Multiple sequence alignment - TraesCS2B01G038700

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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 TraesCS2B01G038700 chr2B 100.000 3394 0 0 1 3394 17884297 17880904 0.000000e+00 6268.0
1 TraesCS2B01G038700 chr2B 92.356 1125 68 11 1384 2498 17873752 17872636 0.000000e+00 1585.0
2 TraesCS2B01G038700 chr2B 90.573 1082 92 5 1387 2458 24089827 24090908 0.000000e+00 1424.0
3 TraesCS2B01G038700 chr2B 81.102 254 27 14 679 915 752784792 752785041 2.080000e-42 183.0
4 TraesCS2B01G038700 chr2A 91.222 2062 117 30 1374 3394 12103039 12101001 0.000000e+00 2747.0
5 TraesCS2B01G038700 chr2A 91.921 1510 99 11 1374 2860 12073222 12071713 0.000000e+00 2091.0
6 TraesCS2B01G038700 chr2A 92.955 1022 72 0 1375 2396 12048330 12047309 0.000000e+00 1489.0
7 TraesCS2B01G038700 chr2A 90.175 1140 88 8 1376 2498 15395140 15396272 0.000000e+00 1463.0
8 TraesCS2B01G038700 chr2A 87.852 922 94 5 4 917 12104336 12103425 0.000000e+00 1066.0
9 TraesCS2B01G038700 chr2A 91.392 546 34 6 2858 3394 12071684 12071143 0.000000e+00 736.0
10 TraesCS2B01G038700 chr2A 93.309 269 11 4 994 1257 12073487 12073221 1.140000e-104 390.0
11 TraesCS2B01G038700 chr2A 92.989 271 12 4 994 1257 12103308 12103038 4.110000e-104 388.0
12 TraesCS2B01G038700 chr2A 91.829 257 15 5 995 1248 15394873 15395126 1.500000e-93 353.0
13 TraesCS2B01G038700 chr2A 91.051 257 20 2 995 1248 12048598 12048342 9.020000e-91 344.0
14 TraesCS2B01G038700 chr2A 95.939 197 8 0 997 1193 747087088 747087284 1.520000e-83 320.0
15 TraesCS2B01G038700 chr2A 81.452 248 25 14 682 913 747086693 747086935 2.080000e-42 183.0
16 TraesCS2B01G038700 chr2A 76.136 352 70 7 1 345 327150413 327150757 4.500000e-39 172.0
17 TraesCS2B01G038700 chr2A 75.207 242 53 6 108 345 566082303 566082065 1.290000e-19 108.0
18 TraesCS2B01G038700 chr2D 93.113 1118 45 7 1753 2859 11495755 11494659 0.000000e+00 1609.0
19 TraesCS2B01G038700 chr2D 91.031 1115 92 4 1333 2439 11477781 11476667 0.000000e+00 1498.0
20 TraesCS2B01G038700 chr2D 93.060 1023 71 0 1374 2396 11509647 11508625 0.000000e+00 1496.0
21 TraesCS2B01G038700 chr2D 90.018 1132 97 8 1376 2498 13421721 13422845 0.000000e+00 1450.0
22 TraesCS2B01G038700 chr2D 87.608 1162 128 11 1386 2531 617052665 617053826 0.000000e+00 1334.0
23 TraesCS2B01G038700 chr2D 93.349 421 26 2 2975 3394 11485817 11485398 3.720000e-174 621.0
24 TraesCS2B01G038700 chr2D 84.628 631 44 27 676 1257 11510272 11509646 2.270000e-161 579.0
25 TraesCS2B01G038700 chr2D 94.774 287 12 2 982 1267 11478067 11477783 8.640000e-121 444.0
26 TraesCS2B01G038700 chr2D 91.071 280 9 3 994 1257 13421437 13421716 6.920000e-97 364.0
27 TraesCS2B01G038700 chr2D 88.148 270 22 7 316 580 11510571 11510307 2.540000e-81 313.0
28 TraesCS2B01G038700 chr2D 78.481 316 60 7 15 325 164743337 164743025 2.070000e-47 200.0
29 TraesCS2B01G038700 chr2D 78.161 348 42 18 585 921 11496977 11496653 1.240000e-44 191.0
30 TraesCS2B01G038700 chr2D 82.203 236 24 12 679 898 617050974 617051207 1.610000e-43 187.0
31 TraesCS2B01G038700 chr2D 75.931 349 56 18 1 345 647564518 647564194 1.630000e-33 154.0
32 TraesCS2B01G038700 chr2D 83.824 136 13 6 731 857 11478339 11478204 1.650000e-23 121.0
33 TraesCS2B01G038700 chr2D 83.721 86 3 4 495 579 11497027 11496952 1.690000e-08 71.3
34 TraesCS2B01G038700 chr2D 91.111 45 3 1 1332 1375 199761250 199761206 3.660000e-05 60.2
35 TraesCS2B01G038700 chr3B 78.704 324 55 9 1 323 584532144 584531834 1.600000e-48 204.0
36 TraesCS2B01G038700 chr6D 78.182 330 59 9 1 323 121158882 121158559 7.430000e-47 198.0
37 TraesCS2B01G038700 chr6D 90.667 75 7 0 1256 1330 190909359 190909285 2.150000e-17 100.0
38 TraesCS2B01G038700 chr6D 88.750 80 9 0 1252 1331 414526261 414526182 7.750000e-17 99.0
39 TraesCS2B01G038700 chr6D 89.474 76 8 0 1256 1331 29741081 29741006 2.790000e-16 97.1
40 TraesCS2B01G038700 chr3A 76.486 370 70 13 1 362 717293992 717293632 5.780000e-43 185.0
41 TraesCS2B01G038700 chr3A 92.857 42 2 1 1335 1376 485595246 485595286 3.660000e-05 60.2
42 TraesCS2B01G038700 chr3A 92.857 42 2 1 1335 1376 485679867 485679907 3.660000e-05 60.2
43 TraesCS2B01G038700 chr7B 77.377 305 58 9 1 300 596997165 596996867 1.620000e-38 171.0
44 TraesCS2B01G038700 chr5B 77.134 328 45 23 1 323 606279820 606280122 2.710000e-36 163.0
45 TraesCS2B01G038700 chr1D 76.994 326 48 19 1 323 384471666 384471365 9.750000e-36 161.0
46 TraesCS2B01G038700 chr1D 88.406 69 7 1 355 422 461003091 461003023 7.810000e-12 82.4
47 TraesCS2B01G038700 chr1D 92.683 41 3 0 1335 1375 260568893 260568853 3.660000e-05 60.2
48 TraesCS2B01G038700 chr1B 74.590 366 84 8 1 362 423715651 423715291 5.870000e-33 152.0
49 TraesCS2B01G038700 chr4A 86.466 133 18 0 1 133 503239868 503240000 2.730000e-31 147.0
50 TraesCS2B01G038700 chr6A 76.923 260 49 8 90 345 79308747 79308495 1.640000e-28 137.0
51 TraesCS2B01G038700 chr6A 97.059 34 1 0 389 422 531331462 531331429 1.320000e-04 58.4
52 TraesCS2B01G038700 chr3D 90.909 77 7 0 1255 1331 368377685 368377761 1.670000e-18 104.0
53 TraesCS2B01G038700 chr3D 90.789 76 7 0 1256 1331 398703775 398703850 5.990000e-18 102.0
54 TraesCS2B01G038700 chr3D 89.610 77 8 0 1255 1331 517884733 517884809 7.750000e-17 99.0
55 TraesCS2B01G038700 chr5D 89.610 77 8 0 1255 1331 277816471 277816395 7.750000e-17 99.0
56 TraesCS2B01G038700 chr1A 91.549 71 6 0 1256 1326 411923352 411923422 7.750000e-17 99.0
57 TraesCS2B01G038700 chr1A 89.286 56 5 1 367 421 64515715 64515770 6.080000e-08 69.4
58 TraesCS2B01G038700 chr4B 95.122 41 2 0 1337 1377 43110916 43110876 7.860000e-07 65.8
59 TraesCS2B01G038700 chr5A 89.583 48 4 1 1332 1378 536862516 536862563 3.660000e-05 60.2
60 TraesCS2B01G038700 chr7D 89.362 47 4 1 1331 1376 556998817 556998771 1.320000e-04 58.4


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 TraesCS2B01G038700 chr2B 17880904 17884297 3393 True 6268.000000 6268 100.000000 1 3394 1 chr2B.!!$R2 3393
1 TraesCS2B01G038700 chr2B 17872636 17873752 1116 True 1585.000000 1585 92.356000 1384 2498 1 chr2B.!!$R1 1114
2 TraesCS2B01G038700 chr2B 24089827 24090908 1081 False 1424.000000 1424 90.573000 1387 2458 1 chr2B.!!$F1 1071
3 TraesCS2B01G038700 chr2A 12101001 12104336 3335 True 1400.333333 2747 90.687667 4 3394 3 chr2A.!!$R4 3390
4 TraesCS2B01G038700 chr2A 12071143 12073487 2344 True 1072.333333 2091 92.207333 994 3394 3 chr2A.!!$R3 2400
5 TraesCS2B01G038700 chr2A 12047309 12048598 1289 True 916.500000 1489 92.003000 995 2396 2 chr2A.!!$R2 1401
6 TraesCS2B01G038700 chr2A 15394873 15396272 1399 False 908.000000 1463 91.002000 995 2498 2 chr2A.!!$F2 1503
7 TraesCS2B01G038700 chr2A 747086693 747087284 591 False 251.500000 320 88.695500 682 1193 2 chr2A.!!$F3 511
8 TraesCS2B01G038700 chr2D 13421437 13422845 1408 False 907.000000 1450 90.544500 994 2498 2 chr2D.!!$F1 1504
9 TraesCS2B01G038700 chr2D 11508625 11510571 1946 True 796.000000 1496 88.612000 316 2396 3 chr2D.!!$R7 2080
10 TraesCS2B01G038700 chr2D 617050974 617053826 2852 False 760.500000 1334 84.905500 679 2531 2 chr2D.!!$F2 1852
11 TraesCS2B01G038700 chr2D 11476667 11478339 1672 True 687.666667 1498 89.876333 731 2439 3 chr2D.!!$R5 1708
12 TraesCS2B01G038700 chr2D 11494659 11497027 2368 True 623.766667 1609 84.998333 495 2859 3 chr2D.!!$R6 2364

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
764 828 0.108709 TGGTTGGTATGGACGTACGC 60.109 55.0 16.72 8.19 0.0 4.42 F
2126 3367 0.032678 CCGTCTTCTGGATAGCGCAT 59.967 55.0 11.47 0.06 0.0 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2199 3445 0.673985 TATTCGGAGAGGACATGCCG 59.326 55.0 0.0 0.0 44.83 5.69 R
3227 4560 0.463654 TGCTTGCAACGGAGACAACT 60.464 50.0 0.0 0.0 0.00 3.16 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
25 26 0.241213 TTGCTCAGGAAGACGAGACG 59.759 55.000 0.00 0.00 0.00 4.18
30 31 2.126031 GGAAGACGAGACGGTGGC 60.126 66.667 0.00 0.00 0.00 5.01
52 53 3.697166 GGCTCCCTGAAGTTGGAATAAA 58.303 45.455 0.00 0.00 0.00 1.40
59 60 5.122396 CCCTGAAGTTGGAATAAAGTTCTCG 59.878 44.000 6.18 0.00 39.32 4.04
61 62 5.305585 TGAAGTTGGAATAAAGTTCTCGCT 58.694 37.500 6.18 0.00 39.32 4.93
71 72 3.068691 TTCTCGCTGCGTAGGCCT 61.069 61.111 22.48 11.78 38.85 5.19
76 77 3.188786 GCTGCGTAGGCCTCGTTG 61.189 66.667 9.68 10.91 38.85 4.10
77 78 2.571757 CTGCGTAGGCCTCGTTGA 59.428 61.111 9.68 0.00 38.85 3.18
106 107 2.045242 TAGCGTCGTCAGAGGGCT 60.045 61.111 0.00 0.00 39.65 5.19
108 109 1.934220 TAGCGTCGTCAGAGGGCTTG 61.934 60.000 0.00 0.00 38.08 4.01
110 111 1.734477 CGTCGTCAGAGGGCTTGTG 60.734 63.158 0.00 0.00 0.00 3.33
122 123 0.179018 GGCTTGTGGAGGTGTGTCTT 60.179 55.000 0.00 0.00 0.00 3.01
136 137 1.337071 GTGTCTTCGGCGGATCTCATA 59.663 52.381 7.21 0.00 0.00 2.15
159 160 4.098196 AGGATTTAGTCGGTGCTAGTCTTC 59.902 45.833 0.00 0.00 0.00 2.87
174 175 1.817099 CTTCGGTGGATCTGCCTGC 60.817 63.158 0.00 0.00 37.63 4.85
180 181 0.818445 GTGGATCTGCCTGCATCCAG 60.818 60.000 13.35 6.11 43.13 3.86
183 184 0.469070 GATCTGCCTGCATCCAGTCT 59.531 55.000 11.96 3.56 37.38 3.24
186 187 0.809385 CTGCCTGCATCCAGTCTTTG 59.191 55.000 5.77 0.00 37.38 2.77
195 196 4.937620 TGCATCCAGTCTTTGTATGTCTTC 59.062 41.667 0.00 0.00 0.00 2.87
206 207 3.472652 TGTATGTCTTCGTTTGTGCCTT 58.527 40.909 0.00 0.00 0.00 4.35
209 210 5.703592 TGTATGTCTTCGTTTGTGCCTTTAT 59.296 36.000 0.00 0.00 0.00 1.40
217 218 3.754323 CGTTTGTGCCTTTATAGGTTGGA 59.246 43.478 0.90 0.00 44.00 3.53
223 224 5.201243 GTGCCTTTATAGGTTGGATCCTTT 58.799 41.667 14.23 0.00 44.00 3.11
225 226 4.515567 GCCTTTATAGGTTGGATCCTTTCG 59.484 45.833 14.23 0.00 44.00 3.46
226 227 5.681639 CCTTTATAGGTTGGATCCTTTCGT 58.318 41.667 14.23 7.45 38.86 3.85
237 238 7.983484 GGTTGGATCCTTTCGTTTATACTTCTA 59.017 37.037 14.23 0.00 0.00 2.10
249 250 9.731819 TCGTTTATACTTCTATTCATCAGTGAC 57.268 33.333 0.00 0.00 33.11 3.67
268 269 1.299089 GGTTGTTGTTCTGGTGCGC 60.299 57.895 0.00 0.00 0.00 6.09
277 278 3.730761 CTGGTGCGCTGGTTCTGC 61.731 66.667 9.73 0.00 0.00 4.26
287 288 0.466189 CTGGTTCTGCGGGGCATTAT 60.466 55.000 0.00 0.00 38.13 1.28
299 300 2.277084 GGGCATTATCACGACGACTTT 58.723 47.619 0.00 0.00 0.00 2.66
314 315 5.503683 CGACGACTTTCCGATTGTCTACTAT 60.504 44.000 0.00 0.00 0.00 2.12
327 328 7.277981 CGATTGTCTACTATAACAAGTTTGGCT 59.722 37.037 0.00 0.00 38.66 4.75
345 346 1.476110 GCTTAGCTCCGGAGAGAGAGA 60.476 57.143 35.69 12.26 43.39 3.10
346 347 2.814097 GCTTAGCTCCGGAGAGAGAGAT 60.814 54.545 35.69 9.07 43.39 2.75
375 378 1.022735 CGTCGCTAGGTGGTCTACAT 58.977 55.000 0.00 0.00 0.00 2.29
381 384 3.568430 CGCTAGGTGGTCTACATACATGA 59.432 47.826 0.00 0.00 0.00 3.07
425 433 1.346395 TCTTTGTACTGCCATGGTCGT 59.654 47.619 14.67 12.99 0.00 4.34
427 435 2.264005 TTGTACTGCCATGGTCGTTT 57.736 45.000 14.67 0.00 0.00 3.60
429 437 1.202710 TGTACTGCCATGGTCGTTTGT 60.203 47.619 14.67 6.19 0.00 2.83
432 440 0.950836 CTGCCATGGTCGTTTGTTCA 59.049 50.000 14.67 0.00 0.00 3.18
442 450 4.022242 TGGTCGTTTGTTCAAAAGTTTCCA 60.022 37.500 9.98 12.54 0.00 3.53
443 451 5.106442 GGTCGTTTGTTCAAAAGTTTCCAT 58.894 37.500 9.98 0.00 0.00 3.41
445 453 4.564769 TCGTTTGTTCAAAAGTTTCCATGC 59.435 37.500 9.98 0.00 0.00 4.06
453 461 7.336427 TGTTCAAAAGTTTCCATGCAAGAAAAT 59.664 29.630 14.74 11.89 35.13 1.82
492 500 4.048241 AGCGAGGTATAGAAAGCAAGTC 57.952 45.455 0.00 0.00 0.00 3.01
520 528 7.060633 AGCAAATATCGAACAATTGTCGTTTTC 59.939 33.333 12.39 4.33 0.00 2.29
560 568 2.124570 CGGCCACATCTTCCCCTG 60.125 66.667 2.24 0.00 0.00 4.45
591 600 5.402292 CCCTACCTACCTATTAGTTCCCCTT 60.402 48.000 0.00 0.00 0.00 3.95
593 602 4.969133 ACCTACCTATTAGTTCCCCTTGT 58.031 43.478 0.00 0.00 0.00 3.16
623 632 6.474630 CCTACCTACCTAGTAGATGTGGTAG 58.525 48.000 19.96 19.96 39.71 3.18
755 812 0.395036 TGGCCGGATTGGTTGGTATG 60.395 55.000 5.05 0.00 41.21 2.39
764 828 0.108709 TGGTTGGTATGGACGTACGC 60.109 55.000 16.72 8.19 0.00 4.42
919 1003 1.813337 CATATCACCACACCGCGCA 60.813 57.895 8.75 0.00 0.00 6.09
920 1004 1.813753 ATATCACCACACCGCGCAC 60.814 57.895 8.75 0.00 0.00 5.34
940 1075 2.557372 TACGCGTCACACAGAGCCA 61.557 57.895 18.63 0.00 0.00 4.75
1227 2419 6.947733 TCCATTCTTCTTTGCCATCTCTTTTA 59.052 34.615 0.00 0.00 0.00 1.52
1230 2425 7.765695 TTCTTCTTTGCCATCTCTTTTATGT 57.234 32.000 0.00 0.00 0.00 2.29
1343 2541 0.033366 TGAGACGCACTAGCTTGCAA 59.967 50.000 10.83 0.00 43.15 4.08
1562 2765 0.597568 CGGCACAGAAGGCAATCAAA 59.402 50.000 0.00 0.00 0.00 2.69
1577 2780 2.860971 AAAGAGTGGGGCCAGCCT 60.861 61.111 4.39 0.00 36.10 4.58
1667 2870 1.522580 GACCAAGATGCTCGGCCTC 60.523 63.158 0.00 0.00 0.00 4.70
1763 2966 0.180406 ACCTTGCTGAGAACAACCGT 59.820 50.000 0.00 0.00 0.00 4.83
2060 3301 0.173481 TCTCCAAGAACATCGAGCGG 59.827 55.000 0.00 0.00 0.00 5.52
2126 3367 0.032678 CCGTCTTCTGGATAGCGCAT 59.967 55.000 11.47 0.06 0.00 4.73
2535 3801 6.091986 TGCATTCTCCTGTTTGTTTGTTTTTC 59.908 34.615 0.00 0.00 0.00 2.29
2553 3820 7.488322 TGTTTTTCGTTTTTGATTGAGAGGAT 58.512 30.769 0.00 0.00 0.00 3.24
2650 3917 1.652563 GTTTTCGTGGGCTCACACC 59.347 57.895 18.70 0.00 43.79 4.16
2667 3934 2.004017 CACCGCGCATTTACTTCCTTA 58.996 47.619 8.75 0.00 0.00 2.69
2686 3953 1.008538 GCACGGGTTGTTTCAGCAG 60.009 57.895 0.00 0.00 0.00 4.24
2699 3966 4.127171 GTTTCAGCAGTGTCTTCCTTACA 58.873 43.478 0.00 0.00 0.00 2.41
2755 4033 2.156051 AACCAAGTCTCGGCCGAGTC 62.156 60.000 44.61 40.01 42.49 3.36
2772 4050 7.586300 CGGCCGAGTCATAAAACATATAAAAAG 59.414 37.037 24.07 0.00 0.00 2.27
2905 4232 5.946942 TCTCTATCATTTCTCTTGCTGGT 57.053 39.130 0.00 0.00 0.00 4.00
2906 4233 5.911752 TCTCTATCATTTCTCTTGCTGGTC 58.088 41.667 0.00 0.00 0.00 4.02
2920 4247 1.069204 GCTGGTCAAGCGATCCTATGA 59.931 52.381 0.00 0.00 43.45 2.15
2930 4257 2.349817 GCGATCCTATGAAAACGCATGG 60.350 50.000 0.00 0.00 39.52 3.66
2942 4269 2.887360 GCATGGCCATTTCAGCGT 59.113 55.556 17.92 0.00 0.00 5.07
2943 4270 1.226773 GCATGGCCATTTCAGCGTC 60.227 57.895 17.92 0.00 0.00 5.19
2952 4279 2.222213 CCATTTCAGCGTCGTGTAAACA 59.778 45.455 0.00 0.00 0.00 2.83
3105 4437 5.492895 CTCTCCCATACGATAGCTAGAAGA 58.507 45.833 0.00 0.00 42.67 2.87
3215 4548 2.743718 CCACTGCCAGACGAGGTT 59.256 61.111 0.00 0.00 0.00 3.50
3227 4560 3.079578 AGACGAGGTTCTTGTCGACATA 58.920 45.455 20.80 8.12 46.37 2.29
3244 4577 3.067106 ACATAGTTGTCTCCGTTGCAAG 58.933 45.455 0.00 0.00 0.00 4.01
3253 4586 2.127118 CGTTGCAAGCAAGCTCCG 60.127 61.111 7.88 4.51 36.52 4.63
3296 4629 5.130477 TGCCCTTCCACTAGAAACTAATAGG 59.870 44.000 0.00 0.00 32.88 2.57
3308 4641 5.893255 AGAAACTAATAGGGCATTTGCATCA 59.107 36.000 4.74 0.00 44.36 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.000163 TCGTCTTCCTGAGCAAGACAC 60.000 52.381 15.86 0.00 46.99 3.67
2 3 1.270826 CTCGTCTTCCTGAGCAAGACA 59.729 52.381 15.86 3.29 46.99 3.41
8 9 1.137825 CCGTCTCGTCTTCCTGAGC 59.862 63.158 0.00 0.00 32.20 4.26
25 26 4.785453 CTTCAGGGAGCCGCCACC 62.785 72.222 0.00 0.00 38.95 4.61
30 31 0.035056 ATTCCAACTTCAGGGAGCCG 60.035 55.000 0.00 0.00 34.02 5.52
37 38 5.409826 AGCGAGAACTTTATTCCAACTTCAG 59.590 40.000 0.00 0.00 0.00 3.02
52 53 2.182030 GCCTACGCAGCGAGAACT 59.818 61.111 24.65 0.00 34.03 3.01
59 60 3.188786 CAACGAGGCCTACGCAGC 61.189 66.667 20.11 0.97 36.38 5.25
61 62 2.571757 CTCAACGAGGCCTACGCA 59.428 61.111 20.11 7.56 36.38 5.24
71 72 2.481969 GCTAGATGCATCACCTCAACGA 60.482 50.000 27.81 1.59 42.31 3.85
76 77 1.777101 GACGCTAGATGCATCACCTC 58.223 55.000 27.81 12.68 43.06 3.85
77 78 0.031314 CGACGCTAGATGCATCACCT 59.969 55.000 27.81 10.67 43.06 4.00
79 80 1.124462 GACGACGCTAGATGCATCAC 58.876 55.000 27.81 15.54 43.06 3.06
86 87 1.448922 GCCCTCTGACGACGCTAGAT 61.449 60.000 0.00 0.00 0.00 1.98
96 97 1.298014 CCTCCACAAGCCCTCTGAC 59.702 63.158 0.00 0.00 0.00 3.51
106 107 0.105964 CCGAAGACACACCTCCACAA 59.894 55.000 0.00 0.00 0.00 3.33
108 109 1.668151 GCCGAAGACACACCTCCAC 60.668 63.158 0.00 0.00 0.00 4.02
110 111 2.432628 CGCCGAAGACACACCTCC 60.433 66.667 0.00 0.00 0.00 4.30
122 123 1.924731 AATCCTATGAGATCCGCCGA 58.075 50.000 0.00 0.00 0.00 5.54
136 137 3.633418 AGACTAGCACCGACTAAATCCT 58.367 45.455 0.00 0.00 0.00 3.24
159 160 1.890979 GATGCAGGCAGATCCACCG 60.891 63.158 0.00 0.00 37.29 4.94
180 181 4.904154 GCACAAACGAAGACATACAAAGAC 59.096 41.667 0.00 0.00 0.00 3.01
183 184 3.880490 AGGCACAAACGAAGACATACAAA 59.120 39.130 0.00 0.00 0.00 2.83
186 187 4.483476 AAAGGCACAAACGAAGACATAC 57.517 40.909 0.00 0.00 0.00 2.39
206 207 9.768662 GTATAAACGAAAGGATCCAACCTATAA 57.231 33.333 15.82 0.00 39.62 0.98
209 210 7.427989 AGTATAAACGAAAGGATCCAACCTA 57.572 36.000 15.82 0.00 39.62 3.08
223 224 9.731819 GTCACTGATGAATAGAAGTATAAACGA 57.268 33.333 0.00 0.00 36.31 3.85
225 226 8.969267 CCGTCACTGATGAATAGAAGTATAAAC 58.031 37.037 0.00 0.00 36.31 2.01
226 227 8.692710 ACCGTCACTGATGAATAGAAGTATAAA 58.307 33.333 0.00 0.00 36.31 1.40
237 238 3.476552 ACAACAACCGTCACTGATGAAT 58.523 40.909 0.00 0.00 36.31 2.57
243 244 1.330521 CCAGAACAACAACCGTCACTG 59.669 52.381 0.00 0.00 0.00 3.66
246 247 1.374560 CACCAGAACAACAACCGTCA 58.625 50.000 0.00 0.00 0.00 4.35
247 248 0.028902 GCACCAGAACAACAACCGTC 59.971 55.000 0.00 0.00 0.00 4.79
249 250 1.010125 CGCACCAGAACAACAACCG 60.010 57.895 0.00 0.00 0.00 4.44
268 269 0.466189 ATAATGCCCCGCAGAACCAG 60.466 55.000 0.00 0.00 43.65 4.00
277 278 1.066752 TCGTCGTGATAATGCCCCG 59.933 57.895 0.00 0.00 0.00 5.73
284 285 3.770263 ATCGGAAAGTCGTCGTGATAA 57.230 42.857 0.00 0.00 0.00 1.75
287 288 1.001048 ACAATCGGAAAGTCGTCGTGA 60.001 47.619 0.00 0.00 0.00 4.35
299 300 7.762615 CCAAACTTGTTATAGTAGACAATCGGA 59.237 37.037 3.23 0.00 35.44 4.55
314 315 3.071479 CGGAGCTAAGCCAAACTTGTTA 58.929 45.455 0.00 0.00 39.58 2.41
327 328 2.439880 TCATCTCTCTCTCCGGAGCTAA 59.560 50.000 27.39 12.85 39.31 3.09
345 346 1.266175 CCTAGCGACGACCGTTATCAT 59.734 52.381 0.00 0.00 41.15 2.45
346 347 0.659427 CCTAGCGACGACCGTTATCA 59.341 55.000 0.00 0.00 41.15 2.15
425 433 6.169094 TCTTGCATGGAAACTTTTGAACAAA 58.831 32.000 0.00 0.00 0.00 2.83
427 435 5.336150 TCTTGCATGGAAACTTTTGAACA 57.664 34.783 0.00 0.00 0.00 3.18
429 437 7.862512 ATTTTCTTGCATGGAAACTTTTGAA 57.137 28.000 8.14 0.00 33.22 2.69
442 450 7.219322 ACTTTGAGCCTTTTATTTTCTTGCAT 58.781 30.769 0.00 0.00 0.00 3.96
443 451 6.581712 ACTTTGAGCCTTTTATTTTCTTGCA 58.418 32.000 0.00 0.00 0.00 4.08
445 453 8.822652 ATGACTTTGAGCCTTTTATTTTCTTG 57.177 30.769 0.00 0.00 0.00 3.02
453 461 4.827692 TCGCTATGACTTTGAGCCTTTTA 58.172 39.130 0.00 0.00 32.35 1.52
492 500 5.794945 ACGACAATTGTTCGATATTTGCTTG 59.205 36.000 26.23 4.20 0.00 4.01
520 528 2.229543 CCACATCACCATTCACACCAAG 59.770 50.000 0.00 0.00 0.00 3.61
560 568 4.756203 AATAGGTAGGTAGGGGAGTACC 57.244 50.000 0.00 0.00 42.68 3.34
591 600 3.752596 ACTAGGTAGGTAGGGGAGTACA 58.247 50.000 0.00 0.00 0.00 2.90
593 602 5.440179 TCTACTAGGTAGGTAGGGGAGTA 57.560 47.826 0.00 0.00 36.83 2.59
623 632 3.093278 CTTGAACCGCTCCGATGC 58.907 61.111 0.00 0.00 0.00 3.91
628 637 1.373748 TACGTGCTTGAACCGCTCC 60.374 57.895 0.00 0.00 0.00 4.70
779 843 1.270305 CGAATGCGGGGTATGAGATGT 60.270 52.381 0.00 0.00 0.00 3.06
925 1009 3.044305 GGTGGCTCTGTGTGACGC 61.044 66.667 0.00 0.00 0.00 5.19
928 1012 0.610174 GAGATGGTGGCTCTGTGTGA 59.390 55.000 0.00 0.00 0.00 3.58
929 1013 0.738762 CGAGATGGTGGCTCTGTGTG 60.739 60.000 0.00 0.00 0.00 3.82
930 1014 1.593787 CGAGATGGTGGCTCTGTGT 59.406 57.895 0.00 0.00 0.00 3.72
982 1117 1.131504 CATCGATCTCCGGCTAGCTAC 59.868 57.143 15.72 0.00 39.14 3.58
1227 2419 2.739943 TGTCCATCCGAGAGAAGACAT 58.260 47.619 0.00 0.00 0.00 3.06
1230 2425 1.410517 GCATGTCCATCCGAGAGAAGA 59.589 52.381 0.00 0.00 0.00 2.87
1364 2562 6.542005 TGAAGCATTGTTTGTTACTCTCTTCA 59.458 34.615 0.00 0.00 35.35 3.02
1367 2565 7.516198 AATGAAGCATTGTTTGTTACTCTCT 57.484 32.000 0.00 0.00 32.39 3.10
1372 2570 6.701400 ACCTGAAATGAAGCATTGTTTGTTAC 59.299 34.615 0.00 0.00 34.04 2.50
1556 2759 0.613012 GCTGGCCCCACTCTTTGATT 60.613 55.000 0.00 0.00 0.00 2.57
1577 2780 1.006758 AGGTGGGTGATCTTAGACCGA 59.993 52.381 0.00 0.00 32.48 4.69
1646 2849 1.078848 GCCGAGCATCTTGGTCAGT 60.079 57.895 7.39 0.00 44.51 3.41
1667 2870 2.809601 CGCTTCACGGAAGGACGG 60.810 66.667 13.33 0.00 39.76 4.79
1670 2873 3.296709 GAGGCGCTTCACGGAAGGA 62.297 63.158 15.47 0.00 43.93 3.36
1673 2876 1.741401 CATGAGGCGCTTCACGGAA 60.741 57.895 25.51 0.95 43.93 4.30
2060 3301 1.069935 GAATGCGTCCTCTAGGGCC 59.930 63.158 0.00 0.00 36.14 5.80
2199 3445 0.673985 TATTCGGAGAGGACATGCCG 59.326 55.000 0.00 0.00 44.83 5.69
2535 3801 5.824904 ATCCATCCTCTCAATCAAAAACG 57.175 39.130 0.00 0.00 0.00 3.60
2650 3917 1.663643 TGCTAAGGAAGTAAATGCGCG 59.336 47.619 0.00 0.00 0.00 6.86
2667 3934 1.447317 CTGCTGAAACAACCCGTGCT 61.447 55.000 0.00 0.00 0.00 4.40
2686 3953 3.265791 CTGGCTCATGTAAGGAAGACAC 58.734 50.000 0.00 0.00 0.00 3.67
2805 4085 9.268268 GTTGATGTTATATTCGTGGGATCTTTA 57.732 33.333 0.00 0.00 0.00 1.85
2905 4232 2.607635 GCGTTTTCATAGGATCGCTTGA 59.392 45.455 12.35 0.00 40.39 3.02
2906 4233 2.351418 TGCGTTTTCATAGGATCGCTTG 59.649 45.455 17.58 0.00 43.23 4.01
2915 4242 3.441496 AATGGCCATGCGTTTTCATAG 57.559 42.857 21.63 0.00 0.00 2.23
2920 4247 1.940752 GCTGAAATGGCCATGCGTTTT 60.941 47.619 21.63 10.36 0.00 2.43
2930 4257 0.793861 TTACACGACGCTGAAATGGC 59.206 50.000 0.00 0.00 0.00 4.40
2952 4279 6.699204 CAGTCTGACAGCGAACATAGAATAAT 59.301 38.462 10.88 0.00 0.00 1.28
3105 4437 2.351276 GGTCGTGGCATTCCTGGT 59.649 61.111 0.00 0.00 0.00 4.00
3227 4560 0.463654 TGCTTGCAACGGAGACAACT 60.464 50.000 0.00 0.00 0.00 3.16
3238 4571 3.673484 GCCGGAGCTTGCTTGCAA 61.673 61.111 5.05 7.83 35.50 4.08
3253 4586 2.229784 GCATGCCATAAAGGTGATAGCC 59.770 50.000 6.36 0.00 40.61 3.93
3258 4591 0.630673 AGGGCATGCCATAAAGGTGA 59.369 50.000 36.56 0.00 40.61 4.02
3296 4629 6.238610 TGTACAAAATTTGATGCAAATGCC 57.761 33.333 13.19 0.00 42.32 4.40
3308 4641 6.701400 GCTTCCATCTGTGTTGTACAAAATTT 59.299 34.615 10.51 0.00 39.20 1.82


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

AutoCloner maintained by Alex Coulton.