Multiple sequence alignment - TraesCS3D01G341500

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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 TraesCS3D01G341500 chr3D 100.000 6425 0 0 1 6425 454702263 454695839 0.000000e+00 11865.0
1 TraesCS3D01G341500 chr3D 98.363 611 7 3 1 608 364981024 364981634 0.000000e+00 1070.0
2 TraesCS3D01G341500 chr3D 88.107 412 23 8 5367 5770 610093178 610093571 3.510000e-127 466.0
3 TraesCS3D01G341500 chr3D 97.761 134 2 1 3396 3529 283321120 283321252 5.010000e-56 230.0
4 TraesCS3D01G341500 chr3D 92.357 157 7 4 3374 3530 554058090 554058241 1.080000e-52 219.0
5 TraesCS3D01G341500 chr3A 96.972 2807 62 8 617 3403 596774727 596771924 0.000000e+00 4691.0
6 TraesCS3D01G341500 chr3A 95.859 966 27 6 3526 4485 596771923 596770965 0.000000e+00 1550.0
7 TraesCS3D01G341500 chr3A 87.848 897 76 18 4722 5606 596770547 596769672 0.000000e+00 1022.0
8 TraesCS3D01G341500 chr3A 87.685 406 23 5 5893 6283 596769185 596768792 1.270000e-121 448.0
9 TraesCS3D01G341500 chr3A 97.458 236 6 0 4486 4721 596770809 596770574 2.790000e-108 403.0
10 TraesCS3D01G341500 chr3A 91.286 241 20 1 2532 2771 611188968 611188728 1.730000e-85 327.0
11 TraesCS3D01G341500 chr3A 85.930 199 10 5 5590 5784 596769561 596769377 5.080000e-46 196.0
12 TraesCS3D01G341500 chr3A 100.000 46 0 0 6380 6425 596768727 596768682 1.150000e-12 86.1
13 TraesCS3D01G341500 chr3B 95.677 2799 74 17 626 3404 597479510 597476739 0.000000e+00 4455.0
14 TraesCS3D01G341500 chr3B 95.389 1041 27 10 3526 4553 597476742 597475710 0.000000e+00 1637.0
15 TraesCS3D01G341500 chr3B 87.853 1169 89 18 4533 5662 597475670 597474516 0.000000e+00 1323.0
16 TraesCS3D01G341500 chr3B 86.243 567 42 16 5887 6425 597474036 597473478 3.340000e-162 582.0
17 TraesCS3D01G341500 chr6D 98.860 614 4 3 1 611 162223903 162223290 0.000000e+00 1092.0
18 TraesCS3D01G341500 chr6D 98.061 619 8 4 1 616 436857361 436857978 0.000000e+00 1074.0
19 TraesCS3D01G341500 chr6D 81.579 228 27 6 3936 4162 31106152 31105939 2.380000e-39 174.0
20 TraesCS3D01G341500 chr7D 98.697 614 5 3 1 611 153661776 153662389 0.000000e+00 1086.0
21 TraesCS3D01G341500 chr7D 96.992 133 4 0 3396 3528 134065450 134065318 2.330000e-54 224.0
22 TraesCS3D01G341500 chr7D 95.105 143 5 2 3386 3528 251084836 251084976 2.330000e-54 224.0
23 TraesCS3D01G341500 chr4D 98.369 613 8 2 1 611 416421538 416422150 0.000000e+00 1075.0
24 TraesCS3D01G341500 chr1D 98.371 614 7 3 1 611 442082168 442082781 0.000000e+00 1075.0
25 TraesCS3D01G341500 chr1D 96.992 133 4 0 3396 3528 258059672 258059540 2.330000e-54 224.0
26 TraesCS3D01G341500 chr2D 98.058 618 8 4 1 615 78071224 78071840 0.000000e+00 1072.0
27 TraesCS3D01G341500 chr2D 98.208 614 8 3 1 611 422562678 422563291 0.000000e+00 1070.0
28 TraesCS3D01G341500 chr2D 93.182 88 6 0 3976 4063 608572456 608572369 5.230000e-26 130.0
29 TraesCS3D01G341500 chr5D 98.046 614 9 3 1 611 151927621 151928234 0.000000e+00 1064.0
30 TraesCS3D01G341500 chr5D 96.429 140 3 2 3391 3529 447459579 447459717 5.010000e-56 230.0
31 TraesCS3D01G341500 chr1A 92.116 241 18 1 2532 2771 34347118 34347358 7.980000e-89 339.0
32 TraesCS3D01G341500 chr1A 91.701 241 19 1 2532 2771 481641552 481641792 3.710000e-87 333.0
33 TraesCS3D01G341500 chr7A 90.871 241 21 1 2532 2771 158277516 158277276 8.040000e-84 322.0
34 TraesCS3D01G341500 chr1B 99.237 131 1 0 3398 3528 683747956 683748086 2.990000e-58 237.0
35 TraesCS3D01G341500 chr6A 98.485 132 2 0 3398 3529 542709478 542709347 3.870000e-57 233.0
36 TraesCS3D01G341500 chr4B 95.105 143 5 2 3386 3528 499755994 499756134 2.330000e-54 224.0
37 TraesCS3D01G341500 chr4A 92.045 88 7 0 3976 4063 102624451 102624538 2.430000e-24 124.0


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 TraesCS3D01G341500 chr3D 454695839 454702263 6424 True 11865.000000 11865 100.000000 1 6425 1 chr3D.!!$R1 6424
1 TraesCS3D01G341500 chr3D 364981024 364981634 610 False 1070.000000 1070 98.363000 1 608 1 chr3D.!!$F2 607
2 TraesCS3D01G341500 chr3A 596768682 596774727 6045 True 1199.442857 4691 93.107429 617 6425 7 chr3A.!!$R2 5808
3 TraesCS3D01G341500 chr3B 597473478 597479510 6032 True 1999.250000 4455 91.290500 626 6425 4 chr3B.!!$R1 5799
4 TraesCS3D01G341500 chr6D 162223290 162223903 613 True 1092.000000 1092 98.860000 1 611 1 chr6D.!!$R2 610
5 TraesCS3D01G341500 chr6D 436857361 436857978 617 False 1074.000000 1074 98.061000 1 616 1 chr6D.!!$F1 615
6 TraesCS3D01G341500 chr7D 153661776 153662389 613 False 1086.000000 1086 98.697000 1 611 1 chr7D.!!$F1 610
7 TraesCS3D01G341500 chr4D 416421538 416422150 612 False 1075.000000 1075 98.369000 1 611 1 chr4D.!!$F1 610
8 TraesCS3D01G341500 chr1D 442082168 442082781 613 False 1075.000000 1075 98.371000 1 611 1 chr1D.!!$F1 610
9 TraesCS3D01G341500 chr2D 78071224 78071840 616 False 1072.000000 1072 98.058000 1 615 1 chr2D.!!$F1 614
10 TraesCS3D01G341500 chr2D 422562678 422563291 613 False 1070.000000 1070 98.208000 1 611 1 chr2D.!!$F2 610
11 TraesCS3D01G341500 chr5D 151927621 151928234 613 False 1064.000000 1064 98.046000 1 611 1 chr5D.!!$F1 610

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
918 935 1.307430 GCCTTTCTCCCTCCCTCCT 60.307 63.158 0.00 0.00 0.00 3.69 F
970 987 1.977293 GCCAGATCTCGCTTTCCCCT 61.977 60.000 4.92 0.00 0.00 4.79 F
1864 1881 1.001641 AAGGCCAAGCTCGAGCAAT 60.002 52.632 36.87 23.42 45.16 3.56 F
3418 3456 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28 F
3524 3562 0.323451 AGAATTTTGGGACGGAGGGC 60.323 55.000 0.00 0.00 0.00 5.19 F
5102 5401 0.031449 TTTAGCTTTGCAACACCGCC 59.969 50.000 0.00 0.00 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 1881 1.962822 CTGCGAGTTGCTGCTCCAA 60.963 57.895 3.50 0.00 46.63 3.53 R
2538 2569 3.065786 AGCGATCAGTAAATGCATTGTGG 59.934 43.478 13.82 3.59 0.00 4.17 R
3505 3543 0.323451 GCCCTCCGTCCCAAAATTCT 60.323 55.000 0.00 0.00 0.00 2.40 R
5002 5299 0.179124 GCGCAACAGTGGACCAAAAA 60.179 50.000 0.30 0.00 0.00 1.94 R
5409 5712 0.898320 TACTTCAGCTGCTCCTGTCC 59.102 55.000 9.47 0.00 34.47 4.02 R
6344 7249 0.109272 TGCACAGCAGAGCTACGTAC 60.109 55.000 0.00 0.00 36.40 3.67 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
186 187 2.697229 TGGATTGGTGAACAAATGCACA 59.303 40.909 0.98 0.00 43.46 4.57
251 253 4.783621 GAGTGCAGATGGCCGCCA 62.784 66.667 16.17 16.17 43.89 5.69
611 615 5.683681 AGGTCAAAATTGTCAAATTTGCCT 58.316 33.333 22.84 22.84 43.63 4.75
624 628 2.550830 TTTGCCTCTCTTGTGACCTC 57.449 50.000 0.00 0.00 0.00 3.85
642 646 3.588842 ACCTCATCCAAGGACTTTGATGA 59.411 43.478 20.77 20.77 44.38 2.92
714 723 7.461182 TCTGAGTGTTTTTGGAAGAGAAAAA 57.539 32.000 0.00 0.00 31.43 1.94
912 929 2.202810 CGCTCGCCTTTCTCCCTC 60.203 66.667 0.00 0.00 0.00 4.30
913 930 2.188207 GCTCGCCTTTCTCCCTCC 59.812 66.667 0.00 0.00 0.00 4.30
918 935 1.307430 GCCTTTCTCCCTCCCTCCT 60.307 63.158 0.00 0.00 0.00 3.69
970 987 1.977293 GCCAGATCTCGCTTTCCCCT 61.977 60.000 4.92 0.00 0.00 4.79
1075 1092 3.930012 CCCTCGCCCTCGATTCCC 61.930 72.222 0.00 0.00 44.56 3.97
1134 1151 4.825679 CACCCTCCTCCCTCCCCC 62.826 77.778 0.00 0.00 0.00 5.40
1194 1211 3.468780 GTTCGTCGAAGAGAACGGT 57.531 52.632 8.18 0.00 36.95 4.83
1610 1627 3.744719 CCGGAGCGACGACTTCCA 61.745 66.667 0.00 0.00 35.47 3.53
1638 1655 2.894126 CCTCACTGATCCTAGCGGTATT 59.106 50.000 0.00 0.00 0.00 1.89
1864 1881 1.001641 AAGGCCAAGCTCGAGCAAT 60.002 52.632 36.87 23.42 45.16 3.56
1964 1987 8.200120 TCATGTTACTCTCATTCTGATGGTTAG 58.800 37.037 0.00 0.00 33.93 2.34
2538 2569 2.159310 CCTGGAGACGATGACTTCTGTC 60.159 54.545 0.00 0.00 43.20 3.51
2574 2605 2.868583 TGATCGCTCTAATGCTTTGCTC 59.131 45.455 0.00 0.00 0.00 4.26
2958 2989 4.736126 AGCACAATTAAGTATTTGGGGC 57.264 40.909 0.00 0.00 0.00 5.80
3128 3159 9.974980 TCTGTATATATGCATCGTTTGACTTTA 57.025 29.630 0.19 0.00 0.00 1.85
3182 3219 5.211973 ACCATAGTGATGTCTGAGGTGTAT 58.788 41.667 0.00 0.00 0.00 2.29
3307 3345 9.134734 GGATATTCGTTTTGCTAAAAATTCACA 57.865 29.630 0.00 0.00 37.59 3.58
3377 3415 9.095065 GTATTCCGAGTACATTAATTGTCAGTT 57.905 33.333 0.00 0.00 39.87 3.16
3408 3446 8.514533 ACTGAAGTCTCTATATAGTACTCCCT 57.485 38.462 15.98 5.99 0.00 4.20
3410 3448 7.920227 TGAAGTCTCTATATAGTACTCCCTCC 58.080 42.308 15.98 8.06 0.00 4.30
3411 3449 6.549433 AGTCTCTATATAGTACTCCCTCCG 57.451 45.833 9.58 0.00 0.00 4.63
3412 3450 6.024893 AGTCTCTATATAGTACTCCCTCCGT 58.975 44.000 9.58 0.00 0.00 4.69
3413 3451 6.155049 AGTCTCTATATAGTACTCCCTCCGTC 59.845 46.154 9.58 0.00 0.00 4.79
3414 3452 5.424895 TCTCTATATAGTACTCCCTCCGTCC 59.575 48.000 9.58 0.00 0.00 4.79
3415 3453 3.735720 ATATAGTACTCCCTCCGTCCC 57.264 52.381 0.00 0.00 0.00 4.46
3416 3454 1.229131 ATAGTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
3417 3455 1.002069 TAGTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
3418 3456 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
3419 3457 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
3420 3458 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
3421 3459 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
3422 3460 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
3423 3461 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
3424 3462 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
3425 3463 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
3426 3464 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
3427 3465 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
3428 3466 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
3429 3467 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
3430 3468 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
3431 3469 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
3432 3470 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
3433 3471 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
3434 3472 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
3435 3473 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
3436 3474 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
3437 3475 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
3438 3476 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
3439 3477 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
3447 3485 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
3448 3486 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
3449 3487 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
3450 3488 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
3451 3489 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
3452 3490 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
3463 3501 4.913335 ATACGGATGTATCAAGTCACGT 57.087 40.909 0.00 0.00 36.56 4.49
3464 3502 3.587797 ACGGATGTATCAAGTCACGTT 57.412 42.857 0.00 0.00 0.00 3.99
3465 3503 3.921677 ACGGATGTATCAAGTCACGTTT 58.078 40.909 0.00 0.00 0.00 3.60
3466 3504 4.312443 ACGGATGTATCAAGTCACGTTTT 58.688 39.130 0.00 0.00 0.00 2.43
3467 3505 5.472148 ACGGATGTATCAAGTCACGTTTTA 58.528 37.500 0.00 0.00 0.00 1.52
3468 3506 5.575606 ACGGATGTATCAAGTCACGTTTTAG 59.424 40.000 0.00 0.00 0.00 1.85
3469 3507 5.575606 CGGATGTATCAAGTCACGTTTTAGT 59.424 40.000 0.00 0.00 0.00 2.24
3470 3508 6.748658 CGGATGTATCAAGTCACGTTTTAGTA 59.251 38.462 0.00 0.00 0.00 1.82
3471 3509 7.434307 CGGATGTATCAAGTCACGTTTTAGTAT 59.566 37.037 0.00 0.00 0.00 2.12
3472 3510 9.095065 GGATGTATCAAGTCACGTTTTAGTATT 57.905 33.333 0.00 0.00 0.00 1.89
3482 3520 9.962783 AGTCACGTTTTAGTATTAGATACATCC 57.037 33.333 0.00 0.00 38.21 3.51
3483 3521 8.899776 GTCACGTTTTAGTATTAGATACATCCG 58.100 37.037 0.00 0.00 38.21 4.18
3484 3522 8.623903 TCACGTTTTAGTATTAGATACATCCGT 58.376 33.333 0.00 0.00 38.21 4.69
3485 3523 9.882996 CACGTTTTAGTATTAGATACATCCGTA 57.117 33.333 0.00 0.00 38.21 4.02
3502 3540 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
3503 3541 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
3504 3542 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
3505 3543 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
3506 3544 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
3507 3545 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
3515 3553 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
3516 3554 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
3517 3555 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
3518 3556 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
3519 3557 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
3520 3558 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
3521 3559 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
3522 3560 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
3523 3561 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
3524 3562 0.323451 AGAATTTTGGGACGGAGGGC 60.323 55.000 0.00 0.00 0.00 5.19
3525 3563 1.654023 GAATTTTGGGACGGAGGGCG 61.654 60.000 0.00 0.00 0.00 6.13
3526 3564 2.420466 AATTTTGGGACGGAGGGCGT 62.420 55.000 0.00 0.00 0.00 5.68
3527 3565 1.555477 ATTTTGGGACGGAGGGCGTA 61.555 55.000 0.00 0.00 0.00 4.42
3528 3566 1.555477 TTTTGGGACGGAGGGCGTAT 61.555 55.000 0.00 0.00 0.00 3.06
3529 3567 0.687098 TTTGGGACGGAGGGCGTATA 60.687 55.000 0.00 0.00 0.00 1.47
3530 3568 0.470456 TTGGGACGGAGGGCGTATAT 60.470 55.000 0.00 0.00 0.00 0.86
3531 3569 0.405198 TGGGACGGAGGGCGTATATA 59.595 55.000 0.00 0.00 0.00 0.86
3532 3570 0.813821 GGGACGGAGGGCGTATATAC 59.186 60.000 2.53 2.53 0.00 1.47
3562 3600 7.095229 TGACCATTAGTTTTCAAGACAGATTCG 60.095 37.037 0.00 0.00 0.00 3.34
3645 3683 0.687354 TGGGACAGGTTTCTCTCAGC 59.313 55.000 0.00 0.00 0.00 4.26
3784 3824 6.161855 TGACTGAGAAATATTACGAGGCAT 57.838 37.500 0.00 0.00 0.00 4.40
3827 3868 4.261614 CCTTTCAAGTCAAGTAAAGTGCCC 60.262 45.833 0.00 0.00 0.00 5.36
3871 3913 2.241176 TCTTTCTTGGTGTGGGAAGTGT 59.759 45.455 0.00 0.00 0.00 3.55
4144 4186 9.903682 TCAAACTTCAATTCTGAATCATTCTTC 57.096 29.630 2.92 0.00 40.78 2.87
4314 4357 7.418483 CCCATATTAACCCAAAATGTTACCCAG 60.418 40.741 0.00 0.00 0.00 4.45
4489 4695 6.086222 GCACAACTTTGGATTGTACTGTATG 58.914 40.000 0.00 0.00 38.22 2.39
4542 4808 2.030805 GTCCACTTGATGTTTGCAGTCC 60.031 50.000 0.00 0.00 0.00 3.85
4654 4920 5.748152 GCTTGAGCAACACATAAAGAAACAA 59.252 36.000 0.00 0.00 41.59 2.83
4694 4960 2.674796 AGAAACCATGTCGACCTAGC 57.325 50.000 14.12 0.00 0.00 3.42
4718 4984 0.683179 GGTAGGGGTGTCCAATTGCC 60.683 60.000 0.00 0.00 38.24 4.52
4731 5023 3.692101 TCCAATTGCCACGTGTTATTAGG 59.308 43.478 15.65 9.62 0.00 2.69
4827 5120 8.211629 TCTCTATAGCAAAGGAAAGGATAAACC 58.788 37.037 0.00 0.00 39.35 3.27
4838 5131 8.119062 AGGAAAGGATAAACCCTGATTAAGAT 57.881 34.615 0.00 0.00 40.05 2.40
4852 5145 5.653507 TGATTAAGATGAGCAAACCAATGC 58.346 37.500 0.00 0.00 46.78 3.56
4867 5160 3.195396 ACCAATGCCCATATGTCAAACAC 59.805 43.478 1.24 0.00 0.00 3.32
4869 5162 4.426416 CAATGCCCATATGTCAAACACTG 58.574 43.478 1.24 0.00 0.00 3.66
4923 5216 8.721478 GTGAAAATCTACACTGTGTATGACATT 58.279 33.333 19.99 15.62 31.66 2.71
4939 5232 8.729756 TGTATGACATTGTTTTGGAAGACATAG 58.270 33.333 0.00 0.00 0.00 2.23
4941 5234 7.202016 TGACATTGTTTTGGAAGACATAGTC 57.798 36.000 0.00 0.00 33.87 2.59
4949 5242 4.193826 TGGAAGACATAGTCTGTTCTGC 57.806 45.455 0.00 0.00 42.59 4.26
4958 5255 3.834489 AGTCTGTTCTGCATGGATAGG 57.166 47.619 0.00 0.00 0.00 2.57
4961 5258 2.702478 TCTGTTCTGCATGGATAGGGAG 59.298 50.000 0.00 0.00 0.00 4.30
5017 5314 6.098124 TCTGAAATGATTTTTGGTCCACTGTT 59.902 34.615 0.00 0.00 0.00 3.16
5030 5327 2.126228 CTGTTGCGCATTGGCAGG 60.126 61.111 12.75 0.00 44.94 4.85
5032 5329 4.360964 GTTGCGCATTGGCAGGCA 62.361 61.111 12.75 7.16 44.94 4.75
5037 5334 1.079681 CGCATTGGCAGGCAATGTT 60.080 52.632 36.84 12.66 40.91 2.71
5038 5335 1.355796 CGCATTGGCAGGCAATGTTG 61.356 55.000 36.84 28.85 40.91 3.33
5071 5369 1.269448 GGCCAAGAAAAGTTCATCGCA 59.731 47.619 0.00 0.00 0.00 5.10
5101 5400 1.846541 TTTTAGCTTTGCAACACCGC 58.153 45.000 0.00 0.00 0.00 5.68
5102 5401 0.031449 TTTAGCTTTGCAACACCGCC 59.969 50.000 0.00 0.00 0.00 6.13
5103 5402 0.821711 TTAGCTTTGCAACACCGCCT 60.822 50.000 0.00 0.00 0.00 5.52
5104 5403 1.234615 TAGCTTTGCAACACCGCCTC 61.235 55.000 0.00 0.00 0.00 4.70
5105 5404 2.844451 GCTTTGCAACACCGCCTCA 61.844 57.895 0.00 0.00 0.00 3.86
5106 5405 1.283793 CTTTGCAACACCGCCTCAG 59.716 57.895 0.00 0.00 0.00 3.35
5114 5413 3.377172 GCAACACCGCCTCAGTAAATAAT 59.623 43.478 0.00 0.00 0.00 1.28
5119 5418 5.124936 ACACCGCCTCAGTAAATAATTTTCC 59.875 40.000 0.00 0.00 0.00 3.13
5199 5498 4.439153 CCAGTAGGTGCATACAATTTGCTG 60.439 45.833 0.00 0.00 40.77 4.41
5200 5499 3.696051 AGTAGGTGCATACAATTTGCTGG 59.304 43.478 0.00 0.00 40.77 4.85
5201 5500 2.528564 AGGTGCATACAATTTGCTGGT 58.471 42.857 0.00 0.00 40.77 4.00
5202 5501 2.231964 AGGTGCATACAATTTGCTGGTG 59.768 45.455 0.00 0.00 40.77 4.17
5203 5502 2.609350 GTGCATACAATTTGCTGGTGG 58.391 47.619 0.00 0.00 40.77 4.61
5204 5503 1.549620 TGCATACAATTTGCTGGTGGG 59.450 47.619 2.52 0.00 40.77 4.61
5205 5504 1.824230 GCATACAATTTGCTGGTGGGA 59.176 47.619 0.00 0.00 37.14 4.37
5206 5505 2.159198 GCATACAATTTGCTGGTGGGAG 60.159 50.000 0.00 0.00 37.14 4.30
5207 5506 2.969821 TACAATTTGCTGGTGGGAGT 57.030 45.000 0.00 0.00 0.00 3.85
5208 5507 1.331214 ACAATTTGCTGGTGGGAGTG 58.669 50.000 0.00 0.00 0.00 3.51
5236 5535 4.097892 GGACACCATCTTGTTTTCAACACT 59.902 41.667 0.00 0.00 41.97 3.55
5239 5538 7.346751 ACACCATCTTGTTTTCAACACTTAT 57.653 32.000 0.00 0.00 41.97 1.73
5243 5542 7.285401 ACCATCTTGTTTTCAACACTTATGAGT 59.715 33.333 6.60 0.00 41.97 3.41
5250 5549 9.778741 TGTTTTCAACACTTATGAGTTCTCTAT 57.221 29.630 1.53 0.00 36.25 1.98
5310 5609 4.813027 ACAATTTGATCATCGCAAAAGCT 58.187 34.783 2.79 0.00 38.57 3.74
5323 5626 4.022762 TCGCAAAAGCTAACTAAATTGCCA 60.023 37.500 0.00 0.00 37.06 4.92
5326 5629 5.639082 GCAAAAGCTAACTAAATTGCCATGT 59.361 36.000 0.00 0.00 35.60 3.21
5348 5651 2.222007 TTTGTCAATGTGCAGGTTGC 57.778 45.000 6.20 0.00 45.29 4.17
5358 5661 1.944778 GCAGGTTGCACAGTCAGAC 59.055 57.895 0.00 0.00 44.26 3.51
5400 5703 4.972440 GCAAAGTTAGCAGAAGACACAAAG 59.028 41.667 0.00 0.00 0.00 2.77
5409 5712 1.659098 GAAGACACAAAGGGATACGCG 59.341 52.381 3.53 3.53 37.60 6.01
5412 5715 0.390735 ACACAAAGGGATACGCGGAC 60.391 55.000 12.47 0.29 37.60 4.79
5416 5719 0.974010 AAAGGGATACGCGGACAGGA 60.974 55.000 12.47 0.00 37.60 3.86
5460 5763 6.699575 ATATAGGTGTGAATTTTGAGCCAC 57.300 37.500 0.00 0.00 0.00 5.01
5468 5771 4.456911 GTGAATTTTGAGCCACTCATCTGA 59.543 41.667 0.00 0.00 40.39 3.27
5488 5793 4.148079 TGAAGCATCAACATTGGTTACCA 58.852 39.130 0.00 0.00 35.12 3.25
5500 5805 5.123820 ACATTGGTTACCACATTGAGATTCG 59.876 40.000 2.39 0.00 30.78 3.34
5540 5845 4.151335 GTGATTTAGGCGATATGTGCAGAG 59.849 45.833 0.00 0.00 0.00 3.35
5572 5877 3.621419 CCCAAGGGGCATTGAGATT 57.379 52.632 0.00 0.00 35.35 2.40
5592 5897 5.713861 AGATTGGTCAAGGATTTTCTTGGAG 59.286 40.000 4.99 0.00 43.05 3.86
5652 6086 6.317391 CAGGAAAGATAGAACAAATCCTGGAC 59.683 42.308 10.35 0.00 45.49 4.02
5662 6096 1.241315 AATCCTGGACCGCAAAACCG 61.241 55.000 0.00 0.00 0.00 4.44
5663 6097 2.119484 ATCCTGGACCGCAAAACCGA 62.119 55.000 0.00 0.00 0.00 4.69
5664 6098 2.613506 CCTGGACCGCAAAACCGAC 61.614 63.158 0.00 0.00 0.00 4.79
5665 6099 1.890041 CTGGACCGCAAAACCGACA 60.890 57.895 0.00 0.00 0.00 4.35
5666 6100 2.113131 CTGGACCGCAAAACCGACAC 62.113 60.000 0.00 0.00 0.00 3.67
5667 6101 2.181521 GGACCGCAAAACCGACACA 61.182 57.895 0.00 0.00 0.00 3.72
5668 6102 1.512156 GGACCGCAAAACCGACACAT 61.512 55.000 0.00 0.00 0.00 3.21
5671 6105 0.110238 CCGCAAAACCGACACATCTG 60.110 55.000 0.00 0.00 0.00 2.90
5676 6110 3.300009 CAAAACCGACACATCTGCTTTC 58.700 45.455 0.00 0.00 0.00 2.62
5748 6182 0.108329 ACAATTACGCGGCACTAGCT 60.108 50.000 12.47 0.00 41.70 3.32
5772 6513 0.251634 GGAGTTCCCTGCTTCCTGAG 59.748 60.000 0.00 0.00 0.00 3.35
5784 6525 5.279406 CCTGCTTCCTGAGAGAACCATATAG 60.279 48.000 0.00 0.00 0.00 1.31
5785 6526 4.039730 TGCTTCCTGAGAGAACCATATAGC 59.960 45.833 0.00 0.00 0.00 2.97
5786 6527 4.039730 GCTTCCTGAGAGAACCATATAGCA 59.960 45.833 0.00 0.00 0.00 3.49
5796 6537 7.215789 AGAGAACCATATAGCACATGAGAAAG 58.784 38.462 0.00 0.00 0.00 2.62
5809 6676 7.663081 AGCACATGAGAAAGATTCTTTTCAGTA 59.337 33.333 12.73 0.38 40.87 2.74
5844 6711 3.351020 CAGGCTTGCATTTGCTATCTC 57.649 47.619 3.94 0.00 42.66 2.75
5845 6712 1.945394 AGGCTTGCATTTGCTATCTCG 59.055 47.619 3.94 0.00 42.66 4.04
5846 6713 1.942657 GGCTTGCATTTGCTATCTCGA 59.057 47.619 3.94 0.00 42.66 4.04
5847 6714 2.032204 GGCTTGCATTTGCTATCTCGAG 60.032 50.000 5.93 5.93 42.66 4.04
5848 6715 2.868583 GCTTGCATTTGCTATCTCGAGA 59.131 45.455 19.19 19.19 42.66 4.04
5849 6716 3.497640 GCTTGCATTTGCTATCTCGAGAT 59.502 43.478 29.58 29.58 42.66 2.75
5850 6717 4.610905 GCTTGCATTTGCTATCTCGAGATG 60.611 45.833 33.22 23.72 42.66 2.90
5851 6718 4.063998 TGCATTTGCTATCTCGAGATGT 57.936 40.909 33.22 15.40 42.66 3.06
5852 6719 5.200368 TGCATTTGCTATCTCGAGATGTA 57.800 39.130 33.22 20.63 42.66 2.29
5853 6720 5.787380 TGCATTTGCTATCTCGAGATGTAT 58.213 37.500 33.22 14.30 42.66 2.29
5854 6721 6.226052 TGCATTTGCTATCTCGAGATGTATT 58.774 36.000 33.22 13.93 42.66 1.89
5855 6722 6.707608 TGCATTTGCTATCTCGAGATGTATTT 59.292 34.615 33.22 13.20 42.66 1.40
5856 6723 7.227314 TGCATTTGCTATCTCGAGATGTATTTT 59.773 33.333 33.22 12.48 42.66 1.82
5857 6724 7.743838 GCATTTGCTATCTCGAGATGTATTTTC 59.256 37.037 33.22 15.89 38.21 2.29
5858 6725 7.715265 TTTGCTATCTCGAGATGTATTTTCC 57.285 36.000 33.22 14.51 36.05 3.13
5859 6726 6.656632 TGCTATCTCGAGATGTATTTTCCT 57.343 37.500 33.22 10.32 36.05 3.36
5860 6727 7.055667 TGCTATCTCGAGATGTATTTTCCTT 57.944 36.000 33.22 9.81 36.05 3.36
5861 6728 7.500992 TGCTATCTCGAGATGTATTTTCCTTT 58.499 34.615 33.22 9.61 36.05 3.11
5862 6729 7.439356 TGCTATCTCGAGATGTATTTTCCTTTG 59.561 37.037 33.22 9.31 36.05 2.77
5863 6730 7.439655 GCTATCTCGAGATGTATTTTCCTTTGT 59.560 37.037 33.22 8.55 36.05 2.83
5864 6731 9.319143 CTATCTCGAGATGTATTTTCCTTTGTT 57.681 33.333 33.22 8.18 36.05 2.83
5865 6732 7.979444 TCTCGAGATGTATTTTCCTTTGTTT 57.021 32.000 12.08 0.00 0.00 2.83
5866 6733 8.391075 TCTCGAGATGTATTTTCCTTTGTTTT 57.609 30.769 12.08 0.00 0.00 2.43
5867 6734 8.504005 TCTCGAGATGTATTTTCCTTTGTTTTC 58.496 33.333 12.08 0.00 0.00 2.29
5868 6735 8.391075 TCGAGATGTATTTTCCTTTGTTTTCT 57.609 30.769 0.00 0.00 0.00 2.52
5869 6736 8.846211 TCGAGATGTATTTTCCTTTGTTTTCTT 58.154 29.630 0.00 0.00 0.00 2.52
5870 6737 9.463443 CGAGATGTATTTTCCTTTGTTTTCTTT 57.537 29.630 0.00 0.00 0.00 2.52
5874 6741 8.940768 TGTATTTTCCTTTGTTTTCTTTCAGG 57.059 30.769 0.00 0.00 0.00 3.86
5875 6742 8.754080 TGTATTTTCCTTTGTTTTCTTTCAGGA 58.246 29.630 0.00 0.00 0.00 3.86
5876 6743 9.594478 GTATTTTCCTTTGTTTTCTTTCAGGAA 57.406 29.630 0.00 0.00 33.05 3.36
5878 6745 8.546597 TTTTCCTTTGTTTTCTTTCAGGAAAG 57.453 30.769 14.17 14.17 46.82 2.62
5879 6746 6.220726 TCCTTTGTTTTCTTTCAGGAAAGG 57.779 37.500 18.74 0.00 45.80 3.11
5880 6747 5.128663 TCCTTTGTTTTCTTTCAGGAAAGGG 59.871 40.000 18.74 10.96 45.80 3.95
5881 6748 5.128663 CCTTTGTTTTCTTTCAGGAAAGGGA 59.871 40.000 18.74 7.91 45.80 4.20
5882 6749 6.183361 CCTTTGTTTTCTTTCAGGAAAGGGAT 60.183 38.462 18.74 0.00 45.80 3.85
5883 6750 6.806668 TTGTTTTCTTTCAGGAAAGGGATT 57.193 33.333 18.74 0.00 45.80 3.01
5884 6751 6.160576 TGTTTTCTTTCAGGAAAGGGATTG 57.839 37.500 18.74 0.00 45.80 2.67
5885 6752 5.070313 TGTTTTCTTTCAGGAAAGGGATTGG 59.930 40.000 18.74 0.00 45.80 3.16
5886 6753 3.456380 TCTTTCAGGAAAGGGATTGGG 57.544 47.619 18.74 0.00 45.80 4.12
5887 6754 2.721906 TCTTTCAGGAAAGGGATTGGGT 59.278 45.455 18.74 0.00 45.80 4.51
5888 6755 3.142028 TCTTTCAGGAAAGGGATTGGGTT 59.858 43.478 18.74 0.00 45.80 4.11
5889 6756 3.628832 TTCAGGAAAGGGATTGGGTTT 57.371 42.857 0.00 0.00 0.00 3.27
5890 6757 2.888212 TCAGGAAAGGGATTGGGTTTG 58.112 47.619 0.00 0.00 0.00 2.93
5891 6758 2.448961 TCAGGAAAGGGATTGGGTTTGA 59.551 45.455 0.00 0.00 0.00 2.69
5937 6808 3.059982 CGGAAGGTGAGCCACTCA 58.940 61.111 5.48 0.00 38.25 3.41
5961 6835 1.374758 GACGAGGCTGACTGGTTGG 60.375 63.158 0.00 0.00 38.35 3.77
6086 6960 3.261951 GACGCCGCGTATGCATGT 61.262 61.111 20.22 1.45 41.37 3.21
6092 6966 0.589729 CCGCGTATGCATGTTCAAGC 60.590 55.000 10.16 1.99 42.97 4.01
6102 6976 3.423154 GTTCAAGCTCCCGCCACG 61.423 66.667 0.00 0.00 36.60 4.94
6124 6998 1.096416 ACCCGAAGAACGAGAGCTAG 58.904 55.000 0.00 0.00 45.77 3.42
6137 7011 3.436704 CGAGAGCTAGTTGCCATGAAAAA 59.563 43.478 0.00 0.00 44.23 1.94
6171 7046 1.797348 CGAATTCCGCCCAAAAATCCG 60.797 52.381 0.00 0.00 0.00 4.18
6242 7135 1.726853 CCTCTTTGTCCGCTACTTGG 58.273 55.000 0.00 0.00 0.00 3.61
6325 7230 5.389859 TGATTTTTACTGGGCATGTCTTG 57.610 39.130 0.00 0.00 0.00 3.02
6339 7244 3.244887 TGTCTTGGAGAGGTGAGAAGA 57.755 47.619 0.00 0.00 0.00 2.87
6340 7245 3.576861 TGTCTTGGAGAGGTGAGAAGAA 58.423 45.455 0.00 0.00 0.00 2.52
6342 7247 3.056179 GTCTTGGAGAGGTGAGAAGAAGG 60.056 52.174 0.00 0.00 0.00 3.46
6343 7248 1.270907 TGGAGAGGTGAGAAGAAGGC 58.729 55.000 0.00 0.00 0.00 4.35
6344 7249 0.174617 GGAGAGGTGAGAAGAAGGCG 59.825 60.000 0.00 0.00 0.00 5.52
6346 7251 2.093106 GAGAGGTGAGAAGAAGGCGTA 58.907 52.381 0.00 0.00 0.00 4.42
6347 7252 1.819903 AGAGGTGAGAAGAAGGCGTAC 59.180 52.381 0.00 0.00 0.00 3.67
6348 7253 0.526662 AGGTGAGAAGAAGGCGTACG 59.473 55.000 11.84 11.84 0.00 3.67
6349 7254 0.243095 GGTGAGAAGAAGGCGTACGT 59.757 55.000 17.90 0.00 0.00 3.57
6350 7255 1.470098 GGTGAGAAGAAGGCGTACGTA 59.530 52.381 17.90 0.00 0.00 3.57
6351 7256 2.477525 GGTGAGAAGAAGGCGTACGTAG 60.478 54.545 17.90 0.00 0.00 3.51
6352 7257 1.131883 TGAGAAGAAGGCGTACGTAGC 59.868 52.381 17.90 1.78 0.00 3.58
6358 7263 1.313812 AAGGCGTACGTAGCTCTGCT 61.314 55.000 17.90 0.00 43.41 4.24
6361 7266 1.134530 GCGTACGTAGCTCTGCTGTG 61.135 60.000 17.90 0.00 40.10 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
186 187 0.102481 CCGATCCGACGATTTGGTCT 59.898 55.000 0.00 0.00 34.75 3.85
611 615 2.568956 CCTTGGATGAGGTCACAAGAGA 59.431 50.000 10.45 0.00 42.07 3.10
642 646 7.907841 ACACCCCTGAAAAGTAAATAAGTTT 57.092 32.000 0.00 0.00 31.80 2.66
912 929 1.192146 TCAAGTCGGGTGAAGGAGGG 61.192 60.000 0.00 0.00 0.00 4.30
913 930 0.037232 GTCAAGTCGGGTGAAGGAGG 60.037 60.000 0.00 0.00 0.00 4.30
918 935 0.313043 GACGAGTCAAGTCGGGTGAA 59.687 55.000 11.57 0.00 44.53 3.18
970 987 2.897762 GCGGTTAGGTGGGGGTTGA 61.898 63.158 0.00 0.00 0.00 3.18
1602 1619 2.761208 AGTGAGGAAGGTATGGAAGTCG 59.239 50.000 0.00 0.00 0.00 4.18
1610 1627 4.156477 GCTAGGATCAGTGAGGAAGGTAT 58.844 47.826 0.00 0.00 0.00 2.73
1638 1655 3.640257 CTCACCCTCGGAGGTCGGA 62.640 68.421 22.07 14.53 38.39 4.55
1707 1724 0.672889 TTGTAGGCGTCGTTGGTGTA 59.327 50.000 0.00 0.00 0.00 2.90
1864 1881 1.962822 CTGCGAGTTGCTGCTCCAA 60.963 57.895 3.50 0.00 46.63 3.53
1964 1987 9.638300 CACGAGTTATGCATAAGAAATTAAGAC 57.362 33.333 19.41 4.70 0.00 3.01
1985 2008 3.802139 TGCTTCTGTCAAAACTACACGAG 59.198 43.478 0.00 0.00 0.00 4.18
1987 2010 4.201773 TGTTGCTTCTGTCAAAACTACACG 60.202 41.667 0.00 0.00 0.00 4.49
2538 2569 3.065786 AGCGATCAGTAAATGCATTGTGG 59.934 43.478 13.82 3.59 0.00 4.17
2775 2806 7.589954 ACGCACATTGTACTCTTAATTCAAAAC 59.410 33.333 0.00 0.00 0.00 2.43
2958 2989 3.126073 TGCAGTATGAAGCTATTGCTCG 58.874 45.455 1.10 0.00 42.93 5.03
3182 3219 7.081349 GTGCATAACACTGTGTTTGCTAATAA 58.919 34.615 33.76 22.97 46.41 1.40
3307 3345 8.543774 ACCATACTGAACTAATGATCTTGACTT 58.456 33.333 0.00 0.00 0.00 3.01
3404 3442 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
3405 3443 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
3406 3444 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
3407 3445 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
3408 3446 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
3410 3448 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
3411 3449 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
3412 3450 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
3413 3451 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
3421 3459 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
3422 3460 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
3423 3461 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
3424 3462 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
3425 3463 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
3426 3464 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
3442 3480 4.913335 ACGTGACTTGATACATCCGTAT 57.087 40.909 0.00 0.00 41.16 3.06
3443 3481 4.707030 AACGTGACTTGATACATCCGTA 57.293 40.909 0.00 0.00 0.00 4.02
3444 3482 3.587797 AACGTGACTTGATACATCCGT 57.412 42.857 0.00 0.00 0.00 4.69
3445 3483 4.921470 AAAACGTGACTTGATACATCCG 57.079 40.909 0.00 0.00 0.00 4.18
3446 3484 6.963049 ACTAAAACGTGACTTGATACATCC 57.037 37.500 0.00 0.00 0.00 3.51
3456 3494 9.962783 GGATGTATCTAATACTAAAACGTGACT 57.037 33.333 0.00 0.00 36.70 3.41
3457 3495 8.899776 CGGATGTATCTAATACTAAAACGTGAC 58.100 37.037 0.00 0.00 36.70 3.67
3458 3496 8.623903 ACGGATGTATCTAATACTAAAACGTGA 58.376 33.333 0.00 0.00 36.70 4.35
3459 3497 8.792831 ACGGATGTATCTAATACTAAAACGTG 57.207 34.615 0.00 0.00 36.70 4.49
3476 3514 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
3477 3515 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
3478 3516 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
3479 3517 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
3480 3518 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
3481 3519 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
3489 3527 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
3490 3528 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
3491 3529 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
3492 3530 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
3493 3531 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
3494 3532 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
3495 3533 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
3496 3534 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
3497 3535 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
3498 3536 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
3499 3537 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
3500 3538 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
3501 3539 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
3502 3540 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
3503 3541 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
3504 3542 1.891011 GCCCTCCGTCCCAAAATTCTT 60.891 52.381 0.00 0.00 0.00 2.52
3505 3543 0.323451 GCCCTCCGTCCCAAAATTCT 60.323 55.000 0.00 0.00 0.00 2.40
3506 3544 1.654023 CGCCCTCCGTCCCAAAATTC 61.654 60.000 0.00 0.00 0.00 2.17
3507 3545 1.677633 CGCCCTCCGTCCCAAAATT 60.678 57.895 0.00 0.00 0.00 1.82
3508 3546 2.045340 CGCCCTCCGTCCCAAAAT 60.045 61.111 0.00 0.00 0.00 1.82
3528 3566 9.878667 TCTTGAAAACTAATGGTCAATCGTATA 57.121 29.630 0.00 0.00 30.06 1.47
3529 3567 8.665685 GTCTTGAAAACTAATGGTCAATCGTAT 58.334 33.333 0.00 0.00 30.06 3.06
3530 3568 7.658167 TGTCTTGAAAACTAATGGTCAATCGTA 59.342 33.333 0.00 0.00 30.06 3.43
3531 3569 6.485313 TGTCTTGAAAACTAATGGTCAATCGT 59.515 34.615 0.00 0.00 30.06 3.73
3532 3570 6.898041 TGTCTTGAAAACTAATGGTCAATCG 58.102 36.000 0.00 0.00 30.06 3.34
3562 3600 9.669353 CTGGCATTGTCATCATTTAAATAGTAC 57.331 33.333 0.00 0.00 0.00 2.73
3871 3913 1.075970 AGGCTACAGAGGGATGCGA 60.076 57.895 0.00 0.00 0.00 5.10
3913 3955 6.778069 TCATGTCCCAAGTGTTACCAAAATTA 59.222 34.615 0.00 0.00 0.00 1.40
4144 4186 1.301087 TCGTACAACCGGCAACCAG 60.301 57.895 0.00 0.00 0.00 4.00
4283 4326 8.846423 AACATTTTGGGTTAATATGGGATACA 57.154 30.769 0.00 0.00 33.58 2.29
4314 4357 4.141287 TGGGCAATACTATGCAATGGTAC 58.859 43.478 0.00 0.00 43.28 3.34
4419 4470 4.282195 GGTCACCACATACCAATTTCCAAA 59.718 41.667 0.00 0.00 35.73 3.28
4542 4808 3.941483 ACGATGCAAGATAAGAAAGGTGG 59.059 43.478 0.00 0.00 0.00 4.61
4654 4920 2.601905 ACTTTCTGCAAGCCTTGGAAT 58.398 42.857 6.57 0.00 35.65 3.01
4694 4960 1.189524 TTGGACACCCCTACCAGTCG 61.190 60.000 0.00 0.00 35.08 4.18
4718 4984 5.717119 ACTCCTACAACCTAATAACACGTG 58.283 41.667 15.48 15.48 0.00 4.49
4731 5023 3.125829 TCGACACGATGTACTCCTACAAC 59.874 47.826 0.00 0.00 36.43 3.32
4827 5120 5.902613 TTGGTTTGCTCATCTTAATCAGG 57.097 39.130 0.00 0.00 0.00 3.86
4852 5145 4.883585 AGCATACAGTGTTTGACATATGGG 59.116 41.667 16.75 0.00 31.22 4.00
4867 5160 6.455360 ACCAAATTACCATGAAGCATACAG 57.545 37.500 0.00 0.00 0.00 2.74
4869 5162 7.282224 TCACTACCAAATTACCATGAAGCATAC 59.718 37.037 0.00 0.00 0.00 2.39
4923 5216 6.483307 CAGAACAGACTATGTCTTCCAAAACA 59.517 38.462 0.00 0.00 43.00 2.83
4939 5232 2.435805 TCCCTATCCATGCAGAACAGAC 59.564 50.000 0.00 0.00 0.00 3.51
4941 5234 2.224475 CCTCCCTATCCATGCAGAACAG 60.224 54.545 0.00 0.00 0.00 3.16
4949 5242 4.408921 TCAAACACTACCTCCCTATCCATG 59.591 45.833 0.00 0.00 0.00 3.66
4958 5255 5.990668 ACTATCCAATCAAACACTACCTCC 58.009 41.667 0.00 0.00 0.00 4.30
5001 5298 1.537990 GCGCAACAGTGGACCAAAAAT 60.538 47.619 0.30 0.00 0.00 1.82
5002 5299 0.179124 GCGCAACAGTGGACCAAAAA 60.179 50.000 0.30 0.00 0.00 1.94
5017 5314 3.383681 ATTGCCTGCCAATGCGCA 61.384 55.556 14.96 14.96 42.44 6.09
5030 5327 1.864565 AAAAAGGCGACCAACATTGC 58.135 45.000 0.00 0.00 0.00 3.56
5071 5369 6.588719 TGCAAAGCTAAAATAGTTCCATGT 57.411 33.333 0.00 0.00 0.00 3.21
5114 5413 5.350504 TGCCTGATTTGAACTTTGGAAAA 57.649 34.783 0.00 0.00 0.00 2.29
5119 5418 4.326504 AGGTTGCCTGATTTGAACTTTG 57.673 40.909 0.00 0.00 29.57 2.77
5180 5479 3.443329 CACCAGCAAATTGTATGCACCTA 59.557 43.478 3.58 0.00 46.22 3.08
5192 5491 1.077265 CCCACTCCCACCAGCAAAT 59.923 57.895 0.00 0.00 0.00 2.32
5193 5492 2.391130 ACCCACTCCCACCAGCAAA 61.391 57.895 0.00 0.00 0.00 3.68
5196 5495 4.351054 CCACCCACTCCCACCAGC 62.351 72.222 0.00 0.00 0.00 4.85
5199 5498 3.647771 GTCCCACCCACTCCCACC 61.648 72.222 0.00 0.00 0.00 4.61
5200 5499 2.852075 TGTCCCACCCACTCCCAC 60.852 66.667 0.00 0.00 0.00 4.61
5201 5500 2.852075 GTGTCCCACCCACTCCCA 60.852 66.667 0.00 0.00 0.00 4.37
5270 5569 8.081633 TCAAATTGTTGATACTGTGAAATCCAC 58.918 33.333 0.00 0.00 41.22 4.02
5285 5584 5.118971 GCTTTTGCGATGATCAAATTGTTGA 59.881 36.000 0.00 0.00 41.15 3.18
5304 5603 9.942850 AAATACATGGCAATTTAGTTAGCTTTT 57.057 25.926 0.00 0.00 0.00 2.27
5323 5626 5.726980 ACCTGCACATTGACAAAATACAT 57.273 34.783 0.00 0.00 0.00 2.29
5326 5629 4.305769 GCAACCTGCACATTGACAAAATA 58.694 39.130 8.98 0.00 44.26 1.40
5348 5651 9.920133 ATATACTAGCAATATTGTCTGACTGTG 57.080 33.333 16.61 5.64 0.00 3.66
5358 5661 8.340618 ACTTTGCCCATATACTAGCAATATTG 57.659 34.615 11.27 11.27 44.10 1.90
5400 5703 2.728817 CTCCTGTCCGCGTATCCC 59.271 66.667 4.92 0.00 0.00 3.85
5409 5712 0.898320 TACTTCAGCTGCTCCTGTCC 59.102 55.000 9.47 0.00 34.47 4.02
5412 5715 1.189752 TCCTACTTCAGCTGCTCCTG 58.810 55.000 9.47 0.00 0.00 3.86
5416 5719 4.826274 TTTACATCCTACTTCAGCTGCT 57.174 40.909 9.47 0.00 0.00 4.24
5460 5763 4.398358 ACCAATGTTGATGCTTCAGATGAG 59.602 41.667 2.23 0.00 32.27 2.90
5468 5771 3.894427 TGTGGTAACCAATGTTGATGCTT 59.106 39.130 0.00 0.00 34.18 3.91
5500 5805 1.073216 CACCGAGCGAGTGATGACAC 61.073 60.000 5.86 0.00 46.24 3.67
5524 5829 1.068281 CTGTCTCTGCACATATCGCCT 59.932 52.381 0.00 0.00 0.00 5.52
5540 5845 1.545651 CCTTGGGGAGTGGAAACTGTC 60.546 57.143 0.00 0.00 33.58 3.51
5565 5870 6.015180 CCAAGAAAATCCTTGACCAATCTCAA 60.015 38.462 5.32 0.00 44.66 3.02
5566 5871 5.477984 CCAAGAAAATCCTTGACCAATCTCA 59.522 40.000 5.32 0.00 44.66 3.27
5568 5873 5.644188 TCCAAGAAAATCCTTGACCAATCT 58.356 37.500 5.32 0.00 44.66 2.40
5569 5874 5.105595 CCTCCAAGAAAATCCTTGACCAATC 60.106 44.000 5.32 0.00 44.66 2.67
5570 5875 4.774200 CCTCCAAGAAAATCCTTGACCAAT 59.226 41.667 5.32 0.00 44.66 3.16
5571 5876 4.151883 CCTCCAAGAAAATCCTTGACCAA 58.848 43.478 5.32 0.00 44.66 3.67
5572 5877 3.140144 ACCTCCAAGAAAATCCTTGACCA 59.860 43.478 5.32 0.00 44.66 4.02
5592 5897 2.240279 ACACATCCGGAGATAGCTACC 58.760 52.381 11.34 0.00 0.00 3.18
5636 6070 1.626321 TGCGGTCCAGGATTTGTTCTA 59.374 47.619 0.00 0.00 0.00 2.10
5649 6083 1.512156 ATGTGTCGGTTTTGCGGTCC 61.512 55.000 0.00 0.00 0.00 4.46
5652 6086 0.110238 CAGATGTGTCGGTTTTGCGG 60.110 55.000 0.00 0.00 0.00 5.69
5662 6096 2.873797 GGGGGAAAGCAGATGTGTC 58.126 57.895 0.00 0.00 0.00 3.67
5702 6136 6.369890 CAGAGAAAACTCAGCATTACAGCTAA 59.630 38.462 0.00 0.00 44.54 3.09
5748 6182 0.687354 GAAGCAGGGAACTCCAGTCA 59.313 55.000 0.00 0.00 40.21 3.41
5749 6183 0.035915 GGAAGCAGGGAACTCCAGTC 60.036 60.000 0.00 0.00 40.21 3.51
5750 6184 0.474660 AGGAAGCAGGGAACTCCAGT 60.475 55.000 0.00 0.00 40.21 4.00
5751 6185 0.035630 CAGGAAGCAGGGAACTCCAG 60.036 60.000 0.00 0.00 40.21 3.86
5752 6186 0.473694 TCAGGAAGCAGGGAACTCCA 60.474 55.000 0.00 0.00 40.21 3.86
5753 6187 0.251634 CTCAGGAAGCAGGGAACTCC 59.748 60.000 0.00 0.00 40.21 3.85
5772 6513 7.212976 TCTTTCTCATGTGCTATATGGTTCTC 58.787 38.462 0.00 0.00 0.00 2.87
5784 6525 6.675987 ACTGAAAAGAATCTTTCTCATGTGC 58.324 36.000 8.86 0.00 39.61 4.57
5785 6526 8.997323 AGTACTGAAAAGAATCTTTCTCATGTG 58.003 33.333 8.86 6.46 39.61 3.21
5786 6527 9.566432 AAGTACTGAAAAGAATCTTTCTCATGT 57.434 29.630 8.86 14.13 39.61 3.21
5809 6676 3.214696 AGCCTGCAACACTTCTTAAGT 57.785 42.857 1.63 0.00 44.06 2.24
5842 6709 8.507249 AGAAAACAAAGGAAAATACATCTCGAG 58.493 33.333 5.93 5.93 0.00 4.04
5844 6711 9.463443 AAAGAAAACAAAGGAAAATACATCTCG 57.537 29.630 0.00 0.00 0.00 4.04
5848 6715 9.546428 CCTGAAAGAAAACAAAGGAAAATACAT 57.454 29.630 0.00 0.00 34.07 2.29
5849 6716 8.754080 TCCTGAAAGAAAACAAAGGAAAATACA 58.246 29.630 0.00 0.00 34.07 2.29
5850 6717 9.594478 TTCCTGAAAGAAAACAAAGGAAAATAC 57.406 29.630 0.00 0.00 38.76 1.89
5867 6734 3.175438 ACCCAATCCCTTTCCTGAAAG 57.825 47.619 11.78 11.78 45.47 2.62
5868 6735 3.628832 AACCCAATCCCTTTCCTGAAA 57.371 42.857 0.00 0.00 0.00 2.69
5869 6736 3.116939 TCAAACCCAATCCCTTTCCTGAA 60.117 43.478 0.00 0.00 0.00 3.02
5870 6737 2.448961 TCAAACCCAATCCCTTTCCTGA 59.551 45.455 0.00 0.00 0.00 3.86
5871 6738 2.888212 TCAAACCCAATCCCTTTCCTG 58.112 47.619 0.00 0.00 0.00 3.86
5872 6739 3.852858 ATCAAACCCAATCCCTTTCCT 57.147 42.857 0.00 0.00 0.00 3.36
5873 6740 7.670364 CATAATATCAAACCCAATCCCTTTCC 58.330 38.462 0.00 0.00 0.00 3.13
5874 6741 7.015584 AGCATAATATCAAACCCAATCCCTTTC 59.984 37.037 0.00 0.00 0.00 2.62
5875 6742 6.845975 AGCATAATATCAAACCCAATCCCTTT 59.154 34.615 0.00 0.00 0.00 3.11
5876 6743 6.268387 CAGCATAATATCAAACCCAATCCCTT 59.732 38.462 0.00 0.00 0.00 3.95
5877 6744 5.776716 CAGCATAATATCAAACCCAATCCCT 59.223 40.000 0.00 0.00 0.00 4.20
5878 6745 5.567423 GCAGCATAATATCAAACCCAATCCC 60.567 44.000 0.00 0.00 0.00 3.85
5879 6746 5.473039 GCAGCATAATATCAAACCCAATCC 58.527 41.667 0.00 0.00 0.00 3.01
5880 6747 5.156355 CGCAGCATAATATCAAACCCAATC 58.844 41.667 0.00 0.00 0.00 2.67
5881 6748 5.125100 CGCAGCATAATATCAAACCCAAT 57.875 39.130 0.00 0.00 0.00 3.16
5882 6749 4.566545 CGCAGCATAATATCAAACCCAA 57.433 40.909 0.00 0.00 0.00 4.12
5909 6776 1.528309 ACCTTCCGCACAAACCTGG 60.528 57.895 0.00 0.00 0.00 4.45
5937 6808 1.077357 AGTCAGCCTCGTCGGAGAT 60.077 57.895 0.00 0.00 43.27 2.75
5961 6835 1.442857 CGTCTCCGCGAGCATATCC 60.443 63.158 8.23 0.00 0.00 2.59
6102 6976 1.069255 GCTCTCGTTCTTCGGGTTTC 58.931 55.000 0.00 0.00 41.36 2.78
6137 7011 0.613572 AATTCGCCGGGGTGGAATTT 60.614 50.000 19.13 0.00 42.00 1.82
6138 7012 1.000145 AATTCGCCGGGGTGGAATT 60.000 52.632 19.13 13.83 42.00 2.17
6139 7013 1.453197 GAATTCGCCGGGGTGGAAT 60.453 57.895 19.13 8.23 42.00 3.01
6171 7046 1.079266 CAGAGACAGGGACAGCAGC 60.079 63.158 0.00 0.00 0.00 5.25
6242 7135 1.291877 AAGCTGGTCGACATTGCGTC 61.292 55.000 18.91 0.00 41.62 5.19
6256 7149 2.378806 CGTTTGAAGTGCTTGAAGCTG 58.621 47.619 18.94 0.00 42.97 4.24
6325 7230 0.174617 CGCCTTCTTCTCACCTCTCC 59.825 60.000 0.00 0.00 0.00 3.71
6339 7244 1.139095 GCAGAGCTACGTACGCCTT 59.861 57.895 16.72 0.00 0.00 4.35
6340 7245 1.749638 AGCAGAGCTACGTACGCCT 60.750 57.895 16.72 9.34 36.99 5.52
6342 7247 1.134530 CACAGCAGAGCTACGTACGC 61.135 60.000 16.72 0.00 36.40 4.42
6343 7248 1.134530 GCACAGCAGAGCTACGTACG 61.135 60.000 15.01 15.01 36.40 3.67
6344 7249 0.109272 TGCACAGCAGAGCTACGTAC 60.109 55.000 0.00 0.00 36.40 3.67
6346 7251 0.249868 TTTGCACAGCAGAGCTACGT 60.250 50.000 0.00 0.00 40.61 3.57
6347 7252 0.164647 GTTTGCACAGCAGAGCTACG 59.835 55.000 0.00 0.00 40.61 3.51
6348 7253 1.196354 CTGTTTGCACAGCAGAGCTAC 59.804 52.381 5.67 0.00 44.16 3.58
6349 7254 1.516161 CTGTTTGCACAGCAGAGCTA 58.484 50.000 5.67 0.00 44.16 3.32
6350 7255 2.328235 CTGTTTGCACAGCAGAGCT 58.672 52.632 5.67 0.00 44.16 4.09
6351 7256 4.937781 CTGTTTGCACAGCAGAGC 57.062 55.556 5.67 0.00 44.16 4.09
6358 7263 3.504134 ACAACTGTACAACTGTTTGCACA 59.496 39.130 0.00 0.00 38.03 4.57
6376 7281 1.068474 CTACAGCACGGCAGTACAAC 58.932 55.000 0.00 0.00 29.63 3.32


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

AutoCloner maintained by Alex Coulton.