Multiple sequence alignment - TraesCS3A01G401600

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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 TraesCS3A01G401600 chr3A 100.000 6965 0 0 1 6965 647473159 647480123 0.000000e+00 12863
1 TraesCS3A01G401600 chr3B 95.514 2675 92 9 3500 6148 672867743 672870415 0.000000e+00 4250
2 TraesCS3A01G401600 chr3B 91.602 2596 124 36 116 2675 672864336 672866873 0.000000e+00 3500
3 TraesCS3A01G401600 chr3B 95.346 795 27 6 6176 6965 672870412 672871201 0.000000e+00 1254
4 TraesCS3A01G401600 chr3B 90.818 795 44 19 2674 3444 672866955 672867744 0.000000e+00 1037
5 TraesCS3A01G401600 chr3D 96.066 2135 65 6 3500 5619 511344307 511346437 0.000000e+00 3459
6 TraesCS3A01G401600 chr3D 95.619 1689 65 4 992 2675 511341764 511343448 0.000000e+00 2700
7 TraesCS3A01G401600 chr3D 95.214 794 22 7 6176 6965 511347164 511347945 0.000000e+00 1242
8 TraesCS3A01G401600 chr3D 91.741 787 42 14 2674 3444 511343529 511344308 0.000000e+00 1072
9 TraesCS3A01G401600 chr3D 86.538 780 38 27 116 866 511340966 511341707 0.000000e+00 797
10 TraesCS3A01G401600 chr3D 89.910 555 30 19 5616 6148 511346617 511347167 0.000000e+00 691
11 TraesCS3A01G401600 chr3D 90.909 110 4 3 1 110 511340788 511340891 7.280000e-30 143
12 TraesCS3A01G401600 chr5B 93.609 798 37 6 6177 6965 437803525 437802733 0.000000e+00 1179
13 TraesCS3A01G401600 chr5B 97.222 288 7 1 5766 6052 437806102 437805815 2.920000e-133 486
14 TraesCS3A01G401600 chr5B 91.753 97 7 1 6056 6151 437803616 437803520 4.380000e-27 134
15 TraesCS3A01G401600 chr2A 83.380 355 32 11 4378 4714 630588749 630589094 3.160000e-78 303
16 TraesCS3A01G401600 chr6D 87.204 211 23 2 4398 4607 401168957 401168750 3.250000e-58 237
17 TraesCS3A01G401600 chr1A 82.576 264 44 2 4825 5087 452863813 452864075 1.510000e-56 231
18 TraesCS3A01G401600 chr1D 82.197 264 45 2 4825 5087 352415654 352415916 7.030000e-55 226
19 TraesCS3A01G401600 chr1B 82.197 264 45 2 4825 5087 474685912 474686174 7.030000e-55 226
20 TraesCS3A01G401600 chr1B 91.398 93 6 2 3153 3244 474684680 474684771 7.330000e-25 126


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 TraesCS3A01G401600 chr3A 647473159 647480123 6964 False 12863.000000 12863 100.000000 1 6965 1 chr3A.!!$F1 6964
1 TraesCS3A01G401600 chr3B 672864336 672871201 6865 False 2510.250000 4250 93.320000 116 6965 4 chr3B.!!$F1 6849
2 TraesCS3A01G401600 chr3D 511340788 511347945 7157 False 1443.428571 3459 92.285286 1 6965 7 chr3D.!!$F1 6964
3 TraesCS3A01G401600 chr5B 437802733 437806102 3369 True 599.666667 1179 94.194667 5766 6965 3 chr5B.!!$R1 1199

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
707 828 0.181350 CATCTAACCACTCCCCCAGC 59.819 60.000 0.00 0.00 0.00 4.85 F
1875 2004 0.322366 TTCACCGCATTCCAGCATCA 60.322 50.000 0.00 0.00 0.00 3.07 F
2918 3136 0.650512 CCATCGACATTGTACGGTGC 59.349 55.000 13.13 0.00 38.97 5.01 F
3560 3802 0.538287 AGCTCAGGAACCAACCTTGC 60.538 55.000 0.00 0.00 38.32 4.01 F
3634 3876 1.490574 ATGCAGTGAGGGTAGAGTCC 58.509 55.000 0.00 0.00 0.00 3.85 F
4203 4453 1.526686 CTGCTGGACTGCAACACCA 60.527 57.895 5.42 6.12 42.83 4.17 F
5465 5734 0.827507 AAAACCCAAGCACGGCATCT 60.828 50.000 0.00 0.00 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1986 2115 1.911293 TTGCGTCGGCTTGCATCTTC 61.911 55.000 0.00 0.0 41.42 2.87 R
3534 3776 0.183492 TGGTTCCTGAGCTTTGCAGT 59.817 50.000 0.00 0.0 0.00 4.40 R
4352 4604 2.064434 TTCAACCTGTGTGCCATGAA 57.936 45.000 0.00 0.0 0.00 2.57 R
5122 5383 2.161855 TGCATGCTCCGAGTTTTCAAT 58.838 42.857 20.33 0.0 0.00 2.57 R
5303 5572 3.822167 CCATGGCATGTGCATATACAGAA 59.178 43.478 24.80 0.0 44.36 3.02 R
5827 6318 0.681733 GCTGACCTGGTGTCTTCAGA 59.318 55.000 14.63 0.0 44.75 3.27 R
6558 9257 0.109597 GTGAACATGCTTTGCTCGGG 60.110 55.000 0.00 0.0 0.00 5.14 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
22 23 4.722700 CAACCTGGGACGGCCTGG 62.723 72.222 7.57 13.28 35.11 4.45
46 47 1.301637 CCTCGTGCACCATCACACA 60.302 57.895 12.15 0.00 36.57 3.72
47 48 1.568612 CCTCGTGCACCATCACACAC 61.569 60.000 12.15 0.00 36.57 3.82
48 49 0.879839 CTCGTGCACCATCACACACA 60.880 55.000 12.15 0.00 36.57 3.72
49 50 1.157257 TCGTGCACCATCACACACAC 61.157 55.000 12.15 0.00 36.57 3.82
50 51 1.159713 CGTGCACCATCACACACACT 61.160 55.000 12.15 0.00 36.57 3.55
51 52 1.024271 GTGCACCATCACACACACTT 58.976 50.000 5.22 0.00 36.77 3.16
52 53 1.002468 GTGCACCATCACACACACTTC 60.002 52.381 5.22 0.00 36.77 3.01
103 104 0.873054 CCAGCAGCTGAGTGAAACAG 59.127 55.000 24.90 0.00 41.43 3.16
106 107 0.871057 GCAGCTGAGTGAAACAGACC 59.129 55.000 20.43 0.00 41.43 3.85
109 110 2.945008 CAGCTGAGTGAAACAGACCAAA 59.055 45.455 8.42 0.00 41.43 3.28
110 111 3.378112 CAGCTGAGTGAAACAGACCAAAA 59.622 43.478 8.42 0.00 41.43 2.44
112 113 3.378427 GCTGAGTGAAACAGACCAAAACT 59.622 43.478 0.00 0.00 41.43 2.66
113 114 4.142381 GCTGAGTGAAACAGACCAAAACTT 60.142 41.667 0.00 0.00 41.43 2.66
114 115 5.622233 GCTGAGTGAAACAGACCAAAACTTT 60.622 40.000 0.00 0.00 41.43 2.66
131 200 2.300437 ACTTTCAGCTACCAGACCAGAC 59.700 50.000 0.00 0.00 0.00 3.51
271 362 4.426313 CCAACGGCCCCTCCTTCC 62.426 72.222 0.00 0.00 0.00 3.46
325 423 1.065272 CCCCCAATTTGCCAAATCCAG 60.065 52.381 2.61 0.00 0.00 3.86
333 432 3.904586 GCCAAATCCAGGCGAAAAA 57.095 47.368 0.00 0.00 43.15 1.94
335 434 1.939381 GCCAAATCCAGGCGAAAAACC 60.939 52.381 0.00 0.00 43.15 3.27
336 435 1.337728 CCAAATCCAGGCGAAAAACCC 60.338 52.381 0.00 0.00 0.00 4.11
362 461 1.283793 CTGCAGAACAGCCAAACCG 59.716 57.895 8.42 0.00 40.19 4.44
379 478 8.962679 AGCCAAACCGAAAAATAATCAGTATAA 58.037 29.630 0.00 0.00 0.00 0.98
392 491 6.460103 AATCAGTATAAGATCCCTTGGCAT 57.540 37.500 0.00 0.00 33.94 4.40
421 520 6.402550 CGGTTCCACATTTTAGTGAAGATGAG 60.403 42.308 0.00 0.00 42.05 2.90
491 595 2.226437 ACAGCGGCAACAAATTACAGAG 59.774 45.455 1.45 0.00 0.00 3.35
533 637 1.408702 GCCTGCTTTGACAAACCTGAA 59.591 47.619 0.00 0.00 0.00 3.02
556 664 7.563924 TGAACCCTCCAGGCTATATATACATAC 59.436 40.741 0.00 0.00 40.58 2.39
700 821 2.043227 CCTCCCTCCATCTAACCACTC 58.957 57.143 0.00 0.00 0.00 3.51
701 822 2.043227 CTCCCTCCATCTAACCACTCC 58.957 57.143 0.00 0.00 0.00 3.85
702 823 1.132500 CCCTCCATCTAACCACTCCC 58.868 60.000 0.00 0.00 0.00 4.30
703 824 1.132500 CCTCCATCTAACCACTCCCC 58.868 60.000 0.00 0.00 0.00 4.81
704 825 1.132500 CTCCATCTAACCACTCCCCC 58.868 60.000 0.00 0.00 0.00 5.40
705 826 0.419865 TCCATCTAACCACTCCCCCA 59.580 55.000 0.00 0.00 0.00 4.96
706 827 0.839946 CCATCTAACCACTCCCCCAG 59.160 60.000 0.00 0.00 0.00 4.45
707 828 0.181350 CATCTAACCACTCCCCCAGC 59.819 60.000 0.00 0.00 0.00 4.85
764 886 3.764466 CGCCTCACGCTCCTCCTT 61.764 66.667 0.00 0.00 34.21 3.36
766 888 2.896443 CCTCACGCTCCTCCTTCC 59.104 66.667 0.00 0.00 0.00 3.46
767 889 1.684049 CCTCACGCTCCTCCTTCCT 60.684 63.158 0.00 0.00 0.00 3.36
768 890 1.671901 CCTCACGCTCCTCCTTCCTC 61.672 65.000 0.00 0.00 0.00 3.71
769 891 0.682855 CTCACGCTCCTCCTTCCTCT 60.683 60.000 0.00 0.00 0.00 3.69
770 892 0.624254 TCACGCTCCTCCTTCCTCTA 59.376 55.000 0.00 0.00 0.00 2.43
777 901 1.854280 TCCTCCTTCCTCTACCTCCTC 59.146 57.143 0.00 0.00 0.00 3.71
778 902 1.133294 CCTCCTTCCTCTACCTCCTCC 60.133 61.905 0.00 0.00 0.00 4.30
901 1025 4.357097 AGGAGGGTTTTCCAATTCCTACTT 59.643 41.667 0.00 0.00 41.64 2.24
938 1062 0.388520 GTTGCCGCATTGTTCCTTCC 60.389 55.000 0.00 0.00 0.00 3.46
940 1064 2.332654 GCCGCATTGTTCCTTCCGT 61.333 57.895 0.00 0.00 0.00 4.69
944 1068 1.243902 GCATTGTTCCTTCCGTTCCA 58.756 50.000 0.00 0.00 0.00 3.53
946 1070 3.013921 GCATTGTTCCTTCCGTTCCATA 58.986 45.455 0.00 0.00 0.00 2.74
947 1071 3.181500 GCATTGTTCCTTCCGTTCCATAC 60.181 47.826 0.00 0.00 0.00 2.39
950 1074 3.934068 TGTTCCTTCCGTTCCATACTTC 58.066 45.455 0.00 0.00 0.00 3.01
988 1112 3.423154 GACTGCGGCGGGTTCTTG 61.423 66.667 14.26 0.00 0.00 3.02
1028 1155 4.742649 TCTGCGGCTCCTCCTCGT 62.743 66.667 0.00 0.00 0.00 4.18
1132 1259 1.497991 GCTCTACGTCAGCAACAACA 58.502 50.000 13.27 0.00 36.82 3.33
1233 1360 1.282875 GAAGCTGAACCACAACGCC 59.717 57.895 0.00 0.00 0.00 5.68
1342 1469 4.543590 ATCCGATGAACTGTGAGTTTCT 57.456 40.909 0.00 0.00 38.80 2.52
1359 1486 6.051646 AGTTTCTTCACAAATTGCAAATGC 57.948 33.333 1.71 0.00 42.50 3.56
1379 1506 1.869767 CCTGACTCTGTTGCTGTTCAC 59.130 52.381 0.00 0.00 0.00 3.18
1466 1593 0.961857 TGCATGCGCAGATTGAGGTT 60.962 50.000 18.32 0.00 45.36 3.50
1518 1645 9.300681 TGAAAATTCCTAATATAATGCTCTGGG 57.699 33.333 0.00 0.00 0.00 4.45
1571 1698 5.047660 ACTTCTAGTTACTGCAACTCCTCTG 60.048 44.000 0.00 0.00 44.48 3.35
1573 1700 3.669251 AGTTACTGCAACTCCTCTGTC 57.331 47.619 0.00 0.00 44.48 3.51
1574 1701 2.300437 AGTTACTGCAACTCCTCTGTCC 59.700 50.000 0.00 0.00 44.48 4.02
1678 1805 5.046014 AGACTTCAGATGTGGCATAGAGTTT 60.046 40.000 0.00 0.00 0.00 2.66
1768 1895 8.052748 TGAAGATAAAACCCAGTTGCTACATAT 58.947 33.333 0.13 0.00 0.00 1.78
1875 2004 0.322366 TTCACCGCATTCCAGCATCA 60.322 50.000 0.00 0.00 0.00 3.07
1891 2020 4.036380 CAGCATCACTTGTGACATGCATAT 59.964 41.667 22.93 0.00 43.48 1.78
1986 2115 8.991243 AATGAGTGATGTGTTCAAATTTATGG 57.009 30.769 0.00 0.00 35.70 2.74
2325 2459 6.704493 GTGTGATATTATCTAACTTTCGCCCA 59.296 38.462 5.33 0.00 0.00 5.36
2347 2481 6.295011 CCCAACAAGCAGTTATTGTATTCCAA 60.295 38.462 0.00 0.00 39.91 3.53
2608 2743 2.353208 GGCATTATCTTCCTCTCGCGAT 60.353 50.000 10.36 0.00 0.00 4.58
2679 2897 9.113838 GTCTGATGACCATTCAATACTAATTGT 57.886 33.333 0.00 0.00 39.19 2.71
2686 2904 9.378551 GACCATTCAATACTAATTGTGTGACTA 57.621 33.333 0.00 0.00 42.66 2.59
2772 2990 5.268118 TGATACCATGCACTCTTACTCTG 57.732 43.478 0.00 0.00 0.00 3.35
2849 3067 7.014230 CCGATTGAAATACCTTCATACCCAAAT 59.986 37.037 0.00 0.00 43.64 2.32
2876 3094 5.522824 GTGGAACGGTTCATACTCTTATTCC 59.477 44.000 21.36 1.76 34.85 3.01
2892 3110 7.068839 ACTCTTATTCCGAGAGATACACAATGT 59.931 37.037 8.03 0.00 42.57 2.71
2909 3127 2.696989 TGTCTGATGCCATCGACATT 57.303 45.000 20.59 0.00 37.65 2.71
2918 3136 0.650512 CCATCGACATTGTACGGTGC 59.349 55.000 13.13 0.00 38.97 5.01
2924 3142 2.155347 CGACATTGTACGGTGCGTTTTA 59.845 45.455 0.00 0.00 41.54 1.52
2931 3149 4.525686 TGTACGGTGCGTTTTATTTTCAC 58.474 39.130 0.00 0.00 41.54 3.18
3005 3223 5.412904 AGCAAAGAAAGCTAACAGGTGTATC 59.587 40.000 0.00 0.00 41.32 2.24
3012 3230 8.763601 AGAAAGCTAACAGGTGTATCTTCTTAT 58.236 33.333 0.00 0.00 0.00 1.73
3013 3231 8.723942 AAAGCTAACAGGTGTATCTTCTTATG 57.276 34.615 0.00 0.00 0.00 1.90
3037 3255 6.986231 TGATCGTAATTCACATCTGCACTTAT 59.014 34.615 0.00 0.00 0.00 1.73
3086 3304 9.491675 GAGATGGCATAGATAATAGATTCCATG 57.508 37.037 0.00 0.00 32.52 3.66
3087 3305 9.000978 AGATGGCATAGATAATAGATTCCATGT 57.999 33.333 0.00 0.00 32.52 3.21
3141 3375 8.091449 AGCTATGACACTAGAAATAATGTAGCC 58.909 37.037 0.00 0.00 28.64 3.93
3159 3393 2.762327 AGCCAATCCATAACTTTGCAGG 59.238 45.455 0.00 0.00 0.00 4.85
3192 3426 2.038557 ACGAGGTGTAAATGTCTTGGCT 59.961 45.455 0.00 0.00 0.00 4.75
3219 3453 2.045926 GTTCCTGGCCATGCTCGT 60.046 61.111 5.51 0.00 0.00 4.18
3238 3472 5.097742 TCGTTCATGGTAAGACATTCCAT 57.902 39.130 0.00 0.00 41.88 3.41
3243 3477 6.065976 TCATGGTAAGACATTCCATTCTGT 57.934 37.500 0.00 0.00 39.57 3.41
3249 3483 6.431234 GGTAAGACATTCCATTCTGTTCAGTT 59.569 38.462 0.00 0.00 0.00 3.16
3278 3512 9.599322 GTATATTGAAAATAGGCAAGATTGACG 57.401 33.333 0.00 0.00 42.41 4.35
3279 3513 6.757897 ATTGAAAATAGGCAAGATTGACGA 57.242 33.333 0.00 0.00 42.41 4.20
3280 3514 5.545658 TGAAAATAGGCAAGATTGACGAC 57.454 39.130 0.00 0.00 42.41 4.34
3286 3520 1.363744 GCAAGATTGACGACTCCCAG 58.636 55.000 0.00 0.00 0.00 4.45
3310 3544 3.401182 GCTTCAATTGGTTGGCATTTGA 58.599 40.909 5.42 0.00 35.99 2.69
3322 3556 5.508489 GGTTGGCATTTGATGGATCATACTG 60.508 44.000 0.00 0.00 36.56 2.74
3328 3562 8.025445 GGCATTTGATGGATCATACTGTAAATC 58.975 37.037 0.00 0.00 36.56 2.17
3350 3592 9.669353 AAATCGATAATTTGCTCATGTACATTC 57.331 29.630 5.37 0.00 36.20 2.67
3351 3593 8.613060 ATCGATAATTTGCTCATGTACATTCT 57.387 30.769 5.37 0.00 0.00 2.40
3365 3607 9.671279 TCATGTACATTCTAAAATCATGACTGT 57.329 29.630 5.37 0.00 32.73 3.55
3378 3620 4.702831 TCATGACTGTTTGCTAGAACACA 58.297 39.130 0.00 0.00 35.76 3.72
3388 3630 2.000447 GCTAGAACACATCGGACCAAC 59.000 52.381 0.00 0.00 0.00 3.77
3397 3639 6.677781 ACACATCGGACCAACTAAAATATG 57.322 37.500 0.00 0.00 0.00 1.78
3444 3686 2.557924 CAGGTGTGAAAATGCTGGCTTA 59.442 45.455 0.00 0.00 0.00 3.09
3445 3687 3.005684 CAGGTGTGAAAATGCTGGCTTAA 59.994 43.478 0.00 0.00 0.00 1.85
3446 3688 3.256631 AGGTGTGAAAATGCTGGCTTAAG 59.743 43.478 0.00 0.00 0.00 1.85
3447 3689 3.005791 GGTGTGAAAATGCTGGCTTAAGT 59.994 43.478 4.02 0.00 0.00 2.24
3448 3690 4.501400 GGTGTGAAAATGCTGGCTTAAGTT 60.501 41.667 4.02 0.00 0.00 2.66
3449 3691 5.049828 GTGTGAAAATGCTGGCTTAAGTTT 58.950 37.500 4.02 0.00 0.00 2.66
3450 3692 5.523552 GTGTGAAAATGCTGGCTTAAGTTTT 59.476 36.000 4.02 1.88 0.00 2.43
3451 3693 5.752955 TGTGAAAATGCTGGCTTAAGTTTTC 59.247 36.000 14.93 14.93 36.57 2.29
3452 3694 5.752955 GTGAAAATGCTGGCTTAAGTTTTCA 59.247 36.000 18.27 18.27 40.90 2.69
3453 3695 6.424812 GTGAAAATGCTGGCTTAAGTTTTCAT 59.575 34.615 22.09 11.90 43.27 2.57
3454 3696 6.646240 TGAAAATGCTGGCTTAAGTTTTCATC 59.354 34.615 18.27 5.36 39.33 2.92
3455 3697 4.725790 ATGCTGGCTTAAGTTTTCATCC 57.274 40.909 4.02 0.00 0.00 3.51
3456 3698 2.825532 TGCTGGCTTAAGTTTTCATCCC 59.174 45.455 4.02 0.00 0.00 3.85
3457 3699 2.825532 GCTGGCTTAAGTTTTCATCCCA 59.174 45.455 4.02 0.00 0.00 4.37
3458 3700 3.448660 GCTGGCTTAAGTTTTCATCCCAT 59.551 43.478 4.02 0.00 0.00 4.00
3459 3701 4.081476 GCTGGCTTAAGTTTTCATCCCATT 60.081 41.667 4.02 0.00 0.00 3.16
3460 3702 5.569428 GCTGGCTTAAGTTTTCATCCCATTT 60.569 40.000 4.02 0.00 0.00 2.32
3461 3703 6.036577 TGGCTTAAGTTTTCATCCCATTTC 57.963 37.500 4.02 0.00 0.00 2.17
3462 3704 5.779771 TGGCTTAAGTTTTCATCCCATTTCT 59.220 36.000 4.02 0.00 0.00 2.52
3463 3705 6.071391 TGGCTTAAGTTTTCATCCCATTTCTC 60.071 38.462 4.02 0.00 0.00 2.87
3464 3706 6.153510 GGCTTAAGTTTTCATCCCATTTCTCT 59.846 38.462 4.02 0.00 0.00 3.10
3465 3707 7.031975 GCTTAAGTTTTCATCCCATTTCTCTG 58.968 38.462 4.02 0.00 0.00 3.35
3466 3708 5.397142 AAGTTTTCATCCCATTTCTCTGC 57.603 39.130 0.00 0.00 0.00 4.26
3467 3709 4.670765 AGTTTTCATCCCATTTCTCTGCT 58.329 39.130 0.00 0.00 0.00 4.24
3468 3710 5.819991 AGTTTTCATCCCATTTCTCTGCTA 58.180 37.500 0.00 0.00 0.00 3.49
3469 3711 5.884792 AGTTTTCATCCCATTTCTCTGCTAG 59.115 40.000 0.00 0.00 0.00 3.42
3470 3712 5.698741 TTTCATCCCATTTCTCTGCTAGA 57.301 39.130 0.00 0.00 0.00 2.43
3471 3713 4.952071 TCATCCCATTTCTCTGCTAGAG 57.048 45.455 0.00 6.79 43.64 2.43
3472 3714 4.293494 TCATCCCATTTCTCTGCTAGAGT 58.707 43.478 11.37 0.00 42.83 3.24
3473 3715 4.718774 TCATCCCATTTCTCTGCTAGAGTT 59.281 41.667 11.37 0.00 42.83 3.01
3474 3716 4.744795 TCCCATTTCTCTGCTAGAGTTC 57.255 45.455 11.37 0.00 42.83 3.01
3475 3717 4.096681 TCCCATTTCTCTGCTAGAGTTCA 58.903 43.478 11.37 0.95 42.83 3.18
3476 3718 4.718774 TCCCATTTCTCTGCTAGAGTTCAT 59.281 41.667 11.37 2.70 42.83 2.57
3477 3719 5.899547 TCCCATTTCTCTGCTAGAGTTCATA 59.100 40.000 11.37 0.00 42.83 2.15
3478 3720 6.556495 TCCCATTTCTCTGCTAGAGTTCATAT 59.444 38.462 11.37 0.77 42.83 1.78
3479 3721 6.649973 CCCATTTCTCTGCTAGAGTTCATATG 59.350 42.308 11.37 0.00 42.83 1.78
3480 3722 7.215789 CCATTTCTCTGCTAGAGTTCATATGT 58.784 38.462 1.90 0.00 42.83 2.29
3481 3723 7.714377 CCATTTCTCTGCTAGAGTTCATATGTT 59.286 37.037 1.90 0.00 42.83 2.71
3482 3724 8.763356 CATTTCTCTGCTAGAGTTCATATGTTC 58.237 37.037 1.90 0.05 42.83 3.18
3483 3725 6.398234 TCTCTGCTAGAGTTCATATGTTCC 57.602 41.667 1.90 0.00 42.83 3.62
3484 3726 5.009110 TCTCTGCTAGAGTTCATATGTTCCG 59.991 44.000 1.90 0.00 42.83 4.30
3485 3727 4.038042 TCTGCTAGAGTTCATATGTTCCGG 59.962 45.833 1.90 0.00 0.00 5.14
3486 3728 3.060602 GCTAGAGTTCATATGTTCCGGC 58.939 50.000 0.00 3.93 0.00 6.13
3487 3729 3.243907 GCTAGAGTTCATATGTTCCGGCT 60.244 47.826 0.00 0.00 0.00 5.52
3488 3730 4.022242 GCTAGAGTTCATATGTTCCGGCTA 60.022 45.833 0.00 0.00 0.00 3.93
3489 3731 5.509163 GCTAGAGTTCATATGTTCCGGCTAA 60.509 44.000 0.00 0.00 0.00 3.09
3490 3732 5.552870 AGAGTTCATATGTTCCGGCTAAT 57.447 39.130 0.00 0.00 0.00 1.73
3491 3733 5.300752 AGAGTTCATATGTTCCGGCTAATG 58.699 41.667 0.00 0.00 0.00 1.90
3492 3734 4.389374 AGTTCATATGTTCCGGCTAATGG 58.611 43.478 0.00 0.00 0.00 3.16
3493 3735 2.778299 TCATATGTTCCGGCTAATGGC 58.222 47.619 0.00 0.00 40.90 4.40
3494 3736 2.105649 TCATATGTTCCGGCTAATGGCA 59.894 45.455 0.00 0.00 44.01 4.92
3495 3737 2.949177 TATGTTCCGGCTAATGGCAT 57.051 45.000 0.00 0.00 44.01 4.40
3496 3738 2.949177 ATGTTCCGGCTAATGGCATA 57.051 45.000 0.00 0.00 44.01 3.14
3497 3739 2.719531 TGTTCCGGCTAATGGCATAA 57.280 45.000 0.00 0.00 44.01 1.90
3498 3740 3.222173 TGTTCCGGCTAATGGCATAAT 57.778 42.857 0.00 0.00 44.01 1.28
3499 3741 3.561143 TGTTCCGGCTAATGGCATAATT 58.439 40.909 0.00 0.00 44.01 1.40
3500 3742 3.957497 TGTTCCGGCTAATGGCATAATTT 59.043 39.130 0.00 0.00 44.01 1.82
3527 3769 5.596836 ATGTCCCGCAAACAATTATCAAT 57.403 34.783 0.00 0.00 0.00 2.57
3534 3776 7.872993 TCCCGCAAACAATTATCAATTTTGTAA 59.127 29.630 0.00 0.00 33.44 2.41
3545 3787 8.519492 TTATCAATTTTGTAACTGCAAAGCTC 57.481 30.769 0.00 0.00 39.20 4.09
3560 3802 0.538287 AGCTCAGGAACCAACCTTGC 60.538 55.000 0.00 0.00 38.32 4.01
3576 3818 3.144506 CCTTGCCTTGCATATAGTCCAG 58.855 50.000 0.00 0.00 38.76 3.86
3585 3827 5.290493 TGCATATAGTCCAGAATTCCGTT 57.710 39.130 0.65 0.00 0.00 4.44
3617 3859 6.867816 TCTGTAGCAAAAAGGCACATTTTATG 59.132 34.615 0.00 0.00 37.11 1.90
3625 3867 2.756760 AGGCACATTTTATGCAGTGAGG 59.243 45.455 5.76 0.00 45.27 3.86
3634 3876 1.490574 ATGCAGTGAGGGTAGAGTCC 58.509 55.000 0.00 0.00 0.00 3.85
3665 3907 3.451141 TTGGAGTTCAAATGTGCAACC 57.549 42.857 0.00 0.00 30.49 3.77
3900 4148 9.936759 TTGTTTATTCAAAAGACCATTTATCCC 57.063 29.630 0.00 0.00 0.00 3.85
3904 4152 5.429681 TCAAAAGACCATTTATCCCGAGA 57.570 39.130 0.00 0.00 0.00 4.04
3993 4241 7.598869 TCAGTAGCTATTGGCAAATATTAGTCG 59.401 37.037 15.46 0.00 44.79 4.18
4018 4266 7.976734 CGACAGTCTAAATGGATTCTTAACTCT 59.023 37.037 0.00 0.00 0.00 3.24
4019 4267 9.092876 GACAGTCTAAATGGATTCTTAACTCTG 57.907 37.037 0.00 0.00 0.00 3.35
4096 4346 7.680730 AGGTGATGAAGTCAATACAAGTAAGT 58.319 34.615 0.00 0.00 38.90 2.24
4203 4453 1.526686 CTGCTGGACTGCAACACCA 60.527 57.895 5.42 6.12 42.83 4.17
4221 4471 5.826643 ACACCACACATTAAGGAATGGTAT 58.173 37.500 16.02 6.23 45.83 2.73
4279 4530 2.804986 TGCCTGATGTGCTTCCATAA 57.195 45.000 0.00 0.00 0.00 1.90
4312 4563 6.689554 TCAATGCAAAAGCAAATCAGTCATA 58.310 32.000 0.00 0.00 0.00 2.15
4314 4565 8.468399 TCAATGCAAAAGCAAATCAGTCATATA 58.532 29.630 0.00 0.00 0.00 0.86
4352 4604 8.854117 GCCAGTTAATCTAATGATCATCCTTTT 58.146 33.333 9.06 4.18 31.51 2.27
4550 4810 3.731652 CATGTTTGCAGGGAAGAAACA 57.268 42.857 0.00 0.00 42.22 2.83
4622 4882 7.177878 ACTGGTACTTCCTCAATCATGAAAAT 58.822 34.615 0.00 0.00 34.49 1.82
4728 4989 8.044060 TGGAATTAGACTCATTTACAAGCTTG 57.956 34.615 24.84 24.84 0.00 4.01
4795 5056 2.092968 TCTCAGACACTTGTTGCTGGTT 60.093 45.455 0.00 0.00 32.96 3.67
4810 5071 6.371809 TTGCTGGTTTCAGTAACTAACAAG 57.628 37.500 0.00 0.00 39.95 3.16
5094 5355 4.384056 CAGCAGCTGCAGGTAAGTAATAT 58.616 43.478 38.24 11.97 45.16 1.28
5222 5491 4.855340 TCCTTCATGATTAAAGGGACACC 58.145 43.478 10.61 0.00 42.00 4.16
5254 5523 7.761409 TGTTGCCTGATTAGACATATTCAAAC 58.239 34.615 0.00 0.00 0.00 2.93
5303 5572 7.072454 TGGTATACTTGGAATGATAGCTTCCTT 59.928 37.037 2.25 0.00 42.27 3.36
5321 5590 4.136796 TCCTTTCTGTATATGCACATGCC 58.863 43.478 0.49 0.00 41.18 4.40
5367 5636 2.864343 AGCACACTCAGAAACGTGTAAC 59.136 45.455 0.00 0.00 42.05 2.50
5465 5734 0.827507 AAAACCCAAGCACGGCATCT 60.828 50.000 0.00 0.00 0.00 2.90
5573 5842 5.371526 TCCTAATTCCTCATGAATGCTCAC 58.628 41.667 0.00 0.00 42.97 3.51
5582 5851 5.176223 CCTCATGAATGCTCACAACAAAAAC 59.824 40.000 0.00 0.00 33.30 2.43
5584 5853 3.443037 TGAATGCTCACAACAAAAACCG 58.557 40.909 0.00 0.00 0.00 4.44
5590 5859 3.672241 GCTCACAACAAAAACCGTCTTGT 60.672 43.478 0.00 0.00 37.36 3.16
5679 6131 8.837788 ATGCAATCTTGTCGATTCTGATATTA 57.162 30.769 0.00 0.00 40.33 0.98
5686 6138 9.521503 TCTTGTCGATTCTGATATTACTTTCTG 57.478 33.333 0.00 0.00 0.00 3.02
5687 6139 9.307121 CTTGTCGATTCTGATATTACTTTCTGT 57.693 33.333 0.00 0.00 0.00 3.41
5689 6141 9.731819 TGTCGATTCTGATATTACTTTCTGTAC 57.268 33.333 0.00 0.00 0.00 2.90
5690 6142 9.731819 GTCGATTCTGATATTACTTTCTGTACA 57.268 33.333 0.00 0.00 0.00 2.90
5696 6148 9.803315 TCTGATATTACTTTCTGTACATGTCAC 57.197 33.333 0.00 0.00 0.00 3.67
5697 6149 9.586435 CTGATATTACTTTCTGTACATGTCACA 57.414 33.333 0.00 4.84 0.00 3.58
5700 6152 6.944557 TTACTTTCTGTACATGTCACATCG 57.055 37.500 0.00 0.00 0.00 3.84
5701 6153 5.134202 ACTTTCTGTACATGTCACATCGA 57.866 39.130 0.00 0.00 0.00 3.59
5827 6318 2.373169 TGGAGTCCACTTGAGCAGATTT 59.627 45.455 8.12 0.00 0.00 2.17
6045 6537 7.281774 AGTGTTAGTTCAGCATTATGAATCTGG 59.718 37.037 0.00 0.00 41.05 3.86
6084 8771 7.406031 TGTGTAGACTATAGAAGGTTTCAGG 57.594 40.000 6.78 0.00 0.00 3.86
6095 8782 2.267192 AGGTTTCAGGGAGTCCTTACC 58.733 52.381 9.58 6.37 42.67 2.85
6123 8813 2.274542 TGTATTTCTGCCCCTCTCCAA 58.725 47.619 0.00 0.00 0.00 3.53
6129 8819 1.710244 TCTGCCCCTCTCCAATTTTCA 59.290 47.619 0.00 0.00 0.00 2.69
6134 8824 3.696548 GCCCCTCTCCAATTTTCAACTAG 59.303 47.826 0.00 0.00 0.00 2.57
6156 8846 8.450578 CTAGAATAGTTTGAATGGTAATGCCA 57.549 34.615 0.00 0.00 42.36 4.92
6157 8847 9.071276 CTAGAATAGTTTGAATGGTAATGCCAT 57.929 33.333 0.00 0.00 46.38 4.40
6201 8891 2.781667 AGGGGCATCAGGAGATTAGTT 58.218 47.619 0.00 0.00 30.20 2.24
6202 8892 2.441001 AGGGGCATCAGGAGATTAGTTG 59.559 50.000 0.00 0.00 30.20 3.16
6206 8896 5.136105 GGGCATCAGGAGATTAGTTGAATT 58.864 41.667 0.00 0.00 30.20 2.17
6220 8910 9.696917 GATTAGTTGAATTTGACAGAAAATGGT 57.303 29.630 0.00 0.00 30.21 3.55
6261 8951 5.480422 ACAAATCCAGTAGGTTCCCAAATTC 59.520 40.000 0.00 0.00 35.89 2.17
6263 8953 4.733077 TCCAGTAGGTTCCCAAATTCAA 57.267 40.909 0.00 0.00 35.89 2.69
6264 8954 5.269554 TCCAGTAGGTTCCCAAATTCAAT 57.730 39.130 0.00 0.00 35.89 2.57
6265 8955 5.016173 TCCAGTAGGTTCCCAAATTCAATG 58.984 41.667 0.00 0.00 35.89 2.82
6267 8965 5.245977 CCAGTAGGTTCCCAAATTCAATGTT 59.754 40.000 0.00 0.00 0.00 2.71
6313 9011 4.976864 TCCTACACATCAGCATGCATTAT 58.023 39.130 21.98 7.05 34.76 1.28
6320 9018 5.793457 CACATCAGCATGCATTATATTCACG 59.207 40.000 21.98 0.00 34.76 4.35
6349 9048 6.703319 TGGTTACTATCGACAAAGAATCCAA 58.297 36.000 0.00 0.00 0.00 3.53
6456 9155 1.652563 GTTGTGAACTGCCCCGTTC 59.347 57.895 4.29 4.29 42.73 3.95
6459 9158 2.429930 TGAACTGCCCCGTTCAGG 59.570 61.111 8.65 0.00 45.92 3.86
6463 9162 4.020617 CTGCCCCGTTCAGGAGCA 62.021 66.667 0.00 0.00 45.00 4.26
6464 9163 3.329889 TGCCCCGTTCAGGAGCAT 61.330 61.111 0.00 0.00 45.00 3.79
6465 9164 2.044946 GCCCCGTTCAGGAGCATT 60.045 61.111 0.00 0.00 45.00 3.56
6466 9165 1.678970 GCCCCGTTCAGGAGCATTT 60.679 57.895 0.00 0.00 45.00 2.32
6558 9257 6.623767 GCTGACTACATTCATCAGGGTTTTTC 60.624 42.308 2.90 0.00 40.23 2.29
6662 9361 2.089201 CTTCATGCTCTCAACATGCCA 58.911 47.619 0.00 0.00 43.71 4.92
6806 9505 2.038952 CACCATCTCTCAGTCCAACCAA 59.961 50.000 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 2.098607 TGTCTCGTTGAAGTCGAAGTGT 59.901 45.455 0.00 0.00 36.89 3.55
47 48 2.468040 GTGTCTCGTTGAAGTCGAAGTG 59.532 50.000 0.00 0.00 36.89 3.16
48 49 2.543238 GGTGTCTCGTTGAAGTCGAAGT 60.543 50.000 0.00 0.00 36.89 3.01
49 50 2.052157 GGTGTCTCGTTGAAGTCGAAG 58.948 52.381 0.00 0.00 36.89 3.79
50 51 1.679680 AGGTGTCTCGTTGAAGTCGAA 59.320 47.619 0.00 0.00 36.89 3.71
51 52 1.001706 CAGGTGTCTCGTTGAAGTCGA 60.002 52.381 0.00 0.00 35.96 4.20
52 53 1.409412 CAGGTGTCTCGTTGAAGTCG 58.591 55.000 0.00 0.00 0.00 4.18
103 104 4.023963 GTCTGGTAGCTGAAAGTTTTGGTC 60.024 45.833 2.84 0.00 35.30 4.02
106 107 3.882888 TGGTCTGGTAGCTGAAAGTTTTG 59.117 43.478 2.84 0.00 35.30 2.44
109 110 2.972713 TCTGGTCTGGTAGCTGAAAGTT 59.027 45.455 2.84 0.00 35.30 2.66
110 111 2.300437 GTCTGGTCTGGTAGCTGAAAGT 59.700 50.000 2.84 0.00 35.63 2.66
112 113 2.300152 CAGTCTGGTCTGGTAGCTGAAA 59.700 50.000 2.84 0.00 35.63 2.69
113 114 1.895798 CAGTCTGGTCTGGTAGCTGAA 59.104 52.381 2.84 0.00 35.63 3.02
114 115 1.550327 CAGTCTGGTCTGGTAGCTGA 58.450 55.000 0.00 0.00 0.00 4.26
203 272 0.744281 TTCACGCTGTCTGTCACTCA 59.256 50.000 0.00 0.00 0.00 3.41
265 334 2.110899 AGTGTGAGAAGAGAGGGAAGGA 59.889 50.000 0.00 0.00 0.00 3.36
267 336 3.056891 GTCAGTGTGAGAAGAGAGGGAAG 60.057 52.174 0.00 0.00 0.00 3.46
268 337 2.894126 GTCAGTGTGAGAAGAGAGGGAA 59.106 50.000 0.00 0.00 0.00 3.97
271 362 1.201181 CGGTCAGTGTGAGAAGAGAGG 59.799 57.143 0.00 0.00 0.00 3.69
325 423 2.951458 CTCCGTGGGTTTTTCGCC 59.049 61.111 0.00 0.00 0.00 5.54
328 427 1.956802 CAGGCTCCGTGGGTTTTTC 59.043 57.895 0.00 0.00 0.00 2.29
335 434 2.743928 GTTCTGCAGGCTCCGTGG 60.744 66.667 15.13 0.00 0.00 4.94
336 435 2.031012 TGTTCTGCAGGCTCCGTG 59.969 61.111 15.13 0.00 0.00 4.94
379 478 1.533711 CGGGAATGCCAAGGGATCT 59.466 57.895 0.00 0.00 35.15 2.75
392 491 3.150767 CACTAAAATGTGGAACCGGGAA 58.849 45.455 6.32 0.00 34.36 3.97
421 520 4.536687 GGCGTGCCGTGCTTATGC 62.537 66.667 0.00 0.00 40.20 3.14
473 574 1.068610 TGCTCTGTAATTTGTTGCCGC 60.069 47.619 0.00 0.00 0.00 6.53
491 595 5.334337 GGCTTCCAAATTTCATTTCAAGTGC 60.334 40.000 0.00 0.00 0.00 4.40
587 700 2.078392 CACGGCTAATTTTGGTACGGT 58.922 47.619 0.00 0.00 0.00 4.83
704 825 4.767255 GAGTGGCGTGGAGGGCTG 62.767 72.222 0.00 0.00 0.00 4.85
706 827 4.459089 GAGAGTGGCGTGGAGGGC 62.459 72.222 0.00 0.00 0.00 5.19
707 828 2.997315 TGAGAGTGGCGTGGAGGG 60.997 66.667 0.00 0.00 0.00 4.30
764 886 1.847737 GAGTGAGGAGGAGGTAGAGGA 59.152 57.143 0.00 0.00 0.00 3.71
766 888 1.210967 ACGAGTGAGGAGGAGGTAGAG 59.789 57.143 0.00 0.00 0.00 2.43
767 889 1.287217 ACGAGTGAGGAGGAGGTAGA 58.713 55.000 0.00 0.00 0.00 2.59
768 890 2.018515 GAACGAGTGAGGAGGAGGTAG 58.981 57.143 0.00 0.00 0.00 3.18
769 891 1.353358 TGAACGAGTGAGGAGGAGGTA 59.647 52.381 0.00 0.00 0.00 3.08
770 892 0.112606 TGAACGAGTGAGGAGGAGGT 59.887 55.000 0.00 0.00 0.00 3.85
777 901 0.875728 AGACGAGTGAACGAGTGAGG 59.124 55.000 0.00 0.00 37.03 3.86
778 902 1.135916 GGAGACGAGTGAACGAGTGAG 60.136 57.143 0.00 0.00 37.03 3.51
938 1062 5.207110 AGAGATGATGGAAGTATGGAACG 57.793 43.478 0.00 0.00 0.00 3.95
940 1064 5.072329 GGGAAGAGATGATGGAAGTATGGAA 59.928 44.000 0.00 0.00 0.00 3.53
944 1068 3.913163 GGGGGAAGAGATGATGGAAGTAT 59.087 47.826 0.00 0.00 0.00 2.12
946 1070 2.131023 GGGGGAAGAGATGATGGAAGT 58.869 52.381 0.00 0.00 0.00 3.01
947 1071 2.947127 GGGGGAAGAGATGATGGAAG 57.053 55.000 0.00 0.00 0.00 3.46
975 1099 3.683587 GAATGCAAGAACCCGCCGC 62.684 63.158 0.00 0.00 0.00 6.53
976 1100 2.485122 GAATGCAAGAACCCGCCG 59.515 61.111 0.00 0.00 0.00 6.46
978 1102 2.202479 GCGAATGCAAGAACCCGC 60.202 61.111 0.00 0.00 42.15 6.13
979 1103 1.906994 TTCGCGAATGCAAGAACCCG 61.907 55.000 19.38 0.00 42.97 5.28
981 1105 0.796312 TCTTCGCGAATGCAAGAACC 59.204 50.000 23.67 0.00 42.97 3.62
983 1107 1.398041 CCATCTTCGCGAATGCAAGAA 59.602 47.619 23.67 0.00 42.97 2.52
984 1108 1.009078 CCATCTTCGCGAATGCAAGA 58.991 50.000 23.67 16.06 42.97 3.02
985 1109 0.590732 GCCATCTTCGCGAATGCAAG 60.591 55.000 23.67 10.46 42.97 4.01
1028 1155 1.358787 AGGATCCAATTGCCAGGAACA 59.641 47.619 15.82 0.00 37.48 3.18
1161 1288 4.514577 ATCGCCTTGCCGTCGGAG 62.515 66.667 17.49 3.96 0.00 4.63
1233 1360 2.637025 CTTGGGTTTGCACCGTCG 59.363 61.111 0.00 0.00 45.39 5.12
1342 1469 3.808726 GTCAGGCATTTGCAATTTGTGAA 59.191 39.130 0.00 0.00 44.36 3.18
1359 1486 1.869767 GTGAACAGCAACAGAGTCAGG 59.130 52.381 0.00 0.00 0.00 3.86
1379 1506 3.618780 AAAGCCGAGCTGCAGAGGG 62.619 63.158 20.43 15.51 39.62 4.30
1518 1645 6.566753 GCAACCAAGTAAGTTCTGATGTCTTC 60.567 42.308 0.00 0.00 0.00 2.87
1571 1698 4.943705 TCAGGCAATTATCACAAAGAGGAC 59.056 41.667 0.00 0.00 0.00 3.85
1573 1700 4.701651 TGTCAGGCAATTATCACAAAGAGG 59.298 41.667 0.00 0.00 0.00 3.69
1574 1701 5.645067 TCTGTCAGGCAATTATCACAAAGAG 59.355 40.000 0.00 0.00 0.00 2.85
1619 1746 9.647797 TGTATAGAACAGTAACTGTATGGTTTG 57.352 33.333 0.00 0.00 44.62 2.93
1792 1919 6.509656 TCCGTAGTATGTAATAACTTGCCTG 58.490 40.000 0.00 0.00 0.00 4.85
1891 2020 3.215975 GTTGGTAACCAGGTTACAGCAA 58.784 45.455 34.04 27.36 46.94 3.91
1986 2115 1.911293 TTGCGTCGGCTTGCATCTTC 61.911 55.000 0.00 0.00 41.42 2.87
2175 2309 4.994852 GTGACACAGTTGGCTAAATGTCTA 59.005 41.667 13.22 0.19 42.61 2.59
2347 2481 8.936864 CGAAAACAAGGTTCTGATTCTAGTTAT 58.063 33.333 0.00 0.00 0.00 1.89
2357 2491 5.630661 TTTGAACGAAAACAAGGTTCTGA 57.369 34.783 0.00 0.00 40.44 3.27
2459 2594 7.176340 GCCTATGAGAGAATTTTGGCATAGAAT 59.824 37.037 15.22 0.00 38.14 2.40
2608 2743 9.187996 TCATTGCATCAATCACTCCTTTAATTA 57.812 29.630 0.00 0.00 31.05 1.40
2679 2897 4.921515 GTCTCGTGCAACTTATTAGTCACA 59.078 41.667 0.00 0.00 31.77 3.58
2686 2904 6.371809 TTTTGAAGTCTCGTGCAACTTATT 57.628 33.333 1.55 0.00 35.90 1.40
2772 2990 1.387084 GAGAACGTTCTGCATGACGAC 59.613 52.381 34.23 13.26 37.73 4.34
2849 3067 3.162666 AGAGTATGAACCGTTCCACAGA 58.837 45.455 8.80 0.00 0.00 3.41
2876 3094 4.443725 GCATCAGACATTGTGTATCTCTCG 59.556 45.833 0.00 0.00 0.00 4.04
2892 3110 2.696989 ACAATGTCGATGGCATCAGA 57.303 45.000 25.88 19.86 0.00 3.27
2909 3127 4.272991 AGTGAAAATAAAACGCACCGTACA 59.727 37.500 0.00 0.00 39.99 2.90
3005 3223 8.219769 GCAGATGTGAATTACGATCATAAGAAG 58.780 37.037 0.00 0.00 0.00 2.85
3012 3230 4.758688 AGTGCAGATGTGAATTACGATCA 58.241 39.130 0.00 0.00 0.00 2.92
3013 3231 5.725110 AAGTGCAGATGTGAATTACGATC 57.275 39.130 0.00 0.00 0.00 3.69
3046 3264 1.671328 CCATCTCTTCATGCTGCAGTG 59.329 52.381 16.64 6.80 0.00 3.66
3062 3280 9.624373 AACATGGAATCTATTATCTATGCCATC 57.376 33.333 0.00 0.00 37.87 3.51
3136 3370 4.202050 CCTGCAAAGTTATGGATTGGCTAC 60.202 45.833 0.00 0.00 0.00 3.58
3159 3393 5.600908 TTACACCTCGTTTTTCAGCATAC 57.399 39.130 0.00 0.00 0.00 2.39
3172 3406 2.416547 CAGCCAAGACATTTACACCTCG 59.583 50.000 0.00 0.00 0.00 4.63
3192 3426 1.634973 TGGCCAGGAACATCAATCTCA 59.365 47.619 0.00 0.00 0.00 3.27
3219 3453 6.484288 ACAGAATGGAATGTCTTACCATGAA 58.516 36.000 0.00 0.00 42.59 2.57
3278 3512 0.678048 AATTGAAGCGCCTGGGAGTC 60.678 55.000 2.29 0.00 0.00 3.36
3279 3513 0.962356 CAATTGAAGCGCCTGGGAGT 60.962 55.000 2.29 0.00 0.00 3.85
3280 3514 1.660560 CCAATTGAAGCGCCTGGGAG 61.661 60.000 7.12 0.00 0.00 4.30
3286 3520 1.737735 GCCAACCAATTGAAGCGCC 60.738 57.895 7.12 0.00 38.15 6.53
3350 3592 8.506437 TGTTCTAGCAAACAGTCATGATTTTAG 58.494 33.333 0.00 0.00 34.31 1.85
3351 3593 8.289618 GTGTTCTAGCAAACAGTCATGATTTTA 58.710 33.333 0.00 0.00 39.69 1.52
3365 3607 2.037902 TGGTCCGATGTGTTCTAGCAAA 59.962 45.455 0.00 0.00 0.00 3.68
3378 3620 6.411376 TGTGACATATTTTAGTTGGTCCGAT 58.589 36.000 0.00 0.00 0.00 4.18
3424 3666 1.708341 AAGCCAGCATTTTCACACCT 58.292 45.000 0.00 0.00 0.00 4.00
3444 3686 5.082425 AGCAGAGAAATGGGATGAAAACTT 58.918 37.500 0.00 0.00 0.00 2.66
3445 3687 4.670765 AGCAGAGAAATGGGATGAAAACT 58.329 39.130 0.00 0.00 0.00 2.66
3446 3688 5.882557 TCTAGCAGAGAAATGGGATGAAAAC 59.117 40.000 0.00 0.00 0.00 2.43
3447 3689 6.065976 TCTAGCAGAGAAATGGGATGAAAA 57.934 37.500 0.00 0.00 0.00 2.29
3448 3690 5.190528 ACTCTAGCAGAGAAATGGGATGAAA 59.809 40.000 16.81 0.00 45.07 2.69
3449 3691 4.718774 ACTCTAGCAGAGAAATGGGATGAA 59.281 41.667 16.81 0.00 45.07 2.57
3450 3692 4.293494 ACTCTAGCAGAGAAATGGGATGA 58.707 43.478 16.81 0.00 45.07 2.92
3451 3693 4.686191 ACTCTAGCAGAGAAATGGGATG 57.314 45.455 16.81 0.00 45.07 3.51
3452 3694 4.718774 TGAACTCTAGCAGAGAAATGGGAT 59.281 41.667 16.81 0.00 45.07 3.85
3453 3695 4.096681 TGAACTCTAGCAGAGAAATGGGA 58.903 43.478 16.81 0.00 45.07 4.37
3454 3696 4.478206 TGAACTCTAGCAGAGAAATGGG 57.522 45.455 16.81 0.00 45.07 4.00
3455 3697 7.215789 ACATATGAACTCTAGCAGAGAAATGG 58.784 38.462 10.38 8.47 45.07 3.16
3456 3698 8.659925 AACATATGAACTCTAGCAGAGAAATG 57.340 34.615 10.38 13.48 45.07 2.32
3457 3699 7.930865 GGAACATATGAACTCTAGCAGAGAAAT 59.069 37.037 10.38 10.50 45.07 2.17
3458 3700 7.268586 GGAACATATGAACTCTAGCAGAGAAA 58.731 38.462 10.38 5.42 45.07 2.52
3459 3701 6.460261 CGGAACATATGAACTCTAGCAGAGAA 60.460 42.308 10.38 5.69 45.07 2.87
3460 3702 5.009110 CGGAACATATGAACTCTAGCAGAGA 59.991 44.000 10.38 4.47 45.07 3.10
3462 3704 4.038042 CCGGAACATATGAACTCTAGCAGA 59.962 45.833 10.38 0.00 0.00 4.26
3463 3705 4.302455 CCGGAACATATGAACTCTAGCAG 58.698 47.826 10.38 0.00 0.00 4.24
3464 3706 3.492656 GCCGGAACATATGAACTCTAGCA 60.493 47.826 5.05 0.00 0.00 3.49
3465 3707 3.060602 GCCGGAACATATGAACTCTAGC 58.939 50.000 5.05 6.51 0.00 3.42
3466 3708 4.592485 AGCCGGAACATATGAACTCTAG 57.408 45.455 5.05 2.53 0.00 2.43
3467 3709 6.455647 CATTAGCCGGAACATATGAACTCTA 58.544 40.000 5.05 0.63 0.00 2.43
3468 3710 5.300752 CATTAGCCGGAACATATGAACTCT 58.699 41.667 5.05 1.54 0.00 3.24
3469 3711 4.452455 CCATTAGCCGGAACATATGAACTC 59.548 45.833 5.05 2.89 0.00 3.01
3470 3712 4.389374 CCATTAGCCGGAACATATGAACT 58.611 43.478 5.05 0.00 0.00 3.01
3471 3713 3.058224 GCCATTAGCCGGAACATATGAAC 60.058 47.826 5.05 2.63 34.35 3.18
3472 3714 3.146066 GCCATTAGCCGGAACATATGAA 58.854 45.455 5.05 0.00 34.35 2.57
3473 3715 2.105649 TGCCATTAGCCGGAACATATGA 59.894 45.455 5.05 0.00 42.71 2.15
3474 3716 2.503331 TGCCATTAGCCGGAACATATG 58.497 47.619 5.05 0.00 42.71 1.78
3475 3717 2.949177 TGCCATTAGCCGGAACATAT 57.051 45.000 5.05 0.00 42.71 1.78
3476 3718 2.949177 ATGCCATTAGCCGGAACATA 57.051 45.000 5.05 0.00 42.71 2.29
3477 3719 2.949177 TATGCCATTAGCCGGAACAT 57.051 45.000 5.05 0.00 42.71 2.71
3478 3720 2.719531 TTATGCCATTAGCCGGAACA 57.280 45.000 5.05 0.00 42.71 3.18
3479 3721 4.546570 GAAATTATGCCATTAGCCGGAAC 58.453 43.478 5.05 0.00 42.71 3.62
3480 3722 3.572255 GGAAATTATGCCATTAGCCGGAA 59.428 43.478 5.05 0.00 42.71 4.30
3481 3723 3.153919 GGAAATTATGCCATTAGCCGGA 58.846 45.455 5.05 0.00 42.71 5.14
3482 3724 3.157087 AGGAAATTATGCCATTAGCCGG 58.843 45.455 0.00 0.00 42.71 6.13
3483 3725 5.957842 TTAGGAAATTATGCCATTAGCCG 57.042 39.130 0.00 0.00 42.71 5.52
3484 3726 7.232118 ACATTAGGAAATTATGCCATTAGCC 57.768 36.000 0.00 0.00 42.71 3.93
3485 3727 7.315890 GGACATTAGGAAATTATGCCATTAGC 58.684 38.462 0.00 0.00 44.14 3.09
3486 3728 7.362056 CGGGACATTAGGAAATTATGCCATTAG 60.362 40.741 0.00 0.00 0.00 1.73
3487 3729 6.432783 CGGGACATTAGGAAATTATGCCATTA 59.567 38.462 0.00 0.00 0.00 1.90
3488 3730 5.243730 CGGGACATTAGGAAATTATGCCATT 59.756 40.000 0.00 0.00 0.00 3.16
3489 3731 4.766891 CGGGACATTAGGAAATTATGCCAT 59.233 41.667 0.00 0.00 0.00 4.40
3490 3732 4.141287 CGGGACATTAGGAAATTATGCCA 58.859 43.478 0.00 0.00 0.00 4.92
3491 3733 3.057526 GCGGGACATTAGGAAATTATGCC 60.058 47.826 0.00 0.00 0.00 4.40
3492 3734 3.568007 TGCGGGACATTAGGAAATTATGC 59.432 43.478 0.00 0.00 0.00 3.14
3493 3735 5.766150 TTGCGGGACATTAGGAAATTATG 57.234 39.130 0.00 0.00 0.00 1.90
3494 3736 5.654650 TGTTTGCGGGACATTAGGAAATTAT 59.345 36.000 0.00 0.00 0.00 1.28
3495 3737 5.010933 TGTTTGCGGGACATTAGGAAATTA 58.989 37.500 0.00 0.00 0.00 1.40
3496 3738 3.829601 TGTTTGCGGGACATTAGGAAATT 59.170 39.130 0.00 0.00 0.00 1.82
3497 3739 3.426615 TGTTTGCGGGACATTAGGAAAT 58.573 40.909 0.00 0.00 0.00 2.17
3498 3740 2.865079 TGTTTGCGGGACATTAGGAAA 58.135 42.857 0.00 0.00 0.00 3.13
3499 3741 2.570415 TGTTTGCGGGACATTAGGAA 57.430 45.000 0.00 0.00 0.00 3.36
3500 3742 2.570415 TTGTTTGCGGGACATTAGGA 57.430 45.000 0.00 0.00 0.00 2.94
3527 3769 3.951037 TCCTGAGCTTTGCAGTTACAAAA 59.049 39.130 0.00 0.00 38.96 2.44
3534 3776 0.183492 TGGTTCCTGAGCTTTGCAGT 59.817 50.000 0.00 0.00 0.00 4.40
3545 3787 0.675633 CAAGGCAAGGTTGGTTCCTG 59.324 55.000 0.00 0.00 37.93 3.86
3560 3802 4.692625 CGGAATTCTGGACTATATGCAAGG 59.307 45.833 6.36 0.00 0.00 3.61
3576 3818 5.810587 TGCTACAGAAGACATAACGGAATTC 59.189 40.000 0.00 0.00 0.00 2.17
3585 3827 5.181245 GTGCCTTTTTGCTACAGAAGACATA 59.819 40.000 0.00 0.00 0.00 2.29
3617 3859 0.820871 CTGGACTCTACCCTCACTGC 59.179 60.000 0.00 0.00 0.00 4.40
3625 3867 6.075984 TCCAATAAGGTATCTGGACTCTACC 58.924 44.000 0.00 0.00 39.02 3.18
3634 3876 8.400947 CACATTTGAACTCCAATAAGGTATCTG 58.599 37.037 0.00 0.00 39.02 2.90
3692 3940 5.126067 AGTGCAACATCTACAACTTTCAGT 58.874 37.500 0.00 0.00 41.43 3.41
3739 3987 2.440627 AGCTATCTGATGGCCACAATGA 59.559 45.455 20.51 4.60 37.49 2.57
3740 3988 2.552743 CAGCTATCTGATGGCCACAATG 59.447 50.000 20.51 9.56 42.95 2.82
3900 4148 4.495844 GGTTTCTTTTGGAACACACTCTCG 60.496 45.833 0.00 0.00 39.29 4.04
3904 4152 4.082245 CACTGGTTTCTTTTGGAACACACT 60.082 41.667 0.00 0.00 39.29 3.55
3960 4208 5.474578 TGCCAATAGCTACTGAATCTAGG 57.525 43.478 3.20 0.00 44.23 3.02
3993 4241 9.092876 CAGAGTTAAGAATCCATTTAGACTGTC 57.907 37.037 0.00 0.00 0.00 3.51
4166 4416 4.285260 AGCAGCCTGAAATTCAAAGGAAAT 59.715 37.500 5.56 0.00 36.43 2.17
4196 4446 4.280677 ACCATTCCTTAATGTGTGGTGTTG 59.719 41.667 8.25 0.00 40.84 3.33
4352 4604 2.064434 TTCAACCTGTGTGCCATGAA 57.936 45.000 0.00 0.00 0.00 2.57
4622 4882 2.703536 TCTACAGTTTCCAACAGAGCCA 59.296 45.455 0.00 0.00 0.00 4.75
4728 4989 5.413499 AGCATAAATGTCAAGAACAATGGC 58.587 37.500 0.00 0.00 42.37 4.40
4795 5056 6.093495 GTGCATATGGCTTGTTAGTTACTGAA 59.907 38.462 4.56 0.00 45.15 3.02
4810 5071 5.634859 GCCTGTTAATTTATGTGCATATGGC 59.365 40.000 6.16 3.20 45.13 4.40
5122 5383 2.161855 TGCATGCTCCGAGTTTTCAAT 58.838 42.857 20.33 0.00 0.00 2.57
5222 5491 5.125356 TGTCTAATCAGGCAACATGGTATG 58.875 41.667 0.00 0.00 32.05 2.39
5254 5523 7.028962 CCATTATATTGCATCAACATAACCGG 58.971 38.462 0.00 0.00 27.74 5.28
5303 5572 3.822167 CCATGGCATGTGCATATACAGAA 59.178 43.478 24.80 0.00 44.36 3.02
5367 5636 8.464404 CAATTGCACTATATGGGAATAGGAATG 58.536 37.037 0.00 0.00 34.34 2.67
5573 5842 5.916320 GGGTATAACAAGACGGTTTTTGTTG 59.084 40.000 23.43 9.39 44.63 3.33
5582 5851 7.646314 CCGATATATAGGGTATAACAAGACGG 58.354 42.308 4.01 0.00 0.00 4.79
5584 5853 8.004087 TGCCGATATATAGGGTATAACAAGAC 57.996 38.462 13.15 0.00 0.00 3.01
5679 6131 5.134202 TCGATGTGACATGTACAGAAAGT 57.866 39.130 1.23 0.00 0.00 2.66
5827 6318 0.681733 GCTGACCTGGTGTCTTCAGA 59.318 55.000 14.63 0.00 44.75 3.27
6084 8771 6.997942 ATACATAAAGAGGGTAAGGACTCC 57.002 41.667 0.00 0.00 34.27 3.85
6095 8782 5.053978 AGGGGCAGAAATACATAAAGAGG 57.946 43.478 0.00 0.00 0.00 3.69
6129 8819 8.903820 GGCATTACCATTCAAACTATTCTAGTT 58.096 33.333 0.00 0.00 44.14 2.24
6161 8851 9.161572 TGCCCCTATCATTTTGTAGTTATACTA 57.838 33.333 0.00 0.00 32.75 1.82
6162 8852 8.041143 TGCCCCTATCATTTTGTAGTTATACT 57.959 34.615 0.00 0.00 32.75 2.12
6163 8853 8.863872 ATGCCCCTATCATTTTGTAGTTATAC 57.136 34.615 0.00 0.00 0.00 1.47
6164 8854 8.664992 TGATGCCCCTATCATTTTGTAGTTATA 58.335 33.333 0.00 0.00 32.39 0.98
6165 8855 7.526041 TGATGCCCCTATCATTTTGTAGTTAT 58.474 34.615 0.00 0.00 32.39 1.89
6166 8856 6.905736 TGATGCCCCTATCATTTTGTAGTTA 58.094 36.000 0.00 0.00 32.39 2.24
6167 8857 5.765510 TGATGCCCCTATCATTTTGTAGTT 58.234 37.500 0.00 0.00 32.39 2.24
6168 8858 5.380043 CTGATGCCCCTATCATTTTGTAGT 58.620 41.667 0.00 0.00 36.55 2.73
6169 8859 4.763793 CCTGATGCCCCTATCATTTTGTAG 59.236 45.833 0.00 0.00 36.55 2.74
6170 8860 4.415179 TCCTGATGCCCCTATCATTTTGTA 59.585 41.667 0.00 0.00 36.55 2.41
6171 8861 3.205056 TCCTGATGCCCCTATCATTTTGT 59.795 43.478 0.00 0.00 36.55 2.83
6172 8862 3.825014 CTCCTGATGCCCCTATCATTTTG 59.175 47.826 0.00 0.00 36.55 2.44
6173 8863 3.723681 TCTCCTGATGCCCCTATCATTTT 59.276 43.478 0.00 0.00 36.55 1.82
6174 8864 3.330198 TCTCCTGATGCCCCTATCATTT 58.670 45.455 0.00 0.00 36.55 2.32
6175 8865 2.995746 TCTCCTGATGCCCCTATCATT 58.004 47.619 0.00 0.00 36.55 2.57
6201 8891 9.695526 CTTTATGACCATTTTCTGTCAAATTCA 57.304 29.630 0.00 0.00 44.04 2.57
6202 8892 9.143631 CCTTTATGACCATTTTCTGTCAAATTC 57.856 33.333 0.00 0.00 44.04 2.17
6206 8896 7.432869 CAACCTTTATGACCATTTTCTGTCAA 58.567 34.615 0.00 0.00 44.04 3.18
6220 8910 5.047377 GGATTTGTTCAGGCAACCTTTATGA 60.047 40.000 0.00 0.00 33.51 2.15
6261 8951 9.897744 ATGACTGAGTGTTTGTAATAAACATTG 57.102 29.630 8.26 3.26 41.51 2.82
6263 8953 9.507329 AGATGACTGAGTGTTTGTAATAAACAT 57.493 29.630 8.26 0.00 41.51 2.71
6264 8954 8.902540 AGATGACTGAGTGTTTGTAATAAACA 57.097 30.769 0.00 1.42 37.76 2.83
6265 8955 9.209175 AGAGATGACTGAGTGTTTGTAATAAAC 57.791 33.333 0.00 0.00 0.00 2.01
6267 8965 8.035394 GGAGAGATGACTGAGTGTTTGTAATAA 58.965 37.037 0.00 0.00 0.00 1.40
6279 8977 4.886489 TGATGTGTAGGAGAGATGACTGAG 59.114 45.833 0.00 0.00 0.00 3.35
6313 9011 5.532032 TCGATAGTAACCATGTCCGTGAATA 59.468 40.000 0.00 0.00 37.40 1.75
6320 9018 5.657474 TCTTTGTCGATAGTAACCATGTCC 58.343 41.667 0.00 0.00 37.40 4.02
6349 9048 9.757227 GTCTGATTTACATCTCTAGTAAGCATT 57.243 33.333 0.00 0.00 33.44 3.56
6380 9079 1.406539 GGTTGCATATGACAGGCCAAG 59.593 52.381 5.01 0.00 31.20 3.61
6466 9165 9.503369 TCAGCCTGTCCTAGTATAGTATAGATA 57.497 37.037 0.00 0.00 36.82 1.98
6482 9181 0.826715 TAGCATGTCTCAGCCTGTCC 59.173 55.000 0.00 0.00 0.00 4.02
6558 9257 0.109597 GTGAACATGCTTTGCTCGGG 60.110 55.000 0.00 0.00 0.00 5.14
6662 9361 7.180766 GGATGAAGATGGGATTAGATCTCTCTT 59.819 40.741 0.00 0.00 33.16 2.85
6806 9505 2.145397 TCGACAAGCCTACCAGATCT 57.855 50.000 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.