Multiple sequence alignment - TraesCS3B01G436500

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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 TraesCS3B01G436500 chr3B 100.000 5000 0 0 1 5000 675037423 675042422 0.000000e+00 9234.0
1 TraesCS3B01G436500 chr3B 97.297 37 1 0 2111 2147 675039478 675039514 4.180000e-06 63.9
2 TraesCS3B01G436500 chr3B 97.297 37 1 0 2056 2092 675039533 675039569 4.180000e-06 63.9
3 TraesCS3B01G436500 chr3D 89.784 3240 177 70 1808 5000 512677460 512674328 0.000000e+00 4008.0
4 TraesCS3B01G436500 chr3D 92.334 1187 53 14 648 1806 512678681 512677505 0.000000e+00 1653.0
5 TraesCS3B01G436500 chr3D 92.138 318 18 2 1 315 550254588 550254275 4.590000e-120 442.0
6 TraesCS3B01G436500 chr3D 94.275 262 14 1 316 577 550254243 550253983 2.800000e-107 399.0
7 TraesCS3B01G436500 chr3D 83.193 238 36 4 312 548 511683180 511682946 1.090000e-51 215.0
8 TraesCS3B01G436500 chr3A 91.875 1477 74 24 3543 5000 648263178 648261729 0.000000e+00 2021.0
9 TraesCS3B01G436500 chr3A 88.330 994 66 25 1856 2807 648264928 648263943 0.000000e+00 1147.0
10 TraesCS3B01G436500 chr3A 88.616 571 36 17 2878 3435 648263923 648263369 0.000000e+00 667.0
11 TraesCS3B01G436500 chr3A 87.278 338 29 7 808 1145 648266044 648265721 1.700000e-99 374.0
12 TraesCS3B01G436500 chr2A 85.882 595 43 21 1 578 726420391 726420961 3.330000e-166 595.0
13 TraesCS3B01G436500 chr2A 74.766 214 49 4 3207 3416 535836841 535836629 1.920000e-14 91.6
14 TraesCS3B01G436500 chr4D 92.138 318 21 2 1 315 484167479 484167163 3.550000e-121 446.0
15 TraesCS3B01G436500 chr4D 92.748 262 18 1 318 578 484167129 484166868 1.310000e-100 377.0
16 TraesCS3B01G436500 chr2B 91.698 265 20 2 316 578 628945323 628945587 2.840000e-97 366.0
17 TraesCS3B01G436500 chr2B 75.701 214 47 4 3207 3416 471322220 471322432 8.860000e-18 102.0
18 TraesCS3B01G436500 chr7A 87.952 249 28 2 332 578 613031032 613030784 4.900000e-75 292.0
19 TraesCS3B01G436500 chr7D 88.333 180 20 1 401 579 533637182 533637003 1.090000e-51 215.0
20 TraesCS3B01G436500 chr7D 98.000 50 1 0 340 389 533639624 533639575 2.480000e-13 87.9
21 TraesCS3B01G436500 chr5B 80.608 263 48 3 318 578 107390901 107391162 3.050000e-47 200.0
22 TraesCS3B01G436500 chr1D 81.818 220 40 0 3207 3426 355470720 355470501 8.550000e-43 185.0
23 TraesCS3B01G436500 chr1A 80.909 220 42 0 3207 3426 455819493 455819274 1.850000e-39 174.0
24 TraesCS3B01G436500 chr2D 75.234 214 48 4 3207 3416 398668464 398668252 4.120000e-16 97.1
25 TraesCS3B01G436500 chr6D 88.000 50 6 0 3746 3795 127138151 127138102 5.410000e-05 60.2
26 TraesCS3B01G436500 chr6B 88.000 50 6 0 3746 3795 226187714 226187665 5.410000e-05 60.2
27 TraesCS3B01G436500 chr6A 94.737 38 2 0 3746 3783 151491426 151491463 5.410000e-05 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 TraesCS3B01G436500 chr3B 675037423 675042422 4999 False 3120.60 9234 98.19800 1 5000 3 chr3B.!!$F1 4999
1 TraesCS3B01G436500 chr3D 512674328 512678681 4353 True 2830.50 4008 91.05900 648 5000 2 chr3D.!!$R2 4352
2 TraesCS3B01G436500 chr3D 550253983 550254588 605 True 420.50 442 93.20650 1 577 2 chr3D.!!$R3 576
3 TraesCS3B01G436500 chr3A 648261729 648266044 4315 True 1052.25 2021 89.02475 808 5000 4 chr3A.!!$R1 4192
4 TraesCS3B01G436500 chr2A 726420391 726420961 570 False 595.00 595 85.88200 1 578 1 chr2A.!!$F1 577
5 TraesCS3B01G436500 chr4D 484166868 484167479 611 True 411.50 446 92.44300 1 578 2 chr4D.!!$R1 577

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
614 658 0.097674 CTTCGAAATGAGGCCAAGCG 59.902 55.000 5.01 0.00 0.00 4.68 F
767 830 0.307760 GAGTGAACTGGCCAACGTTG 59.692 55.000 21.47 21.47 0.00 4.10 F
1609 1747 0.036875 GCTGGACCAACTACCTGCTT 59.963 55.000 0.00 0.00 44.05 3.91 F
3074 3430 2.034124 TCGTATACCCTACCCACTTGC 58.966 52.381 0.00 0.00 0.00 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1572 1710 0.394762 GCTGGGAGGAATGCATGTCA 60.395 55.0 0.00 0.0 0.00 3.58 R
2327 2661 0.807496 GCAGTTCCAGAGGATTGCAC 59.193 55.0 14.43 0.0 40.23 4.57 R
3078 3434 0.035725 CAGCCTGCAGGTCAATCAGA 60.036 55.0 32.81 0.0 37.57 3.27 R
4006 4488 0.593128 CTTTGGTTCTTCTGGCCGTG 59.407 55.0 0.00 0.0 0.00 4.94 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
62 63 1.622811 GGATTGTTGCCAATTGGGTCA 59.377 47.619 25.73 13.31 41.37 4.02
70 71 3.772387 TGCCAATTGGGTCACAGATAAA 58.228 40.909 25.73 0.00 39.65 1.40
80 81 5.763204 TGGGTCACAGATAAAAAGACAGTTC 59.237 40.000 0.00 0.00 0.00 3.01
136 145 7.867403 GCATCGGGATGTATAAAATTGAATGTT 59.133 33.333 10.14 0.00 40.80 2.71
292 304 4.214332 GTGCTATTAGGCTTATGACTTGCC 59.786 45.833 0.00 0.00 46.42 4.52
338 381 1.067776 GGCTATACAGAATCCGTCCGG 60.068 57.143 0.00 0.00 0.00 5.14
389 432 2.789213 TGATTGCCGGAAGTTGATGAA 58.211 42.857 5.05 0.00 0.00 2.57
410 453 5.049680 TGAATTCTTTTGACAAGGCGACTAC 60.050 40.000 7.05 0.00 42.68 2.73
417 460 2.101750 TGACAAGGCGACTACAAGTCAA 59.898 45.455 11.81 0.00 45.30 3.18
418 461 3.128349 GACAAGGCGACTACAAGTCAAA 58.872 45.455 0.00 0.00 45.30 2.69
421 464 4.202182 ACAAGGCGACTACAAGTCAAAGTA 60.202 41.667 0.00 0.00 45.30 2.24
430 473 5.756347 ACTACAAGTCAAAGTATGCGTGAAA 59.244 36.000 0.00 0.00 0.00 2.69
506 549 3.308832 GGGGTGTGGAATGATAAACCTCA 60.309 47.826 0.00 0.00 0.00 3.86
516 559 7.182026 TGGAATGATAAACCTCAAGACTTCCTA 59.818 37.037 0.00 0.00 34.13 2.94
599 643 9.893305 AAAAATATAAAACTCTGGACAACTTCG 57.107 29.630 0.00 0.00 0.00 3.79
600 644 8.842358 AAATATAAAACTCTGGACAACTTCGA 57.158 30.769 0.00 0.00 0.00 3.71
601 645 8.842358 AATATAAAACTCTGGACAACTTCGAA 57.158 30.769 0.00 0.00 0.00 3.71
602 646 8.842358 ATATAAAACTCTGGACAACTTCGAAA 57.158 30.769 0.00 0.00 0.00 3.46
603 647 7.745620 ATAAAACTCTGGACAACTTCGAAAT 57.254 32.000 0.00 0.00 0.00 2.17
604 648 5.424121 AAACTCTGGACAACTTCGAAATG 57.576 39.130 0.00 4.15 0.00 2.32
605 649 4.336889 ACTCTGGACAACTTCGAAATGA 57.663 40.909 15.34 0.00 0.00 2.57
606 650 4.310769 ACTCTGGACAACTTCGAAATGAG 58.689 43.478 15.34 3.30 0.00 2.90
607 651 3.664107 TCTGGACAACTTCGAAATGAGG 58.336 45.455 15.34 0.00 0.00 3.86
608 652 2.151202 TGGACAACTTCGAAATGAGGC 58.849 47.619 15.34 1.47 0.00 4.70
609 653 1.468914 GGACAACTTCGAAATGAGGCC 59.531 52.381 15.34 0.00 0.00 5.19
610 654 2.151202 GACAACTTCGAAATGAGGCCA 58.849 47.619 5.01 0.00 0.00 5.36
611 655 2.552315 GACAACTTCGAAATGAGGCCAA 59.448 45.455 5.01 0.00 0.00 4.52
612 656 2.554032 ACAACTTCGAAATGAGGCCAAG 59.446 45.455 5.01 0.00 0.00 3.61
613 657 1.168714 ACTTCGAAATGAGGCCAAGC 58.831 50.000 5.01 0.00 0.00 4.01
614 658 0.097674 CTTCGAAATGAGGCCAAGCG 59.902 55.000 5.01 0.00 0.00 4.68
615 659 0.605319 TTCGAAATGAGGCCAAGCGT 60.605 50.000 5.01 0.00 0.00 5.07
616 660 1.019278 TCGAAATGAGGCCAAGCGTC 61.019 55.000 5.01 2.45 42.76 5.19
617 661 1.021390 CGAAATGAGGCCAAGCGTCT 61.021 55.000 5.01 0.00 42.87 4.18
618 662 1.168714 GAAATGAGGCCAAGCGTCTT 58.831 50.000 5.01 1.91 42.87 3.01
619 663 2.356135 GAAATGAGGCCAAGCGTCTTA 58.644 47.619 5.01 0.00 42.87 2.10
620 664 2.489938 AATGAGGCCAAGCGTCTTAA 57.510 45.000 5.01 0.00 42.87 1.85
621 665 2.717639 ATGAGGCCAAGCGTCTTAAT 57.282 45.000 5.01 0.00 42.87 1.40
622 666 3.838244 ATGAGGCCAAGCGTCTTAATA 57.162 42.857 5.01 0.00 42.87 0.98
623 667 2.901249 TGAGGCCAAGCGTCTTAATAC 58.099 47.619 5.01 0.00 42.87 1.89
624 668 2.235155 TGAGGCCAAGCGTCTTAATACA 59.765 45.455 5.01 0.00 42.87 2.29
625 669 3.118408 TGAGGCCAAGCGTCTTAATACAT 60.118 43.478 5.01 0.00 42.87 2.29
626 670 4.100344 TGAGGCCAAGCGTCTTAATACATA 59.900 41.667 5.01 0.00 42.87 2.29
627 671 5.221641 TGAGGCCAAGCGTCTTAATACATAT 60.222 40.000 5.01 0.00 42.87 1.78
628 672 4.997395 AGGCCAAGCGTCTTAATACATATG 59.003 41.667 5.01 0.00 0.00 1.78
629 673 4.378459 GGCCAAGCGTCTTAATACATATGC 60.378 45.833 1.58 0.00 0.00 3.14
630 674 4.213270 GCCAAGCGTCTTAATACATATGCA 59.787 41.667 1.58 0.00 0.00 3.96
631 675 5.277779 GCCAAGCGTCTTAATACATATGCAA 60.278 40.000 1.58 0.00 0.00 4.08
632 676 6.724263 CCAAGCGTCTTAATACATATGCAAA 58.276 36.000 1.58 0.00 0.00 3.68
633 677 7.192913 CCAAGCGTCTTAATACATATGCAAAA 58.807 34.615 1.58 0.00 0.00 2.44
634 678 7.700234 CCAAGCGTCTTAATACATATGCAAAAA 59.300 33.333 1.58 0.00 0.00 1.94
747 810 4.996434 GGGCTCACGCTGTGCAGT 62.996 66.667 11.95 0.00 38.50 4.40
767 830 0.307760 GAGTGAACTGGCCAACGTTG 59.692 55.000 21.47 21.47 0.00 4.10
776 839 1.281353 GCCAACGTTGCATCGAACA 59.719 52.632 22.93 0.00 34.70 3.18
782 845 1.132640 GTTGCATCGAACAGACGCC 59.867 57.895 0.00 0.00 37.23 5.68
785 848 2.126071 CATCGAACAGACGCCGGT 60.126 61.111 1.90 0.00 0.00 5.28
795 858 1.658673 GACGCCGGTCGAATAGGAT 59.341 57.895 22.10 0.83 41.67 3.24
798 861 1.682854 ACGCCGGTCGAATAGGATTTA 59.317 47.619 22.10 0.00 41.67 1.40
799 862 2.056577 CGCCGGTCGAATAGGATTTAC 58.943 52.381 12.11 0.00 41.67 2.01
800 863 2.410939 GCCGGTCGAATAGGATTTACC 58.589 52.381 1.90 0.00 39.35 2.85
1157 1244 1.386772 TGACCCCAACCCCAGTCTT 60.387 57.895 0.00 0.00 0.00 3.01
1172 1289 2.361757 CAGTCTTGCCGATGATCTCTCT 59.638 50.000 0.00 0.00 0.00 3.10
1179 1296 2.744494 GCCGATGATCTCTCTTTGCCTT 60.744 50.000 0.00 0.00 0.00 4.35
1313 1451 6.319658 TCTTCAGAGTTTCAACAGCATTTCTT 59.680 34.615 0.00 0.00 0.00 2.52
1350 1488 4.280789 TCTTCCCTCTGCTCCCTTTATA 57.719 45.455 0.00 0.00 0.00 0.98
1351 1489 3.967987 TCTTCCCTCTGCTCCCTTTATAC 59.032 47.826 0.00 0.00 0.00 1.47
1352 1490 3.414759 TCCCTCTGCTCCCTTTATACA 57.585 47.619 0.00 0.00 0.00 2.29
1353 1491 3.731431 TCCCTCTGCTCCCTTTATACAA 58.269 45.455 0.00 0.00 0.00 2.41
1354 1492 4.307259 TCCCTCTGCTCCCTTTATACAAT 58.693 43.478 0.00 0.00 0.00 2.71
1355 1493 5.473273 TCCCTCTGCTCCCTTTATACAATA 58.527 41.667 0.00 0.00 0.00 1.90
1356 1494 6.091555 TCCCTCTGCTCCCTTTATACAATAT 58.908 40.000 0.00 0.00 0.00 1.28
1393 1531 2.239654 CAAAATGAGGGGGTAGCTCAGA 59.760 50.000 0.00 0.00 0.00 3.27
1499 1637 1.837439 TCAGACTGTCTTTGGGTGTGT 59.163 47.619 7.77 0.00 0.00 3.72
1500 1638 1.942657 CAGACTGTCTTTGGGTGTGTG 59.057 52.381 7.77 0.00 0.00 3.82
1609 1747 0.036875 GCTGGACCAACTACCTGCTT 59.963 55.000 0.00 0.00 44.05 3.91
1708 1846 2.034558 CGACCATTGCAGAAACAAGGTT 59.965 45.455 0.00 0.00 33.81 3.50
1725 1864 2.306512 AGGTTGATGGGCCGTTAGTTTA 59.693 45.455 0.00 0.00 0.00 2.01
1731 1870 4.020039 TGATGGGCCGTTAGTTTAAAGAGA 60.020 41.667 0.00 0.00 0.00 3.10
1759 1898 9.206870 ACCTTTTGTTTAATTATGCACTTCATG 57.793 29.630 0.00 0.00 36.63 3.07
1795 1934 8.140112 ACAATCTCACTCTAATTCAGGTTAGT 57.860 34.615 0.00 0.00 34.16 2.24
1806 1946 8.248945 TCTAATTCAGGTTAGTTAGTGCACTAC 58.751 37.037 26.02 19.41 34.16 2.73
1829 2117 7.440523 ACTACCTTGCTCACTGAATTTTAAG 57.559 36.000 0.00 0.00 0.00 1.85
1833 2121 6.205658 ACCTTGCTCACTGAATTTTAAGAGTC 59.794 38.462 0.00 0.00 0.00 3.36
1864 2175 6.779117 CACAAAGACAAAGAGTGCTATATGG 58.221 40.000 0.00 0.00 0.00 2.74
1882 2193 2.593026 TGGCTTTAACCCCAGTTCTTG 58.407 47.619 0.00 0.00 37.42 3.02
1894 2205 4.280677 CCCCAGTTCTTGCAACATCTTAAA 59.719 41.667 0.00 0.00 0.00 1.52
1946 2258 4.699925 ACCTTGTGCTAACTCCAGTTTA 57.300 40.909 0.00 0.00 39.31 2.01
2105 2417 6.461110 TTCATAACACCGGTTTTGGTTTAA 57.539 33.333 16.26 5.22 41.38 1.52
2108 2420 3.100658 ACACCGGTTTTGGTTTAATGC 57.899 42.857 2.97 0.00 41.38 3.56
2111 2423 3.492756 CACCGGTTTTGGTTTAATGCTTG 59.507 43.478 2.97 0.00 41.38 4.01
2112 2424 3.385111 ACCGGTTTTGGTTTAATGCTTGA 59.615 39.130 0.00 0.00 39.99 3.02
2113 2425 4.039852 ACCGGTTTTGGTTTAATGCTTGAT 59.960 37.500 0.00 0.00 39.99 2.57
2115 2427 5.468409 CCGGTTTTGGTTTAATGCTTGATTT 59.532 36.000 0.00 0.00 0.00 2.17
2116 2428 6.017523 CCGGTTTTGGTTTAATGCTTGATTTT 60.018 34.615 0.00 0.00 0.00 1.82
2117 2429 7.171678 CCGGTTTTGGTTTAATGCTTGATTTTA 59.828 33.333 0.00 0.00 0.00 1.52
2118 2430 8.220434 CGGTTTTGGTTTAATGCTTGATTTTAG 58.780 33.333 0.00 0.00 0.00 1.85
2119 2431 8.503196 GGTTTTGGTTTAATGCTTGATTTTAGG 58.497 33.333 0.00 0.00 0.00 2.69
2120 2432 9.267084 GTTTTGGTTTAATGCTTGATTTTAGGA 57.733 29.630 0.00 0.00 0.00 2.94
2121 2433 9.487790 TTTTGGTTTAATGCTTGATTTTAGGAG 57.512 29.630 0.00 0.00 0.00 3.69
2122 2434 7.169158 TGGTTTAATGCTTGATTTTAGGAGG 57.831 36.000 0.00 0.00 0.00 4.30
2123 2435 6.951198 TGGTTTAATGCTTGATTTTAGGAGGA 59.049 34.615 0.00 0.00 0.00 3.71
2124 2436 7.122650 TGGTTTAATGCTTGATTTTAGGAGGAG 59.877 37.037 0.00 0.00 0.00 3.69
2125 2437 6.699575 TTAATGCTTGATTTTAGGAGGAGC 57.300 37.500 0.00 0.00 0.00 4.70
2126 2438 3.004752 TGCTTGATTTTAGGAGGAGCC 57.995 47.619 0.00 0.00 0.00 4.70
2127 2439 2.308570 TGCTTGATTTTAGGAGGAGCCA 59.691 45.455 0.00 0.00 40.02 4.75
2129 2441 3.379688 GCTTGATTTTAGGAGGAGCCAAG 59.620 47.826 0.00 0.00 40.02 3.61
2130 2442 3.652057 TGATTTTAGGAGGAGCCAAGG 57.348 47.619 0.00 0.00 40.02 3.61
2131 2443 2.919602 TGATTTTAGGAGGAGCCAAGGT 59.080 45.455 0.00 0.00 40.02 3.50
2133 2445 4.538490 TGATTTTAGGAGGAGCCAAGGTAA 59.462 41.667 0.00 0.00 40.02 2.85
2134 2446 5.014755 TGATTTTAGGAGGAGCCAAGGTAAA 59.985 40.000 0.00 0.00 40.02 2.01
2135 2447 3.994931 TTAGGAGGAGCCAAGGTAAAC 57.005 47.619 0.00 0.00 40.02 2.01
2137 2449 2.349445 AGGAGGAGCCAAGGTAAACTT 58.651 47.619 0.00 0.00 41.00 2.66
2140 2452 3.497942 GGAGGAGCCAAGGTAAACTTTCA 60.498 47.826 0.00 0.00 37.29 2.69
2141 2453 4.336280 GAGGAGCCAAGGTAAACTTTCAT 58.664 43.478 0.00 0.00 37.29 2.57
2337 2671 3.019564 AGTTATGGCTTGTGCAATCCTC 58.980 45.455 6.40 0.00 41.91 3.71
2493 2840 3.329929 AAACACCACCGTATCCTCTTC 57.670 47.619 0.00 0.00 0.00 2.87
2498 2845 2.621998 ACCACCGTATCCTCTTCATACG 59.378 50.000 5.45 5.45 45.72 3.06
2549 2901 4.953579 TGCCCTACTAATCAAAACATTCCC 59.046 41.667 0.00 0.00 0.00 3.97
2595 2947 6.597672 AGTTTTATGCATCGGTCACTAAATCA 59.402 34.615 0.19 0.00 0.00 2.57
2669 3025 2.770802 AGCATGCTGACAACTCTATCCT 59.229 45.455 21.98 0.00 0.00 3.24
2819 3175 4.947388 TGGCATAAGGTAATCCAAACTCAC 59.053 41.667 0.00 0.00 35.89 3.51
2845 3201 7.552050 AATTGTGTTTTTGATAATCCCCAGA 57.448 32.000 0.00 0.00 0.00 3.86
2868 3224 3.189702 TCGATGTTTCGGGTGAAAATTCC 59.810 43.478 0.00 0.00 45.22 3.01
2874 3230 4.965200 TTCGGGTGAAAATTCCCAATTT 57.035 36.364 1.20 0.00 43.57 1.82
2913 3269 2.203195 TGTTGAGCAGCGCAACCT 60.203 55.556 31.55 1.34 42.00 3.50
2976 3332 3.118519 GGTGGTACCTGTGGATATTCGTT 60.119 47.826 14.36 0.00 34.73 3.85
3012 3368 3.496884 TGCTGAACGTCAATGGTAAGTTC 59.503 43.478 0.00 0.28 40.90 3.01
3021 3377 5.616866 CGTCAATGGTAAGTTCCAATCACAC 60.617 44.000 0.00 0.00 41.09 3.82
3028 3384 3.719268 AGTTCCAATCACACTGCCATA 57.281 42.857 0.00 0.00 0.00 2.74
3048 3404 7.282224 TGCCATATCCAGTGTTTACAACTATTC 59.718 37.037 0.00 0.00 0.00 1.75
3063 3419 6.285990 ACAACTATTCCAACATCGTATACCC 58.714 40.000 0.00 0.00 0.00 3.69
3064 3420 6.099269 ACAACTATTCCAACATCGTATACCCT 59.901 38.462 0.00 0.00 0.00 4.34
3065 3421 7.288389 ACAACTATTCCAACATCGTATACCCTA 59.712 37.037 0.00 0.00 0.00 3.53
3066 3422 7.224522 ACTATTCCAACATCGTATACCCTAC 57.775 40.000 0.00 0.00 0.00 3.18
3067 3423 4.942761 TTCCAACATCGTATACCCTACC 57.057 45.455 0.00 0.00 0.00 3.18
3068 3424 3.233507 TCCAACATCGTATACCCTACCC 58.766 50.000 0.00 0.00 0.00 3.69
3069 3425 2.967201 CCAACATCGTATACCCTACCCA 59.033 50.000 0.00 0.00 0.00 4.51
3070 3426 3.243975 CCAACATCGTATACCCTACCCAC 60.244 52.174 0.00 0.00 0.00 4.61
3071 3427 3.607490 ACATCGTATACCCTACCCACT 57.393 47.619 0.00 0.00 0.00 4.00
3072 3428 3.919834 ACATCGTATACCCTACCCACTT 58.080 45.455 0.00 0.00 0.00 3.16
3073 3429 3.640029 ACATCGTATACCCTACCCACTTG 59.360 47.826 0.00 0.00 0.00 3.16
3074 3430 2.034124 TCGTATACCCTACCCACTTGC 58.966 52.381 0.00 0.00 0.00 4.01
3075 3431 2.037144 CGTATACCCTACCCACTTGCT 58.963 52.381 0.00 0.00 0.00 3.91
3076 3432 2.223971 CGTATACCCTACCCACTTGCTG 60.224 54.545 0.00 0.00 0.00 4.41
3077 3433 2.263895 ATACCCTACCCACTTGCTGA 57.736 50.000 0.00 0.00 0.00 4.26
3078 3434 2.263895 TACCCTACCCACTTGCTGAT 57.736 50.000 0.00 0.00 0.00 2.90
3138 3494 3.556999 TCCTTCCTTCCTCTCATCGTAG 58.443 50.000 0.00 0.00 0.00 3.51
3163 3521 1.078497 CTGAACCCCAGCACGCATA 60.078 57.895 0.00 0.00 35.89 3.14
3176 3534 3.120199 AGCACGCATATCAAAGTGTGAAC 60.120 43.478 9.96 0.00 46.27 3.18
3179 3537 4.847757 CACGCATATCAAAGTGTGAACTTG 59.152 41.667 0.00 0.00 46.27 3.16
3184 3542 7.530010 GCATATCAAAGTGTGAACTTGTGTAT 58.470 34.615 0.00 0.00 40.50 2.29
3191 3549 8.721478 CAAAGTGTGAACTTGTGTATATAAGCT 58.279 33.333 0.00 0.00 0.00 3.74
3197 3555 8.604890 GTGAACTTGTGTATATAAGCTTCCTTC 58.395 37.037 0.00 0.00 32.47 3.46
3198 3556 7.769044 TGAACTTGTGTATATAAGCTTCCTTCC 59.231 37.037 0.00 0.00 32.47 3.46
3199 3557 7.439108 ACTTGTGTATATAAGCTTCCTTCCT 57.561 36.000 0.00 0.00 32.47 3.36
3200 3558 7.862675 ACTTGTGTATATAAGCTTCCTTCCTT 58.137 34.615 0.00 0.00 32.47 3.36
3201 3559 7.770897 ACTTGTGTATATAAGCTTCCTTCCTTG 59.229 37.037 0.00 0.00 32.47 3.61
3202 3560 7.195374 TGTGTATATAAGCTTCCTTCCTTGT 57.805 36.000 0.00 0.00 32.47 3.16
3203 3561 7.047891 TGTGTATATAAGCTTCCTTCCTTGTG 58.952 38.462 0.00 0.00 32.47 3.33
3204 3562 6.483640 GTGTATATAAGCTTCCTTCCTTGTGG 59.516 42.308 0.00 0.00 32.47 4.17
3262 3637 1.142748 GTGATAGCTCAGCTGGCGT 59.857 57.895 10.31 10.33 40.10 5.68
3420 3795 1.134551 GCGCTCTTCTTCTGGATCCTT 60.135 52.381 14.23 0.00 0.00 3.36
3423 3798 3.269178 GCTCTTCTTCTGGATCCTTGTG 58.731 50.000 14.23 1.26 0.00 3.33
3442 3817 3.324846 TGTGAGTGTCCTCTGCAAAGTAT 59.675 43.478 0.00 0.00 38.61 2.12
3473 3934 8.820831 TCAGTAGAAGAGAAAAGAAGAATGGAT 58.179 33.333 0.00 0.00 0.00 3.41
3474 3935 8.881743 CAGTAGAAGAGAAAAGAAGAATGGATG 58.118 37.037 0.00 0.00 0.00 3.51
3476 3937 7.025520 AGAAGAGAAAAGAAGAATGGATGGA 57.974 36.000 0.00 0.00 0.00 3.41
3478 3939 7.556996 AGAAGAGAAAAGAAGAATGGATGGATG 59.443 37.037 0.00 0.00 0.00 3.51
3479 3940 6.127793 AGAGAAAAGAAGAATGGATGGATGG 58.872 40.000 0.00 0.00 0.00 3.51
3480 3941 6.069206 AGAGAAAAGAAGAATGGATGGATGGA 60.069 38.462 0.00 0.00 0.00 3.41
3483 3944 4.383931 AGAAGAATGGATGGATGGATGG 57.616 45.455 0.00 0.00 0.00 3.51
3484 3945 3.985452 AGAAGAATGGATGGATGGATGGA 59.015 43.478 0.00 0.00 0.00 3.41
3485 3946 4.606697 AGAAGAATGGATGGATGGATGGAT 59.393 41.667 0.00 0.00 0.00 3.41
3526 3990 3.697166 ACTGTGTCTCTGTTGGGTTTTT 58.303 40.909 0.00 0.00 0.00 1.94
3624 4088 3.144871 TCATCGGGTCGGTCGCAT 61.145 61.111 0.00 0.00 0.00 4.73
3625 4089 2.658593 CATCGGGTCGGTCGCATC 60.659 66.667 0.00 0.00 0.00 3.91
3626 4090 4.266070 ATCGGGTCGGTCGCATCG 62.266 66.667 0.00 0.00 0.00 3.84
3636 4100 3.806422 TCGCATCGCTTCCGTCGA 61.806 61.111 0.00 0.00 40.45 4.20
3647 4111 2.671351 GCTTCCGTCGATTCACTCTTCA 60.671 50.000 0.00 0.00 0.00 3.02
3652 4116 3.061295 CCGTCGATTCACTCTTCACATTG 59.939 47.826 0.00 0.00 0.00 2.82
3681 4154 1.667151 GCAGGCAGCCATGTTTTCA 59.333 52.632 15.80 0.00 37.23 2.69
3682 4155 0.248289 GCAGGCAGCCATGTTTTCAT 59.752 50.000 15.80 0.00 41.78 2.57
3683 4156 1.738030 GCAGGCAGCCATGTTTTCATC 60.738 52.381 15.80 0.00 38.64 2.92
3709 4182 1.771255 AGGTTCAGGCTCAAAGACAGT 59.229 47.619 0.00 0.00 0.00 3.55
3728 4201 2.569404 AGTTGTTGGTTTTGCCCTTTGA 59.431 40.909 0.00 0.00 36.04 2.69
3886 4359 1.145819 GCCAGGATGAGGACAGAGC 59.854 63.158 0.00 0.00 39.69 4.09
4005 4487 4.192000 CTGCCAAGGTAGCTCGTG 57.808 61.111 0.00 0.00 0.00 4.35
4006 4488 2.047274 TGCCAAGGTAGCTCGTGC 60.047 61.111 0.07 0.07 40.05 5.34
4008 4490 2.391389 GCCAAGGTAGCTCGTGCAC 61.391 63.158 12.58 6.82 42.74 4.57
4009 4491 2.094659 CCAAGGTAGCTCGTGCACG 61.095 63.158 32.76 32.76 42.74 5.34
4010 4492 2.094659 CAAGGTAGCTCGTGCACGG 61.095 63.158 36.41 27.12 42.74 4.94
4014 4496 4.435436 TAGCTCGTGCACGGCCAG 62.435 66.667 36.41 27.16 42.74 4.85
4017 4499 3.114616 CTCGTGCACGGCCAGAAG 61.115 66.667 36.41 22.31 40.29 2.85
4018 4500 3.573772 CTCGTGCACGGCCAGAAGA 62.574 63.158 36.41 15.58 40.29 2.87
4019 4501 2.664851 CGTGCACGGCCAGAAGAA 60.665 61.111 31.15 0.00 35.37 2.52
4020 4502 2.946762 GTGCACGGCCAGAAGAAC 59.053 61.111 2.24 0.00 0.00 3.01
4021 4503 2.281484 TGCACGGCCAGAAGAACC 60.281 61.111 2.24 0.00 0.00 3.62
4022 4504 2.281484 GCACGGCCAGAAGAACCA 60.281 61.111 2.24 0.00 0.00 3.67
4023 4505 1.896660 GCACGGCCAGAAGAACCAA 60.897 57.895 2.24 0.00 0.00 3.67
4024 4506 1.452145 GCACGGCCAGAAGAACCAAA 61.452 55.000 2.24 0.00 0.00 3.28
4025 4507 0.593128 CACGGCCAGAAGAACCAAAG 59.407 55.000 2.24 0.00 0.00 2.77
4039 4521 7.939039 AGAAGAACCAAAGATTGAAGTGTCATA 59.061 33.333 0.00 0.00 32.48 2.15
4063 4545 2.031807 TCAGTAAGACACGATCTAGCGC 59.968 50.000 0.00 0.00 36.27 5.92
4064 4546 1.003759 AGTAAGACACGATCTAGCGCG 60.004 52.381 0.00 0.00 36.27 6.86
4128 4610 5.845391 TGGTTTTGCTTTAGTAAACTGCT 57.155 34.783 7.98 0.00 33.44 4.24
4130 4612 6.966021 TGGTTTTGCTTTAGTAAACTGCTAG 58.034 36.000 7.98 0.00 33.44 3.42
4131 4613 6.544564 TGGTTTTGCTTTAGTAAACTGCTAGT 59.455 34.615 7.98 0.00 33.44 2.57
4185 4667 9.310716 TGATAATAGTACGAGATACCAGTATCG 57.689 37.037 11.21 5.87 44.93 2.92
4187 4669 4.005487 AGTACGAGATACCAGTATCGCT 57.995 45.455 16.24 8.47 44.93 4.93
4188 4670 4.387598 AGTACGAGATACCAGTATCGCTT 58.612 43.478 16.24 11.23 44.93 4.68
4189 4671 3.900388 ACGAGATACCAGTATCGCTTC 57.100 47.619 16.24 7.42 44.93 3.86
4274 4761 7.778083 ACTGACAACGGAAATATACTCATACA 58.222 34.615 0.00 0.00 0.00 2.29
4281 4768 7.948357 ACGGAAATATACTCATACAACTAGCA 58.052 34.615 0.00 0.00 0.00 3.49
4284 4771 8.713271 GGAAATATACTCATACAACTAGCAAGC 58.287 37.037 0.00 0.00 0.00 4.01
4293 4780 4.148825 CTAGCAAGCCCGCTCGGT 62.149 66.667 7.59 0.00 42.62 4.69
4390 4877 1.487976 CAGGCTTGCCTCTGGATCTTA 59.512 52.381 11.72 0.00 0.00 2.10
4408 4895 3.055094 TCTTAGAGTTCATGGTGCCCTTC 60.055 47.826 0.00 0.00 0.00 3.46
4453 4940 2.121832 TTGAGGGGCCTTCTCCGA 59.878 61.111 17.30 8.97 0.00 4.55
4543 5030 3.201353 TCCTCAGTATCCTCAGACGAG 57.799 52.381 0.00 0.00 39.16 4.18
4544 5031 2.506231 TCCTCAGTATCCTCAGACGAGT 59.494 50.000 0.00 0.00 37.59 4.18
4545 5032 3.054287 TCCTCAGTATCCTCAGACGAGTT 60.054 47.826 0.00 0.00 37.59 3.01
4612 5099 1.153449 GCCATCGTCGGTTGGATCA 60.153 57.895 16.37 0.00 35.40 2.92
4615 5102 1.405526 CCATCGTCGGTTGGATCAGTT 60.406 52.381 8.88 0.00 35.40 3.16
4668 5155 1.709147 GCATGCTGCAAGGTAGGTCG 61.709 60.000 11.37 0.00 44.26 4.79
4669 5156 0.108186 CATGCTGCAAGGTAGGTCGA 60.108 55.000 6.36 0.00 0.00 4.20
4769 5260 7.273320 AGCTTCATGTTTATCTGAATCCATG 57.727 36.000 0.00 0.00 31.39 3.66
4822 5313 6.071447 TCCTGAACAATATCCACCAAAACATG 60.071 38.462 0.00 0.00 0.00 3.21
4836 5327 5.523552 ACCAAAACATGCTTCAAAAACTAGC 59.476 36.000 0.00 0.00 0.00 3.42
4850 5341 8.500753 TCAAAAACTAGCAACTGAGAAAACTA 57.499 30.769 0.00 0.00 0.00 2.24
4857 5348 6.566197 AGCAACTGAGAAAACTAAATCTGG 57.434 37.500 0.00 0.00 0.00 3.86
4890 5381 2.501602 GCAGTGGGCAAAGCTTGGT 61.502 57.895 0.00 0.00 43.97 3.67
4896 5387 1.109323 GGGCAAAGCTTGGTGACACT 61.109 55.000 0.00 0.00 42.67 3.55
4908 5399 6.483640 AGCTTGGTGACACTTTTAAGTTAGAG 59.516 38.462 5.39 0.00 42.67 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 0.824759 GTAGGGCAGATCGAGTTGGT 59.175 55.000 0.00 0.00 0.00 3.67
62 63 5.073144 TCTGGGGAACTGTCTTTTTATCTGT 59.927 40.000 0.00 0.00 0.00 3.41
136 145 0.389296 CCACGTGGTACGAAGCATCA 60.389 55.000 26.95 0.00 46.05 3.07
284 296 2.429930 CAACCCCTCGGCAAGTCA 59.570 61.111 0.00 0.00 0.00 3.41
292 304 1.413077 GAGAGAATACCCAACCCCTCG 59.587 57.143 0.00 0.00 0.00 4.63
338 381 1.591863 GCTCTTGACGCCCGATACC 60.592 63.158 0.00 0.00 0.00 2.73
352 395 1.478631 TCATCGGTGATCACTGCTCT 58.521 50.000 26.94 12.86 37.60 4.09
389 432 4.385825 TGTAGTCGCCTTGTCAAAAGAAT 58.614 39.130 0.00 0.00 0.00 2.40
410 453 5.095691 AGTTTCACGCATACTTTGACTTG 57.904 39.130 0.00 0.00 0.00 3.16
417 460 4.394920 CACCCATTAGTTTCACGCATACTT 59.605 41.667 0.00 0.00 0.00 2.24
418 461 3.938963 CACCCATTAGTTTCACGCATACT 59.061 43.478 0.00 0.00 0.00 2.12
421 464 2.487762 CACACCCATTAGTTTCACGCAT 59.512 45.455 0.00 0.00 0.00 4.73
430 473 3.009473 AGTTCATGAGCACACCCATTAGT 59.991 43.478 12.41 0.00 0.00 2.24
516 559 7.345392 AGCATGTCCTTTACAATAAATGGGATT 59.655 33.333 0.00 0.00 42.70 3.01
578 622 8.717821 CATTTCGAAGTTGTCCAGAGTTTTATA 58.282 33.333 0.00 0.00 0.00 0.98
580 624 6.764085 TCATTTCGAAGTTGTCCAGAGTTTTA 59.236 34.615 0.00 0.00 0.00 1.52
581 625 5.588648 TCATTTCGAAGTTGTCCAGAGTTTT 59.411 36.000 0.00 0.00 0.00 2.43
582 626 5.123227 TCATTTCGAAGTTGTCCAGAGTTT 58.877 37.500 0.00 0.00 0.00 2.66
583 627 4.703897 TCATTTCGAAGTTGTCCAGAGTT 58.296 39.130 0.00 0.00 0.00 3.01
584 628 4.310769 CTCATTTCGAAGTTGTCCAGAGT 58.689 43.478 0.00 0.00 0.00 3.24
585 629 3.681897 CCTCATTTCGAAGTTGTCCAGAG 59.318 47.826 0.00 0.00 0.00 3.35
586 630 3.664107 CCTCATTTCGAAGTTGTCCAGA 58.336 45.455 0.00 0.00 0.00 3.86
587 631 2.160417 GCCTCATTTCGAAGTTGTCCAG 59.840 50.000 0.00 0.00 0.00 3.86
588 632 2.151202 GCCTCATTTCGAAGTTGTCCA 58.849 47.619 0.00 0.00 0.00 4.02
589 633 1.468914 GGCCTCATTTCGAAGTTGTCC 59.531 52.381 0.00 1.63 0.00 4.02
590 634 2.151202 TGGCCTCATTTCGAAGTTGTC 58.849 47.619 3.32 0.00 0.00 3.18
591 635 2.270352 TGGCCTCATTTCGAAGTTGT 57.730 45.000 3.32 0.00 0.00 3.32
592 636 2.669391 GCTTGGCCTCATTTCGAAGTTG 60.669 50.000 3.32 0.73 0.00 3.16
593 637 1.541588 GCTTGGCCTCATTTCGAAGTT 59.458 47.619 3.32 0.00 0.00 2.66
594 638 1.168714 GCTTGGCCTCATTTCGAAGT 58.831 50.000 3.32 0.00 0.00 3.01
595 639 0.097674 CGCTTGGCCTCATTTCGAAG 59.902 55.000 3.32 0.00 0.00 3.79
596 640 0.605319 ACGCTTGGCCTCATTTCGAA 60.605 50.000 3.32 0.00 0.00 3.71
597 641 1.003839 ACGCTTGGCCTCATTTCGA 60.004 52.632 3.32 0.00 0.00 3.71
598 642 1.021390 AGACGCTTGGCCTCATTTCG 61.021 55.000 3.32 1.48 0.00 3.46
599 643 1.168714 AAGACGCTTGGCCTCATTTC 58.831 50.000 3.32 0.00 0.00 2.17
600 644 2.489938 TAAGACGCTTGGCCTCATTT 57.510 45.000 3.32 0.00 0.00 2.32
601 645 2.489938 TTAAGACGCTTGGCCTCATT 57.510 45.000 3.32 0.00 0.00 2.57
602 646 2.717639 ATTAAGACGCTTGGCCTCAT 57.282 45.000 3.32 0.00 0.00 2.90
603 647 2.235155 TGTATTAAGACGCTTGGCCTCA 59.765 45.455 3.32 0.00 0.00 3.86
604 648 2.901249 TGTATTAAGACGCTTGGCCTC 58.099 47.619 3.32 0.00 0.00 4.70
605 649 3.560636 ATGTATTAAGACGCTTGGCCT 57.439 42.857 3.32 0.00 0.00 5.19
606 650 4.378459 GCATATGTATTAAGACGCTTGGCC 60.378 45.833 4.29 0.00 0.00 5.36
607 651 4.213270 TGCATATGTATTAAGACGCTTGGC 59.787 41.667 4.29 0.00 0.00 4.52
608 652 5.922739 TGCATATGTATTAAGACGCTTGG 57.077 39.130 4.29 0.00 0.00 3.61
609 653 8.613613 TTTTTGCATATGTATTAAGACGCTTG 57.386 30.769 4.29 0.00 0.00 4.01
633 677 8.070171 GTGATCCGATCGACAATAATGATTTTT 58.930 33.333 18.66 0.00 0.00 1.94
634 678 7.226523 TGTGATCCGATCGACAATAATGATTTT 59.773 33.333 18.66 0.00 0.00 1.82
635 679 6.705825 TGTGATCCGATCGACAATAATGATTT 59.294 34.615 18.66 0.00 0.00 2.17
636 680 6.146184 GTGTGATCCGATCGACAATAATGATT 59.854 38.462 18.66 0.00 0.00 2.57
637 681 5.635280 GTGTGATCCGATCGACAATAATGAT 59.365 40.000 18.66 7.83 0.00 2.45
638 682 4.982295 GTGTGATCCGATCGACAATAATGA 59.018 41.667 18.66 2.47 0.00 2.57
639 683 4.143535 CGTGTGATCCGATCGACAATAATG 60.144 45.833 18.66 0.00 0.00 1.90
640 684 3.981416 CGTGTGATCCGATCGACAATAAT 59.019 43.478 18.66 0.00 0.00 1.28
641 685 3.368495 CGTGTGATCCGATCGACAATAA 58.632 45.455 18.66 0.00 0.00 1.40
642 686 2.287368 CCGTGTGATCCGATCGACAATA 60.287 50.000 18.66 4.24 0.00 1.90
643 687 1.536072 CCGTGTGATCCGATCGACAAT 60.536 52.381 18.66 7.01 0.00 2.71
644 688 0.179148 CCGTGTGATCCGATCGACAA 60.179 55.000 18.66 1.56 0.00 3.18
645 689 1.431845 CCGTGTGATCCGATCGACA 59.568 57.895 18.66 10.15 0.00 4.35
646 690 1.944676 GCCGTGTGATCCGATCGAC 60.945 63.158 18.66 7.24 0.00 4.20
653 697 1.669760 TTGTTCGGCCGTGTGATCC 60.670 57.895 27.15 6.74 0.00 3.36
747 810 0.107410 AACGTTGGCCAGTTCACTCA 60.107 50.000 5.11 0.00 0.00 3.41
776 839 0.822532 ATCCTATTCGACCGGCGTCT 60.823 55.000 16.00 8.66 41.80 4.18
791 854 9.685979 CTGTCCCGATCAGAAAAGGTAAATCCT 62.686 44.444 0.00 0.00 40.56 3.24
795 858 4.575885 CTGTCCCGATCAGAAAAGGTAAA 58.424 43.478 0.00 0.00 35.20 2.01
798 861 1.339151 GCTGTCCCGATCAGAAAAGGT 60.339 52.381 0.00 0.00 35.20 3.50
799 862 1.339055 TGCTGTCCCGATCAGAAAAGG 60.339 52.381 0.00 0.00 35.20 3.11
800 863 1.734465 GTGCTGTCCCGATCAGAAAAG 59.266 52.381 0.00 0.00 35.20 2.27
1157 1244 1.473965 GGCAAAGAGAGATCATCGGCA 60.474 52.381 0.00 0.00 0.00 5.69
1172 1289 3.486708 CGTATTAAGCGCATCAAGGCAAA 60.487 43.478 11.47 0.00 0.00 3.68
1179 1296 2.469826 CACTCCGTATTAAGCGCATCA 58.530 47.619 11.47 0.00 0.00 3.07
1325 1463 0.758123 GGGAGCAGAGGGAAGATGAG 59.242 60.000 0.00 0.00 0.00 2.90
1332 1470 3.414759 TGTATAAAGGGAGCAGAGGGA 57.585 47.619 0.00 0.00 0.00 4.20
1355 1493 9.991906 CCTCATTTTGCAATTAATAAGATGGAT 57.008 29.630 0.00 0.00 0.00 3.41
1356 1494 8.423349 CCCTCATTTTGCAATTAATAAGATGGA 58.577 33.333 0.00 0.00 0.00 3.41
1367 1505 2.501316 GCTACCCCCTCATTTTGCAATT 59.499 45.455 0.00 0.00 0.00 2.32
1464 1602 3.825328 AGTCTGAAACTGGAAATGCAGT 58.175 40.909 1.35 1.35 36.65 4.40
1499 1637 2.561569 CATCAGCTCTGCATCATCACA 58.438 47.619 0.00 0.00 0.00 3.58
1500 1638 1.264557 GCATCAGCTCTGCATCATCAC 59.735 52.381 11.94 0.00 39.46 3.06
1572 1710 0.394762 GCTGGGAGGAATGCATGTCA 60.395 55.000 0.00 0.00 0.00 3.58
1609 1747 0.914644 CCTCCATCTTCTTGCAGGGA 59.085 55.000 0.00 0.00 0.00 4.20
1708 1846 4.020039 TCTCTTTAAACTAACGGCCCATCA 60.020 41.667 0.00 0.00 0.00 3.07
1775 1914 7.489757 GCACTAACTAACCTGAATTAGAGTGAG 59.510 40.741 14.07 0.00 38.28 3.51
1794 1933 4.174762 GAGCAAGGTAGTAGTGCACTAAC 58.825 47.826 27.61 21.68 46.33 2.34
1795 1934 3.830178 TGAGCAAGGTAGTAGTGCACTAA 59.170 43.478 27.61 11.20 41.45 2.24
1806 1946 7.389053 ACTCTTAAAATTCAGTGAGCAAGGTAG 59.611 37.037 0.00 0.00 0.00 3.18
1829 2117 1.954146 TCTTTGTGCGCACCGACTC 60.954 57.895 35.72 12.44 0.00 3.36
1833 2121 0.929824 CTTTGTCTTTGTGCGCACCG 60.930 55.000 35.72 23.66 0.00 4.94
1864 2175 1.960689 TGCAAGAACTGGGGTTAAAGC 59.039 47.619 0.00 0.00 35.58 3.51
1894 2205 6.002704 GGATCATTCCAGCATTAGACATCTT 58.997 40.000 0.00 0.00 42.12 2.40
1901 2212 5.495926 ACCTAGGATCATTCCAGCATTAG 57.504 43.478 17.98 0.00 45.30 1.73
1902 2213 6.239887 GGTTACCTAGGATCATTCCAGCATTA 60.240 42.308 17.98 0.00 45.30 1.90
1946 2258 2.086610 ACTTTTCCCTGCCAACACAT 57.913 45.000 0.00 0.00 0.00 3.21
2105 2417 3.053395 TGGCTCCTCCTAAAATCAAGCAT 60.053 43.478 0.00 0.00 35.26 3.79
2108 2420 3.950395 CCTTGGCTCCTCCTAAAATCAAG 59.050 47.826 0.00 0.00 35.26 3.02
2111 2423 3.653835 ACCTTGGCTCCTCCTAAAATC 57.346 47.619 0.00 0.00 35.26 2.17
2112 2424 5.015284 AGTTTACCTTGGCTCCTCCTAAAAT 59.985 40.000 0.00 0.00 35.26 1.82
2113 2425 4.352893 AGTTTACCTTGGCTCCTCCTAAAA 59.647 41.667 0.00 0.00 35.26 1.52
2115 2427 3.527937 AGTTTACCTTGGCTCCTCCTAA 58.472 45.455 0.00 0.00 35.26 2.69
2116 2428 3.200958 AGTTTACCTTGGCTCCTCCTA 57.799 47.619 0.00 0.00 35.26 2.94
2117 2429 2.046280 AGTTTACCTTGGCTCCTCCT 57.954 50.000 0.00 0.00 35.26 3.69
2118 2430 2.881111 AAGTTTACCTTGGCTCCTCC 57.119 50.000 0.00 0.00 30.18 4.30
2119 2431 3.751518 TGAAAGTTTACCTTGGCTCCTC 58.248 45.455 0.00 0.00 32.32 3.71
2120 2432 3.876309 TGAAAGTTTACCTTGGCTCCT 57.124 42.857 0.00 0.00 32.32 3.69
2121 2433 5.475564 TGTTATGAAAGTTTACCTTGGCTCC 59.524 40.000 0.00 0.00 32.32 4.70
2122 2434 6.206829 AGTGTTATGAAAGTTTACCTTGGCTC 59.793 38.462 0.00 0.00 32.32 4.70
2123 2435 6.016276 CAGTGTTATGAAAGTTTACCTTGGCT 60.016 38.462 0.00 0.00 32.32 4.75
2124 2436 6.149633 CAGTGTTATGAAAGTTTACCTTGGC 58.850 40.000 0.00 0.00 32.32 4.52
2125 2437 7.272037 ACAGTGTTATGAAAGTTTACCTTGG 57.728 36.000 0.00 0.00 32.32 3.61
2126 2438 8.621286 AGAACAGTGTTATGAAAGTTTACCTTG 58.379 33.333 8.88 0.00 32.32 3.61
2127 2439 8.747538 AGAACAGTGTTATGAAAGTTTACCTT 57.252 30.769 8.88 0.00 33.79 3.50
2133 2445 8.396272 AGCAATAGAACAGTGTTATGAAAGTT 57.604 30.769 13.34 0.00 0.00 2.66
2134 2446 7.661437 TGAGCAATAGAACAGTGTTATGAAAGT 59.339 33.333 13.34 0.00 0.00 2.66
2135 2447 8.032952 TGAGCAATAGAACAGTGTTATGAAAG 57.967 34.615 13.34 2.29 0.00 2.62
2137 2449 7.386059 TCTGAGCAATAGAACAGTGTTATGAA 58.614 34.615 13.34 0.00 0.00 2.57
2140 2452 7.223582 CGAATCTGAGCAATAGAACAGTGTTAT 59.776 37.037 8.88 8.63 0.00 1.89
2141 2453 6.531594 CGAATCTGAGCAATAGAACAGTGTTA 59.468 38.462 8.88 0.00 0.00 2.41
2327 2661 0.807496 GCAGTTCCAGAGGATTGCAC 59.193 55.000 14.43 0.00 40.23 4.57
2337 2671 1.902508 TCTTAGGTCCTGCAGTTCCAG 59.097 52.381 21.17 13.29 0.00 3.86
2481 2828 4.563337 TGTTCGTATGAAGAGGATACGG 57.437 45.455 11.26 0.00 45.64 4.02
2482 2829 7.753659 AGATATGTTCGTATGAAGAGGATACG 58.246 38.462 0.00 0.00 46.52 3.06
2516 2867 3.906720 TTAGTAGGGCAGGTTTAGCAG 57.093 47.619 0.00 0.00 0.00 4.24
2519 2871 6.657541 TGTTTTGATTAGTAGGGCAGGTTTAG 59.342 38.462 0.00 0.00 0.00 1.85
2527 2879 5.201243 AGGGAATGTTTTGATTAGTAGGGC 58.799 41.667 0.00 0.00 0.00 5.19
2549 2901 5.766222 ACTGCTTAACAAAAGAATGCTGAG 58.234 37.500 0.00 0.00 0.00 3.35
2580 2932 4.497674 GCGTAGTCTGATTTAGTGACCGAT 60.498 45.833 0.00 0.00 0.00 4.18
2819 3175 7.877097 TCTGGGGATTATCAAAAACACAATTTG 59.123 33.333 0.00 0.00 38.76 2.32
2839 3195 0.532862 CCCGAAACATCGATCTGGGG 60.533 60.000 0.00 0.00 34.64 4.96
2845 3201 4.142469 GGAATTTTCACCCGAAACATCGAT 60.142 41.667 0.00 0.00 40.84 3.59
2936 3292 1.073923 ACCTAAGTGGAAGCAAGGGTG 59.926 52.381 0.00 0.00 39.71 4.61
2937 3293 1.073923 CACCTAAGTGGAAGCAAGGGT 59.926 52.381 0.00 0.00 40.55 4.34
2976 3332 3.310501 CGTTCAGCAGCATGAATATCACA 59.689 43.478 0.00 0.00 41.05 3.58
3012 3368 2.882761 CTGGATATGGCAGTGTGATTGG 59.117 50.000 0.00 0.00 0.00 3.16
3048 3404 2.967201 TGGGTAGGGTATACGATGTTGG 59.033 50.000 0.00 0.00 0.00 3.77
3063 3419 3.834489 ATCAGATCAGCAAGTGGGTAG 57.166 47.619 0.00 0.00 0.00 3.18
3064 3420 3.519107 TCAATCAGATCAGCAAGTGGGTA 59.481 43.478 0.00 0.00 0.00 3.69
3065 3421 2.306805 TCAATCAGATCAGCAAGTGGGT 59.693 45.455 0.00 0.00 0.00 4.51
3066 3422 2.681848 GTCAATCAGATCAGCAAGTGGG 59.318 50.000 0.00 0.00 0.00 4.61
3067 3423 2.681848 GGTCAATCAGATCAGCAAGTGG 59.318 50.000 0.00 0.00 0.00 4.00
3068 3424 3.374367 CAGGTCAATCAGATCAGCAAGTG 59.626 47.826 0.00 0.00 0.00 3.16
3069 3425 3.607741 CAGGTCAATCAGATCAGCAAGT 58.392 45.455 0.00 0.00 0.00 3.16
3070 3426 2.355132 GCAGGTCAATCAGATCAGCAAG 59.645 50.000 0.00 0.00 39.48 4.01
3071 3427 2.290450 TGCAGGTCAATCAGATCAGCAA 60.290 45.455 0.00 0.00 45.48 3.91
3072 3428 1.279846 TGCAGGTCAATCAGATCAGCA 59.720 47.619 0.00 0.00 46.15 4.41
3073 3429 1.941294 CTGCAGGTCAATCAGATCAGC 59.059 52.381 5.57 0.00 40.05 4.26
3074 3430 2.562635 CCTGCAGGTCAATCAGATCAG 58.437 52.381 25.53 0.00 0.00 2.90
3075 3431 1.407851 GCCTGCAGGTCAATCAGATCA 60.408 52.381 32.81 0.00 37.57 2.92
3076 3432 1.134159 AGCCTGCAGGTCAATCAGATC 60.134 52.381 32.81 12.74 37.57 2.75
3077 3433 0.917533 AGCCTGCAGGTCAATCAGAT 59.082 50.000 32.81 0.39 37.57 2.90
3078 3434 0.035725 CAGCCTGCAGGTCAATCAGA 60.036 55.000 32.81 0.00 37.57 3.27
3138 3494 2.757077 CTGGGGTTCAGGGACACC 59.243 66.667 0.00 0.00 43.68 4.16
3176 3534 7.770897 ACAAGGAAGGAAGCTTATATACACAAG 59.229 37.037 0.00 0.00 0.00 3.16
3179 3537 6.483640 CCACAAGGAAGGAAGCTTATATACAC 59.516 42.308 0.00 0.00 36.89 2.90
3184 3542 5.253330 CAACCACAAGGAAGGAAGCTTATA 58.747 41.667 0.00 0.00 38.69 0.98
3191 3549 1.691196 CTGCAACCACAAGGAAGGAA 58.309 50.000 0.00 0.00 38.69 3.36
3197 3555 2.198287 AGCAGCTGCAACCACAAGG 61.198 57.895 38.24 0.00 45.16 3.61
3198 3556 1.007734 CAGCAGCTGCAACCACAAG 60.008 57.895 38.24 14.36 45.16 3.16
3199 3557 3.121934 CAGCAGCTGCAACCACAA 58.878 55.556 38.24 0.00 45.16 3.33
3262 3637 2.780643 CTTCTCCGCGACGTCGTA 59.219 61.111 35.48 21.50 42.22 3.43
3339 3714 3.419858 AGGATCACCCTGGGCTTG 58.580 61.111 14.08 4.61 45.61 4.01
3420 3795 1.486310 ACTTTGCAGAGGACACTCACA 59.514 47.619 9.34 0.00 46.44 3.58
3423 3798 4.193826 TGATACTTTGCAGAGGACACTC 57.806 45.455 9.34 0.00 44.31 3.51
3473 3934 2.136974 TCCATCCATCCATCCATCCA 57.863 50.000 0.00 0.00 0.00 3.41
3474 3935 2.949054 GCATCCATCCATCCATCCATCC 60.949 54.545 0.00 0.00 0.00 3.51
3476 3937 2.000803 AGCATCCATCCATCCATCCAT 58.999 47.619 0.00 0.00 0.00 3.41
3478 3939 2.575279 ACTAGCATCCATCCATCCATCC 59.425 50.000 0.00 0.00 0.00 3.51
3479 3940 3.262660 TCACTAGCATCCATCCATCCATC 59.737 47.826 0.00 0.00 0.00 3.51
3480 3941 3.008813 GTCACTAGCATCCATCCATCCAT 59.991 47.826 0.00 0.00 0.00 3.41
3483 3944 5.011533 AGTTAGTCACTAGCATCCATCCATC 59.988 44.000 1.08 0.00 31.97 3.51
3484 3945 4.904251 AGTTAGTCACTAGCATCCATCCAT 59.096 41.667 1.08 0.00 31.97 3.41
3485 3946 4.100035 CAGTTAGTCACTAGCATCCATCCA 59.900 45.833 1.08 0.00 32.76 3.41
3526 3990 3.576550 GGTCTTGCAAATTGGTAAAGGGA 59.423 43.478 0.00 0.00 0.00 4.20
3529 3993 4.039124 AGGTGGTCTTGCAAATTGGTAAAG 59.961 41.667 0.00 0.00 0.00 1.85
3532 3996 3.237268 AGGTGGTCTTGCAAATTGGTA 57.763 42.857 0.00 0.00 0.00 3.25
3533 3997 2.086610 AGGTGGTCTTGCAAATTGGT 57.913 45.000 0.00 0.00 0.00 3.67
3535 3999 3.201726 CGTAGGTGGTCTTGCAAATTG 57.798 47.619 0.00 0.00 0.00 2.32
3624 4088 0.179171 GAGTGAATCGACGGAAGCGA 60.179 55.000 0.00 0.00 42.00 4.93
3625 4089 0.179161 AGAGTGAATCGACGGAAGCG 60.179 55.000 0.00 0.00 0.00 4.68
3626 4090 1.921230 GAAGAGTGAATCGACGGAAGC 59.079 52.381 0.00 0.00 0.00 3.86
3627 4091 2.917971 GTGAAGAGTGAATCGACGGAAG 59.082 50.000 0.00 0.00 0.00 3.46
3628 4092 2.295070 TGTGAAGAGTGAATCGACGGAA 59.705 45.455 0.00 0.00 0.00 4.30
3636 4100 4.401022 TCTTGGCAATGTGAAGAGTGAAT 58.599 39.130 0.00 0.00 0.00 2.57
3647 4111 1.891150 CCTGCTTCTTCTTGGCAATGT 59.109 47.619 0.00 0.00 35.49 2.71
3652 4116 1.881602 CTGCCTGCTTCTTCTTGGC 59.118 57.895 0.00 0.00 43.49 4.52
3681 4154 5.249393 TCTTTGAGCCTGAACCTTAGAAGAT 59.751 40.000 0.00 0.00 0.00 2.40
3682 4155 4.593206 TCTTTGAGCCTGAACCTTAGAAGA 59.407 41.667 0.00 0.00 0.00 2.87
3683 4156 4.693095 GTCTTTGAGCCTGAACCTTAGAAG 59.307 45.833 0.00 0.00 0.00 2.85
3709 4182 3.922171 ATCAAAGGGCAAAACCAACAA 57.078 38.095 0.00 0.00 42.05 2.83
3728 4201 0.107508 CTGGATGACGACCCTGCAAT 60.108 55.000 0.00 0.00 0.00 3.56
3886 4359 1.233285 GCGGCAGCATCCTTGGATAG 61.233 60.000 3.18 0.00 44.35 2.08
4003 4485 2.617274 GGTTCTTCTGGCCGTGCAC 61.617 63.158 6.82 6.82 0.00 4.57
4004 4486 2.281484 GGTTCTTCTGGCCGTGCA 60.281 61.111 0.00 0.00 0.00 4.57
4005 4487 1.452145 TTTGGTTCTTCTGGCCGTGC 61.452 55.000 0.00 0.00 0.00 5.34
4006 4488 0.593128 CTTTGGTTCTTCTGGCCGTG 59.407 55.000 0.00 0.00 0.00 4.94
4008 4490 1.826385 ATCTTTGGTTCTTCTGGCCG 58.174 50.000 0.00 0.00 0.00 6.13
4009 4491 3.157087 TCAATCTTTGGTTCTTCTGGCC 58.843 45.455 0.00 0.00 0.00 5.36
4010 4492 4.279420 ACTTCAATCTTTGGTTCTTCTGGC 59.721 41.667 0.00 0.00 0.00 4.85
4014 4496 6.377327 TGACACTTCAATCTTTGGTTCTTC 57.623 37.500 0.00 0.00 0.00 2.87
4015 4497 6.966534 ATGACACTTCAATCTTTGGTTCTT 57.033 33.333 0.00 0.00 34.61 2.52
4018 4500 9.685276 TGATATATGACACTTCAATCTTTGGTT 57.315 29.630 0.00 0.00 34.61 3.67
4019 4501 9.334947 CTGATATATGACACTTCAATCTTTGGT 57.665 33.333 0.00 0.00 34.61 3.67
4020 4502 9.334947 ACTGATATATGACACTTCAATCTTTGG 57.665 33.333 0.00 0.00 34.61 3.28
4039 4521 5.391097 GCGCTAGATCGTGTCTTACTGATAT 60.391 44.000 0.00 0.00 38.42 1.63
4063 4545 2.660236 GTGTAACTAGTTGCCGTTCTCG 59.340 50.000 18.56 0.00 0.00 4.04
4064 4546 2.991866 GGTGTAACTAGTTGCCGTTCTC 59.008 50.000 18.56 3.65 36.74 2.87
4293 4780 4.329545 GGTGCGGTCTTGAGCCCA 62.330 66.667 0.00 0.00 0.00 5.36
4295 4782 1.896660 TTTGGTGCGGTCTTGAGCC 60.897 57.895 0.00 0.00 0.00 4.70
4296 4783 1.282875 GTTTGGTGCGGTCTTGAGC 59.717 57.895 0.00 0.00 0.00 4.26
4408 4895 3.203716 GAACGCTTACAAGGATAAGGGG 58.796 50.000 12.46 0.00 45.01 4.79
4543 5030 1.971336 CGACGACGACGATGACAAC 59.029 57.895 15.32 0.00 42.66 3.32
4544 5031 1.794785 GCGACGACGACGATGACAA 60.795 57.895 22.94 0.00 42.66 3.18
4545 5032 2.202260 GCGACGACGACGATGACA 60.202 61.111 22.94 0.00 42.66 3.58
4612 5099 2.549754 CAGTGGCGAGAACAAATCAACT 59.450 45.455 0.00 0.00 0.00 3.16
4615 5102 1.522668 CCAGTGGCGAGAACAAATCA 58.477 50.000 0.00 0.00 0.00 2.57
4665 5152 5.348986 TGGATATTGCTTACTTCTGTCGAC 58.651 41.667 9.11 9.11 0.00 4.20
4668 5155 7.792374 TCAATGGATATTGCTTACTTCTGTC 57.208 36.000 0.00 0.00 42.71 3.51
4669 5156 9.851686 TTATCAATGGATATTGCTTACTTCTGT 57.148 29.630 0.00 0.00 42.71 3.41
4747 5238 8.217131 TGTCATGGATTCAGATAAACATGAAG 57.783 34.615 0.00 0.00 44.10 3.02
4769 5260 1.537202 GGTGTGCCTGATCTTGTTGTC 59.463 52.381 0.00 0.00 0.00 3.18
4822 5313 5.424121 TCTCAGTTGCTAGTTTTTGAAGC 57.576 39.130 0.00 0.00 0.00 3.86
4836 5327 6.486657 TCCACCAGATTTAGTTTTCTCAGTTG 59.513 38.462 0.00 0.00 0.00 3.16
4850 5341 4.467769 CCAAGCTATCATCCACCAGATTT 58.532 43.478 0.00 0.00 30.59 2.17
4857 5348 1.945394 CACTGCCAAGCTATCATCCAC 59.055 52.381 0.00 0.00 0.00 4.02
4908 5399 9.717942 AGGTATTGATCTGCATCTAAATACTTC 57.282 33.333 15.95 6.57 32.91 3.01


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

AutoCloner maintained by Alex Coulton.