Multiple sequence alignment - TraesCS1D01G160500

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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 TraesCS1D01G160500 chr1D 100.000 5212 0 0 1 5212 227372126 227377337 0.000000e+00 9625.0
1 TraesCS1D01G160500 chr1D 88.730 1952 126 39 2500 4416 226944077 226945969 0.000000e+00 2300.0
2 TraesCS1D01G160500 chr1D 90.089 1352 107 19 1085 2422 226942754 226944092 0.000000e+00 1729.0
3 TraesCS1D01G160500 chr1D 90.234 1024 75 14 2604 3608 226826316 226827333 0.000000e+00 1314.0
4 TraesCS1D01G160500 chr1D 89.220 974 63 14 3621 4570 226827568 226828523 0.000000e+00 1179.0
5 TraesCS1D01G160500 chr1D 90.054 925 62 7 2498 3411 208415848 208414943 0.000000e+00 1171.0
6 TraesCS1D01G160500 chr1D 86.106 1058 100 23 3406 4446 208413314 208412287 0.000000e+00 1096.0
7 TraesCS1D01G160500 chr1D 86.368 983 95 11 1449 2421 226825345 226826298 0.000000e+00 1037.0
8 TraesCS1D01G160500 chr1D 85.363 977 114 18 1450 2421 223162335 223163287 0.000000e+00 985.0
9 TraesCS1D01G160500 chr1D 85.636 912 77 25 3494 4385 223164290 223165167 0.000000e+00 909.0
10 TraesCS1D01G160500 chr1D 91.860 602 33 3 1822 2421 208416420 208415833 0.000000e+00 826.0
11 TraesCS1D01G160500 chr1D 89.917 605 42 5 1822 2421 227647998 227648588 0.000000e+00 761.0
12 TraesCS1D01G160500 chr1D 87.537 674 58 12 442 1111 226942167 226942818 0.000000e+00 756.0
13 TraesCS1D01G160500 chr1D 84.397 705 82 8 2741 3418 223163457 223164160 0.000000e+00 667.0
14 TraesCS1D01G160500 chr1D 89.901 505 50 1 2739 3242 261723862 261724366 0.000000e+00 649.0
15 TraesCS1D01G160500 chr1D 83.956 642 63 22 1220 1822 208417602 208416962 3.500000e-161 579.0
16 TraesCS1D01G160500 chr1D 92.746 386 19 6 57 440 226941979 226942357 2.740000e-152 549.0
17 TraesCS1D01G160500 chr1D 78.185 573 77 24 502 1058 261722005 261722545 6.510000e-84 322.0
18 TraesCS1D01G160500 chr1D 86.170 282 24 6 34 306 261721867 261722142 1.840000e-74 291.0
19 TraesCS1D01G160500 chr1D 84.667 300 34 9 734 1031 226824469 226824758 6.600000e-74 289.0
20 TraesCS1D01G160500 chr1D 84.490 245 27 8 4210 4443 227650294 227650538 1.130000e-56 231.0
21 TraesCS1D01G160500 chr1D 91.045 134 10 2 4450 4582 226947922 226948054 4.150000e-41 180.0
22 TraesCS1D01G160500 chr1D 90.299 134 11 2 4450 4582 227115193 227115325 1.930000e-39 174.0
23 TraesCS1D01G160500 chr1D 76.855 337 42 22 524 844 227645841 227646157 1.940000e-34 158.0
24 TraesCS1D01G160500 chr1D 88.372 129 10 4 1226 1349 226824887 226825015 3.250000e-32 150.0
25 TraesCS1D01G160500 chr1D 85.430 151 12 6 302 451 227372299 227372440 1.170000e-31 148.0
26 TraesCS1D01G160500 chr1D 85.430 151 12 6 174 315 227372427 227372576 1.170000e-31 148.0
27 TraesCS1D01G160500 chr1D 83.221 149 14 8 305 451 226942099 226942238 5.480000e-25 126.0
28 TraesCS1D01G160500 chr1D 97.183 71 2 0 2427 2497 20340324 20340394 2.550000e-23 121.0
29 TraesCS1D01G160500 chr1D 93.506 77 2 3 2421 2496 3658958 3659032 1.530000e-20 111.0
30 TraesCS1D01G160500 chr1D 89.535 86 2 1 951 1029 227646605 227646690 9.230000e-18 102.0
31 TraesCS1D01G160500 chr1D 94.828 58 3 0 2500 2557 226826285 226826342 2.000000e-14 91.6
32 TraesCS1D01G160500 chr1B 94.296 2770 79 26 2498 5212 327228590 327231335 0.000000e+00 4167.0
33 TraesCS1D01G160500 chr1B 93.759 1987 77 19 442 2421 327226659 327228605 0.000000e+00 2939.0
34 TraesCS1D01G160500 chr1B 87.687 1941 136 50 2500 4416 326913190 326915051 0.000000e+00 2165.0
35 TraesCS1D01G160500 chr1B 91.135 1004 76 9 1085 2083 326911842 326912837 0.000000e+00 1349.0
36 TraesCS1D01G160500 chr1B 86.077 1063 117 19 3398 4443 327345107 327346155 0.000000e+00 1114.0
37 TraesCS1D01G160500 chr1B 90.025 802 55 5 2619 3411 327343065 327343850 0.000000e+00 1014.0
38 TraesCS1D01G160500 chr1B 84.592 980 117 22 1450 2421 322473546 322474499 0.000000e+00 942.0
39 TraesCS1D01G160500 chr1B 83.811 908 84 29 3494 4378 322475491 322476358 0.000000e+00 804.0
40 TraesCS1D01G160500 chr1B 86.311 694 65 14 442 1129 326911253 326911922 0.000000e+00 728.0
41 TraesCS1D01G160500 chr1B 95.078 447 19 3 3 447 327226126 327226571 0.000000e+00 701.0
42 TraesCS1D01G160500 chr1B 93.316 389 18 5 57 443 326911066 326911448 7.570000e-158 568.0
43 TraesCS1D01G160500 chr1B 83.437 646 62 25 1220 1822 327339079 327339722 4.560000e-155 558.0
44 TraesCS1D01G160500 chr1B 78.407 565 70 23 502 1058 350444616 350444096 2.340000e-83 320.0
45 TraesCS1D01G160500 chr1B 93.284 134 9 0 2497 2630 327341515 327341648 1.140000e-46 198.0
46 TraesCS1D01G160500 chr1B 87.248 149 7 6 174 311 327226425 327226572 5.400000e-35 159.0
47 TraesCS1D01G160500 chr1B 83.784 148 14 6 305 451 327226300 327226438 1.180000e-26 132.0
48 TraesCS1D01G160500 chr1B 83.108 148 15 7 305 451 326911186 326911324 5.480000e-25 126.0
49 TraesCS1D01G160500 chr1B 95.833 72 2 1 2427 2498 83631965 83631895 1.190000e-21 115.0
50 TraesCS1D01G160500 chr1B 87.500 64 5 3 1045 1107 327227295 327227356 2.600000e-08 71.3
51 TraesCS1D01G160500 chr1B 100.000 29 0 0 2648 2676 327341580 327341608 3.000000e-03 54.7
52 TraesCS1D01G160500 chr1A 93.375 2400 88 25 2498 4865 294040382 294042742 0.000000e+00 3485.0
53 TraesCS1D01G160500 chr1A 91.057 2024 88 33 442 2421 294038423 294040397 0.000000e+00 2649.0
54 TraesCS1D01G160500 chr1A 85.261 977 111 21 1450 2421 290124482 290125430 0.000000e+00 976.0
55 TraesCS1D01G160500 chr1A 83.402 976 94 31 3494 4446 290126417 290127347 0.000000e+00 843.0
56 TraesCS1D01G160500 chr1A 95.157 413 14 3 34 443 294037925 294038334 0.000000e+00 647.0
57 TraesCS1D01G160500 chr1A 79.329 566 73 24 502 1051 338596612 338596075 1.780000e-94 357.0
58 TraesCS1D01G160500 chr1A 95.960 198 8 0 5015 5212 294042973 294043170 6.510000e-84 322.0
59 TraesCS1D01G160500 chr1A 90.206 194 12 5 154 345 294038335 294038523 4.030000e-61 246.0
60 TraesCS1D01G160500 chr1A 89.362 141 11 2 305 443 338596612 338596474 1.930000e-39 174.0
61 TraesCS1D01G160500 chr1A 87.413 143 8 5 174 306 294038192 294038334 6.990000e-34 156.0
62 TraesCS1D01G160500 chr1A 86.066 122 9 3 34 151 338597258 338597141 1.970000e-24 124.0
63 TraesCS1D01G160500 chr1A 100.000 37 0 0 1 37 294037843 294037879 9.370000e-08 69.4
64 TraesCS1D01G160500 chr7B 81.657 507 68 12 3707 4211 41286383 41286866 1.050000e-106 398.0
65 TraesCS1D01G160500 chr2B 88.732 142 16 0 5055 5196 786478139 786478280 1.930000e-39 174.0
66 TraesCS1D01G160500 chr2B 86.905 84 11 0 4793 4876 786477396 786477479 1.550000e-15 95.3
67 TraesCS1D01G160500 chr7D 82.840 169 16 5 3511 3679 90410250 90410405 7.040000e-29 139.0
68 TraesCS1D01G160500 chr7D 95.890 73 2 1 2427 2498 533430928 533430856 3.300000e-22 117.0
69 TraesCS1D01G160500 chr6D 97.101 69 2 0 2427 2495 65995173 65995105 3.300000e-22 117.0
70 TraesCS1D01G160500 chr6D 92.683 82 3 3 2418 2498 23437254 23437333 1.190000e-21 115.0
71 TraesCS1D01G160500 chr6D 92.593 81 4 2 2418 2497 31767373 31767452 1.190000e-21 115.0
72 TraesCS1D01G160500 chr5D 95.775 71 2 1 2427 2497 60469037 60468968 4.270000e-21 113.0
73 TraesCS1D01G160500 chr5B 93.506 77 2 3 2421 2496 692747539 692747613 1.530000e-20 111.0


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 TraesCS1D01G160500 chr1D 227372126 227377337 5211 False 9625.000000 9625 100.000000 1 5212 1 chr1D.!!$F4 5211
1 TraesCS1D01G160500 chr1D 226941979 226948054 6075 False 940.000000 2300 88.894667 57 4582 6 chr1D.!!$F7 4525
2 TraesCS1D01G160500 chr1D 208412287 208417602 5315 True 918.000000 1171 87.994000 1220 4446 4 chr1D.!!$R1 3226
3 TraesCS1D01G160500 chr1D 223162335 223165167 2832 False 853.666667 985 85.132000 1450 4385 3 chr1D.!!$F5 2935
4 TraesCS1D01G160500 chr1D 226824469 226828523 4054 False 676.766667 1314 88.948167 734 4570 6 chr1D.!!$F6 3836
5 TraesCS1D01G160500 chr1D 261721867 261724366 2499 False 420.666667 649 84.752000 34 3242 3 chr1D.!!$F10 3208
6 TraesCS1D01G160500 chr1D 227645841 227650538 4697 False 313.000000 761 85.199250 524 4443 4 chr1D.!!$F9 3919
7 TraesCS1D01G160500 chr1B 327226126 327231335 5209 False 1361.550000 4167 90.277500 3 5212 6 chr1B.!!$F3 5209
8 TraesCS1D01G160500 chr1B 326911066 326915051 3985 False 987.200000 2165 88.311400 57 4416 5 chr1B.!!$F2 4359
9 TraesCS1D01G160500 chr1B 322473546 322476358 2812 False 873.000000 942 84.201500 1450 4378 2 chr1B.!!$F1 2928
10 TraesCS1D01G160500 chr1B 327339079 327346155 7076 False 587.740000 1114 90.564600 1220 4443 5 chr1B.!!$F4 3223
11 TraesCS1D01G160500 chr1B 350444096 350444616 520 True 320.000000 320 78.407000 502 1058 1 chr1B.!!$R2 556
12 TraesCS1D01G160500 chr1A 294037843 294043170 5327 False 1082.057143 3485 93.309714 1 5212 7 chr1A.!!$F2 5211
13 TraesCS1D01G160500 chr1A 290124482 290127347 2865 False 909.500000 976 84.331500 1450 4446 2 chr1A.!!$F1 2996
14 TraesCS1D01G160500 chr1A 338596075 338597258 1183 True 218.333333 357 84.919000 34 1051 3 chr1A.!!$R1 1017

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
458 514 1.003696 GGGTTCTTCTGGAGTTGAGGG 59.996 57.143 0.00 0.0 0.00 4.30 F
466 522 1.518367 TGGAGTTGAGGGTTTCCAGT 58.482 50.000 0.00 0.0 34.90 4.00 F
2085 4868 1.626825 TCCTTTACCAGGTACCTGCAC 59.373 52.381 32.98 0.0 44.37 4.57 F
2465 5254 1.455217 ATTGCCCAGATGCAGAGGC 60.455 57.895 11.10 11.1 43.21 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2067 4819 1.001633 ACGTGCAGGTACCTGGTAAAG 59.998 52.381 36.91 16.13 43.77 1.85 R
2447 5236 1.455217 GCCTCTGCATCTGGGCAAT 60.455 57.895 12.40 0.00 44.40 3.56 R
4067 10486 0.672401 CGCATCCACCCGTAAACACT 60.672 55.000 0.00 0.00 0.00 3.55 R
4448 12807 2.229792 GGTCAGCTGAACCAAACATCA 58.770 47.619 21.71 0.00 0.00 3.07 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
242 298 2.031682 GCATCGTGCTGTTCTTCACTTT 60.032 45.455 3.20 0.00 40.96 2.66
294 350 8.699749 AGTTTTTCTTTTCTTTTCACGAAACAG 58.300 29.630 0.00 0.00 30.72 3.16
360 416 1.134788 CGGATTATCGCATCCTACCCC 60.135 57.143 6.56 0.00 40.80 4.95
409 465 4.610333 AGGGTTTTTCAGACTTCCAGTTT 58.390 39.130 0.00 0.00 0.00 2.66
410 466 5.023452 AGGGTTTTTCAGACTTCCAGTTTT 58.977 37.500 0.00 0.00 0.00 2.43
411 467 6.192044 AGGGTTTTTCAGACTTCCAGTTTTA 58.808 36.000 0.00 0.00 0.00 1.52
412 468 6.839134 AGGGTTTTTCAGACTTCCAGTTTTAT 59.161 34.615 0.00 0.00 0.00 1.40
413 469 7.344612 AGGGTTTTTCAGACTTCCAGTTTTATT 59.655 33.333 0.00 0.00 0.00 1.40
414 470 7.985184 GGGTTTTTCAGACTTCCAGTTTTATTT 59.015 33.333 0.00 0.00 0.00 1.40
415 471 9.378551 GGTTTTTCAGACTTCCAGTTTTATTTT 57.621 29.630 0.00 0.00 0.00 1.82
438 494 9.762933 TTTTATTTTCAAGAAACAGGGATTCAG 57.237 29.630 0.00 0.00 0.00 3.02
439 495 5.789643 TTTTCAAGAAACAGGGATTCAGG 57.210 39.130 0.00 0.00 0.00 3.86
440 496 3.439857 TCAAGAAACAGGGATTCAGGG 57.560 47.619 0.00 0.00 0.00 4.45
441 497 2.716424 TCAAGAAACAGGGATTCAGGGT 59.284 45.455 0.00 0.00 0.00 4.34
442 498 3.140144 TCAAGAAACAGGGATTCAGGGTT 59.860 43.478 0.00 0.00 0.00 4.11
443 499 3.441500 AGAAACAGGGATTCAGGGTTC 57.558 47.619 0.00 0.00 0.00 3.62
444 500 2.989571 AGAAACAGGGATTCAGGGTTCT 59.010 45.455 0.00 0.00 0.00 3.01
445 501 3.399305 AGAAACAGGGATTCAGGGTTCTT 59.601 43.478 0.00 0.00 0.00 2.52
446 502 3.441500 AACAGGGATTCAGGGTTCTTC 57.558 47.619 0.00 0.00 0.00 2.87
447 503 2.637165 ACAGGGATTCAGGGTTCTTCT 58.363 47.619 0.00 0.00 0.00 2.85
448 504 2.307098 ACAGGGATTCAGGGTTCTTCTG 59.693 50.000 0.00 0.00 0.00 3.02
449 505 1.918957 AGGGATTCAGGGTTCTTCTGG 59.081 52.381 0.00 0.00 33.36 3.86
450 506 1.916181 GGGATTCAGGGTTCTTCTGGA 59.084 52.381 0.00 0.00 33.36 3.86
451 507 2.092699 GGGATTCAGGGTTCTTCTGGAG 60.093 54.545 0.00 0.00 33.36 3.86
452 508 2.573915 GGATTCAGGGTTCTTCTGGAGT 59.426 50.000 0.00 0.00 33.36 3.85
453 509 3.009584 GGATTCAGGGTTCTTCTGGAGTT 59.990 47.826 0.00 0.00 33.36 3.01
454 510 3.492102 TTCAGGGTTCTTCTGGAGTTG 57.508 47.619 0.00 0.00 33.36 3.16
455 511 2.689658 TCAGGGTTCTTCTGGAGTTGA 58.310 47.619 0.00 0.00 33.36 3.18
456 512 2.634940 TCAGGGTTCTTCTGGAGTTGAG 59.365 50.000 0.00 0.00 33.36 3.02
457 513 1.981495 AGGGTTCTTCTGGAGTTGAGG 59.019 52.381 0.00 0.00 0.00 3.86
458 514 1.003696 GGGTTCTTCTGGAGTTGAGGG 59.996 57.143 0.00 0.00 0.00 4.30
459 515 1.700186 GGTTCTTCTGGAGTTGAGGGT 59.300 52.381 0.00 0.00 0.00 4.34
460 516 2.106684 GGTTCTTCTGGAGTTGAGGGTT 59.893 50.000 0.00 0.00 0.00 4.11
461 517 3.435169 GGTTCTTCTGGAGTTGAGGGTTT 60.435 47.826 0.00 0.00 0.00 3.27
462 518 3.771577 TCTTCTGGAGTTGAGGGTTTC 57.228 47.619 0.00 0.00 0.00 2.78
463 519 2.372172 TCTTCTGGAGTTGAGGGTTTCC 59.628 50.000 0.00 0.00 0.00 3.13
464 520 1.814429 TCTGGAGTTGAGGGTTTCCA 58.186 50.000 0.00 0.00 37.38 3.53
466 522 1.518367 TGGAGTTGAGGGTTTCCAGT 58.482 50.000 0.00 0.00 34.90 4.00
467 523 1.850345 TGGAGTTGAGGGTTTCCAGTT 59.150 47.619 0.00 0.00 34.90 3.16
468 524 2.243736 TGGAGTTGAGGGTTTCCAGTTT 59.756 45.455 0.00 0.00 34.90 2.66
469 525 3.296854 GGAGTTGAGGGTTTCCAGTTTT 58.703 45.455 0.00 0.00 34.83 2.43
470 526 3.704566 GGAGTTGAGGGTTTCCAGTTTTT 59.295 43.478 0.00 0.00 34.83 1.94
471 527 4.202121 GGAGTTGAGGGTTTCCAGTTTTTC 60.202 45.833 0.00 0.00 34.83 2.29
472 528 4.610333 AGTTGAGGGTTTCCAGTTTTTCT 58.390 39.130 0.00 0.00 34.83 2.52
473 529 5.023452 AGTTGAGGGTTTCCAGTTTTTCTT 58.977 37.500 0.00 0.00 34.83 2.52
474 530 5.483937 AGTTGAGGGTTTCCAGTTTTTCTTT 59.516 36.000 0.00 0.00 34.83 2.52
475 531 6.013725 AGTTGAGGGTTTCCAGTTTTTCTTTT 60.014 34.615 0.00 0.00 34.83 2.27
476 532 6.367374 TGAGGGTTTCCAGTTTTTCTTTTT 57.633 33.333 0.00 0.00 34.83 1.94
477 533 6.403049 TGAGGGTTTCCAGTTTTTCTTTTTC 58.597 36.000 0.00 0.00 34.83 2.29
478 534 6.212589 TGAGGGTTTCCAGTTTTTCTTTTTCT 59.787 34.615 0.00 0.00 34.83 2.52
479 535 7.016153 AGGGTTTCCAGTTTTTCTTTTTCTT 57.984 32.000 0.00 0.00 34.83 2.52
480 536 7.458397 AGGGTTTCCAGTTTTTCTTTTTCTTT 58.542 30.769 0.00 0.00 34.83 2.52
481 537 7.942341 AGGGTTTCCAGTTTTTCTTTTTCTTTT 59.058 29.630 0.00 0.00 34.83 2.27
482 538 8.234546 GGGTTTCCAGTTTTTCTTTTTCTTTTC 58.765 33.333 0.00 0.00 0.00 2.29
483 539 8.999431 GGTTTCCAGTTTTTCTTTTTCTTTTCT 58.001 29.630 0.00 0.00 0.00 2.52
485 541 8.460831 TTCCAGTTTTTCTTTTTCTTTTCTCG 57.539 30.769 0.00 0.00 0.00 4.04
486 542 7.822658 TCCAGTTTTTCTTTTTCTTTTCTCGA 58.177 30.769 0.00 0.00 0.00 4.04
487 543 8.301002 TCCAGTTTTTCTTTTTCTTTTCTCGAA 58.699 29.630 0.00 0.00 0.00 3.71
488 544 8.921670 CCAGTTTTTCTTTTTCTTTTCTCGAAA 58.078 29.630 0.00 0.00 0.00 3.46
489 545 9.727403 CAGTTTTTCTTTTTCTTTTCTCGAAAC 57.273 29.630 0.00 0.00 30.72 2.78
490 546 9.471084 AGTTTTTCTTTTTCTTTTCTCGAAACA 57.529 25.926 0.00 0.00 30.72 2.83
491 547 9.727403 GTTTTTCTTTTTCTTTTCTCGAAACAG 57.273 29.630 0.00 0.00 32.31 3.16
492 548 8.460831 TTTTCTTTTTCTTTTCTCGAAACAGG 57.539 30.769 0.00 0.00 32.07 4.00
493 549 6.995511 TCTTTTTCTTTTCTCGAAACAGGA 57.004 33.333 0.00 0.00 32.07 3.86
494 550 7.568199 TCTTTTTCTTTTCTCGAAACAGGAT 57.432 32.000 0.00 0.00 32.07 3.24
495 551 7.996385 TCTTTTTCTTTTCTCGAAACAGGATT 58.004 30.769 0.00 0.00 32.07 3.01
496 552 8.129211 TCTTTTTCTTTTCTCGAAACAGGATTC 58.871 33.333 0.00 0.00 32.07 2.52
497 553 6.935741 TTTCTTTTCTCGAAACAGGATTCA 57.064 33.333 0.00 0.00 0.00 2.57
498 554 6.545504 TTCTTTTCTCGAAACAGGATTCAG 57.454 37.500 0.00 0.00 0.00 3.02
499 555 4.452455 TCTTTTCTCGAAACAGGATTCAGC 59.548 41.667 0.00 0.00 0.00 4.26
500 556 1.996292 TCTCGAAACAGGATTCAGCG 58.004 50.000 0.00 0.00 0.00 5.18
512 746 2.352960 GGATTCAGCGTTCTTCATGGAC 59.647 50.000 0.00 0.00 0.00 4.02
580 1259 9.674068 ATCCTACTATTCTTCACTTTTTCTTCC 57.326 33.333 0.00 0.00 0.00 3.46
601 1280 3.412386 CGGAGTTGAGGGTTTTTCAGAT 58.588 45.455 0.00 0.00 0.00 2.90
605 1284 5.301805 GGAGTTGAGGGTTTTTCAGATTTCA 59.698 40.000 0.00 0.00 0.00 2.69
677 1362 6.334989 TCTTGGCTTTCTTTCGTAATCGATA 58.665 36.000 0.00 0.00 45.65 2.92
1051 2114 3.202906 GCCTAGCCAATCGTGATGTTTA 58.797 45.455 0.00 0.00 0.00 2.01
1061 2124 3.909430 TCGTGATGTTTAGACTGTGTCC 58.091 45.455 0.00 0.00 32.18 4.02
1121 2187 9.744468 TCTGTCTTCTAAAAACCAAATAAAAGC 57.256 29.630 0.00 0.00 0.00 3.51
1136 2202 7.442062 CCAAATAAAAGCTTGATGTTTGGACTT 59.558 33.333 30.08 10.83 44.10 3.01
1145 2211 6.978080 GCTTGATGTTTGGACTTTGTCTTTTA 59.022 34.615 0.00 0.00 32.47 1.52
1189 2258 9.249053 TGTAATTTACAGCATTAAATCCTTGGA 57.751 29.630 5.14 0.00 31.67 3.53
1336 2488 4.275810 TGATTAGAAGCGGTAGTACAGGT 58.724 43.478 2.06 0.40 0.00 4.00
1387 2651 4.986054 TTTCTGCTTTGTTCTACCCCTA 57.014 40.909 0.00 0.00 0.00 3.53
1392 2656 5.013704 TCTGCTTTGTTCTACCCCTAATTGA 59.986 40.000 0.00 0.00 0.00 2.57
1397 2661 6.636454 TTGTTCTACCCCTAATTGATGACT 57.364 37.500 0.00 0.00 0.00 3.41
1552 2980 5.911752 TCTCATAGCATGTTCTCTCTTTCC 58.088 41.667 0.00 0.00 0.00 3.13
1770 3205 3.441101 TCACTGCTCTGGGTATAACTGT 58.559 45.455 0.00 0.00 0.00 3.55
1850 4579 8.008513 ACCATCTAGCTTATTTTCGTAGAAGA 57.991 34.615 0.00 0.00 45.90 2.87
1897 4628 7.342799 ACACATTGATTTAGGATGCCATTTACT 59.657 33.333 0.00 0.00 0.00 2.24
1898 4629 8.849168 CACATTGATTTAGGATGCCATTTACTA 58.151 33.333 0.00 0.00 0.00 1.82
1899 4630 9.420118 ACATTGATTTAGGATGCCATTTACTAA 57.580 29.630 0.00 0.00 0.00 2.24
1900 4631 9.683069 CATTGATTTAGGATGCCATTTACTAAC 57.317 33.333 0.00 0.00 0.00 2.34
1901 4632 8.815565 TTGATTTAGGATGCCATTTACTAACA 57.184 30.769 0.00 0.00 0.00 2.41
1902 4633 8.815565 TGATTTAGGATGCCATTTACTAACAA 57.184 30.769 0.00 0.00 0.00 2.83
1903 4634 9.420118 TGATTTAGGATGCCATTTACTAACAAT 57.580 29.630 0.00 0.00 0.00 2.71
1904 4635 9.683069 GATTTAGGATGCCATTTACTAACAATG 57.317 33.333 0.00 0.00 0.00 2.82
1905 4636 8.815565 TTTAGGATGCCATTTACTAACAATGA 57.184 30.769 0.00 0.00 34.05 2.57
2067 4819 3.848272 TGGTTTCTTCGCATGATTTCC 57.152 42.857 0.00 0.00 0.00 3.13
2085 4868 1.626825 TCCTTTACCAGGTACCTGCAC 59.373 52.381 32.98 0.00 44.37 4.57
2123 4906 2.955660 AGGAAATTGGTTCTGAAACGCA 59.044 40.909 0.36 0.00 36.16 5.24
2416 5205 9.667989 AATACAACGTTTTACCATTAACAAGTC 57.332 29.630 0.00 0.00 0.00 3.01
2417 5206 6.193761 ACAACGTTTTACCATTAACAAGTCG 58.806 36.000 0.00 0.00 0.00 4.18
2418 5207 4.775664 ACGTTTTACCATTAACAAGTCGC 58.224 39.130 0.00 0.00 0.00 5.19
2419 5208 4.512571 ACGTTTTACCATTAACAAGTCGCT 59.487 37.500 0.00 0.00 0.00 4.93
2420 5209 5.007921 ACGTTTTACCATTAACAAGTCGCTT 59.992 36.000 0.00 0.00 0.00 4.68
2421 5210 5.338559 CGTTTTACCATTAACAAGTCGCTTG 59.661 40.000 15.16 15.16 45.85 4.01
2422 5211 6.432107 GTTTTACCATTAACAAGTCGCTTGA 58.568 36.000 21.19 4.80 43.42 3.02
2423 5212 5.856126 TTACCATTAACAAGTCGCTTGAG 57.144 39.130 21.19 8.91 43.42 3.02
2424 5213 4.002906 ACCATTAACAAGTCGCTTGAGA 57.997 40.909 21.19 9.24 43.42 3.27
2425 5214 3.746492 ACCATTAACAAGTCGCTTGAGAC 59.254 43.478 21.19 0.00 43.42 3.36
2426 5215 3.745975 CCATTAACAAGTCGCTTGAGACA 59.254 43.478 21.19 7.07 43.42 3.41
2427 5216 4.393062 CCATTAACAAGTCGCTTGAGACAT 59.607 41.667 21.19 8.55 43.42 3.06
2428 5217 5.106555 CCATTAACAAGTCGCTTGAGACATT 60.107 40.000 21.19 10.39 43.42 2.71
2429 5218 6.092122 CCATTAACAAGTCGCTTGAGACATTA 59.908 38.462 21.19 9.65 43.42 1.90
2430 5219 7.360861 CCATTAACAAGTCGCTTGAGACATTAA 60.361 37.037 21.19 15.47 43.42 1.40
2431 5220 7.667043 TTAACAAGTCGCTTGAGACATTAAT 57.333 32.000 21.19 0.00 43.42 1.40
2432 5221 8.766000 TTAACAAGTCGCTTGAGACATTAATA 57.234 30.769 21.19 0.00 43.42 0.98
2433 5222 7.667043 AACAAGTCGCTTGAGACATTAATAA 57.333 32.000 21.19 0.00 43.42 1.40
2434 5223 7.667043 ACAAGTCGCTTGAGACATTAATAAA 57.333 32.000 21.19 0.00 43.42 1.40
2435 5224 7.743104 ACAAGTCGCTTGAGACATTAATAAAG 58.257 34.615 21.19 0.00 43.42 1.85
2436 5225 7.387948 ACAAGTCGCTTGAGACATTAATAAAGT 59.612 33.333 21.19 0.00 43.42 2.66
2437 5226 7.295952 AGTCGCTTGAGACATTAATAAAGTG 57.704 36.000 7.21 0.00 43.24 3.16
2438 5227 6.313905 AGTCGCTTGAGACATTAATAAAGTGG 59.686 38.462 7.21 0.00 43.24 4.00
2439 5228 5.064707 TCGCTTGAGACATTAATAAAGTGGC 59.935 40.000 0.00 0.00 0.00 5.01
2440 5229 5.065218 CGCTTGAGACATTAATAAAGTGGCT 59.935 40.000 0.00 0.00 32.88 4.75
2441 5230 6.261118 GCTTGAGACATTAATAAAGTGGCTG 58.739 40.000 0.00 0.00 29.60 4.85
2442 5231 5.818136 TGAGACATTAATAAAGTGGCTGC 57.182 39.130 0.00 0.00 29.60 5.25
2443 5232 5.252547 TGAGACATTAATAAAGTGGCTGCA 58.747 37.500 0.50 0.00 29.60 4.41
2444 5233 5.887598 TGAGACATTAATAAAGTGGCTGCAT 59.112 36.000 0.50 0.00 29.60 3.96
2445 5234 6.140303 AGACATTAATAAAGTGGCTGCATG 57.860 37.500 0.50 0.00 27.96 4.06
2446 5235 4.685924 ACATTAATAAAGTGGCTGCATGC 58.314 39.130 11.82 11.82 41.94 4.06
2447 5236 4.160065 ACATTAATAAAGTGGCTGCATGCA 59.840 37.500 21.29 21.29 45.15 3.96
2448 5237 5.163385 ACATTAATAAAGTGGCTGCATGCAT 60.163 36.000 22.97 6.91 45.15 3.96
2449 5238 3.899052 AATAAAGTGGCTGCATGCATT 57.101 38.095 22.97 13.89 45.15 3.56
2450 5239 2.658373 TAAAGTGGCTGCATGCATTG 57.342 45.000 22.97 12.00 45.15 2.82
2458 5247 4.750460 GCATGCATTGCCCAGATG 57.250 55.556 14.21 4.34 46.15 2.90
2459 5248 1.594293 GCATGCATTGCCCAGATGC 60.594 57.895 14.21 13.74 46.15 3.91
2462 5251 3.929002 GCATTGCCCAGATGCAGA 58.071 55.556 0.00 0.00 46.96 4.26
2463 5252 1.734137 GCATTGCCCAGATGCAGAG 59.266 57.895 0.00 0.00 46.96 3.35
2464 5253 1.735376 GCATTGCCCAGATGCAGAGG 61.735 60.000 0.00 0.00 46.96 3.69
2465 5254 1.455217 ATTGCCCAGATGCAGAGGC 60.455 57.895 11.10 11.10 43.21 4.70
2466 5255 2.923634 ATTGCCCAGATGCAGAGGCC 62.924 60.000 14.36 0.00 45.14 5.19
2468 5257 4.559063 CCCAGATGCAGAGGCCGG 62.559 72.222 0.00 0.00 40.13 6.13
2469 5258 4.559063 CCAGATGCAGAGGCCGGG 62.559 72.222 2.18 0.00 40.13 5.73
2470 5259 4.559063 CAGATGCAGAGGCCGGGG 62.559 72.222 2.18 0.00 40.13 5.73
2476 5265 3.787001 CAGAGGCCGGGGGTCTTC 61.787 72.222 2.18 0.00 38.01 2.87
2489 5278 4.652679 GGGGTCTTCCTCCTTTTCTAAA 57.347 45.455 0.00 0.00 35.33 1.85
2490 5279 4.994282 GGGGTCTTCCTCCTTTTCTAAAA 58.006 43.478 0.00 0.00 35.33 1.52
2491 5280 5.010933 GGGGTCTTCCTCCTTTTCTAAAAG 58.989 45.833 8.00 8.00 39.31 2.27
2492 5281 5.222068 GGGGTCTTCCTCCTTTTCTAAAAGA 60.222 44.000 15.16 3.02 40.60 2.52
2493 5282 6.304624 GGGTCTTCCTCCTTTTCTAAAAGAA 58.695 40.000 15.16 0.00 46.39 2.52
2494 5283 6.776116 GGGTCTTCCTCCTTTTCTAAAAGAAA 59.224 38.462 15.16 1.37 46.39 2.52
2683 6904 8.243426 TGGCATACACATGTTTCTCTTTAAATC 58.757 33.333 0.00 0.00 34.40 2.17
2916 7217 8.671921 TGAAATCATCTGCTTTTCTAGTTGATC 58.328 33.333 0.00 0.00 34.14 2.92
2974 7275 6.617782 TGATGTCTCTTCTCCTGAAAAGAT 57.382 37.500 0.00 0.00 32.61 2.40
3045 7346 3.118186 TCAGAAGAAGGGGTTCGTCAAAA 60.118 43.478 4.31 0.00 32.95 2.44
3080 7381 5.841810 TGGAACATGAACAATTTCCTTGAC 58.158 37.500 0.00 0.00 38.70 3.18
3104 7405 2.095718 GGACTTGGATCACTTTGTTCGC 60.096 50.000 0.00 0.00 0.00 4.70
3124 7425 4.021456 TCGCTCTCCTACATTTGAAGTTGA 60.021 41.667 0.00 0.00 0.00 3.18
3152 7453 5.299279 GCATAAATGGTATGCACCTGTTACT 59.701 40.000 12.32 0.00 46.89 2.24
3221 7552 9.289303 CATGTGTTATCCAACATTTTAGCTTAC 57.711 33.333 0.00 0.00 46.03 2.34
3223 7554 8.851145 TGTGTTATCCAACATTTTAGCTTACAA 58.149 29.630 0.00 0.00 46.03 2.41
3230 7563 7.065324 TCCAACATTTTAGCTTACAAGTATCCG 59.935 37.037 0.00 0.00 0.00 4.18
3264 7615 2.433239 ACCTGGTCACTGTACGAACTTT 59.567 45.455 0.00 0.00 0.00 2.66
3618 10006 8.251026 TCCATTATCTTGTACTGTAGTGAACTG 58.749 37.037 0.00 0.00 0.00 3.16
3634 10022 7.346751 AGTGAACTGGTGATGTTTTGTTTAT 57.653 32.000 0.00 0.00 0.00 1.40
3686 10078 3.006112 TGTGTCCAAAGTTAACCTGCA 57.994 42.857 0.88 0.00 0.00 4.41
3817 10215 1.880675 CAGGTACGTCCGCATCTATCT 59.119 52.381 0.00 0.00 41.99 1.98
4035 10451 7.047891 TGTAACCTCATGATGATTACAGTTCC 58.952 38.462 14.40 0.26 30.99 3.62
4067 10486 1.847328 TGGTGATCGCAGGTCTCTTA 58.153 50.000 8.82 0.00 0.00 2.10
4351 10792 4.471904 AATGAGCTGGATTTGAGACGTA 57.528 40.909 0.00 0.00 0.00 3.57
4446 12788 5.696822 CATGGATGATGCAACTATGTTAGC 58.303 41.667 0.00 0.00 0.00 3.09
4448 12807 5.439721 TGGATGATGCAACTATGTTAGCTT 58.560 37.500 0.00 0.00 0.00 3.74
4545 12905 9.896645 AATCATATAGTCATATGGTTCCATGTC 57.103 33.333 13.86 0.00 42.37 3.06
4592 12952 3.953712 TGAGAGCGAAGGTGTTTCATA 57.046 42.857 0.00 0.00 39.88 2.15
4593 12953 3.849911 TGAGAGCGAAGGTGTTTCATAG 58.150 45.455 0.00 0.00 39.88 2.23
4594 12954 3.258372 TGAGAGCGAAGGTGTTTCATAGT 59.742 43.478 0.00 0.00 39.88 2.12
4595 12955 4.246458 GAGAGCGAAGGTGTTTCATAGTT 58.754 43.478 0.00 0.00 39.88 2.24
4596 12956 4.642429 AGAGCGAAGGTGTTTCATAGTTT 58.358 39.130 0.00 0.00 39.88 2.66
4597 12957 4.691216 AGAGCGAAGGTGTTTCATAGTTTC 59.309 41.667 0.00 0.00 39.88 2.78
4598 12958 4.385825 AGCGAAGGTGTTTCATAGTTTCA 58.614 39.130 0.00 0.00 36.17 2.69
4599 12959 5.003804 AGCGAAGGTGTTTCATAGTTTCAT 58.996 37.500 0.00 0.00 36.17 2.57
4672 13032 6.295011 CCACACCATAGAATTAAGGTTTGCAA 60.295 38.462 0.00 0.00 30.59 4.08
4739 13102 0.391263 AGTAGTAGGCAAAGTGCGGC 60.391 55.000 0.00 0.00 46.21 6.53
4831 13194 9.748708 TTGAAAGATCAAGTGAAAAATGGTAAG 57.251 29.630 0.00 0.00 40.59 2.34
4918 13307 8.408601 ACATCTTGTGTTCTAATAAATGGATGC 58.591 33.333 0.00 0.00 38.01 3.91
4933 13322 0.810648 GATGCGCCAGTTTTCCATCA 59.189 50.000 4.18 0.00 34.09 3.07
5169 13721 7.891183 TCAGATAACTACAAAGAGCTGAAAC 57.109 36.000 0.00 0.00 0.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 173 3.265791 GAGAGTACCTCACAATGGCTTG 58.734 50.000 6.51 0.00 41.58 4.01
159 215 0.744281 GAAGCCGAGGAAGAGAGAGG 59.256 60.000 0.00 0.00 0.00 3.69
226 282 5.741040 CAGAAGAAAAAGTGAAGAACAGCAC 59.259 40.000 0.00 0.00 35.30 4.40
242 298 4.461198 GAAACCCTCAACTCCAGAAGAAA 58.539 43.478 0.00 0.00 0.00 2.52
294 350 3.652057 TCCATGAAGAACCCTGAATCC 57.348 47.619 0.00 0.00 0.00 3.01
360 416 5.294552 ACTCCAGAAGAAAAAGTGAAGAACG 59.705 40.000 0.00 0.00 0.00 3.95
412 468 9.762933 CTGAATCCCTGTTTCTTGAAAATAAAA 57.237 29.630 0.00 0.00 0.00 1.52
413 469 8.367156 CCTGAATCCCTGTTTCTTGAAAATAAA 58.633 33.333 0.00 0.00 0.00 1.40
414 470 7.039082 CCCTGAATCCCTGTTTCTTGAAAATAA 60.039 37.037 0.00 0.00 0.00 1.40
415 471 6.437162 CCCTGAATCCCTGTTTCTTGAAAATA 59.563 38.462 0.00 0.00 0.00 1.40
416 472 5.246883 CCCTGAATCCCTGTTTCTTGAAAAT 59.753 40.000 0.00 0.00 0.00 1.82
417 473 4.588528 CCCTGAATCCCTGTTTCTTGAAAA 59.411 41.667 0.00 0.00 0.00 2.29
418 474 4.151883 CCCTGAATCCCTGTTTCTTGAAA 58.848 43.478 0.00 0.00 0.00 2.69
419 475 3.140144 ACCCTGAATCCCTGTTTCTTGAA 59.860 43.478 0.00 0.00 0.00 2.69
420 476 2.716424 ACCCTGAATCCCTGTTTCTTGA 59.284 45.455 0.00 0.00 0.00 3.02
421 477 3.160679 ACCCTGAATCCCTGTTTCTTG 57.839 47.619 0.00 0.00 0.00 3.02
422 478 3.399305 AGAACCCTGAATCCCTGTTTCTT 59.601 43.478 0.00 0.00 0.00 2.52
423 479 2.989571 AGAACCCTGAATCCCTGTTTCT 59.010 45.455 0.00 0.00 0.00 2.52
424 480 3.441500 AGAACCCTGAATCCCTGTTTC 57.558 47.619 0.00 0.00 0.00 2.78
425 481 3.399305 AGAAGAACCCTGAATCCCTGTTT 59.601 43.478 0.00 0.00 0.00 2.83
426 482 2.989571 AGAAGAACCCTGAATCCCTGTT 59.010 45.455 0.00 0.00 0.00 3.16
427 483 2.307098 CAGAAGAACCCTGAATCCCTGT 59.693 50.000 0.00 0.00 33.65 4.00
428 484 2.356535 CCAGAAGAACCCTGAATCCCTG 60.357 54.545 0.00 0.00 33.65 4.45
429 485 1.918957 CCAGAAGAACCCTGAATCCCT 59.081 52.381 0.00 0.00 33.65 4.20
430 486 1.916181 TCCAGAAGAACCCTGAATCCC 59.084 52.381 0.00 0.00 33.65 3.85
431 487 2.573915 ACTCCAGAAGAACCCTGAATCC 59.426 50.000 0.00 0.00 33.65 3.01
432 488 3.990959 ACTCCAGAAGAACCCTGAATC 57.009 47.619 0.00 0.00 33.65 2.52
433 489 3.652869 TCAACTCCAGAAGAACCCTGAAT 59.347 43.478 0.00 0.00 33.65 2.57
434 490 3.045634 TCAACTCCAGAAGAACCCTGAA 58.954 45.455 0.00 0.00 33.65 3.02
435 491 2.634940 CTCAACTCCAGAAGAACCCTGA 59.365 50.000 0.00 0.00 33.65 3.86
436 492 2.289945 CCTCAACTCCAGAAGAACCCTG 60.290 54.545 0.00 0.00 0.00 4.45
437 493 1.981495 CCTCAACTCCAGAAGAACCCT 59.019 52.381 0.00 0.00 0.00 4.34
438 494 1.003696 CCCTCAACTCCAGAAGAACCC 59.996 57.143 0.00 0.00 0.00 4.11
439 495 1.700186 ACCCTCAACTCCAGAAGAACC 59.300 52.381 0.00 0.00 0.00 3.62
440 496 3.493767 AACCCTCAACTCCAGAAGAAC 57.506 47.619 0.00 0.00 0.00 3.01
441 497 3.181443 GGAAACCCTCAACTCCAGAAGAA 60.181 47.826 0.00 0.00 0.00 2.52
442 498 2.372172 GGAAACCCTCAACTCCAGAAGA 59.628 50.000 0.00 0.00 0.00 2.87
443 499 2.106511 TGGAAACCCTCAACTCCAGAAG 59.893 50.000 0.00 0.00 32.97 2.85
444 500 2.131854 TGGAAACCCTCAACTCCAGAA 58.868 47.619 0.00 0.00 32.97 3.02
445 501 1.814429 TGGAAACCCTCAACTCCAGA 58.186 50.000 0.00 0.00 32.97 3.86
446 502 2.191128 CTGGAAACCCTCAACTCCAG 57.809 55.000 2.74 2.74 46.66 3.86
447 503 1.518367 ACTGGAAACCCTCAACTCCA 58.482 50.000 0.00 0.00 36.53 3.86
448 504 2.658807 AACTGGAAACCCTCAACTCC 57.341 50.000 0.00 0.00 0.00 3.85
449 505 4.645136 AGAAAAACTGGAAACCCTCAACTC 59.355 41.667 0.00 0.00 0.00 3.01
450 506 4.610333 AGAAAAACTGGAAACCCTCAACT 58.390 39.130 0.00 0.00 0.00 3.16
451 507 5.339008 AAGAAAAACTGGAAACCCTCAAC 57.661 39.130 0.00 0.00 0.00 3.18
452 508 6.367374 AAAAGAAAAACTGGAAACCCTCAA 57.633 33.333 0.00 0.00 0.00 3.02
453 509 6.212589 AGAAAAAGAAAAACTGGAAACCCTCA 59.787 34.615 0.00 0.00 0.00 3.86
454 510 6.640518 AGAAAAAGAAAAACTGGAAACCCTC 58.359 36.000 0.00 0.00 0.00 4.30
455 511 6.620877 AGAAAAAGAAAAACTGGAAACCCT 57.379 33.333 0.00 0.00 0.00 4.34
456 512 7.681939 AAAGAAAAAGAAAAACTGGAAACCC 57.318 32.000 0.00 0.00 0.00 4.11
457 513 8.999431 AGAAAAGAAAAAGAAAAACTGGAAACC 58.001 29.630 0.00 0.00 0.00 3.27
459 515 8.921670 CGAGAAAAGAAAAAGAAAAACTGGAAA 58.078 29.630 0.00 0.00 0.00 3.13
460 516 8.301002 TCGAGAAAAGAAAAAGAAAAACTGGAA 58.699 29.630 0.00 0.00 0.00 3.53
461 517 7.822658 TCGAGAAAAGAAAAAGAAAAACTGGA 58.177 30.769 0.00 0.00 0.00 3.86
462 518 8.460831 TTCGAGAAAAGAAAAAGAAAAACTGG 57.539 30.769 0.00 0.00 0.00 4.00
463 519 9.727403 GTTTCGAGAAAAGAAAAAGAAAAACTG 57.273 29.630 0.00 0.00 39.03 3.16
464 520 9.471084 TGTTTCGAGAAAAGAAAAAGAAAAACT 57.529 25.926 0.00 0.00 39.03 2.66
465 521 9.727403 CTGTTTCGAGAAAAGAAAAAGAAAAAC 57.273 29.630 0.00 0.00 42.59 2.43
466 522 8.921670 CCTGTTTCGAGAAAAGAAAAAGAAAAA 58.078 29.630 9.67 0.00 42.59 1.94
467 523 8.301002 TCCTGTTTCGAGAAAAGAAAAAGAAAA 58.699 29.630 9.67 0.00 42.59 2.29
468 524 7.822658 TCCTGTTTCGAGAAAAGAAAAAGAAA 58.177 30.769 9.67 0.00 42.59 2.52
469 525 7.385778 TCCTGTTTCGAGAAAAGAAAAAGAA 57.614 32.000 9.67 0.00 42.59 2.52
470 526 6.995511 TCCTGTTTCGAGAAAAGAAAAAGA 57.004 33.333 9.67 0.00 42.59 2.52
471 527 7.915397 TGAATCCTGTTTCGAGAAAAGAAAAAG 59.085 33.333 0.00 2.74 40.72 2.27
472 528 7.767261 TGAATCCTGTTTCGAGAAAAGAAAAA 58.233 30.769 0.00 0.00 39.03 1.94
473 529 7.328277 TGAATCCTGTTTCGAGAAAAGAAAA 57.672 32.000 0.00 0.00 39.03 2.29
474 530 6.513393 GCTGAATCCTGTTTCGAGAAAAGAAA 60.513 38.462 0.00 0.00 35.49 2.52
475 531 5.049405 GCTGAATCCTGTTTCGAGAAAAGAA 60.049 40.000 0.00 0.00 31.33 2.52
476 532 4.452455 GCTGAATCCTGTTTCGAGAAAAGA 59.548 41.667 0.00 0.00 31.33 2.52
477 533 4.667668 CGCTGAATCCTGTTTCGAGAAAAG 60.668 45.833 0.00 1.48 31.33 2.27
478 534 3.186409 CGCTGAATCCTGTTTCGAGAAAA 59.814 43.478 0.00 0.00 31.33 2.29
479 535 2.736721 CGCTGAATCCTGTTTCGAGAAA 59.263 45.455 0.00 0.00 0.00 2.52
480 536 2.288825 ACGCTGAATCCTGTTTCGAGAA 60.289 45.455 0.00 0.00 0.00 2.87
481 537 1.272490 ACGCTGAATCCTGTTTCGAGA 59.728 47.619 0.00 0.00 0.00 4.04
482 538 1.714794 ACGCTGAATCCTGTTTCGAG 58.285 50.000 0.00 0.00 0.00 4.04
483 539 2.066262 GAACGCTGAATCCTGTTTCGA 58.934 47.619 0.00 0.00 0.00 3.71
484 540 2.069273 AGAACGCTGAATCCTGTTTCG 58.931 47.619 0.00 0.00 0.00 3.46
485 541 3.498397 TGAAGAACGCTGAATCCTGTTTC 59.502 43.478 0.00 0.00 0.00 2.78
486 542 3.476552 TGAAGAACGCTGAATCCTGTTT 58.523 40.909 0.00 0.00 0.00 2.83
487 543 3.126001 TGAAGAACGCTGAATCCTGTT 57.874 42.857 0.00 0.00 0.00 3.16
488 544 2.839486 TGAAGAACGCTGAATCCTGT 57.161 45.000 0.00 0.00 0.00 4.00
489 545 2.353889 CCATGAAGAACGCTGAATCCTG 59.646 50.000 0.00 0.00 0.00 3.86
490 546 2.237143 TCCATGAAGAACGCTGAATCCT 59.763 45.455 0.00 0.00 0.00 3.24
491 547 2.352960 GTCCATGAAGAACGCTGAATCC 59.647 50.000 0.00 0.00 0.00 3.01
492 548 2.029728 CGTCCATGAAGAACGCTGAATC 59.970 50.000 0.00 0.00 0.00 2.52
493 549 2.002586 CGTCCATGAAGAACGCTGAAT 58.997 47.619 0.00 0.00 0.00 2.57
494 550 1.270094 ACGTCCATGAAGAACGCTGAA 60.270 47.619 0.00 0.00 39.93 3.02
495 551 0.317160 ACGTCCATGAAGAACGCTGA 59.683 50.000 0.00 0.00 39.93 4.26
496 552 0.716108 GACGTCCATGAAGAACGCTG 59.284 55.000 3.51 0.00 39.93 5.18
497 553 0.732880 CGACGTCCATGAAGAACGCT 60.733 55.000 10.58 0.00 39.93 5.07
498 554 1.702299 CGACGTCCATGAAGAACGC 59.298 57.895 10.58 0.00 39.93 4.84
499 555 1.006825 TGCGACGTCCATGAAGAACG 61.007 55.000 10.58 1.21 41.93 3.95
500 556 1.144969 TTGCGACGTCCATGAAGAAC 58.855 50.000 10.58 0.00 0.00 3.01
512 746 1.618861 AAGAGACGAGATTTGCGACG 58.381 50.000 0.00 0.00 0.00 5.12
580 1259 2.846193 TCTGAAAAACCCTCAACTCCG 58.154 47.619 0.00 0.00 0.00 4.63
677 1362 1.673808 CTACGCGCTTTACCCCCTCT 61.674 60.000 5.73 0.00 0.00 3.69
683 1368 2.975410 AAAAACCTACGCGCTTTACC 57.025 45.000 5.73 0.00 0.00 2.85
915 1971 5.700402 ATCTCAGGTAAAGGTAGCACATT 57.300 39.130 0.00 0.00 0.00 2.71
1051 2114 9.802039 TTATTTGGTTTATTAAGGACACAGTCT 57.198 29.630 0.00 0.00 32.47 3.24
1121 2187 8.925161 TTAAAAGACAAAGTCCAAACATCAAG 57.075 30.769 0.00 0.00 32.18 3.02
1123 2189 9.145865 GTTTTAAAAGACAAAGTCCAAACATCA 57.854 29.630 0.00 0.00 32.18 3.07
1189 2258 6.916360 TTCATATTCCTGCCTTGACTTTTT 57.084 33.333 0.00 0.00 0.00 1.94
1392 2656 8.887036 TGAACGCATATAGTTATTCAAGTCAT 57.113 30.769 0.00 0.00 31.14 3.06
1444 2723 4.732285 ACAACAGCACATAAGTTCTTCG 57.268 40.909 0.00 0.00 0.00 3.79
1527 2955 6.479660 GGAAAGAGAGAACATGCTATGAGAAG 59.520 42.308 0.00 0.00 0.00 2.85
1897 4628 8.063630 CGATGATCGATTGAAACATCATTGTTA 58.936 33.333 22.18 0.00 43.09 2.41
1898 4629 6.908820 CGATGATCGATTGAAACATCATTGTT 59.091 34.615 22.18 0.00 44.63 2.83
1899 4630 6.258507 TCGATGATCGATTGAAACATCATTGT 59.741 34.615 14.25 0.00 44.82 2.71
1900 4631 6.652245 TCGATGATCGATTGAAACATCATTG 58.348 36.000 14.25 14.87 44.82 2.82
1901 4632 6.849588 TCGATGATCGATTGAAACATCATT 57.150 33.333 14.25 1.44 44.82 2.57
2067 4819 1.001633 ACGTGCAGGTACCTGGTAAAG 59.998 52.381 36.91 16.13 43.77 1.85
2085 4868 2.905075 TCCTTATGCATTGGACTCACG 58.095 47.619 3.54 0.00 0.00 4.35
2123 4906 7.527084 GTCTTAAGACGAAGAGCAACATATT 57.473 36.000 19.39 0.00 36.13 1.28
2405 5194 4.990543 TGTCTCAAGCGACTTGTTAATG 57.009 40.909 15.83 6.36 41.66 1.90
2406 5195 7.667043 TTAATGTCTCAAGCGACTTGTTAAT 57.333 32.000 15.83 6.69 41.66 1.40
2407 5196 7.667043 ATTAATGTCTCAAGCGACTTGTTAA 57.333 32.000 15.83 13.18 41.66 2.01
2408 5197 8.766000 TTATTAATGTCTCAAGCGACTTGTTA 57.234 30.769 15.83 7.21 41.66 2.41
2409 5198 7.667043 TTATTAATGTCTCAAGCGACTTGTT 57.333 32.000 15.83 7.93 41.66 2.83
2410 5199 7.387948 ACTTTATTAATGTCTCAAGCGACTTGT 59.612 33.333 15.83 2.83 41.66 3.16
2411 5200 7.689812 CACTTTATTAATGTCTCAAGCGACTTG 59.310 37.037 11.78 11.78 42.25 3.16
2412 5201 7.148407 CCACTTTATTAATGTCTCAAGCGACTT 60.148 37.037 0.00 0.00 35.00 3.01
2413 5202 6.313905 CCACTTTATTAATGTCTCAAGCGACT 59.686 38.462 0.00 0.00 35.00 4.18
2414 5203 6.478588 CCACTTTATTAATGTCTCAAGCGAC 58.521 40.000 0.00 0.00 34.52 5.19
2415 5204 5.064707 GCCACTTTATTAATGTCTCAAGCGA 59.935 40.000 0.00 0.00 0.00 4.93
2416 5205 5.065218 AGCCACTTTATTAATGTCTCAAGCG 59.935 40.000 0.00 0.00 0.00 4.68
2417 5206 6.261118 CAGCCACTTTATTAATGTCTCAAGC 58.739 40.000 0.00 0.00 0.00 4.01
2418 5207 6.127925 TGCAGCCACTTTATTAATGTCTCAAG 60.128 38.462 0.00 0.00 0.00 3.02
2419 5208 5.709631 TGCAGCCACTTTATTAATGTCTCAA 59.290 36.000 0.00 0.00 0.00 3.02
2420 5209 5.252547 TGCAGCCACTTTATTAATGTCTCA 58.747 37.500 0.00 0.00 0.00 3.27
2421 5210 5.818136 TGCAGCCACTTTATTAATGTCTC 57.182 39.130 0.00 0.00 0.00 3.36
2422 5211 5.450965 GCATGCAGCCACTTTATTAATGTCT 60.451 40.000 14.21 0.00 37.23 3.41
2423 5212 4.741676 GCATGCAGCCACTTTATTAATGTC 59.258 41.667 14.21 0.00 37.23 3.06
2424 5213 4.160065 TGCATGCAGCCACTTTATTAATGT 59.840 37.500 18.46 0.00 44.83 2.71
2425 5214 4.684877 TGCATGCAGCCACTTTATTAATG 58.315 39.130 18.46 0.00 44.83 1.90
2426 5215 5.540400 ATGCATGCAGCCACTTTATTAAT 57.460 34.783 26.69 0.11 44.83 1.40
2427 5216 5.110598 CAATGCATGCAGCCACTTTATTAA 58.889 37.500 26.69 0.00 44.83 1.40
2428 5217 4.684877 CAATGCATGCAGCCACTTTATTA 58.315 39.130 26.69 0.00 44.83 0.98
2429 5218 3.527533 CAATGCATGCAGCCACTTTATT 58.472 40.909 26.69 9.04 44.83 1.40
2430 5219 3.173668 CAATGCATGCAGCCACTTTAT 57.826 42.857 26.69 2.26 44.83 1.40
2431 5220 2.658373 CAATGCATGCAGCCACTTTA 57.342 45.000 26.69 0.00 44.83 1.85
2432 5221 3.525619 CAATGCATGCAGCCACTTT 57.474 47.368 26.69 11.37 44.83 2.66
2442 5231 4.750460 GCATCTGGGCAATGCATG 57.250 55.556 7.79 3.08 46.93 4.06
2446 5235 1.735376 GCCTCTGCATCTGGGCAATG 61.735 60.000 12.40 0.00 44.40 2.82
2447 5236 1.455217 GCCTCTGCATCTGGGCAAT 60.455 57.895 12.40 0.00 44.40 3.56
2448 5237 2.044650 GCCTCTGCATCTGGGCAA 60.045 61.111 12.40 0.00 44.40 4.52
2449 5238 4.119363 GGCCTCTGCATCTGGGCA 62.119 66.667 17.30 0.00 45.68 5.36
2451 5240 4.559063 CCGGCCTCTGCATCTGGG 62.559 72.222 0.00 0.00 40.13 4.45
2452 5241 4.559063 CCCGGCCTCTGCATCTGG 62.559 72.222 0.00 0.00 40.13 3.86
2453 5242 4.559063 CCCCGGCCTCTGCATCTG 62.559 72.222 0.00 0.00 40.13 2.90
2459 5248 3.787001 GAAGACCCCCGGCCTCTG 61.787 72.222 0.00 0.00 0.00 3.35
2465 5254 1.498176 AAAAGGAGGAAGACCCCCGG 61.498 60.000 0.00 0.00 36.73 5.73
2466 5255 0.035343 GAAAAGGAGGAAGACCCCCG 60.035 60.000 0.00 0.00 36.73 5.73
2467 5256 1.373536 AGAAAAGGAGGAAGACCCCC 58.626 55.000 0.00 0.00 36.73 5.40
2468 5257 4.652679 TTTAGAAAAGGAGGAAGACCCC 57.347 45.455 0.00 0.00 36.73 4.95
2469 5258 5.877491 TCTTTTAGAAAAGGAGGAAGACCC 58.123 41.667 13.40 0.00 44.22 4.46
2470 5259 7.818997 TTTCTTTTAGAAAAGGAGGAAGACC 57.181 36.000 13.40 0.00 40.89 3.85
2484 5273 9.977762 GAGACTTGTTAACGTTTTTCTTTTAGA 57.022 29.630 5.91 0.00 0.00 2.10
2485 5274 9.983804 AGAGACTTGTTAACGTTTTTCTTTTAG 57.016 29.630 5.91 0.00 0.00 1.85
2487 5276 9.687210 AAAGAGACTTGTTAACGTTTTTCTTTT 57.313 25.926 5.91 0.00 0.00 2.27
2488 5277 9.124807 CAAAGAGACTTGTTAACGTTTTTCTTT 57.875 29.630 5.91 7.08 0.00 2.52
2489 5278 8.294577 ACAAAGAGACTTGTTAACGTTTTTCTT 58.705 29.630 5.91 0.54 36.05 2.52
2490 5279 7.813645 ACAAAGAGACTTGTTAACGTTTTTCT 58.186 30.769 5.91 0.00 36.05 2.52
2491 5280 9.712359 ATACAAAGAGACTTGTTAACGTTTTTC 57.288 29.630 5.91 0.00 40.08 2.29
2495 5284 9.712359 GAAAATACAAAGAGACTTGTTAACGTT 57.288 29.630 5.88 5.88 40.08 3.99
2496 5285 9.106070 AGAAAATACAAAGAGACTTGTTAACGT 57.894 29.630 0.26 0.00 40.08 3.99
2509 5298 7.771183 ACTTGACAGCAAAGAAAATACAAAGA 58.229 30.769 0.00 0.00 32.73 2.52
2916 7217 1.995484 CACACCGAAGACACAGCTATG 59.005 52.381 0.00 0.00 0.00 2.23
2974 7275 1.211703 TCTTCTGAACCACAACAGCCA 59.788 47.619 0.00 0.00 34.57 4.75
3045 7346 4.908601 TCATGTTCCAAGTGTATGTCCT 57.091 40.909 0.00 0.00 0.00 3.85
3080 7381 3.146104 ACAAAGTGATCCAAGTCCAGG 57.854 47.619 0.00 0.00 0.00 4.45
3104 7405 4.627467 CCGTCAACTTCAAATGTAGGAGAG 59.373 45.833 0.00 0.00 0.00 3.20
3152 7453 7.390823 TCATTTGTGATGTAACTGCCTAACTA 58.609 34.615 0.00 0.00 0.00 2.24
3221 7552 5.924825 GGTATGGTAAGCTAACGGATACTTG 59.075 44.000 0.00 0.00 0.00 3.16
3223 7554 5.243283 CAGGTATGGTAAGCTAACGGATACT 59.757 44.000 0.00 0.00 0.00 2.12
3264 7615 7.531857 TGTCCATTGGCATAAAAGAGTAAAA 57.468 32.000 0.00 0.00 0.00 1.52
3268 7619 7.338800 CTAATGTCCATTGGCATAAAAGAGT 57.661 36.000 11.42 0.59 32.50 3.24
3423 9476 2.610232 GGTGCAGCGTGAATCCAAAAAT 60.610 45.455 0.00 0.00 0.00 1.82
3432 9485 2.100584 AGAATTTTTGGTGCAGCGTGAA 59.899 40.909 11.91 5.80 0.00 3.18
3436 9489 2.420628 TCAGAATTTTTGGTGCAGCG 57.579 45.000 11.91 0.00 0.00 5.18
3686 10078 1.833630 TGTAGCTGAGCTTGGCTGTAT 59.166 47.619 14.14 0.00 39.88 2.29
3751 10147 6.494146 ACTTCAAAAATAATTTGGTACCCGGA 59.506 34.615 10.07 0.00 0.00 5.14
3817 10215 0.878523 GCTGTACTTGTCACCACGCA 60.879 55.000 0.00 0.00 0.00 5.24
4035 10451 6.293081 CCTGCGATCACCATAAAAGTAAGATG 60.293 42.308 0.00 0.00 0.00 2.90
4067 10486 0.672401 CGCATCCACCCGTAAACACT 60.672 55.000 0.00 0.00 0.00 3.55
4385 10828 5.222631 TCCGATGACATAATCTGTTCGATG 58.777 41.667 0.00 0.00 39.41 3.84
4446 12788 3.304928 GGTCAGCTGAACCAAACATCAAG 60.305 47.826 21.71 0.00 0.00 3.02
4448 12807 2.229792 GGTCAGCTGAACCAAACATCA 58.770 47.619 21.71 0.00 0.00 3.07
4545 12905 7.910162 ACATAAATTATAGACGCAAAGTGCTTG 59.090 33.333 0.00 0.00 42.25 4.01
4570 12930 2.210116 TGAAACACCTTCGCTCTCAAC 58.790 47.619 0.00 0.00 36.78 3.18
4592 12952 1.534729 GACGGAGGGCAAATGAAACT 58.465 50.000 0.00 0.00 0.00 2.66
4593 12953 0.526211 GGACGGAGGGCAAATGAAAC 59.474 55.000 0.00 0.00 0.00 2.78
4594 12954 0.111446 TGGACGGAGGGCAAATGAAA 59.889 50.000 0.00 0.00 0.00 2.69
4595 12955 0.322456 CTGGACGGAGGGCAAATGAA 60.322 55.000 0.00 0.00 0.00 2.57
4596 12956 1.299648 CTGGACGGAGGGCAAATGA 59.700 57.895 0.00 0.00 0.00 2.57
4597 12957 1.002134 ACTGGACGGAGGGCAAATG 60.002 57.895 0.00 0.00 0.00 2.32
4598 12958 1.002134 CACTGGACGGAGGGCAAAT 60.002 57.895 0.00 0.00 0.00 2.32
4599 12959 2.429930 CACTGGACGGAGGGCAAA 59.570 61.111 0.00 0.00 0.00 3.68
4688 13051 7.843490 ATGCGTACACAAACTGTATCTAAAT 57.157 32.000 0.00 0.00 37.69 1.40
4721 13084 1.693083 CGCCGCACTTTGCCTACTAC 61.693 60.000 0.00 0.00 41.12 2.73
4750 13113 1.609208 AACAATGGGCACTGAGACAC 58.391 50.000 0.00 0.00 0.00 3.67
4754 13117 5.431765 ACTAATCTAACAATGGGCACTGAG 58.568 41.667 0.00 0.00 0.00 3.35
4756 13119 7.307396 CGATAACTAATCTAACAATGGGCACTG 60.307 40.741 0.00 0.00 31.87 3.66
4789 13152 8.889717 TGATCTTTCAAATAAGAATAACGACCC 58.110 33.333 0.00 0.00 37.66 4.46
4831 13194 5.504665 CCATTAACATTACTACAGCTGCTGC 60.505 44.000 28.39 7.62 34.37 5.25
4913 13302 0.101219 GATGGAAAACTGGCGCATCC 59.899 55.000 10.83 7.17 0.00 3.51
4918 13307 1.154225 GCGTGATGGAAAACTGGCG 60.154 57.895 0.00 0.00 0.00 5.69
4933 13322 9.113876 CTTTCGTAAAGATTCTTAAAAATGCGT 57.886 29.630 0.00 0.00 41.02 5.24
5135 13687 8.644216 TCTTTGTAGTTATCTGAAACCTGTGTA 58.356 33.333 0.00 0.00 0.00 2.90
5169 13721 8.687242 TGTTCTTCTACTGATATGACTAACCTG 58.313 37.037 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.