Multiple sequence alignment - TraesCS3B01G325100

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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 TraesCS3B01G325100 chr3B 100.000 9251 0 0 1 9251 525998937 525989687 0.000000e+00 17084.0
1 TraesCS3B01G325100 chr3B 83.871 496 65 5 1523 2015 525993208 525992725 8.940000e-125 459.0
2 TraesCS3B01G325100 chr3B 83.871 496 65 5 5730 6213 525997415 525996923 8.940000e-125 459.0
3 TraesCS3B01G325100 chr3B 100.000 205 0 0 9563 9767 525989375 525989171 7.160000e-101 379.0
4 TraesCS3B01G325100 chr3B 87.065 201 25 1 1469 1668 526001690 526001490 9.870000e-55 226.0
5 TraesCS3B01G325100 chr3B 79.638 221 22 11 5370 5577 525993505 525993295 4.760000e-28 137.0
6 TraesCS3B01G325100 chr3B 79.638 221 22 11 5433 5643 525993568 525993361 4.760000e-28 137.0
7 TraesCS3B01G325100 chr3B 79.861 144 23 4 6951 7091 416809443 416809303 6.240000e-17 100.0
8 TraesCS3B01G325100 chr3B 96.000 50 2 0 650 699 526014655 526014606 2.260000e-11 82.4
9 TraesCS3B01G325100 chr3B 78.899 109 20 3 9640 9746 451310088 451309981 4.890000e-08 71.3
10 TraesCS3B01G325100 chr3B 91.111 45 2 1 767 809 526002113 526002069 1.060000e-04 60.2
11 TraesCS3B01G325100 chr3D 89.394 5695 361 98 3712 9251 400316299 400310693 0.000000e+00 6946.0
12 TraesCS3B01G325100 chr3D 88.828 2175 139 38 2 2122 400320424 400318300 0.000000e+00 2575.0
13 TraesCS3B01G325100 chr3D 85.282 496 58 7 1523 2015 400314249 400313766 1.890000e-136 497.0
14 TraesCS3B01G325100 chr3D 83.394 548 75 7 5679 6218 400318949 400318410 2.450000e-135 494.0
15 TraesCS3B01G325100 chr3D 81.102 508 65 21 5779 6259 400322798 400322295 2.570000e-100 377.0
16 TraesCS3B01G325100 chr3D 95.610 205 8 1 9563 9767 400310635 400310432 2.630000e-85 327.0
17 TraesCS3B01G325100 chr3D 78.112 498 83 16 1572 2053 400322798 400322311 9.590000e-75 292.0
18 TraesCS3B01G325100 chr3D 87.417 151 19 0 1518 1668 400322798 400322648 3.630000e-39 174.0
19 TraesCS3B01G325100 chr3D 89.781 137 10 4 641 773 400323388 400323252 1.300000e-38 172.0
20 TraesCS3B01G325100 chr3D 79.638 221 22 11 5433 5643 400314618 400314411 4.760000e-28 137.0
21 TraesCS3B01G325100 chr3D 78.571 224 25 11 5367 5577 400314558 400314345 1.030000e-24 126.0
22 TraesCS3B01G325100 chr3D 74.150 294 67 8 6804 7091 304978065 304978355 8.020000e-21 113.0
23 TraesCS3B01G325100 chr3D 91.111 45 2 1 767 809 400323217 400323173 1.060000e-04 60.2
24 TraesCS3B01G325100 chr3A 86.822 2193 145 49 4512 6612 519248771 519246631 0.000000e+00 2316.0
25 TraesCS3B01G325100 chr3A 90.618 1343 49 24 6576 7872 519246630 519245319 0.000000e+00 1711.0
26 TraesCS3B01G325100 chr3A 88.492 1121 68 22 1 1089 519252612 519251521 0.000000e+00 1299.0
27 TraesCS3B01G325100 chr3A 94.744 704 26 5 8324 9020 519244959 519244260 0.000000e+00 1085.0
28 TraesCS3B01G325100 chr3A 91.055 559 29 9 1071 1617 519251572 519251023 0.000000e+00 736.0
29 TraesCS3B01G325100 chr3A 90.214 562 34 10 1577 2126 519251117 519250565 0.000000e+00 713.0
30 TraesCS3B01G325100 chr3A 93.275 342 15 2 7926 8262 519245321 519244983 1.890000e-136 497.0
31 TraesCS3B01G325100 chr3A 83.521 443 64 2 5782 6218 519251119 519250680 1.180000e-108 405.0
32 TraesCS3B01G325100 chr3A 89.000 300 29 4 4125 4423 519249098 519248802 1.550000e-97 368.0
33 TraesCS3B01G325100 chr3A 86.145 332 36 5 5931 6253 519254876 519254546 5.610000e-92 350.0
34 TraesCS3B01G325100 chr3A 93.659 205 12 1 9563 9767 519243780 519243577 1.230000e-78 305.0
35 TraesCS3B01G325100 chr3A 78.499 493 80 14 1577 2053 519255038 519254556 5.730000e-77 300.0
36 TraesCS3B01G325100 chr3A 87.333 150 16 1 1198 1347 519251397 519251251 1.690000e-37 169.0
37 TraesCS3B01G325100 chr3A 74.229 454 59 35 5433 5863 519247880 519247462 4.760000e-28 137.0
38 TraesCS3B01G325100 chr3A 84.286 140 10 5 5367 5494 519247820 519247681 1.030000e-24 126.0
39 TraesCS3B01G325100 chr3A 91.111 45 2 1 767 809 519255543 519255499 1.060000e-04 60.2
40 TraesCS3B01G325100 chr2B 82.625 800 90 21 2369 3156 781532627 781531865 0.000000e+00 662.0
41 TraesCS3B01G325100 chr2B 84.281 299 40 3 3329 3620 781531540 781531242 1.610000e-72 285.0
42 TraesCS3B01G325100 chr2B 89.116 147 16 0 3185 3331 781531865 781531719 6.020000e-42 183.0
43 TraesCS3B01G325100 chr6B 89.412 255 9 6 2938 3184 707528126 707527882 1.230000e-78 305.0
44 TraesCS3B01G325100 chr6B 100.000 30 0 0 2373 2402 563127576 563127547 1.000000e-03 56.5
45 TraesCS3B01G325100 chr1B 80.758 343 50 10 6768 7096 580622544 580622884 4.530000e-63 254.0
46 TraesCS3B01G325100 chr1B 87.342 79 10 0 9682 9760 514823648 514823726 3.760000e-14 91.6
47 TraesCS3B01G325100 chr1D 80.702 342 50 11 6768 7095 429599513 429599852 1.630000e-62 252.0
48 TraesCS3B01G325100 chr4D 81.754 285 43 6 6804 7079 394967809 394968093 7.630000e-56 230.0
49 TraesCS3B01G325100 chr4D 84.286 70 11 0 7360 7429 394968274 394968343 1.760000e-07 69.4
50 TraesCS3B01G325100 chr4D 85.000 60 7 2 3680 3738 465162310 465162252 1.060000e-04 60.2
51 TraesCS3B01G325100 chr4A 81.754 285 43 6 6804 7079 76627427 76627711 7.630000e-56 230.0
52 TraesCS3B01G325100 chr4A 93.182 44 3 0 7360 7403 76627888 76627931 2.280000e-06 65.8
53 TraesCS3B01G325100 chr4B 80.135 297 50 7 6804 7091 486207201 486206905 7.680000e-51 213.0
54 TraesCS3B01G325100 chr4B 82.895 76 13 0 7360 7435 486206742 486206667 1.760000e-07 69.4
55 TraesCS3B01G325100 chr5D 83.908 87 12 2 9682 9767 319262087 319262002 2.260000e-11 82.4
56 TraesCS3B01G325100 chr5A 86.792 53 6 1 4514 4566 657391124 657391175 3.810000e-04 58.4


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 TraesCS3B01G325100 chr3B 525989171 525998937 9766 True 8731.500000 17084 100.000000 1 9767 2 chr3B.!!$R4 9766
1 TraesCS3B01G325100 chr3B 525992725 525997415 4690 True 298.000000 459 81.754500 1523 6213 4 chr3B.!!$R5 4690
2 TraesCS3B01G325100 chr3D 400310432 400323388 12956 True 1014.766667 6946 85.686667 2 9767 12 chr3D.!!$R1 9765
3 TraesCS3B01G325100 chr3A 519243577 519255543 11966 True 661.075000 2316 87.687687 1 9767 16 chr3A.!!$R1 9766
4 TraesCS3B01G325100 chr2B 781531242 781532627 1385 True 376.666667 662 85.340667 2369 3620 3 chr2B.!!$R1 1251

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
477 3469 0.102120 CGGACTCATCTCCACAGCTC 59.898 60.0 0.00 0.00 0.00 4.09 F
1059 4092 0.029035 CGGTTACTCCATCTCCGACG 59.971 60.0 0.00 0.00 43.22 5.12 F
1179 4233 0.044092 TGAATAGCCCACCTCCTCCA 59.956 55.0 0.00 0.00 0.00 3.86 F
1504 4570 0.107654 CCCGGTGAATTCTCCTCCAC 60.108 60.0 21.11 4.80 0.00 4.02 F
1505 4571 0.107654 CCGGTGAATTCTCCTCCACC 60.108 60.0 21.11 12.12 44.08 4.61 F
6412 12095 0.179062 GCGCCATTCTCTCCTGATGT 60.179 55.0 0.00 0.00 0.00 3.06 F
6895 12636 0.250124 TGTACAAGGGCACGGTGAAG 60.250 55.0 13.29 0.00 0.00 3.02 F
7161 12912 0.387367 CCGACCGACTGACACAAGAG 60.387 60.0 0.00 0.00 0.00 2.85 F
7163 12914 0.674534 GACCGACTGACACAAGAGGT 59.325 55.0 0.00 0.00 35.53 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1479 4545 0.037734 GAGAATTCACCGGGGGTTGT 59.962 55.000 2.42 0.0 31.02 3.32 R
6252 11926 2.203195 GACCGGGCATATGCAGCA 60.203 61.111 28.07 0.0 44.36 4.41 R
6273 11948 0.725784 GCGTGTCAAGAATGGCGTTG 60.726 55.000 0.00 0.0 32.34 4.10 R
6625 12362 0.240945 AATCCGCTGGCACGAAAAAG 59.759 50.000 10.33 0.0 34.06 2.27 R
6797 12538 2.483745 CAGCTCGTCGTAGCCGAA 59.516 61.111 11.45 0.0 37.54 4.30 R
7701 13495 0.032403 CGGTGGCGTAATATTCCGGA 59.968 55.000 0.00 0.0 35.25 5.14 R
7903 13699 0.108138 GGCGCAACCATCTCAGTACT 60.108 55.000 10.83 0.0 38.86 2.73 R
8333 14136 0.110464 GAGCGAGTCACTTTGCTTGC 60.110 55.000 6.92 0.0 41.24 4.01 R
8785 14595 0.174845 TTGATCACCCGCTCGTAAGG 59.825 55.000 0.00 0.0 38.47 2.69 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
49 3013 7.283329 AGATGATAGATGCATGCATGATACAT 58.717 34.615 36.73 29.82 36.70 2.29
71 3038 7.414436 ACATATGCTCGTGCGTATTTTAAAAT 58.586 30.769 18.88 17.18 45.99 1.82
231 3223 6.115448 ACTACTCTTAGTCACCAATGCTTT 57.885 37.500 0.00 0.00 32.67 3.51
234 3226 5.865085 ACTCTTAGTCACCAATGCTTTGTA 58.135 37.500 11.03 0.00 0.00 2.41
276 3268 3.655777 TCTTTCTCCCACCCATGTTAGTT 59.344 43.478 0.00 0.00 0.00 2.24
308 3300 0.176680 CTGGCCTCATAGTGTTCGCT 59.823 55.000 3.32 0.00 0.00 4.93
318 3310 0.396435 AGTGTTCGCTTCACCCATGA 59.604 50.000 0.00 0.00 36.58 3.07
322 3314 0.534873 TTCGCTTCACCCATGATCGA 59.465 50.000 0.00 0.00 37.98 3.59
388 3380 2.475466 CGAGCCTCTACGCCCGTTA 61.475 63.158 0.00 0.00 0.00 3.18
432 3424 1.708551 CCTAAAAACCACTCCTCCCCA 59.291 52.381 0.00 0.00 0.00 4.96
455 3447 2.679996 GCACCCCCACCATCAACC 60.680 66.667 0.00 0.00 0.00 3.77
456 3448 2.037208 CACCCCCACCATCAACCC 59.963 66.667 0.00 0.00 0.00 4.11
465 3457 2.264480 CATCAACCCGCGGACTCA 59.736 61.111 30.73 8.15 0.00 3.41
474 3466 1.226802 CGCGGACTCATCTCCACAG 60.227 63.158 0.00 0.00 0.00 3.66
475 3467 1.520342 GCGGACTCATCTCCACAGC 60.520 63.158 0.00 0.00 0.00 4.40
476 3468 1.954362 GCGGACTCATCTCCACAGCT 61.954 60.000 0.00 0.00 0.00 4.24
477 3469 0.102120 CGGACTCATCTCCACAGCTC 59.898 60.000 0.00 0.00 0.00 4.09
478 3470 1.189752 GGACTCATCTCCACAGCTCA 58.810 55.000 0.00 0.00 0.00 4.26
479 3471 1.134848 GGACTCATCTCCACAGCTCAC 60.135 57.143 0.00 0.00 0.00 3.51
480 3472 0.529833 ACTCATCTCCACAGCTCACG 59.470 55.000 0.00 0.00 0.00 4.35
603 3601 1.974265 TGCATCTTGACCGAAACCAA 58.026 45.000 0.00 0.00 0.00 3.67
604 3602 2.302260 TGCATCTTGACCGAAACCAAA 58.698 42.857 0.00 0.00 0.00 3.28
605 3603 2.890311 TGCATCTTGACCGAAACCAAAT 59.110 40.909 0.00 0.00 0.00 2.32
606 3604 3.320541 TGCATCTTGACCGAAACCAAATT 59.679 39.130 0.00 0.00 0.00 1.82
609 3607 5.107491 GCATCTTGACCGAAACCAAATTTTC 60.107 40.000 0.00 0.00 32.92 2.29
615 3613 7.066374 TGACCGAAACCAAATTTTCTTTTTG 57.934 32.000 0.00 0.00 33.93 2.44
698 3703 3.071167 GGCCCGGTCAATCTTATCTAACT 59.929 47.826 0.00 0.00 0.00 2.24
704 3709 6.041751 CCGGTCAATCTTATCTAACTAACCCT 59.958 42.308 0.00 0.00 0.00 4.34
764 3772 3.632604 GCCTATTCTTTTACAGAAGCCCC 59.367 47.826 0.00 0.00 45.11 5.80
810 3823 2.767505 CTTGAACCCAGTAAGCGAAGT 58.232 47.619 0.00 0.00 0.00 3.01
836 3849 3.598019 GAAGAATTCTGCATGGCCAAA 57.402 42.857 10.96 0.00 43.23 3.28
837 3850 3.256558 GAAGAATTCTGCATGGCCAAAC 58.743 45.455 10.96 5.25 43.23 2.93
838 3851 2.532843 AGAATTCTGCATGGCCAAACT 58.467 42.857 10.96 0.00 0.00 2.66
839 3852 3.700538 AGAATTCTGCATGGCCAAACTA 58.299 40.909 10.96 0.00 0.00 2.24
840 3853 4.088634 AGAATTCTGCATGGCCAAACTAA 58.911 39.130 10.96 0.85 0.00 2.24
841 3854 4.159135 AGAATTCTGCATGGCCAAACTAAG 59.841 41.667 10.96 3.54 0.00 2.18
842 3855 1.176527 TCTGCATGGCCAAACTAAGC 58.823 50.000 10.96 8.13 0.00 3.09
843 3856 0.889994 CTGCATGGCCAAACTAAGCA 59.110 50.000 10.96 12.50 0.00 3.91
844 3857 1.273048 CTGCATGGCCAAACTAAGCAA 59.727 47.619 10.96 0.00 0.00 3.91
845 3858 1.690893 TGCATGGCCAAACTAAGCAAA 59.309 42.857 10.96 0.00 0.00 3.68
846 3859 2.068519 GCATGGCCAAACTAAGCAAAC 58.931 47.619 10.96 0.00 0.00 2.93
847 3860 2.687370 CATGGCCAAACTAAGCAAACC 58.313 47.619 10.96 0.00 0.00 3.27
848 3861 1.044611 TGGCCAAACTAAGCAAACCC 58.955 50.000 0.61 0.00 0.00 4.11
895 3922 3.370103 CCGTACTGAGTCTTCTCCTCTCT 60.370 52.174 0.00 0.00 39.75 3.10
915 3942 1.956869 TCTCCTCTCTTTGCCCATCA 58.043 50.000 0.00 0.00 0.00 3.07
921 3948 4.345257 TCCTCTCTTTGCCCATCAGTATAC 59.655 45.833 0.00 0.00 0.00 1.47
924 3951 6.212388 CCTCTCTTTGCCCATCAGTATACTAT 59.788 42.308 4.74 0.00 0.00 2.12
963 3993 3.818773 GCCTTGCTCACAGTTAAACCTTA 59.181 43.478 0.00 0.00 0.00 2.69
1047 4080 3.698820 GGGTCGCCACCGGTTACT 61.699 66.667 2.97 0.00 44.91 2.24
1048 4081 2.125793 GGTCGCCACCGGTTACTC 60.126 66.667 2.97 0.00 31.06 2.59
1049 4082 2.125793 GTCGCCACCGGTTACTCC 60.126 66.667 2.97 0.00 34.56 3.85
1050 4083 2.601067 TCGCCACCGGTTACTCCA 60.601 61.111 2.97 0.00 35.57 3.86
1051 4084 1.985662 TCGCCACCGGTTACTCCAT 60.986 57.895 2.97 0.00 35.57 3.41
1052 4085 1.520787 CGCCACCGGTTACTCCATC 60.521 63.158 2.97 0.00 35.57 3.51
1053 4086 1.905512 GCCACCGGTTACTCCATCT 59.094 57.895 2.97 0.00 35.57 2.90
1054 4087 0.179081 GCCACCGGTTACTCCATCTC 60.179 60.000 2.97 0.00 35.57 2.75
1055 4088 0.464452 CCACCGGTTACTCCATCTCC 59.536 60.000 2.97 0.00 35.57 3.71
1056 4089 0.102481 CACCGGTTACTCCATCTCCG 59.898 60.000 2.97 0.00 40.72 4.63
1057 4090 0.033796 ACCGGTTACTCCATCTCCGA 60.034 55.000 0.00 0.00 43.22 4.55
1058 4091 0.384669 CCGGTTACTCCATCTCCGAC 59.615 60.000 0.00 0.00 43.22 4.79
1059 4092 0.029035 CGGTTACTCCATCTCCGACG 59.971 60.000 0.00 0.00 43.22 5.12
1060 4093 0.248949 GGTTACTCCATCTCCGACGC 60.249 60.000 0.00 0.00 35.97 5.19
1061 4094 0.248949 GTTACTCCATCTCCGACGCC 60.249 60.000 0.00 0.00 0.00 5.68
1062 4095 1.721664 TTACTCCATCTCCGACGCCG 61.722 60.000 0.00 0.00 0.00 6.46
1063 4096 4.933064 CTCCATCTCCGACGCCGC 62.933 72.222 0.00 0.00 0.00 6.53
1069 4102 4.124351 CTCCGACGCCGCCTGTTA 62.124 66.667 0.00 0.00 0.00 2.41
1070 4103 4.424566 TCCGACGCCGCCTGTTAC 62.425 66.667 0.00 0.00 0.00 2.50
1071 4104 4.728102 CCGACGCCGCCTGTTACA 62.728 66.667 0.00 0.00 0.00 2.41
1072 4105 3.475774 CGACGCCGCCTGTTACAC 61.476 66.667 0.00 0.00 0.00 2.90
1073 4106 3.116531 GACGCCGCCTGTTACACC 61.117 66.667 0.00 0.00 0.00 4.16
1074 4107 3.869473 GACGCCGCCTGTTACACCA 62.869 63.158 0.00 0.00 0.00 4.17
1179 4233 0.044092 TGAATAGCCCACCTCCTCCA 59.956 55.000 0.00 0.00 0.00 3.86
1196 4250 4.530553 TCCTCCAGACACTAGCATGTTTAA 59.469 41.667 0.00 0.00 31.24 1.52
1245 4302 3.787001 CCTCCGGAAGCCACTCCC 61.787 72.222 5.23 0.00 31.03 4.30
1280 4337 1.990060 CATCACCACCTCCTCCGGT 60.990 63.158 0.00 0.00 37.93 5.28
1290 4347 2.088674 CTCCTCCGGTAGCCATTCCG 62.089 65.000 0.00 0.00 45.42 4.30
1324 4381 2.187946 CATCACCACCTCCTCCGC 59.812 66.667 0.00 0.00 0.00 5.54
1326 4383 3.625632 ATCACCACCTCCTCCGCCT 62.626 63.158 0.00 0.00 0.00 5.52
1327 4384 3.775654 CACCACCTCCTCCGCCTC 61.776 72.222 0.00 0.00 0.00 4.70
1398 4455 2.749621 GGTAGCAATTCCACCTTCACTG 59.250 50.000 0.00 0.00 0.00 3.66
1465 4531 0.861837 CATCGTAAATCCTCCAGCGC 59.138 55.000 0.00 0.00 0.00 5.92
1467 4533 2.237751 CGTAAATCCTCCAGCGCCG 61.238 63.158 2.29 0.00 0.00 6.46
1470 4536 1.618876 TAAATCCTCCAGCGCCGGAA 61.619 55.000 14.48 0.00 33.65 4.30
1474 4540 4.394712 CTCCAGCGCCGGAACCTT 62.395 66.667 14.48 0.00 33.65 3.50
1478 4544 3.626924 AGCGCCGGAACCTTCAGT 61.627 61.111 5.05 0.00 0.00 3.41
1479 4545 2.263540 GCGCCGGAACCTTCAGTA 59.736 61.111 5.05 0.00 0.00 2.74
1480 4546 2.098831 GCGCCGGAACCTTCAGTAC 61.099 63.158 5.05 0.00 0.00 2.73
1495 4561 1.069775 AGTACAACCCCCGGTGAATT 58.930 50.000 0.00 0.00 35.34 2.17
1503 4569 1.271840 CCCCGGTGAATTCTCCTCCA 61.272 60.000 21.11 0.00 0.00 3.86
1504 4570 0.107654 CCCGGTGAATTCTCCTCCAC 60.108 60.000 21.11 4.80 0.00 4.02
1505 4571 0.107654 CCGGTGAATTCTCCTCCACC 60.108 60.000 21.11 12.12 44.08 4.61
1509 4575 0.909610 TGAATTCTCCTCCACCGCCT 60.910 55.000 7.05 0.00 0.00 5.52
6254 11928 3.615056 TGCGTACACATTACTGTACATGC 59.385 43.478 0.00 6.42 44.68 4.06
6261 11935 6.057533 ACACATTACTGTACATGCTGCATAT 58.942 36.000 15.78 6.75 33.14 1.78
6273 11948 2.665185 GCATATGCCCGGTCGGAC 60.665 66.667 17.26 0.00 37.50 4.79
6289 11964 1.234821 GGACAACGCCATTCTTGACA 58.765 50.000 0.00 0.00 0.00 3.58
6313 11996 0.789383 CGTGACTTTTTCCGCGATGC 60.789 55.000 8.23 0.00 38.42 3.91
6314 11997 0.454452 GTGACTTTTTCCGCGATGCC 60.454 55.000 8.23 0.00 0.00 4.40
6336 12019 1.742900 GCCATCATGTGACGTCGTCG 61.743 60.000 19.81 6.30 43.34 5.12
6364 12047 2.177977 CAACTGCAAACAACGCGTTAA 58.822 42.857 26.11 5.41 36.59 2.01
6407 12090 4.880537 CGCGCGCCATTCTCTCCT 62.881 66.667 27.72 0.00 0.00 3.69
6412 12095 0.179062 GCGCCATTCTCTCCTGATGT 60.179 55.000 0.00 0.00 0.00 3.06
6448 12131 1.005630 GACAGGCTGACAGCGACTT 60.006 57.895 23.66 5.32 43.62 3.01
6566 12266 7.066284 CCGATTTTCCATCTAGAAACTGAACAT 59.934 37.037 0.00 0.00 35.53 2.71
6569 12269 7.912056 TTTCCATCTAGAAACTGAACATCTG 57.088 36.000 0.00 0.00 30.87 2.90
6572 12272 5.518128 CCATCTAGAAACTGAACATCTGTCG 59.482 44.000 0.00 0.00 0.00 4.35
6609 12346 1.225855 GAATGTGTTGGTGCGAGTGA 58.774 50.000 0.00 0.00 0.00 3.41
6625 12362 0.924090 GTGATGAACTGACCGATCGC 59.076 55.000 10.32 0.00 0.00 4.58
6843 12584 2.721167 CGGATGGGTTCGCAGAGGA 61.721 63.158 0.00 0.00 38.43 3.71
6895 12636 0.250124 TGTACAAGGGCACGGTGAAG 60.250 55.000 13.29 0.00 0.00 3.02
7084 12825 0.471211 ACAAGACCCTCGAGTCCCAA 60.471 55.000 12.31 0.00 37.49 4.12
7112 12853 1.079681 GGTACGCACACCCATCGAA 60.080 57.895 0.00 0.00 31.91 3.71
7143 12894 0.673985 GTTTTGGAAGTGCTGGGACC 59.326 55.000 0.00 0.00 0.00 4.46
7147 12898 2.047179 GAAGTGCTGGGACCGACC 60.047 66.667 0.00 0.00 38.08 4.79
7148 12899 3.934391 GAAGTGCTGGGACCGACCG 62.934 68.421 0.00 0.00 40.11 4.79
7150 12901 4.736896 GTGCTGGGACCGACCGAC 62.737 72.222 0.00 0.00 40.11 4.79
7151 12902 4.988716 TGCTGGGACCGACCGACT 62.989 66.667 0.00 0.00 40.11 4.18
7152 12903 4.436998 GCTGGGACCGACCGACTG 62.437 72.222 0.00 0.00 40.11 3.51
7153 12904 2.675423 CTGGGACCGACCGACTGA 60.675 66.667 0.00 0.00 40.11 3.41
7154 12905 2.987547 TGGGACCGACCGACTGAC 60.988 66.667 0.00 0.00 40.11 3.51
7155 12906 2.987547 GGGACCGACCGACTGACA 60.988 66.667 0.00 0.00 40.11 3.58
7156 12907 2.257676 GGACCGACCGACTGACAC 59.742 66.667 0.00 0.00 0.00 3.67
7157 12908 2.558286 GGACCGACCGACTGACACA 61.558 63.158 0.00 0.00 0.00 3.72
7158 12909 1.361271 GACCGACCGACTGACACAA 59.639 57.895 0.00 0.00 0.00 3.33
7159 12910 0.663568 GACCGACCGACTGACACAAG 60.664 60.000 0.00 0.00 0.00 3.16
7160 12911 1.105167 ACCGACCGACTGACACAAGA 61.105 55.000 0.00 0.00 0.00 3.02
7161 12912 0.387367 CCGACCGACTGACACAAGAG 60.387 60.000 0.00 0.00 0.00 2.85
7162 12913 0.387367 CGACCGACTGACACAAGAGG 60.387 60.000 0.00 0.00 0.00 3.69
7163 12914 0.674534 GACCGACTGACACAAGAGGT 59.325 55.000 0.00 0.00 35.53 3.85
7164 12915 1.068741 GACCGACTGACACAAGAGGTT 59.931 52.381 0.00 0.00 33.93 3.50
7165 12916 1.202533 ACCGACTGACACAAGAGGTTG 60.203 52.381 0.00 0.00 39.82 3.77
7166 12917 1.502231 CGACTGACACAAGAGGTTGG 58.498 55.000 0.00 0.00 38.07 3.77
7167 12918 1.202533 CGACTGACACAAGAGGTTGGT 60.203 52.381 0.00 0.00 38.07 3.67
7168 12919 2.741878 CGACTGACACAAGAGGTTGGTT 60.742 50.000 0.00 0.00 38.07 3.67
7169 12920 3.279434 GACTGACACAAGAGGTTGGTTT 58.721 45.455 0.00 0.00 38.07 3.27
7170 12921 3.694566 GACTGACACAAGAGGTTGGTTTT 59.305 43.478 0.00 0.00 38.07 2.43
7171 12922 3.443681 ACTGACACAAGAGGTTGGTTTTG 59.556 43.478 0.00 0.00 38.07 2.44
7172 12923 2.757868 TGACACAAGAGGTTGGTTTTGG 59.242 45.455 0.00 0.00 38.07 3.28
7173 12924 1.480545 ACACAAGAGGTTGGTTTTGGC 59.519 47.619 0.00 0.00 38.07 4.52
7174 12925 1.756538 CACAAGAGGTTGGTTTTGGCT 59.243 47.619 0.00 0.00 38.07 4.75
7175 12926 1.756538 ACAAGAGGTTGGTTTTGGCTG 59.243 47.619 0.00 0.00 38.07 4.85
7267 13018 1.226575 CCTCGCGTATCTGCACGAA 60.227 57.895 5.77 0.00 44.69 3.85
7288 13063 6.073548 ACGAAGACTGTGAGTTCATTTCATTC 60.074 38.462 0.00 0.00 0.00 2.67
7311 13086 2.004583 TACGGATTTTGTCGCCTGAG 57.995 50.000 0.00 0.00 0.00 3.35
7313 13088 1.803289 GGATTTTGTCGCCTGAGGC 59.197 57.895 14.89 14.89 46.75 4.70
7339 13114 6.839124 TTCTGGCACTGAATATTTGAATGT 57.161 33.333 0.00 0.00 41.26 2.71
7463 13244 6.093357 GTCAAAACCCAACAACAACAATTGAT 59.907 34.615 13.59 0.00 33.57 2.57
7494 13287 7.036220 GTCTGCTTGTATCTAACTCTTGCTAA 58.964 38.462 0.00 0.00 0.00 3.09
7584 13377 5.106436 CGTAATGGGAACTTTTGGGTAAGAC 60.106 44.000 0.00 0.00 0.00 3.01
7585 13378 2.853705 TGGGAACTTTTGGGTAAGACG 58.146 47.619 0.00 0.00 0.00 4.18
7586 13379 2.156917 GGGAACTTTTGGGTAAGACGG 58.843 52.381 0.00 0.00 0.00 4.79
7587 13380 2.487805 GGGAACTTTTGGGTAAGACGGT 60.488 50.000 0.00 0.00 0.00 4.83
7588 13381 3.216800 GGAACTTTTGGGTAAGACGGTT 58.783 45.455 0.00 0.00 0.00 4.44
7589 13382 3.004002 GGAACTTTTGGGTAAGACGGTTG 59.996 47.826 0.00 0.00 0.00 3.77
7591 13384 4.094830 ACTTTTGGGTAAGACGGTTGAT 57.905 40.909 0.00 0.00 0.00 2.57
7593 13386 5.623169 ACTTTTGGGTAAGACGGTTGATTA 58.377 37.500 0.00 0.00 0.00 1.75
7594 13387 5.471116 ACTTTTGGGTAAGACGGTTGATTAC 59.529 40.000 0.00 4.29 0.00 1.89
7595 13388 4.895668 TTGGGTAAGACGGTTGATTACT 57.104 40.909 9.95 0.00 31.53 2.24
7596 13389 5.999205 TTGGGTAAGACGGTTGATTACTA 57.001 39.130 9.95 1.52 31.53 1.82
7597 13390 5.329035 TGGGTAAGACGGTTGATTACTAC 57.671 43.478 9.95 6.23 31.53 2.73
7598 13391 5.018809 TGGGTAAGACGGTTGATTACTACT 58.981 41.667 9.95 0.00 31.53 2.57
7599 13392 5.126061 TGGGTAAGACGGTTGATTACTACTC 59.874 44.000 9.95 0.00 31.53 2.59
7600 13393 5.451103 GGGTAAGACGGTTGATTACTACTCC 60.451 48.000 9.95 0.00 31.53 3.85
7605 13398 5.821995 AGACGGTTGATTACTACTCCTAGTC 59.178 44.000 0.00 0.00 34.79 2.59
7606 13399 4.886489 ACGGTTGATTACTACTCCTAGTCC 59.114 45.833 0.00 0.00 34.79 3.85
7613 13406 7.284074 TGATTACTACTCCTAGTCCTCAGAAG 58.716 42.308 0.00 0.00 34.79 2.85
7630 13423 3.223589 GCCCAACAAACTGCCCGT 61.224 61.111 0.00 0.00 0.00 5.28
7672 13466 5.239306 ACATGTGGACTAATCTTGTGTTGTG 59.761 40.000 0.00 0.00 0.00 3.33
7673 13467 4.776349 TGTGGACTAATCTTGTGTTGTGT 58.224 39.130 0.00 0.00 0.00 3.72
7674 13468 4.814234 TGTGGACTAATCTTGTGTTGTGTC 59.186 41.667 0.00 0.00 0.00 3.67
7678 13472 6.375736 TGGACTAATCTTGTGTTGTGTCAAAA 59.624 34.615 0.00 0.00 0.00 2.44
7679 13473 6.691388 GGACTAATCTTGTGTTGTGTCAAAAC 59.309 38.462 0.00 0.00 0.00 2.43
7682 13476 7.968405 ACTAATCTTGTGTTGTGTCAAAACTTC 59.032 33.333 7.41 1.97 0.00 3.01
7683 13477 5.054390 TCTTGTGTTGTGTCAAAACTTCC 57.946 39.130 7.41 0.00 0.00 3.46
7701 13495 3.619900 TCCATCTACAGATACCTGGCT 57.380 47.619 0.00 0.00 44.60 4.75
7896 13692 5.615925 ACAAGGAAGAACTGTTAGTGAGT 57.384 39.130 0.00 0.00 0.00 3.41
7897 13693 5.360591 ACAAGGAAGAACTGTTAGTGAGTG 58.639 41.667 0.00 0.00 0.00 3.51
7898 13694 5.104900 ACAAGGAAGAACTGTTAGTGAGTGT 60.105 40.000 0.00 0.00 0.00 3.55
7899 13695 5.203060 AGGAAGAACTGTTAGTGAGTGTC 57.797 43.478 0.00 0.00 0.00 3.67
7900 13696 4.039366 AGGAAGAACTGTTAGTGAGTGTCC 59.961 45.833 0.00 0.00 0.00 4.02
7901 13697 4.039366 GGAAGAACTGTTAGTGAGTGTCCT 59.961 45.833 0.00 0.00 0.00 3.85
7902 13698 5.453480 GGAAGAACTGTTAGTGAGTGTCCTT 60.453 44.000 0.00 0.00 0.00 3.36
7903 13699 6.239232 GGAAGAACTGTTAGTGAGTGTCCTTA 60.239 42.308 0.00 0.00 0.00 2.69
7904 13700 6.334102 AGAACTGTTAGTGAGTGTCCTTAG 57.666 41.667 0.00 0.00 0.00 2.18
7919 13715 4.081642 TGTCCTTAGTACTGAGATGGTTGC 60.082 45.833 15.88 0.00 0.00 4.17
7926 13722 0.962356 CTGAGATGGTTGCGCCCTTT 60.962 55.000 4.18 0.00 36.04 3.11
7944 13740 5.161358 CCCTTTTAATTCCTTCTCGCAAAC 58.839 41.667 0.00 0.00 0.00 2.93
7965 13767 3.739300 ACTTATCCACTCGTGTTTGAACG 59.261 43.478 0.00 0.00 44.92 3.95
7990 13793 6.358991 AGTAGAACTGTGTAGAGTAGGATCC 58.641 44.000 2.48 2.48 0.00 3.36
8010 13813 2.679837 CCTGTTTGATCCCACTTGATCG 59.320 50.000 0.00 0.00 43.34 3.69
8013 13816 2.293677 TTGATCCCACTTGATCGTCG 57.706 50.000 0.00 0.00 43.34 5.12
8022 13825 3.364062 CACTTGATCGTCGGATGTCTAC 58.636 50.000 0.00 0.00 31.51 2.59
8180 13983 4.865761 GCCTACGACATGGCGCGA 62.866 66.667 23.72 8.65 39.71 5.87
8271 14074 1.338136 CCAATCCCCTCGCCTACAGT 61.338 60.000 0.00 0.00 0.00 3.55
8333 14136 1.209128 CCGCCGCTGTACTTCATTAG 58.791 55.000 0.00 0.00 0.00 1.73
8339 14142 2.672874 CGCTGTACTTCATTAGCAAGCA 59.327 45.455 0.00 0.00 35.98 3.91
8347 14150 4.823989 ACTTCATTAGCAAGCAAAGTGACT 59.176 37.500 0.00 0.00 0.00 3.41
8379 14182 5.755375 GTCAATGGTATGTGATCAGATCGTT 59.245 40.000 8.90 1.19 0.00 3.85
8742 14545 4.254709 TTCAGCAGGCGCACCACT 62.255 61.111 10.83 0.00 42.27 4.00
8755 14558 1.835267 ACCACTGGCAGACGTACCA 60.835 57.895 23.66 4.54 0.00 3.25
8785 14595 4.493872 GGTGACGAGACGTACTGAATACTC 60.494 50.000 0.00 0.00 41.37 2.59
8786 14596 3.620374 TGACGAGACGTACTGAATACTCC 59.380 47.826 0.00 0.00 41.37 3.85
8847 14657 2.821366 GATGCTGTCGCTGTGGGG 60.821 66.667 0.00 0.00 36.97 4.96
8951 14761 5.473846 TGCGTCCATTAATTAACCACAAAGA 59.526 36.000 0.00 0.00 0.00 2.52
9043 15044 1.674322 AATCGGCCGAACAAGGGTG 60.674 57.895 34.66 0.00 0.00 4.61
9075 15076 3.037549 AGGAAATCCTCGAGAGCTCATT 58.962 45.455 17.77 2.49 44.77 2.57
9077 15078 3.181471 GGAAATCCTCGAGAGCTCATTGA 60.181 47.826 17.77 9.33 0.00 2.57
9078 15079 4.437239 GAAATCCTCGAGAGCTCATTGAA 58.563 43.478 17.77 0.00 0.00 2.69
9113 15116 4.391523 ACAAAACACACCAAAGATGCAAAC 59.608 37.500 0.00 0.00 0.00 2.93
9131 15135 4.336101 CAAACGAAAAACGCACAAGAGTA 58.664 39.130 0.00 0.00 46.94 2.59
9158 15163 2.277373 CGCCGCTAGAGTGTCGTC 60.277 66.667 0.00 0.00 0.00 4.20
9175 15180 0.458543 GTCGAGGAGAAGCGCATGAA 60.459 55.000 11.47 0.00 0.00 2.57
9193 15198 2.748058 AAAATCGCCGCCAGGAGTGT 62.748 55.000 0.00 0.00 41.02 3.55
9219 15224 0.179127 CCTGCACTCATCGACGATGT 60.179 55.000 31.06 15.11 40.55 3.06
9221 15226 0.179137 TGCACTCATCGACGATGTCC 60.179 55.000 31.06 19.62 40.55 4.02
9585 15591 4.115199 GTGGCGCTCCAAGGGGAT 62.115 66.667 7.64 0.00 45.53 3.85
9608 15614 4.644234 TGAAGATTTTCACCAAGAGTGCAA 59.356 37.500 0.00 0.00 46.81 4.08
9678 15684 8.710835 TTATGTGAGTTGCGATCTTTATTGTA 57.289 30.769 0.00 0.00 0.00 2.41
9691 15697 7.592533 CGATCTTTATTGTAATCATGGGCTTTG 59.407 37.037 0.00 0.00 0.00 2.77
9707 15713 7.775053 TGGGCTTTGTTAATAGAGTTGAATT 57.225 32.000 0.00 0.00 0.00 2.17
9726 15732 5.353956 TGAATTATGTGATGTGTTCCCTTCG 59.646 40.000 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.606668 GTTGGTTTGAGATTCGTGGCA 59.393 47.619 0.00 0.00 0.00 4.92
1 2 1.606668 TGTTGGTTTGAGATTCGTGGC 59.393 47.619 0.00 0.00 0.00 5.01
2 3 3.980646 TTGTTGGTTTGAGATTCGTGG 57.019 42.857 0.00 0.00 0.00 4.94
3 4 6.480524 TCTATTGTTGGTTTGAGATTCGTG 57.519 37.500 0.00 0.00 0.00 4.35
4 5 6.878923 TCATCTATTGTTGGTTTGAGATTCGT 59.121 34.615 0.00 0.00 0.00 3.85
49 3013 8.819015 TCTTATTTTAAAATACGCACGAGCATA 58.181 29.630 18.16 0.00 42.27 3.14
129 3098 9.846248 GTGCTAATCATGTCAAGTTTAGAAAAT 57.154 29.630 9.17 0.00 0.00 1.82
133 3102 7.764443 GGTAGTGCTAATCATGTCAAGTTTAGA 59.236 37.037 9.17 0.00 0.00 2.10
135 3104 6.821665 GGGTAGTGCTAATCATGTCAAGTTTA 59.178 38.462 0.00 0.00 0.00 2.01
214 3206 7.144722 TGAATACAAAGCATTGGTGACTAAG 57.855 36.000 6.62 0.00 41.01 2.18
231 3223 3.388024 CGGGGAGAAGAGGAATGAATACA 59.612 47.826 0.00 0.00 0.00 2.29
234 3226 2.436173 GACGGGGAGAAGAGGAATGAAT 59.564 50.000 0.00 0.00 0.00 2.57
276 3268 2.190313 GCCAGTGATGATGGGCGA 59.810 61.111 0.00 0.00 38.33 5.54
308 3300 1.754226 TCGACATCGATCATGGGTGAA 59.246 47.619 0.00 0.00 44.22 3.18
322 3314 2.317371 ATAGAGAGGGGCATCGACAT 57.683 50.000 0.00 0.00 0.00 3.06
384 3376 0.854062 TTGGCAACGACGACTTAACG 59.146 50.000 0.00 0.00 42.51 3.18
388 3380 0.935196 GACTTTGGCAACGACGACTT 59.065 50.000 10.99 0.00 42.51 3.01
455 3447 2.105128 GTGGAGATGAGTCCGCGG 59.895 66.667 22.12 22.12 39.81 6.46
465 3457 2.581354 GCCGTGAGCTGTGGAGAT 59.419 61.111 0.00 0.00 38.99 2.75
528 3521 2.048503 GTCCGAGGGTTGACCGTG 60.049 66.667 0.00 0.00 46.96 4.94
562 3555 1.742761 CTCAAAGATGCGGACATGGT 58.257 50.000 0.00 0.00 36.35 3.55
603 3601 3.312146 CGGGCAACTGCAAAAAGAAAATT 59.688 39.130 3.76 0.00 44.36 1.82
604 3602 2.871633 CGGGCAACTGCAAAAAGAAAAT 59.128 40.909 3.76 0.00 44.36 1.82
605 3603 2.093973 TCGGGCAACTGCAAAAAGAAAA 60.094 40.909 3.76 0.00 45.18 2.29
606 3604 1.478510 TCGGGCAACTGCAAAAAGAAA 59.521 42.857 3.76 0.00 45.18 2.52
609 3607 1.933247 TTTCGGGCAACTGCAAAAAG 58.067 45.000 3.76 0.00 45.18 2.27
615 3613 3.569250 TTCTATTTTTCGGGCAACTGC 57.431 42.857 0.00 0.00 45.18 4.40
658 3662 1.266718 GCCAAAGTCAACGAGCATGAA 59.733 47.619 0.00 0.00 0.00 2.57
662 3666 1.896660 GGGCCAAAGTCAACGAGCA 60.897 57.895 4.39 0.00 0.00 4.26
698 3703 6.791847 TCTAGTATCCACTATCCAGGGTTA 57.208 41.667 0.00 0.00 36.66 2.85
764 3772 6.571154 CGACAGCAACATATCATACGAATTTG 59.429 38.462 0.00 0.00 0.00 2.32
806 3819 6.458478 CCATGCAGAATTCTTCTCATGACTTC 60.458 42.308 27.24 2.77 41.97 3.01
810 3823 3.630769 GCCATGCAGAATTCTTCTCATGA 59.369 43.478 27.24 0.00 41.97 3.07
835 3848 3.421844 GATGAGGTGGGTTTGCTTAGTT 58.578 45.455 0.00 0.00 0.00 2.24
836 3849 2.615493 CGATGAGGTGGGTTTGCTTAGT 60.615 50.000 0.00 0.00 0.00 2.24
837 3850 2.009774 CGATGAGGTGGGTTTGCTTAG 58.990 52.381 0.00 0.00 0.00 2.18
838 3851 1.948611 GCGATGAGGTGGGTTTGCTTA 60.949 52.381 0.00 0.00 0.00 3.09
839 3852 1.244019 GCGATGAGGTGGGTTTGCTT 61.244 55.000 0.00 0.00 0.00 3.91
840 3853 1.675641 GCGATGAGGTGGGTTTGCT 60.676 57.895 0.00 0.00 0.00 3.91
841 3854 0.392461 TAGCGATGAGGTGGGTTTGC 60.392 55.000 0.00 0.00 0.00 3.68
842 3855 1.737793 GTTAGCGATGAGGTGGGTTTG 59.262 52.381 0.00 0.00 0.00 2.93
843 3856 1.628846 AGTTAGCGATGAGGTGGGTTT 59.371 47.619 0.00 0.00 0.00 3.27
844 3857 1.066143 CAGTTAGCGATGAGGTGGGTT 60.066 52.381 0.00 0.00 0.00 4.11
845 3858 0.537188 CAGTTAGCGATGAGGTGGGT 59.463 55.000 0.00 0.00 0.00 4.51
846 3859 0.811616 GCAGTTAGCGATGAGGTGGG 60.812 60.000 0.00 0.00 0.00 4.61
847 3860 2.682893 GCAGTTAGCGATGAGGTGG 58.317 57.895 0.00 0.00 0.00 4.61
880 3907 4.080299 AGAGGAGAAGAGAGGAGAAGACTC 60.080 50.000 0.00 0.00 41.94 3.36
895 3922 2.238144 CTGATGGGCAAAGAGAGGAGAA 59.762 50.000 0.00 0.00 0.00 2.87
944 3974 4.277423 GCCTTAAGGTTTAACTGTGAGCAA 59.723 41.667 22.55 0.00 37.57 3.91
1042 4075 0.248949 GGCGTCGGAGATGGAGTAAC 60.249 60.000 0.00 0.00 45.11 2.50
1043 4076 1.721664 CGGCGTCGGAGATGGAGTAA 61.722 60.000 0.00 0.00 45.11 2.24
1044 4077 2.184830 CGGCGTCGGAGATGGAGTA 61.185 63.158 0.00 0.00 45.11 2.59
1045 4078 3.518998 CGGCGTCGGAGATGGAGT 61.519 66.667 0.00 0.00 45.11 3.85
1046 4079 4.933064 GCGGCGTCGGAGATGGAG 62.933 72.222 13.05 0.00 45.11 3.86
1052 4085 4.124351 TAACAGGCGGCGTCGGAG 62.124 66.667 20.18 9.45 36.79 4.63
1053 4086 4.424566 GTAACAGGCGGCGTCGGA 62.425 66.667 20.18 0.00 36.79 4.55
1054 4087 4.728102 TGTAACAGGCGGCGTCGG 62.728 66.667 13.05 10.69 36.79 4.79
1055 4088 3.475774 GTGTAACAGGCGGCGTCG 61.476 66.667 4.29 4.29 36.32 5.12
1056 4089 3.116531 GGTGTAACAGGCGGCGTC 61.117 66.667 1.71 1.71 39.98 5.19
1057 4090 3.876589 CTGGTGTAACAGGCGGCGT 62.877 63.158 9.37 1.45 39.98 5.68
1058 4091 3.118454 CTGGTGTAACAGGCGGCG 61.118 66.667 0.51 0.51 39.98 6.46
1059 4092 0.320946 TAACTGGTGTAACAGGCGGC 60.321 55.000 0.00 0.00 42.75 6.53
1060 4093 1.001633 AGTAACTGGTGTAACAGGCGG 59.998 52.381 1.56 0.00 42.75 6.13
1061 4094 2.334838 GAGTAACTGGTGTAACAGGCG 58.665 52.381 1.56 0.00 42.75 5.52
1062 4095 2.038033 TGGAGTAACTGGTGTAACAGGC 59.962 50.000 1.56 0.00 42.75 4.85
1063 4096 4.223032 AGATGGAGTAACTGGTGTAACAGG 59.777 45.833 1.56 0.00 42.75 4.00
1064 4097 5.407407 AGATGGAGTAACTGGTGTAACAG 57.593 43.478 0.00 0.00 44.03 3.16
1065 4098 4.222145 GGAGATGGAGTAACTGGTGTAACA 59.778 45.833 0.00 0.00 39.98 2.41
1066 4099 4.677250 CGGAGATGGAGTAACTGGTGTAAC 60.677 50.000 0.00 0.00 0.00 2.50
1067 4100 3.446161 CGGAGATGGAGTAACTGGTGTAA 59.554 47.826 0.00 0.00 0.00 2.41
1068 4101 3.021695 CGGAGATGGAGTAACTGGTGTA 58.978 50.000 0.00 0.00 0.00 2.90
1069 4102 1.825474 CGGAGATGGAGTAACTGGTGT 59.175 52.381 0.00 0.00 0.00 4.16
1070 4103 2.100197 TCGGAGATGGAGTAACTGGTG 58.900 52.381 0.00 0.00 0.00 4.17
1071 4104 2.100989 GTCGGAGATGGAGTAACTGGT 58.899 52.381 0.00 0.00 40.67 4.00
1072 4105 1.065701 CGTCGGAGATGGAGTAACTGG 59.934 57.143 0.00 0.00 40.43 4.00
1073 4106 1.534175 GCGTCGGAGATGGAGTAACTG 60.534 57.143 0.00 0.00 45.11 3.16
1074 4107 0.739561 GCGTCGGAGATGGAGTAACT 59.260 55.000 0.00 0.00 45.11 2.24
1155 4209 1.204146 GAGGTGGGCTATTCACTGGA 58.796 55.000 0.00 0.00 35.61 3.86
1179 4233 3.871594 GCGGATTAAACATGCTAGTGTCT 59.128 43.478 0.00 0.00 0.00 3.41
1196 4250 2.060980 GTCACTGGAGGAGGCGGAT 61.061 63.158 0.00 0.00 0.00 4.18
1245 4302 3.775654 GGAGTCACAGGAGGCGGG 61.776 72.222 0.00 0.00 0.00 6.13
1290 4347 1.043673 ATGGAGTCACCGGAGTAGGC 61.044 60.000 9.46 0.00 42.61 3.93
1329 4386 1.300481 GAGAAGGCGGAATTGCTACC 58.700 55.000 0.00 0.00 34.52 3.18
1330 4387 1.300481 GGAGAAGGCGGAATTGCTAC 58.700 55.000 0.00 0.00 34.52 3.58
1331 4388 0.179084 CGGAGAAGGCGGAATTGCTA 60.179 55.000 0.00 0.00 34.52 3.49
1398 4455 2.063378 AGCTGCTACCTGAGGAGGC 61.063 63.158 4.99 9.53 43.67 4.70
1465 4531 1.609841 GGGTTGTACTGAAGGTTCCGG 60.610 57.143 0.00 0.00 0.00 5.14
1467 4533 1.271762 GGGGGTTGTACTGAAGGTTCC 60.272 57.143 0.00 0.00 0.00 3.62
1470 4536 1.486145 CCGGGGGTTGTACTGAAGGT 61.486 60.000 0.00 0.00 0.00 3.50
1474 4540 0.763604 TTCACCGGGGGTTGTACTGA 60.764 55.000 2.42 0.00 31.02 3.41
1478 4544 1.279846 GAGAATTCACCGGGGGTTGTA 59.720 52.381 2.42 0.00 31.02 2.41
1479 4545 0.037734 GAGAATTCACCGGGGGTTGT 59.962 55.000 2.42 0.00 31.02 3.32
1480 4546 0.679960 GGAGAATTCACCGGGGGTTG 60.680 60.000 2.42 0.00 31.02 3.77
1495 4561 3.992641 TGGAGGCGGTGGAGGAGA 61.993 66.667 0.00 0.00 0.00 3.71
6252 11926 2.203195 GACCGGGCATATGCAGCA 60.203 61.111 28.07 0.00 44.36 4.41
6254 11928 2.666190 CCGACCGGGCATATGCAG 60.666 66.667 28.07 20.21 44.36 4.41
6273 11948 0.725784 GCGTGTCAAGAATGGCGTTG 60.726 55.000 0.00 0.00 32.34 4.10
6289 11964 2.629763 GGAAAAAGTCACGCGCGT 59.370 55.556 32.73 32.73 0.00 6.01
6407 12090 2.030401 GCACCGTGCCGTAACATCA 61.030 57.895 12.80 0.00 37.42 3.07
6483 12166 2.450609 AATCAAGTCGGTTACGTGCT 57.549 45.000 0.00 0.00 41.85 4.40
6484 12167 3.060363 CACTAATCAAGTCGGTTACGTGC 59.940 47.826 0.00 0.00 41.85 5.34
6491 12174 1.899814 TGGAGCACTAATCAAGTCGGT 59.100 47.619 0.00 0.00 35.76 4.69
6609 12346 2.386661 AAAGCGATCGGTCAGTTCAT 57.613 45.000 21.51 0.00 0.00 2.57
6625 12362 0.240945 AATCCGCTGGCACGAAAAAG 59.759 50.000 10.33 0.00 34.06 2.27
6797 12538 2.483745 CAGCTCGTCGTAGCCGAA 59.516 61.111 11.45 0.00 37.54 4.30
6824 12565 2.579201 CTCTGCGAACCCATCCGT 59.421 61.111 0.00 0.00 0.00 4.69
6829 12570 1.671742 GTTCTCCTCTGCGAACCCA 59.328 57.895 0.00 0.00 34.83 4.51
6838 12579 1.614824 CCCCAGCAGGTTCTCCTCT 60.615 63.158 0.00 0.00 43.07 3.69
7084 12825 3.918977 TGCGTACCGTGGTGCAGT 61.919 61.111 7.88 0.00 32.73 4.40
7103 12844 0.687354 AACAGAGCAGTTCGATGGGT 59.313 50.000 0.00 0.00 0.00 4.51
7105 12846 1.081892 CCAACAGAGCAGTTCGATGG 58.918 55.000 0.00 0.00 0.00 3.51
7108 12849 2.325583 AAACCAACAGAGCAGTTCGA 57.674 45.000 0.00 0.00 0.00 3.71
7110 12851 2.687935 TCCAAAACCAACAGAGCAGTTC 59.312 45.455 0.00 0.00 0.00 3.01
7112 12853 2.435372 TCCAAAACCAACAGAGCAGT 57.565 45.000 0.00 0.00 0.00 4.40
7143 12894 0.387367 CCTCTTGTGTCAGTCGGTCG 60.387 60.000 0.00 0.00 0.00 4.79
7147 12898 1.202533 ACCAACCTCTTGTGTCAGTCG 60.203 52.381 0.00 0.00 0.00 4.18
7148 12899 2.622064 ACCAACCTCTTGTGTCAGTC 57.378 50.000 0.00 0.00 0.00 3.51
7150 12901 3.181487 CCAAAACCAACCTCTTGTGTCAG 60.181 47.826 0.00 0.00 0.00 3.51
7151 12902 2.757868 CCAAAACCAACCTCTTGTGTCA 59.242 45.455 0.00 0.00 0.00 3.58
7152 12903 2.481276 GCCAAAACCAACCTCTTGTGTC 60.481 50.000 0.00 0.00 0.00 3.67
7153 12904 1.480545 GCCAAAACCAACCTCTTGTGT 59.519 47.619 0.00 0.00 0.00 3.72
7154 12905 1.756538 AGCCAAAACCAACCTCTTGTG 59.243 47.619 0.00 0.00 0.00 3.33
7155 12906 1.756538 CAGCCAAAACCAACCTCTTGT 59.243 47.619 0.00 0.00 0.00 3.16
7156 12907 1.756538 ACAGCCAAAACCAACCTCTTG 59.243 47.619 0.00 0.00 0.00 3.02
7157 12908 1.756538 CACAGCCAAAACCAACCTCTT 59.243 47.619 0.00 0.00 0.00 2.85
7158 12909 1.402787 CACAGCCAAAACCAACCTCT 58.597 50.000 0.00 0.00 0.00 3.69
7159 12910 0.389025 CCACAGCCAAAACCAACCTC 59.611 55.000 0.00 0.00 0.00 3.85
7160 12911 0.325203 ACCACAGCCAAAACCAACCT 60.325 50.000 0.00 0.00 0.00 3.50
7161 12912 0.104120 GACCACAGCCAAAACCAACC 59.896 55.000 0.00 0.00 0.00 3.77
7162 12913 1.067060 GAGACCACAGCCAAAACCAAC 59.933 52.381 0.00 0.00 0.00 3.77
7163 12914 1.341482 TGAGACCACAGCCAAAACCAA 60.341 47.619 0.00 0.00 0.00 3.67
7164 12915 0.257328 TGAGACCACAGCCAAAACCA 59.743 50.000 0.00 0.00 0.00 3.67
7165 12916 0.954452 CTGAGACCACAGCCAAAACC 59.046 55.000 0.00 0.00 0.00 3.27
7166 12917 0.954452 CCTGAGACCACAGCCAAAAC 59.046 55.000 0.00 0.00 36.67 2.43
7167 12918 0.178992 CCCTGAGACCACAGCCAAAA 60.179 55.000 0.00 0.00 36.67 2.44
7168 12919 1.059584 TCCCTGAGACCACAGCCAAA 61.060 55.000 0.00 0.00 36.67 3.28
7169 12920 1.461268 TCCCTGAGACCACAGCCAA 60.461 57.895 0.00 0.00 36.67 4.52
7170 12921 1.915266 CTCCCTGAGACCACAGCCA 60.915 63.158 0.00 0.00 36.67 4.75
7171 12922 2.985456 CTCCCTGAGACCACAGCC 59.015 66.667 0.00 0.00 36.67 4.85
7172 12923 2.267324 GCTCCCTGAGACCACAGC 59.733 66.667 0.00 0.00 36.67 4.40
7173 12924 2.575993 CGCTCCCTGAGACCACAG 59.424 66.667 0.00 0.00 37.61 3.66
7174 12925 3.695606 GCGCTCCCTGAGACCACA 61.696 66.667 0.00 0.00 0.00 4.17
7175 12926 4.459089 GGCGCTCCCTGAGACCAC 62.459 72.222 7.64 0.00 30.87 4.16
7213 12964 4.508128 GCGATCTTCCACCGGCGA 62.508 66.667 9.30 0.00 0.00 5.54
7267 13018 6.528321 TCAGAATGAAATGAACTCACAGTCT 58.472 36.000 0.00 0.00 45.97 3.24
7288 13063 2.285220 CAGGCGACAAAATCCGTATCAG 59.715 50.000 0.00 0.00 0.00 2.90
7311 13086 2.113860 TATTCAGTGCCAGAACAGCC 57.886 50.000 0.00 0.00 0.00 4.85
7313 13088 5.885230 TCAAATATTCAGTGCCAGAACAG 57.115 39.130 0.00 0.00 0.00 3.16
7330 13105 5.713389 TGAGATCAAAGCCAGACATTCAAAT 59.287 36.000 0.00 0.00 0.00 2.32
7334 13109 3.626670 CCTGAGATCAAAGCCAGACATTC 59.373 47.826 0.00 0.00 0.00 2.67
7339 13114 2.259917 TGACCTGAGATCAAAGCCAGA 58.740 47.619 0.00 0.00 0.00 3.86
7390 13165 1.153349 GTCGAGGAGGATGTTGGCC 60.153 63.158 0.00 0.00 0.00 5.36
7503 13296 2.157305 TTGCCAGCCCAAAATCTGCG 62.157 55.000 0.00 0.00 0.00 5.18
7584 13377 5.131784 AGGACTAGGAGTAGTAATCAACCG 58.868 45.833 0.00 0.00 39.78 4.44
7585 13378 6.127793 TGAGGACTAGGAGTAGTAATCAACC 58.872 44.000 0.00 0.00 39.78 3.77
7586 13379 7.055378 TCTGAGGACTAGGAGTAGTAATCAAC 58.945 42.308 0.00 0.00 39.78 3.18
7587 13380 7.209340 TCTGAGGACTAGGAGTAGTAATCAA 57.791 40.000 0.00 0.00 39.78 2.57
7588 13381 6.826632 TCTGAGGACTAGGAGTAGTAATCA 57.173 41.667 0.00 0.00 39.78 2.57
7589 13382 6.206048 GCTTCTGAGGACTAGGAGTAGTAATC 59.794 46.154 0.00 0.00 39.78 1.75
7591 13384 5.438833 GCTTCTGAGGACTAGGAGTAGTAA 58.561 45.833 0.00 0.00 39.78 2.24
7593 13386 3.372241 GGCTTCTGAGGACTAGGAGTAGT 60.372 52.174 0.00 0.00 42.59 2.73
7594 13387 3.219281 GGCTTCTGAGGACTAGGAGTAG 58.781 54.545 0.00 0.00 0.00 2.57
7595 13388 2.091775 GGGCTTCTGAGGACTAGGAGTA 60.092 54.545 0.00 0.00 0.00 2.59
7596 13389 1.342574 GGGCTTCTGAGGACTAGGAGT 60.343 57.143 0.00 0.00 0.00 3.85
7597 13390 1.342474 TGGGCTTCTGAGGACTAGGAG 60.342 57.143 0.00 0.00 0.00 3.69
7598 13391 0.710588 TGGGCTTCTGAGGACTAGGA 59.289 55.000 0.00 0.00 0.00 2.94
7599 13392 1.208293 GTTGGGCTTCTGAGGACTAGG 59.792 57.143 0.00 0.00 0.00 3.02
7600 13393 1.902508 TGTTGGGCTTCTGAGGACTAG 59.097 52.381 0.00 0.00 0.00 2.57
7605 13398 1.610522 CAGTTTGTTGGGCTTCTGAGG 59.389 52.381 0.00 0.00 0.00 3.86
7606 13399 1.000938 GCAGTTTGTTGGGCTTCTGAG 60.001 52.381 0.00 0.00 0.00 3.35
7613 13406 3.223589 ACGGGCAGTTTGTTGGGC 61.224 61.111 0.00 0.00 0.00 5.36
7648 13441 5.239306 CACAACACAAGATTAGTCCACATGT 59.761 40.000 0.00 0.00 0.00 3.21
7672 13466 7.278868 CAGGTATCTGTAGATGGAAGTTTTGAC 59.721 40.741 4.67 0.00 36.30 3.18
7673 13467 7.331026 CAGGTATCTGTAGATGGAAGTTTTGA 58.669 38.462 4.67 0.00 36.30 2.69
7674 13468 6.540189 CCAGGTATCTGTAGATGGAAGTTTTG 59.460 42.308 1.52 0.00 39.31 2.44
7678 13472 3.643792 GCCAGGTATCTGTAGATGGAAGT 59.356 47.826 1.52 0.00 39.31 3.01
7679 13473 3.900601 AGCCAGGTATCTGTAGATGGAAG 59.099 47.826 1.52 0.00 39.31 3.46
7682 13476 2.564947 GGAGCCAGGTATCTGTAGATGG 59.435 54.545 1.52 0.32 39.31 3.51
7683 13477 2.230025 CGGAGCCAGGTATCTGTAGATG 59.770 54.545 1.52 0.00 39.31 2.90
7701 13495 0.032403 CGGTGGCGTAATATTCCGGA 59.968 55.000 0.00 0.00 35.25 5.14
7877 13673 4.039366 GGACACTCACTAACAGTTCTTCCT 59.961 45.833 0.00 0.00 0.00 3.36
7882 13678 6.086785 ACTAAGGACACTCACTAACAGTTC 57.913 41.667 0.00 0.00 0.00 3.01
7896 13692 4.081642 GCAACCATCTCAGTACTAAGGACA 60.082 45.833 0.00 0.00 0.00 4.02
7897 13693 4.434520 GCAACCATCTCAGTACTAAGGAC 58.565 47.826 0.00 0.00 0.00 3.85
7898 13694 3.130516 CGCAACCATCTCAGTACTAAGGA 59.869 47.826 0.00 0.00 0.00 3.36
7899 13695 3.448686 CGCAACCATCTCAGTACTAAGG 58.551 50.000 0.00 0.00 0.00 2.69
7900 13696 2.860735 GCGCAACCATCTCAGTACTAAG 59.139 50.000 0.30 0.00 0.00 2.18
7901 13697 2.418197 GGCGCAACCATCTCAGTACTAA 60.418 50.000 10.83 0.00 38.86 2.24
7902 13698 1.136305 GGCGCAACCATCTCAGTACTA 59.864 52.381 10.83 0.00 38.86 1.82
7903 13699 0.108138 GGCGCAACCATCTCAGTACT 60.108 55.000 10.83 0.00 38.86 2.73
7904 13700 1.090052 GGGCGCAACCATCTCAGTAC 61.090 60.000 10.83 0.00 42.05 2.73
7919 13715 2.223272 GCGAGAAGGAATTAAAAGGGCG 60.223 50.000 0.00 0.00 0.00 6.13
7926 13722 6.882140 TGGATAAGTTTGCGAGAAGGAATTAA 59.118 34.615 0.00 0.00 0.00 1.40
7944 13740 3.985279 TCGTTCAAACACGAGTGGATAAG 59.015 43.478 8.19 0.00 44.18 1.73
7965 13767 6.484308 GGATCCTACTCTACACAGTTCTACTC 59.516 46.154 3.84 0.00 0.00 2.59
7966 13768 6.159046 AGGATCCTACTCTACACAGTTCTACT 59.841 42.308 14.27 0.00 0.00 2.57
7967 13769 6.261381 CAGGATCCTACTCTACACAGTTCTAC 59.739 46.154 15.67 0.00 0.00 2.59
7990 13793 3.338249 ACGATCAAGTGGGATCAAACAG 58.662 45.455 0.00 0.00 43.07 3.16
8013 13816 2.029307 GCGGTGGGAGGTAGACATCC 62.029 65.000 4.76 4.76 45.46 3.51
8022 13825 2.676121 TGCATTTGCGGTGGGAGG 60.676 61.111 0.00 0.00 45.83 4.30
8159 13962 2.183300 GCCATGTCGTAGGCGTCA 59.817 61.111 0.00 0.00 41.70 4.35
8271 14074 0.243907 CGCGGGAGAGAAAAGACAGA 59.756 55.000 0.00 0.00 0.00 3.41
8326 14129 4.083855 CGAGTCACTTTGCTTGCTAATGAA 60.084 41.667 0.00 0.00 0.00 2.57
8333 14136 0.110464 GAGCGAGTCACTTTGCTTGC 60.110 55.000 6.92 0.00 41.24 4.01
8339 14142 0.384309 TGACACGAGCGAGTCACTTT 59.616 50.000 16.87 0.00 39.92 2.66
8347 14150 1.203758 ACATACCATTGACACGAGCGA 59.796 47.619 0.00 0.00 0.00 4.93
8379 14182 4.051167 TCGCCCTCCAGGTACCGA 62.051 66.667 6.18 0.00 38.26 4.69
8744 14547 4.814294 CCCGGCTGGTACGTCTGC 62.814 72.222 11.58 0.00 0.00 4.26
8785 14595 0.174845 TTGATCACCCGCTCGTAAGG 59.825 55.000 0.00 0.00 38.47 2.69
8786 14596 1.560923 CTTGATCACCCGCTCGTAAG 58.439 55.000 0.00 0.00 0.00 2.34
8847 14657 4.655440 AACAAAGAAACGCAAACCAAAC 57.345 36.364 0.00 0.00 0.00 2.93
8951 14761 9.690913 TCCATCATCTCTTTCTGTTTTATTCAT 57.309 29.630 0.00 0.00 0.00 2.57
9043 15044 2.519013 AGGATTTCCTCAACACCTTGC 58.481 47.619 0.00 0.00 44.77 4.01
9113 15116 4.433304 CAGTTTACTCTTGTGCGTTTTTCG 59.567 41.667 0.00 0.00 43.12 3.46
9131 15135 0.882927 TCTAGCGGCGTTTGCAGTTT 60.883 50.000 9.37 0.00 45.35 2.66
9158 15163 1.078709 TTTTCATGCGCTTCTCCTCG 58.921 50.000 9.73 0.00 0.00 4.63
9175 15180 2.436646 CACTCCTGGCGGCGATTT 60.437 61.111 12.98 0.00 0.00 2.17
9193 15198 1.621317 TCGATGAGTGCAGGTGGTTAA 59.379 47.619 0.00 0.00 0.00 2.01
9221 15226 2.626467 CCTTGAAGGGGGAAGGGGG 61.626 68.421 2.50 0.00 35.93 5.40
9608 15614 6.318144 CACATGGCTAATGAGTGAAAATCTCT 59.682 38.462 0.00 0.00 38.72 3.10
9678 15684 7.615365 TCAACTCTATTAACAAAGCCCATGATT 59.385 33.333 0.00 0.00 0.00 2.57
9707 15713 3.973206 ACGAAGGGAACACATCACATA 57.027 42.857 0.00 0.00 32.04 2.29


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

AutoCloner maintained by Alex Coulton.