Multiple sequence alignment - TraesCS3D01G471800

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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 TraesCS3D01G471800 chr3D 100.000 3703 0 0 1 3703 573922227 573918525 0.000000e+00 6839
1 TraesCS3D01G471800 chr3D 87.654 243 22 7 3465 3703 7443229 7443467 3.640000e-70 276
2 TraesCS3D01G471800 chr3D 83.401 247 41 0 1224 1470 514680942 514680696 2.880000e-56 230
3 TraesCS3D01G471800 chr3A 94.991 2935 106 12 580 3475 709070954 709068022 0.000000e+00 4567
4 TraesCS3D01G471800 chr3A 90.657 578 31 6 1 576 709071591 709071035 0.000000e+00 747
5 TraesCS3D01G471800 chr3A 89.451 237 17 6 3471 3703 99563773 99563541 3.620000e-75 292
6 TraesCS3D01G471800 chr3B 96.101 2129 78 3 901 3027 763226839 763228964 0.000000e+00 3467
7 TraesCS3D01G471800 chr3B 95.309 405 15 2 3071 3472 763229058 763229461 1.120000e-179 640
8 TraesCS3D01G471800 chr3B 87.316 339 14 8 1 335 763225806 763226119 9.780000e-96 361
9 TraesCS3D01G471800 chr3B 86.722 241 24 7 3467 3703 304089987 304089751 1.020000e-65 261
10 TraesCS3D01G471800 chr3B 81.633 294 20 17 580 864 763226567 763226835 2.900000e-51 213
11 TraesCS3D01G471800 chr3B 92.366 131 9 1 445 574 763226379 763226509 6.320000e-43 185
12 TraesCS3D01G471800 chr5A 88.136 236 20 6 3472 3703 101500756 101500987 1.310000e-69 274
13 TraesCS3D01G471800 chr5A 86.667 240 24 7 3468 3703 444341432 444341667 3.670000e-65 259
14 TraesCS3D01G471800 chr5A 85.833 240 26 7 3468 3703 106921269 106921504 7.940000e-62 248
15 TraesCS3D01G471800 chr1D 85.171 263 39 0 1219 1481 7372271 7372533 1.690000e-68 270
16 TraesCS3D01G471800 chr1D 87.500 240 22 7 3468 3703 216793424 216793189 1.690000e-68 270
17 TraesCS3D01G471800 chr5B 87.931 232 20 6 3468 3695 403844306 403844079 2.190000e-67 267
18 TraesCS3D01G471800 chr1A 84.733 262 40 0 1220 1481 9532815 9532554 2.840000e-66 263
19 TraesCS3D01G471800 chr4B 85.714 252 26 9 3458 3703 212948598 212948845 1.320000e-64 257
20 TraesCS3D01G471800 chr1B 84.030 263 42 0 1219 1481 9647615 9647877 1.710000e-63 254
21 TraesCS3D01G471800 chr2B 83.969 262 38 3 1219 1476 775385988 775386249 7.940000e-62 248


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 TraesCS3D01G471800 chr3D 573918525 573922227 3702 True 6839.0 6839 100.000 1 3703 1 chr3D.!!$R2 3702
1 TraesCS3D01G471800 chr3A 709068022 709071591 3569 True 2657.0 4567 92.824 1 3475 2 chr3A.!!$R2 3474
2 TraesCS3D01G471800 chr3B 763225806 763229461 3655 False 973.2 3467 90.545 1 3472 5 chr3B.!!$F1 3471

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
989 1312 0.595095 GGTACGTGGTTCGAGACACT 59.405 55.000 16.28 8.49 42.86 3.55 F
1188 1511 1.064685 GCAGTTTACACCCTGGGCTAT 60.065 52.381 14.08 0.29 0.00 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2244 2567 0.250081 GCCGGGGATCTCTGTTGATC 60.250 60.0 2.18 0.0 41.39 2.92 R
3167 3575 0.184692 TGTTCTGCCCACATGGACAA 59.815 50.0 0.00 0.0 37.39 3.18 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
25 26 2.697431 TGAAAATCCGTTTCCGCTTG 57.303 45.000 0.00 0.00 44.41 4.01
40 42 1.007422 CGCTTGTGTAAGACGCATACG 60.007 52.381 0.00 0.00 38.53 3.06
47 49 2.256174 GTAAGACGCATACGCTGTGAA 58.744 47.619 6.18 0.00 45.53 3.18
59 61 1.127951 CGCTGTGAAAATACGGTCCAC 59.872 52.381 0.00 0.00 0.00 4.02
131 134 2.038975 AGCTCCCCTTCCGCACTA 59.961 61.111 0.00 0.00 0.00 2.74
136 139 3.771160 CCCTTCCGCACTAGCCGT 61.771 66.667 0.00 0.00 37.52 5.68
142 145 3.760035 CGCACTAGCCGTCCACCT 61.760 66.667 0.00 0.00 37.52 4.00
143 146 2.125512 GCACTAGCCGTCCACCTG 60.126 66.667 0.00 0.00 33.58 4.00
227 230 0.933097 CTCGCCCGACTCATCATTTG 59.067 55.000 0.00 0.00 0.00 2.32
243 246 1.845627 TTTGCTCTGCTCCTCCCCAG 61.846 60.000 0.00 0.00 0.00 4.45
309 315 4.813750 TTTCTTTAGAACGGGTAGAGGG 57.186 45.455 0.00 0.00 33.13 4.30
315 321 1.203149 AGAACGGGTAGAGGGACAAGT 60.203 52.381 0.00 0.00 0.00 3.16
351 357 3.723235 CTGTGGCCATCTCCGACGG 62.723 68.421 9.72 7.84 0.00 4.79
378 384 2.735772 GGCCGGCTCTCATTCCTGA 61.736 63.158 28.56 0.00 0.00 3.86
424 430 2.749800 GCAACAACCTCTTCCCTCTTGT 60.750 50.000 0.00 0.00 0.00 3.16
522 749 4.367023 CTCGGGCCGGTCGTTTCA 62.367 66.667 27.98 2.24 0.00 2.69
576 803 3.066064 CCAATGAAACGACCAAACACAGA 59.934 43.478 0.00 0.00 0.00 3.41
580 807 1.021968 AACGACCAAACACAGAAGGC 58.978 50.000 0.00 0.00 0.00 4.35
581 808 0.818040 ACGACCAAACACAGAAGGCC 60.818 55.000 0.00 0.00 0.00 5.19
582 809 1.841663 CGACCAAACACAGAAGGCCG 61.842 60.000 0.00 0.00 0.00 6.13
583 810 2.130073 GACCAAACACAGAAGGCCGC 62.130 60.000 0.00 0.00 0.00 6.53
584 811 2.644992 CAAACACAGAAGGCCGCC 59.355 61.111 0.00 0.00 0.00 6.13
585 812 1.898574 CAAACACAGAAGGCCGCCT 60.899 57.895 5.94 5.94 33.87 5.52
592 897 1.612442 AGAAGGCCGCCTTAGTCCA 60.612 57.895 24.89 0.00 44.82 4.02
593 898 1.153349 GAAGGCCGCCTTAGTCCAG 60.153 63.158 24.89 0.00 44.82 3.86
603 908 3.425162 CCTTAGTCCAGGCCCATATTC 57.575 52.381 0.00 0.00 0.00 1.75
696 1007 5.447818 GCGAATTTCTGAAAGTACATCCCTG 60.448 44.000 8.95 0.00 33.76 4.45
715 1026 5.046663 TCCCTGATTTGCATTTCCCTTTTAC 60.047 40.000 0.00 0.00 0.00 2.01
720 1031 2.865079 TGCATTTCCCTTTTACGTCCA 58.135 42.857 0.00 0.00 0.00 4.02
769 1081 3.820195 TCTACTTCCCCACACTGACTA 57.180 47.619 0.00 0.00 0.00 2.59
777 1089 2.305927 CCCCACACTGACTAACTGGATT 59.694 50.000 0.00 0.00 0.00 3.01
919 1241 5.353938 TCAAGTGTGTCGTACTAAAAGCTT 58.646 37.500 0.00 0.00 0.00 3.74
980 1303 0.831966 TGTCCAACAGGTACGTGGTT 59.168 50.000 19.03 8.60 0.00 3.67
989 1312 0.595095 GGTACGTGGTTCGAGACACT 59.405 55.000 16.28 8.49 42.86 3.55
1089 1412 3.744660 ACAAATGTTCCTCTTCTTCGCT 58.255 40.909 0.00 0.00 0.00 4.93
1137 1460 3.132289 ACTCGTTTCTCAGGTTCTTCACA 59.868 43.478 0.00 0.00 0.00 3.58
1188 1511 1.064685 GCAGTTTACACCCTGGGCTAT 60.065 52.381 14.08 0.29 0.00 2.97
1371 1694 9.606631 CTAGCTTTATATGTTTTCTGGAAGTCT 57.393 33.333 0.00 0.00 33.76 3.24
1629 1952 2.891580 ACGATCAGGTGATAGCGGTAAT 59.108 45.455 0.00 0.00 34.37 1.89
1698 2021 2.032549 GCTTGGCATGATGTACGATGAC 60.033 50.000 4.32 1.79 0.00 3.06
2117 2440 3.567164 ACAGTGATCAAAAGCTTGGTGAG 59.433 43.478 15.92 6.99 33.01 3.51
2199 2522 1.414181 CACGTGGAGGCAGATAAGGAT 59.586 52.381 7.95 0.00 0.00 3.24
2244 2567 4.505922 GGAATTACTGACTTCGATGCTGAG 59.494 45.833 0.00 0.00 0.00 3.35
2265 2588 0.982852 TCAACAGAGATCCCCGGCAT 60.983 55.000 0.00 0.00 0.00 4.40
2334 2657 2.368548 AGATTTTGGTGGAAAGGTTGCC 59.631 45.455 0.00 0.00 0.00 4.52
2415 2738 1.244816 TGGAGACAGACACAGGTACG 58.755 55.000 0.00 0.00 35.01 3.67
2423 2746 0.108615 GACACAGGTACGAGCTGCAT 60.109 55.000 1.02 3.32 46.94 3.96
2442 2765 3.758554 GCATTGTCTTGGTGGAAGTATGT 59.241 43.478 0.00 0.00 32.90 2.29
2478 2801 8.287807 CCAACTACATGGCATACCTTTTGGTC 62.288 46.154 0.00 0.00 42.37 4.02
2491 2814 1.346479 TTTGGTCACCCACCCTTCGA 61.346 55.000 0.00 0.00 46.18 3.71
2494 2817 1.745489 GTCACCCACCCTTCGATGC 60.745 63.158 0.00 0.00 0.00 3.91
2912 3235 8.673711 TCCGTTCTTCATTCGATTTGATTTTAT 58.326 29.630 0.00 0.00 0.00 1.40
2934 3257 1.270305 CCTCTTCTGTTTGCGTCTGGA 60.270 52.381 0.00 0.00 0.00 3.86
2947 3270 2.007608 CGTCTGGAGTATCTCACGACA 58.992 52.381 13.59 0.00 34.74 4.35
3122 3530 2.357009 CACTGCAGCTACAATTGGGATC 59.643 50.000 15.27 0.00 0.00 3.36
3167 3575 8.011844 ACTGAAGCCAGAAAAAGAACTTAATT 57.988 30.769 0.00 0.00 43.02 1.40
3271 3681 4.018484 AGCTTTCAAGACTGCTTCTGAT 57.982 40.909 0.00 0.00 33.46 2.90
3360 3770 3.624410 CACCCTAACTAATTAACACGGCC 59.376 47.826 0.00 0.00 0.00 6.13
3388 3798 4.142271 TGTGAAATGATCCCAAATAACGCC 60.142 41.667 0.00 0.00 0.00 5.68
3472 3885 8.964476 AGTATGATCAAACATGGTAACTAAGG 57.036 34.615 0.00 0.00 37.61 2.69
3475 3888 5.943416 TGATCAAACATGGTAACTAAGGGTG 59.057 40.000 0.00 0.00 37.61 4.61
3476 3889 5.313280 TCAAACATGGTAACTAAGGGTGT 57.687 39.130 0.00 0.00 37.61 4.16
3477 3890 5.067273 TCAAACATGGTAACTAAGGGTGTG 58.933 41.667 0.00 0.00 37.61 3.82
3478 3891 4.717279 AACATGGTAACTAAGGGTGTGT 57.283 40.909 0.00 0.00 37.61 3.72
3479 3892 4.717279 ACATGGTAACTAAGGGTGTGTT 57.283 40.909 0.00 0.00 37.61 3.32
3480 3893 5.056553 ACATGGTAACTAAGGGTGTGTTT 57.943 39.130 0.00 0.00 37.61 2.83
3481 3894 4.825085 ACATGGTAACTAAGGGTGTGTTTG 59.175 41.667 0.00 0.00 37.61 2.93
3482 3895 3.822940 TGGTAACTAAGGGTGTGTTTGG 58.177 45.455 0.00 0.00 37.61 3.28
3483 3896 3.202595 TGGTAACTAAGGGTGTGTTTGGT 59.797 43.478 0.00 0.00 37.61 3.67
3484 3897 4.209538 GGTAACTAAGGGTGTGTTTGGTT 58.790 43.478 0.00 0.00 33.45 3.67
3485 3898 4.276678 GGTAACTAAGGGTGTGTTTGGTTC 59.723 45.833 0.00 0.00 31.67 3.62
3486 3899 3.655615 ACTAAGGGTGTGTTTGGTTCA 57.344 42.857 0.00 0.00 0.00 3.18
3487 3900 3.970842 ACTAAGGGTGTGTTTGGTTCAA 58.029 40.909 0.00 0.00 0.00 2.69
3488 3901 3.951680 ACTAAGGGTGTGTTTGGTTCAAG 59.048 43.478 0.00 0.00 0.00 3.02
3489 3902 2.818751 AGGGTGTGTTTGGTTCAAGA 57.181 45.000 0.00 0.00 0.00 3.02
3490 3903 3.094484 AGGGTGTGTTTGGTTCAAGAA 57.906 42.857 0.00 0.00 0.00 2.52
3491 3904 2.758423 AGGGTGTGTTTGGTTCAAGAAC 59.242 45.455 4.39 4.39 40.45 3.01
3492 3905 2.478879 GGGTGTGTTTGGTTCAAGAACG 60.479 50.000 6.84 0.00 42.02 3.95
3493 3906 2.420722 GGTGTGTTTGGTTCAAGAACGA 59.579 45.455 6.84 0.31 42.02 3.85
3494 3907 3.119779 GGTGTGTTTGGTTCAAGAACGAA 60.120 43.478 6.33 6.33 42.02 3.85
3495 3908 4.095610 GTGTGTTTGGTTCAAGAACGAAG 58.904 43.478 9.69 0.00 39.51 3.79
3497 3910 4.095610 GTGTTTGGTTCAAGAACGAAGTG 58.904 43.478 9.69 0.00 45.00 3.16
3498 3911 3.127895 TGTTTGGTTCAAGAACGAAGTGG 59.872 43.478 9.69 0.00 45.00 4.00
3499 3912 2.992124 TGGTTCAAGAACGAAGTGGA 57.008 45.000 6.84 0.00 45.00 4.02
3500 3913 3.269538 TGGTTCAAGAACGAAGTGGAA 57.730 42.857 6.84 0.00 45.00 3.53
3501 3914 2.940410 TGGTTCAAGAACGAAGTGGAAC 59.060 45.455 6.84 0.00 45.00 3.62
3502 3915 2.033151 GGTTCAAGAACGAAGTGGAACG 60.033 50.000 6.84 0.00 45.00 3.95
3503 3916 1.860676 TCAAGAACGAAGTGGAACGG 58.139 50.000 0.00 0.00 45.00 4.44
3504 3917 1.409790 TCAAGAACGAAGTGGAACGGA 59.590 47.619 0.00 0.00 45.00 4.69
3505 3918 2.159071 TCAAGAACGAAGTGGAACGGAA 60.159 45.455 0.00 0.00 45.00 4.30
3506 3919 2.806244 CAAGAACGAAGTGGAACGGAAT 59.194 45.455 0.00 0.00 45.00 3.01
3507 3920 2.413837 AGAACGAAGTGGAACGGAATG 58.586 47.619 0.00 0.00 45.00 2.67
3508 3921 2.140717 GAACGAAGTGGAACGGAATGT 58.859 47.619 0.00 0.00 45.00 2.71
3509 3922 1.792006 ACGAAGTGGAACGGAATGTC 58.208 50.000 0.00 0.00 45.86 3.06
3510 3923 1.069513 ACGAAGTGGAACGGAATGTCA 59.930 47.619 0.00 0.00 45.86 3.58
3511 3924 2.289444 ACGAAGTGGAACGGAATGTCAT 60.289 45.455 0.00 0.00 45.86 3.06
3512 3925 2.094258 CGAAGTGGAACGGAATGTCATG 59.906 50.000 0.00 0.00 45.86 3.07
3513 3926 2.113860 AGTGGAACGGAATGTCATGG 57.886 50.000 0.00 0.00 45.86 3.66
3514 3927 1.351017 AGTGGAACGGAATGTCATGGT 59.649 47.619 0.00 0.00 45.86 3.55
3515 3928 2.159382 GTGGAACGGAATGTCATGGTT 58.841 47.619 0.00 0.00 0.00 3.67
3516 3929 2.161609 GTGGAACGGAATGTCATGGTTC 59.838 50.000 12.73 12.73 37.00 3.62
3517 3930 2.224646 TGGAACGGAATGTCATGGTTCA 60.225 45.455 18.65 8.52 38.90 3.18
3518 3931 3.016736 GGAACGGAATGTCATGGTTCAT 58.983 45.455 18.65 3.15 38.90 2.57
3519 3932 3.443681 GGAACGGAATGTCATGGTTCATT 59.556 43.478 18.65 9.90 38.90 2.57
3520 3933 4.438744 GGAACGGAATGTCATGGTTCATTC 60.439 45.833 20.30 20.30 45.03 2.67
3524 3937 4.019919 GAATGTCATGGTTCATTCCACG 57.980 45.455 18.96 0.00 42.03 4.94
3525 3938 1.819928 TGTCATGGTTCATTCCACGG 58.180 50.000 0.00 0.00 40.51 4.94
3526 3939 1.349357 TGTCATGGTTCATTCCACGGA 59.651 47.619 0.00 0.00 40.51 4.69
3527 3940 2.224646 TGTCATGGTTCATTCCACGGAA 60.225 45.455 0.00 0.00 40.51 4.30
3528 3941 2.817258 GTCATGGTTCATTCCACGGAAA 59.183 45.455 1.93 0.00 40.51 3.13
3529 3942 3.443681 GTCATGGTTCATTCCACGGAAAT 59.556 43.478 1.93 0.00 40.51 2.17
3530 3943 3.443329 TCATGGTTCATTCCACGGAAATG 59.557 43.478 1.93 1.48 40.51 2.32
3531 3944 2.166829 TGGTTCATTCCACGGAAATGG 58.833 47.619 1.93 0.00 41.57 3.16
3532 3945 1.476488 GGTTCATTCCACGGAAATGGG 59.524 52.381 1.93 0.00 40.49 4.00
3533 3946 2.167662 GTTCATTCCACGGAAATGGGT 58.832 47.619 1.93 0.00 40.49 4.51
3534 3947 2.560981 GTTCATTCCACGGAAATGGGTT 59.439 45.455 1.93 0.00 40.49 4.11
3535 3948 2.166829 TCATTCCACGGAAATGGGTTG 58.833 47.619 1.93 0.00 40.49 3.77
3536 3949 1.204467 CATTCCACGGAAATGGGTTGG 59.796 52.381 1.93 0.00 40.49 3.77
3537 3950 0.186386 TTCCACGGAAATGGGTTGGT 59.814 50.000 0.00 0.00 40.49 3.67
3538 3951 0.186386 TCCACGGAAATGGGTTGGTT 59.814 50.000 0.00 0.00 40.49 3.67
3539 3952 0.601057 CCACGGAAATGGGTTGGTTC 59.399 55.000 0.00 0.00 35.95 3.62
3540 3953 0.601057 CACGGAAATGGGTTGGTTCC 59.399 55.000 0.00 0.00 37.95 3.62
3542 3955 3.045518 GGAAATGGGTTGGTTCCGT 57.954 52.632 0.00 0.00 32.03 4.69
3543 3956 1.334160 GGAAATGGGTTGGTTCCGTT 58.666 50.000 0.00 0.00 35.20 4.44
3544 3957 1.271379 GGAAATGGGTTGGTTCCGTTC 59.729 52.381 0.00 0.00 32.77 3.95
3545 3958 1.271379 GAAATGGGTTGGTTCCGTTCC 59.729 52.381 0.00 0.00 32.77 3.62
3546 3959 0.481128 AATGGGTTGGTTCCGTTCCT 59.519 50.000 0.00 0.00 0.00 3.36
3547 3960 1.364269 ATGGGTTGGTTCCGTTCCTA 58.636 50.000 0.00 0.00 0.00 2.94
3548 3961 1.364269 TGGGTTGGTTCCGTTCCTAT 58.636 50.000 0.00 0.00 0.00 2.57
3549 3962 1.003812 TGGGTTGGTTCCGTTCCTATG 59.996 52.381 0.00 0.00 0.00 2.23
3550 3963 1.003928 GGGTTGGTTCCGTTCCTATGT 59.996 52.381 0.00 0.00 0.00 2.29
3551 3964 2.553685 GGGTTGGTTCCGTTCCTATGTT 60.554 50.000 0.00 0.00 0.00 2.71
3552 3965 3.151554 GGTTGGTTCCGTTCCTATGTTT 58.848 45.455 0.00 0.00 0.00 2.83
3553 3966 3.057806 GGTTGGTTCCGTTCCTATGTTTG 60.058 47.826 0.00 0.00 0.00 2.93
3554 3967 2.785562 TGGTTCCGTTCCTATGTTTGG 58.214 47.619 0.00 0.00 0.00 3.28
3555 3968 2.106857 TGGTTCCGTTCCTATGTTTGGT 59.893 45.455 0.00 0.00 0.00 3.67
3556 3969 3.151554 GGTTCCGTTCCTATGTTTGGTT 58.848 45.455 0.00 0.00 0.00 3.67
3557 3970 4.202440 TGGTTCCGTTCCTATGTTTGGTTA 60.202 41.667 0.00 0.00 0.00 2.85
3558 3971 4.945543 GGTTCCGTTCCTATGTTTGGTTAT 59.054 41.667 0.00 0.00 0.00 1.89
3559 3972 5.163693 GGTTCCGTTCCTATGTTTGGTTATG 60.164 44.000 0.00 0.00 0.00 1.90
3560 3973 5.423704 TCCGTTCCTATGTTTGGTTATGA 57.576 39.130 0.00 0.00 0.00 2.15
3561 3974 5.424757 TCCGTTCCTATGTTTGGTTATGAG 58.575 41.667 0.00 0.00 0.00 2.90
3562 3975 5.046159 TCCGTTCCTATGTTTGGTTATGAGT 60.046 40.000 0.00 0.00 0.00 3.41
3563 3976 6.154877 TCCGTTCCTATGTTTGGTTATGAGTA 59.845 38.462 0.00 0.00 0.00 2.59
3564 3977 6.990349 CCGTTCCTATGTTTGGTTATGAGTAT 59.010 38.462 0.00 0.00 0.00 2.12
3565 3978 7.497909 CCGTTCCTATGTTTGGTTATGAGTATT 59.502 37.037 0.00 0.00 0.00 1.89
3566 3979 9.537192 CGTTCCTATGTTTGGTTATGAGTATTA 57.463 33.333 0.00 0.00 0.00 0.98
3573 3986 9.784531 ATGTTTGGTTATGAGTATTAGAGATGG 57.215 33.333 0.00 0.00 0.00 3.51
3574 3987 8.988060 TGTTTGGTTATGAGTATTAGAGATGGA 58.012 33.333 0.00 0.00 0.00 3.41
3575 3988 9.832445 GTTTGGTTATGAGTATTAGAGATGGAA 57.168 33.333 0.00 0.00 0.00 3.53
3578 3991 8.597167 TGGTTATGAGTATTAGAGATGGAATGG 58.403 37.037 0.00 0.00 0.00 3.16
3579 3992 8.816894 GGTTATGAGTATTAGAGATGGAATGGA 58.183 37.037 0.00 0.00 0.00 3.41
3583 3996 7.683578 TGAGTATTAGAGATGGAATGGAATGG 58.316 38.462 0.00 0.00 0.00 3.16
3584 3997 7.293299 TGAGTATTAGAGATGGAATGGAATGGT 59.707 37.037 0.00 0.00 0.00 3.55
3585 3998 8.050316 AGTATTAGAGATGGAATGGAATGGTT 57.950 34.615 0.00 0.00 0.00 3.67
3586 3999 9.170890 AGTATTAGAGATGGAATGGAATGGTTA 57.829 33.333 0.00 0.00 0.00 2.85
3587 4000 9.220767 GTATTAGAGATGGAATGGAATGGTTAC 57.779 37.037 0.00 0.00 0.00 2.50
3588 4001 4.708177 AGAGATGGAATGGAATGGTTACG 58.292 43.478 0.00 0.00 0.00 3.18
3589 4002 4.164221 AGAGATGGAATGGAATGGTTACGT 59.836 41.667 0.00 0.00 0.00 3.57
3590 4003 4.855340 AGATGGAATGGAATGGTTACGTT 58.145 39.130 0.00 0.00 0.00 3.99
3591 4004 4.881850 AGATGGAATGGAATGGTTACGTTC 59.118 41.667 0.00 0.00 41.01 3.95
3592 4005 4.295141 TGGAATGGAATGGTTACGTTCT 57.705 40.909 0.00 0.00 41.39 3.01
3593 4006 5.423704 TGGAATGGAATGGTTACGTTCTA 57.576 39.130 0.00 0.00 41.39 2.10
3594 4007 5.424757 TGGAATGGAATGGTTACGTTCTAG 58.575 41.667 0.00 0.00 41.39 2.43
3595 4008 5.046159 TGGAATGGAATGGTTACGTTCTAGT 60.046 40.000 0.00 0.00 41.39 2.57
3596 4009 5.293569 GGAATGGAATGGTTACGTTCTAGTG 59.706 44.000 0.00 0.00 41.39 2.74
3597 4010 4.877378 TGGAATGGTTACGTTCTAGTGT 57.123 40.909 0.00 0.00 41.39 3.55
3598 4011 5.217978 TGGAATGGTTACGTTCTAGTGTT 57.782 39.130 0.00 0.00 41.39 3.32
3599 4012 5.613329 TGGAATGGTTACGTTCTAGTGTTT 58.387 37.500 0.00 0.00 41.39 2.83
3600 4013 5.467399 TGGAATGGTTACGTTCTAGTGTTTG 59.533 40.000 0.00 0.00 41.39 2.93
3601 4014 5.106830 GGAATGGTTACGTTCTAGTGTTTGG 60.107 44.000 0.00 0.00 41.39 3.28
3602 4015 4.405116 TGGTTACGTTCTAGTGTTTGGT 57.595 40.909 0.00 0.00 0.00 3.67
3603 4016 4.768583 TGGTTACGTTCTAGTGTTTGGTT 58.231 39.130 0.00 0.00 0.00 3.67
3604 4017 4.810491 TGGTTACGTTCTAGTGTTTGGTTC 59.190 41.667 0.00 0.00 0.00 3.62
3605 4018 5.052481 GGTTACGTTCTAGTGTTTGGTTCT 58.948 41.667 0.00 0.00 0.00 3.01
3606 4019 5.050567 GGTTACGTTCTAGTGTTTGGTTCTG 60.051 44.000 0.00 0.00 0.00 3.02
3607 4020 3.463944 ACGTTCTAGTGTTTGGTTCTGG 58.536 45.455 0.00 0.00 0.00 3.86
3608 4021 3.133362 ACGTTCTAGTGTTTGGTTCTGGA 59.867 43.478 0.00 0.00 0.00 3.86
3609 4022 3.741344 CGTTCTAGTGTTTGGTTCTGGAG 59.259 47.826 0.00 0.00 0.00 3.86
3610 4023 3.402628 TCTAGTGTTTGGTTCTGGAGC 57.597 47.619 0.00 0.00 0.00 4.70
3611 4024 2.972713 TCTAGTGTTTGGTTCTGGAGCT 59.027 45.455 0.00 0.00 0.00 4.09
3612 4025 2.262423 AGTGTTTGGTTCTGGAGCTC 57.738 50.000 4.71 4.71 0.00 4.09
3613 4026 0.868406 GTGTTTGGTTCTGGAGCTCG 59.132 55.000 7.83 0.00 0.00 5.03
3614 4027 0.756294 TGTTTGGTTCTGGAGCTCGA 59.244 50.000 7.83 2.19 0.00 4.04
3615 4028 1.140052 TGTTTGGTTCTGGAGCTCGAA 59.860 47.619 7.83 3.67 0.00 3.71
3616 4029 2.224523 TGTTTGGTTCTGGAGCTCGAAT 60.225 45.455 7.83 0.00 0.00 3.34
3617 4030 2.099141 TTGGTTCTGGAGCTCGAATG 57.901 50.000 7.83 0.00 0.00 2.67
3618 4031 1.266178 TGGTTCTGGAGCTCGAATGA 58.734 50.000 7.83 0.07 0.00 2.57
3619 4032 1.623311 TGGTTCTGGAGCTCGAATGAA 59.377 47.619 7.83 6.45 0.00 2.57
3620 4033 2.038426 TGGTTCTGGAGCTCGAATGAAA 59.962 45.455 7.83 0.00 0.00 2.69
3621 4034 3.274288 GGTTCTGGAGCTCGAATGAAAT 58.726 45.455 7.83 0.00 0.00 2.17
3622 4035 3.064545 GGTTCTGGAGCTCGAATGAAATG 59.935 47.826 7.83 0.00 0.00 2.32
3623 4036 3.893326 TCTGGAGCTCGAATGAAATGA 57.107 42.857 7.83 0.00 0.00 2.57
3624 4037 4.412796 TCTGGAGCTCGAATGAAATGAT 57.587 40.909 7.83 0.00 0.00 2.45
3625 4038 4.774124 TCTGGAGCTCGAATGAAATGATT 58.226 39.130 7.83 0.00 0.00 2.57
3626 4039 5.188434 TCTGGAGCTCGAATGAAATGATTT 58.812 37.500 7.83 0.00 0.00 2.17
3627 4040 5.649395 TCTGGAGCTCGAATGAAATGATTTT 59.351 36.000 7.83 0.00 0.00 1.82
3628 4041 5.883661 TGGAGCTCGAATGAAATGATTTTC 58.116 37.500 7.83 0.00 41.39 2.29
3629 4042 5.649395 TGGAGCTCGAATGAAATGATTTTCT 59.351 36.000 7.83 0.00 41.54 2.52
3630 4043 5.970023 GGAGCTCGAATGAAATGATTTTCTG 59.030 40.000 7.83 0.00 41.54 3.02
3631 4044 5.338365 AGCTCGAATGAAATGATTTTCTGC 58.662 37.500 0.00 0.00 41.54 4.26
3632 4045 5.097529 GCTCGAATGAAATGATTTTCTGCA 58.902 37.500 0.00 0.00 41.54 4.41
3633 4046 5.574055 GCTCGAATGAAATGATTTTCTGCAA 59.426 36.000 0.00 0.00 41.54 4.08
3634 4047 6.453396 GCTCGAATGAAATGATTTTCTGCAAC 60.453 38.462 0.00 0.00 41.54 4.17
3635 4048 6.445475 TCGAATGAAATGATTTTCTGCAACA 58.555 32.000 0.00 0.00 41.54 3.33
3636 4049 6.583427 TCGAATGAAATGATTTTCTGCAACAG 59.417 34.615 0.00 0.00 41.54 3.16
3637 4050 6.476243 AATGAAATGATTTTCTGCAACAGC 57.524 33.333 0.00 0.00 41.54 4.40
3638 4051 4.946445 TGAAATGATTTTCTGCAACAGCA 58.054 34.783 0.00 0.00 41.54 4.41
3639 4052 5.543714 TGAAATGATTTTCTGCAACAGCAT 58.456 33.333 0.00 0.00 41.54 3.79
3640 4053 5.407084 TGAAATGATTTTCTGCAACAGCATG 59.593 36.000 0.00 0.00 41.54 4.06
3641 4054 4.794278 ATGATTTTCTGCAACAGCATGA 57.206 36.364 0.00 0.00 39.69 3.07
3642 4055 4.587584 TGATTTTCTGCAACAGCATGAA 57.412 36.364 0.00 0.00 39.69 2.57
3643 4056 5.142061 TGATTTTCTGCAACAGCATGAAT 57.858 34.783 0.00 0.00 39.69 2.57
3644 4057 6.270156 TGATTTTCTGCAACAGCATGAATA 57.730 33.333 0.00 0.00 39.69 1.75
3645 4058 6.327154 TGATTTTCTGCAACAGCATGAATAG 58.673 36.000 0.00 0.00 39.69 1.73
3646 4059 5.710513 TTTTCTGCAACAGCATGAATAGT 57.289 34.783 0.00 0.00 39.69 2.12
3647 4060 5.710513 TTTCTGCAACAGCATGAATAGTT 57.289 34.783 0.00 0.00 39.69 2.24
3648 4061 6.816134 TTTCTGCAACAGCATGAATAGTTA 57.184 33.333 0.00 0.00 39.69 2.24
3649 4062 5.801350 TCTGCAACAGCATGAATAGTTAC 57.199 39.130 0.00 0.00 39.69 2.50
3650 4063 5.491070 TCTGCAACAGCATGAATAGTTACT 58.509 37.500 0.00 0.00 39.69 2.24
3651 4064 5.582269 TCTGCAACAGCATGAATAGTTACTC 59.418 40.000 0.00 0.00 39.69 2.59
3652 4065 5.491070 TGCAACAGCATGAATAGTTACTCT 58.509 37.500 0.00 0.00 39.69 3.24
3653 4066 5.939883 TGCAACAGCATGAATAGTTACTCTT 59.060 36.000 0.00 0.00 39.69 2.85
3654 4067 6.430925 TGCAACAGCATGAATAGTTACTCTTT 59.569 34.615 0.00 0.00 39.69 2.52
3655 4068 6.744537 GCAACAGCATGAATAGTTACTCTTTG 59.255 38.462 0.00 0.00 39.69 2.77
3656 4069 7.573843 GCAACAGCATGAATAGTTACTCTTTGT 60.574 37.037 0.00 0.00 39.69 2.83
3657 4070 8.935844 CAACAGCATGAATAGTTACTCTTTGTA 58.064 33.333 0.00 0.00 39.69 2.41
3658 4071 9.672673 AACAGCATGAATAGTTACTCTTTGTAT 57.327 29.630 0.00 0.00 39.69 2.29
3659 4072 9.319143 ACAGCATGAATAGTTACTCTTTGTATC 57.681 33.333 0.00 0.00 39.69 2.24
3660 4073 9.317936 CAGCATGAATAGTTACTCTTTGTATCA 57.682 33.333 0.00 0.00 39.69 2.15
3670 4083 9.319143 AGTTACTCTTTGTATCATATCAGCAAC 57.681 33.333 0.00 0.00 0.00 4.17
3671 4084 9.098355 GTTACTCTTTGTATCATATCAGCAACA 57.902 33.333 0.00 0.00 0.00 3.33
3672 4085 7.783090 ACTCTTTGTATCATATCAGCAACAG 57.217 36.000 0.00 0.00 0.00 3.16
3673 4086 7.559486 ACTCTTTGTATCATATCAGCAACAGA 58.441 34.615 0.00 0.00 0.00 3.41
3674 4087 7.710044 ACTCTTTGTATCATATCAGCAACAGAG 59.290 37.037 0.00 0.00 34.49 3.35
3675 4088 7.559486 TCTTTGTATCATATCAGCAACAGAGT 58.441 34.615 0.00 0.00 0.00 3.24
3676 4089 8.695456 TCTTTGTATCATATCAGCAACAGAGTA 58.305 33.333 0.00 0.00 0.00 2.59
3677 4090 8.877808 TTTGTATCATATCAGCAACAGAGTAG 57.122 34.615 0.00 0.00 0.00 2.57
3678 4091 7.588497 TGTATCATATCAGCAACAGAGTAGT 57.412 36.000 0.00 0.00 0.00 2.73
3679 4092 7.652727 TGTATCATATCAGCAACAGAGTAGTC 58.347 38.462 0.00 0.00 0.00 2.59
3680 4093 6.721704 ATCATATCAGCAACAGAGTAGTCA 57.278 37.500 0.00 0.00 0.00 3.41
3681 4094 6.530019 TCATATCAGCAACAGAGTAGTCAA 57.470 37.500 0.00 0.00 0.00 3.18
3682 4095 6.567959 TCATATCAGCAACAGAGTAGTCAAG 58.432 40.000 0.00 0.00 0.00 3.02
3683 4096 4.881019 ATCAGCAACAGAGTAGTCAAGT 57.119 40.909 0.00 0.00 0.00 3.16
3684 4097 4.672587 TCAGCAACAGAGTAGTCAAGTT 57.327 40.909 0.00 1.71 0.00 2.66
3685 4098 4.371786 TCAGCAACAGAGTAGTCAAGTTG 58.628 43.478 22.01 22.01 40.87 3.16
3686 4099 4.122776 CAGCAACAGAGTAGTCAAGTTGT 58.877 43.478 24.62 15.16 40.43 3.32
3687 4100 4.025396 CAGCAACAGAGTAGTCAAGTTGTG 60.025 45.833 24.62 19.64 40.43 3.33
3688 4101 4.119862 GCAACAGAGTAGTCAAGTTGTGA 58.880 43.478 24.62 0.00 40.43 3.58
3689 4102 4.210120 GCAACAGAGTAGTCAAGTTGTGAG 59.790 45.833 24.62 9.97 40.43 3.51
3690 4103 5.592054 CAACAGAGTAGTCAAGTTGTGAGA 58.408 41.667 19.72 0.00 36.74 3.27
3691 4104 5.854010 ACAGAGTAGTCAAGTTGTGAGAA 57.146 39.130 2.11 0.00 36.74 2.87
3692 4105 6.222038 ACAGAGTAGTCAAGTTGTGAGAAA 57.778 37.500 2.11 0.00 36.74 2.52
3693 4106 6.043411 ACAGAGTAGTCAAGTTGTGAGAAAC 58.957 40.000 2.11 0.00 36.74 2.78
3694 4107 6.042777 CAGAGTAGTCAAGTTGTGAGAAACA 58.957 40.000 2.11 0.00 36.74 2.83
3695 4108 6.703607 CAGAGTAGTCAAGTTGTGAGAAACAT 59.296 38.462 2.11 0.00 38.99 2.71
3696 4109 7.225538 CAGAGTAGTCAAGTTGTGAGAAACATT 59.774 37.037 2.11 0.00 38.99 2.71
3697 4110 7.770897 AGAGTAGTCAAGTTGTGAGAAACATTT 59.229 33.333 2.11 0.00 38.99 2.32
3698 4111 7.697691 AGTAGTCAAGTTGTGAGAAACATTTG 58.302 34.615 2.11 0.00 38.99 2.32
3699 4112 6.757897 AGTCAAGTTGTGAGAAACATTTGA 57.242 33.333 2.11 0.00 38.97 2.69
3700 4113 7.156876 AGTCAAGTTGTGAGAAACATTTGAA 57.843 32.000 2.11 0.00 41.00 2.69
3701 4114 7.775120 AGTCAAGTTGTGAGAAACATTTGAAT 58.225 30.769 2.11 4.81 41.00 2.57
3702 4115 8.253113 AGTCAAGTTGTGAGAAACATTTGAATT 58.747 29.630 2.11 0.00 41.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 42 2.415512 GAGTGGACCGTATTTTCACAGC 59.584 50.000 0.00 0.00 0.00 4.40
47 49 1.207329 GAGGCAGAGTGGACCGTATTT 59.793 52.381 0.00 0.00 0.00 1.40
121 124 2.202756 GGACGGCTAGTGCGGAAG 60.203 66.667 0.00 0.00 41.29 3.46
131 134 2.997897 GGTCTCAGGTGGACGGCT 60.998 66.667 0.00 0.00 34.82 5.52
136 139 2.283676 GTCCGGGTCTCAGGTGGA 60.284 66.667 0.00 0.00 0.00 4.02
142 145 2.603473 CCACTGGTCCGGGTCTCA 60.603 66.667 0.00 0.00 0.00 3.27
143 146 4.083862 GCCACTGGTCCGGGTCTC 62.084 72.222 0.00 0.00 0.00 3.36
227 230 3.478274 CCTGGGGAGGAGCAGAGC 61.478 72.222 0.00 0.00 0.00 4.09
243 246 0.540923 AGCAGAAGCAGAGTGGATCC 59.459 55.000 4.20 4.20 45.49 3.36
309 315 3.422343 CGAGATTTCTTGACGCACTTGTC 60.422 47.826 0.00 0.00 39.37 3.18
315 321 0.037326 AGCCGAGATTTCTTGACGCA 60.037 50.000 0.00 0.00 0.00 5.24
362 368 1.144936 GGTCAGGAATGAGAGCCGG 59.855 63.158 0.00 0.00 0.00 6.13
363 369 1.144936 GGGTCAGGAATGAGAGCCG 59.855 63.158 0.00 0.00 41.89 5.52
371 377 0.976073 ATGGTCGTCGGGTCAGGAAT 60.976 55.000 0.00 0.00 0.00 3.01
442 448 8.929487 AGACATGGAAAAGGGTAAAAATGTTTA 58.071 29.630 0.00 0.00 0.00 2.01
511 738 1.666872 GACCAGGTGAAACGACCGG 60.667 63.158 0.00 0.00 41.35 5.28
555 782 4.285807 TCTGTGTTTGGTCGTTTCATTG 57.714 40.909 0.00 0.00 0.00 2.82
576 803 2.670148 CCTGGACTAAGGCGGCCTT 61.670 63.158 34.37 34.37 46.63 4.35
583 810 2.289694 CGAATATGGGCCTGGACTAAGG 60.290 54.545 4.53 0.00 40.63 2.69
584 811 2.368875 ACGAATATGGGCCTGGACTAAG 59.631 50.000 4.53 0.00 0.00 2.18
585 812 2.404559 ACGAATATGGGCCTGGACTAA 58.595 47.619 4.53 0.00 0.00 2.24
586 813 2.097110 ACGAATATGGGCCTGGACTA 57.903 50.000 4.53 0.00 0.00 2.59
592 897 0.814010 GCGACAACGAATATGGGCCT 60.814 55.000 4.53 0.00 42.66 5.19
593 898 0.814010 AGCGACAACGAATATGGGCC 60.814 55.000 0.00 0.00 42.66 5.80
603 908 4.383774 TGAAAAACTATCAGCGACAACG 57.616 40.909 0.00 0.00 42.93 4.10
652 962 2.539274 GCAATGCGCAGTTTTCTCAAAA 59.461 40.909 18.32 0.00 41.79 2.44
668 978 6.470235 GGATGTACTTTCAGAAATTCGCAATG 59.530 38.462 0.00 0.00 0.00 2.82
696 1007 4.862574 GGACGTAAAAGGGAAATGCAAATC 59.137 41.667 0.00 0.00 0.00 2.17
715 1026 8.504005 ACTTCAATCTTTAATTTGTACTGGACG 58.496 33.333 0.00 0.00 0.00 4.79
790 1102 7.589574 AGCGTAAACTCAAAAACAACAAAAT 57.410 28.000 0.00 0.00 0.00 1.82
794 1106 4.324936 GCAAGCGTAAACTCAAAAACAACA 59.675 37.500 0.00 0.00 0.00 3.33
795 1107 4.324936 TGCAAGCGTAAACTCAAAAACAAC 59.675 37.500 0.00 0.00 0.00 3.32
806 1119 7.054998 GTCATTTTAGTTTTGCAAGCGTAAAC 58.945 34.615 0.00 12.03 33.16 2.01
864 1186 8.802267 AGCAAGAATCCTTCTCAGTAGTATATC 58.198 37.037 0.00 0.00 39.61 1.63
867 1189 7.782644 AGTAGCAAGAATCCTTCTCAGTAGTAT 59.217 37.037 0.00 0.00 39.61 2.12
874 1196 6.533730 TGAAAAGTAGCAAGAATCCTTCTCA 58.466 36.000 0.00 0.00 39.61 3.27
980 1303 4.339530 CCATCTAGATTTCCAGTGTCTCGA 59.660 45.833 1.33 0.00 0.00 4.04
989 1312 5.726560 TGATACTCCCCATCTAGATTTCCA 58.273 41.667 1.33 0.00 0.00 3.53
1026 1349 0.038166 GCACCTGGATTTCCCACTCA 59.962 55.000 0.00 0.00 40.82 3.41
1109 1432 3.045601 ACCTGAGAAACGAGTTGATGG 57.954 47.619 0.00 0.00 0.00 3.51
1137 1460 1.065854 GCGCCCAGATAAGCTATCCAT 60.066 52.381 0.00 0.00 35.79 3.41
1263 1586 2.234908 GAGAGCAGTAATGGTGTCCTGT 59.765 50.000 8.18 0.00 0.00 4.00
1371 1694 0.869068 CCACGCCGTGTTTGTCAATA 59.131 50.000 16.99 0.00 0.00 1.90
1629 1952 3.161866 GCTTGGGGTTTCTTGGATAACA 58.838 45.455 0.00 0.00 0.00 2.41
1698 2021 4.402793 AGCACACAGGACTTAGTATACAGG 59.597 45.833 5.50 0.00 0.00 4.00
1992 2315 6.773638 TGAATTTAGATATGGCTTCCTCTCC 58.226 40.000 0.00 0.00 0.00 3.71
2077 2400 1.080093 TGGTCATTGCTCGTCGACC 60.080 57.895 10.58 0.00 46.69 4.79
2117 2440 3.020984 TCCTCTTTGACACCAACCAAAC 58.979 45.455 0.00 0.00 30.88 2.93
2199 2522 3.554129 CCTTCACAACACACTCCATCGTA 60.554 47.826 0.00 0.00 0.00 3.43
2244 2567 0.250081 GCCGGGGATCTCTGTTGATC 60.250 60.000 2.18 0.00 41.39 2.92
2334 2657 5.355071 TGCCTCTGTGATAAAATGCACTAAG 59.645 40.000 0.00 0.00 36.05 2.18
2415 2738 0.524862 CCACCAAGACAATGCAGCTC 59.475 55.000 0.00 0.00 0.00 4.09
2423 2746 3.556213 CCGACATACTTCCACCAAGACAA 60.556 47.826 0.00 0.00 35.82 3.18
2478 2801 1.746615 CAGCATCGAAGGGTGGGTG 60.747 63.158 10.72 0.11 0.00 4.61
2494 2817 2.789917 GCTGTCATTGAGCGGCAG 59.210 61.111 1.45 6.46 37.00 4.85
2700 3023 2.158295 GGTGATAAGCTCCCCTCCTCTA 60.158 54.545 0.00 0.00 0.00 2.43
2912 3235 2.483876 CAGACGCAAACAGAAGAGGAA 58.516 47.619 0.00 0.00 0.00 3.36
2947 3270 9.609346 ACTGTATAAACTTCAGTACTGTTTTGT 57.391 29.630 21.99 17.82 40.06 2.83
3018 3341 6.012658 TCAGTTTTGAAGTGATGCCATTAC 57.987 37.500 0.00 0.00 35.98 1.89
3122 3530 7.154435 TCAGTTAGTACAGTAACAGCTAAGG 57.846 40.000 9.11 0.00 35.65 2.69
3167 3575 0.184692 TGTTCTGCCCACATGGACAA 59.815 50.000 0.00 0.00 37.39 3.18
3222 3632 8.382030 TGCTCCATACAAATATGTTATGACTG 57.618 34.615 0.00 0.00 41.05 3.51
3316 3726 5.123979 GTGGGTTATAAACTTTGAGCCTGAG 59.876 44.000 0.00 0.00 0.00 3.35
3360 3770 4.700268 TTTGGGATCATTTCACACATCG 57.300 40.909 0.00 0.00 37.53 3.84
3388 3798 4.613622 CGCTATTTGGAAAGAACAGTGGTG 60.614 45.833 0.00 0.00 0.00 4.17
3472 3885 2.420722 TCGTTCTTGAACCAAACACACC 59.579 45.455 7.78 0.00 0.00 4.16
3475 3888 4.095610 CACTTCGTTCTTGAACCAAACAC 58.904 43.478 7.78 0.00 0.00 3.32
3476 3889 3.127895 CCACTTCGTTCTTGAACCAAACA 59.872 43.478 7.78 0.00 0.00 2.83
3477 3890 3.375922 TCCACTTCGTTCTTGAACCAAAC 59.624 43.478 7.78 0.00 0.00 2.93
3478 3891 3.611970 TCCACTTCGTTCTTGAACCAAA 58.388 40.909 7.78 2.85 0.00 3.28
3479 3892 3.269538 TCCACTTCGTTCTTGAACCAA 57.730 42.857 7.78 1.30 0.00 3.67
3480 3893 2.940410 GTTCCACTTCGTTCTTGAACCA 59.060 45.455 7.78 0.00 0.00 3.67
3481 3894 2.033151 CGTTCCACTTCGTTCTTGAACC 60.033 50.000 7.78 0.00 30.88 3.62
3482 3895 2.033151 CCGTTCCACTTCGTTCTTGAAC 60.033 50.000 3.60 3.60 0.00 3.18
3483 3896 2.159071 TCCGTTCCACTTCGTTCTTGAA 60.159 45.455 0.00 0.00 0.00 2.69
3484 3897 1.409790 TCCGTTCCACTTCGTTCTTGA 59.590 47.619 0.00 0.00 0.00 3.02
3485 3898 1.860676 TCCGTTCCACTTCGTTCTTG 58.139 50.000 0.00 0.00 0.00 3.02
3486 3899 2.607631 TTCCGTTCCACTTCGTTCTT 57.392 45.000 0.00 0.00 0.00 2.52
3487 3900 2.224209 ACATTCCGTTCCACTTCGTTCT 60.224 45.455 0.00 0.00 0.00 3.01
3488 3901 2.140717 ACATTCCGTTCCACTTCGTTC 58.859 47.619 0.00 0.00 0.00 3.95
3489 3902 2.140717 GACATTCCGTTCCACTTCGTT 58.859 47.619 0.00 0.00 0.00 3.85
3490 3903 1.069513 TGACATTCCGTTCCACTTCGT 59.930 47.619 0.00 0.00 0.00 3.85
3491 3904 1.790755 TGACATTCCGTTCCACTTCG 58.209 50.000 0.00 0.00 0.00 3.79
3492 3905 2.420022 CCATGACATTCCGTTCCACTTC 59.580 50.000 0.00 0.00 0.00 3.01
3493 3906 2.224769 ACCATGACATTCCGTTCCACTT 60.225 45.455 0.00 0.00 0.00 3.16
3494 3907 1.351017 ACCATGACATTCCGTTCCACT 59.649 47.619 0.00 0.00 0.00 4.00
3495 3908 1.821216 ACCATGACATTCCGTTCCAC 58.179 50.000 0.00 0.00 0.00 4.02
3496 3909 2.224646 TGAACCATGACATTCCGTTCCA 60.225 45.455 13.42 4.12 33.48 3.53
3497 3910 2.432444 TGAACCATGACATTCCGTTCC 58.568 47.619 13.42 2.37 33.48 3.62
3498 3911 4.662145 GAATGAACCATGACATTCCGTTC 58.338 43.478 19.62 12.48 43.45 3.95
3499 3912 4.701956 GAATGAACCATGACATTCCGTT 57.298 40.909 19.62 5.36 43.45 4.44
3503 3916 3.181497 CCGTGGAATGAACCATGACATTC 60.181 47.826 20.95 20.95 46.43 2.67
3504 3917 2.754552 CCGTGGAATGAACCATGACATT 59.245 45.455 8.30 10.73 46.43 2.71
3505 3918 2.026356 TCCGTGGAATGAACCATGACAT 60.026 45.455 8.30 0.00 46.43 3.06
3506 3919 1.349357 TCCGTGGAATGAACCATGACA 59.651 47.619 8.30 0.00 46.43 3.58
3507 3920 2.107950 TCCGTGGAATGAACCATGAC 57.892 50.000 8.30 0.00 46.43 3.06
3508 3921 2.869101 TTCCGTGGAATGAACCATGA 57.131 45.000 8.30 0.00 46.43 3.07
3509 3922 3.429272 CCATTTCCGTGGAATGAACCATG 60.429 47.826 1.47 2.38 42.02 3.66
3510 3923 2.760092 CCATTTCCGTGGAATGAACCAT 59.240 45.455 1.47 0.00 42.02 3.55
3511 3924 2.166829 CCATTTCCGTGGAATGAACCA 58.833 47.619 1.47 0.00 42.02 3.67
3512 3925 1.476488 CCCATTTCCGTGGAATGAACC 59.524 52.381 1.47 0.00 42.02 3.62
3513 3926 2.167662 ACCCATTTCCGTGGAATGAAC 58.832 47.619 1.47 0.00 42.02 3.18
3514 3927 2.560542 CAACCCATTTCCGTGGAATGAA 59.439 45.455 1.47 0.00 42.02 2.57
3515 3928 2.166829 CAACCCATTTCCGTGGAATGA 58.833 47.619 1.47 0.00 42.02 2.57
3516 3929 1.204467 CCAACCCATTTCCGTGGAATG 59.796 52.381 1.47 3.61 42.02 2.67
3517 3930 1.203125 ACCAACCCATTTCCGTGGAAT 60.203 47.619 1.47 0.00 42.02 3.01
3518 3931 0.186386 ACCAACCCATTTCCGTGGAA 59.814 50.000 0.00 0.00 42.02 3.53
3519 3932 0.186386 AACCAACCCATTTCCGTGGA 59.814 50.000 0.00 0.00 42.02 4.02
3520 3933 0.601057 GAACCAACCCATTTCCGTGG 59.399 55.000 0.00 0.00 39.05 4.94
3521 3934 0.601057 GGAACCAACCCATTTCCGTG 59.399 55.000 0.00 0.00 29.89 4.94
3522 3935 3.045518 GGAACCAACCCATTTCCGT 57.954 52.632 0.00 0.00 29.89 4.69
3524 3937 1.271379 GAACGGAACCAACCCATTTCC 59.729 52.381 0.00 0.00 36.24 3.13
3525 3938 1.271379 GGAACGGAACCAACCCATTTC 59.729 52.381 0.00 0.00 0.00 2.17
3526 3939 1.133294 AGGAACGGAACCAACCCATTT 60.133 47.619 0.00 0.00 0.00 2.32
3527 3940 0.481128 AGGAACGGAACCAACCCATT 59.519 50.000 0.00 0.00 0.00 3.16
3528 3941 1.364269 TAGGAACGGAACCAACCCAT 58.636 50.000 0.00 0.00 0.00 4.00
3529 3942 1.003812 CATAGGAACGGAACCAACCCA 59.996 52.381 0.00 0.00 0.00 4.51
3530 3943 1.003928 ACATAGGAACGGAACCAACCC 59.996 52.381 0.00 0.00 0.00 4.11
3531 3944 2.484742 ACATAGGAACGGAACCAACC 57.515 50.000 0.00 0.00 0.00 3.77
3532 3945 3.057806 CCAAACATAGGAACGGAACCAAC 60.058 47.826 0.00 0.00 0.00 3.77
3533 3946 3.150767 CCAAACATAGGAACGGAACCAA 58.849 45.455 0.00 0.00 0.00 3.67
3534 3947 2.106857 ACCAAACATAGGAACGGAACCA 59.893 45.455 0.00 0.00 0.00 3.67
3535 3948 2.786777 ACCAAACATAGGAACGGAACC 58.213 47.619 0.00 0.00 0.00 3.62
3536 3949 5.644636 TCATAACCAAACATAGGAACGGAAC 59.355 40.000 0.00 0.00 0.00 3.62
3537 3950 5.806818 TCATAACCAAACATAGGAACGGAA 58.193 37.500 0.00 0.00 0.00 4.30
3538 3951 5.046159 ACTCATAACCAAACATAGGAACGGA 60.046 40.000 0.00 0.00 0.00 4.69
3539 3952 5.183228 ACTCATAACCAAACATAGGAACGG 58.817 41.667 0.00 0.00 0.00 4.44
3540 3953 8.433421 AATACTCATAACCAAACATAGGAACG 57.567 34.615 0.00 0.00 0.00 3.95
3547 3960 9.784531 CCATCTCTAATACTCATAACCAAACAT 57.215 33.333 0.00 0.00 0.00 2.71
3548 3961 8.988060 TCCATCTCTAATACTCATAACCAAACA 58.012 33.333 0.00 0.00 0.00 2.83
3549 3962 9.832445 TTCCATCTCTAATACTCATAACCAAAC 57.168 33.333 0.00 0.00 0.00 2.93
3552 3965 8.597167 CCATTCCATCTCTAATACTCATAACCA 58.403 37.037 0.00 0.00 0.00 3.67
3553 3966 8.816894 TCCATTCCATCTCTAATACTCATAACC 58.183 37.037 0.00 0.00 0.00 2.85
3557 3970 8.327271 CCATTCCATTCCATCTCTAATACTCAT 58.673 37.037 0.00 0.00 0.00 2.90
3558 3971 7.293299 ACCATTCCATTCCATCTCTAATACTCA 59.707 37.037 0.00 0.00 0.00 3.41
3559 3972 7.684529 ACCATTCCATTCCATCTCTAATACTC 58.315 38.462 0.00 0.00 0.00 2.59
3560 3973 7.639062 ACCATTCCATTCCATCTCTAATACT 57.361 36.000 0.00 0.00 0.00 2.12
3561 3974 9.220767 GTAACCATTCCATTCCATCTCTAATAC 57.779 37.037 0.00 0.00 0.00 1.89
3562 3975 8.094548 CGTAACCATTCCATTCCATCTCTAATA 58.905 37.037 0.00 0.00 0.00 0.98
3563 3976 6.936900 CGTAACCATTCCATTCCATCTCTAAT 59.063 38.462 0.00 0.00 0.00 1.73
3564 3977 6.126883 ACGTAACCATTCCATTCCATCTCTAA 60.127 38.462 0.00 0.00 0.00 2.10
3565 3978 5.365605 ACGTAACCATTCCATTCCATCTCTA 59.634 40.000 0.00 0.00 0.00 2.43
3566 3979 4.164221 ACGTAACCATTCCATTCCATCTCT 59.836 41.667 0.00 0.00 0.00 3.10
3567 3980 4.451900 ACGTAACCATTCCATTCCATCTC 58.548 43.478 0.00 0.00 0.00 2.75
3568 3981 4.503714 ACGTAACCATTCCATTCCATCT 57.496 40.909 0.00 0.00 0.00 2.90
3569 3982 4.881850 AGAACGTAACCATTCCATTCCATC 59.118 41.667 0.00 0.00 0.00 3.51
3570 3983 4.855340 AGAACGTAACCATTCCATTCCAT 58.145 39.130 0.00 0.00 0.00 3.41
3571 3984 4.295141 AGAACGTAACCATTCCATTCCA 57.705 40.909 0.00 0.00 0.00 3.53
3572 3985 5.293569 CACTAGAACGTAACCATTCCATTCC 59.706 44.000 0.00 0.00 0.00 3.01
3573 3986 5.873164 ACACTAGAACGTAACCATTCCATTC 59.127 40.000 0.00 0.00 0.00 2.67
3574 3987 5.801380 ACACTAGAACGTAACCATTCCATT 58.199 37.500 0.00 0.00 0.00 3.16
3575 3988 5.416271 ACACTAGAACGTAACCATTCCAT 57.584 39.130 0.00 0.00 0.00 3.41
3576 3989 4.877378 ACACTAGAACGTAACCATTCCA 57.123 40.909 0.00 0.00 0.00 3.53
3577 3990 5.106830 CCAAACACTAGAACGTAACCATTCC 60.107 44.000 0.00 0.00 0.00 3.01
3578 3991 5.467735 ACCAAACACTAGAACGTAACCATTC 59.532 40.000 0.00 0.00 0.00 2.67
3579 3992 5.370679 ACCAAACACTAGAACGTAACCATT 58.629 37.500 0.00 0.00 0.00 3.16
3580 3993 4.964593 ACCAAACACTAGAACGTAACCAT 58.035 39.130 0.00 0.00 0.00 3.55
3581 3994 4.405116 ACCAAACACTAGAACGTAACCA 57.595 40.909 0.00 0.00 0.00 3.67
3582 3995 5.050567 CAGAACCAAACACTAGAACGTAACC 60.051 44.000 0.00 0.00 0.00 2.85
3583 3996 5.050567 CCAGAACCAAACACTAGAACGTAAC 60.051 44.000 0.00 0.00 0.00 2.50
3584 3997 5.051816 CCAGAACCAAACACTAGAACGTAA 58.948 41.667 0.00 0.00 0.00 3.18
3585 3998 4.341806 TCCAGAACCAAACACTAGAACGTA 59.658 41.667 0.00 0.00 0.00 3.57
3586 3999 3.133362 TCCAGAACCAAACACTAGAACGT 59.867 43.478 0.00 0.00 0.00 3.99
3587 4000 3.724374 TCCAGAACCAAACACTAGAACG 58.276 45.455 0.00 0.00 0.00 3.95
3588 4001 3.498777 GCTCCAGAACCAAACACTAGAAC 59.501 47.826 0.00 0.00 0.00 3.01
3589 4002 3.391296 AGCTCCAGAACCAAACACTAGAA 59.609 43.478 0.00 0.00 0.00 2.10
3590 4003 2.972713 AGCTCCAGAACCAAACACTAGA 59.027 45.455 0.00 0.00 0.00 2.43
3591 4004 3.330267 GAGCTCCAGAACCAAACACTAG 58.670 50.000 0.87 0.00 0.00 2.57
3592 4005 2.288825 CGAGCTCCAGAACCAAACACTA 60.289 50.000 8.47 0.00 0.00 2.74
3593 4006 1.541233 CGAGCTCCAGAACCAAACACT 60.541 52.381 8.47 0.00 0.00 3.55
3594 4007 0.868406 CGAGCTCCAGAACCAAACAC 59.132 55.000 8.47 0.00 0.00 3.32
3595 4008 0.756294 TCGAGCTCCAGAACCAAACA 59.244 50.000 8.47 0.00 0.00 2.83
3596 4009 1.878953 TTCGAGCTCCAGAACCAAAC 58.121 50.000 8.47 0.00 0.00 2.93
3597 4010 2.038426 TCATTCGAGCTCCAGAACCAAA 59.962 45.455 8.47 0.00 0.00 3.28
3598 4011 1.623311 TCATTCGAGCTCCAGAACCAA 59.377 47.619 8.47 0.00 0.00 3.67
3599 4012 1.266178 TCATTCGAGCTCCAGAACCA 58.734 50.000 8.47 0.00 0.00 3.67
3600 4013 2.386661 TTCATTCGAGCTCCAGAACC 57.613 50.000 8.47 0.00 0.00 3.62
3601 4014 3.935203 TCATTTCATTCGAGCTCCAGAAC 59.065 43.478 8.47 0.00 0.00 3.01
3602 4015 4.206477 TCATTTCATTCGAGCTCCAGAA 57.794 40.909 8.47 7.34 0.00 3.02
3603 4016 3.893326 TCATTTCATTCGAGCTCCAGA 57.107 42.857 8.47 0.00 0.00 3.86
3604 4017 5.496133 AAATCATTTCATTCGAGCTCCAG 57.504 39.130 8.47 0.00 0.00 3.86
3605 4018 5.649395 AGAAAATCATTTCATTCGAGCTCCA 59.351 36.000 8.47 0.00 46.03 3.86
3606 4019 5.970023 CAGAAAATCATTTCATTCGAGCTCC 59.030 40.000 8.47 0.00 46.03 4.70
3607 4020 5.454877 GCAGAAAATCATTTCATTCGAGCTC 59.545 40.000 2.73 2.73 46.03 4.09
3608 4021 5.106038 TGCAGAAAATCATTTCATTCGAGCT 60.106 36.000 4.34 0.00 46.03 4.09
3609 4022 5.097529 TGCAGAAAATCATTTCATTCGAGC 58.902 37.500 4.34 0.00 46.03 5.03
3610 4023 6.583427 TGTTGCAGAAAATCATTTCATTCGAG 59.417 34.615 4.34 0.00 46.03 4.04
3611 4024 6.445475 TGTTGCAGAAAATCATTTCATTCGA 58.555 32.000 4.34 0.00 46.03 3.71
3612 4025 6.669032 GCTGTTGCAGAAAATCATTTCATTCG 60.669 38.462 0.00 0.00 46.03 3.34
3613 4026 6.146510 TGCTGTTGCAGAAAATCATTTCATTC 59.853 34.615 0.00 0.00 45.31 2.67
3614 4027 5.992829 TGCTGTTGCAGAAAATCATTTCATT 59.007 32.000 0.00 0.00 45.31 2.57
3615 4028 5.543714 TGCTGTTGCAGAAAATCATTTCAT 58.456 33.333 0.00 0.00 45.31 2.57
3616 4029 4.946445 TGCTGTTGCAGAAAATCATTTCA 58.054 34.783 0.00 0.00 45.31 2.69
3630 4043 6.428385 AAGAGTAACTATTCATGCTGTTGC 57.572 37.500 0.00 0.00 40.20 4.17
3631 4044 7.810658 ACAAAGAGTAACTATTCATGCTGTTG 58.189 34.615 0.00 0.00 0.00 3.33
3632 4045 7.986085 ACAAAGAGTAACTATTCATGCTGTT 57.014 32.000 0.00 0.00 0.00 3.16
3633 4046 9.319143 GATACAAAGAGTAACTATTCATGCTGT 57.681 33.333 0.00 0.00 36.05 4.40
3634 4047 9.317936 TGATACAAAGAGTAACTATTCATGCTG 57.682 33.333 0.00 0.00 36.05 4.41
3644 4057 9.319143 GTTGCTGATATGATACAAAGAGTAACT 57.681 33.333 0.00 0.00 36.05 2.24
3645 4058 9.098355 TGTTGCTGATATGATACAAAGAGTAAC 57.902 33.333 0.00 0.00 36.05 2.50
3646 4059 9.317936 CTGTTGCTGATATGATACAAAGAGTAA 57.682 33.333 0.00 0.00 36.05 2.24
3647 4060 8.695456 TCTGTTGCTGATATGATACAAAGAGTA 58.305 33.333 0.00 0.00 37.06 2.59
3648 4061 7.559486 TCTGTTGCTGATATGATACAAAGAGT 58.441 34.615 0.00 0.00 0.00 3.24
3649 4062 7.710044 ACTCTGTTGCTGATATGATACAAAGAG 59.290 37.037 0.00 0.00 34.86 2.85
3650 4063 7.559486 ACTCTGTTGCTGATATGATACAAAGA 58.441 34.615 0.00 0.00 0.00 2.52
3651 4064 7.783090 ACTCTGTTGCTGATATGATACAAAG 57.217 36.000 0.00 0.00 0.00 2.77
3652 4065 8.478066 ACTACTCTGTTGCTGATATGATACAAA 58.522 33.333 0.00 0.00 0.00 2.83
3653 4066 8.011844 ACTACTCTGTTGCTGATATGATACAA 57.988 34.615 0.00 0.00 0.00 2.41
3654 4067 7.285401 TGACTACTCTGTTGCTGATATGATACA 59.715 37.037 0.00 0.00 0.00 2.29
3655 4068 7.652727 TGACTACTCTGTTGCTGATATGATAC 58.347 38.462 0.00 0.00 0.00 2.24
3656 4069 7.823745 TGACTACTCTGTTGCTGATATGATA 57.176 36.000 0.00 0.00 0.00 2.15
3657 4070 6.721704 TGACTACTCTGTTGCTGATATGAT 57.278 37.500 0.00 0.00 0.00 2.45
3658 4071 6.153510 ACTTGACTACTCTGTTGCTGATATGA 59.846 38.462 0.00 0.00 0.00 2.15
3659 4072 6.336566 ACTTGACTACTCTGTTGCTGATATG 58.663 40.000 0.00 0.00 0.00 1.78
3660 4073 6.537453 ACTTGACTACTCTGTTGCTGATAT 57.463 37.500 0.00 0.00 0.00 1.63
3661 4074 5.984695 ACTTGACTACTCTGTTGCTGATA 57.015 39.130 0.00 0.00 0.00 2.15
3662 4075 4.881019 ACTTGACTACTCTGTTGCTGAT 57.119 40.909 0.00 0.00 0.00 2.90
3663 4076 4.141937 ACAACTTGACTACTCTGTTGCTGA 60.142 41.667 0.00 0.00 40.88 4.26
3664 4077 4.025396 CACAACTTGACTACTCTGTTGCTG 60.025 45.833 0.00 0.00 40.88 4.41
3665 4078 4.122776 CACAACTTGACTACTCTGTTGCT 58.877 43.478 0.00 0.00 40.88 3.91
3666 4079 4.119862 TCACAACTTGACTACTCTGTTGC 58.880 43.478 0.00 0.00 40.88 4.17
3667 4080 5.592054 TCTCACAACTTGACTACTCTGTTG 58.408 41.667 0.00 0.00 42.31 3.33
3668 4081 5.854010 TCTCACAACTTGACTACTCTGTT 57.146 39.130 0.00 0.00 0.00 3.16
3669 4082 5.854010 TTCTCACAACTTGACTACTCTGT 57.146 39.130 0.00 0.00 0.00 3.41
3670 4083 6.042777 TGTTTCTCACAACTTGACTACTCTG 58.957 40.000 0.00 0.00 29.87 3.35
3671 4084 6.222038 TGTTTCTCACAACTTGACTACTCT 57.778 37.500 0.00 0.00 29.87 3.24
3672 4085 7.484035 AATGTTTCTCACAACTTGACTACTC 57.516 36.000 0.00 0.00 39.50 2.59
3673 4086 7.552687 TCAAATGTTTCTCACAACTTGACTACT 59.447 33.333 0.00 0.00 39.50 2.57
3674 4087 7.693952 TCAAATGTTTCTCACAACTTGACTAC 58.306 34.615 0.00 0.00 39.50 2.73
3675 4088 7.857734 TCAAATGTTTCTCACAACTTGACTA 57.142 32.000 0.00 0.00 39.50 2.59
3676 4089 6.757897 TCAAATGTTTCTCACAACTTGACT 57.242 33.333 0.00 0.00 39.50 3.41
3677 4090 7.992180 ATTCAAATGTTTCTCACAACTTGAC 57.008 32.000 0.00 0.00 39.37 3.18


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

AutoCloner maintained by Alex Coulton.