Multiple sequence alignment - TraesCS1B01G285700

Loading Multiple Alignment...

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 TraesCS1B01G285700 chr1B 100.000 5250 0 0 1 5250 496572904 496567655 0.000000e+00 9696.0
1 TraesCS1B01G285700 chr1B 95.200 125 6 0 3405 3529 677378495 677378371 1.150000e-46 198.0
2 TraesCS1B01G285700 chr1B 94.444 126 7 0 3405 3530 439402936 439402811 1.490000e-45 195.0
3 TraesCS1B01G285700 chr1A 89.590 2661 175 46 39 2636 471508513 471505892 0.000000e+00 3286.0
4 TraesCS1B01G285700 chr1A 88.028 1303 82 36 3592 4850 471504733 471503461 0.000000e+00 1474.0
5 TraesCS1B01G285700 chr1A 91.822 428 18 8 4836 5250 471494383 471493960 9.800000e-162 580.0
6 TraesCS1B01G285700 chr1A 92.714 398 24 4 3007 3401 471505202 471504807 2.120000e-158 569.0
7 TraesCS1B01G285700 chr1A 91.026 390 21 4 2590 2965 471505865 471505476 1.010000e-141 514.0
8 TraesCS1B01G285700 chr1D 92.253 1833 102 12 39 1848 371787173 371785358 0.000000e+00 2562.0
9 TraesCS1B01G285700 chr1D 93.920 1546 75 13 1874 3401 371784723 371783179 0.000000e+00 2316.0
10 TraesCS1B01G285700 chr1D 90.501 1158 68 21 3522 4639 371783170 371782015 0.000000e+00 1491.0
11 TraesCS1B01G285700 chr1D 93.432 609 23 13 4654 5250 371756743 371756140 0.000000e+00 887.0
12 TraesCS1B01G285700 chr4A 84.753 223 32 2 5028 5250 592477118 592477338 6.840000e-54 222.0
13 TraesCS1B01G285700 chr4A 84.753 223 32 2 5028 5250 592755925 592756145 6.840000e-54 222.0
14 TraesCS1B01G285700 chr4A 83.408 223 35 2 5028 5250 591566157 591565937 6.890000e-49 206.0
15 TraesCS1B01G285700 chr4A 97.561 41 1 0 1 41 594269027 594269067 2.620000e-08 71.3
16 TraesCS1B01G285700 chr5B 96.694 121 4 0 3406 3526 629275118 629275238 8.910000e-48 202.0
17 TraesCS1B01G285700 chr5B 97.436 117 3 0 3406 3522 403545718 403545834 3.210000e-47 200.0
18 TraesCS1B01G285700 chr5B 94.488 127 7 0 3406 3532 278754929 278755055 4.150000e-46 196.0
19 TraesCS1B01G285700 chr5B 95.902 122 4 1 3406 3527 478495170 478495050 4.150000e-46 196.0
20 TraesCS1B01G285700 chr5B 95.868 121 5 0 3406 3526 629357688 629357808 4.150000e-46 196.0
21 TraesCS1B01G285700 chr5B 97.619 42 0 1 6 47 632113745 632113785 2.620000e-08 71.3
22 TraesCS1B01G285700 chr6B 95.902 122 5 0 3403 3524 672946721 672946842 1.150000e-46 198.0
23 TraesCS1B01G285700 chr5D 93.077 130 9 0 3398 3527 464292873 464292744 1.930000e-44 191.0
24 TraesCS1B01G285700 chr3D 90.625 96 6 1 5155 5250 575279277 575279185 1.990000e-24 124.0
25 TraesCS1B01G285700 chr5A 100.000 40 0 0 1 40 219265046 219265085 2.030000e-09 75.0
26 TraesCS1B01G285700 chr5A 97.619 42 1 0 1 42 606398582 606398623 7.290000e-09 73.1
27 TraesCS1B01G285700 chr4B 100.000 40 0 0 4 43 92922475 92922436 2.030000e-09 75.0
28 TraesCS1B01G285700 chrUn 100.000 39 0 0 4 42 334746742 334746704 7.290000e-09 73.1
29 TraesCS1B01G285700 chr7A 95.556 45 2 0 1 45 661880001 661880045 7.290000e-09 73.1
30 TraesCS1B01G285700 chr3A 95.556 45 1 1 1 45 747649653 747649696 2.620000e-08 71.3
31 TraesCS1B01G285700 chr7B 97.500 40 1 0 1 40 49033557 49033596 9.430000e-08 69.4


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 TraesCS1B01G285700 chr1B 496567655 496572904 5249 True 9696.00 9696 100.000000 1 5250 1 chr1B.!!$R2 5249
1 TraesCS1B01G285700 chr1A 471503461 471508513 5052 True 1460.75 3286 90.339500 39 4850 4 chr1A.!!$R2 4811
2 TraesCS1B01G285700 chr1D 371782015 371787173 5158 True 2123.00 2562 92.224667 39 4639 3 chr1D.!!$R2 4600
3 TraesCS1B01G285700 chr1D 371756140 371756743 603 True 887.00 887 93.432000 4654 5250 1 chr1D.!!$R1 596

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
579 593 0.247460 AGCTATGCTCAGTTCGCACA 59.753 50.000 0.0 0.0 40.65 4.57 F
1123 1172 0.036875 CCTGAGGAAGAGGCGGTTTT 59.963 55.000 0.0 0.0 0.00 2.43 F
1290 1339 1.526225 GCAGGGTATCGGGAAAGCC 60.526 63.158 0.0 0.0 0.00 4.35 F
1338 1387 1.605710 TCTATCGCCTACCGCTACAAC 59.394 52.381 0.0 0.0 36.73 3.32 F
3161 4168 0.817013 CAACAGCCACACCAACAACT 59.183 50.000 0.0 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 2582 0.104855 CTGCTATAACAGGCGCTCCA 59.895 55.000 7.64 0.0 33.85 3.86 R
2096 2753 1.597742 TTGGAGAAACAGCAGTCAGC 58.402 50.000 0.00 0.0 46.19 4.26 R
3161 4168 3.008049 GGACAAAAGAGAGAGGGTAAGCA 59.992 47.826 0.00 0.0 0.00 3.91 R
3403 4411 0.033405 TTCTGGACGGAGGGAGTAGG 60.033 60.000 0.00 0.0 0.00 3.18 R
4898 5975 0.036765 TCTCCGGTTGGTGGATTTCG 60.037 55.000 0.00 0.0 34.32 3.46 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
17 18 2.743718 ACCACCAGAAGCACTCCG 59.256 61.111 0.00 0.00 0.00 4.63
18 19 2.140792 ACCACCAGAAGCACTCCGT 61.141 57.895 0.00 0.00 0.00 4.69
19 20 1.669115 CCACCAGAAGCACTCCGTG 60.669 63.158 0.00 0.00 36.51 4.94
33 34 4.369182 CACTCCGTGCTTTATTAGTAGGG 58.631 47.826 0.00 0.00 43.43 3.53
34 35 4.098960 CACTCCGTGCTTTATTAGTAGGGA 59.901 45.833 0.00 0.00 46.81 4.20
36 37 5.680594 TCCGTGCTTTATTAGTAGGGAAA 57.319 39.130 2.51 0.00 46.26 3.13
37 38 5.667466 TCCGTGCTTTATTAGTAGGGAAAG 58.333 41.667 2.51 0.00 46.26 2.62
51 52 3.084786 AGGGAAAGATTGTGCTTGCTAC 58.915 45.455 0.00 0.00 0.00 3.58
63 64 3.194968 GTGCTTGCTACCAACTACTCCTA 59.805 47.826 0.00 0.00 0.00 2.94
110 111 7.458409 AAGAGAAATGTTGATGTAGCACAAT 57.542 32.000 0.00 0.00 0.00 2.71
148 149 7.412853 TGCCTTAGTTAAGAAACAAGGTTTT 57.587 32.000 14.90 0.00 41.28 2.43
149 150 7.262048 TGCCTTAGTTAAGAAACAAGGTTTTG 58.738 34.615 14.90 0.00 41.28 2.44
150 151 6.700081 GCCTTAGTTAAGAAACAAGGTTTTGG 59.300 38.462 14.90 0.00 41.28 3.28
151 152 7.632028 GCCTTAGTTAAGAAACAAGGTTTTGGT 60.632 37.037 14.90 0.00 41.28 3.67
152 153 8.255206 CCTTAGTTAAGAAACAAGGTTTTGGTT 58.745 33.333 0.51 0.00 46.60 3.67
153 154 9.647797 CTTAGTTAAGAAACAAGGTTTTGGTTT 57.352 29.630 0.00 0.00 44.05 3.27
178 179 2.436417 GAACCAATAGAGCCTTGCACA 58.564 47.619 0.00 0.00 0.00 4.57
190 191 4.971939 AGCCTTGCACAAAAATTAACCAT 58.028 34.783 0.00 0.00 0.00 3.55
287 288 0.784778 GTACAAGCGCAGACACTCAC 59.215 55.000 11.47 0.00 0.00 3.51
293 294 0.994995 GCGCAGACACTCACATACAG 59.005 55.000 0.30 0.00 0.00 2.74
315 316 2.874086 TCATCCTTATGAATGCACGCAG 59.126 45.455 0.00 0.00 39.20 5.18
329 334 2.042259 CGCAGGCACACACATCCAT 61.042 57.895 0.00 0.00 0.00 3.41
341 346 2.984604 ACACATCCATCCCTATGAGCAT 59.015 45.455 0.00 0.00 34.84 3.79
346 351 2.158112 TCCATCCCTATGAGCATCTCCA 60.158 50.000 0.00 0.00 34.84 3.86
347 352 2.236644 CCATCCCTATGAGCATCTCCAG 59.763 54.545 0.00 0.00 34.84 3.86
357 362 3.891977 TGAGCATCTCCAGGATACAGTAC 59.108 47.826 0.00 0.00 35.07 2.73
361 366 4.022416 GCATCTCCAGGATACAGTACTGAG 60.022 50.000 29.30 13.09 41.74 3.35
362 367 4.864483 TCTCCAGGATACAGTACTGAGT 57.136 45.455 29.30 16.21 41.74 3.41
371 376 5.163642 GGATACAGTACTGAGTCGACACAAT 60.164 44.000 29.30 10.51 0.00 2.71
402 407 2.826428 TGAAGAAGTCATCATAGGCGC 58.174 47.619 0.00 0.00 0.00 6.53
406 411 1.069204 GAAGTCATCATAGGCGCCTCA 59.931 52.381 36.73 19.27 0.00 3.86
415 420 1.617322 TAGGCGCCTCATAAGTCGAT 58.383 50.000 36.73 6.99 0.00 3.59
450 455 1.604438 CCACCGAACGAACATCACAGA 60.604 52.381 0.00 0.00 0.00 3.41
511 517 8.338259 CAGTGTCAAATCTAGAATTTAATCCCG 58.662 37.037 0.00 0.00 0.00 5.14
515 521 6.770785 TCAAATCTAGAATTTAATCCCGGGTG 59.229 38.462 22.86 4.79 0.00 4.61
516 522 4.699925 TCTAGAATTTAATCCCGGGTGG 57.300 45.455 22.86 0.00 0.00 4.61
578 592 3.056628 AGCTATGCTCAGTTCGCAC 57.943 52.632 0.00 0.00 40.65 5.34
579 593 0.247460 AGCTATGCTCAGTTCGCACA 59.753 50.000 0.00 0.00 40.65 4.57
713 735 0.749091 CATCAAATCTGCGCCCTCCA 60.749 55.000 4.18 0.00 0.00 3.86
913 943 4.063967 CTACCGCAGCACCGTCCA 62.064 66.667 0.00 0.00 0.00 4.02
1123 1172 0.036875 CCTGAGGAAGAGGCGGTTTT 59.963 55.000 0.00 0.00 0.00 2.43
1137 1186 2.915137 TTTTCCGGTTGCCCTGGC 60.915 61.111 0.00 0.00 42.35 4.85
1290 1339 1.526225 GCAGGGTATCGGGAAAGCC 60.526 63.158 0.00 0.00 0.00 4.35
1296 1345 2.650322 GGTATCGGGAAAGCCATTGAA 58.350 47.619 0.00 0.00 35.15 2.69
1314 1363 2.269172 GAAACCTTACCGCTAGCAGAC 58.731 52.381 16.45 0.00 0.00 3.51
1326 1375 3.619054 GCAGACGCTTCTATCGCC 58.381 61.111 0.00 0.00 34.30 5.54
1338 1387 1.605710 TCTATCGCCTACCGCTACAAC 59.394 52.381 0.00 0.00 36.73 3.32
1425 1474 1.863155 GCTCCATGAAGGGGGTGGAA 61.863 60.000 0.00 0.00 41.21 3.53
1467 1516 2.477104 TCCAGGCTATGAGGATGTCA 57.523 50.000 0.00 0.00 40.38 3.58
1624 1673 5.065988 GCTGATATGGTTTTTGTCACGGTAT 59.934 40.000 0.00 0.00 0.00 2.73
1685 1734 9.624697 TGCTTAATTGATGTAGAATTTGTGAAC 57.375 29.630 0.00 0.00 0.00 3.18
1746 1795 7.856145 AGAACACATCAGGAATTGATCTTAC 57.144 36.000 0.00 0.00 44.76 2.34
1833 1882 3.631145 TCATTTCTGTGCTTTGACTGC 57.369 42.857 0.00 0.00 0.00 4.40
1841 1890 2.694628 TGTGCTTTGACTGCAAGGAATT 59.305 40.909 0.00 0.00 42.41 2.17
2096 2753 8.153479 TGATCGTAATCCCAAATGATAAGTTG 57.847 34.615 0.00 0.00 0.00 3.16
2239 2912 7.632680 GCCCCATGTTAGCTATTTTACATTTGT 60.633 37.037 6.12 0.00 0.00 2.83
2279 2953 3.009473 AGGTGGCATGTGATGTCTTAAGT 59.991 43.478 1.63 0.00 35.48 2.24
2280 2954 3.127548 GGTGGCATGTGATGTCTTAAGTG 59.872 47.826 1.63 0.00 35.48 3.16
2354 3028 4.827284 TCTCCTTTGACCATTTCCTTGTTC 59.173 41.667 0.00 0.00 0.00 3.18
2399 3074 3.599343 TCATCACCTTCACACTATGCAC 58.401 45.455 0.00 0.00 0.00 4.57
2438 3123 9.660180 ATTACTGATTCCTAGTTCTTTCTTGAC 57.340 33.333 0.00 0.00 0.00 3.18
2553 3238 8.966868 GGATAAAAGTAGAATCCCATTGTTGAA 58.033 33.333 0.00 0.00 34.30 2.69
2564 3253 4.832266 TCCCATTGTTGAATACTGCACTTT 59.168 37.500 0.00 0.00 0.00 2.66
2568 3257 6.479660 CCATTGTTGAATACTGCACTTTGTTT 59.520 34.615 0.00 0.00 0.00 2.83
2732 3494 3.577667 TGCAGCTAAACATGTGATTTGC 58.422 40.909 0.00 3.74 0.00 3.68
2860 3622 3.578282 AGCAACAGGTTAAATTTCAGGGG 59.422 43.478 0.00 0.00 0.00 4.79
2946 3711 3.996150 ATGCTTGTTGTGAAACTCCTG 57.004 42.857 0.00 0.00 38.04 3.86
3015 4012 4.508461 TTTCTCCGTCGAAAGTCATGTA 57.492 40.909 0.00 0.00 0.00 2.29
3016 4013 4.508461 TTCTCCGTCGAAAGTCATGTAA 57.492 40.909 0.00 0.00 0.00 2.41
3161 4168 0.817013 CAACAGCCACACCAACAACT 59.183 50.000 0.00 0.00 0.00 3.16
3411 4419 9.872721 GCTTAATAGTTTATATGACCTACTCCC 57.127 37.037 0.00 0.00 0.00 4.30
3414 4422 8.667592 AATAGTTTATATGACCTACTCCCTCC 57.332 38.462 0.00 0.00 0.00 4.30
3415 4423 5.078256 AGTTTATATGACCTACTCCCTCCG 58.922 45.833 0.00 0.00 0.00 4.63
3416 4424 4.736611 TTATATGACCTACTCCCTCCGT 57.263 45.455 0.00 0.00 0.00 4.69
3417 4425 2.653234 TATGACCTACTCCCTCCGTC 57.347 55.000 0.00 0.00 0.00 4.79
3418 4426 0.106116 ATGACCTACTCCCTCCGTCC 60.106 60.000 0.00 0.00 0.00 4.79
3419 4427 1.305623 GACCTACTCCCTCCGTCCA 59.694 63.158 0.00 0.00 0.00 4.02
3420 4428 0.752376 GACCTACTCCCTCCGTCCAG 60.752 65.000 0.00 0.00 0.00 3.86
3421 4429 1.212934 ACCTACTCCCTCCGTCCAGA 61.213 60.000 0.00 0.00 0.00 3.86
3422 4430 0.033405 CCTACTCCCTCCGTCCAGAA 60.033 60.000 0.00 0.00 0.00 3.02
3423 4431 1.618888 CCTACTCCCTCCGTCCAGAAA 60.619 57.143 0.00 0.00 0.00 2.52
3424 4432 2.389715 CTACTCCCTCCGTCCAGAAAT 58.610 52.381 0.00 0.00 0.00 2.17
3425 4433 2.544844 ACTCCCTCCGTCCAGAAATA 57.455 50.000 0.00 0.00 0.00 1.40
3426 4434 2.108970 ACTCCCTCCGTCCAGAAATAC 58.891 52.381 0.00 0.00 0.00 1.89
3427 4435 2.292323 ACTCCCTCCGTCCAGAAATACT 60.292 50.000 0.00 0.00 0.00 2.12
3428 4436 2.362717 CTCCCTCCGTCCAGAAATACTC 59.637 54.545 0.00 0.00 0.00 2.59
3429 4437 1.067212 CCCTCCGTCCAGAAATACTCG 59.933 57.143 0.00 0.00 0.00 4.18
3430 4438 1.749634 CCTCCGTCCAGAAATACTCGT 59.250 52.381 0.00 0.00 0.00 4.18
3431 4439 2.223525 CCTCCGTCCAGAAATACTCGTC 60.224 54.545 0.00 0.00 0.00 4.20
3432 4440 1.399440 TCCGTCCAGAAATACTCGTCG 59.601 52.381 0.00 0.00 0.00 5.12
3433 4441 1.533338 CCGTCCAGAAATACTCGTCGG 60.533 57.143 0.00 0.00 0.00 4.79
3434 4442 1.399440 CGTCCAGAAATACTCGTCGGA 59.601 52.381 0.00 0.00 0.00 4.55
3435 4443 2.539142 CGTCCAGAAATACTCGTCGGAG 60.539 54.545 0.00 0.00 46.13 4.63
3436 4444 2.022195 TCCAGAAATACTCGTCGGAGG 58.978 52.381 0.00 0.00 44.93 4.30
3437 4445 2.022195 CCAGAAATACTCGTCGGAGGA 58.978 52.381 0.00 0.00 44.93 3.71
3438 4446 2.426024 CCAGAAATACTCGTCGGAGGAA 59.574 50.000 1.73 0.00 44.93 3.36
3439 4447 3.068307 CCAGAAATACTCGTCGGAGGAAT 59.932 47.826 1.73 0.00 44.93 3.01
3440 4448 4.045104 CAGAAATACTCGTCGGAGGAATG 58.955 47.826 1.73 0.00 44.93 2.67
3441 4449 3.068307 AGAAATACTCGTCGGAGGAATGG 59.932 47.826 1.73 0.00 44.93 3.16
3442 4450 2.359981 ATACTCGTCGGAGGAATGGA 57.640 50.000 1.73 0.00 44.93 3.41
3443 4451 2.359981 TACTCGTCGGAGGAATGGAT 57.640 50.000 1.73 0.00 44.93 3.41
3444 4452 0.747255 ACTCGTCGGAGGAATGGATG 59.253 55.000 1.73 0.00 44.93 3.51
3445 4453 0.598680 CTCGTCGGAGGAATGGATGC 60.599 60.000 1.73 0.00 36.61 3.91
3446 4454 1.143838 CGTCGGAGGAATGGATGCA 59.856 57.895 0.00 0.00 0.00 3.96
3447 4455 0.250038 CGTCGGAGGAATGGATGCAT 60.250 55.000 0.00 0.00 0.00 3.96
3448 4456 1.517242 GTCGGAGGAATGGATGCATC 58.483 55.000 18.81 18.81 0.00 3.91
3449 4457 1.071385 GTCGGAGGAATGGATGCATCT 59.929 52.381 25.28 6.65 0.00 2.90
3450 4458 2.300152 GTCGGAGGAATGGATGCATCTA 59.700 50.000 25.28 20.79 0.00 1.98
3451 4459 2.564504 TCGGAGGAATGGATGCATCTAG 59.435 50.000 25.28 6.75 0.00 2.43
3452 4460 2.564504 CGGAGGAATGGATGCATCTAGA 59.435 50.000 25.28 10.86 0.00 2.43
3453 4461 3.197333 CGGAGGAATGGATGCATCTAGAT 59.803 47.826 25.28 13.14 0.00 1.98
3454 4462 4.515361 GGAGGAATGGATGCATCTAGATG 58.485 47.826 25.64 25.64 41.60 2.90
3455 4463 4.019501 GGAGGAATGGATGCATCTAGATGT 60.020 45.833 28.92 14.10 40.80 3.06
3456 4464 5.188555 GGAGGAATGGATGCATCTAGATGTA 59.811 44.000 28.92 26.27 40.80 2.29
3457 4465 6.126825 GGAGGAATGGATGCATCTAGATGTAT 60.127 42.308 29.54 29.54 44.84 2.29
3458 4466 7.268212 AGGAATGGATGCATCTAGATGTATT 57.732 36.000 29.66 18.66 42.77 1.89
3459 4467 7.696981 AGGAATGGATGCATCTAGATGTATTT 58.303 34.615 29.66 22.13 42.77 1.40
3460 4468 8.168725 AGGAATGGATGCATCTAGATGTATTTT 58.831 33.333 29.66 23.41 42.77 1.82
3461 4469 9.453572 GGAATGGATGCATCTAGATGTATTTTA 57.546 33.333 29.66 20.90 42.77 1.52
3465 4473 9.494271 TGGATGCATCTAGATGTATTTTAGTTC 57.506 33.333 29.66 18.97 42.77 3.01
3466 4474 9.717942 GGATGCATCTAGATGTATTTTAGTTCT 57.282 33.333 29.66 11.50 42.77 3.01
3496 4504 8.335532 ACATTCATTTTTAGACATTTCTCCGA 57.664 30.769 0.00 0.00 32.75 4.55
3497 4505 8.237267 ACATTCATTTTTAGACATTTCTCCGAC 58.763 33.333 0.00 0.00 32.75 4.79
3498 4506 7.737972 TTCATTTTTAGACATTTCTCCGACA 57.262 32.000 0.00 0.00 32.75 4.35
3499 4507 7.737972 TCATTTTTAGACATTTCTCCGACAA 57.262 32.000 0.00 0.00 32.75 3.18
3500 4508 7.806690 TCATTTTTAGACATTTCTCCGACAAG 58.193 34.615 0.00 0.00 32.75 3.16
3501 4509 7.444183 TCATTTTTAGACATTTCTCCGACAAGT 59.556 33.333 0.00 0.00 32.75 3.16
3502 4510 8.717821 CATTTTTAGACATTTCTCCGACAAGTA 58.282 33.333 0.00 0.00 32.75 2.24
3503 4511 8.842358 TTTTTAGACATTTCTCCGACAAGTAT 57.158 30.769 0.00 0.00 32.75 2.12
3504 4512 8.842358 TTTTAGACATTTCTCCGACAAGTATT 57.158 30.769 0.00 0.00 32.75 1.89
3505 4513 8.842358 TTTAGACATTTCTCCGACAAGTATTT 57.158 30.769 0.00 0.00 32.75 1.40
3506 4514 6.969828 AGACATTTCTCCGACAAGTATTTC 57.030 37.500 0.00 0.00 0.00 2.17
3507 4515 5.875359 AGACATTTCTCCGACAAGTATTTCC 59.125 40.000 0.00 0.00 0.00 3.13
3508 4516 4.630069 ACATTTCTCCGACAAGTATTTCCG 59.370 41.667 0.00 0.00 0.00 4.30
3509 4517 2.953466 TCTCCGACAAGTATTTCCGG 57.047 50.000 0.00 0.00 41.36 5.14
3510 4518 2.449464 TCTCCGACAAGTATTTCCGGA 58.551 47.619 0.00 0.00 45.74 5.14
3511 4519 2.165030 TCTCCGACAAGTATTTCCGGAC 59.835 50.000 1.83 0.00 43.47 4.79
3512 4520 1.135315 TCCGACAAGTATTTCCGGACG 60.135 52.381 1.83 0.00 43.47 4.79
3513 4521 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
3514 4522 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
3515 4523 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
3516 4524 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
3517 4525 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
3518 4526 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
3519 4527 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
3520 4528 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
3613 4634 4.082125 AGGCCTGATTCCTTTGTAACTTG 58.918 43.478 3.11 0.00 0.00 3.16
3710 4731 9.964354 CCATCATATATTTGGTCATCCTCTTTA 57.036 33.333 4.02 0.00 34.23 1.85
3818 4839 9.078990 TCATATACTGGTCAGGTAAGTAATCAG 57.921 37.037 2.87 0.00 30.61 2.90
3953 4975 1.099295 ACGCATGGCATCATCCACAG 61.099 55.000 0.00 0.00 39.25 3.66
3966 4988 5.628797 TCATCCACAGGCTAATAACATGA 57.371 39.130 0.00 0.00 0.00 3.07
3990 5012 2.025887 CCCCTTTCAGGTGAGCATAACT 60.026 50.000 0.00 0.00 31.93 2.24
4059 5081 1.374947 GCAGGTACACCCTCTTGCA 59.625 57.895 5.69 0.00 43.86 4.08
4061 5083 2.014068 GCAGGTACACCCTCTTGCATC 61.014 57.143 5.69 0.00 43.86 3.91
4135 5161 3.859414 GCTCAGGCTGGAGGCGAT 61.859 66.667 15.73 0.00 46.23 4.58
4138 5164 2.249413 CTCAGGCTGGAGGCGATGTT 62.249 60.000 15.73 0.00 46.23 2.71
4171 5197 2.500910 CAGCTCCAGGTTCTCTTCATCT 59.499 50.000 0.00 0.00 0.00 2.90
4199 5225 4.729918 AAGGCCCGAAGCTGCAGG 62.730 66.667 17.12 0.00 43.05 4.85
4229 5255 1.810030 CTACAGCGGAAAGGGCGTC 60.810 63.158 0.00 0.00 35.00 5.19
4231 5257 4.697756 CAGCGGAAAGGGCGTCCA 62.698 66.667 9.71 0.00 34.56 4.02
4248 5274 0.991920 CCAGGGTTTTCCAGAGGCTA 59.008 55.000 0.00 0.00 42.91 3.93
4252 5278 1.819288 GGGTTTTCCAGAGGCTAAAGC 59.181 52.381 0.00 0.00 42.91 3.51
4253 5279 2.514803 GGTTTTCCAGAGGCTAAAGCA 58.485 47.619 4.07 0.00 40.63 3.91
4254 5280 3.092301 GGTTTTCCAGAGGCTAAAGCAT 58.908 45.455 4.07 0.00 40.63 3.79
4255 5281 3.511540 GGTTTTCCAGAGGCTAAAGCATT 59.488 43.478 4.07 0.00 40.63 3.56
4256 5282 4.021104 GGTTTTCCAGAGGCTAAAGCATTT 60.021 41.667 4.07 0.00 40.63 2.32
4277 5323 3.777106 TTTCCAGTGTCATGAGCTTCT 57.223 42.857 0.00 0.00 0.00 2.85
4284 5330 2.999355 GTGTCATGAGCTTCTCAGTTCC 59.001 50.000 0.00 0.00 44.08 3.62
4286 5332 3.056250 TGTCATGAGCTTCTCAGTTCCTC 60.056 47.826 0.00 0.00 44.08 3.71
4287 5333 3.195396 GTCATGAGCTTCTCAGTTCCTCT 59.805 47.826 0.00 0.00 44.08 3.69
4288 5334 4.400884 GTCATGAGCTTCTCAGTTCCTCTA 59.599 45.833 0.00 0.00 44.08 2.43
4296 5342 3.892284 TCTCAGTTCCTCTAGCAGTAGG 58.108 50.000 0.00 0.00 0.00 3.18
4309 5355 3.990318 GCAGTAGGCTCTTTGTTTTGT 57.010 42.857 0.00 0.00 40.25 2.83
4310 5356 4.307443 GCAGTAGGCTCTTTGTTTTGTT 57.693 40.909 0.00 0.00 40.25 2.83
4312 5358 4.740205 GCAGTAGGCTCTTTGTTTTGTTTC 59.260 41.667 0.00 0.00 40.25 2.78
4313 5359 4.970003 CAGTAGGCTCTTTGTTTTGTTTCG 59.030 41.667 0.00 0.00 0.00 3.46
4314 5360 4.638865 AGTAGGCTCTTTGTTTTGTTTCGT 59.361 37.500 0.00 0.00 0.00 3.85
4328 5394 2.051423 GTTTCGTTGCAAGCTTTAGGC 58.949 47.619 0.00 0.00 42.19 3.93
4357 5423 5.171476 ACTGTGTGTGTGATAGCATTAGAC 58.829 41.667 0.00 0.00 0.00 2.59
4369 5435 8.777413 GTGATAGCATTAGACTGCATATGAAAA 58.223 33.333 6.97 0.00 44.77 2.29
4371 5437 6.382869 AGCATTAGACTGCATATGAAAACC 57.617 37.500 6.97 0.00 44.77 3.27
4379 5445 8.218338 AGACTGCATATGAAAACCTATCTTTG 57.782 34.615 6.97 0.00 0.00 2.77
4380 5446 7.831193 AGACTGCATATGAAAACCTATCTTTGT 59.169 33.333 6.97 0.00 0.00 2.83
4381 5447 7.989826 ACTGCATATGAAAACCTATCTTTGTC 58.010 34.615 6.97 0.00 0.00 3.18
4382 5448 7.611467 ACTGCATATGAAAACCTATCTTTGTCA 59.389 33.333 6.97 0.00 0.00 3.58
4383 5449 7.988737 TGCATATGAAAACCTATCTTTGTCAG 58.011 34.615 6.97 0.00 0.00 3.51
4384 5450 6.914757 GCATATGAAAACCTATCTTTGTCAGC 59.085 38.462 6.97 0.00 0.00 4.26
4385 5451 5.551760 ATGAAAACCTATCTTTGTCAGCG 57.448 39.130 0.00 0.00 0.00 5.18
4386 5452 4.385825 TGAAAACCTATCTTTGTCAGCGT 58.614 39.130 0.00 0.00 0.00 5.07
4387 5453 4.213270 TGAAAACCTATCTTTGTCAGCGTG 59.787 41.667 0.00 0.00 0.00 5.34
4388 5454 3.402628 AACCTATCTTTGTCAGCGTGT 57.597 42.857 0.00 0.00 0.00 4.49
4395 5461 3.064207 TCTTTGTCAGCGTGTAACCATC 58.936 45.455 0.00 0.00 0.00 3.51
4412 5478 1.688735 CATCCATGGCGGTCTCTTCTA 59.311 52.381 6.96 0.00 35.57 2.10
4420 5486 1.866063 GCGGTCTCTTCTAAGCCATCG 60.866 57.143 0.00 0.00 0.00 3.84
4421 5487 1.859383 GGTCTCTTCTAAGCCATCGC 58.141 55.000 0.00 0.00 0.00 4.58
4437 5503 2.274645 CGCATGGCCCTGTTTGGAA 61.275 57.895 9.95 0.00 38.35 3.53
4441 5507 1.273327 CATGGCCCTGTTTGGAACTTC 59.727 52.381 0.00 0.00 38.35 3.01
4442 5508 0.555769 TGGCCCTGTTTGGAACTTCT 59.444 50.000 0.00 0.00 38.35 2.85
4476 5543 5.447818 CGGGAAATAAGCTGATTCTTGTGAC 60.448 44.000 0.00 0.00 0.00 3.67
4486 5553 3.433274 TGATTCTTGTGACATTCTCGTGC 59.567 43.478 0.00 0.00 0.00 5.34
4488 5555 2.407090 TCTTGTGACATTCTCGTGCTG 58.593 47.619 0.00 0.00 0.00 4.41
4504 5571 2.435938 TGGAAACGCGCCTGGATC 60.436 61.111 5.73 0.00 0.00 3.36
4600 5667 2.884894 AGACGACGAGGTTTTGAACT 57.115 45.000 0.00 0.00 0.00 3.01
4603 5670 2.728318 GACGACGAGGTTTTGAACTACC 59.272 50.000 0.00 0.00 34.54 3.18
4645 5715 4.335315 ACATTTTCTCTTGCTTTGTCACGA 59.665 37.500 0.00 0.00 0.00 4.35
4652 5723 2.605837 TGCTTTGTCACGACCAAGTA 57.394 45.000 11.38 5.54 36.69 2.24
4677 5748 4.132336 CCTGAATCGTGAATCACATGGAT 58.868 43.478 14.24 5.41 38.05 3.41
4678 5749 5.299949 CCTGAATCGTGAATCACATGGATA 58.700 41.667 14.24 0.00 34.28 2.59
4679 5750 5.407691 CCTGAATCGTGAATCACATGGATAG 59.592 44.000 14.24 4.26 34.28 2.08
4680 5751 5.299949 TGAATCGTGAATCACATGGATAGG 58.700 41.667 14.24 0.00 34.28 2.57
4681 5752 3.751479 TCGTGAATCACATGGATAGGG 57.249 47.619 14.24 0.00 34.28 3.53
4682 5753 3.304829 TCGTGAATCACATGGATAGGGA 58.695 45.455 14.24 0.00 34.28 4.20
4683 5754 3.903714 TCGTGAATCACATGGATAGGGAT 59.096 43.478 14.24 0.00 34.28 3.85
4703 5774 3.385384 TGGTCGAGGCAGCTCAGG 61.385 66.667 0.00 0.00 0.00 3.86
4704 5775 3.386237 GGTCGAGGCAGCTCAGGT 61.386 66.667 0.00 0.00 0.00 4.00
4708 5785 2.503546 GAGGCAGCTCAGGTAGGC 59.496 66.667 0.00 0.00 0.00 3.93
4853 5930 0.881796 GCACGAAAGAGGAAAAGGGG 59.118 55.000 0.00 0.00 0.00 4.79
4855 5932 2.858745 CACGAAAGAGGAAAAGGGGAA 58.141 47.619 0.00 0.00 0.00 3.97
4860 5937 0.851332 AGAGGAAAAGGGGAAGGGGG 60.851 60.000 0.00 0.00 0.00 5.40
4895 5972 2.291741 GCAACAGAAAACCAGTCCAGAG 59.708 50.000 0.00 0.00 0.00 3.35
4898 5975 0.402121 AGAAAACCAGTCCAGAGCCC 59.598 55.000 0.00 0.00 0.00 5.19
5062 6146 3.147595 CGCTGGGAGTCGGATCCA 61.148 66.667 13.41 0.00 41.52 3.41
5117 6201 1.878656 CGACAGGTTCGGCTCCTTCT 61.879 60.000 0.00 0.00 44.60 2.85
5123 6207 2.711922 TTCGGCTCCTTCTCTCCGC 61.712 63.158 0.00 0.00 41.49 5.54
5152 6236 4.790962 ATCTGCTGCCCGCTGGTG 62.791 66.667 0.00 0.00 40.11 4.17
5190 6275 1.901650 CTTCGGTTGCTTGTCTCGCC 61.902 60.000 0.00 0.00 0.00 5.54
5241 6326 2.401766 CGGGTTCTGAGCATGTGGC 61.402 63.158 0.00 0.00 45.30 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.140792 ACGGAGTGCTTCTGGTGGT 61.141 57.895 3.27 0.00 42.51 4.16
1 2 2.743718 ACGGAGTGCTTCTGGTGG 59.256 61.111 3.27 0.00 42.51 4.61
13 14 4.931661 TCCCTACTAATAAAGCACGGAG 57.068 45.455 0.00 0.00 0.00 4.63
14 15 5.422970 TCTTTCCCTACTAATAAAGCACGGA 59.577 40.000 0.00 0.00 0.00 4.69
15 16 5.667466 TCTTTCCCTACTAATAAAGCACGG 58.333 41.667 0.00 0.00 0.00 4.94
16 17 7.280205 ACAATCTTTCCCTACTAATAAAGCACG 59.720 37.037 0.00 0.00 0.00 5.34
17 18 8.398665 CACAATCTTTCCCTACTAATAAAGCAC 58.601 37.037 0.00 0.00 0.00 4.40
18 19 7.067008 GCACAATCTTTCCCTACTAATAAAGCA 59.933 37.037 0.00 0.00 0.00 3.91
19 20 7.283354 AGCACAATCTTTCCCTACTAATAAAGC 59.717 37.037 0.00 0.00 0.00 3.51
20 21 8.738645 AGCACAATCTTTCCCTACTAATAAAG 57.261 34.615 0.00 0.00 0.00 1.85
21 22 8.956426 CAAGCACAATCTTTCCCTACTAATAAA 58.044 33.333 0.00 0.00 0.00 1.40
22 23 7.067008 GCAAGCACAATCTTTCCCTACTAATAA 59.933 37.037 0.00 0.00 0.00 1.40
23 24 6.542370 GCAAGCACAATCTTTCCCTACTAATA 59.458 38.462 0.00 0.00 0.00 0.98
24 25 5.358160 GCAAGCACAATCTTTCCCTACTAAT 59.642 40.000 0.00 0.00 0.00 1.73
25 26 4.700213 GCAAGCACAATCTTTCCCTACTAA 59.300 41.667 0.00 0.00 0.00 2.24
26 27 4.019321 AGCAAGCACAATCTTTCCCTACTA 60.019 41.667 0.00 0.00 0.00 1.82
27 28 3.084786 GCAAGCACAATCTTTCCCTACT 58.915 45.455 0.00 0.00 0.00 2.57
28 29 3.084786 AGCAAGCACAATCTTTCCCTAC 58.915 45.455 0.00 0.00 0.00 3.18
29 30 3.439857 AGCAAGCACAATCTTTCCCTA 57.560 42.857 0.00 0.00 0.00 3.53
30 31 2.299326 AGCAAGCACAATCTTTCCCT 57.701 45.000 0.00 0.00 0.00 4.20
31 32 2.164422 GGTAGCAAGCACAATCTTTCCC 59.836 50.000 0.00 0.00 0.00 3.97
32 33 2.819608 TGGTAGCAAGCACAATCTTTCC 59.180 45.455 0.00 0.00 0.00 3.13
33 34 4.022849 AGTTGGTAGCAAGCACAATCTTTC 60.023 41.667 7.79 0.00 31.49 2.62
34 35 3.891366 AGTTGGTAGCAAGCACAATCTTT 59.109 39.130 7.79 0.00 31.49 2.52
35 36 3.490348 AGTTGGTAGCAAGCACAATCTT 58.510 40.909 7.79 0.00 31.49 2.40
36 37 3.146104 AGTTGGTAGCAAGCACAATCT 57.854 42.857 7.79 0.00 31.49 2.40
37 38 4.003648 AGTAGTTGGTAGCAAGCACAATC 58.996 43.478 7.79 0.00 31.49 2.67
51 52 5.831702 ACAACTCGTATAGGAGTAGTTGG 57.168 43.478 24.33 15.14 46.21 3.77
63 64 4.998672 TCGGAAAAATCCAACAACTCGTAT 59.001 37.500 0.00 0.00 0.00 3.06
125 126 6.700081 CCAAAACCTTGTTTCTTAACTAAGGC 59.300 38.462 13.93 0.00 41.35 4.35
150 151 6.487103 CAAGGCTCTATTGGTTCGATTAAAC 58.513 40.000 0.00 0.00 0.00 2.01
151 152 5.065988 GCAAGGCTCTATTGGTTCGATTAAA 59.934 40.000 0.00 0.00 0.00 1.52
152 153 4.574828 GCAAGGCTCTATTGGTTCGATTAA 59.425 41.667 0.00 0.00 0.00 1.40
153 154 4.127171 GCAAGGCTCTATTGGTTCGATTA 58.873 43.478 0.00 0.00 0.00 1.75
164 165 6.014669 TGGTTAATTTTTGTGCAAGGCTCTAT 60.015 34.615 0.00 0.00 0.00 1.98
274 275 0.994995 CTGTATGTGAGTGTCTGCGC 59.005 55.000 0.00 0.00 0.00 6.09
287 288 6.347160 CGTGCATTCATAAGGATGACTGTATG 60.347 42.308 0.00 4.83 42.13 2.39
293 294 2.613595 TGCGTGCATTCATAAGGATGAC 59.386 45.455 0.00 0.00 41.92 3.06
315 316 0.546122 TAGGGATGGATGTGTGTGCC 59.454 55.000 0.00 0.00 0.00 5.01
320 325 2.411583 TGCTCATAGGGATGGATGTGT 58.588 47.619 0.00 0.00 33.49 3.72
329 334 1.505098 TCCTGGAGATGCTCATAGGGA 59.495 52.381 13.50 5.50 37.15 4.20
341 346 4.683671 CGACTCAGTACTGTATCCTGGAGA 60.684 50.000 21.99 0.00 0.00 3.71
346 351 3.940221 GTGTCGACTCAGTACTGTATCCT 59.060 47.826 21.99 1.95 0.00 3.24
347 352 3.688185 TGTGTCGACTCAGTACTGTATCC 59.312 47.826 21.99 9.40 0.00 2.59
357 362 9.694520 CAATCTTAAAATATTGTGTCGACTCAG 57.305 33.333 18.61 6.01 0.00 3.35
415 420 1.550524 CGGTGGGAAGAGATGTTCTCA 59.449 52.381 7.24 0.00 45.73 3.27
424 429 0.032952 TGTTCGTTCGGTGGGAAGAG 59.967 55.000 0.00 0.00 34.69 2.85
450 455 9.271828 ACTTTTTGAATTTGTGTTCAGACTTTT 57.728 25.926 0.00 0.00 39.13 2.27
461 467 6.587990 TGGTGTACACACTTTTTGAATTTGTG 59.412 34.615 26.51 3.25 45.73 3.33
462 468 6.692486 TGGTGTACACACTTTTTGAATTTGT 58.308 32.000 26.51 0.00 45.73 2.83
463 469 6.811170 ACTGGTGTACACACTTTTTGAATTTG 59.189 34.615 26.51 3.21 45.73 2.32
713 735 0.394352 GATTCGTTGGCTGGGTGGAT 60.394 55.000 0.00 0.00 0.00 3.41
786 816 4.941263 GGAAAACCCTTTGCTGTTTTTCTT 59.059 37.500 0.00 0.00 42.87 2.52
787 817 4.513442 GGAAAACCCTTTGCTGTTTTTCT 58.487 39.130 0.00 0.00 42.87 2.52
788 818 3.308595 CGGAAAACCCTTTGCTGTTTTTC 59.691 43.478 0.00 0.00 42.87 2.29
789 819 3.266636 CGGAAAACCCTTTGCTGTTTTT 58.733 40.909 0.00 0.00 42.87 1.94
955 1004 3.756727 GACGGGGTGGAGACGGAC 61.757 72.222 0.00 0.00 0.00 4.79
993 1042 2.025155 GTGGAGAAGCTCATACCTCGA 58.975 52.381 0.00 0.00 31.08 4.04
1044 1093 3.928779 GGCGGATCCAGATGGCGA 61.929 66.667 13.41 0.00 34.44 5.54
1068 1117 1.142060 ACACCACGAAATGTCTTCCCA 59.858 47.619 0.00 0.00 0.00 4.37
1101 1150 1.219393 CCGCCTCTTCCTCAGGAAC 59.781 63.158 0.34 0.00 36.71 3.62
1290 1339 3.006940 TGCTAGCGGTAAGGTTTCAATG 58.993 45.455 10.77 0.00 0.00 2.82
1296 1345 0.172803 CGTCTGCTAGCGGTAAGGTT 59.827 55.000 22.76 0.00 0.00 3.50
1314 1363 1.729838 GCGGTAGGCGATAGAAGCG 60.730 63.158 0.00 0.00 38.29 4.68
1326 1375 1.226888 GGGCTCGTTGTAGCGGTAG 60.227 63.158 0.00 0.00 43.74 3.18
1338 1387 0.177141 TGACTTTAATCCGGGGCTCG 59.823 55.000 0.00 0.00 38.88 5.03
1425 1474 3.961480 TCAGTGTTCACGATCCAGAAT 57.039 42.857 0.00 0.00 0.00 2.40
1467 1516 0.333312 TATTTGCCGGGTCAATGGGT 59.667 50.000 2.18 0.00 0.00 4.51
1646 1695 5.299148 TCAATTAAGCAACAGCAAAAGCAT 58.701 33.333 0.00 0.00 0.00 3.79
1746 1795 9.878667 TCTATCTAGGATATCGTTACTCTCAAG 57.121 37.037 2.78 0.00 0.00 3.02
1841 1890 9.154847 CGACCAATAGAGCATATCAATTATCAA 57.845 33.333 0.00 0.00 0.00 2.57
1885 2542 2.431782 CCCATTCCAGCCTGTAAAATGG 59.568 50.000 17.44 17.44 43.84 3.16
1925 2582 0.104855 CTGCTATAACAGGCGCTCCA 59.895 55.000 7.64 0.00 33.85 3.86
2096 2753 1.597742 TTGGAGAAACAGCAGTCAGC 58.402 50.000 0.00 0.00 46.19 4.26
2239 2912 6.436847 TGCCACCTCTTTGAAATCATATTTGA 59.563 34.615 0.00 0.00 36.00 2.69
2243 2916 5.895534 ACATGCCACCTCTTTGAAATCATAT 59.104 36.000 0.00 0.00 0.00 1.78
2258 2931 3.127548 CACTTAAGACATCACATGCCACC 59.872 47.826 10.09 0.00 0.00 4.61
2315 2989 8.131731 GTCAAAGGAGATTGTTAATCCATAAGC 58.868 37.037 0.00 0.00 38.71 3.09
2316 2990 8.624776 GGTCAAAGGAGATTGTTAATCCATAAG 58.375 37.037 0.00 0.00 38.71 1.73
2371 3046 4.473444 AGTGTGAAGGTGATGATTTTGGT 58.527 39.130 0.00 0.00 0.00 3.67
2399 3074 8.459911 AGGAATCAGTAATAATTTAAACCCGG 57.540 34.615 0.00 0.00 0.00 5.73
2434 3119 9.747898 AAAGAAGTGTATATAATGTTGGGTCAA 57.252 29.630 0.00 0.00 0.00 3.18
2438 3123 8.746052 TCCAAAGAAGTGTATATAATGTTGGG 57.254 34.615 0.00 0.00 34.02 4.12
2553 3238 5.536161 ACAATGGAGAAACAAAGTGCAGTAT 59.464 36.000 0.00 0.00 0.00 2.12
2556 3245 4.311816 ACAATGGAGAAACAAAGTGCAG 57.688 40.909 0.00 0.00 0.00 4.41
2564 3253 9.905713 ATAATAGCTAGAAACAATGGAGAAACA 57.094 29.630 0.00 0.00 0.00 2.83
2860 3622 7.599998 AGCATTTGATGTTGAACAAATAAGGTC 59.400 33.333 0.62 0.00 42.35 3.85
3003 3888 6.202188 ACTTGTGGTTAGTTACATGACTTTCG 59.798 38.462 0.00 0.00 0.00 3.46
3071 4076 4.970662 ATAACTGCATAAAGCCACACAG 57.029 40.909 0.00 0.00 44.83 3.66
3161 4168 3.008049 GGACAAAAGAGAGAGGGTAAGCA 59.992 47.826 0.00 0.00 0.00 3.91
3401 4409 0.752376 CTGGACGGAGGGAGTAGGTC 60.752 65.000 0.00 0.00 0.00 3.85
3402 4410 1.212934 TCTGGACGGAGGGAGTAGGT 61.213 60.000 0.00 0.00 0.00 3.08
3403 4411 0.033405 TTCTGGACGGAGGGAGTAGG 60.033 60.000 0.00 0.00 0.00 3.18
3404 4412 1.848652 TTTCTGGACGGAGGGAGTAG 58.151 55.000 0.00 0.00 0.00 2.57
3405 4413 2.544844 ATTTCTGGACGGAGGGAGTA 57.455 50.000 0.00 0.00 0.00 2.59
3406 4414 2.108970 GTATTTCTGGACGGAGGGAGT 58.891 52.381 0.00 0.00 0.00 3.85
3408 4416 2.385803 GAGTATTTCTGGACGGAGGGA 58.614 52.381 0.00 0.00 0.00 4.20
3409 4417 1.067212 CGAGTATTTCTGGACGGAGGG 59.933 57.143 0.00 0.00 0.00 4.30
3410 4418 1.749634 ACGAGTATTTCTGGACGGAGG 59.250 52.381 0.00 0.00 0.00 4.30
3411 4419 2.539142 CGACGAGTATTTCTGGACGGAG 60.539 54.545 0.00 0.00 36.75 4.63
3412 4420 1.399440 CGACGAGTATTTCTGGACGGA 59.601 52.381 0.00 0.00 36.75 4.69
3413 4421 1.823828 CGACGAGTATTTCTGGACGG 58.176 55.000 0.00 0.00 36.75 4.79
3414 4422 1.399440 TCCGACGAGTATTTCTGGACG 59.601 52.381 0.00 0.00 38.91 4.79
3415 4423 2.223525 CCTCCGACGAGTATTTCTGGAC 60.224 54.545 0.00 0.00 33.93 4.02
3416 4424 2.022195 CCTCCGACGAGTATTTCTGGA 58.978 52.381 0.00 0.00 33.93 3.86
3417 4425 2.022195 TCCTCCGACGAGTATTTCTGG 58.978 52.381 0.00 0.00 33.93 3.86
3418 4426 3.777465 TTCCTCCGACGAGTATTTCTG 57.223 47.619 0.00 0.00 33.93 3.02
3419 4427 3.068307 CCATTCCTCCGACGAGTATTTCT 59.932 47.826 0.00 0.00 33.93 2.52
3420 4428 3.067742 TCCATTCCTCCGACGAGTATTTC 59.932 47.826 0.00 0.00 33.93 2.17
3421 4429 3.028850 TCCATTCCTCCGACGAGTATTT 58.971 45.455 0.00 0.00 33.93 1.40
3422 4430 2.662866 TCCATTCCTCCGACGAGTATT 58.337 47.619 0.00 0.00 33.93 1.89
3423 4431 2.359981 TCCATTCCTCCGACGAGTAT 57.640 50.000 0.00 0.00 33.93 2.12
3424 4432 1.954382 CATCCATTCCTCCGACGAGTA 59.046 52.381 0.00 0.00 33.93 2.59
3425 4433 0.747255 CATCCATTCCTCCGACGAGT 59.253 55.000 0.00 0.00 33.93 4.18
3426 4434 0.598680 GCATCCATTCCTCCGACGAG 60.599 60.000 0.00 0.00 35.72 4.18
3427 4435 1.326951 TGCATCCATTCCTCCGACGA 61.327 55.000 0.00 0.00 0.00 4.20
3428 4436 0.250038 ATGCATCCATTCCTCCGACG 60.250 55.000 0.00 0.00 0.00 5.12
3429 4437 1.071385 AGATGCATCCATTCCTCCGAC 59.929 52.381 23.06 0.00 0.00 4.79
3430 4438 1.427809 AGATGCATCCATTCCTCCGA 58.572 50.000 23.06 0.00 0.00 4.55
3431 4439 2.564504 TCTAGATGCATCCATTCCTCCG 59.435 50.000 23.06 0.00 0.00 4.63
3432 4440 4.019501 ACATCTAGATGCATCCATTCCTCC 60.020 45.833 28.86 0.00 42.39 4.30
3433 4441 5.163281 ACATCTAGATGCATCCATTCCTC 57.837 43.478 28.86 0.00 42.39 3.71
3434 4442 6.887886 ATACATCTAGATGCATCCATTCCT 57.112 37.500 28.86 10.75 42.39 3.36
3435 4443 7.934855 AAATACATCTAGATGCATCCATTCC 57.065 36.000 28.86 0.00 42.39 3.01
3439 4447 9.494271 GAACTAAAATACATCTAGATGCATCCA 57.506 33.333 28.86 9.05 42.39 3.41
3440 4448 9.717942 AGAACTAAAATACATCTAGATGCATCC 57.282 33.333 28.86 5.58 42.39 3.51
3470 4478 9.443323 TCGGAGAAATGTCTAAAAATGAATGTA 57.557 29.630 0.00 0.00 32.80 2.29
3471 4479 8.237267 GTCGGAGAAATGTCTAAAAATGAATGT 58.763 33.333 0.00 0.00 39.69 2.71
3472 4480 8.236586 TGTCGGAGAAATGTCTAAAAATGAATG 58.763 33.333 0.00 0.00 39.69 2.67
3473 4481 8.335532 TGTCGGAGAAATGTCTAAAAATGAAT 57.664 30.769 0.00 0.00 39.69 2.57
3474 4482 7.737972 TGTCGGAGAAATGTCTAAAAATGAA 57.262 32.000 0.00 0.00 39.69 2.57
3475 4483 7.444183 ACTTGTCGGAGAAATGTCTAAAAATGA 59.556 33.333 0.00 0.00 39.69 2.57
3476 4484 7.584987 ACTTGTCGGAGAAATGTCTAAAAATG 58.415 34.615 0.00 0.00 39.69 2.32
3477 4485 7.745620 ACTTGTCGGAGAAATGTCTAAAAAT 57.254 32.000 0.00 0.00 39.69 1.82
3478 4486 8.842358 ATACTTGTCGGAGAAATGTCTAAAAA 57.158 30.769 0.00 0.00 39.69 1.94
3479 4487 8.842358 AATACTTGTCGGAGAAATGTCTAAAA 57.158 30.769 0.00 0.00 39.69 1.52
3480 4488 8.842358 AAATACTTGTCGGAGAAATGTCTAAA 57.158 30.769 0.00 0.00 39.69 1.85
3481 4489 7.548075 GGAAATACTTGTCGGAGAAATGTCTAA 59.452 37.037 0.00 0.00 39.69 2.10
3482 4490 7.039882 GGAAATACTTGTCGGAGAAATGTCTA 58.960 38.462 0.00 0.00 39.69 2.59
3483 4491 5.875359 GGAAATACTTGTCGGAGAAATGTCT 59.125 40.000 0.00 0.00 39.69 3.41
3484 4492 5.220416 CGGAAATACTTGTCGGAGAAATGTC 60.220 44.000 0.00 0.00 39.69 3.06
3485 4493 4.630069 CGGAAATACTTGTCGGAGAAATGT 59.370 41.667 0.00 0.00 39.69 2.71
3486 4494 4.034048 CCGGAAATACTTGTCGGAGAAATG 59.966 45.833 0.00 0.00 42.94 2.32
3487 4495 4.081309 TCCGGAAATACTTGTCGGAGAAAT 60.081 41.667 0.00 0.00 43.84 2.17
3488 4496 3.258872 TCCGGAAATACTTGTCGGAGAAA 59.741 43.478 0.00 0.00 43.84 2.52
3489 4497 2.827322 TCCGGAAATACTTGTCGGAGAA 59.173 45.455 0.00 0.00 43.84 2.87
3490 4498 2.449464 TCCGGAAATACTTGTCGGAGA 58.551 47.619 0.00 0.00 43.84 3.71
3491 4499 2.953466 TCCGGAAATACTTGTCGGAG 57.047 50.000 0.00 0.00 43.84 4.63
3492 4500 1.135315 CGTCCGGAAATACTTGTCGGA 60.135 52.381 5.23 0.00 46.06 4.55
3493 4501 1.274596 CGTCCGGAAATACTTGTCGG 58.725 55.000 5.23 0.00 41.80 4.79
3494 4502 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
3495 4503 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
3496 4504 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
3497 4505 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
3498 4506 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
3499 4507 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
3500 4508 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
3501 4509 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
3502 4510 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
3503 4511 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
3504 4512 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
3505 4513 1.929860 ATGTACTCCCTCCGTCCGGA 61.930 60.000 0.00 0.00 42.90 5.14
3506 4514 0.179009 TATGTACTCCCTCCGTCCGG 60.179 60.000 0.00 0.00 0.00 5.14
3507 4515 1.336125 GTTATGTACTCCCTCCGTCCG 59.664 57.143 0.00 0.00 0.00 4.79
3508 4516 2.381911 TGTTATGTACTCCCTCCGTCC 58.618 52.381 0.00 0.00 0.00 4.79
3509 4517 3.737355 GCTTGTTATGTACTCCCTCCGTC 60.737 52.174 0.00 0.00 0.00 4.79
3510 4518 2.167900 GCTTGTTATGTACTCCCTCCGT 59.832 50.000 0.00 0.00 0.00 4.69
3511 4519 2.431057 AGCTTGTTATGTACTCCCTCCG 59.569 50.000 0.00 0.00 0.00 4.63
3512 4520 5.602628 CTTAGCTTGTTATGTACTCCCTCC 58.397 45.833 0.00 0.00 0.00 4.30
3513 4521 5.051153 GCTTAGCTTGTTATGTACTCCCTC 58.949 45.833 0.00 0.00 0.00 4.30
3514 4522 4.469945 TGCTTAGCTTGTTATGTACTCCCT 59.530 41.667 5.60 0.00 0.00 4.20
3515 4523 4.766375 TGCTTAGCTTGTTATGTACTCCC 58.234 43.478 5.60 0.00 0.00 4.30
3516 4524 6.737254 TTTGCTTAGCTTGTTATGTACTCC 57.263 37.500 5.60 0.00 0.00 3.85
3517 4525 8.202745 AGATTTGCTTAGCTTGTTATGTACTC 57.797 34.615 5.60 0.00 0.00 2.59
3518 4526 9.838339 ATAGATTTGCTTAGCTTGTTATGTACT 57.162 29.630 5.60 0.00 0.00 2.73
3597 4618 5.703876 CAAGCTCCAAGTTACAAAGGAATC 58.296 41.667 0.00 0.00 0.00 2.52
3613 4634 2.039405 CAGGCTCAGTGCAAGCTCC 61.039 63.158 8.68 0.00 45.15 4.70
3710 4731 1.211212 TCAGCTGCTGCATTCACCTAT 59.789 47.619 24.38 0.00 42.74 2.57
3818 4839 3.112709 GACTCTTGTGACGGGCGC 61.113 66.667 0.00 0.00 0.00 6.53
3894 4915 7.697291 TGTGTTTTAACGGTCTTTGAATTGTAC 59.303 33.333 0.00 0.00 0.00 2.90
3953 4975 5.420739 TGAAAGGGGTTTCATGTTATTAGCC 59.579 40.000 0.00 0.00 36.15 3.93
3990 5012 4.309099 GCTTGAATCCAGTTGCAATCAAA 58.691 39.130 0.59 0.00 33.37 2.69
4059 5081 1.207329 GCAGAAAGTAGTCGGTGGGAT 59.793 52.381 0.00 0.00 0.00 3.85
4061 5083 0.608640 AGCAGAAAGTAGTCGGTGGG 59.391 55.000 0.00 0.00 0.00 4.61
4157 5183 2.843113 CCTGGGAAGATGAAGAGAACCT 59.157 50.000 0.00 0.00 0.00 3.50
4171 5197 3.327404 GGGCCTTCGTCCTGGGAA 61.327 66.667 0.84 0.00 0.00 3.97
4199 5225 0.458025 CGCTGTAGGAACTCGGGAAC 60.458 60.000 0.00 0.00 41.75 3.62
4229 5255 0.991920 TAGCCTCTGGAAAACCCTGG 59.008 55.000 0.00 0.00 34.88 4.45
4231 5257 2.555448 GCTTTAGCCTCTGGAAAACCCT 60.555 50.000 0.00 0.00 33.18 4.34
4255 5281 4.464008 AGAAGCTCATGACACTGGAAAAA 58.536 39.130 0.00 0.00 0.00 1.94
4256 5282 4.067896 GAGAAGCTCATGACACTGGAAAA 58.932 43.478 0.00 0.00 0.00 2.29
4277 5323 2.379972 GCCTACTGCTAGAGGAACTGA 58.620 52.381 0.00 0.00 35.99 3.41
4296 5342 3.366422 TGCAACGAAACAAAACAAAGAGC 59.634 39.130 0.00 0.00 0.00 4.09
4302 5348 2.953020 AGCTTGCAACGAAACAAAACA 58.047 38.095 0.00 0.00 0.00 2.83
4306 5352 3.701241 CCTAAAGCTTGCAACGAAACAA 58.299 40.909 0.00 0.00 0.00 2.83
4309 5355 1.334599 CGCCTAAAGCTTGCAACGAAA 60.335 47.619 0.00 0.00 40.39 3.46
4310 5356 0.237235 CGCCTAAAGCTTGCAACGAA 59.763 50.000 0.00 0.00 40.39 3.85
4312 5358 0.447801 ATCGCCTAAAGCTTGCAACG 59.552 50.000 0.00 2.57 40.39 4.10
4313 5359 2.936498 TCTATCGCCTAAAGCTTGCAAC 59.064 45.455 0.00 0.00 40.39 4.17
4314 5360 2.936498 GTCTATCGCCTAAAGCTTGCAA 59.064 45.455 0.00 0.00 40.39 4.08
4328 5394 4.038361 GCTATCACACACACAGTCTATCG 58.962 47.826 0.00 0.00 0.00 2.92
4336 5402 5.170748 CAGTCTAATGCTATCACACACACA 58.829 41.667 0.00 0.00 0.00 3.72
4357 5423 7.988737 TGACAAAGATAGGTTTTCATATGCAG 58.011 34.615 0.00 0.00 0.00 4.41
4369 5435 4.243270 GTTACACGCTGACAAAGATAGGT 58.757 43.478 0.00 0.00 0.00 3.08
4371 5437 4.242475 TGGTTACACGCTGACAAAGATAG 58.758 43.478 0.00 0.00 0.00 2.08
4379 5445 1.665679 CATGGATGGTTACACGCTGAC 59.334 52.381 0.00 0.00 0.00 3.51
4380 5446 1.406751 CCATGGATGGTTACACGCTGA 60.407 52.381 5.56 0.00 43.05 4.26
4381 5447 1.016627 CCATGGATGGTTACACGCTG 58.983 55.000 5.56 0.00 43.05 5.18
4382 5448 3.476740 CCATGGATGGTTACACGCT 57.523 52.632 5.56 0.00 43.05 5.07
4395 5461 1.808133 GCTTAGAAGAGACCGCCATGG 60.808 57.143 7.63 7.63 46.41 3.66
4420 5486 1.187567 AGTTCCAAACAGGGCCATGC 61.188 55.000 19.26 0.00 38.24 4.06
4421 5487 1.273327 GAAGTTCCAAACAGGGCCATG 59.727 52.381 17.55 17.55 38.24 3.66
4464 5531 3.433274 GCACGAGAATGTCACAAGAATCA 59.567 43.478 0.00 0.00 0.00 2.57
4476 5543 0.179215 GCGTTTCCAGCACGAGAATG 60.179 55.000 0.00 0.00 40.20 2.67
4486 5553 2.436646 ATCCAGGCGCGTTTCCAG 60.437 61.111 8.43 0.00 0.00 3.86
4488 5555 3.564027 CGATCCAGGCGCGTTTCC 61.564 66.667 8.43 0.00 0.00 3.13
4579 5646 4.311816 AGTTCAAAACCTCGTCGTCTAA 57.688 40.909 0.00 0.00 0.00 2.10
4600 5667 5.702209 TGTCGAGATAATGCTACATACGGTA 59.298 40.000 0.00 0.00 0.00 4.02
4603 5670 7.568267 AAATGTCGAGATAATGCTACATACG 57.432 36.000 0.00 0.00 0.00 3.06
4616 5686 5.471456 ACAAAGCAAGAGAAAATGTCGAGAT 59.529 36.000 0.00 0.00 0.00 2.75
4645 5715 2.236146 TCACGATTCAGGCATACTTGGT 59.764 45.455 0.00 0.00 0.00 3.67
4652 5723 2.989909 TGTGATTCACGATTCAGGCAT 58.010 42.857 11.97 0.00 37.14 4.40
4677 5748 1.760875 GCCTCGACCACCATCCCTA 60.761 63.158 0.00 0.00 0.00 3.53
4678 5749 3.083997 GCCTCGACCACCATCCCT 61.084 66.667 0.00 0.00 0.00 4.20
4679 5750 3.391665 CTGCCTCGACCACCATCCC 62.392 68.421 0.00 0.00 0.00 3.85
4680 5751 2.187946 CTGCCTCGACCACCATCC 59.812 66.667 0.00 0.00 0.00 3.51
4681 5752 2.512515 GCTGCCTCGACCACCATC 60.513 66.667 0.00 0.00 0.00 3.51
4682 5753 3.005539 AGCTGCCTCGACCACCAT 61.006 61.111 0.00 0.00 0.00 3.55
4683 5754 3.695606 GAGCTGCCTCGACCACCA 61.696 66.667 0.00 0.00 0.00 4.17
4703 5774 2.031944 GCAGCTTAAAATAGGCGCCTAC 60.032 50.000 37.53 22.43 35.71 3.18
4704 5775 2.218603 GCAGCTTAAAATAGGCGCCTA 58.781 47.619 36.88 36.88 35.71 3.93
4708 5785 3.126858 TCAGTTGCAGCTTAAAATAGGCG 59.873 43.478 0.00 0.00 35.71 5.52
4860 5937 2.035442 GTTGCGTTCCTCCTGCTCC 61.035 63.158 0.00 0.00 0.00 4.70
4861 5938 1.294659 CTGTTGCGTTCCTCCTGCTC 61.295 60.000 0.00 0.00 0.00 4.26
4895 5972 2.696759 CGGTTGGTGGATTTCGGGC 61.697 63.158 0.00 0.00 0.00 6.13
4898 5975 0.036765 TCTCCGGTTGGTGGATTTCG 60.037 55.000 0.00 0.00 34.32 3.46
5117 6201 0.970937 ATCACGAAAGGAGGCGGAGA 60.971 55.000 0.00 0.00 0.00 3.71
5123 6207 1.649664 CAGCAGATCACGAAAGGAGG 58.350 55.000 0.00 0.00 0.00 4.30
5166 6251 1.578206 GACAAGCAACCGAAGCTCCC 61.578 60.000 0.00 0.00 42.53 4.30
5212 6297 0.673644 CAGAACCCGCACCGAATTCT 60.674 55.000 3.52 0.00 33.52 2.40


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

AutoCloner maintained by Alex Coulton.