Multiple sequence alignment - TraesCS1A01G254400

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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 TraesCS1A01G254400 chr1A 100.000 4431 0 0 1 4431 445914042 445918472 0.000000e+00 8183
1 TraesCS1A01G254400 chr1A 83.668 698 86 13 3760 4431 445934595 445935290 2.250000e-177 632
2 TraesCS1A01G254400 chr1D 94.722 2406 84 17 1316 3700 345712919 345715302 0.000000e+00 3699
3 TraesCS1A01G254400 chr1D 95.179 726 32 2 3708 4431 345715356 345716080 0.000000e+00 1144
4 TraesCS1A01G254400 chr1D 86.172 687 78 13 3760 4431 345721399 345722083 0.000000e+00 726
5 TraesCS1A01G254400 chr1D 97.531 324 8 0 998 1321 345712570 345712893 5.010000e-154 555
6 TraesCS1A01G254400 chr1D 88.517 418 17 21 574 965 345711871 345712283 1.120000e-130 477
7 TraesCS1A01G254400 chr1D 75.518 531 127 3 19 547 416786451 416786980 1.580000e-64 257
8 TraesCS1A01G254400 chr1B 94.121 1837 78 15 1446 3280 464483554 464481746 0.000000e+00 2767
9 TraesCS1A01G254400 chr1B 94.613 724 36 1 3708 4431 464481144 464480424 0.000000e+00 1118
10 TraesCS1A01G254400 chr1B 87.011 793 50 26 574 1320 464484472 464483687 0.000000e+00 845
11 TraesCS1A01G254400 chr1B 98.383 433 7 0 3277 3709 464481624 464481192 0.000000e+00 761
12 TraesCS1A01G254400 chr1B 86.831 691 71 9 3760 4431 464151131 464150442 0.000000e+00 754
13 TraesCS1A01G254400 chr4A 92.948 553 37 2 10 560 285949585 285949033 0.000000e+00 804
14 TraesCS1A01G254400 chr4A 91.084 572 38 5 7 576 2781838 2781278 0.000000e+00 761
15 TraesCS1A01G254400 chr3D 92.922 551 38 1 10 559 127220749 127220199 0.000000e+00 800
16 TraesCS1A01G254400 chr2B 91.972 436 32 3 139 574 65437321 65436889 3.790000e-170 608
17 TraesCS1A01G254400 chr6B 89.568 278 29 0 1008 1285 223657721 223657444 1.960000e-93 353
18 TraesCS1A01G254400 chr6B 77.281 537 113 9 41 574 563087392 563086862 1.550000e-79 307
19 TraesCS1A01G254400 chr5B 78.378 481 91 13 101 576 73389784 73389312 2.590000e-77 300
20 TraesCS1A01G254400 chr5B 76.000 525 124 2 19 541 655075216 655074692 2.030000e-68 270
21 TraesCS1A01G254400 chr7A 76.376 436 96 6 115 547 40429099 40428668 1.240000e-55 228
22 TraesCS1A01G254400 chr5A 95.161 62 3 0 10 71 69221760 69221821 1.010000e-16 99


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 TraesCS1A01G254400 chr1A 445914042 445918472 4430 False 8183.00 8183 100.00000 1 4431 1 chr1A.!!$F1 4430
1 TraesCS1A01G254400 chr1A 445934595 445935290 695 False 632.00 632 83.66800 3760 4431 1 chr1A.!!$F2 671
2 TraesCS1A01G254400 chr1D 345711871 345716080 4209 False 1468.75 3699 93.98725 574 4431 4 chr1D.!!$F3 3857
3 TraesCS1A01G254400 chr1D 345721399 345722083 684 False 726.00 726 86.17200 3760 4431 1 chr1D.!!$F1 671
4 TraesCS1A01G254400 chr1D 416786451 416786980 529 False 257.00 257 75.51800 19 547 1 chr1D.!!$F2 528
5 TraesCS1A01G254400 chr1B 464480424 464484472 4048 True 1372.75 2767 93.53200 574 4431 4 chr1B.!!$R2 3857
6 TraesCS1A01G254400 chr1B 464150442 464151131 689 True 754.00 754 86.83100 3760 4431 1 chr1B.!!$R1 671
7 TraesCS1A01G254400 chr4A 285949033 285949585 552 True 804.00 804 92.94800 10 560 1 chr4A.!!$R2 550
8 TraesCS1A01G254400 chr4A 2781278 2781838 560 True 761.00 761 91.08400 7 576 1 chr4A.!!$R1 569
9 TraesCS1A01G254400 chr3D 127220199 127220749 550 True 800.00 800 92.92200 10 559 1 chr3D.!!$R1 549
10 TraesCS1A01G254400 chr6B 563086862 563087392 530 True 307.00 307 77.28100 41 574 1 chr6B.!!$R2 533
11 TraesCS1A01G254400 chr5B 655074692 655075216 524 True 270.00 270 76.00000 19 541 1 chr5B.!!$R2 522

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
977 1029 0.039911 AGACAGAGTTAGGCGGAGGT 59.960 55.0 0.0 0.0 0.00 3.85 F
1544 1908 0.034337 TGTCGCCAAGGTAACAGGAC 59.966 55.0 0.0 0.0 36.21 3.85 F
1609 1974 1.427809 TGCCTGTCTGCTATATGCCT 58.572 50.0 0.0 0.0 42.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1887 2256 0.321298 GCGTAACCAAGCAGGAGGAA 60.321 55.000 1.83 0.0 41.22 3.36 R
2349 2724 1.183030 AGTGGCTAGTGCGTGTACCA 61.183 55.000 0.00 0.0 40.82 3.25 R
3453 3954 1.423541 TGGCTCACAGTTAACCATGGT 59.576 47.619 13.00 13.0 0.00 3.55 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
195 201 2.039746 TGTTGGAGTGACGGATCCATTT 59.960 45.455 13.41 0.00 44.87 2.32
219 225 1.837051 TGAGACCTTGGCACTCCGT 60.837 57.895 10.31 0.00 34.14 4.69
341 347 2.489938 TCTGTGATGGCACCTTTACC 57.510 50.000 0.00 0.00 44.51 2.85
378 384 8.462016 GGAGAGCTTGCTTTATCTTTTGATTTA 58.538 33.333 0.00 0.00 40.19 1.40
408 414 2.899900 TCAATATGTATCCAGAGCGGCT 59.100 45.455 0.00 0.00 33.14 5.52
449 463 2.889578 CAAAACATGCTTGCACGCT 58.110 47.368 16.80 0.00 0.00 5.07
464 478 1.215382 CGCTGATGGTCACCGAGAA 59.785 57.895 0.00 0.00 27.45 2.87
471 485 0.323629 TGGTCACCGAGAATTGGACC 59.676 55.000 0.00 0.00 45.05 4.46
490 504 1.455248 CGACTCGAGACCTTCCTTCT 58.545 55.000 21.68 0.00 0.00 2.85
517 531 4.883585 TCACCAGTTTATTGGCTGATGATC 59.116 41.667 0.00 0.00 42.18 2.92
518 532 4.885907 CACCAGTTTATTGGCTGATGATCT 59.114 41.667 0.00 0.00 42.18 2.75
522 536 6.994496 CCAGTTTATTGGCTGATGATCTAAGA 59.006 38.462 0.00 0.00 34.87 2.10
560 574 1.986882 AAGCTCCCAGGTTTGAACAG 58.013 50.000 0.00 0.00 30.79 3.16
562 576 1.202818 AGCTCCCAGGTTTGAACAGAC 60.203 52.381 0.00 0.00 0.00 3.51
563 577 1.476833 GCTCCCAGGTTTGAACAGACA 60.477 52.381 0.00 0.00 0.00 3.41
564 578 2.222027 CTCCCAGGTTTGAACAGACAC 58.778 52.381 0.00 0.00 0.00 3.67
565 579 1.562008 TCCCAGGTTTGAACAGACACA 59.438 47.619 0.00 0.00 0.00 3.72
566 580 1.676006 CCCAGGTTTGAACAGACACAC 59.324 52.381 0.00 0.00 0.00 3.82
624 644 3.195661 CCGTCCAGATTAAAGTACAGCC 58.804 50.000 0.00 0.00 0.00 4.85
628 648 3.589735 TCCAGATTAAAGTACAGCCCCAA 59.410 43.478 0.00 0.00 0.00 4.12
716 736 1.301479 CGGCGAGCCTTATTACCCC 60.301 63.158 12.70 0.00 0.00 4.95
758 790 4.488136 CCGCCCTGGCTGCACATA 62.488 66.667 6.60 0.00 39.32 2.29
759 791 3.204827 CGCCCTGGCTGCACATAC 61.205 66.667 6.60 0.00 39.32 2.39
760 792 2.045045 GCCCTGGCTGCACATACA 60.045 61.111 0.50 0.00 38.26 2.29
761 793 1.454479 GCCCTGGCTGCACATACAT 60.454 57.895 0.50 0.00 38.26 2.29
770 803 0.389166 TGCACATACATCACGCACGA 60.389 50.000 0.00 0.00 0.00 4.35
772 805 1.908065 CACATACATCACGCACGAGA 58.092 50.000 0.00 0.00 0.00 4.04
882 932 2.441532 TCCCGTCCCGTGATCCTC 60.442 66.667 0.00 0.00 0.00 3.71
909 959 4.179599 GGCTAGCCTCCCTCCCCT 62.180 72.222 27.17 0.00 0.00 4.79
925 977 4.403734 CTCCCCTCTCCTAGATAACACTC 58.596 52.174 0.00 0.00 0.00 3.51
959 1011 4.856607 GGCGAGGCGACGAGGAAG 62.857 72.222 0.00 0.00 35.09 3.46
965 1017 1.137825 GGCGACGAGGAAGACAGAG 59.862 63.158 0.00 0.00 0.00 3.35
966 1018 1.587933 GGCGACGAGGAAGACAGAGT 61.588 60.000 0.00 0.00 0.00 3.24
967 1019 0.241481 GCGACGAGGAAGACAGAGTT 59.759 55.000 0.00 0.00 0.00 3.01
971 1023 1.819903 ACGAGGAAGACAGAGTTAGGC 59.180 52.381 0.00 0.00 0.00 3.93
972 1024 1.202200 CGAGGAAGACAGAGTTAGGCG 60.202 57.143 0.00 0.00 0.00 5.52
975 1027 1.135333 GGAAGACAGAGTTAGGCGGAG 59.865 57.143 0.00 0.00 0.00 4.63
976 1028 1.135333 GAAGACAGAGTTAGGCGGAGG 59.865 57.143 0.00 0.00 0.00 4.30
977 1029 0.039911 AGACAGAGTTAGGCGGAGGT 59.960 55.000 0.00 0.00 0.00 3.85
978 1030 0.896226 GACAGAGTTAGGCGGAGGTT 59.104 55.000 0.00 0.00 0.00 3.50
979 1031 0.896226 ACAGAGTTAGGCGGAGGTTC 59.104 55.000 0.00 0.00 0.00 3.62
981 1033 1.141234 GAGTTAGGCGGAGGTTCGG 59.859 63.158 0.00 0.00 0.00 4.30
1011 1317 0.524392 GAGCAGTGATGTCGGACGAG 60.524 60.000 3.34 0.00 0.00 4.18
1302 1608 1.801765 GCCGAGGACGACAAGGTAATC 60.802 57.143 0.00 0.00 42.66 1.75
1352 1698 2.174349 CGGCTTTCGCTGACAAGC 59.826 61.111 12.31 12.31 45.62 4.01
1432 1787 0.167470 CAGTGCTCCAGTGCGAATTG 59.833 55.000 0.00 0.00 35.36 2.32
1539 1903 2.271800 CAGAGATGTCGCCAAGGTAAC 58.728 52.381 0.00 0.00 0.00 2.50
1540 1904 1.899814 AGAGATGTCGCCAAGGTAACA 59.100 47.619 0.00 0.00 41.41 2.41
1541 1905 2.093973 AGAGATGTCGCCAAGGTAACAG 60.094 50.000 2.96 0.00 41.41 3.16
1542 1906 1.066143 AGATGTCGCCAAGGTAACAGG 60.066 52.381 2.96 0.00 41.41 4.00
1543 1907 0.981183 ATGTCGCCAAGGTAACAGGA 59.019 50.000 0.00 0.00 36.21 3.86
1544 1908 0.034337 TGTCGCCAAGGTAACAGGAC 59.966 55.000 0.00 0.00 36.21 3.85
1588 1953 8.362860 TGCATTTTTGAATCAAAATTCGAGAA 57.637 26.923 20.15 5.72 43.61 2.87
1593 1958 6.949578 TTGAATCAAAATTCGAGAAATGCC 57.050 33.333 0.00 0.00 43.61 4.40
1599 1964 4.691860 AAATTCGAGAAATGCCTGTCTG 57.308 40.909 0.00 0.00 0.00 3.51
1606 1971 4.388165 CGAGAAATGCCTGTCTGCTATATG 59.612 45.833 0.00 0.00 0.00 1.78
1607 1972 4.070716 AGAAATGCCTGTCTGCTATATGC 58.929 43.478 0.00 0.00 43.25 3.14
1608 1973 2.486472 ATGCCTGTCTGCTATATGCC 57.514 50.000 0.00 0.00 42.00 4.40
1609 1974 1.427809 TGCCTGTCTGCTATATGCCT 58.572 50.000 0.00 0.00 42.00 4.75
1610 1975 2.608623 TGCCTGTCTGCTATATGCCTA 58.391 47.619 0.00 0.00 42.00 3.93
1611 1976 3.176411 TGCCTGTCTGCTATATGCCTAT 58.824 45.455 0.00 0.00 42.00 2.57
1612 1977 4.352893 TGCCTGTCTGCTATATGCCTATA 58.647 43.478 0.00 0.00 42.00 1.31
1613 1978 4.964897 TGCCTGTCTGCTATATGCCTATAT 59.035 41.667 0.00 0.00 42.00 0.86
1614 1979 6.136155 TGCCTGTCTGCTATATGCCTATATA 58.864 40.000 0.00 0.00 42.00 0.86
1615 1980 6.784473 TGCCTGTCTGCTATATGCCTATATAT 59.216 38.462 0.00 0.00 42.00 0.86
1692 2057 2.093869 TGTTAAGGTCACCTATGCCGAC 60.094 50.000 0.00 0.00 31.13 4.79
1733 2098 6.952938 TCATGGCCTGGATTGCAAATTATATA 59.047 34.615 1.71 0.00 0.00 0.86
1800 2169 8.986477 AATCAACTTGTTAGTATGAAAATGCC 57.014 30.769 0.00 0.00 33.17 4.40
1837 2206 3.851098 CTGTAGCCTGTACAGAGGTTTC 58.149 50.000 24.68 14.69 45.69 2.78
1887 2256 2.529151 CGTGCTTTGCTTTCTGTTTGT 58.471 42.857 0.00 0.00 0.00 2.83
1965 2334 4.639078 TCAGGAAGATGATGACAAACCA 57.361 40.909 0.00 0.00 0.00 3.67
2010 2385 7.624360 TGTTATAATGGTTTAGTTCCTGCAG 57.376 36.000 6.78 6.78 0.00 4.41
2011 2386 7.172342 TGTTATAATGGTTTAGTTCCTGCAGT 58.828 34.615 13.81 0.00 0.00 4.40
2148 2523 2.354821 CGAAACATCGAATTTCTCCCCC 59.645 50.000 18.19 0.00 34.50 5.40
2275 2650 8.661352 TTTATCAGATGACGATTCAGCATTTA 57.339 30.769 0.00 0.00 40.89 1.40
2286 2661 8.094798 ACGATTCAGCATTTACAACTTCTAAA 57.905 30.769 0.00 0.00 0.00 1.85
2349 2724 0.108207 GTAGCCATGCTGAGCCAGAT 59.892 55.000 0.23 0.00 40.10 2.90
2357 2732 0.807667 GCTGAGCCAGATGGTACACG 60.808 60.000 6.40 0.00 34.10 4.49
2446 2821 4.497291 AACACCCTTTTACACTCACAGA 57.503 40.909 0.00 0.00 0.00 3.41
2447 2822 4.497291 ACACCCTTTTACACTCACAGAA 57.503 40.909 0.00 0.00 0.00 3.02
2723 3098 9.989869 GTTATCTGTAAAATACTTGCTTCCTTC 57.010 33.333 0.00 0.00 0.00 3.46
2809 3185 7.341805 ACAGCTGTGATTCTTAAGGACATAAT 58.658 34.615 20.97 0.00 0.00 1.28
2953 3329 2.105477 AGCTCAACTCTGGAACACACAT 59.895 45.455 0.00 0.00 0.00 3.21
2967 3343 7.950512 TGGAACACACATTATTTCAATCTGTT 58.049 30.769 0.00 0.00 0.00 3.16
3078 3454 5.752955 TGTACAAGCTTTTGAATGCTTTTCC 59.247 36.000 12.48 1.63 44.07 3.13
3152 3528 1.754226 CTCTACTGCCCTCTTGACCTC 59.246 57.143 0.00 0.00 0.00 3.85
3802 4354 1.228552 TCCAGGTGGAGCTTTTGGC 60.229 57.895 0.00 0.00 39.78 4.52
3821 4375 6.773976 TTGGCAGTAATCTTTATTCCCTTG 57.226 37.500 0.00 0.00 0.00 3.61
3873 4427 1.225373 AGGCCCTGAATTATCTGGCA 58.775 50.000 0.00 0.00 42.47 4.92
4088 4642 1.448985 TTCGCTTGGGCATTACTGTC 58.551 50.000 0.00 0.00 38.60 3.51
4292 4868 6.985059 CACATGATGATAGAGCTTCTCTTTGA 59.015 38.462 0.00 0.00 41.50 2.69
4315 4891 4.584874 TCCGAAGTTCCTTCAATAATGCA 58.415 39.130 0.00 0.00 40.17 3.96
4342 4918 2.726760 CTCTCGGACAAACTTTGACTCG 59.273 50.000 8.55 8.10 0.00 4.18
4410 4986 2.050985 AGCTTTTCGTTGCGCTGC 60.051 55.556 9.73 0.00 0.00 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.377690 TGGGCCTGTGGGATTTCTAA 58.622 50.000 4.53 0.00 33.58 2.10
1 2 1.215173 CATGGGCCTGTGGGATTTCTA 59.785 52.381 4.53 0.00 33.58 2.10
2 3 0.032813 CATGGGCCTGTGGGATTTCT 60.033 55.000 4.53 0.00 33.58 2.52
3 4 1.679559 GCATGGGCCTGTGGGATTTC 61.680 60.000 4.53 0.00 33.58 2.17
4 5 1.686800 GCATGGGCCTGTGGGATTT 60.687 57.895 4.53 0.00 33.58 2.17
5 6 2.042639 GCATGGGCCTGTGGGATT 60.043 61.111 4.53 0.00 33.58 3.01
17 18 1.270518 CCTGGGAGTATCGAAGCATGG 60.271 57.143 0.00 0.00 34.37 3.66
195 201 1.985159 AGTGCCAAGGTCTCACCAATA 59.015 47.619 0.00 0.00 41.95 1.90
297 303 5.461032 AACTATTGTGGCGATTTTTCCAA 57.539 34.783 0.00 0.00 33.57 3.53
341 347 3.195396 AGCAAGCTCTCCAACTTCTAGAG 59.805 47.826 0.00 0.00 39.81 2.43
442 456 2.358615 GGTGACCATCAGCGTGCA 60.359 61.111 0.00 0.00 35.04 4.57
447 461 1.667724 CAATTCTCGGTGACCATCAGC 59.332 52.381 1.11 0.00 41.16 4.26
448 462 2.093500 TCCAATTCTCGGTGACCATCAG 60.093 50.000 1.11 0.00 0.00 2.90
449 463 1.905894 TCCAATTCTCGGTGACCATCA 59.094 47.619 1.11 0.00 0.00 3.07
464 478 0.323542 AGGTCTCGAGTCGGTCCAAT 60.324 55.000 13.54 0.00 0.00 3.16
471 485 1.455248 AGAAGGAAGGTCTCGAGTCG 58.545 55.000 13.13 6.09 0.00 4.18
490 504 2.557924 CAGCCAATAAACTGGTGAGCAA 59.442 45.455 0.00 0.00 38.86 3.91
518 532 9.659830 GCTTTTATTCAACGAAAGAACTTCTTA 57.340 29.630 4.41 0.00 35.27 2.10
522 536 7.139392 GGAGCTTTTATTCAACGAAAGAACTT 58.861 34.615 0.00 0.00 33.35 2.66
617 637 1.750778 CATGGATTGTTGGGGCTGTAC 59.249 52.381 0.00 0.00 0.00 2.90
624 644 1.512230 CGGTGCATGGATTGTTGGG 59.488 57.895 0.00 0.00 0.00 4.12
628 648 3.133464 CGCCGGTGCATGGATTGT 61.133 61.111 11.80 0.00 37.32 2.71
758 790 1.154207 CTCGTCTCGTGCGTGATGT 60.154 57.895 13.22 0.00 0.00 3.06
759 791 0.859374 CTCTCGTCTCGTGCGTGATG 60.859 60.000 8.90 8.90 32.67 3.07
760 792 1.425825 CTCTCGTCTCGTGCGTGAT 59.574 57.895 0.00 0.00 32.67 3.06
761 793 2.861006 CTCTCGTCTCGTGCGTGA 59.139 61.111 0.00 0.00 0.00 4.35
770 803 2.820479 CCCTCGTCGCTCTCGTCT 60.820 66.667 0.00 0.00 36.96 4.18
772 805 2.820479 CTCCCTCGTCGCTCTCGT 60.820 66.667 0.00 0.00 36.96 4.18
833 883 2.920076 TTTCTGTGGTGGTGGTGGCC 62.920 60.000 0.00 0.00 0.00 5.36
907 957 3.892588 GTGGGAGTGTTATCTAGGAGAGG 59.107 52.174 0.00 0.00 0.00 3.69
909 959 3.271225 TGGTGGGAGTGTTATCTAGGAGA 59.729 47.826 0.00 0.00 0.00 3.71
942 994 4.856607 CTTCCTCGTCGCCTCGCC 62.857 72.222 0.00 0.00 0.00 5.54
943 995 3.812019 TCTTCCTCGTCGCCTCGC 61.812 66.667 0.00 0.00 0.00 5.03
948 1000 0.241481 AACTCTGTCTTCCTCGTCGC 59.759 55.000 0.00 0.00 0.00 5.19
949 1001 2.096174 CCTAACTCTGTCTTCCTCGTCG 59.904 54.545 0.00 0.00 0.00 5.12
959 1011 0.896226 AACCTCCGCCTAACTCTGTC 59.104 55.000 0.00 0.00 0.00 3.51
965 1017 2.510918 GCCGAACCTCCGCCTAAC 60.511 66.667 0.00 0.00 0.00 2.34
966 1018 2.998480 TGCCGAACCTCCGCCTAA 60.998 61.111 0.00 0.00 0.00 2.69
967 1019 3.458163 CTGCCGAACCTCCGCCTA 61.458 66.667 0.00 0.00 0.00 3.93
976 1028 4.373116 TCCTCCGTGCTGCCGAAC 62.373 66.667 11.24 0.00 0.00 3.95
977 1029 4.069232 CTCCTCCGTGCTGCCGAA 62.069 66.667 11.24 0.00 0.00 4.30
981 1033 4.385405 ACTGCTCCTCCGTGCTGC 62.385 66.667 0.00 0.00 32.50 5.25
982 1034 2.236223 ATCACTGCTCCTCCGTGCTG 62.236 60.000 0.00 0.00 34.65 4.41
983 1035 1.986757 ATCACTGCTCCTCCGTGCT 60.987 57.895 0.00 0.00 0.00 4.40
984 1036 1.812922 CATCACTGCTCCTCCGTGC 60.813 63.158 0.00 0.00 0.00 5.34
996 1061 2.052690 CCCCTCGTCCGACATCACT 61.053 63.158 0.00 0.00 0.00 3.41
1302 1608 4.368808 CGCCGCGGACAAACTGTG 62.369 66.667 33.48 0.68 35.38 3.66
1352 1698 1.856539 ATGGCCTGGACCACTTGAGG 61.857 60.000 3.32 0.00 44.17 3.86
1353 1699 0.393537 GATGGCCTGGACCACTTGAG 60.394 60.000 3.32 0.00 44.17 3.02
1432 1787 8.749499 CAAAAGACAGAGAAACATCATTTTGTC 58.251 33.333 0.00 0.00 32.96 3.18
1599 1964 9.987272 TGTGTCATTGATATATAGGCATATAGC 57.013 33.333 4.23 0.00 44.65 2.97
1606 1971 9.929180 TTAAGACTGTGTCATTGATATATAGGC 57.071 33.333 0.46 0.00 34.60 3.93
1655 2020 9.630098 TGACCTTAACAAGTAGAAAATACTACG 57.370 33.333 0.00 0.00 44.91 3.51
1659 2024 8.843885 AGGTGACCTTAACAAGTAGAAAATAC 57.156 34.615 0.00 0.00 0.00 1.89
1664 2029 6.403878 GCATAGGTGACCTTAACAAGTAGAA 58.596 40.000 10.53 0.00 34.61 2.10
1666 2031 5.116882 GGCATAGGTGACCTTAACAAGTAG 58.883 45.833 10.53 0.00 34.61 2.57
1667 2032 4.382254 CGGCATAGGTGACCTTAACAAGTA 60.382 45.833 10.53 0.00 34.61 2.24
1675 2040 0.537188 CAGTCGGCATAGGTGACCTT 59.463 55.000 10.53 0.00 34.61 3.50
1692 2057 3.770666 CCATGAGTAACGACTACACCAG 58.229 50.000 0.00 0.00 35.45 4.00
1784 2153 7.593825 AGAACTTGTGGCATTTTCATACTAAC 58.406 34.615 0.00 0.00 0.00 2.34
1800 2169 2.540265 ACAGCAGGAGAGAACTTGTG 57.460 50.000 0.00 0.00 0.00 3.33
1837 2206 8.244802 TCTTTAGACTCTGAAATCGTAAAGAGG 58.755 37.037 3.80 0.00 40.41 3.69
1887 2256 0.321298 GCGTAACCAAGCAGGAGGAA 60.321 55.000 1.83 0.00 41.22 3.36
1965 2334 7.645058 AACATATAAATGCAGGCAACTTACT 57.355 32.000 0.00 0.00 39.79 2.24
2010 2385 1.661341 CAGAGTCATTGCTGGGCTAC 58.339 55.000 0.00 0.00 0.00 3.58
2011 2386 0.543277 CCAGAGTCATTGCTGGGCTA 59.457 55.000 0.00 0.00 46.24 3.93
2275 2650 7.807977 ACAACTGTGATGATTTAGAAGTTGT 57.192 32.000 11.39 11.39 46.82 3.32
2349 2724 1.183030 AGTGGCTAGTGCGTGTACCA 61.183 55.000 0.00 0.00 40.82 3.25
2357 2732 2.072298 CAACTGAGAAGTGGCTAGTGC 58.928 52.381 0.00 0.00 38.76 4.40
2364 2739 2.614057 GTGTGAACCAACTGAGAAGTGG 59.386 50.000 0.00 0.00 0.00 4.00
2937 3313 7.581213 TTGAAATAATGTGTGTTCCAGAGTT 57.419 32.000 0.00 0.00 0.00 3.01
2953 3329 9.693739 TTCCTGCCTAATAACAGATTGAAATAA 57.306 29.630 0.00 0.00 35.90 1.40
2967 3343 6.327781 TGGTATATCCACTTCCTGCCTAATA 58.672 40.000 0.00 0.00 41.93 0.98
3078 3454 7.901377 CCATAAACATTTTACGTACTCCGAAAG 59.099 37.037 0.00 0.00 40.70 2.62
3152 3528 5.616866 CGGTTTCTGCATGGTTGTTAAGTAG 60.617 44.000 0.00 0.00 0.00 2.57
3295 3796 7.829211 AGCTTTAGTGAGCACCAGAAAAATATA 59.171 33.333 0.00 0.00 45.12 0.86
3453 3954 1.423541 TGGCTCACAGTTAACCATGGT 59.576 47.619 13.00 13.00 0.00 3.55
3579 4080 5.821204 ACTTTACATTGACTGCAACAAGAC 58.179 37.500 10.81 0.00 36.72 3.01
3802 4354 7.770897 ACTGCTACAAGGGAATAAAGATTACTG 59.229 37.037 0.00 0.00 0.00 2.74
3873 4427 0.543646 AAGGCAATTTGGAGCAGGCT 60.544 50.000 0.00 0.00 36.60 4.58
4088 4642 4.128925 TCAAGGATCTGACCTGAAATCG 57.871 45.455 0.00 0.00 40.49 3.34
4315 4891 6.766467 AGTCAAAGTTTGTCCGAGAGTTATTT 59.234 34.615 15.08 0.00 0.00 1.40
4342 4918 1.115326 AGCAAACCCAGCAAACTCCC 61.115 55.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.