Multiple sequence alignment - TraesCS2D01G460500

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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 TraesCS2D01G460500 chr2D 100.000 3551 0 0 1 3551 566997266 567000816 0.000000e+00 6558.0
1 TraesCS2D01G460500 chr2D 77.778 171 31 5 3244 3408 10539005 10538836 8.110000e-17 99.0
2 TraesCS2D01G460500 chr2B 91.775 2626 139 34 965 3550 679909361 679911949 0.000000e+00 3581.0
3 TraesCS2D01G460500 chr2B 87.149 996 72 21 1 962 679908013 679908986 0.000000e+00 1079.0
4 TraesCS2D01G460500 chr2B 82.796 93 13 3 3321 3412 745043182 745043272 2.940000e-11 80.5
5 TraesCS2D01G460500 chr2A 94.248 2173 71 23 965 3097 706763384 706765542 0.000000e+00 3271.0
6 TraesCS2D01G460500 chr2A 92.508 654 27 11 317 962 706762683 706763322 0.000000e+00 917.0
7 TraesCS2D01G460500 chr2A 88.421 380 31 7 2846 3216 706766673 706767048 2.520000e-121 446.0
8 TraesCS2D01G460500 chr2A 91.822 269 20 2 1 269 706762249 706762515 1.200000e-99 374.0
9 TraesCS2D01G460500 chr2A 85.859 297 40 2 3080 3375 706765560 706765855 7.400000e-82 315.0
10 TraesCS2D01G460500 chr5D 82.825 623 82 9 1373 1995 15329775 15329178 5.220000e-148 534.0
11 TraesCS2D01G460500 chr5D 87.654 81 6 1 294 370 319372168 319372088 1.360000e-14 91.6
12 TraesCS2D01G460500 chr5B 87.912 182 21 1 2171 2352 322749212 322749032 2.780000e-51 213.0
13 TraesCS2D01G460500 chr5B 90.667 75 7 0 294 368 526822620 526822546 2.260000e-17 100.0
14 TraesCS2D01G460500 chr7A 82.143 168 21 7 3244 3404 560301712 560301547 6.180000e-28 135.0
15 TraesCS2D01G460500 chr7A 77.914 163 30 5 3250 3408 7573817 7573657 2.920000e-16 97.1
16 TraesCS2D01G460500 chr7D 78.788 165 31 3 3244 3405 48244969 48245132 1.350000e-19 108.0
17 TraesCS2D01G460500 chr7D 88.312 77 8 1 294 369 34961971 34961895 1.360000e-14 91.6
18 TraesCS2D01G460500 chr5A 89.333 75 8 0 294 368 51604502 51604576 1.050000e-15 95.3
19 TraesCS2D01G460500 chr1D 88.750 80 6 1 294 370 471188840 471188919 1.050000e-15 95.3
20 TraesCS2D01G460500 chr6B 87.059 85 4 5 294 378 67506130 67506207 4.880000e-14 89.8
21 TraesCS2D01G460500 chr6B 91.304 46 3 1 3244 3288 686216369 686216324 1.060000e-05 62.1
22 TraesCS2D01G460500 chr3A 85.714 84 10 2 286 368 823725 823643 1.760000e-13 87.9
23 TraesCS2D01G460500 chr3A 82.105 95 17 0 3314 3408 49332448 49332542 8.170000e-12 82.4
24 TraesCS2D01G460500 chr3A 83.544 79 12 1 3320 3397 9142811 9142889 4.920000e-09 73.1
25 TraesCS2D01G460500 chr3A 82.051 78 13 1 3321 3397 26529497 26529574 8.230000e-07 65.8


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 TraesCS2D01G460500 chr2D 566997266 567000816 3550 False 6558.0 6558 100.0000 1 3551 1 chr2D.!!$F1 3550
1 TraesCS2D01G460500 chr2B 679908013 679911949 3936 False 2330.0 3581 89.4620 1 3550 2 chr2B.!!$F2 3549
2 TraesCS2D01G460500 chr2A 706762249 706767048 4799 False 1064.6 3271 90.5716 1 3375 5 chr2A.!!$F1 3374
3 TraesCS2D01G460500 chr5D 15329178 15329775 597 True 534.0 534 82.8250 1373 1995 1 chr5D.!!$R1 622

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
438 573 0.110192 CTCTTCGTTGAAAAGGGCGC 60.110 55.0 0.0 0.0 31.46 6.53 F
959 1102 0.248458 GAACACAAGCAACCCACACG 60.248 55.0 0.0 0.0 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1932 2449 1.284982 GATGCGGCGCGAAGTCATAT 61.285 55.0 28.09 12.32 0.00 1.78 R
2568 3099 0.391130 AACCATGACGTCCATCGGTG 60.391 55.0 14.12 2.50 44.69 4.94 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
72 75 0.249073 CGGCCATCTCTCTAACACCG 60.249 60.000 2.24 0.00 0.00 4.94
74 77 2.029623 GGCCATCTCTCTAACACCGTA 58.970 52.381 0.00 0.00 0.00 4.02
103 106 1.771646 GGGCCTCAAACCCTAACCA 59.228 57.895 0.84 0.00 44.68 3.67
117 120 1.410153 CTAACCAATCATTGCCCCTGC 59.590 52.381 0.00 0.00 38.26 4.85
141 144 7.093858 TGCAGACCATCATTTCAAACAATATGA 60.094 33.333 0.00 0.00 0.00 2.15
152 155 6.721571 TCAAACAATATGAAGGAACTCGAC 57.278 37.500 0.00 0.00 38.49 4.20
181 184 5.335897 CGACCAAACTTCATGTTGATCCAAT 60.336 40.000 0.00 0.00 39.13 3.16
202 205 2.163010 TGGTGAGTAAATCGACCGAGAC 59.837 50.000 0.00 0.00 33.96 3.36
239 242 6.806388 AGGCAATTGTGAAATTTCAAATCC 57.194 33.333 22.07 18.14 39.21 3.01
278 281 9.872757 CTAACGTAATCAATATTTGGCGTAAAT 57.127 29.630 0.00 5.38 41.68 1.40
280 283 7.699566 ACGTAATCAATATTTGGCGTAAATGT 58.300 30.769 9.19 1.72 39.29 2.71
318 412 5.240121 TCCGTCCCAAATTACTTGTCTTAC 58.760 41.667 0.00 0.00 32.65 2.34
321 415 6.183360 CCGTCCCAAATTACTTGTCTTACATC 60.183 42.308 0.00 0.00 32.65 3.06
405 540 2.680805 CGCTTCAGCTCATCCCCTTTTA 60.681 50.000 0.00 0.00 39.32 1.52
437 572 0.517316 CCTCTTCGTTGAAAAGGGCG 59.483 55.000 0.00 0.00 31.46 6.13
438 573 0.110192 CTCTTCGTTGAAAAGGGCGC 60.110 55.000 0.00 0.00 31.46 6.53
471 606 6.206395 TCAAATACGGTGGAAACTCGTATA 57.794 37.500 7.81 0.00 45.54 1.47
472 607 6.808829 TCAAATACGGTGGAAACTCGTATAT 58.191 36.000 7.81 0.00 45.54 0.86
473 608 7.939782 TCAAATACGGTGGAAACTCGTATATA 58.060 34.615 7.81 0.00 45.54 0.86
474 609 8.579006 TCAAATACGGTGGAAACTCGTATATAT 58.421 33.333 7.81 0.00 45.54 0.86
537 672 6.147164 CCGATGTATACACGCCTGATTAATTT 59.853 38.462 7.96 0.00 0.00 1.82
548 683 5.560148 GCCTGATTAATTTGTAGTGTGTCG 58.440 41.667 0.00 0.00 0.00 4.35
679 815 4.448537 TCCAAATGCCCTTTGTTAATCG 57.551 40.909 7.75 0.00 42.29 3.34
685 823 4.712122 TGCCCTTTGTTAATCGGATTTC 57.288 40.909 8.76 3.93 0.00 2.17
710 848 8.394877 TCTTTTAGAATACCAATGTTATGCACG 58.605 33.333 0.00 0.00 0.00 5.34
711 849 6.612247 TTAGAATACCAATGTTATGCACGG 57.388 37.500 0.00 0.00 0.00 4.94
712 850 3.315191 AGAATACCAATGTTATGCACGGC 59.685 43.478 0.00 0.00 0.00 5.68
737 875 1.432270 GAGCCATACGCAGCCAAGTC 61.432 60.000 0.00 0.00 41.38 3.01
816 956 9.860898 GACAGAATGCTAAAATACTCCATTTTT 57.139 29.630 0.74 0.00 41.12 1.94
905 1045 6.734137 TCACTACAAAAACAACCATAAGCAG 58.266 36.000 0.00 0.00 0.00 4.24
931 1074 7.147976 AGAAGCAATTAACACCAAGTCAATTC 58.852 34.615 0.00 0.00 0.00 2.17
933 1076 5.009610 AGCAATTAACACCAAGTCAATTCGT 59.990 36.000 0.00 0.00 0.00 3.85
954 1097 0.249447 GCCAAGAACACAAGCAACCC 60.249 55.000 0.00 0.00 0.00 4.11
955 1098 1.110442 CCAAGAACACAAGCAACCCA 58.890 50.000 0.00 0.00 0.00 4.51
956 1099 1.202405 CCAAGAACACAAGCAACCCAC 60.202 52.381 0.00 0.00 0.00 4.61
957 1100 1.476085 CAAGAACACAAGCAACCCACA 59.524 47.619 0.00 0.00 0.00 4.17
958 1101 1.102978 AGAACACAAGCAACCCACAC 58.897 50.000 0.00 0.00 0.00 3.82
959 1102 0.248458 GAACACAAGCAACCCACACG 60.248 55.000 0.00 0.00 0.00 4.49
961 1104 3.216292 ACAAGCAACCCACACGCC 61.216 61.111 0.00 0.00 0.00 5.68
1005 1519 0.742505 CATGCGTGAAGGCCATGAAT 59.257 50.000 5.01 0.00 33.60 2.57
1022 1536 3.114606 TGAATTACCATGAGCAGGAGGA 58.885 45.455 0.00 0.00 0.00 3.71
1028 1542 1.202782 CCATGAGCAGGAGGATCAAGG 60.203 57.143 0.00 0.00 46.46 3.61
1845 2362 2.049156 TTGCTGGAGTCGCTCACG 60.049 61.111 8.71 0.00 42.01 4.35
2391 2908 1.890510 GTTCGACCAGGTGGCGTTT 60.891 57.895 0.00 0.00 39.32 3.60
2593 3124 3.242413 CGATGGACGTCATGGTTTTGATC 60.242 47.826 18.91 3.41 35.97 2.92
2594 3125 3.133141 TGGACGTCATGGTTTTGATCA 57.867 42.857 18.91 0.00 0.00 2.92
2595 3126 3.684908 TGGACGTCATGGTTTTGATCAT 58.315 40.909 18.91 0.00 0.00 2.45
2596 3127 4.078537 TGGACGTCATGGTTTTGATCATT 58.921 39.130 18.91 0.00 0.00 2.57
2597 3128 4.522405 TGGACGTCATGGTTTTGATCATTT 59.478 37.500 18.91 0.00 0.00 2.32
2598 3129 4.858692 GGACGTCATGGTTTTGATCATTTG 59.141 41.667 18.91 0.00 0.00 2.32
2599 3130 5.335583 GGACGTCATGGTTTTGATCATTTGA 60.336 40.000 18.91 0.00 0.00 2.69
2600 3131 6.271488 ACGTCATGGTTTTGATCATTTGAT 57.729 33.333 0.00 0.00 37.51 2.57
2601 3132 6.094719 ACGTCATGGTTTTGATCATTTGATG 58.905 36.000 0.00 2.59 34.37 3.07
2602 3133 5.517411 CGTCATGGTTTTGATCATTTGATGG 59.483 40.000 0.00 0.00 34.37 3.51
2603 3134 5.292589 GTCATGGTTTTGATCATTTGATGGC 59.707 40.000 0.00 0.00 34.37 4.40
2604 3135 3.847542 TGGTTTTGATCATTTGATGGCG 58.152 40.909 0.00 0.00 34.37 5.69
2605 3136 3.509184 TGGTTTTGATCATTTGATGGCGA 59.491 39.130 0.00 0.00 34.37 5.54
2606 3137 3.859386 GGTTTTGATCATTTGATGGCGAC 59.141 43.478 0.00 0.00 34.37 5.19
2607 3138 3.781079 TTTGATCATTTGATGGCGACC 57.219 42.857 0.00 0.00 34.37 4.79
2608 3139 1.298602 TGATCATTTGATGGCGACCG 58.701 50.000 0.00 0.00 34.37 4.79
2713 3244 1.578206 GCAACTTTGACCGGAGAGCC 61.578 60.000 9.46 0.00 0.00 4.70
2839 3381 0.611618 AATCAAGGGTTGGCGCATGA 60.612 50.000 10.83 1.76 39.07 3.07
2840 3382 0.396139 ATCAAGGGTTGGCGCATGAT 60.396 50.000 10.83 4.18 39.86 2.45
2841 3383 1.031571 TCAAGGGTTGGCGCATGATC 61.032 55.000 10.83 0.00 31.84 2.92
2842 3384 1.754234 AAGGGTTGGCGCATGATCC 60.754 57.895 10.83 3.58 0.00 3.36
2843 3385 3.219198 GGGTTGGCGCATGATCCC 61.219 66.667 10.83 9.66 0.00 3.85
2846 3388 1.153086 GTTGGCGCATGATCCCTCT 60.153 57.895 10.83 0.00 0.00 3.69
2848 3390 2.031768 GGCGCATGATCCCTCTCC 59.968 66.667 10.83 0.00 0.00 3.71
2849 3391 2.811514 GGCGCATGATCCCTCTCCA 61.812 63.158 10.83 0.00 0.00 3.86
2850 3392 1.374190 GCGCATGATCCCTCTCCAT 59.626 57.895 0.30 0.00 0.00 3.41
2873 3428 5.344743 TTTCTGATTTCTCTATGCGTCCT 57.655 39.130 0.00 0.00 0.00 3.85
2874 3429 4.576216 TCTGATTTCTCTATGCGTCCTC 57.424 45.455 0.00 0.00 0.00 3.71
2924 3479 5.183530 TGGTGATCTCATCAAGTTGGATT 57.816 39.130 2.34 0.00 41.69 3.01
2936 3494 6.961359 TCAAGTTGGATTATCACTAACGTG 57.039 37.500 2.34 12.12 42.59 4.49
3017 3577 9.372369 GTATATTCCAAGTGGTATATTCTGCTC 57.628 37.037 12.92 0.00 38.55 4.26
3111 3706 6.566141 TGATTGATTTGTCAACTATGCCATG 58.434 36.000 0.00 0.00 31.89 3.66
3128 3723 3.245016 GCCATGGAATCTGGATGGTGATA 60.245 47.826 18.40 0.00 39.17 2.15
3241 3837 8.540388 AGCTTGGTTATTAGACTATCTTCAACA 58.460 33.333 0.00 0.00 0.00 3.33
3248 3844 4.744795 AGACTATCTTCAACAGGCGAAT 57.255 40.909 0.00 0.00 0.00 3.34
3273 3869 4.330250 ACTTGTGATTGGATGGTCAGAAG 58.670 43.478 9.75 9.75 45.78 2.85
3274 3870 4.042062 ACTTGTGATTGGATGGTCAGAAGA 59.958 41.667 16.06 0.00 44.15 2.87
3281 3877 2.038952 TGGATGGTCAGAAGAACAGTGG 59.961 50.000 0.00 0.00 46.36 4.00
3287 3883 3.260884 GGTCAGAAGAACAGTGGTATCCA 59.739 47.826 0.00 0.00 0.00 3.41
3304 3901 5.589050 GGTATCCACTATCCAAAGGTTCAAC 59.411 44.000 0.00 0.00 0.00 3.18
3312 3909 8.960591 CACTATCCAAAGGTTCAACTCATAAAT 58.039 33.333 0.00 0.00 0.00 1.40
3325 3922 7.950512 TCAACTCATAAATTTGACATTGGTGT 58.049 30.769 0.00 0.00 42.49 4.16
3329 3926 6.976088 TCATAAATTTGACATTGGTGTTCGT 58.024 32.000 0.00 0.00 39.09 3.85
3335 3932 9.921637 AAATTTGACATTGGTGTTCGTATTATT 57.078 25.926 0.00 0.00 39.09 1.40
3362 3959 0.316841 TTTTTCAGCCATTCCGGTGC 59.683 50.000 0.00 0.06 36.97 5.01
3376 3973 0.735978 CGGTGCTATGCGTTCAGTGA 60.736 55.000 0.00 0.00 0.00 3.41
3404 4001 1.706443 GTTCCCGTCGACTACAAAGG 58.294 55.000 14.70 5.96 0.00 3.11
3405 4002 1.000171 GTTCCCGTCGACTACAAAGGT 60.000 52.381 14.70 0.00 0.00 3.50
3408 4005 1.541147 CCCGTCGACTACAAAGGTGTA 59.459 52.381 14.70 0.00 39.30 2.90
3410 4007 2.227388 CCGTCGACTACAAAGGTGTACT 59.773 50.000 14.70 0.00 39.30 2.73
3415 4012 1.001633 ACTACAAAGGTGTACTGGCCG 59.998 52.381 0.00 0.00 39.30 6.13
3421 4018 0.542232 AGGTGTACTGGCCGAGTCTT 60.542 55.000 10.60 0.00 35.96 3.01
3440 4039 7.467947 CGAGTCTTTCAGTTGCTCATAGAGATA 60.468 40.741 0.00 0.00 0.00 1.98
3441 4040 7.715657 AGTCTTTCAGTTGCTCATAGAGATAG 58.284 38.462 0.00 0.00 0.00 2.08
3442 4041 6.922957 GTCTTTCAGTTGCTCATAGAGATAGG 59.077 42.308 0.00 0.00 0.00 2.57
3444 4043 4.809193 TCAGTTGCTCATAGAGATAGGGT 58.191 43.478 0.00 0.00 0.00 4.34
3445 4044 5.953571 TCAGTTGCTCATAGAGATAGGGTA 58.046 41.667 0.00 0.00 0.00 3.69
3446 4045 6.556639 TCAGTTGCTCATAGAGATAGGGTAT 58.443 40.000 0.00 0.00 0.00 2.73
3451 4050 5.128335 TGCTCATAGAGATAGGGTATGCATG 59.872 44.000 10.16 0.00 0.00 4.06
3453 4052 5.025453 TCATAGAGATAGGGTATGCATGCA 58.975 41.667 25.04 25.04 0.00 3.96
3457 4056 4.779489 AGAGATAGGGTATGCATGCATGTA 59.221 41.667 37.43 23.60 37.82 2.29
3465 4064 5.066893 GGGTATGCATGCATGTATTCATAGG 59.933 44.000 37.43 2.34 37.82 2.57
3466 4065 5.882000 GGTATGCATGCATGTATTCATAGGA 59.118 40.000 37.43 14.56 37.82 2.94
3471 4070 6.661805 TGCATGCATGTATTCATAGGAATGAT 59.338 34.615 26.79 2.27 43.47 2.45
3488 4087 8.703604 AGGAATGATTGTATATGCGTATGTAC 57.296 34.615 12.38 12.38 33.09 2.90
3493 4092 7.779349 TGATTGTATATGCGTATGTACAAACG 58.221 34.615 29.16 0.00 46.74 3.60
3494 4093 7.648510 TGATTGTATATGCGTATGTACAAACGA 59.351 33.333 29.16 18.30 46.74 3.85
3501 4100 4.143284 TGCGTATGTACAAACGATGTGTTC 60.143 41.667 0.00 0.00 43.77 3.18
3502 4101 4.143284 GCGTATGTACAAACGATGTGTTCA 60.143 41.667 0.00 4.75 43.77 3.18
3506 4105 7.008901 CGTATGTACAAACGATGTGTTCATACT 59.991 37.037 25.27 8.65 43.77 2.12
3534 4135 6.432607 AAAAACTATCTTTAACGGCTAGCC 57.567 37.500 24.75 24.75 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 2.238646 AGATGGCCGTGTGAGGAAATTA 59.761 45.455 0.00 0.00 0.00 1.40
86 89 2.100197 GATTGGTTAGGGTTTGAGGCC 58.900 52.381 0.00 0.00 0.00 5.19
117 120 9.297586 CTTCATATTGTTTGAAATGATGGTCTG 57.702 33.333 0.00 0.00 32.98 3.51
141 144 0.319641 GTCGCCTTGTCGAGTTCCTT 60.320 55.000 0.00 0.00 39.34 3.36
152 155 1.608590 ACATGAAGTTTGGTCGCCTTG 59.391 47.619 0.00 0.00 0.00 3.61
181 184 2.163010 GTCTCGGTCGATTTACTCACCA 59.837 50.000 0.00 0.00 0.00 4.17
202 205 7.988737 TCACAATTGCCTAAGAATTCACTATG 58.011 34.615 8.44 0.00 0.00 2.23
246 249 9.724839 GCCAAATATTGATTACGTTAGCTTTAA 57.275 29.630 0.00 0.00 0.00 1.52
256 259 8.555166 AACATTTACGCCAAATATTGATTACG 57.445 30.769 0.00 0.00 34.99 3.18
278 281 6.156602 TGGGACGGAGGTTATATTTCTTAACA 59.843 38.462 0.00 0.00 32.38 2.41
280 283 6.811634 TGGGACGGAGGTTATATTTCTTAA 57.188 37.500 0.00 0.00 0.00 1.85
290 310 4.041938 ACAAGTAATTTGGGACGGAGGTTA 59.958 41.667 0.00 0.00 41.25 2.85
291 311 3.181437 ACAAGTAATTTGGGACGGAGGTT 60.181 43.478 0.00 0.00 41.25 3.50
318 412 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
321 415 9.751542 ATTTGTCTTAGATTTGTCTAGATACGG 57.248 33.333 0.00 0.00 0.00 4.02
358 493 6.851965 ATCCTTCTTAGTAGTACTCCCTCT 57.148 41.667 5.96 0.00 0.00 3.69
405 540 7.504924 TCAACGAAGAGGTAAATGATTGTTT 57.495 32.000 0.00 0.00 0.00 2.83
437 572 5.235616 TCCACCGTATTTGAAAGATTATCGC 59.764 40.000 0.00 0.00 0.00 4.58
438 573 6.838198 TCCACCGTATTTGAAAGATTATCG 57.162 37.500 0.00 0.00 0.00 2.92
537 672 2.253154 CGACGGCGACACACTACA 59.747 61.111 16.62 0.00 40.82 2.74
685 823 7.643764 CCGTGCATAACATTGGTATTCTAAAAG 59.356 37.037 0.00 0.00 0.00 2.27
712 850 4.155733 TGCGTATGGCTCCCGTGG 62.156 66.667 0.00 0.00 44.05 4.94
816 956 2.072487 GGGAGCAGGACCAGGCATA 61.072 63.158 10.37 0.00 0.00 3.14
905 1045 5.689383 TGACTTGGTGTTAATTGCTTCTC 57.311 39.130 0.00 0.00 0.00 2.87
931 1074 0.100325 TGCTTGTGTTCTTGGCAACG 59.900 50.000 0.00 0.00 42.51 4.10
933 1076 1.134848 GGTTGCTTGTGTTCTTGGCAA 60.135 47.619 0.00 0.00 39.99 4.52
954 1097 1.597027 AAGAACGAAGGGGCGTGTG 60.597 57.895 0.00 0.00 44.86 3.82
955 1098 1.597027 CAAGAACGAAGGGGCGTGT 60.597 57.895 0.00 0.00 44.86 4.49
956 1099 2.966309 GCAAGAACGAAGGGGCGTG 61.966 63.158 0.00 0.00 44.86 5.34
958 1101 3.788766 CGCAAGAACGAAGGGGCG 61.789 66.667 0.00 0.00 43.02 6.13
1005 1519 2.763039 TGATCCTCCTGCTCATGGTAA 58.237 47.619 0.00 0.00 0.00 2.85
1022 1536 4.514577 CGACGGCGAGCCCTTGAT 62.515 66.667 16.62 0.00 40.82 2.57
1049 1563 1.594293 CAGTCCAAGCCGTCGTTGT 60.594 57.895 0.00 0.00 0.00 3.32
1350 1864 3.996124 CCCGGCCTATCCTGCTCG 61.996 72.222 0.00 0.00 0.00 5.03
1929 2446 2.365068 CGGCGCGAAGTCATATCCG 61.365 63.158 12.10 5.85 0.00 4.18
1932 2449 1.284982 GATGCGGCGCGAAGTCATAT 61.285 55.000 28.09 12.32 0.00 1.78
2563 3089 2.602267 ACGTCCATCGGTGTCCCA 60.602 61.111 0.00 0.00 44.69 4.37
2568 3099 0.391130 AACCATGACGTCCATCGGTG 60.391 55.000 14.12 2.50 44.69 4.94
2593 3124 1.226379 GTGCGGTCGCCATCAAATG 60.226 57.895 12.94 0.00 41.09 2.32
2594 3125 1.031571 ATGTGCGGTCGCCATCAAAT 61.032 50.000 12.94 0.00 41.09 2.32
2595 3126 1.643868 GATGTGCGGTCGCCATCAAA 61.644 55.000 26.17 4.50 42.64 2.69
2596 3127 2.046411 ATGTGCGGTCGCCATCAA 60.046 55.556 12.94 0.00 41.09 2.57
2597 3128 2.511373 GATGTGCGGTCGCCATCA 60.511 61.111 26.17 17.95 42.64 3.07
2598 3129 3.272334 GGATGTGCGGTCGCCATC 61.272 66.667 24.61 24.61 42.51 3.51
2599 3130 4.856801 GGGATGTGCGGTCGCCAT 62.857 66.667 12.94 14.34 41.09 4.40
2603 3134 2.593468 AATCCTGGGATGTGCGGTCG 62.593 60.000 2.59 0.00 34.70 4.79
2604 3135 1.097547 CAATCCTGGGATGTGCGGTC 61.098 60.000 2.59 0.00 34.70 4.79
2605 3136 1.077501 CAATCCTGGGATGTGCGGT 60.078 57.895 2.59 0.00 34.70 5.68
2606 3137 1.825191 CCAATCCTGGGATGTGCGG 60.825 63.158 2.59 0.00 39.30 5.69
2607 3138 3.831883 CCAATCCTGGGATGTGCG 58.168 61.111 2.59 0.00 39.30 5.34
2617 3148 1.333636 CCTCGCTCTCCACCAATCCT 61.334 60.000 0.00 0.00 0.00 3.24
2809 3351 5.867174 GCCAACCCTTGATTAATTTGTACAC 59.133 40.000 0.00 0.00 0.00 2.90
2839 3381 6.160105 AGAGAAATCAGAAAATGGAGAGGGAT 59.840 38.462 0.00 0.00 0.00 3.85
2840 3382 5.490357 AGAGAAATCAGAAAATGGAGAGGGA 59.510 40.000 0.00 0.00 0.00 4.20
2841 3383 5.753716 AGAGAAATCAGAAAATGGAGAGGG 58.246 41.667 0.00 0.00 0.00 4.30
2842 3384 7.041235 GCATAGAGAAATCAGAAAATGGAGAGG 60.041 40.741 0.00 0.00 0.00 3.69
2843 3385 7.307278 CGCATAGAGAAATCAGAAAATGGAGAG 60.307 40.741 0.00 0.00 0.00 3.20
2846 3388 6.115446 ACGCATAGAGAAATCAGAAAATGGA 58.885 36.000 0.00 0.00 0.00 3.41
2848 3390 6.259608 AGGACGCATAGAGAAATCAGAAAATG 59.740 38.462 0.00 0.00 0.00 2.32
2849 3391 6.352516 AGGACGCATAGAGAAATCAGAAAAT 58.647 36.000 0.00 0.00 0.00 1.82
2850 3392 5.734720 AGGACGCATAGAGAAATCAGAAAA 58.265 37.500 0.00 0.00 0.00 2.29
3248 3844 4.074259 CTGACCATCCAATCACAAGTTGA 58.926 43.478 10.54 0.00 39.11 3.18
3262 3858 3.409026 ACCACTGTTCTTCTGACCATC 57.591 47.619 0.00 0.00 0.00 3.51
3281 3877 6.415573 AGTTGAACCTTTGGATAGTGGATAC 58.584 40.000 0.00 0.00 0.00 2.24
3287 3883 9.533831 AATTTATGAGTTGAACCTTTGGATAGT 57.466 29.630 0.00 0.00 0.00 2.12
3290 3886 8.869109 TCAAATTTATGAGTTGAACCTTTGGAT 58.131 29.630 0.00 0.00 39.20 3.41
3295 3891 9.480053 CAATGTCAAATTTATGAGTTGAACCTT 57.520 29.630 0.00 0.00 43.20 3.50
3304 3901 7.083858 ACGAACACCAATGTCAAATTTATGAG 58.916 34.615 0.00 0.00 38.45 2.90
3344 3941 0.539438 AGCACCGGAATGGCTGAAAA 60.539 50.000 9.46 0.00 43.94 2.29
3352 3949 0.304705 GAACGCATAGCACCGGAATG 59.695 55.000 9.46 7.47 0.00 2.67
3360 3957 2.076100 CCTTTCACTGAACGCATAGCA 58.924 47.619 0.00 0.00 0.00 3.49
3362 3959 3.614616 GTCTCCTTTCACTGAACGCATAG 59.385 47.826 0.00 0.00 0.00 2.23
3388 3985 0.316204 ACACCTTTGTAGTCGACGGG 59.684 55.000 10.46 9.14 32.60 5.28
3404 4001 1.000506 TGAAAGACTCGGCCAGTACAC 59.999 52.381 2.24 0.00 34.41 2.90
3405 4002 1.272490 CTGAAAGACTCGGCCAGTACA 59.728 52.381 2.24 4.24 34.41 2.90
3408 4005 0.759346 AACTGAAAGACTCGGCCAGT 59.241 50.000 2.24 5.43 39.49 4.00
3410 4007 0.884704 GCAACTGAAAGACTCGGCCA 60.885 55.000 2.24 0.00 37.43 5.36
3415 4012 5.960113 TCTCTATGAGCAACTGAAAGACTC 58.040 41.667 0.00 0.00 37.43 3.36
3421 4018 5.211973 ACCCTATCTCTATGAGCAACTGAA 58.788 41.667 0.00 0.00 0.00 3.02
3440 4039 4.103013 TGAATACATGCATGCATACCCT 57.897 40.909 31.73 17.10 34.91 4.34
3441 4040 5.066893 CCTATGAATACATGCATGCATACCC 59.933 44.000 31.73 18.61 37.87 3.69
3442 4041 5.882000 TCCTATGAATACATGCATGCATACC 59.118 40.000 31.73 18.29 37.87 2.73
3444 4043 7.830201 TCATTCCTATGAATACATGCATGCATA 59.170 33.333 31.73 18.79 39.20 3.14
3445 4044 6.661805 TCATTCCTATGAATACATGCATGCAT 59.338 34.615 27.46 27.46 39.20 3.96
3446 4045 6.005198 TCATTCCTATGAATACATGCATGCA 58.995 36.000 26.53 25.04 39.20 3.96
3471 4070 7.435784 ACATCGTTTGTACATACGCATATACAA 59.564 33.333 27.35 12.73 36.57 2.41
3477 4076 3.930229 ACACATCGTTTGTACATACGCAT 59.070 39.130 27.35 19.75 36.57 4.73
3491 4090 9.431887 AGTTTTTATACAGTATGAACACATCGT 57.568 29.630 13.86 0.00 39.69 3.73


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

AutoCloner maintained by Alex Coulton.