Multiple sequence alignment - TraesCS7A01G132100

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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 TraesCS7A01G132100 chr7A 100.000 2849 0 0 1 2849 85161827 85158979 0.000000e+00 5262.0
1 TraesCS7A01G132100 chr7A 85.915 426 22 7 1006 1429 68202263 68202652 1.220000e-113 420.0
2 TraesCS7A01G132100 chr7D 89.092 2292 128 54 19 2267 83475037 83472825 0.000000e+00 2736.0
3 TraesCS7A01G132100 chr7D 84.333 300 36 8 2266 2562 83472732 83472441 1.670000e-72 283.0
4 TraesCS7A01G132100 chr7B 86.889 1800 122 40 496 2243 32665239 32663502 0.000000e+00 1912.0
5 TraesCS7A01G132100 chr2A 86.936 421 23 11 1012 1430 505416784 505417174 7.240000e-121 444.0
6 TraesCS7A01G132100 chr2A 83.776 339 22 15 1010 1346 519936796 519936489 9.990000e-75 291.0
7 TraesCS7A01G132100 chr1B 78.423 241 37 13 2276 2508 288648840 288648607 2.960000e-30 143.0
8 TraesCS7A01G132100 chr1B 83.333 114 16 3 2392 2503 66518471 66518359 5.020000e-18 102.0
9 TraesCS7A01G132100 chr1B 79.195 149 19 9 2354 2493 14508891 14509036 3.020000e-15 93.5
10 TraesCS7A01G132100 chr1B 97.959 49 1 0 2560 2608 402041907 402041955 5.060000e-13 86.1
11 TraesCS7A01G132100 chr1B 100.000 28 0 0 1897 1924 645356002 645355975 5.000000e-03 52.8
12 TraesCS7A01G132100 chr2D 75.954 262 36 15 2278 2526 537530679 537530432 3.000000e-20 110.0
13 TraesCS7A01G132100 chr2D 84.783 92 12 2 2395 2484 36787361 36787270 1.090000e-14 91.6
14 TraesCS7A01G132100 chr2D 95.918 49 2 0 2560 2608 617967496 617967448 2.350000e-11 80.5
15 TraesCS7A01G132100 chr2D 100.000 28 0 0 2246 2273 354387093 354387120 5.000000e-03 52.8
16 TraesCS7A01G132100 chr4A 74.903 259 44 13 2321 2563 714071049 714070796 6.500000e-17 99.0
17 TraesCS7A01G132100 chr4A 95.918 49 2 0 2560 2608 672266453 672266501 2.350000e-11 80.5
18 TraesCS7A01G132100 chr3D 84.314 102 11 4 2406 2503 426839402 426839302 8.400000e-16 95.3
19 TraesCS7A01G132100 chr2B 83.000 100 15 2 2395 2493 63219684 63219586 3.910000e-14 89.8
20 TraesCS7A01G132100 chr6B 95.918 49 2 0 2560 2608 599762502 599762550 2.350000e-11 80.5
21 TraesCS7A01G132100 chr6A 95.918 49 2 0 2560 2608 489860616 489860664 2.350000e-11 80.5
22 TraesCS7A01G132100 chr5B 95.918 49 2 0 2560 2608 419522769 419522721 2.350000e-11 80.5
23 TraesCS7A01G132100 chr5B 95.918 49 2 0 2560 2608 491851253 491851205 2.350000e-11 80.5
24 TraesCS7A01G132100 chr5B 94.231 52 3 0 2557 2608 518995587 518995638 2.350000e-11 80.5
25 TraesCS7A01G132100 chr1D 95.918 49 2 0 2560 2608 411297588 411297540 2.350000e-11 80.5
26 TraesCS7A01G132100 chr1D 100.000 28 0 0 1897 1924 467522768 467522741 5.000000e-03 52.8
27 TraesCS7A01G132100 chr1A 100.000 29 0 0 1897 1925 560465332 560465360 1.000000e-03 54.7


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 TraesCS7A01G132100 chr7A 85158979 85161827 2848 True 5262.0 5262 100.0000 1 2849 1 chr7A.!!$R1 2848
1 TraesCS7A01G132100 chr7D 83472441 83475037 2596 True 1509.5 2736 86.7125 19 2562 2 chr7D.!!$R1 2543
2 TraesCS7A01G132100 chr7B 32663502 32665239 1737 True 1912.0 1912 86.8890 496 2243 1 chr7B.!!$R1 1747

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
189 190 0.035458 AGGAGCAAGAAAGTGTCCCG 59.965 55.0 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1883 1942 0.807275 TGGCATCTGCACTTCGATCG 60.807 55.0 9.36 9.36 44.36 3.69 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
36 37 2.104792 GGTAAGCTCACATAGGATGGCA 59.895 50.000 0.00 0.00 33.60 4.92
49 50 1.685148 GATGGCATCTTCAACCTCCC 58.315 55.000 20.08 0.00 0.00 4.30
51 52 0.329261 TGGCATCTTCAACCTCCCTG 59.671 55.000 0.00 0.00 0.00 4.45
84 85 2.206036 AACCTCCGTCCTTCCCCA 59.794 61.111 0.00 0.00 0.00 4.96
91 92 3.787001 GTCCTTCCCCAGAGCCCG 61.787 72.222 0.00 0.00 0.00 6.13
117 118 6.676558 ACATTGACTATGGAAGGGAAATGAT 58.323 36.000 1.98 0.00 38.64 2.45
119 120 7.941238 ACATTGACTATGGAAGGGAAATGATAG 59.059 37.037 1.98 0.00 38.64 2.08
134 135 7.379750 GGAAATGATAGCTCTAAATCTACCGT 58.620 38.462 0.00 0.00 0.00 4.83
161 162 8.867935 CAAACATGTAAAAGACATCACAAACAA 58.132 29.630 0.00 0.00 46.33 2.83
179 180 2.365617 ACAAAGACTTCGAGGAGCAAGA 59.634 45.455 0.00 0.00 0.00 3.02
189 190 0.035458 AGGAGCAAGAAAGTGTCCCG 59.965 55.000 0.00 0.00 0.00 5.14
197 198 1.202770 AGAAAGTGTCCCGTCCCAAAG 60.203 52.381 0.00 0.00 0.00 2.77
210 211 1.214424 TCCCAAAGGGCAAGTATAGGC 59.786 52.381 0.00 0.00 43.94 3.93
273 274 3.366052 AGAGAAGAGGAGGAGAGACAC 57.634 52.381 0.00 0.00 0.00 3.67
274 275 2.647299 AGAGAAGAGGAGGAGAGACACA 59.353 50.000 0.00 0.00 0.00 3.72
275 276 2.752903 GAGAAGAGGAGGAGAGACACAC 59.247 54.545 0.00 0.00 0.00 3.82
303 304 1.446272 CGAAGACGAGGGGACAAGC 60.446 63.158 0.00 0.00 42.66 4.01
315 316 0.895100 GGACAAGCAGTTGCCCATCA 60.895 55.000 0.00 0.00 43.38 3.07
389 390 4.208873 TCACAAAAATCAAAACATGAGCGC 59.791 37.500 0.00 0.00 42.53 5.92
423 424 2.124507 AACCAGATCCACCACCACCG 62.125 60.000 0.00 0.00 0.00 4.94
431 432 1.961277 CACCACCACCGAAGCTCAC 60.961 63.158 0.00 0.00 0.00 3.51
434 435 2.029073 ACCACCGAAGCTCACACG 59.971 61.111 0.00 0.00 0.00 4.49
481 482 3.057019 CTCCGATGAAACACAGACGAAA 58.943 45.455 0.00 0.00 35.52 3.46
482 483 3.459145 TCCGATGAAACACAGACGAAAA 58.541 40.909 0.00 0.00 35.52 2.29
483 484 3.246699 TCCGATGAAACACAGACGAAAAC 59.753 43.478 0.00 0.00 35.52 2.43
484 485 3.001838 CCGATGAAACACAGACGAAAACA 59.998 43.478 0.00 0.00 35.52 2.83
486 487 4.026062 CGATGAAACACAGACGAAAACAGA 60.026 41.667 0.00 0.00 35.52 3.41
487 488 5.501736 CGATGAAACACAGACGAAAACAGAA 60.502 40.000 0.00 0.00 35.52 3.02
488 489 5.614923 TGAAACACAGACGAAAACAGAAA 57.385 34.783 0.00 0.00 0.00 2.52
489 490 5.627172 TGAAACACAGACGAAAACAGAAAG 58.373 37.500 0.00 0.00 0.00 2.62
490 491 5.410132 TGAAACACAGACGAAAACAGAAAGA 59.590 36.000 0.00 0.00 0.00 2.52
491 492 4.859629 ACACAGACGAAAACAGAAAGAC 57.140 40.909 0.00 0.00 0.00 3.01
492 493 4.250464 ACACAGACGAAAACAGAAAGACA 58.750 39.130 0.00 0.00 0.00 3.41
493 494 4.876107 ACACAGACGAAAACAGAAAGACAT 59.124 37.500 0.00 0.00 0.00 3.06
531 532 1.078497 CACTTATGCCGCCACCTGA 60.078 57.895 0.00 0.00 0.00 3.86
567 568 3.801307 AACCGAAACAAGGGACCTATT 57.199 42.857 0.00 0.00 0.00 1.73
575 576 3.648914 AGGGACCTATTTACGCCCT 57.351 52.632 0.00 0.00 44.17 5.19
640 641 1.000993 ATGAGAGGAGTGAGCCGGT 59.999 57.895 1.90 0.00 0.00 5.28
643 644 1.228894 AGAGGAGTGAGCCGGTGAA 60.229 57.895 1.90 0.00 0.00 3.18
645 646 1.228894 AGGAGTGAGCCGGTGAAGA 60.229 57.895 1.90 0.00 0.00 2.87
699 700 2.183046 GACCGCCTCTCTCTGTGC 59.817 66.667 0.00 0.00 0.00 4.57
721 722 2.622436 GAAGGTTCGAGAAGGACATGG 58.378 52.381 0.00 0.00 0.00 3.66
722 723 1.645710 AGGTTCGAGAAGGACATGGT 58.354 50.000 0.00 0.00 0.00 3.55
723 724 2.816411 AGGTTCGAGAAGGACATGGTA 58.184 47.619 0.00 0.00 0.00 3.25
724 725 3.170717 AGGTTCGAGAAGGACATGGTAA 58.829 45.455 0.00 0.00 0.00 2.85
725 726 3.056035 AGGTTCGAGAAGGACATGGTAAC 60.056 47.826 0.00 0.00 0.00 2.50
763 764 1.607251 CGGCCTACAAAGTCGGTCTTT 60.607 52.381 0.00 0.00 45.96 2.52
820 821 2.346803 TGGCGAAAGAGACAAGCATAC 58.653 47.619 0.00 0.00 0.00 2.39
823 824 3.375299 GGCGAAAGAGACAAGCATACAAT 59.625 43.478 0.00 0.00 0.00 2.71
828 829 7.624344 GCGAAAGAGACAAGCATACAATAAGTT 60.624 37.037 0.00 0.00 0.00 2.66
841 842 2.869503 ATAAGTTGCTGGTCGGCCGG 62.870 60.000 27.83 11.60 44.07 6.13
885 886 1.337118 GCTCAACCCAATCAACCCAA 58.663 50.000 0.00 0.00 0.00 4.12
886 887 1.273327 GCTCAACCCAATCAACCCAAG 59.727 52.381 0.00 0.00 0.00 3.61
887 888 2.597455 CTCAACCCAATCAACCCAAGT 58.403 47.619 0.00 0.00 0.00 3.16
974 988 3.648067 TCCCTCCACCTCAGCTATTTATG 59.352 47.826 0.00 0.00 0.00 1.90
1049 1063 0.034198 TGCTCCGTTGACCGATCAAA 59.966 50.000 0.00 0.00 46.40 2.69
1052 1066 0.668096 TCCGTTGACCGATCAAACCG 60.668 55.000 0.00 0.00 46.40 4.44
1064 1078 2.781681 TCAAACCGAGAAATCCTCCC 57.218 50.000 0.00 0.00 38.71 4.30
1070 1084 1.147153 GAGAAATCCTCCCCAGCGG 59.853 63.158 0.00 0.00 35.87 5.52
1078 1092 2.525629 TCCCCAGCGGAGTGACAA 60.526 61.111 0.00 0.00 34.86 3.18
1083 1097 2.357517 AGCGGAGTGACAAAGCCG 60.358 61.111 0.00 0.00 46.14 5.52
1089 1103 1.294659 GAGTGACAAAGCCGGCAGAG 61.295 60.000 31.54 19.58 0.00 3.35
1091 1105 2.347490 GACAAAGCCGGCAGAGGA 59.653 61.111 31.54 0.00 0.00 3.71
1094 1108 1.600636 CAAAGCCGGCAGAGGACAA 60.601 57.895 31.54 0.00 0.00 3.18
1453 1470 2.282251 ACCTGCTCTCCGACGTCA 60.282 61.111 17.16 0.00 0.00 4.35
1455 1472 1.251527 ACCTGCTCTCCGACGTCAAT 61.252 55.000 17.16 0.00 0.00 2.57
1558 1578 4.767255 CCTCTGCTGCGTGGACCC 62.767 72.222 0.00 0.00 0.00 4.46
1812 1847 2.249844 CCGACAACAGTGTAGGGTTT 57.750 50.000 0.00 0.00 44.48 3.27
1883 1942 0.893447 AGCAAAGGAAAGATGCCAGC 59.107 50.000 0.00 0.00 40.93 4.85
1884 1943 0.457337 GCAAAGGAAAGATGCCAGCG 60.457 55.000 0.00 0.00 34.03 5.18
1885 1944 1.167851 CAAAGGAAAGATGCCAGCGA 58.832 50.000 0.00 0.00 0.00 4.93
1886 1945 1.747355 CAAAGGAAAGATGCCAGCGAT 59.253 47.619 0.00 0.00 0.00 4.58
2029 2096 1.133869 GATGACGCGGGTTTTTCGG 59.866 57.895 12.47 0.00 0.00 4.30
2039 2106 1.133869 GTTTTTCGGTCGATGGGCG 59.866 57.895 0.00 0.00 42.69 6.13
2040 2107 1.301874 TTTTTCGGTCGATGGGCGT 60.302 52.632 0.00 0.00 41.80 5.68
2044 2111 1.031235 TTCGGTCGATGGGCGTAATA 58.969 50.000 0.00 0.00 41.80 0.98
2046 2113 1.614903 TCGGTCGATGGGCGTAATATT 59.385 47.619 0.00 0.00 41.80 1.28
2073 2140 3.491964 CCATCGGTGAACTAGGCGATTAA 60.492 47.826 0.00 0.00 0.00 1.40
2101 2168 5.416639 ACTTCCTCGGTTTGTTGTTAGTTTT 59.583 36.000 0.00 0.00 0.00 2.43
2102 2169 6.598850 ACTTCCTCGGTTTGTTGTTAGTTTTA 59.401 34.615 0.00 0.00 0.00 1.52
2103 2170 7.283807 ACTTCCTCGGTTTGTTGTTAGTTTTAT 59.716 33.333 0.00 0.00 0.00 1.40
2104 2171 7.571080 TCCTCGGTTTGTTGTTAGTTTTATT 57.429 32.000 0.00 0.00 0.00 1.40
2132 2199 9.399797 TGTGCTAAGATGAATAAAGAATCATGT 57.600 29.630 0.00 0.00 36.45 3.21
2178 2254 1.268352 TCATTTTACCGTTGCCAGTGC 59.732 47.619 0.00 0.00 38.26 4.40
2191 2267 4.235079 TGCCAGTGCTTATGGATAAAGT 57.765 40.909 6.60 0.00 40.51 2.66
2201 2279 8.523658 GTGCTTATGGATAAAGTTTTCTTTCCT 58.476 33.333 0.00 0.00 45.77 3.36
2232 2310 2.543037 TCTGCACCCAGGTGTATCTA 57.457 50.000 17.82 0.35 46.90 1.98
2250 2328 3.239449 TCTACACCTGGATGTGAACAGT 58.761 45.455 0.00 0.00 39.57 3.55
2299 2471 2.620112 GCTCATGTGCGCAAGGTGT 61.620 57.895 14.00 0.00 38.28 4.16
2302 2474 1.100463 TCATGTGCGCAAGGTGTGTT 61.100 50.000 14.00 0.00 38.28 3.32
2311 2483 5.232414 GTGCGCAAGGTGTGTTTAATTTTTA 59.768 36.000 14.00 0.00 38.28 1.52
2312 2484 5.986135 TGCGCAAGGTGTGTTTAATTTTTAT 59.014 32.000 8.16 0.00 38.28 1.40
2316 2488 7.042389 CGCAAGGTGTGTTTAATTTTTATTGGT 60.042 33.333 0.00 0.00 0.00 3.67
2331 2503 6.573664 TTTATTGGTGTTTGGACATCTGAG 57.426 37.500 0.00 0.00 37.78 3.35
2332 2504 3.855255 TTGGTGTTTGGACATCTGAGA 57.145 42.857 0.00 0.00 37.78 3.27
2335 2507 3.136443 TGGTGTTTGGACATCTGAGAAGT 59.864 43.478 0.00 0.00 37.78 3.01
2338 2510 4.214332 GTGTTTGGACATCTGAGAAGTTCC 59.786 45.833 0.00 0.00 38.23 3.62
2375 2547 7.653311 GCAGGTGTATGAGAAACTTTGAAAAAT 59.347 33.333 0.00 0.00 0.00 1.82
2430 2603 4.641396 CTCCTCAGATGTGTAAACACCAA 58.359 43.478 10.58 0.00 45.88 3.67
2442 2616 6.039829 TGTGTAAACACCAAGAAATATGCACA 59.960 34.615 10.58 0.00 45.88 4.57
2451 2625 3.722147 AGAAATATGCACACTCCTAGCG 58.278 45.455 0.00 0.00 0.00 4.26
2466 2640 1.260825 CTAGCGCACATGAGCATCTTG 59.739 52.381 11.47 8.31 44.95 3.02
2477 2651 3.966979 TGAGCATCTTGGATGCCTAAAA 58.033 40.909 23.37 7.26 45.59 1.52
2481 2655 6.070653 TGAGCATCTTGGATGCCTAAAATTTT 60.071 34.615 23.37 8.75 45.59 1.82
2486 2660 6.924111 TCTTGGATGCCTAAAATTTTCAGAC 58.076 36.000 6.72 0.00 0.00 3.51
2489 2663 8.415950 TTGGATGCCTAAAATTTTCAGACTTA 57.584 30.769 6.72 0.00 0.00 2.24
2495 2669 9.691362 TGCCTAAAATTTTCAGACTTATTTGAC 57.309 29.630 6.72 0.00 0.00 3.18
2582 2756 3.594603 TTTTGAAACGGTGGCAAAAGA 57.405 38.095 13.87 0.00 36.80 2.52
2583 2757 3.810310 TTTGAAACGGTGGCAAAAGAT 57.190 38.095 6.29 0.00 0.00 2.40
2584 2758 3.810310 TTGAAACGGTGGCAAAAGATT 57.190 38.095 0.00 0.00 0.00 2.40
2585 2759 3.810310 TGAAACGGTGGCAAAAGATTT 57.190 38.095 0.00 0.00 0.00 2.17
2586 2760 3.452474 TGAAACGGTGGCAAAAGATTTG 58.548 40.909 0.00 0.00 0.00 2.32
2587 2761 1.864565 AACGGTGGCAAAAGATTTGC 58.135 45.000 17.18 17.18 44.22 3.68
2595 2769 3.492421 GCAAAAGATTTGCCTCATCGA 57.508 42.857 15.12 0.00 39.38 3.59
2596 2770 4.037858 GCAAAAGATTTGCCTCATCGAT 57.962 40.909 15.12 0.00 39.38 3.59
2597 2771 4.427312 GCAAAAGATTTGCCTCATCGATT 58.573 39.130 15.12 0.00 39.38 3.34
2598 2772 5.581605 GCAAAAGATTTGCCTCATCGATTA 58.418 37.500 15.12 0.00 39.38 1.75
2599 2773 6.035843 GCAAAAGATTTGCCTCATCGATTAA 58.964 36.000 15.12 0.00 39.38 1.40
2600 2774 6.698766 GCAAAAGATTTGCCTCATCGATTAAT 59.301 34.615 15.12 0.00 39.38 1.40
2601 2775 7.223387 GCAAAAGATTTGCCTCATCGATTAATT 59.777 33.333 15.12 0.00 39.38 1.40
2602 2776 9.734620 CAAAAGATTTGCCTCATCGATTAATTA 57.265 29.630 0.00 0.00 0.00 1.40
2608 2782 8.925161 TTTGCCTCATCGATTAATTAAAAAGG 57.075 30.769 1.21 4.71 0.00 3.11
2609 2783 7.639113 TGCCTCATCGATTAATTAAAAAGGT 57.361 32.000 1.21 0.00 0.00 3.50
2610 2784 7.479980 TGCCTCATCGATTAATTAAAAAGGTG 58.520 34.615 1.21 3.83 0.00 4.00
2611 2785 7.122055 TGCCTCATCGATTAATTAAAAAGGTGT 59.878 33.333 1.21 0.00 0.00 4.16
2612 2786 8.617809 GCCTCATCGATTAATTAAAAAGGTGTA 58.382 33.333 1.21 0.00 0.00 2.90
2624 2798 9.516546 AATTAAAAAGGTGTAGAAGAACCTAGG 57.483 33.333 7.41 7.41 46.29 3.02
2625 2799 4.554960 AAAGGTGTAGAAGAACCTAGGC 57.445 45.455 9.30 0.00 46.29 3.93
2626 2800 3.185880 AGGTGTAGAAGAACCTAGGCA 57.814 47.619 9.30 0.00 45.15 4.75
2627 2801 2.832733 AGGTGTAGAAGAACCTAGGCAC 59.167 50.000 9.30 6.02 45.15 5.01
2628 2802 2.093606 GGTGTAGAAGAACCTAGGCACC 60.094 54.545 9.30 11.72 38.37 5.01
2629 2803 2.093606 GTGTAGAAGAACCTAGGCACCC 60.094 54.545 9.30 0.00 0.00 4.61
2630 2804 2.225547 TGTAGAAGAACCTAGGCACCCT 60.226 50.000 9.30 2.65 37.71 4.34
2631 2805 2.046280 AGAAGAACCTAGGCACCCTT 57.954 50.000 9.30 6.96 34.61 3.95
2632 2806 2.349445 AGAAGAACCTAGGCACCCTTT 58.651 47.619 9.30 0.00 34.61 3.11
2633 2807 3.527937 AGAAGAACCTAGGCACCCTTTA 58.472 45.455 9.30 0.00 34.61 1.85
2634 2808 3.519913 AGAAGAACCTAGGCACCCTTTAG 59.480 47.826 9.30 0.00 34.61 1.85
2635 2809 3.200958 AGAACCTAGGCACCCTTTAGA 57.799 47.619 9.30 0.00 34.61 2.10
2636 2810 3.527937 AGAACCTAGGCACCCTTTAGAA 58.472 45.455 9.30 0.00 34.61 2.10
2637 2811 4.112331 AGAACCTAGGCACCCTTTAGAAT 58.888 43.478 9.30 0.00 34.61 2.40
2638 2812 4.540502 AGAACCTAGGCACCCTTTAGAATT 59.459 41.667 9.30 0.00 34.61 2.17
2639 2813 4.236527 ACCTAGGCACCCTTTAGAATTG 57.763 45.455 9.30 0.00 34.61 2.32
2640 2814 3.591977 ACCTAGGCACCCTTTAGAATTGT 59.408 43.478 9.30 0.00 34.61 2.71
2641 2815 4.200092 CCTAGGCACCCTTTAGAATTGTC 58.800 47.826 0.00 0.00 34.61 3.18
2642 2816 2.711542 AGGCACCCTTTAGAATTGTCG 58.288 47.619 0.00 0.00 0.00 4.35
2643 2817 2.039879 AGGCACCCTTTAGAATTGTCGT 59.960 45.455 0.00 0.00 0.00 4.34
2644 2818 2.817844 GGCACCCTTTAGAATTGTCGTT 59.182 45.455 0.00 0.00 0.00 3.85
2645 2819 3.254903 GGCACCCTTTAGAATTGTCGTTT 59.745 43.478 0.00 0.00 0.00 3.60
2646 2820 4.473199 GCACCCTTTAGAATTGTCGTTTC 58.527 43.478 0.00 0.00 0.00 2.78
2647 2821 4.215613 GCACCCTTTAGAATTGTCGTTTCT 59.784 41.667 0.00 0.00 37.25 2.52
2648 2822 5.278315 GCACCCTTTAGAATTGTCGTTTCTT 60.278 40.000 0.00 0.00 35.19 2.52
2649 2823 6.142817 CACCCTTTAGAATTGTCGTTTCTTG 58.857 40.000 0.00 0.00 35.19 3.02
2650 2824 5.154222 CCCTTTAGAATTGTCGTTTCTTGC 58.846 41.667 0.00 0.00 35.19 4.01
2651 2825 5.154222 CCTTTAGAATTGTCGTTTCTTGCC 58.846 41.667 0.00 0.00 35.19 4.52
2652 2826 4.759516 TTAGAATTGTCGTTTCTTGCCC 57.240 40.909 0.00 0.00 35.19 5.36
2653 2827 2.863809 AGAATTGTCGTTTCTTGCCCT 58.136 42.857 0.00 0.00 29.12 5.19
2654 2828 4.015872 AGAATTGTCGTTTCTTGCCCTA 57.984 40.909 0.00 0.00 29.12 3.53
2655 2829 4.589908 AGAATTGTCGTTTCTTGCCCTAT 58.410 39.130 0.00 0.00 29.12 2.57
2656 2830 4.396166 AGAATTGTCGTTTCTTGCCCTATG 59.604 41.667 0.00 0.00 29.12 2.23
2657 2831 2.851263 TGTCGTTTCTTGCCCTATGT 57.149 45.000 0.00 0.00 0.00 2.29
2658 2832 3.134574 TGTCGTTTCTTGCCCTATGTT 57.865 42.857 0.00 0.00 0.00 2.71
2659 2833 3.482436 TGTCGTTTCTTGCCCTATGTTT 58.518 40.909 0.00 0.00 0.00 2.83
2660 2834 3.886505 TGTCGTTTCTTGCCCTATGTTTT 59.113 39.130 0.00 0.00 0.00 2.43
2661 2835 5.064558 TGTCGTTTCTTGCCCTATGTTTTA 58.935 37.500 0.00 0.00 0.00 1.52
2662 2836 5.531659 TGTCGTTTCTTGCCCTATGTTTTAA 59.468 36.000 0.00 0.00 0.00 1.52
2663 2837 5.854866 GTCGTTTCTTGCCCTATGTTTTAAC 59.145 40.000 0.00 0.00 0.00 2.01
2664 2838 5.766174 TCGTTTCTTGCCCTATGTTTTAACT 59.234 36.000 0.00 0.00 0.00 2.24
2665 2839 6.072893 TCGTTTCTTGCCCTATGTTTTAACTC 60.073 38.462 0.00 0.00 0.00 3.01
2666 2840 6.293735 CGTTTCTTGCCCTATGTTTTAACTCA 60.294 38.462 0.00 0.00 0.00 3.41
2667 2841 7.430441 GTTTCTTGCCCTATGTTTTAACTCAA 58.570 34.615 0.00 0.00 0.00 3.02
2668 2842 7.775053 TTCTTGCCCTATGTTTTAACTCAAT 57.225 32.000 0.00 0.00 0.00 2.57
2669 2843 7.156876 TCTTGCCCTATGTTTTAACTCAATG 57.843 36.000 0.00 0.00 0.00 2.82
2670 2844 6.945435 TCTTGCCCTATGTTTTAACTCAATGA 59.055 34.615 0.00 0.00 0.00 2.57
2671 2845 7.615365 TCTTGCCCTATGTTTTAACTCAATGAT 59.385 33.333 0.00 0.00 0.00 2.45
2672 2846 8.815565 TTGCCCTATGTTTTAACTCAATGATA 57.184 30.769 0.00 0.00 0.00 2.15
2673 2847 8.220755 TGCCCTATGTTTTAACTCAATGATAC 57.779 34.615 0.00 0.00 0.00 2.24
2674 2848 7.011950 TGCCCTATGTTTTAACTCAATGATACG 59.988 37.037 0.00 0.00 0.00 3.06
2675 2849 7.519970 GCCCTATGTTTTAACTCAATGATACGG 60.520 40.741 0.00 0.00 0.00 4.02
2676 2850 7.041372 CCCTATGTTTTAACTCAATGATACGGG 60.041 40.741 0.00 0.00 0.00 5.28
2677 2851 7.497909 CCTATGTTTTAACTCAATGATACGGGT 59.502 37.037 0.00 0.00 0.00 5.28
2678 2852 7.696992 ATGTTTTAACTCAATGATACGGGTT 57.303 32.000 0.00 0.00 0.00 4.11
2679 2853 7.513371 TGTTTTAACTCAATGATACGGGTTT 57.487 32.000 0.00 0.00 0.00 3.27
2680 2854 7.942990 TGTTTTAACTCAATGATACGGGTTTT 58.057 30.769 0.00 0.00 0.00 2.43
2681 2855 9.064706 TGTTTTAACTCAATGATACGGGTTTTA 57.935 29.630 0.00 0.00 0.00 1.52
2682 2856 9.550811 GTTTTAACTCAATGATACGGGTTTTAG 57.449 33.333 0.00 0.00 0.00 1.85
2683 2857 5.813080 AACTCAATGATACGGGTTTTAGC 57.187 39.130 0.00 0.00 0.00 3.09
2684 2858 4.839121 ACTCAATGATACGGGTTTTAGCA 58.161 39.130 0.00 0.00 0.00 3.49
2685 2859 4.876107 ACTCAATGATACGGGTTTTAGCAG 59.124 41.667 0.00 0.00 0.00 4.24
2686 2860 4.839121 TCAATGATACGGGTTTTAGCAGT 58.161 39.130 0.00 0.00 0.00 4.40
2687 2861 5.979993 TCAATGATACGGGTTTTAGCAGTA 58.020 37.500 0.00 0.00 31.51 2.74
2688 2862 6.408035 TCAATGATACGGGTTTTAGCAGTAA 58.592 36.000 0.00 0.00 30.82 2.24
2689 2863 6.314400 TCAATGATACGGGTTTTAGCAGTAAC 59.686 38.462 0.00 0.00 30.82 2.50
2690 2864 5.410355 TGATACGGGTTTTAGCAGTAACT 57.590 39.130 0.00 0.00 30.82 2.24
2691 2865 5.172934 TGATACGGGTTTTAGCAGTAACTG 58.827 41.667 0.00 0.00 30.82 3.16
2692 2866 3.480505 ACGGGTTTTAGCAGTAACTGT 57.519 42.857 0.00 0.00 33.43 3.55
2693 2867 4.605640 ACGGGTTTTAGCAGTAACTGTA 57.394 40.909 0.00 0.00 33.43 2.74
2694 2868 5.156608 ACGGGTTTTAGCAGTAACTGTAT 57.843 39.130 0.00 0.00 33.43 2.29
2695 2869 5.554070 ACGGGTTTTAGCAGTAACTGTATT 58.446 37.500 0.00 0.00 33.43 1.89
2696 2870 5.640783 ACGGGTTTTAGCAGTAACTGTATTC 59.359 40.000 0.00 0.00 33.43 1.75
2697 2871 5.064325 CGGGTTTTAGCAGTAACTGTATTCC 59.936 44.000 0.00 0.00 33.43 3.01
2698 2872 5.941647 GGGTTTTAGCAGTAACTGTATTCCA 59.058 40.000 0.00 0.00 33.43 3.53
2699 2873 6.602009 GGGTTTTAGCAGTAACTGTATTCCAT 59.398 38.462 0.00 0.00 33.43 3.41
2700 2874 7.771826 GGGTTTTAGCAGTAACTGTATTCCATA 59.228 37.037 0.00 0.00 33.43 2.74
2701 2875 9.169592 GGTTTTAGCAGTAACTGTATTCCATAA 57.830 33.333 0.00 0.00 33.43 1.90
2702 2876 9.983804 GTTTTAGCAGTAACTGTATTCCATAAC 57.016 33.333 0.00 0.00 33.43 1.89
2703 2877 9.953565 TTTTAGCAGTAACTGTATTCCATAACT 57.046 29.630 0.00 0.00 33.43 2.24
2704 2878 9.953565 TTTAGCAGTAACTGTATTCCATAACTT 57.046 29.630 0.00 0.00 33.43 2.66
2705 2879 7.849804 AGCAGTAACTGTATTCCATAACTTG 57.150 36.000 0.00 0.00 33.43 3.16
2706 2880 7.620880 AGCAGTAACTGTATTCCATAACTTGA 58.379 34.615 0.00 0.00 33.43 3.02
2707 2881 7.766278 AGCAGTAACTGTATTCCATAACTTGAG 59.234 37.037 0.00 0.00 33.43 3.02
2708 2882 7.549488 GCAGTAACTGTATTCCATAACTTGAGT 59.451 37.037 0.00 0.00 33.43 3.41
2722 2896 9.915629 CCATAACTTGAGTAACTAGATGATACC 57.084 37.037 0.00 0.00 0.00 2.73
2723 2897 9.915629 CATAACTTGAGTAACTAGATGATACCC 57.084 37.037 0.00 0.00 0.00 3.69
2724 2898 6.980416 ACTTGAGTAACTAGATGATACCCC 57.020 41.667 0.00 0.00 0.00 4.95
2725 2899 6.441222 ACTTGAGTAACTAGATGATACCCCA 58.559 40.000 0.00 0.00 0.00 4.96
2726 2900 7.076446 ACTTGAGTAACTAGATGATACCCCAT 58.924 38.462 0.00 0.00 0.00 4.00
2727 2901 8.232412 ACTTGAGTAACTAGATGATACCCCATA 58.768 37.037 0.00 0.00 0.00 2.74
2728 2902 9.261035 CTTGAGTAACTAGATGATACCCCATAT 57.739 37.037 0.00 0.00 0.00 1.78
2729 2903 8.595362 TGAGTAACTAGATGATACCCCATATG 57.405 38.462 0.00 0.00 0.00 1.78
2730 2904 8.177456 TGAGTAACTAGATGATACCCCATATGT 58.823 37.037 0.00 0.00 0.00 2.29
2731 2905 8.974292 AGTAACTAGATGATACCCCATATGTT 57.026 34.615 0.00 0.00 0.00 2.71
2734 2908 8.974292 AACTAGATGATACCCCATATGTTACT 57.026 34.615 0.00 0.00 0.00 2.24
2735 2909 8.367660 ACTAGATGATACCCCATATGTTACTG 57.632 38.462 0.00 0.00 0.00 2.74
2736 2910 6.054860 AGATGATACCCCATATGTTACTGC 57.945 41.667 1.24 0.00 0.00 4.40
2737 2911 4.265904 TGATACCCCATATGTTACTGCG 57.734 45.455 1.24 0.00 0.00 5.18
2738 2912 3.007506 TGATACCCCATATGTTACTGCGG 59.992 47.826 1.24 0.00 0.00 5.69
2739 2913 0.472471 ACCCCATATGTTACTGCGGG 59.528 55.000 8.85 8.85 35.06 6.13
2740 2914 0.762418 CCCCATATGTTACTGCGGGA 59.238 55.000 5.29 0.00 35.57 5.14
2741 2915 1.142060 CCCCATATGTTACTGCGGGAA 59.858 52.381 5.29 0.00 35.57 3.97
2742 2916 2.224769 CCCCATATGTTACTGCGGGAAT 60.225 50.000 5.29 0.00 35.57 3.01
2743 2917 3.074412 CCCATATGTTACTGCGGGAATC 58.926 50.000 1.24 0.00 35.57 2.52
2744 2918 2.736721 CCATATGTTACTGCGGGAATCG 59.263 50.000 1.24 0.00 42.76 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.483106 GCTTACCGTCTTCAACCTTTCC 59.517 50.000 0.00 0.00 0.00 3.13
1 2 3.400255 AGCTTACCGTCTTCAACCTTTC 58.600 45.455 0.00 0.00 0.00 2.62
2 3 3.181458 TGAGCTTACCGTCTTCAACCTTT 60.181 43.478 0.00 0.00 0.00 3.11
3 4 2.367567 TGAGCTTACCGTCTTCAACCTT 59.632 45.455 0.00 0.00 0.00 3.50
4 5 1.968493 TGAGCTTACCGTCTTCAACCT 59.032 47.619 0.00 0.00 0.00 3.50
5 6 2.067013 GTGAGCTTACCGTCTTCAACC 58.933 52.381 0.00 0.00 0.00 3.77
6 7 2.750948 TGTGAGCTTACCGTCTTCAAC 58.249 47.619 6.13 0.00 0.00 3.18
7 8 3.678056 ATGTGAGCTTACCGTCTTCAA 57.322 42.857 6.13 0.00 0.00 2.69
8 9 3.130516 CCTATGTGAGCTTACCGTCTTCA 59.869 47.826 6.13 0.00 0.00 3.02
9 10 3.380637 TCCTATGTGAGCTTACCGTCTTC 59.619 47.826 6.13 0.00 0.00 2.87
10 11 3.362706 TCCTATGTGAGCTTACCGTCTT 58.637 45.455 6.13 0.00 0.00 3.01
11 12 3.014304 TCCTATGTGAGCTTACCGTCT 57.986 47.619 6.13 0.00 0.00 4.18
12 13 3.553096 CCATCCTATGTGAGCTTACCGTC 60.553 52.174 6.13 0.00 0.00 4.79
13 14 2.365617 CCATCCTATGTGAGCTTACCGT 59.634 50.000 6.13 0.00 0.00 4.83
14 15 2.868044 GCCATCCTATGTGAGCTTACCG 60.868 54.545 6.13 0.00 0.00 4.02
15 16 2.104792 TGCCATCCTATGTGAGCTTACC 59.895 50.000 6.13 0.00 0.00 2.85
16 17 3.475566 TGCCATCCTATGTGAGCTTAC 57.524 47.619 0.78 0.78 0.00 2.34
17 18 3.906218 AGATGCCATCCTATGTGAGCTTA 59.094 43.478 0.00 0.00 0.00 3.09
36 37 0.329596 GTGCCAGGGAGGTTGAAGAT 59.670 55.000 0.00 0.00 40.61 2.40
62 63 1.671379 GAAGGACGGAGGTTGCACC 60.671 63.158 0.00 0.00 38.99 5.01
73 74 3.787001 GGGCTCTGGGGAAGGACG 61.787 72.222 0.00 0.00 0.00 4.79
77 78 3.787001 GTCCGGGCTCTGGGGAAG 61.787 72.222 0.00 0.00 0.00 3.46
84 85 1.414181 CATAGTCAATGTCCGGGCTCT 59.586 52.381 7.97 0.57 0.00 4.09
91 92 4.503714 TTCCCTTCCATAGTCAATGTCC 57.496 45.455 0.00 0.00 33.34 4.02
117 118 6.519679 TGTTTGACGGTAGATTTAGAGCTA 57.480 37.500 0.00 0.00 0.00 3.32
119 120 5.581085 ACATGTTTGACGGTAGATTTAGAGC 59.419 40.000 0.00 0.00 0.00 4.09
161 162 3.070302 ACTTTCTTGCTCCTCGAAGTCTT 59.930 43.478 0.00 0.00 0.00 3.01
179 180 0.179001 CCTTTGGGACGGGACACTTT 60.179 55.000 0.00 0.00 33.58 2.66
197 198 1.583054 CAAGTCGCCTATACTTGCCC 58.417 55.000 3.29 0.00 45.15 5.36
273 274 2.656897 CTCGTCTTCGTGTATGTGTGTG 59.343 50.000 0.00 0.00 38.33 3.82
274 275 2.351447 CCTCGTCTTCGTGTATGTGTGT 60.351 50.000 0.00 0.00 38.33 3.72
275 276 2.251040 CCTCGTCTTCGTGTATGTGTG 58.749 52.381 0.00 0.00 38.33 3.82
315 316 3.380004 TCTGAACAGTTGTTTTGCCGATT 59.620 39.130 0.00 0.00 38.56 3.34
423 424 0.885196 AGAGAGTCCGTGTGAGCTTC 59.115 55.000 0.00 0.00 0.00 3.86
431 432 5.060662 TCTATTTCAACAGAGAGTCCGTG 57.939 43.478 0.00 0.00 0.00 4.94
434 435 5.352846 GGCTTTCTATTTCAACAGAGAGTCC 59.647 44.000 0.00 0.00 0.00 3.85
481 482 7.337942 GTCTCATGGGAATAATGTCTTTCTGTT 59.662 37.037 0.00 0.00 0.00 3.16
482 483 6.825721 GTCTCATGGGAATAATGTCTTTCTGT 59.174 38.462 0.00 0.00 0.00 3.41
483 484 6.825213 TGTCTCATGGGAATAATGTCTTTCTG 59.175 38.462 0.00 0.00 0.00 3.02
484 485 6.962182 TGTCTCATGGGAATAATGTCTTTCT 58.038 36.000 0.00 0.00 0.00 2.52
486 487 6.947733 TGTTGTCTCATGGGAATAATGTCTTT 59.052 34.615 0.00 0.00 0.00 2.52
487 488 6.375455 GTGTTGTCTCATGGGAATAATGTCTT 59.625 38.462 0.00 0.00 0.00 3.01
488 489 5.882557 GTGTTGTCTCATGGGAATAATGTCT 59.117 40.000 0.00 0.00 0.00 3.41
489 490 5.066505 GGTGTTGTCTCATGGGAATAATGTC 59.933 44.000 0.00 0.00 0.00 3.06
490 491 4.949856 GGTGTTGTCTCATGGGAATAATGT 59.050 41.667 0.00 0.00 0.00 2.71
491 492 4.949238 TGGTGTTGTCTCATGGGAATAATG 59.051 41.667 0.00 0.00 0.00 1.90
492 493 4.949856 GTGGTGTTGTCTCATGGGAATAAT 59.050 41.667 0.00 0.00 0.00 1.28
493 494 4.042809 AGTGGTGTTGTCTCATGGGAATAA 59.957 41.667 0.00 0.00 0.00 1.40
531 532 2.106857 TCGGTTAGTTGGGGTTGATGTT 59.893 45.455 0.00 0.00 0.00 2.71
567 568 3.081409 GGGAGCTCCAGGGCGTAA 61.081 66.667 33.29 0.00 37.91 3.18
629 630 1.444553 CGTCTTCACCGGCTCACTC 60.445 63.158 0.00 0.00 0.00 3.51
630 631 2.143594 GACGTCTTCACCGGCTCACT 62.144 60.000 8.70 0.00 0.00 3.41
640 641 0.886043 TCCTTCCGTCGACGTCTTCA 60.886 55.000 33.49 13.84 37.74 3.02
643 644 1.168407 TTGTCCTTCCGTCGACGTCT 61.168 55.000 33.49 0.00 37.74 4.18
645 646 1.168407 TCTTGTCCTTCCGTCGACGT 61.168 55.000 33.49 0.00 37.74 4.34
699 700 0.601558 TGTCCTTCTCGAACCTTCCG 59.398 55.000 0.00 0.00 0.00 4.30
721 722 4.443394 CGGTGTCAACTCTGTTACTGTTAC 59.557 45.833 0.00 0.00 0.00 2.50
722 723 4.500205 CCGGTGTCAACTCTGTTACTGTTA 60.500 45.833 0.00 0.00 0.00 2.41
723 724 3.454375 CGGTGTCAACTCTGTTACTGTT 58.546 45.455 0.00 0.00 0.00 3.16
724 725 2.223971 CCGGTGTCAACTCTGTTACTGT 60.224 50.000 0.00 0.00 0.00 3.55
725 726 2.404215 CCGGTGTCAACTCTGTTACTG 58.596 52.381 0.00 0.00 0.00 2.74
726 727 1.270147 GCCGGTGTCAACTCTGTTACT 60.270 52.381 1.90 0.00 0.00 2.24
763 764 1.604438 CCGGACAAGTCACGATCAACA 60.604 52.381 0.00 0.00 0.00 3.33
806 807 6.656693 AGCAACTTATTGTATGCTTGTCTCTT 59.343 34.615 0.00 0.00 46.36 2.85
820 821 0.451783 GGCCGACCAGCAACTTATTG 59.548 55.000 0.00 0.00 35.82 1.90
823 824 2.047655 CGGCCGACCAGCAACTTA 60.048 61.111 24.07 0.00 34.57 2.24
828 829 3.561120 AATTTCCGGCCGACCAGCA 62.561 57.895 30.73 4.08 34.57 4.41
841 842 7.254151 GCGAGACTGTAGTTTATGAGGAATTTC 60.254 40.741 0.00 0.00 0.00 2.17
885 886 3.964875 CCGCGCAAAGTTGGCACT 61.965 61.111 8.75 0.00 33.11 4.40
940 941 2.301738 GGAGGGAGAAGGTGGGGTG 61.302 68.421 0.00 0.00 0.00 4.61
993 1007 0.809636 TGTGTGTGAGTGTGAAGCGG 60.810 55.000 0.00 0.00 0.00 5.52
1049 1063 1.627297 GCTGGGGAGGATTTCTCGGT 61.627 60.000 0.00 0.00 43.34 4.69
1052 1066 1.147153 CCGCTGGGGAGGATTTCTC 59.853 63.158 4.46 0.00 41.71 2.87
1064 1078 2.328099 GGCTTTGTCACTCCGCTGG 61.328 63.158 0.00 0.00 0.00 4.85
1070 1084 1.294659 CTCTGCCGGCTTTGTCACTC 61.295 60.000 29.70 0.00 0.00 3.51
1075 1089 2.032681 GTCCTCTGCCGGCTTTGT 59.967 61.111 29.70 0.00 0.00 2.83
1078 1092 2.348998 CTTGTCCTCTGCCGGCTT 59.651 61.111 29.70 0.00 0.00 4.35
1083 1097 1.751927 CATGCCCTTGTCCTCTGCC 60.752 63.158 0.00 0.00 0.00 4.85
1089 1103 1.452833 GCTCTCCATGCCCTTGTCC 60.453 63.158 0.00 0.00 0.00 4.02
1091 1105 1.841302 TTCGCTCTCCATGCCCTTGT 61.841 55.000 0.00 0.00 0.00 3.16
1094 1108 2.739996 CCTTCGCTCTCCATGCCCT 61.740 63.158 0.00 0.00 0.00 5.19
1167 1181 2.436115 GGACAGTACAAGGCCGCC 60.436 66.667 0.00 0.00 0.00 6.13
1233 1247 4.821589 GAGGCCAGAGGGTTCGCG 62.822 72.222 5.01 0.00 36.17 5.87
1236 1250 3.787001 CGGGAGGCCAGAGGGTTC 61.787 72.222 5.01 0.00 36.17 3.62
1316 1330 4.717629 CGCCTTCGTCGTCAGCCA 62.718 66.667 0.00 0.00 0.00 4.75
1453 1470 4.778143 GCCGGTGGCCACGAGATT 62.778 66.667 29.08 0.00 44.06 2.40
1812 1847 1.355381 ACTCCATGGGATGCAACTTGA 59.645 47.619 13.02 0.00 0.00 3.02
1883 1942 0.807275 TGGCATCTGCACTTCGATCG 60.807 55.000 9.36 9.36 44.36 3.69
1884 1943 1.263484 CATGGCATCTGCACTTCGATC 59.737 52.381 0.00 0.00 44.36 3.69
1885 1944 1.306148 CATGGCATCTGCACTTCGAT 58.694 50.000 0.00 0.00 44.36 3.59
1886 1945 1.371337 GCATGGCATCTGCACTTCGA 61.371 55.000 8.15 0.00 44.36 3.71
1968 2034 6.270064 CGGGTTTTTACCATGAATATTGACC 58.730 40.000 0.00 0.00 0.00 4.02
2029 2096 4.565564 GGACATAATATTACGCCCATCGAC 59.434 45.833 0.00 0.00 41.67 4.20
2039 2106 9.355215 CTAGTTCACCGATGGACATAATATTAC 57.645 37.037 0.00 0.00 36.69 1.89
2040 2107 8.528643 CCTAGTTCACCGATGGACATAATATTA 58.471 37.037 0.00 0.00 36.69 0.98
2044 2111 4.503296 GCCTAGTTCACCGATGGACATAAT 60.503 45.833 0.00 0.00 36.69 1.28
2046 2113 2.364324 GCCTAGTTCACCGATGGACATA 59.636 50.000 0.00 0.00 36.69 2.29
2073 2140 4.081322 ACAACAAACCGAGGAAGTACAT 57.919 40.909 0.00 0.00 0.00 2.29
2132 2199 4.211125 TCAGTGTGGCCACAAGAATTTAA 58.789 39.130 39.23 16.07 44.39 1.52
2134 2201 2.665165 TCAGTGTGGCCACAAGAATTT 58.335 42.857 39.23 17.63 44.39 1.82
2191 2267 6.656693 CAGAATTGCCTCTCTAGGAAAGAAAA 59.343 38.462 0.00 0.00 44.19 2.29
2232 2310 4.431416 TTTACTGTTCACATCCAGGTGT 57.569 40.909 0.00 0.00 39.76 4.16
2235 2313 6.573664 TTGAATTTACTGTTCACATCCAGG 57.426 37.500 0.00 0.00 35.47 4.45
2299 2471 9.667107 TGTCCAAACACCAATAAAAATTAAACA 57.333 25.926 0.00 0.00 0.00 2.83
2311 2483 4.371624 TCTCAGATGTCCAAACACCAAT 57.628 40.909 0.00 0.00 38.48 3.16
2312 2484 3.855255 TCTCAGATGTCCAAACACCAA 57.145 42.857 0.00 0.00 38.48 3.67
2316 2488 4.103153 AGGAACTTCTCAGATGTCCAAACA 59.897 41.667 10.06 0.00 35.28 2.83
2348 2520 4.973168 TCAAAGTTTCTCATACACCTGCT 58.027 39.130 0.00 0.00 0.00 4.24
2349 2521 5.689383 TTCAAAGTTTCTCATACACCTGC 57.311 39.130 0.00 0.00 0.00 4.85
2404 2577 3.182967 GTTTACACATCTGAGGAGCTCG 58.817 50.000 7.83 0.00 32.35 5.03
2430 2603 3.722147 CGCTAGGAGTGTGCATATTTCT 58.278 45.455 0.00 0.00 0.00 2.52
2442 2616 1.142748 GCTCATGTGCGCTAGGAGT 59.857 57.895 21.45 0.00 0.00 3.85
2451 2625 1.269102 GCATCCAAGATGCTCATGTGC 60.269 52.381 19.69 12.78 41.52 4.57
2466 2640 9.875691 AAATAAGTCTGAAAATTTTAGGCATCC 57.124 29.630 2.75 0.00 0.00 3.51
2511 2685 8.567948 CCTAGTGAACACTGAACAATACATTTT 58.432 33.333 16.37 0.00 42.52 1.82
2512 2686 7.719633 ACCTAGTGAACACTGAACAATACATTT 59.280 33.333 16.37 0.00 42.52 2.32
2513 2687 7.173218 CACCTAGTGAACACTGAACAATACATT 59.827 37.037 16.37 0.00 42.52 2.71
2515 2689 5.989168 CACCTAGTGAACACTGAACAATACA 59.011 40.000 16.37 0.00 42.52 2.29
2516 2690 5.989777 ACACCTAGTGAACACTGAACAATAC 59.010 40.000 16.37 0.00 42.52 1.89
2518 2692 5.036117 ACACCTAGTGAACACTGAACAAT 57.964 39.130 16.37 0.00 42.52 2.71
2519 2693 4.481368 ACACCTAGTGAACACTGAACAA 57.519 40.909 16.37 0.00 42.52 2.83
2520 2694 4.891168 TCTACACCTAGTGAACACTGAACA 59.109 41.667 16.37 0.00 42.52 3.18
2521 2695 5.449107 TCTACACCTAGTGAACACTGAAC 57.551 43.478 16.37 0.00 42.52 3.18
2522 2696 5.831525 TCTTCTACACCTAGTGAACACTGAA 59.168 40.000 16.37 8.88 42.52 3.02
2523 2697 5.382616 TCTTCTACACCTAGTGAACACTGA 58.617 41.667 16.37 2.00 42.52 3.41
2524 2698 5.707242 TCTTCTACACCTAGTGAACACTG 57.293 43.478 16.37 4.55 42.52 3.66
2525 2699 5.010820 GGTTCTTCTACACCTAGTGAACACT 59.989 44.000 12.10 12.10 45.02 3.55
2526 2700 5.010820 AGGTTCTTCTACACCTAGTGAACAC 59.989 44.000 0.96 0.00 41.97 3.32
2534 2708 2.185387 GCCCAGGTTCTTCTACACCTA 58.815 52.381 0.00 0.00 41.86 3.08
2535 2709 0.984995 GCCCAGGTTCTTCTACACCT 59.015 55.000 0.00 0.00 44.88 4.00
2562 2736 3.594603 TCTTTTGCCACCGTTTCAAAA 57.405 38.095 7.21 7.21 37.36 2.44
2563 2737 3.810310 ATCTTTTGCCACCGTTTCAAA 57.190 38.095 0.00 0.00 0.00 2.69
2564 2738 3.810310 AATCTTTTGCCACCGTTTCAA 57.190 38.095 0.00 0.00 0.00 2.69
2565 2739 3.452474 CAAATCTTTTGCCACCGTTTCA 58.548 40.909 0.00 0.00 0.00 2.69
2566 2740 2.220824 GCAAATCTTTTGCCACCGTTTC 59.779 45.455 12.74 0.00 39.38 2.78
2567 2741 2.209273 GCAAATCTTTTGCCACCGTTT 58.791 42.857 12.74 0.00 39.38 3.60
2568 2742 1.864565 GCAAATCTTTTGCCACCGTT 58.135 45.000 12.74 0.00 39.38 4.44
2569 2743 3.586430 GCAAATCTTTTGCCACCGT 57.414 47.368 12.74 0.00 39.38 4.83
2575 2749 3.492421 TCGATGAGGCAAATCTTTTGC 57.508 42.857 14.88 14.88 44.22 3.68
2576 2750 8.638685 AATTAATCGATGAGGCAAATCTTTTG 57.361 30.769 0.00 0.00 0.00 2.44
2582 2756 9.533253 CCTTTTTAATTAATCGATGAGGCAAAT 57.467 29.630 0.00 0.00 0.00 2.32
2583 2757 8.527810 ACCTTTTTAATTAATCGATGAGGCAAA 58.472 29.630 0.00 0.00 0.00 3.68
2584 2758 7.973388 CACCTTTTTAATTAATCGATGAGGCAA 59.027 33.333 0.00 0.00 0.00 4.52
2585 2759 7.122055 ACACCTTTTTAATTAATCGATGAGGCA 59.878 33.333 0.00 0.00 0.00 4.75
2586 2760 7.480810 ACACCTTTTTAATTAATCGATGAGGC 58.519 34.615 0.00 0.00 0.00 4.70
2598 2772 9.516546 CCTAGGTTCTTCTACACCTTTTTAATT 57.483 33.333 0.00 0.00 40.85 1.40
2599 2773 7.610692 GCCTAGGTTCTTCTACACCTTTTTAAT 59.389 37.037 11.31 0.00 40.85 1.40
2600 2774 6.938596 GCCTAGGTTCTTCTACACCTTTTTAA 59.061 38.462 11.31 0.00 40.85 1.52
2601 2775 6.043474 TGCCTAGGTTCTTCTACACCTTTTTA 59.957 38.462 11.31 0.00 40.85 1.52
2602 2776 5.163131 TGCCTAGGTTCTTCTACACCTTTTT 60.163 40.000 11.31 0.00 40.85 1.94
2603 2777 4.349930 TGCCTAGGTTCTTCTACACCTTTT 59.650 41.667 11.31 0.00 40.85 2.27
2604 2778 3.908103 TGCCTAGGTTCTTCTACACCTTT 59.092 43.478 11.31 0.00 40.85 3.11
2605 2779 3.261137 GTGCCTAGGTTCTTCTACACCTT 59.739 47.826 11.31 0.00 40.85 3.50
2606 2780 2.832733 GTGCCTAGGTTCTTCTACACCT 59.167 50.000 11.31 0.00 45.85 4.00
2607 2781 2.093606 GGTGCCTAGGTTCTTCTACACC 60.094 54.545 11.31 12.43 39.52 4.16
2608 2782 2.093606 GGGTGCCTAGGTTCTTCTACAC 60.094 54.545 11.31 6.98 0.00 2.90
2609 2783 2.185387 GGGTGCCTAGGTTCTTCTACA 58.815 52.381 11.31 0.00 0.00 2.74
2610 2784 2.468915 AGGGTGCCTAGGTTCTTCTAC 58.531 52.381 11.31 0.00 28.47 2.59
2611 2785 2.942604 AGGGTGCCTAGGTTCTTCTA 57.057 50.000 11.31 0.00 28.47 2.10
2612 2786 2.046280 AAGGGTGCCTAGGTTCTTCT 57.954 50.000 11.31 0.00 31.13 2.85
2613 2787 2.881111 AAAGGGTGCCTAGGTTCTTC 57.119 50.000 11.31 0.00 31.13 2.87
2614 2788 3.527937 TCTAAAGGGTGCCTAGGTTCTT 58.472 45.455 11.31 6.45 31.13 2.52
2615 2789 3.200958 TCTAAAGGGTGCCTAGGTTCT 57.799 47.619 11.31 0.14 31.13 3.01
2616 2790 3.994931 TTCTAAAGGGTGCCTAGGTTC 57.005 47.619 11.31 3.71 31.13 3.62
2617 2791 4.044191 ACAATTCTAAAGGGTGCCTAGGTT 59.956 41.667 11.31 0.00 31.13 3.50
2618 2792 3.591977 ACAATTCTAAAGGGTGCCTAGGT 59.408 43.478 11.31 0.00 31.13 3.08
2619 2793 4.200092 GACAATTCTAAAGGGTGCCTAGG 58.800 47.826 3.67 3.67 31.13 3.02
2620 2794 3.871594 CGACAATTCTAAAGGGTGCCTAG 59.128 47.826 0.00 0.00 31.13 3.02
2621 2795 3.262405 ACGACAATTCTAAAGGGTGCCTA 59.738 43.478 0.00 0.00 31.13 3.93
2622 2796 2.039879 ACGACAATTCTAAAGGGTGCCT 59.960 45.455 0.00 0.00 33.87 4.75
2623 2797 2.433436 ACGACAATTCTAAAGGGTGCC 58.567 47.619 0.00 0.00 0.00 5.01
2624 2798 4.215613 AGAAACGACAATTCTAAAGGGTGC 59.784 41.667 0.00 0.00 35.43 5.01
2625 2799 5.941948 AGAAACGACAATTCTAAAGGGTG 57.058 39.130 0.00 0.00 35.43 4.61
2626 2800 5.278315 GCAAGAAACGACAATTCTAAAGGGT 60.278 40.000 0.00 0.00 36.14 4.34
2627 2801 5.154222 GCAAGAAACGACAATTCTAAAGGG 58.846 41.667 0.00 0.00 36.14 3.95
2628 2802 5.154222 GGCAAGAAACGACAATTCTAAAGG 58.846 41.667 0.00 0.00 36.14 3.11
2629 2803 5.048713 AGGGCAAGAAACGACAATTCTAAAG 60.049 40.000 0.00 0.00 36.14 1.85
2630 2804 4.825085 AGGGCAAGAAACGACAATTCTAAA 59.175 37.500 0.00 0.00 36.14 1.85
2631 2805 4.394729 AGGGCAAGAAACGACAATTCTAA 58.605 39.130 0.00 0.00 36.14 2.10
2632 2806 4.015872 AGGGCAAGAAACGACAATTCTA 57.984 40.909 0.00 0.00 36.14 2.10
2633 2807 2.863809 AGGGCAAGAAACGACAATTCT 58.136 42.857 0.00 0.00 38.75 2.40
2634 2808 4.156008 ACATAGGGCAAGAAACGACAATTC 59.844 41.667 0.00 0.00 0.00 2.17
2635 2809 4.079253 ACATAGGGCAAGAAACGACAATT 58.921 39.130 0.00 0.00 0.00 2.32
2636 2810 3.686016 ACATAGGGCAAGAAACGACAAT 58.314 40.909 0.00 0.00 0.00 2.71
2637 2811 3.134574 ACATAGGGCAAGAAACGACAA 57.865 42.857 0.00 0.00 0.00 3.18
2638 2812 2.851263 ACATAGGGCAAGAAACGACA 57.149 45.000 0.00 0.00 0.00 4.35
2639 2813 4.499037 AAAACATAGGGCAAGAAACGAC 57.501 40.909 0.00 0.00 0.00 4.34
2640 2814 5.766174 AGTTAAAACATAGGGCAAGAAACGA 59.234 36.000 0.00 0.00 0.00 3.85
2641 2815 6.009115 AGTTAAAACATAGGGCAAGAAACG 57.991 37.500 0.00 0.00 0.00 3.60
2642 2816 6.977213 TGAGTTAAAACATAGGGCAAGAAAC 58.023 36.000 0.00 0.00 0.00 2.78
2643 2817 7.589958 TTGAGTTAAAACATAGGGCAAGAAA 57.410 32.000 0.00 0.00 0.00 2.52
2644 2818 7.450014 TCATTGAGTTAAAACATAGGGCAAGAA 59.550 33.333 0.00 0.00 0.00 2.52
2645 2819 6.945435 TCATTGAGTTAAAACATAGGGCAAGA 59.055 34.615 0.00 0.00 0.00 3.02
2646 2820 7.156876 TCATTGAGTTAAAACATAGGGCAAG 57.843 36.000 0.00 0.00 0.00 4.01
2647 2821 7.716799 ATCATTGAGTTAAAACATAGGGCAA 57.283 32.000 0.00 0.00 0.00 4.52
2648 2822 7.011950 CGTATCATTGAGTTAAAACATAGGGCA 59.988 37.037 0.00 0.00 0.00 5.36
2649 2823 7.352739 CGTATCATTGAGTTAAAACATAGGGC 58.647 38.462 0.00 0.00 0.00 5.19
2650 2824 7.041372 CCCGTATCATTGAGTTAAAACATAGGG 60.041 40.741 0.00 0.00 0.00 3.53
2651 2825 7.497909 ACCCGTATCATTGAGTTAAAACATAGG 59.502 37.037 0.00 0.00 0.00 2.57
2652 2826 8.433421 ACCCGTATCATTGAGTTAAAACATAG 57.567 34.615 0.00 0.00 0.00 2.23
2653 2827 8.795842 AACCCGTATCATTGAGTTAAAACATA 57.204 30.769 0.00 0.00 0.00 2.29
2654 2828 7.696992 AACCCGTATCATTGAGTTAAAACAT 57.303 32.000 0.00 0.00 0.00 2.71
2655 2829 7.513371 AAACCCGTATCATTGAGTTAAAACA 57.487 32.000 0.00 0.00 0.00 2.83
2656 2830 9.550811 CTAAAACCCGTATCATTGAGTTAAAAC 57.449 33.333 0.00 0.00 0.00 2.43
2657 2831 8.238631 GCTAAAACCCGTATCATTGAGTTAAAA 58.761 33.333 0.00 0.00 0.00 1.52
2658 2832 7.390996 TGCTAAAACCCGTATCATTGAGTTAAA 59.609 33.333 0.00 0.00 0.00 1.52
2659 2833 6.879993 TGCTAAAACCCGTATCATTGAGTTAA 59.120 34.615 0.00 0.00 0.00 2.01
2660 2834 6.408035 TGCTAAAACCCGTATCATTGAGTTA 58.592 36.000 0.00 0.00 0.00 2.24
2661 2835 5.250200 TGCTAAAACCCGTATCATTGAGTT 58.750 37.500 0.00 0.00 0.00 3.01
2662 2836 4.839121 TGCTAAAACCCGTATCATTGAGT 58.161 39.130 0.00 0.00 0.00 3.41
2663 2837 4.876107 ACTGCTAAAACCCGTATCATTGAG 59.124 41.667 0.00 0.00 0.00 3.02
2664 2838 4.839121 ACTGCTAAAACCCGTATCATTGA 58.161 39.130 0.00 0.00 0.00 2.57
2665 2839 6.315393 AGTTACTGCTAAAACCCGTATCATTG 59.685 38.462 0.00 0.00 0.00 2.82
2666 2840 6.315393 CAGTTACTGCTAAAACCCGTATCATT 59.685 38.462 0.00 0.00 0.00 2.57
2667 2841 5.815740 CAGTTACTGCTAAAACCCGTATCAT 59.184 40.000 0.00 0.00 0.00 2.45
2668 2842 5.172934 CAGTTACTGCTAAAACCCGTATCA 58.827 41.667 0.00 0.00 0.00 2.15
2669 2843 5.173664 ACAGTTACTGCTAAAACCCGTATC 58.826 41.667 12.80 0.00 34.37 2.24
2670 2844 5.156608 ACAGTTACTGCTAAAACCCGTAT 57.843 39.130 12.80 0.00 34.37 3.06
2671 2845 4.605640 ACAGTTACTGCTAAAACCCGTA 57.394 40.909 12.80 0.00 34.37 4.02
2672 2846 3.480505 ACAGTTACTGCTAAAACCCGT 57.519 42.857 12.80 0.00 34.37 5.28
2673 2847 5.064325 GGAATACAGTTACTGCTAAAACCCG 59.936 44.000 12.80 0.00 34.37 5.28
2674 2848 5.941647 TGGAATACAGTTACTGCTAAAACCC 59.058 40.000 12.80 5.67 34.37 4.11
2675 2849 7.625828 ATGGAATACAGTTACTGCTAAAACC 57.374 36.000 12.80 9.13 34.37 3.27
2676 2850 9.983804 GTTATGGAATACAGTTACTGCTAAAAC 57.016 33.333 12.80 3.37 34.37 2.43
2677 2851 9.953565 AGTTATGGAATACAGTTACTGCTAAAA 57.046 29.630 12.80 0.00 34.37 1.52
2678 2852 9.953565 AAGTTATGGAATACAGTTACTGCTAAA 57.046 29.630 12.80 0.00 34.37 1.85
2679 2853 9.378551 CAAGTTATGGAATACAGTTACTGCTAA 57.621 33.333 12.80 0.00 34.37 3.09
2680 2854 8.755028 TCAAGTTATGGAATACAGTTACTGCTA 58.245 33.333 12.80 4.86 34.37 3.49
2681 2855 7.620880 TCAAGTTATGGAATACAGTTACTGCT 58.379 34.615 12.80 2.68 34.37 4.24
2682 2856 7.549488 ACTCAAGTTATGGAATACAGTTACTGC 59.451 37.037 12.80 0.00 34.37 4.40
2696 2870 9.915629 GGTATCATCTAGTTACTCAAGTTATGG 57.084 37.037 0.00 0.00 0.00 2.74
2697 2871 9.915629 GGGTATCATCTAGTTACTCAAGTTATG 57.084 37.037 0.00 0.00 0.00 1.90
2698 2872 9.091220 GGGGTATCATCTAGTTACTCAAGTTAT 57.909 37.037 0.00 0.00 0.00 1.89
2699 2873 8.063153 TGGGGTATCATCTAGTTACTCAAGTTA 58.937 37.037 0.00 0.00 0.00 2.24
2700 2874 6.901300 TGGGGTATCATCTAGTTACTCAAGTT 59.099 38.462 0.00 0.00 0.00 2.66
2701 2875 6.441222 TGGGGTATCATCTAGTTACTCAAGT 58.559 40.000 0.00 0.00 0.00 3.16
2702 2876 6.978674 TGGGGTATCATCTAGTTACTCAAG 57.021 41.667 0.00 0.00 0.00 3.02
2703 2877 9.035890 CATATGGGGTATCATCTAGTTACTCAA 57.964 37.037 0.00 0.00 0.00 3.02
2704 2878 8.177456 ACATATGGGGTATCATCTAGTTACTCA 58.823 37.037 7.80 0.00 0.00 3.41
2705 2879 8.596781 ACATATGGGGTATCATCTAGTTACTC 57.403 38.462 7.80 0.00 0.00 2.59
2706 2880 8.974292 AACATATGGGGTATCATCTAGTTACT 57.026 34.615 7.80 0.00 0.00 2.24
2709 2883 8.816894 CAGTAACATATGGGGTATCATCTAGTT 58.183 37.037 7.80 0.00 0.00 2.24
2710 2884 7.093289 GCAGTAACATATGGGGTATCATCTAGT 60.093 40.741 7.80 0.00 0.00 2.57
2711 2885 7.268586 GCAGTAACATATGGGGTATCATCTAG 58.731 42.308 7.80 0.00 0.00 2.43
2712 2886 6.127451 CGCAGTAACATATGGGGTATCATCTA 60.127 42.308 7.80 0.00 0.00 1.98
2713 2887 5.337571 CGCAGTAACATATGGGGTATCATCT 60.338 44.000 7.80 0.00 0.00 2.90
2714 2888 4.870426 CGCAGTAACATATGGGGTATCATC 59.130 45.833 7.80 0.00 0.00 2.92
2715 2889 4.323485 CCGCAGTAACATATGGGGTATCAT 60.323 45.833 7.80 0.00 42.81 2.45
2716 2890 3.007506 CCGCAGTAACATATGGGGTATCA 59.992 47.826 7.80 0.00 42.81 2.15
2717 2891 3.596214 CCGCAGTAACATATGGGGTATC 58.404 50.000 7.80 0.00 42.81 2.24
2718 2892 2.304761 CCCGCAGTAACATATGGGGTAT 59.695 50.000 7.80 0.00 45.47 2.73
2719 2893 1.695242 CCCGCAGTAACATATGGGGTA 59.305 52.381 7.80 0.00 45.47 3.69
2720 2894 0.472471 CCCGCAGTAACATATGGGGT 59.528 55.000 7.80 0.00 45.47 4.95
2721 2895 0.762418 TCCCGCAGTAACATATGGGG 59.238 55.000 7.80 6.16 46.24 4.96
2722 2896 2.631160 TTCCCGCAGTAACATATGGG 57.369 50.000 7.80 0.00 38.02 4.00
2723 2897 2.736721 CGATTCCCGCAGTAACATATGG 59.263 50.000 7.80 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.