Multiple sequence alignment - TraesCS4A01G404700

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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 TraesCS4A01G404700 chr4A 100.000 4133 0 0 1 4133 678216789 678220921 0.000000e+00 7633.0
1 TraesCS4A01G404700 chr4A 100.000 35 0 0 1615 1649 678218207 678218241 9.590000e-07 65.8
2 TraesCS4A01G404700 chr4A 100.000 35 0 0 1419 1453 678218403 678218437 9.590000e-07 65.8
3 TraesCS4A01G404700 chr4B 92.897 3435 140 56 1 3394 592818553 592821924 0.000000e+00 4896.0
4 TraesCS4A01G404700 chr4B 90.397 479 23 8 3677 4133 592821924 592822401 3.530000e-170 608.0
5 TraesCS4A01G404700 chr4B 95.238 42 1 1 1469 1510 592820120 592820160 9.590000e-07 65.8
6 TraesCS4A01G404700 chr4D 91.642 2752 113 38 670 3394 470506391 470509052 0.000000e+00 3699.0
7 TraesCS4A01G404700 chr4D 91.871 652 34 4 1 640 470505652 470506296 0.000000e+00 893.0
8 TraesCS4A01G404700 chr4D 91.810 464 16 9 3677 4126 470509052 470509507 9.750000e-176 627.0
9 TraesCS4A01G404700 chr4D 84.615 286 28 9 3397 3678 37612344 37612071 1.890000e-68 270.0
10 TraesCS4A01G404700 chr2B 84.965 286 28 9 3397 3678 485763588 485763314 4.070000e-70 276.0
11 TraesCS4A01G404700 chr2B 86.667 240 23 6 3446 3684 375576704 375576473 1.470000e-64 257.0
12 TraesCS4A01G404700 chrUn 83.775 302 34 10 3381 3678 353135599 353135889 5.260000e-69 272.0
13 TraesCS4A01G404700 chrUn 83.775 302 34 10 3381 3678 406546678 406546968 5.260000e-69 272.0
14 TraesCS4A01G404700 chrUn 83.775 302 34 10 3381 3678 474599966 474600256 5.260000e-69 272.0
15 TraesCS4A01G404700 chr7A 83.681 288 29 13 3397 3678 50002694 50002969 5.300000e-64 255.0
16 TraesCS4A01G404700 chr2D 83.039 283 33 8 3400 3678 639306057 639305786 4.130000e-60 243.0
17 TraesCS4A01G404700 chr2D 84.337 166 23 2 1252 1414 557795287 557795122 4.280000e-35 159.0
18 TraesCS4A01G404700 chr1B 81.944 288 36 15 3397 3680 278458500 278458225 3.210000e-56 230.0
19 TraesCS4A01G404700 chr2A 83.133 166 25 2 1252 1414 698134341 698134176 9.260000e-32 148.0
20 TraesCS4A01G404700 chr6D 89.474 76 5 2 1515 1587 139418337 139418412 4.400000e-15 93.5
21 TraesCS4A01G404700 chr3B 83.750 80 10 3 1507 1585 773009247 773009170 5.730000e-09 73.1
22 TraesCS4A01G404700 chr3A 86.275 51 5 2 1525 1573 46042779 46042829 2.000000e-03 54.7


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G404700 chr4A 678216789 678220921 4132 False 2588.200000 7633 100.000000 1 4133 3 chr4A.!!$F1 4132
1 TraesCS4A01G404700 chr4B 592818553 592822401 3848 False 1856.600000 4896 92.844000 1 4133 3 chr4B.!!$F1 4132
2 TraesCS4A01G404700 chr4D 470505652 470509507 3855 False 1739.666667 3699 91.774333 1 4126 3 chr4D.!!$F1 4125

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
922 1016 0.105964 TGTGTGTGCCACCTGTCTAC 59.894 55.000 0.0 0.0 43.85 2.59 F
1816 1912 1.407258 GCTCTCAACGAGTATCTGCCT 59.593 52.381 0.0 0.0 41.98 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2304 2406 0.527565 CAGGCGAACCCCTTTTCATG 59.472 55.0 0.00 0.00 36.11 3.07 R
3664 3794 0.254178 CACTTCAGGCTGGCCATAGT 59.746 55.0 15.73 10.23 38.92 2.12 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
74 75 3.460648 CCTACAGGCTACAGGCAAC 57.539 57.895 5.52 0.00 44.01 4.17
75 76 0.107654 CCTACAGGCTACAGGCAACC 60.108 60.000 5.52 0.00 44.01 3.77
83 84 1.876416 GCTACAGGCAACCGAAAGACA 60.876 52.381 0.00 0.00 41.35 3.41
107 110 4.145365 TGCGCCATATAACCTTTGTAGT 57.855 40.909 4.18 0.00 0.00 2.73
125 128 3.746900 TGAGATGTCACATGAGGCG 57.253 52.632 0.00 0.00 0.00 5.52
239 254 3.555168 GGCTAGTCCGAACCTTCATATGG 60.555 52.174 2.13 0.00 0.00 2.74
244 259 1.475751 CCGAACCTTCATATGGCTGCT 60.476 52.381 2.13 0.00 0.00 4.24
262 277 0.665835 CTCTAGCCGTCTAGCCAGTG 59.334 60.000 0.00 0.00 41.59 3.66
292 307 2.203195 AGTTGGCGCTGCAGTGAA 60.203 55.556 30.83 14.15 0.00 3.18
307 322 3.439293 CAGTGAAGCTGTAGACGTATGG 58.561 50.000 0.00 0.00 40.27 2.74
308 323 3.090037 AGTGAAGCTGTAGACGTATGGT 58.910 45.455 0.00 0.00 0.00 3.55
324 339 0.615331 TGGTGAGGCTTTGAGCTAGG 59.385 55.000 0.00 0.00 41.99 3.02
343 358 2.377531 AGGTTAGGTTAGTTTGGGTGGG 59.622 50.000 0.00 0.00 0.00 4.61
513 528 1.933853 ACTCTCGCATAATTTGACCGC 59.066 47.619 0.00 0.00 0.00 5.68
514 529 1.261619 CTCTCGCATAATTTGACCGCC 59.738 52.381 0.00 0.00 0.00 6.13
569 590 1.275010 CCCAGTTTGCAAATACACCCC 59.725 52.381 16.21 0.02 0.00 4.95
599 620 0.244721 GTGGATTTGCAACCCTCTGC 59.755 55.000 15.66 0.00 42.95 4.26
797 891 2.072487 ATGGTGATGGTCCCCTCCG 61.072 63.158 0.00 0.00 0.00 4.63
911 1005 4.072088 GCCGCGTACTGTGTGTGC 62.072 66.667 4.92 0.00 0.00 4.57
922 1016 0.105964 TGTGTGTGCCACCTGTCTAC 59.894 55.000 0.00 0.00 43.85 2.59
936 1030 4.589374 ACCTGTCTACTAGCTTGTCTTGTT 59.411 41.667 3.45 0.00 33.04 2.83
991 1085 3.498401 AACCTTTTGCCGCTTGCCG 62.498 57.895 0.00 0.00 40.16 5.69
1329 1423 2.819595 CGGAGGACCCACATTGCG 60.820 66.667 0.00 0.00 34.14 4.85
1419 1513 4.080356 TCCTACGCTCAAAGGGTACTACTA 60.080 45.833 0.26 0.00 41.82 1.82
1420 1514 4.826183 CCTACGCTCAAAGGGTACTACTAT 59.174 45.833 0.26 0.00 41.82 2.12
1421 1515 5.301298 CCTACGCTCAAAGGGTACTACTATT 59.699 44.000 0.26 0.00 41.82 1.73
1422 1516 5.672421 ACGCTCAAAGGGTACTACTATTT 57.328 39.130 0.00 0.00 39.78 1.40
1423 1517 6.780457 ACGCTCAAAGGGTACTACTATTTA 57.220 37.500 0.00 0.00 39.78 1.40
1424 1518 6.567959 ACGCTCAAAGGGTACTACTATTTAC 58.432 40.000 0.00 0.00 39.78 2.01
1425 1519 6.379417 ACGCTCAAAGGGTACTACTATTTACT 59.621 38.462 0.00 0.00 39.78 2.24
1426 1520 7.557719 ACGCTCAAAGGGTACTACTATTTACTA 59.442 37.037 0.00 0.00 39.78 1.82
1427 1521 8.408601 CGCTCAAAGGGTACTACTATTTACTAA 58.591 37.037 0.00 0.00 0.00 2.24
1428 1522 9.747293 GCTCAAAGGGTACTACTATTTACTAAG 57.253 37.037 0.00 0.00 0.00 2.18
1429 1523 9.747293 CTCAAAGGGTACTACTATTTACTAAGC 57.253 37.037 0.00 0.00 0.00 3.09
1430 1524 9.258629 TCAAAGGGTACTACTATTTACTAAGCA 57.741 33.333 0.00 0.00 0.00 3.91
1433 1527 9.430399 AAGGGTACTACTATTTACTAAGCATCA 57.570 33.333 0.00 0.00 0.00 3.07
1434 1528 9.603189 AGGGTACTACTATTTACTAAGCATCAT 57.397 33.333 0.00 0.00 0.00 2.45
1460 1554 5.525378 AGCTTTACTCGATTTTATCTGCCTG 59.475 40.000 0.00 0.00 0.00 4.85
1470 1564 5.920193 TTTTATCTGCCTGCTTATTTGCT 57.080 34.783 0.00 0.00 0.00 3.91
1539 1633 5.476254 TCATAAGAATTGGTTGTGTGCATCA 59.524 36.000 0.00 0.00 0.00 3.07
1581 1676 7.899178 GGTTTCAACCTTCTTTTCAAAAGAA 57.101 32.000 21.49 21.49 45.75 2.52
1650 1745 8.765219 GCATCATAAGCTTTACTCGATTTTAGA 58.235 33.333 3.20 0.00 0.00 2.10
1756 1852 4.518590 TCTGATGATTTTCCAACTCGCAAA 59.481 37.500 0.00 0.00 0.00 3.68
1789 1885 3.881220 TCCCCTTTTGCTATAAGAACCG 58.119 45.455 0.00 0.00 0.00 4.44
1815 1911 1.846541 GCTCTCAACGAGTATCTGCC 58.153 55.000 0.00 0.00 41.98 4.85
1816 1912 1.407258 GCTCTCAACGAGTATCTGCCT 59.593 52.381 0.00 0.00 41.98 4.75
1817 1913 2.542824 GCTCTCAACGAGTATCTGCCTC 60.543 54.545 0.00 0.00 41.98 4.70
1880 1976 1.593209 GAACCGGTCAACACTCGCA 60.593 57.895 8.04 0.00 0.00 5.10
1990 2086 6.899393 TGAGCAACTAATGAATGAAAAGGT 57.101 33.333 0.00 0.00 0.00 3.50
2106 2204 4.340666 TGATTTTAGCATCTCTCGAGCTCT 59.659 41.667 12.85 2.54 39.68 4.09
2200 2299 4.637534 TGCTCCAACTCAGCATATTTCTTC 59.362 41.667 0.00 0.00 42.09 2.87
2261 2360 7.387397 GTCATTTCCATTGAGCAATTAACCAAA 59.613 33.333 0.00 0.00 0.00 3.28
2262 2361 7.603404 TCATTTCCATTGAGCAATTAACCAAAG 59.397 33.333 0.00 0.00 0.00 2.77
2379 2483 7.639039 TCGTATGATTCAAATAAATGAGTGGC 58.361 34.615 0.00 0.00 0.00 5.01
2455 2559 4.876701 GGCGACCAAGCATCCATA 57.123 55.556 0.00 0.00 39.27 2.74
2753 2857 2.124778 GGCAGCTCCTGAGGCTTC 60.125 66.667 0.00 0.00 38.03 3.86
2888 2994 9.760077 ACGTGCTATGCTACTTAGTTTATTTAT 57.240 29.630 0.00 0.00 0.00 1.40
2924 3030 3.259592 TGGAGACAGATCGACGGAA 57.740 52.632 0.00 0.00 35.01 4.30
2948 3054 3.103911 GTGGCTCGTCGACGGTTG 61.104 66.667 35.05 25.10 40.29 3.77
2991 3106 2.125673 GTCCGGTGGTGGTGATCG 60.126 66.667 0.00 0.00 0.00 3.69
2994 3109 2.032634 CCGGTGGTGGTGATCGTTG 61.033 63.158 0.00 0.00 0.00 4.10
2998 3113 1.679153 GGTGGTGGTGATCGTTGTTTT 59.321 47.619 0.00 0.00 0.00 2.43
3226 3349 1.080093 CATGTCGTGTACCTGCCGT 60.080 57.895 0.00 0.00 0.00 5.68
3245 3368 3.081061 CGTGTCCTGGAAAATGGAATCA 58.919 45.455 0.00 0.00 33.72 2.57
3360 3490 7.261325 ACACACTATGACAAGATAACTAGCTG 58.739 38.462 0.00 0.00 0.00 4.24
3378 3508 0.515127 TGTACATCAAAACTGGCGCG 59.485 50.000 0.00 0.00 0.00 6.86
3393 3523 4.849329 GCGCTGCATGCTTGGCTC 62.849 66.667 20.33 11.57 40.11 4.70
3394 3524 4.189188 CGCTGCATGCTTGGCTCC 62.189 66.667 20.33 0.00 40.11 4.70
3395 3525 4.189188 GCTGCATGCTTGGCTCCG 62.189 66.667 20.33 0.00 38.95 4.63
3396 3526 2.437180 CTGCATGCTTGGCTCCGA 60.437 61.111 20.33 0.00 0.00 4.55
3397 3527 2.437180 TGCATGCTTGGCTCCGAG 60.437 61.111 20.33 0.00 0.00 4.63
3398 3528 3.207669 GCATGCTTGGCTCCGAGG 61.208 66.667 11.37 0.00 0.00 4.63
3399 3529 3.207669 CATGCTTGGCTCCGAGGC 61.208 66.667 14.94 14.94 41.77 4.70
3400 3530 3.406200 ATGCTTGGCTCCGAGGCT 61.406 61.111 21.49 0.00 41.96 4.58
3401 3531 2.066393 ATGCTTGGCTCCGAGGCTA 61.066 57.895 21.49 13.88 41.96 3.93
3402 3532 2.202946 GCTTGGCTCCGAGGCTAC 60.203 66.667 21.49 8.30 41.96 3.58
3403 3533 2.726351 GCTTGGCTCCGAGGCTACT 61.726 63.158 21.49 0.00 41.96 2.57
3404 3534 1.439644 CTTGGCTCCGAGGCTACTC 59.560 63.158 21.49 0.00 41.96 2.59
3405 3535 1.304962 TTGGCTCCGAGGCTACTCA 60.305 57.895 21.49 0.00 44.17 3.41
3406 3536 0.687757 TTGGCTCCGAGGCTACTCAT 60.688 55.000 21.49 0.00 44.17 2.90
3407 3537 0.185175 TGGCTCCGAGGCTACTCATA 59.815 55.000 21.49 0.00 44.17 2.15
3408 3538 0.885196 GGCTCCGAGGCTACTCATAG 59.115 60.000 14.56 0.00 44.17 2.23
3409 3539 1.611519 GCTCCGAGGCTACTCATAGT 58.388 55.000 0.00 0.00 44.17 2.12
3410 3540 1.268352 GCTCCGAGGCTACTCATAGTG 59.732 57.143 0.00 0.00 44.17 2.74
3411 3541 1.883275 CTCCGAGGCTACTCATAGTGG 59.117 57.143 0.00 0.00 44.17 4.00
3412 3542 1.493446 TCCGAGGCTACTCATAGTGGA 59.507 52.381 0.00 0.00 44.17 4.02
3413 3543 2.092049 TCCGAGGCTACTCATAGTGGAA 60.092 50.000 0.00 0.00 44.17 3.53
3414 3544 2.294791 CCGAGGCTACTCATAGTGGAAG 59.705 54.545 0.00 0.00 44.17 3.46
3415 3545 2.952978 CGAGGCTACTCATAGTGGAAGT 59.047 50.000 0.00 0.00 44.17 3.01
3416 3546 4.135306 CGAGGCTACTCATAGTGGAAGTA 58.865 47.826 0.00 0.00 44.17 2.24
3417 3547 4.762765 CGAGGCTACTCATAGTGGAAGTAT 59.237 45.833 0.00 0.00 44.17 2.12
3418 3548 5.106475 CGAGGCTACTCATAGTGGAAGTATC 60.106 48.000 0.00 0.00 44.17 2.24
3419 3549 4.762765 AGGCTACTCATAGTGGAAGTATCG 59.237 45.833 0.00 0.00 27.50 2.92
3420 3550 4.519730 GGCTACTCATAGTGGAAGTATCGT 59.480 45.833 0.00 0.00 27.50 3.73
3421 3551 5.009811 GGCTACTCATAGTGGAAGTATCGTT 59.990 44.000 0.00 0.00 27.50 3.85
3422 3552 6.206243 GGCTACTCATAGTGGAAGTATCGTTA 59.794 42.308 0.00 0.00 27.50 3.18
3423 3553 7.094291 GGCTACTCATAGTGGAAGTATCGTTAT 60.094 40.741 0.00 0.00 27.50 1.89
3424 3554 8.944029 GCTACTCATAGTGGAAGTATCGTTATA 58.056 37.037 0.00 0.00 27.50 0.98
3426 3556 8.921353 ACTCATAGTGGAAGTATCGTTATAGT 57.079 34.615 0.00 0.00 27.50 2.12
3427 3557 8.784994 ACTCATAGTGGAAGTATCGTTATAGTG 58.215 37.037 0.00 0.00 27.50 2.74
3428 3558 8.687292 TCATAGTGGAAGTATCGTTATAGTGT 57.313 34.615 0.00 0.00 27.50 3.55
3429 3559 8.781196 TCATAGTGGAAGTATCGTTATAGTGTC 58.219 37.037 0.00 0.00 27.50 3.67
3430 3560 8.565416 CATAGTGGAAGTATCGTTATAGTGTCA 58.435 37.037 0.00 0.00 27.50 3.58
3431 3561 7.584122 AGTGGAAGTATCGTTATAGTGTCAT 57.416 36.000 0.00 0.00 0.00 3.06
3432 3562 7.426410 AGTGGAAGTATCGTTATAGTGTCATG 58.574 38.462 0.00 0.00 0.00 3.07
3433 3563 6.144080 GTGGAAGTATCGTTATAGTGTCATGC 59.856 42.308 0.00 0.00 0.00 4.06
3434 3564 6.183360 TGGAAGTATCGTTATAGTGTCATGCA 60.183 38.462 0.00 0.00 0.00 3.96
3435 3565 6.868864 GGAAGTATCGTTATAGTGTCATGCAT 59.131 38.462 0.00 0.00 0.00 3.96
3436 3566 8.027189 GGAAGTATCGTTATAGTGTCATGCATA 58.973 37.037 0.00 0.00 0.00 3.14
3437 3567 8.744008 AAGTATCGTTATAGTGTCATGCATAC 57.256 34.615 0.00 0.00 0.00 2.39
3438 3568 7.021790 AGTATCGTTATAGTGTCATGCATACG 58.978 38.462 0.00 2.35 0.00 3.06
3439 3569 5.427036 TCGTTATAGTGTCATGCATACGA 57.573 39.130 10.56 10.56 0.00 3.43
3440 3570 6.009115 TCGTTATAGTGTCATGCATACGAT 57.991 37.500 10.56 5.46 0.00 3.73
3441 3571 7.136289 TCGTTATAGTGTCATGCATACGATA 57.864 36.000 10.56 4.61 0.00 2.92
3442 3572 7.019418 TCGTTATAGTGTCATGCATACGATAC 58.981 38.462 10.56 8.24 0.00 2.24
3443 3573 7.021790 CGTTATAGTGTCATGCATACGATACT 58.978 38.462 16.92 16.92 37.38 2.12
3444 3574 8.173130 CGTTATAGTGTCATGCATACGATACTA 58.827 37.037 19.26 19.26 39.29 1.82
3445 3575 9.491934 GTTATAGTGTCATGCATACGATACTAG 57.508 37.037 20.64 0.00 38.65 2.57
3446 3576 7.689446 ATAGTGTCATGCATACGATACTAGT 57.311 36.000 20.64 0.00 38.65 2.57
3447 3577 5.763088 AGTGTCATGCATACGATACTAGTG 58.237 41.667 12.80 0.00 32.54 2.74
3448 3578 5.299531 AGTGTCATGCATACGATACTAGTGT 59.700 40.000 12.80 0.00 32.54 3.55
3449 3579 6.485648 AGTGTCATGCATACGATACTAGTGTA 59.514 38.462 12.80 0.00 32.54 2.90
3450 3580 7.175119 AGTGTCATGCATACGATACTAGTGTAT 59.825 37.037 12.80 2.02 41.65 2.29
3451 3581 7.271438 GTGTCATGCATACGATACTAGTGTATG 59.729 40.741 20.00 20.00 45.15 2.39
3452 3582 7.174253 TGTCATGCATACGATACTAGTGTATGA 59.826 37.037 25.10 15.74 45.17 2.15
3453 3583 8.184848 GTCATGCATACGATACTAGTGTATGAT 58.815 37.037 25.10 16.39 45.17 2.45
3454 3584 9.391006 TCATGCATACGATACTAGTGTATGATA 57.609 33.333 25.10 17.00 45.17 2.15
3455 3585 9.439537 CATGCATACGATACTAGTGTATGATAC 57.560 37.037 25.10 13.96 45.17 2.24
3456 3586 8.788325 TGCATACGATACTAGTGTATGATACT 57.212 34.615 25.10 0.00 45.17 2.12
3457 3587 9.880157 TGCATACGATACTAGTGTATGATACTA 57.120 33.333 25.10 10.20 45.17 1.82
3511 3641 9.331282 GTATCATAGATGACCTTATTTATGGCC 57.669 37.037 0.00 0.00 40.03 5.36
3512 3642 7.328404 TCATAGATGACCTTATTTATGGCCA 57.672 36.000 8.56 8.56 30.30 5.36
3513 3643 7.932134 TCATAGATGACCTTATTTATGGCCAT 58.068 34.615 24.45 24.45 30.30 4.40
3514 3644 7.830697 TCATAGATGACCTTATTTATGGCCATG 59.169 37.037 29.04 11.95 30.30 3.66
3515 3645 4.768968 AGATGACCTTATTTATGGCCATGC 59.231 41.667 29.04 6.49 0.00 4.06
3516 3646 3.908476 TGACCTTATTTATGGCCATGCA 58.092 40.909 29.04 14.74 0.00 3.96
3517 3647 4.482030 TGACCTTATTTATGGCCATGCAT 58.518 39.130 29.04 20.50 0.00 3.96
3518 3648 4.281435 TGACCTTATTTATGGCCATGCATG 59.719 41.667 29.04 20.19 0.00 4.06
3519 3649 4.482030 ACCTTATTTATGGCCATGCATGA 58.518 39.130 29.04 14.64 0.00 3.07
3520 3650 4.281688 ACCTTATTTATGGCCATGCATGAC 59.718 41.667 29.04 17.06 0.00 3.06
3521 3651 4.281435 CCTTATTTATGGCCATGCATGACA 59.719 41.667 29.04 24.11 0.00 3.58
3522 3652 3.738830 ATTTATGGCCATGCATGACAC 57.261 42.857 29.04 16.71 0.00 3.67
3523 3653 2.140839 TTATGGCCATGCATGACACA 57.859 45.000 29.04 21.39 0.00 3.72
3524 3654 2.140839 TATGGCCATGCATGACACAA 57.859 45.000 29.04 14.29 0.00 3.33
3525 3655 1.268066 ATGGCCATGCATGACACAAA 58.732 45.000 28.31 9.31 0.00 2.83
3526 3656 0.604073 TGGCCATGCATGACACAAAG 59.396 50.000 28.31 10.23 0.00 2.77
3527 3657 0.604578 GGCCATGCATGACACAAAGT 59.395 50.000 28.31 0.00 0.00 2.66
3528 3658 1.670674 GGCCATGCATGACACAAAGTG 60.671 52.381 28.31 8.75 39.75 3.16
3529 3659 1.270274 GCCATGCATGACACAAAGTGA 59.730 47.619 28.31 0.00 36.96 3.41
3530 3660 2.094390 GCCATGCATGACACAAAGTGAT 60.094 45.455 28.31 0.00 36.96 3.06
3531 3661 3.129113 GCCATGCATGACACAAAGTGATA 59.871 43.478 28.31 0.00 36.96 2.15
3532 3662 4.202080 GCCATGCATGACACAAAGTGATAT 60.202 41.667 28.31 0.00 36.96 1.63
3533 3663 5.008911 GCCATGCATGACACAAAGTGATATA 59.991 40.000 28.31 0.00 36.96 0.86
3534 3664 6.459985 GCCATGCATGACACAAAGTGATATAA 60.460 38.462 28.31 0.00 36.96 0.98
3535 3665 6.914215 CCATGCATGACACAAAGTGATATAAC 59.086 38.462 28.31 0.00 36.96 1.89
3536 3666 7.415429 CCATGCATGACACAAAGTGATATAACA 60.415 37.037 28.31 1.49 36.96 2.41
3537 3667 7.628769 TGCATGACACAAAGTGATATAACAT 57.371 32.000 3.88 0.00 36.96 2.71
3538 3668 8.054152 TGCATGACACAAAGTGATATAACATT 57.946 30.769 3.88 0.00 36.96 2.71
3539 3669 8.522003 TGCATGACACAAAGTGATATAACATTT 58.478 29.630 3.88 0.00 36.96 2.32
3584 3714 9.787435 TCTATGTTAATCTAACTCTCTCTCTCC 57.213 37.037 0.00 0.00 39.38 3.71
3585 3715 7.833285 ATGTTAATCTAACTCTCTCTCTCCC 57.167 40.000 0.00 0.00 39.38 4.30
3586 3716 6.130569 TGTTAATCTAACTCTCTCTCTCCCC 58.869 44.000 0.00 0.00 39.38 4.81
3587 3717 3.895704 ATCTAACTCTCTCTCTCCCCC 57.104 52.381 0.00 0.00 0.00 5.40
3588 3718 2.866515 TCTAACTCTCTCTCTCCCCCT 58.133 52.381 0.00 0.00 0.00 4.79
3589 3719 3.203059 TCTAACTCTCTCTCTCCCCCTT 58.797 50.000 0.00 0.00 0.00 3.95
3590 3720 3.598782 TCTAACTCTCTCTCTCCCCCTTT 59.401 47.826 0.00 0.00 0.00 3.11
3591 3721 3.283712 AACTCTCTCTCTCCCCCTTTT 57.716 47.619 0.00 0.00 0.00 2.27
3592 3722 2.827755 ACTCTCTCTCTCCCCCTTTTC 58.172 52.381 0.00 0.00 0.00 2.29
3593 3723 2.385417 ACTCTCTCTCTCCCCCTTTTCT 59.615 50.000 0.00 0.00 0.00 2.52
3594 3724 3.181400 ACTCTCTCTCTCCCCCTTTTCTT 60.181 47.826 0.00 0.00 0.00 2.52
3595 3725 3.843619 CTCTCTCTCTCCCCCTTTTCTTT 59.156 47.826 0.00 0.00 0.00 2.52
3596 3726 5.024803 TCTCTCTCTCCCCCTTTTCTTTA 57.975 43.478 0.00 0.00 0.00 1.85
3597 3727 5.412384 TCTCTCTCTCCCCCTTTTCTTTAA 58.588 41.667 0.00 0.00 0.00 1.52
3598 3728 6.032693 TCTCTCTCTCCCCCTTTTCTTTAAT 58.967 40.000 0.00 0.00 0.00 1.40
3599 3729 6.505700 TCTCTCTCTCCCCCTTTTCTTTAATT 59.494 38.462 0.00 0.00 0.00 1.40
3600 3730 6.722328 TCTCTCTCCCCCTTTTCTTTAATTC 58.278 40.000 0.00 0.00 0.00 2.17
3601 3731 6.505700 TCTCTCTCCCCCTTTTCTTTAATTCT 59.494 38.462 0.00 0.00 0.00 2.40
3602 3732 6.722328 TCTCTCCCCCTTTTCTTTAATTCTC 58.278 40.000 0.00 0.00 0.00 2.87
3603 3733 6.505700 TCTCTCCCCCTTTTCTTTAATTCTCT 59.494 38.462 0.00 0.00 0.00 3.10
3604 3734 6.485171 TCTCCCCCTTTTCTTTAATTCTCTG 58.515 40.000 0.00 0.00 0.00 3.35
3605 3735 5.016831 TCCCCCTTTTCTTTAATTCTCTGC 58.983 41.667 0.00 0.00 0.00 4.26
3606 3736 5.019470 CCCCCTTTTCTTTAATTCTCTGCT 58.981 41.667 0.00 0.00 0.00 4.24
3607 3737 6.011981 TCCCCCTTTTCTTTAATTCTCTGCTA 60.012 38.462 0.00 0.00 0.00 3.49
3608 3738 6.095580 CCCCCTTTTCTTTAATTCTCTGCTAC 59.904 42.308 0.00 0.00 0.00 3.58
3609 3739 6.183360 CCCCTTTTCTTTAATTCTCTGCTACG 60.183 42.308 0.00 0.00 0.00 3.51
3610 3740 6.183360 CCCTTTTCTTTAATTCTCTGCTACGG 60.183 42.308 0.00 0.00 0.00 4.02
3611 3741 6.371825 CCTTTTCTTTAATTCTCTGCTACGGT 59.628 38.462 0.00 0.00 0.00 4.83
3612 3742 7.548075 CCTTTTCTTTAATTCTCTGCTACGGTA 59.452 37.037 0.00 0.00 0.00 4.02
3613 3743 9.099454 CTTTTCTTTAATTCTCTGCTACGGTAT 57.901 33.333 0.00 0.00 0.00 2.73
3614 3744 8.644318 TTTCTTTAATTCTCTGCTACGGTATC 57.356 34.615 0.00 0.00 0.00 2.24
3615 3745 7.584122 TCTTTAATTCTCTGCTACGGTATCT 57.416 36.000 0.00 0.00 0.00 1.98
3616 3746 8.687292 TCTTTAATTCTCTGCTACGGTATCTA 57.313 34.615 0.00 0.00 0.00 1.98
3617 3747 9.298250 TCTTTAATTCTCTGCTACGGTATCTAT 57.702 33.333 0.00 0.00 0.00 1.98
3618 3748 9.562583 CTTTAATTCTCTGCTACGGTATCTATC 57.437 37.037 0.00 0.00 0.00 2.08
3619 3749 8.865420 TTAATTCTCTGCTACGGTATCTATCT 57.135 34.615 0.00 0.00 0.00 1.98
3620 3750 9.955102 TTAATTCTCTGCTACGGTATCTATCTA 57.045 33.333 0.00 0.00 0.00 1.98
3627 3757 8.622157 TCTGCTACGGTATCTATCTATATTTGC 58.378 37.037 0.00 0.00 0.00 3.68
3628 3758 8.521170 TGCTACGGTATCTATCTATATTTGCT 57.479 34.615 0.00 0.00 0.00 3.91
3629 3759 9.623000 TGCTACGGTATCTATCTATATTTGCTA 57.377 33.333 0.00 0.00 0.00 3.49
3641 3771 8.607441 ATCTATATTTGCTATTTTCGAGTGCA 57.393 30.769 0.00 0.00 0.00 4.57
3642 3772 8.607441 TCTATATTTGCTATTTTCGAGTGCAT 57.393 30.769 0.00 0.00 33.50 3.96
3643 3773 9.056005 TCTATATTTGCTATTTTCGAGTGCATT 57.944 29.630 0.00 0.00 33.50 3.56
3648 3778 6.539649 TGCTATTTTCGAGTGCATTATACC 57.460 37.500 0.00 0.00 0.00 2.73
3649 3779 5.176774 TGCTATTTTCGAGTGCATTATACCG 59.823 40.000 0.00 0.00 0.00 4.02
3650 3780 5.404366 GCTATTTTCGAGTGCATTATACCGA 59.596 40.000 0.00 0.00 0.00 4.69
3651 3781 5.652744 ATTTTCGAGTGCATTATACCGAC 57.347 39.130 0.00 0.00 0.00 4.79
3652 3782 4.380841 TTTCGAGTGCATTATACCGACT 57.619 40.909 0.00 0.00 0.00 4.18
3653 3783 5.503662 TTTCGAGTGCATTATACCGACTA 57.496 39.130 0.00 0.00 0.00 2.59
3654 3784 5.700722 TTCGAGTGCATTATACCGACTAT 57.299 39.130 0.00 0.00 0.00 2.12
3655 3785 5.043189 TCGAGTGCATTATACCGACTATG 57.957 43.478 0.00 0.00 0.00 2.23
3656 3786 4.758165 TCGAGTGCATTATACCGACTATGA 59.242 41.667 0.00 0.00 0.00 2.15
3657 3787 5.414765 TCGAGTGCATTATACCGACTATGAT 59.585 40.000 0.00 0.00 0.00 2.45
3658 3788 6.596497 TCGAGTGCATTATACCGACTATGATA 59.404 38.462 0.00 0.00 0.00 2.15
3659 3789 6.687531 CGAGTGCATTATACCGACTATGATAC 59.312 42.308 0.00 0.00 0.00 2.24
3660 3790 6.864342 AGTGCATTATACCGACTATGATACC 58.136 40.000 0.00 0.00 0.00 2.73
3661 3791 6.663953 AGTGCATTATACCGACTATGATACCT 59.336 38.462 0.00 0.00 0.00 3.08
3662 3792 6.973474 GTGCATTATACCGACTATGATACCTC 59.027 42.308 0.00 0.00 0.00 3.85
3663 3793 6.890268 TGCATTATACCGACTATGATACCTCT 59.110 38.462 0.00 0.00 0.00 3.69
3664 3794 8.050930 TGCATTATACCGACTATGATACCTCTA 58.949 37.037 0.00 0.00 0.00 2.43
3665 3795 8.344098 GCATTATACCGACTATGATACCTCTAC 58.656 40.741 0.00 0.00 0.00 2.59
3666 3796 9.616156 CATTATACCGACTATGATACCTCTACT 57.384 37.037 0.00 0.00 0.00 2.57
3670 3800 6.416415 ACCGACTATGATACCTCTACTATGG 58.584 44.000 0.00 0.00 0.00 2.74
3671 3801 5.297278 CCGACTATGATACCTCTACTATGGC 59.703 48.000 0.00 0.00 0.00 4.40
3672 3802 5.297278 CGACTATGATACCTCTACTATGGCC 59.703 48.000 0.00 0.00 0.00 5.36
3673 3803 6.153942 ACTATGATACCTCTACTATGGCCA 57.846 41.667 8.56 8.56 0.00 5.36
3674 3804 6.191315 ACTATGATACCTCTACTATGGCCAG 58.809 44.000 13.05 0.00 0.00 4.85
3675 3805 3.165875 TGATACCTCTACTATGGCCAGC 58.834 50.000 13.05 0.00 0.00 4.85
3681 3811 2.036992 CTCTACTATGGCCAGCCTGAAG 59.963 54.545 13.05 3.88 36.94 3.02
3700 3830 4.099266 TGAAGTGAACACATCCTTTTTGGG 59.901 41.667 7.68 0.00 36.20 4.12
3717 3847 0.737219 GGGAGTCGTACATGCGTACT 59.263 55.000 0.00 0.00 44.97 2.73
3750 3880 4.850859 TCACGGATTTACTTTACATGCG 57.149 40.909 0.00 0.00 37.72 4.73
3767 3897 1.976478 GCGTGCACACAGACACACAA 61.976 55.000 18.64 0.00 36.57 3.33
3804 3942 4.495349 CGAATCCATTCACATGCTTCTGTC 60.495 45.833 0.00 0.00 36.61 3.51
3867 4017 3.150335 CAGAGCTAGCCGGCAGGA 61.150 66.667 31.54 12.70 41.02 3.86
3887 4037 2.936919 AGCAGAATGATTGCCCGATA 57.063 45.000 0.00 0.00 42.48 2.92
3991 4143 1.405105 GTGGGCGAATAATGCATGTGT 59.595 47.619 0.00 0.00 0.00 3.72
4072 4226 4.091945 CAGACAACATGAGTGGTATTCGTG 59.908 45.833 0.00 0.00 37.54 4.35
4088 4242 2.214347 TCGTGAGAGGCTAGAGATTCG 58.786 52.381 0.00 0.00 34.84 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 1.813513 CATCTGTCTTTCGGTTGCCT 58.186 50.000 0.00 0.00 0.00 4.75
69 70 0.169009 GCATCTGTCTTTCGGTTGCC 59.831 55.000 0.00 0.00 40.37 4.52
70 71 0.179215 CGCATCTGTCTTTCGGTTGC 60.179 55.000 0.00 0.00 41.87 4.17
71 72 0.179215 GCGCATCTGTCTTTCGGTTG 60.179 55.000 0.30 0.00 0.00 3.77
72 73 1.298859 GGCGCATCTGTCTTTCGGTT 61.299 55.000 10.83 0.00 0.00 4.44
73 74 1.741770 GGCGCATCTGTCTTTCGGT 60.742 57.895 10.83 0.00 0.00 4.69
74 75 1.091771 ATGGCGCATCTGTCTTTCGG 61.092 55.000 10.83 0.00 0.00 4.30
75 76 1.570813 TATGGCGCATCTGTCTTTCG 58.429 50.000 10.83 0.00 0.00 3.46
83 84 3.820557 ACAAAGGTTATATGGCGCATCT 58.179 40.909 10.83 0.00 0.00 2.90
107 110 0.460811 GCGCCTCATGTGACATCTCA 60.461 55.000 0.00 0.00 0.00 3.27
125 128 1.062525 CAATTCAACTAGGCGCCGC 59.937 57.895 23.20 0.00 0.00 6.53
132 135 4.759693 TGGCCACTTGTACAATTCAACTAG 59.240 41.667 9.13 0.00 0.00 2.57
210 225 2.282783 TTCGGACTAGCCAGCTGCA 61.283 57.895 8.66 0.00 44.83 4.41
211 226 1.811679 GTTCGGACTAGCCAGCTGC 60.812 63.158 8.66 3.91 41.71 5.25
212 227 1.153549 GGTTCGGACTAGCCAGCTG 60.154 63.158 6.78 6.78 35.94 4.24
213 228 0.905337 AAGGTTCGGACTAGCCAGCT 60.905 55.000 0.00 0.00 35.94 4.24
244 259 1.384989 GCACTGGCTAGACGGCTAGA 61.385 60.000 29.79 8.08 45.71 2.43
292 307 2.025155 CCTCACCATACGTCTACAGCT 58.975 52.381 0.00 0.00 0.00 4.24
301 316 1.009829 GCTCAAAGCCTCACCATACG 58.990 55.000 0.00 0.00 34.48 3.06
307 322 2.481289 AACCTAGCTCAAAGCCTCAC 57.519 50.000 0.00 0.00 43.77 3.51
308 323 2.501723 CCTAACCTAGCTCAAAGCCTCA 59.498 50.000 0.00 0.00 43.77 3.86
324 339 3.151554 CACCCACCCAAACTAACCTAAC 58.848 50.000 0.00 0.00 0.00 2.34
343 358 1.659098 CGAGATTTTACGGTGAGCCAC 59.341 52.381 0.00 0.00 34.09 5.01
355 370 1.808945 CCAGCTTGCTGTCGAGATTTT 59.191 47.619 19.49 0.00 0.00 1.82
514 529 4.617200 TTTTTCAGGTGCAGGGGG 57.383 55.556 0.00 0.00 0.00 5.40
569 590 3.622060 AAATCCACAGGTCCCGGCG 62.622 63.158 0.00 0.00 0.00 6.46
617 639 7.968405 CGAGGAAAAATATACTGAAAACTTGGG 59.032 37.037 0.00 0.00 0.00 4.12
797 891 2.913060 CGGACGGAGGGAGGGATC 60.913 72.222 0.00 0.00 0.00 3.36
817 911 1.219522 CCCGCGTTTTATAGGGAGCG 61.220 60.000 4.92 0.36 46.64 5.03
911 1005 3.093057 AGACAAGCTAGTAGACAGGTGG 58.907 50.000 0.00 0.00 0.00 4.61
922 1016 3.862267 CGGAGATCAACAAGACAAGCTAG 59.138 47.826 0.00 0.00 0.00 3.42
936 1030 2.833582 GGAGACGGCCGGAGATCA 60.834 66.667 31.76 0.00 0.00 2.92
1099 1193 0.907486 TGATCCCAGCAGTCTTCCAG 59.093 55.000 0.00 0.00 0.00 3.86
1427 1521 7.559590 AAAATCGAGTAAAGCTTATGATGCT 57.440 32.000 0.00 0.00 43.32 3.79
1428 1522 9.535270 GATAAAATCGAGTAAAGCTTATGATGC 57.465 33.333 0.00 0.00 0.00 3.91
1431 1525 8.765219 GCAGATAAAATCGAGTAAAGCTTATGA 58.235 33.333 0.00 0.00 0.00 2.15
1432 1526 8.012241 GGCAGATAAAATCGAGTAAAGCTTATG 58.988 37.037 0.00 0.00 0.00 1.90
1433 1527 7.934120 AGGCAGATAAAATCGAGTAAAGCTTAT 59.066 33.333 0.00 0.00 0.00 1.73
1434 1528 7.224753 CAGGCAGATAAAATCGAGTAAAGCTTA 59.775 37.037 0.00 0.00 0.00 3.09
1435 1529 6.037610 CAGGCAGATAAAATCGAGTAAAGCTT 59.962 38.462 0.00 0.00 0.00 3.74
1436 1530 5.525378 CAGGCAGATAAAATCGAGTAAAGCT 59.475 40.000 0.00 0.00 0.00 3.74
1437 1531 5.742446 CAGGCAGATAAAATCGAGTAAAGC 58.258 41.667 0.00 0.00 0.00 3.51
1438 1532 5.525378 AGCAGGCAGATAAAATCGAGTAAAG 59.475 40.000 0.00 0.00 0.00 1.85
1439 1533 5.428253 AGCAGGCAGATAAAATCGAGTAAA 58.572 37.500 0.00 0.00 0.00 2.01
1440 1534 5.023533 AGCAGGCAGATAAAATCGAGTAA 57.976 39.130 0.00 0.00 0.00 2.24
1441 1535 4.672587 AGCAGGCAGATAAAATCGAGTA 57.327 40.909 0.00 0.00 0.00 2.59
1442 1536 3.550437 AGCAGGCAGATAAAATCGAGT 57.450 42.857 0.00 0.00 0.00 4.18
1443 1537 6.551385 AATAAGCAGGCAGATAAAATCGAG 57.449 37.500 0.00 0.00 0.00 4.04
1444 1538 6.728200 CAAATAAGCAGGCAGATAAAATCGA 58.272 36.000 0.00 0.00 0.00 3.59
1460 1554 8.983724 AGATAAAATCGAGTAGAGCAAATAAGC 58.016 33.333 0.00 0.00 0.00 3.09
1539 1633 1.006281 ACCCCACATCTGCATCATTGT 59.994 47.619 0.00 0.00 0.00 2.71
1650 1745 7.613801 AGTGACACTATAGACACTTGAGAGATT 59.386 37.037 6.24 3.23 40.03 2.40
1756 1852 3.168292 CAAAAGGGGAATGGAAAGAGCT 58.832 45.455 0.00 0.00 0.00 4.09
1789 1885 2.435741 CTCGTTGAGAGCGTTGACC 58.564 57.895 0.00 0.00 40.54 4.02
1815 1911 3.885297 AGGGTTGTGAGTTTGAACATGAG 59.115 43.478 0.00 0.00 0.00 2.90
1816 1912 3.882888 GAGGGTTGTGAGTTTGAACATGA 59.117 43.478 0.00 0.00 0.00 3.07
1817 1913 3.885297 AGAGGGTTGTGAGTTTGAACATG 59.115 43.478 0.00 0.00 0.00 3.21
1880 1976 1.630244 GCAGAACAATCGCTGCGACT 61.630 55.000 28.41 14.90 46.66 4.18
1891 1987 3.753272 GAGTTGGAGCATTAGCAGAACAA 59.247 43.478 0.00 0.00 45.49 2.83
2261 2360 6.844097 TTTTCTTGCGAATTATTAACCCCT 57.156 33.333 0.00 0.00 0.00 4.79
2294 2396 2.170397 CCCCTTTTCATGCATTAACCCC 59.830 50.000 0.00 0.00 0.00 4.95
2301 2403 0.532115 GCGAACCCCTTTTCATGCAT 59.468 50.000 0.00 0.00 0.00 3.96
2302 2404 1.531739 GGCGAACCCCTTTTCATGCA 61.532 55.000 0.00 0.00 0.00 3.96
2303 2405 1.215382 GGCGAACCCCTTTTCATGC 59.785 57.895 0.00 0.00 0.00 4.06
2304 2406 0.527565 CAGGCGAACCCCTTTTCATG 59.472 55.000 0.00 0.00 36.11 3.07
2338 2440 4.567959 TCATACGATTGAAGCAGTGATGTG 59.432 41.667 0.00 0.00 0.00 3.21
2419 2523 5.048573 GTCGCCCTACCAAAATGTAAAAGAA 60.049 40.000 0.00 0.00 0.00 2.52
2423 2527 3.083293 GGTCGCCCTACCAAAATGTAAA 58.917 45.455 0.00 0.00 39.50 2.01
2425 2529 1.629353 TGGTCGCCCTACCAAAATGTA 59.371 47.619 0.00 0.00 46.55 2.29
2434 2538 1.523938 GGATGCTTGGTCGCCCTAC 60.524 63.158 0.00 0.00 0.00 3.18
2455 2559 0.779997 AGTTGATTGCCCCTCCAACT 59.220 50.000 0.00 0.00 42.85 3.16
2736 2840 2.124778 GAAGCCTCAGGAGCTGCC 60.125 66.667 0.00 0.00 40.49 4.85
2791 2895 1.663702 GACGGTGGTCACGTTGAGG 60.664 63.158 0.00 0.00 45.68 3.86
2855 2959 1.600957 GTAGCATAGCACGTACGGAGA 59.399 52.381 21.06 1.87 0.00 3.71
2888 2994 7.073208 TGTCTCCATCACCTTATACTCCATTA 58.927 38.462 0.00 0.00 0.00 1.90
2889 2995 5.905331 TGTCTCCATCACCTTATACTCCATT 59.095 40.000 0.00 0.00 0.00 3.16
2936 3042 1.300080 GGAAACCAACCGTCGACGA 60.300 57.895 37.65 0.00 43.02 4.20
2998 3113 1.865970 CACCTACCGTACGTGCAAAAA 59.134 47.619 15.21 0.00 0.00 1.94
3226 3349 6.018469 AGAATTGATTCCATTTTCCAGGACA 58.982 36.000 0.00 0.00 37.51 4.02
3257 3380 5.813157 TCATTCACAGTTTCACGTACAAAGA 59.187 36.000 0.00 0.00 0.00 2.52
3311 3436 2.046023 CGCCATTGCTCTGGACCA 60.046 61.111 9.04 0.00 38.69 4.02
3312 3437 0.960364 TTTCGCCATTGCTCTGGACC 60.960 55.000 9.04 0.00 38.69 4.46
3337 3467 7.411486 ACAGCTAGTTATCTTGTCATAGTGT 57.589 36.000 0.00 0.00 0.00 3.55
3338 3468 8.406297 TGTACAGCTAGTTATCTTGTCATAGTG 58.594 37.037 0.00 0.00 0.00 2.74
3339 3469 8.521170 TGTACAGCTAGTTATCTTGTCATAGT 57.479 34.615 0.00 0.00 0.00 2.12
3340 3470 9.619316 GATGTACAGCTAGTTATCTTGTCATAG 57.381 37.037 3.28 0.00 0.00 2.23
3341 3471 9.131791 TGATGTACAGCTAGTTATCTTGTCATA 57.868 33.333 13.05 0.00 0.00 2.15
3342 3472 8.011844 TGATGTACAGCTAGTTATCTTGTCAT 57.988 34.615 13.05 0.00 0.00 3.06
3343 3473 7.404671 TGATGTACAGCTAGTTATCTTGTCA 57.595 36.000 13.05 0.00 0.00 3.58
3360 3490 0.793104 GCGCGCCAGTTTTGATGTAC 60.793 55.000 23.24 0.00 0.00 2.90
3378 3508 4.189188 CGGAGCCAAGCATGCAGC 62.189 66.667 21.98 19.01 46.19 5.25
3386 3516 1.323271 TGAGTAGCCTCGGAGCCAAG 61.323 60.000 0.00 0.00 40.85 3.61
3393 3523 1.982660 TCCACTATGAGTAGCCTCGG 58.017 55.000 0.00 0.00 40.85 4.63
3394 3524 2.952978 ACTTCCACTATGAGTAGCCTCG 59.047 50.000 0.00 0.00 40.85 4.63
3395 3525 5.106475 CGATACTTCCACTATGAGTAGCCTC 60.106 48.000 0.00 0.00 38.27 4.70
3396 3526 4.762765 CGATACTTCCACTATGAGTAGCCT 59.237 45.833 0.00 0.00 30.66 4.58
3397 3527 4.519730 ACGATACTTCCACTATGAGTAGCC 59.480 45.833 0.00 0.00 30.66 3.93
3398 3528 5.692613 ACGATACTTCCACTATGAGTAGC 57.307 43.478 0.00 0.00 30.19 3.58
3401 3531 8.784994 CACTATAACGATACTTCCACTATGAGT 58.215 37.037 0.00 0.00 0.00 3.41
3402 3532 8.784994 ACACTATAACGATACTTCCACTATGAG 58.215 37.037 0.00 0.00 0.00 2.90
3403 3533 8.687292 ACACTATAACGATACTTCCACTATGA 57.313 34.615 0.00 0.00 0.00 2.15
3404 3534 8.565416 TGACACTATAACGATACTTCCACTATG 58.435 37.037 0.00 0.00 0.00 2.23
3405 3535 8.687292 TGACACTATAACGATACTTCCACTAT 57.313 34.615 0.00 0.00 0.00 2.12
3406 3536 8.565416 CATGACACTATAACGATACTTCCACTA 58.435 37.037 0.00 0.00 0.00 2.74
3407 3537 7.426410 CATGACACTATAACGATACTTCCACT 58.574 38.462 0.00 0.00 0.00 4.00
3408 3538 6.144080 GCATGACACTATAACGATACTTCCAC 59.856 42.308 0.00 0.00 0.00 4.02
3409 3539 6.183360 TGCATGACACTATAACGATACTTCCA 60.183 38.462 0.00 0.00 0.00 3.53
3410 3540 6.213677 TGCATGACACTATAACGATACTTCC 58.786 40.000 0.00 0.00 0.00 3.46
3411 3541 7.875316 ATGCATGACACTATAACGATACTTC 57.125 36.000 0.00 0.00 0.00 3.01
3412 3542 7.537649 CGTATGCATGACACTATAACGATACTT 59.462 37.037 10.16 0.00 0.00 2.24
3413 3543 7.021790 CGTATGCATGACACTATAACGATACT 58.978 38.462 10.16 0.00 0.00 2.12
3414 3544 7.019418 TCGTATGCATGACACTATAACGATAC 58.981 38.462 10.16 0.00 0.00 2.24
3415 3545 7.136289 TCGTATGCATGACACTATAACGATA 57.864 36.000 10.16 0.00 0.00 2.92
3416 3546 6.009115 TCGTATGCATGACACTATAACGAT 57.991 37.500 10.16 0.00 0.00 3.73
3417 3547 5.427036 TCGTATGCATGACACTATAACGA 57.573 39.130 10.16 10.40 0.00 3.85
3418 3548 7.021790 AGTATCGTATGCATGACACTATAACG 58.978 38.462 10.16 8.00 25.27 3.18
3419 3549 9.491934 CTAGTATCGTATGCATGACACTATAAC 57.508 37.037 10.16 0.00 31.02 1.89
3420 3550 9.227777 ACTAGTATCGTATGCATGACACTATAA 57.772 33.333 10.16 0.00 31.02 0.98
3421 3551 8.665685 CACTAGTATCGTATGCATGACACTATA 58.334 37.037 10.16 0.00 31.02 1.31
3422 3552 7.175119 ACACTAGTATCGTATGCATGACACTAT 59.825 37.037 10.16 0.00 31.02 2.12
3423 3553 6.485648 ACACTAGTATCGTATGCATGACACTA 59.514 38.462 10.16 7.20 30.14 2.74
3424 3554 5.299531 ACACTAGTATCGTATGCATGACACT 59.700 40.000 10.16 6.32 32.24 3.55
3425 3555 5.520632 ACACTAGTATCGTATGCATGACAC 58.479 41.667 10.16 0.00 0.00 3.67
3426 3556 5.767816 ACACTAGTATCGTATGCATGACA 57.232 39.130 10.16 0.00 0.00 3.58
3427 3557 7.527457 TCATACACTAGTATCGTATGCATGAC 58.473 38.462 19.71 2.94 41.37 3.06
3428 3558 7.681939 TCATACACTAGTATCGTATGCATGA 57.318 36.000 19.71 0.00 41.37 3.07
3429 3559 9.439537 GTATCATACACTAGTATCGTATGCATG 57.560 37.037 19.71 6.51 41.37 4.06
3430 3560 9.397280 AGTATCATACACTAGTATCGTATGCAT 57.603 33.333 19.71 3.79 41.37 3.96
3431 3561 8.788325 AGTATCATACACTAGTATCGTATGCA 57.212 34.615 19.71 12.72 41.37 3.96
3485 3615 9.331282 GGCCATAAATAAGGTCATCTATGATAC 57.669 37.037 0.00 0.00 39.30 2.24
3486 3616 9.056799 TGGCCATAAATAAGGTCATCTATGATA 57.943 33.333 0.00 0.00 39.30 2.15
3487 3617 7.932134 TGGCCATAAATAAGGTCATCTATGAT 58.068 34.615 0.00 0.00 39.30 2.45
3488 3618 7.328404 TGGCCATAAATAAGGTCATCTATGA 57.672 36.000 0.00 0.00 33.91 2.15
3489 3619 7.415989 GCATGGCCATAAATAAGGTCATCTATG 60.416 40.741 20.30 1.47 46.80 2.23
3490 3620 6.604795 GCATGGCCATAAATAAGGTCATCTAT 59.395 38.462 20.30 0.00 46.80 1.98
3491 3621 5.945784 GCATGGCCATAAATAAGGTCATCTA 59.054 40.000 20.30 0.00 46.80 1.98
3492 3622 4.768968 GCATGGCCATAAATAAGGTCATCT 59.231 41.667 20.30 0.00 46.80 2.90
3493 3623 4.523943 TGCATGGCCATAAATAAGGTCATC 59.476 41.667 20.30 0.00 46.80 2.92
3495 3625 3.908476 TGCATGGCCATAAATAAGGTCA 58.092 40.909 20.30 4.16 44.75 4.02
3496 3626 4.523943 TCATGCATGGCCATAAATAAGGTC 59.476 41.667 25.97 1.55 0.00 3.85
3497 3627 4.281688 GTCATGCATGGCCATAAATAAGGT 59.718 41.667 25.97 0.00 0.00 3.50
3498 3628 4.281435 TGTCATGCATGGCCATAAATAAGG 59.719 41.667 27.59 5.13 0.00 2.69
3499 3629 5.221283 TGTGTCATGCATGGCCATAAATAAG 60.221 40.000 27.59 5.96 0.00 1.73
3500 3630 4.648307 TGTGTCATGCATGGCCATAAATAA 59.352 37.500 27.59 4.13 0.00 1.40
3501 3631 4.213513 TGTGTCATGCATGGCCATAAATA 58.786 39.130 27.59 4.92 0.00 1.40
3502 3632 3.032459 TGTGTCATGCATGGCCATAAAT 58.968 40.909 27.59 12.26 0.00 1.40
3503 3633 2.454538 TGTGTCATGCATGGCCATAAA 58.545 42.857 27.59 10.18 0.00 1.40
3504 3634 2.140839 TGTGTCATGCATGGCCATAA 57.859 45.000 27.59 10.60 0.00 1.90
3505 3635 2.140839 TTGTGTCATGCATGGCCATA 57.859 45.000 27.59 18.14 0.00 2.74
3506 3636 1.206132 CTTTGTGTCATGCATGGCCAT 59.794 47.619 27.59 14.09 0.00 4.40
3507 3637 0.604073 CTTTGTGTCATGCATGGCCA 59.396 50.000 27.59 20.99 0.00 5.36
3508 3638 0.604578 ACTTTGTGTCATGCATGGCC 59.395 50.000 27.59 18.76 0.00 5.36
3509 3639 1.270274 TCACTTTGTGTCATGCATGGC 59.730 47.619 24.40 24.40 34.79 4.40
3510 3640 3.861276 ATCACTTTGTGTCATGCATGG 57.139 42.857 25.97 10.76 34.79 3.66
3511 3641 7.474190 TGTTATATCACTTTGTGTCATGCATG 58.526 34.615 21.07 21.07 34.79 4.06
3512 3642 7.628769 TGTTATATCACTTTGTGTCATGCAT 57.371 32.000 0.00 0.00 34.79 3.96
3513 3643 7.628769 ATGTTATATCACTTTGTGTCATGCA 57.371 32.000 0.00 0.00 34.79 3.96
3514 3644 8.915871 AAATGTTATATCACTTTGTGTCATGC 57.084 30.769 0.00 0.00 34.79 4.06
3558 3688 9.787435 GGAGAGAGAGAGTTAGATTAACATAGA 57.213 37.037 2.24 0.00 41.07 1.98
3559 3689 9.010029 GGGAGAGAGAGAGTTAGATTAACATAG 57.990 40.741 2.24 0.00 41.07 2.23
3560 3690 7.945664 GGGGAGAGAGAGAGTTAGATTAACATA 59.054 40.741 2.24 0.00 41.07 2.29
3561 3691 6.780522 GGGGAGAGAGAGAGTTAGATTAACAT 59.219 42.308 2.24 0.00 41.07 2.71
3562 3692 6.130569 GGGGAGAGAGAGAGTTAGATTAACA 58.869 44.000 2.24 0.00 41.07 2.41
3563 3693 5.537295 GGGGGAGAGAGAGAGTTAGATTAAC 59.463 48.000 0.00 0.00 38.94 2.01
3564 3694 5.437043 AGGGGGAGAGAGAGAGTTAGATTAA 59.563 44.000 0.00 0.00 0.00 1.40
3565 3695 4.985583 AGGGGGAGAGAGAGAGTTAGATTA 59.014 45.833 0.00 0.00 0.00 1.75
3566 3696 3.797269 AGGGGGAGAGAGAGAGTTAGATT 59.203 47.826 0.00 0.00 0.00 2.40
3567 3697 3.413075 AGGGGGAGAGAGAGAGTTAGAT 58.587 50.000 0.00 0.00 0.00 1.98
3568 3698 2.866515 AGGGGGAGAGAGAGAGTTAGA 58.133 52.381 0.00 0.00 0.00 2.10
3569 3699 3.680777 AAGGGGGAGAGAGAGAGTTAG 57.319 52.381 0.00 0.00 0.00 2.34
3570 3700 4.046103 AGAAAAGGGGGAGAGAGAGAGTTA 59.954 45.833 0.00 0.00 0.00 2.24
3571 3701 3.178046 GAAAAGGGGGAGAGAGAGAGTT 58.822 50.000 0.00 0.00 0.00 3.01
3572 3702 2.385417 AGAAAAGGGGGAGAGAGAGAGT 59.615 50.000 0.00 0.00 0.00 3.24
3573 3703 3.114643 AGAAAAGGGGGAGAGAGAGAG 57.885 52.381 0.00 0.00 0.00 3.20
3574 3704 3.569135 AAGAAAAGGGGGAGAGAGAGA 57.431 47.619 0.00 0.00 0.00 3.10
3575 3705 5.763876 TTAAAGAAAAGGGGGAGAGAGAG 57.236 43.478 0.00 0.00 0.00 3.20
3576 3706 6.505700 AGAATTAAAGAAAAGGGGGAGAGAGA 59.494 38.462 0.00 0.00 0.00 3.10
3577 3707 6.726379 AGAATTAAAGAAAAGGGGGAGAGAG 58.274 40.000 0.00 0.00 0.00 3.20
3578 3708 6.505700 AGAGAATTAAAGAAAAGGGGGAGAGA 59.494 38.462 0.00 0.00 0.00 3.10
3579 3709 6.601217 CAGAGAATTAAAGAAAAGGGGGAGAG 59.399 42.308 0.00 0.00 0.00 3.20
3580 3710 6.485171 CAGAGAATTAAAGAAAAGGGGGAGA 58.515 40.000 0.00 0.00 0.00 3.71
3581 3711 5.126222 GCAGAGAATTAAAGAAAAGGGGGAG 59.874 44.000 0.00 0.00 0.00 4.30
3582 3712 5.016831 GCAGAGAATTAAAGAAAAGGGGGA 58.983 41.667 0.00 0.00 0.00 4.81
3583 3713 5.019470 AGCAGAGAATTAAAGAAAAGGGGG 58.981 41.667 0.00 0.00 0.00 5.40
3584 3714 6.183360 CGTAGCAGAGAATTAAAGAAAAGGGG 60.183 42.308 0.00 0.00 0.00 4.79
3585 3715 6.183360 CCGTAGCAGAGAATTAAAGAAAAGGG 60.183 42.308 0.00 0.00 0.00 3.95
3586 3716 6.371825 ACCGTAGCAGAGAATTAAAGAAAAGG 59.628 38.462 0.00 0.00 0.00 3.11
3587 3717 7.365840 ACCGTAGCAGAGAATTAAAGAAAAG 57.634 36.000 0.00 0.00 0.00 2.27
3588 3718 9.095065 GATACCGTAGCAGAGAATTAAAGAAAA 57.905 33.333 0.00 0.00 0.00 2.29
3589 3719 8.475639 AGATACCGTAGCAGAGAATTAAAGAAA 58.524 33.333 0.00 0.00 0.00 2.52
3590 3720 8.008513 AGATACCGTAGCAGAGAATTAAAGAA 57.991 34.615 0.00 0.00 0.00 2.52
3591 3721 7.584122 AGATACCGTAGCAGAGAATTAAAGA 57.416 36.000 0.00 0.00 0.00 2.52
3592 3722 9.562583 GATAGATACCGTAGCAGAGAATTAAAG 57.437 37.037 0.00 0.00 0.00 1.85
3593 3723 9.298250 AGATAGATACCGTAGCAGAGAATTAAA 57.702 33.333 0.00 0.00 0.00 1.52
3594 3724 8.865420 AGATAGATACCGTAGCAGAGAATTAA 57.135 34.615 0.00 0.00 0.00 1.40
3601 3731 8.622157 GCAAATATAGATAGATACCGTAGCAGA 58.378 37.037 0.00 0.00 0.00 4.26
3602 3732 8.625651 AGCAAATATAGATAGATACCGTAGCAG 58.374 37.037 0.00 0.00 0.00 4.24
3603 3733 8.521170 AGCAAATATAGATAGATACCGTAGCA 57.479 34.615 0.00 0.00 0.00 3.49
3615 3745 9.705290 TGCACTCGAAAATAGCAAATATAGATA 57.295 29.630 0.00 0.00 31.42 1.98
3616 3746 8.607441 TGCACTCGAAAATAGCAAATATAGAT 57.393 30.769 0.00 0.00 31.42 1.98
3617 3747 8.607441 ATGCACTCGAAAATAGCAAATATAGA 57.393 30.769 0.00 0.00 38.85 1.98
3622 3752 8.076178 GGTATAATGCACTCGAAAATAGCAAAT 58.924 33.333 0.00 0.00 38.85 2.32
3623 3753 7.414436 GGTATAATGCACTCGAAAATAGCAAA 58.586 34.615 0.00 0.00 38.85 3.68
3624 3754 6.292649 CGGTATAATGCACTCGAAAATAGCAA 60.293 38.462 0.00 0.00 38.85 3.91
3625 3755 5.176774 CGGTATAATGCACTCGAAAATAGCA 59.823 40.000 0.00 0.00 39.79 3.49
3626 3756 5.404366 TCGGTATAATGCACTCGAAAATAGC 59.596 40.000 0.00 0.00 0.00 2.97
3627 3757 6.641314 AGTCGGTATAATGCACTCGAAAATAG 59.359 38.462 0.00 0.00 0.00 1.73
3628 3758 6.509656 AGTCGGTATAATGCACTCGAAAATA 58.490 36.000 0.00 0.00 0.00 1.40
3629 3759 5.357257 AGTCGGTATAATGCACTCGAAAAT 58.643 37.500 0.00 0.00 0.00 1.82
3630 3760 4.751060 AGTCGGTATAATGCACTCGAAAA 58.249 39.130 0.00 0.00 0.00 2.29
3631 3761 4.380841 AGTCGGTATAATGCACTCGAAA 57.619 40.909 0.00 0.00 0.00 3.46
3632 3762 5.239963 TCATAGTCGGTATAATGCACTCGAA 59.760 40.000 0.00 0.00 0.00 3.71
3633 3763 4.758165 TCATAGTCGGTATAATGCACTCGA 59.242 41.667 0.00 0.00 0.00 4.04
3634 3764 5.043189 TCATAGTCGGTATAATGCACTCG 57.957 43.478 0.00 0.00 0.00 4.18
3635 3765 6.973474 GGTATCATAGTCGGTATAATGCACTC 59.027 42.308 0.00 0.00 0.00 3.51
3636 3766 6.663953 AGGTATCATAGTCGGTATAATGCACT 59.336 38.462 0.00 0.00 0.00 4.40
3637 3767 6.864342 AGGTATCATAGTCGGTATAATGCAC 58.136 40.000 0.00 0.00 0.00 4.57
3638 3768 6.890268 AGAGGTATCATAGTCGGTATAATGCA 59.110 38.462 0.00 0.00 0.00 3.96
3639 3769 7.336161 AGAGGTATCATAGTCGGTATAATGC 57.664 40.000 0.00 0.00 0.00 3.56
3640 3770 9.616156 AGTAGAGGTATCATAGTCGGTATAATG 57.384 37.037 0.00 0.00 0.00 1.90
3644 3774 8.212312 CCATAGTAGAGGTATCATAGTCGGTAT 58.788 40.741 0.00 0.00 0.00 2.73
3645 3775 7.563020 CCATAGTAGAGGTATCATAGTCGGTA 58.437 42.308 0.00 0.00 0.00 4.02
3646 3776 6.416415 CCATAGTAGAGGTATCATAGTCGGT 58.584 44.000 0.00 0.00 0.00 4.69
3647 3777 5.297278 GCCATAGTAGAGGTATCATAGTCGG 59.703 48.000 0.00 0.00 0.00 4.79
3648 3778 5.297278 GGCCATAGTAGAGGTATCATAGTCG 59.703 48.000 0.00 0.00 0.00 4.18
3649 3779 6.188407 TGGCCATAGTAGAGGTATCATAGTC 58.812 44.000 0.00 0.00 0.00 2.59
3650 3780 6.153942 TGGCCATAGTAGAGGTATCATAGT 57.846 41.667 0.00 0.00 0.00 2.12
3651 3781 5.068460 GCTGGCCATAGTAGAGGTATCATAG 59.932 48.000 5.51 0.00 0.00 2.23
3652 3782 4.956700 GCTGGCCATAGTAGAGGTATCATA 59.043 45.833 5.51 0.00 0.00 2.15
3653 3783 3.772025 GCTGGCCATAGTAGAGGTATCAT 59.228 47.826 5.51 0.00 0.00 2.45
3654 3784 3.165875 GCTGGCCATAGTAGAGGTATCA 58.834 50.000 5.51 0.00 0.00 2.15
3655 3785 2.498078 GGCTGGCCATAGTAGAGGTATC 59.502 54.545 5.51 0.00 35.81 2.24
3656 3786 2.112691 AGGCTGGCCATAGTAGAGGTAT 59.887 50.000 5.51 0.00 38.92 2.73
3657 3787 1.503784 AGGCTGGCCATAGTAGAGGTA 59.496 52.381 5.51 0.00 38.92 3.08
3658 3788 0.266152 AGGCTGGCCATAGTAGAGGT 59.734 55.000 5.51 0.00 38.92 3.85
3659 3789 0.683973 CAGGCTGGCCATAGTAGAGG 59.316 60.000 5.51 0.00 38.92 3.69
3660 3790 1.709578 TCAGGCTGGCCATAGTAGAG 58.290 55.000 15.73 0.00 38.92 2.43
3661 3791 2.042464 CTTCAGGCTGGCCATAGTAGA 58.958 52.381 15.73 0.00 38.92 2.59
3662 3792 1.765314 ACTTCAGGCTGGCCATAGTAG 59.235 52.381 15.73 1.85 38.92 2.57
3663 3793 1.486310 CACTTCAGGCTGGCCATAGTA 59.514 52.381 15.73 0.00 38.92 1.82
3664 3794 0.254178 CACTTCAGGCTGGCCATAGT 59.746 55.000 15.73 10.23 38.92 2.12
3665 3795 0.543277 TCACTTCAGGCTGGCCATAG 59.457 55.000 15.73 9.65 38.92 2.23
3666 3796 0.991146 TTCACTTCAGGCTGGCCATA 59.009 50.000 15.73 0.00 38.92 2.74
3667 3797 0.610232 GTTCACTTCAGGCTGGCCAT 60.610 55.000 15.73 0.00 38.92 4.40
3668 3798 1.228245 GTTCACTTCAGGCTGGCCA 60.228 57.895 15.73 4.71 38.92 5.36
3669 3799 1.228245 TGTTCACTTCAGGCTGGCC 60.228 57.895 15.73 3.00 0.00 5.36
3670 3800 0.819259 TGTGTTCACTTCAGGCTGGC 60.819 55.000 15.73 0.00 0.00 4.85
3671 3801 1.808945 GATGTGTTCACTTCAGGCTGG 59.191 52.381 15.73 1.44 0.00 4.85
3672 3802 1.808945 GGATGTGTTCACTTCAGGCTG 59.191 52.381 8.58 8.58 0.00 4.85
3673 3803 1.701847 AGGATGTGTTCACTTCAGGCT 59.298 47.619 16.58 5.99 0.00 4.58
3674 3804 2.191128 AGGATGTGTTCACTTCAGGC 57.809 50.000 16.58 4.31 0.00 4.85
3675 3805 5.284079 CAAAAAGGATGTGTTCACTTCAGG 58.716 41.667 16.58 1.37 0.00 3.86
3681 3811 3.636764 ACTCCCAAAAAGGATGTGTTCAC 59.363 43.478 0.00 0.00 41.22 3.18
3717 3847 1.175654 ATCCGTGAATGCATGCACAA 58.824 45.000 32.31 21.91 34.78 3.33
3750 3880 1.086696 AGTTGTGTGTCTGTGTGCAC 58.913 50.000 10.75 10.75 36.26 4.57
3767 3897 1.337260 GGATTCGAGACACACAGCAGT 60.337 52.381 0.00 0.00 0.00 4.40
3867 4017 2.062971 ATCGGGCAATCATTCTGCTT 57.937 45.000 0.00 0.00 39.82 3.91
3887 4037 2.834549 AGAGGATCCAACTCGTCACATT 59.165 45.455 15.82 0.00 39.90 2.71
3991 4143 2.551887 ACGCACATTTATGTCTGCACAA 59.448 40.909 6.25 0.00 39.39 3.33
4072 4226 4.320935 GGTCAATCGAATCTCTAGCCTCTC 60.321 50.000 0.00 0.00 0.00 3.20
4088 4242 3.308866 CGACAACTATTTCCCGGTCAATC 59.691 47.826 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.