Multiple sequence alignment - TraesCS5B01G492600

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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 TraesCS5B01G492600 chr5B 100.000 3613 0 0 1 3613 660587862 660591474 0.000000e+00 6673
1 TraesCS5B01G492600 chr5B 85.845 219 28 2 1616 1831 112194761 112194543 2.810000e-56 230
2 TraesCS5B01G492600 chr5D 96.131 3360 65 26 1 3323 525956291 525959622 0.000000e+00 5424
3 TraesCS5B01G492600 chr5D 85.388 219 29 2 1616 1831 103176003 103175785 1.310000e-54 224
4 TraesCS5B01G492600 chr5D 93.985 133 3 2 3486 3613 525959621 525959753 2.850000e-46 196
5 TraesCS5B01G492600 chr5A 91.895 3393 114 66 1 3311 652645923 652649236 0.000000e+00 4593
6 TraesCS5B01G492600 chr5A 94.505 182 7 3 3309 3490 290391872 290391694 9.880000e-71 278
7 TraesCS5B01G492600 chr5A 92.063 189 13 2 3313 3501 570081586 570081400 7.690000e-67 265
8 TraesCS5B01G492600 chr5A 86.301 219 27 2 1616 1831 95869179 95869397 6.030000e-58 235
9 TraesCS5B01G492600 chr3D 96.532 173 4 2 3319 3491 361805865 361805695 5.900000e-73 285
10 TraesCS5B01G492600 chr3D 88.995 209 21 2 1620 1827 610544049 610544256 1.290000e-64 257
11 TraesCS5B01G492600 chr1D 95.480 177 6 2 3314 3490 490423145 490423319 7.640000e-72 281
12 TraesCS5B01G492600 chr3B 96.471 170 5 1 3318 3487 279592 279424 2.750000e-71 279
13 TraesCS5B01G492600 chr3B 88.995 209 21 2 1620 1827 828111449 828111656 1.290000e-64 257
14 TraesCS5B01G492600 chr2B 93.478 184 9 3 3314 3496 648880201 648880020 1.650000e-68 270
15 TraesCS5B01G492600 chr7D 90.732 205 13 6 3309 3512 39001273 39001472 5.950000e-68 268
16 TraesCS5B01G492600 chr2D 90.594 202 13 6 3302 3500 32474488 32474290 2.770000e-66 263
17 TraesCS5B01G492600 chr2D 89.423 208 15 5 3285 3489 500764602 500764805 4.630000e-64 255
18 TraesCS5B01G492600 chr3A 87.981 208 25 0 1620 1827 744879519 744879726 2.790000e-61 246
19 TraesCS5B01G492600 chr1A 89.005 191 18 1 1654 1841 18461727 18461537 2.170000e-57 233


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 TraesCS5B01G492600 chr5B 660587862 660591474 3612 False 6673 6673 100.000 1 3613 1 chr5B.!!$F1 3612
1 TraesCS5B01G492600 chr5D 525956291 525959753 3462 False 2810 5424 95.058 1 3613 2 chr5D.!!$F1 3612
2 TraesCS5B01G492600 chr5A 652645923 652649236 3313 False 4593 4593 91.895 1 3311 1 chr5A.!!$F2 3310

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
216 236 1.000521 CCAGCCAGCTCCAATCCAA 60.001 57.895 0.00 0.0 0.00 3.53 F
1180 1237 1.067213 GGAGATATTCCTCTGCGCTCC 60.067 57.143 9.73 0.0 43.16 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1364 1437 0.037139 TTGCAAACATCTGGCCATGC 60.037 50.0 17.91 17.91 0.00 4.06 R
2760 2878 1.308069 CGCCACCAGAACTCCATTGG 61.308 60.0 0.00 0.00 37.98 3.16 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
37 38 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
38 39 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
111 125 8.059798 ACTTTTACTGATTGATCCCTTTCATG 57.940 34.615 0.00 0.00 0.00 3.07
195 209 5.088739 GTGTTGCTCATTTTGATAACCTCG 58.911 41.667 0.00 0.00 0.00 4.63
216 236 1.000521 CCAGCCAGCTCCAATCCAA 60.001 57.895 0.00 0.00 0.00 3.53
217 237 1.318158 CCAGCCAGCTCCAATCCAAC 61.318 60.000 0.00 0.00 0.00 3.77
220 240 1.926511 GCCAGCTCCAATCCAACGTG 61.927 60.000 0.00 0.00 0.00 4.49
237 257 2.029828 ACGTGTTTGTTTGGTTGCTGAA 60.030 40.909 0.00 0.00 0.00 3.02
485 510 3.132646 CAGGCTAAGCAACTGATCTCTCT 59.867 47.826 0.00 0.00 34.21 3.10
486 511 3.384467 AGGCTAAGCAACTGATCTCTCTC 59.616 47.826 0.00 0.00 0.00 3.20
518 543 4.083862 GCTTCCTTCCCCGTCGCT 62.084 66.667 0.00 0.00 0.00 4.93
694 719 1.387926 CATCTTCCCCCTCCCCCAT 60.388 63.158 0.00 0.00 0.00 4.00
803 835 4.672587 TTCTCCATCGATCCACCTTTAG 57.327 45.455 0.00 0.00 0.00 1.85
804 836 2.365617 TCTCCATCGATCCACCTTTAGC 59.634 50.000 0.00 0.00 0.00 3.09
805 837 2.366916 CTCCATCGATCCACCTTTAGCT 59.633 50.000 0.00 0.00 0.00 3.32
806 838 2.771943 TCCATCGATCCACCTTTAGCTT 59.228 45.455 0.00 0.00 0.00 3.74
872 905 2.657143 CTATATACCCCTCGCCTCTCC 58.343 57.143 0.00 0.00 0.00 3.71
979 1012 9.137459 TCAAAAGAAACCAAATTCTATACCACA 57.863 29.630 0.00 0.00 38.69 4.17
980 1013 9.191995 CAAAAGAAACCAAATTCTATACCACAC 57.808 33.333 0.00 0.00 38.69 3.82
981 1014 7.462571 AAGAAACCAAATTCTATACCACACC 57.537 36.000 0.00 0.00 38.69 4.16
982 1015 6.548321 AGAAACCAAATTCTATACCACACCA 58.452 36.000 0.00 0.00 37.88 4.17
983 1016 6.433093 AGAAACCAAATTCTATACCACACCAC 59.567 38.462 0.00 0.00 37.88 4.16
984 1017 4.595986 ACCAAATTCTATACCACACCACC 58.404 43.478 0.00 0.00 0.00 4.61
985 1018 4.043561 ACCAAATTCTATACCACACCACCA 59.956 41.667 0.00 0.00 0.00 4.17
986 1019 4.398044 CCAAATTCTATACCACACCACCAC 59.602 45.833 0.00 0.00 0.00 4.16
1180 1237 1.067213 GGAGATATTCCTCTGCGCTCC 60.067 57.143 9.73 0.00 43.16 4.70
1271 1329 9.599322 CTAGTTTTGTGTGATTGTGATTAGTTC 57.401 33.333 0.00 0.00 0.00 3.01
1298 1356 4.276926 AGCTTTGATTCTCTTGCTTTTCGT 59.723 37.500 0.00 0.00 0.00 3.85
1301 1359 3.141398 TGATTCTCTTGCTTTTCGTGCT 58.859 40.909 0.00 0.00 0.00 4.40
1364 1437 2.979197 GCAGCAGCAACTGAGCCAG 61.979 63.158 9.94 1.16 40.25 4.85
1539 1624 2.106332 CGGACGGCATGGGTAGTC 59.894 66.667 0.00 0.00 0.00 2.59
1913 2007 0.319555 CGTCCACAACATCGTCCACT 60.320 55.000 0.00 0.00 0.00 4.00
1994 2112 4.316823 TCGTCTCAGGGCCAGGGT 62.317 66.667 6.18 0.00 0.00 4.34
2210 2328 0.836400 AGCAGTTCCCCTTCTTCGGA 60.836 55.000 0.00 0.00 0.00 4.55
2403 2521 3.409605 AACCCGCCGTCCAACAACT 62.410 57.895 0.00 0.00 0.00 3.16
2760 2878 6.879188 ATCGATCGAGAAAGAGAAAAGAAC 57.121 37.500 23.84 0.00 0.00 3.01
2771 2889 6.641169 AAGAGAAAAGAACCAATGGAGTTC 57.359 37.500 6.16 0.00 43.22 3.01
2785 2903 3.364441 GTTCTGGTGGCGCATGCA 61.364 61.111 19.57 0.00 45.35 3.96
2845 2963 3.128349 CTCTCGAGTGAGTCCTAGCTAC 58.872 54.545 13.13 0.00 43.09 3.58
2854 2972 7.562259 AGTGAGTCCTAGCTACATCTATCTA 57.438 40.000 0.00 0.00 0.00 1.98
2928 3047 4.497473 TGTTTAAGGTGCTGGATTTTCG 57.503 40.909 0.00 0.00 0.00 3.46
2952 3071 8.314751 TCGATATTCTTGGATCTCCTTAATTCC 58.685 37.037 0.00 0.00 36.82 3.01
2953 3072 7.276658 CGATATTCTTGGATCTCCTTAATTCCG 59.723 40.741 0.00 0.00 36.82 4.30
3018 3139 5.003804 AGCTTGGTTCGATTAATGTGTTCT 58.996 37.500 0.00 0.00 0.00 3.01
3153 3281 4.345257 ACCCCATGTATGACAGTATGAGTC 59.655 45.833 0.00 0.00 39.69 3.36
3160 3288 2.167662 TGACAGTATGAGTCGCTTGGA 58.832 47.619 0.00 0.00 39.69 3.53
3269 3402 9.541143 TGCAATTCTACTCGATGTTTATATCAA 57.459 29.630 0.00 0.00 0.00 2.57
3328 3461 8.923838 ATCCAATACATTGATATCTACTCCCT 57.076 34.615 3.98 0.00 40.14 4.20
3329 3462 8.367660 TCCAATACATTGATATCTACTCCCTC 57.632 38.462 3.98 0.00 40.14 4.30
3330 3463 7.400339 TCCAATACATTGATATCTACTCCCTCC 59.600 40.741 3.98 0.00 40.14 4.30
3331 3464 7.261325 CAATACATTGATATCTACTCCCTCCG 58.739 42.308 3.98 0.00 40.14 4.63
3332 3465 4.742012 ACATTGATATCTACTCCCTCCGT 58.258 43.478 3.98 0.00 0.00 4.69
3333 3466 5.148502 ACATTGATATCTACTCCCTCCGTT 58.851 41.667 3.98 0.00 0.00 4.44
3334 3467 5.244178 ACATTGATATCTACTCCCTCCGTTC 59.756 44.000 3.98 0.00 0.00 3.95
3335 3468 3.764218 TGATATCTACTCCCTCCGTTCC 58.236 50.000 3.98 0.00 0.00 3.62
3336 3469 3.398292 TGATATCTACTCCCTCCGTTCCT 59.602 47.826 3.98 0.00 0.00 3.36
3337 3470 4.600547 TGATATCTACTCCCTCCGTTCCTA 59.399 45.833 3.98 0.00 0.00 2.94
3338 3471 3.967467 ATCTACTCCCTCCGTTCCTAA 57.033 47.619 0.00 0.00 0.00 2.69
3339 3472 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
3340 3473 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
3341 3474 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
3342 3475 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
3343 3476 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
3344 3477 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
3345 3478 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
3346 3479 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
3347 3480 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
3348 3481 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
3349 3482 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
3350 3483 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
3351 3484 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
3352 3485 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
3353 3486 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
3354 3487 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
3355 3488 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
3372 3505 9.436957 TCTTTCTAGACATTTCAAATGGACTAC 57.563 33.333 14.70 1.26 0.00 2.73
3373 3506 8.561738 TTTCTAGACATTTCAAATGGACTACC 57.438 34.615 14.70 0.00 0.00 3.18
3383 3516 3.575506 TGGACTACCACGTACGGAT 57.424 52.632 21.06 6.82 41.77 4.18
3384 3517 1.097232 TGGACTACCACGTACGGATG 58.903 55.000 21.06 9.60 41.77 3.51
3385 3518 1.098050 GGACTACCACGTACGGATGT 58.902 55.000 21.06 15.02 35.97 3.06
3386 3519 2.288666 GGACTACCACGTACGGATGTA 58.711 52.381 21.06 15.33 35.97 2.29
3387 3520 2.880890 GGACTACCACGTACGGATGTAT 59.119 50.000 21.06 0.21 35.97 2.29
3388 3521 3.304257 GGACTACCACGTACGGATGTATG 60.304 52.174 21.06 7.27 42.24 2.39
3390 3523 4.450976 ACTACCACGTACGGATGTATGTA 58.549 43.478 21.06 6.74 46.55 2.29
3391 3524 3.976793 ACCACGTACGGATGTATGTAG 57.023 47.619 21.06 0.00 46.55 2.74
3392 3525 3.544684 ACCACGTACGGATGTATGTAGA 58.455 45.455 21.06 0.00 46.55 2.59
3393 3526 3.313526 ACCACGTACGGATGTATGTAGAC 59.686 47.826 21.06 0.00 46.55 2.59
3394 3527 3.313249 CCACGTACGGATGTATGTAGACA 59.687 47.826 21.06 0.00 46.55 3.41
3395 3528 4.023450 CCACGTACGGATGTATGTAGACAT 60.023 45.833 21.06 0.08 46.55 3.06
3396 3529 5.179929 CCACGTACGGATGTATGTAGACATA 59.820 44.000 21.06 0.00 46.55 2.29
3397 3530 6.128090 CCACGTACGGATGTATGTAGACATAT 60.128 42.308 21.06 0.00 46.55 1.78
3398 3531 7.303261 CACGTACGGATGTATGTAGACATATT 58.697 38.462 21.06 0.00 46.55 1.28
3399 3532 7.806487 CACGTACGGATGTATGTAGACATATTT 59.194 37.037 21.06 0.00 46.55 1.40
3400 3533 8.355169 ACGTACGGATGTATGTAGACATATTTT 58.645 33.333 21.06 0.00 46.45 1.82
3401 3534 9.830294 CGTACGGATGTATGTAGACATATTTTA 57.170 33.333 7.57 0.00 40.18 1.52
3427 3560 7.138692 AGTGTAAGATTCACTCATTTTGCTC 57.861 36.000 0.00 0.00 41.52 4.26
3428 3561 6.150140 AGTGTAAGATTCACTCATTTTGCTCC 59.850 38.462 0.00 0.00 41.52 4.70
3429 3562 6.003326 TGTAAGATTCACTCATTTTGCTCCA 58.997 36.000 0.00 0.00 0.00 3.86
3430 3563 6.660521 TGTAAGATTCACTCATTTTGCTCCAT 59.339 34.615 0.00 0.00 0.00 3.41
3431 3564 7.828717 TGTAAGATTCACTCATTTTGCTCCATA 59.171 33.333 0.00 0.00 0.00 2.74
3432 3565 7.893124 AAGATTCACTCATTTTGCTCCATAT 57.107 32.000 0.00 0.00 0.00 1.78
3433 3566 8.985315 AAGATTCACTCATTTTGCTCCATATA 57.015 30.769 0.00 0.00 0.00 0.86
3434 3567 9.584008 AAGATTCACTCATTTTGCTCCATATAT 57.416 29.630 0.00 0.00 0.00 0.86
3438 3571 9.494271 TTCACTCATTTTGCTCCATATATAGTC 57.506 33.333 0.00 0.00 0.00 2.59
3439 3572 8.650490 TCACTCATTTTGCTCCATATATAGTCA 58.350 33.333 0.00 0.00 0.00 3.41
3440 3573 8.715998 CACTCATTTTGCTCCATATATAGTCAC 58.284 37.037 0.00 0.00 0.00 3.67
3441 3574 8.654997 ACTCATTTTGCTCCATATATAGTCACT 58.345 33.333 0.00 0.00 0.00 3.41
3442 3575 9.499479 CTCATTTTGCTCCATATATAGTCACTT 57.501 33.333 0.00 0.00 0.00 3.16
3443 3576 9.276590 TCATTTTGCTCCATATATAGTCACTTG 57.723 33.333 0.00 0.00 0.00 3.16
3444 3577 9.060347 CATTTTGCTCCATATATAGTCACTTGT 57.940 33.333 0.00 0.00 0.00 3.16
3445 3578 9.632638 ATTTTGCTCCATATATAGTCACTTGTT 57.367 29.630 0.00 0.00 0.00 2.83
3446 3579 8.437360 TTTGCTCCATATATAGTCACTTGTTG 57.563 34.615 0.00 0.00 0.00 3.33
3447 3580 7.360113 TGCTCCATATATAGTCACTTGTTGA 57.640 36.000 0.00 0.00 0.00 3.18
3448 3581 7.791029 TGCTCCATATATAGTCACTTGTTGAA 58.209 34.615 0.00 0.00 35.39 2.69
3449 3582 8.264347 TGCTCCATATATAGTCACTTGTTGAAA 58.736 33.333 0.00 0.00 35.39 2.69
3450 3583 9.277783 GCTCCATATATAGTCACTTGTTGAAAT 57.722 33.333 0.00 0.00 35.39 2.17
3459 3592 9.778741 ATAGTCACTTGTTGAAATGTCTAGAAA 57.221 29.630 0.00 0.00 35.39 2.52
3460 3593 8.147642 AGTCACTTGTTGAAATGTCTAGAAAG 57.852 34.615 0.00 0.00 35.39 2.62
3461 3594 7.987458 AGTCACTTGTTGAAATGTCTAGAAAGA 59.013 33.333 0.00 0.00 35.39 2.52
3462 3595 8.064814 GTCACTTGTTGAAATGTCTAGAAAGAC 58.935 37.037 0.00 0.00 43.53 3.01
3478 3611 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
3479 3612 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
3480 3613 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
3481 3614 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
3482 3615 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3483 3616 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
3484 3617 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
3493 3626 2.028930 GGAACGGAGGGAGTATATGCTG 60.029 54.545 0.00 0.00 0.00 4.41
3598 3736 9.607988 TCCTTATAAAATTTAGTCTTGCATCGA 57.392 29.630 0.00 0.00 0.00 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 7.512705 CCAAGTAGTGGTGGTGAAGAATTCTC 61.513 46.154 8.78 3.35 43.85 2.87
38 39 5.746065 CCAAGTAGTGGTGGTGAAGAATTCT 60.746 44.000 0.88 0.88 43.85 2.40
111 125 6.473455 GCAGGTGCAACTTTATGTCAATATTC 59.527 38.462 0.00 0.00 41.59 1.75
140 154 2.092646 GGGGTGTTCAGGTGCATGTATA 60.093 50.000 0.00 0.00 0.00 1.47
216 236 1.542030 TCAGCAACCAAACAAACACGT 59.458 42.857 0.00 0.00 0.00 4.49
217 237 2.270275 TCAGCAACCAAACAAACACG 57.730 45.000 0.00 0.00 0.00 4.49
220 240 3.616821 GGTTCTTCAGCAACCAAACAAAC 59.383 43.478 0.00 0.00 42.68 2.93
237 257 0.555769 TTCTTGGCAACTGGGGTTCT 59.444 50.000 0.00 0.00 32.73 3.01
485 510 5.450818 AGGAAGCTTAGAGAGAAGAGAGA 57.549 43.478 0.00 0.00 0.00 3.10
486 511 5.067805 GGAAGGAAGCTTAGAGAGAAGAGAG 59.932 48.000 0.00 0.00 0.00 3.20
694 719 0.115152 TCTCACAAGGAGCTGAGGGA 59.885 55.000 0.00 0.00 43.70 4.20
803 835 4.802051 TGGATGGCGAGGGCAAGC 62.802 66.667 0.00 0.00 42.43 4.01
804 836 2.825836 GTGGATGGCGAGGGCAAG 60.826 66.667 0.00 0.00 42.43 4.01
805 837 4.424711 GGTGGATGGCGAGGGCAA 62.425 66.667 0.00 0.00 42.43 4.52
978 1011 2.518349 GTGGTGGTGGTGGTGGTG 60.518 66.667 0.00 0.00 0.00 4.17
979 1012 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.00 0.00 4.16
980 1013 3.814906 TGGTGGTGGTGGTGGTGG 61.815 66.667 0.00 0.00 0.00 4.61
981 1014 2.518349 GTGGTGGTGGTGGTGGTG 60.518 66.667 0.00 0.00 0.00 4.17
982 1015 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.00 0.00 4.16
983 1016 3.145473 ATGGTGGTGGTGGTGGTGG 62.145 63.158 0.00 0.00 0.00 4.61
984 1017 1.902918 CATGGTGGTGGTGGTGGTG 60.903 63.158 0.00 0.00 0.00 4.17
985 1018 2.520458 CATGGTGGTGGTGGTGGT 59.480 61.111 0.00 0.00 0.00 4.16
986 1019 2.283101 CCATGGTGGTGGTGGTGG 60.283 66.667 2.57 0.00 34.46 4.61
1180 1237 5.582689 AGAAGGGGATTTAATTCGCAAAG 57.417 39.130 14.13 0.00 0.00 2.77
1271 1329 3.345414 AGCAAGAGAATCAAAGCTGAGG 58.655 45.455 0.00 0.00 37.36 3.86
1298 1356 5.757320 CCATGGTTTACAATCAAAACAAGCA 59.243 36.000 2.57 0.00 38.53 3.91
1301 1359 5.525378 GCACCATGGTTTACAATCAAAACAA 59.475 36.000 16.84 0.00 38.53 2.83
1342 1415 1.966972 CTCAGTTGCTGCTGCTGCT 60.967 57.895 27.67 11.22 40.48 4.24
1343 1416 2.561885 CTCAGTTGCTGCTGCTGC 59.438 61.111 22.51 22.51 40.48 5.25
1344 1417 2.561885 GCTCAGTTGCTGCTGCTG 59.438 61.111 17.00 14.62 40.48 4.41
1345 1418 2.672307 GGCTCAGTTGCTGCTGCT 60.672 61.111 17.00 0.00 40.48 4.24
1346 1419 2.979197 CTGGCTCAGTTGCTGCTGC 61.979 63.158 8.89 8.89 36.49 5.25
1347 1420 2.979197 GCTGGCTCAGTTGCTGCTG 61.979 63.158 0.00 2.36 37.81 4.41
1364 1437 0.037139 TTGCAAACATCTGGCCATGC 60.037 50.000 17.91 17.91 0.00 4.06
1539 1624 4.404654 GCCGCTCAAAGCAACCGG 62.405 66.667 0.00 0.00 42.58 5.28
1994 2112 2.436469 AATGGCATCTGCGCGTGA 60.436 55.556 8.43 7.24 43.26 4.35
2363 2481 1.519455 CTCCATCTTCACCGACGCC 60.519 63.158 0.00 0.00 0.00 5.68
2760 2878 1.308069 CGCCACCAGAACTCCATTGG 61.308 60.000 0.00 0.00 37.98 3.16
2771 2889 1.940883 ATCTTTGCATGCGCCACCAG 61.941 55.000 14.09 2.42 37.32 4.00
2785 2903 4.625028 TCGATCGATCAGCAATGATCTTT 58.375 39.130 24.40 3.84 41.74 2.52
2845 2963 5.932883 AGAACAGCATGCATGTAGATAGATG 59.067 40.000 26.79 11.20 42.53 2.90
2854 2972 2.489329 GGTACAAGAACAGCATGCATGT 59.511 45.455 26.79 17.58 42.53 3.21
2928 3047 7.065204 GCGGAATTAAGGAGATCCAAGAATATC 59.935 40.741 0.92 0.00 38.89 1.63
2952 3071 3.409851 ACATGCATTACAATGACAGCG 57.590 42.857 0.00 2.91 38.70 5.18
2953 3072 7.254185 CCAATTAACATGCATTACAATGACAGC 60.254 37.037 0.00 0.00 38.70 4.40
3005 3126 5.476945 ACCTTCCACCAAGAACACATTAATC 59.523 40.000 0.00 0.00 33.29 1.75
3153 3281 3.674753 GGAAACATTGAACATTCCAAGCG 59.325 43.478 0.00 0.00 40.81 4.68
3160 3288 6.469782 AAGTGAGTGGAAACATTGAACATT 57.530 33.333 0.00 0.00 46.14 2.71
3251 3384 7.504574 TGGACCTCTTGATATAAACATCGAGTA 59.495 37.037 0.00 0.00 37.59 2.59
3269 3402 5.463051 AAGGATGAATGAAATGGACCTCT 57.537 39.130 0.00 0.00 0.00 3.69
3321 3454 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
3322 3455 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
3323 3456 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
3324 3457 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
3325 3458 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3326 3459 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
3327 3460 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
3328 3461 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
3329 3462 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
3346 3479 9.436957 GTAGTCCATTTGAAATGTCTAGAAAGA 57.563 33.333 15.93 1.84 0.00 2.52
3347 3480 8.669243 GGTAGTCCATTTGAAATGTCTAGAAAG 58.331 37.037 15.93 0.00 0.00 2.62
3348 3481 8.160765 TGGTAGTCCATTTGAAATGTCTAGAAA 58.839 33.333 15.93 0.00 39.03 2.52
3349 3482 7.606456 GTGGTAGTCCATTTGAAATGTCTAGAA 59.394 37.037 15.93 7.22 46.20 2.10
3350 3483 7.103641 GTGGTAGTCCATTTGAAATGTCTAGA 58.896 38.462 15.93 4.16 46.20 2.43
3351 3484 6.036083 CGTGGTAGTCCATTTGAAATGTCTAG 59.964 42.308 15.93 1.90 46.20 2.43
3352 3485 5.872617 CGTGGTAGTCCATTTGAAATGTCTA 59.127 40.000 15.93 13.97 46.20 2.59
3353 3486 4.695455 CGTGGTAGTCCATTTGAAATGTCT 59.305 41.667 15.93 14.81 46.20 3.41
3354 3487 4.454504 ACGTGGTAGTCCATTTGAAATGTC 59.545 41.667 15.93 9.10 46.20 3.06
3355 3488 4.394729 ACGTGGTAGTCCATTTGAAATGT 58.605 39.130 15.93 1.43 46.20 2.71
3356 3489 5.445407 CGTACGTGGTAGTCCATTTGAAATG 60.445 44.000 10.84 10.84 46.20 2.32
3357 3490 4.628333 CGTACGTGGTAGTCCATTTGAAAT 59.372 41.667 7.22 0.00 46.20 2.17
3358 3491 3.989167 CGTACGTGGTAGTCCATTTGAAA 59.011 43.478 7.22 0.00 46.20 2.69
3359 3492 3.577667 CGTACGTGGTAGTCCATTTGAA 58.422 45.455 7.22 0.00 46.20 2.69
3360 3493 2.094597 CCGTACGTGGTAGTCCATTTGA 60.095 50.000 15.21 0.00 46.20 2.69
3361 3494 2.094597 TCCGTACGTGGTAGTCCATTTG 60.095 50.000 15.21 0.00 46.20 2.32
3362 3495 2.170166 TCCGTACGTGGTAGTCCATTT 58.830 47.619 15.21 0.00 46.20 2.32
3363 3496 1.838112 TCCGTACGTGGTAGTCCATT 58.162 50.000 15.21 0.00 46.20 3.16
3364 3497 1.679680 CATCCGTACGTGGTAGTCCAT 59.320 52.381 15.21 0.00 46.20 3.41
3365 3498 1.097232 CATCCGTACGTGGTAGTCCA 58.903 55.000 15.21 0.00 42.05 4.02
3366 3499 1.098050 ACATCCGTACGTGGTAGTCC 58.902 55.000 15.21 0.00 0.00 3.85
3367 3500 3.313526 ACATACATCCGTACGTGGTAGTC 59.686 47.826 15.21 0.00 0.00 2.59
3368 3501 3.282021 ACATACATCCGTACGTGGTAGT 58.718 45.455 15.21 7.78 0.00 2.73
3369 3502 3.976793 ACATACATCCGTACGTGGTAG 57.023 47.619 15.21 9.35 0.00 3.18
3370 3503 4.511454 GTCTACATACATCCGTACGTGGTA 59.489 45.833 15.21 13.05 0.00 3.25
3371 3504 3.313526 GTCTACATACATCCGTACGTGGT 59.686 47.826 15.21 11.27 0.00 4.16
3372 3505 3.313249 TGTCTACATACATCCGTACGTGG 59.687 47.826 15.21 5.54 0.00 4.94
3373 3506 4.541085 TGTCTACATACATCCGTACGTG 57.459 45.455 15.21 9.44 0.00 4.49
3374 3507 7.444629 AATATGTCTACATACATCCGTACGT 57.555 36.000 15.21 0.00 41.15 3.57
3375 3508 8.738199 AAAATATGTCTACATACATCCGTACG 57.262 34.615 8.69 8.69 41.15 3.67
3404 3537 6.072508 TGGAGCAAAATGAGTGAATCTTACAC 60.073 38.462 0.00 0.00 38.38 2.90
3405 3538 6.003326 TGGAGCAAAATGAGTGAATCTTACA 58.997 36.000 0.00 0.00 0.00 2.41
3406 3539 6.500684 TGGAGCAAAATGAGTGAATCTTAC 57.499 37.500 0.00 0.00 0.00 2.34
3407 3540 8.985315 ATATGGAGCAAAATGAGTGAATCTTA 57.015 30.769 0.00 0.00 0.00 2.10
3408 3541 7.893124 ATATGGAGCAAAATGAGTGAATCTT 57.107 32.000 0.00 0.00 0.00 2.40
3412 3545 9.494271 GACTATATATGGAGCAAAATGAGTGAA 57.506 33.333 2.68 0.00 0.00 3.18
3413 3546 8.650490 TGACTATATATGGAGCAAAATGAGTGA 58.350 33.333 2.68 0.00 0.00 3.41
3414 3547 8.715998 GTGACTATATATGGAGCAAAATGAGTG 58.284 37.037 2.68 0.00 0.00 3.51
3415 3548 8.654997 AGTGACTATATATGGAGCAAAATGAGT 58.345 33.333 2.68 0.00 0.00 3.41
3416 3549 9.499479 AAGTGACTATATATGGAGCAAAATGAG 57.501 33.333 2.68 0.00 0.00 2.90
3417 3550 9.276590 CAAGTGACTATATATGGAGCAAAATGA 57.723 33.333 2.68 0.00 0.00 2.57
3418 3551 9.060347 ACAAGTGACTATATATGGAGCAAAATG 57.940 33.333 2.68 4.07 0.00 2.32
3419 3552 9.632638 AACAAGTGACTATATATGGAGCAAAAT 57.367 29.630 2.68 0.00 0.00 1.82
3420 3553 8.892723 CAACAAGTGACTATATATGGAGCAAAA 58.107 33.333 2.68 0.00 0.00 2.44
3421 3554 8.264347 TCAACAAGTGACTATATATGGAGCAAA 58.736 33.333 2.68 0.00 0.00 3.68
3422 3555 7.791029 TCAACAAGTGACTATATATGGAGCAA 58.209 34.615 2.68 0.00 0.00 3.91
3423 3556 7.360113 TCAACAAGTGACTATATATGGAGCA 57.640 36.000 2.68 0.00 0.00 4.26
3424 3557 8.662781 TTTCAACAAGTGACTATATATGGAGC 57.337 34.615 2.68 0.00 35.39 4.70
3433 3566 9.778741 TTTCTAGACATTTCAACAAGTGACTAT 57.221 29.630 0.00 0.00 35.39 2.12
3434 3567 9.261180 CTTTCTAGACATTTCAACAAGTGACTA 57.739 33.333 0.00 0.00 35.39 2.59
3435 3568 7.987458 TCTTTCTAGACATTTCAACAAGTGACT 59.013 33.333 0.00 0.00 35.39 3.41
3436 3569 8.142994 TCTTTCTAGACATTTCAACAAGTGAC 57.857 34.615 0.00 0.00 35.39 3.67
3452 3585 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
3453 3586 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
3454 3587 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
3455 3588 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
3456 3589 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
3457 3590 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
3458 3591 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
3459 3592 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
3460 3593 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
3461 3594 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
3462 3595 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
3463 3596 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
3464 3597 8.759782 CATATACTCCCTCCGTTCCTAAATATT 58.240 37.037 0.00 0.00 0.00 1.28
3465 3598 7.147707 GCATATACTCCCTCCGTTCCTAAATAT 60.148 40.741 0.00 0.00 0.00 1.28
3466 3599 6.154021 GCATATACTCCCTCCGTTCCTAAATA 59.846 42.308 0.00 0.00 0.00 1.40
3467 3600 5.046520 GCATATACTCCCTCCGTTCCTAAAT 60.047 44.000 0.00 0.00 0.00 1.40
3468 3601 4.282703 GCATATACTCCCTCCGTTCCTAAA 59.717 45.833 0.00 0.00 0.00 1.85
3469 3602 3.830755 GCATATACTCCCTCCGTTCCTAA 59.169 47.826 0.00 0.00 0.00 2.69
3470 3603 3.075582 AGCATATACTCCCTCCGTTCCTA 59.924 47.826 0.00 0.00 0.00 2.94
3471 3604 2.158295 AGCATATACTCCCTCCGTTCCT 60.158 50.000 0.00 0.00 0.00 3.36
3472 3605 2.028930 CAGCATATACTCCCTCCGTTCC 60.029 54.545 0.00 0.00 0.00 3.62
3473 3606 2.891580 TCAGCATATACTCCCTCCGTTC 59.108 50.000 0.00 0.00 0.00 3.95
3474 3607 2.958818 TCAGCATATACTCCCTCCGTT 58.041 47.619 0.00 0.00 0.00 4.44
3475 3608 2.677542 TCAGCATATACTCCCTCCGT 57.322 50.000 0.00 0.00 0.00 4.69
3476 3609 4.543590 AATTCAGCATATACTCCCTCCG 57.456 45.455 0.00 0.00 0.00 4.63
3477 3610 5.877564 GCTAAATTCAGCATATACTCCCTCC 59.122 44.000 0.00 0.00 41.40 4.30
3478 3611 6.706295 AGCTAAATTCAGCATATACTCCCTC 58.294 40.000 2.78 0.00 44.35 4.30
3479 3612 6.694445 AGCTAAATTCAGCATATACTCCCT 57.306 37.500 2.78 0.00 44.35 4.20
3480 3613 9.103861 GATAAGCTAAATTCAGCATATACTCCC 57.896 37.037 2.78 0.00 44.35 4.30
3481 3614 9.658799 TGATAAGCTAAATTCAGCATATACTCC 57.341 33.333 2.78 0.00 44.35 3.85
3577 3711 9.722056 GTGAATCGATGCAAGACTAAATTTTAT 57.278 29.630 7.92 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.