Multiple sequence alignment - TraesCS3B01G262500

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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 TraesCS3B01G262500 chr3B 100.000 3374 0 0 1 3374 421213073 421216446 0.000000e+00 6231.0
1 TraesCS3B01G262500 chr3D 91.323 3423 192 37 1 3374 299927805 299924439 0.000000e+00 4578.0
2 TraesCS3B01G262500 chr3D 82.991 341 54 4 2973 3310 553748013 553747674 4.230000e-79 305.0
3 TraesCS3B01G262500 chr3D 87.029 239 27 4 3062 3298 41420794 41420558 2.000000e-67 267.0
4 TraesCS3B01G262500 chr3D 82.566 304 41 6 3062 3355 38908172 38907871 1.200000e-64 257.0
5 TraesCS3B01G262500 chr3D 82.000 300 43 6 3058 3347 427287635 427287933 9.350000e-61 244.0
6 TraesCS3B01G262500 chr3D 81.513 119 19 3 3107 3223 431363472 431363589 9.970000e-16 95.3
7 TraesCS3B01G262500 chr3D 88.462 52 3 2 2962 3010 146266397 146266448 3.640000e-05 60.2
8 TraesCS3B01G262500 chr3A 90.980 1663 101 23 1 1646 435773328 435774958 0.000000e+00 2194.0
9 TraesCS3B01G262500 chr3A 94.922 965 25 8 1671 2627 435775046 435775994 0.000000e+00 1489.0
10 TraesCS3B01G262500 chr6A 79.310 493 84 11 2831 3317 601943579 601944059 2.510000e-86 329.0
11 TraesCS3B01G262500 chr6A 88.462 52 3 2 2962 3010 72333658 72333709 3.640000e-05 60.2
12 TraesCS3B01G262500 chr7D 82.895 304 39 8 3062 3355 453107314 453107614 9.290000e-66 261.0
13 TraesCS3B01G262500 chr4B 84.980 253 31 5 3061 3310 514588773 514588525 2.010000e-62 250.0
14 TraesCS3B01G262500 chr7A 84.314 255 37 3 3058 3310 34974757 34974504 2.600000e-61 246.0
15 TraesCS3B01G262500 chr7A 88.462 52 3 2 2962 3010 170474499 170474448 3.640000e-05 60.2
16 TraesCS3B01G262500 chr1A 73.077 598 128 29 2738 3310 522077089 522076500 7.440000e-42 182.0
17 TraesCS3B01G262500 chr6D 80.769 130 20 5 3097 3223 64296266 64296393 2.770000e-16 97.1
18 TraesCS3B01G262500 chr5D 88.462 52 3 2 2962 3010 191468549 191468498 3.640000e-05 60.2
19 TraesCS3B01G262500 chr5D 88.235 51 4 2 2962 3010 428940914 428940864 3.640000e-05 60.2


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 TraesCS3B01G262500 chr3B 421213073 421216446 3373 False 6231.0 6231 100.000 1 3374 1 chr3B.!!$F1 3373
1 TraesCS3B01G262500 chr3D 299924439 299927805 3366 True 4578.0 4578 91.323 1 3374 1 chr3D.!!$R3 3373
2 TraesCS3B01G262500 chr3A 435773328 435775994 2666 False 1841.5 2194 92.951 1 2627 2 chr3A.!!$F1 2626

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
263 264 0.320421 GGCTTACAAGGCGTGACAGA 60.320 55.0 7.60 0.00 41.93 3.41 F
514 516 0.390735 GTGAAGTAATGCGTCCCCGT 60.391 55.0 0.00 0.00 36.15 5.28 F
707 715 0.736636 ACGAGGCATGCATCACATTG 59.263 50.0 29.58 16.38 36.64 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1685 1785 0.036306 GGCGAAGAGAAACCTTGGGA 59.964 55.0 0.00 0.0 0.0 4.37 R
1687 1787 0.320421 TCGGCGAAGAGAAACCTTGG 60.320 55.0 7.35 0.0 0.0 3.61 R
2543 2652 0.607620 TCACACAGGATCATGTCGCA 59.392 50.0 10.64 0.0 0.0 5.10 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
69 70 1.138661 CTTCTCCCCTAGCAAGCTCTG 59.861 57.143 0.00 0.00 0.00 3.35
72 73 1.142748 CCCCTAGCAAGCTCTGTCG 59.857 63.158 0.00 0.00 0.00 4.35
79 80 4.749310 AAGCTCTGTCGCTGCCGG 62.749 66.667 0.00 0.00 40.79 6.13
98 99 3.426117 GACCGCGGACACCATCGAT 62.426 63.158 35.90 4.22 0.00 3.59
117 118 2.436109 CCCTGGAGGTGGTTGGTG 59.564 66.667 0.00 0.00 0.00 4.17
149 150 0.453793 CTCCAACCGTGCAACAACAA 59.546 50.000 0.00 0.00 35.74 2.83
154 155 2.407210 CGTGCAACAACAACGCCT 59.593 55.556 0.00 0.00 35.74 5.52
156 157 1.588667 GTGCAACAACAACGCCTGG 60.589 57.895 0.00 0.00 36.32 4.45
186 187 1.002684 CGAATAGAAGGACGTCGAGGG 60.003 57.143 9.92 0.00 0.00 4.30
215 216 0.868406 GGTGTTGCACTTCTTCCTCG 59.132 55.000 0.00 0.00 34.40 4.63
217 218 0.884704 TGTTGCACTTCTTCCTCGCC 60.885 55.000 0.00 0.00 0.00 5.54
219 220 0.973632 TTGCACTTCTTCCTCGCCTA 59.026 50.000 0.00 0.00 0.00 3.93
221 222 0.802607 GCACTTCTTCCTCGCCTACG 60.803 60.000 0.00 0.00 42.01 3.51
263 264 0.320421 GGCTTACAAGGCGTGACAGA 60.320 55.000 7.60 0.00 41.93 3.41
271 272 1.557099 AGGCGTGACAGAGGTATTGA 58.443 50.000 0.00 0.00 0.00 2.57
336 337 0.957888 GGCTCTTCAGTTGCTCCCAC 60.958 60.000 0.00 0.00 0.00 4.61
347 348 1.451927 GCTCCCACGATGATGCCAA 60.452 57.895 0.00 0.00 0.00 4.52
355 356 1.139520 GATGATGCCAAACGCCCAC 59.860 57.895 0.00 0.00 36.24 4.61
356 357 1.594194 GATGATGCCAAACGCCCACA 61.594 55.000 0.00 0.00 36.24 4.17
398 400 4.429212 CGATGTCGCCCGTGGTGA 62.429 66.667 2.49 2.49 40.17 4.02
463 465 2.582436 CGGAGCGGGGCTTTTCTA 59.418 61.111 0.00 0.00 39.88 2.10
514 516 0.390735 GTGAAGTAATGCGTCCCCGT 60.391 55.000 0.00 0.00 36.15 5.28
524 526 3.468140 GTCCCCGTGAGTAGGCCC 61.468 72.222 0.00 0.00 0.00 5.80
532 534 1.019805 GTGAGTAGGCCCGAAGCAAC 61.020 60.000 0.00 0.00 46.50 4.17
535 537 1.206371 GAGTAGGCCCGAAGCAACTAA 59.794 52.381 0.00 0.00 46.50 2.24
549 551 8.184192 CCGAAGCAACTAATGAAGTAATCAAAT 58.816 33.333 0.00 0.00 42.54 2.32
625 633 7.253190 GCGGTGATTTTTATGACGAAATGTAAC 60.253 37.037 0.00 0.00 0.00 2.50
629 637 8.496751 TGATTTTTATGACGAAATGTAACGTGA 58.503 29.630 0.00 0.00 42.74 4.35
659 667 3.081061 TGCTAATGACATTGTGGTGGTC 58.919 45.455 11.05 0.00 0.00 4.02
672 680 3.123050 GTGGTGGTCTTTTGCATTTCAC 58.877 45.455 0.00 0.00 0.00 3.18
692 700 4.095036 TCACTGCATAGACTCACTAACGAG 59.905 45.833 0.00 0.00 39.05 4.18
693 701 3.378742 ACTGCATAGACTCACTAACGAGG 59.621 47.826 0.00 0.00 37.34 4.63
707 715 0.736636 ACGAGGCATGCATCACATTG 59.263 50.000 29.58 16.38 36.64 2.82
763 772 3.070018 CGGAGAGCAGAGAACACAAAAT 58.930 45.455 0.00 0.00 0.00 1.82
804 818 3.747854 ATAAAGTTAGCCGAGCCCTAC 57.252 47.619 0.00 0.00 0.00 3.18
825 839 7.108847 CCTACAAAACATCTCTCTTTCATCCT 58.891 38.462 0.00 0.00 0.00 3.24
826 840 7.279758 CCTACAAAACATCTCTCTTTCATCCTC 59.720 40.741 0.00 0.00 0.00 3.71
870 884 7.499232 CCAAAACCCGATGAACTAGAGATTTAT 59.501 37.037 0.00 0.00 0.00 1.40
1386 1402 2.023791 GGGAGAGGACCTCTACTTCCTT 60.024 54.545 29.36 4.52 42.68 3.36
1464 1480 3.462678 GACCTCTCGGCCCAGTCC 61.463 72.222 0.00 0.00 0.00 3.85
1650 1746 2.668457 CAGCACTAACCTTGACGATGAC 59.332 50.000 0.00 0.00 0.00 3.06
1671 1767 7.045725 TGACGATACGTTTCATCTTTCTTTC 57.954 36.000 6.81 0.00 41.37 2.62
1674 1774 8.084590 ACGATACGTTTCATCTTTCTTTCTTT 57.915 30.769 6.81 0.00 36.35 2.52
1676 1776 9.382244 CGATACGTTTCATCTTTCTTTCTTTTT 57.618 29.630 6.81 0.00 0.00 1.94
1878 1978 0.530744 GCGTGATGGTGTACTCAGGA 59.469 55.000 6.70 0.00 30.74 3.86
2010 2110 0.387622 GATCAACGGTGGTCGACGAA 60.388 55.000 9.92 0.00 42.43 3.85
2043 2143 3.670377 GTGAAGTTGGTGGCGGGC 61.670 66.667 0.00 0.00 0.00 6.13
2337 2437 1.524863 CCGTGTCGTCCACCTTCTCT 61.525 60.000 3.10 0.00 41.26 3.10
2409 2518 2.427232 TGCTTGTGTCTGTACGTACC 57.573 50.000 22.43 8.27 0.00 3.34
2543 2652 3.849951 CTGGGGCCGTCGCATAGT 61.850 66.667 0.00 0.00 37.69 2.12
2544 2653 4.155733 TGGGGCCGTCGCATAGTG 62.156 66.667 0.00 0.00 36.38 2.74
2652 2764 3.287867 AATCTGGTATGTGCCTTCCTG 57.712 47.619 0.00 0.00 0.00 3.86
2696 2808 9.609950 GTATGTACCTAGAAAATCGTGTATCTC 57.390 37.037 0.00 0.00 0.00 2.75
2715 2827 2.410638 CTTCGTGTTCACGTCCGGGA 62.411 60.000 21.61 0.00 0.00 5.14
2723 2835 3.692406 ACGTCCGGGAGCCAAGAC 61.692 66.667 0.00 0.00 0.00 3.01
2729 2841 1.376037 CGGGAGCCAAGACAGAACC 60.376 63.158 0.00 0.00 0.00 3.62
2730 2842 1.376037 GGGAGCCAAGACAGAACCG 60.376 63.158 0.00 0.00 0.00 4.44
2731 2843 2.035442 GGAGCCAAGACAGAACCGC 61.035 63.158 0.00 0.00 0.00 5.68
2732 2844 1.301716 GAGCCAAGACAGAACCGCA 60.302 57.895 0.00 0.00 0.00 5.69
2733 2845 1.294659 GAGCCAAGACAGAACCGCAG 61.295 60.000 0.00 0.00 0.00 5.18
2734 2846 1.598130 GCCAAGACAGAACCGCAGT 60.598 57.895 0.00 0.00 0.00 4.40
2735 2847 1.845809 GCCAAGACAGAACCGCAGTG 61.846 60.000 0.00 0.00 0.00 3.66
2736 2848 1.230635 CCAAGACAGAACCGCAGTGG 61.231 60.000 0.00 0.00 46.41 4.00
2776 2888 3.982516 ACTGTCTACTAAGGGCATCTCA 58.017 45.455 0.00 0.00 0.00 3.27
2785 2897 3.287867 AAGGGCATCTCAAATGACGAT 57.712 42.857 0.00 0.00 0.00 3.73
2789 2901 2.289002 GGCATCTCAAATGACGATCCAC 59.711 50.000 0.00 0.00 0.00 4.02
2802 2914 4.642885 TGACGATCCACAAATTTTATCCCC 59.357 41.667 0.00 0.00 0.00 4.81
2817 2929 4.189580 CCCCATCCGGCCGTGAAT 62.190 66.667 26.12 11.82 0.00 2.57
2824 2960 1.067582 CCGGCCGTGAATAGAGGAC 59.932 63.158 26.12 0.00 0.00 3.85
2827 2963 0.105039 GGCCGTGAATAGAGGACCAG 59.895 60.000 0.00 0.00 0.00 4.00
2830 2966 2.379972 CCGTGAATAGAGGACCAGTCT 58.620 52.381 0.00 0.00 0.00 3.24
2836 2972 0.259065 TAGAGGACCAGTCTGCGGAT 59.741 55.000 0.00 0.00 0.00 4.18
2859 2995 3.757248 ATGCGGGAGGGCGTCATTC 62.757 63.158 9.66 0.00 35.06 2.67
2860 2996 4.467084 GCGGGAGGGCGTCATTCA 62.467 66.667 9.66 0.00 0.00 2.57
2863 2999 0.105964 CGGGAGGGCGTCATTCAATA 59.894 55.000 9.66 0.00 0.00 1.90
2864 3000 1.270839 CGGGAGGGCGTCATTCAATAT 60.271 52.381 9.66 0.00 0.00 1.28
2870 3006 3.067180 AGGGCGTCATTCAATATTGCTTG 59.933 43.478 10.76 10.20 0.00 4.01
2878 3014 7.380333 CGTCATTCAATATTGCTTGCATACATT 59.620 33.333 10.76 0.00 0.00 2.71
2880 3016 9.602568 TCATTCAATATTGCTTGCATACATTTT 57.397 25.926 10.76 0.00 0.00 1.82
2942 3083 5.668558 AGATTTCATATAAACCGAACGCC 57.331 39.130 0.00 0.00 0.00 5.68
2953 3094 2.006888 ACCGAACGCCATTCATGTAAG 58.993 47.619 0.00 0.00 37.12 2.34
2954 3095 1.330521 CCGAACGCCATTCATGTAAGG 59.669 52.381 0.00 0.00 37.12 2.69
2955 3096 1.330521 CGAACGCCATTCATGTAAGGG 59.669 52.381 0.00 0.00 42.15 3.95
2956 3097 2.639065 GAACGCCATTCATGTAAGGGA 58.361 47.619 11.23 0.00 41.79 4.20
2957 3098 3.214328 GAACGCCATTCATGTAAGGGAT 58.786 45.455 11.23 0.00 41.79 3.85
2958 3099 3.297134 ACGCCATTCATGTAAGGGATT 57.703 42.857 11.23 0.00 41.79 3.01
2959 3100 4.431416 ACGCCATTCATGTAAGGGATTA 57.569 40.909 11.23 0.00 41.79 1.75
2960 3101 4.389374 ACGCCATTCATGTAAGGGATTAG 58.611 43.478 11.23 3.89 41.79 1.73
2961 3102 4.102524 ACGCCATTCATGTAAGGGATTAGA 59.897 41.667 11.23 0.00 41.79 2.10
2967 3108 7.339212 CCATTCATGTAAGGGATTAGAACACAA 59.661 37.037 3.42 0.00 41.79 3.33
2968 3109 7.681939 TTCATGTAAGGGATTAGAACACAAC 57.318 36.000 0.00 0.00 0.00 3.32
3059 3200 1.518367 TGTTCCCTTCCTTGGACTGT 58.482 50.000 0.00 0.00 0.00 3.55
3066 3207 1.552792 CTTCCTTGGACTGTCTCCTCC 59.447 57.143 7.85 0.00 40.26 4.30
3072 3213 1.439644 GACTGTCTCCTCCATCCGC 59.560 63.158 0.00 0.00 0.00 5.54
3073 3214 2.343163 GACTGTCTCCTCCATCCGCG 62.343 65.000 0.00 0.00 0.00 6.46
3079 3220 4.514577 CCTCCATCCGCGCGTCTT 62.515 66.667 29.95 9.99 0.00 3.01
3080 3221 2.956964 CTCCATCCGCGCGTCTTC 60.957 66.667 29.95 0.00 0.00 2.87
3131 3272 1.888436 AACTGCGATCTCCGGCAAGA 61.888 55.000 0.00 0.00 39.04 3.02
3188 3329 1.093159 CACAAGATCTTGCTGCCTCC 58.907 55.000 30.95 0.00 44.03 4.30
3203 3344 1.742768 CTCCCGTGCCCTACTCATC 59.257 63.158 0.00 0.00 0.00 2.92
3270 3411 1.729881 GATGGAAATGGTGGCGCTC 59.270 57.895 7.64 0.23 0.00 5.03
3290 3431 2.509336 GCTGTCATCGTCCCACCG 60.509 66.667 0.00 0.00 0.00 4.94
3310 3451 1.437986 GCCGCCTGATAGTTCGTCT 59.562 57.895 0.00 0.00 0.00 4.18
3313 3454 1.674441 CCGCCTGATAGTTCGTCTACA 59.326 52.381 0.00 0.00 0.00 2.74
3315 3456 2.733517 GCCTGATAGTTCGTCTACAGC 58.266 52.381 0.00 0.00 32.13 4.40
3316 3457 2.099263 GCCTGATAGTTCGTCTACAGCA 59.901 50.000 0.00 0.00 32.13 4.41
3342 3485 1.663702 CGGCGTTGTTCTCCTTCGT 60.664 57.895 0.00 0.00 0.00 3.85
3344 3487 0.599204 GGCGTTGTTCTCCTTCGTGA 60.599 55.000 0.00 0.00 0.00 4.35
3347 3490 1.993370 CGTTGTTCTCCTTCGTGATCC 59.007 52.381 0.00 0.00 0.00 3.36
3357 3500 3.083349 CGTGATCCCCTGGAGGCA 61.083 66.667 0.00 0.00 34.05 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 97 1.379044 CAACCACCTCCAGGGCATC 60.379 63.158 0.00 0.00 40.27 3.91
98 99 3.579302 CCAACCACCTCCAGGGCA 61.579 66.667 0.00 0.00 40.27 5.36
117 118 3.254024 TTGGAGCGAGGGCCTTGTC 62.254 63.158 21.87 16.45 41.24 3.18
154 155 0.975556 TCTATTCGAGTGCTGGGCCA 60.976 55.000 5.85 5.85 0.00 5.36
156 157 1.576356 CTTCTATTCGAGTGCTGGGC 58.424 55.000 0.00 0.00 0.00 5.36
193 194 1.082756 GAAGAAGTGCAACACCGCG 60.083 57.895 0.00 0.00 41.43 6.46
203 204 0.179134 CCGTAGGCGAGGAAGAAGTG 60.179 60.000 0.00 0.00 46.14 3.16
221 222 1.922135 ATGGACAATTGCACGTCGCC 61.922 55.000 5.05 0.00 41.33 5.54
255 256 2.492088 TGACCTCAATACCTCTGTCACG 59.508 50.000 0.00 0.00 0.00 4.35
259 260 2.840038 TGCATGACCTCAATACCTCTGT 59.160 45.455 0.00 0.00 0.00 3.41
263 264 1.555075 ACGTGCATGACCTCAATACCT 59.445 47.619 14.17 0.00 0.00 3.08
298 299 2.665185 GTTGAGTTGCCGGAGCGT 60.665 61.111 5.05 0.00 44.31 5.07
309 310 2.843701 CAACTGAAGAGCCTGTTGAGT 58.156 47.619 0.00 0.00 43.91 3.41
336 337 2.405805 TGGGCGTTTGGCATCATCG 61.406 57.895 0.00 0.00 46.16 3.84
347 348 3.542676 TCGTGGTCTGTGGGCGTT 61.543 61.111 0.00 0.00 0.00 4.84
389 391 1.078426 GTCCAAGGATCACCACGGG 60.078 63.158 0.00 0.00 38.94 5.28
398 400 2.185350 CTCGCTGCGTCCAAGGAT 59.815 61.111 22.48 0.00 0.00 3.24
463 465 2.588877 CGATCGCCGGAATGCCTT 60.589 61.111 5.05 0.00 33.91 4.35
491 493 2.934553 GGGGACGCATTACTTCACTAAC 59.065 50.000 0.00 0.00 0.00 2.34
514 516 1.192146 AGTTGCTTCGGGCCTACTCA 61.192 55.000 0.84 0.00 40.92 3.41
524 526 9.214953 GATTTGATTACTTCATTAGTTGCTTCG 57.785 33.333 0.00 0.00 38.33 3.79
580 586 1.404047 GCACCGGAAAATTGACATGGG 60.404 52.381 9.46 0.00 0.00 4.00
595 603 2.780993 GTCATAAAAATCACCGCACCG 58.219 47.619 0.00 0.00 0.00 4.94
612 620 3.655486 ACCATCACGTTACATTTCGTCA 58.345 40.909 0.00 0.00 38.23 4.35
625 633 2.419673 TCATTAGCAGCAAACCATCACG 59.580 45.455 0.00 0.00 0.00 4.35
629 637 4.221262 ACAATGTCATTAGCAGCAAACCAT 59.779 37.500 0.00 0.00 0.00 3.55
672 680 3.793801 GCCTCGTTAGTGAGTCTATGCAG 60.794 52.174 0.00 0.00 34.04 4.41
677 685 2.099263 GCATGCCTCGTTAGTGAGTCTA 59.901 50.000 6.36 0.00 34.04 2.59
679 687 1.281899 GCATGCCTCGTTAGTGAGTC 58.718 55.000 6.36 0.00 34.04 3.36
680 688 0.608130 TGCATGCCTCGTTAGTGAGT 59.392 50.000 16.68 0.00 34.04 3.41
692 700 0.818938 TGTCCAATGTGATGCATGCC 59.181 50.000 16.68 0.28 37.96 4.40
693 701 1.796253 CGTGTCCAATGTGATGCATGC 60.796 52.381 11.82 11.82 37.96 4.06
707 715 2.486592 CCCACTAAAATGGTTCGTGTCC 59.513 50.000 0.00 0.00 38.16 4.02
782 796 3.646736 AGGGCTCGGCTAACTTTATTT 57.353 42.857 0.00 0.00 0.00 1.40
791 805 0.978151 TGTTTTGTAGGGCTCGGCTA 59.022 50.000 0.00 0.00 0.00 3.93
795 809 3.118956 AGAGAGATGTTTTGTAGGGCTCG 60.119 47.826 0.00 0.00 0.00 5.03
804 818 5.641209 ACGAGGATGAAAGAGAGATGTTTTG 59.359 40.000 0.00 0.00 0.00 2.44
825 839 4.079980 TGGATTTCTTTCTTGTGGACGA 57.920 40.909 0.00 0.00 0.00 4.20
826 840 4.829064 TTGGATTTCTTTCTTGTGGACG 57.171 40.909 0.00 0.00 0.00 4.79
870 884 1.098712 GGTTGTTTGACCTGGTGCGA 61.099 55.000 2.82 0.00 36.73 5.10
1068 1084 4.357279 GGCAGGAGCAGCAGGGTT 62.357 66.667 0.00 0.00 44.61 4.11
1336 1352 2.427753 GGGGGAGATGATGTCCGC 59.572 66.667 16.06 16.06 44.45 5.54
1627 1652 0.320421 TCGTCAAGGTTAGTGCTGCC 60.320 55.000 0.00 0.00 0.00 4.85
1628 1653 1.394917 CATCGTCAAGGTTAGTGCTGC 59.605 52.381 0.00 0.00 0.00 5.25
1650 1746 8.934973 AAAAGAAAGAAAGATGAAACGTATCG 57.065 30.769 0.00 0.00 0.00 2.92
1679 1779 4.503296 CGAAGAGAAACCTTGGGAGAGAAA 60.503 45.833 0.00 0.00 0.00 2.52
1680 1780 3.006967 CGAAGAGAAACCTTGGGAGAGAA 59.993 47.826 0.00 0.00 0.00 2.87
1681 1781 2.563179 CGAAGAGAAACCTTGGGAGAGA 59.437 50.000 0.00 0.00 0.00 3.10
1682 1782 2.933056 GCGAAGAGAAACCTTGGGAGAG 60.933 54.545 0.00 0.00 0.00 3.20
1683 1783 1.002087 GCGAAGAGAAACCTTGGGAGA 59.998 52.381 0.00 0.00 0.00 3.71
1684 1784 1.443802 GCGAAGAGAAACCTTGGGAG 58.556 55.000 0.00 0.00 0.00 4.30
1685 1785 0.036306 GGCGAAGAGAAACCTTGGGA 59.964 55.000 0.00 0.00 0.00 4.37
1686 1786 1.298859 CGGCGAAGAGAAACCTTGGG 61.299 60.000 0.00 0.00 0.00 4.12
1687 1787 0.320421 TCGGCGAAGAGAAACCTTGG 60.320 55.000 7.35 0.00 0.00 3.61
1764 1864 3.157252 AGCACCGCCTCCGATGAT 61.157 61.111 0.00 0.00 36.29 2.45
2043 2143 3.352338 GAGCCCGTACAGGTCCACG 62.352 68.421 0.00 0.00 38.74 4.94
2358 2458 1.220749 GGTTCAGCGGCAGATGGTA 59.779 57.895 1.43 0.00 33.94 3.25
2409 2518 3.118454 CACGCTACCTTGCCCACG 61.118 66.667 0.00 0.00 0.00 4.94
2538 2647 2.798847 CACAGGATCATGTCGCACTATG 59.201 50.000 10.64 0.00 0.00 2.23
2539 2648 2.432146 ACACAGGATCATGTCGCACTAT 59.568 45.455 10.64 0.00 0.00 2.12
2540 2649 1.824852 ACACAGGATCATGTCGCACTA 59.175 47.619 10.64 0.00 0.00 2.74
2541 2650 0.610174 ACACAGGATCATGTCGCACT 59.390 50.000 10.64 0.00 0.00 4.40
2542 2651 0.723414 CACACAGGATCATGTCGCAC 59.277 55.000 10.64 0.00 0.00 5.34
2543 2652 0.607620 TCACACAGGATCATGTCGCA 59.392 50.000 10.64 0.00 0.00 5.10
2544 2653 1.945387 ATCACACAGGATCATGTCGC 58.055 50.000 10.64 0.00 0.00 5.19
2545 2654 3.055591 GCTATCACACAGGATCATGTCG 58.944 50.000 10.64 8.98 0.00 4.35
2546 2655 4.333913 AGCTATCACACAGGATCATGTC 57.666 45.455 10.64 0.00 0.00 3.06
2715 2827 1.302033 CTGCGGTTCTGTCTTGGCT 60.302 57.895 0.00 0.00 0.00 4.75
2735 2847 5.743302 CAGTAACTGATAGCATGGCACACC 61.743 50.000 0.00 0.00 35.22 4.16
2736 2848 3.310774 CAGTAACTGATAGCATGGCACAC 59.689 47.826 0.00 0.00 35.22 3.82
2737 2849 3.055167 ACAGTAACTGATAGCATGGCACA 60.055 43.478 0.00 0.00 37.83 4.57
2742 2854 8.079203 CCTTAGTAGACAGTAACTGATAGCATG 58.921 40.741 0.00 0.00 35.18 4.06
2776 2888 7.264947 GGGATAAAATTTGTGGATCGTCATTT 58.735 34.615 0.00 0.00 0.00 2.32
2785 2897 4.294347 GGATGGGGGATAAAATTTGTGGA 58.706 43.478 0.00 0.00 0.00 4.02
2789 2901 2.037121 GCCGGATGGGGGATAAAATTTG 59.963 50.000 5.05 0.00 35.78 2.32
2802 2914 0.319900 CTCTATTCACGGCCGGATGG 60.320 60.000 31.76 20.75 38.77 3.51
2817 2929 0.259065 ATCCGCAGACTGGTCCTCTA 59.741 55.000 4.26 0.00 0.00 2.43
2824 2960 0.319040 CATCCGTATCCGCAGACTGG 60.319 60.000 4.26 0.00 0.00 4.00
2827 2963 2.016704 CGCATCCGTATCCGCAGAC 61.017 63.158 0.00 0.00 0.00 3.51
2830 2966 4.293648 CCCGCATCCGTATCCGCA 62.294 66.667 0.00 0.00 0.00 5.69
2844 2980 0.105964 TATTGAATGACGCCCTCCCG 59.894 55.000 0.00 0.00 0.00 5.14
2847 2983 2.880890 AGCAATATTGAATGACGCCCTC 59.119 45.455 19.73 0.00 0.00 4.30
2918 3059 6.932400 TGGCGTTCGGTTTATATGAAATCTAT 59.068 34.615 0.00 0.00 0.00 1.98
2919 3060 6.282167 TGGCGTTCGGTTTATATGAAATCTA 58.718 36.000 0.00 0.00 0.00 1.98
2920 3061 5.120399 TGGCGTTCGGTTTATATGAAATCT 58.880 37.500 0.00 0.00 0.00 2.40
2926 3067 4.804608 TGAATGGCGTTCGGTTTATATG 57.195 40.909 14.33 0.00 39.80 1.78
2942 3083 7.864108 TGTGTTCTAATCCCTTACATGAATG 57.136 36.000 0.00 0.00 0.00 2.67
2953 3094 7.214467 TGAAAATCTGTTGTGTTCTAATCCC 57.786 36.000 0.00 0.00 0.00 3.85
2961 3102 9.814899 TGAAATGTAATGAAAATCTGTTGTGTT 57.185 25.926 0.00 0.00 0.00 3.32
3001 3142 2.418609 GGCAGCCGCTGGATTTATTTTT 60.419 45.455 21.77 0.00 38.60 1.94
3002 3143 1.136891 GGCAGCCGCTGGATTTATTTT 59.863 47.619 21.77 0.00 38.60 1.82
3003 3144 0.746659 GGCAGCCGCTGGATTTATTT 59.253 50.000 21.77 0.00 38.60 1.40
3004 3145 1.447317 CGGCAGCCGCTGGATTTATT 61.447 55.000 23.64 0.00 41.17 1.40
3005 3146 1.893808 CGGCAGCCGCTGGATTTAT 60.894 57.895 23.64 0.00 41.17 1.40
3006 3147 2.513666 CGGCAGCCGCTGGATTTA 60.514 61.111 23.64 0.00 41.17 1.40
3016 3157 4.043200 GCTTTGACACCGGCAGCC 62.043 66.667 0.00 0.00 0.00 4.85
3025 3166 1.754226 GGAACAACAAGGGCTTTGACA 59.246 47.619 16.87 0.00 39.21 3.58
3029 3170 2.039418 GAAGGGAACAACAAGGGCTTT 58.961 47.619 0.00 0.00 0.00 3.51
3066 3207 1.815212 CTCATGAAGACGCGCGGATG 61.815 60.000 35.22 24.07 0.00 3.51
3072 3213 2.792290 CGGTGCTCATGAAGACGCG 61.792 63.158 3.53 3.53 0.00 6.01
3073 3214 2.456119 CCGGTGCTCATGAAGACGC 61.456 63.158 0.00 0.00 0.00 5.19
3079 3220 0.249447 CTTATCGCCGGTGCTCATGA 60.249 55.000 11.05 0.00 34.43 3.07
3080 3221 0.249447 TCTTATCGCCGGTGCTCATG 60.249 55.000 11.05 0.00 34.43 3.07
3100 3241 4.744570 AGATCGCAGTTTCACTTTATCGA 58.255 39.130 0.00 0.00 0.00 3.59
3105 3246 2.069273 CGGAGATCGCAGTTTCACTTT 58.931 47.619 0.00 0.00 0.00 2.66
3113 3254 1.888436 TTCTTGCCGGAGATCGCAGT 61.888 55.000 5.05 0.00 37.59 4.40
3114 3255 0.740868 TTTCTTGCCGGAGATCGCAG 60.741 55.000 5.05 0.00 37.59 5.18
3119 3260 4.162320 TGTTCTATCTTTCTTGCCGGAGAT 59.838 41.667 5.05 5.91 33.68 2.75
3131 3272 2.165845 CCGTCTCCCGTGTTCTATCTTT 59.834 50.000 0.00 0.00 33.66 2.52
3155 3296 0.327924 CTTGTGTCCCATGTAGGCCA 59.672 55.000 5.01 0.00 35.39 5.36
3156 3297 0.618458 TCTTGTGTCCCATGTAGGCC 59.382 55.000 0.00 0.00 35.39 5.19
3160 3301 3.264193 AGCAAGATCTTGTGTCCCATGTA 59.736 43.478 30.88 0.00 42.31 2.29
3175 3316 2.270205 CACGGGAGGCAGCAAGAT 59.730 61.111 0.00 0.00 0.00 2.40
3188 3329 1.742768 GAGGATGAGTAGGGCACGG 59.257 63.158 0.00 0.00 0.00 4.94
3216 3357 4.681978 AGTGACGGACAAGGCGGC 62.682 66.667 0.00 0.00 0.00 6.53
3270 3411 4.794439 TGGGACGATGACAGCGCG 62.794 66.667 13.92 0.00 0.00 6.86
3290 3431 2.280186 CGAACTATCAGGCGGCCC 60.280 66.667 17.02 0.00 0.00 5.80
3310 3451 2.856628 CGCCGCCTCCTATGCTGTA 61.857 63.158 0.00 0.00 0.00 2.74
3313 3454 3.470888 AACGCCGCCTCCTATGCT 61.471 61.111 0.00 0.00 0.00 3.79
3315 3456 1.429148 GAACAACGCCGCCTCCTATG 61.429 60.000 0.00 0.00 0.00 2.23
3316 3457 1.153429 GAACAACGCCGCCTCCTAT 60.153 57.895 0.00 0.00 0.00 2.57
3342 3485 3.083349 CGTGCCTCCAGGGGATCA 61.083 66.667 0.00 0.00 37.86 2.92


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

AutoCloner maintained by Alex Coulton.