Multiple sequence alignment - TraesCS7A01G136500

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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 TraesCS7A01G136500 chr7A 100.000 3785 0 0 1 3785 89045587 89041803 0.000000e+00 6990
1 TraesCS7A01G136500 chr7A 88.700 646 70 2 2146 2790 89035844 89035201 0.000000e+00 785
2 TraesCS7A01G136500 chr7A 86.003 643 69 14 1495 2134 89036628 89036004 0.000000e+00 669
3 TraesCS7A01G136500 chr7A 83.908 522 73 7 842 1355 89037490 89036972 4.390000e-134 488
4 TraesCS7A01G136500 chr7D 91.765 2198 161 10 1359 3548 87506994 87504809 0.000000e+00 3038
5 TraesCS7A01G136500 chr7D 87.532 770 63 18 599 1357 87507781 87507034 0.000000e+00 859
6 TraesCS7A01G136500 chr7D 86.842 646 66 11 1495 2130 87486961 87486325 0.000000e+00 704
7 TraesCS7A01G136500 chr7D 83.080 526 69 9 846 1355 87489029 87488508 9.580000e-126 460
8 TraesCS7A01G136500 chr7D 77.996 509 56 24 1 457 87508635 87508131 6.230000e-68 268
9 TraesCS7A01G136500 chr7D 91.566 166 14 0 2169 2334 87486179 87486014 2.940000e-56 230
10 TraesCS7A01G136500 chr7B 89.434 1325 109 17 2154 3466 36490172 36488867 0.000000e+00 1642
11 TraesCS7A01G136500 chr7B 92.468 624 41 3 1495 2114 36490911 36490290 0.000000e+00 887
12 TraesCS7A01G136500 chr7B 84.642 879 90 28 484 1357 36491904 36491066 0.000000e+00 833
13 TraesCS7A01G136500 chr7B 87.307 646 63 11 1495 2130 36473555 36472919 0.000000e+00 721
14 TraesCS7A01G136500 chr7B 85.772 499 57 4 2293 2790 36469684 36469199 2.020000e-142 516
15 TraesCS7A01G136500 chr7B 84.302 516 73 4 847 1355 36474398 36473884 7.300000e-137 497
16 TraesCS7A01G136500 chr7B 83.658 514 47 13 9 486 36492445 36491933 2.070000e-122 449
17 TraesCS7A01G136500 chr7B 85.593 236 28 3 3544 3779 162626167 162626396 3.780000e-60 243
18 TraesCS7A01G136500 chr7B 85.000 240 29 4 3547 3785 508824001 508823768 1.760000e-58 237
19 TraesCS7A01G136500 chr7B 85.470 234 27 4 3547 3779 698864807 698865034 1.760000e-58 237
20 TraesCS7A01G136500 chr7B 84.937 239 28 6 3544 3782 506986684 506986914 6.320000e-58 235
21 TraesCS7A01G136500 chr7B 89.474 133 14 0 2169 2301 36472773 36472641 6.500000e-38 169
22 TraesCS7A01G136500 chr4D 86.885 244 24 4 3544 3785 390266877 390266640 2.240000e-67 267
23 TraesCS7A01G136500 chr1D 86.864 236 25 3 3547 3782 379732316 379732545 3.750000e-65 259
24 TraesCS7A01G136500 chr5B 85.897 234 26 4 3546 3779 252323904 252323678 3.780000e-60 243
25 TraesCS7A01G136500 chr3A 85.356 239 29 2 3547 3785 76648401 76648169 3.780000e-60 243
26 TraesCS7A01G136500 chr3A 85.837 233 26 4 3547 3779 490624532 490624307 1.360000e-59 241


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 TraesCS7A01G136500 chr7A 89041803 89045587 3784 True 6990.000000 6990 100.000000 1 3785 1 chr7A.!!$R1 3784
1 TraesCS7A01G136500 chr7A 89035201 89037490 2289 True 647.333333 785 86.203667 842 2790 3 chr7A.!!$R2 1948
2 TraesCS7A01G136500 chr7D 87504809 87508635 3826 True 1388.333333 3038 85.764333 1 3548 3 chr7D.!!$R2 3547
3 TraesCS7A01G136500 chr7D 87486014 87489029 3015 True 464.666667 704 87.162667 846 2334 3 chr7D.!!$R1 1488
4 TraesCS7A01G136500 chr7B 36488867 36492445 3578 True 952.750000 1642 87.550500 9 3466 4 chr7B.!!$R3 3457
5 TraesCS7A01G136500 chr7B 36469199 36474398 5199 True 475.750000 721 86.713750 847 2790 4 chr7B.!!$R2 1943

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
611 903 0.033504 GGTCAGTTGCAGTTCTCCGA 59.966 55.0 0.00 0.00 0.0 4.55 F
613 905 0.033504 TCAGTTGCAGTTCTCCGACC 59.966 55.0 0.00 0.00 0.0 4.79 F
914 1242 0.036010 AGCCCAATCAGTGAAGACGG 60.036 55.0 0.00 0.00 0.0 4.79 F
2370 7375 0.319900 TCAAAGAGACACTGCGCCTC 60.320 55.0 4.18 3.32 0.0 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2272 4312 0.879090 CCGCCAACCAAACTCCTTAC 59.121 55.000 0.00 0.00 0.00 2.34 R
2403 7408 1.428912 ACCTTCACATGGTCCATGGTT 59.571 47.619 30.96 12.38 45.16 3.67 R
2634 7639 1.704582 GCTAGCAAGCGTGAACTCG 59.295 57.895 10.63 0.00 39.39 4.18 R
3599 8623 0.620556 ATCTCGGTCAAACATGGCCT 59.379 50.000 3.32 0.00 0.00 5.19 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.218603 ACACAGTTGAATCGGTTGGTC 58.781 47.619 0.00 0.00 0.00 4.02
51 52 2.094545 GCAGCTACATTTGGAAGTTGGG 60.095 50.000 0.00 0.00 0.00 4.12
55 56 1.047801 ACATTTGGAAGTTGGGCCAC 58.952 50.000 5.23 1.08 33.01 5.01
95 96 5.004448 AGTGTTCGTCTTCTATCAGTCAGA 58.996 41.667 0.00 0.00 0.00 3.27
181 186 5.702209 GCAATTCCAAAGTTTGTCATCCAAT 59.298 36.000 14.36 0.93 31.81 3.16
223 250 8.879342 ATCCTAAGATTCTATGAGAAACAACG 57.121 34.615 0.00 0.00 37.82 4.10
224 251 7.265673 TCCTAAGATTCTATGAGAAACAACGG 58.734 38.462 0.00 0.00 37.82 4.44
254 282 7.881232 TCGTATTTAGACCCATTTCAGTTTTCT 59.119 33.333 0.00 0.00 0.00 2.52
261 289 4.342092 ACCCATTTCAGTTTTCTTGGTGAG 59.658 41.667 0.00 0.00 0.00 3.51
263 291 5.163416 CCCATTTCAGTTTTCTTGGTGAGTT 60.163 40.000 0.00 0.00 0.00 3.01
300 338 3.133542 TGCTCTCCAGTTCATACATCCAG 59.866 47.826 0.00 0.00 0.00 3.86
309 347 2.042464 TCATACATCCAGACAGAGCCC 58.958 52.381 0.00 0.00 0.00 5.19
394 444 6.399639 TTTCAAAACCTAGAATGTGGGTTC 57.600 37.500 0.00 0.00 41.78 3.62
401 451 2.671619 AATGTGGGTTCGGGCGTG 60.672 61.111 0.00 0.00 0.00 5.34
414 464 0.530288 GGGCGTGCACCATTGTAAAT 59.470 50.000 12.15 0.00 0.00 1.40
419 469 3.489059 GCGTGCACCATTGTAAATATGCT 60.489 43.478 12.15 0.00 34.18 3.79
474 735 8.693542 TCAACATGCTATCATATTATCGACTG 57.306 34.615 0.00 0.00 0.00 3.51
507 798 5.939764 TCAGTGAAAGGCTACATGTATCT 57.060 39.130 5.91 4.64 0.00 1.98
516 807 5.414360 AGGCTACATGTATCTATTGATGCG 58.586 41.667 5.91 0.00 37.99 4.73
533 824 1.302671 CGGAGGCCGGGTTTTTACA 60.303 57.895 2.18 0.00 44.15 2.41
540 832 2.363038 GGCCGGGTTTTTACACTCTTTT 59.637 45.455 2.18 0.00 0.00 2.27
602 894 1.296392 CCGAGATGGGTCAGTTGCA 59.704 57.895 0.00 0.00 0.00 4.08
603 895 0.742281 CCGAGATGGGTCAGTTGCAG 60.742 60.000 0.00 0.00 0.00 4.41
604 896 0.036952 CGAGATGGGTCAGTTGCAGT 60.037 55.000 0.00 0.00 0.00 4.40
606 898 2.079925 GAGATGGGTCAGTTGCAGTTC 58.920 52.381 0.00 0.00 0.00 3.01
608 900 2.079925 GATGGGTCAGTTGCAGTTCTC 58.920 52.381 0.00 0.00 0.00 2.87
609 901 0.108585 TGGGTCAGTTGCAGTTCTCC 59.891 55.000 0.00 0.00 0.00 3.71
610 902 0.951040 GGGTCAGTTGCAGTTCTCCG 60.951 60.000 0.00 0.00 0.00 4.63
611 903 0.033504 GGTCAGTTGCAGTTCTCCGA 59.966 55.000 0.00 0.00 0.00 4.55
612 904 1.140816 GTCAGTTGCAGTTCTCCGAC 58.859 55.000 0.00 0.00 0.00 4.79
613 905 0.033504 TCAGTTGCAGTTCTCCGACC 59.966 55.000 0.00 0.00 0.00 4.79
614 906 0.249868 CAGTTGCAGTTCTCCGACCA 60.250 55.000 0.00 0.00 0.00 4.02
615 907 0.249911 AGTTGCAGTTCTCCGACCAC 60.250 55.000 0.00 0.00 0.00 4.16
616 908 0.249911 GTTGCAGTTCTCCGACCACT 60.250 55.000 0.00 0.00 0.00 4.00
617 909 1.000506 GTTGCAGTTCTCCGACCACTA 59.999 52.381 0.00 0.00 0.00 2.74
618 910 1.334160 TGCAGTTCTCCGACCACTAA 58.666 50.000 0.00 0.00 0.00 2.24
619 911 1.899814 TGCAGTTCTCCGACCACTAAT 59.100 47.619 0.00 0.00 0.00 1.73
624 947 3.129988 AGTTCTCCGACCACTAATTACCG 59.870 47.826 0.00 0.00 0.00 4.02
626 949 2.684881 TCTCCGACCACTAATTACCGAC 59.315 50.000 0.00 0.00 0.00 4.79
641 964 2.454538 ACCGACGAGTTCCCTTCTAAT 58.545 47.619 0.00 0.00 0.00 1.73
646 969 5.393896 CCGACGAGTTCCCTTCTAATAGTTT 60.394 44.000 0.00 0.00 0.00 2.66
662 985 6.361768 AATAGTTTACCCATCTAGCTAGCC 57.638 41.667 16.35 0.00 0.00 3.93
699 1027 6.748333 TCTGCTCTGAATTATTTCCTTGTG 57.252 37.500 0.00 0.00 0.00 3.33
700 1028 6.475504 TCTGCTCTGAATTATTTCCTTGTGA 58.524 36.000 0.00 0.00 0.00 3.58
727 1055 6.934056 TGTCCATACAAAGGATTCCAAATTG 58.066 36.000 5.29 9.46 37.52 2.32
728 1056 6.723515 TGTCCATACAAAGGATTCCAAATTGA 59.276 34.615 17.57 6.67 37.52 2.57
729 1057 7.093814 TGTCCATACAAAGGATTCCAAATTGAG 60.094 37.037 17.57 9.78 37.52 3.02
730 1058 6.953520 TCCATACAAAGGATTCCAAATTGAGT 59.046 34.615 17.57 5.38 0.00 3.41
731 1059 8.112822 TCCATACAAAGGATTCCAAATTGAGTA 58.887 33.333 17.57 6.90 0.00 2.59
732 1060 8.917088 CCATACAAAGGATTCCAAATTGAGTAT 58.083 33.333 17.57 8.35 0.00 2.12
780 1108 4.183865 TCTCAAAGTCCAATGCGTGATAG 58.816 43.478 0.00 0.00 0.00 2.08
802 1130 3.243101 GGCGTGATCGAGACTGAAAGATA 60.243 47.826 0.00 0.00 39.71 1.98
810 1138 5.344066 TCGAGACTGAAAGATATTGCAGAC 58.656 41.667 15.15 8.68 37.43 3.51
844 1172 1.917495 CTGAGCCCCATGGTGATCA 59.083 57.895 14.63 14.63 0.00 2.92
849 1177 1.153168 CCCCATGGTGATCACGACC 60.153 63.158 19.33 6.83 0.00 4.79
856 1184 0.605319 GGTGATCACGACCTGCCAAA 60.605 55.000 19.33 0.00 0.00 3.28
858 1186 0.396435 TGATCACGACCTGCCAAACT 59.604 50.000 0.00 0.00 0.00 2.66
885 1213 1.106285 GGCACCTCAATCATTCACCC 58.894 55.000 0.00 0.00 0.00 4.61
914 1242 0.036010 AGCCCAATCAGTGAAGACGG 60.036 55.000 0.00 0.00 0.00 4.79
915 1243 1.026718 GCCCAATCAGTGAAGACGGG 61.027 60.000 12.82 12.82 36.89 5.28
916 1244 0.613260 CCCAATCAGTGAAGACGGGA 59.387 55.000 12.08 0.00 36.23 5.14
920 1248 3.056107 CCAATCAGTGAAGACGGGAACTA 60.056 47.826 0.00 0.00 0.00 2.24
921 1249 4.562757 CCAATCAGTGAAGACGGGAACTAA 60.563 45.833 0.00 0.00 0.00 2.24
923 1251 3.228453 TCAGTGAAGACGGGAACTAACT 58.772 45.455 0.00 0.00 0.00 2.24
924 1252 3.255149 TCAGTGAAGACGGGAACTAACTC 59.745 47.826 0.00 0.00 0.00 3.01
925 1253 3.005472 CAGTGAAGACGGGAACTAACTCA 59.995 47.826 0.00 0.00 0.00 3.41
926 1254 3.640029 AGTGAAGACGGGAACTAACTCAA 59.360 43.478 0.00 0.00 0.00 3.02
927 1255 4.283722 AGTGAAGACGGGAACTAACTCAAT 59.716 41.667 0.00 0.00 0.00 2.57
928 1256 4.626172 GTGAAGACGGGAACTAACTCAATC 59.374 45.833 0.00 0.00 0.00 2.67
929 1257 4.527038 TGAAGACGGGAACTAACTCAATCT 59.473 41.667 0.00 0.00 0.00 2.40
931 1259 4.345854 AGACGGGAACTAACTCAATCTCT 58.654 43.478 0.00 0.00 0.00 3.10
941 1269 7.807977 ACTAACTCAATCTCTCATCTCTCTC 57.192 40.000 0.00 0.00 0.00 3.20
962 1307 3.515502 TCTGTGTATATATCCAGCTGCCC 59.484 47.826 8.66 0.00 0.00 5.36
964 1309 3.261643 TGTGTATATATCCAGCTGCCCAG 59.738 47.826 8.66 0.00 0.00 4.45
1053 1405 2.976490 GCATGCCCTCCTGTGGTCT 61.976 63.158 6.36 0.00 0.00 3.85
1284 1636 1.736645 CATCGTGGTTTCGTCGCCT 60.737 57.895 0.00 0.00 0.00 5.52
1357 1709 1.271543 CCTCATCACCAGGCAAGTTCA 60.272 52.381 0.00 0.00 0.00 3.18
1409 3130 9.645059 TTCTGTAAACATCAACAATTGTTTGAA 57.355 25.926 23.43 13.08 43.76 2.69
1466 3188 4.099881 ACTCATTGTTGTTTGTGCTGGAAT 59.900 37.500 0.00 0.00 0.00 3.01
1479 3201 5.637127 TGTGCTGGAATGGAATATCATCAT 58.363 37.500 0.00 0.00 0.00 2.45
1482 3204 7.108194 GTGCTGGAATGGAATATCATCATCTA 58.892 38.462 0.00 0.00 0.00 1.98
1513 3339 9.995003 AATCTTTCAGGTGCAAAATTAATTACA 57.005 25.926 0.01 0.00 0.00 2.41
1540 3366 1.792367 CAACAAGACATCGCGTTCTCA 59.208 47.619 5.77 0.00 0.00 3.27
1552 3378 0.935831 CGTTCTCACCGTACAACGCA 60.936 55.000 1.64 0.00 40.91 5.24
1591 3417 0.965439 AGCTGTTCGTCTCAGAGCTT 59.035 50.000 0.00 0.00 35.20 3.74
1618 3444 1.782028 GCAAACGCGTCCAGTCCTTT 61.782 55.000 14.44 0.00 0.00 3.11
1817 3643 1.375908 GTGTTCAGCGAGGCCATGA 60.376 57.895 5.01 0.00 0.00 3.07
1861 3687 2.654877 GACTTCTTCCCGGCGTCA 59.345 61.111 6.01 0.00 0.00 4.35
1882 3708 1.144057 GATGAGCCGGTGGTTCGAT 59.856 57.895 1.90 0.00 35.65 3.59
1912 3738 2.499205 CTGGAGGCGCGATACCAA 59.501 61.111 12.10 0.00 31.85 3.67
2254 4294 1.375523 AAGAACCCGACGGTGATGC 60.376 57.895 13.94 0.00 43.71 3.91
2272 4312 1.163554 GCAGAAGGCACAAAGAGAGG 58.836 55.000 0.00 0.00 43.97 3.69
2313 7318 3.733337 CAAACAGAGACTAGTGCAGGTT 58.267 45.455 0.00 0.00 0.00 3.50
2370 7375 0.319900 TCAAAGAGACACTGCGCCTC 60.320 55.000 4.18 3.32 0.00 4.70
2475 7480 2.589442 TTCGTGAACGTGTGGGCC 60.589 61.111 0.00 0.00 40.80 5.80
2541 7546 1.361668 CGGAGAGGTTTGACGGCATG 61.362 60.000 0.00 0.00 0.00 4.06
2561 7566 5.533903 GCATGGACACTGATTTCTATGGATT 59.466 40.000 0.00 0.00 32.76 3.01
2568 7573 6.540189 ACACTGATTTCTATGGATTGCACTAC 59.460 38.462 0.00 0.00 0.00 2.73
2634 7639 2.824041 ATGGGCGCCACAATCGTC 60.824 61.111 30.85 8.62 35.80 4.20
2773 7778 5.511373 CCTCTGTGTCTTGTTCCATCTGTTA 60.511 44.000 0.00 0.00 0.00 2.41
2867 7872 7.414222 TCTCGCTCTTCCCTTTAGTATTTAA 57.586 36.000 0.00 0.00 0.00 1.52
2871 7876 9.106070 TCGCTCTTCCCTTTAGTATTTAAAATC 57.894 33.333 0.00 0.00 0.00 2.17
2905 7919 5.299028 AGTTGTCACATGCATGTTTCACTAA 59.701 36.000 29.48 17.35 39.39 2.24
3018 8032 9.596308 ACTATAAAACACCCTCCAACTTATTTT 57.404 29.630 0.00 0.00 0.00 1.82
3055 8069 6.681571 GCTTTTGCTTTCTGATACAACTTC 57.318 37.500 0.00 0.00 43.35 3.01
3107 8122 8.173542 TGATGCATGCTTCTCAATAATGTAAT 57.826 30.769 27.81 5.55 0.00 1.89
3120 8135 7.771183 TCAATAATGTAATTGGGTTCTTCAGC 58.229 34.615 0.00 0.00 36.99 4.26
3122 8137 5.649782 AATGTAATTGGGTTCTTCAGCTG 57.350 39.130 7.63 7.63 33.44 4.24
3156 8171 4.636206 GCTGTAGTATGGAGGAAACTTTGG 59.364 45.833 0.00 0.00 44.43 3.28
3180 8195 8.637986 TGGAAATTACACTTCTAAAATGTTGCT 58.362 29.630 0.00 0.00 0.00 3.91
3189 8204 7.119846 CACTTCTAAAATGTTGCTTAGGCTAGT 59.880 37.037 0.00 0.00 39.59 2.57
3190 8205 7.665974 ACTTCTAAAATGTTGCTTAGGCTAGTT 59.334 33.333 0.00 0.00 39.59 2.24
3191 8206 9.162764 CTTCTAAAATGTTGCTTAGGCTAGTTA 57.837 33.333 0.00 0.00 39.59 2.24
3192 8207 8.718102 TCTAAAATGTTGCTTAGGCTAGTTAG 57.282 34.615 0.00 0.00 39.59 2.34
3193 8208 8.319146 TCTAAAATGTTGCTTAGGCTAGTTAGT 58.681 33.333 0.00 0.00 39.59 2.24
3194 8209 9.595823 CTAAAATGTTGCTTAGGCTAGTTAGTA 57.404 33.333 0.00 0.00 39.59 1.82
3196 8211 9.462606 AAAATGTTGCTTAGGCTAGTTAGTATT 57.537 29.630 0.00 0.00 39.59 1.89
3197 8212 8.664211 AATGTTGCTTAGGCTAGTTAGTATTC 57.336 34.615 0.00 0.00 39.59 1.75
3198 8213 6.270815 TGTTGCTTAGGCTAGTTAGTATTCG 58.729 40.000 0.00 0.00 39.59 3.34
3199 8214 6.095860 TGTTGCTTAGGCTAGTTAGTATTCGA 59.904 38.462 0.00 0.00 39.59 3.71
3200 8215 6.704289 TGCTTAGGCTAGTTAGTATTCGAA 57.296 37.500 0.00 0.00 39.59 3.71
3201 8216 6.736123 TGCTTAGGCTAGTTAGTATTCGAAG 58.264 40.000 3.35 0.00 39.59 3.79
3202 8217 5.630264 GCTTAGGCTAGTTAGTATTCGAAGC 59.370 44.000 3.35 0.00 35.22 3.86
3203 8218 6.515365 GCTTAGGCTAGTTAGTATTCGAAGCT 60.515 42.308 3.35 7.11 33.38 3.74
3204 8219 7.308469 GCTTAGGCTAGTTAGTATTCGAAGCTA 60.308 40.741 3.35 6.09 33.38 3.32
3205 8220 6.956202 AGGCTAGTTAGTATTCGAAGCTAA 57.044 37.500 16.28 16.28 0.00 3.09
3206 8221 6.737118 AGGCTAGTTAGTATTCGAAGCTAAC 58.263 40.000 29.04 29.04 42.69 2.34
3207 8222 6.320672 AGGCTAGTTAGTATTCGAAGCTAACA 59.679 38.462 33.01 24.51 43.98 2.41
3208 8223 6.637658 GGCTAGTTAGTATTCGAAGCTAACAG 59.362 42.308 33.01 28.85 43.98 3.16
3209 8224 6.142639 GCTAGTTAGTATTCGAAGCTAACAGC 59.857 42.308 33.01 31.47 43.98 4.40
3220 8243 0.109735 GCTAACAGCTTTTCGCCACC 60.110 55.000 0.00 0.00 38.45 4.61
3224 8247 0.533308 ACAGCTTTTCGCCACCGTTA 60.533 50.000 0.00 0.00 40.39 3.18
3333 8357 4.476297 TGGATGGATTTATGCTTGCTCAT 58.524 39.130 0.00 0.00 0.00 2.90
3348 8372 6.317140 TGCTTGCTCATGTTAGATAAAGAAGG 59.683 38.462 0.00 0.00 0.00 3.46
3350 8374 5.126067 TGCTCATGTTAGATAAAGAAGGGC 58.874 41.667 0.00 0.00 0.00 5.19
3353 8377 6.293845 GCTCATGTTAGATAAAGAAGGGCATG 60.294 42.308 0.00 0.00 34.33 4.06
3380 8404 7.427989 AGAGAAATGAATGGGTAAATGCATT 57.572 32.000 5.99 5.99 37.39 3.56
3383 8407 5.954153 AATGAATGGGTAAATGCATTGGA 57.046 34.783 13.82 0.97 34.96 3.53
3420 8444 7.675062 AGTATTAGGGCTTAGATGAGTTGATG 58.325 38.462 0.00 0.00 0.00 3.07
3439 8463 6.496144 TGATGGATCAAATCTGAGATGACT 57.504 37.500 0.00 0.00 34.23 3.41
3445 8469 6.424509 GGATCAAATCTGAGATGACTGCTTAG 59.575 42.308 0.00 0.00 34.23 2.18
3456 8480 7.286316 TGAGATGACTGCTTAGATGAATACTGA 59.714 37.037 0.00 0.00 0.00 3.41
3466 8490 8.934825 GCTTAGATGAATACTGAGATGGATTTC 58.065 37.037 0.00 0.00 0.00 2.17
3467 8491 9.138062 CTTAGATGAATACTGAGATGGATTTCG 57.862 37.037 0.00 0.00 0.00 3.46
3482 8506 9.573133 AGATGGATTTCGTTTAACAATGAATTC 57.427 29.630 0.00 0.00 37.68 2.17
3521 8545 5.521735 GCACTCGATTCACAACTCTAATGAT 59.478 40.000 0.00 0.00 0.00 2.45
3524 8548 8.750416 CACTCGATTCACAACTCTAATGATAAG 58.250 37.037 0.00 0.00 0.00 1.73
3531 8555 7.568349 TCACAACTCTAATGATAAGGATGCTT 58.432 34.615 4.41 4.41 0.00 3.91
3553 8577 9.720874 TGCTTATCATCTATTGATATACTCCCT 57.279 33.333 0.00 0.00 44.77 4.20
3558 8582 9.781425 ATCATCTATTGATATACTCCCTCTGTT 57.219 33.333 0.00 0.00 43.43 3.16
3559 8583 9.249053 TCATCTATTGATATACTCCCTCTGTTC 57.751 37.037 0.00 0.00 0.00 3.18
3560 8584 8.474025 CATCTATTGATATACTCCCTCTGTTCC 58.526 40.741 0.00 0.00 0.00 3.62
3561 8585 7.770662 TCTATTGATATACTCCCTCTGTTCCT 58.229 38.462 0.00 0.00 0.00 3.36
3562 8586 8.235230 TCTATTGATATACTCCCTCTGTTCCTT 58.765 37.037 0.00 0.00 0.00 3.36
3563 8587 7.698163 ATTGATATACTCCCTCTGTTCCTTT 57.302 36.000 0.00 0.00 0.00 3.11
3564 8588 8.798975 ATTGATATACTCCCTCTGTTCCTTTA 57.201 34.615 0.00 0.00 0.00 1.85
3565 8589 8.798975 TTGATATACTCCCTCTGTTCCTTTAT 57.201 34.615 0.00 0.00 0.00 1.40
3566 8590 9.892444 TTGATATACTCCCTCTGTTCCTTTATA 57.108 33.333 0.00 0.00 0.00 0.98
3571 8595 7.619512 ACTCCCTCTGTTCCTTTATATAAGG 57.380 40.000 0.00 0.00 38.78 2.69
3572 8596 6.043358 ACTCCCTCTGTTCCTTTATATAAGGC 59.957 42.308 0.00 0.00 37.34 4.35
3573 8597 5.011738 TCCCTCTGTTCCTTTATATAAGGCG 59.988 44.000 0.00 0.00 37.34 5.52
3574 8598 5.221661 CCCTCTGTTCCTTTATATAAGGCGT 60.222 44.000 0.00 0.00 37.34 5.68
3575 8599 6.014840 CCCTCTGTTCCTTTATATAAGGCGTA 60.015 42.308 0.00 0.00 37.34 4.42
3576 8600 7.310485 CCCTCTGTTCCTTTATATAAGGCGTAT 60.310 40.741 0.00 0.00 37.34 3.06
3577 8601 8.095169 CCTCTGTTCCTTTATATAAGGCGTATT 58.905 37.037 0.00 0.00 37.34 1.89
3578 8602 9.490379 CTCTGTTCCTTTATATAAGGCGTATTT 57.510 33.333 0.00 0.00 37.34 1.40
3579 8603 9.268268 TCTGTTCCTTTATATAAGGCGTATTTG 57.732 33.333 0.00 0.00 37.34 2.32
3580 8604 8.967664 TGTTCCTTTATATAAGGCGTATTTGT 57.032 30.769 0.00 0.00 37.34 2.83
3581 8605 9.398538 TGTTCCTTTATATAAGGCGTATTTGTT 57.601 29.630 0.00 0.00 37.34 2.83
3603 8627 5.767816 TTTTTCAGAAGTCAAACTAGGCC 57.232 39.130 0.00 0.00 0.00 5.19
3604 8628 4.431416 TTTCAGAAGTCAAACTAGGCCA 57.569 40.909 5.01 0.00 0.00 5.36
3605 8629 4.640771 TTCAGAAGTCAAACTAGGCCAT 57.359 40.909 5.01 0.00 0.00 4.40
3606 8630 3.942829 TCAGAAGTCAAACTAGGCCATG 58.057 45.455 5.01 0.00 0.00 3.66
3607 8631 3.327757 TCAGAAGTCAAACTAGGCCATGT 59.672 43.478 5.01 0.00 0.00 3.21
3608 8632 4.074970 CAGAAGTCAAACTAGGCCATGTT 58.925 43.478 5.01 6.53 0.00 2.71
3609 8633 4.520492 CAGAAGTCAAACTAGGCCATGTTT 59.480 41.667 16.98 16.98 36.91 2.83
3614 8638 1.821216 AACTAGGCCATGTTTGACCG 58.179 50.000 5.01 0.00 0.00 4.79
3615 8639 0.981183 ACTAGGCCATGTTTGACCGA 59.019 50.000 5.01 0.00 0.00 4.69
3616 8640 1.066143 ACTAGGCCATGTTTGACCGAG 60.066 52.381 5.01 0.00 0.00 4.63
3617 8641 1.207089 CTAGGCCATGTTTGACCGAGA 59.793 52.381 5.01 0.00 0.00 4.04
3618 8642 0.620556 AGGCCATGTTTGACCGAGAT 59.379 50.000 5.01 0.00 0.00 2.75
3619 8643 1.004745 AGGCCATGTTTGACCGAGATT 59.995 47.619 5.01 0.00 0.00 2.40
3620 8644 1.818674 GGCCATGTTTGACCGAGATTT 59.181 47.619 0.00 0.00 0.00 2.17
3621 8645 2.231235 GGCCATGTTTGACCGAGATTTT 59.769 45.455 0.00 0.00 0.00 1.82
3622 8646 3.244976 GCCATGTTTGACCGAGATTTTG 58.755 45.455 0.00 0.00 0.00 2.44
3623 8647 3.836949 CCATGTTTGACCGAGATTTTGG 58.163 45.455 0.00 0.00 0.00 3.28
3624 8648 3.505680 CCATGTTTGACCGAGATTTTGGA 59.494 43.478 0.00 0.00 0.00 3.53
3625 8649 4.022416 CCATGTTTGACCGAGATTTTGGAA 60.022 41.667 0.00 0.00 0.00 3.53
3626 8650 5.508825 CCATGTTTGACCGAGATTTTGGAAA 60.509 40.000 0.00 0.00 0.00 3.13
3627 8651 5.584253 TGTTTGACCGAGATTTTGGAAAA 57.416 34.783 0.00 0.00 0.00 2.29
3628 8652 5.967088 TGTTTGACCGAGATTTTGGAAAAA 58.033 33.333 0.00 0.00 0.00 1.94
3629 8653 6.578023 TGTTTGACCGAGATTTTGGAAAAAT 58.422 32.000 0.00 0.00 0.00 1.82
3630 8654 7.717568 TGTTTGACCGAGATTTTGGAAAAATA 58.282 30.769 0.00 0.00 0.00 1.40
3631 8655 8.364142 TGTTTGACCGAGATTTTGGAAAAATAT 58.636 29.630 0.00 0.00 0.00 1.28
3632 8656 9.849166 GTTTGACCGAGATTTTGGAAAAATATA 57.151 29.630 0.00 0.00 0.00 0.86
3635 8659 8.846211 TGACCGAGATTTTGGAAAAATATATCC 58.154 33.333 0.00 0.00 36.21 2.59
3636 8660 8.760980 ACCGAGATTTTGGAAAAATATATCCA 57.239 30.769 0.00 1.68 43.84 3.41
3637 8661 9.367160 ACCGAGATTTTGGAAAAATATATCCAT 57.633 29.630 0.00 0.00 44.83 3.41
3685 8709 9.695526 TCATTTGAACCATCATGAAAAGTTAAG 57.304 29.630 0.00 0.00 34.96 1.85
3686 8710 9.480053 CATTTGAACCATCATGAAAAGTTAAGT 57.520 29.630 0.00 0.00 34.96 2.24
3687 8711 8.870160 TTTGAACCATCATGAAAAGTTAAGTG 57.130 30.769 0.00 0.00 34.96 3.16
3688 8712 6.980593 TGAACCATCATGAAAAGTTAAGTGG 58.019 36.000 0.00 1.70 0.00 4.00
3689 8713 6.549364 TGAACCATCATGAAAAGTTAAGTGGT 59.451 34.615 0.00 2.43 38.97 4.16
3690 8714 6.976934 ACCATCATGAAAAGTTAAGTGGTT 57.023 33.333 0.00 0.00 33.97 3.67
3691 8715 7.360113 ACCATCATGAAAAGTTAAGTGGTTT 57.640 32.000 0.00 0.00 33.97 3.27
3692 8716 7.433680 ACCATCATGAAAAGTTAAGTGGTTTC 58.566 34.615 0.00 1.91 33.97 2.78
3693 8717 7.069331 ACCATCATGAAAAGTTAAGTGGTTTCA 59.931 33.333 10.95 10.95 42.42 2.69
3694 8718 8.090214 CCATCATGAAAAGTTAAGTGGTTTCAT 58.910 33.333 13.63 13.63 46.47 2.57
3703 8727 9.840427 AAAGTTAAGTGGTTTCATATTTCATCG 57.160 29.630 0.00 0.00 0.00 3.84
3704 8728 8.786826 AGTTAAGTGGTTTCATATTTCATCGA 57.213 30.769 0.00 0.00 0.00 3.59
3705 8729 9.396022 AGTTAAGTGGTTTCATATTTCATCGAT 57.604 29.630 0.00 0.00 0.00 3.59
3708 8732 8.915871 AAGTGGTTTCATATTTCATCGATTTG 57.084 30.769 0.00 0.00 0.00 2.32
3709 8733 7.483307 AGTGGTTTCATATTTCATCGATTTGG 58.517 34.615 0.00 0.00 0.00 3.28
3710 8734 7.122650 AGTGGTTTCATATTTCATCGATTTGGT 59.877 33.333 0.00 0.00 0.00 3.67
3711 8735 8.402472 GTGGTTTCATATTTCATCGATTTGGTA 58.598 33.333 0.00 0.00 0.00 3.25
3712 8736 9.130661 TGGTTTCATATTTCATCGATTTGGTAT 57.869 29.630 0.00 0.00 0.00 2.73
3713 8737 9.965824 GGTTTCATATTTCATCGATTTGGTATT 57.034 29.630 0.00 0.00 0.00 1.89
3716 8740 8.916628 TCATATTTCATCGATTTGGTATTCCA 57.083 30.769 0.00 0.00 42.66 3.53
3717 8741 9.519191 TCATATTTCATCGATTTGGTATTCCAT 57.481 29.630 0.00 0.00 43.91 3.41
3721 8745 8.690203 TTTCATCGATTTGGTATTCCATATGT 57.310 30.769 0.00 0.00 43.91 2.29
3722 8746 8.690203 TTCATCGATTTGGTATTCCATATGTT 57.310 30.769 0.00 0.00 43.91 2.71
3723 8747 8.098220 TCATCGATTTGGTATTCCATATGTTG 57.902 34.615 0.00 0.07 43.91 3.33
3724 8748 7.719193 TCATCGATTTGGTATTCCATATGTTGT 59.281 33.333 0.00 0.00 43.91 3.32
3725 8749 7.873719 TCGATTTGGTATTCCATATGTTGTT 57.126 32.000 1.24 0.00 43.91 2.83
3726 8750 7.702386 TCGATTTGGTATTCCATATGTTGTTG 58.298 34.615 1.24 0.00 43.91 3.33
3727 8751 6.917477 CGATTTGGTATTCCATATGTTGTTGG 59.083 38.462 1.24 0.00 43.91 3.77
3728 8752 7.416213 CGATTTGGTATTCCATATGTTGTTGGT 60.416 37.037 1.24 0.00 43.91 3.67
3729 8753 7.546250 TTTGGTATTCCATATGTTGTTGGTT 57.454 32.000 1.24 0.00 43.91 3.67
3730 8754 7.546250 TTGGTATTCCATATGTTGTTGGTTT 57.454 32.000 1.24 0.00 43.91 3.27
3731 8755 8.651589 TTGGTATTCCATATGTTGTTGGTTTA 57.348 30.769 1.24 0.00 43.91 2.01
3732 8756 8.830915 TGGTATTCCATATGTTGTTGGTTTAT 57.169 30.769 1.24 0.00 39.03 1.40
3733 8757 9.261035 TGGTATTCCATATGTTGTTGGTTTATT 57.739 29.630 1.24 0.00 39.03 1.40
3738 8762 8.877864 TCCATATGTTGTTGGTTTATTTCTCT 57.122 30.769 1.24 0.00 34.48 3.10
3739 8763 9.967451 TCCATATGTTGTTGGTTTATTTCTCTA 57.033 29.630 1.24 0.00 34.48 2.43
3746 8770 9.573133 GTTGTTGGTTTATTTCTCTAATCATGG 57.427 33.333 0.00 0.00 0.00 3.66
3747 8771 8.877864 TGTTGGTTTATTTCTCTAATCATGGT 57.122 30.769 0.00 0.00 0.00 3.55
3748 8772 8.956426 TGTTGGTTTATTTCTCTAATCATGGTC 58.044 33.333 0.00 0.00 0.00 4.02
3749 8773 8.956426 GTTGGTTTATTTCTCTAATCATGGTCA 58.044 33.333 0.00 0.00 0.00 4.02
3750 8774 9.527157 TTGGTTTATTTCTCTAATCATGGTCAA 57.473 29.630 0.00 0.00 0.00 3.18
3751 8775 9.527157 TGGTTTATTTCTCTAATCATGGTCAAA 57.473 29.630 0.00 0.00 0.00 2.69
3752 8776 9.788960 GGTTTATTTCTCTAATCATGGTCAAAC 57.211 33.333 0.00 0.00 0.00 2.93
3757 8781 8.634335 TTTCTCTAATCATGGTCAAACATTCA 57.366 30.769 0.00 0.00 0.00 2.57
3758 8782 8.634335 TTCTCTAATCATGGTCAAACATTCAA 57.366 30.769 0.00 0.00 0.00 2.69
3759 8783 8.634335 TCTCTAATCATGGTCAAACATTCAAA 57.366 30.769 0.00 0.00 0.00 2.69
3760 8784 9.246670 TCTCTAATCATGGTCAAACATTCAAAT 57.753 29.630 0.00 0.00 0.00 2.32
3761 8785 9.297586 CTCTAATCATGGTCAAACATTCAAATG 57.702 33.333 1.20 1.20 42.10 2.32
3762 8786 8.252417 TCTAATCATGGTCAAACATTCAAATGG 58.748 33.333 7.58 0.00 40.70 3.16
3763 8787 5.804944 TCATGGTCAAACATTCAAATGGT 57.195 34.783 7.58 0.00 40.70 3.55
3764 8788 6.172136 TCATGGTCAAACATTCAAATGGTT 57.828 33.333 7.58 4.05 46.69 3.67
3771 8795 5.989551 AAACATTCAAATGGTTGACTTGC 57.010 34.783 5.24 0.00 44.21 4.01
3772 8796 4.669206 ACATTCAAATGGTTGACTTGCA 57.331 36.364 7.58 0.00 43.52 4.08
3773 8797 4.370917 ACATTCAAATGGTTGACTTGCAC 58.629 39.130 7.58 0.00 43.52 4.57
3774 8798 2.772568 TCAAATGGTTGACTTGCACG 57.227 45.000 0.00 0.00 38.88 5.34
3775 8799 2.293170 TCAAATGGTTGACTTGCACGA 58.707 42.857 0.00 0.00 38.88 4.35
3776 8800 2.685388 TCAAATGGTTGACTTGCACGAA 59.315 40.909 0.00 0.00 38.88 3.85
3777 8801 3.129462 TCAAATGGTTGACTTGCACGAAA 59.871 39.130 0.00 0.00 38.88 3.46
3778 8802 3.791973 AATGGTTGACTTGCACGAAAA 57.208 38.095 0.00 0.00 0.00 2.29
3779 8803 3.791973 ATGGTTGACTTGCACGAAAAA 57.208 38.095 0.00 0.00 0.00 1.94
3780 8804 2.869897 TGGTTGACTTGCACGAAAAAC 58.130 42.857 0.00 0.00 0.00 2.43
3781 8805 2.229062 TGGTTGACTTGCACGAAAAACA 59.771 40.909 0.00 0.00 0.00 2.83
3782 8806 2.851824 GGTTGACTTGCACGAAAAACAG 59.148 45.455 0.00 0.00 0.00 3.16
3783 8807 3.498082 GTTGACTTGCACGAAAAACAGT 58.502 40.909 0.00 0.00 0.00 3.55
3784 8808 4.437659 GGTTGACTTGCACGAAAAACAGTA 60.438 41.667 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.194547 CGACCAACCGATTCAACTGTG 59.805 52.381 0.00 0.00 0.00 3.66
22 23 2.413239 CCAAATGTAGCTGCTTGTGTCG 60.413 50.000 7.79 0.00 0.00 4.35
51 52 0.984995 ACTTTAGGAGAGGTGGTGGC 59.015 55.000 0.00 0.00 0.00 5.01
55 56 2.900546 ACACTGACTTTAGGAGAGGTGG 59.099 50.000 0.00 0.00 32.00 4.61
181 186 9.650714 ATCTTAGGATTCAATTCCAAATCATGA 57.349 29.630 0.00 0.00 38.32 3.07
223 250 7.282450 ACTGAAATGGGTCTAAATACGAATTCC 59.718 37.037 0.00 0.00 0.00 3.01
224 251 8.209917 ACTGAAATGGGTCTAAATACGAATTC 57.790 34.615 0.00 0.00 0.00 2.17
254 282 2.554344 GGGCTGGAATACAACTCACCAA 60.554 50.000 0.00 0.00 0.00 3.67
261 289 2.584492 GCATTGGGCTGGAATACAAC 57.416 50.000 0.00 0.00 40.25 3.32
287 325 3.462021 GGCTCTGTCTGGATGTATGAAC 58.538 50.000 0.00 0.00 0.00 3.18
300 338 2.550180 GAGTTGAAACTTGGGCTCTGTC 59.450 50.000 0.00 0.00 39.88 3.51
394 444 1.857318 TTTACAATGGTGCACGCCCG 61.857 55.000 11.45 1.96 0.00 6.13
401 451 7.382218 GGTCAATAAGCATATTTACAATGGTGC 59.618 37.037 7.95 0.00 35.36 5.01
414 464 8.018537 TGCTACTTTCTAGGTCAATAAGCATA 57.981 34.615 0.00 0.00 31.78 3.14
451 508 8.306761 TCACAGTCGATAATATGATAGCATGTT 58.693 33.333 8.08 8.08 38.97 2.71
455 716 7.687941 TCTCACAGTCGATAATATGATAGCA 57.312 36.000 0.00 0.00 0.00 3.49
474 735 3.120511 GCCTTTCACTGATTCGTTCTCAC 60.121 47.826 0.00 0.00 0.00 3.51
507 798 2.425592 CCGGCCTCCGCATCAATA 59.574 61.111 0.00 0.00 46.86 1.90
516 807 0.251033 AGTGTAAAAACCCGGCCTCC 60.251 55.000 0.00 0.00 0.00 4.30
533 824 5.036117 TCAGGAGCACAGTTTAAAAGAGT 57.964 39.130 0.00 0.00 0.00 3.24
540 832 5.483685 ACAAGTATCAGGAGCACAGTTTA 57.516 39.130 0.00 0.00 0.00 2.01
585 877 0.036952 ACTGCAACTGACCCATCTCG 60.037 55.000 0.00 0.00 0.00 4.04
590 882 0.108585 GGAGAACTGCAACTGACCCA 59.891 55.000 0.00 0.00 0.00 4.51
604 896 3.129287 GTCGGTAATTAGTGGTCGGAGAA 59.871 47.826 0.00 0.00 39.69 2.87
606 898 2.540361 CGTCGGTAATTAGTGGTCGGAG 60.540 54.545 0.00 0.00 0.00 4.63
608 900 1.401552 TCGTCGGTAATTAGTGGTCGG 59.598 52.381 0.00 0.00 0.00 4.79
609 901 2.096496 ACTCGTCGGTAATTAGTGGTCG 59.904 50.000 0.00 0.00 0.00 4.79
610 902 3.772060 ACTCGTCGGTAATTAGTGGTC 57.228 47.619 0.00 0.00 0.00 4.02
611 903 3.119352 GGAACTCGTCGGTAATTAGTGGT 60.119 47.826 0.00 0.00 0.00 4.16
612 904 3.442100 GGAACTCGTCGGTAATTAGTGG 58.558 50.000 0.00 0.00 0.00 4.00
613 905 3.129988 AGGGAACTCGTCGGTAATTAGTG 59.870 47.826 0.00 0.00 32.90 2.74
614 906 3.359950 AGGGAACTCGTCGGTAATTAGT 58.640 45.455 0.00 0.00 32.90 2.24
615 907 4.097589 AGAAGGGAACTCGTCGGTAATTAG 59.902 45.833 0.00 0.00 42.68 1.73
616 908 4.019174 AGAAGGGAACTCGTCGGTAATTA 58.981 43.478 0.00 0.00 42.68 1.40
617 909 2.830321 AGAAGGGAACTCGTCGGTAATT 59.170 45.455 0.00 0.00 42.68 1.40
618 910 2.454538 AGAAGGGAACTCGTCGGTAAT 58.545 47.619 0.00 0.00 42.68 1.89
619 911 1.915141 AGAAGGGAACTCGTCGGTAA 58.085 50.000 0.00 0.00 42.68 2.85
624 947 6.977502 GGTAAACTATTAGAAGGGAACTCGTC 59.022 42.308 0.00 0.00 42.68 4.20
626 949 6.127253 TGGGTAAACTATTAGAAGGGAACTCG 60.127 42.308 0.00 0.00 42.68 4.18
641 964 4.811498 TGGCTAGCTAGATGGGTAAACTA 58.189 43.478 25.15 0.00 0.00 2.24
646 969 1.633774 GCTGGCTAGCTAGATGGGTA 58.366 55.000 30.17 2.38 46.57 3.69
660 983 1.867698 GCAGATAGAAGACTCGCTGGC 60.868 57.143 0.00 0.00 32.10 4.85
662 985 2.618241 AGAGCAGATAGAAGACTCGCTG 59.382 50.000 0.00 0.00 33.52 5.18
670 998 9.558396 AAGGAAATAATTCAGAGCAGATAGAAG 57.442 33.333 0.00 0.00 37.29 2.85
725 1053 7.483375 GCACGTGCACAAAATATTAATACTCAA 59.517 33.333 34.52 0.00 41.59 3.02
727 1055 7.363589 GCACGTGCACAAAATATTAATACTC 57.636 36.000 34.52 0.00 41.59 2.59
752 1080 3.003689 CGCATTGGACTTTGAGAAACAGT 59.996 43.478 0.00 0.00 0.00 3.55
780 1108 1.135373 TCTTTCAGTCTCGATCACGCC 60.135 52.381 0.00 0.00 39.58 5.68
810 1138 0.662619 TCAGCCAACGCAGAAACTTG 59.337 50.000 0.00 0.00 37.52 3.16
844 1172 1.371558 GGAGAGTTTGGCAGGTCGT 59.628 57.895 0.00 0.00 0.00 4.34
849 1177 1.239968 GCCTGTGGAGAGTTTGGCAG 61.240 60.000 0.00 0.00 40.04 4.85
856 1184 0.764369 TTGAGGTGCCTGTGGAGAGT 60.764 55.000 0.00 0.00 0.00 3.24
858 1186 0.615331 GATTGAGGTGCCTGTGGAGA 59.385 55.000 0.00 0.00 0.00 3.71
885 1213 3.332493 GATTGGGCTGTGCAGTGCG 62.332 63.158 11.20 0.00 0.00 5.34
914 1242 7.285401 AGAGAGATGAGAGATTGAGTTAGTTCC 59.715 40.741 0.00 0.00 0.00 3.62
915 1243 8.225603 AGAGAGATGAGAGATTGAGTTAGTTC 57.774 38.462 0.00 0.00 0.00 3.01
916 1244 8.055181 AGAGAGAGATGAGAGATTGAGTTAGTT 58.945 37.037 0.00 0.00 0.00 2.24
920 1248 6.095860 CACAGAGAGAGATGAGAGATTGAGTT 59.904 42.308 0.00 0.00 0.00 3.01
921 1249 5.591472 CACAGAGAGAGATGAGAGATTGAGT 59.409 44.000 0.00 0.00 0.00 3.41
923 1251 5.508567 ACACAGAGAGAGATGAGAGATTGA 58.491 41.667 0.00 0.00 0.00 2.57
924 1252 5.840243 ACACAGAGAGAGATGAGAGATTG 57.160 43.478 0.00 0.00 0.00 2.67
928 1256 9.330063 GGATATATACACAGAGAGAGATGAGAG 57.670 40.741 0.00 0.00 0.00 3.20
929 1257 8.830741 TGGATATATACACAGAGAGAGATGAGA 58.169 37.037 0.00 0.00 0.00 3.27
931 1259 7.555914 GCTGGATATATACACAGAGAGAGATGA 59.444 40.741 15.95 0.00 32.86 2.92
941 1269 3.261643 TGGGCAGCTGGATATATACACAG 59.738 47.826 17.12 9.92 0.00 3.66
964 1309 1.005630 AGAAGACAGTGGAGCACGC 60.006 57.895 0.00 0.00 39.64 5.34
965 1310 0.389166 GGAGAAGACAGTGGAGCACG 60.389 60.000 0.00 0.00 39.64 5.34
970 1315 1.620819 GCTCTTGGAGAAGACAGTGGA 59.379 52.381 0.00 0.00 34.36 4.02
1053 1405 4.827835 GGAGCTATGATGAGTAGTGGTACA 59.172 45.833 0.00 0.00 0.00 2.90
1233 1585 3.941657 GAGCTGCAGGTGGACGACC 62.942 68.421 25.60 2.56 46.58 4.79
1260 1612 2.024868 CGAAACCACGATGTCCGCA 61.025 57.895 0.00 0.00 43.32 5.69
1265 1617 2.025418 GGCGACGAAACCACGATGT 61.025 57.895 0.00 0.00 37.03 3.06
1284 1636 2.530151 ACCTCCTTGGCAGCCTCA 60.530 61.111 14.15 0.00 40.22 3.86
1378 3099 9.683069 ACAATTGTTGATGTTTACAGAATCTTC 57.317 29.630 4.92 0.00 0.00 2.87
1383 3104 9.645059 TTCAAACAATTGTTGATGTTTACAGAA 57.355 25.926 23.93 11.76 45.31 3.02
1428 3150 9.062524 ACAACAATGAGTTAGTATGCAACTTTA 57.937 29.630 6.82 0.00 38.74 1.85
1448 3170 2.762887 TCCATTCCAGCACAAACAACAA 59.237 40.909 0.00 0.00 0.00 2.83
1479 3201 7.523293 TTTGCACCTGAAAGATTCAAATAGA 57.477 32.000 0.00 0.00 39.58 1.98
1482 3204 9.558396 TTAATTTTGCACCTGAAAGATTCAAAT 57.442 25.926 0.00 0.00 39.58 2.32
1507 3333 4.328536 TGTCTTGTTGGCCGTATGTAATT 58.671 39.130 0.00 0.00 0.00 1.40
1513 3339 1.651987 CGATGTCTTGTTGGCCGTAT 58.348 50.000 0.00 0.00 0.00 3.06
1540 3366 1.959226 CCAGCTTGCGTTGTACGGT 60.959 57.895 1.14 0.00 42.82 4.83
1591 3417 1.567537 GACGCGTTTGCTGCTTACA 59.432 52.632 15.53 0.00 39.65 2.41
1817 3643 2.124695 GAAGGCGGAAAGGGCGAT 60.125 61.111 0.00 0.00 37.59 4.58
1882 3708 2.361992 TCCAGCCCGACGAGCTTA 60.362 61.111 0.00 0.00 38.95 3.09
1906 3732 6.214412 CCAGCTCTAGGAATATCCTTTGGTAT 59.786 42.308 3.90 0.00 46.91 2.73
1912 3738 5.083821 GAGTCCAGCTCTAGGAATATCCTT 58.916 45.833 3.90 0.00 41.70 3.36
2173 4213 1.365699 GTCGTGCCACCGATAAATGT 58.634 50.000 0.00 0.00 39.34 2.71
2254 4294 2.557920 ACCTCTCTTTGTGCCTTCTG 57.442 50.000 0.00 0.00 0.00 3.02
2265 4305 4.202472 CCAACCAAACTCCTTACCTCTCTT 60.202 45.833 0.00 0.00 0.00 2.85
2266 4306 3.328050 CCAACCAAACTCCTTACCTCTCT 59.672 47.826 0.00 0.00 0.00 3.10
2267 4307 3.676093 CCAACCAAACTCCTTACCTCTC 58.324 50.000 0.00 0.00 0.00 3.20
2272 4312 0.879090 CCGCCAACCAAACTCCTTAC 59.121 55.000 0.00 0.00 0.00 2.34
2313 7318 4.142790 AGTTGAGTTTAGAGAGGTCGTCA 58.857 43.478 0.00 0.00 0.00 4.35
2403 7408 1.428912 ACCTTCACATGGTCCATGGTT 59.571 47.619 30.96 12.38 45.16 3.67
2502 7507 3.072211 CGGGTAAAACTCCTCAGGTTTC 58.928 50.000 0.00 0.00 38.94 2.78
2541 7546 4.883585 TGCAATCCATAGAAATCAGTGTCC 59.116 41.667 0.00 0.00 0.00 4.02
2568 7573 2.391389 GCCAAACGGAAGGAGCTCG 61.391 63.158 7.83 0.00 0.00 5.03
2634 7639 1.704582 GCTAGCAAGCGTGAACTCG 59.295 57.895 10.63 0.00 39.39 4.18
2773 7778 8.624776 GTCTAAATTCATGCTTTAGCCAGTATT 58.375 33.333 16.66 0.00 41.18 1.89
2827 7832 4.148838 AGCGAGAAATACTGCTATCTCCT 58.851 43.478 0.00 0.00 35.91 3.69
2945 7959 6.467677 ACATATGTGCTAGAGTTGACAAAGT 58.532 36.000 7.78 0.00 0.00 2.66
2987 8001 8.631480 AGTTGGAGGGTGTTTTATAGTTTAAG 57.369 34.615 0.00 0.00 0.00 1.85
3014 8028 7.079475 GCAAAAGCACATTATTGCAAGAAAAT 58.921 30.769 11.02 4.72 45.61 1.82
3092 8106 9.527157 TGAAGAACCCAATTACATTATTGAGAA 57.473 29.630 0.00 0.00 37.65 2.87
3107 8122 1.271379 GCTACCAGCTGAAGAACCCAA 60.271 52.381 17.39 0.00 38.45 4.12
3133 8148 4.636206 CCAAAGTTTCCTCCATACTACAGC 59.364 45.833 0.00 0.00 0.00 4.40
3180 8195 6.956202 AGCTTCGAATACTAACTAGCCTAA 57.044 37.500 0.00 0.00 0.00 2.69
3224 8247 1.990614 GGGAAGAGGAAGAGGCGGT 60.991 63.158 0.00 0.00 0.00 5.68
3333 8357 7.857456 TCTAACATGCCCTTCTTTATCTAACA 58.143 34.615 0.00 0.00 0.00 2.41
3348 8372 4.646492 ACCCATTCATTTCTCTAACATGCC 59.354 41.667 0.00 0.00 0.00 4.40
3350 8374 9.740239 CATTTACCCATTCATTTCTCTAACATG 57.260 33.333 0.00 0.00 0.00 3.21
3353 8377 7.771183 TGCATTTACCCATTCATTTCTCTAAC 58.229 34.615 0.00 0.00 0.00 2.34
3380 8404 9.003145 AGCCCTAATACTTTATATGCATATCCA 57.997 33.333 22.33 8.33 0.00 3.41
3392 8416 9.209048 TCAACTCATCTAAGCCCTAATACTTTA 57.791 33.333 0.00 0.00 0.00 1.85
3393 8417 8.090788 TCAACTCATCTAAGCCCTAATACTTT 57.909 34.615 0.00 0.00 0.00 2.66
3394 8418 7.676683 TCAACTCATCTAAGCCCTAATACTT 57.323 36.000 0.00 0.00 0.00 2.24
3395 8419 7.256475 CCATCAACTCATCTAAGCCCTAATACT 60.256 40.741 0.00 0.00 0.00 2.12
3420 8444 4.706035 AGCAGTCATCTCAGATTTGATCC 58.294 43.478 0.00 0.00 31.68 3.36
3427 8451 6.728089 TTCATCTAAGCAGTCATCTCAGAT 57.272 37.500 0.00 0.00 0.00 2.90
3439 8463 6.983906 TCCATCTCAGTATTCATCTAAGCA 57.016 37.500 0.00 0.00 0.00 3.91
3445 8469 7.721286 AACGAAATCCATCTCAGTATTCATC 57.279 36.000 0.00 0.00 0.00 2.92
3456 8480 9.573133 GAATTCATTGTTAAACGAAATCCATCT 57.427 29.630 0.00 0.00 0.00 2.90
3466 8490 8.464770 AACATCCATGAATTCATTGTTAAACG 57.535 30.769 25.18 11.42 34.74 3.60
3482 8506 5.233957 TCGAGTGCAAAATAACATCCATG 57.766 39.130 0.00 0.00 0.00 3.66
3495 8519 3.111853 AGAGTTGTGAATCGAGTGCAA 57.888 42.857 0.00 0.00 0.00 4.08
3548 8572 6.468543 GCCTTATATAAAGGAACAGAGGGAG 58.531 44.000 7.97 0.00 39.81 4.30
3549 8573 5.011738 CGCCTTATATAAAGGAACAGAGGGA 59.988 44.000 7.97 0.00 39.81 4.20
3550 8574 5.221661 ACGCCTTATATAAAGGAACAGAGGG 60.222 44.000 7.97 1.92 39.81 4.30
3551 8575 5.855045 ACGCCTTATATAAAGGAACAGAGG 58.145 41.667 7.97 2.27 39.81 3.69
3552 8576 9.490379 AAATACGCCTTATATAAAGGAACAGAG 57.510 33.333 7.97 0.00 39.81 3.35
3553 8577 9.268268 CAAATACGCCTTATATAAAGGAACAGA 57.732 33.333 7.97 0.00 39.81 3.41
3554 8578 9.052759 ACAAATACGCCTTATATAAAGGAACAG 57.947 33.333 7.97 0.00 39.81 3.16
3555 8579 8.967664 ACAAATACGCCTTATATAAAGGAACA 57.032 30.769 7.97 0.00 39.81 3.18
3581 8605 5.197451 TGGCCTAGTTTGACTTCTGAAAAA 58.803 37.500 3.32 0.00 0.00 1.94
3582 8606 4.787551 TGGCCTAGTTTGACTTCTGAAAA 58.212 39.130 3.32 0.00 0.00 2.29
3583 8607 4.431416 TGGCCTAGTTTGACTTCTGAAA 57.569 40.909 3.32 0.00 0.00 2.69
3584 8608 4.202461 ACATGGCCTAGTTTGACTTCTGAA 60.202 41.667 3.32 0.00 0.00 3.02
3585 8609 3.327757 ACATGGCCTAGTTTGACTTCTGA 59.672 43.478 3.32 0.00 0.00 3.27
3586 8610 3.679389 ACATGGCCTAGTTTGACTTCTG 58.321 45.455 3.32 0.00 0.00 3.02
3587 8611 4.373156 AACATGGCCTAGTTTGACTTCT 57.627 40.909 3.32 0.00 0.00 2.85
3594 8618 2.159382 CGGTCAAACATGGCCTAGTTT 58.841 47.619 16.98 16.98 38.40 2.66
3595 8619 1.349688 TCGGTCAAACATGGCCTAGTT 59.650 47.619 3.32 5.87 0.00 2.24
3596 8620 0.981183 TCGGTCAAACATGGCCTAGT 59.019 50.000 3.32 0.00 0.00 2.57
3597 8621 1.207089 TCTCGGTCAAACATGGCCTAG 59.793 52.381 3.32 0.00 0.00 3.02
3598 8622 1.271856 TCTCGGTCAAACATGGCCTA 58.728 50.000 3.32 0.00 0.00 3.93
3599 8623 0.620556 ATCTCGGTCAAACATGGCCT 59.379 50.000 3.32 0.00 0.00 5.19
3600 8624 1.463674 AATCTCGGTCAAACATGGCC 58.536 50.000 0.00 0.00 0.00 5.36
3601 8625 3.244976 CAAAATCTCGGTCAAACATGGC 58.755 45.455 0.00 0.00 0.00 4.40
3602 8626 3.505680 TCCAAAATCTCGGTCAAACATGG 59.494 43.478 0.00 0.00 0.00 3.66
3603 8627 4.764679 TCCAAAATCTCGGTCAAACATG 57.235 40.909 0.00 0.00 0.00 3.21
3604 8628 5.782893 TTTCCAAAATCTCGGTCAAACAT 57.217 34.783 0.00 0.00 0.00 2.71
3605 8629 5.584253 TTTTCCAAAATCTCGGTCAAACA 57.416 34.783 0.00 0.00 0.00 2.83
3606 8630 8.757164 ATATTTTTCCAAAATCTCGGTCAAAC 57.243 30.769 0.00 0.00 0.00 2.93
3609 8633 8.846211 GGATATATTTTTCCAAAATCTCGGTCA 58.154 33.333 0.00 0.00 31.99 4.02
3610 8634 8.846211 TGGATATATTTTTCCAAAATCTCGGTC 58.154 33.333 0.00 0.00 39.05 4.79
3611 8635 8.760980 TGGATATATTTTTCCAAAATCTCGGT 57.239 30.769 0.00 0.00 39.05 4.69
3659 8683 9.695526 CTTAACTTTTCATGATGGTTCAAATGA 57.304 29.630 0.00 0.00 34.96 2.57
3660 8684 9.480053 ACTTAACTTTTCATGATGGTTCAAATG 57.520 29.630 0.00 0.00 34.96 2.32
3661 8685 9.480053 CACTTAACTTTTCATGATGGTTCAAAT 57.520 29.630 0.00 0.00 34.96 2.32
3662 8686 7.925483 CCACTTAACTTTTCATGATGGTTCAAA 59.075 33.333 0.00 0.00 34.96 2.69
3663 8687 7.069331 ACCACTTAACTTTTCATGATGGTTCAA 59.931 33.333 6.10 0.00 34.25 2.69
3664 8688 6.549364 ACCACTTAACTTTTCATGATGGTTCA 59.451 34.615 6.10 0.00 34.25 3.18
3665 8689 6.981722 ACCACTTAACTTTTCATGATGGTTC 58.018 36.000 6.10 0.00 34.25 3.62
3666 8690 6.976934 ACCACTTAACTTTTCATGATGGTT 57.023 33.333 6.10 9.05 34.25 3.67
3667 8691 6.976934 AACCACTTAACTTTTCATGATGGT 57.023 33.333 6.10 6.10 39.59 3.55
3668 8692 7.432869 TGAAACCACTTAACTTTTCATGATGG 58.567 34.615 0.00 0.00 33.96 3.51
3677 8701 9.840427 CGATGAAATATGAAACCACTTAACTTT 57.160 29.630 0.00 0.00 0.00 2.66
3678 8702 9.226606 TCGATGAAATATGAAACCACTTAACTT 57.773 29.630 0.00 0.00 0.00 2.66
3679 8703 8.786826 TCGATGAAATATGAAACCACTTAACT 57.213 30.769 0.00 0.00 0.00 2.24
3683 8707 7.975616 CCAAATCGATGAAATATGAAACCACTT 59.024 33.333 0.00 0.00 0.00 3.16
3684 8708 7.122650 ACCAAATCGATGAAATATGAAACCACT 59.877 33.333 0.00 0.00 0.00 4.00
3685 8709 7.257722 ACCAAATCGATGAAATATGAAACCAC 58.742 34.615 0.00 0.00 0.00 4.16
3686 8710 7.403312 ACCAAATCGATGAAATATGAAACCA 57.597 32.000 0.00 0.00 0.00 3.67
3687 8711 9.965824 AATACCAAATCGATGAAATATGAAACC 57.034 29.630 0.00 0.00 0.00 3.27
3690 8714 9.348476 TGGAATACCAAATCGATGAAATATGAA 57.652 29.630 0.00 0.00 43.91 2.57
3691 8715 8.916628 TGGAATACCAAATCGATGAAATATGA 57.083 30.769 0.00 0.00 43.91 2.15
3712 8736 9.308000 AGAGAAATAAACCAACAACATATGGAA 57.692 29.630 7.80 0.00 39.12 3.53
3713 8737 8.877864 AGAGAAATAAACCAACAACATATGGA 57.122 30.769 7.80 0.00 39.12 3.41
3720 8744 9.573133 CCATGATTAGAGAAATAAACCAACAAC 57.427 33.333 0.00 0.00 0.00 3.32
3721 8745 9.308000 ACCATGATTAGAGAAATAAACCAACAA 57.692 29.630 0.00 0.00 0.00 2.83
3722 8746 8.877864 ACCATGATTAGAGAAATAAACCAACA 57.122 30.769 0.00 0.00 0.00 3.33
3723 8747 8.956426 TGACCATGATTAGAGAAATAAACCAAC 58.044 33.333 0.00 0.00 0.00 3.77
3724 8748 9.527157 TTGACCATGATTAGAGAAATAAACCAA 57.473 29.630 0.00 0.00 0.00 3.67
3725 8749 9.527157 TTTGACCATGATTAGAGAAATAAACCA 57.473 29.630 0.00 0.00 0.00 3.67
3726 8750 9.788960 GTTTGACCATGATTAGAGAAATAAACC 57.211 33.333 0.00 0.00 0.00 3.27
3731 8755 9.246670 TGAATGTTTGACCATGATTAGAGAAAT 57.753 29.630 0.00 0.00 0.00 2.17
3732 8756 8.634335 TGAATGTTTGACCATGATTAGAGAAA 57.366 30.769 0.00 0.00 0.00 2.52
3733 8757 8.634335 TTGAATGTTTGACCATGATTAGAGAA 57.366 30.769 0.00 0.00 0.00 2.87
3734 8758 8.634335 TTTGAATGTTTGACCATGATTAGAGA 57.366 30.769 0.00 0.00 0.00 3.10
3735 8759 9.297586 CATTTGAATGTTTGACCATGATTAGAG 57.702 33.333 0.00 0.00 0.00 2.43
3736 8760 8.252417 CCATTTGAATGTTTGACCATGATTAGA 58.748 33.333 0.00 0.00 34.60 2.10
3737 8761 8.036575 ACCATTTGAATGTTTGACCATGATTAG 58.963 33.333 0.00 0.00 34.60 1.73
3738 8762 7.905265 ACCATTTGAATGTTTGACCATGATTA 58.095 30.769 0.00 0.00 34.60 1.75
3739 8763 6.771573 ACCATTTGAATGTTTGACCATGATT 58.228 32.000 0.00 0.00 34.60 2.57
3740 8764 6.363167 ACCATTTGAATGTTTGACCATGAT 57.637 33.333 0.00 0.00 34.60 2.45
3741 8765 5.804944 ACCATTTGAATGTTTGACCATGA 57.195 34.783 0.00 0.00 34.60 3.07
3742 8766 5.990386 TCAACCATTTGAATGTTTGACCATG 59.010 36.000 11.22 0.00 41.11 3.66
3743 8767 6.172136 TCAACCATTTGAATGTTTGACCAT 57.828 33.333 11.22 0.00 41.11 3.55
3744 8768 5.604758 TCAACCATTTGAATGTTTGACCA 57.395 34.783 11.22 0.00 41.11 4.02
3747 8771 5.523188 GCAAGTCAACCATTTGAATGTTTGA 59.477 36.000 11.22 11.22 42.89 2.69
3748 8772 5.293814 TGCAAGTCAACCATTTGAATGTTTG 59.706 36.000 7.44 7.44 43.52 2.93
3749 8773 5.294060 GTGCAAGTCAACCATTTGAATGTTT 59.706 36.000 0.00 0.00 43.52 2.83
3750 8774 4.810491 GTGCAAGTCAACCATTTGAATGTT 59.190 37.500 0.00 0.00 43.52 2.71
3751 8775 4.370917 GTGCAAGTCAACCATTTGAATGT 58.629 39.130 0.00 0.00 43.52 2.71
3752 8776 3.426191 CGTGCAAGTCAACCATTTGAATG 59.574 43.478 0.00 0.00 43.52 2.67
3753 8777 3.317711 TCGTGCAAGTCAACCATTTGAAT 59.682 39.130 0.00 0.00 43.52 2.57
3754 8778 2.685388 TCGTGCAAGTCAACCATTTGAA 59.315 40.909 0.00 0.00 43.52 2.69
3755 8779 2.293170 TCGTGCAAGTCAACCATTTGA 58.707 42.857 0.00 0.00 39.55 2.69
3756 8780 2.772568 TCGTGCAAGTCAACCATTTG 57.227 45.000 0.00 0.00 0.00 2.32
3757 8781 3.791973 TTTCGTGCAAGTCAACCATTT 57.208 38.095 0.00 0.00 0.00 2.32
3758 8782 3.791973 TTTTCGTGCAAGTCAACCATT 57.208 38.095 0.00 0.00 0.00 3.16
3759 8783 3.119316 TGTTTTTCGTGCAAGTCAACCAT 60.119 39.130 0.00 0.00 0.00 3.55
3760 8784 2.229062 TGTTTTTCGTGCAAGTCAACCA 59.771 40.909 0.00 0.00 0.00 3.67
3761 8785 2.851824 CTGTTTTTCGTGCAAGTCAACC 59.148 45.455 0.00 0.00 0.00 3.77
3762 8786 3.498082 ACTGTTTTTCGTGCAAGTCAAC 58.502 40.909 0.00 2.50 0.00 3.18
3763 8787 3.840890 ACTGTTTTTCGTGCAAGTCAA 57.159 38.095 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.