Multiple sequence alignment - TraesCS6B01G063500

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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 TraesCS6B01G063500 chr6B 100.000 3357 0 0 1 3357 42213097 42209741 0.000000e+00 6200.0
1 TraesCS6B01G063500 chr6B 81.511 1509 202 42 835 2314 42392777 42394237 0.000000e+00 1170.0
2 TraesCS6B01G063500 chr6B 80.238 1513 203 58 835 2297 42006014 42004548 0.000000e+00 1050.0
3 TraesCS6B01G063500 chr6B 85.532 940 121 9 1391 2327 42318474 42317547 0.000000e+00 968.0
4 TraesCS6B01G063500 chr6B 88.615 527 50 5 858 1380 42231897 42231377 1.700000e-177 632.0
5 TraesCS6B01G063500 chr6B 91.983 237 19 0 1391 1627 42231340 42231104 1.930000e-87 333.0
6 TraesCS6B01G063500 chr6B 85.549 173 19 4 233 400 42376902 42376731 3.440000e-40 176.0
7 TraesCS6B01G063500 chr6A 91.813 2394 106 34 1 2344 23953496 23951143 0.000000e+00 3253.0
8 TraesCS6B01G063500 chr6A 82.368 1537 200 36 810 2314 24031728 24030231 0.000000e+00 1271.0
9 TraesCS6B01G063500 chr6A 86.416 876 103 12 1418 2289 24048988 24049851 0.000000e+00 944.0
10 TraesCS6B01G063500 chr6A 86.248 589 47 11 2378 2946 23951139 23950565 2.860000e-170 608.0
11 TraesCS6B01G063500 chr6A 85.586 555 55 16 835 1380 24048351 24048889 2.930000e-155 558.0
12 TraesCS6B01G063500 chr6A 84.673 535 58 14 101 629 23964756 23964240 2.310000e-141 512.0
13 TraesCS6B01G063500 chr6A 87.696 382 40 6 999 1380 23963284 23962910 3.980000e-119 438.0
14 TraesCS6B01G063500 chr6A 92.405 237 18 0 1391 1627 23962876 23962640 4.150000e-89 339.0
15 TraesCS6B01G063500 chr6A 88.776 196 15 4 810 1003 23963728 23963538 2.010000e-57 233.0
16 TraesCS6B01G063500 chr6A 91.892 37 3 0 2341 2377 597866459 597866495 6.000000e-03 52.8
17 TraesCS6B01G063500 chr6D 93.458 1819 79 14 656 2444 25828079 25826271 0.000000e+00 2663.0
18 TraesCS6B01G063500 chr6D 84.314 1428 189 23 883 2306 25880321 25878925 0.000000e+00 1363.0
19 TraesCS6B01G063500 chr6D 82.958 933 121 23 1391 2317 25852337 25851437 0.000000e+00 808.0
20 TraesCS6B01G063500 chr6D 86.288 722 74 10 2440 3154 25826130 25825427 0.000000e+00 761.0
21 TraesCS6B01G063500 chr6D 82.256 913 123 27 1391 2297 25804757 25803878 0.000000e+00 752.0
22 TraesCS6B01G063500 chr6D 86.796 568 71 4 1724 2289 25915648 25916213 6.110000e-177 630.0
23 TraesCS6B01G063500 chr6D 82.985 717 72 28 60 746 25854038 25853342 1.330000e-168 603.0
24 TraesCS6B01G063500 chr6D 90.862 383 34 1 999 1380 25852753 25852371 2.310000e-141 512.0
25 TraesCS6B01G063500 chr6D 88.776 196 15 4 810 1003 25853201 25853011 2.010000e-57 233.0
26 TraesCS6B01G063500 chr2D 100.000 28 0 0 2349 2376 535731154 535731181 6.000000e-03 52.8


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 TraesCS6B01G063500 chr6B 42209741 42213097 3356 True 6200.0 6200 100.00000 1 3357 1 chr6B.!!$R2 3356
1 TraesCS6B01G063500 chr6B 42392777 42394237 1460 False 1170.0 1170 81.51100 835 2314 1 chr6B.!!$F1 1479
2 TraesCS6B01G063500 chr6B 42004548 42006014 1466 True 1050.0 1050 80.23800 835 2297 1 chr6B.!!$R1 1462
3 TraesCS6B01G063500 chr6B 42317547 42318474 927 True 968.0 968 85.53200 1391 2327 1 chr6B.!!$R3 936
4 TraesCS6B01G063500 chr6B 42231104 42231897 793 True 482.5 632 90.29900 858 1627 2 chr6B.!!$R5 769
5 TraesCS6B01G063500 chr6A 23950565 23953496 2931 True 1930.5 3253 89.03050 1 2946 2 chr6A.!!$R2 2945
6 TraesCS6B01G063500 chr6A 24030231 24031728 1497 True 1271.0 1271 82.36800 810 2314 1 chr6A.!!$R1 1504
7 TraesCS6B01G063500 chr6A 24048351 24049851 1500 False 751.0 944 86.00100 835 2289 2 chr6A.!!$F2 1454
8 TraesCS6B01G063500 chr6A 23962640 23964756 2116 True 380.5 512 88.38750 101 1627 4 chr6A.!!$R3 1526
9 TraesCS6B01G063500 chr6D 25825427 25828079 2652 True 1712.0 2663 89.87300 656 3154 2 chr6D.!!$R3 2498
10 TraesCS6B01G063500 chr6D 25878925 25880321 1396 True 1363.0 1363 84.31400 883 2306 1 chr6D.!!$R2 1423
11 TraesCS6B01G063500 chr6D 25803878 25804757 879 True 752.0 752 82.25600 1391 2297 1 chr6D.!!$R1 906
12 TraesCS6B01G063500 chr6D 25915648 25916213 565 False 630.0 630 86.79600 1724 2289 1 chr6D.!!$F1 565
13 TraesCS6B01G063500 chr6D 25851437 25854038 2601 True 539.0 808 86.39525 60 2317 4 chr6D.!!$R4 2257

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
918 1352 0.454196 GCAACCACGTGGAACTTGTT 59.546 50.0 40.21 20.26 33.71 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2760 3745 0.036858 GCCACTTCGCTTCTCTCCTT 60.037 55.0 0.0 0.0 0.0 3.36 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
99 100 7.626452 GCCTAACAATTCATTCAAGTGGAGTAC 60.626 40.741 0.00 0.00 34.18 2.73
328 339 8.087750 TCAACCCAATTATTTGAATTGAGTGAC 58.912 33.333 10.79 0.00 39.36 3.67
335 346 3.319137 TTGAATTGAGTGACGAGGGAG 57.681 47.619 0.00 0.00 0.00 4.30
336 347 2.248248 TGAATTGAGTGACGAGGGAGT 58.752 47.619 0.00 0.00 0.00 3.85
337 348 2.029020 TGAATTGAGTGACGAGGGAGTG 60.029 50.000 0.00 0.00 0.00 3.51
338 349 0.898320 ATTGAGTGACGAGGGAGTGG 59.102 55.000 0.00 0.00 0.00 4.00
339 350 0.469331 TTGAGTGACGAGGGAGTGGT 60.469 55.000 0.00 0.00 0.00 4.16
340 351 0.469331 TGAGTGACGAGGGAGTGGTT 60.469 55.000 0.00 0.00 0.00 3.67
341 352 1.202964 TGAGTGACGAGGGAGTGGTTA 60.203 52.381 0.00 0.00 0.00 2.85
342 353 1.473278 GAGTGACGAGGGAGTGGTTAG 59.527 57.143 0.00 0.00 0.00 2.34
343 354 1.203025 AGTGACGAGGGAGTGGTTAGT 60.203 52.381 0.00 0.00 0.00 2.24
344 355 1.617357 GTGACGAGGGAGTGGTTAGTT 59.383 52.381 0.00 0.00 0.00 2.24
345 356 2.036862 GTGACGAGGGAGTGGTTAGTTT 59.963 50.000 0.00 0.00 0.00 2.66
346 357 2.701951 TGACGAGGGAGTGGTTAGTTTT 59.298 45.455 0.00 0.00 0.00 2.43
347 358 3.064931 GACGAGGGAGTGGTTAGTTTTG 58.935 50.000 0.00 0.00 0.00 2.44
348 359 1.804748 CGAGGGAGTGGTTAGTTTTGC 59.195 52.381 0.00 0.00 0.00 3.68
349 360 2.160205 GAGGGAGTGGTTAGTTTTGCC 58.840 52.381 0.00 0.00 0.00 4.52
350 361 0.879090 GGGAGTGGTTAGTTTTGCCG 59.121 55.000 0.00 0.00 0.00 5.69
351 362 0.879090 GGAGTGGTTAGTTTTGCCGG 59.121 55.000 0.00 0.00 0.00 6.13
352 363 1.601166 GAGTGGTTAGTTTTGCCGGT 58.399 50.000 1.90 0.00 0.00 5.28
370 399 1.694696 GGTGTCTGGTGTTTCTCTCCT 59.305 52.381 0.00 0.00 0.00 3.69
388 417 1.336609 CCTGCTTTTTGGAGCTGCTTC 60.337 52.381 6.82 0.96 43.11 3.86
490 521 6.808704 CAGGAATTGGAGCTAGCTTTTAAAAC 59.191 38.462 20.42 8.10 0.00 2.43
549 580 5.022282 AGGTAAGCTTGTGTTGCAAATTT 57.978 34.783 9.86 0.00 36.53 1.82
604 636 6.821388 AGATAGACATGGGTTTACTCACATC 58.179 40.000 0.00 0.00 0.00 3.06
789 1187 1.270518 CCATAGAGATCGGCAACCAGG 60.271 57.143 0.00 0.00 0.00 4.45
808 1206 1.607148 GGGCGCTCACTAACAGTTTTT 59.393 47.619 7.64 0.00 0.00 1.94
887 1321 5.643777 AGAGATGCGTTGCTGTTAATTAGTT 59.356 36.000 0.00 0.00 0.00 2.24
918 1352 0.454196 GCAACCACGTGGAACTTGTT 59.546 50.000 40.21 20.26 33.71 2.83
1051 1748 2.205022 ATGCAAAGCCACTGAGCTAA 57.795 45.000 0.00 0.00 44.11 3.09
1181 1895 1.380515 CCTCCTCTCCTCTTCCGCA 60.381 63.158 0.00 0.00 0.00 5.69
1238 1952 1.079127 CCCGACGCTGGAACTCATT 60.079 57.895 0.00 0.00 0.00 2.57
1511 2301 1.567537 CAACGTGAATTCGGTGCGT 59.432 52.632 0.04 6.21 41.45 5.24
1523 2313 2.260434 GTGCGTGGCTTCGAGGTA 59.740 61.111 6.82 0.00 0.00 3.08
1526 2316 0.036765 TGCGTGGCTTCGAGGTAATT 60.037 50.000 6.82 0.00 0.00 1.40
1627 2417 0.457337 GGCGTGGTTCTGGTACGTAG 60.457 60.000 0.00 0.00 39.79 3.51
1629 2419 1.336240 GCGTGGTTCTGGTACGTAGTT 60.336 52.381 0.00 0.00 37.78 2.24
1630 2420 2.095263 GCGTGGTTCTGGTACGTAGTTA 60.095 50.000 0.00 0.00 37.78 2.24
1631 2421 3.492313 CGTGGTTCTGGTACGTAGTTAC 58.508 50.000 0.00 0.00 37.78 2.50
1667 2464 4.175337 AGTGGGCACGTGCACTGT 62.175 61.111 39.61 25.62 46.62 3.55
1726 2543 1.035139 ACGTACGTTGTTCCTCCAGT 58.965 50.000 16.72 0.00 0.00 4.00
1728 2545 1.790623 CGTACGTTGTTCCTCCAGTTG 59.209 52.381 7.22 0.00 0.00 3.16
1824 2641 1.315690 TCCCGACGCCTGACTATAAG 58.684 55.000 0.00 0.00 0.00 1.73
2022 2839 2.515901 GCCCCCAATGGCGATACT 59.484 61.111 0.00 0.00 42.54 2.12
2115 2932 2.586792 GGCCTGCTGAACTCCGAT 59.413 61.111 0.00 0.00 0.00 4.18
2344 3163 4.334759 CGTCCGTCCTAAGTTAGATTCAGA 59.665 45.833 11.66 0.00 0.00 3.27
2493 3457 7.817418 AGCCGTTTGGTTCACATAATAATAT 57.183 32.000 0.00 0.00 37.67 1.28
2494 3458 8.911918 AGCCGTTTGGTTCACATAATAATATA 57.088 30.769 0.00 0.00 37.67 0.86
2495 3459 8.999431 AGCCGTTTGGTTCACATAATAATATAG 58.001 33.333 0.00 0.00 37.67 1.31
2553 3526 4.035208 GGTCGTTTATGCAACATCTAAGGG 59.965 45.833 0.00 0.00 34.68 3.95
2582 3560 4.694339 ACGCTCCTAAACTATTGACATCC 58.306 43.478 0.00 0.00 0.00 3.51
2586 3564 5.686124 GCTCCTAAACTATTGACATCCTGCT 60.686 44.000 0.00 0.00 0.00 4.24
2657 3640 1.184431 TTGTACGGAGCCGGTTCATA 58.816 50.000 20.67 8.91 44.69 2.15
2717 3701 5.577164 ACATAAGCACGCTACAAGAGTTAAG 59.423 40.000 0.00 0.00 0.00 1.85
2720 3704 4.177026 AGCACGCTACAAGAGTTAAGATG 58.823 43.478 0.00 0.00 0.00 2.90
2724 3708 6.453922 GCACGCTACAAGAGTTAAGATGTTAC 60.454 42.308 0.00 0.00 0.00 2.50
2725 3709 6.807230 CACGCTACAAGAGTTAAGATGTTACT 59.193 38.462 0.00 0.00 0.00 2.24
2726 3710 7.966753 CACGCTACAAGAGTTAAGATGTTACTA 59.033 37.037 0.00 0.00 0.00 1.82
2727 3711 7.967303 ACGCTACAAGAGTTAAGATGTTACTAC 59.033 37.037 0.00 0.00 0.00 2.73
2728 3712 7.966753 CGCTACAAGAGTTAAGATGTTACTACA 59.033 37.037 0.00 0.00 38.95 2.74
2749 3734 6.076981 ACATTTGTGCTTAGTTGAAGGAAG 57.923 37.500 0.00 0.00 37.23 3.46
2752 3737 4.431416 TGTGCTTAGTTGAAGGAAGGAA 57.569 40.909 0.00 0.00 37.23 3.36
2759 3744 4.105754 AGTTGAAGGAAGGAAAAGAGGG 57.894 45.455 0.00 0.00 0.00 4.30
2760 3745 3.722101 AGTTGAAGGAAGGAAAAGAGGGA 59.278 43.478 0.00 0.00 0.00 4.20
2840 3827 8.006564 AGACAATTTGTGGATTATATGATGGGT 58.993 33.333 6.80 0.00 0.00 4.51
2915 3902 6.862090 CGACTATTAGGTTGGCTATAAGTGAC 59.138 42.308 0.00 0.00 0.00 3.67
2919 3906 6.808321 TTAGGTTGGCTATAAGTGACTGAT 57.192 37.500 0.00 0.00 0.00 2.90
2957 3944 6.262273 CCGATTGTTGGCTACATTATTAACCT 59.738 38.462 1.93 0.00 36.44 3.50
2960 3947 6.202516 TGTTGGCTACATTATTAACCTTGC 57.797 37.500 0.00 0.00 0.00 4.01
2966 3953 7.715249 TGGCTACATTATTAACCTTGCTCTTAG 59.285 37.037 0.00 0.00 0.00 2.18
2977 3964 0.617820 TGCTCTTAGGGGAGGTCCAC 60.618 60.000 0.00 0.00 40.63 4.02
2978 3965 0.617820 GCTCTTAGGGGAGGTCCACA 60.618 60.000 0.00 0.00 43.57 4.17
3001 3988 0.729116 GTGGACGGTCTGCATGATTG 59.271 55.000 8.23 0.00 0.00 2.67
3002 3989 0.612744 TGGACGGTCTGCATGATTGA 59.387 50.000 8.23 0.00 0.00 2.57
3008 3995 2.743664 CGGTCTGCATGATTGAAGTTCA 59.256 45.455 0.08 0.08 29.62 3.18
3009 3996 3.376234 CGGTCTGCATGATTGAAGTTCAT 59.624 43.478 6.36 0.00 34.15 2.57
3015 4002 1.750193 TGATTGAAGTTCATCGGCCC 58.250 50.000 6.36 0.00 0.00 5.80
3026 4013 1.694169 ATCGGCCCCATTGACCTCT 60.694 57.895 0.00 0.00 0.00 3.69
3028 4015 2.276740 GGCCCCATTGACCTCTGG 59.723 66.667 0.00 0.00 0.00 3.86
3032 4019 1.752084 GCCCCATTGACCTCTGGAATC 60.752 57.143 0.00 0.00 34.24 2.52
3048 4035 3.144506 GGAATCGCATCTCATGGTTCAT 58.855 45.455 0.00 0.00 0.00 2.57
3049 4036 4.202346 TGGAATCGCATCTCATGGTTCATA 60.202 41.667 0.00 0.00 0.00 2.15
3051 4038 2.742774 TCGCATCTCATGGTTCATACG 58.257 47.619 0.00 0.00 0.00 3.06
3101 4088 2.046507 CGCTTCTTCCTGCTGGCT 60.047 61.111 4.42 0.00 0.00 4.75
3113 4100 1.003355 GCTGGCTGCAACTAGACCA 60.003 57.895 11.80 0.00 42.31 4.02
3116 4103 0.692476 TGGCTGCAACTAGACCATGT 59.308 50.000 0.50 0.00 0.00 3.21
3122 4109 3.261580 TGCAACTAGACCATGTTCATCG 58.738 45.455 0.00 0.00 0.00 3.84
3124 4111 3.307242 GCAACTAGACCATGTTCATCGTC 59.693 47.826 0.00 3.10 0.00 4.20
3159 4146 4.781959 CAACGCTGGCCGGCATTG 62.782 66.667 35.00 32.03 42.52 2.82
3163 4150 3.830192 GCTGGCCGGCATTGGAAG 61.830 66.667 32.13 15.55 0.00 3.46
3164 4151 3.142838 CTGGCCGGCATTGGAAGG 61.143 66.667 30.85 4.31 0.00 3.46
3167 4154 3.521796 GCCGGCATTGGAAGGCTC 61.522 66.667 24.80 0.00 45.67 4.70
3168 4155 2.273449 CCGGCATTGGAAGGCTCT 59.727 61.111 0.00 0.00 35.75 4.09
3169 4156 1.821332 CCGGCATTGGAAGGCTCTC 60.821 63.158 0.00 0.00 35.75 3.20
3170 4157 1.821332 CGGCATTGGAAGGCTCTCC 60.821 63.158 8.30 8.30 35.75 3.71
3171 4158 1.304282 GGCATTGGAAGGCTCTCCA 59.696 57.895 12.50 12.50 43.99 3.86
3172 4159 1.034292 GGCATTGGAAGGCTCTCCAC 61.034 60.000 15.16 6.95 45.37 4.02
3173 4160 1.372087 GCATTGGAAGGCTCTCCACG 61.372 60.000 15.16 11.54 45.37 4.94
3174 4161 0.250234 CATTGGAAGGCTCTCCACGA 59.750 55.000 15.16 5.58 45.37 4.35
3175 4162 1.134280 CATTGGAAGGCTCTCCACGAT 60.134 52.381 15.16 7.25 45.37 3.73
3176 4163 0.250234 TTGGAAGGCTCTCCACGATG 59.750 55.000 15.16 0.00 45.37 3.84
3177 4164 1.522580 GGAAGGCTCTCCACGATGC 60.523 63.158 9.85 0.00 35.36 3.91
3178 4165 1.219124 GAAGGCTCTCCACGATGCA 59.781 57.895 0.00 0.00 33.74 3.96
3179 4166 0.179062 GAAGGCTCTCCACGATGCAT 60.179 55.000 0.00 0.00 33.74 3.96
3180 4167 0.463295 AAGGCTCTCCACGATGCATG 60.463 55.000 2.46 0.00 33.74 4.06
3181 4168 1.153289 GGCTCTCCACGATGCATGT 60.153 57.895 2.46 0.00 0.00 3.21
3182 4169 1.156645 GGCTCTCCACGATGCATGTC 61.157 60.000 2.46 0.00 0.00 3.06
3183 4170 0.179089 GCTCTCCACGATGCATGTCT 60.179 55.000 2.46 0.00 0.00 3.41
3184 4171 1.568606 CTCTCCACGATGCATGTCTG 58.431 55.000 2.46 0.00 0.00 3.51
3194 4181 3.786656 GCATGTCTGCCACATAGGA 57.213 52.632 0.00 0.00 44.60 2.94
3195 4182 2.042686 GCATGTCTGCCACATAGGAA 57.957 50.000 0.00 0.00 44.60 3.36
3196 4183 1.945394 GCATGTCTGCCACATAGGAAG 59.055 52.381 0.00 0.00 44.60 3.46
3197 4184 2.569059 CATGTCTGCCACATAGGAAGG 58.431 52.381 0.00 0.00 44.60 3.46
3198 4185 0.911769 TGTCTGCCACATAGGAAGGG 59.088 55.000 0.00 0.00 44.19 3.95
3199 4186 0.181350 GTCTGCCACATAGGAAGGGG 59.819 60.000 0.00 0.00 44.19 4.79
3200 4187 0.988145 TCTGCCACATAGGAAGGGGG 60.988 60.000 0.00 0.00 44.19 5.40
3224 4211 2.783609 GGGGGACTTGTTTCTCTACC 57.216 55.000 0.00 0.00 0.00 3.18
3225 4212 1.982958 GGGGGACTTGTTTCTCTACCA 59.017 52.381 0.00 0.00 0.00 3.25
3226 4213 2.374170 GGGGGACTTGTTTCTCTACCAA 59.626 50.000 0.00 0.00 0.00 3.67
3227 4214 3.559384 GGGGGACTTGTTTCTCTACCAAG 60.559 52.174 0.00 0.00 41.02 3.61
3228 4215 3.559384 GGGGACTTGTTTCTCTACCAAGG 60.559 52.174 0.00 0.00 39.85 3.61
3229 4216 3.072622 GGGACTTGTTTCTCTACCAAGGT 59.927 47.826 0.00 0.00 39.85 3.50
3230 4217 4.316645 GGACTTGTTTCTCTACCAAGGTC 58.683 47.826 0.00 0.00 39.85 3.85
3231 4218 3.988517 GACTTGTTTCTCTACCAAGGTCG 59.011 47.826 0.00 0.00 39.85 4.79
3232 4219 3.640029 ACTTGTTTCTCTACCAAGGTCGA 59.360 43.478 0.00 0.00 39.85 4.20
3233 4220 4.100498 ACTTGTTTCTCTACCAAGGTCGAA 59.900 41.667 0.00 0.00 39.85 3.71
3234 4221 4.252971 TGTTTCTCTACCAAGGTCGAAG 57.747 45.455 0.00 0.00 0.00 3.79
3235 4222 3.006537 TGTTTCTCTACCAAGGTCGAAGG 59.993 47.826 0.00 0.00 0.00 3.46
3236 4223 1.848652 TCTCTACCAAGGTCGAAGGG 58.151 55.000 0.00 0.00 0.00 3.95
3237 4224 1.076677 TCTCTACCAAGGTCGAAGGGT 59.923 52.381 0.00 0.00 37.43 4.34
3238 4225 1.204941 CTCTACCAAGGTCGAAGGGTG 59.795 57.143 0.00 0.00 34.88 4.61
3239 4226 0.974383 CTACCAAGGTCGAAGGGTGT 59.026 55.000 0.00 0.00 34.88 4.16
3240 4227 0.682852 TACCAAGGTCGAAGGGTGTG 59.317 55.000 0.00 0.00 34.88 3.82
3241 4228 1.966451 CCAAGGTCGAAGGGTGTGC 60.966 63.158 0.00 0.00 0.00 4.57
3242 4229 1.227823 CAAGGTCGAAGGGTGTGCA 60.228 57.895 0.00 0.00 0.00 4.57
3243 4230 0.606401 CAAGGTCGAAGGGTGTGCAT 60.606 55.000 0.00 0.00 0.00 3.96
3244 4231 0.981183 AAGGTCGAAGGGTGTGCATA 59.019 50.000 0.00 0.00 0.00 3.14
3245 4232 0.981183 AGGTCGAAGGGTGTGCATAA 59.019 50.000 0.00 0.00 0.00 1.90
3246 4233 1.066143 AGGTCGAAGGGTGTGCATAAG 60.066 52.381 0.00 0.00 0.00 1.73
3247 4234 1.369625 GTCGAAGGGTGTGCATAAGG 58.630 55.000 0.00 0.00 0.00 2.69
3248 4235 0.251916 TCGAAGGGTGTGCATAAGGG 59.748 55.000 0.00 0.00 0.00 3.95
3249 4236 0.251916 CGAAGGGTGTGCATAAGGGA 59.748 55.000 0.00 0.00 0.00 4.20
3250 4237 1.134098 CGAAGGGTGTGCATAAGGGAT 60.134 52.381 0.00 0.00 0.00 3.85
3251 4238 2.104111 CGAAGGGTGTGCATAAGGGATA 59.896 50.000 0.00 0.00 0.00 2.59
3252 4239 3.244561 CGAAGGGTGTGCATAAGGGATAT 60.245 47.826 0.00 0.00 0.00 1.63
3253 4240 3.795688 AGGGTGTGCATAAGGGATATG 57.204 47.619 0.00 0.00 43.64 1.78
3254 4241 3.056080 AGGGTGTGCATAAGGGATATGT 58.944 45.455 0.00 0.00 42.89 2.29
3255 4242 3.463329 AGGGTGTGCATAAGGGATATGTT 59.537 43.478 0.00 0.00 42.89 2.71
3256 4243 4.079212 AGGGTGTGCATAAGGGATATGTTT 60.079 41.667 0.00 0.00 42.89 2.83
3257 4244 4.278419 GGGTGTGCATAAGGGATATGTTTC 59.722 45.833 0.00 0.00 42.89 2.78
3258 4245 4.278419 GGTGTGCATAAGGGATATGTTTCC 59.722 45.833 0.00 0.00 42.89 3.13
3259 4246 4.024048 GTGTGCATAAGGGATATGTTTCCG 60.024 45.833 0.00 0.00 42.89 4.30
3260 4247 4.134563 GTGCATAAGGGATATGTTTCCGT 58.865 43.478 0.00 0.00 42.89 4.69
3261 4248 4.213482 GTGCATAAGGGATATGTTTCCGTC 59.787 45.833 0.00 0.00 42.89 4.79
3262 4249 4.102524 TGCATAAGGGATATGTTTCCGTCT 59.897 41.667 0.00 0.00 42.89 4.18
3263 4250 5.063880 GCATAAGGGATATGTTTCCGTCTT 58.936 41.667 0.00 0.00 42.89 3.01
3264 4251 5.531287 GCATAAGGGATATGTTTCCGTCTTT 59.469 40.000 0.00 0.00 42.89 2.52
3265 4252 6.513393 GCATAAGGGATATGTTTCCGTCTTTG 60.513 42.308 0.00 0.00 42.89 2.77
3266 4253 4.837093 AGGGATATGTTTCCGTCTTTGA 57.163 40.909 0.00 0.00 36.58 2.69
3267 4254 4.514401 AGGGATATGTTTCCGTCTTTGAC 58.486 43.478 0.00 0.00 36.58 3.18
3268 4255 4.019681 AGGGATATGTTTCCGTCTTTGACA 60.020 41.667 0.00 0.00 36.58 3.58
3269 4256 4.881850 GGGATATGTTTCCGTCTTTGACAT 59.118 41.667 0.00 0.00 36.58 3.06
3270 4257 5.220854 GGGATATGTTTCCGTCTTTGACATG 60.221 44.000 0.00 0.00 36.58 3.21
3271 4258 5.220854 GGATATGTTTCCGTCTTTGACATGG 60.221 44.000 0.00 0.00 33.42 3.66
3272 4259 3.201353 TGTTTCCGTCTTTGACATGGA 57.799 42.857 0.00 0.00 32.09 3.41
3273 4260 3.750371 TGTTTCCGTCTTTGACATGGAT 58.250 40.909 0.00 0.00 32.09 3.41
3274 4261 4.141287 TGTTTCCGTCTTTGACATGGATT 58.859 39.130 0.00 0.00 32.09 3.01
3275 4262 4.582656 TGTTTCCGTCTTTGACATGGATTT 59.417 37.500 0.00 0.00 32.09 2.17
3276 4263 5.068460 TGTTTCCGTCTTTGACATGGATTTT 59.932 36.000 0.00 0.00 32.09 1.82
3277 4264 4.764679 TCCGTCTTTGACATGGATTTTG 57.235 40.909 0.00 0.00 32.09 2.44
3278 4265 4.141287 TCCGTCTTTGACATGGATTTTGT 58.859 39.130 0.00 0.00 32.09 2.83
3279 4266 4.582656 TCCGTCTTTGACATGGATTTTGTT 59.417 37.500 0.00 0.00 32.09 2.83
3280 4267 5.765677 TCCGTCTTTGACATGGATTTTGTTA 59.234 36.000 0.00 0.00 32.09 2.41
3281 4268 6.432783 TCCGTCTTTGACATGGATTTTGTTAT 59.567 34.615 0.00 0.00 32.09 1.89
3282 4269 6.747280 CCGTCTTTGACATGGATTTTGTTATC 59.253 38.462 0.00 0.00 32.09 1.75
3283 4270 7.362056 CCGTCTTTGACATGGATTTTGTTATCT 60.362 37.037 0.00 0.00 32.09 1.98
3284 4271 7.482743 CGTCTTTGACATGGATTTTGTTATCTG 59.517 37.037 0.00 0.00 32.09 2.90
3285 4272 7.756722 GTCTTTGACATGGATTTTGTTATCTGG 59.243 37.037 0.00 0.00 32.09 3.86
3286 4273 7.451255 TCTTTGACATGGATTTTGTTATCTGGT 59.549 33.333 0.00 0.00 0.00 4.00
3287 4274 6.513806 TGACATGGATTTTGTTATCTGGTG 57.486 37.500 0.00 0.00 0.00 4.17
3288 4275 5.418524 TGACATGGATTTTGTTATCTGGTGG 59.581 40.000 0.00 0.00 0.00 4.61
3289 4276 5.579047 ACATGGATTTTGTTATCTGGTGGA 58.421 37.500 0.00 0.00 0.00 4.02
3290 4277 6.015918 ACATGGATTTTGTTATCTGGTGGAA 58.984 36.000 0.00 0.00 0.00 3.53
3291 4278 6.496565 ACATGGATTTTGTTATCTGGTGGAAA 59.503 34.615 0.00 0.00 0.00 3.13
3292 4279 7.180766 ACATGGATTTTGTTATCTGGTGGAAAT 59.819 33.333 0.00 0.00 0.00 2.17
3293 4280 7.552050 TGGATTTTGTTATCTGGTGGAAATT 57.448 32.000 0.00 0.00 0.00 1.82
3294 4281 7.972301 TGGATTTTGTTATCTGGTGGAAATTT 58.028 30.769 0.00 0.00 0.00 1.82
3295 4282 8.435982 TGGATTTTGTTATCTGGTGGAAATTTT 58.564 29.630 0.00 0.00 0.00 1.82
3296 4283 8.720562 GGATTTTGTTATCTGGTGGAAATTTTG 58.279 33.333 0.00 0.00 0.00 2.44
3297 4284 8.620116 ATTTTGTTATCTGGTGGAAATTTTGG 57.380 30.769 0.00 0.00 0.00 3.28
3298 4285 6.739331 TTGTTATCTGGTGGAAATTTTGGT 57.261 33.333 0.00 0.00 0.00 3.67
3299 4286 6.739331 TGTTATCTGGTGGAAATTTTGGTT 57.261 33.333 0.00 0.00 0.00 3.67
3300 4287 7.130681 TGTTATCTGGTGGAAATTTTGGTTT 57.869 32.000 0.00 0.00 0.00 3.27
3301 4288 7.569240 TGTTATCTGGTGGAAATTTTGGTTTT 58.431 30.769 0.00 0.00 0.00 2.43
3302 4289 8.049721 TGTTATCTGGTGGAAATTTTGGTTTTT 58.950 29.630 0.00 0.00 0.00 1.94
3303 4290 8.556194 GTTATCTGGTGGAAATTTTGGTTTTTC 58.444 33.333 0.00 0.00 0.00 2.29
3312 4299 8.083462 GGAAATTTTGGTTTTTCCTCATACAC 57.917 34.615 7.09 0.00 44.86 2.90
3313 4300 7.095816 GGAAATTTTGGTTTTTCCTCATACACG 60.096 37.037 7.09 0.00 44.86 4.49
3314 4301 6.642707 ATTTTGGTTTTTCCTCATACACGA 57.357 33.333 0.00 0.00 37.07 4.35
3315 4302 6.452494 TTTTGGTTTTTCCTCATACACGAA 57.548 33.333 0.00 0.00 37.07 3.85
3316 4303 5.682943 TTGGTTTTTCCTCATACACGAAG 57.317 39.130 0.00 0.00 37.07 3.79
3317 4304 4.963373 TGGTTTTTCCTCATACACGAAGA 58.037 39.130 0.00 0.00 37.07 2.87
3318 4305 4.994852 TGGTTTTTCCTCATACACGAAGAG 59.005 41.667 0.00 0.00 37.07 2.85
3319 4306 5.221561 TGGTTTTTCCTCATACACGAAGAGA 60.222 40.000 0.00 0.00 37.07 3.10
3320 4307 5.699458 GGTTTTTCCTCATACACGAAGAGAA 59.301 40.000 0.00 0.00 0.00 2.87
3321 4308 6.204108 GGTTTTTCCTCATACACGAAGAGAAA 59.796 38.462 0.00 0.00 0.00 2.52
3322 4309 7.094762 GGTTTTTCCTCATACACGAAGAGAAAT 60.095 37.037 0.00 0.00 0.00 2.17
3323 4310 8.932791 GTTTTTCCTCATACACGAAGAGAAATA 58.067 33.333 0.00 0.00 0.00 1.40
3324 4311 8.703604 TTTTCCTCATACACGAAGAGAAATAG 57.296 34.615 0.00 0.00 0.00 1.73
3325 4312 7.640597 TTCCTCATACACGAAGAGAAATAGA 57.359 36.000 0.00 0.00 0.00 1.98
3326 4313 7.028926 TCCTCATACACGAAGAGAAATAGAC 57.971 40.000 0.00 0.00 0.00 2.59
3327 4314 6.829298 TCCTCATACACGAAGAGAAATAGACT 59.171 38.462 0.00 0.00 0.00 3.24
3328 4315 7.339721 TCCTCATACACGAAGAGAAATAGACTT 59.660 37.037 0.00 0.00 0.00 3.01
3329 4316 7.976734 CCTCATACACGAAGAGAAATAGACTTT 59.023 37.037 0.00 0.00 0.00 2.66
3330 4317 9.360093 CTCATACACGAAGAGAAATAGACTTTT 57.640 33.333 0.00 0.00 0.00 2.27
3331 4318 9.355215 TCATACACGAAGAGAAATAGACTTTTC 57.645 33.333 0.00 0.00 36.13 2.29
3332 4319 9.140286 CATACACGAAGAGAAATAGACTTTTCA 57.860 33.333 0.00 0.00 37.93 2.69
3333 4320 9.706691 ATACACGAAGAGAAATAGACTTTTCAA 57.293 29.630 0.00 0.00 37.93 2.69
3334 4321 8.077836 ACACGAAGAGAAATAGACTTTTCAAG 57.922 34.615 0.00 0.00 37.93 3.02
3335 4322 7.012358 CACGAAGAGAAATAGACTTTTCAAGC 58.988 38.462 0.00 0.00 37.93 4.01
3336 4323 6.706270 ACGAAGAGAAATAGACTTTTCAAGCA 59.294 34.615 0.00 0.00 37.93 3.91
3337 4324 7.226720 ACGAAGAGAAATAGACTTTTCAAGCAA 59.773 33.333 0.00 0.00 37.93 3.91
3338 4325 8.070171 CGAAGAGAAATAGACTTTTCAAGCAAA 58.930 33.333 10.65 0.00 37.93 3.68
3339 4326 9.736023 GAAGAGAAATAGACTTTTCAAGCAAAA 57.264 29.630 10.65 0.00 37.93 2.44
3341 4328 9.521503 AGAGAAATAGACTTTTCAAGCAAAAAC 57.478 29.630 10.65 0.00 37.93 2.43
3342 4329 9.301153 GAGAAATAGACTTTTCAAGCAAAAACA 57.699 29.630 10.65 0.00 37.93 2.83
3343 4330 9.651913 AGAAATAGACTTTTCAAGCAAAAACAA 57.348 25.926 10.65 0.00 37.93 2.83
3346 4333 9.598517 AATAGACTTTTCAAGCAAAAACAATGA 57.401 25.926 0.00 0.00 33.40 2.57
3347 4334 7.903995 AGACTTTTCAAGCAAAAACAATGAA 57.096 28.000 0.00 0.00 33.40 2.57
3348 4335 8.496707 AGACTTTTCAAGCAAAAACAATGAAT 57.503 26.923 0.00 0.00 33.40 2.57
3349 4336 8.949177 AGACTTTTCAAGCAAAAACAATGAATT 58.051 25.926 0.00 0.00 33.40 2.17
3350 4337 9.558648 GACTTTTCAAGCAAAAACAATGAATTT 57.441 25.926 0.00 0.00 33.40 1.82
3351 4338 9.911138 ACTTTTCAAGCAAAAACAATGAATTTT 57.089 22.222 0.00 0.00 33.40 1.82
3353 4340 9.903682 TTTTCAAGCAAAAACAATGAATTTTGA 57.096 22.222 22.69 8.00 45.09 2.69
3354 4341 9.903682 TTTCAAGCAAAAACAATGAATTTTGAA 57.096 22.222 22.69 11.81 45.09 2.69
3355 4342 9.903682 TTCAAGCAAAAACAATGAATTTTGAAA 57.096 22.222 22.69 12.87 45.09 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
328 339 1.804748 GCAAAACTAACCACTCCCTCG 59.195 52.381 0.00 0.00 0.00 4.63
335 346 1.002142 GACACCGGCAAAACTAACCAC 60.002 52.381 0.00 0.00 0.00 4.16
336 347 1.134037 AGACACCGGCAAAACTAACCA 60.134 47.619 0.00 0.00 0.00 3.67
337 348 1.265905 CAGACACCGGCAAAACTAACC 59.734 52.381 0.00 0.00 0.00 2.85
338 349 1.265905 CCAGACACCGGCAAAACTAAC 59.734 52.381 0.00 0.00 0.00 2.34
339 350 1.134037 ACCAGACACCGGCAAAACTAA 60.134 47.619 0.00 0.00 0.00 2.24
340 351 0.470766 ACCAGACACCGGCAAAACTA 59.529 50.000 0.00 0.00 0.00 2.24
341 352 1.101049 CACCAGACACCGGCAAAACT 61.101 55.000 0.00 0.00 0.00 2.66
342 353 1.358759 CACCAGACACCGGCAAAAC 59.641 57.895 0.00 0.00 0.00 2.43
343 354 0.681564 AACACCAGACACCGGCAAAA 60.682 50.000 0.00 0.00 0.00 2.44
344 355 0.681564 AAACACCAGACACCGGCAAA 60.682 50.000 0.00 0.00 0.00 3.68
345 356 1.077357 AAACACCAGACACCGGCAA 60.077 52.632 0.00 0.00 0.00 4.52
346 357 1.525077 GAAACACCAGACACCGGCA 60.525 57.895 0.00 0.00 0.00 5.69
347 358 1.227853 AGAAACACCAGACACCGGC 60.228 57.895 0.00 0.00 0.00 6.13
348 359 0.393077 AGAGAAACACCAGACACCGG 59.607 55.000 0.00 0.00 0.00 5.28
349 360 1.605712 GGAGAGAAACACCAGACACCG 60.606 57.143 0.00 0.00 0.00 4.94
350 361 1.694696 AGGAGAGAAACACCAGACACC 59.305 52.381 0.00 0.00 0.00 4.16
351 362 2.760374 CAGGAGAGAAACACCAGACAC 58.240 52.381 0.00 0.00 0.00 3.67
352 363 1.070758 GCAGGAGAGAAACACCAGACA 59.929 52.381 0.00 0.00 0.00 3.41
370 399 0.311790 CGAAGCAGCTCCAAAAAGCA 59.688 50.000 0.00 0.00 45.00 3.91
388 417 6.219473 ACAAACAGGAGCATAGAGAATATCG 58.781 40.000 0.00 0.00 0.00 2.92
503 534 3.509575 CCTGCCTGCCTTGTTATGTTTTA 59.490 43.478 0.00 0.00 0.00 1.52
582 614 6.560003 TGATGTGAGTAAACCCATGTCTAT 57.440 37.500 0.00 0.00 0.00 1.98
685 734 6.573434 AGGGTTGTTTCATGAACTTCTTTTC 58.427 36.000 7.89 0.00 39.08 2.29
887 1321 2.158871 ACGTGGTTGCTTTCTCTGGTTA 60.159 45.455 0.00 0.00 0.00 2.85
918 1352 4.620332 CGTACGGGGTTGTGGAAAAGTATA 60.620 45.833 7.57 0.00 0.00 1.47
1051 1748 4.623932 TCTTCACTGTAAGCAGGATTGT 57.376 40.909 0.00 0.00 46.62 2.71
1238 1952 4.961511 GTCACCGTGGAGCGCACA 62.962 66.667 11.47 5.21 39.71 4.57
1511 2301 1.546923 TCGTCAATTACCTCGAAGCCA 59.453 47.619 0.00 0.00 0.00 4.75
1523 2313 5.119279 CACGTTCTTCTTGATCTCGTCAATT 59.881 40.000 0.00 0.00 45.36 2.32
1526 2316 3.565516 CACGTTCTTCTTGATCTCGTCA 58.434 45.455 0.00 0.00 34.25 4.35
1627 2417 5.863898 TGTCATTGATTGTATGCACGTAAC 58.136 37.500 0.00 0.00 0.00 2.50
1628 2418 5.641636 ACTGTCATTGATTGTATGCACGTAA 59.358 36.000 0.00 0.00 0.00 3.18
1629 2419 5.063312 CACTGTCATTGATTGTATGCACGTA 59.937 40.000 0.00 0.00 0.00 3.57
1630 2420 4.002982 ACTGTCATTGATTGTATGCACGT 58.997 39.130 0.00 0.00 0.00 4.49
1631 2421 4.336932 CACTGTCATTGATTGTATGCACG 58.663 43.478 0.00 0.00 0.00 5.34
1632 2422 4.439153 CCCACTGTCATTGATTGTATGCAC 60.439 45.833 0.00 0.00 0.00 4.57
1633 2423 3.695556 CCCACTGTCATTGATTGTATGCA 59.304 43.478 0.00 0.00 0.00 3.96
1634 2424 3.489738 GCCCACTGTCATTGATTGTATGC 60.490 47.826 0.00 0.00 0.00 3.14
1667 2464 6.296026 AGCATTGTCAGTAACCAGAAAACTA 58.704 36.000 0.00 0.00 0.00 2.24
2013 2830 1.440060 CGCCAGGTTAGTATCGCCA 59.560 57.895 0.00 0.00 0.00 5.69
2022 2839 1.448893 GTCGAATGGCGCCAGGTTA 60.449 57.895 35.36 17.44 40.61 2.85
2115 2932 1.293498 GCCGTTGAAGAGCTCCTGA 59.707 57.895 10.93 0.00 0.00 3.86
2361 3180 1.613836 ACACGTACTTCCTCCGTCTT 58.386 50.000 0.00 0.00 31.46 3.01
2371 3190 5.232838 GCACTTAACACTGTAACACGTACTT 59.767 40.000 0.00 0.00 33.46 2.24
2414 3233 8.975410 TGGTTACATATCATGCGTACTTATAC 57.025 34.615 0.00 0.00 0.00 1.47
2494 3458 9.525409 GTTTCCGTTATAGTATTGTCACATACT 57.475 33.333 10.53 10.53 37.38 2.12
2495 3459 9.304731 TGTTTCCGTTATAGTATTGTCACATAC 57.695 33.333 0.00 0.00 0.00 2.39
2553 3526 5.865552 TCAATAGTTTAGGAGCGTACACAAC 59.134 40.000 0.00 0.00 0.00 3.32
2689 3673 4.503910 TCTTGTAGCGTGCTTATGTCATT 58.496 39.130 0.00 0.00 0.00 2.57
2702 3686 7.966753 TGTAGTAACATCTTAACTCTTGTAGCG 59.033 37.037 0.00 0.00 0.00 4.26
2717 3701 8.717821 TCAACTAAGCACAAATGTAGTAACATC 58.282 33.333 0.00 0.00 45.79 3.06
2720 3704 8.015658 CCTTCAACTAAGCACAAATGTAGTAAC 58.984 37.037 0.00 0.00 33.49 2.50
2724 3708 6.801539 TCCTTCAACTAAGCACAAATGTAG 57.198 37.500 0.00 0.00 33.49 2.74
2725 3709 6.206634 CCTTCCTTCAACTAAGCACAAATGTA 59.793 38.462 0.00 0.00 33.49 2.29
2726 3710 5.010012 CCTTCCTTCAACTAAGCACAAATGT 59.990 40.000 0.00 0.00 33.49 2.71
2727 3711 5.241506 TCCTTCCTTCAACTAAGCACAAATG 59.758 40.000 0.00 0.00 33.49 2.32
2728 3712 5.385198 TCCTTCCTTCAACTAAGCACAAAT 58.615 37.500 0.00 0.00 33.49 2.32
2729 3713 4.787551 TCCTTCCTTCAACTAAGCACAAA 58.212 39.130 0.00 0.00 33.49 2.83
2734 3718 5.182190 CCTCTTTTCCTTCCTTCAACTAAGC 59.818 44.000 0.00 0.00 33.49 3.09
2749 3734 3.621214 GCTTCTCTCCTTCCCTCTTTTCC 60.621 52.174 0.00 0.00 0.00 3.13
2752 3737 1.552792 CGCTTCTCTCCTTCCCTCTTT 59.447 52.381 0.00 0.00 0.00 2.52
2759 3744 2.003196 CCACTTCGCTTCTCTCCTTC 57.997 55.000 0.00 0.00 0.00 3.46
2760 3745 0.036858 GCCACTTCGCTTCTCTCCTT 60.037 55.000 0.00 0.00 0.00 3.36
2876 3863 5.577164 CCTAATAGTCGGCATGTACAATAGC 59.423 44.000 0.00 4.63 0.00 2.97
2915 3902 5.186021 ACAATCGGCTATAGGGAGTTATCAG 59.814 44.000 1.04 0.00 0.00 2.90
2919 3906 4.039973 CCAACAATCGGCTATAGGGAGTTA 59.960 45.833 1.04 0.00 0.00 2.24
2946 3933 6.601332 TCCCCTAAGAGCAAGGTTAATAATG 58.399 40.000 0.00 0.00 31.70 1.90
2957 3944 0.118346 TGGACCTCCCCTAAGAGCAA 59.882 55.000 0.00 0.00 34.29 3.91
2960 3947 1.196012 GTGTGGACCTCCCCTAAGAG 58.804 60.000 0.00 0.00 34.29 2.85
2966 3953 1.002134 CACATGTGTGGACCTCCCC 60.002 63.158 18.03 0.00 42.10 4.81
2977 3964 0.674581 ATGCAGACCGTCCACATGTG 60.675 55.000 19.31 19.31 0.00 3.21
2978 3965 0.674581 CATGCAGACCGTCCACATGT 60.675 55.000 17.45 0.00 34.73 3.21
2988 3975 4.495349 CGATGAACTTCAATCATGCAGACC 60.495 45.833 0.00 0.00 37.64 3.85
2990 3977 3.624410 CCGATGAACTTCAATCATGCAGA 59.376 43.478 0.00 0.00 37.64 4.26
3001 3988 0.740737 CAATGGGGCCGATGAACTTC 59.259 55.000 0.30 0.00 0.00 3.01
3002 3989 0.331278 TCAATGGGGCCGATGAACTT 59.669 50.000 0.30 0.00 0.00 2.66
3008 3995 1.694169 AGAGGTCAATGGGGCCGAT 60.694 57.895 0.00 0.00 0.00 4.18
3009 3996 2.285368 AGAGGTCAATGGGGCCGA 60.285 61.111 0.00 0.00 0.00 5.54
3015 4002 1.303309 GCGATTCCAGAGGTCAATGG 58.697 55.000 0.00 0.00 37.97 3.16
3026 4013 2.093021 TGAACCATGAGATGCGATTCCA 60.093 45.455 0.00 0.00 0.00 3.53
3028 4015 4.143242 CGTATGAACCATGAGATGCGATTC 60.143 45.833 0.00 0.00 0.00 2.52
3032 4019 1.794701 CCGTATGAACCATGAGATGCG 59.205 52.381 0.00 0.00 0.00 4.73
3061 4048 1.591183 CAAAATGAGCGGTTGGGGG 59.409 57.895 0.00 0.00 0.00 5.40
3062 4049 1.184970 ACCAAAATGAGCGGTTGGGG 61.185 55.000 7.17 0.00 45.09 4.96
3066 4053 1.665442 GCCACCAAAATGAGCGGTT 59.335 52.632 0.00 0.00 0.00 4.44
3067 4054 2.625823 CGCCACCAAAATGAGCGGT 61.626 57.895 0.00 0.00 42.93 5.68
3068 4055 2.179018 CGCCACCAAAATGAGCGG 59.821 61.111 0.00 0.00 42.93 5.52
3071 4058 0.883833 AGAAGCGCCACCAAAATGAG 59.116 50.000 2.29 0.00 0.00 2.90
3072 4059 1.269448 GAAGAAGCGCCACCAAAATGA 59.731 47.619 2.29 0.00 0.00 2.57
3073 4060 1.669795 GGAAGAAGCGCCACCAAAATG 60.670 52.381 2.29 0.00 0.00 2.32
3074 4061 0.603065 GGAAGAAGCGCCACCAAAAT 59.397 50.000 2.29 0.00 0.00 1.82
3101 4088 3.261580 CGATGAACATGGTCTAGTTGCA 58.738 45.455 12.94 0.00 0.00 4.08
3113 4100 2.743938 GCCATAGACGACGATGAACAT 58.256 47.619 9.30 0.00 32.28 2.71
3116 4103 1.018910 TCGCCATAGACGACGATGAA 58.981 50.000 9.30 0.00 33.96 2.57
3122 4109 1.772182 CCTTCATCGCCATAGACGAC 58.228 55.000 0.00 0.00 43.23 4.34
3124 4111 0.249447 TGCCTTCATCGCCATAGACG 60.249 55.000 0.00 0.00 0.00 4.18
3158 4145 1.900351 CATCGTGGAGAGCCTTCCA 59.100 57.895 2.77 2.77 44.84 3.53
3159 4146 1.522580 GCATCGTGGAGAGCCTTCC 60.523 63.158 0.00 0.00 37.77 3.46
3160 4147 0.179062 ATGCATCGTGGAGAGCCTTC 60.179 55.000 0.00 0.00 34.31 3.46
3161 4148 0.463295 CATGCATCGTGGAGAGCCTT 60.463 55.000 0.00 0.00 34.31 4.35
3162 4149 1.145598 CATGCATCGTGGAGAGCCT 59.854 57.895 0.00 0.00 34.31 4.58
3163 4150 1.153289 ACATGCATCGTGGAGAGCC 60.153 57.895 0.00 0.00 0.00 4.70
3164 4151 0.179089 AGACATGCATCGTGGAGAGC 60.179 55.000 0.00 0.00 0.00 4.09
3165 4152 1.568606 CAGACATGCATCGTGGAGAG 58.431 55.000 0.00 0.00 0.00 3.20
3166 4153 3.746900 CAGACATGCATCGTGGAGA 57.253 52.632 0.00 0.00 0.00 3.71
3177 4164 2.569059 CCTTCCTATGTGGCAGACATG 58.431 52.381 10.14 0.00 45.43 3.21
3179 4166 0.911769 CCCTTCCTATGTGGCAGACA 59.088 55.000 0.00 0.00 39.53 3.41
3180 4167 0.181350 CCCCTTCCTATGTGGCAGAC 59.819 60.000 0.00 0.00 30.20 3.51
3181 4168 0.988145 CCCCCTTCCTATGTGGCAGA 60.988 60.000 0.00 0.00 30.20 4.26
3182 4169 1.533711 CCCCCTTCCTATGTGGCAG 59.466 63.158 0.00 0.00 35.26 4.85
3183 4170 3.754043 CCCCCTTCCTATGTGGCA 58.246 61.111 0.00 0.00 35.26 4.92
3205 4192 1.982958 TGGTAGAGAAACAAGTCCCCC 59.017 52.381 0.00 0.00 0.00 5.40
3206 4193 3.559384 CCTTGGTAGAGAAACAAGTCCCC 60.559 52.174 2.43 0.00 39.85 4.81
3207 4194 3.072622 ACCTTGGTAGAGAAACAAGTCCC 59.927 47.826 2.43 0.00 39.85 4.46
3208 4195 4.316645 GACCTTGGTAGAGAAACAAGTCC 58.683 47.826 2.43 0.00 39.85 3.85
3209 4196 3.988517 CGACCTTGGTAGAGAAACAAGTC 59.011 47.826 2.43 0.42 39.85 3.01
3210 4197 3.640029 TCGACCTTGGTAGAGAAACAAGT 59.360 43.478 2.43 0.00 39.85 3.16
3211 4198 4.252971 TCGACCTTGGTAGAGAAACAAG 57.747 45.455 0.00 0.00 40.85 3.16
3212 4199 4.502604 CCTTCGACCTTGGTAGAGAAACAA 60.503 45.833 3.08 0.00 0.00 2.83
3213 4200 3.006537 CCTTCGACCTTGGTAGAGAAACA 59.993 47.826 3.08 0.00 0.00 2.83
3214 4201 3.586892 CCTTCGACCTTGGTAGAGAAAC 58.413 50.000 3.08 0.00 0.00 2.78
3215 4202 2.565834 CCCTTCGACCTTGGTAGAGAAA 59.434 50.000 3.08 0.00 0.00 2.52
3216 4203 2.176889 CCCTTCGACCTTGGTAGAGAA 58.823 52.381 3.08 4.34 0.00 2.87
3217 4204 1.076677 ACCCTTCGACCTTGGTAGAGA 59.923 52.381 3.08 0.00 0.00 3.10
3218 4205 1.204941 CACCCTTCGACCTTGGTAGAG 59.795 57.143 3.08 0.00 0.00 2.43
3219 4206 1.263356 CACCCTTCGACCTTGGTAGA 58.737 55.000 0.00 0.00 0.00 2.59
3220 4207 0.974383 ACACCCTTCGACCTTGGTAG 59.026 55.000 0.00 0.00 0.00 3.18
3221 4208 0.682852 CACACCCTTCGACCTTGGTA 59.317 55.000 0.00 0.00 0.00 3.25
3222 4209 1.450211 CACACCCTTCGACCTTGGT 59.550 57.895 0.00 0.00 0.00 3.67
3223 4210 1.966451 GCACACCCTTCGACCTTGG 60.966 63.158 0.00 0.00 0.00 3.61
3224 4211 0.606401 ATGCACACCCTTCGACCTTG 60.606 55.000 0.00 0.00 0.00 3.61
3225 4212 0.981183 TATGCACACCCTTCGACCTT 59.019 50.000 0.00 0.00 0.00 3.50
3226 4213 0.981183 TTATGCACACCCTTCGACCT 59.019 50.000 0.00 0.00 0.00 3.85
3227 4214 1.369625 CTTATGCACACCCTTCGACC 58.630 55.000 0.00 0.00 0.00 4.79
3228 4215 1.369625 CCTTATGCACACCCTTCGAC 58.630 55.000 0.00 0.00 0.00 4.20
3229 4216 0.251916 CCCTTATGCACACCCTTCGA 59.748 55.000 0.00 0.00 0.00 3.71
3230 4217 0.251916 TCCCTTATGCACACCCTTCG 59.748 55.000 0.00 0.00 0.00 3.79
3231 4218 2.736670 ATCCCTTATGCACACCCTTC 57.263 50.000 0.00 0.00 0.00 3.46
3232 4219 3.463329 ACATATCCCTTATGCACACCCTT 59.537 43.478 0.00 0.00 41.29 3.95
3233 4220 3.056080 ACATATCCCTTATGCACACCCT 58.944 45.455 0.00 0.00 41.29 4.34
3234 4221 3.508845 ACATATCCCTTATGCACACCC 57.491 47.619 0.00 0.00 41.29 4.61
3235 4222 4.278419 GGAAACATATCCCTTATGCACACC 59.722 45.833 0.00 0.00 41.29 4.16
3236 4223 4.024048 CGGAAACATATCCCTTATGCACAC 60.024 45.833 0.00 0.00 41.29 3.82
3237 4224 4.133820 CGGAAACATATCCCTTATGCACA 58.866 43.478 0.00 0.00 41.29 4.57
3238 4225 4.134563 ACGGAAACATATCCCTTATGCAC 58.865 43.478 0.00 0.00 41.29 4.57
3239 4226 4.102524 AGACGGAAACATATCCCTTATGCA 59.897 41.667 0.00 0.00 41.29 3.96
3240 4227 4.642429 AGACGGAAACATATCCCTTATGC 58.358 43.478 0.00 0.00 41.29 3.14
3241 4228 6.765989 TCAAAGACGGAAACATATCCCTTATG 59.234 38.462 0.00 0.00 42.94 1.90
3242 4229 6.766467 GTCAAAGACGGAAACATATCCCTTAT 59.234 38.462 0.00 0.00 36.00 1.73
3243 4230 6.110707 GTCAAAGACGGAAACATATCCCTTA 58.889 40.000 0.00 0.00 36.00 2.69
3244 4231 4.941873 GTCAAAGACGGAAACATATCCCTT 59.058 41.667 0.00 0.00 36.00 3.95
3245 4232 4.019681 TGTCAAAGACGGAAACATATCCCT 60.020 41.667 0.00 0.00 36.00 4.20
3246 4233 4.258543 TGTCAAAGACGGAAACATATCCC 58.741 43.478 0.00 0.00 36.00 3.85
3247 4234 5.220854 CCATGTCAAAGACGGAAACATATCC 60.221 44.000 0.00 0.00 34.95 2.59
3248 4235 5.584649 TCCATGTCAAAGACGGAAACATATC 59.415 40.000 0.00 0.00 34.95 1.63
3249 4236 5.496556 TCCATGTCAAAGACGGAAACATAT 58.503 37.500 0.00 0.00 34.95 1.78
3250 4237 4.900684 TCCATGTCAAAGACGGAAACATA 58.099 39.130 0.00 0.00 34.95 2.29
3251 4238 3.750371 TCCATGTCAAAGACGGAAACAT 58.250 40.909 0.00 0.00 34.95 2.71
3252 4239 3.201353 TCCATGTCAAAGACGGAAACA 57.799 42.857 0.00 0.00 34.95 2.83
3253 4240 4.766404 AATCCATGTCAAAGACGGAAAC 57.234 40.909 0.00 0.00 34.95 2.78
3254 4241 5.068460 ACAAAATCCATGTCAAAGACGGAAA 59.932 36.000 0.00 0.00 34.95 3.13
3255 4242 4.582656 ACAAAATCCATGTCAAAGACGGAA 59.417 37.500 0.00 0.00 34.95 4.30
3256 4243 4.141287 ACAAAATCCATGTCAAAGACGGA 58.859 39.130 0.00 0.00 34.95 4.69
3257 4244 4.503741 ACAAAATCCATGTCAAAGACGG 57.496 40.909 0.00 0.00 34.95 4.79
3258 4245 7.482743 CAGATAACAAAATCCATGTCAAAGACG 59.517 37.037 0.00 0.00 34.95 4.18
3259 4246 7.756722 CCAGATAACAAAATCCATGTCAAAGAC 59.243 37.037 0.00 0.00 0.00 3.01
3260 4247 7.451255 ACCAGATAACAAAATCCATGTCAAAGA 59.549 33.333 0.00 0.00 0.00 2.52
3261 4248 7.543172 CACCAGATAACAAAATCCATGTCAAAG 59.457 37.037 0.00 0.00 0.00 2.77
3262 4249 7.377398 CACCAGATAACAAAATCCATGTCAAA 58.623 34.615 0.00 0.00 0.00 2.69
3263 4250 6.071447 CCACCAGATAACAAAATCCATGTCAA 60.071 38.462 0.00 0.00 0.00 3.18
3264 4251 5.418524 CCACCAGATAACAAAATCCATGTCA 59.581 40.000 0.00 0.00 0.00 3.58
3265 4252 5.652014 TCCACCAGATAACAAAATCCATGTC 59.348 40.000 0.00 0.00 0.00 3.06
3266 4253 5.579047 TCCACCAGATAACAAAATCCATGT 58.421 37.500 0.00 0.00 0.00 3.21
3267 4254 6.528537 TTCCACCAGATAACAAAATCCATG 57.471 37.500 0.00 0.00 0.00 3.66
3268 4255 7.738437 ATTTCCACCAGATAACAAAATCCAT 57.262 32.000 0.00 0.00 0.00 3.41
3269 4256 7.552050 AATTTCCACCAGATAACAAAATCCA 57.448 32.000 0.00 0.00 0.00 3.41
3270 4257 8.720562 CAAAATTTCCACCAGATAACAAAATCC 58.279 33.333 0.00 0.00 0.00 3.01
3271 4258 8.720562 CCAAAATTTCCACCAGATAACAAAATC 58.279 33.333 0.00 0.00 0.00 2.17
3272 4259 8.217111 ACCAAAATTTCCACCAGATAACAAAAT 58.783 29.630 0.00 0.00 0.00 1.82
3273 4260 7.569240 ACCAAAATTTCCACCAGATAACAAAA 58.431 30.769 0.00 0.00 0.00 2.44
3274 4261 7.130681 ACCAAAATTTCCACCAGATAACAAA 57.869 32.000 0.00 0.00 0.00 2.83
3275 4262 6.739331 ACCAAAATTTCCACCAGATAACAA 57.261 33.333 0.00 0.00 0.00 2.83
3276 4263 6.739331 AACCAAAATTTCCACCAGATAACA 57.261 33.333 0.00 0.00 0.00 2.41
3277 4264 8.445275 AAAAACCAAAATTTCCACCAGATAAC 57.555 30.769 0.00 0.00 0.00 1.89
3278 4265 8.669946 GAAAAACCAAAATTTCCACCAGATAA 57.330 30.769 0.00 0.00 30.98 1.75
3288 4275 7.650104 TCGTGTATGAGGAAAAACCAAAATTTC 59.350 33.333 0.00 0.00 42.04 2.17
3289 4276 7.493367 TCGTGTATGAGGAAAAACCAAAATTT 58.507 30.769 0.00 0.00 42.04 1.82
3290 4277 7.045126 TCGTGTATGAGGAAAAACCAAAATT 57.955 32.000 0.00 0.00 42.04 1.82
3291 4278 6.642707 TCGTGTATGAGGAAAAACCAAAAT 57.357 33.333 0.00 0.00 42.04 1.82
3292 4279 6.319152 TCTTCGTGTATGAGGAAAAACCAAAA 59.681 34.615 0.00 0.00 42.04 2.44
3293 4280 5.823570 TCTTCGTGTATGAGGAAAAACCAAA 59.176 36.000 0.00 0.00 42.04 3.28
3294 4281 5.369833 TCTTCGTGTATGAGGAAAAACCAA 58.630 37.500 0.00 0.00 42.04 3.67
3295 4282 4.963373 TCTTCGTGTATGAGGAAAAACCA 58.037 39.130 0.00 0.00 42.04 3.67
3296 4283 5.235516 TCTCTTCGTGTATGAGGAAAAACC 58.764 41.667 0.00 0.00 39.35 3.27
3297 4284 6.780706 TTCTCTTCGTGTATGAGGAAAAAC 57.219 37.500 0.00 0.00 31.71 2.43
3298 4285 7.979444 ATTTCTCTTCGTGTATGAGGAAAAA 57.021 32.000 0.00 0.00 32.21 1.94
3299 4286 8.528643 TCTATTTCTCTTCGTGTATGAGGAAAA 58.471 33.333 0.00 0.00 32.21 2.29
3300 4287 7.974501 GTCTATTTCTCTTCGTGTATGAGGAAA 59.025 37.037 0.00 0.00 32.21 3.13
3301 4288 7.339721 AGTCTATTTCTCTTCGTGTATGAGGAA 59.660 37.037 0.00 0.00 32.81 3.36
3302 4289 6.829298 AGTCTATTTCTCTTCGTGTATGAGGA 59.171 38.462 0.00 0.00 31.71 3.71
3303 4290 7.033530 AGTCTATTTCTCTTCGTGTATGAGG 57.966 40.000 0.00 0.00 31.71 3.86
3304 4291 8.918961 AAAGTCTATTTCTCTTCGTGTATGAG 57.081 34.615 0.00 0.00 0.00 2.90
3305 4292 9.355215 GAAAAGTCTATTTCTCTTCGTGTATGA 57.645 33.333 0.00 0.00 36.57 2.15
3306 4293 9.140286 TGAAAAGTCTATTTCTCTTCGTGTATG 57.860 33.333 1.99 0.00 39.51 2.39
3307 4294 9.706691 TTGAAAAGTCTATTTCTCTTCGTGTAT 57.293 29.630 1.99 0.00 39.51 2.29
3308 4295 9.193133 CTTGAAAAGTCTATTTCTCTTCGTGTA 57.807 33.333 1.99 0.00 39.70 2.90
3309 4296 8.077836 CTTGAAAAGTCTATTTCTCTTCGTGT 57.922 34.615 1.99 0.00 39.70 4.49
3327 4314 9.903682 TCAAAATTCATTGTTTTTGCTTGAAAA 57.096 22.222 16.08 0.00 40.78 2.29
3328 4315 9.903682 TTCAAAATTCATTGTTTTTGCTTGAAA 57.096 22.222 16.08 7.77 40.78 2.69
3329 4316 9.903682 TTTCAAAATTCATTGTTTTTGCTTGAA 57.096 22.222 16.08 0.00 40.78 2.69


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

AutoCloner maintained by Alex Coulton.