Multiple sequence alignment - TraesCS3D01G381400

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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 TraesCS3D01G381400 chr3D 100.000 4023 0 0 1 4023 497605146 497601124 0.000000e+00 7430.0
1 TraesCS3D01G381400 chr3D 88.041 393 31 8 3124 3512 40808779 40809159 6.130000e-123 451.0
2 TraesCS3D01G381400 chr3D 88.929 280 24 4 3186 3463 595030128 595029854 4.980000e-89 339.0
3 TraesCS3D01G381400 chr3D 82.833 233 40 0 467 699 445041360 445041128 4.070000e-50 209.0
4 TraesCS3D01G381400 chr3D 80.711 197 36 2 467 662 595887474 595887669 6.960000e-33 152.0
5 TraesCS3D01G381400 chr3D 77.021 235 49 4 440 671 544278624 544278392 3.260000e-26 130.0
6 TraesCS3D01G381400 chr3A 93.827 2365 71 32 1673 4023 637110818 637113121 0.000000e+00 3489.0
7 TraesCS3D01G381400 chr3A 92.179 959 37 17 717 1661 637109824 637110758 0.000000e+00 1321.0
8 TraesCS3D01G381400 chr3A 85.324 695 93 7 1 690 637108891 637109581 0.000000e+00 710.0
9 TraesCS3D01G381400 chr3A 81.538 130 23 1 435 564 710744073 710744201 5.500000e-19 106.0
10 TraesCS3D01G381400 chr3B 93.359 2379 100 30 1681 4023 657650968 657648612 0.000000e+00 3465.0
11 TraesCS3D01G381400 chr3B 91.173 929 34 16 753 1661 657651930 657651030 0.000000e+00 1218.0
12 TraesCS3D01G381400 chr3B 82.578 706 103 14 1 698 657697741 657697048 4.450000e-169 604.0
13 TraesCS3D01G381400 chr3B 87.500 392 34 6 3124 3512 811123691 811124070 4.770000e-119 438.0
14 TraesCS3D01G381400 chr3B 89.781 274 20 4 3192 3463 798486850 798486583 1.070000e-90 344.0
15 TraesCS3D01G381400 chr3B 87.719 285 25 4 3128 3411 727505627 727505352 1.390000e-84 324.0
16 TraesCS3D01G381400 chr3B 79.695 197 36 4 467 661 116084537 116084343 5.420000e-29 139.0
17 TraesCS3D01G381400 chr6A 87.686 471 39 8 3331 3787 568178460 568177995 7.660000e-147 531.0
18 TraesCS3D01G381400 chr6A 88.312 154 16 2 3085 3237 568178717 568178565 2.470000e-42 183.0
19 TraesCS3D01G381400 chr1B 87.234 470 49 9 3338 3801 192674109 192674573 3.560000e-145 525.0
20 TraesCS3D01G381400 chr1B 85.208 480 50 10 3338 3801 177158815 177159289 1.310000e-129 473.0
21 TraesCS3D01G381400 chr1D 87.076 472 41 11 3333 3789 348124690 348125156 2.140000e-142 516.0
22 TraesCS3D01G381400 chr1D 84.532 278 31 8 3085 3355 348124373 348124645 8.570000e-67 265.0
23 TraesCS3D01G381400 chr2D 85.361 485 48 13 3333 3801 244754490 244754967 7.820000e-132 481.0
24 TraesCS3D01G381400 chr2D 78.689 244 44 8 1242 1481 424036878 424036639 5.380000e-34 156.0
25 TraesCS3D01G381400 chr2D 91.818 110 9 0 3126 3235 373852714 373852605 1.940000e-33 154.0
26 TraesCS3D01G381400 chr2D 77.982 218 43 5 1251 1464 424041657 424041441 9.070000e-27 132.0
27 TraesCS3D01G381400 chr6D 85.470 468 51 10 3333 3789 77328119 77328580 4.710000e-129 472.0
28 TraesCS3D01G381400 chr6D 85.657 251 27 3 3128 3378 161304005 161303764 5.160000e-64 255.0
29 TraesCS3D01G381400 chr5B 85.683 461 47 11 3343 3789 176793548 176793093 6.090000e-128 468.0
30 TraesCS3D01G381400 chr5B 92.500 40 3 0 660 699 41956222 41956183 1.560000e-04 58.4
31 TraesCS3D01G381400 chr5A 86.331 278 28 8 3085 3355 73840993 73841267 1.090000e-75 294.0
32 TraesCS3D01G381400 chr7D 78.800 250 51 2 446 694 474255697 474255945 2.490000e-37 167.0
33 TraesCS3D01G381400 chr7D 78.235 170 35 2 494 662 434268874 434269042 1.530000e-19 108.0
34 TraesCS3D01G381400 chr7D 81.343 134 19 3 554 681 504539977 504540110 1.980000e-18 104.0
35 TraesCS3D01G381400 chr7B 78.601 243 47 4 441 683 474460884 474460647 5.380000e-34 156.0
36 TraesCS3D01G381400 chr2A 78.226 248 44 10 1239 1481 564105194 564105436 2.500000e-32 150.0
37 TraesCS3D01G381400 chr2A 88.571 105 12 0 1242 1346 564098428 564098532 1.170000e-25 128.0
38 TraesCS3D01G381400 chr2B 77.869 244 46 8 1242 1481 498418407 498418168 1.170000e-30 145.0
39 TraesCS3D01G381400 chr2B 78.440 218 42 5 1251 1464 498427131 498426915 1.950000e-28 137.0


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 TraesCS3D01G381400 chr3D 497601124 497605146 4022 True 7430.0 7430 100.000000 1 4023 1 chr3D.!!$R2 4022
1 TraesCS3D01G381400 chr3A 637108891 637113121 4230 False 1840.0 3489 90.443333 1 4023 3 chr3A.!!$F2 4022
2 TraesCS3D01G381400 chr3B 657648612 657651930 3318 True 2341.5 3465 92.266000 753 4023 2 chr3B.!!$R5 3270
3 TraesCS3D01G381400 chr3B 657697048 657697741 693 True 604.0 604 82.578000 1 698 1 chr3B.!!$R2 697
4 TraesCS3D01G381400 chr6A 568177995 568178717 722 True 357.0 531 87.999000 3085 3787 2 chr6A.!!$R1 702
5 TraesCS3D01G381400 chr1D 348124373 348125156 783 False 390.5 516 85.804000 3085 3789 2 chr1D.!!$F1 704

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
623 629 0.107459 GGCATCTCCTCCCACTGAAC 60.107 60.0 0.0 0.0 0.0 3.18 F
629 635 0.391597 TCCTCCCACTGAACGAACAC 59.608 55.0 0.0 0.0 0.0 3.32 F
1736 2042 0.761187 TTCTCCTTGTGTGCTCTGCT 59.239 50.0 0.0 0.0 0.0 4.24 F
2451 2778 1.267574 TGTGCCTCATCCTCCACCTC 61.268 60.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1736 2042 0.737367 CTCCTGATCGCACTTCGCAA 60.737 55.000 0.00 0.0 42.6 4.85 R
2451 2778 2.158564 ACTGACCTGATATGCCCCAATG 60.159 50.000 0.00 0.0 0.0 2.82 R
2788 3115 1.205064 CAGCACCGCGTTGAAGAAG 59.795 57.895 8.22 0.0 0.0 2.85 R
3899 4317 1.069159 GCGAGAAGAGAGTGACGTGAA 60.069 52.381 0.00 0.0 0.0 3.18 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
43 44 8.151141 TGCAAAGAATTGAATTTATGTTGCAA 57.849 26.923 19.55 0.00 44.03 4.08
49 50 9.275398 AGAATTGAATTTATGTTGCAAATGTGT 57.725 25.926 0.00 0.00 0.00 3.72
50 51 9.320406 GAATTGAATTTATGTTGCAAATGTGTG 57.680 29.630 0.00 0.00 0.00 3.82
51 52 8.604640 ATTGAATTTATGTTGCAAATGTGTGA 57.395 26.923 0.00 0.00 0.00 3.58
68 69 3.689649 GTGTGAGTACATCATTGGTTCCC 59.310 47.826 0.00 0.00 40.92 3.97
87 88 1.269726 CCTTGTTCCGCATGTTGCTTT 60.270 47.619 0.00 0.00 42.25 3.51
111 112 3.120234 CGTTGCTTCTGTATGTTGCATGA 60.120 43.478 0.00 0.00 33.50 3.07
113 114 5.221880 GTTGCTTCTGTATGTTGCATGAAA 58.778 37.500 0.00 0.00 33.50 2.69
119 120 7.953710 GCTTCTGTATGTTGCATGAAAATTTTC 59.046 33.333 21.60 21.60 37.69 2.29
171 172 9.053840 CATACTCGGAGTACTTGAGTAATCTTA 57.946 37.037 28.23 15.91 45.38 2.10
175 176 8.969260 TCGGAGTACTTGAGTAATCTTATACA 57.031 34.615 15.57 0.00 43.01 2.29
177 178 8.291032 CGGAGTACTTGAGTAATCTTATACAGG 58.709 40.741 15.57 0.00 43.01 4.00
183 184 6.073327 TGAGTAATCTTATACAGGTCGCAG 57.927 41.667 0.00 0.00 0.00 5.18
186 187 2.579207 TCTTATACAGGTCGCAGTGC 57.421 50.000 4.58 4.58 0.00 4.40
223 224 2.219903 CGTCTCATACACACGCAAAACA 59.780 45.455 0.00 0.00 0.00 2.83
224 225 3.541711 GTCTCATACACACGCAAAACAC 58.458 45.455 0.00 0.00 0.00 3.32
265 266 3.101209 CATGGATCGGGTGTTGCG 58.899 61.111 0.00 0.00 0.00 4.85
273 274 2.472059 CGGGTGTTGCGGGATCATG 61.472 63.158 0.00 0.00 0.00 3.07
329 331 4.080015 TGAGAAAATTATCACCCCGACCAT 60.080 41.667 0.00 0.00 0.00 3.55
330 332 4.461198 AGAAAATTATCACCCCGACCATC 58.539 43.478 0.00 0.00 0.00 3.51
382 386 7.343057 ACTTTGATGTAGATACAGTCATCAGGA 59.657 37.037 0.00 0.00 44.38 3.86
399 403 4.602107 TCAGGATGGATTCTGCAATTTGA 58.398 39.130 0.00 0.00 36.16 2.69
438 442 7.087409 TGAGCAATTAATGACCAATGTAGTG 57.913 36.000 0.00 0.00 0.00 2.74
465 471 7.892778 TTTTAATACAGTACATTCGCAGTCA 57.107 32.000 0.00 0.00 0.00 3.41
472 478 1.502231 ACATTCGCAGTCACTCACAC 58.498 50.000 0.00 0.00 0.00 3.82
477 483 1.811217 CGCAGTCACTCACACACACG 61.811 60.000 0.00 0.00 0.00 4.49
486 492 1.721389 CTCACACACACGAGCATACAC 59.279 52.381 0.00 0.00 0.00 2.90
487 493 0.790207 CACACACACGAGCATACACC 59.210 55.000 0.00 0.00 0.00 4.16
492 498 1.295101 CACGAGCATACACCCACCA 59.705 57.895 0.00 0.00 0.00 4.17
497 503 2.803133 CGAGCATACACCCACCACTATG 60.803 54.545 0.00 0.00 0.00 2.23
499 505 2.843730 AGCATACACCCACCACTATGAA 59.156 45.455 0.00 0.00 0.00 2.57
502 508 0.321298 ACACCCACCACTATGAACGC 60.321 55.000 0.00 0.00 0.00 4.84
521 527 2.809601 CGCACGCACACTCTACCC 60.810 66.667 0.00 0.00 0.00 3.69
528 534 1.754803 CGCACACTCTACCCCTATGAA 59.245 52.381 0.00 0.00 0.00 2.57
540 546 2.320781 CCCTATGAACACCTCCGAGAT 58.679 52.381 0.00 0.00 0.00 2.75
546 552 3.427573 TGAACACCTCCGAGATACTGAA 58.572 45.455 0.00 0.00 0.00 3.02
550 556 0.669077 CCTCCGAGATACTGAACCGG 59.331 60.000 0.00 0.00 41.36 5.28
551 557 1.390565 CTCCGAGATACTGAACCGGT 58.609 55.000 0.00 0.00 40.87 5.28
564 570 2.565391 TGAACCGGTCTAGCATCTTGAA 59.435 45.455 8.04 0.00 0.00 2.69
579 585 7.078228 AGCATCTTGAAATTTTACGAAGTCAC 58.922 34.615 0.00 0.00 43.93 3.67
585 591 5.008217 TGAAATTTTACGAAGTCACCACTGG 59.992 40.000 0.00 0.00 43.93 4.00
586 592 3.547054 TTTTACGAAGTCACCACTGGT 57.453 42.857 0.00 0.00 43.93 4.00
598 604 1.665916 CACTGGTGCCTCACAGTCG 60.666 63.158 0.00 0.00 35.86 4.18
622 628 1.274703 GGGCATCTCCTCCCACTGAA 61.275 60.000 0.00 0.00 42.18 3.02
623 629 0.107459 GGCATCTCCTCCCACTGAAC 60.107 60.000 0.00 0.00 0.00 3.18
629 635 0.391597 TCCTCCCACTGAACGAACAC 59.608 55.000 0.00 0.00 0.00 3.32
640 646 3.838468 CGAACACCGTCGGAAGTC 58.162 61.111 20.51 10.25 37.37 3.01
642 648 1.002250 CGAACACCGTCGGAAGTCTG 61.002 60.000 20.51 7.85 37.37 3.51
649 655 3.991773 CACCGTCGGAAGTCTGAAATAAA 59.008 43.478 20.51 0.00 32.23 1.40
651 657 4.868734 ACCGTCGGAAGTCTGAAATAAATC 59.131 41.667 20.51 0.00 32.23 2.17
683 689 9.850628 ATAATTCAAACATCAATGTCAAGTCTG 57.149 29.630 0.00 0.00 40.80 3.51
701 917 3.045634 TCTGGGACTTCAACTCTGGAAA 58.954 45.455 0.00 0.00 0.00 3.13
706 922 3.315470 GGACTTCAACTCTGGAAAACCAC 59.685 47.826 0.00 0.00 0.00 4.16
707 923 3.288092 ACTTCAACTCTGGAAAACCACC 58.712 45.455 0.00 0.00 0.00 4.61
713 929 2.176798 ACTCTGGAAAACCACCATCCAA 59.823 45.455 0.00 0.00 42.41 3.53
717 933 1.618343 GGAAAACCACCATCCAACCAG 59.382 52.381 0.00 0.00 33.30 4.00
718 934 1.618343 GAAAACCACCATCCAACCAGG 59.382 52.381 0.00 0.00 39.47 4.45
758 980 9.210426 CAATGTAGTTAACGCAGTGATTTAATC 57.790 33.333 20.73 0.00 45.00 1.75
957 1191 4.087892 CACCCGCCCCTCTGTCTG 62.088 72.222 0.00 0.00 0.00 3.51
958 1192 4.316823 ACCCGCCCCTCTGTCTGA 62.317 66.667 0.00 0.00 0.00 3.27
959 1193 3.775654 CCCGCCCCTCTGTCTGAC 61.776 72.222 0.00 0.00 0.00 3.51
960 1194 2.681778 CCGCCCCTCTGTCTGACT 60.682 66.667 9.51 0.00 0.00 3.41
1104 1338 4.864334 CCGCCCATCCCTGTGCTC 62.864 72.222 0.00 0.00 0.00 4.26
1105 1339 3.790437 CGCCCATCCCTGTGCTCT 61.790 66.667 0.00 0.00 0.00 4.09
1106 1340 2.191641 GCCCATCCCTGTGCTCTC 59.808 66.667 0.00 0.00 0.00 3.20
1107 1341 2.373707 GCCCATCCCTGTGCTCTCT 61.374 63.158 0.00 0.00 0.00 3.10
1108 1342 1.828768 CCCATCCCTGTGCTCTCTC 59.171 63.158 0.00 0.00 0.00 3.20
1109 1343 1.440893 CCATCCCTGTGCTCTCTCG 59.559 63.158 0.00 0.00 0.00 4.04
1110 1344 1.039785 CCATCCCTGTGCTCTCTCGA 61.040 60.000 0.00 0.00 0.00 4.04
1116 1350 1.678728 CCTGTGCTCTCTCGACTCTCT 60.679 57.143 0.00 0.00 0.00 3.10
1117 1351 2.083774 CTGTGCTCTCTCGACTCTCTT 58.916 52.381 0.00 0.00 0.00 2.85
1228 1466 2.319096 CGGCGGCGGTCTTTGTTTA 61.319 57.895 25.36 0.00 0.00 2.01
1233 1471 1.727880 CGGCGGTCTTTGTTTATTCGA 59.272 47.619 0.00 0.00 0.00 3.71
1240 1478 5.389098 CGGTCTTTGTTTATTCGATCGTTGT 60.389 40.000 15.94 5.02 0.00 3.32
1484 1722 2.286872 CGATCCTACCTCAGTACGTGT 58.713 52.381 0.00 0.00 0.00 4.49
1487 1743 1.101331 CCTACCTCAGTACGTGTCCC 58.899 60.000 0.00 0.00 0.00 4.46
1519 1775 3.800685 TTCCTCCACACGCACACCG 62.801 63.158 0.00 0.00 44.21 4.94
1520 1776 4.293648 CCTCCACACGCACACCGA 62.294 66.667 0.00 0.00 41.02 4.69
1524 1780 1.025113 TCCACACGCACACCGAAAAA 61.025 50.000 0.00 0.00 41.02 1.94
1526 1782 1.394697 CACACGCACACCGAAAAATC 58.605 50.000 0.00 0.00 41.02 2.17
1661 1919 3.979101 TCAGCATGGTGTGAGTATCAA 57.021 42.857 23.35 0.00 42.79 2.57
1662 1920 4.284829 TCAGCATGGTGTGAGTATCAAA 57.715 40.909 23.35 0.00 42.79 2.69
1684 1990 6.851222 AACTTCAGTCTGTGACAAGTTATG 57.149 37.500 13.12 0.00 37.17 1.90
1722 2028 6.422100 GCTGAATCCTGTTTTTCTTTTTCTCC 59.578 38.462 0.00 0.00 0.00 3.71
1736 2042 0.761187 TTCTCCTTGTGTGCTCTGCT 59.239 50.000 0.00 0.00 0.00 4.24
1768 2074 3.063084 AGGAGGTCGGACTGCGTC 61.063 66.667 8.23 0.79 33.63 5.19
1834 2140 2.125512 ATGCTCGCCTTCACCGTC 60.126 61.111 0.00 0.00 0.00 4.79
1852 2158 2.828868 GTCCAGGTGGTGCTGTCA 59.171 61.111 0.00 0.00 36.34 3.58
2451 2778 1.267574 TGTGCCTCATCCTCCACCTC 61.268 60.000 0.00 0.00 0.00 3.85
2487 2814 5.359292 TCAGGTCAGTACATCTCAATCAGAG 59.641 44.000 0.00 0.00 46.14 3.35
2576 2903 5.011451 CTGTTCAACAGCTCGAACTAAAG 57.989 43.478 4.15 6.66 39.62 1.85
2702 3029 2.203112 GCATCCCGCTCATGCAGA 60.203 61.111 0.00 0.00 45.19 4.26
2788 3115 1.956477 GTGGTGGCAATGATGATACCC 59.044 52.381 0.00 0.00 34.80 3.69
2806 3133 1.205064 CTTCTTCAACGCGGTGCTG 59.795 57.895 21.87 14.58 0.00 4.41
3261 3590 9.268268 TGTGAAATAGGAAGTACTGTGTTAAAG 57.732 33.333 0.00 0.00 0.00 1.85
3501 3917 2.289320 ACTTGCTTCCAGCTCACTAGTG 60.289 50.000 17.17 17.17 42.97 2.74
3541 3958 3.032017 TCTGCTACTTCAGAGTGTTGC 57.968 47.619 5.55 5.55 38.11 4.17
3740 4158 7.296628 ACAATTTAGACAAGGGCAATGTTAA 57.703 32.000 0.00 0.00 0.00 2.01
3801 4219 5.814705 ACTTATAGATCAAACTGCTGCAGTC 59.185 40.000 33.00 20.71 44.62 3.51
3881 4299 4.413969 GCTACGTCCACTAAGAAACTCTC 58.586 47.826 0.00 0.00 0.00 3.20
3883 4301 4.506886 ACGTCCACTAAGAAACTCTCAG 57.493 45.455 0.00 0.00 0.00 3.35
3899 4317 2.175202 CTCAGGGCACAAGACTAGAGT 58.825 52.381 0.00 0.00 0.00 3.24
3983 4401 6.586844 AGCTGACGTAAGACTTAAATCTTCAC 59.413 38.462 3.33 0.36 39.65 3.18
3984 4402 6.452611 GCTGACGTAAGACTTAAATCTTCACG 60.453 42.308 18.33 18.33 39.65 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 7.725818 TGCAACATAAATTCAATTCTTTGCA 57.274 28.000 12.94 12.94 43.24 4.08
24 25 9.320406 CACACATTTGCAACATAAATTCAATTC 57.680 29.630 0.00 0.00 0.00 2.17
40 41 5.097529 CCAATGATGTACTCACACATTTGC 58.902 41.667 0.00 0.00 39.25 3.68
43 44 5.415701 GGAACCAATGATGTACTCACACATT 59.584 40.000 0.00 0.00 39.25 2.71
87 88 1.069296 GCAACATACAGAAGCAACGCA 60.069 47.619 0.00 0.00 0.00 5.24
119 120 7.432252 GCAAACAGATCCCATTTATTAAACTCG 59.568 37.037 0.00 0.00 0.00 4.18
129 130 4.336433 CGAGTATGCAAACAGATCCCATTT 59.664 41.667 0.00 0.00 0.00 2.32
138 139 4.111375 AGTACTCCGAGTATGCAAACAG 57.889 45.455 11.43 0.00 32.65 3.16
183 184 1.782023 CGTCGTTGCAATAGTTCGCAC 60.782 52.381 0.59 1.31 38.00 5.34
186 187 1.983605 AGACGTCGTTGCAATAGTTCG 59.016 47.619 10.46 11.71 0.00 3.95
190 191 4.027621 GTGTATGAGACGTCGTTGCAATAG 60.028 45.833 10.46 0.00 0.00 1.73
192 193 2.666508 GTGTATGAGACGTCGTTGCAAT 59.333 45.455 10.46 1.84 0.00 3.56
223 224 1.929806 TAAGTCTCCGCATGCGACGT 61.930 55.000 39.90 28.13 42.83 4.34
224 225 0.595053 ATAAGTCTCCGCATGCGACG 60.595 55.000 39.90 28.01 42.83 5.12
265 266 2.807108 GCCCGAGTTAAGTCATGATCCC 60.807 54.545 10.83 0.00 0.00 3.85
273 274 1.362406 GCAGCTGCCCGAGTTAAGTC 61.362 60.000 28.76 0.00 34.31 3.01
329 331 8.645730 TTTTGGTGTATTTTATATCTACGCGA 57.354 30.769 15.93 0.00 0.00 5.87
358 362 7.660030 TCCTGATGACTGTATCTACATCAAA 57.340 36.000 0.00 0.00 45.01 2.69
365 369 7.178097 CAGAATCCATCCTGATGACTGTATCTA 59.822 40.741 8.69 0.00 41.20 1.98
373 377 3.204306 TGCAGAATCCATCCTGATGAC 57.796 47.619 8.69 0.00 41.20 3.06
382 386 7.279313 GCAAAAGTATCAAATTGCAGAATCCAT 59.721 33.333 4.60 0.00 45.61 3.41
456 462 0.174617 TGTGTGTGAGTGACTGCGAA 59.825 50.000 0.00 0.00 0.00 4.70
459 465 0.527600 TCGTGTGTGTGAGTGACTGC 60.528 55.000 0.00 0.00 0.00 4.40
465 471 1.339929 TGTATGCTCGTGTGTGTGAGT 59.660 47.619 0.00 0.00 34.67 3.41
472 478 1.019278 GGTGGGTGTATGCTCGTGTG 61.019 60.000 0.00 0.00 0.00 3.82
477 483 2.434336 TCATAGTGGTGGGTGTATGCTC 59.566 50.000 0.00 0.00 0.00 4.26
486 492 1.358725 CGTGCGTTCATAGTGGTGGG 61.359 60.000 0.00 0.00 0.00 4.61
487 493 1.966493 GCGTGCGTTCATAGTGGTGG 61.966 60.000 0.00 0.00 0.00 4.61
492 498 2.726691 GCGTGCGTGCGTTCATAGT 61.727 57.895 3.11 0.00 0.00 2.12
502 508 2.372690 GGTAGAGTGTGCGTGCGTG 61.373 63.158 0.00 0.00 0.00 5.34
515 521 2.688817 CGGAGGTGTTCATAGGGGTAGA 60.689 54.545 0.00 0.00 0.00 2.59
516 522 1.687123 CGGAGGTGTTCATAGGGGTAG 59.313 57.143 0.00 0.00 0.00 3.18
521 527 4.022762 CAGTATCTCGGAGGTGTTCATAGG 60.023 50.000 4.96 0.00 0.00 2.57
528 534 2.100989 GGTTCAGTATCTCGGAGGTGT 58.899 52.381 4.96 0.00 0.00 4.16
540 546 3.014304 AGATGCTAGACCGGTTCAGTA 57.986 47.619 9.42 9.21 0.00 2.74
546 552 3.914426 ATTTCAAGATGCTAGACCGGT 57.086 42.857 6.92 6.92 0.00 5.28
550 556 8.443937 ACTTCGTAAAATTTCAAGATGCTAGAC 58.556 33.333 0.00 0.00 0.00 2.59
551 557 8.547967 ACTTCGTAAAATTTCAAGATGCTAGA 57.452 30.769 0.00 0.00 0.00 2.43
564 570 4.457466 ACCAGTGGTGACTTCGTAAAATT 58.543 39.130 15.86 0.00 32.98 1.82
579 585 1.302033 GACTGTGAGGCACCAGTGG 60.302 63.158 7.91 7.91 32.73 4.00
604 610 0.107459 GTTCAGTGGGAGGAGATGCC 60.107 60.000 0.00 0.00 40.61 4.40
605 611 0.460987 CGTTCAGTGGGAGGAGATGC 60.461 60.000 0.00 0.00 0.00 3.91
606 612 1.186200 TCGTTCAGTGGGAGGAGATG 58.814 55.000 0.00 0.00 0.00 2.90
607 613 1.550976 GTTCGTTCAGTGGGAGGAGAT 59.449 52.381 0.00 0.00 0.00 2.75
623 629 1.002250 CAGACTTCCGACGGTGTTCG 61.002 60.000 14.79 6.01 45.88 3.95
629 635 5.109903 AGATTTATTTCAGACTTCCGACGG 58.890 41.667 7.84 7.84 0.00 4.79
662 668 4.520111 CCCAGACTTGACATTGATGTTTGA 59.480 41.667 0.00 0.00 41.95 2.69
664 670 4.520492 GTCCCAGACTTGACATTGATGTTT 59.480 41.667 0.00 0.00 41.95 2.83
666 672 3.328931 AGTCCCAGACTTGACATTGATGT 59.671 43.478 0.00 0.00 40.28 3.06
683 689 2.885266 GGTTTTCCAGAGTTGAAGTCCC 59.115 50.000 0.00 0.00 40.31 4.46
701 917 0.560688 AACCTGGTTGGATGGTGGTT 59.439 50.000 12.11 0.00 39.71 3.67
728 950 3.743911 CACTGCGTTAACTACATTGGTCA 59.256 43.478 3.71 0.00 0.00 4.02
758 980 1.526917 GGATCCAATGCCCCGACTG 60.527 63.158 6.95 0.00 0.00 3.51
812 1034 1.135803 CCTGTAAAACACCGGCATTCG 60.136 52.381 0.00 0.00 38.88 3.34
954 1188 2.450243 GAGGGGGTGGGAGTCAGA 59.550 66.667 0.00 0.00 0.00 3.27
957 1191 3.391382 CGTGAGGGGGTGGGAGTC 61.391 72.222 0.00 0.00 0.00 3.36
1093 1327 0.033601 AGTCGAGAGAGCACAGGGAT 60.034 55.000 0.00 0.00 43.49 3.85
1096 1330 0.732571 GAGAGTCGAGAGAGCACAGG 59.267 60.000 0.00 0.00 43.49 4.00
1097 1331 1.737838 AGAGAGTCGAGAGAGCACAG 58.262 55.000 0.00 0.00 43.49 3.66
1098 1332 2.192664 AAGAGAGTCGAGAGAGCACA 57.807 50.000 0.00 0.00 43.49 4.57
1099 1333 3.569250 AAAAGAGAGTCGAGAGAGCAC 57.431 47.619 0.00 0.00 43.49 4.40
1125 1359 2.426023 GCCCTATACACCAGGCCG 59.574 66.667 0.00 0.00 39.60 6.13
1126 1360 2.426023 CGCCCTATACACCAGGCC 59.574 66.667 0.00 0.00 42.66 5.19
1134 1368 3.063861 CCGTTAAACAAACCGCCCTATAC 59.936 47.826 0.00 0.00 34.33 1.47
1142 1376 2.975193 GCTAAAGCCGTTAAACAAACCG 59.025 45.455 0.00 0.00 34.33 4.44
1143 1377 2.975193 CGCTAAAGCCGTTAAACAAACC 59.025 45.455 0.00 0.00 37.91 3.27
1228 1466 1.066605 CCGTCCCTACAACGATCGAAT 59.933 52.381 24.34 7.28 42.62 3.34
1233 1471 1.684983 CCATACCGTCCCTACAACGAT 59.315 52.381 0.00 0.00 42.62 3.73
1240 1478 1.829533 GCCGTCCATACCGTCCCTA 60.830 63.158 0.00 0.00 0.00 3.53
1487 1743 2.692741 GGAACAGAGGGGGAGGGG 60.693 72.222 0.00 0.00 0.00 4.79
1519 1775 3.261643 AGGCATTGGGTTCAGGATTTTTC 59.738 43.478 0.00 0.00 0.00 2.29
1520 1776 3.008266 CAGGCATTGGGTTCAGGATTTTT 59.992 43.478 0.00 0.00 0.00 1.94
1524 1780 1.002069 TCAGGCATTGGGTTCAGGAT 58.998 50.000 0.00 0.00 0.00 3.24
1526 1782 1.273327 GTTTCAGGCATTGGGTTCAGG 59.727 52.381 0.00 0.00 0.00 3.86
1661 1919 6.582636 TCATAACTTGTCACAGACTGAAGTT 58.417 36.000 18.58 18.58 39.92 2.66
1662 1920 6.161855 TCATAACTTGTCACAGACTGAAGT 57.838 37.500 10.08 5.46 32.63 3.01
1663 1921 7.386025 TGAATCATAACTTGTCACAGACTGAAG 59.614 37.037 10.08 4.79 33.15 3.02
1664 1922 7.216494 TGAATCATAACTTGTCACAGACTGAA 58.784 34.615 10.08 0.00 33.15 3.02
1665 1923 6.758254 TGAATCATAACTTGTCACAGACTGA 58.242 36.000 10.08 0.00 33.15 3.41
1667 1925 6.169094 CCTGAATCATAACTTGTCACAGACT 58.831 40.000 0.00 0.00 33.15 3.24
1668 1926 5.352569 CCCTGAATCATAACTTGTCACAGAC 59.647 44.000 0.00 0.00 0.00 3.51
1669 1927 5.248248 TCCCTGAATCATAACTTGTCACAGA 59.752 40.000 0.00 0.00 0.00 3.41
1671 1929 5.221823 TGTCCCTGAATCATAACTTGTCACA 60.222 40.000 0.00 0.00 0.00 3.58
1722 2028 1.082300 CGCAAGCAGAGCACACAAG 60.082 57.895 0.00 0.00 0.00 3.16
1736 2042 0.737367 CTCCTGATCGCACTTCGCAA 60.737 55.000 0.00 0.00 42.60 4.85
1768 2074 4.760047 CCCTGGCCGTTCTCGTGG 62.760 72.222 0.00 0.00 35.01 4.94
1834 2140 2.357517 GACAGCACCACCTGGACG 60.358 66.667 0.00 0.00 37.16 4.79
1852 2158 4.974438 TCCAGGCCGGGGAACTGT 62.974 66.667 22.79 0.00 34.36 3.55
2083 2389 3.181436 CCATGCCTACCTGGATCTCAATT 60.181 47.826 0.00 0.00 38.35 2.32
2176 2503 5.183904 GCCACTTGGAGTAATGTTCTGAAAT 59.816 40.000 0.00 0.00 37.39 2.17
2451 2778 2.158564 ACTGACCTGATATGCCCCAATG 60.159 50.000 0.00 0.00 0.00 2.82
2560 2887 5.220796 GGAAAACACTTTAGTTCGAGCTGTT 60.221 40.000 12.54 5.08 0.00 3.16
2567 2894 5.625311 GCATTGAGGAAAACACTTTAGTTCG 59.375 40.000 0.00 0.00 0.00 3.95
2576 2903 2.887152 AGACCTGCATTGAGGAAAACAC 59.113 45.455 8.56 0.00 36.51 3.32
2788 3115 1.205064 CAGCACCGCGTTGAAGAAG 59.795 57.895 8.22 0.00 0.00 2.85
3117 3445 2.585845 CGGAACTGATCGGATATCACG 58.414 52.381 9.00 6.18 0.00 4.35
3430 3834 3.567397 AGGTGTAGTAGCCTCATAGGTG 58.433 50.000 0.00 0.00 37.80 4.00
3501 3917 7.902087 AGCAGATTAGGACCTTAGAATGTATC 58.098 38.462 0.00 0.00 0.00 2.24
3541 3958 5.105146 AGGACCTTTACACTCAGAATAGCAG 60.105 44.000 0.00 0.00 0.00 4.24
3657 4074 8.891671 AGTTGTGAAAATGCTTATTGACATTT 57.108 26.923 0.00 0.00 45.84 2.32
3820 4238 3.541632 TGAAGGTGAACTGGAAACTGTC 58.458 45.455 0.00 0.00 42.21 3.51
3881 4299 2.300152 TGAACTCTAGTCTTGTGCCCTG 59.700 50.000 0.00 0.00 0.00 4.45
3883 4301 2.689646 GTGAACTCTAGTCTTGTGCCC 58.310 52.381 0.00 0.00 0.00 5.36
3899 4317 1.069159 GCGAGAAGAGAGTGACGTGAA 60.069 52.381 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.