Multiple sequence alignment - TraesCS1D01G147100

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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 TraesCS1D01G147100 chr1D 100.000 4710 0 0 1 4710 203297126 203292417 0.000000e+00 8698
1 TraesCS1D01G147100 chr1D 99.121 2957 17 6 1 2951 127668032 127665079 0.000000e+00 5308
2 TraesCS1D01G147100 chr5D 98.514 2625 29 7 1 2617 42998774 43001396 0.000000e+00 4623
3 TraesCS1D01G147100 chr5D 100.000 176 0 0 2776 2951 43001395 43001570 4.550000e-85 326
4 TraesCS1D01G147100 chr3B 94.965 2582 80 12 379 2951 595836569 595834029 0.000000e+00 4002
5 TraesCS1D01G147100 chr3B 83.942 274 26 8 1 274 757757456 757757711 3.640000e-61 246
6 TraesCS1D01G147100 chr6D 96.436 2441 59 15 530 2951 457716264 457718695 0.000000e+00 4000
7 TraesCS1D01G147100 chr4B 95.455 2222 65 8 379 2592 593951789 593953982 0.000000e+00 3511
8 TraesCS1D01G147100 chr4B 82.213 461 53 13 458 900 24996893 24996444 2.070000e-98 370
9 TraesCS1D01G147100 chr4B 96.000 75 3 0 1 75 593951680 593951754 6.400000e-24 122
10 TraesCS1D01G147100 chr5B 95.397 1651 46 5 379 2027 34158260 34159882 0.000000e+00 2601
11 TraesCS1D01G147100 chr5B 97.484 795 20 0 1343 2137 268247072 268246278 0.000000e+00 1358
12 TraesCS1D01G147100 chr5B 93.792 451 19 6 2250 2693 268246281 268245833 0.000000e+00 669
13 TraesCS1D01G147100 chr5B 94.937 158 6 1 387 542 268247211 268247054 3.640000e-61 246
14 TraesCS1D01G147100 chr5B 87.692 130 11 1 1141 1270 133661642 133661766 3.800000e-31 147
15 TraesCS1D01G147100 chr5B 97.403 77 2 0 1 77 268247328 268247252 1.060000e-26 132
16 TraesCS1D01G147100 chr5B 97.333 75 2 0 1 75 34158151 34158225 1.380000e-25 128
17 TraesCS1D01G147100 chr7B 94.559 1507 50 17 379 1882 266858643 266857166 0.000000e+00 2300
18 TraesCS1D01G147100 chr7B 95.005 1081 47 4 1878 2951 266842387 266841307 0.000000e+00 1690
19 TraesCS1D01G147100 chr7B 97.403 77 2 0 1 77 266858752 266858676 1.060000e-26 132
20 TraesCS1D01G147100 chr6B 96.212 1188 35 7 1769 2949 244566408 244565224 0.000000e+00 1936
21 TraesCS1D01G147100 chr6B 93.817 841 20 7 552 1388 244582665 244583477 0.000000e+00 1236
22 TraesCS1D01G147100 chr6B 93.286 566 29 4 1 559 244568063 244568626 0.000000e+00 826
23 TraesCS1D01G147100 chrUn 97.233 795 22 0 1343 2137 42463621 42462827 0.000000e+00 1347
24 TraesCS1D01G147100 chrUn 94.457 451 18 4 2250 2693 42462830 42462380 0.000000e+00 688
25 TraesCS1D01G147100 chrUn 94.578 166 7 1 379 542 42463768 42463603 6.050000e-64 255
26 TraesCS1D01G147100 chrUn 96.104 77 3 0 1 77 42463877 42463801 4.950000e-25 126
27 TraesCS1D01G147100 chr1B 92.921 777 39 8 2987 3758 297100776 297100011 0.000000e+00 1116
28 TraesCS1D01G147100 chr1B 97.086 549 15 1 4162 4710 297099642 297099095 0.000000e+00 924
29 TraesCS1D01G147100 chr1B 91.322 242 10 4 3810 4048 297100026 297099793 2.110000e-83 320
30 TraesCS1D01G147100 chr1B 95.238 105 5 0 4062 4166 297099808 297099704 2.920000e-37 167
31 TraesCS1D01G147100 chr1A 95.000 560 12 6 4162 4710 257558713 257558159 0.000000e+00 865
32 TraesCS1D01G147100 chr1A 92.759 580 26 7 2988 3561 257565301 257564732 0.000000e+00 824
33 TraesCS1D01G147100 chr1A 94.355 496 25 1 3556 4048 257559366 257558871 0.000000e+00 758
34 TraesCS1D01G147100 chr1A 95.098 102 5 0 4062 4163 257558886 257558785 1.360000e-35 161
35 TraesCS1D01G147100 chr3A 90.618 469 37 5 2486 2951 13839440 13839904 2.410000e-172 616
36 TraesCS1D01G147100 chr4A 87.905 463 47 6 2403 2861 676083271 676082814 1.930000e-148 536
37 TraesCS1D01G147100 chr4A 84.328 268 30 9 2687 2951 188763305 188763047 7.820000e-63 252
38 TraesCS1D01G147100 chr5A 87.600 250 26 4 26 274 536251736 536251491 7.710000e-73 285
39 TraesCS1D01G147100 chr7D 89.744 78 8 0 1182 1259 39064489 39064412 3.000000e-17 100


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 TraesCS1D01G147100 chr1D 203292417 203297126 4709 True 8698.000000 8698 100.000000 1 4710 1 chr1D.!!$R2 4709
1 TraesCS1D01G147100 chr1D 127665079 127668032 2953 True 5308.000000 5308 99.121000 1 2951 1 chr1D.!!$R1 2950
2 TraesCS1D01G147100 chr5D 42998774 43001570 2796 False 2474.500000 4623 99.257000 1 2951 2 chr5D.!!$F1 2950
3 TraesCS1D01G147100 chr3B 595834029 595836569 2540 True 4002.000000 4002 94.965000 379 2951 1 chr3B.!!$R1 2572
4 TraesCS1D01G147100 chr6D 457716264 457718695 2431 False 4000.000000 4000 96.436000 530 2951 1 chr6D.!!$F1 2421
5 TraesCS1D01G147100 chr4B 593951680 593953982 2302 False 1816.500000 3511 95.727500 1 2592 2 chr4B.!!$F1 2591
6 TraesCS1D01G147100 chr5B 34158151 34159882 1731 False 1364.500000 2601 96.365000 1 2027 2 chr5B.!!$F2 2026
7 TraesCS1D01G147100 chr5B 268245833 268247328 1495 True 601.250000 1358 95.904000 1 2693 4 chr5B.!!$R1 2692
8 TraesCS1D01G147100 chr7B 266841307 266842387 1080 True 1690.000000 1690 95.005000 1878 2951 1 chr7B.!!$R1 1073
9 TraesCS1D01G147100 chr7B 266857166 266858752 1586 True 1216.000000 2300 95.981000 1 1882 2 chr7B.!!$R2 1881
10 TraesCS1D01G147100 chr6B 244565224 244566408 1184 True 1936.000000 1936 96.212000 1769 2949 1 chr6B.!!$R1 1180
11 TraesCS1D01G147100 chr6B 244582665 244583477 812 False 1236.000000 1236 93.817000 552 1388 1 chr6B.!!$F2 836
12 TraesCS1D01G147100 chr6B 244568063 244568626 563 False 826.000000 826 93.286000 1 559 1 chr6B.!!$F1 558
13 TraesCS1D01G147100 chrUn 42462380 42463877 1497 True 604.000000 1347 95.593000 1 2693 4 chrUn.!!$R1 2692
14 TraesCS1D01G147100 chr1B 297099095 297100776 1681 True 631.750000 1116 94.141750 2987 4710 4 chr1B.!!$R1 1723
15 TraesCS1D01G147100 chr1A 257564732 257565301 569 True 824.000000 824 92.759000 2988 3561 1 chr1A.!!$R1 573
16 TraesCS1D01G147100 chr1A 257558159 257559366 1207 True 594.666667 865 94.817667 3556 4710 3 chr1A.!!$R2 1154

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
373 381 0.253160 TCAGGGCCCCTCTGTGTTAT 60.253 55.000 21.43 0.00 34.15 1.89 F
1039 1061 2.433318 GGACGTGGAGCTGCACTC 60.433 66.667 31.82 25.86 45.45 3.51 F
2952 2990 0.176680 CACGGGCATCTTGCTAGTCT 59.823 55.000 0.00 0.00 44.28 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1975 1997 8.807948 AAATGATACAATAGGCATATGGTACC 57.192 34.615 7.75 4.43 31.84 3.34 R
3005 3043 0.036388 GGCGTGAATCAGTGGAAGGA 60.036 55.000 0.00 0.00 0.00 3.36 R
4550 4680 0.034059 ACTCAGGGTGTTTCTGCTCG 59.966 55.000 0.00 0.00 32.63 5.03 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
373 381 0.253160 TCAGGGCCCCTCTGTGTTAT 60.253 55.000 21.43 0.00 34.15 1.89
1039 1061 2.433318 GGACGTGGAGCTGCACTC 60.433 66.667 31.82 25.86 45.45 3.51
1975 1997 0.667487 CTGTGTGCCGGACTGTAGTG 60.667 60.000 5.05 0.00 0.00 2.74
2951 2989 1.432270 GCACGGGCATCTTGCTAGTC 61.432 60.000 3.77 0.00 44.28 2.59
2952 2990 0.176680 CACGGGCATCTTGCTAGTCT 59.823 55.000 0.00 0.00 44.28 3.24
2953 2991 0.461961 ACGGGCATCTTGCTAGTCTC 59.538 55.000 0.00 0.00 44.28 3.36
2954 2992 0.749649 CGGGCATCTTGCTAGTCTCT 59.250 55.000 0.00 0.00 44.28 3.10
2955 2993 1.137872 CGGGCATCTTGCTAGTCTCTT 59.862 52.381 0.00 0.00 44.28 2.85
2956 2994 2.801342 CGGGCATCTTGCTAGTCTCTTC 60.801 54.545 0.00 0.00 44.28 2.87
2957 2995 2.433970 GGGCATCTTGCTAGTCTCTTCT 59.566 50.000 0.00 0.00 44.28 2.85
2958 2996 3.639094 GGGCATCTTGCTAGTCTCTTCTA 59.361 47.826 0.00 0.00 44.28 2.10
2959 2997 4.500716 GGGCATCTTGCTAGTCTCTTCTAC 60.501 50.000 0.00 0.00 44.28 2.59
2960 2998 4.098654 GGCATCTTGCTAGTCTCTTCTACA 59.901 45.833 0.00 0.00 44.28 2.74
2961 2999 5.394663 GGCATCTTGCTAGTCTCTTCTACAA 60.395 44.000 0.00 0.00 44.28 2.41
2962 3000 6.102663 GCATCTTGCTAGTCTCTTCTACAAA 58.897 40.000 0.00 0.00 40.96 2.83
2963 3001 6.591834 GCATCTTGCTAGTCTCTTCTACAAAA 59.408 38.462 0.00 0.00 40.96 2.44
2964 3002 7.412455 GCATCTTGCTAGTCTCTTCTACAAAAC 60.412 40.741 0.00 0.00 40.96 2.43
2965 3003 6.456501 TCTTGCTAGTCTCTTCTACAAAACC 58.543 40.000 0.00 0.00 0.00 3.27
2966 3004 4.806330 TGCTAGTCTCTTCTACAAAACCG 58.194 43.478 0.00 0.00 0.00 4.44
2967 3005 4.280174 TGCTAGTCTCTTCTACAAAACCGT 59.720 41.667 0.00 0.00 0.00 4.83
2968 3006 4.621886 GCTAGTCTCTTCTACAAAACCGTG 59.378 45.833 0.00 0.00 0.00 4.94
2969 3007 4.931661 AGTCTCTTCTACAAAACCGTGA 57.068 40.909 0.00 0.00 0.00 4.35
2970 3008 5.470047 AGTCTCTTCTACAAAACCGTGAT 57.530 39.130 0.00 0.00 0.00 3.06
2971 3009 6.585695 AGTCTCTTCTACAAAACCGTGATA 57.414 37.500 0.00 0.00 0.00 2.15
2972 3010 6.622549 AGTCTCTTCTACAAAACCGTGATAG 58.377 40.000 0.00 0.00 0.00 2.08
2973 3011 6.433404 AGTCTCTTCTACAAAACCGTGATAGA 59.567 38.462 0.00 0.00 0.00 1.98
2974 3012 7.122948 AGTCTCTTCTACAAAACCGTGATAGAT 59.877 37.037 0.00 0.00 0.00 1.98
2975 3013 7.760340 GTCTCTTCTACAAAACCGTGATAGATT 59.240 37.037 0.00 0.00 0.00 2.40
2976 3014 8.311836 TCTCTTCTACAAAACCGTGATAGATTT 58.688 33.333 0.00 0.00 0.00 2.17
2977 3015 8.842358 TCTTCTACAAAACCGTGATAGATTTT 57.158 30.769 0.00 0.00 0.00 1.82
2978 3016 8.932791 TCTTCTACAAAACCGTGATAGATTTTC 58.067 33.333 0.00 0.00 0.00 2.29
2979 3017 8.842358 TTCTACAAAACCGTGATAGATTTTCT 57.158 30.769 0.00 0.00 0.00 2.52
2980 3018 8.842358 TCTACAAAACCGTGATAGATTTTCTT 57.158 30.769 0.00 0.00 0.00 2.52
2981 3019 8.717821 TCTACAAAACCGTGATAGATTTTCTTG 58.282 33.333 0.00 0.00 0.00 3.02
2982 3020 6.677913 ACAAAACCGTGATAGATTTTCTTGG 58.322 36.000 0.00 0.00 0.00 3.61
2983 3021 6.488683 ACAAAACCGTGATAGATTTTCTTGGA 59.511 34.615 0.00 0.00 0.00 3.53
2984 3022 7.176690 ACAAAACCGTGATAGATTTTCTTGGAT 59.823 33.333 0.00 0.00 0.00 3.41
2985 3023 6.683974 AACCGTGATAGATTTTCTTGGATG 57.316 37.500 0.00 0.00 0.00 3.51
3005 3043 8.523915 TGGATGTTCTATTTGCTAATGTTCAT 57.476 30.769 3.49 3.73 0.00 2.57
3021 3059 4.326826 TGTTCATCCTTCCACTGATTCAC 58.673 43.478 0.00 0.00 0.00 3.18
3158 3196 6.672147 CAGTTGAGGAGTTCATAAAAAGTGG 58.328 40.000 0.00 0.00 35.27 4.00
3207 3245 3.738791 CCAAAGGTTTTGCGGATACAAAC 59.261 43.478 0.00 0.00 39.18 2.93
3270 3308 0.250295 TCGACCAGGAGGCACAAAAG 60.250 55.000 0.00 0.00 39.06 2.27
3326 3364 6.433847 TGAACTACAAGAGAAGGGATTTGA 57.566 37.500 0.00 0.00 0.00 2.69
3392 3435 3.132289 TGCTAGAGTTATCTTTGGACCGG 59.868 47.826 0.00 0.00 36.96 5.28
3393 3436 3.132467 GCTAGAGTTATCTTTGGACCGGT 59.868 47.826 6.92 6.92 36.96 5.28
3415 3458 2.556144 AGCTCTGCTGATTGACACAA 57.444 45.000 0.00 0.00 37.57 3.33
3416 3459 3.069079 AGCTCTGCTGATTGACACAAT 57.931 42.857 0.00 0.00 37.57 2.71
3464 3507 8.911965 TGCAAATATTAAACATGGAGCTTATGA 58.088 29.630 16.11 0.00 0.00 2.15
3476 3519 7.124901 ACATGGAGCTTATGATACGATTATCCT 59.875 37.037 16.11 0.00 34.18 3.24
3477 3520 7.101652 TGGAGCTTATGATACGATTATCCTC 57.898 40.000 0.00 0.00 34.18 3.71
3478 3521 6.892456 TGGAGCTTATGATACGATTATCCTCT 59.108 38.462 0.00 0.00 34.18 3.69
3479 3522 7.397476 TGGAGCTTATGATACGATTATCCTCTT 59.603 37.037 0.00 0.00 34.18 2.85
3480 3523 8.254508 GGAGCTTATGATACGATTATCCTCTTT 58.745 37.037 0.00 0.00 34.18 2.52
3481 3524 9.296400 GAGCTTATGATACGATTATCCTCTTTC 57.704 37.037 0.00 0.00 34.18 2.62
3482 3525 9.030452 AGCTTATGATACGATTATCCTCTTTCT 57.970 33.333 0.00 0.00 34.18 2.52
3483 3526 9.646427 GCTTATGATACGATTATCCTCTTTCTT 57.354 33.333 0.00 0.00 34.18 2.52
3519 3562 3.618690 CCTGCCTGGGCTATATCTTAC 57.381 52.381 13.05 0.00 42.51 2.34
3523 3566 2.166664 GCCTGGGCTATATCTTACTCCG 59.833 54.545 4.12 0.00 38.26 4.63
3568 3611 5.142061 TCTACGTTATGTTGTGTCCATGT 57.858 39.130 0.00 0.00 0.00 3.21
3575 3618 7.766738 ACGTTATGTTGTGTCCATGTCAATATA 59.233 33.333 0.00 0.00 0.00 0.86
3615 3658 9.567776 TGTTCCATTTCTTCTGTTACTGATTTA 57.432 29.630 0.00 0.00 0.00 1.40
3678 3721 9.810545 CCTTATTTTCCTGTTTTCACAAACTTA 57.189 29.630 0.00 0.00 42.61 2.24
3704 3747 8.962679 AGAGTTATTTTCTGGTGTTTACAAACA 58.037 29.630 3.44 3.44 45.88 2.83
3862 3905 1.904287 TAATGGTGGCGCTCTTGTTT 58.096 45.000 7.64 0.00 0.00 2.83
3926 3969 9.559732 TGATAAATCATAAACAGGTCCATGTAG 57.440 33.333 0.00 0.00 31.70 2.74
3928 3971 7.630242 AAATCATAAACAGGTCCATGTAGTG 57.370 36.000 0.00 0.00 31.70 2.74
3929 3972 5.755409 TCATAAACAGGTCCATGTAGTGT 57.245 39.130 0.00 0.00 31.70 3.55
3930 3973 6.860790 TCATAAACAGGTCCATGTAGTGTA 57.139 37.500 0.00 0.00 31.70 2.90
3931 3974 7.432148 TCATAAACAGGTCCATGTAGTGTAT 57.568 36.000 0.00 0.00 31.70 2.29
4044 4090 4.387862 GGTATCTTACTGTGTGTCAAACCG 59.612 45.833 0.00 0.00 0.00 4.44
4048 4094 0.393808 ACTGTGTGTCAAACCGCCTT 60.394 50.000 0.00 0.00 0.00 4.35
4049 4095 0.738389 CTGTGTGTCAAACCGCCTTT 59.262 50.000 0.00 0.00 0.00 3.11
4050 4096 1.134175 CTGTGTGTCAAACCGCCTTTT 59.866 47.619 0.00 0.00 0.00 2.27
4051 4097 1.546476 TGTGTGTCAAACCGCCTTTTT 59.454 42.857 0.00 0.00 0.00 1.94
4071 4117 5.917541 TTTTCGATAAAGGTGTGTCAGAC 57.082 39.130 0.00 0.00 0.00 3.51
4072 4118 3.587797 TCGATAAAGGTGTGTCAGACC 57.412 47.619 11.24 11.24 0.00 3.85
4073 4119 2.894765 TCGATAAAGGTGTGTCAGACCA 59.105 45.455 20.54 1.06 35.76 4.02
4074 4120 2.993899 CGATAAAGGTGTGTCAGACCAC 59.006 50.000 20.54 11.71 35.76 4.16
4075 4121 2.519377 TAAAGGTGTGTCAGACCACG 57.481 50.000 20.54 0.00 38.20 4.94
4076 4122 0.539986 AAAGGTGTGTCAGACCACGT 59.460 50.000 20.54 11.58 38.20 4.49
4157 4203 8.102484 AGGTCTAAATTCCTATTTTGCCTCTA 57.898 34.615 0.00 0.00 32.98 2.43
4396 4526 8.462143 AACGAGTAAGTAACATGTACATTCAG 57.538 34.615 5.37 0.00 0.00 3.02
4550 4680 3.888930 TCATGGTTCAAAAGTTGGGACTC 59.111 43.478 0.00 0.00 34.21 3.36
4630 4760 0.829990 CTTCCTCCCTCTTCCTCTGC 59.170 60.000 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.776933 TTATAAGCAGTTGCATCTGTTCTAG 57.223 36.000 22.50 0.67 45.16 2.43
825 836 1.742308 AGGCCCTGACCTCTAAAACA 58.258 50.000 0.00 0.00 33.62 2.83
1039 1061 3.443045 GGTGCACCAATGGAGGCG 61.443 66.667 31.23 0.00 35.64 5.52
1975 1997 8.807948 AAATGATACAATAGGCATATGGTACC 57.192 34.615 7.75 4.43 31.84 3.34
2461 2491 2.031870 AGGAGTGAGTGCGCATATACA 58.968 47.619 15.91 9.04 0.00 2.29
2951 2989 8.480643 AAATCTATCACGGTTTTGTAGAAGAG 57.519 34.615 0.00 0.00 0.00 2.85
2952 2990 8.842358 AAAATCTATCACGGTTTTGTAGAAGA 57.158 30.769 0.00 0.00 0.00 2.87
2953 2991 8.936864 AGAAAATCTATCACGGTTTTGTAGAAG 58.063 33.333 0.00 0.00 0.00 2.85
2954 2992 8.842358 AGAAAATCTATCACGGTTTTGTAGAA 57.158 30.769 0.00 0.00 0.00 2.10
2955 2993 8.717821 CAAGAAAATCTATCACGGTTTTGTAGA 58.282 33.333 0.00 0.00 0.00 2.59
2956 2994 7.962918 CCAAGAAAATCTATCACGGTTTTGTAG 59.037 37.037 0.00 0.00 0.00 2.74
2957 2995 7.662258 TCCAAGAAAATCTATCACGGTTTTGTA 59.338 33.333 0.00 0.00 0.00 2.41
2958 2996 6.488683 TCCAAGAAAATCTATCACGGTTTTGT 59.511 34.615 0.00 0.00 0.00 2.83
2959 2997 6.908825 TCCAAGAAAATCTATCACGGTTTTG 58.091 36.000 0.00 0.00 0.00 2.44
2960 2998 7.176690 ACATCCAAGAAAATCTATCACGGTTTT 59.823 33.333 0.00 0.00 0.00 2.43
2961 2999 6.659242 ACATCCAAGAAAATCTATCACGGTTT 59.341 34.615 0.00 0.00 0.00 3.27
2962 3000 6.180472 ACATCCAAGAAAATCTATCACGGTT 58.820 36.000 0.00 0.00 0.00 4.44
2963 3001 5.745227 ACATCCAAGAAAATCTATCACGGT 58.255 37.500 0.00 0.00 0.00 4.83
2964 3002 6.540189 AGAACATCCAAGAAAATCTATCACGG 59.460 38.462 0.00 0.00 0.00 4.94
2965 3003 7.545362 AGAACATCCAAGAAAATCTATCACG 57.455 36.000 0.00 0.00 0.00 4.35
2970 3008 9.466497 AGCAAATAGAACATCCAAGAAAATCTA 57.534 29.630 0.00 0.00 0.00 1.98
2971 3009 8.358582 AGCAAATAGAACATCCAAGAAAATCT 57.641 30.769 0.00 0.00 0.00 2.40
2974 3012 9.859427 CATTAGCAAATAGAACATCCAAGAAAA 57.141 29.630 0.00 0.00 0.00 2.29
2975 3013 9.023962 ACATTAGCAAATAGAACATCCAAGAAA 57.976 29.630 0.00 0.00 0.00 2.52
2976 3014 8.579850 ACATTAGCAAATAGAACATCCAAGAA 57.420 30.769 0.00 0.00 0.00 2.52
2977 3015 8.579850 AACATTAGCAAATAGAACATCCAAGA 57.420 30.769 0.00 0.00 0.00 3.02
2978 3016 8.461222 TGAACATTAGCAAATAGAACATCCAAG 58.539 33.333 0.00 0.00 0.00 3.61
2979 3017 8.347004 TGAACATTAGCAAATAGAACATCCAA 57.653 30.769 0.00 0.00 0.00 3.53
2980 3018 7.936496 TGAACATTAGCAAATAGAACATCCA 57.064 32.000 0.00 0.00 0.00 3.41
2981 3019 8.078596 GGATGAACATTAGCAAATAGAACATCC 58.921 37.037 0.00 0.00 40.83 3.51
2982 3020 8.844244 AGGATGAACATTAGCAAATAGAACATC 58.156 33.333 0.00 0.00 0.00 3.06
2983 3021 8.757982 AGGATGAACATTAGCAAATAGAACAT 57.242 30.769 0.00 0.00 0.00 2.71
2984 3022 8.579850 AAGGATGAACATTAGCAAATAGAACA 57.420 30.769 0.00 0.00 0.00 3.18
2985 3023 8.131731 GGAAGGATGAACATTAGCAAATAGAAC 58.868 37.037 0.00 0.00 0.00 3.01
3005 3043 0.036388 GGCGTGAATCAGTGGAAGGA 60.036 55.000 0.00 0.00 0.00 3.36
3021 3059 4.941873 AGAAAACTATAAACTGGAAGGGCG 59.058 41.667 0.00 0.00 39.30 6.13
3079 3117 4.675510 CGCTCATAAAGATGTGCCATTTT 58.324 39.130 6.43 0.00 45.62 1.82
3158 3196 1.673808 CGTGGTACCTAGAGCACCCC 61.674 65.000 14.36 0.00 43.40 4.95
3207 3245 2.862536 CTGCATGTTATCAGAGTCCACG 59.137 50.000 0.00 0.00 32.26 4.94
3270 3308 0.537188 TCCTCATTCGGAACCAGAGC 59.463 55.000 9.80 0.00 0.00 4.09
3349 3387 4.646492 GCATGACACCATTTCCTCCTTTAT 59.354 41.667 0.00 0.00 0.00 1.40
3351 3389 2.827921 GCATGACACCATTTCCTCCTTT 59.172 45.455 0.00 0.00 0.00 3.11
3354 3392 2.134789 AGCATGACACCATTTCCTCC 57.865 50.000 0.00 0.00 0.00 4.30
3356 3394 3.521126 ACTCTAGCATGACACCATTTCCT 59.479 43.478 0.00 0.00 0.00 3.36
3357 3395 3.878778 ACTCTAGCATGACACCATTTCC 58.121 45.455 0.00 0.00 0.00 3.13
3434 3477 9.452287 AAGCTCCATGTTTAATATTTGCATTTT 57.548 25.926 0.00 0.00 0.00 1.82
3519 3562 2.336554 CAAAGACATTTGCCACGGAG 57.663 50.000 0.00 0.00 39.43 4.63
3554 3597 9.412460 AGATTTATATTGACATGGACACAACAT 57.588 29.630 0.00 0.00 0.00 2.71
3558 3601 8.806429 ACAAGATTTATATTGACATGGACACA 57.194 30.769 4.26 0.00 33.49 3.72
3568 3611 8.250332 GGAACAAGCCAACAAGATTTATATTGA 58.750 33.333 4.26 0.00 33.49 2.57
3615 3658 9.685276 TGGTTGATAACATGTCTTAAAGATCAT 57.315 29.630 0.00 0.00 0.00 2.45
3678 3721 8.962679 TGTTTGTAAACACCAGAAAATAACTCT 58.037 29.630 6.11 0.00 43.45 3.24
3704 3747 1.627864 AAATAAGGGCACAACGGCTT 58.372 45.000 0.00 0.00 40.90 4.35
3790 3833 5.798125 TGTTAATGAAATGGTTCAAGCCA 57.202 34.783 0.00 0.00 46.66 4.75
3791 3834 7.671495 AAATGTTAATGAAATGGTTCAAGCC 57.329 32.000 0.00 0.00 46.66 4.35
3862 3905 2.650116 GGTCTCAGCAGCCCGAGAA 61.650 63.158 12.63 0.00 39.88 2.87
3926 3969 7.644490 TGTTCCACACTTCAACATTTATACAC 58.356 34.615 0.00 0.00 0.00 2.90
3928 3971 7.803189 CACTGTTCCACACTTCAACATTTATAC 59.197 37.037 0.00 0.00 29.82 1.47
3929 3972 7.040755 CCACTGTTCCACACTTCAACATTTATA 60.041 37.037 0.00 0.00 29.82 0.98
3930 3973 6.239008 CCACTGTTCCACACTTCAACATTTAT 60.239 38.462 0.00 0.00 29.82 1.40
3931 3974 5.067153 CCACTGTTCCACACTTCAACATTTA 59.933 40.000 0.00 0.00 29.82 1.40
4048 4094 5.237779 GGTCTGACACACCTTTATCGAAAAA 59.762 40.000 10.38 0.00 0.00 1.94
4049 4095 4.753107 GGTCTGACACACCTTTATCGAAAA 59.247 41.667 10.38 0.00 0.00 2.29
4050 4096 4.202274 TGGTCTGACACACCTTTATCGAAA 60.202 41.667 10.38 0.00 34.66 3.46
4051 4097 3.322541 TGGTCTGACACACCTTTATCGAA 59.677 43.478 10.38 0.00 34.66 3.71
4052 4098 2.894765 TGGTCTGACACACCTTTATCGA 59.105 45.455 10.38 0.00 34.66 3.59
4053 4099 2.993899 GTGGTCTGACACACCTTTATCG 59.006 50.000 10.38 0.00 40.99 2.92
4054 4100 2.993899 CGTGGTCTGACACACCTTTATC 59.006 50.000 17.77 0.00 41.38 1.75
4055 4101 2.367567 ACGTGGTCTGACACACCTTTAT 59.632 45.455 17.77 3.25 41.38 1.40
4056 4102 1.758280 ACGTGGTCTGACACACCTTTA 59.242 47.619 17.77 0.00 41.38 1.85
4057 4103 0.539986 ACGTGGTCTGACACACCTTT 59.460 50.000 17.77 5.83 41.38 3.11
4058 4104 1.068127 GTACGTGGTCTGACACACCTT 59.932 52.381 17.77 11.00 41.38 3.50
4059 4105 0.672342 GTACGTGGTCTGACACACCT 59.328 55.000 17.77 11.95 41.38 4.00
4060 4106 0.386476 TGTACGTGGTCTGACACACC 59.614 55.000 17.77 0.00 41.38 4.16
4061 4107 2.058798 CATGTACGTGGTCTGACACAC 58.941 52.381 10.38 13.34 41.38 3.82
4062 4108 1.684450 ACATGTACGTGGTCTGACACA 59.316 47.619 19.05 5.30 41.38 3.72
4063 4109 2.058798 CACATGTACGTGGTCTGACAC 58.941 52.381 19.05 5.37 37.99 3.67
4064 4110 1.957877 TCACATGTACGTGGTCTGACA 59.042 47.619 19.05 0.00 37.50 3.58
4065 4111 2.717580 TCACATGTACGTGGTCTGAC 57.282 50.000 19.05 0.00 37.50 3.51
4066 4112 3.737032 TTTCACATGTACGTGGTCTGA 57.263 42.857 19.05 10.81 37.50 3.27
4067 4113 4.245660 AGATTTCACATGTACGTGGTCTG 58.754 43.478 19.05 8.68 37.50 3.51
4068 4114 4.537135 AGATTTCACATGTACGTGGTCT 57.463 40.909 19.05 10.57 37.50 3.85
4069 4115 5.607119 AAAGATTTCACATGTACGTGGTC 57.393 39.130 19.05 8.74 37.50 4.02
4070 4116 5.529430 TGAAAAGATTTCACATGTACGTGGT 59.471 36.000 19.05 2.52 37.50 4.16
4071 4117 5.996219 TGAAAAGATTTCACATGTACGTGG 58.004 37.500 19.05 8.37 37.50 4.94
4072 4118 7.906611 TTTGAAAAGATTTCACATGTACGTG 57.093 32.000 13.64 13.64 38.29 4.49
4073 4119 7.971168 TGTTTTGAAAAGATTTCACATGTACGT 59.029 29.630 0.00 0.00 0.00 3.57
4074 4120 8.334016 TGTTTTGAAAAGATTTCACATGTACG 57.666 30.769 0.00 0.00 0.00 3.67
4076 4122 8.763356 GCATGTTTTGAAAAGATTTCACATGTA 58.237 29.630 22.30 4.43 35.07 2.29
4370 4500 9.563898 CTGAATGTACATGTTACTTACTCGTTA 57.436 33.333 9.63 0.00 0.00 3.18
4373 4503 8.584600 GTTCTGAATGTACATGTTACTTACTCG 58.415 37.037 9.63 0.00 0.00 4.18
4550 4680 0.034059 ACTCAGGGTGTTTCTGCTCG 59.966 55.000 0.00 0.00 32.63 5.03
4630 4760 1.331756 GAGGACGCAATGGCATACTTG 59.668 52.381 0.00 0.00 41.24 3.16
4647 4777 8.648557 TTTACATATCAAATCAGAAGTCGAGG 57.351 34.615 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.