Multiple sequence alignment - TraesCS2B01G197200

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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 TraesCS2B01G197200 chr2B 100.000 2438 0 0 1 2438 175059227 175061664 0.000000e+00 4503.0
1 TraesCS2B01G197200 chr2B 90.499 421 26 6 1928 2341 739876586 739876173 5.930000e-151 544.0
2 TraesCS2B01G197200 chr2B 92.573 377 23 3 1955 2327 676211934 676211559 9.920000e-149 536.0
3 TraesCS2B01G197200 chr2B 91.111 45 3 1 1871 1914 739876672 739876628 2.620000e-05 60.2
4 TraesCS2B01G197200 chr2A 89.342 1792 100 37 582 2318 126471843 126473598 0.000000e+00 2167.0
5 TraesCS2B01G197200 chr2A 82.822 163 20 3 368 525 126471289 126471448 3.270000e-29 139.0
6 TraesCS2B01G197200 chr2D 89.757 1689 109 26 126 1763 122031718 122033393 0.000000e+00 2102.0
7 TraesCS2B01G197200 chr2D 78.293 410 45 21 2019 2425 122033684 122034052 8.770000e-55 224.0
8 TraesCS2B01G197200 chr2D 89.600 125 13 0 1 125 122031552 122031676 2.510000e-35 159.0
9 TraesCS2B01G197200 chr6B 87.071 758 48 11 1675 2425 691467554 691466840 0.000000e+00 811.0
10 TraesCS2B01G197200 chr6B 92.593 459 21 5 1878 2331 152337006 152337456 0.000000e+00 647.0
11 TraesCS2B01G197200 chr6B 85.075 67 9 1 1697 1763 691467464 691467399 1.560000e-07 67.6
12 TraesCS2B01G197200 chr7B 92.375 459 22 5 1878 2331 692772637 692773087 2.040000e-180 641.0
13 TraesCS2B01G197200 chr7B 91.463 410 22 5 1927 2331 615592805 615592404 3.540000e-153 551.0
14 TraesCS2B01G197200 chr3B 91.285 459 27 5 1872 2325 329494341 329493891 4.460000e-172 614.0
15 TraesCS2B01G197200 chr4B 90.343 466 31 7 1872 2331 647875023 647874566 1.250000e-167 599.0
16 TraesCS2B01G197200 chr4B 92.670 382 23 3 1955 2331 613133515 613133896 1.650000e-151 545.0
17 TraesCS2B01G197200 chr4A 92.932 382 22 3 1955 2331 689805984 689806365 3.540000e-153 551.0
18 TraesCS2B01G197200 chr5B 91.198 409 23 5 1928 2331 638203085 638202685 5.930000e-151 544.0
19 TraesCS2B01G197200 chr5B 93.478 46 2 1 1871 1915 638203171 638203126 1.560000e-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 TraesCS2B01G197200 chr2B 175059227 175061664 2437 False 4503.000000 4503 100.000000 1 2438 1 chr2B.!!$F1 2437
1 TraesCS2B01G197200 chr2A 126471289 126473598 2309 False 1153.000000 2167 86.082000 368 2318 2 chr2A.!!$F1 1950
2 TraesCS2B01G197200 chr2D 122031552 122034052 2500 False 828.333333 2102 85.883333 1 2425 3 chr2D.!!$F1 2424
3 TraesCS2B01G197200 chr6B 691466840 691467554 714 True 439.300000 811 86.073000 1675 2425 2 chr6B.!!$R1 750

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
257 302 0.403750 TACCTCCCACCCCAAAACCT 60.404 55.0 0.0 0.0 0.0 3.50 F
260 305 0.539669 CTCCCACCCCAAAACCTGAC 60.540 60.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1216 1648 0.453793 CAGAGCCTCTCGACGTTGAT 59.546 55.0 5.82 0.0 35.36 2.57 R
1748 2190 2.236146 CAGTTACCATGACTACCAGGCA 59.764 50.0 0.00 0.0 37.84 4.75 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
51 52 8.373992 GCTTAAACTTATTCGTAGTGAGAACAG 58.626 37.037 0.00 0.00 0.00 3.16
53 54 9.622004 TTAAACTTATTCGTAGTGAGAACAGAG 57.378 33.333 0.00 0.00 0.00 3.35
61 62 5.125578 TCGTAGTGAGAACAGAGTTGCATAT 59.874 40.000 0.00 0.00 0.00 1.78
64 65 5.344066 AGTGAGAACAGAGTTGCATATACG 58.656 41.667 0.00 0.00 0.00 3.06
66 67 5.004821 GTGAGAACAGAGTTGCATATACGTG 59.995 44.000 0.00 0.00 0.00 4.49
76 77 4.551702 TGCATATACGTGGGCAAGATAT 57.448 40.909 0.00 0.00 32.54 1.63
78 79 5.660460 TGCATATACGTGGGCAAGATATAG 58.340 41.667 0.00 0.00 32.54 1.31
84 85 3.243771 ACGTGGGCAAGATATAGCTGTAC 60.244 47.826 0.00 0.00 0.00 2.90
86 87 4.561105 GTGGGCAAGATATAGCTGTACTC 58.439 47.826 0.00 0.00 0.00 2.59
96 97 2.349297 AGCTGTACTCAACGTAGCAC 57.651 50.000 6.97 0.00 0.00 4.40
133 175 6.653020 TGTACTCCCTACGTAATGTCTAGAA 58.347 40.000 0.00 0.00 0.00 2.10
139 181 6.040166 TCCCTACGTAATGTCTAGAAACATCC 59.960 42.308 0.00 0.00 38.92 3.51
140 182 5.913514 CCTACGTAATGTCTAGAAACATCCG 59.086 44.000 0.00 4.79 38.92 4.18
144 186 8.158169 ACGTAATGTCTAGAAACATCCGTATA 57.842 34.615 14.95 0.00 41.39 1.47
211 256 9.713713 AAGGAAATCTTCTCTAGTTTGTAACTC 57.286 33.333 0.00 0.00 41.77 3.01
257 302 0.403750 TACCTCCCACCCCAAAACCT 60.404 55.000 0.00 0.00 0.00 3.50
260 305 0.539669 CTCCCACCCCAAAACCTGAC 60.540 60.000 0.00 0.00 0.00 3.51
269 314 3.639094 CCCCAAAACCTGACAATGTTACA 59.361 43.478 0.00 0.00 0.00 2.41
271 316 5.229423 CCCAAAACCTGACAATGTTACATG 58.771 41.667 0.00 0.00 0.00 3.21
288 333 4.785453 GGAGAGGGGTGGCAAGCG 62.785 72.222 0.00 0.00 0.00 4.68
304 349 2.100605 AGCGAACCCTCTTTGATGAC 57.899 50.000 0.00 0.00 0.00 3.06
336 381 8.879342 AGTTATGAGAAGAGATAAAACGATGG 57.121 34.615 0.00 0.00 0.00 3.51
339 384 5.111989 TGAGAAGAGATAAAACGATGGCAG 58.888 41.667 0.00 0.00 0.00 4.85
350 395 3.276882 ACGATGGCAGGTTTTTAAACG 57.723 42.857 0.00 0.00 39.77 3.60
356 401 5.975410 TGGCAGGTTTTTAAACGAAAATG 57.025 34.783 0.00 0.00 39.77 2.32
376 421 4.974645 TGGCCTTCTCAGAAAGAAACTA 57.025 40.909 3.32 0.00 43.39 2.24
381 426 6.879458 GGCCTTCTCAGAAAGAAACTAACATA 59.121 38.462 0.00 0.00 43.39 2.29
384 429 9.883142 CCTTCTCAGAAAGAAACTAACATATCT 57.117 33.333 0.00 0.00 43.39 1.98
406 451 0.748450 TCGAGGAAAACGTCACCACT 59.252 50.000 0.00 0.00 0.00 4.00
421 466 3.136443 TCACCACTCAACCACTTTCTCAT 59.864 43.478 0.00 0.00 0.00 2.90
469 514 6.747414 TGTATATGTCACCCTCTAGCAAAT 57.253 37.500 0.00 0.00 0.00 2.32
470 515 6.524734 TGTATATGTCACCCTCTAGCAAATG 58.475 40.000 0.00 0.00 0.00 2.32
474 519 3.327757 TGTCACCCTCTAGCAAATGTTCT 59.672 43.478 0.00 0.00 0.00 3.01
477 522 2.093447 ACCCTCTAGCAAATGTTCTCCG 60.093 50.000 0.00 0.00 0.00 4.63
489 534 2.607499 TGTTCTCCGGTTAACAGGGTA 58.393 47.619 22.44 9.83 32.11 3.69
492 537 4.141528 TGTTCTCCGGTTAACAGGGTAAAA 60.142 41.667 22.44 10.79 32.11 1.52
493 538 4.703379 TCTCCGGTTAACAGGGTAAAAA 57.297 40.909 22.44 3.53 0.00 1.94
530 591 1.069204 ACGATCACAATATGCGAGCCT 59.931 47.619 0.00 0.00 0.00 4.58
561 938 2.933495 CGGACTATGTTCTTCCGTCA 57.067 50.000 1.03 0.00 45.95 4.35
575 952 2.379005 TCCGTCATGACAGCTGACTAT 58.621 47.619 24.93 8.48 40.68 2.12
608 996 1.072154 GCAAGAAAACTTTCGCAACGC 60.072 47.619 0.00 0.00 41.92 4.84
621 1015 0.775861 GCAACGCGACCATGTTTTTC 59.224 50.000 15.93 0.00 0.00 2.29
627 1021 2.908626 CGCGACCATGTTTTTCTTAAGC 59.091 45.455 0.00 0.00 0.00 3.09
635 1029 4.223320 TGTTTTTCTTAAGCCGAGCAAG 57.777 40.909 0.00 0.00 0.00 4.01
644 1038 1.195115 AGCCGAGCAAGGAGACAATA 58.805 50.000 1.32 0.00 0.00 1.90
734 1158 2.167693 CCCGAGCCTATCACACAAAGTA 59.832 50.000 0.00 0.00 0.00 2.24
812 1240 1.960689 GCACCAAAGCAAAACCCTAGA 59.039 47.619 0.00 0.00 0.00 2.43
814 1242 3.552890 GCACCAAAGCAAAACCCTAGAAG 60.553 47.826 0.00 0.00 0.00 2.85
899 1327 4.750096 GCCTTATAAGTCCTTCCATTCCCC 60.750 50.000 11.50 0.00 0.00 4.81
960 1388 4.862823 CTCCCCGACCCCTCTCCC 62.863 77.778 0.00 0.00 0.00 4.30
1012 1444 4.944372 CGGCTATGACGACCCGCC 62.944 72.222 0.00 0.00 35.20 6.13
1026 1458 2.391389 CCGCCTCAAGAAGAACCGC 61.391 63.158 0.00 0.00 0.00 5.68
1086 1518 2.034687 AAGCACCGCAAGCATCCT 59.965 55.556 0.00 0.00 0.00 3.24
1209 1641 2.548920 GCTCAGCAACAGGTTCTACACT 60.549 50.000 0.00 0.00 0.00 3.55
1216 1648 1.162698 CAGGTTCTACACTCCGACGA 58.837 55.000 0.00 0.00 0.00 4.20
1245 1677 0.339859 AGAGGCTCTGGTCCATGGTA 59.660 55.000 17.96 0.00 0.00 3.25
1249 1681 1.823295 CTCTGGTCCATGGTACCGG 59.177 63.158 25.16 25.16 43.63 5.28
1453 1885 0.526662 CTAGGGTTCTGTTCGCGACT 59.473 55.000 9.15 1.95 0.00 4.18
1477 1909 9.099071 ACTGTGCCTTGAGATCTATTATATCTT 57.901 33.333 0.00 0.00 33.82 2.40
1478 1910 9.941325 CTGTGCCTTGAGATCTATTATATCTTT 57.059 33.333 0.00 0.00 33.82 2.52
1542 1974 7.660208 ACAAGACATCGTTAGTTTGTTATCCTT 59.340 33.333 0.00 0.00 0.00 3.36
1583 2015 6.150976 ACCAACATCTTATGAGAATTTTGCGA 59.849 34.615 0.00 0.00 35.07 5.10
1686 2124 4.955811 TCGATCCCTAATGCATGTACTT 57.044 40.909 0.00 0.00 0.00 2.24
1701 2139 6.153510 TGCATGTACTTTTATTTGCCATGGTA 59.846 34.615 14.67 5.86 31.29 3.25
1737 2179 3.371034 TGCCTGCTAGTCATGGTAACTA 58.629 45.455 0.00 0.00 37.61 2.24
1751 2193 9.319143 GTCATGGTAACTATATGATTCTATGCC 57.681 37.037 0.00 0.00 33.82 4.40
1752 2194 9.271921 TCATGGTAACTATATGATTCTATGCCT 57.728 33.333 0.00 0.00 37.61 4.75
1753 2195 9.322773 CATGGTAACTATATGATTCTATGCCTG 57.677 37.037 0.00 0.00 37.61 4.85
1754 2196 7.851228 TGGTAACTATATGATTCTATGCCTGG 58.149 38.462 0.00 0.00 37.61 4.45
1755 2197 7.457852 TGGTAACTATATGATTCTATGCCTGGT 59.542 37.037 0.00 0.00 37.61 4.00
1756 2198 8.978472 GGTAACTATATGATTCTATGCCTGGTA 58.022 37.037 0.00 0.00 0.00 3.25
1758 2200 8.671987 AACTATATGATTCTATGCCTGGTAGT 57.328 34.615 0.00 0.00 0.00 2.73
1759 2201 8.299990 ACTATATGATTCTATGCCTGGTAGTC 57.700 38.462 0.00 0.00 0.00 2.59
1760 2202 7.895962 ACTATATGATTCTATGCCTGGTAGTCA 59.104 37.037 0.00 0.00 0.00 3.41
1761 2203 7.746243 ATATGATTCTATGCCTGGTAGTCAT 57.254 36.000 0.00 0.13 0.00 3.06
1762 2204 5.219343 TGATTCTATGCCTGGTAGTCATG 57.781 43.478 0.00 0.00 0.00 3.07
1763 2205 4.040829 TGATTCTATGCCTGGTAGTCATGG 59.959 45.833 0.00 0.00 0.00 3.66
1764 2206 3.046283 TCTATGCCTGGTAGTCATGGT 57.954 47.619 0.00 0.00 0.00 3.55
1765 2207 4.193240 TCTATGCCTGGTAGTCATGGTA 57.807 45.455 0.00 0.00 0.00 3.25
1766 2208 4.552674 TCTATGCCTGGTAGTCATGGTAA 58.447 43.478 0.00 0.00 0.00 2.85
1767 2209 3.560636 ATGCCTGGTAGTCATGGTAAC 57.439 47.619 0.00 0.00 0.00 2.50
1768 2210 2.546899 TGCCTGGTAGTCATGGTAACT 58.453 47.619 0.00 0.00 37.61 2.24
1769 2211 2.236146 TGCCTGGTAGTCATGGTAACTG 59.764 50.000 0.00 0.00 37.61 3.16
1770 2212 2.236395 GCCTGGTAGTCATGGTAACTGT 59.764 50.000 0.00 0.00 37.61 3.55
1771 2213 3.449737 GCCTGGTAGTCATGGTAACTGTA 59.550 47.826 0.00 0.00 37.61 2.74
1772 2214 4.101119 GCCTGGTAGTCATGGTAACTGTAT 59.899 45.833 0.00 0.00 37.61 2.29
1773 2215 5.601662 CCTGGTAGTCATGGTAACTGTATG 58.398 45.833 0.00 0.00 37.61 2.39
1774 2216 5.128827 CCTGGTAGTCATGGTAACTGTATGT 59.871 44.000 0.00 0.00 37.61 2.29
1775 2217 5.972935 TGGTAGTCATGGTAACTGTATGTG 58.027 41.667 0.00 0.00 37.61 3.21
1776 2218 5.482526 TGGTAGTCATGGTAACTGTATGTGT 59.517 40.000 0.00 0.00 37.61 3.72
1777 2219 6.040878 GGTAGTCATGGTAACTGTATGTGTC 58.959 44.000 0.00 0.00 37.61 3.67
1778 2220 6.127423 GGTAGTCATGGTAACTGTATGTGTCT 60.127 42.308 0.00 0.00 37.61 3.41
1779 2221 7.067859 GGTAGTCATGGTAACTGTATGTGTCTA 59.932 40.741 0.00 0.00 37.61 2.59
1789 2231 4.405680 ACTGTATGTGTCTATGCCTGCTAA 59.594 41.667 0.00 0.00 0.00 3.09
1795 2237 4.101430 TGTGTCTATGCCTGCTAATCATGA 59.899 41.667 0.00 0.00 0.00 3.07
1863 2336 6.215121 TGTATGATTTTTGTTTGCACTCTGG 58.785 36.000 0.00 0.00 0.00 3.86
1879 2352 5.507985 GCACTCTGGTATGCTTTGTTTTCTT 60.508 40.000 0.00 0.00 38.84 2.52
1881 2354 6.418819 CACTCTGGTATGCTTTGTTTTCTTTG 59.581 38.462 0.00 0.00 0.00 2.77
1883 2356 6.872920 TCTGGTATGCTTTGTTTTCTTTGTT 58.127 32.000 0.00 0.00 0.00 2.83
1946 2454 8.798859 ATTTCTTGTAGTCATAGTGATTTGCT 57.201 30.769 0.00 0.00 0.00 3.91
1947 2455 8.621532 TTTCTTGTAGTCATAGTGATTTGCTT 57.378 30.769 0.00 0.00 0.00 3.91
1948 2456 7.601073 TCTTGTAGTCATAGTGATTTGCTTG 57.399 36.000 0.00 0.00 0.00 4.01
1949 2457 5.801350 TGTAGTCATAGTGATTTGCTTGC 57.199 39.130 0.00 0.00 0.00 4.01
1951 2459 5.939883 TGTAGTCATAGTGATTTGCTTGCTT 59.060 36.000 0.00 0.00 0.00 3.91
1952 2460 7.102993 TGTAGTCATAGTGATTTGCTTGCTTA 58.897 34.615 0.00 0.00 0.00 3.09
1958 2481 4.741342 AGTGATTTGCTTGCTTAATGCTC 58.259 39.130 0.00 0.00 43.37 4.26
2006 2532 6.483640 GGAAGAGGTTTGTAGCCATACTAATG 59.516 42.308 0.00 0.00 30.99 1.90
2149 2728 4.256920 CTGGAGTAAGCTATTGTGCTGTT 58.743 43.478 0.00 0.00 43.24 3.16
2177 2756 3.255395 TGTGCCATTGTGTGAAGTATTGG 59.745 43.478 0.00 0.00 0.00 3.16
2194 2773 7.516198 AGTATTGGTATCCATTTGCATCTTC 57.484 36.000 0.00 0.00 31.53 2.87
2231 2810 7.446001 ACATGTTCTTTGAGAAATCTTCCTC 57.554 36.000 0.00 0.00 35.75 3.71
2238 2817 4.897509 TGAGAAATCTTCCTCTGAAGCA 57.102 40.909 0.00 0.00 46.28 3.91
2297 2877 7.436673 TGTTATTCTTTTTGGGTGTTCGATTTG 59.563 33.333 0.00 0.00 0.00 2.32
2307 2887 3.302415 GGTGTTCGATTTGTTTTGCTTGC 60.302 43.478 0.00 0.00 0.00 4.01
2368 2948 5.163864 CGCATAGCAGTTGTTTTATCAGTCA 60.164 40.000 0.00 0.00 0.00 3.41
2380 2960 9.862371 TTGTTTTATCAGTCAAGCTTTGTTTTA 57.138 25.926 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 8.958119 TTAAGCGAAATAAACTCTCCATACAT 57.042 30.769 0.00 0.00 0.00 2.29
21 22 7.809331 TCTCACTACGAATAAGTTTAAGCGAAA 59.191 33.333 0.00 0.00 0.00 3.46
51 52 1.948104 TGCCCACGTATATGCAACTC 58.052 50.000 0.00 0.00 0.00 3.01
53 54 2.285083 TCTTGCCCACGTATATGCAAC 58.715 47.619 8.54 0.00 38.68 4.17
61 62 2.963101 ACAGCTATATCTTGCCCACGTA 59.037 45.455 0.00 0.00 0.00 3.57
64 65 4.039245 TGAGTACAGCTATATCTTGCCCAC 59.961 45.833 0.00 0.00 0.00 4.61
66 67 4.873746 TGAGTACAGCTATATCTTGCCC 57.126 45.455 0.00 0.00 0.00 5.36
76 77 2.163010 GGTGCTACGTTGAGTACAGCTA 59.837 50.000 8.53 0.00 35.88 3.32
78 79 1.347320 GGTGCTACGTTGAGTACAGC 58.653 55.000 8.53 3.39 35.53 4.40
84 85 3.179265 CGGCGGTGCTACGTTGAG 61.179 66.667 0.00 0.00 35.98 3.02
96 97 0.719465 GAGTACATGTCAAACGGCGG 59.281 55.000 13.24 0.00 0.00 6.13
235 280 1.965643 GTTTTGGGGTGGGAGGTAAAC 59.034 52.381 0.00 0.00 0.00 2.01
257 302 3.054434 CCCCTCTCCATGTAACATTGTCA 60.054 47.826 0.00 0.00 0.00 3.58
260 305 3.282021 CACCCCTCTCCATGTAACATTG 58.718 50.000 0.00 0.00 0.00 2.82
269 314 2.988839 GCTTGCCACCCCTCTCCAT 61.989 63.158 0.00 0.00 0.00 3.41
271 316 4.785453 CGCTTGCCACCCCTCTCC 62.785 72.222 0.00 0.00 0.00 3.71
288 333 7.886338 ACTAAAAATGTCATCAAAGAGGGTTC 58.114 34.615 0.00 0.00 0.00 3.62
323 368 5.722021 AAAAACCTGCCATCGTTTTATCT 57.278 34.783 3.93 0.00 40.39 1.98
331 376 3.546002 TCGTTTAAAAACCTGCCATCG 57.454 42.857 0.19 0.00 35.51 3.84
336 381 4.319190 GGCCATTTTCGTTTAAAAACCTGC 60.319 41.667 0.00 0.00 40.37 4.85
339 384 5.756347 AGAAGGCCATTTTCGTTTAAAAACC 59.244 36.000 5.01 0.00 40.37 3.27
350 395 5.712152 TTCTTTCTGAGAAGGCCATTTTC 57.288 39.130 5.01 0.00 39.44 2.29
356 401 5.063880 TGTTAGTTTCTTTCTGAGAAGGCC 58.936 41.667 0.00 0.00 44.80 5.19
376 421 5.721232 ACGTTTTCCTCGAGAAGATATGTT 58.279 37.500 15.71 0.00 35.40 2.71
381 426 3.576648 GTGACGTTTTCCTCGAGAAGAT 58.423 45.455 15.71 0.00 35.40 2.40
384 429 1.409790 TGGTGACGTTTTCCTCGAGAA 59.590 47.619 15.71 3.49 0.00 2.87
386 431 1.137513 GTGGTGACGTTTTCCTCGAG 58.862 55.000 5.13 5.13 0.00 4.04
387 432 0.748450 AGTGGTGACGTTTTCCTCGA 59.252 50.000 0.00 0.00 0.00 4.04
388 433 1.137513 GAGTGGTGACGTTTTCCTCG 58.862 55.000 0.00 0.00 0.00 4.63
406 451 8.836413 CAGTTTTAGTTATGAGAAAGTGGTTGA 58.164 33.333 0.00 0.00 31.84 3.18
421 466 9.039870 CAAATGATTTTGTGGCAGTTTTAGTTA 57.960 29.630 0.00 0.00 37.92 2.24
463 508 3.482436 TGTTAACCGGAGAACATTTGCT 58.518 40.909 9.46 0.00 30.72 3.91
469 514 1.426751 ACCCTGTTAACCGGAGAACA 58.573 50.000 16.92 19.88 34.49 3.18
470 515 3.683365 TTACCCTGTTAACCGGAGAAC 57.317 47.619 16.92 12.49 0.00 3.01
492 537 7.876068 TGTGATCGTATAGAACAGGAACTTTTT 59.124 33.333 0.00 0.00 34.60 1.94
493 538 7.383687 TGTGATCGTATAGAACAGGAACTTTT 58.616 34.615 0.00 0.00 34.60 2.27
494 539 6.931838 TGTGATCGTATAGAACAGGAACTTT 58.068 36.000 0.00 0.00 34.60 2.66
495 540 6.525578 TGTGATCGTATAGAACAGGAACTT 57.474 37.500 0.00 0.00 34.60 2.66
496 541 6.525578 TTGTGATCGTATAGAACAGGAACT 57.474 37.500 0.00 0.00 43.88 3.01
530 591 1.551430 CATAGTCCGTTGGTGGGTGTA 59.449 52.381 0.00 0.00 0.00 2.90
575 952 6.431198 AGTTTTCTTGCGTTTGAGACTAAA 57.569 33.333 0.00 0.00 0.00 1.85
608 996 3.187637 TCGGCTTAAGAAAAACATGGTCG 59.812 43.478 6.67 0.00 0.00 4.79
621 1015 1.066858 TGTCTCCTTGCTCGGCTTAAG 60.067 52.381 0.00 0.00 0.00 1.85
627 1021 5.567138 AAAAATATTGTCTCCTTGCTCGG 57.433 39.130 0.00 0.00 0.00 4.63
651 1045 0.036010 CATTGTCTCGTTGCTCCCCT 60.036 55.000 0.00 0.00 0.00 4.79
652 1046 0.036388 TCATTGTCTCGTTGCTCCCC 60.036 55.000 0.00 0.00 0.00 4.81
710 1108 1.144057 GTGTGATAGGCTCGGGTGG 59.856 63.158 0.00 0.00 0.00 4.61
734 1158 2.303022 TCGGTTGAGGCTTCATCTTTCT 59.697 45.455 0.00 0.00 32.27 2.52
812 1240 4.637771 GCCGTTGGATGTAGGCTT 57.362 55.556 0.00 0.00 45.67 4.35
941 1369 3.752167 GAGAGGGGTCGGGGAGGA 61.752 72.222 0.00 0.00 0.00 3.71
999 1431 0.681887 TCTTGAGGCGGGTCGTCATA 60.682 55.000 0.00 0.00 39.10 2.15
1012 1444 2.096019 GCTTCTTGCGGTTCTTCTTGAG 60.096 50.000 0.00 0.00 0.00 3.02
1216 1648 0.453793 CAGAGCCTCTCGACGTTGAT 59.546 55.000 5.82 0.00 35.36 2.57
1477 1909 7.238486 TGGTACGGGAAACAACTAATAGTAA 57.762 36.000 0.00 0.00 0.00 2.24
1478 1910 6.627953 GCTGGTACGGGAAACAACTAATAGTA 60.628 42.308 0.00 0.00 33.56 1.82
1583 2015 9.371136 CGTCTGATATAAACTGGCATAACATAT 57.629 33.333 0.00 0.00 0.00 1.78
1701 2139 8.372877 ACTAGCAGGCATAGAATCATATAGTT 57.627 34.615 0.00 0.00 0.00 2.24
1708 2150 4.262765 CCATGACTAGCAGGCATAGAATCA 60.263 45.833 4.46 0.00 43.49 2.57
1737 2179 7.365384 CCATGACTACCAGGCATAGAATCATAT 60.365 40.741 0.00 0.00 43.49 1.78
1748 2190 2.236146 CAGTTACCATGACTACCAGGCA 59.764 50.000 0.00 0.00 37.84 4.75
1749 2191 2.236395 ACAGTTACCATGACTACCAGGC 59.764 50.000 0.00 0.00 0.00 4.85
1750 2192 5.128827 ACATACAGTTACCATGACTACCAGG 59.871 44.000 0.00 0.00 0.00 4.45
1751 2193 6.042777 CACATACAGTTACCATGACTACCAG 58.957 44.000 0.00 0.00 0.00 4.00
1752 2194 5.482526 ACACATACAGTTACCATGACTACCA 59.517 40.000 0.00 0.00 0.00 3.25
1753 2195 5.974108 ACACATACAGTTACCATGACTACC 58.026 41.667 0.00 0.00 0.00 3.18
1754 2196 6.864342 AGACACATACAGTTACCATGACTAC 58.136 40.000 0.00 0.00 0.00 2.73
1755 2197 8.630037 CATAGACACATACAGTTACCATGACTA 58.370 37.037 0.00 0.00 0.00 2.59
1756 2198 7.492524 CATAGACACATACAGTTACCATGACT 58.507 38.462 0.00 0.00 0.00 3.41
1757 2199 6.201044 GCATAGACACATACAGTTACCATGAC 59.799 42.308 0.00 0.00 0.00 3.06
1758 2200 6.280643 GCATAGACACATACAGTTACCATGA 58.719 40.000 0.00 0.00 0.00 3.07
1759 2201 5.466728 GGCATAGACACATACAGTTACCATG 59.533 44.000 0.00 0.00 0.00 3.66
1760 2202 5.366768 AGGCATAGACACATACAGTTACCAT 59.633 40.000 0.00 0.00 0.00 3.55
1761 2203 4.714802 AGGCATAGACACATACAGTTACCA 59.285 41.667 0.00 0.00 0.00 3.25
1762 2204 5.050490 CAGGCATAGACACATACAGTTACC 58.950 45.833 0.00 0.00 0.00 2.85
1763 2205 4.508124 GCAGGCATAGACACATACAGTTAC 59.492 45.833 0.00 0.00 0.00 2.50
1764 2206 4.405680 AGCAGGCATAGACACATACAGTTA 59.594 41.667 0.00 0.00 0.00 2.24
1765 2207 3.198635 AGCAGGCATAGACACATACAGTT 59.801 43.478 0.00 0.00 0.00 3.16
1766 2208 2.768527 AGCAGGCATAGACACATACAGT 59.231 45.455 0.00 0.00 0.00 3.55
1767 2209 3.465742 AGCAGGCATAGACACATACAG 57.534 47.619 0.00 0.00 0.00 2.74
1768 2210 5.070313 TGATTAGCAGGCATAGACACATACA 59.930 40.000 0.00 0.00 0.00 2.29
1769 2211 5.541845 TGATTAGCAGGCATAGACACATAC 58.458 41.667 0.00 0.00 0.00 2.39
1770 2212 5.806654 TGATTAGCAGGCATAGACACATA 57.193 39.130 0.00 0.00 0.00 2.29
1771 2213 4.694760 TGATTAGCAGGCATAGACACAT 57.305 40.909 0.00 0.00 0.00 3.21
1772 2214 4.101430 TCATGATTAGCAGGCATAGACACA 59.899 41.667 0.00 0.00 0.00 3.72
1773 2215 4.635223 TCATGATTAGCAGGCATAGACAC 58.365 43.478 0.00 0.00 0.00 3.67
1774 2216 4.961438 TCATGATTAGCAGGCATAGACA 57.039 40.909 0.00 0.00 0.00 3.41
1775 2217 7.064371 CAGTTATCATGATTAGCAGGCATAGAC 59.936 40.741 14.65 0.00 0.00 2.59
1776 2218 7.101700 CAGTTATCATGATTAGCAGGCATAGA 58.898 38.462 14.65 0.00 0.00 1.98
1777 2219 6.877855 ACAGTTATCATGATTAGCAGGCATAG 59.122 38.462 14.65 0.00 0.00 2.23
1778 2220 6.772605 ACAGTTATCATGATTAGCAGGCATA 58.227 36.000 14.65 0.00 0.00 3.14
1779 2221 5.628130 ACAGTTATCATGATTAGCAGGCAT 58.372 37.500 14.65 0.00 0.00 4.40
1789 2231 9.610705 GGCATAGAATCATACAGTTATCATGAT 57.389 33.333 13.81 13.81 40.31 2.45
1795 2237 7.013823 AGCAGGCATAGAATCATACAGTTAT 57.986 36.000 0.00 0.00 0.00 1.89
1908 2412 7.766278 TGACTACAAGAAATAGAATCCTGAAGC 59.234 37.037 0.00 0.00 0.00 3.86
1948 2456 4.801147 TCAATGTCATCGAGCATTAAGC 57.199 40.909 10.82 0.00 46.19 3.09
1949 2457 6.355397 ACTTCAATGTCATCGAGCATTAAG 57.645 37.500 10.82 14.21 34.01 1.85
1951 2459 5.874261 TCAACTTCAATGTCATCGAGCATTA 59.126 36.000 10.82 0.00 34.01 1.90
1952 2460 4.696877 TCAACTTCAATGTCATCGAGCATT 59.303 37.500 6.78 6.78 35.91 3.56
1982 2505 6.483640 CCATTAGTATGGCTACAAACCTCTTC 59.516 42.308 0.00 0.00 44.64 2.87
2017 2543 8.272889 AGGGATTCCAAAGATAAAACTACTACC 58.727 37.037 4.80 0.00 34.83 3.18
2103 2681 7.878127 CAGGTTCTTATTTAACTCAAGAGGTGA 59.122 37.037 0.00 0.00 30.43 4.02
2177 2756 3.561310 TCTGCGAAGATGCAAATGGATAC 59.439 43.478 0.00 0.00 45.74 2.24
2206 2785 7.390162 AGAGGAAGATTTCTCAAAGAACATGTC 59.610 37.037 0.00 0.00 33.26 3.06
2231 2810 5.179045 ACAAAACAGACAGAATGCTTCAG 57.821 39.130 0.00 0.00 42.53 3.02
2238 2817 8.621532 TCTAGCAAATACAAAACAGACAGAAT 57.378 30.769 0.00 0.00 0.00 2.40
2368 2948 8.981647 CAAATGCTTGACTATAAAACAAAGCTT 58.018 29.630 0.00 0.00 34.14 3.74
2381 2961 8.726988 GGAAATACAGTAACAAATGCTTGACTA 58.273 33.333 0.00 0.00 36.33 2.59
2383 2963 6.806739 GGGAAATACAGTAACAAATGCTTGAC 59.193 38.462 0.00 0.00 36.33 3.18


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

AutoCloner maintained by Alex Coulton.