Multiple sequence alignment - TraesCS1D01G263900

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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 TraesCS1D01G263900 chr1D 100.000 6696 0 0 1 6696 359726610 359719915 0.000000e+00 12366.0
1 TraesCS1D01G263900 chr1A 95.011 2746 106 13 782 3510 459275685 459272954 0.000000e+00 4283.0
2 TraesCS1D01G263900 chr1A 95.511 1604 44 9 3504 5107 459272925 459271350 0.000000e+00 2538.0
3 TraesCS1D01G263900 chr1A 92.615 826 40 7 5118 5923 459271104 459270280 0.000000e+00 1168.0
4 TraesCS1D01G263900 chr1A 81.891 497 50 17 6202 6696 459270117 459269659 3.790000e-102 383.0
5 TraesCS1D01G263900 chr1A 92.806 139 8 1 3088 3224 155857706 155857844 4.100000e-47 200.0
6 TraesCS1D01G263900 chr1A 74.346 191 31 9 237 412 308950630 308950443 1.560000e-06 65.8
7 TraesCS1D01G263900 chr1A 97.368 38 1 0 6142 6179 459270204 459270167 1.560000e-06 65.8
8 TraesCS1D01G263900 chr1B 96.693 2026 65 2 777 2802 481713049 481711026 0.000000e+00 3369.0
9 TraesCS1D01G263900 chr1B 93.345 1773 94 13 3231 4982 481710601 481708832 0.000000e+00 2599.0
10 TraesCS1D01G263900 chr1B 89.167 1237 64 35 2284 3510 642795255 642794079 0.000000e+00 1478.0
11 TraesCS1D01G263900 chr1B 95.479 730 23 4 5284 6008 481708446 481707722 0.000000e+00 1157.0
12 TraesCS1D01G263900 chr1B 95.516 669 23 5 6000 6664 481705892 481705227 0.000000e+00 1062.0
13 TraesCS1D01G263900 chr1B 92.445 503 34 3 3504 4006 642794050 642793552 0.000000e+00 715.0
14 TraesCS1D01G263900 chr1B 85.202 446 45 9 1 433 481713831 481713394 7.970000e-119 438.0
15 TraesCS1D01G263900 chr1B 91.620 179 13 2 2794 2972 481710977 481710801 5.190000e-61 246.0
16 TraesCS1D01G263900 chr1B 89.167 120 9 3 2971 3089 481710716 481710600 5.410000e-31 147.0
17 TraesCS1D01G263900 chr1B 100.000 29 0 0 724 752 104467128 104467156 3.000000e-03 54.7
18 TraesCS1D01G263900 chr7B 90.756 1244 64 23 2277 3510 380858572 380859774 0.000000e+00 1613.0
19 TraesCS1D01G263900 chr7B 92.402 408 27 3 3501 3908 380859800 380860203 4.500000e-161 579.0
20 TraesCS1D01G263900 chr2D 87.500 216 24 3 3 216 644282124 644282338 5.190000e-61 246.0
21 TraesCS1D01G263900 chr2D 83.265 245 22 10 2 241 18635995 18636225 2.450000e-49 207.0
22 TraesCS1D01G263900 chr2D 82.731 249 27 10 1 235 56804097 56804343 2.450000e-49 207.0
23 TraesCS1D01G263900 chr2D 80.380 158 27 4 6450 6605 561318999 561319154 4.240000e-22 117.0
24 TraesCS1D01G263900 chr2D 90.000 60 6 0 6533 6592 549858446 549858387 2.000000e-10 78.7
25 TraesCS1D01G263900 chr2D 97.143 35 1 0 378 412 579378086 579378052 7.250000e-05 60.2
26 TraesCS1D01G263900 chr6B 84.298 242 31 6 1 237 27127435 27127196 5.220000e-56 230.0
27 TraesCS1D01G263900 chr6B 76.800 125 26 3 290 412 544404040 544403917 4.330000e-07 67.6
28 TraesCS1D01G263900 chr3D 84.337 249 24 8 1 235 488120953 488121200 5.220000e-56 230.0
29 TraesCS1D01G263900 chr3D 84.167 240 25 6 9 235 8368161 8367922 3.140000e-53 220.0
30 TraesCS1D01G263900 chr5D 84.146 246 25 7 3 235 329771314 329771070 6.760000e-55 226.0
31 TraesCS1D01G263900 chr7D 83.871 248 15 4 1 235 75346841 75347076 5.260000e-51 213.0
32 TraesCS1D01G263900 chr7D 93.525 139 6 2 3088 3224 34757018 34756881 3.170000e-48 204.0
33 TraesCS1D01G263900 chr7D 92.254 142 9 1 3085 3224 454079074 454079215 4.100000e-47 200.0
34 TraesCS1D01G263900 chr6D 93.525 139 7 1 3088 3224 303059853 303059991 8.800000e-49 206.0
35 TraesCS1D01G263900 chr6D 76.000 125 21 7 290 409 390006481 390006601 1.000000e-03 56.5
36 TraesCS1D01G263900 chr7A 93.525 139 6 2 3088 3224 579808374 579808511 3.170000e-48 204.0
37 TraesCS1D01G263900 chr2B 82.833 233 33 4 3 235 198720496 198720271 1.140000e-47 202.0
38 TraesCS1D01G263900 chr2B 79.424 243 44 6 2 240 53418064 53417824 4.150000e-37 167.0
39 TraesCS1D01G263900 chr2B 96.970 33 0 1 378 409 418651251 418651283 3.000000e-03 54.7
40 TraesCS1D01G263900 chr2B 96.970 33 0 1 378 409 418652632 418652664 3.000000e-03 54.7
41 TraesCS1D01G263900 chr2B 100.000 28 0 0 724 751 156612516 156612489 1.200000e-02 52.8
42 TraesCS1D01G263900 chr4D 92.806 139 8 1 3088 3224 74079351 74079489 4.100000e-47 200.0
43 TraesCS1D01G263900 chr4D 75.148 169 33 8 6507 6668 18205019 18204853 3.350000e-08 71.3
44 TraesCS1D01G263900 chr4D 77.966 118 19 4 6536 6650 486396941 486397054 4.330000e-07 67.6
45 TraesCS1D01G263900 chr4D 100.000 30 0 0 568 597 471960557 471960586 1.000000e-03 56.5
46 TraesCS1D01G263900 chr5B 82.906 234 24 14 1 230 26960733 26960954 5.300000e-46 196.0
47 TraesCS1D01G263900 chr5A 83.019 159 15 2 1 147 590673571 590673413 4.210000e-27 134.0
48 TraesCS1D01G263900 chrUn 85.217 115 16 1 6499 6612 150822519 150822405 4.240000e-22 117.0
49 TraesCS1D01G263900 chrUn 92.500 40 0 3 378 416 363025597 363025560 3.000000e-03 54.7
50 TraesCS1D01G263900 chrUn 92.500 40 0 3 378 416 363026978 363026941 3.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G263900 chr1D 359719915 359726610 6695 True 12366.000000 12366 100.000000 1 6696 1 chr1D.!!$R1 6695
1 TraesCS1D01G263900 chr1A 459269659 459275685 6026 True 1687.560000 4283 92.479200 782 6696 5 chr1A.!!$R2 5914
2 TraesCS1D01G263900 chr1B 481705227 481713831 8604 True 1288.285714 3369 92.431714 1 6664 7 chr1B.!!$R1 6663
3 TraesCS1D01G263900 chr1B 642793552 642795255 1703 True 1096.500000 1478 90.806000 2284 4006 2 chr1B.!!$R2 1722
4 TraesCS1D01G263900 chr7B 380858572 380860203 1631 False 1096.000000 1613 91.579000 2277 3908 2 chr7B.!!$F1 1631

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
486 499 0.108615 CGGCCGTGAGAAGATGTTCT 60.109 55.000 19.50 4.50 46.32 3.01 F
713 768 0.178967 TGGGATTGCTGAGCCAAACA 60.179 50.000 0.23 0.00 34.70 2.83 F
884 1082 0.602905 GCACGGTCCATACTATGCCC 60.603 60.000 0.00 0.00 33.15 5.36 F
2044 2248 0.620556 AATTCTGAGGGACGCCACAT 59.379 50.000 0.00 0.00 0.00 3.21 F
2229 2433 1.134487 CGCTGCATTGGTTGGTACG 59.866 57.895 0.00 0.00 0.00 3.67 F
3510 3870 2.105649 TGCAGGTATGAAACTGTGGTGA 59.894 45.455 0.00 0.00 37.07 4.02 F
4740 5141 0.037303 TGGCCTTGAAGCTTCTCCAG 59.963 55.000 26.09 18.01 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1794 1998 1.071471 CCGAGCCACAGTTTCCAGT 59.929 57.895 0.00 0.0 0.00 4.00 R
2522 2726 1.315690 AACAGACTCACCGTTCGAGA 58.684 50.000 0.00 0.0 34.47 4.04 R
2693 2897 1.436600 GCATGACAGGATATGCCTCG 58.563 55.000 0.00 0.0 46.97 4.63 R
3732 4128 1.344763 ACTGCCACTGTCTCCACTTAC 59.655 52.381 0.00 0.0 0.00 2.34 R
4207 4606 1.202830 ACACGGTTGATTTGTGGCCTA 60.203 47.619 3.32 0.0 37.92 3.93 R
5328 6092 1.256812 TGTGCTCTCGAGATGACCAA 58.743 50.000 17.03 0.0 0.00 3.67 R
6119 8729 1.122019 AGGAGGTTTGGTGAGTCGCT 61.122 55.000 3.25 0.0 0.00 4.93 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
18 19 3.225272 CCCTATGAACGCACACACA 57.775 52.632 0.00 0.00 0.00 3.72
28 29 0.944311 CGCACACACACAGACCCTAC 60.944 60.000 0.00 0.00 0.00 3.18
30 31 1.048601 CACACACACAGACCCTACCT 58.951 55.000 0.00 0.00 0.00 3.08
35 36 3.131223 CACACACAGACCCTACCTCTATG 59.869 52.174 0.00 0.00 0.00 2.23
53 54 1.153667 GAGCACCTTCGAGAGCCTG 60.154 63.158 0.00 0.00 0.00 4.85
66 67 3.161067 GAGAGCCTGAGCCAGTATATCA 58.839 50.000 2.18 0.00 41.25 2.15
68 69 3.768757 AGAGCCTGAGCCAGTATATCATC 59.231 47.826 2.18 0.00 41.25 2.92
108 121 0.751452 GTAGGGACGGGAACATCTCC 59.249 60.000 0.00 0.00 44.54 3.71
121 134 1.280421 ACATCTCCTCCCACTGAAAGC 59.720 52.381 0.00 0.00 37.60 3.51
122 135 0.539051 ATCTCCTCCCACTGAAAGCG 59.461 55.000 0.00 0.00 37.60 4.68
139 152 2.517598 CGTATCGCCGGAAATCCTG 58.482 57.895 5.05 0.00 0.00 3.86
148 161 3.377172 CGCCGGAAATCCTGAAATAAGTT 59.623 43.478 5.05 0.00 0.00 2.66
150 163 4.495844 GCCGGAAATCCTGAAATAAGTTCG 60.496 45.833 5.05 0.00 39.30 3.95
169 182 0.947244 GGGAATAATGCGAGCACCAG 59.053 55.000 0.00 0.00 0.00 4.00
179 192 0.951040 CGAGCACCAGGACTTGAACC 60.951 60.000 0.00 0.00 0.00 3.62
180 193 0.606673 GAGCACCAGGACTTGAACCC 60.607 60.000 0.00 0.00 0.00 4.11
215 228 3.004752 ACCATTGTGCCTCTAACCATC 57.995 47.619 0.00 0.00 0.00 3.51
217 230 2.092212 CCATTGTGCCTCTAACCATCCT 60.092 50.000 0.00 0.00 0.00 3.24
224 237 1.687123 CCTCTAACCATCCTACCACGG 59.313 57.143 0.00 0.00 0.00 4.94
244 257 3.734293 CGGGTTGGTTCGCTAAAACAAAA 60.734 43.478 1.26 0.00 45.89 2.44
248 261 6.440436 GGTTGGTTCGCTAAAACAAAAGATA 58.560 36.000 1.26 0.00 45.89 1.98
282 295 4.436332 GTTGGAATGGATGCTTGATTTCC 58.564 43.478 0.00 0.00 34.54 3.13
288 301 6.944862 GGAATGGATGCTTGATTTCCTACTAT 59.055 38.462 0.00 0.00 31.90 2.12
329 342 8.888579 AAATTTCTATAGGGTTCAGTCATACG 57.111 34.615 0.00 0.00 0.00 3.06
331 344 6.630444 TTCTATAGGGTTCAGTCATACGAC 57.370 41.667 0.00 0.00 42.95 4.34
353 366 1.198867 CGGACAATCACGGCATGAAAA 59.801 47.619 0.00 0.00 41.93 2.29
354 367 2.159393 CGGACAATCACGGCATGAAAAT 60.159 45.455 0.00 0.00 41.93 1.82
355 368 3.673052 CGGACAATCACGGCATGAAAATT 60.673 43.478 0.00 0.00 41.93 1.82
356 369 3.859386 GGACAATCACGGCATGAAAATTC 59.141 43.478 0.00 0.00 41.93 2.17
357 370 3.848726 ACAATCACGGCATGAAAATTCC 58.151 40.909 0.00 0.00 41.93 3.01
358 371 3.511146 ACAATCACGGCATGAAAATTCCT 59.489 39.130 0.00 0.00 41.93 3.36
359 372 4.704540 ACAATCACGGCATGAAAATTCCTA 59.295 37.500 0.00 0.00 41.93 2.94
360 373 5.360714 ACAATCACGGCATGAAAATTCCTAT 59.639 36.000 0.00 0.00 41.93 2.57
361 374 4.898829 TCACGGCATGAAAATTCCTATG 57.101 40.909 0.00 0.00 33.02 2.23
362 375 4.522114 TCACGGCATGAAAATTCCTATGA 58.478 39.130 0.00 0.00 33.02 2.15
363 376 4.946772 TCACGGCATGAAAATTCCTATGAA 59.053 37.500 0.00 0.00 33.02 2.57
364 377 5.593909 TCACGGCATGAAAATTCCTATGAAT 59.406 36.000 0.00 0.00 37.29 2.57
365 378 6.096705 TCACGGCATGAAAATTCCTATGAATT 59.903 34.615 0.00 0.57 41.48 2.17
366 379 7.681782 TCACGGCATGAAAATTCCTATGAATTC 60.682 37.037 6.46 0.00 39.44 2.17
407 420 9.989296 TCCTATAAAAATCCTTTGAATCAAGGA 57.011 29.630 6.68 10.86 34.66 3.36
410 423 5.411831 AAAATCCTTTGAATCAAGGAGGC 57.588 39.130 6.68 0.00 33.55 4.70
411 424 2.514458 TCCTTTGAATCAAGGAGGCC 57.486 50.000 6.68 0.00 0.00 5.19
412 425 1.995542 TCCTTTGAATCAAGGAGGCCT 59.004 47.619 3.86 3.86 33.87 5.19
413 426 2.097825 CCTTTGAATCAAGGAGGCCTG 58.902 52.381 12.00 0.00 32.13 4.85
414 427 2.556114 CCTTTGAATCAAGGAGGCCTGT 60.556 50.000 12.00 0.00 32.13 4.00
415 428 3.308402 CCTTTGAATCAAGGAGGCCTGTA 60.308 47.826 12.00 0.00 32.13 2.74
416 429 4.335416 CTTTGAATCAAGGAGGCCTGTAA 58.665 43.478 12.00 0.00 32.13 2.41
417 430 3.350219 TGAATCAAGGAGGCCTGTAAC 57.650 47.619 12.00 0.00 32.13 2.50
418 431 2.912956 TGAATCAAGGAGGCCTGTAACT 59.087 45.455 12.00 0.00 32.13 2.24
419 432 4.101114 TGAATCAAGGAGGCCTGTAACTA 58.899 43.478 12.00 0.00 32.13 2.24
420 433 4.721776 TGAATCAAGGAGGCCTGTAACTAT 59.278 41.667 12.00 0.00 32.13 2.12
421 434 5.903010 TGAATCAAGGAGGCCTGTAACTATA 59.097 40.000 12.00 0.00 32.13 1.31
422 435 6.558775 TGAATCAAGGAGGCCTGTAACTATAT 59.441 38.462 12.00 0.00 32.13 0.86
423 436 7.733047 TGAATCAAGGAGGCCTGTAACTATATA 59.267 37.037 12.00 0.00 32.13 0.86
424 437 8.506196 AATCAAGGAGGCCTGTAACTATATAA 57.494 34.615 12.00 0.00 32.13 0.98
425 438 7.299246 TCAAGGAGGCCTGTAACTATATAAC 57.701 40.000 12.00 0.00 32.13 1.89
426 439 7.073854 TCAAGGAGGCCTGTAACTATATAACT 58.926 38.462 12.00 0.00 32.13 2.24
427 440 8.229605 TCAAGGAGGCCTGTAACTATATAACTA 58.770 37.037 12.00 0.00 32.13 2.24
428 441 8.524487 CAAGGAGGCCTGTAACTATATAACTAG 58.476 40.741 12.00 0.00 32.13 2.57
429 442 7.997915 AGGAGGCCTGTAACTATATAACTAGA 58.002 38.462 12.00 0.00 29.57 2.43
430 443 8.110908 AGGAGGCCTGTAACTATATAACTAGAG 58.889 40.741 12.00 0.00 29.57 2.43
431 444 8.108364 GGAGGCCTGTAACTATATAACTAGAGA 58.892 40.741 12.00 0.00 0.00 3.10
432 445 8.866970 AGGCCTGTAACTATATAACTAGAGAC 57.133 38.462 3.11 0.00 0.00 3.36
433 446 8.446394 AGGCCTGTAACTATATAACTAGAGACA 58.554 37.037 3.11 0.00 0.00 3.41
434 447 9.245481 GGCCTGTAACTATATAACTAGAGACAT 57.755 37.037 0.00 0.00 0.00 3.06
447 460 6.963083 ACTAGAGACATGTCAGTAATACCC 57.037 41.667 27.02 5.17 0.00 3.69
448 461 6.674573 ACTAGAGACATGTCAGTAATACCCT 58.325 40.000 27.02 11.30 0.00 4.34
449 462 7.126733 ACTAGAGACATGTCAGTAATACCCTT 58.873 38.462 27.02 1.97 0.00 3.95
450 463 6.227298 AGAGACATGTCAGTAATACCCTTG 57.773 41.667 27.02 0.00 0.00 3.61
451 464 4.770795 AGACATGTCAGTAATACCCTTGC 58.229 43.478 27.02 0.00 0.00 4.01
452 465 4.471386 AGACATGTCAGTAATACCCTTGCT 59.529 41.667 27.02 0.00 0.00 3.91
453 466 5.661312 AGACATGTCAGTAATACCCTTGCTA 59.339 40.000 27.02 0.00 0.00 3.49
454 467 6.327626 AGACATGTCAGTAATACCCTTGCTAT 59.672 38.462 27.02 0.00 0.00 2.97
455 468 6.291377 ACATGTCAGTAATACCCTTGCTATG 58.709 40.000 0.00 0.00 0.00 2.23
456 469 5.950544 TGTCAGTAATACCCTTGCTATGT 57.049 39.130 0.00 0.00 0.00 2.29
457 470 7.070696 ACATGTCAGTAATACCCTTGCTATGTA 59.929 37.037 0.00 0.00 0.00 2.29
458 471 7.050970 TGTCAGTAATACCCTTGCTATGTAG 57.949 40.000 0.00 0.00 0.00 2.74
469 482 1.151668 GCTATGTAGCCTCATTGCGG 58.848 55.000 0.48 0.00 43.39 5.69
476 489 3.197790 CCTCATTGCGGCCGTGAG 61.198 66.667 28.39 28.39 39.20 3.51
477 490 2.125552 CTCATTGCGGCCGTGAGA 60.126 61.111 30.44 20.52 41.38 3.27
478 491 1.741401 CTCATTGCGGCCGTGAGAA 60.741 57.895 30.44 17.96 41.38 2.87
479 492 1.699656 CTCATTGCGGCCGTGAGAAG 61.700 60.000 30.44 18.30 41.38 2.85
480 493 1.741401 CATTGCGGCCGTGAGAAGA 60.741 57.895 28.70 5.35 0.00 2.87
481 494 1.091771 CATTGCGGCCGTGAGAAGAT 61.092 55.000 28.70 7.53 0.00 2.40
482 495 1.091771 ATTGCGGCCGTGAGAAGATG 61.092 55.000 28.70 0.00 0.00 2.90
483 496 2.125512 GCGGCCGTGAGAAGATGT 60.126 61.111 28.70 0.00 0.00 3.06
484 497 1.741770 GCGGCCGTGAGAAGATGTT 60.742 57.895 28.70 0.00 0.00 2.71
485 498 1.696832 GCGGCCGTGAGAAGATGTTC 61.697 60.000 28.70 0.08 0.00 3.18
486 499 0.108615 CGGCCGTGAGAAGATGTTCT 60.109 55.000 19.50 4.50 46.32 3.01
487 500 1.363744 GGCCGTGAGAAGATGTTCTG 58.636 55.000 10.29 0.00 43.50 3.02
488 501 0.723981 GCCGTGAGAAGATGTTCTGC 59.276 55.000 10.29 3.40 43.50 4.26
489 502 1.674221 GCCGTGAGAAGATGTTCTGCT 60.674 52.381 10.29 0.00 43.50 4.24
490 503 2.417379 GCCGTGAGAAGATGTTCTGCTA 60.417 50.000 10.29 0.00 43.50 3.49
491 504 3.443037 CCGTGAGAAGATGTTCTGCTAG 58.557 50.000 10.29 0.00 43.50 3.42
492 505 2.857152 CGTGAGAAGATGTTCTGCTAGC 59.143 50.000 10.29 8.10 43.50 3.42
493 506 3.194062 GTGAGAAGATGTTCTGCTAGCC 58.806 50.000 10.29 0.00 43.50 3.93
494 507 3.102972 TGAGAAGATGTTCTGCTAGCCT 58.897 45.455 10.29 0.00 43.50 4.58
495 508 3.131933 TGAGAAGATGTTCTGCTAGCCTC 59.868 47.826 10.29 7.74 43.50 4.70
496 509 3.102972 AGAAGATGTTCTGCTAGCCTCA 58.897 45.455 13.29 6.49 41.78 3.86
497 510 2.977772 AGATGTTCTGCTAGCCTCAC 57.022 50.000 13.29 6.30 0.00 3.51
498 511 2.465813 AGATGTTCTGCTAGCCTCACT 58.534 47.619 13.29 0.00 0.00 3.41
499 512 2.430332 AGATGTTCTGCTAGCCTCACTC 59.570 50.000 13.29 2.36 0.00 3.51
500 513 1.632589 TGTTCTGCTAGCCTCACTCA 58.367 50.000 13.29 1.44 0.00 3.41
501 514 1.970640 TGTTCTGCTAGCCTCACTCAA 59.029 47.619 13.29 0.00 0.00 3.02
502 515 2.289072 TGTTCTGCTAGCCTCACTCAAC 60.289 50.000 13.29 5.11 0.00 3.18
503 516 1.930251 TCTGCTAGCCTCACTCAACT 58.070 50.000 13.29 0.00 0.00 3.16
504 517 2.251818 TCTGCTAGCCTCACTCAACTT 58.748 47.619 13.29 0.00 0.00 2.66
505 518 2.634940 TCTGCTAGCCTCACTCAACTTT 59.365 45.455 13.29 0.00 0.00 2.66
506 519 3.832490 TCTGCTAGCCTCACTCAACTTTA 59.168 43.478 13.29 0.00 0.00 1.85
507 520 4.467795 TCTGCTAGCCTCACTCAACTTTAT 59.532 41.667 13.29 0.00 0.00 1.40
508 521 5.046304 TCTGCTAGCCTCACTCAACTTTATT 60.046 40.000 13.29 0.00 0.00 1.40
509 522 5.560724 TGCTAGCCTCACTCAACTTTATTT 58.439 37.500 13.29 0.00 0.00 1.40
510 523 6.707290 TGCTAGCCTCACTCAACTTTATTTA 58.293 36.000 13.29 0.00 0.00 1.40
511 524 6.818644 TGCTAGCCTCACTCAACTTTATTTAG 59.181 38.462 13.29 0.00 0.00 1.85
512 525 6.238239 GCTAGCCTCACTCAACTTTATTTAGC 60.238 42.308 2.29 0.00 0.00 3.09
513 526 4.944317 AGCCTCACTCAACTTTATTTAGCC 59.056 41.667 0.00 0.00 0.00 3.93
514 527 4.944317 GCCTCACTCAACTTTATTTAGCCT 59.056 41.667 0.00 0.00 0.00 4.58
515 528 5.065346 GCCTCACTCAACTTTATTTAGCCTC 59.935 44.000 0.00 0.00 0.00 4.70
516 529 6.173339 CCTCACTCAACTTTATTTAGCCTCA 58.827 40.000 0.00 0.00 0.00 3.86
517 530 6.825721 CCTCACTCAACTTTATTTAGCCTCAT 59.174 38.462 0.00 0.00 0.00 2.90
518 531 7.337942 CCTCACTCAACTTTATTTAGCCTCATT 59.662 37.037 0.00 0.00 0.00 2.57
519 532 8.044060 TCACTCAACTTTATTTAGCCTCATTG 57.956 34.615 0.00 0.00 0.00 2.82
520 533 6.749118 CACTCAACTTTATTTAGCCTCATTGC 59.251 38.462 0.00 0.00 0.00 3.56
521 534 5.879237 TCAACTTTATTTAGCCTCATTGCG 58.121 37.500 0.00 0.00 36.02 4.85
522 535 4.900635 ACTTTATTTAGCCTCATTGCGG 57.099 40.909 0.00 0.00 36.02 5.69
529 542 3.197790 CCTCATTGCGGCCGTGAG 61.198 66.667 28.39 28.39 39.20 3.51
530 543 2.125552 CTCATTGCGGCCGTGAGA 60.126 61.111 30.44 20.52 41.38 3.27
531 544 1.741401 CTCATTGCGGCCGTGAGAA 60.741 57.895 30.44 17.96 41.38 2.87
532 545 1.078497 TCATTGCGGCCGTGAGAAT 60.078 52.632 28.70 16.39 0.00 2.40
548 561 7.335422 GCCGTGAGAATATTCCTATGAATTCAT 59.665 37.037 23.75 23.75 41.44 2.57
598 611 5.705609 TTTGAATCAAAGAGGCCTGTAAC 57.294 39.130 12.00 0.00 0.00 2.50
599 612 4.365514 TGAATCAAAGAGGCCTGTAACA 57.634 40.909 12.00 0.00 0.00 2.41
600 613 4.724399 TGAATCAAAGAGGCCTGTAACAA 58.276 39.130 12.00 0.00 0.00 2.83
601 614 5.324409 TGAATCAAAGAGGCCTGTAACAAT 58.676 37.500 12.00 0.00 0.00 2.71
602 615 5.415701 TGAATCAAAGAGGCCTGTAACAATC 59.584 40.000 12.00 3.84 0.00 2.67
604 617 4.072131 TCAAAGAGGCCTGTAACAATCAC 58.928 43.478 12.00 0.00 0.00 3.06
605 618 2.386661 AGAGGCCTGTAACAATCACG 57.613 50.000 12.00 0.00 0.00 4.35
606 619 1.066143 AGAGGCCTGTAACAATCACGG 60.066 52.381 12.00 0.00 0.00 4.94
608 621 0.958382 GGCCTGTAACAATCACGGCA 60.958 55.000 0.00 0.00 37.34 5.69
609 622 1.094785 GCCTGTAACAATCACGGCAT 58.905 50.000 0.00 0.00 36.36 4.40
610 623 2.285083 GCCTGTAACAATCACGGCATA 58.715 47.619 0.00 0.00 36.36 3.14
611 624 2.680841 GCCTGTAACAATCACGGCATAA 59.319 45.455 0.00 0.00 36.36 1.90
612 625 3.315191 GCCTGTAACAATCACGGCATAAT 59.685 43.478 0.00 0.00 36.36 1.28
613 626 4.202010 GCCTGTAACAATCACGGCATAATT 60.202 41.667 0.00 0.00 36.36 1.40
614 627 5.678616 GCCTGTAACAATCACGGCATAATTT 60.679 40.000 0.00 0.00 36.36 1.82
615 628 6.329496 CCTGTAACAATCACGGCATAATTTT 58.671 36.000 0.00 0.00 0.00 1.82
616 629 6.811170 CCTGTAACAATCACGGCATAATTTTT 59.189 34.615 0.00 0.00 0.00 1.94
670 724 8.714179 TCATTCAACTTTATTTAATCGTGACGT 58.286 29.630 4.40 0.00 0.00 4.34
685 739 7.837202 ATCGTGACGTTTAAAAGGATCATTA 57.163 32.000 4.40 0.00 0.00 1.90
713 768 0.178967 TGGGATTGCTGAGCCAAACA 60.179 50.000 0.23 0.00 34.70 2.83
744 799 7.765307 TCACGTACTCCTTCGTAAAGAAATAT 58.235 34.615 0.00 0.00 38.57 1.28
745 800 8.892723 TCACGTACTCCTTCGTAAAGAAATATA 58.107 33.333 0.00 0.00 38.57 0.86
746 801 9.507280 CACGTACTCCTTCGTAAAGAAATATAA 57.493 33.333 0.00 0.00 38.57 0.98
747 802 9.727627 ACGTACTCCTTCGTAAAGAAATATAAG 57.272 33.333 0.00 0.00 38.57 1.73
748 803 9.941664 CGTACTCCTTCGTAAAGAAATATAAGA 57.058 33.333 0.00 0.00 38.57 2.10
751 806 8.697292 ACTCCTTCGTAAAGAAATATAAGAGCT 58.303 33.333 0.00 0.00 38.57 4.09
752 807 9.187455 CTCCTTCGTAAAGAAATATAAGAGCTC 57.813 37.037 5.27 5.27 38.57 4.09
754 809 9.535878 CCTTCGTAAAGAAATATAAGAGCTCTT 57.464 33.333 30.63 30.63 38.57 2.85
830 1026 1.133823 TGAACTCTTCAGGCTTTGGCA 60.134 47.619 0.00 0.00 35.90 4.92
857 1053 1.227141 CGAAATTCGTCGCGTTGTTC 58.773 50.000 5.77 2.08 34.72 3.18
884 1082 0.602905 GCACGGTCCATACTATGCCC 60.603 60.000 0.00 0.00 33.15 5.36
1350 1554 2.123077 CTCCCTCTCCCGCTCCAT 60.123 66.667 0.00 0.00 0.00 3.41
1541 1745 3.606662 CCCGATCGATGCTCCCGT 61.607 66.667 18.66 0.00 0.00 5.28
1543 1747 2.721859 CGATCGATGCTCCCGTCA 59.278 61.111 10.26 0.00 0.00 4.35
1794 1998 1.173913 TGAATGAGAGGAGCGACGAA 58.826 50.000 0.00 0.00 0.00 3.85
1870 2074 4.467084 GATTGCACGGCGAGGGGA 62.467 66.667 16.62 0.08 0.00 4.81
2044 2248 0.620556 AATTCTGAGGGACGCCACAT 59.379 50.000 0.00 0.00 0.00 3.21
2130 2334 2.186532 TATTGGTGGCGCTTGTTACA 57.813 45.000 7.64 0.00 0.00 2.41
2229 2433 1.134487 CGCTGCATTGGTTGGTACG 59.866 57.895 0.00 0.00 0.00 3.67
2246 2450 2.561478 ACGCAGTTAGAACCATTGGT 57.439 45.000 1.37 1.37 37.78 3.67
2397 2601 4.837896 AGCTCAGAAAAGTTTTAGGTGC 57.162 40.909 0.00 8.81 0.00 5.01
2651 2855 5.518865 AGCCATTGGAGGTATAAACACAAT 58.481 37.500 6.95 0.00 30.76 2.71
2755 2959 4.961438 AAAACATTTTGATCTGGGCACT 57.039 36.364 0.00 0.00 0.00 4.40
3099 3448 3.959449 ACCTTTCTATTACTCCCTCCGTC 59.041 47.826 0.00 0.00 0.00 4.79
3152 3501 7.519032 TGTGAATCGGATGTATATAGACACA 57.481 36.000 1.52 0.00 30.52 3.72
3229 3587 9.713684 ATCCAAAACATCTTATATTTGAGGGAA 57.286 29.630 0.00 0.00 35.34 3.97
3282 3640 7.389884 ACTTCATAGTCTGACGTCTTACTTACA 59.610 37.037 22.53 10.18 31.06 2.41
3331 3689 5.708948 TGTGCTATGTTATTTGGTTTCTGC 58.291 37.500 0.00 0.00 0.00 4.26
3354 3714 2.202878 GCCATCGCTCGCCTTACA 60.203 61.111 0.00 0.00 0.00 2.41
3365 3725 3.067742 GCTCGCCTTACAATACTAGTGGA 59.932 47.826 5.39 0.00 0.00 4.02
3366 3726 4.262079 GCTCGCCTTACAATACTAGTGGAT 60.262 45.833 5.39 0.00 0.00 3.41
3409 3769 7.987458 TGACCAGAATTATGACTCAAGTAATCC 59.013 37.037 0.54 0.00 0.00 3.01
3463 3823 7.399191 GGGGGATTTTTGTTTAGTTCTTCCTAT 59.601 37.037 0.00 0.00 0.00 2.57
3506 3866 3.187227 GTCACTGCAGGTATGAAACTGTG 59.813 47.826 19.93 3.22 37.07 3.66
3508 3868 2.106511 ACTGCAGGTATGAAACTGTGGT 59.893 45.455 19.93 0.00 37.07 4.16
3509 3869 2.485426 CTGCAGGTATGAAACTGTGGTG 59.515 50.000 5.57 0.00 37.07 4.17
3510 3870 2.105649 TGCAGGTATGAAACTGTGGTGA 59.894 45.455 0.00 0.00 37.07 4.02
3511 3871 2.744202 GCAGGTATGAAACTGTGGTGAG 59.256 50.000 0.00 0.00 37.07 3.51
3512 3872 3.807209 GCAGGTATGAAACTGTGGTGAGT 60.807 47.826 0.00 0.00 37.07 3.41
3513 3873 4.389374 CAGGTATGAAACTGTGGTGAGTT 58.611 43.478 0.00 0.00 37.81 3.01
3514 3874 4.821805 CAGGTATGAAACTGTGGTGAGTTT 59.178 41.667 0.00 0.00 46.57 2.66
3522 3882 5.505173 AACTGTGGTGAGTTTCATTCTTG 57.495 39.130 0.00 0.00 31.92 3.02
3523 3883 4.780815 ACTGTGGTGAGTTTCATTCTTGA 58.219 39.130 0.00 0.00 0.00 3.02
3524 3884 5.192927 ACTGTGGTGAGTTTCATTCTTGAA 58.807 37.500 0.00 0.00 40.09 2.69
3525 3885 5.652014 ACTGTGGTGAGTTTCATTCTTGAAA 59.348 36.000 0.00 0.00 46.88 2.69
3539 3910 9.545105 TTCATTCTTGAAATAAACAACATGCTT 57.455 25.926 0.00 0.00 38.90 3.91
3732 4128 6.427853 TGACAATGATAACCAGTCTCTTTGTG 59.572 38.462 14.14 0.00 37.39 3.33
4110 4506 6.039717 GCCTGTATCTTCTGGCATTCATAAAA 59.960 38.462 9.14 0.00 46.73 1.52
4156 4555 9.657419 ATTTTGGCAATTTAAGAATGTTAGGAG 57.343 29.630 0.00 0.00 0.00 3.69
4207 4606 7.392673 GGATTATTCACTTGGATGCACTATGAT 59.607 37.037 0.00 0.00 0.00 2.45
4492 4891 8.384607 TGTGTTATAATGTTTGCTTACAGTCA 57.615 30.769 0.00 0.00 0.00 3.41
4650 5051 4.986054 AAATGGCTATATACCGGTGGAA 57.014 40.909 19.93 1.99 0.00 3.53
4740 5141 0.037303 TGGCCTTGAAGCTTCTCCAG 59.963 55.000 26.09 18.01 0.00 3.86
4802 5203 7.642082 TGGTCAACTCTTCTATAGGAGTTAC 57.358 40.000 18.42 16.13 46.82 2.50
4982 5383 7.043565 ACATCATTTCCTTTGCATGTTATTCC 58.956 34.615 0.00 0.00 0.00 3.01
4983 5384 5.976458 TCATTTCCTTTGCATGTTATTCCC 58.024 37.500 0.00 0.00 0.00 3.97
4984 5385 4.817318 TTTCCTTTGCATGTTATTCCCC 57.183 40.909 0.00 0.00 0.00 4.81
4985 5386 3.756082 TCCTTTGCATGTTATTCCCCT 57.244 42.857 0.00 0.00 0.00 4.79
4988 5389 4.222588 TCCTTTGCATGTTATTCCCCTTTG 59.777 41.667 0.00 0.00 0.00 2.77
4989 5390 4.020307 CCTTTGCATGTTATTCCCCTTTGT 60.020 41.667 0.00 0.00 0.00 2.83
4990 5391 5.512921 CCTTTGCATGTTATTCCCCTTTGTT 60.513 40.000 0.00 0.00 0.00 2.83
4991 5392 6.295575 CCTTTGCATGTTATTCCCCTTTGTTA 60.296 38.462 0.00 0.00 0.00 2.41
4992 5393 6.865834 TTGCATGTTATTCCCCTTTGTTAT 57.134 33.333 0.00 0.00 0.00 1.89
4993 5394 6.219417 TGCATGTTATTCCCCTTTGTTATG 57.781 37.500 0.00 0.00 0.00 1.90
4994 5395 5.049828 GCATGTTATTCCCCTTTGTTATGC 58.950 41.667 0.00 0.00 0.00 3.14
4995 5396 5.395103 GCATGTTATTCCCCTTTGTTATGCA 60.395 40.000 0.00 0.00 37.65 3.96
4996 5397 6.686126 GCATGTTATTCCCCTTTGTTATGCAT 60.686 38.462 3.79 3.79 37.65 3.96
4997 5398 6.865834 TGTTATTCCCCTTTGTTATGCATT 57.134 33.333 3.54 0.00 0.00 3.56
4998 5399 6.872920 TGTTATTCCCCTTTGTTATGCATTC 58.127 36.000 3.54 0.00 0.00 2.67
4999 5400 6.438741 TGTTATTCCCCTTTGTTATGCATTCA 59.561 34.615 3.54 1.97 0.00 2.57
5000 5401 7.125507 TGTTATTCCCCTTTGTTATGCATTCAT 59.874 33.333 3.54 0.00 36.73 2.57
5001 5402 8.637986 GTTATTCCCCTTTGTTATGCATTCATA 58.362 33.333 3.54 0.00 34.22 2.15
5002 5403 6.463995 TTCCCCTTTGTTATGCATTCATAC 57.536 37.500 3.54 0.00 35.07 2.39
5003 5404 5.514169 TCCCCTTTGTTATGCATTCATACA 58.486 37.500 3.54 1.95 35.07 2.29
5004 5405 5.954752 TCCCCTTTGTTATGCATTCATACAA 59.045 36.000 3.54 8.26 35.07 2.41
5005 5406 6.042143 CCCCTTTGTTATGCATTCATACAAC 58.958 40.000 3.54 2.31 35.07 3.32
5006 5407 6.350864 CCCCTTTGTTATGCATTCATACAACA 60.351 38.462 3.54 5.35 35.07 3.33
5007 5408 7.267128 CCCTTTGTTATGCATTCATACAACAT 58.733 34.615 3.54 0.00 33.57 2.71
5008 5409 7.765360 CCCTTTGTTATGCATTCATACAACATT 59.235 33.333 3.54 0.00 33.57 2.71
5009 5410 9.153721 CCTTTGTTATGCATTCATACAACATTT 57.846 29.630 3.54 0.00 33.57 2.32
5012 5413 9.926158 TTGTTATGCATTCATACAACATTTTCT 57.074 25.926 3.54 0.00 33.57 2.52
5041 5442 9.649167 GTTCTAGAGTAATTTAAAGGTGCACTA 57.351 33.333 17.98 0.00 0.00 2.74
5049 5450 8.957466 GTAATTTAAAGGTGCACTAAGGAGAAT 58.043 33.333 17.98 6.25 0.00 2.40
5065 5466 1.425066 AGAATGTGCTCCCTGGTGAAA 59.575 47.619 0.00 0.00 0.00 2.69
5163 5798 8.367943 TGTGATTGTCAAATTTCATGGAAAAG 57.632 30.769 0.00 0.00 35.11 2.27
5278 5928 7.386059 AGTTTTCCCCAAGTAAATTATGCAAG 58.614 34.615 0.00 0.00 0.00 4.01
5328 6092 7.226720 GGAATTGTCTGACACGTATGGATTTAT 59.773 37.037 10.56 0.00 0.00 1.40
5337 6101 6.591935 ACACGTATGGATTTATTGGTCATCT 58.408 36.000 0.00 0.00 0.00 2.90
5372 6136 4.201950 GCTAGGAGCCATTTTACATGTGTG 60.202 45.833 9.11 2.16 34.48 3.82
5496 6260 7.497249 CCTCTAGGGAAACAATAACTTCTCATG 59.503 40.741 0.00 0.00 37.23 3.07
5568 6332 5.584442 TGATCAGTGCATGTTTGATATTGC 58.416 37.500 0.00 0.00 32.03 3.56
5625 6389 2.353803 GGAACGAGCATTCTGGTACACT 60.354 50.000 0.00 0.00 30.75 3.55
5832 6601 6.150318 CCGATGAACTATGATACACCTGTAC 58.850 44.000 0.00 0.00 32.72 2.90
5961 6730 7.174946 GGTTGAATTTCAAGTGATTAGGTCTGA 59.825 37.037 12.02 0.00 37.00 3.27
5975 6744 4.148128 AGGTCTGAACTTGGATGCTATG 57.852 45.455 0.00 0.00 0.00 2.23
5989 6758 5.111293 GGATGCTATGTGGGTTGAAATTTG 58.889 41.667 0.00 0.00 0.00 2.32
6014 8621 2.297701 GATTACGTCCACATGCCCAAT 58.702 47.619 0.00 0.00 0.00 3.16
6068 8678 9.945633 AAATAAATAAAGGTTTATCCCTGCCTA 57.054 29.630 0.00 0.00 34.16 3.93
6083 8693 3.627577 CCTGCCTAACATGTACAACCATC 59.372 47.826 0.00 0.00 0.00 3.51
6256 8900 1.072505 CGGCCCAACAAGGTGTACT 59.927 57.895 0.00 0.00 34.66 2.73
6335 8979 0.683412 AGGTTCTACGCGGGTTCTTT 59.317 50.000 11.50 0.00 0.00 2.52
6369 9014 8.737168 TGATTTTCTCTATCGGTTTTCATCAT 57.263 30.769 0.00 0.00 0.00 2.45
6473 9118 9.881529 AATTCAAATACACATTGCACATTTTTC 57.118 25.926 0.00 0.00 0.00 2.29
6476 9121 1.786004 ACACATTGCACATTTTTCGCG 59.214 42.857 0.00 0.00 0.00 5.87
6572 9218 8.877808 TGTTGAACATTTGTAAAATGCACATA 57.122 26.923 11.62 4.10 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.245028 TGCTCATAGAGGTAGGGTCTGT 59.755 50.000 0.00 0.00 0.00 3.41
28 29 2.293122 CTCTCGAAGGTGCTCATAGAGG 59.707 54.545 6.17 0.00 0.00 3.69
30 31 1.678627 GCTCTCGAAGGTGCTCATAGA 59.321 52.381 0.00 0.00 0.00 1.98
35 36 1.153667 CAGGCTCTCGAAGGTGCTC 60.154 63.158 0.00 0.00 0.00 4.26
53 54 9.364989 GTAAATCTCAAGATGATATACTGGCTC 57.635 37.037 0.00 0.00 34.49 4.70
66 67 9.790389 CTACAGTTACTTCGTAAATCTCAAGAT 57.210 33.333 0.00 0.00 36.07 2.40
68 69 7.488471 CCCTACAGTTACTTCGTAAATCTCAAG 59.512 40.741 0.00 0.00 29.42 3.02
85 86 1.553704 GATGTTCCCGTCCCTACAGTT 59.446 52.381 0.00 0.00 0.00 3.16
108 121 1.560923 CGATACGCTTTCAGTGGGAG 58.439 55.000 0.00 0.00 0.00 4.30
121 134 0.031585 TCAGGATTTCCGGCGATACG 59.968 55.000 9.30 0.00 42.08 3.06
122 135 2.234300 TTCAGGATTTCCGGCGATAC 57.766 50.000 9.30 0.00 42.08 2.24
128 141 4.035208 CCGAACTTATTTCAGGATTTCCGG 59.965 45.833 0.00 0.00 42.08 5.14
133 146 8.850156 CATTATTCCCGAACTTATTTCAGGATT 58.150 33.333 0.00 0.00 40.02 3.01
135 148 6.262273 GCATTATTCCCGAACTTATTTCAGGA 59.738 38.462 0.00 0.00 38.80 3.86
136 149 6.438763 GCATTATTCCCGAACTTATTTCAGG 58.561 40.000 0.00 0.00 33.43 3.86
139 152 6.295039 TCGCATTATTCCCGAACTTATTTC 57.705 37.500 0.00 0.00 0.00 2.17
148 161 0.531974 GGTGCTCGCATTATTCCCGA 60.532 55.000 0.00 0.00 0.00 5.14
150 163 0.947244 CTGGTGCTCGCATTATTCCC 59.053 55.000 0.00 0.00 0.00 3.97
169 182 0.035343 GCCTACCAGGGTTCAAGTCC 60.035 60.000 0.00 0.00 35.37 3.85
179 192 0.399949 TGGTATCCCAGCCTACCAGG 60.400 60.000 0.00 0.00 41.85 4.45
180 193 3.240670 TGGTATCCCAGCCTACCAG 57.759 57.895 0.00 0.00 41.85 4.00
183 196 2.851195 CACAATGGTATCCCAGCCTAC 58.149 52.381 0.00 0.00 46.15 3.18
185 198 0.106519 GCACAATGGTATCCCAGCCT 60.107 55.000 0.00 0.00 46.15 4.58
224 237 4.674475 TCTTTTGTTTTAGCGAACCAACC 58.326 39.130 0.00 0.00 0.00 3.77
244 257 8.781951 TCCATTCCAACCTCTTAGAAAATATCT 58.218 33.333 0.00 0.00 42.48 1.98
248 261 6.097412 GCATCCATTCCAACCTCTTAGAAAAT 59.903 38.462 0.00 0.00 0.00 1.82
266 279 8.829746 TCATATAGTAGGAAATCAAGCATCCAT 58.170 33.333 0.00 0.00 35.62 3.41
306 319 7.659186 GTCGTATGACTGAACCCTATAGAAAT 58.341 38.462 7.88 0.00 42.08 2.17
308 321 6.630444 GTCGTATGACTGAACCCTATAGAA 57.370 41.667 7.88 0.00 42.08 2.10
322 335 3.106672 GTGATTGTCCGAGTCGTATGAC 58.893 50.000 12.31 12.09 45.86 3.06
329 342 0.460284 ATGCCGTGATTGTCCGAGTC 60.460 55.000 0.00 0.00 0.00 3.36
331 344 0.460109 TCATGCCGTGATTGTCCGAG 60.460 55.000 0.00 0.00 0.00 4.63
334 347 3.508744 ATTTTCATGCCGTGATTGTCC 57.491 42.857 0.00 0.00 36.54 4.02
335 348 3.859386 GGAATTTTCATGCCGTGATTGTC 59.141 43.478 0.00 0.00 36.54 3.18
393 406 2.097825 CAGGCCTCCTTGATTCAAAGG 58.902 52.381 0.00 11.34 46.99 3.11
394 407 2.800250 ACAGGCCTCCTTGATTCAAAG 58.200 47.619 0.00 0.00 0.00 2.77
395 408 2.978156 ACAGGCCTCCTTGATTCAAA 57.022 45.000 0.00 0.00 0.00 2.69
396 409 3.330701 AGTTACAGGCCTCCTTGATTCAA 59.669 43.478 0.00 0.00 0.00 2.69
397 410 2.912956 AGTTACAGGCCTCCTTGATTCA 59.087 45.455 0.00 0.00 0.00 2.57
398 411 3.636153 AGTTACAGGCCTCCTTGATTC 57.364 47.619 0.00 0.00 0.00 2.52
399 412 8.376270 GTTATATAGTTACAGGCCTCCTTGATT 58.624 37.037 0.00 0.00 0.00 2.57
400 413 7.735321 AGTTATATAGTTACAGGCCTCCTTGAT 59.265 37.037 0.00 0.00 0.00 2.57
401 414 7.073854 AGTTATATAGTTACAGGCCTCCTTGA 58.926 38.462 0.00 0.00 0.00 3.02
402 415 7.304497 AGTTATATAGTTACAGGCCTCCTTG 57.696 40.000 0.00 0.00 0.00 3.61
403 416 8.454494 TCTAGTTATATAGTTACAGGCCTCCTT 58.546 37.037 0.00 0.00 0.00 3.36
404 417 7.997915 TCTAGTTATATAGTTACAGGCCTCCT 58.002 38.462 0.00 0.00 0.00 3.69
405 418 8.108364 TCTCTAGTTATATAGTTACAGGCCTCC 58.892 40.741 0.00 0.00 0.00 4.30
406 419 8.949177 GTCTCTAGTTATATAGTTACAGGCCTC 58.051 40.741 0.00 0.00 0.00 4.70
407 420 8.446394 TGTCTCTAGTTATATAGTTACAGGCCT 58.554 37.037 0.00 0.00 0.00 5.19
408 421 8.632906 TGTCTCTAGTTATATAGTTACAGGCC 57.367 38.462 0.00 0.00 0.00 5.19
421 434 9.080097 GGGTATTACTGACATGTCTCTAGTTAT 57.920 37.037 25.55 19.93 0.00 1.89
422 435 8.280084 AGGGTATTACTGACATGTCTCTAGTTA 58.720 37.037 25.55 15.01 0.00 2.24
423 436 7.126733 AGGGTATTACTGACATGTCTCTAGTT 58.873 38.462 25.55 10.06 0.00 2.24
424 437 6.674573 AGGGTATTACTGACATGTCTCTAGT 58.325 40.000 25.55 21.46 0.00 2.57
425 438 7.429633 CAAGGGTATTACTGACATGTCTCTAG 58.570 42.308 25.55 17.13 0.00 2.43
426 439 6.183360 GCAAGGGTATTACTGACATGTCTCTA 60.183 42.308 25.55 12.25 0.00 2.43
427 440 5.395768 GCAAGGGTATTACTGACATGTCTCT 60.396 44.000 25.55 13.21 0.00 3.10
428 441 4.811557 GCAAGGGTATTACTGACATGTCTC 59.188 45.833 25.55 2.29 0.00 3.36
429 442 4.471386 AGCAAGGGTATTACTGACATGTCT 59.529 41.667 25.55 9.97 0.00 3.41
430 443 4.770795 AGCAAGGGTATTACTGACATGTC 58.229 43.478 19.27 19.27 0.00 3.06
431 444 4.844349 AGCAAGGGTATTACTGACATGT 57.156 40.909 0.00 0.00 0.00 3.21
432 445 6.291377 ACATAGCAAGGGTATTACTGACATG 58.709 40.000 0.00 0.00 0.00 3.21
433 446 6.500589 ACATAGCAAGGGTATTACTGACAT 57.499 37.500 0.00 0.00 0.00 3.06
434 447 5.950544 ACATAGCAAGGGTATTACTGACA 57.049 39.130 0.00 0.00 0.00 3.58
459 472 3.197790 CTCACGGCCGCAATGAGG 61.198 66.667 27.92 14.60 36.92 3.86
460 473 1.699656 CTTCTCACGGCCGCAATGAG 61.700 60.000 29.07 29.07 41.06 2.90
461 474 1.741401 CTTCTCACGGCCGCAATGA 60.741 57.895 28.58 20.85 0.00 2.57
462 475 1.091771 ATCTTCTCACGGCCGCAATG 61.092 55.000 28.58 17.25 0.00 2.82
463 476 1.091771 CATCTTCTCACGGCCGCAAT 61.092 55.000 28.58 1.81 0.00 3.56
464 477 1.741401 CATCTTCTCACGGCCGCAA 60.741 57.895 28.58 13.09 0.00 4.85
465 478 2.125552 CATCTTCTCACGGCCGCA 60.126 61.111 28.58 11.76 0.00 5.69
466 479 1.696832 GAACATCTTCTCACGGCCGC 61.697 60.000 28.58 0.00 0.00 6.53
467 480 0.108615 AGAACATCTTCTCACGGCCG 60.109 55.000 26.86 26.86 30.11 6.13
468 481 1.363744 CAGAACATCTTCTCACGGCC 58.636 55.000 0.00 0.00 34.20 6.13
469 482 0.723981 GCAGAACATCTTCTCACGGC 59.276 55.000 0.00 0.00 34.20 5.68
470 483 2.376808 AGCAGAACATCTTCTCACGG 57.623 50.000 0.00 0.00 34.20 4.94
471 484 2.857152 GCTAGCAGAACATCTTCTCACG 59.143 50.000 10.63 0.00 34.20 4.35
472 485 3.118811 AGGCTAGCAGAACATCTTCTCAC 60.119 47.826 18.24 0.00 34.20 3.51
473 486 3.102972 AGGCTAGCAGAACATCTTCTCA 58.897 45.455 18.24 0.00 34.20 3.27
474 487 3.131933 TGAGGCTAGCAGAACATCTTCTC 59.868 47.826 18.24 9.90 34.20 2.87
475 488 3.102972 TGAGGCTAGCAGAACATCTTCT 58.897 45.455 18.24 0.00 37.19 2.85
476 489 3.118811 AGTGAGGCTAGCAGAACATCTTC 60.119 47.826 18.24 0.00 0.00 2.87
477 490 2.836981 AGTGAGGCTAGCAGAACATCTT 59.163 45.455 18.24 0.00 0.00 2.40
478 491 2.430332 GAGTGAGGCTAGCAGAACATCT 59.570 50.000 18.24 1.61 0.00 2.90
479 492 2.167281 TGAGTGAGGCTAGCAGAACATC 59.833 50.000 18.24 7.52 0.00 3.06
480 493 2.182827 TGAGTGAGGCTAGCAGAACAT 58.817 47.619 18.24 0.00 0.00 2.71
481 494 1.632589 TGAGTGAGGCTAGCAGAACA 58.367 50.000 18.24 7.61 0.00 3.18
482 495 2.028567 AGTTGAGTGAGGCTAGCAGAAC 60.029 50.000 18.24 10.72 0.00 3.01
483 496 2.251818 AGTTGAGTGAGGCTAGCAGAA 58.748 47.619 18.24 0.00 0.00 3.02
484 497 1.930251 AGTTGAGTGAGGCTAGCAGA 58.070 50.000 18.24 0.00 0.00 4.26
485 498 2.758736 AAGTTGAGTGAGGCTAGCAG 57.241 50.000 18.24 0.00 0.00 4.24
486 499 4.826274 ATAAAGTTGAGTGAGGCTAGCA 57.174 40.909 18.24 0.00 0.00 3.49
487 500 6.238239 GCTAAATAAAGTTGAGTGAGGCTAGC 60.238 42.308 6.04 6.04 0.00 3.42
488 501 6.258947 GGCTAAATAAAGTTGAGTGAGGCTAG 59.741 42.308 0.00 0.00 0.00 3.42
489 502 6.070194 AGGCTAAATAAAGTTGAGTGAGGCTA 60.070 38.462 0.00 0.00 35.75 3.93
490 503 4.944317 GGCTAAATAAAGTTGAGTGAGGCT 59.056 41.667 0.00 0.00 0.00 4.58
491 504 4.944317 AGGCTAAATAAAGTTGAGTGAGGC 59.056 41.667 0.00 0.00 0.00 4.70
492 505 6.173339 TGAGGCTAAATAAAGTTGAGTGAGG 58.827 40.000 0.00 0.00 0.00 3.86
493 506 7.856145 ATGAGGCTAAATAAAGTTGAGTGAG 57.144 36.000 0.00 0.00 0.00 3.51
494 507 7.362056 GCAATGAGGCTAAATAAAGTTGAGTGA 60.362 37.037 0.00 0.00 0.00 3.41
495 508 6.749118 GCAATGAGGCTAAATAAAGTTGAGTG 59.251 38.462 0.00 0.00 0.00 3.51
496 509 6.403636 CGCAATGAGGCTAAATAAAGTTGAGT 60.404 38.462 0.00 0.00 0.00 3.41
497 510 5.967674 CGCAATGAGGCTAAATAAAGTTGAG 59.032 40.000 0.00 0.00 0.00 3.02
498 511 5.163663 CCGCAATGAGGCTAAATAAAGTTGA 60.164 40.000 0.00 0.00 0.00 3.18
499 512 5.036737 CCGCAATGAGGCTAAATAAAGTTG 58.963 41.667 0.00 0.00 0.00 3.16
500 513 5.248870 CCGCAATGAGGCTAAATAAAGTT 57.751 39.130 0.00 0.00 0.00 2.66
501 514 4.900635 CCGCAATGAGGCTAAATAAAGT 57.099 40.909 0.00 0.00 0.00 2.66
512 525 3.197790 CTCACGGCCGCAATGAGG 61.198 66.667 27.92 14.60 36.92 3.86
513 526 1.091771 ATTCTCACGGCCGCAATGAG 61.092 55.000 29.07 29.07 41.06 2.90
514 527 0.176910 TATTCTCACGGCCGCAATGA 59.823 50.000 28.58 20.85 0.00 2.57
515 528 1.229428 ATATTCTCACGGCCGCAATG 58.771 50.000 28.58 17.25 0.00 2.82
516 529 1.873591 GAATATTCTCACGGCCGCAAT 59.126 47.619 28.58 19.76 0.00 3.56
517 530 1.295792 GAATATTCTCACGGCCGCAA 58.704 50.000 28.58 13.09 0.00 4.85
518 531 0.531974 GGAATATTCTCACGGCCGCA 60.532 55.000 28.58 11.76 0.00 5.69
519 532 0.249911 AGGAATATTCTCACGGCCGC 60.250 55.000 28.58 3.96 0.00 6.53
520 533 3.056821 TCATAGGAATATTCTCACGGCCG 60.057 47.826 26.86 26.86 0.00 6.13
521 534 4.537135 TCATAGGAATATTCTCACGGCC 57.463 45.455 14.95 0.00 0.00 6.13
522 535 6.650807 TGAATTCATAGGAATATTCTCACGGC 59.349 38.462 14.95 0.00 42.87 5.68
523 536 8.783833 ATGAATTCATAGGAATATTCTCACGG 57.216 34.615 19.42 2.62 42.87 4.94
585 598 2.615493 CCGTGATTGTTACAGGCCTCTT 60.615 50.000 0.00 0.00 0.00 2.85
685 739 4.333690 GCTCAGCAATCCCATGATCTTAT 58.666 43.478 0.00 0.00 0.00 1.73
694 748 0.178967 TGTTTGGCTCAGCAATCCCA 60.179 50.000 0.00 0.00 0.00 4.37
722 777 9.941664 TCTTATATTTCTTTACGAAGGAGTACG 57.058 33.333 0.00 0.00 33.56 3.67
762 817 7.235079 TGAACATTGGTATCCCTCTGTAAAAA 58.765 34.615 0.00 0.00 0.00 1.94
763 818 6.785076 TGAACATTGGTATCCCTCTGTAAAA 58.215 36.000 0.00 0.00 0.00 1.52
766 821 5.277250 TCTGAACATTGGTATCCCTCTGTA 58.723 41.667 0.00 0.00 0.00 2.74
767 822 4.104086 TCTGAACATTGGTATCCCTCTGT 58.896 43.478 0.00 0.00 0.00 3.41
770 825 7.410120 AATTTTCTGAACATTGGTATCCCTC 57.590 36.000 1.22 0.00 0.00 4.30
771 826 6.381133 GGAATTTTCTGAACATTGGTATCCCT 59.619 38.462 6.51 0.00 0.00 4.20
772 827 6.154363 TGGAATTTTCTGAACATTGGTATCCC 59.846 38.462 6.51 2.05 0.00 3.85
773 828 7.169158 TGGAATTTTCTGAACATTGGTATCC 57.831 36.000 6.51 2.67 0.00 2.59
774 829 6.753744 GCTGGAATTTTCTGAACATTGGTATC 59.246 38.462 6.51 0.00 0.00 2.24
884 1082 3.812019 CCCGAGGAGGACGTGTCG 61.812 72.222 0.00 0.00 45.00 4.35
1794 1998 1.071471 CCGAGCCACAGTTTCCAGT 59.929 57.895 0.00 0.00 0.00 4.00
1822 2026 2.270352 TCACACACCTCCATTCCAAC 57.730 50.000 0.00 0.00 0.00 3.77
1870 2074 2.036256 GAGGCAACCCAGCACCAT 59.964 61.111 0.00 0.00 35.83 3.55
1998 2202 2.282180 TCGGGAGCAACCAAAGCC 60.282 61.111 2.58 0.00 41.20 4.35
2044 2248 3.706086 TCGAAATCATGACTCCTCATCCA 59.294 43.478 0.00 0.00 34.65 3.41
2130 2334 4.443266 GCAAGCCGCTCGTCTCCT 62.443 66.667 0.00 0.00 37.77 3.69
2229 2433 2.295909 TGCAACCAATGGTTCTAACTGC 59.704 45.455 15.79 15.57 43.05 4.40
2246 2450 2.892373 GCATAACGCTGTAGTTGCAA 57.108 45.000 0.00 0.00 37.77 4.08
2441 2645 5.162794 GCTGCACTATATCATCTGACTCAG 58.837 45.833 0.00 0.00 0.00 3.35
2522 2726 1.315690 AACAGACTCACCGTTCGAGA 58.684 50.000 0.00 0.00 34.47 4.04
2685 2889 4.836825 ACAGGATATGCCTCGAATAATGG 58.163 43.478 0.00 0.00 46.97 3.16
2693 2897 1.436600 GCATGACAGGATATGCCTCG 58.563 55.000 0.00 0.00 46.97 4.63
2755 2959 6.099159 TCCAGAATTTTTCATGTTGCATCA 57.901 33.333 0.00 0.00 0.00 3.07
2833 3095 6.067263 TCTTCTAACACATTTTGGGTTTCG 57.933 37.500 0.00 0.00 42.12 3.46
2872 3134 6.657875 ACCAAAATGGAGGTTTCATTCAAAA 58.342 32.000 2.85 0.00 40.96 2.44
3033 3382 6.326375 TGGTTTCGGCATAAAATGAACATAC 58.674 36.000 0.00 0.00 0.00 2.39
3152 3501 9.301153 GAAATGAGTGAACAAACACACTAAAAT 57.699 29.630 0.00 0.00 45.54 1.82
3365 3725 6.101734 TCTGGTCAAAGGCATTAGGAAGATAT 59.898 38.462 0.00 0.00 0.00 1.63
3366 3726 5.428457 TCTGGTCAAAGGCATTAGGAAGATA 59.572 40.000 0.00 0.00 0.00 1.98
3409 3769 7.426456 GCAATACAGTAAAGATTCATCAACACG 59.574 37.037 0.00 0.00 0.00 4.49
3463 3823 7.014134 AGTGACCATACATTGATTGTTTTGTCA 59.986 33.333 0.00 2.44 38.62 3.58
3513 3873 9.545105 AAGCATGTTGTTTATTTCAAGAATGAA 57.455 25.926 0.00 0.00 43.70 2.57
3514 3874 9.545105 AAAGCATGTTGTTTATTTCAAGAATGA 57.455 25.926 0.00 0.00 0.00 2.57
3519 3879 8.209869 CGAGAAAAGCATGTTGTTTATTTCAAG 58.790 33.333 6.48 0.00 0.00 3.02
3520 3880 7.168972 CCGAGAAAAGCATGTTGTTTATTTCAA 59.831 33.333 6.48 0.00 0.00 2.69
3522 3882 6.861055 TCCGAGAAAAGCATGTTGTTTATTTC 59.139 34.615 0.00 0.00 0.00 2.17
3523 3883 6.744112 TCCGAGAAAAGCATGTTGTTTATTT 58.256 32.000 0.00 0.00 0.00 1.40
3524 3884 6.325919 TCCGAGAAAAGCATGTTGTTTATT 57.674 33.333 0.00 0.00 0.00 1.40
3525 3885 5.957842 TCCGAGAAAAGCATGTTGTTTAT 57.042 34.783 0.00 0.00 0.00 1.40
3526 3886 5.759506 TTCCGAGAAAAGCATGTTGTTTA 57.240 34.783 0.00 0.00 0.00 2.01
3527 3887 4.647424 TTCCGAGAAAAGCATGTTGTTT 57.353 36.364 0.00 0.00 0.00 2.83
3528 3888 4.278170 TCATTCCGAGAAAAGCATGTTGTT 59.722 37.500 0.00 0.00 0.00 2.83
3530 3890 4.409570 CTCATTCCGAGAAAAGCATGTTG 58.590 43.478 0.00 0.00 45.45 3.33
3531 3891 4.691860 CTCATTCCGAGAAAAGCATGTT 57.308 40.909 0.00 0.00 45.45 2.71
3732 4128 1.344763 ACTGCCACTGTCTCCACTTAC 59.655 52.381 0.00 0.00 0.00 2.34
4110 4506 2.665165 TGGTTTGGCAGATTCAACAGT 58.335 42.857 1.86 0.00 0.00 3.55
4156 4555 6.913170 TGCCAAAGAGAGATTGTGAATTAAC 58.087 36.000 0.00 0.00 0.00 2.01
4207 4606 1.202830 ACACGGTTGATTTGTGGCCTA 60.203 47.619 3.32 0.00 37.92 3.93
4465 4864 9.840427 GACTGTAAGCAAACATTATAACACAAT 57.160 29.630 0.00 0.00 37.60 2.71
4676 5077 6.747280 GCACCAAATATGTGTCAGAAATACAC 59.253 38.462 0.00 0.00 45.96 2.90
4740 5141 7.254084 GCAAGGCAACAAATAATATGTTAGCAC 60.254 37.037 12.36 5.78 38.90 4.40
4802 5203 5.713792 TCCAACTCTGACTTGTCTTCTAG 57.286 43.478 2.35 0.00 0.00 2.43
4811 5212 5.815233 TCTCTGATTTCCAACTCTGACTT 57.185 39.130 0.00 0.00 0.00 3.01
4949 5350 6.044046 TGCAAAGGAAATGATGTATGAATGC 58.956 36.000 0.00 0.00 0.00 3.56
4982 5383 6.629128 TGTTGTATGAATGCATAACAAAGGG 58.371 36.000 14.62 0.00 38.64 3.95
4983 5384 8.706492 AATGTTGTATGAATGCATAACAAAGG 57.294 30.769 12.98 0.00 36.85 3.11
4990 5391 9.926158 ACAAAGAAAATGTTGTATGAATGCATA 57.074 25.926 0.00 0.00 36.22 3.14
4991 5392 8.836268 ACAAAGAAAATGTTGTATGAATGCAT 57.164 26.923 0.00 0.00 36.22 3.96
4992 5393 8.659925 AACAAAGAAAATGTTGTATGAATGCA 57.340 26.923 0.00 0.00 39.43 3.96
4993 5394 8.981647 AGAACAAAGAAAATGTTGTATGAATGC 58.018 29.630 0.00 0.00 40.90 3.56
5011 5412 9.827411 GCACCTTTAAATTACTCTAGAACAAAG 57.173 33.333 0.00 0.00 0.00 2.77
5012 5413 9.344772 TGCACCTTTAAATTACTCTAGAACAAA 57.655 29.630 0.00 0.00 0.00 2.83
5049 5450 3.913855 TTTTTCACCAGGGAGCACA 57.086 47.368 0.00 0.00 0.00 4.57
5065 5466 5.280654 ACAAGTGGAACATCAGCATTTTT 57.719 34.783 0.00 0.00 44.52 1.94
5107 5508 9.349145 GGACACAAAAACTTATATGCGTAAATT 57.651 29.630 0.00 0.00 0.00 1.82
5110 5511 7.675962 AGGACACAAAAACTTATATGCGTAA 57.324 32.000 0.00 0.00 0.00 3.18
5114 5515 9.855021 ACATAAAGGACACAAAAACTTATATGC 57.145 29.630 0.00 0.00 0.00 3.14
5129 5763 8.637099 TGAAATTTGACAATCACATAAAGGACA 58.363 29.630 0.00 0.00 0.00 4.02
5143 5777 8.646004 TGATACCTTTTCCATGAAATTTGACAA 58.354 29.630 0.00 0.00 31.34 3.18
5163 5798 5.376854 ACACAAGATGCAAAACTGATACC 57.623 39.130 0.00 0.00 0.00 2.73
5212 5854 5.752955 AGACGAAAACCAAATTTCACAATGG 59.247 36.000 0.00 0.00 38.87 3.16
5278 5928 8.768955 TCCAAAAACAATTACACATGTAAATGC 58.231 29.630 16.30 0.00 42.28 3.56
5288 5938 8.539674 GTCAGACAATTCCAAAAACAATTACAC 58.460 33.333 0.00 0.00 0.00 2.90
5328 6092 1.256812 TGTGCTCTCGAGATGACCAA 58.743 50.000 17.03 0.00 0.00 3.67
5421 6185 5.321102 AGTAATAACTGTTGTGGATTGGCA 58.679 37.500 2.69 0.00 33.57 4.92
5832 6601 4.684242 GCATTTCCCTTCAAACTTTTACCG 59.316 41.667 0.00 0.00 0.00 4.02
5961 6730 3.091545 CAACCCACATAGCATCCAAGTT 58.908 45.455 0.00 0.00 0.00 2.66
5975 6744 6.362283 CGTAATCACTTCAAATTTCAACCCAC 59.638 38.462 0.00 0.00 0.00 4.61
5989 6758 2.351726 GGCATGTGGACGTAATCACTTC 59.648 50.000 14.42 6.23 35.15 3.01
6068 8678 4.574892 TGATGACGATGGTTGTACATGTT 58.425 39.130 2.30 0.00 0.00 2.71
6083 8693 4.934075 ATATCGCATTTGGATGATGACG 57.066 40.909 0.00 0.00 35.16 4.35
6119 8729 1.122019 AGGAGGTTTGGTGAGTCGCT 61.122 55.000 3.25 0.00 0.00 4.93
6256 8900 3.297134 AAAGCTTCTCAAACCCACTCA 57.703 42.857 0.00 0.00 0.00 3.41
6335 8979 8.792830 ACCGATAGAGAAAATCATGAAGAAAA 57.207 30.769 0.00 0.00 39.76 2.29
6390 9035 4.082125 AGGAACGGAAGCAAAGATGAAAT 58.918 39.130 0.00 0.00 0.00 2.17
6429 9074 8.754230 TTTGAATTATTTCGACATGCATTTGA 57.246 26.923 0.00 0.00 34.39 2.69
6448 9093 8.222433 CGAAAAATGTGCAATGTGTATTTGAAT 58.778 29.630 0.00 0.00 0.00 2.57
6473 9118 8.429739 TCTAACAAAATTTCAATTTCTACGCG 57.570 30.769 3.53 3.53 37.62 6.01
6588 9234 5.289917 TGTGTGTAAAACTGTTCACTGTG 57.710 39.130 0.17 0.17 0.00 3.66


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

AutoCloner maintained by Alex Coulton.