Multiple sequence alignment - TraesCS4D01G069500

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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 TraesCS4D01G069500 chr4D 100.000 3560 0 0 1 3560 44757649 44754090 0.000000e+00 6575.0
1 TraesCS4D01G069500 chr4B 90.818 2592 166 28 9 2594 64776133 64773608 0.000000e+00 3402.0
2 TraesCS4D01G069500 chr4B 90.889 900 76 5 3 899 64785242 64784346 0.000000e+00 1203.0
3 TraesCS4D01G069500 chr4A 90.346 1533 104 22 1 1524 554852346 554853843 0.000000e+00 1971.0
4 TraesCS4D01G069500 chr4A 92.448 1205 65 12 1604 2790 554853868 554855064 0.000000e+00 1698.0
5 TraesCS4D01G069500 chr4A 90.495 768 54 12 2802 3557 554855109 554855869 0.000000e+00 996.0
6 TraesCS4D01G069500 chr7A 81.081 481 71 11 1051 1523 671305685 671306153 2.020000e-97 366.0
7 TraesCS4D01G069500 chr7D 78.794 481 72 14 1051 1523 579570463 579570921 2.690000e-76 296.0
8 TraesCS4D01G069500 chr3A 84.932 146 21 1 1052 1197 728225084 728225228 2.860000e-31 147.0
9 TraesCS4D01G069500 chr3A 83.688 141 23 0 1057 1197 728094999 728095139 2.230000e-27 134.0
10 TraesCS4D01G069500 chr3A 71.053 418 117 4 1971 2386 728100406 728100821 8.130000e-17 99.0
11 TraesCS4D01G069500 chr3B 83.448 145 23 1 1054 1197 805093958 805094102 2.230000e-27 134.0
12 TraesCS4D01G069500 chr3B 72.619 420 107 7 1971 2386 805099381 805099796 8.020000e-27 132.0
13 TraesCS4D01G069500 chr3B 82.877 146 24 1 1052 1197 805118217 805118361 2.880000e-26 130.0
14 TraesCS4D01G069500 chr3B 82.877 146 24 1 1052 1197 805121481 805121625 2.880000e-26 130.0
15 TraesCS4D01G069500 chr3B 70.476 420 116 6 1971 2386 805127927 805128342 8.190000e-12 82.4
16 TraesCS4D01G069500 chr3D 71.531 418 115 4 1971 2386 598080227 598080642 3.760000e-20 110.0
17 TraesCS4D01G069500 chrUn 70.476 420 116 6 1971 2386 291744735 291744320 8.190000e-12 82.4
18 TraesCS4D01G069500 chr6B 84.127 63 10 0 1427 1489 56011494 56011432 1.070000e-05 62.1


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 TraesCS4D01G069500 chr4D 44754090 44757649 3559 True 6575 6575 100.000000 1 3560 1 chr4D.!!$R1 3559
1 TraesCS4D01G069500 chr4B 64773608 64776133 2525 True 3402 3402 90.818000 9 2594 1 chr4B.!!$R1 2585
2 TraesCS4D01G069500 chr4B 64784346 64785242 896 True 1203 1203 90.889000 3 899 1 chr4B.!!$R2 896
3 TraesCS4D01G069500 chr4A 554852346 554855869 3523 False 1555 1971 91.096333 1 3557 3 chr4A.!!$F1 3556

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
173 176 0.469892 CCAAGCCCCAAGTCCAAGTT 60.470 55.0 0.0 0.0 0.00 2.66 F
392 396 0.475906 GGCTAGGGTCTGCATTGGAT 59.524 55.0 0.0 0.0 0.00 3.41 F
2109 2129 0.310854 CTTTTCTGTGGGTTGTCCGC 59.689 55.0 0.0 0.0 46.03 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 1871 0.535335 GGCGTATCCTGTCCAGTTCA 59.465 55.0 0.00 0.0 0.00 3.18 R
2361 2381 0.179134 CCTCGAGCTCAAACCCTACG 60.179 60.0 15.40 0.0 0.00 3.51 R
3443 3521 0.045778 AGGGCCAGGTTGGGTACTAT 59.954 55.0 6.18 0.0 38.19 2.12 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
39 42 1.475403 GTCTCCTCTCATTGTCCGGA 58.525 55.000 0.00 0.00 0.00 5.14
136 139 1.744639 GAGCGGCATCCTCTCATCA 59.255 57.895 1.45 0.00 0.00 3.07
173 176 0.469892 CCAAGCCCCAAGTCCAAGTT 60.470 55.000 0.00 0.00 0.00 2.66
177 180 1.187567 GCCCCAAGTCCAAGTTGCAT 61.188 55.000 0.00 0.00 0.00 3.96
392 396 0.475906 GGCTAGGGTCTGCATTGGAT 59.524 55.000 0.00 0.00 0.00 3.41
569 573 4.771356 GCAGCCACGCGTACGAGA 62.771 66.667 25.90 0.00 43.93 4.04
664 669 6.713450 ACTTAGGTTTATTCCGTCATGTTTGT 59.287 34.615 0.00 0.00 0.00 2.83
734 739 1.678970 GTTGGATGGCCGGCTTTCT 60.679 57.895 28.56 8.44 36.79 2.52
739 746 1.338020 GGATGGCCGGCTTTCTTATTG 59.662 52.381 28.56 0.00 0.00 1.90
745 752 1.062587 CCGGCTTTCTTATTGCTGTCG 59.937 52.381 0.00 0.00 0.00 4.35
791 798 4.202326 GCTTCATCTTTCCCCTTCCGTATA 60.202 45.833 0.00 0.00 0.00 1.47
811 818 1.133809 ACTGTAGCATGGTGGGGTGT 61.134 55.000 7.89 0.00 0.00 4.16
830 838 4.163649 GGTGTAGCCACTACTTTCCCTTAT 59.836 45.833 6.34 0.00 41.53 1.73
854 862 0.976641 GGTGATCACTCCACAGTCCA 59.023 55.000 24.50 0.00 36.31 4.02
920 928 6.924060 TGTAAGAACTAAGAAGTGAGAACTGC 59.076 38.462 0.00 0.00 35.62 4.40
954 962 1.856629 ACCCATGGAGATTTTGGCAG 58.143 50.000 15.22 0.00 0.00 4.85
982 994 3.002759 GCTTGCTAAGATCGGATCAAACC 59.997 47.826 19.47 6.33 0.00 3.27
1036 1048 2.182284 CATCCCGTGGCGACGTTA 59.818 61.111 20.00 7.82 44.54 3.18
1037 1049 1.876714 CATCCCGTGGCGACGTTAG 60.877 63.158 20.00 8.50 44.54 2.34
1047 1059 2.431260 GACGTTAGCCGGCGACAA 60.431 61.111 27.67 18.62 42.24 3.18
1122 1134 4.542390 ATGCTGCAGCTCGCCGAT 62.542 61.111 36.61 19.64 42.66 4.18
1215 1227 1.337817 CTGAGTTCACCTTCGTCGCG 61.338 60.000 0.00 0.00 0.00 5.87
1473 1485 1.306642 CCTGCTTCAGCTGCTTCCTG 61.307 60.000 9.47 1.55 42.66 3.86
1482 1494 1.704007 GCTGCTTCCTGGCCTATCCT 61.704 60.000 3.32 0.00 35.26 3.24
1529 1541 5.845391 CCTCCAAAAGGTCAGTAAACAAA 57.155 39.130 0.00 0.00 40.67 2.83
1530 1542 6.405278 CCTCCAAAAGGTCAGTAAACAAAT 57.595 37.500 0.00 0.00 40.67 2.32
1531 1543 7.519032 CCTCCAAAAGGTCAGTAAACAAATA 57.481 36.000 0.00 0.00 40.67 1.40
1532 1544 7.368059 CCTCCAAAAGGTCAGTAAACAAATAC 58.632 38.462 0.00 0.00 40.67 1.89
1533 1545 6.961576 TCCAAAAGGTCAGTAAACAAATACG 58.038 36.000 0.00 0.00 0.00 3.06
1534 1546 6.543100 TCCAAAAGGTCAGTAAACAAATACGT 59.457 34.615 0.00 0.00 0.00 3.57
1535 1547 7.714377 TCCAAAAGGTCAGTAAACAAATACGTA 59.286 33.333 0.00 0.00 0.00 3.57
1536 1548 7.799914 CCAAAAGGTCAGTAAACAAATACGTAC 59.200 37.037 0.00 0.00 0.00 3.67
1537 1549 8.336806 CAAAAGGTCAGTAAACAAATACGTACA 58.663 33.333 0.00 0.00 0.00 2.90
1552 1564 7.900782 AATACGTACAGCCAATATAATCACC 57.099 36.000 0.00 0.00 0.00 4.02
1553 1565 5.284861 ACGTACAGCCAATATAATCACCA 57.715 39.130 0.00 0.00 0.00 4.17
1579 1594 2.586648 TAGGATGAGATCTGCGCCTA 57.413 50.000 4.18 4.97 0.00 3.93
1599 1614 6.402875 CGCCTAATCATGTATTGTGATCCATG 60.403 42.308 0.00 0.00 35.35 3.66
1600 1615 6.624423 GCCTAATCATGTATTGTGATCCATGC 60.624 42.308 0.00 0.00 35.35 4.06
1601 1616 6.431852 CCTAATCATGTATTGTGATCCATGCA 59.568 38.462 0.00 0.00 35.35 3.96
1602 1617 6.911250 AATCATGTATTGTGATCCATGCAT 57.089 33.333 0.00 0.00 35.35 3.96
1635 1650 4.560108 GCACCTTGAGATTTTGCTGATTGT 60.560 41.667 0.00 0.00 0.00 2.71
1636 1651 5.535333 CACCTTGAGATTTTGCTGATTGTT 58.465 37.500 0.00 0.00 0.00 2.83
1645 1660 8.524870 AGATTTTGCTGATTGTTTGTTATGTC 57.475 30.769 0.00 0.00 0.00 3.06
1734 1754 2.047844 CTGCGTGTCAGGGACCTG 60.048 66.667 12.16 12.16 44.86 4.00
1748 1768 3.414700 CCTGTTCCGCACGAGCAC 61.415 66.667 5.50 0.00 42.27 4.40
1773 1793 2.983433 CCACAAAATGGTGCGCAAA 58.017 47.368 14.00 3.42 44.46 3.68
1851 1871 3.444805 GACGCTCTGGAGACCGCT 61.445 66.667 1.35 0.00 0.00 5.52
1854 1874 2.973899 GCTCTGGAGACCGCTGAA 59.026 61.111 1.35 0.00 0.00 3.02
1978 1998 1.219124 CGTAGCTGCATGGAGTGGT 59.781 57.895 16.22 3.79 0.00 4.16
2097 2117 1.402787 ACAGTGGCCAACCTTTTCTG 58.597 50.000 7.24 11.71 36.63 3.02
2109 2129 0.310854 CTTTTCTGTGGGTTGTCCGC 59.689 55.000 0.00 0.00 46.03 5.54
2112 2132 4.619227 CTGTGGGTTGTCCGCCGT 62.619 66.667 0.00 0.00 45.26 5.68
2130 2150 4.222847 GACCTCGTGCGGGGATCC 62.223 72.222 18.21 1.92 38.23 3.36
2340 2360 4.665212 CGGATCAAATGATGAACACAAGG 58.335 43.478 0.00 0.00 42.54 3.61
2343 2363 6.555315 GGATCAAATGATGAACACAAGGTAC 58.445 40.000 0.00 0.00 42.54 3.34
2418 2438 3.065655 CAAAATCGCCAAGGCAATTCAA 58.934 40.909 12.19 0.00 42.06 2.69
2517 2537 2.938956 AAAGTGGTGGGTCTTCTCTG 57.061 50.000 0.00 0.00 0.00 3.35
2623 2644 4.901868 TGGAACTGGATAAGTGGTGTTAC 58.098 43.478 0.00 0.00 39.81 2.50
2636 2657 3.255642 GTGGTGTTACTGGCATTGATGTT 59.744 43.478 0.00 0.00 0.00 2.71
2637 2658 3.505680 TGGTGTTACTGGCATTGATGTTC 59.494 43.478 0.00 0.00 0.00 3.18
2640 2661 3.505680 TGTTACTGGCATTGATGTTCCAC 59.494 43.478 0.00 0.00 0.00 4.02
2645 2678 3.927854 TGGCATTGATGTTCCACAATTG 58.072 40.909 3.24 3.24 35.01 2.32
2648 2681 4.807304 GGCATTGATGTTCCACAATTGATC 59.193 41.667 13.59 4.06 35.01 2.92
2659 2692 4.452114 TCCACAATTGATCTTGAAGTGACG 59.548 41.667 13.59 0.00 0.00 4.35
2679 2712 3.245754 ACGTTGTTTGCATGCATGAAAAG 59.754 39.130 29.51 20.60 36.04 2.27
2682 2715 4.597404 TGTTTGCATGCATGAAAAGGTA 57.403 36.364 29.51 17.49 36.04 3.08
2724 2757 6.629128 TGTGTGTGTGAATTGAACTTTCATT 58.371 32.000 0.00 0.00 37.00 2.57
2728 2761 9.814899 TGTGTGTGAATTGAACTTTCATTAATT 57.185 25.926 0.00 0.00 37.00 1.40
2773 2806 2.037251 GGACTTGACTTCTGCAGGTGTA 59.963 50.000 15.13 0.00 0.00 2.90
2790 2823 3.429272 GGTGTAATACGAATCCACACCGA 60.429 47.826 6.45 0.00 46.84 4.69
2791 2824 3.795101 GTGTAATACGAATCCACACCGAG 59.205 47.826 0.00 0.00 34.74 4.63
2793 2826 4.639755 TGTAATACGAATCCACACCGAGTA 59.360 41.667 0.00 0.00 0.00 2.59
2794 2827 4.724074 AATACGAATCCACACCGAGTAA 57.276 40.909 0.00 0.00 0.00 2.24
2795 2828 2.649331 ACGAATCCACACCGAGTAAG 57.351 50.000 0.00 0.00 0.00 2.34
2796 2829 1.203994 ACGAATCCACACCGAGTAAGG 59.796 52.381 0.00 0.00 37.30 2.69
2825 2891 2.113860 TTTGCTCCCTACTCACATGC 57.886 50.000 0.00 0.00 0.00 4.06
2832 2898 4.082190 GCTCCCTACTCACATGCGATATAA 60.082 45.833 0.00 0.00 0.00 0.98
2849 2915 6.388278 CGATATAACAAACTCCCTACCTAGC 58.612 44.000 0.00 0.00 0.00 3.42
2867 2933 4.745620 CCTAGCCATAGTAAAAGCTTCGTC 59.254 45.833 0.00 0.00 36.79 4.20
2871 2937 4.033014 GCCATAGTAAAAGCTTCGTCTCAC 59.967 45.833 0.00 0.00 0.00 3.51
2913 2981 0.971447 CTATCGGGGGCTAGGTAGGC 60.971 65.000 1.94 1.94 47.00 3.93
2924 2992 3.578716 GGCTAGGTAGGCTATCATGTCAA 59.421 47.826 7.67 0.00 44.61 3.18
2931 2999 5.590259 GGTAGGCTATCATGTCAACAACAAT 59.410 40.000 0.00 0.00 42.37 2.71
2941 3009 7.160726 TCATGTCAACAACAATGATGAGTCTA 58.839 34.615 0.00 0.00 42.37 2.59
2945 3013 8.849168 TGTCAACAACAATGATGAGTCTATTTT 58.151 29.630 0.00 0.00 38.80 1.82
2971 3039 2.609747 TGAAGGTGTCTAAGCTCCACT 58.390 47.619 0.00 0.00 34.84 4.00
3036 3104 0.736053 CCAGAGCACTCGAGTAGGTC 59.264 60.000 26.02 26.02 34.09 3.85
3041 3109 2.610374 GAGCACTCGAGTAGGTCTACAG 59.390 54.545 26.04 12.45 38.48 2.74
3052 3120 3.594603 AGGTCTACAGGAAACGACATG 57.405 47.619 0.00 0.00 0.00 3.21
3059 3127 4.008074 ACAGGAAACGACATGAAGTGAT 57.992 40.909 0.00 0.00 0.00 3.06
3060 3128 4.389374 ACAGGAAACGACATGAAGTGATT 58.611 39.130 0.00 0.00 0.00 2.57
3061 3129 4.214119 ACAGGAAACGACATGAAGTGATTG 59.786 41.667 0.00 0.00 0.00 2.67
3062 3130 3.753272 AGGAAACGACATGAAGTGATTGG 59.247 43.478 0.00 0.00 0.00 3.16
3079 3157 6.039941 AGTGATTGGTTGTTACGGAAAATCAA 59.960 34.615 6.09 5.11 0.00 2.57
3087 3165 4.756135 TGTTACGGAAAATCAACCTACCAC 59.244 41.667 0.00 0.00 0.00 4.16
3088 3166 2.786777 ACGGAAAATCAACCTACCACC 58.213 47.619 0.00 0.00 0.00 4.61
3119 3197 3.629398 CCATCTTCTTTGAGGTATGCACC 59.371 47.826 0.00 0.00 46.19 5.01
3146 3224 7.837863 TCTATAGTGAGTTTAGTCCAACTTGG 58.162 38.462 0.74 0.74 37.11 3.61
3172 3250 2.606378 GGGGGTTAGTCCATCTACGAT 58.394 52.381 0.00 0.00 38.11 3.73
3182 3260 1.136891 CCATCTACGATGGTGTGAGCA 59.863 52.381 13.45 0.00 34.56 4.26
3205 3283 2.097680 ATTTCTGCGGCATTTTTGGG 57.902 45.000 1.75 0.00 0.00 4.12
3207 3285 2.434709 CTGCGGCATTTTTGGGCC 60.435 61.111 1.75 0.00 46.80 5.80
3213 3291 0.975887 GGCATTTTTGGGCCTTCTCA 59.024 50.000 4.53 0.00 46.74 3.27
3228 3306 4.447054 GCCTTCTCATCTACAACATGATCG 59.553 45.833 0.00 0.00 29.78 3.69
3263 3341 1.838077 CTTCCCTTTAGGTGGATCGGT 59.162 52.381 0.00 0.00 36.75 4.69
3285 3363 1.304134 GGGGTGTTGGCGGATTTCT 60.304 57.895 0.00 0.00 0.00 2.52
3296 3374 2.480759 GGCGGATTTCTAGAAGCGTGTA 60.481 50.000 5.12 0.00 0.00 2.90
3297 3375 2.789893 GCGGATTTCTAGAAGCGTGTAG 59.210 50.000 5.12 0.00 0.00 2.74
3298 3376 3.734293 GCGGATTTCTAGAAGCGTGTAGT 60.734 47.826 5.12 0.00 0.00 2.73
3299 3377 4.036352 CGGATTTCTAGAAGCGTGTAGTC 58.964 47.826 5.12 0.00 0.00 2.59
3309 3387 1.743958 AGCGTGTAGTCGATGTAGCTT 59.256 47.619 0.00 0.00 0.00 3.74
3313 3391 3.786576 CGTGTAGTCGATGTAGCTTGAAG 59.213 47.826 0.00 0.00 0.00 3.02
3318 3396 5.091261 AGTCGATGTAGCTTGAAGGAAAT 57.909 39.130 0.00 0.00 0.00 2.17
3344 3422 4.451096 TCAAGACAATTTAGTCGTTGGAGC 59.549 41.667 0.00 0.00 43.24 4.70
3345 3423 4.273148 AGACAATTTAGTCGTTGGAGCT 57.727 40.909 0.00 0.00 43.24 4.09
3370 3448 0.586319 CAGGTGCGTGATTTCGTTGT 59.414 50.000 0.00 0.00 0.00 3.32
3378 3456 2.218603 GTGATTTCGTTGTGGACCTGT 58.781 47.619 0.00 0.00 0.00 4.00
3385 3463 2.066262 CGTTGTGGACCTGTCATGTAC 58.934 52.381 0.00 0.00 0.00 2.90
3419 3497 2.998667 CATCGAAAGGCGCTCGTC 59.001 61.111 15.83 6.13 40.61 4.20
3443 3521 0.178068 GTGCGCCCTTTGAGGAGATA 59.822 55.000 4.18 0.00 37.67 1.98
3453 3531 5.844516 CCCTTTGAGGAGATATAGTACCCAA 59.155 44.000 0.00 0.00 37.67 4.12
3516 3594 2.034558 CCAAACTTCACTCATGGCGTTT 59.965 45.455 0.00 0.00 32.45 3.60
3523 3601 0.687354 ACTCATGGCGTTTCAGAGGT 59.313 50.000 0.00 0.00 0.00 3.85
3530 3608 0.596600 GCGTTTCAGAGGTCACGTGA 60.597 55.000 15.76 15.76 35.06 4.35
3541 3619 2.509336 CACGTGACCGAGGGCATC 60.509 66.667 10.90 0.00 37.88 3.91
3557 3635 7.323420 CGAGGGCATCTATAGAATACATGAAA 58.677 38.462 6.52 0.00 0.00 2.69
3558 3636 7.490725 CGAGGGCATCTATAGAATACATGAAAG 59.509 40.741 6.52 0.00 0.00 2.62
3559 3637 7.628234 AGGGCATCTATAGAATACATGAAAGG 58.372 38.462 6.52 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.438795 GAGACGAGACCGCTCCCT 60.439 66.667 0.00 0.00 37.91 4.20
39 42 4.651503 ACTACCATCTTCGTCTCAATCCAT 59.348 41.667 0.00 0.00 0.00 3.41
239 242 5.365314 ACTCCCATGTACAAAACCAACATTT 59.635 36.000 0.00 0.00 31.60 2.32
242 245 3.904717 ACTCCCATGTACAAAACCAACA 58.095 40.909 0.00 0.00 0.00 3.33
253 256 4.469945 CCTCCTTGTTCTAACTCCCATGTA 59.530 45.833 0.00 0.00 0.00 2.29
335 339 4.148825 ACCTCACTGATCCGCGGC 62.149 66.667 23.51 8.29 0.00 6.53
383 387 2.829914 GCCGCCTCATCCAATGCA 60.830 61.111 0.00 0.00 0.00 3.96
412 416 2.669569 GCACCGCTTCCTTCTGCA 60.670 61.111 0.00 0.00 0.00 4.41
569 573 3.837146 ACTATCTTGGAGCGGATGATGAT 59.163 43.478 0.00 0.00 0.00 2.45
644 649 7.079182 TCATACAAACATGACGGAATAAACC 57.921 36.000 0.00 0.00 29.93 3.27
664 669 9.878667 ATTTGAACAAGCATGATGAATTTCATA 57.121 25.926 11.79 2.22 37.20 2.15
734 739 4.195308 GTCGGCCGACAGCAATAA 57.805 55.556 44.88 13.64 46.50 1.40
745 752 0.958822 AAAATGGACACTTGTCGGCC 59.041 50.000 3.32 0.00 45.65 6.13
791 798 0.038166 CACCCCACCATGCTACAGTT 59.962 55.000 0.00 0.00 0.00 3.16
811 818 4.368067 ACCATAAGGGAAAGTAGTGGCTA 58.632 43.478 0.00 0.00 41.15 3.93
830 838 2.179427 CTGTGGAGTGATCACCTACCA 58.821 52.381 22.21 23.18 34.46 3.25
854 862 2.928396 CGGGAGGGGAGTTGGTGT 60.928 66.667 0.00 0.00 0.00 4.16
920 928 6.373216 TCTCCATGGGTTTTTATAAACACTCG 59.627 38.462 13.02 3.76 45.85 4.18
954 962 1.936547 CCGATCTTAGCAAGCTGGAAC 59.063 52.381 4.53 1.66 0.00 3.62
982 994 1.996786 ATTTTGCTGATGCTCGGGCG 61.997 55.000 1.14 0.00 42.25 6.13
1197 1209 1.371267 CGCGACGAAGGTGAACTCA 60.371 57.895 0.00 0.00 0.00 3.41
1425 1437 2.452813 GGTACGCAGCACCATCGTG 61.453 63.158 0.00 0.00 43.35 4.35
1526 1538 8.227791 GGTGATTATATTGGCTGTACGTATTTG 58.772 37.037 0.00 0.00 0.00 2.32
1527 1539 7.934665 TGGTGATTATATTGGCTGTACGTATTT 59.065 33.333 0.00 0.00 0.00 1.40
1528 1540 7.386848 GTGGTGATTATATTGGCTGTACGTATT 59.613 37.037 0.00 0.00 0.00 1.89
1529 1541 6.872020 GTGGTGATTATATTGGCTGTACGTAT 59.128 38.462 0.00 0.00 0.00 3.06
1530 1542 6.218019 GTGGTGATTATATTGGCTGTACGTA 58.782 40.000 0.00 0.00 0.00 3.57
1531 1543 5.054477 GTGGTGATTATATTGGCTGTACGT 58.946 41.667 0.00 0.00 0.00 3.57
1532 1544 4.149922 CGTGGTGATTATATTGGCTGTACG 59.850 45.833 0.00 0.00 0.00 3.67
1533 1545 5.054477 ACGTGGTGATTATATTGGCTGTAC 58.946 41.667 0.00 0.00 0.00 2.90
1534 1546 5.284861 ACGTGGTGATTATATTGGCTGTA 57.715 39.130 0.00 0.00 0.00 2.74
1535 1547 4.150897 ACGTGGTGATTATATTGGCTGT 57.849 40.909 0.00 0.00 0.00 4.40
1536 1548 6.801539 ATTACGTGGTGATTATATTGGCTG 57.198 37.500 0.00 0.00 0.00 4.85
1537 1549 7.606456 CCTAATTACGTGGTGATTATATTGGCT 59.394 37.037 0.00 0.00 0.00 4.75
1547 1559 6.495181 AGATCTCATCCTAATTACGTGGTGAT 59.505 38.462 0.00 0.00 0.00 3.06
1549 1561 5.923114 CAGATCTCATCCTAATTACGTGGTG 59.077 44.000 0.00 0.00 0.00 4.17
1552 1564 4.618912 CGCAGATCTCATCCTAATTACGTG 59.381 45.833 0.00 0.00 0.00 4.49
1553 1565 4.799678 CGCAGATCTCATCCTAATTACGT 58.200 43.478 0.00 0.00 0.00 3.57
1608 1623 2.555757 AGCAAAATCTCAAGGTGCAGAC 59.444 45.455 0.00 0.00 37.68 3.51
1734 1754 3.414700 CTGGTGCTCGTGCGGAAC 61.415 66.667 4.84 0.00 43.34 3.62
1759 1779 2.888834 AGAACTTTGCGCACCATTTT 57.111 40.000 11.12 0.00 0.00 1.82
1773 1793 1.040339 CAGAGGCTCGGGCTAGAACT 61.040 60.000 7.48 0.00 38.98 3.01
1851 1871 0.535335 GGCGTATCCTGTCCAGTTCA 59.465 55.000 0.00 0.00 0.00 3.18
1854 1874 3.077519 GCGGCGTATCCTGTCCAGT 62.078 63.158 9.37 0.00 0.00 4.00
2097 2117 4.612412 TCACGGCGGACAACCCAC 62.612 66.667 13.24 0.00 34.14 4.61
2112 2132 3.458163 GATCCCCGCACGAGGTCA 61.458 66.667 0.00 0.00 0.00 4.02
2151 2171 0.744414 CCACCGCACGATCAAATCCT 60.744 55.000 0.00 0.00 0.00 3.24
2340 2360 1.374252 CCACACTGCCTCCACGTAC 60.374 63.158 0.00 0.00 0.00 3.67
2343 2363 4.704833 CCCCACACTGCCTCCACG 62.705 72.222 0.00 0.00 0.00 4.94
2361 2381 0.179134 CCTCGAGCTCAAACCCTACG 60.179 60.000 15.40 0.00 0.00 3.51
2418 2438 5.192522 TCCTTCCCTCTCATTCATAAGCTTT 59.807 40.000 3.20 0.00 0.00 3.51
2486 2506 1.400142 CACCACTTTTCAAGCACGACA 59.600 47.619 0.00 0.00 0.00 4.35
2497 2517 2.749800 GCAGAGAAGACCCACCACTTTT 60.750 50.000 0.00 0.00 0.00 2.27
2501 2521 1.205893 CTAGCAGAGAAGACCCACCAC 59.794 57.143 0.00 0.00 0.00 4.16
2517 2537 6.346199 GCTCGACAAGTTTATCAATAGCTAGC 60.346 42.308 6.62 6.62 0.00 3.42
2603 2624 4.935808 CCAGTAACACCACTTATCCAGTTC 59.064 45.833 0.00 0.00 30.92 3.01
2636 2657 4.452114 CGTCACTTCAAGATCAATTGTGGA 59.548 41.667 5.13 0.00 0.00 4.02
2637 2658 4.214119 ACGTCACTTCAAGATCAATTGTGG 59.786 41.667 5.13 0.00 0.00 4.17
2640 2661 5.751680 ACAACGTCACTTCAAGATCAATTG 58.248 37.500 0.00 0.00 0.00 2.32
2645 2678 3.968724 GCAAACAACGTCACTTCAAGATC 59.031 43.478 0.00 0.00 0.00 2.75
2648 2681 3.129852 TGCAAACAACGTCACTTCAAG 57.870 42.857 0.00 0.00 0.00 3.02
2659 2692 3.560896 ACCTTTTCATGCATGCAAACAAC 59.439 39.130 26.68 0.00 0.00 3.32
2697 2730 6.925718 TGAAAGTTCAATTCACACACACAAAA 59.074 30.769 0.00 0.00 33.55 2.44
2701 2734 8.627487 TTAATGAAAGTTCAATTCACACACAC 57.373 30.769 0.00 0.00 41.13 3.82
2724 2757 8.544622 TGTGACTGTAGTGATCCCATTTAATTA 58.455 33.333 0.00 0.00 0.00 1.40
2728 2761 6.367374 TTGTGACTGTAGTGATCCCATTTA 57.633 37.500 0.00 0.00 0.00 1.40
2729 2762 4.908601 TGTGACTGTAGTGATCCCATTT 57.091 40.909 0.00 0.00 0.00 2.32
2730 2763 4.323792 CCTTGTGACTGTAGTGATCCCATT 60.324 45.833 0.00 0.00 0.00 3.16
2731 2764 3.198635 CCTTGTGACTGTAGTGATCCCAT 59.801 47.826 0.00 0.00 0.00 4.00
2732 2765 2.567169 CCTTGTGACTGTAGTGATCCCA 59.433 50.000 0.00 0.00 0.00 4.37
2733 2766 2.832129 TCCTTGTGACTGTAGTGATCCC 59.168 50.000 0.00 0.00 0.00 3.85
2773 2806 4.441079 CCTTACTCGGTGTGGATTCGTATT 60.441 45.833 0.00 0.00 0.00 1.89
2790 2823 4.327680 GAGCAAAACCATCTCACCTTACT 58.672 43.478 0.00 0.00 0.00 2.24
2791 2824 3.440522 GGAGCAAAACCATCTCACCTTAC 59.559 47.826 0.00 0.00 0.00 2.34
2793 2826 2.519013 GGAGCAAAACCATCTCACCTT 58.481 47.619 0.00 0.00 0.00 3.50
2794 2827 1.272147 GGGAGCAAAACCATCTCACCT 60.272 52.381 0.00 0.00 0.00 4.00
2795 2828 1.177401 GGGAGCAAAACCATCTCACC 58.823 55.000 0.00 0.00 0.00 4.02
2796 2829 2.206576 AGGGAGCAAAACCATCTCAC 57.793 50.000 0.00 0.00 0.00 3.51
2799 2832 2.912956 TGAGTAGGGAGCAAAACCATCT 59.087 45.455 0.00 0.00 0.00 2.90
2800 2833 3.010420 GTGAGTAGGGAGCAAAACCATC 58.990 50.000 0.00 0.00 0.00 3.51
2825 2891 6.388278 GCTAGGTAGGGAGTTTGTTATATCG 58.612 44.000 0.00 0.00 0.00 2.92
2832 2898 2.337359 TGGCTAGGTAGGGAGTTTGT 57.663 50.000 0.00 0.00 0.00 2.83
2849 2915 4.567159 GGTGAGACGAAGCTTTTACTATGG 59.433 45.833 0.00 0.00 0.00 2.74
2867 2933 1.901591 AGTGGCATCTTGTTGGTGAG 58.098 50.000 0.00 0.00 0.00 3.51
2871 2937 0.604578 CCCAAGTGGCATCTTGTTGG 59.395 55.000 20.56 14.61 42.01 3.77
2890 2958 0.041386 ACCTAGCCCCCGATAGATCC 59.959 60.000 0.00 0.00 39.76 3.36
2898 2966 0.971447 GATAGCCTACCTAGCCCCCG 60.971 65.000 0.00 0.00 0.00 5.73
2913 2981 7.982224 ACTCATCATTGTTGTTGACATGATAG 58.018 34.615 0.00 0.00 38.26 2.08
2924 2992 7.884877 TCCTCAAAATAGACTCATCATTGTTGT 59.115 33.333 0.00 0.00 0.00 3.32
2931 2999 7.092712 ACCTTCATCCTCAAAATAGACTCATCA 60.093 37.037 0.00 0.00 0.00 3.07
2941 3009 5.649831 GCTTAGACACCTTCATCCTCAAAAT 59.350 40.000 0.00 0.00 0.00 1.82
2945 3013 3.445008 AGCTTAGACACCTTCATCCTCA 58.555 45.455 0.00 0.00 0.00 3.86
3036 3104 4.556233 TCACTTCATGTCGTTTCCTGTAG 58.444 43.478 0.00 0.00 0.00 2.74
3041 3109 3.502211 ACCAATCACTTCATGTCGTTTCC 59.498 43.478 0.00 0.00 0.00 3.13
3052 3120 5.427036 TTTCCGTAACAACCAATCACTTC 57.573 39.130 0.00 0.00 0.00 3.01
3062 3130 5.239087 TGGTAGGTTGATTTTCCGTAACAAC 59.761 40.000 0.00 0.00 39.67 3.32
3088 3166 1.571773 AAAGAAGATGGGACCGGGGG 61.572 60.000 6.32 0.00 0.00 5.40
3119 3197 9.307121 CAAGTTGGACTAAACTCACTATAGATG 57.693 37.037 6.78 1.48 39.48 2.90
3123 3201 6.070424 CCCCAAGTTGGACTAAACTCACTATA 60.070 42.308 24.06 0.00 40.96 1.31
3124 3202 5.280521 CCCCAAGTTGGACTAAACTCACTAT 60.281 44.000 24.06 0.00 40.96 2.12
3125 3203 4.041198 CCCCAAGTTGGACTAAACTCACTA 59.959 45.833 24.06 0.00 40.96 2.74
3127 3205 3.146847 CCCCAAGTTGGACTAAACTCAC 58.853 50.000 24.06 0.00 40.96 3.51
3156 3234 4.097437 TCACACCATCGTAGATGGACTAAC 59.903 45.833 29.37 0.00 45.12 2.34
3172 3250 1.610038 CAGAAATTGCTGCTCACACCA 59.390 47.619 0.00 0.00 0.00 4.17
3186 3264 1.945355 GCCCAAAAATGCCGCAGAAAT 60.945 47.619 0.00 0.00 0.00 2.17
3190 3268 2.434709 GGCCCAAAAATGCCGCAG 60.435 61.111 0.00 0.00 38.00 5.18
3205 3283 4.447054 CGATCATGTTGTAGATGAGAAGGC 59.553 45.833 0.00 0.00 33.38 4.35
3207 3285 6.860539 CCTACGATCATGTTGTAGATGAGAAG 59.139 42.308 17.49 3.35 44.48 2.85
3213 3291 5.221263 GGTGACCTACGATCATGTTGTAGAT 60.221 44.000 17.49 6.73 44.48 1.98
3228 3306 0.245813 GGAAGTCGGTGGTGACCTAC 59.754 60.000 2.11 0.00 40.58 3.18
3263 3341 1.628238 AATCCGCCAACACCCCGATA 61.628 55.000 0.00 0.00 0.00 2.92
3285 3363 3.002042 GCTACATCGACTACACGCTTCTA 59.998 47.826 0.00 0.00 0.00 2.10
3296 3374 4.537135 TTTCCTTCAAGCTACATCGACT 57.463 40.909 0.00 0.00 0.00 4.18
3297 3375 4.870426 TGATTTCCTTCAAGCTACATCGAC 59.130 41.667 0.00 0.00 0.00 4.20
3298 3376 5.084818 TGATTTCCTTCAAGCTACATCGA 57.915 39.130 0.00 0.00 0.00 3.59
3299 3377 5.525012 TGATGATTTCCTTCAAGCTACATCG 59.475 40.000 0.00 0.00 35.76 3.84
3309 3387 9.300681 ACTAAATTGTCTTGATGATTTCCTTCA 57.699 29.630 0.00 0.00 0.00 3.02
3313 3391 7.752695 ACGACTAAATTGTCTTGATGATTTCC 58.247 34.615 0.00 0.00 35.00 3.13
3318 3396 6.227522 TCCAACGACTAAATTGTCTTGATGA 58.772 36.000 0.00 0.00 35.00 2.92
3333 3411 1.203523 CTGAAGCTAGCTCCAACGACT 59.796 52.381 19.65 0.00 0.00 4.18
3344 3422 2.015736 AATCACGCACCTGAAGCTAG 57.984 50.000 0.00 0.00 0.00 3.42
3345 3423 2.346803 GAAATCACGCACCTGAAGCTA 58.653 47.619 0.00 0.00 0.00 3.32
3370 3448 1.188871 TGGCGTACATGACAGGTCCA 61.189 55.000 0.00 0.00 0.00 4.02
3385 3463 3.038017 CGATGCTTATGAAAATGTGGCG 58.962 45.455 0.00 0.00 0.00 5.69
3428 3506 4.223255 GGGTACTATATCTCCTCAAAGGGC 59.777 50.000 0.00 0.00 35.59 5.19
3430 3508 6.239629 GGTTGGGTACTATATCTCCTCAAAGG 60.240 46.154 0.00 0.00 36.46 3.11
3431 3509 6.555360 AGGTTGGGTACTATATCTCCTCAAAG 59.445 42.308 0.00 0.00 0.00 2.77
3443 3521 0.045778 AGGGCCAGGTTGGGTACTAT 59.954 55.000 6.18 0.00 38.19 2.12
3453 3531 1.691219 CACCAACATAGGGCCAGGT 59.309 57.895 6.18 0.21 0.00 4.00
3523 3601 2.994995 ATGCCCTCGGTCACGTGA 60.995 61.111 15.76 15.76 41.85 4.35
3530 3608 4.673968 TGTATTCTATAGATGCCCTCGGT 58.326 43.478 2.58 0.00 0.00 4.69
3532 3610 6.456795 TCATGTATTCTATAGATGCCCTCG 57.543 41.667 2.58 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.