Multiple sequence alignment - TraesCS4A01G230200

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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 TraesCS4A01G230200 chr4A 100.000 3976 0 0 1 3976 539300560 539296585 0.000000e+00 7343
1 TraesCS4A01G230200 chr4D 91.082 3409 194 35 55 3423 57474181 57477519 0.000000e+00 4510
2 TraesCS4A01G230200 chr4D 81.475 583 48 35 3425 3961 57477595 57478163 1.320000e-114 424
3 TraesCS4A01G230200 chr4B 91.607 2228 141 25 46 2247 86060716 86062923 0.000000e+00 3037
4 TraesCS4A01G230200 chr4B 91.085 673 44 12 2764 3424 86062917 86063585 0.000000e+00 896
5 TraesCS4A01G230200 chr4B 83.103 580 39 35 3425 3961 86063659 86064222 1.290000e-129 473
6 TraesCS4A01G230200 chr6B 93.860 1189 69 2 1226 2413 551792826 551794011 0.000000e+00 1788
7 TraesCS4A01G230200 chr6B 87.171 912 73 20 60 939 551791549 551792448 0.000000e+00 996
8 TraesCS4A01G230200 chr6B 95.142 494 19 3 2442 2931 551794010 551794502 0.000000e+00 774
9 TraesCS4A01G230200 chr6B 91.356 509 35 7 2919 3421 551794520 551795025 0.000000e+00 688
10 TraesCS4A01G230200 chr6B 82.423 586 33 41 3425 3961 551795102 551795666 7.840000e-122 448
11 TraesCS4A01G230200 chr6B 91.284 218 13 1 940 1151 551792612 551792829 3.890000e-75 292


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 TraesCS4A01G230200 chr4A 539296585 539300560 3975 True 7343.000000 7343 100.000000 1 3976 1 chr4A.!!$R1 3975
1 TraesCS4A01G230200 chr4D 57474181 57478163 3982 False 2467.000000 4510 86.278500 55 3961 2 chr4D.!!$F1 3906
2 TraesCS4A01G230200 chr4B 86060716 86064222 3506 False 1468.666667 3037 88.598333 46 3961 3 chr4B.!!$F1 3915
3 TraesCS4A01G230200 chr6B 551791549 551795666 4117 False 831.000000 1788 90.206000 60 3961 6 chr6B.!!$F1 3901

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
471 489 0.460284 GCGTGAACAGGTCCATCGAT 60.460 55.0 0.00 0.0 0.0 3.59 F
2356 2619 0.458716 GCTACTCTGGCCTCGTTGAC 60.459 60.0 3.32 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2452 2715 0.035317 ATGCTTCGACAAGTCTGCCA 59.965 50.000 0.0 0.0 31.45 4.92 R
3574 3972 1.133792 CCACAAACACTTCCTGGGACT 60.134 52.381 0.0 0.0 0.00 3.85 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
47 48 8.934507 AGTAATTTCTAACATACAGTCTGAGC 57.065 34.615 6.91 0.00 0.00 4.26
48 49 8.531982 AGTAATTTCTAACATACAGTCTGAGCA 58.468 33.333 6.91 0.00 0.00 4.26
49 50 7.840342 AATTTCTAACATACAGTCTGAGCAG 57.160 36.000 6.91 0.00 0.00 4.24
50 51 5.984695 TTCTAACATACAGTCTGAGCAGT 57.015 39.130 6.91 0.00 0.00 4.40
51 52 5.984695 TCTAACATACAGTCTGAGCAGTT 57.015 39.130 6.91 8.13 0.00 3.16
52 53 7.462571 TTCTAACATACAGTCTGAGCAGTTA 57.537 36.000 6.91 8.77 0.00 2.24
53 54 7.089770 TCTAACATACAGTCTGAGCAGTTAG 57.910 40.000 20.42 20.42 38.82 2.34
54 55 5.984695 AACATACAGTCTGAGCAGTTAGA 57.015 39.130 6.91 0.00 0.00 2.10
55 56 5.317733 ACATACAGTCTGAGCAGTTAGAC 57.682 43.478 6.91 0.00 42.77 2.59
56 57 4.767409 ACATACAGTCTGAGCAGTTAGACA 59.233 41.667 6.91 0.00 44.41 3.41
57 58 5.420421 ACATACAGTCTGAGCAGTTAGACAT 59.580 40.000 6.91 0.00 44.41 3.06
58 59 6.603599 ACATACAGTCTGAGCAGTTAGACATA 59.396 38.462 6.91 0.47 44.41 2.29
65 66 7.806374 GTCTGAGCAGTTAGACATAGGGAACT 61.806 46.154 0.00 0.00 42.18 3.01
79 80 7.645058 CATAGGGAACTGTGGTCATTTATTT 57.355 36.000 0.00 0.00 45.01 1.40
80 81 5.982890 AGGGAACTGTGGTCATTTATTTG 57.017 39.130 0.00 0.00 41.13 2.32
82 83 4.165779 GGAACTGTGGTCATTTATTTGCG 58.834 43.478 0.00 0.00 0.00 4.85
85 86 5.046910 ACTGTGGTCATTTATTTGCGAAG 57.953 39.130 0.00 0.00 0.00 3.79
88 89 6.071952 ACTGTGGTCATTTATTTGCGAAGAAT 60.072 34.615 0.00 0.00 0.00 2.40
100 101 5.413969 TTGCGAAGAATTGAGCATGATAG 57.586 39.130 0.00 0.00 37.99 2.08
124 125 5.954434 CATGTAATGCTTGGTTGCAATAC 57.046 39.130 0.59 7.51 46.61 1.89
128 129 3.658757 ATGCTTGGTTGCAATACGTTT 57.341 38.095 0.59 0.00 46.61 3.60
129 130 3.444703 TGCTTGGTTGCAATACGTTTT 57.555 38.095 0.59 0.00 40.29 2.43
130 131 3.376540 TGCTTGGTTGCAATACGTTTTC 58.623 40.909 0.59 0.00 40.29 2.29
142 148 5.308927 CAATACGTTTTCTTTCAGAGCTCG 58.691 41.667 8.37 3.55 0.00 5.03
144 150 1.461127 CGTTTTCTTTCAGAGCTCGGG 59.539 52.381 14.13 8.02 0.00 5.14
145 151 1.197949 GTTTTCTTTCAGAGCTCGGGC 59.802 52.381 14.13 0.00 39.06 6.13
153 159 2.032681 GAGCTCGGGCCTTTGTGT 59.967 61.111 2.00 0.00 39.73 3.72
181 187 7.715657 TGCTATTTAAGGGCATACATTTTCTG 58.284 34.615 0.00 0.00 0.00 3.02
182 188 7.341769 TGCTATTTAAGGGCATACATTTTCTGT 59.658 33.333 0.00 0.00 42.13 3.41
196 202 4.647424 TTTTCTGTACTTTGCAGGGTTG 57.353 40.909 0.00 0.00 34.89 3.77
208 215 1.164411 CAGGGTTGCATACGCTTCAA 58.836 50.000 13.29 0.00 46.90 2.69
293 302 1.135972 CATATATCGGCCAGCGCAAAC 60.136 52.381 11.47 0.00 36.38 2.93
348 366 7.231722 GTCTAAGCTGAGATGTATCCTTCCTTA 59.768 40.741 3.44 0.00 0.00 2.69
462 480 2.022129 GGAGTCGTGCGTGAACAGG 61.022 63.158 0.00 0.00 0.00 4.00
471 489 0.460284 GCGTGAACAGGTCCATCGAT 60.460 55.000 0.00 0.00 0.00 3.59
560 587 7.436933 AGGAATCAGAAACTTTCAAATTGTCC 58.563 34.615 4.34 3.46 0.00 4.02
611 638 6.003326 TGAATCTATCCAGAGTCTCTAGCAG 58.997 44.000 0.94 0.00 44.44 4.24
627 654 2.350522 AGCAGCACTAGTGTAACATGC 58.649 47.619 23.44 22.01 41.43 4.06
636 664 6.237942 GCACTAGTGTAACATGCTCATTACTG 60.238 42.308 23.44 0.00 41.43 2.74
648 676 3.998913 TCATTACTGCCATGAGAACCA 57.001 42.857 0.00 0.00 0.00 3.67
649 677 4.508551 TCATTACTGCCATGAGAACCAT 57.491 40.909 0.00 0.00 35.44 3.55
689 742 3.279434 TGCTGAGAGATTAGTGCGTCTA 58.721 45.455 0.00 0.00 0.00 2.59
703 756 2.108157 TCTAAATGGCGCCGCGAT 59.892 55.556 23.90 6.99 0.00 4.58
706 759 1.897398 CTAAATGGCGCCGCGATACC 61.897 60.000 23.90 9.07 0.00 2.73
851 924 6.488817 GCATTTCATAATGGCACCAAATTTC 58.511 36.000 0.00 0.00 41.21 2.17
999 1244 1.374190 CCCAACTCAGTCAGCAGCT 59.626 57.895 0.00 0.00 0.00 4.24
1545 1808 4.354943 CCAGGAGGGGGAGGTGGT 62.355 72.222 0.00 0.00 0.00 4.16
1576 1839 4.389576 GTGTTCTTGGCAGCCGCG 62.390 66.667 7.03 0.00 39.92 6.46
1777 2040 2.280628 GAGATGGTTCATGGGTTCGTC 58.719 52.381 0.00 0.00 0.00 4.20
1816 2079 1.091771 CGAATCTGCCGCTGGTGAAT 61.092 55.000 0.00 0.00 0.00 2.57
1867 2130 1.225745 CATTGCGTCGGCGAAAGAC 60.226 57.895 16.53 0.00 39.28 3.01
1888 2151 1.630223 TGTTTGATGGAATGGCTGCA 58.370 45.000 0.50 0.00 0.00 4.41
2101 2364 1.153549 GAGTCATGGGCTCGACACC 60.154 63.158 0.00 0.00 34.48 4.16
2110 2373 2.791927 CTCGACACCGATGCGAGA 59.208 61.111 15.74 0.00 46.43 4.04
2252 2515 0.883833 CAACCATGGTGAGCCTGAAC 59.116 55.000 20.60 0.00 35.27 3.18
2266 2529 2.903798 CCTGAACAGGCTCTCAATCTC 58.096 52.381 7.95 0.00 42.44 2.75
2272 2535 2.765699 ACAGGCTCTCAATCTCTTCTCC 59.234 50.000 0.00 0.00 0.00 3.71
2283 2546 1.135139 TCTCTTCTCCGCGATGAAAGG 59.865 52.381 8.23 7.06 0.00 3.11
2293 2556 1.453155 CGATGAAAGGTCAAGGGGTG 58.547 55.000 0.00 0.00 37.30 4.61
2356 2619 0.458716 GCTACTCTGGCCTCGTTGAC 60.459 60.000 3.32 0.00 0.00 3.18
2369 2632 4.697756 TTGACGAAGGGCTGGCGG 62.698 66.667 0.00 0.00 0.00 6.13
2388 2651 3.044986 CGGTTTTCAACAGCATTGTCAG 58.955 45.455 1.17 0.00 36.23 3.51
2404 2667 5.977489 TTGTCAGGGACTACCATATATCG 57.023 43.478 0.00 0.00 43.89 2.92
2407 2670 3.011369 TCAGGGACTACCATATATCGCCT 59.989 47.826 0.00 0.00 43.89 5.52
2413 2676 5.066246 GGACTACCATATATCGCCTACACTC 59.934 48.000 0.00 0.00 35.97 3.51
2419 2682 5.066634 CCATATATCGCCTACACTCGAGAAT 59.933 44.000 21.68 8.98 38.17 2.40
2452 2715 0.608130 TTGACATGCTAGGACGTGCT 59.392 50.000 15.78 15.78 0.00 4.40
2464 2727 1.560860 GACGTGCTGGCAGACTTGTC 61.561 60.000 20.86 15.23 0.00 3.18
2470 2733 0.601046 CTGGCAGACTTGTCGAAGCA 60.601 55.000 9.42 0.00 31.68 3.91
2602 2865 1.045911 ATCTCTTCCTGTCGGGCTCC 61.046 60.000 0.00 0.00 34.39 4.70
2662 2925 1.523258 CGAGGCTGGAATGCTGGAG 60.523 63.158 0.00 0.00 0.00 3.86
2701 2964 2.368221 GAGGACCATGAAGGAGATGGAG 59.632 54.545 5.78 0.00 42.81 3.86
2760 3023 5.108517 CAGTAGAGAAAGAAGAGCCATCAC 58.891 45.833 0.00 0.00 0.00 3.06
2805 3070 9.931210 CAAGTTTTAGGTTAGACTGTTTGTAAG 57.069 33.333 0.00 0.00 0.00 2.34
2815 3080 6.246420 AGACTGTTTGTAAGCAGCTATTTG 57.754 37.500 8.16 0.00 40.41 2.32
2834 3099 1.168714 GCACATGTTCTCTCCCCAAC 58.831 55.000 0.00 0.00 0.00 3.77
3051 3349 7.765307 ACAATGCTCCAGAAAATAATGTACTG 58.235 34.615 0.00 0.00 0.00 2.74
3060 3358 8.398665 CCAGAAAATAATGTACTGCCTAGTTTC 58.601 37.037 0.00 2.47 38.36 2.78
3061 3359 9.167311 CAGAAAATAATGTACTGCCTAGTTTCT 57.833 33.333 10.73 10.73 38.51 2.52
3168 3467 3.386726 TCGGTGATCGGTGAGGAATAATT 59.613 43.478 0.00 0.00 39.77 1.40
3193 3492 7.262772 TGTTTTCATACTACAGGAGAATACCG 58.737 38.462 0.00 0.00 34.73 4.02
3239 3538 0.967380 GTTTCATGGCTCAGGTGGGG 60.967 60.000 0.00 0.00 0.00 4.96
3263 3562 3.265791 GGCAGAGAATTGTAGTCACAGG 58.734 50.000 0.00 0.00 35.67 4.00
3280 3579 3.820467 CACAGGTGCTATTTTCCACTGAA 59.180 43.478 0.00 0.00 32.68 3.02
3306 3606 6.686630 TGCATCGACAGTCCAAATTATTTTT 58.313 32.000 0.00 0.00 0.00 1.94
3390 3699 2.043664 AGTGGGATGAGTTCAGAGAGGA 59.956 50.000 0.00 0.00 0.00 3.71
3400 3709 3.326297 AGTTCAGAGAGGAAGGACAAAGG 59.674 47.826 0.00 0.00 0.00 3.11
3410 3719 3.321968 GGAAGGACAAAGGAGTTGCAAAT 59.678 43.478 0.00 0.00 41.31 2.32
3442 3827 3.629855 TGGCACGAGAAAGTTTCAAATCA 59.370 39.130 17.65 5.56 0.00 2.57
3507 3905 6.194796 TGTCTTCTAGCATTTTGTATTGCC 57.805 37.500 0.00 0.00 39.72 4.52
3529 3927 3.706594 CCTCCTAGGAAGTGTGCATTCTA 59.293 47.826 13.77 0.00 37.67 2.10
3530 3928 4.346418 CCTCCTAGGAAGTGTGCATTCTAT 59.654 45.833 13.77 0.00 37.67 1.98
3567 3965 9.188588 CGATTCATAATCTAGCATTTTGCATTT 57.811 29.630 1.93 0.00 39.77 2.32
3596 3995 1.463553 CCCAGGAAGTGTTTGTGGGC 61.464 60.000 0.00 0.00 41.53 5.36
3597 3996 0.754957 CCAGGAAGTGTTTGTGGGCA 60.755 55.000 0.00 0.00 0.00 5.36
3598 3997 1.110442 CAGGAAGTGTTTGTGGGCAA 58.890 50.000 0.00 0.00 0.00 4.52
3626 4025 7.549839 ACAGCACAGTATATAAAGTTCGGTAA 58.450 34.615 0.00 0.00 0.00 2.85
3636 4035 4.911514 AAAGTTCGGTAAGTGTGCATTT 57.088 36.364 0.00 0.00 0.00 2.32
3641 4040 4.217754 TCGGTAAGTGTGCATTTGTTTC 57.782 40.909 0.00 0.00 0.00 2.78
3644 4043 4.260990 CGGTAAGTGTGCATTTGTTTCTCA 60.261 41.667 0.00 0.00 0.00 3.27
3645 4044 5.587289 GGTAAGTGTGCATTTGTTTCTCAA 58.413 37.500 0.00 0.00 0.00 3.02
3684 4110 2.203195 TCAGTGCACACCTGCCAC 60.203 61.111 21.04 0.00 43.51 5.01
3745 4173 9.832445 TTCATAACTAATCAGGGTAACATCTTC 57.168 33.333 0.00 0.00 39.74 2.87
3749 4177 8.840200 AACTAATCAGGGTAACATCTTCTAGA 57.160 34.615 0.00 0.00 39.74 2.43
3751 4179 9.268282 ACTAATCAGGGTAACATCTTCTAGAAA 57.732 33.333 6.63 0.00 39.74 2.52
3754 4182 7.792364 TCAGGGTAACATCTTCTAGAAAAGA 57.208 36.000 6.63 1.36 39.49 2.52
3755 4183 8.380742 TCAGGGTAACATCTTCTAGAAAAGAT 57.619 34.615 6.63 3.89 44.84 2.40
3776 4204 2.225934 TGGTACAATACAAGGAGGGGGA 60.226 50.000 0.00 0.00 31.92 4.81
3777 4205 3.053826 GGTACAATACAAGGAGGGGGAT 58.946 50.000 0.00 0.00 0.00 3.85
3778 4206 3.462205 GGTACAATACAAGGAGGGGGATT 59.538 47.826 0.00 0.00 0.00 3.01
3801 4248 1.889829 CTAACCAAATGCCCGGTTCAA 59.110 47.619 0.00 0.00 44.40 2.69
3819 4266 5.229423 GTTCAACATATTTTGCCAAGCTGA 58.771 37.500 0.00 0.00 0.00 4.26
3888 4335 0.392461 ACGTGTTGCCACTTGTGAGT 60.392 50.000 1.89 0.00 39.55 3.41
3913 4364 6.700081 TGTAATACTGAATGCAAGGTCGATAC 59.300 38.462 0.00 0.00 0.00 2.24
3956 4410 4.083324 CGACAACAAAGAACCATGCTATGT 60.083 41.667 0.00 0.00 0.00 2.29
3969 4423 2.910199 TGCTATGTCATGGAGAAGTGC 58.090 47.619 0.00 0.00 0.00 4.40
3970 4424 2.236893 TGCTATGTCATGGAGAAGTGCA 59.763 45.455 0.00 0.00 0.00 4.57
3971 4425 3.118149 TGCTATGTCATGGAGAAGTGCAT 60.118 43.478 0.00 0.00 34.48 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 9.372369 GCTCAGACTGTATGTTAGAAATTACTT 57.628 33.333 1.59 0.00 0.00 2.24
22 23 8.531982 TGCTCAGACTGTATGTTAGAAATTACT 58.468 33.333 1.59 0.00 0.00 2.24
23 24 8.703604 TGCTCAGACTGTATGTTAGAAATTAC 57.296 34.615 1.59 0.00 0.00 1.89
24 25 8.531982 ACTGCTCAGACTGTATGTTAGAAATTA 58.468 33.333 1.59 0.00 0.00 1.40
25 26 7.390027 ACTGCTCAGACTGTATGTTAGAAATT 58.610 34.615 1.59 0.00 0.00 1.82
26 27 6.940739 ACTGCTCAGACTGTATGTTAGAAAT 58.059 36.000 1.59 0.00 0.00 2.17
27 28 6.346477 ACTGCTCAGACTGTATGTTAGAAA 57.654 37.500 1.59 0.00 0.00 2.52
28 29 5.984695 ACTGCTCAGACTGTATGTTAGAA 57.015 39.130 1.59 0.00 0.00 2.10
29 30 5.984695 AACTGCTCAGACTGTATGTTAGA 57.015 39.130 1.59 0.00 0.00 2.10
30 31 6.970043 GTCTAACTGCTCAGACTGTATGTTAG 59.030 42.308 20.64 20.64 38.50 2.34
31 32 6.433093 TGTCTAACTGCTCAGACTGTATGTTA 59.567 38.462 1.59 7.41 41.46 2.41
32 33 5.243954 TGTCTAACTGCTCAGACTGTATGTT 59.756 40.000 1.59 6.71 41.46 2.71
33 34 4.767409 TGTCTAACTGCTCAGACTGTATGT 59.233 41.667 1.59 0.00 41.46 2.29
34 35 5.316327 TGTCTAACTGCTCAGACTGTATG 57.684 43.478 1.59 0.00 41.46 2.39
35 36 6.264292 CCTATGTCTAACTGCTCAGACTGTAT 59.736 42.308 1.59 0.00 41.46 2.29
36 37 5.590663 CCTATGTCTAACTGCTCAGACTGTA 59.409 44.000 1.59 0.00 41.46 2.74
37 38 4.400884 CCTATGTCTAACTGCTCAGACTGT 59.599 45.833 1.59 0.00 41.46 3.55
38 39 4.202101 CCCTATGTCTAACTGCTCAGACTG 60.202 50.000 3.60 0.00 41.46 3.51
39 40 3.957497 CCCTATGTCTAACTGCTCAGACT 59.043 47.826 3.60 0.00 41.46 3.24
40 41 3.954904 TCCCTATGTCTAACTGCTCAGAC 59.045 47.826 3.60 0.00 41.31 3.51
41 42 4.251103 TCCCTATGTCTAACTGCTCAGA 57.749 45.455 3.60 0.00 0.00 3.27
42 43 4.404073 AGTTCCCTATGTCTAACTGCTCAG 59.596 45.833 0.00 0.00 31.20 3.35
43 44 4.160439 CAGTTCCCTATGTCTAACTGCTCA 59.840 45.833 0.00 0.00 41.49 4.26
44 45 4.688021 CAGTTCCCTATGTCTAACTGCTC 58.312 47.826 0.00 0.00 41.49 4.26
45 46 4.744795 CAGTTCCCTATGTCTAACTGCT 57.255 45.455 0.00 0.00 41.49 4.24
48 49 4.426704 ACCACAGTTCCCTATGTCTAACT 58.573 43.478 0.00 0.00 32.52 2.24
49 50 4.222145 TGACCACAGTTCCCTATGTCTAAC 59.778 45.833 0.00 0.00 0.00 2.34
50 51 4.422057 TGACCACAGTTCCCTATGTCTAA 58.578 43.478 0.00 0.00 0.00 2.10
51 52 4.055710 TGACCACAGTTCCCTATGTCTA 57.944 45.455 0.00 0.00 0.00 2.59
52 53 2.902608 TGACCACAGTTCCCTATGTCT 58.097 47.619 0.00 0.00 0.00 3.41
53 54 3.914426 ATGACCACAGTTCCCTATGTC 57.086 47.619 0.00 0.00 0.00 3.06
54 55 4.657814 AAATGACCACAGTTCCCTATGT 57.342 40.909 0.00 0.00 27.75 2.29
55 56 7.483307 CAAATAAATGACCACAGTTCCCTATG 58.517 38.462 0.00 0.00 35.87 2.23
56 57 6.096846 GCAAATAAATGACCACAGTTCCCTAT 59.903 38.462 0.00 0.00 35.87 2.57
57 58 5.417580 GCAAATAAATGACCACAGTTCCCTA 59.582 40.000 0.00 0.00 35.87 3.53
58 59 4.220602 GCAAATAAATGACCACAGTTCCCT 59.779 41.667 0.00 0.00 35.87 4.20
65 66 5.697473 TTCTTCGCAAATAAATGACCACA 57.303 34.783 0.00 0.00 0.00 4.17
79 80 4.509230 GTCTATCATGCTCAATTCTTCGCA 59.491 41.667 0.00 0.00 36.75 5.10
80 81 4.509230 TGTCTATCATGCTCAATTCTTCGC 59.491 41.667 0.00 0.00 0.00 4.70
100 101 3.574284 TGCAACCAAGCATTACATGTC 57.426 42.857 0.00 0.00 40.11 3.06
105 106 4.091453 ACGTATTGCAACCAAGCATTAC 57.909 40.909 0.00 9.63 45.19 1.89
114 115 5.516090 TCTGAAAGAAAACGTATTGCAACC 58.484 37.500 0.00 0.00 42.31 3.77
115 116 5.115622 GCTCTGAAAGAAAACGTATTGCAAC 59.884 40.000 0.00 0.00 46.34 4.17
121 122 3.927142 CCGAGCTCTGAAAGAAAACGTAT 59.073 43.478 12.85 0.00 46.34 3.06
124 125 1.461127 CCCGAGCTCTGAAAGAAAACG 59.539 52.381 12.85 0.00 46.34 3.60
128 129 1.194781 AGGCCCGAGCTCTGAAAGAA 61.195 55.000 12.85 0.00 46.34 2.52
129 130 1.194781 AAGGCCCGAGCTCTGAAAGA 61.195 55.000 12.85 0.00 43.34 2.52
130 131 0.322008 AAAGGCCCGAGCTCTGAAAG 60.322 55.000 12.85 0.00 39.73 2.62
142 148 4.736126 AAATAGCAATACACAAAGGCCC 57.264 40.909 0.00 0.00 0.00 5.80
144 150 6.273071 CCCTTAAATAGCAATACACAAAGGC 58.727 40.000 0.00 0.00 31.61 4.35
145 151 6.127479 TGCCCTTAAATAGCAATACACAAAGG 60.127 38.462 0.00 0.00 32.56 3.11
293 302 6.017109 GCACCAGGGTGTAAATGATACAATAG 60.017 42.308 18.99 0.00 46.90 1.73
348 366 2.755103 GCGATTCAACCTTTCCTGGAAT 59.245 45.455 10.45 0.00 0.00 3.01
390 408 3.004734 GGAGCTTTGCTGCTTCAAACTTA 59.995 43.478 0.00 0.00 43.58 2.24
471 489 1.985614 CAGGACCCTGATGCTGTCA 59.014 57.895 10.47 0.00 46.30 3.58
560 587 4.050934 GGCAAAAACGAGCCGGGG 62.051 66.667 2.18 0.00 41.70 5.73
611 638 5.812642 AGTAATGAGCATGTTACACTAGTGC 59.187 40.000 22.90 6.96 34.14 4.40
689 742 3.276846 GGTATCGCGGCGCCATTT 61.277 61.111 28.98 10.40 0.00 2.32
703 756 4.817464 ACGTTTGCAACATTTAGTCTGGTA 59.183 37.500 0.00 0.00 0.00 3.25
706 759 4.846137 GCTACGTTTGCAACATTTAGTCTG 59.154 41.667 0.00 0.00 0.00 3.51
727 780 9.933723 AAGATTTTAAGATGTTATGCAAAAGCT 57.066 25.926 0.00 0.00 34.23 3.74
766 819 7.064134 GCAAATTGCAGAGATCATGAATGAAAA 59.936 33.333 13.73 0.00 44.26 2.29
822 875 1.955778 TGCCATTATGAAATGCCCTCG 59.044 47.619 0.00 0.00 41.06 4.63
877 959 9.387257 GCTTGGGATATTTGAATTTCTTTGAAT 57.613 29.630 0.00 0.00 0.00 2.57
878 960 8.373981 TGCTTGGGATATTTGAATTTCTTTGAA 58.626 29.630 0.00 0.00 0.00 2.69
879 961 7.905265 TGCTTGGGATATTTGAATTTCTTTGA 58.095 30.769 0.00 0.00 0.00 2.69
880 962 8.550710 TTGCTTGGGATATTTGAATTTCTTTG 57.449 30.769 0.00 0.00 0.00 2.77
881 963 9.002600 GTTTGCTTGGGATATTTGAATTTCTTT 57.997 29.630 0.00 0.00 0.00 2.52
884 966 6.878389 TGGTTTGCTTGGGATATTTGAATTTC 59.122 34.615 0.00 0.00 0.00 2.17
898 980 5.799435 GTCAAAATTTGTTTGGTTTGCTTGG 59.201 36.000 5.56 0.00 0.00 3.61
999 1244 1.918293 ATCTGTTGGACCTCGGGCA 60.918 57.895 0.00 0.00 0.00 5.36
1071 1327 1.109920 TGAGAGGAGGCCGATGTAGC 61.110 60.000 0.00 0.00 0.00 3.58
1097 1353 2.277404 GAGGGAGGAGGAGACGCT 59.723 66.667 0.00 0.00 0.00 5.07
1120 1382 1.152525 GGCGTGGATAGGGAGGAGA 60.153 63.158 0.00 0.00 0.00 3.71
1738 2001 2.185350 CCGGCAGCGAGACATTCT 59.815 61.111 0.00 0.00 0.00 2.40
1777 2040 1.079127 ATCGAACCCCAGCTTGACG 60.079 57.895 0.00 0.00 0.00 4.35
1852 2115 2.028484 AAGTCTTTCGCCGACGCA 59.972 55.556 0.00 0.00 39.84 5.24
1867 2130 2.028839 TGCAGCCATTCCATCAAACAAG 60.029 45.455 0.00 0.00 0.00 3.16
2101 2364 0.110956 CATTGCCGATTCTCGCATCG 60.111 55.000 4.93 4.93 44.78 3.84
2110 2373 1.086696 CCACGAGAACATTGCCGATT 58.913 50.000 0.00 0.00 0.00 3.34
2170 2433 0.594796 CGCGCAAACCTTCAAAAGCT 60.595 50.000 8.75 0.00 0.00 3.74
2252 2515 2.223782 CGGAGAAGAGATTGAGAGCCTG 60.224 54.545 0.00 0.00 0.00 4.85
2266 2529 1.281899 GACCTTTCATCGCGGAGAAG 58.718 55.000 6.13 5.89 0.00 2.85
2272 2535 1.369091 CCCCTTGACCTTTCATCGCG 61.369 60.000 0.00 0.00 0.00 5.87
2283 2546 2.808906 ATTAGGCTTCACCCCTTGAC 57.191 50.000 0.00 0.00 40.58 3.18
2293 2556 2.609916 GAGCGTGAAGGAATTAGGCTTC 59.390 50.000 0.00 0.00 35.89 3.86
2350 2613 3.423154 GCCAGCCCTTCGTCAACG 61.423 66.667 0.00 0.00 41.45 4.10
2356 2619 2.978018 GAAAACCGCCAGCCCTTCG 61.978 63.158 0.00 0.00 0.00 3.79
2369 2632 5.028741 GTCCCTGACAATGCTGTTGAAAAC 61.029 45.833 8.99 0.00 38.85 2.43
2388 2651 4.097589 GTGTAGGCGATATATGGTAGTCCC 59.902 50.000 0.00 0.00 0.00 4.46
2404 2667 3.060602 GGCATAATTCTCGAGTGTAGGC 58.939 50.000 13.13 14.85 0.00 3.93
2407 2670 3.132111 TGCAGGCATAATTCTCGAGTGTA 59.868 43.478 13.13 3.75 0.00 2.90
2413 2676 2.224606 ACCATGCAGGCATAATTCTCG 58.775 47.619 6.42 0.00 43.14 4.04
2419 2682 2.212812 TGTCAACCATGCAGGCATAA 57.787 45.000 6.42 0.00 43.14 1.90
2452 2715 0.035317 ATGCTTCGACAAGTCTGCCA 59.965 50.000 0.00 0.00 31.45 4.92
2464 2727 4.155462 CCCCTGATGATTTCATATGCTTCG 59.845 45.833 0.00 0.00 36.57 3.79
2470 2733 5.942236 CGACATTCCCCTGATGATTTCATAT 59.058 40.000 0.00 0.00 36.57 1.78
2592 2855 2.264480 CGTCATTGGAGCCCGACA 59.736 61.111 0.00 0.00 0.00 4.35
2662 2925 2.506438 CTCGTCCTTTCCGCGTCC 60.506 66.667 4.92 0.00 0.00 4.79
2701 2964 1.743252 CCCAGCCGTCTTCTTGAGC 60.743 63.158 0.00 0.00 0.00 4.26
2760 3023 1.067669 TGCATCTAGCTTGCTACCTCG 59.932 52.381 10.10 0.00 45.94 4.63
2805 3070 3.128242 AGAGAACATGTGCAAATAGCTGC 59.872 43.478 6.60 0.00 45.94 5.25
2815 3080 1.168714 GTTGGGGAGAGAACATGTGC 58.831 55.000 0.00 0.00 0.00 4.57
2857 3122 6.998673 ACGAGCCTATGATAAAGCCTAATTTT 59.001 34.615 0.00 0.00 0.00 1.82
3005 3303 2.452295 TTCAGTCTCTTCTGCAGCTG 57.548 50.000 10.11 10.11 35.63 4.24
3130 3429 0.585357 CCGATCGTAGTCCAGTACCG 59.415 60.000 15.09 0.00 0.00 4.02
3168 3467 7.093640 ACGGTATTCTCCTGTAGTATGAAAACA 60.094 37.037 0.00 0.00 0.00 2.83
3193 3492 9.860898 AAATTTCTATGCCAATCAACTTAGAAC 57.139 29.630 0.00 0.00 34.28 3.01
3239 3538 3.055819 TGTGACTACAATTCTCTGCCCTC 60.056 47.826 0.00 0.00 32.88 4.30
3263 3562 4.808558 TGCATTTCAGTGGAAAATAGCAC 58.191 39.130 9.61 0.00 45.52 4.40
3280 3579 6.455360 AATAATTTGGACTGTCGATGCATT 57.545 33.333 0.00 0.73 0.00 3.56
3306 3606 2.542595 GGCGTTCTTGTTTCTTCGAAGA 59.457 45.455 23.74 23.74 0.00 2.87
3357 3660 6.252599 ACTCATCCCACTAGCATGAAATAA 57.747 37.500 0.00 0.00 0.00 1.40
3359 3662 4.785346 ACTCATCCCACTAGCATGAAAT 57.215 40.909 0.00 0.00 0.00 2.17
3390 3699 4.405358 TCAATTTGCAACTCCTTTGTCCTT 59.595 37.500 0.00 0.00 37.54 3.36
3400 3709 5.179742 TGCCATCATTTTCAATTTGCAACTC 59.820 36.000 0.00 0.00 0.00 3.01
3410 3719 4.278170 ACTTTCTCGTGCCATCATTTTCAA 59.722 37.500 0.00 0.00 0.00 2.69
3476 3861 5.415415 AAATGCTAGAAGACATGAATCGC 57.585 39.130 0.00 0.00 0.00 4.58
3507 3905 2.503356 AGAATGCACACTTCCTAGGAGG 59.497 50.000 18.95 18.95 36.46 4.30
3567 3965 3.711849 CTTCCTGGGACTGGGAGTA 57.288 57.895 0.00 0.00 46.62 2.59
3568 3966 4.569214 CTTCCTGGGACTGGGAGT 57.431 61.111 0.00 0.00 46.62 3.85
3573 3971 1.949525 CACAAACACTTCCTGGGACTG 59.050 52.381 0.00 0.00 0.00 3.51
3574 3972 1.133792 CCACAAACACTTCCTGGGACT 60.134 52.381 0.00 0.00 0.00 3.85
3575 3973 1.318576 CCACAAACACTTCCTGGGAC 58.681 55.000 0.00 0.00 0.00 4.46
3596 3995 7.688167 CGAACTTTATATACTGTGCTGTTGTTG 59.312 37.037 0.00 0.00 0.00 3.33
3597 3996 7.148474 CCGAACTTTATATACTGTGCTGTTGTT 60.148 37.037 0.00 0.00 0.00 2.83
3598 3997 6.312918 CCGAACTTTATATACTGTGCTGTTGT 59.687 38.462 0.00 0.00 0.00 3.32
3724 4152 8.840200 TCTAGAAGATGTTACCCTGATTAGTT 57.160 34.615 0.00 0.00 0.00 2.24
3725 4153 8.840200 TTCTAGAAGATGTTACCCTGATTAGT 57.160 34.615 0.00 0.00 0.00 2.24
3745 4173 9.319143 CTCCTTGTATTGTACCATCTTTTCTAG 57.681 37.037 0.00 0.00 0.00 2.43
3749 4177 6.187682 CCCTCCTTGTATTGTACCATCTTTT 58.812 40.000 0.00 0.00 0.00 2.27
3751 4179 4.166144 CCCCTCCTTGTATTGTACCATCTT 59.834 45.833 0.00 0.00 0.00 2.40
3753 4181 3.181443 CCCCCTCCTTGTATTGTACCATC 60.181 52.174 0.00 0.00 0.00 3.51
3754 4182 2.783510 CCCCCTCCTTGTATTGTACCAT 59.216 50.000 0.00 0.00 0.00 3.55
3755 4183 2.201830 CCCCCTCCTTGTATTGTACCA 58.798 52.381 0.00 0.00 0.00 3.25
3776 4204 4.178956 ACCGGGCATTTGGTTAGATAAT 57.821 40.909 6.32 0.00 33.81 1.28
3777 4205 3.655615 ACCGGGCATTTGGTTAGATAA 57.344 42.857 6.32 0.00 33.81 1.75
3778 4206 3.655615 AACCGGGCATTTGGTTAGATA 57.344 42.857 6.32 0.00 46.34 1.98
3801 4248 3.164268 TGGTCAGCTTGGCAAAATATGT 58.836 40.909 0.00 0.00 0.00 2.29
3819 4266 2.281692 TGCAGCGCATGAACTGGT 60.282 55.556 11.47 0.00 31.71 4.00
3888 4335 5.079689 TCGACCTTGCATTCAGTATTACA 57.920 39.130 0.00 0.00 0.00 2.41
3889 4336 6.145696 GGTATCGACCTTGCATTCAGTATTAC 59.854 42.308 0.00 0.00 43.16 1.89
3913 4364 2.107366 GGAGGAAGAGGAGTCTGAAGG 58.893 57.143 0.00 0.00 31.37 3.46


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

AutoCloner maintained by Alex Coulton.