Multiple sequence alignment - TraesCS7D01G403300

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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 TraesCS7D01G403300 chr7D 100.000 4619 0 0 1 4619 520409525 520404907 0.000000e+00 8530.0
1 TraesCS7D01G403300 chr7D 82.456 114 17 3 271 384 80795837 80795727 3.800000e-16 97.1
2 TraesCS7D01G403300 chr7B 88.410 3063 207 64 778 3747 553632915 553629908 0.000000e+00 3554.0
3 TraesCS7D01G403300 chr7B 91.096 292 16 4 4329 4619 553628906 553628624 2.020000e-103 387.0
4 TraesCS7D01G403300 chr7B 81.752 411 45 17 1 384 553633964 553633557 2.680000e-82 316.0
5 TraesCS7D01G403300 chr7B 90.805 87 4 3 593 677 553633181 553633097 3.780000e-21 113.0
6 TraesCS7D01G403300 chr7B 81.746 126 21 1 259 384 28319998 28319875 2.270000e-18 104.0
7 TraesCS7D01G403300 chr7B 100.000 28 0 0 536 563 223809883 223809910 8.000000e-03 52.8
8 TraesCS7D01G403300 chr7A 86.478 3313 221 109 541 3772 596725952 596722786 0.000000e+00 3426.0
9 TraesCS7D01G403300 chr7A 90.287 453 32 10 4175 4619 596719826 596719378 2.400000e-162 582.0
10 TraesCS7D01G403300 chr7A 84.046 351 29 11 1 325 596726718 596726369 3.470000e-81 313.0
11 TraesCS7D01G403300 chr6A 81.967 122 18 3 263 384 471534302 471534419 2.940000e-17 100.0
12 TraesCS7D01G403300 chr6B 97.059 34 1 0 530 563 705137515 705137548 1.800000e-04 58.4
13 TraesCS7D01G403300 chr2B 100.000 28 0 0 536 563 412641579 412641552 8.000000e-03 52.8
14 TraesCS7D01G403300 chr2B 100.000 28 0 0 536 563 412656675 412656648 8.000000e-03 52.8
15 TraesCS7D01G403300 chr2B 100.000 28 0 0 536 563 412710839 412710812 8.000000e-03 52.8


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 TraesCS7D01G403300 chr7D 520404907 520409525 4618 True 8530.000000 8530 100.00000 1 4619 1 chr7D.!!$R2 4618
1 TraesCS7D01G403300 chr7B 553628624 553633964 5340 True 1092.500000 3554 88.01575 1 4619 4 chr7B.!!$R2 4618
2 TraesCS7D01G403300 chr7A 596719378 596726718 7340 True 1440.333333 3426 86.93700 1 4619 3 chr7A.!!$R1 4618

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
248 275 0.102481 GTCGATGCGAAGGCCTAGAA 59.898 55.0 5.16 0.0 37.72 2.10 F
1198 1622 0.253894 TCATCCACCTCGTCCGTCTA 59.746 55.0 0.00 0.0 0.00 2.59 F
2010 2472 0.108186 TCTGCACAGGTATGCTTCCG 60.108 55.0 0.00 0.0 46.28 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1416 1870 0.249868 CCTTGTGCGTCACCTCAGAA 60.250 55.0 7.38 0.0 32.73 3.02 R
2456 2939 0.458716 GCTACTCCTTGAGACCGTGC 60.459 60.0 0.00 0.0 33.32 5.34 R
3747 4277 0.250684 TCGGCCAACAATCTTGCAGA 60.251 50.0 2.24 0.0 0.00 4.26 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 5.472478 ACGAGTGGAGCTATATATTTGACGA 59.528 40.000 0.00 0.00 0.00 4.20
41 42 5.795939 GTGGAGCTATATATTTGACGAGTCG 59.204 44.000 11.85 11.85 0.00 4.18
47 48 6.639686 GCTATATATTTGACGAGTCGTTTGGA 59.360 38.462 20.91 7.01 41.37 3.53
78 79 3.390311 GGTTTAGGTATCCGGTGGATCTT 59.610 47.826 0.00 0.00 42.11 2.40
83 84 5.531753 AGGTATCCGGTGGATCTTATCTA 57.468 43.478 0.00 0.00 42.11 1.98
91 92 5.012148 CCGGTGGATCTTATCTAGATTTGGT 59.988 44.000 11.25 0.15 43.75 3.67
149 150 0.249398 CGACATCCTTTTCTCCGGGT 59.751 55.000 0.00 0.00 0.00 5.28
154 155 1.133363 TCCTTTTCTCCGGGTTGTCA 58.867 50.000 0.00 0.00 0.00 3.58
155 156 1.071699 TCCTTTTCTCCGGGTTGTCAG 59.928 52.381 0.00 0.00 0.00 3.51
156 157 0.875059 CTTTTCTCCGGGTTGTCAGC 59.125 55.000 0.00 0.00 0.00 4.26
157 158 0.181587 TTTTCTCCGGGTTGTCAGCA 59.818 50.000 0.00 0.00 0.00 4.41
190 217 1.530013 ATCAACGACTTCCCGACCGT 61.530 55.000 0.00 0.00 36.77 4.83
201 228 0.320073 CCCGACCGTTGCTTCTACAA 60.320 55.000 0.00 0.00 0.00 2.41
202 229 1.504359 CCGACCGTTGCTTCTACAAA 58.496 50.000 0.00 0.00 0.00 2.83
238 265 1.306148 AGTTAGGATCGTCGATGCGA 58.694 50.000 19.29 12.77 45.32 5.10
244 271 2.685387 GATCGTCGATGCGAAGGCCT 62.685 60.000 13.54 0.00 44.38 5.19
248 275 0.102481 GTCGATGCGAAGGCCTAGAA 59.898 55.000 5.16 0.00 37.72 2.10
315 342 0.545548 AAGAAGACTTCGGCTCCCCT 60.546 55.000 9.53 0.00 34.02 4.79
334 361 8.138074 GCTCCCCTAAGATTTTGAATGTATTTC 58.862 37.037 0.00 0.00 34.72 2.17
387 415 7.850935 AAGGACCGATGATACTTAATAAGGA 57.149 36.000 4.92 0.00 0.00 3.36
389 417 7.897864 AGGACCGATGATACTTAATAAGGAAG 58.102 38.462 4.92 0.00 0.00 3.46
431 592 4.191544 ACGCGTGATACACCTACTTACTA 58.808 43.478 12.93 0.00 0.00 1.82
432 593 4.272018 ACGCGTGATACACCTACTTACTAG 59.728 45.833 12.93 0.00 0.00 2.57
433 594 4.509230 CGCGTGATACACCTACTTACTAGA 59.491 45.833 0.00 0.00 0.00 2.43
434 595 5.557893 CGCGTGATACACCTACTTACTAGAC 60.558 48.000 0.00 0.00 0.00 2.59
449 620 4.946478 ACTAGACCCAACATGATAGAGC 57.054 45.455 0.00 0.00 0.00 4.09
462 633 4.901197 TGATAGAGCTGTAACAAACCCA 57.099 40.909 0.00 0.00 0.00 4.51
467 638 3.883489 AGAGCTGTAACAAACCCAAGTTC 59.117 43.478 0.00 0.00 34.19 3.01
502 673 8.826710 CCGCAAGATCTAAATGTATTACTTTCA 58.173 33.333 0.00 0.00 43.02 2.69
547 837 5.279256 CCCCATCCGTTTCAAAATAAGTGTT 60.279 40.000 0.00 0.00 0.00 3.32
577 867 7.878477 TTTAGTTCAATACCACGACACTTAG 57.122 36.000 0.00 0.00 0.00 2.18
591 881 3.872771 GACACTTAGTTTTGAACGGTGGA 59.127 43.478 13.99 0.00 36.42 4.02
607 923 5.238583 ACGGTGGATCAACTCTCTAAAAAG 58.761 41.667 0.00 0.00 0.00 2.27
608 924 5.011738 ACGGTGGATCAACTCTCTAAAAAGA 59.988 40.000 0.00 0.00 0.00 2.52
609 925 5.578727 CGGTGGATCAACTCTCTAAAAAGAG 59.421 44.000 0.00 0.00 46.78 2.85
666 984 9.915629 GTGAAATAGTGTTAGAAGAGAGAGAAA 57.084 33.333 0.00 0.00 0.00 2.52
700 1027 5.183140 TGCATAACAGGGAAAAAGAGTTAGC 59.817 40.000 0.00 0.00 0.00 3.09
741 1085 4.945543 GGTACCCACTGAAATTACCGAAAT 59.054 41.667 0.00 0.00 0.00 2.17
754 1098 8.587952 AAATTACCGAAATTTCAGAAGTTTGG 57.412 30.769 17.99 11.45 42.88 3.28
757 1101 5.181690 CCGAAATTTCAGAAGTTTGGTGA 57.818 39.130 17.99 0.00 38.82 4.02
758 1102 5.772521 CCGAAATTTCAGAAGTTTGGTGAT 58.227 37.500 17.99 0.00 38.82 3.06
831 1250 5.675538 AGTGGAATCTAGTGTTCCTTATGC 58.324 41.667 21.80 11.91 44.36 3.14
890 1309 3.314553 CAAAGCAAAAGAGCAGTCATGG 58.685 45.455 0.00 0.00 36.85 3.66
932 1356 2.203640 TGAGGCCGTGGTCTGACT 60.204 61.111 7.85 0.00 0.00 3.41
1038 1462 4.497340 CGAGTAAACAGATCTGCTCTCTCC 60.497 50.000 22.83 6.10 29.16 3.71
1040 1464 2.548464 AACAGATCTGCTCTCTCCCT 57.452 50.000 22.83 0.00 29.16 4.20
1041 1465 2.071778 ACAGATCTGCTCTCTCCCTC 57.928 55.000 22.83 0.00 29.16 4.30
1042 1466 1.570501 ACAGATCTGCTCTCTCCCTCT 59.429 52.381 22.83 0.00 29.16 3.69
1043 1467 2.233271 CAGATCTGCTCTCTCCCTCTC 58.767 57.143 10.38 0.00 29.16 3.20
1044 1468 2.138542 AGATCTGCTCTCTCCCTCTCT 58.861 52.381 0.00 0.00 0.00 3.10
1045 1469 2.515429 AGATCTGCTCTCTCCCTCTCTT 59.485 50.000 0.00 0.00 0.00 2.85
1097 1521 4.899239 CGATGAGGGCGTGGAGGC 62.899 72.222 0.00 0.00 45.91 4.70
1198 1622 0.253894 TCATCCACCTCGTCCGTCTA 59.746 55.000 0.00 0.00 0.00 2.59
1416 1870 2.158325 TCAGGGCAAGAAATCCAACCTT 60.158 45.455 0.00 0.00 0.00 3.50
1532 1986 1.630244 GCGCGATGTATCATCCCAGC 61.630 60.000 12.10 4.32 0.00 4.85
1567 2021 5.578005 GTAGACTGCTACTGATACAACCA 57.422 43.478 0.00 0.00 42.96 3.67
1582 2036 1.677576 CAACCAATATCGCATGCCTGT 59.322 47.619 13.15 0.34 0.00 4.00
1588 2048 1.667236 TATCGCATGCCTGTTTCCTG 58.333 50.000 13.15 0.00 0.00 3.86
1614 2074 3.671716 AGAAAGCCCGGTTTGTAGTTAG 58.328 45.455 0.00 0.00 0.00 2.34
1619 2079 2.867647 GCCCGGTTTGTAGTTAGACGTT 60.868 50.000 0.00 0.00 0.00 3.99
1638 2098 4.097892 ACGTTGAGTGATTCCTTTTGCTTT 59.902 37.500 0.00 0.00 0.00 3.51
1702 2162 2.368439 TCATGTTTAGATGGCTGCACC 58.632 47.619 0.50 0.00 39.84 5.01
1705 2165 2.106074 TTTAGATGGCTGCACCGCG 61.106 57.895 0.00 0.00 43.94 6.46
1726 2186 6.308282 CCGCGCCTAATTTTGTTTTATGTTTA 59.692 34.615 0.00 0.00 0.00 2.01
1727 2187 7.009723 CCGCGCCTAATTTTGTTTTATGTTTAT 59.990 33.333 0.00 0.00 0.00 1.40
1728 2188 9.011407 CGCGCCTAATTTTGTTTTATGTTTATA 57.989 29.630 0.00 0.00 0.00 0.98
1758 2218 8.353423 AGAAAAATATTCACTGGTGTGCTATT 57.647 30.769 0.53 1.57 43.49 1.73
1765 2225 5.357742 TCACTGGTGTGCTATTCATGTAT 57.642 39.130 0.53 0.00 43.49 2.29
1773 2233 7.992608 TGGTGTGCTATTCATGTATGTTCTTAT 59.007 33.333 0.00 0.00 0.00 1.73
1776 2236 9.394767 TGTGCTATTCATGTATGTTCTTATTGT 57.605 29.630 0.00 0.00 0.00 2.71
1777 2237 9.655769 GTGCTATTCATGTATGTTCTTATTGTG 57.344 33.333 0.00 0.00 0.00 3.33
1778 2238 8.344831 TGCTATTCATGTATGTTCTTATTGTGC 58.655 33.333 0.00 0.00 0.00 4.57
1779 2239 8.344831 GCTATTCATGTATGTTCTTATTGTGCA 58.655 33.333 0.00 0.00 0.00 4.57
1782 2242 8.510243 TTCATGTATGTTCTTATTGTGCATCT 57.490 30.769 0.00 0.00 0.00 2.90
1787 2249 8.668353 TGTATGTTCTTATTGTGCATCTCTTTC 58.332 33.333 0.00 0.00 0.00 2.62
1806 2268 4.717233 TTCCATTGTTTGATTGATCCGG 57.283 40.909 0.00 0.00 0.00 5.14
1912 2374 6.192234 TCATCTCCTTACTGTTCGAGTTAC 57.808 41.667 0.00 0.00 35.96 2.50
1928 2390 6.460781 TCGAGTTACAAACCATGTACTCATT 58.539 36.000 0.00 0.00 44.11 2.57
1931 2393 8.166706 CGAGTTACAAACCATGTACTCATTTAC 58.833 37.037 0.00 0.00 44.11 2.01
1956 2418 4.023365 GGATGACAGAAATGCTAATGGCTC 60.023 45.833 0.00 0.00 42.39 4.70
2010 2472 0.108186 TCTGCACAGGTATGCTTCCG 60.108 55.000 0.00 0.00 46.28 4.30
2014 2476 1.134788 GCACAGGTATGCTTCCGTACT 60.135 52.381 0.00 0.00 42.62 2.73
2030 2503 3.176708 CGTACTACTTGCGCTGTTACAT 58.823 45.455 9.73 0.00 0.00 2.29
2031 2504 3.611113 CGTACTACTTGCGCTGTTACATT 59.389 43.478 9.73 0.00 0.00 2.71
2033 2506 3.926616 ACTACTTGCGCTGTTACATTCT 58.073 40.909 9.73 0.00 0.00 2.40
2037 2510 5.030874 ACTTGCGCTGTTACATTCTTTAC 57.969 39.130 9.73 0.00 0.00 2.01
2053 2526 1.225376 TTACGCCGTCTGCTTGTTGG 61.225 55.000 0.00 0.00 38.05 3.77
2060 2533 1.264288 CGTCTGCTTGTTGGAGTTTCC 59.736 52.381 0.00 0.00 35.48 3.13
2103 2577 3.119137 AGGCTGGCGTTTGGAATAAAATC 60.119 43.478 0.00 0.00 0.00 2.17
2112 2586 6.853362 GCGTTTGGAATAAAATCTGCTCTATC 59.147 38.462 0.00 0.00 0.00 2.08
2117 2591 9.425248 TTGGAATAAAATCTGCTCTATCCAATT 57.575 29.630 0.00 0.00 0.00 2.32
2124 2598 9.905713 AAAATCTGCTCTATCCAATTACTGTTA 57.094 29.630 0.00 0.00 0.00 2.41
2151 2628 9.696917 CTTGTTATTTTGGCTAATCTTCAAGTT 57.303 29.630 0.00 0.00 0.00 2.66
2207 2684 7.978414 TCAGAAAGTCAAAACATAATTGCACAA 59.022 29.630 0.00 0.00 0.00 3.33
2350 2832 9.003658 CAAGTTTACCATTCTAGACACAAGAAT 57.996 33.333 0.00 0.00 42.95 2.40
2377 2859 0.681175 GAATGGTGGCAGCCTGTTTT 59.319 50.000 14.15 1.30 0.00 2.43
2397 2879 2.247358 TCCTGCAAAGTTTTGGGGATC 58.753 47.619 6.72 0.00 38.57 3.36
2415 2897 6.728164 TGGGGATCATCTGTTTAAATTCCAAA 59.272 34.615 0.00 0.00 0.00 3.28
2417 2899 7.041721 GGGATCATCTGTTTAAATTCCAAACC 58.958 38.462 11.18 0.00 35.46 3.27
2456 2939 7.962964 TGAAGGTTCTATGTTGTAAGTTCTG 57.037 36.000 0.00 0.00 0.00 3.02
2460 2943 5.389516 GGTTCTATGTTGTAAGTTCTGCACG 60.390 44.000 0.00 0.00 0.00 5.34
2574 3083 9.967346 AAAAAGAGAAGAAATTAAGTAACTGGC 57.033 29.630 0.00 0.00 0.00 4.85
2647 3165 4.618920 AGAAAGGTGGATAACTGTCGTT 57.381 40.909 0.00 0.00 37.15 3.85
2649 3167 5.476614 AGAAAGGTGGATAACTGTCGTTAC 58.523 41.667 0.00 0.00 38.35 2.50
2660 3178 7.972277 GGATAACTGTCGTTACACTCTTCATAA 59.028 37.037 0.00 0.00 38.35 1.90
2661 3179 8.912787 ATAACTGTCGTTACACTCTTCATAAG 57.087 34.615 0.00 0.00 38.35 1.73
2662 3180 6.328641 ACTGTCGTTACACTCTTCATAAGT 57.671 37.500 0.00 0.00 0.00 2.24
2663 3181 6.746120 ACTGTCGTTACACTCTTCATAAGTT 58.254 36.000 0.00 0.00 0.00 2.66
2664 3182 6.862090 ACTGTCGTTACACTCTTCATAAGTTC 59.138 38.462 0.00 0.00 0.00 3.01
2665 3183 6.741109 TGTCGTTACACTCTTCATAAGTTCA 58.259 36.000 0.00 0.00 0.00 3.18
2666 3184 7.375834 TGTCGTTACACTCTTCATAAGTTCAT 58.624 34.615 0.00 0.00 0.00 2.57
2667 3185 8.517056 TGTCGTTACACTCTTCATAAGTTCATA 58.483 33.333 0.00 0.00 0.00 2.15
2668 3186 9.517609 GTCGTTACACTCTTCATAAGTTCATAT 57.482 33.333 0.00 0.00 0.00 1.78
2699 3217 8.298140 ACATAGAGTATTACGAAAGCCTATCAC 58.702 37.037 0.00 0.00 0.00 3.06
2778 3297 9.665719 TCTGTATAGTAGCTTCTCTCTATGATG 57.334 37.037 0.00 0.00 0.00 3.07
2813 3332 2.301346 CTGACCATGCCCCACTTAATC 58.699 52.381 0.00 0.00 0.00 1.75
2833 3352 3.698289 TCGTCATACAGGAGAGAAAGGT 58.302 45.455 0.00 0.00 0.00 3.50
2914 3433 1.133853 AGCTTCATGATCCAAGGAGGC 60.134 52.381 0.00 0.00 37.29 4.70
2929 3448 0.318762 GAGGCGACTTCACTCTTGGT 59.681 55.000 0.00 0.00 44.43 3.67
2941 3460 0.995024 CTCTTGGTGATGGAAGGGGT 59.005 55.000 0.00 0.00 0.00 4.95
2970 3489 1.722011 ATCTACGGCACAAAGTTCGG 58.278 50.000 0.00 0.00 0.00 4.30
3016 3535 2.774234 CACTGGACCAGGTAATGATCCT 59.226 50.000 25.34 0.00 35.51 3.24
3033 3552 7.729124 ATGATCCTTGTTTCTTGAAATCCAT 57.271 32.000 0.00 0.00 0.00 3.41
3036 3555 8.431222 TGATCCTTGTTTCTTGAAATCCATTTT 58.569 29.630 0.00 0.00 0.00 1.82
3037 3556 8.611654 ATCCTTGTTTCTTGAAATCCATTTTG 57.388 30.769 0.00 0.00 0.00 2.44
3044 3563 5.299148 TCTTGAAATCCATTTTGCAACTGG 58.701 37.500 17.52 17.52 0.00 4.00
3048 3567 5.070180 TGAAATCCATTTTGCAACTGGAAGA 59.930 36.000 25.84 10.48 42.12 2.87
3052 3571 3.572584 CATTTTGCAACTGGAAGAGCTC 58.427 45.455 5.27 5.27 38.81 4.09
3070 3589 2.300437 GCTCCGTTAGAATGATAGCCCT 59.700 50.000 0.00 0.00 0.00 5.19
3078 3597 4.092116 AGAATGATAGCCCTGGTTAAGC 57.908 45.455 0.00 0.00 0.00 3.09
3079 3598 2.959465 ATGATAGCCCTGGTTAAGCC 57.041 50.000 1.51 0.00 37.90 4.35
3080 3599 1.590591 TGATAGCCCTGGTTAAGCCA 58.409 50.000 1.51 0.00 46.95 4.75
3151 3670 3.209410 CAATGCTGGGAGAGATACCAAC 58.791 50.000 0.00 0.00 36.09 3.77
3181 3700 5.300752 CAGTTCTTCATCACCACTGTAACT 58.699 41.667 0.00 0.00 31.91 2.24
3196 3715 5.515626 CACTGTAACTACGAGCTGGTAATTC 59.484 44.000 5.84 0.41 0.00 2.17
3201 3720 4.745649 ACTACGAGCTGGTAATTCTTCAC 58.254 43.478 10.00 0.00 0.00 3.18
3205 3724 3.243877 CGAGCTGGTAATTCTTCACGATG 59.756 47.826 0.00 0.00 0.00 3.84
3212 3731 5.935206 TGGTAATTCTTCACGATGCTTTGTA 59.065 36.000 0.00 0.00 0.00 2.41
3215 3734 7.640240 GGTAATTCTTCACGATGCTTTGTAATC 59.360 37.037 0.00 0.00 0.00 1.75
3222 3741 4.514545 CGATGCTTTGTAATCGCAGTAA 57.485 40.909 0.00 0.00 39.22 2.24
3240 3759 6.345723 CGCAGTAATTTGTGCTAAACCTTTTG 60.346 38.462 9.34 0.00 37.55 2.44
3246 3766 5.652994 TTGTGCTAAACCTTTTGTTCTGT 57.347 34.783 0.00 0.00 35.67 3.41
3247 3767 5.652994 TGTGCTAAACCTTTTGTTCTGTT 57.347 34.783 0.00 0.00 35.67 3.16
3248 3768 5.406649 TGTGCTAAACCTTTTGTTCTGTTG 58.593 37.500 0.00 0.00 35.67 3.33
3249 3769 4.803613 GTGCTAAACCTTTTGTTCTGTTGG 59.196 41.667 0.00 0.00 35.67 3.77
3250 3770 4.142049 TGCTAAACCTTTTGTTCTGTTGGG 60.142 41.667 0.00 0.00 35.67 4.12
3251 3771 4.098807 GCTAAACCTTTTGTTCTGTTGGGA 59.901 41.667 0.00 0.00 35.67 4.37
3252 3772 4.736126 AAACCTTTTGTTCTGTTGGGAG 57.264 40.909 0.00 0.00 35.67 4.30
3253 3773 3.382083 ACCTTTTGTTCTGTTGGGAGT 57.618 42.857 0.00 0.00 0.00 3.85
3257 3777 2.065899 TTGTTCTGTTGGGAGTTGGG 57.934 50.000 0.00 0.00 0.00 4.12
3356 3876 0.963962 TGGACGTGGTCTACAAGGTC 59.036 55.000 0.00 2.37 35.29 3.85
3383 3903 2.281484 GGCAAGCAGAACGGGACA 60.281 61.111 0.00 0.00 0.00 4.02
3395 3915 0.106918 ACGGGACACCAAAGAGCAAA 60.107 50.000 0.00 0.00 36.13 3.68
3442 3964 0.798776 CCGCTGTGATGACCTGAAAC 59.201 55.000 0.00 0.00 0.00 2.78
3475 3997 3.925299 GGAAAGCTACGGTGACTAGTTTC 59.075 47.826 0.00 0.00 0.00 2.78
3486 4008 4.922103 GGTGACTAGTTTCCGTTGTAGAAG 59.078 45.833 0.00 0.00 0.00 2.85
3538 4067 3.103793 CGTGTGAATTTAGACGGCAAG 57.896 47.619 11.49 0.00 34.17 4.01
3539 4068 2.478894 CGTGTGAATTTAGACGGCAAGT 59.521 45.455 11.49 0.00 34.17 3.16
3608 4137 0.396974 TGGCTGGCAACTTTGAAGGT 60.397 50.000 0.00 0.00 37.61 3.50
3645 4174 6.346919 CCGTTCTGTTGTCAGTATCTCTTTTG 60.347 42.308 0.00 0.00 41.91 2.44
3679 4208 5.104652 TGCTGGGGTTATTTACCTTAGAGAC 60.105 44.000 0.00 0.00 46.86 3.36
3681 4210 6.409349 GCTGGGGTTATTTACCTTAGAGACAT 60.409 42.308 0.00 0.00 46.86 3.06
3728 4257 6.951643 TGAACGATAAATGATCATCAGCAAG 58.048 36.000 9.06 2.41 33.73 4.01
3747 4277 4.440112 GCAAGCAAATATTCCCGCTTAGTT 60.440 41.667 15.41 0.00 42.60 2.24
3755 4285 0.973632 TCCCGCTTAGTTCTGCAAGA 59.026 50.000 0.00 0.00 44.68 3.02
3756 4286 1.555075 TCCCGCTTAGTTCTGCAAGAT 59.445 47.619 0.00 0.00 46.36 2.40
3758 4288 2.096496 CCCGCTTAGTTCTGCAAGATTG 59.904 50.000 0.00 0.00 46.36 2.67
3759 4289 2.744202 CCGCTTAGTTCTGCAAGATTGT 59.256 45.455 0.00 0.00 46.36 2.71
3760 4290 3.189287 CCGCTTAGTTCTGCAAGATTGTT 59.811 43.478 0.00 0.00 46.36 2.83
3772 4302 3.016736 CAAGATTGTTGGCCGATACCTT 58.983 45.455 0.00 0.00 0.00 3.50
3773 4303 3.366052 AGATTGTTGGCCGATACCTTT 57.634 42.857 0.00 0.00 0.00 3.11
3777 4307 3.420300 TGTTGGCCGATACCTTTGTTA 57.580 42.857 0.00 0.00 0.00 2.41
3778 4308 3.075884 TGTTGGCCGATACCTTTGTTAC 58.924 45.455 0.00 0.00 0.00 2.50
3789 4334 4.223320 ACCTTTGTTACAAACGCATGAG 57.777 40.909 6.41 0.00 0.00 2.90
3794 4339 2.729360 TGTTACAAACGCATGAGTCTCG 59.271 45.455 1.45 0.00 0.00 4.04
3795 4340 2.717580 TACAAACGCATGAGTCTCGT 57.282 45.000 1.45 3.32 38.15 4.18
3805 4350 5.288712 ACGCATGAGTCTCGTAGTAATTTTG 59.711 40.000 0.00 0.00 34.41 2.44
3826 4372 8.833231 TTTTGTACTGTGAAAATCTCTAGAGG 57.167 34.615 19.67 2.83 0.00 3.69
3832 4378 7.327214 ACTGTGAAAATCTCTAGAGGAACATC 58.673 38.462 19.67 11.88 0.00 3.06
3875 4445 3.679389 CAGTTGAAGCACTGTCCCTATT 58.321 45.455 0.00 0.00 39.59 1.73
3879 4449 2.375174 TGAAGCACTGTCCCTATTGGTT 59.625 45.455 0.00 0.00 34.77 3.67
3883 4453 4.526970 AGCACTGTCCCTATTGGTTTATG 58.473 43.478 0.00 0.00 34.77 1.90
3900 4470 3.466879 GCAAATGCTGCGCCTTTC 58.533 55.556 4.18 0.00 42.37 2.62
3904 4474 1.199789 CAAATGCTGCGCCTTTCTGTA 59.800 47.619 4.18 0.00 0.00 2.74
3907 4477 0.670546 TGCTGCGCCTTTCTGTAGAC 60.671 55.000 4.18 0.00 0.00 2.59
3932 4508 2.579201 CACCACTGCCCCGTAGAG 59.421 66.667 0.00 0.00 0.00 2.43
3957 4533 0.923358 TCCAACAAACCTCCACCACT 59.077 50.000 0.00 0.00 0.00 4.00
3963 4539 2.158813 ACAAACCTCCACCACTACACAG 60.159 50.000 0.00 0.00 0.00 3.66
3966 4542 3.185880 ACCTCCACCACTACACAGTAT 57.814 47.619 0.00 0.00 32.21 2.12
3968 4544 4.021916 ACCTCCACCACTACACAGTATAC 58.978 47.826 0.00 0.00 32.21 1.47
3969 4545 4.021229 CCTCCACCACTACACAGTATACA 58.979 47.826 5.50 0.00 32.21 2.29
3970 4546 4.098044 CCTCCACCACTACACAGTATACAG 59.902 50.000 5.50 0.00 32.21 2.74
3971 4547 3.446161 TCCACCACTACACAGTATACAGC 59.554 47.826 5.50 0.00 32.21 4.40
3972 4548 3.194755 CCACCACTACACAGTATACAGCA 59.805 47.826 5.50 0.00 32.21 4.41
3973 4549 4.322424 CCACCACTACACAGTATACAGCAA 60.322 45.833 5.50 0.00 32.21 3.91
3976 4552 7.210174 CACCACTACACAGTATACAGCAATAT 58.790 38.462 5.50 0.00 32.21 1.28
3977 4553 7.710907 CACCACTACACAGTATACAGCAATATT 59.289 37.037 5.50 0.00 32.21 1.28
3978 4554 7.926555 ACCACTACACAGTATACAGCAATATTC 59.073 37.037 5.50 0.00 32.21 1.75
3979 4555 8.144478 CCACTACACAGTATACAGCAATATTCT 58.856 37.037 5.50 0.00 32.21 2.40
3980 4556 9.186323 CACTACACAGTATACAGCAATATTCTC 57.814 37.037 5.50 0.00 32.21 2.87
3981 4557 9.137459 ACTACACAGTATACAGCAATATTCTCT 57.863 33.333 5.50 0.00 31.45 3.10
4001 4577 0.736053 TTTTTCCTTTGACGCGTGCT 59.264 45.000 20.70 0.00 0.00 4.40
4003 4579 2.387125 TTTCCTTTGACGCGTGCTGC 62.387 55.000 20.70 1.49 41.47 5.25
4011 4587 2.025359 GACGCGTGCTGCAGTATTCC 62.025 60.000 20.70 2.57 46.97 3.01
4028 4604 0.036306 TCCCTTTCCCTCGCAGAAAC 59.964 55.000 0.00 0.00 34.09 2.78
4038 4614 4.635765 TCCCTCGCAGAAACAGAAATATTG 59.364 41.667 0.00 0.00 34.09 1.90
4041 4617 5.447818 CCTCGCAGAAACAGAAATATTGTCC 60.448 44.000 0.00 0.00 34.09 4.02
4046 4622 6.381801 CAGAAACAGAAATATTGTCCACCAC 58.618 40.000 0.00 0.00 0.00 4.16
4049 4625 7.390718 AGAAACAGAAATATTGTCCACCACTAC 59.609 37.037 0.00 0.00 0.00 2.73
4052 7275 5.642063 CAGAAATATTGTCCACCACTACGTT 59.358 40.000 0.00 0.00 0.00 3.99
4055 7278 3.764237 ATTGTCCACCACTACGTTTCT 57.236 42.857 0.00 0.00 0.00 2.52
4060 7283 4.171754 GTCCACCACTACGTTTCTCATAC 58.828 47.826 0.00 0.00 0.00 2.39
4065 7288 5.907945 CACCACTACGTTTCTCATACGATAG 59.092 44.000 0.00 3.69 41.33 2.08
4071 7294 5.770417 ACGTTTCTCATACGATAGAATCCC 58.230 41.667 2.12 0.00 41.33 3.85
4072 7295 4.852104 CGTTTCTCATACGATAGAATCCCG 59.148 45.833 0.00 0.00 41.33 5.14
4075 7298 5.624344 TCTCATACGATAGAATCCCGTTC 57.376 43.478 0.00 0.00 37.69 3.95
4106 7335 8.282455 TCTCATACGATAATCTACAATCCTCC 57.718 38.462 0.00 0.00 0.00 4.30
4120 7349 4.106197 CAATCCTCCTTTTCTCGTACGAG 58.894 47.826 34.21 34.21 43.21 4.18
4137 7366 7.573627 TCGTACGAGAGACACTATAATGAATG 58.426 38.462 15.28 0.00 0.00 2.67
4138 7367 7.440255 TCGTACGAGAGACACTATAATGAATGA 59.560 37.037 15.28 0.00 0.00 2.57
4142 7371 9.900710 ACGAGAGACACTATAATGAATGAATAC 57.099 33.333 0.00 0.00 0.00 1.89
4148 7377 9.167311 GACACTATAATGAATGAATACATCCCC 57.833 37.037 0.00 0.00 35.50 4.81
4149 7378 8.894592 ACACTATAATGAATGAATACATCCCCT 58.105 33.333 0.00 0.00 35.50 4.79
4219 7448 4.649088 GCCCGTGGCTTAAATAAAGAAT 57.351 40.909 7.58 0.00 46.69 2.40
4221 7450 5.758924 GCCCGTGGCTTAAATAAAGAATAG 58.241 41.667 7.58 0.00 46.69 1.73
4226 7455 9.849166 CCGTGGCTTAAATAAAGAATAGAAAAA 57.151 29.630 0.00 0.00 37.38 1.94
4279 7508 1.071385 CCTAGAAGCCGCATCTTCCAT 59.929 52.381 3.01 0.00 42.52 3.41
4280 7509 2.411904 CTAGAAGCCGCATCTTCCATC 58.588 52.381 3.01 0.00 42.52 3.51
4306 7964 8.096414 CCAACCAACATATTTTTCTTCCATCTT 58.904 33.333 0.00 0.00 0.00 2.40
4307 7965 9.492973 CAACCAACATATTTTTCTTCCATCTTT 57.507 29.630 0.00 0.00 0.00 2.52
4308 7966 9.710900 AACCAACATATTTTTCTTCCATCTTTC 57.289 29.630 0.00 0.00 0.00 2.62
4343 8002 5.458451 AAAAAGGAGGAATCCTAGAAGGG 57.542 43.478 0.00 0.00 39.65 3.95
4344 8003 2.110753 AGGAGGAATCCTAGAAGGGC 57.889 55.000 0.00 0.00 38.58 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.099652 CTCCACTCGTGCTCCACCAA 62.100 60.000 0.00 0.00 0.00 3.67
13 14 5.472478 TCGTCAAATATATAGCTCCACTCGT 59.528 40.000 0.00 0.00 0.00 4.18
16 17 6.348622 CGACTCGTCAAATATATAGCTCCACT 60.349 42.308 0.00 0.00 0.00 4.00
41 42 3.439129 CCTAAACCGTCTGGAATCCAAAC 59.561 47.826 2.61 0.00 39.21 2.93
47 48 3.069158 CGGATACCTAAACCGTCTGGAAT 59.931 47.826 0.00 0.00 41.47 3.01
78 79 4.098960 ACGAAAGCCGACCAAATCTAGATA 59.901 41.667 5.46 0.00 41.76 1.98
83 84 1.156736 CACGAAAGCCGACCAAATCT 58.843 50.000 0.00 0.00 41.76 2.40
91 92 0.242825 CTGAGTACCACGAAAGCCGA 59.757 55.000 0.00 0.00 41.76 5.54
149 150 3.244526 TGCAGACTAGGAAATGCTGACAA 60.245 43.478 10.67 0.00 39.42 3.18
154 155 3.920231 TGATGCAGACTAGGAAATGCT 57.080 42.857 10.67 0.00 39.42 3.79
155 156 3.242543 CGTTGATGCAGACTAGGAAATGC 60.243 47.826 0.00 0.00 39.14 3.56
156 157 4.033358 GTCGTTGATGCAGACTAGGAAATG 59.967 45.833 0.00 0.00 32.58 2.32
157 158 4.081420 AGTCGTTGATGCAGACTAGGAAAT 60.081 41.667 3.88 0.00 42.71 2.17
190 217 6.489700 TGAAATCCATGAGTTTGTAGAAGCAA 59.510 34.615 0.00 0.00 0.00 3.91
201 228 8.477419 TCCTAACTTTTTGAAATCCATGAGTT 57.523 30.769 0.00 0.00 0.00 3.01
202 229 8.655935 ATCCTAACTTTTTGAAATCCATGAGT 57.344 30.769 0.00 0.00 0.00 3.41
244 271 2.759191 CATAGCTTGATGCCGCTTCTA 58.241 47.619 7.69 0.00 44.23 2.10
248 275 3.741860 GCATAGCTTGATGCCGCT 58.258 55.556 9.91 0.00 45.41 5.52
346 374 5.123344 CGGTCCTTATAAAAAGACACCCTTG 59.877 44.000 10.47 0.00 34.79 3.61
384 412 5.091552 TGTTGTGATTACTACTCCCTTCCT 58.908 41.667 4.07 0.00 34.31 3.36
385 413 5.416271 TGTTGTGATTACTACTCCCTTCC 57.584 43.478 4.07 0.00 34.31 3.46
386 414 6.128634 CGTTTGTTGTGATTACTACTCCCTTC 60.129 42.308 4.07 0.00 34.31 3.46
387 415 5.699458 CGTTTGTTGTGATTACTACTCCCTT 59.301 40.000 4.07 0.00 34.31 3.95
389 417 4.142966 GCGTTTGTTGTGATTACTACTCCC 60.143 45.833 4.07 0.00 34.31 4.30
431 592 3.110705 ACAGCTCTATCATGTTGGGTCT 58.889 45.455 0.00 0.00 0.00 3.85
432 593 3.550437 ACAGCTCTATCATGTTGGGTC 57.450 47.619 0.00 0.00 0.00 4.46
433 594 4.225042 TGTTACAGCTCTATCATGTTGGGT 59.775 41.667 0.00 0.00 0.00 4.51
434 595 4.769688 TGTTACAGCTCTATCATGTTGGG 58.230 43.478 0.00 0.00 0.00 4.12
462 633 7.923414 AGATCTTGCGGTTAATTAAGAACTT 57.077 32.000 0.00 0.00 31.03 2.66
502 673 6.957020 TGGGGGTAAACAAGAATTATGTTCAT 59.043 34.615 8.96 0.00 39.98 2.57
503 674 6.315714 TGGGGGTAAACAAGAATTATGTTCA 58.684 36.000 8.96 1.28 39.98 3.18
504 675 6.844097 TGGGGGTAAACAAGAATTATGTTC 57.156 37.500 8.96 0.17 39.98 3.18
547 837 7.118101 GTGTCGTGGTATTGAACTAAAACCATA 59.882 37.037 0.00 0.00 41.93 2.74
563 853 4.503734 CGTTCAAAACTAAGTGTCGTGGTA 59.496 41.667 0.00 0.00 0.00 3.25
577 867 3.564225 AGAGTTGATCCACCGTTCAAAAC 59.436 43.478 0.00 0.00 33.90 2.43
607 923 6.305693 AGAAGCACACAAGTATTTTGACTC 57.694 37.500 0.00 0.00 0.00 3.36
608 924 6.699575 AAGAAGCACACAAGTATTTTGACT 57.300 33.333 0.00 0.00 0.00 3.41
609 925 6.751888 ACAAAGAAGCACACAAGTATTTTGAC 59.248 34.615 0.00 0.00 0.00 3.18
610 926 6.751425 CACAAAGAAGCACACAAGTATTTTGA 59.249 34.615 0.00 0.00 0.00 2.69
611 927 6.751425 TCACAAAGAAGCACACAAGTATTTTG 59.249 34.615 0.00 0.00 0.00 2.44
681 1008 4.793201 ACTGCTAACTCTTTTTCCCTGTT 58.207 39.130 0.00 0.00 0.00 3.16
816 1235 3.243569 CCTCCTCGCATAAGGAACACTAG 60.244 52.174 1.57 0.00 44.81 2.57
818 1237 1.482593 CCTCCTCGCATAAGGAACACT 59.517 52.381 1.57 0.00 44.81 3.55
831 1250 1.279271 ACCAAATTCCACTCCTCCTCG 59.721 52.381 0.00 0.00 0.00 4.63
932 1356 1.754380 CTGACAGGTGGGGTCGAACA 61.754 60.000 1.31 0.00 38.10 3.18
1038 1462 1.668751 CGGACGAGAGAGAAAGAGAGG 59.331 57.143 0.00 0.00 0.00 3.69
1040 1464 1.088306 GCGGACGAGAGAGAAAGAGA 58.912 55.000 0.00 0.00 0.00 3.10
1041 1465 0.247894 CGCGGACGAGAGAGAAAGAG 60.248 60.000 0.00 0.00 43.93 2.85
1042 1466 1.645704 CCGCGGACGAGAGAGAAAGA 61.646 60.000 24.07 0.00 43.93 2.52
1043 1467 1.226435 CCGCGGACGAGAGAGAAAG 60.226 63.158 24.07 0.00 43.93 2.62
1044 1468 2.875485 CCGCGGACGAGAGAGAAA 59.125 61.111 24.07 0.00 43.93 2.52
1045 1469 3.812019 GCCGCGGACGAGAGAGAA 61.812 66.667 33.48 0.00 43.93 2.87
1416 1870 0.249868 CCTTGTGCGTCACCTCAGAA 60.250 55.000 7.38 0.00 32.73 3.02
1493 1947 4.674211 GCGCTGATCTGAAAATAAATCTGC 59.326 41.667 0.00 0.00 38.78 4.26
1532 1986 1.134580 CAGTCTACTGTCTGCCCCATG 60.135 57.143 1.81 0.00 39.09 3.66
1567 2021 2.620115 CAGGAAACAGGCATGCGATATT 59.380 45.455 12.44 4.33 0.00 1.28
1614 2074 3.251004 AGCAAAAGGAATCACTCAACGTC 59.749 43.478 0.00 0.00 0.00 4.34
1619 2079 4.214310 TCCAAAGCAAAAGGAATCACTCA 58.786 39.130 0.00 0.00 0.00 3.41
1653 2113 7.381766 TCAATTTCAATGTCGATCTCACAAT 57.618 32.000 0.00 0.00 0.00 2.71
1654 2114 6.799926 TCAATTTCAATGTCGATCTCACAA 57.200 33.333 0.00 0.00 0.00 3.33
1702 2162 5.755330 AACATAAAACAAAATTAGGCGCG 57.245 34.783 0.00 0.00 0.00 6.86
1726 2186 9.520515 ACACCAGTGAATATTTTTCTCACTTAT 57.479 29.630 4.48 0.00 45.85 1.73
1727 2187 8.783093 CACACCAGTGAATATTTTTCTCACTTA 58.217 33.333 4.48 0.00 45.85 2.24
1728 2188 7.651808 CACACCAGTGAATATTTTTCTCACTT 58.348 34.615 4.48 0.00 45.85 3.16
1758 2218 7.989170 AGAGATGCACAATAAGAACATACATGA 59.011 33.333 0.00 0.00 0.00 3.07
1765 2225 6.003326 TGGAAAGAGATGCACAATAAGAACA 58.997 36.000 0.00 0.00 0.00 3.18
1773 2233 5.068855 TCAAACAATGGAAAGAGATGCACAA 59.931 36.000 0.00 0.00 0.00 3.33
1776 2236 5.988310 ATCAAACAATGGAAAGAGATGCA 57.012 34.783 0.00 0.00 0.00 3.96
1777 2237 6.392354 TCAATCAAACAATGGAAAGAGATGC 58.608 36.000 0.00 0.00 0.00 3.91
1778 2238 7.705325 GGATCAATCAAACAATGGAAAGAGATG 59.295 37.037 0.00 0.00 0.00 2.90
1779 2239 7.415989 CGGATCAATCAAACAATGGAAAGAGAT 60.416 37.037 0.00 0.00 0.00 2.75
1780 2240 6.127925 CGGATCAATCAAACAATGGAAAGAGA 60.128 38.462 0.00 0.00 0.00 3.10
1781 2241 6.032094 CGGATCAATCAAACAATGGAAAGAG 58.968 40.000 0.00 0.00 0.00 2.85
1782 2242 5.105797 CCGGATCAATCAAACAATGGAAAGA 60.106 40.000 0.00 0.00 0.00 2.52
1787 2249 3.429272 CCACCGGATCAATCAAACAATGG 60.429 47.826 9.46 0.00 0.00 3.16
1806 2268 8.938906 ACAATTCAGAATCAATTTAAATGCCAC 58.061 29.630 0.39 0.00 0.00 5.01
1912 2374 7.336679 TCATCCAGTAAATGAGTACATGGTTTG 59.663 37.037 0.00 0.00 36.79 2.93
1928 2390 6.543465 CCATTAGCATTTCTGTCATCCAGTAA 59.457 38.462 0.00 0.00 42.19 2.24
1931 2393 4.261489 GCCATTAGCATTTCTGTCATCCAG 60.261 45.833 0.00 0.00 42.97 3.86
2010 2472 4.863131 AGAATGTAACAGCGCAAGTAGTAC 59.137 41.667 11.47 8.84 41.68 2.73
2014 2476 5.164031 CGTAAAGAATGTAACAGCGCAAGTA 60.164 40.000 11.47 0.00 41.68 2.24
2053 2526 6.705381 CCATCAGACTAATCATCTGGAAACTC 59.295 42.308 2.37 0.00 43.25 3.01
2060 2533 4.755629 CCTTGCCATCAGACTAATCATCTG 59.244 45.833 0.00 0.00 44.22 2.90
2089 2562 8.225603 TGGATAGAGCAGATTTTATTCCAAAC 57.774 34.615 0.00 0.00 0.00 2.93
2090 2563 8.821686 TTGGATAGAGCAGATTTTATTCCAAA 57.178 30.769 0.00 0.00 30.63 3.28
2103 2577 7.766278 ACAAGTAACAGTAATTGGATAGAGCAG 59.234 37.037 0.00 0.00 39.16 4.24
2112 2586 8.921670 GCCAAAATAACAAGTAACAGTAATTGG 58.078 33.333 0.00 0.00 39.16 3.16
2124 2598 8.860088 ACTTGAAGATTAGCCAAAATAACAAGT 58.140 29.630 0.00 0.00 34.97 3.16
2175 2652 7.510549 TTATGTTTTGACTTTCTGAGGAAGG 57.489 36.000 5.33 0.00 35.12 3.46
2350 2832 1.208052 GCTGCCACCATTCTCTCTACA 59.792 52.381 0.00 0.00 0.00 2.74
2377 2859 2.247358 GATCCCCAAAACTTTGCAGGA 58.753 47.619 12.09 12.09 40.79 3.86
2397 2879 5.248248 AGGGGGTTTGGAATTTAAACAGATG 59.752 40.000 16.29 0.00 39.24 2.90
2415 2897 1.507140 TCAATTATGCTCGAGGGGGT 58.493 50.000 15.58 0.00 0.00 4.95
2417 2899 2.158755 ACCTTCAATTATGCTCGAGGGG 60.159 50.000 15.58 0.00 0.00 4.79
2456 2939 0.458716 GCTACTCCTTGAGACCGTGC 60.459 60.000 0.00 0.00 33.32 5.34
2460 2943 0.827368 CAGGGCTACTCCTTGAGACC 59.173 60.000 0.00 0.00 44.14 3.85
2574 3083 4.159857 GCACTAGACAACTACGAACTCAG 58.840 47.826 0.00 0.00 0.00 3.35
2625 3143 4.618920 ACGACAGTTATCCACCTTTCTT 57.381 40.909 0.00 0.00 0.00 2.52
2627 3145 5.119743 GTGTAACGACAGTTATCCACCTTTC 59.880 44.000 0.00 0.00 43.80 2.62
2649 3167 9.166173 TGTTGGAATATGAACTTATGAAGAGTG 57.834 33.333 0.00 0.00 0.00 3.51
2666 3184 9.472361 GCTTTCGTAATACTCTATGTTGGAATA 57.528 33.333 0.00 0.00 0.00 1.75
2667 3185 7.441458 GGCTTTCGTAATACTCTATGTTGGAAT 59.559 37.037 0.00 0.00 0.00 3.01
2668 3186 6.759827 GGCTTTCGTAATACTCTATGTTGGAA 59.240 38.462 0.00 0.00 0.00 3.53
2669 3187 6.097839 AGGCTTTCGTAATACTCTATGTTGGA 59.902 38.462 0.00 0.00 0.00 3.53
2670 3188 6.281405 AGGCTTTCGTAATACTCTATGTTGG 58.719 40.000 0.00 0.00 0.00 3.77
2671 3189 9.130312 GATAGGCTTTCGTAATACTCTATGTTG 57.870 37.037 0.00 0.00 0.00 3.33
2672 3190 8.857098 TGATAGGCTTTCGTAATACTCTATGTT 58.143 33.333 0.00 0.00 0.00 2.71
2673 3191 8.298140 GTGATAGGCTTTCGTAATACTCTATGT 58.702 37.037 0.00 0.00 0.00 2.29
2759 3278 5.241506 GCAGACATCATAGAGAGAAGCTACT 59.758 44.000 0.00 0.00 0.00 2.57
2778 3297 1.433534 GTCAGCAACCACTAGCAGAC 58.566 55.000 0.00 0.00 39.48 3.51
2813 3332 5.508153 CCATACCTTTCTCTCCTGTATGACG 60.508 48.000 8.98 0.00 40.60 4.35
2833 3352 1.604879 TTTGCCGCTGTTGCCCATA 60.605 52.632 0.00 0.00 35.36 2.74
2929 3448 1.284785 GATTCACCACCCCTTCCATCA 59.715 52.381 0.00 0.00 0.00 3.07
2941 3460 2.027653 TGTGCCGTAGATTGATTCACCA 60.028 45.455 0.00 0.00 0.00 4.17
2970 3489 2.341257 TGAGCTTGAAGTTCTCATCGC 58.659 47.619 10.35 0.11 32.78 4.58
3016 3535 7.336427 AGTTGCAAAATGGATTTCAAGAAACAA 59.664 29.630 0.00 0.00 32.51 2.83
3033 3552 1.956477 GGAGCTCTTCCAGTTGCAAAA 59.044 47.619 14.64 0.00 46.01 2.44
3044 3563 4.920927 GCTATCATTCTAACGGAGCTCTTC 59.079 45.833 14.64 0.00 0.00 2.87
3048 3567 2.300437 GGGCTATCATTCTAACGGAGCT 59.700 50.000 0.00 0.00 0.00 4.09
3052 3571 2.368875 ACCAGGGCTATCATTCTAACGG 59.631 50.000 0.00 0.00 0.00 4.44
3055 3574 5.456186 GGCTTAACCAGGGCTATCATTCTAA 60.456 44.000 0.00 0.00 38.86 2.10
3078 3597 4.159135 CCAGTCAATGAAAAAGGAGGATGG 59.841 45.833 0.00 0.00 0.00 3.51
3079 3598 4.768968 ACCAGTCAATGAAAAAGGAGGATG 59.231 41.667 0.00 0.00 0.00 3.51
3080 3599 5.003096 ACCAGTCAATGAAAAAGGAGGAT 57.997 39.130 0.00 0.00 0.00 3.24
3151 3670 2.555199 GTGATGAAGAACTGGGATCCG 58.445 52.381 5.45 0.00 0.00 4.18
3181 3700 3.441222 TCGTGAAGAATTACCAGCTCGTA 59.559 43.478 0.00 0.00 0.00 3.43
3196 3715 3.181521 TGCGATTACAAAGCATCGTGAAG 60.182 43.478 4.13 0.00 43.49 3.02
3201 3720 4.514545 TTACTGCGATTACAAAGCATCG 57.485 40.909 0.00 0.00 44.24 3.84
3205 3724 5.220024 GCACAAATTACTGCGATTACAAAGC 60.220 40.000 0.00 0.00 0.00 3.51
3212 3731 5.183140 AGGTTTAGCACAAATTACTGCGATT 59.817 36.000 0.00 0.00 38.51 3.34
3215 3734 4.419522 AGGTTTAGCACAAATTACTGCG 57.580 40.909 2.47 0.00 38.51 5.18
3220 3739 8.254508 ACAGAACAAAAGGTTTAGCACAAATTA 58.745 29.630 0.00 0.00 40.63 1.40
3222 3741 6.639563 ACAGAACAAAAGGTTTAGCACAAAT 58.360 32.000 0.00 0.00 40.63 2.32
3240 3759 1.143073 AGTCCCAACTCCCAACAGAAC 59.857 52.381 0.00 0.00 0.00 3.01
3246 3766 2.291930 ACAACAAAGTCCCAACTCCCAA 60.292 45.455 0.00 0.00 33.48 4.12
3247 3767 1.286553 ACAACAAAGTCCCAACTCCCA 59.713 47.619 0.00 0.00 33.48 4.37
3248 3768 2.067365 ACAACAAAGTCCCAACTCCC 57.933 50.000 0.00 0.00 33.48 4.30
3249 3769 3.020984 TCAACAACAAAGTCCCAACTCC 58.979 45.455 0.00 0.00 33.48 3.85
3250 3770 4.338118 TCATCAACAACAAAGTCCCAACTC 59.662 41.667 0.00 0.00 33.48 3.01
3251 3771 4.277476 TCATCAACAACAAAGTCCCAACT 58.723 39.130 0.00 0.00 37.32 3.16
3252 3772 4.647424 TCATCAACAACAAAGTCCCAAC 57.353 40.909 0.00 0.00 0.00 3.77
3253 3773 7.667635 TGTATATCATCAACAACAAAGTCCCAA 59.332 33.333 0.00 0.00 0.00 4.12
3257 3777 9.155975 AGAGTGTATATCATCAACAACAAAGTC 57.844 33.333 0.00 0.00 0.00 3.01
3383 3903 4.685924 CAATGACAACTTTGCTCTTTGGT 58.314 39.130 0.00 0.00 0.00 3.67
3395 3915 0.870393 CGCTGTCAGCAATGACAACT 59.130 50.000 24.13 0.00 46.60 3.16
3407 3927 4.329545 GGCACTTCCCCGCTGTCA 62.330 66.667 0.00 0.00 0.00 3.58
3416 3936 1.375908 TCATCACAGCGGCACTTCC 60.376 57.895 1.45 0.00 0.00 3.46
3442 3964 0.895530 TAGCTTTCCACCAGAGACCG 59.104 55.000 0.00 0.00 0.00 4.79
3475 3997 4.147653 CGGATAATAACGCTTCTACAACGG 59.852 45.833 0.00 0.00 0.00 4.44
3486 4008 4.549489 CGAAAACAGTCCGGATAATAACGC 60.549 45.833 7.81 0.00 0.00 4.84
3566 4095 2.422597 TCACGGGTAAGCAAGTCATTG 58.577 47.619 0.00 0.00 39.57 2.82
3608 4137 4.020928 ACAACAGAACGGTGGTGTATGATA 60.021 41.667 3.78 0.00 46.79 2.15
3728 4257 4.789802 GCAGAACTAAGCGGGAATATTTGC 60.790 45.833 0.00 0.00 0.00 3.68
3747 4277 0.250684 TCGGCCAACAATCTTGCAGA 60.251 50.000 2.24 0.00 0.00 4.26
3755 4285 2.802719 ACAAAGGTATCGGCCAACAAT 58.197 42.857 2.24 0.00 0.00 2.71
3756 4286 2.279935 ACAAAGGTATCGGCCAACAA 57.720 45.000 2.24 0.00 0.00 2.83
3758 4288 3.075884 TGTAACAAAGGTATCGGCCAAC 58.924 45.455 2.24 0.00 0.00 3.77
3759 4289 3.420300 TGTAACAAAGGTATCGGCCAA 57.580 42.857 2.24 0.00 0.00 4.52
3760 4290 3.420300 TTGTAACAAAGGTATCGGCCA 57.580 42.857 2.24 0.00 0.00 5.36
3772 4302 3.183574 CGAGACTCATGCGTTTGTAACAA 59.816 43.478 2.82 0.00 0.00 2.83
3773 4303 2.729360 CGAGACTCATGCGTTTGTAACA 59.271 45.455 2.82 0.00 0.00 2.41
3777 4307 2.030185 ACTACGAGACTCATGCGTTTGT 60.030 45.455 2.82 0.00 39.24 2.83
3778 4308 2.596452 ACTACGAGACTCATGCGTTTG 58.404 47.619 2.82 0.00 39.24 2.93
3789 4334 8.511465 TTCACAGTACAAAATTACTACGAGAC 57.489 34.615 0.00 0.00 30.76 3.36
3805 4350 7.603651 TGTTCCTCTAGAGATTTTCACAGTAC 58.396 38.462 21.76 5.65 0.00 2.73
3859 4429 2.789409 ACCAATAGGGACAGTGCTTC 57.211 50.000 0.00 0.00 41.15 3.86
3868 4438 4.961730 AGCATTTGCATAAACCAATAGGGA 59.038 37.500 5.20 0.00 45.16 4.20
3894 4464 2.263945 GAGCTTCGTCTACAGAAAGGC 58.736 52.381 0.00 0.00 0.00 4.35
3900 4470 0.888619 TGGTGGAGCTTCGTCTACAG 59.111 55.000 0.00 0.00 29.74 2.74
3904 4474 1.668294 CAGTGGTGGAGCTTCGTCT 59.332 57.895 0.00 0.00 0.00 4.18
3907 4477 2.743928 GGCAGTGGTGGAGCTTCG 60.744 66.667 0.00 0.00 0.00 3.79
3932 4508 2.820197 GTGGAGGTTTGTTGGAGATTCC 59.180 50.000 0.00 0.00 36.96 3.01
3987 4563 3.584250 CTGCAGCACGCGTCAAAGG 62.584 63.158 9.86 0.00 46.97 3.11
3988 4564 1.556591 TACTGCAGCACGCGTCAAAG 61.557 55.000 15.27 5.55 46.97 2.77
3998 4574 1.340991 GGGAAAGGGAATACTGCAGCA 60.341 52.381 15.27 0.00 0.00 4.41
3999 4575 1.064389 AGGGAAAGGGAATACTGCAGC 60.064 52.381 15.27 0.00 0.00 5.25
4001 4577 1.209504 CGAGGGAAAGGGAATACTGCA 59.790 52.381 0.00 0.00 0.00 4.41
4003 4579 1.209504 TGCGAGGGAAAGGGAATACTG 59.790 52.381 0.00 0.00 0.00 2.74
4011 4587 1.160137 CTGTTTCTGCGAGGGAAAGG 58.840 55.000 0.00 0.00 34.02 3.11
4028 4604 5.175859 ACGTAGTGGTGGACAATATTTCTG 58.824 41.667 0.00 0.00 42.51 3.02
4038 4614 2.806608 TGAGAAACGTAGTGGTGGAC 57.193 50.000 0.00 0.00 45.00 4.02
4041 4617 4.087510 TCGTATGAGAAACGTAGTGGTG 57.912 45.455 0.00 0.00 45.00 4.17
4046 4622 7.022384 GGGATTCTATCGTATGAGAAACGTAG 58.978 42.308 0.00 0.00 41.08 3.51
4049 4625 4.852104 CGGGATTCTATCGTATGAGAAACG 59.148 45.833 0.00 0.00 41.64 3.60
4052 7275 5.048224 GGAACGGGATTCTATCGTATGAGAA 60.048 44.000 0.00 0.00 37.48 2.87
4055 7278 4.404640 AGGAACGGGATTCTATCGTATGA 58.595 43.478 0.00 0.00 37.48 2.15
4060 7283 5.116882 AGAAAAAGGAACGGGATTCTATCG 58.883 41.667 0.00 0.00 37.48 2.92
4065 7288 5.220605 CGTATGAGAAAAAGGAACGGGATTC 60.221 44.000 0.00 0.00 36.48 2.52
4071 7294 8.354011 AGATTATCGTATGAGAAAAAGGAACG 57.646 34.615 0.00 0.00 0.00 3.95
4121 7350 9.950496 GGGATGTATTCATTCATTATAGTGTCT 57.050 33.333 0.00 0.00 34.06 3.41
4123 7352 8.894592 AGGGGATGTATTCATTCATTATAGTGT 58.105 33.333 0.00 0.00 34.06 3.55
4199 7428 7.562454 TTCTATTCTTTATTTAAGCCACGGG 57.438 36.000 0.00 0.00 33.66 5.28
4231 7460 2.076863 GCCGTGTCTTTGCATAACTCT 58.923 47.619 0.00 0.00 0.00 3.24
4279 7508 6.985653 TGGAAGAAAAATATGTTGGTTGGA 57.014 33.333 0.00 0.00 0.00 3.53
4280 7509 7.614494 AGATGGAAGAAAAATATGTTGGTTGG 58.386 34.615 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.