Multiple sequence alignment - TraesCS4D01G240900

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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 TraesCS4D01G240900 chr4D 100.000 3575 0 0 1 3575 403198766 403202340 0.000000e+00 6602.0
1 TraesCS4D01G240900 chr4D 87.460 1882 180 36 803 2656 403181965 403183818 0.000000e+00 2117.0
2 TraesCS4D01G240900 chr4B 92.252 2607 159 25 976 3575 500079122 500081692 0.000000e+00 3655.0
3 TraesCS4D01G240900 chr4B 88.711 1807 164 19 866 2656 500052695 500054477 0.000000e+00 2170.0
4 TraesCS4D01G240900 chr4B 90.244 451 23 7 173 605 500076287 500076734 1.440000e-158 569.0
5 TraesCS4D01G240900 chr4B 84.034 357 26 15 594 931 500078770 500079114 7.450000e-82 315.0
6 TraesCS4D01G240900 chr4B 89.706 136 13 1 46 180 500076040 500076175 4.750000e-39 172.0
7 TraesCS4D01G240900 chr4B 76.879 346 55 16 2733 3070 663103342 663103670 4.750000e-39 172.0
8 TraesCS4D01G240900 chr4A 92.410 2108 100 20 711 2796 60879694 60881763 0.000000e+00 2952.0
9 TraesCS4D01G240900 chr4A 88.598 1798 168 19 866 2651 60730374 60732146 0.000000e+00 2150.0
10 TraesCS4D01G240900 chr4A 82.938 211 18 6 3379 3572 60882665 60882874 1.320000e-39 174.0
11 TraesCS4D01G240900 chr4A 80.435 230 22 5 2786 3015 60882462 60882668 1.720000e-33 154.0
12 TraesCS4D01G240900 chr4A 84.672 137 18 3 46 180 153457350 153457485 2.240000e-27 134.0
13 TraesCS4D01G240900 chr4A 95.349 43 1 1 608 650 60739320 60739361 2.300000e-07 67.6
14 TraesCS4D01G240900 chr2D 87.397 1460 157 14 1120 2567 645838270 645839714 0.000000e+00 1652.0
15 TraesCS4D01G240900 chr2A 85.923 1577 173 29 996 2561 771538641 771540179 0.000000e+00 1637.0
16 TraesCS4D01G240900 chr2B 87.475 495 62 0 1120 1614 789672745 789673239 4.000000e-159 571.0
17 TraesCS4D01G240900 chr2B 89.600 250 23 1 2317 2563 789673367 789673616 7.450000e-82 315.0
18 TraesCS4D01G240900 chr2B 85.124 121 16 2 2869 2988 25810213 25810332 4.850000e-24 122.0
19 TraesCS4D01G240900 chr3D 77.551 637 105 32 1860 2484 438435618 438436228 2.040000e-92 350.0
20 TraesCS4D01G240900 chr3A 77.936 562 97 23 1930 2484 576683173 576683714 3.440000e-85 326.0
21 TraesCS4D01G240900 chr5A 82.428 313 39 10 2764 3069 559739184 559738881 3.540000e-65 259.0
22 TraesCS4D01G240900 chr5A 88.889 117 12 1 195 311 470763226 470763341 3.720000e-30 143.0
23 TraesCS4D01G240900 chr7D 84.151 265 35 7 2769 3028 204256281 204256019 2.130000e-62 250.0
24 TraesCS4D01G240900 chr7A 83.394 277 29 9 173 434 597528572 597528298 1.280000e-59 241.0
25 TraesCS4D01G240900 chr7A 79.741 232 37 7 2769 2999 36394516 36394294 3.690000e-35 159.0
26 TraesCS4D01G240900 chr5D 81.433 307 39 10 2772 3069 443498429 443498132 5.970000e-58 235.0
27 TraesCS4D01G240900 chr5B 80.645 310 42 11 2769 3069 539929181 539928881 1.290000e-54 224.0
28 TraesCS4D01G240900 chr3B 82.949 217 29 5 2784 2999 71334176 71334385 4.710000e-44 189.0
29 TraesCS4D01G240900 chr6D 87.943 141 14 3 173 311 25367581 25367442 2.860000e-36 163.0
30 TraesCS4D01G240900 chr1A 88.889 117 12 1 195 311 577988995 577988880 3.720000e-30 143.0
31 TraesCS4D01G240900 chr1A 87.324 71 9 0 2771 2841 432632160 432632230 8.230000e-12 82.4
32 TraesCS4D01G240900 chr6A 87.179 117 12 3 195 311 408021524 408021411 2.900000e-26 130.0


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 TraesCS4D01G240900 chr4D 403198766 403202340 3574 False 6602.000000 6602 100.0000 1 3575 1 chr4D.!!$F2 3574
1 TraesCS4D01G240900 chr4D 403181965 403183818 1853 False 2117.000000 2117 87.4600 803 2656 1 chr4D.!!$F1 1853
2 TraesCS4D01G240900 chr4B 500052695 500054477 1782 False 2170.000000 2170 88.7110 866 2656 1 chr4B.!!$F1 1790
3 TraesCS4D01G240900 chr4B 500076040 500081692 5652 False 1177.750000 3655 89.0590 46 3575 4 chr4B.!!$F3 3529
4 TraesCS4D01G240900 chr4A 60730374 60732146 1772 False 2150.000000 2150 88.5980 866 2651 1 chr4A.!!$F1 1785
5 TraesCS4D01G240900 chr4A 60879694 60882874 3180 False 1093.333333 2952 85.2610 711 3572 3 chr4A.!!$F4 2861
6 TraesCS4D01G240900 chr2D 645838270 645839714 1444 False 1652.000000 1652 87.3970 1120 2567 1 chr2D.!!$F1 1447
7 TraesCS4D01G240900 chr2A 771538641 771540179 1538 False 1637.000000 1637 85.9230 996 2561 1 chr2A.!!$F1 1565
8 TraesCS4D01G240900 chr2B 789672745 789673616 871 False 443.000000 571 88.5375 1120 2563 2 chr2B.!!$F2 1443
9 TraesCS4D01G240900 chr3D 438435618 438436228 610 False 350.000000 350 77.5510 1860 2484 1 chr3D.!!$F1 624
10 TraesCS4D01G240900 chr3A 576683173 576683714 541 False 326.000000 326 77.9360 1930 2484 1 chr3A.!!$F1 554

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
653 2840 0.179189 GAAGTTACGTGCATGCTGCC 60.179 55.0 20.33 5.89 44.23 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2576 4899 0.458543 CCCTCCATCTTGTCGTCGTG 60.459 60.0 0.0 0.0 0.0 4.35 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
22 23 5.663795 CATCATCTTCGATTTCGTTGGAT 57.336 39.130 0.00 0.75 40.80 3.41
23 24 5.674008 CATCATCTTCGATTTCGTTGGATC 58.326 41.667 0.00 0.00 40.80 3.36
24 25 4.119862 TCATCTTCGATTTCGTTGGATCC 58.880 43.478 4.20 4.20 40.80 3.36
25 26 3.603158 TCTTCGATTTCGTTGGATCCA 57.397 42.857 11.44 11.44 40.80 3.41
26 27 3.932822 TCTTCGATTTCGTTGGATCCAA 58.067 40.909 23.63 23.63 40.80 3.53
39 40 4.591321 TGGATCCAACCTAAATTCTGCT 57.409 40.909 13.46 0.00 0.00 4.24
40 41 5.708736 TGGATCCAACCTAAATTCTGCTA 57.291 39.130 13.46 0.00 0.00 3.49
41 42 5.684704 TGGATCCAACCTAAATTCTGCTAG 58.315 41.667 13.46 0.00 0.00 3.42
42 43 5.191722 TGGATCCAACCTAAATTCTGCTAGT 59.808 40.000 13.46 0.00 0.00 2.57
43 44 6.385759 TGGATCCAACCTAAATTCTGCTAGTA 59.614 38.462 13.46 0.00 0.00 1.82
44 45 6.706716 GGATCCAACCTAAATTCTGCTAGTAC 59.293 42.308 6.95 0.00 0.00 2.73
70 71 0.321298 TTTGCTGGAACCCGCTCTAC 60.321 55.000 8.53 0.00 0.00 2.59
84 85 3.002656 CCGCTCTACATTTTGCTACCATG 59.997 47.826 0.00 0.00 0.00 3.66
125 126 6.294843 GGATCCAACCTAGATTCTGCTACTAC 60.295 46.154 6.95 0.00 0.00 2.73
132 133 6.377712 ACCTAGATTCTGCTACTACGTTTCTT 59.622 38.462 0.00 0.00 0.00 2.52
155 156 2.719531 TGCTGGAACAAGTGTACCAA 57.280 45.000 0.00 0.00 38.70 3.67
166 167 6.969993 ACAAGTGTACCAATTTGTTACCAT 57.030 33.333 2.15 0.00 30.05 3.55
170 171 7.391148 AGTGTACCAATTTGTTACCATCATC 57.609 36.000 2.15 0.00 0.00 2.92
201 324 1.225855 TGAGGTTGCACAATCGTGAC 58.774 50.000 0.00 0.00 46.80 3.67
205 328 3.674997 AGGTTGCACAATCGTGACTATT 58.325 40.909 0.00 0.00 46.80 1.73
243 366 7.484959 GCAACCATTACTGATTTTTGCTACTAC 59.515 37.037 0.00 0.00 35.95 2.73
246 369 6.238374 CCATTACTGATTTTTGCTACTACGGG 60.238 42.308 0.00 0.00 0.00 5.28
247 370 4.546829 ACTGATTTTTGCTACTACGGGA 57.453 40.909 0.00 0.00 0.00 5.14
248 371 4.504858 ACTGATTTTTGCTACTACGGGAG 58.495 43.478 0.00 0.00 0.00 4.30
275 406 1.835927 GAGCCTGGACCAGAAGCTGT 61.836 60.000 24.79 7.01 31.23 4.40
283 414 2.287849 GGACCAGAAGCTGTTTTTGAGC 60.288 50.000 0.00 0.00 36.65 4.26
305 436 3.000277 CGTTTCTGCGATTTTTGTTGCAA 60.000 39.130 0.00 0.00 38.01 4.08
308 439 1.189884 CTGCGATTTTTGTTGCAACCG 59.810 47.619 26.14 20.58 38.01 4.44
325 456 2.356194 GGCACCCGCAAAAGCTTG 60.356 61.111 0.00 0.00 41.24 4.01
326 457 2.727544 GCACCCGCAAAAGCTTGA 59.272 55.556 0.00 0.00 38.36 3.02
327 458 1.661509 GCACCCGCAAAAGCTTGAC 60.662 57.895 0.00 0.00 38.36 3.18
328 459 1.732917 CACCCGCAAAAGCTTGACA 59.267 52.632 0.00 0.00 34.14 3.58
329 460 0.314935 CACCCGCAAAAGCTTGACAT 59.685 50.000 0.00 0.00 34.14 3.06
358 497 2.291365 TGCTACCATGTAAGCTGCATG 58.709 47.619 19.11 19.11 42.29 4.06
370 509 1.746615 CTGCATGCGGCTGTTAGGT 60.747 57.895 14.81 0.00 45.15 3.08
462 601 4.681978 GCGACGGGACCTGCAAGT 62.682 66.667 0.00 0.00 0.00 3.16
511 650 1.153061 GGGCTAGGGGGCATTTACC 59.847 63.158 0.00 0.00 42.84 2.85
553 692 3.117372 GCGAGAGGTAGCGGCTTA 58.883 61.111 8.26 0.00 0.00 3.09
556 695 1.931263 GCGAGAGGTAGCGGCTTAATC 60.931 57.143 8.26 3.81 0.00 1.75
639 2826 3.142174 GGTTGCAGCTCTAGTTGAAGTT 58.858 45.455 0.00 0.00 0.00 2.66
650 2837 2.494059 AGTTGAAGTTACGTGCATGCT 58.506 42.857 20.33 0.40 0.00 3.79
651 2838 2.224079 AGTTGAAGTTACGTGCATGCTG 59.776 45.455 20.33 13.87 0.00 4.41
652 2839 0.516877 TGAAGTTACGTGCATGCTGC 59.483 50.000 20.33 10.84 45.29 5.25
653 2840 0.179189 GAAGTTACGTGCATGCTGCC 60.179 55.000 20.33 5.89 44.23 4.85
654 2841 1.586154 AAGTTACGTGCATGCTGCCC 61.586 55.000 20.33 3.29 44.23 5.36
683 2877 7.698550 CACGCCTTAGCTACTATACATATCAAG 59.301 40.741 0.00 0.00 36.60 3.02
725 2934 8.439971 TGCATGTATAAACAAATATCTCTCCCT 58.560 33.333 0.00 0.00 39.58 4.20
731 2940 4.810191 ACAAATATCTCTCCCTATCCGC 57.190 45.455 0.00 0.00 0.00 5.54
757 2971 4.675404 ACGGAGTTCAGCGGAAAG 57.325 55.556 0.00 0.00 37.78 2.62
761 2975 2.034221 AGTTCAGCGGAAAGGGCC 59.966 61.111 0.00 0.00 34.13 5.80
798 3012 0.881118 GAAGTTCCCATTTCGCAGCA 59.119 50.000 0.00 0.00 0.00 4.41
799 3013 1.269448 GAAGTTCCCATTTCGCAGCAA 59.731 47.619 0.00 0.00 0.00 3.91
800 3014 0.598065 AGTTCCCATTTCGCAGCAAC 59.402 50.000 0.00 0.00 0.00 4.17
801 3015 0.729140 GTTCCCATTTCGCAGCAACG 60.729 55.000 0.00 0.00 0.00 4.10
851 3065 0.861837 GTCAGCACAAGAACTCACCG 59.138 55.000 0.00 0.00 0.00 4.94
932 3166 3.564225 CCTTCACCTACACTCCACAAAAC 59.436 47.826 0.00 0.00 0.00 2.43
934 3168 2.506231 TCACCTACACTCCACAAAACCA 59.494 45.455 0.00 0.00 0.00 3.67
935 3169 3.054287 TCACCTACACTCCACAAAACCAA 60.054 43.478 0.00 0.00 0.00 3.67
936 3170 3.697045 CACCTACACTCCACAAAACCAAA 59.303 43.478 0.00 0.00 0.00 3.28
937 3171 3.697542 ACCTACACTCCACAAAACCAAAC 59.302 43.478 0.00 0.00 0.00 2.93
938 3172 3.067601 CCTACACTCCACAAAACCAAACC 59.932 47.826 0.00 0.00 0.00 3.27
939 3173 2.530701 ACACTCCACAAAACCAAACCA 58.469 42.857 0.00 0.00 0.00 3.67
940 3174 2.900546 ACACTCCACAAAACCAAACCAA 59.099 40.909 0.00 0.00 0.00 3.67
941 3175 3.056179 ACACTCCACAAAACCAAACCAAG 60.056 43.478 0.00 0.00 0.00 3.61
971 3205 2.668144 AAACCCCACGAATTTCCTCA 57.332 45.000 0.00 0.00 0.00 3.86
1047 3295 1.339610 CTGATACCGCTCTTCTCCCTG 59.660 57.143 0.00 0.00 0.00 4.45
1429 3689 1.602165 CCAGCTACGAGTTCAACACGT 60.602 52.381 17.21 17.21 46.35 4.49
1437 3697 1.201825 GTTCAACACGTGCTCGCTC 59.798 57.895 17.22 0.00 41.18 5.03
1541 3801 1.000993 AGCTCGACCTCCAGGACAT 59.999 57.895 0.00 0.00 38.94 3.06
1653 3949 2.578178 CCAGAAGTCGAGAGCGCG 60.578 66.667 0.00 0.00 37.46 6.86
1927 4229 1.360194 CGAGAGCTACACCGAGACGT 61.360 60.000 0.00 0.00 0.00 4.34
2287 4594 2.842058 CCATGGGGAGGATGGAGC 59.158 66.667 2.85 0.00 42.81 4.70
2576 4899 3.620821 GTGAAGGCTAGAGTGAATTGAGC 59.379 47.826 0.00 0.00 0.00 4.26
2669 4994 9.512435 GAAAGATGAATTCCAGAATACACAATG 57.488 33.333 2.27 0.00 0.00 2.82
2714 5042 1.816074 TTCTACGCCCACCAACATTC 58.184 50.000 0.00 0.00 0.00 2.67
2727 5055 1.135603 CAACATTCCACCTGATGCACG 60.136 52.381 0.00 0.00 0.00 5.34
2729 5057 2.108514 ATTCCACCTGATGCACGCG 61.109 57.895 3.53 3.53 0.00 6.01
2745 5073 0.229753 CGCGTGATCGGAAACATAGC 59.770 55.000 0.00 0.00 37.56 2.97
2746 5074 1.286501 GCGTGATCGGAAACATAGCA 58.713 50.000 0.00 0.00 37.56 3.49
2749 5077 3.425625 GCGTGATCGGAAACATAGCAAAA 60.426 43.478 0.00 0.00 37.56 2.44
2853 5889 0.951558 GACATCCGAGGAGCTCTCTC 59.048 60.000 14.64 16.43 40.30 3.20
2867 5903 6.324561 GAGCTCTCTCCAAAGAACAATTTT 57.675 37.500 6.43 0.00 33.19 1.82
2868 5904 6.721704 AGCTCTCTCCAAAGAACAATTTTT 57.278 33.333 0.00 0.00 0.00 1.94
2876 5913 6.347696 TCCAAAGAACAATTTTTGTGCTCAT 58.652 32.000 1.43 0.00 46.78 2.90
2879 5916 3.737266 AGAACAATTTTTGTGCTCATGCG 59.263 39.130 0.00 0.00 46.78 4.73
2910 5947 7.169645 TGCACTTTCAAGCAGAATTTGTATTTC 59.830 33.333 0.00 0.00 35.83 2.17
2912 5949 6.863126 ACTTTCAAGCAGAATTTGTATTTCGG 59.137 34.615 0.00 0.00 35.83 4.30
2915 5952 6.744112 TCAAGCAGAATTTGTATTTCGGTTT 58.256 32.000 0.00 0.00 0.00 3.27
2916 5953 6.640499 TCAAGCAGAATTTGTATTTCGGTTTG 59.360 34.615 6.74 6.74 39.21 2.93
2917 5954 6.084326 AGCAGAATTTGTATTTCGGTTTGT 57.916 33.333 0.00 0.00 0.00 2.83
2918 5955 7.209471 AGCAGAATTTGTATTTCGGTTTGTA 57.791 32.000 0.00 0.00 0.00 2.41
2919 5956 7.081976 AGCAGAATTTGTATTTCGGTTTGTAC 58.918 34.615 0.00 0.00 0.00 2.90
2920 5957 6.858993 GCAGAATTTGTATTTCGGTTTGTACA 59.141 34.615 0.00 0.00 0.00 2.90
2959 5996 1.145819 GGCCACCAAGCTTTGCAAA 59.854 52.632 12.14 12.14 0.00 3.68
2990 6027 8.851541 AAAACATTTGTTCATAATCAATGCCT 57.148 26.923 0.00 0.00 37.25 4.75
2999 6036 8.149647 TGTTCATAATCAATGCCTTGAAGTTTT 58.850 29.630 8.55 1.59 44.29 2.43
3003 6040 9.294030 CATAATCAATGCCTTGAAGTTTTAGAC 57.706 33.333 8.55 0.00 44.29 2.59
3004 6041 7.530426 AATCAATGCCTTGAAGTTTTAGACT 57.470 32.000 8.55 0.00 44.29 3.24
3053 6090 2.198827 TGTGGGTACAATGAGCTTGG 57.801 50.000 0.00 0.00 39.30 3.61
3059 6096 3.307480 GGGTACAATGAGCTTGGTGTAGT 60.307 47.826 0.00 0.00 39.30 2.73
3131 6169 0.610785 GAACCCGGCTTCCATTTGGA 60.611 55.000 0.00 0.00 43.73 3.53
3150 6188 2.093128 GGAAGAGAAAAGCGTATGGGGA 60.093 50.000 0.00 0.00 0.00 4.81
3155 6193 4.007659 GAGAAAAGCGTATGGGGAAAAGA 58.992 43.478 0.00 0.00 0.00 2.52
3229 6268 6.817140 AGTCGGCTAAAATAAGTAAGAAGTGG 59.183 38.462 0.00 0.00 0.00 4.00
3240 6279 5.695851 AGTAAGAAGTGGAGTGCAAATTG 57.304 39.130 0.00 0.00 0.00 2.32
3241 6280 5.133221 AGTAAGAAGTGGAGTGCAAATTGT 58.867 37.500 0.00 0.00 0.00 2.71
3282 6321 8.255111 AGAATCATATTCATCAGACACAGGTA 57.745 34.615 2.74 0.00 0.00 3.08
3328 6367 8.636843 CGTACAAATAGTTCTAACACAGTCTTC 58.363 37.037 0.00 0.00 0.00 2.87
3329 6368 7.639162 ACAAATAGTTCTAACACAGTCTTCG 57.361 36.000 0.00 0.00 0.00 3.79
3333 6372 5.707242 AGTTCTAACACAGTCTTCGATGA 57.293 39.130 0.00 0.00 0.00 2.92
3433 6473 0.109723 ACCTGCGCCCTAAAGTTGAA 59.890 50.000 4.18 0.00 0.00 2.69
3446 6486 1.745232 AGTTGAAAGTTGGACACGCA 58.255 45.000 0.00 0.00 0.00 5.24
3453 6493 2.254546 AGTTGGACACGCATCTTCAA 57.745 45.000 0.00 0.00 0.00 2.69
3458 6498 2.076100 GGACACGCATCTTCAATGTCA 58.924 47.619 5.18 0.00 41.18 3.58
3500 6540 0.622665 CCAGGTGCCTTGAGGAGAAT 59.377 55.000 0.06 0.00 37.39 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.333645 GGATCCAACGAAATCGAAGATGATG 60.334 44.000 6.95 0.00 45.12 3.07
1 2 4.752101 GGATCCAACGAAATCGAAGATGAT 59.248 41.667 6.95 4.24 45.12 2.45
2 3 4.119862 GGATCCAACGAAATCGAAGATGA 58.880 43.478 6.95 0.00 45.12 2.92
3 4 3.871006 TGGATCCAACGAAATCGAAGATG 59.129 43.478 13.46 3.30 45.12 2.90
4 5 4.137116 TGGATCCAACGAAATCGAAGAT 57.863 40.909 13.46 8.03 45.12 2.40
6 7 4.003519 GTTGGATCCAACGAAATCGAAG 57.996 45.455 35.47 1.37 45.24 3.79
17 18 4.934356 AGCAGAATTTAGGTTGGATCCAA 58.066 39.130 23.63 23.63 0.00 3.53
18 19 4.591321 AGCAGAATTTAGGTTGGATCCA 57.409 40.909 11.44 11.44 0.00 3.41
19 20 5.685728 ACTAGCAGAATTTAGGTTGGATCC 58.314 41.667 4.20 4.20 0.00 3.36
20 21 6.421202 CGTACTAGCAGAATTTAGGTTGGATC 59.579 42.308 0.00 0.00 0.00 3.36
21 22 6.127140 ACGTACTAGCAGAATTTAGGTTGGAT 60.127 38.462 0.00 0.00 0.00 3.41
22 23 5.186409 ACGTACTAGCAGAATTTAGGTTGGA 59.814 40.000 0.00 0.00 0.00 3.53
23 24 5.416947 ACGTACTAGCAGAATTTAGGTTGG 58.583 41.667 0.00 0.00 0.00 3.77
24 25 6.963049 AACGTACTAGCAGAATTTAGGTTG 57.037 37.500 0.00 0.00 0.00 3.77
25 26 7.974482 AAAACGTACTAGCAGAATTTAGGTT 57.026 32.000 0.00 0.00 0.00 3.50
26 27 7.974482 AAAAACGTACTAGCAGAATTTAGGT 57.026 32.000 0.00 0.00 0.00 3.08
55 56 2.403252 AAATGTAGAGCGGGTTCCAG 57.597 50.000 0.00 0.00 0.00 3.86
63 64 3.002656 CCATGGTAGCAAAATGTAGAGCG 59.997 47.826 2.57 0.00 0.00 5.03
64 65 3.947834 ACCATGGTAGCAAAATGTAGAGC 59.052 43.478 18.10 0.00 0.00 4.09
70 71 3.689161 TCGAAGACCATGGTAGCAAAATG 59.311 43.478 19.80 2.81 0.00 2.32
84 85 3.756434 TGGATCCAACAAAATCGAAGACC 59.244 43.478 13.46 0.00 42.51 3.85
132 133 3.764434 TGGTACACTTGTTCCAGCAAAAA 59.236 39.130 3.74 0.00 39.98 1.94
166 167 5.047802 GCAACCTCATGAAAAAGGAAGATGA 60.048 40.000 5.76 0.00 36.46 2.92
170 171 4.202141 TGTGCAACCTCATGAAAAAGGAAG 60.202 41.667 5.76 0.00 36.46 3.46
213 336 3.492421 AAATCAGTAATGGTTGCAGCG 57.508 42.857 0.00 0.00 0.00 5.18
223 346 6.646267 TCCCGTAGTAGCAAAAATCAGTAAT 58.354 36.000 0.00 0.00 0.00 1.89
224 347 6.040209 TCCCGTAGTAGCAAAAATCAGTAA 57.960 37.500 0.00 0.00 0.00 2.24
246 369 4.168291 CCAGGCTCGGGGCTTCTC 62.168 72.222 9.54 0.00 46.62 2.87
247 370 4.722535 TCCAGGCTCGGGGCTTCT 62.723 66.667 9.54 0.00 46.62 2.85
248 371 4.475135 GTCCAGGCTCGGGGCTTC 62.475 72.222 9.54 0.00 46.62 3.86
260 391 2.951642 TCAAAAACAGCTTCTGGTCCAG 59.048 45.455 13.21 13.21 35.51 3.86
261 392 2.951642 CTCAAAAACAGCTTCTGGTCCA 59.048 45.455 0.00 0.00 35.51 4.02
275 406 3.347958 AATCGCAGAAACGCTCAAAAA 57.652 38.095 0.00 0.00 43.58 1.94
283 414 2.533535 TGCAACAAAAATCGCAGAAACG 59.466 40.909 0.00 0.00 43.58 3.60
358 497 1.359459 CGAGGAAACCTAACAGCCGC 61.359 60.000 0.00 0.00 31.76 6.53
391 530 2.032634 CAGCTCGCCGGTAGCAAAA 61.033 57.895 26.23 0.00 44.04 2.44
462 601 2.747686 GCCCCAAGTTGTCTCCGA 59.252 61.111 1.45 0.00 0.00 4.55
473 612 1.899437 CTACTTGCTCCTCGCCCCAA 61.899 60.000 0.00 0.00 38.05 4.12
490 629 0.272543 TAAATGCCCCCTAGCCCCTA 59.727 55.000 0.00 0.00 0.00 3.53
511 650 0.798771 CGGTCTTCTTCTTCCTCGCG 60.799 60.000 0.00 0.00 0.00 5.87
579 718 2.655364 CACTGATAGGCGCCGTCG 60.655 66.667 23.20 19.54 39.07 5.12
580 719 2.279517 CCACTGATAGGCGCCGTC 60.280 66.667 23.20 23.05 0.00 4.79
581 720 4.530857 GCCACTGATAGGCGCCGT 62.531 66.667 23.20 14.73 43.15 5.68
652 2839 3.845259 TAGCTAAGGCGTGCGGGG 61.845 66.667 0.00 0.00 44.37 5.73
653 2840 1.731433 TAGTAGCTAAGGCGTGCGGG 61.731 60.000 0.00 0.00 44.37 6.13
654 2841 0.314302 ATAGTAGCTAAGGCGTGCGG 59.686 55.000 0.00 0.00 44.37 5.69
683 2877 2.096442 GCAGCCGGCATTTCTTTGC 61.096 57.895 31.54 23.61 43.97 3.68
705 2899 8.475639 GCGGATAGGGAGAGATATTTGTTTATA 58.524 37.037 0.00 0.00 0.00 0.98
725 2934 1.066752 CCGTCACATTCGGCGGATA 59.933 57.895 7.21 0.00 46.33 2.59
798 3012 2.432628 GTCTGCCGCAGCTACGTT 60.433 61.111 15.98 0.00 40.80 3.99
799 3013 4.436998 GGTCTGCCGCAGCTACGT 62.437 66.667 15.98 0.00 40.80 3.57
932 3166 1.755179 ATCTCCATCGCTTGGTTTGG 58.245 50.000 4.43 0.00 46.52 3.28
934 3168 3.694566 GGTTTATCTCCATCGCTTGGTTT 59.305 43.478 4.43 0.00 46.52 3.27
935 3169 3.279434 GGTTTATCTCCATCGCTTGGTT 58.721 45.455 4.43 0.00 46.52 3.67
936 3170 2.421529 GGGTTTATCTCCATCGCTTGGT 60.422 50.000 4.43 0.00 46.52 3.67
937 3171 5.578615 TGGGGTTTATCTCCATCGCTTGG 62.579 52.174 0.00 0.00 42.62 3.61
938 3172 2.222027 GGGGTTTATCTCCATCGCTTG 58.778 52.381 0.00 0.00 36.51 4.01
939 3173 1.843851 TGGGGTTTATCTCCATCGCTT 59.156 47.619 0.00 0.00 42.62 4.68
940 3174 1.507140 TGGGGTTTATCTCCATCGCT 58.493 50.000 0.00 0.00 42.62 4.93
971 3205 1.755380 GCTGGATTCTACCTACCGTGT 59.245 52.381 0.00 0.00 0.00 4.49
1047 3295 3.991536 GAGGACGAAGACTGCGCCC 62.992 68.421 4.18 0.08 0.00 6.13
1075 3323 2.437343 GCGCCTTCTTGTCGAGTCG 61.437 63.158 6.09 6.09 0.00 4.18
1260 3520 4.324991 AGGTTGGTCGGGTTCGCC 62.325 66.667 0.00 0.00 36.13 5.54
1634 3906 2.202676 CGCTCTCGACTTCTGGGC 60.203 66.667 0.00 0.00 38.10 5.36
1635 3907 2.202676 GCGCTCTCGACTTCTGGG 60.203 66.667 0.00 0.00 38.10 4.45
1636 3908 2.578178 CGCGCTCTCGACTTCTGG 60.578 66.667 5.56 0.00 38.10 3.86
1637 3909 2.578178 CCGCGCTCTCGACTTCTG 60.578 66.667 5.56 0.00 38.10 3.02
1638 3910 4.484258 GCCGCGCTCTCGACTTCT 62.484 66.667 5.56 0.00 38.10 2.85
1927 4229 4.631773 CACTACGTCTCGGAGGGA 57.368 61.111 4.96 0.00 45.26 4.20
1983 4285 1.004440 GAAGAACCAGGTGAGCGCT 60.004 57.895 11.27 11.27 0.00 5.92
2077 4379 1.226717 GTCTGCCGAGATCACCGAC 60.227 63.158 8.78 0.00 0.00 4.79
2518 4841 3.418913 CGCCATCCGCAACGTCAA 61.419 61.111 0.00 0.00 37.30 3.18
2576 4899 0.458543 CCCTCCATCTTGTCGTCGTG 60.459 60.000 0.00 0.00 0.00 4.35
2669 4994 4.715713 ACCACTCTCCTAAGAAAAACACC 58.284 43.478 0.00 0.00 0.00 4.16
2696 5024 0.035820 GGAATGTTGGTGGGCGTAGA 60.036 55.000 0.00 0.00 0.00 2.59
2707 5035 1.135603 CGTGCATCAGGTGGAATGTTG 60.136 52.381 0.00 0.00 0.00 3.33
2708 5036 1.167851 CGTGCATCAGGTGGAATGTT 58.832 50.000 0.00 0.00 0.00 2.71
2714 5042 3.792047 CACGCGTGCATCAGGTGG 61.792 66.667 28.16 0.00 34.62 4.61
2727 5055 1.286501 TGCTATGTTTCCGATCACGC 58.713 50.000 0.00 0.00 38.29 5.34
2760 5088 8.627208 AAGCAATCAAGTTTCAGATCTTTCTA 57.373 30.769 0.00 0.00 0.00 2.10
2762 5090 7.864379 TCAAAGCAATCAAGTTTCAGATCTTTC 59.136 33.333 0.00 0.00 0.00 2.62
2765 5093 6.889301 TCAAAGCAATCAAGTTTCAGATCT 57.111 33.333 0.00 0.00 0.00 2.75
2781 5109 7.440198 TGAAACATTTGGTCATAATCAAAGCA 58.560 30.769 0.00 0.00 36.49 3.91
2853 5889 6.423862 CATGAGCACAAAAATTGTTCTTTGG 58.576 36.000 5.56 0.00 43.23 3.28
2854 5890 5.905181 GCATGAGCACAAAAATTGTTCTTTG 59.095 36.000 0.00 0.00 43.23 2.77
2861 5897 6.560799 GCATATACGCATGAGCACAAAAATTG 60.561 38.462 0.00 0.00 42.27 2.32
2867 5903 2.559440 TGCATATACGCATGAGCACAA 58.441 42.857 0.00 0.00 42.27 3.33
2868 5904 2.237393 TGCATATACGCATGAGCACA 57.763 45.000 0.00 0.00 42.27 4.57
2876 5913 3.006247 TGCTTGAAAGTGCATATACGCA 58.994 40.909 0.00 0.00 40.32 5.24
2879 5916 7.756722 ACAAATTCTGCTTGAAAGTGCATATAC 59.243 33.333 0.00 0.00 38.29 1.47
2910 5947 8.964420 ACATTAAATGATCTTTGTACAAACCG 57.036 30.769 17.01 8.91 0.00 4.44
2918 5955 9.382275 GGCCAAATAACATTAAATGATCTTTGT 57.618 29.630 0.00 0.00 0.00 2.83
2919 5956 9.381033 TGGCCAAATAACATTAAATGATCTTTG 57.619 29.630 0.61 0.00 0.00 2.77
2920 5957 9.382275 GTGGCCAAATAACATTAAATGATCTTT 57.618 29.630 7.24 0.00 0.00 2.52
2931 5968 2.905736 AGCTTGGTGGCCAAATAACATT 59.094 40.909 7.24 0.00 43.44 2.71
3043 6080 4.528596 AGTAGTGACTACACCAAGCTCATT 59.471 41.667 23.28 0.00 46.99 2.57
3046 6083 4.522722 AAGTAGTGACTACACCAAGCTC 57.477 45.455 23.28 0.00 46.99 4.09
3080 6117 9.942850 TGAACAACAGTTCAAATGATATCTAGA 57.057 29.630 8.46 0.00 46.21 2.43
3106 6144 0.838987 TGGAAGCCGGGTTCCTAACT 60.839 55.000 46.98 18.45 45.63 2.24
3131 6169 3.713826 TTCCCCATACGCTTTTCTCTT 57.286 42.857 0.00 0.00 0.00 2.85
3139 6177 4.563140 TTTAGTCTTTTCCCCATACGCT 57.437 40.909 0.00 0.00 0.00 5.07
3140 6178 7.227910 TGAATATTTAGTCTTTTCCCCATACGC 59.772 37.037 0.00 0.00 0.00 4.42
3187 6225 7.923414 AGCCGACTTAATTCTTTTCTATTGT 57.077 32.000 0.00 0.00 0.00 2.71
3201 6239 9.933723 ACTTCTTACTTATTTTAGCCGACTTAA 57.066 29.630 0.00 0.00 0.00 1.85
3202 6240 9.362539 CACTTCTTACTTATTTTAGCCGACTTA 57.637 33.333 0.00 0.00 0.00 2.24
3208 6246 7.414208 GCACTCCACTTCTTACTTATTTTAGCC 60.414 40.741 0.00 0.00 0.00 3.93
3216 6254 6.770785 ACAATTTGCACTCCACTTCTTACTTA 59.229 34.615 0.00 0.00 0.00 2.24
3223 6261 5.831997 AGTAAACAATTTGCACTCCACTTC 58.168 37.500 0.00 0.00 0.00 3.01
3300 6339 5.636543 ACTGTGTTAGAACTATTTGTACGCC 59.363 40.000 0.00 0.00 0.00 5.68
3302 6341 8.516811 AAGACTGTGTTAGAACTATTTGTACG 57.483 34.615 0.00 0.00 0.00 3.67
3351 6390 9.631257 TGGTGTTGAAATGACATATCTGATTAT 57.369 29.630 0.00 0.00 0.00 1.28
3356 6395 8.131100 GGTATTGGTGTTGAAATGACATATCTG 58.869 37.037 0.00 0.00 0.00 2.90
3357 6396 7.833682 TGGTATTGGTGTTGAAATGACATATCT 59.166 33.333 0.00 0.00 0.00 1.98
3358 6397 7.915397 GTGGTATTGGTGTTGAAATGACATATC 59.085 37.037 0.00 0.00 0.00 1.63
3420 6460 3.634910 TGTCCAACTTTCAACTTTAGGGC 59.365 43.478 0.00 0.00 0.00 5.19
3433 6473 2.254546 TGAAGATGCGTGTCCAACTT 57.745 45.000 0.00 0.00 31.56 2.66
3446 6486 9.118300 GGTTAGATGAAGATTGACATTGAAGAT 57.882 33.333 0.00 0.00 0.00 2.40
3453 6493 8.868522 TTTCTTGGTTAGATGAAGATTGACAT 57.131 30.769 0.00 0.00 31.54 3.06
3458 6498 6.721208 TGGCTTTTCTTGGTTAGATGAAGATT 59.279 34.615 0.00 0.00 32.37 2.40
3516 6573 4.619863 CGTTCTCCTTCGACATTCCCTTTA 60.620 45.833 0.00 0.00 0.00 1.85
3520 6577 1.203994 TCGTTCTCCTTCGACATTCCC 59.796 52.381 0.00 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.