Multiple sequence alignment - TraesCS2D01G186600

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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 TraesCS2D01G186600 chr2D 100.000 2450 0 0 1 2450 131123464 131125913 0.000000e+00 4525.0
1 TraesCS2D01G186600 chr2D 88.964 1178 102 16 1187 2357 131134472 131135628 0.000000e+00 1430.0
2 TraesCS2D01G186600 chr2D 90.079 504 29 9 853 1346 131134187 131134679 3.440000e-178 634.0
3 TraesCS2D01G186600 chr2D 82.333 583 83 7 807 1386 130987624 130988189 2.830000e-134 488.0
4 TraesCS2D01G186600 chr2D 79.274 661 94 23 1130 1765 130987999 130988641 2.910000e-114 422.0
5 TraesCS2D01G186600 chr2D 83.632 446 67 5 807 1248 131041980 131042423 4.870000e-112 414.0
6 TraesCS2D01G186600 chr2D 79.789 569 96 15 839 1406 131052276 131052826 1.770000e-106 396.0
7 TraesCS2D01G186600 chr2D 80.000 435 50 18 1187 1609 131042998 131043407 1.110000e-73 287.0
8 TraesCS2D01G186600 chr2D 78.140 430 59 19 1186 1599 131042304 131042714 8.750000e-60 241.0
9 TraesCS2D01G186600 chr2D 83.412 211 32 3 432 639 130986602 130986812 2.490000e-45 193.0
10 TraesCS2D01G186600 chr2D 81.567 217 31 6 1382 1590 131002635 131002850 1.160000e-38 171.0
11 TraesCS2D01G186600 chr2A 88.060 1918 158 34 468 2357 137212248 137214122 0.000000e+00 2207.0
12 TraesCS2D01G186600 chr2A 79.429 700 91 28 712 1373 137128941 137129625 1.730000e-121 446.0
13 TraesCS2D01G186600 chr2A 92.884 267 13 3 218 482 137211820 137212082 1.370000e-102 383.0
14 TraesCS2D01G186600 chr2A 79.480 346 38 16 1284 1597 137129479 137129823 5.310000e-52 215.0
15 TraesCS2D01G186600 chr2A 83.412 211 31 4 432 638 137128050 137128260 2.490000e-45 193.0
16 TraesCS2D01G186600 chr2A 87.591 137 17 0 1250 1386 137140922 137141058 2.520000e-35 159.0
17 TraesCS2D01G186600 chr2A 97.222 36 1 0 2365 2400 722168749 722168784 7.320000e-06 62.1
18 TraesCS2D01G186600 chrUn 92.019 1040 65 9 41 1068 428032560 428033593 0.000000e+00 1445.0
19 TraesCS2D01G186600 chrUn 85.535 719 74 17 1133 1844 17496755 17496060 0.000000e+00 725.0
20 TraesCS2D01G186600 chrUn 85.457 722 75 17 1130 1844 302453990 302454688 0.000000e+00 725.0
21 TraesCS2D01G186600 chrUn 85.457 722 75 17 1130 1844 330583694 330584392 0.000000e+00 725.0
22 TraesCS2D01G186600 chrUn 88.528 523 47 7 1838 2357 302454850 302455362 2.680000e-174 621.0
23 TraesCS2D01G186600 chrUn 88.528 523 47 7 1838 2357 330584554 330585066 2.680000e-174 621.0
24 TraesCS2D01G186600 chrUn 88.337 523 48 7 1838 2357 17495898 17495386 1.240000e-172 616.0
25 TraesCS2D01G186600 chrUn 93.798 258 7 2 1072 1329 17496873 17496625 1.780000e-101 379.0
26 TraesCS2D01G186600 chrUn 93.798 258 7 2 1072 1329 302453875 302454123 1.780000e-101 379.0
27 TraesCS2D01G186600 chrUn 93.798 258 7 2 1072 1329 330583579 330583827 1.780000e-101 379.0
28 TraesCS2D01G186600 chrUn 87.591 137 17 0 1250 1386 13406521 13406657 2.520000e-35 159.0
29 TraesCS2D01G186600 chr2B 88.528 523 46 7 1838 2357 184593037 184593548 2.680000e-174 621.0
30 TraesCS2D01G186600 chr2B 79.339 726 114 31 691 1406 184513225 184513924 6.130000e-131 477.0
31 TraesCS2D01G186600 chr2B 83.412 211 32 3 432 639 184493477 184493687 2.490000e-45 193.0
32 TraesCS2D01G186600 chr2B 91.111 45 4 0 2365 2409 703840195 703840151 7.320000e-06 62.1
33 TraesCS2D01G186600 chr6B 93.258 89 2 2 2365 2449 52151740 52151652 7.110000e-26 128.0
34 TraesCS2D01G186600 chr6B 91.176 68 5 1 2364 2430 712073013 712073080 9.330000e-15 91.6
35 TraesCS2D01G186600 chr1B 93.182 88 3 1 2365 2449 586140743 586140656 2.560000e-25 126.0
36 TraesCS2D01G186600 chr1B 92.647 68 4 1 2364 2430 354915443 354915510 2.010000e-16 97.1
37 TraesCS2D01G186600 chr1D 89.655 87 3 2 2364 2450 371254224 371254304 3.330000e-19 106.0
38 TraesCS2D01G186600 chr7B 92.537 67 4 1 2365 2430 148955286 148955220 7.210000e-16 95.3
39 TraesCS2D01G186600 chr3A 97.143 35 1 0 2365 2399 57224827 57224793 2.630000e-05 60.2
40 TraesCS2D01G186600 chr7A 96.875 32 1 0 316 347 720949390 720949359 1.000000e-03 54.7


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 TraesCS2D01G186600 chr2D 131123464 131125913 2449 False 4525.000000 4525 100.000000 1 2450 1 chr2D.!!$F3 2449
1 TraesCS2D01G186600 chr2D 131134187 131135628 1441 False 1032.000000 1430 89.521500 853 2357 2 chr2D.!!$F6 1504
2 TraesCS2D01G186600 chr2D 131052276 131052826 550 False 396.000000 396 79.789000 839 1406 1 chr2D.!!$F2 567
3 TraesCS2D01G186600 chr2D 130986602 130988641 2039 False 367.666667 488 81.673000 432 1765 3 chr2D.!!$F4 1333
4 TraesCS2D01G186600 chr2D 131041980 131043407 1427 False 314.000000 414 80.590667 807 1609 3 chr2D.!!$F5 802
5 TraesCS2D01G186600 chr2A 137211820 137214122 2302 False 1295.000000 2207 90.472000 218 2357 2 chr2A.!!$F4 2139
6 TraesCS2D01G186600 chr2A 137128050 137129823 1773 False 284.666667 446 80.773667 432 1597 3 chr2A.!!$F3 1165
7 TraesCS2D01G186600 chrUn 428032560 428033593 1033 False 1445.000000 1445 92.019000 41 1068 1 chrUn.!!$F2 1027
8 TraesCS2D01G186600 chrUn 302453875 302455362 1487 False 575.000000 725 89.261000 1072 2357 3 chrUn.!!$F3 1285
9 TraesCS2D01G186600 chrUn 330583579 330585066 1487 False 575.000000 725 89.261000 1072 2357 3 chrUn.!!$F4 1285
10 TraesCS2D01G186600 chrUn 17495386 17496873 1487 True 573.333333 725 89.223333 1072 2357 3 chrUn.!!$R1 1285
11 TraesCS2D01G186600 chr2B 184593037 184593548 511 False 621.000000 621 88.528000 1838 2357 1 chr2B.!!$F3 519
12 TraesCS2D01G186600 chr2B 184513225 184513924 699 False 477.000000 477 79.339000 691 1406 1 chr2B.!!$F2 715

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
145 146 0.038159 CTTGCGAGAACCGAGGAAGT 60.038 55.0 0.0 0.0 41.76 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1850 3579 0.033796 ATGCATGCACTAGTTGGCCT 60.034 50.0 25.37 0.0 0.0 5.19 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
30 31 2.572284 GCTCCCAGCGTCTACGTT 59.428 61.111 0.00 0.00 42.22 3.99
31 32 1.516603 GCTCCCAGCGTCTACGTTC 60.517 63.158 0.00 0.00 42.22 3.95
32 33 1.935327 GCTCCCAGCGTCTACGTTCT 61.935 60.000 0.00 0.00 42.22 3.01
33 34 1.376543 CTCCCAGCGTCTACGTTCTA 58.623 55.000 0.00 0.00 42.22 2.10
34 35 1.741706 CTCCCAGCGTCTACGTTCTAA 59.258 52.381 0.00 0.00 42.22 2.10
35 36 2.161855 TCCCAGCGTCTACGTTCTAAA 58.838 47.619 0.00 0.00 42.22 1.85
36 37 2.557924 TCCCAGCGTCTACGTTCTAAAA 59.442 45.455 0.00 0.00 42.22 1.52
37 38 3.005684 TCCCAGCGTCTACGTTCTAAAAA 59.994 43.478 0.00 0.00 42.22 1.94
145 146 0.038159 CTTGCGAGAACCGAGGAAGT 60.038 55.000 0.00 0.00 41.76 3.01
154 155 6.448006 CGAGAACCGAGGAAGTATATTCATT 58.552 40.000 0.00 0.00 41.76 2.57
254 256 8.702438 CATAACTGCACAAAACTTATTTCCTTG 58.298 33.333 0.00 0.00 0.00 3.61
264 266 4.934356 ACTTATTTCCTTGCCATCTCCAA 58.066 39.130 0.00 0.00 0.00 3.53
265 267 5.332743 ACTTATTTCCTTGCCATCTCCAAA 58.667 37.500 0.00 0.00 0.00 3.28
266 268 5.779771 ACTTATTTCCTTGCCATCTCCAAAA 59.220 36.000 0.00 0.00 0.00 2.44
267 269 6.269769 ACTTATTTCCTTGCCATCTCCAAAAA 59.730 34.615 0.00 0.00 0.00 1.94
270 272 5.565455 TTCCTTGCCATCTCCAAAAATTT 57.435 34.783 0.00 0.00 0.00 1.82
271 273 5.565455 TCCTTGCCATCTCCAAAAATTTT 57.435 34.783 0.00 0.00 0.00 1.82
355 359 6.300354 AGAAAACACTATGTTCCTTGTTCG 57.700 37.500 0.00 0.00 40.14 3.95
395 399 5.959618 TTCTTCTAACAAAAAGGCTAGCC 57.040 39.130 27.19 27.19 0.00 3.93
435 439 7.663081 TCTCTTCACATTCAAGCTGAATAGTTT 59.337 33.333 9.96 0.00 44.60 2.66
638 1464 4.392138 CCACAACGAGAAGGTATCCTTTTC 59.608 45.833 8.44 8.44 44.82 2.29
653 1483 5.545658 TCCTTTTCTACTTAAGCATTGCG 57.454 39.130 1.29 0.00 0.00 4.85
657 1487 6.260050 CCTTTTCTACTTAAGCATTGCGGATA 59.740 38.462 1.29 0.00 0.00 2.59
663 1493 9.582431 TCTACTTAAGCATTGCGGATAATATAC 57.418 33.333 1.29 0.00 0.00 1.47
676 1506 6.183359 GCGGATAATATACGTACTTGCTTGTC 60.183 42.308 6.75 0.00 39.30 3.18
722 1555 4.756642 CAGAACATTTGGTCTTCACAGCTA 59.243 41.667 0.00 0.00 39.48 3.32
760 1593 3.190118 GTGCTTGTACTGTCGTACCTACT 59.810 47.826 0.00 0.00 44.27 2.57
761 1594 4.393062 GTGCTTGTACTGTCGTACCTACTA 59.607 45.833 0.00 0.00 44.27 1.82
762 1595 4.393062 TGCTTGTACTGTCGTACCTACTAC 59.607 45.833 0.00 0.00 44.27 2.73
840 1703 6.821388 AGCAGATATAGACTCCAAAACGAAT 58.179 36.000 0.00 0.00 0.00 3.34
864 1745 5.914033 TGCATACAAGTAGATGACCTAACC 58.086 41.667 0.00 0.00 0.00 2.85
881 1762 2.629656 CCTGTTGCAAAGCTCCGGG 61.630 63.158 0.00 0.00 0.00 5.73
952 1845 3.776969 TGCTATCTCTCCCACACTCAAAT 59.223 43.478 0.00 0.00 0.00 2.32
1033 1942 2.167398 CTCCGCCGTTTTCCTCCTCA 62.167 60.000 0.00 0.00 0.00 3.86
1240 2263 4.431131 ACCTGCCATCCAAGCCGG 62.431 66.667 0.00 0.00 40.19 6.13
1248 2271 3.008517 TCCAAGCCGGAGATGCCA 61.009 61.111 5.05 0.00 39.64 4.92
1347 2370 0.606401 CAACGTTCCCAGAGGTGCAT 60.606 55.000 0.00 0.00 0.00 3.96
1351 2374 0.326264 GTTCCCAGAGGTGCATCTGT 59.674 55.000 2.86 0.00 44.35 3.41
1354 2377 0.545171 CCCAGAGGTGCATCTGTCAT 59.455 55.000 2.86 0.00 44.35 3.06
1457 2585 2.753966 CCAAGCCATGAGAACCGCG 61.754 63.158 0.00 0.00 0.00 6.46
1485 2613 6.801575 ACCAACATTGTTATTTCGTTGTTCT 58.198 32.000 0.86 0.00 36.15 3.01
1498 2633 2.407361 CGTTGTTCTTCGCTCGTACATT 59.593 45.455 0.00 0.00 0.00 2.71
1549 2685 6.491394 TCTGATTGTTTAGTTGTGGTTTTCG 58.509 36.000 0.00 0.00 0.00 3.46
1627 2780 4.074970 ACACCCTTTTGTCATAAGAGCAG 58.925 43.478 4.74 0.00 0.00 4.24
1692 2853 3.686227 TGCACCTATCCATTTCCCATT 57.314 42.857 0.00 0.00 0.00 3.16
1695 2856 3.960102 GCACCTATCCATTTCCCATTGAA 59.040 43.478 0.00 0.00 0.00 2.69
1807 2969 8.918202 ATCAGTAAGTTTTTGTGAATGGTCTA 57.082 30.769 0.00 0.00 0.00 2.59
1813 2976 6.569780 AGTTTTTGTGAATGGTCTAAACACC 58.430 36.000 0.00 0.00 36.90 4.16
1831 3005 2.057922 ACCAGTGATCAAGAGGGTGTT 58.942 47.619 0.00 0.00 0.00 3.32
1883 3612 3.319122 TGCATGCATGACTACTATCGAGT 59.681 43.478 30.64 0.00 39.92 4.18
1916 3645 2.432146 GCAGAGATCTGGGTGTCATGTA 59.568 50.000 11.63 0.00 43.94 2.29
1925 3654 6.499106 TCTGGGTGTCATGTATCAACATAT 57.501 37.500 0.00 0.00 44.70 1.78
1926 3655 7.610580 TCTGGGTGTCATGTATCAACATATA 57.389 36.000 0.00 0.00 44.70 0.86
1927 3656 8.206126 TCTGGGTGTCATGTATCAACATATAT 57.794 34.615 0.00 0.00 44.70 0.86
1928 3657 9.320295 TCTGGGTGTCATGTATCAACATATATA 57.680 33.333 0.00 0.00 44.70 0.86
1962 3692 1.202651 AGGGGTGTCAGACAACTTTCG 60.203 52.381 18.31 0.00 35.75 3.46
1990 3721 3.852471 TTCATCGAACGTGTTCACTTG 57.148 42.857 12.76 6.83 39.46 3.16
1996 3727 2.546778 GAACGTGTTCACTTGAGTGGA 58.453 47.619 10.97 0.00 45.65 4.02
2020 3751 9.620660 GGACAAATACGTTCAAATTGTTCTATT 57.379 29.630 0.00 0.00 34.59 1.73
2055 3790 8.093659 TGACATGTCGACAAATATTCAAAAGA 57.906 30.769 24.13 0.00 0.00 2.52
2104 3839 2.482721 CCAACATTACGAGTGTCCAACC 59.517 50.000 0.00 0.00 0.00 3.77
2168 3904 3.908382 CACAAGTTAAGCAATCGAGCAAC 59.092 43.478 0.00 0.00 36.85 4.17
2170 3906 1.732259 AGTTAAGCAATCGAGCAACCG 59.268 47.619 0.00 0.00 36.85 4.44
2185 3921 2.285977 CAACCGAACTATAACCAGGGC 58.714 52.381 0.00 0.00 0.00 5.19
2196 3932 0.251077 AACCAGGGCTTGAAGCTCAG 60.251 55.000 20.53 11.50 46.44 3.35
2208 3944 7.663493 GGGCTTGAAGCTCAGAAATAGTTATAT 59.337 37.037 17.59 0.00 42.59 0.86
2306 4042 7.737972 TGAACTCAAATATTCGGACTTTCAA 57.262 32.000 0.00 0.00 0.00 2.69
2318 4054 7.938563 TTCGGACTTTCAAATTTGTTAATGG 57.061 32.000 17.47 6.47 0.00 3.16
2319 4055 6.451393 TCGGACTTTCAAATTTGTTAATGGG 58.549 36.000 17.47 4.94 0.00 4.00
2320 4056 5.120053 CGGACTTTCAAATTTGTTAATGGGC 59.880 40.000 17.47 6.00 0.00 5.36
2321 4057 6.230472 GGACTTTCAAATTTGTTAATGGGCT 58.770 36.000 17.47 0.00 0.00 5.19
2376 4112 8.050325 TCATCTAGATGAGAACTAGCTATACCC 58.950 40.741 27.93 0.00 42.42 3.69
2377 4113 6.408035 TCTAGATGAGAACTAGCTATACCCG 58.592 44.000 0.00 0.00 37.73 5.28
2378 4114 4.988029 AGATGAGAACTAGCTATACCCGT 58.012 43.478 0.00 0.00 0.00 5.28
2379 4115 4.762765 AGATGAGAACTAGCTATACCCGTG 59.237 45.833 0.00 0.00 0.00 4.94
2380 4116 2.621998 TGAGAACTAGCTATACCCGTGC 59.378 50.000 0.00 0.00 0.00 5.34
2381 4117 1.607628 AGAACTAGCTATACCCGTGCG 59.392 52.381 0.00 0.00 0.00 5.34
2382 4118 0.672342 AACTAGCTATACCCGTGCGG 59.328 55.000 3.25 3.25 37.81 5.69
2383 4119 1.080705 CTAGCTATACCCGTGCGGC 60.081 63.158 4.91 0.00 33.26 6.53
2384 4120 2.797866 CTAGCTATACCCGTGCGGCG 62.798 65.000 0.51 0.51 40.95 6.46
2403 4139 4.386951 CACGCCACACCCCATCGA 62.387 66.667 0.00 0.00 0.00 3.59
2404 4140 3.399181 ACGCCACACCCCATCGAT 61.399 61.111 0.00 0.00 0.00 3.59
2405 4141 2.061578 ACGCCACACCCCATCGATA 61.062 57.895 0.00 0.00 0.00 2.92
2406 4142 1.300931 CGCCACACCCCATCGATAG 60.301 63.158 0.00 0.00 0.00 2.08
2423 4159 5.792631 TCGATAGATACGCGTGTGTATATG 58.207 41.667 24.59 18.03 42.67 1.78
2424 4160 4.433624 CGATAGATACGCGTGTGTATATGC 59.566 45.833 24.59 10.70 35.24 3.14
2425 4161 3.917329 AGATACGCGTGTGTATATGCT 57.083 42.857 24.59 3.39 35.24 3.79
2426 4162 6.509039 CGATAGATACGCGTGTGTATATGCTA 60.509 42.308 24.59 11.20 35.24 3.49
2427 4163 4.720090 AGATACGCGTGTGTATATGCTAC 58.280 43.478 24.59 0.00 35.24 3.58
2428 4164 4.454847 AGATACGCGTGTGTATATGCTACT 59.545 41.667 24.59 0.93 35.24 2.57
2429 4165 3.431922 ACGCGTGTGTATATGCTACTT 57.568 42.857 12.93 0.00 0.00 2.24
2430 4166 3.113322 ACGCGTGTGTATATGCTACTTG 58.887 45.455 12.93 0.00 0.00 3.16
2431 4167 3.113322 CGCGTGTGTATATGCTACTTGT 58.887 45.455 0.00 0.00 0.00 3.16
2432 4168 3.179795 CGCGTGTGTATATGCTACTTGTC 59.820 47.826 0.00 0.00 0.00 3.18
2433 4169 3.179795 GCGTGTGTATATGCTACTTGTCG 59.820 47.826 0.00 0.00 0.00 4.35
2434 4170 4.348656 CGTGTGTATATGCTACTTGTCGT 58.651 43.478 0.00 0.00 0.00 4.34
2435 4171 4.204370 CGTGTGTATATGCTACTTGTCGTG 59.796 45.833 0.00 0.00 0.00 4.35
2436 4172 4.503007 GTGTGTATATGCTACTTGTCGTGG 59.497 45.833 0.00 0.00 0.00 4.94
2437 4173 4.158949 TGTGTATATGCTACTTGTCGTGGT 59.841 41.667 0.00 0.00 0.00 4.16
2438 4174 5.357596 TGTGTATATGCTACTTGTCGTGGTA 59.642 40.000 0.00 0.00 0.00 3.25
2439 4175 5.684626 GTGTATATGCTACTTGTCGTGGTAC 59.315 44.000 0.00 0.00 0.00 3.34
2440 4176 5.591472 TGTATATGCTACTTGTCGTGGTACT 59.409 40.000 0.00 0.00 0.00 2.73
2441 4177 3.955650 ATGCTACTTGTCGTGGTACTT 57.044 42.857 0.00 0.00 0.00 2.24
2442 4178 3.738830 TGCTACTTGTCGTGGTACTTT 57.261 42.857 0.00 0.00 0.00 2.66
2443 4179 3.645884 TGCTACTTGTCGTGGTACTTTC 58.354 45.455 0.00 0.00 0.00 2.62
2444 4180 3.068448 TGCTACTTGTCGTGGTACTTTCA 59.932 43.478 0.00 0.00 0.00 2.69
2445 4181 4.243270 GCTACTTGTCGTGGTACTTTCAT 58.757 43.478 0.00 0.00 0.00 2.57
2446 4182 4.326548 GCTACTTGTCGTGGTACTTTCATC 59.673 45.833 0.00 0.00 0.00 2.92
2447 4183 4.602340 ACTTGTCGTGGTACTTTCATCT 57.398 40.909 0.00 0.00 0.00 2.90
2448 4184 4.957296 ACTTGTCGTGGTACTTTCATCTT 58.043 39.130 0.00 0.00 0.00 2.40
2449 4185 4.989168 ACTTGTCGTGGTACTTTCATCTTC 59.011 41.667 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.516603 GAACGTAGACGCTGGGAGC 60.517 63.158 1.14 0.00 44.43 4.70
14 15 1.376543 TAGAACGTAGACGCTGGGAG 58.623 55.000 1.14 0.00 44.43 4.30
15 16 1.825090 TTAGAACGTAGACGCTGGGA 58.175 50.000 1.14 0.00 44.43 4.37
16 17 2.642139 TTTAGAACGTAGACGCTGGG 57.358 50.000 1.14 0.00 44.43 4.45
68 69 4.448395 CCAAAATGTGCAAACGTGAATCAT 59.552 37.500 0.00 0.00 0.00 2.45
104 105 7.651808 CAAGAGGCAAAACTGAGAGATAAAAA 58.348 34.615 0.00 0.00 0.00 1.94
154 155 6.413783 TGTTTGGACTGTACAGATTAGTCA 57.586 37.500 29.30 16.52 41.93 3.41
254 256 4.186856 TCCGAAAATTTTTGGAGATGGC 57.813 40.909 28.94 3.58 44.01 4.40
270 272 8.289618 CAGTGAAGAGATTACAAAAATTCCGAA 58.710 33.333 0.00 0.00 0.00 4.30
271 273 7.659799 TCAGTGAAGAGATTACAAAAATTCCGA 59.340 33.333 0.00 0.00 0.00 4.55
395 399 8.970859 AATGTGAAGAGAACTGAATAATAGGG 57.029 34.615 0.00 0.00 0.00 3.53
435 439 5.725325 TGATGGCATCAAATGAAACAAGA 57.275 34.783 27.03 0.00 36.11 3.02
638 1464 8.532341 CGTATATTATCCGCAATGCTTAAGTAG 58.468 37.037 2.94 0.00 0.00 2.57
653 1483 8.813643 AAGACAAGCAAGTACGTATATTATCC 57.186 34.615 0.00 0.00 0.00 2.59
684 1514 9.184523 CCAAATGTTCTGTCAAAGGGTATATTA 57.815 33.333 0.00 0.00 0.00 0.98
685 1515 7.673926 ACCAAATGTTCTGTCAAAGGGTATATT 59.326 33.333 0.00 0.00 0.00 1.28
686 1516 7.182060 ACCAAATGTTCTGTCAAAGGGTATAT 58.818 34.615 0.00 0.00 0.00 0.86
688 1518 5.393866 ACCAAATGTTCTGTCAAAGGGTAT 58.606 37.500 0.00 0.00 0.00 2.73
696 1529 4.522114 TGTGAAGACCAAATGTTCTGTCA 58.478 39.130 0.00 0.00 31.74 3.58
701 1534 5.452777 GTTAGCTGTGAAGACCAAATGTTC 58.547 41.667 0.00 0.00 0.00 3.18
722 1555 3.703001 AGCACATACAGCTGTTAGGTT 57.297 42.857 27.06 7.80 41.61 3.50
840 1703 6.156256 AGGTTAGGTCATCTACTTGTATGCAA 59.844 38.462 0.00 0.00 0.00 4.08
864 1745 2.956987 CCCGGAGCTTTGCAACAG 59.043 61.111 0.73 1.22 0.00 3.16
952 1845 3.774528 CTAGCCTGGGCAGTGCGA 61.775 66.667 14.39 0.00 44.88 5.10
1033 1942 3.583806 CAACGCATGAGAGAAGAAGACT 58.416 45.455 2.50 0.00 0.00 3.24
1245 2268 1.751927 CACCTTGGGCATCTCTGGC 60.752 63.158 0.00 0.00 46.82 4.85
1246 2269 1.077212 CCACCTTGGGCATCTCTGG 60.077 63.158 0.00 0.00 32.67 3.86
1247 2270 0.107312 CTCCACCTTGGGCATCTCTG 60.107 60.000 0.00 0.00 38.32 3.35
1248 2271 1.919600 GCTCCACCTTGGGCATCTCT 61.920 60.000 0.00 0.00 38.32 3.10
1347 2370 4.128580 TCCGGCTTGGATGACAGA 57.871 55.556 0.00 0.00 43.74 3.41
1457 2585 6.639279 ACAACGAAATAACAATGTTGGTAAGC 59.361 34.615 9.15 0.00 43.08 3.09
1485 2613 3.581024 ACAGGTAAATGTACGAGCGAA 57.419 42.857 0.00 0.00 0.00 4.70
1498 2633 1.134640 ACACGACACAGCAACAGGTAA 60.135 47.619 0.00 0.00 0.00 2.85
1549 2685 1.512926 AATCACTCACAACACTCGCC 58.487 50.000 0.00 0.00 0.00 5.54
1627 2780 7.308435 ACTTAGAAGCATGCATACTTTTGAAC 58.692 34.615 21.98 0.87 0.00 3.18
1718 2879 8.851145 GGAGACTTAAGGTTGAAGAGAAAAATT 58.149 33.333 7.53 0.00 0.00 1.82
1786 2948 9.016623 GTGTTTAGACCATTCACAAAAACTTAC 57.983 33.333 0.00 0.00 0.00 2.34
1794 2956 4.578516 CACTGGTGTTTAGACCATTCACAA 59.421 41.667 0.00 0.00 45.19 3.33
1795 2957 4.133820 CACTGGTGTTTAGACCATTCACA 58.866 43.478 0.00 0.00 45.19 3.58
1798 2960 5.245531 TGATCACTGGTGTTTAGACCATTC 58.754 41.667 0.00 0.00 45.19 2.67
1801 2963 4.346709 TCTTGATCACTGGTGTTTAGACCA 59.653 41.667 0.00 0.00 44.09 4.02
1807 2969 2.443255 ACCCTCTTGATCACTGGTGTTT 59.557 45.455 0.00 0.00 0.00 2.83
1813 2976 4.013267 AGAAACACCCTCTTGATCACTG 57.987 45.455 0.00 0.00 0.00 3.66
1821 2984 3.174779 GAGACCCTAGAAACACCCTCTT 58.825 50.000 0.00 0.00 0.00 2.85
1831 3005 3.117813 GCCTCTCTAGTGAGACCCTAGAA 60.118 52.174 20.81 0.00 43.73 2.10
1850 3579 0.033796 ATGCATGCACTAGTTGGCCT 60.034 50.000 25.37 0.00 0.00 5.19
1854 3583 4.186926 AGTAGTCATGCATGCACTAGTTG 58.813 43.478 25.37 17.25 0.00 3.16
1883 3612 0.969149 ATCTCTGCCACGTCTGTTCA 59.031 50.000 0.00 0.00 0.00 3.18
1916 3645 8.306761 TCATCAGCGTTGTCTATATATGTTGAT 58.693 33.333 0.00 0.00 31.57 2.57
1925 3654 2.628178 CCCCTCATCAGCGTTGTCTATA 59.372 50.000 0.00 0.00 0.00 1.31
1926 3655 1.414181 CCCCTCATCAGCGTTGTCTAT 59.586 52.381 0.00 0.00 0.00 1.98
1927 3656 0.824109 CCCCTCATCAGCGTTGTCTA 59.176 55.000 0.00 0.00 0.00 2.59
1928 3657 1.194781 ACCCCTCATCAGCGTTGTCT 61.195 55.000 0.00 0.00 0.00 3.41
1962 3692 6.138081 GTGAACACGTTCGATGAAAGTAAAAC 59.862 38.462 5.51 0.00 42.28 2.43
1990 3721 6.435428 ACAATTTGAACGTATTTGTCCACTC 58.565 36.000 2.79 0.00 0.00 3.51
1996 3727 9.405587 CCAATAGAACAATTTGAACGTATTTGT 57.594 29.630 2.79 0.00 32.19 2.83
2020 3751 3.244044 TGTCGACATGTCAGTTTCATCCA 60.244 43.478 24.93 5.23 0.00 3.41
2104 3839 5.006746 GGCGTCTCAGTCAATATTTTGTAGG 59.993 44.000 0.00 0.00 34.32 3.18
2149 3885 2.159627 CGGTTGCTCGATTGCTTAACTT 59.840 45.455 0.00 0.00 0.00 2.66
2158 3894 4.117685 GGTTATAGTTCGGTTGCTCGATT 58.882 43.478 0.00 0.00 39.03 3.34
2168 3904 2.169769 TCAAGCCCTGGTTATAGTTCGG 59.830 50.000 0.00 0.00 0.00 4.30
2170 3906 3.628032 GCTTCAAGCCCTGGTTATAGTTC 59.372 47.826 0.00 0.00 34.48 3.01
2185 3921 9.770097 TCCATATAACTATTTCTGAGCTTCAAG 57.230 33.333 0.00 0.00 0.00 3.02
2208 3944 3.916359 TGGTCGTTGCCTATTTATCCA 57.084 42.857 0.00 0.00 0.00 3.41
2212 3948 5.644636 CCTAAAGTTGGTCGTTGCCTATTTA 59.355 40.000 0.00 0.00 0.00 1.40
2300 4036 8.619546 TGAAAAGCCCATTAACAAATTTGAAAG 58.380 29.630 24.64 6.53 0.00 2.62
2306 4042 6.880529 CCAGATGAAAAGCCCATTAACAAATT 59.119 34.615 0.00 0.00 0.00 1.82
2317 4053 3.287867 TCTCATCCAGATGAAAAGCCC 57.712 47.619 11.30 0.00 46.10 5.19
2318 4054 5.848833 AATTCTCATCCAGATGAAAAGCC 57.151 39.130 11.30 0.00 46.10 4.35
2319 4055 7.714377 TCTCTAATTCTCATCCAGATGAAAAGC 59.286 37.037 11.30 0.00 46.10 3.51
2320 4056 9.610705 TTCTCTAATTCTCATCCAGATGAAAAG 57.389 33.333 11.30 1.16 46.10 2.27
2321 4057 9.610705 CTTCTCTAATTCTCATCCAGATGAAAA 57.389 33.333 11.30 5.41 46.10 2.29
2357 4093 4.616373 GCACGGGTATAGCTAGTTCTCATC 60.616 50.000 0.00 0.00 0.00 2.92
2358 4094 3.256136 GCACGGGTATAGCTAGTTCTCAT 59.744 47.826 0.00 0.00 0.00 2.90
2359 4095 2.621998 GCACGGGTATAGCTAGTTCTCA 59.378 50.000 0.00 0.00 0.00 3.27
2360 4096 2.350580 CGCACGGGTATAGCTAGTTCTC 60.351 54.545 0.00 0.00 0.00 2.87
2361 4097 1.607628 CGCACGGGTATAGCTAGTTCT 59.392 52.381 0.00 0.00 0.00 3.01
2362 4098 1.335689 CCGCACGGGTATAGCTAGTTC 60.336 57.143 0.00 0.00 0.00 3.01
2363 4099 0.672342 CCGCACGGGTATAGCTAGTT 59.328 55.000 0.00 0.00 0.00 2.24
2364 4100 1.803366 GCCGCACGGGTATAGCTAGT 61.803 60.000 11.65 0.13 38.44 2.57
2365 4101 1.080705 GCCGCACGGGTATAGCTAG 60.081 63.158 11.65 0.00 38.44 3.42
2366 4102 2.911484 CGCCGCACGGGTATAGCTA 61.911 63.158 11.65 0.00 38.44 3.32
2367 4103 4.280494 CGCCGCACGGGTATAGCT 62.280 66.667 11.65 0.00 38.44 3.32
2386 4122 2.304901 TATCGATGGGGTGTGGCGTG 62.305 60.000 8.54 0.00 0.00 5.34
2387 4123 2.028125 CTATCGATGGGGTGTGGCGT 62.028 60.000 8.54 0.00 0.00 5.68
2388 4124 1.300931 CTATCGATGGGGTGTGGCG 60.301 63.158 8.54 0.00 0.00 5.69
2389 4125 0.687354 ATCTATCGATGGGGTGTGGC 59.313 55.000 8.54 0.00 0.00 5.01
2390 4126 2.094700 CGTATCTATCGATGGGGTGTGG 60.095 54.545 8.54 0.00 0.00 4.17
2391 4127 2.671351 GCGTATCTATCGATGGGGTGTG 60.671 54.545 8.54 0.00 0.00 3.82
2392 4128 1.544691 GCGTATCTATCGATGGGGTGT 59.455 52.381 8.54 0.00 0.00 4.16
2393 4129 1.467543 CGCGTATCTATCGATGGGGTG 60.468 57.143 8.54 0.00 0.00 4.61
2394 4130 0.809385 CGCGTATCTATCGATGGGGT 59.191 55.000 8.54 0.00 0.00 4.95
2395 4131 0.809385 ACGCGTATCTATCGATGGGG 59.191 55.000 11.67 0.00 0.00 4.96
2396 4132 1.199327 ACACGCGTATCTATCGATGGG 59.801 52.381 13.44 0.73 0.00 4.00
2397 4133 2.242564 CACACGCGTATCTATCGATGG 58.757 52.381 13.44 5.03 0.00 3.51
2398 4134 2.917363 ACACACGCGTATCTATCGATG 58.083 47.619 13.44 0.00 0.00 3.84
2399 4135 4.941325 ATACACACGCGTATCTATCGAT 57.059 40.909 13.44 2.16 0.00 3.59
2400 4136 5.725864 GCATATACACACGCGTATCTATCGA 60.726 44.000 13.44 0.00 34.03 3.59
2401 4137 4.433624 GCATATACACACGCGTATCTATCG 59.566 45.833 13.44 0.00 34.03 2.92
2402 4138 5.570344 AGCATATACACACGCGTATCTATC 58.430 41.667 13.44 0.00 34.03 2.08
2403 4139 5.562506 AGCATATACACACGCGTATCTAT 57.437 39.130 13.44 9.11 34.03 1.98
2404 4140 5.640783 AGTAGCATATACACACGCGTATCTA 59.359 40.000 13.44 0.82 34.03 1.98
2405 4141 3.917329 AGCATATACACACGCGTATCT 57.083 42.857 13.44 0.00 34.03 1.98
2406 4142 4.720090 AGTAGCATATACACACGCGTATC 58.280 43.478 13.44 0.00 34.03 2.24
2407 4143 4.761235 AGTAGCATATACACACGCGTAT 57.239 40.909 13.44 0.00 36.13 3.06
2408 4144 4.201940 ACAAGTAGCATATACACACGCGTA 60.202 41.667 13.44 0.00 0.00 4.42
2409 4145 3.113322 CAAGTAGCATATACACACGCGT 58.887 45.455 5.58 5.58 0.00 6.01
2410 4146 3.113322 ACAAGTAGCATATACACACGCG 58.887 45.455 3.53 3.53 0.00 6.01
2411 4147 3.179795 CGACAAGTAGCATATACACACGC 59.820 47.826 0.00 0.00 0.00 5.34
2412 4148 4.204370 CACGACAAGTAGCATATACACACG 59.796 45.833 0.00 0.00 0.00 4.49
2413 4149 4.503007 CCACGACAAGTAGCATATACACAC 59.497 45.833 0.00 0.00 0.00 3.82
2414 4150 4.158949 ACCACGACAAGTAGCATATACACA 59.841 41.667 0.00 0.00 0.00 3.72
2415 4151 4.679662 ACCACGACAAGTAGCATATACAC 58.320 43.478 0.00 0.00 0.00 2.90
2416 4152 4.994907 ACCACGACAAGTAGCATATACA 57.005 40.909 0.00 0.00 0.00 2.29
2417 4153 6.069684 AGTACCACGACAAGTAGCATATAC 57.930 41.667 0.00 0.00 0.00 1.47
2418 4154 6.704289 AAGTACCACGACAAGTAGCATATA 57.296 37.500 0.00 0.00 0.00 0.86
2419 4155 5.593679 AAGTACCACGACAAGTAGCATAT 57.406 39.130 0.00 0.00 0.00 1.78
2420 4156 5.047872 TGAAAGTACCACGACAAGTAGCATA 60.048 40.000 0.00 0.00 0.00 3.14
2421 4157 3.955650 AAGTACCACGACAAGTAGCAT 57.044 42.857 0.00 0.00 0.00 3.79
2422 4158 3.068448 TGAAAGTACCACGACAAGTAGCA 59.932 43.478 0.00 0.00 0.00 3.49
2423 4159 3.645884 TGAAAGTACCACGACAAGTAGC 58.354 45.455 0.00 0.00 0.00 3.58
2424 4160 5.710984 AGATGAAAGTACCACGACAAGTAG 58.289 41.667 0.00 0.00 0.00 2.57
2425 4161 5.717078 AGATGAAAGTACCACGACAAGTA 57.283 39.130 0.00 0.00 0.00 2.24
2426 4162 4.602340 AGATGAAAGTACCACGACAAGT 57.398 40.909 0.00 0.00 0.00 3.16
2427 4163 5.517037 GAAGATGAAAGTACCACGACAAG 57.483 43.478 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.