Multiple sequence alignment - TraesCS1B01G141800

Loading Multiple Alignment...

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 TraesCS1B01G141800 chr1B 100.000 2639 0 0 1 2639 189587240 189589878 0 4874
1 TraesCS1B01G141800 chr7B 90.841 2653 217 19 1 2639 151132760 151130120 0 3530
2 TraesCS1B01G141800 chr7B 89.444 2662 228 22 1 2639 396280760 396278129 0 3310
3 TraesCS1B01G141800 chr7B 87.851 1745 194 14 904 2639 506241333 506239598 0 2032
4 TraesCS1B01G141800 chr7B 83.271 1327 197 24 649 1964 361254992 361256304 0 1197
5 TraesCS1B01G141800 chr1D 90.762 2652 218 26 1 2639 307650904 307648267 0 3515
6 TraesCS1B01G141800 chr1D 82.850 2105 313 38 1 2079 69098931 69101013 0 1844
7 TraesCS1B01G141800 chr1D 82.938 2110 295 53 1 2079 397992003 397994078 0 1842
8 TraesCS1B01G141800 chr6D 88.075 2675 270 35 1 2639 333794254 333791593 0 3127
9 TraesCS1B01G141800 chr6D 91.085 1346 98 11 147 1488 364247743 364246416 0 1801
10 TraesCS1B01G141800 chr6D 82.312 2024 313 32 1 2003 321241398 321239399 0 1712
11 TraesCS1B01G141800 chr2B 86.882 2668 288 31 1 2639 263700354 263702988 0 2931
12 TraesCS1B01G141800 chr4D 89.228 2358 220 26 301 2639 393474112 393471770 0 2916
13 TraesCS1B01G141800 chr4A 85.732 2432 298 35 165 2579 48884550 48882151 0 2523
14 TraesCS1B01G141800 chr2D 91.338 1293 89 19 1 1274 162338479 162337191 0 1746
15 TraesCS1B01G141800 chr2D 85.142 1622 204 31 1 1606 260490827 260489227 0 1626
16 TraesCS1B01G141800 chr2D 87.993 1166 119 15 1488 2639 162321159 162320001 0 1358


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 TraesCS1B01G141800 chr1B 189587240 189589878 2638 False 4874 4874 100.000 1 2639 1 chr1B.!!$F1 2638
1 TraesCS1B01G141800 chr7B 151130120 151132760 2640 True 3530 3530 90.841 1 2639 1 chr7B.!!$R1 2638
2 TraesCS1B01G141800 chr7B 396278129 396280760 2631 True 3310 3310 89.444 1 2639 1 chr7B.!!$R2 2638
3 TraesCS1B01G141800 chr7B 506239598 506241333 1735 True 2032 2032 87.851 904 2639 1 chr7B.!!$R3 1735
4 TraesCS1B01G141800 chr7B 361254992 361256304 1312 False 1197 1197 83.271 649 1964 1 chr7B.!!$F1 1315
5 TraesCS1B01G141800 chr1D 307648267 307650904 2637 True 3515 3515 90.762 1 2639 1 chr1D.!!$R1 2638
6 TraesCS1B01G141800 chr1D 69098931 69101013 2082 False 1844 1844 82.850 1 2079 1 chr1D.!!$F1 2078
7 TraesCS1B01G141800 chr1D 397992003 397994078 2075 False 1842 1842 82.938 1 2079 1 chr1D.!!$F2 2078
8 TraesCS1B01G141800 chr6D 333791593 333794254 2661 True 3127 3127 88.075 1 2639 1 chr6D.!!$R2 2638
9 TraesCS1B01G141800 chr6D 364246416 364247743 1327 True 1801 1801 91.085 147 1488 1 chr6D.!!$R3 1341
10 TraesCS1B01G141800 chr6D 321239399 321241398 1999 True 1712 1712 82.312 1 2003 1 chr6D.!!$R1 2002
11 TraesCS1B01G141800 chr2B 263700354 263702988 2634 False 2931 2931 86.882 1 2639 1 chr2B.!!$F1 2638
12 TraesCS1B01G141800 chr4D 393471770 393474112 2342 True 2916 2916 89.228 301 2639 1 chr4D.!!$R1 2338
13 TraesCS1B01G141800 chr4A 48882151 48884550 2399 True 2523 2523 85.732 165 2579 1 chr4A.!!$R1 2414
14 TraesCS1B01G141800 chr2D 162337191 162338479 1288 True 1746 1746 91.338 1 1274 1 chr2D.!!$R2 1273
15 TraesCS1B01G141800 chr2D 260489227 260490827 1600 True 1626 1626 85.142 1 1606 1 chr2D.!!$R3 1605
16 TraesCS1B01G141800 chr2D 162320001 162321159 1158 True 1358 1358 87.993 1488 2639 1 chr2D.!!$R1 1151

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
195 198 0.690762 AGTACTGCGGGTTGTGGATT 59.309 50.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1715 1815 0.598065 ATTCCACCAAGAAAGTGCGC 59.402 50.0 0.0 0.0 33.75 6.09 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 5.078411 TGAGATTGGAGAGCTCTTGTTAC 57.922 43.478 19.36 10.02 41.40 2.50
67 68 4.154737 CGTGATTCCTTGAGAAATTGCTCA 59.845 41.667 12.45 12.45 42.81 4.26
83 84 3.888583 TGCTCATAATTCATGCTCCACA 58.111 40.909 0.00 0.00 34.35 4.17
180 182 1.606224 CGTGGTTGTGTGGGGTAGTAC 60.606 57.143 0.00 0.00 0.00 2.73
195 198 0.690762 AGTACTGCGGGTTGTGGATT 59.309 50.000 0.00 0.00 0.00 3.01
221 224 3.921119 ATGTTCGAATTGCAAGCTTCA 57.079 38.095 4.94 0.00 0.00 3.02
355 362 3.165087 TGTACTCCCTCTTCTCCGAAA 57.835 47.619 0.00 0.00 0.00 3.46
381 388 3.466836 GGTCGCATCATCTGGTATTCAA 58.533 45.455 0.00 0.00 0.00 2.69
544 567 3.256879 TCTTTGTGTTTGCACCAAGTTCA 59.743 39.130 10.09 0.00 44.19 3.18
567 596 1.065401 CCGAAGCTGCTGTTGTTTTCA 59.935 47.619 1.35 0.00 0.00 2.69
744 811 1.094785 AGTGTTGCAGCTCAAACGTT 58.905 45.000 1.17 0.00 36.26 3.99
847 929 1.139058 CCAGATCCACCTAGAAACCGG 59.861 57.143 0.00 0.00 0.00 5.28
880 962 1.541310 TTCATTCGCCCGTCCACTCT 61.541 55.000 0.00 0.00 0.00 3.24
929 1012 7.684428 GCCAAGGAATCATTAGAATTTGGGTAC 60.684 40.741 0.00 0.00 35.52 3.34
997 1091 6.147864 TGTCCACTTTCTTCCAAAAGATTG 57.852 37.500 3.56 0.00 41.12 2.67
1019 1113 1.841302 ATGGCAGGCTCCAACTCGAA 61.841 55.000 9.27 0.00 39.96 3.71
1072 1166 2.048222 CCAAGACTCGAGCCGCAA 60.048 61.111 13.61 0.00 0.00 4.85
1146 1240 1.874345 GACGTCTTCCTCTTGCGGGA 61.874 60.000 8.70 0.00 0.00 5.14
1157 1251 0.106519 CTTGCGGGAAATGGGGATCT 60.107 55.000 0.00 0.00 0.00 2.75
1457 1552 5.047847 CCCAAATCATAACGATGAGTACGT 58.952 41.667 0.00 0.00 45.29 3.57
1496 1595 2.093658 AGTCATATTCCACGCCTCGTTT 60.094 45.455 0.00 0.00 38.32 3.60
1583 1682 0.948678 GCAAGGGTGAAGTTACGCAA 59.051 50.000 0.00 0.00 36.11 4.85
1635 1735 4.591321 TGCTTATTTTGAGTGGGAGGAT 57.409 40.909 0.00 0.00 0.00 3.24
1636 1736 4.934356 TGCTTATTTTGAGTGGGAGGATT 58.066 39.130 0.00 0.00 0.00 3.01
1715 1815 8.091449 ACTCACTCTTAATAAGTTCTCTGGTTG 58.909 37.037 0.00 0.00 0.00 3.77
1716 1816 6.874134 TCACTCTTAATAAGTTCTCTGGTTGC 59.126 38.462 0.00 0.00 0.00 4.17
1750 1850 4.262592 GGTGGAATCAGTTGCAAAAGGATT 60.263 41.667 16.75 16.75 37.42 3.01
1784 1884 3.323403 GGAGGTGACTATATCTGCAGCTT 59.677 47.826 9.47 1.05 44.43 3.74
1842 1942 9.967346 TTCGTTCCATTATACTATGAGAAGAAG 57.033 33.333 0.00 0.00 0.00 2.85
1943 2043 2.092321 TCCGGACAAAAACCCAAGAGAA 60.092 45.455 0.00 0.00 0.00 2.87
1946 2046 3.305335 CGGACAAAAACCCAAGAGAATGG 60.305 47.826 0.00 0.00 40.35 3.16
2080 2182 6.650807 GTGGAGAAGAAGAACATGTGTAATCA 59.349 38.462 0.00 0.00 0.00 2.57
2100 2202 5.839517 TCATTGGTCCCAAAATTTCCAAT 57.160 34.783 12.89 12.89 45.83 3.16
2106 2208 6.315714 TGGTCCCAAAATTTCCAATACTGTA 58.684 36.000 0.00 0.00 0.00 2.74
2200 2302 5.665459 AGATAGAAGAATCGTGGTTTCAGG 58.335 41.667 0.00 0.00 0.00 3.86
2202 2304 4.884668 AGAAGAATCGTGGTTTCAGGTA 57.115 40.909 0.00 0.00 0.00 3.08
2367 2870 6.544928 AAGAGTGTCCACTTCCAAAAATTT 57.455 33.333 0.79 0.00 42.66 1.82
2376 2879 9.271828 GTCCACTTCCAAAAATTTCACATATTT 57.728 29.630 0.00 0.00 0.00 1.40
2383 2886 9.638239 TCCAAAAATTTCACATATTTAGAGTGC 57.362 29.630 0.00 0.00 33.44 4.40
2390 2893 8.948631 TTTCACATATTTAGAGTGCTAAGAGG 57.051 34.615 0.00 0.00 37.84 3.69
2393 2896 5.905913 ACATATTTAGAGTGCTAAGAGGGGT 59.094 40.000 0.00 0.00 37.84 4.95
2417 2920 3.117888 AGTTGAGTGACTCCACCAAATGT 60.118 43.478 12.58 0.00 44.22 2.71
2418 2921 2.849942 TGAGTGACTCCACCAAATGTG 58.150 47.619 10.52 0.00 44.22 3.21
2430 2933 4.170468 ACCAAATGTGAGGAAGAGTGTT 57.830 40.909 0.00 0.00 0.00 3.32
2462 2965 7.972277 CCAAAAATTCCACATATTGAGAGTGAG 59.028 37.037 0.00 0.00 35.33 3.51
2517 3099 5.073144 TGTGAGAAAGAGGGTACATTTTCCT 59.927 40.000 0.00 0.00 31.56 3.36
2518 3100 6.271391 TGTGAGAAAGAGGGTACATTTTCCTA 59.729 38.462 0.00 0.00 31.56 2.94
2519 3101 7.166167 GTGAGAAAGAGGGTACATTTTCCTAA 58.834 38.462 0.00 0.00 31.56 2.69
2520 3102 7.664318 GTGAGAAAGAGGGTACATTTTCCTAAA 59.336 37.037 0.00 0.00 31.56 1.85
2521 3103 8.221944 TGAGAAAGAGGGTACATTTTCCTAAAA 58.778 33.333 0.00 0.00 31.56 1.52
2522 3104 9.244292 GAGAAAGAGGGTACATTTTCCTAAAAT 57.756 33.333 0.00 0.00 41.57 1.82
2523 3105 9.601810 AGAAAGAGGGTACATTTTCCTAAAATT 57.398 29.630 0.00 0.00 38.97 1.82
2525 3107 9.996554 AAAGAGGGTACATTTTCCTAAAATTTG 57.003 29.630 0.00 0.00 38.97 2.32
2526 3108 8.721133 AGAGGGTACATTTTCCTAAAATTTGT 57.279 30.769 0.00 0.00 38.97 2.83
2527 3109 9.816787 AGAGGGTACATTTTCCTAAAATTTGTA 57.183 29.630 0.00 0.00 38.97 2.41
2549 3131 8.768501 TGTATATTGAGAGTGATAAGAGTGGT 57.231 34.615 0.00 0.00 0.00 4.16
2550 3132 8.633561 TGTATATTGAGAGTGATAAGAGTGGTG 58.366 37.037 0.00 0.00 0.00 4.17
2551 3133 7.667575 ATATTGAGAGTGATAAGAGTGGTGT 57.332 36.000 0.00 0.00 0.00 4.16
2552 3134 8.768501 ATATTGAGAGTGATAAGAGTGGTGTA 57.231 34.615 0.00 0.00 0.00 2.90
2553 3135 7.667575 ATTGAGAGTGATAAGAGTGGTGTAT 57.332 36.000 0.00 0.00 0.00 2.29
2554 3136 6.701145 TGAGAGTGATAAGAGTGGTGTATC 57.299 41.667 0.00 0.00 0.00 2.24
2555 3137 5.297029 TGAGAGTGATAAGAGTGGTGTATCG 59.703 44.000 0.00 0.00 0.00 2.92
2556 3138 5.437946 AGAGTGATAAGAGTGGTGTATCGA 58.562 41.667 0.00 0.00 0.00 3.59
2557 3139 5.529430 AGAGTGATAAGAGTGGTGTATCGAG 59.471 44.000 0.00 0.00 0.00 4.04
2558 3140 5.194432 AGTGATAAGAGTGGTGTATCGAGT 58.806 41.667 0.00 0.00 0.00 4.18
2559 3141 5.066634 AGTGATAAGAGTGGTGTATCGAGTG 59.933 44.000 0.00 0.00 0.00 3.51
2560 3142 5.066117 GTGATAAGAGTGGTGTATCGAGTGA 59.934 44.000 0.00 0.00 0.00 3.41
2561 3143 5.828328 TGATAAGAGTGGTGTATCGAGTGAT 59.172 40.000 0.00 0.00 38.67 3.06
2562 3144 6.321435 TGATAAGAGTGGTGTATCGAGTGATT 59.679 38.462 0.00 0.00 35.99 2.57
2563 3145 4.640789 AGAGTGGTGTATCGAGTGATTC 57.359 45.455 0.00 0.00 35.99 2.52
2564 3146 3.381908 AGAGTGGTGTATCGAGTGATTCC 59.618 47.826 0.00 0.00 35.99 3.01
2565 3147 3.096852 AGTGGTGTATCGAGTGATTCCA 58.903 45.455 0.00 0.00 35.99 3.53
2566 3148 3.119101 AGTGGTGTATCGAGTGATTCCAC 60.119 47.826 14.84 14.84 42.79 4.02
2567 3149 2.167693 TGGTGTATCGAGTGATTCCACC 59.832 50.000 14.77 14.77 45.95 4.61
2568 3150 2.167693 GGTGTATCGAGTGATTCCACCA 59.832 50.000 15.92 0.00 45.53 4.17
2569 3151 3.369052 GGTGTATCGAGTGATTCCACCAA 60.369 47.826 15.92 0.00 45.53 3.67
2570 3152 4.250464 GTGTATCGAGTGATTCCACCAAA 58.750 43.478 0.00 0.00 44.22 3.28
2571 3153 4.876107 GTGTATCGAGTGATTCCACCAAAT 59.124 41.667 0.00 0.00 44.22 2.32
2572 3154 4.875536 TGTATCGAGTGATTCCACCAAATG 59.124 41.667 0.00 0.00 44.22 2.32
2573 3155 2.083774 TCGAGTGATTCCACCAAATGC 58.916 47.619 0.00 0.00 44.22 3.56
2574 3156 1.811965 CGAGTGATTCCACCAAATGCA 59.188 47.619 0.00 0.00 44.22 3.96
2575 3157 2.228582 CGAGTGATTCCACCAAATGCAA 59.771 45.455 0.00 0.00 44.22 4.08
2576 3158 3.671433 CGAGTGATTCCACCAAATGCAAG 60.671 47.826 0.00 0.00 44.22 4.01
2577 3159 2.564062 AGTGATTCCACCAAATGCAAGG 59.436 45.455 0.00 0.00 44.22 3.61
2578 3160 2.562298 GTGATTCCACCAAATGCAAGGA 59.438 45.455 9.85 0.00 37.33 3.36
2579 3161 3.006752 GTGATTCCACCAAATGCAAGGAA 59.993 43.478 9.85 8.04 42.05 3.36
2580 3162 3.258872 TGATTCCACCAAATGCAAGGAAG 59.741 43.478 9.85 2.83 41.24 3.46
2581 3163 2.673775 TCCACCAAATGCAAGGAAGA 57.326 45.000 9.85 3.77 0.00 2.87
2582 3164 2.517959 TCCACCAAATGCAAGGAAGAG 58.482 47.619 9.85 0.00 0.00 2.85
2583 3165 2.158475 TCCACCAAATGCAAGGAAGAGT 60.158 45.455 9.85 0.00 0.00 3.24
2584 3166 2.029649 CCACCAAATGCAAGGAAGAGTG 60.030 50.000 9.85 3.06 0.00 3.51
2585 3167 2.624838 CACCAAATGCAAGGAAGAGTGT 59.375 45.455 9.85 0.00 0.00 3.55
2586 3168 2.887152 ACCAAATGCAAGGAAGAGTGTC 59.113 45.455 9.85 0.00 0.00 3.67
2587 3169 2.229784 CCAAATGCAAGGAAGAGTGTCC 59.770 50.000 0.00 0.00 38.03 4.02
2588 3170 2.886523 CAAATGCAAGGAAGAGTGTCCA 59.113 45.455 0.00 0.00 40.48 4.02
2589 3171 2.191128 ATGCAAGGAAGAGTGTCCAC 57.809 50.000 0.00 0.00 40.48 4.02
2590 3172 1.131638 TGCAAGGAAGAGTGTCCACT 58.868 50.000 0.00 0.00 45.84 4.00
2591 3173 1.490490 TGCAAGGAAGAGTGTCCACTT 59.510 47.619 0.79 0.00 42.66 3.16
2592 3174 1.876156 GCAAGGAAGAGTGTCCACTTG 59.124 52.381 0.79 0.00 42.66 3.16
2593 3175 1.876156 CAAGGAAGAGTGTCCACTTGC 59.124 52.381 0.79 0.00 42.66 4.01
2594 3176 1.131638 AGGAAGAGTGTCCACTTGCA 58.868 50.000 0.79 0.00 42.66 4.08
2617 3199 6.035327 GCAAAAATTCCACATATTGAGAGTGC 59.965 38.462 0.00 0.00 32.09 4.40
2625 3207 5.982516 CCACATATTGAGAGTGCTAAGAGAC 59.017 44.000 0.00 0.00 32.09 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.630644 AACAAGAGCTCTCCAATCTCAA 57.369 40.909 18.55 0.00 0.00 3.02
34 35 5.023533 TCAAGGAATCACGAGAATAAGGG 57.976 43.478 0.00 0.00 0.00 3.95
67 68 6.648310 CGATCTAGTTGTGGAGCATGAATTAT 59.352 38.462 0.00 0.00 0.00 1.28
83 84 4.537135 ATCCACACAACACGATCTAGTT 57.463 40.909 0.00 0.00 0.00 2.24
180 182 2.993471 GCCAATCCACAACCCGCAG 61.993 63.158 0.00 0.00 0.00 5.18
221 224 1.379309 GACGAGGAGGAGGCTCACT 60.379 63.158 17.69 10.95 0.00 3.41
355 362 0.107508 CCAGATGATGCGACCCTGTT 60.108 55.000 0.00 0.00 0.00 3.16
381 388 2.369532 TCCTACCGTGTAAACCTTGCTT 59.630 45.455 0.00 0.00 0.00 3.91
544 567 1.609208 AACAACAGCAGCTTCGGATT 58.391 45.000 0.00 0.00 0.00 3.01
567 596 6.966534 AAAGATCCAACAACAAGACTCAAT 57.033 33.333 0.00 0.00 0.00 2.57
847 929 2.159462 CGAATGAAAGGAAGGAAGCTGC 60.159 50.000 0.00 0.00 0.00 5.25
880 962 4.713553 TGTTGTGAGGAAGTAGCAATCAA 58.286 39.130 0.00 0.00 0.00 2.57
929 1012 2.029828 ACACTCAGCTCACCTTCTTACG 60.030 50.000 0.00 0.00 0.00 3.18
997 1091 1.001641 AGTTGGAGCCTGCCATGTC 60.002 57.895 0.00 0.00 37.86 3.06
1019 1113 6.554784 TCCATAATATTTCCTCCATGTGCAT 58.445 36.000 0.00 0.00 0.00 3.96
1072 1166 6.906157 ACTTTCTTCAATCACATCACCAAT 57.094 33.333 0.00 0.00 0.00 3.16
1146 1240 3.075283 TGTGTTGGTGTAGATCCCCATTT 59.925 43.478 0.00 0.00 0.00 2.32
1157 1251 2.428187 CGGGGCTGTGTTGGTGTA 59.572 61.111 0.00 0.00 0.00 2.90
1391 1486 1.968017 CCACCATGTGCAGCTCGTT 60.968 57.895 0.00 0.00 31.34 3.85
1457 1552 3.776417 TGACTCATCATCCACCATCTCAA 59.224 43.478 0.00 0.00 0.00 3.02
1561 1660 1.607148 GCGTAACTTCACCCTTGCTTT 59.393 47.619 0.00 0.00 0.00 3.51
1583 1682 6.267471 GTCCTCTTCTCTAGTGAATGATGGAT 59.733 42.308 7.65 0.00 0.00 3.41
1635 1735 9.452287 TGAGTATTGAAGATTTGATCACATCAA 57.548 29.630 20.98 12.98 46.77 2.57
1636 1736 9.623000 ATGAGTATTGAAGATTTGATCACATCA 57.377 29.630 20.98 5.32 37.55 3.07
1715 1815 0.598065 ATTCCACCAAGAAAGTGCGC 59.402 50.000 0.00 0.00 33.75 6.09
1716 1816 1.879380 TGATTCCACCAAGAAAGTGCG 59.121 47.619 0.00 0.00 33.75 5.34
1750 1850 2.912956 AGTCACCTCCCAAAGCAAGATA 59.087 45.455 0.00 0.00 0.00 1.98
1784 1884 6.825213 CCTCATGACTCTTTTCATTGTATCCA 59.175 38.462 0.00 0.00 33.74 3.41
1842 1942 3.146847 CCCCTTCAACCTCTTGTACAAC 58.853 50.000 3.59 0.00 0.00 3.32
1943 2043 4.564782 TCTCTCATCTTTGCTTCACCAT 57.435 40.909 0.00 0.00 0.00 3.55
1946 2046 6.740411 AAGAATCTCTCATCTTTGCTTCAC 57.260 37.500 0.00 0.00 32.05 3.18
2100 2202 4.954202 CCATGAAGGAGTAGTGGTACAGTA 59.046 45.833 0.00 0.00 41.21 2.74
2106 2208 1.556911 CTGCCATGAAGGAGTAGTGGT 59.443 52.381 0.00 0.00 41.22 4.16
2190 2292 5.735766 AGAATAAGCTCTACCTGAAACCAC 58.264 41.667 0.00 0.00 0.00 4.16
2200 2302 3.322541 GGGTGGAGGAGAATAAGCTCTAC 59.677 52.174 0.00 0.00 35.26 2.59
2202 2304 2.293184 TGGGTGGAGGAGAATAAGCTCT 60.293 50.000 0.00 0.00 35.26 4.09
2367 2870 6.042093 CCCCTCTTAGCACTCTAAATATGTGA 59.958 42.308 0.00 0.00 34.62 3.58
2376 2879 2.312140 ACTCACCCCTCTTAGCACTCTA 59.688 50.000 0.00 0.00 0.00 2.43
2381 2884 1.902508 CTCAACTCACCCCTCTTAGCA 59.097 52.381 0.00 0.00 0.00 3.49
2383 2886 3.056465 GTCACTCAACTCACCCCTCTTAG 60.056 52.174 0.00 0.00 0.00 2.18
2386 2889 1.133009 AGTCACTCAACTCACCCCTCT 60.133 52.381 0.00 0.00 0.00 3.69
2390 2893 1.048601 TGGAGTCACTCAACTCACCC 58.951 55.000 7.24 0.00 46.15 4.61
2393 2896 1.788229 TGGTGGAGTCACTCAACTCA 58.212 50.000 12.34 5.91 46.15 3.41
2430 2933 8.187913 TCAATATGTGGAATTTTTGGAAGTGA 57.812 30.769 0.00 0.00 0.00 3.41
2462 2965 3.572255 AGTCACTCAACTCACCTCTCTTC 59.428 47.826 0.00 0.00 0.00 2.87
2499 3080 9.996554 CAAATTTTAGGAAAATGTACCCTCTTT 57.003 29.630 0.00 0.00 40.05 2.52
2523 3105 9.201989 ACCACTCTTATCACTCTCAATATACAA 57.798 33.333 0.00 0.00 0.00 2.41
2524 3106 8.633561 CACCACTCTTATCACTCTCAATATACA 58.366 37.037 0.00 0.00 0.00 2.29
2525 3107 8.634444 ACACCACTCTTATCACTCTCAATATAC 58.366 37.037 0.00 0.00 0.00 1.47
2526 3108 8.768501 ACACCACTCTTATCACTCTCAATATA 57.231 34.615 0.00 0.00 0.00 0.86
2527 3109 7.667575 ACACCACTCTTATCACTCTCAATAT 57.332 36.000 0.00 0.00 0.00 1.28
2528 3110 8.768501 ATACACCACTCTTATCACTCTCAATA 57.231 34.615 0.00 0.00 0.00 1.90
2529 3111 7.469318 CGATACACCACTCTTATCACTCTCAAT 60.469 40.741 0.00 0.00 0.00 2.57
2530 3112 6.183360 CGATACACCACTCTTATCACTCTCAA 60.183 42.308 0.00 0.00 0.00 3.02
2531 3113 5.297029 CGATACACCACTCTTATCACTCTCA 59.703 44.000 0.00 0.00 0.00 3.27
2532 3114 5.527951 TCGATACACCACTCTTATCACTCTC 59.472 44.000 0.00 0.00 0.00 3.20
2533 3115 5.437946 TCGATACACCACTCTTATCACTCT 58.562 41.667 0.00 0.00 0.00 3.24
2534 3116 5.297278 ACTCGATACACCACTCTTATCACTC 59.703 44.000 0.00 0.00 0.00 3.51
2535 3117 5.066634 CACTCGATACACCACTCTTATCACT 59.933 44.000 0.00 0.00 0.00 3.41
2536 3118 5.066117 TCACTCGATACACCACTCTTATCAC 59.934 44.000 0.00 0.00 0.00 3.06
2537 3119 5.190677 TCACTCGATACACCACTCTTATCA 58.809 41.667 0.00 0.00 0.00 2.15
2538 3120 5.752892 TCACTCGATACACCACTCTTATC 57.247 43.478 0.00 0.00 0.00 1.75
2539 3121 6.239064 GGAATCACTCGATACACCACTCTTAT 60.239 42.308 0.00 0.00 0.00 1.73
2540 3122 5.067413 GGAATCACTCGATACACCACTCTTA 59.933 44.000 0.00 0.00 0.00 2.10
2541 3123 4.142138 GGAATCACTCGATACACCACTCTT 60.142 45.833 0.00 0.00 0.00 2.85
2542 3124 3.381908 GGAATCACTCGATACACCACTCT 59.618 47.826 0.00 0.00 0.00 3.24
2543 3125 3.130516 TGGAATCACTCGATACACCACTC 59.869 47.826 0.00 0.00 30.09 3.51
2544 3126 3.096852 TGGAATCACTCGATACACCACT 58.903 45.455 0.00 0.00 30.09 4.00
2545 3127 3.187700 GTGGAATCACTCGATACACCAC 58.812 50.000 0.00 0.00 40.15 4.16
2546 3128 3.520290 GTGGAATCACTCGATACACCA 57.480 47.619 0.00 0.00 40.58 4.17
2547 3129 2.822764 GGTGGAATCACTCGATACACC 58.177 52.381 1.64 1.64 45.15 4.16
2548 3130 3.520290 TGGTGGAATCACTCGATACAC 57.480 47.619 0.00 0.00 43.17 2.90
2549 3131 4.545208 TTTGGTGGAATCACTCGATACA 57.455 40.909 0.00 0.00 43.17 2.29
2550 3132 4.260784 GCATTTGGTGGAATCACTCGATAC 60.261 45.833 0.00 0.00 43.17 2.24
2551 3133 3.876914 GCATTTGGTGGAATCACTCGATA 59.123 43.478 0.00 0.00 43.17 2.92
2552 3134 2.684881 GCATTTGGTGGAATCACTCGAT 59.315 45.455 0.00 0.00 43.17 3.59
2553 3135 2.083774 GCATTTGGTGGAATCACTCGA 58.916 47.619 0.00 0.00 43.17 4.04
2554 3136 1.811965 TGCATTTGGTGGAATCACTCG 59.188 47.619 0.00 0.00 43.17 4.18
2555 3137 3.367703 CCTTGCATTTGGTGGAATCACTC 60.368 47.826 0.00 0.00 43.17 3.51
2556 3138 2.564062 CCTTGCATTTGGTGGAATCACT 59.436 45.455 0.00 0.00 43.17 3.41
2557 3139 2.562298 TCCTTGCATTTGGTGGAATCAC 59.438 45.455 0.00 0.00 37.53 3.06
2558 3140 2.886913 TCCTTGCATTTGGTGGAATCA 58.113 42.857 0.00 0.00 37.53 2.57
2559 3141 3.511146 TCTTCCTTGCATTTGGTGGAATC 59.489 43.478 0.00 0.00 37.53 2.52
2560 3142 3.509442 TCTTCCTTGCATTTGGTGGAAT 58.491 40.909 0.00 0.00 37.53 3.01
2561 3143 2.892852 CTCTTCCTTGCATTTGGTGGAA 59.107 45.455 0.00 0.00 36.65 3.53
2562 3144 2.158475 ACTCTTCCTTGCATTTGGTGGA 60.158 45.455 0.00 0.00 0.00 4.02
2563 3145 2.029649 CACTCTTCCTTGCATTTGGTGG 60.030 50.000 0.00 0.00 0.00 4.61
2564 3146 2.624838 ACACTCTTCCTTGCATTTGGTG 59.375 45.455 0.00 0.00 0.00 4.17
2565 3147 2.887152 GACACTCTTCCTTGCATTTGGT 59.113 45.455 0.00 0.00 0.00 3.67
2566 3148 2.229784 GGACACTCTTCCTTGCATTTGG 59.770 50.000 0.00 0.00 32.24 3.28
2567 3149 2.886523 TGGACACTCTTCCTTGCATTTG 59.113 45.455 0.00 0.00 36.51 2.32
2568 3150 2.887152 GTGGACACTCTTCCTTGCATTT 59.113 45.455 0.00 0.00 36.51 2.32
2569 3151 2.107204 AGTGGACACTCTTCCTTGCATT 59.893 45.455 0.00 0.00 36.92 3.56
2570 3152 1.701847 AGTGGACACTCTTCCTTGCAT 59.298 47.619 0.00 0.00 36.92 3.96
2571 3153 1.131638 AGTGGACACTCTTCCTTGCA 58.868 50.000 0.00 0.00 36.92 4.08
2572 3154 1.876156 CAAGTGGACACTCTTCCTTGC 59.124 52.381 5.30 0.00 41.58 4.01
2573 3155 1.876156 GCAAGTGGACACTCTTCCTTG 59.124 52.381 5.30 0.64 41.58 3.61
2574 3156 1.490490 TGCAAGTGGACACTCTTCCTT 59.510 47.619 5.30 0.00 41.58 3.36
2575 3157 1.131638 TGCAAGTGGACACTCTTCCT 58.868 50.000 5.30 0.00 41.58 3.36
2576 3158 1.967319 TTGCAAGTGGACACTCTTCC 58.033 50.000 5.30 0.00 41.58 3.46
2577 3159 4.370364 TTTTTGCAAGTGGACACTCTTC 57.630 40.909 5.30 0.00 41.58 2.87
2578 3160 5.343307 AATTTTTGCAAGTGGACACTCTT 57.657 34.783 5.30 0.00 41.58 2.85
2579 3161 4.202151 GGAATTTTTGCAAGTGGACACTCT 60.202 41.667 5.30 0.00 41.58 3.24
2580 3162 4.051237 GGAATTTTTGCAAGTGGACACTC 58.949 43.478 5.30 0.00 41.58 3.51
2581 3163 3.450457 TGGAATTTTTGCAAGTGGACACT 59.550 39.130 0.00 0.00 44.94 3.55
2582 3164 3.555547 GTGGAATTTTTGCAAGTGGACAC 59.444 43.478 0.00 3.08 30.97 3.67
2583 3165 3.196469 TGTGGAATTTTTGCAAGTGGACA 59.804 39.130 0.00 0.00 30.97 4.02
2584 3166 3.791245 TGTGGAATTTTTGCAAGTGGAC 58.209 40.909 0.00 0.00 30.97 4.02
2585 3167 4.686191 ATGTGGAATTTTTGCAAGTGGA 57.314 36.364 0.00 0.00 30.97 4.02
2586 3168 6.649973 TCAATATGTGGAATTTTTGCAAGTGG 59.350 34.615 0.00 0.00 30.97 4.00
2587 3169 7.599621 TCTCAATATGTGGAATTTTTGCAAGTG 59.400 33.333 0.00 0.00 30.97 3.16
2588 3170 7.669427 TCTCAATATGTGGAATTTTTGCAAGT 58.331 30.769 0.00 0.00 30.97 3.16
2589 3171 7.816031 ACTCTCAATATGTGGAATTTTTGCAAG 59.184 33.333 0.00 0.00 30.97 4.01
2590 3172 7.599621 CACTCTCAATATGTGGAATTTTTGCAA 59.400 33.333 0.00 0.00 30.97 4.08
2591 3173 7.092079 CACTCTCAATATGTGGAATTTTTGCA 58.908 34.615 0.00 0.00 0.00 4.08
2592 3174 6.035327 GCACTCTCAATATGTGGAATTTTTGC 59.965 38.462 0.00 0.00 32.85 3.68
2593 3175 7.318141 AGCACTCTCAATATGTGGAATTTTTG 58.682 34.615 0.00 0.00 32.85 2.44
2594 3176 7.472334 AGCACTCTCAATATGTGGAATTTTT 57.528 32.000 0.00 0.00 32.85 1.94


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

AutoCloner maintained by Alex Coulton.