Multiple sequence alignment - TraesCS3B01G116500

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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 TraesCS3B01G116500 chr3B 100.000 4721 0 0 1 4721 82855255 82850535 0.000000e+00 8719.0
1 TraesCS3B01G116500 chr3B 100.000 1653 0 0 1111 2763 83271314 83272966 0.000000e+00 3053.0
2 TraesCS3B01G116500 chr3B 90.657 867 48 20 2120 2971 83469759 83468911 0.000000e+00 1122.0
3 TraesCS3B01G116500 chr3B 87.815 714 56 14 877 1577 83470648 83469953 0.000000e+00 808.0
4 TraesCS3B01G116500 chr3B 90.940 596 40 5 3480 4062 83272974 83273568 0.000000e+00 789.0
5 TraesCS3B01G116500 chr3B 77.961 726 77 39 3373 4056 83515014 83515698 1.240000e-100 377.0
6 TraesCS3B01G116500 chr3B 79.305 604 52 31 2668 3243 83512848 83513406 5.810000e-94 355.0
7 TraesCS3B01G116500 chr3B 100.000 178 0 0 1 178 83270599 83270776 3.520000e-86 329.0
8 TraesCS3B01G116500 chr3B 95.477 199 9 0 1716 1914 83469958 83469760 7.620000e-83 318.0
9 TraesCS3B01G116500 chr3B 76.112 607 116 21 1918 2511 115236278 115236868 1.660000e-74 291.0
10 TraesCS3B01G116500 chr3B 93.023 43 3 0 867 909 115275856 115275898 3.940000e-06 63.9
11 TraesCS3B01G116500 chr3D 89.684 2404 165 33 1683 4062 51788906 51786562 0.000000e+00 2988.0
12 TraesCS3B01G116500 chr3D 86.243 1054 105 16 615 1659 51790367 51789345 0.000000e+00 1107.0
13 TraesCS3B01G116500 chr3D 85.452 708 86 11 863 1567 52840254 52840947 0.000000e+00 721.0
14 TraesCS3B01G116500 chr3D 83.459 532 61 6 1735 2263 52840959 52841466 1.990000e-128 470.0
15 TraesCS3B01G116500 chr3D 79.733 750 70 39 2635 3363 52851946 52852634 7.150000e-128 468.0
16 TraesCS3B01G116500 chr3D 77.486 724 86 37 3380 4056 53101598 53102291 3.470000e-96 363.0
17 TraesCS3B01G116500 chr3D 73.684 1045 185 61 1918 2937 69456010 69456989 1.640000e-84 324.0
18 TraesCS3B01G116500 chr3D 86.567 268 27 7 2276 2543 52851221 52851479 2.150000e-73 287.0
19 TraesCS3B01G116500 chr3D 73.412 677 104 44 746 1386 71368699 71368063 2.900000e-42 183.0
20 TraesCS3B01G116500 chr3D 74.263 373 68 13 992 1362 69460132 69460478 1.070000e-26 132.0
21 TraesCS3B01G116500 chr5B 91.994 687 25 12 4065 4721 6826652 6827338 0.000000e+00 937.0
22 TraesCS3B01G116500 chr5B 85.517 145 18 3 3 145 38016198 38016341 1.060000e-31 148.0
23 TraesCS3B01G116500 chr3A 89.867 750 45 15 2292 3030 64317709 64316980 0.000000e+00 935.0
24 TraesCS3B01G116500 chr3A 89.367 743 48 14 864 1576 64319227 64318486 0.000000e+00 905.0
25 TraesCS3B01G116500 chr3A 90.000 680 42 7 4068 4721 690963146 690962467 0.000000e+00 856.0
26 TraesCS3B01G116500 chr3A 91.795 585 27 7 1735 2298 64318477 64317893 0.000000e+00 795.0
27 TraesCS3B01G116500 chr3A 80.837 1075 125 37 1717 2778 64342970 64343976 0.000000e+00 769.0
28 TraesCS3B01G116500 chr3A 86.741 626 37 20 3022 3624 64309468 64308866 0.000000e+00 654.0
29 TraesCS3B01G116500 chr3A 84.980 506 64 3 981 1483 64340839 64341335 1.960000e-138 503.0
30 TraesCS3B01G116500 chr3A 76.565 751 118 33 1931 2661 83394568 83395280 4.490000e-95 359.0
31 TraesCS3B01G116500 chr3A 75.602 623 123 17 1931 2543 80546067 80546670 1.000000e-71 281.0
32 TraesCS3B01G116500 chr3A 85.496 262 25 12 3112 3363 64344850 64345108 1.300000e-65 261.0
33 TraesCS3B01G116500 chr3A 72.538 528 93 25 877 1386 74218763 74219256 1.780000e-24 124.0
34 TraesCS3B01G116500 chr3A 93.651 63 4 0 867 929 80514510 80514572 1.400000e-15 95.3
35 TraesCS3B01G116500 chr4D 95.379 541 23 1 4065 4603 386481326 386480786 0.000000e+00 859.0
36 TraesCS3B01G116500 chr4D 97.778 135 2 1 4588 4721 386481339 386481473 1.020000e-56 231.0
37 TraesCS3B01G116500 chr2B 93.284 536 36 0 4065 4600 609148863 609148328 0.000000e+00 791.0
38 TraesCS3B01G116500 chr2B 96.269 134 5 0 4588 4721 609148312 609148179 2.210000e-53 220.0
39 TraesCS3B01G116500 chr2B 80.822 146 20 7 1 142 11442231 11442090 1.800000e-19 108.0
40 TraesCS3B01G116500 chr1B 92.072 555 26 6 4061 4597 635437258 635437812 0.000000e+00 765.0
41 TraesCS3B01G116500 chr1B 98.319 119 2 0 4603 4721 635437856 635437974 4.790000e-50 209.0
42 TraesCS3B01G116500 chr2A 88.199 322 12 11 4426 4721 773199719 773200040 1.250000e-95 361.0
43 TraesCS3B01G116500 chr2A 94.048 168 10 0 4063 4230 773199546 773199713 6.060000e-64 255.0
44 TraesCS3B01G116500 chr1A 92.500 200 14 1 4400 4598 574236498 574236299 7.730000e-73 285.0
45 TraesCS3B01G116500 chr1A 83.333 138 21 2 11 146 23824673 23824810 4.960000e-25 126.0
46 TraesCS3B01G116500 chr2D 84.407 295 23 9 4145 4426 633876436 633876720 7.790000e-68 268.0
47 TraesCS3B01G116500 chr2D 79.200 250 47 5 4065 4309 11236559 11236808 8.120000e-38 169.0
48 TraesCS3B01G116500 chr2D 85.124 121 13 5 4 122 9670741 9670858 8.300000e-23 119.0
49 TraesCS3B01G116500 chr7A 87.218 133 14 3 6 136 459636243 459636112 1.060000e-31 148.0
50 TraesCS3B01G116500 chr7A 89.899 99 9 1 49 146 663450986 663451084 4.960000e-25 126.0
51 TraesCS3B01G116500 chr7D 86.777 121 11 4 3 122 401847283 401847167 3.830000e-26 130.0
52 TraesCS3B01G116500 chr5D 83.099 142 19 5 4060 4198 556376648 556376509 1.780000e-24 124.0
53 TraesCS3B01G116500 chr6A 80.000 150 23 5 6 154 481029517 481029374 2.320000e-18 104.0


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 TraesCS3B01G116500 chr3B 82850535 82855255 4720 True 8719.000000 8719 100.000000 1 4721 1 chr3B.!!$R1 4720
1 TraesCS3B01G116500 chr3B 83270599 83273568 2969 False 1390.333333 3053 96.980000 1 4062 3 chr3B.!!$F3 4061
2 TraesCS3B01G116500 chr3B 83468911 83470648 1737 True 749.333333 1122 91.316333 877 2971 3 chr3B.!!$R2 2094
3 TraesCS3B01G116500 chr3B 83512848 83515698 2850 False 366.000000 377 78.633000 2668 4056 2 chr3B.!!$F4 1388
4 TraesCS3B01G116500 chr3B 115236278 115236868 590 False 291.000000 291 76.112000 1918 2511 1 chr3B.!!$F1 593
5 TraesCS3B01G116500 chr3D 51786562 51790367 3805 True 2047.500000 2988 87.963500 615 4062 2 chr3D.!!$R2 3447
6 TraesCS3B01G116500 chr3D 52840254 52841466 1212 False 595.500000 721 84.455500 863 2263 2 chr3D.!!$F2 1400
7 TraesCS3B01G116500 chr3D 52851221 52852634 1413 False 377.500000 468 83.150000 2276 3363 2 chr3D.!!$F3 1087
8 TraesCS3B01G116500 chr3D 53101598 53102291 693 False 363.000000 363 77.486000 3380 4056 1 chr3D.!!$F1 676
9 TraesCS3B01G116500 chr3D 69456010 69460478 4468 False 228.000000 324 73.973500 992 2937 2 chr3D.!!$F4 1945
10 TraesCS3B01G116500 chr5B 6826652 6827338 686 False 937.000000 937 91.994000 4065 4721 1 chr5B.!!$F1 656
11 TraesCS3B01G116500 chr3A 64316980 64319227 2247 True 878.333333 935 90.343000 864 3030 3 chr3A.!!$R3 2166
12 TraesCS3B01G116500 chr3A 690962467 690963146 679 True 856.000000 856 90.000000 4068 4721 1 chr3A.!!$R2 653
13 TraesCS3B01G116500 chr3A 64308866 64309468 602 True 654.000000 654 86.741000 3022 3624 1 chr3A.!!$R1 602
14 TraesCS3B01G116500 chr3A 64340839 64345108 4269 False 511.000000 769 83.771000 981 3363 3 chr3A.!!$F5 2382
15 TraesCS3B01G116500 chr3A 83394568 83395280 712 False 359.000000 359 76.565000 1931 2661 1 chr3A.!!$F4 730
16 TraesCS3B01G116500 chr3A 80546067 80546670 603 False 281.000000 281 75.602000 1931 2543 1 chr3A.!!$F3 612
17 TraesCS3B01G116500 chr4D 386480786 386481326 540 True 859.000000 859 95.379000 4065 4603 1 chr4D.!!$R1 538
18 TraesCS3B01G116500 chr2B 609148179 609148863 684 True 505.500000 791 94.776500 4065 4721 2 chr2B.!!$R2 656
19 TraesCS3B01G116500 chr1B 635437258 635437974 716 False 487.000000 765 95.195500 4061 4721 2 chr1B.!!$F1 660

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
508 509 0.031721 GCCGTATAGGAGTCCCAACG 59.968 60.000 17.34 17.34 45.00 4.10 F
509 510 0.031721 CCGTATAGGAGTCCCAACGC 59.968 60.000 18.38 1.77 45.00 4.84 F
518 519 0.036306 AGTCCCAACGCGAGGAATTT 59.964 50.000 15.93 2.64 32.81 1.82 F
573 574 0.179034 GTTGGAGATGCCCTAGCCAG 60.179 60.000 0.00 0.00 38.69 4.85 F
762 764 0.179150 CGGAGAGAGAAACAGAGGCG 60.179 60.000 0.00 0.00 0.00 5.52 F
823 828 0.491823 TTCTTCCTCCTCCCACTCCA 59.508 55.000 0.00 0.00 0.00 3.86 F
837 842 1.003718 CTCCAACTCCGACCCCAAC 60.004 63.158 0.00 0.00 0.00 3.77 F
1008 1021 1.683385 TCCAGATCTACCATGTCGCTG 59.317 52.381 0.00 0.00 0.00 5.18 F
3084 6174 2.289756 GGTGGTTTGTTTGGTGGTTTGT 60.290 45.455 0.00 0.00 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2780 5503 6.798427 AGCTAGTTCTAGAATGAACATCCA 57.202 37.500 8.75 0.00 46.19 3.41 R
2781 5504 8.172352 TCTAGCTAGTTCTAGAATGAACATCC 57.828 38.462 20.10 0.00 46.19 3.51 R
2942 5694 2.276430 GCGCACGCCGTTTCATAC 60.276 61.111 0.30 0.00 39.71 2.39 R
2963 5715 1.528292 GCGAGCGGATCCCATAGACT 61.528 60.000 6.06 0.00 0.00 3.24 R
3236 6667 5.087323 CACCTGGAGGGAGCTCTAAATATA 58.913 45.833 14.64 0.00 40.27 0.86 R
3503 9127 7.272948 GTGGTAACGTAATCGGATCTTCATATC 59.727 40.741 0.00 0.00 41.85 1.63 R
3527 9578 1.266446 TGGTGCGTGAATGACATTGTG 59.734 47.619 5.14 0.00 0.00 3.33 R
3695 10735 2.812358 TCGTGACCCCATATCAATCG 57.188 50.000 0.00 0.00 0.00 3.34 R
4578 11757 1.352352 AGAAGCTGGCTTTAAGCAGGA 59.648 47.619 19.10 1.04 44.75 3.86 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
200 201 9.672673 TTTTGACTTTTTATGAACATTTTGGGA 57.327 25.926 0.00 0.00 0.00 4.37
201 202 9.672673 TTTGACTTTTTATGAACATTTTGGGAA 57.327 25.926 0.00 0.00 0.00 3.97
202 203 9.672673 TTGACTTTTTATGAACATTTTGGGAAA 57.327 25.926 0.00 0.00 0.00 3.13
203 204 9.103861 TGACTTTTTATGAACATTTTGGGAAAC 57.896 29.630 0.00 0.00 0.00 2.78
204 205 9.325198 GACTTTTTATGAACATTTTGGGAAACT 57.675 29.630 0.00 0.00 0.00 2.66
212 213 9.844257 ATGAACATTTTGGGAAACTATGAAAAA 57.156 25.926 0.00 0.00 0.00 1.94
267 268 9.781633 ATCTTGATGAACAAATTTTGAATTCCA 57.218 25.926 15.81 5.44 38.08 3.53
268 269 9.781633 TCTTGATGAACAAATTTTGAATTCCAT 57.218 25.926 15.81 10.00 38.08 3.41
269 270 9.820229 CTTGATGAACAAATTTTGAATTCCATG 57.180 29.630 15.81 6.61 38.08 3.66
270 271 9.557061 TTGATGAACAAATTTTGAATTCCATGA 57.443 25.926 15.81 3.53 35.39 3.07
271 272 8.991026 TGATGAACAAATTTTGAATTCCATGAC 58.009 29.630 15.81 2.66 0.00 3.06
272 273 7.727331 TGAACAAATTTTGAATTCCATGACC 57.273 32.000 15.81 0.00 0.00 4.02
273 274 6.709846 TGAACAAATTTTGAATTCCATGACCC 59.290 34.615 15.81 0.00 0.00 4.46
274 275 6.438186 ACAAATTTTGAATTCCATGACCCT 57.562 33.333 15.81 0.00 0.00 4.34
275 276 6.840527 ACAAATTTTGAATTCCATGACCCTT 58.159 32.000 15.81 0.00 0.00 3.95
276 277 7.289310 ACAAATTTTGAATTCCATGACCCTTT 58.711 30.769 15.81 0.00 0.00 3.11
277 278 7.779326 ACAAATTTTGAATTCCATGACCCTTTT 59.221 29.630 15.81 0.00 0.00 2.27
278 279 8.631797 CAAATTTTGAATTCCATGACCCTTTTT 58.368 29.630 2.88 0.00 0.00 1.94
300 301 8.961294 TTTTTGTGTCCATTGAACAATTTTTG 57.039 26.923 0.00 0.00 34.04 2.44
301 302 7.912056 TTTGTGTCCATTGAACAATTTTTGA 57.088 28.000 0.00 0.00 34.04 2.69
302 303 7.912056 TTGTGTCCATTGAACAATTTTTGAA 57.088 28.000 0.00 0.00 0.00 2.69
303 304 8.503458 TTGTGTCCATTGAACAATTTTTGAAT 57.497 26.923 0.00 0.00 0.00 2.57
304 305 8.503458 TGTGTCCATTGAACAATTTTTGAATT 57.497 26.923 0.00 0.00 0.00 2.17
305 306 8.954350 TGTGTCCATTGAACAATTTTTGAATTT 58.046 25.926 0.00 0.00 0.00 1.82
306 307 9.224058 GTGTCCATTGAACAATTTTTGAATTTG 57.776 29.630 0.00 0.00 0.00 2.32
307 308 9.170734 TGTCCATTGAACAATTTTTGAATTTGA 57.829 25.926 0.00 0.00 0.00 2.69
339 340 9.757227 AAAAATGTTCGTGGATATGAAAAGAAA 57.243 25.926 0.00 0.00 33.82 2.52
340 341 9.757227 AAAATGTTCGTGGATATGAAAAGAAAA 57.243 25.926 0.00 0.00 33.82 2.29
341 342 9.927668 AAATGTTCGTGGATATGAAAAGAAAAT 57.072 25.926 0.00 0.00 33.82 1.82
342 343 9.927668 AATGTTCGTGGATATGAAAAGAAAATT 57.072 25.926 0.00 0.00 33.82 1.82
343 344 8.964420 TGTTCGTGGATATGAAAAGAAAATTC 57.036 30.769 0.00 0.00 33.82 2.17
344 345 7.748683 TGTTCGTGGATATGAAAAGAAAATTCG 59.251 33.333 0.00 0.00 33.82 3.34
345 346 6.255215 TCGTGGATATGAAAAGAAAATTCGC 58.745 36.000 0.00 0.00 0.00 4.70
346 347 6.027131 CGTGGATATGAAAAGAAAATTCGCA 58.973 36.000 0.00 0.00 0.00 5.10
347 348 6.526325 CGTGGATATGAAAAGAAAATTCGCAA 59.474 34.615 0.00 0.00 0.00 4.85
348 349 7.061673 CGTGGATATGAAAAGAAAATTCGCAAA 59.938 33.333 0.00 0.00 0.00 3.68
349 350 8.707839 GTGGATATGAAAAGAAAATTCGCAAAA 58.292 29.630 0.00 0.00 0.00 2.44
350 351 9.265901 TGGATATGAAAAGAAAATTCGCAAAAA 57.734 25.926 0.00 0.00 0.00 1.94
425 426 8.940768 TGAAAGAAAAAGAAACAGGTAAATGG 57.059 30.769 0.00 0.00 0.00 3.16
426 427 7.984617 TGAAAGAAAAAGAAACAGGTAAATGGG 59.015 33.333 0.00 0.00 0.00 4.00
427 428 5.853936 AGAAAAAGAAACAGGTAAATGGGC 58.146 37.500 0.00 0.00 0.00 5.36
428 429 4.617253 AAAAGAAACAGGTAAATGGGCC 57.383 40.909 0.00 0.00 0.00 5.80
429 430 1.834188 AGAAACAGGTAAATGGGCCG 58.166 50.000 0.00 0.00 0.00 6.13
430 431 0.815095 GAAACAGGTAAATGGGCCGG 59.185 55.000 0.00 0.00 0.00 6.13
431 432 1.254975 AAACAGGTAAATGGGCCGGC 61.255 55.000 21.18 21.18 0.00 6.13
432 433 2.833121 CAGGTAAATGGGCCGGCC 60.833 66.667 38.57 38.57 0.00 6.13
444 445 4.540735 CCGGCCCATACGACACCC 62.541 72.222 0.00 0.00 0.00 4.61
445 446 4.540735 CGGCCCATACGACACCCC 62.541 72.222 0.00 0.00 0.00 4.95
446 447 4.185286 GGCCCATACGACACCCCC 62.185 72.222 0.00 0.00 0.00 5.40
447 448 4.540735 GCCCATACGACACCCCCG 62.541 72.222 0.00 0.00 0.00 5.73
448 449 4.540735 CCCATACGACACCCCCGC 62.541 72.222 0.00 0.00 0.00 6.13
449 450 3.467226 CCATACGACACCCCCGCT 61.467 66.667 0.00 0.00 0.00 5.52
450 451 2.202878 CATACGACACCCCCGCTG 60.203 66.667 0.00 0.00 0.00 5.18
451 452 4.157120 ATACGACACCCCCGCTGC 62.157 66.667 0.00 0.00 0.00 5.25
481 482 4.217159 GGGGGTACGCGCTACAGG 62.217 72.222 18.21 0.00 44.67 4.00
482 483 4.217159 GGGGTACGCGCTACAGGG 62.217 72.222 5.73 0.00 0.00 4.45
483 484 3.142838 GGGTACGCGCTACAGGGA 61.143 66.667 5.73 0.00 0.00 4.20
484 485 2.713967 GGGTACGCGCTACAGGGAA 61.714 63.158 5.73 0.00 0.00 3.97
485 486 1.216178 GGTACGCGCTACAGGGAAA 59.784 57.895 5.73 0.00 0.00 3.13
486 487 0.179092 GGTACGCGCTACAGGGAAAT 60.179 55.000 5.73 0.00 0.00 2.17
487 488 0.928229 GTACGCGCTACAGGGAAATG 59.072 55.000 5.73 0.00 0.00 2.32
488 489 0.179094 TACGCGCTACAGGGAAATGG 60.179 55.000 5.73 0.00 0.00 3.16
489 490 2.180204 CGCGCTACAGGGAAATGGG 61.180 63.158 5.56 0.00 0.00 4.00
490 491 2.481471 GCGCTACAGGGAAATGGGC 61.481 63.158 0.00 0.00 0.00 5.36
491 492 1.823899 CGCTACAGGGAAATGGGCC 60.824 63.158 0.00 0.00 0.00 5.80
492 493 1.823899 GCTACAGGGAAATGGGCCG 60.824 63.158 0.00 0.00 0.00 6.13
493 494 1.607612 CTACAGGGAAATGGGCCGT 59.392 57.895 0.00 0.00 0.00 5.68
494 495 0.834612 CTACAGGGAAATGGGCCGTA 59.165 55.000 0.00 0.00 0.00 4.02
495 496 1.420138 CTACAGGGAAATGGGCCGTAT 59.580 52.381 0.00 0.00 0.00 3.06
496 497 1.513858 ACAGGGAAATGGGCCGTATA 58.486 50.000 0.00 0.00 0.00 1.47
497 498 1.420138 ACAGGGAAATGGGCCGTATAG 59.580 52.381 0.00 0.00 0.00 1.31
498 499 1.064825 AGGGAAATGGGCCGTATAGG 58.935 55.000 0.00 0.00 44.97 2.57
499 500 1.061546 GGGAAATGGGCCGTATAGGA 58.938 55.000 0.00 0.00 45.00 2.94
500 501 1.003233 GGGAAATGGGCCGTATAGGAG 59.997 57.143 0.00 0.00 45.00 3.69
501 502 1.697982 GGAAATGGGCCGTATAGGAGT 59.302 52.381 0.00 0.00 45.00 3.85
502 503 2.289506 GGAAATGGGCCGTATAGGAGTC 60.290 54.545 0.00 0.00 45.00 3.36
503 504 1.349067 AATGGGCCGTATAGGAGTCC 58.651 55.000 0.00 0.00 45.00 3.85
504 505 0.544595 ATGGGCCGTATAGGAGTCCC 60.545 60.000 5.25 9.18 45.00 4.46
505 506 1.152398 GGGCCGTATAGGAGTCCCA 60.152 63.158 5.25 0.00 45.00 4.37
506 507 0.761702 GGGCCGTATAGGAGTCCCAA 60.762 60.000 5.25 0.00 45.00 4.12
507 508 0.391966 GGCCGTATAGGAGTCCCAAC 59.608 60.000 5.25 0.60 45.00 3.77
508 509 0.031721 GCCGTATAGGAGTCCCAACG 59.968 60.000 17.34 17.34 45.00 4.10
509 510 0.031721 CCGTATAGGAGTCCCAACGC 59.968 60.000 18.38 1.77 45.00 4.84
510 511 0.317603 CGTATAGGAGTCCCAACGCG 60.318 60.000 3.53 3.53 31.83 6.01
511 512 1.027357 GTATAGGAGTCCCAACGCGA 58.973 55.000 15.93 0.00 33.88 5.87
512 513 1.001597 GTATAGGAGTCCCAACGCGAG 60.002 57.143 15.93 4.40 33.88 5.03
513 514 1.392710 ATAGGAGTCCCAACGCGAGG 61.393 60.000 15.93 14.73 33.88 4.63
514 515 2.488771 TAGGAGTCCCAACGCGAGGA 62.489 60.000 15.93 13.54 33.88 3.71
515 516 2.654877 GAGTCCCAACGCGAGGAA 59.345 61.111 15.93 0.00 32.81 3.36
516 517 1.218316 GAGTCCCAACGCGAGGAAT 59.782 57.895 15.93 15.42 32.81 3.01
517 518 0.391263 GAGTCCCAACGCGAGGAATT 60.391 55.000 15.93 7.77 32.81 2.17
518 519 0.036306 AGTCCCAACGCGAGGAATTT 59.964 50.000 15.93 2.64 32.81 1.82
519 520 0.879090 GTCCCAACGCGAGGAATTTT 59.121 50.000 15.93 0.00 32.81 1.82
520 521 1.268625 GTCCCAACGCGAGGAATTTTT 59.731 47.619 15.93 0.00 32.81 1.94
536 537 3.780357 TTTTTAGGGGCCCAACGC 58.220 55.556 27.72 5.74 0.00 4.84
537 538 2.269529 TTTTTAGGGGCCCAACGCG 61.270 57.895 27.72 3.53 38.94 6.01
538 539 2.693896 TTTTTAGGGGCCCAACGCGA 62.694 55.000 27.72 1.40 38.94 5.87
539 540 3.615509 TTTAGGGGCCCAACGCGAG 62.616 63.158 27.72 4.40 38.94 5.03
543 544 4.796495 GGGCCCAACGCGAGGAAT 62.796 66.667 19.95 0.00 38.94 3.01
544 545 2.188469 GGCCCAACGCGAGGAATA 59.812 61.111 15.93 0.00 38.94 1.75
545 546 1.887707 GGCCCAACGCGAGGAATAG 60.888 63.158 15.93 2.51 38.94 1.73
546 547 1.887707 GCCCAACGCGAGGAATAGG 60.888 63.158 15.93 4.32 0.00 2.57
547 548 1.887707 CCCAACGCGAGGAATAGGC 60.888 63.158 15.93 0.00 0.00 3.93
557 558 3.937062 GAATAGGCGCGCCCGTTG 61.937 66.667 44.47 0.00 39.21 4.10
567 568 4.115199 GCCCGTTGGAGATGCCCT 62.115 66.667 0.00 0.00 34.97 5.19
568 569 2.742116 GCCCGTTGGAGATGCCCTA 61.742 63.158 0.00 0.00 34.97 3.53
569 570 1.447643 CCCGTTGGAGATGCCCTAG 59.552 63.158 0.00 0.00 34.97 3.02
570 571 1.227674 CCGTTGGAGATGCCCTAGC 60.228 63.158 0.00 0.00 40.48 3.42
571 572 1.227674 CGTTGGAGATGCCCTAGCC 60.228 63.158 0.00 0.00 38.69 3.93
572 573 1.915228 GTTGGAGATGCCCTAGCCA 59.085 57.895 0.00 0.00 38.69 4.75
573 574 0.179034 GTTGGAGATGCCCTAGCCAG 60.179 60.000 0.00 0.00 38.69 4.85
574 575 1.987807 TTGGAGATGCCCTAGCCAGC 61.988 60.000 0.00 0.00 38.69 4.85
575 576 2.429494 GAGATGCCCTAGCCAGCC 59.571 66.667 0.00 0.00 38.69 4.85
576 577 2.367377 AGATGCCCTAGCCAGCCA 60.367 61.111 0.00 0.00 38.69 4.75
577 578 1.773391 AGATGCCCTAGCCAGCCAT 60.773 57.895 0.00 0.00 38.69 4.40
578 579 1.602888 GATGCCCTAGCCAGCCATG 60.603 63.158 0.00 0.00 38.69 3.66
579 580 3.804638 ATGCCCTAGCCAGCCATGC 62.805 63.158 0.00 0.00 38.69 4.06
581 582 3.865383 CCCTAGCCAGCCATGCGA 61.865 66.667 0.00 0.00 0.00 5.10
582 583 2.429058 CCTAGCCAGCCATGCGAT 59.571 61.111 0.00 0.00 0.00 4.58
583 584 1.964891 CCTAGCCAGCCATGCGATG 60.965 63.158 0.00 0.00 0.00 3.84
584 585 2.592574 TAGCCAGCCATGCGATGC 60.593 61.111 0.00 0.00 0.00 3.91
592 593 3.945434 CATGCGATGCGGGCTGTC 61.945 66.667 0.00 0.00 0.00 3.51
593 594 4.471908 ATGCGATGCGGGCTGTCA 62.472 61.111 0.00 0.00 0.00 3.58
594 595 3.974835 ATGCGATGCGGGCTGTCAA 62.975 57.895 0.00 0.00 0.00 3.18
595 596 3.430862 GCGATGCGGGCTGTCAAA 61.431 61.111 0.00 0.00 0.00 2.69
596 597 2.480555 CGATGCGGGCTGTCAAAC 59.519 61.111 0.00 0.00 0.00 2.93
597 598 2.034879 CGATGCGGGCTGTCAAACT 61.035 57.895 0.00 0.00 0.00 2.66
598 599 1.796796 GATGCGGGCTGTCAAACTC 59.203 57.895 0.00 0.00 0.00 3.01
599 600 0.955428 GATGCGGGCTGTCAAACTCA 60.955 55.000 0.00 0.00 0.00 3.41
600 601 0.957395 ATGCGGGCTGTCAAACTCAG 60.957 55.000 0.00 0.00 36.18 3.35
601 602 1.598130 GCGGGCTGTCAAACTCAGT 60.598 57.895 0.00 0.00 35.60 3.41
602 603 0.320421 GCGGGCTGTCAAACTCAGTA 60.320 55.000 0.00 0.00 35.60 2.74
603 604 1.876416 GCGGGCTGTCAAACTCAGTAA 60.876 52.381 0.00 0.00 35.60 2.24
604 605 2.489971 CGGGCTGTCAAACTCAGTAAA 58.510 47.619 0.00 0.00 35.60 2.01
605 606 2.480419 CGGGCTGTCAAACTCAGTAAAG 59.520 50.000 0.00 0.00 35.60 1.85
606 607 3.740115 GGGCTGTCAAACTCAGTAAAGA 58.260 45.455 0.00 0.00 35.60 2.52
607 608 3.748568 GGGCTGTCAAACTCAGTAAAGAG 59.251 47.826 0.00 0.00 41.44 2.85
608 609 3.748568 GGCTGTCAAACTCAGTAAAGAGG 59.251 47.826 0.00 0.00 39.97 3.69
609 610 3.748568 GCTGTCAAACTCAGTAAAGAGGG 59.251 47.826 0.00 0.00 39.97 4.30
610 611 4.503296 GCTGTCAAACTCAGTAAAGAGGGA 60.503 45.833 0.00 0.00 39.97 4.20
611 612 5.215252 TGTCAAACTCAGTAAAGAGGGAG 57.785 43.478 0.00 0.00 39.97 4.30
612 613 4.040461 TGTCAAACTCAGTAAAGAGGGAGG 59.960 45.833 0.00 0.00 39.97 4.30
613 614 3.583086 TCAAACTCAGTAAAGAGGGAGGG 59.417 47.826 0.00 0.00 39.97 4.30
642 643 3.329542 GATGCGTGAGGAGGCCCAA 62.330 63.158 0.00 0.00 33.88 4.12
649 650 1.009997 TGAGGAGGCCCAAAATCCAT 58.990 50.000 10.41 0.00 35.45 3.41
654 655 1.278699 GAGGCCCAAAATCCATGCAAA 59.721 47.619 0.00 0.00 0.00 3.68
675 677 1.612146 TAGCCCTAGGTGTGCAGCA 60.612 57.895 8.29 0.00 0.00 4.41
684 686 4.560743 TGTGCAGCAGACGGGCAA 62.561 61.111 0.00 0.00 39.57 4.52
685 687 3.730761 GTGCAGCAGACGGGCAAG 61.731 66.667 0.00 0.00 39.57 4.01
686 688 3.939939 TGCAGCAGACGGGCAAGA 61.940 61.111 0.00 0.00 34.05 3.02
687 689 3.123620 GCAGCAGACGGGCAAGAG 61.124 66.667 0.00 0.00 35.83 2.85
688 690 2.659016 CAGCAGACGGGCAAGAGA 59.341 61.111 0.00 0.00 35.83 3.10
690 692 2.125350 GCAGACGGGCAAGAGAGG 60.125 66.667 0.00 0.00 0.00 3.69
691 693 2.650116 GCAGACGGGCAAGAGAGGA 61.650 63.158 0.00 0.00 0.00 3.71
692 694 1.515020 CAGACGGGCAAGAGAGGAG 59.485 63.158 0.00 0.00 0.00 3.69
741 743 0.522495 GCCGTGTGTTGTGTTGTGTC 60.522 55.000 0.00 0.00 0.00 3.67
761 763 1.178276 TCGGAGAGAGAAACAGAGGC 58.822 55.000 0.00 0.00 0.00 4.70
762 764 0.179150 CGGAGAGAGAAACAGAGGCG 60.179 60.000 0.00 0.00 0.00 5.52
763 765 0.892063 GGAGAGAGAAACAGAGGCGT 59.108 55.000 0.00 0.00 0.00 5.68
767 769 3.134458 AGAGAGAAACAGAGGCGTTTTG 58.866 45.455 0.00 0.00 39.17 2.44
823 828 0.491823 TTCTTCCTCCTCCCACTCCA 59.508 55.000 0.00 0.00 0.00 3.86
830 835 1.609501 CCTCCCACTCCAACTCCGA 60.610 63.158 0.00 0.00 0.00 4.55
831 836 1.592223 CTCCCACTCCAACTCCGAC 59.408 63.158 0.00 0.00 0.00 4.79
832 837 1.889530 CTCCCACTCCAACTCCGACC 61.890 65.000 0.00 0.00 0.00 4.79
833 838 2.663196 CCACTCCAACTCCGACCC 59.337 66.667 0.00 0.00 0.00 4.46
834 839 2.663196 CACTCCAACTCCGACCCC 59.337 66.667 0.00 0.00 0.00 4.95
835 840 2.203182 ACTCCAACTCCGACCCCA 59.797 61.111 0.00 0.00 0.00 4.96
836 841 1.460689 ACTCCAACTCCGACCCCAA 60.461 57.895 0.00 0.00 0.00 4.12
837 842 1.003718 CTCCAACTCCGACCCCAAC 60.004 63.158 0.00 0.00 0.00 3.77
838 843 2.033602 CCAACTCCGACCCCAACC 59.966 66.667 0.00 0.00 0.00 3.77
839 844 2.033602 CAACTCCGACCCCAACCC 59.966 66.667 0.00 0.00 0.00 4.11
840 845 3.254617 AACTCCGACCCCAACCCC 61.255 66.667 0.00 0.00 0.00 4.95
1008 1021 1.683385 TCCAGATCTACCATGTCGCTG 59.317 52.381 0.00 0.00 0.00 5.18
2780 5503 7.966246 TTTCTTTTTCTTAACATGCATGCAT 57.034 28.000 27.46 27.46 37.08 3.96
2942 5694 3.750652 GCAGTTTCAAAGGAGAAGGAGAG 59.249 47.826 0.00 0.00 0.00 3.20
3084 6174 2.289756 GGTGGTTTGTTTGGTGGTTTGT 60.290 45.455 0.00 0.00 0.00 2.83
3166 6592 2.558286 CCATGCCATCCACCATCGC 61.558 63.158 0.00 0.00 0.00 4.58
3308 6805 4.452825 TGTGCTCTAGGTAGCTAGTACAG 58.547 47.826 24.45 17.06 43.19 2.74
3395 8886 9.878667 TTGTTAAGGTTATTATGAATGTCTCGA 57.121 29.630 0.00 0.00 0.00 4.04
3416 8998 4.375706 CGACTGCGTTTTGACCTTACTTAC 60.376 45.833 0.00 0.00 0.00 2.34
3503 9127 3.242706 TGTGCAAAGTGTCAATCTTGTCG 60.243 43.478 0.00 0.00 0.00 4.35
3527 9578 6.468319 CGATATGAAGATCCGATTACGTTACC 59.532 42.308 0.00 0.00 37.88 2.85
3695 10735 5.359716 TCGTTTCTCTGTCTTACTCAGTC 57.640 43.478 0.00 0.00 34.86 3.51
3914 11002 2.931325 CAATATTGCCAAAATGCACGCT 59.069 40.909 1.74 0.00 41.88 5.07
3933 11021 3.549794 GCTGAGGCTTGGTGAATTCTAT 58.450 45.455 7.05 0.00 35.22 1.98
3940 11028 4.103311 GGCTTGGTGAATTCTATAGACCCT 59.897 45.833 0.67 0.00 0.00 4.34
3942 11030 5.531122 TTGGTGAATTCTATAGACCCTCG 57.469 43.478 0.67 0.00 0.00 4.63
3984 11074 0.677288 CTCCATTATACCGGCGGTGA 59.323 55.000 39.80 25.54 36.19 4.02
4042 11135 5.007234 TGAATTAACAGAAATACCCGATGCG 59.993 40.000 0.00 0.00 0.00 4.73
4063 11156 4.092968 GCGCCTTCATATATACGGAAAAGG 59.907 45.833 0.00 0.00 35.88 3.11
4174 11272 0.916086 AGCCCGGTCAATATCAACCA 59.084 50.000 0.00 0.00 35.13 3.67
4179 11277 2.886523 CCGGTCAATATCAACCATGCAT 59.113 45.455 0.00 0.00 35.13 3.96
4199 11299 6.007076 TGCATTGATCCTAAACCTGTTTGTA 58.993 36.000 5.55 0.00 34.23 2.41
4243 11343 2.892215 CCGGGATTACTAGGTTCTCTCC 59.108 54.545 0.00 0.00 0.00 3.71
4291 11391 8.134895 TCATATTTTTCTTTCTCGCTGTTGTTT 58.865 29.630 0.00 0.00 0.00 2.83
4448 11555 1.304282 GGTCCCATGTCACCTGCAT 59.696 57.895 3.50 0.00 0.00 3.96
4518 11631 3.386078 AGATCGATCAAAGCTAGAAGGCA 59.614 43.478 26.47 0.00 34.17 4.75
4532 11645 7.569240 AGCTAGAAGGCATGTAAATTTCTACT 58.431 34.615 0.00 0.00 34.17 2.57
4578 11757 8.220559 AGAATACATTATACATTCACCTGCCTT 58.779 33.333 0.00 0.00 32.27 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
178 179 9.325198 AGTTTCCCAAAATGTTCATAAAAAGTC 57.675 29.630 0.00 0.00 0.00 3.01
186 187 9.844257 TTTTTCATAGTTTCCCAAAATGTTCAT 57.156 25.926 0.00 0.00 0.00 2.57
241 242 9.781633 TGGAATTCAAAATTTGTTCATCAAGAT 57.218 25.926 7.93 0.00 37.35 2.40
242 243 9.781633 ATGGAATTCAAAATTTGTTCATCAAGA 57.218 25.926 7.93 0.00 37.35 3.02
243 244 9.820229 CATGGAATTCAAAATTTGTTCATCAAG 57.180 29.630 7.93 0.00 37.35 3.02
244 245 9.557061 TCATGGAATTCAAAATTTGTTCATCAA 57.443 25.926 7.93 0.00 0.00 2.57
245 246 8.991026 GTCATGGAATTCAAAATTTGTTCATCA 58.009 29.630 7.93 1.82 0.00 3.07
246 247 8.445493 GGTCATGGAATTCAAAATTTGTTCATC 58.555 33.333 7.93 1.31 0.00 2.92
247 248 7.391275 GGGTCATGGAATTCAAAATTTGTTCAT 59.609 33.333 7.93 0.00 0.00 2.57
248 249 6.709846 GGGTCATGGAATTCAAAATTTGTTCA 59.290 34.615 7.93 0.00 0.00 3.18
249 250 6.936335 AGGGTCATGGAATTCAAAATTTGTTC 59.064 34.615 7.93 3.41 0.00 3.18
250 251 6.840527 AGGGTCATGGAATTCAAAATTTGTT 58.159 32.000 7.93 0.00 0.00 2.83
251 252 6.438186 AGGGTCATGGAATTCAAAATTTGT 57.562 33.333 7.93 0.00 0.00 2.83
252 253 7.748691 AAAGGGTCATGGAATTCAAAATTTG 57.251 32.000 7.93 0.00 0.00 2.32
253 254 8.765488 AAAAAGGGTCATGGAATTCAAAATTT 57.235 26.923 7.93 0.00 0.00 1.82
275 276 8.786898 TCAAAAATTGTTCAATGGACACAAAAA 58.213 25.926 0.00 0.00 34.19 1.94
276 277 8.327941 TCAAAAATTGTTCAATGGACACAAAA 57.672 26.923 0.00 0.00 34.19 2.44
277 278 7.912056 TCAAAAATTGTTCAATGGACACAAA 57.088 28.000 0.00 0.00 34.19 2.83
278 279 7.912056 TTCAAAAATTGTTCAATGGACACAA 57.088 28.000 0.00 0.00 34.97 3.33
279 280 8.503458 AATTCAAAAATTGTTCAATGGACACA 57.497 26.923 0.00 0.00 33.78 3.72
280 281 9.224058 CAAATTCAAAAATTGTTCAATGGACAC 57.776 29.630 0.00 0.00 35.27 3.67
281 282 9.170734 TCAAATTCAAAAATTGTTCAATGGACA 57.829 25.926 0.00 0.00 35.27 4.02
313 314 9.757227 TTTCTTTTCATATCCACGAACATTTTT 57.243 25.926 0.00 0.00 0.00 1.94
314 315 9.757227 TTTTCTTTTCATATCCACGAACATTTT 57.243 25.926 0.00 0.00 0.00 1.82
315 316 9.927668 ATTTTCTTTTCATATCCACGAACATTT 57.072 25.926 0.00 0.00 0.00 2.32
316 317 9.927668 AATTTTCTTTTCATATCCACGAACATT 57.072 25.926 0.00 0.00 0.00 2.71
317 318 9.573133 GAATTTTCTTTTCATATCCACGAACAT 57.427 29.630 0.00 0.00 0.00 2.71
318 319 7.748683 CGAATTTTCTTTTCATATCCACGAACA 59.251 33.333 0.00 0.00 0.00 3.18
319 320 7.253321 GCGAATTTTCTTTTCATATCCACGAAC 60.253 37.037 0.00 0.00 0.00 3.95
320 321 6.745450 GCGAATTTTCTTTTCATATCCACGAA 59.255 34.615 0.00 0.00 0.00 3.85
321 322 6.128145 TGCGAATTTTCTTTTCATATCCACGA 60.128 34.615 0.00 0.00 0.00 4.35
322 323 6.027131 TGCGAATTTTCTTTTCATATCCACG 58.973 36.000 0.00 0.00 0.00 4.94
323 324 7.810766 TTGCGAATTTTCTTTTCATATCCAC 57.189 32.000 0.00 0.00 0.00 4.02
324 325 8.824159 TTTTGCGAATTTTCTTTTCATATCCA 57.176 26.923 0.00 0.00 0.00 3.41
399 400 9.546428 CCATTTACCTGTTTCTTTTTCTTTCAT 57.454 29.630 0.00 0.00 0.00 2.57
400 401 7.984617 CCCATTTACCTGTTTCTTTTTCTTTCA 59.015 33.333 0.00 0.00 0.00 2.69
401 402 7.042051 GCCCATTTACCTGTTTCTTTTTCTTTC 60.042 37.037 0.00 0.00 0.00 2.62
402 403 6.765989 GCCCATTTACCTGTTTCTTTTTCTTT 59.234 34.615 0.00 0.00 0.00 2.52
403 404 6.288294 GCCCATTTACCTGTTTCTTTTTCTT 58.712 36.000 0.00 0.00 0.00 2.52
404 405 5.221641 GGCCCATTTACCTGTTTCTTTTTCT 60.222 40.000 0.00 0.00 0.00 2.52
405 406 4.994852 GGCCCATTTACCTGTTTCTTTTTC 59.005 41.667 0.00 0.00 0.00 2.29
406 407 4.502431 CGGCCCATTTACCTGTTTCTTTTT 60.502 41.667 0.00 0.00 0.00 1.94
407 408 3.006430 CGGCCCATTTACCTGTTTCTTTT 59.994 43.478 0.00 0.00 0.00 2.27
408 409 2.560981 CGGCCCATTTACCTGTTTCTTT 59.439 45.455 0.00 0.00 0.00 2.52
409 410 2.167662 CGGCCCATTTACCTGTTTCTT 58.832 47.619 0.00 0.00 0.00 2.52
410 411 1.615919 CCGGCCCATTTACCTGTTTCT 60.616 52.381 0.00 0.00 0.00 2.52
411 412 0.815095 CCGGCCCATTTACCTGTTTC 59.185 55.000 0.00 0.00 0.00 2.78
412 413 1.254975 GCCGGCCCATTTACCTGTTT 61.255 55.000 18.11 0.00 0.00 2.83
413 414 1.680989 GCCGGCCCATTTACCTGTT 60.681 57.895 18.11 0.00 0.00 3.16
414 415 2.044352 GCCGGCCCATTTACCTGT 60.044 61.111 18.11 0.00 0.00 4.00
415 416 2.833121 GGCCGGCCCATTTACCTG 60.833 66.667 36.64 0.00 0.00 4.00
427 428 4.540735 GGGTGTCGTATGGGCCGG 62.541 72.222 0.00 0.00 0.00 6.13
428 429 4.540735 GGGGTGTCGTATGGGCCG 62.541 72.222 0.00 0.00 0.00 6.13
429 430 4.185286 GGGGGTGTCGTATGGGCC 62.185 72.222 0.00 0.00 0.00 5.80
430 431 4.540735 CGGGGGTGTCGTATGGGC 62.541 72.222 0.00 0.00 0.00 5.36
431 432 4.540735 GCGGGGGTGTCGTATGGG 62.541 72.222 0.00 0.00 0.00 4.00
432 433 3.467226 AGCGGGGGTGTCGTATGG 61.467 66.667 0.00 0.00 0.00 2.74
433 434 2.202878 CAGCGGGGGTGTCGTATG 60.203 66.667 0.00 0.00 0.00 2.39
434 435 4.157120 GCAGCGGGGGTGTCGTAT 62.157 66.667 0.00 0.00 33.19 3.06
464 465 4.217159 CCTGTAGCGCGTACCCCC 62.217 72.222 8.43 0.00 0.00 5.40
465 466 4.217159 CCCTGTAGCGCGTACCCC 62.217 72.222 8.43 0.00 0.00 4.95
466 467 2.229690 TTTCCCTGTAGCGCGTACCC 62.230 60.000 8.43 0.00 0.00 3.69
467 468 0.179092 ATTTCCCTGTAGCGCGTACC 60.179 55.000 8.43 0.00 0.00 3.34
468 469 0.928229 CATTTCCCTGTAGCGCGTAC 59.072 55.000 8.43 9.82 0.00 3.67
469 470 0.179094 CCATTTCCCTGTAGCGCGTA 60.179 55.000 8.43 0.00 0.00 4.42
470 471 1.449601 CCATTTCCCTGTAGCGCGT 60.450 57.895 8.43 0.00 0.00 6.01
471 472 2.180204 CCCATTTCCCTGTAGCGCG 61.180 63.158 0.00 0.00 0.00 6.86
472 473 2.481471 GCCCATTTCCCTGTAGCGC 61.481 63.158 0.00 0.00 0.00 5.92
473 474 1.823899 GGCCCATTTCCCTGTAGCG 60.824 63.158 0.00 0.00 0.00 4.26
474 475 1.823899 CGGCCCATTTCCCTGTAGC 60.824 63.158 0.00 0.00 0.00 3.58
475 476 0.834612 TACGGCCCATTTCCCTGTAG 59.165 55.000 0.00 0.00 0.00 2.74
476 477 1.513858 ATACGGCCCATTTCCCTGTA 58.486 50.000 0.00 0.00 0.00 2.74
477 478 1.420138 CTATACGGCCCATTTCCCTGT 59.580 52.381 0.00 0.00 0.00 4.00
478 479 1.271379 CCTATACGGCCCATTTCCCTG 60.271 57.143 0.00 0.00 0.00 4.45
479 480 1.064825 CCTATACGGCCCATTTCCCT 58.935 55.000 0.00 0.00 0.00 4.20
480 481 1.003233 CTCCTATACGGCCCATTTCCC 59.997 57.143 0.00 0.00 0.00 3.97
481 482 1.697982 ACTCCTATACGGCCCATTTCC 59.302 52.381 0.00 0.00 0.00 3.13
482 483 2.289506 GGACTCCTATACGGCCCATTTC 60.290 54.545 0.00 0.00 0.00 2.17
483 484 1.697982 GGACTCCTATACGGCCCATTT 59.302 52.381 0.00 0.00 0.00 2.32
484 485 1.349067 GGACTCCTATACGGCCCATT 58.651 55.000 0.00 0.00 0.00 3.16
485 486 0.544595 GGGACTCCTATACGGCCCAT 60.545 60.000 0.00 0.00 33.86 4.00
486 487 1.152398 GGGACTCCTATACGGCCCA 60.152 63.158 0.00 0.00 33.86 5.36
487 488 0.761702 TTGGGACTCCTATACGGCCC 60.762 60.000 0.00 0.00 34.18 5.80
488 489 0.391966 GTTGGGACTCCTATACGGCC 59.608 60.000 0.00 0.00 0.00 6.13
489 490 0.031721 CGTTGGGACTCCTATACGGC 59.968 60.000 0.00 0.00 33.10 5.68
490 491 0.031721 GCGTTGGGACTCCTATACGG 59.968 60.000 14.60 0.00 35.34 4.02
491 492 0.317603 CGCGTTGGGACTCCTATACG 60.318 60.000 0.00 10.76 36.69 3.06
492 493 1.001597 CTCGCGTTGGGACTCCTATAC 60.002 57.143 5.77 0.00 0.00 1.47
493 494 1.315690 CTCGCGTTGGGACTCCTATA 58.684 55.000 5.77 0.00 0.00 1.31
494 495 1.392710 CCTCGCGTTGGGACTCCTAT 61.393 60.000 5.77 0.00 0.00 2.57
495 496 2.050350 CCTCGCGTTGGGACTCCTA 61.050 63.158 5.77 0.00 0.00 2.94
496 497 3.382832 CCTCGCGTTGGGACTCCT 61.383 66.667 5.77 0.00 0.00 3.69
497 498 2.240162 ATTCCTCGCGTTGGGACTCC 62.240 60.000 17.69 0.00 0.00 3.85
498 499 0.391263 AATTCCTCGCGTTGGGACTC 60.391 55.000 17.69 0.00 0.00 3.36
499 500 0.036306 AAATTCCTCGCGTTGGGACT 59.964 50.000 17.69 10.54 0.00 3.85
500 501 0.879090 AAAATTCCTCGCGTTGGGAC 59.121 50.000 17.69 0.00 0.00 4.46
501 502 1.611519 AAAAATTCCTCGCGTTGGGA 58.388 45.000 17.69 15.09 0.00 4.37
519 520 2.269529 CGCGTTGGGCCCCTAAAAA 61.270 57.895 22.27 2.59 38.94 1.94
520 521 2.673687 CGCGTTGGGCCCCTAAAA 60.674 61.111 22.27 3.06 38.94 1.52
521 522 3.615509 CTCGCGTTGGGCCCCTAAA 62.616 63.158 22.27 3.53 38.94 1.85
522 523 4.090588 CTCGCGTTGGGCCCCTAA 62.091 66.667 22.27 4.46 38.94 2.69
526 527 3.394635 TATTCCTCGCGTTGGGCCC 62.395 63.158 17.59 17.59 38.94 5.80
527 528 1.887707 CTATTCCTCGCGTTGGGCC 60.888 63.158 17.69 0.00 38.94 5.80
528 529 1.887707 CCTATTCCTCGCGTTGGGC 60.888 63.158 17.69 0.00 38.69 5.36
529 530 1.887707 GCCTATTCCTCGCGTTGGG 60.888 63.158 17.69 13.29 0.00 4.12
530 531 2.237751 CGCCTATTCCTCGCGTTGG 61.238 63.158 5.77 10.41 40.99 3.77
531 532 3.309675 CGCCTATTCCTCGCGTTG 58.690 61.111 5.77 0.00 40.99 4.10
540 541 3.937062 CAACGGGCGCGCCTATTC 61.937 66.667 45.23 29.48 36.10 1.75
550 551 2.666596 CTAGGGCATCTCCAACGGGC 62.667 65.000 0.00 0.00 36.21 6.13
551 552 1.447643 CTAGGGCATCTCCAACGGG 59.552 63.158 0.00 0.00 36.21 5.28
552 553 1.227674 GCTAGGGCATCTCCAACGG 60.228 63.158 0.00 0.00 38.54 4.44
553 554 1.227674 GGCTAGGGCATCTCCAACG 60.228 63.158 0.00 0.00 40.87 4.10
554 555 0.179034 CTGGCTAGGGCATCTCCAAC 60.179 60.000 0.00 0.00 40.87 3.77
555 556 1.987807 GCTGGCTAGGGCATCTCCAA 61.988 60.000 0.00 0.00 40.87 3.53
556 557 2.446848 GCTGGCTAGGGCATCTCCA 61.447 63.158 0.00 0.00 40.87 3.86
557 558 2.429494 GCTGGCTAGGGCATCTCC 59.571 66.667 0.00 0.00 40.87 3.71
558 559 1.776975 ATGGCTGGCTAGGGCATCTC 61.777 60.000 0.00 0.00 44.74 2.75
559 560 1.773391 ATGGCTGGCTAGGGCATCT 60.773 57.895 0.00 0.00 44.74 2.90
560 561 1.602888 CATGGCTGGCTAGGGCATC 60.603 63.158 0.00 0.00 45.88 3.91
562 563 4.511246 GCATGGCTGGCTAGGGCA 62.511 66.667 0.00 0.93 43.10 5.36
564 565 3.188015 ATCGCATGGCTGGCTAGGG 62.188 63.158 0.00 3.66 0.00 3.53
565 566 1.964891 CATCGCATGGCTGGCTAGG 60.965 63.158 0.00 0.00 0.00 3.02
566 567 2.614446 GCATCGCATGGCTGGCTAG 61.614 63.158 2.00 0.00 0.00 3.42
567 568 2.592574 GCATCGCATGGCTGGCTA 60.593 61.111 2.00 0.00 0.00 3.93
575 576 3.945434 GACAGCCCGCATCGCATG 61.945 66.667 0.00 0.00 0.00 4.06
576 577 3.974835 TTGACAGCCCGCATCGCAT 62.975 57.895 0.00 0.00 0.00 4.73
577 578 4.695993 TTGACAGCCCGCATCGCA 62.696 61.111 0.00 0.00 0.00 5.10
578 579 3.430862 TTTGACAGCCCGCATCGC 61.431 61.111 0.00 0.00 0.00 4.58
579 580 1.970917 GAGTTTGACAGCCCGCATCG 61.971 60.000 0.00 0.00 0.00 3.84
580 581 0.955428 TGAGTTTGACAGCCCGCATC 60.955 55.000 0.00 0.00 0.00 3.91
581 582 0.957395 CTGAGTTTGACAGCCCGCAT 60.957 55.000 0.00 0.00 0.00 4.73
582 583 1.597854 CTGAGTTTGACAGCCCGCA 60.598 57.895 0.00 0.00 0.00 5.69
583 584 0.320421 TACTGAGTTTGACAGCCCGC 60.320 55.000 0.00 0.00 38.74 6.13
584 585 2.163818 TTACTGAGTTTGACAGCCCG 57.836 50.000 0.00 0.00 38.74 6.13
585 586 3.740115 TCTTTACTGAGTTTGACAGCCC 58.260 45.455 0.00 0.00 38.74 5.19
586 587 3.748568 CCTCTTTACTGAGTTTGACAGCC 59.251 47.826 0.00 0.00 38.74 4.85
587 588 3.748568 CCCTCTTTACTGAGTTTGACAGC 59.251 47.826 0.00 0.00 38.74 4.40
588 589 5.215252 TCCCTCTTTACTGAGTTTGACAG 57.785 43.478 0.00 0.00 40.68 3.51
589 590 4.040461 CCTCCCTCTTTACTGAGTTTGACA 59.960 45.833 0.00 0.00 32.50 3.58
590 591 4.563786 CCCTCCCTCTTTACTGAGTTTGAC 60.564 50.000 0.00 0.00 32.50 3.18
591 592 3.583086 CCCTCCCTCTTTACTGAGTTTGA 59.417 47.826 0.00 0.00 32.50 2.69
592 593 3.870299 GCCCTCCCTCTTTACTGAGTTTG 60.870 52.174 0.00 0.00 32.50 2.93
593 594 2.306219 GCCCTCCCTCTTTACTGAGTTT 59.694 50.000 0.00 0.00 32.50 2.66
594 595 1.909986 GCCCTCCCTCTTTACTGAGTT 59.090 52.381 0.00 0.00 32.50 3.01
595 596 1.574263 GCCCTCCCTCTTTACTGAGT 58.426 55.000 0.00 0.00 32.50 3.41
596 597 0.833949 GGCCCTCCCTCTTTACTGAG 59.166 60.000 0.00 0.00 0.00 3.35
597 598 0.976073 CGGCCCTCCCTCTTTACTGA 60.976 60.000 0.00 0.00 0.00 3.41
598 599 1.522569 CGGCCCTCCCTCTTTACTG 59.477 63.158 0.00 0.00 0.00 2.74
599 600 1.689582 CCGGCCCTCCCTCTTTACT 60.690 63.158 0.00 0.00 0.00 2.24
600 601 2.743179 CCCGGCCCTCCCTCTTTAC 61.743 68.421 0.00 0.00 0.00 2.01
601 602 2.366435 CCCGGCCCTCCCTCTTTA 60.366 66.667 0.00 0.00 0.00 1.85
629 630 0.039618 TGGATTTTGGGCCTCCTCAC 59.960 55.000 4.53 0.00 0.00 3.51
642 643 2.110578 GGGCTAGGTTTGCATGGATTT 58.889 47.619 0.00 0.00 0.00 2.17
668 670 3.730761 CTTGCCCGTCTGCTGCAC 61.731 66.667 0.00 0.00 34.16 4.57
675 677 1.684049 CCTCCTCTCTTGCCCGTCT 60.684 63.158 0.00 0.00 0.00 4.18
684 686 4.824515 CGGACGGCCCTCCTCTCT 62.825 72.222 17.50 0.00 0.00 3.10
685 687 3.711059 TACGGACGGCCCTCCTCTC 62.711 68.421 17.50 0.00 0.00 3.20
686 688 3.717924 CTACGGACGGCCCTCCTCT 62.718 68.421 17.50 6.22 0.00 3.69
687 689 3.217743 CTACGGACGGCCCTCCTC 61.218 72.222 17.50 0.00 0.00 3.71
690 692 4.208686 CTGCTACGGACGGCCCTC 62.209 72.222 0.00 0.00 0.00 4.30
722 724 0.522495 GACACAACACAACACACGGC 60.522 55.000 0.00 0.00 0.00 5.68
730 732 2.028876 TCTCTCCGAGACACAACACAA 58.971 47.619 0.00 0.00 33.35 3.33
741 743 1.134175 GCCTCTGTTTCTCTCTCCGAG 59.866 57.143 0.00 0.00 41.30 4.63
753 755 3.740115 ACATCTACAAAACGCCTCTGTT 58.260 40.909 0.00 0.00 0.00 3.16
754 756 3.402628 ACATCTACAAAACGCCTCTGT 57.597 42.857 0.00 0.00 0.00 3.41
755 757 4.378459 GGAAACATCTACAAAACGCCTCTG 60.378 45.833 0.00 0.00 0.00 3.35
757 759 3.424433 CGGAAACATCTACAAAACGCCTC 60.424 47.826 0.00 0.00 0.00 4.70
758 760 2.482721 CGGAAACATCTACAAAACGCCT 59.517 45.455 0.00 0.00 0.00 5.52
759 761 2.846693 CGGAAACATCTACAAAACGCC 58.153 47.619 0.00 0.00 0.00 5.68
761 763 2.723618 CGGCGGAAACATCTACAAAACG 60.724 50.000 0.00 0.00 0.00 3.60
762 764 2.846693 CGGCGGAAACATCTACAAAAC 58.153 47.619 0.00 0.00 0.00 2.43
763 765 1.198178 GCGGCGGAAACATCTACAAAA 59.802 47.619 9.78 0.00 0.00 2.44
767 769 2.522638 CGGCGGCGGAAACATCTAC 61.523 63.158 25.36 0.00 0.00 2.59
787 789 1.713078 AGAAAGGGAAATGGAGTGGCT 59.287 47.619 0.00 0.00 0.00 4.75
797 802 1.993301 GGGAGGAGGAAGAAAGGGAAA 59.007 52.381 0.00 0.00 0.00 3.13
823 828 3.254617 GGGGTTGGGGTCGGAGTT 61.255 66.667 0.00 0.00 0.00 3.01
833 838 2.863988 AAGGGGACAGGGGGTTGG 60.864 66.667 0.00 0.00 0.00 3.77
834 839 1.435346 AAGAAGGGGACAGGGGGTTG 61.435 60.000 0.00 0.00 0.00 3.77
835 840 1.072143 AAGAAGGGGACAGGGGGTT 60.072 57.895 0.00 0.00 0.00 4.11
836 841 1.541620 GAAGAAGGGGACAGGGGGT 60.542 63.158 0.00 0.00 0.00 4.95
837 842 0.846870 AAGAAGAAGGGGACAGGGGG 60.847 60.000 0.00 0.00 0.00 5.40
838 843 0.621082 GAAGAAGAAGGGGACAGGGG 59.379 60.000 0.00 0.00 0.00 4.79
839 844 0.621082 GGAAGAAGAAGGGGACAGGG 59.379 60.000 0.00 0.00 0.00 4.45
840 845 0.250513 CGGAAGAAGAAGGGGACAGG 59.749 60.000 0.00 0.00 0.00 4.00
841 846 0.391793 GCGGAAGAAGAAGGGGACAG 60.392 60.000 0.00 0.00 0.00 3.51
842 847 1.677552 GCGGAAGAAGAAGGGGACA 59.322 57.895 0.00 0.00 0.00 4.02
843 848 1.078356 GGCGGAAGAAGAAGGGGAC 60.078 63.158 0.00 0.00 0.00 4.46
875 880 0.597072 AAACACGAGACGGAGAGGAC 59.403 55.000 0.00 0.00 0.00 3.85
960 965 4.338118 ACACAGACACAGGGTATTTGTTTG 59.662 41.667 0.00 0.00 32.91 2.93
2780 5503 6.798427 AGCTAGTTCTAGAATGAACATCCA 57.202 37.500 8.75 0.00 46.19 3.41
2781 5504 8.172352 TCTAGCTAGTTCTAGAATGAACATCC 57.828 38.462 20.10 0.00 46.19 3.51
2942 5694 2.276430 GCGCACGCCGTTTCATAC 60.276 61.111 0.30 0.00 39.71 2.39
2963 5715 1.528292 GCGAGCGGATCCCATAGACT 61.528 60.000 6.06 0.00 0.00 3.24
3236 6667 5.087323 CACCTGGAGGGAGCTCTAAATATA 58.913 45.833 14.64 0.00 40.27 0.86
3503 9127 7.272948 GTGGTAACGTAATCGGATCTTCATATC 59.727 40.741 0.00 0.00 41.85 1.63
3527 9578 1.266446 TGGTGCGTGAATGACATTGTG 59.734 47.619 5.14 0.00 0.00 3.33
3695 10735 2.812358 TCGTGACCCCATATCAATCG 57.188 50.000 0.00 0.00 0.00 3.34
3885 10963 2.937469 TTGGCAATATTGAAGGCGTG 57.063 45.000 19.73 0.00 0.00 5.34
3914 11002 5.163301 GGTCTATAGAATTCACCAAGCCTCA 60.163 44.000 8.44 0.00 0.00 3.86
3933 11021 5.684030 GCACATAGGAATTTTCGAGGGTCTA 60.684 44.000 0.00 0.00 0.00 2.59
3940 11028 6.017934 GCTTGATAGCACATAGGAATTTTCGA 60.018 38.462 0.00 0.00 46.95 3.71
4014 11104 9.801873 CATCGGGTATTTCTGTTAATTCATTTT 57.198 29.630 0.00 0.00 0.00 1.82
4036 11129 2.789339 CCGTATATATGAAGGCGCATCG 59.211 50.000 10.83 0.00 0.00 3.84
4042 11135 5.411669 CACCCTTTTCCGTATATATGAAGGC 59.588 44.000 12.46 0.00 32.74 4.35
4174 11272 5.481473 ACAAACAGGTTTAGGATCAATGCAT 59.519 36.000 0.00 0.00 0.00 3.96
4179 11277 5.626142 TGCTACAAACAGGTTTAGGATCAA 58.374 37.500 0.00 0.00 0.00 2.57
4199 11299 4.340381 GTCAGGATTGCCTATTTTCATGCT 59.660 41.667 0.00 0.00 44.80 3.79
4291 11391 4.135153 GCTCGGGCAGCTCGAAGA 62.135 66.667 20.12 0.00 45.83 2.87
4532 11645 2.349590 TGAGCTAGCTCACGTACGTAA 58.650 47.619 37.64 16.32 46.80 3.18
4578 11757 1.352352 AGAAGCTGGCTTTAAGCAGGA 59.648 47.619 19.10 1.04 44.75 3.86


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

AutoCloner maintained by Alex Coulton.