Multiple sequence alignment - TraesCS3D01G385200

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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 TraesCS3D01G385200 chr3D 100.000 3635 0 0 1 3635 500543873 500540239 0.000000e+00 6713
1 TraesCS3D01G385200 chr3D 91.360 544 41 5 2159 2702 500534831 500534294 0.000000e+00 739
2 TraesCS3D01G385200 chr3D 78.209 1005 146 37 1189 2162 500535959 500534997 3.150000e-160 575
3 TraesCS3D01G385200 chr3D 83.005 406 54 9 3095 3485 500534032 500533627 1.610000e-93 353
4 TraesCS3D01G385200 chr3D 84.641 306 31 7 3346 3635 500532968 500532663 1.280000e-74 291
5 TraesCS3D01G385200 chr3D 84.685 222 30 3 2704 2924 500534260 500534042 6.110000e-53 219
6 TraesCS3D01G385200 chr3A 91.960 1791 87 25 1 1762 639702543 639700781 0.000000e+00 2457
7 TraesCS3D01G385200 chr3A 94.582 1052 44 5 1660 2702 639700787 639699740 0.000000e+00 1615
8 TraesCS3D01G385200 chr3A 82.506 806 110 18 2704 3485 639699706 639698908 0.000000e+00 678
9 TraesCS3D01G385200 chr3B 90.421 1806 96 32 952 2702 661826744 661824961 0.000000e+00 2305
10 TraesCS3D01G385200 chr3B 95.284 827 27 6 1 817 661827699 661826875 0.000000e+00 1301
11 TraesCS3D01G385200 chr3B 82.903 310 32 9 3346 3635 661811758 661811450 3.600000e-65 259
12 TraesCS3D01G385200 chr3B 80.161 373 51 11 3032 3401 661824667 661824315 1.300000e-64 257
13 TraesCS3D01G385200 chr3B 85.271 258 21 7 3346 3588 661812267 661812012 2.170000e-62 250
14 TraesCS3D01G385200 chr3B 85.375 253 22 5 3346 3583 661579438 661579186 7.790000e-62 248
15 TraesCS3D01G385200 chr3B 84.231 260 21 8 3346 3588 661812778 661812522 6.070000e-58 235
16 TraesCS3D01G385200 chr3B 81.967 244 31 9 2704 2943 661824927 661824693 1.030000e-45 195
17 TraesCS3D01G385200 chr3B 86.087 115 1 7 844 953 661826877 661826773 3.840000e-20 110


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 TraesCS3D01G385200 chr3D 500540239 500543873 3634 True 6713.000000 6713 100.000000 1 3635 1 chr3D.!!$R1 3634
1 TraesCS3D01G385200 chr3D 500532663 500535959 3296 True 435.400000 739 84.380000 1189 3635 5 chr3D.!!$R2 2446
2 TraesCS3D01G385200 chr3A 639698908 639702543 3635 True 1583.333333 2457 89.682667 1 3485 3 chr3A.!!$R1 3484
3 TraesCS3D01G385200 chr3B 661824315 661827699 3384 True 833.600000 2305 86.784000 1 3401 5 chr3B.!!$R3 3400
4 TraesCS3D01G385200 chr3B 661811450 661812778 1328 True 248.000000 259 84.135000 3346 3635 3 chr3B.!!$R2 289

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
234 235 0.036732 TGTGGCATCTGTTGGAGTCC 59.963 55.0 0.73 0.73 0.00 3.85 F
489 492 0.458260 ACAACGAAAACCAGCCAACC 59.542 50.0 0.00 0.00 0.00 3.77 F
1464 1566 0.182061 GCTCAGGAATCTGGCATCCA 59.818 55.0 8.26 0.00 41.23 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1440 1542 0.249405 GCCAGATTCCTGAGCTCTCG 60.249 60.0 16.19 5.95 43.02 4.04 R
2082 2322 0.779997 ATCAGGCCCTCACCAACTTT 59.220 50.0 0.00 0.00 0.00 2.66 R
3028 3474 0.106819 AGCTCATTGACTCCATGGCC 60.107 55.0 6.96 0.00 0.00 5.36 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
205 206 9.185192 GAAATAAAAGGTGAAAGAATGTGAGTG 57.815 33.333 0.00 0.00 0.00 3.51
209 210 4.899502 AGGTGAAAGAATGTGAGTGTAGG 58.100 43.478 0.00 0.00 0.00 3.18
214 215 5.778241 TGAAAGAATGTGAGTGTAGGTAGGA 59.222 40.000 0.00 0.00 0.00 2.94
234 235 0.036732 TGTGGCATCTGTTGGAGTCC 59.963 55.000 0.73 0.73 0.00 3.85
323 324 0.940991 GGGCAAAACAGAAAGCAGCG 60.941 55.000 0.00 0.00 0.00 5.18
420 421 2.439701 CTGCTCCCACATGGCCTG 60.440 66.667 3.32 2.01 0.00 4.85
472 475 3.170672 AGCTGGCACACCTGGACA 61.171 61.111 0.00 0.00 35.49 4.02
473 476 2.203337 GCTGGCACACCTGGACAA 60.203 61.111 0.00 0.00 35.49 3.18
474 477 2.555547 GCTGGCACACCTGGACAAC 61.556 63.158 0.00 0.00 35.49 3.32
475 478 2.203139 TGGCACACCTGGACAACG 60.203 61.111 0.00 0.00 36.63 4.10
489 492 0.458260 ACAACGAAAACCAGCCAACC 59.542 50.000 0.00 0.00 0.00 3.77
502 508 1.098712 GCCAACCAAACACCGTGAGA 61.099 55.000 5.28 0.00 0.00 3.27
813 827 2.651361 CGACTCGTGGCTCCAAGT 59.349 61.111 2.00 0.00 0.00 3.16
1006 1059 0.824109 TCAGTAGTTCTCCATGGCGG 59.176 55.000 6.96 2.23 0.00 6.13
1007 1060 0.811616 CAGTAGTTCTCCATGGCGGC 60.812 60.000 6.96 0.00 33.14 6.53
1008 1061 1.883084 GTAGTTCTCCATGGCGGCG 60.883 63.158 6.96 0.51 33.14 6.46
1009 1062 3.088941 TAGTTCTCCATGGCGGCGG 62.089 63.158 9.78 0.00 33.14 6.13
1010 1063 4.778143 GTTCTCCATGGCGGCGGT 62.778 66.667 9.78 0.00 33.14 5.68
1011 1064 4.028490 TTCTCCATGGCGGCGGTT 62.028 61.111 9.78 0.00 33.14 4.44
1140 1202 2.430610 CCCTTCTCCTCTCCCTGCG 61.431 68.421 0.00 0.00 0.00 5.18
1183 1245 2.257391 TCCCCTCCGATTTACCTGAA 57.743 50.000 0.00 0.00 0.00 3.02
1207 1277 1.841103 TGCTACTGTGGGCTGGTGA 60.841 57.895 8.53 0.00 0.00 4.02
1223 1293 3.273434 TGGTGATAACTGCTCTGATTGC 58.727 45.455 0.00 0.00 0.00 3.56
1259 1330 2.342279 CCGTTCGGTGCTTCCAGA 59.658 61.111 2.82 0.00 35.57 3.86
1368 1457 3.138304 TGAAACTGACGTGAAATCCTGG 58.862 45.455 0.00 0.00 0.00 4.45
1395 1484 2.739996 CCATGGCGAGCTTCCTCCT 61.740 63.158 0.00 0.00 34.49 3.69
1401 1490 1.270041 GGCGAGCTTCCTCCTAATCTG 60.270 57.143 0.00 0.00 34.49 2.90
1440 1542 2.476320 GCCTCGCATTCTCCTTGCC 61.476 63.158 0.00 0.00 36.75 4.52
1449 1551 0.900182 TTCTCCTTGCCGAGAGCTCA 60.900 55.000 17.77 0.00 44.23 4.26
1463 1565 0.473326 AGCTCAGGAATCTGGCATCC 59.527 55.000 0.00 0.00 41.23 3.51
1464 1566 0.182061 GCTCAGGAATCTGGCATCCA 59.818 55.000 8.26 0.00 41.23 3.41
1465 1567 1.202903 GCTCAGGAATCTGGCATCCAT 60.203 52.381 8.26 0.00 41.23 3.41
1467 1569 2.885266 CTCAGGAATCTGGCATCCATTG 59.115 50.000 8.26 0.00 41.23 2.82
1469 1571 1.572415 AGGAATCTGGCATCCATTGGT 59.428 47.619 8.26 0.00 38.23 3.67
1471 1573 3.205056 AGGAATCTGGCATCCATTGGTTA 59.795 43.478 8.26 0.00 38.23 2.85
1495 1597 1.825474 CATTCCTGACCAGTCGTACCT 59.175 52.381 0.00 0.00 0.00 3.08
1599 1734 4.740634 GCTGGTATCTTGACGGATCAATCA 60.741 45.833 0.00 0.00 43.92 2.57
1700 1932 3.686016 TCTTATTTCTGTCTGCAACCCC 58.314 45.455 0.00 0.00 0.00 4.95
1734 1966 5.392380 GGCATCTGGTATGACTGAAACAAAG 60.392 44.000 0.00 0.00 0.00 2.77
1741 1973 6.018588 TGGTATGACTGAAACAAAGTTACACG 60.019 38.462 0.00 0.00 0.00 4.49
1815 2055 4.959723 AGCACATAAAGTTGGTTGCAAAT 58.040 34.783 0.00 0.00 0.00 2.32
1872 2112 4.529897 TGCTGCAAATGTCCTATCTCATT 58.470 39.130 0.00 0.00 36.07 2.57
2021 2261 4.130118 CAATAGCTGGCGAGAAGGTAAAT 58.870 43.478 0.00 0.00 31.85 1.40
2181 2591 6.821160 ACAAAAACTTGAACAATACCCCTTTG 59.179 34.615 0.00 0.00 0.00 2.77
2229 2639 7.916450 GTGGTGTGTATTTAGTTGTTTGCTAAA 59.084 33.333 0.00 0.00 41.04 1.85
2284 2694 1.506262 GCGCCGACATGTTGGAATT 59.494 52.632 32.76 0.00 36.15 2.17
2293 2703 4.496341 CGACATGTTGGAATTATGTCAGCC 60.496 45.833 15.25 0.00 46.82 4.85
2329 2739 3.450115 GGAGTCCGGTGAGGGTCG 61.450 72.222 0.00 0.00 41.52 4.79
2413 2823 3.425193 GCAGAAAATAGTTTGTTGTGCCG 59.575 43.478 0.00 0.00 0.00 5.69
2423 2833 4.219944 AGTTTGTTGTGCCGTCTCTATCTA 59.780 41.667 0.00 0.00 0.00 1.98
2424 2834 4.794278 TTGTTGTGCCGTCTCTATCTAA 57.206 40.909 0.00 0.00 0.00 2.10
2568 2978 5.997746 TCTGGGTTCTAACAAATTCAGTCTG 59.002 40.000 0.00 0.00 0.00 3.51
2585 2995 8.996024 TTCAGTCTGTCACGAAATTATATCAA 57.004 30.769 0.00 0.00 0.00 2.57
2628 3038 1.566703 AGTCGGGATCCTCAGAGAAGA 59.433 52.381 12.58 0.00 0.00 2.87
2637 3047 5.764192 GGATCCTCAGAGAAGAAAATGATGG 59.236 44.000 3.84 0.00 0.00 3.51
2653 3063 9.341899 GAAAATGATGGTAAGTATTTGTGTGTC 57.658 33.333 0.00 0.00 0.00 3.67
2658 3068 9.214957 TGATGGTAAGTATTTGTGTGTCTTAAG 57.785 33.333 0.00 0.00 0.00 1.85
2666 3076 5.940192 TTTGTGTGTCTTAAGCATGTAGG 57.060 39.130 0.00 0.00 0.00 3.18
2687 3097 2.667473 ACGACGGAACTCAAATAGGG 57.333 50.000 0.00 0.00 0.00 3.53
2695 3105 3.193479 GGAACTCAAATAGGGTTTGCCTG 59.807 47.826 0.00 0.00 34.45 4.85
2702 3112 0.611618 TAGGGTTTGCCTGCCATGTG 60.612 55.000 0.00 0.00 34.45 3.21
2719 3161 2.763039 TGTGGATGGATGGAGCTTCTA 58.237 47.619 0.00 0.00 0.00 2.10
2726 3168 2.216898 GGATGGAGCTTCTACATGTGC 58.783 52.381 9.11 2.80 34.80 4.57
2731 3173 2.416747 GAGCTTCTACATGTGCACACA 58.583 47.619 24.37 9.60 46.44 3.72
2732 3174 2.807967 GAGCTTCTACATGTGCACACAA 59.192 45.455 24.37 9.58 45.41 3.33
2741 3183 6.934083 TCTACATGTGCACACAAAATCTCTTA 59.066 34.615 24.37 0.00 45.41 2.10
2745 3187 7.596248 ACATGTGCACACAAAATCTCTTAATTC 59.404 33.333 24.37 0.00 45.41 2.17
2781 3223 6.604735 ACATAGTGTCAGAAACTGTGTTTC 57.395 37.500 15.71 13.41 44.56 2.78
2783 3225 3.950397 AGTGTCAGAAACTGTGTTTCCA 58.050 40.909 16.51 7.67 32.61 3.53
2786 3228 5.418840 AGTGTCAGAAACTGTGTTTCCATTT 59.581 36.000 16.51 0.00 32.61 2.32
2788 3230 6.912591 GTGTCAGAAACTGTGTTTCCATTTAG 59.087 38.462 16.51 4.30 32.61 1.85
2859 3301 6.655003 TGGGATTGTATGTCTTTCTTGAGTTC 59.345 38.462 0.00 0.00 0.00 3.01
2862 3304 7.389053 GGATTGTATGTCTTTCTTGAGTTCTGT 59.611 37.037 0.00 0.00 0.00 3.41
2863 3305 7.715265 TTGTATGTCTTTCTTGAGTTCTGTC 57.285 36.000 0.00 0.00 0.00 3.51
2867 3309 4.340097 TGTCTTTCTTGAGTTCTGTCGGTA 59.660 41.667 0.00 0.00 0.00 4.02
2869 3311 4.825634 TCTTTCTTGAGTTCTGTCGGTAGA 59.174 41.667 0.00 0.00 0.00 2.59
2883 3329 6.014840 TCTGTCGGTAGAACTATTTTCCTGTT 60.015 38.462 0.00 0.00 0.00 3.16
2966 3412 3.057456 GGAAAGATCATCATGGCAGCATC 60.057 47.826 0.00 0.00 0.00 3.91
2978 3424 1.417890 GGCAGCATCCTACATGTACCT 59.582 52.381 0.08 0.00 0.00 3.08
2982 3428 3.638627 CAGCATCCTACATGTACCTCTGA 59.361 47.826 0.08 0.00 0.00 3.27
2985 3431 4.281941 GCATCCTACATGTACCTCTGATCA 59.718 45.833 0.08 0.00 0.00 2.92
2996 3442 7.848223 TGTACCTCTGATCATGTAAACAATG 57.152 36.000 0.00 0.00 0.00 2.82
2998 3444 4.641989 ACCTCTGATCATGTAAACAATGCC 59.358 41.667 0.00 0.00 0.00 4.40
3002 3448 4.343231 TGATCATGTAAACAATGCCACCT 58.657 39.130 0.00 0.00 0.00 4.00
3004 3450 4.517952 TCATGTAAACAATGCCACCTTG 57.482 40.909 0.00 0.00 0.00 3.61
3005 3451 4.148079 TCATGTAAACAATGCCACCTTGA 58.852 39.130 0.00 0.00 0.00 3.02
3007 3453 5.069648 TCATGTAAACAATGCCACCTTGAAA 59.930 36.000 0.00 0.00 0.00 2.69
3009 3455 4.404073 TGTAAACAATGCCACCTTGAAAGT 59.596 37.500 0.00 0.00 0.00 2.66
3011 3457 4.853924 AACAATGCCACCTTGAAAGTAG 57.146 40.909 0.00 0.00 0.00 2.57
3012 3458 2.558359 ACAATGCCACCTTGAAAGTAGC 59.442 45.455 0.00 0.00 0.00 3.58
3013 3459 1.839424 ATGCCACCTTGAAAGTAGCC 58.161 50.000 0.00 0.00 0.00 3.93
3014 3460 0.771127 TGCCACCTTGAAAGTAGCCT 59.229 50.000 0.00 0.00 0.00 4.58
3015 3461 1.271379 TGCCACCTTGAAAGTAGCCTC 60.271 52.381 0.00 0.00 0.00 4.70
3016 3462 1.726853 CCACCTTGAAAGTAGCCTCG 58.273 55.000 0.00 0.00 0.00 4.63
3017 3463 1.676014 CCACCTTGAAAGTAGCCTCGG 60.676 57.143 0.00 0.00 0.00 4.63
3078 3530 0.542467 ATGCCCATGAACACCTTGCA 60.542 50.000 0.00 0.00 0.00 4.08
3079 3531 0.542467 TGCCCATGAACACCTTGCAT 60.542 50.000 0.00 0.00 0.00 3.96
3088 3540 3.444742 TGAACACCTTGCATCATTCATCC 59.555 43.478 0.00 0.00 0.00 3.51
3124 3576 0.113190 TCTCACTGGTCAGGAGCTCA 59.887 55.000 17.19 0.00 0.00 4.26
3131 3583 0.673022 GGTCAGGAGCTCACAGCAAG 60.673 60.000 17.19 0.00 45.56 4.01
3136 3588 0.035630 GGAGCTCACAGCAAGATGGT 60.036 55.000 17.19 0.00 45.56 3.55
3138 3590 0.390866 AGCTCACAGCAAGATGGTCG 60.391 55.000 0.00 0.00 45.56 4.79
3147 3599 1.293924 CAAGATGGTCGCCTCATGAC 58.706 55.000 0.00 0.00 35.60 3.06
3148 3600 1.134580 CAAGATGGTCGCCTCATGACT 60.135 52.381 0.00 0.00 36.58 3.41
3149 3602 2.073252 AGATGGTCGCCTCATGACTA 57.927 50.000 0.00 0.00 36.58 2.59
3210 3663 2.642311 TCAAGGATCTTAGTTGTGCCCA 59.358 45.455 0.00 0.00 0.00 5.36
3236 3689 2.888534 GCCATGCATGCCGCTTTG 60.889 61.111 21.69 6.82 43.06 2.77
3260 3713 2.903855 CATGGCAGCACCGATCCC 60.904 66.667 0.00 0.00 43.94 3.85
3266 3719 2.685017 AGCACCGATCCCAGCTCA 60.685 61.111 0.00 0.00 30.05 4.26
3267 3720 2.202987 GCACCGATCCCAGCTCAG 60.203 66.667 0.00 0.00 0.00 3.35
3284 3737 4.462394 GCCATCAGCTTGCCGATA 57.538 55.556 0.00 0.00 38.99 2.92
3326 3779 0.600255 CGGTGTCGTTGCTCCTTCTT 60.600 55.000 0.00 0.00 0.00 2.52
3329 3782 0.179059 TGTCGTTGCTCCTTCTTGCA 60.179 50.000 0.00 0.00 37.42 4.08
3335 3790 3.246403 GCTCCTTCTTGCAAGAGCT 57.754 52.632 27.02 0.00 46.50 4.09
3389 3844 6.516739 TTACTCCAGTATCTCACTTCACAG 57.483 41.667 0.00 0.00 34.26 3.66
3416 3873 4.999311 CCAGTAGTAAGGTACACCCAAAAC 59.001 45.833 0.00 0.00 36.42 2.43
3430 4092 5.182380 ACACCCAAAACGGTTAAGATACATG 59.818 40.000 0.00 0.00 32.17 3.21
3432 4094 5.413523 ACCCAAAACGGTTAAGATACATGTC 59.586 40.000 0.00 0.00 29.19 3.06
3433 4095 5.413213 CCCAAAACGGTTAAGATACATGTCA 59.587 40.000 0.00 0.00 0.00 3.58
3438 4100 5.175859 ACGGTTAAGATACATGTCACTTGG 58.824 41.667 20.43 12.57 0.00 3.61
3439 4101 4.034048 CGGTTAAGATACATGTCACTTGGC 59.966 45.833 20.43 14.56 0.00 4.52
3442 4104 4.833478 AAGATACATGTCACTTGGCTCT 57.167 40.909 0.00 0.00 0.00 4.09
3443 4105 4.134379 AGATACATGTCACTTGGCTCTG 57.866 45.455 0.00 0.00 0.00 3.35
3450 4429 2.288666 GTCACTTGGCTCTGACAACAA 58.711 47.619 5.30 0.00 37.36 2.83
3496 5440 4.348461 ACAGATGATTGATCAGAGCTGGAT 59.652 41.667 16.45 0.00 40.64 3.41
3532 5476 1.236616 TGTCCCGAGCATGCAACTTG 61.237 55.000 21.98 2.82 0.00 3.16
3547 5491 3.728864 GCAACTTGCTTGGATATCACACG 60.729 47.826 6.50 0.00 40.96 4.49
3566 5510 1.532505 CGTAGCTCATGCACATTTGGC 60.533 52.381 0.00 0.00 42.74 4.52
3626 5576 6.258727 GGACACCAATTCATAGACACATACTG 59.741 42.308 0.00 0.00 0.00 2.74
3628 5578 4.811024 ACCAATTCATAGACACATACTGCG 59.189 41.667 0.00 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
205 206 2.700897 ACAGATGCCACATCCTACCTAC 59.299 50.000 4.00 0.00 0.00 3.18
209 210 2.092968 TCCAACAGATGCCACATCCTAC 60.093 50.000 4.00 0.00 0.00 3.18
214 215 1.340405 GGACTCCAACAGATGCCACAT 60.340 52.381 0.00 0.00 0.00 3.21
234 235 1.221466 TGACTTTGTGAGGCTTCGCG 61.221 55.000 0.00 0.00 36.61 5.87
323 324 3.732849 CAAGGTCCCTCCCTGCCC 61.733 72.222 0.00 0.00 34.19 5.36
420 421 2.439104 AAGGATGAGGAGGAGCGGC 61.439 63.158 0.00 0.00 0.00 6.53
472 475 1.187087 TTGGTTGGCTGGTTTTCGTT 58.813 45.000 0.00 0.00 0.00 3.85
473 476 1.134936 GTTTGGTTGGCTGGTTTTCGT 60.135 47.619 0.00 0.00 0.00 3.85
474 477 1.134965 TGTTTGGTTGGCTGGTTTTCG 60.135 47.619 0.00 0.00 0.00 3.46
475 478 2.276201 GTGTTTGGTTGGCTGGTTTTC 58.724 47.619 0.00 0.00 0.00 2.29
502 508 0.248012 TTCGGTGGTATGCGTGTGAT 59.752 50.000 0.00 0.00 0.00 3.06
547 555 1.306141 TCCTCCTGTTCCATCGGCT 60.306 57.895 0.00 0.00 0.00 5.52
733 744 6.629156 AGATTCTAGACTACATCCATTCCCT 58.371 40.000 0.00 0.00 0.00 4.20
931 950 2.126071 CGATCACAGCCGTCCGTT 60.126 61.111 0.00 0.00 0.00 4.44
977 1027 3.379057 GGAGAACTACTGACTAGCTCACC 59.621 52.174 0.00 0.00 0.00 4.02
1140 1202 1.740664 GGAGGAGGAAAACGTCGCC 60.741 63.158 0.00 0.00 0.00 5.54
1183 1245 0.911525 AGCCCACAGTAGCACAGGAT 60.912 55.000 0.00 0.00 0.00 3.24
1207 1277 1.938577 CGCAGCAATCAGAGCAGTTAT 59.061 47.619 0.00 0.00 0.00 1.89
1259 1330 6.857964 CGTGAACTTTTACATTTCAGCTGAAT 59.142 34.615 28.89 17.15 33.54 2.57
1389 1478 1.508185 CCCCTACCCAGATTAGGAGGA 59.492 57.143 0.00 0.00 38.84 3.71
1395 1484 1.766496 CGCTTTCCCCTACCCAGATTA 59.234 52.381 0.00 0.00 0.00 1.75
1401 1490 0.255033 AATGTCGCTTTCCCCTACCC 59.745 55.000 0.00 0.00 0.00 3.69
1440 1542 0.249405 GCCAGATTCCTGAGCTCTCG 60.249 60.000 16.19 5.95 43.02 4.04
1449 1551 1.572415 ACCAATGGATGCCAGATTCCT 59.428 47.619 6.16 0.00 36.75 3.36
1467 1569 4.200092 GACTGGTCAGGAATGGATTAACC 58.800 47.826 2.87 0.00 39.54 2.85
1469 1571 3.517901 ACGACTGGTCAGGAATGGATTAA 59.482 43.478 2.87 0.00 0.00 1.40
1471 1573 1.909302 ACGACTGGTCAGGAATGGATT 59.091 47.619 2.87 0.00 0.00 3.01
1495 1597 8.270080 TGAAATGCATACTGTACCGAAAATAA 57.730 30.769 0.00 0.00 0.00 1.40
1508 1610 7.062322 TGGATAAGGTCATTGAAATGCATACT 58.938 34.615 0.00 0.00 36.36 2.12
1700 1932 1.471119 ACCAGATGCCTGATGCTTTG 58.529 50.000 0.00 0.00 43.02 2.77
1734 1966 4.516359 TGTAACAAATTGTCGCGTGTAAC 58.484 39.130 5.77 0.00 0.00 2.50
1741 1973 5.846473 GTCTTTCTCTGTAACAAATTGTCGC 59.154 40.000 0.00 0.00 0.00 5.19
1815 2055 8.723365 TCAGGGAGAAATAATTTCCTAGCAATA 58.277 33.333 0.00 0.00 40.54 1.90
1872 2112 6.483307 CCAGAAACATAGTTCAACTCACTGAA 59.517 38.462 0.00 0.00 32.89 3.02
2082 2322 0.779997 ATCAGGCCCTCACCAACTTT 59.220 50.000 0.00 0.00 0.00 2.66
2135 2375 2.338809 AGGACAGGTCAACATTCCAGA 58.661 47.619 1.41 0.00 0.00 3.86
2284 2694 5.545063 TTCCTATTGATTCGGCTGACATA 57.455 39.130 0.00 0.00 0.00 2.29
2293 2703 6.647067 GGACTCCATAGTTTCCTATTGATTCG 59.353 42.308 0.00 0.00 35.56 3.34
2404 2814 3.508402 TGTTAGATAGAGACGGCACAACA 59.492 43.478 0.00 0.00 0.00 3.33
2585 2995 3.617284 AGACCGTGTTTCCTCAAAGTTT 58.383 40.909 0.00 0.00 0.00 2.66
2601 3011 0.953003 GAGGATCCCGACTAAGACCG 59.047 60.000 8.55 0.00 0.00 4.79
2628 3038 9.077885 AGACACACAAATACTTACCATCATTTT 57.922 29.630 0.00 0.00 0.00 1.82
2637 3047 8.504005 ACATGCTTAAGACACACAAATACTTAC 58.496 33.333 6.67 0.00 0.00 2.34
2648 3058 4.460034 TCGTACCTACATGCTTAAGACACA 59.540 41.667 6.67 0.00 0.00 3.72
2653 3063 3.065786 TCCGTCGTACCTACATGCTTAAG 59.934 47.826 0.00 0.00 0.00 1.85
2658 3068 1.133790 AGTTCCGTCGTACCTACATGC 59.866 52.381 0.00 0.00 0.00 4.06
2666 3076 3.119352 ACCCTATTTGAGTTCCGTCGTAC 60.119 47.826 0.00 0.00 0.00 3.67
2687 3097 0.108520 CATCCACATGGCAGGCAAAC 60.109 55.000 0.00 0.00 34.44 2.93
2702 3112 3.072184 ACATGTAGAAGCTCCATCCATCC 59.928 47.826 0.00 0.00 0.00 3.51
2719 3161 4.924305 AAGAGATTTTGTGTGCACATGT 57.076 36.364 24.69 4.53 41.52 3.21
2755 3197 8.677148 AAACACAGTTTCTGACACTATGTAAT 57.323 30.769 8.17 0.00 35.18 1.89
2811 3253 3.007831 TCCAGCACATGTGTATGAACTCA 59.992 43.478 26.01 6.29 37.73 3.41
2817 3259 1.951602 CCCATCCAGCACATGTGTATG 59.048 52.381 26.01 22.65 40.24 2.39
2821 3263 1.407618 CAATCCCATCCAGCACATGTG 59.592 52.381 21.83 21.83 0.00 3.21
2822 3264 1.006281 ACAATCCCATCCAGCACATGT 59.994 47.619 0.00 0.00 0.00 3.21
2823 3265 1.771565 ACAATCCCATCCAGCACATG 58.228 50.000 0.00 0.00 0.00 3.21
2859 3301 5.721232 ACAGGAAAATAGTTCTACCGACAG 58.279 41.667 0.00 0.00 0.00 3.51
2862 3304 6.349243 TGAACAGGAAAATAGTTCTACCGA 57.651 37.500 0.00 0.00 41.56 4.69
2863 3305 7.611213 AATGAACAGGAAAATAGTTCTACCG 57.389 36.000 0.00 0.00 41.56 4.02
2877 3323 6.829811 TCATGCAGAAATCATAATGAACAGGA 59.170 34.615 0.00 0.00 0.00 3.86
2879 3325 8.920509 TTTCATGCAGAAATCATAATGAACAG 57.079 30.769 7.09 0.00 41.17 3.16
2911 3357 8.199449 TCCTGTTCCACCGTAAATATAAAGTAG 58.801 37.037 0.00 0.00 0.00 2.57
2916 3362 5.426185 ACCTCCTGTTCCACCGTAAATATAA 59.574 40.000 0.00 0.00 0.00 0.98
2924 3370 1.458777 TCACCTCCTGTTCCACCGT 60.459 57.895 0.00 0.00 0.00 4.83
2929 3375 1.003696 CTTTCCCTCACCTCCTGTTCC 59.996 57.143 0.00 0.00 0.00 3.62
2978 3424 4.398988 GGTGGCATTGTTTACATGATCAGA 59.601 41.667 0.00 0.00 0.00 3.27
2982 3428 4.771577 TCAAGGTGGCATTGTTTACATGAT 59.228 37.500 0.00 0.00 0.00 2.45
2985 3431 5.070313 ACTTTCAAGGTGGCATTGTTTACAT 59.930 36.000 0.00 0.00 0.00 2.29
2996 3442 1.454201 GAGGCTACTTTCAAGGTGGC 58.546 55.000 0.00 0.00 39.81 5.01
2998 3444 1.676014 CCCGAGGCTACTTTCAAGGTG 60.676 57.143 0.00 0.00 0.00 4.00
3020 3466 3.849951 CTCCATGGCCGGCGTAGT 61.850 66.667 22.54 2.59 0.00 2.73
3022 3468 3.845259 GACTCCATGGCCGGCGTA 61.845 66.667 22.54 12.99 0.00 4.42
3024 3470 4.776322 TTGACTCCATGGCCGGCG 62.776 66.667 22.54 7.92 0.00 6.46
3025 3471 2.124151 ATTGACTCCATGGCCGGC 60.124 61.111 21.18 21.18 0.00 6.13
3026 3472 0.816825 CTCATTGACTCCATGGCCGG 60.817 60.000 6.96 0.00 0.00 6.13
3027 3473 1.442526 GCTCATTGACTCCATGGCCG 61.443 60.000 6.96 2.80 0.00 6.13
3028 3474 0.106819 AGCTCATTGACTCCATGGCC 60.107 55.000 6.96 0.00 0.00 5.36
3029 3475 1.404391 CAAGCTCATTGACTCCATGGC 59.596 52.381 6.96 0.00 41.83 4.40
3030 3476 1.404391 GCAAGCTCATTGACTCCATGG 59.596 52.381 4.97 4.97 41.83 3.66
3058 3510 1.272369 TGCAAGGTGTTCATGGGCATA 60.272 47.619 0.00 0.00 0.00 3.14
3078 3530 1.133294 TGGCATGCAGGGATGAATGAT 60.133 47.619 21.36 0.00 0.00 2.45
3079 3531 0.259356 TGGCATGCAGGGATGAATGA 59.741 50.000 21.36 0.00 0.00 2.57
3101 3553 1.405256 GCTCCTGACCAGTGAGATGTG 60.405 57.143 15.11 0.00 31.59 3.21
3102 3554 0.901124 GCTCCTGACCAGTGAGATGT 59.099 55.000 15.11 0.00 31.59 3.06
3124 3576 1.078848 GAGGCGACCATCTTGCTGT 60.079 57.895 0.00 0.00 0.00 4.40
3131 3583 2.866762 GTTTAGTCATGAGGCGACCATC 59.133 50.000 0.00 0.00 33.70 3.51
3136 3588 0.174845 CCGGTTTAGTCATGAGGCGA 59.825 55.000 0.00 0.00 0.00 5.54
3138 3590 2.093869 TGTACCGGTTTAGTCATGAGGC 60.094 50.000 15.04 0.00 0.00 4.70
3147 3599 1.065926 GTTCCCCCTGTACCGGTTTAG 60.066 57.143 15.04 11.84 0.00 1.85
3148 3600 0.983467 GTTCCCCCTGTACCGGTTTA 59.017 55.000 15.04 0.33 0.00 2.01
3149 3602 1.763120 GTTCCCCCTGTACCGGTTT 59.237 57.895 15.04 0.00 0.00 3.27
3210 3663 3.731728 ATGCATGGCCGTGGAGGT 61.732 61.111 26.22 6.94 43.70 3.85
3236 3689 1.527844 GGTGCTGCCATGGGAGATC 60.528 63.158 35.08 24.24 35.50 2.75
3267 3720 1.242076 AATATCGGCAAGCTGATGGC 58.758 50.000 23.04 1.93 41.64 4.40
3329 3782 2.165998 GTCAATCCCAAGCAAGCTCTT 58.834 47.619 0.00 0.00 0.00 2.85
3335 3790 4.275443 GCAAATTTTGTCAATCCCAAGCAA 59.725 37.500 10.65 0.00 0.00 3.91
3340 3795 4.686191 AGTGCAAATTTTGTCAATCCCA 57.314 36.364 10.65 0.00 0.00 4.37
3389 3844 3.698539 GGGTGTACCTTACTACTGGTCTC 59.301 52.174 0.44 0.00 37.74 3.36
3416 3873 4.034048 GCCAAGTGACATGTATCTTAACCG 59.966 45.833 0.00 0.00 0.00 4.44
3430 4092 1.953559 TGTTGTCAGAGCCAAGTGAC 58.046 50.000 0.00 0.00 42.93 3.67
3432 4094 3.144506 AGATTGTTGTCAGAGCCAAGTG 58.855 45.455 0.00 0.00 0.00 3.16
3433 4095 3.498774 AGATTGTTGTCAGAGCCAAGT 57.501 42.857 0.00 0.00 0.00 3.16
3443 4105 9.155975 ACTGTATGATTAGACAAGATTGTTGTC 57.844 33.333 16.64 16.64 46.71 3.18
3496 5440 3.571590 GGACATATAAATGGGGCCAACA 58.428 45.455 4.39 2.74 37.43 3.33
3532 5476 3.053455 GAGCTACGTGTGATATCCAAGC 58.947 50.000 0.00 4.65 0.00 4.01
3547 5491 1.202336 GGCCAAATGTGCATGAGCTAC 60.202 52.381 0.00 0.00 42.74 3.58
3566 5510 0.679002 CCTCCTGCATGACTGGTTGG 60.679 60.000 0.00 5.44 38.49 3.77
3596 5540 1.593006 CTATGAATTGGTGTCCGTCGC 59.407 52.381 0.00 0.00 0.00 5.19
3600 5544 3.595173 TGTGTCTATGAATTGGTGTCCG 58.405 45.455 0.00 0.00 0.00 4.79
3603 5552 5.586243 GCAGTATGTGTCTATGAATTGGTGT 59.414 40.000 0.00 0.00 39.31 4.16


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

AutoCloner maintained by Alex Coulton.