Multiple sequence alignment - TraesCS7B01G028200

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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 TraesCS7B01G028200 chr7B 100.000 9297 0 0 1 9297 26756590 26747294 0.000000e+00 17169.0
1 TraesCS7B01G028200 chr7B 82.341 1025 138 30 2833 3836 26884465 26883463 0.000000e+00 850.0
2 TraesCS7B01G028200 chr7B 76.904 788 117 32 7534 8285 26878684 26877926 4.070000e-103 387.0
3 TraesCS7B01G028200 chr7B 77.121 660 114 22 5135 5786 26882439 26881809 1.920000e-91 348.0
4 TraesCS7B01G028200 chr7B 83.077 390 55 10 1592 1976 26885119 26884736 2.490000e-90 344.0
5 TraesCS7B01G028200 chr7B 84.416 308 43 4 4267 4570 26883443 26883137 1.960000e-76 298.0
6 TraesCS7B01G028200 chr7B 77.826 460 71 22 6059 6497 26881133 26880684 1.200000e-63 255.0
7 TraesCS7B01G028200 chr7D 95.045 6054 169 45 2660 8664 79547224 79541253 0.000000e+00 9396.0
8 TraesCS7B01G028200 chr7D 93.067 2553 88 44 138 2666 79549811 79547324 0.000000e+00 3651.0
9 TraesCS7B01G028200 chr7D 81.854 1025 143 31 2833 3836 79633461 79632459 0.000000e+00 822.0
10 TraesCS7B01G028200 chr7D 83.043 631 43 20 8664 9289 79541128 79540557 1.790000e-141 514.0
11 TraesCS7B01G028200 chr7D 77.820 789 109 33 7534 8285 79627868 79627109 2.400000e-115 427.0
12 TraesCS7B01G028200 chr7D 84.000 375 51 8 1592 1962 79634115 79633746 1.490000e-92 351.0
13 TraesCS7B01G028200 chr7D 76.935 672 113 26 5135 5795 79631354 79630714 2.490000e-90 344.0
14 TraesCS7B01G028200 chr7D 84.365 307 45 2 4267 4570 79632439 79632133 1.960000e-76 298.0
15 TraesCS7B01G028200 chr7D 86.275 204 23 3 6331 6533 79629665 79629466 5.650000e-52 217.0
16 TraesCS7B01G028200 chr7A 91.677 2535 117 43 7 2509 82208870 82206398 0.000000e+00 3426.0
17 TraesCS7B01G028200 chr7A 97.002 1968 48 6 2660 4623 82206170 82204210 0.000000e+00 3297.0
18 TraesCS7B01G028200 chr7A 90.735 1619 123 20 4927 6533 82198306 82196703 0.000000e+00 2134.0
19 TraesCS7B01G028200 chr7A 91.989 724 39 9 7944 8664 82194716 82194009 0.000000e+00 998.0
20 TraesCS7B01G028200 chr7A 82.049 1025 143 29 2832 3836 82513765 82512762 0.000000e+00 835.0
21 TraesCS7B01G028200 chr7A 89.449 635 40 12 8664 9279 82193879 82193253 0.000000e+00 776.0
22 TraesCS7B01G028200 chr7A 93.487 522 31 3 7352 7872 82195259 82194740 0.000000e+00 773.0
23 TraesCS7B01G028200 chr7A 93.296 358 21 3 6955 7310 82195619 82195263 8.270000e-145 525.0
24 TraesCS7B01G028200 chr7A 91.401 314 23 4 4624 4933 82204122 82203809 2.400000e-115 427.0
25 TraesCS7B01G028200 chr7A 87.062 371 31 8 6595 6956 82196075 82195713 4.040000e-108 403.0
26 TraesCS7B01G028200 chr7A 76.553 789 119 35 7534 8285 82507414 82506655 1.140000e-98 372.0
27 TraesCS7B01G028200 chr7A 83.590 390 54 9 1592 1976 82514421 82514037 3.190000e-94 357.0
28 TraesCS7B01G028200 chr7A 76.490 621 108 23 5186 5795 82511796 82511203 4.220000e-78 303.0
29 TraesCS7B01G028200 chr7A 83.442 308 43 6 4267 4570 82512742 82512439 7.110000e-71 279.0
30 TraesCS7B01G028200 chr7A 89.286 168 16 2 6331 6497 82509992 82509826 9.460000e-50 209.0
31 TraesCS7B01G028200 chr5A 85.588 1131 130 22 4523 5635 610213040 610214155 0.000000e+00 1155.0
32 TraesCS7B01G028200 chr4D 100.000 32 0 0 5688 5719 322855683 322855714 1.010000e-04 60.2
33 TraesCS7B01G028200 chr4B 100.000 32 0 0 5688 5719 398235546 398235515 1.010000e-04 60.2
34 TraesCS7B01G028200 chr4A 100.000 32 0 0 5688 5719 149651280 149651249 1.010000e-04 60.2


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 TraesCS7B01G028200 chr7B 26747294 26756590 9296 True 17169.000000 17169 100.000000 1 9297 1 chr7B.!!$R1 9296
1 TraesCS7B01G028200 chr7B 26877926 26885119 7193 True 413.666667 850 80.280833 1592 8285 6 chr7B.!!$R2 6693
2 TraesCS7B01G028200 chr7D 79540557 79549811 9254 True 4520.333333 9396 90.385000 138 9289 3 chr7D.!!$R1 9151
3 TraesCS7B01G028200 chr7D 79627109 79634115 7006 True 409.833333 822 81.874833 1592 8285 6 chr7D.!!$R2 6693
4 TraesCS7B01G028200 chr7A 82203809 82208870 5061 True 2383.333333 3426 93.360000 7 4933 3 chr7A.!!$R2 4926
5 TraesCS7B01G028200 chr7A 82193253 82198306 5053 True 934.833333 2134 91.003000 4927 9279 6 chr7A.!!$R1 4352
6 TraesCS7B01G028200 chr7A 82506655 82514421 7766 True 392.500000 835 81.901667 1592 8285 6 chr7A.!!$R3 6693
7 TraesCS7B01G028200 chr5A 610213040 610214155 1115 False 1155.000000 1155 85.588000 4523 5635 1 chr5A.!!$F1 1112

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
545 592 0.639756 TCGTTCGTTTTATACCGCGC 59.360 50.000 0.0 0.0 0.00 6.86 F
2380 2452 0.886490 ACAGCAGTAGTGTGCAAGGC 60.886 55.000 0.0 0.0 46.60 4.35 F
2580 2652 0.250901 AATCTTTGCGGGCACTCTGT 60.251 50.000 0.0 0.0 0.00 3.41 F
3864 4081 1.065199 CAGGCTCCTAAACCAGATGCA 60.065 52.381 0.0 0.0 0.00 3.96 F
4562 4782 1.700186 GAACAGGTTGGACCCTTCTCT 59.300 52.381 0.0 0.0 39.75 3.10 F
5153 5804 1.683943 ATTGTTGCTGCTCACAGTGT 58.316 45.000 0.0 0.0 46.30 3.55 F
6051 7317 2.439507 TCAGTTCTGAGTTGCTTTCCCT 59.560 45.455 0.0 0.0 0.00 4.20 F
7522 11295 1.341080 ATGCCTGGGTTCTGTTTTGG 58.659 50.000 0.0 0.0 0.00 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2501 2573 0.038251 CACGCTAACTGCACTCCAGA 60.038 55.000 0.00 0.0 44.64 3.86 R
3760 3977 2.997980 TGTCAGACAAGACAAGCCAAA 58.002 42.857 0.00 0.0 44.92 3.28 R
4251 4468 3.062099 CCTTGTGTCCATTTCGTGTATCG 59.938 47.826 0.00 0.0 41.41 2.92 R
5153 5804 3.459227 TGGATCCCAGATTAATGTGCTCA 59.541 43.478 9.90 0.0 0.00 4.26 R
6515 8271 3.210358 TGCAATTAACTACAAAGCCGC 57.790 42.857 0.00 0.0 0.00 6.53 R
6725 9107 2.284754 TGGAACAGCTTAATGCACCA 57.715 45.000 0.00 0.0 45.94 4.17 R
7887 11691 1.278985 CAGACCAGCATGTAACCCTGA 59.721 52.381 0.00 0.0 0.00 3.86 R
8814 12776 0.179034 GCCTCGGCAATCTCTCCAAT 60.179 55.000 2.41 0.0 41.49 3.16 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
43 44 2.594592 GTCCAGCACCACCACCAC 60.595 66.667 0.00 0.00 0.00 4.16
44 45 3.884774 TCCAGCACCACCACCACC 61.885 66.667 0.00 0.00 0.00 4.61
45 46 4.202574 CCAGCACCACCACCACCA 62.203 66.667 0.00 0.00 0.00 4.17
46 47 2.906897 CAGCACCACCACCACCAC 60.907 66.667 0.00 0.00 0.00 4.16
47 48 4.204028 AGCACCACCACCACCACC 62.204 66.667 0.00 0.00 0.00 4.61
51 52 2.281484 CCACCACCACCACCTTCG 60.281 66.667 0.00 0.00 0.00 3.79
88 89 4.180817 CCCGCATTTCAAAAACTAATCCC 58.819 43.478 0.00 0.00 0.00 3.85
89 90 4.180817 CCGCATTTCAAAAACTAATCCCC 58.819 43.478 0.00 0.00 0.00 4.81
90 91 4.081697 CCGCATTTCAAAAACTAATCCCCT 60.082 41.667 0.00 0.00 0.00 4.79
91 92 5.102313 CGCATTTCAAAAACTAATCCCCTC 58.898 41.667 0.00 0.00 0.00 4.30
92 93 5.419542 GCATTTCAAAAACTAATCCCCTCC 58.580 41.667 0.00 0.00 0.00 4.30
93 94 5.626809 GCATTTCAAAAACTAATCCCCTCCC 60.627 44.000 0.00 0.00 0.00 4.30
94 95 3.750501 TCAAAAACTAATCCCCTCCCC 57.249 47.619 0.00 0.00 0.00 4.81
95 96 3.274383 TCAAAAACTAATCCCCTCCCCT 58.726 45.455 0.00 0.00 0.00 4.79
106 107 4.548513 CTCCCCTCCTCTCCCCCG 62.549 77.778 0.00 0.00 0.00 5.73
387 422 1.696314 TCCCAGGTATGCCCTTCCC 60.696 63.158 0.00 0.00 42.73 3.97
463 498 2.377628 TTAGATCCGTCCATGGCGCC 62.378 60.000 22.73 22.73 0.00 6.53
530 577 0.680061 GGGTGGAGTCTGAGTTCGTT 59.320 55.000 0.00 0.00 0.00 3.85
545 592 0.639756 TCGTTCGTTTTATACCGCGC 59.360 50.000 0.00 0.00 0.00 6.86
580 633 2.434884 AGCATTCACGAGCCACCG 60.435 61.111 0.00 0.00 0.00 4.94
657 710 7.243487 TCATTTATTTTCGAGTGCAGTCATTC 58.757 34.615 21.15 0.00 0.00 2.67
817 870 1.844357 CAGTTAGTAATCACGACGCCG 59.156 52.381 0.00 0.00 42.50 6.46
867 920 9.476202 AAAATTTTGAGACCAACTAATTAGTGC 57.524 29.630 18.70 8.94 36.50 4.40
868 921 5.856126 TTTGAGACCAACTAATTAGTGCG 57.144 39.130 18.70 13.46 36.50 5.34
895 949 3.018423 AGTTGGTTGTCTTCTGGCTTT 57.982 42.857 0.00 0.00 0.00 3.51
900 954 4.072131 TGGTTGTCTTCTGGCTTTGATAC 58.928 43.478 0.00 0.00 0.00 2.24
1124 1188 5.409520 TGCTTTGAGATCACACATTCTGTAC 59.590 40.000 0.00 0.00 0.00 2.90
1436 1504 6.548321 ACTGTTATGTTGGGTGGAAATCTAA 58.452 36.000 0.00 0.00 0.00 2.10
1558 1626 1.004044 CATGCACTTCTCAACCTCCCT 59.996 52.381 0.00 0.00 0.00 4.20
1574 1642 1.600107 CCTAAACCCCTGCTGCGTA 59.400 57.895 0.00 0.00 0.00 4.42
1613 1682 5.605488 TCAGTAAGGTCTTGTAGGGTTTCTT 59.395 40.000 0.00 0.00 0.00 2.52
1614 1683 5.701290 CAGTAAGGTCTTGTAGGGTTTCTTG 59.299 44.000 0.00 0.00 0.00 3.02
1615 1684 5.605488 AGTAAGGTCTTGTAGGGTTTCTTGA 59.395 40.000 0.00 0.00 0.00 3.02
1616 1685 4.625607 AGGTCTTGTAGGGTTTCTTGAG 57.374 45.455 0.00 0.00 0.00 3.02
1617 1686 4.232091 AGGTCTTGTAGGGTTTCTTGAGA 58.768 43.478 0.00 0.00 0.00 3.27
1618 1687 4.040584 AGGTCTTGTAGGGTTTCTTGAGAC 59.959 45.833 0.00 0.00 0.00 3.36
1629 1698 6.437477 AGGGTTTCTTGAGACAAAGTTTTCTT 59.563 34.615 0.00 0.00 42.58 2.52
1972 2041 8.715191 TTCTTTGAAGCAATACATTTGTTGTT 57.285 26.923 0.00 0.00 39.87 2.83
2037 2106 6.423182 AGCAGCTTATGGTTTTAGGATACAA 58.577 36.000 0.00 0.00 35.67 2.41
2088 2157 4.561735 ACGGTTGGACACAATTTACTTG 57.438 40.909 0.00 0.00 39.13 3.16
2158 2229 3.583966 TCCGTTCCTATTTAGGTGGTGTT 59.416 43.478 3.62 0.00 44.02 3.32
2159 2230 3.937079 CCGTTCCTATTTAGGTGGTGTTC 59.063 47.826 3.62 0.00 44.02 3.18
2160 2231 4.323257 CCGTTCCTATTTAGGTGGTGTTCT 60.323 45.833 3.62 0.00 44.02 3.01
2161 2232 5.243207 CGTTCCTATTTAGGTGGTGTTCTT 58.757 41.667 3.62 0.00 44.02 2.52
2262 2333 8.410673 TCACTAATCTCTAATCGGCTCTTAAT 57.589 34.615 0.00 0.00 0.00 1.40
2280 2351 7.014038 GCTCTTAATCCATTGATCTCCACAATT 59.986 37.037 0.00 0.00 36.07 2.32
2287 2358 5.303589 CCATTGATCTCCACAATTTATGGCT 59.696 40.000 0.00 0.00 36.07 4.75
2317 2388 3.443045 CCCAGAACACATGCCCGC 61.443 66.667 0.00 0.00 0.00 6.13
2326 2397 1.210478 ACACATGCCCGCTATCTTCTT 59.790 47.619 0.00 0.00 0.00 2.52
2373 2445 2.440946 TGCAGGACAGCAGTAGTGT 58.559 52.632 0.00 0.00 40.11 3.55
2380 2452 0.886490 ACAGCAGTAGTGTGCAAGGC 60.886 55.000 0.00 0.00 46.60 4.35
2437 2509 4.431986 CGAATCTGTTTGCAATTTTCGCAG 60.432 41.667 0.00 2.98 41.18 5.18
2462 2534 2.289820 AGCGCGTTATGAATACGAGAGA 59.710 45.455 8.43 0.00 40.51 3.10
2467 2539 4.558898 GCGTTATGAATACGAGAGATGGGT 60.559 45.833 0.00 0.00 41.33 4.51
2471 2543 7.361799 CGTTATGAATACGAGAGATGGGTGATA 60.362 40.741 0.00 0.00 41.33 2.15
2501 2573 8.890718 CAGTTATGAGATGATGTGAACAAAGAT 58.109 33.333 0.00 0.00 0.00 2.40
2506 2578 6.058553 AGATGATGTGAACAAAGATCTGGA 57.941 37.500 0.00 0.00 0.00 3.86
2510 2582 3.141398 TGTGAACAAAGATCTGGAGTGC 58.859 45.455 0.00 0.00 0.00 4.40
2511 2583 3.141398 GTGAACAAAGATCTGGAGTGCA 58.859 45.455 0.00 0.00 0.00 4.57
2512 2584 3.188048 GTGAACAAAGATCTGGAGTGCAG 59.812 47.826 5.07 5.07 0.00 4.41
2513 2585 3.181451 TGAACAAAGATCTGGAGTGCAGT 60.181 43.478 11.78 0.00 0.00 4.40
2514 2586 3.498774 ACAAAGATCTGGAGTGCAGTT 57.501 42.857 11.78 2.92 0.00 3.16
2515 2587 4.623932 ACAAAGATCTGGAGTGCAGTTA 57.376 40.909 11.78 0.00 0.00 2.24
2516 2588 4.573900 ACAAAGATCTGGAGTGCAGTTAG 58.426 43.478 11.78 0.00 0.00 2.34
2517 2589 2.977772 AGATCTGGAGTGCAGTTAGC 57.022 50.000 11.78 0.00 45.96 3.09
2532 2604 5.657499 GCAGTTAGCGTGATAAATAAGACG 58.343 41.667 0.00 0.00 34.93 4.18
2533 2605 5.332355 GCAGTTAGCGTGATAAATAAGACGG 60.332 44.000 0.00 0.00 32.45 4.79
2534 2606 5.175126 CAGTTAGCGTGATAAATAAGACGGG 59.825 44.000 0.00 0.00 32.45 5.28
2535 2607 3.107642 AGCGTGATAAATAAGACGGGG 57.892 47.619 0.00 0.00 32.45 5.73
2536 2608 2.140717 GCGTGATAAATAAGACGGGGG 58.859 52.381 0.00 0.00 32.45 5.40
2537 2609 2.140717 CGTGATAAATAAGACGGGGGC 58.859 52.381 0.00 0.00 0.00 5.80
2538 2610 2.140717 GTGATAAATAAGACGGGGGCG 58.859 52.381 0.00 0.00 0.00 6.13
2542 2614 2.472414 AAATAAGACGGGGGCGTGCA 62.472 55.000 0.00 0.00 0.00 4.57
2546 2618 4.856801 GACGGGGGCGTGCATGAT 62.857 66.667 10.93 0.00 0.00 2.45
2580 2652 0.250901 AATCTTTGCGGGCACTCTGT 60.251 50.000 0.00 0.00 0.00 3.41
2607 2679 3.751479 AATCCTTGGTCTTGGCAAAAC 57.249 42.857 0.00 0.00 0.00 2.43
2734 2917 6.930164 TGCATTGCTTCACTTTATTTTCATGT 59.070 30.769 10.49 0.00 0.00 3.21
2735 2918 7.441760 TGCATTGCTTCACTTTATTTTCATGTT 59.558 29.630 10.49 0.00 0.00 2.71
2736 2919 8.284693 GCATTGCTTCACTTTATTTTCATGTTT 58.715 29.630 0.16 0.00 0.00 2.83
2737 2920 9.801714 CATTGCTTCACTTTATTTTCATGTTTC 57.198 29.630 0.00 0.00 0.00 2.78
2738 2921 8.939201 TTGCTTCACTTTATTTTCATGTTTCA 57.061 26.923 0.00 0.00 0.00 2.69
2739 2922 9.545105 TTGCTTCACTTTATTTTCATGTTTCAT 57.455 25.926 0.00 0.00 0.00 2.57
2740 2923 8.980610 TGCTTCACTTTATTTTCATGTTTCATG 58.019 29.630 3.65 3.65 0.00 3.07
2813 2997 2.366533 TCTACCTAAGGTGAGACTGCG 58.633 52.381 0.00 0.00 36.19 5.18
2830 3014 6.149633 AGACTGCGAAATGTTTAATTGGTTC 58.850 36.000 0.00 0.00 0.00 3.62
2877 3078 4.505808 GACCTCCAGAAAAGTAGGCTTAC 58.494 47.826 0.00 0.00 33.95 2.34
2921 3126 4.447724 TGCTTTGTTTCTAGCGTACTCTTG 59.552 41.667 0.00 0.00 40.26 3.02
2969 3175 4.444720 GTTGTCCAACTATATCTGCGTAGC 59.555 45.833 2.95 0.00 46.08 3.58
3259 3471 3.066380 CCATTTGGGCTTTTCCTTTTCG 58.934 45.455 0.00 0.00 34.39 3.46
3344 3557 4.316025 TCCTAAATGGGGAGAAAACTGG 57.684 45.455 0.00 0.00 36.20 4.00
3361 3574 4.808767 ACTGGGGGTTCTCTTAAAAAGT 57.191 40.909 0.00 0.00 0.00 2.66
3864 4081 1.065199 CAGGCTCCTAAACCAGATGCA 60.065 52.381 0.00 0.00 0.00 3.96
3867 4084 1.745653 GCTCCTAAACCAGATGCAACC 59.254 52.381 0.00 0.00 0.00 3.77
4078 4295 5.129634 TGAGCACTAAATCTCCACAACAAA 58.870 37.500 0.00 0.00 0.00 2.83
4251 4468 4.133078 CAAGGGACATGAAGCTTAGATCC 58.867 47.826 0.00 4.43 0.00 3.36
4433 4650 3.382546 GCAACAGATGGCCATGATAGTTT 59.617 43.478 26.56 4.36 0.00 2.66
4455 4675 8.492782 AGTTTGATGATAGAAGATGTTGAGGAT 58.507 33.333 0.00 0.00 0.00 3.24
4562 4782 1.700186 GAACAGGTTGGACCCTTCTCT 59.300 52.381 0.00 0.00 39.75 3.10
4734 5300 6.096141 TGAATTGTTTTAAACTCTGCCACTCA 59.904 34.615 9.33 0.00 0.00 3.41
4843 5426 4.532126 TCTCACCATCTTACAAGTGTGGAT 59.468 41.667 17.17 0.00 36.81 3.41
4936 5527 9.672673 CCATCCCCTCAAAACTATATATTACAG 57.327 37.037 0.00 0.00 0.00 2.74
4958 5569 8.862325 ACAGACATATTTTCCACTAATGACAA 57.138 30.769 0.00 0.00 0.00 3.18
5029 5640 7.500141 AGTTTAAAATGTGAACTGCAAGGATT 58.500 30.769 0.00 0.00 39.30 3.01
5056 5668 7.202526 CACCACCACTTATATTTTTAGGCATG 58.797 38.462 0.00 0.00 0.00 4.06
5153 5804 1.683943 ATTGTTGCTGCTCACAGTGT 58.316 45.000 0.00 0.00 46.30 3.55
5172 5823 4.202441 GTGTGAGCACATTAATCTGGGAT 58.798 43.478 6.59 0.00 43.97 3.85
5771 6427 9.922305 CTTGCACTATTATAGCAAAAGTTCTAC 57.078 33.333 0.00 0.00 46.30 2.59
5778 6434 8.712285 ATTATAGCAAAAGTTCTACGCAACTA 57.288 30.769 0.00 0.00 35.45 2.24
6051 7317 2.439507 TCAGTTCTGAGTTGCTTTCCCT 59.560 45.455 0.00 0.00 0.00 4.20
6114 7380 8.506168 TCGAAGCTAGTATTGGATTCAAAAAT 57.494 30.769 0.00 0.00 36.36 1.82
6515 8271 8.474006 TTTGCAAAATCTGATCAATCATTGAG 57.526 30.769 10.02 0.00 43.98 3.02
6703 9085 6.361748 GCTTGAAATGTTGTTGTCTCATCTTC 59.638 38.462 0.00 0.00 0.00 2.87
6736 9446 7.707464 TGCAGAATAAATCATTGGTGCATTAAG 59.293 33.333 0.00 0.00 37.87 1.85
6816 9526 3.932710 GAGGCGATAATTATGAATGCCGA 59.067 43.478 1.78 0.00 45.44 5.54
6855 9565 9.594478 CTTCTTAAACAACAACAAAGGGTAAAT 57.406 29.630 0.00 0.00 0.00 1.40
6945 9657 4.952071 TGATGATTTCTTTGGTTGGCAA 57.048 36.364 0.00 0.00 0.00 4.52
6946 9658 4.630111 TGATGATTTCTTTGGTTGGCAAC 58.370 39.130 21.92 21.92 0.00 4.17
6948 9660 4.057406 TGATTTCTTTGGTTGGCAACTG 57.943 40.909 27.77 15.99 37.61 3.16
6949 9661 3.450457 TGATTTCTTTGGTTGGCAACTGT 59.550 39.130 27.77 7.09 37.61 3.55
6950 9662 3.518634 TTTCTTTGGTTGGCAACTGTC 57.481 42.857 27.77 13.46 37.61 3.51
6952 9664 2.665165 TCTTTGGTTGGCAACTGTCAT 58.335 42.857 27.77 0.00 37.61 3.06
6953 9665 2.622942 TCTTTGGTTGGCAACTGTCATC 59.377 45.455 27.77 12.06 37.61 2.92
7126 10156 9.196552 AGCAATAATTTAAAACTTCTGAGCAAC 57.803 29.630 0.00 0.00 0.00 4.17
7128 10158 9.393249 CAATAATTTAAAACTTCTGAGCAACGA 57.607 29.630 0.00 0.00 0.00 3.85
7198 10886 5.793026 TGATTTTGATTTAAATTGGGCGC 57.207 34.783 0.00 0.00 0.00 6.53
7263 10989 8.219105 GCACATCATTTTTCTTCTGAAATCAAC 58.781 33.333 0.00 0.00 41.24 3.18
7343 11070 4.376413 GCATTAACAGATATCGAGGCAACG 60.376 45.833 0.00 0.00 46.39 4.10
7344 11071 4.642445 TTAACAGATATCGAGGCAACGA 57.358 40.909 8.96 8.96 46.04 3.85
7350 11077 3.561429 TCGAGGCAACGATGTTGC 58.439 55.556 22.75 22.75 44.22 4.17
7461 11189 5.767665 TGACACAACACATAAAATAGCTGGT 59.232 36.000 0.00 0.00 0.00 4.00
7462 11190 6.937465 TGACACAACACATAAAATAGCTGGTA 59.063 34.615 0.00 0.00 0.00 3.25
7463 11191 7.445707 TGACACAACACATAAAATAGCTGGTAA 59.554 33.333 0.00 0.00 0.00 2.85
7464 11192 8.172352 ACACAACACATAAAATAGCTGGTAAA 57.828 30.769 0.00 0.00 0.00 2.01
7465 11193 8.634444 ACACAACACATAAAATAGCTGGTAAAA 58.366 29.630 0.00 0.00 0.00 1.52
7466 11194 9.128107 CACAACACATAAAATAGCTGGTAAAAG 57.872 33.333 0.00 0.00 0.00 2.27
7467 11195 9.073475 ACAACACATAAAATAGCTGGTAAAAGA 57.927 29.630 0.00 0.00 0.00 2.52
7468 11196 9.341899 CAACACATAAAATAGCTGGTAAAAGAC 57.658 33.333 0.00 0.00 0.00 3.01
7469 11197 8.630054 ACACATAAAATAGCTGGTAAAAGACA 57.370 30.769 0.00 0.00 0.00 3.41
7470 11198 9.243105 ACACATAAAATAGCTGGTAAAAGACAT 57.757 29.630 0.00 0.00 0.00 3.06
7471 11199 9.507280 CACATAAAATAGCTGGTAAAAGACATG 57.493 33.333 0.00 0.00 0.00 3.21
7472 11200 8.190784 ACATAAAATAGCTGGTAAAAGACATGC 58.809 33.333 0.00 0.00 0.00 4.06
7473 11201 6.840780 AAAATAGCTGGTAAAAGACATGCT 57.159 33.333 0.00 0.00 40.04 3.79
7474 11202 6.840780 AAATAGCTGGTAAAAGACATGCTT 57.159 33.333 0.00 0.00 38.52 3.91
7475 11203 6.442513 AATAGCTGGTAAAAGACATGCTTC 57.557 37.500 0.00 0.00 38.52 3.86
7476 11204 4.026356 AGCTGGTAAAAGACATGCTTCT 57.974 40.909 0.00 0.00 35.47 2.85
7477 11205 4.006319 AGCTGGTAAAAGACATGCTTCTC 58.994 43.478 0.00 0.00 35.47 2.87
7478 11206 3.181516 GCTGGTAAAAGACATGCTTCTCG 60.182 47.826 0.00 0.00 35.24 4.04
7479 11207 4.245660 CTGGTAAAAGACATGCTTCTCGA 58.754 43.478 0.00 0.00 35.24 4.04
7485 11213 7.905493 GGTAAAAGACATGCTTCTCGATAAAAG 59.095 37.037 0.00 0.00 35.24 2.27
7488 11216 5.971763 AGACATGCTTCTCGATAAAAGACT 58.028 37.500 0.00 0.00 0.00 3.24
7522 11295 1.341080 ATGCCTGGGTTCTGTTTTGG 58.659 50.000 0.00 0.00 0.00 3.28
7584 11371 5.118729 TGTTTTCAGGTCTTACTTGGGAA 57.881 39.130 0.00 0.00 0.00 3.97
7628 11415 5.649831 GGAGCATTTCTCAAGGTAAGATTGT 59.350 40.000 0.00 0.00 43.70 2.71
7784 11586 7.493971 GCAGATAAGCGTGGAAAGATATATGAT 59.506 37.037 0.00 0.00 0.00 2.45
7871 11675 7.016153 ACAGTATTCTCAACATTCAGGGTTA 57.984 36.000 0.00 0.00 0.00 2.85
7872 11676 6.879458 ACAGTATTCTCAACATTCAGGGTTAC 59.121 38.462 0.00 0.00 0.00 2.50
7873 11677 6.878923 CAGTATTCTCAACATTCAGGGTTACA 59.121 38.462 0.00 0.00 0.00 2.41
7874 11678 7.065085 CAGTATTCTCAACATTCAGGGTTACAG 59.935 40.741 0.00 0.00 0.00 2.74
7875 11679 4.974645 TCTCAACATTCAGGGTTACAGT 57.025 40.909 0.00 0.00 0.00 3.55
7876 11680 4.894784 TCTCAACATTCAGGGTTACAGTC 58.105 43.478 0.00 0.00 0.00 3.51
7877 11681 4.593206 TCTCAACATTCAGGGTTACAGTCT 59.407 41.667 0.00 0.00 0.00 3.24
7878 11682 5.071788 TCTCAACATTCAGGGTTACAGTCTT 59.928 40.000 0.00 0.00 0.00 3.01
7879 11683 5.305585 TCAACATTCAGGGTTACAGTCTTC 58.694 41.667 0.00 0.00 0.00 2.87
7880 11684 5.071788 TCAACATTCAGGGTTACAGTCTTCT 59.928 40.000 0.00 0.00 0.00 2.85
7881 11685 5.153950 ACATTCAGGGTTACAGTCTTCTC 57.846 43.478 0.00 0.00 0.00 2.87
7882 11686 4.593206 ACATTCAGGGTTACAGTCTTCTCA 59.407 41.667 0.00 0.00 0.00 3.27
7883 11687 5.071788 ACATTCAGGGTTACAGTCTTCTCAA 59.928 40.000 0.00 0.00 0.00 3.02
7884 11688 4.602340 TCAGGGTTACAGTCTTCTCAAC 57.398 45.455 0.00 0.00 0.00 3.18
7885 11689 3.964688 TCAGGGTTACAGTCTTCTCAACA 59.035 43.478 0.00 0.00 0.00 3.33
7886 11690 4.593206 TCAGGGTTACAGTCTTCTCAACAT 59.407 41.667 0.00 0.00 0.00 2.71
7887 11691 5.071788 TCAGGGTTACAGTCTTCTCAACATT 59.928 40.000 0.00 0.00 0.00 2.71
7888 11692 5.409826 CAGGGTTACAGTCTTCTCAACATTC 59.590 44.000 0.00 0.00 0.00 2.67
7889 11693 5.071788 AGGGTTACAGTCTTCTCAACATTCA 59.928 40.000 0.00 0.00 0.00 2.57
7890 11694 5.409826 GGGTTACAGTCTTCTCAACATTCAG 59.590 44.000 0.00 0.00 0.00 3.02
7891 11695 5.409826 GGTTACAGTCTTCTCAACATTCAGG 59.590 44.000 0.00 0.00 0.00 3.86
7892 11696 4.013267 ACAGTCTTCTCAACATTCAGGG 57.987 45.455 0.00 0.00 0.00 4.45
7893 11697 3.392616 ACAGTCTTCTCAACATTCAGGGT 59.607 43.478 0.00 0.00 0.00 4.34
7894 11698 4.141390 ACAGTCTTCTCAACATTCAGGGTT 60.141 41.667 0.00 0.00 0.00 4.11
7904 11708 2.041620 ACATTCAGGGTTACATGCTGGT 59.958 45.455 0.00 0.00 0.00 4.00
7998 11814 2.325583 TTACATCTGATCCAACCGCC 57.674 50.000 0.00 0.00 0.00 6.13
8017 11837 2.479901 GCCGTTGCCTTACTCTACTCTC 60.480 54.545 0.00 0.00 0.00 3.20
8053 11873 1.213678 CTGGATGCCTTCAGAATGGGA 59.786 52.381 0.00 0.00 36.16 4.37
8062 11882 3.560882 CCTTCAGAATGGGAGACAAGCTT 60.561 47.826 0.00 0.00 36.16 3.74
8194 12014 7.122715 AGGAGATCTTCTATGATTACCGCTAT 58.877 38.462 0.02 0.00 32.00 2.97
8304 12127 0.389166 CTCGCCCACTGAAGAGACAC 60.389 60.000 0.00 0.00 32.84 3.67
8305 12128 1.734477 CGCCCACTGAAGAGACACG 60.734 63.158 0.00 0.00 0.00 4.49
8454 12277 0.320374 GTGTCGGAACCTGTGGATGA 59.680 55.000 0.00 0.00 0.00 2.92
8530 12355 0.534873 GCCTTTGGTGGTGTGTTTGT 59.465 50.000 0.00 0.00 0.00 2.83
8531 12356 1.066502 GCCTTTGGTGGTGTGTTTGTT 60.067 47.619 0.00 0.00 0.00 2.83
8532 12357 2.614229 GCCTTTGGTGGTGTGTTTGTTT 60.614 45.455 0.00 0.00 0.00 2.83
8533 12358 2.999355 CCTTTGGTGGTGTGTTTGTTTG 59.001 45.455 0.00 0.00 0.00 2.93
8593 12418 1.771565 CTGCATGGGTTGATCATGGT 58.228 50.000 0.00 0.00 41.49 3.55
8602 12427 3.561313 GGGTTGATCATGGTACCACAACT 60.561 47.826 30.10 11.85 38.02 3.16
8626 12451 0.730265 TGCGAGCGACTTGTTTGTTT 59.270 45.000 0.00 0.00 0.00 2.83
8639 12464 2.093288 TGTTTGTTTGAGCAATGCCCAA 60.093 40.909 0.00 0.00 0.00 4.12
8644 12469 0.749649 TTGAGCAATGCCCAACGTTT 59.250 45.000 0.00 0.00 0.00 3.60
8646 12471 1.269517 TGAGCAATGCCCAACGTTTTC 60.270 47.619 0.00 0.00 0.00 2.29
8661 12618 1.859080 GTTTTCGTTCGCAGACTCACT 59.141 47.619 0.00 0.00 34.32 3.41
8662 12619 5.678428 CGTTTTCGTTCGCAGACTCACTG 62.678 52.174 0.00 0.00 42.64 3.66
8687 12645 5.088739 GGAAAACAGAAGATGCAACATACG 58.911 41.667 0.00 0.00 0.00 3.06
8723 12685 0.451383 TCACAATATGCAAGCGCCAC 59.549 50.000 2.29 0.00 37.32 5.01
8765 12727 7.172875 CCAGCCTGAGAATCTTAATCATGTTAG 59.827 40.741 0.00 0.00 34.92 2.34
8814 12776 4.487714 ACACAAAGAACTCAAGGTCAGA 57.512 40.909 0.00 0.00 0.00 3.27
8858 12820 1.280133 CATTCCTCCTGCTCCAACTCA 59.720 52.381 0.00 0.00 0.00 3.41
8873 12835 3.985925 CCAACTCAAGCAAGAAATGAAGC 59.014 43.478 0.00 0.00 0.00 3.86
8903 12865 6.463995 TTGCTCTTGTTGAAAATTACACCT 57.536 33.333 0.00 0.00 0.00 4.00
8904 12866 5.830912 TGCTCTTGTTGAAAATTACACCTG 58.169 37.500 0.00 0.00 0.00 4.00
8906 12868 5.915196 GCTCTTGTTGAAAATTACACCTGAC 59.085 40.000 0.00 0.00 0.00 3.51
8907 12869 6.385649 TCTTGTTGAAAATTACACCTGACC 57.614 37.500 0.00 0.00 0.00 4.02
9050 13015 4.022589 CACTGCAATGGGATGCCTAATTAG 60.023 45.833 4.35 5.43 45.83 1.73
9086 13051 3.375299 CCTCGGTAGAAAAGAAATGGCAG 59.625 47.826 0.00 0.00 0.00 4.85
9122 13087 1.481363 CTCCTCTCAAGAGCAGCATCA 59.519 52.381 1.28 0.00 40.75 3.07
9142 13107 3.041211 CACTGGAACCATGATCCCTCTA 58.959 50.000 13.12 0.00 36.04 2.43
9189 13170 0.800631 GCGGTTGGTAACTTGGTAGC 59.199 55.000 0.00 0.00 37.61 3.58
9202 13183 0.543277 TGGTAGCAGCCATCTCCAAG 59.457 55.000 0.00 0.00 32.81 3.61
9203 13184 0.179034 GGTAGCAGCCATCTCCAAGG 60.179 60.000 0.00 0.00 0.00 3.61
9208 13189 2.105766 GCAGCCATCTCCAAGGAAAAT 58.894 47.619 0.00 0.00 0.00 1.82
9240 13221 2.045524 CACATCTAGCAGACCCTGGAT 58.954 52.381 0.00 0.00 33.89 3.41
9254 13235 2.749621 CCCTGGATGTTAAGAGCAACAC 59.250 50.000 0.00 0.00 41.02 3.32
9255 13236 3.411446 CCTGGATGTTAAGAGCAACACA 58.589 45.455 0.00 0.00 41.02 3.72
9257 13238 4.278170 CCTGGATGTTAAGAGCAACACAAA 59.722 41.667 0.00 0.00 41.02 2.83
9263 13244 5.280945 TGTTAAGAGCAACACAAAATCAGC 58.719 37.500 0.00 0.00 33.55 4.26
9264 13245 5.163571 TGTTAAGAGCAACACAAAATCAGCA 60.164 36.000 0.00 0.00 33.55 4.41
9267 13248 5.051891 AGAGCAACACAAAATCAGCATAC 57.948 39.130 0.00 0.00 0.00 2.39
9270 13251 5.224888 AGCAACACAAAATCAGCATACAAG 58.775 37.500 0.00 0.00 0.00 3.16
9276 13257 6.919662 ACACAAAATCAGCATACAAGTTTCAG 59.080 34.615 0.00 0.00 0.00 3.02
9280 13261 3.674997 TCAGCATACAAGTTTCAGACCC 58.325 45.455 0.00 0.00 0.00 4.46
9281 13262 3.072330 TCAGCATACAAGTTTCAGACCCA 59.928 43.478 0.00 0.00 0.00 4.51
9283 13264 3.821033 AGCATACAAGTTTCAGACCCAAC 59.179 43.478 0.00 0.00 0.00 3.77
9284 13265 3.568007 GCATACAAGTTTCAGACCCAACA 59.432 43.478 0.00 0.00 0.00 3.33
9285 13266 4.218417 GCATACAAGTTTCAGACCCAACAT 59.782 41.667 0.00 0.00 0.00 2.71
9286 13267 5.702865 CATACAAGTTTCAGACCCAACATG 58.297 41.667 0.00 0.00 0.00 3.21
9296 13277 4.213630 CCAACATGGGGTTTGCCT 57.786 55.556 0.00 0.00 37.72 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 4.204028 GGTGGTGGTGGTGGTGCT 62.204 66.667 0.00 0.00 0.00 4.40
43 44 3.330720 AGGGGGAAGCGAAGGTGG 61.331 66.667 0.00 0.00 39.47 4.61
44 45 2.269241 GAGGGGGAAGCGAAGGTG 59.731 66.667 0.00 0.00 39.47 4.00
45 46 3.009714 GGAGGGGGAAGCGAAGGT 61.010 66.667 0.00 0.00 44.60 3.50
46 47 3.798511 GGGAGGGGGAAGCGAAGG 61.799 72.222 0.00 0.00 0.00 3.46
47 48 2.689034 AGGGAGGGGGAAGCGAAG 60.689 66.667 0.00 0.00 0.00 3.79
88 89 4.179599 GGGGGAGAGGAGGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
89 90 4.548513 CGGGGGAGAGGAGGGGAG 62.549 77.778 0.00 0.00 0.00 4.30
91 92 4.862823 GACGGGGGAGAGGAGGGG 62.863 77.778 0.00 0.00 0.00 4.79
92 93 3.742248 GAGACGGGGGAGAGGAGGG 62.742 73.684 0.00 0.00 0.00 4.30
93 94 2.123640 GAGACGGGGGAGAGGAGG 60.124 72.222 0.00 0.00 0.00 4.30
94 95 2.517402 CGAGACGGGGGAGAGGAG 60.517 72.222 0.00 0.00 0.00 3.69
95 96 3.336568 ACGAGACGGGGGAGAGGA 61.337 66.667 0.00 0.00 0.00 3.71
106 107 1.950909 CAGGGAGATAGGTCACGAGAC 59.049 57.143 4.21 4.21 44.21 3.36
209 210 3.024356 AGCGGAGGAGGAGGAGGA 61.024 66.667 0.00 0.00 0.00 3.71
444 479 1.069090 GCGCCATGGACGGATCTAA 59.931 57.895 18.40 0.00 0.00 2.10
495 542 2.742372 CCGTTTCAGGCCGTCAGG 60.742 66.667 0.00 0.00 41.62 3.86
530 577 2.187707 GAGAAGCGCGGTATAAAACGA 58.812 47.619 12.91 0.00 0.00 3.85
545 592 3.904717 TGCTCCTACTAGAAGGGAGAAG 58.095 50.000 23.78 8.28 46.82 2.85
580 633 0.827368 TGACAAAAACCCAACAGGCC 59.173 50.000 0.00 0.00 40.58 5.19
582 635 2.433970 ACCATGACAAAAACCCAACAGG 59.566 45.455 0.00 0.00 43.78 4.00
583 636 3.492482 GGACCATGACAAAAACCCAACAG 60.492 47.826 0.00 0.00 0.00 3.16
584 637 2.432510 GGACCATGACAAAAACCCAACA 59.567 45.455 0.00 0.00 0.00 3.33
585 638 2.544903 CGGACCATGACAAAAACCCAAC 60.545 50.000 0.00 0.00 0.00 3.77
586 639 1.683917 CGGACCATGACAAAAACCCAA 59.316 47.619 0.00 0.00 0.00 4.12
588 641 0.038618 GCGGACCATGACAAAAACCC 60.039 55.000 0.00 0.00 0.00 4.11
589 642 0.038618 GGCGGACCATGACAAAAACC 60.039 55.000 0.00 0.00 35.26 3.27
590 643 0.038618 GGGCGGACCATGACAAAAAC 60.039 55.000 0.00 0.00 39.85 2.43
678 731 2.309528 AGCGTCCAATATTTCTGCGA 57.690 45.000 0.00 0.00 0.00 5.10
770 823 5.983720 AGCGAATAATGATACTGTACACCAC 59.016 40.000 0.00 0.00 0.00 4.16
790 843 5.327091 GTCGTGATTACTAACTGTAAGCGA 58.673 41.667 0.00 0.00 46.95 4.93
817 870 7.038154 TCAGGCATAATGTTAGGCATAAAAC 57.962 36.000 10.97 0.00 41.81 2.43
867 920 4.058817 AGAAGACAACCAACTTTAGAGCG 58.941 43.478 0.00 0.00 0.00 5.03
868 921 4.214332 CCAGAAGACAACCAACTTTAGAGC 59.786 45.833 0.00 0.00 0.00 4.09
895 949 9.613428 CTGTATGATTGAAGGGTAAAAGTATCA 57.387 33.333 0.00 0.00 0.00 2.15
900 954 8.562892 CATAGCTGTATGATTGAAGGGTAAAAG 58.437 37.037 0.00 0.00 38.76 2.27
1436 1504 3.077359 GCCTAGTGACATTCTTTGCAGT 58.923 45.455 0.00 0.00 0.00 4.40
1525 1593 6.149308 TGAGAAGTGCATGTGGTTATAAACAG 59.851 38.462 2.67 0.00 0.00 3.16
1526 1594 6.000840 TGAGAAGTGCATGTGGTTATAAACA 58.999 36.000 0.00 0.00 0.00 2.83
1527 1595 6.494893 TGAGAAGTGCATGTGGTTATAAAC 57.505 37.500 0.00 0.00 0.00 2.01
1528 1596 6.072175 GGTTGAGAAGTGCATGTGGTTATAAA 60.072 38.462 0.00 0.00 0.00 1.40
1558 1626 0.397187 TTGTACGCAGCAGGGGTTTA 59.603 50.000 3.55 0.00 43.28 2.01
1601 1669 5.367945 ACTTTGTCTCAAGAAACCCTACA 57.632 39.130 0.00 0.00 0.00 2.74
1613 1682 3.976015 ACCCCAAGAAAACTTTGTCTCA 58.024 40.909 0.00 0.00 0.00 3.27
1614 1683 5.105513 TGAAACCCCAAGAAAACTTTGTCTC 60.106 40.000 0.00 0.00 0.00 3.36
1615 1684 4.775253 TGAAACCCCAAGAAAACTTTGTCT 59.225 37.500 0.00 0.00 0.00 3.41
1616 1685 5.079689 TGAAACCCCAAGAAAACTTTGTC 57.920 39.130 0.00 0.00 0.00 3.18
1617 1686 5.427378 CATGAAACCCCAAGAAAACTTTGT 58.573 37.500 0.00 0.00 0.00 2.83
1618 1687 4.273235 GCATGAAACCCCAAGAAAACTTTG 59.727 41.667 0.00 0.00 0.00 2.77
1629 1698 0.541764 GGTTCCTGCATGAAACCCCA 60.542 55.000 8.45 0.00 0.00 4.96
1972 2041 4.818546 TGGTTCCCGTACGAAAATACAAAA 59.181 37.500 18.76 0.00 0.00 2.44
2000 2069 5.106396 CCATAAGCTGCTTGTATCCTAATGC 60.106 44.000 24.35 0.00 0.00 3.56
2262 2333 5.302568 GCCATAAATTGTGGAGATCAATGGA 59.697 40.000 13.12 0.00 39.12 3.41
2287 2358 6.422344 TGTGTTCTGGGTGTATTTAGTACA 57.578 37.500 0.00 0.00 40.93 2.90
2317 2388 8.267894 TGGATAAAGGAGGAACAAAGAAGATAG 58.732 37.037 0.00 0.00 0.00 2.08
2326 2397 4.837093 ATCGTGGATAAAGGAGGAACAA 57.163 40.909 0.00 0.00 0.00 2.83
2373 2445 0.397564 TCTCACACATCAGCCTTGCA 59.602 50.000 0.00 0.00 0.00 4.08
2380 2452 5.579564 TCTCTCTTGATCTCACACATCAG 57.420 43.478 0.00 0.00 31.84 2.90
2437 2509 3.495193 TCGTATTCATAACGCGCTATCC 58.505 45.455 5.73 0.00 40.12 2.59
2462 2534 4.655649 TCTCATAACTGCACTATCACCCAT 59.344 41.667 0.00 0.00 0.00 4.00
2467 2539 6.927381 CACATCATCTCATAACTGCACTATCA 59.073 38.462 0.00 0.00 0.00 2.15
2471 2543 5.349061 TCACATCATCTCATAACTGCACT 57.651 39.130 0.00 0.00 0.00 4.40
2501 2573 0.038251 CACGCTAACTGCACTCCAGA 60.038 55.000 0.00 0.00 44.64 3.86
2506 2578 6.255887 GTCTTATTTATCACGCTAACTGCACT 59.744 38.462 0.00 0.00 43.06 4.40
2510 2582 5.175126 CCCGTCTTATTTATCACGCTAACTG 59.825 44.000 0.00 0.00 0.00 3.16
2511 2583 5.287226 CCCGTCTTATTTATCACGCTAACT 58.713 41.667 0.00 0.00 0.00 2.24
2512 2584 4.446719 CCCCGTCTTATTTATCACGCTAAC 59.553 45.833 0.00 0.00 0.00 2.34
2513 2585 4.501915 CCCCCGTCTTATTTATCACGCTAA 60.502 45.833 0.00 0.00 0.00 3.09
2514 2586 3.006110 CCCCCGTCTTATTTATCACGCTA 59.994 47.826 0.00 0.00 0.00 4.26
2515 2587 2.224209 CCCCCGTCTTATTTATCACGCT 60.224 50.000 0.00 0.00 0.00 5.07
2516 2588 2.140717 CCCCCGTCTTATTTATCACGC 58.859 52.381 0.00 0.00 0.00 5.34
2517 2589 2.140717 GCCCCCGTCTTATTTATCACG 58.859 52.381 0.00 0.00 0.00 4.35
2518 2590 2.140717 CGCCCCCGTCTTATTTATCAC 58.859 52.381 0.00 0.00 0.00 3.06
2519 2591 1.764134 ACGCCCCCGTCTTATTTATCA 59.236 47.619 0.00 0.00 46.39 2.15
2520 2592 2.140717 CACGCCCCCGTCTTATTTATC 58.859 52.381 0.00 0.00 46.39 1.75
2521 2593 1.812708 GCACGCCCCCGTCTTATTTAT 60.813 52.381 0.00 0.00 46.39 1.40
2522 2594 0.462403 GCACGCCCCCGTCTTATTTA 60.462 55.000 0.00 0.00 46.39 1.40
2523 2595 1.747745 GCACGCCCCCGTCTTATTT 60.748 57.895 0.00 0.00 46.39 1.40
2524 2596 2.124860 GCACGCCCCCGTCTTATT 60.125 61.111 0.00 0.00 46.39 1.40
2525 2597 2.742116 ATGCACGCCCCCGTCTTAT 61.742 57.895 0.00 0.00 46.39 1.73
2526 2598 3.395702 ATGCACGCCCCCGTCTTA 61.396 61.111 0.00 0.00 46.39 2.10
2529 2601 4.856801 ATCATGCACGCCCCCGTC 62.857 66.667 0.00 0.00 46.39 4.79
2532 2604 2.902423 TTACCATCATGCACGCCCCC 62.902 60.000 0.00 0.00 0.00 5.40
2533 2605 1.034838 TTTACCATCATGCACGCCCC 61.035 55.000 0.00 0.00 0.00 5.80
2534 2606 0.814457 TTTTACCATCATGCACGCCC 59.186 50.000 0.00 0.00 0.00 6.13
2535 2607 2.098934 TCATTTTACCATCATGCACGCC 59.901 45.455 0.00 0.00 0.00 5.68
2536 2608 3.108144 GTCATTTTACCATCATGCACGC 58.892 45.455 0.00 0.00 0.00 5.34
2537 2609 3.128415 TGGTCATTTTACCATCATGCACG 59.872 43.478 0.00 0.00 44.68 5.34
2538 2610 4.717233 TGGTCATTTTACCATCATGCAC 57.283 40.909 0.00 0.00 44.68 4.57
2580 2652 2.517959 CAAGACCAAGGATTTCCAGCA 58.482 47.619 0.00 0.00 38.89 4.41
2607 2679 1.384525 TTTCGGTGGTGTGTTTCCAG 58.615 50.000 0.00 0.00 35.49 3.86
2754 2937 9.295825 AGACACAAAAGTGGTATTGAATTATCA 57.704 29.630 0.38 0.00 0.00 2.15
2830 3014 5.950758 AGCTAGTCTAGTCCGATTATGTG 57.049 43.478 8.68 0.00 0.00 3.21
2877 3078 3.840890 TGCAGCCCATTTTAAGTAACG 57.159 42.857 0.00 0.00 0.00 3.18
2921 3126 8.793592 ACATAAACTCCACATTAAAGTTCCTTC 58.206 33.333 0.00 0.00 32.24 3.46
2969 3175 4.389374 AGGTGTGTAAACTCATCAACAGG 58.611 43.478 0.00 0.00 0.00 4.00
3259 3471 5.927030 TGTCAATAGCGAAAATGTGAACTC 58.073 37.500 0.00 0.00 0.00 3.01
3344 3557 7.342769 TCAGAAAACTTTTTAAGAGAACCCC 57.657 36.000 0.00 0.00 0.00 4.95
3361 3574 6.097554 TCCACTTTGGCATTAAGTTCAGAAAA 59.902 34.615 1.86 0.00 37.47 2.29
3680 3895 4.456911 GGTATACCATCATCCATGCTGTTG 59.543 45.833 17.44 0.00 35.64 3.33
3760 3977 2.997980 TGTCAGACAAGACAAGCCAAA 58.002 42.857 0.00 0.00 44.92 3.28
3864 4081 3.214328 GTCAGAATCAACTGTGGTGGTT 58.786 45.455 0.00 0.00 38.79 3.67
3867 4084 3.365666 GCATGTCAGAATCAACTGTGGTG 60.366 47.826 0.00 0.00 38.79 4.17
4078 4295 9.603921 AATTTTGACTTTTGATTGACAAGATGT 57.396 25.926 0.00 0.00 39.77 3.06
4251 4468 3.062099 CCTTGTGTCCATTTCGTGTATCG 59.938 47.826 0.00 0.00 41.41 2.92
4562 4782 7.379059 AACCACTGATATAGATGGTCATCAA 57.621 36.000 12.75 0.00 38.80 2.57
4734 5300 5.544176 TGAGGAACCATAGTCAAAGTCTTCT 59.456 40.000 0.00 0.00 0.00 2.85
5029 5640 5.889289 GCCTAAAAATATAAGTGGTGGTGGA 59.111 40.000 0.00 0.00 0.00 4.02
5153 5804 3.459227 TGGATCCCAGATTAATGTGCTCA 59.541 43.478 9.90 0.00 0.00 4.26
5172 5823 3.795688 AAAGGAGAGCAGTGATTTGGA 57.204 42.857 0.00 0.00 0.00 3.53
5222 5873 4.636206 GTGTGGCTATTAACTCTGGGAAAG 59.364 45.833 0.00 0.00 0.00 2.62
5232 5883 5.009010 CCATGGATTCAGTGTGGCTATTAAC 59.991 44.000 5.56 0.00 0.00 2.01
5448 6103 7.606456 CACTAAAATAAGAAACTAGCTGGGTGA 59.394 37.037 0.85 0.00 0.00 4.02
5897 7162 7.161404 AGCATTCTTAGTTCACATGTAACAGA 58.839 34.615 15.75 10.25 0.00 3.41
6035 7301 4.706842 AGTAAAGGGAAAGCAACTCAGA 57.293 40.909 0.00 0.00 0.00 3.27
6051 7317 3.756434 GTCCAGGCATGCTAACAAGTAAA 59.244 43.478 18.92 0.00 0.00 2.01
6510 8266 5.640732 CAATTAACTACAAAGCCGCTCAAT 58.359 37.500 0.00 0.00 0.00 2.57
6515 8271 3.210358 TGCAATTAACTACAAAGCCGC 57.790 42.857 0.00 0.00 0.00 6.53
6570 8361 6.665992 ACTCTGGTACAAGTGAGATTGTAA 57.334 37.500 6.33 0.00 44.83 2.41
6703 9085 9.027129 CACCAATGATTTATTCTGCAATACTTG 57.973 33.333 0.00 0.00 0.00 3.16
6725 9107 2.284754 TGGAACAGCTTAATGCACCA 57.715 45.000 0.00 0.00 45.94 4.17
6765 9475 3.372440 GGAACTCCCAATGAACCATCT 57.628 47.619 0.00 0.00 34.14 2.90
6816 9526 8.682710 TGTTGTTTAAGAAGTAGCTTCATGTTT 58.317 29.630 10.91 0.41 42.37 2.83
7126 10156 5.061808 CGGAACTAACCATAAACAAGAGTCG 59.938 44.000 0.00 0.00 0.00 4.18
7128 10158 6.105397 TCGGAACTAACCATAAACAAGAGT 57.895 37.500 0.00 0.00 0.00 3.24
7263 10989 3.859386 GCATTGCCCTGTTCTATTTTTCG 59.141 43.478 0.00 0.00 0.00 3.46
7319 11046 4.335400 TGCCTCGATATCTGTTAATGCA 57.665 40.909 0.34 0.00 0.00 3.96
7347 11074 8.839343 CATAGTCATTATCACAACTAATGGCAA 58.161 33.333 9.52 0.00 41.47 4.52
7348 11075 8.210265 TCATAGTCATTATCACAACTAATGGCA 58.790 33.333 9.52 0.00 41.47 4.92
7349 11076 8.607441 TCATAGTCATTATCACAACTAATGGC 57.393 34.615 0.57 0.57 40.07 4.40
7383 11110 1.788308 CGTCGTGTACAACAATTCGGT 59.212 47.619 0.00 0.00 0.00 4.69
7450 11178 6.840780 AGCATGTCTTTTACCAGCTATTTT 57.159 33.333 0.00 0.00 35.98 1.82
7461 11189 8.656849 GTCTTTTATCGAGAAGCATGTCTTTTA 58.343 33.333 0.00 0.00 34.56 1.52
7462 11190 7.389053 AGTCTTTTATCGAGAAGCATGTCTTTT 59.611 33.333 0.00 0.00 34.56 2.27
7463 11191 6.876257 AGTCTTTTATCGAGAAGCATGTCTTT 59.124 34.615 0.00 0.00 34.56 2.52
7464 11192 6.402222 AGTCTTTTATCGAGAAGCATGTCTT 58.598 36.000 0.00 0.00 37.83 3.01
7465 11193 5.971763 AGTCTTTTATCGAGAAGCATGTCT 58.028 37.500 0.00 0.00 0.00 3.41
7466 11194 6.473521 CAAGTCTTTTATCGAGAAGCATGTC 58.526 40.000 0.00 0.00 0.00 3.06
7467 11195 5.163814 GCAAGTCTTTTATCGAGAAGCATGT 60.164 40.000 0.00 0.00 0.00 3.21
7468 11196 5.064452 AGCAAGTCTTTTATCGAGAAGCATG 59.936 40.000 0.00 0.00 0.00 4.06
7469 11197 5.064452 CAGCAAGTCTTTTATCGAGAAGCAT 59.936 40.000 0.00 0.00 0.00 3.79
7470 11198 4.389992 CAGCAAGTCTTTTATCGAGAAGCA 59.610 41.667 0.00 0.00 0.00 3.91
7471 11199 4.390297 ACAGCAAGTCTTTTATCGAGAAGC 59.610 41.667 0.00 0.00 0.00 3.86
7472 11200 5.062809 GGACAGCAAGTCTTTTATCGAGAAG 59.937 44.000 8.88 0.00 46.72 2.85
7473 11201 4.929808 GGACAGCAAGTCTTTTATCGAGAA 59.070 41.667 8.88 0.00 46.72 2.87
7474 11202 4.021456 TGGACAGCAAGTCTTTTATCGAGA 60.021 41.667 8.88 0.00 46.72 4.04
7475 11203 4.245660 TGGACAGCAAGTCTTTTATCGAG 58.754 43.478 8.88 0.00 46.72 4.04
7476 11204 4.265904 TGGACAGCAAGTCTTTTATCGA 57.734 40.909 8.88 0.00 46.72 3.59
7477 11205 5.551760 AATGGACAGCAAGTCTTTTATCG 57.448 39.130 8.88 0.00 46.72 2.92
7485 11213 4.823989 AGGCATTATAATGGACAGCAAGTC 59.176 41.667 23.57 5.88 46.83 3.01
7488 11216 3.890756 CCAGGCATTATAATGGACAGCAA 59.109 43.478 23.57 0.00 36.90 3.91
7522 11295 8.081633 TCAATACCATGAACAGAACATTTTGTC 58.918 33.333 0.00 0.00 0.00 3.18
7584 11371 2.622452 CCCCAGCCAGAAACATCAGATT 60.622 50.000 0.00 0.00 0.00 2.40
7628 11415 3.198635 AGCGATGAAGAAGATGGAAGGAA 59.801 43.478 0.00 0.00 0.00 3.36
7784 11586 2.168496 AGGAAGGACGAATTCTCACGA 58.832 47.619 3.52 0.00 0.00 4.35
7871 11675 3.392616 ACCCTGAATGTTGAGAAGACTGT 59.607 43.478 0.00 0.00 0.00 3.55
7872 11676 4.013267 ACCCTGAATGTTGAGAAGACTG 57.987 45.455 0.00 0.00 0.00 3.51
7873 11677 4.713792 AACCCTGAATGTTGAGAAGACT 57.286 40.909 0.00 0.00 0.00 3.24
7874 11678 5.305585 TGTAACCCTGAATGTTGAGAAGAC 58.694 41.667 0.00 0.00 0.00 3.01
7875 11679 5.560722 TGTAACCCTGAATGTTGAGAAGA 57.439 39.130 0.00 0.00 0.00 2.87
7876 11680 5.392380 GCATGTAACCCTGAATGTTGAGAAG 60.392 44.000 0.00 0.00 0.00 2.85
7877 11681 4.458989 GCATGTAACCCTGAATGTTGAGAA 59.541 41.667 0.00 0.00 0.00 2.87
7878 11682 4.009675 GCATGTAACCCTGAATGTTGAGA 58.990 43.478 0.00 0.00 0.00 3.27
7879 11683 4.012374 AGCATGTAACCCTGAATGTTGAG 58.988 43.478 0.00 0.00 0.00 3.02
7880 11684 3.758023 CAGCATGTAACCCTGAATGTTGA 59.242 43.478 0.00 0.00 34.34 3.18
7881 11685 3.119388 CCAGCATGTAACCCTGAATGTTG 60.119 47.826 0.00 0.00 32.83 3.33
7882 11686 3.091545 CCAGCATGTAACCCTGAATGTT 58.908 45.455 0.00 0.00 0.00 2.71
7883 11687 2.041620 ACCAGCATGTAACCCTGAATGT 59.958 45.455 0.00 0.00 0.00 2.71
7884 11688 2.684881 GACCAGCATGTAACCCTGAATG 59.315 50.000 0.00 0.00 0.00 2.67
7885 11689 2.578021 AGACCAGCATGTAACCCTGAAT 59.422 45.455 0.00 0.00 0.00 2.57
7886 11690 1.985159 AGACCAGCATGTAACCCTGAA 59.015 47.619 0.00 0.00 0.00 3.02
7887 11691 1.278985 CAGACCAGCATGTAACCCTGA 59.721 52.381 0.00 0.00 0.00 3.86
7888 11692 1.278985 TCAGACCAGCATGTAACCCTG 59.721 52.381 0.00 0.00 0.00 4.45
7889 11693 1.656587 TCAGACCAGCATGTAACCCT 58.343 50.000 0.00 0.00 0.00 4.34
7890 11694 2.092968 TGATCAGACCAGCATGTAACCC 60.093 50.000 0.00 0.00 0.00 4.11
7891 11695 2.939103 GTGATCAGACCAGCATGTAACC 59.061 50.000 0.00 0.00 0.00 2.85
7892 11696 3.866651 AGTGATCAGACCAGCATGTAAC 58.133 45.455 0.00 0.00 0.00 2.50
7893 11697 4.956075 TCTAGTGATCAGACCAGCATGTAA 59.044 41.667 0.00 0.00 0.00 2.41
7894 11698 4.536765 TCTAGTGATCAGACCAGCATGTA 58.463 43.478 0.00 0.00 0.00 2.29
7904 11708 9.752228 AGAAATGAGCTATATCTAGTGATCAGA 57.248 33.333 0.00 0.00 34.32 3.27
7998 11814 3.690139 TCAGAGAGTAGAGTAAGGCAACG 59.310 47.826 0.00 0.00 46.39 4.10
8017 11837 4.482386 CATCCAGAACAAACTGCATTCAG 58.518 43.478 0.22 0.00 45.71 3.02
8053 11873 3.068165 GGTTGGCAAACTTAAGCTTGTCT 59.932 43.478 20.53 0.00 36.48 3.41
8062 11882 1.479757 GGGGAGTGGTTGGCAAACTTA 60.480 52.381 17.39 0.00 36.48 2.24
8239 12062 4.814294 CCGGGGTCTTTCGCTCCG 62.814 72.222 0.00 0.00 40.32 4.63
8304 12127 5.762045 ACAAAAGAATCAACCAATGACTCG 58.238 37.500 0.00 0.00 39.27 4.18
8305 12128 7.202526 TGAACAAAAGAATCAACCAATGACTC 58.797 34.615 0.00 0.00 41.93 3.36
8476 12299 3.539253 GCATGAAGCAACCATAGCG 57.461 52.632 0.00 0.00 44.79 4.26
8509 12334 1.138661 CAAACACACCACCAAAGGCAT 59.861 47.619 0.00 0.00 0.00 4.40
8530 12355 4.023291 ACAAGAACTTTTGAGAGGGCAAA 58.977 39.130 0.00 0.00 36.08 3.68
8531 12356 3.631250 ACAAGAACTTTTGAGAGGGCAA 58.369 40.909 0.00 0.00 0.00 4.52
8532 12357 3.297134 ACAAGAACTTTTGAGAGGGCA 57.703 42.857 0.00 0.00 0.00 5.36
8533 12358 4.762251 ACATACAAGAACTTTTGAGAGGGC 59.238 41.667 0.00 0.00 0.00 5.19
8593 12418 0.317160 CTCGCAGGACAGTTGTGGTA 59.683 55.000 0.00 0.00 0.00 3.25
8602 12427 2.049156 CAAGTCGCTCGCAGGACA 60.049 61.111 3.13 0.00 35.63 4.02
8626 12451 0.749649 AAAACGTTGGGCATTGCTCA 59.250 45.000 7.23 7.23 37.19 4.26
8639 12464 0.850856 GAGTCTGCGAACGAAAACGT 59.149 50.000 0.00 0.00 0.00 3.99
8644 12469 0.318699 CCAGTGAGTCTGCGAACGAA 60.319 55.000 0.00 0.00 42.38 3.85
8646 12471 1.734477 CCCAGTGAGTCTGCGAACG 60.734 63.158 0.00 0.00 42.38 3.95
8651 12476 1.239347 GTTTTCCCCAGTGAGTCTGC 58.761 55.000 0.00 0.00 42.38 4.26
8653 12478 2.408565 TCTGTTTTCCCCAGTGAGTCT 58.591 47.619 0.00 0.00 0.00 3.24
8654 12479 2.930826 TCTGTTTTCCCCAGTGAGTC 57.069 50.000 0.00 0.00 0.00 3.36
8655 12480 2.777692 TCTTCTGTTTTCCCCAGTGAGT 59.222 45.455 0.00 0.00 0.00 3.41
8656 12481 3.492102 TCTTCTGTTTTCCCCAGTGAG 57.508 47.619 0.00 0.00 0.00 3.51
8657 12482 3.754965 CATCTTCTGTTTTCCCCAGTGA 58.245 45.455 0.00 0.00 0.00 3.41
8661 12618 2.627699 GTTGCATCTTCTGTTTTCCCCA 59.372 45.455 0.00 0.00 0.00 4.96
8662 12619 2.627699 TGTTGCATCTTCTGTTTTCCCC 59.372 45.455 0.00 0.00 0.00 4.81
8687 12645 9.241317 CATATTGTGAATTGTGATTTTAGCCTC 57.759 33.333 0.00 0.00 0.00 4.70
8723 12685 4.763793 CAGGCTGGTTCTATATTTGATGGG 59.236 45.833 6.61 0.00 0.00 4.00
8765 12727 7.011482 GTCACCAAATTGTATCTAGACCATGAC 59.989 40.741 0.00 1.70 0.00 3.06
8814 12776 0.179034 GCCTCGGCAATCTCTCCAAT 60.179 55.000 2.41 0.00 41.49 3.16
8858 12820 2.798976 TTGCGCTTCATTTCTTGCTT 57.201 40.000 9.73 0.00 0.00 3.91
8907 12869 3.788766 CCTTGGCCGAGAAACGCG 61.789 66.667 22.68 3.53 41.07 6.01
9050 13015 0.752376 CCGAGGGTGGAGTCTAGGAC 60.752 65.000 0.00 0.00 0.00 3.85
9086 13051 2.364002 GAGGAGTGGCTATTCTGTCCTC 59.636 54.545 0.60 0.60 42.44 3.71
9122 13087 2.277008 AGAGGGATCATGGTTCCAGT 57.723 50.000 5.94 0.00 34.77 4.00
9142 13107 4.153475 CGTGGATCTTTTGTCAACCGTTAT 59.847 41.667 0.00 0.00 0.00 1.89
9189 13170 4.020839 ACAAATTTTCCTTGGAGATGGCTG 60.021 41.667 0.00 0.00 0.00 4.85
9208 13189 7.041372 GGTCTGCTAGATGTGTTTCTTTACAAA 60.041 37.037 0.00 0.00 0.00 2.83
9240 13221 5.163571 TGCTGATTTTGTGTTGCTCTTAACA 60.164 36.000 0.00 0.00 38.17 2.41
9254 13235 6.583806 GGTCTGAAACTTGTATGCTGATTTTG 59.416 38.462 0.00 0.00 0.00 2.44
9255 13236 6.294731 GGGTCTGAAACTTGTATGCTGATTTT 60.295 38.462 0.00 0.00 0.00 1.82
9257 13238 4.702131 GGGTCTGAAACTTGTATGCTGATT 59.298 41.667 0.00 0.00 0.00 2.57
9263 13244 5.335897 CCATGTTGGGTCTGAAACTTGTATG 60.336 44.000 0.00 0.00 32.67 2.39
9264 13245 4.766891 CCATGTTGGGTCTGAAACTTGTAT 59.233 41.667 0.00 0.00 32.67 2.29
9267 13248 3.648339 CCATGTTGGGTCTGAAACTTG 57.352 47.619 0.00 0.00 32.67 3.16


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

AutoCloner maintained by Alex Coulton.