Multiple sequence alignment - TraesCS7B01G278200

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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 TraesCS7B01G278200 chr7B 100.000 3509 0 0 1 3509 509511360 509514868 0.000000e+00 6481.0
1 TraesCS7B01G278200 chr7A 97.863 1872 36 4 808 2675 550051863 550053734 0.000000e+00 3232.0
2 TraesCS7B01G278200 chr7A 87.979 757 63 13 2761 3509 550053826 550054562 0.000000e+00 869.0
3 TraesCS7B01G278200 chr7A 86.245 807 85 13 2 797 550050989 550051780 0.000000e+00 852.0
4 TraesCS7B01G278200 chr7D 97.693 1777 36 4 829 2600 483877358 483879134 0.000000e+00 3049.0
5 TraesCS7B01G278200 chr7D 88.111 757 68 8 2756 3509 483908057 483908794 0.000000e+00 880.0
6 TraesCS7B01G278200 chr7D 88.037 535 37 15 275 797 483876756 483877275 3.000000e-170 608.0
7 TraesCS7B01G278200 chr7D 83.691 233 36 2 2 233 483876148 483876379 5.900000e-53 219.0
8 TraesCS7B01G278200 chr7D 82.653 98 7 7 3297 3386 345676633 345676728 1.040000e-10 78.7
9 TraesCS7B01G278200 chr7D 94.595 37 2 0 2639 2675 483908023 483908059 1.360000e-04 58.4
10 TraesCS7B01G278200 chr3A 82.774 923 130 17 1032 1927 647690294 647689374 0.000000e+00 797.0
11 TraesCS7B01G278200 chr3A 82.075 106 14 4 155 258 669177382 669177484 6.240000e-13 86.1
12 TraesCS7B01G278200 chr3B 81.458 933 145 12 1021 1927 673847018 673846088 0.000000e+00 739.0
13 TraesCS7B01G278200 chr3B 75.862 232 51 5 37 265 736667407 736667636 2.860000e-21 113.0
14 TraesCS7B01G278200 chr3B 81.102 127 9 6 3213 3325 253890616 253890741 1.740000e-13 87.9
15 TraesCS7B01G278200 chr4B 82.650 317 30 14 3213 3509 440619334 440619023 1.250000e-64 257.0
16 TraesCS7B01G278200 chr1B 77.574 272 55 5 7 275 633321799 633321531 3.630000e-35 159.0
17 TraesCS7B01G278200 chr1B 81.967 122 20 2 7 128 408654973 408654854 6.200000e-18 102.0
18 TraesCS7B01G278200 chr1B 76.166 193 31 11 143 325 4086661 4086474 1.740000e-13 87.9
19 TraesCS7B01G278200 chr1A 78.313 249 48 5 7 251 552203250 552203004 4.690000e-34 156.0
20 TraesCS7B01G278200 chr1A 76.871 294 51 13 3228 3509 494896936 494896648 2.180000e-32 150.0
21 TraesCS7B01G278200 chr1A 89.189 111 11 1 2652 2762 209362174 209362065 1.700000e-28 137.0
22 TraesCS7B01G278200 chr1A 84.466 103 16 0 7 109 470397057 470397159 6.200000e-18 102.0
23 TraesCS7B01G278200 chr2D 95.745 94 2 2 2666 2758 14893729 14893821 2.180000e-32 150.0
24 TraesCS7B01G278200 chr2D 90.090 111 8 3 2652 2760 518804188 518804297 1.310000e-29 141.0
25 TraesCS7B01G278200 chr2D 75.732 239 54 4 88 322 459323498 459323260 2.210000e-22 117.0
26 TraesCS7B01G278200 chr1D 77.600 250 52 3 6 251 461118430 461118181 7.850000e-32 148.0
27 TraesCS7B01G278200 chr1D 84.466 103 16 0 7 109 371220119 371220221 6.200000e-18 102.0
28 TraesCS7B01G278200 chr6B 93.878 98 4 2 2663 2759 458503578 458503482 2.820000e-31 147.0
29 TraesCS7B01G278200 chr6B 93.000 100 5 2 2662 2760 48874028 48874126 1.020000e-30 145.0
30 TraesCS7B01G278200 chr6B 93.000 100 5 2 2662 2760 48981421 48981519 1.020000e-30 145.0
31 TraesCS7B01G278200 chr6B 90.566 106 10 0 2672 2777 646750058 646750163 1.310000e-29 141.0
32 TraesCS7B01G278200 chr5D 95.604 91 3 1 2673 2762 128577672 128577582 1.020000e-30 145.0
33 TraesCS7B01G278200 chr5B 95.604 91 3 1 2673 2762 140966014 140965924 1.020000e-30 145.0
34 TraesCS7B01G278200 chr4D 77.489 231 46 4 7 232 8920821 8921050 2.200000e-27 134.0
35 TraesCS7B01G278200 chr6D 76.538 260 28 13 3213 3447 294165116 294164865 1.030000e-20 111.0


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 TraesCS7B01G278200 chr7B 509511360 509514868 3508 False 6481.0 6481 100.000000 1 3509 1 chr7B.!!$F1 3508
1 TraesCS7B01G278200 chr7A 550050989 550054562 3573 False 1651.0 3232 90.695667 2 3509 3 chr7A.!!$F1 3507
2 TraesCS7B01G278200 chr7D 483876148 483879134 2986 False 1292.0 3049 89.807000 2 2600 3 chr7D.!!$F2 2598
3 TraesCS7B01G278200 chr7D 483908023 483908794 771 False 469.2 880 91.353000 2639 3509 2 chr7D.!!$F3 870
4 TraesCS7B01G278200 chr3A 647689374 647690294 920 True 797.0 797 82.774000 1032 1927 1 chr3A.!!$R1 895
5 TraesCS7B01G278200 chr3B 673846088 673847018 930 True 739.0 739 81.458000 1021 1927 1 chr3B.!!$R1 906

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
259 261 0.103876 AAACCAAGGAGGGAGAGGGT 60.104 55.0 0.0 0.0 43.89 4.34 F
260 262 0.842467 AACCAAGGAGGGAGAGGGTG 60.842 60.0 0.0 0.0 43.89 4.61 F
1180 1601 0.712979 ACTCCATCTCCTCCTCCACA 59.287 55.0 0.0 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1180 1601 0.964358 CGTTGAGGTCGTAGGGAGGT 60.964 60.000 0.00 0.00 0.00 3.85 R
1324 1745 3.678717 GAGCTCGTACGCGCAGGAA 62.679 63.158 29.55 1.58 38.14 3.36 R
3170 3639 0.608035 TTTGTGATCACCTTCCGCCC 60.608 55.000 22.85 0.00 0.00 6.13 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
64 65 5.353938 TGATTTAGTTATTCGTCGGGGAAG 58.646 41.667 0.00 0.00 0.00 3.46
65 66 2.877043 TAGTTATTCGTCGGGGAAGC 57.123 50.000 0.00 0.00 0.00 3.86
74 75 0.881796 GTCGGGGAAGCAAAGGAAAG 59.118 55.000 0.00 0.00 0.00 2.62
76 77 1.133606 TCGGGGAAGCAAAGGAAAGTT 60.134 47.619 0.00 0.00 0.00 2.66
78 79 2.102420 CGGGGAAGCAAAGGAAAGTTTT 59.898 45.455 0.00 0.00 0.00 2.43
80 81 3.118408 GGGGAAGCAAAGGAAAGTTTTGT 60.118 43.478 0.00 0.00 37.73 2.83
90 91 8.927721 GCAAAGGAAAGTTTTGTTTTAGTTGTA 58.072 29.630 0.00 0.00 37.73 2.41
152 153 2.173569 GGGCATCATCTTGGGAAGTACT 59.826 50.000 0.00 0.00 0.00 2.73
154 155 3.370953 GGCATCATCTTGGGAAGTACTGT 60.371 47.826 0.00 0.00 0.00 3.55
155 156 4.265073 GCATCATCTTGGGAAGTACTGTT 58.735 43.478 0.00 0.00 0.00 3.16
229 230 4.447138 AACATGGGTTGAGAGTACCAAA 57.553 40.909 0.00 0.00 37.40 3.28
232 233 5.393866 ACATGGGTTGAGAGTACCAAAAAT 58.606 37.500 0.00 0.00 37.40 1.82
236 238 7.279750 TGGGTTGAGAGTACCAAAAATTAAC 57.720 36.000 0.00 0.00 37.40 2.01
238 240 7.507616 TGGGTTGAGAGTACCAAAAATTAACAT 59.492 33.333 0.00 0.00 37.40 2.71
253 255 8.499288 AAAATTAACATAAAACCAAGGAGGGA 57.501 30.769 0.00 0.00 43.89 4.20
255 257 6.457159 TTAACATAAAACCAAGGAGGGAGA 57.543 37.500 0.00 0.00 43.89 3.71
256 258 4.576330 ACATAAAACCAAGGAGGGAGAG 57.424 45.455 0.00 0.00 43.89 3.20
258 260 1.076438 AAAACCAAGGAGGGAGAGGG 58.924 55.000 0.00 0.00 43.89 4.30
259 261 0.103876 AAACCAAGGAGGGAGAGGGT 60.104 55.000 0.00 0.00 43.89 4.34
260 262 0.842467 AACCAAGGAGGGAGAGGGTG 60.842 60.000 0.00 0.00 43.89 4.61
261 263 2.674220 CCAAGGAGGGAGAGGGTGC 61.674 68.421 0.00 0.00 0.00 5.01
262 264 1.920325 CAAGGAGGGAGAGGGTGCA 60.920 63.158 0.00 0.00 0.00 4.57
263 265 1.083706 AAGGAGGGAGAGGGTGCAT 59.916 57.895 0.00 0.00 0.00 3.96
264 266 1.277580 AAGGAGGGAGAGGGTGCATG 61.278 60.000 0.00 0.00 0.00 4.06
265 267 1.690633 GGAGGGAGAGGGTGCATGA 60.691 63.158 0.00 0.00 0.00 3.07
271 273 2.692368 GAGGGTGCATGAGGGGGA 60.692 66.667 0.00 0.00 0.00 4.81
281 618 1.570501 CATGAGGGGGAAAATGAGGGA 59.429 52.381 0.00 0.00 0.00 4.20
295 632 1.127343 GAGGGATGAGGGGAGTCAAG 58.873 60.000 0.00 0.00 0.00 3.02
297 634 1.348775 GGGATGAGGGGAGTCAAGGG 61.349 65.000 0.00 0.00 0.00 3.95
359 696 3.430042 AATGACATCACTGCTGACCTT 57.570 42.857 0.00 0.00 0.00 3.50
396 733 3.262420 GTCATTGCTGACTTCACGGTAT 58.738 45.455 0.00 0.00 46.84 2.73
425 762 8.911247 AATAAAAATGACTTGCCGATTTACTC 57.089 30.769 0.00 0.00 0.00 2.59
444 783 2.808543 CTCCTTTTCAGGGTTTGACTCG 59.191 50.000 0.00 0.00 41.25 4.18
447 786 2.249844 TTTCAGGGTTTGACTCGACC 57.750 50.000 0.00 0.00 34.94 4.79
452 791 1.909302 AGGGTTTGACTCGACCATGAT 59.091 47.619 0.00 0.00 37.68 2.45
453 792 2.009774 GGGTTTGACTCGACCATGATG 58.990 52.381 0.00 0.00 37.68 3.07
464 803 3.501828 TCGACCATGATGACCAAAACAAG 59.498 43.478 0.00 0.00 0.00 3.16
466 805 4.261572 CGACCATGATGACCAAAACAAGTT 60.262 41.667 0.00 0.00 0.00 2.66
467 806 5.049060 CGACCATGATGACCAAAACAAGTTA 60.049 40.000 0.00 0.00 0.00 2.24
468 807 6.514212 CGACCATGATGACCAAAACAAGTTAA 60.514 38.462 0.00 0.00 0.00 2.01
470 809 7.734942 ACCATGATGACCAAAACAAGTTAATT 58.265 30.769 0.00 0.00 0.00 1.40
471 810 7.872483 ACCATGATGACCAAAACAAGTTAATTC 59.128 33.333 0.00 0.00 0.00 2.17
472 811 7.062138 CCATGATGACCAAAACAAGTTAATTCG 59.938 37.037 0.00 0.00 0.00 3.34
477 820 4.039032 CCAAAACAAGTTAATTCGCGTGT 58.961 39.130 5.77 0.00 0.00 4.49
478 821 4.085822 CCAAAACAAGTTAATTCGCGTGTG 60.086 41.667 5.77 0.00 0.00 3.82
487 830 1.767127 ATTCGCGTGTGTTGCAACGA 61.767 50.000 23.79 13.70 36.54 3.85
627 972 8.958043 CAAGAAAAGTTTTTGATTTAGTCGAGG 58.042 33.333 1.64 0.00 0.00 4.63
632 977 8.851960 AAGTTTTTGATTTAGTCGAGGTTTTC 57.148 30.769 0.00 0.00 0.00 2.29
737 1083 9.806203 TGCGAAGATTTGATTGATTTAATTGAT 57.194 25.926 0.00 0.00 0.00 2.57
767 1113 8.121305 TGCAGTACATGATTTTAGAAAATGGT 57.879 30.769 0.00 3.99 38.64 3.55
947 1368 3.513515 AGATATTTCGCCTCTCATCCTCC 59.486 47.826 0.00 0.00 0.00 4.30
1079 1500 2.588989 CCTCCAGCCTCCTCAAGC 59.411 66.667 0.00 0.00 0.00 4.01
1180 1601 0.712979 ACTCCATCTCCTCCTCCACA 59.287 55.000 0.00 0.00 0.00 4.17
2011 2463 0.603975 GACTTGTGCTGGACTGACCC 60.604 60.000 0.00 0.00 38.00 4.46
2269 2724 0.704551 CGTACGTACGCTGGTGTTTC 59.295 55.000 32.36 0.00 43.14 2.78
2304 2759 5.309638 TCAATAAGATGGTTCGGTGAAACA 58.690 37.500 0.00 0.00 43.65 2.83
2325 2780 0.032017 AGGATGCTTAGGGACGAGGT 60.032 55.000 0.00 0.00 0.00 3.85
2632 3089 5.713025 ACCTAGCATACAACTTGCAAAATG 58.287 37.500 0.00 5.06 42.62 2.32
2668 3125 7.041107 ACACAAACATGCACAAGAAATTTAGT 58.959 30.769 0.00 0.00 0.00 2.24
2675 3132 9.231297 ACATGCACAAGAAATTTAGTGTATACT 57.769 29.630 15.74 0.00 35.59 2.12
2676 3133 9.708222 CATGCACAAGAAATTTAGTGTATACTC 57.292 33.333 15.74 0.09 35.59 2.59
2678 3135 7.335924 TGCACAAGAAATTTAGTGTATACTCCC 59.664 37.037 15.22 0.00 38.36 4.30
2679 3136 7.553044 GCACAAGAAATTTAGTGTATACTCCCT 59.447 37.037 15.22 0.48 38.36 4.20
2680 3137 9.099454 CACAAGAAATTTAGTGTATACTCCCTC 57.901 37.037 4.17 0.00 38.36 4.30
2681 3138 9.047947 ACAAGAAATTTAGTGTATACTCCCTCT 57.952 33.333 4.17 0.00 38.36 3.69
2682 3139 9.319143 CAAGAAATTTAGTGTATACTCCCTCTG 57.681 37.037 4.17 0.00 38.36 3.35
2683 3140 8.611051 AGAAATTTAGTGTATACTCCCTCTGT 57.389 34.615 4.17 0.00 38.36 3.41
2689 3146 9.537852 TTTAGTGTATACTCCCTCTGTAAAGAA 57.462 33.333 4.17 0.00 38.36 2.52
2690 3147 9.537852 TTAGTGTATACTCCCTCTGTAAAGAAA 57.462 33.333 4.17 0.00 38.36 2.52
2691 3148 8.611051 AGTGTATACTCCCTCTGTAAAGAAAT 57.389 34.615 4.17 0.00 28.79 2.17
2692 3149 9.710818 AGTGTATACTCCCTCTGTAAAGAAATA 57.289 33.333 4.17 0.00 28.79 1.40
2699 3156 8.425703 ACTCCCTCTGTAAAGAAATATAAGAGC 58.574 37.037 0.00 0.00 0.00 4.09
2700 3157 8.319057 TCCCTCTGTAAAGAAATATAAGAGCA 57.681 34.615 0.00 0.00 0.00 4.26
2701 3158 8.938883 TCCCTCTGTAAAGAAATATAAGAGCAT 58.061 33.333 0.00 0.00 0.00 3.79
2751 3208 8.943909 AACACTCTTATATTTCTTTACGGAGG 57.056 34.615 0.00 0.00 0.00 4.30
2753 3210 7.343833 ACACTCTTATATTTCTTTACGGAGGGA 59.656 37.037 0.00 0.00 0.00 4.20
2754 3211 7.868415 CACTCTTATATTTCTTTACGGAGGGAG 59.132 40.741 0.00 0.00 0.00 4.30
2757 3214 8.854117 TCTTATATTTCTTTACGGAGGGAGTAC 58.146 37.037 0.00 0.00 0.00 2.73
2758 3215 8.537728 TTATATTTCTTTACGGAGGGAGTACA 57.462 34.615 0.00 0.00 0.00 2.90
2759 3216 5.952347 ATTTCTTTACGGAGGGAGTACAT 57.048 39.130 0.00 0.00 0.00 2.29
2760 3217 4.996788 TTCTTTACGGAGGGAGTACATC 57.003 45.455 0.00 0.00 0.00 3.06
2762 3219 3.952323 TCTTTACGGAGGGAGTACATCTG 59.048 47.826 0.00 0.00 0.00 2.90
2783 3246 5.091261 TGTAAAAATGCTGTTGTGGGTTT 57.909 34.783 0.00 0.00 0.00 3.27
2796 3259 7.524038 GCTGTTGTGGGTTTGTATTATTACCAA 60.524 37.037 0.00 0.00 32.20 3.67
2888 3356 6.839124 TCATGATCATTAAAAGTGCCAACT 57.161 33.333 5.16 0.00 38.71 3.16
2909 3377 7.499232 CCAACTGTTTCTATAAAATCGGATCCT 59.501 37.037 10.75 0.00 0.00 3.24
2933 3401 0.807667 AGCGCCAACGATGACTCATC 60.808 55.000 2.29 8.78 43.93 2.92
3016 3484 7.654022 AATTCGCCTAAAAAGGATATGGAAA 57.346 32.000 0.00 0.00 0.00 3.13
3017 3485 7.839680 ATTCGCCTAAAAAGGATATGGAAAT 57.160 32.000 0.00 0.00 0.00 2.17
3018 3486 7.654022 TTCGCCTAAAAAGGATATGGAAATT 57.346 32.000 0.00 0.00 0.00 1.82
3035 3503 4.339530 GGAAATTGTTAAGATCTGAGGCCC 59.660 45.833 0.00 0.00 0.00 5.80
3036 3504 4.591321 AATTGTTAAGATCTGAGGCCCA 57.409 40.909 0.00 0.00 0.00 5.36
3058 3526 2.121963 TCAGTCCCCAAGGCACCT 60.122 61.111 0.00 0.00 0.00 4.00
3072 3540 2.409948 GCACCTAGAGGAATTGTGCT 57.590 50.000 1.60 0.00 46.56 4.40
3152 3621 6.547141 CACATCCTATTTCCCACATGTTACAT 59.453 38.462 0.00 0.00 0.00 2.29
3163 3632 4.462483 CCACATGTTACATTTAGCCACCTT 59.538 41.667 0.00 0.00 0.00 3.50
3168 3637 4.890581 TGTTACATTTAGCCACCTTTGTGT 59.109 37.500 0.00 0.00 41.09 3.72
3170 3639 2.552315 ACATTTAGCCACCTTTGTGTCG 59.448 45.455 0.00 0.00 41.09 4.35
3195 3664 2.224769 GGAAGGTGATCACAAAGGTGGA 60.225 50.000 26.47 0.00 45.32 4.02
3239 3708 4.468153 AGGGAGAAGATTAGAACCACACTC 59.532 45.833 0.00 0.00 0.00 3.51
3240 3709 4.223032 GGGAGAAGATTAGAACCACACTCA 59.777 45.833 0.00 0.00 0.00 3.41
3242 3711 5.046950 GGAGAAGATTAGAACCACACTCAGT 60.047 44.000 0.00 0.00 0.00 3.41
3281 3750 9.255029 GGATTAGAAAGGATCTAGATCTAGCTT 57.745 37.037 27.65 20.24 41.59 3.74
3312 3781 2.047002 ACTAGAACTCGAGGAGGCTC 57.953 55.000 18.41 5.78 33.35 4.70
3418 3889 1.615424 GTACTGGCCAAGGGGAGGA 60.615 63.158 7.01 0.00 35.59 3.71
3452 3923 1.296002 ATTCGGCCTCCCCTTACTTT 58.704 50.000 0.00 0.00 0.00 2.66
3454 3925 1.069775 TCGGCCTCCCCTTACTTTTT 58.930 50.000 0.00 0.00 0.00 1.94
3466 3937 7.351166 TCCCCTTACTTTTTCAAGAAGAAAGA 58.649 34.615 16.76 0.00 46.24 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.810545 CTTACCAAAACCTCAACTAAATCAAAA 57.189 29.630 0.00 0.00 0.00 2.44
49 50 2.352388 CTTTGCTTCCCCGACGAATAA 58.648 47.619 0.00 0.00 0.00 1.40
57 58 1.328279 AACTTTCCTTTGCTTCCCCG 58.672 50.000 0.00 0.00 0.00 5.73
64 65 7.802738 ACAACTAAAACAAAACTTTCCTTTGC 58.197 30.769 0.00 0.00 37.29 3.68
74 75 9.827411 TTGCCAAAATTACAACTAAAACAAAAC 57.173 25.926 0.00 0.00 0.00 2.43
76 77 9.436957 TCTTGCCAAAATTACAACTAAAACAAA 57.563 25.926 0.00 0.00 0.00 2.83
78 79 9.606631 AATCTTGCCAAAATTACAACTAAAACA 57.393 25.926 0.00 0.00 0.00 2.83
120 121 7.004086 CCCAAGATGATGCCCTAAATTAACTA 58.996 38.462 0.00 0.00 0.00 2.24
128 129 2.852449 ACTTCCCAAGATGATGCCCTAA 59.148 45.455 0.00 0.00 0.00 2.69
135 136 5.178797 CGAAACAGTACTTCCCAAGATGAT 58.821 41.667 0.00 0.00 0.00 2.45
137 138 3.684788 CCGAAACAGTACTTCCCAAGATG 59.315 47.826 0.00 0.00 0.00 2.90
140 141 3.121738 ACCGAAACAGTACTTCCCAAG 57.878 47.619 0.00 0.00 0.00 3.61
189 190 6.740453 CCATGTTGCACAAAACTAAAAACAAC 59.260 34.615 0.00 0.00 37.31 3.32
192 193 5.352846 ACCCATGTTGCACAAAACTAAAAAC 59.647 36.000 0.00 0.00 0.00 2.43
208 209 4.447138 TTTGGTACTCTCAACCCATGTT 57.553 40.909 0.00 0.00 36.06 2.71
213 214 7.279750 TGTTAATTTTTGGTACTCTCAACCC 57.720 36.000 0.00 0.00 36.06 4.11
229 230 7.953493 TCTCCCTCCTTGGTTTTATGTTAATTT 59.047 33.333 0.00 0.00 0.00 1.82
232 233 6.457159 TCTCCCTCCTTGGTTTTATGTTAA 57.543 37.500 0.00 0.00 0.00 2.01
236 238 3.372025 CCCTCTCCCTCCTTGGTTTTATG 60.372 52.174 0.00 0.00 0.00 1.90
238 240 2.275466 CCCTCTCCCTCCTTGGTTTTA 58.725 52.381 0.00 0.00 0.00 1.52
243 245 2.674220 GCACCCTCTCCCTCCTTGG 61.674 68.421 0.00 0.00 0.00 3.61
253 255 2.693864 CCCCCTCATGCACCCTCT 60.694 66.667 0.00 0.00 0.00 3.69
255 257 1.442886 TTTTCCCCCTCATGCACCCT 61.443 55.000 0.00 0.00 0.00 4.34
256 258 0.325577 ATTTTCCCCCTCATGCACCC 60.326 55.000 0.00 0.00 0.00 4.61
258 260 1.753073 CTCATTTTCCCCCTCATGCAC 59.247 52.381 0.00 0.00 0.00 4.57
259 261 1.342275 CCTCATTTTCCCCCTCATGCA 60.342 52.381 0.00 0.00 0.00 3.96
260 262 1.406903 CCTCATTTTCCCCCTCATGC 58.593 55.000 0.00 0.00 0.00 4.06
261 263 1.570501 TCCCTCATTTTCCCCCTCATG 59.429 52.381 0.00 0.00 0.00 3.07
262 264 2.000290 TCCCTCATTTTCCCCCTCAT 58.000 50.000 0.00 0.00 0.00 2.90
263 265 1.570501 CATCCCTCATTTTCCCCCTCA 59.429 52.381 0.00 0.00 0.00 3.86
264 266 1.852965 TCATCCCTCATTTTCCCCCTC 59.147 52.381 0.00 0.00 0.00 4.30
265 267 1.855599 CTCATCCCTCATTTTCCCCCT 59.144 52.381 0.00 0.00 0.00 4.79
271 273 2.511637 GACTCCCCTCATCCCTCATTTT 59.488 50.000 0.00 0.00 0.00 1.82
281 618 0.621862 GTCCCCTTGACTCCCCTCAT 60.622 60.000 0.00 0.00 41.03 2.90
295 632 6.063496 ACTATTAAAGAAGAGTTGGTCCCC 57.937 41.667 0.00 0.00 33.23 4.81
297 634 8.968969 TCTCTACTATTAAAGAAGAGTTGGTCC 58.031 37.037 0.00 0.00 38.14 4.46
333 670 6.051717 GGTCAGCAGTGATGTCATTTAGTAT 58.948 40.000 8.47 0.00 34.36 2.12
359 696 5.130975 AGCAATGACATCAACCTAGGACATA 59.869 40.000 17.98 0.00 0.00 2.29
392 729 9.575783 TCGGCAAGTCATTTTTATTTTTATACC 57.424 29.630 0.00 0.00 0.00 2.73
425 762 2.548480 GTCGAGTCAAACCCTGAAAAGG 59.452 50.000 0.00 0.00 35.22 3.11
444 783 4.853924 ACTTGTTTTGGTCATCATGGTC 57.146 40.909 0.00 0.00 0.00 4.02
447 786 7.410728 GCGAATTAACTTGTTTTGGTCATCATG 60.411 37.037 0.00 0.00 0.00 3.07
452 791 4.201930 ACGCGAATTAACTTGTTTTGGTCA 60.202 37.500 15.93 0.00 0.00 4.02
453 792 4.145756 CACGCGAATTAACTTGTTTTGGTC 59.854 41.667 15.93 0.00 0.00 4.02
464 803 2.025544 TGCAACACACGCGAATTAAC 57.974 45.000 15.93 0.00 0.00 2.01
466 805 1.657816 CGTTGCAACACACGCGAATTA 60.658 47.619 28.01 0.00 0.00 1.40
467 806 0.927994 CGTTGCAACACACGCGAATT 60.928 50.000 28.01 0.00 0.00 2.17
468 807 1.368731 CGTTGCAACACACGCGAAT 60.369 52.632 28.01 0.00 0.00 3.34
470 809 1.767127 ATTCGTTGCAACACACGCGA 61.767 50.000 28.01 15.99 35.11 5.87
471 810 1.368731 ATTCGTTGCAACACACGCG 60.369 52.632 28.01 13.89 0.00 6.01
472 811 2.123990 CATTCGTTGCAACACACGC 58.876 52.632 28.01 1.21 0.00 5.34
487 830 8.978874 TGAACCACTAGAATAATGTATGCATT 57.021 30.769 13.75 13.75 46.14 3.56
582 925 4.345257 TCTTGCATTCCACTATCCCTACTC 59.655 45.833 0.00 0.00 0.00 2.59
587 932 4.706962 ACTTTTCTTGCATTCCACTATCCC 59.293 41.667 0.00 0.00 0.00 3.85
623 968 9.793252 ATCAAATCAAATCTTATGAAAACCTCG 57.207 29.630 0.00 0.00 0.00 4.63
653 998 7.534852 TCCCTTATGCTTATGAATACCCAATT 58.465 34.615 0.00 0.00 0.00 2.32
656 1001 6.467194 CCTTCCCTTATGCTTATGAATACCCA 60.467 42.308 0.00 0.00 0.00 4.51
657 1002 5.946377 CCTTCCCTTATGCTTATGAATACCC 59.054 44.000 0.00 0.00 0.00 3.69
658 1003 6.779860 TCCTTCCCTTATGCTTATGAATACC 58.220 40.000 0.00 0.00 0.00 2.73
659 1004 8.691661 TTTCCTTCCCTTATGCTTATGAATAC 57.308 34.615 0.00 0.00 0.00 1.89
660 1005 9.300681 CATTTCCTTCCCTTATGCTTATGAATA 57.699 33.333 0.00 0.00 0.00 1.75
661 1006 8.006564 TCATTTCCTTCCCTTATGCTTATGAAT 58.993 33.333 0.00 0.00 0.00 2.57
662 1007 7.353525 TCATTTCCTTCCCTTATGCTTATGAA 58.646 34.615 0.00 0.00 0.00 2.57
663 1008 6.910191 TCATTTCCTTCCCTTATGCTTATGA 58.090 36.000 0.00 0.00 0.00 2.15
664 1009 7.587037 TTCATTTCCTTCCCTTATGCTTATG 57.413 36.000 0.00 0.00 0.00 1.90
665 1010 7.841222 ACTTTCATTTCCTTCCCTTATGCTTAT 59.159 33.333 0.00 0.00 0.00 1.73
666 1011 7.182060 ACTTTCATTTCCTTCCCTTATGCTTA 58.818 34.615 0.00 0.00 0.00 3.09
667 1012 6.019108 ACTTTCATTTCCTTCCCTTATGCTT 58.981 36.000 0.00 0.00 0.00 3.91
668 1013 5.583932 ACTTTCATTTCCTTCCCTTATGCT 58.416 37.500 0.00 0.00 0.00 3.79
669 1014 5.921962 ACTTTCATTTCCTTCCCTTATGC 57.078 39.130 0.00 0.00 0.00 3.14
670 1015 7.029563 CGAAACTTTCATTTCCTTCCCTTATG 58.970 38.462 2.49 0.00 35.52 1.90
671 1016 6.946009 TCGAAACTTTCATTTCCTTCCCTTAT 59.054 34.615 2.49 0.00 35.52 1.73
764 1110 6.715718 TGAAATAACCTAAACCAAATCGACCA 59.284 34.615 0.00 0.00 0.00 4.02
815 1231 7.122055 CCTCTGTCAATCACTAGTTCTCTACTT 59.878 40.741 0.00 0.00 38.33 2.24
947 1368 2.766263 TGTGAGTGGCAGGGTATAAGAG 59.234 50.000 0.00 0.00 0.00 2.85
1079 1500 3.839432 GACGCCGGAGAAGGAGGG 61.839 72.222 13.83 0.00 35.27 4.30
1180 1601 0.964358 CGTTGAGGTCGTAGGGAGGT 60.964 60.000 0.00 0.00 0.00 3.85
1324 1745 3.678717 GAGCTCGTACGCGCAGGAA 62.679 63.158 29.55 1.58 38.14 3.36
1976 2428 5.615764 GCACAAGTCGAAAAGAGATTCTTCC 60.616 44.000 0.00 0.00 35.27 3.46
2011 2463 6.580476 GCCACAAGACAAAACAAATTAATCG 58.420 36.000 0.00 0.00 0.00 3.34
2269 2724 4.290155 CATCTTATTGATTTTTCGCCCCG 58.710 43.478 0.00 0.00 32.05 5.73
2276 2731 7.461182 TCACCGAACCATCTTATTGATTTTT 57.539 32.000 0.00 0.00 32.05 1.94
2304 2759 1.698506 CTCGTCCCTAAGCATCCTCT 58.301 55.000 0.00 0.00 0.00 3.69
2325 2780 6.115446 AGTCTGACAAATCACAAAGACAAGA 58.885 36.000 10.88 0.00 31.72 3.02
2472 2928 5.796502 TTTATTCCCTCCTCTTGTTCCAT 57.203 39.130 0.00 0.00 0.00 3.41
2514 2970 2.486548 GGAGTAAACAGAGCCCACACAA 60.487 50.000 0.00 0.00 0.00 3.33
2610 3067 4.563976 GCATTTTGCAAGTTGTATGCTAGG 59.436 41.667 18.55 2.28 44.26 3.02
2632 3089 1.388547 TGTTTGTGTTGGTCCTCTGC 58.611 50.000 0.00 0.00 0.00 4.26
2675 3132 8.319057 TGCTCTTATATTTCTTTACAGAGGGA 57.681 34.615 0.00 0.00 0.00 4.20
2676 3133 9.566432 AATGCTCTTATATTTCTTTACAGAGGG 57.434 33.333 0.00 0.00 0.00 4.30
2725 3182 9.379791 CCTCCGTAAAGAAATATAAGAGTGTTT 57.620 33.333 0.00 0.00 0.00 2.83
2726 3183 7.985752 CCCTCCGTAAAGAAATATAAGAGTGTT 59.014 37.037 0.00 0.00 0.00 3.32
2727 3184 7.343833 TCCCTCCGTAAAGAAATATAAGAGTGT 59.656 37.037 0.00 0.00 0.00 3.55
2728 3185 7.723324 TCCCTCCGTAAAGAAATATAAGAGTG 58.277 38.462 0.00 0.00 0.00 3.51
2730 3187 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
2732 3189 8.636213 TGTACTCCCTCCGTAAAGAAATATAAG 58.364 37.037 0.00 0.00 0.00 1.73
2733 3190 8.537728 TGTACTCCCTCCGTAAAGAAATATAA 57.462 34.615 0.00 0.00 0.00 0.98
2734 3191 8.716674 ATGTACTCCCTCCGTAAAGAAATATA 57.283 34.615 0.00 0.00 0.00 0.86
2735 3192 7.509659 AGATGTACTCCCTCCGTAAAGAAATAT 59.490 37.037 0.00 0.00 0.00 1.28
2736 3193 6.837568 AGATGTACTCCCTCCGTAAAGAAATA 59.162 38.462 0.00 0.00 0.00 1.40
2737 3194 5.661759 AGATGTACTCCCTCCGTAAAGAAAT 59.338 40.000 0.00 0.00 0.00 2.17
2738 3195 5.021458 AGATGTACTCCCTCCGTAAAGAAA 58.979 41.667 0.00 0.00 0.00 2.52
2740 3197 3.952323 CAGATGTACTCCCTCCGTAAAGA 59.048 47.826 0.00 0.00 0.00 2.52
2741 3198 3.700038 ACAGATGTACTCCCTCCGTAAAG 59.300 47.826 0.00 0.00 0.00 1.85
2742 3199 3.705051 ACAGATGTACTCCCTCCGTAAA 58.295 45.455 0.00 0.00 0.00 2.01
2743 3200 3.377253 ACAGATGTACTCCCTCCGTAA 57.623 47.619 0.00 0.00 0.00 3.18
2744 3201 4.508551 TTACAGATGTACTCCCTCCGTA 57.491 45.455 0.00 0.00 0.00 4.02
2745 3202 3.377253 TTACAGATGTACTCCCTCCGT 57.623 47.619 0.00 0.00 0.00 4.69
2747 3204 5.297029 GCATTTTTACAGATGTACTCCCTCC 59.703 44.000 0.00 0.00 0.00 4.30
2749 3206 5.882557 CAGCATTTTTACAGATGTACTCCCT 59.117 40.000 0.00 0.00 0.00 4.20
2751 3208 6.743575 ACAGCATTTTTACAGATGTACTCC 57.256 37.500 0.00 0.00 29.02 3.85
2753 3210 7.362662 CACAACAGCATTTTTACAGATGTACT 58.637 34.615 0.00 0.00 30.86 2.73
2754 3211 6.582295 CCACAACAGCATTTTTACAGATGTAC 59.418 38.462 0.00 0.00 30.86 2.90
2757 3214 4.925054 CCCACAACAGCATTTTTACAGATG 59.075 41.667 0.00 0.00 0.00 2.90
2758 3215 4.588528 ACCCACAACAGCATTTTTACAGAT 59.411 37.500 0.00 0.00 0.00 2.90
2759 3216 3.957497 ACCCACAACAGCATTTTTACAGA 59.043 39.130 0.00 0.00 0.00 3.41
2760 3217 4.320608 ACCCACAACAGCATTTTTACAG 57.679 40.909 0.00 0.00 0.00 2.74
2762 3219 4.873259 ACAAACCCACAACAGCATTTTTAC 59.127 37.500 0.00 0.00 0.00 2.01
2842 3305 7.490840 TGATTAATGCATTGTGGAATCGAATT 58.509 30.769 22.27 0.00 0.00 2.17
2909 3377 2.147958 AGTCATCGTTGGCGCTTTAAA 58.852 42.857 7.64 0.00 38.14 1.52
2933 3401 2.385315 ACATATCGTGATCGTTCTGCG 58.615 47.619 0.00 0.66 43.01 5.18
2953 3421 6.038609 AGGGGCCTCTTATGAATTCCATATA 58.961 40.000 0.00 0.00 37.56 0.86
2974 3442 1.856629 TTACAACGGTAGGAGGAGGG 58.143 55.000 0.00 0.00 0.00 4.30
3016 3484 3.372025 GGTGGGCCTCAGATCTTAACAAT 60.372 47.826 4.53 0.00 0.00 2.71
3017 3485 2.026262 GGTGGGCCTCAGATCTTAACAA 60.026 50.000 4.53 0.00 0.00 2.83
3018 3486 1.559682 GGTGGGCCTCAGATCTTAACA 59.440 52.381 4.53 0.00 0.00 2.41
3035 3503 1.376466 CCTTGGGGACTGAGTGGTG 59.624 63.158 0.00 0.00 33.58 4.17
3036 3504 2.529744 GCCTTGGGGACTGAGTGGT 61.530 63.158 0.00 0.00 33.58 4.16
3058 3526 1.275010 TGTCGCAGCACAATTCCTCTA 59.725 47.619 0.00 0.00 0.00 2.43
3072 3540 2.613026 TTTCCTTCTCTTGTGTCGCA 57.387 45.000 0.00 0.00 0.00 5.10
3131 3600 7.284489 GCTAAATGTAACATGTGGGAAATAGGA 59.716 37.037 0.00 0.00 0.00 2.94
3163 3632 3.552384 ACCTTCCGCCCGACACAA 61.552 61.111 0.00 0.00 0.00 3.33
3168 3637 2.682136 TGATCACCTTCCGCCCGA 60.682 61.111 0.00 0.00 0.00 5.14
3170 3639 0.608035 TTTGTGATCACCTTCCGCCC 60.608 55.000 22.85 0.00 0.00 6.13
3195 3664 6.442564 TCCCTCTAACCACATGTTACACTTAT 59.557 38.462 0.00 0.00 38.42 1.73
3281 3750 8.974238 TCCTCGAGTTCTAGTTAATCCAATTAA 58.026 33.333 12.31 0.00 32.64 1.40
3291 3760 3.543665 GAGCCTCCTCGAGTTCTAGTTA 58.456 50.000 12.31 0.00 0.00 2.24
3302 3771 1.160137 CAAGTTTTGGAGCCTCCTCG 58.840 55.000 12.94 0.00 39.06 4.63
3312 3781 7.359681 GGTCACTTTTAAACACACAAGTTTTGG 60.360 37.037 0.00 0.00 41.58 3.28
3402 3873 2.612115 CTCCTCCCCTTGGCCAGT 60.612 66.667 5.11 0.00 0.00 4.00
3452 3923 2.504367 CGCCCCTCTTTCTTCTTGAAA 58.496 47.619 0.00 0.00 41.85 2.69
3454 3925 0.321653 GCGCCCCTCTTTCTTCTTGA 60.322 55.000 0.00 0.00 0.00 3.02
3466 3937 4.499116 ATAGGAGGTGGCGCCCCT 62.499 66.667 29.74 29.74 39.93 4.79


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

AutoCloner maintained by Alex Coulton.