Multiple sequence alignment - TraesCS3A01G238300

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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 TraesCS3A01G238300 chr3A 100.000 3565 0 0 1 3565 445282297 445278733 0.000000e+00 6584
1 TraesCS3A01G238300 chr3D 89.856 3066 107 77 532 3524 330064126 330061192 0.000000e+00 3751
2 TraesCS3A01G238300 chr3D 89.931 437 25 7 11 441 330064773 330064350 2.420000e-151 545
3 TraesCS3A01G238300 chr3B 89.879 2480 114 67 1089 3513 427590978 427588581 0.000000e+00 3062
4 TraesCS3A01G238300 chr3B 88.868 530 25 14 532 1051 427591480 427590975 3.910000e-174 621
5 TraesCS3A01G238300 chr3B 89.120 432 33 6 11 441 427592110 427591692 3.150000e-145 525
6 TraesCS3A01G238300 chr4D 84.337 166 19 6 1892 2052 479525195 479525358 4.770000e-34 156
7 TraesCS3A01G238300 chr4D 86.667 120 13 1 1890 2006 739003 739122 2.890000e-26 130
8 TraesCS3A01G238300 chr4A 83.133 166 21 7 1892 2052 685826807 685826970 1.030000e-30 145
9 TraesCS3A01G238300 chr4B 82.530 166 22 7 1892 2052 606755170 606755333 4.800000e-29 139
10 TraesCS3A01G238300 chr2A 81.111 180 26 6 1895 2071 680357724 680357550 1.730000e-28 137
11 TraesCS3A01G238300 chr2B 80.423 189 28 7 1886 2071 640765320 640765138 6.210000e-28 135
12 TraesCS3A01G238300 chr1D 81.757 148 22 4 1898 2041 307420812 307420666 6.250000e-23 119


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 TraesCS3A01G238300 chr3A 445278733 445282297 3564 True 6584.000000 6584 100.0000 1 3565 1 chr3A.!!$R1 3564
1 TraesCS3A01G238300 chr3D 330061192 330064773 3581 True 2148.000000 3751 89.8935 11 3524 2 chr3D.!!$R1 3513
2 TraesCS3A01G238300 chr3B 427588581 427592110 3529 True 1402.666667 3062 89.2890 11 3513 3 chr3B.!!$R1 3502

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
302 308 0.037790 GTGGCAGTGAGGAGAGTGTC 60.038 60.0 0.00 0.00 0.0 3.67 F
305 311 0.109504 GCAGTGAGGAGAGTGTCGAC 60.110 60.0 9.11 9.11 0.0 4.20 F
795 945 0.248458 CCGTAAACCAATGCCATCGC 60.248 55.0 0.00 0.00 0.0 4.58 F
1589 1778 0.036010 CGGCATCCTCCTTTCTGTGT 60.036 55.0 0.00 0.00 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1313 1489 0.107165 GGCAATAAAGACGGCCTCCT 60.107 55.000 0.0 0.0 43.09 3.69 R
1317 1493 0.738975 GGAAGGCAATAAAGACGGCC 59.261 55.000 0.0 0.0 46.77 6.13 R
2182 2380 1.811266 CTCCGCCAAGGACGACATG 60.811 63.158 0.0 0.0 45.98 3.21 R
3406 3686 0.322816 CTTCCCCATGTGGTCACCTG 60.323 60.000 0.0 0.0 0.00 4.00 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
184 185 4.838486 CCGTCTCTCGCTCGCACC 62.838 72.222 0.00 0.00 38.35 5.01
302 308 0.037790 GTGGCAGTGAGGAGAGTGTC 60.038 60.000 0.00 0.00 0.00 3.67
305 311 0.109504 GCAGTGAGGAGAGTGTCGAC 60.110 60.000 9.11 9.11 0.00 4.20
363 369 1.808390 CCGGGAATCGTCGACCAAC 60.808 63.158 10.58 0.00 37.11 3.77
367 373 2.049802 AATCGTCGACCAACGCGT 60.050 55.556 5.58 5.58 42.31 6.01
408 414 1.296392 CCTTCGTGGCATCACTCCA 59.704 57.895 0.00 0.00 41.53 3.86
414 420 1.959042 GTGGCATCACTCCACCTATG 58.041 55.000 0.00 0.00 46.26 2.23
421 427 1.204704 TCACTCCACCTATGTTCAGCG 59.795 52.381 0.00 0.00 0.00 5.18
428 434 3.334691 CACCTATGTTCAGCGAGGAAAA 58.665 45.455 0.00 0.00 33.04 2.29
429 435 3.125316 CACCTATGTTCAGCGAGGAAAAC 59.875 47.826 0.00 0.00 33.04 2.43
430 436 3.244422 ACCTATGTTCAGCGAGGAAAACA 60.244 43.478 0.00 0.00 36.19 2.83
431 437 3.372206 CCTATGTTCAGCGAGGAAAACAG 59.628 47.826 0.00 0.00 35.30 3.16
441 447 1.807142 GAGGAAAACAGTGCAGCTACC 59.193 52.381 0.00 0.00 0.00 3.18
442 448 1.142870 AGGAAAACAGTGCAGCTACCA 59.857 47.619 0.00 0.00 0.00 3.25
443 449 2.162681 GGAAAACAGTGCAGCTACCAT 58.837 47.619 0.00 0.00 0.00 3.55
446 533 0.391661 AACAGTGCAGCTACCATCCG 60.392 55.000 0.00 0.00 0.00 4.18
451 538 0.613260 TGCAGCTACCATCCGTCTTT 59.387 50.000 0.00 0.00 0.00 2.52
454 541 2.815478 CAGCTACCATCCGTCTTTCTC 58.185 52.381 0.00 0.00 0.00 2.87
471 558 3.519908 TCTCAAAGAATTCACAACGCG 57.480 42.857 3.53 3.53 0.00 6.01
472 559 1.971962 CTCAAAGAATTCACAACGCGC 59.028 47.619 5.73 0.00 0.00 6.86
473 560 0.697010 CAAAGAATTCACAACGCGCG 59.303 50.000 30.96 30.96 0.00 6.86
475 562 1.503818 AAGAATTCACAACGCGCGGT 61.504 50.000 35.22 28.24 0.00 5.68
476 563 1.792057 GAATTCACAACGCGCGGTG 60.792 57.895 43.19 43.19 39.06 4.94
483 570 4.373116 AACGCGCGGTGGAGTGAT 62.373 61.111 35.22 6.31 0.00 3.06
509 615 2.320587 GCGTCACAGTTGGAGCAGG 61.321 63.158 0.00 0.00 0.00 4.85
515 621 4.357279 AGTTGGAGCAGGCCAGCC 62.357 66.667 17.68 8.27 39.69 4.85
526 632 3.467226 GCCAGCCCGTACTGCCTA 61.467 66.667 1.09 0.00 36.29 3.93
527 633 2.499685 CCAGCCCGTACTGCCTAC 59.500 66.667 1.09 0.00 36.29 3.18
528 634 2.499685 CAGCCCGTACTGCCTACC 59.500 66.667 1.09 0.00 0.00 3.18
529 635 2.762875 AGCCCGTACTGCCTACCC 60.763 66.667 1.09 0.00 0.00 3.69
530 636 3.078836 GCCCGTACTGCCTACCCA 61.079 66.667 0.00 0.00 0.00 4.51
537 676 0.266453 TACTGCCTACCCAGCCCATA 59.734 55.000 0.00 0.00 36.29 2.74
543 682 1.307170 TACCCAGCCCATACCCGTT 60.307 57.895 0.00 0.00 0.00 4.44
597 738 2.669229 CGGCACTGCACACATCCA 60.669 61.111 2.82 0.00 0.00 3.41
598 739 2.683859 CGGCACTGCACACATCCAG 61.684 63.158 2.82 0.00 35.26 3.86
599 740 2.564975 GCACTGCACACATCCAGC 59.435 61.111 0.00 0.00 32.37 4.85
600 741 2.986306 GCACTGCACACATCCAGCC 61.986 63.158 0.00 0.00 32.37 4.85
601 742 1.601477 CACTGCACACATCCAGCCA 60.601 57.895 0.00 0.00 32.37 4.75
602 743 1.303074 ACTGCACACATCCAGCCAG 60.303 57.895 0.00 0.00 32.37 4.85
603 744 2.674033 TGCACACATCCAGCCAGC 60.674 61.111 0.00 0.00 0.00 4.85
604 745 3.446570 GCACACATCCAGCCAGCC 61.447 66.667 0.00 0.00 0.00 4.85
610 751 3.664888 ATCCAGCCAGCCAGCCAA 61.665 61.111 0.00 0.00 0.00 4.52
645 786 0.606401 CCAGTTACCCACAGTGCCAG 60.606 60.000 0.00 0.00 0.00 4.85
721 871 3.519930 GAGGCGTCCTCGTCCTCC 61.520 72.222 9.63 0.00 45.35 4.30
722 872 3.999297 GAGGCGTCCTCGTCCTCCT 62.999 68.421 9.63 3.17 45.35 3.69
723 873 3.519930 GGCGTCCTCGTCCTCCTC 61.520 72.222 0.00 0.00 39.49 3.71
724 874 3.519930 GCGTCCTCGTCCTCCTCC 61.520 72.222 0.00 0.00 39.49 4.30
725 875 2.272797 CGTCCTCGTCCTCCTCCT 59.727 66.667 0.00 0.00 0.00 3.69
726 876 1.820481 CGTCCTCGTCCTCCTCCTC 60.820 68.421 0.00 0.00 0.00 3.71
733 883 2.038975 TCCTCCTCCTCGGGGTTG 59.961 66.667 0.00 0.00 0.00 3.77
792 942 1.326951 GCCCCGTAAACCAATGCCAT 61.327 55.000 0.00 0.00 0.00 4.40
794 944 0.380378 CCCGTAAACCAATGCCATCG 59.620 55.000 0.00 0.00 0.00 3.84
795 945 0.248458 CCGTAAACCAATGCCATCGC 60.248 55.000 0.00 0.00 0.00 4.58
804 954 3.684113 TGCCATCGCATTGCAAGT 58.316 50.000 9.69 0.00 41.12 3.16
805 955 2.865492 TGCCATCGCATTGCAAGTA 58.135 47.368 9.69 0.00 41.12 2.24
806 956 0.734309 TGCCATCGCATTGCAAGTAG 59.266 50.000 9.69 0.00 41.12 2.57
807 957 0.593263 GCCATCGCATTGCAAGTAGC 60.593 55.000 9.69 8.23 38.32 3.58
808 958 3.204360 GCCATCGCATTGCAAGTAGCA 62.204 52.381 17.77 8.30 43.38 3.49
823 973 4.460873 GCAGCAGTAAACGCGGCC 62.461 66.667 12.47 0.00 43.59 6.13
964 1119 3.184003 GACGGCGCTAACGAACCC 61.184 66.667 6.90 0.00 43.93 4.11
1058 1213 2.512057 GCTCAGCTCAGCTCAGCC 60.512 66.667 12.39 0.00 46.82 4.85
1059 1214 2.979649 CTCAGCTCAGCTCAGCCA 59.020 61.111 5.75 0.00 40.65 4.75
1060 1215 1.523046 CTCAGCTCAGCTCAGCCAT 59.477 57.895 5.75 0.00 40.65 4.40
1061 1216 0.531090 CTCAGCTCAGCTCAGCCATC 60.531 60.000 5.75 0.00 40.65 3.51
1062 1217 0.976590 TCAGCTCAGCTCAGCCATCT 60.977 55.000 5.75 0.00 40.65 2.90
1063 1218 0.531090 CAGCTCAGCTCAGCCATCTC 60.531 60.000 5.75 0.00 40.65 2.75
1064 1219 1.227615 GCTCAGCTCAGCCATCTCC 60.228 63.158 0.00 0.00 32.76 3.71
1065 1220 1.067749 CTCAGCTCAGCCATCTCCG 59.932 63.158 0.00 0.00 0.00 4.63
1066 1221 1.380380 TCAGCTCAGCCATCTCCGA 60.380 57.895 0.00 0.00 0.00 4.55
1067 1222 1.067749 CAGCTCAGCCATCTCCGAG 59.932 63.158 0.00 0.00 0.00 4.63
1083 1238 1.752694 GAGTCCGAGGCTCTGCTCT 60.753 63.158 13.50 7.90 0.00 4.09
1084 1239 1.724582 GAGTCCGAGGCTCTGCTCTC 61.725 65.000 13.50 12.63 0.00 3.20
1085 1240 2.049185 GTCCGAGGCTCTGCTCTCA 61.049 63.158 13.50 0.00 0.00 3.27
1086 1241 1.076412 TCCGAGGCTCTGCTCTCAT 60.076 57.895 13.50 0.00 0.00 2.90
1087 1242 0.685785 TCCGAGGCTCTGCTCTCATT 60.686 55.000 13.50 0.00 0.00 2.57
1088 1243 0.249405 CCGAGGCTCTGCTCTCATTC 60.249 60.000 13.50 0.00 0.00 2.67
1089 1244 0.746063 CGAGGCTCTGCTCTCATTCT 59.254 55.000 13.50 0.00 0.00 2.40
1090 1245 1.269206 CGAGGCTCTGCTCTCATTCTC 60.269 57.143 13.50 0.00 0.00 2.87
1113 1268 2.107366 CTCTTCTCTTCTCCACTCCCC 58.893 57.143 0.00 0.00 0.00 4.81
1131 1286 1.807573 CTCCTTGTTCCTCGCGCTC 60.808 63.158 5.56 0.00 0.00 5.03
1313 1489 2.298951 AGGTAAAGAGGAGGAGGAGGA 58.701 52.381 0.00 0.00 0.00 3.71
1314 1490 2.246327 AGGTAAAGAGGAGGAGGAGGAG 59.754 54.545 0.00 0.00 0.00 3.69
1315 1491 2.673258 GTAAAGAGGAGGAGGAGGAGG 58.327 57.143 0.00 0.00 0.00 4.30
1316 1492 1.398799 AAAGAGGAGGAGGAGGAGGA 58.601 55.000 0.00 0.00 0.00 3.71
1317 1493 0.933700 AAGAGGAGGAGGAGGAGGAG 59.066 60.000 0.00 0.00 0.00 3.69
1318 1494 0.998945 AGAGGAGGAGGAGGAGGAGG 60.999 65.000 0.00 0.00 0.00 4.30
1404 1580 3.078837 TGCCGTTCCTTTGGTCTTTATC 58.921 45.455 0.00 0.00 0.00 1.75
1412 1588 0.629058 TTGGTCTTTATCCCCCTGCC 59.371 55.000 0.00 0.00 0.00 4.85
1470 1646 0.302890 CAATCGATCGTCAGCTTGCC 59.697 55.000 15.94 0.00 0.00 4.52
1589 1778 0.036010 CGGCATCCTCCTTTCTGTGT 60.036 55.000 0.00 0.00 0.00 3.72
1590 1779 1.457346 GGCATCCTCCTTTCTGTGTG 58.543 55.000 0.00 0.00 0.00 3.82
1687 1882 2.043852 TCCAGCGAGGAGGAGGAC 60.044 66.667 0.00 0.00 43.07 3.85
1996 2191 3.608662 ACCTTCGACACCGCCGAA 61.609 61.111 0.00 0.00 42.79 4.30
2227 2425 2.888863 GACTCGGAGGCCTGTCAG 59.111 66.667 12.00 4.71 0.00 3.51
2344 2545 2.507324 GACTTCGAGCCGCAGTCC 60.507 66.667 13.44 0.95 42.37 3.85
2368 2569 4.592936 CTCTACGCCGAGCCGTCG 62.593 72.222 0.00 0.00 46.39 5.12
2447 2654 2.229302 GTGCAGGAGAACGACTACTTCT 59.771 50.000 0.00 0.00 37.78 2.85
2448 2655 2.891580 TGCAGGAGAACGACTACTTCTT 59.108 45.455 0.00 0.00 37.78 2.52
2449 2656 3.057456 TGCAGGAGAACGACTACTTCTTC 60.057 47.826 0.00 0.00 37.78 2.87
2501 2708 1.207329 AGCTTCCCGCGATTTTCTAGT 59.793 47.619 8.23 0.00 45.59 2.57
2621 2840 2.353839 GCGTTGCTGCTGTGTTGG 60.354 61.111 0.00 0.00 0.00 3.77
2628 2847 1.227527 CTGCTGTGTTGGGTCGACA 60.228 57.895 18.91 0.00 0.00 4.35
2736 2969 0.870307 GATACGCTGCAGGGTGTACG 60.870 60.000 38.13 23.59 41.49 3.67
2737 2970 1.601419 ATACGCTGCAGGGTGTACGT 61.601 55.000 38.13 27.34 41.49 3.57
2738 2971 0.959867 TACGCTGCAGGGTGTACGTA 60.960 55.000 38.13 26.40 41.49 3.57
2739 2972 1.804326 CGCTGCAGGGTGTACGTAC 60.804 63.158 21.92 18.90 0.00 3.67
2740 2973 1.290955 GCTGCAGGGTGTACGTACA 59.709 57.895 24.10 24.10 0.00 2.90
2741 2974 0.108329 GCTGCAGGGTGTACGTACAT 60.108 55.000 29.58 12.85 38.63 2.29
2742 2975 1.640428 CTGCAGGGTGTACGTACATG 58.360 55.000 29.58 23.70 38.63 3.21
2743 2976 0.970640 TGCAGGGTGTACGTACATGT 59.029 50.000 29.58 15.25 38.63 3.21
2744 2977 2.164827 CTGCAGGGTGTACGTACATGTA 59.835 50.000 29.58 21.31 38.63 2.29
2745 2978 2.094597 TGCAGGGTGTACGTACATGTAC 60.095 50.000 29.58 23.53 43.95 2.90
2887 3136 0.592247 GGCCATGATTTAGTTGCGCG 60.592 55.000 0.00 0.00 0.00 6.86
3063 3329 0.384309 GGACATGTCCGTGCGATAGA 59.616 55.000 28.52 0.00 40.36 1.98
3064 3330 1.000163 GGACATGTCCGTGCGATAGAT 60.000 52.381 28.52 0.00 40.36 1.98
3117 3383 3.091545 AGCAGGTGTTTGGGTATTCATG 58.908 45.455 0.00 0.00 0.00 3.07
3118 3384 2.166254 GCAGGTGTTTGGGTATTCATGG 59.834 50.000 0.00 0.00 0.00 3.66
3119 3385 2.166254 CAGGTGTTTGGGTATTCATGGC 59.834 50.000 0.00 0.00 0.00 4.40
3204 3472 2.510906 CCGGGCAGGGAGTTATGG 59.489 66.667 0.00 0.00 35.97 2.74
3245 3513 0.517316 GCGTGTGAATCTTGTGACCC 59.483 55.000 0.00 0.00 0.00 4.46
3246 3514 0.790207 CGTGTGAATCTTGTGACCCG 59.210 55.000 0.00 0.00 0.00 5.28
3258 3526 4.436998 GACCCGACAGTGGCGAGG 62.437 72.222 22.85 21.37 0.00 4.63
3279 3547 0.933097 CGAGGGAGTGAATGCGAATG 59.067 55.000 0.00 0.00 0.00 2.67
3406 3686 1.012486 CCGAGCAAGAACACGTACCC 61.012 60.000 0.00 0.00 0.00 3.69
3432 3712 0.254178 CCACATGGGGAAGGAGACAG 59.746 60.000 8.91 0.00 0.00 3.51
3447 3727 2.352960 GAGACAGCGCAAAAGATAAGGG 59.647 50.000 11.47 0.00 0.00 3.95
3454 3734 2.027385 GCAAAAGATAAGGGGGAGCTG 58.973 52.381 0.00 0.00 0.00 4.24
3458 3738 3.359110 AAGATAAGGGGGAGCTGAGAT 57.641 47.619 0.00 0.00 0.00 2.75
3531 3811 4.990543 TTTGAGACAAAGATGCGTACTG 57.009 40.909 0.00 0.00 0.00 2.74
3532 3812 2.337583 TGAGACAAAGATGCGTACTGC 58.662 47.619 3.22 3.22 46.70 4.40
3533 3813 2.029020 TGAGACAAAGATGCGTACTGCT 60.029 45.455 10.27 0.00 46.63 4.24
3534 3814 2.996621 GAGACAAAGATGCGTACTGCTT 59.003 45.455 10.27 4.92 46.63 3.91
3535 3815 3.403038 AGACAAAGATGCGTACTGCTTT 58.597 40.909 10.27 0.00 46.63 3.51
3536 3816 3.815401 AGACAAAGATGCGTACTGCTTTT 59.185 39.130 10.27 6.48 46.63 2.27
3537 3817 4.275936 AGACAAAGATGCGTACTGCTTTTT 59.724 37.500 10.27 4.23 46.63 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.673665 GATGGATGGAGGATGGCGC 60.674 63.158 0.00 0.00 0.00 6.53
3 4 1.381851 GGGATGGATGGAGGATGGC 59.618 63.158 0.00 0.00 0.00 4.40
5 6 0.990374 GAGGGGATGGATGGAGGATG 59.010 60.000 0.00 0.00 0.00 3.51
6 7 0.880357 AGAGGGGATGGATGGAGGAT 59.120 55.000 0.00 0.00 0.00 3.24
7 8 0.104777 CAGAGGGGATGGATGGAGGA 60.105 60.000 0.00 0.00 0.00 3.71
8 9 1.776975 GCAGAGGGGATGGATGGAGG 61.777 65.000 0.00 0.00 0.00 4.30
9 10 1.759881 GCAGAGGGGATGGATGGAG 59.240 63.158 0.00 0.00 0.00 3.86
10 11 2.142761 CGCAGAGGGGATGGATGGA 61.143 63.158 0.00 0.00 0.00 3.41
11 12 2.388890 GACGCAGAGGGGATGGATGG 62.389 65.000 0.00 0.00 0.00 3.51
12 13 1.070445 GACGCAGAGGGGATGGATG 59.930 63.158 0.00 0.00 0.00 3.51
13 14 2.143419 GGACGCAGAGGGGATGGAT 61.143 63.158 0.00 0.00 0.00 3.41
14 15 2.764128 GGACGCAGAGGGGATGGA 60.764 66.667 0.00 0.00 0.00 3.41
15 16 3.866582 GGGACGCAGAGGGGATGG 61.867 72.222 0.00 0.00 0.00 3.51
133 134 1.484356 CGTCCCCGTCGTCATATTTC 58.516 55.000 0.00 0.00 0.00 2.17
204 205 3.338250 TGCCCCAGTCACCCCATC 61.338 66.667 0.00 0.00 0.00 3.51
302 308 4.189188 ACGGCCGATTCCTCGTCG 62.189 66.667 35.90 0.00 43.49 5.12
305 311 3.833645 TGGACGGCCGATTCCTCG 61.834 66.667 35.90 1.83 44.62 4.63
343 349 2.103736 GGTCGACGATTCCCGGTC 59.896 66.667 9.92 0.00 43.93 4.79
400 406 2.159043 CGCTGAACATAGGTGGAGTGAT 60.159 50.000 0.00 0.00 0.00 3.06
403 409 1.478510 CTCGCTGAACATAGGTGGAGT 59.521 52.381 0.00 0.00 0.00 3.85
408 414 3.244422 TGTTTTCCTCGCTGAACATAGGT 60.244 43.478 0.00 0.00 0.00 3.08
411 417 3.745975 CACTGTTTTCCTCGCTGAACATA 59.254 43.478 0.00 0.00 32.23 2.29
413 419 1.939934 CACTGTTTTCCTCGCTGAACA 59.060 47.619 0.00 0.00 0.00 3.18
414 420 1.334149 GCACTGTTTTCCTCGCTGAAC 60.334 52.381 0.00 0.00 0.00 3.18
421 427 1.807142 GGTAGCTGCACTGTTTTCCTC 59.193 52.381 3.61 0.00 0.00 3.71
428 434 1.219124 CGGATGGTAGCTGCACTGT 59.781 57.895 3.61 0.00 0.00 3.55
429 435 0.807667 GACGGATGGTAGCTGCACTG 60.808 60.000 3.61 2.42 0.00 3.66
430 436 0.972983 AGACGGATGGTAGCTGCACT 60.973 55.000 3.61 0.00 0.00 4.40
431 437 0.108138 AAGACGGATGGTAGCTGCAC 60.108 55.000 3.61 0.00 0.00 4.57
441 447 6.073058 TGTGAATTCTTTGAGAAAGACGGATG 60.073 38.462 7.05 0.00 46.53 3.51
442 448 5.997746 TGTGAATTCTTTGAGAAAGACGGAT 59.002 36.000 7.05 0.00 46.53 4.18
443 449 5.364778 TGTGAATTCTTTGAGAAAGACGGA 58.635 37.500 7.05 0.00 46.53 4.69
446 533 5.396654 GCGTTGTGAATTCTTTGAGAAAGAC 59.603 40.000 7.05 0.00 46.53 3.01
451 538 2.349438 GCGCGTTGTGAATTCTTTGAGA 60.349 45.455 8.43 0.00 0.00 3.27
454 541 0.697010 CGCGCGTTGTGAATTCTTTG 59.303 50.000 24.19 0.00 0.00 2.77
461 548 4.893601 TCCACCGCGCGTTGTGAA 62.894 61.111 31.69 16.24 34.37 3.18
466 553 4.373116 ATCACTCCACCGCGCGTT 62.373 61.111 29.95 13.03 0.00 4.84
471 558 2.265739 TGAGCATCACTCCACCGC 59.734 61.111 0.00 0.00 42.56 5.68
480 567 2.432456 GTGACGCCGTGAGCATCA 60.432 61.111 0.00 0.00 42.45 3.07
481 568 2.432456 TGTGACGCCGTGAGCATC 60.432 61.111 0.00 0.00 44.04 3.91
482 569 2.433145 CTGTGACGCCGTGAGCAT 60.433 61.111 0.00 0.00 44.04 3.79
483 570 3.439513 AACTGTGACGCCGTGAGCA 62.440 57.895 0.00 0.00 44.04 4.26
515 621 2.499685 GCTGGGTAGGCAGTACGG 59.500 66.667 0.00 0.00 31.59 4.02
523 629 2.516888 CGGGTATGGGCTGGGTAGG 61.517 68.421 0.00 0.00 0.00 3.18
525 631 0.031313 TAACGGGTATGGGCTGGGTA 60.031 55.000 0.00 0.00 0.00 3.69
526 632 1.307170 TAACGGGTATGGGCTGGGT 60.307 57.895 0.00 0.00 0.00 4.51
527 633 1.147600 GTAACGGGTATGGGCTGGG 59.852 63.158 0.00 0.00 0.00 4.45
528 634 1.227438 CGTAACGGGTATGGGCTGG 60.227 63.158 0.00 0.00 0.00 4.85
529 635 1.885850 GCGTAACGGGTATGGGCTG 60.886 63.158 0.00 0.00 0.00 4.85
530 636 1.692173 ATGCGTAACGGGTATGGGCT 61.692 55.000 0.00 0.00 0.00 5.19
537 676 4.825252 GGGCGATGCGTAACGGGT 62.825 66.667 5.22 0.00 0.00 5.28
543 682 3.598715 CTACGGGGGCGATGCGTA 61.599 66.667 0.00 0.00 0.00 4.42
645 786 1.658409 GCAAAACTGCTGCCGTGTC 60.658 57.895 0.00 0.00 33.51 3.67
721 871 0.916809 AATTACCCAACCCCGAGGAG 59.083 55.000 0.00 0.00 36.73 3.69
722 872 2.267160 TAATTACCCAACCCCGAGGA 57.733 50.000 0.00 0.00 36.73 3.71
723 873 3.018856 GTTTAATTACCCAACCCCGAGG 58.981 50.000 0.00 0.00 40.04 4.63
724 874 3.959293 AGTTTAATTACCCAACCCCGAG 58.041 45.455 0.00 0.00 0.00 4.63
725 875 4.535692 ACTAGTTTAATTACCCAACCCCGA 59.464 41.667 0.00 0.00 0.00 5.14
726 876 4.637091 CACTAGTTTAATTACCCAACCCCG 59.363 45.833 0.00 0.00 0.00 5.73
733 883 2.286025 CGCGCCACTAGTTTAATTACCC 59.714 50.000 0.00 0.00 0.00 3.69
799 949 1.464189 GCGTTTACTGCTGCTACTTGC 60.464 52.381 0.00 0.00 43.25 4.01
800 950 1.201812 CGCGTTTACTGCTGCTACTTG 60.202 52.381 0.00 0.00 0.00 3.16
801 951 1.068474 CGCGTTTACTGCTGCTACTT 58.932 50.000 0.00 0.00 0.00 2.24
802 952 0.736325 CCGCGTTTACTGCTGCTACT 60.736 55.000 4.92 0.00 0.00 2.57
803 953 1.708027 CCGCGTTTACTGCTGCTAC 59.292 57.895 4.92 0.00 0.00 3.58
804 954 2.098233 GCCGCGTTTACTGCTGCTA 61.098 57.895 4.92 0.00 39.17 3.49
805 955 3.423154 GCCGCGTTTACTGCTGCT 61.423 61.111 4.92 0.00 39.17 4.24
806 956 4.460873 GGCCGCGTTTACTGCTGC 62.461 66.667 4.92 0.00 41.17 5.25
807 957 4.147322 CGGCCGCGTTTACTGCTG 62.147 66.667 14.67 0.50 0.00 4.41
823 973 0.175073 CGGGTTTAACCTCTCCTCCG 59.825 60.000 14.27 3.32 38.64 4.63
869 1019 6.128634 CCGTGAAAGCGTTTTTAACTATCTCT 60.129 38.462 0.00 0.00 0.00 3.10
870 1020 6.013689 CCGTGAAAGCGTTTTTAACTATCTC 58.986 40.000 0.00 0.00 0.00 2.75
871 1021 5.616204 GCCGTGAAAGCGTTTTTAACTATCT 60.616 40.000 0.00 0.00 0.00 1.98
873 1023 4.469552 GCCGTGAAAGCGTTTTTAACTAT 58.530 39.130 0.00 0.00 0.00 2.12
874 1024 3.875884 GCCGTGAAAGCGTTTTTAACTA 58.124 40.909 0.00 0.00 0.00 2.24
937 1092 3.243336 GTTAGCGCCGTCTTATAGGATG 58.757 50.000 2.29 0.00 0.00 3.51
964 1119 2.664081 GGGAGAGTGGACTGGCTGG 61.664 68.421 0.00 0.00 0.00 4.85
1049 1204 1.067749 CTCGGAGATGGCTGAGCTG 59.932 63.158 3.72 0.00 34.76 4.24
1050 1205 1.381056 ACTCGGAGATGGCTGAGCT 60.381 57.895 12.86 0.00 43.56 4.09
1051 1206 1.067250 GACTCGGAGATGGCTGAGC 59.933 63.158 12.86 0.00 43.56 4.26
1052 1207 1.739049 GGACTCGGAGATGGCTGAG 59.261 63.158 12.86 0.00 44.92 3.35
1053 1208 2.121538 CGGACTCGGAGATGGCTGA 61.122 63.158 12.86 0.00 33.89 4.26
1054 1209 2.069465 CTCGGACTCGGAGATGGCTG 62.069 65.000 12.86 3.58 33.89 4.85
1055 1210 1.826054 CTCGGACTCGGAGATGGCT 60.826 63.158 12.86 0.00 33.89 4.75
1056 1211 2.725008 CTCGGACTCGGAGATGGC 59.275 66.667 12.86 0.00 33.89 4.40
1057 1212 2.851071 GCCTCGGACTCGGAGATGG 61.851 68.421 12.86 7.01 33.89 3.51
1058 1213 1.791103 GAGCCTCGGACTCGGAGATG 61.791 65.000 12.86 0.89 33.89 2.90
1059 1214 1.527380 GAGCCTCGGACTCGGAGAT 60.527 63.158 12.86 3.77 33.89 2.75
1060 1215 2.124653 GAGCCTCGGACTCGGAGA 60.125 66.667 12.86 0.00 36.95 3.71
1061 1216 2.124487 AGAGCCTCGGACTCGGAG 60.124 66.667 2.83 2.83 39.23 4.63
1062 1217 2.438614 CAGAGCCTCGGACTCGGA 60.439 66.667 0.00 0.00 39.23 4.55
1063 1218 4.200283 GCAGAGCCTCGGACTCGG 62.200 72.222 0.00 0.00 39.23 4.63
1064 1219 3.119709 GAGCAGAGCCTCGGACTCG 62.120 68.421 0.00 0.00 39.23 4.18
1065 1220 1.724582 GAGAGCAGAGCCTCGGACTC 61.725 65.000 0.00 2.47 36.95 3.36
1066 1221 1.752694 GAGAGCAGAGCCTCGGACT 60.753 63.158 0.00 0.00 36.95 3.85
1067 1222 1.391157 ATGAGAGCAGAGCCTCGGAC 61.391 60.000 0.00 0.00 36.95 4.79
1083 1238 6.152661 GTGGAGAAGAGAAGAGAAGAGAATGA 59.847 42.308 0.00 0.00 0.00 2.57
1084 1239 6.153340 AGTGGAGAAGAGAAGAGAAGAGAATG 59.847 42.308 0.00 0.00 0.00 2.67
1085 1240 6.256053 AGTGGAGAAGAGAAGAGAAGAGAAT 58.744 40.000 0.00 0.00 0.00 2.40
1086 1241 5.640147 AGTGGAGAAGAGAAGAGAAGAGAA 58.360 41.667 0.00 0.00 0.00 2.87
1087 1242 5.253330 GAGTGGAGAAGAGAAGAGAAGAGA 58.747 45.833 0.00 0.00 0.00 3.10
1088 1243 4.399303 GGAGTGGAGAAGAGAAGAGAAGAG 59.601 50.000 0.00 0.00 0.00 2.85
1089 1244 4.340617 GGAGTGGAGAAGAGAAGAGAAGA 58.659 47.826 0.00 0.00 0.00 2.87
1090 1245 3.447229 GGGAGTGGAGAAGAGAAGAGAAG 59.553 52.174 0.00 0.00 0.00 2.85
1113 1268 1.807573 GAGCGCGAGGAACAAGGAG 60.808 63.158 12.10 0.00 0.00 3.69
1202 1362 1.180029 GAGGCGCCGGGATAATACTA 58.820 55.000 23.20 0.00 0.00 1.82
1203 1363 1.874345 CGAGGCGCCGGGATAATACT 61.874 60.000 23.20 0.00 0.00 2.12
1204 1364 1.445582 CGAGGCGCCGGGATAATAC 60.446 63.158 23.20 4.36 0.00 1.89
1235 1395 3.849953 GTAAAGCCGCGAGCCGTG 61.850 66.667 8.23 1.74 45.47 4.94
1236 1396 4.065281 AGTAAAGCCGCGAGCCGT 62.065 61.111 8.23 2.72 45.47 5.68
1237 1397 3.554692 CAGTAAAGCCGCGAGCCG 61.555 66.667 8.23 0.00 45.47 5.52
1238 1398 3.865830 GCAGTAAAGCCGCGAGCC 61.866 66.667 8.23 0.00 45.47 4.70
1239 1399 2.803713 GAGCAGTAAAGCCGCGAGC 61.804 63.158 8.23 9.98 44.25 5.03
1240 1400 1.153745 AGAGCAGTAAAGCCGCGAG 60.154 57.895 8.23 0.00 34.23 5.03
1241 1401 1.446099 CAGAGCAGTAAAGCCGCGA 60.446 57.895 8.23 0.00 34.23 5.87
1242 1402 1.291877 AACAGAGCAGTAAAGCCGCG 61.292 55.000 0.00 0.00 34.23 6.46
1243 1403 1.393883 GTAACAGAGCAGTAAAGCCGC 59.606 52.381 0.00 0.00 34.23 6.53
1244 1404 2.683968 TGTAACAGAGCAGTAAAGCCG 58.316 47.619 0.00 0.00 34.23 5.52
1256 1429 2.028112 AGGCGAGCAGAAATGTAACAGA 60.028 45.455 0.00 0.00 0.00 3.41
1313 1489 0.107165 GGCAATAAAGACGGCCTCCT 60.107 55.000 0.00 0.00 43.09 3.69
1314 1490 2.405143 GGCAATAAAGACGGCCTCC 58.595 57.895 0.00 0.00 43.09 4.30
1317 1493 0.738975 GGAAGGCAATAAAGACGGCC 59.261 55.000 0.00 0.00 46.77 6.13
1318 1494 0.738975 GGGAAGGCAATAAAGACGGC 59.261 55.000 0.00 0.00 0.00 5.68
1470 1646 1.648467 GAAGCTGCAGCCTTAACCGG 61.648 60.000 34.39 0.00 43.38 5.28
1573 1762 2.867109 ACCACACAGAAAGGAGGATG 57.133 50.000 0.00 0.00 0.00 3.51
1589 1778 4.939368 CGCCACCACCGGAAACCA 62.939 66.667 9.46 0.00 0.00 3.67
2182 2380 1.811266 CTCCGCCAAGGACGACATG 60.811 63.158 0.00 0.00 45.98 3.21
2344 2545 3.122250 CTCGGCGTAGAGGAACCCG 62.122 68.421 6.85 0.00 40.25 5.28
2447 2654 2.038269 GGTCGCGCAAATCCTGGAA 61.038 57.895 8.75 0.00 0.00 3.53
2448 2655 2.435938 GGTCGCGCAAATCCTGGA 60.436 61.111 8.75 0.00 0.00 3.86
2449 2656 2.436646 AGGTCGCGCAAATCCTGG 60.437 61.111 8.75 0.00 0.00 4.45
2549 2763 3.120923 CCACACGTACACGACAAAATACC 60.121 47.826 9.04 0.00 43.02 2.73
2621 2840 6.100004 TCATACATTTCTCTTCTTGTCGACC 58.900 40.000 14.12 0.00 0.00 4.79
2628 2847 5.131142 ACCCGGATCATACATTTCTCTTCTT 59.869 40.000 0.73 0.00 0.00 2.52
2736 2969 6.287107 ACACCTATACGTACGTACATGTAC 57.713 41.667 28.99 23.53 41.01 2.90
2737 2970 6.315144 ACAACACCTATACGTACGTACATGTA 59.685 38.462 28.99 18.51 33.01 2.29
2738 2971 5.123820 ACAACACCTATACGTACGTACATGT 59.876 40.000 28.99 24.10 33.01 3.21
2739 2972 5.572211 ACAACACCTATACGTACGTACATG 58.428 41.667 28.99 23.54 33.01 3.21
2740 2973 5.818136 ACAACACCTATACGTACGTACAT 57.182 39.130 28.99 18.34 33.01 2.29
2741 2974 5.180304 TGAACAACACCTATACGTACGTACA 59.820 40.000 28.99 18.21 33.01 2.90
2742 2975 5.508224 GTGAACAACACCTATACGTACGTAC 59.492 44.000 28.99 15.90 43.05 3.67
2743 2976 5.627172 GTGAACAACACCTATACGTACGTA 58.373 41.667 28.62 28.62 43.05 3.57
2744 2977 4.475944 GTGAACAACACCTATACGTACGT 58.524 43.478 25.98 25.98 43.05 3.57
2887 3136 0.599991 CCAAAACCCGCAAGCTTTCC 60.600 55.000 0.00 0.00 0.00 3.13
2923 3172 0.940126 CGGCAGATAATTTCGCAGCT 59.060 50.000 0.00 0.00 0.00 4.24
2925 3180 1.581934 TCCGGCAGATAATTTCGCAG 58.418 50.000 0.00 0.00 0.00 5.18
3006 3261 0.390603 TGTACCGATGCAAACTCCGG 60.391 55.000 0.00 0.00 46.65 5.14
3063 3329 1.146930 CCAGCGGCCATGTCTGTAT 59.853 57.895 2.24 0.00 0.00 2.29
3064 3330 2.584064 CCAGCGGCCATGTCTGTA 59.416 61.111 2.24 0.00 0.00 2.74
3187 3453 2.510906 CCATAACTCCCTGCCCGG 59.489 66.667 0.00 0.00 0.00 5.73
3246 3514 4.803426 CTCGCCCTCGCCACTGTC 62.803 72.222 0.00 0.00 35.26 3.51
3258 3526 2.852495 TTCGCATTCACTCCCTCGCC 62.852 60.000 0.00 0.00 0.00 5.54
3310 3582 4.803426 CACGCCGCTCTCACTCCC 62.803 72.222 0.00 0.00 0.00 4.30
3406 3686 0.322816 CTTCCCCATGTGGTCACCTG 60.323 60.000 0.00 0.00 0.00 4.00
3432 3712 1.025041 CTCCCCCTTATCTTTTGCGC 58.975 55.000 0.00 0.00 0.00 6.09
3447 3727 4.292178 CCGCCGATCTCAGCTCCC 62.292 72.222 0.00 0.00 0.00 4.30
3454 3734 2.279784 CTCCTTGCCGCCGATCTC 60.280 66.667 0.00 0.00 0.00 2.75
3513 3793 2.611518 AGCAGTACGCATCTTTGTCTC 58.388 47.619 11.30 0.00 46.13 3.36
3514 3794 2.751166 AGCAGTACGCATCTTTGTCT 57.249 45.000 11.30 0.00 46.13 3.41


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

AutoCloner maintained by Alex Coulton.