Multiple sequence alignment - TraesCS7B01G402300

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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 TraesCS7B01G402300 chr7B 100.000 3912 0 0 1 3912 668931624 668927713 0.000000e+00 7225.0
1 TraesCS7B01G402300 chr7B 86.687 1307 89 33 462 1695 668906680 668907974 0.000000e+00 1371.0
2 TraesCS7B01G402300 chr7B 84.934 1135 83 44 745 1809 669141716 669140600 0.000000e+00 1068.0
3 TraesCS7B01G402300 chr7B 86.207 899 74 21 2264 3123 669140080 669139193 0.000000e+00 928.0
4 TraesCS7B01G402300 chr7B 80.287 279 37 10 502 763 669175049 669174772 1.110000e-45 195.0
5 TraesCS7B01G402300 chr7B 93.750 128 7 1 2063 2189 669140406 669140279 1.430000e-44 191.0
6 TraesCS7B01G402300 chr7B 87.719 57 3 3 2087 2139 668908531 668908587 3.260000e-06 63.9
7 TraesCS7B01G402300 chr7D 92.917 1186 55 8 1958 3123 592818441 592819617 0.000000e+00 1698.0
8 TraesCS7B01G402300 chr7D 91.684 986 45 9 982 1958 592816335 592817292 0.000000e+00 1332.0
9 TraesCS7B01G402300 chr7D 86.898 1038 81 29 1963 2974 592678584 592679592 0.000000e+00 1112.0
10 TraesCS7B01G402300 chr7D 87.962 947 99 15 1 935 592815399 592816342 0.000000e+00 1103.0
11 TraesCS7B01G402300 chr7D 86.567 871 56 20 811 1647 592677218 592678061 0.000000e+00 904.0
12 TraesCS7B01G402300 chr7D 83.987 943 56 36 811 1695 592860385 592859480 0.000000e+00 817.0
13 TraesCS7B01G402300 chr7D 85.515 718 69 18 983 1672 592632301 592633011 0.000000e+00 717.0
14 TraesCS7B01G402300 chr7D 94.118 425 21 3 3488 3912 592819787 592820207 0.000000e+00 643.0
15 TraesCS7B01G402300 chr7D 86.494 385 33 13 462 831 592860809 592860429 4.710000e-109 405.0
16 TraesCS7B01G402300 chr7D 77.054 645 84 38 2281 2868 592858667 592858030 2.930000e-81 313.0
17 TraesCS7B01G402300 chr7D 96.571 175 6 0 3221 3395 592819618 592819792 1.380000e-74 291.0
18 TraesCS7B01G402300 chr7D 80.399 301 35 12 476 753 592675547 592675846 1.420000e-49 207.0
19 TraesCS7B01G402300 chr7D 87.069 116 10 5 1694 1807 592678426 592678538 4.100000e-25 126.0
20 TraesCS7B01G402300 chr7A 86.167 1453 110 40 1687 3060 685213430 685214870 0.000000e+00 1485.0
21 TraesCS7B01G402300 chr7A 91.180 907 45 16 804 1688 685212487 685213380 0.000000e+00 1199.0
22 TraesCS7B01G402300 chr7A 89.290 831 46 21 838 1647 685090000 685090808 0.000000e+00 1002.0
23 TraesCS7B01G402300 chr7A 84.598 896 67 30 817 1650 685230879 685229993 0.000000e+00 824.0
24 TraesCS7B01G402300 chr7A 82.081 865 97 25 838 1671 684292405 684293242 0.000000e+00 686.0
25 TraesCS7B01G402300 chr7A 84.895 523 39 16 1899 2416 685094858 685095345 3.510000e-135 492.0
26 TraesCS7B01G402300 chr7A 78.193 830 104 32 2280 3070 684296585 684297376 3.560000e-125 459.0
27 TraesCS7B01G402300 chr7A 82.885 520 49 12 2457 2937 685095344 685095862 7.770000e-117 431.0
28 TraesCS7B01G402300 chr7A 87.778 360 32 9 446 796 685212157 685212513 1.010000e-110 411.0
29 TraesCS7B01G402300 chr7A 76.516 643 85 34 2281 2864 685228845 685228210 1.380000e-74 291.0
30 TraesCS7B01G402300 chr7A 83.860 285 33 5 1756 2033 684293389 684293667 3.880000e-65 259.0
31 TraesCS7B01G402300 chr7A 83.815 173 11 2 1694 1859 685094685 685094847 8.760000e-32 148.0
32 TraesCS7B01G402300 chr7A 77.193 171 20 11 2028 2190 684296427 684296586 9.010000e-12 82.4
33 TraesCS7B01G402300 chr7A 88.000 50 4 2 2092 2139 685229096 685229047 1.520000e-04 58.4
34 TraesCS7B01G402300 chr3B 84.706 85 11 2 3607 3690 418332732 418332649 2.500000e-12 84.2
35 TraesCS7B01G402300 chr2A 81.319 91 15 2 3124 3212 20562738 20562828 5.420000e-09 73.1


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 TraesCS7B01G402300 chr7B 668927713 668931624 3911 True 7225.000000 7225 100.000000 1 3912 1 chr7B.!!$R1 3911
1 TraesCS7B01G402300 chr7B 669139193 669141716 2523 True 729.000000 1068 88.297000 745 3123 3 chr7B.!!$R3 2378
2 TraesCS7B01G402300 chr7B 668906680 668908587 1907 False 717.450000 1371 87.203000 462 2139 2 chr7B.!!$F1 1677
3 TraesCS7B01G402300 chr7D 592815399 592820207 4808 False 1013.400000 1698 92.650400 1 3912 5 chr7D.!!$F3 3911
4 TraesCS7B01G402300 chr7D 592632301 592633011 710 False 717.000000 717 85.515000 983 1672 1 chr7D.!!$F1 689
5 TraesCS7B01G402300 chr7D 592675547 592679592 4045 False 587.250000 1112 85.233250 476 2974 4 chr7D.!!$F2 2498
6 TraesCS7B01G402300 chr7D 592858030 592860809 2779 True 511.666667 817 82.511667 462 2868 3 chr7D.!!$R1 2406
7 TraesCS7B01G402300 chr7A 685212157 685214870 2713 False 1031.666667 1485 88.375000 446 3060 3 chr7A.!!$F3 2614
8 TraesCS7B01G402300 chr7A 685090000 685095862 5862 False 518.250000 1002 85.221250 838 2937 4 chr7A.!!$F2 2099
9 TraesCS7B01G402300 chr7A 685228210 685230879 2669 True 391.133333 824 83.038000 817 2864 3 chr7A.!!$R1 2047
10 TraesCS7B01G402300 chr7A 684292405 684297376 4971 False 371.600000 686 80.331750 838 3070 4 chr7A.!!$F1 2232


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
492 493 0.251297 TTGGACACATGGGGCTCAAG 60.251 55.000 0.0 0.0 0.00 3.02 F
976 2405 0.718343 CGGCTTTCTCTTCTTGAGCG 59.282 55.000 0.0 0.0 42.38 5.03 F
1797 7174 1.329292 CGCTCTGTTTTTGGTTCACGA 59.671 47.619 0.0 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1662 3169 0.543749 GAGTTGATGGAGAGTGGGGG 59.456 60.0 0.00 0.0 0.00 5.40 R
2852 12594 0.375803 GCGTTGTCGTTGTTCTGGTT 59.624 50.0 0.00 0.0 39.49 3.67 R
3123 12940 0.037326 AGCGAATGCCTGTTTCGAGA 60.037 50.0 9.74 0.0 46.73 4.04 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
25 26 2.513897 CCGGATCCGAAACCAGGC 60.514 66.667 35.42 0.00 42.83 4.85
26 27 2.584608 CGGATCCGAAACCAGGCT 59.415 61.111 30.62 0.00 42.83 4.58
28 29 1.908483 GGATCCGAAACCAGGCTCT 59.092 57.895 0.00 0.00 0.00 4.09
36 37 1.062488 AAACCAGGCTCTGACCCACT 61.062 55.000 4.00 0.00 32.44 4.00
39 40 1.757306 CAGGCTCTGACCCACTTGT 59.243 57.895 0.00 0.00 32.44 3.16
69 70 3.190878 GCTTCTTGCCCATCACGG 58.809 61.111 0.00 0.00 35.15 4.94
84 85 4.323477 CGGCAACCGGTCCTGGAA 62.323 66.667 8.04 0.00 44.15 3.53
108 109 1.669115 CTGGTGTGCGAAGGAGGTG 60.669 63.158 0.00 0.00 0.00 4.00
113 114 2.525629 TGCGAAGGAGGTGGGACA 60.526 61.111 0.00 0.00 0.00 4.02
114 115 2.266055 GCGAAGGAGGTGGGACAG 59.734 66.667 0.00 0.00 41.80 3.51
137 138 1.418264 GAGGAGGAGGATAGGGTTTGC 59.582 57.143 0.00 0.00 0.00 3.68
141 142 1.847088 AGGAGGATAGGGTTTGCTTCC 59.153 52.381 0.00 0.00 0.00 3.46
145 146 2.048312 GATAGGGTTTGCTTCCGCGC 62.048 60.000 0.00 0.00 39.65 6.86
146 147 2.536997 ATAGGGTTTGCTTCCGCGCT 62.537 55.000 5.56 0.00 39.65 5.92
161 162 1.567504 GCGCTCGTCTGGCTTTAATA 58.432 50.000 0.00 0.00 0.00 0.98
162 163 1.523095 GCGCTCGTCTGGCTTTAATAG 59.477 52.381 0.00 0.00 0.00 1.73
188 189 2.218603 GAAGGGTTGTCGAAGCTTCAA 58.781 47.619 25.47 10.86 0.00 2.69
191 192 2.814336 AGGGTTGTCGAAGCTTCAATTC 59.186 45.455 25.47 12.46 0.00 2.17
192 193 2.814336 GGGTTGTCGAAGCTTCAATTCT 59.186 45.455 25.47 0.00 0.00 2.40
215 216 1.378124 GAGTAGGCTTCTCGGTCGCT 61.378 60.000 5.34 0.00 0.00 4.93
219 220 3.482783 GCTTCTCGGTCGCTGCAC 61.483 66.667 0.00 0.00 0.00 4.57
220 221 2.259818 CTTCTCGGTCGCTGCACT 59.740 61.111 0.00 0.00 0.00 4.40
223 224 2.749110 TTCTCGGTCGCTGCACTGAC 62.749 60.000 0.00 5.23 0.00 3.51
229 230 1.227118 TCGCTGCACTGACGTGAAA 60.227 52.632 0.00 0.00 43.97 2.69
230 231 1.083401 CGCTGCACTGACGTGAAAC 60.083 57.895 0.00 0.00 43.97 2.78
231 232 1.761244 CGCTGCACTGACGTGAAACA 61.761 55.000 0.00 0.00 43.97 2.83
248 249 0.326595 ACACGTATTGGTGGATGGCA 59.673 50.000 0.00 0.00 42.23 4.92
250 251 1.334556 CACGTATTGGTGGATGGCATG 59.665 52.381 3.81 0.00 34.27 4.06
288 289 2.234300 ACGAAGTTTTCCAGAGCGAA 57.766 45.000 0.00 0.00 37.78 4.70
297 298 2.310233 CCAGAGCGAACACACACGG 61.310 63.158 0.00 0.00 0.00 4.94
304 305 1.802337 CGAACACACACGGGAGAGGA 61.802 60.000 0.00 0.00 0.00 3.71
311 312 1.070134 CACACGGGAGAGGAGTTTTGA 59.930 52.381 0.00 0.00 0.00 2.69
319 320 4.445019 GGGAGAGGAGTTTTGAGTGAGTTT 60.445 45.833 0.00 0.00 0.00 2.66
325 326 2.097466 AGTTTTGAGTGAGTTTGGTGCG 59.903 45.455 0.00 0.00 0.00 5.34
327 328 1.295792 TTGAGTGAGTTTGGTGCGTC 58.704 50.000 0.00 0.00 0.00 5.19
334 335 2.355363 TTTGGTGCGTCGGAGTCG 60.355 61.111 0.00 0.00 42.81 4.18
352 353 2.551270 GTTGCGGCAGACGTTCAG 59.449 61.111 1.67 0.00 46.52 3.02
358 359 3.555428 GCAGACGTTCAGACTGGC 58.445 61.111 1.81 0.00 41.73 4.85
359 360 2.029844 GCAGACGTTCAGACTGGCC 61.030 63.158 1.81 0.00 41.73 5.36
360 361 1.374758 CAGACGTTCAGACTGGCCC 60.375 63.158 0.00 0.00 38.63 5.80
375 376 0.808755 GGCCCGGACAATGTTTGTAG 59.191 55.000 0.73 0.00 45.52 2.74
381 382 1.127951 GGACAATGTTTGTAGCCGTCG 59.872 52.381 0.00 0.00 45.52 5.12
436 437 4.136796 CCAGACAGTTGAGGTTGATTTGA 58.863 43.478 0.00 0.00 0.00 2.69
440 441 5.471456 AGACAGTTGAGGTTGATTTGATGAC 59.529 40.000 0.00 0.00 0.00 3.06
444 445 5.593909 AGTTGAGGTTGATTTGATGACACAA 59.406 36.000 0.00 0.00 0.00 3.33
455 456 3.213506 TGATGACACAAGTTGGAGTTGG 58.786 45.455 7.96 0.00 32.93 3.77
459 460 0.670162 CACAAGTTGGAGTTGGCCTG 59.330 55.000 3.32 0.00 32.93 4.85
468 469 1.517242 GAGTTGGCCTGAGAACACAG 58.483 55.000 3.32 0.00 37.61 3.66
469 470 1.070758 GAGTTGGCCTGAGAACACAGA 59.929 52.381 3.32 0.00 39.94 3.41
471 472 2.092429 AGTTGGCCTGAGAACACAGAAA 60.092 45.455 3.32 0.00 39.94 2.52
483 484 4.336433 AGAACACAGAAAGTTGGACACATG 59.664 41.667 0.00 0.00 0.00 3.21
492 493 0.251297 TTGGACACATGGGGCTCAAG 60.251 55.000 0.00 0.00 0.00 3.02
541 544 8.867097 AGCCAGAATCATATTTAGATTTTGCAT 58.133 29.630 0.00 0.00 36.69 3.96
562 569 2.111756 GCACAAGAAAAACAGTGCGAG 58.888 47.619 0.00 0.00 46.35 5.03
572 596 7.797819 AGAAAAACAGTGCGAGATAAGTAAAG 58.202 34.615 0.00 0.00 0.00 1.85
606 634 3.008813 AGTGTCCATGCATGTCTTCTCTT 59.991 43.478 24.58 0.70 0.00 2.85
672 703 1.615392 GCACCAAAACAGCAAGGAGAT 59.385 47.619 0.00 0.00 0.00 2.75
797 2108 1.847737 TCCCTCCTCCACTCTCTCTAC 59.152 57.143 0.00 0.00 0.00 2.59
798 2109 1.566703 CCCTCCTCCACTCTCTCTACA 59.433 57.143 0.00 0.00 0.00 2.74
799 2110 2.650322 CCTCCTCCACTCTCTCTACAC 58.350 57.143 0.00 0.00 0.00 2.90
830 2204 4.230502 ACCCTCTCAATCTCTTCTCTCTCT 59.769 45.833 0.00 0.00 0.00 3.10
913 2334 3.634448 ACTGATTCATACAGCTAGCGAGT 59.366 43.478 17.79 17.79 38.74 4.18
914 2335 3.969899 TGATTCATACAGCTAGCGAGTG 58.030 45.455 21.32 12.44 0.00 3.51
915 2336 3.632145 TGATTCATACAGCTAGCGAGTGA 59.368 43.478 21.32 15.56 0.00 3.41
916 2337 3.699779 TTCATACAGCTAGCGAGTGAG 57.300 47.619 21.32 14.72 0.00 3.51
917 2338 1.335182 TCATACAGCTAGCGAGTGAGC 59.665 52.381 21.32 0.00 39.08 4.26
953 2382 1.894756 ACGCCTCCTAGCTAGCTCG 60.895 63.158 23.26 19.42 0.00 5.03
976 2405 0.718343 CGGCTTTCTCTTCTTGAGCG 59.282 55.000 0.00 0.00 42.38 5.03
1153 2626 2.922950 AACTTCGACTACGCGGCCA 61.923 57.895 12.47 0.00 39.58 5.36
1285 2773 2.592574 TGCAGATGCCGCCTATGC 60.593 61.111 8.17 8.17 41.18 3.14
1288 2776 3.958860 AGATGCCGCCTATGCCCC 61.959 66.667 0.00 0.00 0.00 5.80
1289 2777 4.269523 GATGCCGCCTATGCCCCA 62.270 66.667 0.00 0.00 0.00 4.96
1290 2778 4.586235 ATGCCGCCTATGCCCCAC 62.586 66.667 0.00 0.00 0.00 4.61
1347 2835 3.371097 GATGGTGAAGCGCGAGGGA 62.371 63.158 12.10 0.00 0.00 4.20
1526 3023 1.462238 AGGTGGAGGACTGCAAGGT 60.462 57.895 0.00 0.00 39.30 3.50
1647 3144 1.677966 CCAGCAATGCAGCAGGTCT 60.678 57.895 8.35 0.00 36.52 3.85
1662 3169 2.852075 TCTGACCCCACACCCCAC 60.852 66.667 0.00 0.00 0.00 4.61
1797 7174 1.329292 CGCTCTGTTTTTGGTTCACGA 59.671 47.619 0.00 0.00 0.00 4.35
1940 7404 2.281276 GCCGTTTTCCCGTCCTGT 60.281 61.111 0.00 0.00 0.00 4.00
2065 11503 2.500714 CCTGTGGCAGGCTTTTGCA 61.501 57.895 1.93 0.00 45.13 4.08
2208 11729 7.558435 AATTTTGTTGAGTAGTACGTACGAG 57.442 36.000 24.41 0.00 36.66 4.18
2214 11735 7.635423 TGTTGAGTAGTACGTACGAGTTAAAA 58.365 34.615 24.41 12.46 36.66 1.52
2242 11781 2.355209 GGTGCTCAAGGTTAGCTAGCTT 60.355 50.000 24.88 7.25 45.15 3.74
2244 11783 4.116238 GTGCTCAAGGTTAGCTAGCTTAG 58.884 47.826 24.88 10.05 42.49 2.18
2245 11784 3.769844 TGCTCAAGGTTAGCTAGCTTAGT 59.230 43.478 24.88 0.00 42.49 2.24
2246 11785 4.223032 TGCTCAAGGTTAGCTAGCTTAGTT 59.777 41.667 24.88 7.49 42.49 2.24
2483 12158 1.531149 CAACAGTAAGCCGACACCTTG 59.469 52.381 0.00 0.00 0.00 3.61
2533 12220 5.237048 TGCGATTGATCATCATTTATCGGA 58.763 37.500 20.77 17.25 36.37 4.55
2619 12315 2.816958 CACCAGCGCGATCAGCTT 60.817 61.111 12.10 0.00 44.06 3.74
2852 12594 2.342279 CAAACGGCGAGGTCTCCA 59.658 61.111 16.62 0.00 0.00 3.86
2987 12776 5.648092 AGAACACCACATTAGATTGTAAGCC 59.352 40.000 0.00 0.00 0.00 4.35
3013 12802 3.543099 GTGTTTTGTTTTCACCGGTTACG 59.457 43.478 2.97 0.00 40.55 3.18
3065 12866 5.293560 GGGCTAAACAGCAACAAAACATTA 58.706 37.500 0.00 0.00 36.33 1.90
3075 12876 9.638239 ACAGCAACAAAACATTATACTAATTGG 57.362 29.630 0.00 0.00 0.00 3.16
3114 12931 5.012561 AGTGGACTTTGAGATAGTTTCAGCT 59.987 40.000 0.00 0.00 0.00 4.24
3123 12940 7.661536 TGAGATAGTTTCAGCTACCAAGTAT 57.338 36.000 0.00 0.00 0.00 2.12
3124 12941 7.717568 TGAGATAGTTTCAGCTACCAAGTATC 58.282 38.462 13.76 13.76 34.80 2.24
3125 12942 7.561722 TGAGATAGTTTCAGCTACCAAGTATCT 59.438 37.037 19.59 19.59 42.24 1.98
3126 12943 7.947282 AGATAGTTTCAGCTACCAAGTATCTC 58.053 38.462 16.43 3.13 38.16 2.75
3127 12944 5.000012 AGTTTCAGCTACCAAGTATCTCG 58.000 43.478 0.00 0.00 0.00 4.04
3128 12945 4.705507 AGTTTCAGCTACCAAGTATCTCGA 59.294 41.667 0.00 0.00 0.00 4.04
3129 12946 5.185249 AGTTTCAGCTACCAAGTATCTCGAA 59.815 40.000 0.00 0.00 0.00 3.71
3130 12947 5.654603 TTCAGCTACCAAGTATCTCGAAA 57.345 39.130 0.00 0.00 0.00 3.46
3131 12948 4.995124 TCAGCTACCAAGTATCTCGAAAC 58.005 43.478 0.00 0.00 0.00 2.78
3132 12949 4.461431 TCAGCTACCAAGTATCTCGAAACA 59.539 41.667 0.00 0.00 0.00 2.83
3133 12950 4.800993 CAGCTACCAAGTATCTCGAAACAG 59.199 45.833 0.00 0.00 0.00 3.16
3134 12951 4.113354 GCTACCAAGTATCTCGAAACAGG 58.887 47.826 0.00 0.00 0.00 4.00
3135 12952 2.973945 ACCAAGTATCTCGAAACAGGC 58.026 47.619 0.00 0.00 0.00 4.85
3136 12953 2.301870 ACCAAGTATCTCGAAACAGGCA 59.698 45.455 0.00 0.00 0.00 4.75
3137 12954 3.055094 ACCAAGTATCTCGAAACAGGCAT 60.055 43.478 0.00 0.00 0.00 4.40
3138 12955 3.941483 CCAAGTATCTCGAAACAGGCATT 59.059 43.478 0.00 0.00 0.00 3.56
3139 12956 4.034510 CCAAGTATCTCGAAACAGGCATTC 59.965 45.833 0.00 0.00 0.00 2.67
3141 12958 1.009829 ATCTCGAAACAGGCATTCGC 58.990 50.000 13.09 0.00 46.85 4.70
3142 12959 0.037326 TCTCGAAACAGGCATTCGCT 60.037 50.000 13.09 0.00 46.85 4.93
3143 12960 0.371645 CTCGAAACAGGCATTCGCTC 59.628 55.000 13.09 0.00 46.85 5.03
3144 12961 1.019278 TCGAAACAGGCATTCGCTCC 61.019 55.000 13.09 0.00 46.85 4.70
3145 12962 1.425428 GAAACAGGCATTCGCTCCG 59.575 57.895 0.00 0.00 38.60 4.63
3146 12963 2.583685 GAAACAGGCATTCGCTCCGC 62.584 60.000 0.00 0.00 38.60 5.54
3147 12964 3.612247 AACAGGCATTCGCTCCGCT 62.612 57.895 0.00 0.00 38.60 5.52
3148 12965 2.821366 CAGGCATTCGCTCCGCTT 60.821 61.111 0.00 0.00 38.60 4.68
3149 12966 2.045926 AGGCATTCGCTCCGCTTT 60.046 55.556 0.00 0.00 38.60 3.51
3150 12967 1.089481 CAGGCATTCGCTCCGCTTTA 61.089 55.000 0.00 0.00 38.60 1.85
3151 12968 0.179045 AGGCATTCGCTCCGCTTTAT 60.179 50.000 0.00 0.00 38.60 1.40
3152 12969 1.070134 AGGCATTCGCTCCGCTTTATA 59.930 47.619 0.00 0.00 38.60 0.98
3153 12970 1.871039 GGCATTCGCTCCGCTTTATAA 59.129 47.619 0.00 0.00 38.60 0.98
3154 12971 2.289547 GGCATTCGCTCCGCTTTATAAA 59.710 45.455 0.00 0.00 38.60 1.40
3155 12972 3.058224 GGCATTCGCTCCGCTTTATAAAT 60.058 43.478 0.00 0.00 38.60 1.40
3156 12973 4.153475 GGCATTCGCTCCGCTTTATAAATA 59.847 41.667 0.00 0.00 38.60 1.40
3157 12974 5.334569 GGCATTCGCTCCGCTTTATAAATAA 60.335 40.000 0.00 0.00 38.60 1.40
3158 12975 6.140110 GCATTCGCTCCGCTTTATAAATAAA 58.860 36.000 0.00 0.00 34.30 1.40
3159 12976 6.635239 GCATTCGCTCCGCTTTATAAATAAAA 59.365 34.615 0.00 0.00 31.75 1.52
3160 12977 7.357287 GCATTCGCTCCGCTTTATAAATAAAAC 60.357 37.037 0.00 0.00 31.75 2.43
3161 12978 6.665474 TCGCTCCGCTTTATAAATAAAACA 57.335 33.333 0.00 0.00 32.39 2.83
3162 12979 7.074507 TCGCTCCGCTTTATAAATAAAACAA 57.925 32.000 0.00 0.00 32.39 2.83
3163 12980 6.962678 TCGCTCCGCTTTATAAATAAAACAAC 59.037 34.615 0.00 0.00 32.39 3.32
3164 12981 6.743627 CGCTCCGCTTTATAAATAAAACAACA 59.256 34.615 0.00 0.00 32.39 3.33
3165 12982 7.271653 CGCTCCGCTTTATAAATAAAACAACAA 59.728 33.333 0.00 0.00 32.39 2.83
3166 12983 8.370321 GCTCCGCTTTATAAATAAAACAACAAC 58.630 33.333 0.00 0.00 32.39 3.32
3167 12984 8.745464 TCCGCTTTATAAATAAAACAACAACC 57.255 30.769 0.00 0.00 32.39 3.77
3168 12985 8.358148 TCCGCTTTATAAATAAAACAACAACCA 58.642 29.630 0.00 0.00 32.39 3.67
3169 12986 9.145865 CCGCTTTATAAATAAAACAACAACCAT 57.854 29.630 0.00 0.00 32.39 3.55
3179 12996 9.453325 AATAAAACAACAACCATAAGTTACACG 57.547 29.630 0.00 0.00 36.18 4.49
3180 12997 5.427036 AACAACAACCATAAGTTACACGG 57.573 39.130 0.00 0.00 36.18 4.94
3181 12998 3.251487 ACAACAACCATAAGTTACACGGC 59.749 43.478 0.00 0.00 36.18 5.68
3182 12999 2.070783 ACAACCATAAGTTACACGGCG 58.929 47.619 4.80 4.80 36.18 6.46
3183 13000 2.288948 ACAACCATAAGTTACACGGCGA 60.289 45.455 16.62 0.00 36.18 5.54
3184 13001 2.737783 CAACCATAAGTTACACGGCGAA 59.262 45.455 16.62 0.00 36.18 4.70
3185 13002 3.042871 ACCATAAGTTACACGGCGAAA 57.957 42.857 16.62 1.36 0.00 3.46
3186 13003 3.401182 ACCATAAGTTACACGGCGAAAA 58.599 40.909 16.62 0.94 0.00 2.29
3187 13004 3.434299 ACCATAAGTTACACGGCGAAAAG 59.566 43.478 16.62 2.56 0.00 2.27
3188 13005 3.680937 CCATAAGTTACACGGCGAAAAGA 59.319 43.478 16.62 0.00 0.00 2.52
3189 13006 4.331717 CCATAAGTTACACGGCGAAAAGAT 59.668 41.667 16.62 0.00 0.00 2.40
3190 13007 5.521010 CCATAAGTTACACGGCGAAAAGATA 59.479 40.000 16.62 0.00 0.00 1.98
3191 13008 4.916099 AAGTTACACGGCGAAAAGATAC 57.084 40.909 16.62 1.99 0.00 2.24
3192 13009 3.916761 AGTTACACGGCGAAAAGATACA 58.083 40.909 16.62 0.00 0.00 2.29
3193 13010 4.309099 AGTTACACGGCGAAAAGATACAA 58.691 39.130 16.62 0.00 0.00 2.41
3194 13011 4.933400 AGTTACACGGCGAAAAGATACAAT 59.067 37.500 16.62 0.00 0.00 2.71
3195 13012 6.101332 AGTTACACGGCGAAAAGATACAATA 58.899 36.000 16.62 0.00 0.00 1.90
3196 13013 6.759827 AGTTACACGGCGAAAAGATACAATAT 59.240 34.615 16.62 0.00 0.00 1.28
3197 13014 5.403897 ACACGGCGAAAAGATACAATATG 57.596 39.130 16.62 0.00 0.00 1.78
3198 13015 5.113383 ACACGGCGAAAAGATACAATATGA 58.887 37.500 16.62 0.00 0.00 2.15
3199 13016 5.758296 ACACGGCGAAAAGATACAATATGAT 59.242 36.000 16.62 0.00 0.00 2.45
3200 13017 6.073369 CACGGCGAAAAGATACAATATGATG 58.927 40.000 16.62 0.00 0.00 3.07
3201 13018 5.989168 ACGGCGAAAAGATACAATATGATGA 59.011 36.000 16.62 0.00 0.00 2.92
3202 13019 6.146184 ACGGCGAAAAGATACAATATGATGAG 59.854 38.462 16.62 0.00 0.00 2.90
3203 13020 6.401474 CGGCGAAAAGATACAATATGATGAGG 60.401 42.308 0.00 0.00 0.00 3.86
3204 13021 6.428159 GGCGAAAAGATACAATATGATGAGGT 59.572 38.462 0.00 0.00 0.00 3.85
3205 13022 7.602644 GGCGAAAAGATACAATATGATGAGGTA 59.397 37.037 0.00 0.00 0.00 3.08
3206 13023 8.988934 GCGAAAAGATACAATATGATGAGGTAA 58.011 33.333 0.00 0.00 0.00 2.85
3209 13026 9.574516 AAAAGATACAATATGATGAGGTAACCC 57.425 33.333 0.00 0.00 37.17 4.11
3210 13027 8.511748 AAGATACAATATGATGAGGTAACCCT 57.488 34.615 0.00 0.00 46.66 4.34
3228 13045 2.215907 CTCTCACATAGAGCAACCGG 57.784 55.000 0.00 0.00 45.22 5.28
3233 13050 4.038042 TCTCACATAGAGCAACCGGATAAG 59.962 45.833 9.46 0.00 44.35 1.73
3254 13071 6.655078 AAGAGAACAATAAGCACAAATGGT 57.345 33.333 0.00 0.00 38.52 3.55
3306 13123 3.187842 AGAAAACGGGAATAAGAACACGC 59.812 43.478 0.00 0.00 36.31 5.34
3396 13213 8.934507 ACTCTAGAATTTACAATACACTCAGC 57.065 34.615 0.00 0.00 0.00 4.26
3397 13214 8.531982 ACTCTAGAATTTACAATACACTCAGCA 58.468 33.333 0.00 0.00 0.00 4.41
3398 13215 8.703604 TCTAGAATTTACAATACACTCAGCAC 57.296 34.615 0.00 0.00 0.00 4.40
3399 13216 6.743575 AGAATTTACAATACACTCAGCACC 57.256 37.500 0.00 0.00 0.00 5.01
3400 13217 6.476378 AGAATTTACAATACACTCAGCACCT 58.524 36.000 0.00 0.00 0.00 4.00
3401 13218 6.942576 AGAATTTACAATACACTCAGCACCTT 59.057 34.615 0.00 0.00 0.00 3.50
3402 13219 8.100791 AGAATTTACAATACACTCAGCACCTTA 58.899 33.333 0.00 0.00 0.00 2.69
3403 13220 7.611213 ATTTACAATACACTCAGCACCTTAC 57.389 36.000 0.00 0.00 0.00 2.34
3404 13221 3.939066 ACAATACACTCAGCACCTTACC 58.061 45.455 0.00 0.00 0.00 2.85
3405 13222 3.326588 ACAATACACTCAGCACCTTACCA 59.673 43.478 0.00 0.00 0.00 3.25
3406 13223 4.202419 ACAATACACTCAGCACCTTACCAA 60.202 41.667 0.00 0.00 0.00 3.67
3407 13224 2.256117 ACACTCAGCACCTTACCAAC 57.744 50.000 0.00 0.00 0.00 3.77
3408 13225 1.768870 ACACTCAGCACCTTACCAACT 59.231 47.619 0.00 0.00 0.00 3.16
3409 13226 2.969950 ACACTCAGCACCTTACCAACTA 59.030 45.455 0.00 0.00 0.00 2.24
3410 13227 3.006967 ACACTCAGCACCTTACCAACTAG 59.993 47.826 0.00 0.00 0.00 2.57
3411 13228 2.028020 ACTCAGCACCTTACCAACTAGC 60.028 50.000 0.00 0.00 0.00 3.42
3412 13229 1.974957 TCAGCACCTTACCAACTAGCA 59.025 47.619 0.00 0.00 0.00 3.49
3413 13230 2.028112 TCAGCACCTTACCAACTAGCAG 60.028 50.000 0.00 0.00 0.00 4.24
3414 13231 1.087501 GCACCTTACCAACTAGCAGC 58.912 55.000 0.00 0.00 0.00 5.25
3415 13232 1.610624 GCACCTTACCAACTAGCAGCA 60.611 52.381 0.00 0.00 0.00 4.41
3416 13233 2.778299 CACCTTACCAACTAGCAGCAA 58.222 47.619 0.00 0.00 0.00 3.91
3417 13234 2.484264 CACCTTACCAACTAGCAGCAAC 59.516 50.000 0.00 0.00 0.00 4.17
3418 13235 2.084546 CCTTACCAACTAGCAGCAACC 58.915 52.381 0.00 0.00 0.00 3.77
3419 13236 2.552155 CCTTACCAACTAGCAGCAACCA 60.552 50.000 0.00 0.00 0.00 3.67
3420 13237 2.178912 TACCAACTAGCAGCAACCAC 57.821 50.000 0.00 0.00 0.00 4.16
3421 13238 0.182537 ACCAACTAGCAGCAACCACA 59.817 50.000 0.00 0.00 0.00 4.17
3422 13239 1.317613 CCAACTAGCAGCAACCACAA 58.682 50.000 0.00 0.00 0.00 3.33
3423 13240 1.267806 CCAACTAGCAGCAACCACAAG 59.732 52.381 0.00 0.00 0.00 3.16
3424 13241 1.949525 CAACTAGCAGCAACCACAAGT 59.050 47.619 0.00 0.00 0.00 3.16
3425 13242 1.597742 ACTAGCAGCAACCACAAGTG 58.402 50.000 0.00 0.00 0.00 3.16
3436 13253 2.223537 CCACAAGTGGCAAGAAAACC 57.776 50.000 6.27 0.00 44.73 3.27
3437 13254 1.480137 CCACAAGTGGCAAGAAAACCA 59.520 47.619 6.27 0.00 44.73 3.67
3444 13261 3.685139 TGGCAAGAAAACCACAAAACA 57.315 38.095 0.00 0.00 0.00 2.83
3445 13262 4.008074 TGGCAAGAAAACCACAAAACAA 57.992 36.364 0.00 0.00 0.00 2.83
3446 13263 4.389374 TGGCAAGAAAACCACAAAACAAA 58.611 34.783 0.00 0.00 0.00 2.83
3447 13264 4.453819 TGGCAAGAAAACCACAAAACAAAG 59.546 37.500 0.00 0.00 0.00 2.77
3448 13265 4.454161 GGCAAGAAAACCACAAAACAAAGT 59.546 37.500 0.00 0.00 0.00 2.66
3449 13266 5.049060 GGCAAGAAAACCACAAAACAAAGTT 60.049 36.000 0.00 0.00 0.00 2.66
3450 13267 6.147985 GGCAAGAAAACCACAAAACAAAGTTA 59.852 34.615 0.00 0.00 0.00 2.24
3451 13268 7.308049 GGCAAGAAAACCACAAAACAAAGTTAA 60.308 33.333 0.00 0.00 0.00 2.01
3452 13269 8.233868 GCAAGAAAACCACAAAACAAAGTTAAT 58.766 29.630 0.00 0.00 0.00 1.40
3453 13270 9.540431 CAAGAAAACCACAAAACAAAGTTAATG 57.460 29.630 0.00 0.00 0.00 1.90
3454 13271 7.747888 AGAAAACCACAAAACAAAGTTAATGC 58.252 30.769 0.00 0.00 0.00 3.56
3455 13272 7.389053 AGAAAACCACAAAACAAAGTTAATGCA 59.611 29.630 0.00 0.00 0.00 3.96
3456 13273 6.660887 AACCACAAAACAAAGTTAATGCAG 57.339 33.333 0.00 0.00 0.00 4.41
3457 13274 5.971763 ACCACAAAACAAAGTTAATGCAGA 58.028 33.333 0.00 0.00 0.00 4.26
3458 13275 6.581712 ACCACAAAACAAAGTTAATGCAGAT 58.418 32.000 0.00 0.00 0.00 2.90
3459 13276 7.047271 ACCACAAAACAAAGTTAATGCAGATT 58.953 30.769 0.00 0.00 0.00 2.40
3460 13277 8.200792 ACCACAAAACAAAGTTAATGCAGATTA 58.799 29.630 0.00 0.00 0.00 1.75
3461 13278 9.206870 CCACAAAACAAAGTTAATGCAGATTAT 57.793 29.630 0.00 0.00 0.00 1.28
3463 13280 9.762933 ACAAAACAAAGTTAATGCAGATTATGT 57.237 25.926 0.00 0.00 0.00 2.29
3467 13284 9.855021 AACAAAGTTAATGCAGATTATGTTACC 57.145 29.630 0.00 0.00 28.46 2.85
3468 13285 9.243105 ACAAAGTTAATGCAGATTATGTTACCT 57.757 29.630 0.00 0.00 0.00 3.08
3471 13288 8.142994 AGTTAATGCAGATTATGTTACCTTCG 57.857 34.615 0.00 0.00 0.00 3.79
3472 13289 7.985184 AGTTAATGCAGATTATGTTACCTTCGA 59.015 33.333 0.00 0.00 0.00 3.71
3473 13290 8.774586 GTTAATGCAGATTATGTTACCTTCGAT 58.225 33.333 0.00 0.00 0.00 3.59
3474 13291 9.990360 TTAATGCAGATTATGTTACCTTCGATA 57.010 29.630 0.00 0.00 0.00 2.92
3475 13292 8.902540 AATGCAGATTATGTTACCTTCGATAA 57.097 30.769 0.00 0.00 0.00 1.75
3476 13293 7.709269 TGCAGATTATGTTACCTTCGATAAC 57.291 36.000 1.28 1.28 33.85 1.89
3477 13294 6.704493 TGCAGATTATGTTACCTTCGATAACC 59.296 38.462 5.24 0.00 32.52 2.85
3478 13295 6.929606 GCAGATTATGTTACCTTCGATAACCT 59.070 38.462 5.24 0.00 32.52 3.50
3479 13296 8.086522 GCAGATTATGTTACCTTCGATAACCTA 58.913 37.037 5.24 0.00 32.52 3.08
3484 13301 5.839621 TGTTACCTTCGATAACCTATGAGC 58.160 41.667 5.24 0.00 32.52 4.26
3485 13302 5.597182 TGTTACCTTCGATAACCTATGAGCT 59.403 40.000 5.24 0.00 32.52 4.09
3486 13303 4.592485 ACCTTCGATAACCTATGAGCTG 57.408 45.455 0.00 0.00 0.00 4.24
3503 13320 1.932511 GCTGCTCTCATACTGCTGAAC 59.067 52.381 0.00 0.00 0.00 3.18
3516 13333 1.586028 CTGAACCAAATGGCACGGG 59.414 57.895 0.00 0.00 39.32 5.28
3519 13336 0.894835 GAACCAAATGGCACGGGATT 59.105 50.000 7.80 0.00 39.32 3.01
3520 13337 1.275010 GAACCAAATGGCACGGGATTT 59.725 47.619 7.80 0.00 39.32 2.17
3521 13338 0.607620 ACCAAATGGCACGGGATTTG 59.392 50.000 7.80 5.13 38.67 2.32
3522 13339 3.439494 CAAATGGCACGGGATTTGG 57.561 52.632 4.33 0.00 36.37 3.28
3560 13377 9.856488 ATATGTAAGCTCGAAACATATACGAAT 57.144 29.630 16.31 1.70 42.27 3.34
3835 13652 1.133513 TGGAAGAACCATTGTGCCACT 60.134 47.619 0.00 0.00 44.64 4.00
3843 13660 3.700538 ACCATTGTGCCACTAACATCAT 58.299 40.909 0.00 0.00 0.00 2.45
3845 13662 4.883585 ACCATTGTGCCACTAACATCATAG 59.116 41.667 0.00 0.00 0.00 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.513897 GCCTGGTTTCGGATCCGG 60.514 66.667 32.79 16.38 40.25 5.14
17 18 1.062488 AGTGGGTCAGAGCCTGGTTT 61.062 55.000 19.59 0.00 36.53 3.27
36 37 1.774894 AAGCCCTACGCCTCCAACAA 61.775 55.000 0.00 0.00 38.78 2.83
39 40 1.198759 AAGAAGCCCTACGCCTCCAA 61.199 55.000 0.00 0.00 38.78 3.53
69 70 1.966451 CACTTCCAGGACCGGTTGC 60.966 63.158 9.42 0.00 0.00 4.17
81 82 2.896801 CGCACACCAGCACACTTCC 61.897 63.158 0.00 0.00 0.00 3.46
84 85 1.889105 CTTCGCACACCAGCACACT 60.889 57.895 0.00 0.00 0.00 3.55
108 109 1.075600 CCTCCTCCTCTCCTGTCCC 60.076 68.421 0.00 0.00 0.00 4.46
113 114 1.348160 ACCCTATCCTCCTCCTCTCCT 60.348 57.143 0.00 0.00 0.00 3.69
114 115 1.163408 ACCCTATCCTCCTCCTCTCC 58.837 60.000 0.00 0.00 0.00 3.71
141 142 1.421410 ATTAAAGCCAGACGAGCGCG 61.421 55.000 8.75 8.75 44.79 6.86
161 162 3.647771 GACAACCCTTCCCCGGCT 61.648 66.667 0.00 0.00 0.00 5.52
163 164 2.798148 CTTCGACAACCCTTCCCCGG 62.798 65.000 0.00 0.00 0.00 5.73
164 165 1.375523 CTTCGACAACCCTTCCCCG 60.376 63.158 0.00 0.00 0.00 5.73
171 172 2.814336 AGAATTGAAGCTTCGACAACCC 59.186 45.455 18.81 6.54 0.00 4.11
179 180 5.044558 CCTACTCCGTAGAATTGAAGCTTC 58.955 45.833 19.89 19.89 38.29 3.86
188 189 2.879646 CGAGAAGCCTACTCCGTAGAAT 59.120 50.000 2.74 0.00 38.29 2.40
191 192 0.945813 CCGAGAAGCCTACTCCGTAG 59.054 60.000 0.00 0.00 36.04 3.51
192 193 0.254178 ACCGAGAAGCCTACTCCGTA 59.746 55.000 0.00 0.00 0.00 4.02
209 210 3.406361 CACGTCAGTGCAGCGACC 61.406 66.667 9.30 0.00 41.94 4.79
229 230 0.326595 TGCCATCCACCAATACGTGT 59.673 50.000 0.00 0.00 31.47 4.49
230 231 1.334556 CATGCCATCCACCAATACGTG 59.665 52.381 0.00 0.00 0.00 4.49
231 232 1.064758 ACATGCCATCCACCAATACGT 60.065 47.619 0.00 0.00 0.00 3.57
248 249 3.693085 GTCACATTCATTCTGGCTGACAT 59.307 43.478 0.00 0.00 0.00 3.06
250 251 2.094894 CGTCACATTCATTCTGGCTGAC 59.905 50.000 0.00 0.00 0.00 3.51
258 259 5.757886 TGGAAAACTTCGTCACATTCATTC 58.242 37.500 0.00 0.00 0.00 2.67
288 289 0.759436 AACTCCTCTCCCGTGTGTGT 60.759 55.000 0.00 0.00 0.00 3.72
297 298 4.344359 AACTCACTCAAAACTCCTCTCC 57.656 45.455 0.00 0.00 0.00 3.71
304 305 2.097466 CGCACCAAACTCACTCAAAACT 59.903 45.455 0.00 0.00 0.00 2.66
311 312 1.594293 CCGACGCACCAAACTCACT 60.594 57.895 0.00 0.00 0.00 3.41
334 335 2.954753 CTGAACGTCTGCCGCAACC 61.955 63.158 0.00 0.00 41.42 3.77
352 353 0.893727 AAACATTGTCCGGGCCAGTC 60.894 55.000 2.12 0.00 0.00 3.51
358 359 0.808755 GGCTACAAACATTGTCCGGG 59.191 55.000 0.00 0.00 44.12 5.73
359 360 0.446222 CGGCTACAAACATTGTCCGG 59.554 55.000 12.82 0.00 43.39 5.14
360 361 3.967734 CGGCTACAAACATTGTCCG 57.032 52.632 8.38 8.38 44.12 4.79
381 382 5.351740 ACTCGAAAGCTTTTAGCCATCTAAC 59.648 40.000 14.05 0.00 43.77 2.34
436 437 1.956477 GCCAACTCCAACTTGTGTCAT 59.044 47.619 0.00 0.00 0.00 3.06
440 441 0.670162 CAGGCCAACTCCAACTTGTG 59.330 55.000 5.01 0.00 0.00 3.33
444 445 1.140312 TTCTCAGGCCAACTCCAACT 58.860 50.000 5.01 0.00 0.00 3.16
455 456 2.291741 CCAACTTTCTGTGTTCTCAGGC 59.708 50.000 2.76 0.00 36.25 4.85
459 460 3.938963 TGTGTCCAACTTTCTGTGTTCTC 59.061 43.478 0.00 0.00 0.00 2.87
468 469 0.603065 GCCCCATGTGTCCAACTTTC 59.397 55.000 0.00 0.00 0.00 2.62
469 470 0.188342 AGCCCCATGTGTCCAACTTT 59.812 50.000 0.00 0.00 0.00 2.66
471 472 1.380302 GAGCCCCATGTGTCCAACT 59.620 57.895 0.00 0.00 0.00 3.16
483 484 0.460987 CACGTGATCTCTTGAGCCCC 60.461 60.000 10.90 0.00 0.00 5.80
492 493 3.786576 CGAACATGTACTCACGTGATCTC 59.213 47.826 20.40 12.22 43.26 2.75
516 519 8.922676 CATGCAAAATCTAAATATGATTCTGGC 58.077 33.333 0.00 0.00 33.54 4.85
559 562 4.288531 CGTGGGCTACTTTACTTATCTCG 58.711 47.826 0.00 0.00 0.00 4.04
562 569 3.788937 TGCGTGGGCTACTTTACTTATC 58.211 45.455 0.00 0.00 40.82 1.75
572 596 2.033194 GGACACTTGCGTGGGCTAC 61.033 63.158 0.00 0.00 45.50 3.58
606 634 0.184451 AGAGAAGCGTATACCCCCGA 59.816 55.000 0.00 0.00 0.00 5.14
797 2108 3.695060 AGATTGAGAGGGTAGTGTACGTG 59.305 47.826 0.00 0.00 0.00 4.49
798 2109 3.946558 GAGATTGAGAGGGTAGTGTACGT 59.053 47.826 0.00 0.00 0.00 3.57
799 2110 4.200874 AGAGATTGAGAGGGTAGTGTACG 58.799 47.826 0.00 0.00 0.00 3.67
913 2334 0.036010 GGTTGGCTAAGCTCAGCTCA 60.036 55.000 9.21 2.16 38.25 4.26
914 2335 0.036010 TGGTTGGCTAAGCTCAGCTC 60.036 55.000 9.21 0.00 38.25 4.09
915 2336 0.322008 GTGGTTGGCTAAGCTCAGCT 60.322 55.000 9.21 0.00 42.56 4.24
916 2337 0.606401 TGTGGTTGGCTAAGCTCAGC 60.606 55.000 13.36 0.00 41.02 4.26
917 2338 1.160137 GTGTGGTTGGCTAAGCTCAG 58.840 55.000 15.62 0.00 38.14 3.35
953 2382 1.002011 AAGAAGAGAAAGCCGGGGC 60.002 57.895 2.18 0.18 42.33 5.80
976 2405 3.628280 GAGTGAGTGGTCGGTCGGC 62.628 68.421 0.00 0.00 0.00 5.54
1281 2763 2.459969 ATGCATCCCGTGGGGCATA 61.460 57.895 17.01 0.00 43.94 3.14
1288 2776 3.520862 GTGGCCATGCATCCCGTG 61.521 66.667 9.72 0.00 0.00 4.94
1662 3169 0.543749 GAGTTGATGGAGAGTGGGGG 59.456 60.000 0.00 0.00 0.00 5.40
1753 7130 2.687935 GACTGGAAAGGCAAACAGTTCA 59.312 45.455 0.00 0.00 43.61 3.18
1940 7404 2.242926 GATCCTGTCTCCATCGATCCA 58.757 52.381 0.00 0.00 0.00 3.41
2197 11712 7.653311 ACCAAAATCTTTTAACTCGTACGTACT 59.347 33.333 22.55 7.25 0.00 2.73
2208 11729 6.280643 ACCTTGAGCACCAAAATCTTTTAAC 58.719 36.000 0.00 0.00 33.76 2.01
2214 11735 3.507622 GCTAACCTTGAGCACCAAAATCT 59.492 43.478 0.00 0.00 39.84 2.40
2245 11784 9.921637 CCAATTACAAGAACAATTTAGGCTAAA 57.078 29.630 21.05 21.05 0.00 1.85
2246 11785 9.303116 TCCAATTACAAGAACAATTTAGGCTAA 57.697 29.630 2.04 2.04 0.00 3.09
2386 12061 1.206072 CGGAGTCTTTCGACGACGT 59.794 57.895 0.00 0.00 44.93 4.34
2443 12118 2.125793 GTCGGCGGTGTAGGAACC 60.126 66.667 7.21 0.00 36.82 3.62
2650 12352 4.719369 GTCGTCGGCCTTGTCGCT 62.719 66.667 0.00 0.00 0.00 4.93
2656 12358 4.719369 GTGAGCGTCGTCGGCCTT 62.719 66.667 0.00 0.00 37.56 4.35
2720 12443 1.378250 GCTGCTGCTCCTGATGGTT 60.378 57.895 8.53 0.00 36.03 3.67
2836 12578 1.301479 GTTGGAGACCTCGCCGTTT 60.301 57.895 0.00 0.00 38.78 3.60
2852 12594 0.375803 GCGTTGTCGTTGTTCTGGTT 59.624 50.000 0.00 0.00 39.49 3.67
2987 12776 2.849473 CCGGTGAAAACAAAACACTTCG 59.151 45.455 0.00 0.00 35.28 3.79
3075 12876 5.354842 AGTCCACTATAAACTAAGGGTGC 57.645 43.478 0.00 0.00 0.00 5.01
3110 12927 4.744570 TGTTTCGAGATACTTGGTAGCTG 58.255 43.478 0.00 0.00 34.77 4.24
3114 12931 3.512329 TGCCTGTTTCGAGATACTTGGTA 59.488 43.478 0.00 0.00 0.00 3.25
3123 12940 0.037326 AGCGAATGCCTGTTTCGAGA 60.037 50.000 9.74 0.00 46.73 4.04
3124 12941 0.371645 GAGCGAATGCCTGTTTCGAG 59.628 55.000 9.74 0.00 46.73 4.04
3125 12942 1.019278 GGAGCGAATGCCTGTTTCGA 61.019 55.000 9.74 0.00 46.73 3.71
3126 12943 1.425428 GGAGCGAATGCCTGTTTCG 59.575 57.895 1.70 1.70 46.56 3.46
3127 12944 1.425428 CGGAGCGAATGCCTGTTTC 59.575 57.895 0.00 0.00 44.31 2.78
3128 12945 3.578456 CGGAGCGAATGCCTGTTT 58.422 55.556 0.00 0.00 44.31 2.83
3141 12958 8.856247 GGTTGTTGTTTTATTTATAAAGCGGAG 58.144 33.333 3.94 0.00 36.59 4.63
3142 12959 8.358148 TGGTTGTTGTTTTATTTATAAAGCGGA 58.642 29.630 3.94 0.00 36.59 5.54
3143 12960 8.522178 TGGTTGTTGTTTTATTTATAAAGCGG 57.478 30.769 3.94 0.00 36.59 5.52
3153 12970 9.453325 CGTGTAACTTATGGTTGTTGTTTTATT 57.547 29.630 0.00 0.00 38.75 1.40
3154 12971 8.077386 CCGTGTAACTTATGGTTGTTGTTTTAT 58.923 33.333 0.00 0.00 38.75 1.40
3155 12972 7.416022 CCGTGTAACTTATGGTTGTTGTTTTA 58.584 34.615 0.00 0.00 38.75 1.52
3156 12973 6.267070 CCGTGTAACTTATGGTTGTTGTTTT 58.733 36.000 0.00 0.00 38.75 2.43
3157 12974 5.733937 GCCGTGTAACTTATGGTTGTTGTTT 60.734 40.000 0.00 0.00 38.75 2.83
3158 12975 4.261280 GCCGTGTAACTTATGGTTGTTGTT 60.261 41.667 0.00 0.00 38.75 2.83
3159 12976 3.251487 GCCGTGTAACTTATGGTTGTTGT 59.749 43.478 0.00 0.00 38.75 3.32
3160 12977 3.665848 CGCCGTGTAACTTATGGTTGTTG 60.666 47.826 0.00 0.00 38.75 3.33
3161 12978 2.481185 CGCCGTGTAACTTATGGTTGTT 59.519 45.455 0.00 0.00 38.75 2.83
3162 12979 2.070783 CGCCGTGTAACTTATGGTTGT 58.929 47.619 0.00 0.00 38.75 3.32
3163 12980 2.339418 TCGCCGTGTAACTTATGGTTG 58.661 47.619 0.00 0.00 38.75 3.77
3164 12981 2.747396 TCGCCGTGTAACTTATGGTT 57.253 45.000 0.00 0.00 41.54 3.67
3165 12982 2.747396 TTCGCCGTGTAACTTATGGT 57.253 45.000 0.00 0.00 31.75 3.55
3166 12983 3.680937 TCTTTTCGCCGTGTAACTTATGG 59.319 43.478 0.00 0.00 31.75 2.74
3167 12984 4.914312 TCTTTTCGCCGTGTAACTTATG 57.086 40.909 0.00 0.00 31.75 1.90
3168 12985 6.101332 TGTATCTTTTCGCCGTGTAACTTAT 58.899 36.000 0.00 0.00 31.75 1.73
3169 12986 5.468592 TGTATCTTTTCGCCGTGTAACTTA 58.531 37.500 0.00 0.00 31.75 2.24
3170 12987 4.309099 TGTATCTTTTCGCCGTGTAACTT 58.691 39.130 0.00 0.00 31.75 2.66
3171 12988 3.916761 TGTATCTTTTCGCCGTGTAACT 58.083 40.909 0.00 0.00 31.75 2.24
3172 12989 4.650545 TTGTATCTTTTCGCCGTGTAAC 57.349 40.909 0.00 0.00 0.00 2.50
3173 12990 6.757478 TCATATTGTATCTTTTCGCCGTGTAA 59.243 34.615 0.00 0.00 0.00 2.41
3174 12991 6.274579 TCATATTGTATCTTTTCGCCGTGTA 58.725 36.000 0.00 0.00 0.00 2.90
3175 12992 5.113383 TCATATTGTATCTTTTCGCCGTGT 58.887 37.500 0.00 0.00 0.00 4.49
3176 12993 5.651172 TCATATTGTATCTTTTCGCCGTG 57.349 39.130 0.00 0.00 0.00 4.94
3177 12994 5.989168 TCATCATATTGTATCTTTTCGCCGT 59.011 36.000 0.00 0.00 0.00 5.68
3178 12995 6.401474 CCTCATCATATTGTATCTTTTCGCCG 60.401 42.308 0.00 0.00 0.00 6.46
3179 12996 6.428159 ACCTCATCATATTGTATCTTTTCGCC 59.572 38.462 0.00 0.00 0.00 5.54
3180 12997 7.426929 ACCTCATCATATTGTATCTTTTCGC 57.573 36.000 0.00 0.00 0.00 4.70
3183 13000 9.574516 GGGTTACCTCATCATATTGTATCTTTT 57.425 33.333 0.00 0.00 0.00 2.27
3184 13001 8.949421 AGGGTTACCTCATCATATTGTATCTTT 58.051 33.333 0.00 0.00 46.95 2.52
3185 13002 8.511748 AGGGTTACCTCATCATATTGTATCTT 57.488 34.615 0.00 0.00 46.95 2.40
3210 13027 1.847328 TCCGGTTGCTCTATGTGAGA 58.153 50.000 0.00 0.00 45.39 3.27
3211 13028 2.898729 ATCCGGTTGCTCTATGTGAG 57.101 50.000 0.00 0.00 45.33 3.51
3212 13029 3.958147 TCTTATCCGGTTGCTCTATGTGA 59.042 43.478 0.00 0.00 0.00 3.58
3213 13030 4.038042 TCTCTTATCCGGTTGCTCTATGTG 59.962 45.833 0.00 0.00 0.00 3.21
3214 13031 4.215908 TCTCTTATCCGGTTGCTCTATGT 58.784 43.478 0.00 0.00 0.00 2.29
3215 13032 4.855715 TCTCTTATCCGGTTGCTCTATG 57.144 45.455 0.00 0.00 0.00 2.23
3216 13033 4.649674 TGTTCTCTTATCCGGTTGCTCTAT 59.350 41.667 0.00 0.00 0.00 1.98
3217 13034 4.021229 TGTTCTCTTATCCGGTTGCTCTA 58.979 43.478 0.00 0.00 0.00 2.43
3218 13035 2.832129 TGTTCTCTTATCCGGTTGCTCT 59.168 45.455 0.00 0.00 0.00 4.09
3219 13036 3.247006 TGTTCTCTTATCCGGTTGCTC 57.753 47.619 0.00 0.00 0.00 4.26
3220 13037 3.695830 TTGTTCTCTTATCCGGTTGCT 57.304 42.857 0.00 0.00 0.00 3.91
3221 13038 5.504173 GCTTATTGTTCTCTTATCCGGTTGC 60.504 44.000 0.00 0.00 0.00 4.17
3222 13039 5.584649 TGCTTATTGTTCTCTTATCCGGTTG 59.415 40.000 0.00 0.00 0.00 3.77
3223 13040 5.585047 GTGCTTATTGTTCTCTTATCCGGTT 59.415 40.000 0.00 0.00 0.00 4.44
3224 13041 5.116882 GTGCTTATTGTTCTCTTATCCGGT 58.883 41.667 0.00 0.00 0.00 5.28
3225 13042 5.116180 TGTGCTTATTGTTCTCTTATCCGG 58.884 41.667 0.00 0.00 0.00 5.14
3226 13043 6.662414 TTGTGCTTATTGTTCTCTTATCCG 57.338 37.500 0.00 0.00 0.00 4.18
3227 13044 7.917505 CCATTTGTGCTTATTGTTCTCTTATCC 59.082 37.037 0.00 0.00 0.00 2.59
3228 13045 8.462016 ACCATTTGTGCTTATTGTTCTCTTATC 58.538 33.333 0.00 0.00 0.00 1.75
3233 13050 6.908825 TGTACCATTTGTGCTTATTGTTCTC 58.091 36.000 0.00 0.00 0.00 2.87
3254 13071 8.240682 GGTTCTTGCACATGTACAAATATTGTA 58.759 33.333 12.47 0.00 43.27 2.41
3268 13085 2.957402 TTCTGGAGGTTCTTGCACAT 57.043 45.000 0.00 0.00 0.00 3.21
3389 13206 2.550830 AGTTGGTAAGGTGCTGAGTG 57.449 50.000 0.00 0.00 0.00 3.51
3390 13207 2.028020 GCTAGTTGGTAAGGTGCTGAGT 60.028 50.000 0.00 0.00 0.00 3.41
3391 13208 2.028112 TGCTAGTTGGTAAGGTGCTGAG 60.028 50.000 0.00 0.00 0.00 3.35
3392 13209 1.974957 TGCTAGTTGGTAAGGTGCTGA 59.025 47.619 0.00 0.00 0.00 4.26
3393 13210 2.350522 CTGCTAGTTGGTAAGGTGCTG 58.649 52.381 0.00 0.00 0.00 4.41
3394 13211 1.339151 GCTGCTAGTTGGTAAGGTGCT 60.339 52.381 0.00 0.00 0.00 4.40
3395 13212 1.087501 GCTGCTAGTTGGTAAGGTGC 58.912 55.000 0.00 0.00 0.00 5.01
3396 13213 2.472695 TGCTGCTAGTTGGTAAGGTG 57.527 50.000 0.00 0.00 0.00 4.00
3397 13214 2.552373 GGTTGCTGCTAGTTGGTAAGGT 60.552 50.000 0.00 0.00 0.00 3.50
3398 13215 2.084546 GGTTGCTGCTAGTTGGTAAGG 58.915 52.381 0.00 0.00 0.00 2.69
3399 13216 2.484264 GTGGTTGCTGCTAGTTGGTAAG 59.516 50.000 0.00 0.00 0.00 2.34
3400 13217 2.158740 TGTGGTTGCTGCTAGTTGGTAA 60.159 45.455 0.00 0.00 0.00 2.85
3401 13218 1.418264 TGTGGTTGCTGCTAGTTGGTA 59.582 47.619 0.00 0.00 0.00 3.25
3402 13219 0.182537 TGTGGTTGCTGCTAGTTGGT 59.817 50.000 0.00 0.00 0.00 3.67
3403 13220 1.267806 CTTGTGGTTGCTGCTAGTTGG 59.732 52.381 0.00 0.00 0.00 3.77
3404 13221 1.949525 ACTTGTGGTTGCTGCTAGTTG 59.050 47.619 0.00 0.00 0.00 3.16
3405 13222 1.949525 CACTTGTGGTTGCTGCTAGTT 59.050 47.619 0.00 0.00 0.00 2.24
3406 13223 1.597742 CACTTGTGGTTGCTGCTAGT 58.402 50.000 0.00 0.00 0.00 2.57
3407 13224 0.877071 CCACTTGTGGTTGCTGCTAG 59.123 55.000 11.39 0.00 0.00 3.42
3408 13225 1.172180 GCCACTTGTGGTTGCTGCTA 61.172 55.000 19.47 0.00 34.27 3.49
3409 13226 2.492773 GCCACTTGTGGTTGCTGCT 61.493 57.895 19.47 0.00 34.27 4.24
3410 13227 2.028043 GCCACTTGTGGTTGCTGC 59.972 61.111 19.47 0.00 34.27 5.25
3411 13228 0.249155 CTTGCCACTTGTGGTTGCTG 60.249 55.000 19.47 4.43 37.46 4.41
3412 13229 0.395586 TCTTGCCACTTGTGGTTGCT 60.396 50.000 19.47 0.00 37.46 3.91
3413 13230 0.459489 TTCTTGCCACTTGTGGTTGC 59.541 50.000 19.47 7.45 37.14 4.17
3414 13231 2.929398 GTTTTCTTGCCACTTGTGGTTG 59.071 45.455 19.47 10.80 0.00 3.77
3415 13232 2.093711 GGTTTTCTTGCCACTTGTGGTT 60.094 45.455 19.47 0.00 0.00 3.67
3416 13233 1.480545 GGTTTTCTTGCCACTTGTGGT 59.519 47.619 19.47 0.00 0.00 4.16
3417 13234 1.480137 TGGTTTTCTTGCCACTTGTGG 59.520 47.619 14.94 14.94 0.00 4.17
3418 13235 2.957491 TGGTTTTCTTGCCACTTGTG 57.043 45.000 0.00 0.00 0.00 3.33
3424 13241 3.685139 TGTTTTGTGGTTTTCTTGCCA 57.315 38.095 0.00 0.00 0.00 4.92
3425 13242 4.454161 ACTTTGTTTTGTGGTTTTCTTGCC 59.546 37.500 0.00 0.00 0.00 4.52
3426 13243 5.605564 ACTTTGTTTTGTGGTTTTCTTGC 57.394 34.783 0.00 0.00 0.00 4.01
3427 13244 9.540431 CATTAACTTTGTTTTGTGGTTTTCTTG 57.460 29.630 0.00 0.00 0.00 3.02
3428 13245 8.233868 GCATTAACTTTGTTTTGTGGTTTTCTT 58.766 29.630 0.00 0.00 0.00 2.52
3429 13246 7.389053 TGCATTAACTTTGTTTTGTGGTTTTCT 59.611 29.630 0.00 0.00 0.00 2.52
3430 13247 7.522374 TGCATTAACTTTGTTTTGTGGTTTTC 58.478 30.769 0.00 0.00 0.00 2.29
3431 13248 7.389053 TCTGCATTAACTTTGTTTTGTGGTTTT 59.611 29.630 0.00 0.00 0.00 2.43
3432 13249 6.876257 TCTGCATTAACTTTGTTTTGTGGTTT 59.124 30.769 0.00 0.00 0.00 3.27
3433 13250 6.402222 TCTGCATTAACTTTGTTTTGTGGTT 58.598 32.000 0.00 0.00 0.00 3.67
3434 13251 5.971763 TCTGCATTAACTTTGTTTTGTGGT 58.028 33.333 0.00 0.00 0.00 4.16
3435 13252 7.481275 AATCTGCATTAACTTTGTTTTGTGG 57.519 32.000 0.00 0.00 0.00 4.17
3437 13254 9.762933 ACATAATCTGCATTAACTTTGTTTTGT 57.237 25.926 0.00 0.00 0.00 2.83
3441 13258 9.855021 GGTAACATAATCTGCATTAACTTTGTT 57.145 29.630 0.00 0.00 32.47 2.83
3442 13259 9.243105 AGGTAACATAATCTGCATTAACTTTGT 57.757 29.630 0.00 0.00 41.41 2.83
3445 13262 8.612619 CGAAGGTAACATAATCTGCATTAACTT 58.387 33.333 4.38 4.38 35.89 2.66
3446 13263 7.985184 TCGAAGGTAACATAATCTGCATTAACT 59.015 33.333 0.00 0.00 41.41 2.24
3447 13264 8.138365 TCGAAGGTAACATAATCTGCATTAAC 57.862 34.615 0.00 0.00 41.41 2.01
3448 13265 8.902540 ATCGAAGGTAACATAATCTGCATTAA 57.097 30.769 0.00 0.00 41.41 1.40
3449 13266 9.990360 TTATCGAAGGTAACATAATCTGCATTA 57.010 29.630 0.00 0.00 41.41 1.90
3450 13267 8.774586 GTTATCGAAGGTAACATAATCTGCATT 58.225 33.333 0.00 0.00 41.41 3.56
3451 13268 7.387948 GGTTATCGAAGGTAACATAATCTGCAT 59.612 37.037 9.07 0.00 41.41 3.96
3452 13269 6.704493 GGTTATCGAAGGTAACATAATCTGCA 59.296 38.462 9.07 0.00 41.41 4.41
3453 13270 6.929606 AGGTTATCGAAGGTAACATAATCTGC 59.070 38.462 9.07 0.00 41.41 4.26
3458 13275 8.086522 GCTCATAGGTTATCGAAGGTAACATAA 58.913 37.037 9.07 0.00 33.65 1.90
3459 13276 7.450634 AGCTCATAGGTTATCGAAGGTAACATA 59.549 37.037 9.07 6.91 41.41 2.29
3460 13277 6.267928 AGCTCATAGGTTATCGAAGGTAACAT 59.732 38.462 9.07 5.12 41.41 2.71
3461 13278 5.597182 AGCTCATAGGTTATCGAAGGTAACA 59.403 40.000 9.07 0.00 41.41 2.41
3462 13279 5.921408 CAGCTCATAGGTTATCGAAGGTAAC 59.079 44.000 0.00 0.00 0.00 2.50
3463 13280 5.509163 GCAGCTCATAGGTTATCGAAGGTAA 60.509 44.000 0.00 0.00 0.00 2.85
3464 13281 4.022242 GCAGCTCATAGGTTATCGAAGGTA 60.022 45.833 0.00 0.00 0.00 3.08
3465 13282 3.243907 GCAGCTCATAGGTTATCGAAGGT 60.244 47.826 0.00 0.00 0.00 3.50
3466 13283 3.006323 AGCAGCTCATAGGTTATCGAAGG 59.994 47.826 0.00 0.00 0.00 3.46
3467 13284 4.022416 AGAGCAGCTCATAGGTTATCGAAG 60.022 45.833 24.64 0.00 32.06 3.79
3468 13285 3.891977 AGAGCAGCTCATAGGTTATCGAA 59.108 43.478 24.64 0.00 32.06 3.71
3469 13286 3.491342 AGAGCAGCTCATAGGTTATCGA 58.509 45.455 24.64 0.00 32.06 3.59
3470 13287 3.832276 GAGAGCAGCTCATAGGTTATCG 58.168 50.000 24.64 0.00 43.38 2.92
3481 13298 1.408340 TCAGCAGTATGAGAGCAGCTC 59.592 52.381 15.25 15.25 44.21 4.09
3482 13299 1.482954 TCAGCAGTATGAGAGCAGCT 58.517 50.000 0.00 0.00 39.69 4.24
3483 13300 1.932511 GTTCAGCAGTATGAGAGCAGC 59.067 52.381 0.00 0.00 39.69 5.25
3484 13301 2.093816 TGGTTCAGCAGTATGAGAGCAG 60.094 50.000 0.00 0.00 39.69 4.24
3485 13302 1.901833 TGGTTCAGCAGTATGAGAGCA 59.098 47.619 0.00 0.00 39.69 4.26
3486 13303 2.680312 TGGTTCAGCAGTATGAGAGC 57.320 50.000 0.00 0.00 39.69 4.09
3493 13310 1.885887 GTGCCATTTGGTTCAGCAGTA 59.114 47.619 0.00 0.00 37.57 2.74
3496 13313 1.659233 CGTGCCATTTGGTTCAGCA 59.341 52.632 0.00 0.00 37.57 4.41
3503 13320 3.439494 CAAATCCCGTGCCATTTGG 57.561 52.632 0.00 0.00 36.66 3.28
3537 13354 7.197703 TGATTCGTATATGTTTCGAGCTTACA 58.802 34.615 0.00 0.00 35.13 2.41
3593 13410 1.302366 CGTATCAGCCATGCACACAT 58.698 50.000 0.00 0.00 36.79 3.21
3704 13521 4.461081 GTGGGCACTGGATTAATGTGTTAA 59.539 41.667 0.00 0.00 34.50 2.01
3822 13639 3.153369 TGATGTTAGTGGCACAATGGT 57.847 42.857 21.41 0.31 44.16 3.55
3835 13652 2.062636 GCCCCCTTCCCTATGATGTTA 58.937 52.381 0.00 0.00 0.00 2.41
3843 13660 3.961651 TGGTGGCCCCCTTCCCTA 61.962 66.667 5.62 0.00 0.00 3.53



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

AutoCloner maintained by Alex Coulton.