Multiple sequence alignment - TraesCS1D01G042600

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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 TraesCS1D01G042600 chr1D 100.000 3500 0 0 1 3500 21149442 21145943 0.000000e+00 6464
1 TraesCS1D01G042600 chr1A 95.611 2028 83 5 903 2927 22973598 22971574 0.000000e+00 3247
2 TraesCS1D01G042600 chr1A 89.141 396 30 5 2926 3310 22971511 22971118 6.790000e-132 481
3 TraesCS1D01G042600 chr1A 92.582 337 19 1 573 903 22973966 22973630 2.440000e-131 479
4 TraesCS1D01G042600 chr1A 92.958 71 5 0 3430 3500 22931991 22931921 1.720000e-18 104
5 TraesCS1D01G042600 chr1B 95.423 2032 78 9 903 2927 35451937 35453960 0.000000e+00 3223
6 TraesCS1D01G042600 chr1B 92.368 2031 143 11 903 2927 34781626 34779602 0.000000e+00 2881
7 TraesCS1D01G042600 chr1B 92.368 2031 143 11 903 2927 34798953 34796929 0.000000e+00 2881
8 TraesCS1D01G042600 chr1B 82.323 1748 205 49 64 1740 35001646 35003360 0.000000e+00 1421
9 TraesCS1D01G042600 chr1B 91.603 786 59 7 1986 2769 35003354 35004134 0.000000e+00 1079
10 TraesCS1D01G042600 chr1B 85.810 895 63 34 46 902 35451036 35451904 0.000000e+00 891
11 TraesCS1D01G042600 chr1B 80.804 771 80 28 180 903 34799734 34798985 3.070000e-150 542
12 TraesCS1D01G042600 chr1B 85.185 351 29 9 180 511 34782828 34782482 4.330000e-89 339
13 TraesCS1D01G042600 chr1B 79.310 406 50 13 526 903 34782057 34781658 1.610000e-63 254
14 TraesCS1D01G042600 chr1B 95.070 142 6 1 2786 2927 35006203 35006343 4.550000e-54 222
15 TraesCS1D01G042600 chr4D 89.304 2113 198 15 757 2847 73883614 73881508 0.000000e+00 2625
16 TraesCS1D01G042600 chr4D 95.158 888 39 3 2041 2927 73966447 73965563 0.000000e+00 1399
17 TraesCS1D01G042600 chr4D 95.254 611 29 0 1470 2080 73967057 73966447 0.000000e+00 968
18 TraesCS1D01G042600 chr4D 85.556 900 65 30 46 903 73968507 73967631 0.000000e+00 881
19 TraesCS1D01G042600 chr4D 94.505 546 27 2 903 1446 73967599 73967055 0.000000e+00 839
20 TraesCS1D01G042600 chr4D 89.349 338 31 3 2965 3298 73881501 73881165 1.500000e-113 420
21 TraesCS1D01G042600 chr4D 79.906 637 63 20 46 657 73884357 73883761 1.170000e-109 407
22 TraesCS1D01G042600 chrUn 82.323 1748 205 49 64 1740 3003682 3001968 0.000000e+00 1421
23 TraesCS1D01G042600 chrUn 91.892 777 56 7 1995 2769 3001965 3001194 0.000000e+00 1079
24 TraesCS1D01G042600 chrUn 95.070 142 6 1 2786 2927 2995701 2995841 4.550000e-54 222
25 TraesCS1D01G042600 chr6D 75.585 1495 310 37 998 2454 450344707 450343230 0.000000e+00 688
26 TraesCS1D01G042600 chr6B 75.084 1493 308 43 1000 2451 683486874 683488343 3.810000e-179 638
27 TraesCS1D01G042600 chr3D 72.349 1490 338 49 998 2454 426000170 425998722 5.440000e-108 401


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 TraesCS1D01G042600 chr1D 21145943 21149442 3499 True 6464.000000 6464 100.000000 1 3500 1 chr1D.!!$R1 3499
1 TraesCS1D01G042600 chr1A 22971118 22973966 2848 True 1402.333333 3247 92.444667 573 3310 3 chr1A.!!$R2 2737
2 TraesCS1D01G042600 chr1B 35451036 35453960 2924 False 2057.000000 3223 90.616500 46 2927 2 chr1B.!!$F2 2881
3 TraesCS1D01G042600 chr1B 34796929 34799734 2805 True 1711.500000 2881 86.586000 180 2927 2 chr1B.!!$R2 2747
4 TraesCS1D01G042600 chr1B 34779602 34782828 3226 True 1158.000000 2881 85.621000 180 2927 3 chr1B.!!$R1 2747
5 TraesCS1D01G042600 chr1B 35001646 35006343 4697 False 907.333333 1421 89.665333 64 2927 3 chr1B.!!$F1 2863
6 TraesCS1D01G042600 chr4D 73881165 73884357 3192 True 1150.666667 2625 86.186333 46 3298 3 chr4D.!!$R1 3252
7 TraesCS1D01G042600 chr4D 73965563 73968507 2944 True 1021.750000 1399 92.618250 46 2927 4 chr4D.!!$R2 2881
8 TraesCS1D01G042600 chrUn 3001194 3003682 2488 True 1250.000000 1421 87.107500 64 2769 2 chrUn.!!$R1 2705
9 TraesCS1D01G042600 chr6D 450343230 450344707 1477 True 688.000000 688 75.585000 998 2454 1 chr6D.!!$R1 1456
10 TraesCS1D01G042600 chr6B 683486874 683488343 1469 False 638.000000 638 75.084000 1000 2451 1 chr6B.!!$F1 1451
11 TraesCS1D01G042600 chr3D 425998722 426000170 1448 True 401.000000 401 72.349000 998 2454 1 chr3D.!!$R1 1456

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
126 127 0.178932 ATCGGGATCGGGAATGAGGA 60.179 55.0 0.0 0.0 36.95 3.71 F
464 520 0.611896 GCTGCCCACCACCATTAACT 60.612 55.0 0.0 0.0 0.00 2.24 F
696 1210 2.289195 TGACAAGTACGTCCACCATTCC 60.289 50.0 0.0 0.0 34.88 3.01 F
1342 1933 0.371645 CGGAATCACGAGCTTCTTGC 59.628 55.0 0.0 0.0 43.29 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1203 1790 0.448990 CGACGGTCCGTTCATACTCA 59.551 55.000 19.95 0.00 41.37 3.41 R
1342 1933 0.609957 TCATGGCCACCTTCTGCTTG 60.610 55.000 8.16 0.00 0.00 4.01 R
1773 2389 1.271102 GAGCACTCTTCAAGGACGAGT 59.729 52.381 0.11 0.11 40.88 4.18 R
2947 5758 0.762418 ACCGATTGATATGGGCGGAA 59.238 50.000 0.00 0.00 44.43 4.30 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
28 29 9.490379 TCAACCAAGACTATTTTCTTTCTAGTC 57.510 33.333 0.00 0.00 40.98 2.59
29 30 8.436200 CAACCAAGACTATTTTCTTTCTAGTCG 58.564 37.037 0.00 0.00 43.86 4.18
30 31 7.893658 ACCAAGACTATTTTCTTTCTAGTCGA 58.106 34.615 0.00 0.00 43.86 4.20
31 32 8.030106 ACCAAGACTATTTTCTTTCTAGTCGAG 58.970 37.037 0.00 0.00 43.86 4.04
32 33 7.489757 CCAAGACTATTTTCTTTCTAGTCGAGG 59.510 40.741 0.00 0.00 43.86 4.63
33 34 7.941431 AGACTATTTTCTTTCTAGTCGAGGA 57.059 36.000 0.00 0.00 43.86 3.71
34 35 8.528044 AGACTATTTTCTTTCTAGTCGAGGAT 57.472 34.615 0.00 0.00 43.86 3.24
35 36 8.410141 AGACTATTTTCTTTCTAGTCGAGGATG 58.590 37.037 0.00 0.00 43.86 3.51
36 37 7.493367 ACTATTTTCTTTCTAGTCGAGGATGG 58.507 38.462 0.00 0.00 0.00 3.51
37 38 5.995565 TTTTCTTTCTAGTCGAGGATGGA 57.004 39.130 0.00 0.00 0.00 3.41
38 39 6.546428 TTTTCTTTCTAGTCGAGGATGGAT 57.454 37.500 0.00 0.00 0.00 3.41
39 40 5.776173 TTCTTTCTAGTCGAGGATGGATC 57.224 43.478 0.00 0.00 0.00 3.36
40 41 5.055265 TCTTTCTAGTCGAGGATGGATCT 57.945 43.478 0.00 0.00 0.00 2.75
41 42 5.067273 TCTTTCTAGTCGAGGATGGATCTC 58.933 45.833 0.00 0.00 0.00 2.75
42 43 4.715534 TTCTAGTCGAGGATGGATCTCT 57.284 45.455 0.00 0.00 0.00 3.10
43 44 4.280436 TCTAGTCGAGGATGGATCTCTC 57.720 50.000 0.00 0.00 0.00 3.20
44 45 1.890876 AGTCGAGGATGGATCTCTCG 58.109 55.000 15.64 15.64 43.03 4.04
45 46 1.142060 AGTCGAGGATGGATCTCTCGT 59.858 52.381 18.67 8.35 42.64 4.18
46 47 2.369203 AGTCGAGGATGGATCTCTCGTA 59.631 50.000 18.67 9.41 42.64 3.43
47 48 2.481185 GTCGAGGATGGATCTCTCGTAC 59.519 54.545 18.67 14.23 42.64 3.67
48 49 2.369203 TCGAGGATGGATCTCTCGTACT 59.631 50.000 18.67 2.33 42.64 2.73
49 50 3.577415 TCGAGGATGGATCTCTCGTACTA 59.423 47.826 18.67 5.60 42.64 1.82
50 51 4.223255 TCGAGGATGGATCTCTCGTACTAT 59.777 45.833 18.67 0.00 42.64 2.12
51 52 4.331443 CGAGGATGGATCTCTCGTACTATG 59.669 50.000 14.42 0.00 39.99 2.23
52 53 4.594970 AGGATGGATCTCTCGTACTATGG 58.405 47.826 0.00 0.00 0.00 2.74
53 54 3.129638 GGATGGATCTCTCGTACTATGGC 59.870 52.174 0.00 0.00 0.00 4.40
88 89 4.556912 CGATGCGCTAATTTTTGTGCTAAA 59.443 37.500 9.73 0.00 39.53 1.85
107 108 8.248945 GTGCTAAATCCTAATACGCCTAAGATA 58.751 37.037 0.00 0.00 0.00 1.98
108 109 8.978472 TGCTAAATCCTAATACGCCTAAGATAT 58.022 33.333 0.00 0.00 0.00 1.63
109 110 9.465985 GCTAAATCCTAATACGCCTAAGATATC 57.534 37.037 0.00 0.00 0.00 1.63
110 111 9.666626 CTAAATCCTAATACGCCTAAGATATCG 57.333 37.037 0.00 0.00 0.00 2.92
111 112 6.636562 ATCCTAATACGCCTAAGATATCGG 57.363 41.667 0.00 0.00 0.00 4.18
112 113 4.885907 TCCTAATACGCCTAAGATATCGGG 59.114 45.833 0.00 2.87 0.00 5.14
126 127 0.178932 ATCGGGATCGGGAATGAGGA 60.179 55.000 0.00 0.00 36.95 3.71
134 135 4.444306 GGATCGGGAATGAGGATGTACAAA 60.444 45.833 0.00 0.00 0.00 2.83
156 157 2.038557 TCTGTTTCCAGAGTTAGCCCAC 59.961 50.000 0.00 0.00 42.80 4.61
163 164 2.294791 CCAGAGTTAGCCCACTCGATAG 59.705 54.545 7.14 0.92 46.85 2.08
363 392 2.031012 CGCCACCAGAGACAGCAA 59.969 61.111 0.00 0.00 0.00 3.91
366 395 1.071987 CCACCAGAGACAGCAAGCA 59.928 57.895 0.00 0.00 0.00 3.91
368 397 1.302351 ACCAGAGACAGCAAGCAGC 60.302 57.895 0.00 0.00 46.19 5.25
388 438 2.944542 GCCTAAAGGAGTTGGTAAGCCC 60.945 54.545 0.00 0.00 37.39 5.19
436 488 0.666913 CTGATGCCCTGCTGTATTGC 59.333 55.000 0.00 0.00 0.00 3.56
441 493 0.677731 GCCCTGCTGTATTGCTGTGA 60.678 55.000 0.00 0.00 0.00 3.58
442 494 1.825090 CCCTGCTGTATTGCTGTGAA 58.175 50.000 0.00 0.00 0.00 3.18
453 509 3.357079 CTGTGAACGGCTGCCCAC 61.357 66.667 14.12 15.61 0.00 4.61
455 511 4.947147 GTGAACGGCTGCCCACCA 62.947 66.667 14.12 5.26 0.00 4.17
464 520 0.611896 GCTGCCCACCACCATTAACT 60.612 55.000 0.00 0.00 0.00 2.24
477 536 5.955355 CCACCATTAACTCTAAATCCCCAAA 59.045 40.000 0.00 0.00 0.00 3.28
538 1018 8.915871 ATTGTTATTGTGTGTTGCAGATATTC 57.084 30.769 0.00 0.00 0.00 1.75
549 1029 2.972021 TGCAGATATTCTCGGAATCCCA 59.028 45.455 0.00 0.00 0.00 4.37
562 1042 5.811190 TCGGAATCCCAAACTTATTTCTGA 58.189 37.500 0.00 0.00 0.00 3.27
564 1044 7.570132 TCGGAATCCCAAACTTATTTCTGATA 58.430 34.615 0.00 0.00 0.00 2.15
646 1133 8.412456 TGAACTACAATGTTGTGAATCAATTGT 58.588 29.630 13.45 13.45 42.31 2.71
686 1200 9.377383 CGATATTTTTCTTTTTGACAAGTACGT 57.623 29.630 0.00 0.00 0.00 3.57
696 1210 2.289195 TGACAAGTACGTCCACCATTCC 60.289 50.000 0.00 0.00 34.88 3.01
755 1292 5.825593 ATCACCTCCACTCTTCTGTTTTA 57.174 39.130 0.00 0.00 0.00 1.52
793 1330 8.863872 AGTTTCTTATGCTAGTTTGGTGTTAT 57.136 30.769 0.00 0.00 0.00 1.89
926 1505 7.009357 GCTTCTTTTCGGTAAGACTGTACTATG 59.991 40.741 0.00 0.00 34.04 2.23
1342 1933 0.371645 CGGAATCACGAGCTTCTTGC 59.628 55.000 0.00 0.00 43.29 4.01
1350 1941 0.870393 CGAGCTTCTTGCAAGCAGAA 59.130 50.000 27.24 13.90 45.30 3.02
1536 2148 1.604593 CTTCCCCCACAACTGCCTG 60.605 63.158 0.00 0.00 0.00 4.85
1641 2257 0.607620 TCATCCTGCGTGACATGTCA 59.392 50.000 24.56 24.56 37.24 3.58
1753 2369 1.602888 ACTCTAGTGGTGGACGCGT 60.603 57.895 13.85 13.85 33.90 6.01
1773 2389 3.674955 CGTCGTGTTCACATATCAGGGAA 60.675 47.826 3.87 0.00 0.00 3.97
1782 2398 3.133003 CACATATCAGGGAACTCGTCCTT 59.867 47.826 0.00 0.00 46.92 3.36
1887 2503 5.441718 AGATTCTATTTGGCTCAGTTCCA 57.558 39.130 0.00 0.00 0.00 3.53
2226 2894 2.290641 CGGGATGAATTGGTCGAAATCC 59.709 50.000 0.00 0.00 34.14 3.01
2496 3176 3.251484 TCTTCCTGAACTGATCTTGGGT 58.749 45.455 0.00 0.00 0.00 4.51
2498 3178 4.844085 TCTTCCTGAACTGATCTTGGGTTA 59.156 41.667 0.00 0.00 0.00 2.85
2575 3263 8.512966 TGTGATCGATGGGAAAAATATGTTTA 57.487 30.769 0.54 0.00 0.00 2.01
2611 3299 3.706698 TCACTCGATCGATGTCCATTTC 58.293 45.455 19.78 0.00 0.00 2.17
2669 3357 2.093447 AGTAGCACCAAGAGTATGCCAC 60.093 50.000 0.00 0.00 40.33 5.01
2700 3388 0.179171 CGCCTGCAATCTCAAGCTTG 60.179 55.000 20.81 20.81 0.00 4.01
2848 5595 3.216800 ACATTCATGATCATCAACCGGG 58.783 45.455 6.32 0.00 0.00 5.73
2871 5618 1.355381 TGGTGGAGCCAACATCTGAAT 59.645 47.619 2.46 0.00 45.94 2.57
2886 5633 8.559536 CAACATCTGAATAATGGGTGTACATAC 58.440 37.037 0.00 0.00 0.00 2.39
2947 5758 2.690840 ACACCCAAGTCCTCAACTAGT 58.309 47.619 0.00 0.00 37.17 2.57
2957 5768 1.760613 CCTCAACTAGTTCCGCCCATA 59.239 52.381 4.77 0.00 0.00 2.74
2962 5773 4.102524 TCAACTAGTTCCGCCCATATCAAT 59.897 41.667 4.77 0.00 0.00 2.57
3039 5852 5.125578 CACAGTACTAGGATGTAGCTTGTCA 59.874 44.000 0.00 0.00 0.00 3.58
3125 5949 4.066646 TCTCATTCGTTTGAGAACCACA 57.933 40.909 14.72 0.00 46.92 4.17
3136 5960 7.040755 TCGTTTGAGAACCACAAATCATATGTT 60.041 33.333 1.90 0.00 39.01 2.71
3157 5981 5.746245 TGTTCCATTTCAAGTTTACTTTGCG 59.254 36.000 0.00 0.00 33.11 4.85
3172 5996 9.182933 GTTTACTTTGCGGTTTTACAATATTCA 57.817 29.630 0.00 0.00 0.00 2.57
3213 6037 2.046892 CACCTAAGCTGGCACGCT 60.047 61.111 5.75 5.75 39.56 5.07
3252 6076 5.934625 ACAGGTTCTGCAACACTAGATAAAG 59.065 40.000 0.00 0.00 34.37 1.85
3311 6136 2.505628 TGCAAAATCGTGTGCATTGT 57.494 40.000 0.00 0.00 45.52 2.71
3312 6137 2.125685 TGCAAAATCGTGTGCATTGTG 58.874 42.857 0.00 0.00 45.52 3.33
3313 6138 2.126467 GCAAAATCGTGTGCATTGTGT 58.874 42.857 0.00 0.00 40.58 3.72
3314 6139 2.539274 GCAAAATCGTGTGCATTGTGTT 59.461 40.909 0.00 0.00 40.58 3.32
3315 6140 3.361917 GCAAAATCGTGTGCATTGTGTTC 60.362 43.478 0.00 0.00 40.58 3.18
3316 6141 3.988379 AAATCGTGTGCATTGTGTTCT 57.012 38.095 0.00 0.00 0.00 3.01
3317 6142 3.988379 AATCGTGTGCATTGTGTTCTT 57.012 38.095 0.00 0.00 0.00 2.52
3318 6143 3.542712 ATCGTGTGCATTGTGTTCTTC 57.457 42.857 0.00 0.00 0.00 2.87
3319 6144 2.284190 TCGTGTGCATTGTGTTCTTCA 58.716 42.857 0.00 0.00 0.00 3.02
3320 6145 2.680339 TCGTGTGCATTGTGTTCTTCAA 59.320 40.909 0.00 0.00 0.00 2.69
3321 6146 3.314913 TCGTGTGCATTGTGTTCTTCAAT 59.685 39.130 0.00 0.00 36.16 2.57
3322 6147 3.665409 CGTGTGCATTGTGTTCTTCAATC 59.335 43.478 0.00 0.00 33.92 2.67
3323 6148 3.665409 GTGTGCATTGTGTTCTTCAATCG 59.335 43.478 0.00 0.00 33.92 3.34
3324 6149 3.314913 TGTGCATTGTGTTCTTCAATCGT 59.685 39.130 0.00 0.00 33.92 3.73
3325 6150 4.202000 TGTGCATTGTGTTCTTCAATCGTT 60.202 37.500 0.00 0.00 33.92 3.85
3326 6151 4.379793 GTGCATTGTGTTCTTCAATCGTTC 59.620 41.667 0.00 0.00 33.92 3.95
3327 6152 4.036144 TGCATTGTGTTCTTCAATCGTTCA 59.964 37.500 0.00 0.00 33.92 3.18
3328 6153 5.156355 GCATTGTGTTCTTCAATCGTTCAT 58.844 37.500 0.00 0.00 33.92 2.57
3329 6154 5.060077 GCATTGTGTTCTTCAATCGTTCATG 59.940 40.000 0.00 0.00 33.92 3.07
3330 6155 6.372981 CATTGTGTTCTTCAATCGTTCATGA 58.627 36.000 0.00 0.00 33.92 3.07
3331 6156 6.558771 TTGTGTTCTTCAATCGTTCATGAT 57.441 33.333 0.00 0.00 0.00 2.45
3332 6157 6.558771 TGTGTTCTTCAATCGTTCATGATT 57.441 33.333 0.00 0.00 39.10 2.57
3333 6158 7.665561 TGTGTTCTTCAATCGTTCATGATTA 57.334 32.000 0.00 0.00 36.46 1.75
3334 6159 7.518161 TGTGTTCTTCAATCGTTCATGATTAC 58.482 34.615 0.00 0.00 36.46 1.89
3335 6160 7.387673 TGTGTTCTTCAATCGTTCATGATTACT 59.612 33.333 0.00 0.00 36.46 2.24
3336 6161 7.689812 GTGTTCTTCAATCGTTCATGATTACTG 59.310 37.037 0.00 0.00 36.46 2.74
3337 6162 7.602265 TGTTCTTCAATCGTTCATGATTACTGA 59.398 33.333 0.00 0.00 36.46 3.41
3338 6163 8.607459 GTTCTTCAATCGTTCATGATTACTGAT 58.393 33.333 0.00 0.00 36.46 2.90
3339 6164 8.134905 TCTTCAATCGTTCATGATTACTGATG 57.865 34.615 0.00 0.00 36.46 3.07
3340 6165 7.765819 TCTTCAATCGTTCATGATTACTGATGT 59.234 33.333 0.00 0.00 36.46 3.06
3341 6166 8.940768 TTCAATCGTTCATGATTACTGATGTA 57.059 30.769 0.00 0.00 36.46 2.29
3342 6167 8.352752 TCAATCGTTCATGATTACTGATGTAC 57.647 34.615 0.00 0.00 36.46 2.90
3343 6168 8.197439 TCAATCGTTCATGATTACTGATGTACT 58.803 33.333 0.00 0.00 36.46 2.73
3344 6169 8.483218 CAATCGTTCATGATTACTGATGTACTC 58.517 37.037 0.00 0.00 36.46 2.59
3345 6170 7.095695 TCGTTCATGATTACTGATGTACTCA 57.904 36.000 0.00 0.00 40.78 3.41
3346 6171 7.716612 TCGTTCATGATTACTGATGTACTCAT 58.283 34.615 0.00 4.08 44.51 2.90
3347 6172 7.862873 TCGTTCATGATTACTGATGTACTCATC 59.137 37.037 0.00 1.80 42.97 2.92
3357 6182 4.864916 GATGTACTCATCGTGTGCATTT 57.135 40.909 0.00 0.00 39.98 2.32
3358 6183 4.826500 GATGTACTCATCGTGTGCATTTC 58.173 43.478 0.00 0.00 39.98 2.17
3359 6184 3.925379 TGTACTCATCGTGTGCATTTCT 58.075 40.909 0.00 0.00 0.00 2.52
3360 6185 4.314961 TGTACTCATCGTGTGCATTTCTT 58.685 39.130 0.00 0.00 0.00 2.52
3361 6186 4.754618 TGTACTCATCGTGTGCATTTCTTT 59.245 37.500 0.00 0.00 0.00 2.52
3362 6187 4.410492 ACTCATCGTGTGCATTTCTTTC 57.590 40.909 0.00 0.00 0.00 2.62
3363 6188 3.120546 ACTCATCGTGTGCATTTCTTTCG 60.121 43.478 0.00 0.00 0.00 3.46
3364 6189 2.805671 TCATCGTGTGCATTTCTTTCGT 59.194 40.909 0.00 0.00 0.00 3.85
3365 6190 2.941891 TCGTGTGCATTTCTTTCGTC 57.058 45.000 0.00 0.00 0.00 4.20
3366 6191 1.529438 TCGTGTGCATTTCTTTCGTCC 59.471 47.619 0.00 0.00 0.00 4.79
3367 6192 1.399727 CGTGTGCATTTCTTTCGTCCC 60.400 52.381 0.00 0.00 0.00 4.46
3368 6193 1.606668 GTGTGCATTTCTTTCGTCCCA 59.393 47.619 0.00 0.00 0.00 4.37
3369 6194 1.606668 TGTGCATTTCTTTCGTCCCAC 59.393 47.619 0.00 0.00 0.00 4.61
3370 6195 1.068541 GTGCATTTCTTTCGTCCCACC 60.069 52.381 0.00 0.00 0.00 4.61
3371 6196 0.526211 GCATTTCTTTCGTCCCACCC 59.474 55.000 0.00 0.00 0.00 4.61
3372 6197 1.886655 GCATTTCTTTCGTCCCACCCT 60.887 52.381 0.00 0.00 0.00 4.34
3373 6198 2.514803 CATTTCTTTCGTCCCACCCTT 58.485 47.619 0.00 0.00 0.00 3.95
3374 6199 2.265589 TTTCTTTCGTCCCACCCTTC 57.734 50.000 0.00 0.00 0.00 3.46
3375 6200 0.399075 TTCTTTCGTCCCACCCTTCC 59.601 55.000 0.00 0.00 0.00 3.46
3376 6201 1.002502 CTTTCGTCCCACCCTTCCC 60.003 63.158 0.00 0.00 0.00 3.97
3377 6202 1.462627 TTTCGTCCCACCCTTCCCT 60.463 57.895 0.00 0.00 0.00 4.20
3378 6203 1.486145 TTTCGTCCCACCCTTCCCTC 61.486 60.000 0.00 0.00 0.00 4.30
3379 6204 2.284699 CGTCCCACCCTTCCCTCT 60.285 66.667 0.00 0.00 0.00 3.69
3380 6205 1.918800 CGTCCCACCCTTCCCTCTT 60.919 63.158 0.00 0.00 0.00 2.85
3381 6206 1.489560 CGTCCCACCCTTCCCTCTTT 61.490 60.000 0.00 0.00 0.00 2.52
3382 6207 0.778083 GTCCCACCCTTCCCTCTTTT 59.222 55.000 0.00 0.00 0.00 2.27
3383 6208 1.147191 GTCCCACCCTTCCCTCTTTTT 59.853 52.381 0.00 0.00 0.00 1.94
3384 6209 1.427753 TCCCACCCTTCCCTCTTTTTC 59.572 52.381 0.00 0.00 0.00 2.29
3385 6210 1.550179 CCCACCCTTCCCTCTTTTTCC 60.550 57.143 0.00 0.00 0.00 3.13
3386 6211 1.550179 CCACCCTTCCCTCTTTTTCCC 60.550 57.143 0.00 0.00 0.00 3.97
3387 6212 0.404426 ACCCTTCCCTCTTTTTCCCG 59.596 55.000 0.00 0.00 0.00 5.14
3388 6213 0.965866 CCCTTCCCTCTTTTTCCCGC 60.966 60.000 0.00 0.00 0.00 6.13
3389 6214 0.965866 CCTTCCCTCTTTTTCCCGCC 60.966 60.000 0.00 0.00 0.00 6.13
3390 6215 0.251165 CTTCCCTCTTTTTCCCGCCA 60.251 55.000 0.00 0.00 0.00 5.69
3391 6216 0.407918 TTCCCTCTTTTTCCCGCCAT 59.592 50.000 0.00 0.00 0.00 4.40
3392 6217 0.034477 TCCCTCTTTTTCCCGCCATC 60.034 55.000 0.00 0.00 0.00 3.51
3393 6218 0.034089 CCCTCTTTTTCCCGCCATCT 60.034 55.000 0.00 0.00 0.00 2.90
3394 6219 1.383523 CCTCTTTTTCCCGCCATCTC 58.616 55.000 0.00 0.00 0.00 2.75
3395 6220 1.009829 CTCTTTTTCCCGCCATCTCG 58.990 55.000 0.00 0.00 0.00 4.04
3396 6221 1.024579 TCTTTTTCCCGCCATCTCGC 61.025 55.000 0.00 0.00 0.00 5.03
3397 6222 1.002624 TTTTTCCCGCCATCTCGCT 60.003 52.632 0.00 0.00 0.00 4.93
3398 6223 1.305219 TTTTTCCCGCCATCTCGCTG 61.305 55.000 0.00 0.00 0.00 5.18
3399 6224 4.838152 TTCCCGCCATCTCGCTGC 62.838 66.667 0.00 0.00 0.00 5.25
3404 6229 4.925861 GCCATCTCGCTGCCTCCC 62.926 72.222 0.00 0.00 0.00 4.30
3405 6230 4.247380 CCATCTCGCTGCCTCCCC 62.247 72.222 0.00 0.00 0.00 4.81
3406 6231 3.473647 CATCTCGCTGCCTCCCCA 61.474 66.667 0.00 0.00 0.00 4.96
3407 6232 3.474570 ATCTCGCTGCCTCCCCAC 61.475 66.667 0.00 0.00 0.00 4.61
3408 6233 3.991924 ATCTCGCTGCCTCCCCACT 62.992 63.158 0.00 0.00 0.00 4.00
3409 6234 4.154347 CTCGCTGCCTCCCCACTC 62.154 72.222 0.00 0.00 0.00 3.51
3410 6235 4.704103 TCGCTGCCTCCCCACTCT 62.704 66.667 0.00 0.00 0.00 3.24
3411 6236 4.154347 CGCTGCCTCCCCACTCTC 62.154 72.222 0.00 0.00 0.00 3.20
3412 6237 2.686835 GCTGCCTCCCCACTCTCT 60.687 66.667 0.00 0.00 0.00 3.10
3413 6238 3.028921 GCTGCCTCCCCACTCTCTG 62.029 68.421 0.00 0.00 0.00 3.35
3414 6239 2.284921 TGCCTCCCCACTCTCTGG 60.285 66.667 0.00 0.00 40.26 3.86
3415 6240 2.284995 GCCTCCCCACTCTCTGGT 60.285 66.667 0.00 0.00 38.60 4.00
3416 6241 2.363172 GCCTCCCCACTCTCTGGTC 61.363 68.421 0.00 0.00 38.60 4.02
3417 6242 1.390125 CCTCCCCACTCTCTGGTCT 59.610 63.158 0.00 0.00 38.60 3.85
3418 6243 0.631753 CCTCCCCACTCTCTGGTCTA 59.368 60.000 0.00 0.00 38.60 2.59
3419 6244 1.219213 CCTCCCCACTCTCTGGTCTAT 59.781 57.143 0.00 0.00 38.60 1.98
3420 6245 2.359781 CCTCCCCACTCTCTGGTCTATT 60.360 54.545 0.00 0.00 38.60 1.73
3421 6246 3.117093 CCTCCCCACTCTCTGGTCTATTA 60.117 52.174 0.00 0.00 38.60 0.98
3422 6247 4.148838 CTCCCCACTCTCTGGTCTATTAG 58.851 52.174 0.00 0.00 38.60 1.73
3423 6248 3.532232 TCCCCACTCTCTGGTCTATTAGT 59.468 47.826 0.00 0.00 38.60 2.24
3424 6249 4.730392 TCCCCACTCTCTGGTCTATTAGTA 59.270 45.833 0.00 0.00 38.60 1.82
3425 6250 4.828387 CCCCACTCTCTGGTCTATTAGTAC 59.172 50.000 0.00 0.00 38.60 2.73
3426 6251 4.515944 CCCACTCTCTGGTCTATTAGTACG 59.484 50.000 0.00 0.00 38.60 3.67
3427 6252 5.366460 CCACTCTCTGGTCTATTAGTACGA 58.634 45.833 0.00 0.00 34.90 3.43
3428 6253 5.467399 CCACTCTCTGGTCTATTAGTACGAG 59.533 48.000 0.00 0.00 34.90 4.18
3429 6254 6.050432 CACTCTCTGGTCTATTAGTACGAGT 58.950 44.000 0.00 0.00 0.00 4.18
3430 6255 6.018588 CACTCTCTGGTCTATTAGTACGAGTG 60.019 46.154 0.00 0.00 38.78 3.51
3431 6256 5.987098 TCTCTGGTCTATTAGTACGAGTGT 58.013 41.667 0.00 0.00 0.00 3.55
3432 6257 6.047870 TCTCTGGTCTATTAGTACGAGTGTC 58.952 44.000 0.00 0.00 0.00 3.67
3433 6258 5.737860 TCTGGTCTATTAGTACGAGTGTCA 58.262 41.667 0.00 0.00 0.00 3.58
3434 6259 5.583854 TCTGGTCTATTAGTACGAGTGTCAC 59.416 44.000 0.00 0.00 0.00 3.67
3435 6260 4.637534 TGGTCTATTAGTACGAGTGTCACC 59.362 45.833 0.00 0.00 0.00 4.02
3436 6261 4.260538 GGTCTATTAGTACGAGTGTCACCG 60.261 50.000 10.96 10.96 0.00 4.94
3437 6262 2.556534 ATTAGTACGAGTGTCACCGC 57.443 50.000 12.07 0.00 0.00 5.68
3438 6263 0.523072 TTAGTACGAGTGTCACCGCC 59.477 55.000 12.07 5.37 0.00 6.13
3439 6264 1.638388 TAGTACGAGTGTCACCGCCG 61.638 60.000 12.07 10.05 0.00 6.46
3440 6265 3.740397 TACGAGTGTCACCGCCGG 61.740 66.667 0.00 0.00 0.00 6.13
3456 6281 2.668212 GGCTGCCGTGTGCTACAA 60.668 61.111 1.35 0.00 42.00 2.41
3457 6282 2.680913 GGCTGCCGTGTGCTACAAG 61.681 63.158 1.35 0.00 42.00 3.16
3458 6283 1.961277 GCTGCCGTGTGCTACAAGT 60.961 57.895 0.00 0.00 42.00 3.16
3459 6284 1.901650 GCTGCCGTGTGCTACAAGTC 61.902 60.000 0.00 0.00 42.00 3.01
3460 6285 1.291877 CTGCCGTGTGCTACAAGTCC 61.292 60.000 0.00 0.00 42.00 3.85
3461 6286 1.301401 GCCGTGTGCTACAAGTCCA 60.301 57.895 0.00 0.00 36.87 4.02
3462 6287 0.673644 GCCGTGTGCTACAAGTCCAT 60.674 55.000 0.00 0.00 36.87 3.41
3463 6288 1.404986 GCCGTGTGCTACAAGTCCATA 60.405 52.381 0.00 0.00 36.87 2.74
3464 6289 2.933492 GCCGTGTGCTACAAGTCCATAA 60.933 50.000 0.00 0.00 36.87 1.90
3465 6290 3.331150 CCGTGTGCTACAAGTCCATAAA 58.669 45.455 0.00 0.00 0.00 1.40
3466 6291 3.370978 CCGTGTGCTACAAGTCCATAAAG 59.629 47.826 0.00 0.00 0.00 1.85
3467 6292 3.994392 CGTGTGCTACAAGTCCATAAAGT 59.006 43.478 0.00 0.00 0.00 2.66
3468 6293 4.091509 CGTGTGCTACAAGTCCATAAAGTC 59.908 45.833 0.00 0.00 0.00 3.01
3469 6294 4.392138 GTGTGCTACAAGTCCATAAAGTCC 59.608 45.833 0.00 0.00 0.00 3.85
3470 6295 3.939592 GTGCTACAAGTCCATAAAGTCCC 59.060 47.826 0.00 0.00 0.00 4.46
3471 6296 3.844211 TGCTACAAGTCCATAAAGTCCCT 59.156 43.478 0.00 0.00 0.00 4.20
3472 6297 4.081087 TGCTACAAGTCCATAAAGTCCCTC 60.081 45.833 0.00 0.00 0.00 4.30
3473 6298 4.081087 GCTACAAGTCCATAAAGTCCCTCA 60.081 45.833 0.00 0.00 0.00 3.86
3474 6299 4.287766 ACAAGTCCATAAAGTCCCTCAC 57.712 45.455 0.00 0.00 0.00 3.51
3475 6300 3.262420 CAAGTCCATAAAGTCCCTCACG 58.738 50.000 0.00 0.00 0.00 4.35
3476 6301 2.816411 AGTCCATAAAGTCCCTCACGA 58.184 47.619 0.00 0.00 0.00 4.35
3477 6302 2.761208 AGTCCATAAAGTCCCTCACGAG 59.239 50.000 0.00 0.00 0.00 4.18
3478 6303 2.758979 GTCCATAAAGTCCCTCACGAGA 59.241 50.000 0.00 0.00 0.00 4.04
3479 6304 3.385111 GTCCATAAAGTCCCTCACGAGAT 59.615 47.826 0.00 0.00 0.00 2.75
3480 6305 3.384789 TCCATAAAGTCCCTCACGAGATG 59.615 47.826 0.00 0.00 0.00 2.90
3481 6306 3.493350 CCATAAAGTCCCTCACGAGATGG 60.493 52.174 0.00 0.00 0.00 3.51
3482 6307 0.250513 AAAGTCCCTCACGAGATGGC 59.749 55.000 0.00 0.00 30.36 4.40
3483 6308 0.904865 AAGTCCCTCACGAGATGGCA 60.905 55.000 0.00 0.00 30.36 4.92
3484 6309 0.904865 AGTCCCTCACGAGATGGCAA 60.905 55.000 0.00 0.00 30.36 4.52
3485 6310 0.460987 GTCCCTCACGAGATGGCAAG 60.461 60.000 0.00 0.00 30.36 4.01
3486 6311 0.904865 TCCCTCACGAGATGGCAAGT 60.905 55.000 0.00 0.00 30.36 3.16
3487 6312 0.036010 CCCTCACGAGATGGCAAGTT 60.036 55.000 0.00 0.00 0.00 2.66
3488 6313 1.363744 CCTCACGAGATGGCAAGTTC 58.636 55.000 0.00 0.00 0.00 3.01
3489 6314 1.363744 CTCACGAGATGGCAAGTTCC 58.636 55.000 0.00 0.00 0.00 3.62
3490 6315 0.389817 TCACGAGATGGCAAGTTCCG 60.390 55.000 0.00 0.00 0.00 4.30
3491 6316 0.389817 CACGAGATGGCAAGTTCCGA 60.390 55.000 0.00 0.00 0.00 4.55
3492 6317 0.320374 ACGAGATGGCAAGTTCCGAA 59.680 50.000 0.00 0.00 0.00 4.30
3493 6318 1.066143 ACGAGATGGCAAGTTCCGAAT 60.066 47.619 0.00 0.00 0.00 3.34
3494 6319 1.594862 CGAGATGGCAAGTTCCGAATC 59.405 52.381 0.00 0.00 0.00 2.52
3495 6320 1.943340 GAGATGGCAAGTTCCGAATCC 59.057 52.381 0.00 0.00 0.00 3.01
3496 6321 1.281867 AGATGGCAAGTTCCGAATCCA 59.718 47.619 0.00 0.00 0.00 3.41
3497 6322 2.092212 AGATGGCAAGTTCCGAATCCAT 60.092 45.455 0.00 0.00 37.05 3.41
3498 6323 2.214376 TGGCAAGTTCCGAATCCATT 57.786 45.000 0.00 0.00 0.00 3.16
3499 6324 2.091541 TGGCAAGTTCCGAATCCATTC 58.908 47.619 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.490379 GACTAGAAAGAAAATAGTCTTGGTTGA 57.510 33.333 0.00 0.00 41.34 3.18
3 4 8.436200 CGACTAGAAAGAAAATAGTCTTGGTTG 58.564 37.037 0.00 0.00 42.04 3.77
5 6 7.893658 TCGACTAGAAAGAAAATAGTCTTGGT 58.106 34.615 0.00 0.00 42.04 3.67
6 7 7.489757 CCTCGACTAGAAAGAAAATAGTCTTGG 59.510 40.741 0.00 7.36 42.04 3.61
8 9 8.350852 TCCTCGACTAGAAAGAAAATAGTCTT 57.649 34.615 0.00 0.00 42.04 3.01
9 10 7.941431 TCCTCGACTAGAAAGAAAATAGTCT 57.059 36.000 0.00 0.00 42.04 3.24
10 11 7.650104 CCATCCTCGACTAGAAAGAAAATAGTC 59.350 40.741 0.00 0.00 41.21 2.59
11 12 7.342284 TCCATCCTCGACTAGAAAGAAAATAGT 59.658 37.037 0.00 0.00 32.53 2.12
12 13 7.717568 TCCATCCTCGACTAGAAAGAAAATAG 58.282 38.462 0.00 0.00 0.00 1.73
13 14 7.655521 TCCATCCTCGACTAGAAAGAAAATA 57.344 36.000 0.00 0.00 0.00 1.40
14 15 6.546428 TCCATCCTCGACTAGAAAGAAAAT 57.454 37.500 0.00 0.00 0.00 1.82
15 16 5.995565 TCCATCCTCGACTAGAAAGAAAA 57.004 39.130 0.00 0.00 0.00 2.29
16 17 5.894393 AGATCCATCCTCGACTAGAAAGAAA 59.106 40.000 0.00 0.00 0.00 2.52
17 18 5.450453 AGATCCATCCTCGACTAGAAAGAA 58.550 41.667 0.00 0.00 0.00 2.52
18 19 5.055265 AGATCCATCCTCGACTAGAAAGA 57.945 43.478 0.00 0.00 0.00 2.52
19 20 5.070001 AGAGATCCATCCTCGACTAGAAAG 58.930 45.833 0.00 0.00 35.88 2.62
20 21 5.055265 AGAGATCCATCCTCGACTAGAAA 57.945 43.478 0.00 0.00 35.88 2.52
21 22 4.647611 GAGAGATCCATCCTCGACTAGAA 58.352 47.826 0.00 0.00 35.88 2.10
22 23 3.306433 CGAGAGATCCATCCTCGACTAGA 60.306 52.174 16.33 0.00 43.68 2.43
23 24 3.000041 CGAGAGATCCATCCTCGACTAG 59.000 54.545 16.33 0.00 43.68 2.57
24 25 2.369203 ACGAGAGATCCATCCTCGACTA 59.631 50.000 23.11 0.00 43.68 2.59
25 26 1.142060 ACGAGAGATCCATCCTCGACT 59.858 52.381 23.11 8.50 43.68 4.18
26 27 1.600023 ACGAGAGATCCATCCTCGAC 58.400 55.000 23.11 5.34 43.68 4.20
27 28 2.369203 AGTACGAGAGATCCATCCTCGA 59.631 50.000 23.11 11.47 43.68 4.04
28 29 2.773487 AGTACGAGAGATCCATCCTCG 58.227 52.381 18.27 18.27 45.02 4.63
29 30 4.638421 CCATAGTACGAGAGATCCATCCTC 59.362 50.000 0.00 0.00 0.00 3.71
30 31 4.594970 CCATAGTACGAGAGATCCATCCT 58.405 47.826 0.00 0.00 0.00 3.24
31 32 3.129638 GCCATAGTACGAGAGATCCATCC 59.870 52.174 0.00 0.00 0.00 3.51
32 33 3.129638 GGCCATAGTACGAGAGATCCATC 59.870 52.174 0.00 0.00 0.00 3.51
33 34 3.093057 GGCCATAGTACGAGAGATCCAT 58.907 50.000 0.00 0.00 0.00 3.41
34 35 2.158519 TGGCCATAGTACGAGAGATCCA 60.159 50.000 0.00 0.00 0.00 3.41
35 36 2.229302 GTGGCCATAGTACGAGAGATCC 59.771 54.545 9.72 0.00 0.00 3.36
36 37 2.095668 CGTGGCCATAGTACGAGAGATC 60.096 54.545 9.72 0.00 40.01 2.75
37 38 1.880675 CGTGGCCATAGTACGAGAGAT 59.119 52.381 9.72 0.00 40.01 2.75
38 39 1.306148 CGTGGCCATAGTACGAGAGA 58.694 55.000 9.72 0.00 40.01 3.10
39 40 1.022735 ACGTGGCCATAGTACGAGAG 58.977 55.000 18.43 0.00 40.01 3.20
40 41 2.330440 TACGTGGCCATAGTACGAGA 57.670 50.000 18.43 4.20 40.01 4.04
41 42 2.542411 GGTTACGTGGCCATAGTACGAG 60.542 54.545 18.43 2.02 40.01 4.18
42 43 1.405105 GGTTACGTGGCCATAGTACGA 59.595 52.381 18.43 5.81 40.01 3.43
43 44 1.134753 TGGTTACGTGGCCATAGTACG 59.865 52.381 19.58 15.63 42.98 3.67
44 45 2.543641 GTGGTTACGTGGCCATAGTAC 58.456 52.381 19.58 15.03 37.09 2.73
45 46 1.481772 GGTGGTTACGTGGCCATAGTA 59.518 52.381 9.72 14.45 37.09 1.82
46 47 0.251073 GGTGGTTACGTGGCCATAGT 59.749 55.000 9.72 15.61 37.09 2.12
47 48 0.808453 CGGTGGTTACGTGGCCATAG 60.808 60.000 9.72 9.48 37.09 2.23
48 49 1.218585 CGGTGGTTACGTGGCCATA 59.781 57.895 9.72 0.00 37.09 2.74
49 50 1.906105 ATCGGTGGTTACGTGGCCAT 61.906 55.000 9.72 0.00 37.09 4.40
50 51 2.585341 ATCGGTGGTTACGTGGCCA 61.585 57.895 0.00 0.00 0.00 5.36
51 52 2.104253 CATCGGTGGTTACGTGGCC 61.104 63.158 0.00 0.00 0.00 5.36
52 53 2.746803 GCATCGGTGGTTACGTGGC 61.747 63.158 0.00 0.00 0.00 5.01
53 54 2.449525 CGCATCGGTGGTTACGTGG 61.450 63.158 0.00 0.00 0.00 4.94
88 89 5.535406 CCCGATATCTTAGGCGTATTAGGAT 59.465 44.000 0.34 0.00 0.00 3.24
107 108 0.178932 TCCTCATTCCCGATCCCGAT 60.179 55.000 0.00 0.00 38.22 4.18
108 109 0.178932 ATCCTCATTCCCGATCCCGA 60.179 55.000 0.00 0.00 38.22 5.14
109 110 0.036952 CATCCTCATTCCCGATCCCG 60.037 60.000 0.00 0.00 0.00 5.14
110 111 1.059913 ACATCCTCATTCCCGATCCC 58.940 55.000 0.00 0.00 0.00 3.85
111 112 2.632996 TGTACATCCTCATTCCCGATCC 59.367 50.000 0.00 0.00 0.00 3.36
112 113 4.336889 TTGTACATCCTCATTCCCGATC 57.663 45.455 0.00 0.00 0.00 3.69
148 149 6.069331 AGAAAGTATCTATCGAGTGGGCTAA 58.931 40.000 0.00 0.00 36.32 3.09
156 157 7.658167 TGAGTGTAGGAGAAAGTATCTATCGAG 59.342 40.741 0.00 0.00 38.96 4.04
163 164 7.422399 GTGATCTGAGTGTAGGAGAAAGTATC 58.578 42.308 0.00 0.00 0.00 2.24
263 292 2.284995 GGTGGAGGAGGTGAGGCT 60.285 66.667 0.00 0.00 0.00 4.58
363 392 1.068121 ACCAACTCCTTTAGGCTGCT 58.932 50.000 0.00 0.00 34.44 4.24
366 395 2.026169 GGCTTACCAACTCCTTTAGGCT 60.026 50.000 0.00 0.00 35.26 4.58
368 397 2.679930 CGGGCTTACCAACTCCTTTAGG 60.680 54.545 0.00 0.00 40.22 2.69
370 399 1.339342 GCGGGCTTACCAACTCCTTTA 60.339 52.381 0.00 0.00 40.22 1.85
436 488 3.357079 GTGGGCAGCCGTTCACAG 61.357 66.667 12.99 0.00 0.00 3.66
453 509 5.124036 TGGGGATTTAGAGTTAATGGTGG 57.876 43.478 0.00 0.00 0.00 4.61
455 511 5.656859 GCTTTGGGGATTTAGAGTTAATGGT 59.343 40.000 0.00 0.00 0.00 3.55
464 520 2.944094 GCTTCGGCTTTGGGGATTTAGA 60.944 50.000 0.00 0.00 38.08 2.10
477 536 0.605589 GTAACACTTGGGCTTCGGCT 60.606 55.000 0.00 0.00 41.44 5.52
516 575 6.901887 CGAGAATATCTGCAACACACAATAAC 59.098 38.462 0.00 0.00 0.00 1.89
518 577 5.523552 CCGAGAATATCTGCAACACACAATA 59.476 40.000 0.00 0.00 0.00 1.90
519 578 4.333649 CCGAGAATATCTGCAACACACAAT 59.666 41.667 0.00 0.00 0.00 2.71
520 579 3.684305 CCGAGAATATCTGCAACACACAA 59.316 43.478 0.00 0.00 0.00 3.33
521 580 3.056179 TCCGAGAATATCTGCAACACACA 60.056 43.478 0.00 0.00 0.00 3.72
522 581 3.521560 TCCGAGAATATCTGCAACACAC 58.478 45.455 0.00 0.00 0.00 3.82
531 1011 5.896073 AGTTTGGGATTCCGAGAATATCT 57.104 39.130 0.00 0.00 35.24 1.98
538 1018 5.880332 TCAGAAATAAGTTTGGGATTCCGAG 59.120 40.000 0.00 0.00 35.24 4.63
646 1133 8.437360 AGAAAAATATCGCACATATGAACAGA 57.563 30.769 10.38 3.75 0.00 3.41
686 1200 4.088634 CCAGAAAGAAATGGAATGGTGGA 58.911 43.478 0.00 0.00 39.02 4.02
755 1292 8.798859 AGCATAAGAAACTAGTGAATTGACAT 57.201 30.769 0.00 0.00 0.00 3.06
851 1393 5.940470 AGCAAATACAAGTAGTTGGGAAGAG 59.060 40.000 18.40 1.75 40.32 2.85
965 1551 4.562082 CAATGGCAGAGCAGAAAATTTCA 58.438 39.130 8.55 0.00 0.00 2.69
1203 1790 0.448990 CGACGGTCCGTTCATACTCA 59.551 55.000 19.95 0.00 41.37 3.41
1342 1933 0.609957 TCATGGCCACCTTCTGCTTG 60.610 55.000 8.16 0.00 0.00 4.01
1753 2369 3.513912 AGTTCCCTGATATGTGAACACGA 59.486 43.478 0.00 0.00 39.57 4.35
1773 2389 1.271102 GAGCACTCTTCAAGGACGAGT 59.729 52.381 0.11 0.11 40.88 4.18
1782 2398 2.866156 CACAAAGAACGAGCACTCTTCA 59.134 45.455 0.00 0.00 30.57 3.02
1887 2503 2.237392 GAGGTTAGTGTCCATGAGGCTT 59.763 50.000 0.00 0.00 33.74 4.35
2644 3332 1.471119 TACTCTTGGTGCTACTCCCG 58.529 55.000 0.00 0.00 0.00 5.14
2669 3357 2.401766 GCAGGCGTCCAAGGATGTG 61.402 63.158 9.88 2.93 33.91 3.21
2700 3388 1.654023 GGCCCTTGCACGTACCATTC 61.654 60.000 0.00 0.00 40.13 2.67
2947 5758 0.762418 ACCGATTGATATGGGCGGAA 59.238 50.000 0.00 0.00 44.43 4.30
2957 5768 3.903714 TGGTATCAGATGGACCGATTGAT 59.096 43.478 8.79 8.79 35.91 2.57
2962 5773 2.307768 GACTGGTATCAGATGGACCGA 58.692 52.381 10.76 0.00 43.49 4.69
3136 5960 4.339814 ACCGCAAAGTAAACTTGAAATGGA 59.660 37.500 0.00 0.00 36.12 3.41
3172 5996 8.893727 GTGACCAAAGCATACATCTTAGTTAAT 58.106 33.333 0.00 0.00 0.00 1.40
3179 6003 4.307032 AGGTGACCAAAGCATACATCTT 57.693 40.909 3.63 0.00 0.00 2.40
3213 6037 5.646793 CAGAACCTGTAGTAGTGCTGTACTA 59.353 44.000 1.22 1.22 40.89 1.82
3222 6046 3.641906 AGTGTTGCAGAACCTGTAGTAGT 59.358 43.478 0.00 0.00 33.43 2.73
3224 6048 5.074804 TCTAGTGTTGCAGAACCTGTAGTA 58.925 41.667 0.00 0.00 33.43 1.82
3252 6076 6.647895 AGGAACTTGCAAAATTGATGAACATC 59.352 34.615 0.00 7.73 34.52 3.06
3298 6123 2.877786 TGAAGAACACAATGCACACGAT 59.122 40.909 0.00 0.00 0.00 3.73
3299 6124 2.284190 TGAAGAACACAATGCACACGA 58.716 42.857 0.00 0.00 0.00 4.35
3300 6125 2.753989 TGAAGAACACAATGCACACG 57.246 45.000 0.00 0.00 0.00 4.49
3301 6126 3.665409 CGATTGAAGAACACAATGCACAC 59.335 43.478 0.00 0.00 37.96 3.82
3302 6127 3.314913 ACGATTGAAGAACACAATGCACA 59.685 39.130 0.00 0.00 37.96 4.57
3303 6128 3.888934 ACGATTGAAGAACACAATGCAC 58.111 40.909 0.00 0.00 37.96 4.57
3310 6135 7.689812 CAGTAATCATGAACGATTGAAGAACAC 59.310 37.037 0.00 0.00 36.31 3.32
3311 6136 7.602265 TCAGTAATCATGAACGATTGAAGAACA 59.398 33.333 0.00 0.00 36.31 3.18
3312 6137 7.963981 TCAGTAATCATGAACGATTGAAGAAC 58.036 34.615 0.00 0.00 36.31 3.01
3313 6138 8.606602 CATCAGTAATCATGAACGATTGAAGAA 58.393 33.333 0.00 0.00 36.31 2.52
3314 6139 7.765819 ACATCAGTAATCATGAACGATTGAAGA 59.234 33.333 0.00 0.00 36.31 2.87
3315 6140 7.913423 ACATCAGTAATCATGAACGATTGAAG 58.087 34.615 0.00 0.83 36.31 3.02
3316 6141 7.848223 ACATCAGTAATCATGAACGATTGAA 57.152 32.000 0.00 0.00 36.31 2.69
3317 6142 8.197439 AGTACATCAGTAATCATGAACGATTGA 58.803 33.333 0.00 1.09 36.31 2.57
3318 6143 8.357796 AGTACATCAGTAATCATGAACGATTG 57.642 34.615 0.00 0.00 36.31 2.67
3319 6144 8.197439 TGAGTACATCAGTAATCATGAACGATT 58.803 33.333 0.00 0.00 46.72 3.34
3320 6145 7.716612 TGAGTACATCAGTAATCATGAACGAT 58.283 34.615 0.00 0.00 46.72 3.73
3321 6146 7.095695 TGAGTACATCAGTAATCATGAACGA 57.904 36.000 0.00 0.00 46.72 3.85
3336 6161 4.568359 AGAAATGCACACGATGAGTACATC 59.432 41.667 0.00 0.00 46.50 3.06
3337 6162 4.507710 AGAAATGCACACGATGAGTACAT 58.492 39.130 0.00 0.00 39.67 2.29
3338 6163 3.925379 AGAAATGCACACGATGAGTACA 58.075 40.909 0.00 0.00 0.00 2.90
3339 6164 4.928661 AAGAAATGCACACGATGAGTAC 57.071 40.909 0.00 0.00 0.00 2.73
3340 6165 4.091365 CGAAAGAAATGCACACGATGAGTA 59.909 41.667 0.00 0.00 0.00 2.59
3341 6166 3.120546 CGAAAGAAATGCACACGATGAGT 60.121 43.478 0.00 0.00 0.00 3.41
3342 6167 3.120546 ACGAAAGAAATGCACACGATGAG 60.121 43.478 0.00 0.00 0.00 2.90
3343 6168 2.805671 ACGAAAGAAATGCACACGATGA 59.194 40.909 0.00 0.00 0.00 2.92
3344 6169 3.155998 GACGAAAGAAATGCACACGATG 58.844 45.455 0.00 0.00 0.00 3.84
3345 6170 2.159627 GGACGAAAGAAATGCACACGAT 59.840 45.455 0.00 0.00 0.00 3.73
3346 6171 1.529438 GGACGAAAGAAATGCACACGA 59.471 47.619 0.00 0.00 0.00 4.35
3347 6172 1.399727 GGGACGAAAGAAATGCACACG 60.400 52.381 0.00 0.00 0.00 4.49
3348 6173 1.606668 TGGGACGAAAGAAATGCACAC 59.393 47.619 0.00 0.00 0.00 3.82
3349 6174 1.606668 GTGGGACGAAAGAAATGCACA 59.393 47.619 0.00 0.00 0.00 4.57
3350 6175 1.068541 GGTGGGACGAAAGAAATGCAC 60.069 52.381 0.00 0.00 0.00 4.57
3351 6176 1.243902 GGTGGGACGAAAGAAATGCA 58.756 50.000 0.00 0.00 0.00 3.96
3352 6177 0.526211 GGGTGGGACGAAAGAAATGC 59.474 55.000 0.00 0.00 0.00 3.56
3353 6178 2.200373 AGGGTGGGACGAAAGAAATG 57.800 50.000 0.00 0.00 0.00 2.32
3354 6179 2.554564 GGAAGGGTGGGACGAAAGAAAT 60.555 50.000 0.00 0.00 0.00 2.17
3355 6180 1.202842 GGAAGGGTGGGACGAAAGAAA 60.203 52.381 0.00 0.00 0.00 2.52
3356 6181 0.399075 GGAAGGGTGGGACGAAAGAA 59.601 55.000 0.00 0.00 0.00 2.52
3357 6182 1.486145 GGGAAGGGTGGGACGAAAGA 61.486 60.000 0.00 0.00 0.00 2.52
3358 6183 1.002502 GGGAAGGGTGGGACGAAAG 60.003 63.158 0.00 0.00 0.00 2.62
3359 6184 1.462627 AGGGAAGGGTGGGACGAAA 60.463 57.895 0.00 0.00 0.00 3.46
3360 6185 1.916777 GAGGGAAGGGTGGGACGAA 60.917 63.158 0.00 0.00 0.00 3.85
3361 6186 2.284405 GAGGGAAGGGTGGGACGA 60.284 66.667 0.00 0.00 0.00 4.20
3362 6187 1.489560 AAAGAGGGAAGGGTGGGACG 61.490 60.000 0.00 0.00 0.00 4.79
3363 6188 0.778083 AAAAGAGGGAAGGGTGGGAC 59.222 55.000 0.00 0.00 0.00 4.46
3364 6189 1.427753 GAAAAAGAGGGAAGGGTGGGA 59.572 52.381 0.00 0.00 0.00 4.37
3365 6190 1.550179 GGAAAAAGAGGGAAGGGTGGG 60.550 57.143 0.00 0.00 0.00 4.61
3366 6191 1.550179 GGGAAAAAGAGGGAAGGGTGG 60.550 57.143 0.00 0.00 0.00 4.61
3367 6192 1.886655 CGGGAAAAAGAGGGAAGGGTG 60.887 57.143 0.00 0.00 0.00 4.61
3368 6193 0.404426 CGGGAAAAAGAGGGAAGGGT 59.596 55.000 0.00 0.00 0.00 4.34
3369 6194 0.965866 GCGGGAAAAAGAGGGAAGGG 60.966 60.000 0.00 0.00 0.00 3.95
3370 6195 0.965866 GGCGGGAAAAAGAGGGAAGG 60.966 60.000 0.00 0.00 0.00 3.46
3371 6196 0.251165 TGGCGGGAAAAAGAGGGAAG 60.251 55.000 0.00 0.00 0.00 3.46
3372 6197 0.407918 ATGGCGGGAAAAAGAGGGAA 59.592 50.000 0.00 0.00 0.00 3.97
3373 6198 0.034477 GATGGCGGGAAAAAGAGGGA 60.034 55.000 0.00 0.00 0.00 4.20
3374 6199 0.034089 AGATGGCGGGAAAAAGAGGG 60.034 55.000 0.00 0.00 0.00 4.30
3375 6200 1.383523 GAGATGGCGGGAAAAAGAGG 58.616 55.000 0.00 0.00 0.00 3.69
3376 6201 1.009829 CGAGATGGCGGGAAAAAGAG 58.990 55.000 0.00 0.00 0.00 2.85
3377 6202 1.024579 GCGAGATGGCGGGAAAAAGA 61.025 55.000 0.00 0.00 0.00 2.52
3378 6203 1.026718 AGCGAGATGGCGGGAAAAAG 61.027 55.000 0.00 0.00 38.18 2.27
3379 6204 1.002624 AGCGAGATGGCGGGAAAAA 60.003 52.632 0.00 0.00 38.18 1.94
3380 6205 1.745115 CAGCGAGATGGCGGGAAAA 60.745 57.895 0.00 0.00 38.18 2.29
3381 6206 2.125147 CAGCGAGATGGCGGGAAA 60.125 61.111 0.00 0.00 38.18 3.13
3382 6207 4.838152 GCAGCGAGATGGCGGGAA 62.838 66.667 0.00 0.00 38.18 3.97
3387 6212 4.925861 GGGAGGCAGCGAGATGGC 62.926 72.222 6.81 6.81 45.63 4.40
3388 6213 4.247380 GGGGAGGCAGCGAGATGG 62.247 72.222 0.00 0.00 0.00 3.51
3389 6214 3.473647 TGGGGAGGCAGCGAGATG 61.474 66.667 0.00 0.00 0.00 2.90
3390 6215 3.474570 GTGGGGAGGCAGCGAGAT 61.475 66.667 0.00 0.00 0.00 2.75
3391 6216 4.704103 AGTGGGGAGGCAGCGAGA 62.704 66.667 0.00 0.00 0.00 4.04
3392 6217 4.154347 GAGTGGGGAGGCAGCGAG 62.154 72.222 0.00 0.00 0.00 5.03
3393 6218 4.704103 AGAGTGGGGAGGCAGCGA 62.704 66.667 0.00 0.00 0.00 4.93
3394 6219 4.154347 GAGAGTGGGGAGGCAGCG 62.154 72.222 0.00 0.00 0.00 5.18
3395 6220 2.686835 AGAGAGTGGGGAGGCAGC 60.687 66.667 0.00 0.00 0.00 5.25
3396 6221 2.365586 CCAGAGAGTGGGGAGGCAG 61.366 68.421 0.00 0.00 43.63 4.85
3397 6222 2.284921 CCAGAGAGTGGGGAGGCA 60.285 66.667 0.00 0.00 43.63 4.75
3405 6230 6.018588 CACTCGTACTAATAGACCAGAGAGTG 60.019 46.154 13.35 13.35 43.43 3.51
3406 6231 6.050432 CACTCGTACTAATAGACCAGAGAGT 58.950 44.000 0.00 0.00 35.88 3.24
3407 6232 6.050432 ACACTCGTACTAATAGACCAGAGAG 58.950 44.000 0.00 0.00 0.00 3.20
3408 6233 5.987098 ACACTCGTACTAATAGACCAGAGA 58.013 41.667 0.00 0.00 0.00 3.10
3409 6234 5.816258 TGACACTCGTACTAATAGACCAGAG 59.184 44.000 0.00 0.49 0.00 3.35
3410 6235 5.583854 GTGACACTCGTACTAATAGACCAGA 59.416 44.000 0.00 0.00 0.00 3.86
3411 6236 5.220815 GGTGACACTCGTACTAATAGACCAG 60.221 48.000 5.39 0.00 0.00 4.00
3412 6237 4.637534 GGTGACACTCGTACTAATAGACCA 59.362 45.833 5.39 0.00 0.00 4.02
3413 6238 4.260538 CGGTGACACTCGTACTAATAGACC 60.261 50.000 5.39 0.00 0.00 3.85
3414 6239 4.784710 GCGGTGACACTCGTACTAATAGAC 60.785 50.000 14.95 0.00 0.00 2.59
3415 6240 3.310774 GCGGTGACACTCGTACTAATAGA 59.689 47.826 14.95 0.00 0.00 1.98
3416 6241 3.547613 GGCGGTGACACTCGTACTAATAG 60.548 52.174 14.95 0.00 0.00 1.73
3417 6242 2.355756 GGCGGTGACACTCGTACTAATA 59.644 50.000 14.95 0.00 0.00 0.98
3418 6243 1.133790 GGCGGTGACACTCGTACTAAT 59.866 52.381 14.95 0.00 0.00 1.73
3419 6244 0.523072 GGCGGTGACACTCGTACTAA 59.477 55.000 14.95 0.00 0.00 2.24
3420 6245 1.638388 CGGCGGTGACACTCGTACTA 61.638 60.000 14.95 0.00 0.00 1.82
3421 6246 2.960170 GGCGGTGACACTCGTACT 59.040 61.111 14.95 0.00 0.00 2.73
3422 6247 2.503375 CGGCGGTGACACTCGTAC 60.503 66.667 14.95 9.37 0.00 3.67
3423 6248 3.740397 CCGGCGGTGACACTCGTA 61.740 66.667 19.97 0.00 0.00 3.43
3443 6268 0.673644 ATGGACTTGTAGCACACGGC 60.674 55.000 0.00 0.00 45.30 5.68
3444 6269 2.665649 TATGGACTTGTAGCACACGG 57.334 50.000 0.00 0.00 0.00 4.94
3445 6270 3.994392 ACTTTATGGACTTGTAGCACACG 59.006 43.478 0.00 0.00 0.00 4.49
3446 6271 4.392138 GGACTTTATGGACTTGTAGCACAC 59.608 45.833 0.00 0.00 0.00 3.82
3447 6272 4.564821 GGGACTTTATGGACTTGTAGCACA 60.565 45.833 0.00 0.00 0.00 4.57
3448 6273 3.939592 GGGACTTTATGGACTTGTAGCAC 59.060 47.826 0.00 0.00 0.00 4.40
3449 6274 3.844211 AGGGACTTTATGGACTTGTAGCA 59.156 43.478 0.00 0.00 27.25 3.49
3450 6275 4.081087 TGAGGGACTTTATGGACTTGTAGC 60.081 45.833 0.00 0.00 41.55 3.58
3451 6276 5.420409 GTGAGGGACTTTATGGACTTGTAG 58.580 45.833 0.00 0.00 41.55 2.74
3452 6277 4.081862 CGTGAGGGACTTTATGGACTTGTA 60.082 45.833 0.00 0.00 41.55 2.41
3453 6278 3.306780 CGTGAGGGACTTTATGGACTTGT 60.307 47.826 0.00 0.00 41.55 3.16
3454 6279 3.056107 TCGTGAGGGACTTTATGGACTTG 60.056 47.826 0.00 0.00 41.55 3.16
3455 6280 3.170717 TCGTGAGGGACTTTATGGACTT 58.829 45.455 0.00 0.00 41.55 3.01
3456 6281 2.761208 CTCGTGAGGGACTTTATGGACT 59.239 50.000 0.00 0.00 41.55 3.85
3457 6282 2.758979 TCTCGTGAGGGACTTTATGGAC 59.241 50.000 0.00 0.00 41.55 4.02
3458 6283 3.095912 TCTCGTGAGGGACTTTATGGA 57.904 47.619 0.00 0.00 41.55 3.41
3468 6293 0.036010 AACTTGCCATCTCGTGAGGG 60.036 55.000 13.55 13.55 46.10 4.30
3469 6294 1.363744 GAACTTGCCATCTCGTGAGG 58.636 55.000 0.00 0.00 0.00 3.86
3470 6295 1.363744 GGAACTTGCCATCTCGTGAG 58.636 55.000 0.00 0.00 0.00 3.51
3471 6296 0.389817 CGGAACTTGCCATCTCGTGA 60.390 55.000 0.00 0.00 0.00 4.35
3472 6297 0.389817 TCGGAACTTGCCATCTCGTG 60.390 55.000 0.00 0.00 0.00 4.35
3473 6298 0.320374 TTCGGAACTTGCCATCTCGT 59.680 50.000 0.00 0.00 0.00 4.18
3474 6299 1.594862 GATTCGGAACTTGCCATCTCG 59.405 52.381 0.00 0.00 0.00 4.04
3475 6300 1.943340 GGATTCGGAACTTGCCATCTC 59.057 52.381 0.00 0.00 0.00 2.75
3476 6301 1.281867 TGGATTCGGAACTTGCCATCT 59.718 47.619 0.00 0.00 0.00 2.90
3477 6302 1.750193 TGGATTCGGAACTTGCCATC 58.250 50.000 0.00 0.00 0.00 3.51
3478 6303 2.442236 ATGGATTCGGAACTTGCCAT 57.558 45.000 9.24 9.24 0.00 4.40
3479 6304 2.091541 GAATGGATTCGGAACTTGCCA 58.908 47.619 0.00 0.00 0.00 4.92
3480 6305 2.851805 GAATGGATTCGGAACTTGCC 57.148 50.000 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.