Multiple sequence alignment - TraesCS5B01G375400

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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 TraesCS5B01G375400 chr5B 100.000 2986 0 0 1 2986 552839367 552842352 0.000000e+00 5515.0
1 TraesCS5B01G375400 chr5B 100.000 2006 0 0 3190 5195 552842556 552844561 0.000000e+00 3705.0
2 TraesCS5B01G375400 chr5B 92.453 53 4 0 3190 3242 570749956 570750008 5.580000e-10 76.8
3 TraesCS5B01G375400 chr5B 86.207 58 7 1 1219 1275 690024980 690025037 1.560000e-05 62.1
4 TraesCS5B01G375400 chr5D 92.911 2243 89 18 702 2918 452495802 452498000 0.000000e+00 3197.0
5 TraesCS5B01G375400 chr5D 95.003 1741 56 14 3340 5062 452498149 452499876 0.000000e+00 2704.0
6 TraesCS5B01G375400 chr5D 86.391 338 34 10 375 702 519092620 519092285 4.950000e-95 359.0
7 TraesCS5B01G375400 chr5D 82.160 426 59 12 291 708 99351019 99351435 2.980000e-92 350.0
8 TraesCS5B01G375400 chr5D 96.552 87 3 0 3260 3346 452497983 452498069 1.510000e-30 145.0
9 TraesCS5B01G375400 chr5D 90.476 84 8 0 1219 1302 546858322 546858405 1.530000e-20 111.0
10 TraesCS5B01G375400 chr5D 97.619 42 1 0 3204 3245 203991823 203991864 7.220000e-09 73.1
11 TraesCS5B01G375400 chr5D 97.619 42 1 0 3204 3245 498936824 498936783 7.220000e-09 73.1
12 TraesCS5B01G375400 chr5D 97.619 42 1 0 3204 3245 501729575 501729534 7.220000e-09 73.1
13 TraesCS5B01G375400 chr5D 90.196 51 5 0 3211 3261 36180576 36180526 3.360000e-07 67.6
14 TraesCS5B01G375400 chr5D 90.385 52 3 1 3212 3261 114379802 114379853 3.360000e-07 67.6
15 TraesCS5B01G375400 chr5A 93.062 2090 100 21 844 2915 571427755 571429817 0.000000e+00 3014.0
16 TraesCS5B01G375400 chr5A 92.918 1765 87 16 3340 5089 571429970 571431711 0.000000e+00 2532.0
17 TraesCS5B01G375400 chr5A 88.991 109 8 3 5059 5166 571431770 571431875 1.170000e-26 132.0
18 TraesCS5B01G375400 chr5A 93.023 86 5 1 3260 3344 571429802 571429887 1.960000e-24 124.0
19 TraesCS5B01G375400 chr3D 81.301 615 64 23 130 708 613584659 613585258 7.930000e-123 451.0
20 TraesCS5B01G375400 chr3D 97.727 44 1 0 3202 3245 352226156 352226113 5.580000e-10 76.8
21 TraesCS5B01G375400 chr1D 80.968 599 63 23 130 689 415986079 415986665 1.340000e-115 427.0
22 TraesCS5B01G375400 chr1D 79.125 594 81 25 128 702 467415813 467416382 2.280000e-98 370.0
23 TraesCS5B01G375400 chr1D 97.727 44 1 0 3202 3245 156926053 156926010 5.580000e-10 76.8
24 TraesCS5B01G375400 chr1D 100.000 37 0 0 3211 3247 320706479 320706443 9.330000e-08 69.4
25 TraesCS5B01G375400 chr7A 80.239 587 94 12 128 702 230487663 230488239 6.220000e-114 422.0
26 TraesCS5B01G375400 chr7B 80.409 587 82 19 130 696 725523261 725523834 2.890000e-112 416.0
27 TraesCS5B01G375400 chr2A 80.711 591 66 21 130 699 603860259 603859696 2.890000e-112 416.0
28 TraesCS5B01G375400 chr2A 85.000 360 36 17 352 699 29800541 29800894 2.980000e-92 350.0
29 TraesCS5B01G375400 chr3B 81.055 512 69 20 168 662 796891559 796892059 2.930000e-102 383.0
30 TraesCS5B01G375400 chr3B 89.333 75 7 1 3190 3263 60035865 60035791 5.540000e-15 93.5
31 TraesCS5B01G375400 chr3A 78.686 624 81 25 126 708 516888516 516889128 8.220000e-98 368.0
32 TraesCS5B01G375400 chr3A 86.095 338 38 9 375 708 10959781 10960113 6.400000e-94 355.0
33 TraesCS5B01G375400 chr6A 79.463 521 75 20 128 639 196314802 196315299 1.790000e-89 340.0
34 TraesCS5B01G375400 chr4D 79.368 538 60 25 132 656 29001307 29000808 1.080000e-86 331.0
35 TraesCS5B01G375400 chr4D 97.727 44 1 0 3202 3245 67761692 67761649 5.580000e-10 76.8
36 TraesCS5B01G375400 chr4D 97.727 44 1 0 3202 3245 432040367 432040410 5.580000e-10 76.8
37 TraesCS5B01G375400 chr4D 97.674 43 1 0 3202 3244 19449411 19449369 2.010000e-09 75.0
38 TraesCS5B01G375400 chr4D 90.909 55 5 0 3190 3244 156067363 156067417 2.010000e-09 75.0
39 TraesCS5B01G375400 chr4D 85.135 74 10 1 3190 3262 194048416 194048343 2.010000e-09 75.0
40 TraesCS5B01G375400 chr4D 95.455 44 2 0 3202 3245 317505354 317505311 2.600000e-08 71.3
41 TraesCS5B01G375400 chr4D 100.000 34 0 0 3212 3245 331684146 331684113 4.340000e-06 63.9
42 TraesCS5B01G375400 chr4D 96.875 32 1 0 3213 3244 282308072 282308041 3.000000e-03 54.7
43 TraesCS5B01G375400 chrUn 77.513 587 76 26 130 702 157055 156511 8.450000e-78 302.0
44 TraesCS5B01G375400 chr4B 100.000 70 0 0 3190 3259 471240102 471240171 4.220000e-26 130.0
45 TraesCS5B01G375400 chr4B 91.429 70 5 1 3190 3259 142837729 142837797 1.540000e-15 95.3
46 TraesCS5B01G375400 chr4B 93.103 58 2 1 2917 2974 142837606 142837661 3.330000e-12 84.2
47 TraesCS5B01G375400 chr4B 87.097 62 5 3 3211 3270 517267331 517267271 3.360000e-07 67.6
48 TraesCS5B01G375400 chr4A 97.778 45 1 0 3202 3246 54257598 54257642 1.550000e-10 78.7
49 TraesCS5B01G375400 chr7D 97.727 44 1 0 3202 3245 312872276 312872233 5.580000e-10 76.8
50 TraesCS5B01G375400 chr7D 97.727 44 1 0 3202 3245 412472572 412472529 5.580000e-10 76.8
51 TraesCS5B01G375400 chr6D 97.727 44 1 0 3202 3245 443032403 443032446 5.580000e-10 76.8
52 TraesCS5B01G375400 chr6D 97.500 40 1 0 3206 3245 91292378 91292339 9.330000e-08 69.4
53 TraesCS5B01G375400 chr6D 100.000 36 0 0 3212 3247 326427751 326427716 3.360000e-07 67.6
54 TraesCS5B01G375400 chr6B 83.544 79 9 4 3191 3267 439753335 439753259 2.600000e-08 71.3


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 TraesCS5B01G375400 chr5B 552839367 552844561 5194 False 4610.000000 5515 100.0000 1 5195 2 chr5B.!!$F3 5194
1 TraesCS5B01G375400 chr5D 452495802 452499876 4074 False 2015.333333 3197 94.8220 702 5062 3 chr5D.!!$F5 4360
2 TraesCS5B01G375400 chr5A 571427755 571431875 4120 False 1450.500000 3014 91.9985 844 5166 4 chr5A.!!$F1 4322
3 TraesCS5B01G375400 chr3D 613584659 613585258 599 False 451.000000 451 81.3010 130 708 1 chr3D.!!$F1 578
4 TraesCS5B01G375400 chr1D 415986079 415986665 586 False 427.000000 427 80.9680 130 689 1 chr1D.!!$F1 559
5 TraesCS5B01G375400 chr1D 467415813 467416382 569 False 370.000000 370 79.1250 128 702 1 chr1D.!!$F2 574
6 TraesCS5B01G375400 chr7A 230487663 230488239 576 False 422.000000 422 80.2390 128 702 1 chr7A.!!$F1 574
7 TraesCS5B01G375400 chr7B 725523261 725523834 573 False 416.000000 416 80.4090 130 696 1 chr7B.!!$F1 566
8 TraesCS5B01G375400 chr2A 603859696 603860259 563 True 416.000000 416 80.7110 130 699 1 chr2A.!!$R1 569
9 TraesCS5B01G375400 chr3B 796891559 796892059 500 False 383.000000 383 81.0550 168 662 1 chr3B.!!$F1 494
10 TraesCS5B01G375400 chr3A 516888516 516889128 612 False 368.000000 368 78.6860 126 708 1 chr3A.!!$F2 582
11 TraesCS5B01G375400 chrUn 156511 157055 544 True 302.000000 302 77.5130 130 702 1 chrUn.!!$R1 572

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
177 178 0.602638 AAGCCTCGCAACGATCAACA 60.603 50.0 0.0 0.0 34.61 3.33 F
1615 1783 0.037697 TGCCTGTACGCAAGATCGTT 60.038 50.0 0.0 0.0 43.15 3.85 F
2607 2790 0.895100 CTGGCTGGCTTGGTGCTAAA 60.895 55.0 2.0 0.0 42.39 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2075 2258 0.250338 AGGTTGCGTTGGGAGAGAAC 60.250 55.0 0.00 0.0 0.00 3.01 R
2718 2906 0.178944 TCCCTTCCCTCGACAAGTCA 60.179 55.0 0.72 0.0 0.00 3.41 R
4246 4619 0.827368 GAGCTCCCCTTGAGTACAGG 59.173 60.0 0.87 0.0 43.48 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
124 125 8.828688 TTTTTCTAAAAACAAAAGGACCGAAA 57.171 26.923 0.00 0.00 33.29 3.46
125 126 8.468720 TTTTCTAAAAACAAAAGGACCGAAAG 57.531 30.769 0.00 0.00 0.00 2.62
157 158 1.884579 AGTTAACGAGTGCTCCTTCGA 59.115 47.619 0.00 0.00 0.00 3.71
158 159 2.295349 AGTTAACGAGTGCTCCTTCGAA 59.705 45.455 0.00 0.00 0.00 3.71
175 176 0.796312 GAAAGCCTCGCAACGATCAA 59.204 50.000 0.00 0.00 34.61 2.57
177 178 0.602638 AAGCCTCGCAACGATCAACA 60.603 50.000 0.00 0.00 34.61 3.33
209 210 1.783031 CTCTCAGCCATTCGCCATGC 61.783 60.000 0.00 0.00 38.78 4.06
241 242 2.164219 TGATGCTCCCTTCGAATTTTGC 59.836 45.455 0.00 2.40 0.00 3.68
244 245 2.627699 TGCTCCCTTCGAATTTTGCTTT 59.372 40.909 0.00 0.00 0.00 3.51
333 366 2.742589 CCACCGGTCTTTCTTAGCTTTC 59.257 50.000 2.59 0.00 0.00 2.62
414 536 1.154073 GCTTTCGCGAGAGTACGGT 60.154 57.895 25.34 0.00 43.69 4.83
415 537 0.731855 GCTTTCGCGAGAGTACGGTT 60.732 55.000 25.34 0.00 43.69 4.44
503 627 4.116328 CTTCCGCGAGAGGCACGA 62.116 66.667 8.23 0.00 43.84 4.35
599 734 2.639065 AGAGTCACGGTTTTGCTTTCA 58.361 42.857 0.00 0.00 0.00 2.69
625 760 2.893404 ACGGTTGTGCTTTCGCGT 60.893 55.556 5.77 0.00 39.65 6.01
792 935 1.175983 CCCTTTTACAGCGGTTGCCA 61.176 55.000 0.00 0.00 44.31 4.92
967 1111 4.131596 AGTTTTAAAGTCGGTAAGCTGCA 58.868 39.130 1.02 0.00 0.00 4.41
1095 1254 2.674380 AACCGCGTCTACGACCCT 60.674 61.111 4.92 0.00 43.02 4.34
1182 1341 1.433879 CTTCTACTCCGGCTCCACG 59.566 63.158 0.00 0.00 0.00 4.94
1283 1442 0.250295 CTCACCGTCAACACCACCAT 60.250 55.000 0.00 0.00 0.00 3.55
1284 1443 0.181587 TCACCGTCAACACCACCATT 59.818 50.000 0.00 0.00 0.00 3.16
1313 1472 3.912907 CGTAAGCGCGATCCCCCT 61.913 66.667 12.10 0.00 0.00 4.79
1314 1473 2.504519 GTAAGCGCGATCCCCCTT 59.495 61.111 12.10 4.77 0.00 3.95
1315 1474 1.594564 GTAAGCGCGATCCCCCTTC 60.595 63.158 12.10 0.00 0.00 3.46
1316 1475 2.803817 TAAGCGCGATCCCCCTTCC 61.804 63.158 12.10 0.00 0.00 3.46
1319 1478 3.930012 CGCGATCCCCCTTCCCTC 61.930 72.222 0.00 0.00 0.00 4.30
1320 1479 2.768344 GCGATCCCCCTTCCCTCA 60.768 66.667 0.00 0.00 0.00 3.86
1321 1480 2.375345 GCGATCCCCCTTCCCTCAA 61.375 63.158 0.00 0.00 0.00 3.02
1435 1595 0.539986 GAAATGCGGGAGTAGGTGGA 59.460 55.000 0.00 0.00 0.00 4.02
1615 1783 0.037697 TGCCTGTACGCAAGATCGTT 60.038 50.000 0.00 0.00 43.15 3.85
1622 1790 4.171005 TGTACGCAAGATCGTTTTCCTAG 58.829 43.478 0.00 0.00 43.15 3.02
1738 1906 4.442192 GCGTGAGGGAAGTTGAGATAATCT 60.442 45.833 0.00 0.00 0.00 2.40
1783 1951 2.564062 GGTAGGGTTAGCACTGTGTGTA 59.436 50.000 9.86 0.00 35.75 2.90
1913 2081 7.309133 CCTTAAGCACCAAGTCAACATGAATTA 60.309 37.037 0.00 0.00 31.77 1.40
1980 2163 8.641499 TTTCAAGTTCAAATACCATTTGTGTC 57.359 30.769 10.51 4.40 0.00 3.67
2068 2251 3.390967 TGGATGAAGTCACTTTCACCAGA 59.609 43.478 0.00 0.00 39.68 3.86
2069 2252 4.141505 TGGATGAAGTCACTTTCACCAGAA 60.142 41.667 0.00 0.00 39.68 3.02
2075 2258 7.035004 TGAAGTCACTTTCACCAGAAAAATTG 58.965 34.615 0.00 0.00 42.78 2.32
2129 2312 5.200483 TGAAACTCCAAGAAGATGTTTGGT 58.800 37.500 3.46 0.00 43.43 3.67
2161 2344 5.897250 GGAATGCCTCCTATAAAAGGGAAAA 59.103 40.000 0.00 0.00 46.55 2.29
2162 2345 6.382859 GGAATGCCTCCTATAAAAGGGAAAAA 59.617 38.462 0.00 0.00 46.55 1.94
2326 2509 4.074970 ACCACACTTCACTGATGAATTCC 58.925 43.478 2.27 0.00 43.92 3.01
2349 2532 7.541162 TCCTTTTTGATATCTGACTGCATTTG 58.459 34.615 3.98 0.00 0.00 2.32
2403 2586 9.823647 TTAAGGAGACATCATTATGAGAGTTTC 57.176 33.333 0.29 6.78 36.54 2.78
2404 2587 6.825610 AGGAGACATCATTATGAGAGTTTCC 58.174 40.000 21.60 21.60 38.63 3.13
2427 2610 9.527157 TTCCAAGGACTATTTTGTGATTCATTA 57.473 29.630 0.00 0.00 0.00 1.90
2456 2639 8.636213 CAACCATCCATTTAGAATGCTAGAAAT 58.364 33.333 0.00 0.00 0.00 2.17
2607 2790 0.895100 CTGGCTGGCTTGGTGCTAAA 60.895 55.000 2.00 0.00 42.39 1.85
2620 2803 5.058149 TGGTGCTAAAATGTTGCTATGTG 57.942 39.130 0.00 0.00 0.00 3.21
2621 2804 4.082300 TGGTGCTAAAATGTTGCTATGTGG 60.082 41.667 0.00 0.00 0.00 4.17
2622 2805 3.859386 GTGCTAAAATGTTGCTATGTGGC 59.141 43.478 0.00 0.00 0.00 5.01
2623 2806 3.119173 TGCTAAAATGTTGCTATGTGGCC 60.119 43.478 0.00 0.00 0.00 5.36
2624 2807 3.119173 GCTAAAATGTTGCTATGTGGCCA 60.119 43.478 0.00 0.00 0.00 5.36
2683 2871 1.868997 GTGAACCAGACATGTGCCG 59.131 57.895 1.15 0.00 0.00 5.69
2691 2879 2.807967 CCAGACATGTGCCGGTATTATG 59.192 50.000 1.15 14.98 0.00 1.90
2718 2906 2.452600 TTTCCAGCAGTGGGAAACTT 57.547 45.000 8.94 0.00 46.58 2.66
2748 2936 1.140772 GGGAAGGGAAGGAGGGTGTT 61.141 60.000 0.00 0.00 0.00 3.32
2763 2951 4.215109 AGGGTGTTAAGTGTCAAATTGCT 58.785 39.130 0.00 0.00 0.00 3.91
2915 3103 4.578105 CCCTATCAACTGAAAATGGAGCTC 59.422 45.833 4.71 4.71 0.00 4.09
2916 3104 5.435291 CCTATCAACTGAAAATGGAGCTCT 58.565 41.667 14.64 0.00 0.00 4.09
2917 3105 5.296283 CCTATCAACTGAAAATGGAGCTCTG 59.704 44.000 14.64 0.00 0.00 3.35
2918 3106 4.356405 TCAACTGAAAATGGAGCTCTGA 57.644 40.909 14.64 2.14 0.00 3.27
2919 3107 4.914983 TCAACTGAAAATGGAGCTCTGAT 58.085 39.130 14.64 3.22 0.00 2.90
2920 3108 6.053632 TCAACTGAAAATGGAGCTCTGATA 57.946 37.500 14.64 0.00 0.00 2.15
2921 3109 5.877012 TCAACTGAAAATGGAGCTCTGATAC 59.123 40.000 14.64 0.00 0.00 2.24
2922 3110 5.426689 ACTGAAAATGGAGCTCTGATACA 57.573 39.130 14.64 2.55 0.00 2.29
2923 3111 5.999044 ACTGAAAATGGAGCTCTGATACAT 58.001 37.500 14.64 5.10 0.00 2.29
2924 3112 7.129457 ACTGAAAATGGAGCTCTGATACATA 57.871 36.000 14.64 0.00 0.00 2.29
2925 3113 7.215789 ACTGAAAATGGAGCTCTGATACATAG 58.784 38.462 14.64 5.03 0.00 2.23
2926 3114 6.528321 TGAAAATGGAGCTCTGATACATAGG 58.472 40.000 14.64 0.00 0.00 2.57
2927 3115 6.327365 TGAAAATGGAGCTCTGATACATAGGA 59.673 38.462 14.64 0.00 0.00 2.94
2928 3116 5.736951 AATGGAGCTCTGATACATAGGAC 57.263 43.478 14.64 0.00 0.00 3.85
2929 3117 4.461450 TGGAGCTCTGATACATAGGACT 57.539 45.455 14.64 0.00 0.00 3.85
2930 3118 4.809193 TGGAGCTCTGATACATAGGACTT 58.191 43.478 14.64 0.00 0.00 3.01
2931 3119 4.830046 TGGAGCTCTGATACATAGGACTTC 59.170 45.833 14.64 0.00 0.00 3.01
2932 3120 5.076873 GGAGCTCTGATACATAGGACTTCT 58.923 45.833 14.64 0.00 0.00 2.85
2933 3121 5.048083 GGAGCTCTGATACATAGGACTTCTG 60.048 48.000 14.64 0.00 0.00 3.02
2934 3122 5.700183 AGCTCTGATACATAGGACTTCTGA 58.300 41.667 0.00 0.00 0.00 3.27
2935 3123 5.769662 AGCTCTGATACATAGGACTTCTGAG 59.230 44.000 0.00 0.00 36.23 3.35
2936 3124 5.767665 GCTCTGATACATAGGACTTCTGAGA 59.232 44.000 12.83 0.00 35.58 3.27
2937 3125 6.264292 GCTCTGATACATAGGACTTCTGAGAA 59.736 42.308 12.83 0.00 35.58 2.87
2938 3126 7.201866 GCTCTGATACATAGGACTTCTGAGAAA 60.202 40.741 0.00 0.00 35.58 2.52
2939 3127 8.595362 TCTGATACATAGGACTTCTGAGAAAA 57.405 34.615 0.00 0.00 0.00 2.29
2940 3128 9.035890 TCTGATACATAGGACTTCTGAGAAAAA 57.964 33.333 0.00 0.00 0.00 1.94
2970 3158 8.502161 CAGTGTTTATTACTGCCTTTGTAAAC 57.498 34.615 0.00 0.00 39.09 2.01
2971 3159 8.349983 CAGTGTTTATTACTGCCTTTGTAAACT 58.650 33.333 0.00 0.00 39.09 2.66
2972 3160 8.565416 AGTGTTTATTACTGCCTTTGTAAACTC 58.435 33.333 0.00 0.00 34.70 3.01
2973 3161 7.806487 GTGTTTATTACTGCCTTTGTAAACTCC 59.194 37.037 0.00 0.00 34.70 3.85
2974 3162 7.722285 TGTTTATTACTGCCTTTGTAAACTCCT 59.278 33.333 0.00 0.00 34.70 3.69
2975 3163 7.916914 TTATTACTGCCTTTGTAAACTCCTC 57.083 36.000 0.00 0.00 34.20 3.71
2976 3164 5.562298 TTACTGCCTTTGTAAACTCCTCT 57.438 39.130 0.00 0.00 0.00 3.69
2977 3165 4.439253 ACTGCCTTTGTAAACTCCTCTT 57.561 40.909 0.00 0.00 0.00 2.85
2978 3166 4.137543 ACTGCCTTTGTAAACTCCTCTTG 58.862 43.478 0.00 0.00 0.00 3.02
2979 3167 4.137543 CTGCCTTTGTAAACTCCTCTTGT 58.862 43.478 0.00 0.00 0.00 3.16
2980 3168 3.882888 TGCCTTTGTAAACTCCTCTTGTG 59.117 43.478 0.00 0.00 0.00 3.33
2981 3169 3.253432 GCCTTTGTAAACTCCTCTTGTGG 59.747 47.826 0.00 0.00 0.00 4.17
2982 3170 3.821033 CCTTTGTAAACTCCTCTTGTGGG 59.179 47.826 0.00 0.00 0.00 4.61
2983 3171 4.461198 CTTTGTAAACTCCTCTTGTGGGT 58.539 43.478 0.00 0.00 0.00 4.51
2984 3172 3.485463 TGTAAACTCCTCTTGTGGGTG 57.515 47.619 0.00 0.00 0.00 4.61
2985 3173 2.775384 TGTAAACTCCTCTTGTGGGTGT 59.225 45.455 0.00 0.00 32.78 4.16
3211 3399 3.892284 TGTAACATTTGTGTGAGTGGGT 58.108 40.909 0.00 0.00 0.00 4.51
3212 3400 5.037383 TGTAACATTTGTGTGAGTGGGTA 57.963 39.130 0.00 0.00 0.00 3.69
3213 3401 5.437946 TGTAACATTTGTGTGAGTGGGTAA 58.562 37.500 0.00 0.00 0.00 2.85
3214 3402 6.065374 TGTAACATTTGTGTGAGTGGGTAAT 58.935 36.000 0.00 0.00 0.00 1.89
3215 3403 7.225011 TGTAACATTTGTGTGAGTGGGTAATA 58.775 34.615 0.00 0.00 0.00 0.98
3216 3404 7.885922 TGTAACATTTGTGTGAGTGGGTAATAT 59.114 33.333 0.00 0.00 0.00 1.28
3217 3405 9.386010 GTAACATTTGTGTGAGTGGGTAATATA 57.614 33.333 0.00 0.00 0.00 0.86
3222 3410 8.615878 TTTGTGTGAGTGGGTAATATATATGC 57.384 34.615 0.00 0.00 0.00 3.14
3223 3411 7.309770 TGTGTGAGTGGGTAATATATATGCA 57.690 36.000 0.00 0.00 0.00 3.96
3224 3412 7.386059 TGTGTGAGTGGGTAATATATATGCAG 58.614 38.462 0.00 0.00 0.00 4.41
3225 3413 7.016170 TGTGTGAGTGGGTAATATATATGCAGT 59.984 37.037 0.00 0.00 0.00 4.40
3226 3414 8.528643 GTGTGAGTGGGTAATATATATGCAGTA 58.471 37.037 0.00 0.00 0.00 2.74
3227 3415 8.749354 TGTGAGTGGGTAATATATATGCAGTAG 58.251 37.037 0.00 0.00 0.00 2.57
3228 3416 8.198109 GTGAGTGGGTAATATATATGCAGTAGG 58.802 40.741 0.00 0.00 0.00 3.18
3229 3417 8.119891 TGAGTGGGTAATATATATGCAGTAGGA 58.880 37.037 0.00 0.00 0.00 2.94
3230 3418 8.540507 AGTGGGTAATATATATGCAGTAGGAG 57.459 38.462 0.00 0.00 0.00 3.69
3231 3419 7.070074 AGTGGGTAATATATATGCAGTAGGAGC 59.930 40.741 0.00 0.00 0.00 4.70
3232 3420 6.326583 TGGGTAATATATATGCAGTAGGAGCC 59.673 42.308 0.00 0.00 0.00 4.70
3233 3421 6.555360 GGGTAATATATATGCAGTAGGAGCCT 59.445 42.308 0.00 0.00 0.00 4.58
3234 3422 7.071321 GGGTAATATATATGCAGTAGGAGCCTT 59.929 40.741 0.00 0.00 0.00 4.35
3235 3423 8.487028 GGTAATATATATGCAGTAGGAGCCTTT 58.513 37.037 0.00 0.00 0.00 3.11
3236 3424 9.535878 GTAATATATATGCAGTAGGAGCCTTTC 57.464 37.037 0.00 0.00 0.00 2.62
3246 3434 1.574263 GGAGCCTTTCCTACTGTCCT 58.426 55.000 0.00 0.00 43.16 3.85
3247 3435 1.909986 GGAGCCTTTCCTACTGTCCTT 59.090 52.381 0.00 0.00 43.16 3.36
3248 3436 2.306219 GGAGCCTTTCCTACTGTCCTTT 59.694 50.000 0.00 0.00 43.16 3.11
3249 3437 3.244946 GGAGCCTTTCCTACTGTCCTTTT 60.245 47.826 0.00 0.00 43.16 2.27
3250 3438 3.753797 GAGCCTTTCCTACTGTCCTTTTG 59.246 47.826 0.00 0.00 0.00 2.44
3251 3439 3.394606 AGCCTTTCCTACTGTCCTTTTGA 59.605 43.478 0.00 0.00 0.00 2.69
3252 3440 4.043435 AGCCTTTCCTACTGTCCTTTTGAT 59.957 41.667 0.00 0.00 0.00 2.57
3253 3441 5.250774 AGCCTTTCCTACTGTCCTTTTGATA 59.749 40.000 0.00 0.00 0.00 2.15
3254 3442 5.944007 GCCTTTCCTACTGTCCTTTTGATAA 59.056 40.000 0.00 0.00 0.00 1.75
3255 3443 6.433093 GCCTTTCCTACTGTCCTTTTGATAAA 59.567 38.462 0.00 0.00 0.00 1.40
3256 3444 7.039993 GCCTTTCCTACTGTCCTTTTGATAAAA 60.040 37.037 0.00 0.00 0.00 1.52
3257 3445 8.856103 CCTTTCCTACTGTCCTTTTGATAAAAA 58.144 33.333 0.00 0.00 0.00 1.94
3295 3483 4.066490 CCTGTGTGTTTCGGTAAACCATA 58.934 43.478 0.00 0.00 43.66 2.74
3296 3484 4.515944 CCTGTGTGTTTCGGTAAACCATAA 59.484 41.667 0.00 0.00 43.66 1.90
3330 3518 8.020819 TGTAGTAGCATTTTGTTAATTCACTGC 58.979 33.333 0.00 0.00 0.00 4.40
3376 3737 7.038302 TGTGGATATTGAACTTTCAGGACTAGT 60.038 37.037 0.00 0.00 38.61 2.57
3425 3786 4.112331 ACTATGCCTATCCCCCTAATTCC 58.888 47.826 0.00 0.00 0.00 3.01
3480 3841 1.558294 TGATCATCTCCTGCTGCAACT 59.442 47.619 3.02 0.00 0.00 3.16
3487 3848 2.156917 CTCCTGCTGCAACTGATGAAA 58.843 47.619 3.02 0.00 0.00 2.69
3573 3935 8.556213 TTACCTGTGTGATAACCTGAATTTAC 57.444 34.615 0.00 0.00 0.00 2.01
3812 4176 3.306225 GGACCACAGATGTACCGTTGTTA 60.306 47.826 0.00 0.00 0.00 2.41
3861 4225 1.098050 ATTCTGAATGTTGCCGCTCC 58.902 50.000 1.31 0.00 0.00 4.70
4244 4617 3.972971 CTCTCCTGCCACTGCCTGC 62.973 68.421 0.00 0.00 36.33 4.85
4270 4643 2.132300 CTCAAGGGGAGCTCTAGCC 58.868 63.158 14.64 6.30 43.38 3.93
4271 4644 0.398381 CTCAAGGGGAGCTCTAGCCT 60.398 60.000 14.64 0.00 43.38 4.58
4272 4645 0.689080 TCAAGGGGAGCTCTAGCCTG 60.689 60.000 14.64 5.45 43.38 4.85
4310 4683 1.135689 CCAGCTGATTGTACGCAAACC 60.136 52.381 17.39 0.00 38.21 3.27
4433 4809 3.501828 TGAACTTCAAATCATGTGACGGG 59.498 43.478 0.00 0.00 0.00 5.28
4443 4819 0.245539 ATGTGACGGGTCGATCGTTT 59.754 50.000 15.94 0.00 41.22 3.60
4455 4831 1.359848 GATCGTTTGCTGTCGATGGT 58.640 50.000 13.10 0.00 44.90 3.55
4457 4833 1.154413 CGTTTGCTGTCGATGGTGC 60.154 57.895 0.00 0.00 0.00 5.01
4475 4851 1.287815 CCGTGTGCCGTACTGAAGA 59.712 57.895 0.00 0.00 33.66 2.87
4482 4858 3.880490 TGTGCCGTACTGAAGAAAACATT 59.120 39.130 0.00 0.00 0.00 2.71
4493 4869 1.545582 AGAAAACATTGTCATGCCCGG 59.454 47.619 0.00 0.00 33.05 5.73
4497 4873 0.960364 ACATTGTCATGCCCGGTCAC 60.960 55.000 0.00 0.00 33.05 3.67
4514 4890 1.257675 TCACAATGCGCGTTGATATCG 59.742 47.619 40.73 24.44 33.37 2.92
4515 4891 1.005032 CACAATGCGCGTTGATATCGT 60.005 47.619 40.73 20.11 33.37 3.73
4521 4897 1.200483 CGCGTTGATATCGTCAGCTT 58.800 50.000 0.00 0.00 38.29 3.74
4667 5048 5.642063 TCGCAGGTCCACTCTTTTATTTTAG 59.358 40.000 0.00 0.00 0.00 1.85
4716 5104 0.985490 CCAAGAGAGGGAAGGGGAGG 60.985 65.000 0.00 0.00 0.00 4.30
4726 5114 1.486726 GGAAGGGGAGGTGTATGTCTG 59.513 57.143 0.00 0.00 0.00 3.51
4731 5119 1.207329 GGGAGGTGTATGTCTGTGTCC 59.793 57.143 0.00 0.00 0.00 4.02
4857 5246 5.767665 GTCCATTACCATTACCATGTGCATA 59.232 40.000 0.00 0.00 0.00 3.14
4897 5287 2.886523 CCTCCAGCTGTTTGTTTCATGA 59.113 45.455 13.81 0.00 0.00 3.07
4898 5288 3.318839 CCTCCAGCTGTTTGTTTCATGAA 59.681 43.478 13.81 3.38 0.00 2.57
4899 5289 4.202141 CCTCCAGCTGTTTGTTTCATGAAA 60.202 41.667 16.91 16.91 0.00 2.69
4900 5290 5.336150 TCCAGCTGTTTGTTTCATGAAAA 57.664 34.783 22.07 10.15 31.33 2.29
4901 5291 5.728471 TCCAGCTGTTTGTTTCATGAAAAA 58.272 33.333 22.07 14.81 31.33 1.94
4959 5349 2.214387 TAGCTGATGCATCACAGTCG 57.786 50.000 25.42 15.96 42.74 4.18
5047 5437 2.038814 ATGGCGATGCGACCATACCA 62.039 55.000 11.92 2.56 40.09 3.25
5049 5439 2.585869 GCGATGCGACCATACCACG 61.586 63.158 0.00 0.00 0.00 4.94
5089 5479 4.699925 ACCACCTGCAACTAAAGAACTA 57.300 40.909 0.00 0.00 0.00 2.24
5115 5591 3.256383 TGACATGGAAAAAGATGTGCCTG 59.744 43.478 0.00 0.00 32.85 4.85
5118 5594 0.109132 GGAAAAAGATGTGCCTGGCG 60.109 55.000 14.98 0.00 0.00 5.69
5119 5595 0.733909 GAAAAAGATGTGCCTGGCGC 60.734 55.000 24.80 24.80 39.75 6.53
5158 5634 5.262455 AGCTCTAAGGGGATTCAACTTTT 57.738 39.130 0.00 0.00 0.00 2.27
5159 5635 5.012893 AGCTCTAAGGGGATTCAACTTTTG 58.987 41.667 0.00 0.00 0.00 2.44
5160 5636 4.767409 GCTCTAAGGGGATTCAACTTTTGT 59.233 41.667 0.00 0.00 0.00 2.83
5174 5650 5.649602 AACTTTTGTTGTGTTGTGTTGTG 57.350 34.783 0.00 0.00 41.77 3.33
5175 5651 4.688021 ACTTTTGTTGTGTTGTGTTGTGT 58.312 34.783 0.00 0.00 0.00 3.72
5176 5652 4.742659 ACTTTTGTTGTGTTGTGTTGTGTC 59.257 37.500 0.00 0.00 0.00 3.67
5177 5653 3.990318 TTGTTGTGTTGTGTTGTGTCA 57.010 38.095 0.00 0.00 0.00 3.58
5178 5654 4.511617 TTGTTGTGTTGTGTTGTGTCAT 57.488 36.364 0.00 0.00 0.00 3.06
5179 5655 4.090138 TGTTGTGTTGTGTTGTGTCATC 57.910 40.909 0.00 0.00 0.00 2.92
5180 5656 3.119673 TGTTGTGTTGTGTTGTGTCATCC 60.120 43.478 0.00 0.00 0.00 3.51
5181 5657 2.716217 TGTGTTGTGTTGTGTCATCCA 58.284 42.857 0.00 0.00 0.00 3.41
5182 5658 3.286353 TGTGTTGTGTTGTGTCATCCAT 58.714 40.909 0.00 0.00 0.00 3.41
5183 5659 3.314913 TGTGTTGTGTTGTGTCATCCATC 59.685 43.478 0.00 0.00 0.00 3.51
5184 5660 2.884012 TGTTGTGTTGTGTCATCCATCC 59.116 45.455 0.00 0.00 0.00 3.51
5185 5661 2.198827 TGTGTTGTGTCATCCATCCC 57.801 50.000 0.00 0.00 0.00 3.85
5186 5662 1.423161 TGTGTTGTGTCATCCATCCCA 59.577 47.619 0.00 0.00 0.00 4.37
5187 5663 2.158549 TGTGTTGTGTCATCCATCCCAA 60.159 45.455 0.00 0.00 0.00 4.12
5188 5664 2.890311 GTGTTGTGTCATCCATCCCAAA 59.110 45.455 0.00 0.00 0.00 3.28
5189 5665 3.057315 GTGTTGTGTCATCCATCCCAAAG 60.057 47.826 0.00 0.00 0.00 2.77
5190 5666 3.181435 TGTTGTGTCATCCATCCCAAAGA 60.181 43.478 0.00 0.00 0.00 2.52
5191 5667 3.805066 TGTGTCATCCATCCCAAAGAA 57.195 42.857 0.00 0.00 0.00 2.52
5192 5668 3.689347 TGTGTCATCCATCCCAAAGAAG 58.311 45.455 0.00 0.00 0.00 2.85
5193 5669 2.424956 GTGTCATCCATCCCAAAGAAGC 59.575 50.000 0.00 0.00 0.00 3.86
5194 5670 2.041485 TGTCATCCATCCCAAAGAAGCA 59.959 45.455 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 8.828688 TTTCGGTCCTTTTGTTTTTAGAAAAA 57.171 26.923 0.00 0.00 35.67 1.94
100 101 7.546316 CCTTTCGGTCCTTTTGTTTTTAGAAAA 59.454 33.333 0.00 0.00 0.00 2.29
101 102 7.036829 CCTTTCGGTCCTTTTGTTTTTAGAAA 58.963 34.615 0.00 0.00 0.00 2.52
102 103 6.406065 CCCTTTCGGTCCTTTTGTTTTTAGAA 60.406 38.462 0.00 0.00 0.00 2.10
103 104 5.068067 CCCTTTCGGTCCTTTTGTTTTTAGA 59.932 40.000 0.00 0.00 0.00 2.10
104 105 5.068067 TCCCTTTCGGTCCTTTTGTTTTTAG 59.932 40.000 0.00 0.00 0.00 1.85
105 106 4.954826 TCCCTTTCGGTCCTTTTGTTTTTA 59.045 37.500 0.00 0.00 0.00 1.52
106 107 3.770388 TCCCTTTCGGTCCTTTTGTTTTT 59.230 39.130 0.00 0.00 0.00 1.94
107 108 3.367321 TCCCTTTCGGTCCTTTTGTTTT 58.633 40.909 0.00 0.00 0.00 2.43
108 109 2.956333 CTCCCTTTCGGTCCTTTTGTTT 59.044 45.455 0.00 0.00 0.00 2.83
109 110 2.173996 TCTCCCTTTCGGTCCTTTTGTT 59.826 45.455 0.00 0.00 0.00 2.83
110 111 1.772453 TCTCCCTTTCGGTCCTTTTGT 59.228 47.619 0.00 0.00 0.00 2.83
111 112 2.427506 CTCTCCCTTTCGGTCCTTTTG 58.572 52.381 0.00 0.00 0.00 2.44
112 113 1.271434 GCTCTCCCTTTCGGTCCTTTT 60.271 52.381 0.00 0.00 0.00 2.27
113 114 0.325272 GCTCTCCCTTTCGGTCCTTT 59.675 55.000 0.00 0.00 0.00 3.11
114 115 0.836400 TGCTCTCCCTTTCGGTCCTT 60.836 55.000 0.00 0.00 0.00 3.36
115 116 0.836400 TTGCTCTCCCTTTCGGTCCT 60.836 55.000 0.00 0.00 0.00 3.85
116 117 0.673956 GTTGCTCTCCCTTTCGGTCC 60.674 60.000 0.00 0.00 0.00 4.46
117 118 0.321996 AGTTGCTCTCCCTTTCGGTC 59.678 55.000 0.00 0.00 0.00 4.79
118 119 1.550976 CTAGTTGCTCTCCCTTTCGGT 59.449 52.381 0.00 0.00 0.00 4.69
119 120 1.550976 ACTAGTTGCTCTCCCTTTCGG 59.449 52.381 0.00 0.00 0.00 4.30
120 121 3.320673 AACTAGTTGCTCTCCCTTTCG 57.679 47.619 7.48 0.00 0.00 3.46
121 122 4.626172 CGTTAACTAGTTGCTCTCCCTTTC 59.374 45.833 18.56 0.00 0.00 2.62
122 123 4.282703 TCGTTAACTAGTTGCTCTCCCTTT 59.717 41.667 18.56 0.00 0.00 3.11
123 124 3.830755 TCGTTAACTAGTTGCTCTCCCTT 59.169 43.478 18.56 0.00 0.00 3.95
124 125 3.428532 TCGTTAACTAGTTGCTCTCCCT 58.571 45.455 18.56 0.00 0.00 4.20
125 126 3.193056 ACTCGTTAACTAGTTGCTCTCCC 59.807 47.826 18.56 0.00 0.00 4.30
126 127 4.167268 CACTCGTTAACTAGTTGCTCTCC 58.833 47.826 18.56 0.00 0.00 3.71
157 158 0.517316 GTTGATCGTTGCGAGGCTTT 59.483 50.000 0.00 0.00 39.91 3.51
158 159 0.602638 TGTTGATCGTTGCGAGGCTT 60.603 50.000 0.00 0.00 39.91 4.35
211 212 3.267860 GGAGCATCAAGAGCGCGG 61.268 66.667 8.83 0.00 36.25 6.46
220 221 2.164219 GCAAAATTCGAAGGGAGCATCA 59.836 45.455 3.35 0.00 36.25 3.07
244 245 6.764877 TGCGTGCGGAAAAATAAAATAAAA 57.235 29.167 0.00 0.00 0.00 1.52
248 249 5.854431 AAATGCGTGCGGAAAAATAAAAT 57.146 30.435 0.00 0.00 0.00 1.82
460 584 1.186200 CATGACTCTCACGGAAGGGA 58.814 55.000 0.00 0.00 44.68 4.20
461 585 0.176680 CCATGACTCTCACGGAAGGG 59.823 60.000 0.00 0.00 29.76 3.95
466 590 1.197721 GCAAAACCATGACTCTCACGG 59.802 52.381 0.00 0.00 35.52 4.94
503 627 2.996621 GTGACTCTCGCTAAAGCACAAT 59.003 45.455 2.44 0.00 42.21 2.71
576 706 4.636648 TGAAAGCAAAACCGTGACTCTTAA 59.363 37.500 0.00 0.00 0.00 1.85
578 713 3.013921 TGAAAGCAAAACCGTGACTCTT 58.986 40.909 0.00 0.00 0.00 2.85
599 734 2.029073 CACAACCGTGCCTCTCGT 59.971 61.111 0.00 0.00 36.06 4.18
676 818 3.452786 TGCCTCTCGCGGAAGGAG 61.453 66.667 25.65 17.82 42.08 3.69
724 867 1.892391 GCCAGTTATACAGGCCGGC 60.892 63.158 21.18 21.18 44.02 6.13
765 908 0.972471 GCTGTAAAAGGGCCTGGCAT 60.972 55.000 22.05 5.29 0.00 4.40
829 972 5.240844 CGGGGAACAGTTCAGTTCTTTTATT 59.759 40.000 15.36 0.00 45.52 1.40
832 975 2.949644 CGGGGAACAGTTCAGTTCTTTT 59.050 45.455 15.36 0.00 45.52 2.27
833 976 2.572290 CGGGGAACAGTTCAGTTCTTT 58.428 47.619 15.36 0.00 45.52 2.52
834 977 1.814248 GCGGGGAACAGTTCAGTTCTT 60.814 52.381 15.36 0.00 45.52 2.52
950 1094 2.088950 GGTGCAGCTTACCGACTTTA 57.911 50.000 9.07 0.00 0.00 1.85
1095 1254 0.605319 GGATCTTGGTGTCGGTGCAA 60.605 55.000 0.00 0.00 0.00 4.08
1309 1468 0.553333 GGAAGGATTGAGGGAAGGGG 59.447 60.000 0.00 0.00 0.00 4.79
1313 1472 1.921869 GCGGGGAAGGATTGAGGGAA 61.922 60.000 0.00 0.00 0.00 3.97
1314 1473 2.375345 GCGGGGAAGGATTGAGGGA 61.375 63.158 0.00 0.00 0.00 4.20
1315 1474 2.193248 GCGGGGAAGGATTGAGGG 59.807 66.667 0.00 0.00 0.00 4.30
1316 1475 2.203070 CGCGGGGAAGGATTGAGG 60.203 66.667 0.00 0.00 0.00 3.86
1317 1476 2.897350 GCGCGGGGAAGGATTGAG 60.897 66.667 8.83 0.00 0.00 3.02
1318 1477 4.483243 GGCGCGGGGAAGGATTGA 62.483 66.667 8.83 0.00 0.00 2.57
1319 1478 3.995506 AAGGCGCGGGGAAGGATTG 62.996 63.158 8.83 0.00 0.00 2.67
1320 1479 3.699134 GAAGGCGCGGGGAAGGATT 62.699 63.158 8.83 0.00 0.00 3.01
1321 1480 4.176752 GAAGGCGCGGGGAAGGAT 62.177 66.667 8.83 0.00 0.00 3.24
1435 1595 1.152839 CAACAACCCCAACCGACCT 60.153 57.895 0.00 0.00 0.00 3.85
1486 1646 1.888018 CATCCAGCACAGGCCAAAG 59.112 57.895 5.01 0.00 42.56 2.77
1615 1783 3.244526 TGTCACAATGCAGAGCTAGGAAA 60.245 43.478 0.00 0.00 0.00 3.13
1622 1790 1.068055 CCCTTTGTCACAATGCAGAGC 60.068 52.381 0.00 0.00 0.00 4.09
1738 1906 9.308000 ACCATTGTTCATAGAGGAAAATTGTTA 57.692 29.630 0.00 0.00 0.00 2.41
1880 2048 2.079925 CTTGGTGCTTAAGGCTCTCAC 58.920 52.381 4.29 3.27 42.39 3.51
1881 2049 1.699634 ACTTGGTGCTTAAGGCTCTCA 59.300 47.619 4.29 0.00 42.39 3.27
1882 2050 2.289694 TGACTTGGTGCTTAAGGCTCTC 60.290 50.000 4.29 0.00 42.39 3.20
1890 2058 7.517614 TTAATTCATGTTGACTTGGTGCTTA 57.482 32.000 0.00 0.00 0.00 3.09
1980 2163 7.589221 CAGAGGTTTCTCATTTCTTTTCTTTCG 59.411 37.037 0.00 0.00 42.34 3.46
2033 2216 9.118300 AGTGACTTCATCCATTCATATTCTTTC 57.882 33.333 0.00 0.00 0.00 2.62
2068 2251 3.383185 TGCGTTGGGAGAGAACAATTTTT 59.617 39.130 0.00 0.00 0.00 1.94
2069 2252 2.955660 TGCGTTGGGAGAGAACAATTTT 59.044 40.909 0.00 0.00 0.00 1.82
2075 2258 0.250338 AGGTTGCGTTGGGAGAGAAC 60.250 55.000 0.00 0.00 0.00 3.01
2161 2344 8.487176 GTTTAAGCAACGATTCAACATGAAATT 58.513 29.630 0.00 0.00 40.12 1.82
2162 2345 7.651304 TGTTTAAGCAACGATTCAACATGAAAT 59.349 29.630 0.00 0.00 37.82 2.17
2326 2509 7.218145 GCAAATGCAGTCAGATATCAAAAAG 57.782 36.000 5.32 0.00 41.59 2.27
2349 2532 7.009540 GCAATAACCATGTTGTCTCTAAAATGC 59.990 37.037 0.00 0.00 30.94 3.56
2403 2586 9.956720 GATAATGAATCACAAAATAGTCCTTGG 57.043 33.333 0.00 0.00 34.46 3.61
2404 2587 9.956720 GGATAATGAATCACAAAATAGTCCTTG 57.043 33.333 0.00 0.00 36.20 3.61
2427 2610 5.461327 AGCATTCTAAATGGATGGTTGGAT 58.539 37.500 2.17 0.00 0.00 3.41
2548 2731 9.392259 TGATATACCTAGTTATCTGTCGGTATG 57.608 37.037 14.91 0.00 35.68 2.39
2607 2790 2.220653 ACTGGCCACATAGCAACATT 57.779 45.000 0.00 0.00 0.00 2.71
2620 2803 0.322456 TCACAGCAACCATACTGGCC 60.322 55.000 0.00 0.00 42.67 5.36
2621 2804 1.755179 ATCACAGCAACCATACTGGC 58.245 50.000 0.00 0.00 42.67 4.85
2622 2805 4.142609 ACTATCACAGCAACCATACTGG 57.857 45.455 0.00 0.00 45.02 4.00
2623 2806 5.163723 CCAAACTATCACAGCAACCATACTG 60.164 44.000 0.00 0.00 39.86 2.74
2624 2807 4.943705 CCAAACTATCACAGCAACCATACT 59.056 41.667 0.00 0.00 0.00 2.12
2683 2871 5.248870 CTGGAAACCAGCAACATAATACC 57.751 43.478 4.84 0.00 45.13 2.73
2718 2906 0.178944 TCCCTTCCCTCGACAAGTCA 60.179 55.000 0.72 0.00 0.00 3.41
2748 2936 8.134895 CAGAAACCTTTAGCAATTTGACACTTA 58.865 33.333 0.00 0.00 0.00 2.24
2763 2951 6.855763 AATTGCATCATCCAGAAACCTTTA 57.144 33.333 0.00 0.00 0.00 1.85
2945 3133 8.349983 AGTTTACAAAGGCAGTAATAAACACTG 58.650 33.333 12.04 0.00 45.08 3.66
2946 3134 8.459911 AGTTTACAAAGGCAGTAATAAACACT 57.540 30.769 12.04 4.64 35.79 3.55
2947 3135 7.806487 GGAGTTTACAAAGGCAGTAATAAACAC 59.194 37.037 12.04 7.50 35.79 3.32
2948 3136 7.722285 AGGAGTTTACAAAGGCAGTAATAAACA 59.278 33.333 12.04 0.00 35.79 2.83
2949 3137 8.107399 AGGAGTTTACAAAGGCAGTAATAAAC 57.893 34.615 0.00 0.00 34.31 2.01
2950 3138 8.161425 AGAGGAGTTTACAAAGGCAGTAATAAA 58.839 33.333 0.00 0.00 32.07 1.40
2951 3139 7.686434 AGAGGAGTTTACAAAGGCAGTAATAA 58.314 34.615 0.00 0.00 32.07 1.40
2952 3140 7.253905 AGAGGAGTTTACAAAGGCAGTAATA 57.746 36.000 0.00 0.00 32.07 0.98
2953 3141 6.128138 AGAGGAGTTTACAAAGGCAGTAAT 57.872 37.500 0.00 0.00 32.07 1.89
2954 3142 5.562298 AGAGGAGTTTACAAAGGCAGTAA 57.438 39.130 0.00 0.00 0.00 2.24
2955 3143 5.163237 ACAAGAGGAGTTTACAAAGGCAGTA 60.163 40.000 0.00 0.00 0.00 2.74
2956 3144 4.137543 CAAGAGGAGTTTACAAAGGCAGT 58.862 43.478 0.00 0.00 0.00 4.40
2957 3145 4.023707 CACAAGAGGAGTTTACAAAGGCAG 60.024 45.833 0.00 0.00 0.00 4.85
2958 3146 3.882888 CACAAGAGGAGTTTACAAAGGCA 59.117 43.478 0.00 0.00 0.00 4.75
2959 3147 3.253432 CCACAAGAGGAGTTTACAAAGGC 59.747 47.826 0.00 0.00 0.00 4.35
2960 3148 3.821033 CCCACAAGAGGAGTTTACAAAGG 59.179 47.826 0.00 0.00 0.00 3.11
2961 3149 4.275936 CACCCACAAGAGGAGTTTACAAAG 59.724 45.833 0.00 0.00 0.00 2.77
2962 3150 4.204012 CACCCACAAGAGGAGTTTACAAA 58.796 43.478 0.00 0.00 0.00 2.83
2963 3151 3.201266 ACACCCACAAGAGGAGTTTACAA 59.799 43.478 0.00 0.00 0.00 2.41
2964 3152 2.775384 ACACCCACAAGAGGAGTTTACA 59.225 45.455 0.00 0.00 0.00 2.41
2965 3153 3.487120 ACACCCACAAGAGGAGTTTAC 57.513 47.619 0.00 0.00 0.00 2.01
3189 3377 4.469657 ACCCACTCACACAAATGTTACAT 58.530 39.130 0.00 0.00 36.72 2.29
3190 3378 3.892284 ACCCACTCACACAAATGTTACA 58.108 40.909 0.00 0.00 36.72 2.41
3191 3379 6.569179 ATTACCCACTCACACAAATGTTAC 57.431 37.500 0.00 0.00 36.72 2.50
3196 3384 9.231297 GCATATATATTACCCACTCACACAAAT 57.769 33.333 0.00 0.00 0.00 2.32
3197 3385 8.214364 TGCATATATATTACCCACTCACACAAA 58.786 33.333 0.00 0.00 0.00 2.83
3198 3386 7.740805 TGCATATATATTACCCACTCACACAA 58.259 34.615 0.00 0.00 0.00 3.33
3199 3387 7.016170 ACTGCATATATATTACCCACTCACACA 59.984 37.037 0.00 0.00 0.00 3.72
3200 3388 7.386851 ACTGCATATATATTACCCACTCACAC 58.613 38.462 0.00 0.00 0.00 3.82
3201 3389 7.553504 ACTGCATATATATTACCCACTCACA 57.446 36.000 0.00 0.00 0.00 3.58
3202 3390 8.198109 CCTACTGCATATATATTACCCACTCAC 58.802 40.741 0.00 0.00 0.00 3.51
3203 3391 8.119891 TCCTACTGCATATATATTACCCACTCA 58.880 37.037 0.00 0.00 0.00 3.41
3204 3392 8.534954 TCCTACTGCATATATATTACCCACTC 57.465 38.462 0.00 0.00 0.00 3.51
3205 3393 7.070074 GCTCCTACTGCATATATATTACCCACT 59.930 40.741 0.00 0.00 0.00 4.00
3206 3394 7.210873 GCTCCTACTGCATATATATTACCCAC 58.789 42.308 0.00 0.00 0.00 4.61
3207 3395 6.326583 GGCTCCTACTGCATATATATTACCCA 59.673 42.308 0.00 0.00 0.00 4.51
3208 3396 6.555360 AGGCTCCTACTGCATATATATTACCC 59.445 42.308 0.00 0.00 0.00 3.69
3209 3397 7.604657 AGGCTCCTACTGCATATATATTACC 57.395 40.000 0.00 0.00 0.00 2.85
3210 3398 9.535878 GAAAGGCTCCTACTGCATATATATTAC 57.464 37.037 0.00 0.00 0.00 1.89
3211 3399 8.705594 GGAAAGGCTCCTACTGCATATATATTA 58.294 37.037 0.00 0.00 41.61 0.98
3212 3400 7.569240 GGAAAGGCTCCTACTGCATATATATT 58.431 38.462 0.00 0.00 41.61 1.28
3213 3401 7.130681 GGAAAGGCTCCTACTGCATATATAT 57.869 40.000 0.00 0.00 41.61 0.86
3214 3402 6.546428 GGAAAGGCTCCTACTGCATATATA 57.454 41.667 0.00 0.00 41.61 0.86
3215 3403 5.428184 GGAAAGGCTCCTACTGCATATAT 57.572 43.478 0.00 0.00 41.61 0.86
3216 3404 4.891992 GGAAAGGCTCCTACTGCATATA 57.108 45.455 0.00 0.00 41.61 0.86
3217 3405 3.778954 GGAAAGGCTCCTACTGCATAT 57.221 47.619 0.00 0.00 41.61 1.78
3227 3415 1.574263 AGGACAGTAGGAAAGGCTCC 58.426 55.000 0.00 0.00 45.81 4.70
3228 3416 3.704800 AAAGGACAGTAGGAAAGGCTC 57.295 47.619 0.00 0.00 0.00 4.70
3229 3417 3.394606 TCAAAAGGACAGTAGGAAAGGCT 59.605 43.478 0.00 0.00 0.00 4.58
3230 3418 3.751518 TCAAAAGGACAGTAGGAAAGGC 58.248 45.455 0.00 0.00 0.00 4.35
3231 3419 7.996098 TTTATCAAAAGGACAGTAGGAAAGG 57.004 36.000 0.00 0.00 0.00 3.11
3256 3444 4.162131 ACACAGGCTCCATTTTCAGTTTTT 59.838 37.500 0.00 0.00 0.00 1.94
3257 3445 3.706086 ACACAGGCTCCATTTTCAGTTTT 59.294 39.130 0.00 0.00 0.00 2.43
3258 3446 3.068590 CACACAGGCTCCATTTTCAGTTT 59.931 43.478 0.00 0.00 0.00 2.66
3295 3483 6.010219 ACAAAATGCTACTACAGGTTCCATT 58.990 36.000 0.00 0.00 32.64 3.16
3296 3484 5.570320 ACAAAATGCTACTACAGGTTCCAT 58.430 37.500 0.00 0.00 0.00 3.41
3376 3737 7.711772 TGAGAAGGAAACTAAACAACGAATGTA 59.288 33.333 0.00 0.00 40.57 2.29
3425 3786 2.224450 ACCAACTACCCTGGAGTTTTCG 60.224 50.000 0.00 0.00 34.90 3.46
3480 3841 5.538053 TGGGACAAACTATGCTTTTTCATCA 59.462 36.000 0.00 0.00 31.92 3.07
3706 4068 2.104451 AGATCTGGCTGCATACTTCCTG 59.896 50.000 0.50 0.00 0.00 3.86
3861 4225 6.446781 AGAACCTAGAAATGCATCAACATG 57.553 37.500 0.00 0.00 0.00 3.21
4246 4619 0.827368 GAGCTCCCCTTGAGTACAGG 59.173 60.000 0.87 0.00 43.48 4.00
4433 4809 1.007011 CATCGACAGCAAACGATCGAC 60.007 52.381 24.34 8.07 45.50 4.20
4443 4819 4.002506 ACGGCACCATCGACAGCA 62.003 61.111 0.00 0.00 0.00 4.41
4475 4851 1.272212 GACCGGGCATGACAATGTTTT 59.728 47.619 0.00 0.00 36.08 2.43
4482 4858 0.959867 CATTGTGACCGGGCATGACA 60.960 55.000 16.47 3.31 0.00 3.58
4493 4869 2.629022 GATATCAACGCGCATTGTGAC 58.371 47.619 16.56 3.25 0.00 3.67
4497 4873 1.257675 TGACGATATCAACGCGCATTG 59.742 47.619 10.48 10.48 33.02 2.82
4521 4897 5.163673 TGAGCAAAATATACAAAGATGCGCA 60.164 36.000 14.96 14.96 39.24 6.09
4589 4967 9.184523 CCTGAAATATAGACATAAACAACCCAA 57.815 33.333 0.00 0.00 0.00 4.12
4667 5048 2.112815 CATTCGCCTCCCGGGAAAC 61.113 63.158 26.68 18.29 45.53 2.78
4716 5104 1.276622 AGGGGGACACAGACATACAC 58.723 55.000 0.00 0.00 0.00 2.90
4726 5114 1.002502 GCTACCACAAGGGGGACAC 60.003 63.158 0.00 0.00 42.91 3.67
4731 5119 2.044946 GCCTGCTACCACAAGGGG 60.045 66.667 0.00 0.00 42.91 4.79
4791 5179 1.153289 CAACAGCTCAGGATCCCCG 60.153 63.158 8.55 0.00 37.58 5.73
5078 5468 8.918202 TTTCCATGTCACAATAGTTCTTTAGT 57.082 30.769 0.00 0.00 0.00 2.24
5089 5479 5.232463 GCACATCTTTTTCCATGTCACAAT 58.768 37.500 0.00 0.00 30.48 2.71
5119 5595 3.411703 CTTTAGTGAGCTGCGCGCG 62.412 63.158 28.44 28.44 45.59 6.86
5158 5634 3.119673 GGATGACACAACACAACACAACA 60.120 43.478 0.00 0.00 0.00 3.33
5159 5635 3.119673 TGGATGACACAACACAACACAAC 60.120 43.478 0.00 0.00 0.00 3.32
5160 5636 3.084786 TGGATGACACAACACAACACAA 58.915 40.909 0.00 0.00 0.00 3.33
5162 5638 3.304659 GGATGGATGACACAACACAACAC 60.305 47.826 0.00 0.00 0.00 3.32
5163 5639 2.884012 GGATGGATGACACAACACAACA 59.116 45.455 0.00 0.00 0.00 3.33
5164 5640 2.228822 GGGATGGATGACACAACACAAC 59.771 50.000 0.00 0.00 0.00 3.32
5165 5641 2.158549 TGGGATGGATGACACAACACAA 60.159 45.455 0.00 0.00 0.00 3.33
5167 5643 2.198827 TGGGATGGATGACACAACAC 57.801 50.000 0.00 0.00 0.00 3.32
5168 5644 2.967745 TTGGGATGGATGACACAACA 57.032 45.000 0.00 0.00 0.00 3.33
5169 5645 3.420893 TCTTTGGGATGGATGACACAAC 58.579 45.455 0.00 0.00 0.00 3.32
5170 5646 3.805066 TCTTTGGGATGGATGACACAA 57.195 42.857 0.00 0.00 0.00 3.33
5171 5647 3.689347 CTTCTTTGGGATGGATGACACA 58.311 45.455 0.00 0.00 0.00 3.72
5172 5648 2.424956 GCTTCTTTGGGATGGATGACAC 59.575 50.000 0.00 0.00 0.00 3.67
5173 5649 2.041485 TGCTTCTTTGGGATGGATGACA 59.959 45.455 0.00 0.00 0.00 3.58
5174 5650 2.726821 TGCTTCTTTGGGATGGATGAC 58.273 47.619 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.