.179 55.000 0.00 0.00 0.00 4.52
2594 2663 1.966354 CCCATCTCGATGACATCCTCA 59.034 52.381 9.87 0.00 41.20 3.86
2667 2737 2.238942 TTAATGCGTCTCATGGCGAT 57.761 45.000 8.88 0.00 35.13 4.58
2673 2743 5.497474 AGGGTTAAGTTTAATGCGTCTCAT 58.503 37.500 0.00 0.00 36.87 2.90
2676 2746 6.470278 AGTTAGGGTTAAGTTTAATGCGTCT 58.530 36.000 0.00 0.00 0.00 4.18
2680 2750 7.414873 GGCTGTAGTTAGGGTTAAGTTTAATGC 60.415 40.741 0.00 0.00 0.00 3.56
2835 3272 6.488683 TGGTAACACTTCTGTTATTTCCCTTG 59.511 38.462 0.00 0.00 46.17 3.61
2903 3340 9.556030 CGTGATAACGATGTTCATGTATACTAT 57.444 33.333 0.00 0.00 34.64 2.12
2948 3385 6.351711 TGCTGCTAAGTTGTGATCTATTGAT 58.648 36.000 0.00 0.00 35.26 2.57
2956 3393 3.260380 ACTCTCTGCTGCTAAGTTGTGAT 59.740 43.478 0.00 0.00 0.00 3.06
2973 3410 4.034975 GCAGGCAACAAGATAATCACTCTC 59.965 45.833 0.00 0.00 41.41 3.20
2974 3411 3.944015 GCAGGCAACAAGATAATCACTCT 59.056 43.478 0.00 0.00 41.41 3.24
2975 3412 3.065925 GGCAGGCAACAAGATAATCACTC 59.934 47.826 0.00 0.00 41.41 3.51
2976 3413 3.019564 GGCAGGCAACAAGATAATCACT 58.980 45.455 0.00 0.00 41.41 3.41
2977 3414 2.099756 GGGCAGGCAACAAGATAATCAC 59.900 50.000 0.00 0.00 41.41 3.06
2978 3415 2.378038 GGGCAGGCAACAAGATAATCA 58.622 47.619 0.00 0.00 41.41 2.57
2979 3416 1.683385 GGGGCAGGCAACAAGATAATC 59.317 52.381 0.00 0.00 41.41 1.75
2980 3417 1.780503 GGGGCAGGCAACAAGATAAT 58.219 50.000 0.00 0.00 41.41 1.28
2981 3418 0.679640 CGGGGCAGGCAACAAGATAA 60.680 55.000 0.00 0.00 41.41 1.75
2982 3419 1.077787 CGGGGCAGGCAACAAGATA 60.078 57.895 0.00 0.00 41.41 1.98
2983 3420 2.361610 CGGGGCAGGCAACAAGAT 60.362 61.111 0.00 0.00 41.41 2.40
2993 3430 2.966309 GAAAACTCACGCGGGGCAG 61.966 63.158 9.32 0.79 0.00 4.85
2994 3431 2.975799 GAAAACTCACGCGGGGCA 60.976 61.111 9.32 0.00 0.00 5.36
2995 3432 2.253414 GATGAAAACTCACGCGGGGC 62.253 60.000 9.32 0.00 0.00 5.80
2996 3433 1.644786 GGATGAAAACTCACGCGGGG 61.645 60.000 9.32 0.91 0.00 5.73
2997 3434 0.673644 AGGATGAAAACTCACGCGGG 60.674 55.000 12.47 6.51 0.00 6.13
2998 3435 1.128692 GAAGGATGAAAACTCACGCGG 59.871 52.381 12.47 0.00 0.00 6.46
2999 3436 1.128692 GGAAGGATGAAAACTCACGCG 59.871 52.381 3.53 3.53 0.00 6.01
3000 3437 2.151202 TGGAAGGATGAAAACTCACGC 58.849 47.619 0.00 0.00 0.00 5.34
3001 3438 3.403038 ACTGGAAGGATGAAAACTCACG 58.597 45.455 0.00 0.00 39.30 4.35
3002 3439 3.433615 CGACTGGAAGGATGAAAACTCAC 59.566 47.826 0.00 0.00 39.30 3.51
3003 3440 3.071023 ACGACTGGAAGGATGAAAACTCA 59.929 43.478 0.00 0.00 39.30 3.41
3004 3441 3.665190 ACGACTGGAAGGATGAAAACTC 58.335 45.455 0.00 0.00 39.30 3.01
3005 3442 3.325135 AGACGACTGGAAGGATGAAAACT 59.675 43.478 0.00 0.00 39.30 2.66
3006 3443 3.665190 AGACGACTGGAAGGATGAAAAC 58.335 45.455 0.00 0.00 39.30 2.43
3007 3444 3.323691 TGAGACGACTGGAAGGATGAAAA 59.676 43.478 0.00 0.00 39.30 2.29
3008 3445 2.897326 TGAGACGACTGGAAGGATGAAA 59.103 45.455 0.00 0.00 39.30 2.69
3009 3446 2.525368 TGAGACGACTGGAAGGATGAA 58.475 47.619 0.00 0.00 39.30 2.57
3010 3447 2.215942 TGAGACGACTGGAAGGATGA 57.784 50.000 0.00 0.00 39.30 2.92
3011 3448 2.819115 CATGAGACGACTGGAAGGATG 58.181 52.381 0.00 0.00 39.30 3.51
3012 3449 1.137872 GCATGAGACGACTGGAAGGAT 59.862 52.381 0.00 0.00 39.30 3.24
3013 3450 0.532573 GCATGAGACGACTGGAAGGA 59.467 55.000 0.00 0.00 39.30 3.36
3014 3451 0.534412 AGCATGAGACGACTGGAAGG 59.466 55.000 0.00 0.00 39.30 3.46
3015 3452 1.919918 GAGCATGAGACGACTGGAAG 58.080 55.000 0.00 0.00 42.29 3.46


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

AutoCloner maintained by Alex Coulton.