Multiple sequence alignment - TraesCS4B01G280100

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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 TraesCS4B01G280100 chr4B 100.000 3531 0 0 1 3531 562929287 562925757 0.000000e+00 6521.0
1 TraesCS4B01G280100 chr4B 91.373 1020 72 15 2522 3530 562913377 562912363 0.000000e+00 1382.0
2 TraesCS4B01G280100 chr4B 86.310 840 99 10 2637 3464 562885685 562884850 0.000000e+00 900.0
3 TraesCS4B01G280100 chr4B 94.574 129 7 0 2522 2650 562912104 562911976 2.150000e-47 200.0
4 TraesCS4B01G280100 chr4A 91.263 1980 85 41 531 2464 16505187 16507124 0.000000e+00 2617.0
5 TraesCS4B01G280100 chr4A 90.207 868 53 17 2522 3370 16507547 16508401 0.000000e+00 1103.0
6 TraesCS4B01G280100 chr4A 87.293 362 17 5 7 366 16504609 16504943 1.540000e-103 387.0
7 TraesCS4B01G280100 chr4D 88.949 2018 87 55 513 2467 450149102 450147158 0.000000e+00 2366.0
8 TraesCS4B01G280100 chr4D 86.047 559 26 12 11 548 450149629 450149102 1.430000e-153 553.0
9 TraesCS4B01G280100 chr5B 86.922 887 89 23 2576 3442 550420134 550421013 0.000000e+00 970.0
10 TraesCS4B01G280100 chr5B 86.944 674 58 18 2725 3393 705876903 705876255 0.000000e+00 730.0
11 TraesCS4B01G280100 chr5B 79.781 638 103 20 2767 3389 606837333 606836707 1.160000e-119 440.0
12 TraesCS4B01G280100 chr5B 80.503 318 45 11 3080 3389 606844526 606844218 9.860000e-56 228.0
13 TraesCS4B01G280100 chr5A 79.896 766 97 27 2538 3291 693652026 693651306 3.140000e-140 508.0
14 TraesCS4B01G280100 chr5D 90.032 311 23 8 2756 3062 438341372 438341678 2.550000e-106 396.0
15 TraesCS4B01G280100 chr5D 85.323 402 33 15 2522 2918 438340869 438341249 3.300000e-105 392.0
16 TraesCS4B01G280100 chr1A 77.641 407 70 7 1373 1779 426882260 426881875 9.860000e-56 228.0
17 TraesCS4B01G280100 chr1A 77.821 257 42 12 3081 3325 550823338 550823591 1.020000e-30 145.0
18 TraesCS4B01G280100 chr1D 81.685 273 47 2 1507 1779 329725997 329725728 1.280000e-54 224.0
19 TraesCS4B01G280100 chr1B 77.396 407 71 7 1373 1779 444682785 444682400 4.590000e-54 222.0
20 TraesCS4B01G280100 chr1B 76.825 315 50 18 3024 3325 629071210 629071514 4.720000e-34 156.0
21 TraesCS4B01G280100 chr2A 82.963 135 19 3 2842 2975 72756890 72756759 6.190000e-23 119.0
22 TraesCS4B01G280100 chr2A 75.833 240 40 12 2713 2942 775010616 775010385 4.820000e-19 106.0
23 TraesCS4B01G280100 chr3B 100.000 28 0 0 2711 2738 42184454 42184427 6.000000e-03 52.8
24 TraesCS4B01G280100 chr3A 100.000 28 0 0 2711 2738 655575311 655575338 6.000000e-03 52.8


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 TraesCS4B01G280100 chr4B 562925757 562929287 3530 True 6521.0 6521 100.000000 1 3531 1 chr4B.!!$R2 3530
1 TraesCS4B01G280100 chr4B 562884850 562885685 835 True 900.0 900 86.310000 2637 3464 1 chr4B.!!$R1 827
2 TraesCS4B01G280100 chr4B 562911976 562913377 1401 True 791.0 1382 92.973500 2522 3530 2 chr4B.!!$R3 1008
3 TraesCS4B01G280100 chr4A 16504609 16508401 3792 False 1369.0 2617 89.587667 7 3370 3 chr4A.!!$F1 3363
4 TraesCS4B01G280100 chr4D 450147158 450149629 2471 True 1459.5 2366 87.498000 11 2467 2 chr4D.!!$R1 2456
5 TraesCS4B01G280100 chr5B 550420134 550421013 879 False 970.0 970 86.922000 2576 3442 1 chr5B.!!$F1 866
6 TraesCS4B01G280100 chr5B 705876255 705876903 648 True 730.0 730 86.944000 2725 3393 1 chr5B.!!$R3 668
7 TraesCS4B01G280100 chr5B 606836707 606837333 626 True 440.0 440 79.781000 2767 3389 1 chr5B.!!$R1 622
8 TraesCS4B01G280100 chr5A 693651306 693652026 720 True 508.0 508 79.896000 2538 3291 1 chr5A.!!$R1 753
9 TraesCS4B01G280100 chr5D 438340869 438341678 809 False 394.0 396 87.677500 2522 3062 2 chr5D.!!$F1 540

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
804 1078 0.108089 TTTATTAGCGACGCAGGCCA 60.108 50.0 23.7 0.0 0.0 5.36 F
876 1164 0.320374 TGCAACGTTACCCTCTCTGG 59.680 55.0 0.0 0.0 0.0 3.86 F
1573 1894 0.601841 GAGTTCGCCCGGTTCAAGAA 60.602 55.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1993 2326 1.984570 CCGAACTCCTCCTCCAGCA 60.985 63.158 0.00 0.00 0.00 4.41 R
2153 2486 3.758088 CTCCATGTCGGCGTCGGAG 62.758 68.421 10.62 17.24 37.52 4.63 R
3509 4579 0.035056 ATCTCCAAGGGAAGCAACGG 60.035 55.000 0.00 0.00 0.00 4.44 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
108 115 0.458669 CTTCACATGCAAGATGGGGC 59.541 55.000 0.00 0.00 0.00 5.80
148 155 7.833682 TGTCAAAAATAGATCATCTGCCCTTAA 59.166 33.333 0.00 0.00 0.00 1.85
182 194 6.146673 GCAACAAATCTCAAGAAAAATGGAGG 59.853 38.462 0.00 0.00 0.00 4.30
183 195 7.436118 CAACAAATCTCAAGAAAAATGGAGGA 58.564 34.615 0.00 0.00 0.00 3.71
226 238 2.127758 CACGACCAAAGCGCGTTC 60.128 61.111 8.43 0.00 35.90 3.95
238 250 1.636340 CGCGTTCCCAAATAGCTCG 59.364 57.895 0.00 0.00 0.00 5.03
242 254 2.095415 GCGTTCCCAAATAGCTCGTTTT 60.095 45.455 0.00 0.00 0.00 2.43
243 255 3.743886 CGTTCCCAAATAGCTCGTTTTC 58.256 45.455 0.00 0.00 0.00 2.29
244 256 3.435671 CGTTCCCAAATAGCTCGTTTTCT 59.564 43.478 0.00 0.00 0.00 2.52
245 257 4.628333 CGTTCCCAAATAGCTCGTTTTCTA 59.372 41.667 0.00 0.00 0.00 2.10
246 258 5.121142 CGTTCCCAAATAGCTCGTTTTCTAA 59.879 40.000 0.00 0.00 0.00 2.10
247 259 6.183360 CGTTCCCAAATAGCTCGTTTTCTAAT 60.183 38.462 0.00 0.00 0.00 1.73
248 260 6.920569 TCCCAAATAGCTCGTTTTCTAATC 57.079 37.500 0.00 0.00 0.00 1.75
249 261 6.650120 TCCCAAATAGCTCGTTTTCTAATCT 58.350 36.000 0.00 0.00 0.00 2.40
250 262 7.788026 TCCCAAATAGCTCGTTTTCTAATCTA 58.212 34.615 0.00 0.00 0.00 1.98
251 263 8.262227 TCCCAAATAGCTCGTTTTCTAATCTAA 58.738 33.333 0.00 0.00 0.00 2.10
252 264 9.057089 CCCAAATAGCTCGTTTTCTAATCTAAT 57.943 33.333 0.00 0.00 0.00 1.73
316 330 1.135199 ACGAGCACGACGGAACATAAT 60.135 47.619 11.40 0.00 42.66 1.28
317 331 2.097954 ACGAGCACGACGGAACATAATA 59.902 45.455 11.40 0.00 42.66 0.98
318 332 2.466571 CGAGCACGACGGAACATAATAC 59.533 50.000 0.00 0.00 42.66 1.89
356 370 2.549563 CCACGAGGATTGGGAGATGATG 60.550 54.545 0.00 0.00 36.89 3.07
399 624 2.225041 TGAGAGAGAGGGAGAAACGGAA 60.225 50.000 0.00 0.00 0.00 4.30
424 649 3.936453 CGTGAGTTACTGAGAGCTCTACT 59.064 47.826 18.25 16.09 0.00 2.57
426 651 5.756347 CGTGAGTTACTGAGAGCTCTACTAT 59.244 44.000 18.25 5.35 0.00 2.12
472 697 2.480845 GTGTGAAACGTAGCTCAAGGT 58.519 47.619 0.00 0.00 42.39 3.50
488 713 3.505680 TCAAGGTTGCATTACATGGACAC 59.494 43.478 0.00 0.00 0.00 3.67
495 720 5.109500 TGCATTACATGGACACATCCTTA 57.891 39.130 0.00 0.00 46.43 2.69
505 730 1.884579 ACACATCCTTACACTCGTCGT 59.115 47.619 0.00 0.00 0.00 4.34
516 741 0.526662 ACTCGTCGTGTCCCATCTTC 59.473 55.000 0.00 0.00 0.00 2.87
566 827 9.962759 TTCTTCTTAAATTTTATTAGCGACGTC 57.037 29.630 5.18 5.18 0.00 4.34
579 840 1.709760 GACGTCGACACATGCATGG 59.290 57.895 29.41 20.05 0.00 3.66
610 871 1.083489 TGCTTTCCTAATGAACGGCG 58.917 50.000 4.80 4.80 35.77 6.46
638 899 5.005586 CCATGTGTTGCCAATAAATTTAGCG 59.994 40.000 3.94 0.00 0.00 4.26
662 933 7.148355 GGGGACGTTGAACTAATTAATTCAA 57.852 36.000 16.02 16.02 41.38 2.69
687 960 0.393077 GTGCCCACGCCTATATCTGT 59.607 55.000 0.00 0.00 0.00 3.41
691 964 1.273606 CCCACGCCTATATCTGTCCAG 59.726 57.143 0.00 0.00 0.00 3.86
756 1030 1.978080 TGGCCATCATGCACACCAC 60.978 57.895 0.00 0.00 0.00 4.16
757 1031 2.713967 GGCCATCATGCACACCACC 61.714 63.158 0.00 0.00 0.00 4.61
758 1032 1.978080 GCCATCATGCACACCACCA 60.978 57.895 0.00 0.00 0.00 4.17
766 1040 0.826672 TGCACACCACCATGAATGCA 60.827 50.000 0.00 0.00 40.57 3.96
772 1046 3.579586 ACACCACCATGAATGCAATTTCT 59.420 39.130 0.00 0.00 36.07 2.52
775 1049 4.186159 CCACCATGAATGCAATTTCTTCC 58.814 43.478 0.00 0.00 36.07 3.46
802 1076 2.817538 TTTTTATTAGCGACGCAGGC 57.182 45.000 23.70 0.00 0.00 4.85
803 1077 1.011333 TTTTATTAGCGACGCAGGCC 58.989 50.000 23.70 0.00 0.00 5.19
804 1078 0.108089 TTTATTAGCGACGCAGGCCA 60.108 50.000 23.70 0.00 0.00 5.36
805 1079 0.529773 TTATTAGCGACGCAGGCCAG 60.530 55.000 23.70 0.00 0.00 4.85
829 1103 1.412710 AGGGCGAATTCGATGCTTCTA 59.587 47.619 31.01 0.00 43.02 2.10
830 1104 2.037772 AGGGCGAATTCGATGCTTCTAT 59.962 45.455 31.01 3.11 43.02 1.98
872 1160 0.608640 CTCCTGCAACGTTACCCTCT 59.391 55.000 0.00 0.00 0.00 3.69
873 1161 0.606604 TCCTGCAACGTTACCCTCTC 59.393 55.000 0.00 0.00 0.00 3.20
874 1162 0.608640 CCTGCAACGTTACCCTCTCT 59.391 55.000 0.00 0.00 0.00 3.10
875 1163 1.673033 CCTGCAACGTTACCCTCTCTG 60.673 57.143 0.00 0.00 0.00 3.35
876 1164 0.320374 TGCAACGTTACCCTCTCTGG 59.680 55.000 0.00 0.00 0.00 3.86
877 1165 0.606604 GCAACGTTACCCTCTCTGGA 59.393 55.000 0.00 0.00 38.35 3.86
878 1166 1.207329 GCAACGTTACCCTCTCTGGAT 59.793 52.381 0.00 0.00 38.35 3.41
879 1167 2.354805 GCAACGTTACCCTCTCTGGATT 60.355 50.000 0.00 0.00 38.35 3.01
882 1170 3.170717 ACGTTACCCTCTCTGGATTGAA 58.829 45.455 0.00 0.00 38.35 2.69
909 1197 7.874016 TGAATTGTAATCAAGTTGGTACGTAGT 59.126 33.333 2.34 0.00 40.06 2.73
973 1266 1.961277 CGATGGGCAAGGCGGTATC 60.961 63.158 0.00 0.00 0.00 2.24
980 1273 2.064014 GGCAAGGCGGTATCGTATTAC 58.936 52.381 0.00 0.00 38.89 1.89
989 1285 6.038050 AGGCGGTATCGTATTACTATTCTAGC 59.962 42.308 0.00 0.00 38.89 3.42
1178 1481 1.685077 CCCAGGAGAGAGCAGCAGA 60.685 63.158 0.00 0.00 0.00 4.26
1179 1482 1.678598 CCCAGGAGAGAGCAGCAGAG 61.679 65.000 0.00 0.00 0.00 3.35
1180 1483 1.142314 CAGGAGAGAGCAGCAGAGC 59.858 63.158 0.00 0.00 0.00 4.09
1181 1484 2.059786 AGGAGAGAGCAGCAGAGCC 61.060 63.158 0.00 0.00 34.23 4.70
1182 1485 2.357575 GGAGAGAGCAGCAGAGCCA 61.358 63.158 0.00 0.00 34.23 4.75
1183 1486 1.142314 GAGAGAGCAGCAGAGCCAG 59.858 63.158 0.00 0.00 34.23 4.85
1184 1487 1.305129 AGAGAGCAGCAGAGCCAGA 60.305 57.895 0.00 0.00 34.23 3.86
1185 1488 1.142314 GAGAGCAGCAGAGCCAGAG 59.858 63.158 0.00 0.00 34.23 3.35
1186 1489 2.512057 GAGCAGCAGAGCCAGAGC 60.512 66.667 0.00 0.00 40.32 4.09
1270 1579 2.411904 ACGTACGGCGAACCAAATTAA 58.588 42.857 21.06 0.00 44.77 1.40
1271 1580 2.157474 ACGTACGGCGAACCAAATTAAC 59.843 45.455 21.06 0.00 44.77 2.01
1272 1581 2.474361 CGTACGGCGAACCAAATTAACC 60.474 50.000 16.62 0.00 44.77 2.85
1278 1589 2.295070 GCGAACCAAATTAACCACCTGT 59.705 45.455 0.00 0.00 0.00 4.00
1279 1590 3.610821 GCGAACCAAATTAACCACCTGTC 60.611 47.826 0.00 0.00 0.00 3.51
1287 1598 2.943036 TAACCACCTGTCCTGAAACC 57.057 50.000 0.00 0.00 0.00 3.27
1292 1603 0.834612 ACCTGTCCTGAAACCGAACA 59.165 50.000 0.00 0.00 0.00 3.18
1309 1620 4.624882 CCGAACAGTGATCTCTTCTTCTTG 59.375 45.833 0.00 0.00 0.00 3.02
1310 1621 5.465051 CGAACAGTGATCTCTTCTTCTTGA 58.535 41.667 0.00 0.00 0.00 3.02
1314 1635 5.417266 ACAGTGATCTCTTCTTCTTGATCGA 59.583 40.000 0.00 0.00 38.40 3.59
1340 1661 1.750193 TTGGTTTCGGATGCTCCATC 58.250 50.000 3.57 0.00 39.87 3.51
1342 1663 1.160329 GGTTTCGGATGCTCCATCGG 61.160 60.000 6.47 6.47 41.35 4.18
1343 1664 1.523711 TTTCGGATGCTCCATCGGC 60.524 57.895 7.61 0.00 41.35 5.54
1344 1665 1.971505 TTTCGGATGCTCCATCGGCT 61.972 55.000 7.61 0.00 41.35 5.52
1345 1666 1.112916 TTCGGATGCTCCATCGGCTA 61.113 55.000 7.61 0.00 41.35 3.93
1347 1668 0.817654 CGGATGCTCCATCGGCTATA 59.182 55.000 3.57 0.00 41.35 1.31
1348 1669 1.410517 CGGATGCTCCATCGGCTATAT 59.589 52.381 3.57 0.00 41.35 0.86
1350 1671 2.169352 GGATGCTCCATCGGCTATATGT 59.831 50.000 0.00 0.00 41.35 2.29
1351 1672 3.369892 GGATGCTCCATCGGCTATATGTT 60.370 47.826 0.00 0.00 41.35 2.71
1352 1673 3.769739 TGCTCCATCGGCTATATGTTT 57.230 42.857 0.00 0.00 0.00 2.83
1353 1674 4.085357 TGCTCCATCGGCTATATGTTTT 57.915 40.909 0.00 0.00 0.00 2.43
1354 1675 4.065088 TGCTCCATCGGCTATATGTTTTC 58.935 43.478 0.00 0.00 0.00 2.29
1355 1676 3.123621 GCTCCATCGGCTATATGTTTTCG 59.876 47.826 0.00 0.00 0.00 3.46
1356 1677 4.307432 CTCCATCGGCTATATGTTTTCGT 58.693 43.478 0.00 0.00 0.00 3.85
1357 1678 4.699637 TCCATCGGCTATATGTTTTCGTT 58.300 39.130 0.00 0.00 0.00 3.85
1358 1679 4.748102 TCCATCGGCTATATGTTTTCGTTC 59.252 41.667 0.00 0.00 0.00 3.95
1359 1680 4.376008 CCATCGGCTATATGTTTTCGTTCG 60.376 45.833 0.00 0.00 0.00 3.95
1360 1681 3.117794 TCGGCTATATGTTTTCGTTCGG 58.882 45.455 0.00 0.00 0.00 4.30
1361 1682 3.117794 CGGCTATATGTTTTCGTTCGGA 58.882 45.455 0.00 0.00 0.00 4.55
1479 1800 2.351276 GCTTCCCGGGCTTCTTCA 59.649 61.111 18.49 0.00 0.00 3.02
1573 1894 0.601841 GAGTTCGCCCGGTTCAAGAA 60.602 55.000 0.00 0.00 0.00 2.52
1986 2319 1.544825 GCTGTACAGGGAGCTCCACA 61.545 60.000 33.29 25.65 38.24 4.17
2204 2537 0.034896 CCTACCTGAAACAGCACGGT 59.965 55.000 0.00 0.00 0.00 4.83
2296 2629 3.325293 GAAGTGATCCACTGAAGCTCA 57.675 47.619 0.00 0.00 44.62 4.26
2480 3162 7.815840 TCTTTCCATGACACATTTTTCTGTA 57.184 32.000 0.00 0.00 0.00 2.74
2684 3431 6.735510 CGAAATCTAATATTTCTGCATGAGCG 59.264 38.462 0.00 0.00 36.56 5.03
2749 3506 6.917477 TGAAATCTGTTTTTCGATTTGACTGG 59.083 34.615 2.36 0.00 39.29 4.00
2948 3990 9.950680 TTGTTTTAGACAAGTGAAATCATTCTC 57.049 29.630 0.00 0.00 43.13 2.87
3050 4100 4.472691 TCAGCGTTTTGAAATGAGTGAG 57.527 40.909 0.04 0.00 0.00 3.51
3063 4113 3.407424 TGAGTGAGATCAGTGTTTGGG 57.593 47.619 0.00 0.00 0.00 4.12
3372 4436 0.683412 AGCTGACACATCTGAGCACA 59.317 50.000 0.00 0.00 33.67 4.57
3389 4453 4.363999 AGCACACTTTCTATGCGTATCTC 58.636 43.478 0.00 0.00 44.25 2.75
3420 4489 4.214971 GCTTGTGTATTCTATGGCAGATGG 59.785 45.833 0.00 0.00 31.77 3.51
3471 4540 1.967319 TGCGCTTCCTCAAGAAAAGT 58.033 45.000 9.73 0.00 32.88 2.66
3480 4550 6.401581 GCTTCCTCAAGAAAAGTGATTCTACG 60.402 42.308 0.00 0.00 38.69 3.51
3513 4583 4.778143 GTGCCTCCATCCGCCGTT 62.778 66.667 0.00 0.00 0.00 4.44
3530 4600 1.756430 GTTGCTTCCCTTGGAGATCC 58.244 55.000 0.00 0.00 31.21 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.015367 TGATTAATTAGTAGAGCTAGCTGTAGG 57.985 37.037 24.99 0.00 0.00 3.18
108 115 5.688348 TTTTTGACAAAACAATCGGTTCG 57.312 34.783 12.86 0.00 39.29 3.95
148 155 5.764686 TCTTGAGATTTGTTGCAGTGTGTAT 59.235 36.000 0.00 0.00 0.00 2.29
182 194 4.963878 ATCCACCGGATGCAACTC 57.036 55.556 9.46 0.00 41.43 3.01
226 238 6.927294 AGATTAGAAAACGAGCTATTTGGG 57.073 37.500 0.00 0.00 0.00 4.12
316 330 4.116961 GTGGAAAGCACACGCATATAGTA 58.883 43.478 0.00 0.00 42.27 1.82
317 331 2.936498 GTGGAAAGCACACGCATATAGT 59.064 45.455 0.00 0.00 42.27 2.12
318 332 3.592381 GTGGAAAGCACACGCATATAG 57.408 47.619 0.00 0.00 42.27 1.31
356 370 7.660617 TCTCATCTCTCATTTAGCAATCAATCC 59.339 37.037 0.00 0.00 0.00 3.01
399 624 4.013728 AGAGCTCTCAGTAACTCACGATT 58.986 43.478 11.45 0.00 0.00 3.34
410 635 3.201353 TCGCATAGTAGAGCTCTCAGT 57.799 47.619 22.17 11.98 0.00 3.41
411 636 3.750652 TCATCGCATAGTAGAGCTCTCAG 59.249 47.826 22.17 7.91 0.00 3.35
415 640 7.757173 TGAATATTTCATCGCATAGTAGAGCTC 59.243 37.037 5.27 5.27 34.08 4.09
426 651 7.429051 CGATTTTCTGTTGAATATTTCATCGCA 59.571 33.333 0.00 0.00 39.84 5.10
464 689 2.754552 TCCATGTAATGCAACCTTGAGC 59.245 45.455 0.00 0.00 44.97 4.26
471 696 4.032703 GGATGTGTCCATGTAATGCAAC 57.967 45.455 0.00 0.00 44.97 4.17
506 731 3.320673 ACGAAGAACAGAAGATGGGAC 57.679 47.619 0.00 0.00 0.00 4.46
516 741 8.620533 AAGAAGAAAAATGAAACGAAGAACAG 57.379 30.769 0.00 0.00 0.00 3.16
550 811 4.168014 TGTGTCGACGTCGCTAATAAAAT 58.832 39.130 32.19 0.00 39.60 1.82
566 827 2.101575 GCTGCCATGCATGTGTCG 59.898 61.111 24.58 10.82 38.13 4.35
579 840 1.515736 GAAAGCAATCCAGCGCTGC 60.516 57.895 31.96 20.91 38.82 5.25
638 899 6.746745 TGAATTAATTAGTTCAACGTCCCC 57.253 37.500 18.06 0.00 30.44 4.81
676 947 2.352225 CGACAGCTGGACAGATATAGGC 60.352 54.545 19.93 0.00 0.00 3.93
682 953 1.244697 ACGACGACAGCTGGACAGAT 61.245 55.000 19.93 0.00 0.00 2.90
687 960 2.067091 AACGAACGACGACAGCTGGA 62.067 55.000 19.93 0.00 45.77 3.86
691 964 1.818221 AAGCAACGAACGACGACAGC 61.818 55.000 0.00 11.87 45.77 4.40
756 1030 3.119029 ACCGGAAGAAATTGCATTCATGG 60.119 43.478 9.46 4.82 0.00 3.66
757 1031 4.114058 ACCGGAAGAAATTGCATTCATG 57.886 40.909 9.46 0.00 0.00 3.07
758 1032 4.021192 ACAACCGGAAGAAATTGCATTCAT 60.021 37.500 9.46 0.00 0.00 2.57
802 1076 2.830370 GAATTCGCCCTGGCCTGG 60.830 66.667 21.51 21.51 37.98 4.45
803 1077 2.947938 ATCGAATTCGCCCTGGCCTG 62.948 60.000 22.90 2.54 39.60 4.85
804 1078 2.746375 ATCGAATTCGCCCTGGCCT 61.746 57.895 22.90 0.00 39.60 5.19
805 1079 2.203209 ATCGAATTCGCCCTGGCC 60.203 61.111 22.90 0.00 39.60 5.36
829 1103 1.210478 ACTAGCTGATTGCCGTTCCAT 59.790 47.619 0.00 0.00 44.23 3.41
830 1104 0.613260 ACTAGCTGATTGCCGTTCCA 59.387 50.000 0.00 0.00 44.23 3.53
872 1160 9.246670 ACTTGATTACAATTCATTCAATCCAGA 57.753 29.630 0.00 0.00 35.37 3.86
873 1161 9.865321 AACTTGATTACAATTCATTCAATCCAG 57.135 29.630 0.00 0.00 35.37 3.86
874 1162 9.642327 CAACTTGATTACAATTCATTCAATCCA 57.358 29.630 0.00 0.00 35.37 3.41
875 1163 9.090692 CCAACTTGATTACAATTCATTCAATCC 57.909 33.333 0.00 0.00 35.37 3.01
876 1164 9.643693 ACCAACTTGATTACAATTCATTCAATC 57.356 29.630 0.00 0.00 35.37 2.67
878 1166 9.906660 GTACCAACTTGATTACAATTCATTCAA 57.093 29.630 0.00 0.00 35.37 2.69
879 1167 8.233868 CGTACCAACTTGATTACAATTCATTCA 58.766 33.333 0.00 0.00 35.37 2.57
882 1170 7.681939 ACGTACCAACTTGATTACAATTCAT 57.318 32.000 0.00 0.00 35.37 2.57
934 1226 0.318441 TCCTTCCTGCAACGTCTCTG 59.682 55.000 0.00 0.00 0.00 3.35
989 1285 5.879223 TGGCCCAAATGCTTGTTAATTTATG 59.121 36.000 0.00 0.00 0.00 1.90
1159 1462 3.388703 CTGCTGCTCTCTCCTGGGC 62.389 68.421 0.00 0.00 0.00 5.36
1178 1481 1.559965 TTGATGCTCTGGCTCTGGCT 61.560 55.000 0.00 0.00 39.59 4.75
1179 1482 1.077930 TTGATGCTCTGGCTCTGGC 60.078 57.895 0.00 0.00 39.59 4.85
1180 1483 0.464013 CCTTGATGCTCTGGCTCTGG 60.464 60.000 0.00 0.00 39.59 3.86
1181 1484 0.540454 TCCTTGATGCTCTGGCTCTG 59.460 55.000 0.00 0.00 39.59 3.35
1182 1485 0.831966 CTCCTTGATGCTCTGGCTCT 59.168 55.000 0.00 0.00 39.59 4.09
1183 1486 0.179051 CCTCCTTGATGCTCTGGCTC 60.179 60.000 0.00 0.00 39.59 4.70
1184 1487 1.913722 CCTCCTTGATGCTCTGGCT 59.086 57.895 0.00 0.00 39.59 4.75
1185 1488 1.823041 GCCTCCTTGATGCTCTGGC 60.823 63.158 0.00 0.00 39.26 4.85
1186 1489 1.523258 CGCCTCCTTGATGCTCTGG 60.523 63.158 0.00 0.00 0.00 3.86
1270 1579 1.052124 TCGGTTTCAGGACAGGTGGT 61.052 55.000 0.00 0.00 0.00 4.16
1271 1580 0.107831 TTCGGTTTCAGGACAGGTGG 59.892 55.000 0.00 0.00 0.00 4.61
1272 1581 1.226746 GTTCGGTTTCAGGACAGGTG 58.773 55.000 0.00 0.00 0.00 4.00
1278 1589 2.632996 AGATCACTGTTCGGTTTCAGGA 59.367 45.455 0.00 0.00 36.17 3.86
1279 1590 2.996621 GAGATCACTGTTCGGTTTCAGG 59.003 50.000 0.00 0.00 36.17 3.86
1287 1598 5.465051 TCAAGAAGAAGAGATCACTGTTCG 58.535 41.667 0.00 0.00 46.54 3.95
1292 1603 6.320926 TGATCGATCAAGAAGAAGAGATCACT 59.679 38.462 25.44 0.00 38.42 3.41
1309 1620 3.682858 TCCGAAACCAAAAGTGATCGATC 59.317 43.478 18.72 18.72 39.66 3.69
1310 1621 3.670625 TCCGAAACCAAAAGTGATCGAT 58.329 40.909 0.00 0.00 39.66 3.59
1314 1635 3.157087 AGCATCCGAAACCAAAAGTGAT 58.843 40.909 0.00 0.00 0.00 3.06
1340 1661 3.117794 TCCGAACGAAAACATATAGCCG 58.882 45.455 0.00 0.00 0.00 5.52
1342 1663 5.612709 GCAGATCCGAACGAAAACATATAGC 60.613 44.000 0.00 0.00 0.00 2.97
1343 1664 5.462068 TGCAGATCCGAACGAAAACATATAG 59.538 40.000 0.00 0.00 0.00 1.31
1344 1665 5.353111 TGCAGATCCGAACGAAAACATATA 58.647 37.500 0.00 0.00 0.00 0.86
1345 1666 4.188462 TGCAGATCCGAACGAAAACATAT 58.812 39.130 0.00 0.00 0.00 1.78
1347 1668 2.416547 CTGCAGATCCGAACGAAAACAT 59.583 45.455 8.42 0.00 0.00 2.71
1348 1669 1.798223 CTGCAGATCCGAACGAAAACA 59.202 47.619 8.42 0.00 0.00 2.83
1350 1671 1.438651 CCTGCAGATCCGAACGAAAA 58.561 50.000 17.39 0.00 0.00 2.29
1351 1672 0.391130 CCCTGCAGATCCGAACGAAA 60.391 55.000 17.39 0.00 0.00 3.46
1352 1673 1.218047 CCCTGCAGATCCGAACGAA 59.782 57.895 17.39 0.00 0.00 3.85
1353 1674 1.043116 ATCCCTGCAGATCCGAACGA 61.043 55.000 17.39 0.00 0.00 3.85
1354 1675 0.877649 CATCCCTGCAGATCCGAACG 60.878 60.000 17.39 0.00 0.00 3.95
1355 1676 0.533755 CCATCCCTGCAGATCCGAAC 60.534 60.000 17.39 0.00 0.00 3.95
1356 1677 1.699054 CCCATCCCTGCAGATCCGAA 61.699 60.000 17.39 0.00 0.00 4.30
1357 1678 2.142761 CCCATCCCTGCAGATCCGA 61.143 63.158 17.39 5.23 0.00 4.55
1358 1679 2.429058 CCCATCCCTGCAGATCCG 59.571 66.667 17.39 0.00 0.00 4.18
1359 1680 2.114838 GCCCATCCCTGCAGATCC 59.885 66.667 17.39 0.00 0.00 3.36
1360 1681 2.281345 CGCCCATCCCTGCAGATC 60.281 66.667 17.39 0.00 0.00 2.75
1361 1682 3.882326 CCGCCCATCCCTGCAGAT 61.882 66.667 17.39 0.00 0.00 2.90
1993 2326 1.984570 CCGAACTCCTCCTCCAGCA 60.985 63.158 0.00 0.00 0.00 4.41
2153 2486 3.758088 CTCCATGTCGGCGTCGGAG 62.758 68.421 10.62 17.24 37.52 4.63
2701 3455 9.663904 TTCACTCATTTCAAAAGAGTTATTTCG 57.336 29.630 5.26 0.00 40.42 3.46
2709 3463 9.525409 AAACAGATTTCACTCATTTCAAAAGAG 57.475 29.630 0.70 0.70 35.56 2.85
2749 3506 8.633075 TTTCACTCATTTCAAACAACTGATTC 57.367 30.769 0.00 0.00 0.00 2.52
2785 3542 7.325821 GCGATTTCACTCATTTCACACAATTTA 59.674 33.333 0.00 0.00 0.00 1.40
2786 3543 6.144402 GCGATTTCACTCATTTCACACAATTT 59.856 34.615 0.00 0.00 0.00 1.82
2930 3972 9.520204 TTTTCAAAGAGAATGATTTCACTTGTC 57.480 29.630 0.31 0.00 40.48 3.18
3050 4100 6.712095 TGCTGAATATATCCCAAACACTGATC 59.288 38.462 0.00 0.00 0.00 2.92
3063 4113 9.120538 TCTTTAAAACTGGGTGCTGAATATATC 57.879 33.333 0.00 0.00 0.00 1.63
3295 4357 3.176411 ACACATGATTCTCTCTCCACCA 58.824 45.455 0.00 0.00 0.00 4.17
3372 4436 7.148641 CCATTAGTGAGATACGCATAGAAAGT 58.851 38.462 0.00 0.00 0.00 2.66
3389 4453 6.293626 GCCATAGAATACACAAGCCATTAGTG 60.294 42.308 0.00 0.00 39.12 2.74
3442 4511 0.038166 AGGAAGCGCAAAATCTCCCA 59.962 50.000 11.47 0.00 0.00 4.37
3471 4540 0.172578 CTCCCGTGCACGTAGAATCA 59.827 55.000 34.81 11.18 37.74 2.57
3509 4579 0.035056 ATCTCCAAGGGAAGCAACGG 60.035 55.000 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.