Multiple sequence alignment - TraesCS7A01G082900

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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 TraesCS7A01G082900 chr7A 100.000 3017 0 0 1 3017 47899183 47902199 0.000000e+00 5572
1 TraesCS7A01G082900 chr7A 90.222 450 44 0 1462 1911 47781102 47780653 3.350000e-164 588
2 TraesCS7A01G082900 chr7A 93.353 346 13 9 2287 2626 133934364 133934023 1.250000e-138 503
3 TraesCS7A01G082900 chr7A 84.036 332 32 15 1921 2245 47780389 47780072 1.760000e-77 300
4 TraesCS7A01G082900 chr4A 88.135 2343 165 61 1 2304 658896291 658898559 0.000000e+00 2682
5 TraesCS7A01G082900 chr4A 90.299 1072 74 19 890 1946 658343043 658344099 0.000000e+00 1376
6 TraesCS7A01G082900 chr4A 87.246 690 72 7 1461 2149 658108879 658108205 0.000000e+00 773
7 TraesCS7A01G082900 chr4A 87.101 690 73 7 1461 2149 658069899 658069225 0.000000e+00 767
8 TraesCS7A01G082900 chr4A 94.294 333 15 4 2297 2627 731427386 731427716 9.650000e-140 507
9 TraesCS7A01G082900 chr4A 87.970 266 15 7 612 868 658342669 658342926 6.320000e-77 298
10 TraesCS7A01G082900 chr4A 93.333 75 4 1 2618 2691 658898560 658898634 3.180000e-20 110
11 TraesCS7A01G082900 chr7D 89.273 2200 121 38 176 2309 45702574 45704724 0.000000e+00 2649
12 TraesCS7A01G082900 chr7D 91.832 404 18 6 2618 3017 45704719 45705111 1.580000e-152 549
13 TraesCS7A01G082900 chr7D 84.708 497 50 16 1756 2244 45605985 45605507 9.790000e-130 473
14 TraesCS7A01G082900 chr7D 88.612 281 31 1 1461 1740 45619856 45619576 1.040000e-89 340
15 TraesCS7A01G082900 chr6D 86.926 566 63 6 1340 1898 9973259 9973820 2.550000e-175 625
16 TraesCS7A01G082900 chr2A 97.125 313 8 1 2307 2619 597848123 597847812 7.410000e-146 527
17 TraesCS7A01G082900 chr6B 96.795 312 9 1 2308 2619 547713957 547713647 1.240000e-143 520
18 TraesCS7A01G082900 chr3A 96.497 314 11 0 2308 2621 78194916 78194603 1.240000e-143 520
19 TraesCS7A01G082900 chr3A 95.385 325 12 3 2298 2621 451653207 451653529 5.770000e-142 514
20 TraesCS7A01G082900 chr1A 96.508 315 9 2 2308 2621 385654649 385654962 1.240000e-143 520
21 TraesCS7A01G082900 chr5A 96.203 316 11 1 2308 2622 350901555 350901240 1.600000e-142 516
22 TraesCS7A01G082900 chr5A 95.342 322 13 2 2308 2629 23935876 23936195 7.460000e-141 510
23 TraesCS7A01G082900 chrUn 85.756 344 20 9 2674 3017 320963602 320963288 1.340000e-88 337


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 TraesCS7A01G082900 chr7A 47899183 47902199 3016 False 5572 5572 100.0000 1 3017 1 chr7A.!!$F1 3016
1 TraesCS7A01G082900 chr7A 47780072 47781102 1030 True 444 588 87.1290 1462 2245 2 chr7A.!!$R2 783
2 TraesCS7A01G082900 chr4A 658896291 658898634 2343 False 1396 2682 90.7340 1 2691 2 chr4A.!!$F3 2690
3 TraesCS7A01G082900 chr4A 658342669 658344099 1430 False 837 1376 89.1345 612 1946 2 chr4A.!!$F2 1334
4 TraesCS7A01G082900 chr4A 658108205 658108879 674 True 773 773 87.2460 1461 2149 1 chr4A.!!$R2 688
5 TraesCS7A01G082900 chr4A 658069225 658069899 674 True 767 767 87.1010 1461 2149 1 chr4A.!!$R1 688
6 TraesCS7A01G082900 chr7D 45702574 45705111 2537 False 1599 2649 90.5525 176 3017 2 chr7D.!!$F1 2841
7 TraesCS7A01G082900 chr6D 9973259 9973820 561 False 625 625 86.9260 1340 1898 1 chr6D.!!$F1 558

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
540 558 0.375106 CAGGAAAAGAATCGAGCGGC 59.625 55.0 0.0 0.0 0.0 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2230 2711 0.029567 ACTCCGAATAGAAGCTCGCG 59.97 55.0 0.0 0.0 33.7 5.87 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
37 38 2.736719 CGAGCAGGTGTTCATACTCCAG 60.737 54.545 0.00 0.00 39.80 3.86
42 43 2.572104 AGGTGTTCATACTCCAGGGTTC 59.428 50.000 0.00 0.00 39.80 3.62
44 45 1.553248 TGTTCATACTCCAGGGTTCGG 59.447 52.381 0.00 0.00 0.00 4.30
83 84 3.266510 ACACTGAAACAGAAGTGCTCA 57.733 42.857 5.76 0.00 46.28 4.26
90 91 2.988010 ACAGAAGTGCTCAGTGAACA 57.012 45.000 0.00 0.00 0.00 3.18
104 105 1.066430 GTGAACATGCCGAGGAACCTA 60.066 52.381 0.00 0.00 0.00 3.08
105 106 1.626321 TGAACATGCCGAGGAACCTAA 59.374 47.619 0.00 0.00 0.00 2.69
114 115 3.366171 GCCGAGGAACCTAAGATATCGTC 60.366 52.174 0.00 0.00 0.00 4.20
115 116 3.120269 CCGAGGAACCTAAGATATCGTCG 60.120 52.174 9.07 9.07 44.90 5.12
116 117 3.497640 CGAGGAACCTAAGATATCGTCGT 59.502 47.826 8.14 0.00 42.15 4.34
117 118 4.687948 CGAGGAACCTAAGATATCGTCGTA 59.312 45.833 8.14 0.00 42.15 3.43
142 143 3.274095 AGTTTAAGGCAGAGGAGCATC 57.726 47.619 0.00 0.00 35.83 3.91
144 145 3.009473 AGTTTAAGGCAGAGGAGCATCAA 59.991 43.478 0.00 0.00 36.25 2.57
145 146 2.996249 TAAGGCAGAGGAGCATCAAG 57.004 50.000 0.00 0.00 36.25 3.02
209 210 0.592637 TTTCAGTCCAACAGCATGCG 59.407 50.000 13.01 9.99 42.53 4.73
216 217 2.436469 AACAGCATGCGCATCGGA 60.436 55.556 22.51 0.00 42.53 4.55
223 224 3.086391 ATGCGCATCGGAGTGCTCT 62.086 57.895 19.28 0.00 44.96 4.09
288 289 1.078988 GGACGGATGGCGGTACAAA 60.079 57.895 0.00 0.00 0.00 2.83
359 363 0.603569 GAGAGAGGAAGTGCGACCAA 59.396 55.000 0.00 0.00 0.00 3.67
396 400 1.289109 CTTCATTGCCCGAACGACGT 61.289 55.000 0.00 0.00 40.78 4.34
418 422 6.011277 CGTGCATCTTAGTAACCGTAAAAAC 58.989 40.000 0.00 0.00 0.00 2.43
447 451 5.365605 TGATTCACCGGACCTTAGATAATGT 59.634 40.000 9.46 0.00 0.00 2.71
474 478 2.439156 GGCAGCTGCTCCCGAAAT 60.439 61.111 35.82 0.00 41.70 2.17
539 557 1.394917 CACAGGAAAAGAATCGAGCGG 59.605 52.381 0.00 0.00 0.00 5.52
540 558 0.375106 CAGGAAAAGAATCGAGCGGC 59.625 55.000 0.00 0.00 0.00 6.53
541 559 0.744771 AGGAAAAGAATCGAGCGGCC 60.745 55.000 0.00 0.00 0.00 6.13
542 560 1.348594 GAAAAGAATCGAGCGGCCG 59.651 57.895 24.05 24.05 0.00 6.13
543 561 1.079405 AAAAGAATCGAGCGGCCGA 60.079 52.632 33.48 8.40 43.16 5.54
544 562 0.672401 AAAAGAATCGAGCGGCCGAA 60.672 50.000 33.48 11.25 42.22 4.30
545 563 1.359459 AAAGAATCGAGCGGCCGAAC 61.359 55.000 33.48 20.43 42.22 3.95
546 564 3.617538 GAATCGAGCGGCCGAACG 61.618 66.667 33.48 30.62 42.22 3.95
547 565 4.124351 AATCGAGCGGCCGAACGA 62.124 61.111 34.90 34.90 42.22 3.85
548 566 4.554363 ATCGAGCGGCCGAACGAG 62.554 66.667 35.23 21.01 42.22 4.18
600 644 4.096682 GGCGGATAGTCTAGCGAGATTTAT 59.903 45.833 0.00 1.99 33.14 1.40
601 645 5.296283 GGCGGATAGTCTAGCGAGATTTATA 59.704 44.000 0.00 0.00 33.14 0.98
602 646 6.193761 GCGGATAGTCTAGCGAGATTTATAC 58.806 44.000 0.00 2.21 33.14 1.47
663 707 2.010145 ATCGACACGCACAAGCTTAT 57.990 45.000 0.00 0.00 39.10 1.73
664 708 2.640346 TCGACACGCACAAGCTTATA 57.360 45.000 0.00 0.00 39.10 0.98
665 709 3.159353 TCGACACGCACAAGCTTATAT 57.841 42.857 0.00 0.00 39.10 0.86
666 710 4.295857 TCGACACGCACAAGCTTATATA 57.704 40.909 0.00 0.00 39.10 0.86
667 711 4.866921 TCGACACGCACAAGCTTATATAT 58.133 39.130 0.00 0.00 39.10 0.86
852 905 8.325787 TCTGGGTAAAGCAACAGAATTTCTATA 58.674 33.333 0.00 0.00 37.06 1.31
853 906 9.125026 CTGGGTAAAGCAACAGAATTTCTATAT 57.875 33.333 0.00 0.00 32.86 0.86
854 907 8.902806 TGGGTAAAGCAACAGAATTTCTATATG 58.097 33.333 0.00 0.46 0.00 1.78
855 908 8.352942 GGGTAAAGCAACAGAATTTCTATATGG 58.647 37.037 0.00 0.00 0.00 2.74
856 909 7.862873 GGTAAAGCAACAGAATTTCTATATGGC 59.137 37.037 0.00 0.00 0.00 4.40
857 910 6.396829 AAGCAACAGAATTTCTATATGGCC 57.603 37.500 0.00 0.00 0.00 5.36
858 911 5.448654 AGCAACAGAATTTCTATATGGCCA 58.551 37.500 8.56 8.56 0.00 5.36
860 913 6.040166 AGCAACAGAATTTCTATATGGCCAAG 59.960 38.462 10.96 2.10 0.00 3.61
957 1113 4.096984 GCAATCTGTAACCAGCTAGCATTT 59.903 41.667 18.83 9.00 38.66 2.32
979 1139 5.477607 TTCATCGGTCGATATAAACCCAT 57.522 39.130 5.50 0.00 32.93 4.00
982 1142 5.947566 TCATCGGTCGATATAAACCCATAGA 59.052 40.000 5.50 0.00 32.93 1.98
989 1149 5.185249 TCGATATAAACCCATAGAGCCAGTC 59.815 44.000 0.00 0.00 0.00 3.51
990 1150 5.186021 CGATATAAACCCATAGAGCCAGTCT 59.814 44.000 0.00 0.00 39.59 3.24
991 1151 6.377429 CGATATAAACCCATAGAGCCAGTCTA 59.623 42.308 0.00 0.00 42.22 2.59
992 1152 5.810080 ATAAACCCATAGAGCCAGTCTAC 57.190 43.478 0.00 0.00 40.76 2.59
1055 1218 1.271001 CCAACAGTGACATGGAGCTCA 60.271 52.381 17.19 1.87 36.27 4.26
1270 1433 4.049640 GCCGCCGCCATTTTCACA 62.050 61.111 0.00 0.00 0.00 3.58
1301 1464 1.170442 CAACTCTGCATGCATGGACA 58.830 50.000 27.34 16.52 0.00 4.02
1410 1608 4.619227 ACGACCTGGGCAACGTGG 62.619 66.667 0.00 0.00 37.58 4.94
1467 1665 3.031417 GCTGGACGGGTGGCAGTAT 62.031 63.158 0.00 0.00 0.00 2.12
1505 1703 1.334869 GCACCTCAACAAGTTCCTGTG 59.665 52.381 0.00 0.00 0.00 3.66
1752 1950 1.444119 GCTTCTGGAACAACACGGCA 61.444 55.000 0.00 0.00 38.70 5.69
1779 1977 3.469970 ATCCACCATCAGCCGCGA 61.470 61.111 8.23 0.00 0.00 5.87
1836 2034 1.739667 GTGGGACAAGGTGTTTGGC 59.260 57.895 0.00 0.00 44.16 4.52
1867 2068 1.204704 CCTATGTTGTCGAGCACAGGA 59.795 52.381 3.55 0.00 35.97 3.86
1919 2375 5.827797 TGGAAGCCCTTAACTAAGCATATTG 59.172 40.000 0.00 0.00 32.02 1.90
1939 2395 9.467258 CATATTGTTGTGTTTCAGATTTGACTT 57.533 29.630 0.00 0.00 31.71 3.01
1951 2407 8.722480 TTCAGATTTGACTTATATGTCACCAG 57.278 34.615 18.30 9.62 45.32 4.00
2063 2530 2.280524 CTGTCGGCGGTGGTTTGA 60.281 61.111 7.21 0.00 0.00 2.69
2098 2565 3.373130 TCGAGCATCTGAGCAATTTCTTG 59.627 43.478 0.00 0.00 36.85 3.02
2100 2567 4.660105 GAGCATCTGAGCAATTTCTTGTC 58.340 43.478 0.00 0.00 36.85 3.18
2127 2597 0.613853 ATGGCATGCTTCAAGGCTGT 60.614 50.000 18.92 0.00 0.00 4.40
2151 2621 7.118825 TGTCAGAGAAAAGAATTGCTACATCTG 59.881 37.037 0.00 0.00 0.00 2.90
2152 2622 6.093219 TCAGAGAAAAGAATTGCTACATCTGC 59.907 38.462 0.00 0.00 0.00 4.26
2157 2627 6.519679 AAAGAATTGCTACATCTGCATCAA 57.480 33.333 0.00 0.00 40.34 2.57
2160 2630 6.561614 AGAATTGCTACATCTGCATCAAAAG 58.438 36.000 0.00 0.00 40.34 2.27
2161 2631 5.909621 ATTGCTACATCTGCATCAAAAGT 57.090 34.783 0.00 0.00 40.34 2.66
2162 2632 5.710513 TTGCTACATCTGCATCAAAAGTT 57.289 34.783 0.00 0.00 40.34 2.66
2163 2633 5.300969 TGCTACATCTGCATCAAAAGTTC 57.699 39.130 0.00 0.00 35.31 3.01
2201 2682 1.577468 TTCTGTACAACAGCACCACG 58.423 50.000 0.00 0.00 45.54 4.94
2226 2707 7.589587 CGTCAGACTAGATAGTAAAGCTTCATG 59.410 40.741 0.00 0.00 36.50 3.07
2230 2711 8.417884 AGACTAGATAGTAAAGCTTCATGTTCC 58.582 37.037 0.00 0.00 36.50 3.62
2300 2784 1.593006 CATTCGTGCTGACCGGATTAC 59.407 52.381 9.46 0.00 0.00 1.89
2304 2788 1.127951 CGTGCTGACCGGATTACAAAC 59.872 52.381 9.46 3.74 0.00 2.93
2305 2789 2.147958 GTGCTGACCGGATTACAAACA 58.852 47.619 9.46 1.65 0.00 2.83
2306 2790 2.550606 GTGCTGACCGGATTACAAACAA 59.449 45.455 9.46 0.00 0.00 2.83
2307 2791 3.190535 GTGCTGACCGGATTACAAACAAT 59.809 43.478 9.46 0.00 0.00 2.71
2308 2792 4.393680 GTGCTGACCGGATTACAAACAATA 59.606 41.667 9.46 0.00 0.00 1.90
2309 2793 5.004448 TGCTGACCGGATTACAAACAATAA 58.996 37.500 9.46 0.00 0.00 1.40
2310 2794 5.123186 TGCTGACCGGATTACAAACAATAAG 59.877 40.000 9.46 0.00 0.00 1.73
2311 2795 5.448632 GCTGACCGGATTACAAACAATAAGG 60.449 44.000 9.46 0.00 0.00 2.69
2312 2796 4.396790 TGACCGGATTACAAACAATAAGGC 59.603 41.667 9.46 0.00 0.00 4.35
2313 2797 3.697542 ACCGGATTACAAACAATAAGGCC 59.302 43.478 9.46 0.00 0.00 5.19
2314 2798 3.951680 CCGGATTACAAACAATAAGGCCT 59.048 43.478 0.00 0.00 0.00 5.19
2315 2799 4.036380 CCGGATTACAAACAATAAGGCCTC 59.964 45.833 5.23 0.00 0.00 4.70
2316 2800 4.036380 CGGATTACAAACAATAAGGCCTCC 59.964 45.833 5.23 0.00 0.00 4.30
2317 2801 5.201243 GGATTACAAACAATAAGGCCTCCT 58.799 41.667 5.23 0.00 33.87 3.69
2318 2802 5.656859 GGATTACAAACAATAAGGCCTCCTT 59.343 40.000 5.23 0.00 46.63 3.36
2319 2803 6.154534 GGATTACAAACAATAAGGCCTCCTTT 59.845 38.462 5.23 0.00 41.69 3.11
2320 2804 4.871933 ACAAACAATAAGGCCTCCTTTG 57.128 40.909 5.23 13.04 41.69 2.77
2321 2805 3.578282 ACAAACAATAAGGCCTCCTTTGG 59.422 43.478 20.26 9.75 41.69 3.28
2322 2806 3.542969 AACAATAAGGCCTCCTTTGGT 57.457 42.857 20.26 14.33 41.69 3.67
2323 2807 3.542969 ACAATAAGGCCTCCTTTGGTT 57.457 42.857 20.26 1.54 41.69 3.67
2324 2808 3.856900 ACAATAAGGCCTCCTTTGGTTT 58.143 40.909 20.26 0.88 41.69 3.27
2325 2809 5.005628 ACAATAAGGCCTCCTTTGGTTTA 57.994 39.130 20.26 2.98 41.69 2.01
2326 2810 5.016831 ACAATAAGGCCTCCTTTGGTTTAG 58.983 41.667 20.26 3.33 41.69 1.85
2327 2811 5.222254 ACAATAAGGCCTCCTTTGGTTTAGA 60.222 40.000 20.26 0.00 41.69 2.10
2328 2812 3.441500 AAGGCCTCCTTTGGTTTAGAG 57.558 47.619 5.23 0.00 41.69 2.43
2329 2813 2.041755 AAGGCCTCCTTTGGTTTAGAGG 59.958 50.000 5.23 0.43 41.69 3.69
2337 2821 7.709149 CTCCTTTGGTTTAGAGGAATTTCAT 57.291 36.000 0.00 0.00 39.00 2.57
2338 2822 8.807948 CTCCTTTGGTTTAGAGGAATTTCATA 57.192 34.615 0.00 0.00 39.00 2.15
2339 2823 8.807948 TCCTTTGGTTTAGAGGAATTTCATAG 57.192 34.615 0.00 0.00 36.67 2.23
2340 2824 7.834181 TCCTTTGGTTTAGAGGAATTTCATAGG 59.166 37.037 0.00 0.00 36.67 2.57
2341 2825 7.834181 CCTTTGGTTTAGAGGAATTTCATAGGA 59.166 37.037 0.00 0.00 32.11 2.94
2342 2826 9.243105 CTTTGGTTTAGAGGAATTTCATAGGAA 57.757 33.333 0.00 0.00 0.00 3.36
2343 2827 9.768215 TTTGGTTTAGAGGAATTTCATAGGAAT 57.232 29.630 0.00 0.00 31.93 3.01
2344 2828 9.768215 TTGGTTTAGAGGAATTTCATAGGAATT 57.232 29.630 0.00 0.00 31.93 2.17
2345 2829 9.408648 TGGTTTAGAGGAATTTCATAGGAATTC 57.591 33.333 0.00 0.00 31.93 2.17
2346 2830 9.634021 GGTTTAGAGGAATTTCATAGGAATTCT 57.366 33.333 5.23 0.00 31.93 2.40
2351 2835 9.667607 AGAGGAATTTCATAGGAATTCTAGAGA 57.332 33.333 5.23 0.00 31.93 3.10
2395 2879 5.784578 TTTTCTTTAGAGCCCTTTGGTTC 57.215 39.130 0.00 0.00 41.91 3.62
2396 2880 4.447138 TTCTTTAGAGCCCTTTGGTTCA 57.553 40.909 0.00 0.00 43.89 3.18
2397 2881 4.657814 TCTTTAGAGCCCTTTGGTTCAT 57.342 40.909 0.00 0.00 43.89 2.57
2398 2882 5.772393 TCTTTAGAGCCCTTTGGTTCATA 57.228 39.130 0.00 0.00 43.89 2.15
2399 2883 5.745227 TCTTTAGAGCCCTTTGGTTCATAG 58.255 41.667 0.00 0.00 43.89 2.23
2400 2884 5.487488 TCTTTAGAGCCCTTTGGTTCATAGA 59.513 40.000 0.00 0.00 43.89 1.98
2401 2885 5.772393 TTAGAGCCCTTTGGTTCATAGAA 57.228 39.130 0.00 0.00 43.89 2.10
2402 2886 4.657814 AGAGCCCTTTGGTTCATAGAAA 57.342 40.909 0.00 0.00 43.89 2.52
2403 2887 5.198602 AGAGCCCTTTGGTTCATAGAAAT 57.801 39.130 0.00 0.00 43.89 2.17
2404 2888 4.952335 AGAGCCCTTTGGTTCATAGAAATG 59.048 41.667 0.00 0.00 43.89 2.32
2405 2889 4.026052 AGCCCTTTGGTTCATAGAAATGG 58.974 43.478 0.00 0.00 33.61 3.16
2406 2890 4.023291 GCCCTTTGGTTCATAGAAATGGA 58.977 43.478 0.00 0.00 33.61 3.41
2407 2891 4.651045 GCCCTTTGGTTCATAGAAATGGAT 59.349 41.667 0.00 0.00 33.61 3.41
2408 2892 5.129320 GCCCTTTGGTTCATAGAAATGGATT 59.871 40.000 0.00 0.00 33.61 3.01
2409 2893 6.683861 GCCCTTTGGTTCATAGAAATGGATTC 60.684 42.308 0.00 0.00 38.39 2.52
2410 2894 6.183360 CCCTTTGGTTCATAGAAATGGATTCC 60.183 42.308 0.00 0.00 38.94 3.01
2411 2895 6.608808 CCTTTGGTTCATAGAAATGGATTCCT 59.391 38.462 3.95 0.00 38.94 3.36
2412 2896 7.779798 CCTTTGGTTCATAGAAATGGATTCCTA 59.220 37.037 3.95 0.00 38.94 2.94
2413 2897 9.359653 CTTTGGTTCATAGAAATGGATTCCTAT 57.640 33.333 3.95 0.00 38.94 2.57
2414 2898 9.713684 TTTGGTTCATAGAAATGGATTCCTATT 57.286 29.630 3.95 0.00 38.94 1.73
2415 2899 8.924511 TGGTTCATAGAAATGGATTCCTATTC 57.075 34.615 3.95 8.33 38.94 1.75
2416 2900 7.944554 TGGTTCATAGAAATGGATTCCTATTCC 59.055 37.037 13.88 0.00 38.94 3.01
2417 2901 8.166726 GGTTCATAGAAATGGATTCCTATTCCT 58.833 37.037 13.88 5.21 38.94 3.36
2420 2904 9.392506 TCATAGAAATGGATTCCTATTCCTACA 57.607 33.333 13.88 0.00 38.94 2.74
2424 2908 8.830741 AGAAATGGATTCCTATTCCTACATAGG 58.169 37.037 13.88 0.00 45.32 2.57
2437 2921 4.911390 CCTACATAGGATTGGTTCCCATC 58.089 47.826 0.00 0.00 46.81 3.51
2438 2922 3.884037 ACATAGGATTGGTTCCCATCC 57.116 47.619 12.39 12.39 46.81 3.51
2439 2923 3.407209 ACATAGGATTGGTTCCCATCCT 58.593 45.455 22.40 22.40 46.81 3.24
2440 2924 3.395941 ACATAGGATTGGTTCCCATCCTC 59.604 47.826 22.43 3.33 46.81 3.71
2441 2925 1.226311 AGGATTGGTTCCCATCCTCC 58.774 55.000 15.92 7.39 46.81 4.30
2442 2926 0.926293 GGATTGGTTCCCATCCTCCA 59.074 55.000 12.86 0.00 38.75 3.86
2443 2927 1.410224 GGATTGGTTCCCATCCTCCAC 60.410 57.143 12.86 0.00 38.75 4.02
2444 2928 1.284785 GATTGGTTCCCATCCTCCACA 59.715 52.381 0.00 0.00 31.53 4.17
2445 2929 1.381867 TTGGTTCCCATCCTCCACAT 58.618 50.000 0.00 0.00 31.53 3.21
2446 2930 1.381867 TGGTTCCCATCCTCCACATT 58.618 50.000 0.00 0.00 0.00 2.71
2447 2931 1.715931 TGGTTCCCATCCTCCACATTT 59.284 47.619 0.00 0.00 0.00 2.32
2448 2932 2.291540 TGGTTCCCATCCTCCACATTTC 60.292 50.000 0.00 0.00 0.00 2.17
2449 2933 2.291540 GGTTCCCATCCTCCACATTTCA 60.292 50.000 0.00 0.00 0.00 2.69
2450 2934 3.628257 GGTTCCCATCCTCCACATTTCAT 60.628 47.826 0.00 0.00 0.00 2.57
2451 2935 4.386312 GGTTCCCATCCTCCACATTTCATA 60.386 45.833 0.00 0.00 0.00 2.15
2452 2936 4.712051 TCCCATCCTCCACATTTCATAG 57.288 45.455 0.00 0.00 0.00 2.23
2453 2937 3.395607 TCCCATCCTCCACATTTCATAGG 59.604 47.826 0.00 0.00 0.00 2.57
2454 2938 3.395607 CCCATCCTCCACATTTCATAGGA 59.604 47.826 0.00 0.00 40.50 2.94
2455 2939 4.141181 CCCATCCTCCACATTTCATAGGAA 60.141 45.833 0.00 0.00 39.68 3.36
2456 2940 5.448654 CCATCCTCCACATTTCATAGGAAA 58.551 41.667 4.85 4.85 46.36 3.13
2457 2941 5.893255 CCATCCTCCACATTTCATAGGAAAA 59.107 40.000 6.65 0.00 45.52 2.29
2458 2942 6.552350 CCATCCTCCACATTTCATAGGAAAAT 59.448 38.462 6.65 0.00 45.52 1.82
2459 2943 7.725397 CCATCCTCCACATTTCATAGGAAAATA 59.275 37.037 6.65 0.00 45.52 1.40
2460 2944 9.135189 CATCCTCCACATTTCATAGGAAAATAA 57.865 33.333 6.65 0.00 45.52 1.40
2461 2945 9.713684 ATCCTCCACATTTCATAGGAAAATAAA 57.286 29.630 6.65 0.00 45.52 1.40
2462 2946 9.540538 TCCTCCACATTTCATAGGAAAATAAAA 57.459 29.630 6.65 0.00 45.52 1.52
2489 2973 9.914131 AAAAGCCTAGACTCAATGTAAAAATTC 57.086 29.630 0.00 0.00 0.00 2.17
2490 2974 7.631717 AGCCTAGACTCAATGTAAAAATTCC 57.368 36.000 0.00 0.00 0.00 3.01
2491 2975 7.406104 AGCCTAGACTCAATGTAAAAATTCCT 58.594 34.615 0.00 0.00 0.00 3.36
2492 2976 7.890655 AGCCTAGACTCAATGTAAAAATTCCTT 59.109 33.333 0.00 0.00 0.00 3.36
2493 2977 8.523658 GCCTAGACTCAATGTAAAAATTCCTTT 58.476 33.333 0.00 0.00 0.00 3.11
2494 2978 9.846248 CCTAGACTCAATGTAAAAATTCCTTTG 57.154 33.333 0.00 0.00 0.00 2.77
2495 2979 9.846248 CTAGACTCAATGTAAAAATTCCTTTGG 57.154 33.333 0.00 0.00 0.00 3.28
2496 2980 8.250143 AGACTCAATGTAAAAATTCCTTTGGT 57.750 30.769 0.00 0.00 0.00 3.67
2497 2981 8.143835 AGACTCAATGTAAAAATTCCTTTGGTG 58.856 33.333 0.00 0.00 0.00 4.17
2498 2982 7.791029 ACTCAATGTAAAAATTCCTTTGGTGT 58.209 30.769 0.00 0.00 0.00 4.16
2499 2983 7.926018 ACTCAATGTAAAAATTCCTTTGGTGTC 59.074 33.333 0.00 0.00 0.00 3.67
2500 2984 7.786030 TCAATGTAAAAATTCCTTTGGTGTCA 58.214 30.769 0.00 0.00 0.00 3.58
2501 2985 8.260818 TCAATGTAAAAATTCCTTTGGTGTCAA 58.739 29.630 0.00 0.00 0.00 3.18
2502 2986 8.334632 CAATGTAAAAATTCCTTTGGTGTCAAC 58.665 33.333 0.00 0.00 31.78 3.18
2521 3005 5.841810 TCAACCAAATGACATCTTGTTTCC 58.158 37.500 0.00 0.00 0.00 3.13
2522 3006 5.598005 TCAACCAAATGACATCTTGTTTCCT 59.402 36.000 0.00 0.00 0.00 3.36
2523 3007 6.775142 TCAACCAAATGACATCTTGTTTCCTA 59.225 34.615 0.00 0.00 0.00 2.94
2524 3008 7.451255 TCAACCAAATGACATCTTGTTTCCTAT 59.549 33.333 0.00 0.00 0.00 2.57
2525 3009 7.781324 ACCAAATGACATCTTGTTTCCTATT 57.219 32.000 0.00 0.00 0.00 1.73
2526 3010 7.830739 ACCAAATGACATCTTGTTTCCTATTC 58.169 34.615 0.00 0.00 0.00 1.75
2527 3011 7.093771 ACCAAATGACATCTTGTTTCCTATTCC 60.094 37.037 0.00 0.00 0.00 3.01
2528 3012 7.123247 CCAAATGACATCTTGTTTCCTATTCCT 59.877 37.037 0.00 0.00 0.00 3.36
2529 3013 9.177608 CAAATGACATCTTGTTTCCTATTCCTA 57.822 33.333 0.00 0.00 0.00 2.94
2530 3014 8.738645 AATGACATCTTGTTTCCTATTCCTAC 57.261 34.615 0.00 0.00 0.00 3.18
2531 3015 7.496346 TGACATCTTGTTTCCTATTCCTACT 57.504 36.000 0.00 0.00 0.00 2.57
2532 3016 7.556844 TGACATCTTGTTTCCTATTCCTACTC 58.443 38.462 0.00 0.00 0.00 2.59
2533 3017 7.180229 TGACATCTTGTTTCCTATTCCTACTCA 59.820 37.037 0.00 0.00 0.00 3.41
2534 3018 8.095452 ACATCTTGTTTCCTATTCCTACTCAT 57.905 34.615 0.00 0.00 0.00 2.90
2535 3019 9.213777 ACATCTTGTTTCCTATTCCTACTCATA 57.786 33.333 0.00 0.00 0.00 2.15
2536 3020 9.703892 CATCTTGTTTCCTATTCCTACTCATAG 57.296 37.037 0.00 0.00 0.00 2.23
2553 3037 9.853555 CTACTCATAGGATTTGAGATACATGTC 57.146 37.037 0.00 0.00 42.63 3.06
2554 3038 8.255111 ACTCATAGGATTTGAGATACATGTCA 57.745 34.615 0.00 0.00 42.63 3.58
2555 3039 8.878211 ACTCATAGGATTTGAGATACATGTCAT 58.122 33.333 0.00 0.00 42.63 3.06
2556 3040 9.368674 CTCATAGGATTTGAGATACATGTCATC 57.631 37.037 0.00 4.47 42.63 2.92
2557 3041 9.097946 TCATAGGATTTGAGATACATGTCATCT 57.902 33.333 0.00 9.42 35.43 2.90
2558 3042 9.368674 CATAGGATTTGAGATACATGTCATCTC 57.631 37.037 24.04 24.04 45.76 2.75
2568 3052 9.755804 GAGATACATGTCATCTCATTTTCTACA 57.244 33.333 24.95 0.00 45.17 2.74
2573 3057 9.458727 ACATGTCATCTCATTTTCTACAAGATT 57.541 29.630 0.00 0.00 0.00 2.40
2574 3058 9.717892 CATGTCATCTCATTTTCTACAAGATTG 57.282 33.333 0.00 0.00 0.00 2.67
2575 3059 7.755591 TGTCATCTCATTTTCTACAAGATTGC 58.244 34.615 0.00 0.00 0.00 3.56
2576 3060 7.609146 TGTCATCTCATTTTCTACAAGATTGCT 59.391 33.333 0.00 0.00 0.00 3.91
2577 3061 9.102757 GTCATCTCATTTTCTACAAGATTGCTA 57.897 33.333 0.00 0.00 0.00 3.49
2578 3062 9.842775 TCATCTCATTTTCTACAAGATTGCTAT 57.157 29.630 0.00 0.00 0.00 2.97
2581 3065 9.113838 TCTCATTTTCTACAAGATTGCTATTCC 57.886 33.333 0.00 0.00 0.00 3.01
2582 3066 9.118300 CTCATTTTCTACAAGATTGCTATTCCT 57.882 33.333 0.00 0.00 0.00 3.36
2592 3076 9.678260 ACAAGATTGCTATTCCTATGATAATCC 57.322 33.333 0.00 0.00 0.00 3.01
2593 3077 9.902684 CAAGATTGCTATTCCTATGATAATCCT 57.097 33.333 0.00 0.00 0.00 3.24
2598 3082 9.735362 TTGCTATTCCTATGATAATCCTATCCT 57.265 33.333 0.00 0.00 34.10 3.24
2605 3089 9.661954 TCCTATGATAATCCTATCCTATGAACC 57.338 37.037 0.00 0.00 34.10 3.62
2606 3090 9.439461 CCTATGATAATCCTATCCTATGAACCA 57.561 37.037 0.00 0.00 34.10 3.67
2613 3097 6.500589 TCCTATCCTATGAACCAAAAGAGG 57.499 41.667 0.00 0.00 0.00 3.69
2614 3098 5.066593 CCTATCCTATGAACCAAAAGAGGC 58.933 45.833 0.00 0.00 0.00 4.70
2615 3099 3.366052 TCCTATGAACCAAAAGAGGCC 57.634 47.619 0.00 0.00 0.00 5.19
2616 3100 2.919602 TCCTATGAACCAAAAGAGGCCT 59.080 45.455 3.86 3.86 0.00 5.19
2681 3165 1.003464 TGAAACTCTGGCATGCAGCTA 59.997 47.619 21.36 1.38 44.79 3.32
2710 3194 8.025445 AGAAATCAGTGTTGCAATTCAGATTAC 58.975 33.333 17.51 0.17 0.00 1.89
2711 3195 5.627499 TCAGTGTTGCAATTCAGATTACC 57.373 39.130 0.59 0.00 0.00 2.85
2712 3196 5.316167 TCAGTGTTGCAATTCAGATTACCT 58.684 37.500 0.59 0.00 0.00 3.08
2713 3197 5.769662 TCAGTGTTGCAATTCAGATTACCTT 59.230 36.000 0.59 0.00 0.00 3.50
2714 3198 5.860182 CAGTGTTGCAATTCAGATTACCTTG 59.140 40.000 0.59 0.00 0.00 3.61
2715 3199 5.536161 AGTGTTGCAATTCAGATTACCTTGT 59.464 36.000 0.59 0.00 0.00 3.16
2716 3200 5.858581 GTGTTGCAATTCAGATTACCTTGTC 59.141 40.000 0.59 0.00 0.00 3.18
2717 3201 4.944962 TGCAATTCAGATTACCTTGTCG 57.055 40.909 0.00 0.00 0.00 4.35
2718 3202 3.126858 TGCAATTCAGATTACCTTGTCGC 59.873 43.478 0.00 0.00 0.00 5.19
2726 3210 0.947180 TTACCTTGTCGCCTTGTCGC 60.947 55.000 0.00 0.00 0.00 5.19
2731 3215 2.665185 GTCGCCTTGTCGCCTTGT 60.665 61.111 0.00 0.00 0.00 3.16
2797 3281 4.044317 AGTGTACCCCAGATCCGAGTATAT 59.956 45.833 0.00 0.00 0.00 0.86
2805 3293 6.717540 CCCCAGATCCGAGTATATAAGATAGG 59.282 46.154 0.00 0.00 0.00 2.57
2837 3325 6.744175 AATCTCAGGAGCATCTATCTGAAA 57.256 37.500 0.00 0.00 36.06 2.69
2878 3366 6.706270 ACAACTATGTATCCCATTAAAGCGAG 59.294 38.462 0.00 0.00 38.24 5.03
2890 3378 6.594159 CCCATTAAAGCGAGAGAGTTCTTTTA 59.406 38.462 0.00 0.00 32.53 1.52
2925 3413 5.297547 ACGAAAGATCACAGTAAGAAAGCA 58.702 37.500 0.00 0.00 0.00 3.91
2935 3423 7.148641 TCACAGTAAGAAAGCAGAGAAGTAAG 58.851 38.462 0.00 0.00 0.00 2.34
2949 3437 6.978080 CAGAGAAGTAAGTAAGAGAAGATGCC 59.022 42.308 0.00 0.00 0.00 4.40
2960 3448 2.416893 GAGAAGATGCCGACCAAGAAAC 59.583 50.000 0.00 0.00 0.00 2.78
2981 3469 8.834465 AGAAACATAAATATGTGATCAGACAGC 58.166 33.333 6.82 0.00 45.55 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.614983 TGAACACCTGCTCGTTTTTACC 59.385 45.455 0.00 0.00 0.00 2.85
37 38 1.004595 GCAATCGAAGTACCGAACCC 58.995 55.000 0.00 0.00 42.22 4.11
42 43 4.986034 TGTAATATGGCAATCGAAGTACCG 59.014 41.667 0.00 0.00 0.00 4.02
44 45 6.700081 TCAGTGTAATATGGCAATCGAAGTAC 59.300 38.462 0.00 0.00 0.00 2.73
83 84 0.321653 GGTTCCTCGGCATGTTCACT 60.322 55.000 0.00 0.00 0.00 3.41
90 91 3.193691 CGATATCTTAGGTTCCTCGGCAT 59.806 47.826 0.34 0.00 0.00 4.40
104 105 7.487189 CCTTAAACTTGTGTACGACGATATCTT 59.513 37.037 0.00 0.00 0.00 2.40
105 106 6.971184 CCTTAAACTTGTGTACGACGATATCT 59.029 38.462 0.00 0.00 0.00 1.98
114 115 3.432252 CCTCTGCCTTAAACTTGTGTACG 59.568 47.826 0.00 0.00 0.00 3.67
115 116 4.638304 TCCTCTGCCTTAAACTTGTGTAC 58.362 43.478 0.00 0.00 0.00 2.90
116 117 4.802918 GCTCCTCTGCCTTAAACTTGTGTA 60.803 45.833 0.00 0.00 0.00 2.90
117 118 3.744660 CTCCTCTGCCTTAAACTTGTGT 58.255 45.455 0.00 0.00 0.00 3.72
142 143 2.285198 GCTTTCTTTTTGTGCGTGCTTG 60.285 45.455 0.00 0.00 0.00 4.01
144 145 1.559831 GCTTTCTTTTTGTGCGTGCT 58.440 45.000 0.00 0.00 0.00 4.40
145 146 0.576798 GGCTTTCTTTTTGTGCGTGC 59.423 50.000 0.00 0.00 0.00 5.34
148 149 2.472816 ACATGGCTTTCTTTTTGTGCG 58.527 42.857 0.00 0.00 0.00 5.34
185 186 4.293415 CATGCTGTTGGACTGAAAAGAAC 58.707 43.478 0.00 0.00 0.00 3.01
209 210 1.285578 GAAAGAGAGCACTCCGATGC 58.714 55.000 7.60 0.00 46.50 3.91
216 217 2.708325 AGAACAAGGGAAAGAGAGCACT 59.292 45.455 0.00 0.00 0.00 4.40
223 224 4.207165 CAAGACCAAGAACAAGGGAAAGA 58.793 43.478 0.00 0.00 0.00 2.52
359 363 3.451178 TGAAGCGAGGCCTAGAAACTATT 59.549 43.478 18.16 0.68 0.00 1.73
396 400 8.090214 ACTAGTTTTTACGGTTACTAAGATGCA 58.910 33.333 0.00 0.00 0.00 3.96
418 422 3.611766 AAGGTCCGGTGAATCAACTAG 57.388 47.619 0.00 0.00 0.00 2.57
464 468 5.248870 ACATTCACATTTATTTCGGGAGC 57.751 39.130 0.00 0.00 0.00 4.70
498 502 4.705519 CCGTTTTGGCTGCTGGCG 62.706 66.667 12.46 0.00 42.94 5.69
499 503 3.273080 CTCCGTTTTGGCTGCTGGC 62.273 63.158 10.40 10.40 37.80 4.85
549 567 1.465991 GCATATTTGTGTGCGCTGCG 61.466 55.000 19.17 19.17 0.00 5.18
550 568 1.141591 GGCATATTTGTGTGCGCTGC 61.142 55.000 9.73 6.43 42.15 5.25
551 569 0.452987 AGGCATATTTGTGTGCGCTG 59.547 50.000 9.73 0.00 42.15 5.18
552 570 0.734889 GAGGCATATTTGTGTGCGCT 59.265 50.000 9.73 0.00 42.15 5.92
553 571 0.248621 GGAGGCATATTTGTGTGCGC 60.249 55.000 0.00 0.00 42.15 6.09
554 572 0.027979 CGGAGGCATATTTGTGTGCG 59.972 55.000 0.00 0.00 42.15 5.34
555 573 0.381801 CCGGAGGCATATTTGTGTGC 59.618 55.000 0.00 0.00 46.14 4.57
582 626 9.962809 AACCTAGTATAAATCTCGCTAGACTAT 57.037 33.333 0.00 0.00 33.57 2.12
600 644 8.431910 AACTCAAAACCTCATCTAACCTAGTA 57.568 34.615 0.00 0.00 0.00 1.82
601 645 6.936968 ACTCAAAACCTCATCTAACCTAGT 57.063 37.500 0.00 0.00 0.00 2.57
602 646 8.507249 CAAAACTCAAAACCTCATCTAACCTAG 58.493 37.037 0.00 0.00 0.00 3.02
643 687 1.790755 TAAGCTTGTGCGTGTCGATT 58.209 45.000 9.86 0.00 45.42 3.34
665 709 9.926158 TGTGTGGATTTTAGTCGTTTAGTAATA 57.074 29.630 0.00 0.00 0.00 0.98
666 710 8.836268 TGTGTGGATTTTAGTCGTTTAGTAAT 57.164 30.769 0.00 0.00 0.00 1.89
667 711 8.714179 CATGTGTGGATTTTAGTCGTTTAGTAA 58.286 33.333 0.00 0.00 0.00 2.24
738 783 6.524101 TTTTAGTCAAAAGTGGTTCAAGCT 57.476 33.333 0.00 0.00 0.00 3.74
775 822 1.213537 CAAGCAAGGCGTTCCATGG 59.786 57.895 4.97 4.97 31.94 3.66
852 905 3.581101 TCTAGCAGTAGATCTTGGCCAT 58.419 45.455 6.09 0.00 29.69 4.40
853 906 3.032265 TCTAGCAGTAGATCTTGGCCA 57.968 47.619 0.00 0.00 29.69 5.36
854 907 4.615588 AATCTAGCAGTAGATCTTGGCC 57.384 45.455 0.00 0.00 44.04 5.36
855 908 8.438676 TTTAAAATCTAGCAGTAGATCTTGGC 57.561 34.615 0.00 2.46 44.04 4.52
856 909 9.823647 TCTTTAAAATCTAGCAGTAGATCTTGG 57.176 33.333 0.00 0.00 44.04 3.61
957 1113 4.940905 TGGGTTTATATCGACCGATGAA 57.059 40.909 14.42 6.37 36.78 2.57
979 1139 4.967442 TCTGGTAGTAGTAGACTGGCTCTA 59.033 45.833 0.00 0.00 39.39 2.43
982 1142 3.266254 TGTCTGGTAGTAGTAGACTGGCT 59.734 47.826 12.50 0.00 41.01 4.75
989 1149 2.641305 AGCGGTGTCTGGTAGTAGTAG 58.359 52.381 0.00 0.00 0.00 2.57
990 1150 2.795231 AGCGGTGTCTGGTAGTAGTA 57.205 50.000 0.00 0.00 0.00 1.82
991 1151 2.641305 CTAGCGGTGTCTGGTAGTAGT 58.359 52.381 0.00 0.00 33.78 2.73
992 1152 1.334243 GCTAGCGGTGTCTGGTAGTAG 59.666 57.143 0.00 0.00 39.13 2.57
1055 1218 3.661944 CCAGCGCTTCATCAGAGAATAT 58.338 45.455 7.50 0.00 0.00 1.28
1270 1433 5.812642 GCATGCAGAGTTGTACTAACATACT 59.187 40.000 14.21 0.00 34.97 2.12
1280 1443 2.290197 TGTCCATGCATGCAGAGTTGTA 60.290 45.455 26.69 3.13 0.00 2.41
1411 1609 3.490759 CTGCATCGCCACCGTCAC 61.491 66.667 0.00 0.00 35.54 3.67
1467 1665 4.010224 ATGTACCGGTGCCACGCA 62.010 61.111 19.93 6.80 35.60 5.24
1752 1950 2.103094 CTGATGGTGGATGTCGTGGTAT 59.897 50.000 0.00 0.00 0.00 2.73
1779 1977 2.417924 CGAGAAGTTGTATCTGCTGGCT 60.418 50.000 0.00 0.00 0.00 4.75
1836 2034 4.223800 ACATAGGGCATGTGCGTG 57.776 55.556 0.00 0.00 46.41 5.34
1854 2052 2.099652 CTTGGGTCCTGTGCTCGACA 62.100 60.000 0.00 0.00 0.00 4.35
1894 2095 3.067684 TGCTTAGTTAAGGGCTTCCAC 57.932 47.619 1.44 0.00 33.95 4.02
1940 2396 8.598041 GGAAGGATAAATACTCTGGTGACATAT 58.402 37.037 0.00 0.00 41.51 1.78
1951 2407 5.869579 TGCATGAGGGAAGGATAAATACTC 58.130 41.667 0.00 0.00 0.00 2.59
2025 2486 5.008331 CAGGAAATGCACATGCTCCTATAT 58.992 41.667 11.60 0.00 42.66 0.86
2026 2487 4.141413 ACAGGAAATGCACATGCTCCTATA 60.141 41.667 11.60 0.00 42.66 1.31
2027 2488 3.220110 CAGGAAATGCACATGCTCCTAT 58.780 45.455 11.60 0.00 42.66 2.57
2028 2489 2.025981 ACAGGAAATGCACATGCTCCTA 60.026 45.455 11.60 0.00 42.66 2.94
2029 2490 1.272313 ACAGGAAATGCACATGCTCCT 60.272 47.619 7.21 7.21 42.66 3.69
2030 2491 1.133790 GACAGGAAATGCACATGCTCC 59.866 52.381 5.31 4.06 42.66 4.70
2031 2492 1.202110 CGACAGGAAATGCACATGCTC 60.202 52.381 5.31 0.00 42.66 4.26
2032 2493 0.806868 CGACAGGAAATGCACATGCT 59.193 50.000 5.31 0.00 42.66 3.79
2033 2494 0.179156 CCGACAGGAAATGCACATGC 60.179 55.000 0.00 0.00 41.02 4.06
2034 2495 0.179156 GCCGACAGGAAATGCACATG 60.179 55.000 0.00 0.00 41.02 3.21
2036 2497 2.324330 CGCCGACAGGAAATGCACA 61.324 57.895 0.00 0.00 41.02 4.57
2038 2499 2.745884 CCGCCGACAGGAAATGCA 60.746 61.111 0.00 0.00 41.02 3.96
2063 2530 6.519382 TCAGATGCTCGAATGACAGATATTT 58.481 36.000 0.00 0.00 0.00 1.40
2098 2565 2.857592 AGCATGCCATTTTCATCGAC 57.142 45.000 15.66 0.00 0.00 4.20
2100 2567 3.153676 TGAAGCATGCCATTTTCATCG 57.846 42.857 15.66 0.00 0.00 3.84
2127 2597 6.093219 GCAGATGTAGCAATTCTTTTCTCTGA 59.907 38.462 0.00 0.00 30.49 3.27
2151 2621 5.447144 GGTGTTGGTTTTGAACTTTTGATGC 60.447 40.000 0.00 0.00 0.00 3.91
2152 2622 5.874261 AGGTGTTGGTTTTGAACTTTTGATG 59.126 36.000 0.00 0.00 0.00 3.07
2157 2627 5.476091 TCAAGGTGTTGGTTTTGAACTTT 57.524 34.783 0.00 0.00 34.09 2.66
2201 2682 8.410141 ACATGAAGCTTTACTATCTAGTCTGAC 58.590 37.037 0.00 0.00 37.73 3.51
2226 2707 0.847035 CGAATAGAAGCTCGCGGAAC 59.153 55.000 6.13 0.00 0.00 3.62
2230 2711 0.029567 ACTCCGAATAGAAGCTCGCG 59.970 55.000 0.00 0.00 33.70 5.87
2300 2784 3.578282 ACCAAAGGAGGCCTTATTGTTTG 59.422 43.478 6.77 12.26 43.92 2.93
2304 2788 5.261216 TCTAAACCAAAGGAGGCCTTATTG 58.739 41.667 6.77 12.69 43.92 1.90
2305 2789 5.510430 CTCTAAACCAAAGGAGGCCTTATT 58.490 41.667 6.77 1.29 43.92 1.40
2306 2790 4.079730 CCTCTAAACCAAAGGAGGCCTTAT 60.080 45.833 6.77 0.00 43.92 1.73
2307 2791 3.265995 CCTCTAAACCAAAGGAGGCCTTA 59.734 47.826 6.77 0.00 43.92 2.69
2309 2793 1.636003 CCTCTAAACCAAAGGAGGCCT 59.364 52.381 3.86 3.86 38.82 5.19
2310 2794 1.633945 TCCTCTAAACCAAAGGAGGCC 59.366 52.381 0.00 0.00 43.46 5.19
2311 2795 3.434940 TTCCTCTAAACCAAAGGAGGC 57.565 47.619 0.00 0.00 43.46 4.70
2312 2796 6.010219 TGAAATTCCTCTAAACCAAAGGAGG 58.990 40.000 0.00 0.00 44.69 4.30
2313 2797 7.709149 ATGAAATTCCTCTAAACCAAAGGAG 57.291 36.000 0.00 0.00 40.21 3.69
2314 2798 7.834181 CCTATGAAATTCCTCTAAACCAAAGGA 59.166 37.037 0.00 0.00 37.42 3.36
2315 2799 7.834181 TCCTATGAAATTCCTCTAAACCAAAGG 59.166 37.037 0.00 0.00 0.00 3.11
2316 2800 8.807948 TCCTATGAAATTCCTCTAAACCAAAG 57.192 34.615 0.00 0.00 0.00 2.77
2317 2801 9.768215 ATTCCTATGAAATTCCTCTAAACCAAA 57.232 29.630 0.00 0.00 33.32 3.28
2318 2802 9.768215 AATTCCTATGAAATTCCTCTAAACCAA 57.232 29.630 0.00 0.00 33.32 3.67
2319 2803 9.408648 GAATTCCTATGAAATTCCTCTAAACCA 57.591 33.333 0.00 0.00 33.32 3.67
2320 2804 9.634021 AGAATTCCTATGAAATTCCTCTAAACC 57.366 33.333 0.65 0.00 33.32 3.27
2325 2809 9.667607 TCTCTAGAATTCCTATGAAATTCCTCT 57.332 33.333 0.65 0.00 33.32 3.69
2372 2856 5.659079 TGAACCAAAGGGCTCTAAAGAAAAA 59.341 36.000 0.00 0.00 37.90 1.94
2373 2857 5.205056 TGAACCAAAGGGCTCTAAAGAAAA 58.795 37.500 0.00 0.00 37.90 2.29
2374 2858 4.798882 TGAACCAAAGGGCTCTAAAGAAA 58.201 39.130 0.00 0.00 37.90 2.52
2375 2859 4.447138 TGAACCAAAGGGCTCTAAAGAA 57.553 40.909 0.00 0.00 37.90 2.52
2376 2860 4.657814 ATGAACCAAAGGGCTCTAAAGA 57.342 40.909 0.00 0.00 37.90 2.52
2377 2861 5.745227 TCTATGAACCAAAGGGCTCTAAAG 58.255 41.667 0.00 0.00 37.90 1.85
2378 2862 5.772393 TCTATGAACCAAAGGGCTCTAAA 57.228 39.130 0.00 0.00 37.90 1.85
2379 2863 5.772393 TTCTATGAACCAAAGGGCTCTAA 57.228 39.130 0.00 0.00 37.90 2.10
2380 2864 5.772393 TTTCTATGAACCAAAGGGCTCTA 57.228 39.130 0.00 0.00 37.90 2.43
2381 2865 4.657814 TTTCTATGAACCAAAGGGCTCT 57.342 40.909 0.00 0.00 37.90 4.09
2382 2866 4.098501 CCATTTCTATGAACCAAAGGGCTC 59.901 45.833 0.00 0.00 33.50 4.70
2383 2867 4.026052 CCATTTCTATGAACCAAAGGGCT 58.974 43.478 0.00 0.00 33.50 5.19
2384 2868 4.023291 TCCATTTCTATGAACCAAAGGGC 58.977 43.478 0.00 0.00 33.50 5.19
2385 2869 6.183360 GGAATCCATTTCTATGAACCAAAGGG 60.183 42.308 0.00 0.00 35.88 3.95
2386 2870 6.608808 AGGAATCCATTTCTATGAACCAAAGG 59.391 38.462 0.61 0.00 34.56 3.11
2387 2871 7.651027 AGGAATCCATTTCTATGAACCAAAG 57.349 36.000 0.61 0.00 34.56 2.77
2388 2872 9.713684 AATAGGAATCCATTTCTATGAACCAAA 57.286 29.630 0.61 0.00 37.55 3.28
2389 2873 9.354673 GAATAGGAATCCATTTCTATGAACCAA 57.645 33.333 0.61 0.00 37.55 3.67
2390 2874 7.944554 GGAATAGGAATCCATTTCTATGAACCA 59.055 37.037 0.61 0.00 37.55 3.67
2391 2875 8.166726 AGGAATAGGAATCCATTTCTATGAACC 58.833 37.037 0.61 6.01 37.55 3.62
2394 2878 9.392506 TGTAGGAATAGGAATCCATTTCTATGA 57.607 33.333 0.61 0.00 37.55 2.15
2429 2913 3.085952 TGAAATGTGGAGGATGGGAAC 57.914 47.619 0.00 0.00 0.00 3.62
2430 2914 4.141181 CCTATGAAATGTGGAGGATGGGAA 60.141 45.833 0.00 0.00 0.00 3.97
2431 2915 3.395607 CCTATGAAATGTGGAGGATGGGA 59.604 47.826 0.00 0.00 0.00 4.37
2432 2916 3.395607 TCCTATGAAATGTGGAGGATGGG 59.604 47.826 0.00 0.00 31.25 4.00
2433 2917 4.712051 TCCTATGAAATGTGGAGGATGG 57.288 45.455 0.00 0.00 31.25 3.51
2434 2918 7.592885 ATTTTCCTATGAAATGTGGAGGATG 57.407 36.000 0.00 0.00 40.08 3.51
2435 2919 9.713684 TTTATTTTCCTATGAAATGTGGAGGAT 57.286 29.630 0.00 0.00 40.08 3.24
2436 2920 9.540538 TTTTATTTTCCTATGAAATGTGGAGGA 57.459 29.630 0.00 0.00 40.08 3.71
2463 2947 9.914131 GAATTTTTACATTGAGTCTAGGCTTTT 57.086 29.630 0.00 0.00 0.00 2.27
2464 2948 8.523658 GGAATTTTTACATTGAGTCTAGGCTTT 58.476 33.333 0.00 0.00 0.00 3.51
2465 2949 7.890655 AGGAATTTTTACATTGAGTCTAGGCTT 59.109 33.333 0.00 0.00 0.00 4.35
2466 2950 7.406104 AGGAATTTTTACATTGAGTCTAGGCT 58.594 34.615 0.00 0.00 0.00 4.58
2467 2951 7.631717 AGGAATTTTTACATTGAGTCTAGGC 57.368 36.000 0.00 0.00 0.00 3.93
2468 2952 9.846248 CAAAGGAATTTTTACATTGAGTCTAGG 57.154 33.333 0.00 0.00 0.00 3.02
2469 2953 9.846248 CCAAAGGAATTTTTACATTGAGTCTAG 57.154 33.333 0.00 0.00 0.00 2.43
2470 2954 9.362151 ACCAAAGGAATTTTTACATTGAGTCTA 57.638 29.630 0.00 0.00 0.00 2.59
2471 2955 8.143835 CACCAAAGGAATTTTTACATTGAGTCT 58.856 33.333 0.00 0.00 0.00 3.24
2472 2956 7.926018 ACACCAAAGGAATTTTTACATTGAGTC 59.074 33.333 0.00 0.00 0.00 3.36
2473 2957 7.791029 ACACCAAAGGAATTTTTACATTGAGT 58.209 30.769 0.00 0.00 0.00 3.41
2474 2958 7.925483 TGACACCAAAGGAATTTTTACATTGAG 59.075 33.333 0.00 0.00 0.00 3.02
2475 2959 7.786030 TGACACCAAAGGAATTTTTACATTGA 58.214 30.769 0.00 0.00 0.00 2.57
2476 2960 8.334632 GTTGACACCAAAGGAATTTTTACATTG 58.665 33.333 0.00 0.00 33.49 2.82
2477 2961 7.497579 GGTTGACACCAAAGGAATTTTTACATT 59.502 33.333 0.00 0.00 43.61 2.71
2478 2962 6.989759 GGTTGACACCAAAGGAATTTTTACAT 59.010 34.615 0.00 0.00 43.61 2.29
2479 2963 6.342111 GGTTGACACCAAAGGAATTTTTACA 58.658 36.000 0.00 0.00 43.61 2.41
2480 2964 6.838198 GGTTGACACCAAAGGAATTTTTAC 57.162 37.500 0.00 0.00 43.61 2.01
2497 2981 5.691754 GGAAACAAGATGTCATTTGGTTGAC 59.308 40.000 12.70 0.00 45.05 3.18
2498 2982 5.598005 AGGAAACAAGATGTCATTTGGTTGA 59.402 36.000 12.70 0.00 34.55 3.18
2499 2983 5.846203 AGGAAACAAGATGTCATTTGGTTG 58.154 37.500 12.70 6.32 34.55 3.77
2500 2984 7.781324 ATAGGAAACAAGATGTCATTTGGTT 57.219 32.000 9.41 9.41 36.95 3.67
2501 2985 7.093771 GGAATAGGAAACAAGATGTCATTTGGT 60.094 37.037 10.50 3.75 0.00 3.67
2502 2986 7.123247 AGGAATAGGAAACAAGATGTCATTTGG 59.877 37.037 10.50 0.00 0.00 3.28
2503 2987 8.059798 AGGAATAGGAAACAAGATGTCATTTG 57.940 34.615 0.00 0.00 0.00 2.32
2504 2988 9.178758 GTAGGAATAGGAAACAAGATGTCATTT 57.821 33.333 0.00 0.00 0.00 2.32
2505 2989 8.552296 AGTAGGAATAGGAAACAAGATGTCATT 58.448 33.333 0.00 0.00 0.00 2.57
2506 2990 8.095452 AGTAGGAATAGGAAACAAGATGTCAT 57.905 34.615 0.00 0.00 0.00 3.06
2507 2991 7.180229 TGAGTAGGAATAGGAAACAAGATGTCA 59.820 37.037 0.00 0.00 0.00 3.58
2508 2992 7.556844 TGAGTAGGAATAGGAAACAAGATGTC 58.443 38.462 0.00 0.00 0.00 3.06
2509 2993 7.496346 TGAGTAGGAATAGGAAACAAGATGT 57.504 36.000 0.00 0.00 0.00 3.06
2510 2994 9.703892 CTATGAGTAGGAATAGGAAACAAGATG 57.296 37.037 0.00 0.00 0.00 2.90
2527 3011 9.853555 GACATGTATCTCAAATCCTATGAGTAG 57.146 37.037 0.00 0.00 43.77 2.57
2528 3012 9.367160 TGACATGTATCTCAAATCCTATGAGTA 57.633 33.333 0.00 0.00 43.77 2.59
2529 3013 8.255111 TGACATGTATCTCAAATCCTATGAGT 57.745 34.615 0.00 0.00 43.77 3.41
2530 3014 9.368674 GATGACATGTATCTCAAATCCTATGAG 57.631 37.037 0.00 0.00 44.53 2.90
2531 3015 9.097946 AGATGACATGTATCTCAAATCCTATGA 57.902 33.333 0.00 0.00 29.05 2.15
2532 3016 9.368674 GAGATGACATGTATCTCAAATCCTATG 57.631 37.037 24.95 0.00 46.22 2.23
2542 3026 9.755804 TGTAGAAAATGAGATGACATGTATCTC 57.244 33.333 24.04 24.04 46.82 2.75
2547 3031 9.458727 AATCTTGTAGAAAATGAGATGACATGT 57.541 29.630 0.00 0.00 0.00 3.21
2548 3032 9.717892 CAATCTTGTAGAAAATGAGATGACATG 57.282 33.333 0.00 0.00 0.00 3.21
2549 3033 8.404000 GCAATCTTGTAGAAAATGAGATGACAT 58.596 33.333 0.00 0.00 0.00 3.06
2550 3034 7.609146 AGCAATCTTGTAGAAAATGAGATGACA 59.391 33.333 0.00 0.00 0.00 3.58
2551 3035 7.983307 AGCAATCTTGTAGAAAATGAGATGAC 58.017 34.615 0.00 0.00 0.00 3.06
2552 3036 9.842775 ATAGCAATCTTGTAGAAAATGAGATGA 57.157 29.630 0.00 0.00 0.00 2.92
2555 3039 9.113838 GGAATAGCAATCTTGTAGAAAATGAGA 57.886 33.333 0.00 0.00 0.00 3.27
2556 3040 9.118300 AGGAATAGCAATCTTGTAGAAAATGAG 57.882 33.333 0.00 0.00 0.00 2.90
2566 3050 9.678260 GGATTATCATAGGAATAGCAATCTTGT 57.322 33.333 0.00 0.00 0.00 3.16
2567 3051 9.902684 AGGATTATCATAGGAATAGCAATCTTG 57.097 33.333 0.00 0.00 0.00 3.02
2572 3056 9.735362 AGGATAGGATTATCATAGGAATAGCAA 57.265 33.333 0.00 0.00 37.92 3.91
2579 3063 9.661954 GGTTCATAGGATAGGATTATCATAGGA 57.338 37.037 0.00 1.09 39.88 2.94
2580 3064 9.439461 TGGTTCATAGGATAGGATTATCATAGG 57.561 37.037 0.00 0.00 36.37 2.57
2587 3071 8.660435 CCTCTTTTGGTTCATAGGATAGGATTA 58.340 37.037 0.00 0.00 28.27 1.75
2588 3072 7.521669 CCTCTTTTGGTTCATAGGATAGGATT 58.478 38.462 0.00 0.00 28.27 3.01
2589 3073 6.466470 GCCTCTTTTGGTTCATAGGATAGGAT 60.466 42.308 0.00 0.00 28.27 3.24
2590 3074 5.163195 GCCTCTTTTGGTTCATAGGATAGGA 60.163 44.000 0.00 0.00 0.00 2.94
2591 3075 5.066593 GCCTCTTTTGGTTCATAGGATAGG 58.933 45.833 0.00 0.00 0.00 2.57
2592 3076 5.066593 GGCCTCTTTTGGTTCATAGGATAG 58.933 45.833 0.00 0.00 0.00 2.08
2593 3077 4.726825 AGGCCTCTTTTGGTTCATAGGATA 59.273 41.667 0.00 0.00 0.00 2.59
2594 3078 3.529319 AGGCCTCTTTTGGTTCATAGGAT 59.471 43.478 0.00 0.00 0.00 3.24
2595 3079 2.919602 AGGCCTCTTTTGGTTCATAGGA 59.080 45.455 0.00 0.00 0.00 2.94
2596 3080 3.372440 AGGCCTCTTTTGGTTCATAGG 57.628 47.619 0.00 0.00 0.00 2.57
2597 3081 6.834168 TTTTAGGCCTCTTTTGGTTCATAG 57.166 37.500 9.68 0.00 0.00 2.23
2598 3082 8.113462 ACTATTTTAGGCCTCTTTTGGTTCATA 58.887 33.333 9.68 0.00 0.00 2.15
2599 3083 6.954102 ACTATTTTAGGCCTCTTTTGGTTCAT 59.046 34.615 9.68 0.00 0.00 2.57
2600 3084 6.311735 ACTATTTTAGGCCTCTTTTGGTTCA 58.688 36.000 9.68 0.00 0.00 3.18
2601 3085 6.835819 ACTATTTTAGGCCTCTTTTGGTTC 57.164 37.500 9.68 0.00 0.00 3.62
2602 3086 7.467650 AGTACTATTTTAGGCCTCTTTTGGTT 58.532 34.615 9.68 0.00 0.00 3.67
2603 3087 7.029053 AGTACTATTTTAGGCCTCTTTTGGT 57.971 36.000 9.68 6.01 0.00 3.67
2604 3088 7.715686 CCTAGTACTATTTTAGGCCTCTTTTGG 59.284 40.741 9.68 0.00 0.00 3.28
2605 3089 8.664211 CCTAGTACTATTTTAGGCCTCTTTTG 57.336 38.462 9.68 0.00 0.00 2.44
2681 3165 7.267128 TCTGAATTGCAACACTGATTTCTTTT 58.733 30.769 0.00 0.00 0.00 2.27
2710 3194 3.423154 GGCGACAAGGCGACAAGG 61.423 66.667 0.00 0.00 39.62 3.61
2718 3202 1.080093 TAGCGACAAGGCGACAAGG 60.080 57.895 0.00 0.00 38.18 3.61
2771 3255 1.006758 TCGGATCTGGGGTACACTCTT 59.993 52.381 0.62 0.00 0.00 2.85
2797 3281 9.439461 TCCTGAGATTTCATTCTTCCTATCTTA 57.561 33.333 0.00 0.00 31.68 2.10
2805 3293 6.056884 AGATGCTCCTGAGATTTCATTCTTC 58.943 40.000 0.00 0.00 31.68 2.87
2822 3310 6.765036 TGATGGTTTCTTTCAGATAGATGCTC 59.235 38.462 0.00 0.00 0.00 4.26
2858 3346 6.493802 ACTCTCTCGCTTTAATGGGATACATA 59.506 38.462 8.31 0.00 39.40 2.29
2864 3352 3.769844 AGAACTCTCTCGCTTTAATGGGA 59.230 43.478 7.71 7.71 0.00 4.37
2865 3353 4.130286 AGAACTCTCTCGCTTTAATGGG 57.870 45.455 0.00 0.00 0.00 4.00
2925 3413 6.183360 CGGCATCTTCTCTTACTTACTTCTCT 60.183 42.308 0.00 0.00 0.00 3.10
2935 3423 2.961526 TGGTCGGCATCTTCTCTTAC 57.038 50.000 0.00 0.00 0.00 2.34
2949 3437 8.611757 TGATCACATATTTATGTTTCTTGGTCG 58.388 33.333 0.45 0.00 43.99 4.79
2960 3448 8.319143 TGATGCTGTCTGATCACATATTTATG 57.681 34.615 0.00 0.00 39.55 1.90
2981 3469 4.039004 TCCAACCTGGAACATGTTTTGATG 59.961 41.667 13.36 7.63 44.36 3.07


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

AutoCloner maintained by Alex Coulton.