Multiple sequence alignment - TraesCS3D01G374500

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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 TraesCS3D01G374500 chr3D 100.000 3900 0 0 1 3900 488054383 488058282 0.000000e+00 7203
1 TraesCS3D01G374500 chr3B 94.951 2951 112 15 2 2942 650829667 650832590 0.000000e+00 4590
2 TraesCS3D01G374500 chr3B 91.549 284 20 4 3551 3831 650837763 650838045 4.730000e-104 388
3 TraesCS3D01G374500 chr3B 83.673 245 20 7 3005 3239 650832599 650832833 3.050000e-51 213
4 TraesCS3D01G374500 chr3B 82.840 169 24 4 3395 3562 773386398 773386234 3.140000e-31 147
5 TraesCS3D01G374500 chr3A 95.340 2468 87 12 897 3342 631613971 631616432 0.000000e+00 3895
6 TraesCS3D01G374500 chr3A 92.299 883 35 18 1 858 631613098 631613972 0.000000e+00 1223
7 TraesCS3D01G374500 chr3A 90.972 288 25 1 3551 3837 631616431 631616718 1.700000e-103 387
8 TraesCS3D01G374500 chr3A 87.736 106 11 2 3454 3559 34605258 34605361 5.290000e-24 122
9 TraesCS3D01G374500 chr2D 92.938 354 15 7 327 670 632562657 632563010 1.250000e-139 507
10 TraesCS3D01G374500 chr7B 88.315 368 19 7 327 670 648222996 648223363 1.680000e-113 420
11 TraesCS3D01G374500 chr7B 86.765 136 8 4 544 670 704165707 704165573 4.060000e-30 143
12 TraesCS3D01G374500 chr4B 90.431 209 20 0 3353 3561 601294467 601294259 3.840000e-70 276
13 TraesCS3D01G374500 chr4B 86.029 136 9 7 544 670 631973385 631973519 1.890000e-28 137
14 TraesCS3D01G374500 chr4D 75.139 539 111 18 1979 2510 468593002 468593524 8.430000e-57 231
15 TraesCS3D01G374500 chr4A 89.610 154 13 3 463 616 656046069 656045919 3.980000e-45 193
16 TraesCS3D01G374500 chr5D 87.349 166 21 0 3394 3559 513022611 513022446 1.430000e-44 191
17 TraesCS3D01G374500 chr1B 88.194 144 14 3 3417 3559 509568683 509568542 6.700000e-38 169
18 TraesCS3D01G374500 chr1B 86.765 136 8 4 544 670 554153635 554153501 4.060000e-30 143
19 TraesCS3D01G374500 chr5B 87.500 136 7 4 544 670 521347057 521346923 8.730000e-32 148
20 TraesCS3D01G374500 chr7A 84.615 143 18 2 3417 3559 240115761 240115623 5.250000e-29 139
21 TraesCS3D01G374500 chr5A 82.517 143 25 0 3416 3558 58470208 58470350 4.090000e-25 126
22 TraesCS3D01G374500 chr6B 90.000 90 9 0 3470 3559 364442416 364442327 2.460000e-22 117
23 TraesCS3D01G374500 chr7D 88.660 97 8 3 3467 3561 564574928 564574833 8.860000e-22 115


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 TraesCS3D01G374500 chr3D 488054383 488058282 3899 False 7203.0 7203 100.000000 1 3900 1 chr3D.!!$F1 3899
1 TraesCS3D01G374500 chr3B 650829667 650832833 3166 False 2401.5 4590 89.312000 2 3239 2 chr3B.!!$F2 3237
2 TraesCS3D01G374500 chr3A 631613098 631616718 3620 False 1835.0 3895 92.870333 1 3837 3 chr3A.!!$F2 3836
3 TraesCS3D01G374500 chr4D 468593002 468593524 522 False 231.0 231 75.139000 1979 2510 1 chr4D.!!$F1 531

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
914 940 0.04087 CGGATGAGATCGTCGACCAG 60.041 60.0 10.58 0.0 32.78 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2905 2991 1.299541 CATAGGTACAAGCAAGCGGG 58.7 55.0 0.0 0.0 0.0 6.13 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
34 35 4.949966 TTAGAGAGAGAGTAGTTGGGGT 57.050 45.455 0.00 0.00 0.00 4.95
71 73 3.122278 TGAACTAAAGATGTAACACGCGC 59.878 43.478 5.73 0.00 0.00 6.86
111 113 6.647895 ACGTCAAATAAACCGAACTATCTGTT 59.352 34.615 0.00 0.00 42.38 3.16
112 114 6.953743 CGTCAAATAAACCGAACTATCTGTTG 59.046 38.462 0.00 0.00 39.30 3.33
114 116 5.813080 AATAAACCGAACTATCTGTTGCC 57.187 39.130 0.00 0.00 39.30 4.52
115 117 2.851263 AACCGAACTATCTGTTGCCA 57.149 45.000 0.00 0.00 39.30 4.92
149 151 9.857656 ATCAATTAGGAGTCACAATCATACAAT 57.142 29.630 0.00 0.00 0.00 2.71
172 174 1.270465 TGATCGATGCCATGGTGCTAG 60.270 52.381 14.67 1.86 0.00 3.42
452 460 5.856156 TGACCAAGCAAATCAAATCATGTT 58.144 33.333 0.00 0.00 0.00 2.71
490 502 5.388944 CATCAAGACAAGCTAGCACTTTTC 58.611 41.667 18.83 6.14 0.00 2.29
491 503 4.450976 TCAAGACAAGCTAGCACTTTTCA 58.549 39.130 18.83 1.37 30.37 2.69
492 504 4.512944 TCAAGACAAGCTAGCACTTTTCAG 59.487 41.667 18.83 3.74 30.37 3.02
493 505 4.342862 AGACAAGCTAGCACTTTTCAGA 57.657 40.909 18.83 0.00 30.37 3.27
642 661 2.737830 GGCCAGGCCTATCGAGAC 59.262 66.667 24.99 0.00 46.69 3.36
701 720 0.674534 CCACGGCCTACCTATCACTC 59.325 60.000 0.00 0.00 0.00 3.51
702 721 1.693627 CACGGCCTACCTATCACTCT 58.306 55.000 0.00 0.00 0.00 3.24
821 846 0.387202 TGGCTTGAGAGATAGAGCGC 59.613 55.000 0.00 0.00 36.02 5.92
912 938 0.875728 ATCGGATGAGATCGTCGACC 59.124 55.000 10.58 0.00 32.78 4.79
913 939 0.463116 TCGGATGAGATCGTCGACCA 60.463 55.000 10.58 0.00 32.78 4.02
914 940 0.040870 CGGATGAGATCGTCGACCAG 60.041 60.000 10.58 0.00 32.78 4.00
970 996 0.324943 GTGGAGAACTAAGCAGGGCA 59.675 55.000 0.00 0.00 0.00 5.36
1018 1044 0.035176 GATGGCTCCTCATGCTCTCC 59.965 60.000 0.00 0.00 0.00 3.71
1192 1218 0.532417 GCAGAGAAGATCATGGCGCT 60.532 55.000 7.64 0.00 0.00 5.92
1195 1221 1.068895 AGAGAAGATCATGGCGCTGAG 59.931 52.381 7.64 0.00 0.00 3.35
1291 1320 0.249699 TGTCCGTCGTGCTCATGTTT 60.250 50.000 0.00 0.00 0.00 2.83
1349 1378 0.393944 ACTCCGTCATCGTCCAGCTA 60.394 55.000 0.00 0.00 35.01 3.32
1414 1443 2.737180 CAGTGGGACAGCGTCACT 59.263 61.111 11.28 5.28 41.80 3.41
1804 1836 1.673400 CATGTCCTCGTCGTCTCTGAT 59.327 52.381 0.00 0.00 0.00 2.90
2461 2541 4.118995 TCGTACAACGGCGGCGAT 62.119 61.111 38.93 25.17 42.81 4.58
2555 2641 2.678934 AACAGGGCCATGCTGCTG 60.679 61.111 19.26 10.22 0.00 4.41
2729 2815 1.811266 CACGACAGGATCAAGCCGG 60.811 63.158 0.00 0.00 0.00 6.13
2905 2991 1.299541 CACCCACCGCATGATTCTAC 58.700 55.000 0.00 0.00 0.00 2.59
2982 3069 4.963276 TTTCTAATCATTTCACAGCGGG 57.037 40.909 0.00 0.00 0.00 6.13
3017 3107 4.782019 ATTGCTTTAAAATCTGACGCCA 57.218 36.364 0.00 0.00 0.00 5.69
3090 3180 1.201429 TTGCTCCCAACCCCTCTCTC 61.201 60.000 0.00 0.00 0.00 3.20
3116 3209 2.680352 TGAGCACCCTCCTCGTCC 60.680 66.667 0.00 0.00 37.29 4.79
3225 3327 1.680651 CTCACCCTCAGAGCTCCGT 60.681 63.158 10.93 0.00 0.00 4.69
3279 3381 1.148310 ATGTCACTCGCTTTTCCACG 58.852 50.000 0.00 0.00 0.00 4.94
3338 3440 5.645624 ACGAACATCATCAAGTCTAGAGTG 58.354 41.667 0.00 0.00 0.00 3.51
3342 3444 5.728471 ACATCATCAAGTCTAGAGTGTTGG 58.272 41.667 0.00 0.00 0.00 3.77
3343 3445 4.193826 TCATCAAGTCTAGAGTGTTGGC 57.806 45.455 0.00 0.00 0.00 4.52
3346 3448 2.072298 CAAGTCTAGAGTGTTGGCTGC 58.928 52.381 0.00 0.00 0.00 5.25
3347 3449 0.610687 AGTCTAGAGTGTTGGCTGCC 59.389 55.000 12.87 12.87 0.00 4.85
3348 3450 0.391793 GTCTAGAGTGTTGGCTGCCC 60.392 60.000 17.53 1.56 0.00 5.36
3349 3451 0.545309 TCTAGAGTGTTGGCTGCCCT 60.545 55.000 17.53 5.44 0.00 5.19
3350 3452 0.326264 CTAGAGTGTTGGCTGCCCTT 59.674 55.000 17.53 0.00 0.00 3.95
3351 3453 1.555075 CTAGAGTGTTGGCTGCCCTTA 59.445 52.381 17.53 0.00 0.00 2.69
3352 3454 0.771127 AGAGTGTTGGCTGCCCTTAA 59.229 50.000 17.53 0.22 0.00 1.85
3353 3455 1.144913 AGAGTGTTGGCTGCCCTTAAA 59.855 47.619 17.53 0.00 0.00 1.52
3354 3456 2.171003 GAGTGTTGGCTGCCCTTAAAT 58.829 47.619 17.53 0.00 0.00 1.40
3355 3457 2.562738 GAGTGTTGGCTGCCCTTAAATT 59.437 45.455 17.53 0.00 0.00 1.82
3356 3458 2.562738 AGTGTTGGCTGCCCTTAAATTC 59.437 45.455 17.53 1.63 0.00 2.17
3357 3459 1.543802 TGTTGGCTGCCCTTAAATTCG 59.456 47.619 17.53 0.00 0.00 3.34
3358 3460 1.544246 GTTGGCTGCCCTTAAATTCGT 59.456 47.619 17.53 0.00 0.00 3.85
3359 3461 1.173043 TGGCTGCCCTTAAATTCGTG 58.827 50.000 17.53 0.00 0.00 4.35
3360 3462 0.179137 GGCTGCCCTTAAATTCGTGC 60.179 55.000 7.66 0.00 0.00 5.34
3361 3463 0.525761 GCTGCCCTTAAATTCGTGCA 59.474 50.000 0.00 0.00 0.00 4.57
3362 3464 1.732405 GCTGCCCTTAAATTCGTGCAC 60.732 52.381 6.82 6.82 0.00 4.57
3363 3465 1.539388 CTGCCCTTAAATTCGTGCACA 59.461 47.619 18.64 0.00 0.00 4.57
3364 3466 1.268352 TGCCCTTAAATTCGTGCACAC 59.732 47.619 18.64 0.00 0.00 3.82
3365 3467 1.268352 GCCCTTAAATTCGTGCACACA 59.732 47.619 18.64 1.99 0.00 3.72
3366 3468 2.094752 GCCCTTAAATTCGTGCACACAT 60.095 45.455 18.64 4.68 0.00 3.21
3367 3469 3.500982 CCCTTAAATTCGTGCACACATG 58.499 45.455 18.64 0.00 0.00 3.21
3377 3479 1.430632 GCACACATGCGATGGAAGG 59.569 57.895 0.00 0.00 43.33 3.46
3378 3480 1.996786 GCACACATGCGATGGAAGGG 61.997 60.000 0.00 0.00 43.33 3.95
3379 3481 0.677731 CACACATGCGATGGAAGGGT 60.678 55.000 0.00 0.00 33.60 4.34
3380 3482 0.677731 ACACATGCGATGGAAGGGTG 60.678 55.000 0.00 0.00 33.60 4.61
3381 3483 0.677731 CACATGCGATGGAAGGGTGT 60.678 55.000 0.00 0.00 33.60 4.16
3382 3484 0.677731 ACATGCGATGGAAGGGTGTG 60.678 55.000 0.00 0.00 33.60 3.82
3383 3485 1.077501 ATGCGATGGAAGGGTGTGG 60.078 57.895 0.00 0.00 0.00 4.17
3384 3486 2.438434 GCGATGGAAGGGTGTGGG 60.438 66.667 0.00 0.00 0.00 4.61
3385 3487 2.966732 GCGATGGAAGGGTGTGGGA 61.967 63.158 0.00 0.00 0.00 4.37
3386 3488 1.915228 CGATGGAAGGGTGTGGGAT 59.085 57.895 0.00 0.00 0.00 3.85
3387 3489 0.464373 CGATGGAAGGGTGTGGGATG 60.464 60.000 0.00 0.00 0.00 3.51
3388 3490 0.106519 GATGGAAGGGTGTGGGATGG 60.107 60.000 0.00 0.00 0.00 3.51
3389 3491 2.043953 GGAAGGGTGTGGGATGGC 60.044 66.667 0.00 0.00 0.00 4.40
3390 3492 2.763215 GAAGGGTGTGGGATGGCA 59.237 61.111 0.00 0.00 0.00 4.92
3391 3493 1.379044 GAAGGGTGTGGGATGGCAG 60.379 63.158 0.00 0.00 0.00 4.85
3392 3494 3.590466 AAGGGTGTGGGATGGCAGC 62.590 63.158 0.00 0.00 0.00 5.25
3395 3497 4.722700 GTGTGGGATGGCAGCGGT 62.723 66.667 0.00 0.00 0.00 5.68
3396 3498 4.408821 TGTGGGATGGCAGCGGTC 62.409 66.667 0.00 0.00 0.00 4.79
3399 3501 4.554036 GGGATGGCAGCGGTCCTC 62.554 72.222 12.89 2.36 32.55 3.71
3400 3502 4.899239 GGATGGCAGCGGTCCTCG 62.899 72.222 7.31 0.00 42.76 4.63
3401 3503 3.838271 GATGGCAGCGGTCCTCGA 61.838 66.667 0.00 0.00 42.43 4.04
3402 3504 3.157217 GATGGCAGCGGTCCTCGAT 62.157 63.158 0.00 0.00 42.43 3.59
3403 3505 3.157217 ATGGCAGCGGTCCTCGATC 62.157 63.158 0.00 0.00 42.43 3.69
3404 3506 4.593864 GGCAGCGGTCCTCGATCC 62.594 72.222 0.00 0.00 42.43 3.36
3409 3511 4.904466 CGGTCCTCGATCCGTTTT 57.096 55.556 13.25 0.00 42.43 2.43
3410 3512 2.369870 CGGTCCTCGATCCGTTTTG 58.630 57.895 13.25 0.00 42.43 2.44
3411 3513 0.389426 CGGTCCTCGATCCGTTTTGT 60.389 55.000 13.25 0.00 42.43 2.83
3412 3514 1.076332 GGTCCTCGATCCGTTTTGTG 58.924 55.000 0.00 0.00 0.00 3.33
3413 3515 0.442699 GTCCTCGATCCGTTTTGTGC 59.557 55.000 0.00 0.00 0.00 4.57
3414 3516 1.011968 TCCTCGATCCGTTTTGTGCG 61.012 55.000 0.00 0.00 0.00 5.34
3415 3517 1.225745 CTCGATCCGTTTTGTGCGC 60.226 57.895 0.00 0.00 0.00 6.09
3416 3518 1.626654 CTCGATCCGTTTTGTGCGCT 61.627 55.000 9.73 0.00 0.00 5.92
3417 3519 1.509787 CGATCCGTTTTGTGCGCTG 60.510 57.895 9.73 0.00 0.00 5.18
3418 3520 1.154225 GATCCGTTTTGTGCGCTGG 60.154 57.895 9.73 0.00 0.00 4.85
3419 3521 1.852067 GATCCGTTTTGTGCGCTGGT 61.852 55.000 9.73 0.00 0.00 4.00
3420 3522 0.604243 ATCCGTTTTGTGCGCTGGTA 60.604 50.000 9.73 0.00 0.00 3.25
3421 3523 0.814410 TCCGTTTTGTGCGCTGGTAA 60.814 50.000 9.73 0.00 0.00 2.85
3422 3524 0.659123 CCGTTTTGTGCGCTGGTAAC 60.659 55.000 9.73 7.42 0.00 2.50
3434 3536 2.534038 TGGTAACAGCAGGGTGACA 58.466 52.632 5.37 0.00 46.17 3.58
3435 3537 1.064003 TGGTAACAGCAGGGTGACAT 58.936 50.000 5.37 0.00 46.17 3.06
3436 3538 1.271325 TGGTAACAGCAGGGTGACATG 60.271 52.381 5.37 0.00 46.17 3.21
3437 3539 1.453155 GTAACAGCAGGGTGACATGG 58.547 55.000 5.37 0.00 43.79 3.66
3438 3540 0.322456 TAACAGCAGGGTGACATGGC 60.322 55.000 5.37 0.00 43.79 4.40
3439 3541 2.034532 CAGCAGGGTGACATGGCA 59.965 61.111 0.00 0.00 43.79 4.92
3440 3542 1.379443 CAGCAGGGTGACATGGCAT 60.379 57.895 3.50 0.00 43.79 4.40
3441 3543 1.379443 AGCAGGGTGACATGGCATG 60.379 57.895 25.31 25.31 43.79 4.06
3442 3544 1.378911 GCAGGGTGACATGGCATGA 60.379 57.895 32.74 9.75 43.79 3.07
3443 3545 0.754217 GCAGGGTGACATGGCATGAT 60.754 55.000 32.74 17.23 43.79 2.45
3444 3546 1.029681 CAGGGTGACATGGCATGATG 58.970 55.000 32.74 16.13 38.79 3.07
3445 3547 0.754217 AGGGTGACATGGCATGATGC 60.754 55.000 32.74 20.36 44.08 3.91
3460 3562 6.564709 GCATGATGCATGTTAGGAATTAGA 57.435 37.500 13.36 0.00 44.26 2.10
3461 3563 7.154435 GCATGATGCATGTTAGGAATTAGAT 57.846 36.000 13.36 0.00 44.26 1.98
3462 3564 7.600065 GCATGATGCATGTTAGGAATTAGATT 58.400 34.615 13.36 0.00 44.26 2.40
3463 3565 8.086522 GCATGATGCATGTTAGGAATTAGATTT 58.913 33.333 13.36 0.00 44.26 2.17
3477 3579 9.950496 AGGAATTAGATTTATATGAACGCTGAT 57.050 29.630 0.00 0.00 0.00 2.90
3478 3580 9.979270 GGAATTAGATTTATATGAACGCTGATG 57.021 33.333 0.00 0.00 0.00 3.07
3481 3583 6.791887 AGATTTATATGAACGCTGATGTGG 57.208 37.500 0.00 0.00 0.00 4.17
3482 3584 4.811555 TTTATATGAACGCTGATGTGGC 57.188 40.909 0.00 0.00 0.00 5.01
3483 3585 2.330440 ATATGAACGCTGATGTGGCA 57.670 45.000 0.00 0.00 0.00 4.92
3484 3586 2.330440 TATGAACGCTGATGTGGCAT 57.670 45.000 0.00 0.00 0.00 4.40
3485 3587 0.736636 ATGAACGCTGATGTGGCATG 59.263 50.000 0.00 0.00 0.00 4.06
3486 3588 0.321475 TGAACGCTGATGTGGCATGA 60.321 50.000 0.00 0.00 0.00 3.07
3487 3589 0.804364 GAACGCTGATGTGGCATGAA 59.196 50.000 0.00 0.00 0.00 2.57
3488 3590 0.806868 AACGCTGATGTGGCATGAAG 59.193 50.000 0.00 0.00 0.00 3.02
3489 3591 1.063649 CGCTGATGTGGCATGAAGC 59.936 57.895 0.00 0.00 44.65 3.86
3490 3592 1.374343 CGCTGATGTGGCATGAAGCT 61.374 55.000 0.00 0.00 44.79 3.74
3491 3593 0.100682 GCTGATGTGGCATGAAGCTG 59.899 55.000 0.00 0.00 44.79 4.24
3492 3594 0.738975 CTGATGTGGCATGAAGCTGG 59.261 55.000 0.00 0.00 44.79 4.85
3493 3595 0.038599 TGATGTGGCATGAAGCTGGT 59.961 50.000 0.00 0.00 44.79 4.00
3494 3596 0.454600 GATGTGGCATGAAGCTGGTG 59.545 55.000 0.00 0.00 44.79 4.17
3495 3597 0.251474 ATGTGGCATGAAGCTGGTGT 60.251 50.000 0.00 0.00 44.79 4.16
3496 3598 1.174078 TGTGGCATGAAGCTGGTGTG 61.174 55.000 0.00 0.00 44.79 3.82
3497 3599 1.604308 TGGCATGAAGCTGGTGTGG 60.604 57.895 0.00 0.00 44.79 4.17
3498 3600 1.303561 GGCATGAAGCTGGTGTGGA 60.304 57.895 0.00 0.00 44.79 4.02
3499 3601 0.682209 GGCATGAAGCTGGTGTGGAT 60.682 55.000 0.00 0.00 44.79 3.41
3500 3602 1.408683 GGCATGAAGCTGGTGTGGATA 60.409 52.381 0.00 0.00 44.79 2.59
3501 3603 1.945394 GCATGAAGCTGGTGTGGATAG 59.055 52.381 0.00 0.00 41.15 2.08
3502 3604 2.681976 GCATGAAGCTGGTGTGGATAGT 60.682 50.000 0.00 0.00 41.15 2.12
3503 3605 2.768253 TGAAGCTGGTGTGGATAGTG 57.232 50.000 0.00 0.00 0.00 2.74
3504 3606 1.977854 TGAAGCTGGTGTGGATAGTGT 59.022 47.619 0.00 0.00 0.00 3.55
3505 3607 2.289631 TGAAGCTGGTGTGGATAGTGTG 60.290 50.000 0.00 0.00 0.00 3.82
3506 3608 0.036010 AGCTGGTGTGGATAGTGTGC 60.036 55.000 0.00 0.00 0.00 4.57
3507 3609 0.321564 GCTGGTGTGGATAGTGTGCA 60.322 55.000 0.00 0.00 0.00 4.57
3508 3610 1.679944 GCTGGTGTGGATAGTGTGCAT 60.680 52.381 0.00 0.00 0.00 3.96
3509 3611 2.011947 CTGGTGTGGATAGTGTGCATG 58.988 52.381 0.00 0.00 0.00 4.06
3510 3612 1.350684 TGGTGTGGATAGTGTGCATGT 59.649 47.619 0.00 0.00 0.00 3.21
3511 3613 2.224744 TGGTGTGGATAGTGTGCATGTT 60.225 45.455 0.00 0.00 0.00 2.71
3512 3614 2.162208 GGTGTGGATAGTGTGCATGTTG 59.838 50.000 0.00 0.00 0.00 3.33
3513 3615 3.073678 GTGTGGATAGTGTGCATGTTGA 58.926 45.455 0.00 0.00 0.00 3.18
3514 3616 3.125829 GTGTGGATAGTGTGCATGTTGAG 59.874 47.826 0.00 0.00 0.00 3.02
3515 3617 3.007831 TGTGGATAGTGTGCATGTTGAGA 59.992 43.478 0.00 0.00 0.00 3.27
3516 3618 3.620374 GTGGATAGTGTGCATGTTGAGAG 59.380 47.826 0.00 0.00 0.00 3.20
3517 3619 3.515104 TGGATAGTGTGCATGTTGAGAGA 59.485 43.478 0.00 0.00 0.00 3.10
3518 3620 4.020307 TGGATAGTGTGCATGTTGAGAGAA 60.020 41.667 0.00 0.00 0.00 2.87
3519 3621 5.121811 GGATAGTGTGCATGTTGAGAGAAT 58.878 41.667 0.00 0.00 0.00 2.40
3520 3622 5.587844 GGATAGTGTGCATGTTGAGAGAATT 59.412 40.000 0.00 0.00 0.00 2.17
3521 3623 4.761235 AGTGTGCATGTTGAGAGAATTG 57.239 40.909 0.00 0.00 0.00 2.32
3522 3624 3.504906 AGTGTGCATGTTGAGAGAATTGG 59.495 43.478 0.00 0.00 0.00 3.16
3523 3625 3.254166 GTGTGCATGTTGAGAGAATTGGT 59.746 43.478 0.00 0.00 0.00 3.67
3524 3626 3.890756 TGTGCATGTTGAGAGAATTGGTT 59.109 39.130 0.00 0.00 0.00 3.67
3525 3627 5.048782 GTGTGCATGTTGAGAGAATTGGTTA 60.049 40.000 0.00 0.00 0.00 2.85
3526 3628 5.711506 TGTGCATGTTGAGAGAATTGGTTAT 59.288 36.000 0.00 0.00 0.00 1.89
3527 3629 6.883756 TGTGCATGTTGAGAGAATTGGTTATA 59.116 34.615 0.00 0.00 0.00 0.98
3528 3630 7.066163 TGTGCATGTTGAGAGAATTGGTTATAG 59.934 37.037 0.00 0.00 0.00 1.31
3529 3631 7.066284 GTGCATGTTGAGAGAATTGGTTATAGT 59.934 37.037 0.00 0.00 0.00 2.12
3530 3632 7.066163 TGCATGTTGAGAGAATTGGTTATAGTG 59.934 37.037 0.00 0.00 0.00 2.74
3531 3633 7.467811 GCATGTTGAGAGAATTGGTTATAGTGG 60.468 40.741 0.00 0.00 0.00 4.00
3532 3634 6.414732 TGTTGAGAGAATTGGTTATAGTGGG 58.585 40.000 0.00 0.00 0.00 4.61
3533 3635 5.630415 TGAGAGAATTGGTTATAGTGGGG 57.370 43.478 0.00 0.00 0.00 4.96
3534 3636 5.285401 TGAGAGAATTGGTTATAGTGGGGA 58.715 41.667 0.00 0.00 0.00 4.81
3535 3637 5.366768 TGAGAGAATTGGTTATAGTGGGGAG 59.633 44.000 0.00 0.00 0.00 4.30
3536 3638 4.103311 AGAGAATTGGTTATAGTGGGGAGC 59.897 45.833 0.00 0.00 0.00 4.70
3537 3639 3.785887 AGAATTGGTTATAGTGGGGAGCA 59.214 43.478 0.00 0.00 0.00 4.26
3538 3640 4.229582 AGAATTGGTTATAGTGGGGAGCAA 59.770 41.667 0.00 0.00 34.51 3.91
3539 3641 3.359695 TTGGTTATAGTGGGGAGCAAC 57.640 47.619 0.00 0.00 0.00 4.17
3540 3642 2.557869 TGGTTATAGTGGGGAGCAACT 58.442 47.619 0.00 0.00 0.00 3.16
3541 3643 2.916934 TGGTTATAGTGGGGAGCAACTT 59.083 45.455 0.00 0.00 0.00 2.66
3542 3644 3.054655 TGGTTATAGTGGGGAGCAACTTC 60.055 47.826 0.00 0.00 0.00 3.01
3543 3645 3.200165 GGTTATAGTGGGGAGCAACTTCT 59.800 47.826 0.00 0.00 0.00 2.85
3544 3646 4.324331 GGTTATAGTGGGGAGCAACTTCTT 60.324 45.833 0.00 0.00 0.00 2.52
3545 3647 5.104652 GGTTATAGTGGGGAGCAACTTCTTA 60.105 44.000 0.00 0.00 0.00 2.10
3546 3648 6.412214 GTTATAGTGGGGAGCAACTTCTTAA 58.588 40.000 0.00 0.00 0.00 1.85
3547 3649 3.425162 AGTGGGGAGCAACTTCTTAAG 57.575 47.619 0.00 0.00 0.00 1.85
3548 3650 2.979678 AGTGGGGAGCAACTTCTTAAGA 59.020 45.455 0.00 0.00 0.00 2.10
3549 3651 3.008485 AGTGGGGAGCAACTTCTTAAGAG 59.992 47.826 5.12 3.14 0.00 2.85
3550 3652 2.979678 TGGGGAGCAACTTCTTAAGAGT 59.020 45.455 5.12 3.76 0.00 3.24
3551 3653 3.244561 TGGGGAGCAACTTCTTAAGAGTG 60.245 47.826 5.12 6.86 0.00 3.51
3552 3654 3.244596 GGGGAGCAACTTCTTAAGAGTGT 60.245 47.826 5.12 6.35 0.00 3.55
3553 3655 4.020485 GGGGAGCAACTTCTTAAGAGTGTA 60.020 45.833 5.12 0.00 0.00 2.90
3554 3656 5.512576 GGGGAGCAACTTCTTAAGAGTGTAA 60.513 44.000 5.12 0.00 0.00 2.41
3555 3657 5.639931 GGGAGCAACTTCTTAAGAGTGTAAG 59.360 44.000 5.12 2.52 33.16 2.34
3580 3682 8.512956 AGATATGACTAAATGATGAAATGCAGC 58.487 33.333 0.00 0.00 0.00 5.25
3590 3692 4.020928 TGATGAAATGCAGCAACCTTGATT 60.021 37.500 0.00 0.00 40.49 2.57
3617 3719 8.954950 AGACAATTACTCATCAGTTATCTTGG 57.045 34.615 0.00 0.00 33.62 3.61
3650 3752 2.231235 CACCACCTTAAAGCCAATGGTC 59.769 50.000 0.00 0.00 38.38 4.02
3658 3760 8.157476 CACCTTAAAGCCAATGGTCTATATAGT 58.843 37.037 9.58 0.00 0.00 2.12
3685 3787 3.050089 ATGGCAAAACCCATGACGT 57.950 47.368 0.00 0.00 43.80 4.34
3691 3793 3.192633 GGCAAAACCCATGACGTTTATCT 59.807 43.478 10.21 0.00 33.17 1.98
3720 3822 4.574759 CGTAATACGGCTTTGAATGTGAC 58.425 43.478 4.68 0.00 38.08 3.67
3753 3855 9.495572 CTTAGTTGGAGGATACCATAAAAGATC 57.504 37.037 0.00 0.00 39.82 2.75
3756 3858 6.346477 TGGAGGATACCATAAAAGATCGAG 57.654 41.667 0.00 0.00 34.77 4.04
3757 3859 5.172205 GGAGGATACCATAAAAGATCGAGC 58.828 45.833 0.00 0.00 37.17 5.03
3772 3874 2.489971 TCGAGCAAACCAACGAGATTT 58.510 42.857 0.00 0.00 0.00 2.17
3804 3906 2.904866 GCCTCCAACGCAACCACA 60.905 61.111 0.00 0.00 0.00 4.17
3809 3911 2.631428 CAACGCAACCACAGGTCG 59.369 61.111 0.00 0.00 33.12 4.79
3833 3935 6.347644 CGTGAGACTGCTGAATTATCAACAAA 60.348 38.462 0.00 0.00 31.60 2.83
3881 3983 8.925161 AAAAACAGTTTCAATCGATTCAGAAA 57.075 26.923 15.78 15.78 0.00 2.52
3882 3984 7.914537 AAACAGTTTCAATCGATTCAGAAAC 57.085 32.000 29.12 29.12 46.15 2.78
3888 3990 8.097514 GTTTCAATCGATTCAGAAACTAATGC 57.902 34.615 29.06 14.13 43.81 3.56
3889 3991 7.615582 TTCAATCGATTCAGAAACTAATGCT 57.384 32.000 7.92 0.00 0.00 3.79
3890 3992 7.615582 TCAATCGATTCAGAAACTAATGCTT 57.384 32.000 7.92 0.00 0.00 3.91
3891 3993 7.466805 TCAATCGATTCAGAAACTAATGCTTG 58.533 34.615 7.92 0.00 0.00 4.01
3892 3994 5.801350 TCGATTCAGAAACTAATGCTTGG 57.199 39.130 0.00 0.00 0.00 3.61
3893 3995 5.487433 TCGATTCAGAAACTAATGCTTGGA 58.513 37.500 0.00 0.00 0.00 3.53
3894 3996 5.582269 TCGATTCAGAAACTAATGCTTGGAG 59.418 40.000 0.00 0.00 0.00 3.86
3895 3997 5.573337 ATTCAGAAACTAATGCTTGGAGC 57.427 39.130 0.00 0.00 42.82 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 5.202004 TCAATACCCCAACTACTCTCTCTC 58.798 45.833 0.00 0.00 0.00 3.20
32 33 7.681939 TTAGTTCACATCCAACTTCAATACC 57.318 36.000 0.00 0.00 35.63 2.73
34 35 9.739276 ATCTTTAGTTCACATCCAACTTCAATA 57.261 29.630 0.00 0.00 35.63 1.90
71 73 2.880879 CGTGGATCGGTGACTGCG 60.881 66.667 0.00 0.00 35.71 5.18
111 113 4.650734 TCCTAATTGATTATCGCATGGCA 58.349 39.130 0.00 0.00 0.00 4.92
112 114 4.697352 ACTCCTAATTGATTATCGCATGGC 59.303 41.667 0.00 0.00 0.00 4.40
114 116 6.424812 TGTGACTCCTAATTGATTATCGCATG 59.575 38.462 0.00 0.00 0.00 4.06
115 117 6.524734 TGTGACTCCTAATTGATTATCGCAT 58.475 36.000 0.00 0.00 0.00 4.73
149 151 2.153645 GCACCATGGCATCGATCATAA 58.846 47.619 13.04 0.00 0.00 1.90
172 174 0.591170 CTCGCCTGTCTAGCTAGCTC 59.409 60.000 23.26 7.84 0.00 4.09
188 190 2.094906 TCGTATTGTTCACCTCACCTCG 60.095 50.000 0.00 0.00 0.00 4.63
530 544 2.635915 TCCAAGTTCTTCTCCGGCTTAA 59.364 45.455 0.00 0.00 0.00 1.85
539 558 5.799213 ACATCGATCTTTCCAAGTTCTTCT 58.201 37.500 0.00 0.00 0.00 2.85
542 561 6.702329 ACTAACATCGATCTTTCCAAGTTCT 58.298 36.000 0.00 0.00 0.00 3.01
639 658 5.144100 AGATTAATCCTGACCTCGATGTCT 58.856 41.667 19.56 4.03 36.21 3.41
642 661 4.281941 TGGAGATTAATCCTGACCTCGATG 59.718 45.833 11.92 0.00 40.29 3.84
701 720 8.562892 GGAGGTGATTAATCATGTGATTACAAG 58.437 37.037 20.65 0.00 44.13 3.16
702 721 8.052141 TGGAGGTGATTAATCATGTGATTACAA 58.948 33.333 20.65 4.63 44.13 2.41
829 854 1.950216 GCTGGGAATGGTTAAGCTAGC 59.050 52.381 6.62 6.62 0.00 3.42
830 855 2.092429 TGGCTGGGAATGGTTAAGCTAG 60.092 50.000 6.19 0.00 34.29 3.42
831 856 1.919654 TGGCTGGGAATGGTTAAGCTA 59.080 47.619 6.19 0.00 34.29 3.32
832 857 0.704076 TGGCTGGGAATGGTTAAGCT 59.296 50.000 6.19 0.00 34.29 3.74
970 996 3.740128 GATCACTCGGCCCGTGCAT 62.740 63.158 13.57 8.89 40.13 3.96
1291 1320 0.473694 TTCTGGTCTTGAGGAGGGCA 60.474 55.000 0.00 0.00 0.00 5.36
1398 1427 2.737180 CAGTGACGCTGTCCCACT 59.263 61.111 7.89 0.00 41.35 4.00
1804 1836 2.451493 TTGGGGAGTGGGAGGCAA 60.451 61.111 0.00 0.00 0.00 4.52
2065 2097 2.997315 CTGGTGGAGCCCGACTGA 60.997 66.667 0.00 0.00 36.04 3.41
2165 2236 4.856801 GATGCGGCCGTCCATGGT 62.857 66.667 28.70 1.61 0.00 3.55
2305 2376 3.576648 GTCGAAGAGGAAGTCGATGTTT 58.423 45.455 0.00 0.00 46.91 2.83
2461 2541 2.362242 CTCGTTGAGGAACCCCTGA 58.638 57.895 0.00 0.00 44.53 3.86
2717 2803 2.770048 CTCCCCCGGCTTGATCCT 60.770 66.667 0.00 0.00 0.00 3.24
2743 2829 2.740826 GGCAACGCGCAGAACCTA 60.741 61.111 5.73 0.00 45.17 3.08
2905 2991 1.299541 CATAGGTACAAGCAAGCGGG 58.700 55.000 0.00 0.00 0.00 6.13
3017 3107 2.943033 CCAACGGCTAGGAAAATCGATT 59.057 45.455 4.39 4.39 0.00 3.34
3067 3157 2.361737 GGGGTTGGGAGCAAGAGC 60.362 66.667 0.00 0.00 42.56 4.09
3073 3163 2.371259 GGAGAGAGGGGTTGGGAGC 61.371 68.421 0.00 0.00 0.00 4.70
3113 3206 3.066233 GCGTCCGGAAGAGGAGGAC 62.066 68.421 22.33 3.93 46.06 3.85
3116 3209 2.046864 TGAGCGTCCGGAAGAGGAG 61.047 63.158 22.33 2.89 41.68 3.69
3195 3297 6.995091 GCTCTGAGGGTGAGACAAATATAATT 59.005 38.462 6.83 0.00 33.68 1.40
3199 3301 4.036518 AGCTCTGAGGGTGAGACAAATAT 58.963 43.478 6.83 0.00 33.68 1.28
3236 3338 3.067833 GTCGGTTTTCTGGGAGAAGAAG 58.932 50.000 0.00 0.00 37.48 2.85
3237 3339 2.704065 AGTCGGTTTTCTGGGAGAAGAA 59.296 45.455 0.00 0.00 35.37 2.52
3238 3340 2.326428 AGTCGGTTTTCTGGGAGAAGA 58.674 47.619 0.00 0.00 35.37 2.87
3279 3381 8.889849 ATGTGTATTTGTTATTTGTAAGTCGC 57.110 30.769 0.00 0.00 0.00 5.19
3330 3432 0.545309 AGGGCAGCCAACACTCTAGA 60.545 55.000 15.19 0.00 0.00 2.43
3338 3440 1.544246 ACGAATTTAAGGGCAGCCAAC 59.456 47.619 15.19 0.00 0.00 3.77
3342 3444 0.525761 TGCACGAATTTAAGGGCAGC 59.474 50.000 2.89 0.00 42.46 5.25
3346 3448 3.500982 CATGTGTGCACGAATTTAAGGG 58.499 45.455 13.13 0.00 0.00 3.95
3360 3462 0.677731 ACCCTTCCATCGCATGTGTG 60.678 55.000 6.09 4.20 0.00 3.82
3361 3463 0.677731 CACCCTTCCATCGCATGTGT 60.678 55.000 6.09 0.00 0.00 3.72
3362 3464 0.677731 ACACCCTTCCATCGCATGTG 60.678 55.000 0.00 0.00 0.00 3.21
3363 3465 0.677731 CACACCCTTCCATCGCATGT 60.678 55.000 0.00 0.00 0.00 3.21
3364 3466 1.378882 CCACACCCTTCCATCGCATG 61.379 60.000 0.00 0.00 0.00 4.06
3365 3467 1.077501 CCACACCCTTCCATCGCAT 60.078 57.895 0.00 0.00 0.00 4.73
3366 3468 2.350895 CCACACCCTTCCATCGCA 59.649 61.111 0.00 0.00 0.00 5.10
3367 3469 2.270874 ATCCCACACCCTTCCATCGC 62.271 60.000 0.00 0.00 0.00 4.58
3368 3470 0.464373 CATCCCACACCCTTCCATCG 60.464 60.000 0.00 0.00 0.00 3.84
3369 3471 0.106519 CCATCCCACACCCTTCCATC 60.107 60.000 0.00 0.00 0.00 3.51
3370 3472 2.010067 CCATCCCACACCCTTCCAT 58.990 57.895 0.00 0.00 0.00 3.41
3371 3473 2.917897 GCCATCCCACACCCTTCCA 61.918 63.158 0.00 0.00 0.00 3.53
3372 3474 2.043953 GCCATCCCACACCCTTCC 60.044 66.667 0.00 0.00 0.00 3.46
3373 3475 1.379044 CTGCCATCCCACACCCTTC 60.379 63.158 0.00 0.00 0.00 3.46
3374 3476 2.765969 CTGCCATCCCACACCCTT 59.234 61.111 0.00 0.00 0.00 3.95
3375 3477 4.052518 GCTGCCATCCCACACCCT 62.053 66.667 0.00 0.00 0.00 4.34
3378 3480 4.722700 ACCGCTGCCATCCCACAC 62.723 66.667 0.00 0.00 0.00 3.82
3379 3481 4.408821 GACCGCTGCCATCCCACA 62.409 66.667 0.00 0.00 0.00 4.17
3382 3484 4.554036 GAGGACCGCTGCCATCCC 62.554 72.222 12.02 0.93 32.47 3.85
3383 3485 4.899239 CGAGGACCGCTGCCATCC 62.899 72.222 8.43 8.43 0.00 3.51
3384 3486 3.157217 ATCGAGGACCGCTGCCATC 62.157 63.158 0.00 0.00 38.37 3.51
3385 3487 3.157217 GATCGAGGACCGCTGCCAT 62.157 63.158 0.00 0.00 38.37 4.40
3386 3488 3.838271 GATCGAGGACCGCTGCCA 61.838 66.667 0.00 0.00 38.37 4.92
3387 3489 4.593864 GGATCGAGGACCGCTGCC 62.594 72.222 0.00 0.00 38.37 4.85
3388 3490 4.933064 CGGATCGAGGACCGCTGC 62.933 72.222 13.69 0.00 42.55 5.25
3393 3495 1.076332 CACAAAACGGATCGAGGACC 58.924 55.000 0.00 0.00 0.00 4.46
3394 3496 0.442699 GCACAAAACGGATCGAGGAC 59.557 55.000 0.00 0.00 0.00 3.85
3395 3497 1.011968 CGCACAAAACGGATCGAGGA 61.012 55.000 0.00 0.00 0.00 3.71
3396 3498 1.419922 CGCACAAAACGGATCGAGG 59.580 57.895 0.00 0.00 0.00 4.63
3397 3499 1.225745 GCGCACAAAACGGATCGAG 60.226 57.895 0.30 0.00 0.00 4.04
3398 3500 1.666553 AGCGCACAAAACGGATCGA 60.667 52.632 11.47 0.00 0.00 3.59
3399 3501 1.509787 CAGCGCACAAAACGGATCG 60.510 57.895 11.47 0.00 0.00 3.69
3400 3502 1.154225 CCAGCGCACAAAACGGATC 60.154 57.895 11.47 0.00 0.00 3.36
3401 3503 0.604243 TACCAGCGCACAAAACGGAT 60.604 50.000 11.47 0.00 0.00 4.18
3402 3504 0.814410 TTACCAGCGCACAAAACGGA 60.814 50.000 11.47 0.00 0.00 4.69
3403 3505 0.659123 GTTACCAGCGCACAAAACGG 60.659 55.000 11.47 0.03 0.00 4.44
3404 3506 0.028242 TGTTACCAGCGCACAAAACG 59.972 50.000 11.47 0.00 0.00 3.60
3405 3507 1.753956 CTGTTACCAGCGCACAAAAC 58.246 50.000 11.47 9.43 0.00 2.43
3415 3517 0.396435 TGTCACCCTGCTGTTACCAG 59.604 55.000 0.00 0.00 41.91 4.00
3416 3518 1.064003 ATGTCACCCTGCTGTTACCA 58.936 50.000 0.00 0.00 0.00 3.25
3417 3519 1.453155 CATGTCACCCTGCTGTTACC 58.547 55.000 0.00 0.00 0.00 2.85
3418 3520 1.453155 CCATGTCACCCTGCTGTTAC 58.547 55.000 0.00 0.00 0.00 2.50
3419 3521 0.322456 GCCATGTCACCCTGCTGTTA 60.322 55.000 0.00 0.00 0.00 2.41
3420 3522 1.604593 GCCATGTCACCCTGCTGTT 60.605 57.895 0.00 0.00 0.00 3.16
3421 3523 2.034687 GCCATGTCACCCTGCTGT 59.965 61.111 0.00 0.00 0.00 4.40
3422 3524 1.379443 ATGCCATGTCACCCTGCTG 60.379 57.895 0.00 0.00 0.00 4.41
3423 3525 1.379443 CATGCCATGTCACCCTGCT 60.379 57.895 0.00 0.00 0.00 4.24
3424 3526 0.754217 ATCATGCCATGTCACCCTGC 60.754 55.000 4.31 0.00 0.00 4.85
3425 3527 1.029681 CATCATGCCATGTCACCCTG 58.970 55.000 4.31 0.00 0.00 4.45
3426 3528 0.754217 GCATCATGCCATGTCACCCT 60.754 55.000 4.31 0.00 37.42 4.34
3427 3529 1.038681 TGCATCATGCCATGTCACCC 61.039 55.000 7.30 0.00 44.23 4.61
3428 3530 1.037493 ATGCATCATGCCATGTCACC 58.963 50.000 7.30 0.00 44.23 4.02
3429 3531 1.407618 ACATGCATCATGCCATGTCAC 59.592 47.619 17.13 0.00 44.80 3.67
3430 3532 1.770294 ACATGCATCATGCCATGTCA 58.230 45.000 17.13 2.42 44.80 3.58
3431 3533 2.882927 AACATGCATCATGCCATGTC 57.117 45.000 20.88 5.07 44.80 3.06
3432 3534 2.626266 CCTAACATGCATCATGCCATGT 59.374 45.455 17.13 17.13 44.80 3.21
3433 3535 2.888414 TCCTAACATGCATCATGCCATG 59.112 45.455 7.30 12.98 44.80 3.66
3434 3536 3.232720 TCCTAACATGCATCATGCCAT 57.767 42.857 7.30 0.00 44.80 4.40
3435 3537 2.732844 TCCTAACATGCATCATGCCA 57.267 45.000 7.30 0.00 44.80 4.92
3436 3538 4.595762 AATTCCTAACATGCATCATGCC 57.404 40.909 7.30 0.00 44.80 4.40
3437 3539 6.564709 TCTAATTCCTAACATGCATCATGC 57.435 37.500 1.35 1.35 44.80 4.06
3451 3553 9.950496 ATCAGCGTTCATATAAATCTAATTCCT 57.050 29.630 0.00 0.00 0.00 3.36
3452 3554 9.979270 CATCAGCGTTCATATAAATCTAATTCC 57.021 33.333 0.00 0.00 0.00 3.01
3455 3557 8.939929 CCACATCAGCGTTCATATAAATCTAAT 58.060 33.333 0.00 0.00 0.00 1.73
3456 3558 7.095229 GCCACATCAGCGTTCATATAAATCTAA 60.095 37.037 0.00 0.00 0.00 2.10
3457 3559 6.368791 GCCACATCAGCGTTCATATAAATCTA 59.631 38.462 0.00 0.00 0.00 1.98
3458 3560 5.180117 GCCACATCAGCGTTCATATAAATCT 59.820 40.000 0.00 0.00 0.00 2.40
3459 3561 5.049474 TGCCACATCAGCGTTCATATAAATC 60.049 40.000 0.00 0.00 0.00 2.17
3460 3562 4.821260 TGCCACATCAGCGTTCATATAAAT 59.179 37.500 0.00 0.00 0.00 1.40
3461 3563 4.195416 TGCCACATCAGCGTTCATATAAA 58.805 39.130 0.00 0.00 0.00 1.40
3462 3564 3.802866 TGCCACATCAGCGTTCATATAA 58.197 40.909 0.00 0.00 0.00 0.98
3463 3565 3.467374 TGCCACATCAGCGTTCATATA 57.533 42.857 0.00 0.00 0.00 0.86
3464 3566 2.330440 TGCCACATCAGCGTTCATAT 57.670 45.000 0.00 0.00 0.00 1.78
3465 3567 1.941975 CATGCCACATCAGCGTTCATA 59.058 47.619 0.00 0.00 0.00 2.15
3466 3568 0.736636 CATGCCACATCAGCGTTCAT 59.263 50.000 0.00 0.00 0.00 2.57
3467 3569 0.321475 TCATGCCACATCAGCGTTCA 60.321 50.000 0.00 0.00 0.00 3.18
3468 3570 0.804364 TTCATGCCACATCAGCGTTC 59.196 50.000 0.00 0.00 0.00 3.95
3469 3571 0.806868 CTTCATGCCACATCAGCGTT 59.193 50.000 0.00 0.00 0.00 4.84
3470 3572 1.651240 GCTTCATGCCACATCAGCGT 61.651 55.000 0.00 0.00 35.15 5.07
3471 3573 1.063649 GCTTCATGCCACATCAGCG 59.936 57.895 0.00 0.00 35.15 5.18
3472 3574 0.100682 CAGCTTCATGCCACATCAGC 59.899 55.000 0.00 1.58 44.23 4.26
3473 3575 0.738975 CCAGCTTCATGCCACATCAG 59.261 55.000 0.00 0.00 44.23 2.90
3474 3576 0.038599 ACCAGCTTCATGCCACATCA 59.961 50.000 0.00 0.00 44.23 3.07
3475 3577 0.454600 CACCAGCTTCATGCCACATC 59.545 55.000 0.00 0.00 44.23 3.06
3476 3578 0.251474 ACACCAGCTTCATGCCACAT 60.251 50.000 0.00 0.00 44.23 3.21
3477 3579 1.151221 ACACCAGCTTCATGCCACA 59.849 52.632 0.00 0.00 44.23 4.17
3478 3580 1.582968 CACACCAGCTTCATGCCAC 59.417 57.895 0.00 0.00 44.23 5.01
3479 3581 1.604308 CCACACCAGCTTCATGCCA 60.604 57.895 0.00 0.00 44.23 4.92
3480 3582 0.682209 ATCCACACCAGCTTCATGCC 60.682 55.000 0.00 0.00 44.23 4.40
3481 3583 1.945394 CTATCCACACCAGCTTCATGC 59.055 52.381 0.00 0.00 43.29 4.06
3482 3584 2.941064 CACTATCCACACCAGCTTCATG 59.059 50.000 0.00 0.00 0.00 3.07
3483 3585 2.573462 ACACTATCCACACCAGCTTCAT 59.427 45.455 0.00 0.00 0.00 2.57
3484 3586 1.977854 ACACTATCCACACCAGCTTCA 59.022 47.619 0.00 0.00 0.00 3.02
3485 3587 2.350522 CACACTATCCACACCAGCTTC 58.649 52.381 0.00 0.00 0.00 3.86
3486 3588 1.611673 GCACACTATCCACACCAGCTT 60.612 52.381 0.00 0.00 0.00 3.74
3487 3589 0.036010 GCACACTATCCACACCAGCT 60.036 55.000 0.00 0.00 0.00 4.24
3488 3590 0.321564 TGCACACTATCCACACCAGC 60.322 55.000 0.00 0.00 0.00 4.85
3489 3591 2.011947 CATGCACACTATCCACACCAG 58.988 52.381 0.00 0.00 0.00 4.00
3490 3592 1.350684 ACATGCACACTATCCACACCA 59.649 47.619 0.00 0.00 0.00 4.17
3491 3593 2.113860 ACATGCACACTATCCACACC 57.886 50.000 0.00 0.00 0.00 4.16
3492 3594 3.073678 TCAACATGCACACTATCCACAC 58.926 45.455 0.00 0.00 0.00 3.82
3493 3595 3.007831 TCTCAACATGCACACTATCCACA 59.992 43.478 0.00 0.00 0.00 4.17
3494 3596 3.599343 TCTCAACATGCACACTATCCAC 58.401 45.455 0.00 0.00 0.00 4.02
3495 3597 3.515104 TCTCTCAACATGCACACTATCCA 59.485 43.478 0.00 0.00 0.00 3.41
3496 3598 4.128925 TCTCTCAACATGCACACTATCC 57.871 45.455 0.00 0.00 0.00 2.59
3497 3599 6.457934 CCAATTCTCTCAACATGCACACTATC 60.458 42.308 0.00 0.00 0.00 2.08
3498 3600 5.356190 CCAATTCTCTCAACATGCACACTAT 59.644 40.000 0.00 0.00 0.00 2.12
3499 3601 4.696877 CCAATTCTCTCAACATGCACACTA 59.303 41.667 0.00 0.00 0.00 2.74
3500 3602 3.504906 CCAATTCTCTCAACATGCACACT 59.495 43.478 0.00 0.00 0.00 3.55
3501 3603 3.254166 ACCAATTCTCTCAACATGCACAC 59.746 43.478 0.00 0.00 0.00 3.82
3502 3604 3.489355 ACCAATTCTCTCAACATGCACA 58.511 40.909 0.00 0.00 0.00 4.57
3503 3605 4.510038 AACCAATTCTCTCAACATGCAC 57.490 40.909 0.00 0.00 0.00 4.57
3504 3606 7.066163 CACTATAACCAATTCTCTCAACATGCA 59.934 37.037 0.00 0.00 0.00 3.96
3505 3607 7.412853 CACTATAACCAATTCTCTCAACATGC 58.587 38.462 0.00 0.00 0.00 4.06
3506 3608 7.012704 CCCACTATAACCAATTCTCTCAACATG 59.987 40.741 0.00 0.00 0.00 3.21
3507 3609 7.056635 CCCACTATAACCAATTCTCTCAACAT 58.943 38.462 0.00 0.00 0.00 2.71
3508 3610 6.414732 CCCACTATAACCAATTCTCTCAACA 58.585 40.000 0.00 0.00 0.00 3.33
3509 3611 5.823045 CCCCACTATAACCAATTCTCTCAAC 59.177 44.000 0.00 0.00 0.00 3.18
3510 3612 5.729229 TCCCCACTATAACCAATTCTCTCAA 59.271 40.000 0.00 0.00 0.00 3.02
3511 3613 5.285401 TCCCCACTATAACCAATTCTCTCA 58.715 41.667 0.00 0.00 0.00 3.27
3512 3614 5.743422 GCTCCCCACTATAACCAATTCTCTC 60.743 48.000 0.00 0.00 0.00 3.20
3513 3615 4.103311 GCTCCCCACTATAACCAATTCTCT 59.897 45.833 0.00 0.00 0.00 3.10
3514 3616 4.141482 TGCTCCCCACTATAACCAATTCTC 60.141 45.833 0.00 0.00 0.00 2.87
3515 3617 3.785887 TGCTCCCCACTATAACCAATTCT 59.214 43.478 0.00 0.00 0.00 2.40
3516 3618 4.164843 TGCTCCCCACTATAACCAATTC 57.835 45.455 0.00 0.00 0.00 2.17
3517 3619 4.017499 AGTTGCTCCCCACTATAACCAATT 60.017 41.667 0.00 0.00 0.00 2.32
3518 3620 3.527665 AGTTGCTCCCCACTATAACCAAT 59.472 43.478 0.00 0.00 0.00 3.16
3519 3621 2.916934 AGTTGCTCCCCACTATAACCAA 59.083 45.455 0.00 0.00 0.00 3.67
3520 3622 2.557869 AGTTGCTCCCCACTATAACCA 58.442 47.619 0.00 0.00 0.00 3.67
3521 3623 3.200165 AGAAGTTGCTCCCCACTATAACC 59.800 47.826 0.00 0.00 0.00 2.85
3522 3624 4.489306 AGAAGTTGCTCCCCACTATAAC 57.511 45.455 0.00 0.00 0.00 1.89
3523 3625 6.442564 TCTTAAGAAGTTGCTCCCCACTATAA 59.557 38.462 1.68 0.00 0.00 0.98
3524 3626 5.962031 TCTTAAGAAGTTGCTCCCCACTATA 59.038 40.000 1.68 0.00 0.00 1.31
3525 3627 4.783227 TCTTAAGAAGTTGCTCCCCACTAT 59.217 41.667 1.68 0.00 0.00 2.12
3526 3628 4.164981 TCTTAAGAAGTTGCTCCCCACTA 58.835 43.478 1.68 0.00 0.00 2.74
3527 3629 2.979678 TCTTAAGAAGTTGCTCCCCACT 59.020 45.455 1.68 0.00 0.00 4.00
3528 3630 3.244596 ACTCTTAAGAAGTTGCTCCCCAC 60.245 47.826 6.63 0.00 0.00 4.61
3529 3631 2.979678 ACTCTTAAGAAGTTGCTCCCCA 59.020 45.455 6.63 0.00 0.00 4.96
3530 3632 3.244596 ACACTCTTAAGAAGTTGCTCCCC 60.245 47.826 6.63 0.00 0.00 4.81
3531 3633 4.009370 ACACTCTTAAGAAGTTGCTCCC 57.991 45.455 6.63 0.00 0.00 4.30
3532 3634 6.456501 TCTTACACTCTTAAGAAGTTGCTCC 58.543 40.000 13.56 0.00 35.55 4.70
3533 3635 9.810545 ATATCTTACACTCTTAAGAAGTTGCTC 57.189 33.333 13.56 0.00 40.62 4.26
3534 3636 9.593134 CATATCTTACACTCTTAAGAAGTTGCT 57.407 33.333 13.56 4.72 40.62 3.91
3535 3637 9.587772 TCATATCTTACACTCTTAAGAAGTTGC 57.412 33.333 13.56 0.00 40.62 4.17
3554 3656 8.512956 GCTGCATTTCATCATTTAGTCATATCT 58.487 33.333 0.00 0.00 0.00 1.98
3555 3657 8.294577 TGCTGCATTTCATCATTTAGTCATATC 58.705 33.333 0.00 0.00 0.00 1.63
3580 3682 7.439157 TGAGTAATTGTCTCAATCAAGGTTG 57.561 36.000 11.10 0.00 38.71 3.77
3590 3692 9.591792 CAAGATAACTGATGAGTAATTGTCTCA 57.408 33.333 14.42 14.42 44.37 3.27
3617 3719 3.385193 AAGGTGGTGCTATTTTGTTGC 57.615 42.857 0.00 0.00 0.00 4.17
3658 3760 5.485353 TCATGGGTTTTGCCATGGTTATTTA 59.515 36.000 14.67 0.00 42.62 1.40
3670 3772 4.434713 AGATAAACGTCATGGGTTTTGC 57.565 40.909 17.07 11.39 38.47 3.68
3699 3801 4.634443 AGGTCACATTCAAAGCCGTATTAC 59.366 41.667 0.00 0.00 0.00 1.89
3702 3804 3.350219 AGGTCACATTCAAAGCCGTAT 57.650 42.857 0.00 0.00 0.00 3.06
3707 3809 5.438761 AAGTTGTAGGTCACATTCAAAGC 57.561 39.130 0.00 0.00 36.90 3.51
3720 3822 5.424252 TGGTATCCTCCAACTAAGTTGTAGG 59.576 44.000 0.00 0.00 46.49 3.18
3743 3845 4.788100 CGTTGGTTTGCTCGATCTTTTATG 59.212 41.667 0.00 0.00 0.00 1.90
3744 3846 4.693566 TCGTTGGTTTGCTCGATCTTTTAT 59.306 37.500 0.00 0.00 0.00 1.40
3753 3855 2.969443 AAATCTCGTTGGTTTGCTCG 57.031 45.000 0.00 0.00 0.00 5.03
3756 3858 5.038033 TGTTGTTAAATCTCGTTGGTTTGC 58.962 37.500 1.00 0.00 0.00 3.68
3757 3859 6.143758 CCATGTTGTTAAATCTCGTTGGTTTG 59.856 38.462 0.00 0.00 0.00 2.93
3772 3874 2.040947 TGGAGGCATGACCATGTTGTTA 59.959 45.455 11.17 0.00 43.14 2.41
3804 3906 1.261480 ATTCAGCAGTCTCACGACCT 58.739 50.000 0.00 0.00 41.16 3.85
3809 3911 6.486253 TTGTTGATAATTCAGCAGTCTCAC 57.514 37.500 0.00 0.00 42.92 3.51
3856 3958 8.807581 GTTTCTGAATCGATTGAAACTGTTTTT 58.192 29.630 29.06 3.49 42.62 1.94
3857 3959 8.340230 GTTTCTGAATCGATTGAAACTGTTTT 57.660 30.769 29.06 3.66 42.62 2.43
3858 3960 7.914537 GTTTCTGAATCGATTGAAACTGTTT 57.085 32.000 29.06 5.29 42.62 2.83
3863 3965 7.965107 AGCATTAGTTTCTGAATCGATTGAAAC 59.035 33.333 29.12 29.12 44.80 2.78
3864 3966 8.044060 AGCATTAGTTTCTGAATCGATTGAAA 57.956 30.769 16.96 16.23 0.00 2.69
3865 3967 7.615582 AGCATTAGTTTCTGAATCGATTGAA 57.384 32.000 16.96 10.96 0.00 2.69
3866 3968 7.414429 CCAAGCATTAGTTTCTGAATCGATTGA 60.414 37.037 16.96 6.19 0.00 2.57
3867 3969 6.690098 CCAAGCATTAGTTTCTGAATCGATTG 59.310 38.462 16.96 1.85 0.00 2.67
3868 3970 6.599244 TCCAAGCATTAGTTTCTGAATCGATT 59.401 34.615 11.20 11.20 0.00 3.34
3869 3971 6.115446 TCCAAGCATTAGTTTCTGAATCGAT 58.885 36.000 0.00 0.00 0.00 3.59
3870 3972 5.487433 TCCAAGCATTAGTTTCTGAATCGA 58.513 37.500 0.00 0.00 0.00 3.59
3871 3973 5.728898 GCTCCAAGCATTAGTTTCTGAATCG 60.729 44.000 0.00 0.00 41.89 3.34
3872 3974 5.576895 GCTCCAAGCATTAGTTTCTGAATC 58.423 41.667 0.00 0.00 41.89 2.52
3873 3975 5.573337 GCTCCAAGCATTAGTTTCTGAAT 57.427 39.130 0.00 0.00 41.89 2.57


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

AutoCloner maintained by Alex Coulton.