Multiple sequence alignment - TraesCS6D01G385400

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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 TraesCS6D01G385400 chr6D 100.000 3572 0 0 1 3572 463448701 463445130 0.000000e+00 6597.0
1 TraesCS6D01G385400 chr6D 92.771 166 9 1 2910 3075 463445746 463445584 1.660000e-58 237.0
2 TraesCS6D01G385400 chr6D 92.771 166 9 1 2956 3118 463445792 463445627 1.660000e-58 237.0
3 TraesCS6D01G385400 chr6D 96.403 139 2 1 2907 3045 463445703 463445568 3.590000e-55 226.0
4 TraesCS6D01G385400 chr6D 96.403 139 2 1 2999 3134 463445795 463445657 3.590000e-55 226.0
5 TraesCS6D01G385400 chr6D 91.111 90 5 1 2910 2999 463445654 463445568 6.260000e-23 119.0
6 TraesCS6D01G385400 chr6D 95.745 47 2 0 2907 2953 463445614 463445568 3.820000e-10 76.8
7 TraesCS6D01G385400 chr6B 89.662 2457 181 41 418 2843 706628172 706625758 0.000000e+00 3062.0
8 TraesCS6D01G385400 chr6B 93.252 489 19 5 3092 3572 613301599 613302081 0.000000e+00 708.0
9 TraesCS6D01G385400 chr6B 87.119 427 29 15 7 425 706628782 706628374 9.040000e-126 460.0
10 TraesCS6D01G385400 chr6B 81.395 172 23 8 260 422 696463520 696463691 8.050000e-27 132.0
11 TraesCS6D01G385400 chr6A 92.505 2028 132 11 827 2843 609974063 609972045 0.000000e+00 2885.0
12 TraesCS6D01G385400 chr6A 91.331 496 26 11 3088 3572 594313566 594314055 0.000000e+00 662.0
13 TraesCS6D01G385400 chr6A 79.677 310 24 24 64 348 609974984 609974689 1.690000e-43 187.0
14 TraesCS6D01G385400 chr6A 87.059 85 11 0 621 705 609974063 609973979 2.940000e-16 97.1
15 TraesCS6D01G385400 chr4B 94.274 489 14 3 3092 3572 69147581 69148063 0.000000e+00 736.0
16 TraesCS6D01G385400 chr4B 89.769 303 26 4 773 1074 402794664 402794366 2.010000e-102 383.0
17 TraesCS6D01G385400 chr4B 89.000 300 28 4 773 1071 138680172 138680467 2.030000e-97 366.0
18 TraesCS6D01G385400 chr1B 93.509 493 18 6 3088 3572 130553251 130552765 0.000000e+00 721.0
19 TraesCS6D01G385400 chr1B 92.292 493 19 4 3088 3572 171012039 171011558 0.000000e+00 682.0
20 TraesCS6D01G385400 chr1B 88.816 304 27 6 773 1074 123149696 123149994 2.030000e-97 366.0
21 TraesCS6D01G385400 chr1B 88.487 304 28 7 773 1074 123078817 123079115 9.430000e-96 361.0
22 TraesCS6D01G385400 chr1B 89.286 112 7 3 260 366 510003112 510003223 6.220000e-28 135.0
23 TraesCS6D01G385400 chr1B 82.456 114 13 3 2841 2953 171012100 171011993 3.800000e-15 93.5
24 TraesCS6D01G385400 chr7D 93.131 495 18 6 3088 3572 10753918 10754406 0.000000e+00 712.0
25 TraesCS6D01G385400 chr7D 83.333 120 14 4 2831 2950 10753848 10753961 4.880000e-19 106.0
26 TraesCS6D01G385400 chr7A 93.252 489 19 2 3092 3572 383961844 383961362 0.000000e+00 708.0
27 TraesCS6D01G385400 chr7A 91.129 496 27 11 3088 3572 27647521 27647032 0.000000e+00 656.0
28 TraesCS6D01G385400 chr7A 91.129 496 27 11 3088 3572 27672168 27671679 0.000000e+00 656.0
29 TraesCS6D01G385400 chr5B 93.103 493 19 6 3088 3572 155287214 155287699 0.000000e+00 708.0
30 TraesCS6D01G385400 chr5B 93.878 49 3 0 2708 2756 23363345 23363297 1.380000e-09 75.0
31 TraesCS6D01G385400 chr2D 93.075 491 18 7 3092 3572 7472650 7472166 0.000000e+00 704.0
32 TraesCS6D01G385400 chr4D 92.525 495 15 8 3088 3572 213332226 213332708 0.000000e+00 689.0
33 TraesCS6D01G385400 chr4D 84.545 110 12 3 2841 2950 213332165 213332269 1.750000e-18 104.0
34 TraesCS6D01G385400 chr4A 83.598 189 18 8 419 604 590625966 590626144 7.930000e-37 165.0
35 TraesCS6D01G385400 chr4A 90.265 113 5 3 260 366 590625769 590625881 3.720000e-30 143.0
36 TraesCS6D01G385400 chr3A 83.069 189 19 8 419 604 37766280 37766458 3.690000e-35 159.0
37 TraesCS6D01G385400 chr2B 83.140 172 20 6 260 422 3086026 3086197 7.990000e-32 148.0
38 TraesCS6D01G385400 chr3B 82.558 172 21 7 260 422 665496241 665496412 3.720000e-30 143.0
39 TraesCS6D01G385400 chr2A 90.179 112 6 3 260 366 35225493 35225604 1.340000e-29 141.0
40 TraesCS6D01G385400 chr2A 97.059 34 0 1 571 604 196308731 196308699 4.980000e-04 56.5
41 TraesCS6D01G385400 chr7B 81.818 176 22 7 260 425 134439190 134439015 4.810000e-29 139.0
42 TraesCS6D01G385400 chr5A 87.719 114 7 4 266 372 121944417 121944304 3.740000e-25 126.0


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 TraesCS6D01G385400 chr6D 463445130 463448701 3571 True 1102.685714 6597 95.029143 1 3572 7 chr6D.!!$R1 3571
1 TraesCS6D01G385400 chr6B 706625758 706628782 3024 True 1761.000000 3062 88.390500 7 2843 2 chr6B.!!$R1 2836
2 TraesCS6D01G385400 chr6A 609972045 609974984 2939 True 1056.366667 2885 86.413667 64 2843 3 chr6A.!!$R1 2779
3 TraesCS6D01G385400 chr1B 171011558 171012100 542 True 387.750000 682 87.374000 2841 3572 2 chr1B.!!$R2 731
4 TraesCS6D01G385400 chr7D 10753848 10754406 558 False 409.000000 712 88.232000 2831 3572 2 chr7D.!!$F1 741
5 TraesCS6D01G385400 chr4D 213332165 213332708 543 False 396.500000 689 88.535000 2841 3572 2 chr4D.!!$F1 731

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
182 193 0.033894 GTCCTCGTCCTCTTCCTCCT 60.034 60.0 0.0 0.0 0.00 3.69 F
1086 1455 0.032952 TCACCGCTTCAAACTACGCT 59.967 50.0 0.0 0.0 0.00 5.07 F
1227 1596 0.037882 CGCAGAGTGAGGCTGAGAAA 60.038 55.0 0.0 0.0 35.54 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1434 1806 0.108138 CTTCCCCAGCCTGACTAACG 60.108 60.0 0.0 0.0 0.0 3.18 R
2550 2931 0.034186 AGCCCAATCGAGCATTTCCA 60.034 50.0 0.0 0.0 0.0 3.53 R
3022 3407 0.179081 GCCCCGATGTCCACTAGTTC 60.179 60.0 0.0 0.0 0.0 3.01 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
57 58 4.142049 CGGCAGTAGAAAAGATCTCCTCTT 60.142 45.833 10.82 0.00 46.44 2.85
81 82 0.896226 GTCTCCACCACCTCCACTAC 59.104 60.000 0.00 0.00 0.00 2.73
97 98 6.037830 CCTCCACTACGAACAAAAAGAAAAGA 59.962 38.462 0.00 0.00 0.00 2.52
169 180 3.203412 CTCCGTCCCTCGTCCTCG 61.203 72.222 0.00 0.00 37.94 4.63
182 193 0.033894 GTCCTCGTCCTCTTCCTCCT 60.034 60.000 0.00 0.00 0.00 3.69
183 194 0.256464 TCCTCGTCCTCTTCCTCCTC 59.744 60.000 0.00 0.00 0.00 3.71
184 195 0.257616 CCTCGTCCTCTTCCTCCTCT 59.742 60.000 0.00 0.00 0.00 3.69
199 210 1.918800 CTCTCCCCACTTTCCCCGT 60.919 63.158 0.00 0.00 0.00 5.28
200 211 1.462627 TCTCCCCACTTTCCCCGTT 60.463 57.895 0.00 0.00 0.00 4.44
202 213 0.694196 CTCCCCACTTTCCCCGTTAA 59.306 55.000 0.00 0.00 0.00 2.01
212 223 3.278668 TTCCCCGTTAATAATTCGGCA 57.721 42.857 0.00 0.00 42.48 5.69
254 265 2.047844 TGCGACTGAAGCCTCTGC 60.048 61.111 0.00 0.00 37.95 4.26
378 412 4.659172 CCGGCTGCTGGGTTTCCA 62.659 66.667 20.04 0.00 41.58 3.53
400 435 3.141488 CGCTCCCGTCCAGCTAGT 61.141 66.667 0.00 0.00 34.45 2.57
409 444 2.358267 CCGTCCAGCTAGTCGATTAACT 59.642 50.000 0.00 0.00 0.00 2.24
483 737 1.942657 TCACTGCACTTGCTCTGTTTC 59.057 47.619 2.33 0.00 42.66 2.78
484 738 1.945394 CACTGCACTTGCTCTGTTTCT 59.055 47.619 2.33 0.00 42.66 2.52
485 739 1.945394 ACTGCACTTGCTCTGTTTCTG 59.055 47.619 2.33 0.00 42.66 3.02
505 759 3.930336 TGAACTCTGTTACTCCTGCATG 58.070 45.455 0.00 0.00 0.00 4.06
521 781 4.095483 CCTGCATGGTCTTGTAGCTTAAAG 59.905 45.833 0.00 0.00 0.00 1.85
537 803 6.720012 GCTTAAAGCAGCTCCTCTAATATC 57.280 41.667 0.00 0.00 41.89 1.63
557 828 2.435586 ATCTGGACAGTGCGCTGC 60.436 61.111 26.78 18.36 46.30 5.25
567 838 2.002586 CAGTGCGCTGCTTATTACAGT 58.997 47.619 15.44 0.00 37.47 3.55
603 875 5.978322 GTCTTATATTCGTTCACAGAGGGAC 59.022 44.000 0.00 0.00 0.00 4.46
611 885 3.988517 CGTTCACAGAGGGACTACTTTTC 59.011 47.826 0.00 0.00 41.55 2.29
651 925 5.531287 AGTTGTTGTAAATTCCCAGTCAGTC 59.469 40.000 0.00 0.00 0.00 3.51
742 1106 5.842907 AGCTATGTTACGTCTGCATATTCA 58.157 37.500 0.00 0.00 0.00 2.57
744 1108 6.931281 AGCTATGTTACGTCTGCATATTCATT 59.069 34.615 0.00 0.00 0.00 2.57
746 1110 7.116948 GCTATGTTACGTCTGCATATTCATTCT 59.883 37.037 0.00 0.00 0.00 2.40
747 1111 7.792374 ATGTTACGTCTGCATATTCATTCTT 57.208 32.000 0.00 0.00 0.00 2.52
750 1114 5.980698 ACGTCTGCATATTCATTCTTCTG 57.019 39.130 0.00 0.00 0.00 3.02
758 1122 6.484643 TGCATATTCATTCTTCTGGTAGCTTC 59.515 38.462 0.00 0.00 0.00 3.86
772 1136 2.596776 GCTTCTCACAGCTCCCCTA 58.403 57.895 0.00 0.00 36.79 3.53
845 1209 9.341078 AGTTTTTACGGACCAGTTATTCTAAAA 57.659 29.630 0.00 0.00 0.00 1.52
846 1210 9.949174 GTTTTTACGGACCAGTTATTCTAAAAA 57.051 29.630 0.00 0.00 0.00 1.94
850 1214 7.387119 ACGGACCAGTTATTCTAAAAATTCC 57.613 36.000 0.00 0.00 0.00 3.01
851 1215 6.376299 ACGGACCAGTTATTCTAAAAATTCCC 59.624 38.462 0.00 0.00 0.00 3.97
852 1216 6.376018 CGGACCAGTTATTCTAAAAATTCCCA 59.624 38.462 0.00 0.00 0.00 4.37
853 1217 7.094118 CGGACCAGTTATTCTAAAAATTCCCAA 60.094 37.037 0.00 0.00 0.00 4.12
864 1232 4.718940 AAAATTCCCAATCGCAGGTAAG 57.281 40.909 0.00 0.00 0.00 2.34
894 1262 4.158384 CCGCACAGCTTAATTTTACACTG 58.842 43.478 0.00 0.00 0.00 3.66
927 1296 5.473039 GTGCAAGTTATGATTCCTTTGCTT 58.527 37.500 8.26 0.00 0.00 3.91
930 1299 7.274250 GTGCAAGTTATGATTCCTTTGCTTAAG 59.726 37.037 0.00 0.00 0.00 1.85
957 1326 4.578105 GCATGTCTCTAGCTAAATTGCCTT 59.422 41.667 0.00 0.00 0.00 4.35
968 1337 6.762333 AGCTAAATTGCCTTTCATGAGTTTT 58.238 32.000 0.00 0.00 0.00 2.43
969 1338 7.219322 AGCTAAATTGCCTTTCATGAGTTTTT 58.781 30.769 0.00 0.00 0.00 1.94
979 1348 6.698766 CCTTTCATGAGTTTTTCTGACTTTGG 59.301 38.462 0.00 0.00 0.00 3.28
1086 1455 0.032952 TCACCGCTTCAAACTACGCT 59.967 50.000 0.00 0.00 0.00 5.07
1119 1488 1.014564 CGGCGAGAACTGAACCTTCC 61.015 60.000 0.00 0.00 0.00 3.46
1148 1517 0.253044 GCTGAAGGCCAGGTGTATGA 59.747 55.000 5.01 0.00 43.13 2.15
1214 1583 1.448540 ATTTCTCGGTGCCGCAGAG 60.449 57.895 5.64 0.00 40.15 3.35
1227 1596 0.037882 CGCAGAGTGAGGCTGAGAAA 60.038 55.000 0.00 0.00 35.54 2.52
1255 1624 6.127111 CCTCATGGAAGCTGATACTAGCATAT 60.127 42.308 0.00 0.00 39.97 1.78
1257 1626 8.544687 TCATGGAAGCTGATACTAGCATATAT 57.455 34.615 0.00 0.00 46.07 0.86
1304 1673 0.954452 GCAGTTTCTGACAAGGGTGG 59.046 55.000 0.66 0.00 32.44 4.61
1347 1719 2.678324 CAGGAGAAACTGAAGGACGAC 58.322 52.381 0.00 0.00 40.97 4.34
1425 1797 2.264480 CCTGACGATGGGAACGCA 59.736 61.111 0.00 0.00 0.00 5.24
1434 1806 2.126346 GGGAACGCATTGCACAGC 60.126 61.111 9.69 0.00 0.00 4.40
1494 1866 1.148310 CTGGTTACAGTGCAACGGAG 58.852 55.000 0.13 0.00 45.86 4.63
1508 1880 1.343069 ACGGAGGCTGAGAAAGAAGT 58.657 50.000 0.00 0.00 0.00 3.01
1543 1915 5.940470 GCCAAGGAGAAGACTGAAGAAAATA 59.060 40.000 0.00 0.00 0.00 1.40
1544 1916 6.601217 GCCAAGGAGAAGACTGAAGAAAATAT 59.399 38.462 0.00 0.00 0.00 1.28
1558 1930 8.909708 TGAAGAAAATATAACGCTCCAAAATG 57.090 30.769 0.00 0.00 0.00 2.32
1602 1974 1.238439 ATGTTGTTGCTTCCGGTGAG 58.762 50.000 0.00 1.83 0.00 3.51
1740 2112 1.753848 CGCTTTGATGGGGATGGCA 60.754 57.895 0.00 0.00 0.00 4.92
1913 2285 7.977818 TGAAATTCAGGTAGGTGATAGCATAT 58.022 34.615 0.00 0.00 34.15 1.78
2034 2409 6.446781 AATAGATTGTTGCCTCTGTCATTG 57.553 37.500 0.00 0.00 0.00 2.82
2110 2485 6.537453 AGCTCTGCTTGTTATCTTCTCTTA 57.463 37.500 0.00 0.00 33.89 2.10
2133 2508 2.465860 TGGCCGTCCAATATTATCCG 57.534 50.000 0.00 0.00 39.99 4.18
2185 2561 7.208080 TCTTGCCTTTCTAATTCCGATAGTAC 58.792 38.462 0.00 0.00 0.00 2.73
2186 2562 6.726490 TGCCTTTCTAATTCCGATAGTACT 57.274 37.500 0.00 0.00 0.00 2.73
2187 2563 7.828508 TGCCTTTCTAATTCCGATAGTACTA 57.171 36.000 4.77 4.77 0.00 1.82
2237 2613 9.740239 ATTCATATGTTCATTTTATCTGTGTGC 57.260 29.630 1.90 0.00 0.00 4.57
2238 2614 8.510243 TCATATGTTCATTTTATCTGTGTGCT 57.490 30.769 1.90 0.00 0.00 4.40
2267 2645 4.407818 CTGTGCTTGTTACGTTTTGTTGA 58.592 39.130 0.00 0.00 0.00 3.18
2341 2719 5.590663 TGTCTGAGTTAGTCTGTAGCCTATG 59.409 44.000 0.00 0.00 0.00 2.23
2350 2728 6.798427 AGTCTGTAGCCTATGAGAATTTCA 57.202 37.500 0.00 0.00 40.85 2.69
2352 2730 7.800092 AGTCTGTAGCCTATGAGAATTTCATT 58.200 34.615 7.96 0.00 44.14 2.57
2399 2780 9.593134 TTTTGTTAAGTGTCAATTTTGCACTAT 57.407 25.926 15.65 10.93 41.34 2.12
2414 2795 6.603237 TTGCACTATCATGTTCGGATTTAG 57.397 37.500 0.00 0.00 0.00 1.85
2431 2812 3.412237 TTAGTGTTCCAACTGGTAGCC 57.588 47.619 0.00 0.00 36.34 3.93
2657 3039 0.529773 GATGCCGCAGAACGTATGGA 60.530 55.000 0.00 0.00 41.42 3.41
2706 3088 1.435346 CCCCAAAACTCCTCCTGGGT 61.435 60.000 5.31 0.00 46.18 4.51
2800 3185 1.285023 GCTGCTGCAGTTTGTCAGG 59.715 57.895 28.50 3.51 39.41 3.86
2821 3206 3.128349 GCACTGTAACTTCTTCCGTTGA 58.872 45.455 0.00 0.00 0.00 3.18
2823 3208 4.213482 GCACTGTAACTTCTTCCGTTGATT 59.787 41.667 0.00 0.00 0.00 2.57
2824 3209 5.277828 GCACTGTAACTTCTTCCGTTGATTT 60.278 40.000 0.00 0.00 0.00 2.17
2832 3217 3.670625 TCTTCCGTTGATTTCGTGGATT 58.329 40.909 0.00 0.00 0.00 3.01
2834 3219 4.153475 TCTTCCGTTGATTTCGTGGATTTC 59.847 41.667 0.00 0.00 0.00 2.17
2849 3234 9.768662 TTCGTGGATTTCTTTTAACTAGTAAGT 57.231 29.630 0.00 0.00 37.65 2.24
2860 3245 0.708370 CTAGTAAGTGTGCACGTGCG 59.292 55.000 33.22 12.79 45.83 5.34
2861 3246 0.031043 TAGTAAGTGTGCACGTGCGT 59.969 50.000 33.22 18.55 45.83 5.24
2862 3247 0.808453 AGTAAGTGTGCACGTGCGTT 60.808 50.000 33.22 24.41 45.83 4.84
2892 3277 2.025969 CAGTGGCACGTCTCTGCAG 61.026 63.158 12.71 7.63 39.08 4.41
2937 3322 1.226746 GCAAGGCGTGTTGAACTAGT 58.773 50.000 1.69 0.00 0.00 2.57
2938 3323 1.069906 GCAAGGCGTGTTGAACTAGTG 60.070 52.381 0.00 0.00 0.00 2.74
2939 3324 1.531149 CAAGGCGTGTTGAACTAGTGG 59.469 52.381 0.00 0.00 0.00 4.00
2940 3325 1.045407 AGGCGTGTTGAACTAGTGGA 58.955 50.000 0.00 0.00 0.00 4.02
2941 3326 1.145803 GGCGTGTTGAACTAGTGGAC 58.854 55.000 0.00 0.00 0.00 4.02
2942 3327 1.539496 GGCGTGTTGAACTAGTGGACA 60.539 52.381 0.00 0.00 0.00 4.02
2943 3328 2.413837 GCGTGTTGAACTAGTGGACAT 58.586 47.619 0.00 0.00 0.00 3.06
2944 3329 2.412089 GCGTGTTGAACTAGTGGACATC 59.588 50.000 0.00 0.00 0.00 3.06
2945 3330 2.661675 CGTGTTGAACTAGTGGACATCG 59.338 50.000 0.00 5.42 0.00 3.84
2946 3331 2.993899 GTGTTGAACTAGTGGACATCGG 59.006 50.000 0.00 0.00 0.00 4.18
2947 3332 2.028476 TGTTGAACTAGTGGACATCGGG 60.028 50.000 0.00 0.00 0.00 5.14
2948 3333 1.191535 TGAACTAGTGGACATCGGGG 58.808 55.000 0.00 0.00 0.00 5.73
2949 3334 0.179081 GAACTAGTGGACATCGGGGC 60.179 60.000 0.00 0.00 0.00 5.80
2950 3335 1.623542 AACTAGTGGACATCGGGGCC 61.624 60.000 0.00 0.00 0.00 5.80
2951 3336 3.151710 TAGTGGACATCGGGGCCG 61.152 66.667 0.00 0.00 41.35 6.13
2968 3353 3.741476 GCCAGTTGAGGGCGCAAG 61.741 66.667 10.83 0.00 42.39 4.01
2969 3354 3.058160 CCAGTTGAGGGCGCAAGG 61.058 66.667 10.83 0.00 38.28 3.61
2983 3368 1.226746 GCAAGGCGTGTTGAACTAGT 58.773 50.000 1.69 0.00 0.00 2.57
2984 3369 1.069906 GCAAGGCGTGTTGAACTAGTG 60.070 52.381 0.00 0.00 0.00 2.74
2985 3370 1.531149 CAAGGCGTGTTGAACTAGTGG 59.469 52.381 0.00 0.00 0.00 4.00
2986 3371 1.045407 AGGCGTGTTGAACTAGTGGA 58.955 50.000 0.00 0.00 0.00 4.02
2987 3372 1.145803 GGCGTGTTGAACTAGTGGAC 58.854 55.000 0.00 0.00 0.00 4.02
2988 3373 1.539496 GGCGTGTTGAACTAGTGGACA 60.539 52.381 0.00 0.00 0.00 4.02
2989 3374 2.413837 GCGTGTTGAACTAGTGGACAT 58.586 47.619 0.00 0.00 0.00 3.06
2990 3375 2.806244 GCGTGTTGAACTAGTGGACATT 59.194 45.455 0.00 0.00 0.00 2.71
2991 3376 3.363970 GCGTGTTGAACTAGTGGACATTG 60.364 47.826 0.00 1.12 0.00 2.82
2992 3377 3.186409 CGTGTTGAACTAGTGGACATTGG 59.814 47.826 0.00 0.00 0.00 3.16
2993 3378 3.502211 GTGTTGAACTAGTGGACATTGGG 59.498 47.826 0.00 0.00 0.00 4.12
2994 3379 3.081804 GTTGAACTAGTGGACATTGGGG 58.918 50.000 0.00 0.00 0.00 4.96
2995 3380 1.004277 TGAACTAGTGGACATTGGGGC 59.996 52.381 0.00 0.00 0.00 5.80
2996 3381 0.331616 AACTAGTGGACATTGGGGCC 59.668 55.000 0.00 0.00 0.00 5.80
2997 3382 1.153168 CTAGTGGACATTGGGGCCG 60.153 63.158 0.00 0.00 0.00 6.13
2998 3383 3.338275 TAGTGGACATTGGGGCCGC 62.338 63.158 14.01 14.01 0.00 6.53
3002 3387 4.875713 GACATTGGGGCCGCCGAT 62.876 66.667 18.45 12.01 0.00 4.18
3003 3388 4.440829 ACATTGGGGCCGCCGATT 62.441 61.111 18.45 3.89 0.00 3.34
3004 3389 3.903282 CATTGGGGCCGCCGATTG 61.903 66.667 18.45 5.71 0.00 2.67
3005 3390 4.122149 ATTGGGGCCGCCGATTGA 62.122 61.111 18.45 0.00 0.00 2.57
3006 3391 4.794648 TTGGGGCCGCCGATTGAG 62.795 66.667 18.45 0.00 0.00 3.02
3014 3399 3.880846 GCCGATTGAGGGCGCAAG 61.881 66.667 10.83 0.00 41.39 4.01
3015 3400 3.204827 CCGATTGAGGGCGCAAGG 61.205 66.667 10.83 0.00 38.28 3.61
3029 3414 1.226746 GCAAGGCGTGTTGAACTAGT 58.773 50.000 1.69 0.00 0.00 2.57
3030 3415 1.069906 GCAAGGCGTGTTGAACTAGTG 60.070 52.381 0.00 0.00 0.00 2.74
3031 3416 1.531149 CAAGGCGTGTTGAACTAGTGG 59.469 52.381 0.00 0.00 0.00 4.00
3032 3417 1.045407 AGGCGTGTTGAACTAGTGGA 58.955 50.000 0.00 0.00 0.00 4.02
3033 3418 1.145803 GGCGTGTTGAACTAGTGGAC 58.854 55.000 0.00 0.00 0.00 4.02
3034 3419 1.539496 GGCGTGTTGAACTAGTGGACA 60.539 52.381 0.00 0.00 0.00 4.02
3035 3420 2.413837 GCGTGTTGAACTAGTGGACAT 58.586 47.619 0.00 0.00 0.00 3.06
3036 3421 2.412089 GCGTGTTGAACTAGTGGACATC 59.588 50.000 0.00 0.00 0.00 3.06
3037 3422 2.661675 CGTGTTGAACTAGTGGACATCG 59.338 50.000 0.00 5.42 0.00 3.84
3038 3423 2.993899 GTGTTGAACTAGTGGACATCGG 59.006 50.000 0.00 0.00 0.00 4.18
3039 3424 2.028476 TGTTGAACTAGTGGACATCGGG 60.028 50.000 0.00 0.00 0.00 5.14
3040 3425 1.191535 TGAACTAGTGGACATCGGGG 58.808 55.000 0.00 0.00 0.00 5.73
3041 3426 0.179081 GAACTAGTGGACATCGGGGC 60.179 60.000 0.00 0.00 0.00 5.80
3042 3427 1.623542 AACTAGTGGACATCGGGGCC 61.624 60.000 0.00 0.00 0.00 5.80
3043 3428 3.151710 TAGTGGACATCGGGGCCG 61.152 66.667 0.00 0.00 41.35 6.13
3060 3445 3.741476 GCCAGTTGAGGGCGCAAG 61.741 66.667 10.83 0.00 42.39 4.01
3061 3446 3.058160 CCAGTTGAGGGCGCAAGG 61.058 66.667 10.83 0.00 38.28 3.61
3075 3460 1.508632 GCAAGGCGTGTTGAACTAGA 58.491 50.000 0.00 0.00 0.00 2.43
3076 3461 1.194772 GCAAGGCGTGTTGAACTAGAC 59.805 52.381 0.00 0.00 0.00 2.59
3077 3462 2.479837 CAAGGCGTGTTGAACTAGACA 58.520 47.619 0.00 0.00 0.00 3.41
3078 3463 3.067106 CAAGGCGTGTTGAACTAGACAT 58.933 45.455 0.00 0.00 0.00 3.06
3079 3464 3.402628 AGGCGTGTTGAACTAGACATT 57.597 42.857 0.00 0.00 0.00 2.71
3080 3465 3.067106 AGGCGTGTTGAACTAGACATTG 58.933 45.455 0.00 0.00 0.00 2.82
3081 3466 2.159627 GGCGTGTTGAACTAGACATTGG 59.840 50.000 0.00 0.00 0.00 3.16
3082 3467 2.159627 GCGTGTTGAACTAGACATTGGG 59.840 50.000 0.00 0.00 0.00 4.12
3083 3468 2.742053 CGTGTTGAACTAGACATTGGGG 59.258 50.000 0.00 0.00 0.00 4.96
3084 3469 2.488153 GTGTTGAACTAGACATTGGGGC 59.512 50.000 0.00 0.00 0.00 5.80
3085 3470 2.092323 GTTGAACTAGACATTGGGGCC 58.908 52.381 0.00 0.00 0.00 5.80
3086 3471 0.251916 TGAACTAGACATTGGGGCCG 59.748 55.000 0.00 0.00 0.00 6.13
3087 3472 1.077716 AACTAGACATTGGGGCCGC 60.078 57.895 14.01 14.01 0.00 6.53
3088 3473 2.203209 CTAGACATTGGGGCCGCC 60.203 66.667 18.45 10.45 0.00 6.13
3089 3474 4.169696 TAGACATTGGGGCCGCCG 62.170 66.667 18.45 8.37 0.00 6.46
3091 3476 4.875713 GACATTGGGGCCGCCGAT 62.876 66.667 18.45 12.01 0.00 4.18
3092 3477 4.440829 ACATTGGGGCCGCCGATT 62.441 61.111 18.45 3.89 0.00 3.34
3093 3478 3.903282 CATTGGGGCCGCCGATTG 61.903 66.667 18.45 5.71 0.00 2.67
3094 3479 4.122149 ATTGGGGCCGCCGATTGA 62.122 61.111 18.45 0.00 0.00 2.57
3095 3480 4.794648 TTGGGGCCGCCGATTGAG 62.795 66.667 18.45 0.00 0.00 3.02
3103 3488 3.880846 GCCGATTGAGGGCGCAAG 61.881 66.667 10.83 0.00 41.39 4.01
3104 3489 3.204827 CCGATTGAGGGCGCAAGG 61.205 66.667 10.83 0.00 38.28 3.61
3123 3508 1.539496 GGCGTGTTGAACTAGTGGACA 60.539 52.381 0.00 0.00 0.00 4.02
3418 3813 6.602179 TCTGCTTAATCAATGAAACGTCAAG 58.398 36.000 0.00 0.00 37.30 3.02
3537 3932 6.865205 GGCATGCTAAGCAAAAAGGATAATAG 59.135 38.462 18.92 0.00 43.62 1.73
3557 3952 2.039348 AGCCATGCCTGCTTTGAAAATT 59.961 40.909 0.00 0.00 34.87 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 0.836400 GGAGGTGGTGGAGACTGGAA 60.836 60.000 0.00 0.00 0.00 3.53
61 62 0.784495 TAGTGGAGGTGGTGGAGACT 59.216 55.000 0.00 0.00 0.00 3.24
109 120 2.771639 GCGCCCCGGGAGATTTTTC 61.772 63.158 26.32 0.00 0.00 2.29
157 168 1.849975 AAGAGGACGAGGACGAGGGA 61.850 60.000 0.00 0.00 42.66 4.20
169 180 0.397957 GGGGAGAGGAGGAAGAGGAC 60.398 65.000 0.00 0.00 0.00 3.85
182 193 0.178897 TAACGGGGAAAGTGGGGAGA 60.179 55.000 0.00 0.00 0.00 3.71
183 194 0.694196 TTAACGGGGAAAGTGGGGAG 59.306 55.000 0.00 0.00 0.00 4.30
184 195 1.374572 ATTAACGGGGAAAGTGGGGA 58.625 50.000 0.00 0.00 0.00 4.81
237 248 2.047844 GCAGAGGCTTCAGTCGCA 60.048 61.111 0.00 0.00 36.96 5.10
267 278 4.129737 GTACCGGCGAGCAGAGCA 62.130 66.667 9.30 0.00 36.08 4.26
328 362 2.336478 CGAGAGGGGATCCGATCGG 61.336 68.421 28.62 28.62 40.09 4.18
400 435 0.459585 GGGCACGAGCAGTTAATCGA 60.460 55.000 7.26 0.00 44.61 3.59
409 444 3.670637 GATCAGCAGGGCACGAGCA 62.671 63.158 7.26 0.00 44.61 4.26
483 737 3.667497 TGCAGGAGTAACAGAGTTCAG 57.333 47.619 0.00 0.00 0.00 3.02
484 738 3.306989 CCATGCAGGAGTAACAGAGTTCA 60.307 47.826 0.00 0.00 41.22 3.18
485 739 3.265791 CCATGCAGGAGTAACAGAGTTC 58.734 50.000 0.00 0.00 41.22 3.01
505 759 3.748868 GCTGCTTTAAGCTACAAGACC 57.251 47.619 18.20 0.00 42.97 3.85
521 781 2.732412 TGCGATATTAGAGGAGCTGC 57.268 50.000 0.00 0.00 0.00 5.25
603 875 9.420551 ACTGATCCGTAAAAACTAGAAAAGTAG 57.579 33.333 0.00 0.00 37.50 2.57
611 885 7.186021 ACAACAACTGATCCGTAAAAACTAG 57.814 36.000 0.00 0.00 0.00 2.57
742 1106 4.622695 GCTGTGAGAAGCTACCAGAAGAAT 60.623 45.833 0.00 0.00 40.20 2.40
744 1108 2.232452 GCTGTGAGAAGCTACCAGAAGA 59.768 50.000 0.00 0.00 40.20 2.87
746 1110 2.751166 GCTGTGAGAAGCTACCAGAA 57.249 50.000 0.00 0.00 40.20 3.02
758 1122 2.369860 TGCAATATAGGGGAGCTGTGAG 59.630 50.000 0.00 0.00 0.00 3.51
772 1136 3.386078 AGTGGACTGTCGAGATGCAATAT 59.614 43.478 1.07 0.00 0.00 1.28
807 1171 9.777297 TGGTCCGTAAAAACTAAAATAACTACT 57.223 29.630 0.00 0.00 0.00 2.57
809 1173 9.777297 ACTGGTCCGTAAAAACTAAAATAACTA 57.223 29.630 0.00 0.00 0.00 2.24
810 1174 8.681486 ACTGGTCCGTAAAAACTAAAATAACT 57.319 30.769 0.00 0.00 0.00 2.24
825 1189 7.553760 GGGAATTTTTAGAATAACTGGTCCGTA 59.446 37.037 0.00 0.00 0.00 4.02
831 1195 7.435192 GCGATTGGGAATTTTTAGAATAACTGG 59.565 37.037 0.00 0.00 0.00 4.00
845 1209 3.016736 CACTTACCTGCGATTGGGAATT 58.983 45.455 0.00 0.00 0.00 2.17
846 1210 2.643551 CACTTACCTGCGATTGGGAAT 58.356 47.619 0.00 0.00 0.00 3.01
848 1212 0.392461 GCACTTACCTGCGATTGGGA 60.392 55.000 0.00 0.00 0.00 4.37
894 1262 3.255642 TCATAACTTGCACCCTTTTCAGC 59.744 43.478 0.00 0.00 0.00 4.26
927 1296 2.392662 AGCTAGAGACATGCAGGCTTA 58.607 47.619 0.00 0.00 33.72 3.09
930 1299 2.898729 TTAGCTAGAGACATGCAGGC 57.101 50.000 0.00 0.00 0.00 4.85
957 1326 6.458206 CGACCAAAGTCAGAAAAACTCATGAA 60.458 38.462 0.00 0.00 43.73 2.57
968 1337 3.615110 GCAGAGATCGACCAAAGTCAGAA 60.615 47.826 0.00 0.00 43.73 3.02
969 1338 2.094494 GCAGAGATCGACCAAAGTCAGA 60.094 50.000 0.00 0.00 43.73 3.27
979 1348 0.174389 TTCCAGCTGCAGAGATCGAC 59.826 55.000 20.43 0.00 0.00 4.20
1077 1446 1.512926 CAGGTGCAGAAGCGTAGTTT 58.487 50.000 0.00 0.00 46.23 2.66
1086 1455 4.329545 GCCGGACCAGGTGCAGAA 62.330 66.667 12.28 0.00 0.00 3.02
1119 1488 2.492090 CCTTCAGCCTCCTCGTCG 59.508 66.667 0.00 0.00 0.00 5.12
1177 1546 2.125391 GCCAGACATGAGCAGCGA 60.125 61.111 0.00 0.00 0.00 4.93
1179 1548 1.035932 AATGGCCAGACATGAGCAGC 61.036 55.000 13.05 0.00 0.00 5.25
1185 1554 1.019673 CCGAGAAATGGCCAGACATG 58.980 55.000 13.05 0.00 0.00 3.21
1214 1583 2.378445 GAGGAGTTTCTCAGCCTCAC 57.622 55.000 0.00 0.00 44.91 3.51
1227 1596 3.652055 AGTATCAGCTTCCATGAGGAGT 58.348 45.455 0.00 0.00 46.74 3.85
1255 1624 4.592192 GCGCGCCTCCTGCTGATA 62.592 66.667 23.24 0.00 38.05 2.15
1304 1673 4.793353 GCTGGTCTTCGTACATACCATCTC 60.793 50.000 6.19 0.00 41.04 2.75
1347 1719 1.141881 CGGGATCCTGTCAAGACCG 59.858 63.158 12.93 0.00 0.00 4.79
1393 1765 2.804572 CGTCAGGCTCCATATCAACAGG 60.805 54.545 0.00 0.00 0.00 4.00
1425 1797 1.442769 CCTGACTAACGCTGTGCAAT 58.557 50.000 0.00 0.00 0.00 3.56
1434 1806 0.108138 CTTCCCCAGCCTGACTAACG 60.108 60.000 0.00 0.00 0.00 3.18
1494 1866 3.056749 TCTCGGTAACTTCTTTCTCAGCC 60.057 47.826 0.00 0.00 0.00 4.85
1508 1880 0.895530 CTCCTTGGCACTCTCGGTAA 59.104 55.000 0.00 0.00 0.00 2.85
1543 1915 2.676342 GGTCGACATTTTGGAGCGTTAT 59.324 45.455 18.91 0.00 0.00 1.89
1544 1916 2.070783 GGTCGACATTTTGGAGCGTTA 58.929 47.619 18.91 0.00 0.00 3.18
1558 1930 1.732732 CGAATCAGTGACAGGGTCGAC 60.733 57.143 7.13 7.13 34.95 4.20
1602 1974 2.125350 CCGTCAGGCTTGCTCTCC 60.125 66.667 0.00 0.00 0.00 3.71
1722 2094 1.111116 ATGCCATCCCCATCAAAGCG 61.111 55.000 0.00 0.00 0.00 4.68
1726 2098 3.509442 GGAAATATGCCATCCCCATCAA 58.491 45.455 0.00 0.00 0.00 2.57
1740 2112 2.972505 CAGCGCCGCCGGAAATAT 60.973 61.111 7.68 0.00 34.32 1.28
1932 2304 9.309516 CTTTGATGAAAGCAGCACAAATAATAT 57.690 29.630 0.00 0.00 40.65 1.28
2095 2470 5.584649 CGGCCAACATAAGAGAAGATAACAA 59.415 40.000 2.24 0.00 0.00 2.83
2131 2506 3.057734 GTTTCCTCGCAATACTATCCGG 58.942 50.000 0.00 0.00 0.00 5.14
2133 2508 5.297547 TGATGTTTCCTCGCAATACTATCC 58.702 41.667 0.00 0.00 0.00 2.59
2185 2561 4.755123 GGATGATCCAACAACCCGTAATAG 59.245 45.833 6.60 0.00 36.28 1.73
2186 2562 4.164413 TGGATGATCCAACAACCCGTAATA 59.836 41.667 12.63 0.00 45.00 0.98
2187 2563 3.053991 TGGATGATCCAACAACCCGTAAT 60.054 43.478 12.63 0.00 45.00 1.89
2251 2629 6.922247 TGGATAGTCAACAAAACGTAACAA 57.078 33.333 0.00 0.00 0.00 2.83
2267 2645 7.068702 TGGAAATTCTGGCAATATTGGATAGT 58.931 34.615 17.02 0.00 0.00 2.12
2327 2705 6.798427 TGAAATTCTCATAGGCTACAGACT 57.202 37.500 0.00 0.00 37.13 3.24
2350 2728 9.768662 AAAAGTTGCTGAAATAGAAATGTCAAT 57.231 25.926 0.00 0.00 28.62 2.57
2351 2729 9.033481 CAAAAGTTGCTGAAATAGAAATGTCAA 57.967 29.630 0.00 0.00 28.62 3.18
2352 2730 8.196771 ACAAAAGTTGCTGAAATAGAAATGTCA 58.803 29.630 0.00 0.00 0.00 3.58
2399 2780 4.900684 TGGAACACTAAATCCGAACATGA 58.099 39.130 0.00 0.00 38.63 3.07
2414 2795 0.034337 TCGGCTACCAGTTGGAACAC 59.966 55.000 4.92 0.00 39.29 3.32
2431 2812 9.318041 CAAGTGTTTGATGTTTATTAGAACTCG 57.682 33.333 0.00 0.00 36.36 4.18
2545 2926 2.947652 CCAATCGAGCATTTCCATGAGT 59.052 45.455 0.00 0.00 31.07 3.41
2550 2931 0.034186 AGCCCAATCGAGCATTTCCA 60.034 50.000 0.00 0.00 0.00 3.53
2752 3134 1.002011 GGCCAAGGTGGGAGTTCTC 60.002 63.158 0.00 0.00 38.19 2.87
2800 3185 3.128349 TCAACGGAAGAAGTTACAGTGC 58.872 45.455 0.00 0.00 0.00 4.40
2823 3208 9.768662 ACTTACTAGTTAAAAGAAATCCACGAA 57.231 29.630 10.24 0.00 0.00 3.85
2824 3209 9.199982 CACTTACTAGTTAAAAGAAATCCACGA 57.800 33.333 10.24 0.00 30.26 4.35
2832 3217 6.757947 ACGTGCACACTTACTAGTTAAAAGAA 59.242 34.615 18.64 0.00 30.26 2.52
2834 3219 6.352526 CACGTGCACACTTACTAGTTAAAAG 58.647 40.000 18.64 1.00 30.26 2.27
2892 3277 2.151049 AACCGGTAGAGACGTGCCAC 62.151 60.000 8.00 0.00 0.00 5.01
2897 3282 0.964358 CCCTCAACCGGTAGAGACGT 60.964 60.000 8.00 0.00 33.74 4.34
2898 3283 1.807886 CCCTCAACCGGTAGAGACG 59.192 63.158 8.00 0.56 33.74 4.18
2899 3284 1.516423 GCCCTCAACCGGTAGAGAC 59.484 63.158 8.00 0.00 33.74 3.36
2900 3285 2.050350 CGCCCTCAACCGGTAGAGA 61.050 63.158 8.00 5.76 33.74 3.10
2901 3286 2.494918 CGCCCTCAACCGGTAGAG 59.505 66.667 8.00 0.41 0.00 2.43
2902 3287 3.766691 GCGCCCTCAACCGGTAGA 61.767 66.667 8.00 0.00 0.00 2.59
2934 3319 3.151710 CGGCCCCGATGTCCACTA 61.152 66.667 0.00 0.00 42.83 2.74
2951 3336 3.741476 CTTGCGCCCTCAACTGGC 61.741 66.667 4.18 0.00 45.70 4.85
2952 3337 3.058160 CCTTGCGCCCTCAACTGG 61.058 66.667 4.18 0.00 0.00 4.00
2953 3338 3.741476 GCCTTGCGCCCTCAACTG 61.741 66.667 4.18 0.00 0.00 3.16
2964 3349 1.069906 CACTAGTTCAACACGCCTTGC 60.070 52.381 0.00 0.00 0.00 4.01
2965 3350 1.531149 CCACTAGTTCAACACGCCTTG 59.469 52.381 0.00 0.00 0.00 3.61
2966 3351 1.414919 TCCACTAGTTCAACACGCCTT 59.585 47.619 0.00 0.00 0.00 4.35
2967 3352 1.045407 TCCACTAGTTCAACACGCCT 58.955 50.000 0.00 0.00 0.00 5.52
2968 3353 1.145803 GTCCACTAGTTCAACACGCC 58.854 55.000 0.00 0.00 0.00 5.68
2969 3354 1.860676 TGTCCACTAGTTCAACACGC 58.139 50.000 0.00 0.00 0.00 5.34
2970 3355 3.186409 CCAATGTCCACTAGTTCAACACG 59.814 47.826 0.00 0.00 0.00 4.49
2971 3356 3.502211 CCCAATGTCCACTAGTTCAACAC 59.498 47.826 0.00 0.00 0.00 3.32
2972 3357 3.497763 CCCCAATGTCCACTAGTTCAACA 60.498 47.826 0.00 0.00 0.00 3.33
2973 3358 3.081804 CCCCAATGTCCACTAGTTCAAC 58.918 50.000 0.00 0.00 0.00 3.18
2974 3359 2.554344 GCCCCAATGTCCACTAGTTCAA 60.554 50.000 0.00 0.00 0.00 2.69
2975 3360 1.004277 GCCCCAATGTCCACTAGTTCA 59.996 52.381 0.00 0.00 0.00 3.18
2976 3361 1.682087 GGCCCCAATGTCCACTAGTTC 60.682 57.143 0.00 0.00 0.00 3.01
2977 3362 0.331616 GGCCCCAATGTCCACTAGTT 59.668 55.000 0.00 0.00 0.00 2.24
2978 3363 1.910580 CGGCCCCAATGTCCACTAGT 61.911 60.000 0.00 0.00 0.00 2.57
2979 3364 1.153168 CGGCCCCAATGTCCACTAG 60.153 63.158 0.00 0.00 0.00 2.57
2980 3365 2.994699 CGGCCCCAATGTCCACTA 59.005 61.111 0.00 0.00 0.00 2.74
2981 3366 4.740822 GCGGCCCCAATGTCCACT 62.741 66.667 0.00 0.00 0.00 4.00
2985 3370 4.875713 ATCGGCGGCCCCAATGTC 62.876 66.667 14.55 0.00 0.00 3.06
2986 3371 4.440829 AATCGGCGGCCCCAATGT 62.441 61.111 14.55 0.00 0.00 2.71
2987 3372 3.903282 CAATCGGCGGCCCCAATG 61.903 66.667 14.55 3.90 0.00 2.82
2988 3373 4.122149 TCAATCGGCGGCCCCAAT 62.122 61.111 14.55 1.66 0.00 3.16
2989 3374 4.794648 CTCAATCGGCGGCCCCAA 62.795 66.667 14.55 0.00 0.00 4.12
2997 3382 3.880846 CTTGCGCCCTCAATCGGC 61.881 66.667 4.18 0.00 43.38 5.54
2998 3383 3.204827 CCTTGCGCCCTCAATCGG 61.205 66.667 4.18 0.00 0.00 4.18
2999 3384 3.880846 GCCTTGCGCCCTCAATCG 61.881 66.667 4.18 0.00 0.00 3.34
3010 3395 1.069906 CACTAGTTCAACACGCCTTGC 60.070 52.381 0.00 0.00 0.00 4.01
3011 3396 1.531149 CCACTAGTTCAACACGCCTTG 59.469 52.381 0.00 0.00 0.00 3.61
3012 3397 1.414919 TCCACTAGTTCAACACGCCTT 59.585 47.619 0.00 0.00 0.00 4.35
3013 3398 1.045407 TCCACTAGTTCAACACGCCT 58.955 50.000 0.00 0.00 0.00 5.52
3014 3399 1.145803 GTCCACTAGTTCAACACGCC 58.854 55.000 0.00 0.00 0.00 5.68
3015 3400 1.860676 TGTCCACTAGTTCAACACGC 58.139 50.000 0.00 0.00 0.00 5.34
3016 3401 2.661675 CGATGTCCACTAGTTCAACACG 59.338 50.000 0.00 2.01 0.00 4.49
3017 3402 2.993899 CCGATGTCCACTAGTTCAACAC 59.006 50.000 0.00 0.00 0.00 3.32
3018 3403 2.028476 CCCGATGTCCACTAGTTCAACA 60.028 50.000 0.00 0.00 0.00 3.33
3019 3404 2.618053 CCCGATGTCCACTAGTTCAAC 58.382 52.381 0.00 0.00 0.00 3.18
3020 3405 1.553248 CCCCGATGTCCACTAGTTCAA 59.447 52.381 0.00 0.00 0.00 2.69
3021 3406 1.191535 CCCCGATGTCCACTAGTTCA 58.808 55.000 0.00 0.00 0.00 3.18
3022 3407 0.179081 GCCCCGATGTCCACTAGTTC 60.179 60.000 0.00 0.00 0.00 3.01
3023 3408 1.623542 GGCCCCGATGTCCACTAGTT 61.624 60.000 0.00 0.00 0.00 2.24
3024 3409 2.064581 GGCCCCGATGTCCACTAGT 61.065 63.158 0.00 0.00 0.00 2.57
3025 3410 2.822399 GGCCCCGATGTCCACTAG 59.178 66.667 0.00 0.00 0.00 2.57
3026 3411 3.151710 CGGCCCCGATGTCCACTA 61.152 66.667 0.00 0.00 42.83 2.74
3043 3428 3.741476 CTTGCGCCCTCAACTGGC 61.741 66.667 4.18 0.00 45.70 4.85
3044 3429 3.058160 CCTTGCGCCCTCAACTGG 61.058 66.667 4.18 0.00 0.00 4.00
3045 3430 3.741476 GCCTTGCGCCCTCAACTG 61.741 66.667 4.18 0.00 0.00 3.16
3056 3441 1.194772 GTCTAGTTCAACACGCCTTGC 59.805 52.381 0.00 0.00 0.00 4.01
3057 3442 2.479837 TGTCTAGTTCAACACGCCTTG 58.520 47.619 0.00 0.00 0.00 3.61
3058 3443 2.902705 TGTCTAGTTCAACACGCCTT 57.097 45.000 0.00 0.00 0.00 4.35
3059 3444 3.067106 CAATGTCTAGTTCAACACGCCT 58.933 45.455 0.00 0.00 0.00 5.52
3060 3445 2.159627 CCAATGTCTAGTTCAACACGCC 59.840 50.000 0.00 0.00 0.00 5.68
3061 3446 2.159627 CCCAATGTCTAGTTCAACACGC 59.840 50.000 0.00 0.00 0.00 5.34
3062 3447 2.742053 CCCCAATGTCTAGTTCAACACG 59.258 50.000 0.00 0.00 0.00 4.49
3063 3448 2.488153 GCCCCAATGTCTAGTTCAACAC 59.512 50.000 0.00 0.00 0.00 3.32
3064 3449 2.554344 GGCCCCAATGTCTAGTTCAACA 60.554 50.000 0.00 0.00 0.00 3.33
3065 3450 2.092323 GGCCCCAATGTCTAGTTCAAC 58.908 52.381 0.00 0.00 0.00 3.18
3066 3451 1.339631 CGGCCCCAATGTCTAGTTCAA 60.340 52.381 0.00 0.00 0.00 2.69
3067 3452 0.251916 CGGCCCCAATGTCTAGTTCA 59.748 55.000 0.00 0.00 0.00 3.18
3068 3453 1.095807 GCGGCCCCAATGTCTAGTTC 61.096 60.000 0.00 0.00 0.00 3.01
3069 3454 1.077716 GCGGCCCCAATGTCTAGTT 60.078 57.895 0.00 0.00 0.00 2.24
3070 3455 2.590092 GCGGCCCCAATGTCTAGT 59.410 61.111 0.00 0.00 0.00 2.57
3071 3456 2.203209 GGCGGCCCCAATGTCTAG 60.203 66.667 8.12 0.00 0.00 2.43
3072 3457 4.169696 CGGCGGCCCCAATGTCTA 62.170 66.667 14.55 0.00 0.00 2.59
3074 3459 4.875713 ATCGGCGGCCCCAATGTC 62.876 66.667 14.55 0.00 0.00 3.06
3075 3460 4.440829 AATCGGCGGCCCCAATGT 62.441 61.111 14.55 0.00 0.00 2.71
3076 3461 3.903282 CAATCGGCGGCCCCAATG 61.903 66.667 14.55 3.90 0.00 2.82
3077 3462 4.122149 TCAATCGGCGGCCCCAAT 62.122 61.111 14.55 1.66 0.00 3.16
3078 3463 4.794648 CTCAATCGGCGGCCCCAA 62.795 66.667 14.55 0.00 0.00 4.12
3086 3471 3.880846 CTTGCGCCCTCAATCGGC 61.881 66.667 4.18 0.00 43.38 5.54
3087 3472 3.204827 CCTTGCGCCCTCAATCGG 61.205 66.667 4.18 0.00 0.00 4.18
3088 3473 3.880846 GCCTTGCGCCCTCAATCG 61.881 66.667 4.18 0.00 0.00 3.34
3099 3484 1.069906 CACTAGTTCAACACGCCTTGC 60.070 52.381 0.00 0.00 0.00 4.01
3100 3485 1.531149 CCACTAGTTCAACACGCCTTG 59.469 52.381 0.00 0.00 0.00 3.61
3101 3486 1.414919 TCCACTAGTTCAACACGCCTT 59.585 47.619 0.00 0.00 0.00 4.35
3102 3487 1.045407 TCCACTAGTTCAACACGCCT 58.955 50.000 0.00 0.00 0.00 5.52
3103 3488 1.145803 GTCCACTAGTTCAACACGCC 58.854 55.000 0.00 0.00 0.00 5.68
3104 3489 1.860676 TGTCCACTAGTTCAACACGC 58.139 50.000 0.00 0.00 0.00 5.34
3105 3490 2.661675 CGATGTCCACTAGTTCAACACG 59.338 50.000 0.00 2.01 0.00 4.49
3106 3491 2.993899 CCGATGTCCACTAGTTCAACAC 59.006 50.000 0.00 0.00 0.00 3.32
3107 3492 2.028476 CCCGATGTCCACTAGTTCAACA 60.028 50.000 0.00 0.00 0.00 3.33
3108 3493 2.618053 CCCGATGTCCACTAGTTCAAC 58.382 52.381 0.00 0.00 0.00 3.18
3109 3494 1.553248 CCCCGATGTCCACTAGTTCAA 59.447 52.381 0.00 0.00 0.00 2.69
3110 3495 1.191535 CCCCGATGTCCACTAGTTCA 58.808 55.000 0.00 0.00 0.00 3.18
3111 3496 0.179081 GCCCCGATGTCCACTAGTTC 60.179 60.000 0.00 0.00 0.00 3.01
3112 3497 1.905512 GCCCCGATGTCCACTAGTT 59.094 57.895 0.00 0.00 0.00 2.24
3113 3498 2.423898 CGCCCCGATGTCCACTAGT 61.424 63.158 0.00 0.00 0.00 2.57
3114 3499 2.417516 CGCCCCGATGTCCACTAG 59.582 66.667 0.00 0.00 0.00 2.57
3115 3500 3.151710 CCGCCCCGATGTCCACTA 61.152 66.667 0.00 0.00 0.00 2.74
3140 3525 4.722700 TGCAAAGCTCTCGGGGGC 62.723 66.667 0.00 0.00 0.00 5.80
3141 3526 2.034066 TTGCAAAGCTCTCGGGGG 59.966 61.111 0.00 0.00 0.00 5.40
3184 3569 2.157834 TGTAGTAGTTGCAACCCACG 57.842 50.000 25.62 0.00 0.00 4.94
3418 3813 3.414549 TTCAGACACGAAGCAAAAACC 57.585 42.857 0.00 0.00 0.00 3.27
3537 3932 2.103537 ATTTTCAAAGCAGGCATGGC 57.896 45.000 12.14 12.14 0.00 4.40


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

AutoCloner maintained by Alex Coulton.