Multiple sequence alignment - TraesCS3B01G237700

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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 TraesCS3B01G237700 chr3B 100.000 4319 0 0 1 4319 372897928 372893610 0.000000e+00 7976.0
1 TraesCS3B01G237700 chr3B 86.634 404 52 2 1342 1744 95461696 95461294 3.060000e-121 446.0
2 TraesCS3B01G237700 chr3D 92.683 4182 111 79 1 4058 277220743 277224853 0.000000e+00 5847.0
3 TraesCS3B01G237700 chr3D 87.097 403 52 0 1342 1744 59856443 59856041 1.420000e-124 457.0
4 TraesCS3B01G237700 chr3D 94.361 266 12 3 4057 4319 277225037 277225302 5.200000e-109 405.0
5 TraesCS3B01G237700 chr3A 89.277 4523 156 107 1 4319 362203531 362199134 0.000000e+00 5361.0
6 TraesCS3B01G237700 chr3A 86.667 405 47 5 1342 1744 178987287 178986888 3.960000e-120 442.0
7 TraesCS3B01G237700 chr3A 86.352 403 55 0 1342 1744 68869406 68869004 1.430000e-119 440.0
8 TraesCS3B01G237700 chr4B 86.946 406 50 1 1353 1758 531580972 531580570 1.830000e-123 453.0
9 TraesCS3B01G237700 chr4B 79.538 303 27 22 474 769 476641375 476641101 2.650000e-42 183.0
10 TraesCS3B01G237700 chr4B 79.208 303 28 22 474 769 44947352 44947626 1.230000e-40 178.0
11 TraesCS3B01G237700 chr4B 100.000 35 0 0 403 437 44947312 44947346 1.000000e-06 65.8
12 TraesCS3B01G237700 chr4D 87.532 393 46 1 1353 1745 433393640 433393251 6.590000e-123 451.0
13 TraesCS3B01G237700 chr4D 95.000 40 1 1 3650 3689 16054690 16054652 1.300000e-05 62.1
14 TraesCS3B01G237700 chr4A 87.310 394 45 3 1353 1745 34787845 34787456 3.060000e-121 446.0
15 TraesCS3B01G237700 chr4A 95.238 42 1 1 3648 3689 584545455 584545415 1.000000e-06 65.8
16 TraesCS3B01G237700 chr4A 100.000 29 0 0 403 431 624767738 624767710 2.000000e-03 54.7
17 TraesCS3B01G237700 chr4A 94.444 36 1 1 3653 3688 743700511 743700545 2.000000e-03 54.7
18 TraesCS3B01G237700 chr1A 79.866 149 25 3 3730 3873 309456959 309457107 2.120000e-18 104.0
19 TraesCS3B01G237700 chr1A 100.000 35 0 0 403 437 569343146 569343180 1.000000e-06 65.8
20 TraesCS3B01G237700 chr1B 100.000 35 0 0 403 437 52491300 52491266 1.000000e-06 65.8
21 TraesCS3B01G237700 chr2D 97.143 35 1 0 403 437 614808168 614808202 4.660000e-05 60.2
22 TraesCS3B01G237700 chr7D 97.059 34 0 1 3654 3687 421141262 421141230 6.030000e-04 56.5
23 TraesCS3B01G237700 chr7B 92.105 38 1 1 3640 3675 84392706 84392743 8.000000e-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 TraesCS3B01G237700 chr3B 372893610 372897928 4318 True 7976 7976 100.000 1 4319 1 chr3B.!!$R2 4318
1 TraesCS3B01G237700 chr3D 277220743 277225302 4559 False 3126 5847 93.522 1 4319 2 chr3D.!!$F1 4318
2 TraesCS3B01G237700 chr3A 362199134 362203531 4397 True 5361 5361 89.277 1 4319 1 chr3A.!!$R3 4318

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
615 699 0.601057 TACGCTTGTACTGCTGCAGA 59.399 50.0 34.28 16.05 35.18 4.26 F
1269 1400 0.321919 ACTGGACTGATGCGCATGTT 60.322 50.0 30.76 11.47 0.00 2.71 F
1936 2084 0.582005 GATCGTGAACATTAGGGCGC 59.418 55.0 0.00 0.00 0.00 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1992 2145 0.392193 CTTCTGCGTTGCCTCATCCT 60.392 55.000 0.00 0.0 0.00 3.24 R
2478 2677 1.079819 CGTGATGAAGCTGTCCCGT 60.080 57.895 0.00 0.0 0.00 5.28 R
3584 3867 0.038021 TAGGCAATGCAGCTGACCAA 59.962 50.000 20.43 0.0 34.17 3.67 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
131 143 8.487970 CACAATGTTATATACAGTCCGTGATTC 58.512 37.037 0.00 0.00 40.83 2.52
294 322 4.528076 TTTTTAGCATACCCATAGGCCA 57.472 40.909 5.01 0.00 38.94 5.36
295 323 4.740154 TTTTAGCATACCCATAGGCCAT 57.260 40.909 5.01 0.00 38.94 4.40
296 324 5.851808 TTTTAGCATACCCATAGGCCATA 57.148 39.130 5.01 0.00 38.94 2.74
297 325 5.435686 TTTAGCATACCCATAGGCCATAG 57.564 43.478 5.01 0.00 38.94 2.23
478 530 3.325753 AGCACTGTGGCCTCTCCC 61.326 66.667 10.21 0.00 0.00 4.30
495 547 3.054802 TCTCCCTTTTTCTCTCTCATGGC 60.055 47.826 0.00 0.00 0.00 4.40
513 565 2.436824 GGCCGTCTTCTTCCAGCC 60.437 66.667 0.00 0.00 0.00 4.85
550 634 2.170607 CTCCGTTCCTCTCTCTCTCTCT 59.829 54.545 0.00 0.00 0.00 3.10
552 636 2.170607 CCGTTCCTCTCTCTCTCTCTCT 59.829 54.545 0.00 0.00 0.00 3.10
554 638 3.133003 CGTTCCTCTCTCTCTCTCTCTCT 59.867 52.174 0.00 0.00 0.00 3.10
555 639 4.698575 GTTCCTCTCTCTCTCTCTCTCTC 58.301 52.174 0.00 0.00 0.00 3.20
556 640 3.309296 TCCTCTCTCTCTCTCTCTCTCC 58.691 54.545 0.00 0.00 0.00 3.71
615 699 0.601057 TACGCTTGTACTGCTGCAGA 59.399 50.000 34.28 16.05 35.18 4.26
734 826 1.855451 TTTGTCCCCTTCCCCTCCC 60.855 63.158 0.00 0.00 0.00 4.30
802 903 3.621953 GCAAGTGGCTCTCTGAACT 57.378 52.632 0.00 0.00 40.25 3.01
803 904 1.437625 GCAAGTGGCTCTCTGAACTC 58.562 55.000 0.00 0.00 40.25 3.01
804 905 1.001860 GCAAGTGGCTCTCTGAACTCT 59.998 52.381 0.00 0.00 40.25 3.24
805 906 2.686235 CAAGTGGCTCTCTGAACTCTG 58.314 52.381 0.00 0.00 0.00 3.35
830 936 3.161067 TCTCTCCTCTTGTCACTCTTGG 58.839 50.000 0.00 0.00 0.00 3.61
957 1075 6.603997 GTGTTTAGAGGGAGAGAGAGATAACA 59.396 42.308 0.00 0.00 0.00 2.41
994 1112 2.709397 ACCCCTAGCACTACAAGTTTGT 59.291 45.455 2.75 2.75 44.86 2.83
1050 1172 1.447838 GCGTGGAGAATCGGAAGCA 60.448 57.895 0.00 0.00 34.37 3.91
1109 1231 4.394712 CACCTCCGCCTCCGCTTT 62.395 66.667 0.00 0.00 0.00 3.51
1227 1355 7.447374 TCTTGTTTGTTTTCTCTCAAGTCAA 57.553 32.000 0.00 0.00 35.35 3.18
1228 1356 7.530010 TCTTGTTTGTTTTCTCTCAAGTCAAG 58.470 34.615 0.00 0.00 37.88 3.02
1229 1357 5.640732 TGTTTGTTTTCTCTCAAGTCAAGC 58.359 37.500 0.00 0.00 0.00 4.01
1231 1359 3.792401 TGTTTTCTCTCAAGTCAAGCGA 58.208 40.909 0.00 0.00 0.00 4.93
1232 1360 4.380531 TGTTTTCTCTCAAGTCAAGCGAT 58.619 39.130 0.00 0.00 0.00 4.58
1240 1371 0.888619 AAGTCAAGCGATCGAGGACA 59.111 50.000 21.57 0.00 0.00 4.02
1269 1400 0.321919 ACTGGACTGATGCGCATGTT 60.322 50.000 30.76 11.47 0.00 2.71
1671 1802 2.430244 AAGTACGCCGTGCAGTCG 60.430 61.111 8.30 0.00 0.00 4.18
1767 1898 6.374613 GGTTCTTATCCGTTTCTTCCAATCTT 59.625 38.462 0.00 0.00 0.00 2.40
1782 1913 5.280499 TCCAATCTTGATCCACCTCTTCTA 58.720 41.667 0.00 0.00 0.00 2.10
1785 1916 6.325028 CCAATCTTGATCCACCTCTTCTACTA 59.675 42.308 0.00 0.00 0.00 1.82
1786 1917 7.016072 CCAATCTTGATCCACCTCTTCTACTAT 59.984 40.741 0.00 0.00 0.00 2.12
1787 1918 7.775053 ATCTTGATCCACCTCTTCTACTATC 57.225 40.000 0.00 0.00 0.00 2.08
1788 1919 6.916909 TCTTGATCCACCTCTTCTACTATCT 58.083 40.000 0.00 0.00 0.00 1.98
1789 1920 8.046867 TCTTGATCCACCTCTTCTACTATCTA 57.953 38.462 0.00 0.00 0.00 1.98
1838 1978 3.494626 TGCAGTCTTGTTGATTTCTCGTC 59.505 43.478 0.00 0.00 0.00 4.20
1860 2000 8.135529 TCGTCACTATATATTCTTGTGTCTTGG 58.864 37.037 0.00 0.00 0.00 3.61
1861 2001 7.096023 CGTCACTATATATTCTTGTGTCTTGGC 60.096 40.741 0.00 0.00 0.00 4.52
1862 2002 6.923508 TCACTATATATTCTTGTGTCTTGGCG 59.076 38.462 0.00 0.00 0.00 5.69
1863 2003 5.696724 ACTATATATTCTTGTGTCTTGGCGC 59.303 40.000 0.00 0.00 0.00 6.53
1898 2046 5.665459 AGTGCACTGCCTAGAAATTACTAG 58.335 41.667 20.97 0.00 39.40 2.57
1934 2082 2.103263 AGAGGATCGTGAACATTAGGGC 59.897 50.000 0.00 0.00 42.67 5.19
1935 2083 1.202533 AGGATCGTGAACATTAGGGCG 60.203 52.381 0.00 0.00 0.00 6.13
1936 2084 0.582005 GATCGTGAACATTAGGGCGC 59.418 55.000 0.00 0.00 0.00 6.53
1937 2085 0.814010 ATCGTGAACATTAGGGCGCC 60.814 55.000 21.18 21.18 0.00 6.53
2132 2304 1.134551 GTGTGGAAGGAGAGAGATGCC 60.135 57.143 0.00 0.00 0.00 4.40
2306 2482 3.490348 CTCTCCTCCCTGATTCTCTCTC 58.510 54.545 0.00 0.00 0.00 3.20
2307 2483 3.130450 TCTCCTCCCTGATTCTCTCTCT 58.870 50.000 0.00 0.00 0.00 3.10
2308 2484 3.138283 TCTCCTCCCTGATTCTCTCTCTC 59.862 52.174 0.00 0.00 0.00 3.20
2309 2485 3.130450 TCCTCCCTGATTCTCTCTCTCT 58.870 50.000 0.00 0.00 0.00 3.10
2317 2493 5.296151 TGATTCTCTCTCTCTCTCTCTCC 57.704 47.826 0.00 0.00 0.00 3.71
2378 2573 7.692291 CGTACCATATGACAAATGAACAAAGAC 59.308 37.037 3.65 0.00 0.00 3.01
2384 2579 5.436175 TGACAAATGAACAAAGACTCAGGA 58.564 37.500 0.00 0.00 0.00 3.86
2686 2891 1.986413 GACCAGCATCACCAGGTCT 59.014 57.895 0.00 0.00 45.46 3.85
3247 3458 4.451150 CGCCCTGCTACGAGCCAA 62.451 66.667 0.00 0.00 41.51 4.52
3266 3477 4.043200 GCAACAAGGACAGCCGCC 62.043 66.667 0.00 0.00 39.96 6.13
3387 3614 2.591923 TGCTGCTACCCTCTAGATCAG 58.408 52.381 0.00 0.00 0.00 2.90
3388 3615 1.272212 GCTGCTACCCTCTAGATCAGC 59.728 57.143 0.00 0.63 38.62 4.26
3389 3616 1.539388 CTGCTACCCTCTAGATCAGCG 59.461 57.143 0.00 0.00 0.00 5.18
3390 3617 0.242555 GCTACCCTCTAGATCAGCGC 59.757 60.000 0.00 0.00 0.00 5.92
3391 3618 1.904287 CTACCCTCTAGATCAGCGCT 58.096 55.000 2.64 2.64 0.00 5.92
3397 3624 0.753111 TCTAGATCAGCGCTGCAGGA 60.753 55.000 32.44 20.30 0.00 3.86
3428 3655 5.923733 TTGAACTGGGTAATCTCTCTCTC 57.076 43.478 0.00 0.00 0.00 3.20
3473 3731 3.004734 GCAAGTTAAGCAAGCTTTGGAGA 59.995 43.478 13.06 0.00 37.47 3.71
3570 3853 2.027929 TCCGTCGTCTCTTCTCTCTCTT 60.028 50.000 0.00 0.00 0.00 2.85
3584 3867 4.070716 CTCTCTCTTTGGCACTCAACAAT 58.929 43.478 0.00 0.00 34.67 2.71
3610 3893 1.134401 AGCTGCATTGCCTACATACGT 60.134 47.619 6.12 0.00 0.00 3.57
3611 3894 2.102420 AGCTGCATTGCCTACATACGTA 59.898 45.455 6.12 0.00 0.00 3.57
3612 3895 2.869801 GCTGCATTGCCTACATACGTAA 59.130 45.455 6.12 0.00 0.00 3.18
3699 3990 1.826096 GAGAAGTACACACTCCCTCCC 59.174 57.143 0.00 0.00 32.29 4.30
3713 4004 4.235372 CTCCCTCCCTTCCATATGTAGTT 58.765 47.826 1.24 0.00 0.00 2.24
3918 4219 5.854010 ATACGCTACATTATGGATCGGAT 57.146 39.130 5.65 0.00 0.00 4.18
3919 4220 3.849911 ACGCTACATTATGGATCGGATG 58.150 45.455 5.65 0.00 0.00 3.51
3920 4221 3.509967 ACGCTACATTATGGATCGGATGA 59.490 43.478 5.65 0.00 0.00 2.92
3952 4253 1.806542 CATGGCCACACACTACAAGTC 59.193 52.381 8.16 0.00 0.00 3.01
3974 4275 5.988561 GTCTTATATTCTCTGACTTGGGCAG 59.011 44.000 0.00 0.00 34.71 4.85
3994 4295 6.879458 GGGCAGAACAAAGTTTTCTCTATCTA 59.121 38.462 0.00 0.00 30.56 1.98
4024 4325 5.853282 GGTACACGTTGATCGGTATATGTAC 59.147 44.000 12.67 12.67 41.67 2.90
4051 4352 2.166907 ATCCAGATATAGAGCCCCCG 57.833 55.000 0.00 0.00 0.00 5.73
4054 4355 1.978580 CCAGATATAGAGCCCCCGTTT 59.021 52.381 0.00 0.00 0.00 3.60
4058 4543 5.424252 CCAGATATAGAGCCCCCGTTTATAA 59.576 44.000 0.00 0.00 0.00 0.98
4070 4555 5.221165 CCCCCGTTTATAATAAACCAGCAAG 60.221 44.000 0.00 0.00 0.00 4.01
4108 4593 2.028020 AGGGAGTACTTTGCTTCTTCGG 60.028 50.000 0.00 0.00 0.00 4.30
4109 4594 2.347731 GGAGTACTTTGCTTCTTCGGG 58.652 52.381 0.00 0.00 0.00 5.14
4110 4595 2.347731 GAGTACTTTGCTTCTTCGGGG 58.652 52.381 0.00 0.00 0.00 5.73
4111 4596 1.003233 AGTACTTTGCTTCTTCGGGGG 59.997 52.381 0.00 0.00 0.00 5.40
4218 4721 1.003233 GTGGTCACTTGGGAGCTCC 60.003 63.158 25.59 25.59 36.30 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
273 301 4.528076 TGGCCTATGGGTATGCTAAAAA 57.472 40.909 3.32 0.00 34.45 1.94
274 302 4.740154 ATGGCCTATGGGTATGCTAAAA 57.260 40.909 3.32 0.00 34.45 1.52
275 303 4.324254 GCTATGGCCTATGGGTATGCTAAA 60.324 45.833 3.32 0.00 34.45 1.85
276 304 3.199946 GCTATGGCCTATGGGTATGCTAA 59.800 47.826 3.32 0.00 34.45 3.09
277 305 2.771943 GCTATGGCCTATGGGTATGCTA 59.228 50.000 3.32 0.00 34.45 3.49
278 306 1.561542 GCTATGGCCTATGGGTATGCT 59.438 52.381 3.32 0.00 34.45 3.79
279 307 1.561542 AGCTATGGCCTATGGGTATGC 59.438 52.381 3.32 0.17 39.73 3.14
280 308 4.290093 TCTAGCTATGGCCTATGGGTATG 58.710 47.826 3.32 3.42 39.73 2.39
281 309 4.233053 TCTCTAGCTATGGCCTATGGGTAT 59.767 45.833 3.32 0.00 39.73 2.73
282 310 3.596500 TCTCTAGCTATGGCCTATGGGTA 59.403 47.826 3.32 7.23 39.73 3.69
283 311 2.383683 TCTCTAGCTATGGCCTATGGGT 59.616 50.000 3.32 6.39 39.73 4.51
284 312 3.030291 CTCTCTAGCTATGGCCTATGGG 58.970 54.545 3.32 0.00 39.73 4.00
285 313 3.953612 CTCTCTCTAGCTATGGCCTATGG 59.046 52.174 3.32 0.00 39.73 2.74
286 314 3.381272 GCTCTCTCTAGCTATGGCCTATG 59.619 52.174 3.32 0.00 39.50 2.23
287 315 3.011144 TGCTCTCTCTAGCTATGGCCTAT 59.989 47.826 3.32 0.00 43.19 2.57
288 316 2.376855 TGCTCTCTCTAGCTATGGCCTA 59.623 50.000 3.32 0.00 43.19 3.93
289 317 1.146774 TGCTCTCTCTAGCTATGGCCT 59.853 52.381 3.32 0.00 43.19 5.19
290 318 1.626686 TGCTCTCTCTAGCTATGGCC 58.373 55.000 0.00 0.00 43.19 5.36
291 319 2.824936 TCATGCTCTCTCTAGCTATGGC 59.175 50.000 0.00 0.00 43.19 4.40
292 320 4.082081 CCTTCATGCTCTCTCTAGCTATGG 60.082 50.000 0.00 0.00 43.19 2.74
293 321 4.082081 CCCTTCATGCTCTCTCTAGCTATG 60.082 50.000 0.00 0.00 43.19 2.23
294 322 4.088634 CCCTTCATGCTCTCTCTAGCTAT 58.911 47.826 0.00 0.00 43.19 2.97
295 323 3.139211 TCCCTTCATGCTCTCTCTAGCTA 59.861 47.826 0.00 0.00 43.19 3.32
296 324 2.091389 TCCCTTCATGCTCTCTCTAGCT 60.091 50.000 0.00 0.00 43.19 3.32
297 325 2.315176 TCCCTTCATGCTCTCTCTAGC 58.685 52.381 0.00 0.00 43.08 3.42
478 530 1.399791 GCCGCCATGAGAGAGAAAAAG 59.600 52.381 0.00 0.00 0.00 2.27
495 547 2.815647 GCTGGAAGAAGACGGCCG 60.816 66.667 26.86 26.86 34.07 6.13
513 565 1.067706 CGGAGATCAGGAGCTATGCAG 60.068 57.143 0.00 0.00 0.00 4.41
550 634 4.074526 GCTGGCAGTGCGGAGAGA 62.075 66.667 17.16 0.00 0.00 3.10
615 699 9.362151 TCTTCTTTCTCTCTCTACTTTCTTTCT 57.638 33.333 0.00 0.00 0.00 2.52
680 767 2.288395 GGTTGGTCAATGACTGCAAAGG 60.288 50.000 13.53 0.00 32.47 3.11
685 772 0.539438 TGGGGTTGGTCAATGACTGC 60.539 55.000 13.53 3.91 32.47 4.40
734 826 5.131142 AGGGAATAACACAGGTATCAAGGAG 59.869 44.000 0.00 0.00 0.00 3.69
785 886 2.298446 TCAGAGTTCAGAGAGCCACTTG 59.702 50.000 0.00 0.00 0.00 3.16
786 887 2.603021 TCAGAGTTCAGAGAGCCACTT 58.397 47.619 0.00 0.00 0.00 3.16
799 900 4.479158 ACAAGAGGAGAGAGTTCAGAGTT 58.521 43.478 0.00 0.00 0.00 3.01
800 901 4.079253 GACAAGAGGAGAGAGTTCAGAGT 58.921 47.826 0.00 0.00 0.00 3.24
801 902 4.078537 TGACAAGAGGAGAGAGTTCAGAG 58.921 47.826 0.00 0.00 0.00 3.35
802 903 3.823873 GTGACAAGAGGAGAGAGTTCAGA 59.176 47.826 0.00 0.00 0.00 3.27
803 904 3.826157 AGTGACAAGAGGAGAGAGTTCAG 59.174 47.826 0.00 0.00 0.00 3.02
804 905 3.823873 GAGTGACAAGAGGAGAGAGTTCA 59.176 47.826 0.00 0.00 0.00 3.18
805 906 4.079253 AGAGTGACAAGAGGAGAGAGTTC 58.921 47.826 0.00 0.00 0.00 3.01
830 936 2.037847 AACAGGATGGGGGCAAGC 59.962 61.111 0.00 0.00 43.62 4.01
957 1075 2.587307 AGGGGTTTGATTCAGGCCTTAT 59.413 45.455 0.00 0.00 0.00 1.73
994 1112 3.641436 AGGTGGTGATGATACATAAGCGA 59.359 43.478 0.00 0.00 0.00 4.93
1050 1172 3.804153 CTGATCTGCCGATGCCGCT 62.804 63.158 0.00 0.00 36.33 5.52
1061 1183 1.300481 CATGCTGCTGTCCTGATCTG 58.700 55.000 0.00 0.00 0.00 2.90
1109 1231 2.683933 GAGGAGGAGGGTTGGCGA 60.684 66.667 0.00 0.00 0.00 5.54
1184 1312 6.531021 ACAAGAAATTAAACCGAGGAGAAGA 58.469 36.000 0.00 0.00 0.00 2.87
1227 1355 0.737715 GCAACTTGTCCTCGATCGCT 60.738 55.000 11.09 0.00 0.00 4.93
1228 1356 0.737715 AGCAACTTGTCCTCGATCGC 60.738 55.000 11.09 0.00 0.00 4.58
1229 1357 0.994995 CAGCAACTTGTCCTCGATCG 59.005 55.000 9.36 9.36 0.00 3.69
1231 1359 0.976641 TCCAGCAACTTGTCCTCGAT 59.023 50.000 0.00 0.00 0.00 3.59
1232 1360 0.033504 GTCCAGCAACTTGTCCTCGA 59.966 55.000 0.00 0.00 0.00 4.04
1240 1371 1.131638 TCAGTCCAGTCCAGCAACTT 58.868 50.000 0.00 0.00 0.00 2.66
1269 1400 2.499693 TGCAACGATCCTCCAGATACAA 59.500 45.455 0.00 0.00 34.42 2.41
1671 1802 2.435059 GAGTGCGCCTTCCAGTCC 60.435 66.667 4.18 0.00 0.00 3.85
1767 1898 6.102762 TGGTAGATAGTAGAAGAGGTGGATCA 59.897 42.308 0.00 0.00 0.00 2.92
1782 1913 5.704515 GCTTTCATGATGCATGGTAGATAGT 59.295 40.000 2.46 0.00 41.66 2.12
1785 1916 4.726583 AGCTTTCATGATGCATGGTAGAT 58.273 39.130 19.07 2.16 41.66 1.98
1786 1917 4.160642 AGCTTTCATGATGCATGGTAGA 57.839 40.909 19.07 0.00 41.66 2.59
1787 1918 4.913335 AAGCTTTCATGATGCATGGTAG 57.087 40.909 19.07 6.48 41.66 3.18
1788 1919 4.951715 AGAAAGCTTTCATGATGCATGGTA 59.048 37.500 34.39 0.00 41.66 3.25
1789 1920 3.767673 AGAAAGCTTTCATGATGCATGGT 59.232 39.130 34.39 11.80 41.66 3.55
1838 1978 6.346919 GCGCCAAGACACAAGAATATATAGTG 60.347 42.308 0.00 0.00 36.34 2.74
1898 2046 8.838365 TCACGATCCTCTACTTAAATTCTACTC 58.162 37.037 0.00 0.00 0.00 2.59
1908 2056 6.264744 CCCTAATGTTCACGATCCTCTACTTA 59.735 42.308 0.00 0.00 0.00 2.24
1934 2082 4.327982 TCCTTCTCTCAGATTAATGGCG 57.672 45.455 0.00 0.00 0.00 5.69
1935 2083 5.062528 CCTTCCTTCTCTCAGATTAATGGC 58.937 45.833 0.00 0.00 0.00 4.40
1936 2084 6.491714 TCCTTCCTTCTCTCAGATTAATGG 57.508 41.667 0.00 0.00 0.00 3.16
1937 2085 7.563906 AGTTCCTTCCTTCTCTCAGATTAATG 58.436 38.462 0.00 0.00 0.00 1.90
1992 2145 0.392193 CTTCTGCGTTGCCTCATCCT 60.392 55.000 0.00 0.00 0.00 3.24
2132 2304 1.269174 AGCTCGATCCTCATCATCACG 59.731 52.381 0.00 0.00 0.00 4.35
2353 2529 8.730680 AGTCTTTGTTCATTTGTCATATGGTAC 58.269 33.333 2.13 0.00 0.00 3.34
2378 2573 6.937465 AGGTAAAGCTAAAACTTTCTCCTGAG 59.063 38.462 10.66 0.00 39.95 3.35
2384 2579 9.409918 AGAGAAAAGGTAAAGCTAAAACTTTCT 57.590 29.630 10.71 9.54 40.32 2.52
2478 2677 1.079819 CGTGATGAAGCTGTCCCGT 60.080 57.895 0.00 0.00 0.00 5.28
2634 2833 3.174987 TCCTGGTGGTGGTGGTGG 61.175 66.667 0.00 0.00 34.23 4.61
2635 2834 2.431683 CTCCTGGTGGTGGTGGTG 59.568 66.667 0.00 0.00 34.23 4.17
2636 2835 3.570212 GCTCCTGGTGGTGGTGGT 61.570 66.667 0.00 0.00 34.23 4.16
2637 2836 3.252284 AGCTCCTGGTGGTGGTGG 61.252 66.667 0.00 0.00 36.37 4.61
2638 2837 2.348998 GAGCTCCTGGTGGTGGTG 59.651 66.667 0.87 0.00 37.64 4.17
2639 2838 3.314331 CGAGCTCCTGGTGGTGGT 61.314 66.667 8.47 0.00 39.85 4.16
2673 2872 1.930908 GCTGCAAGACCTGGTGATGC 61.931 60.000 20.77 20.77 34.07 3.91
3247 3458 2.555547 GCGGCTGTCCTTGTTGCTT 61.556 57.895 0.00 0.00 0.00 3.91
3266 3477 2.900167 TTGCTGTTCTGCTGCTGCG 61.900 57.895 11.21 6.13 43.34 5.18
3278 3501 3.058160 GCCATGGCTCGTTGCTGT 61.058 61.111 29.98 0.00 42.39 4.40
3291 3514 1.532316 GCTACCCATGCCATGCCAT 60.532 57.895 0.00 0.00 0.00 4.40
3397 3624 1.981256 ACCCAGTTCAAAACGCATCT 58.019 45.000 0.00 0.00 36.23 2.90
3479 3737 1.347707 CAGTTGGCTTCTACTCCCACA 59.652 52.381 0.00 0.00 0.00 4.17
3480 3738 1.348036 ACAGTTGGCTTCTACTCCCAC 59.652 52.381 0.00 0.00 0.00 4.61
3481 3739 1.729586 ACAGTTGGCTTCTACTCCCA 58.270 50.000 0.00 0.00 0.00 4.37
3483 3741 3.261137 ACCTTACAGTTGGCTTCTACTCC 59.739 47.826 0.00 0.00 0.00 3.85
3484 3742 4.538746 ACCTTACAGTTGGCTTCTACTC 57.461 45.455 0.00 0.00 0.00 2.59
3485 3743 6.429521 TTTACCTTACAGTTGGCTTCTACT 57.570 37.500 0.00 0.00 0.00 2.57
3570 3853 2.361757 CTGACCAATTGTTGAGTGCCAA 59.638 45.455 4.43 0.00 0.00 4.52
3584 3867 0.038021 TAGGCAATGCAGCTGACCAA 59.962 50.000 20.43 0.00 34.17 3.67
3610 3893 6.978659 CAGCAAACGGAGACAGTAGATATTTA 59.021 38.462 0.00 0.00 0.00 1.40
3611 3894 5.812642 CAGCAAACGGAGACAGTAGATATTT 59.187 40.000 0.00 0.00 0.00 1.40
3612 3895 5.352284 CAGCAAACGGAGACAGTAGATATT 58.648 41.667 0.00 0.00 0.00 1.28
3757 4048 9.103048 GTTAGATGTAAATGTTCTTCACAAACG 57.897 33.333 0.00 0.00 39.50 3.60
3900 4201 5.482908 ACTTCATCCGATCCATAATGTAGC 58.517 41.667 0.00 0.00 0.00 3.58
3913 4214 4.202151 CCATGAGACATGTACTTCATCCGA 60.202 45.833 13.94 0.00 34.09 4.55
3914 4215 4.053983 CCATGAGACATGTACTTCATCCG 58.946 47.826 13.94 7.14 34.09 4.18
3918 4219 2.571202 TGGCCATGAGACATGTACTTCA 59.429 45.455 0.00 3.89 0.00 3.02
3919 4220 2.939103 GTGGCCATGAGACATGTACTTC 59.061 50.000 9.72 0.00 0.00 3.01
3920 4221 2.305635 TGTGGCCATGAGACATGTACTT 59.694 45.455 9.72 0.00 0.00 2.24
3952 4253 6.166984 TCTGCCCAAGTCAGAGAATATAAG 57.833 41.667 0.00 0.00 35.81 1.73
3994 4295 3.256631 ACCGATCAACGTGTACCTTAGTT 59.743 43.478 0.00 0.00 40.78 2.24
4024 4325 5.942826 GGGCTCTATATCTGGATTTTCCTTG 59.057 44.000 0.00 0.00 37.46 3.61
4043 4344 4.463070 TGGTTTATTATAAACGGGGGCTC 58.537 43.478 18.08 6.46 0.00 4.70
4045 4346 3.005050 GCTGGTTTATTATAAACGGGGGC 59.995 47.826 18.08 15.04 0.00 5.80
4225 4728 1.599542 GTAGGCCGCATTTTAGCTCTG 59.400 52.381 0.00 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.