Multiple sequence alignment - TraesCS3D01G137000

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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 TraesCS3D01G137000 chr3D 100.000 3053 0 0 1 3053 95610503 95613555 0.000000e+00 5638.0
1 TraesCS3D01G137000 chr3B 90.721 2748 161 28 1 2688 146658800 146661513 0.000000e+00 3576.0
2 TraesCS3D01G137000 chr3B 90.449 356 33 1 2699 3053 146661767 146662122 4.610000e-128 468.0
3 TraesCS3D01G137000 chr3B 80.000 105 20 1 2587 2691 354663603 354663500 3.260000e-10 76.8
4 TraesCS3D01G137000 chr3B 78.431 102 21 1 2587 2688 357461522 357461622 7.070000e-07 65.8
5 TraesCS3D01G137000 chr3A 83.907 2268 209 80 66 2250 113869705 113871899 0.000000e+00 2023.0
6 TraesCS3D01G137000 chr3A 87.912 91 2 3 1 82 113869597 113869687 6.970000e-17 99.0
7 TraesCS3D01G137000 chrUn 79.612 103 20 1 2589 2691 31126068 31125967 4.220000e-09 73.1
8 TraesCS3D01G137000 chr4B 79.048 105 21 1 2587 2691 80274400 80274297 1.520000e-08 71.3
9 TraesCS3D01G137000 chr4D 78.302 106 20 3 2587 2691 41876389 41876286 7.070000e-07 65.8
10 TraesCS3D01G137000 chr4A 78.431 102 21 1 2587 2688 693452842 693452942 7.070000e-07 65.8
11 TraesCS3D01G137000 chr1A 78.095 105 22 1 2587 2691 64151073 64150970 7.070000e-07 65.8
12 TraesCS3D01G137000 chr7B 77.670 103 22 1 2589 2691 261379780 261379679 9.140000e-06 62.1
13 TraesCS3D01G137000 chr6D 77.451 102 22 1 2587 2688 252275476 252275576 3.290000e-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 TraesCS3D01G137000 chr3D 95610503 95613555 3052 False 5638 5638 100.0000 1 3053 1 chr3D.!!$F1 3052
1 TraesCS3D01G137000 chr3B 146658800 146662122 3322 False 2022 3576 90.5850 1 3053 2 chr3B.!!$F2 3052
2 TraesCS3D01G137000 chr3A 113869597 113871899 2302 False 1061 2023 85.9095 1 2250 2 chr3A.!!$F1 2249

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
826 978 0.034059 CAGTGACGGTCTCCTTGCTT 59.966 55.0 9.88 0.0 0.0 3.91 F
850 1002 0.457851 CCAAGAACCACACCGCAAAA 59.542 50.0 0.00 0.0 0.0 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1907 2066 0.033699 GCTTTGCTCCTTCCCATCCT 60.034 55.0 0.0 0.0 0.0 3.24 R
2570 2760 0.239879 TCGTTCAAAAAGCATCCGGC 59.760 50.0 0.0 0.0 45.3 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
91 138 2.286523 CGGTCTCTTCACCCTGCCT 61.287 63.158 0.00 0.00 31.99 4.75
236 312 1.577328 GCAGTTGACACATCCCCACG 61.577 60.000 0.00 0.00 0.00 4.94
326 402 9.965824 GAATATTATTTGTGTTCATAAGGTGGG 57.034 33.333 0.00 0.00 0.00 4.61
358 434 5.613358 AACTTTTGGCTAATTCTCAGTCG 57.387 39.130 0.00 0.00 0.00 4.18
360 436 2.024176 TTGGCTAATTCTCAGTCGCC 57.976 50.000 0.00 0.00 38.01 5.54
361 437 1.195115 TGGCTAATTCTCAGTCGCCT 58.805 50.000 0.00 0.00 38.33 5.52
363 439 1.410882 GGCTAATTCTCAGTCGCCTCT 59.589 52.381 0.00 0.00 34.80 3.69
364 440 2.468831 GCTAATTCTCAGTCGCCTCTG 58.531 52.381 0.00 0.00 36.85 3.35
365 441 2.099921 GCTAATTCTCAGTCGCCTCTGA 59.900 50.000 5.57 5.57 41.40 3.27
372 450 2.734079 CTCAGTCGCCTCTGAAACTTTC 59.266 50.000 6.88 0.00 42.73 2.62
386 464 8.110860 TCTGAAACTTTCTTGAAAACTTCAGT 57.889 30.769 25.73 10.03 41.38 3.41
387 465 8.237267 TCTGAAACTTTCTTGAAAACTTCAGTC 58.763 33.333 25.73 10.25 41.38 3.51
396 474 7.940850 TCTTGAAAACTTCAGTCCCTAAAATG 58.059 34.615 0.00 0.00 41.38 2.32
400 478 2.304761 ACTTCAGTCCCTAAAATGGCGA 59.695 45.455 0.00 0.00 0.00 5.54
402 480 2.985896 TCAGTCCCTAAAATGGCGAAG 58.014 47.619 0.00 0.00 0.00 3.79
403 481 2.569853 TCAGTCCCTAAAATGGCGAAGA 59.430 45.455 0.00 0.00 0.00 2.87
404 482 3.199946 TCAGTCCCTAAAATGGCGAAGAT 59.800 43.478 0.00 0.00 0.00 2.40
420 525 4.745620 GCGAAGATAGGTAAAGGTGTGATC 59.254 45.833 0.00 0.00 0.00 2.92
428 533 4.003648 GGTAAAGGTGTGATCTGGTGAAG 58.996 47.826 0.00 0.00 0.00 3.02
440 545 3.141398 TCTGGTGAAGCATTGAGACAAC 58.859 45.455 0.00 0.00 0.00 3.32
459 565 4.520492 ACAACAGCTGGGACTGAAATTTAG 59.480 41.667 19.93 0.00 40.25 1.85
460 566 4.373156 ACAGCTGGGACTGAAATTTAGT 57.627 40.909 19.93 0.00 40.25 2.24
544 677 0.821301 TTGTGCTGATGCCGGTTTGA 60.821 50.000 1.90 0.00 38.71 2.69
555 688 2.287909 TGCCGGTTTGAAGTATTTGCAC 60.288 45.455 1.90 0.00 0.00 4.57
565 698 2.076863 AGTATTTGCACGAGTGGCTTC 58.923 47.619 5.32 0.00 0.00 3.86
618 751 0.388134 CAGGTACGTGTCAGGTTCCG 60.388 60.000 13.61 7.06 30.24 4.30
649 788 0.467290 ATGGAGCCCGAGAGAGACTC 60.467 60.000 0.00 0.00 41.79 3.36
674 825 1.570347 TTTCCAATCCACCGAACGCG 61.570 55.000 3.53 3.53 37.24 6.01
677 828 1.419922 CAATCCACCGAACGCGAAG 59.580 57.895 15.93 2.74 40.82 3.79
695 846 5.382573 CGAAGCAAAATAGTAGAGCAGAC 57.617 43.478 0.00 0.00 0.00 3.51
696 847 5.105752 CGAAGCAAAATAGTAGAGCAGACT 58.894 41.667 0.00 0.00 0.00 3.24
697 848 6.266323 CGAAGCAAAATAGTAGAGCAGACTA 58.734 40.000 0.00 0.00 34.01 2.59
698 849 6.416455 CGAAGCAAAATAGTAGAGCAGACTAG 59.584 42.308 0.00 0.00 33.03 2.57
699 850 5.596845 AGCAAAATAGTAGAGCAGACTAGC 58.403 41.667 0.00 0.00 33.03 3.42
700 851 4.747605 GCAAAATAGTAGAGCAGACTAGCC 59.252 45.833 0.00 0.00 33.03 3.93
753 904 2.673775 TTGAAAGCTGACCATGGGAA 57.326 45.000 18.09 2.17 0.00 3.97
763 914 3.153919 TGACCATGGGAAAACTAAGCAC 58.846 45.455 18.09 0.00 0.00 4.40
766 917 3.964031 ACCATGGGAAAACTAAGCACAAA 59.036 39.130 18.09 0.00 0.00 2.83
804 956 3.363673 GCGTTAACACAGCTAAGGTTCAC 60.364 47.826 6.39 0.78 0.00 3.18
822 974 0.822532 ACGACAGTGACGGTCTCCTT 60.823 55.000 18.67 0.00 33.11 3.36
823 975 0.387367 CGACAGTGACGGTCTCCTTG 60.387 60.000 13.61 4.08 33.11 3.61
824 976 0.667792 GACAGTGACGGTCTCCTTGC 60.668 60.000 8.62 0.00 32.54 4.01
825 977 1.115930 ACAGTGACGGTCTCCTTGCT 61.116 55.000 9.88 0.00 0.00 3.91
826 978 0.034059 CAGTGACGGTCTCCTTGCTT 59.966 55.000 9.88 0.00 0.00 3.91
850 1002 0.457851 CCAAGAACCACACCGCAAAA 59.542 50.000 0.00 0.00 0.00 2.44
877 1030 3.712091 AATCTACGTGCAGGCTAGTAC 57.288 47.619 6.26 0.00 0.00 2.73
878 1031 2.414994 TCTACGTGCAGGCTAGTACT 57.585 50.000 6.26 0.00 0.00 2.73
879 1032 3.548745 TCTACGTGCAGGCTAGTACTA 57.451 47.619 6.26 1.89 0.00 1.82
906 1059 2.420890 GAGAGCCATCTCCCGCTG 59.579 66.667 0.00 0.00 45.41 5.18
919 1072 2.267351 CCGCTGGTTTCATGCACCA 61.267 57.895 14.10 14.10 42.34 4.17
923 1076 1.404583 GCTGGTTTCATGCACCAATCC 60.405 52.381 15.28 0.00 43.96 3.01
943 1096 2.787680 CCATCTCGTCGGAAATCGTAAC 59.212 50.000 0.00 0.00 40.32 2.50
944 1097 3.431856 CATCTCGTCGGAAATCGTAACA 58.568 45.455 0.00 0.00 40.32 2.41
985 1144 1.545614 CGACCAAACAGACGACACGG 61.546 60.000 0.00 0.00 0.00 4.94
1521 1680 0.818040 GCGAGGTGCGGGGATTTTAT 60.818 55.000 0.00 0.00 41.29 1.40
1552 1711 1.114119 GGACTACTCCCGTGGGATCC 61.114 65.000 8.37 8.78 44.24 3.36
1668 1827 3.945434 GCCGCCGTCGACGAGATA 61.945 66.667 37.65 0.00 43.02 1.98
1670 1829 1.368969 CCGCCGTCGACGAGATAAG 60.369 63.158 37.65 20.96 43.02 1.73
1680 1839 2.539142 CGACGAGATAAGGGAGAACACG 60.539 54.545 0.00 0.00 0.00 4.49
1793 1952 2.943978 CGCTCAAGGTCGGGAAGGT 61.944 63.158 0.00 0.00 0.00 3.50
1907 2066 0.907704 ATGGTGGCCGAGGTGAGTAA 60.908 55.000 0.00 0.00 0.00 2.24
2083 2245 7.225538 CGAGCTTCTCATCAAATTAACCATACT 59.774 37.037 0.00 0.00 0.00 2.12
2239 2429 5.824904 AGAAAAGCCTAGTGCATTGTATG 57.175 39.130 0.00 0.00 44.83 2.39
2261 2451 4.589798 TGTTGCACTCTAAACTACACCCTA 59.410 41.667 0.00 0.00 0.00 3.53
2267 2457 6.313164 GCACTCTAAACTACACCCTATGTTTC 59.687 42.308 0.00 0.00 43.19 2.78
2268 2458 6.530534 CACTCTAAACTACACCCTATGTTTCG 59.469 42.308 0.00 0.00 43.19 3.46
2273 2463 6.980051 AACTACACCCTATGTTTCGAAATC 57.020 37.500 14.69 8.51 43.19 2.17
2284 2474 7.962918 CCTATGTTTCGAAATCTAAGGTGTTTG 59.037 37.037 14.69 0.00 0.00 2.93
2292 2482 3.306472 TCTAAGGTGTTTGGGCAGTTT 57.694 42.857 0.00 0.00 0.00 2.66
2324 2514 5.622770 ACGCCAAAACTTCCTACATTTAG 57.377 39.130 0.00 0.00 0.00 1.85
2361 2551 0.037975 GTGATACCCCACGACGTTGT 60.038 55.000 1.48 1.48 0.00 3.32
2364 2554 0.952010 ATACCCCACGACGTTGTTGC 60.952 55.000 5.46 0.00 0.00 4.17
2478 2668 9.845214 ATGTTGAGAGGAATATATTAGTAGGGT 57.155 33.333 0.00 0.00 0.00 4.34
2481 2671 8.880991 TGAGAGGAATATATTAGTAGGGTCAC 57.119 38.462 0.00 0.00 0.00 3.67
2482 2672 8.453681 TGAGAGGAATATATTAGTAGGGTCACA 58.546 37.037 0.00 0.00 0.00 3.58
2532 2722 8.144478 TGCTTAGATACATTTCATCTAGTGGTC 58.856 37.037 0.00 0.00 36.59 4.02
2570 2760 2.332514 CCACACTGGCAACGCTTG 59.667 61.111 0.00 0.00 42.51 4.01
2585 2775 0.038343 GCTTGCCGGATGCTTTTTGA 60.038 50.000 5.05 0.00 42.00 2.69
2635 2825 4.632153 ACCTATTCCATCATGACTTACGC 58.368 43.478 0.00 0.00 0.00 4.42
2638 2828 0.468226 TCCATCATGACTTACGCCCC 59.532 55.000 0.00 0.00 0.00 5.80
2639 2829 0.880278 CCATCATGACTTACGCCCCG 60.880 60.000 0.00 0.00 0.00 5.73
2640 2830 1.227556 ATCATGACTTACGCCCCGC 60.228 57.895 0.00 0.00 0.00 6.13
2653 2843 1.820581 CCCCGCGAAGGACTAATCA 59.179 57.895 8.23 0.00 45.00 2.57
2673 2863 5.515797 TCACATTAGGGTAGATCTTCACG 57.484 43.478 0.00 0.00 0.00 4.35
2683 2873 4.398673 GGTAGATCTTCACGAAGTAGGTGT 59.601 45.833 0.00 0.00 41.61 4.16
2688 2878 4.142790 TCTTCACGAAGTAGGTGTTCTCT 58.857 43.478 6.68 0.00 41.61 3.10
2689 2879 4.583489 TCTTCACGAAGTAGGTGTTCTCTT 59.417 41.667 6.68 0.00 41.61 2.85
2690 2880 4.931661 TCACGAAGTAGGTGTTCTCTTT 57.068 40.909 0.00 0.00 41.61 2.52
2691 2881 5.272283 TCACGAAGTAGGTGTTCTCTTTT 57.728 39.130 0.00 0.00 41.61 2.27
2693 2883 5.068723 TCACGAAGTAGGTGTTCTCTTTTCT 59.931 40.000 0.00 0.00 41.61 2.52
2694 2884 6.263842 TCACGAAGTAGGTGTTCTCTTTTCTA 59.736 38.462 0.00 0.00 41.61 2.10
2695 2885 7.039923 TCACGAAGTAGGTGTTCTCTTTTCTAT 60.040 37.037 0.00 0.00 41.61 1.98
2696 2886 7.062371 CACGAAGTAGGTGTTCTCTTTTCTATG 59.938 40.741 0.00 0.00 41.61 2.23
2697 2887 6.035112 CGAAGTAGGTGTTCTCTTTTCTATGC 59.965 42.308 0.00 0.00 0.00 3.14
2721 3154 6.127310 GCATTAGAAGGTGGAGTTCTCTCTTA 60.127 42.308 0.00 0.00 40.29 2.10
2742 3175 7.730084 TCTTAGAACATATGATGGGAGTGAAG 58.270 38.462 10.38 1.07 33.60 3.02
2768 3201 4.518970 TGCTTCAAGTTAAACTGATGGGAC 59.481 41.667 0.00 0.00 0.00 4.46
2834 3268 0.169009 GTTTTGCACATCTCGGAGGC 59.831 55.000 4.96 1.05 0.00 4.70
2842 3276 2.780094 ATCTCGGAGGCTCGCACTG 61.780 63.158 8.69 0.00 0.00 3.66
2881 3315 9.092876 GTTTCCAAAGTGAACATAAATGACAAA 57.907 29.630 0.00 0.00 0.00 2.83
2894 3328 9.345517 ACATAAATGACAAATTTCAGATGTTCG 57.654 29.630 0.00 0.00 29.46 3.95
2901 3335 2.859165 TTTCAGATGTTCGGAGCCTT 57.141 45.000 0.00 0.00 0.00 4.35
2910 3344 2.218603 GTTCGGAGCCTTTGAAGTGAA 58.781 47.619 0.00 0.00 0.00 3.18
2917 3351 4.565652 GGAGCCTTTGAAGTGAATACCTCA 60.566 45.833 0.00 0.00 0.00 3.86
2918 3352 4.985538 AGCCTTTGAAGTGAATACCTCAA 58.014 39.130 0.00 0.00 35.90 3.02
2922 3356 5.997746 CCTTTGAAGTGAATACCTCAACAGA 59.002 40.000 0.00 0.00 37.07 3.41
2941 3375 2.807045 GCACACTCTCTGTCGGCG 60.807 66.667 0.00 0.00 0.00 6.46
2954 3388 1.066430 TGTCGGCGCTTAGGAAATTCT 60.066 47.619 7.64 0.00 0.00 2.40
2957 3391 2.158957 TCGGCGCTTAGGAAATTCTGAT 60.159 45.455 7.64 0.00 0.00 2.90
2958 3392 2.614057 CGGCGCTTAGGAAATTCTGATT 59.386 45.455 7.64 0.00 0.00 2.57
2959 3393 3.546815 CGGCGCTTAGGAAATTCTGATTG 60.547 47.826 7.64 0.00 0.00 2.67
2980 3414 3.005367 TGGAAAGGCTCAAAATTTCGGAC 59.995 43.478 0.00 0.00 34.47 4.79
2981 3415 3.255888 GGAAAGGCTCAAAATTTCGGACT 59.744 43.478 0.00 0.00 34.47 3.85
2988 3422 4.676924 GCTCAAAATTTCGGACTTGACAAG 59.323 41.667 13.77 13.77 0.00 3.16
2990 3424 6.060028 TCAAAATTTCGGACTTGACAAGAG 57.940 37.500 21.95 11.93 0.00 2.85
2999 3433 4.448060 CGGACTTGACAAGAGAAGGTTTAC 59.552 45.833 21.95 0.00 0.00 2.01
3010 3444 3.813724 GAGAAGGTTTACGAGGTTGCTTT 59.186 43.478 0.00 0.00 0.00 3.51
3019 3453 0.538287 GAGGTTGCTTTGGTGGCTCT 60.538 55.000 0.00 0.00 0.00 4.09
3023 3457 1.174712 TTGCTTTGGTGGCTCTGAGC 61.175 55.000 21.17 21.17 41.46 4.26
3036 3470 0.391661 TCTGAGCGGAATGTTGGAGC 60.392 55.000 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 68 0.608582 AGAGACCGAGCACCGTTACT 60.609 55.000 0.00 0.00 36.31 2.24
63 70 0.524862 GAAGAGACCGAGCACCGTTA 59.475 55.000 0.00 0.00 36.31 3.18
64 71 1.289380 GAAGAGACCGAGCACCGTT 59.711 57.895 0.00 0.00 36.31 4.44
202 256 4.214119 GTCAACTGCATGTGTATGTGTCTT 59.786 41.667 0.00 0.00 36.65 3.01
358 434 5.895928 AGTTTTCAAGAAAGTTTCAGAGGC 58.104 37.500 17.65 8.63 0.00 4.70
360 436 8.239998 ACTGAAGTTTTCAAGAAAGTTTCAGAG 58.760 33.333 31.14 20.01 44.42 3.35
361 437 8.110860 ACTGAAGTTTTCAAGAAAGTTTCAGA 57.889 30.769 31.14 11.70 44.42 3.27
363 439 7.312899 GGACTGAAGTTTTCAAGAAAGTTTCA 58.687 34.615 17.65 16.12 39.58 2.69
364 440 6.752351 GGGACTGAAGTTTTCAAGAAAGTTTC 59.248 38.462 7.57 7.57 39.58 2.78
365 441 6.437477 AGGGACTGAAGTTTTCAAGAAAGTTT 59.563 34.615 0.00 0.00 39.58 2.66
372 450 7.147976 CCATTTTAGGGACTGAAGTTTTCAAG 58.852 38.462 0.00 0.00 41.52 3.02
386 464 3.714798 ACCTATCTTCGCCATTTTAGGGA 59.285 43.478 0.00 0.00 32.30 4.20
387 465 4.086706 ACCTATCTTCGCCATTTTAGGG 57.913 45.455 0.00 0.00 32.30 3.53
396 474 3.118884 TCACACCTTTACCTATCTTCGCC 60.119 47.826 0.00 0.00 0.00 5.54
400 478 5.726793 ACCAGATCACACCTTTACCTATCTT 59.273 40.000 0.00 0.00 0.00 2.40
402 480 5.128827 TCACCAGATCACACCTTTACCTATC 59.871 44.000 0.00 0.00 0.00 2.08
403 481 5.030147 TCACCAGATCACACCTTTACCTAT 58.970 41.667 0.00 0.00 0.00 2.57
404 482 4.422057 TCACCAGATCACACCTTTACCTA 58.578 43.478 0.00 0.00 0.00 3.08
420 525 2.880268 TGTTGTCTCAATGCTTCACCAG 59.120 45.455 0.00 0.00 0.00 4.00
428 533 0.524862 CCCAGCTGTTGTCTCAATGC 59.475 55.000 13.81 0.00 0.00 3.56
440 545 6.173339 TCTTACTAAATTTCAGTCCCAGCTG 58.827 40.000 6.78 6.78 37.81 4.24
497 603 8.491152 AGTAATCTGATGATCTTTTTAATCGCG 58.509 33.333 0.00 0.00 31.51 5.87
509 615 7.312657 TCAGCACAAAAGTAATCTGATGATC 57.687 36.000 0.00 0.00 31.51 2.92
526 633 0.821301 TTCAAACCGGCATCAGCACA 60.821 50.000 0.00 0.00 44.61 4.57
544 677 2.185004 AGCCACTCGTGCAAATACTT 57.815 45.000 0.00 0.00 0.00 2.24
565 698 4.978186 CAGTCAGAATACAACTGGCAATG 58.022 43.478 0.00 0.00 41.68 2.82
618 751 1.673168 GGCTCCATGTCAAGATCACC 58.327 55.000 0.00 0.00 0.00 4.02
649 788 4.546570 GTTCGGTGGATTGGAAAAAGAAG 58.453 43.478 0.00 0.00 0.00 2.85
674 825 6.200097 GCTAGTCTGCTCTACTATTTTGCTTC 59.800 42.308 0.00 0.00 0.00 3.86
677 828 4.747605 GGCTAGTCTGCTCTACTATTTTGC 59.252 45.833 0.00 0.00 0.00 3.68
684 835 3.194542 CACTTTGGCTAGTCTGCTCTACT 59.805 47.826 0.00 0.00 0.00 2.57
686 837 3.193691 GTCACTTTGGCTAGTCTGCTCTA 59.806 47.826 0.00 0.00 0.00 2.43
687 838 2.028567 GTCACTTTGGCTAGTCTGCTCT 60.029 50.000 0.00 0.00 0.00 4.09
688 839 2.342179 GTCACTTTGGCTAGTCTGCTC 58.658 52.381 0.00 0.00 0.00 4.26
690 841 1.071605 CGTCACTTTGGCTAGTCTGC 58.928 55.000 0.00 0.00 0.00 4.26
691 842 2.229062 TCTCGTCACTTTGGCTAGTCTG 59.771 50.000 0.00 0.00 0.00 3.51
692 843 2.229302 GTCTCGTCACTTTGGCTAGTCT 59.771 50.000 0.00 0.00 0.00 3.24
693 844 2.597520 GTCTCGTCACTTTGGCTAGTC 58.402 52.381 0.00 0.00 0.00 2.59
695 846 1.272490 TGGTCTCGTCACTTTGGCTAG 59.728 52.381 0.00 0.00 0.00 3.42
696 847 1.334160 TGGTCTCGTCACTTTGGCTA 58.666 50.000 0.00 0.00 0.00 3.93
697 848 0.687354 ATGGTCTCGTCACTTTGGCT 59.313 50.000 0.00 0.00 0.00 4.75
698 849 1.079503 GATGGTCTCGTCACTTTGGC 58.920 55.000 0.00 0.00 0.00 4.52
699 850 1.350193 CGATGGTCTCGTCACTTTGG 58.650 55.000 0.00 0.00 42.56 3.28
700 851 1.067846 TCCGATGGTCTCGTCACTTTG 60.068 52.381 0.00 0.00 46.18 2.77
732 883 3.173953 TCCCATGGTCAGCTTTCAAAT 57.826 42.857 11.73 0.00 0.00 2.32
741 892 3.191371 GTGCTTAGTTTTCCCATGGTCAG 59.809 47.826 11.73 0.00 0.00 3.51
747 898 5.869649 ACTTTTGTGCTTAGTTTTCCCAT 57.130 34.783 0.00 0.00 0.00 4.00
753 904 5.049886 GCCTACGTACTTTTGTGCTTAGTTT 60.050 40.000 0.00 0.00 35.95 2.66
763 914 1.529010 GCGCATGCCTACGTACTTTTG 60.529 52.381 13.15 0.00 33.98 2.44
766 917 1.876714 CGCGCATGCCTACGTACTT 60.877 57.895 13.15 0.00 38.08 2.24
804 956 0.387367 CAAGGAGACCGTCACTGTCG 60.387 60.000 0.40 0.00 37.80 4.35
822 974 1.214175 TGTGGTTCTTGGAAGGAAGCA 59.786 47.619 4.56 4.56 45.05 3.91
823 975 1.609072 GTGTGGTTCTTGGAAGGAAGC 59.391 52.381 0.00 0.00 40.33 3.86
824 976 2.230660 GGTGTGGTTCTTGGAAGGAAG 58.769 52.381 0.00 0.00 0.00 3.46
825 977 1.476110 CGGTGTGGTTCTTGGAAGGAA 60.476 52.381 0.00 0.00 0.00 3.36
826 978 0.107831 CGGTGTGGTTCTTGGAAGGA 59.892 55.000 0.00 0.00 0.00 3.36
850 1002 3.317993 AGCCTGCACGTAGATTTTGTTTT 59.682 39.130 0.00 0.00 0.00 2.43
877 1030 7.012894 CGGGAGATGGCTCTCTATTTATACTAG 59.987 44.444 11.84 0.00 46.11 2.57
878 1031 6.829298 CGGGAGATGGCTCTCTATTTATACTA 59.171 42.308 11.84 0.00 46.11 1.82
879 1032 5.654650 CGGGAGATGGCTCTCTATTTATACT 59.345 44.000 11.84 0.00 46.11 2.12
906 1059 2.762327 AGATGGATTGGTGCATGAAACC 59.238 45.455 10.33 10.33 36.44 3.27
919 1072 2.100916 ACGATTTCCGACGAGATGGATT 59.899 45.455 0.00 0.00 41.76 3.01
923 1076 3.431856 TGTTACGATTTCCGACGAGATG 58.568 45.455 0.00 0.00 41.76 2.90
943 1096 1.144565 CGTGCAGGCTCGAGAAGATG 61.145 60.000 18.75 9.29 35.30 2.90
944 1097 1.140589 CGTGCAGGCTCGAGAAGAT 59.859 57.895 18.75 0.00 35.30 2.40
985 1144 0.518636 TGCATGCACGAGAAAGAAGC 59.481 50.000 18.46 0.00 0.00 3.86
1022 1181 4.241999 CTGCCGCGCTAATGCCAC 62.242 66.667 5.56 0.00 35.36 5.01
1181 1340 1.822186 GCCTTGTTGGTGACCACGT 60.822 57.895 2.46 0.00 38.35 4.49
1441 1600 3.116531 GTACCGTTCCAGCACCGC 61.117 66.667 0.00 0.00 0.00 5.68
1514 1673 0.501435 CGCGTCCGTCCGATAAAATC 59.499 55.000 0.00 0.00 0.00 2.17
1515 1674 0.872881 CCGCGTCCGTCCGATAAAAT 60.873 55.000 4.92 0.00 0.00 1.82
1521 1680 4.758251 TAGTCCGCGTCCGTCCGA 62.758 66.667 4.92 0.00 0.00 4.55
1668 1827 1.071471 CCTGCACGTGTTCTCCCTT 59.929 57.895 18.38 0.00 0.00 3.95
1670 1829 3.050275 GCCTGCACGTGTTCTCCC 61.050 66.667 18.38 0.00 0.00 4.30
1680 1839 3.667282 CTGCACACCAGCCTGCAC 61.667 66.667 0.00 0.00 38.49 4.57
1793 1952 0.243907 CTCCGCTTCTTCGTCCTTCA 59.756 55.000 0.00 0.00 0.00 3.02
1873 2032 2.626950 CCACCATCCCTCCAAGAGAGTA 60.627 54.545 0.00 0.00 41.47 2.59
1907 2066 0.033699 GCTTTGCTCCTTCCCATCCT 60.034 55.000 0.00 0.00 0.00 3.24
2239 2429 4.004196 AGGGTGTAGTTTAGAGTGCAAC 57.996 45.455 0.00 0.00 0.00 4.17
2261 2451 6.294508 CCCAAACACCTTAGATTTCGAAACAT 60.295 38.462 13.81 7.32 0.00 2.71
2267 2457 2.817258 TGCCCAAACACCTTAGATTTCG 59.183 45.455 0.00 0.00 0.00 3.46
2268 2458 3.826729 ACTGCCCAAACACCTTAGATTTC 59.173 43.478 0.00 0.00 0.00 2.17
2273 2463 5.523438 TTAAAACTGCCCAAACACCTTAG 57.477 39.130 0.00 0.00 0.00 2.18
2292 2482 6.865411 AGGAAGTTTTGGCGTTTTAGTTTAA 58.135 32.000 0.00 0.00 0.00 1.52
2324 2514 4.207891 TCACATCTACTGCCTTCTTTCC 57.792 45.455 0.00 0.00 0.00 3.13
2330 2520 2.706190 GGGGTATCACATCTACTGCCTT 59.294 50.000 0.00 0.00 0.00 4.35
2333 2523 2.545952 CGTGGGGTATCACATCTACTGC 60.546 54.545 0.00 0.00 37.50 4.40
2334 2524 2.956333 TCGTGGGGTATCACATCTACTG 59.044 50.000 0.00 0.00 37.50 2.74
2426 2616 9.567776 TTCAACCATGTATTAGAAAAGTCTTCA 57.432 29.630 0.00 0.00 35.12 3.02
2442 2632 4.371624 TCCTCTCAACATTCAACCATGT 57.628 40.909 0.00 0.00 39.17 3.21
2519 2709 7.921041 ATTAAGATCCAGACCACTAGATGAA 57.079 36.000 0.00 0.00 0.00 2.57
2532 2722 6.154445 GTGGCAAATGCATATTAAGATCCAG 58.846 40.000 0.00 0.00 44.36 3.86
2570 2760 0.239879 TCGTTCAAAAAGCATCCGGC 59.760 50.000 0.00 0.00 45.30 6.13
2571 2761 2.584791 CTTCGTTCAAAAAGCATCCGG 58.415 47.619 0.00 0.00 0.00 5.14
2572 2762 2.584791 CCTTCGTTCAAAAAGCATCCG 58.415 47.619 0.00 0.00 0.00 4.18
2573 2763 2.296190 ACCCTTCGTTCAAAAAGCATCC 59.704 45.455 0.00 0.00 0.00 3.51
2585 2775 2.580601 CCTCCGTGGACCCTTCGTT 61.581 63.158 0.00 0.00 38.35 3.85
2607 2797 4.137543 GTCATGATGGAATAGGTTGGGTC 58.862 47.826 0.00 0.00 0.00 4.46
2609 2799 4.443978 AGTCATGATGGAATAGGTTGGG 57.556 45.455 0.00 0.00 0.00 4.12
2635 2825 0.529992 GTGATTAGTCCTTCGCGGGG 60.530 60.000 6.13 9.66 0.00 5.73
2638 2828 3.736252 CCTAATGTGATTAGTCCTTCGCG 59.264 47.826 0.00 0.00 40.44 5.87
2639 2829 4.058817 CCCTAATGTGATTAGTCCTTCGC 58.941 47.826 0.00 0.00 40.44 4.70
2640 2830 5.277857 ACCCTAATGTGATTAGTCCTTCG 57.722 43.478 0.00 0.00 40.44 3.79
2650 2840 5.833667 TCGTGAAGATCTACCCTAATGTGAT 59.166 40.000 0.00 0.00 0.00 3.06
2653 2843 5.657302 ACTTCGTGAAGATCTACCCTAATGT 59.343 40.000 16.10 0.00 40.79 2.71
2673 2863 6.874134 TGCATAGAAAAGAGAACACCTACTTC 59.126 38.462 0.00 0.00 0.00 3.01
2690 2880 5.957771 ACTCCACCTTCTAATGCATAGAA 57.042 39.130 0.00 8.78 46.09 2.10
2691 2881 5.663106 AGAACTCCACCTTCTAATGCATAGA 59.337 40.000 0.00 0.48 38.90 1.98
2693 2883 5.663106 AGAGAACTCCACCTTCTAATGCATA 59.337 40.000 0.00 0.00 0.00 3.14
2694 2884 4.472833 AGAGAACTCCACCTTCTAATGCAT 59.527 41.667 0.00 0.00 0.00 3.96
2695 2885 3.840666 AGAGAACTCCACCTTCTAATGCA 59.159 43.478 0.00 0.00 0.00 3.96
2696 2886 4.161377 AGAGAGAACTCCACCTTCTAATGC 59.839 45.833 0.00 0.00 43.53 3.56
2697 2887 5.930837 AGAGAGAACTCCACCTTCTAATG 57.069 43.478 0.00 0.00 43.53 1.90
2721 3154 5.965033 ACTTCACTCCCATCATATGTTCT 57.035 39.130 1.90 0.00 0.00 3.01
2742 3175 5.691754 CCCATCAGTTTAACTTGAAGCAAAC 59.308 40.000 12.50 12.50 0.00 2.93
2751 3184 4.827284 CCACTTGTCCCATCAGTTTAACTT 59.173 41.667 0.00 0.00 0.00 2.66
2757 3190 0.405585 CCCCACTTGTCCCATCAGTT 59.594 55.000 0.00 0.00 0.00 3.16
2761 3194 0.988832 TGTACCCCACTTGTCCCATC 59.011 55.000 0.00 0.00 0.00 3.51
2762 3195 1.681229 ATGTACCCCACTTGTCCCAT 58.319 50.000 0.00 0.00 0.00 4.00
2768 3201 3.072476 CCACCCTATATGTACCCCACTTG 59.928 52.174 0.00 0.00 0.00 3.16
2779 3212 8.055790 TGTCAGATATCTAGTCCACCCTATATG 58.944 40.741 4.54 0.00 0.00 1.78
2834 3268 1.154525 CGAGCAAAAGCAGTGCGAG 60.155 57.895 10.00 2.12 46.86 5.03
2842 3276 0.383949 TGGAAACACCGAGCAAAAGC 59.616 50.000 0.00 0.00 42.61 3.51
2843 3277 2.861462 TTGGAAACACCGAGCAAAAG 57.139 45.000 0.00 0.00 42.67 2.27
2881 3315 3.356529 AAGGCTCCGAACATCTGAAAT 57.643 42.857 0.00 0.00 0.00 2.17
2894 3328 3.942115 GAGGTATTCACTTCAAAGGCTCC 59.058 47.826 0.00 0.00 31.28 4.70
2922 3356 2.936912 GCCGACAGAGAGTGTGCCT 61.937 63.158 0.00 0.00 40.56 4.75
2924 3358 2.807045 CGCCGACAGAGAGTGTGC 60.807 66.667 0.00 0.00 40.56 4.57
2941 3375 6.567959 CCTTTCCAATCAGAATTTCCTAAGC 58.432 40.000 0.00 0.00 0.00 3.09
2954 3388 5.229423 CGAAATTTTGAGCCTTTCCAATCA 58.771 37.500 0.00 0.00 0.00 2.57
2957 3391 3.639094 TCCGAAATTTTGAGCCTTTCCAA 59.361 39.130 7.02 0.00 0.00 3.53
2958 3392 3.005367 GTCCGAAATTTTGAGCCTTTCCA 59.995 43.478 7.02 0.00 0.00 3.53
2959 3393 3.255888 AGTCCGAAATTTTGAGCCTTTCC 59.744 43.478 7.02 0.00 0.00 3.13
2980 3414 4.686554 CCTCGTAAACCTTCTCTTGTCAAG 59.313 45.833 6.21 6.21 0.00 3.02
2981 3415 4.100498 ACCTCGTAAACCTTCTCTTGTCAA 59.900 41.667 0.00 0.00 0.00 3.18
2988 3422 3.041508 AGCAACCTCGTAAACCTTCTC 57.958 47.619 0.00 0.00 0.00 2.87
2990 3424 3.304458 CCAAAGCAACCTCGTAAACCTTC 60.304 47.826 0.00 0.00 0.00 3.46
2999 3433 1.856265 GAGCCACCAAAGCAACCTCG 61.856 60.000 0.00 0.00 0.00 4.63
3010 3444 2.293318 ATTCCGCTCAGAGCCACCA 61.293 57.895 17.16 0.00 38.18 4.17
3019 3453 1.377202 GGCTCCAACATTCCGCTCA 60.377 57.895 0.00 0.00 0.00 4.26
3023 3457 0.250234 TCAGAGGCTCCAACATTCCG 59.750 55.000 11.71 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.