Multiple sequence alignment - TraesCS7A01G529700

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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 TraesCS7A01G529700 chr7A 100.000 3421 0 0 1 3421 709267240 709263820 0.000000e+00 6318.0
1 TraesCS7A01G529700 chr7A 80.869 1542 244 27 1739 3257 709755449 709756962 0.000000e+00 1166.0
2 TraesCS7A01G529700 chr7A 80.987 1520 234 37 1760 3258 709285518 709284033 0.000000e+00 1155.0
3 TraesCS7A01G529700 chr7A 87.143 350 29 9 962 1310 709286253 709285919 1.930000e-102 383.0
4 TraesCS7A01G529700 chr7A 79.920 498 91 7 1539 2029 709788133 709788628 1.170000e-94 357.0
5 TraesCS7A01G529700 chr7A 93.103 232 16 0 1445 1676 709285782 709285551 1.180000e-89 340.0
6 TraesCS7A01G529700 chr7A 84.951 206 29 2 1524 1729 709755275 709755478 1.240000e-49 207.0
7 TraesCS7A01G529700 chr7D 93.603 2001 102 11 1445 3421 616219818 616221816 0.000000e+00 2963.0
8 TraesCS7A01G529700 chr7D 89.439 1515 131 8 1522 3025 616257599 616256103 0.000000e+00 1884.0
9 TraesCS7A01G529700 chr7D 81.108 1498 241 24 1772 3257 616276222 616274755 0.000000e+00 1160.0
10 TraesCS7A01G529700 chr7D 80.337 1541 250 27 1739 3257 617027978 617029487 0.000000e+00 1118.0
11 TraesCS7A01G529700 chr7D 79.707 1434 246 29 1846 3257 616331549 616330139 0.000000e+00 994.0
12 TraesCS7A01G529700 chr7D 81.967 1098 146 36 401 1476 616258772 616257705 0.000000e+00 883.0
13 TraesCS7A01G529700 chr7D 86.043 609 38 23 904 1476 616219167 616219764 8.120000e-171 610.0
14 TraesCS7A01G529700 chr7D 77.526 881 159 31 1772 2635 617010154 617011012 8.530000e-136 494.0
15 TraesCS7A01G529700 chr7D 92.145 331 19 5 3098 3421 616256075 616255745 8.650000e-126 460.0
16 TraesCS7A01G529700 chr7D 81.870 353 48 9 38 387 616217901 616218240 2.010000e-72 283.0
17 TraesCS7A01G529700 chr7D 81.173 324 38 12 46 356 616259423 616259110 4.410000e-59 239.0
18 TraesCS7A01G529700 chr7D 80.892 314 46 8 1423 1729 617027701 617028007 5.710000e-58 235.0
19 TraesCS7A01G529700 chr7D 91.489 47 2 2 1445 1490 616257645 616257600 2.850000e-06 63.9
20 TraesCS7A01G529700 chr7B 81.126 1510 220 38 1773 3257 709591701 709590232 0.000000e+00 1149.0
21 TraesCS7A01G529700 chr7B 80.084 1426 227 28 1780 3196 709530403 709529026 0.000000e+00 1007.0
22 TraesCS7A01G529700 chr7B 85.851 629 30 25 876 1476 709531348 709530751 6.270000e-172 614.0
23 TraesCS7A01G529700 chr7B 93.162 234 14 2 1445 1676 709530689 709530456 3.270000e-90 342.0
24 TraesCS7A01G529700 chr7B 83.077 390 24 19 918 1300 709516870 709516516 1.980000e-82 316.0
25 TraesCS7A01G529700 chr7B 82.886 298 49 1 2897 3194 709514308 709514013 2.020000e-67 267.0
26 TraesCS7A01G529700 chr7B 81.553 309 37 10 1438 1732 709592005 709591703 1.590000e-58 237.0
27 TraesCS7A01G529700 chr7B 78.707 263 40 11 2980 3230 711206550 711206808 9.820000e-36 161.0
28 TraesCS7A01G529700 chr7B 79.221 231 33 1 161 391 709532283 709532068 2.750000e-31 147.0
29 TraesCS7A01G529700 chr7B 90.769 65 5 1 1445 1508 709515732 709515668 6.080000e-13 86.1
30 TraesCS7A01G529700 chr1B 76.384 1499 283 42 1770 3244 677254878 677256329 0.000000e+00 741.0
31 TraesCS7A01G529700 chr1A 76.259 1449 273 33 1770 3194 583924634 583926035 0.000000e+00 704.0
32 TraesCS7A01G529700 chr1D 81.919 271 42 3 1465 1729 408625905 408626174 4.440000e-54 222.0
33 TraesCS7A01G529700 chr6B 78.417 278 50 8 552 827 76484507 76484776 4.540000e-39 172.0


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 TraesCS7A01G529700 chr7A 709263820 709267240 3420 True 6318.000000 6318 100.000000 1 3421 1 chr7A.!!$R1 3420
1 TraesCS7A01G529700 chr7A 709755275 709756962 1687 False 686.500000 1166 82.910000 1524 3257 2 chr7A.!!$F2 1733
2 TraesCS7A01G529700 chr7A 709284033 709286253 2220 True 626.000000 1155 87.077667 962 3258 3 chr7A.!!$R2 2296
3 TraesCS7A01G529700 chr7D 616217901 616221816 3915 False 1285.333333 2963 87.172000 38 3421 3 chr7D.!!$F2 3383
4 TraesCS7A01G529700 chr7D 616274755 616276222 1467 True 1160.000000 1160 81.108000 1772 3257 1 chr7D.!!$R1 1485
5 TraesCS7A01G529700 chr7D 616330139 616331549 1410 True 994.000000 994 79.707000 1846 3257 1 chr7D.!!$R2 1411
6 TraesCS7A01G529700 chr7D 616255745 616259423 3678 True 705.980000 1884 87.242600 46 3421 5 chr7D.!!$R3 3375
7 TraesCS7A01G529700 chr7D 617027701 617029487 1786 False 676.500000 1118 80.614500 1423 3257 2 chr7D.!!$F3 1834
8 TraesCS7A01G529700 chr7D 617010154 617011012 858 False 494.000000 494 77.526000 1772 2635 1 chr7D.!!$F1 863
9 TraesCS7A01G529700 chr7B 709590232 709592005 1773 True 693.000000 1149 81.339500 1438 3257 2 chr7B.!!$R3 1819
10 TraesCS7A01G529700 chr7B 709529026 709532283 3257 True 527.500000 1007 84.579500 161 3196 4 chr7B.!!$R2 3035
11 TraesCS7A01G529700 chr7B 709514013 709516870 2857 True 223.033333 316 85.577333 918 3194 3 chr7B.!!$R1 2276
12 TraesCS7A01G529700 chr1B 677254878 677256329 1451 False 741.000000 741 76.384000 1770 3244 1 chr1B.!!$F1 1474
13 TraesCS7A01G529700 chr1A 583924634 583926035 1401 False 704.000000 704 76.259000 1770 3194 1 chr1A.!!$F1 1424

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
676 1018 0.303796 GCGGTCCTAATAAAGCACGC 59.696 55.0 0.0 0.0 38.94 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2423 3654 2.158475 TCTTCACTGGGGAAATGCTTGT 60.158 45.455 0.0 0.0 0.0 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
26 27 2.202987 CCCGATGAGGCTGCAGTC 60.203 66.667 11.28 11.28 39.21 3.51
27 28 2.729479 CCCGATGAGGCTGCAGTCT 61.729 63.158 23.48 23.48 39.21 3.24
28 29 1.227205 CCGATGAGGCTGCAGTCTC 60.227 63.158 36.05 36.05 46.44 3.36
52 53 1.796749 GTCGACGACGCTTGAGGAC 60.797 63.158 12.94 0.00 39.58 3.85
53 54 2.504244 CGACGACGCTTGAGGACC 60.504 66.667 0.00 0.00 0.00 4.46
54 55 2.126031 GACGACGCTTGAGGACCC 60.126 66.667 0.00 0.00 0.00 4.46
70 71 2.580815 CCTGCGACTCTCATGGCA 59.419 61.111 0.00 0.00 0.00 4.92
71 72 4.105727 CTGCGACTCTCATGGCAG 57.894 61.111 5.21 5.21 43.64 4.85
72 73 2.125391 TGCGACTCTCATGGCAGC 60.125 61.111 0.00 0.00 0.00 5.25
120 121 3.161450 GGACTGCCGGCCATAGGA 61.161 66.667 26.77 2.02 0.00 2.94
123 124 1.460305 ACTGCCGGCCATAGGATCT 60.460 57.895 26.77 0.00 0.00 2.75
144 145 2.761465 CCATTGGGAGGAGGGGAGC 61.761 68.421 0.00 0.00 35.59 4.70
202 215 2.569373 GATGGGGGAGGGGAAGAGGT 62.569 65.000 0.00 0.00 0.00 3.85
227 240 2.238395 GGAGGCAGAAAGAAGAGTGGAT 59.762 50.000 0.00 0.00 0.00 3.41
228 241 3.308046 GGAGGCAGAAAGAAGAGTGGATT 60.308 47.826 0.00 0.00 0.00 3.01
249 263 2.438951 TTTTTACTCCCGCGCCGAGT 62.439 55.000 24.49 24.49 43.05 4.18
278 292 7.017155 TGGAGTAAATATTGGCTAGGCATAAGA 59.983 37.037 20.94 5.22 0.00 2.10
318 332 0.319555 CACGTGGGAATGACTGTCGT 60.320 55.000 7.95 0.00 0.00 4.34
322 336 0.762418 TGGGAATGACTGTCGTTGGT 59.238 50.000 19.26 0.00 0.00 3.67
331 345 7.094933 GGAATGACTGTCGTTGGTTAAATTAGT 60.095 37.037 19.26 0.00 0.00 2.24
340 354 5.650543 GTTGGTTAAATTAGTGGCATCTGG 58.349 41.667 0.00 0.00 0.00 3.86
406 748 7.496920 TCCTGTAAATTGAATAGAGTGCATCTG 59.503 37.037 8.40 0.00 39.20 2.90
420 762 3.824815 TCTGCAAGATGGGGAGCA 58.175 55.556 0.00 0.00 38.67 4.26
427 769 2.094675 CAAGATGGGGAGCATCGTTTT 58.905 47.619 0.00 0.00 34.37 2.43
462 804 2.111878 CCATCGAGGACATGGGGC 59.888 66.667 0.00 0.00 41.22 5.80
493 835 3.933048 GAGGTCGTCCCGAGGGTGA 62.933 68.421 8.20 5.01 36.23 4.02
534 876 2.906897 CGCACCACCACCAAAGCT 60.907 61.111 0.00 0.00 0.00 3.74
573 915 4.485834 CGGCTACCGCGCTACACA 62.486 66.667 5.56 0.00 41.17 3.72
609 951 2.605094 GCGAAGGCGATATGCTTCA 58.395 52.632 0.00 0.00 45.43 3.02
654 996 0.755079 CGGCCTCCATGATCTCTTCA 59.245 55.000 0.00 0.00 39.12 3.02
665 1007 2.032620 GATCTCTTCAAGGCGGTCCTA 58.967 52.381 0.00 0.00 43.40 2.94
666 1008 1.933021 TCTCTTCAAGGCGGTCCTAA 58.067 50.000 0.00 0.00 43.40 2.69
667 1009 2.467880 TCTCTTCAAGGCGGTCCTAAT 58.532 47.619 0.00 0.00 43.40 1.73
668 1010 3.638860 TCTCTTCAAGGCGGTCCTAATA 58.361 45.455 0.00 0.00 43.40 0.98
669 1011 4.028131 TCTCTTCAAGGCGGTCCTAATAA 58.972 43.478 0.00 0.00 43.40 1.40
670 1012 4.468510 TCTCTTCAAGGCGGTCCTAATAAA 59.531 41.667 0.00 0.00 43.40 1.40
671 1013 4.766375 TCTTCAAGGCGGTCCTAATAAAG 58.234 43.478 0.00 0.00 43.40 1.85
672 1014 2.914059 TCAAGGCGGTCCTAATAAAGC 58.086 47.619 0.00 0.00 43.40 3.51
673 1015 2.237643 TCAAGGCGGTCCTAATAAAGCA 59.762 45.455 0.00 0.00 43.40 3.91
674 1016 2.327200 AGGCGGTCCTAATAAAGCAC 57.673 50.000 0.00 0.00 42.06 4.40
675 1017 0.935196 GGCGGTCCTAATAAAGCACG 59.065 55.000 0.00 0.00 0.00 5.34
676 1018 0.303796 GCGGTCCTAATAAAGCACGC 59.696 55.000 0.00 0.00 38.94 5.34
677 1019 1.935933 CGGTCCTAATAAAGCACGCT 58.064 50.000 0.00 0.00 0.00 5.07
678 1020 1.593006 CGGTCCTAATAAAGCACGCTG 59.407 52.381 0.00 0.00 0.00 5.18
679 1021 1.330829 GGTCCTAATAAAGCACGCTGC 59.669 52.381 0.00 2.28 45.46 5.25
777 1140 5.488645 TTTCAGGGTTTTCGTGTTACTTC 57.511 39.130 0.00 0.00 33.36 3.01
787 1150 4.996788 TCGTGTTACTTCTTAGGGATCC 57.003 45.455 1.92 1.92 0.00 3.36
807 1170 7.011763 GGGATCCGGTTGTAAATTTAACTACTC 59.988 40.741 5.45 0.00 0.00 2.59
861 1224 6.431198 TTTTTGCGGAATCTATTCTACCAC 57.569 37.500 0.00 0.00 37.00 4.16
870 1233 7.196331 GGAATCTATTCTACCACAACAAATGC 58.804 38.462 2.91 0.00 37.00 3.56
1040 1526 3.569361 AAGCAGCTCCTCCTCCCCA 62.569 63.158 0.00 0.00 0.00 4.96
1041 1527 2.771762 GCAGCTCCTCCTCCCCAT 60.772 66.667 0.00 0.00 0.00 4.00
1042 1528 2.817056 GCAGCTCCTCCTCCCCATC 61.817 68.421 0.00 0.00 0.00 3.51
1043 1529 2.146061 CAGCTCCTCCTCCCCATCC 61.146 68.421 0.00 0.00 0.00 3.51
1044 1530 2.851588 GCTCCTCCTCCCCATCCC 60.852 72.222 0.00 0.00 0.00 3.85
1045 1531 2.122189 CTCCTCCTCCCCATCCCC 60.122 72.222 0.00 0.00 0.00 4.81
1072 1570 4.979335 TCTAGATCGACAGGTGATCATCT 58.021 43.478 1.50 1.50 43.73 2.90
1079 1577 3.037549 GACAGGTGATCATCTTCTCCCT 58.962 50.000 5.51 0.00 31.05 4.20
1080 1578 3.037549 ACAGGTGATCATCTTCTCCCTC 58.962 50.000 5.51 0.00 31.05 4.30
1083 1581 3.044894 GGTGATCATCTTCTCCCTCCTT 58.955 50.000 0.00 0.00 0.00 3.36
1088 1586 3.796111 TCATCTTCTCCCTCCTTCTGTT 58.204 45.455 0.00 0.00 0.00 3.16
1089 1587 4.947883 TCATCTTCTCCCTCCTTCTGTTA 58.052 43.478 0.00 0.00 0.00 2.41
1090 1588 5.342017 TCATCTTCTCCCTCCTTCTGTTAA 58.658 41.667 0.00 0.00 0.00 2.01
1144 1642 2.106477 GAGTGCCCTCCTTTTCTCTG 57.894 55.000 0.00 0.00 0.00 3.35
1196 1698 4.496336 GCCCATGGAAGAGGCGCT 62.496 66.667 15.22 0.00 36.84 5.92
1197 1699 2.515523 CCCATGGAAGAGGCGCTG 60.516 66.667 15.22 0.00 0.00 5.18
1228 1733 0.968393 GAGGAGAAGGTCGGAGCACT 60.968 60.000 10.15 8.15 0.00 4.40
1325 1831 1.562475 TCAATTTCCCCCTTAGACGGG 59.438 52.381 0.00 0.00 44.27 5.28
1327 1833 1.979619 ATTTCCCCCTTAGACGGGCG 61.980 60.000 0.13 0.00 43.25 6.13
1392 2433 0.828762 TTTGCTGCTGTGGCCTTCAT 60.829 50.000 3.32 0.00 37.74 2.57
1393 2434 0.828762 TTGCTGCTGTGGCCTTCATT 60.829 50.000 3.32 0.00 37.74 2.57
1394 2435 1.214589 GCTGCTGTGGCCTTCATTG 59.785 57.895 3.32 0.00 37.74 2.82
1395 2436 1.246056 GCTGCTGTGGCCTTCATTGA 61.246 55.000 3.32 0.00 37.74 2.57
1407 2478 3.624410 GCCTTCATTGATTTGAATTGGGC 59.376 43.478 0.00 0.00 37.33 5.36
1684 2885 5.142635 TGCGATCTATGTTTCAATGAACG 57.857 39.130 0.00 0.00 32.18 3.95
1687 2888 4.518217 GATCTATGTTTCAATGAACGCGG 58.482 43.478 12.47 0.00 32.18 6.46
1814 3033 7.862372 GCAAAGTTCATTGAGACTGTAAATTCA 59.138 33.333 3.36 0.00 31.84 2.57
1836 3056 4.336433 CAGTTATTCAACAGCATAGTGGGG 59.664 45.833 0.00 0.00 37.10 4.96
1876 3096 0.330604 ATCAAGTGTGGCCTGCTCAT 59.669 50.000 3.32 0.00 0.00 2.90
1877 3097 0.321919 TCAAGTGTGGCCTGCTCATC 60.322 55.000 3.32 0.00 0.00 2.92
1936 3156 2.476241 CCGCTTCATCAAAGGCAAAAAC 59.524 45.455 0.00 0.00 35.37 2.43
1988 3208 2.225117 CCCAGTTGAAGAAGTTCCCCAT 60.225 50.000 0.00 0.00 0.00 4.00
2025 3248 2.977772 AGATGCTCAAGGTAGCTCAC 57.022 50.000 0.00 0.00 43.19 3.51
2210 3434 2.808543 GTGTTCTGGTGTGGATGACTTC 59.191 50.000 0.00 0.00 0.00 3.01
2224 3448 5.456192 GATGACTTCATCGTACCAAACAG 57.544 43.478 3.49 0.00 42.66 3.16
2279 3509 1.351017 ACGGATGTCCAGATGGTTGTT 59.649 47.619 0.00 0.00 36.34 2.83
2312 3542 6.038382 CAGCTGATCTTGCTCATTTTGAGTAT 59.962 38.462 8.42 0.00 45.94 2.12
2417 3648 2.033372 CACTGGCCCATGCATTCAATA 58.967 47.619 0.00 0.00 40.13 1.90
2423 3654 6.725369 ACTGGCCCATGCATTCAATATAATTA 59.275 34.615 0.00 0.00 40.13 1.40
2492 3732 8.978874 ATCAACATATGCACAGGTTATCTTAA 57.021 30.769 1.58 0.00 0.00 1.85
2751 4013 4.726416 CACTTGCATGTGAGTACCATTTC 58.274 43.478 24.41 0.00 40.12 2.17
2823 4173 3.569701 AGTTTGACCGAATGATTGCAAGT 59.430 39.130 4.94 0.00 0.00 3.16
2995 4350 4.400567 GTGCTCTATCTTGGGAAATGCTTT 59.599 41.667 0.00 0.00 0.00 3.51
2999 4354 6.095440 GCTCTATCTTGGGAAATGCTTTTGTA 59.905 38.462 1.76 0.00 0.00 2.41
3017 4372 3.329386 TGTACTTGAGCAGCTGACAATC 58.671 45.455 20.43 9.69 0.00 2.67
3053 4411 5.240183 CACAGAAGCAATATGGGGTGATAAG 59.760 44.000 0.00 0.00 0.00 1.73
3055 4413 5.471456 CAGAAGCAATATGGGGTGATAAGTC 59.529 44.000 0.00 0.00 0.00 3.01
3060 4418 5.705905 GCAATATGGGGTGATAAGTCTTACC 59.294 44.000 0.00 0.00 0.00 2.85
3070 4428 7.202102 GGGTGATAAGTCTTACCAGTGGAATAT 60.202 40.741 18.40 0.00 34.89 1.28
3269 4639 0.761802 GGGAGAATGCCCCTGTAGAG 59.238 60.000 0.00 0.00 43.14 2.43
3293 4663 5.989777 GTGTAGTGACTGTTTTGGTGTCTAT 59.010 40.000 0.00 0.00 0.00 1.98
3305 4675 7.671819 TGTTTTGGTGTCTATAAATGGAATCCA 59.328 33.333 3.67 3.67 38.19 3.41
3353 4736 8.463930 AAAAACAAGTAATCTCTGGTTCATCA 57.536 30.769 0.00 0.00 0.00 3.07
3402 4787 1.205655 GTGTCTCCAGTGCATCTGCTA 59.794 52.381 9.88 1.85 42.38 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.227205 GAGACTGCAGCCTCATCGG 60.227 63.158 23.48 0.00 0.00 4.18
11 12 1.588403 CGAGACTGCAGCCTCATCG 60.588 63.158 26.80 18.27 0.00 3.84
12 13 1.882167 GCGAGACTGCAGCCTCATC 60.882 63.158 26.80 15.33 34.15 2.92
13 14 2.186384 GCGAGACTGCAGCCTCAT 59.814 61.111 26.80 1.82 34.15 2.90
14 15 4.426112 CGCGAGACTGCAGCCTCA 62.426 66.667 26.80 0.00 34.15 3.86
34 35 1.796749 GTCCTCAAGCGTCGTCGAC 60.797 63.158 15.51 15.51 39.71 4.20
35 36 2.559840 GTCCTCAAGCGTCGTCGA 59.440 61.111 6.17 0.00 39.71 4.20
36 37 2.504244 GGTCCTCAAGCGTCGTCG 60.504 66.667 0.00 0.00 40.37 5.12
41 42 4.379243 CGCAGGGTCCTCAAGCGT 62.379 66.667 10.75 0.00 43.08 5.07
44 45 1.216710 GAGTCGCAGGGTCCTCAAG 59.783 63.158 0.00 0.00 0.00 3.02
52 53 2.202987 GCCATGAGAGTCGCAGGG 60.203 66.667 21.48 21.48 38.09 4.45
53 54 1.521010 CTGCCATGAGAGTCGCAGG 60.521 63.158 10.50 1.70 43.96 4.85
54 55 4.105727 CTGCCATGAGAGTCGCAG 57.894 61.111 2.26 2.72 42.42 5.18
116 117 1.438469 CTCCCAATGGCCAGATCCTA 58.562 55.000 13.05 0.00 0.00 2.94
117 118 1.358830 CCTCCCAATGGCCAGATCCT 61.359 60.000 13.05 0.00 0.00 3.24
120 121 1.358830 CCTCCTCCCAATGGCCAGAT 61.359 60.000 13.05 0.00 0.00 2.90
123 124 3.023116 CCCTCCTCCCAATGGCCA 61.023 66.667 8.56 8.56 0.00 5.36
147 148 3.831727 TTCCTCCCGTCGTTCCCCA 62.832 63.158 0.00 0.00 0.00 4.96
194 207 1.063567 TCTGCCTCCTCTACCTCTTCC 60.064 57.143 0.00 0.00 0.00 3.46
202 215 3.766591 CACTCTTCTTTCTGCCTCCTCTA 59.233 47.826 0.00 0.00 0.00 2.43
241 254 2.775032 TTTACTCCACCACTCGGCGC 62.775 60.000 0.00 0.00 34.57 6.53
249 263 4.445735 GCCTAGCCAATATTTACTCCACCA 60.446 45.833 0.00 0.00 0.00 4.17
301 315 0.790207 CAACGACAGTCATTCCCACG 59.210 55.000 0.41 0.00 0.00 4.94
318 332 5.329399 ACCAGATGCCACTAATTTAACCAA 58.671 37.500 0.00 0.00 0.00 3.67
322 336 7.432148 TCTCTACCAGATGCCACTAATTTAA 57.568 36.000 0.00 0.00 0.00 1.52
376 390 8.704668 TGCACTCTATTCAATTTACAGGATCTA 58.295 33.333 0.00 0.00 0.00 1.98
406 748 0.749454 AACGATGCTCCCCATCTTGC 60.749 55.000 0.00 0.00 46.61 4.01
411 753 2.192605 GCAAAACGATGCTCCCCAT 58.807 52.632 0.00 0.00 43.06 4.00
412 754 3.680156 GCAAAACGATGCTCCCCA 58.320 55.556 0.00 0.00 43.06 4.96
485 827 2.125912 CTGCCTCGTTCACCCTCG 60.126 66.667 0.00 0.00 0.00 4.63
493 835 2.342648 GAACCCGACTGCCTCGTT 59.657 61.111 0.75 0.00 41.18 3.85
561 903 1.798234 TACACAGTGTGTAGCGCGGT 61.798 55.000 28.24 17.70 45.56 5.68
571 913 1.819288 CCTCCATCTCGTACACAGTGT 59.181 52.381 11.87 11.87 0.00 3.55
573 915 0.818296 GCCTCCATCTCGTACACAGT 59.182 55.000 0.00 0.00 0.00 3.55
644 986 0.537188 GGACCGCCTTGAAGAGATCA 59.463 55.000 0.00 0.00 35.85 2.92
654 996 2.640184 GTGCTTTATTAGGACCGCCTT 58.360 47.619 0.00 0.00 43.90 4.35
676 1018 4.426112 TGCTCGAGTCAGGCGCAG 62.426 66.667 15.13 0.00 0.00 5.18
677 1019 4.724602 GTGCTCGAGTCAGGCGCA 62.725 66.667 15.13 1.16 36.61 6.09
681 1023 4.056125 TGGCGTGCTCGAGTCAGG 62.056 66.667 15.13 17.42 39.71 3.86
682 1024 2.807045 GTGGCGTGCTCGAGTCAG 60.807 66.667 15.13 6.55 39.71 3.51
683 1025 4.700365 CGTGGCGTGCTCGAGTCA 62.700 66.667 15.13 9.82 39.71 3.41
767 1129 3.490419 CCGGATCCCTAAGAAGTAACACG 60.490 52.174 6.06 0.00 0.00 4.49
777 1140 7.555195 AGTTAAATTTACAACCGGATCCCTAAG 59.445 37.037 9.46 0.00 0.00 2.18
787 1150 9.887406 ATTTGTGAGTAGTTAAATTTACAACCG 57.113 29.630 0.00 0.00 0.00 4.44
807 1170 7.765819 TCATGTTAGATGTAGAGTCCATTTGTG 59.234 37.037 0.00 0.00 0.00 3.33
861 1224 5.755813 GAGCATCTAGTATGGCATTTGTTG 58.244 41.667 4.78 0.00 0.00 3.33
1040 1526 2.447429 TGTCGATCTAGAGAAGGGGGAT 59.553 50.000 0.00 0.00 0.00 3.85
1041 1527 1.850998 TGTCGATCTAGAGAAGGGGGA 59.149 52.381 0.00 0.00 0.00 4.81
1042 1528 2.235016 CTGTCGATCTAGAGAAGGGGG 58.765 57.143 0.00 0.00 0.00 5.40
1043 1529 2.235016 CCTGTCGATCTAGAGAAGGGG 58.765 57.143 0.00 0.00 0.00 4.79
1044 1530 2.621055 CACCTGTCGATCTAGAGAAGGG 59.379 54.545 0.00 0.09 0.00 3.95
1045 1531 3.546724 TCACCTGTCGATCTAGAGAAGG 58.453 50.000 0.00 3.28 0.00 3.46
1072 1570 3.870559 AGGTTAACAGAAGGAGGGAGAA 58.129 45.455 8.10 0.00 0.00 2.87
1079 1577 5.609708 AGGAAAACCTAGGTTAACAGAAGGA 59.390 40.000 27.33 0.00 37.35 3.36
1080 1578 5.877491 AGGAAAACCTAGGTTAACAGAAGG 58.123 41.667 27.33 12.36 37.35 3.46
1083 1581 4.909088 TGGAGGAAAACCTAGGTTAACAGA 59.091 41.667 27.33 6.15 37.35 3.41
1088 1586 4.440808 TCCATGGAGGAAAACCTAGGTTA 58.559 43.478 27.33 10.49 45.65 2.85
1089 1587 3.265489 TCCATGGAGGAAAACCTAGGTT 58.735 45.455 21.96 21.96 45.65 3.50
1090 1588 2.929301 TCCATGGAGGAAAACCTAGGT 58.071 47.619 11.44 9.21 45.65 3.08
1104 1602 2.005560 CGCAGATCGATCCATCCATGG 61.006 57.143 21.66 4.97 44.66 3.66
1105 1603 1.356938 CGCAGATCGATCCATCCATG 58.643 55.000 21.66 13.02 41.67 3.66
1106 1604 0.248565 CCGCAGATCGATCCATCCAT 59.751 55.000 21.66 0.00 41.67 3.41
1167 1665 3.664888 ATGGGCTGCTGCAGGGAA 61.665 61.111 29.05 0.00 41.91 3.97
1210 1715 0.331954 TAGTGCTCCGACCTTCTCCT 59.668 55.000 0.00 0.00 0.00 3.69
1215 1720 1.874345 CGTGGTAGTGCTCCGACCTT 61.874 60.000 8.46 0.00 34.13 3.50
1325 1831 0.526524 CAGAGTTCCAGATCCGTCGC 60.527 60.000 0.00 0.00 0.00 5.19
1327 1833 0.461961 CCCAGAGTTCCAGATCCGTC 59.538 60.000 0.00 0.00 0.00 4.79
1392 2433 4.020039 AGCAAGATGCCCAATTCAAATCAA 60.020 37.500 0.00 0.00 46.52 2.57
1393 2434 3.516300 AGCAAGATGCCCAATTCAAATCA 59.484 39.130 0.00 0.00 46.52 2.57
1394 2435 4.133013 AGCAAGATGCCCAATTCAAATC 57.867 40.909 0.00 0.00 46.52 2.17
1395 2436 4.563140 AAGCAAGATGCCCAATTCAAAT 57.437 36.364 0.00 0.00 46.52 2.32
1407 2478 7.592938 TGTAGTTTCACCAATTAAGCAAGATG 58.407 34.615 0.00 0.00 0.00 2.90
1684 2885 2.351726 GTGTTAGAATCCACATCACCGC 59.648 50.000 0.00 0.00 0.00 5.68
1687 2888 3.857052 TCGGTGTTAGAATCCACATCAC 58.143 45.455 0.00 0.00 33.19 3.06
1814 3033 4.018415 ACCCCACTATGCTGTTGAATAACT 60.018 41.667 0.00 0.00 37.68 2.24
1836 3056 7.792374 TGATGCTGAACTTATTGATTCCTAC 57.208 36.000 0.00 0.00 0.00 3.18
1876 3096 3.191581 GTCAAGATGTTCAGAGTCCTCGA 59.808 47.826 0.00 0.00 34.09 4.04
1877 3097 3.057245 TGTCAAGATGTTCAGAGTCCTCG 60.057 47.826 0.00 0.00 34.09 4.63
1950 3170 9.527157 TTCAACTGGGTAATCAAATATCTTCAA 57.473 29.630 0.00 0.00 0.00 2.69
2025 3248 2.540265 AGAGACAAGGACTGCACAAG 57.460 50.000 0.00 0.00 0.00 3.16
2210 3434 3.211803 TCGAGTCTGTTTGGTACGATG 57.788 47.619 0.00 0.00 0.00 3.84
2220 3444 9.450807 CAAATTTTGAAGTTTATCGAGTCTGTT 57.549 29.630 2.88 0.00 0.00 3.16
2224 3448 7.803189 TCAGCAAATTTTGAAGTTTATCGAGTC 59.197 33.333 13.26 0.00 0.00 3.36
2279 3509 3.813724 GAGCAAGATCAGCTGCATGAATA 59.186 43.478 16.22 0.00 43.58 1.75
2312 3542 2.820728 TAGGGATCAGTCGTCCTTCA 57.179 50.000 0.00 0.00 36.00 3.02
2417 3648 6.194235 TCACTGGGGAAATGCTTGTAATTAT 58.806 36.000 0.00 0.00 0.00 1.28
2423 3654 2.158475 TCTTCACTGGGGAAATGCTTGT 60.158 45.455 0.00 0.00 0.00 3.16
2788 4138 7.789273 TTCGGTCAAACTAATCAAACTACAA 57.211 32.000 0.00 0.00 0.00 2.41
2839 4189 0.033011 AGCACCGGGACTCAGATAGT 60.033 55.000 6.32 0.00 42.80 2.12
2850 4200 1.856265 GCACTGAAGAAAGCACCGGG 61.856 60.000 6.32 0.00 0.00 5.73
2995 4350 2.908688 TGTCAGCTGCTCAAGTACAA 57.091 45.000 9.47 0.00 0.00 2.41
2999 4354 1.001293 TCGATTGTCAGCTGCTCAAGT 59.999 47.619 21.72 13.72 0.00 3.16
3017 4372 1.151668 CTTCTGTGAGCCTTGGTTCG 58.848 55.000 0.00 0.00 0.00 3.95
3053 4411 4.593634 AGGCCTATATTCCACTGGTAAGAC 59.406 45.833 1.29 0.00 0.00 3.01
3055 4413 5.071788 TCAAGGCCTATATTCCACTGGTAAG 59.928 44.000 5.16 0.00 0.00 2.34
3060 4418 5.684704 TCTTTCAAGGCCTATATTCCACTG 58.315 41.667 5.16 0.00 0.00 3.66
3070 4428 6.210584 CCTTGGTAAAATTCTTTCAAGGCCTA 59.789 38.462 5.16 0.00 38.59 3.93
3269 4639 4.189231 AGACACCAAAACAGTCACTACAC 58.811 43.478 0.00 0.00 34.80 2.90
3293 4663 4.588528 GCAAAGCCCTATGGATTCCATTTA 59.411 41.667 22.87 5.77 42.23 1.40


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

AutoCloner maintained by Alex Coulton.