Multiple sequence alignment - TraesCS3B01G349100

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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 TraesCS3B01G349100 chr3B 100.000 6548 0 0 1 6548 559334783 559341330 0.000000e+00 12092.0
1 TraesCS3B01G349100 chr3D 91.839 3431 159 46 3201 6548 427813505 427816897 0.000000e+00 4673.0
2 TraesCS3B01G349100 chr3D 89.638 2268 141 33 564 2763 427810886 427813127 0.000000e+00 2800.0
3 TraesCS3B01G349100 chr3D 94.150 359 20 1 1 359 427810373 427810730 4.460000e-151 545.0
4 TraesCS3B01G349100 chr3D 88.830 376 26 9 2749 3119 427813142 427813506 1.300000e-121 448.0
5 TraesCS3B01G349100 chr3D 90.588 85 8 0 3118 3202 60275859 60275943 5.370000e-21 113.0
6 TraesCS3B01G349100 chr3D 90.196 51 3 2 401 450 213396624 213396575 1.520000e-06 65.8
7 TraesCS3B01G349100 chr3A 93.919 1480 77 5 3201 4671 557953162 557951687 0.000000e+00 2222.0
8 TraesCS3B01G349100 chr3A 95.472 1303 40 6 5247 6548 557951041 557949757 0.000000e+00 2061.0
9 TraesCS3B01G349100 chr3A 89.415 1436 84 25 564 1945 557955683 557954262 0.000000e+00 1748.0
10 TraesCS3B01G349100 chr3A 92.098 1101 49 16 2053 3119 557954257 557953161 0.000000e+00 1517.0
11 TraesCS3B01G349100 chr3A 88.689 610 36 6 4672 5261 557951655 557951059 0.000000e+00 713.0
12 TraesCS3B01G349100 chr3A 88.267 554 42 9 1 532 557956238 557955686 5.540000e-180 641.0
13 TraesCS3B01G349100 chr3A 90.588 85 8 0 3118 3202 299209386 299209470 5.370000e-21 113.0
14 TraesCS3B01G349100 chr2B 90.868 219 18 2 6325 6542 751841802 751842019 6.420000e-75 292.0
15 TraesCS3B01G349100 chr2D 90.541 222 16 4 6329 6545 616634858 616635079 8.310000e-74 289.0
16 TraesCS3B01G349100 chr2D 90.588 85 8 0 3118 3202 525600399 525600483 5.370000e-21 113.0
17 TraesCS3B01G349100 chr2A 90.090 222 19 3 6326 6545 746851959 746852179 1.070000e-72 285.0
18 TraesCS3B01G349100 chr2A 90.588 85 8 0 3118 3202 412059347 412059431 5.370000e-21 113.0
19 TraesCS3B01G349100 chrUn 89.041 146 16 0 6392 6537 98211522 98211667 1.450000e-41 182.0
20 TraesCS3B01G349100 chr6B 89.041 146 16 0 6392 6537 107771734 107771879 1.450000e-41 182.0
21 TraesCS3B01G349100 chr6A 89.041 146 16 0 6392 6537 53156746 53156891 1.450000e-41 182.0
22 TraesCS3B01G349100 chr5B 85.802 162 17 5 6390 6547 562048474 562048315 4.060000e-37 167.0
23 TraesCS3B01G349100 chr6D 91.765 85 7 0 3118 3202 190909275 190909359 1.150000e-22 119.0
24 TraesCS3B01G349100 chr6D 89.362 94 8 2 3118 3210 414526173 414526265 4.150000e-22 117.0
25 TraesCS3B01G349100 chr1A 90.588 85 8 0 3118 3202 411923436 411923352 5.370000e-21 113.0
26 TraesCS3B01G349100 chr7A 88.298 94 9 2 3113 3205 138751779 138751687 1.930000e-20 111.0
27 TraesCS3B01G349100 chr5D 89.011 91 8 2 3118 3207 277816386 277816475 1.930000e-20 111.0


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 TraesCS3B01G349100 chr3B 559334783 559341330 6547 False 12092.000000 12092 100.00000 1 6548 1 chr3B.!!$F1 6547
1 TraesCS3B01G349100 chr3D 427810373 427816897 6524 False 2116.500000 4673 91.11425 1 6548 4 chr3D.!!$F2 6547
2 TraesCS3B01G349100 chr3A 557949757 557956238 6481 True 1483.666667 2222 91.31000 1 6548 6 chr3A.!!$R1 6547

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
980 1043 0.178995 CGGAGGAGGAGGGTAGTACC 60.179 65.0 11.20 11.20 37.60 3.34 F
1637 1729 0.520404 CTGCTGCCACTGAATGTGTC 59.480 55.0 0.00 0.00 44.81 3.67 F
1929 2030 0.599558 GCCTGTGCTTCAATTGAGCA 59.400 50.0 21.22 21.22 36.09 4.26 F
3199 3386 0.902531 ATATTATGGGACGGCGGGAG 59.097 55.0 13.24 0.00 0.00 4.30 F
3786 3977 0.969149 CTCTTCTTTTGGGTTGGGCC 59.031 55.0 0.00 0.00 0.00 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2520 2643 1.010170 AGGGGAGCCTGAGGTAAATCT 59.990 52.381 0.0 0.0 0.00 2.40 R
3187 3374 0.393402 AAAATTACTCCCGCCGTCCC 60.393 55.000 0.0 0.0 0.00 4.46 R
3846 4038 1.054231 TATCTGCTGCTCATCTGGGG 58.946 55.000 0.0 0.0 0.00 4.96 R
4728 4967 0.179073 AGTCGGCACATCCAGCATAC 60.179 55.000 0.0 0.0 34.01 2.39 R
5643 5946 0.894141 TTCTCTCTCAGCCAGACAGC 59.106 55.000 0.0 0.0 0.00 4.40 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
105 106 6.097270 TGGAGATGAATGAATGAATGGGAAAC 59.903 38.462 0.00 0.00 0.00 2.78
159 160 3.242641 GGTCTTCGTTTTCTGTGGTGTTC 60.243 47.826 0.00 0.00 0.00 3.18
192 193 3.131577 CCATTAGCCGTGTGGTAGAAGTA 59.868 47.826 0.00 0.00 37.67 2.24
292 304 5.360591 CCTAGGACTGCTCGTTTGAATATT 58.639 41.667 1.05 0.00 0.00 1.28
335 347 2.623416 ACTTGGCTGCTAAGGAAACAAC 59.377 45.455 26.18 0.00 0.00 3.32
361 373 0.838122 AAGTCTACCACCAGCTGGCT 60.838 55.000 33.06 16.54 45.32 4.75
372 384 3.769201 GCTGGCTGCTGTTTTCCT 58.231 55.556 9.31 0.00 38.95 3.36
430 463 7.174253 TGGGATTCTGTGTAATAAGTTGTTGAC 59.826 37.037 0.00 0.00 0.00 3.18
452 485 8.534333 TGACTATCAACAAGTCAGTGTAATTC 57.466 34.615 1.92 0.00 46.38 2.17
455 488 9.337396 ACTATCAACAAGTCAGTGTAATTCAAA 57.663 29.630 0.00 0.00 0.00 2.69
497 540 5.921962 AGTAATCACAGATCTAGTGTGCA 57.078 39.130 18.61 6.66 44.22 4.57
498 541 5.655488 AGTAATCACAGATCTAGTGTGCAC 58.345 41.667 10.75 10.75 44.22 4.57
499 542 3.533606 ATCACAGATCTAGTGTGCACC 57.466 47.619 15.69 5.76 44.22 5.01
500 543 2.247358 TCACAGATCTAGTGTGCACCA 58.753 47.619 15.69 0.00 44.22 4.17
540 588 8.404889 CATAAATCAAAACATTTATGGACGCA 57.595 30.769 14.30 0.00 45.29 5.24
541 589 9.033481 CATAAATCAAAACATTTATGGACGCAT 57.967 29.630 14.30 0.00 45.29 4.73
543 591 8.994429 AAATCAAAACATTTATGGACGCATAA 57.006 26.923 0.00 0.00 0.00 1.90
544 592 7.985634 ATCAAAACATTTATGGACGCATAAC 57.014 32.000 0.00 0.00 0.00 1.89
545 593 6.914259 TCAAAACATTTATGGACGCATAACA 58.086 32.000 0.00 0.00 0.00 2.41
546 594 7.542890 TCAAAACATTTATGGACGCATAACAT 58.457 30.769 0.00 0.00 0.00 2.71
547 595 8.031864 TCAAAACATTTATGGACGCATAACATT 58.968 29.630 0.00 0.00 0.00 2.71
548 596 8.655092 CAAAACATTTATGGACGCATAACATTT 58.345 29.630 0.00 0.00 0.00 2.32
549 597 7.985634 AACATTTATGGACGCATAACATTTC 57.014 32.000 0.00 0.00 0.00 2.17
550 598 7.333528 ACATTTATGGACGCATAACATTTCT 57.666 32.000 0.00 0.00 0.00 2.52
551 599 7.195646 ACATTTATGGACGCATAACATTTCTG 58.804 34.615 0.00 0.00 0.00 3.02
552 600 6.751514 TTTATGGACGCATAACATTTCTGT 57.248 33.333 0.00 0.00 37.12 3.41
553 601 4.882671 ATGGACGCATAACATTTCTGTC 57.117 40.909 0.00 0.00 33.36 3.51
554 602 3.006940 TGGACGCATAACATTTCTGTCC 58.993 45.455 1.66 1.66 43.60 4.02
555 603 3.270877 GGACGCATAACATTTCTGTCCT 58.729 45.455 1.42 0.00 40.88 3.85
556 604 3.689649 GGACGCATAACATTTCTGTCCTT 59.310 43.478 1.42 0.00 40.88 3.36
557 605 4.156008 GGACGCATAACATTTCTGTCCTTT 59.844 41.667 1.42 0.00 40.88 3.11
558 606 5.046910 ACGCATAACATTTCTGTCCTTTG 57.953 39.130 0.00 0.00 33.36 2.77
559 607 4.518970 ACGCATAACATTTCTGTCCTTTGT 59.481 37.500 0.00 0.00 33.36 2.83
560 608 5.009610 ACGCATAACATTTCTGTCCTTTGTT 59.990 36.000 0.00 0.00 33.36 2.83
561 609 5.343058 CGCATAACATTTCTGTCCTTTGTTG 59.657 40.000 0.00 0.00 33.36 3.33
562 610 6.446318 GCATAACATTTCTGTCCTTTGTTGA 58.554 36.000 0.00 0.00 33.36 3.18
567 615 2.655090 TCTGTCCTTTGTTGATGGCA 57.345 45.000 0.00 0.00 0.00 4.92
618 670 1.523758 GTTAGGCCCCATCTAATGCG 58.476 55.000 0.00 0.00 0.00 4.73
638 690 1.928868 CCCTTTTGTCCCTGAATGCT 58.071 50.000 0.00 0.00 0.00 3.79
879 932 3.175240 CAGTTGGTCGCTCGCTCG 61.175 66.667 0.00 0.00 0.00 5.03
980 1043 0.178995 CGGAGGAGGAGGGTAGTACC 60.179 65.000 11.20 11.20 37.60 3.34
989 1052 0.794934 AGGGTAGTACCACCAGGGAA 59.205 55.000 20.97 0.00 41.02 3.97
1079 1142 1.254954 AGTCGCCTACTCCGTTTCTT 58.745 50.000 0.00 0.00 30.33 2.52
1148 1211 2.657237 CGGTCCGCCTTGTCTTCT 59.343 61.111 0.00 0.00 0.00 2.85
1204 1267 3.479269 CGCCGTCGGAGTTGCTTC 61.479 66.667 17.49 0.00 0.00 3.86
1215 1278 0.668535 AGTTGCTTCTTGCGGGTTTC 59.331 50.000 0.00 0.00 46.63 2.78
1216 1279 0.668535 GTTGCTTCTTGCGGGTTTCT 59.331 50.000 0.00 0.00 46.63 2.52
1219 1282 1.518903 GCTTCTTGCGGGTTTCTGCT 61.519 55.000 0.00 0.00 45.25 4.24
1348 1412 1.739929 TTGTGTTGCCGATCGCGAT 60.740 52.632 23.97 23.97 42.08 4.58
1393 1457 1.018910 CTTCCGTGTTCGTTTTGGGT 58.981 50.000 0.00 0.00 35.01 4.51
1418 1508 5.576563 TTTCAGGGTAGAAATGAACTGGA 57.423 39.130 0.00 0.00 32.91 3.86
1463 1553 3.046968 TGCGGTTTACTAGATGTGCAA 57.953 42.857 0.00 0.00 0.00 4.08
1465 1555 3.815962 TGCGGTTTACTAGATGTGCAAAA 59.184 39.130 0.00 0.00 0.00 2.44
1474 1564 6.076981 ACTAGATGTGCAAAACTTTGGAAG 57.923 37.500 0.00 0.00 40.21 3.46
1476 1566 6.770785 ACTAGATGTGCAAAACTTTGGAAGTA 59.229 34.615 0.00 0.00 41.91 2.24
1496 1586 1.541588 AGGCGATTTGCTCTTCCAAAC 59.458 47.619 0.00 0.00 45.43 2.93
1534 1626 6.652062 ACGAAAAATGGAAAATACCTCGTACT 59.348 34.615 0.00 0.00 35.30 2.73
1535 1627 7.818930 ACGAAAAATGGAAAATACCTCGTACTA 59.181 33.333 0.00 0.00 35.30 1.82
1536 1628 8.112449 CGAAAAATGGAAAATACCTCGTACTAC 58.888 37.037 0.00 0.00 0.00 2.73
1626 1718 1.139654 GTGTCTATGGATCTGCTGCCA 59.860 52.381 0.00 0.00 38.78 4.92
1637 1729 0.520404 CTGCTGCCACTGAATGTGTC 59.480 55.000 0.00 0.00 44.81 3.67
1646 1738 4.021544 GCCACTGAATGTGTCCCATTTTAA 60.022 41.667 0.00 0.00 43.87 1.52
1647 1739 5.337491 GCCACTGAATGTGTCCCATTTTAAT 60.337 40.000 0.00 0.00 43.87 1.40
1648 1740 6.127479 GCCACTGAATGTGTCCCATTTTAATA 60.127 38.462 0.00 0.00 43.87 0.98
1650 1742 7.975616 CCACTGAATGTGTCCCATTTTAATAAG 59.024 37.037 0.00 0.00 43.87 1.73
1651 1743 8.739039 CACTGAATGTGTCCCATTTTAATAAGA 58.261 33.333 0.00 0.00 43.87 2.10
1652 1744 8.739972 ACTGAATGTGTCCCATTTTAATAAGAC 58.260 33.333 0.00 0.00 43.87 3.01
1654 1746 9.083422 TGAATGTGTCCCATTTTAATAAGACAA 57.917 29.630 7.79 2.42 43.87 3.18
1676 1768 9.982651 GACAATAATCCTTATCTACAGTAGCAA 57.017 33.333 2.26 0.00 0.00 3.91
1701 1793 2.423538 GGATTGCCGTGCTAACTTTCAT 59.576 45.455 0.00 0.00 0.00 2.57
1704 1796 2.226330 TGCCGTGCTAACTTTCATTGT 58.774 42.857 0.00 0.00 0.00 2.71
1714 1814 6.088824 GCTAACTTTCATTGTCCTGATTGTG 58.911 40.000 0.00 0.00 0.00 3.33
1724 1824 4.842574 TGTCCTGATTGTGCATAAGCTTA 58.157 39.130 12.73 8.99 42.74 3.09
1727 1827 7.226441 TGTCCTGATTGTGCATAAGCTTATAT 58.774 34.615 18.45 8.38 42.74 0.86
1847 1948 1.216710 GCCACCTCTTCCTCACGAG 59.783 63.158 0.00 0.00 0.00 4.18
1874 1975 5.174395 GCTGGATTCTATAATGATCGTGCT 58.826 41.667 0.00 0.00 0.00 4.40
1929 2030 0.599558 GCCTGTGCTTCAATTGAGCA 59.400 50.000 21.22 21.22 36.09 4.26
1948 2049 8.621532 TTGAGCATGTCAATTCTTTACTTACT 57.378 30.769 6.62 0.00 40.45 2.24
1949 2050 8.621532 TGAGCATGTCAATTCTTTACTTACTT 57.378 30.769 0.00 0.00 29.64 2.24
1950 2051 9.719355 TGAGCATGTCAATTCTTTACTTACTTA 57.281 29.630 0.00 0.00 29.64 2.24
1993 2102 2.242882 ATTGAAAGGCCAGGCAGAAT 57.757 45.000 15.19 0.32 0.00 2.40
2012 2121 6.802608 CAGAATGCAATTGACTATTGACCAT 58.197 36.000 10.34 5.62 45.35 3.55
2014 2123 7.762615 CAGAATGCAATTGACTATTGACCATTT 59.237 33.333 10.34 4.10 45.35 2.32
2025 2134 9.685276 TGACTATTGACCATTTATGAATGTTCT 57.315 29.630 8.81 0.00 40.85 3.01
2029 2138 8.585471 ATTGACCATTTATGAATGTTCTCACT 57.415 30.769 8.81 0.30 40.85 3.41
2042 2151 8.777413 TGAATGTTCTCACTATTCTTTGTCAAG 58.223 33.333 0.00 0.00 33.21 3.02
2046 2155 9.645059 TGTTCTCACTATTCTTTGTCAAGATAG 57.355 33.333 9.42 9.42 38.89 2.08
2085 2194 7.509141 TTGATTACAGAATTCTTTCACAGCA 57.491 32.000 4.86 0.00 34.08 4.41
2238 2347 5.049405 ACTTGAAATTCCAGCTTTACACTCG 60.049 40.000 0.00 0.00 0.00 4.18
2245 2354 2.341257 CAGCTTTACACTCGCATCACT 58.659 47.619 0.00 0.00 0.00 3.41
2379 2496 3.267031 ACCTTAAGTTCCCCTGGATGAAG 59.733 47.826 0.97 0.00 0.00 3.02
2380 2497 3.267031 CCTTAAGTTCCCCTGGATGAAGT 59.733 47.826 0.97 0.00 0.00 3.01
2395 2512 4.279420 GGATGAAGTTTTGTGAAGCTTCCT 59.721 41.667 23.42 9.26 46.46 3.36
2396 2513 4.637483 TGAAGTTTTGTGAAGCTTCCTG 57.363 40.909 23.42 0.00 46.46 3.86
2520 2643 3.774766 ACTGGTGAGCTATGGTTGACATA 59.225 43.478 0.00 0.00 41.03 2.29
2574 2697 6.676950 ACTGCTCTAACTATTGATCAGATCG 58.323 40.000 5.91 0.00 32.67 3.69
2664 2809 1.412343 GGTGGTTGTGCTTGTGGAAAT 59.588 47.619 0.00 0.00 0.00 2.17
2684 2829 8.811017 TGGAAATTGCCTATTGTTATCAAAAGA 58.189 29.630 3.49 0.00 37.11 2.52
2708 2853 7.980662 AGATTTCATATAGCCATCATCTCTTCG 59.019 37.037 0.00 0.00 0.00 3.79
2792 2969 2.603560 GCAGTGGTTCTACGTAATCAGC 59.396 50.000 0.00 0.00 0.00 4.26
2802 2979 7.095102 GGTTCTACGTAATCAGCAAAACCTTTA 60.095 37.037 0.00 0.00 32.74 1.85
2819 2996 4.753107 ACCTTTATCGACAACGTTTCACAT 59.247 37.500 0.00 0.00 40.69 3.21
2970 3149 5.822132 AGTTCTTCCTATAGCTGATGCAT 57.178 39.130 0.00 0.00 42.74 3.96
3042 3229 4.758773 ATTGGCCCAAGTTGATTAATGG 57.241 40.909 3.87 0.00 0.00 3.16
3113 3300 7.092137 TGAATGATTCAGTGAAAGGCTATTG 57.908 36.000 10.14 0.00 34.08 1.90
3114 3301 6.885918 TGAATGATTCAGTGAAAGGCTATTGA 59.114 34.615 10.14 0.00 34.08 2.57
3115 3302 6.939132 ATGATTCAGTGAAAGGCTATTGAG 57.061 37.500 10.14 0.00 0.00 3.02
3128 3315 4.776795 GCTATTGAGCTACTCCCTCTAC 57.223 50.000 0.00 0.00 45.98 2.59
3129 3316 3.508402 GCTATTGAGCTACTCCCTCTACC 59.492 52.174 0.00 0.00 45.98 3.18
3130 3317 3.983533 ATTGAGCTACTCCCTCTACCT 57.016 47.619 0.00 0.00 0.00 3.08
3131 3318 3.300239 TTGAGCTACTCCCTCTACCTC 57.700 52.381 0.00 0.00 0.00 3.85
3132 3319 2.206223 TGAGCTACTCCCTCTACCTCA 58.794 52.381 0.00 0.00 0.00 3.86
3133 3320 2.092321 TGAGCTACTCCCTCTACCTCAC 60.092 54.545 0.00 0.00 0.00 3.51
3134 3321 1.923850 AGCTACTCCCTCTACCTCACA 59.076 52.381 0.00 0.00 0.00 3.58
3135 3322 2.312140 AGCTACTCCCTCTACCTCACAA 59.688 50.000 0.00 0.00 0.00 3.33
3136 3323 3.052490 AGCTACTCCCTCTACCTCACAAT 60.052 47.826 0.00 0.00 0.00 2.71
3137 3324 4.168283 AGCTACTCCCTCTACCTCACAATA 59.832 45.833 0.00 0.00 0.00 1.90
3138 3325 5.081032 GCTACTCCCTCTACCTCACAATAT 58.919 45.833 0.00 0.00 0.00 1.28
3139 3326 6.045695 AGCTACTCCCTCTACCTCACAATATA 59.954 42.308 0.00 0.00 0.00 0.86
3140 3327 6.720288 GCTACTCCCTCTACCTCACAATATAA 59.280 42.308 0.00 0.00 0.00 0.98
3141 3328 7.094118 GCTACTCCCTCTACCTCACAATATAAG 60.094 44.444 0.00 0.00 0.00 1.73
3142 3329 6.923670 ACTCCCTCTACCTCACAATATAAGA 58.076 40.000 0.00 0.00 0.00 2.10
3143 3330 6.778559 ACTCCCTCTACCTCACAATATAAGAC 59.221 42.308 0.00 0.00 0.00 3.01
3144 3331 5.768662 TCCCTCTACCTCACAATATAAGACG 59.231 44.000 0.00 0.00 0.00 4.18
3145 3332 5.535406 CCCTCTACCTCACAATATAAGACGT 59.465 44.000 0.00 0.00 0.00 4.34
3146 3333 6.040616 CCCTCTACCTCACAATATAAGACGTT 59.959 42.308 0.00 0.00 0.00 3.99
3147 3334 7.417570 CCCTCTACCTCACAATATAAGACGTTT 60.418 40.741 0.00 0.00 0.00 3.60
3148 3335 7.980099 CCTCTACCTCACAATATAAGACGTTTT 59.020 37.037 0.00 0.00 0.00 2.43
3149 3336 9.367444 CTCTACCTCACAATATAAGACGTTTTT 57.633 33.333 0.00 0.00 0.00 1.94
3150 3337 9.146984 TCTACCTCACAATATAAGACGTTTTTG 57.853 33.333 0.00 0.00 0.00 2.44
3151 3338 6.608610 ACCTCACAATATAAGACGTTTTTGC 58.391 36.000 0.00 0.00 0.00 3.68
3152 3339 6.205853 ACCTCACAATATAAGACGTTTTTGCA 59.794 34.615 0.00 0.00 0.00 4.08
3153 3340 7.081349 CCTCACAATATAAGACGTTTTTGCAA 58.919 34.615 0.00 0.00 0.00 4.08
3154 3341 7.271223 CCTCACAATATAAGACGTTTTTGCAAG 59.729 37.037 0.00 0.00 0.00 4.01
3155 3342 6.580791 TCACAATATAAGACGTTTTTGCAAGC 59.419 34.615 0.00 0.00 0.00 4.01
3156 3343 6.582295 CACAATATAAGACGTTTTTGCAAGCT 59.418 34.615 0.00 0.00 0.00 3.74
3157 3344 7.748683 CACAATATAAGACGTTTTTGCAAGCTA 59.251 33.333 0.00 0.00 0.00 3.32
3158 3345 7.962918 ACAATATAAGACGTTTTTGCAAGCTAG 59.037 33.333 0.00 0.00 0.00 3.42
3159 3346 5.941948 ATAAGACGTTTTTGCAAGCTAGT 57.058 34.783 0.00 0.00 0.00 2.57
3160 3347 4.632538 AAGACGTTTTTGCAAGCTAGTT 57.367 36.364 0.00 0.00 0.00 2.24
3161 3348 4.632538 AGACGTTTTTGCAAGCTAGTTT 57.367 36.364 0.00 0.00 0.00 2.66
3162 3349 5.744666 AGACGTTTTTGCAAGCTAGTTTA 57.255 34.783 0.00 0.00 0.00 2.01
3163 3350 5.748592 AGACGTTTTTGCAAGCTAGTTTAG 58.251 37.500 0.00 0.00 0.00 1.85
3193 3380 9.109393 CCATAAACATCTTATATTATGGGACGG 57.891 37.037 13.19 0.00 45.66 4.79
3194 3381 8.612619 CATAAACATCTTATATTATGGGACGGC 58.387 37.037 0.00 0.00 33.94 5.68
3195 3382 4.755411 ACATCTTATATTATGGGACGGCG 58.245 43.478 4.80 4.80 0.00 6.46
3196 3383 3.880047 TCTTATATTATGGGACGGCGG 57.120 47.619 13.24 0.00 0.00 6.13
3197 3384 2.498481 TCTTATATTATGGGACGGCGGG 59.502 50.000 13.24 0.00 0.00 6.13
3198 3385 2.234896 TATATTATGGGACGGCGGGA 57.765 50.000 13.24 0.00 0.00 5.14
3199 3386 0.902531 ATATTATGGGACGGCGGGAG 59.097 55.000 13.24 0.00 0.00 4.30
3207 3394 1.456296 GGACGGCGGGAGTAATTTTT 58.544 50.000 13.24 0.00 0.00 1.94
3280 3467 6.750501 TCAACGTCATACTATCTTCCTTTTCG 59.249 38.462 0.00 0.00 0.00 3.46
3307 3494 4.737054 CAGCTGGTATTGTCATTGAAACC 58.263 43.478 5.57 0.00 0.00 3.27
3513 3700 9.982291 GAATATCGCAAACACTATTTTTACTGA 57.018 29.630 0.00 0.00 0.00 3.41
3520 3707 7.255486 GCAAACACTATTTTTACTGAGGACCTT 60.255 37.037 0.00 0.00 0.00 3.50
3521 3708 7.745620 AACACTATTTTTACTGAGGACCTTG 57.254 36.000 0.00 0.00 0.00 3.61
3523 3710 5.940470 CACTATTTTTACTGAGGACCTTGCT 59.060 40.000 0.00 0.00 0.00 3.91
3574 3765 3.003394 TCACCTGGATCAATGCGATTT 57.997 42.857 0.00 0.00 33.17 2.17
3599 3790 5.279708 CCATATCATCTCCTAGGGTGTGAAC 60.280 48.000 9.46 0.00 0.00 3.18
3600 3791 3.184382 TCATCTCCTAGGGTGTGAACA 57.816 47.619 9.46 0.00 0.00 3.18
3603 3794 3.184382 TCTCCTAGGGTGTGAACATGA 57.816 47.619 9.46 0.00 0.00 3.07
3786 3977 0.969149 CTCTTCTTTTGGGTTGGGCC 59.031 55.000 0.00 0.00 0.00 5.80
3799 3990 2.903784 GGTTGGGCCTAAACTTCCAATT 59.096 45.455 10.11 0.00 40.77 2.32
3809 4001 6.587608 GCCTAAACTTCCAATTGTCATGAAAG 59.412 38.462 4.43 0.00 0.00 2.62
3819 4011 7.038870 TCCAATTGTCATGAAAGAATGTCCAAT 60.039 33.333 4.43 0.00 34.60 3.16
3846 4038 6.633500 TGCTAGTAATCAAATAATGGTGGC 57.367 37.500 0.00 0.00 0.00 5.01
3896 4088 9.844257 AATTAGGAGATTCAAGTCTAAGATTGG 57.156 33.333 0.00 0.00 0.00 3.16
3897 4089 6.245890 AGGAGATTCAAGTCTAAGATTGGG 57.754 41.667 0.00 0.00 0.00 4.12
3927 4119 3.146618 CACAGATTGCTGATTTCTGCC 57.853 47.619 6.93 0.00 45.17 4.85
3947 4139 2.285083 CAATTTTGATGCCATGCAGGG 58.715 47.619 14.45 14.45 43.65 4.45
4087 4279 1.615392 GCACCTGAAACAAATCTGGCT 59.385 47.619 0.75 0.00 40.90 4.75
4089 4281 1.615392 ACCTGAAACAAATCTGGCTGC 59.385 47.619 0.00 0.00 40.90 5.25
4127 4319 3.273434 TGTCATCTGGTTGCTAGCAATC 58.727 45.455 31.46 30.68 38.28 2.67
4214 4406 7.315142 CAATGAGGTTTGTGTACATGCTTATT 58.685 34.615 0.00 0.00 0.00 1.40
4215 4407 8.458052 CAATGAGGTTTGTGTACATGCTTATTA 58.542 33.333 0.00 0.00 0.00 0.98
4221 4413 8.379902 GGTTTGTGTACATGCTTATTATTTTGC 58.620 33.333 0.00 0.00 0.00 3.68
4268 4460 3.681593 TGTCTTTACACCTTATGCCACC 58.318 45.455 0.00 0.00 0.00 4.61
4381 4575 7.235812 ACTCTTCTAGACTAAATGGTTTCCACT 59.764 37.037 0.00 0.00 35.80 4.00
4591 4796 1.401761 ACTTCTGTTTGTGCCATGCA 58.598 45.000 0.00 0.00 35.60 3.96
4651 4860 2.865119 TGGACACACTGAATGCATCT 57.135 45.000 0.00 0.00 0.00 2.90
4653 4862 3.076621 TGGACACACTGAATGCATCTTC 58.923 45.455 0.00 0.00 0.00 2.87
4656 4865 4.157289 GGACACACTGAATGCATCTTCAAT 59.843 41.667 0.00 0.00 34.86 2.57
4671 4880 7.280428 TGCATCTTCAATGAATTTTGTGTGTTT 59.720 29.630 0.00 0.00 0.00 2.83
4672 4881 8.763356 GCATCTTCAATGAATTTTGTGTGTTTA 58.237 29.630 0.00 0.00 0.00 2.01
4705 4944 2.837291 GCACCACCACCAAAGCCA 60.837 61.111 0.00 0.00 0.00 4.75
4725 4964 2.363306 TTGTGGCTCCTTTGTCACAT 57.637 45.000 2.78 0.00 39.45 3.21
4726 4965 1.896220 TGTGGCTCCTTTGTCACATC 58.104 50.000 0.00 0.00 35.52 3.06
4727 4966 1.421268 TGTGGCTCCTTTGTCACATCT 59.579 47.619 0.00 0.00 35.52 2.90
4728 4967 1.808945 GTGGCTCCTTTGTCACATCTG 59.191 52.381 0.00 0.00 0.00 2.90
4743 4982 1.878088 CATCTGTATGCTGGATGTGCC 59.122 52.381 8.35 0.00 34.08 5.01
4884 5124 9.189723 GTAATACTACCCTAAAGAATAGCAACG 57.810 37.037 0.00 0.00 0.00 4.10
4893 5133 1.134491 AGAATAGCAACGCCACCTACC 60.134 52.381 0.00 0.00 0.00 3.18
4986 5226 2.288666 GGATCAATTCGGTTGCTGCTA 58.711 47.619 0.00 0.00 37.74 3.49
4996 5236 4.069304 TCGGTTGCTGCTATAAACTGTTT 58.931 39.130 10.98 10.98 32.98 2.83
5035 5275 4.774726 AGCAACTCTCTTTCAGACTATCCA 59.225 41.667 0.00 0.00 0.00 3.41
5041 5281 5.197451 TCTCTTTCAGACTATCCACTCTCC 58.803 45.833 0.00 0.00 0.00 3.71
5061 5301 8.646900 ACTCTCCTTTCAAATCATAGATAGGTC 58.353 37.037 0.00 0.00 35.36 3.85
5078 5336 4.392921 AGGTCGGTATCAACTCATTCAG 57.607 45.455 0.00 0.00 0.00 3.02
5099 5357 7.187824 TCAGATTATCTAACTTTGCCTGTCT 57.812 36.000 0.00 0.00 0.00 3.41
5132 5390 2.429250 GTGTTACAGTGGGTTTTTGCCT 59.571 45.455 0.00 0.00 0.00 4.75
5153 5411 2.009774 GCAATTGACGTCATAGGCAGT 58.990 47.619 20.80 0.00 0.00 4.40
5182 5440 3.359695 TGTGGGGGTAAGTATTTCTGC 57.640 47.619 0.00 0.00 0.00 4.26
5222 5482 0.315251 GGCTGCTTTTCTGGGTGTTC 59.685 55.000 0.00 0.00 0.00 3.18
5233 5493 1.667724 CTGGGTGTTCGATGAAGCATC 59.332 52.381 0.00 0.00 37.50 3.91
5234 5494 1.003003 TGGGTGTTCGATGAAGCATCA 59.997 47.619 8.02 0.00 40.54 3.07
5309 5612 8.773033 ACATTTTCTCCTGGCAGATATTTTAT 57.227 30.769 17.94 0.00 0.00 1.40
5410 5713 1.543429 CCGTGCCTTCTGTTTCCTTCT 60.543 52.381 0.00 0.00 0.00 2.85
5412 5715 2.806745 CGTGCCTTCTGTTTCCTTCTCA 60.807 50.000 0.00 0.00 0.00 3.27
5561 5864 1.944024 CTTCTGATAGAGCGGTCTCGT 59.056 52.381 22.33 11.37 44.02 4.18
5637 5940 9.601810 TTTGTACATCCCTATACATATCTCTGT 57.398 33.333 0.00 0.00 31.55 3.41
5639 5942 6.537453 ACATCCCTATACATATCTCTGTGC 57.463 41.667 0.00 0.00 0.00 4.57
5640 5943 5.126222 ACATCCCTATACATATCTCTGTGCG 59.874 44.000 0.00 0.00 0.00 5.34
5641 5944 4.663334 TCCCTATACATATCTCTGTGCGT 58.337 43.478 0.00 0.00 0.00 5.24
5642 5945 4.459337 TCCCTATACATATCTCTGTGCGTG 59.541 45.833 0.00 0.00 0.00 5.34
5643 5946 4.380973 CCCTATACATATCTCTGTGCGTGG 60.381 50.000 0.00 0.00 0.00 4.94
5644 5947 2.509052 TACATATCTCTGTGCGTGGC 57.491 50.000 0.00 0.00 0.00 5.01
5645 5948 0.826715 ACATATCTCTGTGCGTGGCT 59.173 50.000 0.00 0.00 0.00 4.75
5646 5949 1.215244 CATATCTCTGTGCGTGGCTG 58.785 55.000 0.00 0.00 0.00 4.85
5647 5950 0.826715 ATATCTCTGTGCGTGGCTGT 59.173 50.000 0.00 0.00 0.00 4.40
5648 5951 0.173481 TATCTCTGTGCGTGGCTGTC 59.827 55.000 0.00 0.00 0.00 3.51
5666 5969 3.953612 CTGTCTGGCTGAGAGAGAATACT 59.046 47.826 12.39 0.00 43.51 2.12
5684 5987 9.982291 GAGAATACTTGTAGCTATAGATCTTCG 57.018 37.037 0.00 0.00 0.00 3.79
5820 6123 1.000607 AGCTTGCTTGCAATGTCACTG 60.001 47.619 8.55 0.00 34.99 3.66
5884 6188 1.654954 CCCATGCAGAGCTGAAGCAC 61.655 60.000 4.90 0.00 45.16 4.40
5972 6276 6.927294 AATGAAAATGGGAGACGAATCTAC 57.073 37.500 0.00 0.00 34.34 2.59
5981 6287 4.883006 GGGAGACGAATCTACTAACTCTGT 59.117 45.833 0.00 0.00 35.87 3.41
5985 6291 5.642919 AGACGAATCTACTAACTCTGTCGTT 59.357 40.000 0.00 0.00 40.27 3.85
6025 6333 1.303317 TTTTTGGGGCGCCTCTCTC 60.303 57.895 29.93 9.83 0.00 3.20
6026 6334 1.779061 TTTTTGGGGCGCCTCTCTCT 61.779 55.000 29.93 0.00 0.00 3.10
6147 6455 2.224572 GGATCTCCTGCTTCATGCTCAT 60.225 50.000 0.00 0.00 43.37 2.90
6529 6837 3.343788 CTCCGACTCCGACAGCCAC 62.344 68.421 0.00 0.00 38.22 5.01
6530 6838 4.778415 CCGACTCCGACAGCCACG 62.778 72.222 0.00 0.00 38.22 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 106 1.204941 AGGACTAAACTAGCAGGCGTG 59.795 52.381 1.01 1.01 0.00 5.34
159 160 1.429148 GGCTAATGGTGGAGCGAACG 61.429 60.000 0.00 0.00 39.72 3.95
192 193 4.080638 GGAGGAGAGATGGTTGTCTTCAAT 60.081 45.833 0.00 0.00 35.92 2.57
292 304 8.783093 CAAGTATGAGTTCACATTTTTAGGACA 58.217 33.333 0.00 0.00 0.00 4.02
335 347 2.744202 GCTGGTGGTAGACTTCACAATG 59.256 50.000 9.76 0.00 35.74 2.82
359 371 0.962855 GGAGGGAGGAAAACAGCAGC 60.963 60.000 0.00 0.00 0.00 5.25
361 373 1.073923 GAAGGAGGGAGGAAAACAGCA 59.926 52.381 0.00 0.00 0.00 4.41
370 382 1.557371 GAGTTGAAGGAAGGAGGGAGG 59.443 57.143 0.00 0.00 0.00 4.30
371 383 2.235898 CTGAGTTGAAGGAAGGAGGGAG 59.764 54.545 0.00 0.00 0.00 4.30
372 384 2.260822 CTGAGTTGAAGGAAGGAGGGA 58.739 52.381 0.00 0.00 0.00 4.20
460 493 9.391006 TCTGTGATTACTTTTTACACTGAGTTT 57.609 29.630 0.00 0.00 35.64 2.66
463 496 9.429359 AGATCTGTGATTACTTTTTACACTGAG 57.571 33.333 0.00 0.00 40.54 3.35
476 517 4.806247 GGTGCACACTAGATCTGTGATTAC 59.194 45.833 20.43 18.16 41.43 1.89
518 561 8.868916 GTTATGCGTCCATAAATGTTTTGATTT 58.131 29.630 0.00 0.00 43.48 2.17
523 571 8.770438 AAATGTTATGCGTCCATAAATGTTTT 57.230 26.923 0.00 0.00 43.48 2.43
532 580 3.627577 GGACAGAAATGTTATGCGTCCAT 59.372 43.478 0.00 0.00 40.90 3.41
534 582 3.270877 AGGACAGAAATGTTATGCGTCC 58.729 45.455 0.00 0.00 41.41 4.79
535 583 4.946784 AAGGACAGAAATGTTATGCGTC 57.053 40.909 0.00 0.00 0.00 5.19
536 584 4.518970 ACAAAGGACAGAAATGTTATGCGT 59.481 37.500 0.00 0.00 0.00 5.24
537 585 5.046910 ACAAAGGACAGAAATGTTATGCG 57.953 39.130 0.00 0.00 0.00 4.73
538 586 6.446318 TCAACAAAGGACAGAAATGTTATGC 58.554 36.000 0.00 0.00 33.24 3.14
539 587 7.543172 CCATCAACAAAGGACAGAAATGTTATG 59.457 37.037 0.00 0.00 33.24 1.90
540 588 7.605449 CCATCAACAAAGGACAGAAATGTTAT 58.395 34.615 0.00 0.00 33.24 1.89
541 589 6.516527 GCCATCAACAAAGGACAGAAATGTTA 60.517 38.462 0.00 0.00 33.24 2.41
542 590 5.739935 GCCATCAACAAAGGACAGAAATGTT 60.740 40.000 0.00 0.00 34.74 2.71
543 591 4.262164 GCCATCAACAAAGGACAGAAATGT 60.262 41.667 0.00 0.00 0.00 2.71
544 592 4.240096 GCCATCAACAAAGGACAGAAATG 58.760 43.478 0.00 0.00 0.00 2.32
545 593 3.896888 TGCCATCAACAAAGGACAGAAAT 59.103 39.130 0.00 0.00 0.00 2.17
546 594 3.295093 TGCCATCAACAAAGGACAGAAA 58.705 40.909 0.00 0.00 0.00 2.52
547 595 2.942804 TGCCATCAACAAAGGACAGAA 58.057 42.857 0.00 0.00 0.00 3.02
548 596 2.655090 TGCCATCAACAAAGGACAGA 57.345 45.000 0.00 0.00 0.00 3.41
549 597 3.947910 AATGCCATCAACAAAGGACAG 57.052 42.857 0.00 0.00 0.00 3.51
550 598 3.006752 GGAAATGCCATCAACAAAGGACA 59.993 43.478 0.00 0.00 36.34 4.02
551 599 3.006752 TGGAAATGCCATCAACAAAGGAC 59.993 43.478 0.00 0.00 43.33 3.85
552 600 3.237746 TGGAAATGCCATCAACAAAGGA 58.762 40.909 0.00 0.00 43.33 3.36
553 601 3.681593 TGGAAATGCCATCAACAAAGG 57.318 42.857 0.00 0.00 43.33 3.11
567 615 1.355720 ACTGCAGCCTAACCTGGAAAT 59.644 47.619 15.27 0.00 32.63 2.17
618 670 0.247460 GCATTCAGGGACAAAAGGGC 59.753 55.000 0.00 0.00 0.00 5.19
980 1043 2.674220 GCCTCCTCCTTCCCTGGTG 61.674 68.421 0.00 0.00 0.00 4.17
1079 1142 2.718073 GGCGAGGCGGGTAGAAAGA 61.718 63.158 0.00 0.00 0.00 2.52
1164 1227 1.665679 CCGGACCAAATTCGACATCTG 59.334 52.381 0.00 0.00 0.00 2.90
1165 1228 1.553248 TCCGGACCAAATTCGACATCT 59.447 47.619 0.00 0.00 0.00 2.90
1193 1256 2.680913 CCCGCAAGAAGCAACTCCG 61.681 63.158 0.00 0.00 46.13 4.63
1204 1267 3.181500 GGTTATAAGCAGAAACCCGCAAG 60.181 47.826 9.77 0.00 37.31 4.01
1215 1278 3.203716 GAAACGAGGGGGTTATAAGCAG 58.796 50.000 16.07 4.82 0.00 4.24
1216 1279 2.419021 CGAAACGAGGGGGTTATAAGCA 60.419 50.000 16.07 0.00 0.00 3.91
1219 1282 1.134431 GGCGAAACGAGGGGGTTATAA 60.134 52.381 0.00 0.00 0.00 0.98
1463 1553 4.558697 GCAAATCGCCTACTTCCAAAGTTT 60.559 41.667 0.00 0.00 37.54 2.66
1465 1555 2.488153 GCAAATCGCCTACTTCCAAAGT 59.512 45.455 0.00 0.00 39.12 2.66
1474 1564 2.024176 TGGAAGAGCAAATCGCCTAC 57.976 50.000 0.00 0.00 44.04 3.18
1476 1566 1.541588 GTTTGGAAGAGCAAATCGCCT 59.458 47.619 0.00 0.00 44.04 5.52
1496 1586 4.440758 CCATTTTTCGTTTGCGGCATATAG 59.559 41.667 2.28 0.00 38.89 1.31
1534 1626 1.977854 TCTTCAGCCAGCAAGAAGGTA 59.022 47.619 18.61 4.48 39.30 3.08
1535 1627 0.767375 TCTTCAGCCAGCAAGAAGGT 59.233 50.000 18.61 0.00 39.30 3.50
1536 1628 2.125773 ATCTTCAGCCAGCAAGAAGG 57.874 50.000 18.61 6.53 39.30 3.46
1605 1697 1.139654 GGCAGCAGATCCATAGACACA 59.860 52.381 0.00 0.00 0.00 3.72
1650 1742 9.982651 TTGCTACTGTAGATAAGGATTATTGTC 57.017 33.333 18.64 0.00 42.35 3.18
1654 1746 9.862371 CGAATTGCTACTGTAGATAAGGATTAT 57.138 33.333 18.64 0.00 45.61 1.28
1655 1747 8.304596 CCGAATTGCTACTGTAGATAAGGATTA 58.695 37.037 18.64 0.00 33.48 1.75
1656 1748 7.015292 TCCGAATTGCTACTGTAGATAAGGATT 59.985 37.037 18.64 7.87 0.00 3.01
1657 1749 6.493802 TCCGAATTGCTACTGTAGATAAGGAT 59.506 38.462 18.64 4.09 0.00 3.24
1658 1750 5.831525 TCCGAATTGCTACTGTAGATAAGGA 59.168 40.000 18.64 13.87 0.00 3.36
1659 1751 6.085555 TCCGAATTGCTACTGTAGATAAGG 57.914 41.667 18.64 12.06 0.00 2.69
1660 1752 8.012151 CAATCCGAATTGCTACTGTAGATAAG 57.988 38.462 18.64 4.22 36.15 1.73
1687 1779 3.745975 TCAGGACAATGAAAGTTAGCACG 59.254 43.478 0.00 0.00 0.00 5.34
1692 1784 5.534278 TGCACAATCAGGACAATGAAAGTTA 59.466 36.000 0.00 0.00 31.76 2.24
1701 1793 3.689347 AGCTTATGCACAATCAGGACAA 58.311 40.909 3.16 0.00 42.74 3.18
1750 1851 4.150451 GGAAAATCAGCCAAACGATTGTTG 59.850 41.667 4.63 3.21 38.62 3.33
1754 1855 2.817258 TCGGAAAATCAGCCAAACGATT 59.183 40.909 0.00 0.00 33.27 3.34
1757 1858 2.697431 TTCGGAAAATCAGCCAAACG 57.303 45.000 0.00 0.00 0.00 3.60
1808 1909 1.771565 TCCGAGAATTAGAAGCCGGA 58.228 50.000 5.05 0.00 42.92 5.14
1811 1912 2.147150 GGCATCCGAGAATTAGAAGCC 58.853 52.381 0.00 0.00 37.24 4.35
1847 1948 4.569966 CGATCATTATAGAATCCAGCAGGC 59.430 45.833 0.00 0.00 33.74 4.85
1874 1975 1.108776 GAGGTATGTCCACGGTAGCA 58.891 55.000 0.00 0.00 39.02 3.49
1970 2079 1.829222 CTGCCTGGCCTTTCAATTCAT 59.171 47.619 17.53 0.00 0.00 2.57
1993 2102 8.291191 TCATAAATGGTCAATAGTCAATTGCA 57.709 30.769 0.00 0.00 44.03 4.08
2014 2123 9.942850 TGACAAAGAATAGTGAGAACATTCATA 57.057 29.630 0.00 0.00 32.27 2.15
2022 2131 9.645059 CACTATCTTGACAAAGAATAGTGAGAA 57.355 33.333 24.29 0.09 45.44 2.87
2025 2134 9.208022 CAACACTATCTTGACAAAGAATAGTGA 57.792 33.333 29.46 10.33 45.44 3.41
2045 2154 8.783093 TCTGTAATCAATTTCGAAATCAACACT 58.217 29.630 22.93 4.31 0.00 3.55
2046 2155 8.948853 TCTGTAATCAATTTCGAAATCAACAC 57.051 30.769 22.93 16.41 0.00 3.32
2069 2178 4.067896 ACGACATGCTGTGAAAGAATTCT 58.932 39.130 0.88 0.88 36.48 2.40
2085 2194 2.032054 CCGCATAAGCAATCAACGACAT 59.968 45.455 0.00 0.00 42.27 3.06
2136 2245 4.202050 TGCAGTTCTTTCTCCTTTTGCTTC 60.202 41.667 0.00 0.00 0.00 3.86
2238 2347 8.783833 ATGACATATAGGATAACAAGTGATGC 57.216 34.615 0.00 0.00 0.00 3.91
2368 2485 3.305608 GCTTCACAAAACTTCATCCAGGG 60.306 47.826 0.00 0.00 0.00 4.45
2379 2496 4.762251 AGTATCCAGGAAGCTTCACAAAAC 59.238 41.667 27.02 16.40 0.00 2.43
2380 2497 4.761739 CAGTATCCAGGAAGCTTCACAAAA 59.238 41.667 27.02 9.21 0.00 2.44
2395 2512 5.738619 TCTAAGCAGTTTGTCAGTATCCA 57.261 39.130 0.00 0.00 0.00 3.41
2396 2513 7.928706 ACATATCTAAGCAGTTTGTCAGTATCC 59.071 37.037 0.00 0.00 0.00 2.59
2520 2643 1.010170 AGGGGAGCCTGAGGTAAATCT 59.990 52.381 0.00 0.00 0.00 2.40
2574 2697 2.160417 GCATGAGGCAAGTACTGTCAAC 59.840 50.000 0.00 0.00 43.97 3.18
2684 2829 7.619050 ACGAAGAGATGATGGCTATATGAAAT 58.381 34.615 0.00 0.00 0.00 2.17
2708 2853 8.506168 TTTATCATCTGATTGTCTGGGTTAAC 57.494 34.615 0.00 0.00 36.05 2.01
2792 2969 5.966503 TGAAACGTTGTCGATAAAGGTTTTG 59.033 36.000 23.58 4.24 42.48 2.44
2802 2979 4.450757 TCAATCATGTGAAACGTTGTCGAT 59.549 37.500 0.00 0.00 42.39 3.59
2819 2996 2.821378 CACATCTGGGCTGTTTCAATCA 59.179 45.455 0.00 0.00 0.00 2.57
2899 3076 7.364320 CCCTTCTTTTAAGTTCCTGGTTTCAAA 60.364 37.037 0.00 0.00 0.00 2.69
2900 3077 6.097696 CCCTTCTTTTAAGTTCCTGGTTTCAA 59.902 38.462 0.00 0.00 0.00 2.69
3042 3229 7.255139 CGGAACAAGTTTCCAGATAAATATCCC 60.255 40.741 4.02 0.00 38.49 3.85
3113 3300 2.092321 TGTGAGGTAGAGGGAGTAGCTC 60.092 54.545 0.00 3.00 42.76 4.09
3114 3301 1.923850 TGTGAGGTAGAGGGAGTAGCT 59.076 52.381 0.00 0.00 0.00 3.32
3115 3302 2.438800 TGTGAGGTAGAGGGAGTAGC 57.561 55.000 0.00 0.00 0.00 3.58
3116 3303 8.164733 TCTTATATTGTGAGGTAGAGGGAGTAG 58.835 40.741 0.00 0.00 0.00 2.57
3117 3304 7.943447 GTCTTATATTGTGAGGTAGAGGGAGTA 59.057 40.741 0.00 0.00 0.00 2.59
3118 3305 6.778559 GTCTTATATTGTGAGGTAGAGGGAGT 59.221 42.308 0.00 0.00 0.00 3.85
3119 3306 6.072397 CGTCTTATATTGTGAGGTAGAGGGAG 60.072 46.154 0.00 0.00 0.00 4.30
3120 3307 5.768662 CGTCTTATATTGTGAGGTAGAGGGA 59.231 44.000 0.00 0.00 0.00 4.20
3121 3308 5.535406 ACGTCTTATATTGTGAGGTAGAGGG 59.465 44.000 0.00 0.00 0.00 4.30
3122 3309 6.636562 ACGTCTTATATTGTGAGGTAGAGG 57.363 41.667 0.00 0.00 0.00 3.69
3123 3310 8.928270 AAAACGTCTTATATTGTGAGGTAGAG 57.072 34.615 0.00 0.00 0.00 2.43
3124 3311 9.146984 CAAAAACGTCTTATATTGTGAGGTAGA 57.853 33.333 0.00 0.00 0.00 2.59
3125 3312 7.903431 GCAAAAACGTCTTATATTGTGAGGTAG 59.097 37.037 0.00 0.00 0.00 3.18
3126 3313 7.388224 TGCAAAAACGTCTTATATTGTGAGGTA 59.612 33.333 0.00 0.00 0.00 3.08
3127 3314 6.205853 TGCAAAAACGTCTTATATTGTGAGGT 59.794 34.615 0.00 0.00 0.00 3.85
3128 3315 6.607689 TGCAAAAACGTCTTATATTGTGAGG 58.392 36.000 0.00 0.00 0.00 3.86
3129 3316 7.201266 GCTTGCAAAAACGTCTTATATTGTGAG 60.201 37.037 0.00 0.00 0.00 3.51
3130 3317 6.580791 GCTTGCAAAAACGTCTTATATTGTGA 59.419 34.615 0.00 0.00 0.00 3.58
3131 3318 6.582295 AGCTTGCAAAAACGTCTTATATTGTG 59.418 34.615 0.00 0.00 0.00 3.33
3132 3319 6.677913 AGCTTGCAAAAACGTCTTATATTGT 58.322 32.000 0.00 0.00 0.00 2.71
3133 3320 7.962918 ACTAGCTTGCAAAAACGTCTTATATTG 59.037 33.333 0.00 0.00 0.00 1.90
3134 3321 8.040716 ACTAGCTTGCAAAAACGTCTTATATT 57.959 30.769 0.00 0.00 0.00 1.28
3135 3322 7.611213 ACTAGCTTGCAAAAACGTCTTATAT 57.389 32.000 0.00 0.00 0.00 0.86
3136 3323 7.429636 AACTAGCTTGCAAAAACGTCTTATA 57.570 32.000 0.00 0.00 0.00 0.98
3137 3324 5.941948 ACTAGCTTGCAAAAACGTCTTAT 57.058 34.783 0.00 0.00 0.00 1.73
3138 3325 5.744666 AACTAGCTTGCAAAAACGTCTTA 57.255 34.783 0.00 0.00 0.00 2.10
3139 3326 4.632538 AACTAGCTTGCAAAAACGTCTT 57.367 36.364 0.00 0.00 0.00 3.01
3140 3327 4.632538 AAACTAGCTTGCAAAAACGTCT 57.367 36.364 0.00 0.00 0.00 4.18
3167 3354 9.109393 CCGTCCCATAATATAAGATGTTTATGG 57.891 37.037 11.76 11.76 45.52 2.74
3168 3355 8.612619 GCCGTCCCATAATATAAGATGTTTATG 58.387 37.037 0.00 0.00 33.72 1.90
3169 3356 7.494625 CGCCGTCCCATAATATAAGATGTTTAT 59.505 37.037 0.00 0.00 0.00 1.40
3170 3357 6.814644 CGCCGTCCCATAATATAAGATGTTTA 59.185 38.462 0.00 0.00 0.00 2.01
3171 3358 5.642063 CGCCGTCCCATAATATAAGATGTTT 59.358 40.000 0.00 0.00 0.00 2.83
3172 3359 5.175859 CGCCGTCCCATAATATAAGATGTT 58.824 41.667 0.00 0.00 0.00 2.71
3173 3360 4.382685 CCGCCGTCCCATAATATAAGATGT 60.383 45.833 0.00 0.00 0.00 3.06
3174 3361 4.119862 CCGCCGTCCCATAATATAAGATG 58.880 47.826 0.00 0.00 0.00 2.90
3175 3362 3.134081 CCCGCCGTCCCATAATATAAGAT 59.866 47.826 0.00 0.00 0.00 2.40
3176 3363 2.498481 CCCGCCGTCCCATAATATAAGA 59.502 50.000 0.00 0.00 0.00 2.10
3177 3364 2.498481 TCCCGCCGTCCCATAATATAAG 59.502 50.000 0.00 0.00 0.00 1.73
3178 3365 2.498481 CTCCCGCCGTCCCATAATATAA 59.502 50.000 0.00 0.00 0.00 0.98
3179 3366 2.104967 CTCCCGCCGTCCCATAATATA 58.895 52.381 0.00 0.00 0.00 0.86
3180 3367 0.902531 CTCCCGCCGTCCCATAATAT 59.097 55.000 0.00 0.00 0.00 1.28
3181 3368 0.470456 ACTCCCGCCGTCCCATAATA 60.470 55.000 0.00 0.00 0.00 0.98
3182 3369 0.470456 TACTCCCGCCGTCCCATAAT 60.470 55.000 0.00 0.00 0.00 1.28
3183 3370 0.687098 TTACTCCCGCCGTCCCATAA 60.687 55.000 0.00 0.00 0.00 1.90
3184 3371 0.470456 ATTACTCCCGCCGTCCCATA 60.470 55.000 0.00 0.00 0.00 2.74
3185 3372 1.342672 AATTACTCCCGCCGTCCCAT 61.343 55.000 0.00 0.00 0.00 4.00
3186 3373 1.555477 AAATTACTCCCGCCGTCCCA 61.555 55.000 0.00 0.00 0.00 4.37
3187 3374 0.393402 AAAATTACTCCCGCCGTCCC 60.393 55.000 0.00 0.00 0.00 4.46
3188 3375 1.456296 AAAAATTACTCCCGCCGTCC 58.544 50.000 0.00 0.00 0.00 4.79
3207 3394 5.356751 ACTGTAACAACAACAGCAGAATGAA 59.643 36.000 3.24 0.00 46.73 2.57
3213 3400 2.942376 TGGACTGTAACAACAACAGCAG 59.058 45.455 3.24 0.00 46.73 4.24
3218 3405 8.349983 AGTGAAATATTGGACTGTAACAACAAC 58.650 33.333 0.00 0.00 0.00 3.32
3280 3467 3.855689 ATGACAATACCAGCTGCAAAC 57.144 42.857 8.66 0.00 0.00 2.93
3307 3494 3.436359 GCATAAATGGTGGCCAGTTTTTG 59.564 43.478 5.11 13.88 38.77 2.44
3487 3674 9.982291 TCAGTAAAAATAGTGTTTGCGATATTC 57.018 29.630 0.00 0.00 0.00 1.75
3493 3680 6.077838 GTCCTCAGTAAAAATAGTGTTTGCG 58.922 40.000 0.00 0.00 0.00 4.85
3513 3700 2.887152 GTGAATGTGAAAGCAAGGTCCT 59.113 45.455 0.00 0.00 0.00 3.85
3520 3707 2.618241 GGACAGTGTGAATGTGAAAGCA 59.382 45.455 0.00 0.00 0.00 3.91
3521 3708 2.618241 TGGACAGTGTGAATGTGAAAGC 59.382 45.455 0.00 0.00 0.00 3.51
3523 3710 4.269183 AGTTGGACAGTGTGAATGTGAAA 58.731 39.130 0.00 0.00 0.00 2.69
3574 3765 4.107961 TCACACCCTAGGAGATGATATGGA 59.892 45.833 11.48 0.00 0.00 3.41
3599 3790 5.121925 CCACTTCTCAGAAGACAATGTCATG 59.878 44.000 21.82 10.93 34.60 3.07
3600 3791 5.243981 CCACTTCTCAGAAGACAATGTCAT 58.756 41.667 21.82 2.97 34.60 3.06
3603 3794 3.181451 TGCCACTTCTCAGAAGACAATGT 60.181 43.478 21.82 0.00 0.00 2.71
3786 3977 9.918630 ATTCTTTCATGACAATTGGAAGTTTAG 57.081 29.630 10.83 0.19 32.48 1.85
3799 3990 7.760794 GCATTTATTGGACATTCTTTCATGACA 59.239 33.333 0.00 0.00 0.00 3.58
3846 4038 1.054231 TATCTGCTGCTCATCTGGGG 58.946 55.000 0.00 0.00 0.00 4.96
3855 4047 7.789202 TCTCCTAATTCTAATATCTGCTGCT 57.211 36.000 0.00 0.00 0.00 4.24
3883 4075 4.891756 CCAATGCATCCCAATCTTAGACTT 59.108 41.667 0.00 0.00 0.00 3.01
3927 4119 2.285083 CCCTGCATGGCATCAAAATTG 58.715 47.619 0.00 0.00 38.13 2.32
3947 4139 3.500680 TCCAAAAGAGGCATAACGTCAAC 59.499 43.478 0.00 0.00 35.56 3.18
4087 4279 2.301870 ACAACACCTATCGAAAGGAGCA 59.698 45.455 0.00 0.00 39.15 4.26
4089 4281 4.188247 TGACAACACCTATCGAAAGGAG 57.812 45.455 0.00 0.00 39.15 3.69
4127 4319 4.202202 GGGACACCAGAGATGAAGTAGATG 60.202 50.000 0.00 0.00 36.50 2.90
4157 4349 2.991190 CGGCCGATACCATAACACATAC 59.009 50.000 24.07 0.00 0.00 2.39
4214 4406 9.337091 GAAGCGACTTGTAAAAATAGCAAAATA 57.663 29.630 0.00 0.00 0.00 1.40
4215 4407 8.082242 AGAAGCGACTTGTAAAAATAGCAAAAT 58.918 29.630 0.00 0.00 0.00 1.82
4268 4460 6.480524 TTCAGTCCTGTAACATGAATTTCG 57.519 37.500 0.00 0.00 0.00 3.46
4416 4610 4.433382 AATATTAGCTCGTCGCGAAAAC 57.567 40.909 12.06 0.00 45.59 2.43
4457 4653 1.238615 ATGGATCTGGAAGGGGCAAT 58.761 50.000 0.00 0.00 0.00 3.56
4591 4796 9.284968 GCCACAGTGAATAACTACCATATTTAT 57.715 33.333 0.62 0.00 36.83 1.40
4671 4880 6.948886 TGGTGGTGCCTTTTTATCAGTTAATA 59.051 34.615 0.00 0.00 38.35 0.98
4672 4881 5.777732 TGGTGGTGCCTTTTTATCAGTTAAT 59.222 36.000 0.00 0.00 38.35 1.40
4674 4883 4.521256 GTGGTGGTGCCTTTTTATCAGTTA 59.479 41.667 0.00 0.00 38.35 2.24
4675 4884 3.320826 GTGGTGGTGCCTTTTTATCAGTT 59.679 43.478 0.00 0.00 38.35 3.16
4676 4885 2.890945 GTGGTGGTGCCTTTTTATCAGT 59.109 45.455 0.00 0.00 38.35 3.41
4679 4888 2.243810 TGGTGGTGGTGCCTTTTTATC 58.756 47.619 0.00 0.00 38.35 1.75
4680 4889 2.390225 TGGTGGTGGTGCCTTTTTAT 57.610 45.000 0.00 0.00 38.35 1.40
4681 4890 2.160721 TTGGTGGTGGTGCCTTTTTA 57.839 45.000 0.00 0.00 38.35 1.52
4682 4891 1.209261 CTTTGGTGGTGGTGCCTTTTT 59.791 47.619 0.00 0.00 38.35 1.94
4705 4944 2.363306 TGTGACAAAGGAGCCACAAT 57.637 45.000 0.00 0.00 36.69 2.71
4725 4964 0.179076 CGGCACATCCAGCATACAGA 60.179 55.000 0.00 0.00 34.01 3.41
4726 4965 0.179076 TCGGCACATCCAGCATACAG 60.179 55.000 0.00 0.00 34.01 2.74
4727 4966 0.461870 GTCGGCACATCCAGCATACA 60.462 55.000 0.00 0.00 34.01 2.29
4728 4967 0.179073 AGTCGGCACATCCAGCATAC 60.179 55.000 0.00 0.00 34.01 2.39
4884 5124 1.280998 ACAATGTACTGGGTAGGTGGC 59.719 52.381 0.00 0.00 0.00 5.01
4893 5133 4.503007 GTGCTATACGTGACAATGTACTGG 59.497 45.833 0.00 0.00 30.58 4.00
4996 5236 9.422681 AGAGAGTTGCTAGGTATTCTTAACATA 57.577 33.333 0.00 0.00 0.00 2.29
5035 5275 8.560124 ACCTATCTATGATTTGAAAGGAGAGT 57.440 34.615 0.00 0.00 0.00 3.24
5041 5281 9.360093 GATACCGACCTATCTATGATTTGAAAG 57.640 37.037 0.00 0.00 0.00 2.62
5061 5301 9.914131 TTAGATAATCTGAATGAGTTGATACCG 57.086 33.333 0.00 0.00 0.00 4.02
5099 5357 5.533154 CCCACTGTAACACCAGAAACAATAA 59.467 40.000 0.00 0.00 36.30 1.40
5132 5390 2.009051 CTGCCTATGACGTCAATTGCA 58.991 47.619 26.84 26.84 0.00 4.08
5153 5411 9.411189 GAAATACTTACCCCCACAATAACATTA 57.589 33.333 0.00 0.00 0.00 1.90
5182 5440 4.320494 GCCATGCCAAATTAACTCGATAGG 60.320 45.833 0.00 0.00 0.00 2.57
5309 5612 4.036262 CAGAACAGTCCGAATCCAACAAAA 59.964 41.667 0.00 0.00 0.00 2.44
5561 5864 7.664318 CACATCCTATTCTCATCCATTCATCAA 59.336 37.037 0.00 0.00 0.00 2.57
5634 5937 3.046087 CCAGACAGCCACGCACAG 61.046 66.667 0.00 0.00 0.00 3.66
5637 5940 4.994471 CAGCCAGACAGCCACGCA 62.994 66.667 0.00 0.00 0.00 5.24
5639 5942 2.433838 CTCAGCCAGACAGCCACG 60.434 66.667 0.00 0.00 0.00 4.94
5640 5943 1.079266 CTCTCAGCCAGACAGCCAC 60.079 63.158 0.00 0.00 0.00 5.01
5641 5944 1.228988 TCTCTCAGCCAGACAGCCA 60.229 57.895 0.00 0.00 0.00 4.75
5642 5945 0.969917 TCTCTCTCAGCCAGACAGCC 60.970 60.000 0.00 0.00 0.00 4.85
5643 5946 0.894141 TTCTCTCTCAGCCAGACAGC 59.106 55.000 0.00 0.00 0.00 4.40
5644 5947 3.953612 AGTATTCTCTCTCAGCCAGACAG 59.046 47.826 0.00 0.00 0.00 3.51
5645 5948 3.974719 AGTATTCTCTCTCAGCCAGACA 58.025 45.455 0.00 0.00 0.00 3.41
5646 5949 4.159506 ACAAGTATTCTCTCTCAGCCAGAC 59.840 45.833 0.00 0.00 0.00 3.51
5647 5950 4.348486 ACAAGTATTCTCTCTCAGCCAGA 58.652 43.478 0.00 0.00 0.00 3.86
5648 5951 4.734398 ACAAGTATTCTCTCTCAGCCAG 57.266 45.455 0.00 0.00 0.00 4.85
5666 5969 5.767816 TGCACGAAGATCTATAGCTACAA 57.232 39.130 0.00 0.00 0.00 2.41
5684 5987 9.979270 GCACTCATATATATTACAAGAATGCAC 57.021 33.333 7.97 0.00 0.00 4.57
5704 6007 5.248640 CCTAGGAAAGAAATGAAGCACTCA 58.751 41.667 1.05 0.00 38.81 3.41
5783 6086 4.428209 CAAGCTCGTCAGAATAGTGATGT 58.572 43.478 0.00 0.00 35.33 3.06
5820 6123 9.273016 AGCACTTCACATACATAACCATAATAC 57.727 33.333 0.00 0.00 0.00 1.89
5981 6287 6.701145 AGAGTATGAAATCTCAGCTAACGA 57.299 37.500 0.00 0.00 34.23 3.85
6147 6455 1.548357 GGAGCTGGAGAAGGAGTGCA 61.548 60.000 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.