Multiple sequence alignment - TraesCS1A01G340700

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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 TraesCS1A01G340700 chr1A 100.000 5658 0 0 1 5658 530737249 530731592 0.000000e+00 10449.0
1 TraesCS1A01G340700 chr1A 84.402 936 114 10 1 911 530754244 530753316 0.000000e+00 891.0
2 TraesCS1A01G340700 chr1D 93.528 3600 159 34 826 4397 432210258 432206705 0.000000e+00 5289.0
3 TraesCS1A01G340700 chr1D 89.385 1300 75 28 946 2224 432232977 432231720 0.000000e+00 1578.0
4 TraesCS1A01G340700 chr1D 85.256 936 106 13 1 911 432308925 432307997 0.000000e+00 935.0
5 TraesCS1A01G340700 chr1D 87.709 716 72 9 2442 3147 432231728 432231019 0.000000e+00 821.0
6 TraesCS1A01G340700 chr1D 95.000 460 23 0 1 460 432214298 432213839 0.000000e+00 723.0
7 TraesCS1A01G340700 chr1D 80.810 667 69 19 3292 3918 432230869 432230222 8.580000e-128 468.0
8 TraesCS1A01G340700 chr1D 89.855 345 28 5 4571 4909 432229884 432229541 2.420000e-118 436.0
9 TraesCS1A01G340700 chr1D 95.572 271 12 0 423 693 432213841 432213571 8.710000e-118 435.0
10 TraesCS1A01G340700 chr1D 81.958 521 23 20 5188 5658 432206058 432205559 5.350000e-100 375.0
11 TraesCS1A01G340700 chr1D 91.026 234 15 5 4811 5043 432206574 432206346 1.530000e-80 311.0
12 TraesCS1A01G340700 chr1D 97.059 170 5 0 4394 4563 476231388 476231219 2.580000e-73 287.0
13 TraesCS1A01G340700 chr1D 96.850 127 4 0 4558 4684 432206706 432206580 4.440000e-51 213.0
14 TraesCS1A01G340700 chr1D 91.743 109 9 0 3187 3295 432231019 432230911 9.820000e-33 152.0
15 TraesCS1A01G340700 chr1D 93.651 63 4 0 4158 4220 432230058 432229996 1.680000e-15 95.3
16 TraesCS1A01G340700 chr1D 92.308 65 2 2 744 808 432213569 432213508 7.810000e-14 89.8
17 TraesCS1A01G340700 chr1B 91.308 1116 72 9 3296 4396 583690823 583689718 0.000000e+00 1500.0
18 TraesCS1A01G340700 chr1B 91.132 936 39 12 1 925 583694389 583693487 0.000000e+00 1229.0
19 TraesCS1A01G340700 chr1B 87.862 1071 94 18 4597 5658 583689710 583688667 0.000000e+00 1225.0
20 TraesCS1A01G340700 chr1B 95.080 691 27 3 939 1627 583693116 583692431 0.000000e+00 1081.0
21 TraesCS1A01G340700 chr1B 87.389 674 77 7 1 668 583736180 583735509 0.000000e+00 767.0
22 TraesCS1A01G340700 chr1B 85.762 604 53 19 1632 2224 583692342 583691761 4.850000e-170 608.0
23 TraesCS1A01G340700 chr1B 92.123 292 17 2 2442 2727 583691769 583691478 1.900000e-109 407.0
24 TraesCS1A01G340700 chr1B 96.364 220 8 0 2225 2444 98964730 98964511 4.170000e-96 363.0
25 TraesCS1A01G340700 chr1B 84.211 247 18 13 666 900 583735484 583735247 2.650000e-53 220.0
26 TraesCS1A01G340700 chr7A 93.871 620 32 1 1 614 547143415 547142796 0.000000e+00 929.0
27 TraesCS1A01G340700 chr7A 86.698 421 16 9 598 1002 547122615 547122219 1.130000e-116 431.0
28 TraesCS1A01G340700 chr2D 85.493 841 73 18 955 1769 571919784 571920601 0.000000e+00 832.0
29 TraesCS1A01G340700 chr2D 95.122 41 2 0 3144 3184 558182826 558182786 1.320000e-06 65.8
30 TraesCS1A01G340700 chr2B 83.288 730 74 24 1061 1769 683767774 683768476 3.720000e-176 628.0
31 TraesCS1A01G340700 chr2B 78.400 250 18 23 833 1067 683765544 683765772 4.600000e-26 130.0
32 TraesCS1A01G340700 chr2A 84.387 538 60 13 993 1521 710376574 710377096 1.820000e-139 507.0
33 TraesCS1A01G340700 chr2A 96.364 220 8 0 2223 2442 510431379 510431160 4.170000e-96 363.0
34 TraesCS1A01G340700 chr2A 93.182 44 3 0 3141 3184 117530061 117530104 1.320000e-06 65.8
35 TraesCS1A01G340700 chr2A 90.196 51 3 2 3134 3183 187954996 187954947 1.320000e-06 65.8
36 TraesCS1A01G340700 chr5D 96.818 220 7 0 2223 2442 67584760 67584541 8.960000e-98 368.0
37 TraesCS1A01G340700 chr5D 96.380 221 8 0 2223 2443 292147892 292148112 1.160000e-96 364.0
38 TraesCS1A01G340700 chr5D 97.561 41 1 0 3143 3183 109811419 109811379 2.830000e-08 71.3
39 TraesCS1A01G340700 chr3D 96.818 220 7 0 2223 2442 313292364 313292583 8.960000e-98 368.0
40 TraesCS1A01G340700 chr3D 96.804 219 7 0 2224 2442 324319277 324319059 3.220000e-97 366.0
41 TraesCS1A01G340700 chr3D 96.364 220 8 0 2223 2442 225855207 225854988 4.170000e-96 363.0
42 TraesCS1A01G340700 chr3D 97.500 40 1 0 3144 3183 27936655 27936616 1.020000e-07 69.4
43 TraesCS1A01G340700 chr5A 96.364 220 8 0 2223 2442 366234822 366235041 4.170000e-96 363.0
44 TraesCS1A01G340700 chr5A 97.647 170 4 0 4394 4563 676319132 676319301 5.540000e-75 292.0
45 TraesCS1A01G340700 chr5A 95.122 41 2 0 3144 3184 509644409 509644369 1.320000e-06 65.8
46 TraesCS1A01G340700 chrUn 98.795 166 2 0 4395 4560 318699530 318699365 4.290000e-76 296.0
47 TraesCS1A01G340700 chrUn 96.111 180 6 1 4394 4572 61009609 61009430 5.540000e-75 292.0
48 TraesCS1A01G340700 chr6A 98.193 166 3 0 4395 4560 573643312 573643477 1.990000e-74 291.0
49 TraesCS1A01G340700 chr6A 98.193 166 3 0 4395 4560 574214913 574214748 1.990000e-74 291.0
50 TraesCS1A01G340700 chr4D 98.193 166 3 0 4394 4559 281177086 281177251 1.990000e-74 291.0
51 TraesCS1A01G340700 chr4A 97.110 173 4 1 4391 4562 185555348 185555176 1.990000e-74 291.0
52 TraesCS1A01G340700 chr4A 97.619 168 4 0 4396 4563 560316465 560316298 7.170000e-74 289.0
53 TraesCS1A01G340700 chr5B 97.500 40 1 0 3144 3183 536586947 536586986 1.020000e-07 69.4
54 TraesCS1A01G340700 chr5B 95.122 41 2 0 3143 3183 123689219 123689179 1.320000e-06 65.8


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 TraesCS1A01G340700 chr1A 530731592 530737249 5657 True 10449.000000 10449 100.000000 1 5658 1 chr1A.!!$R1 5657
1 TraesCS1A01G340700 chr1A 530753316 530754244 928 True 891.000000 891 84.402000 1 911 1 chr1A.!!$R2 910
2 TraesCS1A01G340700 chr1D 432205559 432214298 8739 True 1062.257143 5289 92.320286 1 5658 7 chr1D.!!$R3 5657
3 TraesCS1A01G340700 chr1D 432307997 432308925 928 True 935.000000 935 85.256000 1 911 1 chr1D.!!$R1 910
4 TraesCS1A01G340700 chr1D 432229541 432232977 3436 True 591.716667 1578 88.858833 946 4909 6 chr1D.!!$R4 3963
5 TraesCS1A01G340700 chr1B 583688667 583694389 5722 True 1008.333333 1500 90.544500 1 5658 6 chr1B.!!$R2 5657
6 TraesCS1A01G340700 chr1B 583735247 583736180 933 True 493.500000 767 85.800000 1 900 2 chr1B.!!$R3 899
7 TraesCS1A01G340700 chr7A 547142796 547143415 619 True 929.000000 929 93.871000 1 614 1 chr7A.!!$R2 613
8 TraesCS1A01G340700 chr2D 571919784 571920601 817 False 832.000000 832 85.493000 955 1769 1 chr2D.!!$F1 814
9 TraesCS1A01G340700 chr2B 683765544 683768476 2932 False 379.000000 628 80.844000 833 1769 2 chr2B.!!$F1 936
10 TraesCS1A01G340700 chr2A 710376574 710377096 522 False 507.000000 507 84.387000 993 1521 1 chr2A.!!$F2 528

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
886 4211 1.749286 GCCGGCCCATTACACAATAGT 60.749 52.381 18.11 0.0 0.00 2.12 F
1717 7612 0.185175 GGAGTTGTTTGTGGGGGAGT 59.815 55.000 0.00 0.0 0.00 3.85 F
2062 7966 1.100510 GCCCGTAAGTTCCATTTCCC 58.899 55.000 0.00 0.0 0.00 3.97 F
2804 8798 0.248866 GTCTGTGTTTTTGCACGGGG 60.249 55.000 5.37 0.0 43.81 5.73 F
2936 8942 0.457851 CATCAGACGAGTCCCCAGAC 59.542 60.000 0.00 0.0 43.89 3.51 F
3684 9764 0.550914 AAACAGCCCTCTGACACCAA 59.449 50.000 0.00 0.0 42.95 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2417 8330 0.035247 AAGAGAGGTCGGCGTAGACT 60.035 55.000 6.85 2.86 40.76 3.24 R
2791 8785 0.458260 ACTGAACCCCGTGCAAAAAC 59.542 50.000 0.00 0.00 0.00 2.43 R
3616 9694 1.133199 TCCCAAAGAAACCCAGCACAT 60.133 47.619 0.00 0.00 0.00 3.21 R
4547 10662 0.541863 CTGCCAAATACTCCCTCCGT 59.458 55.000 0.00 0.00 0.00 4.69 R
4548 10663 0.830648 TCTGCCAAATACTCCCTCCG 59.169 55.000 0.00 0.00 0.00 4.63 R
5365 11666 0.693622 TACACATTTGGGGCGGAGAA 59.306 50.000 0.00 0.00 0.00 2.87 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
786 871 2.611971 CGGATAGAGAGAGACGAGGGAG 60.612 59.091 0.00 0.00 0.00 4.30
886 4211 1.749286 GCCGGCCCATTACACAATAGT 60.749 52.381 18.11 0.00 0.00 2.12
1276 7009 2.203938 TCCTGGAGGCCGAGGTTT 60.204 61.111 15.73 0.00 34.44 3.27
1387 7165 1.666189 GTAAGATGAACCTCGCCTTGC 59.334 52.381 0.00 0.00 0.00 4.01
1403 7181 2.159240 CCTTGCTATACTGACAGTGCGA 60.159 50.000 18.58 11.59 0.00 5.10
1425 7203 5.277974 CGACATCCACATGATTTTATCCCAC 60.278 44.000 0.00 0.00 33.72 4.61
1429 7207 3.287222 CACATGATTTTATCCCACCCGT 58.713 45.455 0.00 0.00 0.00 5.28
1464 7250 1.724623 CGTGTACAGTCCACAATTCCG 59.275 52.381 0.00 0.00 33.00 4.30
1553 7351 4.124851 ACATGAATTCGTAGGTGAGGAC 57.875 45.455 0.00 0.00 0.00 3.85
1556 7354 5.362717 ACATGAATTCGTAGGTGAGGACATA 59.637 40.000 0.00 0.00 0.00 2.29
1557 7355 5.258456 TGAATTCGTAGGTGAGGACATAC 57.742 43.478 0.04 0.00 36.25 2.39
1558 7356 4.707934 TGAATTCGTAGGTGAGGACATACA 59.292 41.667 0.04 0.00 38.94 2.29
1559 7357 4.920640 ATTCGTAGGTGAGGACATACAG 57.079 45.455 0.00 0.00 38.94 2.74
1560 7358 3.361281 TCGTAGGTGAGGACATACAGT 57.639 47.619 0.00 0.00 38.94 3.55
1650 7537 0.691904 TCATGCTCCATGTCACACCA 59.308 50.000 5.24 0.00 41.98 4.17
1663 7550 0.963962 CACACCATTTGCTCTGCCTT 59.036 50.000 0.00 0.00 0.00 4.35
1717 7612 0.185175 GGAGTTGTTTGTGGGGGAGT 59.815 55.000 0.00 0.00 0.00 3.85
1720 7615 2.105993 GAGTTGTTTGTGGGGGAGTAGT 59.894 50.000 0.00 0.00 0.00 2.73
1741 7639 5.321516 AGTACTCGCGCATTTAAATTTGTC 58.678 37.500 8.75 0.00 0.00 3.18
1781 7679 9.298250 TGAATGACTAGTACAGGATATAGGTTC 57.702 37.037 0.00 0.00 0.00 3.62
1828 7727 8.625786 TTACATGTAAGGATGATGATGAATGG 57.374 34.615 14.35 0.00 0.00 3.16
1843 7742 7.885009 TGATGAATGGTGATGATGTAAACAT 57.115 32.000 0.00 0.00 39.70 2.71
1850 7749 8.806429 ATGGTGATGATGTAAACATGACTTTA 57.194 30.769 0.00 0.00 33.93 1.85
1878 7777 6.073222 GCCGATTAACATATTTACAGGAGTGG 60.073 42.308 0.00 0.00 0.00 4.00
1879 7778 6.426937 CCGATTAACATATTTACAGGAGTGGG 59.573 42.308 0.00 0.00 0.00 4.61
1880 7779 6.990349 CGATTAACATATTTACAGGAGTGGGT 59.010 38.462 0.00 0.00 0.00 4.51
1908 7812 5.221641 ACTGATCACTTAGGCTGTGTTTACA 60.222 40.000 0.00 0.00 36.83 2.41
2062 7966 1.100510 GCCCGTAAGTTCCATTTCCC 58.899 55.000 0.00 0.00 0.00 3.97
2227 8140 3.455990 TTAAGCCGTCTGTGTACAACA 57.544 42.857 0.00 0.00 37.22 3.33
2228 8141 2.319136 AAGCCGTCTGTGTACAACAA 57.681 45.000 0.00 0.00 38.67 2.83
2229 8142 1.578583 AGCCGTCTGTGTACAACAAC 58.421 50.000 0.00 0.00 38.67 3.32
2343 8256 3.570212 AAGCTTCCACGCACCCCT 61.570 61.111 0.00 0.00 0.00 4.79
2377 8290 5.178797 AGTTCTTTGGTGATACTCCAATCG 58.821 41.667 6.20 2.59 43.25 3.34
2417 8330 3.308402 GGACTCCTCCCATGTCAAATTCA 60.308 47.826 0.00 0.00 32.84 2.57
2712 8635 2.546789 GACAAGTAGGGTTGGTTTGACG 59.453 50.000 0.00 0.00 0.00 4.35
2791 8785 3.494626 ACTATGCGAGTTTGTTGTCTGTG 59.505 43.478 0.00 0.00 33.13 3.66
2804 8798 0.248866 GTCTGTGTTTTTGCACGGGG 60.249 55.000 5.37 0.00 43.81 5.73
2879 8873 7.701539 TGCATGGGTGGCTATTATATTTAAG 57.298 36.000 0.00 0.00 0.00 1.85
2882 8876 8.585018 GCATGGGTGGCTATTATATTTAAGTTT 58.415 33.333 0.00 0.00 0.00 2.66
2886 8880 8.297426 GGGTGGCTATTATATTTAAGTTTGAGC 58.703 37.037 0.00 0.00 0.00 4.26
2936 8942 0.457851 CATCAGACGAGTCCCCAGAC 59.542 60.000 0.00 0.00 43.89 3.51
3170 9177 8.074991 ACTCCCTCCCTAAAGAAATATAAGAGT 58.925 37.037 0.00 0.00 0.00 3.24
3195 9202 6.984474 TGTTTAGACCACTGAGTACTTTCTTG 59.016 38.462 0.00 0.00 0.00 3.02
3221 9228 5.786401 AAGCAAAGAACGATCATAGTGTC 57.214 39.130 0.00 0.00 0.00 3.67
3307 9365 4.380233 GGAGCTGTTTGTCCAGAATCATTG 60.380 45.833 0.00 0.00 34.23 2.82
3353 9411 1.407258 CAGCAACCGGGTTCTTTTGAA 59.593 47.619 10.04 0.00 35.84 2.69
3488 9549 9.023962 TGGATTATGATGTAGCACTTTCTTTTT 57.976 29.630 0.00 0.00 0.00 1.94
3499 9560 4.032104 GCACTTTCTTTTTCTGCTTGTGTG 59.968 41.667 0.00 0.00 0.00 3.82
3592 9653 3.490078 CCGCACACAGGTTTGTTTTATGT 60.490 43.478 0.00 0.00 34.62 2.29
3679 9759 2.814336 CCTGTAAAAACAGCCCTCTGAC 59.186 50.000 0.00 0.00 42.95 3.51
3684 9764 0.550914 AAACAGCCCTCTGACACCAA 59.449 50.000 0.00 0.00 42.95 3.67
3694 9774 3.256383 CCTCTGACACCAATTCAATTGCA 59.744 43.478 4.40 0.00 38.92 4.08
3782 9879 8.945481 TTGAATAATTGTGATTAGGGCAAATG 57.055 30.769 0.00 0.00 31.58 2.32
3791 9888 5.066505 GTGATTAGGGCAAATGTCTTACTGG 59.933 44.000 0.00 0.00 0.00 4.00
3875 9974 6.935741 TGCTTATGTTATAGCCAACGATTT 57.064 33.333 0.00 0.00 36.56 2.17
3930 10041 2.384382 CTGTAGCAACGCCAAACAAAG 58.616 47.619 0.00 0.00 0.00 2.77
3943 10054 5.625311 CGCCAAACAAAGAAATAGTTGAGAC 59.375 40.000 0.00 0.00 0.00 3.36
4073 10185 5.603170 ACCAAATGATTGTGATCCCATTC 57.397 39.130 0.00 0.00 34.60 2.67
4078 10190 2.310538 GATTGTGATCCCATTCACCCC 58.689 52.381 2.43 0.00 44.37 4.95
4153 10265 9.525826 AAGTGATCTTTACCAATTCTCATTCTT 57.474 29.630 0.00 0.00 0.00 2.52
4221 10333 5.123027 CCAGGTTAGTTTCTCAATCAGAAGC 59.877 44.000 0.00 0.00 42.37 3.86
4260 10374 8.976353 TCTCTTAGCTACTCAGATCTTTTTCAT 58.024 33.333 0.00 0.00 0.00 2.57
4269 10383 7.173722 ACTCAGATCTTTTTCATGAGTCCAAT 58.826 34.615 5.87 0.00 45.60 3.16
4270 10384 7.668886 ACTCAGATCTTTTTCATGAGTCCAATT 59.331 33.333 5.87 0.00 45.60 2.32
4341 10456 9.453325 GTTCTTTATAGAGTATGTGCTACTGAC 57.547 37.037 0.00 0.00 40.88 3.51
4358 10473 7.280428 TGCTACTGACAGAGTGATAGTAGTTAC 59.720 40.741 10.08 7.30 38.45 2.50
4396 10511 6.103997 CGTGAAGCCTGGTAATACTTTTCTA 58.896 40.000 0.00 0.00 0.00 2.10
4397 10512 6.035758 CGTGAAGCCTGGTAATACTTTTCTAC 59.964 42.308 0.00 0.00 0.00 2.59
4399 10514 7.278203 GTGAAGCCTGGTAATACTTTTCTACTC 59.722 40.741 0.00 0.00 0.00 2.59
4400 10515 6.236558 AGCCTGGTAATACTTTTCTACTCC 57.763 41.667 0.00 0.00 0.00 3.85
4401 10516 5.130643 AGCCTGGTAATACTTTTCTACTCCC 59.869 44.000 0.00 0.00 0.00 4.30
4402 10517 5.130643 GCCTGGTAATACTTTTCTACTCCCT 59.869 44.000 0.00 0.00 0.00 4.20
4403 10518 6.685873 GCCTGGTAATACTTTTCTACTCCCTC 60.686 46.154 0.00 0.00 0.00 4.30
4404 10519 6.612049 CCTGGTAATACTTTTCTACTCCCTCT 59.388 42.308 0.00 0.00 0.00 3.69
4405 10520 7.418025 CCTGGTAATACTTTTCTACTCCCTCTG 60.418 44.444 0.00 0.00 0.00 3.35
4406 10521 6.958192 TGGTAATACTTTTCTACTCCCTCTGT 59.042 38.462 0.00 0.00 0.00 3.41
4407 10522 7.456902 TGGTAATACTTTTCTACTCCCTCTGTT 59.543 37.037 0.00 0.00 0.00 3.16
4408 10523 7.980662 GGTAATACTTTTCTACTCCCTCTGTTC 59.019 40.741 0.00 0.00 0.00 3.18
4409 10524 4.893829 ACTTTTCTACTCCCTCTGTTCC 57.106 45.455 0.00 0.00 0.00 3.62
4410 10525 4.494591 ACTTTTCTACTCCCTCTGTTCCT 58.505 43.478 0.00 0.00 0.00 3.36
4411 10526 5.652324 ACTTTTCTACTCCCTCTGTTCCTA 58.348 41.667 0.00 0.00 0.00 2.94
4412 10527 6.082707 ACTTTTCTACTCCCTCTGTTCCTAA 58.917 40.000 0.00 0.00 0.00 2.69
4413 10528 6.557633 ACTTTTCTACTCCCTCTGTTCCTAAA 59.442 38.462 0.00 0.00 0.00 1.85
4414 10529 7.237887 ACTTTTCTACTCCCTCTGTTCCTAAAT 59.762 37.037 0.00 0.00 0.00 1.40
4415 10530 8.674925 TTTTCTACTCCCTCTGTTCCTAAATA 57.325 34.615 0.00 0.00 0.00 1.40
4416 10531 8.855804 TTTCTACTCCCTCTGTTCCTAAATAT 57.144 34.615 0.00 0.00 0.00 1.28
4417 10532 8.855804 TTCTACTCCCTCTGTTCCTAAATATT 57.144 34.615 0.00 0.00 0.00 1.28
4418 10533 8.855804 TCTACTCCCTCTGTTCCTAAATATTT 57.144 34.615 5.89 5.89 0.00 1.40
4419 10534 8.705594 TCTACTCCCTCTGTTCCTAAATATTTG 58.294 37.037 11.05 1.40 0.00 2.32
4420 10535 7.272144 ACTCCCTCTGTTCCTAAATATTTGT 57.728 36.000 11.05 0.00 0.00 2.83
4421 10536 7.339482 ACTCCCTCTGTTCCTAAATATTTGTC 58.661 38.462 11.05 0.00 0.00 3.18
4422 10537 7.182930 ACTCCCTCTGTTCCTAAATATTTGTCT 59.817 37.037 11.05 0.00 0.00 3.41
4423 10538 7.928873 TCCCTCTGTTCCTAAATATTTGTCTT 58.071 34.615 11.05 0.00 0.00 3.01
4424 10539 8.390921 TCCCTCTGTTCCTAAATATTTGTCTTT 58.609 33.333 11.05 0.00 0.00 2.52
4425 10540 8.678199 CCCTCTGTTCCTAAATATTTGTCTTTC 58.322 37.037 11.05 0.00 0.00 2.62
4426 10541 9.454859 CCTCTGTTCCTAAATATTTGTCTTTCT 57.545 33.333 11.05 0.00 0.00 2.52
4442 10557 8.924511 TTGTCTTTCTAGAGATTTCAAATGGT 57.075 30.769 0.00 0.00 0.00 3.55
4443 10558 8.553459 TGTCTTTCTAGAGATTTCAAATGGTC 57.447 34.615 0.00 0.00 0.00 4.02
4444 10559 8.156820 TGTCTTTCTAGAGATTTCAAATGGTCA 58.843 33.333 0.00 0.00 0.00 4.02
4445 10560 8.447053 GTCTTTCTAGAGATTTCAAATGGTCAC 58.553 37.037 0.00 0.00 0.00 3.67
4446 10561 7.607991 TCTTTCTAGAGATTTCAAATGGTCACC 59.392 37.037 0.00 0.00 0.00 4.02
4447 10562 6.373005 TCTAGAGATTTCAAATGGTCACCA 57.627 37.500 0.00 0.00 38.19 4.17
4448 10563 6.173339 TCTAGAGATTTCAAATGGTCACCAC 58.827 40.000 0.00 0.00 35.80 4.16
4449 10564 4.728772 AGAGATTTCAAATGGTCACCACA 58.271 39.130 0.00 0.00 35.80 4.17
4450 10565 5.327732 AGAGATTTCAAATGGTCACCACAT 58.672 37.500 0.00 0.00 35.80 3.21
4451 10566 6.484288 AGAGATTTCAAATGGTCACCACATA 58.516 36.000 0.00 0.00 35.80 2.29
4452 10567 6.375455 AGAGATTTCAAATGGTCACCACATAC 59.625 38.462 0.00 0.00 35.80 2.39
4453 10568 4.757799 TTTCAAATGGTCACCACATACG 57.242 40.909 0.00 0.00 35.80 3.06
4454 10569 2.705730 TCAAATGGTCACCACATACGG 58.294 47.619 0.00 0.00 35.80 4.02
4455 10570 2.303311 TCAAATGGTCACCACATACGGA 59.697 45.455 0.00 0.00 35.80 4.69
4456 10571 3.054728 TCAAATGGTCACCACATACGGAT 60.055 43.478 0.00 0.00 35.80 4.18
4457 10572 2.620251 ATGGTCACCACATACGGATG 57.380 50.000 5.94 5.94 35.80 3.51
4459 10574 2.458620 TGGTCACCACATACGGATGTA 58.541 47.619 14.23 0.00 44.82 2.29
4460 10575 3.035363 TGGTCACCACATACGGATGTAT 58.965 45.455 14.23 1.38 44.82 2.29
4461 10576 4.216708 TGGTCACCACATACGGATGTATA 58.783 43.478 14.23 0.00 44.82 1.47
4462 10577 4.836175 TGGTCACCACATACGGATGTATAT 59.164 41.667 14.23 0.00 44.82 0.86
4463 10578 6.011481 TGGTCACCACATACGGATGTATATA 58.989 40.000 14.23 0.00 44.82 0.86
4464 10579 6.152154 TGGTCACCACATACGGATGTATATAG 59.848 42.308 14.23 0.00 44.82 1.31
4465 10580 6.376299 GGTCACCACATACGGATGTATATAGA 59.624 42.308 14.23 4.80 44.82 1.98
4466 10581 7.249147 GTCACCACATACGGATGTATATAGAC 58.751 42.308 14.23 12.97 44.82 2.59
4467 10582 6.943718 TCACCACATACGGATGTATATAGACA 59.056 38.462 14.23 2.07 44.82 3.41
4468 10583 7.614192 TCACCACATACGGATGTATATAGACAT 59.386 37.037 14.23 12.70 44.82 3.06
4469 10584 8.899771 CACCACATACGGATGTATATAGACATA 58.100 37.037 14.23 0.00 44.82 2.29
4470 10585 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
4497 10612 9.677567 TTTAAAGTGTAGATTCACTCATTTTGC 57.322 29.630 0.00 0.00 46.25 3.68
4498 10613 7.516198 AAAGTGTAGATTCACTCATTTTGCT 57.484 32.000 0.00 0.00 46.25 3.91
4499 10614 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
4500 10615 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
4501 10616 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
4502 10617 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
4503 10618 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
4504 10619 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
4505 10620 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
4506 10621 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
4507 10622 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
4508 10623 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
4509 10624 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
4510 10625 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
4511 10626 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
4512 10627 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
4513 10628 2.953466 TTGCTCCGTATGTAGTCACC 57.047 50.000 0.00 0.00 0.00 4.02
4514 10629 1.842052 TGCTCCGTATGTAGTCACCA 58.158 50.000 0.00 0.00 0.00 4.17
4515 10630 2.384828 TGCTCCGTATGTAGTCACCAT 58.615 47.619 0.00 0.00 0.00 3.55
4516 10631 2.764010 TGCTCCGTATGTAGTCACCATT 59.236 45.455 0.00 0.00 0.00 3.16
4517 10632 3.196901 TGCTCCGTATGTAGTCACCATTT 59.803 43.478 0.00 0.00 0.00 2.32
4518 10633 3.555956 GCTCCGTATGTAGTCACCATTTG 59.444 47.826 0.00 0.00 0.00 2.32
4519 10634 4.679639 GCTCCGTATGTAGTCACCATTTGA 60.680 45.833 0.00 0.00 0.00 2.69
4520 10635 5.408880 TCCGTATGTAGTCACCATTTGAA 57.591 39.130 0.00 0.00 35.39 2.69
4521 10636 5.795972 TCCGTATGTAGTCACCATTTGAAA 58.204 37.500 0.00 0.00 35.39 2.69
4522 10637 5.640357 TCCGTATGTAGTCACCATTTGAAAC 59.360 40.000 0.00 0.00 35.39 2.78
4523 10638 5.163794 CCGTATGTAGTCACCATTTGAAACC 60.164 44.000 0.00 0.00 35.39 3.27
4524 10639 5.642063 CGTATGTAGTCACCATTTGAAACCT 59.358 40.000 0.00 0.00 35.39 3.50
4525 10640 6.183360 CGTATGTAGTCACCATTTGAAACCTC 60.183 42.308 0.00 0.00 35.39 3.85
4526 10641 5.304686 TGTAGTCACCATTTGAAACCTCT 57.695 39.130 0.00 0.00 35.39 3.69
4527 10642 6.428083 TGTAGTCACCATTTGAAACCTCTA 57.572 37.500 0.00 0.00 35.39 2.43
4528 10643 6.464222 TGTAGTCACCATTTGAAACCTCTAG 58.536 40.000 0.00 0.00 35.39 2.43
4529 10644 5.825593 AGTCACCATTTGAAACCTCTAGA 57.174 39.130 0.00 0.00 35.39 2.43
4530 10645 6.187727 AGTCACCATTTGAAACCTCTAGAA 57.812 37.500 0.00 0.00 35.39 2.10
4531 10646 6.601332 AGTCACCATTTGAAACCTCTAGAAA 58.399 36.000 0.00 0.00 35.39 2.52
4532 10647 6.712547 AGTCACCATTTGAAACCTCTAGAAAG 59.287 38.462 0.00 0.00 35.39 2.62
4533 10648 6.710744 GTCACCATTTGAAACCTCTAGAAAGA 59.289 38.462 0.00 0.00 35.39 2.52
4534 10649 6.710744 TCACCATTTGAAACCTCTAGAAAGAC 59.289 38.462 0.00 0.00 0.00 3.01
4535 10650 6.486657 CACCATTTGAAACCTCTAGAAAGACA 59.513 38.462 0.00 0.00 0.00 3.41
4536 10651 7.013274 CACCATTTGAAACCTCTAGAAAGACAA 59.987 37.037 0.00 0.00 0.00 3.18
4537 10652 7.559897 ACCATTTGAAACCTCTAGAAAGACAAA 59.440 33.333 0.00 4.41 0.00 2.83
4538 10653 8.579863 CCATTTGAAACCTCTAGAAAGACAAAT 58.420 33.333 13.64 13.64 36.38 2.32
4550 10665 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
4551 10666 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
4552 10667 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
4553 10668 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
4554 10669 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
4555 10670 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
4556 10671 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
4636 10751 6.258947 GGAAAGCAGACATAGATTCAGTTACC 59.741 42.308 0.00 0.00 0.00 2.85
4660 10775 1.379527 AATTGCGCCTACTGTAAGCC 58.620 50.000 4.18 0.00 37.60 4.35
4691 10806 4.381411 GGCATGGTTAGTCTATTCCTCAC 58.619 47.826 0.00 0.00 0.00 3.51
4694 10809 5.755861 GCATGGTTAGTCTATTCCTCACTTC 59.244 44.000 0.00 0.00 0.00 3.01
4704 10819 3.340814 TTCCTCACTTCTTCCTGATGC 57.659 47.619 0.00 0.00 0.00 3.91
4706 10821 2.909006 TCCTCACTTCTTCCTGATGCTT 59.091 45.455 0.00 0.00 0.00 3.91
4715 10830 2.220653 TCCTGATGCTTTTCCCCTTG 57.779 50.000 0.00 0.00 0.00 3.61
4723 10838 2.172293 TGCTTTTCCCCTTGCAAACATT 59.828 40.909 0.00 0.00 32.12 2.71
4728 10843 3.534357 TCCCCTTGCAAACATTTAGGA 57.466 42.857 0.00 0.00 0.00 2.94
4737 10852 8.527810 CCTTGCAAACATTTAGGACCTTTTATA 58.472 33.333 0.00 0.00 0.00 0.98
4796 10916 5.011738 TCACCAAGTTTTAGAGTCCCTACAG 59.988 44.000 0.00 0.00 0.00 2.74
4807 10927 2.586792 CCTACAGGACCAGGCAGC 59.413 66.667 0.00 0.00 37.39 5.25
4828 10948 3.561213 CAGAGTGCTGGCGATGCG 61.561 66.667 0.00 0.00 38.51 4.73
4960 11084 1.004560 CTCGCAGTTGAAGGCCAGA 60.005 57.895 5.01 0.00 0.00 3.86
4965 11089 1.887956 GCAGTTGAAGGCCAGAATCCA 60.888 52.381 5.01 0.00 0.00 3.41
4968 11092 3.512724 CAGTTGAAGGCCAGAATCCATTT 59.487 43.478 5.01 0.00 0.00 2.32
4979 11103 3.129287 CAGAATCCATTTGCTGTACCCAC 59.871 47.826 0.00 0.00 0.00 4.61
4980 11104 2.897271 ATCCATTTGCTGTACCCACA 57.103 45.000 0.00 0.00 0.00 4.17
5037 11161 2.481952 GCAGACTCTAGTGCTTGGTTTG 59.518 50.000 0.00 0.00 36.71 2.93
5063 11187 1.376295 ACCGCCCGCGAATACTTTT 60.376 52.632 8.23 0.00 42.83 2.27
5065 11189 0.247934 CCGCCCGCGAATACTTTTTC 60.248 55.000 8.23 0.00 42.83 2.29
5067 11191 0.247934 GCCCGCGAATACTTTTTCGG 60.248 55.000 8.23 0.00 46.52 4.30
5074 11198 4.491441 CGCGAATACTTTTTCGGTTACCTC 60.491 45.833 0.00 0.00 46.52 3.85
5075 11199 4.628766 GCGAATACTTTTTCGGTTACCTCT 59.371 41.667 0.00 0.00 46.52 3.69
5077 11201 6.531439 CGAATACTTTTTCGGTTACCTCTTG 58.469 40.000 0.00 0.00 43.59 3.02
5078 11202 6.366877 CGAATACTTTTTCGGTTACCTCTTGA 59.633 38.462 0.00 0.00 43.59 3.02
5097 11221 7.772757 CCTCTTGATGATGATGATGATGATGAT 59.227 37.037 0.00 0.00 0.00 2.45
5123 11247 2.724744 GCAACACAGCTTTGCTTTTG 57.275 45.000 13.22 5.96 44.96 2.44
5150 11274 2.356553 TTCCCTTTCCGCGACACG 60.357 61.111 8.23 0.00 43.15 4.49
5160 11284 2.742372 GCGACACGGGACAAGCAT 60.742 61.111 0.00 0.00 0.00 3.79
5175 11299 5.806654 ACAAGCATTTGTAATCCCAAACT 57.193 34.783 0.00 0.00 45.45 2.66
5176 11300 5.540911 ACAAGCATTTGTAATCCCAAACTG 58.459 37.500 0.00 0.00 45.45 3.16
5242 11521 2.277247 GTGCGTGTGTGTGTGTGC 60.277 61.111 0.00 0.00 0.00 4.57
5332 11633 1.299468 CTCGTGGCATCTCCGCTAC 60.299 63.158 0.00 0.00 43.21 3.58
5365 11666 1.066908 CTGGACCGTTTTGTGTTGCAT 59.933 47.619 0.00 0.00 0.00 3.96
5370 11671 2.223711 ACCGTTTTGTGTTGCATTCTCC 60.224 45.455 0.00 0.00 0.00 3.71
5373 11674 0.313672 TTTGTGTTGCATTCTCCGCC 59.686 50.000 0.00 0.00 0.00 6.13
5380 11681 1.321805 TGCATTCTCCGCCCCAAATG 61.322 55.000 0.00 0.00 33.31 2.32
5390 11691 2.755655 CCGCCCCAAATGTGTATGTAAA 59.244 45.455 0.00 0.00 0.00 2.01
5413 11714 5.565509 ACTTTGATCTTCTCCTTTCCTTCC 58.434 41.667 0.00 0.00 0.00 3.46
5425 11726 3.307059 CCTTTCCTTCCTCGTGAACATCT 60.307 47.826 0.00 0.00 0.00 2.90
5432 11733 5.348997 CCTTCCTCGTGAACATCTAGTTTTC 59.651 44.000 0.00 0.00 41.51 2.29
5433 11734 5.723672 TCCTCGTGAACATCTAGTTTTCT 57.276 39.130 0.00 0.00 41.51 2.52
5434 11735 6.097915 TCCTCGTGAACATCTAGTTTTCTT 57.902 37.500 0.00 0.00 41.51 2.52
5435 11736 6.522054 TCCTCGTGAACATCTAGTTTTCTTT 58.478 36.000 0.00 0.00 41.51 2.52
5436 11737 6.990349 TCCTCGTGAACATCTAGTTTTCTTTT 59.010 34.615 0.00 0.00 41.51 2.27
5437 11738 7.497909 TCCTCGTGAACATCTAGTTTTCTTTTT 59.502 33.333 0.00 0.00 41.51 1.94
5438 11739 7.798982 CCTCGTGAACATCTAGTTTTCTTTTTC 59.201 37.037 0.00 0.00 41.51 2.29
5439 11740 8.433421 TCGTGAACATCTAGTTTTCTTTTTCT 57.567 30.769 0.00 0.00 41.51 2.52
5440 11741 8.889717 TCGTGAACATCTAGTTTTCTTTTTCTT 58.110 29.630 0.00 0.00 41.51 2.52
5441 11742 9.159470 CGTGAACATCTAGTTTTCTTTTTCTTC 57.841 33.333 0.00 0.00 41.51 2.87
5442 11743 9.452065 GTGAACATCTAGTTTTCTTTTTCTTCC 57.548 33.333 0.00 0.00 41.51 3.46
5538 11873 4.054780 TCTCGAAATTAACTCGGATGGG 57.945 45.455 8.49 0.00 36.93 4.00
5617 11958 1.582610 AAAAGCATACCGCCACCACG 61.583 55.000 0.00 0.00 44.04 4.94
5643 11984 2.280186 GGCATCCACCCGATCGAC 60.280 66.667 18.66 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 4.528206 TCCTACTTCATCGATGCCACATAT 59.472 41.667 20.81 4.27 0.00 1.78
242 243 2.100418 GCCCCTTCTTTCTCATCAATGC 59.900 50.000 0.00 0.00 0.00 3.56
427 428 3.381169 CTCGGCGGCCATGAAAACG 62.381 63.158 20.71 2.02 0.00 3.60
664 737 2.428569 GAACACGTCGCGCAGAGA 60.429 61.111 8.75 0.00 0.00 3.10
786 871 3.192466 AGACATAAACGTGCCCGATTAC 58.808 45.455 0.00 0.00 34.72 1.89
873 4198 6.258160 GCCAGCAGTTTACTATTGTGTAATG 58.742 40.000 0.00 0.00 33.16 1.90
886 4211 0.616371 ATACGTGGGCCAGCAGTTTA 59.384 50.000 6.40 0.00 0.00 2.01
1345 7123 1.449246 CTTGAGCTCTTCGCCTGGG 60.449 63.158 16.19 0.00 40.39 4.45
1387 7165 3.066760 TGGATGTCGCACTGTCAGTATAG 59.933 47.826 4.85 0.32 0.00 1.31
1403 7181 4.895297 GGTGGGATAAAATCATGTGGATGT 59.105 41.667 0.00 0.00 36.02 3.06
1425 7203 1.076332 GGTCGTTTCAGATCAACGGG 58.924 55.000 14.55 0.00 45.70 5.28
1429 7207 2.519377 ACACGGTCGTTTCAGATCAA 57.481 45.000 0.00 0.00 0.00 2.57
1464 7250 5.762218 CCCTTGGAGTCAATCAATCAGATAC 59.238 44.000 0.00 0.00 35.39 2.24
1553 7351 5.524284 CAGGTGCTTAGCTAGTACTGTATG 58.476 45.833 5.39 0.00 39.23 2.39
1556 7354 2.166664 GCAGGTGCTTAGCTAGTACTGT 59.833 50.000 5.39 0.00 39.23 3.55
1557 7355 2.482142 GGCAGGTGCTTAGCTAGTACTG 60.482 54.545 5.39 7.63 39.23 2.74
1558 7356 1.757699 GGCAGGTGCTTAGCTAGTACT 59.242 52.381 5.60 0.00 39.23 2.73
1559 7357 1.202545 GGGCAGGTGCTTAGCTAGTAC 60.203 57.143 5.60 0.00 41.70 2.73
1560 7358 1.120530 GGGCAGGTGCTTAGCTAGTA 58.879 55.000 5.60 0.00 41.70 1.82
1650 7537 0.039326 AGAGCCAAGGCAGAGCAAAT 59.961 50.000 14.40 0.00 44.88 2.32
1717 7612 6.091034 TGACAAATTTAAATGCGCGAGTACTA 59.909 34.615 12.10 0.00 0.00 1.82
1720 7615 5.284428 TGACAAATTTAAATGCGCGAGTA 57.716 34.783 12.10 0.00 0.00 2.59
1754 7652 8.638629 ACCTATATCCTGTACTAGTCATTCAC 57.361 38.462 0.00 0.00 0.00 3.18
1828 7727 7.645340 GCCATAAAGTCATGTTTACATCATCAC 59.355 37.037 0.00 0.00 33.61 3.06
1843 7742 8.458573 AAATATGTTAATCGGCCATAAAGTCA 57.541 30.769 2.24 0.00 0.00 3.41
1850 7749 6.539173 TCCTGTAAATATGTTAATCGGCCAT 58.461 36.000 2.24 0.00 0.00 4.40
1878 7777 5.986135 CACAGCCTAAGTGATCAGTATTACC 59.014 44.000 2.79 0.00 39.30 2.85
1879 7778 6.574350 ACACAGCCTAAGTGATCAGTATTAC 58.426 40.000 2.79 0.00 40.16 1.89
1880 7779 6.791867 ACACAGCCTAAGTGATCAGTATTA 57.208 37.500 2.79 0.00 40.16 0.98
1908 7812 7.654022 TTCCAACAGAAAACCAAGAGTATTT 57.346 32.000 0.00 0.00 0.00 1.40
2227 8140 4.142026 GGGACTAAAGGCTTTGTTGTTGTT 60.142 41.667 22.32 0.00 0.00 2.83
2228 8141 3.383505 GGGACTAAAGGCTTTGTTGTTGT 59.616 43.478 22.32 10.58 0.00 3.32
2229 8142 3.383185 TGGGACTAAAGGCTTTGTTGTTG 59.617 43.478 22.32 7.79 0.00 3.33
2343 8256 4.530553 TCACCAAAGAACTAGCTATGGACA 59.469 41.667 14.35 0.00 0.00 4.02
2377 8290 5.449451 GGAGTCCGTAAAGAGAGATCTGAAC 60.449 48.000 0.00 0.00 0.00 3.18
2417 8330 0.035247 AAGAGAGGTCGGCGTAGACT 60.035 55.000 6.85 2.86 40.76 3.24
2791 8785 0.458260 ACTGAACCCCGTGCAAAAAC 59.542 50.000 0.00 0.00 0.00 2.43
2804 8798 5.007626 TGCTAAATCAAGTGTGACACTGAAC 59.992 40.000 20.19 4.19 44.62 3.18
2879 8873 7.442666 ACTTAGGCTAGCATTTATAGCTCAAAC 59.557 37.037 18.24 0.00 44.16 2.93
2882 8876 6.672266 ACTTAGGCTAGCATTTATAGCTCA 57.328 37.500 18.24 0.00 44.16 4.26
2963 8969 6.559810 TCACTGAAAACATAACCAACAACAG 58.440 36.000 0.00 0.00 0.00 3.16
3057 9064 4.991687 CACTCCTCTTTTCAGTCCACTTAC 59.008 45.833 0.00 0.00 0.00 2.34
3170 9177 6.726490 AGAAAGTACTCAGTGGTCTAAACA 57.274 37.500 0.00 0.00 0.00 2.83
3195 9202 6.017933 CACTATGATCGTTCTTTGCTTTCAC 58.982 40.000 0.00 0.00 0.00 3.18
3210 9217 7.615582 TTTGAACTTCATGGACACTATGATC 57.384 36.000 0.00 0.00 34.76 2.92
3221 9228 6.072286 AGTCTAGTGCAATTTGAACTTCATGG 60.072 38.462 15.20 2.57 37.46 3.66
3307 9365 8.838365 GCAAAGGGATATATCAGATGAATGATC 58.162 37.037 14.60 0.00 40.40 2.92
3353 9411 2.227194 GTCCGAACTGTTCCCATTGTT 58.773 47.619 14.48 0.00 0.00 2.83
3460 9521 7.129457 AGAAAGTGCTACATCATAATCCAGA 57.871 36.000 0.00 0.00 0.00 3.86
3488 9549 1.693606 TCCTGATGACACACAAGCAGA 59.306 47.619 0.00 0.00 37.24 4.26
3490 9551 2.221169 GTTCCTGATGACACACAAGCA 58.779 47.619 0.00 0.00 0.00 3.91
3491 9552 2.221169 TGTTCCTGATGACACACAAGC 58.779 47.619 0.00 0.00 0.00 4.01
3499 9560 5.359194 TCCTTTATCCTGTTCCTGATGAC 57.641 43.478 0.00 0.00 0.00 3.06
3616 9694 1.133199 TCCCAAAGAAACCCAGCACAT 60.133 47.619 0.00 0.00 0.00 3.21
3679 9759 4.318689 GGACGTTTTGCAATTGAATTGGTG 60.319 41.667 18.52 0.00 40.57 4.17
3684 9764 4.984161 CAGAAGGACGTTTTGCAATTGAAT 59.016 37.500 10.34 0.00 0.00 2.57
3756 9853 9.550406 CATTTGCCCTAATCACAATTATTCAAT 57.450 29.630 0.00 0.00 0.00 2.57
3777 9874 5.745294 GTGCATTATGCCAGTAAGACATTTG 59.255 40.000 15.06 0.00 44.23 2.32
3782 9879 2.287915 CGGTGCATTATGCCAGTAAGAC 59.712 50.000 15.06 3.98 44.23 3.01
3791 9888 1.467374 GGTCAACACGGTGCATTATGC 60.467 52.381 10.65 10.65 45.29 3.14
3802 9899 2.223688 TGGCTCAAAATTGGTCAACACG 60.224 45.455 0.00 0.00 0.00 4.49
3803 9900 3.068024 TCTGGCTCAAAATTGGTCAACAC 59.932 43.478 0.00 0.00 0.00 3.32
3930 10041 5.587289 AGCATCTCTCGTCTCAACTATTTC 58.413 41.667 0.00 0.00 0.00 2.17
4030 10141 9.860650 TTTGGTATATACATAGAAAACTGCCAT 57.139 29.630 14.70 0.00 0.00 4.40
4031 10142 9.860650 ATTTGGTATATACATAGAAAACTGCCA 57.139 29.630 14.70 0.00 0.00 4.92
4073 10185 2.710096 AGTTGGTAATGATCGGGGTG 57.290 50.000 0.00 0.00 0.00 4.61
4078 10190 8.593492 TCAAGAATGATAGTTGGTAATGATCG 57.407 34.615 0.00 0.00 0.00 3.69
4135 10247 8.726988 CCTACGAAAAGAATGAGAATTGGTAAA 58.273 33.333 0.00 0.00 0.00 2.01
4147 10259 4.330074 CAGCCACTACCTACGAAAAGAATG 59.670 45.833 0.00 0.00 0.00 2.67
4153 10265 0.899720 CCCAGCCACTACCTACGAAA 59.100 55.000 0.00 0.00 0.00 3.46
4156 10268 0.683504 AGACCCAGCCACTACCTACG 60.684 60.000 0.00 0.00 0.00 3.51
4221 10333 8.430801 AGTAGCTAAGAGAATAAAACAGCATG 57.569 34.615 0.00 0.00 46.00 4.06
4274 10388 6.058833 TGTAACAGAATTAGCACAAGGTGAA 58.941 36.000 0.00 0.00 35.23 3.18
4341 10456 7.827701 TCAGTTTGGTAACTACTATCACTCTG 58.172 38.462 0.00 0.00 42.67 3.35
4358 10473 2.614057 GCTTCACGGGATATCAGTTTGG 59.386 50.000 4.83 0.00 0.00 3.28
4396 10511 7.182930 AGACAAATATTTAGGAACAGAGGGAGT 59.817 37.037 0.00 0.00 0.00 3.85
4397 10512 7.569240 AGACAAATATTTAGGAACAGAGGGAG 58.431 38.462 0.00 0.00 0.00 4.30
4399 10514 8.581253 AAAGACAAATATTTAGGAACAGAGGG 57.419 34.615 0.00 0.00 0.00 4.30
4400 10515 9.454859 AGAAAGACAAATATTTAGGAACAGAGG 57.545 33.333 0.00 0.00 0.00 3.69
4416 10531 9.354673 ACCATTTGAAATCTCTAGAAAGACAAA 57.645 29.630 0.00 4.41 0.00 2.83
4417 10532 8.924511 ACCATTTGAAATCTCTAGAAAGACAA 57.075 30.769 0.00 0.00 0.00 3.18
4418 10533 8.156820 TGACCATTTGAAATCTCTAGAAAGACA 58.843 33.333 0.00 0.00 0.00 3.41
4419 10534 8.447053 GTGACCATTTGAAATCTCTAGAAAGAC 58.553 37.037 0.00 0.00 0.00 3.01
4420 10535 7.607991 GGTGACCATTTGAAATCTCTAGAAAGA 59.392 37.037 0.00 0.00 0.00 2.52
4421 10536 7.391554 TGGTGACCATTTGAAATCTCTAGAAAG 59.608 37.037 0.00 0.00 0.00 2.62
4422 10537 7.174946 GTGGTGACCATTTGAAATCTCTAGAAA 59.825 37.037 7.94 0.00 35.28 2.52
4423 10538 6.655003 GTGGTGACCATTTGAAATCTCTAGAA 59.345 38.462 7.94 0.00 35.28 2.10
4424 10539 6.173339 GTGGTGACCATTTGAAATCTCTAGA 58.827 40.000 7.94 0.00 35.28 2.43
4425 10540 5.939883 TGTGGTGACCATTTGAAATCTCTAG 59.060 40.000 7.94 0.00 35.28 2.43
4426 10541 5.875224 TGTGGTGACCATTTGAAATCTCTA 58.125 37.500 7.94 0.00 35.28 2.43
4427 10542 4.728772 TGTGGTGACCATTTGAAATCTCT 58.271 39.130 7.94 0.00 35.28 3.10
4428 10543 5.649782 ATGTGGTGACCATTTGAAATCTC 57.350 39.130 7.94 0.00 35.28 2.75
4429 10544 5.123820 CGTATGTGGTGACCATTTGAAATCT 59.876 40.000 7.94 0.00 35.28 2.40
4430 10545 5.331902 CGTATGTGGTGACCATTTGAAATC 58.668 41.667 7.94 0.00 35.28 2.17
4431 10546 4.157656 CCGTATGTGGTGACCATTTGAAAT 59.842 41.667 7.94 0.00 35.28 2.17
4432 10547 3.504134 CCGTATGTGGTGACCATTTGAAA 59.496 43.478 7.94 0.00 35.28 2.69
4433 10548 3.078097 CCGTATGTGGTGACCATTTGAA 58.922 45.455 7.94 0.00 35.28 2.69
4434 10549 2.303311 TCCGTATGTGGTGACCATTTGA 59.697 45.455 7.94 0.00 35.28 2.69
4435 10550 2.705730 TCCGTATGTGGTGACCATTTG 58.294 47.619 7.94 0.00 35.28 2.32
4436 10551 3.278574 CATCCGTATGTGGTGACCATTT 58.721 45.455 7.94 0.45 35.28 2.32
4437 10552 2.238646 ACATCCGTATGTGGTGACCATT 59.761 45.455 7.94 0.86 44.79 3.16
4438 10553 1.837439 ACATCCGTATGTGGTGACCAT 59.163 47.619 7.94 0.00 44.79 3.55
4439 10554 1.271856 ACATCCGTATGTGGTGACCA 58.728 50.000 0.00 0.00 44.79 4.02
4440 10555 3.746045 ATACATCCGTATGTGGTGACC 57.254 47.619 3.56 0.00 45.99 4.02
4441 10556 7.094506 TGTCTATATACATCCGTATGTGGTGAC 60.095 40.741 3.56 5.93 45.99 3.67
4442 10557 6.943718 TGTCTATATACATCCGTATGTGGTGA 59.056 38.462 3.56 0.00 45.99 4.02
4443 10558 7.153217 TGTCTATATACATCCGTATGTGGTG 57.847 40.000 3.56 0.00 45.99 4.17
4444 10559 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
4477 10592 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
4478 10593 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
4479 10594 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
4480 10595 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
4481 10596 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
4482 10597 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
4483 10598 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
4484 10599 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
4485 10600 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
4486 10601 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
4487 10602 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
4488 10603 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
4489 10604 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
4490 10605 4.034048 GGTGACTACATACGGAGCAAAATG 59.966 45.833 0.00 0.00 0.00 2.32
4491 10606 4.189231 GGTGACTACATACGGAGCAAAAT 58.811 43.478 0.00 0.00 0.00 1.82
4492 10607 3.007074 TGGTGACTACATACGGAGCAAAA 59.993 43.478 0.00 0.00 0.00 2.44
4493 10608 2.563620 TGGTGACTACATACGGAGCAAA 59.436 45.455 0.00 0.00 0.00 3.68
4494 10609 2.172679 TGGTGACTACATACGGAGCAA 58.827 47.619 0.00 0.00 0.00 3.91
4495 10610 1.842052 TGGTGACTACATACGGAGCA 58.158 50.000 0.00 0.00 0.00 4.26
4496 10611 3.454371 AATGGTGACTACATACGGAGC 57.546 47.619 0.00 0.00 0.00 4.70
4497 10612 5.006153 TCAAATGGTGACTACATACGGAG 57.994 43.478 0.00 0.00 0.00 4.63
4498 10613 5.408880 TTCAAATGGTGACTACATACGGA 57.591 39.130 0.00 0.00 35.39 4.69
4499 10614 5.163794 GGTTTCAAATGGTGACTACATACGG 60.164 44.000 0.00 0.00 35.39 4.02
4500 10615 5.642063 AGGTTTCAAATGGTGACTACATACG 59.358 40.000 0.00 0.00 35.39 3.06
4501 10616 6.879458 AGAGGTTTCAAATGGTGACTACATAC 59.121 38.462 0.00 0.00 35.39 2.39
4502 10617 7.016153 AGAGGTTTCAAATGGTGACTACATA 57.984 36.000 0.00 0.00 35.39 2.29
4503 10618 5.880901 AGAGGTTTCAAATGGTGACTACAT 58.119 37.500 0.00 0.00 35.39 2.29
4504 10619 5.304686 AGAGGTTTCAAATGGTGACTACA 57.695 39.130 0.00 0.00 35.39 2.74
4505 10620 6.698380 TCTAGAGGTTTCAAATGGTGACTAC 58.302 40.000 0.00 0.00 35.39 2.73
4506 10621 6.928348 TCTAGAGGTTTCAAATGGTGACTA 57.072 37.500 0.00 0.00 35.39 2.59
4507 10622 5.825593 TCTAGAGGTTTCAAATGGTGACT 57.174 39.130 0.00 0.00 35.39 3.41
4508 10623 6.710744 TCTTTCTAGAGGTTTCAAATGGTGAC 59.289 38.462 0.00 0.00 35.39 3.67
4509 10624 6.710744 GTCTTTCTAGAGGTTTCAAATGGTGA 59.289 38.462 0.00 0.00 0.00 4.02
4510 10625 6.486657 TGTCTTTCTAGAGGTTTCAAATGGTG 59.513 38.462 0.00 0.00 0.00 4.17
4511 10626 6.601332 TGTCTTTCTAGAGGTTTCAAATGGT 58.399 36.000 0.00 0.00 0.00 3.55
4512 10627 7.510549 TTGTCTTTCTAGAGGTTTCAAATGG 57.489 36.000 0.00 0.00 0.00 3.16
4524 10639 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
4525 10640 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
4526 10641 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
4527 10642 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
4528 10643 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
4529 10644 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
4530 10645 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
4531 10646 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
4532 10647 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
4533 10648 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
4534 10649 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
4535 10650 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
4536 10651 7.628501 AATACTCCCTCCGTTCCTAAATATT 57.371 36.000 0.00 0.00 0.00 1.28
4537 10652 7.450903 CAAATACTCCCTCCGTTCCTAAATAT 58.549 38.462 0.00 0.00 0.00 1.28
4538 10653 6.183361 CCAAATACTCCCTCCGTTCCTAAATA 60.183 42.308 0.00 0.00 0.00 1.40
4539 10654 5.397559 CCAAATACTCCCTCCGTTCCTAAAT 60.398 44.000 0.00 0.00 0.00 1.40
4540 10655 4.080751 CCAAATACTCCCTCCGTTCCTAAA 60.081 45.833 0.00 0.00 0.00 1.85
4541 10656 3.453353 CCAAATACTCCCTCCGTTCCTAA 59.547 47.826 0.00 0.00 0.00 2.69
4542 10657 3.036091 CCAAATACTCCCTCCGTTCCTA 58.964 50.000 0.00 0.00 0.00 2.94
4543 10658 1.838077 CCAAATACTCCCTCCGTTCCT 59.162 52.381 0.00 0.00 0.00 3.36
4544 10659 1.746171 GCCAAATACTCCCTCCGTTCC 60.746 57.143 0.00 0.00 0.00 3.62
4545 10660 1.065709 TGCCAAATACTCCCTCCGTTC 60.066 52.381 0.00 0.00 0.00 3.95
4546 10661 0.988832 TGCCAAATACTCCCTCCGTT 59.011 50.000 0.00 0.00 0.00 4.44
4547 10662 0.541863 CTGCCAAATACTCCCTCCGT 59.458 55.000 0.00 0.00 0.00 4.69
4548 10663 0.830648 TCTGCCAAATACTCCCTCCG 59.169 55.000 0.00 0.00 0.00 4.63
4549 10664 3.217626 CATTCTGCCAAATACTCCCTCC 58.782 50.000 0.00 0.00 0.00 4.30
4550 10665 3.217626 CCATTCTGCCAAATACTCCCTC 58.782 50.000 0.00 0.00 0.00 4.30
4551 10666 2.687914 GCCATTCTGCCAAATACTCCCT 60.688 50.000 0.00 0.00 0.00 4.20
4552 10667 1.683385 GCCATTCTGCCAAATACTCCC 59.317 52.381 0.00 0.00 0.00 4.30
4553 10668 2.360165 CTGCCATTCTGCCAAATACTCC 59.640 50.000 0.00 0.00 0.00 3.85
4554 10669 3.282021 TCTGCCATTCTGCCAAATACTC 58.718 45.455 0.00 0.00 0.00 2.59
4555 10670 3.285484 CTCTGCCATTCTGCCAAATACT 58.715 45.455 0.00 0.00 0.00 2.12
4556 10671 2.223665 GCTCTGCCATTCTGCCAAATAC 60.224 50.000 0.00 0.00 0.00 1.89
4636 10751 1.024579 ACAGTAGGCGCAATTTCCCG 61.025 55.000 10.83 0.00 0.00 5.14
4660 10775 1.224069 CTAACCATGCCCGAGATGCG 61.224 60.000 0.00 0.00 40.47 4.73
4691 10806 2.757314 GGGGAAAAGCATCAGGAAGAAG 59.243 50.000 0.00 0.00 0.00 2.85
4694 10809 2.494870 CAAGGGGAAAAGCATCAGGAAG 59.505 50.000 0.00 0.00 0.00 3.46
4704 10819 4.996758 CCTAAATGTTTGCAAGGGGAAAAG 59.003 41.667 0.00 0.00 36.03 2.27
4706 10821 4.039852 GTCCTAAATGTTTGCAAGGGGAAA 59.960 41.667 0.00 0.00 31.39 3.13
4737 10852 5.674525 TCACGAGCCTTCAGAATTCATAAT 58.325 37.500 8.44 0.00 0.00 1.28
4747 10866 2.897436 TCATGAATCACGAGCCTTCAG 58.103 47.619 0.00 0.00 32.82 3.02
4828 10948 4.708726 AGCAATACCAAAGATGCAACTC 57.291 40.909 0.00 0.00 41.18 3.01
4838 10958 8.540388 AGACTAGTTATCAGAAGCAATACCAAA 58.460 33.333 0.00 0.00 0.00 3.28
4960 11084 2.825532 GTGTGGGTACAGCAAATGGATT 59.174 45.455 0.00 0.00 37.52 3.01
4979 11103 1.306148 ATCAAGCGATGCATGAGGTG 58.694 50.000 2.46 0.00 39.56 4.00
4980 11104 1.945394 GAATCAAGCGATGCATGAGGT 59.055 47.619 2.46 0.00 39.56 3.85
5056 11180 7.391620 TCATCAAGAGGTAACCGAAAAAGTAT 58.608 34.615 0.00 0.00 37.17 2.12
5063 11187 5.128663 TCATCATCATCAAGAGGTAACCGAA 59.871 40.000 0.00 0.00 37.17 4.30
5065 11189 4.948847 TCATCATCATCAAGAGGTAACCG 58.051 43.478 0.00 0.00 37.17 4.44
5066 11190 6.528321 TCATCATCATCATCAAGAGGTAACC 58.472 40.000 0.00 0.00 37.17 2.85
5067 11191 7.876582 TCATCATCATCATCATCAAGAGGTAAC 59.123 37.037 0.00 0.00 0.00 2.50
5074 11198 8.498054 TCATCATCATCATCATCATCATCAAG 57.502 34.615 0.00 0.00 0.00 3.02
5077 11201 9.771534 ACTATCATCATCATCATCATCATCATC 57.228 33.333 0.00 0.00 0.00 2.92
5078 11202 9.553064 CACTATCATCATCATCATCATCATCAT 57.447 33.333 0.00 0.00 0.00 2.45
5097 11221 3.902261 CAAAGCTGTGTTGCACTATCA 57.098 42.857 0.00 0.00 35.11 2.15
5132 11256 2.664436 CGTGTCGCGGAAAGGGAAC 61.664 63.158 6.13 0.00 43.70 3.62
5133 11257 2.356553 CGTGTCGCGGAAAGGGAA 60.357 61.111 6.13 0.00 43.70 3.97
5150 11274 3.096092 TGGGATTACAAATGCTTGTCCC 58.904 45.455 6.99 6.99 42.25 4.46
5152 11276 5.634859 CAGTTTGGGATTACAAATGCTTGTC 59.365 40.000 0.00 0.00 42.25 3.18
5160 11284 8.387813 AGATAACCTACAGTTTGGGATTACAAA 58.612 33.333 0.00 0.00 40.05 2.83
5169 11293 5.429130 GGGAGAAGATAACCTACAGTTTGG 58.571 45.833 0.00 0.00 40.05 3.28
5229 11508 4.250431 GGGCGCACACACACACAC 62.250 66.667 10.83 0.00 0.00 3.82
5230 11509 4.785453 TGGGCGCACACACACACA 62.785 61.111 9.15 0.00 0.00 3.72
5231 11510 3.468266 CTTGGGCGCACACACACAC 62.468 63.158 14.54 0.00 0.00 3.82
5232 11511 3.208383 CTTGGGCGCACACACACA 61.208 61.111 14.54 0.00 0.00 3.72
5242 11521 4.303257 GAGGTTTCCTCTTGGGCG 57.697 61.111 8.38 0.00 46.41 6.13
5351 11652 2.043411 CGGAGAATGCAACACAAAACG 58.957 47.619 0.00 0.00 0.00 3.60
5365 11666 0.693622 TACACATTTGGGGCGGAGAA 59.306 50.000 0.00 0.00 0.00 2.87
5370 11671 3.442273 AGTTTACATACACATTTGGGGCG 59.558 43.478 0.00 0.00 0.00 6.13
5373 11674 8.522830 AGATCAAAGTTTACATACACATTTGGG 58.477 33.333 0.00 0.00 0.00 4.12
5380 11681 8.779354 AGGAGAAGATCAAAGTTTACATACAC 57.221 34.615 0.00 0.00 0.00 2.90
5390 11691 5.311913 AGGAAGGAAAGGAGAAGATCAAAGT 59.688 40.000 0.00 0.00 0.00 2.66
5413 11714 8.552034 AGAAAAAGAAAACTAGATGTTCACGAG 58.448 33.333 0.00 0.00 38.03 4.18
5511 11846 3.491267 CCGAGTTAATTTCGAGATCCTGC 59.509 47.826 12.28 0.00 40.36 4.85
5518 11853 3.793559 ACCCATCCGAGTTAATTTCGAG 58.206 45.455 12.28 4.89 40.36 4.04


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

AutoCloner maintained by Alex Coulton.