Multiple sequence alignment - TraesCS2A01G527300

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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 TraesCS2A01G527300 chr2A 100.000 3423 0 0 1 3423 746938231 746941653 0.000000e+00 6322.0
1 TraesCS2A01G527300 chr2A 87.962 2517 217 43 983 3423 746956270 746958776 0.000000e+00 2891.0
2 TraesCS2A01G527300 chr2A 100.000 32 0 0 935 966 746956177 746956208 3.690000e-05 60.2
3 TraesCS2A01G527300 chr2D 98.487 2709 36 4 719 3423 616942301 616945008 0.000000e+00 4771.0
4 TraesCS2A01G527300 chr2D 92.013 313 23 1 1 313 616941653 616941963 4.060000e-119 438.0
5 TraesCS2A01G527300 chr2B 88.176 2495 230 37 979 3423 752480122 752482601 0.000000e+00 2913.0
6 TraesCS2A01G527300 chr2B 88.703 1850 170 18 1579 3423 752411849 752413664 0.000000e+00 2222.0
7 TraesCS2A01G527300 chr2B 89.377 546 49 9 993 1535 752410951 752411490 0.000000e+00 678.0
8 TraesCS2A01G527300 chr2B 88.596 114 12 1 668 780 752479538 752479651 1.660000e-28 137.0
9 TraesCS2A01G527300 chr2B 80.342 117 17 4 18 129 752486193 752486308 2.190000e-12 84.2
10 TraesCS2A01G527300 chr6D 77.778 1872 352 41 1583 3423 468872445 468874283 0.000000e+00 1094.0
11 TraesCS2A01G527300 chr6D 77.515 1690 318 42 1770 3423 468941591 468943254 0.000000e+00 959.0
12 TraesCS2A01G527300 chr6D 77.916 1123 213 24 2271 3379 468588736 468587635 0.000000e+00 667.0
13 TraesCS2A01G527300 chr6D 74.780 341 71 9 3049 3387 468860465 468860792 4.610000e-29 139.0
14 TraesCS2A01G527300 chr6D 74.621 264 57 10 1025 1283 468255954 468255696 1.300000e-19 108.0
15 TraesCS2A01G527300 chr6B 77.211 1843 347 44 1583 3391 715154735 715156538 0.000000e+00 1009.0
16 TraesCS2A01G527300 chrUn 100.000 388 0 0 2648 3035 480372188 480371801 0.000000e+00 717.0
17 TraesCS2A01G527300 chrUn 76.056 284 58 10 1005 1283 75218285 75218563 4.610000e-29 139.0
18 TraesCS2A01G527300 chrUn 93.056 72 3 2 776 845 9577458 9577529 1.680000e-18 104.0


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 TraesCS2A01G527300 chr2A 746938231 746941653 3422 False 6322.000000 6322 100.000000 1 3423 1 chr2A.!!$F1 3422
1 TraesCS2A01G527300 chr2A 746956177 746958776 2599 False 1475.600000 2891 93.981000 935 3423 2 chr2A.!!$F2 2488
2 TraesCS2A01G527300 chr2D 616941653 616945008 3355 False 2604.500000 4771 95.250000 1 3423 2 chr2D.!!$F1 3422
3 TraesCS2A01G527300 chr2B 752410951 752413664 2713 False 1450.000000 2222 89.040000 993 3423 2 chr2B.!!$F1 2430
4 TraesCS2A01G527300 chr2B 752479538 752486308 6770 False 1044.733333 2913 85.704667 18 3423 3 chr2B.!!$F2 3405
5 TraesCS2A01G527300 chr6D 468872445 468874283 1838 False 1094.000000 1094 77.778000 1583 3423 1 chr6D.!!$F2 1840
6 TraesCS2A01G527300 chr6D 468941591 468943254 1663 False 959.000000 959 77.515000 1770 3423 1 chr6D.!!$F3 1653
7 TraesCS2A01G527300 chr6D 468587635 468588736 1101 True 667.000000 667 77.916000 2271 3379 1 chr6D.!!$R2 1108
8 TraesCS2A01G527300 chr6B 715154735 715156538 1803 False 1009.000000 1009 77.211000 1583 3391 1 chr6B.!!$F1 1808

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
568 569 0.039618 TGGATTGTTGCTCCTTCCCC 59.96 55.0 0.0 0.0 33.69 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2562 3295 1.839994 TCTGGGAAGAGGGCACAATAG 59.16 52.381 0.0 0.0 0.0 1.73 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
24 25 5.241728 GGTGCTGACTAACAAAAGGAATTCT 59.758 40.000 5.23 0.00 0.00 2.40
26 27 7.203218 GTGCTGACTAACAAAAGGAATTCTTT 58.797 34.615 5.23 0.35 46.82 2.52
42 43 7.122799 AGGAATTCTTTACTTAATGCAGGAACC 59.877 37.037 5.23 0.00 0.00 3.62
50 51 1.117150 AATGCAGGAACCATCATGGC 58.883 50.000 2.52 0.00 42.67 4.40
54 55 0.323633 CAGGAACCATCATGGCCACA 60.324 55.000 8.16 0.00 42.67 4.17
112 113 2.949447 ACAGGTTTCAAGGCTGTGAAT 58.051 42.857 11.19 0.00 37.36 2.57
127 128 2.424601 TGTGAATAATTCAGCAGGCTGC 59.575 45.455 31.56 31.56 45.46 5.25
178 179 1.134007 TGAAGCCGGAGCATCATTGAT 60.134 47.619 5.05 0.00 41.55 2.57
179 180 1.952296 GAAGCCGGAGCATCATTGATT 59.048 47.619 5.05 0.00 43.56 2.57
190 191 6.239232 GGAGCATCATTGATTTTGGATAGCTT 60.239 38.462 0.00 0.00 36.25 3.74
194 195 8.086522 GCATCATTGATTTTGGATAGCTTATGT 58.913 33.333 0.00 0.00 0.00 2.29
199 200 8.750515 TTGATTTTGGATAGCTTATGTGATCA 57.249 30.769 0.00 0.00 0.00 2.92
220 221 3.914426 ACTCGGCAGTTGATTAGGATT 57.086 42.857 0.00 0.00 0.00 3.01
231 232 5.491078 AGTTGATTAGGATTCCACACCCTAA 59.509 40.000 5.29 0.00 44.02 2.69
261 262 5.048013 AGTGGGTTAGTTAGAAATGCTTTGC 60.048 40.000 0.00 0.00 0.00 3.68
271 272 2.228138 AATGCTTTGCAAGTGGTGTG 57.772 45.000 0.00 0.00 43.62 3.82
272 273 1.113788 ATGCTTTGCAAGTGGTGTGT 58.886 45.000 0.00 0.00 43.62 3.72
273 274 0.173029 TGCTTTGCAAGTGGTGTGTG 59.827 50.000 0.00 0.00 34.76 3.82
283 284 1.974957 AGTGGTGTGTGCCATGTACTA 59.025 47.619 0.00 0.00 41.08 1.82
287 288 2.355716 GGTGTGTGCCATGTACTACCAT 60.356 50.000 13.92 0.00 31.26 3.55
315 316 3.399440 GGTTTGCCCATTCATTCAACA 57.601 42.857 0.00 0.00 0.00 3.33
316 317 3.737850 GGTTTGCCCATTCATTCAACAA 58.262 40.909 0.00 0.00 0.00 2.83
318 319 4.502950 GGTTTGCCCATTCATTCAACAAGA 60.503 41.667 0.00 0.00 0.00 3.02
319 320 4.524316 TTGCCCATTCATTCAACAAGAG 57.476 40.909 0.00 0.00 0.00 2.85
320 321 3.765381 TGCCCATTCATTCAACAAGAGA 58.235 40.909 0.00 0.00 0.00 3.10
321 322 4.346730 TGCCCATTCATTCAACAAGAGAT 58.653 39.130 0.00 0.00 0.00 2.75
323 324 5.591472 TGCCCATTCATTCAACAAGAGATAG 59.409 40.000 0.00 0.00 0.00 2.08
324 325 5.824624 GCCCATTCATTCAACAAGAGATAGA 59.175 40.000 0.00 0.00 0.00 1.98
325 326 6.489361 GCCCATTCATTCAACAAGAGATAGAT 59.511 38.462 0.00 0.00 0.00 1.98
326 327 7.521748 GCCCATTCATTCAACAAGAGATAGATG 60.522 40.741 0.00 0.00 0.00 2.90
327 328 7.718314 CCCATTCATTCAACAAGAGATAGATGA 59.282 37.037 0.00 0.00 0.00 2.92
328 329 8.557864 CCATTCATTCAACAAGAGATAGATGAC 58.442 37.037 0.00 0.00 0.00 3.06
329 330 8.557864 CATTCATTCAACAAGAGATAGATGACC 58.442 37.037 0.00 0.00 0.00 4.02
330 331 6.276091 TCATTCAACAAGAGATAGATGACCG 58.724 40.000 0.00 0.00 0.00 4.79
331 332 5.661056 TTCAACAAGAGATAGATGACCGT 57.339 39.130 0.00 0.00 0.00 4.83
332 333 5.250235 TCAACAAGAGATAGATGACCGTC 57.750 43.478 0.00 0.00 0.00 4.79
333 334 4.705023 TCAACAAGAGATAGATGACCGTCA 59.295 41.667 3.10 3.10 0.00 4.35
334 335 4.640789 ACAAGAGATAGATGACCGTCAC 57.359 45.455 2.57 0.00 0.00 3.67
335 336 4.017126 ACAAGAGATAGATGACCGTCACA 58.983 43.478 2.57 0.00 0.00 3.58
336 337 4.097135 ACAAGAGATAGATGACCGTCACAG 59.903 45.833 2.57 0.00 0.00 3.66
337 338 2.621055 AGAGATAGATGACCGTCACAGC 59.379 50.000 2.57 0.00 0.00 4.40
338 339 2.359214 GAGATAGATGACCGTCACAGCA 59.641 50.000 2.57 0.00 0.00 4.41
339 340 2.099921 AGATAGATGACCGTCACAGCAC 59.900 50.000 2.57 0.00 0.00 4.40
340 341 1.545841 TAGATGACCGTCACAGCACT 58.454 50.000 2.57 2.01 0.00 4.40
341 342 0.681733 AGATGACCGTCACAGCACTT 59.318 50.000 2.57 0.00 0.00 3.16
342 343 1.071605 GATGACCGTCACAGCACTTC 58.928 55.000 2.57 0.00 0.00 3.01
343 344 0.392706 ATGACCGTCACAGCACTTCA 59.607 50.000 2.57 0.00 0.00 3.02
344 345 0.392706 TGACCGTCACAGCACTTCAT 59.607 50.000 0.00 0.00 0.00 2.57
345 346 1.202639 TGACCGTCACAGCACTTCATT 60.203 47.619 0.00 0.00 0.00 2.57
346 347 1.873591 GACCGTCACAGCACTTCATTT 59.126 47.619 0.00 0.00 0.00 2.32
347 348 2.290641 GACCGTCACAGCACTTCATTTT 59.709 45.455 0.00 0.00 0.00 1.82
348 349 2.033299 ACCGTCACAGCACTTCATTTTG 59.967 45.455 0.00 0.00 0.00 2.44
349 350 2.605338 CCGTCACAGCACTTCATTTTGG 60.605 50.000 0.00 0.00 0.00 3.28
350 351 2.290367 CGTCACAGCACTTCATTTTGGA 59.710 45.455 0.00 0.00 0.00 3.53
351 352 3.607775 CGTCACAGCACTTCATTTTGGAG 60.608 47.826 0.00 0.00 0.00 3.86
352 353 2.886523 TCACAGCACTTCATTTTGGAGG 59.113 45.455 0.00 0.00 0.00 4.30
353 354 2.624838 CACAGCACTTCATTTTGGAGGT 59.375 45.455 0.00 0.00 0.00 3.85
354 355 3.068590 CACAGCACTTCATTTTGGAGGTT 59.931 43.478 0.00 0.00 0.00 3.50
355 356 3.706086 ACAGCACTTCATTTTGGAGGTTT 59.294 39.130 0.00 0.00 0.00 3.27
356 357 4.162131 ACAGCACTTCATTTTGGAGGTTTT 59.838 37.500 0.00 0.00 0.00 2.43
399 400 2.418368 TGCTGAATTGTTAGGGCGAT 57.582 45.000 0.00 0.00 0.00 4.58
402 403 2.945668 GCTGAATTGTTAGGGCGATTCT 59.054 45.455 7.34 0.00 39.08 2.40
449 450 8.976986 AATTTTGTTGCTTGATAGTTCAGATC 57.023 30.769 0.00 0.00 32.27 2.75
467 468 2.284263 TCTTGATAGTGCAGAGCGTG 57.716 50.000 0.00 0.00 0.00 5.34
524 525 6.318144 CCTGAACATCTGCTCTATGAACAAAT 59.682 38.462 0.00 0.00 0.00 2.32
535 536 8.959548 TGCTCTATGAACAAATTTGTGATGTAT 58.040 29.630 23.93 15.09 41.31 2.29
536 537 9.443283 GCTCTATGAACAAATTTGTGATGTATC 57.557 33.333 23.93 16.21 41.31 2.24
550 551 5.535753 TGATGTATCACCCTGTCATAGTG 57.464 43.478 0.00 0.00 0.00 2.74
551 552 4.344968 TGATGTATCACCCTGTCATAGTGG 59.655 45.833 3.32 0.00 32.29 4.00
562 563 3.609853 TGTCATAGTGGATTGTTGCTCC 58.390 45.455 0.00 0.00 0.00 4.70
564 565 4.263462 TGTCATAGTGGATTGTTGCTCCTT 60.263 41.667 0.00 0.00 33.69 3.36
565 566 4.333926 GTCATAGTGGATTGTTGCTCCTTC 59.666 45.833 0.00 0.00 33.69 3.46
566 567 2.206576 AGTGGATTGTTGCTCCTTCC 57.793 50.000 0.00 0.00 33.69 3.46
567 568 1.177401 GTGGATTGTTGCTCCTTCCC 58.823 55.000 0.00 0.00 33.69 3.97
568 569 0.039618 TGGATTGTTGCTCCTTCCCC 59.960 55.000 0.00 0.00 33.69 4.81
569 570 0.039618 GGATTGTTGCTCCTTCCCCA 59.960 55.000 0.00 0.00 0.00 4.96
570 571 1.342374 GGATTGTTGCTCCTTCCCCAT 60.342 52.381 0.00 0.00 0.00 4.00
571 572 2.027385 GATTGTTGCTCCTTCCCCATC 58.973 52.381 0.00 0.00 0.00 3.51
573 574 1.002069 TGTTGCTCCTTCCCCATCAT 58.998 50.000 0.00 0.00 0.00 2.45
574 575 1.341285 TGTTGCTCCTTCCCCATCATG 60.341 52.381 0.00 0.00 0.00 3.07
575 576 0.396139 TTGCTCCTTCCCCATCATGC 60.396 55.000 0.00 0.00 0.00 4.06
576 577 1.284111 TGCTCCTTCCCCATCATGCT 61.284 55.000 0.00 0.00 0.00 3.79
577 578 0.536915 GCTCCTTCCCCATCATGCTC 60.537 60.000 0.00 0.00 0.00 4.26
578 579 0.841961 CTCCTTCCCCATCATGCTCA 59.158 55.000 0.00 0.00 0.00 4.26
582 583 2.374504 CCTTCCCCATCATGCTCATAGT 59.625 50.000 0.00 0.00 0.00 2.12
583 584 3.409570 CTTCCCCATCATGCTCATAGTG 58.590 50.000 0.00 0.00 0.00 2.74
584 585 1.701292 TCCCCATCATGCTCATAGTGG 59.299 52.381 0.00 5.99 0.00 4.00
586 587 2.639347 CCCCATCATGCTCATAGTGGTA 59.361 50.000 10.07 0.00 0.00 3.25
587 588 3.072915 CCCCATCATGCTCATAGTGGTAA 59.927 47.826 10.07 0.00 0.00 2.85
588 589 4.067896 CCCATCATGCTCATAGTGGTAAC 58.932 47.826 10.07 0.00 0.00 2.50
590 591 4.202398 CCATCATGCTCATAGTGGTAACCT 60.202 45.833 0.00 0.00 0.00 3.50
610 644 3.485346 TTGCCCCGGACACCTTCAC 62.485 63.158 0.73 0.00 0.00 3.18
614 648 2.357034 CCGGACACCTTCACGTGG 60.357 66.667 17.00 1.58 38.11 4.94
633 667 2.458592 GTGTTCTTGCACACAGTCAC 57.541 50.000 0.60 1.22 45.57 3.67
635 669 1.286501 GTTCTTGCACACAGTCACGA 58.713 50.000 0.00 0.00 0.00 4.35
654 691 3.682858 ACGATGGTGTAAATTTCCTGACG 59.317 43.478 0.00 1.32 0.00 4.35
663 700 2.063015 ATTTCCTGACGTGGGTGCCA 62.063 55.000 0.00 0.00 0.00 4.92
664 701 2.063015 TTTCCTGACGTGGGTGCCAT 62.063 55.000 0.00 0.00 35.28 4.40
665 702 2.034066 CCTGACGTGGGTGCCATT 59.966 61.111 0.00 0.00 35.28 3.16
666 703 1.603455 CCTGACGTGGGTGCCATTT 60.603 57.895 0.00 0.00 35.28 2.32
667 704 1.178534 CCTGACGTGGGTGCCATTTT 61.179 55.000 0.00 0.00 35.28 1.82
668 705 0.673437 CTGACGTGGGTGCCATTTTT 59.327 50.000 0.00 0.00 35.28 1.94
669 706 1.883275 CTGACGTGGGTGCCATTTTTA 59.117 47.619 0.00 0.00 35.28 1.52
670 707 1.609555 TGACGTGGGTGCCATTTTTAC 59.390 47.619 0.00 0.00 35.28 2.01
671 708 1.609555 GACGTGGGTGCCATTTTTACA 59.390 47.619 0.00 0.00 35.28 2.41
681 718 6.348132 GGGTGCCATTTTTACATTTTACAAGC 60.348 38.462 0.00 0.00 0.00 4.01
687 724 8.421701 CCATTTTTACATTTTACAAGCACGTAC 58.578 33.333 0.00 0.00 0.00 3.67
691 728 5.338614 ACATTTTACAAGCACGTACTGTC 57.661 39.130 0.00 0.00 0.00 3.51
694 731 3.994204 TTACAAGCACGTACTGTCTGA 57.006 42.857 0.00 0.00 0.00 3.27
707 744 5.508573 CGTACTGTCTGACTTTTGACTATCG 59.491 44.000 9.51 0.00 34.57 2.92
711 748 3.927142 GTCTGACTTTTGACTATCGGGTG 59.073 47.826 0.00 0.00 0.00 4.61
1138 1471 1.856265 GAACGCCAAGAACCAGCTGG 61.856 60.000 31.60 31.60 42.17 4.85
1837 2542 1.449601 CGGTGGCACCTACCATGAC 60.450 63.158 32.28 4.91 43.01 3.06
1848 2553 4.019681 CACCTACCATGACAAAACCCTCTA 60.020 45.833 0.00 0.00 0.00 2.43
1956 2661 2.471815 CCTGTCAGGGTCTGGGTATA 57.528 55.000 11.46 0.00 31.51 1.47
2136 2868 2.645838 ATGTGGACTTGCAAGAGTGT 57.354 45.000 32.50 11.36 0.00 3.55
2175 2907 0.105760 TTGGCCCCATTCACAACAGT 60.106 50.000 0.00 0.00 0.00 3.55
2562 3295 4.813027 TCCATCTGCAGAAATGCTTTTTC 58.187 39.130 22.50 2.20 35.49 2.29
3115 3863 1.524621 ATGCCACCTAGTGATGCGC 60.525 57.895 0.00 0.00 35.23 6.09
3116 3864 1.976132 ATGCCACCTAGTGATGCGCT 61.976 55.000 9.73 0.00 35.23 5.92
3119 3867 1.680522 CCACCTAGTGATGCGCTCCT 61.681 60.000 9.73 1.19 35.23 3.69
3277 4025 5.643379 TTCTTCCAAAGAATTCCATTCCG 57.357 39.130 0.65 0.00 42.31 4.30
3405 4159 1.610522 CTTGGGCAGCTTGGTATATGC 59.389 52.381 0.00 0.00 37.95 3.14
3411 4165 3.057736 GGCAGCTTGGTATATGCAATCTG 60.058 47.826 0.00 0.00 40.46 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 7.615365 TGATGGTTCCTGCATTAAGTAAAGAAT 59.385 33.333 0.00 0.00 0.00 2.40
24 25 6.096705 CCATGATGGTTCCTGCATTAAGTAAA 59.903 38.462 2.54 0.00 31.35 2.01
26 27 5.132502 CCATGATGGTTCCTGCATTAAGTA 58.867 41.667 2.54 0.00 31.35 2.24
127 128 4.939271 TGGCAATCTATTGATGCACAATG 58.061 39.130 18.73 11.73 46.93 2.82
131 132 3.881688 ACTCTGGCAATCTATTGATGCAC 59.118 43.478 6.87 0.00 40.14 4.57
141 142 4.006319 GCTTCAACTTACTCTGGCAATCT 58.994 43.478 0.00 0.00 0.00 2.40
178 179 7.011389 CGAGTTGATCACATAAGCTATCCAAAA 59.989 37.037 0.00 0.00 0.00 2.44
179 180 6.479990 CGAGTTGATCACATAAGCTATCCAAA 59.520 38.462 0.00 0.00 0.00 3.28
190 191 3.610040 AACTGCCGAGTTGATCACATA 57.390 42.857 0.00 0.00 41.12 2.29
199 200 3.914426 ATCCTAATCAACTGCCGAGTT 57.086 42.857 0.00 0.00 43.63 3.01
220 221 2.635915 CCACTACAGTTTAGGGTGTGGA 59.364 50.000 0.00 0.00 44.21 4.02
231 232 6.653740 GCATTTCTAACTAACCCACTACAGTT 59.346 38.462 0.00 0.00 35.50 3.16
271 272 5.008613 CCATACAAATGGTAGTACATGGCAC 59.991 44.000 2.06 0.00 46.68 5.01
272 273 5.129634 CCATACAAATGGTAGTACATGGCA 58.870 41.667 2.06 0.00 46.68 4.92
273 274 5.689383 CCATACAAATGGTAGTACATGGC 57.311 43.478 2.06 0.00 46.68 4.40
295 296 3.399440 TGTTGAATGAATGGGCAAACC 57.601 42.857 0.00 0.00 40.81 3.27
313 314 4.017126 TGTGACGGTCATCTATCTCTTGT 58.983 43.478 14.78 0.00 0.00 3.16
314 315 4.605968 CTGTGACGGTCATCTATCTCTTG 58.394 47.826 14.78 0.00 0.00 3.02
315 316 3.067461 GCTGTGACGGTCATCTATCTCTT 59.933 47.826 14.78 0.00 0.00 2.85
316 317 2.621055 GCTGTGACGGTCATCTATCTCT 59.379 50.000 14.78 0.00 0.00 3.10
318 319 2.099921 GTGCTGTGACGGTCATCTATCT 59.900 50.000 14.78 0.00 0.00 1.98
319 320 2.099921 AGTGCTGTGACGGTCATCTATC 59.900 50.000 14.78 1.34 0.00 2.08
320 321 2.103373 AGTGCTGTGACGGTCATCTAT 58.897 47.619 14.78 0.00 0.00 1.98
321 322 1.545841 AGTGCTGTGACGGTCATCTA 58.454 50.000 14.78 3.56 0.00 1.98
323 324 1.071605 GAAGTGCTGTGACGGTCATC 58.928 55.000 14.78 8.69 0.00 2.92
324 325 0.392706 TGAAGTGCTGTGACGGTCAT 59.607 50.000 14.78 0.00 0.00 3.06
325 326 0.392706 ATGAAGTGCTGTGACGGTCA 59.607 50.000 6.76 6.76 0.00 4.02
326 327 1.512926 AATGAAGTGCTGTGACGGTC 58.487 50.000 0.00 0.00 0.00 4.79
327 328 1.967319 AAATGAAGTGCTGTGACGGT 58.033 45.000 0.00 0.00 0.00 4.83
328 329 2.605338 CCAAAATGAAGTGCTGTGACGG 60.605 50.000 0.00 0.00 0.00 4.79
329 330 2.290367 TCCAAAATGAAGTGCTGTGACG 59.710 45.455 0.00 0.00 0.00 4.35
330 331 3.304928 CCTCCAAAATGAAGTGCTGTGAC 60.305 47.826 0.00 0.00 0.00 3.67
331 332 2.886523 CCTCCAAAATGAAGTGCTGTGA 59.113 45.455 0.00 0.00 0.00 3.58
332 333 2.624838 ACCTCCAAAATGAAGTGCTGTG 59.375 45.455 0.00 0.00 0.00 3.66
333 334 2.949447 ACCTCCAAAATGAAGTGCTGT 58.051 42.857 0.00 0.00 0.00 4.40
334 335 4.326504 AAACCTCCAAAATGAAGTGCTG 57.673 40.909 0.00 0.00 0.00 4.41
335 336 6.670695 ATAAAACCTCCAAAATGAAGTGCT 57.329 33.333 0.00 0.00 0.00 4.40
336 337 7.575365 CAAATAAAACCTCCAAAATGAAGTGC 58.425 34.615 0.00 0.00 0.00 4.40
337 338 7.569226 CGCAAATAAAACCTCCAAAATGAAGTG 60.569 37.037 0.00 0.00 0.00 3.16
338 339 6.423604 CGCAAATAAAACCTCCAAAATGAAGT 59.576 34.615 0.00 0.00 0.00 3.01
339 340 6.423604 ACGCAAATAAAACCTCCAAAATGAAG 59.576 34.615 0.00 0.00 0.00 3.02
340 341 6.284459 ACGCAAATAAAACCTCCAAAATGAA 58.716 32.000 0.00 0.00 0.00 2.57
341 342 5.848406 ACGCAAATAAAACCTCCAAAATGA 58.152 33.333 0.00 0.00 0.00 2.57
342 343 6.642950 TGTACGCAAATAAAACCTCCAAAATG 59.357 34.615 0.00 0.00 0.00 2.32
343 344 6.750148 TGTACGCAAATAAAACCTCCAAAAT 58.250 32.000 0.00 0.00 0.00 1.82
344 345 6.145338 TGTACGCAAATAAAACCTCCAAAA 57.855 33.333 0.00 0.00 0.00 2.44
345 346 5.764131 CTGTACGCAAATAAAACCTCCAAA 58.236 37.500 0.00 0.00 0.00 3.28
346 347 4.320641 GCTGTACGCAAATAAAACCTCCAA 60.321 41.667 5.07 0.00 38.92 3.53
347 348 3.189702 GCTGTACGCAAATAAAACCTCCA 59.810 43.478 5.07 0.00 38.92 3.86
348 349 3.726782 CGCTGTACGCAAATAAAACCTCC 60.727 47.826 9.69 0.00 39.08 4.30
349 350 3.413558 CGCTGTACGCAAATAAAACCTC 58.586 45.455 9.69 0.00 39.08 3.85
350 351 2.160813 CCGCTGTACGCAAATAAAACCT 59.839 45.455 9.69 0.00 41.76 3.50
351 352 2.160022 TCCGCTGTACGCAAATAAAACC 59.840 45.455 9.69 0.00 41.76 3.27
352 353 3.458779 TCCGCTGTACGCAAATAAAAC 57.541 42.857 9.69 0.00 41.76 2.43
353 354 3.936453 AGATCCGCTGTACGCAAATAAAA 59.064 39.130 9.69 0.00 41.76 1.52
354 355 3.308595 CAGATCCGCTGTACGCAAATAAA 59.691 43.478 9.69 0.00 41.76 1.40
355 356 2.863740 CAGATCCGCTGTACGCAAATAA 59.136 45.455 9.69 0.00 41.76 1.40
356 357 2.469826 CAGATCCGCTGTACGCAAATA 58.530 47.619 9.69 0.00 41.76 1.40
376 377 2.543641 GCCCTAACAATTCAGCAATGC 58.456 47.619 0.00 0.00 0.00 3.56
426 427 7.750229 AGATCTGAACTATCAAGCAACAAAA 57.250 32.000 0.00 0.00 34.49 2.44
444 445 3.051327 CGCTCTGCACTATCAAGATCTG 58.949 50.000 0.00 0.00 0.00 2.90
449 450 2.284263 TCACGCTCTGCACTATCAAG 57.716 50.000 0.00 0.00 0.00 3.02
467 468 4.497340 CCATATAAACACGGCACCATGTTC 60.497 45.833 1.05 0.00 38.08 3.18
493 494 1.484240 GAGCAGATGTTCAGGCCTAGT 59.516 52.381 3.98 0.00 0.00 2.57
497 498 2.103771 TCATAGAGCAGATGTTCAGGCC 59.896 50.000 0.00 0.00 0.00 5.19
535 536 3.181329 ACAATCCACTATGACAGGGTGA 58.819 45.455 10.85 0.90 33.32 4.02
536 537 3.634397 ACAATCCACTATGACAGGGTG 57.366 47.619 4.25 4.25 0.00 4.61
537 538 3.873801 GCAACAATCCACTATGACAGGGT 60.874 47.826 0.00 0.00 0.00 4.34
538 539 2.684881 GCAACAATCCACTATGACAGGG 59.315 50.000 0.00 0.00 0.00 4.45
539 540 3.614092 AGCAACAATCCACTATGACAGG 58.386 45.455 0.00 0.00 0.00 4.00
540 541 3.624861 GGAGCAACAATCCACTATGACAG 59.375 47.826 0.00 0.00 36.79 3.51
541 542 3.264193 AGGAGCAACAATCCACTATGACA 59.736 43.478 0.00 0.00 39.47 3.58
542 543 3.878778 AGGAGCAACAATCCACTATGAC 58.121 45.455 0.00 0.00 39.47 3.06
543 544 4.517285 GAAGGAGCAACAATCCACTATGA 58.483 43.478 0.00 0.00 39.47 2.15
544 545 3.629398 GGAAGGAGCAACAATCCACTATG 59.371 47.826 0.00 0.00 39.47 2.23
545 546 3.372025 GGGAAGGAGCAACAATCCACTAT 60.372 47.826 0.00 0.00 39.47 2.12
546 547 2.026262 GGGAAGGAGCAACAATCCACTA 60.026 50.000 0.00 0.00 39.47 2.74
547 548 1.272147 GGGAAGGAGCAACAATCCACT 60.272 52.381 0.00 0.00 39.47 4.00
548 549 1.177401 GGGAAGGAGCAACAATCCAC 58.823 55.000 0.00 0.00 39.47 4.02
549 550 0.039618 GGGGAAGGAGCAACAATCCA 59.960 55.000 0.00 0.00 39.47 3.41
550 551 0.039618 TGGGGAAGGAGCAACAATCC 59.960 55.000 0.00 0.00 37.07 3.01
551 552 2.027385 GATGGGGAAGGAGCAACAATC 58.973 52.381 0.00 0.00 0.00 2.67
562 563 3.409570 CACTATGAGCATGATGGGGAAG 58.590 50.000 0.00 0.00 0.00 3.46
564 565 1.701292 CCACTATGAGCATGATGGGGA 59.299 52.381 0.00 0.00 0.00 4.81
565 566 1.422781 ACCACTATGAGCATGATGGGG 59.577 52.381 15.18 8.76 0.00 4.96
566 567 2.945080 ACCACTATGAGCATGATGGG 57.055 50.000 15.18 5.67 0.00 4.00
567 568 4.067896 GGTTACCACTATGAGCATGATGG 58.932 47.826 0.00 11.23 0.00 3.51
568 569 4.965814 AGGTTACCACTATGAGCATGATG 58.034 43.478 3.51 0.00 0.00 3.07
569 570 4.904251 AGAGGTTACCACTATGAGCATGAT 59.096 41.667 3.51 0.00 0.00 2.45
570 571 4.290093 AGAGGTTACCACTATGAGCATGA 58.710 43.478 3.51 0.00 0.00 3.07
571 572 4.679373 AGAGGTTACCACTATGAGCATG 57.321 45.455 3.51 0.00 0.00 4.06
573 574 3.369471 GCAAGAGGTTACCACTATGAGCA 60.369 47.826 3.51 0.00 0.00 4.26
574 575 3.198872 GCAAGAGGTTACCACTATGAGC 58.801 50.000 3.51 2.28 0.00 4.26
575 576 3.432326 GGGCAAGAGGTTACCACTATGAG 60.432 52.174 3.51 0.00 0.00 2.90
576 577 2.504175 GGGCAAGAGGTTACCACTATGA 59.496 50.000 3.51 0.00 0.00 2.15
577 578 2.421529 GGGGCAAGAGGTTACCACTATG 60.422 54.545 3.51 5.55 0.00 2.23
578 579 1.844497 GGGGCAAGAGGTTACCACTAT 59.156 52.381 3.51 0.00 0.00 2.12
582 583 2.598787 CCGGGGCAAGAGGTTACCA 61.599 63.158 3.51 0.00 0.00 3.25
583 584 2.271173 CCGGGGCAAGAGGTTACC 59.729 66.667 0.00 0.00 0.00 2.85
584 585 1.078637 GTCCGGGGCAAGAGGTTAC 60.079 63.158 0.00 0.00 0.00 2.50
586 587 2.852075 TGTCCGGGGCAAGAGGTT 60.852 61.111 0.00 0.00 0.00 3.50
587 588 3.637273 GTGTCCGGGGCAAGAGGT 61.637 66.667 1.18 0.00 0.00 3.85
588 589 4.410400 GGTGTCCGGGGCAAGAGG 62.410 72.222 1.18 0.00 0.00 3.69
590 591 2.852075 AAGGTGTCCGGGGCAAGA 60.852 61.111 1.18 0.00 0.00 3.02
610 644 4.996113 GTGTGCAAGAACACCACG 57.004 55.556 0.00 0.00 43.84 4.94
633 667 3.682858 ACGTCAGGAAATTTACACCATCG 59.317 43.478 2.58 3.06 0.00 3.84
635 669 3.756434 CCACGTCAGGAAATTTACACCAT 59.244 43.478 2.58 0.00 0.00 3.55
654 691 5.992217 TGTAAAATGTAAAAATGGCACCCAC 59.008 36.000 0.00 0.00 35.80 4.61
663 700 9.176181 CAGTACGTGCTTGTAAAATGTAAAAAT 57.824 29.630 2.37 0.00 0.00 1.82
664 701 8.182881 ACAGTACGTGCTTGTAAAATGTAAAAA 58.817 29.630 2.37 0.00 0.00 1.94
665 702 7.695820 ACAGTACGTGCTTGTAAAATGTAAAA 58.304 30.769 2.37 0.00 0.00 1.52
666 703 7.225145 AGACAGTACGTGCTTGTAAAATGTAAA 59.775 33.333 2.37 0.00 0.00 2.01
667 704 6.702723 AGACAGTACGTGCTTGTAAAATGTAA 59.297 34.615 2.37 0.00 0.00 2.41
668 705 6.144886 CAGACAGTACGTGCTTGTAAAATGTA 59.855 38.462 2.37 0.00 0.00 2.29
669 706 5.050363 CAGACAGTACGTGCTTGTAAAATGT 60.050 40.000 2.37 0.00 0.00 2.71
670 707 5.176774 TCAGACAGTACGTGCTTGTAAAATG 59.823 40.000 2.37 4.31 0.00 2.32
671 708 5.176958 GTCAGACAGTACGTGCTTGTAAAAT 59.823 40.000 2.37 0.00 0.00 1.82
681 718 4.360563 AGTCAAAAGTCAGACAGTACGTG 58.639 43.478 2.66 0.00 37.23 4.49
687 724 4.177026 CCCGATAGTCAAAAGTCAGACAG 58.823 47.826 2.66 0.00 37.23 3.51
691 728 2.673368 GCACCCGATAGTCAAAAGTCAG 59.327 50.000 0.00 0.00 0.00 3.51
694 731 2.109425 GGCACCCGATAGTCAAAAGT 57.891 50.000 0.00 0.00 0.00 2.66
711 748 2.025699 TGTGGGTCAGGTAATTAAGGGC 60.026 50.000 0.00 0.00 0.00 5.19
997 1330 1.422781 GGCCATCTTCATCTCCATGGA 59.577 52.381 15.27 15.27 38.52 3.41
1138 1471 1.966451 GCAGCCCCTGTGTGTACAC 60.966 63.158 19.36 19.36 46.59 2.90
1837 2542 3.690460 AGGCAGAACATAGAGGGTTTTG 58.310 45.455 0.00 0.00 34.51 2.44
2136 2868 3.547054 ATAGGTTTTCCCAATCGCGTA 57.453 42.857 5.77 0.00 41.86 4.42
2175 2907 2.855770 ATGCTGCCCTTGGTTCCCA 61.856 57.895 0.00 0.00 0.00 4.37
2562 3295 1.839994 TCTGGGAAGAGGGCACAATAG 59.160 52.381 0.00 0.00 0.00 1.73
2646 3379 6.567687 TTCTTATCATTTCGGCAACTTGAA 57.432 33.333 0.00 0.00 0.00 2.69
3035 3777 4.751431 GCAAACTGCCTGGGAGAT 57.249 55.556 22.89 7.27 37.42 2.75
3277 4025 2.764572 TCTTTCCGACCTCAGGAATACC 59.235 50.000 0.00 0.00 46.01 2.73
3340 4088 5.759763 GGCTCAATTCAAATCCAACACTTTT 59.240 36.000 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.