Multiple sequence alignment - TraesCS1B01G136300

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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 TraesCS1B01G136300 chr1B 100.000 4399 0 0 1 4399 174103706 174108104 0.000000e+00 8124.0
1 TraesCS1B01G136300 chr1B 85.874 269 34 3 961 1228 653823535 653823270 2.590000e-72 283.0
2 TraesCS1B01G136300 chr1B 97.959 49 1 0 1 49 463054261 463054213 7.840000e-13 86.1
3 TraesCS1B01G136300 chr1B 95.918 49 2 0 1 49 346895968 346895920 3.650000e-11 80.5
4 TraesCS1B01G136300 chr1B 95.918 49 2 0 1 49 580643712 580643760 3.650000e-11 80.5
5 TraesCS1B01G136300 chr1D 96.529 3400 85 13 682 4070 113911971 113908594 0.000000e+00 5594.0
6 TraesCS1B01G136300 chr1D 86.783 401 47 3 46 446 113912585 113912191 4.040000e-120 442.0
7 TraesCS1B01G136300 chr1D 97.115 208 5 1 4192 4399 113908596 113908390 2.520000e-92 350.0
8 TraesCS1B01G136300 chr1A 97.010 3244 73 11 838 4070 122504005 122500775 0.000000e+00 5432.0
9 TraesCS1B01G136300 chr1A 91.248 617 51 3 50 665 122504904 122504290 0.000000e+00 837.0
10 TraesCS1B01G136300 chr1A 85.317 647 80 5 962 1598 360986360 360987001 0.000000e+00 654.0
11 TraesCS1B01G136300 chr1A 94.712 208 4 1 4192 4399 122500777 122500577 2.550000e-82 316.0
12 TraesCS1B01G136300 chr1A 91.391 151 10 2 4056 4206 284542145 284542292 2.070000e-48 204.0
13 TraesCS1B01G136300 chr5B 85.185 648 80 6 962 1598 591571188 591571830 0.000000e+00 651.0
14 TraesCS1B01G136300 chr2B 82.477 662 91 15 961 1599 482629927 482630586 1.380000e-154 556.0
15 TraesCS1B01G136300 chr2B 82.416 654 77 15 961 1599 725467453 725468083 1.800000e-148 536.0
16 TraesCS1B01G136300 chr2B 77.358 530 66 32 1057 1580 87473287 87473768 9.380000e-67 265.0
17 TraesCS1B01G136300 chr2B 94.245 139 6 2 4065 4202 545760384 545760521 1.240000e-50 211.0
18 TraesCS1B01G136300 chr4A 84.832 567 55 12 1061 1598 4251870 4251306 3.870000e-150 542.0
19 TraesCS1B01G136300 chr4A 94.964 139 4 3 4068 4203 223857834 223857972 9.580000e-52 215.0
20 TraesCS1B01G136300 chr7A 98.438 128 1 1 4068 4194 495545720 495545847 1.590000e-54 224.0
21 TraesCS1B01G136300 chr7A 93.617 141 9 0 4066 4206 552891758 552891898 1.240000e-50 211.0
22 TraesCS1B01G136300 chr7A 98.039 51 1 0 1 51 316348718 316348668 6.060000e-14 89.8
23 TraesCS1B01G136300 chr7B 81.625 283 35 10 987 1268 568667690 568667956 7.410000e-53 219.0
24 TraesCS1B01G136300 chr2D 94.928 138 5 2 4066 4202 619720675 619720539 9.580000e-52 215.0
25 TraesCS1B01G136300 chr2D 98.000 50 1 0 1 50 408328799 408328848 2.180000e-13 87.9
26 TraesCS1B01G136300 chr3A 95.522 134 5 1 4063 4195 644809261 644809128 3.450000e-51 213.0
27 TraesCS1B01G136300 chr3A 93.478 138 9 0 4069 4206 332035496 332035359 5.770000e-49 206.0
28 TraesCS1B01G136300 chr3A 89.130 138 11 2 1442 1576 696200138 696200274 7.570000e-38 169.0
29 TraesCS1B01G136300 chr3A 88.406 138 12 2 1442 1576 628900714 628900850 3.520000e-36 163.0
30 TraesCS1B01G136300 chr3A 78.339 277 37 15 1055 1324 628892685 628892945 1.640000e-34 158.0
31 TraesCS1B01G136300 chr3A 86.957 92 12 0 1321 1412 628900623 628900714 2.160000e-18 104.0
32 TraesCS1B01G136300 chr3A 86.957 92 12 0 1321 1412 696200047 696200138 2.160000e-18 104.0
33 TraesCS1B01G136300 chr6B 91.391 151 9 4 4052 4200 39329381 39329529 2.070000e-48 204.0
34 TraesCS1B01G136300 chr6B 96.000 50 2 0 1 50 634748466 634748417 1.010000e-11 82.4
35 TraesCS1B01G136300 chr6B 95.918 49 2 0 1 49 240036646 240036694 3.650000e-11 80.5
36 TraesCS1B01G136300 chr4B 97.959 49 1 0 1 49 511269603 511269651 7.840000e-13 86.1
37 TraesCS1B01G136300 chr4B 95.918 49 2 0 1 49 478448244 478448196 3.650000e-11 80.5


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 TraesCS1B01G136300 chr1B 174103706 174108104 4398 False 8124.000000 8124 100.000000 1 4399 1 chr1B.!!$F1 4398
1 TraesCS1B01G136300 chr1D 113908390 113912585 4195 True 2128.666667 5594 93.475667 46 4399 3 chr1D.!!$R1 4353
2 TraesCS1B01G136300 chr1A 122500577 122504904 4327 True 2195.000000 5432 94.323333 50 4399 3 chr1A.!!$R1 4349
3 TraesCS1B01G136300 chr1A 360986360 360987001 641 False 654.000000 654 85.317000 962 1598 1 chr1A.!!$F2 636
4 TraesCS1B01G136300 chr5B 591571188 591571830 642 False 651.000000 651 85.185000 962 1598 1 chr5B.!!$F1 636
5 TraesCS1B01G136300 chr2B 482629927 482630586 659 False 556.000000 556 82.477000 961 1599 1 chr2B.!!$F2 638
6 TraesCS1B01G136300 chr2B 725467453 725468083 630 False 536.000000 536 82.416000 961 1599 1 chr2B.!!$F4 638
7 TraesCS1B01G136300 chr4A 4251306 4251870 564 True 542.000000 542 84.832000 1061 1598 1 chr4A.!!$R1 537

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
713 761 0.037303 CACCAAGTGGCTGATGGAGT 59.963 55.0 9.45 0.00 39.32 3.85 F
1576 1874 0.391130 TTACGCTTGTGCCAGGCTAG 60.391 55.0 14.15 8.62 34.24 3.42 F
2532 2832 0.174389 GAGGACGCAGAGCAAGATGA 59.826 55.0 0.00 0.00 0.00 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2066 2366 0.178967 TCCATTGGCTGCAACAGGAA 60.179 50.0 0.50 0.0 31.21 3.36 R
3077 3377 0.864455 GCACAGACAACAGACTGAGC 59.136 55.0 10.08 0.0 41.49 4.26 R
4171 4471 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.0 5.23 0.0 44.66 2.12 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
20 21 2.688477 CTCCTCTCTTTAGCCATCCCT 58.312 52.381 0.00 0.00 0.00 4.20
21 22 3.044894 CTCCTCTCTTTAGCCATCCCTT 58.955 50.000 0.00 0.00 0.00 3.95
22 23 2.774234 TCCTCTCTTTAGCCATCCCTTG 59.226 50.000 0.00 0.00 0.00 3.61
23 24 2.774234 CCTCTCTTTAGCCATCCCTTGA 59.226 50.000 0.00 0.00 0.00 3.02
24 25 3.432890 CCTCTCTTTAGCCATCCCTTGAC 60.433 52.174 0.00 0.00 0.00 3.18
25 26 3.181329 TCTCTTTAGCCATCCCTTGACA 58.819 45.455 0.00 0.00 0.00 3.58
26 27 3.782523 TCTCTTTAGCCATCCCTTGACAT 59.217 43.478 0.00 0.00 0.00 3.06
27 28 4.133078 CTCTTTAGCCATCCCTTGACATC 58.867 47.826 0.00 0.00 0.00 3.06
28 29 3.782523 TCTTTAGCCATCCCTTGACATCT 59.217 43.478 0.00 0.00 0.00 2.90
29 30 4.968719 TCTTTAGCCATCCCTTGACATCTA 59.031 41.667 0.00 0.00 0.00 1.98
30 31 4.689612 TTAGCCATCCCTTGACATCTAC 57.310 45.455 0.00 0.00 0.00 2.59
31 32 1.771255 AGCCATCCCTTGACATCTACC 59.229 52.381 0.00 0.00 0.00 3.18
32 33 1.541233 GCCATCCCTTGACATCTACCG 60.541 57.143 0.00 0.00 0.00 4.02
33 34 1.762957 CCATCCCTTGACATCTACCGT 59.237 52.381 0.00 0.00 0.00 4.83
34 35 2.483714 CCATCCCTTGACATCTACCGTG 60.484 54.545 0.00 0.00 0.00 4.94
35 36 0.535335 TCCCTTGACATCTACCGTGC 59.465 55.000 0.00 0.00 0.00 5.34
36 37 0.806102 CCCTTGACATCTACCGTGCG 60.806 60.000 0.00 0.00 0.00 5.34
37 38 1.421410 CCTTGACATCTACCGTGCGC 61.421 60.000 0.00 0.00 0.00 6.09
38 39 1.421410 CTTGACATCTACCGTGCGCC 61.421 60.000 4.18 0.00 0.00 6.53
39 40 2.585247 GACATCTACCGTGCGCCC 60.585 66.667 4.18 0.00 0.00 6.13
40 41 3.365291 GACATCTACCGTGCGCCCA 62.365 63.158 4.18 0.00 0.00 5.36
41 42 2.890474 CATCTACCGTGCGCCCAC 60.890 66.667 4.18 0.00 38.62 4.61
42 43 4.157120 ATCTACCGTGCGCCCACC 62.157 66.667 4.18 0.00 38.79 4.61
60 61 4.442893 CCCACCACGACACATCTACAATAT 60.443 45.833 0.00 0.00 0.00 1.28
91 92 4.816392 ACATCAAACTACATCTACGTGCA 58.184 39.130 0.00 0.00 0.00 4.57
133 134 6.157123 AGTTTAACCAAATTTTCACCTTGGGA 59.843 34.615 5.16 0.00 43.30 4.37
149 150 3.216187 TGGGAGGATTTTGTCGAACAA 57.784 42.857 0.00 0.00 36.11 2.83
207 208 3.338126 GAGCGTCGATGGTGGTCGT 62.338 63.158 15.18 0.00 42.07 4.34
366 367 1.073199 CGACAACCCCTCCAAGCTT 59.927 57.895 0.00 0.00 0.00 3.74
388 389 2.493278 TGGCAACCCGTAGTTCTACTAC 59.507 50.000 6.87 6.87 45.71 2.73
399 400 1.134877 GTTCTACTACGGAAGGTGGCC 60.135 57.143 0.00 0.00 0.00 5.36
522 563 1.369625 GCGACTACCAGGGTGAAATG 58.630 55.000 0.06 0.00 0.00 2.32
589 630 1.839747 TACCGTCTGGCAGTTGGGT 60.840 57.895 24.38 23.65 39.70 4.51
620 661 0.578211 ACGAGTTGGTTTTACACGCG 59.422 50.000 3.53 3.53 33.78 6.01
636 684 2.125713 CGCGGTGGCTGATGTGTA 60.126 61.111 0.00 0.00 36.88 2.90
637 685 1.521457 CGCGGTGGCTGATGTGTAT 60.521 57.895 0.00 0.00 36.88 2.29
638 686 0.249280 CGCGGTGGCTGATGTGTATA 60.249 55.000 0.00 0.00 36.88 1.47
639 687 1.605457 CGCGGTGGCTGATGTGTATAT 60.605 52.381 0.00 0.00 36.88 0.86
640 688 2.494059 GCGGTGGCTGATGTGTATATT 58.506 47.619 0.00 0.00 35.83 1.28
641 689 2.878406 GCGGTGGCTGATGTGTATATTT 59.122 45.455 0.00 0.00 35.83 1.40
642 690 3.303990 GCGGTGGCTGATGTGTATATTTG 60.304 47.826 0.00 0.00 35.83 2.32
643 691 4.126437 CGGTGGCTGATGTGTATATTTGA 58.874 43.478 0.00 0.00 0.00 2.69
644 692 4.574421 CGGTGGCTGATGTGTATATTTGAA 59.426 41.667 0.00 0.00 0.00 2.69
645 693 5.239306 CGGTGGCTGATGTGTATATTTGAAT 59.761 40.000 0.00 0.00 0.00 2.57
646 694 6.566564 CGGTGGCTGATGTGTATATTTGAATC 60.567 42.308 0.00 0.00 0.00 2.52
647 695 6.262944 GGTGGCTGATGTGTATATTTGAATCA 59.737 38.462 0.00 0.00 0.00 2.57
648 696 7.134815 GTGGCTGATGTGTATATTTGAATCAC 58.865 38.462 0.00 0.00 0.00 3.06
649 697 6.262944 TGGCTGATGTGTATATTTGAATCACC 59.737 38.462 0.00 0.00 0.00 4.02
650 698 6.262944 GGCTGATGTGTATATTTGAATCACCA 59.737 38.462 0.00 0.00 0.00 4.17
651 699 7.201812 GGCTGATGTGTATATTTGAATCACCAA 60.202 37.037 0.00 0.00 0.00 3.67
652 700 7.859377 GCTGATGTGTATATTTGAATCACCAAG 59.141 37.037 0.00 0.00 0.00 3.61
653 701 8.806429 TGATGTGTATATTTGAATCACCAAGT 57.194 30.769 0.00 0.00 0.00 3.16
654 702 8.676401 TGATGTGTATATTTGAATCACCAAGTG 58.324 33.333 0.00 0.00 34.45 3.16
693 741 8.806429 TCACCAAGTGATGTGTATATTTGAAT 57.194 30.769 0.00 0.00 37.67 2.57
694 742 8.892723 TCACCAAGTGATGTGTATATTTGAATC 58.107 33.333 0.00 0.00 37.67 2.52
695 743 8.676401 CACCAAGTGATGTGTATATTTGAATCA 58.324 33.333 0.00 0.00 35.23 2.57
696 744 8.677300 ACCAAGTGATGTGTATATTTGAATCAC 58.323 33.333 5.65 5.65 42.60 3.06
697 745 8.131100 CCAAGTGATGTGTATATTTGAATCACC 58.869 37.037 9.35 0.00 43.04 4.02
698 746 8.676401 CAAGTGATGTGTATATTTGAATCACCA 58.324 33.333 9.35 0.00 43.04 4.17
699 747 8.806429 AGTGATGTGTATATTTGAATCACCAA 57.194 30.769 9.35 0.00 43.04 3.67
700 748 8.896744 AGTGATGTGTATATTTGAATCACCAAG 58.103 33.333 9.35 0.00 43.04 3.61
701 749 8.677300 GTGATGTGTATATTTGAATCACCAAGT 58.323 33.333 0.00 0.00 38.51 3.16
702 750 8.676401 TGATGTGTATATTTGAATCACCAAGTG 58.324 33.333 0.00 0.00 34.45 3.16
703 751 7.389803 TGTGTATATTTGAATCACCAAGTGG 57.610 36.000 0.00 0.00 42.17 4.00
704 752 6.127758 TGTGTATATTTGAATCACCAAGTGGC 60.128 38.462 0.00 0.00 39.32 5.01
705 753 6.095440 GTGTATATTTGAATCACCAAGTGGCT 59.905 38.462 0.00 0.00 39.32 4.75
706 754 3.947910 ATTTGAATCACCAAGTGGCTG 57.052 42.857 0.00 0.00 39.32 4.85
707 755 2.655090 TTGAATCACCAAGTGGCTGA 57.345 45.000 0.00 1.49 39.32 4.26
708 756 2.885135 TGAATCACCAAGTGGCTGAT 57.115 45.000 0.00 3.76 37.46 2.90
709 757 2.439409 TGAATCACCAAGTGGCTGATG 58.561 47.619 12.97 0.00 36.65 3.07
710 758 1.747355 GAATCACCAAGTGGCTGATGG 59.253 52.381 12.97 2.20 36.65 3.51
711 759 0.994247 ATCACCAAGTGGCTGATGGA 59.006 50.000 12.00 0.00 39.32 3.41
712 760 0.325933 TCACCAAGTGGCTGATGGAG 59.674 55.000 9.45 2.88 39.32 3.86
713 761 0.037303 CACCAAGTGGCTGATGGAGT 59.963 55.000 9.45 0.00 39.32 3.85
740 788 3.622630 ACATCTAGAGTAGAACCAGCGT 58.377 45.455 0.00 0.00 38.50 5.07
769 819 8.865590 TTTTTACTGTTGGAGCACTATTTTTC 57.134 30.769 0.00 0.00 0.00 2.29
1229 1453 1.002134 CTCCTTGCCGGTGAATGGT 60.002 57.895 1.90 0.00 0.00 3.55
1546 1844 3.005791 GCTTGCTTTGGTGGTTAGTCATT 59.994 43.478 0.00 0.00 0.00 2.57
1576 1874 0.391130 TTACGCTTGTGCCAGGCTAG 60.391 55.000 14.15 8.62 34.24 3.42
1590 1888 2.028112 CAGGCTAGCTTCTGTTGTGGTA 60.028 50.000 15.72 0.00 0.00 3.25
1608 1906 3.630312 TGGTATAATTTGCGAAGAAGGGC 59.370 43.478 0.00 0.00 0.00 5.19
1633 1931 5.413523 TGCATGCCTGATATGTCATTATCAC 59.586 40.000 16.68 0.00 34.46 3.06
1654 1952 4.869297 CACAGTGGATCTCTCTTTGCTTAG 59.131 45.833 0.00 0.00 0.00 2.18
1656 1954 5.105392 ACAGTGGATCTCTCTTTGCTTAGAG 60.105 44.000 8.76 8.76 42.46 2.43
1679 1977 9.927081 AGAGAAATATTCACAAATACCCTTGAT 57.073 29.630 0.00 0.00 30.27 2.57
1767 2066 3.120321 AGTCAGCACAATTCGGTGTAA 57.880 42.857 4.09 0.00 40.89 2.41
1980 2280 8.978874 TGCTCATGTACCAATTCTACAAATAT 57.021 30.769 0.00 0.00 0.00 1.28
2066 2366 3.004106 GTGCTTGTTGTCTGATGAGCTTT 59.996 43.478 0.00 0.00 0.00 3.51
2096 2396 3.189080 GCAGCCAATGGAAAATTTCAACC 59.811 43.478 2.05 0.00 0.00 3.77
2135 2435 0.471617 CCCACCCTCATCAGATGGTC 59.528 60.000 10.67 0.00 40.32 4.02
2232 2532 1.417890 CCTACATGAGCCAACCCCTAG 59.582 57.143 0.00 0.00 0.00 3.02
2262 2562 3.386078 TCAGCGATTTCTTCTGAGGCTAT 59.614 43.478 0.00 0.00 33.42 2.97
2264 2564 4.025061 CAGCGATTTCTTCTGAGGCTATTG 60.025 45.833 0.00 0.00 0.00 1.90
2284 2584 2.294233 TGCTTTCAATCCTGCTGTCAAC 59.706 45.455 0.00 0.00 0.00 3.18
2408 2708 8.189119 AGAAGTTCCTGAGTCAATATATCTCC 57.811 38.462 0.00 0.00 0.00 3.71
2532 2832 0.174389 GAGGACGCAGAGCAAGATGA 59.826 55.000 0.00 0.00 0.00 2.92
2550 2850 2.257207 TGAAAGTCGTGATTCCTCCCT 58.743 47.619 0.00 0.00 0.00 4.20
2573 2873 3.758023 TGGATTTGATGTGCTCGTTGATT 59.242 39.130 0.00 0.00 0.00 2.57
3077 3377 3.260380 AGAGTTCTTGATGGAGGAGTGTG 59.740 47.826 0.00 0.00 0.00 3.82
3341 3641 3.643792 GCTTCTCAAGGCTAAGGATAGGA 59.356 47.826 0.00 0.00 0.00 2.94
3362 3662 0.607762 TTCAATTAGCCAGCGCACCA 60.608 50.000 11.47 0.00 37.52 4.17
3363 3663 0.394216 TCAATTAGCCAGCGCACCAT 60.394 50.000 11.47 0.00 37.52 3.55
3364 3664 1.134250 TCAATTAGCCAGCGCACCATA 60.134 47.619 11.47 0.00 37.52 2.74
3365 3665 1.002468 CAATTAGCCAGCGCACCATAC 60.002 52.381 11.47 0.00 37.52 2.39
3366 3666 0.469917 ATTAGCCAGCGCACCATACT 59.530 50.000 11.47 0.00 37.52 2.12
3367 3667 0.461870 TTAGCCAGCGCACCATACTG 60.462 55.000 11.47 0.00 37.52 2.74
3421 3721 0.391395 CTCTGCTCAGCTTGGTCAGG 60.391 60.000 0.00 0.00 0.00 3.86
3458 3758 2.171635 GCGTTAGCAACTTGGGAGG 58.828 57.895 0.00 0.00 44.35 4.30
3461 3761 1.270625 CGTTAGCAACTTGGGAGGACA 60.271 52.381 0.00 0.00 0.00 4.02
3720 4020 5.980116 ACTACTTTTCTGTATATCTGCGCAG 59.020 40.000 31.53 31.53 0.00 5.18
3773 4073 5.106555 CCAGGATTAATAGTGCATTAAGGCG 60.107 44.000 7.70 0.00 41.32 5.52
3872 4172 7.040201 AGCTCTTGAATACATCACAACAAACAT 60.040 33.333 0.00 0.00 37.92 2.71
4004 4304 1.971357 TCCTTCGTCTTGAGCCTTCTT 59.029 47.619 0.00 0.00 0.00 2.52
4049 4349 8.877864 ACTCATCCTGAATTTGTTATGGTTAA 57.122 30.769 0.00 0.00 0.00 2.01
4070 4370 7.255139 GGTTAACCTTCCTTGATATGCATGTAC 60.255 40.741 17.83 1.00 0.00 2.90
4071 4371 5.636903 ACCTTCCTTGATATGCATGTACT 57.363 39.130 10.16 0.00 0.00 2.73
4072 4372 5.615289 ACCTTCCTTGATATGCATGTACTC 58.385 41.667 10.16 1.59 0.00 2.59
4073 4373 4.999950 CCTTCCTTGATATGCATGTACTCC 59.000 45.833 10.16 0.00 0.00 3.85
4074 4374 4.623932 TCCTTGATATGCATGTACTCCC 57.376 45.455 10.16 0.00 0.00 4.30
4075 4375 4.234550 TCCTTGATATGCATGTACTCCCT 58.765 43.478 10.16 0.00 0.00 4.20
4076 4376 4.284490 TCCTTGATATGCATGTACTCCCTC 59.716 45.833 10.16 0.00 0.00 4.30
4077 4377 4.564406 CCTTGATATGCATGTACTCCCTCC 60.564 50.000 10.16 0.00 0.00 4.30
4078 4378 2.562738 TGATATGCATGTACTCCCTCCG 59.437 50.000 10.16 0.00 0.00 4.63
4079 4379 2.082140 TATGCATGTACTCCCTCCGT 57.918 50.000 10.16 0.00 0.00 4.69
4080 4380 0.753262 ATGCATGTACTCCCTCCGTC 59.247 55.000 0.00 0.00 0.00 4.79
4081 4381 1.327690 TGCATGTACTCCCTCCGTCC 61.328 60.000 0.00 0.00 0.00 4.79
4082 4382 1.734137 CATGTACTCCCTCCGTCCG 59.266 63.158 0.00 0.00 0.00 4.79
4083 4383 0.750546 CATGTACTCCCTCCGTCCGA 60.751 60.000 0.00 0.00 0.00 4.55
4084 4384 0.033796 ATGTACTCCCTCCGTCCGAA 60.034 55.000 0.00 0.00 0.00 4.30
4085 4385 0.251297 TGTACTCCCTCCGTCCGAAA 60.251 55.000 0.00 0.00 0.00 3.46
4086 4386 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
4087 4387 1.479730 GTACTCCCTCCGTCCGAAAAT 59.520 52.381 0.00 0.00 0.00 1.82
4088 4388 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
4089 4389 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
4090 4390 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
4091 4391 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
4092 4392 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
4093 4393 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
4094 4394 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
4095 4395 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
4096 4396 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
4097 4397 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
4098 4398 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
4099 4399 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
4100 4400 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
4101 4401 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
4102 4402 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
4103 4403 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
4104 4404 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
4105 4405 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
4106 4406 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
4113 4413 7.614494 ACTTGTCATCAAAATGGATAAAAGGG 58.386 34.615 0.00 0.00 33.42 3.95
4114 4414 7.454380 ACTTGTCATCAAAATGGATAAAAGGGA 59.546 33.333 0.00 0.00 33.42 4.20
4115 4415 7.976414 TGTCATCAAAATGGATAAAAGGGAT 57.024 32.000 0.00 0.00 33.42 3.85
4116 4416 7.784037 TGTCATCAAAATGGATAAAAGGGATG 58.216 34.615 0.00 0.00 33.42 3.51
4117 4417 7.399765 TGTCATCAAAATGGATAAAAGGGATGT 59.600 33.333 0.00 0.00 33.29 3.06
4118 4418 8.912988 GTCATCAAAATGGATAAAAGGGATGTA 58.087 33.333 0.00 0.00 33.29 2.29
4119 4419 9.659135 TCATCAAAATGGATAAAAGGGATGTAT 57.341 29.630 0.00 0.00 33.29 2.29
4120 4420 9.918630 CATCAAAATGGATAAAAGGGATGTATC 57.081 33.333 0.00 0.00 0.00 2.24
4121 4421 9.887862 ATCAAAATGGATAAAAGGGATGTATCT 57.112 29.630 0.00 0.00 0.00 1.98
4126 4426 7.228314 TGGATAAAAGGGATGTATCTAGACG 57.772 40.000 0.00 0.00 0.00 4.18
4127 4427 6.781014 TGGATAAAAGGGATGTATCTAGACGT 59.219 38.462 0.00 0.00 0.00 4.34
4128 4428 7.946219 TGGATAAAAGGGATGTATCTAGACGTA 59.054 37.037 0.00 0.00 0.00 3.57
4129 4429 8.968969 GGATAAAAGGGATGTATCTAGACGTAT 58.031 37.037 0.00 0.00 0.00 3.06
4135 4435 8.937207 AGGGATGTATCTAGACGTATTTTAGT 57.063 34.615 0.00 0.00 0.00 2.24
4136 4436 9.364653 AGGGATGTATCTAGACGTATTTTAGTT 57.635 33.333 0.00 0.00 0.00 2.24
4137 4437 9.978044 GGGATGTATCTAGACGTATTTTAGTTT 57.022 33.333 0.00 0.00 0.00 2.66
4165 4465 9.690913 AGATACATCTCTTTTCATCCATTTTGA 57.309 29.630 0.00 0.00 29.30 2.69
4179 4479 8.469200 TCATCCATTTTGATGACAAGTATTTCC 58.531 33.333 0.00 0.00 44.65 3.13
4180 4480 6.851609 TCCATTTTGATGACAAGTATTTCCG 58.148 36.000 0.00 0.00 37.32 4.30
4181 4481 6.035843 CCATTTTGATGACAAGTATTTCCGG 58.964 40.000 0.00 0.00 37.32 5.14
4182 4482 6.127758 CCATTTTGATGACAAGTATTTCCGGA 60.128 38.462 0.00 0.00 37.32 5.14
4183 4483 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
4184 4484 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
4185 4485 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
4186 4486 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
4187 4487 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
4188 4488 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
4189 4489 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
4190 4490 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
4191 4491 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
4192 4492 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
4193 4493 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
4267 4567 3.450904 TGCACCATAGGACTTCTTAGGT 58.549 45.455 0.00 0.00 33.49 3.08
4279 4579 6.497259 AGGACTTCTTAGGTATGAACACTGAA 59.503 38.462 0.00 0.00 0.00 3.02
4379 4679 5.316987 CAAACATTTAGGAGGTCTGGTTCT 58.683 41.667 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.688477 AGGGATGGCTAAAGAGAGGAG 58.312 52.381 0.00 0.00 0.00 3.69
1 2 2.774234 CAAGGGATGGCTAAAGAGAGGA 59.226 50.000 0.00 0.00 0.00 3.71
4 5 3.181329 TGTCAAGGGATGGCTAAAGAGA 58.819 45.455 0.00 0.00 33.68 3.10
5 6 3.634397 TGTCAAGGGATGGCTAAAGAG 57.366 47.619 0.00 0.00 33.68 2.85
6 7 3.782523 AGATGTCAAGGGATGGCTAAAGA 59.217 43.478 0.00 0.00 33.68 2.52
7 8 4.162040 AGATGTCAAGGGATGGCTAAAG 57.838 45.455 0.00 0.00 33.68 1.85
8 9 4.141482 GGTAGATGTCAAGGGATGGCTAAA 60.141 45.833 0.00 0.00 33.68 1.85
9 10 3.391296 GGTAGATGTCAAGGGATGGCTAA 59.609 47.826 0.00 0.00 33.68 3.09
10 11 2.972713 GGTAGATGTCAAGGGATGGCTA 59.027 50.000 0.00 0.00 33.68 3.93
11 12 1.771255 GGTAGATGTCAAGGGATGGCT 59.229 52.381 0.00 0.00 33.68 4.75
12 13 1.541233 CGGTAGATGTCAAGGGATGGC 60.541 57.143 0.00 0.00 0.00 4.40
13 14 1.762957 ACGGTAGATGTCAAGGGATGG 59.237 52.381 0.00 0.00 0.00 3.51
14 15 2.826428 CACGGTAGATGTCAAGGGATG 58.174 52.381 0.00 0.00 0.00 3.51
15 16 1.139058 GCACGGTAGATGTCAAGGGAT 59.861 52.381 0.00 0.00 0.00 3.85
16 17 0.535335 GCACGGTAGATGTCAAGGGA 59.465 55.000 0.00 0.00 0.00 4.20
17 18 0.806102 CGCACGGTAGATGTCAAGGG 60.806 60.000 0.00 0.00 0.00 3.95
18 19 1.421410 GCGCACGGTAGATGTCAAGG 61.421 60.000 0.30 0.00 0.00 3.61
19 20 1.421410 GGCGCACGGTAGATGTCAAG 61.421 60.000 10.83 0.00 0.00 3.02
20 21 1.447140 GGCGCACGGTAGATGTCAA 60.447 57.895 10.83 0.00 0.00 3.18
21 22 2.183300 GGCGCACGGTAGATGTCA 59.817 61.111 10.83 0.00 0.00 3.58
22 23 2.585247 GGGCGCACGGTAGATGTC 60.585 66.667 10.83 0.00 0.00 3.06
23 24 3.387091 TGGGCGCACGGTAGATGT 61.387 61.111 10.83 0.00 0.00 3.06
24 25 2.890474 GTGGGCGCACGGTAGATG 60.890 66.667 18.81 0.00 0.00 2.90
25 26 4.157120 GGTGGGCGCACGGTAGAT 62.157 66.667 25.43 0.00 0.00 1.98
35 36 2.220615 TAGATGTGTCGTGGTGGGCG 62.221 60.000 0.00 0.00 0.00 6.13
36 37 0.739813 GTAGATGTGTCGTGGTGGGC 60.740 60.000 0.00 0.00 0.00 5.36
37 38 0.606096 TGTAGATGTGTCGTGGTGGG 59.394 55.000 0.00 0.00 0.00 4.61
38 39 2.448926 TTGTAGATGTGTCGTGGTGG 57.551 50.000 0.00 0.00 0.00 4.61
39 40 4.507756 CCATATTGTAGATGTGTCGTGGTG 59.492 45.833 0.00 0.00 0.00 4.17
40 41 4.404394 TCCATATTGTAGATGTGTCGTGGT 59.596 41.667 0.00 0.00 0.00 4.16
41 42 4.944048 TCCATATTGTAGATGTGTCGTGG 58.056 43.478 0.00 0.00 0.00 4.94
42 43 6.902224 TTTCCATATTGTAGATGTGTCGTG 57.098 37.500 0.00 0.00 0.00 4.35
43 44 7.272244 TGATTTCCATATTGTAGATGTGTCGT 58.728 34.615 0.00 0.00 0.00 4.34
44 45 7.713764 TGATTTCCATATTGTAGATGTGTCG 57.286 36.000 0.00 0.00 0.00 4.35
45 46 8.892723 TGTTGATTTCCATATTGTAGATGTGTC 58.107 33.333 0.00 0.00 0.00 3.67
46 47 8.806429 TGTTGATTTCCATATTGTAGATGTGT 57.194 30.769 0.00 0.00 0.00 3.72
47 48 9.888878 GATGTTGATTTCCATATTGTAGATGTG 57.111 33.333 0.00 0.00 0.00 3.21
48 49 9.631257 TGATGTTGATTTCCATATTGTAGATGT 57.369 29.630 0.00 0.00 0.00 3.06
60 61 8.946085 GTAGATGTAGTTTGATGTTGATTTCCA 58.054 33.333 0.00 0.00 0.00 3.53
133 134 4.334481 ACGAAACTTGTTCGACAAAATCCT 59.666 37.500 14.78 0.00 43.97 3.24
149 150 0.673644 CTTCATCCCCGCACGAAACT 60.674 55.000 0.00 0.00 0.00 2.66
207 208 2.045438 CACCCACAATAGCCGGCA 60.045 61.111 31.54 15.56 0.00 5.69
215 216 2.199652 CCAACCGCACACCCACAAT 61.200 57.895 0.00 0.00 0.00 2.71
299 300 1.452145 ATTGCTTCGGTTGGCGTTGT 61.452 50.000 0.00 0.00 0.00 3.32
366 367 1.972795 AGTAGAACTACGGGTTGCCAA 59.027 47.619 6.37 0.00 40.80 4.52
516 557 1.001974 CTCCCACTGTCGACCATTTCA 59.998 52.381 14.12 0.00 0.00 2.69
522 563 4.436998 CGCCTCCCACTGTCGACC 62.437 72.222 14.12 0.00 0.00 4.79
576 617 1.227823 CGAACACCCAACTGCCAGA 60.228 57.895 0.00 0.00 0.00 3.86
589 630 4.617486 ACTCGTGTCGCGCGAACA 62.617 61.111 36.57 29.16 45.55 3.18
605 646 1.723197 CCGCGCGTGTAAAACCAAC 60.723 57.895 29.95 0.00 0.00 3.77
620 661 2.169832 ATATACACATCAGCCACCGC 57.830 50.000 0.00 0.00 0.00 5.68
625 673 6.262944 TGGTGATTCAAATATACACATCAGCC 59.737 38.462 11.55 6.88 38.03 4.85
626 674 7.263100 TGGTGATTCAAATATACACATCAGC 57.737 36.000 0.00 0.00 38.85 4.26
627 675 8.896744 ACTTGGTGATTCAAATATACACATCAG 58.103 33.333 0.00 0.00 33.82 2.90
628 676 8.676401 CACTTGGTGATTCAAATATACACATCA 58.324 33.333 0.00 0.00 35.23 3.07
629 677 8.892723 TCACTTGGTGATTCAAATATACACATC 58.107 33.333 0.00 0.00 37.67 3.06
630 678 8.806429 TCACTTGGTGATTCAAATATACACAT 57.194 30.769 0.00 0.00 37.67 3.21
645 693 8.892723 GTGATTCAAATATACATCACTTGGTGA 58.107 33.333 2.80 2.80 46.90 4.02
646 694 8.131100 GGTGATTCAAATATACATCACTTGGTG 58.869 37.037 10.18 0.00 43.42 4.17
647 695 7.833682 TGGTGATTCAAATATACATCACTTGGT 59.166 33.333 10.18 0.00 43.42 3.67
648 696 8.224389 TGGTGATTCAAATATACATCACTTGG 57.776 34.615 10.18 0.00 43.42 3.61
649 697 9.726232 CTTGGTGATTCAAATATACATCACTTG 57.274 33.333 10.18 0.00 43.42 3.16
650 698 9.466497 ACTTGGTGATTCAAATATACATCACTT 57.534 29.630 10.18 0.00 43.42 3.16
651 699 8.896744 CACTTGGTGATTCAAATATACATCACT 58.103 33.333 10.18 0.00 43.42 3.41
652 700 8.892723 TCACTTGGTGATTCAAATATACATCAC 58.107 33.333 3.05 3.05 43.24 3.06
682 730 6.318648 TCAGCCACTTGGTGATTCAAATATAC 59.681 38.462 0.00 0.00 46.14 1.47
683 731 6.422333 TCAGCCACTTGGTGATTCAAATATA 58.578 36.000 0.00 0.00 46.14 0.86
684 732 5.263599 TCAGCCACTTGGTGATTCAAATAT 58.736 37.500 0.00 0.00 46.14 1.28
685 733 4.661222 TCAGCCACTTGGTGATTCAAATA 58.339 39.130 0.00 0.00 46.14 1.40
686 734 3.499338 TCAGCCACTTGGTGATTCAAAT 58.501 40.909 0.00 0.00 46.14 2.32
687 735 2.942804 TCAGCCACTTGGTGATTCAAA 58.057 42.857 0.00 0.00 46.14 2.69
688 736 2.655090 TCAGCCACTTGGTGATTCAA 57.345 45.000 0.00 0.00 46.14 2.69
694 742 0.037303 ACTCCATCAGCCACTTGGTG 59.963 55.000 0.00 0.00 43.96 4.17
695 743 1.656587 TACTCCATCAGCCACTTGGT 58.343 50.000 0.00 0.00 37.57 3.67
696 744 3.287867 AATACTCCATCAGCCACTTGG 57.712 47.619 0.00 0.00 38.53 3.61
697 745 5.647658 TGTAAAATACTCCATCAGCCACTTG 59.352 40.000 0.00 0.00 0.00 3.16
698 746 5.815581 TGTAAAATACTCCATCAGCCACTT 58.184 37.500 0.00 0.00 0.00 3.16
699 747 5.435686 TGTAAAATACTCCATCAGCCACT 57.564 39.130 0.00 0.00 0.00 4.00
700 748 6.058183 AGATGTAAAATACTCCATCAGCCAC 58.942 40.000 0.00 0.00 36.91 5.01
701 749 6.252599 AGATGTAAAATACTCCATCAGCCA 57.747 37.500 0.00 0.00 36.91 4.75
702 750 7.671302 TCTAGATGTAAAATACTCCATCAGCC 58.329 38.462 0.00 0.00 36.91 4.85
703 751 8.364142 ACTCTAGATGTAAAATACTCCATCAGC 58.636 37.037 0.00 0.00 36.91 4.26
712 760 9.465985 GCTGGTTCTACTCTAGATGTAAAATAC 57.534 37.037 0.00 0.00 34.22 1.89
713 761 8.350722 CGCTGGTTCTACTCTAGATGTAAAATA 58.649 37.037 0.00 0.00 34.22 1.40
762 812 9.745880 TTTTTACAGTACAAATGCCGAAAAATA 57.254 25.926 0.00 0.00 0.00 1.40
763 813 8.649973 TTTTTACAGTACAAATGCCGAAAAAT 57.350 26.923 0.00 0.00 0.00 1.82
769 819 4.915085 CCACTTTTTACAGTACAAATGCCG 59.085 41.667 0.00 0.00 0.00 5.69
800 850 4.880120 CAGAGCATGTCCAATGTAGATGTT 59.120 41.667 0.00 0.00 0.00 2.71
832 882 1.985159 TGCATACCAGTCCCTCAAAGT 59.015 47.619 0.00 0.00 0.00 2.66
983 1202 1.228737 CGGTGTGGGAAATGGGGTT 60.229 57.895 0.00 0.00 0.00 4.11
984 1203 2.438795 CGGTGTGGGAAATGGGGT 59.561 61.111 0.00 0.00 0.00 4.95
1229 1453 3.916544 CGAGGCGGCATCCAGCTA 61.917 66.667 13.08 0.00 44.79 3.32
1546 1844 3.126171 GCACAAGCGTAATAATGACACCA 59.874 43.478 0.00 0.00 0.00 4.17
1576 1874 4.793216 CGCAAATTATACCACAACAGAAGC 59.207 41.667 0.00 0.00 0.00 3.86
1590 1888 2.099756 GCAGCCCTTCTTCGCAAATTAT 59.900 45.455 0.00 0.00 0.00 1.28
1608 1906 5.646360 TGATAATGACATATCAGGCATGCAG 59.354 40.000 21.36 11.65 37.37 4.41
1618 1916 8.530311 AGAGATCCACTGTGATAATGACATATC 58.470 37.037 9.86 0.00 33.71 1.63
1633 1931 5.126869 TCTCTAAGCAAAGAGAGATCCACTG 59.873 44.000 12.58 0.00 45.54 3.66
1700 1998 6.599638 GCAAGGTGTAATAGAAGAATTGGAGT 59.400 38.462 0.00 0.00 0.00 3.85
2066 2366 0.178967 TCCATTGGCTGCAACAGGAA 60.179 50.000 0.50 0.00 31.21 3.36
2096 2396 2.135933 GACTGTCAAGGACTTGGTTCG 58.864 52.381 11.76 2.21 40.78 3.95
2135 2435 3.942829 TGGCTGTCTTGACAGAAATAGG 58.057 45.455 28.50 7.14 39.99 2.57
2232 2532 3.373439 AGAAGAAATCGCTGATTCAGTGC 59.627 43.478 20.06 8.10 41.21 4.40
2262 2562 2.585330 TGACAGCAGGATTGAAAGCAA 58.415 42.857 0.00 0.00 38.60 3.91
2264 2564 2.666619 CGTTGACAGCAGGATTGAAAGC 60.667 50.000 0.00 0.00 0.00 3.51
2284 2584 2.279741 TCATCTCCAGCGGAATTTTCG 58.720 47.619 0.00 0.00 0.00 3.46
2408 2708 5.356751 TGACCGAAATAGGACCATCAAATTG 59.643 40.000 0.00 0.00 34.73 2.32
2532 2832 2.290323 CCAAGGGAGGAATCACGACTTT 60.290 50.000 0.00 0.00 0.00 2.66
2550 2850 3.145286 TCAACGAGCACATCAAATCCAA 58.855 40.909 0.00 0.00 0.00 3.53
2573 2873 5.163301 GGTCATTCTTGTTAGAGAGCCCATA 60.163 44.000 0.00 0.00 0.00 2.74
3009 3309 1.068333 CAATGCCTTGGAAACCACTCG 60.068 52.381 0.00 0.00 30.78 4.18
3077 3377 0.864455 GCACAGACAACAGACTGAGC 59.136 55.000 10.08 0.00 41.49 4.26
3341 3641 1.134946 GGTGCGCTGGCTAATTGAAAT 59.865 47.619 9.73 0.00 40.82 2.17
3362 3662 7.041780 GCAGTTTATATGCACTTGCTACAGTAT 60.042 37.037 2.33 0.00 43.31 2.12
3363 3663 6.257849 GCAGTTTATATGCACTTGCTACAGTA 59.742 38.462 2.33 0.00 43.31 2.74
3364 3664 5.065218 GCAGTTTATATGCACTTGCTACAGT 59.935 40.000 2.33 0.00 43.31 3.55
3365 3665 5.505286 GCAGTTTATATGCACTTGCTACAG 58.495 41.667 2.33 0.00 43.31 2.74
3366 3666 5.484173 GCAGTTTATATGCACTTGCTACA 57.516 39.130 2.33 0.00 43.31 2.74
3421 3721 2.603892 CGCAGCTGCCATAAACATCATC 60.604 50.000 32.07 0.44 37.91 2.92
3458 3758 5.296780 TGTTCCATTCTCTTTGACAGTTGTC 59.703 40.000 5.33 5.33 44.97 3.18
3461 3761 6.064060 TCATGTTCCATTCTCTTTGACAGTT 58.936 36.000 0.00 0.00 0.00 3.16
3720 4020 3.549794 AGCAGCTGAAAGGGATATGAAC 58.450 45.455 20.43 0.00 0.00 3.18
3773 4073 6.229733 CAAATATCATCACCCCTCTCTTCTC 58.770 44.000 0.00 0.00 0.00 2.87
3872 4172 7.182817 AGTACTATTAGCTGAAACACCATCA 57.817 36.000 0.00 0.00 0.00 3.07
3984 4284 1.633774 AGAAGGCTCAAGACGAAGGA 58.366 50.000 0.00 0.00 0.00 3.36
4049 4349 5.455326 GGAGTACATGCATATCAAGGAAGGT 60.455 44.000 0.00 0.00 0.00 3.50
4070 4370 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
4071 4371 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
4072 4372 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
4073 4373 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
4074 4374 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
4075 4375 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
4076 4376 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
4077 4377 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
4078 4378 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
4079 4379 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
4080 4380 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
4081 4381 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
4087 4387 8.748412 CCCTTTTATCCATTTTGATGACAAGTA 58.252 33.333 0.00 0.00 37.32 2.24
4088 4388 7.454380 TCCCTTTTATCCATTTTGATGACAAGT 59.546 33.333 0.00 0.00 37.32 3.16
4089 4389 7.839907 TCCCTTTTATCCATTTTGATGACAAG 58.160 34.615 0.00 0.00 37.32 3.16
4090 4390 7.789202 TCCCTTTTATCCATTTTGATGACAA 57.211 32.000 0.00 0.00 0.00 3.18
4091 4391 7.399765 ACATCCCTTTTATCCATTTTGATGACA 59.600 33.333 0.00 0.00 33.22 3.58
4092 4392 7.785033 ACATCCCTTTTATCCATTTTGATGAC 58.215 34.615 0.00 0.00 33.22 3.06
4093 4393 7.976414 ACATCCCTTTTATCCATTTTGATGA 57.024 32.000 0.00 0.00 33.22 2.92
4094 4394 9.918630 GATACATCCCTTTTATCCATTTTGATG 57.081 33.333 0.00 0.00 34.68 3.07
4095 4395 9.887862 AGATACATCCCTTTTATCCATTTTGAT 57.112 29.630 0.00 0.00 0.00 2.57
4100 4400 8.314751 CGTCTAGATACATCCCTTTTATCCATT 58.685 37.037 0.00 0.00 0.00 3.16
4101 4401 7.455008 ACGTCTAGATACATCCCTTTTATCCAT 59.545 37.037 0.00 0.00 0.00 3.41
4102 4402 6.781014 ACGTCTAGATACATCCCTTTTATCCA 59.219 38.462 0.00 0.00 0.00 3.41
4103 4403 7.229581 ACGTCTAGATACATCCCTTTTATCC 57.770 40.000 0.00 0.00 0.00 2.59
4109 4409 9.364653 ACTAAAATACGTCTAGATACATCCCTT 57.635 33.333 0.00 0.00 0.00 3.95
4110 4410 8.937207 ACTAAAATACGTCTAGATACATCCCT 57.063 34.615 0.00 0.00 0.00 4.20
4111 4411 9.978044 AAACTAAAATACGTCTAGATACATCCC 57.022 33.333 0.00 0.00 0.00 3.85
4139 4439 9.690913 TCAAAATGGATGAAAAGAGATGTATCT 57.309 29.630 0.00 0.00 40.50 1.98
4154 4454 7.433131 CGGAAATACTTGTCATCAAAATGGATG 59.567 37.037 0.00 0.00 44.78 3.51
4155 4455 7.416664 CCGGAAATACTTGTCATCAAAATGGAT 60.417 37.037 0.00 0.00 33.42 3.41
4156 4456 6.127758 CCGGAAATACTTGTCATCAAAATGGA 60.128 38.462 0.00 0.00 33.42 3.41
4157 4457 6.035843 CCGGAAATACTTGTCATCAAAATGG 58.964 40.000 0.00 0.00 33.42 3.16
4158 4458 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
4159 4459 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
4160 4460 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
4161 4461 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
4162 4462 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
4163 4463 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
4164 4464 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
4165 4465 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
4166 4466 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
4167 4467 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
4168 4468 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
4169 4469 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
4170 4470 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
4171 4471 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
4172 4472 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
4173 4473 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
4174 4474 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
4175 4475 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
4176 4476 0.846015 TATACTCCCTCCGTCCGGAA 59.154 55.000 5.23 0.00 44.66 4.30
4177 4477 1.070604 ATATACTCCCTCCGTCCGGA 58.929 55.000 0.00 0.00 42.90 5.14
4178 4478 1.920610 AATATACTCCCTCCGTCCGG 58.079 55.000 0.00 0.00 0.00 5.14
4179 4479 5.298777 CCTAATAATATACTCCCTCCGTCCG 59.701 48.000 0.00 0.00 0.00 4.79
4180 4480 6.193504 ACCTAATAATATACTCCCTCCGTCC 58.806 44.000 0.00 0.00 0.00 4.79
4181 4481 7.715266 AACCTAATAATATACTCCCTCCGTC 57.285 40.000 0.00 0.00 0.00 4.79
4182 4482 7.038516 CCAAACCTAATAATATACTCCCTCCGT 60.039 40.741 0.00 0.00 0.00 4.69
4183 4483 7.038516 ACCAAACCTAATAATATACTCCCTCCG 60.039 40.741 0.00 0.00 0.00 4.63
4184 4484 8.215954 ACCAAACCTAATAATATACTCCCTCC 57.784 38.462 0.00 0.00 0.00 4.30
4185 4485 8.877195 TGACCAAACCTAATAATATACTCCCTC 58.123 37.037 0.00 0.00 0.00 4.30
4186 4486 8.808240 TGACCAAACCTAATAATATACTCCCT 57.192 34.615 0.00 0.00 0.00 4.20
4267 4567 5.298276 GTGGGTGTTTCTTTCAGTGTTCATA 59.702 40.000 0.00 0.00 0.00 2.15
4279 4579 2.014128 CTGTGTTCGTGGGTGTTTCTT 58.986 47.619 0.00 0.00 0.00 2.52
4379 4679 1.871418 CCTCCCAGATCAGACCAGAA 58.129 55.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.