Multiple sequence alignment - TraesCS4A01G464200

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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 TraesCS4A01G464200 chr4A 100.000 3952 0 0 1 3952 728091116 728087165 0 7299
1 TraesCS4A01G464200 chr4A 91.160 543 34 6 997 1538 728065014 728064485 0 725
2 TraesCS4A01G464200 chr7D 92.621 1843 81 28 1458 3263 10712627 10714451 0 2599
3 TraesCS4A01G464200 chr7D 92.828 1478 65 20 1 1468 10711152 10712598 0 2104
4 TraesCS4A01G464200 chr7D 92.352 693 33 8 3261 3952 10714477 10715150 0 968
5 TraesCS4A01G464200 chr7A 92.295 1843 83 18 1458 3263 9752422 9754242 0 2562
6 TraesCS4A01G464200 chr7A 91.819 1479 80 23 1 1468 9750945 9752393 0 2023
7 TraesCS4A01G464200 chr7A 93.497 692 26 7 3261 3952 9754268 9754940 0 1011


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 TraesCS4A01G464200 chr4A 728087165 728091116 3951 True 7299.000000 7299 100.000000 1 3952 1 chr4A.!!$R2 3951
1 TraesCS4A01G464200 chr4A 728064485 728065014 529 True 725.000000 725 91.160000 997 1538 1 chr4A.!!$R1 541
2 TraesCS4A01G464200 chr7D 10711152 10715150 3998 False 1890.333333 2599 92.600333 1 3952 3 chr7D.!!$F1 3951
3 TraesCS4A01G464200 chr7A 9750945 9754940 3995 False 1865.333333 2562 92.537000 1 3952 3 chr7A.!!$F1 3951

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
273 284 0.030603 AGGCAAAAACCTTGGGGGAA 60.031 50.0 0.0 0.0 36.28 3.97 F
1593 1653 0.178992 CTTTCACCAACCTGGCTCCA 60.179 55.0 0.0 0.0 42.67 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1887 1947 1.313812 GCCAGATTCTGCTGCTGCTT 61.314 55.0 17.0 0.0 40.48 3.91 R
3551 3681 0.388649 TTTTCTCTCGGTCTGCTCGC 60.389 55.0 0.0 0.0 0.00 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
35 36 5.412640 TGCATGCAAATCAGTTGATAAAGG 58.587 37.500 20.30 0.00 39.87 3.11
37 38 6.152492 TGCATGCAAATCAGTTGATAAAGGTA 59.848 34.615 20.30 0.00 39.87 3.08
97 98 8.907222 AATTCCTGAACAATGTTAATTTGCTT 57.093 26.923 0.00 0.00 0.00 3.91
98 99 8.907222 ATTCCTGAACAATGTTAATTTGCTTT 57.093 26.923 0.00 0.00 0.00 3.51
137 139 5.435686 AGTTACCTGAACATGGATGCTAA 57.564 39.130 0.00 0.00 40.86 3.09
139 141 7.136822 AGTTACCTGAACATGGATGCTAATA 57.863 36.000 0.00 0.00 40.86 0.98
144 154 5.335426 CCTGAACATGGATGCTAATATGCAC 60.335 44.000 0.00 0.00 46.33 4.57
154 164 5.177725 TGCTAATATGCACAATTCAGCAG 57.822 39.130 15.73 5.73 44.94 4.24
270 281 1.071299 GCAGGCAAAAACCTTGGGG 59.929 57.895 0.00 0.00 38.26 4.96
271 282 1.754107 CAGGCAAAAACCTTGGGGG 59.246 57.895 0.00 0.00 38.26 5.40
272 283 0.762461 CAGGCAAAAACCTTGGGGGA 60.762 55.000 0.00 0.00 38.26 4.81
273 284 0.030603 AGGCAAAAACCTTGGGGGAA 60.031 50.000 0.00 0.00 36.28 3.97
274 285 1.064003 GGCAAAAACCTTGGGGGAAT 58.936 50.000 0.00 0.00 38.76 3.01
275 286 1.423541 GGCAAAAACCTTGGGGGAATT 59.576 47.619 0.00 0.00 38.76 2.17
277 288 3.307410 GGCAAAAACCTTGGGGGAATTAG 60.307 47.826 0.00 0.00 38.76 1.73
282 293 5.560722 AAACCTTGGGGGAATTAGTTTTG 57.439 39.130 0.00 0.00 38.76 2.44
295 306 1.298041 GTTTTGTGTCACCGCACCG 60.298 57.895 0.00 0.00 38.52 4.94
311 322 2.231529 CACCGGGTCTGGATCTACTAG 58.768 57.143 6.32 0.00 0.00 2.57
422 433 3.313526 CAGTTGCAGCAAAGTGTAGTTCT 59.686 43.478 10.11 0.00 0.00 3.01
423 434 4.511454 CAGTTGCAGCAAAGTGTAGTTCTA 59.489 41.667 10.11 0.00 0.00 2.10
506 517 3.443925 CTGCTCGTCTCTCGGCCA 61.444 66.667 2.24 0.00 40.32 5.36
540 551 5.498393 CATTATCAAGGGAGATGGATGAGG 58.502 45.833 0.00 0.00 30.71 3.86
598 609 1.707427 ACTCACCATCCTGCTTTCCTT 59.293 47.619 0.00 0.00 0.00 3.36
605 616 3.131755 CCATCCTGCTTTCCTTTGGATTC 59.868 47.826 0.00 0.00 35.57 2.52
607 618 1.135286 CCTGCTTTCCTTTGGATTCGC 60.135 52.381 0.00 0.00 0.00 4.70
655 666 1.938577 CGCAACTGAATAGCTCTGCAT 59.061 47.619 0.00 0.00 0.00 3.96
656 667 2.033065 CGCAACTGAATAGCTCTGCATC 60.033 50.000 0.00 0.00 0.00 3.91
657 668 2.033065 GCAACTGAATAGCTCTGCATCG 60.033 50.000 0.00 0.00 0.00 3.84
663 674 0.250209 ATAGCTCTGCATCGCCCTTG 60.250 55.000 0.00 0.00 0.00 3.61
685 696 4.105217 TGCCATGATGAGAATAGGGTCAAT 59.895 41.667 0.00 0.00 0.00 2.57
703 714 4.749598 GTCAATTTTGTAGCCCAAACAAGG 59.250 41.667 0.00 0.00 42.63 3.61
731 742 0.823460 AACCCACCAAAGTGTGCAAG 59.177 50.000 0.00 0.00 42.88 4.01
742 753 1.227943 TGTGCAAGCAGTGGAGTCC 60.228 57.895 0.73 0.73 0.00 3.85
756 767 2.838202 TGGAGTCCTTTCCATAGTCACC 59.162 50.000 11.33 0.00 42.24 4.02
800 811 5.935789 AGATGCTTCCACCAAAATCAAAATG 59.064 36.000 0.00 0.00 0.00 2.32
842 853 1.339438 GCTTCTCATGGCACTGAAGGA 60.339 52.381 20.08 6.49 37.12 3.36
907 918 9.193133 AGTAATCGCATTATGTGTTATCACTAC 57.807 33.333 5.63 0.00 44.14 2.73
909 920 5.908341 TCGCATTATGTGTTATCACTACCA 58.092 37.500 5.63 0.00 44.14 3.25
931 943 3.895656 ACCTTTTCTTGGAGGGTAAAAGC 59.104 43.478 0.00 0.00 37.52 3.51
938 950 2.432444 TGGAGGGTAAAAGCGTCATTG 58.568 47.619 1.88 0.00 32.71 2.82
1251 1263 0.389948 CACGGTCTTCCTTTCTCCGG 60.390 60.000 0.00 0.00 44.54 5.14
1276 1288 4.378616 CGCATTTTTCAAAGAACGGTACTG 59.621 41.667 0.00 0.00 0.00 2.74
1347 1359 7.603180 TCCTAGAATATGATGCTACTGTTGT 57.397 36.000 0.00 0.00 0.00 3.32
1593 1653 0.178992 CTTTCACCAACCTGGCTCCA 60.179 55.000 0.00 0.00 42.67 3.86
1638 1698 0.827368 TGCTCAGGTGTGTGTGTGTA 59.173 50.000 0.00 0.00 0.00 2.90
1661 1721 7.928706 TGTACCAATTTTCAAATTTACCTGGTG 59.071 33.333 10.23 0.00 36.03 4.17
1662 1722 6.295249 ACCAATTTTCAAATTTACCTGGTGG 58.705 36.000 10.23 0.00 34.75 4.61
1663 1723 6.126623 ACCAATTTTCAAATTTACCTGGTGGT 60.127 34.615 10.23 0.00 41.97 4.16
1686 1746 1.676635 TGCTCATGCACCTTGCTCC 60.677 57.895 0.00 0.00 45.31 4.70
1690 1750 2.362120 ATGCACCTTGCTCCTGCC 60.362 61.111 0.00 0.00 45.31 4.85
1704 1764 3.686691 GCTCCTGCCAATATCTGAAACCT 60.687 47.826 0.00 0.00 0.00 3.50
1705 1765 4.530875 CTCCTGCCAATATCTGAAACCTT 58.469 43.478 0.00 0.00 0.00 3.50
1706 1766 4.526970 TCCTGCCAATATCTGAAACCTTC 58.473 43.478 0.00 0.00 0.00 3.46
1707 1767 3.633986 CCTGCCAATATCTGAAACCTTCC 59.366 47.826 0.00 0.00 0.00 3.46
1710 1770 3.885901 GCCAATATCTGAAACCTTCCCTC 59.114 47.826 0.00 0.00 0.00 4.30
2068 2128 2.930019 CAGGGAGGTGGCCTGACA 60.930 66.667 3.32 0.00 31.76 3.58
2084 2144 4.569023 CAGCGGCGATACAGCGGA 62.569 66.667 12.98 0.00 45.09 5.54
2212 2275 5.757850 AGTGAATTGACTGAACCAAAGAC 57.242 39.130 0.00 0.00 0.00 3.01
2221 2284 3.694566 ACTGAACCAAAGACCACTTGTTC 59.305 43.478 0.00 0.00 38.44 3.18
2288 2351 1.160137 GACATGGTGTGTGGAGAAGC 58.840 55.000 0.00 0.00 42.36 3.86
2296 2359 4.821589 GTGGAGAAGCGAGGGCCG 62.822 72.222 0.00 0.00 41.24 6.13
2403 2466 2.568623 AGGTAAACCTGTCTTGCCTG 57.431 50.000 0.00 0.00 46.55 4.85
2406 2469 2.224548 GGTAAACCTGTCTTGCCTGAGT 60.225 50.000 0.00 0.00 0.00 3.41
2417 2480 7.377766 TGTCTTGCCTGAGTTATTAAATCAC 57.622 36.000 2.59 0.00 0.00 3.06
2421 2484 7.491372 TCTTGCCTGAGTTATTAAATCACTACG 59.509 37.037 2.59 0.00 0.00 3.51
2424 2487 7.147863 TGCCTGAGTTATTAAATCACTACGGTA 60.148 37.037 2.59 0.68 0.00 4.02
2434 2497 9.645059 ATTAAATCACTACGGTATCATGATCAG 57.355 33.333 12.53 7.41 0.00 2.90
2467 2558 9.872684 ATTTCCCATATTCAGTTTATGAGTGAT 57.127 29.630 0.00 0.00 39.68 3.06
2501 2592 5.356882 TTGTACTTGTAGAACTGCAATGC 57.643 39.130 0.00 0.00 34.80 3.56
2520 2611 1.784358 CCTGGTCCAAATGGCATCAT 58.216 50.000 0.00 0.00 34.56 2.45
2684 2776 5.933463 GCAAATCAAATCATGAGGACCAAAA 59.067 36.000 0.09 0.00 42.53 2.44
2700 2792 7.175104 AGGACCAAAACTATGCAATTCTTAGA 58.825 34.615 0.00 0.00 0.00 2.10
2730 2822 8.641498 AAAACTATGGCATATATTCCTCCTTG 57.359 34.615 7.81 0.00 0.00 3.61
2767 2859 4.694037 ACGTAGTTTAACCAAGAGGAATGC 59.306 41.667 0.00 0.00 37.78 3.56
2797 2889 6.645003 CAGTACTGTTAGTAATGCAGTTGTCA 59.355 38.462 15.06 0.00 39.45 3.58
2943 3045 2.102925 TCACATCTGTCACACTGAGCAA 59.897 45.455 0.00 0.00 29.63 3.91
3055 3157 6.730960 ATCAATGCTTTGCGATTTGATTTT 57.269 29.167 7.44 0.00 34.25 1.82
3059 3161 3.740321 TGCTTTGCGATTTGATTTTGACC 59.260 39.130 0.00 0.00 0.00 4.02
3069 3171 7.381139 GCGATTTGATTTTGACCTAAAGAAACA 59.619 33.333 0.00 0.00 0.00 2.83
3079 3181 6.503524 TGACCTAAAGAAACATTTTGCTCAC 58.496 36.000 0.00 0.00 0.00 3.51
3104 3206 0.038744 AAGAGACAGTGGGCATTGGG 59.961 55.000 0.00 0.00 0.00 4.12
3108 3210 0.678048 GACAGTGGGCATTGGGTCTC 60.678 60.000 0.00 0.00 0.00 3.36
3162 3264 9.462606 CTAAATTGTTCCTTGTAGGTCCTAAAT 57.537 33.333 0.00 0.00 36.53 1.40
3276 3406 2.884639 TGCTTGCCTTACTTTGTTCCTC 59.115 45.455 0.00 0.00 0.00 3.71
3318 3448 1.569479 GCTATTCGATTCAGCCGGGC 61.569 60.000 12.11 12.11 0.00 6.13
3411 3541 2.423064 CCCGGGCCATGTTTTAGCC 61.423 63.158 8.08 1.58 46.37 3.93
3489 3619 4.796231 CCGGACCTTCGGCTGTCG 62.796 72.222 0.00 0.00 43.71 4.35
3549 3679 0.389556 CCCATCAGATCATCGAGGCG 60.390 60.000 0.00 0.00 0.00 5.52
3551 3681 0.389556 CATCAGATCATCGAGGCGGG 60.390 60.000 0.00 0.00 0.00 6.13
3554 3684 3.978491 GATCATCGAGGCGGGCGA 61.978 66.667 0.00 2.96 42.48 5.54
3555 3685 3.905705 GATCATCGAGGCGGGCGAG 62.906 68.421 0.00 0.00 41.49 5.03
3566 3696 4.200283 GGGCGAGCAGACCGAGAG 62.200 72.222 0.00 0.00 38.99 3.20
3567 3697 3.134792 GGCGAGCAGACCGAGAGA 61.135 66.667 0.00 0.00 0.00 3.10
3568 3698 2.701780 GGCGAGCAGACCGAGAGAA 61.702 63.158 0.00 0.00 0.00 2.87
3569 3699 1.213013 GCGAGCAGACCGAGAGAAA 59.787 57.895 0.00 0.00 0.00 2.52
3737 3867 0.253044 TGCTGGCCACTGTATTCCTC 59.747 55.000 0.00 0.00 0.00 3.71
3797 3927 9.241317 CATTACTATTATCAAAAGCAAAGGCAG 57.759 33.333 0.00 0.00 44.61 4.85
3841 3971 2.211353 GCAGCTGCTAGTACCAGTAC 57.789 55.000 31.33 0.00 38.21 2.73
3905 4035 2.224018 TGCACATGAACTGGCCTTTTTC 60.224 45.455 3.32 4.39 0.00 2.29
3908 4038 4.301628 CACATGAACTGGCCTTTTTCTTC 58.698 43.478 3.32 0.00 0.00 2.87
3915 4045 5.268118 ACTGGCCTTTTTCTTCTTCTTTG 57.732 39.130 3.32 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 4.858935 TGAGAGTGCAAAGCAAAATGTAC 58.141 39.130 0.00 0.00 41.47 2.90
37 38 4.038282 TCATGAGAGTGCAAAGCAAAATGT 59.962 37.500 0.00 0.00 41.47 2.71
137 139 3.446161 ACAAGCTGCTGAATTGTGCATAT 59.554 39.130 1.35 0.00 38.59 1.78
139 141 1.616865 ACAAGCTGCTGAATTGTGCAT 59.383 42.857 1.35 0.00 38.59 3.96
144 154 2.156917 TCCAGACAAGCTGCTGAATTG 58.843 47.619 1.35 0.00 43.50 2.32
154 164 1.134371 GGGTACTGGATCCAGACAAGC 60.134 57.143 41.91 31.79 46.30 4.01
212 223 2.048127 GCCCACTCGTCGCTTTCT 60.048 61.111 0.00 0.00 0.00 2.52
262 273 3.901222 CACAAAACTAATTCCCCCAAGGT 59.099 43.478 0.00 0.00 36.75 3.50
264 275 4.586841 TGACACAAAACTAATTCCCCCAAG 59.413 41.667 0.00 0.00 0.00 3.61
265 276 4.342665 GTGACACAAAACTAATTCCCCCAA 59.657 41.667 0.00 0.00 0.00 4.12
266 277 3.892588 GTGACACAAAACTAATTCCCCCA 59.107 43.478 0.00 0.00 0.00 4.96
270 281 3.003897 TGCGGTGACACAAAACTAATTCC 59.996 43.478 8.08 0.00 0.00 3.01
271 282 3.972502 GTGCGGTGACACAAAACTAATTC 59.027 43.478 8.08 0.00 40.40 2.17
272 283 3.243267 GGTGCGGTGACACAAAACTAATT 60.243 43.478 8.08 0.00 42.55 1.40
273 284 2.292292 GGTGCGGTGACACAAAACTAAT 59.708 45.455 8.08 0.00 42.55 1.73
274 285 1.671845 GGTGCGGTGACACAAAACTAA 59.328 47.619 8.08 0.00 42.55 2.24
275 286 1.301423 GGTGCGGTGACACAAAACTA 58.699 50.000 8.08 0.00 42.55 2.24
277 288 1.298041 CGGTGCGGTGACACAAAAC 60.298 57.895 8.08 1.79 42.55 2.43
295 306 1.249407 CCGCTAGTAGATCCAGACCC 58.751 60.000 0.00 0.00 0.00 4.46
330 341 5.121768 TCCTAGACGCAGCAATAAGAAAAAC 59.878 40.000 0.00 0.00 0.00 2.43
422 433 2.413963 GGCATTGGCGCACATGGTA 61.414 57.895 10.83 0.00 42.47 3.25
423 434 3.762247 GGCATTGGCGCACATGGT 61.762 61.111 10.83 0.00 42.47 3.55
467 478 1.743252 CCAGTTGCGAAGAGGAGCC 60.743 63.158 0.00 0.00 0.00 4.70
469 480 0.108424 CTCCCAGTTGCGAAGAGGAG 60.108 60.000 0.00 0.00 35.34 3.69
506 517 2.958355 CCTTGATAATGGGAATTGGCGT 59.042 45.455 0.00 0.00 0.00 5.68
540 551 2.436173 ACCTAGTATGAAAGCTCCCTGC 59.564 50.000 0.00 0.00 43.29 4.85
598 609 2.183300 CCGTCCGAGCGAATCCAA 59.817 61.111 0.00 0.00 0.00 3.53
607 618 4.436998 GGTGCTGTCCCGTCCGAG 62.437 72.222 0.00 0.00 0.00 4.63
636 647 2.033065 CGATGCAGAGCTATTCAGTTGC 60.033 50.000 0.00 0.00 0.00 4.17
655 666 1.153107 CTCATCATGGCAAGGGCGA 60.153 57.895 0.00 0.00 42.47 5.54
656 667 0.749091 TTCTCATCATGGCAAGGGCG 60.749 55.000 0.00 0.00 42.47 6.13
657 668 1.700955 ATTCTCATCATGGCAAGGGC 58.299 50.000 0.00 0.00 40.13 5.19
663 674 3.777106 TGACCCTATTCTCATCATGGC 57.223 47.619 0.00 0.00 0.00 4.40
703 714 4.932105 TGGTGGGTTTGGCAGGCC 62.932 66.667 2.62 2.62 0.00 5.19
742 753 1.737793 GTTGGCGGTGACTATGGAAAG 59.262 52.381 0.00 0.00 0.00 2.62
749 760 1.292223 GCTGAGTTGGCGGTGACTA 59.708 57.895 0.00 0.00 0.00 2.59
750 761 2.031163 GCTGAGTTGGCGGTGACT 59.969 61.111 0.00 0.00 0.00 3.41
756 767 2.664851 TCCGTTGCTGAGTTGGCG 60.665 61.111 0.00 0.00 0.00 5.69
800 811 0.179215 CTGGCACGAATCGCAAAGAC 60.179 55.000 1.15 0.00 0.00 3.01
907 918 3.518992 TTACCCTCCAAGAAAAGGTGG 57.481 47.619 0.00 0.00 39.07 4.61
909 920 3.895656 GCTTTTACCCTCCAAGAAAAGGT 59.104 43.478 7.76 0.00 38.66 3.50
931 943 0.855349 GAGGATACGCAGCAATGACG 59.145 55.000 0.00 0.00 46.39 4.35
938 950 1.589196 GTCACGGAGGATACGCAGC 60.589 63.158 0.00 0.00 46.39 5.25
1251 1263 3.368495 ACCGTTCTTTGAAAAATGCGAC 58.632 40.909 0.00 0.00 0.00 5.19
1276 1288 8.875803 TCATCTTCTGCAAATCAAAATTTATGC 58.124 29.630 0.00 0.00 33.27 3.14
1593 1653 1.674221 GCGATGAGGAAAGTCAGCACT 60.674 52.381 0.00 0.00 32.11 4.40
1638 1698 6.295249 CCACCAGGTAAATTTGAAAATTGGT 58.705 36.000 0.00 3.14 38.53 3.67
1679 1739 3.204306 TCAGATATTGGCAGGAGCAAG 57.796 47.619 0.00 0.00 44.61 4.01
1683 1743 4.162040 AGGTTTCAGATATTGGCAGGAG 57.838 45.455 0.00 0.00 0.00 3.69
1686 1746 3.633986 GGGAAGGTTTCAGATATTGGCAG 59.366 47.826 0.00 0.00 0.00 4.85
1690 1750 5.128919 CCAGAGGGAAGGTTTCAGATATTG 58.871 45.833 0.00 0.00 35.59 1.90
1721 1781 2.212752 ACCCTACATCCATGATGGGT 57.787 50.000 12.26 16.25 43.60 4.51
1723 1783 2.039480 CTCCACCCTACATCCATGATGG 59.961 54.545 4.74 4.74 43.60 3.51
1724 1784 2.707791 ACTCCACCCTACATCCATGATG 59.292 50.000 0.00 2.62 44.71 3.07
1725 1785 2.975489 GACTCCACCCTACATCCATGAT 59.025 50.000 0.00 0.00 0.00 2.45
1887 1947 1.313812 GCCAGATTCTGCTGCTGCTT 61.314 55.000 17.00 0.00 40.48 3.91
2068 2128 4.271816 CTCCGCTGTATCGCCGCT 62.272 66.667 0.00 0.00 0.00 5.52
2084 2144 3.717294 GACCCACACCGATGCCCT 61.717 66.667 0.00 0.00 0.00 5.19
2175 2235 9.084533 AGTCAATTCACTAGAGTTCTCTTAACT 57.915 33.333 7.66 0.00 0.00 2.24
2176 2236 9.134734 CAGTCAATTCACTAGAGTTCTCTTAAC 57.865 37.037 7.66 0.00 0.00 2.01
2190 2251 4.580580 GGTCTTTGGTTCAGTCAATTCACT 59.419 41.667 0.00 0.00 0.00 3.41
2191 2252 4.338118 TGGTCTTTGGTTCAGTCAATTCAC 59.662 41.667 0.00 0.00 0.00 3.18
2192 2253 4.338118 GTGGTCTTTGGTTCAGTCAATTCA 59.662 41.667 0.00 0.00 0.00 2.57
2221 2284 3.319972 CCAAGATTCCCTGCAACATATGG 59.680 47.826 7.80 0.00 0.00 2.74
2288 2351 3.530910 AAGTGAACACCGGCCCTCG 62.531 63.158 0.00 0.00 38.88 4.63
2296 2359 1.967319 TGAAGGCTGAAGTGAACACC 58.033 50.000 1.11 0.00 0.00 4.16
2338 2401 7.396907 TGGAGAAAGAAGAAATCAATTATGGCA 59.603 33.333 0.00 0.00 0.00 4.92
2395 2458 7.491372 CGTAGTGATTTAATAACTCAGGCAAGA 59.509 37.037 0.00 0.00 0.00 3.02
2396 2459 7.254455 CCGTAGTGATTTAATAACTCAGGCAAG 60.254 40.741 0.00 0.00 0.00 4.01
2417 2480 6.681777 TGAATGACTGATCATGATACCGTAG 58.318 40.000 8.54 5.21 45.26 3.51
2421 2484 7.094463 GGGAAATGAATGACTGATCATGATACC 60.094 40.741 8.54 0.00 45.26 2.73
2424 2487 6.370453 TGGGAAATGAATGACTGATCATGAT 58.630 36.000 8.25 8.25 45.26 2.45
2471 2562 7.549842 TGCAGTTCTACAAGTACAAAAGTGTAA 59.450 33.333 0.00 0.00 41.89 2.41
2473 2564 5.878116 TGCAGTTCTACAAGTACAAAAGTGT 59.122 36.000 0.00 0.00 42.09 3.55
2482 2573 4.002982 CAGGCATTGCAGTTCTACAAGTA 58.997 43.478 11.39 0.00 0.00 2.24
2501 2592 1.684983 GATGATGCCATTTGGACCAGG 59.315 52.381 0.00 0.00 37.39 4.45
2520 2611 7.627300 GCAAGGCCAAAACAAAAATACAAAAGA 60.627 33.333 5.01 0.00 0.00 2.52
2854 2956 3.243359 TCACCTGAAGAATTTGGGCTT 57.757 42.857 0.00 0.00 0.00 4.35
2981 3083 2.545106 GGTGGTCGTACAAAAATCGTGT 59.455 45.455 0.00 0.00 0.00 4.49
3055 3157 6.460953 GGTGAGCAAAATGTTTCTTTAGGTCA 60.461 38.462 0.00 0.00 0.00 4.02
3059 3161 7.706179 TCTTTGGTGAGCAAAATGTTTCTTTAG 59.294 33.333 11.19 0.00 0.00 1.85
3069 3171 4.889409 TGTCTCTTCTTTGGTGAGCAAAAT 59.111 37.500 11.19 0.00 0.00 1.82
3079 3181 1.202806 TGCCCACTGTCTCTTCTTTGG 60.203 52.381 0.00 0.00 0.00 3.28
3104 3206 4.543590 TCCCATGAGAAAGTTCTGAGAC 57.456 45.455 0.00 0.00 37.73 3.36
3108 3210 2.751806 GCCTTCCCATGAGAAAGTTCTG 59.248 50.000 0.00 0.00 37.73 3.02
3376 3506 2.107953 GGGAGAGGAGCACATCGC 59.892 66.667 0.00 0.00 42.91 4.58
3413 3543 2.526993 TTTTCGCACACGTGACCGG 61.527 57.895 25.01 0.00 41.18 5.28
3448 3578 0.394762 TGGCATCTGAAGGCATGTCC 60.395 55.000 4.96 0.00 36.56 4.02
3489 3619 2.698274 CCATGGTTTTTATAGGGGTGGC 59.302 50.000 2.57 0.00 0.00 5.01
3549 3679 4.200283 CTCTCGGTCTGCTCGCCC 62.200 72.222 0.00 0.00 0.00 6.13
3551 3681 0.388649 TTTTCTCTCGGTCTGCTCGC 60.389 55.000 0.00 0.00 0.00 5.03
3569 3699 2.028748 GCATCCTGCACTCCACATTTTT 60.029 45.455 0.00 0.00 44.26 1.94
3797 3927 7.646922 GCTTTTATCACCATGATGATCTGTTTC 59.353 37.037 5.62 0.00 39.97 2.78
3836 3966 3.008330 ACGACTACTGGTGCTAGTACTG 58.992 50.000 10.95 6.90 32.19 2.74
3837 3967 3.269178 GACGACTACTGGTGCTAGTACT 58.731 50.000 10.95 0.00 32.19 2.73
3838 3968 2.030213 CGACGACTACTGGTGCTAGTAC 59.970 54.545 1.77 1.77 32.19 2.73
3839 3969 2.274437 CGACGACTACTGGTGCTAGTA 58.726 52.381 0.00 0.00 32.19 1.82
3840 3970 1.085091 CGACGACTACTGGTGCTAGT 58.915 55.000 0.00 0.00 34.71 2.57
3841 3971 1.085091 ACGACGACTACTGGTGCTAG 58.915 55.000 0.00 0.00 0.00 3.42
3845 3975 0.313043 ACCAACGACGACTACTGGTG 59.687 55.000 0.00 0.00 38.95 4.17


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

AutoCloner maintained by Alex Coulton.