Multiple sequence alignment - TraesCS5D01G307200

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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 TraesCS5D01G307200 chr5D 100.000 2863 0 0 1333 4195 403939768 403936906 0.000000e+00 5288.0
1 TraesCS5D01G307200 chr5D 100.000 1051 0 0 1 1051 403941100 403940050 0.000000e+00 1941.0
2 TraesCS5D01G307200 chr5A 95.176 2073 74 17 1333 3400 510280618 510278567 0.000000e+00 3251.0
3 TraesCS5D01G307200 chr5A 93.427 426 18 3 632 1051 510281159 510280738 1.280000e-174 623.0
4 TraesCS5D01G307200 chr5A 80.679 383 54 10 1 367 510281716 510281338 3.190000e-71 279.0
5 TraesCS5D01G307200 chr5A 82.353 187 24 7 3831 4009 510278436 510278251 2.020000e-33 154.0
6 TraesCS5D01G307200 chr5A 87.736 106 11 2 3726 3830 510278569 510278465 5.700000e-24 122.0
7 TraesCS5D01G307200 chr5A 89.583 48 5 0 4109 4156 510278173 510278126 1.260000e-05 62.1
8 TraesCS5D01G307200 chr5B 91.508 1943 121 17 1670 3590 484734035 484735955 0.000000e+00 2634.0
9 TraesCS5D01G307200 chr5B 88.988 563 33 13 3638 4195 484736045 484736583 0.000000e+00 669.0
10 TraesCS5D01G307200 chr5B 90.020 511 36 7 541 1051 484732931 484733426 0.000000e+00 647.0
11 TraesCS5D01G307200 chr5B 86.965 514 25 6 6 519 484732473 484732944 1.330000e-149 540.0
12 TraesCS5D01G307200 chr5B 85.714 77 6 4 3327 3400 403701746 403701672 4.500000e-10 76.8
13 TraesCS5D01G307200 chr7B 89.189 74 7 1 3327 3400 89952171 89952243 1.610000e-14 91.6
14 TraesCS5D01G307200 chr7A 89.189 74 7 1 3327 3400 128783043 128783115 1.610000e-14 91.6
15 TraesCS5D01G307200 chr2D 87.838 74 8 1 3327 3400 11394132 11394060 7.470000e-13 86.1
16 TraesCS5D01G307200 chr2B 89.831 59 5 1 3831 3889 717474140 717474197 1.620000e-09 75.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G307200 chr5D 403936906 403941100 4194 True 3614.500000 5288 100.00000 1 4195 2 chr5D.!!$R1 4194
1 TraesCS5D01G307200 chr5A 510278126 510281716 3590 True 748.516667 3251 88.15900 1 4156 6 chr5A.!!$R1 4155
2 TraesCS5D01G307200 chr5B 484732473 484736583 4110 False 1122.500000 2634 89.37025 6 4195 4 chr5B.!!$F1 4189

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
384 397 0.321671 AACTACGGCATGTGTGAGCT 59.678 50.000 0.00 0.0 0.00 4.09 F
895 912 0.837272 AATCAACGGTCGGGATCCAT 59.163 50.000 15.23 0.0 0.00 3.41 F
924 941 1.149401 GATAACTGCCTCCTGCCCC 59.851 63.158 0.00 0.0 40.16 5.80 F
2102 2307 1.275856 GAAAATCCCATGCAAGCACCA 59.724 47.619 0.00 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1680 1874 1.456296 TTCACCATCTGCAGCACATC 58.544 50.0 9.47 0.0 0.00 3.06 R
2882 3089 1.156736 CTTTTGGTACCTGAGCCACG 58.843 55.0 14.36 0.0 34.02 4.94 R
2975 3182 7.759489 TGTAACCTTTTCAACATATTCAGCT 57.241 32.0 0.00 0.0 0.00 4.24 R
3618 3835 0.179081 CTTGGCTAAGGGTACTCGGC 60.179 60.0 1.05 0.0 0.00 5.54 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
47 48 7.337167 AGAGATGTTATGGATGGATATTCAGC 58.663 38.462 0.00 0.00 0.00 4.26
80 90 7.308782 AGGAGATAATTCAACACATCGAAAC 57.691 36.000 0.00 0.00 0.00 2.78
134 144 2.175202 CTGCAGAGGTTCTCCTGTAGT 58.825 52.381 8.42 0.00 45.24 2.73
137 147 2.354203 GCAGAGGTTCTCCTGTAGTTGG 60.354 54.545 0.00 0.00 45.24 3.77
206 216 3.724508 CAGAGGAACGTGATATCTGCT 57.275 47.619 3.98 0.00 31.83 4.24
237 247 5.932303 TCATCAGTGCCAGTTTAGTAAGTTC 59.068 40.000 0.00 0.00 0.00 3.01
256 266 2.927028 TCGCTCCATAGTGCACTAGTA 58.073 47.619 29.05 16.63 33.01 1.82
268 278 2.224646 TGCACTAGTACCAAATGCCACA 60.225 45.455 0.00 0.00 35.37 4.17
272 282 2.489938 AGTACCAAATGCCACACGAT 57.510 45.000 0.00 0.00 0.00 3.73
307 317 1.102154 CGCCCTGCACAATTATTCCA 58.898 50.000 0.00 0.00 0.00 3.53
317 327 4.584325 GCACAATTATTCCATAGCTTCCCA 59.416 41.667 0.00 0.00 0.00 4.37
323 333 7.771927 ATTATTCCATAGCTTCCCAATCAAG 57.228 36.000 0.00 0.00 0.00 3.02
331 341 2.687914 GCTTCCCAATCAAGCTACCCAT 60.688 50.000 0.00 0.00 42.63 4.00
332 342 2.734755 TCCCAATCAAGCTACCCATG 57.265 50.000 0.00 0.00 0.00 3.66
335 345 3.118038 TCCCAATCAAGCTACCCATGTAC 60.118 47.826 0.00 0.00 0.00 2.90
336 346 3.214328 CCAATCAAGCTACCCATGTACC 58.786 50.000 0.00 0.00 0.00 3.34
341 354 2.367567 CAAGCTACCCATGTACCGGTAT 59.632 50.000 19.19 0.00 34.15 2.73
384 397 0.321671 AACTACGGCATGTGTGAGCT 59.678 50.000 0.00 0.00 0.00 4.09
385 398 1.182667 ACTACGGCATGTGTGAGCTA 58.817 50.000 0.00 0.00 0.00 3.32
386 399 1.135139 ACTACGGCATGTGTGAGCTAG 59.865 52.381 0.00 0.00 0.00 3.42
395 408 6.455647 GGCATGTGTGAGCTAGTATATGTTA 58.544 40.000 0.00 0.00 0.00 2.41
425 438 6.096282 ACTCTGAAACTATCTGAACCTAGCTC 59.904 42.308 0.00 0.00 35.82 4.09
426 439 5.066634 TCTGAAACTATCTGAACCTAGCTCG 59.933 44.000 0.00 0.00 33.57 5.03
427 440 4.948004 TGAAACTATCTGAACCTAGCTCGA 59.052 41.667 0.00 0.00 0.00 4.04
428 441 4.904253 AACTATCTGAACCTAGCTCGAC 57.096 45.455 0.00 0.00 0.00 4.20
429 442 4.159244 ACTATCTGAACCTAGCTCGACT 57.841 45.455 0.00 0.00 0.00 4.18
430 443 4.528920 ACTATCTGAACCTAGCTCGACTT 58.471 43.478 0.00 0.00 0.00 3.01
431 444 5.682659 ACTATCTGAACCTAGCTCGACTTA 58.317 41.667 0.00 0.00 0.00 2.24
432 445 6.120905 ACTATCTGAACCTAGCTCGACTTAA 58.879 40.000 0.00 0.00 0.00 1.85
433 446 5.916661 ATCTGAACCTAGCTCGACTTAAA 57.083 39.130 0.00 0.00 0.00 1.52
434 447 5.056894 TCTGAACCTAGCTCGACTTAAAC 57.943 43.478 0.00 0.00 0.00 2.01
435 448 4.082354 TCTGAACCTAGCTCGACTTAAACC 60.082 45.833 0.00 0.00 0.00 3.27
436 449 3.575256 TGAACCTAGCTCGACTTAAACCA 59.425 43.478 0.00 0.00 0.00 3.67
437 450 4.039488 TGAACCTAGCTCGACTTAAACCAA 59.961 41.667 0.00 0.00 0.00 3.67
438 451 4.189639 ACCTAGCTCGACTTAAACCAAG 57.810 45.455 0.00 0.00 40.38 3.61
439 452 2.930682 CCTAGCTCGACTTAAACCAAGC 59.069 50.000 0.00 0.00 37.83 4.01
440 453 1.809684 AGCTCGACTTAAACCAAGCC 58.190 50.000 0.00 0.00 37.83 4.35
499 516 0.964700 TTTGCCACCGAATCATGCAA 59.035 45.000 0.00 0.00 39.92 4.08
512 529 6.347240 CCGAATCATGCAACTCTTATCTTAGC 60.347 42.308 0.00 0.00 0.00 3.09
519 536 6.341316 TGCAACTCTTATCTTAGCGAAGAAT 58.659 36.000 13.49 5.28 44.85 2.40
520 537 6.477033 TGCAACTCTTATCTTAGCGAAGAATC 59.523 38.462 13.49 0.00 44.85 2.52
522 539 7.010552 GCAACTCTTATCTTAGCGAAGAATCAA 59.989 37.037 13.49 7.26 44.85 2.57
523 540 9.039870 CAACTCTTATCTTAGCGAAGAATCAAT 57.960 33.333 13.49 0.00 44.85 2.57
524 541 9.606631 AACTCTTATCTTAGCGAAGAATCAATT 57.393 29.630 13.49 0.00 44.85 2.32
525 542 9.606631 ACTCTTATCTTAGCGAAGAATCAATTT 57.393 29.630 13.49 0.00 44.85 1.82
581 598 5.327091 CAATATCACAGCAAAGAAACGAGG 58.673 41.667 0.00 0.00 0.00 4.63
602 619 1.999735 CGACTTCGCTGCATTTCCTAA 59.000 47.619 0.00 0.00 0.00 2.69
606 623 3.568007 ACTTCGCTGCATTTCCTAAACAA 59.432 39.130 0.00 0.00 0.00 2.83
751 768 1.007964 CCGCAGCATCTCCTCGTAG 60.008 63.158 0.00 0.00 0.00 3.51
895 912 0.837272 AATCAACGGTCGGGATCCAT 59.163 50.000 15.23 0.00 0.00 3.41
924 941 1.149401 GATAACTGCCTCCTGCCCC 59.851 63.158 0.00 0.00 40.16 5.80
998 1021 3.396685 AGCTCTCTTGGACTGGATAGT 57.603 47.619 0.00 0.00 40.66 2.12
1379 1402 4.524316 TGTTGCAATTGAAGAGAATGGG 57.476 40.909 10.34 0.00 0.00 4.00
1382 1405 5.048083 TGTTGCAATTGAAGAGAATGGGTAC 60.048 40.000 10.34 0.00 0.00 3.34
1457 1480 5.728637 CCAGCTCTTGGTTAATTTTCCTT 57.271 39.130 0.00 0.00 42.41 3.36
1458 1481 6.834168 CCAGCTCTTGGTTAATTTTCCTTA 57.166 37.500 0.00 0.00 42.41 2.69
1459 1482 7.410120 CCAGCTCTTGGTTAATTTTCCTTAT 57.590 36.000 0.00 0.00 42.41 1.73
1571 1620 9.474313 AGCATTAATAAGAGATTTAAACCCACA 57.526 29.630 0.00 0.00 0.00 4.17
1576 1625 3.408634 AGAGATTTAAACCCACACACCG 58.591 45.455 0.00 0.00 0.00 4.94
1647 1705 8.162085 AGATATATGTTCAGACAGGCAAATGAT 58.838 33.333 0.00 0.00 39.58 2.45
1884 2078 6.124340 TCGATTGTACTGAGGGAGTAATACA 58.876 40.000 0.00 0.00 38.96 2.29
1949 2146 8.715191 TCATAGTTGCTTGTGAATTTGTTTTT 57.285 26.923 0.00 0.00 0.00 1.94
1996 2193 1.804372 CGCTTCAGGCAGTATCTCCAC 60.804 57.143 0.00 0.00 41.91 4.02
2102 2307 1.275856 GAAAATCCCATGCAAGCACCA 59.724 47.619 0.00 0.00 0.00 4.17
2123 2328 7.084486 CACCAGTAGCCTTTAAAGATTTTCAC 58.916 38.462 16.98 5.71 0.00 3.18
2222 2427 7.714377 TGAAAATAAAATCCAGCTCTTTTGCAA 59.286 29.630 0.00 0.00 34.99 4.08
2389 2594 2.096013 GCGATTGAAAGGAGGTAGCAAC 59.904 50.000 0.00 0.00 0.00 4.17
2458 2663 6.017933 GCAACTCTGTTTCTGTTATTCGATG 58.982 40.000 0.00 0.00 0.00 3.84
2882 3089 2.941720 GACCTGCTCCATGAATCTTGTC 59.058 50.000 0.00 0.00 0.00 3.18
2975 3182 3.871006 AGAAAATCATCAATCGCGCAGTA 59.129 39.130 8.75 0.00 0.00 2.74
2996 3203 7.575720 GCAGTAGCTGAATATGTTGAAAAGGTT 60.576 37.037 0.00 0.00 37.91 3.50
3024 3231 2.439507 ACTATCCATGGGTTGCCTACTG 59.560 50.000 13.02 0.00 0.00 2.74
3043 3250 3.758554 ACTGTAGATGTGAATTGGTTGGC 59.241 43.478 0.00 0.00 0.00 4.52
3168 3375 3.131396 GGAAAAGAGTTCTGCTTCGACA 58.869 45.455 0.00 0.00 0.00 4.35
3346 3557 5.598417 TCTCTACTGGCTAAATATCTGTGCA 59.402 40.000 0.00 0.00 0.00 4.57
3374 3585 2.224066 CGGGGGCAACTCTATTCTAGTG 60.224 54.545 0.00 0.00 37.10 2.74
3382 3593 5.062308 GCAACTCTATTCTAGTGGTTCAACG 59.938 44.000 0.00 0.00 0.00 4.10
3394 3605 6.459670 AGTGGTTCAACGTAGGAAATTTTT 57.540 33.333 4.36 0.00 0.00 1.94
3429 3640 4.165779 GGAAAAATCGTCGTTACCGAGTA 58.834 43.478 0.00 0.00 45.26 2.59
3431 3642 3.829886 AAATCGTCGTTACCGAGTACA 57.170 42.857 0.00 0.00 45.26 2.90
3432 3643 4.361451 AAATCGTCGTTACCGAGTACAT 57.639 40.909 0.00 0.00 45.26 2.29
3433 3644 4.361451 AATCGTCGTTACCGAGTACATT 57.639 40.909 0.00 0.00 45.26 2.71
3434 3645 3.121559 TCGTCGTTACCGAGTACATTG 57.878 47.619 0.00 0.00 45.26 2.82
3435 3646 2.159531 TCGTCGTTACCGAGTACATTGG 60.160 50.000 0.00 0.00 45.26 3.16
3437 3648 3.578688 GTCGTTACCGAGTACATTGGTT 58.421 45.455 8.70 0.00 44.01 3.67
3443 3660 2.295070 ACCGAGTACATTGGTTTTTGCC 59.705 45.455 0.00 0.00 44.01 4.52
3452 3669 1.600023 TGGTTTTTGCCGAGTACCAG 58.400 50.000 0.00 0.00 34.13 4.00
3469 3686 0.528924 CAGAACACGGGATCACGGTA 59.471 55.000 23.42 0.00 38.39 4.02
3484 3701 1.203287 ACGGTAAAGGACTCGTAAGCC 59.797 52.381 0.00 0.00 34.50 4.35
3528 3745 1.352352 AGGGCATGGCATATGGTAGAC 59.648 52.381 22.06 0.00 0.00 2.59
3539 3756 2.508663 GGTAGACGCTGCCGAACC 60.509 66.667 0.00 0.00 38.29 3.62
3540 3757 2.879462 GTAGACGCTGCCGAACCG 60.879 66.667 0.00 0.00 38.29 4.44
3580 3797 1.800805 AACATGACAGAACTCGGCTG 58.199 50.000 0.00 0.00 39.26 4.85
3594 3811 2.962253 GCTGACGGAGCGTATGCC 60.962 66.667 2.51 0.00 41.37 4.40
3595 3812 2.494445 CTGACGGAGCGTATGCCA 59.506 61.111 2.51 0.00 41.37 4.92
3596 3813 1.153647 CTGACGGAGCGTATGCCAA 60.154 57.895 2.51 0.00 41.37 4.52
3597 3814 1.148157 CTGACGGAGCGTATGCCAAG 61.148 60.000 2.51 0.00 41.37 3.61
3598 3815 1.141019 GACGGAGCGTATGCCAAGA 59.859 57.895 2.51 0.00 41.37 3.02
3599 3816 0.872021 GACGGAGCGTATGCCAAGAG 60.872 60.000 2.51 0.00 41.37 2.85
3600 3817 2.240500 CGGAGCGTATGCCAAGAGC 61.241 63.158 2.51 0.00 44.31 4.09
3601 3818 1.889573 GGAGCGTATGCCAAGAGCC 60.890 63.158 2.51 0.00 44.31 4.70
3602 3819 1.144936 GAGCGTATGCCAAGAGCCT 59.855 57.895 2.51 0.00 44.31 4.58
3603 3820 0.878086 GAGCGTATGCCAAGAGCCTC 60.878 60.000 2.51 0.00 44.31 4.70
3604 3821 1.153369 GCGTATGCCAAGAGCCTCA 60.153 57.895 0.00 0.00 42.71 3.86
3605 3822 1.432270 GCGTATGCCAAGAGCCTCAC 61.432 60.000 0.00 0.00 42.71 3.51
3606 3823 1.148157 CGTATGCCAAGAGCCTCACG 61.148 60.000 0.00 0.00 42.71 4.35
3607 3824 0.811616 GTATGCCAAGAGCCTCACGG 60.812 60.000 0.00 0.00 42.71 4.94
3608 3825 0.975556 TATGCCAAGAGCCTCACGGA 60.976 55.000 3.76 0.00 42.71 4.69
3609 3826 1.630126 ATGCCAAGAGCCTCACGGAT 61.630 55.000 3.76 0.00 42.71 4.18
3610 3827 1.817099 GCCAAGAGCCTCACGGATG 60.817 63.158 3.76 0.00 34.35 3.51
3611 3828 1.153289 CCAAGAGCCTCACGGATGG 60.153 63.158 0.00 0.00 0.00 3.51
3612 3829 1.153289 CAAGAGCCTCACGGATGGG 60.153 63.158 0.00 0.00 0.00 4.00
3613 3830 1.613630 AAGAGCCTCACGGATGGGT 60.614 57.895 0.00 0.00 36.70 4.51
3614 3831 1.201429 AAGAGCCTCACGGATGGGTT 61.201 55.000 0.00 0.00 33.83 4.11
3615 3832 1.450312 GAGCCTCACGGATGGGTTG 60.450 63.158 0.00 0.00 33.83 3.77
3616 3833 2.438434 GCCTCACGGATGGGTTGG 60.438 66.667 0.00 0.00 0.00 3.77
3617 3834 2.272146 CCTCACGGATGGGTTGGG 59.728 66.667 0.00 0.00 0.00 4.12
3618 3835 2.272146 CTCACGGATGGGTTGGGG 59.728 66.667 0.00 0.00 0.00 4.96
3619 3836 3.995506 CTCACGGATGGGTTGGGGC 62.996 68.421 0.00 0.00 0.00 5.80
3633 3850 2.820261 GGGCCGAGTACCCTTAGC 59.180 66.667 0.00 0.00 44.68 3.09
3635 3852 2.062177 GGCCGAGTACCCTTAGCCA 61.062 63.158 0.00 0.00 38.44 4.75
3706 4000 0.664224 TTTTTCGGCACTCGGGAAAC 59.336 50.000 0.00 0.00 39.77 2.78
3767 4061 4.414182 TGACGTGGGGAGGGAATTTATAAT 59.586 41.667 0.00 0.00 0.00 1.28
3789 4083 7.976414 AATCAAACATGAGGGGAAATATGAA 57.024 32.000 0.00 0.00 0.00 2.57
3854 4176 9.950680 TTCTATTGGCGATTTATTTGATTTCTC 57.049 29.630 0.00 0.00 0.00 2.87
3963 4289 3.502123 TTTCCCAAGAAACGATGAGGT 57.498 42.857 0.00 0.00 37.07 3.85
3964 4290 2.472695 TCCCAAGAAACGATGAGGTG 57.527 50.000 0.00 0.00 0.00 4.00
3965 4291 1.003118 TCCCAAGAAACGATGAGGTGG 59.997 52.381 0.00 0.00 0.00 4.61
3967 4293 1.271379 CCAAGAAACGATGAGGTGGGT 60.271 52.381 0.00 0.00 0.00 4.51
3980 4306 2.196229 TGGGTGGTCGTTTTGGGG 59.804 61.111 0.00 0.00 0.00 4.96
3981 4307 2.599281 GGGTGGTCGTTTTGGGGG 60.599 66.667 0.00 0.00 0.00 5.40
4028 4357 2.814023 TTTTTGCGGGTCACATGGT 58.186 47.368 0.00 0.00 0.00 3.55
4029 4358 1.115467 TTTTTGCGGGTCACATGGTT 58.885 45.000 0.00 0.00 0.00 3.67
4030 4359 1.115467 TTTTGCGGGTCACATGGTTT 58.885 45.000 0.00 0.00 0.00 3.27
4031 4360 0.387202 TTTGCGGGTCACATGGTTTG 59.613 50.000 0.00 0.00 0.00 2.93
4047 4376 5.798125 TGGTTTGAAAAAGGCATGTATCA 57.202 34.783 0.00 0.00 0.00 2.15
4138 4480 5.819379 TGATCATGGATGCTAGTCTGTTTTC 59.181 40.000 0.00 0.00 0.00 2.29
4145 4487 5.470098 GGATGCTAGTCTGTTTTCTTGTTCA 59.530 40.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.304686 TCTCTCCCTTGCAAAGTAGAAAA 57.695 39.130 0.00 0.00 44.25 2.29
47 48 5.525012 TGTTGAATTATCTCCTTCATCGCTG 59.475 40.000 0.00 0.00 31.83 5.18
206 216 3.769739 ACTGGCACTGATGAACTGTTA 57.230 42.857 0.00 0.00 0.00 2.41
237 247 2.287668 GGTACTAGTGCACTATGGAGCG 60.288 54.545 26.22 15.76 31.76 5.03
256 266 3.879998 TGTATATCGTGTGGCATTTGGT 58.120 40.909 0.00 0.00 0.00 3.67
268 278 8.350722 CAGGGCGACTATATTTATGTATATCGT 58.649 37.037 0.00 0.00 0.00 3.73
272 282 7.093684 TGTGCAGGGCGACTATATTTATGTATA 60.094 37.037 0.00 0.00 0.00 1.47
317 327 2.158813 CCGGTACATGGGTAGCTTGATT 60.159 50.000 0.00 0.00 43.99 2.57
323 333 1.965643 TGATACCGGTACATGGGTAGC 59.034 52.381 18.55 14.66 43.66 3.58
331 341 5.046159 AGGTTCAGAATTTGATACCGGTACA 60.046 40.000 18.55 14.17 39.70 2.90
332 342 5.425630 AGGTTCAGAATTTGATACCGGTAC 58.574 41.667 18.55 11.61 39.70 3.34
335 345 5.523916 CAGTAGGTTCAGAATTTGATACCGG 59.476 44.000 0.00 0.00 39.70 5.28
336 346 5.523916 CCAGTAGGTTCAGAATTTGATACCG 59.476 44.000 0.00 0.00 39.70 4.02
341 354 6.187727 AGTTCCAGTAGGTTCAGAATTTGA 57.812 37.500 0.00 0.00 35.89 2.69
395 408 6.153680 AGGTTCAGATAGTTTCAGAGTTCGAT 59.846 38.462 0.00 0.00 0.00 3.59
426 439 1.162698 GACCCGGCTTGGTTTAAGTC 58.837 55.000 0.00 0.00 39.24 3.01
427 440 0.475044 TGACCCGGCTTGGTTTAAGT 59.525 50.000 0.00 0.00 39.24 2.24
428 441 1.472480 CATGACCCGGCTTGGTTTAAG 59.528 52.381 0.00 0.00 39.24 1.85
429 442 1.202952 ACATGACCCGGCTTGGTTTAA 60.203 47.619 0.00 0.00 39.24 1.52
430 443 0.402504 ACATGACCCGGCTTGGTTTA 59.597 50.000 0.00 0.00 39.24 2.01
431 444 1.152830 ACATGACCCGGCTTGGTTT 59.847 52.632 0.00 0.00 39.24 3.27
432 445 1.603455 CACATGACCCGGCTTGGTT 60.603 57.895 0.00 0.00 39.24 3.67
433 446 2.034066 CACATGACCCGGCTTGGT 59.966 61.111 0.00 0.00 42.79 3.67
434 447 2.751436 CCACATGACCCGGCTTGG 60.751 66.667 0.00 0.00 37.55 3.61
435 448 2.034066 ACCACATGACCCGGCTTG 59.966 61.111 0.00 0.00 0.00 4.01
436 449 2.034066 CACCACATGACCCGGCTT 59.966 61.111 0.00 0.00 0.00 4.35
437 450 4.033776 CCACCACATGACCCGGCT 62.034 66.667 0.00 0.00 0.00 5.52
438 451 3.344137 ATCCACCACATGACCCGGC 62.344 63.158 0.00 0.00 0.00 6.13
439 452 1.451927 CATCCACCACATGACCCGG 60.452 63.158 0.00 0.00 0.00 5.73
440 453 0.322456 AACATCCACCACATGACCCG 60.322 55.000 0.00 0.00 0.00 5.28
499 516 9.606631 AAATTGATTCTTCGCTAAGATAAGAGT 57.393 29.630 0.96 0.00 41.36 3.24
535 552 5.178252 TGCTGATTCTTCGCTAAGATTATGC 59.822 40.000 0.96 6.96 41.36 3.14
536 553 6.775939 TGCTGATTCTTCGCTAAGATTATG 57.224 37.500 0.96 0.00 41.36 1.90
537 554 7.976135 ATTGCTGATTCTTCGCTAAGATTAT 57.024 32.000 0.96 0.00 41.36 1.28
538 555 9.144747 GATATTGCTGATTCTTCGCTAAGATTA 57.855 33.333 0.96 0.00 41.36 1.75
539 556 7.658982 TGATATTGCTGATTCTTCGCTAAGATT 59.341 33.333 0.96 0.00 41.36 2.40
540 557 7.117523 GTGATATTGCTGATTCTTCGCTAAGAT 59.882 37.037 0.96 0.00 41.36 2.40
541 558 6.422100 GTGATATTGCTGATTCTTCGCTAAGA 59.578 38.462 0.00 0.00 40.03 2.10
542 559 6.201615 TGTGATATTGCTGATTCTTCGCTAAG 59.798 38.462 0.00 0.00 0.00 2.18
543 560 6.048509 TGTGATATTGCTGATTCTTCGCTAA 58.951 36.000 0.00 0.00 0.00 3.09
544 561 5.600696 TGTGATATTGCTGATTCTTCGCTA 58.399 37.500 0.00 0.00 0.00 4.26
545 562 4.445453 TGTGATATTGCTGATTCTTCGCT 58.555 39.130 0.00 0.00 0.00 4.93
546 563 4.770287 CTGTGATATTGCTGATTCTTCGC 58.230 43.478 0.00 0.00 0.00 4.70
547 564 4.271776 TGCTGTGATATTGCTGATTCTTCG 59.728 41.667 0.00 0.00 0.00 3.79
548 565 5.746307 TGCTGTGATATTGCTGATTCTTC 57.254 39.130 0.00 0.00 0.00 2.87
549 566 6.376299 TCTTTGCTGTGATATTGCTGATTCTT 59.624 34.615 0.00 0.00 0.00 2.52
550 567 5.884232 TCTTTGCTGTGATATTGCTGATTCT 59.116 36.000 0.00 0.00 0.00 2.40
551 568 6.127810 TCTTTGCTGTGATATTGCTGATTC 57.872 37.500 0.00 0.00 0.00 2.52
552 569 6.519679 TTCTTTGCTGTGATATTGCTGATT 57.480 33.333 0.00 0.00 0.00 2.57
553 570 6.327934 GTTTCTTTGCTGTGATATTGCTGAT 58.672 36.000 0.00 0.00 0.00 2.90
554 571 5.617529 CGTTTCTTTGCTGTGATATTGCTGA 60.618 40.000 0.00 0.00 0.00 4.26
591 608 7.002250 TGATGGAAATTGTTTAGGAAATGCA 57.998 32.000 0.00 0.00 0.00 3.96
602 619 3.766051 GCTTCTCCCTGATGGAAATTGTT 59.234 43.478 0.00 0.00 44.57 2.83
606 623 3.744940 TTGCTTCTCCCTGATGGAAAT 57.255 42.857 0.00 0.00 44.57 2.17
645 662 1.003718 GGTAGGTGCCCACTGACAC 60.004 63.158 0.00 0.00 36.03 3.67
649 666 1.671054 CAACGGTAGGTGCCCACTG 60.671 63.158 0.00 0.00 0.00 3.66
819 836 5.489792 TCACTAGCACTTCCTTCAGATTT 57.510 39.130 0.00 0.00 0.00 2.17
895 912 1.063266 GGCAGTTATCCAATTCCCCCA 60.063 52.381 0.00 0.00 0.00 4.96
924 941 1.286553 AGGAGTGGAGTACTGGAGGAG 59.713 57.143 0.00 0.00 40.53 3.69
1382 1405 8.906867 AGAATGACAAATACATCAACCTAATGG 58.093 33.333 0.00 0.00 39.83 3.16
1453 1476 8.846211 CCAAAGTTCTTCACAAGTTTATAAGGA 58.154 33.333 0.00 0.00 29.45 3.36
1454 1477 8.082242 CCCAAAGTTCTTCACAAGTTTATAAGG 58.918 37.037 0.00 0.00 29.45 2.69
1456 1479 8.528044 ACCCAAAGTTCTTCACAAGTTTATAA 57.472 30.769 0.00 0.00 29.45 0.98
1457 1480 8.528044 AACCCAAAGTTCTTCACAAGTTTATA 57.472 30.769 0.00 0.00 30.99 0.98
1458 1481 7.418337 AACCCAAAGTTCTTCACAAGTTTAT 57.582 32.000 0.00 0.00 30.99 1.40
1459 1482 6.844097 AACCCAAAGTTCTTCACAAGTTTA 57.156 33.333 0.00 0.00 30.99 2.01
1493 1516 9.595823 GTGCAAATTCTCTGGTAAGTATTAGTA 57.404 33.333 0.00 0.00 0.00 1.82
1506 1529 5.237996 TGTTCTCTCTTGTGCAAATTCTCTG 59.762 40.000 0.00 0.00 0.00 3.35
1576 1625 1.519408 AACAATAGCACCCGTGTGTC 58.481 50.000 0.00 0.00 44.65 3.67
1680 1874 1.456296 TTCACCATCTGCAGCACATC 58.544 50.000 9.47 0.00 0.00 3.06
1949 2146 4.159321 TGCAAACTTTGTGGTTGATTCTGA 59.841 37.500 3.48 0.00 45.82 3.27
2102 2307 7.506328 AACGTGAAAATCTTTAAAGGCTACT 57.494 32.000 15.13 0.00 0.00 2.57
2123 2328 4.745125 TCTTCTTCAGTAAGCACAGAAACG 59.255 41.667 0.00 0.00 30.73 3.60
2302 2507 5.622346 AGACTTTCTCAAAGACAGAACCT 57.378 39.130 3.00 0.00 41.02 3.50
2304 2509 8.594881 TGATAAGACTTTCTCAAAGACAGAAC 57.405 34.615 3.00 0.00 41.02 3.01
2389 2594 6.852404 TGAGATGGATAGGGAAATAAAAGGG 58.148 40.000 0.00 0.00 0.00 3.95
2715 2921 2.869801 TGACCAGCGTTAGTTTCACAAG 59.130 45.455 0.00 0.00 0.00 3.16
2882 3089 1.156736 CTTTTGGTACCTGAGCCACG 58.843 55.000 14.36 0.00 34.02 4.94
2975 3182 7.759489 TGTAACCTTTTCAACATATTCAGCT 57.241 32.000 0.00 0.00 0.00 4.24
2996 3203 4.141574 GGCAACCCATGGATAGTAGTTGTA 60.142 45.833 22.38 0.00 37.50 2.41
3024 3231 3.088532 TGGCCAACCAATTCACATCTAC 58.911 45.455 0.61 0.00 45.37 2.59
3043 3250 3.676873 GCCATTGCAACAGAGGTAAATGG 60.677 47.826 0.00 2.27 41.24 3.16
3168 3375 0.537188 CCTGTTAGATGGACAGCCGT 59.463 55.000 0.00 0.00 42.42 5.68
3374 3585 7.568679 GCAATCAAAAATTTCCTACGTTGAACC 60.569 37.037 0.00 0.00 0.00 3.62
3382 3593 7.542130 CCAGTAGTGCAATCAAAAATTTCCTAC 59.458 37.037 0.00 0.00 0.00 3.18
3394 3605 4.759693 ACGATTTTTCCAGTAGTGCAATCA 59.240 37.500 0.00 0.00 0.00 2.57
3429 3640 2.295070 GGTACTCGGCAAAAACCAATGT 59.705 45.455 0.00 0.00 0.00 2.71
3431 3642 2.556622 CTGGTACTCGGCAAAAACCAAT 59.443 45.455 0.00 0.00 39.62 3.16
3432 3643 1.950909 CTGGTACTCGGCAAAAACCAA 59.049 47.619 0.00 0.00 39.62 3.67
3433 3644 1.141254 TCTGGTACTCGGCAAAAACCA 59.859 47.619 0.00 0.00 37.88 3.67
3434 3645 1.886886 TCTGGTACTCGGCAAAAACC 58.113 50.000 0.00 0.00 0.00 3.27
3435 3646 2.614983 TGTTCTGGTACTCGGCAAAAAC 59.385 45.455 0.00 0.00 0.00 2.43
3436 3647 2.614983 GTGTTCTGGTACTCGGCAAAAA 59.385 45.455 0.00 0.00 0.00 1.94
3437 3648 2.215196 GTGTTCTGGTACTCGGCAAAA 58.785 47.619 0.00 0.00 0.00 2.44
3443 3660 0.815734 ATCCCGTGTTCTGGTACTCG 59.184 55.000 0.00 0.00 35.47 4.18
3452 3669 1.997606 CTTTACCGTGATCCCGTGTTC 59.002 52.381 0.00 0.00 0.00 3.18
3501 3718 2.629424 TATGCCATGCCCTGCTGTCC 62.629 60.000 0.00 0.00 0.00 4.02
3514 3731 0.249868 GCAGCGTCTACCATATGCCA 60.250 55.000 0.00 0.00 0.00 4.92
3516 3733 1.284982 CGGCAGCGTCTACCATATGC 61.285 60.000 0.00 0.00 0.00 3.14
3539 3756 1.226323 CGAGTACTTCCTGTCGGCG 60.226 63.158 0.00 0.00 0.00 6.46
3540 3757 1.139095 CCGAGTACTTCCTGTCGGC 59.861 63.158 6.10 0.00 44.99 5.54
3545 3762 2.163818 TGTTTGCCGAGTACTTCCTG 57.836 50.000 0.00 0.00 0.00 3.86
3580 3797 0.872021 CTCTTGGCATACGCTCCGTC 60.872 60.000 0.00 0.00 41.54 4.79
3601 3818 2.272146 CCCCAACCCATCCGTGAG 59.728 66.667 0.00 0.00 0.00 3.51
3602 3819 4.041762 GCCCCAACCCATCCGTGA 62.042 66.667 0.00 0.00 0.00 4.35
3606 3823 4.506255 CTCGGCCCCAACCCATCC 62.506 72.222 0.00 0.00 0.00 3.51
3607 3824 2.372074 TACTCGGCCCCAACCCATC 61.372 63.158 0.00 0.00 0.00 3.51
3608 3825 2.285818 TACTCGGCCCCAACCCAT 60.286 61.111 0.00 0.00 0.00 4.00
3609 3826 3.324108 GTACTCGGCCCCAACCCA 61.324 66.667 0.00 0.00 0.00 4.51
3610 3827 4.105553 GGTACTCGGCCCCAACCC 62.106 72.222 0.00 0.00 0.00 4.11
3611 3828 4.105553 GGGTACTCGGCCCCAACC 62.106 72.222 0.00 0.00 40.88 3.77
3616 3833 2.804912 GGCTAAGGGTACTCGGCCC 61.805 68.421 13.90 0.00 46.43 5.80
3617 3834 1.619807 TTGGCTAAGGGTACTCGGCC 61.620 60.000 16.77 16.77 41.57 6.13
3618 3835 0.179081 CTTGGCTAAGGGTACTCGGC 60.179 60.000 1.05 0.00 0.00 5.54
3619 3836 1.481871 TCTTGGCTAAGGGTACTCGG 58.518 55.000 10.21 0.00 34.59 4.63
3620 3837 2.496470 AGTTCTTGGCTAAGGGTACTCG 59.504 50.000 10.21 0.00 34.59 4.18
3621 3838 4.465305 TGTAGTTCTTGGCTAAGGGTACTC 59.535 45.833 10.21 0.00 34.59 2.59
3622 3839 4.222366 GTGTAGTTCTTGGCTAAGGGTACT 59.778 45.833 10.21 12.66 34.59 2.73
3633 3850 3.214328 AGTTTGCCAGTGTAGTTCTTGG 58.786 45.455 0.00 0.00 0.00 3.61
3635 3852 4.101741 AGAGAGTTTGCCAGTGTAGTTCTT 59.898 41.667 0.00 0.00 0.00 2.52
3767 4061 6.377996 CACTTCATATTTCCCCTCATGTTTGA 59.622 38.462 0.00 0.00 0.00 2.69
3789 4083 5.308014 TGTAAGCACACAATCTCAATCACT 58.692 37.500 0.00 0.00 0.00 3.41
3883 4206 1.933021 TCCCACCGCTCTTTTCTAGA 58.067 50.000 0.00 0.00 0.00 2.43
3891 4214 0.609131 CAAACCAATCCCACCGCTCT 60.609 55.000 0.00 0.00 0.00 4.09
3895 4218 1.904287 TTCTCAAACCAATCCCACCG 58.096 50.000 0.00 0.00 0.00 4.94
3950 4276 0.324943 CCACCCACCTCATCGTTTCT 59.675 55.000 0.00 0.00 0.00 2.52
3958 4284 0.464735 CAAAACGACCACCCACCTCA 60.465 55.000 0.00 0.00 0.00 3.86
3960 4286 1.152839 CCAAAACGACCACCCACCT 60.153 57.895 0.00 0.00 0.00 4.00
3963 4289 2.196229 CCCCAAAACGACCACCCA 59.804 61.111 0.00 0.00 0.00 4.51
3964 4290 2.599281 CCCCCAAAACGACCACCC 60.599 66.667 0.00 0.00 0.00 4.61
3965 4291 0.756070 TTTCCCCCAAAACGACCACC 60.756 55.000 0.00 0.00 0.00 4.61
3967 4293 1.861982 TTTTTCCCCCAAAACGACCA 58.138 45.000 0.00 0.00 33.47 4.02
4010 4339 1.115467 AACCATGTGACCCGCAAAAA 58.885 45.000 0.00 0.00 0.00 1.94
4011 4340 1.115467 AAACCATGTGACCCGCAAAA 58.885 45.000 0.00 0.00 0.00 2.44
4012 4341 0.387202 CAAACCATGTGACCCGCAAA 59.613 50.000 0.00 0.00 0.00 3.68
4013 4342 0.466372 TCAAACCATGTGACCCGCAA 60.466 50.000 0.00 0.00 0.00 4.85
4014 4343 0.466372 TTCAAACCATGTGACCCGCA 60.466 50.000 0.00 0.00 0.00 5.69
4015 4344 0.671251 TTTCAAACCATGTGACCCGC 59.329 50.000 0.00 0.00 0.00 6.13
4016 4345 3.380142 CTTTTTCAAACCATGTGACCCG 58.620 45.455 0.00 0.00 0.00 5.28
4017 4346 3.727726 CCTTTTTCAAACCATGTGACCC 58.272 45.455 0.00 0.00 0.00 4.46
4018 4347 3.130633 GCCTTTTTCAAACCATGTGACC 58.869 45.455 0.00 0.00 0.00 4.02
4019 4348 3.791245 TGCCTTTTTCAAACCATGTGAC 58.209 40.909 0.00 0.00 0.00 3.67
4020 4349 4.141756 ACATGCCTTTTTCAAACCATGTGA 60.142 37.500 3.56 0.00 40.98 3.58
4021 4350 4.128643 ACATGCCTTTTTCAAACCATGTG 58.871 39.130 3.56 0.00 40.98 3.21
4022 4351 4.420522 ACATGCCTTTTTCAAACCATGT 57.579 36.364 0.00 0.00 38.62 3.21
4023 4352 6.164876 TGATACATGCCTTTTTCAAACCATG 58.835 36.000 0.00 0.00 36.90 3.66
4024 4353 6.357579 TGATACATGCCTTTTTCAAACCAT 57.642 33.333 0.00 0.00 0.00 3.55
4025 4354 5.798125 TGATACATGCCTTTTTCAAACCA 57.202 34.783 0.00 0.00 0.00 3.67
4026 4355 6.092533 CCATTGATACATGCCTTTTTCAAACC 59.907 38.462 0.00 0.00 0.00 3.27
4027 4356 6.873076 TCCATTGATACATGCCTTTTTCAAAC 59.127 34.615 0.00 0.00 0.00 2.93
4028 4357 7.002250 TCCATTGATACATGCCTTTTTCAAA 57.998 32.000 0.00 0.00 0.00 2.69
4029 4358 6.602410 TCCATTGATACATGCCTTTTTCAA 57.398 33.333 0.00 0.00 0.00 2.69
4030 4359 6.351202 CCTTCCATTGATACATGCCTTTTTCA 60.351 38.462 0.00 0.00 0.00 2.69
4031 4360 6.044682 CCTTCCATTGATACATGCCTTTTTC 58.955 40.000 0.00 0.00 0.00 2.29
4047 4376 0.486879 TGGCTTTCACCCCTTCCATT 59.513 50.000 0.00 0.00 0.00 3.16
4065 4407 5.009854 AGTTTGTTGGTTTCACTTCCATG 57.990 39.130 0.00 0.00 33.50 3.66
4106 4448 7.620491 AGACTAGCATCCATGATCATCTCTTAT 59.380 37.037 4.86 0.00 0.00 1.73
4107 4449 6.952938 AGACTAGCATCCATGATCATCTCTTA 59.047 38.462 4.86 0.00 0.00 2.10
4159 4501 8.795842 TCAAAGAGAGTACAAGGTAACAAAAA 57.204 30.769 0.00 0.00 41.41 1.94
4168 4510 9.482627 GTAATATGGATCAAAGAGAGTACAAGG 57.517 37.037 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.