Multiple sequence alignment - TraesCS3A01G381300

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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 TraesCS3A01G381300 chr3A 100.000 3809 0 0 1 3809 631613169 631616977 0.000000e+00 7035.0
1 TraesCS3A01G381300 chr3A 75.630 238 52 3 2507 2744 653852357 653852126 3.110000e-21 113.0
2 TraesCS3A01G381300 chr3D 95.340 2468 87 12 803 3264 488055279 488057724 0.000000e+00 3895.0
3 TraesCS3A01G381300 chr3D 92.222 810 31 17 3 804 488054455 488055240 0.000000e+00 1118.0
4 TraesCS3A01G381300 chr3D 87.916 571 36 9 3263 3809 488057933 488058494 3.210000e-180 641.0
5 TraesCS3A01G381300 chr3D 97.561 41 1 0 3738 3778 81716488 81716448 1.900000e-08 71.3
6 TraesCS3A01G381300 chr3B 94.158 2054 96 8 803 2850 650830553 650832588 0.000000e+00 3107.0
7 TraesCS3A01G381300 chr3B 91.439 806 40 15 1 804 650829736 650830514 0.000000e+00 1079.0
8 TraesCS3A01G381300 chr3B 85.075 469 30 11 3234 3701 650837739 650838168 3.490000e-120 442.0
9 TraesCS3A01G381300 chr3B 85.075 268 24 11 2900 3164 650832579 650832833 3.770000e-65 259.0
10 TraesCS3A01G381300 chr3B 100.000 30 0 0 3671 3700 128953757 128953786 5.320000e-04 56.5
11 TraesCS3A01G381300 chr2D 88.154 363 25 15 263 616 632562657 632563010 2.120000e-112 416.0
12 TraesCS3A01G381300 chr7B 85.027 374 30 13 263 616 648222996 648223363 1.300000e-94 357.0
13 TraesCS3A01G381300 chr4A 85.906 149 13 7 414 562 656046059 656045919 6.590000e-33 152.0
14 TraesCS3A01G381300 chr5B 86.765 136 8 4 490 616 521347057 521346923 3.970000e-30 143.0
15 TraesCS3A01G381300 chr2B 86.029 136 9 4 490 616 44383104 44382970 1.850000e-28 137.0
16 TraesCS3A01G381300 chr1B 86.029 136 9 4 490 616 625435513 625435647 1.850000e-28 137.0
17 TraesCS3A01G381300 chr1B 86.029 136 9 4 490 616 670625206 670625340 1.850000e-28 137.0
18 TraesCS3A01G381300 chr5A 82.192 146 15 10 3636 3778 85314046 85313909 8.650000e-22 115.0
19 TraesCS3A01G381300 chr4D 79.412 102 16 2 3656 3757 487046544 487046640 2.460000e-07 67.6


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 TraesCS3A01G381300 chr3A 631613169 631616977 3808 False 7035.000000 7035 100.000 1 3809 1 chr3A.!!$F1 3808
1 TraesCS3A01G381300 chr3D 488054455 488058494 4039 False 1884.666667 3895 91.826 3 3809 3 chr3D.!!$F1 3806
2 TraesCS3A01G381300 chr3B 650829736 650832833 3097 False 1481.666667 3107 90.224 1 3164 3 chr3B.!!$F3 3163

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
870 923 0.037326 TGCGTGGAGAACTAAGCAGG 60.037 55.0 0.0 0.0 37.13 4.85 F
1018 1081 0.169009 GATGGCACGCTTTCTTGGTC 59.831 55.0 0.0 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2541 2610 0.601558 TCCAGTTGCAGTCGTAGTCC 59.398 55.000 0.0 0.0 0.0 3.85 R
2978 3047 1.150135 AGGAGTTGGGAGGAAGAGTGA 59.850 52.381 0.0 0.0 0.0 3.41 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
123 124 1.286553 AGCTAGCTAGACAGGTGAGGT 59.713 52.381 25.15 0.00 33.61 3.85
195 196 2.167487 TGCACCAAACCTGGAAGAAAAC 59.833 45.455 0.00 0.00 46.92 2.43
209 210 4.143263 GGAAGAAAACGTACGTACCACATG 60.143 45.833 23.12 7.97 0.00 3.21
247 248 1.377536 GAGCAAGACCTCCTCAATGC 58.622 55.000 0.00 0.00 35.32 3.56
330 331 4.116113 AGTCTCTCTTCTCCCTCCTCTTA 58.884 47.826 0.00 0.00 0.00 2.10
354 355 1.202927 ACTAGTGCCAACTGCCACAAT 60.203 47.619 0.00 0.00 40.16 2.71
377 378 0.316204 CTGGCCTTGACCAAGCAAAG 59.684 55.000 3.32 0.00 39.86 2.77
382 383 2.476821 CCTTGACCAAGCAAAGCAAAG 58.523 47.619 4.31 0.00 37.11 2.77
385 386 1.206610 TGACCAAGCAAAGCAAAGCAA 59.793 42.857 0.00 0.00 0.00 3.91
386 387 2.158928 TGACCAAGCAAAGCAAAGCAAT 60.159 40.909 0.00 0.00 0.00 3.56
387 388 2.215196 ACCAAGCAAAGCAAAGCAATG 58.785 42.857 0.00 0.00 0.00 2.82
388 389 1.069500 CCAAGCAAAGCAAAGCAATGC 60.069 47.619 0.00 0.00 46.78 3.56
399 400 4.889241 GCAAAGCAATGCAAATCATGTAC 58.111 39.130 8.35 0.00 45.70 2.90
408 409 6.808008 ATGCAAATCATGTACTACTATGCC 57.192 37.500 0.00 0.00 33.26 4.40
464 466 7.987268 AAAAAGAAGCAAACTACTACAAAGC 57.013 32.000 0.00 0.00 0.00 3.51
466 468 3.186613 AGAAGCAAACTACTACAAAGCGC 59.813 43.478 0.00 0.00 0.00 5.92
467 469 2.489971 AGCAAACTACTACAAAGCGCA 58.510 42.857 11.47 0.00 0.00 6.09
468 470 2.480419 AGCAAACTACTACAAAGCGCAG 59.520 45.455 11.47 0.00 0.00 5.18
469 471 2.412847 GCAAACTACTACAAAGCGCAGG 60.413 50.000 11.47 0.00 0.00 4.85
471 473 3.947910 AACTACTACAAAGCGCAGGTA 57.052 42.857 11.47 7.94 37.06 3.08
473 475 4.467198 ACTACTACAAAGCGCAGGTATT 57.533 40.909 11.47 5.74 37.06 1.89
474 476 4.828829 ACTACTACAAAGCGCAGGTATTT 58.171 39.130 11.47 0.00 37.06 1.40
475 477 5.243207 ACTACTACAAAGCGCAGGTATTTT 58.757 37.500 11.47 0.00 37.06 1.82
476 478 5.704053 ACTACTACAAAGCGCAGGTATTTTT 59.296 36.000 11.47 0.00 37.06 1.94
477 479 6.875195 ACTACTACAAAGCGCAGGTATTTTTA 59.125 34.615 11.47 0.00 37.06 1.52
484 486 2.414957 GCGCAGGTATTTTTAAAGCCGT 60.415 45.455 0.30 0.00 0.00 5.68
519 521 1.264557 AGATCGATGTTAGTCGGAGCG 59.735 52.381 0.54 0.00 41.74 5.03
636 638 1.079336 GTGAGTTAGACCACGGCCC 60.079 63.158 0.00 0.00 0.00 5.80
688 692 4.511826 CACCTCCAACTTAGTCAAAGACAC 59.488 45.833 0.00 0.00 38.67 3.67
770 774 3.888930 AGTGTAGCTTGAGAGATAGAGCC 59.111 47.826 0.00 0.00 35.79 4.70
793 801 1.899142 GCAAAGGCTTAACCATTCCCA 59.101 47.619 0.00 0.00 43.14 4.37
794 802 2.094026 GCAAAGGCTTAACCATTCCCAG 60.094 50.000 0.00 0.00 43.14 4.45
795 803 1.852633 AAGGCTTAACCATTCCCAGC 58.147 50.000 0.00 0.00 43.14 4.85
797 805 3.281332 GCTTAACCATTCCCAGCCA 57.719 52.632 0.00 0.00 0.00 4.75
798 806 1.106285 GCTTAACCATTCCCAGCCAG 58.894 55.000 0.00 0.00 0.00 4.85
799 807 1.106285 CTTAACCATTCCCAGCCAGC 58.894 55.000 0.00 0.00 0.00 4.85
801 809 1.505151 TAACCATTCCCAGCCAGCCA 61.505 55.000 0.00 0.00 0.00 4.75
817 866 0.600557 GCCAGGATGAGATCGTCGAT 59.399 55.000 7.63 7.63 39.69 3.59
822 871 1.539388 GGATGAGATCGTCGATCAGCT 59.461 52.381 31.17 17.54 41.12 4.24
868 921 0.666274 CGTGCGTGGAGAACTAAGCA 60.666 55.000 0.00 0.00 39.17 3.91
869 922 1.071605 GTGCGTGGAGAACTAAGCAG 58.928 55.000 0.00 0.00 41.45 4.24
870 923 0.037326 TGCGTGGAGAACTAAGCAGG 60.037 55.000 0.00 0.00 37.13 4.85
871 924 0.741221 GCGTGGAGAACTAAGCAGGG 60.741 60.000 0.00 0.00 33.10 4.45
872 925 0.741221 CGTGGAGAACTAAGCAGGGC 60.741 60.000 0.00 0.00 0.00 5.19
873 926 0.741221 GTGGAGAACTAAGCAGGGCG 60.741 60.000 0.00 0.00 0.00 6.13
874 927 1.192146 TGGAGAACTAAGCAGGGCGT 61.192 55.000 0.00 0.00 0.00 5.68
875 928 0.741221 GGAGAACTAAGCAGGGCGTG 60.741 60.000 2.14 2.14 0.00 5.34
908 971 1.950216 GATCGGAAGGAAAAGATGGCC 59.050 52.381 0.00 0.00 0.00 5.36
914 977 0.332972 AGGAAAAGATGGCCCCTCAC 59.667 55.000 0.00 0.00 0.00 3.51
996 1059 2.875317 TGAGTTGATCGATCGAGGAGAG 59.125 50.000 23.84 0.00 0.00 3.20
997 1060 2.225491 GAGTTGATCGATCGAGGAGAGG 59.775 54.545 23.84 0.00 0.00 3.69
1018 1081 0.169009 GATGGCACGCTTTCTTGGTC 59.831 55.000 0.00 0.00 0.00 4.02
1068 1131 3.119566 TCATGGTGCATGTACGTACGTTA 60.120 43.478 27.92 16.43 41.98 3.18
1084 1147 6.073440 ACGTACGTTATTGTTTTGCAGAGAAT 60.073 34.615 16.72 0.00 0.00 2.40
1095 1158 0.441533 GCAGAGAATATCATGGCGCG 59.558 55.000 0.00 0.00 0.00 6.86
1150 1213 3.273788 AAGGCCGGCAGGAAGAAGG 62.274 63.158 30.85 0.00 41.02 3.46
1151 1214 4.035102 GGCCGGCAGGAAGAAGGT 62.035 66.667 30.85 0.00 41.02 3.50
1152 1215 2.747855 GCCGGCAGGAAGAAGGTG 60.748 66.667 24.80 0.00 41.02 4.00
1153 1216 2.747855 CCGGCAGGAAGAAGGTGC 60.748 66.667 0.00 0.00 41.02 5.01
1154 1217 2.348998 CGGCAGGAAGAAGGTGCT 59.651 61.111 0.00 0.00 37.37 4.40
1199 1262 2.444624 CCGTCGTGCTCATGTTCGG 61.445 63.158 11.31 11.31 33.20 4.30
1396 1459 3.316573 GAGGTGAAGCGGTGGAGGG 62.317 68.421 0.00 0.00 0.00 4.30
1548 1611 1.609501 CTCACTCCCAGACCCCGAA 60.610 63.158 0.00 0.00 0.00 4.30
1601 1664 4.659172 CAACCTCCCCTGCCGCAA 62.659 66.667 0.00 0.00 0.00 4.85
1686 1749 4.477975 CTCGCCGTCTCCGTCCAC 62.478 72.222 0.00 0.00 0.00 4.02
1692 1755 2.322830 CGTCTCCGTCCACTCGTCA 61.323 63.158 0.00 0.00 0.00 4.35
1695 1758 1.081376 CTCCGTCCACTCGTCACAC 60.081 63.158 0.00 0.00 0.00 3.82
1753 1816 1.304381 TTCCCATGCAAGCACCTCC 60.304 57.895 0.00 0.00 0.00 4.30
1760 1823 2.046892 CAAGCACCTCCTCCACCG 60.047 66.667 0.00 0.00 0.00 4.94
1805 1868 4.753662 TCACGCCGCCTACCTCCT 62.754 66.667 0.00 0.00 0.00 3.69
1877 1940 2.104530 GAGTCCTACGAAGCCGCC 59.895 66.667 0.00 0.00 39.95 6.13
1881 1944 1.378911 TCCTACGAAGCCGCCTACA 60.379 57.895 0.00 0.00 39.95 2.74
1894 1957 2.351244 CCTACAGTGCTCAGGCGGA 61.351 63.158 0.00 0.00 42.25 5.54
2283 2346 1.801913 CCGGACGCTCTTCAACTCG 60.802 63.158 0.00 0.00 0.00 4.18
2304 2367 2.821366 GTCATGGTGCTGGAGCCG 60.821 66.667 0.00 0.00 41.18 5.52
2433 2496 3.403057 CGCACCGTCAACGTCCTG 61.403 66.667 1.48 0.00 37.74 3.86
2453 2516 3.576982 CTGAAGTACTACCACCAACAGGA 59.423 47.826 0.00 0.00 0.00 3.86
2819 2888 0.753262 ACCGCTTGATTCTATCCGCT 59.247 50.000 0.00 0.00 0.00 5.52
2850 2919 9.968870 TTGTACCTATGGTGTTTTTGTAAATTC 57.031 29.630 0.00 0.00 36.19 2.17
2892 2961 4.355543 TTTCTAATCATTTCACAGCGGC 57.644 40.909 0.00 0.00 0.00 6.53
2933 3002 5.006358 GCTTTAGAAAAATCTGACGCCGATA 59.994 40.000 0.00 0.00 0.00 2.92
2978 3047 1.229359 CATCCAATGGCCCAGCTCT 59.771 57.895 0.00 0.00 0.00 4.09
2980 3049 1.284111 ATCCAATGGCCCAGCTCTCA 61.284 55.000 0.00 0.00 0.00 3.27
2986 3055 1.220477 GGCCCAGCTCTCACTCTTC 59.780 63.158 0.00 0.00 0.00 2.87
2995 3064 2.534990 CTCTCACTCTTCCTCCCAACT 58.465 52.381 0.00 0.00 0.00 3.16
3029 3098 1.305718 GTGAGCACCCTCCTCCTCT 60.306 63.158 0.00 0.00 37.29 3.69
3032 3101 0.616111 GAGCACCCTCCTCCTCTTCA 60.616 60.000 0.00 0.00 31.68 3.02
3053 3122 2.282958 TCTTCCGGACGCTCACCT 60.283 61.111 1.83 0.00 0.00 4.00
3060 3129 4.803426 GACGCTCACCTCTGGCCG 62.803 72.222 0.00 0.00 0.00 6.13
3092 3161 0.760945 CTTGGGCGAGGTCCTATCCT 60.761 60.000 8.39 0.00 40.97 3.24
3100 3169 1.019650 AGGTCCTATCCTGGTCTGGT 58.980 55.000 0.00 0.00 36.35 4.00
3149 3218 0.613292 GTCTCACCCTCAGAGCTCCA 60.613 60.000 10.93 0.00 33.15 3.86
3201 3273 2.254546 ATGTCACTCGCTTTTCCACA 57.745 45.000 0.00 0.00 0.00 4.17
3260 3332 4.081420 ACGAACATCATCAAGCCTAGAGTT 60.081 41.667 0.00 0.00 0.00 3.01
3264 3336 5.564550 ACATCATCAAGCCTAGAGTTTTGT 58.435 37.500 0.00 0.00 0.00 2.83
3265 3337 6.711277 ACATCATCAAGCCTAGAGTTTTGTA 58.289 36.000 0.00 0.00 0.00 2.41
3268 3340 6.946340 TCATCAAGCCTAGAGTTTTGTATGA 58.054 36.000 0.00 0.00 0.00 2.15
3303 3584 5.957798 TGATGAAATGCAGAAACCTTGATC 58.042 37.500 0.00 0.00 0.00 2.92
3330 3611 9.809096 GAGACAATTACTCATCAGTTATCTTGA 57.191 33.333 6.87 0.00 33.62 3.02
3363 3644 3.426615 CACCACCTTAAAGCCAATGGTA 58.573 45.455 0.00 0.00 38.38 3.25
3371 3652 8.893727 CACCTTAAAGCCAATGGTATATATAGC 58.106 37.037 13.87 13.87 0.00 2.97
3397 3678 2.956132 ACCATGACAAAACCCATGACA 58.044 42.857 0.00 0.00 41.88 3.58
3398 3679 2.627699 ACCATGACAAAACCCATGACAC 59.372 45.455 0.00 0.00 41.88 3.67
3404 3685 4.454161 TGACAAAACCCATGACACTTATCG 59.546 41.667 0.00 0.00 0.00 2.92
3412 3693 0.599060 TGACACTTATCGACGTGCCA 59.401 50.000 0.00 4.27 34.58 4.92
3415 3696 2.787680 GACACTTATCGACGTGCCATAC 59.212 50.000 0.00 0.00 34.58 2.39
3420 3701 1.302366 ATCGACGTGCCATACTACGA 58.698 50.000 0.00 0.00 42.54 3.43
3433 3714 5.523916 GCCATACTACGACTTTGAATGTGAT 59.476 40.000 0.00 0.00 0.00 3.06
3485 3766 5.556915 AGATGGACAAAACCAACGAGATTA 58.443 37.500 0.00 0.00 43.47 1.75
3517 3798 4.025401 GCCTCCAACGCAACCACG 62.025 66.667 0.00 0.00 39.50 4.94
3522 3803 2.897846 CAACGCAACCACGGGTCA 60.898 61.111 0.00 0.00 33.12 4.02
3531 3812 0.832135 ACCACGGGTCATGAGACTGT 60.832 55.000 0.00 0.18 44.36 3.55
3536 3817 2.069273 CGGGTCATGAGACTGTTGAAC 58.931 52.381 0.00 0.00 44.36 3.18
3557 3862 8.781067 TGAACTATCAACAAGAAACAATTTCG 57.219 30.769 0.00 0.00 37.40 3.46
3585 3890 3.002791 TCAGAAACTAATGCTTGGAGCG 58.997 45.455 0.00 0.00 46.26 5.03
3594 3899 2.586245 CTTGGAGCGGCTGGATGA 59.414 61.111 7.50 0.00 0.00 2.92
3651 3956 9.670442 ATCTATCTTTAGTAGGGATGTAAACCA 57.330 33.333 0.00 0.00 0.00 3.67
3654 3959 4.765813 TTAGTAGGGATGTAAACCAGGC 57.234 45.455 0.00 0.00 0.00 4.85
3660 3965 2.301346 GGATGTAAACCAGGCCTCATG 58.699 52.381 0.00 0.00 0.00 3.07
3681 3986 5.093849 TGTAAGCCCACTTATGGTCTAAC 57.906 43.478 0.00 0.00 45.66 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 1.647545 CTGTAGCACCATGGCAACGG 61.648 60.000 13.04 6.24 42.51 4.44
88 89 0.617935 TAGCTGTAGCACCATGGCAA 59.382 50.000 13.04 0.00 45.16 4.52
123 124 2.894765 TCGTATTGTTCACCTCACCTCA 59.105 45.455 0.00 0.00 0.00 3.86
195 196 0.989164 CAGTGCATGTGGTACGTACG 59.011 55.000 18.98 15.01 37.18 3.67
209 210 1.486310 TCCATCCATGTAGACCAGTGC 59.514 52.381 0.00 0.00 0.00 4.40
247 248 7.932335 AGTAGTAGTACAAGCTATGCAACTAG 58.068 38.462 10.33 0.00 33.72 2.57
354 355 1.073722 CTTGGTCAAGGCCAGCTGA 59.926 57.895 17.39 1.02 40.01 4.26
377 378 4.628333 AGTACATGATTTGCATTGCTTTGC 59.372 37.500 10.49 4.71 43.07 3.68
382 383 6.580041 GCATAGTAGTACATGATTTGCATTGC 59.420 38.462 0.00 0.46 34.15 3.56
385 386 6.537355 AGGCATAGTAGTACATGATTTGCAT 58.463 36.000 0.00 2.00 37.85 3.96
386 387 5.928976 AGGCATAGTAGTACATGATTTGCA 58.071 37.500 0.00 0.00 0.00 4.08
387 388 5.991606 TGAGGCATAGTAGTACATGATTTGC 59.008 40.000 0.00 5.83 0.00 3.68
388 389 7.928167 TCTTGAGGCATAGTAGTACATGATTTG 59.072 37.037 0.00 0.00 0.00 2.32
389 390 7.928706 GTCTTGAGGCATAGTAGTACATGATTT 59.071 37.037 0.00 0.00 0.00 2.17
390 391 7.069950 TGTCTTGAGGCATAGTAGTACATGATT 59.930 37.037 0.00 4.23 0.00 2.57
391 392 6.551227 TGTCTTGAGGCATAGTAGTACATGAT 59.449 38.462 0.00 4.70 0.00 2.45
392 393 5.891551 TGTCTTGAGGCATAGTAGTACATGA 59.108 40.000 0.00 0.00 0.00 3.07
394 395 6.684111 GCTTGTCTTGAGGCATAGTAGTACAT 60.684 42.308 2.52 0.00 0.00 2.29
395 396 5.394224 GCTTGTCTTGAGGCATAGTAGTACA 60.394 44.000 2.52 0.00 0.00 2.90
396 397 5.044558 GCTTGTCTTGAGGCATAGTAGTAC 58.955 45.833 0.00 0.00 0.00 2.73
397 398 4.956700 AGCTTGTCTTGAGGCATAGTAGTA 59.043 41.667 0.00 0.00 0.00 1.82
398 399 3.772025 AGCTTGTCTTGAGGCATAGTAGT 59.228 43.478 0.00 0.00 0.00 2.73
399 400 4.399004 AGCTTGTCTTGAGGCATAGTAG 57.601 45.455 0.00 0.00 0.00 2.57
408 409 5.008019 TGAAAAAGTGCTAGCTTGTCTTGAG 59.992 40.000 17.23 0.00 0.00 3.02
457 459 5.859648 GCTTTAAAAATACCTGCGCTTTGTA 59.140 36.000 9.73 7.84 0.00 2.41
459 461 4.091365 GGCTTTAAAAATACCTGCGCTTTG 59.909 41.667 9.73 0.00 0.00 2.77
460 462 4.242475 GGCTTTAAAAATACCTGCGCTTT 58.758 39.130 9.73 0.80 0.00 3.51
461 463 3.672241 CGGCTTTAAAAATACCTGCGCTT 60.672 43.478 9.73 0.00 0.00 4.68
463 465 2.182014 CGGCTTTAAAAATACCTGCGC 58.818 47.619 0.00 0.00 0.00 6.09
464 466 3.168193 CACGGCTTTAAAAATACCTGCG 58.832 45.455 0.00 0.00 0.00 5.18
466 468 4.142469 CCTCCACGGCTTTAAAAATACCTG 60.142 45.833 0.00 0.00 0.00 4.00
467 469 4.014406 CCTCCACGGCTTTAAAAATACCT 58.986 43.478 0.00 0.00 0.00 3.08
468 470 4.011698 TCCTCCACGGCTTTAAAAATACC 58.988 43.478 0.00 0.00 0.00 2.73
469 471 5.182570 AGTTCCTCCACGGCTTTAAAAATAC 59.817 40.000 0.00 0.00 0.00 1.89
471 473 4.149598 AGTTCCTCCACGGCTTTAAAAAT 58.850 39.130 0.00 0.00 0.00 1.82
473 475 3.217681 AGTTCCTCCACGGCTTTAAAA 57.782 42.857 0.00 0.00 0.00 1.52
474 476 2.882137 CAAGTTCCTCCACGGCTTTAAA 59.118 45.455 0.00 0.00 0.00 1.52
475 477 2.500229 CAAGTTCCTCCACGGCTTTAA 58.500 47.619 0.00 0.00 0.00 1.52
476 478 1.271163 CCAAGTTCCTCCACGGCTTTA 60.271 52.381 0.00 0.00 0.00 1.85
477 479 0.537371 CCAAGTTCCTCCACGGCTTT 60.537 55.000 0.00 0.00 0.00 3.51
484 486 2.903784 TCGATCTTTCCAAGTTCCTCCA 59.096 45.455 0.00 0.00 0.00 3.86
519 521 1.777101 CTACATTCAGGCGAGCTAGC 58.223 55.000 10.75 10.75 0.00 3.42
636 638 8.442632 AATCATGTGATTACAAGTGATAGGTG 57.557 34.615 6.46 0.00 42.48 4.00
688 692 2.286184 CCGTGGTTTTCAGTTTGTCTCG 60.286 50.000 0.00 0.00 0.00 4.04
741 745 9.225436 TCTATCTCTCAAGCTACACTGTATATG 57.775 37.037 0.00 0.00 0.00 1.78
742 746 9.448438 CTCTATCTCTCAAGCTACACTGTATAT 57.552 37.037 0.00 0.00 0.00 0.86
743 747 7.389330 GCTCTATCTCTCAAGCTACACTGTATA 59.611 40.741 0.00 0.00 0.00 1.47
744 748 6.206634 GCTCTATCTCTCAAGCTACACTGTAT 59.793 42.308 0.00 0.00 0.00 2.29
745 749 5.529430 GCTCTATCTCTCAAGCTACACTGTA 59.471 44.000 0.00 0.00 0.00 2.74
746 750 4.338118 GCTCTATCTCTCAAGCTACACTGT 59.662 45.833 0.00 0.00 0.00 3.55
747 751 4.261572 GGCTCTATCTCTCAAGCTACACTG 60.262 50.000 0.00 0.00 35.12 3.66
793 801 1.756408 CGATCTCATCCTGGCTGGCT 61.756 60.000 5.39 0.00 35.26 4.75
794 802 1.301558 CGATCTCATCCTGGCTGGC 60.302 63.158 5.39 0.00 35.26 4.85
795 803 0.033228 GACGATCTCATCCTGGCTGG 59.967 60.000 3.65 3.65 37.10 4.85
797 805 0.466372 TCGACGATCTCATCCTGGCT 60.466 55.000 0.00 0.00 0.00 4.75
798 806 0.600557 ATCGACGATCTCATCCTGGC 59.399 55.000 4.05 0.00 0.00 4.85
799 807 1.882623 TGATCGACGATCTCATCCTGG 59.117 52.381 31.65 0.00 39.56 4.45
801 809 1.539388 GCTGATCGACGATCTCATCCT 59.461 52.381 31.65 1.09 39.56 3.24
822 871 1.600076 CCGGCGGAGTAGCTAGCTA 60.600 63.158 24.41 20.67 37.29 3.32
872 925 3.958147 ATCACTCGGCCCTTGCACG 62.958 63.158 0.00 0.00 40.13 5.34
873 926 2.045926 ATCACTCGGCCCTTGCAC 60.046 61.111 0.00 0.00 40.13 4.57
874 927 2.268920 GATCACTCGGCCCTTGCA 59.731 61.111 0.00 0.00 40.13 4.08
875 928 2.892425 CGATCACTCGGCCCTTGC 60.892 66.667 0.00 0.00 41.27 4.01
908 971 0.172352 GAGACAAGAGAGCGTGAGGG 59.828 60.000 0.00 0.00 0.00 4.30
914 977 1.309499 ACTCCGGAGACAAGAGAGCG 61.309 60.000 37.69 7.99 35.07 5.03
996 1059 0.449388 CAAGAAAGCGTGCCATCTCC 59.551 55.000 0.00 0.00 0.00 3.71
997 1060 0.449388 CCAAGAAAGCGTGCCATCTC 59.551 55.000 0.00 0.00 0.00 2.75
1018 1081 4.315803 AGTCCAAAATCCAGACGTACTTG 58.684 43.478 0.00 0.00 35.65 3.16
1068 1131 6.278363 GCCATGATATTCTCTGCAAAACAAT 58.722 36.000 0.00 0.00 0.00 2.71
1150 1213 3.667282 CAGCACCAGCACCAGCAC 61.667 66.667 0.00 0.00 45.49 4.40
1151 1214 3.876236 TCAGCACCAGCACCAGCA 61.876 61.111 0.00 0.00 45.49 4.41
1152 1215 3.360340 GTCAGCACCAGCACCAGC 61.360 66.667 0.00 0.00 45.49 4.85
1153 1216 2.670934 GGTCAGCACCAGCACCAG 60.671 66.667 0.00 0.00 45.49 4.00
1154 1217 4.624364 CGGTCAGCACCAGCACCA 62.624 66.667 0.00 0.00 44.02 4.17
1199 1262 0.035915 GGTTCTGGTCTTGAGGAGGC 60.036 60.000 0.00 0.00 0.00 4.70
1403 1466 3.075005 TCACTGCTCCGGGTAGCC 61.075 66.667 12.28 0.00 42.05 3.93
1406 1469 1.228769 ACTGTCACTGCTCCGGGTA 60.229 57.895 0.00 0.00 0.00 3.69
1409 1472 2.262915 GGACTGTCACTGCTCCGG 59.737 66.667 10.38 0.00 0.00 5.14
1411 1474 1.214062 CTCGGACTGTCACTGCTCC 59.786 63.158 10.38 0.00 0.00 4.70
1412 1475 1.445238 GCTCGGACTGTCACTGCTC 60.445 63.158 10.38 0.00 0.00 4.26
1413 1476 2.653702 GCTCGGACTGTCACTGCT 59.346 61.111 10.38 0.00 0.00 4.24
1414 1477 2.807045 CGCTCGGACTGTCACTGC 60.807 66.667 10.38 8.78 0.00 4.40
1416 1479 2.597805 ACCGCTCGGACTGTCACT 60.598 61.111 15.95 0.00 38.96 3.41
1417 1480 2.430921 CACCGCTCGGACTGTCAC 60.431 66.667 15.95 0.00 38.96 3.67
1418 1481 4.357947 GCACCGCTCGGACTGTCA 62.358 66.667 15.95 0.00 38.96 3.58
1548 1611 2.906458 CGCTGGCCTCCTTGATCT 59.094 61.111 3.32 0.00 0.00 2.75
1695 1758 2.812609 TCCGAGACGACGAGGACG 60.813 66.667 0.00 1.78 45.75 4.79
1710 1773 3.403558 GGGAGTGGGAGGCAGTCC 61.404 72.222 0.00 0.00 46.10 3.85
1862 1925 1.065436 GTAGGCGGCTTCGTAGGAC 59.935 63.158 19.76 2.89 36.07 3.85
1868 1931 3.188786 GCACTGTAGGCGGCTTCG 61.189 66.667 19.76 11.11 0.00 3.79
1877 1940 1.140589 CTCCGCCTGAGCACTGTAG 59.859 63.158 0.00 0.00 39.83 2.74
2283 2346 4.408821 TCCAGCACCATGACGCCC 62.409 66.667 0.00 0.00 0.00 6.13
2433 2496 3.306571 GGTCCTGTTGGTGGTAGTACTTC 60.307 52.174 0.00 0.00 34.23 3.01
2541 2610 0.601558 TCCAGTTGCAGTCGTAGTCC 59.398 55.000 0.00 0.00 0.00 3.85
2805 2874 4.009675 ACAAGCAAAGCGGATAGAATCAA 58.990 39.130 0.00 0.00 0.00 2.57
2819 2888 6.127310 ACAAAAACACCATAGGTACAAGCAAA 60.127 34.615 0.00 0.00 32.11 3.68
2933 3002 3.933861 ATCCAACGGCTAGGAAAATCT 57.066 42.857 0.00 0.00 37.48 2.40
2978 3047 1.150135 AGGAGTTGGGAGGAAGAGTGA 59.850 52.381 0.00 0.00 0.00 3.41
2980 3049 1.435168 AGAGGAGTTGGGAGGAAGAGT 59.565 52.381 0.00 0.00 0.00 3.24
2986 3055 2.246091 AGAAGAGAGGAGTTGGGAGG 57.754 55.000 0.00 0.00 0.00 4.30
2995 3064 2.564947 GCTCACCAAGAAGAAGAGAGGA 59.435 50.000 0.00 0.00 0.00 3.71
3032 3101 1.379977 TGAGCGTCCGGAAGAGGAT 60.380 57.895 22.33 2.25 43.04 3.24
3060 3129 4.208632 CCAAGACAGGGATGTCGC 57.791 61.111 2.94 0.00 43.15 5.19
3092 3161 3.948719 GGCGTCCCAACCAGACCA 61.949 66.667 0.00 0.00 0.00 4.02
3117 3186 5.487488 TGAGGGTGAGACAAATACAATAGGT 59.513 40.000 0.00 0.00 0.00 3.08
3293 3574 6.464222 TGAGTAATTGTCTCGATCAAGGTTT 58.536 36.000 8.65 2.77 34.99 3.27
3303 3584 8.750416 CAAGATAACTGATGAGTAATTGTCTCG 58.250 37.037 0.00 0.00 34.99 4.04
3330 3611 6.472686 TTTAAGGTGGTGCTATTTTGTTGT 57.527 33.333 0.00 0.00 0.00 3.32
3371 3652 6.368516 GTCATGGGTTTTGTCATGGTTATTTG 59.631 38.462 0.00 0.00 40.63 2.32
3383 3664 4.454504 GTCGATAAGTGTCATGGGTTTTGT 59.545 41.667 0.00 0.00 0.00 2.83
3397 3678 3.303593 CGTAGTATGGCACGTCGATAAGT 60.304 47.826 0.00 0.00 33.56 2.24
3398 3679 3.059393 TCGTAGTATGGCACGTCGATAAG 60.059 47.826 0.00 0.00 39.18 1.73
3404 3685 2.556534 AAGTCGTAGTATGGCACGTC 57.443 50.000 0.00 0.00 39.18 4.34
3412 3693 8.683615 TGTAGATCACATTCAAAGTCGTAGTAT 58.316 33.333 0.00 0.00 30.04 2.12
3415 3696 7.542477 AGTTGTAGATCACATTCAAAGTCGTAG 59.458 37.037 0.00 0.00 36.90 3.51
3420 3701 9.561069 AACTAAGTTGTAGATCACATTCAAAGT 57.439 29.630 0.00 0.00 36.90 2.66
3433 3714 6.952358 ACAGTATCCTCCAACTAAGTTGTAGA 59.048 38.462 0.00 0.00 41.41 2.59
3456 3737 5.357314 TCGTTGGTTTTGTCCATCTTTTACA 59.643 36.000 0.00 0.00 37.33 2.41
3457 3738 5.823353 TCGTTGGTTTTGTCCATCTTTTAC 58.177 37.500 0.00 0.00 37.33 2.01
3466 3747 5.823353 TGTTTAATCTCGTTGGTTTTGTCC 58.177 37.500 0.00 0.00 0.00 4.02
3469 3750 7.306515 CCATGTTGTTTAATCTCGTTGGTTTTG 60.307 37.037 0.00 0.00 0.00 2.44
3470 3751 6.699642 CCATGTTGTTTAATCTCGTTGGTTTT 59.300 34.615 0.00 0.00 0.00 2.43
3485 3766 1.895131 GGAGGCATGACCATGTTGTTT 59.105 47.619 11.17 0.00 43.14 2.83
3517 3798 3.409026 AGTTCAACAGTCTCATGACCC 57.591 47.619 0.00 0.00 43.91 4.46
3531 3812 9.232082 CGAAATTGTTTCTTGTTGATAGTTCAA 57.768 29.630 1.52 0.00 37.23 2.69
3536 3817 8.168626 TCGATCGAAATTGTTTCTTGTTGATAG 58.831 33.333 16.99 0.00 37.52 2.08
3546 3827 7.746475 AGTTTCTGAATCGATCGAAATTGTTTC 59.254 33.333 23.50 19.14 35.03 2.78
3552 3857 7.225538 AGCATTAGTTTCTGAATCGATCGAAAT 59.774 33.333 23.50 14.25 35.03 2.17
3557 3862 6.258727 TCCAAGCATTAGTTTCTGAATCGATC 59.741 38.462 0.00 0.00 0.00 3.69
3585 3890 4.886579 AGTCATTTGTTTTTCATCCAGCC 58.113 39.130 0.00 0.00 0.00 4.85
3619 3924 9.781425 ACATCCCTACTAAAGATAGATGATGAT 57.219 33.333 13.65 0.00 34.11 2.45
3624 3929 9.930693 GGTTTACATCCCTACTAAAGATAGATG 57.069 37.037 0.00 0.00 35.16 2.90
3625 3930 9.670442 TGGTTTACATCCCTACTAAAGATAGAT 57.330 33.333 0.00 0.00 33.15 1.98
3639 3944 0.623723 TGAGGCCTGGTTTACATCCC 59.376 55.000 12.00 0.00 0.00 3.85
3654 3959 3.480470 CCATAAGTGGGCTTACATGAGG 58.520 50.000 0.00 0.00 42.11 3.86


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

AutoCloner maintained by Alex Coulton.