Multiple sequence alignment - TraesCS3A01G152000

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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 TraesCS3A01G152000 chr3A 100.000 3904 0 0 1 3904 142578178 142582081 0.000000e+00 7210.0
1 TraesCS3A01G152000 chr3A 95.041 121 6 0 3713 3833 142882947 142883067 1.430000e-44 191.0
2 TraesCS3A01G152000 chr3A 87.333 150 14 2 3293 3442 141894606 141894462 2.410000e-37 167.0
3 TraesCS3A01G152000 chr3A 93.458 107 6 1 3016 3122 142882679 142882784 1.450000e-34 158.0
4 TraesCS3A01G152000 chr3D 94.226 2390 101 21 914 3294 130504852 130507213 0.000000e+00 3615.0
5 TraesCS3A01G152000 chr3D 88.153 498 25 17 3428 3904 130507202 130507686 2.630000e-156 562.0
6 TraesCS3A01G152000 chr3D 88.889 306 10 7 1 294 130503731 130504024 4.800000e-94 355.0
7 TraesCS3A01G152000 chr3D 89.362 188 9 3 570 757 130504540 130504716 3.920000e-55 226.0
8 TraesCS3A01G152000 chr3D 92.308 91 6 1 357 447 130504340 130504429 1.140000e-25 128.0
9 TraesCS3A01G152000 chr3D 96.552 58 2 0 294 351 130504101 130504158 3.210000e-16 97.1
10 TraesCS3A01G152000 chr3D 97.500 40 1 0 1016 1055 130504994 130505033 7.000000e-08 69.4
11 TraesCS3A01G152000 chr3B 93.995 1149 61 5 2150 3294 187330508 187331652 0.000000e+00 1733.0
12 TraesCS3A01G152000 chr3B 88.809 554 43 12 1050 1588 187329961 187330510 0.000000e+00 662.0
13 TraesCS3A01G152000 chr3B 90.625 288 13 7 1 286 187152809 187153084 1.710000e-98 370.0
14 TraesCS3A01G152000 chr3B 86.307 241 14 12 833 1055 187329763 187330002 1.080000e-60 244.0
15 TraesCS3A01G152000 chr3B 89.630 135 7 5 3428 3562 187331641 187331768 8.680000e-37 165.0
16 TraesCS3A01G152000 chr3B 85.897 156 15 6 629 780 187153542 187153694 4.040000e-35 159.0
17 TraesCS3A01G152000 chr4B 94.737 418 11 3 2097 2513 117059581 117059988 1.180000e-179 640.0
18 TraesCS3A01G152000 chr1A 89.024 164 11 4 3293 3455 438341215 438341372 3.080000e-46 196.0
19 TraesCS3A01G152000 chr1A 89.865 148 10 2 3296 3443 85860518 85860376 6.660000e-43 185.0
20 TraesCS3A01G152000 chr5A 90.345 145 9 2 3293 3437 591437156 591437017 6.660000e-43 185.0
21 TraesCS3A01G152000 chr6A 90.278 144 9 2 3294 3437 158314926 158315064 2.400000e-42 183.0
22 TraesCS3A01G152000 chr7D 89.189 148 11 2 3293 3440 3598906 3598764 3.100000e-41 180.0
23 TraesCS3A01G152000 chr2A 89.189 148 11 2 3290 3437 48402671 48402813 3.100000e-41 180.0
24 TraesCS3A01G152000 chr5D 88.158 152 12 3 3290 3441 35825425 35825570 4.010000e-40 176.0
25 TraesCS3A01G152000 chr5D 82.270 141 20 2 3297 3437 364733117 364732982 2.460000e-22 117.0
26 TraesCS3A01G152000 chr6B 100.000 35 0 0 3403 3437 46851248 46851282 9.050000e-07 65.8


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 TraesCS3A01G152000 chr3A 142578178 142582081 3903 False 7210.000000 7210 100.000000 1 3904 1 chr3A.!!$F1 3903
1 TraesCS3A01G152000 chr3D 130503731 130507686 3955 False 721.785714 3615 92.427143 1 3904 7 chr3D.!!$F1 3903
2 TraesCS3A01G152000 chr3B 187329763 187331768 2005 False 701.000000 1733 89.685250 833 3562 4 chr3B.!!$F2 2729
3 TraesCS3A01G152000 chr3B 187152809 187153694 885 False 264.500000 370 88.261000 1 780 2 chr3B.!!$F1 779

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
533 849 0.109597 CTCCAGACATTTGCGGCAAC 60.110 55.000 16.15 3.79 0.0 4.17 F
1386 1781 1.275291 TGACCCGGCTCAGTTTTCTAG 59.725 52.381 0.00 0.00 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1415 1810 0.600255 CACAGGTCACACGACTTCCC 60.600 60.0 0.0 0.0 42.21 3.97 R
3371 3783 0.179018 GGAGTTGGTGGAGTTGCAGT 60.179 55.0 0.0 0.0 0.00 4.40 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 111 4.760757 GCTAACCGAGCCCTCATC 57.239 61.111 0.00 0.00 46.41 2.92
111 112 1.823295 GCTAACCGAGCCCTCATCA 59.177 57.895 0.00 0.00 46.41 3.07
112 113 0.249657 GCTAACCGAGCCCTCATCAG 60.250 60.000 0.00 0.00 46.41 2.90
113 114 1.115467 CTAACCGAGCCCTCATCAGT 58.885 55.000 0.00 0.00 0.00 3.41
171 172 6.406624 GGCATTCCACTTACTGTAAGCTAGTA 60.407 42.308 23.74 9.71 39.39 1.82
175 176 7.096884 TCCACTTACTGTAAGCTAGTATGTG 57.903 40.000 23.74 22.49 46.07 3.21
230 238 0.523966 AGAGCACGGAAAGAGTCGAG 59.476 55.000 0.00 0.00 0.00 4.04
232 240 1.467734 GAGCACGGAAAGAGTCGAGTA 59.532 52.381 0.00 0.00 0.00 2.59
233 241 1.884579 AGCACGGAAAGAGTCGAGTAA 59.115 47.619 0.00 0.00 0.00 2.24
234 242 2.095161 AGCACGGAAAGAGTCGAGTAAG 60.095 50.000 0.00 0.00 0.00 2.34
235 243 2.351544 GCACGGAAAGAGTCGAGTAAGT 60.352 50.000 0.00 0.00 0.00 2.24
236 244 3.490399 CACGGAAAGAGTCGAGTAAGTC 58.510 50.000 0.00 0.00 0.00 3.01
248 256 2.338500 GAGTAAGTCGACAGGCTTTGG 58.662 52.381 19.50 0.00 39.70 3.28
351 444 8.141298 TGTCCCTGTTCTTGTAGATTTATACA 57.859 34.615 0.00 0.00 33.88 2.29
352 445 8.768397 TGTCCCTGTTCTTGTAGATTTATACAT 58.232 33.333 0.00 0.00 35.65 2.29
380 650 8.311650 TGTTGTATAGAAAGAAAGCAAGACTC 57.688 34.615 0.00 0.00 0.00 3.36
386 656 4.273724 AGAAAGAAAGCAAGACTCGGAAAC 59.726 41.667 0.00 0.00 0.00 2.78
447 717 2.479566 TCCACTGTGGCTTCTTGATC 57.520 50.000 22.02 0.00 37.47 2.92
469 784 9.213777 TGATCTATACAGGAGTAAATTTCCACT 57.786 33.333 0.00 0.00 37.18 4.00
481 796 5.596836 AAATTTCCACTGTGACATTGTGT 57.403 34.783 9.86 0.00 0.00 3.72
490 805 3.549794 TGTGACATTGTGTGTGGATCAA 58.450 40.909 0.00 0.00 42.36 2.57
491 806 3.314913 TGTGACATTGTGTGTGGATCAAC 59.685 43.478 0.00 0.00 42.36 3.18
497 813 0.250124 GTGTGTGGATCAACGGACCA 60.250 55.000 0.00 0.00 0.00 4.02
524 840 6.888632 AGAAAATGCTAATGACTCCAGACATT 59.111 34.615 8.88 8.88 41.66 2.71
528 844 3.242543 GCTAATGACTCCAGACATTTGCG 60.243 47.826 16.96 6.70 43.36 4.85
529 845 1.742761 ATGACTCCAGACATTTGCGG 58.257 50.000 0.00 0.00 0.00 5.69
533 849 0.109597 CTCCAGACATTTGCGGCAAC 60.110 55.000 16.15 3.79 0.00 4.17
550 866 5.819825 GGCAACGAATTATCCTTCTTCTT 57.180 39.130 0.00 0.00 0.00 2.52
551 867 6.196079 GGCAACGAATTATCCTTCTTCTTT 57.804 37.500 0.00 0.00 0.00 2.52
552 868 6.621613 GGCAACGAATTATCCTTCTTCTTTT 58.378 36.000 0.00 0.00 0.00 2.27
553 869 7.090808 GGCAACGAATTATCCTTCTTCTTTTT 58.909 34.615 0.00 0.00 0.00 1.94
616 932 1.693606 ACCCAAAAAGTCCAATGCCAG 59.306 47.619 0.00 0.00 0.00 4.85
641 975 2.097466 GGCTTGACACATCCCAATTACG 59.903 50.000 0.00 0.00 0.00 3.18
671 1005 3.436700 AATGTGCACATCATCAGCATG 57.563 42.857 31.45 0.00 40.78 4.06
683 1017 6.592607 ACATCATCAGCATGTTTTTGAATTCC 59.407 34.615 2.27 0.00 37.40 3.01
689 1023 4.039124 AGCATGTTTTTGAATTCCCGAACT 59.961 37.500 2.27 0.00 0.00 3.01
720 1054 8.973378 TGTCAAATCCGTGAATAATTTTTCAAC 58.027 29.630 12.15 6.05 37.36 3.18
915 1254 2.350895 CCATGTCGCACAGGGGAA 59.649 61.111 10.83 0.00 45.60 3.97
917 1256 1.746615 CATGTCGCACAGGGGAAGG 60.747 63.158 0.00 0.00 37.76 3.46
918 1257 1.918293 ATGTCGCACAGGGGAAGGA 60.918 57.895 0.00 0.00 37.76 3.36
920 1259 1.671379 GTCGCACAGGGGAAGGAAC 60.671 63.158 0.00 0.00 37.76 3.62
921 1260 2.144078 TCGCACAGGGGAAGGAACA 61.144 57.895 0.00 0.00 32.40 3.18
923 1262 1.456287 GCACAGGGGAAGGAACAGT 59.544 57.895 0.00 0.00 0.00 3.55
982 1373 3.318017 CAATATAAGCCTCTCCGTTCCG 58.682 50.000 0.00 0.00 0.00 4.30
1127 1522 3.358076 GAAGTCGACAGAGCCCCGG 62.358 68.421 19.50 0.00 0.00 5.73
1377 1772 3.948719 GGTTGGTGACCCGGCTCA 61.949 66.667 0.00 0.00 43.06 4.26
1386 1781 1.275291 TGACCCGGCTCAGTTTTCTAG 59.725 52.381 0.00 0.00 0.00 2.43
1388 1783 1.275573 ACCCGGCTCAGTTTTCTAGTC 59.724 52.381 0.00 0.00 0.00 2.59
1390 1785 2.611518 CCGGCTCAGTTTTCTAGTCTG 58.388 52.381 0.00 0.00 0.00 3.51
1434 1838 0.600255 GGGAAGTCGTGTGACCTGTG 60.600 60.000 0.00 0.00 46.74 3.66
1435 1839 0.104304 GGAAGTCGTGTGACCTGTGT 59.896 55.000 0.00 0.00 46.74 3.72
1436 1840 1.472728 GGAAGTCGTGTGACCTGTGTT 60.473 52.381 0.00 0.00 46.74 3.32
1437 1841 1.859080 GAAGTCGTGTGACCTGTGTTC 59.141 52.381 0.00 0.00 46.74 3.18
1490 1894 6.479001 CGTTCGGTGAGTAATTATGGAGAAAT 59.521 38.462 0.00 0.00 0.00 2.17
1513 1917 8.408043 AATTTGTTGGTCTGTTGATGATCTTA 57.592 30.769 0.00 0.00 0.00 2.10
1544 1949 2.356382 CGGTTTGGTTCAAGCACTTGTA 59.644 45.455 10.05 0.00 41.16 2.41
1553 1958 5.009010 GGTTCAAGCACTTGTATATCATGGG 59.991 44.000 10.05 0.00 41.16 4.00
1572 1977 2.914059 GGGAAAATCCGCACTAGCTTA 58.086 47.619 0.00 0.00 37.43 3.09
1573 1978 3.275999 GGGAAAATCCGCACTAGCTTAA 58.724 45.455 0.00 0.00 37.43 1.85
1594 1999 3.059352 AGCACCTGTGGTTAGACATTC 57.941 47.619 0.00 0.00 38.24 2.67
1595 2000 1.732259 GCACCTGTGGTTAGACATTCG 59.268 52.381 0.00 0.00 31.02 3.34
1605 2010 4.517453 TGGTTAGACATTCGGGTCAAAAAG 59.483 41.667 0.00 0.00 40.29 2.27
1620 2025 5.985781 GTCAAAAAGACACGTGATGTATGT 58.014 37.500 25.01 0.00 46.77 2.29
1633 2038 5.006068 CGTGATGTATGTCATGTTCCTTCAG 59.994 44.000 0.00 0.00 36.83 3.02
1669 2074 9.941664 CTAGCACTTTTATCAGGATAAAACATG 57.058 33.333 18.46 18.61 44.01 3.21
1749 2154 4.899352 AATGGGAGGTAGTCATGATAGC 57.101 45.455 0.00 2.70 0.00 2.97
1795 2200 5.811399 TTCGAACTTGATTGTTCAGTGTT 57.189 34.783 0.00 0.00 44.59 3.32
1859 2264 6.824553 AGAGGATTCTTCATGAATTCGATCA 58.175 36.000 8.96 0.00 44.70 2.92
1908 2313 1.512926 AGCAAGTAAACGTCTGCTGG 58.487 50.000 7.86 0.00 0.00 4.85
1971 2376 7.052248 TCATCATGATGTGAAGCTACTGATTT 58.948 34.615 30.01 0.00 40.97 2.17
1973 2378 6.408869 TCATGATGTGAAGCTACTGATTTGA 58.591 36.000 0.00 0.00 32.78 2.69
1996 2401 1.181098 ATTGCCACCAACTGAGCACC 61.181 55.000 0.00 0.00 34.37 5.01
2001 2406 0.179048 CACCAACTGAGCACCTGACA 60.179 55.000 0.00 0.00 0.00 3.58
2006 2411 2.676839 CAACTGAGCACCTGACATGATC 59.323 50.000 0.00 0.00 33.03 2.92
2076 2481 7.917597 TCTAGAAGAATACAGATACACGTGAC 58.082 38.462 25.01 12.86 0.00 3.67
2263 2672 0.038159 AAAGGGTCGAGCTGAAGACG 60.038 55.000 15.18 0.00 38.20 4.18
2392 2801 3.248024 TGACCTGTATGTGGACTCCTTT 58.752 45.455 0.00 0.00 0.00 3.11
2434 2843 0.041684 TCAGAGGGGAGCATCTGTCA 59.958 55.000 0.00 0.00 42.86 3.58
2497 2906 2.783828 ATGCCATCGAGAACTCTACG 57.216 50.000 0.00 0.00 0.00 3.51
2848 3257 6.486253 TGAGAAAATGCTGTTCTGATACAC 57.514 37.500 2.44 0.00 35.46 2.90
2853 3262 5.779806 AATGCTGTTCTGATACACGTTAC 57.220 39.130 0.00 0.00 0.00 2.50
2854 3263 4.514781 TGCTGTTCTGATACACGTTACT 57.485 40.909 0.00 0.00 0.00 2.24
2855 3264 5.632244 TGCTGTTCTGATACACGTTACTA 57.368 39.130 0.00 0.00 0.00 1.82
2926 3335 6.817765 ACTTGTGTTGTCTCTTTTTCTTCA 57.182 33.333 0.00 0.00 0.00 3.02
2927 3336 6.846350 ACTTGTGTTGTCTCTTTTTCTTCAG 58.154 36.000 0.00 0.00 0.00 3.02
2928 3337 6.431234 ACTTGTGTTGTCTCTTTTTCTTCAGT 59.569 34.615 0.00 0.00 0.00 3.41
3004 3415 9.793259 AGTTAACCTAGAATCTTGAATTGTCAA 57.207 29.630 0.88 0.00 41.57 3.18
3030 3442 7.527568 TTTGGTCGATTTACCCTTACAAATT 57.472 32.000 0.00 0.00 38.90 1.82
3066 3478 5.763204 TGGTTGTGAATCCTACAGAAAGTTC 59.237 40.000 0.00 0.00 0.00 3.01
3100 3512 1.826024 CAGTATGGCGAGCCCTTCT 59.174 57.895 12.05 2.15 34.56 2.85
3135 3547 5.126869 TCACCCAAAACATATAGCATTGGTG 59.873 40.000 0.00 0.00 39.07 4.17
3159 3571 7.432252 GTGCAGTACTTTATTGCCATGTAAATC 59.568 37.037 0.00 0.00 40.27 2.17
3181 3593 5.126067 TCCATCTTAGCTTGGCTATGTTTC 58.874 41.667 0.00 0.00 41.01 2.78
3185 3597 6.500684 TCTTAGCTTGGCTATGTTTCTTTG 57.499 37.500 0.00 0.00 41.01 2.77
3188 3600 3.507622 AGCTTGGCTATGTTTCTTTGGAC 59.492 43.478 0.00 0.00 36.99 4.02
3218 3630 6.930731 AGTTTCTTTCTTTGGTGCTTTGTTA 58.069 32.000 0.00 0.00 0.00 2.41
3219 3631 7.382898 AGTTTCTTTCTTTGGTGCTTTGTTAA 58.617 30.769 0.00 0.00 0.00 2.01
3222 3634 6.512297 TCTTTCTTTGGTGCTTTGTTAATCC 58.488 36.000 0.00 0.00 0.00 3.01
3253 3665 2.509111 CATCCTGTGCGTGCGCTA 60.509 61.111 17.49 6.09 42.51 4.26
3297 3709 3.274288 CTGGATAACAGTTCTCAAGGCC 58.726 50.000 0.00 0.00 42.42 5.19
3298 3710 2.912956 TGGATAACAGTTCTCAAGGCCT 59.087 45.455 0.00 0.00 0.00 5.19
3299 3711 3.274288 GGATAACAGTTCTCAAGGCCTG 58.726 50.000 5.69 0.00 0.00 4.85
3300 3712 3.307762 GGATAACAGTTCTCAAGGCCTGT 60.308 47.826 5.69 0.00 39.73 4.00
3301 3713 2.736670 AACAGTTCTCAAGGCCTGTT 57.263 45.000 5.69 0.47 41.86 3.16
3302 3714 2.262423 ACAGTTCTCAAGGCCTGTTC 57.738 50.000 5.69 0.00 34.64 3.18
3303 3715 1.151668 CAGTTCTCAAGGCCTGTTCG 58.848 55.000 5.69 0.00 0.00 3.95
3304 3716 0.035458 AGTTCTCAAGGCCTGTTCGG 59.965 55.000 5.69 0.00 0.00 4.30
3305 3717 0.034896 GTTCTCAAGGCCTGTTCGGA 59.965 55.000 5.69 0.00 33.16 4.55
3306 3718 0.762418 TTCTCAAGGCCTGTTCGGAA 59.238 50.000 5.69 4.37 33.16 4.30
3307 3719 0.984230 TCTCAAGGCCTGTTCGGAAT 59.016 50.000 5.69 0.00 33.16 3.01
3308 3720 1.351017 TCTCAAGGCCTGTTCGGAATT 59.649 47.619 5.69 0.00 33.16 2.17
3309 3721 2.162681 CTCAAGGCCTGTTCGGAATTT 58.837 47.619 5.69 0.00 33.16 1.82
3310 3722 2.159382 TCAAGGCCTGTTCGGAATTTC 58.841 47.619 5.69 0.00 33.16 2.17
3311 3723 1.885887 CAAGGCCTGTTCGGAATTTCA 59.114 47.619 5.69 0.00 33.16 2.69
3312 3724 1.534729 AGGCCTGTTCGGAATTTCAC 58.465 50.000 3.11 0.00 33.16 3.18
3313 3725 0.526211 GGCCTGTTCGGAATTTCACC 59.474 55.000 0.00 0.00 33.16 4.02
3314 3726 1.243902 GCCTGTTCGGAATTTCACCA 58.756 50.000 0.00 0.00 33.16 4.17
3315 3727 1.200020 GCCTGTTCGGAATTTCACCAG 59.800 52.381 0.00 0.00 33.16 4.00
3316 3728 1.200020 CCTGTTCGGAATTTCACCAGC 59.800 52.381 0.00 0.00 33.16 4.85
3317 3729 2.154462 CTGTTCGGAATTTCACCAGCT 58.846 47.619 0.00 0.00 0.00 4.24
3318 3730 2.151202 TGTTCGGAATTTCACCAGCTC 58.849 47.619 0.00 0.00 0.00 4.09
3319 3731 1.468914 GTTCGGAATTTCACCAGCTCC 59.531 52.381 0.00 0.00 0.00 4.70
3320 3732 0.690192 TCGGAATTTCACCAGCTCCA 59.310 50.000 0.00 0.00 0.00 3.86
3321 3733 0.804989 CGGAATTTCACCAGCTCCAC 59.195 55.000 0.00 0.00 0.00 4.02
3322 3734 0.804989 GGAATTTCACCAGCTCCACG 59.195 55.000 0.00 0.00 0.00 4.94
3323 3735 1.610624 GGAATTTCACCAGCTCCACGA 60.611 52.381 0.00 0.00 0.00 4.35
3324 3736 2.151202 GAATTTCACCAGCTCCACGAA 58.849 47.619 0.00 0.00 0.00 3.85
3325 3737 2.270352 ATTTCACCAGCTCCACGAAA 57.730 45.000 0.00 0.00 0.00 3.46
3326 3738 2.270352 TTTCACCAGCTCCACGAAAT 57.730 45.000 0.00 0.00 0.00 2.17
3327 3739 2.270352 TTCACCAGCTCCACGAAATT 57.730 45.000 0.00 0.00 0.00 1.82
3328 3740 2.270352 TCACCAGCTCCACGAAATTT 57.730 45.000 0.00 0.00 0.00 1.82
3329 3741 2.151202 TCACCAGCTCCACGAAATTTC 58.849 47.619 8.20 8.20 0.00 2.17
3330 3742 1.879380 CACCAGCTCCACGAAATTTCA 59.121 47.619 17.99 0.00 0.00 2.69
3331 3743 2.095567 CACCAGCTCCACGAAATTTCAG 60.096 50.000 17.99 12.49 0.00 3.02
3332 3744 1.470098 CCAGCTCCACGAAATTTCAGG 59.530 52.381 17.99 17.29 0.00 3.86
3333 3745 2.426522 CAGCTCCACGAAATTTCAGGA 58.573 47.619 21.57 21.57 32.32 3.86
3334 3746 2.417933 CAGCTCCACGAAATTTCAGGAG 59.582 50.000 32.58 32.58 45.05 3.69
3335 3747 2.039084 AGCTCCACGAAATTTCAGGAGT 59.961 45.455 34.37 25.57 44.54 3.85
3336 3748 2.814336 GCTCCACGAAATTTCAGGAGTT 59.186 45.455 34.37 9.69 44.54 3.01
3337 3749 3.365364 GCTCCACGAAATTTCAGGAGTTG 60.365 47.826 34.37 22.52 44.54 3.16
3338 3750 3.815401 CTCCACGAAATTTCAGGAGTTGT 59.185 43.478 30.52 14.38 41.00 3.32
3339 3751 3.563808 TCCACGAAATTTCAGGAGTTGTG 59.436 43.478 19.94 15.44 30.46 3.33
3340 3752 3.304659 CCACGAAATTTCAGGAGTTGTGG 60.305 47.826 17.99 18.31 38.46 4.17
3341 3753 3.563808 CACGAAATTTCAGGAGTTGTGGA 59.436 43.478 17.99 0.00 0.00 4.02
3342 3754 3.815401 ACGAAATTTCAGGAGTTGTGGAG 59.185 43.478 17.99 0.00 0.00 3.86
3343 3755 3.815401 CGAAATTTCAGGAGTTGTGGAGT 59.185 43.478 17.99 0.00 0.00 3.85
3344 3756 4.275936 CGAAATTTCAGGAGTTGTGGAGTT 59.724 41.667 17.99 0.00 0.00 3.01
3345 3757 5.468746 CGAAATTTCAGGAGTTGTGGAGTTA 59.531 40.000 17.99 0.00 0.00 2.24
3346 3758 6.347725 CGAAATTTCAGGAGTTGTGGAGTTAG 60.348 42.308 17.99 0.00 0.00 2.34
3347 3759 4.351874 TTTCAGGAGTTGTGGAGTTAGG 57.648 45.455 0.00 0.00 0.00 2.69
3348 3760 3.254093 TCAGGAGTTGTGGAGTTAGGA 57.746 47.619 0.00 0.00 0.00 2.94
3349 3761 3.583228 TCAGGAGTTGTGGAGTTAGGAA 58.417 45.455 0.00 0.00 0.00 3.36
3350 3762 3.971305 TCAGGAGTTGTGGAGTTAGGAAA 59.029 43.478 0.00 0.00 0.00 3.13
3351 3763 4.597507 TCAGGAGTTGTGGAGTTAGGAAAT 59.402 41.667 0.00 0.00 0.00 2.17
3352 3764 5.783360 TCAGGAGTTGTGGAGTTAGGAAATA 59.217 40.000 0.00 0.00 0.00 1.40
3353 3765 6.070767 TCAGGAGTTGTGGAGTTAGGAAATAG 60.071 42.308 0.00 0.00 0.00 1.73
3354 3766 4.876679 GGAGTTGTGGAGTTAGGAAATAGC 59.123 45.833 0.00 0.00 0.00 2.97
3355 3767 5.338463 GGAGTTGTGGAGTTAGGAAATAGCT 60.338 44.000 0.00 0.00 0.00 3.32
3356 3768 5.491982 AGTTGTGGAGTTAGGAAATAGCTG 58.508 41.667 0.00 0.00 0.00 4.24
3357 3769 3.873910 TGTGGAGTTAGGAAATAGCTGC 58.126 45.455 0.00 0.00 34.27 5.25
3358 3770 3.519510 TGTGGAGTTAGGAAATAGCTGCT 59.480 43.478 7.57 7.57 34.69 4.24
3359 3771 4.019321 TGTGGAGTTAGGAAATAGCTGCTT 60.019 41.667 7.79 0.00 34.69 3.91
3360 3772 4.572795 GTGGAGTTAGGAAATAGCTGCTTC 59.427 45.833 7.79 0.00 34.69 3.86
3361 3773 3.804873 GGAGTTAGGAAATAGCTGCTTCG 59.195 47.826 7.79 0.00 31.54 3.79
3362 3774 3.198872 AGTTAGGAAATAGCTGCTTCGC 58.801 45.455 7.79 0.00 0.00 4.70
3363 3775 2.936498 GTTAGGAAATAGCTGCTTCGCA 59.064 45.455 7.79 0.00 36.92 5.10
3383 3795 3.782889 AGTTTTCAACTGCAACTCCAC 57.217 42.857 0.00 0.00 41.01 4.02
3384 3796 2.427095 AGTTTTCAACTGCAACTCCACC 59.573 45.455 0.00 0.00 41.01 4.61
3385 3797 2.136298 TTTCAACTGCAACTCCACCA 57.864 45.000 0.00 0.00 0.00 4.17
3386 3798 2.136298 TTCAACTGCAACTCCACCAA 57.864 45.000 0.00 0.00 0.00 3.67
3387 3799 1.388547 TCAACTGCAACTCCACCAAC 58.611 50.000 0.00 0.00 0.00 3.77
3388 3800 1.064758 TCAACTGCAACTCCACCAACT 60.065 47.619 0.00 0.00 0.00 3.16
3389 3801 1.334869 CAACTGCAACTCCACCAACTC 59.665 52.381 0.00 0.00 0.00 3.01
3390 3802 0.179018 ACTGCAACTCCACCAACTCC 60.179 55.000 0.00 0.00 0.00 3.85
3391 3803 1.227823 TGCAACTCCACCAACTCCG 60.228 57.895 0.00 0.00 0.00 4.63
3392 3804 1.966451 GCAACTCCACCAACTCCGG 60.966 63.158 0.00 0.00 0.00 5.14
3393 3805 1.302511 CAACTCCACCAACTCCGGG 60.303 63.158 0.00 0.00 0.00 5.73
3394 3806 1.460689 AACTCCACCAACTCCGGGA 60.461 57.895 0.00 0.00 0.00 5.14
3395 3807 1.057851 AACTCCACCAACTCCGGGAA 61.058 55.000 0.00 0.00 0.00 3.97
3396 3808 1.057851 ACTCCACCAACTCCGGGAAA 61.058 55.000 0.00 0.00 0.00 3.13
3397 3809 0.328258 CTCCACCAACTCCGGGAAAT 59.672 55.000 0.00 0.00 0.00 2.17
3398 3810 0.774908 TCCACCAACTCCGGGAAATT 59.225 50.000 0.00 0.00 0.00 1.82
3399 3811 1.146152 TCCACCAACTCCGGGAAATTT 59.854 47.619 0.00 0.00 0.00 1.82
3400 3812 1.544246 CCACCAACTCCGGGAAATTTC 59.456 52.381 9.83 9.83 0.00 2.17
3401 3813 2.235016 CACCAACTCCGGGAAATTTCA 58.765 47.619 19.49 0.00 0.00 2.69
3402 3814 2.228822 CACCAACTCCGGGAAATTTCAG 59.771 50.000 19.49 12.24 0.00 3.02
3403 3815 1.818674 CCAACTCCGGGAAATTTCAGG 59.181 52.381 19.49 19.73 0.00 3.86
3404 3816 2.554344 CCAACTCCGGGAAATTTCAGGA 60.554 50.000 24.22 24.22 35.34 3.86
3406 3818 2.789409 CTCCGGGAAATTTCAGGAGT 57.211 50.000 32.47 0.00 43.02 3.85
3407 3819 3.073274 CTCCGGGAAATTTCAGGAGTT 57.927 47.619 32.47 0.00 43.02 3.01
3408 3820 2.749621 CTCCGGGAAATTTCAGGAGTTG 59.250 50.000 32.47 20.15 43.02 3.16
3409 3821 2.107552 TCCGGGAAATTTCAGGAGTTGT 59.892 45.455 22.87 0.00 33.58 3.32
3410 3822 2.228822 CCGGGAAATTTCAGGAGTTGTG 59.771 50.000 20.84 2.02 0.00 3.33
3411 3823 2.228822 CGGGAAATTTCAGGAGTTGTGG 59.771 50.000 19.49 0.00 0.00 4.17
3412 3824 3.496331 GGGAAATTTCAGGAGTTGTGGA 58.504 45.455 19.49 0.00 0.00 4.02
3413 3825 3.507622 GGGAAATTTCAGGAGTTGTGGAG 59.492 47.826 19.49 0.00 0.00 3.86
3414 3826 4.145052 GGAAATTTCAGGAGTTGTGGAGT 58.855 43.478 19.49 0.00 0.00 3.85
3415 3827 4.022849 GGAAATTTCAGGAGTTGTGGAGTG 60.023 45.833 19.49 0.00 0.00 3.51
3416 3828 2.638480 TTTCAGGAGTTGTGGAGTGG 57.362 50.000 0.00 0.00 0.00 4.00
3417 3829 1.801242 TTCAGGAGTTGTGGAGTGGA 58.199 50.000 0.00 0.00 0.00 4.02
3418 3830 1.342074 TCAGGAGTTGTGGAGTGGAG 58.658 55.000 0.00 0.00 0.00 3.86
3419 3831 0.322975 CAGGAGTTGTGGAGTGGAGG 59.677 60.000 0.00 0.00 0.00 4.30
3420 3832 0.104934 AGGAGTTGTGGAGTGGAGGT 60.105 55.000 0.00 0.00 0.00 3.85
3421 3833 0.765510 GGAGTTGTGGAGTGGAGGTT 59.234 55.000 0.00 0.00 0.00 3.50
3422 3834 1.270893 GGAGTTGTGGAGTGGAGGTTC 60.271 57.143 0.00 0.00 0.00 3.62
3423 3835 1.694696 GAGTTGTGGAGTGGAGGTTCT 59.305 52.381 0.00 0.00 0.00 3.01
3424 3836 1.694696 AGTTGTGGAGTGGAGGTTCTC 59.305 52.381 0.00 0.00 0.00 2.87
3433 3845 1.597461 GGAGGTTCTCCGAACAGGG 59.403 63.158 8.76 0.00 41.08 4.45
3434 3846 1.079057 GAGGTTCTCCGAACAGGGC 60.079 63.158 8.76 0.00 41.52 5.19
3490 3902 3.131396 CAGCGACACCTATAACCAATCC 58.869 50.000 0.00 0.00 0.00 3.01
3494 3906 3.378339 GACACCTATAACCAATCCGTCG 58.622 50.000 0.00 0.00 0.00 5.12
3496 3908 1.758280 ACCTATAACCAATCCGTCGCA 59.242 47.619 0.00 0.00 0.00 5.10
3501 3913 2.396590 AACCAATCCGTCGCACTTAT 57.603 45.000 0.00 0.00 0.00 1.73
3518 3930 5.641709 CACTTATGTCGTCACAGTCAGTAT 58.358 41.667 0.00 0.00 35.41 2.12
3519 3931 6.677187 GCACTTATGTCGTCACAGTCAGTATA 60.677 42.308 0.00 0.00 35.41 1.47
3522 3934 5.899120 ATGTCGTCACAGTCAGTATAAGT 57.101 39.130 0.00 0.00 35.41 2.24
3523 3935 5.700722 TGTCGTCACAGTCAGTATAAGTT 57.299 39.130 0.00 0.00 0.00 2.66
3524 3936 6.806388 TGTCGTCACAGTCAGTATAAGTTA 57.194 37.500 0.00 0.00 0.00 2.24
3525 3937 6.605849 TGTCGTCACAGTCAGTATAAGTTAC 58.394 40.000 0.00 0.00 0.00 2.50
3526 3938 6.026513 GTCGTCACAGTCAGTATAAGTTACC 58.973 44.000 0.00 0.00 0.00 2.85
3527 3939 5.124457 TCGTCACAGTCAGTATAAGTTACCC 59.876 44.000 0.00 0.00 0.00 3.69
3630 4043 5.122239 TCAAGATCGGACAATTTAACTGCAG 59.878 40.000 13.48 13.48 0.00 4.41
3631 4044 3.375299 AGATCGGACAATTTAACTGCAGC 59.625 43.478 15.27 0.00 0.00 5.25
3639 4072 0.602562 TTTAACTGCAGCACATGGGC 59.397 50.000 13.49 13.49 0.00 5.36
3647 4080 2.226315 AGCACATGGGCAGTGGAGA 61.226 57.895 24.51 0.00 37.46 3.71
3669 4102 2.524306 CCATAAAGGGTTTGGTCTGCA 58.476 47.619 0.00 0.00 0.00 4.41
3701 4134 6.295349 GCTGCAGTATGTTATCCCTGTAGTAT 60.295 42.308 16.64 0.00 39.11 2.12
3790 4223 4.298103 AGATGTGATATGCATCCCTTCC 57.702 45.455 0.19 0.00 42.58 3.46
3815 4248 4.034510 GCAACACCATGTAATCTCTGCTAC 59.965 45.833 0.00 0.00 0.00 3.58
3829 4262 2.022195 CTGCTACAGCGAAGGTACCTA 58.978 52.381 16.67 0.00 45.83 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 0.329596 GTCTGGGATCACCTTTGCCT 59.670 55.000 0.00 0.00 41.11 4.75
109 110 8.927675 TGCTATTTACCCTTTTCTTAAACTGA 57.072 30.769 0.00 0.00 0.00 3.41
171 172 5.368145 TGTTCTTACAAGACAGCTTCACAT 58.632 37.500 0.00 0.00 34.13 3.21
175 176 5.237344 ACACATGTTCTTACAAGACAGCTTC 59.763 40.000 0.00 0.00 37.91 3.86
230 238 2.067013 GACCAAAGCCTGTCGACTTAC 58.933 52.381 17.92 5.65 0.00 2.34
232 240 3.307379 GACCAAAGCCTGTCGACTT 57.693 52.632 17.92 0.00 0.00 3.01
237 245 0.318762 AGAGACGACCAAAGCCTGTC 59.681 55.000 0.00 0.00 0.00 3.51
238 246 0.759346 AAGAGACGACCAAAGCCTGT 59.241 50.000 0.00 0.00 0.00 4.00
239 247 1.151668 CAAGAGACGACCAAAGCCTG 58.848 55.000 0.00 0.00 0.00 4.85
240 248 0.759346 ACAAGAGACGACCAAAGCCT 59.241 50.000 0.00 0.00 0.00 4.58
248 256 4.111375 ACATCCATGTACAAGAGACGAC 57.889 45.455 0.00 0.00 39.68 4.34
353 446 9.289782 AGTCTTGCTTTCTTTCTATACAACAAT 57.710 29.630 0.00 0.00 0.00 2.71
354 447 8.677148 AGTCTTGCTTTCTTTCTATACAACAA 57.323 30.769 0.00 0.00 0.00 2.83
369 639 1.597663 CACGTTTCCGAGTCTTGCTTT 59.402 47.619 0.00 0.00 37.88 3.51
380 650 4.318546 CCACTTCTTTAGTTCACGTTTCCG 60.319 45.833 0.00 0.00 33.85 4.30
386 656 6.202954 ACAAAGATCCACTTCTTTAGTTCACG 59.797 38.462 0.00 0.00 42.58 4.35
447 717 8.258007 TCACAGTGGAAATTTACTCCTGTATAG 58.742 37.037 19.48 11.71 33.77 1.31
469 784 3.205784 TGATCCACACACAATGTCACA 57.794 42.857 0.00 0.00 40.64 3.58
490 805 2.851263 TAGCATTTTCTGTGGTCCGT 57.149 45.000 0.00 0.00 0.00 4.69
491 806 3.689161 TCATTAGCATTTTCTGTGGTCCG 59.311 43.478 0.00 0.00 0.00 4.79
497 813 5.645497 GTCTGGAGTCATTAGCATTTTCTGT 59.355 40.000 0.00 0.00 0.00 3.41
524 840 1.745232 AGGATAATTCGTTGCCGCAA 58.255 45.000 0.38 0.38 0.00 4.85
528 844 5.819825 AAGAAGAAGGATAATTCGTTGCC 57.180 39.130 0.00 0.00 34.27 4.52
561 877 1.651138 GATAATTCGATGCGCTCCTCG 59.349 52.381 9.73 14.71 42.12 4.63
562 878 1.996191 GGATAATTCGATGCGCTCCTC 59.004 52.381 9.73 1.73 0.00 3.71
563 879 1.338200 GGGATAATTCGATGCGCTCCT 60.338 52.381 9.73 0.00 0.00 3.69
564 880 1.079503 GGGATAATTCGATGCGCTCC 58.920 55.000 9.73 3.09 0.00 4.70
565 881 1.795768 TGGGATAATTCGATGCGCTC 58.204 50.000 9.73 2.56 0.00 5.03
566 882 2.289631 TGATGGGATAATTCGATGCGCT 60.290 45.455 9.73 0.00 0.00 5.92
567 883 2.076100 TGATGGGATAATTCGATGCGC 58.924 47.619 0.00 0.00 0.00 6.09
568 884 3.486375 GCATGATGGGATAATTCGATGCG 60.486 47.826 0.00 0.00 0.00 4.73
569 885 3.441222 TGCATGATGGGATAATTCGATGC 59.559 43.478 0.00 0.00 36.37 3.91
570 886 5.830000 ATGCATGATGGGATAATTCGATG 57.170 39.130 0.00 0.00 0.00 3.84
571 887 7.228108 GTGATATGCATGATGGGATAATTCGAT 59.772 37.037 10.16 0.00 0.00 3.59
572 888 6.539826 GTGATATGCATGATGGGATAATTCGA 59.460 38.462 10.16 0.00 0.00 3.71
616 932 1.909700 TGGGATGTGTCAAGCCTTTC 58.090 50.000 0.00 0.00 0.00 2.62
622 938 5.621197 TTTCGTAATTGGGATGTGTCAAG 57.379 39.130 0.00 0.00 0.00 3.02
624 940 3.438781 GCTTTCGTAATTGGGATGTGTCA 59.561 43.478 0.00 0.00 0.00 3.58
625 941 3.689649 AGCTTTCGTAATTGGGATGTGTC 59.310 43.478 0.00 0.00 0.00 3.67
641 975 4.300803 TGATGTGCACATTTGAAGCTTTC 58.699 39.130 31.82 16.91 36.57 2.62
805 1143 9.344309 CGGTCTGTTTACTTTTAAGTTGAAAAA 57.656 29.630 0.00 0.00 40.37 1.94
861 1200 1.090728 CAGTCAGAGCTAGCGACAGA 58.909 55.000 19.31 12.88 31.92 3.41
907 1246 0.401395 TGGACTGTTCCTTCCCCTGT 60.401 55.000 0.00 0.00 43.31 4.00
915 1254 1.971357 ACAAGACGATGGACTGTTCCT 59.029 47.619 0.00 0.00 43.31 3.36
917 1256 1.461127 GCACAAGACGATGGACTGTTC 59.539 52.381 0.00 0.00 0.00 3.18
918 1257 1.070758 AGCACAAGACGATGGACTGTT 59.929 47.619 0.00 0.00 0.00 3.16
920 1259 1.073964 CAGCACAAGACGATGGACTG 58.926 55.000 0.00 0.00 0.00 3.51
921 1260 0.036952 CCAGCACAAGACGATGGACT 60.037 55.000 0.00 0.00 32.55 3.85
923 1262 1.375908 GCCAGCACAAGACGATGGA 60.376 57.895 0.00 0.00 32.55 3.41
1367 1762 1.275573 ACTAGAAAACTGAGCCGGGTC 59.724 52.381 26.70 26.70 0.00 4.46
1377 1772 4.051922 CTGCAACGACAGACTAGAAAACT 58.948 43.478 0.00 0.00 40.25 2.66
1386 1781 2.658707 GGACGCTGCAACGACAGAC 61.659 63.158 17.68 2.22 40.25 3.51
1388 1783 0.666274 TTAGGACGCTGCAACGACAG 60.666 55.000 17.68 0.00 40.80 3.51
1390 1785 1.852895 CTATTAGGACGCTGCAACGAC 59.147 52.381 17.68 10.19 36.70 4.34
1415 1810 0.600255 CACAGGTCACACGACTTCCC 60.600 60.000 0.00 0.00 42.21 3.97
1434 1838 3.320673 AATGACAGGGAGAGAACGAAC 57.679 47.619 0.00 0.00 0.00 3.95
1435 1839 5.477607 TTAAATGACAGGGAGAGAACGAA 57.522 39.130 0.00 0.00 0.00 3.85
1436 1840 5.477607 TTTAAATGACAGGGAGAGAACGA 57.522 39.130 0.00 0.00 0.00 3.85
1437 1841 4.093556 GCTTTAAATGACAGGGAGAGAACG 59.906 45.833 0.00 0.00 0.00 3.95
1490 1894 9.685276 ATATAAGATCATCAACAGACCAACAAA 57.315 29.630 0.00 0.00 0.00 2.83
1513 1917 4.829872 TGAACCAAACCGTACAGGATAT 57.170 40.909 10.17 0.00 45.00 1.63
1544 1949 3.157087 GTGCGGATTTTCCCCATGATAT 58.843 45.455 0.00 0.00 31.13 1.63
1553 1958 4.730903 GCTTTAAGCTAGTGCGGATTTTCC 60.731 45.833 10.01 0.00 45.42 3.13
1572 1977 3.508845 ATGTCTAACCACAGGTGCTTT 57.491 42.857 0.00 0.00 35.34 3.51
1573 1978 3.412386 GAATGTCTAACCACAGGTGCTT 58.588 45.455 0.00 0.00 35.34 3.91
1588 1993 3.606153 CGTGTCTTTTTGACCCGAATGTC 60.606 47.826 0.00 0.00 46.76 3.06
1595 2000 2.616842 ACATCACGTGTCTTTTTGACCC 59.383 45.455 16.51 0.00 44.75 4.46
1605 2010 4.032900 GGAACATGACATACATCACGTGTC 59.967 45.833 16.51 4.21 42.29 3.67
1610 2015 5.877012 ACTGAAGGAACATGACATACATCAC 59.123 40.000 0.00 0.00 37.07 3.06
1611 2016 6.053632 ACTGAAGGAACATGACATACATCA 57.946 37.500 0.00 0.00 37.07 3.07
1616 2021 5.934043 CAGTGAACTGAAGGAACATGACATA 59.066 40.000 4.36 0.00 46.59 2.29
1620 2025 4.422073 ACAGTGAACTGAAGGAACATGA 57.578 40.909 17.11 0.00 46.59 3.07
1633 2038 7.063544 CCTGATAAAAGTGCTAGTACAGTGAAC 59.936 40.741 13.75 1.76 0.00 3.18
1665 2070 6.808212 CACTGAAGTTTGAAAACAGAACATGT 59.192 34.615 8.53 0.00 46.97 3.21
1669 2074 6.861055 TGAACACTGAAGTTTGAAAACAGAAC 59.139 34.615 8.53 0.00 41.30 3.01
1782 2187 7.584987 ACATACTGCTAAAACACTGAACAATC 58.415 34.615 0.00 0.00 0.00 2.67
1795 2200 9.196552 CGATCAGATTCAATACATACTGCTAAA 57.803 33.333 0.00 0.00 0.00 1.85
1859 2264 6.055588 ACATACTGCTAGCGTTTATCCAATT 58.944 36.000 10.77 0.00 0.00 2.32
1956 2361 7.433425 GGCAATAATTCAAATCAGTAGCTTCAC 59.567 37.037 0.00 0.00 0.00 3.18
1957 2362 7.122501 TGGCAATAATTCAAATCAGTAGCTTCA 59.877 33.333 0.00 0.00 0.00 3.02
1971 2376 3.193267 GCTCAGTTGGTGGCAATAATTCA 59.807 43.478 0.00 0.00 0.00 2.57
1973 2378 3.056607 GTGCTCAGTTGGTGGCAATAATT 60.057 43.478 0.00 0.00 35.09 1.40
1996 2401 6.765036 ACCACTAAGCTAATTGATCATGTCAG 59.235 38.462 0.00 0.00 38.29 3.51
2001 2406 7.341805 AGAACACCACTAAGCTAATTGATCAT 58.658 34.615 0.00 0.00 0.00 2.45
2076 2481 2.758009 CCACAAGGCAAACCAATTGAG 58.242 47.619 7.12 0.00 41.85 3.02
2098 2503 4.290155 CAAAAACCATGAGAGAAACACCG 58.710 43.478 0.00 0.00 0.00 4.94
2141 2546 3.951563 TCTGCCCCAATAATAAGCACT 57.048 42.857 0.00 0.00 0.00 4.40
2192 2599 1.888215 TTGCTGCAAAGGAGACAGAG 58.112 50.000 13.51 0.00 33.10 3.35
2263 2672 3.136763 CACATCTGGTGTATCATGCCTC 58.863 50.000 0.00 0.00 42.75 4.70
2392 2801 4.529769 AGTGTCTTCACATCCTTGATCTCA 59.470 41.667 0.00 0.00 46.01 3.27
2452 2861 0.693049 TCTTGCCTCCTTTCCCTGAC 59.307 55.000 0.00 0.00 0.00 3.51
2497 2906 2.226912 AGCGATAACTATGCGAGTCCTC 59.773 50.000 0.00 0.00 37.44 3.71
2769 3178 0.453793 ACAGATCTCTCGGCACTTCG 59.546 55.000 0.00 0.00 0.00 3.79
2848 3257 6.807708 AGTCGAAGCAAACATATAGTAACG 57.192 37.500 0.00 0.00 0.00 3.18
2895 3304 5.796350 AGAGACAACACAAGTTACACAAC 57.204 39.130 0.00 0.00 35.85 3.32
2904 3313 6.744537 CACTGAAGAAAAAGAGACAACACAAG 59.255 38.462 0.00 0.00 0.00 3.16
3004 3415 7.527568 TTTGTAAGGGTAAATCGACCAAATT 57.472 32.000 0.00 0.00 41.73 1.82
3100 3512 1.059584 TTTGGGTGAGCCTCCTGTGA 61.060 55.000 1.06 0.00 34.45 3.58
3135 3547 6.918022 GGATTTACATGGCAATAAAGTACTGC 59.082 38.462 0.00 0.00 35.28 4.40
3159 3571 5.128919 AGAAACATAGCCAAGCTAAGATGG 58.871 41.667 5.90 0.00 44.62 3.51
3181 3593 4.455877 AGAAAGAAACTATGGCGTCCAAAG 59.544 41.667 2.68 0.00 36.95 2.77
3185 3597 4.379499 CCAAAGAAAGAAACTATGGCGTCC 60.379 45.833 0.00 0.00 0.00 4.79
3188 3600 4.475944 CACCAAAGAAAGAAACTATGGCG 58.524 43.478 0.00 0.00 0.00 5.69
3246 3658 2.432628 AGAAGCACCGTAGCGCAC 60.433 61.111 11.47 4.91 40.15 5.34
3288 3700 0.984230 ATTCCGAACAGGCCTTGAGA 59.016 50.000 0.00 0.00 40.77 3.27
3289 3701 1.826385 AATTCCGAACAGGCCTTGAG 58.174 50.000 0.00 0.00 40.77 3.02
3290 3702 2.159382 GAAATTCCGAACAGGCCTTGA 58.841 47.619 0.00 0.00 40.77 3.02
3291 3703 1.885887 TGAAATTCCGAACAGGCCTTG 59.114 47.619 0.00 0.66 40.77 3.61
3292 3704 1.886542 GTGAAATTCCGAACAGGCCTT 59.113 47.619 0.00 0.00 40.77 4.35
3293 3705 1.534729 GTGAAATTCCGAACAGGCCT 58.465 50.000 0.00 0.00 40.77 5.19
3294 3706 0.526211 GGTGAAATTCCGAACAGGCC 59.474 55.000 0.00 0.00 40.77 5.19
3295 3707 1.200020 CTGGTGAAATTCCGAACAGGC 59.800 52.381 0.00 0.00 40.77 4.85
3296 3708 1.200020 GCTGGTGAAATTCCGAACAGG 59.800 52.381 1.40 0.00 42.97 4.00
3297 3709 2.154462 AGCTGGTGAAATTCCGAACAG 58.846 47.619 0.00 0.00 0.00 3.16
3298 3710 2.151202 GAGCTGGTGAAATTCCGAACA 58.849 47.619 0.00 0.00 0.00 3.18
3299 3711 1.468914 GGAGCTGGTGAAATTCCGAAC 59.531 52.381 0.00 0.00 0.00 3.95
3300 3712 1.073125 TGGAGCTGGTGAAATTCCGAA 59.927 47.619 0.00 0.00 0.00 4.30
3301 3713 0.690192 TGGAGCTGGTGAAATTCCGA 59.310 50.000 0.00 0.00 0.00 4.55
3302 3714 0.804989 GTGGAGCTGGTGAAATTCCG 59.195 55.000 0.00 0.00 0.00 4.30
3303 3715 0.804989 CGTGGAGCTGGTGAAATTCC 59.195 55.000 0.00 0.00 0.00 3.01
3304 3716 1.808411 TCGTGGAGCTGGTGAAATTC 58.192 50.000 0.00 0.00 0.00 2.17
3305 3717 2.270352 TTCGTGGAGCTGGTGAAATT 57.730 45.000 0.00 0.00 0.00 1.82
3306 3718 2.270352 TTTCGTGGAGCTGGTGAAAT 57.730 45.000 0.00 0.00 0.00 2.17
3307 3719 2.270352 ATTTCGTGGAGCTGGTGAAA 57.730 45.000 0.00 0.00 33.56 2.69
3308 3720 2.270352 AATTTCGTGGAGCTGGTGAA 57.730 45.000 0.00 0.00 0.00 3.18
3309 3721 2.151202 GAAATTTCGTGGAGCTGGTGA 58.849 47.619 1.68 0.00 0.00 4.02
3310 3722 1.879380 TGAAATTTCGTGGAGCTGGTG 59.121 47.619 13.34 0.00 0.00 4.17
3311 3723 2.154462 CTGAAATTTCGTGGAGCTGGT 58.846 47.619 13.34 0.00 0.00 4.00
3312 3724 1.470098 CCTGAAATTTCGTGGAGCTGG 59.530 52.381 19.39 3.96 0.00 4.85
3313 3725 2.417933 CTCCTGAAATTTCGTGGAGCTG 59.582 50.000 30.15 17.94 40.75 4.24
3314 3726 2.039084 ACTCCTGAAATTTCGTGGAGCT 59.961 45.455 35.20 26.46 45.84 4.09
3315 3727 2.427506 ACTCCTGAAATTTCGTGGAGC 58.572 47.619 35.20 10.55 45.84 4.70
3316 3728 3.815401 ACAACTCCTGAAATTTCGTGGAG 59.185 43.478 34.44 34.44 46.57 3.86
3317 3729 3.563808 CACAACTCCTGAAATTTCGTGGA 59.436 43.478 22.95 22.95 33.50 4.02
3318 3730 3.304659 CCACAACTCCTGAAATTTCGTGG 60.305 47.826 18.54 18.54 35.83 4.94
3319 3731 3.563808 TCCACAACTCCTGAAATTTCGTG 59.436 43.478 13.34 12.04 0.00 4.35
3320 3732 3.815401 CTCCACAACTCCTGAAATTTCGT 59.185 43.478 13.34 2.44 0.00 3.85
3321 3733 3.815401 ACTCCACAACTCCTGAAATTTCG 59.185 43.478 13.34 8.11 0.00 3.46
3322 3734 5.774498 AACTCCACAACTCCTGAAATTTC 57.226 39.130 11.41 11.41 0.00 2.17
3323 3735 5.770162 CCTAACTCCACAACTCCTGAAATTT 59.230 40.000 0.00 0.00 0.00 1.82
3324 3736 5.073144 TCCTAACTCCACAACTCCTGAAATT 59.927 40.000 0.00 0.00 0.00 1.82
3325 3737 4.597507 TCCTAACTCCACAACTCCTGAAAT 59.402 41.667 0.00 0.00 0.00 2.17
3326 3738 3.971305 TCCTAACTCCACAACTCCTGAAA 59.029 43.478 0.00 0.00 0.00 2.69
3327 3739 3.583228 TCCTAACTCCACAACTCCTGAA 58.417 45.455 0.00 0.00 0.00 3.02
3328 3740 3.254093 TCCTAACTCCACAACTCCTGA 57.746 47.619 0.00 0.00 0.00 3.86
3329 3741 4.351874 TTTCCTAACTCCACAACTCCTG 57.648 45.455 0.00 0.00 0.00 3.86
3330 3742 5.338463 GCTATTTCCTAACTCCACAACTCCT 60.338 44.000 0.00 0.00 0.00 3.69
3331 3743 4.876679 GCTATTTCCTAACTCCACAACTCC 59.123 45.833 0.00 0.00 0.00 3.85
3332 3744 5.582665 CAGCTATTTCCTAACTCCACAACTC 59.417 44.000 0.00 0.00 0.00 3.01
3333 3745 5.491982 CAGCTATTTCCTAACTCCACAACT 58.508 41.667 0.00 0.00 0.00 3.16
3334 3746 4.095036 GCAGCTATTTCCTAACTCCACAAC 59.905 45.833 0.00 0.00 0.00 3.32
3335 3747 4.019321 AGCAGCTATTTCCTAACTCCACAA 60.019 41.667 0.00 0.00 0.00 3.33
3336 3748 3.519510 AGCAGCTATTTCCTAACTCCACA 59.480 43.478 0.00 0.00 0.00 4.17
3337 3749 4.143986 AGCAGCTATTTCCTAACTCCAC 57.856 45.455 0.00 0.00 0.00 4.02
3338 3750 4.680708 CGAAGCAGCTATTTCCTAACTCCA 60.681 45.833 0.00 0.00 0.00 3.86
3339 3751 3.804873 CGAAGCAGCTATTTCCTAACTCC 59.195 47.826 0.00 0.00 0.00 3.85
3365 3777 2.451490 TGGTGGAGTTGCAGTTGAAAA 58.549 42.857 0.00 0.00 0.00 2.29
3366 3778 2.136298 TGGTGGAGTTGCAGTTGAAA 57.864 45.000 0.00 0.00 0.00 2.69
3367 3779 1.748493 GTTGGTGGAGTTGCAGTTGAA 59.252 47.619 0.00 0.00 0.00 2.69
3368 3780 1.064758 AGTTGGTGGAGTTGCAGTTGA 60.065 47.619 0.00 0.00 0.00 3.18
3369 3781 1.334869 GAGTTGGTGGAGTTGCAGTTG 59.665 52.381 0.00 0.00 0.00 3.16
3370 3782 1.680338 GAGTTGGTGGAGTTGCAGTT 58.320 50.000 0.00 0.00 0.00 3.16
3371 3783 0.179018 GGAGTTGGTGGAGTTGCAGT 60.179 55.000 0.00 0.00 0.00 4.40
3372 3784 1.230635 CGGAGTTGGTGGAGTTGCAG 61.231 60.000 0.00 0.00 0.00 4.41
3373 3785 1.227823 CGGAGTTGGTGGAGTTGCA 60.228 57.895 0.00 0.00 0.00 4.08
3374 3786 1.966451 CCGGAGTTGGTGGAGTTGC 60.966 63.158 0.00 0.00 0.00 4.17
3375 3787 1.302511 CCCGGAGTTGGTGGAGTTG 60.303 63.158 0.73 0.00 0.00 3.16
3376 3788 1.057851 TTCCCGGAGTTGGTGGAGTT 61.058 55.000 0.73 0.00 0.00 3.01
3377 3789 1.057851 TTTCCCGGAGTTGGTGGAGT 61.058 55.000 0.73 0.00 0.00 3.85
3378 3790 0.328258 ATTTCCCGGAGTTGGTGGAG 59.672 55.000 0.73 0.00 0.00 3.86
3379 3791 0.774908 AATTTCCCGGAGTTGGTGGA 59.225 50.000 0.73 0.00 0.00 4.02
3380 3792 1.544246 GAAATTTCCCGGAGTTGGTGG 59.456 52.381 0.73 0.00 0.00 4.61
3381 3793 2.228822 CTGAAATTTCCCGGAGTTGGTG 59.771 50.000 15.48 0.00 0.00 4.17
3382 3794 2.514803 CTGAAATTTCCCGGAGTTGGT 58.485 47.619 15.48 0.00 0.00 3.67
3383 3795 1.818674 CCTGAAATTTCCCGGAGTTGG 59.181 52.381 15.48 2.01 0.00 3.77
3384 3796 2.749621 CTCCTGAAATTTCCCGGAGTTG 59.250 50.000 28.57 15.53 38.26 3.16
3385 3797 2.375509 ACTCCTGAAATTTCCCGGAGTT 59.624 45.455 32.70 23.67 46.20 3.01
3386 3798 1.985895 ACTCCTGAAATTTCCCGGAGT 59.014 47.619 32.70 32.70 44.89 3.85
3387 3799 2.749621 CAACTCCTGAAATTTCCCGGAG 59.250 50.000 31.83 31.83 43.65 4.63
3388 3800 2.107552 ACAACTCCTGAAATTTCCCGGA 59.892 45.455 19.41 19.41 0.00 5.14
3389 3801 2.228822 CACAACTCCTGAAATTTCCCGG 59.771 50.000 15.48 14.85 0.00 5.73
3390 3802 2.228822 CCACAACTCCTGAAATTTCCCG 59.771 50.000 15.48 6.66 0.00 5.14
3391 3803 3.496331 TCCACAACTCCTGAAATTTCCC 58.504 45.455 15.48 0.00 0.00 3.97
3392 3804 4.022849 CACTCCACAACTCCTGAAATTTCC 60.023 45.833 15.48 0.00 0.00 3.13
3393 3805 4.022849 CCACTCCACAACTCCTGAAATTTC 60.023 45.833 11.41 11.41 0.00 2.17
3394 3806 3.891366 CCACTCCACAACTCCTGAAATTT 59.109 43.478 0.00 0.00 0.00 1.82
3395 3807 3.138283 TCCACTCCACAACTCCTGAAATT 59.862 43.478 0.00 0.00 0.00 1.82
3396 3808 2.711009 TCCACTCCACAACTCCTGAAAT 59.289 45.455 0.00 0.00 0.00 2.17
3397 3809 2.104792 CTCCACTCCACAACTCCTGAAA 59.895 50.000 0.00 0.00 0.00 2.69
3398 3810 1.694150 CTCCACTCCACAACTCCTGAA 59.306 52.381 0.00 0.00 0.00 3.02
3399 3811 1.342074 CTCCACTCCACAACTCCTGA 58.658 55.000 0.00 0.00 0.00 3.86
3400 3812 0.322975 CCTCCACTCCACAACTCCTG 59.677 60.000 0.00 0.00 0.00 3.86
3401 3813 0.104934 ACCTCCACTCCACAACTCCT 60.105 55.000 0.00 0.00 0.00 3.69
3402 3814 0.765510 AACCTCCACTCCACAACTCC 59.234 55.000 0.00 0.00 0.00 3.85
3403 3815 1.694696 AGAACCTCCACTCCACAACTC 59.305 52.381 0.00 0.00 0.00 3.01
3404 3816 1.694696 GAGAACCTCCACTCCACAACT 59.305 52.381 0.00 0.00 0.00 3.16
3405 3817 2.171341 GAGAACCTCCACTCCACAAC 57.829 55.000 0.00 0.00 0.00 3.32
3415 3827 1.597461 CCCTGTTCGGAGAACCTCC 59.403 63.158 10.00 2.97 46.44 4.30
3416 3828 1.079057 GCCCTGTTCGGAGAACCTC 60.079 63.158 10.00 0.00 45.90 3.85
3417 3829 2.593956 GGCCCTGTTCGGAGAACCT 61.594 63.158 10.00 0.00 45.90 3.50
3418 3830 2.046217 GGCCCTGTTCGGAGAACC 60.046 66.667 10.00 0.00 45.90 3.62
3419 3831 1.079057 GAGGCCCTGTTCGGAGAAC 60.079 63.158 0.00 6.01 45.90 3.01
3420 3832 1.125093 TTGAGGCCCTGTTCGGAGAA 61.125 55.000 0.00 0.00 45.90 2.87
3421 3833 0.909610 ATTGAGGCCCTGTTCGGAGA 60.910 55.000 0.00 0.00 33.16 3.71
3422 3834 0.462759 GATTGAGGCCCTGTTCGGAG 60.463 60.000 0.00 0.00 33.16 4.63
3423 3835 0.909610 AGATTGAGGCCCTGTTCGGA 60.910 55.000 0.00 0.00 33.16 4.55
3424 3836 0.462759 GAGATTGAGGCCCTGTTCGG 60.463 60.000 0.00 0.00 0.00 4.30
3425 3837 0.462759 GGAGATTGAGGCCCTGTTCG 60.463 60.000 0.00 0.00 0.00 3.95
3426 3838 0.915364 AGGAGATTGAGGCCCTGTTC 59.085 55.000 0.00 0.00 0.00 3.18
3427 3839 0.622665 CAGGAGATTGAGGCCCTGTT 59.377 55.000 0.00 0.00 40.84 3.16
3428 3840 1.919600 GCAGGAGATTGAGGCCCTGT 61.920 60.000 0.00 0.00 45.90 4.00
3429 3841 1.153005 GCAGGAGATTGAGGCCCTG 60.153 63.158 0.00 0.00 46.67 4.45
3430 3842 2.381941 GGCAGGAGATTGAGGCCCT 61.382 63.158 0.00 0.00 38.70 5.19
3431 3843 2.194326 GGCAGGAGATTGAGGCCC 59.806 66.667 0.00 0.00 38.70 5.80
3432 3844 1.148048 GAGGCAGGAGATTGAGGCC 59.852 63.158 0.00 0.00 44.92 5.19
3433 3845 1.148048 GGAGGCAGGAGATTGAGGC 59.852 63.158 0.00 0.00 0.00 4.70
3434 3846 0.914644 TTGGAGGCAGGAGATTGAGG 59.085 55.000 0.00 0.00 0.00 3.86
3490 3902 0.633733 GTGACGACATAAGTGCGACG 59.366 55.000 0.00 0.00 0.00 5.12
3494 3906 2.663602 CTGACTGTGACGACATAAGTGC 59.336 50.000 10.03 4.54 0.00 4.40
3496 3908 5.899120 ATACTGACTGTGACGACATAAGT 57.101 39.130 6.03 6.03 0.00 2.24
3501 3913 5.700722 AACTTATACTGACTGTGACGACA 57.299 39.130 0.00 0.00 0.00 4.35
3518 3930 7.093024 CCAAAGTCTGATCCTAAGGGTAACTTA 60.093 40.741 0.00 0.00 40.64 2.24
3519 3931 6.296489 CCAAAGTCTGATCCTAAGGGTAACTT 60.296 42.308 0.00 0.00 43.28 2.66
3522 3934 5.347124 TCCAAAGTCTGATCCTAAGGGTAA 58.653 41.667 0.00 0.00 0.00 2.85
3523 3935 4.955335 TCCAAAGTCTGATCCTAAGGGTA 58.045 43.478 0.00 0.00 0.00 3.69
3524 3936 3.777522 CTCCAAAGTCTGATCCTAAGGGT 59.222 47.826 0.00 0.00 0.00 4.34
3525 3937 4.033709 TCTCCAAAGTCTGATCCTAAGGG 58.966 47.826 0.00 0.00 0.00 3.95
3526 3938 5.396213 CCTTCTCCAAAGTCTGATCCTAAGG 60.396 48.000 0.00 0.00 0.00 2.69
3527 3939 5.188751 ACCTTCTCCAAAGTCTGATCCTAAG 59.811 44.000 0.00 0.00 0.00 2.18
3592 4005 8.350722 TGTCCGATCTTGAGACAGTAATAATAC 58.649 37.037 0.00 0.00 35.67 1.89
3601 4014 6.591834 AGTTAAATTGTCCGATCTTGAGACAG 59.408 38.462 0.00 0.00 41.27 3.51
3607 4020 5.295431 TGCAGTTAAATTGTCCGATCTTG 57.705 39.130 0.00 0.00 0.00 3.02
3614 4027 3.641437 TGTGCTGCAGTTAAATTGTCC 57.359 42.857 16.64 0.00 0.00 4.02
3630 4043 1.748122 CTCTCCACTGCCCATGTGC 60.748 63.158 0.00 0.00 34.38 4.57
3631 4044 1.748122 GCTCTCCACTGCCCATGTG 60.748 63.158 0.00 0.00 35.39 3.21
3639 4072 1.561542 ACCCTTTATGGCTCTCCACTG 59.438 52.381 0.00 0.00 46.92 3.66
3647 4080 2.807676 CAGACCAAACCCTTTATGGCT 58.192 47.619 0.00 0.00 37.77 4.75
3669 4102 4.262808 GGATAACATACTGCAGCAGGAGAT 60.263 45.833 26.38 13.34 36.58 2.75
3679 4112 7.316640 CAGATACTACAGGGATAACATACTGC 58.683 42.308 0.00 0.00 34.40 4.40
3683 4116 8.168058 TGTAGCAGATACTACAGGGATAACATA 58.832 37.037 0.40 0.00 45.79 2.29
3701 4134 8.306313 TCCTTCTATAAACTTCATGTAGCAGA 57.694 34.615 0.00 0.00 0.00 4.26
3746 4179 4.873817 TCTGCATCTTGTCCAAACATTTG 58.126 39.130 0.00 0.00 34.73 2.32
3754 4187 3.008266 TCACATCTTCTGCATCTTGTCCA 59.992 43.478 0.00 0.00 0.00 4.02
3790 4223 2.352651 CAGAGATTACATGGTGTTGCCG 59.647 50.000 0.00 0.00 41.21 5.69
3829 4262 9.490083 AAATAGGTATTAGAACAGAGTACCAGT 57.510 33.333 0.00 0.00 37.78 4.00
3864 4297 5.751586 ACGATTTCTAAGCCCAAGGAATAA 58.248 37.500 0.00 0.00 0.00 1.40
3870 4303 5.163754 CCAGTTAACGATTTCTAAGCCCAAG 60.164 44.000 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.