Multiple sequence alignment - TraesCS6B01G183800

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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 TraesCS6B01G183800 chr6B 100.000 4707 0 0 1 4707 206006402 206011108 0.000000e+00 8693
1 TraesCS6B01G183800 chr6D 96.201 4133 113 22 567 4671 116334346 116338462 0.000000e+00 6722
2 TraesCS6B01G183800 chr6D 93.311 299 14 6 1 296 116333797 116334092 2.010000e-118 436
3 TraesCS6B01G183800 chr6D 82.667 150 9 7 419 551 116334215 116334364 2.980000e-22 117
4 TraesCS6B01G183800 chr6A 94.996 4157 141 26 574 4707 144517336 144521448 0.000000e+00 6462
5 TraesCS6B01G183800 chr6A 93.939 297 14 3 5 298 144516826 144517121 3.340000e-121 446
6 TraesCS6B01G183800 chr6A 83.600 250 14 12 312 548 144517105 144517340 4.770000e-50 209


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 TraesCS6B01G183800 chr6B 206006402 206011108 4706 False 8693.000000 8693 100.000000 1 4707 1 chr6B.!!$F1 4706
1 TraesCS6B01G183800 chr6D 116333797 116338462 4665 False 2425.000000 6722 90.726333 1 4671 3 chr6D.!!$F1 4670
2 TraesCS6B01G183800 chr6A 144516826 144521448 4622 False 2372.333333 6462 90.845000 5 4707 3 chr6A.!!$F1 4702

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
490 555 0.625316 CCAACCACTCCATCCATCCA 59.375 55.000 0.00 0.00 0.00 3.41 F
1127 1201 0.322906 CTCTCCTTTTGGCTGGGGTC 60.323 60.000 0.00 0.00 40.12 4.46 F
1583 1663 1.133025 GCGCTTATGTTCATGCAGGTT 59.867 47.619 0.00 0.00 0.00 3.50 F
2125 2205 1.339055 GGAGGTATGCACTGTGCTTCA 60.339 52.381 30.43 13.62 45.31 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1363 1438 0.877213 GCAGCAAGTTTGGCAGTTGG 60.877 55.000 7.99 0.0 36.43 3.77 R
2880 2969 2.730382 TCATTGAATGTGCTCCATGCT 58.270 42.857 4.93 0.0 43.37 3.79 R
3209 3298 1.949525 TGGCTGCTCAAAGAACTTGTC 59.050 47.619 0.00 0.0 36.34 3.18 R
3829 3922 3.058914 GTGTTGCTCATACACACAAGTCC 60.059 47.826 0.00 0.0 44.08 3.85 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
29 30 2.935446 GACGACCAAACGCGACACC 61.935 63.158 15.93 0.00 36.70 4.16
32 33 3.819877 GACCAAACGCGACACCCCT 62.820 63.158 15.93 0.00 0.00 4.79
34 35 3.353836 CAAACGCGACACCCCTGG 61.354 66.667 15.93 0.00 0.00 4.45
139 143 6.476380 TGACTTTTTGTTTCACATGAATGAGC 59.524 34.615 0.00 0.00 33.54 4.26
216 223 6.090129 TGTTTAGCTTGATTATGCCGAAAAC 58.910 36.000 0.00 9.56 31.98 2.43
298 305 4.557296 CGTGCAATCACCAAGAAATGTCTT 60.557 41.667 0.00 0.00 39.69 3.01
299 306 5.291971 GTGCAATCACCAAGAAATGTCTTT 58.708 37.500 0.00 0.00 37.77 2.52
301 308 6.258507 GTGCAATCACCAAGAAATGTCTTTTT 59.741 34.615 0.00 0.00 37.77 1.94
324 331 7.475137 TTTTTAGGGGTATCACCAAGAAATG 57.525 36.000 0.00 0.00 41.02 2.32
325 332 5.789574 TTAGGGGTATCACCAAGAAATGT 57.210 39.130 0.00 0.00 41.02 2.71
326 333 4.236527 AGGGGTATCACCAAGAAATGTC 57.763 45.455 0.00 0.00 41.02 3.06
327 334 3.852578 AGGGGTATCACCAAGAAATGTCT 59.147 43.478 0.00 0.00 41.02 3.41
328 335 5.036916 AGGGGTATCACCAAGAAATGTCTA 58.963 41.667 0.00 0.00 41.02 2.59
329 336 5.104485 AGGGGTATCACCAAGAAATGTCTAC 60.104 44.000 0.00 0.00 41.02 2.59
330 337 5.104485 GGGGTATCACCAAGAAATGTCTACT 60.104 44.000 0.00 0.00 41.02 2.57
331 338 6.099269 GGGGTATCACCAAGAAATGTCTACTA 59.901 42.308 0.00 0.00 41.02 1.82
332 339 7.210873 GGGTATCACCAAGAAATGTCTACTAG 58.789 42.308 0.00 0.00 41.02 2.57
333 340 6.702282 GGTATCACCAAGAAATGTCTACTAGC 59.298 42.308 0.00 0.00 38.42 3.42
334 341 5.738619 TCACCAAGAAATGTCTACTAGCA 57.261 39.130 0.00 0.00 32.16 3.49
335 342 5.479306 TCACCAAGAAATGTCTACTAGCAC 58.521 41.667 0.00 0.00 32.16 4.40
336 343 5.246203 TCACCAAGAAATGTCTACTAGCACT 59.754 40.000 0.00 0.00 32.16 4.40
354 361 4.863131 AGCACTTTGTATTCTACGTGTAGC 59.137 41.667 0.00 0.00 33.32 3.58
356 363 5.444218 GCACTTTGTATTCTACGTGTAGCAC 60.444 44.000 0.00 1.82 33.32 4.40
358 365 6.310467 CACTTTGTATTCTACGTGTAGCACAT 59.690 38.462 0.00 0.00 33.40 3.21
359 366 6.530534 ACTTTGTATTCTACGTGTAGCACATC 59.469 38.462 0.00 0.00 33.40 3.06
360 367 5.830000 TGTATTCTACGTGTAGCACATCT 57.170 39.130 0.00 0.00 33.40 2.90
361 368 6.930667 TGTATTCTACGTGTAGCACATCTA 57.069 37.500 0.00 0.00 33.40 1.98
362 369 6.956047 TGTATTCTACGTGTAGCACATCTAG 58.044 40.000 0.00 0.00 33.40 2.43
363 370 6.541278 TGTATTCTACGTGTAGCACATCTAGT 59.459 38.462 0.00 0.00 33.40 2.57
364 371 7.712205 TGTATTCTACGTGTAGCACATCTAGTA 59.288 37.037 0.00 0.00 33.40 1.82
365 372 6.990341 TTCTACGTGTAGCACATCTAGTAA 57.010 37.500 0.00 0.00 33.40 2.24
366 373 6.990341 TCTACGTGTAGCACATCTAGTAAA 57.010 37.500 0.00 0.00 33.40 2.01
367 374 6.779117 TCTACGTGTAGCACATCTAGTAAAC 58.221 40.000 0.00 0.00 33.40 2.01
368 375 5.381174 ACGTGTAGCACATCTAGTAAACA 57.619 39.130 0.00 0.00 33.40 2.83
369 376 5.159209 ACGTGTAGCACATCTAGTAAACAC 58.841 41.667 0.00 0.00 35.03 3.32
370 377 5.048224 ACGTGTAGCACATCTAGTAAACACT 60.048 40.000 0.00 0.00 35.66 3.55
393 400 1.847818 TATCACGCGTGTTATGCTCC 58.152 50.000 35.74 0.00 0.00 4.70
412 419 1.067071 CCCCGTGTTGTTCTAGTCCTC 60.067 57.143 0.00 0.00 0.00 3.71
413 420 1.067071 CCCGTGTTGTTCTAGTCCTCC 60.067 57.143 0.00 0.00 0.00 4.30
414 421 1.893801 CCGTGTTGTTCTAGTCCTCCT 59.106 52.381 0.00 0.00 0.00 3.69
415 422 2.352814 CCGTGTTGTTCTAGTCCTCCTG 60.353 54.545 0.00 0.00 0.00 3.86
416 423 2.296471 CGTGTTGTTCTAGTCCTCCTGT 59.704 50.000 0.00 0.00 0.00 4.00
417 424 3.654414 GTGTTGTTCTAGTCCTCCTGTG 58.346 50.000 0.00 0.00 0.00 3.66
487 552 0.921896 CCTCCAACCACTCCATCCAT 59.078 55.000 0.00 0.00 0.00 3.41
488 553 1.133976 CCTCCAACCACTCCATCCATC 60.134 57.143 0.00 0.00 0.00 3.51
489 554 0.918983 TCCAACCACTCCATCCATCC 59.081 55.000 0.00 0.00 0.00 3.51
490 555 0.625316 CCAACCACTCCATCCATCCA 59.375 55.000 0.00 0.00 0.00 3.41
535 600 1.741770 CCCGAGCCGAAAACCAGAG 60.742 63.158 0.00 0.00 0.00 3.35
548 613 5.391310 CGAAAACCAGAGACCATCAATCAAG 60.391 44.000 0.00 0.00 0.00 3.02
549 614 2.996631 ACCAGAGACCATCAATCAAGC 58.003 47.619 0.00 0.00 0.00 4.01
550 615 2.575279 ACCAGAGACCATCAATCAAGCT 59.425 45.455 0.00 0.00 0.00 3.74
551 616 3.204526 CCAGAGACCATCAATCAAGCTC 58.795 50.000 0.00 0.00 0.00 4.09
552 617 3.118334 CCAGAGACCATCAATCAAGCTCT 60.118 47.826 0.00 0.00 0.00 4.09
553 618 4.515361 CAGAGACCATCAATCAAGCTCTT 58.485 43.478 0.00 0.00 0.00 2.85
554 619 4.942483 CAGAGACCATCAATCAAGCTCTTT 59.058 41.667 0.00 0.00 0.00 2.52
555 620 5.415077 CAGAGACCATCAATCAAGCTCTTTT 59.585 40.000 0.00 0.00 0.00 2.27
556 621 6.008960 AGAGACCATCAATCAAGCTCTTTTT 58.991 36.000 0.00 0.00 0.00 1.94
588 653 9.330063 CACTAATAACCATCAATCAAGCTTAGA 57.670 33.333 0.00 0.00 0.00 2.10
600 665 3.498397 TCAAGCTTAGAAAAAGAGGCACG 59.502 43.478 0.00 0.00 0.00 5.34
846 920 4.761304 TCCCTCCCCTCCCTCCCT 62.761 72.222 0.00 0.00 0.00 4.20
858 932 3.801997 CTCCCTCCATTGCCGCCT 61.802 66.667 0.00 0.00 0.00 5.52
911 985 2.354891 CGGGACACGTACGCACAA 60.355 61.111 16.72 0.00 37.93 3.33
922 996 2.639286 CGCACAAGAAAAGGCGCT 59.361 55.556 7.64 0.00 43.14 5.92
1108 1182 0.596341 GATCTCGCGCCTCTCTTTCC 60.596 60.000 0.00 0.00 0.00 3.13
1127 1201 0.322906 CTCTCCTTTTGGCTGGGGTC 60.323 60.000 0.00 0.00 40.12 4.46
1140 1214 1.354368 CTGGGGTCTGGTGGTACAATT 59.646 52.381 0.00 0.00 44.16 2.32
1145 1219 2.890945 GGTCTGGTGGTACAATTGCTTT 59.109 45.455 5.05 0.00 44.16 3.51
1198 1272 8.400947 CAATCCTGTCAAGTTCAATATGGTTAG 58.599 37.037 0.00 0.00 0.00 2.34
1213 1287 1.337447 GGTTAGTCACTTGGCTACGCA 60.337 52.381 0.00 0.00 31.05 5.24
1262 1337 2.214376 TCTTGCCCCATGTGTTAAGG 57.786 50.000 0.00 0.00 0.00 2.69
1334 1409 2.627699 ACCAAGTCGTGCAATCCAAAAT 59.372 40.909 0.00 0.00 0.00 1.82
1363 1438 4.142881 GCTCGGTCAAATGAAGTTTAGGTC 60.143 45.833 0.00 0.00 0.00 3.85
1419 1494 4.547532 TCTTCTCTTTCGTGTAAGCAGAC 58.452 43.478 0.00 0.00 0.00 3.51
1428 1503 2.731976 CGTGTAAGCAGACTCCAAGTTC 59.268 50.000 0.00 0.00 0.00 3.01
1548 1623 7.627513 GCTTTAGAGAGATCATATGTAGGACCG 60.628 44.444 1.90 0.00 0.00 4.79
1565 1645 1.442520 CGCCTCACAAATGGTTGCG 60.443 57.895 0.00 0.00 38.39 4.85
1574 1654 3.364621 CACAAATGGTTGCGCTTATGTTC 59.635 43.478 9.73 0.00 38.39 3.18
1583 1663 1.133025 GCGCTTATGTTCATGCAGGTT 59.867 47.619 0.00 0.00 0.00 3.50
1596 1676 3.634568 TGCAGGTTATTTCGGTGTTTG 57.365 42.857 0.00 0.00 0.00 2.93
1826 1906 2.637382 TGCCTACATCCAGAACTCAACA 59.363 45.455 0.00 0.00 0.00 3.33
1869 1949 7.253905 AGGACACTAAAGGTAATGAGCTTAA 57.746 36.000 0.00 0.00 42.60 1.85
1880 1960 4.796038 AATGAGCTTAACTGCATGCTTT 57.204 36.364 20.33 14.19 35.76 3.51
2125 2205 1.339055 GGAGGTATGCACTGTGCTTCA 60.339 52.381 30.43 13.62 45.31 3.02
2258 2347 5.896432 GCATTGTCGATAATGTTAACTCACG 59.104 40.000 28.46 6.89 39.62 4.35
2425 2514 5.482686 TTTGTTTTGCTGGAAATTGCTTC 57.517 34.783 0.00 0.00 0.00 3.86
2618 2707 3.118738 ACCTACTGATTGTTGTCCGGATC 60.119 47.826 7.81 0.00 0.00 3.36
2642 2731 5.676744 CGCTAAAATGTTGGATATTGACACG 59.323 40.000 0.00 0.00 0.00 4.49
2880 2969 5.368145 GCTATTGTTCCATGTGGTCTGATA 58.632 41.667 0.00 0.00 36.34 2.15
2935 3024 7.362229 CCTTCCAACACAACACTAACAACTTAA 60.362 37.037 0.00 0.00 0.00 1.85
3091 3180 3.221771 TGGGTTTCAATTCCACTCTGTG 58.778 45.455 0.00 0.00 0.00 3.66
3209 3298 8.715998 CGATCATTTTCCATTAGATAGACCAAG 58.284 37.037 0.00 0.00 0.00 3.61
3402 3492 8.458573 AAGAAAATGACACCATTACTGTTACA 57.541 30.769 0.00 0.00 41.84 2.41
3741 3834 3.403613 TGATTTCCGCATTCAACATCG 57.596 42.857 0.00 0.00 0.00 3.84
3755 3848 5.107109 TCAACATCGAACAATTGGTCTTG 57.893 39.130 20.81 18.71 0.00 3.02
3808 3901 5.519927 AGCAATTTTTGTGTACAAGCTGTTC 59.480 36.000 0.00 0.00 37.15 3.18
3829 3922 6.419710 TGTTCTCAAAGTACGTGTATCAAGTG 59.580 38.462 0.00 0.00 0.00 3.16
3983 4079 4.013728 TGCTGTCAGTTTTAAACAGGTGT 58.986 39.130 10.60 0.00 40.57 4.16
4127 4227 9.396022 CTTTGAAGGGTTACAAGATACATATGT 57.604 33.333 13.93 13.93 0.00 2.29
4128 4228 9.747898 TTTGAAGGGTTACAAGATACATATGTT 57.252 29.630 14.77 1.88 0.00 2.71
4129 4229 8.731275 TGAAGGGTTACAAGATACATATGTTG 57.269 34.615 14.77 8.67 41.25 3.33
4144 4244 7.214467 ACATATGTTGTTCTTGTTCGGAAAT 57.786 32.000 1.41 0.00 33.74 2.17
4250 4350 5.992217 ACTGGTCAGTAGAATGTTTTGACTC 59.008 40.000 1.24 0.00 40.43 3.36
4293 4393 5.921408 CGGAGTAAGTAATTGCTGAGATACC 59.079 44.000 0.00 0.00 0.00 2.73
4436 4536 5.697473 TCATCAACGTGGATAAGCAAAAA 57.303 34.783 4.78 0.00 0.00 1.94
4520 4620 4.675510 ACGCATGCCAATATGAAAAGAAG 58.324 39.130 13.15 0.00 0.00 2.85
4536 4636 2.728007 AGAAGCTAAAAGGGCCATGAC 58.272 47.619 6.18 0.00 0.00 3.06
4561 4661 6.757897 ATTCATCGCAAACCTTCTATGAAA 57.242 33.333 0.00 0.00 37.03 2.69
4662 4762 7.569240 AGATTTGAGTAAATAGGACCCAAGAG 58.431 38.462 0.00 0.00 36.66 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 3.986006 AACCGAAGCGAGCGTCCA 61.986 61.111 5.51 0.00 0.00 4.02
34 35 3.479269 CCAACCGAAGCGAGCGTC 61.479 66.667 0.97 0.97 0.00 5.19
201 208 6.226787 ACATTTTTGGTTTTCGGCATAATCA 58.773 32.000 0.00 0.00 0.00 2.57
301 308 6.557568 ACATTTCTTGGTGATACCCCTAAAA 58.442 36.000 0.00 0.00 37.50 1.52
302 309 6.011981 AGACATTTCTTGGTGATACCCCTAAA 60.012 38.462 0.00 0.00 37.50 1.85
304 311 5.036916 AGACATTTCTTGGTGATACCCCTA 58.963 41.667 0.00 0.00 37.50 3.53
305 312 3.852578 AGACATTTCTTGGTGATACCCCT 59.147 43.478 0.00 0.00 37.50 4.79
306 313 4.236527 AGACATTTCTTGGTGATACCCC 57.763 45.455 0.00 0.00 37.50 4.95
307 314 5.990668 AGTAGACATTTCTTGGTGATACCC 58.009 41.667 0.00 0.00 33.24 3.69
308 315 6.702282 GCTAGTAGACATTTCTTGGTGATACC 59.298 42.308 0.00 0.00 34.20 2.73
309 316 7.222999 GTGCTAGTAGACATTTCTTGGTGATAC 59.777 40.741 0.00 0.00 32.75 2.24
310 317 7.124298 AGTGCTAGTAGACATTTCTTGGTGATA 59.876 37.037 0.00 0.00 32.75 2.15
311 318 6.070538 AGTGCTAGTAGACATTTCTTGGTGAT 60.071 38.462 0.00 0.00 32.75 3.06
312 319 5.246203 AGTGCTAGTAGACATTTCTTGGTGA 59.754 40.000 0.00 0.00 32.75 4.02
313 320 5.482908 AGTGCTAGTAGACATTTCTTGGTG 58.517 41.667 0.00 0.00 32.75 4.17
314 321 5.746990 AGTGCTAGTAGACATTTCTTGGT 57.253 39.130 0.00 0.00 32.75 3.67
315 322 6.428159 ACAAAGTGCTAGTAGACATTTCTTGG 59.572 38.462 0.00 0.24 32.75 3.61
316 323 7.426929 ACAAAGTGCTAGTAGACATTTCTTG 57.573 36.000 0.00 1.86 32.75 3.02
317 324 9.726438 AATACAAAGTGCTAGTAGACATTTCTT 57.274 29.630 0.00 0.00 32.75 2.52
318 325 9.372369 GAATACAAAGTGCTAGTAGACATTTCT 57.628 33.333 0.00 0.00 35.66 2.52
319 326 9.372369 AGAATACAAAGTGCTAGTAGACATTTC 57.628 33.333 0.00 0.00 0.00 2.17
321 328 9.804758 GTAGAATACAAAGTGCTAGTAGACATT 57.195 33.333 0.00 0.00 42.43 2.71
322 329 8.129840 CGTAGAATACAAAGTGCTAGTAGACAT 58.870 37.037 0.00 0.00 43.24 3.06
323 330 7.120285 ACGTAGAATACAAAGTGCTAGTAGACA 59.880 37.037 0.00 0.00 43.24 3.41
324 331 7.428761 CACGTAGAATACAAAGTGCTAGTAGAC 59.571 40.741 0.00 0.00 43.24 2.59
325 332 7.120285 ACACGTAGAATACAAAGTGCTAGTAGA 59.880 37.037 0.00 0.00 43.24 2.59
326 333 7.249147 ACACGTAGAATACAAAGTGCTAGTAG 58.751 38.462 0.00 0.00 43.24 2.57
327 334 7.149569 ACACGTAGAATACAAAGTGCTAGTA 57.850 36.000 0.00 0.00 43.24 1.82
328 335 6.022163 ACACGTAGAATACAAAGTGCTAGT 57.978 37.500 0.00 0.00 43.24 2.57
329 336 6.196724 GCTACACGTAGAATACAAAGTGCTAG 59.803 42.308 8.41 0.00 43.24 3.42
330 337 6.032094 GCTACACGTAGAATACAAAGTGCTA 58.968 40.000 8.41 0.00 43.24 3.49
331 338 4.863131 GCTACACGTAGAATACAAAGTGCT 59.137 41.667 8.41 0.00 43.24 4.40
332 339 4.624024 TGCTACACGTAGAATACAAAGTGC 59.376 41.667 8.41 0.00 43.24 4.40
333 340 5.631929 TGTGCTACACGTAGAATACAAAGTG 59.368 40.000 8.41 0.00 43.24 3.16
334 341 5.775686 TGTGCTACACGTAGAATACAAAGT 58.224 37.500 8.41 0.00 43.24 2.66
335 342 6.752351 AGATGTGCTACACGTAGAATACAAAG 59.248 38.462 8.41 0.00 43.24 2.77
336 343 6.627243 AGATGTGCTACACGTAGAATACAAA 58.373 36.000 8.41 0.00 43.24 2.83
346 353 5.048224 AGTGTTTACTAGATGTGCTACACGT 60.048 40.000 0.00 0.00 38.90 4.49
354 361 9.741168 CGTGATAAAAAGTGTTTACTAGATGTG 57.259 33.333 0.00 0.00 35.69 3.21
356 363 7.630987 CGCGTGATAAAAAGTGTTTACTAGATG 59.369 37.037 0.00 0.00 35.69 2.90
358 365 6.642131 ACGCGTGATAAAAAGTGTTTACTAGA 59.358 34.615 12.93 0.00 35.69 2.43
359 366 6.730619 CACGCGTGATAAAAAGTGTTTACTAG 59.269 38.462 34.93 0.00 35.69 2.57
360 367 6.200665 ACACGCGTGATAAAAAGTGTTTACTA 59.799 34.615 42.94 0.00 39.44 1.82
361 368 5.006941 ACACGCGTGATAAAAAGTGTTTACT 59.993 36.000 42.94 13.64 39.44 2.24
362 369 5.199726 ACACGCGTGATAAAAAGTGTTTAC 58.800 37.500 42.94 0.00 39.44 2.01
363 370 5.406767 ACACGCGTGATAAAAAGTGTTTA 57.593 34.783 42.94 0.00 39.44 2.01
364 371 4.281525 ACACGCGTGATAAAAAGTGTTT 57.718 36.364 42.94 15.22 39.44 2.83
365 372 3.955771 ACACGCGTGATAAAAAGTGTT 57.044 38.095 42.94 15.44 39.44 3.32
366 373 3.955771 AACACGCGTGATAAAAAGTGT 57.044 38.095 42.94 16.00 43.56 3.55
367 374 4.259734 GCATAACACGCGTGATAAAAAGTG 59.740 41.667 42.94 28.38 35.89 3.16
368 375 4.153475 AGCATAACACGCGTGATAAAAAGT 59.847 37.500 42.94 18.87 0.00 2.66
369 376 4.647964 AGCATAACACGCGTGATAAAAAG 58.352 39.130 42.94 25.39 0.00 2.27
370 377 4.436317 GGAGCATAACACGCGTGATAAAAA 60.436 41.667 42.94 18.84 0.00 1.94
393 400 1.067071 GGAGGACTAGAACAACACGGG 60.067 57.143 0.00 0.00 0.00 5.28
412 419 1.080093 ATGGTGACGCGTACACAGG 60.080 57.895 29.46 0.00 39.65 4.00
413 420 1.351430 CCATGGTGACGCGTACACAG 61.351 60.000 29.46 21.70 39.65 3.66
414 421 1.373622 CCATGGTGACGCGTACACA 60.374 57.895 29.46 21.70 39.65 3.72
415 422 2.736682 GCCATGGTGACGCGTACAC 61.737 63.158 24.34 24.34 37.51 2.90
416 423 2.433491 GCCATGGTGACGCGTACA 60.433 61.111 13.97 12.88 0.00 2.90
417 424 3.192922 GGCCATGGTGACGCGTAC 61.193 66.667 13.97 11.03 0.00 3.67
436 484 0.037326 TGCTTCGTGGATCTTTCGCT 60.037 50.000 0.00 0.00 0.00 4.93
437 485 0.095417 GTGCTTCGTGGATCTTTCGC 59.905 55.000 0.00 0.00 0.00 4.70
487 552 1.055551 AGTGTAACGGGTGGGTTGGA 61.056 55.000 0.00 0.00 45.86 3.53
488 553 0.686224 TAGTGTAACGGGTGGGTTGG 59.314 55.000 0.00 0.00 45.86 3.77
489 554 1.799544 GTAGTGTAACGGGTGGGTTG 58.200 55.000 0.00 0.00 45.86 3.77
490 555 0.318120 CGTAGTGTAACGGGTGGGTT 59.682 55.000 0.00 0.00 45.86 4.11
558 623 9.461312 AGCTTGATTGATGGTTATTAGTGTAAA 57.539 29.630 0.00 0.00 0.00 2.01
559 624 9.461312 AAGCTTGATTGATGGTTATTAGTGTAA 57.539 29.630 0.00 0.00 0.00 2.41
561 626 7.944729 AAGCTTGATTGATGGTTATTAGTGT 57.055 32.000 0.00 0.00 0.00 3.55
562 627 9.330063 TCTAAGCTTGATTGATGGTTATTAGTG 57.670 33.333 9.86 0.00 0.00 2.74
563 628 9.905713 TTCTAAGCTTGATTGATGGTTATTAGT 57.094 29.630 9.86 0.00 0.00 2.24
568 633 9.295825 TCTTTTTCTAAGCTTGATTGATGGTTA 57.704 29.630 9.86 0.00 0.00 2.85
569 634 8.181904 TCTTTTTCTAAGCTTGATTGATGGTT 57.818 30.769 9.86 0.00 0.00 3.67
570 635 7.094032 CCTCTTTTTCTAAGCTTGATTGATGGT 60.094 37.037 9.86 0.00 0.00 3.55
571 636 7.256286 CCTCTTTTTCTAAGCTTGATTGATGG 58.744 38.462 9.86 0.00 0.00 3.51
572 637 6.750963 GCCTCTTTTTCTAAGCTTGATTGATG 59.249 38.462 9.86 0.00 0.00 3.07
573 638 6.435277 TGCCTCTTTTTCTAAGCTTGATTGAT 59.565 34.615 9.86 0.00 0.00 2.57
574 639 5.769662 TGCCTCTTTTTCTAAGCTTGATTGA 59.230 36.000 9.86 0.00 0.00 2.57
575 640 5.860716 GTGCCTCTTTTTCTAAGCTTGATTG 59.139 40.000 9.86 0.00 0.00 2.67
576 641 5.335191 CGTGCCTCTTTTTCTAAGCTTGATT 60.335 40.000 9.86 0.00 0.00 2.57
577 642 4.154918 CGTGCCTCTTTTTCTAAGCTTGAT 59.845 41.667 9.86 0.00 0.00 2.57
588 653 0.606673 GCTCCTCCGTGCCTCTTTTT 60.607 55.000 0.00 0.00 0.00 1.94
600 665 5.654209 AGATGGTTCTAATTTTTGCTCCTCC 59.346 40.000 0.00 0.00 0.00 4.30
737 807 2.612251 GAGGGAGAGGGAGAGGGG 59.388 72.222 0.00 0.00 0.00 4.79
782 852 3.606065 CTCTTGTTGCTGCCGCTGC 62.606 63.158 14.83 14.83 36.97 5.25
817 888 2.063378 GGAGGGAGGGTGCTCTCTG 61.063 68.421 0.00 0.00 33.68 3.35
818 889 2.366570 GGAGGGAGGGTGCTCTCT 59.633 66.667 0.00 0.00 36.78 3.10
819 890 2.766229 GGGAGGGAGGGTGCTCTC 60.766 72.222 0.00 0.00 0.00 3.20
826 900 4.179599 GAGGGAGGGGAGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
846 920 2.272146 GAGGAAGGCGGCAATGGA 59.728 61.111 13.08 0.00 0.00 3.41
858 932 4.089757 CGGGGAGAGGGGGAGGAA 62.090 72.222 0.00 0.00 0.00 3.36
882 956 4.736896 GTCCCGCGCTCGAGGTTT 62.737 66.667 15.58 0.00 38.10 3.27
908 982 0.675633 ATGCAAGCGCCTTTTCTTGT 59.324 45.000 2.29 0.00 41.15 3.16
911 985 1.666888 CGAAATGCAAGCGCCTTTTCT 60.667 47.619 2.29 0.00 36.28 2.52
922 996 2.976840 GCCGACAGCCGAAATGCAA 61.977 57.895 0.00 0.00 41.76 4.08
1108 1182 0.322906 GACCCCAGCCAAAAGGAGAG 60.323 60.000 0.00 0.00 0.00 3.20
1213 1287 2.442413 CTTTTCCAGGCCCAGGCT 59.558 61.111 8.89 0.00 41.60 4.58
1226 1300 4.243270 GCAAGAATGATGAGCAAGCTTTT 58.757 39.130 0.00 0.00 0.00 2.27
1262 1337 7.648039 TCTAAAGGAAGTCAACTCTCCTATC 57.352 40.000 11.69 0.00 0.00 2.08
1321 1396 3.592059 AGCATGTGATTTTGGATTGCAC 58.408 40.909 0.00 0.00 0.00 4.57
1334 1409 2.470983 TCATTTGACCGAGCATGTGA 57.529 45.000 0.00 0.00 0.00 3.58
1363 1438 0.877213 GCAGCAAGTTTGGCAGTTGG 60.877 55.000 7.99 0.00 36.43 3.77
1419 1494 1.572085 CCTGCTGCGTGAACTTGGAG 61.572 60.000 0.00 0.00 0.00 3.86
1548 1623 1.734117 GCGCAACCATTTGTGAGGC 60.734 57.895 0.30 0.00 44.70 4.70
1565 1645 5.682862 CGAAATAACCTGCATGAACATAAGC 59.317 40.000 0.00 0.00 0.00 3.09
1574 1654 3.848272 AACACCGAAATAACCTGCATG 57.152 42.857 0.00 0.00 0.00 4.06
1583 1663 5.125739 ACCAACAAGAACAAACACCGAAATA 59.874 36.000 0.00 0.00 0.00 1.40
1596 1676 5.290885 GGACAAAAATGACACCAACAAGAAC 59.709 40.000 0.00 0.00 0.00 3.01
1710 1790 6.439675 AGAAACCAACAAACGTTAGCTAAA 57.560 33.333 7.99 0.00 0.00 1.85
1826 1906 5.123936 GTCCTTCGGCAGGTTTTAGATATT 58.876 41.667 0.00 0.00 44.37 1.28
1869 1949 6.425114 CGATTAGACCTATAAAAGCATGCAGT 59.575 38.462 21.98 3.94 0.00 4.40
1880 1960 5.568825 GCCATTCCAGCGATTAGACCTATAA 60.569 44.000 0.00 0.00 0.00 0.98
2125 2205 5.873164 GTCTTTGACATATTGGTAACCTCGT 59.127 40.000 0.00 0.00 32.09 4.18
2169 2249 5.263599 TGGACACATATTTGAGCCAAAGAT 58.736 37.500 0.00 4.75 35.98 2.40
2230 2319 8.175069 TGAGTTAACATTATCGACAATGCTTTC 58.825 33.333 16.15 7.88 39.13 2.62
2258 2347 7.750229 TCCTTTGCATAATCACTATCCATTC 57.250 36.000 0.00 0.00 0.00 2.67
2402 2491 5.295045 AGAAGCAATTTCCAGCAAAACAAAG 59.705 36.000 0.00 0.00 36.40 2.77
2425 2514 5.476091 AGTTTCTTAGGGTCAAGTCAGAG 57.524 43.478 0.00 0.00 0.00 3.35
2618 2707 5.676744 CGTGTCAATATCCAACATTTTAGCG 59.323 40.000 0.00 0.00 0.00 4.26
2642 2731 4.083581 ACTGCTAAAATTGCATGTCGAC 57.916 40.909 9.11 9.11 39.86 4.20
2880 2969 2.730382 TCATTGAATGTGCTCCATGCT 58.270 42.857 4.93 0.00 43.37 3.79
2935 3024 5.189928 AGAGATGTCTGTCTTGTCGATAGT 58.810 41.667 0.00 0.00 33.09 2.12
3105 3194 6.832520 TTGCTTGTCAACCACATATGTAAT 57.167 33.333 8.32 0.00 33.90 1.89
3108 3197 6.832520 TTATTGCTTGTCAACCACATATGT 57.167 33.333 1.41 1.41 37.53 2.29
3151 3240 9.362151 AGGTCAGTTTATCTTTAAATTGGACAA 57.638 29.630 0.00 0.00 36.32 3.18
3209 3298 1.949525 TGGCTGCTCAAAGAACTTGTC 59.050 47.619 0.00 0.00 36.34 3.18
3369 3459 3.888930 TGGTGTCATTTTCTTTGAGGTCC 59.111 43.478 0.00 0.00 0.00 4.46
3402 3492 7.759489 ATATGTGTTGTAATTGTTGTCCAGT 57.241 32.000 0.00 0.00 0.00 4.00
3708 3801 3.814945 CGGAAATCAACTTTCAGAGTGC 58.185 45.455 0.71 0.00 44.29 4.40
3741 3834 6.144078 AGTTAACCACAAGACCAATTGTTC 57.856 37.500 4.43 0.00 41.41 3.18
3755 3848 7.642071 TCGTACAAAGATACAAGTTAACCAC 57.358 36.000 0.88 0.00 0.00 4.16
3808 3901 5.345202 GTCCACTTGATACACGTACTTTGAG 59.655 44.000 0.00 0.00 0.00 3.02
3829 3922 3.058914 GTGTTGCTCATACACACAAGTCC 60.059 47.826 0.00 0.00 44.08 3.85
3883 3979 7.692908 ATTTTCAACAAAAGAACCGTGTATG 57.307 32.000 0.00 0.00 34.92 2.39
4127 4227 7.698970 GTGTAGAAAATTTCCGAACAAGAACAA 59.301 33.333 1.57 0.00 0.00 2.83
4128 4228 7.190871 GTGTAGAAAATTTCCGAACAAGAACA 58.809 34.615 1.57 0.00 0.00 3.18
4129 4229 6.635641 GGTGTAGAAAATTTCCGAACAAGAAC 59.364 38.462 1.57 0.00 0.00 3.01
4250 4350 5.073311 TCCGAGTAATGTGAAGAAGGAAG 57.927 43.478 0.00 0.00 0.00 3.46
4316 4416 1.315690 CAGCTTGCGATCATCCCATT 58.684 50.000 0.00 0.00 0.00 3.16
4436 4536 8.537728 TTGTCTATATTCCATTGCAAATTCCT 57.462 30.769 1.71 0.00 0.00 3.36
4520 4620 4.207165 TGAATAGTCATGGCCCTTTTAGC 58.793 43.478 0.00 0.00 0.00 3.09
4536 4636 7.482654 TTCATAGAAGGTTTGCGATGAATAG 57.517 36.000 0.00 0.00 33.30 1.73
4561 4661 4.828939 TCTTCCAGCATGTCAAACTGAAAT 59.171 37.500 6.97 0.00 33.10 2.17


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

AutoCloner maintained by Alex Coulton.