Multiple sequence alignment - TraesCS4B01G126000

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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 TraesCS4B01G126000 chr4B 100.000 6544 0 0 1 6544 158283031 158276488 0.000000e+00 12085.0
1 TraesCS4B01G126000 chr4B 89.322 974 86 12 4104 5066 351011964 351012930 0.000000e+00 1206.0
2 TraesCS4B01G126000 chr4B 95.775 142 4 2 3513 3653 180671150 180671290 1.840000e-55 228.0
3 TraesCS4B01G126000 chr4B 93.289 149 6 4 3505 3653 363315783 363315927 3.970000e-52 217.0
4 TraesCS4B01G126000 chr4A 96.094 2586 74 16 841 3410 220026291 220023717 0.000000e+00 4191.0
5 TraesCS4B01G126000 chr4A 95.505 1535 57 7 4545 6075 220020870 220019344 0.000000e+00 2442.0
6 TraesCS4B01G126000 chr4A 95.216 857 24 14 3662 4515 220021712 220020870 0.000000e+00 1339.0
7 TraesCS4B01G126000 chr4A 95.798 119 5 0 3409 3527 220021830 220021712 6.700000e-45 193.0
8 TraesCS4B01G126000 chr4A 90.164 61 5 1 6150 6209 741472555 741472615 1.960000e-10 78.7
9 TraesCS4B01G126000 chr4D 97.447 1802 43 3 1729 3527 150002074 150000273 0.000000e+00 3070.0
10 TraesCS4B01G126000 chr4D 93.454 1604 51 18 4992 6543 149998987 149997386 0.000000e+00 2331.0
11 TraesCS4B01G126000 chr4D 97.454 1296 25 5 3650 4944 150000275 149998987 0.000000e+00 2204.0
12 TraesCS4B01G126000 chr4D 98.507 871 12 1 868 1738 150003040 150002171 0.000000e+00 1535.0
13 TraesCS4B01G126000 chr1A 90.452 974 74 13 4104 5066 514933808 514932843 0.000000e+00 1266.0
14 TraesCS4B01G126000 chr1A 89.311 973 77 17 4104 5066 515189846 515188891 0.000000e+00 1195.0
15 TraesCS4B01G126000 chrUn 89.969 977 77 13 4104 5066 31633951 31632982 0.000000e+00 1242.0
16 TraesCS4B01G126000 chrUn 85.168 863 110 12 1 849 290072444 290071586 0.000000e+00 869.0
17 TraesCS4B01G126000 chrUn 85.168 863 110 12 1 849 310231604 310230746 0.000000e+00 869.0
18 TraesCS4B01G126000 chr1B 88.119 808 82 6 1 797 256200121 256199317 0.000000e+00 948.0
19 TraesCS4B01G126000 chr1B 87.300 811 91 6 1 800 645949129 645949938 0.000000e+00 917.0
20 TraesCS4B01G126000 chr1B 86.369 807 94 12 1 797 115448329 115449129 0.000000e+00 867.0
21 TraesCS4B01G126000 chr1B 85.874 807 93 14 1 794 666845464 666846262 0.000000e+00 839.0
22 TraesCS4B01G126000 chr1D 85.921 831 100 13 29 846 363858765 363857939 0.000000e+00 870.0
23 TraesCS4B01G126000 chr1D 94.231 52 2 1 6150 6200 404066319 404066370 1.960000e-10 78.7
24 TraesCS4B01G126000 chr7B 85.168 863 110 12 1 849 642144113 642143255 0.000000e+00 869.0
25 TraesCS4B01G126000 chr7B 97.778 135 2 1 3519 3653 372835115 372834982 1.420000e-56 231.0
26 TraesCS4B01G126000 chr3D 85.697 811 94 16 1 797 945425 946227 0.000000e+00 835.0
27 TraesCS4B01G126000 chr3D 97.761 134 3 0 3523 3656 210622420 210622553 1.420000e-56 231.0
28 TraesCS4B01G126000 chr5B 97.778 135 3 0 3518 3652 165087654 165087788 3.950000e-57 233.0
29 TraesCS4B01G126000 chr5B 96.078 51 2 0 6150 6200 339291164 339291114 4.200000e-12 84.2
30 TraesCS4B01G126000 chr5B 92.308 52 4 0 6149 6200 55269182 55269233 2.530000e-09 75.0
31 TraesCS4B01G126000 chr2B 97.101 138 4 0 3521 3658 662686153 662686290 3.950000e-57 233.0
32 TraesCS4B01G126000 chr2B 94.118 51 3 0 6139 6189 337084147 337084197 1.960000e-10 78.7
33 TraesCS4B01G126000 chr2D 95.139 144 6 1 3519 3661 602705744 602705887 6.600000e-55 226.0
34 TraesCS4B01G126000 chr3A 95.683 139 6 0 3514 3652 642715804 642715942 2.370000e-54 224.0
35 TraesCS4B01G126000 chr5D 91.925 161 10 3 3493 3652 382507938 382508096 8.540000e-54 222.0
36 TraesCS4B01G126000 chr7A 89.655 58 3 1 6150 6207 230872796 230872742 3.270000e-08 71.3
37 TraesCS4B01G126000 chr6A 85.333 75 4 5 6141 6209 509276947 509277020 3.270000e-08 71.3
38 TraesCS4B01G126000 chr3B 85.714 70 6 4 6123 6189 134308712 134308644 3.270000e-08 71.3
39 TraesCS4B01G126000 chr7D 100.000 29 0 0 6515 6543 47517789 47517817 3.000000e-03 54.7


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 TraesCS4B01G126000 chr4B 158276488 158283031 6543 True 12085.00 12085 100.00000 1 6544 1 chr4B.!!$R1 6543
1 TraesCS4B01G126000 chr4B 351011964 351012930 966 False 1206.00 1206 89.32200 4104 5066 1 chr4B.!!$F2 962
2 TraesCS4B01G126000 chr4A 220019344 220026291 6947 True 2041.25 4191 95.65325 841 6075 4 chr4A.!!$R1 5234
3 TraesCS4B01G126000 chr4D 149997386 150003040 5654 True 2285.00 3070 96.71550 868 6543 4 chr4D.!!$R1 5675
4 TraesCS4B01G126000 chr1A 514932843 514933808 965 True 1266.00 1266 90.45200 4104 5066 1 chr1A.!!$R1 962
5 TraesCS4B01G126000 chr1A 515188891 515189846 955 True 1195.00 1195 89.31100 4104 5066 1 chr1A.!!$R2 962
6 TraesCS4B01G126000 chrUn 31632982 31633951 969 True 1242.00 1242 89.96900 4104 5066 1 chrUn.!!$R1 962
7 TraesCS4B01G126000 chrUn 290071586 290072444 858 True 869.00 869 85.16800 1 849 1 chrUn.!!$R2 848
8 TraesCS4B01G126000 chrUn 310230746 310231604 858 True 869.00 869 85.16800 1 849 1 chrUn.!!$R3 848
9 TraesCS4B01G126000 chr1B 256199317 256200121 804 True 948.00 948 88.11900 1 797 1 chr1B.!!$R1 796
10 TraesCS4B01G126000 chr1B 645949129 645949938 809 False 917.00 917 87.30000 1 800 1 chr1B.!!$F2 799
11 TraesCS4B01G126000 chr1B 115448329 115449129 800 False 867.00 867 86.36900 1 797 1 chr1B.!!$F1 796
12 TraesCS4B01G126000 chr1B 666845464 666846262 798 False 839.00 839 85.87400 1 794 1 chr1B.!!$F3 793
13 TraesCS4B01G126000 chr1D 363857939 363858765 826 True 870.00 870 85.92100 29 846 1 chr1D.!!$R1 817
14 TraesCS4B01G126000 chr7B 642143255 642144113 858 True 869.00 869 85.16800 1 849 1 chr7B.!!$R2 848
15 TraesCS4B01G126000 chr3D 945425 946227 802 False 835.00 835 85.69700 1 797 1 chr3D.!!$F1 796

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
779 796 0.872388 CTTCCCACGCGCTAGTTTTT 59.128 50.0 5.73 0.00 0.00 1.94 F
1821 1945 0.109412 GCCTTGTGCTGCAGATTCAC 60.109 55.0 20.43 16.54 36.87 3.18 F
2279 2412 0.320697 GTACGTCCTTTGGCAGGTCT 59.679 55.0 0.00 0.00 44.37 3.85 F
3540 5568 0.338814 ATTGTACTCCCTCCGTCCCT 59.661 55.0 0.00 0.00 0.00 4.20 F
3689 5717 0.320421 TCCGCTTGTAGTCCAACAGC 60.320 55.0 0.00 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2705 2843 2.621998 GCATGAATCACAAGATCCAGGG 59.378 50.000 0.00 0.00 31.90 4.45 R
2791 2929 0.807667 CTAGCACCTCATCGCCACAC 60.808 60.000 0.00 0.00 0.00 3.82 R
3630 5658 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17 R
4798 6844 1.364626 GATGGCAGCAACTGACCGAG 61.365 60.000 0.00 0.00 39.07 4.63 R
5546 7594 1.626654 CCCTACGCGAACAACTGCAG 61.627 60.000 15.93 13.48 0.00 4.41 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
37 38 2.830321 TCCTCATCATCATCCTCATCCG 59.170 50.000 0.00 0.00 0.00 4.18
40 41 2.570302 TCATCATCATCCTCATCCGCAT 59.430 45.455 0.00 0.00 0.00 4.73
107 109 3.654414 GTCTGACGTGAAGATGGACTTT 58.346 45.455 0.00 0.00 39.13 2.66
128 130 2.499693 TCCACCTGCTTCAACGATATCA 59.500 45.455 3.12 0.00 0.00 2.15
323 328 2.523168 TGGTCTGCACGGTCCTGA 60.523 61.111 0.00 0.00 0.00 3.86
336 341 2.558795 CGGTCCTGATCCGTGATAAGAT 59.441 50.000 0.00 0.00 42.62 2.40
379 384 1.951181 GCATGTTCGCGCGTGTAGAA 61.951 55.000 30.98 13.72 0.00 2.10
412 417 1.489649 CATCTGTGATGGAGGCCTCTT 59.510 52.381 31.36 19.55 0.00 2.85
565 571 2.762459 CCCGAAGATCCCCGGTGA 60.762 66.667 18.39 0.00 43.93 4.02
579 585 3.838795 GTGACGCGGCGACATGAC 61.839 66.667 30.94 13.46 34.08 3.06
657 664 1.605165 GGGGAAAATGGGCACGTGA 60.605 57.895 22.23 0.00 0.00 4.35
659 666 1.584495 GGAAAATGGGCACGTGACC 59.416 57.895 34.40 34.40 45.93 4.02
670 677 4.665431 CGTGACCGTGTCATGGAA 57.335 55.556 18.36 2.72 44.63 3.53
708 715 3.663233 GCATATTATTAGTGCGCGCGAAA 60.663 43.478 37.18 20.98 0.00 3.46
755 762 4.569023 CGCTATCTCCCGCGTGCA 62.569 66.667 4.92 0.00 44.01 4.57
779 796 0.872388 CTTCCCACGCGCTAGTTTTT 59.128 50.000 5.73 0.00 0.00 1.94
814 831 1.518572 CTGCTCGTTAATCCCGCGT 60.519 57.895 4.92 0.00 0.00 6.01
837 855 1.657181 CTTTTGGCGTGTCCGTTGC 60.657 57.895 0.00 0.00 37.80 4.17
932 950 2.263741 CGCAGAAAGCTGTGGCCTT 61.264 57.895 3.32 0.00 46.38 4.35
933 951 1.288127 GCAGAAAGCTGTGGCCTTG 59.712 57.895 3.32 0.00 44.17 3.61
934 952 1.174712 GCAGAAAGCTGTGGCCTTGA 61.175 55.000 3.32 0.00 44.17 3.02
935 953 1.321474 CAGAAAGCTGTGGCCTTGAA 58.679 50.000 3.32 0.00 39.73 2.69
1161 1179 2.120718 AACCGCTCCTCCTCCACT 59.879 61.111 0.00 0.00 0.00 4.00
1821 1945 0.109412 GCCTTGTGCTGCAGATTCAC 60.109 55.000 20.43 16.54 36.87 3.18
1830 1954 0.391661 TGCAGATTCACGAAGAGGCC 60.392 55.000 0.00 0.00 0.00 5.19
1976 2100 8.415950 TGTTTCTTATAAAATTTCTGCCCTGA 57.584 30.769 0.00 0.00 0.00 3.86
2251 2384 2.103042 ATCCTTCGTTGCTGAGCGC 61.103 57.895 0.00 0.00 39.77 5.92
2279 2412 0.320697 GTACGTCCTTTGGCAGGTCT 59.679 55.000 0.00 0.00 44.37 3.85
2348 2481 3.245284 CGGTTTAGTGCTTGATCGTATGG 59.755 47.826 0.00 0.00 0.00 2.74
2352 2485 6.349033 GGTTTAGTGCTTGATCGTATGGTTTT 60.349 38.462 0.00 0.00 0.00 2.43
2426 2559 5.815581 TGCCTCCTGTTATGTTCATTAGTT 58.184 37.500 0.00 0.00 0.00 2.24
2510 2647 5.393866 ACCTGATTATGGGTTGTTTTGTCT 58.606 37.500 0.00 0.00 30.80 3.41
2539 2676 4.526262 CCATTGTTCCCCATAGTTTTGTCA 59.474 41.667 0.00 0.00 0.00 3.58
2548 2685 5.048713 CCCCATAGTTTTGTCAGACTTTGTC 60.049 44.000 1.31 0.00 0.00 3.18
2612 2749 2.297701 TGTTGCCACAAAGTTCTCTCC 58.702 47.619 0.00 0.00 0.00 3.71
2650 2788 2.799978 CAACGTTGGGAAAATGGCTTTC 59.200 45.455 20.71 0.00 42.45 2.62
2681 2819 8.388484 AGGATGATGCTGATAGTTTAATTCAC 57.612 34.615 0.00 0.00 0.00 3.18
2705 2843 4.194640 ACATCACTCATGATAACAGTGGC 58.805 43.478 10.99 0.00 44.13 5.01
2751 2889 6.018669 CACCACAAAGTCTTCTCAAAGTAGAC 60.019 42.308 5.81 5.81 41.27 2.59
2791 2929 4.580167 TGTCAATCTGGGTGAGTTTTCAAG 59.420 41.667 0.00 0.00 34.49 3.02
2840 2978 3.181329 TGGTAACACATGATCCCTCTGT 58.819 45.455 0.00 0.00 46.17 3.41
3045 3185 3.451178 GGGCAAGAGTATCCTTACAGTCA 59.549 47.826 0.00 0.00 33.66 3.41
3218 3358 8.428852 ACAGGTTAGCTTTTTATTCCACATTTT 58.571 29.630 0.00 0.00 0.00 1.82
3400 3540 7.321153 TGTCTGATGCTTTACTCTTTAGGTAC 58.679 38.462 0.00 0.00 0.00 3.34
3422 5450 7.665559 GGTACTATGGCATCTTTTCCATGAATA 59.334 37.037 1.65 0.00 42.62 1.75
3423 5451 9.236006 GTACTATGGCATCTTTTCCATGAATAT 57.764 33.333 1.65 0.00 42.62 1.28
3492 5520 7.225784 AGATTTACATGCCATGTGTTGTTAA 57.774 32.000 20.36 2.49 44.60 2.01
3527 5555 8.958175 TGAACATCGAAAAACCAATATTGTAC 57.042 30.769 14.25 0.00 0.00 2.90
3528 5556 8.788806 TGAACATCGAAAAACCAATATTGTACT 58.211 29.630 14.25 0.00 0.00 2.73
3529 5557 9.274065 GAACATCGAAAAACCAATATTGTACTC 57.726 33.333 14.25 3.21 0.00 2.59
3530 5558 7.758495 ACATCGAAAAACCAATATTGTACTCC 58.242 34.615 14.25 0.00 0.00 3.85
3531 5559 6.746745 TCGAAAAACCAATATTGTACTCCC 57.253 37.500 14.25 0.00 0.00 4.30
3532 5560 6.478129 TCGAAAAACCAATATTGTACTCCCT 58.522 36.000 14.25 0.00 0.00 4.20
3533 5561 6.596497 TCGAAAAACCAATATTGTACTCCCTC 59.404 38.462 14.25 1.98 0.00 4.30
3534 5562 6.183360 CGAAAAACCAATATTGTACTCCCTCC 60.183 42.308 14.25 0.00 0.00 4.30
3535 5563 4.417426 AACCAATATTGTACTCCCTCCG 57.583 45.455 14.25 0.00 0.00 4.63
3536 5564 3.381335 ACCAATATTGTACTCCCTCCGT 58.619 45.455 14.25 0.00 0.00 4.69
3537 5565 3.387050 ACCAATATTGTACTCCCTCCGTC 59.613 47.826 14.25 0.00 0.00 4.79
3538 5566 3.244112 CCAATATTGTACTCCCTCCGTCC 60.244 52.174 14.25 0.00 0.00 4.79
3539 5567 2.077687 TATTGTACTCCCTCCGTCCC 57.922 55.000 0.00 0.00 0.00 4.46
3540 5568 0.338814 ATTGTACTCCCTCCGTCCCT 59.661 55.000 0.00 0.00 0.00 4.20
3541 5569 1.002069 TTGTACTCCCTCCGTCCCTA 58.998 55.000 0.00 0.00 0.00 3.53
3542 5570 1.002069 TGTACTCCCTCCGTCCCTAA 58.998 55.000 0.00 0.00 0.00 2.69
3543 5571 1.358787 TGTACTCCCTCCGTCCCTAAA 59.641 52.381 0.00 0.00 0.00 1.85
3544 5572 2.023695 TGTACTCCCTCCGTCCCTAAAT 60.024 50.000 0.00 0.00 0.00 1.40
3545 5573 2.265526 ACTCCCTCCGTCCCTAAATT 57.734 50.000 0.00 0.00 0.00 1.82
3546 5574 2.117051 ACTCCCTCCGTCCCTAAATTC 58.883 52.381 0.00 0.00 0.00 2.17
3547 5575 2.292984 ACTCCCTCCGTCCCTAAATTCT 60.293 50.000 0.00 0.00 0.00 2.40
3548 5576 2.772515 CTCCCTCCGTCCCTAAATTCTT 59.227 50.000 0.00 0.00 0.00 2.52
3549 5577 2.504175 TCCCTCCGTCCCTAAATTCTTG 59.496 50.000 0.00 0.00 0.00 3.02
3550 5578 2.238898 CCCTCCGTCCCTAAATTCTTGT 59.761 50.000 0.00 0.00 0.00 3.16
3551 5579 3.532542 CCTCCGTCCCTAAATTCTTGTC 58.467 50.000 0.00 0.00 0.00 3.18
3552 5580 3.197983 CCTCCGTCCCTAAATTCTTGTCT 59.802 47.826 0.00 0.00 0.00 3.41
3553 5581 4.323562 CCTCCGTCCCTAAATTCTTGTCTT 60.324 45.833 0.00 0.00 0.00 3.01
3554 5582 5.105064 CCTCCGTCCCTAAATTCTTGTCTTA 60.105 44.000 0.00 0.00 0.00 2.10
3555 5583 5.974108 TCCGTCCCTAAATTCTTGTCTTAG 58.026 41.667 0.00 0.00 0.00 2.18
3556 5584 5.718130 TCCGTCCCTAAATTCTTGTCTTAGA 59.282 40.000 0.00 0.00 0.00 2.10
3557 5585 6.383147 TCCGTCCCTAAATTCTTGTCTTAGAT 59.617 38.462 0.00 0.00 0.00 1.98
3558 5586 7.048512 CCGTCCCTAAATTCTTGTCTTAGATT 58.951 38.462 0.00 0.00 0.00 2.40
3559 5587 7.553044 CCGTCCCTAAATTCTTGTCTTAGATTT 59.447 37.037 0.00 0.00 0.00 2.17
3560 5588 8.391106 CGTCCCTAAATTCTTGTCTTAGATTTG 58.609 37.037 0.00 0.00 0.00 2.32
3561 5589 8.184848 GTCCCTAAATTCTTGTCTTAGATTTGC 58.815 37.037 0.00 0.00 0.00 3.68
3562 5590 7.339466 TCCCTAAATTCTTGTCTTAGATTTGCC 59.661 37.037 0.00 0.00 0.00 4.52
3563 5591 7.340487 CCCTAAATTCTTGTCTTAGATTTGCCT 59.660 37.037 0.00 0.00 0.00 4.75
3564 5592 9.396022 CCTAAATTCTTGTCTTAGATTTGCCTA 57.604 33.333 0.00 0.00 0.00 3.93
3567 5595 9.692325 AAATTCTTGTCTTAGATTTGCCTAGAT 57.308 29.630 0.00 0.00 0.00 1.98
3569 5597 9.771534 ATTCTTGTCTTAGATTTGCCTAGATAC 57.228 33.333 0.00 0.00 0.00 2.24
3570 5598 7.426410 TCTTGTCTTAGATTTGCCTAGATACG 58.574 38.462 0.00 0.00 0.00 3.06
3571 5599 6.085555 TGTCTTAGATTTGCCTAGATACGG 57.914 41.667 0.00 0.00 0.00 4.02
3572 5600 5.831525 TGTCTTAGATTTGCCTAGATACGGA 59.168 40.000 0.00 0.00 0.00 4.69
3573 5601 6.493802 TGTCTTAGATTTGCCTAGATACGGAT 59.506 38.462 0.00 0.00 0.00 4.18
3574 5602 6.809196 GTCTTAGATTTGCCTAGATACGGATG 59.191 42.308 0.00 0.00 0.00 3.51
3575 5603 6.493802 TCTTAGATTTGCCTAGATACGGATGT 59.506 38.462 0.00 0.00 0.00 3.06
3576 5604 7.668469 TCTTAGATTTGCCTAGATACGGATGTA 59.332 37.037 0.00 0.00 34.45 2.29
3577 5605 6.859112 AGATTTGCCTAGATACGGATGTAT 57.141 37.500 0.00 0.00 43.97 2.29
3593 5621 8.792831 ACGGATGTATCTAATACTAAAACGTG 57.207 34.615 0.00 0.00 36.70 4.49
3594 5622 8.623903 ACGGATGTATCTAATACTAAAACGTGA 58.376 33.333 0.00 0.00 36.70 4.35
3595 5623 8.899776 CGGATGTATCTAATACTAAAACGTGAC 58.100 37.037 0.00 0.00 36.70 3.67
3596 5624 9.962783 GGATGTATCTAATACTAAAACGTGACT 57.037 33.333 0.00 0.00 36.70 3.41
3606 5634 6.963049 ACTAAAACGTGACTTGATACATCC 57.037 37.500 0.00 0.00 0.00 3.51
3607 5635 4.921470 AAAACGTGACTTGATACATCCG 57.079 40.909 0.00 0.00 0.00 4.18
3608 5636 3.587797 AACGTGACTTGATACATCCGT 57.412 42.857 0.00 0.00 0.00 4.69
3609 5637 4.707030 AACGTGACTTGATACATCCGTA 57.293 40.909 0.00 0.00 0.00 4.02
3610 5638 4.913335 ACGTGACTTGATACATCCGTAT 57.087 40.909 0.00 0.00 41.16 3.06
3611 5639 5.258456 ACGTGACTTGATACATCCGTATT 57.742 39.130 0.00 0.00 38.48 1.89
3612 5640 5.657474 ACGTGACTTGATACATCCGTATTT 58.343 37.500 0.00 0.00 38.48 1.40
3613 5641 6.798482 ACGTGACTTGATACATCCGTATTTA 58.202 36.000 0.00 0.00 38.48 1.40
3614 5642 6.916387 ACGTGACTTGATACATCCGTATTTAG 59.084 38.462 0.00 0.00 38.48 1.85
3615 5643 7.136772 CGTGACTTGATACATCCGTATTTAGA 58.863 38.462 0.00 0.00 38.48 2.10
3616 5644 7.113124 CGTGACTTGATACATCCGTATTTAGAC 59.887 40.741 0.00 0.00 38.48 2.59
3617 5645 7.919091 GTGACTTGATACATCCGTATTTAGACA 59.081 37.037 0.00 0.00 38.48 3.41
3618 5646 8.471609 TGACTTGATACATCCGTATTTAGACAA 58.528 33.333 0.00 0.00 38.48 3.18
3619 5647 9.309516 GACTTGATACATCCGTATTTAGACAAA 57.690 33.333 0.00 0.00 38.48 2.83
3620 5648 9.832445 ACTTGATACATCCGTATTTAGACAAAT 57.168 29.630 0.00 0.00 38.48 2.32
3627 5655 9.530633 ACATCCGTATTTAGACAAATCTAAGAC 57.469 33.333 0.00 0.83 45.93 3.01
3628 5656 9.529325 CATCCGTATTTAGACAAATCTAAGACA 57.471 33.333 9.81 0.00 45.93 3.41
3630 5658 9.582431 TCCGTATTTAGACAAATCTAAGACAAG 57.418 33.333 9.81 3.88 45.93 3.16
3631 5659 9.582431 CCGTATTTAGACAAATCTAAGACAAGA 57.418 33.333 9.81 0.00 45.93 3.02
3639 5667 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
3640 5668 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
3641 5669 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
3642 5670 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
3643 5671 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
3644 5672 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
3645 5673 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
3646 5674 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
3647 5675 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
3648 5676 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
3649 5677 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
3650 5678 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
3651 5679 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
3689 5717 0.320421 TCCGCTTGTAGTCCAACAGC 60.320 55.000 0.00 0.00 0.00 4.40
3848 5876 5.505173 AATTAGTAACATGCACATGCTCC 57.495 39.130 10.50 0.00 42.39 4.70
3872 5900 5.106396 CCTGAAGAGAAAGTTATGCCAACTG 60.106 44.000 1.88 0.00 0.00 3.16
4051 6080 0.899717 TCCTGACTGCATTTTGCCCC 60.900 55.000 0.00 0.00 44.23 5.80
4052 6081 1.593265 CTGACTGCATTTTGCCCCC 59.407 57.895 0.00 0.00 44.23 5.40
4064 6093 0.404040 TTGCCCCCACCTTACTGAAG 59.596 55.000 0.00 0.00 0.00 3.02
4641 6679 1.360393 TGGAGACCAAAAGGGGTGCT 61.360 55.000 0.00 0.00 42.53 4.40
4798 6844 8.511321 TGTTTGTTCACTGGAATGATGTAATAC 58.489 33.333 0.00 0.00 35.05 1.89
5336 7384 2.056223 GGAGGTACCTGCGTGGCTA 61.056 63.158 22.10 0.00 40.22 3.93
5594 7643 7.958053 TCAAGTTAGGTTGCTTTTACTCTAC 57.042 36.000 0.00 0.00 0.00 2.59
5660 7712 1.787155 CAGTACGAGTGAACTGTGTGC 59.213 52.381 0.00 0.00 38.62 4.57
5709 7761 9.308000 CCAAGGTAGTCTTATCTTCAGATATCT 57.692 37.037 0.00 0.00 36.94 1.98
5774 7826 5.007724 GGTTCGCAGTTAGGAATAGGATTTG 59.992 44.000 0.00 0.00 0.00 2.32
5800 7852 4.923415 AGACTGAAATTCCTTGTTAGGGG 58.077 43.478 0.00 0.00 42.26 4.79
5859 7911 6.253746 CGCTTAATGTGGAATTTCTCTCTTG 58.746 40.000 0.00 0.00 0.00 3.02
5933 7987 4.202151 GGGTGCTTCTGTGACTTGATTTTT 60.202 41.667 0.00 0.00 0.00 1.94
5962 8016 6.139679 AGATTTGAGTTTTGATACCCAGGA 57.860 37.500 0.00 0.00 0.00 3.86
5985 8039 3.011821 TGAGGTTGGAGGATCTGTAGTCT 59.988 47.826 0.00 0.00 33.73 3.24
5995 8049 4.161377 AGGATCTGTAGTCTTTGCTCCTTC 59.839 45.833 0.00 0.00 0.00 3.46
6015 8069 5.352569 CCTTCAGATCCTGTTGTAATGTGTC 59.647 44.000 0.00 0.00 32.61 3.67
6083 8137 1.807814 ACGAGGAAGAAGGGGCATAT 58.192 50.000 0.00 0.00 0.00 1.78
6102 8156 6.040842 GGCATATTATGTGATGGGTTTGTTCT 59.959 38.462 5.60 0.00 0.00 3.01
6131 8188 7.878477 AGATGCATGTTGTAGATTTGTTTTG 57.122 32.000 2.46 0.00 0.00 2.44
6179 8236 9.099454 CCTCTGTAAAGAAATATAAGAGCGTTT 57.901 33.333 0.00 0.00 0.00 3.60
6180 8237 9.907576 CTCTGTAAAGAAATATAAGAGCGTTTG 57.092 33.333 0.00 0.00 0.00 2.93
6189 8246 8.958119 AAATATAAGAGCGTTTGGATCACTAA 57.042 30.769 0.00 0.00 32.03 2.24
6201 8283 6.795144 TTGGATCACTAATACTTTACGGGA 57.205 37.500 0.00 0.00 0.00 5.14
6204 8286 6.781014 TGGATCACTAATACTTTACGGGAGAT 59.219 38.462 0.00 0.00 0.00 2.75
6238 8320 5.940470 GTGTGTCTTTATCCAAATGTCTCCT 59.060 40.000 0.00 0.00 0.00 3.69
6244 8326 8.360390 GTCTTTATCCAAATGTCTCCTGTTTTT 58.640 33.333 0.00 0.00 0.00 1.94
6280 8362 3.378339 GCACATATTTGATGCCTTGCTC 58.622 45.455 0.00 0.00 33.06 4.26
6281 8363 3.624900 CACATATTTGATGCCTTGCTCG 58.375 45.455 0.00 0.00 0.00 5.03
6348 8444 5.556355 TTCATGCATTAAGAAGTGAGCTG 57.444 39.130 0.00 0.00 0.00 4.24
6358 8454 5.841957 AAGAAGTGAGCTGAAACAAACAT 57.158 34.783 0.00 0.00 0.00 2.71
6364 8460 5.069516 AGTGAGCTGAAACAAACATTGGATT 59.930 36.000 0.00 0.00 34.12 3.01
6405 8501 1.141053 GGGGTCGATTAATGAGGTGCT 59.859 52.381 0.00 0.00 0.00 4.40
6435 8531 3.633525 TGGAATAACATCATGGCTTGCTC 59.366 43.478 0.00 0.00 0.00 4.26
6441 8537 3.220110 ACATCATGGCTTGCTCTATTGG 58.780 45.455 0.00 0.00 0.00 3.16
6461 8557 3.880490 TGGTTCGGCATAATGGTTACATC 59.120 43.478 0.00 0.00 35.94 3.06
6501 8599 3.864789 AAGACAGGTGGTTCATCAACT 57.135 42.857 0.00 0.00 34.56 3.16
6526 8626 6.366877 TCGGTTACAAGACACTAGTTAAATGC 59.633 38.462 0.00 0.00 0.00 3.56
6528 8628 6.128090 GGTTACAAGACACTAGTTAAATGCCC 60.128 42.308 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 0.889186 ACCTCGGACAACACCAATGC 60.889 55.000 0.00 0.00 0.00 3.56
40 41 1.067425 CGATACCTCGGACAACACCAA 60.067 52.381 0.00 0.00 41.27 3.67
107 109 2.499693 TGATATCGTTGAAGCAGGTGGA 59.500 45.455 0.00 0.00 0.00 4.02
128 130 0.462581 CACTGGCCATATCGCAGTGT 60.463 55.000 5.51 0.00 38.61 3.55
251 256 4.819761 GACGAGCGAGCCATGGCA 62.820 66.667 37.18 0.00 44.88 4.92
323 328 1.273606 CCGCCTCATCTTATCACGGAT 59.726 52.381 0.00 0.00 41.61 4.18
362 367 0.388134 ACTTCTACACGCGCGAACAT 60.388 50.000 39.36 20.00 0.00 2.71
379 384 2.628178 TCACAGATGAACTTCCGTGACT 59.372 45.455 0.00 0.00 28.61 3.41
573 579 4.451150 ATCACCGCGCCGTCATGT 62.451 61.111 0.00 0.00 0.00 3.21
632 639 1.688811 CCCATTTTCCCCGTCTCCA 59.311 57.895 0.00 0.00 0.00 3.86
657 664 2.736995 CGCGTTCCATGACACGGT 60.737 61.111 15.68 0.00 36.88 4.83
659 666 2.469847 CACGCGTTCCATGACACG 59.530 61.111 10.22 11.15 39.49 4.49
690 697 1.331680 CGTTTCGCGCGCACTAATAAT 60.332 47.619 32.61 0.00 0.00 1.28
695 702 3.463690 GTCGTTTCGCGCGCACTA 61.464 61.111 32.61 13.45 41.07 2.74
708 715 0.452987 TGGTAGATTTAGCGCGTCGT 59.547 50.000 8.43 0.00 0.00 4.34
717 724 1.801395 GCAGCTCGCGTGGTAGATTTA 60.801 52.381 12.92 0.00 0.00 1.40
755 762 1.369091 CTAGCGCGTGGGAAGCAATT 61.369 55.000 8.43 0.00 34.19 2.32
797 814 1.807981 CACGCGGGATTAACGAGCA 60.808 57.895 12.47 0.00 34.45 4.26
798 815 3.003478 CACGCGGGATTAACGAGC 58.997 61.111 12.47 0.00 34.45 5.03
799 816 2.856346 CGCACGCGGGATTAACGAG 61.856 63.158 15.48 0.00 37.17 4.18
800 817 2.881827 CGCACGCGGGATTAACGA 60.882 61.111 15.48 0.00 35.56 3.85
801 818 3.134141 GACGCACGCGGGATTAACG 62.134 63.158 15.48 8.47 44.69 3.18
802 819 1.356527 AAGACGCACGCGGGATTAAC 61.357 55.000 15.48 0.00 44.69 2.01
803 820 0.671163 AAAGACGCACGCGGGATTAA 60.671 50.000 15.48 0.00 44.69 1.40
804 821 0.671163 AAAAGACGCACGCGGGATTA 60.671 50.000 15.48 0.00 44.69 1.75
805 822 1.964373 AAAAGACGCACGCGGGATT 60.964 52.632 15.48 0.00 44.69 3.01
806 823 2.358247 AAAAGACGCACGCGGGAT 60.358 55.556 15.48 0.00 44.69 3.85
807 824 3.342627 CAAAAGACGCACGCGGGA 61.343 61.111 15.48 0.00 44.69 5.14
808 825 4.383602 CCAAAAGACGCACGCGGG 62.384 66.667 16.70 7.92 44.69 6.13
814 831 2.539338 GGACACGCCAAAAGACGCA 61.539 57.895 0.00 0.00 36.34 5.24
828 846 4.284123 GAGCATCTGCAACGGACA 57.716 55.556 4.79 0.00 45.16 4.02
866 884 1.050009 GTTTGCGGCTAAAACGAAGC 58.950 50.000 0.00 0.00 39.33 3.86
1821 1945 4.503741 TGAAAATTTTCTGGCCTCTTCG 57.496 40.909 26.73 0.00 38.02 3.79
1830 1954 8.517878 ACACCAGTCTGATATGAAAATTTTCTG 58.482 33.333 26.73 15.98 38.02 3.02
2251 2384 3.124636 GCCAAAGGACGTACTGTGTAATG 59.875 47.826 16.95 2.49 0.00 1.90
2371 2504 7.169158 ACAGAAAGAAAACAGATTTTGGACA 57.831 32.000 0.00 0.00 38.17 4.02
2426 2559 2.832129 AGAAAGATAACTCAGTGCCGGA 59.168 45.455 5.05 0.00 0.00 5.14
2460 2597 5.965033 AACAGACTTATGATCAGGATGGT 57.035 39.130 0.09 0.00 36.16 3.55
2510 2647 7.415004 AAACTATGGGGAACAATGGGATATA 57.585 36.000 0.00 0.00 0.00 0.86
2539 2676 4.564406 CCTGTGCCATCTAAGACAAAGTCT 60.564 45.833 0.00 0.00 45.64 3.24
2612 2749 3.059868 ACGTTGTTTCACTCAGTAATGCG 60.060 43.478 0.00 0.00 0.00 4.73
2650 2788 4.958509 ACTATCAGCATCATCCTTCACAG 58.041 43.478 0.00 0.00 0.00 3.66
2681 2819 5.448225 GCCACTGTTATCATGAGTGATGTTG 60.448 44.000 12.30 1.96 44.62 3.33
2705 2843 2.621998 GCATGAATCACAAGATCCAGGG 59.378 50.000 0.00 0.00 31.90 4.45
2751 2889 4.811555 TGACAAGTCCAATTCTTCAACG 57.188 40.909 0.00 0.00 0.00 4.10
2791 2929 0.807667 CTAGCACCTCATCGCCACAC 60.808 60.000 0.00 0.00 0.00 3.82
2840 2978 7.436080 GCCACGTTAACTAGCTATATAACACAA 59.564 37.037 20.21 0.00 0.00 3.33
3045 3185 6.266131 TCATCAAGGGCAAGGTATCTAATT 57.734 37.500 0.00 0.00 0.00 1.40
3249 3389 8.498054 TTTAAATAGAGTGGAGATGCTTCTTG 57.502 34.615 3.29 0.00 30.30 3.02
3400 3540 8.582437 ACAATATTCATGGAAAAGATGCCATAG 58.418 33.333 0.00 0.00 42.81 2.23
3422 5450 8.034313 TCCAGCATAGATCTAAGGTTAACAAT 57.966 34.615 6.52 0.00 0.00 2.71
3423 5451 7.432148 TCCAGCATAGATCTAAGGTTAACAA 57.568 36.000 6.52 0.00 0.00 2.83
3492 5520 9.607988 TGGTTTTTCGATGTTCATATAGTACAT 57.392 29.630 0.00 0.00 40.43 2.29
3527 5555 2.399580 AGAATTTAGGGACGGAGGGAG 58.600 52.381 0.00 0.00 0.00 4.30
3528 5556 2.504175 CAAGAATTTAGGGACGGAGGGA 59.496 50.000 0.00 0.00 0.00 4.20
3529 5557 2.238898 ACAAGAATTTAGGGACGGAGGG 59.761 50.000 0.00 0.00 0.00 4.30
3530 5558 3.197983 AGACAAGAATTTAGGGACGGAGG 59.802 47.826 0.00 0.00 0.00 4.30
3531 5559 4.473477 AGACAAGAATTTAGGGACGGAG 57.527 45.455 0.00 0.00 0.00 4.63
3532 5560 4.903045 AAGACAAGAATTTAGGGACGGA 57.097 40.909 0.00 0.00 0.00 4.69
3533 5561 5.974108 TCTAAGACAAGAATTTAGGGACGG 58.026 41.667 0.00 0.00 0.00 4.79
3534 5562 8.391106 CAAATCTAAGACAAGAATTTAGGGACG 58.609 37.037 0.00 0.00 0.00 4.79
3535 5563 8.184848 GCAAATCTAAGACAAGAATTTAGGGAC 58.815 37.037 0.00 0.00 0.00 4.46
3536 5564 7.339466 GGCAAATCTAAGACAAGAATTTAGGGA 59.661 37.037 0.00 0.00 0.00 4.20
3537 5565 7.340487 AGGCAAATCTAAGACAAGAATTTAGGG 59.660 37.037 0.00 0.00 0.00 3.53
3538 5566 8.286191 AGGCAAATCTAAGACAAGAATTTAGG 57.714 34.615 0.00 0.00 0.00 2.69
3541 5569 9.692325 ATCTAGGCAAATCTAAGACAAGAATTT 57.308 29.630 0.00 0.00 0.00 1.82
3543 5571 9.771534 GTATCTAGGCAAATCTAAGACAAGAAT 57.228 33.333 0.00 0.00 0.00 2.40
3544 5572 7.921214 CGTATCTAGGCAAATCTAAGACAAGAA 59.079 37.037 0.00 0.00 0.00 2.52
3545 5573 7.426410 CGTATCTAGGCAAATCTAAGACAAGA 58.574 38.462 0.00 0.00 0.00 3.02
3546 5574 6.642950 CCGTATCTAGGCAAATCTAAGACAAG 59.357 42.308 0.00 0.00 0.00 3.16
3547 5575 6.322969 TCCGTATCTAGGCAAATCTAAGACAA 59.677 38.462 0.00 0.00 0.00 3.18
3548 5576 5.831525 TCCGTATCTAGGCAAATCTAAGACA 59.168 40.000 0.00 0.00 0.00 3.41
3549 5577 6.328641 TCCGTATCTAGGCAAATCTAAGAC 57.671 41.667 0.00 0.00 0.00 3.01
3550 5578 6.493802 ACATCCGTATCTAGGCAAATCTAAGA 59.506 38.462 0.00 0.00 0.00 2.10
3551 5579 6.692486 ACATCCGTATCTAGGCAAATCTAAG 58.308 40.000 0.00 0.00 0.00 2.18
3552 5580 6.665992 ACATCCGTATCTAGGCAAATCTAA 57.334 37.500 0.00 0.00 0.00 2.10
3553 5581 7.956328 ATACATCCGTATCTAGGCAAATCTA 57.044 36.000 0.00 0.00 32.66 1.98
3554 5582 6.859112 ATACATCCGTATCTAGGCAAATCT 57.141 37.500 0.00 0.00 32.66 2.40
3567 5595 9.882996 CACGTTTTAGTATTAGATACATCCGTA 57.117 33.333 0.00 0.00 38.21 4.02
3568 5596 8.623903 TCACGTTTTAGTATTAGATACATCCGT 58.376 33.333 0.00 0.00 38.21 4.69
3569 5597 8.899776 GTCACGTTTTAGTATTAGATACATCCG 58.100 37.037 0.00 0.00 38.21 4.18
3570 5598 9.962783 AGTCACGTTTTAGTATTAGATACATCC 57.037 33.333 0.00 0.00 38.21 3.51
3580 5608 9.095065 GGATGTATCAAGTCACGTTTTAGTATT 57.905 33.333 0.00 0.00 0.00 1.89
3581 5609 7.434307 CGGATGTATCAAGTCACGTTTTAGTAT 59.566 37.037 0.00 0.00 0.00 2.12
3582 5610 6.748658 CGGATGTATCAAGTCACGTTTTAGTA 59.251 38.462 0.00 0.00 0.00 1.82
3583 5611 5.575606 CGGATGTATCAAGTCACGTTTTAGT 59.424 40.000 0.00 0.00 0.00 2.24
3584 5612 5.575606 ACGGATGTATCAAGTCACGTTTTAG 59.424 40.000 0.00 0.00 0.00 1.85
3585 5613 5.472148 ACGGATGTATCAAGTCACGTTTTA 58.528 37.500 0.00 0.00 0.00 1.52
3586 5614 4.312443 ACGGATGTATCAAGTCACGTTTT 58.688 39.130 0.00 0.00 0.00 2.43
3587 5615 3.921677 ACGGATGTATCAAGTCACGTTT 58.078 40.909 0.00 0.00 0.00 3.60
3588 5616 3.587797 ACGGATGTATCAAGTCACGTT 57.412 42.857 0.00 0.00 0.00 3.99
3589 5617 4.913335 ATACGGATGTATCAAGTCACGT 57.087 40.909 0.00 0.00 36.56 4.49
3590 5618 7.113124 GTCTAAATACGGATGTATCAAGTCACG 59.887 40.741 0.00 0.00 40.42 4.35
3591 5619 7.919091 TGTCTAAATACGGATGTATCAAGTCAC 59.081 37.037 0.00 0.00 40.42 3.67
3592 5620 8.002984 TGTCTAAATACGGATGTATCAAGTCA 57.997 34.615 0.00 0.00 40.42 3.41
3593 5621 8.867112 TTGTCTAAATACGGATGTATCAAGTC 57.133 34.615 0.00 0.00 40.42 3.01
3594 5622 9.832445 ATTTGTCTAAATACGGATGTATCAAGT 57.168 29.630 0.00 0.00 40.42 3.16
3601 5629 9.530633 GTCTTAGATTTGTCTAAATACGGATGT 57.469 33.333 0.26 0.00 36.66 3.06
3602 5630 9.529325 TGTCTTAGATTTGTCTAAATACGGATG 57.471 33.333 0.26 0.00 36.66 3.51
3604 5632 9.582431 CTTGTCTTAGATTTGTCTAAATACGGA 57.418 33.333 0.26 0.00 36.66 4.69
3605 5633 9.582431 TCTTGTCTTAGATTTGTCTAAATACGG 57.418 33.333 0.26 0.99 36.66 4.02
3613 5641 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
3614 5642 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
3615 5643 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
3616 5644 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
3617 5645 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
3618 5646 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
3619 5647 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
3620 5648 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
3621 5649 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
3622 5650 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
3623 5651 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
3624 5652 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
3625 5653 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
3626 5654 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
3627 5655 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
3628 5656 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
3629 5657 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
3630 5658 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
3631 5659 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
3632 5660 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
3633 5661 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
3634 5662 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
3635 5663 2.852714 TAATACTCCCTCCGTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
3636 5664 2.852714 TTAATACTCCCTCCGTCCCA 57.147 50.000 0.00 0.00 0.00 4.37
3637 5665 4.701651 AATTTAATACTCCCTCCGTCCC 57.298 45.455 0.00 0.00 0.00 4.46
3638 5666 6.492772 TCTCTAATTTAATACTCCCTCCGTCC 59.507 42.308 0.00 0.00 0.00 4.79
3639 5667 7.521871 TCTCTAATTTAATACTCCCTCCGTC 57.478 40.000 0.00 0.00 0.00 4.79
3640 5668 7.909485 TTCTCTAATTTAATACTCCCTCCGT 57.091 36.000 0.00 0.00 0.00 4.69
3641 5669 9.780186 ATTTTCTCTAATTTAATACTCCCTCCG 57.220 33.333 0.00 0.00 0.00 4.63
3689 5717 9.783256 CATATAGGCATATGACAATCATTGTTG 57.217 33.333 12.11 0.00 44.70 3.33
3848 5876 5.006386 AGTTGGCATAACTTTCTCTTCAGG 58.994 41.667 0.00 0.00 0.00 3.86
4014 6043 6.940298 AGTCAGGAAAAGATAATTCAACCGAA 59.060 34.615 0.00 0.00 35.05 4.30
4016 6045 6.546395 CAGTCAGGAAAAGATAATTCAACCG 58.454 40.000 0.00 0.00 0.00 4.44
4051 6080 6.595716 CAGGAAAAGATACTTCAGTAAGGTGG 59.404 42.308 0.00 0.00 37.01 4.61
4052 6081 7.332182 GTCAGGAAAAGATACTTCAGTAAGGTG 59.668 40.741 0.00 0.00 37.01 4.00
4064 6093 6.349300 TGCCAGATTAGTCAGGAAAAGATAC 58.651 40.000 0.46 0.00 33.04 2.24
4200 6229 7.958674 TGCAAACTAAAAACTTTTGACATGAC 58.041 30.769 0.00 0.00 32.91 3.06
4202 6231 9.424659 GAATGCAAACTAAAAACTTTTGACATG 57.575 29.630 0.00 0.00 32.91 3.21
4474 6505 7.404671 ACTAAAGAACAACAAAACATCAGGT 57.595 32.000 0.00 0.00 0.00 4.00
4508 6539 6.323996 CCTCCATAGTACTTCCACAACTGATA 59.676 42.308 0.00 0.00 0.00 2.15
4543 6574 9.912634 CTAGGAATAAAGATCTGCTTTCTCTAG 57.087 37.037 0.00 8.69 43.17 2.43
4641 6679 2.088104 ACCAGTTCTCCAGTGAGTCA 57.912 50.000 0.00 0.00 39.75 3.41
4719 6757 7.397476 GGGAGGTTCTGAAGGAAAAATAAAGAT 59.603 37.037 0.00 0.00 35.51 2.40
4798 6844 1.364626 GATGGCAGCAACTGACCGAG 61.365 60.000 0.00 0.00 39.07 4.63
5038 7086 4.563337 TCCTGTAAGAATCGGTACATCG 57.437 45.455 0.00 0.00 34.07 3.84
5534 7582 3.368248 ACAACTGCAGCATTAATCCCAT 58.632 40.909 15.27 0.00 0.00 4.00
5546 7594 1.626654 CCCTACGCGAACAACTGCAG 61.627 60.000 15.93 13.48 0.00 4.41
5659 7711 2.294449 AACCAGAAGAAAAGGGGAGC 57.706 50.000 0.00 0.00 0.00 4.70
5660 7712 4.367039 TGTAACCAGAAGAAAAGGGGAG 57.633 45.455 0.00 0.00 0.00 4.30
5709 7761 4.033009 TCCTCAAGATGCTCTCCATAACA 58.967 43.478 0.00 0.00 33.29 2.41
5774 7826 6.819146 CCCTAACAAGGAATTTCAGTCTCTAC 59.181 42.308 0.00 0.00 0.00 2.59
5800 7852 6.096564 AGTCTACCAACACCAGCTACTATTAC 59.903 42.308 0.00 0.00 0.00 1.89
5859 7911 2.087646 GAGACAGACCAAGGAAATGCC 58.912 52.381 0.00 0.00 0.00 4.40
5933 7987 5.642063 GGTATCAAAACTCAAATCTCGGACA 59.358 40.000 0.00 0.00 0.00 4.02
5962 8016 3.964031 GACTACAGATCCTCCAACCTCAT 59.036 47.826 0.00 0.00 0.00 2.90
5985 8039 3.181440 ACAACAGGATCTGAAGGAGCAAA 60.181 43.478 1.59 0.00 35.18 3.68
5995 8049 6.533012 CAGTAGACACATTACAACAGGATCTG 59.467 42.308 0.00 0.00 37.52 2.90
6015 8069 0.534412 CCAGCCTGACCTCACAGTAG 59.466 60.000 0.00 0.00 36.30 2.57
6083 8137 5.380900 TGTCAGAACAAACCCATCACATAA 58.619 37.500 0.00 0.00 30.70 1.90
6102 8156 6.207221 ACAAATCTACAACATGCATCTTGTCA 59.793 34.615 21.57 11.59 32.77 3.58
6131 8188 4.040584 GGGAGTGGTAGTTTAGATCCATCC 59.959 50.000 0.00 0.00 32.45 3.51
6179 8236 6.131264 TCTCCCGTAAAGTATTAGTGATCCA 58.869 40.000 0.00 0.00 0.00 3.41
6180 8237 6.645790 TCTCCCGTAAAGTATTAGTGATCC 57.354 41.667 0.00 0.00 0.00 3.36
6201 8283 5.979288 AAAGACACACTACGGAGTAATCT 57.021 39.130 0.00 0.29 45.13 2.40
6204 8286 5.711506 TGGATAAAGACACACTACGGAGTAA 59.288 40.000 0.00 0.00 45.13 2.24
6216 8298 5.940470 ACAGGAGACATTTGGATAAAGACAC 59.060 40.000 0.00 0.00 0.00 3.67
6244 8326 1.689984 TGTGCCATCAACAGCAAGAA 58.310 45.000 0.00 0.00 41.48 2.52
6249 8331 4.374843 TCAAATATGTGCCATCAACAGC 57.625 40.909 0.00 0.00 0.00 4.40
6274 8356 0.882042 ACTGCAGGAACACGAGCAAG 60.882 55.000 19.93 0.00 35.23 4.01
6277 8359 0.880278 TGAACTGCAGGAACACGAGC 60.880 55.000 19.93 0.00 0.00 5.03
6278 8360 1.143305 CTGAACTGCAGGAACACGAG 58.857 55.000 19.93 0.00 41.07 4.18
6307 8399 6.073657 GCATGAAAATGTGCAAACATGTAGTT 60.074 34.615 0.00 0.00 43.89 2.24
6309 8401 5.849858 GCATGAAAATGTGCAAACATGTAG 58.150 37.500 0.00 0.00 40.94 2.74
6310 8402 5.842619 GCATGAAAATGTGCAAACATGTA 57.157 34.783 0.00 0.00 40.94 2.29
6413 8509 3.633525 GAGCAAGCCATGATGTTATTCCA 59.366 43.478 0.00 0.00 0.00 3.53
6435 8531 5.529430 TGTAACCATTATGCCGAACCAATAG 59.471 40.000 0.00 0.00 0.00 1.73
6441 8537 3.558418 ACGATGTAACCATTATGCCGAAC 59.442 43.478 0.00 0.00 0.00 3.95
6478 8574 4.956075 AGTTGATGAACCACCTGTCTTTTT 59.044 37.500 0.00 0.00 31.81 1.94
6480 8576 4.137543 GAGTTGATGAACCACCTGTCTTT 58.862 43.478 0.00 0.00 31.81 2.52
6483 8579 2.069273 CGAGTTGATGAACCACCTGTC 58.931 52.381 0.00 0.00 31.81 3.51
6485 8581 1.270839 ACCGAGTTGATGAACCACCTG 60.271 52.381 0.00 0.00 31.81 4.00
6487 8583 1.892209 AACCGAGTTGATGAACCACC 58.108 50.000 0.00 0.00 31.81 4.61
6489 8585 3.755112 TGTAACCGAGTTGATGAACCA 57.245 42.857 0.00 0.00 31.81 3.67
6501 8599 6.366877 GCATTTAACTAGTGTCTTGTAACCGA 59.633 38.462 0.00 0.00 0.00 4.69


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

AutoCloner maintained by Alex Coulton.