Multiple sequence alignment - TraesCS7A01G465700

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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 TraesCS7A01G465700 chr7A 100.000 2810 0 0 1 2810 662144600 662141791 0.000000e+00 5190.0
1 TraesCS7A01G465700 chr7A 92.075 694 41 7 828 1515 662170004 662169319 0.000000e+00 965.0
2 TraesCS7A01G465700 chr7A 97.403 77 2 0 1878 1954 662142649 662142573 6.990000e-27 132.0
3 TraesCS7A01G465700 chr7A 97.403 77 2 0 1952 2028 662142723 662142647 6.990000e-27 132.0
4 TraesCS7A01G465700 chr7A 100.000 60 0 0 3047 3106 662141554 662141495 9.110000e-21 111.0
5 TraesCS7A01G465700 chr7B 93.763 946 48 7 1792 2736 292798977 292798042 0.000000e+00 1410.0
6 TraesCS7A01G465700 chr7B 86.173 810 56 20 569 1374 630607536 630606779 0.000000e+00 824.0
7 TraesCS7A01G465700 chr7B 87.381 737 50 20 815 1518 630652074 630651348 0.000000e+00 806.0
8 TraesCS7A01G465700 chr7B 92.022 539 38 4 40 575 630650477 630649941 0.000000e+00 752.0
9 TraesCS7A01G465700 chr7B 80.319 376 61 8 92 461 501942601 501942969 3.950000e-69 272.0
10 TraesCS7A01G465700 chr7B 96.053 76 3 0 1878 1953 292798816 292798741 1.170000e-24 124.0
11 TraesCS7A01G465700 chr7D 91.922 718 30 15 67 774 572825484 572824785 0.000000e+00 979.0
12 TraesCS7A01G465700 chr7D 88.905 703 57 8 815 1509 572835735 572835046 0.000000e+00 846.0
13 TraesCS7A01G465700 chr7D 81.938 609 53 22 769 1368 572824746 572824186 2.180000e-126 462.0
14 TraesCS7A01G465700 chr5D 85.130 538 72 5 1 532 232131899 232131364 7.580000e-151 544.0
15 TraesCS7A01G465700 chr5D 78.852 331 50 16 1059 1375 371440862 371440538 4.060000e-49 206.0
16 TraesCS7A01G465700 chr5D 93.814 97 4 1 1697 1791 269021944 269021848 8.980000e-31 145.0
17 TraesCS7A01G465700 chr5A 86.719 256 33 1 278 532 324080898 324081153 1.820000e-72 283.0
18 TraesCS7A01G465700 chr5A 83.916 286 40 4 1 282 324079039 324079322 5.110000e-68 268.0
19 TraesCS7A01G465700 chr5A 81.780 236 37 6 1135 1364 474537493 474537258 3.160000e-45 193.0
20 TraesCS7A01G465700 chr5A 94.059 101 4 2 1693 1791 510559678 510559778 5.360000e-33 152.0
21 TraesCS7A01G465700 chr5A 92.079 101 6 2 1693 1791 680655779 680655879 1.160000e-29 141.0
22 TraesCS7A01G465700 chr2B 77.706 462 90 10 8 461 561856162 561856618 1.420000e-68 270.0
23 TraesCS7A01G465700 chr2B 84.434 212 24 3 144 348 715307678 715307469 1.890000e-47 200.0
24 TraesCS7A01G465700 chr2B 90.654 107 8 1 1692 1796 4635305 4635411 1.160000e-29 141.0
25 TraesCS7A01G465700 chr2B 92.857 98 5 1 1696 1791 757882324 757882421 1.160000e-29 141.0
26 TraesCS7A01G465700 chr4D 81.618 272 44 3 1097 1368 465908857 465908592 1.450000e-53 220.0
27 TraesCS7A01G465700 chr4A 80.612 294 45 8 1066 1350 641602475 641602765 1.880000e-52 217.0
28 TraesCS7A01G465700 chr2D 76.162 495 68 34 893 1363 582495032 582494564 6.750000e-52 215.0
29 TraesCS7A01G465700 chr2D 89.189 111 9 2 1690 1798 417633598 417633707 5.400000e-28 135.0
30 TraesCS7A01G465700 chr2D 81.481 108 18 2 410 516 645948790 645948896 1.530000e-13 87.9
31 TraesCS7A01G465700 chr4B 80.515 272 50 1 1097 1368 582956836 582956568 4.060000e-49 206.0
32 TraesCS7A01G465700 chr6A 91.589 107 5 4 1694 1796 502402528 502402422 8.980000e-31 145.0
33 TraesCS7A01G465700 chr1D 90.385 104 8 1 1690 1791 433922668 433922771 5.400000e-28 135.0
34 TraesCS7A01G465700 chr1D 86.400 125 12 4 1696 1816 490029544 490029667 6.990000e-27 132.0
35 TraesCS7A01G465700 chr3A 95.349 43 1 1 3064 3105 521608563 521608605 2.000000e-07 67.6
36 TraesCS7A01G465700 chr1B 85.075 67 5 4 1496 1560 654816329 654816266 2.590000e-06 63.9
37 TraesCS7A01G465700 chr1A 95.000 40 2 0 1513 1552 360989788 360989749 2.590000e-06 63.9


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 TraesCS7A01G465700 chr7A 662141495 662144600 3105 True 1391.25 5190 98.7015 1 3106 4 chr7A.!!$R2 3105
1 TraesCS7A01G465700 chr7A 662169319 662170004 685 True 965.00 965 92.0750 828 1515 1 chr7A.!!$R1 687
2 TraesCS7A01G465700 chr7B 630606779 630607536 757 True 824.00 824 86.1730 569 1374 1 chr7B.!!$R1 805
3 TraesCS7A01G465700 chr7B 630649941 630652074 2133 True 779.00 806 89.7015 40 1518 2 chr7B.!!$R3 1478
4 TraesCS7A01G465700 chr7B 292798042 292798977 935 True 767.00 1410 94.9080 1792 2736 2 chr7B.!!$R2 944
5 TraesCS7A01G465700 chr7D 572835046 572835735 689 True 846.00 846 88.9050 815 1509 1 chr7D.!!$R1 694
6 TraesCS7A01G465700 chr7D 572824186 572825484 1298 True 720.50 979 86.9300 67 1368 2 chr7D.!!$R2 1301
7 TraesCS7A01G465700 chr5D 232131364 232131899 535 True 544.00 544 85.1300 1 532 1 chr5D.!!$R1 531
8 TraesCS7A01G465700 chr5A 324079039 324081153 2114 False 275.50 283 85.3175 1 532 2 chr5A.!!$F3 531

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
630 2226 0.39382 AACAGTTTCCGTTCCCGCTA 59.606 50.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2278 4278 0.179137 GCGTGTGATCTGATCGTGGA 60.179 55.0 12.65 0.0 0.0 4.02 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
29 30 4.321304 CGAAACCTCTCACACTACATGAGT 60.321 45.833 0.00 0.00 43.47 3.41
38 39 4.772624 TCACACTACATGAGTTAGGAGCTT 59.227 41.667 0.00 0.00 35.64 3.74
59 60 1.306148 CCATCTACTGTGGCATGCAG 58.694 55.000 21.36 11.12 39.67 4.41
60 61 0.661552 CATCTACTGTGGCATGCAGC 59.338 55.000 21.36 11.84 44.65 5.25
72 73 2.663075 ATGCAGCGCTCCTCCTCAA 61.663 57.895 7.13 0.00 0.00 3.02
124 125 9.793259 AGAAATCAGTGAAGTAACCTTTAATCA 57.207 29.630 0.00 0.00 0.00 2.57
140 141 9.784531 ACCTTTAATCAGTCATACTTCATATGG 57.215 33.333 2.13 0.00 41.10 2.74
162 163 4.142600 GGCTCAAAGCATTAGTCGAAACAT 60.143 41.667 0.86 0.00 44.75 2.71
261 267 6.280643 TGGTTACTTGGATGACGAGATTATG 58.719 40.000 0.00 0.00 34.46 1.90
269 275 2.892374 TGACGAGATTATGCCTGTGTG 58.108 47.619 0.00 0.00 0.00 3.82
351 1937 1.377725 CCGCCCATTCTCAGCAACT 60.378 57.895 0.00 0.00 0.00 3.16
516 2111 1.043816 CGGTGTAGATGGAGCAGGAT 58.956 55.000 0.00 0.00 0.00 3.24
538 2133 0.611340 GAGGTCGGTGTAGAGGGTGT 60.611 60.000 0.00 0.00 0.00 4.16
558 2153 4.023622 GTGTTTTCTTGAGAGGAAAGCTCC 60.024 45.833 0.00 0.00 42.81 4.70
592 2187 1.202722 GGACAAGGAAGAAACGGGACA 60.203 52.381 0.00 0.00 0.00 4.02
630 2226 0.393820 AACAGTTTCCGTTCCCGCTA 59.606 50.000 0.00 0.00 0.00 4.26
683 2279 2.745821 GGTGTTTACTTCCAATCCGGAC 59.254 50.000 6.12 0.00 46.36 4.79
705 2301 7.470286 CGGACCCCAAGAATTTGTTTTTACTTA 60.470 37.037 0.00 0.00 32.21 2.24
734 2335 4.898320 TCCATATTCCATGATCCGAAGTG 58.102 43.478 0.00 0.00 0.00 3.16
743 2344 2.816411 TGATCCGAAGTGGTAGTTCCT 58.184 47.619 0.00 0.00 39.52 3.36
746 2347 3.672767 TCCGAAGTGGTAGTTCCTTTC 57.327 47.619 0.00 0.00 39.52 2.62
747 2348 3.236896 TCCGAAGTGGTAGTTCCTTTCT 58.763 45.455 0.00 0.00 39.52 2.52
748 2349 3.644738 TCCGAAGTGGTAGTTCCTTTCTT 59.355 43.478 0.00 0.00 39.52 2.52
749 2350 3.995048 CCGAAGTGGTAGTTCCTTTCTTC 59.005 47.826 0.00 0.00 36.66 2.87
750 2351 4.262506 CCGAAGTGGTAGTTCCTTTCTTCT 60.263 45.833 12.71 0.00 37.19 2.85
751 2352 5.298347 CGAAGTGGTAGTTCCTTTCTTCTT 58.702 41.667 12.71 0.00 37.19 2.52
752 2353 5.405873 CGAAGTGGTAGTTCCTTTCTTCTTC 59.594 44.000 12.71 0.00 37.19 2.87
758 2359 7.915923 GTGGTAGTTCCTTTCTTCTTCTTTTTG 59.084 37.037 0.00 0.00 37.07 2.44
795 2440 3.238108 AGTTCCTCGTGTCATCATGTC 57.762 47.619 0.00 0.00 32.85 3.06
796 2441 2.093973 AGTTCCTCGTGTCATCATGTCC 60.094 50.000 0.00 0.00 32.85 4.02
797 2442 1.555967 TCCTCGTGTCATCATGTCCA 58.444 50.000 0.00 0.00 32.85 4.02
798 2443 2.110578 TCCTCGTGTCATCATGTCCAT 58.889 47.619 0.00 0.00 32.85 3.41
799 2444 2.159057 TCCTCGTGTCATCATGTCCATG 60.159 50.000 0.71 0.71 40.09 3.66
800 2445 2.419159 CCTCGTGTCATCATGTCCATGT 60.419 50.000 7.13 0.00 39.72 3.21
801 2446 2.606272 CTCGTGTCATCATGTCCATGTG 59.394 50.000 7.13 5.61 39.72 3.21
802 2447 1.667212 CGTGTCATCATGTCCATGTGG 59.333 52.381 7.13 0.00 39.72 4.17
803 2448 1.402968 GTGTCATCATGTCCATGTGGC 59.597 52.381 7.13 7.17 39.72 5.01
804 2449 1.027357 GTCATCATGTCCATGTGGCC 58.973 55.000 0.00 0.00 39.72 5.36
805 2450 0.624785 TCATCATGTCCATGTGGCCA 59.375 50.000 0.00 0.00 39.72 5.36
830 2486 6.547510 AGGCCAATTTGTATTCTTATCCAGTC 59.452 38.462 5.01 0.00 0.00 3.51
877 2533 3.319972 TCTCTTTTTCTTCCTCGGTTCGA 59.680 43.478 0.00 0.00 0.00 3.71
939 2595 1.341156 CCCGGCTTCCTCCTCAAGAT 61.341 60.000 0.00 0.00 0.00 2.40
974 2638 2.895404 TGACCGACCCCATATAAGTAGC 59.105 50.000 0.00 0.00 0.00 3.58
988 2652 4.077184 TAGCCACGACCCCGCAAG 62.077 66.667 0.00 0.00 39.95 4.01
995 2659 3.723922 GACCCCGCAAGCCCCTAA 61.724 66.667 0.00 0.00 0.00 2.69
1009 2675 2.686715 GCCCCTAACACCATAGCAACAT 60.687 50.000 0.00 0.00 0.00 2.71
1025 2691 0.675633 ACATGGGCAGCAACAACTTC 59.324 50.000 0.00 0.00 0.00 3.01
1026 2692 0.387622 CATGGGCAGCAACAACTTCG 60.388 55.000 0.00 0.00 0.00 3.79
1027 2693 1.526575 ATGGGCAGCAACAACTTCGG 61.527 55.000 0.00 0.00 0.00 4.30
1028 2694 1.896660 GGGCAGCAACAACTTCGGA 60.897 57.895 0.00 0.00 0.00 4.55
1062 2740 5.628134 GCAAGTTTTCGATAAACCGATCTT 58.372 37.500 15.14 1.92 38.45 2.40
1071 2749 6.554419 TCGATAAACCGATCTTAGTTTTCGA 58.446 36.000 20.17 20.17 39.80 3.71
1198 2879 2.459969 TTGGTGGAGCTGGCCAAGA 61.460 57.895 7.01 0.00 40.20 3.02
1364 3045 4.858140 GCAGTAGATCATCATCGTCATCTG 59.142 45.833 0.00 0.00 33.75 2.90
1449 3149 7.334671 CAGCATTATCAGTCTGCAGATATCATT 59.665 37.037 21.47 5.93 38.37 2.57
1505 3210 8.088981 AGAGTTGTGTGAATCTACGTTCTAAAT 58.911 33.333 0.00 0.00 0.00 1.40
1533 3238 8.967664 TTGAATAATACTAGTTAATTGCCCGT 57.032 30.769 0.00 0.00 0.00 5.28
1535 3240 6.796705 ATAATACTAGTTAATTGCCCGTGC 57.203 37.500 0.00 0.00 38.26 5.34
1536 3241 1.365699 ACTAGTTAATTGCCCGTGCG 58.634 50.000 0.00 0.00 41.78 5.34
1537 3242 1.338389 ACTAGTTAATTGCCCGTGCGT 60.338 47.619 0.00 0.00 41.78 5.24
1539 3244 0.239879 AGTTAATTGCCCGTGCGTTG 59.760 50.000 0.00 0.00 41.78 4.10
1540 3245 1.081108 TTAATTGCCCGTGCGTTGC 60.081 52.632 0.00 0.00 41.78 4.17
1541 3246 1.796190 TTAATTGCCCGTGCGTTGCA 61.796 50.000 2.68 2.68 41.78 4.08
1542 3247 1.590610 TAATTGCCCGTGCGTTGCAT 61.591 50.000 6.82 0.00 41.91 3.96
1543 3248 2.817470 AATTGCCCGTGCGTTGCATC 62.817 55.000 6.82 0.00 41.91 3.91
1548 3253 4.147322 CGTGCGTTGCATCGGGAC 62.147 66.667 18.16 9.52 41.91 4.46
1549 3254 3.799755 GTGCGTTGCATCGGGACC 61.800 66.667 18.16 2.81 41.91 4.46
1550 3255 4.321966 TGCGTTGCATCGGGACCA 62.322 61.111 18.16 5.35 31.71 4.02
1551 3256 2.824041 GCGTTGCATCGGGACCAT 60.824 61.111 18.16 0.00 0.00 3.55
1553 3258 0.884704 GCGTTGCATCGGGACCATAT 60.885 55.000 18.16 0.00 0.00 1.78
1554 3259 1.593196 CGTTGCATCGGGACCATATT 58.407 50.000 9.33 0.00 0.00 1.28
1557 3262 3.181491 CGTTGCATCGGGACCATATTTTT 60.181 43.478 9.33 0.00 0.00 1.94
1584 3583 6.877611 TTTTGACTGTTAAATCTCCACCTC 57.122 37.500 0.00 0.00 0.00 3.85
1585 3584 4.553330 TGACTGTTAAATCTCCACCTCC 57.447 45.455 0.00 0.00 0.00 4.30
1586 3585 3.263425 TGACTGTTAAATCTCCACCTCCC 59.737 47.826 0.00 0.00 0.00 4.30
1587 3586 2.576648 ACTGTTAAATCTCCACCTCCCC 59.423 50.000 0.00 0.00 0.00 4.81
1588 3587 2.846827 CTGTTAAATCTCCACCTCCCCT 59.153 50.000 0.00 0.00 0.00 4.79
1589 3588 2.844348 TGTTAAATCTCCACCTCCCCTC 59.156 50.000 0.00 0.00 0.00 4.30
1590 3589 3.116174 GTTAAATCTCCACCTCCCCTCT 58.884 50.000 0.00 0.00 0.00 3.69
1591 3590 1.886422 AAATCTCCACCTCCCCTCTC 58.114 55.000 0.00 0.00 0.00 3.20
1592 3591 1.022903 AATCTCCACCTCCCCTCTCT 58.977 55.000 0.00 0.00 0.00 3.10
1593 3592 1.022903 ATCTCCACCTCCCCTCTCTT 58.977 55.000 0.00 0.00 0.00 2.85
1594 3593 0.793617 TCTCCACCTCCCCTCTCTTT 59.206 55.000 0.00 0.00 0.00 2.52
1595 3594 1.152271 TCTCCACCTCCCCTCTCTTTT 59.848 52.381 0.00 0.00 0.00 2.27
1596 3595 1.557371 CTCCACCTCCCCTCTCTTTTC 59.443 57.143 0.00 0.00 0.00 2.29
1597 3596 1.152271 TCCACCTCCCCTCTCTTTTCT 59.848 52.381 0.00 0.00 0.00 2.52
1598 3597 1.557371 CCACCTCCCCTCTCTTTTCTC 59.443 57.143 0.00 0.00 0.00 2.87
1599 3598 2.260822 CACCTCCCCTCTCTTTTCTCA 58.739 52.381 0.00 0.00 0.00 3.27
1600 3599 2.843113 CACCTCCCCTCTCTTTTCTCAT 59.157 50.000 0.00 0.00 0.00 2.90
1601 3600 3.111484 ACCTCCCCTCTCTTTTCTCATC 58.889 50.000 0.00 0.00 0.00 2.92
1602 3601 2.437651 CCTCCCCTCTCTTTTCTCATCC 59.562 54.545 0.00 0.00 0.00 3.51
1603 3602 3.110705 CTCCCCTCTCTTTTCTCATCCA 58.889 50.000 0.00 0.00 0.00 3.41
1604 3603 3.521126 CTCCCCTCTCTTTTCTCATCCAA 59.479 47.826 0.00 0.00 0.00 3.53
1605 3604 4.114597 TCCCCTCTCTTTTCTCATCCAAT 58.885 43.478 0.00 0.00 0.00 3.16
1606 3605 4.080129 TCCCCTCTCTTTTCTCATCCAATG 60.080 45.833 0.00 0.00 0.00 2.82
1607 3606 4.324874 CCCCTCTCTTTTCTCATCCAATGT 60.325 45.833 0.00 0.00 0.00 2.71
1608 3607 5.104360 CCCCTCTCTTTTCTCATCCAATGTA 60.104 44.000 0.00 0.00 0.00 2.29
1609 3608 6.410157 CCCCTCTCTTTTCTCATCCAATGTAT 60.410 42.308 0.00 0.00 0.00 2.29
1610 3609 7.059156 CCCTCTCTTTTCTCATCCAATGTATT 58.941 38.462 0.00 0.00 0.00 1.89
1611 3610 7.559170 CCCTCTCTTTTCTCATCCAATGTATTT 59.441 37.037 0.00 0.00 0.00 1.40
1612 3611 8.619546 CCTCTCTTTTCTCATCCAATGTATTTC 58.380 37.037 0.00 0.00 0.00 2.17
1613 3612 8.511604 TCTCTTTTCTCATCCAATGTATTTCC 57.488 34.615 0.00 0.00 0.00 3.13
1614 3613 8.108999 TCTCTTTTCTCATCCAATGTATTTCCA 58.891 33.333 0.00 0.00 0.00 3.53
1615 3614 8.827832 TCTTTTCTCATCCAATGTATTTCCAT 57.172 30.769 0.00 0.00 0.00 3.41
1616 3615 8.689061 TCTTTTCTCATCCAATGTATTTCCATG 58.311 33.333 0.00 0.00 0.00 3.66
1617 3616 7.959658 TTTCTCATCCAATGTATTTCCATGT 57.040 32.000 0.00 0.00 0.00 3.21
1618 3617 7.959658 TTCTCATCCAATGTATTTCCATGTT 57.040 32.000 0.00 0.00 0.00 2.71
1619 3618 9.473007 TTTCTCATCCAATGTATTTCCATGTTA 57.527 29.630 0.00 0.00 0.00 2.41
1620 3619 9.645128 TTCTCATCCAATGTATTTCCATGTTAT 57.355 29.630 0.00 0.00 0.00 1.89
1621 3620 9.645128 TCTCATCCAATGTATTTCCATGTTATT 57.355 29.630 0.00 0.00 0.00 1.40
1622 3621 9.903682 CTCATCCAATGTATTTCCATGTTATTC 57.096 33.333 0.00 0.00 0.00 1.75
1623 3622 9.418839 TCATCCAATGTATTTCCATGTTATTCA 57.581 29.630 0.00 0.00 0.00 2.57
1624 3623 9.687210 CATCCAATGTATTTCCATGTTATTCAG 57.313 33.333 0.00 0.00 0.00 3.02
1625 3624 7.715657 TCCAATGTATTTCCATGTTATTCAGC 58.284 34.615 0.00 0.00 0.00 4.26
1626 3625 6.638063 CCAATGTATTTCCATGTTATTCAGCG 59.362 38.462 0.00 0.00 0.00 5.18
1627 3626 5.168526 TGTATTTCCATGTTATTCAGCGC 57.831 39.130 0.00 0.00 0.00 5.92
1628 3627 3.715628 ATTTCCATGTTATTCAGCGCC 57.284 42.857 2.29 0.00 0.00 6.53
1629 3628 2.121291 TTCCATGTTATTCAGCGCCA 57.879 45.000 2.29 0.00 0.00 5.69
1630 3629 2.121291 TCCATGTTATTCAGCGCCAA 57.879 45.000 2.29 0.00 0.00 4.52
1631 3630 2.441410 TCCATGTTATTCAGCGCCAAA 58.559 42.857 2.29 0.00 0.00 3.28
1632 3631 2.163412 TCCATGTTATTCAGCGCCAAAC 59.837 45.455 2.29 2.23 0.00 2.93
1633 3632 2.164219 CCATGTTATTCAGCGCCAAACT 59.836 45.455 2.29 0.00 0.00 2.66
1634 3633 3.376859 CCATGTTATTCAGCGCCAAACTA 59.623 43.478 2.29 0.00 0.00 2.24
1635 3634 4.036734 CCATGTTATTCAGCGCCAAACTAT 59.963 41.667 2.29 0.00 0.00 2.12
1636 3635 5.238432 CCATGTTATTCAGCGCCAAACTATA 59.762 40.000 2.29 0.00 0.00 1.31
1637 3636 6.072508 CCATGTTATTCAGCGCCAAACTATAT 60.073 38.462 2.29 0.00 0.00 0.86
1638 3637 7.119116 CCATGTTATTCAGCGCCAAACTATATA 59.881 37.037 2.29 0.00 0.00 0.86
1639 3638 8.503196 CATGTTATTCAGCGCCAAACTATATAA 58.497 33.333 2.29 0.00 0.00 0.98
1640 3639 8.083462 TGTTATTCAGCGCCAAACTATATAAG 57.917 34.615 2.29 0.00 0.00 1.73
1641 3640 5.613358 ATTCAGCGCCAAACTATATAAGC 57.387 39.130 2.29 0.00 0.00 3.09
1642 3641 3.399330 TCAGCGCCAAACTATATAAGCC 58.601 45.455 2.29 0.00 0.00 4.35
1643 3642 3.138304 CAGCGCCAAACTATATAAGCCA 58.862 45.455 2.29 0.00 0.00 4.75
1644 3643 3.563808 CAGCGCCAAACTATATAAGCCAA 59.436 43.478 2.29 0.00 0.00 4.52
1645 3644 4.036262 CAGCGCCAAACTATATAAGCCAAA 59.964 41.667 2.29 0.00 0.00 3.28
1646 3645 4.036380 AGCGCCAAACTATATAAGCCAAAC 59.964 41.667 2.29 0.00 0.00 2.93
1647 3646 4.201970 GCGCCAAACTATATAAGCCAAACA 60.202 41.667 0.00 0.00 0.00 2.83
1648 3647 5.510671 CGCCAAACTATATAAGCCAAACAG 58.489 41.667 0.00 0.00 0.00 3.16
1649 3648 5.505654 CGCCAAACTATATAAGCCAAACAGG 60.506 44.000 0.00 0.00 41.84 4.00
1650 3649 5.221244 GCCAAACTATATAAGCCAAACAGGG 60.221 44.000 0.00 0.00 38.09 4.45
1662 3661 5.462530 GCCAAACAGGGTTATACTTGTTT 57.537 39.130 0.00 0.00 38.09 2.83
1663 3662 5.849510 GCCAAACAGGGTTATACTTGTTTT 58.150 37.500 4.07 0.00 38.09 2.43
1664 3663 6.285224 GCCAAACAGGGTTATACTTGTTTTT 58.715 36.000 4.07 0.00 38.09 1.94
1685 3684 5.450818 TTTTCACCCTTCAGCCATATACT 57.549 39.130 0.00 0.00 0.00 2.12
1686 3685 4.422073 TTCACCCTTCAGCCATATACTG 57.578 45.455 0.00 0.00 36.44 2.74
1687 3686 2.104792 TCACCCTTCAGCCATATACTGC 59.895 50.000 0.94 0.00 35.04 4.40
1688 3687 1.421646 ACCCTTCAGCCATATACTGCC 59.578 52.381 0.94 0.00 35.04 4.85
1689 3688 1.701847 CCCTTCAGCCATATACTGCCT 59.298 52.381 0.94 0.00 35.04 4.75
1690 3689 2.289945 CCCTTCAGCCATATACTGCCTC 60.290 54.545 0.94 0.00 35.04 4.70
1691 3690 2.636893 CCTTCAGCCATATACTGCCTCT 59.363 50.000 0.94 0.00 35.04 3.69
1692 3691 3.306641 CCTTCAGCCATATACTGCCTCTC 60.307 52.174 0.94 0.00 35.04 3.20
1693 3692 2.962859 TCAGCCATATACTGCCTCTCA 58.037 47.619 0.94 0.00 35.04 3.27
1694 3693 3.514539 TCAGCCATATACTGCCTCTCAT 58.485 45.455 0.94 0.00 35.04 2.90
1695 3694 3.513119 TCAGCCATATACTGCCTCTCATC 59.487 47.826 0.94 0.00 35.04 2.92
1696 3695 3.514706 CAGCCATATACTGCCTCTCATCT 59.485 47.826 0.00 0.00 0.00 2.90
1697 3696 4.708909 CAGCCATATACTGCCTCTCATCTA 59.291 45.833 0.00 0.00 0.00 1.98
1698 3697 4.709397 AGCCATATACTGCCTCTCATCTAC 59.291 45.833 0.00 0.00 0.00 2.59
1699 3698 4.709397 GCCATATACTGCCTCTCATCTACT 59.291 45.833 0.00 0.00 0.00 2.57
1700 3699 5.163561 GCCATATACTGCCTCTCATCTACTC 60.164 48.000 0.00 0.00 0.00 2.59
1701 3700 5.359576 CCATATACTGCCTCTCATCTACTCC 59.640 48.000 0.00 0.00 0.00 3.85
1702 3701 2.080654 ACTGCCTCTCATCTACTCCC 57.919 55.000 0.00 0.00 0.00 4.30
1703 3702 1.573376 ACTGCCTCTCATCTACTCCCT 59.427 52.381 0.00 0.00 0.00 4.20
1704 3703 2.238521 CTGCCTCTCATCTACTCCCTC 58.761 57.143 0.00 0.00 0.00 4.30
1705 3704 1.133325 TGCCTCTCATCTACTCCCTCC 60.133 57.143 0.00 0.00 0.00 4.30
1706 3705 1.904287 CCTCTCATCTACTCCCTCCG 58.096 60.000 0.00 0.00 0.00 4.63
1707 3706 1.144093 CCTCTCATCTACTCCCTCCGT 59.856 57.143 0.00 0.00 0.00 4.69
1708 3707 2.423660 CCTCTCATCTACTCCCTCCGTT 60.424 54.545 0.00 0.00 0.00 4.44
1718 3717 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
1719 3718 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
1720 3719 5.186198 ACTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
1722 3721 5.183228 TCCCTCCGTTTCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
1723 3722 5.045869 TCCCTCCGTTTCAAAATAGATGACT 60.046 40.000 0.00 0.00 0.00 3.41
1724 3723 5.294552 CCCTCCGTTTCAAAATAGATGACTC 59.705 44.000 0.00 0.00 0.00 3.36
1726 3725 6.371548 CCTCCGTTTCAAAATAGATGACTCAA 59.628 38.462 0.00 0.00 0.00 3.02
1727 3726 7.129109 TCCGTTTCAAAATAGATGACTCAAC 57.871 36.000 0.00 0.00 0.00 3.18
1728 3727 6.934645 TCCGTTTCAAAATAGATGACTCAACT 59.065 34.615 0.00 0.00 0.00 3.16
1730 3729 8.076178 CCGTTTCAAAATAGATGACTCAACTTT 58.924 33.333 0.00 0.00 0.00 2.66
1783 3782 8.893563 AAAGTTGGGTCATCTATTTAAATGGA 57.106 30.769 15.60 15.60 0.00 3.41
1784 3783 8.525290 AAGTTGGGTCATCTATTTAAATGGAG 57.475 34.615 17.77 10.94 29.12 3.86
1785 3784 7.062957 AGTTGGGTCATCTATTTAAATGGAGG 58.937 38.462 17.18 17.18 29.12 4.30
1786 3785 5.952387 TGGGTCATCTATTTAAATGGAGGG 58.048 41.667 21.25 14.78 30.11 4.30
1787 3786 5.674496 TGGGTCATCTATTTAAATGGAGGGA 59.326 40.000 21.25 16.40 30.11 4.20
1788 3787 6.183361 TGGGTCATCTATTTAAATGGAGGGAG 60.183 42.308 21.25 11.15 30.11 4.30
1789 3788 6.183361 GGGTCATCTATTTAAATGGAGGGAGT 60.183 42.308 21.25 3.23 30.11 3.85
1790 3789 7.017254 GGGTCATCTATTTAAATGGAGGGAGTA 59.983 40.741 21.25 4.35 30.11 2.59
1800 3799 1.559682 TGGAGGGAGTAATTGAGTGGC 59.440 52.381 0.00 0.00 0.00 5.01
1839 3839 6.126409 TCCAACTCTTTTCTTTTCTGCCTTA 58.874 36.000 0.00 0.00 0.00 2.69
1874 3874 1.101331 CAGCTTCTCCAATTCCCTGC 58.899 55.000 0.00 0.00 0.00 4.85
1891 3891 6.121776 TCCCTGCTTCAATTAGTTCAGTAA 57.878 37.500 0.00 0.00 0.00 2.24
1960 3960 9.394477 GTGATGGTCAAAGTTAACAATTAGTTC 57.606 33.333 8.61 0.00 41.64 3.01
2013 4013 8.352201 TGTAATTCTTGAAGGAAAAGTGTGATG 58.648 33.333 0.00 0.00 0.00 3.07
2027 4027 6.767524 AAGTGTGATGGTCAAAGTTAACAA 57.232 33.333 8.61 0.00 25.85 2.83
2055 4055 7.016170 AGTGTGTGGGAGTGCATTGTATATATA 59.984 37.037 0.00 0.00 0.00 0.86
2105 4105 8.210946 CCAGATGAAGGTCCACATAGTAATAAA 58.789 37.037 0.00 0.00 0.00 1.40
2111 4111 9.726438 GAAGGTCCACATAGTAATAAAGCATAT 57.274 33.333 0.00 0.00 0.00 1.78
2149 4149 9.860898 ATTTTATCGAAGGAGAAAAGAAAATGG 57.139 29.630 0.00 0.00 44.01 3.16
2220 4220 3.826524 TGAAAGTCATGTAGCAACCCAA 58.173 40.909 0.00 0.00 0.00 4.12
2245 4245 4.275689 TGTGCAACTTGATCGATTTTGACT 59.724 37.500 0.00 0.00 38.04 3.41
2278 4278 1.692173 CCGGTTACCCATCCCGATGT 61.692 60.000 0.00 0.00 44.41 3.06
2296 4296 1.135402 TGTCCACGATCAGATCACACG 60.135 52.381 11.12 0.00 0.00 4.49
2299 4299 0.798389 CACGATCAGATCACACGCGT 60.798 55.000 5.58 5.58 0.00 6.01
2343 4343 1.344953 ACAGACTGGCACTTCCCACA 61.345 55.000 7.51 0.00 0.00 4.17
2352 4352 0.250295 CACTTCCCACACCATGTCGT 60.250 55.000 0.00 0.00 0.00 4.34
2366 4366 2.779755 TGTCGTTCCTACATGCCATT 57.220 45.000 0.00 0.00 0.00 3.16
2367 4367 2.355197 TGTCGTTCCTACATGCCATTG 58.645 47.619 0.00 0.00 0.00 2.82
2368 4368 1.064060 GTCGTTCCTACATGCCATTGC 59.936 52.381 0.00 0.00 38.26 3.56
2369 4369 0.381801 CGTTCCTACATGCCATTGCC 59.618 55.000 0.00 0.00 36.33 4.52
2370 4370 1.473258 GTTCCTACATGCCATTGCCA 58.527 50.000 0.00 0.00 36.33 4.92
2371 4371 1.134946 GTTCCTACATGCCATTGCCAC 59.865 52.381 0.00 0.00 36.33 5.01
2372 4372 0.395586 TCCTACATGCCATTGCCACC 60.396 55.000 0.00 0.00 36.33 4.61
2373 4373 1.394266 CCTACATGCCATTGCCACCC 61.394 60.000 0.00 0.00 36.33 4.61
2374 4374 1.381056 TACATGCCATTGCCACCCC 60.381 57.895 0.00 0.00 36.33 4.95
2403 4403 3.732849 TGGCCACACCACACCACA 61.733 61.111 0.00 0.00 46.36 4.17
2427 4427 0.033920 GACGTTACTTTCCCCACGGT 59.966 55.000 0.00 0.00 36.95 4.83
2444 4444 4.306767 TCGTAGACGCAGCTACCA 57.693 55.556 7.23 0.00 37.96 3.25
2446 4446 0.380733 TCGTAGACGCAGCTACCATG 59.619 55.000 7.23 0.00 37.96 3.66
2453 4453 1.226686 CGCAGCTACCATGAGCCATC 61.227 60.000 2.91 0.00 43.97 3.51
2454 4454 1.226686 GCAGCTACCATGAGCCATCG 61.227 60.000 2.91 0.00 43.97 3.84
2495 4495 1.209275 CCGTCATCGTGCCGAGAATC 61.209 60.000 3.76 0.00 39.91 2.52
2503 4503 3.655486 TCGTGCCGAGAATCAACTTTAA 58.345 40.909 0.00 0.00 33.17 1.52
2536 4536 5.984233 CAGTAGAAACTGTACAAAGCACA 57.016 39.130 0.00 0.00 46.76 4.57
2544 4544 7.499232 AGAAACTGTACAAAGCACATTCTAGTT 59.501 33.333 0.00 0.00 28.35 2.24
2547 4547 8.848474 ACTGTACAAAGCACATTCTAGTTAAT 57.152 30.769 0.00 0.00 0.00 1.40
2560 4560 8.709308 ACATTCTAGTTAATCCTTCAGTAGCAT 58.291 33.333 0.00 0.00 0.00 3.79
2561 4561 9.553064 CATTCTAGTTAATCCTTCAGTAGCATT 57.447 33.333 0.00 0.00 0.00 3.56
2635 4645 5.599732 TGCAGCTTGTACAACATCAAAAAT 58.400 33.333 3.59 0.00 0.00 1.82
2645 4655 9.672086 TGTACAACATCAAAAATAGTTACAAGC 57.328 29.630 0.00 0.00 0.00 4.01
2679 5140 7.550551 TGAAGGTTGCACAAATAATGTCAAAAA 59.449 29.630 0.00 0.00 41.46 1.94
2736 5315 7.061566 TGATGCATATGCCAGTTTAGTACTA 57.938 36.000 24.54 0.00 41.18 1.82
2737 5316 7.679783 TGATGCATATGCCAGTTTAGTACTAT 58.320 34.615 24.54 6.63 41.18 2.12
2739 5318 9.653287 GATGCATATGCCAGTTTAGTACTATAA 57.347 33.333 24.54 0.01 41.18 0.98
2793 5372 9.507329 AAACAGAAGTATGACATCTAACATTGT 57.493 29.630 0.00 0.00 0.00 2.71
2794 5373 9.507329 AACAGAAGTATGACATCTAACATTGTT 57.493 29.630 7.30 7.30 0.00 2.83
2795 5374 9.155975 ACAGAAGTATGACATCTAACATTGTTC 57.844 33.333 5.07 0.00 0.00 3.18
2796 5375 9.376075 CAGAAGTATGACATCTAACATTGTTCT 57.624 33.333 5.07 0.00 32.60 3.01
2797 5376 9.593134 AGAAGTATGACATCTAACATTGTTCTC 57.407 33.333 5.07 0.00 29.55 2.87
2798 5377 9.593134 GAAGTATGACATCTAACATTGTTCTCT 57.407 33.333 5.07 0.00 0.00 3.10
2804 5383 9.208022 TGACATCTAACATTGTTCTCTAAACTG 57.792 33.333 5.07 0.00 0.00 3.16
2806 5385 9.778741 ACATCTAACATTGTTCTCTAAACTGAA 57.221 29.630 5.07 0.00 0.00 3.02
3099 5678 6.136541 GGAACATCTCATTCCATTAACCAC 57.863 41.667 0.00 0.00 44.42 4.16
3100 5679 5.888161 GGAACATCTCATTCCATTAACCACT 59.112 40.000 0.00 0.00 44.42 4.00
3101 5680 7.054124 GGAACATCTCATTCCATTAACCACTA 58.946 38.462 0.00 0.00 44.42 2.74
3102 5681 7.721399 GGAACATCTCATTCCATTAACCACTAT 59.279 37.037 0.00 0.00 44.42 2.12
3103 5682 8.455903 AACATCTCATTCCATTAACCACTATG 57.544 34.615 0.00 0.00 0.00 2.23
3104 5683 7.577303 ACATCTCATTCCATTAACCACTATGT 58.423 34.615 0.00 0.00 0.00 2.29
3105 5684 8.055181 ACATCTCATTCCATTAACCACTATGTT 58.945 33.333 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 5.140747 ACTCATGTAGTGTGAGAGGTTTC 57.859 43.478 9.86 0.00 44.57 2.78
10 11 4.707448 CCTAACTCATGTAGTGTGAGAGGT 59.293 45.833 9.86 0.00 44.57 3.85
17 18 5.127356 GGTAAGCTCCTAACTCATGTAGTGT 59.873 44.000 0.00 0.00 38.88 3.55
29 30 4.649674 CCACAGTAGATGGTAAGCTCCTAA 59.350 45.833 0.00 0.00 32.08 2.69
38 39 1.836802 TGCATGCCACAGTAGATGGTA 59.163 47.619 16.68 0.00 39.63 3.25
59 60 1.936547 CATTTAGTTGAGGAGGAGCGC 59.063 52.381 0.00 0.00 0.00 5.92
60 61 3.131223 TCTCATTTAGTTGAGGAGGAGCG 59.869 47.826 1.94 0.00 42.78 5.03
61 62 4.442753 CCTCTCATTTAGTTGAGGAGGAGC 60.443 50.000 0.00 0.00 46.53 4.70
72 73 5.222337 ACAAACCCATTCCCTCTCATTTAGT 60.222 40.000 0.00 0.00 0.00 2.24
124 125 5.762218 GCTTTGAGCCATATGAAGTATGACT 59.238 40.000 3.65 0.00 42.34 3.41
140 141 4.404507 TGTTTCGACTAATGCTTTGAGC 57.595 40.909 0.00 0.00 42.82 4.26
261 267 1.812571 CATAACCTCAACCACACAGGC 59.187 52.381 0.00 0.00 43.14 4.85
351 1937 1.063912 CGTCGTAGTAACCGGCATACA 59.936 52.381 17.48 4.18 0.00 2.29
382 1968 1.364626 CGGCATGCTTCAGTGGAGAC 61.365 60.000 18.92 0.00 0.00 3.36
516 2111 0.034380 CCCTCTACACCGACCTCTGA 60.034 60.000 0.00 0.00 0.00 3.27
538 2133 3.403038 CGGAGCTTTCCTCTCAAGAAAA 58.597 45.455 0.00 0.00 40.57 2.29
558 2153 4.785453 GTCCCCTGCTCCAAGCCG 62.785 72.222 0.00 0.00 41.51 5.52
559 2154 3.210012 TTGTCCCCTGCTCCAAGCC 62.210 63.158 0.00 0.00 41.51 4.35
561 2156 1.001641 CCTTGTCCCCTGCTCCAAG 60.002 63.158 0.00 0.00 35.26 3.61
562 2157 1.065410 TTCCTTGTCCCCTGCTCCAA 61.065 55.000 0.00 0.00 0.00 3.53
564 2159 1.201429 TCTTCCTTGTCCCCTGCTCC 61.201 60.000 0.00 0.00 0.00 4.70
565 2160 0.693049 TTCTTCCTTGTCCCCTGCTC 59.307 55.000 0.00 0.00 0.00 4.26
566 2161 1.149101 TTTCTTCCTTGTCCCCTGCT 58.851 50.000 0.00 0.00 0.00 4.24
567 2162 1.248486 GTTTCTTCCTTGTCCCCTGC 58.752 55.000 0.00 0.00 0.00 4.85
592 2187 1.633774 TCGTTCTCTCTGCTTCCCTT 58.366 50.000 0.00 0.00 0.00 3.95
705 2301 7.233632 TCGGATCATGGAATATGGAAGAAAAT 58.766 34.615 0.00 0.00 0.00 1.82
734 2335 8.129840 GTCAAAAAGAAGAAGAAAGGAACTACC 58.870 37.037 0.00 0.00 38.49 3.18
743 2344 6.317642 TCGGTGATGTCAAAAAGAAGAAGAAA 59.682 34.615 0.00 0.00 0.00 2.52
746 2347 5.673337 TCGGTGATGTCAAAAAGAAGAAG 57.327 39.130 0.00 0.00 0.00 2.85
747 2348 5.588648 ACTTCGGTGATGTCAAAAAGAAGAA 59.411 36.000 17.07 4.04 37.75 2.52
748 2349 5.123227 ACTTCGGTGATGTCAAAAAGAAGA 58.877 37.500 17.07 0.00 37.75 2.87
749 2350 5.424121 ACTTCGGTGATGTCAAAAAGAAG 57.576 39.130 12.32 12.32 39.54 2.85
750 2351 6.053005 ACTACTTCGGTGATGTCAAAAAGAA 58.947 36.000 7.07 1.35 0.00 2.52
751 2352 5.607477 ACTACTTCGGTGATGTCAAAAAGA 58.393 37.500 7.07 0.00 0.00 2.52
752 2353 5.924475 ACTACTTCGGTGATGTCAAAAAG 57.076 39.130 0.00 0.00 0.00 2.27
758 2359 4.398673 AGGAACTACTACTTCGGTGATGTC 59.601 45.833 0.00 0.00 36.02 3.06
802 2447 3.893326 AAGAATACAAATTGGCCTGGC 57.107 42.857 11.05 11.05 0.00 4.85
803 2448 5.598005 TGGATAAGAATACAAATTGGCCTGG 59.402 40.000 3.32 0.00 0.00 4.45
804 2449 6.322201 ACTGGATAAGAATACAAATTGGCCTG 59.678 38.462 3.32 0.00 0.00 4.85
805 2450 6.435164 ACTGGATAAGAATACAAATTGGCCT 58.565 36.000 3.32 0.00 0.00 5.19
830 2486 2.434336 TCCCGTTAACCTCTGGATGATG 59.566 50.000 0.00 0.00 0.00 3.07
862 2518 3.006537 ACAGAAATCGAACCGAGGAAGAA 59.993 43.478 0.00 0.00 39.91 2.52
877 2533 9.634021 AGTAGGAGAAAAGAAAGAAACAGAAAT 57.366 29.630 0.00 0.00 0.00 2.17
939 2595 2.501128 GTCATGAGGCGCTGGCTA 59.499 61.111 7.64 0.00 38.98 3.93
988 2652 1.340600 TGTTGCTATGGTGTTAGGGGC 60.341 52.381 0.00 0.00 0.00 5.80
994 2658 1.185315 GCCCATGTTGCTATGGTGTT 58.815 50.000 12.20 0.00 44.98 3.32
995 2659 0.039472 TGCCCATGTTGCTATGGTGT 59.961 50.000 12.20 0.00 44.98 4.16
1009 2675 2.192861 CCGAAGTTGTTGCTGCCCA 61.193 57.895 0.00 0.00 0.00 5.36
1025 2691 0.662374 ACTTGCGTACGTGAAGTCCG 60.662 55.000 21.77 6.74 35.16 4.79
1026 2692 1.494824 AACTTGCGTACGTGAAGTCC 58.505 50.000 25.27 7.39 0.00 3.85
1027 2693 3.529085 GAAAACTTGCGTACGTGAAGTC 58.471 45.455 25.27 14.92 0.00 3.01
1028 2694 2.034339 CGAAAACTTGCGTACGTGAAGT 60.034 45.455 21.77 21.77 0.00 3.01
1052 2730 4.928020 GGTCTCGAAAACTAAGATCGGTTT 59.072 41.667 8.09 8.09 37.20 3.27
1062 2740 3.447586 CCTCCATCAGGTCTCGAAAACTA 59.552 47.826 0.00 0.00 37.53 2.24
1071 2749 2.630889 TGTTCTCCTCCATCAGGTCT 57.369 50.000 0.00 0.00 43.95 3.85
1198 2879 0.035458 GTGAACTGCTGGTACTGGCT 59.965 55.000 10.74 0.00 0.00 4.75
1294 2975 4.452733 GGAGTCGCCCTTGGACCG 62.453 72.222 0.00 0.00 34.97 4.79
1364 3045 6.313164 GCGACTAAATTACTAATAGGCCATCC 59.687 42.308 5.01 0.00 0.00 3.51
1515 3220 3.128349 CGCACGGGCAATTAACTAGTAT 58.872 45.455 11.77 0.00 41.24 2.12
1518 3223 1.365699 ACGCACGGGCAATTAACTAG 58.634 50.000 11.77 0.00 41.24 2.57
1519 3224 1.465387 CAACGCACGGGCAATTAACTA 59.535 47.619 11.77 0.00 41.24 2.24
1522 3227 1.081108 GCAACGCACGGGCAATTAA 60.081 52.632 11.77 0.00 41.24 1.40
1523 3228 1.590610 ATGCAACGCACGGGCAATTA 61.591 50.000 11.77 0.00 43.04 1.40
1524 3229 2.817470 GATGCAACGCACGGGCAATT 62.817 55.000 11.77 0.00 43.04 2.32
1526 3231 4.036804 GATGCAACGCACGGGCAA 62.037 61.111 11.77 0.00 43.04 4.52
1531 3236 4.147322 GTCCCGATGCAACGCACG 62.147 66.667 11.32 0.54 43.04 5.34
1532 3237 3.799755 GGTCCCGATGCAACGCAC 61.800 66.667 11.32 9.26 43.04 5.34
1533 3238 2.245438 TATGGTCCCGATGCAACGCA 62.245 55.000 11.32 3.84 44.86 5.24
1535 3240 1.593196 AATATGGTCCCGATGCAACG 58.407 50.000 9.71 9.71 0.00 4.10
1536 3241 4.385358 AAAAATATGGTCCCGATGCAAC 57.615 40.909 0.00 0.00 0.00 4.17
1557 3262 7.559897 AGGTGGAGATTTAACAGTCAAAAAGAA 59.440 33.333 0.00 0.00 0.00 2.52
1559 3264 7.277174 AGGTGGAGATTTAACAGTCAAAAAG 57.723 36.000 0.00 0.00 0.00 2.27
1560 3265 6.264518 GGAGGTGGAGATTTAACAGTCAAAAA 59.735 38.462 0.00 0.00 0.00 1.94
1561 3266 5.768164 GGAGGTGGAGATTTAACAGTCAAAA 59.232 40.000 0.00 0.00 0.00 2.44
1564 3269 3.263425 GGGAGGTGGAGATTTAACAGTCA 59.737 47.826 0.00 0.00 0.00 3.41
1567 3272 2.846827 AGGGGAGGTGGAGATTTAACAG 59.153 50.000 0.00 0.00 0.00 3.16
1568 3273 2.844348 GAGGGGAGGTGGAGATTTAACA 59.156 50.000 0.00 0.00 0.00 2.41
1569 3274 3.116174 AGAGGGGAGGTGGAGATTTAAC 58.884 50.000 0.00 0.00 0.00 2.01
1570 3275 3.014110 AGAGAGGGGAGGTGGAGATTTAA 59.986 47.826 0.00 0.00 0.00 1.52
1577 3576 1.152271 AGAAAAGAGAGGGGAGGTGGA 59.848 52.381 0.00 0.00 0.00 4.02
1584 3583 4.205587 CATTGGATGAGAAAAGAGAGGGG 58.794 47.826 0.00 0.00 0.00 4.79
1585 3584 4.853007 ACATTGGATGAGAAAAGAGAGGG 58.147 43.478 0.00 0.00 0.00 4.30
1586 3585 8.517062 AAATACATTGGATGAGAAAAGAGAGG 57.483 34.615 0.00 0.00 0.00 3.69
1587 3586 8.619546 GGAAATACATTGGATGAGAAAAGAGAG 58.380 37.037 0.00 0.00 0.00 3.20
1588 3587 8.108999 TGGAAATACATTGGATGAGAAAAGAGA 58.891 33.333 0.00 0.00 0.00 3.10
1589 3588 8.284945 TGGAAATACATTGGATGAGAAAAGAG 57.715 34.615 0.00 0.00 0.00 2.85
1590 3589 8.689061 CATGGAAATACATTGGATGAGAAAAGA 58.311 33.333 0.00 0.00 0.00 2.52
1591 3590 8.472413 ACATGGAAATACATTGGATGAGAAAAG 58.528 33.333 0.00 0.00 0.00 2.27
1592 3591 8.365060 ACATGGAAATACATTGGATGAGAAAA 57.635 30.769 0.00 0.00 0.00 2.29
1593 3592 7.959658 ACATGGAAATACATTGGATGAGAAA 57.040 32.000 0.00 0.00 0.00 2.52
1594 3593 7.959658 AACATGGAAATACATTGGATGAGAA 57.040 32.000 0.00 0.00 0.00 2.87
1595 3594 9.645128 AATAACATGGAAATACATTGGATGAGA 57.355 29.630 0.00 0.00 0.00 3.27
1596 3595 9.903682 GAATAACATGGAAATACATTGGATGAG 57.096 33.333 0.00 0.00 0.00 2.90
1597 3596 9.418839 TGAATAACATGGAAATACATTGGATGA 57.581 29.630 0.00 0.00 0.00 2.92
1598 3597 9.687210 CTGAATAACATGGAAATACATTGGATG 57.313 33.333 0.00 0.00 0.00 3.51
1599 3598 8.362639 GCTGAATAACATGGAAATACATTGGAT 58.637 33.333 0.00 0.00 0.00 3.41
1600 3599 7.468494 CGCTGAATAACATGGAAATACATTGGA 60.468 37.037 0.00 0.00 0.00 3.53
1601 3600 6.638063 CGCTGAATAACATGGAAATACATTGG 59.362 38.462 0.00 0.00 0.00 3.16
1602 3601 6.142798 GCGCTGAATAACATGGAAATACATTG 59.857 38.462 0.00 0.00 0.00 2.82
1603 3602 6.208644 GCGCTGAATAACATGGAAATACATT 58.791 36.000 0.00 0.00 0.00 2.71
1604 3603 5.278463 GGCGCTGAATAACATGGAAATACAT 60.278 40.000 7.64 0.00 0.00 2.29
1605 3604 4.036262 GGCGCTGAATAACATGGAAATACA 59.964 41.667 7.64 0.00 0.00 2.29
1606 3605 4.036262 TGGCGCTGAATAACATGGAAATAC 59.964 41.667 7.64 0.00 0.00 1.89
1607 3606 4.203226 TGGCGCTGAATAACATGGAAATA 58.797 39.130 7.64 0.00 0.00 1.40
1608 3607 3.023119 TGGCGCTGAATAACATGGAAAT 58.977 40.909 7.64 0.00 0.00 2.17
1609 3608 2.441410 TGGCGCTGAATAACATGGAAA 58.559 42.857 7.64 0.00 0.00 3.13
1610 3609 2.121291 TGGCGCTGAATAACATGGAA 57.879 45.000 7.64 0.00 0.00 3.53
1611 3610 2.121291 TTGGCGCTGAATAACATGGA 57.879 45.000 7.64 0.00 0.00 3.41
1612 3611 2.164219 AGTTTGGCGCTGAATAACATGG 59.836 45.455 7.64 0.00 0.00 3.66
1613 3612 3.492421 AGTTTGGCGCTGAATAACATG 57.508 42.857 7.64 0.00 0.00 3.21
1614 3613 8.615878 TTATATAGTTTGGCGCTGAATAACAT 57.384 30.769 7.64 0.00 0.00 2.71
1615 3614 7.307751 GCTTATATAGTTTGGCGCTGAATAACA 60.308 37.037 7.64 0.00 0.00 2.41
1616 3615 7.015877 GCTTATATAGTTTGGCGCTGAATAAC 58.984 38.462 7.64 5.02 0.00 1.89
1617 3616 6.148811 GGCTTATATAGTTTGGCGCTGAATAA 59.851 38.462 7.64 0.56 0.00 1.40
1618 3617 5.642063 GGCTTATATAGTTTGGCGCTGAATA 59.358 40.000 7.64 0.00 0.00 1.75
1619 3618 4.455877 GGCTTATATAGTTTGGCGCTGAAT 59.544 41.667 7.64 0.00 0.00 2.57
1620 3619 3.813166 GGCTTATATAGTTTGGCGCTGAA 59.187 43.478 7.64 0.00 0.00 3.02
1621 3620 3.181459 TGGCTTATATAGTTTGGCGCTGA 60.181 43.478 7.64 0.00 0.00 4.26
1622 3621 3.138304 TGGCTTATATAGTTTGGCGCTG 58.862 45.455 7.64 0.00 0.00 5.18
1623 3622 3.485463 TGGCTTATATAGTTTGGCGCT 57.515 42.857 7.64 0.00 0.00 5.92
1624 3623 4.201970 TGTTTGGCTTATATAGTTTGGCGC 60.202 41.667 0.00 0.00 0.00 6.53
1625 3624 5.493133 TGTTTGGCTTATATAGTTTGGCG 57.507 39.130 0.00 0.00 0.00 5.69
1626 3625 5.221244 CCCTGTTTGGCTTATATAGTTTGGC 60.221 44.000 0.00 0.00 0.00 4.52
1627 3626 5.891551 ACCCTGTTTGGCTTATATAGTTTGG 59.108 40.000 0.00 0.00 0.00 3.28
1628 3627 7.404671 AACCCTGTTTGGCTTATATAGTTTG 57.595 36.000 0.00 0.00 0.00 2.93
1630 3629 9.788889 GTATAACCCTGTTTGGCTTATATAGTT 57.211 33.333 0.00 0.00 0.00 2.24
1631 3630 9.167387 AGTATAACCCTGTTTGGCTTATATAGT 57.833 33.333 0.00 0.00 0.00 2.12
1633 3632 9.787435 CAAGTATAACCCTGTTTGGCTTATATA 57.213 33.333 0.00 0.00 0.00 0.86
1634 3633 8.279361 ACAAGTATAACCCTGTTTGGCTTATAT 58.721 33.333 0.00 0.00 0.00 0.86
1635 3634 7.635648 ACAAGTATAACCCTGTTTGGCTTATA 58.364 34.615 0.00 0.00 0.00 0.98
1636 3635 6.490492 ACAAGTATAACCCTGTTTGGCTTAT 58.510 36.000 0.00 0.00 0.00 1.73
1637 3636 5.883180 ACAAGTATAACCCTGTTTGGCTTA 58.117 37.500 0.00 0.00 0.00 3.09
1638 3637 4.736473 ACAAGTATAACCCTGTTTGGCTT 58.264 39.130 0.00 0.00 0.00 4.35
1639 3638 4.382386 ACAAGTATAACCCTGTTTGGCT 57.618 40.909 0.00 0.00 0.00 4.75
1640 3639 5.462530 AAACAAGTATAACCCTGTTTGGC 57.537 39.130 6.93 0.00 0.00 4.52
1662 3661 5.652014 CAGTATATGGCTGAAGGGTGAAAAA 59.348 40.000 3.81 0.00 36.12 1.94
1663 3662 5.192927 CAGTATATGGCTGAAGGGTGAAAA 58.807 41.667 3.81 0.00 36.12 2.29
1664 3663 4.780815 CAGTATATGGCTGAAGGGTGAAA 58.219 43.478 3.81 0.00 36.12 2.69
1665 3664 3.433598 GCAGTATATGGCTGAAGGGTGAA 60.434 47.826 11.72 0.00 36.12 3.18
1666 3665 2.104792 GCAGTATATGGCTGAAGGGTGA 59.895 50.000 11.72 0.00 36.12 4.02
1667 3666 2.498167 GCAGTATATGGCTGAAGGGTG 58.502 52.381 11.72 0.00 36.12 4.61
1668 3667 2.938956 GCAGTATATGGCTGAAGGGT 57.061 50.000 11.72 0.00 36.12 4.34
1677 3676 5.359576 GGAGTAGATGAGAGGCAGTATATGG 59.640 48.000 0.00 0.00 0.00 2.74
1678 3677 5.359576 GGGAGTAGATGAGAGGCAGTATATG 59.640 48.000 0.00 0.00 0.00 1.78
1679 3678 5.255207 AGGGAGTAGATGAGAGGCAGTATAT 59.745 44.000 0.00 0.00 0.00 0.86
1680 3679 4.604050 AGGGAGTAGATGAGAGGCAGTATA 59.396 45.833 0.00 0.00 0.00 1.47
1681 3680 3.401002 AGGGAGTAGATGAGAGGCAGTAT 59.599 47.826 0.00 0.00 0.00 2.12
1682 3681 2.786445 AGGGAGTAGATGAGAGGCAGTA 59.214 50.000 0.00 0.00 0.00 2.74
1683 3682 1.573376 AGGGAGTAGATGAGAGGCAGT 59.427 52.381 0.00 0.00 0.00 4.40
1684 3683 2.238521 GAGGGAGTAGATGAGAGGCAG 58.761 57.143 0.00 0.00 0.00 4.85
1685 3684 1.133325 GGAGGGAGTAGATGAGAGGCA 60.133 57.143 0.00 0.00 0.00 4.75
1686 3685 1.627864 GGAGGGAGTAGATGAGAGGC 58.372 60.000 0.00 0.00 0.00 4.70
1687 3686 1.144093 ACGGAGGGAGTAGATGAGAGG 59.856 57.143 0.00 0.00 0.00 3.69
1688 3687 2.649531 ACGGAGGGAGTAGATGAGAG 57.350 55.000 0.00 0.00 0.00 3.20
1689 3688 3.288964 GAAACGGAGGGAGTAGATGAGA 58.711 50.000 0.00 0.00 0.00 3.27
1690 3689 3.024547 TGAAACGGAGGGAGTAGATGAG 58.975 50.000 0.00 0.00 0.00 2.90
1691 3690 3.095912 TGAAACGGAGGGAGTAGATGA 57.904 47.619 0.00 0.00 0.00 2.92
1692 3691 3.887621 TTGAAACGGAGGGAGTAGATG 57.112 47.619 0.00 0.00 0.00 2.90
1693 3692 4.903045 TTTTGAAACGGAGGGAGTAGAT 57.097 40.909 0.00 0.00 0.00 1.98
1694 3693 4.903045 ATTTTGAAACGGAGGGAGTAGA 57.097 40.909 0.00 0.00 0.00 2.59
1695 3694 5.974108 TCTATTTTGAAACGGAGGGAGTAG 58.026 41.667 0.00 0.00 0.00 2.57
1696 3695 6.155565 TCATCTATTTTGAAACGGAGGGAGTA 59.844 38.462 0.00 0.00 0.00 2.59
1697 3696 4.903045 TCTATTTTGAAACGGAGGGAGT 57.097 40.909 0.00 0.00 0.00 3.85
1698 3697 5.294552 GTCATCTATTTTGAAACGGAGGGAG 59.705 44.000 0.00 0.00 0.00 4.30
1699 3698 5.045869 AGTCATCTATTTTGAAACGGAGGGA 60.046 40.000 0.00 0.00 0.00 4.20
1700 3699 5.186198 AGTCATCTATTTTGAAACGGAGGG 58.814 41.667 0.00 0.00 0.00 4.30
1701 3700 5.874810 TGAGTCATCTATTTTGAAACGGAGG 59.125 40.000 0.00 0.00 0.00 4.30
1702 3701 6.968131 TGAGTCATCTATTTTGAAACGGAG 57.032 37.500 0.00 0.00 0.00 4.63
1703 3702 6.934645 AGTTGAGTCATCTATTTTGAAACGGA 59.065 34.615 1.70 0.00 0.00 4.69
1704 3703 7.133891 AGTTGAGTCATCTATTTTGAAACGG 57.866 36.000 1.70 0.00 0.00 4.44
1757 3756 9.983024 TCCATTTAAATAGATGACCCAACTTTA 57.017 29.630 0.00 0.00 0.00 1.85
1758 3757 8.893563 TCCATTTAAATAGATGACCCAACTTT 57.106 30.769 0.00 0.00 0.00 2.66
1759 3758 7.561356 CCTCCATTTAAATAGATGACCCAACTT 59.439 37.037 0.00 0.00 0.00 2.66
1760 3759 7.062957 CCTCCATTTAAATAGATGACCCAACT 58.937 38.462 0.00 0.00 0.00 3.16
1761 3760 6.265422 CCCTCCATTTAAATAGATGACCCAAC 59.735 42.308 0.00 0.00 0.00 3.77
1762 3761 6.161348 TCCCTCCATTTAAATAGATGACCCAA 59.839 38.462 0.00 0.00 0.00 4.12
1763 3762 5.674496 TCCCTCCATTTAAATAGATGACCCA 59.326 40.000 0.00 0.00 0.00 4.51
1764 3763 6.183361 ACTCCCTCCATTTAAATAGATGACCC 60.183 42.308 0.00 0.00 0.00 4.46
1765 3764 6.842676 ACTCCCTCCATTTAAATAGATGACC 58.157 40.000 0.00 0.00 0.00 4.02
1771 3770 9.853177 ACTCAATTACTCCCTCCATTTAAATAG 57.147 33.333 0.00 0.00 0.00 1.73
1772 3771 9.627123 CACTCAATTACTCCCTCCATTTAAATA 57.373 33.333 0.00 0.00 0.00 1.40
1773 3772 7.561356 CCACTCAATTACTCCCTCCATTTAAAT 59.439 37.037 0.00 0.00 0.00 1.40
1774 3773 6.889722 CCACTCAATTACTCCCTCCATTTAAA 59.110 38.462 0.00 0.00 0.00 1.52
1775 3774 6.423182 CCACTCAATTACTCCCTCCATTTAA 58.577 40.000 0.00 0.00 0.00 1.52
1776 3775 5.631481 GCCACTCAATTACTCCCTCCATTTA 60.631 44.000 0.00 0.00 0.00 1.40
1777 3776 4.860022 CCACTCAATTACTCCCTCCATTT 58.140 43.478 0.00 0.00 0.00 2.32
1778 3777 3.372025 GCCACTCAATTACTCCCTCCATT 60.372 47.826 0.00 0.00 0.00 3.16
1779 3778 2.173569 GCCACTCAATTACTCCCTCCAT 59.826 50.000 0.00 0.00 0.00 3.41
1780 3779 1.559682 GCCACTCAATTACTCCCTCCA 59.440 52.381 0.00 0.00 0.00 3.86
1781 3780 1.559682 TGCCACTCAATTACTCCCTCC 59.440 52.381 0.00 0.00 0.00 4.30
1782 3781 3.350219 TTGCCACTCAATTACTCCCTC 57.650 47.619 0.00 0.00 0.00 4.30
1783 3782 3.181434 TGTTTGCCACTCAATTACTCCCT 60.181 43.478 0.00 0.00 34.12 4.20
1784 3783 3.153919 TGTTTGCCACTCAATTACTCCC 58.846 45.455 0.00 0.00 34.12 4.30
1785 3784 6.509418 TTATGTTTGCCACTCAATTACTCC 57.491 37.500 0.00 0.00 34.12 3.85
1786 3785 6.030228 GCTTATGTTTGCCACTCAATTACTC 58.970 40.000 0.00 0.00 34.12 2.59
1787 3786 5.954335 GCTTATGTTTGCCACTCAATTACT 58.046 37.500 0.00 0.00 34.12 2.24
1800 3799 4.520492 AGAGTTGGAGTTGGCTTATGTTTG 59.480 41.667 0.00 0.00 0.00 2.93
1839 3839 0.674895 GCTGGAGAAGTCGGTTGCAT 60.675 55.000 0.00 0.00 0.00 3.96
1982 3982 7.168135 CACTTTTCCTTCAAGAATTACAACTGC 59.832 37.037 0.00 0.00 0.00 4.40
2013 4013 5.575218 CCACACACTTTTGTTAACTTTGACC 59.425 40.000 7.22 0.00 31.66 4.02
2027 4027 1.682854 CAATGCACTCCCACACACTTT 59.317 47.619 0.00 0.00 0.00 2.66
2070 4070 4.141551 TGGACCTTCATCTGGAGATCATTG 60.142 45.833 0.00 0.00 31.21 2.82
2080 4080 9.265901 CTTTATTACTATGTGGACCTTCATCTG 57.734 37.037 6.12 4.68 0.00 2.90
2111 4111 9.109393 CTCCTTCGATAAAATTTGTGGAATAGA 57.891 33.333 1.09 1.85 0.00 1.98
2127 4127 7.663905 TGTTCCATTTTCTTTTCTCCTTCGATA 59.336 33.333 0.00 0.00 0.00 2.92
2217 4217 3.557577 TCGATCAAGTTGCACAATTGG 57.442 42.857 10.83 0.00 0.00 3.16
2220 4220 5.630680 GTCAAAATCGATCAAGTTGCACAAT 59.369 36.000 0.00 0.00 0.00 2.71
2245 4245 0.397564 AACCGGGAAGGCGTTCTTTA 59.602 50.000 17.90 0.00 46.52 1.85
2278 4278 0.179137 GCGTGTGATCTGATCGTGGA 60.179 55.000 12.65 0.00 0.00 4.02
2296 4296 2.032634 TGGCCGTTGATGAGAACGC 61.033 57.895 0.00 0.00 45.89 4.84
2299 4299 0.321564 CAGGTGGCCGTTGATGAGAA 60.322 55.000 0.00 0.00 0.00 2.87
2352 4352 1.473258 GTGGCAATGGCATGTAGGAA 58.527 50.000 13.81 0.00 43.71 3.36
2393 4393 2.915869 GTCCAGGTGTGGTGTGGT 59.084 61.111 0.00 0.00 45.28 4.16
2403 4403 0.689055 GGGGAAAGTAACGTCCAGGT 59.311 55.000 0.00 0.00 35.44 4.00
2427 4427 0.380733 CATGGTAGCTGCGTCTACGA 59.619 55.000 6.71 5.93 43.02 3.43
2516 4516 7.190920 AGAATGTGCTTTGTACAGTTTCTAC 57.809 36.000 0.00 0.00 30.18 2.59
2523 4523 8.391106 GGATTAACTAGAATGTGCTTTGTACAG 58.609 37.037 0.00 0.00 30.87 2.74
2534 4534 8.079211 TGCTACTGAAGGATTAACTAGAATGT 57.921 34.615 0.00 0.00 0.00 2.71
2635 4645 8.564574 CAACCTTCAATTACTTGCTTGTAACTA 58.435 33.333 4.69 0.00 35.56 2.24
2644 4654 3.976169 TGTGCAACCTTCAATTACTTGC 58.024 40.909 0.00 0.00 38.16 4.01
2645 4655 8.586570 TTATTTGTGCAACCTTCAATTACTTG 57.413 30.769 0.00 0.00 34.36 3.16
2679 5140 0.250234 TTCTAGAAGCGTGCATGCCT 59.750 50.000 26.95 19.40 34.65 4.75
2767 5346 9.507329 ACAATGTTAGATGTCATACTTCTGTTT 57.493 29.630 5.89 0.00 34.84 2.83
2768 5347 9.507329 AACAATGTTAGATGTCATACTTCTGTT 57.493 29.630 0.00 0.00 34.84 3.16
2769 5348 9.155975 GAACAATGTTAGATGTCATACTTCTGT 57.844 33.333 0.00 0.00 34.84 3.41
2772 5351 9.593134 AGAGAACAATGTTAGATGTCATACTTC 57.407 33.333 0.00 0.00 0.00 3.01
2779 5358 9.424319 TCAGTTTAGAGAACAATGTTAGATGTC 57.576 33.333 0.00 0.00 0.00 3.06
2780 5359 9.778741 TTCAGTTTAGAGAACAATGTTAGATGT 57.221 29.630 0.00 0.00 0.00 3.06
3076 5655 5.888161 AGTGGTTAATGGAATGAGATGTTCC 59.112 40.000 0.00 0.00 44.32 3.62
3077 5656 8.562892 CATAGTGGTTAATGGAATGAGATGTTC 58.437 37.037 0.00 0.00 0.00 3.18
3078 5657 8.055181 ACATAGTGGTTAATGGAATGAGATGTT 58.945 33.333 0.00 0.00 0.00 2.71
3079 5658 7.577303 ACATAGTGGTTAATGGAATGAGATGT 58.423 34.615 0.00 0.00 0.00 3.06
3080 5659 8.455903 AACATAGTGGTTAATGGAATGAGATG 57.544 34.615 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.