Multiple sequence alignment - TraesCS7D01G042600

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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 TraesCS7D01G042600 chr7D 100.000 7250 0 0 1 7250 21789076 21781827 0.000000e+00 13389.0
1 TraesCS7D01G042600 chr7D 78.516 768 103 46 1156 1892 21836996 21836260 1.430000e-121 448.0
2 TraesCS7D01G042600 chr7A 90.229 3838 328 38 937 4760 22241341 22237537 0.000000e+00 4966.0
3 TraesCS7D01G042600 chr7A 87.708 1863 169 17 754 2572 22386017 22384171 0.000000e+00 2117.0
4 TraesCS7D01G042600 chr7A 89.735 1169 106 8 5140 6295 22384164 22382997 0.000000e+00 1482.0
5 TraesCS7D01G042600 chr7A 85.800 1338 108 31 451 1756 22412137 22410850 0.000000e+00 1343.0
6 TraesCS7D01G042600 chr7A 89.922 903 75 6 5400 6295 22236811 22235918 0.000000e+00 1149.0
7 TraesCS7D01G042600 chr7A 89.138 893 78 10 5167 6047 22386936 22386051 0.000000e+00 1094.0
8 TraesCS7D01G042600 chr7A 90.390 718 62 6 4778 5490 22237548 22236833 0.000000e+00 937.0
9 TraesCS7D01G042600 chr7A 91.339 635 36 11 4 632 22284376 22283755 0.000000e+00 850.0
10 TraesCS7D01G042600 chr7A 90.379 634 51 5 1787 2413 22387637 22387007 0.000000e+00 824.0
11 TraesCS7D01G042600 chr7A 87.764 474 48 2 6577 7046 22226898 22226431 4.950000e-151 545.0
12 TraesCS7D01G042600 chr7A 92.192 333 25 1 6298 6629 22382951 22382619 3.060000e-128 470.0
13 TraesCS7D01G042600 chr7A 91.958 286 22 1 6294 6579 22235875 22235591 4.070000e-107 399.0
14 TraesCS7D01G042600 chr7A 80.154 519 86 16 1156 1666 22332706 22332197 8.880000e-99 372.0
15 TraesCS7D01G042600 chr4A 88.959 4103 310 49 720 4760 711973477 711977498 0.000000e+00 4935.0
16 TraesCS7D01G042600 chr4A 88.916 4105 312 50 720 4760 711956719 711960744 0.000000e+00 4927.0
17 TraesCS7D01G042600 chr4A 90.885 1536 117 14 4778 6295 711977486 711979016 0.000000e+00 2039.0
18 TraesCS7D01G042600 chr4A 90.761 1537 118 14 4778 6295 711960732 711962263 0.000000e+00 2030.0
19 TraesCS7D01G042600 chr4A 86.639 958 93 14 6297 7250 711979055 711979981 0.000000e+00 1027.0
20 TraesCS7D01G042600 chr4A 86.430 958 95 14 6297 7250 711962302 711963228 0.000000e+00 1016.0
21 TraesCS7D01G042600 chr4A 81.579 608 107 4 6647 7250 722144426 722145032 1.400000e-136 497.0
22 TraesCS7D01G042600 chr4A 81.618 136 23 2 1581 1715 712305998 712306132 2.140000e-20 111.0
23 TraesCS7D01G042600 chr4A 80.147 136 24 3 1581 1715 712269850 712269983 1.660000e-16 99.0
24 TraesCS7D01G042600 chrUn 90.300 2165 155 16 664 2775 50503255 50505417 0.000000e+00 2784.0
25 TraesCS7D01G042600 chrUn 88.912 1957 156 31 2820 4760 50544966 50543055 0.000000e+00 2355.0
26 TraesCS7D01G042600 chrUn 91.253 1532 115 12 4778 6295 50543067 50541541 0.000000e+00 2069.0
27 TraesCS7D01G042600 chrUn 89.049 1251 105 21 1557 2775 50546204 50544954 0.000000e+00 1522.0
28 TraesCS7D01G042600 chrUn 89.843 955 84 9 3562 4511 50506440 50507386 0.000000e+00 1214.0
29 TraesCS7D01G042600 chrUn 92.744 758 49 2 5498 6249 50508647 50509404 0.000000e+00 1090.0
30 TraesCS7D01G042600 chrUn 86.798 962 90 19 6294 7250 50541500 50540571 0.000000e+00 1038.0
31 TraesCS7D01G042600 chrUn 89.821 727 61 10 4778 5496 50507751 50508472 0.000000e+00 920.0
32 TraesCS7D01G042600 chrUn 87.968 748 50 17 2820 3560 50505405 50506119 0.000000e+00 846.0
33 TraesCS7D01G042600 chrUn 88.889 522 43 6 106 623 50502732 50503242 4.770000e-176 628.0
34 TraesCS7D01G042600 chrUn 84.936 624 66 15 6627 7250 50509567 50510162 2.240000e-169 606.0
35 TraesCS7D01G042600 chrUn 91.317 334 24 4 6294 6626 477270758 477270429 1.110000e-122 451.0
36 TraesCS7D01G042600 chrUn 88.492 252 21 6 4513 4760 50507516 50507763 1.530000e-76 298.0
37 TraesCS7D01G042600 chrUn 100.000 30 0 0 2382 2411 50545452 50545423 1.000000e-03 56.5
38 TraesCS7D01G042600 chr5D 86.131 274 38 0 6647 6920 279233084 279233357 5.500000e-76 296.0
39 TraesCS7D01G042600 chr5B 81.560 282 39 8 2159 2437 243916301 243916030 3.400000e-53 220.0


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 TraesCS7D01G042600 chr7D 21781827 21789076 7249 True 13389.000000 13389 100.000000 1 7250 1 chr7D.!!$R1 7249
1 TraesCS7D01G042600 chr7D 21836260 21836996 736 True 448.000000 448 78.516000 1156 1892 1 chr7D.!!$R2 736
2 TraesCS7D01G042600 chr7A 22235591 22241341 5750 True 1862.750000 4966 90.624750 937 6579 4 chr7A.!!$R5 5642
3 TraesCS7D01G042600 chr7A 22410850 22412137 1287 True 1343.000000 1343 85.800000 451 1756 1 chr7A.!!$R4 1305
4 TraesCS7D01G042600 chr7A 22382619 22387637 5018 True 1197.400000 2117 89.830400 754 6629 5 chr7A.!!$R6 5875
5 TraesCS7D01G042600 chr7A 22283755 22284376 621 True 850.000000 850 91.339000 4 632 1 chr7A.!!$R2 628
6 TraesCS7D01G042600 chr7A 22332197 22332706 509 True 372.000000 372 80.154000 1156 1666 1 chr7A.!!$R3 510
7 TraesCS7D01G042600 chr4A 711973477 711979981 6504 False 2667.000000 4935 88.827667 720 7250 3 chr4A.!!$F5 6530
8 TraesCS7D01G042600 chr4A 711956719 711963228 6509 False 2657.666667 4927 88.702333 720 7250 3 chr4A.!!$F4 6530
9 TraesCS7D01G042600 chr4A 722144426 722145032 606 False 497.000000 497 81.579000 6647 7250 1 chr4A.!!$F3 603
10 TraesCS7D01G042600 chrUn 50540571 50546204 5633 True 1408.100000 2355 91.202400 1557 7250 5 chrUn.!!$R2 5693
11 TraesCS7D01G042600 chrUn 50502732 50510162 7430 False 1048.250000 2784 89.124125 106 7250 8 chrUn.!!$F1 7144

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
99 100 0.250727 TTTCTGCACTCTTTCCCCCG 60.251 55.000 0.00 0.0 0.00 5.73 F
248 252 0.321996 GGTGTTGGAGAGGAGGACAC 59.678 60.000 0.00 0.0 39.76 3.67 F
1326 2242 0.748450 TAACCTAACCGCAGATCCCG 59.252 55.000 0.00 0.0 0.00 5.14 F
2497 3479 0.322456 CTTGGCCCCGTCTTCATCAA 60.322 55.000 0.00 0.0 0.00 2.57 F
2573 3555 0.321346 TCGCTCCTGAAACATCAGCA 59.679 50.000 0.28 0.0 36.46 4.41 F
2632 3628 0.821301 TTGCGTGCCCTTTGATGTGA 60.821 50.000 0.00 0.0 0.00 3.58 F
3459 4469 1.617850 CCTAACTTTTGCCATGTGCCA 59.382 47.619 4.07 0.0 40.16 4.92 F
4769 6245 0.031515 TCGGGCTCCTATCCCTCAAA 60.032 55.000 0.00 0.0 41.69 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1450 2378 1.066787 GCTGGCTCTCTTTTCGGTAGT 60.067 52.381 0.00 0.00 0.00 2.73 R
1460 2388 1.603236 CTTCGTCCTGCTGGCTCTCT 61.603 60.000 4.42 0.00 0.00 3.10 R
2503 3485 0.254178 ATGAGCAGTGGCCTAACCTG 59.746 55.000 3.32 6.12 42.56 4.00 R
3436 4446 2.497273 GCACATGGCAAAAGTTAGGGAT 59.503 45.455 0.00 0.00 43.97 3.85 R
4087 5424 3.683365 ATTTCTTGCCATGGTCCAAAC 57.317 42.857 14.67 0.00 0.00 2.93 R
4172 5509 4.805219 AGTTTGCCATTTTATGTTCGGTC 58.195 39.130 0.00 0.00 0.00 4.79 R
5008 6492 0.179029 CTTCTCGGTGTGGGTGGTTT 60.179 55.000 0.00 0.00 0.00 3.27 R
6632 8460 0.179124 GACCAGGACTAGCTTCGCAG 60.179 60.000 0.00 0.00 0.00 5.18 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
36 37 1.365368 GAGAAGCGAGCAAGGGAAGC 61.365 60.000 0.00 0.00 0.00 3.86
39 40 0.610232 AAGCGAGCAAGGGAAGCAAT 60.610 50.000 0.00 0.00 0.00 3.56
42 43 1.472480 GCGAGCAAGGGAAGCAATAAA 59.528 47.619 0.00 0.00 0.00 1.40
43 44 2.094752 GCGAGCAAGGGAAGCAATAAAA 60.095 45.455 0.00 0.00 0.00 1.52
44 45 3.613910 GCGAGCAAGGGAAGCAATAAAAA 60.614 43.478 0.00 0.00 0.00 1.94
88 89 2.036475 TCTGAGTGAGAGGTTTCTGCAC 59.964 50.000 0.00 0.00 34.48 4.57
90 91 2.036475 TGAGTGAGAGGTTTCTGCACTC 59.964 50.000 19.11 19.11 45.89 3.51
99 100 0.250727 TTTCTGCACTCTTTCCCCCG 60.251 55.000 0.00 0.00 0.00 5.73
102 103 0.537371 CTGCACTCTTTCCCCCGTTT 60.537 55.000 0.00 0.00 0.00 3.60
114 115 1.296715 CCCGTTTCTCCTCCAGTGG 59.703 63.158 1.40 1.40 0.00 4.00
248 252 0.321996 GGTGTTGGAGAGGAGGACAC 59.678 60.000 0.00 0.00 39.76 3.67
429 441 6.467677 AGATATTGTGGAATGTATTCGAGGG 58.532 40.000 0.00 0.00 37.67 4.30
430 442 3.992943 TTGTGGAATGTATTCGAGGGT 57.007 42.857 0.00 0.00 37.67 4.34
431 443 3.992943 TGTGGAATGTATTCGAGGGTT 57.007 42.857 0.00 0.00 37.67 4.11
432 444 3.605634 TGTGGAATGTATTCGAGGGTTG 58.394 45.455 0.00 0.00 37.67 3.77
526 538 7.907045 CAGCATATATAGCAAATAAAAGCTCCG 59.093 37.037 9.01 0.00 42.05 4.63
592 609 3.083293 AGAGAGGGAAACTGACGTAGAC 58.917 50.000 0.00 0.00 0.00 2.59
632 650 5.384063 TCAAAGAAAATGTGTGTGTGTGT 57.616 34.783 0.00 0.00 0.00 3.72
642 673 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
644 675 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
645 676 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
646 677 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
647 678 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
650 681 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
651 682 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
652 683 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
653 684 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
655 686 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
657 688 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
658 689 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
659 690 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
660 691 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
661 692 1.265635 GTGTGTGTGTGTGTGTGTGTT 59.734 47.619 0.00 0.00 0.00 3.32
662 693 1.265365 TGTGTGTGTGTGTGTGTGTTG 59.735 47.619 0.00 0.00 0.00 3.33
666 697 3.753797 TGTGTGTGTGTGTGTGTTGTATT 59.246 39.130 0.00 0.00 0.00 1.89
698 729 7.840342 ATCTTCTGTACTTGCAATAGTGAAG 57.160 36.000 0.00 10.60 31.77 3.02
848 1717 3.933515 AGCGAGAGAGCTTCCTCC 58.066 61.111 9.75 4.55 46.80 4.30
923 1810 4.041075 GTCTTCCTCCTTCAGTTTCTTCCT 59.959 45.833 0.00 0.00 0.00 3.36
934 1821 7.335673 CCTTCAGTTTCTTCCTTTTCTATCTCC 59.664 40.741 0.00 0.00 0.00 3.71
942 1858 2.611292 CCTTTTCTATCTCCGCTGCTTG 59.389 50.000 0.00 0.00 0.00 4.01
1193 2109 4.129148 GGCTGGGATGGTGGGGAC 62.129 72.222 0.00 0.00 0.00 4.46
1326 2242 0.748450 TAACCTAACCGCAGATCCCG 59.252 55.000 0.00 0.00 0.00 5.14
1460 2388 1.375013 GGCCGCAGACTACCGAAAA 60.375 57.895 0.00 0.00 0.00 2.29
1465 2393 2.520979 CGCAGACTACCGAAAAGAGAG 58.479 52.381 0.00 0.00 0.00 3.20
1606 2534 4.329545 GGTGGCGCTCTTGGTCCA 62.330 66.667 7.64 0.00 0.00 4.02
1607 2535 2.045926 GTGGCGCTCTTGGTCCAT 60.046 61.111 7.64 0.00 0.00 3.41
1790 2721 2.265739 GATGCAGCTGGACCGACA 59.734 61.111 17.12 3.66 0.00 4.35
1813 2744 4.357947 AGATGGCGCGTGTCACGT 62.358 61.111 25.18 6.19 44.73 4.49
1984 2925 1.338020 CAAACAAGCCACCTTCCTGAC 59.662 52.381 0.00 0.00 0.00 3.51
2263 3212 1.195448 CGTTGAGTTGCCATGTCAGAC 59.805 52.381 0.00 0.00 0.00 3.51
2349 3331 4.279420 CCGATGTCCACTCATCTCTATTCA 59.721 45.833 0.00 0.00 41.17 2.57
2369 3351 4.857679 TCATCATCCATTCACAACCATGA 58.142 39.130 0.00 0.00 0.00 3.07
2380 3362 2.027377 CACAACCATGAGGAAGAGCTCT 60.027 50.000 11.45 11.45 38.69 4.09
2454 3436 1.470285 GCTCGCGTGAATAGGTGGTAA 60.470 52.381 13.13 0.00 0.00 2.85
2497 3479 0.322456 CTTGGCCCCGTCTTCATCAA 60.322 55.000 0.00 0.00 0.00 2.57
2503 3485 0.676782 CCCGTCTTCATCAACCCCAC 60.677 60.000 0.00 0.00 0.00 4.61
2572 3554 1.329906 CATCGCTCCTGAAACATCAGC 59.670 52.381 0.28 0.00 36.46 4.26
2573 3555 0.321346 TCGCTCCTGAAACATCAGCA 59.679 50.000 0.28 0.00 36.46 4.41
2575 3557 1.741706 CGCTCCTGAAACATCAGCATT 59.258 47.619 0.28 0.00 36.46 3.56
2580 3562 5.571784 TCCTGAAACATCAGCATTCAATC 57.428 39.130 0.28 0.00 36.46 2.67
2599 3581 6.687604 TCAATCAGTTCGTGTCAAAGAGATA 58.312 36.000 0.00 0.00 0.00 1.98
2603 3585 5.348724 TCAGTTCGTGTCAAAGAGATATTGC 59.651 40.000 0.00 0.00 0.00 3.56
2616 3598 7.721286 AAGAGATATTGCAGTATAGTGTTGC 57.279 36.000 9.30 1.17 38.30 4.17
2632 3628 0.821301 TTGCGTGCCCTTTGATGTGA 60.821 50.000 0.00 0.00 0.00 3.58
2668 3664 9.985318 GCAGCTATATTGATGTTATTCTTCATC 57.015 33.333 4.41 0.00 40.29 2.92
2703 3700 7.928307 AGCTACAGTAATTTGATCATGTGTT 57.072 32.000 7.48 0.00 0.00 3.32
2737 3734 6.347061 AAGATGATTCCCCTAGGATTGTTT 57.653 37.500 11.48 0.00 43.54 2.83
2739 3736 6.745857 AGATGATTCCCCTAGGATTGTTTTT 58.254 36.000 11.48 0.00 43.54 1.94
2787 3784 3.667087 TGGCACATTTCTGTCCGC 58.333 55.556 0.00 0.00 31.62 5.54
2796 3793 4.023193 CACATTTCTGTCCGCTTTTTAGGT 60.023 41.667 0.00 0.00 31.62 3.08
2856 3853 7.418483 GCAAGTTATAGATAAAATTTGCCCCCA 60.418 37.037 12.13 0.00 34.18 4.96
2860 3857 9.325198 GTTATAGATAAAATTTGCCCCCAAAAG 57.675 33.333 0.00 0.00 43.58 2.27
2885 3882 9.777297 AGAAATTGCAAATTGGTTTACTACATT 57.223 25.926 4.04 0.00 0.00 2.71
3021 4020 7.781693 AGTTTATCTCCTACATCATGGCAAAAT 59.218 33.333 0.00 0.00 0.00 1.82
3324 4326 6.701432 AAGACAAATCTCGTAGTTTTACCG 57.299 37.500 0.00 0.00 32.34 4.02
3326 4328 5.860716 AGACAAATCTCGTAGTTTTACCGTC 59.139 40.000 0.00 0.00 0.00 4.79
3434 4444 6.645700 ACATGTTGTGTTTTTACAAAGCAG 57.354 33.333 0.00 0.00 41.75 4.24
3435 4445 6.393990 ACATGTTGTGTTTTTACAAAGCAGA 58.606 32.000 0.00 0.00 41.75 4.26
3436 4446 6.870965 ACATGTTGTGTTTTTACAAAGCAGAA 59.129 30.769 0.00 0.00 41.75 3.02
3459 4469 1.617850 CCTAACTTTTGCCATGTGCCA 59.382 47.619 4.07 0.00 40.16 4.92
3489 4500 7.926674 AATTCCCTAAAATTGCCATCTTTTG 57.073 32.000 0.00 0.00 0.00 2.44
3683 5013 9.914834 ATGTAACTTTATTTTAGGTAGCATGGA 57.085 29.630 0.00 0.00 0.00 3.41
3814 5145 8.703823 AGAACAACGTCAATTTTATTCGTTAC 57.296 30.769 0.00 0.00 41.58 2.50
3848 5179 6.799512 AGTTTGATAATTTGACCATGCTAGC 58.200 36.000 8.10 8.10 0.00 3.42
3892 5223 9.225436 GGCAATTTTATGGTATTTTGGAAAAGA 57.775 29.630 0.00 0.00 0.00 2.52
3903 5234 9.140286 GGTATTTTGGAAAAGATTCTACTTTGC 57.860 33.333 0.00 0.00 39.57 3.68
4008 5343 8.891720 ACAATGCAATGTTTTGTTTTACTCATT 58.108 25.926 0.28 0.00 35.17 2.57
4079 5414 8.987890 ACAACCATTTGAAATTCCTATTTTTCG 58.012 29.630 0.00 0.00 34.16 3.46
4116 5453 3.007182 CCATGGCAAGAAATTTCACACCT 59.993 43.478 19.99 5.56 0.00 4.00
4141 5478 7.507733 TGGCAATTTTATTCAACAAAGCATT 57.492 28.000 0.00 0.00 0.00 3.56
4159 5496 8.344098 CAAAGCATTGTAAAAACATTGAATGGT 58.656 29.630 10.27 0.00 34.04 3.55
4172 5509 8.550710 AACATTGAATGGTGTGGAAAATTATG 57.449 30.769 10.27 0.00 33.60 1.90
4174 5511 7.818930 ACATTGAATGGTGTGGAAAATTATGAC 59.181 33.333 10.27 0.00 33.60 3.06
4383 5721 7.951530 ATTGAACATGATTTTGTGAGAAACC 57.048 32.000 0.00 0.00 0.00 3.27
4511 5854 5.824904 ACTTAGAGCATGGCAAATGTAAG 57.175 39.130 0.00 1.90 0.00 2.34
4575 6050 8.688747 ATTTTTGTTTATGGCAAAGATTTCCA 57.311 26.923 0.00 0.00 37.18 3.53
4695 6171 2.583441 TTCACTGCAGGGGTCCTCG 61.583 63.158 17.80 0.00 0.00 4.63
4737 6213 2.943265 AGGCAACCCCCAGCTGAT 60.943 61.111 17.39 0.00 37.17 2.90
4755 6231 0.687354 ATGATCACCACCTATCGGGC 59.313 55.000 0.00 0.00 39.10 6.13
4756 6232 0.398522 TGATCACCACCTATCGGGCT 60.399 55.000 0.00 0.00 39.10 5.19
4757 6233 0.318762 GATCACCACCTATCGGGCTC 59.681 60.000 0.00 0.00 39.10 4.70
4758 6234 1.122019 ATCACCACCTATCGGGCTCC 61.122 60.000 0.00 0.00 39.10 4.70
4759 6235 1.762460 CACCACCTATCGGGCTCCT 60.762 63.158 0.00 0.00 39.10 3.69
4760 6236 0.469331 CACCACCTATCGGGCTCCTA 60.469 60.000 0.00 0.00 39.10 2.94
4761 6237 0.487772 ACCACCTATCGGGCTCCTAT 59.512 55.000 0.00 0.00 39.10 2.57
4762 6238 1.187087 CCACCTATCGGGCTCCTATC 58.813 60.000 0.00 0.00 39.10 2.08
4763 6239 1.187087 CACCTATCGGGCTCCTATCC 58.813 60.000 0.00 0.00 39.10 2.59
4764 6240 0.041386 ACCTATCGGGCTCCTATCCC 59.959 60.000 0.00 0.00 40.43 3.85
4765 6241 0.336737 CCTATCGGGCTCCTATCCCT 59.663 60.000 0.00 0.00 41.69 4.20
4766 6242 1.686741 CCTATCGGGCTCCTATCCCTC 60.687 61.905 0.00 0.00 41.69 4.30
4767 6243 1.006043 CTATCGGGCTCCTATCCCTCA 59.994 57.143 0.00 0.00 41.69 3.86
4768 6244 0.191064 ATCGGGCTCCTATCCCTCAA 59.809 55.000 0.00 0.00 41.69 3.02
4769 6245 0.031515 TCGGGCTCCTATCCCTCAAA 60.032 55.000 0.00 0.00 41.69 2.69
4770 6246 0.837272 CGGGCTCCTATCCCTCAAAA 59.163 55.000 0.00 0.00 41.69 2.44
4771 6247 1.211949 CGGGCTCCTATCCCTCAAAAA 59.788 52.381 0.00 0.00 41.69 1.94
4987 6471 3.548818 CGGAGGTTGCAAGACAGAAAAAG 60.549 47.826 0.00 0.00 0.00 2.27
5031 6515 2.266055 CCCACACCGAGAAGAGCC 59.734 66.667 0.00 0.00 0.00 4.70
5052 6536 3.374745 CTCGTTGCAACAAAGAAGCATT 58.625 40.909 28.01 0.00 38.19 3.56
5124 6608 1.135689 CCGCTTGAGCCACACATTAAC 60.136 52.381 0.00 0.00 37.91 2.01
5286 6771 5.854338 GCAAATCAAAACATTTCCTTGCATG 59.146 36.000 0.00 0.00 38.20 4.06
5297 6782 6.437162 ACATTTCCTTGCATGTTAGTACCAAT 59.563 34.615 0.00 0.00 28.73 3.16
5309 6794 9.621629 CATGTTAGTACCAATAAAGGGATGTAA 57.378 33.333 0.00 0.00 0.00 2.41
5325 6810 3.436577 TGTAAAAGGCGGGGTTTATCA 57.563 42.857 0.00 0.00 0.00 2.15
5335 6820 6.370453 AGGCGGGGTTTATCATACTTTTTAT 58.630 36.000 0.00 0.00 0.00 1.40
5446 6933 4.095946 AGATGTACCAATGGGCACAATTT 58.904 39.130 12.02 0.00 43.59 1.82
5461 6948 7.337942 TGGGCACAATTTTGTTCTAATTTTTGT 59.662 29.630 0.00 0.00 39.91 2.83
5566 7330 8.707938 TGCATCCTATTATCTGATCAAATACG 57.292 34.615 0.00 0.00 0.00 3.06
5574 7338 7.800155 TTATCTGATCAAATACGGCATTGAA 57.200 32.000 0.00 0.00 38.88 2.69
5633 7397 3.952323 TGGTAAACCGTGAATTCAAACCA 59.048 39.130 10.35 13.30 39.43 3.67
5637 7401 5.982465 AAACCGTGAATTCAAACCAATTG 57.018 34.783 10.35 0.00 40.58 2.32
5805 7571 9.598517 GGATATATGAGAGTTGATTTCCTGATC 57.401 37.037 0.00 0.00 0.00 2.92
5952 7726 5.950544 AAACTATACTCATAGGGCACACA 57.049 39.130 0.00 0.00 38.82 3.72
5964 7738 1.227943 GCACACACTCCTCAAGCCA 60.228 57.895 0.00 0.00 0.00 4.75
6094 7868 2.125952 GCGCAACCTGGAAATGCC 60.126 61.111 0.30 0.00 36.75 4.40
6232 8006 5.559770 ACATCTGTGTGGTTGTGATTGATA 58.440 37.500 0.00 0.00 37.14 2.15
6284 8058 9.821240 ATCAGATCACCATCTCTATAAGTTACT 57.179 33.333 0.00 0.00 37.25 2.24
6295 8069 8.977267 TCTCTATAAGTTACTACTTGGACCTC 57.023 38.462 0.00 0.00 44.22 3.85
6300 8123 3.893813 AGTTACTACTTGGACCTCGTTGT 59.106 43.478 0.00 0.00 0.00 3.32
6488 8312 9.585099 GGATATGCAGTTGAATTTTATGTTTCA 57.415 29.630 0.00 0.00 0.00 2.69
6496 8320 9.423061 AGTTGAATTTTATGTTTCATGCTTACC 57.577 29.630 0.00 0.00 32.27 2.85
6516 8340 4.847198 ACCGTCCCCGTTATTTTTCTTAT 58.153 39.130 0.00 0.00 0.00 1.73
6517 8341 5.255687 ACCGTCCCCGTTATTTTTCTTATT 58.744 37.500 0.00 0.00 0.00 1.40
6522 8346 7.042254 CGTCCCCGTTATTTTTCTTATTCTAGG 60.042 40.741 0.00 0.00 0.00 3.02
6575 8399 0.759060 AAGGCAAGTGTTGGGTTCCC 60.759 55.000 0.12 0.12 0.00 3.97
6580 8404 0.759060 AAGTGTTGGGTTCCCTTGCC 60.759 55.000 9.43 0.00 0.00 4.52
6654 8482 0.457851 CGAAGCTAGTCCTGGTCCTG 59.542 60.000 0.00 0.00 0.00 3.86
6661 8489 1.229209 GTCCTGGTCCTGGTCCTCA 60.229 63.158 14.11 0.00 0.00 3.86
6704 8532 1.305297 TCTGGACATCCGCTGGAGT 60.305 57.895 3.76 2.54 39.43 3.85
6709 8537 4.864334 CATCCGCTGGAGTGGCCC 62.864 72.222 0.00 0.00 45.04 5.80
6779 8607 3.454812 GTCCATAAAGTAGCCCTCCTCAA 59.545 47.826 0.00 0.00 0.00 3.02
6813 8641 2.513204 CTAGTCGACCTCCGCGGA 60.513 66.667 29.03 29.03 38.37 5.54
6832 8660 4.605968 CGGATATTCTAGCATCCATCTCG 58.394 47.826 14.51 2.26 40.75 4.04
6833 8661 4.367450 GGATATTCTAGCATCCATCTCGC 58.633 47.826 11.07 0.00 40.48 5.03
6864 8692 1.756538 CTTCCTCTGCTCCTTCTCCTC 59.243 57.143 0.00 0.00 0.00 3.71
6881 8709 3.452878 TCCTCATTGGCCCAAAAATCAT 58.547 40.909 0.00 0.00 35.26 2.45
6886 8714 1.941377 TGGCCCAAAAATCATGCTCT 58.059 45.000 0.00 0.00 0.00 4.09
6953 8781 3.122480 TCCTTATTCATCTTGGCCAGGA 58.878 45.455 21.17 21.17 0.00 3.86
6956 8784 1.302907 ATTCATCTTGGCCAGGAGGT 58.697 50.000 26.21 6.91 37.19 3.85
6977 8805 2.750350 CCTTCACCTCCTTGCGGT 59.250 61.111 0.00 0.00 34.38 5.68
6979 8807 0.108138 CCTTCACCTCCTTGCGGTAG 60.108 60.000 0.00 0.00 32.37 3.18
6986 8814 2.032620 CCTCCTTGCGGTAGTACATCT 58.967 52.381 2.06 0.00 0.00 2.90
6988 8816 2.688446 CTCCTTGCGGTAGTACATCTGA 59.312 50.000 2.06 0.00 0.00 3.27
7016 8848 1.039856 GGCAAGGACACATGTTTGGT 58.960 50.000 9.44 0.00 0.00 3.67
7040 8873 0.997363 TCGGGGAAGTCTAGGTCAGA 59.003 55.000 0.00 0.00 0.00 3.27
7075 8908 0.888736 CATGGAAGCCACCACGTCAA 60.889 55.000 1.49 0.00 43.03 3.18
7107 8940 2.358195 GGTGAGCTTGGGGGTATCAAAT 60.358 50.000 0.00 0.00 0.00 2.32
7137 8970 2.494471 CAACAGCCAATCACCATCACAT 59.506 45.455 0.00 0.00 0.00 3.21
7151 8984 2.445565 TCACATATGATCTCAGCGGC 57.554 50.000 10.38 0.00 0.00 6.53
7168 9001 3.285371 CGTAGCAACCCGACTCCT 58.715 61.111 0.00 0.00 0.00 3.69
7181 9014 3.127099 ACTCCTGGAGTCGAACACA 57.873 52.632 23.49 0.00 38.71 3.72
7202 9035 4.699522 AAACCCGGTCGCAGGAGC 62.700 66.667 0.00 0.00 37.32 4.70
7238 9071 0.738762 CTCCTGCACGAGTGTCATGG 60.739 60.000 4.69 7.21 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.105063 GCTTCTCTTTTGAATACAATGGGC 58.895 41.667 0.00 0.00 35.85 5.36
1 2 5.123820 TCGCTTCTCTTTTGAATACAATGGG 59.876 40.000 0.00 0.00 35.85 4.00
2 3 6.182039 TCGCTTCTCTTTTGAATACAATGG 57.818 37.500 0.00 0.00 35.85 3.16
8 9 4.393062 CCTTGCTCGCTTCTCTTTTGAATA 59.607 41.667 0.00 0.00 0.00 1.75
42 43 5.761726 CAGGGAGGACGTTACTTTTACTTTT 59.238 40.000 0.00 0.00 0.00 2.27
43 44 5.163269 ACAGGGAGGACGTTACTTTTACTTT 60.163 40.000 0.00 0.00 0.00 2.66
44 45 4.346127 ACAGGGAGGACGTTACTTTTACTT 59.654 41.667 0.00 0.00 0.00 2.24
84 85 0.536460 GAAACGGGGGAAAGAGTGCA 60.536 55.000 0.00 0.00 0.00 4.57
88 89 0.984995 AGGAGAAACGGGGGAAAGAG 59.015 55.000 0.00 0.00 0.00 2.85
90 91 0.035343 GGAGGAGAAACGGGGGAAAG 60.035 60.000 0.00 0.00 0.00 2.62
99 100 1.276705 GAGGACCACTGGAGGAGAAAC 59.723 57.143 0.71 0.00 0.00 2.78
102 103 1.149782 AGGAGGACCACTGGAGGAGA 61.150 60.000 0.71 0.00 38.94 3.71
114 115 0.534873 GGAGTGCAGAAGAGGAGGAC 59.465 60.000 0.00 0.00 0.00 3.85
219 223 4.597507 TCCTCTCCAACACCTCTAACAATT 59.402 41.667 0.00 0.00 0.00 2.32
220 224 4.168101 TCCTCTCCAACACCTCTAACAAT 58.832 43.478 0.00 0.00 0.00 2.71
222 226 3.165875 CTCCTCTCCAACACCTCTAACA 58.834 50.000 0.00 0.00 0.00 2.41
350 355 3.282021 CCCTTGGTCGTCATCATCATTT 58.718 45.455 0.00 0.00 0.00 2.32
467 479 6.649973 CCAATTCAATTCATTGGTGTTAAGCA 59.350 34.615 14.36 0.00 44.04 3.91
577 594 9.095065 ACATATAAATTGTCTACGTCAGTTTCC 57.905 33.333 0.00 0.00 0.00 3.13
632 650 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
642 673 1.265365 CAACACACACACACACACACA 59.735 47.619 0.00 0.00 0.00 3.72
644 675 1.598882 ACAACACACACACACACACA 58.401 45.000 0.00 0.00 0.00 3.72
645 676 4.349663 AATACAACACACACACACACAC 57.650 40.909 0.00 0.00 0.00 3.82
646 677 5.179533 AGTAATACAACACACACACACACA 58.820 37.500 0.00 0.00 0.00 3.72
647 678 5.522460 AGAGTAATACAACACACACACACAC 59.478 40.000 0.00 0.00 0.00 3.82
650 681 8.896320 ATAAAGAGTAATACAACACACACACA 57.104 30.769 0.00 0.00 0.00 3.72
651 682 9.204570 AGATAAAGAGTAATACAACACACACAC 57.795 33.333 0.00 0.00 0.00 3.82
652 683 9.772973 AAGATAAAGAGTAATACAACACACACA 57.227 29.630 0.00 0.00 0.00 3.72
718 749 8.359875 TGATGGAAAATGGCTTATCTTTGTAA 57.640 30.769 0.00 0.00 0.00 2.41
799 1667 2.223947 GGGGGTTACTTGTTTGTGCTTG 60.224 50.000 0.00 0.00 0.00 4.01
923 1810 2.632377 CCAAGCAGCGGAGATAGAAAA 58.368 47.619 0.00 0.00 0.00 2.29
967 1883 0.249699 TCACGCGAAAGAGGAGCAAA 60.250 50.000 15.93 0.00 34.13 3.68
968 1884 0.944311 GTCACGCGAAAGAGGAGCAA 60.944 55.000 15.93 0.00 34.13 3.91
1193 2109 1.620819 CCTCCATGATCTTCCGGTAGG 59.379 57.143 8.37 0.00 39.46 3.18
1326 2242 3.119245 TGGAGTTGGCACGAGTAAGATAC 60.119 47.826 0.00 0.00 0.00 2.24
1450 2378 1.066787 GCTGGCTCTCTTTTCGGTAGT 60.067 52.381 0.00 0.00 0.00 2.73
1460 2388 1.603236 CTTCGTCCTGCTGGCTCTCT 61.603 60.000 4.42 0.00 0.00 3.10
1465 2393 2.125350 CCTCTTCGTCCTGCTGGC 60.125 66.667 4.42 0.00 0.00 4.85
1505 2433 4.299547 AAGCTCCGCGTCAGTGCA 62.300 61.111 4.92 0.00 34.15 4.57
1606 2534 1.889105 GCCACGATGATGCGACCAT 60.889 57.895 0.00 0.00 34.83 3.55
1607 2535 2.511373 GCCACGATGATGCGACCA 60.511 61.111 0.00 0.00 34.83 4.02
1741 2672 2.986479 GCTAAAATTTGTCCAGCCAACG 59.014 45.455 0.00 0.00 0.00 4.10
1790 2721 3.842923 CACGCGCCATCTCCTCCT 61.843 66.667 5.73 0.00 0.00 3.69
1826 2757 2.377310 CCGCCGTAGTTGAACACCG 61.377 63.158 0.00 0.00 0.00 4.94
1984 2925 3.627577 ACACTGACCAGTAGCAAACAAAG 59.372 43.478 1.95 0.00 40.20 2.77
2263 3212 1.597663 ACTCAAGAGCGAACGGTTTTG 59.402 47.619 18.53 18.53 38.51 2.44
2299 3254 3.116300 CACGTCCATTTCATCTACGAGG 58.884 50.000 0.00 0.00 37.04 4.63
2349 3331 4.079615 TCCTCATGGTTGTGAATGGATGAT 60.080 41.667 0.00 0.00 34.23 2.45
2369 3351 3.080121 CCGGCCAGAGCTCTTCCT 61.080 66.667 15.27 0.00 39.73 3.36
2480 3462 1.002624 GTTGATGAAGACGGGGCCA 60.003 57.895 4.39 0.00 0.00 5.36
2483 3465 1.077716 GGGGTTGATGAAGACGGGG 60.078 63.158 0.00 0.00 0.00 5.73
2503 3485 0.254178 ATGAGCAGTGGCCTAACCTG 59.746 55.000 3.32 6.12 42.56 4.00
2508 3490 1.257750 ACACGATGAGCAGTGGCCTA 61.258 55.000 3.32 0.00 42.25 3.93
2572 3554 5.989249 TCTTTGACACGAACTGATTGAATG 58.011 37.500 0.00 0.00 0.00 2.67
2573 3555 5.991606 TCTCTTTGACACGAACTGATTGAAT 59.008 36.000 0.00 0.00 0.00 2.57
2575 3557 4.944048 TCTCTTTGACACGAACTGATTGA 58.056 39.130 0.00 0.00 0.00 2.57
2580 3562 5.120674 TGCAATATCTCTTTGACACGAACTG 59.879 40.000 0.00 0.00 0.00 3.16
2599 3581 2.095853 GCACGCAACACTATACTGCAAT 59.904 45.455 0.00 0.00 35.78 3.56
2603 3585 1.006832 GGGCACGCAACACTATACTG 58.993 55.000 0.00 0.00 0.00 2.74
2616 3598 2.868583 CTCTATCACATCAAAGGGCACG 59.131 50.000 0.00 0.00 0.00 5.34
2632 3628 6.386342 ACATCAATATAGCTGCATCCCTCTAT 59.614 38.462 1.02 0.00 0.00 1.98
2703 3700 3.826157 GGGAATCATCTTCCACAACACAA 59.174 43.478 6.36 0.00 40.32 3.33
2737 3734 6.870965 ACTTATCACACTTGTGCAAACAAAAA 59.129 30.769 4.38 0.00 45.25 1.94
2739 3736 5.804473 CACTTATCACACTTGTGCAAACAAA 59.196 36.000 4.38 0.00 45.25 2.83
2785 3782 2.793278 AGCCAACAACCTAAAAAGCG 57.207 45.000 0.00 0.00 0.00 4.68
2786 3783 4.033932 CACAAAGCCAACAACCTAAAAAGC 59.966 41.667 0.00 0.00 0.00 3.51
2787 3784 4.570369 CCACAAAGCCAACAACCTAAAAAG 59.430 41.667 0.00 0.00 0.00 2.27
2796 3793 3.409026 ACAAAACCACAAAGCCAACAA 57.591 38.095 0.00 0.00 0.00 2.83
3196 4196 8.266473 TGCATTCCTAAGAAATATTTTGCCATT 58.734 29.630 12.35 3.22 35.09 3.16
3293 4294 9.503427 AAACTACGAGATTTGTCTTTGAAAAAG 57.497 29.630 0.00 0.00 0.00 2.27
3378 4380 7.883391 TTTATAAGTTGGCCGATGGAAATTA 57.117 32.000 0.00 0.00 0.00 1.40
3430 4440 3.092301 GGCAAAAGTTAGGGATTCTGCT 58.908 45.455 0.00 0.00 0.00 4.24
3431 4441 2.825532 TGGCAAAAGTTAGGGATTCTGC 59.174 45.455 0.00 0.00 0.00 4.26
3432 4442 4.463891 ACATGGCAAAAGTTAGGGATTCTG 59.536 41.667 0.00 0.00 0.00 3.02
3433 4443 4.463891 CACATGGCAAAAGTTAGGGATTCT 59.536 41.667 0.00 0.00 0.00 2.40
3434 4444 4.747810 CACATGGCAAAAGTTAGGGATTC 58.252 43.478 0.00 0.00 0.00 2.52
3435 4445 3.055891 GCACATGGCAAAAGTTAGGGATT 60.056 43.478 0.00 0.00 43.97 3.01
3436 4446 2.497273 GCACATGGCAAAAGTTAGGGAT 59.503 45.455 0.00 0.00 43.97 3.85
3459 4469 6.385766 TGGCAATTTTAGGGAATTTCCATT 57.614 33.333 17.08 7.26 37.38 3.16
3469 4479 5.876460 CCTTCAAAAGATGGCAATTTTAGGG 59.124 40.000 15.62 12.51 0.00 3.53
3489 4500 7.230712 TGTCAAAGTTAGGGATTTCTTTCCTTC 59.769 37.037 0.00 0.00 35.97 3.46
3604 4934 8.159447 TCTGAATAATAAGAATGCCATGCTACT 58.841 33.333 0.00 0.00 0.00 2.57
3658 4988 9.742144 TTCCATGCTACCTAAAATAAAGTTACA 57.258 29.630 0.00 0.00 0.00 2.41
3796 5127 6.467682 CCATGGTGTAACGAATAAAATTGACG 59.532 38.462 2.57 0.00 38.12 4.35
3814 5145 7.331687 GGTCAAATTATCAAACTTTCCATGGTG 59.668 37.037 12.58 1.02 0.00 4.17
3848 5179 9.665719 AAAATTGCCATGGTACCTAAAATAAAG 57.334 29.630 14.67 0.00 0.00 1.85
3903 5234 5.452078 TTTTCTCTAAAACAGCCATGTGG 57.548 39.130 0.00 0.00 40.39 4.17
4008 5343 9.632807 GTGTAGTGTGAAATTAAAATTGCCATA 57.367 29.630 0.00 0.00 0.00 2.74
4054 5389 8.987890 ACGAAAAATAGGAATTTCAAATGGTTG 58.012 29.630 0.00 0.00 34.12 3.77
4078 5413 4.156922 TGCCATGGTCCAAACTAATTTACG 59.843 41.667 14.67 0.00 0.00 3.18
4079 5414 5.652994 TGCCATGGTCCAAACTAATTTAC 57.347 39.130 14.67 0.00 0.00 2.01
4087 5424 3.683365 ATTTCTTGCCATGGTCCAAAC 57.317 42.857 14.67 0.00 0.00 2.93
4116 5453 6.932356 TGCTTTGTTGAATAAAATTGCCAA 57.068 29.167 0.00 0.00 0.00 4.52
4141 5478 6.471233 TCCACACCATTCAATGTTTTTACA 57.529 33.333 0.00 0.00 0.00 2.41
4159 5496 7.689446 TTATGTTCGGTCATAATTTTCCACA 57.311 32.000 8.38 0.00 35.99 4.17
4172 5509 4.805219 AGTTTGCCATTTTATGTTCGGTC 58.195 39.130 0.00 0.00 0.00 4.79
4174 5511 4.987912 ACAAGTTTGCCATTTTATGTTCGG 59.012 37.500 0.00 0.00 0.00 4.30
4326 5664 7.809546 TTGTTTGTTGTCATCACATAACCTA 57.190 32.000 0.00 0.00 30.55 3.08
4330 5668 9.591792 TGAAAATTGTTTGTTGTCATCACATAA 57.408 25.926 0.00 0.00 30.55 1.90
4362 5700 7.951530 AATGGTTTCTCACAAAATCATGTTC 57.048 32.000 0.00 0.00 38.66 3.18
4383 5721 8.522830 TCACCTAGCAAATTAAAAGGAGAAATG 58.477 33.333 0.00 0.00 0.00 2.32
4430 5772 7.344093 TGGCATCCACTAATAAATCATGGAAAA 59.656 33.333 0.00 0.00 42.57 2.29
4431 5773 6.838090 TGGCATCCACTAATAAATCATGGAAA 59.162 34.615 0.00 0.00 42.57 3.13
4432 5774 6.372104 TGGCATCCACTAATAAATCATGGAA 58.628 36.000 0.00 0.00 42.57 3.53
4433 5775 5.951204 TGGCATCCACTAATAAATCATGGA 58.049 37.500 0.00 0.00 43.42 3.41
4652 6128 5.337652 CGAAACCCTTTCTCCTGATAGTTCT 60.338 44.000 0.00 0.00 37.52 3.01
4772 6248 4.830600 TGAAAAAGGAGCCCGATAGTTTTT 59.169 37.500 0.00 0.00 31.53 1.94
4773 6249 4.403734 TGAAAAAGGAGCCCGATAGTTTT 58.596 39.130 0.00 0.00 0.00 2.43
4774 6250 4.028993 TGAAAAAGGAGCCCGATAGTTT 57.971 40.909 0.00 0.00 0.00 2.66
4775 6251 3.713826 TGAAAAAGGAGCCCGATAGTT 57.286 42.857 0.00 0.00 0.00 2.24
4776 6252 3.933861 ATGAAAAAGGAGCCCGATAGT 57.066 42.857 0.00 0.00 0.00 2.12
4777 6253 5.582689 AAAATGAAAAAGGAGCCCGATAG 57.417 39.130 0.00 0.00 0.00 2.08
4778 6254 5.392595 CGAAAAATGAAAAAGGAGCCCGATA 60.393 40.000 0.00 0.00 0.00 2.92
4779 6255 4.618227 CGAAAAATGAAAAAGGAGCCCGAT 60.618 41.667 0.00 0.00 0.00 4.18
4780 6256 3.305064 CGAAAAATGAAAAAGGAGCCCGA 60.305 43.478 0.00 0.00 0.00 5.14
4781 6257 2.986479 CGAAAAATGAAAAAGGAGCCCG 59.014 45.455 0.00 0.00 0.00 6.13
4782 6258 3.740832 CACGAAAAATGAAAAAGGAGCCC 59.259 43.478 0.00 0.00 0.00 5.19
4783 6259 4.209080 CACACGAAAAATGAAAAAGGAGCC 59.791 41.667 0.00 0.00 0.00 4.70
4793 6269 2.445316 CAACACGCACACGAAAAATGA 58.555 42.857 0.00 0.00 43.93 2.57
4987 6471 4.481930 TTCATCAACAACATCGTTGGTC 57.518 40.909 11.26 0.00 45.16 4.02
5008 6492 0.179029 CTTCTCGGTGTGGGTGGTTT 60.179 55.000 0.00 0.00 0.00 3.27
5031 6515 2.473530 TGCTTCTTTGTTGCAACGAG 57.526 45.000 23.79 22.04 33.48 4.18
5052 6536 4.980805 GTCCTCGTGGTGGCGCAA 62.981 66.667 10.83 0.00 34.23 4.85
5096 6580 0.596082 TGGCTCAAGCGGCTTAAAAC 59.404 50.000 15.93 7.25 43.26 2.43
5124 6608 5.168569 TCATTTCCTTGTACTCTGCTAACG 58.831 41.667 0.00 0.00 0.00 3.18
5277 6762 6.601613 CCTTTATTGGTACTAACATGCAAGGA 59.398 38.462 0.00 0.00 0.00 3.36
5297 6782 2.357361 CCCCGCCTTTTACATCCCTTTA 60.357 50.000 0.00 0.00 0.00 1.85
5309 6794 3.945640 AGTATGATAAACCCCGCCTTT 57.054 42.857 0.00 0.00 0.00 3.11
5446 6933 7.598493 GGAAGCATGCTACAAAAATTAGAACAA 59.402 33.333 23.00 0.00 0.00 2.83
5566 7330 9.914131 AAGACTTTTAAAAGATAGTTCAATGCC 57.086 29.630 29.97 0.00 39.31 4.40
5586 7350 6.068670 AGTATGGTTGTTAAAGGCAAGACTT 58.931 36.000 0.00 0.00 0.00 3.01
5633 7397 8.738645 CCTTGCTAAAGGTAAGACTATCAATT 57.261 34.615 0.00 0.00 46.97 2.32
5674 7440 9.438228 TCAATTTGACATCAATGTTAATGCAAT 57.562 25.926 0.00 0.00 41.95 3.56
5759 7525 6.875972 ATCCATCAAGACCAAGTAAGTACT 57.124 37.500 0.00 0.00 38.39 2.73
5930 7704 5.425539 AGTGTGTGCCCTATGAGTATAGTTT 59.574 40.000 0.00 0.00 35.51 2.66
5952 7726 1.722034 TCACTTCTGGCTTGAGGAGT 58.278 50.000 0.00 0.00 31.26 3.85
5964 7738 2.363680 CTCCGGCTCACATATCACTTCT 59.636 50.000 0.00 0.00 0.00 2.85
6232 8006 4.298626 TGTAGCTAACCCCTCATCTTCAT 58.701 43.478 0.00 0.00 0.00 2.57
6284 8058 2.485835 CCCAAACAACGAGGTCCAAGTA 60.486 50.000 0.00 0.00 0.00 2.24
6289 8063 1.228154 AGCCCAAACAACGAGGTCC 60.228 57.895 0.00 0.00 0.00 4.46
6295 8069 1.464997 GAGCTAAGAGCCCAAACAACG 59.535 52.381 0.00 0.00 43.77 4.10
6300 8123 2.432510 GCTAGAGAGCTAAGAGCCCAAA 59.567 50.000 0.00 0.00 45.98 3.28
6517 8341 7.799014 ATTGAGAGTGCAAATCACAATCCTAGA 60.799 37.037 15.55 0.00 46.25 2.43
6522 8346 6.154445 ACAATTGAGAGTGCAAATCACAATC 58.846 36.000 19.24 4.19 46.25 2.67
6540 8364 4.734398 TGCCTTGCCCTAATAACAATTG 57.266 40.909 3.24 3.24 0.00 2.32
6575 8399 5.722021 AACACTAAATTTGTAGGGGCAAG 57.278 39.130 0.00 0.00 0.00 4.01
6580 8404 6.808212 CAGATGCAAACACTAAATTTGTAGGG 59.192 38.462 0.00 0.00 38.93 3.53
6632 8460 0.179124 GACCAGGACTAGCTTCGCAG 60.179 60.000 0.00 0.00 0.00 5.18
6640 8468 0.336737 AGGACCAGGACCAGGACTAG 59.663 60.000 10.44 0.00 0.00 2.57
6641 8469 0.335361 GAGGACCAGGACCAGGACTA 59.665 60.000 10.44 0.00 0.00 2.59
6642 8470 1.079438 GAGGACCAGGACCAGGACT 59.921 63.158 10.44 7.24 0.00 3.85
6643 8471 0.618968 ATGAGGACCAGGACCAGGAC 60.619 60.000 10.44 3.07 0.00 3.85
6644 8472 0.325671 GATGAGGACCAGGACCAGGA 60.326 60.000 10.44 0.00 0.00 3.86
6645 8473 1.341156 GGATGAGGACCAGGACCAGG 61.341 65.000 10.90 0.33 0.00 4.45
6648 8476 1.395826 CGAGGATGAGGACCAGGACC 61.396 65.000 0.00 0.00 0.00 4.46
6654 8482 0.395862 TGTCTCCGAGGATGAGGACC 60.396 60.000 6.74 0.00 32.33 4.46
6661 8489 1.550976 GTTGACCTTGTCTCCGAGGAT 59.449 52.381 2.99 0.00 44.19 3.24
6736 8564 0.700269 ATGATGGGGAGGAGGTGCAT 60.700 55.000 0.00 0.00 0.00 3.96
6798 8626 0.822532 AATATCCGCGGAGGTCGACT 60.823 55.000 33.87 17.23 42.43 4.18
6813 8641 3.181482 CGGCGAGATGGATGCTAGAATAT 60.181 47.826 0.00 0.00 0.00 1.28
6832 8660 1.153804 GAGGAAGAACGAGGACGGC 60.154 63.158 0.00 0.00 44.46 5.68
6833 8661 0.171455 CAGAGGAAGAACGAGGACGG 59.829 60.000 0.00 0.00 44.46 4.79
6864 8692 2.940410 GAGCATGATTTTTGGGCCAATG 59.060 45.455 21.65 15.11 0.00 2.82
6881 8709 0.035317 CACCTTGTGGTAGCAGAGCA 59.965 55.000 0.00 0.00 46.60 4.26
6886 8714 2.031919 CCGCACCTTGTGGTAGCA 59.968 61.111 0.00 0.00 46.60 3.49
6905 8733 0.034616 GCTAGGTATGCTGAGGCCAG 59.965 60.000 5.01 0.00 43.22 4.85
6956 8784 1.228245 GCAAGGAGGTGAAGGCACA 60.228 57.895 0.00 0.00 46.96 4.57
6977 8805 4.140782 TGCCCCTCCTTATCAGATGTACTA 60.141 45.833 0.00 0.00 0.00 1.82
6979 8807 2.972713 TGCCCCTCCTTATCAGATGTAC 59.027 50.000 0.00 0.00 0.00 2.90
6986 8814 1.213296 GTCCTTGCCCCTCCTTATCA 58.787 55.000 0.00 0.00 0.00 2.15
6988 8816 0.919710 GTGTCCTTGCCCCTCCTTAT 59.080 55.000 0.00 0.00 0.00 1.73
7016 8848 2.107901 GACCTAGACTTCCCCGAGGATA 59.892 54.545 0.00 0.00 43.54 2.59
7040 8873 3.085952 CCATGTATGGGTGGAAACTGT 57.914 47.619 2.87 0.00 44.31 3.55
7075 8908 3.335534 GCTCACCGTTCGTGCGTT 61.336 61.111 0.00 0.00 42.69 4.84
7081 8914 2.742372 CCCCAAGCTCACCGTTCG 60.742 66.667 0.00 0.00 0.00 3.95
7094 8927 0.707024 TGGCACATTTGATACCCCCA 59.293 50.000 0.00 0.00 0.00 4.96
7107 8940 1.401318 ATTGGCTGTTGCTTGGCACA 61.401 50.000 0.00 0.00 38.71 4.57
7137 8970 0.241213 GCTACGCCGCTGAGATCATA 59.759 55.000 0.00 0.00 0.00 2.15
7151 8984 1.153823 CAGGAGTCGGGTTGCTACG 60.154 63.158 0.00 0.00 0.00 3.51
7164 8997 1.068588 TGTTGTGTTCGACTCCAGGAG 59.931 52.381 15.72 15.72 35.52 3.69
7168 9001 2.420722 GGTTTTGTTGTGTTCGACTCCA 59.579 45.455 0.00 0.00 0.00 3.86
7181 9014 2.190841 CCTGCGACCGGGTTTTGTT 61.191 57.895 6.32 0.00 32.47 2.83


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

AutoCloner maintained by Alex Coulton.