Multiple sequence alignment - TraesCS3B01G468200

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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 TraesCS3B01G468200 chr3B 100.000 5405 0 0 1 5405 712574393 712568989 0.000000e+00 9982.0
1 TraesCS3B01G468200 chr3B 85.714 70 9 1 180 248 631966746 631966677 7.510000e-09 73.1
2 TraesCS3B01G468200 chr3A 94.520 4708 199 33 735 5405 673448912 673444227 0.000000e+00 7210.0
3 TraesCS3B01G468200 chr3A 85.294 136 15 4 228 358 80520009 80519874 9.440000e-28 135.0
4 TraesCS3B01G468200 chr3D 96.263 3880 137 6 610 4487 537918884 537915011 0.000000e+00 6355.0
5 TraesCS3B01G468200 chr3D 90.394 406 33 5 4507 4911 537914867 537914467 3.710000e-146 529.0
6 TraesCS3B01G468200 chr3D 86.139 202 10 8 5218 5405 537914048 537913851 9.180000e-48 202.0
7 TraesCS3B01G468200 chr3D 82.105 95 14 2 10 103 535398933 535399025 1.610000e-10 78.7
8 TraesCS3B01G468200 chr2B 78.674 558 79 27 73 605 733465620 733465078 8.670000e-88 335.0
9 TraesCS3B01G468200 chr5D 81.003 379 60 8 230 602 219518299 219518671 1.900000e-74 291.0
10 TraesCS3B01G468200 chr5D 79.310 145 20 5 117 252 402967462 402967605 5.760000e-15 93.5
11 TraesCS3B01G468200 chr6D 80.070 286 48 9 52 335 432807083 432807361 2.550000e-48 204.0
12 TraesCS3B01G468200 chr7D 85.714 147 9 6 196 336 182332266 182332406 1.570000e-30 145.0
13 TraesCS3B01G468200 chr5A 86.667 135 13 4 229 358 6002655 6002789 1.570000e-30 145.0
14 TraesCS3B01G468200 chr5A 84.536 97 13 1 7 103 557095477 557095383 1.600000e-15 95.3
15 TraesCS3B01G468200 chr5A 87.500 72 7 2 33 103 398293684 398293614 1.250000e-11 82.4
16 TraesCS3B01G468200 chr1D 83.648 159 19 6 32 189 384156997 384156845 5.640000e-30 143.0
17 TraesCS3B01G468200 chr1D 86.139 101 7 5 154 249 338066022 338065924 9.580000e-18 102.0
18 TraesCS3B01G468200 chr1D 82.955 88 7 3 170 250 310878245 310878331 7.510000e-09 73.1
19 TraesCS3B01G468200 chr1D 80.180 111 11 6 149 249 326772792 326772683 7.510000e-09 73.1
20 TraesCS3B01G468200 chr4D 85.926 135 14 3 229 358 390860715 390860849 7.300000e-29 139.0
21 TraesCS3B01G468200 chr1B 85.075 134 15 4 229 358 581313652 581313784 1.220000e-26 132.0
22 TraesCS3B01G468200 chr1B 87.931 58 7 0 3093 3150 474447084 474447141 9.710000e-08 69.4
23 TraesCS3B01G468200 chr2D 84.444 135 16 4 235 365 1611920 1611787 1.580000e-25 128.0
24 TraesCS3B01G468200 chr2D 78.014 141 19 5 172 312 577331788 577331660 1.610000e-10 78.7
25 TraesCS3B01G468200 chr2A 77.826 230 34 8 380 606 23984258 23984473 5.680000e-25 126.0
26 TraesCS3B01G468200 chr2A 78.261 207 20 15 1 189 413486010 413485811 5.720000e-20 110.0
27 TraesCS3B01G468200 chr6A 83.810 105 12 4 1 103 555211636 555211535 1.600000e-15 95.3
28 TraesCS3B01G468200 chr5B 82.143 112 11 7 143 248 267057454 267057562 2.680000e-13 87.9
29 TraesCS3B01G468200 chr7A 86.111 72 4 5 184 249 728332729 728332800 7.510000e-09 73.1
30 TraesCS3B01G468200 chr6B 81.395 86 12 2 20 103 68908510 68908427 3.490000e-07 67.6


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 TraesCS3B01G468200 chr3B 712568989 712574393 5404 True 9982 9982 100.000 1 5405 1 chr3B.!!$R2 5404
1 TraesCS3B01G468200 chr3A 673444227 673448912 4685 True 7210 7210 94.520 735 5405 1 chr3A.!!$R2 4670
2 TraesCS3B01G468200 chr3D 537913851 537918884 5033 True 2362 6355 90.932 610 5405 3 chr3D.!!$R1 4795
3 TraesCS3B01G468200 chr2B 733465078 733465620 542 True 335 335 78.674 73 605 1 chr2B.!!$R1 532

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
830 856 0.036858 AAAGGAGACGAGAAGCAGCC 60.037 55.0 0.0 0.0 0.00 4.85 F
2109 2153 0.692476 TGCTGGCTGGATTGTGTACT 59.308 50.0 0.0 0.0 0.00 2.73 F
2359 2403 0.037590 TTACCATCTGCCACCACACC 59.962 55.0 0.0 0.0 0.00 4.16 F
4284 4328 0.179048 CATTGCCGAGCAGTATCCCA 60.179 55.0 0.0 0.0 40.61 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2267 2311 1.821216 ACTGTTCCAATACCTTGCCG 58.179 50.0 0.00 0.00 0.00 5.69 R
4046 4090 0.675633 CCTTGAACCAACTGGCAAGG 59.324 55.0 16.23 16.23 43.81 3.61 R
4313 4357 1.173444 AGTCAACCTCGAGTCGCACT 61.173 55.0 12.31 5.17 0.00 4.40 R
5143 5347 0.548031 TTCCCCCTCAATGCAGCTAG 59.452 55.0 0.00 0.00 0.00 3.42 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
23 24 6.928979 TCGTGAAAGGAAATACAACAGAAA 57.071 33.333 0.00 0.00 0.00 2.52
24 25 7.323049 TCGTGAAAGGAAATACAACAGAAAA 57.677 32.000 0.00 0.00 0.00 2.29
25 26 7.936584 TCGTGAAAGGAAATACAACAGAAAAT 58.063 30.769 0.00 0.00 0.00 1.82
26 27 7.860373 TCGTGAAAGGAAATACAACAGAAAATG 59.140 33.333 0.00 0.00 0.00 2.32
27 28 7.647715 CGTGAAAGGAAATACAACAGAAAATGT 59.352 33.333 0.00 0.00 46.97 2.71
28 29 8.755018 GTGAAAGGAAATACAACAGAAAATGTG 58.245 33.333 0.00 0.00 43.00 3.21
29 30 8.474025 TGAAAGGAAATACAACAGAAAATGTGT 58.526 29.630 0.00 0.00 43.00 3.72
30 31 9.313118 GAAAGGAAATACAACAGAAAATGTGTT 57.687 29.630 0.00 0.00 43.00 3.32
31 32 9.665719 AAAGGAAATACAACAGAAAATGTGTTT 57.334 25.926 1.15 1.15 43.00 2.83
32 33 9.665719 AAGGAAATACAACAGAAAATGTGTTTT 57.334 25.926 2.89 0.00 43.00 2.43
33 34 9.665719 AGGAAATACAACAGAAAATGTGTTTTT 57.334 25.926 2.89 0.00 43.00 1.94
55 56 3.894257 TCTGTTTCTCAGAGGCACG 57.106 52.632 0.00 0.00 46.77 5.34
56 57 0.318441 TCTGTTTCTCAGAGGCACGG 59.682 55.000 0.00 0.26 46.77 4.94
57 58 1.294659 CTGTTTCTCAGAGGCACGGC 61.295 60.000 0.00 0.00 46.27 5.68
77 78 1.666888 CCATGCCTTTCACGAAAGCAC 60.667 52.381 13.03 8.41 44.76 4.40
84 85 1.937278 TTCACGAAAGCACAACCGTA 58.063 45.000 0.00 0.00 33.62 4.02
88 89 0.788391 CGAAAGCACAACCGTACCTC 59.212 55.000 0.00 0.00 0.00 3.85
90 91 2.490991 GAAAGCACAACCGTACCTCTT 58.509 47.619 0.00 0.00 0.00 2.85
140 143 3.641437 TTTTCGTTTCCAAGAGGCATG 57.359 42.857 0.00 0.00 33.74 4.06
141 144 2.559698 TTCGTTTCCAAGAGGCATGA 57.440 45.000 0.00 0.00 33.74 3.07
143 146 1.347707 TCGTTTCCAAGAGGCATGACT 59.652 47.619 0.00 0.00 33.74 3.41
147 150 1.351076 TCCAAGAGGCATGACTGTGA 58.649 50.000 5.31 0.00 33.74 3.58
154 157 0.801251 GGCATGACTGTGACTCTTGC 59.199 55.000 0.00 4.72 37.83 4.01
171 174 4.614673 CGAAAGCACAACCACTGC 57.385 55.556 0.00 0.00 34.63 4.40
177 181 2.320587 GCACAACCACTGCCTCTCG 61.321 63.158 0.00 0.00 0.00 4.04
227 231 3.390003 TTTTTCGAGAGGCACGGTT 57.610 47.368 0.00 0.00 0.00 4.44
242 246 2.357034 GTTGTGCCTCTCGCGGAA 60.357 61.111 6.13 0.00 42.08 4.30
243 247 2.048222 TTGTGCCTCTCGCGGAAG 60.048 61.111 6.13 3.71 42.08 3.46
244 248 2.570284 TTGTGCCTCTCGCGGAAGA 61.570 57.895 6.13 0.90 42.08 2.87
245 249 2.094757 TTGTGCCTCTCGCGGAAGAA 62.095 55.000 6.13 0.00 42.08 2.52
246 250 1.374252 GTGCCTCTCGCGGAAGAAA 60.374 57.895 6.13 0.00 42.08 2.52
248 252 0.250124 TGCCTCTCGCGGAAGAAAAA 60.250 50.000 6.13 0.00 42.08 1.94
323 334 2.603173 CGAAAGCAAAACTGTGCCTCTC 60.603 50.000 0.00 0.00 46.14 3.20
324 335 2.057137 AAGCAAAACTGTGCCTCTCA 57.943 45.000 0.00 0.00 46.14 3.27
335 346 1.537202 GTGCCTCTCACGAAAGCAAAT 59.463 47.619 0.00 0.00 35.76 2.32
337 348 1.201965 GCCTCTCACGAAAGCAAATCG 60.202 52.381 0.00 4.55 45.47 3.34
344 358 2.130815 CGAAAGCAAATCGTGACTCG 57.869 50.000 0.00 0.00 41.41 4.18
416 431 8.972262 CTTTTTATCCAAAAGCTAAGGAAGAC 57.028 34.615 5.88 0.00 43.87 3.01
417 432 8.472007 TTTTTATCCAAAAGCTAAGGAAGACA 57.528 30.769 5.88 0.00 35.15 3.41
429 444 5.067283 GCTAAGGAAGACAAGTGAAAAACCA 59.933 40.000 0.00 0.00 0.00 3.67
477 492 2.097781 CGTTTAAAAAGCCGAAAACGCC 60.098 45.455 6.30 0.00 44.94 5.68
480 495 0.874175 AAAAAGCCGAAAACGCCTGC 60.874 50.000 0.00 0.00 0.00 4.85
493 508 1.614413 ACGCCTGCGGGAAAATAAAAA 59.386 42.857 18.31 0.00 44.69 1.94
517 537 1.194781 TCCAGAGGGAGTGCCAAGAC 61.195 60.000 2.50 0.00 38.64 3.01
554 574 4.148825 CTGGGAGCGCGCTAGGTT 62.149 66.667 36.69 12.70 0.00 3.50
555 575 4.451150 TGGGAGCGCGCTAGGTTG 62.451 66.667 36.69 0.00 0.00 3.77
563 583 1.756375 CGCGCTAGGTTGCACTGATC 61.756 60.000 5.56 0.00 0.00 2.92
570 590 0.944386 GGTTGCACTGATCGTTGTGT 59.056 50.000 12.63 0.00 36.63 3.72
578 598 1.003839 GATCGTTGTGTGGCTCCCA 60.004 57.895 0.00 0.00 0.00 4.37
592 612 1.302511 TCCCAAAGGAGCGCTTGTC 60.303 57.895 13.26 4.64 37.19 3.18
602 622 2.404215 GAGCGCTTGTCAACTAGTTGA 58.596 47.619 30.07 30.07 46.27 3.18
616 636 2.936919 AGTTGATCCTGTGAGCACAA 57.063 45.000 4.72 0.00 41.33 3.33
618 638 3.759581 AGTTGATCCTGTGAGCACAAAT 58.240 40.909 4.72 1.84 41.33 2.32
628 648 5.168526 TGTGAGCACAAATGAAGTTACAC 57.831 39.130 0.00 0.00 38.56 2.90
633 653 5.591099 AGCACAAATGAAGTTACACCAAAG 58.409 37.500 0.00 0.00 0.00 2.77
635 655 5.591099 CACAAATGAAGTTACACCAAAGCT 58.409 37.500 0.00 0.00 0.00 3.74
652 672 4.920828 TGGGCCACCAGTTCTTTC 57.079 55.556 0.00 0.00 43.37 2.62
656 676 1.454201 GGCCACCAGTTCTTTCTAGC 58.546 55.000 0.00 0.00 0.00 3.42
669 689 5.179452 TCTTTCTAGCTAAACAATGGGCT 57.821 39.130 0.00 0.00 38.62 5.19
685 705 1.527034 GGCTGCAAGTGAAGTGATGA 58.473 50.000 0.50 0.00 35.30 2.92
690 710 3.807553 TGCAAGTGAAGTGATGAACTCA 58.192 40.909 0.00 0.00 38.56 3.41
701 723 8.147704 TGAAGTGATGAACTCAGTACATACAAA 58.852 33.333 0.00 0.00 38.56 2.83
703 725 6.586463 AGTGATGAACTCAGTACATACAAACG 59.414 38.462 0.00 0.00 35.70 3.60
711 733 1.134848 GTACATACAAACGGCCCGGTA 60.135 52.381 8.57 0.00 0.00 4.02
715 737 1.752358 TACAAACGGCCCGGTACACA 61.752 55.000 8.57 0.00 0.00 3.72
716 738 2.281002 AAACGGCCCGGTACACAC 60.281 61.111 8.57 0.00 0.00 3.82
719 741 4.302509 CGGCCCGGTACACACACA 62.303 66.667 0.00 0.00 0.00 3.72
726 748 1.365699 CGGTACACACACAATAGGCC 58.634 55.000 0.00 0.00 0.00 5.19
727 749 1.338294 CGGTACACACACAATAGGCCA 60.338 52.381 5.01 0.00 0.00 5.36
748 770 3.569873 CCAGAGGTAAATTGGCCGT 57.430 52.632 0.00 0.00 0.00 5.68
750 772 2.561569 CCAGAGGTAAATTGGCCGTAG 58.438 52.381 0.00 0.00 0.00 3.51
788 810 2.990066 ATTCCCGATGTGAACCTCTC 57.010 50.000 0.00 0.00 0.00 3.20
789 811 1.938585 TTCCCGATGTGAACCTCTCT 58.061 50.000 0.00 0.00 0.00 3.10
830 856 0.036858 AAAGGAGACGAGAAGCAGCC 60.037 55.000 0.00 0.00 0.00 4.85
855 881 4.844267 ACTTCGTCCAAGTTTCGATTTTG 58.156 39.130 0.00 0.00 43.38 2.44
985 1011 4.034258 CACCAGCAAGCACAGCCG 62.034 66.667 0.00 0.00 0.00 5.52
1004 1030 1.990060 CCTCGACCCCTGACATGGT 60.990 63.158 0.00 0.00 37.64 3.55
1519 1548 4.394712 CCTCTCCGCGGCTTGGTT 62.395 66.667 23.51 0.00 0.00 3.67
1614 1658 3.684788 CCGAACTGATGGAAAGGTTAGTG 59.315 47.826 0.00 0.00 0.00 2.74
1726 1770 1.358046 GCGCAGATGGCCTTCAATC 59.642 57.895 19.98 7.03 40.31 2.67
1733 1777 3.697542 CAGATGGCCTTCAATCATGTGAA 59.302 43.478 19.98 0.00 35.14 3.18
1742 1786 4.305539 TCAATCATGTGAACATCCAGGT 57.694 40.909 0.00 0.00 33.61 4.00
1899 1943 3.360340 GGCTTGCTGCGTTCTGCT 61.360 61.111 0.00 0.00 46.63 4.24
1953 1997 5.132480 TGATGATGTTTGGGATGATAGTGGA 59.868 40.000 0.00 0.00 0.00 4.02
2092 2136 2.887152 GGTGTAAGGATCCCAATGATGC 59.113 50.000 8.55 0.00 41.82 3.91
2104 2148 1.754803 CAATGATGCTGGCTGGATTGT 59.245 47.619 0.00 0.00 0.00 2.71
2109 2153 0.692476 TGCTGGCTGGATTGTGTACT 59.308 50.000 0.00 0.00 0.00 2.73
2157 2201 1.336440 CACGCATTGGGTTGTGAGAAA 59.664 47.619 3.24 0.00 34.29 2.52
2179 2223 5.633830 AAGTTGTGAATATCTGCAGTTGG 57.366 39.130 14.67 0.00 0.00 3.77
2267 2311 3.251004 GGGATGCTTAATGGTGATCGAAC 59.749 47.826 0.00 0.00 0.00 3.95
2307 2351 7.721402 ACAGTATCTTGGAGACAGATATTCAC 58.279 38.462 0.00 0.00 44.54 3.18
2308 2352 7.343057 ACAGTATCTTGGAGACAGATATTCACA 59.657 37.037 0.00 0.00 44.54 3.58
2334 2378 2.418628 CGTTGTCACCACACTTTTGTCT 59.581 45.455 0.00 0.00 31.66 3.41
2359 2403 0.037590 TTACCATCTGCCACCACACC 59.962 55.000 0.00 0.00 0.00 4.16
2421 2465 6.432472 AGAATTGGAAGTTTGAGCCTAAGAAG 59.568 38.462 0.00 0.00 0.00 2.85
2534 2578 7.286316 ACTTTTGTCAAGGTCATTCTTTCAGAT 59.714 33.333 0.00 0.00 0.00 2.90
3033 3077 2.524569 TGCGATATCTTGGCATCGAA 57.475 45.000 11.29 0.00 45.32 3.71
3120 3164 6.385759 AGTTCCATGTTAAAAAGGAAAAGGGT 59.614 34.615 3.90 0.00 41.42 4.34
3401 3445 1.615392 GAGGTGGTTGCAGCTGAAAAT 59.385 47.619 20.43 0.00 32.51 1.82
3626 3670 2.354203 GCTGGACAGGAGAAACTGGTAG 60.354 54.545 1.01 0.00 42.75 3.18
3701 3745 0.600057 GAAGTGCCCTTGCTTCCTTG 59.400 55.000 0.00 0.00 36.14 3.61
3915 3959 4.149922 GTGGCTGCCGAAAAATTTAAGTTC 59.850 41.667 14.98 0.00 0.00 3.01
3942 3986 6.780706 ACATCACTAAGAAAACTACGGTTG 57.219 37.500 0.00 0.00 35.63 3.77
3968 4012 1.132834 GTGCGACATGGATGATGCAAA 59.867 47.619 10.57 0.00 40.75 3.68
3969 4013 2.025898 TGCGACATGGATGATGCAAAT 58.974 42.857 0.00 0.00 38.04 2.32
4046 4090 7.490079 TGACTGCAAGAATATCAAATCATTTGC 59.510 33.333 5.12 0.00 37.78 3.68
4284 4328 0.179048 CATTGCCGAGCAGTATCCCA 60.179 55.000 0.00 0.00 40.61 4.37
4299 4343 0.926293 TCCCACCATCCCTGGAATTC 59.074 55.000 0.00 0.00 46.37 2.17
4313 4357 4.527816 CCTGGAATTCCTTCATTTGGTTGA 59.472 41.667 24.73 0.00 36.82 3.18
4401 4445 7.885399 GCCTTTATCTCCCAAATCACAGTATAT 59.115 37.037 0.00 0.00 0.00 0.86
4419 4463 7.080099 CAGTATATTGATTGTATGGCTTGTGC 58.920 38.462 0.00 0.00 38.76 4.57
4676 4845 5.061179 AGCGTATCAACCTGTGTTTACTTT 58.939 37.500 0.00 0.00 30.42 2.66
4705 4874 6.868864 TCTTTACTGTCTAGTGCACATCTTTC 59.131 38.462 21.04 4.83 37.78 2.62
4922 5125 6.819146 AGGCAATAACAAGAGCTAGTAACTTC 59.181 38.462 0.00 0.00 0.00 3.01
5120 5324 3.574396 TCCCATCTCTAGCTTCCATTACG 59.426 47.826 0.00 0.00 0.00 3.18
5143 5347 7.368833 ACGTTGGTAGCAGAATAGTATGATAC 58.631 38.462 4.75 4.75 37.17 2.24
5147 5351 8.282455 TGGTAGCAGAATAGTATGATACTAGC 57.718 38.462 16.53 13.79 43.85 3.42
5307 5592 0.400213 TGGACCATGGTGTTCCTCAC 59.600 55.000 25.52 4.55 45.47 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.928979 TTTCTGTTGTATTTCCTTTCACGA 57.071 33.333 0.00 0.00 0.00 4.35
1 2 7.647715 ACATTTTCTGTTGTATTTCCTTTCACG 59.352 33.333 0.00 0.00 32.90 4.35
2 3 8.755018 CACATTTTCTGTTGTATTTCCTTTCAC 58.245 33.333 0.00 0.00 35.29 3.18
3 4 8.474025 ACACATTTTCTGTTGTATTTCCTTTCA 58.526 29.630 0.00 0.00 35.29 2.69
4 5 8.871686 ACACATTTTCTGTTGTATTTCCTTTC 57.128 30.769 0.00 0.00 35.29 2.62
5 6 9.665719 AAACACATTTTCTGTTGTATTTCCTTT 57.334 25.926 0.00 0.00 35.29 3.11
6 7 9.665719 AAAACACATTTTCTGTTGTATTTCCTT 57.334 25.926 0.00 0.00 35.29 3.36
7 8 9.665719 AAAAACACATTTTCTGTTGTATTTCCT 57.334 25.926 0.00 0.00 36.49 3.36
38 39 1.294659 GCCGTGCCTCTGAGAAACAG 61.295 60.000 6.17 0.00 46.97 3.16
39 40 1.301716 GCCGTGCCTCTGAGAAACA 60.302 57.895 6.17 0.00 0.00 2.83
40 41 2.035442 GGCCGTGCCTCTGAGAAAC 61.035 63.158 6.17 3.09 46.69 2.78
41 42 2.347490 GGCCGTGCCTCTGAGAAA 59.653 61.111 6.17 0.00 46.69 2.52
56 57 0.733909 GCTTTCGTGAAAGGCATGGC 60.734 55.000 20.53 12.14 45.85 4.40
57 58 0.597568 TGCTTTCGTGAAAGGCATGG 59.402 50.000 20.53 0.00 45.85 3.66
58 59 1.001487 TGTGCTTTCGTGAAAGGCATG 60.001 47.619 20.53 0.00 45.85 4.06
59 60 1.317613 TGTGCTTTCGTGAAAGGCAT 58.682 45.000 20.53 0.00 45.85 4.40
60 61 1.098869 TTGTGCTTTCGTGAAAGGCA 58.901 45.000 20.53 16.07 45.85 4.75
61 62 1.477105 GTTGTGCTTTCGTGAAAGGC 58.523 50.000 20.53 14.16 45.85 4.35
62 63 1.596954 CGGTTGTGCTTTCGTGAAAGG 60.597 52.381 20.53 6.10 45.85 3.11
64 65 1.088306 ACGGTTGTGCTTTCGTGAAA 58.912 45.000 0.00 0.00 34.40 2.69
65 66 1.593933 GTACGGTTGTGCTTTCGTGAA 59.406 47.619 0.00 0.00 37.10 3.18
66 67 1.210870 GTACGGTTGTGCTTTCGTGA 58.789 50.000 0.00 0.00 37.10 4.35
67 68 0.233848 GGTACGGTTGTGCTTTCGTG 59.766 55.000 0.00 0.00 37.10 4.35
68 69 0.105408 AGGTACGGTTGTGCTTTCGT 59.895 50.000 0.00 0.00 39.30 3.85
69 70 0.788391 GAGGTACGGTTGTGCTTTCG 59.212 55.000 0.00 0.00 0.00 3.46
70 71 2.165319 AGAGGTACGGTTGTGCTTTC 57.835 50.000 0.00 0.00 0.00 2.62
71 72 2.218603 CAAGAGGTACGGTTGTGCTTT 58.781 47.619 0.00 0.00 0.00 3.51
77 78 0.320073 TTCCGCAAGAGGTACGGTTG 60.320 55.000 0.00 0.00 46.92 3.77
123 125 1.347707 AGTCATGCCTCTTGGAAACGA 59.652 47.619 0.00 0.00 34.57 3.85
131 134 2.255406 AGAGTCACAGTCATGCCTCTT 58.745 47.619 0.00 0.00 29.69 2.85
152 155 1.726865 CAGTGGTTGTGCTTTCGCA 59.273 52.632 0.00 0.00 45.60 5.10
154 157 1.008538 GGCAGTGGTTGTGCTTTCG 60.009 57.895 0.00 0.00 40.97 3.46
167 170 1.816863 TTTCTTCCGCGAGAGGCAGT 61.817 55.000 8.23 0.00 43.84 4.40
168 171 0.670546 TTTTCTTCCGCGAGAGGCAG 60.671 55.000 8.23 0.00 43.84 4.85
169 172 0.250124 TTTTTCTTCCGCGAGAGGCA 60.250 50.000 8.23 0.00 43.84 4.75
170 173 2.540145 TTTTTCTTCCGCGAGAGGC 58.460 52.632 8.23 0.00 38.69 4.70
211 215 0.878523 CACAACCGTGCCTCTCGAAA 60.879 55.000 0.00 0.00 36.06 3.46
212 216 1.300620 CACAACCGTGCCTCTCGAA 60.301 57.895 0.00 0.00 36.06 3.71
221 225 3.414700 GCGAGAGGCACAACCGTG 61.415 66.667 0.00 0.00 46.52 4.94
224 228 3.876589 TTCCGCGAGAGGCACAACC 62.877 63.158 8.23 0.00 43.84 3.77
225 229 2.357034 TTCCGCGAGAGGCACAAC 60.357 61.111 8.23 0.00 43.84 3.32
226 230 2.048222 CTTCCGCGAGAGGCACAA 60.048 61.111 8.23 0.00 43.84 3.33
227 231 2.094757 TTTCTTCCGCGAGAGGCACA 62.095 55.000 8.23 0.00 43.84 4.57
271 282 2.342279 CGTGCCTCTCGGAAACCA 59.658 61.111 0.00 0.00 0.00 3.67
300 311 0.249031 GGCACAGTTTTGCTTTCGCT 60.249 50.000 0.00 0.00 42.56 4.93
318 329 2.795121 CGATTTGCTTTCGTGAGAGG 57.205 50.000 0.00 0.00 43.69 3.69
397 412 5.474876 CACTTGTCTTCCTTAGCTTTTGGAT 59.525 40.000 0.00 0.00 0.00 3.41
406 421 6.693315 TGGTTTTTCACTTGTCTTCCTTAG 57.307 37.500 0.00 0.00 0.00 2.18
413 428 5.128992 ACGTTTTGGTTTTTCACTTGTCT 57.871 34.783 0.00 0.00 0.00 3.41
416 431 4.159857 TCGACGTTTTGGTTTTTCACTTG 58.840 39.130 0.00 0.00 0.00 3.16
417 432 4.422546 TCGACGTTTTGGTTTTTCACTT 57.577 36.364 0.00 0.00 0.00 3.16
453 468 3.547068 CGTTTTCGGCTTTTTAAACGGTT 59.453 39.130 10.17 0.00 45.26 4.44
454 469 3.107407 CGTTTTCGGCTTTTTAAACGGT 58.893 40.909 10.17 0.00 45.26 4.83
493 508 1.428912 TGGCACTCCCTCTGGATTTTT 59.571 47.619 0.00 0.00 40.80 1.94
501 521 2.286523 CGGTCTTGGCACTCCCTCT 61.287 63.158 0.00 0.00 0.00 3.69
549 569 2.224185 ACACAACGATCAGTGCAACCTA 60.224 45.455 9.18 0.00 39.30 3.08
551 571 0.944386 ACACAACGATCAGTGCAACC 59.056 50.000 9.18 0.00 39.30 3.77
554 574 1.506309 GCCACACAACGATCAGTGCA 61.506 55.000 9.18 0.00 39.30 4.57
555 575 1.207593 GCCACACAACGATCAGTGC 59.792 57.895 9.18 0.00 39.30 4.40
563 583 1.654220 CTTTGGGAGCCACACAACG 59.346 57.895 0.00 0.00 41.98 4.10
578 598 2.224305 ACTAGTTGACAAGCGCTCCTTT 60.224 45.455 12.06 0.00 0.00 3.11
592 612 3.681897 GTGCTCACAGGATCAACTAGTTG 59.318 47.826 26.60 26.60 41.71 3.16
602 622 3.759581 ACTTCATTTGTGCTCACAGGAT 58.240 40.909 2.77 0.00 42.94 3.24
605 625 5.207768 GTGTAACTTCATTTGTGCTCACAG 58.792 41.667 2.77 0.00 42.94 3.66
606 626 4.036262 GGTGTAACTTCATTTGTGCTCACA 59.964 41.667 0.00 0.00 36.83 3.58
607 627 4.036262 TGGTGTAACTTCATTTGTGCTCAC 59.964 41.667 0.00 0.00 36.74 3.51
608 628 4.203226 TGGTGTAACTTCATTTGTGCTCA 58.797 39.130 0.00 0.00 36.74 4.26
616 636 3.573967 CCCAGCTTTGGTGTAACTTCATT 59.426 43.478 0.00 0.00 36.74 2.57
618 638 2.582052 CCCAGCTTTGGTGTAACTTCA 58.418 47.619 0.00 0.00 36.74 3.02
635 655 1.351017 CTAGAAAGAACTGGTGGCCCA 59.649 52.381 0.00 0.00 38.87 5.36
641 661 6.431234 CCATTGTTTAGCTAGAAAGAACTGGT 59.569 38.462 0.00 0.00 0.00 4.00
651 671 2.026356 TGCAGCCCATTGTTTAGCTAGA 60.026 45.455 0.00 0.00 33.33 2.43
652 672 2.368439 TGCAGCCCATTGTTTAGCTAG 58.632 47.619 0.00 0.00 33.33 3.42
656 676 2.557924 TCACTTGCAGCCCATTGTTTAG 59.442 45.455 0.00 0.00 0.00 1.85
669 689 3.807553 TGAGTTCATCACTTCACTTGCA 58.192 40.909 0.00 0.00 35.01 4.08
685 705 3.332034 GGCCGTTTGTATGTACTGAGTT 58.668 45.455 0.00 0.00 0.00 3.01
690 710 0.108041 CCGGGCCGTTTGTATGTACT 60.108 55.000 26.32 0.00 0.00 2.73
701 723 4.303993 GTGTGTGTACCGGGCCGT 62.304 66.667 26.32 15.36 0.00 5.68
703 725 0.036199 TATTGTGTGTGTACCGGGCC 60.036 55.000 6.32 0.00 0.00 5.80
711 733 0.609131 GCCTGGCCTATTGTGTGTGT 60.609 55.000 7.66 0.00 0.00 3.72
748 770 2.686106 GTTGGGCCGGGTCTCCTA 60.686 66.667 2.18 0.00 0.00 2.94
755 777 2.706834 GGAATTTCGTTGGGCCGGG 61.707 63.158 2.18 0.00 0.00 5.73
855 881 0.237498 CGGCCTTGGAAACTTCGAAC 59.763 55.000 0.00 0.00 0.00 3.95
900 926 0.474184 GTCCATGGTGATGTAGGGGG 59.526 60.000 12.58 0.00 0.00 5.40
955 981 1.899437 GCTGGTGGTCCCGAAGATGA 61.899 60.000 0.00 0.00 35.15 2.92
985 1011 2.187946 CATGTCAGGGGTCGAGGC 59.812 66.667 0.00 0.00 0.00 4.70
988 1014 1.550130 GGAACCATGTCAGGGGTCGA 61.550 60.000 15.14 0.00 43.32 4.20
996 1022 0.108377 CGGTCGATGGAACCATGTCA 60.108 55.000 11.27 0.00 36.70 3.58
1461 1487 1.589196 GTGGGCGATCTCAGCGTAC 60.589 63.158 0.00 0.00 35.00 3.67
1519 1548 0.390124 AAGTTCACGGCTGGTTCGTA 59.610 50.000 0.00 0.00 38.94 3.43
1527 1556 1.941668 GCAGAGCTAAAGTTCACGGCT 60.942 52.381 0.00 0.00 35.86 5.52
1532 1561 1.337823 GGACGGCAGAGCTAAAGTTCA 60.338 52.381 0.00 0.00 0.00 3.18
1733 1777 2.834549 AGATCGAAGTGAACCTGGATGT 59.165 45.455 0.00 0.00 0.00 3.06
1742 1786 3.118992 CCACATCTGGAGATCGAAGTGAA 60.119 47.826 5.59 0.00 40.55 3.18
1899 1943 3.820557 CAAGAACCTCTTCCCTTCAACA 58.179 45.455 0.00 0.00 33.78 3.33
1953 1997 2.554032 CACGTTCTGCCAAATCTTCCTT 59.446 45.455 0.00 0.00 0.00 3.36
2092 2136 2.768253 TCAGTACACAATCCAGCCAG 57.232 50.000 0.00 0.00 0.00 4.85
2104 2148 4.085357 ACAACCAATGCTCTTCAGTACA 57.915 40.909 0.00 0.00 0.00 2.90
2109 2153 2.798976 GCAACAACCAATGCTCTTCA 57.201 45.000 0.00 0.00 39.46 3.02
2157 2201 5.316167 TCCAACTGCAGATATTCACAACTT 58.684 37.500 23.35 0.00 0.00 2.66
2179 2223 3.882288 GCAATCTTTCTCCCAATCTCCTC 59.118 47.826 0.00 0.00 0.00 3.71
2267 2311 1.821216 ACTGTTCCAATACCTTGCCG 58.179 50.000 0.00 0.00 0.00 5.69
2334 2378 3.071023 GTGGTGGCAGATGGTAATAGCTA 59.929 47.826 0.00 0.00 0.00 3.32
2421 2465 5.931441 GTGATATCCACATCCTAACAAGC 57.069 43.478 0.00 0.00 45.03 4.01
2445 2489 5.337813 GCCATTTTCCATCTGAATGAAACCT 60.338 40.000 4.94 0.00 34.61 3.50
2534 2578 3.118811 CCTTTTGTTTCCTTGCTTGACCA 60.119 43.478 0.00 0.00 0.00 4.02
2950 2994 4.191544 TGGCACTTCTTCGGAATATCAAG 58.808 43.478 0.00 0.00 33.06 3.02
3120 3164 4.831155 TCCTTCAACTCTTCTAAGGTTCGA 59.169 41.667 0.00 0.00 39.62 3.71
3626 3670 2.021208 GCAGGGAAGGGAGAAATGAGC 61.021 57.143 0.00 0.00 0.00 4.26
3701 3745 8.430828 GTTCTACCGTCACTCTTTTTATTGTAC 58.569 37.037 0.00 0.00 0.00 2.90
3915 3959 7.095270 ACCGTAGTTTTCTTAGTGATGTTAGG 58.905 38.462 0.00 0.00 0.00 2.69
3942 3986 1.746615 ATCCATGTCGCACTGCCAC 60.747 57.895 0.00 0.00 0.00 5.01
4046 4090 0.675633 CCTTGAACCAACTGGCAAGG 59.324 55.000 16.23 16.23 43.81 3.61
4284 4328 2.287584 TGAAGGAATTCCAGGGATGGT 58.712 47.619 26.22 0.00 38.89 3.55
4299 4343 1.879380 TCGCACTCAACCAAATGAAGG 59.121 47.619 0.00 0.00 0.00 3.46
4313 4357 1.173444 AGTCAACCTCGAGTCGCACT 61.173 55.000 12.31 5.17 0.00 4.40
4401 4445 4.588899 ACTAGCACAAGCCATACAATCAA 58.411 39.130 0.00 0.00 43.56 2.57
4403 4447 4.396166 ACAACTAGCACAAGCCATACAATC 59.604 41.667 0.00 0.00 43.56 2.67
4419 4463 3.994392 AGAACATACCGTGCAACAACTAG 59.006 43.478 0.00 0.00 35.74 2.57
4676 4845 6.096673 TGTGCACTAGACAGTAAAGATTCA 57.903 37.500 19.41 0.00 32.21 2.57
4922 5125 1.208358 CACAACACTGCGATGCCAG 59.792 57.895 0.00 0.00 38.78 4.85
5143 5347 0.548031 TTCCCCCTCAATGCAGCTAG 59.452 55.000 0.00 0.00 0.00 3.42
5147 5351 2.833338 TCAAATTTCCCCCTCAATGCAG 59.167 45.455 0.00 0.00 0.00 4.41
5307 5592 4.689812 CAGAGGTGAACAGAAGATGAACTG 59.310 45.833 0.00 0.00 39.65 3.16


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

AutoCloner maintained by Alex Coulton.