Multiple sequence alignment - TraesCS2D01G282800

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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 TraesCS2D01G282800 chr2D 100.000 9906 0 0 1 9906 355675689 355685594 0.000000e+00 18294.0
1 TraesCS2D01G282800 chr2D 81.501 373 62 5 1 368 619937197 619936827 5.820000e-77 300.0
2 TraesCS2D01G282800 chr2D 89.744 78 8 0 6876 6953 433507288 433507365 6.330000e-17 100.0
3 TraesCS2D01G282800 chr2D 95.745 47 0 1 9566 9612 355685211 355685255 3.840000e-09 75.0
4 TraesCS2D01G282800 chr2D 95.745 47 0 1 9523 9567 355685254 355685300 3.840000e-09 75.0
5 TraesCS2D01G282800 chr2A 98.163 5389 86 5 3766 9146 475872698 475878081 0.000000e+00 9391.0
6 TraesCS2D01G282800 chr2A 94.339 3515 134 32 1 3500 475869235 475872699 0.000000e+00 5328.0
7 TraesCS2D01G282800 chr2A 95.894 682 24 3 9228 9906 475878080 475878760 0.000000e+00 1101.0
8 TraesCS2D01G282800 chr2A 95.745 47 1 1 9566 9612 475878375 475878420 3.840000e-09 75.0
9 TraesCS2D01G282800 chr2A 95.745 47 0 1 9523 9567 475878419 475878465 3.840000e-09 75.0
10 TraesCS2D01G282800 chr2A 96.875 32 1 0 431 462 8555711 8555680 5.000000e-03 54.7
11 TraesCS2D01G282800 chr2B 97.218 3703 80 8 5452 9147 423662806 423666492 0.000000e+00 6246.0
12 TraesCS2D01G282800 chr2B 96.778 2607 72 5 2853 5455 423660086 423662684 0.000000e+00 4338.0
13 TraesCS2D01G282800 chr2B 96.219 2195 70 7 566 2758 423657503 423659686 0.000000e+00 3581.0
14 TraesCS2D01G282800 chr2B 92.486 346 23 2 9224 9567 423666493 423666837 8.940000e-135 492.0
15 TraesCS2D01G282800 chr2B 91.691 349 12 10 9567 9906 423666792 423667132 1.510000e-127 468.0
16 TraesCS2D01G282800 chr2B 93.750 96 4 2 9135 9229 230293611 230293517 1.040000e-29 143.0
17 TraesCS2D01G282800 chr2B 98.750 80 1 0 2775 2854 423659893 423659972 1.040000e-29 143.0
18 TraesCS2D01G282800 chr2B 86.957 115 12 2 3101 3213 459576906 459577019 1.040000e-24 126.0
19 TraesCS2D01G282800 chr6A 90.657 792 66 4 6092 6876 395249328 395250118 0.000000e+00 1046.0
20 TraesCS2D01G282800 chr6A 84.043 846 81 26 6969 7772 395250124 395250957 0.000000e+00 765.0
21 TraesCS2D01G282800 chr6A 81.105 688 61 40 3366 4024 395247980 395248627 4.160000e-133 486.0
22 TraesCS2D01G282800 chr6A 85.417 336 39 7 2652 2987 395240920 395241245 3.430000e-89 340.0
23 TraesCS2D01G282800 chr6A 86.957 253 30 3 4271 4522 395248636 395248886 2.110000e-71 281.0
24 TraesCS2D01G282800 chr6A 89.205 176 18 1 3194 3369 395241445 395241619 1.680000e-52 219.0
25 TraesCS2D01G282800 chr6A 91.964 112 8 1 5982 6093 395249002 395249112 1.330000e-33 156.0
26 TraesCS2D01G282800 chr6A 94.382 89 5 0 3088 3176 538097832 538097744 4.830000e-28 137.0
27 TraesCS2D01G282800 chrUn 89.052 749 59 10 1594 2324 360626239 360625496 0.000000e+00 907.0
28 TraesCS2D01G282800 chrUn 85.144 451 51 12 2538 2987 385732732 385732297 1.960000e-121 448.0
29 TraesCS2D01G282800 chrUn 89.385 179 18 1 3194 3372 385732097 385731920 3.600000e-54 224.0
30 TraesCS2D01G282800 chrUn 79.263 217 32 6 1343 1547 360626465 360626250 1.340000e-28 139.0
31 TraesCS2D01G282800 chr6B 89.052 749 59 10 1594 2324 8331683 8330940 0.000000e+00 907.0
32 TraesCS2D01G282800 chr6B 89.052 749 59 10 1594 2324 8342652 8341909 0.000000e+00 907.0
33 TraesCS2D01G282800 chr6B 89.052 749 59 10 1594 2324 8352296 8351553 0.000000e+00 907.0
34 TraesCS2D01G282800 chr6B 89.052 749 59 10 1594 2324 8361943 8361200 0.000000e+00 907.0
35 TraesCS2D01G282800 chr6B 89.052 749 59 10 1594 2324 8371589 8370846 0.000000e+00 907.0
36 TraesCS2D01G282800 chr6B 85.556 450 50 11 2538 2987 8351278 8350844 3.260000e-124 457.0
37 TraesCS2D01G282800 chr6B 85.366 451 50 12 2538 2987 8341634 8341199 4.220000e-123 453.0
38 TraesCS2D01G282800 chr6B 85.398 452 49 12 2538 2987 8370571 8370135 4.220000e-123 453.0
39 TraesCS2D01G282800 chr6B 85.144 451 51 12 2538 2987 8360925 8360490 1.960000e-121 448.0
40 TraesCS2D01G282800 chr6B 89.385 179 18 1 3194 3372 8350644 8350467 3.600000e-54 224.0
41 TraesCS2D01G282800 chr6B 89.385 179 18 1 3194 3372 8360290 8360113 3.600000e-54 224.0
42 TraesCS2D01G282800 chr6B 89.385 179 18 1 3194 3372 8369935 8369758 3.600000e-54 224.0
43 TraesCS2D01G282800 chr6B 88.827 179 19 1 3194 3372 8340999 8340822 1.680000e-52 219.0
44 TraesCS2D01G282800 chr6B 79.263 217 32 6 1343 1547 8331909 8331694 1.340000e-28 139.0
45 TraesCS2D01G282800 chr6B 79.263 217 32 6 1343 1547 8342878 8342663 1.340000e-28 139.0
46 TraesCS2D01G282800 chr6B 79.263 217 32 6 1343 1547 8352522 8352307 1.340000e-28 139.0
47 TraesCS2D01G282800 chr6B 79.263 217 32 6 1343 1547 8362169 8361954 1.340000e-28 139.0
48 TraesCS2D01G282800 chr6B 79.263 217 32 6 1343 1547 8371815 8371600 1.340000e-28 139.0
49 TraesCS2D01G282800 chr6B 89.333 75 7 1 6880 6953 142478860 142478934 1.060000e-14 93.5
50 TraesCS2D01G282800 chr5D 83.862 378 48 11 2 370 421371814 421372187 2.050000e-91 348.0
51 TraesCS2D01G282800 chr5D 83.425 362 45 11 1 358 387926316 387926666 1.240000e-83 322.0
52 TraesCS2D01G282800 chr5D 95.506 89 4 0 9142 9230 464415011 464414923 1.040000e-29 143.0
53 TraesCS2D01G282800 chr5A 80.472 466 78 9 1 458 394263484 394263024 2.650000e-90 344.0
54 TraesCS2D01G282800 chr5A 83.516 91 11 1 6876 6962 580927634 580927544 2.290000e-11 82.4
55 TraesCS2D01G282800 chr5B 82.850 379 53 10 1 370 507652749 507653124 7.420000e-86 329.0
56 TraesCS2D01G282800 chr5B 95.604 91 4 0 9139 9229 617247654 617247744 8.020000e-31 147.0
57 TraesCS2D01G282800 chr5B 95.455 88 4 0 9145 9232 33627051 33626964 3.730000e-29 141.0
58 TraesCS2D01G282800 chr7B 81.205 415 62 12 1 407 466278454 466278048 4.460000e-83 320.0
59 TraesCS2D01G282800 chr7B 92.857 98 5 2 9135 9230 487811870 487811773 3.730000e-29 141.0
60 TraesCS2D01G282800 chr7B 91.026 78 7 0 6878 6955 740993879 740993956 1.360000e-18 106.0
61 TraesCS2D01G282800 chr7B 88.000 75 8 1 6879 6953 120452089 120452016 4.930000e-13 87.9
62 TraesCS2D01G282800 chr7D 81.501 373 62 5 1 370 571238217 571237849 5.820000e-77 300.0
63 TraesCS2D01G282800 chr7D 95.455 88 4 0 9142 9229 622185151 622185064 3.730000e-29 141.0
64 TraesCS2D01G282800 chr7D 91.262 103 6 3 3081 3181 34756856 34756957 4.830000e-28 137.0
65 TraesCS2D01G282800 chr7D 89.189 111 11 1 3101 3211 638458213 638458104 4.830000e-28 137.0
66 TraesCS2D01G282800 chr3B 80.250 400 65 12 1 393 362050511 362050119 1.260000e-73 289.0
67 TraesCS2D01G282800 chr3B 94.382 89 5 0 3088 3176 521797770 521797858 4.830000e-28 137.0
68 TraesCS2D01G282800 chr4B 94.681 94 5 0 9136 9229 631841842 631841935 8.020000e-31 147.0
69 TraesCS2D01G282800 chr4A 95.506 89 4 0 3088 3176 48905991 48905903 1.040000e-29 143.0
70 TraesCS2D01G282800 chr4A 89.062 64 7 0 6890 6953 612373924 612373861 8.250000e-11 80.5
71 TraesCS2D01G282800 chr1D 94.505 91 5 0 9142 9232 28144196 28144106 3.730000e-29 141.0
72 TraesCS2D01G282800 chr1B 95.455 88 4 0 9145 9232 352885039 352884952 3.730000e-29 141.0
73 TraesCS2D01G282800 chr1B 95.402 87 4 0 3089 3175 632020927 632021013 1.340000e-28 139.0
74 TraesCS2D01G282800 chr3A 89.720 107 9 2 3101 3206 36236239 36236344 1.740000e-27 135.0
75 TraesCS2D01G282800 chr4D 86.400 125 12 4 3089 3212 4772132 4772252 2.250000e-26 132.0
76 TraesCS2D01G282800 chr3D 88.608 79 9 0 6888 6966 591606766 591606844 8.190000e-16 97.1


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 TraesCS2D01G282800 chr2D 355675689 355685594 9905 False 6148.000000 18294 97.163333 1 9906 3 chr2D.!!$F2 9905
1 TraesCS2D01G282800 chr2A 475869235 475878760 9525 False 3194.000000 9391 95.977200 1 9906 5 chr2A.!!$F1 9905
2 TraesCS2D01G282800 chr2B 423657503 423667132 9629 False 2544.666667 6246 95.523667 566 9906 6 chr2B.!!$F2 9340
3 TraesCS2D01G282800 chr6A 395247980 395250957 2977 False 546.800000 1046 86.945200 3366 7772 5 chr6A.!!$F2 4406
4 TraesCS2D01G282800 chr6A 395240920 395241619 699 False 279.500000 340 87.311000 2652 3369 2 chr6A.!!$F1 717
5 TraesCS2D01G282800 chrUn 360625496 360626465 969 True 523.000000 907 84.157500 1343 2324 2 chrUn.!!$R1 981
6 TraesCS2D01G282800 chrUn 385731920 385732732 812 True 336.000000 448 87.264500 2538 3372 2 chrUn.!!$R2 834
7 TraesCS2D01G282800 chr6B 8330940 8331909 969 True 523.000000 907 84.157500 1343 2324 2 chr6B.!!$R1 981
8 TraesCS2D01G282800 chr6B 8350467 8352522 2055 True 431.750000 907 85.814000 1343 3372 4 chr6B.!!$R3 2029
9 TraesCS2D01G282800 chr6B 8369758 8371815 2057 True 430.750000 907 85.774500 1343 3372 4 chr6B.!!$R5 2029
10 TraesCS2D01G282800 chr6B 8340822 8342878 2056 True 429.500000 907 85.627000 1343 3372 4 chr6B.!!$R2 2029
11 TraesCS2D01G282800 chr6B 8360113 8362169 2056 True 429.500000 907 85.711000 1343 3372 4 chr6B.!!$R4 2029

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
375 381 0.035915 TTTCGGGCGATTCCATGTGA 60.036 50.000 0.00 0.00 36.21 3.58 F
378 384 0.098728 CGGGCGATTCCATGTGAAAC 59.901 55.000 0.00 0.00 36.33 2.78 F
479 485 0.107214 GGATCAGCCCGACCATTTGA 60.107 55.000 0.00 0.00 0.00 2.69 F
488 494 0.110238 CGACCATTTGAGCACCGTTG 60.110 55.000 0.00 0.00 0.00 4.10 F
493 499 0.598065 ATTTGAGCACCGTTGAAGGC 59.402 50.000 0.00 0.00 33.69 4.35 F
530 536 0.608035 TTTTCATGACTGGGCCGTCC 60.608 55.000 20.48 4.35 32.97 4.79 F
1147 1168 1.863155 TAGCAAGGGGGCCTTCTTGG 61.863 60.000 27.96 16.83 42.67 3.61 F
2404 2616 2.586425 AGCAATACATCGGAATTGGGG 58.414 47.619 3.76 0.00 34.37 4.96 F
3881 4464 2.301870 AGGTCGTTGCACTATTCCAGAA 59.698 45.455 0.00 0.00 0.00 3.02 F
4791 5388 5.939883 CAGATGTACAGGGAAATCAGACAAA 59.060 40.000 0.33 0.00 0.00 2.83 F
6385 7324 2.571212 AGTTTCACAGATTTCGCACCA 58.429 42.857 0.00 0.00 0.00 4.17 F
8038 9034 0.881118 TGATTGGGCTTTGAACTCGC 59.119 50.000 0.00 0.00 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2101 2143 2.288666 GGCAAGAGTGTTGACAAGACA 58.711 47.619 16.90 0.00 0.00 3.41 R
2378 2590 5.392919 CCAATTCCGATGTATTGCTTGACAA 60.393 40.000 0.00 0.00 44.01 3.18 R
2404 2616 2.892374 AGTTGTTTCTTGTTGCCTTGC 58.108 42.857 0.00 0.00 0.00 4.01 R
2719 2935 4.334759 CCTTCTCATTTCTAGGCATGTGTG 59.665 45.833 0.00 0.00 0.00 3.82 R
2742 2958 4.513442 TGATCAGGCTAACCATACAACAC 58.487 43.478 0.00 0.00 39.06 3.32 R
2916 3437 6.038603 TCTGAAAATATGGATTTTGCTCTCCG 59.961 38.462 0.56 0.00 43.76 4.63 R
3296 3859 1.949525 TGCACTGCAGAAAAGGAGAAC 59.050 47.619 23.35 0.00 33.32 3.01 R
4648 5245 1.340017 GCTTGGTTGAGCCCAGATGTA 60.340 52.381 0.00 0.00 36.66 2.29 R
4892 5489 2.390938 CACAAAGCATGCTTGTCAGTG 58.609 47.619 32.54 28.86 36.26 3.66 R
6766 7711 2.168521 AGTCCATCCATTCGAATCACGT 59.831 45.455 7.92 0.00 43.13 4.49 R
8100 9096 3.031736 GGTGACCTCTTACATGAGCCTA 58.968 50.000 0.00 0.00 33.02 3.93 R
9225 10234 0.629058 ACCCGCCATTCCCAATTACT 59.371 50.000 0.00 0.00 0.00 2.24 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
27 28 1.078567 GCTCCAGCAAGTCCAGAGG 60.079 63.158 0.00 0.00 41.59 3.69
83 86 4.292178 GCCCGGATCTCCTGCTCG 62.292 72.222 0.73 0.00 0.00 5.03
97 100 2.782222 GCTCGATCTGGTACCGGCA 61.782 63.158 16.58 5.62 0.00 5.69
115 118 0.807667 CACTCCGGTGTGAGCATAGC 60.808 60.000 28.47 0.00 40.12 2.97
118 121 1.033202 TCCGGTGTGAGCATAGCGTA 61.033 55.000 15.53 0.00 40.86 4.42
128 131 2.978489 GAGCATAGCGTACGTGGTTATC 59.022 50.000 17.90 5.58 0.00 1.75
130 133 2.724690 GCATAGCGTACGTGGTTATCTG 59.275 50.000 17.90 4.99 0.00 2.90
133 136 2.019249 AGCGTACGTGGTTATCTGCTA 58.981 47.619 17.90 0.00 0.00 3.49
135 138 2.724349 CGTACGTGGTTATCTGCTACC 58.276 52.381 7.22 0.00 34.93 3.18
148 153 2.098831 GCTACCGGACCAGCGAAAC 61.099 63.158 9.46 0.00 0.00 2.78
251 256 3.793888 GGCTAGGGTTGGGGGACG 61.794 72.222 0.00 0.00 0.00 4.79
324 329 3.286694 ATGCGGCATTCACACCCCT 62.287 57.895 10.23 0.00 0.00 4.79
332 338 2.923121 CATTCACACCCCTACATGAGG 58.077 52.381 0.00 1.66 46.25 3.86
370 376 1.676303 GGGTTTTCGGGCGATTCCA 60.676 57.895 0.00 0.00 36.21 3.53
375 381 0.035915 TTTCGGGCGATTCCATGTGA 60.036 50.000 0.00 0.00 36.21 3.58
376 382 0.035915 TTCGGGCGATTCCATGTGAA 60.036 50.000 0.00 0.00 37.38 3.18
378 384 0.098728 CGGGCGATTCCATGTGAAAC 59.901 55.000 0.00 0.00 36.33 2.78
388 394 2.044215 TCCATGTGAAACCCCCATCATT 59.956 45.455 0.00 0.00 34.36 2.57
394 400 2.922955 TGAAACCCCCATCATTAGTCCA 59.077 45.455 0.00 0.00 0.00 4.02
396 402 3.382083 AACCCCCATCATTAGTCCAAC 57.618 47.619 0.00 0.00 0.00 3.77
397 403 2.283834 ACCCCCATCATTAGTCCAACA 58.716 47.619 0.00 0.00 0.00 3.33
413 419 3.259625 TCCAACATGATGGACGTGTAAGA 59.740 43.478 19.99 0.00 46.50 2.10
414 420 3.618594 CCAACATGATGGACGTGTAAGAG 59.381 47.826 16.73 0.00 46.50 2.85
424 430 2.092882 GTGTAAGAGCGTGCCCGAC 61.093 63.158 0.00 0.00 35.63 4.79
439 445 1.213094 CCGACGTCCCATATTCGCAC 61.213 60.000 10.58 0.00 0.00 5.34
462 468 0.478072 ATTTGGGCTGGATATGCGGA 59.522 50.000 7.32 0.00 0.00 5.54
469 475 0.392193 CTGGATATGCGGATCAGCCC 60.392 60.000 15.47 9.39 36.02 5.19
477 483 4.986467 GGATCAGCCCGACCATTT 57.014 55.556 0.00 0.00 0.00 2.32
479 485 0.107214 GGATCAGCCCGACCATTTGA 60.107 55.000 0.00 0.00 0.00 2.69
481 487 0.749454 ATCAGCCCGACCATTTGAGC 60.749 55.000 0.00 0.00 0.00 4.26
482 488 1.675310 CAGCCCGACCATTTGAGCA 60.675 57.895 0.00 0.00 0.00 4.26
483 489 1.675641 AGCCCGACCATTTGAGCAC 60.676 57.895 0.00 0.00 0.00 4.40
484 490 2.700773 GCCCGACCATTTGAGCACC 61.701 63.158 0.00 0.00 0.00 5.01
485 491 2.398554 CCCGACCATTTGAGCACCG 61.399 63.158 0.00 0.00 0.00 4.94
486 492 1.671054 CCGACCATTTGAGCACCGT 60.671 57.895 0.00 0.00 0.00 4.83
488 494 0.110238 CGACCATTTGAGCACCGTTG 60.110 55.000 0.00 0.00 0.00 4.10
490 496 1.606668 GACCATTTGAGCACCGTTGAA 59.393 47.619 0.00 0.00 0.00 2.69
491 497 1.608590 ACCATTTGAGCACCGTTGAAG 59.391 47.619 0.00 0.00 0.00 3.02
492 498 1.068333 CCATTTGAGCACCGTTGAAGG 60.068 52.381 0.00 0.00 37.30 3.46
493 499 0.598065 ATTTGAGCACCGTTGAAGGC 59.402 50.000 0.00 0.00 33.69 4.35
494 500 1.781025 TTTGAGCACCGTTGAAGGCG 61.781 55.000 0.00 0.00 33.69 5.52
495 501 2.665185 GAGCACCGTTGAAGGCGT 60.665 61.111 0.00 0.00 33.69 5.68
496 502 2.665185 AGCACCGTTGAAGGCGTC 60.665 61.111 0.00 0.00 33.69 5.19
497 503 3.723348 GCACCGTTGAAGGCGTCC 61.723 66.667 0.00 0.00 33.69 4.79
498 504 2.280524 CACCGTTGAAGGCGTCCA 60.281 61.111 0.00 0.00 33.69 4.02
499 505 1.671054 CACCGTTGAAGGCGTCCAT 60.671 57.895 0.00 0.00 33.69 3.41
500 506 1.375523 ACCGTTGAAGGCGTCCATC 60.376 57.895 0.00 0.00 33.69 3.51
501 507 1.079127 CCGTTGAAGGCGTCCATCT 60.079 57.895 0.00 0.00 0.00 2.90
502 508 0.673644 CCGTTGAAGGCGTCCATCTT 60.674 55.000 0.00 0.00 0.00 2.40
503 509 1.156736 CGTTGAAGGCGTCCATCTTT 58.843 50.000 0.00 0.00 0.00 2.52
504 510 1.135972 CGTTGAAGGCGTCCATCTTTG 60.136 52.381 0.00 0.00 0.00 2.77
515 521 4.730521 GCGTCCATCTTTGATCGAATTTTC 59.269 41.667 0.00 0.00 0.00 2.29
520 526 7.430502 GTCCATCTTTGATCGAATTTTCATGAC 59.569 37.037 0.00 0.00 0.00 3.06
521 527 7.337689 TCCATCTTTGATCGAATTTTCATGACT 59.662 33.333 0.00 0.00 0.00 3.41
524 530 5.565592 TTGATCGAATTTTCATGACTGGG 57.434 39.130 0.00 0.00 0.00 4.45
526 532 2.091541 TCGAATTTTCATGACTGGGCC 58.908 47.619 0.00 0.00 0.00 5.80
529 535 1.463674 ATTTTCATGACTGGGCCGTC 58.536 50.000 17.77 17.77 34.52 4.79
530 536 0.608035 TTTTCATGACTGGGCCGTCC 60.608 55.000 20.48 4.35 32.97 4.79
531 537 2.796483 TTTCATGACTGGGCCGTCCG 62.796 60.000 20.48 13.94 38.76 4.79
532 538 4.082523 CATGACTGGGCCGTCCGT 62.083 66.667 20.48 6.66 38.76 4.69
533 539 3.771160 ATGACTGGGCCGTCCGTC 61.771 66.667 20.48 14.37 38.57 4.79
709 725 2.672874 TCTCCGCGTTGATTCTTGAATG 59.327 45.455 4.92 0.00 0.00 2.67
760 776 2.136878 CCCCTCCATCTCGGGTCAG 61.137 68.421 0.00 0.00 38.88 3.51
1100 1121 2.227089 CTCGACTTCTTGACCCGGGG 62.227 65.000 27.92 12.73 0.00 5.73
1147 1168 1.863155 TAGCAAGGGGGCCTTCTTGG 61.863 60.000 27.96 16.83 42.67 3.61
1186 1207 9.935682 CATTTAACGCTAGATTGTGTATTTCAT 57.064 29.630 0.00 0.00 0.00 2.57
1331 1353 7.203218 TCTTATCACAAGATCAATGGTCGTAG 58.797 38.462 0.00 0.00 35.67 3.51
1381 1403 5.128919 AGAGTTCAACTGTTGCTCAAGATT 58.871 37.500 21.93 6.18 0.00 2.40
1427 1459 5.221783 TGACCTAGGGTTCCAAGTCTTAAAC 60.222 44.000 14.81 2.72 35.25 2.01
1435 1467 5.401376 GGTTCCAAGTCTTAAACATTTTCGC 59.599 40.000 10.54 0.00 0.00 4.70
1479 1512 9.771534 GTAGAATATAAACTTCTGGAAGCAGAT 57.228 33.333 9.91 4.18 41.99 2.90
1680 1713 9.816787 ATAACTAAAGGTTACCTTCATTTTGGA 57.183 29.630 17.77 0.00 43.92 3.53
2378 2590 9.238368 TGCTTTACCATATAGTTTTTACTGCTT 57.762 29.630 0.00 0.00 0.00 3.91
2404 2616 2.586425 AGCAATACATCGGAATTGGGG 58.414 47.619 3.76 0.00 34.37 4.96
2719 2935 3.498927 AGCAATCACAGCAATGCTAAC 57.501 42.857 7.70 0.00 46.61 2.34
2742 2958 4.334759 CACACATGCCTAGAAATGAGAAGG 59.665 45.833 10.53 0.00 0.00 3.46
2771 2987 5.587388 ATGGTTAGCCTGATCATTTTGTG 57.413 39.130 0.00 0.00 35.27 3.33
2916 3437 4.358851 CTCTGAGTTGCTACTATGCTCAC 58.641 47.826 0.00 0.00 33.84 3.51
3056 3577 9.953697 TGCCATTTATAATTTTATGTTACCGTC 57.046 29.630 0.00 0.00 0.00 4.79
3240 3803 8.840321 GCTATTCATTTGCTATCTAGGAAACAA 58.160 33.333 6.11 3.82 44.46 2.83
3281 3844 6.530120 TGCAAAGAAGAGTGATTGGTACTAA 58.470 36.000 0.00 0.00 0.00 2.24
3507 4071 5.204292 TGACTGAGTGAGCTAACATATCCT 58.796 41.667 3.43 0.00 0.00 3.24
3692 4271 6.126863 TCATTAGGAAGTGTCAAACCTGAT 57.873 37.500 0.00 0.00 33.05 2.90
3800 4383 6.774354 AACTTACAGTTATGGTTGTACACG 57.226 37.500 0.00 0.00 36.52 4.49
3881 4464 2.301870 AGGTCGTTGCACTATTCCAGAA 59.698 45.455 0.00 0.00 0.00 3.02
3893 4476 8.855110 TGCACTATTCCAGAAAAATTTCTTACA 58.145 29.630 5.68 0.00 44.70 2.41
3920 4503 6.310224 CCATTTGCGTAATTGGGTCTTTTAAG 59.690 38.462 16.58 0.00 34.94 1.85
4123 4718 7.765360 AGCAGTGATCTTTTCTCTTTATCTCAG 59.235 37.037 0.00 0.00 0.00 3.35
4791 5388 5.939883 CAGATGTACAGGGAAATCAGACAAA 59.060 40.000 0.33 0.00 0.00 2.83
5115 5712 5.869753 ATTATGTCGCATCCTTATTCAGC 57.130 39.130 0.00 0.00 0.00 4.26
5279 5876 9.226606 TGATTTTTACTATCCTCGTGTGATTTT 57.773 29.630 0.00 0.00 0.00 1.82
5381 5978 5.015178 TTCCTGGTTGAATACCTTGGAAGAT 59.985 40.000 13.74 0.00 45.90 2.40
5434 6031 3.923017 AGTTGCTGTGCATTTAAGGTC 57.077 42.857 0.00 0.00 38.76 3.85
5757 6479 6.546484 AGATTTCTTTTGGGATCAGAAGACA 58.454 36.000 0.00 0.00 41.77 3.41
6074 6796 3.181329 TGAGATCACCAAGGTACACCAT 58.819 45.455 0.38 0.00 38.89 3.55
6385 7324 2.571212 AGTTTCACAGATTTCGCACCA 58.429 42.857 0.00 0.00 0.00 4.17
6419 7364 7.284716 TGAAGTCTACTGAAGAGTTGTCACTTA 59.715 37.037 0.00 0.00 45.99 2.24
6455 7400 6.033341 GCAAGAATACTTTTGTGTGACAACA 58.967 36.000 0.00 0.00 37.90 3.33
6766 7711 2.493675 TGCTGGCGTTGGCATAAATTTA 59.506 40.909 0.00 0.00 42.47 1.40
6910 7855 8.433421 ACGTAAAATCAATGGTATAGGACTTG 57.567 34.615 0.00 0.00 0.00 3.16
7128 8083 2.292828 ACAAGTAATGCCCAACTGCT 57.707 45.000 0.00 0.00 0.00 4.24
8036 9032 5.827797 TGGTATATGATTGGGCTTTGAACTC 59.172 40.000 0.00 0.00 0.00 3.01
8037 9033 5.049405 GGTATATGATTGGGCTTTGAACTCG 60.049 44.000 0.00 0.00 0.00 4.18
8038 9034 0.881118 TGATTGGGCTTTGAACTCGC 59.119 50.000 0.00 0.00 0.00 5.03
8039 9035 1.168714 GATTGGGCTTTGAACTCGCT 58.831 50.000 0.00 0.00 0.00 4.93
8040 9036 0.883833 ATTGGGCTTTGAACTCGCTG 59.116 50.000 0.00 0.00 0.00 5.18
8279 9275 3.221771 AGAGGAGGAAGACGATGATGAG 58.778 50.000 0.00 0.00 0.00 2.90
8589 9586 2.039879 GGTGCTAACCTCTTTCAAGGGA 59.960 50.000 0.00 0.00 43.84 4.20
8590 9587 3.497942 GGTGCTAACCTCTTTCAAGGGAA 60.498 47.826 0.00 0.00 43.84 3.97
8595 9592 3.570912 ACCTCTTTCAAGGGAACGAAA 57.429 42.857 0.00 0.00 41.04 3.46
9051 10053 5.482908 ACTGATTGTTGTAGAGTGATGGTC 58.517 41.667 0.00 0.00 0.00 4.02
9120 10122 6.705863 AAAAAGAGGATGATGGTTCTATGC 57.294 37.500 0.00 0.00 0.00 3.14
9149 10158 9.865321 TGTTGTCTGTAAGTTATGTATTACTCC 57.135 33.333 0.00 0.00 33.86 3.85
9150 10159 9.310716 GTTGTCTGTAAGTTATGTATTACTCCC 57.689 37.037 0.00 0.00 33.86 4.30
9151 10160 8.834004 TGTCTGTAAGTTATGTATTACTCCCT 57.166 34.615 0.00 0.00 33.86 4.20
9152 10161 8.910944 TGTCTGTAAGTTATGTATTACTCCCTC 58.089 37.037 0.00 0.00 33.86 4.30
9153 10162 8.358895 GTCTGTAAGTTATGTATTACTCCCTCC 58.641 40.741 0.00 0.00 33.86 4.30
9154 10163 7.230108 TCTGTAAGTTATGTATTACTCCCTCCG 59.770 40.741 0.00 0.00 33.86 4.63
9155 10164 6.835488 TGTAAGTTATGTATTACTCCCTCCGT 59.165 38.462 0.00 0.00 33.86 4.69
9156 10165 6.402456 AAGTTATGTATTACTCCCTCCGTC 57.598 41.667 0.00 0.00 0.00 4.79
9157 10166 4.831710 AGTTATGTATTACTCCCTCCGTCC 59.168 45.833 0.00 0.00 0.00 4.79
9158 10167 2.077687 TGTATTACTCCCTCCGTCCC 57.922 55.000 0.00 0.00 0.00 4.46
9159 10168 1.288633 TGTATTACTCCCTCCGTCCCA 59.711 52.381 0.00 0.00 0.00 4.37
9160 10169 2.090943 TGTATTACTCCCTCCGTCCCAT 60.091 50.000 0.00 0.00 0.00 4.00
9161 10170 3.140707 TGTATTACTCCCTCCGTCCCATA 59.859 47.826 0.00 0.00 0.00 2.74
9162 10171 2.852714 TTACTCCCTCCGTCCCATAA 57.147 50.000 0.00 0.00 0.00 1.90
9163 10172 3.339713 TTACTCCCTCCGTCCCATAAT 57.660 47.619 0.00 0.00 0.00 1.28
9164 10173 4.474303 TTACTCCCTCCGTCCCATAATA 57.526 45.455 0.00 0.00 0.00 0.98
9165 10174 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
9166 10175 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
9167 10176 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
9168 10177 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
9169 10178 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
9170 10179 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
9171 10180 6.269194 TCCCTCCGTCCCATAATATAAGAAT 58.731 40.000 0.00 0.00 0.00 2.40
9172 10181 6.156256 TCCCTCCGTCCCATAATATAAGAATG 59.844 42.308 0.00 0.00 0.00 2.67
9173 10182 5.817816 CCTCCGTCCCATAATATAAGAATGC 59.182 44.000 0.00 0.00 0.00 3.56
9174 10183 6.352222 CCTCCGTCCCATAATATAAGAATGCT 60.352 42.308 0.00 0.00 0.00 3.79
9175 10184 7.016153 TCCGTCCCATAATATAAGAATGCTT 57.984 36.000 0.00 0.00 38.15 3.91
9176 10185 7.458397 TCCGTCCCATAATATAAGAATGCTTT 58.542 34.615 0.00 0.00 35.56 3.51
9177 10186 7.942341 TCCGTCCCATAATATAAGAATGCTTTT 59.058 33.333 0.00 0.00 35.56 2.27
9178 10187 8.023128 CCGTCCCATAATATAAGAATGCTTTTG 58.977 37.037 0.00 0.00 35.56 2.44
9179 10188 8.783093 CGTCCCATAATATAAGAATGCTTTTGA 58.217 33.333 0.00 0.00 35.56 2.69
9221 10230 7.989416 AAACGTTCTTATATTTTGGGACAGA 57.011 32.000 0.00 0.00 42.39 3.41
9222 10231 7.611213 AACGTTCTTATATTTTGGGACAGAG 57.389 36.000 0.00 0.00 42.39 3.35
9223 10232 6.113411 ACGTTCTTATATTTTGGGACAGAGG 58.887 40.000 0.00 0.00 42.39 3.69
9224 10233 5.527582 CGTTCTTATATTTTGGGACAGAGGG 59.472 44.000 0.00 0.00 42.39 4.30
9225 10234 6.631766 CGTTCTTATATTTTGGGACAGAGGGA 60.632 42.308 0.00 0.00 42.39 4.20
9226 10235 6.500589 TCTTATATTTTGGGACAGAGGGAG 57.499 41.667 0.00 0.00 42.39 4.30
9227 10236 5.970640 TCTTATATTTTGGGACAGAGGGAGT 59.029 40.000 0.00 0.00 42.39 3.85
9228 10237 7.136885 TCTTATATTTTGGGACAGAGGGAGTA 58.863 38.462 0.00 0.00 42.39 2.59
9241 10250 1.133792 AGGGAGTAATTGGGAATGGCG 60.134 52.381 0.00 0.00 0.00 5.69
9285 10294 8.793592 CAGGTATCTTTAACTTAAAGGTTGCTT 58.206 33.333 17.55 6.70 44.04 3.91
9351 10360 2.577911 GCCTGCGCAATTTCGAGC 60.578 61.111 13.05 1.99 34.03 5.03
9382 10391 5.962433 TGTTCACATGAGCTACTAGTAACC 58.038 41.667 3.76 0.00 0.00 2.85
9406 10415 2.004583 TGGTTGTTCGATGATCCGTC 57.995 50.000 0.00 0.00 0.00 4.79
9426 10435 4.492570 CGTCTGATCTTTGGACGTAAATGC 60.493 45.833 16.58 0.00 44.93 3.56
9603 10613 7.308830 GCATGAAGATGTTTCTTGGTTAAGAGT 60.309 37.037 0.00 0.00 42.34 3.24
9620 10630 2.579860 AGAGTGAATGGCAGGAATCCTT 59.420 45.455 0.00 0.00 0.00 3.36
9668 10683 6.625532 AACATATTCTTTGGGCCATTCTTT 57.374 33.333 7.26 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 62 4.593864 GAGATCCGGGCGAGGCAC 62.594 72.222 0.00 0.00 0.00 5.01
68 71 0.893270 AGATCGAGCAGGAGATCCGG 60.893 60.000 2.38 0.00 43.03 5.14
69 72 0.240678 CAGATCGAGCAGGAGATCCG 59.759 60.000 2.38 0.00 43.03 4.18
83 86 1.442148 GGAGTGCCGGTACCAGATC 59.558 63.158 19.90 10.01 0.00 2.75
97 100 1.517832 GCTATGCTCACACCGGAGT 59.482 57.895 9.46 2.22 37.24 3.85
104 107 0.179148 CCACGTACGCTATGCTCACA 60.179 55.000 16.72 0.00 0.00 3.58
115 118 2.724349 GGTAGCAGATAACCACGTACG 58.276 52.381 15.01 15.01 35.73 3.67
118 121 0.458669 CCGGTAGCAGATAACCACGT 59.541 55.000 0.00 0.00 35.35 4.49
130 133 2.098831 GTTTCGCTGGTCCGGTAGC 61.099 63.158 15.05 15.05 36.60 3.58
133 136 2.030562 CAGTTTCGCTGGTCCGGT 59.969 61.111 0.00 0.00 41.42 5.28
148 153 1.515020 CTCTTCCCACGCTCTCCAG 59.485 63.158 0.00 0.00 0.00 3.86
177 182 2.039070 GCCCATCCACCTCATCTCTCT 61.039 57.143 0.00 0.00 0.00 3.10
304 309 2.045708 GGGTGTGAATGCCGCATGA 61.046 57.895 6.63 0.00 37.64 3.07
307 312 2.597818 TAGGGGTGTGAATGCCGCA 61.598 57.895 0.00 0.00 39.78 5.69
324 329 1.947456 CGACGGACATCTCCTCATGTA 59.053 52.381 0.00 0.00 37.11 2.29
351 357 2.757056 GGAATCGCCCGAAAACCCG 61.757 63.158 0.00 0.00 0.00 5.28
354 360 0.808755 ACATGGAATCGCCCGAAAAC 59.191 50.000 0.00 0.00 34.97 2.43
359 365 0.098728 GTTTCACATGGAATCGCCCG 59.901 55.000 0.00 0.00 34.91 6.13
362 368 0.455815 GGGGTTTCACATGGAATCGC 59.544 55.000 0.00 5.74 37.40 4.58
364 370 2.230130 TGGGGGTTTCACATGGAATC 57.770 50.000 0.00 0.00 34.91 2.52
370 376 4.536765 GACTAATGATGGGGGTTTCACAT 58.463 43.478 0.00 0.00 0.00 3.21
375 381 3.076785 TGTTGGACTAATGATGGGGGTTT 59.923 43.478 0.00 0.00 0.00 3.27
376 382 2.652348 TGTTGGACTAATGATGGGGGTT 59.348 45.455 0.00 0.00 0.00 4.11
378 384 3.117550 TCATGTTGGACTAATGATGGGGG 60.118 47.826 0.00 0.00 0.00 5.40
394 400 3.262420 GCTCTTACACGTCCATCATGTT 58.738 45.455 0.00 0.00 0.00 2.71
396 402 1.854743 CGCTCTTACACGTCCATCATG 59.145 52.381 0.00 0.00 0.00 3.07
397 403 1.476891 ACGCTCTTACACGTCCATCAT 59.523 47.619 0.00 0.00 38.28 2.45
424 430 2.448926 TATGGTGCGAATATGGGACG 57.551 50.000 0.00 0.00 0.00 4.79
426 432 4.078537 CCAAATATGGTGCGAATATGGGA 58.921 43.478 0.00 0.00 42.18 4.37
450 456 0.392193 GGGCTGATCCGCATATCCAG 60.392 60.000 11.45 0.00 34.94 3.86
462 468 0.749454 GCTCAAATGGTCGGGCTGAT 60.749 55.000 0.00 0.00 0.00 2.90
469 475 0.110238 CAACGGTGCTCAAATGGTCG 60.110 55.000 0.00 0.00 0.00 4.79
473 479 1.666888 GCCTTCAACGGTGCTCAAATG 60.667 52.381 0.00 0.00 0.00 2.32
474 480 0.598065 GCCTTCAACGGTGCTCAAAT 59.402 50.000 0.00 0.00 0.00 2.32
475 481 1.781025 CGCCTTCAACGGTGCTCAAA 61.781 55.000 0.00 0.00 0.00 2.69
476 482 2.250939 CGCCTTCAACGGTGCTCAA 61.251 57.895 0.00 0.00 0.00 3.02
477 483 2.664851 CGCCTTCAACGGTGCTCA 60.665 61.111 0.00 0.00 0.00 4.26
479 485 2.665185 GACGCCTTCAACGGTGCT 60.665 61.111 0.00 0.00 38.11 4.40
481 487 1.635663 GATGGACGCCTTCAACGGTG 61.636 60.000 0.00 0.00 40.39 4.94
482 488 1.375523 GATGGACGCCTTCAACGGT 60.376 57.895 6.82 0.00 34.00 4.83
483 489 0.673644 AAGATGGACGCCTTCAACGG 60.674 55.000 12.12 0.00 31.13 4.44
484 490 1.135972 CAAAGATGGACGCCTTCAACG 60.136 52.381 12.12 0.00 31.13 4.10
485 491 2.151202 TCAAAGATGGACGCCTTCAAC 58.849 47.619 12.12 0.00 31.13 3.18
486 492 2.559698 TCAAAGATGGACGCCTTCAA 57.440 45.000 12.12 0.00 31.13 2.69
488 494 1.594862 CGATCAAAGATGGACGCCTTC 59.405 52.381 0.00 4.34 0.00 3.46
490 496 0.824109 TCGATCAAAGATGGACGCCT 59.176 50.000 0.00 0.00 0.00 5.52
491 497 1.651987 TTCGATCAAAGATGGACGCC 58.348 50.000 0.00 0.00 0.00 5.68
492 498 3.951979 AATTCGATCAAAGATGGACGC 57.048 42.857 0.00 0.00 0.00 5.19
493 499 5.868257 TGAAAATTCGATCAAAGATGGACG 58.132 37.500 0.00 0.00 0.00 4.79
494 500 7.430502 GTCATGAAAATTCGATCAAAGATGGAC 59.569 37.037 0.00 0.00 0.00 4.02
495 501 7.337689 AGTCATGAAAATTCGATCAAAGATGGA 59.662 33.333 0.00 0.00 0.00 3.41
496 502 7.431376 CAGTCATGAAAATTCGATCAAAGATGG 59.569 37.037 0.00 0.00 0.00 3.51
497 503 7.431376 CCAGTCATGAAAATTCGATCAAAGATG 59.569 37.037 0.00 0.00 0.00 2.90
498 504 7.415989 CCCAGTCATGAAAATTCGATCAAAGAT 60.416 37.037 0.00 0.00 0.00 2.40
499 505 6.127925 CCCAGTCATGAAAATTCGATCAAAGA 60.128 38.462 0.00 0.00 0.00 2.52
500 506 6.032094 CCCAGTCATGAAAATTCGATCAAAG 58.968 40.000 0.00 0.00 0.00 2.77
501 507 5.622007 GCCCAGTCATGAAAATTCGATCAAA 60.622 40.000 0.00 0.00 0.00 2.69
502 508 4.142403 GCCCAGTCATGAAAATTCGATCAA 60.142 41.667 0.00 0.00 0.00 2.57
503 509 3.378112 GCCCAGTCATGAAAATTCGATCA 59.622 43.478 0.00 0.00 0.00 2.92
504 510 3.243201 GGCCCAGTCATGAAAATTCGATC 60.243 47.826 0.00 0.00 0.00 3.69
515 521 4.082523 ACGGACGGCCCAGTCATG 62.083 66.667 0.00 6.85 42.62 3.07
526 532 3.927163 CTCAAACCCCGGACGGACG 62.927 68.421 13.13 4.31 37.50 4.79
531 537 4.735358 GGGCCTCAAACCCCGGAC 62.735 72.222 0.73 0.00 42.01 4.79
591 606 2.476947 GCGCGCACGTGGAAATTA 59.523 55.556 29.10 0.00 42.83 1.40
709 725 0.108756 CTCCTTCCTTCCGTTCCGTC 60.109 60.000 0.00 0.00 0.00 4.79
760 776 1.065782 GGAGGGGAAGAGAAGTTGCTC 60.066 57.143 0.00 0.00 35.11 4.26
1100 1121 2.165319 ACCTTAACAAGCACTCGACC 57.835 50.000 0.00 0.00 0.00 4.79
1147 1168 4.083484 AGCGTTAAATGCCTTACACAAGAC 60.083 41.667 0.00 0.00 33.20 3.01
1186 1207 3.828451 CCCAAGAAAGAGCAATTCCAAGA 59.172 43.478 0.00 0.00 0.00 3.02
1312 1334 3.308053 CAGCTACGACCATTGATCTTGTG 59.692 47.826 0.00 0.00 0.00 3.33
1318 1340 2.430694 TGTAGCAGCTACGACCATTGAT 59.569 45.455 24.53 0.00 39.58 2.57
1341 1363 7.482654 TGAACTCTTGTTTGATTAGACAGTG 57.517 36.000 0.00 0.00 36.39 3.66
1347 1369 7.166473 GCAACAGTTGAACTCTTGTTTGATTAG 59.834 37.037 17.99 0.00 36.39 1.73
1381 1403 6.922957 GTCATGGAAAACAAGCTGATTAAACA 59.077 34.615 0.00 0.00 0.00 2.83
1427 1459 7.953305 TTCGATCAGAATTAAAGCGAAAATG 57.047 32.000 0.00 0.00 33.99 2.32
1489 1522 3.260380 TGCCACCCAACAAATCTTAATGG 59.740 43.478 0.00 0.00 0.00 3.16
1905 1938 7.617533 ACAAATGACGCTGTTATTGTAAAAC 57.382 32.000 0.00 0.00 0.00 2.43
2101 2143 2.288666 GGCAAGAGTGTTGACAAGACA 58.711 47.619 16.90 0.00 0.00 3.41
2378 2590 5.392919 CCAATTCCGATGTATTGCTTGACAA 60.393 40.000 0.00 0.00 44.01 3.18
2404 2616 2.892374 AGTTGTTTCTTGTTGCCTTGC 58.108 42.857 0.00 0.00 0.00 4.01
2719 2935 4.334759 CCTTCTCATTTCTAGGCATGTGTG 59.665 45.833 0.00 0.00 0.00 3.82
2742 2958 4.513442 TGATCAGGCTAACCATACAACAC 58.487 43.478 0.00 0.00 39.06 3.32
2916 3437 6.038603 TCTGAAAATATGGATTTTGCTCTCCG 59.961 38.462 0.56 0.00 43.76 4.63
3094 3615 8.917088 CAAAACATCTTATATTTGTGAGGGGAT 58.083 33.333 0.00 0.00 0.00 3.85
3240 3803 7.966246 TCTTTGCATAGAAAAATGTTTGCAT 57.034 28.000 4.20 0.00 36.80 3.96
3296 3859 1.949525 TGCACTGCAGAAAAGGAGAAC 59.050 47.619 23.35 0.00 33.32 3.01
3507 4071 9.109393 GATACTGTTGATTAGCCTTTTACATGA 57.891 33.333 0.00 0.00 0.00 3.07
3624 4203 7.093596 CCTGATATGGACTCATGCTGATAAGTA 60.094 40.741 0.00 0.00 34.96 2.24
3800 4383 9.099454 GGGCAGCAGTTATCACTTATATTATAC 57.901 37.037 0.00 0.00 0.00 1.47
3857 4440 3.857052 TGGAATAGTGCAACGACCTTAG 58.143 45.455 0.00 0.00 45.86 2.18
3881 4464 8.649973 TTACGCAAATGGTTGTAAGAAATTTT 57.350 26.923 0.00 0.00 37.06 1.82
3893 4476 3.161866 AGACCCAATTACGCAAATGGTT 58.838 40.909 1.85 0.00 0.00 3.67
4123 4718 4.455877 AGGGATCAAAATTCTCACGTCAAC 59.544 41.667 0.00 0.00 0.00 3.18
4139 4734 1.750193 GCATTCGTTTGGAGGGATCA 58.250 50.000 0.00 0.00 0.00 2.92
4329 4926 8.888579 ATAATATCGTCCCTGTAAGAAAGTTG 57.111 34.615 0.00 0.00 34.07 3.16
4390 4987 7.888021 TGTATGTCATTTGGATAACTCAAGGTT 59.112 33.333 0.00 0.00 41.54 3.50
4648 5245 1.340017 GCTTGGTTGAGCCCAGATGTA 60.340 52.381 0.00 0.00 36.66 2.29
4791 5388 6.126854 ACCAGAAACTTTACCTAGACTGTTGT 60.127 38.462 0.00 0.00 0.00 3.32
4892 5489 2.390938 CACAAAGCATGCTTGTCAGTG 58.609 47.619 32.54 28.86 36.26 3.66
5115 5712 5.226565 CGAATTTGATTTGCTTCATCGTCAG 59.773 40.000 0.00 0.00 0.00 3.51
5279 5876 7.310072 TCACAACTCATTCTTTACGTTGAAA 57.690 32.000 0.00 0.00 38.55 2.69
5381 5978 8.202137 CCCTCGATGAATTAGTTAAAGAAGGTA 58.798 37.037 0.00 0.00 0.00 3.08
5384 5981 6.538742 TGCCCTCGATGAATTAGTTAAAGAAG 59.461 38.462 0.00 0.00 0.00 2.85
5434 6031 5.552870 AAAGTAGTACTATCATGGCCCAG 57.447 43.478 5.75 0.00 0.00 4.45
5757 6479 8.466617 AAGTTATAAGATGGTGAGTCGATAGT 57.533 34.615 0.00 0.00 37.40 2.12
6074 6796 7.724305 AAGACGTAGAAAGCTAAAATGTTCA 57.276 32.000 0.00 0.00 0.00 3.18
6385 7324 8.995027 ACTCTTCAGTAGACTTCATAGATGAT 57.005 34.615 0.00 0.00 36.56 2.45
6766 7711 2.168521 AGTCCATCCATTCGAATCACGT 59.831 45.455 7.92 0.00 43.13 4.49
7100 8055 5.699097 TGGGCATTACTTGTTACAAAGTC 57.301 39.130 0.00 0.00 40.77 3.01
7128 8083 4.699637 ACTTCATTTGTGACCTACGTTCA 58.300 39.130 0.00 0.00 0.00 3.18
7243 8202 7.081526 ACAAGTCATTTCAAGATATGCTGAC 57.918 36.000 0.00 0.00 35.07 3.51
7278 8237 5.048364 ACGCTAACATATGGAGAGAGATGTC 60.048 44.000 14.65 0.00 31.37 3.06
8036 9032 3.667497 ACCTGATATCATGTACCAGCG 57.333 47.619 11.46 0.00 0.00 5.18
8037 9033 6.102897 ACTTACCTGATATCATGTACCAGC 57.897 41.667 17.39 0.00 28.98 4.85
8038 9034 7.439356 CACAACTTACCTGATATCATGTACCAG 59.561 40.741 17.39 15.42 28.98 4.00
8039 9035 7.093068 ACACAACTTACCTGATATCATGTACCA 60.093 37.037 17.39 6.42 28.98 3.25
8040 9036 7.272978 ACACAACTTACCTGATATCATGTACC 58.727 38.462 17.39 0.00 28.98 3.34
8100 9096 3.031736 GGTGACCTCTTACATGAGCCTA 58.968 50.000 0.00 0.00 33.02 3.93
8279 9275 3.867493 TGACTGCTTCATCATCATCGAAC 59.133 43.478 0.00 0.00 0.00 3.95
8426 9422 7.602644 TGTCAAATCCATGAACTACTTACAGTC 59.397 37.037 0.00 0.00 0.00 3.51
8542 9538 7.538575 TCAGTCCTTTTGTTCTTTTGAGAAAG 58.461 34.615 0.00 0.00 42.92 2.62
8589 9586 8.561738 AAGATTTCACTACATATGGTTTCGTT 57.438 30.769 7.80 0.00 0.00 3.85
8590 9587 9.095065 GTAAGATTTCACTACATATGGTTTCGT 57.905 33.333 7.80 0.00 0.00 3.85
9066 10068 1.673337 GGTGTTACTCCCGGCAACC 60.673 63.158 0.00 0.00 0.00 3.77
9146 10155 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
9147 10156 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
9148 10157 6.349300 CATTCTTATATTATGGGACGGAGGG 58.651 44.000 0.00 0.00 0.00 4.30
9149 10158 5.817816 GCATTCTTATATTATGGGACGGAGG 59.182 44.000 0.00 0.00 0.00 4.30
9150 10159 6.644347 AGCATTCTTATATTATGGGACGGAG 58.356 40.000 0.00 0.00 0.00 4.63
9151 10160 6.620877 AGCATTCTTATATTATGGGACGGA 57.379 37.500 0.00 0.00 0.00 4.69
9152 10161 7.687941 AAAGCATTCTTATATTATGGGACGG 57.312 36.000 0.00 0.00 31.02 4.79
9153 10162 8.783093 TCAAAAGCATTCTTATATTATGGGACG 58.217 33.333 0.00 0.00 31.02 4.79
9195 10204 8.852135 TCTGTCCCAAAATATAAGAACGTTTTT 58.148 29.630 9.22 9.22 0.00 1.94
9196 10205 8.398878 TCTGTCCCAAAATATAAGAACGTTTT 57.601 30.769 0.46 0.00 0.00 2.43
9197 10206 7.120726 CCTCTGTCCCAAAATATAAGAACGTTT 59.879 37.037 0.46 0.00 0.00 3.60
9198 10207 6.598064 CCTCTGTCCCAAAATATAAGAACGTT 59.402 38.462 0.00 0.00 0.00 3.99
9199 10208 6.113411 CCTCTGTCCCAAAATATAAGAACGT 58.887 40.000 0.00 0.00 0.00 3.99
9200 10209 5.527582 CCCTCTGTCCCAAAATATAAGAACG 59.472 44.000 0.00 0.00 0.00 3.95
9201 10210 6.659824 TCCCTCTGTCCCAAAATATAAGAAC 58.340 40.000 0.00 0.00 0.00 3.01
9202 10211 6.447084 ACTCCCTCTGTCCCAAAATATAAGAA 59.553 38.462 0.00 0.00 0.00 2.52
9203 10212 5.970640 ACTCCCTCTGTCCCAAAATATAAGA 59.029 40.000 0.00 0.00 0.00 2.10
9204 10213 6.253946 ACTCCCTCTGTCCCAAAATATAAG 57.746 41.667 0.00 0.00 0.00 1.73
9205 10214 7.758820 TTACTCCCTCTGTCCCAAAATATAA 57.241 36.000 0.00 0.00 0.00 0.98
9206 10215 7.947782 ATTACTCCCTCTGTCCCAAAATATA 57.052 36.000 0.00 0.00 0.00 0.86
9207 10216 6.848562 ATTACTCCCTCTGTCCCAAAATAT 57.151 37.500 0.00 0.00 0.00 1.28
9208 10217 6.423182 CAATTACTCCCTCTGTCCCAAAATA 58.577 40.000 0.00 0.00 0.00 1.40
9209 10218 5.264395 CAATTACTCCCTCTGTCCCAAAAT 58.736 41.667 0.00 0.00 0.00 1.82
9210 10219 4.508405 CCAATTACTCCCTCTGTCCCAAAA 60.508 45.833 0.00 0.00 0.00 2.44
9211 10220 3.010138 CCAATTACTCCCTCTGTCCCAAA 59.990 47.826 0.00 0.00 0.00 3.28
9212 10221 2.576191 CCAATTACTCCCTCTGTCCCAA 59.424 50.000 0.00 0.00 0.00 4.12
9213 10222 2.196595 CCAATTACTCCCTCTGTCCCA 58.803 52.381 0.00 0.00 0.00 4.37
9214 10223 1.490910 CCCAATTACTCCCTCTGTCCC 59.509 57.143 0.00 0.00 0.00 4.46
9215 10224 2.478292 TCCCAATTACTCCCTCTGTCC 58.522 52.381 0.00 0.00 0.00 4.02
9216 10225 4.455606 CATTCCCAATTACTCCCTCTGTC 58.544 47.826 0.00 0.00 0.00 3.51
9217 10226 3.203040 CCATTCCCAATTACTCCCTCTGT 59.797 47.826 0.00 0.00 0.00 3.41
9218 10227 3.825328 CCATTCCCAATTACTCCCTCTG 58.175 50.000 0.00 0.00 0.00 3.35
9219 10228 2.175715 GCCATTCCCAATTACTCCCTCT 59.824 50.000 0.00 0.00 0.00 3.69
9220 10229 2.587522 GCCATTCCCAATTACTCCCTC 58.412 52.381 0.00 0.00 0.00 4.30
9221 10230 1.133792 CGCCATTCCCAATTACTCCCT 60.134 52.381 0.00 0.00 0.00 4.20
9222 10231 1.318576 CGCCATTCCCAATTACTCCC 58.681 55.000 0.00 0.00 0.00 4.30
9223 10232 1.318576 CCGCCATTCCCAATTACTCC 58.681 55.000 0.00 0.00 0.00 3.85
9224 10233 1.318576 CCCGCCATTCCCAATTACTC 58.681 55.000 0.00 0.00 0.00 2.59
9225 10234 0.629058 ACCCGCCATTCCCAATTACT 59.371 50.000 0.00 0.00 0.00 2.24
9226 10235 1.480789 AACCCGCCATTCCCAATTAC 58.519 50.000 0.00 0.00 0.00 1.89
9227 10236 3.117474 TCATAACCCGCCATTCCCAATTA 60.117 43.478 0.00 0.00 0.00 1.40
9228 10237 2.038659 CATAACCCGCCATTCCCAATT 58.961 47.619 0.00 0.00 0.00 2.32
9241 10250 5.048846 ACCTGATATGGTGTTCATAACCC 57.951 43.478 0.00 0.00 41.23 4.11
9285 10294 6.662755 AGAATATGCTGACCAAATTCTACCA 58.337 36.000 0.00 0.00 35.64 3.25
9351 10360 2.747989 AGCTCATGTGAACAATCTGCTG 59.252 45.455 0.00 0.00 0.00 4.41
9353 10362 3.937706 AGTAGCTCATGTGAACAATCTGC 59.062 43.478 0.00 0.00 0.00 4.26
9382 10391 4.097714 CGGATCATCGAACAACCAATTTG 58.902 43.478 0.00 0.00 41.49 2.32
9406 10415 4.944962 TGCATTTACGTCCAAAGATCAG 57.055 40.909 0.00 0.00 0.00 2.90
9603 10613 5.128033 TGATAAAGGATTCCTGCCATTCA 57.872 39.130 5.84 3.36 32.13 2.57
9620 10630 7.984422 ACTTCTGTTCACATTCACATGATAA 57.016 32.000 0.00 0.00 34.11 1.75
9668 10683 4.321718 CATGAGAGTTTCAGAGCCTTTGA 58.678 43.478 0.00 0.00 39.68 2.69


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

AutoCloner maintained by Alex Coulton.