Multiple sequence alignment - TraesCS4A01G314300

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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 TraesCS4A01G314300 chr4A 100.000 4190 0 0 1 4190 604771917 604776106 0.000000e+00 7738.0
1 TraesCS4A01G314300 chr4A 92.650 1347 94 5 2847 4190 604849257 604847913 0.000000e+00 1934.0
2 TraesCS4A01G314300 chr4A 83.303 1102 174 9 2847 3942 604390705 604389608 0.000000e+00 1007.0
3 TraesCS4A01G314300 chr4A 84.942 259 22 10 3948 4190 604839856 604839599 3.240000e-61 246.0
4 TraesCS4A01G314300 chr5D 92.565 1614 92 9 2579 4190 559917214 559918801 0.000000e+00 2290.0
5 TraesCS4A01G314300 chr5D 95.388 1431 53 4 608 2034 559915322 559916743 0.000000e+00 2265.0
6 TraesCS4A01G314300 chr5D 92.558 1478 92 6 2719 4190 559982588 559984053 0.000000e+00 2104.0
7 TraesCS4A01G314300 chr5D 84.853 1360 183 18 2790 4143 555915369 555914027 0.000000e+00 1349.0
8 TraesCS4A01G314300 chr5D 80.297 1345 213 41 608 1936 555917197 555915889 0.000000e+00 968.0
9 TraesCS4A01G314300 chr5D 96.646 477 13 2 2061 2534 559916736 559917212 0.000000e+00 789.0
10 TraesCS4A01G314300 chr5D 82.398 909 141 9 997 1889 559981532 559982437 0.000000e+00 774.0
11 TraesCS4A01G314300 chr5D 81.453 895 153 10 1010 1899 555456615 555455729 0.000000e+00 721.0
12 TraesCS4A01G314300 chr5D 87.943 282 24 2 4 275 559914604 559914885 1.450000e-84 324.0
13 TraesCS4A01G314300 chr5D 93.846 65 3 1 206 270 556112073 556112010 3.450000e-16 97.1
14 TraesCS4A01G314300 chr5B 89.360 1344 140 3 2847 4188 710344222 710345564 0.000000e+00 1687.0
15 TraesCS4A01G314300 chr5B 86.646 1273 155 8 608 1871 710342356 710343622 0.000000e+00 1395.0
16 TraesCS4A01G314300 chr5B 84.464 1371 190 18 2790 4154 695776905 695778258 0.000000e+00 1330.0
17 TraesCS4A01G314300 chr5B 83.859 1363 195 19 2790 4143 695423699 695425045 0.000000e+00 1275.0
18 TraesCS4A01G314300 chr5B 79.227 1372 222 48 602 1953 695421994 695423322 0.000000e+00 896.0
19 TraesCS4A01G314300 chr5B 78.577 1307 260 20 2847 4140 695963005 695964304 0.000000e+00 845.0
20 TraesCS4A01G314300 chr5B 79.079 1238 217 35 726 1947 695775187 695776398 0.000000e+00 813.0
21 TraesCS4A01G314300 chr5B 83.452 840 131 7 991 1825 695967525 695968361 0.000000e+00 774.0
22 TraesCS4A01G314300 chr5B 80.756 899 152 14 1007 1895 695947512 695948399 0.000000e+00 682.0
23 TraesCS4A01G314300 chr5B 81.590 717 97 20 839 1542 695547984 695548678 1.020000e-155 560.0
24 TraesCS4A01G314300 chr5B 89.007 282 21 2 4 275 710341212 710341493 1.440000e-89 340.0
25 TraesCS4A01G314300 chr5B 81.657 169 12 11 737 904 696352195 696352045 5.690000e-24 122.0
26 TraesCS4A01G314300 chr5B 93.846 65 3 1 206 270 695421711 695421774 3.450000e-16 97.1
27 TraesCS4A01G314300 chr5B 93.846 65 3 1 206 270 695774813 695774876 3.450000e-16 97.1
28 TraesCS4A01G314300 chr1B 78.765 810 160 10 1025 1828 25821637 25820834 2.220000e-147 532.0


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 TraesCS4A01G314300 chr4A 604771917 604776106 4189 False 7738.000000 7738 100.000000 1 4190 1 chr4A.!!$F1 4189
1 TraesCS4A01G314300 chr4A 604847913 604849257 1344 True 1934.000000 1934 92.650000 2847 4190 1 chr4A.!!$R3 1343
2 TraesCS4A01G314300 chr4A 604389608 604390705 1097 True 1007.000000 1007 83.303000 2847 3942 1 chr4A.!!$R1 1095
3 TraesCS4A01G314300 chr5D 559981532 559984053 2521 False 1439.000000 2104 87.478000 997 4190 2 chr5D.!!$F2 3193
4 TraesCS4A01G314300 chr5D 559914604 559918801 4197 False 1417.000000 2290 93.135500 4 4190 4 chr5D.!!$F1 4186
5 TraesCS4A01G314300 chr5D 555914027 555917197 3170 True 1158.500000 1349 82.575000 608 4143 2 chr5D.!!$R3 3535
6 TraesCS4A01G314300 chr5D 555455729 555456615 886 True 721.000000 721 81.453000 1010 1899 1 chr5D.!!$R1 889
7 TraesCS4A01G314300 chr5B 710341212 710345564 4352 False 1140.666667 1687 88.337667 4 4188 3 chr5B.!!$F6 4184
8 TraesCS4A01G314300 chr5B 695963005 695968361 5356 False 809.500000 845 81.014500 991 4140 2 chr5B.!!$F5 3149
9 TraesCS4A01G314300 chr5B 695421711 695425045 3334 False 756.033333 1275 85.644000 206 4143 3 chr5B.!!$F3 3937
10 TraesCS4A01G314300 chr5B 695774813 695778258 3445 False 746.700000 1330 85.796333 206 4154 3 chr5B.!!$F4 3948
11 TraesCS4A01G314300 chr5B 695947512 695948399 887 False 682.000000 682 80.756000 1007 1895 1 chr5B.!!$F2 888
12 TraesCS4A01G314300 chr5B 695547984 695548678 694 False 560.000000 560 81.590000 839 1542 1 chr5B.!!$F1 703
13 TraesCS4A01G314300 chr1B 25820834 25821637 803 True 532.000000 532 78.765000 1025 1828 1 chr1B.!!$R1 803

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
285 300 0.107945 GTTACTGCTCTCCCTGCTGG 60.108 60.000 1.89 1.89 34.40 4.85 F
458 931 0.108186 TCCTCTTGGTATGCAGTGCG 60.108 55.000 11.20 0.00 34.23 5.34 F
486 959 0.178767 CAACAGAGGGCATCGATGGA 59.821 55.000 26.00 0.00 0.00 3.41 F
513 988 1.065401 CAGTGAGCCACGCTTTTCAAA 59.935 47.619 0.00 0.00 39.88 2.69 F
519 994 1.455408 GCCACGCTTTTCAAAAATCGG 59.545 47.619 13.83 5.27 40.58 4.18 F
749 1353 2.082629 TTTCGCCTGACACGAGCTGA 62.083 55.000 0.00 0.00 41.18 4.26 F
2295 2962 2.379972 TCCTGACTCCAGCTAGCTTAC 58.620 52.381 16.46 5.54 39.07 2.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1590 2234 0.540830 TTCCCAATCCACCAAACCCG 60.541 55.000 0.00 0.00 0.00 5.28 R
2266 2933 1.815003 CTGGAGTCAGGATTGGTTTGC 59.185 52.381 0.00 0.00 37.36 3.68 R
2278 2945 3.634448 GAGATGTAAGCTAGCTGGAGTCA 59.366 47.826 20.16 13.11 22.26 3.41 R
2386 3053 5.972107 ACTTGATTCTCACAGGGAATTTG 57.028 39.130 0.00 0.00 34.09 2.32 R
2526 3193 6.875948 TTGCATATGATTTAGGTACGCAAT 57.124 33.333 6.97 0.00 32.36 3.56 R
2545 3212 2.964464 ACCATGAAACTCCAACATTGCA 59.036 40.909 0.00 0.00 0.00 4.08 R
3527 4334 0.035317 TATCATGGACTCGGCATGCC 59.965 55.000 27.67 27.67 0.00 4.40 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 6.151144 TCCTTTTCTGAAATAGTAAAGCAGCC 59.849 38.462 3.31 0.00 40.47 4.85
36 37 6.071952 CCTTTTCTGAAATAGTAAAGCAGCCA 60.072 38.462 3.31 0.00 40.47 4.75
39 40 8.752005 TTTCTGAAATAGTAAAGCAGCCATAT 57.248 30.769 0.00 0.00 0.00 1.78
80 90 3.932710 TCGCACTATGTCCAAGTTTGATC 59.067 43.478 0.00 0.00 0.00 2.92
104 114 7.168219 TCCATGGATGTAATACTCCTATTTGC 58.832 38.462 11.44 0.00 32.47 3.68
117 127 0.885196 TATTTGCCCACCGTTTCAGC 59.115 50.000 0.00 0.00 0.00 4.26
128 138 2.304761 ACCGTTTCAGCCTTAAGATGGA 59.695 45.455 3.36 0.00 0.00 3.41
175 186 8.737168 TTAACCTGAATAAGTTCTGATGGATG 57.263 34.615 0.00 0.00 35.89 3.51
177 188 7.437713 ACCTGAATAAGTTCTGATGGATGTA 57.562 36.000 0.00 0.00 35.89 2.29
217 228 0.968405 TGGCAACATTTCCAGGCTTC 59.032 50.000 0.00 0.00 46.17 3.86
258 269 5.048013 GGCAAGATGCTTGGTTTTACTAACT 60.048 40.000 9.01 0.00 44.28 2.24
277 292 8.934507 ACTAACTTGAATATGTTACTGCTCTC 57.065 34.615 0.00 0.00 0.00 3.20
278 293 7.982354 ACTAACTTGAATATGTTACTGCTCTCC 59.018 37.037 0.00 0.00 0.00 3.71
279 294 5.675538 ACTTGAATATGTTACTGCTCTCCC 58.324 41.667 0.00 0.00 0.00 4.30
280 295 5.426833 ACTTGAATATGTTACTGCTCTCCCT 59.573 40.000 0.00 0.00 0.00 4.20
281 296 5.282055 TGAATATGTTACTGCTCTCCCTG 57.718 43.478 0.00 0.00 0.00 4.45
282 297 3.760580 ATATGTTACTGCTCTCCCTGC 57.239 47.619 0.00 0.00 0.00 4.85
283 298 1.577736 ATGTTACTGCTCTCCCTGCT 58.422 50.000 0.00 0.00 0.00 4.24
284 299 0.610174 TGTTACTGCTCTCCCTGCTG 59.390 55.000 0.00 0.00 35.85 4.41
285 300 0.107945 GTTACTGCTCTCCCTGCTGG 60.108 60.000 1.89 1.89 34.40 4.85
286 301 0.252239 TTACTGCTCTCCCTGCTGGA 60.252 55.000 11.88 3.09 42.41 3.86
287 302 0.252239 TACTGCTCTCCCTGCTGGAA 60.252 55.000 11.88 0.00 44.57 3.53
288 303 0.913451 ACTGCTCTCCCTGCTGGAAT 60.913 55.000 11.88 0.00 44.57 3.01
289 304 0.179051 CTGCTCTCCCTGCTGGAATC 60.179 60.000 11.88 0.00 44.57 2.52
290 305 1.148048 GCTCTCCCTGCTGGAATCC 59.852 63.158 11.88 0.00 44.57 3.01
291 306 1.445095 CTCTCCCTGCTGGAATCCG 59.555 63.158 11.88 0.00 44.57 4.18
296 740 1.144936 CCTGCTGGAATCCGAGGTC 59.855 63.158 2.92 0.00 34.57 3.85
297 741 1.333636 CCTGCTGGAATCCGAGGTCT 61.334 60.000 2.92 0.00 34.57 3.85
308 752 1.134367 TCCGAGGTCTGAAAGCATACG 59.866 52.381 0.00 0.00 0.00 3.06
312 756 4.171005 CGAGGTCTGAAAGCATACGTTAA 58.829 43.478 0.00 0.00 0.00 2.01
316 760 7.448748 AGGTCTGAAAGCATACGTTAATTTT 57.551 32.000 0.00 0.00 0.00 1.82
318 762 9.005777 AGGTCTGAAAGCATACGTTAATTTTAA 57.994 29.630 0.00 0.00 0.00 1.52
319 763 9.058424 GGTCTGAAAGCATACGTTAATTTTAAC 57.942 33.333 0.00 3.59 39.62 2.01
354 798 4.460034 ACTTGATGCACATGCTAATTCACA 59.540 37.500 5.31 0.00 42.66 3.58
374 818 6.949715 TCACAACTCCCCGTAAGTAAAATAT 58.050 36.000 0.00 0.00 0.00 1.28
375 819 7.396418 TCACAACTCCCCGTAAGTAAAATATT 58.604 34.615 0.00 0.00 0.00 1.28
380 824 9.551734 AACTCCCCGTAAGTAAAATATTATCAC 57.448 33.333 0.00 0.00 0.00 3.06
393 837 8.902540 AAAATATTATCACTGAGCCATCGTTA 57.097 30.769 0.00 0.00 0.00 3.18
398 842 1.204704 CACTGAGCCATCGTTAGGTGA 59.795 52.381 0.00 0.00 0.00 4.02
421 865 5.059404 GCTAACCAAAGCTTGCAATTAGA 57.941 39.130 14.80 0.00 39.50 2.10
422 866 5.098211 GCTAACCAAAGCTTGCAATTAGAG 58.902 41.667 14.80 0.00 39.50 2.43
423 867 5.335976 GCTAACCAAAGCTTGCAATTAGAGT 60.336 40.000 14.80 1.31 39.50 3.24
424 868 6.128007 GCTAACCAAAGCTTGCAATTAGAGTA 60.128 38.462 14.80 0.00 39.50 2.59
426 870 4.156739 ACCAAAGCTTGCAATTAGAGTAGC 59.843 41.667 0.00 0.00 0.00 3.58
427 871 4.397417 CCAAAGCTTGCAATTAGAGTAGCT 59.603 41.667 0.00 0.00 40.43 3.32
428 872 5.330295 CAAAGCTTGCAATTAGAGTAGCTG 58.670 41.667 0.00 0.00 38.82 4.24
446 919 1.686052 CTGGCTAGCTAGGTCCTCTTG 59.314 57.143 22.10 4.88 0.00 3.02
447 920 1.044611 GGCTAGCTAGGTCCTCTTGG 58.955 60.000 22.10 0.00 0.00 3.61
449 922 2.424523 GGCTAGCTAGGTCCTCTTGGTA 60.425 54.545 22.10 0.00 31.88 3.25
450 923 3.502356 GCTAGCTAGGTCCTCTTGGTAT 58.498 50.000 22.10 0.00 32.57 2.73
451 924 3.257127 GCTAGCTAGGTCCTCTTGGTATG 59.743 52.174 22.10 0.00 32.57 2.39
452 925 2.043227 AGCTAGGTCCTCTTGGTATGC 58.957 52.381 0.00 0.00 34.23 3.14
453 926 1.762957 GCTAGGTCCTCTTGGTATGCA 59.237 52.381 0.00 0.00 34.23 3.96
454 927 2.224161 GCTAGGTCCTCTTGGTATGCAG 60.224 54.545 0.00 0.00 34.23 4.41
455 928 1.958288 AGGTCCTCTTGGTATGCAGT 58.042 50.000 0.00 0.00 34.23 4.40
456 929 1.556911 AGGTCCTCTTGGTATGCAGTG 59.443 52.381 0.00 0.00 34.23 3.66
457 930 1.373570 GTCCTCTTGGTATGCAGTGC 58.626 55.000 8.58 8.58 34.23 4.40
458 931 0.108186 TCCTCTTGGTATGCAGTGCG 60.108 55.000 11.20 0.00 34.23 5.34
460 933 1.078497 TCTTGGTATGCAGTGCGGG 60.078 57.895 11.20 0.00 0.00 6.13
461 934 2.045438 TTGGTATGCAGTGCGGGG 60.045 61.111 11.20 0.00 0.00 5.73
462 935 2.535485 CTTGGTATGCAGTGCGGGGA 62.535 60.000 11.20 0.00 0.00 4.81
464 937 2.267642 GTATGCAGTGCGGGGACA 59.732 61.111 11.20 0.00 0.00 4.02
465 938 1.815421 GTATGCAGTGCGGGGACAG 60.815 63.158 11.20 0.00 0.00 3.51
469 942 4.641645 CAGTGCGGGGACAGCCAA 62.642 66.667 0.00 0.00 35.15 4.52
470 943 4.643387 AGTGCGGGGACAGCCAAC 62.643 66.667 0.00 0.00 35.15 3.77
472 945 4.641645 TGCGGGGACAGCCAACAG 62.642 66.667 0.00 0.00 35.15 3.16
474 947 2.046892 CGGGGACAGCCAACAGAG 60.047 66.667 0.00 0.00 35.15 3.35
476 949 2.352805 GGGACAGCCAACAGAGGG 59.647 66.667 0.00 0.00 35.15 4.30
484 957 2.699073 CCAACAGAGGGCATCGATG 58.301 57.895 21.27 21.27 0.00 3.84
486 959 0.178767 CAACAGAGGGCATCGATGGA 59.821 55.000 26.00 0.00 0.00 3.41
487 960 1.135094 AACAGAGGGCATCGATGGAT 58.865 50.000 26.00 0.96 0.00 3.41
495 968 1.303074 CATCGATGGATGGGGGCAG 60.303 63.158 17.96 0.00 45.15 4.85
496 969 1.771746 ATCGATGGATGGGGGCAGT 60.772 57.895 0.00 0.00 0.00 4.40
497 970 2.060567 ATCGATGGATGGGGGCAGTG 62.061 60.000 0.00 0.00 0.00 3.66
498 971 2.745308 CGATGGATGGGGGCAGTGA 61.745 63.158 0.00 0.00 0.00 3.41
499 972 1.150081 GATGGATGGGGGCAGTGAG 59.850 63.158 0.00 0.00 0.00 3.51
500 973 2.972892 GATGGATGGGGGCAGTGAGC 62.973 65.000 0.00 0.00 44.65 4.26
513 988 1.065401 CAGTGAGCCACGCTTTTCAAA 59.935 47.619 0.00 0.00 39.88 2.69
517 992 3.182372 GTGAGCCACGCTTTTCAAAAATC 59.818 43.478 0.00 0.00 39.88 2.17
519 994 1.455408 GCCACGCTTTTCAAAAATCGG 59.545 47.619 13.83 5.27 40.58 4.18
529 1004 7.114247 CGCTTTTCAAAAATCGGAACTTCATAA 59.886 33.333 4.10 0.00 34.84 1.90
538 1013 8.466086 AAATCGGAACTTCATAATTTTTCTGC 57.534 30.769 0.00 0.00 0.00 4.26
539 1014 5.627172 TCGGAACTTCATAATTTTTCTGCG 58.373 37.500 0.00 0.00 0.00 5.18
541 1016 5.102313 GGAACTTCATAATTTTTCTGCGGG 58.898 41.667 0.00 0.00 0.00 6.13
545 1020 6.935167 ACTTCATAATTTTTCTGCGGGAAAT 58.065 32.000 0.00 1.13 42.63 2.17
546 1021 7.035612 ACTTCATAATTTTTCTGCGGGAAATC 58.964 34.615 0.00 0.00 42.63 2.17
549 1024 8.463930 TCATAATTTTTCTGCGGGAAATCTAT 57.536 30.769 0.00 0.00 42.63 1.98
550 1025 8.567948 TCATAATTTTTCTGCGGGAAATCTATC 58.432 33.333 0.00 0.00 42.63 2.08
551 1026 8.571336 CATAATTTTTCTGCGGGAAATCTATCT 58.429 33.333 0.00 0.00 42.63 1.98
552 1027 5.818136 TTTTTCTGCGGGAAATCTATCTG 57.182 39.130 0.00 0.00 42.63 2.90
553 1028 3.475566 TTCTGCGGGAAATCTATCTGG 57.524 47.619 0.00 0.00 0.00 3.86
555 1030 2.630098 TCTGCGGGAAATCTATCTGGAG 59.370 50.000 0.00 0.00 0.00 3.86
556 1031 2.366916 CTGCGGGAAATCTATCTGGAGT 59.633 50.000 0.00 0.00 0.00 3.85
557 1032 2.103094 TGCGGGAAATCTATCTGGAGTG 59.897 50.000 0.00 0.00 0.00 3.51
558 1033 2.760374 CGGGAAATCTATCTGGAGTGC 58.240 52.381 0.00 0.00 0.00 4.40
560 1035 3.737850 GGGAAATCTATCTGGAGTGCTG 58.262 50.000 0.00 0.00 0.00 4.41
561 1036 3.389329 GGGAAATCTATCTGGAGTGCTGA 59.611 47.826 0.00 0.00 0.00 4.26
562 1037 4.141620 GGGAAATCTATCTGGAGTGCTGAA 60.142 45.833 0.00 0.00 0.00 3.02
563 1038 5.431765 GGAAATCTATCTGGAGTGCTGAAA 58.568 41.667 0.00 0.00 0.00 2.69
564 1039 5.882557 GGAAATCTATCTGGAGTGCTGAAAA 59.117 40.000 0.00 0.00 0.00 2.29
565 1040 6.375455 GGAAATCTATCTGGAGTGCTGAAAAA 59.625 38.462 0.00 0.00 0.00 1.94
567 1042 6.939132 ATCTATCTGGAGTGCTGAAAAATG 57.061 37.500 0.00 0.00 0.00 2.32
570 1045 2.555325 TCTGGAGTGCTGAAAAATGCTG 59.445 45.455 0.00 0.00 0.00 4.41
573 1157 2.325761 GAGTGCTGAAAAATGCTGCAG 58.674 47.619 10.11 10.11 40.17 4.41
578 1162 3.125316 GCTGAAAAATGCTGCAGTTTGA 58.875 40.909 25.98 15.70 32.02 2.69
581 1165 4.757594 TGAAAAATGCTGCAGTTTGAACT 58.242 34.783 25.98 12.34 40.60 3.01
627 1225 3.131223 TGGAGTAGTTCTAGTGATGCTGC 59.869 47.826 0.00 0.00 0.00 5.25
637 1239 2.693069 AGTGATGCTGCTGTACAAGTC 58.307 47.619 0.00 0.00 0.00 3.01
700 1304 3.001127 TGGTTCTGTTAACGTGCGTAAAC 59.999 43.478 0.26 0.00 0.00 2.01
749 1353 2.082629 TTTCGCCTGACACGAGCTGA 62.083 55.000 0.00 0.00 41.18 4.26
840 1444 3.342377 TCATGTGCCTTCCATCGTTAA 57.658 42.857 0.00 0.00 0.00 2.01
891 1507 5.255687 TGCTCATCTTCATTTTCCTGCTAA 58.744 37.500 0.00 0.00 0.00 3.09
921 1537 3.960102 CCCTTGTCTGAGCTATTCTCTCT 59.040 47.826 0.00 0.00 42.38 3.10
935 1551 6.351456 GCTATTCTCTCTACCACTCCAAAGTT 60.351 42.308 0.00 0.00 31.71 2.66
966 1586 2.958355 CCAACAACACCCACAAGAGATT 59.042 45.455 0.00 0.00 0.00 2.40
967 1587 3.243501 CCAACAACACCCACAAGAGATTG 60.244 47.826 0.00 0.00 0.00 2.67
968 1588 3.576078 ACAACACCCACAAGAGATTGA 57.424 42.857 0.00 0.00 0.00 2.57
969 1589 3.214328 ACAACACCCACAAGAGATTGAC 58.786 45.455 0.00 0.00 0.00 3.18
1072 1704 4.680237 CCACCTTGCTCGCCGACA 62.680 66.667 0.00 0.00 0.00 4.35
1175 1807 3.507411 AGTACACCAAGCTAGAAGACCA 58.493 45.455 0.00 0.00 0.00 4.02
1542 2180 4.657504 AGAGATGATCTTGCCAAGTGGATA 59.342 41.667 4.04 0.00 32.99 2.59
1590 2234 4.448732 GGATGCAAGGTTTTGTCAATTGTC 59.551 41.667 5.13 0.00 36.65 3.18
1656 2300 4.701956 TCGCAAGATTGAAGGGAATTTC 57.298 40.909 0.00 0.00 45.01 2.17
2255 2922 5.918608 ACTAGTTACTACATGCAATCCCAG 58.081 41.667 0.00 0.00 0.00 4.45
2278 2945 2.917713 TATGGGTGCAAACCAATCCT 57.082 45.000 14.64 2.23 42.17 3.24
2295 2962 2.379972 TCCTGACTCCAGCTAGCTTAC 58.620 52.381 16.46 5.54 39.07 2.34
2535 3202 7.068692 ACACTTAATTAAGTCATTGCGTACC 57.931 36.000 24.77 0.00 44.19 3.34
2536 3203 6.877322 ACACTTAATTAAGTCATTGCGTACCT 59.123 34.615 24.77 0.00 44.19 3.08
2537 3204 8.036575 ACACTTAATTAAGTCATTGCGTACCTA 58.963 33.333 24.77 0.00 44.19 3.08
2538 3205 8.875803 CACTTAATTAAGTCATTGCGTACCTAA 58.124 33.333 24.77 0.00 44.19 2.69
2539 3206 9.439500 ACTTAATTAAGTCATTGCGTACCTAAA 57.561 29.630 22.49 0.00 42.52 1.85
2542 3209 8.500753 AATTAAGTCATTGCGTACCTAAATCA 57.499 30.769 0.00 0.00 0.00 2.57
2543 3210 8.677148 ATTAAGTCATTGCGTACCTAAATCAT 57.323 30.769 0.00 0.00 0.00 2.45
2544 3211 9.772973 ATTAAGTCATTGCGTACCTAAATCATA 57.227 29.630 0.00 0.00 0.00 2.15
2545 3212 9.772973 TTAAGTCATTGCGTACCTAAATCATAT 57.227 29.630 0.00 0.00 0.00 1.78
2546 3213 7.658179 AGTCATTGCGTACCTAAATCATATG 57.342 36.000 0.00 0.00 0.00 1.78
2547 3214 6.147821 AGTCATTGCGTACCTAAATCATATGC 59.852 38.462 0.00 0.00 0.00 3.14
2548 3215 5.994668 TCATTGCGTACCTAAATCATATGCA 59.005 36.000 0.00 0.00 38.69 3.96
2550 3217 6.875948 TTGCGTACCTAAATCATATGCAAT 57.124 33.333 6.12 0.00 42.82 3.56
2551 3218 6.239908 TGCGTACCTAAATCATATGCAATG 57.760 37.500 0.00 0.00 37.77 2.82
2552 3219 5.762711 TGCGTACCTAAATCATATGCAATGT 59.237 36.000 0.00 0.00 37.77 2.71
2553 3220 6.262049 TGCGTACCTAAATCATATGCAATGTT 59.738 34.615 0.00 0.00 37.77 2.71
2554 3221 6.578545 GCGTACCTAAATCATATGCAATGTTG 59.421 38.462 0.00 0.00 32.22 3.33
2555 3222 7.077605 CGTACCTAAATCATATGCAATGTTGG 58.922 38.462 0.00 0.00 0.00 3.77
2556 3223 7.041440 CGTACCTAAATCATATGCAATGTTGGA 60.041 37.037 0.00 0.00 0.00 3.53
2557 3224 7.281040 ACCTAAATCATATGCAATGTTGGAG 57.719 36.000 0.00 0.00 30.13 3.86
2558 3225 6.835488 ACCTAAATCATATGCAATGTTGGAGT 59.165 34.615 0.00 0.00 30.13 3.85
2559 3226 7.342799 ACCTAAATCATATGCAATGTTGGAGTT 59.657 33.333 0.00 0.00 30.13 3.01
2560 3227 8.199449 CCTAAATCATATGCAATGTTGGAGTTT 58.801 33.333 0.00 0.00 30.13 2.66
2561 3228 9.241317 CTAAATCATATGCAATGTTGGAGTTTC 57.759 33.333 0.00 0.00 30.13 2.78
2562 3229 6.778834 ATCATATGCAATGTTGGAGTTTCA 57.221 33.333 0.00 0.00 30.13 2.69
2563 3230 6.778834 TCATATGCAATGTTGGAGTTTCAT 57.221 33.333 0.00 0.00 30.13 2.57
2564 3231 6.566141 TCATATGCAATGTTGGAGTTTCATG 58.434 36.000 0.00 0.00 30.13 3.07
2565 3232 3.663995 TGCAATGTTGGAGTTTCATGG 57.336 42.857 0.00 0.00 0.00 3.66
2566 3233 2.964464 TGCAATGTTGGAGTTTCATGGT 59.036 40.909 0.00 0.00 0.00 3.55
2567 3234 4.148079 TGCAATGTTGGAGTTTCATGGTA 58.852 39.130 0.00 0.00 0.00 3.25
2568 3235 4.771577 TGCAATGTTGGAGTTTCATGGTAT 59.228 37.500 0.00 0.00 0.00 2.73
2569 3236 5.948758 TGCAATGTTGGAGTTTCATGGTATA 59.051 36.000 0.00 0.00 0.00 1.47
2570 3237 6.435591 TGCAATGTTGGAGTTTCATGGTATAA 59.564 34.615 0.00 0.00 0.00 0.98
2571 3238 6.974622 GCAATGTTGGAGTTTCATGGTATAAG 59.025 38.462 0.00 0.00 0.00 1.73
2572 3239 7.362920 GCAATGTTGGAGTTTCATGGTATAAGT 60.363 37.037 0.00 0.00 0.00 2.24
2573 3240 8.522830 CAATGTTGGAGTTTCATGGTATAAGTT 58.477 33.333 0.00 0.00 0.00 2.66
2574 3241 7.681939 TGTTGGAGTTTCATGGTATAAGTTC 57.318 36.000 0.00 0.00 0.00 3.01
2575 3242 7.227873 TGTTGGAGTTTCATGGTATAAGTTCA 58.772 34.615 0.00 0.00 0.00 3.18
2576 3243 7.888021 TGTTGGAGTTTCATGGTATAAGTTCAT 59.112 33.333 0.00 0.00 0.00 2.57
2577 3244 9.391006 GTTGGAGTTTCATGGTATAAGTTCATA 57.609 33.333 0.00 0.00 0.00 2.15
2905 3709 6.648879 TCATCGATGATGTATGGTCTACAA 57.351 37.500 23.99 0.00 40.55 2.41
3028 3832 2.758423 AGTGCTGATGACCGTGTGTATA 59.242 45.455 0.00 0.00 0.00 1.47
3314 4119 3.496130 CCCTTAGCTACAATGATCTTGCG 59.504 47.826 0.00 0.00 0.00 4.85
3366 4171 3.146847 AGTTTGTTTCCCGAAGACCATC 58.853 45.455 0.00 0.00 0.00 3.51
3527 4334 6.016777 GCATTAAGTATGATGGAAAGGTCCAG 60.017 42.308 1.42 0.00 44.75 3.86
3596 4403 7.573968 ATCAGCTGAAGATAATTTTACCACC 57.426 36.000 22.50 0.00 0.00 4.61
3749 4556 6.941436 TGATAGTAATGCCATCATGTTGCATA 59.059 34.615 15.89 5.22 44.49 3.14
3816 4623 4.766891 TGGATTTTGAAGGTTGTGAGGATC 59.233 41.667 0.00 0.00 0.00 3.36
3821 4628 8.655935 ATTTTGAAGGTTGTGAGGATCTAAAT 57.344 30.769 0.00 0.00 34.92 1.40
3833 4640 9.367160 TGTGAGGATCTAAATGACTGTGATATA 57.633 33.333 0.00 0.00 34.92 0.86
3858 4665 4.870636 AGGCATGGACAAATTATTCCAGA 58.129 39.130 12.30 0.00 45.20 3.86
3896 4703 8.220559 AGCTTTAGGGACACATGTATATCAAAT 58.779 33.333 0.00 0.00 0.00 2.32
3907 4714 6.150641 ACATGTATATCAAATCTGCCATCAGC 59.849 38.462 0.00 0.00 40.13 4.26
3916 4723 4.108902 GCCATCAGCGATCGTCAA 57.891 55.556 17.81 2.34 0.00 3.18
3942 4749 6.529829 GCTAAATAATCTAGAGACGCTGGATG 59.470 42.308 5.84 0.00 43.22 3.51
3961 4768 6.108687 TGGATGTTGAGAATACATCTGTGAC 58.891 40.000 13.70 0.87 47.00 3.67
3974 4781 0.533531 CTGTGACAGAGTTGCCTGCA 60.534 55.000 6.79 0.00 37.68 4.41
4002 4809 3.589061 CTCGGCTAACTACACTACGAG 57.411 52.381 0.00 0.00 40.00 4.18
4078 4888 7.145932 ACTTACAGTTGATGCCAAGATTTAC 57.854 36.000 0.00 0.00 32.06 2.01
4159 4969 4.202264 GGAACTCGATGTGGATCTTGGTAT 60.202 45.833 0.00 0.00 0.00 2.73
4168 4978 7.388776 CGATGTGGATCTTGGTATGAATGTATT 59.611 37.037 0.00 0.00 0.00 1.89
4173 4983 6.491403 GGATCTTGGTATGAATGTATTTGGCT 59.509 38.462 0.00 0.00 0.00 4.75
4174 4984 6.942532 TCTTGGTATGAATGTATTTGGCTC 57.057 37.500 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.745312 ATTTCAGAAAAGGATTGGGTTCC 57.255 39.130 0.00 0.00 35.90 3.62
4 5 8.950007 TTTACTATTTCAGAAAAGGATTGGGT 57.050 30.769 0.00 0.00 0.00 4.51
5 6 7.976175 GCTTTACTATTTCAGAAAAGGATTGGG 59.024 37.037 0.00 0.00 0.00 4.12
6 7 8.522830 TGCTTTACTATTTCAGAAAAGGATTGG 58.477 33.333 0.00 0.00 0.00 3.16
7 8 9.565213 CTGCTTTACTATTTCAGAAAAGGATTG 57.435 33.333 0.00 0.00 29.06 2.67
8 9 8.246871 GCTGCTTTACTATTTCAGAAAAGGATT 58.753 33.333 0.00 0.00 29.06 3.01
39 40 8.902540 AGTGCGAATTAATCAAGGACAATATA 57.097 30.769 10.36 0.00 0.00 0.86
80 90 6.375455 GGCAAATAGGAGTATTACATCCATGG 59.625 42.308 4.97 4.97 38.12 3.66
104 114 1.165270 CTTAAGGCTGAAACGGTGGG 58.835 55.000 0.00 0.00 0.00 4.61
117 127 2.691409 TCTTGCCGTCCATCTTAAGG 57.309 50.000 1.85 0.00 0.00 2.69
128 138 2.888834 AAAAACAAGCATCTTGCCGT 57.111 40.000 6.49 0.00 46.52 5.68
163 174 3.132289 TCCCGTTCTACATCCATCAGAAC 59.868 47.826 4.07 4.07 42.99 3.01
170 181 1.191535 CTGGTCCCGTTCTACATCCA 58.808 55.000 0.00 0.00 0.00 3.41
172 183 3.022406 ACTACTGGTCCCGTTCTACATC 58.978 50.000 0.00 0.00 0.00 3.06
175 186 4.460731 AGTTAACTACTGGTCCCGTTCTAC 59.539 45.833 6.26 0.00 35.19 2.59
177 188 3.504375 AGTTAACTACTGGTCCCGTTCT 58.496 45.455 6.26 0.00 35.19 3.01
202 213 2.693074 ACGTTTGAAGCCTGGAAATGTT 59.307 40.909 0.00 0.00 0.00 2.71
217 228 1.572447 CCGGCCACTTGTACGTTTG 59.428 57.895 2.24 0.00 0.00 2.93
258 269 5.674525 CAGGGAGAGCAGTAACATATTCAA 58.325 41.667 0.00 0.00 0.00 2.69
276 291 2.066393 CCTCGGATTCCAGCAGGGA 61.066 63.158 3.09 0.00 46.61 4.20
277 292 2.317149 GACCTCGGATTCCAGCAGGG 62.317 65.000 14.14 6.22 34.83 4.45
278 293 1.144936 GACCTCGGATTCCAGCAGG 59.855 63.158 3.09 7.10 0.00 4.85
279 294 0.179089 CAGACCTCGGATTCCAGCAG 60.179 60.000 3.09 0.00 0.00 4.24
280 295 0.614697 TCAGACCTCGGATTCCAGCA 60.615 55.000 3.09 0.00 0.00 4.41
281 296 0.537188 TTCAGACCTCGGATTCCAGC 59.463 55.000 3.09 0.00 0.00 4.85
282 297 2.898705 CTTTCAGACCTCGGATTCCAG 58.101 52.381 3.09 0.00 0.00 3.86
283 298 1.066143 GCTTTCAGACCTCGGATTCCA 60.066 52.381 3.09 0.00 0.00 3.53
284 299 1.066143 TGCTTTCAGACCTCGGATTCC 60.066 52.381 0.00 0.00 0.00 3.01
285 300 2.386661 TGCTTTCAGACCTCGGATTC 57.613 50.000 0.00 0.00 0.00 2.52
286 301 3.738281 CGTATGCTTTCAGACCTCGGATT 60.738 47.826 0.00 0.00 31.01 3.01
287 302 2.223829 CGTATGCTTTCAGACCTCGGAT 60.224 50.000 0.00 0.00 31.01 4.18
288 303 1.134367 CGTATGCTTTCAGACCTCGGA 59.866 52.381 0.00 0.00 31.01 4.55
289 304 1.135083 ACGTATGCTTTCAGACCTCGG 60.135 52.381 0.00 0.00 31.01 4.63
290 305 2.279582 ACGTATGCTTTCAGACCTCG 57.720 50.000 0.00 0.00 31.01 4.63
291 306 6.663944 AATTAACGTATGCTTTCAGACCTC 57.336 37.500 0.00 0.00 31.01 3.85
312 756 9.630098 CATCAAGTGTCAGCTAATTGTTAAAAT 57.370 29.630 0.00 0.00 0.00 1.82
316 760 5.704978 TGCATCAAGTGTCAGCTAATTGTTA 59.295 36.000 0.00 0.00 0.00 2.41
318 762 4.074259 TGCATCAAGTGTCAGCTAATTGT 58.926 39.130 0.00 0.00 0.00 2.71
319 763 4.083164 TGTGCATCAAGTGTCAGCTAATTG 60.083 41.667 0.00 0.00 0.00 2.32
323 767 2.837532 TGTGCATCAAGTGTCAGCTA 57.162 45.000 0.00 0.00 0.00 3.32
324 768 1.810755 CATGTGCATCAAGTGTCAGCT 59.189 47.619 0.00 0.00 0.00 4.24
326 770 1.810755 AGCATGTGCATCAAGTGTCAG 59.189 47.619 7.83 0.00 45.16 3.51
327 771 1.900245 AGCATGTGCATCAAGTGTCA 58.100 45.000 7.83 0.00 45.16 3.58
329 773 4.460034 TGAATTAGCATGTGCATCAAGTGT 59.540 37.500 7.83 0.00 45.16 3.55
330 774 4.796830 GTGAATTAGCATGTGCATCAAGTG 59.203 41.667 7.83 0.00 45.16 3.16
331 775 4.460034 TGTGAATTAGCATGTGCATCAAGT 59.540 37.500 7.83 0.00 45.16 3.16
335 779 4.990257 AGTTGTGAATTAGCATGTGCATC 58.010 39.130 7.83 1.19 45.16 3.91
354 798 9.551734 GTGATAATATTTTACTTACGGGGAGTT 57.448 33.333 0.00 0.00 0.00 3.01
374 818 3.704566 ACCTAACGATGGCTCAGTGATAA 59.295 43.478 0.00 0.00 0.00 1.75
375 819 3.068165 CACCTAACGATGGCTCAGTGATA 59.932 47.826 0.00 0.00 0.00 2.15
380 824 1.804372 GCTCACCTAACGATGGCTCAG 60.804 57.143 0.00 0.00 0.00 3.35
426 870 1.686052 CAAGAGGACCTAGCTAGCCAG 59.314 57.143 15.74 7.24 0.00 4.85
427 871 1.689575 CCAAGAGGACCTAGCTAGCCA 60.690 57.143 15.74 0.00 36.89 4.75
428 872 1.044611 CCAAGAGGACCTAGCTAGCC 58.955 60.000 15.74 11.93 36.89 3.93
446 919 2.513897 GTCCCCGCACTGCATACC 60.514 66.667 1.11 0.00 0.00 2.73
447 920 1.815421 CTGTCCCCGCACTGCATAC 60.815 63.158 1.11 0.00 0.00 2.39
452 925 4.641645 TTGGCTGTCCCCGCACTG 62.642 66.667 0.00 0.00 0.00 3.66
453 926 4.643387 GTTGGCTGTCCCCGCACT 62.643 66.667 0.00 0.00 0.00 4.40
454 927 4.947147 TGTTGGCTGTCCCCGCAC 62.947 66.667 0.00 0.00 0.00 5.34
455 928 4.641645 CTGTTGGCTGTCCCCGCA 62.642 66.667 0.00 0.00 0.00 5.69
456 929 4.329545 TCTGTTGGCTGTCCCCGC 62.330 66.667 0.00 0.00 0.00 6.13
457 930 2.046892 CTCTGTTGGCTGTCCCCG 60.047 66.667 0.00 0.00 0.00 5.73
458 931 2.352805 CCTCTGTTGGCTGTCCCC 59.647 66.667 0.00 0.00 0.00 4.81
460 933 2.360475 GCCCTCTGTTGGCTGTCC 60.360 66.667 0.00 0.00 45.70 4.02
468 941 1.135094 ATCCATCGATGCCCTCTGTT 58.865 50.000 20.25 0.00 0.00 3.16
469 942 0.395686 CATCCATCGATGCCCTCTGT 59.604 55.000 20.25 0.00 39.59 3.41
470 943 0.321387 CCATCCATCGATGCCCTCTG 60.321 60.000 20.25 10.94 44.00 3.35
472 945 1.002868 CCCATCCATCGATGCCCTC 60.003 63.158 20.25 0.00 44.00 4.30
474 947 2.034687 CCCCATCCATCGATGCCC 59.965 66.667 20.25 0.00 44.00 5.36
476 949 2.674380 GCCCCCATCCATCGATGC 60.674 66.667 20.25 1.89 44.00 3.91
477 950 1.303074 CTGCCCCCATCCATCGATG 60.303 63.158 18.76 18.76 44.80 3.84
478 951 1.771746 ACTGCCCCCATCCATCGAT 60.772 57.895 0.00 0.00 0.00 3.59
479 952 2.366837 ACTGCCCCCATCCATCGA 60.367 61.111 0.00 0.00 0.00 3.59
481 954 1.150081 CTCACTGCCCCCATCCATC 59.850 63.158 0.00 0.00 0.00 3.51
482 955 3.065787 GCTCACTGCCCCCATCCAT 62.066 63.158 0.00 0.00 35.15 3.41
483 956 3.731728 GCTCACTGCCCCCATCCA 61.732 66.667 0.00 0.00 35.15 3.41
492 965 1.081840 GAAAAGCGTGGCTCACTGC 60.082 57.895 11.25 11.25 38.25 4.40
493 966 0.662619 TTGAAAAGCGTGGCTCACTG 59.337 50.000 4.21 0.23 38.25 3.66
495 968 2.202295 TTTTGAAAAGCGTGGCTCAC 57.798 45.000 0.00 0.00 38.25 3.51
496 969 2.949451 TTTTTGAAAAGCGTGGCTCA 57.051 40.000 0.00 0.00 38.25 4.26
513 988 7.273381 CGCAGAAAAATTATGAAGTTCCGATTT 59.727 33.333 0.00 1.99 0.00 2.17
517 992 4.793216 CCGCAGAAAAATTATGAAGTTCCG 59.207 41.667 0.00 0.00 0.00 4.30
519 994 5.949735 TCCCGCAGAAAAATTATGAAGTTC 58.050 37.500 0.00 0.00 0.00 3.01
533 1008 3.038280 TCCAGATAGATTTCCCGCAGAA 58.962 45.455 0.00 0.00 0.00 3.02
535 1010 2.366916 ACTCCAGATAGATTTCCCGCAG 59.633 50.000 0.00 0.00 0.00 5.18
536 1011 2.103094 CACTCCAGATAGATTTCCCGCA 59.897 50.000 0.00 0.00 0.00 5.69
537 1012 2.760374 CACTCCAGATAGATTTCCCGC 58.240 52.381 0.00 0.00 0.00 6.13
538 1013 2.366916 AGCACTCCAGATAGATTTCCCG 59.633 50.000 0.00 0.00 0.00 5.14
539 1014 3.389329 TCAGCACTCCAGATAGATTTCCC 59.611 47.826 0.00 0.00 0.00 3.97
541 1016 6.992063 TTTTCAGCACTCCAGATAGATTTC 57.008 37.500 0.00 0.00 0.00 2.17
545 1020 4.637534 GCATTTTTCAGCACTCCAGATAGA 59.362 41.667 0.00 0.00 0.00 1.98
546 1021 4.639310 AGCATTTTTCAGCACTCCAGATAG 59.361 41.667 0.00 0.00 0.00 2.08
549 1024 2.555325 CAGCATTTTTCAGCACTCCAGA 59.445 45.455 0.00 0.00 0.00 3.86
550 1025 2.925306 GCAGCATTTTTCAGCACTCCAG 60.925 50.000 0.00 0.00 0.00 3.86
551 1026 1.000060 GCAGCATTTTTCAGCACTCCA 60.000 47.619 0.00 0.00 0.00 3.86
552 1027 1.000060 TGCAGCATTTTTCAGCACTCC 60.000 47.619 0.00 0.00 0.00 3.85
553 1028 2.288030 ACTGCAGCATTTTTCAGCACTC 60.288 45.455 15.27 0.00 0.00 3.51
555 1030 2.144482 ACTGCAGCATTTTTCAGCAC 57.856 45.000 15.27 0.00 0.00 4.40
556 1031 2.867368 CAAACTGCAGCATTTTTCAGCA 59.133 40.909 15.27 0.00 0.00 4.41
557 1032 3.125316 TCAAACTGCAGCATTTTTCAGC 58.875 40.909 15.27 0.00 0.00 4.26
558 1033 4.807304 AGTTCAAACTGCAGCATTTTTCAG 59.193 37.500 15.27 0.00 37.98 3.02
573 1157 7.435068 TTCTAGCAAAGGTATCAGTTCAAAC 57.565 36.000 0.00 0.00 0.00 2.93
593 1177 8.496088 ACTAGAACTACTCCAGCTAGATTTCTA 58.504 37.037 0.00 0.00 34.24 2.10
594 1178 7.284489 CACTAGAACTACTCCAGCTAGATTTCT 59.716 40.741 0.00 0.00 34.24 2.52
627 1225 1.455786 CTTGAACGGCGACTTGTACAG 59.544 52.381 16.62 0.00 0.00 2.74
637 1239 1.442520 CAATGCACCTTGAACGGCG 60.443 57.895 4.80 4.80 0.00 6.46
700 1304 0.319728 AGCCTCGGTATGCAGCATAG 59.680 55.000 15.81 5.64 0.00 2.23
749 1353 4.022416 TGTTTGGTGCAAGCGAATTAAGAT 60.022 37.500 0.00 0.00 40.30 2.40
840 1444 5.012239 TGAGATTTGTTTGGCTCAGCTAAT 58.988 37.500 0.00 0.00 32.85 1.73
891 1507 0.901124 CTCAGACAAGGGCAGCTAGT 59.099 55.000 0.00 0.00 0.00 2.57
900 1516 5.009610 GGTAGAGAGAATAGCTCAGACAAGG 59.990 48.000 0.00 0.00 46.45 3.61
921 1537 5.355910 GTGTCTTTTGAACTTTGGAGTGGTA 59.644 40.000 0.00 0.00 35.91 3.25
935 1551 2.494073 GGGTGTTGTTGGTGTCTTTTGA 59.506 45.455 0.00 0.00 0.00 2.69
966 1586 2.068519 CTTTGTATCTGCACTGCGTCA 58.931 47.619 0.00 0.00 0.00 4.35
967 1587 2.337583 TCTTTGTATCTGCACTGCGTC 58.662 47.619 0.00 0.00 0.00 5.19
968 1588 2.289072 ACTCTTTGTATCTGCACTGCGT 60.289 45.455 0.00 0.00 0.00 5.24
969 1589 2.341257 ACTCTTTGTATCTGCACTGCG 58.659 47.619 0.00 0.00 0.00 5.18
1072 1704 0.886490 CCTTTCAGCCGAGCACACTT 60.886 55.000 0.00 0.00 0.00 3.16
1175 1807 5.139727 TCCATGTCTTCACTTGGTCATTTT 58.860 37.500 6.87 0.00 44.71 1.82
1542 2180 6.418057 TTGGACAAGTTATTTGCTTCCAAT 57.582 33.333 7.94 0.00 42.47 3.16
1590 2234 0.540830 TTCCCAATCCACCAAACCCG 60.541 55.000 0.00 0.00 0.00 5.28
1656 2300 4.037923 ACTGACACAAAAGCCTTACAATGG 59.962 41.667 0.00 0.00 0.00 3.16
2255 2922 3.005791 GGATTGGTTTGCACCCATATAGC 59.994 47.826 5.17 0.00 43.49 2.97
2266 2933 1.815003 CTGGAGTCAGGATTGGTTTGC 59.185 52.381 0.00 0.00 37.36 3.68
2278 2945 3.634448 GAGATGTAAGCTAGCTGGAGTCA 59.366 47.826 20.16 13.11 22.26 3.41
2386 3053 5.972107 ACTTGATTCTCACAGGGAATTTG 57.028 39.130 0.00 0.00 34.09 2.32
2526 3193 6.875948 TTGCATATGATTTAGGTACGCAAT 57.124 33.333 6.97 0.00 32.36 3.56
2534 3201 7.281040 ACTCCAACATTGCATATGATTTAGG 57.719 36.000 6.97 0.00 0.00 2.69
2535 3202 9.241317 GAAACTCCAACATTGCATATGATTTAG 57.759 33.333 6.97 8.84 0.00 1.85
2536 3203 8.747471 TGAAACTCCAACATTGCATATGATTTA 58.253 29.630 6.97 0.00 0.00 1.40
2537 3204 7.613585 TGAAACTCCAACATTGCATATGATTT 58.386 30.769 6.97 6.10 0.00 2.17
2538 3205 7.172868 TGAAACTCCAACATTGCATATGATT 57.827 32.000 6.97 4.41 0.00 2.57
2539 3206 6.778834 TGAAACTCCAACATTGCATATGAT 57.221 33.333 6.97 2.03 0.00 2.45
2540 3207 6.406065 CCATGAAACTCCAACATTGCATATGA 60.406 38.462 6.97 0.00 0.00 2.15
2541 3208 5.751509 CCATGAAACTCCAACATTGCATATG 59.248 40.000 0.00 0.00 0.00 1.78
2542 3209 5.422970 ACCATGAAACTCCAACATTGCATAT 59.577 36.000 0.00 0.00 0.00 1.78
2543 3210 4.771577 ACCATGAAACTCCAACATTGCATA 59.228 37.500 0.00 0.00 0.00 3.14
2544 3211 3.579586 ACCATGAAACTCCAACATTGCAT 59.420 39.130 0.00 0.00 0.00 3.96
2545 3212 2.964464 ACCATGAAACTCCAACATTGCA 59.036 40.909 0.00 0.00 0.00 4.08
2546 3213 3.665745 ACCATGAAACTCCAACATTGC 57.334 42.857 0.00 0.00 0.00 3.56
2547 3214 8.055279 ACTTATACCATGAAACTCCAACATTG 57.945 34.615 0.00 0.00 0.00 2.82
2548 3215 8.650143 AACTTATACCATGAAACTCCAACATT 57.350 30.769 0.00 0.00 0.00 2.71
2549 3216 7.888021 TGAACTTATACCATGAAACTCCAACAT 59.112 33.333 0.00 0.00 0.00 2.71
2550 3217 7.227873 TGAACTTATACCATGAAACTCCAACA 58.772 34.615 0.00 0.00 0.00 3.33
2551 3218 7.681939 TGAACTTATACCATGAAACTCCAAC 57.318 36.000 0.00 0.00 0.00 3.77
2552 3219 9.391006 GTATGAACTTATACCATGAAACTCCAA 57.609 33.333 0.00 0.00 0.00 3.53
2553 3220 8.768397 AGTATGAACTTATACCATGAAACTCCA 58.232 33.333 0.00 0.00 34.75 3.86
2554 3221 9.614792 AAGTATGAACTTATACCATGAAACTCC 57.385 33.333 0.00 0.00 44.26 3.85
2723 3456 6.725246 ACGCTTATTGCTTATGTTTCCATAC 58.275 36.000 0.00 0.00 40.11 2.39
2905 3709 1.402968 CTTGATAGCGTGCCATGCTTT 59.597 47.619 17.89 9.37 41.42 3.51
3028 3832 5.654209 GGAGATCACTTAGGGCTTTCAATTT 59.346 40.000 0.00 0.00 0.00 1.82
3314 4119 2.399916 AGCAAGTCTTGAGATGAGGC 57.600 50.000 16.99 0.00 0.00 4.70
3366 4171 7.309133 CCTCACTAGCCTATCTCTGTAAATCAG 60.309 44.444 0.00 0.00 44.85 2.90
3527 4334 0.035317 TATCATGGACTCGGCATGCC 59.965 55.000 27.67 27.67 0.00 4.40
3596 4403 2.718747 TTTGACCGCCACCTACCACG 62.719 60.000 0.00 0.00 0.00 4.94
3749 4556 2.733956 TCAAGACTGGGCAAGTGTTTT 58.266 42.857 0.00 0.00 39.25 2.43
3816 4623 8.933807 CATGCCTTCTATATCACAGTCATTTAG 58.066 37.037 0.00 0.00 0.00 1.85
3821 4628 4.901250 TCCATGCCTTCTATATCACAGTCA 59.099 41.667 0.00 0.00 0.00 3.41
3833 4640 5.271598 TGGAATAATTTGTCCATGCCTTCT 58.728 37.500 5.84 0.00 39.04 2.85
3858 4665 5.724854 TGTCCCTAAAGCTGAGGTACTTTAT 59.275 40.000 12.75 0.00 41.55 1.40
3896 4703 1.066422 GACGATCGCTGATGGCAGA 59.934 57.895 16.60 0.00 45.17 4.26
3907 4714 8.231161 TCTCTAGATTATTTAGCTTGACGATCG 58.769 37.037 14.88 14.88 0.00 3.69
3916 4723 5.770663 TCCAGCGTCTCTAGATTATTTAGCT 59.229 40.000 0.00 0.00 0.00 3.32
3942 4749 6.393990 ACTCTGTCACAGATGTATTCTCAAC 58.606 40.000 8.28 0.00 39.92 3.18
3974 4781 4.954826 AGTGTAGTTAGCCGAGTAATTCCT 59.045 41.667 0.00 0.00 0.00 3.36
4078 4888 5.812642 ACATCTGTTTCTTGCGAGGTAATAG 59.187 40.000 0.00 4.45 0.00 1.73
4124 4934 2.833794 TCGAGTTCCTCCAAACTTGTG 58.166 47.619 4.42 0.00 39.55 3.33
4159 4969 3.342377 TGTCCGAGCCAAATACATTCA 57.658 42.857 0.00 0.00 0.00 2.57
4168 4978 0.976641 ACATCTCTTGTCCGAGCCAA 59.023 50.000 0.00 0.00 30.89 4.52


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

AutoCloner maintained by Alex Coulton.