Multiple sequence alignment - TraesCS2D01G512300

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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 TraesCS2D01G512300 chr2D 100.000 2231 0 0 1 2231 603633572 603631342 0.000000e+00 4120.0
1 TraesCS2D01G512300 chr2D 93.146 642 42 2 1 640 91797075 91797716 0.000000e+00 941.0
2 TraesCS2D01G512300 chr2D 92.835 642 43 3 1 640 105660761 105660121 0.000000e+00 928.0
3 TraesCS2D01G512300 chr2D 88.710 434 43 6 1 434 123201866 123202293 1.960000e-145 525.0
4 TraesCS2D01G512300 chr2D 94.515 237 12 1 422 657 603638748 603638512 4.530000e-97 364.0
5 TraesCS2D01G512300 chr2D 90.950 221 19 1 422 641 91790698 91790918 1.680000e-76 296.0
6 TraesCS2D01G512300 chr2D 88.123 261 13 3 984 1229 603648478 603648221 6.020000e-76 294.0
7 TraesCS2D01G512300 chr2D 87.342 237 23 4 422 657 105668824 105668594 4.720000e-67 265.0
8 TraesCS2D01G512300 chr2D 81.034 232 25 13 658 876 603648786 603648561 1.370000e-37 167.0
9 TraesCS2D01G512300 chr2B 92.719 1497 44 17 768 2231 734185636 734184172 0.000000e+00 2100.0
10 TraesCS2D01G512300 chr2B 92.483 439 31 2 1 438 155874194 155874631 5.230000e-176 627.0
11 TraesCS2D01G512300 chr2B 88.249 434 44 7 1 434 176166411 176166837 1.530000e-141 512.0
12 TraesCS2D01G512300 chr2B 80.449 624 57 29 658 1229 734200607 734199997 1.230000e-112 416.0
13 TraesCS2D01G512300 chr2B 91.707 205 16 1 437 640 155879494 155879698 1.300000e-72 283.0
14 TraesCS2D01G512300 chr2B 90.526 190 15 3 454 641 155829173 155829361 4.760000e-62 248.0
15 TraesCS2D01G512300 chr5B 91.972 436 30 5 1 434 239250046 239250478 6.810000e-170 606.0
16 TraesCS2D01G512300 chr3B 90.741 432 36 4 2 432 763102196 763101768 6.910000e-160 573.0
17 TraesCS2D01G512300 chr6D 90.553 434 35 4 2 434 89071425 89070997 8.940000e-159 569.0
18 TraesCS2D01G512300 chr6B 89.885 435 35 5 2 434 171066746 171066319 3.240000e-153 551.0
19 TraesCS2D01G512300 chr2A 78.905 621 69 24 658 1229 735788138 735787531 4.530000e-97 364.0
20 TraesCS2D01G512300 chr1D 90.717 237 19 3 418 653 28817757 28817991 1.660000e-81 313.0
21 TraesCS2D01G512300 chr1D 92.105 38 2 1 2132 2169 92965576 92965540 4.000000e-03 52.8
22 TraesCS2D01G512300 chr7D 86.408 206 25 3 452 654 290925520 290925315 2.880000e-54 222.0
23 TraesCS2D01G512300 chr3A 100.000 31 0 0 2129 2159 474843076 474843106 8.610000e-05 58.4
24 TraesCS2D01G512300 chr7B 97.059 34 0 1 2126 2159 696275670 696275638 3.090000e-04 56.5
25 TraesCS2D01G512300 chr5A 96.875 32 1 0 2128 2159 641843937 641843968 1.000000e-03 54.7


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 TraesCS2D01G512300 chr2D 603631342 603633572 2230 True 4120.0 4120 100.0000 1 2231 1 chr2D.!!$R3 2230
1 TraesCS2D01G512300 chr2D 91797075 91797716 641 False 941.0 941 93.1460 1 640 1 chr2D.!!$F2 639
2 TraesCS2D01G512300 chr2D 105660121 105660761 640 True 928.0 928 92.8350 1 640 1 chr2D.!!$R1 639
3 TraesCS2D01G512300 chr2D 603648221 603648786 565 True 230.5 294 84.5785 658 1229 2 chr2D.!!$R5 571
4 TraesCS2D01G512300 chr2B 734184172 734185636 1464 True 2100.0 2100 92.7190 768 2231 1 chr2B.!!$R1 1463
5 TraesCS2D01G512300 chr2B 734199997 734200607 610 True 416.0 416 80.4490 658 1229 1 chr2B.!!$R2 571
6 TraesCS2D01G512300 chr2A 735787531 735788138 607 True 364.0 364 78.9050 658 1229 1 chr2A.!!$R1 571

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
511 513 1.996798 AGGGACGTGTCTCTCTTTCA 58.003 50.0 0.0 0.0 34.85 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1993 2100 0.395724 GTGTTGGGATGCCCTTAGGG 60.396 60.0 14.11 14.11 45.7 3.53 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 6.708054 CACTAAGCATATTTCTCCTAAGTGGG 59.292 42.308 0.00 0.00 36.20 4.61
42 43 6.603599 AGCATATTTCTCCTAAGTGGGTTTTC 59.396 38.462 0.00 0.00 36.20 2.29
44 45 4.799715 TTTCTCCTAAGTGGGTTTTCCA 57.200 40.909 0.00 0.00 44.79 3.53
65 66 4.580167 CCACCATGAACTTCAGAAAAGTGA 59.420 41.667 0.00 0.00 0.00 3.41
90 91 9.346725 GAGGAAATAAACATCTTGCAAGTTAAG 57.653 33.333 25.19 15.40 0.00 1.85
227 228 4.846940 AGTTTCTCCCTGAACTATTCCTGT 59.153 41.667 0.00 0.00 33.88 4.00
272 273 8.616076 ACTCTTTCTCTTTGTGAGTTTATGTTG 58.384 33.333 0.00 0.00 43.13 3.33
288 289 2.507484 TGTTGCAGGTTCTCATCAAGG 58.493 47.619 0.00 0.00 0.00 3.61
329 331 3.832490 TGAGAAGGATCTTTTCGAGGTGA 59.168 43.478 0.00 0.00 35.54 4.02
338 340 6.864165 GGATCTTTTCGAGGTGATGATACTAC 59.136 42.308 0.00 0.00 0.00 2.73
339 341 6.769134 TCTTTTCGAGGTGATGATACTACA 57.231 37.500 0.00 0.00 0.00 2.74
348 350 7.141758 AGGTGATGATACTACAATGGACAAT 57.858 36.000 0.00 0.00 0.00 2.71
352 354 9.764363 GTGATGATACTACAATGGACAATCTTA 57.236 33.333 0.00 0.00 0.00 2.10
354 356 9.429359 GATGATACTACAATGGACAATCTTAGG 57.571 37.037 0.00 0.00 0.00 2.69
359 361 5.715439 ACAATGGACAATCTTAGGGATGA 57.285 39.130 0.00 0.00 34.45 2.92
379 381 5.126396 TGATGATCATACCTAGACAAGCG 57.874 43.478 8.54 0.00 0.00 4.68
386 388 6.650427 TCATACCTAGACAAGCGTATGAAT 57.350 37.500 12.23 0.00 40.98 2.57
403 405 7.385205 GCGTATGAATATTCTACATGGACAAGT 59.615 37.037 16.24 0.00 0.00 3.16
415 417 4.464951 ACATGGACAAGTGTAGATTACGGA 59.535 41.667 0.00 0.00 0.00 4.69
420 422 5.587844 GGACAAGTGTAGATTACGGAGAGTA 59.412 44.000 0.00 0.00 0.00 2.59
475 477 6.154534 AGGGAATCTATTTTTGCCTAAACACC 59.845 38.462 0.00 0.00 42.40 4.16
478 480 5.365403 TCTATTTTTGCCTAAACACCGTG 57.635 39.130 0.00 0.00 0.00 4.94
511 513 1.996798 AGGGACGTGTCTCTCTTTCA 58.003 50.000 0.00 0.00 34.85 2.69
517 519 2.159142 ACGTGTCTCTCTTTCAAACCGT 60.159 45.455 0.00 0.00 0.00 4.83
526 529 2.955660 TCTTTCAAACCGTTGCATCCTT 59.044 40.909 0.00 0.00 34.50 3.36
558 561 3.890147 ACCGACCTAGGATATGACTGTTC 59.110 47.826 17.98 0.00 34.73 3.18
591 594 2.031944 TCTATTCGACGCATCTCTTCCG 60.032 50.000 0.00 0.00 0.00 4.30
593 596 2.884087 TTCGACGCATCTCTTCCGGC 62.884 60.000 0.00 0.00 0.00 6.13
603 606 5.428253 GCATCTCTTCCGGCCATATATAAA 58.572 41.667 2.24 0.00 0.00 1.40
604 607 5.294552 GCATCTCTTCCGGCCATATATAAAC 59.705 44.000 2.24 0.00 0.00 2.01
643 646 9.820725 ATCAATCAAAACAAGTTGATCTTTTCA 57.179 25.926 10.54 0.00 45.42 2.69
644 647 9.086336 TCAATCAAAACAAGTTGATCTTTTCAC 57.914 29.630 10.54 0.00 45.42 3.18
645 648 9.090692 CAATCAAAACAAGTTGATCTTTTCACT 57.909 29.630 10.54 0.00 45.42 3.41
646 649 8.862550 ATCAAAACAAGTTGATCTTTTCACTC 57.137 30.769 10.54 0.00 43.24 3.51
647 650 7.825681 TCAAAACAAGTTGATCTTTTCACTCA 58.174 30.769 10.54 0.00 32.56 3.41
648 651 8.303156 TCAAAACAAGTTGATCTTTTCACTCAA 58.697 29.630 10.54 0.00 32.56 3.02
649 652 8.924691 CAAAACAAGTTGATCTTTTCACTCAAA 58.075 29.630 10.54 0.00 32.84 2.69
650 653 9.487790 AAAACAAGTTGATCTTTTCACTCAAAA 57.512 25.926 10.54 0.00 32.84 2.44
651 654 8.466086 AACAAGTTGATCTTTTCACTCAAAAC 57.534 30.769 10.54 0.00 32.84 2.43
652 655 7.601856 ACAAGTTGATCTTTTCACTCAAAACA 58.398 30.769 10.54 0.00 32.84 2.83
653 656 8.253113 ACAAGTTGATCTTTTCACTCAAAACAT 58.747 29.630 10.54 0.00 32.84 2.71
654 657 8.537223 CAAGTTGATCTTTTCACTCAAAACATG 58.463 33.333 0.00 0.00 32.84 3.21
655 658 7.775120 AGTTGATCTTTTCACTCAAAACATGT 58.225 30.769 0.00 0.00 32.84 3.21
656 659 8.253113 AGTTGATCTTTTCACTCAAAACATGTT 58.747 29.630 4.92 4.92 32.84 2.71
657 660 8.872845 GTTGATCTTTTCACTCAAAACATGTTT 58.127 29.630 18.13 18.13 32.84 2.83
658 661 8.410030 TGATCTTTTCACTCAAAACATGTTTG 57.590 30.769 23.93 16.99 32.36 2.93
659 662 8.034215 TGATCTTTTCACTCAAAACATGTTTGT 58.966 29.630 23.93 14.74 37.82 2.83
660 663 7.810766 TCTTTTCACTCAAAACATGTTTGTC 57.189 32.000 23.93 0.00 34.06 3.18
661 664 7.601856 TCTTTTCACTCAAAACATGTTTGTCT 58.398 30.769 23.93 6.38 34.06 3.41
664 667 6.266168 TCACTCAAAACATGTTTGTCTGTT 57.734 33.333 23.93 4.86 37.19 3.16
676 679 2.684001 TGTCTGTTTGTCTGTCCGTT 57.316 45.000 0.00 0.00 0.00 4.44
678 681 2.675844 TGTCTGTTTGTCTGTCCGTTTG 59.324 45.455 0.00 0.00 0.00 2.93
679 682 2.676342 GTCTGTTTGTCTGTCCGTTTGT 59.324 45.455 0.00 0.00 0.00 2.83
680 683 2.933906 TCTGTTTGTCTGTCCGTTTGTC 59.066 45.455 0.00 0.00 0.00 3.18
681 684 2.936498 CTGTTTGTCTGTCCGTTTGTCT 59.064 45.455 0.00 0.00 0.00 3.41
682 685 2.675844 TGTTTGTCTGTCCGTTTGTCTG 59.324 45.455 0.00 0.00 0.00 3.51
683 686 2.676342 GTTTGTCTGTCCGTTTGTCTGT 59.324 45.455 0.00 0.00 0.00 3.41
684 687 2.218953 TGTCTGTCCGTTTGTCTGTC 57.781 50.000 0.00 0.00 0.00 3.51
721 724 2.169352 GAGCTAGAGCCATTTCAGGTCA 59.831 50.000 0.00 0.00 43.38 4.02
730 733 6.894103 AGAGCCATTTCAGGTCATTTTCTATT 59.106 34.615 0.00 0.00 34.17 1.73
731 734 6.870769 AGCCATTTCAGGTCATTTTCTATTG 58.129 36.000 0.00 0.00 0.00 1.90
739 742 5.580691 CAGGTCATTTTCTATTGCTACGTCA 59.419 40.000 0.00 0.00 0.00 4.35
742 745 5.350365 GTCATTTTCTATTGCTACGTCACCA 59.650 40.000 0.00 0.00 0.00 4.17
743 746 5.935206 TCATTTTCTATTGCTACGTCACCAA 59.065 36.000 0.00 0.00 0.00 3.67
744 747 5.600908 TTTTCTATTGCTACGTCACCAAC 57.399 39.130 0.00 0.00 0.00 3.77
787 794 3.941573 GGTTCTATTTAACCACCACGGA 58.058 45.455 0.94 0.00 46.85 4.69
909 942 2.950172 ATGTGTTTGTCGCGCCGTC 61.950 57.895 0.00 0.00 0.00 4.79
910 943 4.696172 GTGTTTGTCGCGCCGTCG 62.696 66.667 0.00 0.00 39.07 5.12
1247 1323 0.463204 TGATCACCAGAGCTAGCTGC 59.537 55.000 24.99 13.76 43.29 5.25
1248 1324 0.249826 GATCACCAGAGCTAGCTGCC 60.250 60.000 24.99 8.88 44.23 4.85
1259 1344 0.820871 CTAGCTGCCCGTCTTCTTCT 59.179 55.000 0.00 0.00 0.00 2.85
1302 1394 0.393077 CCTGCCCTATGTCCTAACCG 59.607 60.000 0.00 0.00 0.00 4.44
1362 1460 6.076981 AGTGGATGTAAAGAAAGCAAACAG 57.923 37.500 0.00 0.00 0.00 3.16
1399 1497 0.547229 TACCACCCGTAACCCCACAT 60.547 55.000 0.00 0.00 0.00 3.21
1400 1498 1.377987 CCACCCGTAACCCCACATG 60.378 63.158 0.00 0.00 0.00 3.21
1401 1499 2.043980 CACCCGTAACCCCACATGC 61.044 63.158 0.00 0.00 0.00 4.06
1402 1500 2.822255 CCCGTAACCCCACATGCG 60.822 66.667 0.00 0.00 0.00 4.73
1403 1501 2.266372 CCGTAACCCCACATGCGA 59.734 61.111 0.00 0.00 0.00 5.10
1404 1502 1.376166 CCGTAACCCCACATGCGAA 60.376 57.895 0.00 0.00 0.00 4.70
1405 1503 0.746563 CCGTAACCCCACATGCGAAT 60.747 55.000 0.00 0.00 0.00 3.34
1406 1504 0.376852 CGTAACCCCACATGCGAATG 59.623 55.000 0.40 0.40 0.00 2.67
1407 1505 1.745232 GTAACCCCACATGCGAATGA 58.255 50.000 11.32 0.00 0.00 2.57
1408 1506 2.297701 GTAACCCCACATGCGAATGAT 58.702 47.619 11.32 0.00 0.00 2.45
1409 1507 1.105457 AACCCCACATGCGAATGATG 58.895 50.000 11.32 4.72 0.00 3.07
1410 1508 0.034186 ACCCCACATGCGAATGATGT 60.034 50.000 11.32 0.00 34.24 3.06
1411 1509 1.211703 ACCCCACATGCGAATGATGTA 59.788 47.619 11.32 0.00 32.64 2.29
1412 1510 1.875514 CCCCACATGCGAATGATGTAG 59.124 52.381 11.32 0.00 32.64 2.74
1413 1511 1.265095 CCCACATGCGAATGATGTAGC 59.735 52.381 11.32 0.00 32.64 3.58
1414 1512 1.265095 CCACATGCGAATGATGTAGCC 59.735 52.381 11.32 0.00 32.64 3.93
1415 1513 1.070376 CACATGCGAATGATGTAGCCG 60.070 52.381 11.32 0.00 32.64 5.52
1416 1514 0.110509 CATGCGAATGATGTAGCCGC 60.111 55.000 0.00 0.00 45.28 6.53
1417 1515 1.230635 ATGCGAATGATGTAGCCGCC 61.231 55.000 0.00 0.00 44.55 6.13
1418 1516 2.943345 GCGAATGATGTAGCCGCCG 61.943 63.158 0.00 0.00 39.97 6.46
1419 1517 2.939022 GAATGATGTAGCCGCCGC 59.061 61.111 0.00 0.00 0.00 6.53
1420 1518 1.887242 GAATGATGTAGCCGCCGCA 60.887 57.895 0.00 0.00 37.52 5.69
1421 1519 2.105960 GAATGATGTAGCCGCCGCAC 62.106 60.000 0.00 0.00 37.52 5.34
1422 1520 2.867793 AATGATGTAGCCGCCGCACA 62.868 55.000 0.00 2.64 37.52 4.57
1463 1561 7.974730 TCTATCTATCTCTATCTCACCCGTA 57.025 40.000 0.00 0.00 0.00 4.02
1487 1585 3.755378 ACTTGCTCTTCCATTTAGCTGTG 59.245 43.478 0.00 0.00 37.16 3.66
1502 1600 3.891049 AGCTGTGAAAGAACTTCAACCT 58.109 40.909 0.00 0.00 45.67 3.50
1545 1643 7.008859 CGTACGTTTGTTCGGTTAAATTGTAT 58.991 34.615 7.22 0.00 35.53 2.29
1592 1690 6.548441 TCGTTTTGATCACTTTTTATCGGT 57.452 33.333 0.00 0.00 0.00 4.69
1656 1754 5.279384 GGACGTACAAGTACCAGATGTATG 58.721 45.833 0.00 12.64 40.63 2.39
1683 1781 1.202440 AGTTGTGTTTAGTCGTGCGGA 60.202 47.619 0.00 0.00 0.00 5.54
1686 1784 1.795872 TGTGTTTAGTCGTGCGGAATG 59.204 47.619 0.00 0.00 0.00 2.67
1713 1811 3.328505 ACGTACGGTTTCATTGGGTAAG 58.671 45.455 21.06 0.00 0.00 2.34
1723 1821 4.112634 TCATTGGGTAAGCTGTTCCTTT 57.887 40.909 0.00 0.00 0.00 3.11
1728 1826 2.820197 GGGTAAGCTGTTCCTTTCCAAG 59.180 50.000 0.00 0.00 34.89 3.61
1860 1958 1.411394 CAAAATGACTGCCACTTGCG 58.589 50.000 0.00 0.00 45.60 4.85
1861 1959 1.001487 CAAAATGACTGCCACTTGCGA 60.001 47.619 0.00 0.00 45.60 5.10
1871 1978 1.503542 CACTTGCGACCAATCCTGC 59.496 57.895 0.00 0.00 0.00 4.85
1895 2002 7.124599 TGCTTTCCATCATCCATATTTGACTTT 59.875 33.333 0.00 0.00 0.00 2.66
1945 2052 0.653397 TATCCATCACCCCCTCCCTT 59.347 55.000 0.00 0.00 0.00 3.95
1969 2076 7.744087 TTGAAAATAGAAGCAGCTTAGACAA 57.256 32.000 7.92 5.62 0.00 3.18
1993 2100 5.131142 AGCCACCATTATATGCTCTATACCC 59.869 44.000 0.00 0.00 0.00 3.69
2087 2194 0.033601 GCCATCCAACATGGTACCCA 60.034 55.000 10.07 0.00 41.17 4.51
2091 2198 2.818751 TCCAACATGGTACCCAATCC 57.181 50.000 10.07 0.00 39.03 3.01
2094 2201 2.014128 CAACATGGTACCCAATCCGTC 58.986 52.381 10.07 0.00 36.95 4.79
2099 2206 1.520787 GTACCCAATCCGTCCGCAG 60.521 63.158 0.00 0.00 0.00 5.18
2167 2274 3.487202 CGCTGCCACATACGCGTT 61.487 61.111 20.78 1.87 40.64 4.84
2196 2303 4.887655 CCAAGACCCAACCATAAAGATACC 59.112 45.833 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 5.514274 TTCTGAAGTTCATGGTGGAAAAC 57.486 39.130 5.91 0.00 0.00 2.43
42 43 4.580167 TCACTTTTCTGAAGTTCATGGTGG 59.420 41.667 5.91 0.00 0.00 4.61
44 45 4.823989 CCTCACTTTTCTGAAGTTCATGGT 59.176 41.667 5.91 0.00 0.00 3.55
56 57 8.084684 GCAAGATGTTTATTTCCTCACTTTTCT 58.915 33.333 0.00 0.00 0.00 2.52
65 66 8.860088 ACTTAACTTGCAAGATGTTTATTTCCT 58.140 29.630 32.50 2.30 0.00 3.36
90 91 3.988379 TCAGCAAGGTTTTCACATGAC 57.012 42.857 0.00 0.00 0.00 3.06
160 161 2.961526 AGTCGTCGCATACCAATTCT 57.038 45.000 0.00 0.00 0.00 2.40
272 273 2.172293 AGGATCCTTGATGAGAACCTGC 59.828 50.000 9.02 0.00 0.00 4.85
329 331 8.378565 CCCTAAGATTGTCCATTGTAGTATCAT 58.621 37.037 0.00 0.00 0.00 2.45
338 340 6.301486 TCATCATCCCTAAGATTGTCCATTG 58.699 40.000 0.00 0.00 30.59 2.82
339 341 6.520021 TCATCATCCCTAAGATTGTCCATT 57.480 37.500 0.00 0.00 30.59 3.16
348 350 7.836685 GTCTAGGTATGATCATCATCCCTAAGA 59.163 40.741 17.41 13.97 42.49 2.10
352 354 5.908590 TGTCTAGGTATGATCATCATCCCT 58.091 41.667 15.69 15.69 44.20 4.20
354 356 6.105333 GCTTGTCTAGGTATGATCATCATCC 58.895 44.000 12.53 13.06 38.26 3.51
359 361 6.434340 TCATACGCTTGTCTAGGTATGATCAT 59.566 38.462 13.81 13.81 39.47 2.45
371 373 7.600375 CCATGTAGAATATTCATACGCTTGTCT 59.400 37.037 17.56 0.00 0.00 3.41
379 381 9.547753 ACACTTGTCCATGTAGAATATTCATAC 57.452 33.333 17.56 15.21 0.00 2.39
460 462 1.534175 CGCACGGTGTTTAGGCAAAAA 60.534 47.619 10.24 0.00 0.00 1.94
478 480 1.748879 TCCCTTGCTATGCAACCGC 60.749 57.895 0.45 0.00 43.99 5.68
511 513 5.047660 TGCTAATTAAAGGATGCAACGGTTT 60.048 36.000 0.00 0.00 0.00 3.27
517 519 4.702612 TCGGTTGCTAATTAAAGGATGCAA 59.297 37.500 0.00 4.06 37.96 4.08
526 529 5.881923 ATCCTAGGTCGGTTGCTAATTAA 57.118 39.130 9.08 0.00 0.00 1.40
558 561 1.325640 TCGAATAGACTCGACGGTTCG 59.674 52.381 0.00 0.00 42.69 3.95
573 576 0.249073 CCGGAAGAGATGCGTCGAAT 60.249 55.000 0.00 0.00 41.91 3.34
603 606 9.778741 TGTTTTGATTGATAGAAAGAGTACAGT 57.221 29.630 0.00 0.00 0.00 3.55
618 621 9.086336 GTGAAAAGATCAACTTGTTTTGATTGA 57.914 29.630 0.00 0.00 44.59 2.57
626 629 8.087750 TGTTTTGAGTGAAAAGATCAACTTGTT 58.912 29.630 0.00 0.00 40.50 2.83
640 643 6.266168 ACAGACAAACATGTTTTGAGTGAA 57.734 33.333 21.10 0.00 33.83 3.18
641 644 5.895636 ACAGACAAACATGTTTTGAGTGA 57.104 34.783 21.10 0.00 33.83 3.41
642 645 6.365789 ACAAACAGACAAACATGTTTTGAGTG 59.634 34.615 21.10 18.88 44.96 3.51
643 646 6.454795 ACAAACAGACAAACATGTTTTGAGT 58.545 32.000 21.10 15.74 44.96 3.41
644 647 6.808212 AGACAAACAGACAAACATGTTTTGAG 59.192 34.615 21.10 12.66 44.96 3.02
645 648 6.585702 CAGACAAACAGACAAACATGTTTTGA 59.414 34.615 21.10 0.00 44.96 2.69
646 649 6.365789 ACAGACAAACAGACAAACATGTTTTG 59.634 34.615 21.10 18.38 44.96 2.44
647 650 6.454795 ACAGACAAACAGACAAACATGTTTT 58.545 32.000 21.10 12.50 44.96 2.43
649 652 5.393027 GGACAGACAAACAGACAAACATGTT 60.393 40.000 4.92 4.92 41.28 2.71
650 653 4.096382 GGACAGACAAACAGACAAACATGT 59.904 41.667 0.00 0.00 0.00 3.21
651 654 4.601019 GGACAGACAAACAGACAAACATG 58.399 43.478 0.00 0.00 0.00 3.21
652 655 3.312421 CGGACAGACAAACAGACAAACAT 59.688 43.478 0.00 0.00 0.00 2.71
653 656 2.675844 CGGACAGACAAACAGACAAACA 59.324 45.455 0.00 0.00 0.00 2.83
654 657 2.676342 ACGGACAGACAAACAGACAAAC 59.324 45.455 0.00 0.00 0.00 2.93
655 658 2.980568 ACGGACAGACAAACAGACAAA 58.019 42.857 0.00 0.00 0.00 2.83
656 659 2.684001 ACGGACAGACAAACAGACAA 57.316 45.000 0.00 0.00 0.00 3.18
657 660 2.675844 CAAACGGACAGACAAACAGACA 59.324 45.455 0.00 0.00 0.00 3.41
658 661 2.676342 ACAAACGGACAGACAAACAGAC 59.324 45.455 0.00 0.00 0.00 3.51
659 662 2.933906 GACAAACGGACAGACAAACAGA 59.066 45.455 0.00 0.00 0.00 3.41
660 663 2.936498 AGACAAACGGACAGACAAACAG 59.064 45.455 0.00 0.00 0.00 3.16
661 664 2.675844 CAGACAAACGGACAGACAAACA 59.324 45.455 0.00 0.00 0.00 2.83
664 667 2.167693 AGACAGACAAACGGACAGACAA 59.832 45.455 0.00 0.00 0.00 3.18
676 679 3.394274 TGATTGGAGGGAAAGACAGACAA 59.606 43.478 0.00 0.00 0.00 3.18
678 681 3.703001 TGATTGGAGGGAAAGACAGAC 57.297 47.619 0.00 0.00 0.00 3.51
679 682 3.909995 TCTTGATTGGAGGGAAAGACAGA 59.090 43.478 0.00 0.00 0.00 3.41
680 683 4.260170 CTCTTGATTGGAGGGAAAGACAG 58.740 47.826 0.00 0.00 0.00 3.51
681 684 3.560025 GCTCTTGATTGGAGGGAAAGACA 60.560 47.826 0.00 0.00 0.00 3.41
682 685 3.013219 GCTCTTGATTGGAGGGAAAGAC 58.987 50.000 0.00 0.00 0.00 3.01
683 686 2.915604 AGCTCTTGATTGGAGGGAAAGA 59.084 45.455 0.00 0.00 0.00 2.52
684 687 3.362870 AGCTCTTGATTGGAGGGAAAG 57.637 47.619 0.00 0.00 0.00 2.62
730 733 1.372499 GCGAGTTGGTGACGTAGCA 60.372 57.895 0.00 0.00 34.39 3.49
731 734 2.092882 GGCGAGTTGGTGACGTAGC 61.093 63.158 0.00 0.00 0.00 3.58
739 742 2.203294 AAAAGCCGGCGAGTTGGT 60.203 55.556 23.20 0.00 0.00 3.67
787 794 3.210074 AGGAGGAGAATACAGGTGGGTAT 59.790 47.826 0.00 0.00 35.53 2.73
910 943 2.361104 TGAATTCCACCGGCAGCC 60.361 61.111 0.00 0.00 0.00 4.85
911 944 3.056313 GCTGAATTCCACCGGCAGC 62.056 63.158 11.40 11.40 44.11 5.25
912 945 0.107703 TAGCTGAATTCCACCGGCAG 60.108 55.000 0.00 0.00 37.14 4.85
954 1002 1.343506 CCCGGACGAAAAACTCTACG 58.656 55.000 0.73 0.00 0.00 3.51
1247 1323 3.991121 GTGAAGAAGAAGAAGAAGACGGG 59.009 47.826 0.00 0.00 0.00 5.28
1248 1324 4.621991 TGTGAAGAAGAAGAAGAAGACGG 58.378 43.478 0.00 0.00 0.00 4.79
1279 1364 0.104462 TAGGACATAGGGCAGGGCAT 60.104 55.000 0.00 0.00 0.00 4.40
1282 1367 0.765510 GGTTAGGACATAGGGCAGGG 59.234 60.000 0.00 0.00 0.00 4.45
1302 1394 5.277538 GCATATGCTAGCACTAAACTTCACC 60.278 44.000 22.07 0.00 38.21 4.02
1327 1423 2.901249 ACATCCACTATGCAACCGTAC 58.099 47.619 0.00 0.00 39.39 3.67
1399 1497 1.887242 GGCGGCTACATCATTCGCA 60.887 57.895 0.00 0.00 46.95 5.10
1400 1498 2.939022 GGCGGCTACATCATTCGC 59.061 61.111 0.00 0.00 44.80 4.70
1401 1499 2.943345 GCGGCGGCTACATCATTCG 61.943 63.158 9.78 0.00 35.83 3.34
1402 1500 1.887242 TGCGGCGGCTACATCATTC 60.887 57.895 17.76 0.00 40.82 2.67
1403 1501 2.180204 GTGCGGCGGCTACATCATT 61.180 57.895 17.76 0.00 40.82 2.57
1404 1502 2.588877 GTGCGGCGGCTACATCAT 60.589 61.111 17.76 0.00 40.82 2.45
1405 1503 4.075854 TGTGCGGCGGCTACATCA 62.076 61.111 17.76 6.25 40.82 3.07
1406 1504 3.564027 GTGTGCGGCGGCTACATC 61.564 66.667 17.76 10.31 40.82 3.06
1407 1505 4.386951 TGTGTGCGGCGGCTACAT 62.387 61.111 17.76 0.00 40.82 2.29
1410 1508 4.308458 AACTGTGTGCGGCGGCTA 62.308 61.111 17.76 3.80 40.82 3.93
1414 1512 4.312231 CACCAACTGTGTGCGGCG 62.312 66.667 0.51 0.51 40.26 6.46
1415 1513 0.953471 TATCACCAACTGTGTGCGGC 60.953 55.000 0.00 0.00 45.61 6.53
1416 1514 1.398041 CATATCACCAACTGTGTGCGG 59.602 52.381 0.00 0.00 45.61 5.69
1417 1515 2.076100 ACATATCACCAACTGTGTGCG 58.924 47.619 0.00 0.00 45.61 5.34
1418 1516 5.118990 AGATACATATCACCAACTGTGTGC 58.881 41.667 1.88 0.00 45.61 4.57
1419 1517 8.363390 AGATAGATACATATCACCAACTGTGTG 58.637 37.037 1.88 0.00 45.61 3.82
1420 1518 8.484214 AGATAGATACATATCACCAACTGTGT 57.516 34.615 1.88 0.00 45.61 3.72
1463 1561 4.829492 ACAGCTAAATGGAAGAGCAAGTTT 59.171 37.500 0.00 0.00 38.73 2.66
1487 1585 5.869344 AGTTTGCAAAGGTTGAAGTTCTTTC 59.131 36.000 13.26 0.00 36.29 2.62
1502 1600 2.028130 ACGTTGATCCCAGTTTGCAAA 58.972 42.857 8.05 8.05 0.00 3.68
1566 1664 8.723311 ACCGATAAAAAGTGATCAAAACGATTA 58.277 29.630 0.00 0.00 33.17 1.75
1575 1673 5.457140 GCACAAACCGATAAAAAGTGATCA 58.543 37.500 0.00 0.00 0.00 2.92
1656 1754 6.294363 GCACGACTAAACACAACTTGTATAC 58.706 40.000 0.00 0.00 37.51 1.47
1683 1781 3.401182 TGAAACCGTACGTAAAGCCATT 58.599 40.909 15.21 0.00 0.00 3.16
1686 1784 3.425227 CCAATGAAACCGTACGTAAAGCC 60.425 47.826 15.21 0.00 0.00 4.35
1738 1836 9.129532 GGGATCATCTCATCAGTTTTCTTAATT 57.870 33.333 0.00 0.00 0.00 1.40
1739 1837 8.277197 TGGGATCATCTCATCAGTTTTCTTAAT 58.723 33.333 0.00 0.00 0.00 1.40
1748 1846 4.720773 ACTTCTTGGGATCATCTCATCAGT 59.279 41.667 0.00 0.00 0.00 3.41
1750 1848 5.901853 AGTACTTCTTGGGATCATCTCATCA 59.098 40.000 0.00 0.00 0.00 3.07
1860 1958 2.726821 TGATGGAAAGCAGGATTGGTC 58.273 47.619 0.00 0.00 32.95 4.02
1861 1959 2.905415 TGATGGAAAGCAGGATTGGT 57.095 45.000 0.00 0.00 36.38 3.67
1871 1978 8.139989 GGAAAGTCAAATATGGATGATGGAAAG 58.860 37.037 0.00 0.00 0.00 2.62
1945 2052 7.744087 TTGTCTAAGCTGCTTCTATTTTCAA 57.256 32.000 19.62 12.11 0.00 2.69
1969 2076 5.131142 GGGTATAGAGCATATAATGGTGGCT 59.869 44.000 0.00 0.00 41.77 4.75
1993 2100 0.395724 GTGTTGGGATGCCCTTAGGG 60.396 60.000 14.11 14.11 45.70 3.53
2087 2194 3.030415 AAAAACCTGCGGACGGATT 57.970 47.368 0.00 0.00 0.00 3.01
2114 2221 1.377202 GCCCTCTGATTTGCGTCCA 60.377 57.895 0.00 0.00 0.00 4.02
2167 2274 2.522367 GGTTGGGTCTTGGGGACGA 61.522 63.158 0.00 0.00 45.35 4.20


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

AutoCloner maintained by Alex Coulton.