Multiple sequence alignment - TraesCS2A01G515000

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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 TraesCS2A01G515000 chr2A 100.000 6521 0 0 1 6521 739429005 739435525 0.000000e+00 12043.0
1 TraesCS2A01G515000 chr2A 90.096 1878 116 27 3703 5550 739447906 739449743 0.000000e+00 2374.0
2 TraesCS2A01G515000 chr2A 91.601 1262 66 18 1973 3211 739446063 739447307 0.000000e+00 1707.0
3 TraesCS2A01G515000 chr2A 92.659 504 24 3 3201 3697 739447487 739447984 0.000000e+00 713.0
4 TraesCS2A01G515000 chr2A 87.684 544 45 15 5997 6518 739449615 739450158 1.200000e-171 614.0
5 TraesCS2A01G515000 chr2A 85.115 477 40 12 1448 1920 739445595 739446044 5.960000e-125 459.0
6 TraesCS2A01G515000 chr2A 84.697 379 33 15 1060 1420 739445236 739445607 8.040000e-94 355.0
7 TraesCS2A01G515000 chr2A 89.726 146 11 3 3871 4014 739447925 739448068 4.020000e-42 183.0
8 TraesCS2A01G515000 chr2A 90.698 129 11 1 5997 6125 739434427 739434554 3.130000e-38 171.0
9 TraesCS2A01G515000 chr2A 90.698 129 11 1 5423 5550 739435001 739435129 3.130000e-38 171.0
10 TraesCS2A01G515000 chr2D 92.648 5223 241 49 1 5142 607932276 607937436 0.000000e+00 7385.0
11 TraesCS2A01G515000 chr2D 93.366 3919 158 30 2220 6077 607955126 607959003 0.000000e+00 5703.0
12 TraesCS2A01G515000 chr2D 97.055 1392 26 5 5142 6521 607937679 607939067 0.000000e+00 2329.0
13 TraesCS2A01G515000 chr2D 82.773 476 49 19 6072 6521 607960275 607960743 1.700000e-105 394.0
14 TraesCS2A01G515000 chr2D 94.093 237 10 3 5584 5817 607969702 607969937 2.240000e-94 357.0
15 TraesCS2A01G515000 chr2D 84.551 356 38 9 5908 6261 607969956 607970296 2.910000e-88 337.0
16 TraesCS2A01G515000 chr2D 91.473 129 10 1 5997 6125 607937960 607938087 6.720000e-40 176.0
17 TraesCS2A01G515000 chr2D 87.179 156 16 4 5997 6150 607958345 607958498 2.420000e-39 174.0
18 TraesCS2A01G515000 chr2D 90.698 129 11 1 5423 5550 607938544 607938672 3.130000e-38 171.0
19 TraesCS2A01G515000 chr2D 98.913 92 1 0 2127 2218 607952568 607952659 1.450000e-36 165.0
20 TraesCS2A01G515000 chr2B 91.489 3572 196 30 1 3524 741013297 741016808 0.000000e+00 4813.0
21 TraesCS2A01G515000 chr2B 92.501 2267 114 20 3945 6176 741016804 741019049 0.000000e+00 3193.0
22 TraesCS2A01G515000 chr2B 90.996 1888 93 22 1795 3663 741123413 741125242 0.000000e+00 2473.0
23 TraesCS2A01G515000 chr2B 90.969 1218 70 18 5340 6521 741114356 741115569 0.000000e+00 1604.0
24 TraesCS2A01G515000 chr2B 96.110 437 14 1 4097 4533 741085317 741085750 0.000000e+00 710.0
25 TraesCS2A01G515000 chr2B 96.680 241 8 0 4538 4778 741085992 741086232 1.020000e-107 401.0
26 TraesCS2A01G515000 chr2B 82.438 484 59 11 5574 6055 741136717 741137176 3.660000e-107 399.0
27 TraesCS2A01G515000 chr2B 91.429 280 13 3 5018 5296 741112841 741113110 2.220000e-99 374.0
28 TraesCS2A01G515000 chr2B 94.397 232 13 0 6290 6521 741019562 741019793 2.240000e-94 357.0
29 TraesCS2A01G515000 chr2B 94.811 212 9 2 5377 5588 741136491 741136700 4.870000e-86 329.0
30 TraesCS2A01G515000 chr2B 92.544 228 17 0 6294 6521 741137349 741137576 1.750000e-85 327.0
31 TraesCS2A01G515000 chr2B 83.158 380 30 20 6132 6484 741150110 741150482 3.790000e-82 316.0
32 TraesCS2A01G515000 chr2B 93.878 196 11 1 3688 3882 741125385 741125580 1.780000e-75 294.0
33 TraesCS2A01G515000 chr2B 86.667 150 17 3 6002 6150 741136541 741136688 5.230000e-36 163.0
34 TraesCS2A01G515000 chr2B 95.455 44 2 0 4958 5001 741121731 741121774 3.260000e-08 71.3
35 TraesCS2A01G515000 chr2B 92.000 50 4 0 6472 6521 741151721 741151770 3.260000e-08 71.3
36 TraesCS2A01G515000 chr1B 79.048 525 73 18 4362 4882 487776386 487776877 6.310000e-85 326.0
37 TraesCS2A01G515000 chr5D 82.036 334 50 9 5209 5541 37189766 37190090 6.440000e-70 276.0
38 TraesCS2A01G515000 chr5A 85.772 246 23 6 4370 4612 26146527 26146763 3.900000e-62 250.0
39 TraesCS2A01G515000 chr7A 80.061 326 65 0 2 327 403166858 403166533 6.530000e-60 243.0


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 TraesCS2A01G515000 chr2A 739429005 739435525 6520 False 4128.333333 12043 93.798667 1 6521 3 chr2A.!!$F1 6520
1 TraesCS2A01G515000 chr2A 739445236 739450158 4922 False 915.000000 2374 88.796857 1060 6518 7 chr2A.!!$F2 5458
2 TraesCS2A01G515000 chr2D 607932276 607939067 6791 False 2515.250000 7385 92.968500 1 6521 4 chr2D.!!$F1 6520
3 TraesCS2A01G515000 chr2D 607952568 607960743 8175 False 1609.000000 5703 90.557750 2127 6521 4 chr2D.!!$F2 4394
4 TraesCS2A01G515000 chr2D 607969702 607970296 594 False 347.000000 357 89.322000 5584 6261 2 chr2D.!!$F3 677
5 TraesCS2A01G515000 chr2B 741013297 741019793 6496 False 2787.666667 4813 92.795667 1 6521 3 chr2B.!!$F1 6520
6 TraesCS2A01G515000 chr2B 741112841 741115569 2728 False 989.000000 1604 91.199000 5018 6521 2 chr2B.!!$F3 1503
7 TraesCS2A01G515000 chr2B 741121731 741125580 3849 False 946.100000 2473 93.443000 1795 5001 3 chr2B.!!$F4 3206
8 TraesCS2A01G515000 chr2B 741085317 741086232 915 False 555.500000 710 96.395000 4097 4778 2 chr2B.!!$F2 681
9 TraesCS2A01G515000 chr2B 741136491 741137576 1085 False 304.500000 399 89.115000 5377 6521 4 chr2B.!!$F5 1144

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
986 1035 0.031585 CTGACACGACCGAAACTCCA 59.968 55.000 0.00 0.0 0.00 3.86 F
2879 5450 0.388907 GCAATGCCGAATGTGCAGTT 60.389 50.000 0.00 0.0 42.92 3.16 F
3443 6204 1.202806 TGCCAGACCTCTGAAAACCTG 60.203 52.381 3.73 0.0 46.59 4.00 F
4301 7210 2.124507 ATCCCGGGGACAACTGTGTG 62.125 60.000 23.50 0.0 38.41 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2922 5493 0.450983 GAGTAGGTTCCGAGTGTCCG 59.549 60.000 0.00 0.00 0.00 4.79 R
4301 7210 1.061711 GAGTCATCGTGCATGCAGTTC 59.938 52.381 23.41 8.85 31.70 3.01 R
4823 7974 1.466950 CGGAAAAGGCAGCGTGATTTA 59.533 47.619 0.00 0.00 0.00 1.40 R
5801 10483 1.393603 ATGCTCGAGCTGTAGTGCTA 58.606 50.000 35.27 14.55 44.17 3.49 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
90 91 4.134563 ACTTGTCTGACTTAAACCGCAAT 58.865 39.130 9.51 0.00 0.00 3.56
111 112 9.079833 CGCAATGAAATATTGACATCTTTCTTT 57.920 29.630 3.97 0.00 30.34 2.52
177 178 6.477033 CGACTTCTTTACGATCCATCTTCAAT 59.523 38.462 0.00 0.00 0.00 2.57
197 198 6.286758 TCAATCTCCTCATCAAGCAATCTAC 58.713 40.000 0.00 0.00 0.00 2.59
199 200 4.033009 TCTCCTCATCAAGCAATCTACCA 58.967 43.478 0.00 0.00 0.00 3.25
214 215 4.689612 TCTACCAGATAACCATCCAAGC 57.310 45.455 0.00 0.00 0.00 4.01
217 218 2.769663 ACCAGATAACCATCCAAGCGTA 59.230 45.455 0.00 0.00 0.00 4.42
260 261 8.193953 ACATCAGGTTTCCTTTGACATTTAAT 57.806 30.769 0.00 0.00 0.00 1.40
309 310 4.977739 TCCTGGAGGAGACCATGATAATTT 59.022 41.667 0.00 0.00 39.78 1.82
383 384 8.331022 CCTCGTTGAAATCATAAACTCATACAG 58.669 37.037 0.00 0.00 0.00 2.74
439 440 3.821600 GAGAGACGCATCTACTATGGGAA 59.178 47.826 8.78 0.00 34.34 3.97
464 465 2.767505 GTCATGGAGACGACCAAAACT 58.232 47.619 0.00 0.00 43.47 2.66
467 468 3.071023 TCATGGAGACGACCAAAACTTCT 59.929 43.478 0.00 0.00 43.47 2.85
469 470 4.252971 TGGAGACGACCAAAACTTCTAG 57.747 45.455 0.00 0.00 36.96 2.43
470 471 3.640029 TGGAGACGACCAAAACTTCTAGT 59.360 43.478 0.00 0.00 36.96 2.57
566 610 1.545651 GCCAGCAAAACCCTAGTCACT 60.546 52.381 0.00 0.00 0.00 3.41
606 650 1.250328 TTGAGACCGAGCGGAGTTAA 58.750 50.000 16.83 2.48 38.96 2.01
612 656 1.202498 ACCGAGCGGAGTTAATTAGGC 60.202 52.381 16.83 0.00 38.96 3.93
616 660 3.553096 CGAGCGGAGTTAATTAGGCAGAT 60.553 47.826 0.00 0.00 0.00 2.90
618 662 5.539048 GAGCGGAGTTAATTAGGCAGATAA 58.461 41.667 0.00 0.00 0.00 1.75
620 664 5.992217 AGCGGAGTTAATTAGGCAGATAAAG 59.008 40.000 0.00 0.00 0.00 1.85
639 683 1.981495 AGATATTAGCCTGCCTCCCAC 59.019 52.381 0.00 0.00 0.00 4.61
643 687 1.485294 TTAGCCTGCCTCCCACGAAA 61.485 55.000 0.00 0.00 0.00 3.46
644 688 1.271840 TAGCCTGCCTCCCACGAAAT 61.272 55.000 0.00 0.00 0.00 2.17
645 689 2.115291 GCCTGCCTCCCACGAAATC 61.115 63.158 0.00 0.00 0.00 2.17
646 690 1.452108 CCTGCCTCCCACGAAATCC 60.452 63.158 0.00 0.00 0.00 3.01
647 691 1.299648 CTGCCTCCCACGAAATCCA 59.700 57.895 0.00 0.00 0.00 3.41
649 693 0.394216 TGCCTCCCACGAAATCCATG 60.394 55.000 0.00 0.00 0.00 3.66
650 694 0.107214 GCCTCCCACGAAATCCATGA 60.107 55.000 0.00 0.00 0.00 3.07
730 774 4.100808 GTCCGTCTCTCCCTACTACTTCTA 59.899 50.000 0.00 0.00 0.00 2.10
737 781 8.654094 GTCTCTCCCTACTACTTCTACTCTATT 58.346 40.741 0.00 0.00 0.00 1.73
784 829 1.337260 CGTTGGAGACTTGGAGTCCTG 60.337 57.143 11.33 5.98 46.18 3.86
816 861 1.448540 CCTCAATGGACGCGCTTCT 60.449 57.895 14.02 0.00 38.35 2.85
827 872 3.786048 GGACGCGCTTCTCATAAAAATTG 59.214 43.478 14.02 0.00 0.00 2.32
836 881 6.204495 GCTTCTCATAAAAATTGTGCCCAAAA 59.796 34.615 0.00 0.00 33.44 2.44
937 986 5.414765 ACAAATCGGATTAAGAAACCCAGAC 59.585 40.000 3.22 0.00 0.00 3.51
986 1035 0.031585 CTGACACGACCGAAACTCCA 59.968 55.000 0.00 0.00 0.00 3.86
1014 1063 2.607771 CCAAAACATGTTCAGCCTTCGG 60.608 50.000 12.39 3.38 0.00 4.30
1587 1655 5.972935 TCCAGACGCATTTAGAGTTGATTA 58.027 37.500 0.00 0.00 0.00 1.75
1622 1690 3.431912 GTCACATGACACTTTGTATGCGA 59.568 43.478 7.15 0.00 44.18 5.10
1625 1693 0.787787 TGACACTTTGTATGCGACGC 59.212 50.000 14.19 14.19 0.00 5.19
1637 1705 0.389025 TGCGACGCCATGATCATAGT 59.611 50.000 18.69 8.98 0.00 2.12
1718 1786 2.700897 CGATGGATTCTACCTGGACCTT 59.299 50.000 0.00 0.00 0.00 3.50
1759 1827 3.648067 TCCTCAGAGGTTGTGAGATTGTT 59.352 43.478 16.65 0.00 43.65 2.83
1821 1889 7.390823 TGGTTTATTGATCTTGTGCACTACTA 58.609 34.615 19.41 1.14 0.00 1.82
1856 1924 3.308438 AAATGTGCTTGCTGTTCCATC 57.692 42.857 0.00 0.00 0.00 3.51
2000 2068 4.455606 GTGAGCTCCTTTTAGGCATACAT 58.544 43.478 12.15 0.00 34.61 2.29
2002 2070 5.698545 GTGAGCTCCTTTTAGGCATACATAG 59.301 44.000 12.15 0.00 34.61 2.23
2023 2092 9.367444 ACATAGAAGCTAGTATTGTGTTAACAC 57.633 33.333 28.13 28.13 46.59 3.32
2038 2107 7.672240 TGTGTTAACACTGGATATGAACTACA 58.328 34.615 32.58 9.72 46.55 2.74
2070 2139 4.085357 ACTTCTGATTATGGCCGCATTA 57.915 40.909 0.00 0.00 0.00 1.90
2247 4784 6.790285 AGGCAAATCAATTTTCATGTTGTC 57.210 33.333 0.00 0.00 0.00 3.18
2248 4785 5.406175 AGGCAAATCAATTTTCATGTTGTCG 59.594 36.000 0.00 0.00 0.00 4.35
2253 4790 6.741992 ATCAATTTTCATGTTGTCGCTCTA 57.258 33.333 0.00 0.00 0.00 2.43
2289 4826 3.418047 TGGAGGCAACCTTTTAAGCTAC 58.582 45.455 0.00 0.00 31.76 3.58
2290 4827 3.073946 TGGAGGCAACCTTTTAAGCTACT 59.926 43.478 0.00 0.00 31.76 2.57
2291 4828 4.079970 GGAGGCAACCTTTTAAGCTACTT 58.920 43.478 0.00 0.00 31.76 2.24
2292 4829 4.082733 GGAGGCAACCTTTTAAGCTACTTG 60.083 45.833 0.00 0.00 31.76 3.16
2293 4830 3.826729 AGGCAACCTTTTAAGCTACTTGG 59.173 43.478 0.00 0.00 37.17 3.61
2294 4831 3.824443 GGCAACCTTTTAAGCTACTTGGA 59.176 43.478 0.00 0.00 0.00 3.53
2295 4832 4.321008 GGCAACCTTTTAAGCTACTTGGAC 60.321 45.833 0.00 0.00 0.00 4.02
2296 4833 4.519350 GCAACCTTTTAAGCTACTTGGACT 59.481 41.667 0.00 0.00 0.00 3.85
2297 4834 5.009710 GCAACCTTTTAAGCTACTTGGACTT 59.990 40.000 0.00 0.00 0.00 3.01
2298 4835 6.669278 CAACCTTTTAAGCTACTTGGACTTC 58.331 40.000 0.00 0.00 0.00 3.01
2299 4836 6.189036 ACCTTTTAAGCTACTTGGACTTCT 57.811 37.500 0.00 0.00 0.00 2.85
2300 4837 6.231951 ACCTTTTAAGCTACTTGGACTTCTC 58.768 40.000 0.00 0.00 0.00 2.87
2418 4967 2.525105 ACACCCACTTGTTTTCTGGT 57.475 45.000 0.00 0.00 0.00 4.00
2426 4975 5.449999 CCCACTTGTTTTCTGGTTACAGTTC 60.450 44.000 0.00 0.00 45.14 3.01
2439 4988 5.239087 TGGTTACAGTTCGGAAACCATTTAC 59.761 40.000 7.05 0.00 44.84 2.01
2442 4994 7.420002 GTTACAGTTCGGAAACCATTTACTTT 58.580 34.615 0.00 0.00 35.92 2.66
2445 4997 5.912955 CAGTTCGGAAACCATTTACTTTGAC 59.087 40.000 0.00 0.00 35.92 3.18
2458 5010 9.408648 CCATTTACTTTGACCTACCAATATTCT 57.591 33.333 0.00 0.00 0.00 2.40
2468 5020 8.998814 TGACCTACCAATATTCTATTTCCTCAA 58.001 33.333 0.00 0.00 0.00 3.02
2544 5110 8.877195 ACCAGTCTGTTCCTTAACTATCTTTTA 58.123 33.333 0.00 0.00 36.51 1.52
2624 5190 4.473444 ACCATTCTTTCCAGTGTTCATGT 58.527 39.130 0.00 0.00 0.00 3.21
2698 5264 2.616376 ACTGTTTCATTGCGTGCTAACA 59.384 40.909 0.00 0.00 33.78 2.41
2711 5277 3.118738 CGTGCTAACAGGGAAACTAGGAT 60.119 47.826 0.00 0.00 0.00 3.24
2866 5437 3.308438 ACAAGAATTCCACAGCAATGC 57.692 42.857 0.65 0.00 0.00 3.56
2879 5450 0.388907 GCAATGCCGAATGTGCAGTT 60.389 50.000 0.00 0.00 42.92 3.16
2922 5493 8.230486 CACACATTGGTCTTTATTTGTACTCTC 58.770 37.037 0.00 0.00 0.00 3.20
3212 5973 7.496529 TTGACTTTCACTTCAATTGACTAGG 57.503 36.000 7.89 1.78 0.00 3.02
3218 5979 8.777865 TTTCACTTCAATTGACTAGGTCATAG 57.222 34.615 7.89 2.02 42.40 2.23
3246 6007 4.320953 GCAAACGAGTAAATGCTGCTTTAC 59.679 41.667 18.57 18.57 40.38 2.01
3264 6025 7.264221 TGCTTTACAGACACAAACATTCATTT 58.736 30.769 0.00 0.00 0.00 2.32
3291 6052 5.183140 AGTTTCCAACACTATAACCACATGC 59.817 40.000 0.00 0.00 0.00 4.06
3314 6075 4.398549 TGTGTAGCGTTAAATTGTCTGC 57.601 40.909 0.00 0.00 0.00 4.26
3443 6204 1.202806 TGCCAGACCTCTGAAAACCTG 60.203 52.381 3.73 0.00 46.59 4.00
3484 6245 2.554893 GTTTTGTTGGATGCGGAAGGTA 59.445 45.455 0.00 0.00 0.00 3.08
3485 6246 2.799126 TTGTTGGATGCGGAAGGTAT 57.201 45.000 0.00 0.00 0.00 2.73
3486 6247 3.916359 TTGTTGGATGCGGAAGGTATA 57.084 42.857 0.00 0.00 0.00 1.47
3487 6248 4.431416 TTGTTGGATGCGGAAGGTATAT 57.569 40.909 0.00 0.00 0.00 0.86
3501 6262 2.429610 AGGTATATATGCTAACGCCGGG 59.570 50.000 2.18 0.00 34.43 5.73
3582 6343 8.901748 GCATTTTACACCTTTACATAATATGCG 58.098 33.333 0.00 0.00 34.54 4.73
3727 6629 8.442374 AGGAAACCTACATTGGAACTTTACTAA 58.558 33.333 0.00 0.00 28.47 2.24
3729 6631 9.888878 GAAACCTACATTGGAACTTTACTAAAC 57.111 33.333 0.00 0.00 0.00 2.01
3730 6632 7.662604 ACCTACATTGGAACTTTACTAAACG 57.337 36.000 0.00 0.00 0.00 3.60
3777 6680 9.197694 CTACCTGATACATGTCTTTTATGTAGC 57.802 37.037 0.00 6.48 43.84 3.58
3828 6732 8.194104 TCTCATCAGAAGTTCAGAACTAATAGC 58.806 37.037 16.46 4.46 41.91 2.97
3912 6816 5.467668 TTTCTCCTAGACTCCCTGATACA 57.532 43.478 0.00 0.00 0.00 2.29
3998 6906 4.745125 GTCGCTCTGCTATGTGCTATTTTA 59.255 41.667 0.00 0.00 43.37 1.52
4301 7210 2.124507 ATCCCGGGGACAACTGTGTG 62.125 60.000 23.50 0.00 38.41 3.82
4535 7682 5.992217 CAGTGCTCTTTCCTTTGTAGTACTT 59.008 40.000 0.00 0.00 31.87 2.24
4682 7833 8.695284 CATATTGACAGTATTACGAAGCTCTTC 58.305 37.037 0.00 0.00 36.29 2.87
4823 7974 6.396829 AAGTTGCTGAAGTGAGCTTATTTT 57.603 33.333 0.00 0.00 39.90 1.82
4933 8085 3.359194 CTCACGAAGAGCCAGGATG 57.641 57.895 0.00 0.00 37.59 3.51
5287 8707 7.334171 GGTGCCTATATTTTTCATTGCTGTTTT 59.666 33.333 0.00 0.00 0.00 2.43
5524 10149 4.917906 AGCAAGAGAAGGAATTAGTGGT 57.082 40.909 0.00 0.00 0.00 4.16
5667 10337 4.940046 ACTGTGCTAATCAAGTTCATCTGG 59.060 41.667 0.00 0.00 0.00 3.86
6475 12888 1.227380 CGGGAGCAGCACAGGTATC 60.227 63.158 0.00 0.00 0.00 2.24
6508 12921 1.136110 GTTGTGAAGGTTGGTGTTGGG 59.864 52.381 0.00 0.00 0.00 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 112 6.614694 AGTGGTGGTATGTTACTGTTATGA 57.385 37.500 0.00 0.00 0.00 2.15
177 178 4.033009 TGGTAGATTGCTTGATGAGGAGA 58.967 43.478 0.00 0.00 0.00 3.71
197 198 2.332063 ACGCTTGGATGGTTATCTGG 57.668 50.000 0.00 0.00 33.68 3.86
199 200 5.063880 GGAAATACGCTTGGATGGTTATCT 58.936 41.667 0.00 0.00 33.68 1.98
214 215 5.922546 TGTTCATTTTCTGTCGGAAATACG 58.077 37.500 7.67 0.63 42.63 3.06
217 218 6.349611 CCTGATGTTCATTTTCTGTCGGAAAT 60.350 38.462 7.67 0.00 42.63 2.17
232 233 4.531854 TGTCAAAGGAAACCTGATGTTCA 58.468 39.130 0.00 0.00 35.67 3.18
260 261 2.172717 GCTGTGAGGGCCCTTCTTAATA 59.827 50.000 29.39 7.67 0.00 0.98
309 310 6.936335 TCATGCTGATGAAACTTCTTAGTTGA 59.064 34.615 0.00 0.00 43.74 3.18
383 384 5.517054 GTCTTGATCGAAGGAGTATGTGTTC 59.483 44.000 0.00 0.00 31.85 3.18
388 389 5.464722 CCATTGTCTTGATCGAAGGAGTATG 59.535 44.000 0.00 0.00 31.85 2.39
439 440 0.608640 GGTCGTCTCCATGACAGGTT 59.391 55.000 0.00 0.00 45.60 3.50
448 449 3.640029 ACTAGAAGTTTTGGTCGTCTCCA 59.360 43.478 0.00 0.00 35.49 3.86
464 465 4.141574 GGCTGGTCTCTCTCTCTACTAGAA 60.142 50.000 0.00 0.00 32.46 2.10
467 468 3.116174 TGGCTGGTCTCTCTCTCTACTA 58.884 50.000 0.00 0.00 0.00 1.82
469 470 2.021457 GTGGCTGGTCTCTCTCTCTAC 58.979 57.143 0.00 0.00 0.00 2.59
470 471 1.407575 CGTGGCTGGTCTCTCTCTCTA 60.408 57.143 0.00 0.00 0.00 2.43
566 610 1.440618 TTGGTTAGGAGAGCACCCAA 58.559 50.000 0.00 0.00 0.00 4.12
606 650 7.772757 GCAGGCTAATATCTTTATCTGCCTAAT 59.227 37.037 0.00 0.00 40.98 1.73
612 656 6.112058 GGAGGCAGGCTAATATCTTTATCTG 58.888 44.000 0.00 0.00 0.00 2.90
616 660 4.041691 GTGGGAGGCAGGCTAATATCTTTA 59.958 45.833 0.00 0.00 0.00 1.85
618 662 2.373502 GTGGGAGGCAGGCTAATATCTT 59.626 50.000 0.00 0.00 0.00 2.40
620 664 1.338200 CGTGGGAGGCAGGCTAATATC 60.338 57.143 0.00 0.00 0.00 1.63
639 683 8.741101 TGTCTTACAAAAATTCATGGATTTCG 57.259 30.769 12.46 9.38 0.00 3.46
644 688 9.642327 CAATCATGTCTTACAAAAATTCATGGA 57.358 29.630 0.00 0.00 34.11 3.41
645 689 9.642327 TCAATCATGTCTTACAAAAATTCATGG 57.358 29.630 0.00 0.00 34.11 3.66
650 694 8.967218 CGTTGTCAATCATGTCTTACAAAAATT 58.033 29.630 7.62 0.00 0.00 1.82
730 774 3.818295 AGATAGGCTCGGGAATAGAGT 57.182 47.619 0.00 0.00 37.99 3.24
737 781 1.882780 CGCTTCTAGATAGGCTCGGGA 60.883 57.143 0.00 0.00 0.00 5.14
784 829 3.068590 CCATTGAGGCATACCATGGAAAC 59.931 47.826 21.47 4.44 38.68 2.78
816 861 7.814264 ACAATTTTGGGCACAATTTTTATGA 57.186 28.000 0.06 0.00 36.29 2.15
827 872 6.375945 AAAATCTTCAACAATTTTGGGCAC 57.624 33.333 0.00 0.00 34.62 5.01
836 881 7.318141 CACTGATGCCTAAAATCTTCAACAAT 58.682 34.615 0.00 0.00 0.00 2.71
878 927 9.431887 AGCTGTCTAACGAAATGTTATTTCTAA 57.568 29.630 11.25 0.00 42.02 2.10
880 929 7.907214 AGCTGTCTAACGAAATGTTATTTCT 57.093 32.000 11.25 0.00 42.02 2.52
963 1012 2.135581 TTTCGGTCGTGTCAGGGGT 61.136 57.895 0.00 0.00 0.00 4.95
968 1017 0.460722 TTGGAGTTTCGGTCGTGTCA 59.539 50.000 0.00 0.00 0.00 3.58
986 1035 3.622612 GCTGAACATGTTTTGGTTTGCTT 59.377 39.130 13.36 0.00 0.00 3.91
1014 1063 0.802607 GCAACTCGACGGACTGGATC 60.803 60.000 0.00 0.00 0.00 3.36
1420 1485 2.716017 GCCGAGTGAGGGGAGACAG 61.716 68.421 0.00 0.00 0.00 3.51
1587 1655 6.660521 AGTGTCATGTGACCATAATCAAATGT 59.339 34.615 10.40 0.00 42.68 2.71
1622 1690 1.681264 TCGTCACTATGATCATGGCGT 59.319 47.619 18.72 9.51 41.97 5.68
1625 1693 3.593096 CCCATCGTCACTATGATCATGG 58.407 50.000 18.72 17.72 0.00 3.66
1637 1705 0.396695 GGTCCTCTACCCCATCGTCA 60.397 60.000 0.00 0.00 43.16 4.35
1718 1786 1.480954 GACGAGAACCTCCAGCCATTA 59.519 52.381 0.00 0.00 0.00 1.90
1759 1827 6.834451 TCAATAAACCAACCAAGACCAAGTTA 59.166 34.615 0.00 0.00 0.00 2.24
1821 1889 7.632721 CAAGCACATTTTCAAAATTTAGCAGT 58.367 30.769 11.46 0.00 0.00 4.40
1856 1924 2.507102 CACACCTCTACCTGCGCG 60.507 66.667 0.00 0.00 0.00 6.86
2023 2092 6.317140 ACACTTTGCATGTAGTTCATATCCAG 59.683 38.462 0.00 0.00 34.67 3.86
2036 2105 7.148188 CCATAATCAGAAGTACACTTTGCATGT 60.148 37.037 0.00 0.00 36.11 3.21
2038 2107 6.183360 GCCATAATCAGAAGTACACTTTGCAT 60.183 38.462 0.00 0.00 36.11 3.96
2247 4784 4.300189 AGAAGCTGTCTGTAATAGAGCG 57.700 45.455 0.00 0.00 35.70 5.03
2289 4826 4.559862 AACTACATGGGAGAAGTCCAAG 57.440 45.455 0.00 0.00 46.07 3.61
2290 4827 4.597507 AGAAACTACATGGGAGAAGTCCAA 59.402 41.667 0.00 0.00 46.07 3.53
2291 4828 4.168101 AGAAACTACATGGGAGAAGTCCA 58.832 43.478 0.00 0.00 46.07 4.02
2292 4829 4.828072 AGAAACTACATGGGAGAAGTCC 57.172 45.455 0.00 0.00 43.05 3.85
2293 4830 7.113658 TGATAGAAACTACATGGGAGAAGTC 57.886 40.000 0.00 0.00 0.00 3.01
2294 4831 7.496346 TTGATAGAAACTACATGGGAGAAGT 57.504 36.000 0.00 0.00 0.00 3.01
2295 4832 8.970859 ATTTGATAGAAACTACATGGGAGAAG 57.029 34.615 0.00 0.00 0.00 2.85
2296 4833 9.177608 CAATTTGATAGAAACTACATGGGAGAA 57.822 33.333 0.00 0.00 0.00 2.87
2297 4834 7.283127 GCAATTTGATAGAAACTACATGGGAGA 59.717 37.037 0.00 0.00 0.00 3.71
2298 4835 7.067372 TGCAATTTGATAGAAACTACATGGGAG 59.933 37.037 0.00 0.00 0.00 4.30
2299 4836 6.889177 TGCAATTTGATAGAAACTACATGGGA 59.111 34.615 0.00 0.00 0.00 4.37
2300 4837 7.067372 TCTGCAATTTGATAGAAACTACATGGG 59.933 37.037 0.00 0.00 0.00 4.00
2368 4917 9.174166 GTGGATGGTTATACTTAAACAACAGAT 57.826 33.333 0.00 0.00 38.47 2.90
2418 4967 7.282675 TCAAAGTAAATGGTTTCCGAACTGTAA 59.717 33.333 0.00 0.00 36.03 2.41
2426 4975 5.106436 GGTAGGTCAAAGTAAATGGTTTCCG 60.106 44.000 0.00 0.00 0.00 4.30
2439 4988 9.853177 AGGAAATAGAATATTGGTAGGTCAAAG 57.147 33.333 0.00 0.00 0.00 2.77
2442 4994 8.561536 TGAGGAAATAGAATATTGGTAGGTCA 57.438 34.615 0.00 0.00 0.00 4.02
2445 4997 9.853177 AAGTTGAGGAAATAGAATATTGGTAGG 57.147 33.333 0.00 0.00 0.00 3.18
2544 5110 3.074390 TCCAACCTTTCTGGATCACACAT 59.926 43.478 0.00 0.00 38.07 3.21
2553 5119 3.754965 TGTCTTGATCCAACCTTTCTGG 58.245 45.455 0.00 0.00 42.93 3.86
2624 5190 3.625853 TGAACTGACCCACATTGAAACA 58.374 40.909 0.00 0.00 0.00 2.83
2698 5264 5.584551 ACAAAGTGAATCCTAGTTTCCCT 57.415 39.130 0.00 0.00 0.00 4.20
2711 5277 5.885352 TGACTTCCATCTGAAACAAAGTGAA 59.115 36.000 0.00 0.00 31.06 3.18
2866 5437 2.352651 CACCAGATAACTGCACATTCGG 59.647 50.000 0.00 0.00 42.25 4.30
2879 5450 6.983906 ATGTGTGATATCAGTCACCAGATA 57.016 37.500 18.69 5.40 46.17 1.98
2906 5477 6.585695 AGTGTCCGAGAGTACAAATAAAGA 57.414 37.500 0.00 0.00 0.00 2.52
2922 5493 0.450983 GAGTAGGTTCCGAGTGTCCG 59.549 60.000 0.00 0.00 0.00 4.79
3212 5973 7.044706 GCATTTACTCGTTTGCAATTCTATGAC 60.045 37.037 0.00 0.00 35.22 3.06
3218 5979 4.201523 GCAGCATTTACTCGTTTGCAATTC 60.202 41.667 0.00 0.00 37.56 2.17
3246 6007 7.760131 AACTTGAAATGAATGTTTGTGTCTG 57.240 32.000 0.00 0.00 0.00 3.51
3291 6052 4.788100 GCAGACAATTTAACGCTACACATG 59.212 41.667 0.00 0.00 0.00 3.21
3314 6075 3.447918 ACTACGATGGAACCCAATACG 57.552 47.619 0.00 0.00 36.95 3.06
3443 6204 4.142609 ACCACATATCACACAGATCCAC 57.857 45.455 0.00 0.00 38.19 4.02
3501 6262 4.694339 AGTTCTGGTACACTTTCAGTCAC 58.306 43.478 0.00 0.00 0.00 3.67
3562 6323 7.868922 CAGTACCGCATATTATGTAAAGGTGTA 59.131 37.037 17.40 4.60 31.98 2.90
3582 6343 2.168496 TCTACTGAGTGCACCAGTACC 58.832 52.381 29.12 10.50 43.79 3.34
3727 6629 4.527038 TCTGGGAGAAATAGAAGTGACGTT 59.473 41.667 0.00 0.00 0.00 3.99
3729 6631 4.158764 AGTCTGGGAGAAATAGAAGTGACG 59.841 45.833 0.00 0.00 0.00 4.35
3730 6632 5.669164 AGTCTGGGAGAAATAGAAGTGAC 57.331 43.478 0.00 0.00 0.00 3.67
4066 6975 2.327568 GTTGATTTGGGCATGTTGACG 58.672 47.619 0.00 0.00 0.00 4.35
4301 7210 1.061711 GAGTCATCGTGCATGCAGTTC 59.938 52.381 23.41 8.85 31.70 3.01
4625 7776 6.488006 ACACAGGCATATAAATGGATCAGAAC 59.512 38.462 0.00 0.00 33.38 3.01
4682 7833 7.504403 TCCCTTTCTTTCTTAGCATCTGATAG 58.496 38.462 0.00 0.00 0.00 2.08
4823 7974 1.466950 CGGAAAAGGCAGCGTGATTTA 59.533 47.619 0.00 0.00 0.00 1.40
4933 8085 2.018542 TTTACTGTCTGGCGCCATAC 57.981 50.000 31.84 31.84 0.00 2.39
5093 8261 8.824781 CCTCTAAATAAGACTGAACATGACATG 58.175 37.037 14.02 14.02 0.00 3.21
5287 8707 8.857098 ACCTCGAGATATTATAGCTTTTACACA 58.143 33.333 15.71 0.00 0.00 3.72
5308 8826 2.165845 CCTAGTACTGAAACCCACCTCG 59.834 54.545 5.39 0.00 0.00 4.63
5524 10149 6.114767 TCATGCATTCATACTAGCAAAGTCA 58.885 36.000 0.00 0.00 40.76 3.41
5667 10337 7.948278 TTCTACTTTTTCTTGCTGAGAGTAC 57.052 36.000 0.00 0.00 35.37 2.73
5791 10473 5.805486 CGAGCTGTAGTGCTAGAACAATTAA 59.195 40.000 3.00 0.00 44.17 1.40
5801 10483 1.393603 ATGCTCGAGCTGTAGTGCTA 58.606 50.000 35.27 14.55 44.17 3.49
6480 12893 3.813166 ACCAACCTTCACAACATTACTCG 59.187 43.478 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.