Multiple sequence alignment - TraesCS4A01G047000

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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 TraesCS4A01G047000 chr4A 100.000 5705 0 0 1 5705 38639045 38644749 0.000000e+00 10536
1 TraesCS4A01G047000 chr4B 91.757 2584 108 29 308 2851 523454161 523451643 0.000000e+00 3494
2 TraesCS4A01G047000 chr4B 92.544 1824 70 32 3834 5598 523450601 523448785 0.000000e+00 2555
3 TraesCS4A01G047000 chr4B 89.749 517 46 6 3317 3831 523451156 523450645 0.000000e+00 654
4 TraesCS4A01G047000 chr4B 86.890 328 24 10 1 311 523454713 523454388 3.270000e-92 350
5 TraesCS4A01G047000 chr4B 87.171 304 27 6 3019 3314 523451502 523451203 9.160000e-88 335
6 TraesCS4A01G047000 chr4B 90.991 111 10 0 5595 5705 523448754 523448644 3.560000e-32 150
7 TraesCS4A01G047000 chr4D 90.679 2682 123 54 308 2941 427465304 427462702 0.000000e+00 3450
8 TraesCS4A01G047000 chr4D 91.973 1956 67 37 3834 5705 427461785 427459836 0.000000e+00 2660
9 TraesCS4A01G047000 chr4D 92.085 518 37 4 3317 3834 427462350 427461837 0.000000e+00 726
10 TraesCS4A01G047000 chr4D 86.335 322 32 5 1 311 427465855 427465535 1.970000e-89 340
11 TraesCS4A01G047000 chr3D 91.566 83 6 1 1504 1585 585095114 585095032 4.670000e-21 113


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 TraesCS4A01G047000 chr4A 38639045 38644749 5704 False 10536.000000 10536 100.000000 1 5705 1 chr4A.!!$F1 5704
1 TraesCS4A01G047000 chr4B 523448644 523454713 6069 True 1256.333333 3494 89.850333 1 5705 6 chr4B.!!$R1 5704
2 TraesCS4A01G047000 chr4D 427459836 427465855 6019 True 1794.000000 3450 90.268000 1 5705 4 chr4D.!!$R1 5704

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
869 1143 0.033796 AGATTACCAGACCGTCGGGA 60.034 55.000 22.78 7.4 35.20 5.14 F
2560 2872 0.037790 GAGACCCTGCTCACACTCAC 60.038 60.000 0.00 0.0 35.01 3.51 F
3311 3675 0.036010 AGGAAGGCTGTGAACATCCG 60.036 55.000 0.00 0.0 37.24 4.18 F
3579 3987 1.376037 GGAGGAGGTCAAACTGCGG 60.376 63.158 0.00 0.0 33.63 5.69 F
4328 4788 0.037303 TGCAGGGCTTTCTGAAGGAG 59.963 55.000 3.45 0.0 36.93 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2567 2879 1.299541 CGGCATAAACGGATCAAGCT 58.700 50.0 0.00 0.00 0.00 3.74 R
3666 4074 0.380733 CTCGGTACAGCATAGCGTCA 59.619 55.0 16.14 1.62 39.19 4.35 R
4214 4674 0.448197 TCTCGAGCTTGCTGACGTAG 59.552 55.0 7.81 0.00 0.00 3.51 R
4666 5126 0.842030 TCTGCATCTTCACCACCCCT 60.842 55.0 0.00 0.00 0.00 4.79 R
5393 5920 0.901124 GATCTCCTCACCTGTGCAGT 59.099 55.0 0.00 0.00 0.00 4.40 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
38 39 5.506730 TGGCCCCGATTATATAAACATGA 57.493 39.130 0.00 0.00 0.00 3.07
117 118 2.093764 AGCGGAAGATTTGTCTCTCCAG 60.094 50.000 0.00 0.00 0.00 3.86
128 129 6.364568 TTTGTCTCTCCAGAAGATGATCAA 57.635 37.500 0.00 0.00 32.19 2.57
129 130 6.556974 TTGTCTCTCCAGAAGATGATCAAT 57.443 37.500 0.00 0.00 32.19 2.57
224 233 2.003301 GCTCGAAAGTCAGGGTTCATC 58.997 52.381 0.00 0.00 0.00 2.92
231 240 0.652592 GTCAGGGTTCATCGATTGCG 59.347 55.000 0.00 0.00 39.35 4.85
232 241 1.089481 TCAGGGTTCATCGATTGCGC 61.089 55.000 0.00 0.00 37.46 6.09
236 245 0.582005 GGTTCATCGATTGCGCCTAC 59.418 55.000 4.18 0.00 37.46 3.18
238 252 1.258982 GTTCATCGATTGCGCCTACAG 59.741 52.381 4.18 0.00 37.46 2.74
249 263 1.464997 GCGCCTACAGTTTTGAAGGAG 59.535 52.381 0.00 0.00 32.66 3.69
270 286 6.043243 AGGAGATTCTACCTTTGAAACTCACA 59.957 38.462 13.06 0.00 41.80 3.58
272 288 5.998363 AGATTCTACCTTTGAAACTCACACC 59.002 40.000 0.00 0.00 0.00 4.16
275 291 4.903049 TCTACCTTTGAAACTCACACCCTA 59.097 41.667 0.00 0.00 0.00 3.53
278 294 3.496870 CCTTTGAAACTCACACCCTAGCT 60.497 47.826 0.00 0.00 0.00 3.32
321 573 3.478857 AGGACACCATTGACAACGTTA 57.521 42.857 0.00 0.00 0.00 3.18
322 574 4.015872 AGGACACCATTGACAACGTTAT 57.984 40.909 0.00 0.00 0.00 1.89
323 575 5.155278 AGGACACCATTGACAACGTTATA 57.845 39.130 0.00 0.00 0.00 0.98
324 576 5.741011 AGGACACCATTGACAACGTTATAT 58.259 37.500 0.00 0.00 0.00 0.86
325 577 5.584649 AGGACACCATTGACAACGTTATATG 59.415 40.000 0.00 2.53 0.00 1.78
326 578 5.583061 GGACACCATTGACAACGTTATATGA 59.417 40.000 0.00 0.00 0.00 2.15
330 582 6.912051 CACCATTGACAACGTTATATGAATGG 59.088 38.462 23.71 23.71 42.80 3.16
337 589 7.226523 TGACAACGTTATATGAATGGATCAAGG 59.773 37.037 0.00 0.00 42.54 3.61
341 597 9.793259 AACGTTATATGAATGGATCAAGGTAAT 57.207 29.630 0.00 0.00 42.54 1.89
346 602 6.645790 ATGAATGGATCAAGGTAATGAAGC 57.354 37.500 0.00 0.00 42.54 3.86
361 617 2.936202 TGAAGCCAGTCAAAAGAAGCT 58.064 42.857 0.00 0.00 0.00 3.74
366 622 4.826556 AGCCAGTCAAAAGAAGCTACTAG 58.173 43.478 0.00 0.00 0.00 2.57
368 624 5.480772 AGCCAGTCAAAAGAAGCTACTAGTA 59.519 40.000 1.89 1.89 0.00 1.82
369 625 5.577554 GCCAGTCAAAAGAAGCTACTAGTAC 59.422 44.000 0.00 0.00 0.00 2.73
370 626 6.572703 GCCAGTCAAAAGAAGCTACTAGTACT 60.573 42.308 0.00 0.00 0.00 2.73
373 629 9.909644 CAGTCAAAAGAAGCTACTAGTACTAAA 57.090 33.333 3.76 0.00 0.00 1.85
389 645 2.170770 CTAAATTAAAACGGGTGCGCG 58.829 47.619 0.00 0.00 0.00 6.86
390 646 1.004785 AAATTAAAACGGGTGCGCGC 61.005 50.000 27.26 27.26 0.00 6.86
402 658 3.261951 GCGCGCTCTTAATCGGCA 61.262 61.111 26.67 0.00 0.00 5.69
416 672 3.070576 GGCAAGGCCCACATGGTC 61.071 66.667 0.00 0.00 44.06 4.02
422 678 3.978876 GGCCCACATGGTCTTTACT 57.021 52.632 0.00 0.00 35.10 2.24
423 679 1.751437 GGCCCACATGGTCTTTACTC 58.249 55.000 0.00 0.00 35.10 2.59
478 734 6.770542 TGTACTGTACCACCATTTGTTGATA 58.229 36.000 14.91 0.00 0.00 2.15
479 735 7.398829 TGTACTGTACCACCATTTGTTGATAT 58.601 34.615 14.91 0.00 0.00 1.63
480 736 6.757897 ACTGTACCACCATTTGTTGATATG 57.242 37.500 0.00 0.00 0.00 1.78
611 870 1.069500 CACCAAAACCTCCTAAACGCG 60.069 52.381 3.53 3.53 0.00 6.01
614 873 1.571215 AAAACCTCCTAAACGCGGCG 61.571 55.000 22.36 22.36 0.00 6.46
626 885 3.338676 GCGGCGCGAAATCCCTAG 61.339 66.667 19.09 0.00 0.00 3.02
694 958 4.324641 GGGCAGGAAAAAGAGGTTAGATCT 60.325 45.833 0.00 0.00 0.00 2.75
700 964 8.043710 CAGGAAAAAGAGGTTAGATCTACACAT 58.956 37.037 0.67 2.19 0.00 3.21
702 966 9.232473 GGAAAAAGAGGTTAGATCTACACATTT 57.768 33.333 0.67 2.02 0.00 2.32
705 969 9.574516 AAAAGAGGTTAGATCTACACATTTGTT 57.425 29.630 0.67 0.00 37.15 2.83
746 1020 2.540145 GGAGCGCCGAAGAAAAGAA 58.460 52.632 2.29 0.00 0.00 2.52
747 1021 0.872388 GGAGCGCCGAAGAAAAGAAA 59.128 50.000 2.29 0.00 0.00 2.52
748 1022 1.265905 GGAGCGCCGAAGAAAAGAAAA 59.734 47.619 2.29 0.00 0.00 2.29
749 1023 2.575363 GAGCGCCGAAGAAAAGAAAAG 58.425 47.619 2.29 0.00 0.00 2.27
750 1024 2.218603 AGCGCCGAAGAAAAGAAAAGA 58.781 42.857 2.29 0.00 0.00 2.52
756 1030 5.613577 CGCCGAAGAAAAGAAAAGAGAAGAG 60.614 44.000 0.00 0.00 0.00 2.85
820 1094 4.891727 CAGATTCGGGCCGTCGGG 62.892 72.222 27.32 10.94 0.00 5.14
835 1109 4.217159 GGGGGCGCCACGTAGTAG 62.217 72.222 30.85 0.00 41.61 2.57
836 1110 3.455469 GGGGCGCCACGTAGTAGT 61.455 66.667 30.85 0.00 41.61 2.73
865 1139 2.619646 GAGAGGAGATTACCAGACCGTC 59.380 54.545 0.00 0.00 0.00 4.79
867 1141 0.384669 GGAGATTACCAGACCGTCGG 59.615 60.000 10.48 10.48 0.00 4.79
868 1142 0.384669 GAGATTACCAGACCGTCGGG 59.615 60.000 17.28 15.40 37.75 5.14
869 1143 0.033796 AGATTACCAGACCGTCGGGA 60.034 55.000 22.78 7.40 35.20 5.14
870 1144 0.384669 GATTACCAGACCGTCGGGAG 59.615 60.000 22.78 4.54 35.20 4.30
895 1176 1.300971 ATGGTGGCGATCGCATATGC 61.301 55.000 38.00 22.33 44.11 3.14
949 1240 1.725066 GGCGTCTTCTCTCTCCTCG 59.275 63.158 0.00 0.00 0.00 4.63
950 1241 1.720694 GGCGTCTTCTCTCTCCTCGG 61.721 65.000 0.00 0.00 0.00 4.63
951 1242 1.725066 CGTCTTCTCTCTCCTCGGC 59.275 63.158 0.00 0.00 0.00 5.54
1003 1300 0.818296 TCTCACTCTAGAAAGCGGGC 59.182 55.000 0.00 0.00 0.00 6.13
1041 1338 2.159184 GCTCTGGCTTTGGCTTTTATCC 60.159 50.000 0.00 0.00 38.73 2.59
1052 1349 6.824305 TTGGCTTTTATCCTCTTCTTCTTG 57.176 37.500 0.00 0.00 0.00 3.02
1341 1638 2.585153 GGCGACTTCTTCCCTCCC 59.415 66.667 0.00 0.00 0.00 4.30
1413 1719 4.955774 AACACCGTCACCGCCGAC 62.956 66.667 0.00 0.00 0.00 4.79
2169 2475 2.446994 TCCAACCCACCTCCACGT 60.447 61.111 0.00 0.00 0.00 4.49
2181 2493 3.867783 CCACGTCCACCACCACCA 61.868 66.667 0.00 0.00 0.00 4.17
2238 2550 2.032528 TCCAACGCAGCTCCAAGG 59.967 61.111 0.00 0.00 0.00 3.61
2550 2862 1.003580 TCATTCCAGTTGAGACCCTGC 59.996 52.381 0.00 0.00 0.00 4.85
2552 2864 0.687354 TTCCAGTTGAGACCCTGCTC 59.313 55.000 0.00 0.00 35.46 4.26
2553 2865 0.471780 TCCAGTTGAGACCCTGCTCA 60.472 55.000 0.00 0.00 42.81 4.26
2557 2869 0.394565 GTTGAGACCCTGCTCACACT 59.605 55.000 0.00 0.00 44.08 3.55
2559 2871 0.469892 TGAGACCCTGCTCACACTCA 60.470 55.000 0.00 0.00 39.84 3.41
2560 2872 0.037790 GAGACCCTGCTCACACTCAC 60.038 60.000 0.00 0.00 35.01 3.51
2563 2875 0.767375 ACCCTGCTCACACTCACAAT 59.233 50.000 0.00 0.00 0.00 2.71
2564 2876 1.977854 ACCCTGCTCACACTCACAATA 59.022 47.619 0.00 0.00 0.00 1.90
2565 2877 2.371841 ACCCTGCTCACACTCACAATAA 59.628 45.455 0.00 0.00 0.00 1.40
2566 2878 3.181445 ACCCTGCTCACACTCACAATAAA 60.181 43.478 0.00 0.00 0.00 1.40
2567 2879 3.820467 CCCTGCTCACACTCACAATAAAA 59.180 43.478 0.00 0.00 0.00 1.52
2568 2880 4.083110 CCCTGCTCACACTCACAATAAAAG 60.083 45.833 0.00 0.00 0.00 2.27
2571 2883 4.580167 TGCTCACACTCACAATAAAAGCTT 59.420 37.500 0.00 0.00 0.00 3.74
2572 2884 4.913924 GCTCACACTCACAATAAAAGCTTG 59.086 41.667 0.00 0.00 0.00 4.01
2579 2891 5.473504 ACTCACAATAAAAGCTTGATCCGTT 59.526 36.000 0.00 0.00 0.00 4.44
2841 3153 0.038159 CTCCTGGACGGTGAGTGTTC 60.038 60.000 0.00 0.00 0.00 3.18
2853 3165 1.436195 GAGTGTTCGTGCTGCAACCA 61.436 55.000 2.77 0.00 0.00 3.67
2854 3166 1.009675 GTGTTCGTGCTGCAACCAG 60.010 57.895 2.77 0.00 42.13 4.00
2858 3178 1.713937 TTCGTGCTGCAACCAGTGTG 61.714 55.000 2.77 0.00 41.26 3.82
2881 3234 9.932207 TGTGATAATTTTGAGCTCATTTTTCAT 57.068 25.926 19.04 7.07 0.00 2.57
2885 3238 7.900782 AATTTTGAGCTCATTTTTCATCTGG 57.099 32.000 19.04 0.00 0.00 3.86
2911 3264 3.319755 CATTCGCAAAATTGAACCAGCT 58.680 40.909 0.00 0.00 0.00 4.24
2912 3265 3.451141 TTCGCAAAATTGAACCAGCTT 57.549 38.095 0.00 0.00 0.00 3.74
2913 3266 3.451141 TCGCAAAATTGAACCAGCTTT 57.549 38.095 0.00 0.00 0.00 3.51
2966 3319 9.871238 ACTCTATAAGACGTTTATTGACATTGT 57.129 29.630 0.00 0.00 0.00 2.71
2974 3327 9.871238 AGACGTTTATTGACATTGTAATAGAGT 57.129 29.630 0.00 0.00 0.00 3.24
2976 3329 9.647797 ACGTTTATTGACATTGTAATAGAGTCA 57.352 29.630 0.00 0.00 37.43 3.41
3006 3359 9.470399 AAACAACTTATATTAAGTTACAGGGGG 57.530 33.333 11.23 2.49 38.32 5.40
3007 3360 8.396619 ACAACTTATATTAAGTTACAGGGGGA 57.603 34.615 11.23 0.00 38.32 4.81
3008 3361 8.491958 ACAACTTATATTAAGTTACAGGGGGAG 58.508 37.037 11.23 1.37 38.32 4.30
3009 3362 8.491958 CAACTTATATTAAGTTACAGGGGGAGT 58.508 37.037 11.23 0.00 38.32 3.85
3010 3363 9.733907 AACTTATATTAAGTTACAGGGGGAGTA 57.266 33.333 10.17 0.00 38.58 2.59
3011 3364 9.909365 ACTTATATTAAGTTACAGGGGGAGTAT 57.091 33.333 0.00 0.00 0.00 2.12
3013 3366 9.901651 TTATATTAAGTTACAGGGGGAGTATGA 57.098 33.333 0.00 0.00 0.00 2.15
3014 3367 8.990693 ATATTAAGTTACAGGGGGAGTATGAT 57.009 34.615 0.00 0.00 0.00 2.45
3015 3368 7.707467 ATTAAGTTACAGGGGGAGTATGATT 57.293 36.000 0.00 0.00 0.00 2.57
3016 3369 5.632034 AAGTTACAGGGGGAGTATGATTC 57.368 43.478 0.00 0.00 0.00 2.52
3017 3370 4.897051 AGTTACAGGGGGAGTATGATTCT 58.103 43.478 0.00 0.00 0.00 2.40
3083 3436 8.123639 TGTGATTAGGTATCTAGCATAAGGAC 57.876 38.462 0.00 0.00 34.17 3.85
3084 3437 7.950684 TGTGATTAGGTATCTAGCATAAGGACT 59.049 37.037 0.00 0.00 34.17 3.85
3085 3438 9.463902 GTGATTAGGTATCTAGCATAAGGACTA 57.536 37.037 0.00 0.00 34.17 2.59
3088 3441 8.880991 TTAGGTATCTAGCATAAGGACTAAGG 57.119 38.462 0.00 0.00 0.00 2.69
3089 3442 7.104974 AGGTATCTAGCATAAGGACTAAGGA 57.895 40.000 0.00 0.00 0.00 3.36
3098 3451 5.440610 CATAAGGACTAAGGATGCTTTGGT 58.559 41.667 4.26 4.90 0.00 3.67
3106 3459 1.992557 AGGATGCTTTGGTTGGTAGGA 59.007 47.619 0.00 0.00 0.00 2.94
3107 3460 2.582636 AGGATGCTTTGGTTGGTAGGAT 59.417 45.455 0.00 0.00 0.00 3.24
3134 3491 7.811236 GCTCTTTTCATCTGATTTTGTGATTCA 59.189 33.333 0.00 0.00 0.00 2.57
3135 3492 9.343103 CTCTTTTCATCTGATTTTGTGATTCAG 57.657 33.333 0.00 0.00 37.19 3.02
3149 3506 5.728471 TGTGATTCAGGTTTTGCTTTCAAA 58.272 33.333 0.00 0.00 40.17 2.69
3150 3507 6.347696 TGTGATTCAGGTTTTGCTTTCAAAT 58.652 32.000 0.00 0.00 41.37 2.32
3151 3508 6.258287 TGTGATTCAGGTTTTGCTTTCAAATG 59.742 34.615 0.00 0.00 41.37 2.32
3152 3509 6.479660 GTGATTCAGGTTTTGCTTTCAAATGA 59.520 34.615 0.00 0.00 41.37 2.57
3153 3510 6.702723 TGATTCAGGTTTTGCTTTCAAATGAG 59.297 34.615 0.00 0.00 41.37 2.90
3154 3511 4.947645 TCAGGTTTTGCTTTCAAATGAGG 58.052 39.130 0.00 0.00 41.37 3.86
3156 3513 5.104982 TCAGGTTTTGCTTTCAAATGAGGTT 60.105 36.000 0.00 0.00 41.37 3.50
3157 3514 5.234972 CAGGTTTTGCTTTCAAATGAGGTTC 59.765 40.000 0.00 0.00 41.37 3.62
3158 3515 5.104982 AGGTTTTGCTTTCAAATGAGGTTCA 60.105 36.000 0.00 0.00 41.37 3.18
3159 3516 5.234972 GGTTTTGCTTTCAAATGAGGTTCAG 59.765 40.000 0.00 0.00 41.37 3.02
3160 3517 5.850557 TTTGCTTTCAAATGAGGTTCAGA 57.149 34.783 0.00 0.00 37.28 3.27
3167 3530 5.381174 TCAAATGAGGTTCAGATTTGCAG 57.619 39.130 0.00 0.00 30.50 4.41
3168 3531 3.863142 AATGAGGTTCAGATTTGCAGC 57.137 42.857 0.00 0.00 0.00 5.25
3171 3534 2.430465 GAGGTTCAGATTTGCAGCTCA 58.570 47.619 9.62 0.00 42.28 4.26
3179 3542 4.633126 TCAGATTTGCAGCTCAATAGTGAC 59.367 41.667 0.00 0.00 34.12 3.67
3184 3547 2.275318 GCAGCTCAATAGTGACAGGTC 58.725 52.381 0.00 0.00 0.00 3.85
3185 3548 2.093764 GCAGCTCAATAGTGACAGGTCT 60.094 50.000 0.65 0.00 0.00 3.85
3248 3612 7.038302 ACCTCAACAGAATATACAAGGACTTGA 60.038 37.037 18.15 3.33 42.93 3.02
3261 3625 4.526438 AGGACTTGAAATCAATAGGGGG 57.474 45.455 0.00 0.00 35.02 5.40
3273 3637 2.961062 CAATAGGGGGAGAAAATGGCTG 59.039 50.000 0.00 0.00 0.00 4.85
3299 3663 5.126779 CCAATCCTTTTCTAGTAGGAAGGC 58.873 45.833 20.08 0.00 43.44 4.35
3311 3675 0.036010 AGGAAGGCTGTGAACATCCG 60.036 55.000 0.00 0.00 37.24 4.18
3314 3678 2.045926 GGCTGTGAACATCCGGCT 60.046 61.111 0.00 0.00 33.41 5.52
3321 3729 1.591863 GAACATCCGGCTAGCGTCC 60.592 63.158 9.00 0.00 0.00 4.79
3330 3738 1.730451 GGCTAGCGTCCTCTCACTCC 61.730 65.000 9.00 0.00 0.00 3.85
3346 3754 2.618709 CACTCCACTTCCAAAGTCCAAC 59.381 50.000 0.00 0.00 40.46 3.77
3350 3758 1.681264 CACTTCCAAAGTCCAACACCC 59.319 52.381 0.00 0.00 40.46 4.61
3388 3796 5.765677 TGAATCAAACGTTCACCCTGATTTA 59.234 36.000 20.38 15.76 36.97 1.40
3406 3814 9.580916 CCTGATTTATACACATAATCGTTTTCG 57.419 33.333 0.00 0.00 45.64 3.46
3416 3824 8.007716 ACACATAATCGTTTTCGTACTTTTCAG 58.992 33.333 0.00 0.00 44.46 3.02
3422 3830 4.269363 CGTTTTCGTACTTTTCAGTGGAGT 59.731 41.667 0.00 0.00 38.65 3.85
3465 3873 5.112129 TCTCTGTATAGCAGTGTCCACTA 57.888 43.478 0.00 0.00 45.23 2.74
3534 3942 1.600413 GGCAGTGAGCTTTTGGAAACG 60.600 52.381 0.00 0.00 44.79 3.60
3555 3963 3.187700 GTTAGTCAAGATGGCACCTACG 58.812 50.000 0.00 0.00 0.00 3.51
3576 3984 3.669536 GAAAGAGGAGGAGGTCAAACTG 58.330 50.000 0.00 0.00 0.00 3.16
3579 3987 1.376037 GGAGGAGGTCAAACTGCGG 60.376 63.158 0.00 0.00 33.63 5.69
3595 4003 1.520787 CGGGATTACAGTGGCGACC 60.521 63.158 0.00 0.00 0.00 4.79
3598 4006 1.692519 GGGATTACAGTGGCGACCTAT 59.307 52.381 0.00 0.00 0.00 2.57
3666 4074 3.288092 ACCTTTCGCCTTCAAAAGAGTT 58.712 40.909 0.00 0.00 35.02 3.01
3672 4080 1.604278 GCCTTCAAAAGAGTTGACGCT 59.396 47.619 0.00 0.00 0.00 5.07
3753 4161 5.109903 ACGCTAGAGGTATGCTAGTTTTTG 58.890 41.667 0.00 0.00 38.06 2.44
3788 4196 7.804614 TTGTCATTTTTAATAACGCACATCC 57.195 32.000 0.00 0.00 0.00 3.51
3789 4197 7.151999 TGTCATTTTTAATAACGCACATCCT 57.848 32.000 0.00 0.00 0.00 3.24
3843 4303 5.731957 TTCAGCTACTACACATGTGGTTA 57.268 39.130 28.64 15.15 40.33 2.85
3977 4437 3.735037 GAACCGGGGCGAGGCTAAG 62.735 68.421 6.32 0.00 0.00 2.18
4103 4563 4.287720 ACGCGAAATCTGAAAAGGAAAAC 58.712 39.130 15.93 0.00 0.00 2.43
4214 4674 1.291877 ACTTCGATGTTCTGCACGGC 61.292 55.000 0.00 0.00 0.00 5.68
4232 4692 2.937026 CTACGTCAGCAAGCTCGAG 58.063 57.895 8.45 8.45 0.00 4.04
4277 4737 2.099431 GTTGCAGCTCGAGAGGCAG 61.099 63.158 24.18 7.25 37.59 4.85
4303 4763 0.622665 CAGGGCCAGAGGTTCTTCAT 59.377 55.000 6.18 0.00 0.00 2.57
4307 4767 0.391661 GCCAGAGGTTCTTCATCGCA 60.392 55.000 0.00 0.00 31.60 5.10
4328 4788 0.037303 TGCAGGGCTTTCTGAAGGAG 59.963 55.000 3.45 0.00 36.93 3.69
4556 5016 2.804090 GCGAGGTCGTTCCGTGTC 60.804 66.667 0.69 0.00 42.22 3.67
4571 5031 3.371063 GTCTCGACGACAGCCCCA 61.371 66.667 0.00 0.00 42.37 4.96
4586 5046 1.607612 CCCATTGCCGGTCCTAAGT 59.392 57.895 1.90 0.00 0.00 2.24
4656 5116 2.274760 CGTCGTAGGAGAGGGGGT 59.725 66.667 0.00 0.00 0.00 4.95
4663 5123 4.364686 GGAGAGGGGGTTGGGGGA 62.365 72.222 0.00 0.00 0.00 4.81
4666 5126 4.364686 GAGGGGGTTGGGGGAGGA 62.365 72.222 0.00 0.00 0.00 3.71
4679 5140 1.229529 GGAGGAGGGGTGGTGAAGA 60.230 63.158 0.00 0.00 0.00 2.87
4680 5141 0.621862 GGAGGAGGGGTGGTGAAGAT 60.622 60.000 0.00 0.00 0.00 2.40
4880 5341 4.962155 TGACAAGAAGGTCTTCCTCTTTC 58.038 43.478 7.06 0.00 44.35 2.62
4894 5355 3.136992 TCCTCTTTCCGTTGGGTAGTTTT 59.863 43.478 0.00 0.00 33.83 2.43
4946 5421 1.667724 CTAGCAGCAGTTACACATGGC 59.332 52.381 0.00 0.00 0.00 4.40
4948 5423 1.796151 CAGCAGTTACACATGGCCG 59.204 57.895 0.00 0.00 0.00 6.13
5032 5514 6.152661 TGGAAATAATTTTTCAGATGACCGCT 59.847 34.615 12.21 0.00 0.00 5.52
5063 5545 3.126858 GTCTGCGCAAATAATCAGGAACA 59.873 43.478 13.05 0.00 0.00 3.18
5079 5562 5.303333 TCAGGAACAACCCAAAATTAACCTC 59.697 40.000 0.00 0.00 40.05 3.85
5123 5631 7.777910 TGTAGGTTTCCTCTTTCAAATTTCTCA 59.222 33.333 0.00 0.00 34.61 3.27
5141 5649 0.455633 CATGCGCTTGGAAGAACAGC 60.456 55.000 15.12 0.00 0.00 4.40
5142 5650 0.890542 ATGCGCTTGGAAGAACAGCA 60.891 50.000 9.73 0.00 37.54 4.41
5143 5651 1.208614 GCGCTTGGAAGAACAGCAG 59.791 57.895 0.00 0.00 0.00 4.24
5222 5731 2.061061 CTAGGCCATCCTTCCTTCCAT 58.939 52.381 5.01 0.00 40.66 3.41
5380 5907 2.563798 CCGGCAGCAGGCTTTTTCA 61.564 57.895 0.00 0.00 44.01 2.69
5387 5914 3.427233 GCAGCAGGCTTTTTCATCTGTAG 60.427 47.826 0.00 0.00 40.25 2.74
5388 5915 3.755378 CAGCAGGCTTTTTCATCTGTAGT 59.245 43.478 0.00 0.00 0.00 2.73
5389 5916 4.006319 AGCAGGCTTTTTCATCTGTAGTC 58.994 43.478 0.00 0.00 0.00 2.59
5390 5917 4.006319 GCAGGCTTTTTCATCTGTAGTCT 58.994 43.478 0.00 0.00 0.00 3.24
5391 5918 4.142730 GCAGGCTTTTTCATCTGTAGTCTG 60.143 45.833 0.00 0.00 40.56 3.51
5392 5919 4.999950 CAGGCTTTTTCATCTGTAGTCTGT 59.000 41.667 0.00 0.00 34.68 3.41
5393 5920 6.166279 CAGGCTTTTTCATCTGTAGTCTGTA 58.834 40.000 0.00 0.00 34.68 2.74
5397 5924 6.401581 GCTTTTTCATCTGTAGTCTGTACTGC 60.402 42.308 0.00 0.00 38.69 4.40
5408 5940 3.141409 TGTACTGCACAGGTGAGGA 57.859 52.632 3.10 0.00 31.89 3.71
5469 6001 0.683179 ATAAAGAAAGCACCGGGGGC 60.683 55.000 15.02 15.02 0.00 5.80
5490 6022 3.186613 GCATAACTAGGGCGAAAGTATGC 59.813 47.826 0.00 0.00 31.75 3.14
5633 6203 1.544691 GCATCATCAAGGATGGATGGC 59.455 52.381 6.76 2.56 43.85 4.40
5656 6226 2.853159 TGGTGACGCCATGATTGTC 58.147 52.632 2.83 0.00 43.61 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 6.489603 TCATGTTTATATAATCGGGGCCAAT 58.510 36.000 4.39 0.00 0.00 3.16
57 58 6.056884 TCGACTTTAAGTGGTTGTTGGTAAT 58.943 36.000 0.93 0.00 0.00 1.89
117 118 7.361889 AGATTATGACGCATTGATCATCTTC 57.638 36.000 0.00 6.36 36.87 2.87
128 129 7.333528 ACAATTTGGTTAGATTATGACGCAT 57.666 32.000 0.78 0.00 0.00 4.73
129 130 6.751514 ACAATTTGGTTAGATTATGACGCA 57.248 33.333 0.78 0.00 0.00 5.24
171 173 9.878599 CACCTTTACGATTGAATAATATGTTCC 57.121 33.333 0.00 0.00 0.00 3.62
224 233 1.463056 TCAAAACTGTAGGCGCAATCG 59.537 47.619 10.83 0.00 39.07 3.34
231 240 5.249420 AGAATCTCCTTCAAAACTGTAGGC 58.751 41.667 0.00 0.00 36.24 3.93
232 241 6.819146 GGTAGAATCTCCTTCAAAACTGTAGG 59.181 42.308 0.00 0.00 36.24 3.18
236 245 7.445402 TCAAAGGTAGAATCTCCTTCAAAACTG 59.555 37.037 12.22 7.75 42.38 3.16
238 252 7.745620 TCAAAGGTAGAATCTCCTTCAAAAC 57.254 36.000 12.22 0.00 42.38 2.43
249 263 5.181433 GGGTGTGAGTTTCAAAGGTAGAATC 59.819 44.000 0.00 0.00 0.00 2.52
270 286 6.628644 AAGATGAGAAAACTTAGCTAGGGT 57.371 37.500 7.87 0.00 0.00 4.34
272 288 7.106239 TCCAAAGATGAGAAAACTTAGCTAGG 58.894 38.462 0.48 0.48 0.00 3.02
275 291 7.170965 TGATCCAAAGATGAGAAAACTTAGCT 58.829 34.615 0.00 0.00 30.90 3.32
278 294 8.163408 TCCTTGATCCAAAGATGAGAAAACTTA 58.837 33.333 0.00 0.00 30.90 2.24
321 573 7.395489 GGCTTCATTACCTTGATCCATTCATAT 59.605 37.037 0.00 0.00 33.34 1.78
322 574 6.716628 GGCTTCATTACCTTGATCCATTCATA 59.283 38.462 0.00 0.00 33.34 2.15
323 575 5.537674 GGCTTCATTACCTTGATCCATTCAT 59.462 40.000 0.00 0.00 33.34 2.57
324 576 4.889409 GGCTTCATTACCTTGATCCATTCA 59.111 41.667 0.00 0.00 0.00 2.57
325 577 4.889409 TGGCTTCATTACCTTGATCCATTC 59.111 41.667 0.00 0.00 0.00 2.67
326 578 4.870636 TGGCTTCATTACCTTGATCCATT 58.129 39.130 0.00 0.00 0.00 3.16
330 582 4.517285 TGACTGGCTTCATTACCTTGATC 58.483 43.478 0.00 0.00 0.00 2.92
337 589 5.048434 AGCTTCTTTTGACTGGCTTCATTAC 60.048 40.000 0.00 0.00 0.00 1.89
341 597 2.936202 AGCTTCTTTTGACTGGCTTCA 58.064 42.857 0.00 0.00 0.00 3.02
346 602 6.926313 AGTACTAGTAGCTTCTTTTGACTGG 58.074 40.000 1.87 0.00 0.00 4.00
361 617 7.487829 CGCACCCGTTTTAATTTAGTACTAGTA 59.512 37.037 2.23 0.00 0.00 1.82
366 622 4.090729 GCGCACCCGTTTTAATTTAGTAC 58.909 43.478 0.30 0.00 36.67 2.73
368 624 2.413108 CGCGCACCCGTTTTAATTTAGT 60.413 45.455 8.75 0.00 36.67 2.24
369 625 2.170770 CGCGCACCCGTTTTAATTTAG 58.829 47.619 8.75 0.00 36.67 1.85
370 626 1.728502 GCGCGCACCCGTTTTAATTTA 60.729 47.619 29.10 0.00 36.67 1.40
373 629 2.177284 GCGCGCACCCGTTTTAAT 59.823 55.556 29.10 0.00 36.67 1.40
374 630 2.957052 GAGCGCGCACCCGTTTTAA 61.957 57.895 35.10 0.00 36.67 1.52
375 631 3.416382 GAGCGCGCACCCGTTTTA 61.416 61.111 35.10 0.00 36.67 1.52
377 633 3.869473 TAAGAGCGCGCACCCGTTT 62.869 57.895 35.10 18.98 36.67 3.60
378 634 3.869473 TTAAGAGCGCGCACCCGTT 62.869 57.895 35.10 19.35 36.67 4.44
379 635 3.659089 ATTAAGAGCGCGCACCCGT 62.659 57.895 35.10 20.95 36.67 5.28
380 636 2.871427 GATTAAGAGCGCGCACCCG 61.871 63.158 35.10 0.00 37.57 5.28
381 637 2.871427 CGATTAAGAGCGCGCACCC 61.871 63.158 35.10 21.22 0.00 4.61
389 645 2.025719 GGCCTTGCCGATTAAGAGC 58.974 57.895 0.00 0.00 39.62 4.09
450 706 5.001232 ACAAATGGTGGTACAGTACATCAC 58.999 41.667 12.89 11.38 41.80 3.06
453 709 5.626142 TCAACAAATGGTGGTACAGTACAT 58.374 37.500 12.89 0.00 41.80 2.29
478 734 0.326048 ACAGGCCAGCTCTACTCCAT 60.326 55.000 5.01 0.00 0.00 3.41
479 735 0.972983 GACAGGCCAGCTCTACTCCA 60.973 60.000 5.01 0.00 0.00 3.86
480 736 1.819905 GACAGGCCAGCTCTACTCC 59.180 63.158 5.01 0.00 0.00 3.85
535 792 0.168128 CCGCGCAAGGTAAAGGAAAG 59.832 55.000 8.75 0.00 38.28 2.62
536 793 1.858372 GCCGCGCAAGGTAAAGGAAA 61.858 55.000 8.75 0.00 38.28 3.13
537 794 2.329614 GCCGCGCAAGGTAAAGGAA 61.330 57.895 8.75 0.00 38.28 3.36
538 795 2.744709 GCCGCGCAAGGTAAAGGA 60.745 61.111 8.75 0.00 38.28 3.36
539 796 4.160635 CGCCGCGCAAGGTAAAGG 62.161 66.667 8.75 0.00 38.28 3.11
540 797 4.160635 CCGCCGCGCAAGGTAAAG 62.161 66.667 8.75 0.00 38.28 1.85
611 870 1.594564 GGACTAGGGATTTCGCGCC 60.595 63.158 0.00 0.00 0.00 6.53
614 873 1.340248 TGATCGGACTAGGGATTTCGC 59.660 52.381 0.00 0.00 0.00 4.70
624 883 6.335471 TGTACAAGAACTTTGATCGGACTA 57.665 37.500 0.00 0.00 0.00 2.59
626 885 6.481954 AATGTACAAGAACTTTGATCGGAC 57.518 37.500 0.00 0.00 0.00 4.79
694 958 7.825331 TCCCACTATGAAAAACAAATGTGTA 57.175 32.000 0.00 0.00 36.80 2.90
700 964 4.590647 TGGCATCCCACTATGAAAAACAAA 59.409 37.500 0.00 0.00 35.79 2.83
702 966 3.772387 TGGCATCCCACTATGAAAAACA 58.228 40.909 0.00 0.00 35.79 2.83
705 969 3.195396 GCTTTGGCATCCCACTATGAAAA 59.805 43.478 0.00 0.00 41.97 2.29
746 1020 3.500299 GCCGCTTTTCTTCTCTTCTCTTT 59.500 43.478 0.00 0.00 0.00 2.52
747 1021 3.070748 GCCGCTTTTCTTCTCTTCTCTT 58.929 45.455 0.00 0.00 0.00 2.85
748 1022 2.694213 GCCGCTTTTCTTCTCTTCTCT 58.306 47.619 0.00 0.00 0.00 3.10
749 1023 1.391826 CGCCGCTTTTCTTCTCTTCTC 59.608 52.381 0.00 0.00 0.00 2.87
750 1024 1.000955 TCGCCGCTTTTCTTCTCTTCT 59.999 47.619 0.00 0.00 0.00 2.85
756 1030 0.872388 TTTCCTCGCCGCTTTTCTTC 59.128 50.000 0.00 0.00 0.00 2.87
820 1094 1.064783 GTACTACTACGTGGCGCCC 59.935 63.158 26.77 14.70 0.00 6.13
831 1105 5.829062 ATCTCCTCTCCATACGTACTACT 57.171 43.478 0.00 0.00 0.00 2.57
832 1106 6.371271 GGTAATCTCCTCTCCATACGTACTAC 59.629 46.154 0.00 0.00 0.00 2.73
833 1107 6.043590 TGGTAATCTCCTCTCCATACGTACTA 59.956 42.308 0.00 0.00 0.00 1.82
834 1108 5.163120 TGGTAATCTCCTCTCCATACGTACT 60.163 44.000 0.00 0.00 0.00 2.73
835 1109 5.068636 TGGTAATCTCCTCTCCATACGTAC 58.931 45.833 0.00 0.00 0.00 3.67
836 1110 5.072736 TCTGGTAATCTCCTCTCCATACGTA 59.927 44.000 0.00 0.00 0.00 3.57
895 1176 1.335142 GCGGCTTCGGAGATGTACTAG 60.335 57.143 0.00 0.00 35.04 2.57
949 1240 0.907230 AGGGGAGAGAGTGTGAAGCC 60.907 60.000 0.00 0.00 0.00 4.35
950 1241 0.534873 GAGGGGAGAGAGTGTGAAGC 59.465 60.000 0.00 0.00 0.00 3.86
951 1242 1.190643 GGAGGGGAGAGAGTGTGAAG 58.809 60.000 0.00 0.00 0.00 3.02
1041 1338 0.162507 CGCACGCACAAGAAGAAGAG 59.837 55.000 0.00 0.00 0.00 2.85
1821 2127 3.144120 CTCGTCGGAGGAGCCCATG 62.144 68.421 14.05 0.00 36.61 3.66
2169 2475 2.852075 GGAGGTGGTGGTGGTGGA 60.852 66.667 0.00 0.00 0.00 4.02
2181 2493 2.177518 TGGTGGAGGAGGAGGAGGT 61.178 63.158 0.00 0.00 0.00 3.85
2241 2553 3.330720 GGTGGTGGTGGAGGAGGG 61.331 72.222 0.00 0.00 0.00 4.30
2550 2862 6.304356 TCAAGCTTTTATTGTGAGTGTGAG 57.696 37.500 0.00 0.00 0.00 3.51
2552 2864 6.088824 GGATCAAGCTTTTATTGTGAGTGTG 58.911 40.000 0.00 0.00 0.00 3.82
2553 2865 5.106555 CGGATCAAGCTTTTATTGTGAGTGT 60.107 40.000 0.00 0.00 0.00 3.55
2557 2869 5.957842 AACGGATCAAGCTTTTATTGTGA 57.042 34.783 0.00 0.00 0.00 3.58
2559 2871 6.751888 GCATAAACGGATCAAGCTTTTATTGT 59.248 34.615 0.00 0.00 0.00 2.71
2560 2872 6.198966 GGCATAAACGGATCAAGCTTTTATTG 59.801 38.462 0.00 0.00 0.00 1.90
2563 2875 4.201871 CGGCATAAACGGATCAAGCTTTTA 60.202 41.667 0.00 0.00 0.00 1.52
2564 2876 3.427503 CGGCATAAACGGATCAAGCTTTT 60.428 43.478 0.00 0.00 0.00 2.27
2565 2877 2.097466 CGGCATAAACGGATCAAGCTTT 59.903 45.455 0.00 0.00 0.00 3.51
2566 2878 1.670811 CGGCATAAACGGATCAAGCTT 59.329 47.619 0.00 0.00 0.00 3.74
2567 2879 1.299541 CGGCATAAACGGATCAAGCT 58.700 50.000 0.00 0.00 0.00 3.74
2568 2880 3.825812 CGGCATAAACGGATCAAGC 57.174 52.632 0.00 0.00 0.00 4.01
2720 3032 2.125350 CTCCTCCTGCCTGAACGC 60.125 66.667 0.00 0.00 0.00 4.84
2841 3153 1.509644 ATCACACTGGTTGCAGCACG 61.510 55.000 2.05 0.00 0.00 5.34
2853 3165 9.415544 GAAAAATGAGCTCAAAATTATCACACT 57.584 29.630 22.50 0.00 0.00 3.55
2854 3166 9.195411 TGAAAAATGAGCTCAAAATTATCACAC 57.805 29.630 22.50 3.71 0.00 3.82
2881 3234 4.217334 TCAATTTTGCGAATGCTAACCAGA 59.783 37.500 0.00 0.00 43.34 3.86
2885 3238 4.683781 TGGTTCAATTTTGCGAATGCTAAC 59.316 37.500 0.00 0.00 43.34 2.34
2912 3265 8.677148 TTCTTAGCTAAAGAAGAGCAGAAAAA 57.323 30.769 7.74 0.00 46.88 1.94
2948 3301 9.871238 ACTCTATTACAATGTCAATAAACGTCT 57.129 29.630 0.00 0.00 0.00 4.18
2950 3303 9.647797 TGACTCTATTACAATGTCAATAAACGT 57.352 29.630 0.00 0.00 35.15 3.99
2980 3333 9.470399 CCCCCTGTAACTTAATATAAGTTGTTT 57.530 33.333 20.29 2.68 40.38 2.83
2981 3334 8.838741 TCCCCCTGTAACTTAATATAAGTTGTT 58.161 33.333 20.29 2.97 40.38 2.83
2982 3335 8.396619 TCCCCCTGTAACTTAATATAAGTTGT 57.603 34.615 20.29 3.56 40.38 3.32
2983 3336 8.491958 ACTCCCCCTGTAACTTAATATAAGTTG 58.508 37.037 20.29 8.18 40.38 3.16
2984 3337 8.634188 ACTCCCCCTGTAACTTAATATAAGTT 57.366 34.615 16.93 16.93 42.53 2.66
2985 3338 9.909365 ATACTCCCCCTGTAACTTAATATAAGT 57.091 33.333 0.00 0.00 0.00 2.24
2987 3340 9.901651 TCATACTCCCCCTGTAACTTAATATAA 57.098 33.333 0.00 0.00 0.00 0.98
2989 3342 8.990693 ATCATACTCCCCCTGTAACTTAATAT 57.009 34.615 0.00 0.00 0.00 1.28
2990 3343 8.808240 AATCATACTCCCCCTGTAACTTAATA 57.192 34.615 0.00 0.00 0.00 0.98
2991 3344 7.572861 AGAATCATACTCCCCCTGTAACTTAAT 59.427 37.037 0.00 0.00 0.00 1.40
2992 3345 6.906901 AGAATCATACTCCCCCTGTAACTTAA 59.093 38.462 0.00 0.00 0.00 1.85
2993 3346 6.449956 AGAATCATACTCCCCCTGTAACTTA 58.550 40.000 0.00 0.00 0.00 2.24
2994 3347 5.289510 AGAATCATACTCCCCCTGTAACTT 58.710 41.667 0.00 0.00 0.00 2.66
2995 3348 4.897051 AGAATCATACTCCCCCTGTAACT 58.103 43.478 0.00 0.00 0.00 2.24
2996 3349 6.936968 ATAGAATCATACTCCCCCTGTAAC 57.063 41.667 0.00 0.00 0.00 2.50
2997 3350 7.947782 AAATAGAATCATACTCCCCCTGTAA 57.052 36.000 0.00 0.00 0.00 2.41
2998 3351 7.349859 ACAAAATAGAATCATACTCCCCCTGTA 59.650 37.037 0.00 0.00 0.00 2.74
2999 3352 6.160459 ACAAAATAGAATCATACTCCCCCTGT 59.840 38.462 0.00 0.00 0.00 4.00
3000 3353 6.605119 ACAAAATAGAATCATACTCCCCCTG 58.395 40.000 0.00 0.00 0.00 4.45
3001 3354 6.848562 ACAAAATAGAATCATACTCCCCCT 57.151 37.500 0.00 0.00 0.00 4.79
3002 3355 7.684428 GCAAACAAAATAGAATCATACTCCCCC 60.684 40.741 0.00 0.00 0.00 5.40
3003 3356 7.147915 TGCAAACAAAATAGAATCATACTCCCC 60.148 37.037 0.00 0.00 0.00 4.81
3004 3357 7.771183 TGCAAACAAAATAGAATCATACTCCC 58.229 34.615 0.00 0.00 0.00 4.30
3005 3358 9.638239 TTTGCAAACAAAATAGAATCATACTCC 57.362 29.630 8.05 0.00 42.73 3.85
3007 3360 9.423061 GGTTTGCAAACAAAATAGAATCATACT 57.577 29.630 35.95 0.00 46.94 2.12
3008 3361 9.423061 AGGTTTGCAAACAAAATAGAATCATAC 57.577 29.630 35.95 17.22 46.94 2.39
3009 3362 9.995003 AAGGTTTGCAAACAAAATAGAATCATA 57.005 25.926 35.95 0.00 46.94 2.15
3010 3363 8.907222 AAGGTTTGCAAACAAAATAGAATCAT 57.093 26.923 35.95 11.19 46.94 2.45
3011 3364 9.823647 TTAAGGTTTGCAAACAAAATAGAATCA 57.176 25.926 35.95 10.80 46.94 2.57
3083 3436 3.947834 CCTACCAACCAAAGCATCCTTAG 59.052 47.826 0.00 0.00 0.00 2.18
3084 3437 3.589735 TCCTACCAACCAAAGCATCCTTA 59.410 43.478 0.00 0.00 0.00 2.69
3085 3438 2.378547 TCCTACCAACCAAAGCATCCTT 59.621 45.455 0.00 0.00 0.00 3.36
3086 3439 1.992557 TCCTACCAACCAAAGCATCCT 59.007 47.619 0.00 0.00 0.00 3.24
3087 3440 2.507407 TCCTACCAACCAAAGCATCC 57.493 50.000 0.00 0.00 0.00 3.51
3088 3441 2.099756 GCATCCTACCAACCAAAGCATC 59.900 50.000 0.00 0.00 0.00 3.91
3089 3442 2.102578 GCATCCTACCAACCAAAGCAT 58.897 47.619 0.00 0.00 0.00 3.79
3098 3451 5.045651 TCAGATGAAAAGAGCATCCTACCAA 60.046 40.000 0.00 0.00 42.36 3.67
3106 3459 7.223260 TCACAAAATCAGATGAAAAGAGCAT 57.777 32.000 0.00 0.00 0.00 3.79
3107 3460 6.638096 TCACAAAATCAGATGAAAAGAGCA 57.362 33.333 0.00 0.00 0.00 4.26
3134 3491 5.104982 TGAACCTCATTTGAAAGCAAAACCT 60.105 36.000 0.00 0.00 46.19 3.50
3135 3492 5.115480 TGAACCTCATTTGAAAGCAAAACC 58.885 37.500 0.00 0.00 46.19 3.27
3149 3506 3.015327 GAGCTGCAAATCTGAACCTCAT 58.985 45.455 1.02 0.00 0.00 2.90
3150 3507 2.224597 TGAGCTGCAAATCTGAACCTCA 60.225 45.455 1.02 0.00 0.00 3.86
3151 3508 2.430465 TGAGCTGCAAATCTGAACCTC 58.570 47.619 1.02 0.00 0.00 3.85
3152 3509 2.574006 TGAGCTGCAAATCTGAACCT 57.426 45.000 1.02 0.00 0.00 3.50
3153 3510 3.863142 ATTGAGCTGCAAATCTGAACC 57.137 42.857 1.02 0.00 40.48 3.62
3154 3511 5.122869 TCACTATTGAGCTGCAAATCTGAAC 59.877 40.000 1.02 0.00 40.48 3.18
3156 3513 4.633126 GTCACTATTGAGCTGCAAATCTGA 59.367 41.667 1.02 3.87 40.48 3.27
3157 3514 4.393990 TGTCACTATTGAGCTGCAAATCTG 59.606 41.667 1.02 1.71 40.48 2.90
3158 3515 4.582869 TGTCACTATTGAGCTGCAAATCT 58.417 39.130 1.02 0.00 40.48 2.40
3159 3516 4.201891 CCTGTCACTATTGAGCTGCAAATC 60.202 45.833 1.02 0.00 40.48 2.17
3160 3517 3.693085 CCTGTCACTATTGAGCTGCAAAT 59.307 43.478 1.02 4.12 40.48 2.32
3167 3530 5.967088 TCTTAAGACCTGTCACTATTGAGC 58.033 41.667 0.00 0.00 30.10 4.26
3205 3569 8.698973 TGTTGAGGTTTTATTATCAAGAACCA 57.301 30.769 6.37 0.00 41.65 3.67
3221 3585 7.259088 AGTCCTTGTATATTCTGTTGAGGTT 57.741 36.000 0.00 0.00 0.00 3.50
3235 3599 7.062957 CCCCTATTGATTTCAAGTCCTTGTAT 58.937 38.462 6.90 2.84 41.16 2.29
3248 3612 4.655649 GCCATTTTCTCCCCCTATTGATTT 59.344 41.667 0.00 0.00 0.00 2.17
3273 3637 5.952347 TCCTACTAGAAAAGGATTGGTCC 57.048 43.478 0.00 0.00 45.45 4.46
3299 3663 1.148157 CGCTAGCCGGATGTTCACAG 61.148 60.000 5.05 0.00 0.00 3.66
3311 3675 1.730451 GGAGTGAGAGGACGCTAGCC 61.730 65.000 9.66 0.00 0.00 3.93
3314 3678 0.328592 AGTGGAGTGAGAGGACGCTA 59.671 55.000 0.00 0.00 0.00 4.26
3321 3729 3.556004 GGACTTTGGAAGTGGAGTGAGAG 60.556 52.174 0.00 0.00 43.03 3.20
3330 3738 1.681264 GGGTGTTGGACTTTGGAAGTG 59.319 52.381 0.00 0.00 43.03 3.16
3346 3754 4.589216 TTCAGAGAGCAAATTTTGGGTG 57.411 40.909 10.96 0.00 0.00 4.61
3350 3758 6.418819 ACGTTTGATTCAGAGAGCAAATTTTG 59.581 34.615 4.72 4.72 33.43 2.44
3388 3796 9.962759 GAAAAGTACGAAAACGATTATGTGTAT 57.037 29.630 0.00 0.00 0.00 2.29
3406 3814 4.495844 GCACAACACTCCACTGAAAAGTAC 60.496 45.833 0.00 0.00 0.00 2.73
3416 3824 1.064060 GTGAACAGCACAACACTCCAC 59.936 52.381 0.00 0.00 46.91 4.02
3465 3873 5.818678 TGTGGAGACCAAATAGTGTAGTT 57.181 39.130 0.00 0.00 34.18 2.24
3534 3942 3.119245 TCGTAGGTGCCATCTTGACTAAC 60.119 47.826 0.00 0.00 0.00 2.34
3555 3963 3.669536 CAGTTTGACCTCCTCCTCTTTC 58.330 50.000 0.00 0.00 0.00 2.62
3576 3984 2.171725 GTCGCCACTGTAATCCCGC 61.172 63.158 0.00 0.00 0.00 6.13
3579 3987 2.607282 CGATAGGTCGCCACTGTAATCC 60.607 54.545 0.00 0.00 41.49 3.01
3595 4003 0.876342 GCGGTTCCCAGCTTCGATAG 60.876 60.000 0.00 0.00 0.00 2.08
3598 4006 4.735132 CGCGGTTCCCAGCTTCGA 62.735 66.667 0.00 0.00 0.00 3.71
3615 4023 2.221981 CACAGTCTTGAGAAAGCGTTCC 59.778 50.000 8.86 1.74 33.92 3.62
3666 4074 0.380733 CTCGGTACAGCATAGCGTCA 59.619 55.000 16.14 1.62 39.19 4.35
3672 4080 3.202906 GAAATTGGCTCGGTACAGCATA 58.797 45.455 7.43 0.00 41.65 3.14
3774 4182 5.935206 TCAAGTCAAAGGATGTGCGTTATTA 59.065 36.000 0.00 0.00 0.00 0.98
3775 4183 4.759693 TCAAGTCAAAGGATGTGCGTTATT 59.240 37.500 0.00 0.00 0.00 1.40
3776 4184 4.323417 TCAAGTCAAAGGATGTGCGTTAT 58.677 39.130 0.00 0.00 0.00 1.89
3777 4185 3.734463 TCAAGTCAAAGGATGTGCGTTA 58.266 40.909 0.00 0.00 0.00 3.18
3778 4186 2.549754 CTCAAGTCAAAGGATGTGCGTT 59.450 45.455 0.00 0.00 0.00 4.84
3779 4187 2.146342 CTCAAGTCAAAGGATGTGCGT 58.854 47.619 0.00 0.00 0.00 5.24
3780 4188 2.146342 ACTCAAGTCAAAGGATGTGCG 58.854 47.619 0.00 0.00 0.00 5.34
3781 4189 4.937620 TGATACTCAAGTCAAAGGATGTGC 59.062 41.667 0.00 0.00 0.00 4.57
3782 4190 7.439157 TTTGATACTCAAGTCAAAGGATGTG 57.561 36.000 0.00 0.00 38.88 3.21
3783 4191 9.911788 ATATTTGATACTCAAGTCAAAGGATGT 57.088 29.630 6.67 0.00 44.65 3.06
3786 4194 9.958180 TTGATATTTGATACTCAAGTCAAAGGA 57.042 29.630 6.67 0.00 44.65 3.36
3816 4224 6.098266 ACCACATGTGTAGTAGCTGAATATGA 59.902 38.462 23.79 0.00 0.00 2.15
3831 4239 2.928801 TGTGAGCTAACCACATGTGT 57.071 45.000 23.79 9.54 39.36 3.72
3843 4303 5.841957 AAACAAGTGAAGAAATGTGAGCT 57.158 34.783 0.00 0.00 0.00 4.09
3977 4437 0.888619 GGGTGTCAAGCTTAAAGGCC 59.111 55.000 0.00 0.00 0.00 5.19
4121 4581 4.524328 ACAACCTTCAGGCCTTTATCTTTG 59.476 41.667 0.00 5.34 39.32 2.77
4214 4674 0.448197 TCTCGAGCTTGCTGACGTAG 59.552 55.000 7.81 0.00 0.00 3.51
4232 4692 1.360911 GATCTTCTCGAGGCCCGTC 59.639 63.158 13.56 1.52 39.75 4.79
4303 4763 1.303561 AGAAAGCCCTGCATTGCGA 60.304 52.632 3.84 0.00 0.00 5.10
4307 4767 1.076024 TCCTTCAGAAAGCCCTGCATT 59.924 47.619 0.00 0.00 34.28 3.56
4328 4788 1.066587 CTCGATCTCCTTGTCGGCC 59.933 63.158 0.00 0.00 38.34 6.13
4556 5016 1.811266 CAATGGGGCTGTCGTCGAG 60.811 63.158 0.00 0.00 0.00 4.04
4571 5031 2.579410 ACAAACTTAGGACCGGCAAT 57.421 45.000 0.00 0.00 0.00 3.56
4656 5116 4.693915 CCACCCCTCCTCCCCCAA 62.694 72.222 0.00 0.00 0.00 4.12
4663 5123 1.566298 GCATCTTCACCACCCCTCCT 61.566 60.000 0.00 0.00 0.00 3.69
4666 5126 0.842030 TCTGCATCTTCACCACCCCT 60.842 55.000 0.00 0.00 0.00 4.79
4679 5140 5.353123 GTCCATTGCAAAATTCATTCTGCAT 59.647 36.000 1.71 0.00 43.83 3.96
4680 5141 4.691685 GTCCATTGCAAAATTCATTCTGCA 59.308 37.500 1.71 0.00 42.79 4.41
4868 5329 1.071857 ACCCAACGGAAAGAGGAAGAC 59.928 52.381 0.00 0.00 0.00 3.01
4880 5341 4.998672 TCTACATTGAAAACTACCCAACGG 59.001 41.667 0.00 0.00 0.00 4.44
4894 5355 5.586243 GTGAAGCAGCCTATTTCTACATTGA 59.414 40.000 0.00 0.00 0.00 2.57
4946 5421 9.773328 CATAATTATACATAAGAAATGGTGCGG 57.227 33.333 0.00 0.00 0.00 5.69
5030 5512 2.900122 TGCGCAGACAGAAATTTAGC 57.100 45.000 5.66 0.00 0.00 3.09
5032 5514 7.534282 TGATTATTTGCGCAGACAGAAATTTA 58.466 30.769 11.31 0.00 0.00 1.40
5101 5584 6.367149 GCATGAGAAATTTGAAAGAGGAAACC 59.633 38.462 0.00 0.00 0.00 3.27
5123 5631 0.890542 TGCTGTTCTTCCAAGCGCAT 60.891 50.000 11.47 0.00 0.00 4.73
5141 5649 4.829968 CCAAGGTATGGCTGATAGATCTG 58.170 47.826 5.18 0.00 43.80 2.90
5142 5650 5.189342 CATCCAAGGTATGGCTGATAGATCT 59.811 44.000 0.00 0.00 46.27 2.75
5143 5651 5.426504 CATCCAAGGTATGGCTGATAGATC 58.573 45.833 0.00 0.00 46.27 2.75
5195 5704 2.563620 GGAAGGATGGCCTAGTACTAGC 59.436 54.545 22.39 17.14 46.28 3.42
5222 5731 6.986817 GCCTTTCTGTTACTTGCAGAGATATA 59.013 38.462 3.37 0.00 42.95 0.86
5261 5770 7.766219 ACAGTTAAATCGTATACATGGTGAC 57.234 36.000 3.32 0.00 0.00 3.67
5390 5917 0.969149 CTCCTCACCTGTGCAGTACA 59.031 55.000 0.00 0.00 37.78 2.90
5391 5918 1.257743 TCTCCTCACCTGTGCAGTAC 58.742 55.000 0.00 0.00 0.00 2.73
5392 5919 2.103373 GATCTCCTCACCTGTGCAGTA 58.897 52.381 0.00 0.00 0.00 2.74
5393 5920 0.901124 GATCTCCTCACCTGTGCAGT 59.099 55.000 0.00 0.00 0.00 4.40
5397 5924 1.068281 CCATCGATCTCCTCACCTGTG 59.932 57.143 0.00 0.00 0.00 3.66
5408 5940 3.005684 GCTCAAGTGATCTCCATCGATCT 59.994 47.826 0.00 0.00 40.32 2.75
5469 6001 3.746492 GGCATACTTTCGCCCTAGTTATG 59.254 47.826 0.00 0.00 42.82 1.90
5490 6022 2.084546 CTGGGAGAAAAAGGTTAGCGG 58.915 52.381 0.00 0.00 0.00 5.52
5609 6179 0.949397 CCATCCTTGATGATGCCACG 59.051 55.000 5.67 0.00 42.09 4.94
5610 6180 2.353357 TCCATCCTTGATGATGCCAC 57.647 50.000 5.67 0.00 42.09 5.01
5656 6226 2.291741 GAGAATTATGAAGGCAAGGGCG 59.708 50.000 0.00 0.00 42.47 6.13


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

AutoCloner maintained by Alex Coulton.