Multiple sequence alignment - TraesCS1A01G041500

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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 TraesCS1A01G041500 chr1A 100.000 2252 0 0 1 2252 22656694 22658945 0.000000e+00 4159.0
1 TraesCS1A01G041500 chr1B 89.256 1452 95 20 1 1416 16465767 16464341 0.000000e+00 1760.0
2 TraesCS1A01G041500 chr1B 89.644 618 52 8 1644 2252 16464265 16463651 0.000000e+00 776.0
3 TraesCS1A01G041500 chr1B 76.162 495 93 14 812 1289 23840155 23839669 1.040000e-58 237.0
4 TraesCS1A01G041500 chr1B 96.104 77 3 0 1492 1568 16464340 16464264 2.350000e-25 126.0
5 TraesCS1A01G041500 chr1B 84.337 83 12 1 1902 1983 529212727 529212809 1.850000e-11 80.5
6 TraesCS1A01G041500 chr1D 90.637 769 59 8 1 761 10987065 10986302 0.000000e+00 1009.0
7 TraesCS1A01G041500 chr1D 81.400 457 52 7 966 1405 10963774 10963334 2.140000e-90 342.0
8 TraesCS1A01G041500 chr1D 86.111 108 13 2 2002 2109 10957376 10957271 5.080000e-22 115.0
9 TraesCS1A01G041500 chr1D 98.148 54 1 0 1 54 11032814 11032761 6.620000e-16 95.3
10 TraesCS1A01G041500 chr1D 98.148 54 1 0 1 54 11082020 11081967 6.620000e-16 95.3
11 TraesCS1A01G041500 chr1D 98.148 54 1 0 1 54 11116027 11115974 6.620000e-16 95.3
12 TraesCS1A01G041500 chr1D 98.039 51 1 0 4 54 11001941 11001891 3.080000e-14 89.8
13 TraesCS1A01G041500 chr5D 85.859 99 13 1 1902 1999 459067834 459067736 1.100000e-18 104.0
14 TraesCS1A01G041500 chr6B 100.000 50 0 0 1902 1951 225312498 225312449 2.380000e-15 93.5
15 TraesCS1A01G041500 chr6B 87.302 63 7 1 1903 1964 84859912 84859974 1.120000e-08 71.3
16 TraesCS1A01G041500 chr5A 83.721 86 12 2 1916 1999 578048751 578048666 1.850000e-11 80.5
17 TraesCS1A01G041500 chr6D 87.302 63 7 1 1903 1964 36584171 36584233 1.120000e-08 71.3


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 TraesCS1A01G041500 chr1A 22656694 22658945 2251 False 4159.000000 4159 100.000 1 2252 1 chr1A.!!$F1 2251
1 TraesCS1A01G041500 chr1B 16463651 16465767 2116 True 887.333333 1760 91.668 1 2252 3 chr1B.!!$R2 2251
2 TraesCS1A01G041500 chr1D 10986302 10987065 763 True 1009.000000 1009 90.637 1 761 1 chr1D.!!$R3 760

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
486 487 0.03467 GCTGAATGGACCTGAAGCCT 60.035 55.0 0.0 0.0 0.0 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1480 1520 0.108138 ACTAGCACCACCGAGCATTC 60.108 55.0 0.0 0.0 0.0 2.67 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
24 25 2.476185 GCATACATTTCTTCGCGCTTGT 60.476 45.455 5.56 0.93 0.00 3.16
283 284 1.203928 GAGCTCATCGTTGATGGACG 58.796 55.000 9.40 0.00 40.15 4.79
356 357 4.649088 AAGTAGCACCAAAACTGAAACC 57.351 40.909 0.00 0.00 0.00 3.27
357 358 2.616842 AGTAGCACCAAAACTGAAACCG 59.383 45.455 0.00 0.00 0.00 4.44
361 362 2.794350 GCACCAAAACTGAAACCGATTG 59.206 45.455 0.00 0.00 0.00 2.67
364 365 5.288804 CACCAAAACTGAAACCGATTGATT 58.711 37.500 0.00 0.00 0.00 2.57
365 366 5.175491 CACCAAAACTGAAACCGATTGATTG 59.825 40.000 0.00 0.00 0.00 2.67
374 375 4.558538 AACCGATTGATTGATAGCAAGC 57.441 40.909 1.19 1.19 40.69 4.01
428 429 8.660373 AGTTAGCTAAAGATTGATCGACAAAAG 58.340 33.333 7.99 1.33 42.03 2.27
429 430 5.873732 AGCTAAAGATTGATCGACAAAAGC 58.126 37.500 4.87 8.39 42.03 3.51
430 431 5.412594 AGCTAAAGATTGATCGACAAAAGCA 59.587 36.000 4.87 0.00 42.03 3.91
437 438 3.673902 TGATCGACAAAAGCAAGATGGA 58.326 40.909 0.00 0.00 0.00 3.41
438 439 4.264253 TGATCGACAAAAGCAAGATGGAT 58.736 39.130 0.00 0.00 0.00 3.41
439 440 5.427378 TGATCGACAAAAGCAAGATGGATA 58.573 37.500 0.00 0.00 0.00 2.59
440 441 6.057533 TGATCGACAAAAGCAAGATGGATAT 58.942 36.000 0.00 0.00 0.00 1.63
441 442 5.739752 TCGACAAAAGCAAGATGGATATG 57.260 39.130 0.00 0.00 0.00 1.78
442 443 5.185454 TCGACAAAAGCAAGATGGATATGT 58.815 37.500 0.00 0.00 0.00 2.29
443 444 5.065090 TCGACAAAAGCAAGATGGATATGTG 59.935 40.000 0.00 0.00 0.00 3.21
444 445 5.163723 CGACAAAAGCAAGATGGATATGTGT 60.164 40.000 0.00 0.00 0.00 3.72
445 446 6.037062 CGACAAAAGCAAGATGGATATGTGTA 59.963 38.462 0.00 0.00 0.00 2.90
480 481 1.746615 CACCGGCTGAATGGACCTG 60.747 63.158 0.00 0.00 0.00 4.00
484 485 1.372087 CGGCTGAATGGACCTGAAGC 61.372 60.000 0.00 0.00 0.00 3.86
485 486 1.034292 GGCTGAATGGACCTGAAGCC 61.034 60.000 10.87 10.87 43.05 4.35
486 487 0.034670 GCTGAATGGACCTGAAGCCT 60.035 55.000 0.00 0.00 0.00 4.58
487 488 1.210478 GCTGAATGGACCTGAAGCCTA 59.790 52.381 0.00 0.00 0.00 3.93
490 491 4.444876 GCTGAATGGACCTGAAGCCTATTA 60.445 45.833 0.00 0.00 0.00 0.98
502 506 8.425703 ACCTGAAGCCTATTACTTAATCTTCTC 58.574 37.037 0.00 0.00 31.05 2.87
504 508 9.823647 CTGAAGCCTATTACTTAATCTTCTCAA 57.176 33.333 0.00 0.00 31.05 3.02
516 520 8.164070 ACTTAATCTTCTCAACTTGGTTGGTAT 58.836 33.333 9.98 0.00 42.99 2.73
521 525 5.560722 TCTCAACTTGGTTGGTATCTTGA 57.439 39.130 9.98 0.00 42.99 3.02
536 540 5.297776 GGTATCTTGATGCTGCATAAACACT 59.702 40.000 16.23 2.57 0.00 3.55
569 579 4.015764 GGGTACTTATAGGGGAGATCGAC 58.984 52.174 0.00 0.00 0.00 4.20
577 587 0.959553 GGGGAGATCGACATAAGCGA 59.040 55.000 0.00 0.00 42.48 4.93
587 597 2.159973 CGACATAAGCGACACTGTGTTG 60.160 50.000 21.29 21.29 34.88 3.33
635 645 1.829456 CATGCATGTACCGAGGGGA 59.171 57.895 18.91 0.00 36.97 4.81
636 646 0.180171 CATGCATGTACCGAGGGGAA 59.820 55.000 18.91 0.00 36.97 3.97
720 734 2.358267 ACGTACGGATGCTAAGGAAGAG 59.642 50.000 21.06 0.00 0.00 2.85
781 795 3.658709 GCTAGGAGCTCAATGTACCATC 58.341 50.000 17.19 0.00 38.45 3.51
878 892 9.093458 TGATGCTATATCATCAACTTCTCCTTA 57.907 33.333 15.21 0.00 46.84 2.69
922 936 0.107456 CTTCTGGTGAGTGTGTGCCT 59.893 55.000 0.00 0.00 0.00 4.75
955 969 1.904287 TGTTCACCCATTTTCCCTCG 58.096 50.000 0.00 0.00 0.00 4.63
964 978 3.130340 CCCATTTTCCCTCGTGGTTTATG 59.870 47.826 2.33 1.37 34.77 1.90
965 979 3.428862 CCATTTTCCCTCGTGGTTTATGC 60.429 47.826 2.33 0.00 34.77 3.14
966 980 2.871096 TTTCCCTCGTGGTTTATGCT 57.129 45.000 2.33 0.00 34.77 3.79
967 981 2.871096 TTCCCTCGTGGTTTATGCTT 57.129 45.000 2.33 0.00 34.77 3.91
969 983 3.985019 TCCCTCGTGGTTTATGCTTTA 57.015 42.857 2.33 0.00 34.77 1.85
970 984 4.497291 TCCCTCGTGGTTTATGCTTTAT 57.503 40.909 2.33 0.00 34.77 1.40
1025 1052 0.842030 TCCATGGAGGGAAGCACTGT 60.842 55.000 11.44 0.00 38.24 3.55
1038 1065 2.843701 AGCACTGTGAAGTTTCCAGAG 58.156 47.619 12.86 9.02 32.97 3.35
1045 1072 1.133823 TGAAGTTTCCAGAGCCTGCAA 60.134 47.619 0.00 0.00 0.00 4.08
1047 1074 0.475906 AGTTTCCAGAGCCTGCAAGT 59.524 50.000 0.00 0.00 0.00 3.16
1080 1107 0.249447 CCAGCAGTGTGAAGACGTCA 60.249 55.000 19.50 0.00 0.00 4.35
1084 1111 1.605457 GCAGTGTGAAGACGTCATGGA 60.605 52.381 19.50 0.00 38.90 3.41
1104 1131 1.753463 AGAGGTCGTCGGGATGTCC 60.753 63.158 0.00 0.00 0.00 4.02
1128 1155 2.437281 TGAGAAGGCCAAGGAGATCATC 59.563 50.000 5.01 0.00 0.00 2.92
1129 1156 1.415659 AGAAGGCCAAGGAGATCATCG 59.584 52.381 5.01 0.00 0.00 3.84
1130 1157 0.179034 AAGGCCAAGGAGATCATCGC 60.179 55.000 5.01 0.00 0.00 4.58
1133 1160 0.464373 GCCAAGGAGATCATCGCCAA 60.464 55.000 10.43 0.00 38.94 4.52
1166 1193 1.063341 TGCTGAGATAGAGGTCCTGCT 60.063 52.381 0.00 0.00 0.00 4.24
1178 1205 0.179134 GTCCTGCTAGTCGATGCGTT 60.179 55.000 0.00 0.00 0.00 4.84
1182 1209 0.457853 TGCTAGTCGATGCGTTGGTC 60.458 55.000 0.00 0.00 0.00 4.02
1219 1246 1.606994 CCGACCGTGTCCAAATCTTCA 60.607 52.381 0.00 0.00 0.00 3.02
1223 1250 2.289444 ACCGTGTCCAAATCTTCATCGT 60.289 45.455 0.00 0.00 0.00 3.73
1276 1303 6.596888 GCTAGCTTATCAGGCATGAATCATTA 59.403 38.462 4.62 0.00 39.39 1.90
1310 1337 6.753913 AACAGAGGATAAAGATATCTGGCA 57.246 37.500 5.86 0.00 41.32 4.92
1315 1342 6.499699 AGAGGATAAAGATATCTGGCACATCA 59.500 38.462 5.86 0.00 38.39 3.07
1318 1345 2.855209 AGATATCTGGCACATCAGGC 57.145 50.000 3.89 0.00 38.20 4.85
1333 1360 1.143684 TCAGGCAGGCACTTTCTCTTT 59.856 47.619 0.00 0.00 34.60 2.52
1352 1392 8.455903 TCTCTTTGATAAGGAATAAAGGCATG 57.544 34.615 0.00 0.00 32.48 4.06
1398 1438 4.899352 AGTTCAGGCTTCAGTGTATTCT 57.101 40.909 0.00 0.00 0.00 2.40
1407 1447 4.937620 GCTTCAGTGTATTCTTCCATGACA 59.062 41.667 0.00 0.00 0.00 3.58
1416 1456 1.075212 TCTTCCATGACATGTTGGGCA 59.925 47.619 15.13 2.26 33.62 5.36
1417 1457 2.104967 CTTCCATGACATGTTGGGCAT 58.895 47.619 15.13 4.54 38.60 4.40
1430 1470 6.982160 ATGTTGGGCATGACATGTATAATT 57.018 33.333 16.62 0.00 35.31 1.40
1431 1471 6.146601 TGTTGGGCATGACATGTATAATTG 57.853 37.500 16.62 0.00 0.00 2.32
1432 1472 4.852134 TGGGCATGACATGTATAATTGC 57.148 40.909 16.62 3.94 0.00 3.56
1433 1473 3.252944 TGGGCATGACATGTATAATTGCG 59.747 43.478 16.62 0.00 0.00 4.85
1434 1474 3.236816 GGCATGACATGTATAATTGCGC 58.763 45.455 16.62 0.00 0.00 6.09
1435 1475 3.058016 GGCATGACATGTATAATTGCGCT 60.058 43.478 16.62 0.00 0.00 5.92
1436 1476 4.153986 GCATGACATGTATAATTGCGCTC 58.846 43.478 16.62 0.00 0.00 5.03
1437 1477 4.083643 GCATGACATGTATAATTGCGCTCT 60.084 41.667 16.62 0.00 0.00 4.09
1438 1478 5.615708 CATGACATGTATAATTGCGCTCTC 58.384 41.667 9.73 0.00 0.00 3.20
1439 1479 4.948847 TGACATGTATAATTGCGCTCTCT 58.051 39.130 9.73 0.00 0.00 3.10
1440 1480 4.746611 TGACATGTATAATTGCGCTCTCTG 59.253 41.667 9.73 0.00 0.00 3.35
1441 1481 4.697514 ACATGTATAATTGCGCTCTCTGT 58.302 39.130 9.73 0.00 0.00 3.41
1442 1482 5.118990 ACATGTATAATTGCGCTCTCTGTT 58.881 37.500 9.73 0.00 0.00 3.16
1443 1483 5.586243 ACATGTATAATTGCGCTCTCTGTTT 59.414 36.000 9.73 0.00 0.00 2.83
1444 1484 5.718649 TGTATAATTGCGCTCTCTGTTTC 57.281 39.130 9.73 0.00 0.00 2.78
1445 1485 5.175127 TGTATAATTGCGCTCTCTGTTTCA 58.825 37.500 9.73 0.00 0.00 2.69
1446 1486 5.817296 TGTATAATTGCGCTCTCTGTTTCAT 59.183 36.000 9.73 0.00 0.00 2.57
1447 1487 3.754188 AATTGCGCTCTCTGTTTCATC 57.246 42.857 9.73 0.00 0.00 2.92
1448 1488 2.462456 TTGCGCTCTCTGTTTCATCT 57.538 45.000 9.73 0.00 0.00 2.90
1449 1489 3.592898 TTGCGCTCTCTGTTTCATCTA 57.407 42.857 9.73 0.00 0.00 1.98
1450 1490 3.156511 TGCGCTCTCTGTTTCATCTAG 57.843 47.619 9.73 0.00 0.00 2.43
1451 1491 2.755103 TGCGCTCTCTGTTTCATCTAGA 59.245 45.455 9.73 0.00 0.00 2.43
1452 1492 3.382865 TGCGCTCTCTGTTTCATCTAGAT 59.617 43.478 9.73 0.00 0.00 1.98
1453 1493 4.142071 TGCGCTCTCTGTTTCATCTAGATT 60.142 41.667 9.73 0.00 0.00 2.40
1454 1494 5.067805 TGCGCTCTCTGTTTCATCTAGATTA 59.932 40.000 9.73 0.00 0.00 1.75
1455 1495 5.401079 GCGCTCTCTGTTTCATCTAGATTAC 59.599 44.000 1.33 2.71 0.00 1.89
1456 1496 6.734137 CGCTCTCTGTTTCATCTAGATTACT 58.266 40.000 1.33 0.00 0.00 2.24
1457 1497 6.855914 CGCTCTCTGTTTCATCTAGATTACTC 59.144 42.308 1.33 0.00 0.00 2.59
1458 1498 7.255104 CGCTCTCTGTTTCATCTAGATTACTCT 60.255 40.741 1.33 0.00 35.39 3.24
1459 1499 8.413229 GCTCTCTGTTTCATCTAGATTACTCTT 58.587 37.037 1.33 0.00 32.66 2.85
1466 1506 9.902196 GTTTCATCTAGATTACTCTTACTAGGC 57.098 37.037 1.33 0.00 34.80 3.93
1467 1507 9.642343 TTTCATCTAGATTACTCTTACTAGGCA 57.358 33.333 1.33 0.00 34.80 4.75
1468 1508 8.856153 TCATCTAGATTACTCTTACTAGGCAG 57.144 38.462 1.33 0.00 34.80 4.85
1469 1509 7.885922 TCATCTAGATTACTCTTACTAGGCAGG 59.114 40.741 1.33 0.00 34.80 4.85
1470 1510 6.544650 TCTAGATTACTCTTACTAGGCAGGG 58.455 44.000 0.00 0.00 34.80 4.45
1471 1511 5.405063 AGATTACTCTTACTAGGCAGGGA 57.595 43.478 0.00 0.00 0.00 4.20
1472 1512 5.778542 AGATTACTCTTACTAGGCAGGGAA 58.221 41.667 0.00 0.00 0.00 3.97
1473 1513 6.386284 AGATTACTCTTACTAGGCAGGGAAT 58.614 40.000 0.00 0.00 0.00 3.01
1474 1514 5.871396 TTACTCTTACTAGGCAGGGAATG 57.129 43.478 0.00 0.00 0.00 2.67
1475 1515 3.725634 ACTCTTACTAGGCAGGGAATGT 58.274 45.455 0.00 0.00 0.00 2.71
1476 1516 3.452627 ACTCTTACTAGGCAGGGAATGTG 59.547 47.826 0.00 0.00 0.00 3.21
1477 1517 2.170607 TCTTACTAGGCAGGGAATGTGC 59.829 50.000 0.00 0.00 40.42 4.57
1485 1525 2.807622 GGGAATGTGCCCGAATGC 59.192 61.111 0.00 0.00 38.58 3.56
1486 1526 1.754234 GGGAATGTGCCCGAATGCT 60.754 57.895 0.00 0.00 38.58 3.79
1487 1527 1.728490 GGGAATGTGCCCGAATGCTC 61.728 60.000 0.00 0.00 38.58 4.26
1488 1528 1.353103 GAATGTGCCCGAATGCTCG 59.647 57.895 0.00 0.00 45.02 5.03
1506 1546 3.741388 GCTCGGTGGTGCTAGTATTTCAT 60.741 47.826 0.00 0.00 0.00 2.57
1525 1565 6.567769 TTCATGTTGCGAGTTTTTCTTTTC 57.432 33.333 0.00 0.00 0.00 2.29
1556 1596 0.732571 CAAGTTGTGAGTTGGCACGT 59.267 50.000 0.00 0.00 41.63 4.49
1568 1608 2.880268 GTTGGCACGTTAAACCTTAGGT 59.120 45.455 0.00 0.00 37.65 3.08
1581 1621 3.408634 ACCTTAGGTTTGTTCACATCGG 58.591 45.455 0.00 0.00 27.29 4.18
1582 1622 3.181448 ACCTTAGGTTTGTTCACATCGGT 60.181 43.478 0.00 0.00 27.29 4.69
1583 1623 3.818773 CCTTAGGTTTGTTCACATCGGTT 59.181 43.478 0.00 0.00 0.00 4.44
1584 1624 4.998672 CCTTAGGTTTGTTCACATCGGTTA 59.001 41.667 0.00 0.00 0.00 2.85
1585 1625 5.121768 CCTTAGGTTTGTTCACATCGGTTAG 59.878 44.000 0.00 0.00 0.00 2.34
1586 1626 2.812011 AGGTTTGTTCACATCGGTTAGC 59.188 45.455 0.00 0.00 0.00 3.09
1587 1627 2.095415 GGTTTGTTCACATCGGTTAGCC 60.095 50.000 0.00 0.00 0.00 3.93
1600 1640 2.830104 GGTTAGCCGGTCATTTATCGT 58.170 47.619 1.90 0.00 0.00 3.73
1601 1641 3.981211 GGTTAGCCGGTCATTTATCGTA 58.019 45.455 1.90 0.00 0.00 3.43
1602 1642 4.563061 GGTTAGCCGGTCATTTATCGTAT 58.437 43.478 1.90 0.00 0.00 3.06
1603 1643 4.992951 GGTTAGCCGGTCATTTATCGTATT 59.007 41.667 1.90 0.00 0.00 1.89
1604 1644 5.119743 GGTTAGCCGGTCATTTATCGTATTC 59.880 44.000 1.90 0.00 0.00 1.75
1605 1645 3.660865 AGCCGGTCATTTATCGTATTCC 58.339 45.455 1.90 0.00 0.00 3.01
1606 1646 2.740447 GCCGGTCATTTATCGTATTCCC 59.260 50.000 1.90 0.00 0.00 3.97
1607 1647 3.556423 GCCGGTCATTTATCGTATTCCCT 60.556 47.826 1.90 0.00 0.00 4.20
1608 1648 4.322198 GCCGGTCATTTATCGTATTCCCTA 60.322 45.833 1.90 0.00 0.00 3.53
1609 1649 5.408356 CCGGTCATTTATCGTATTCCCTAG 58.592 45.833 0.00 0.00 0.00 3.02
1610 1650 5.184479 CCGGTCATTTATCGTATTCCCTAGA 59.816 44.000 0.00 0.00 0.00 2.43
1611 1651 6.323266 CGGTCATTTATCGTATTCCCTAGAG 58.677 44.000 0.00 0.00 0.00 2.43
1612 1652 6.100668 GGTCATTTATCGTATTCCCTAGAGC 58.899 44.000 0.00 0.00 0.00 4.09
1613 1653 6.295123 GGTCATTTATCGTATTCCCTAGAGCA 60.295 42.308 0.00 0.00 0.00 4.26
1614 1654 7.152645 GTCATTTATCGTATTCCCTAGAGCAA 58.847 38.462 0.00 0.00 0.00 3.91
1615 1655 7.656137 GTCATTTATCGTATTCCCTAGAGCAAA 59.344 37.037 0.00 0.00 0.00 3.68
1616 1656 7.656137 TCATTTATCGTATTCCCTAGAGCAAAC 59.344 37.037 0.00 0.00 0.00 2.93
1617 1657 6.474140 TTATCGTATTCCCTAGAGCAAACA 57.526 37.500 0.00 0.00 0.00 2.83
1618 1658 5.552870 ATCGTATTCCCTAGAGCAAACAT 57.447 39.130 0.00 0.00 0.00 2.71
1619 1659 4.945246 TCGTATTCCCTAGAGCAAACATC 58.055 43.478 0.00 0.00 0.00 3.06
1620 1660 4.058817 CGTATTCCCTAGAGCAAACATCC 58.941 47.826 0.00 0.00 0.00 3.51
1621 1661 4.442893 CGTATTCCCTAGAGCAAACATCCA 60.443 45.833 0.00 0.00 0.00 3.41
1622 1662 4.591321 ATTCCCTAGAGCAAACATCCAA 57.409 40.909 0.00 0.00 0.00 3.53
1623 1663 4.380843 TTCCCTAGAGCAAACATCCAAA 57.619 40.909 0.00 0.00 0.00 3.28
1624 1664 4.380843 TCCCTAGAGCAAACATCCAAAA 57.619 40.909 0.00 0.00 0.00 2.44
1625 1665 4.735369 TCCCTAGAGCAAACATCCAAAAA 58.265 39.130 0.00 0.00 0.00 1.94
1626 1666 4.766891 TCCCTAGAGCAAACATCCAAAAAG 59.233 41.667 0.00 0.00 0.00 2.27
1627 1667 4.766891 CCCTAGAGCAAACATCCAAAAAGA 59.233 41.667 0.00 0.00 0.00 2.52
1628 1668 5.335976 CCCTAGAGCAAACATCCAAAAAGAC 60.336 44.000 0.00 0.00 0.00 3.01
1629 1669 4.228912 AGAGCAAACATCCAAAAAGACG 57.771 40.909 0.00 0.00 0.00 4.18
1630 1670 3.882888 AGAGCAAACATCCAAAAAGACGA 59.117 39.130 0.00 0.00 0.00 4.20
1631 1671 3.964909 AGCAAACATCCAAAAAGACGAC 58.035 40.909 0.00 0.00 0.00 4.34
1632 1672 3.380004 AGCAAACATCCAAAAAGACGACA 59.620 39.130 0.00 0.00 0.00 4.35
1633 1673 4.109050 GCAAACATCCAAAAAGACGACAA 58.891 39.130 0.00 0.00 0.00 3.18
1634 1674 4.026886 GCAAACATCCAAAAAGACGACAAC 60.027 41.667 0.00 0.00 0.00 3.32
1635 1675 4.974368 AACATCCAAAAAGACGACAACA 57.026 36.364 0.00 0.00 0.00 3.33
1636 1676 4.974368 ACATCCAAAAAGACGACAACAA 57.026 36.364 0.00 0.00 0.00 2.83
1637 1677 4.668289 ACATCCAAAAAGACGACAACAAC 58.332 39.130 0.00 0.00 0.00 3.32
1638 1678 4.156922 ACATCCAAAAAGACGACAACAACA 59.843 37.500 0.00 0.00 0.00 3.33
1639 1679 4.768130 TCCAAAAAGACGACAACAACAA 57.232 36.364 0.00 0.00 0.00 2.83
1640 1680 4.728534 TCCAAAAAGACGACAACAACAAG 58.271 39.130 0.00 0.00 0.00 3.16
1641 1681 4.456222 TCCAAAAAGACGACAACAACAAGA 59.544 37.500 0.00 0.00 0.00 3.02
1642 1682 4.793216 CCAAAAAGACGACAACAACAAGAG 59.207 41.667 0.00 0.00 0.00 2.85
1643 1683 4.616181 AAAAGACGACAACAACAAGAGG 57.384 40.909 0.00 0.00 0.00 3.69
1644 1684 2.240493 AGACGACAACAACAAGAGGG 57.760 50.000 0.00 0.00 0.00 4.30
1645 1685 1.760613 AGACGACAACAACAAGAGGGA 59.239 47.619 0.00 0.00 0.00 4.20
1646 1686 2.368875 AGACGACAACAACAAGAGGGAT 59.631 45.455 0.00 0.00 0.00 3.85
1647 1687 3.576982 AGACGACAACAACAAGAGGGATA 59.423 43.478 0.00 0.00 0.00 2.59
1648 1688 4.039973 AGACGACAACAACAAGAGGGATAA 59.960 41.667 0.00 0.00 0.00 1.75
1649 1689 4.906618 ACGACAACAACAAGAGGGATAAT 58.093 39.130 0.00 0.00 0.00 1.28
1650 1690 6.045072 ACGACAACAACAAGAGGGATAATA 57.955 37.500 0.00 0.00 0.00 0.98
1651 1691 6.650120 ACGACAACAACAAGAGGGATAATAT 58.350 36.000 0.00 0.00 0.00 1.28
1681 1721 4.458989 TGGATCTAAGCACAAATTGGTCAC 59.541 41.667 0.00 0.00 33.68 3.67
1699 1739 7.534723 TGGTCACTACTTACAGTAACTGAAT 57.465 36.000 0.00 0.00 35.18 2.57
1722 1762 5.416083 TGTTATGTGTCACCCTAAATCTCG 58.584 41.667 0.00 0.00 0.00 4.04
1724 1764 4.819105 ATGTGTCACCCTAAATCTCGAA 57.181 40.909 0.00 0.00 0.00 3.71
1729 1769 3.933332 GTCACCCTAAATCTCGAACAAGG 59.067 47.826 0.00 0.00 0.00 3.61
1738 1778 2.857483 TCTCGAACAAGGGCAAAATCA 58.143 42.857 0.00 0.00 0.00 2.57
1771 1811 7.642082 TGACACTAGAAGAAATCCTAGTACC 57.358 40.000 0.00 0.00 42.47 3.34
1775 1815 7.013464 ACACTAGAAGAAATCCTAGTACCATCG 59.987 40.741 0.00 0.00 42.47 3.84
1791 1831 3.179830 CCATCGTCGGTACTCAAAGAAG 58.820 50.000 0.00 0.00 0.00 2.85
1824 1864 7.433131 CGCTTTATCTGTTGCACAAATAATGAT 59.567 33.333 0.00 0.00 0.00 2.45
1825 1865 8.537223 GCTTTATCTGTTGCACAAATAATGATG 58.463 33.333 0.00 0.00 0.00 3.07
1828 1868 9.926158 TTATCTGTTGCACAAATAATGATGTTT 57.074 25.926 0.00 0.00 0.00 2.83
1850 1890 9.515020 TGTTTTATCACTTTCACATGAACTTTC 57.485 29.630 0.00 0.00 33.13 2.62
1856 1896 8.450578 TCACTTTCACATGAACTTTCAACTAT 57.549 30.769 0.00 0.00 41.13 2.12
1883 1923 6.828273 TGTAACTTTAATGTGATAGGCATGCT 59.172 34.615 18.92 6.26 0.00 3.79
1908 1948 1.082104 GGACGCGGCTCTTTTTGTG 60.082 57.895 13.91 0.00 0.00 3.33
1946 1987 7.044576 CAAATGTTTGATTGCTTGCAAAGTTTC 60.045 33.333 12.17 6.00 42.67 2.78
1958 1999 5.625921 TGCAAAGTTTCATCATCGAATGA 57.374 34.783 0.00 0.00 44.55 2.57
1975 2016 2.835580 TGACATTCGGGGAAAACGTA 57.164 45.000 0.00 0.00 0.00 3.57
1983 2024 2.885894 TCGGGGAAAACGTAGCAAAAAT 59.114 40.909 0.00 0.00 0.00 1.82
1986 2027 5.032220 CGGGGAAAACGTAGCAAAAATATC 58.968 41.667 0.00 0.00 0.00 1.63
1987 2028 5.032220 GGGGAAAACGTAGCAAAAATATCG 58.968 41.667 0.00 0.00 0.00 2.92
1988 2029 5.163733 GGGGAAAACGTAGCAAAAATATCGA 60.164 40.000 0.00 0.00 0.00 3.59
1989 2030 5.735892 GGGAAAACGTAGCAAAAATATCGAC 59.264 40.000 0.00 0.00 0.00 4.20
1990 2031 6.308675 GGAAAACGTAGCAAAAATATCGACA 58.691 36.000 0.00 0.00 0.00 4.35
2000 2044 7.029563 AGCAAAAATATCGACACTCCAAAATC 58.970 34.615 0.00 0.00 0.00 2.17
2005 2049 1.071542 TCGACACTCCAAAATCCTGCA 59.928 47.619 0.00 0.00 0.00 4.41
2007 2051 2.293122 CGACACTCCAAAATCCTGCAAA 59.707 45.455 0.00 0.00 0.00 3.68
2015 2059 5.144100 TCCAAAATCCTGCAAAGTCCTTTA 58.856 37.500 0.00 0.00 0.00 1.85
2020 2064 6.396829 AATCCTGCAAAGTCCTTTATATGC 57.603 37.500 0.00 0.00 0.00 3.14
2021 2065 5.116084 TCCTGCAAAGTCCTTTATATGCT 57.884 39.130 0.00 0.00 0.00 3.79
2022 2066 4.883585 TCCTGCAAAGTCCTTTATATGCTG 59.116 41.667 0.00 0.00 0.00 4.41
2059 2107 8.760980 TTCCTTAATTTTCTGAGTTCCTGAAA 57.239 30.769 0.00 0.00 39.78 2.69
2153 2201 6.060788 GGAGATCAAGTATGCTTCCTTCAAT 58.939 40.000 0.00 0.00 31.49 2.57
2162 2210 7.824672 AGTATGCTTCCTTCAATCTGAAAAAG 58.175 34.615 6.75 6.75 35.73 2.27
2166 2214 5.176406 GCTTCCTTCAATCTGAAAAAGCAAC 59.824 40.000 20.45 3.47 45.18 4.17
2167 2215 5.850557 TCCTTCAATCTGAAAAAGCAACA 57.149 34.783 0.00 0.00 35.73 3.33
2169 2217 6.042143 TCCTTCAATCTGAAAAAGCAACAAC 58.958 36.000 0.00 0.00 35.73 3.32
2171 2219 4.358851 TCAATCTGAAAAAGCAACAACCG 58.641 39.130 0.00 0.00 0.00 4.44
2196 2245 7.627340 GTCACCAAACCATATAGTTTATGACG 58.373 38.462 18.62 2.57 40.91 4.35
2214 2263 0.863144 CGTACACCGTTTCAACTGGG 59.137 55.000 0.00 0.00 0.00 4.45
2227 2276 2.916934 TCAACTGGGTTGGCTAGGTATT 59.083 45.455 9.98 0.00 42.99 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 3.353836 AACCGCGTGCGCATCTTT 61.354 55.556 15.91 0.00 42.06 2.52
146 147 5.424895 AGAGATCATACTCAAAGACAAGCCT 59.575 40.000 0.00 0.00 39.14 4.58
283 284 7.360353 GCTTTTGGAAAATTGATTTGTAGGCTC 60.360 37.037 0.00 0.00 0.00 4.70
356 357 3.002965 TGCAGCTTGCTATCAATCAATCG 59.997 43.478 9.12 0.00 45.31 3.34
357 358 4.563337 TGCAGCTTGCTATCAATCAATC 57.437 40.909 9.12 0.00 45.31 2.67
361 362 5.184340 AGAAATGCAGCTTGCTATCAATC 57.816 39.130 9.12 1.29 45.31 2.67
364 365 6.704289 AATTAGAAATGCAGCTTGCTATCA 57.296 33.333 9.12 0.00 45.31 2.15
365 366 7.325579 GCTTAATTAGAAATGCAGCTTGCTATC 59.674 37.037 9.12 5.47 45.31 2.08
404 405 7.119116 TGCTTTTGTCGATCAATCTTTAGCTAA 59.881 33.333 0.86 0.86 35.84 3.09
437 438 9.853177 TGAGTCGGATCATAGATATACACATAT 57.147 33.333 0.00 0.00 0.00 1.78
438 439 9.110502 GTGAGTCGGATCATAGATATACACATA 57.889 37.037 0.00 0.00 0.00 2.29
439 440 7.067615 GGTGAGTCGGATCATAGATATACACAT 59.932 40.741 0.00 0.00 0.00 3.21
440 441 6.374613 GGTGAGTCGGATCATAGATATACACA 59.625 42.308 0.00 0.00 0.00 3.72
441 442 6.457122 CGGTGAGTCGGATCATAGATATACAC 60.457 46.154 0.00 0.00 0.00 2.90
442 443 5.585047 CGGTGAGTCGGATCATAGATATACA 59.415 44.000 0.00 0.00 0.00 2.29
443 444 6.050454 CGGTGAGTCGGATCATAGATATAC 57.950 45.833 0.00 0.00 0.00 1.47
444 445 8.545034 AGCCGGTGAGTCGGATCATAGATATA 62.545 46.154 1.90 0.00 46.79 0.86
445 446 7.849435 AGCCGGTGAGTCGGATCATAGATAT 62.849 48.000 1.90 0.00 46.79 1.63
449 450 2.425145 AGCCGGTGAGTCGGATCATAG 61.425 57.143 1.90 0.00 46.79 2.23
451 452 1.758514 AGCCGGTGAGTCGGATCAT 60.759 57.895 1.90 0.00 46.79 2.45
470 471 5.297569 AGTAATAGGCTTCAGGTCCATTC 57.702 43.478 0.00 0.00 0.00 2.67
480 481 9.825109 AGTTGAGAAGATTAAGTAATAGGCTTC 57.175 33.333 0.00 0.00 30.39 3.86
484 485 9.892130 ACCAAGTTGAGAAGATTAAGTAATAGG 57.108 33.333 3.87 0.00 0.00 2.57
487 488 9.014297 CCAACCAAGTTGAGAAGATTAAGTAAT 57.986 33.333 3.87 0.00 45.28 1.89
490 491 6.365520 ACCAACCAAGTTGAGAAGATTAAGT 58.634 36.000 3.87 0.00 45.28 2.24
502 506 4.460382 AGCATCAAGATACCAACCAAGTTG 59.540 41.667 0.00 0.00 42.49 3.16
504 508 4.012374 CAGCATCAAGATACCAACCAAGT 58.988 43.478 0.00 0.00 0.00 3.16
516 520 5.463286 CAAAGTGTTTATGCAGCATCAAGA 58.537 37.500 12.38 2.67 0.00 3.02
521 525 3.663995 TGCAAAGTGTTTATGCAGCAT 57.336 38.095 13.73 13.73 44.52 3.79
536 540 5.457487 CCCTATAAGTACCCATCCATGCAAA 60.457 44.000 0.00 0.00 0.00 3.68
569 579 3.173399 CACAACACAGTGTCGCTTATG 57.827 47.619 6.67 2.84 34.83 1.90
629 639 4.083862 ACGCGCCTTCTTCCCCTC 62.084 66.667 5.73 0.00 0.00 4.30
635 645 2.750815 GTGTATCACGCGCCTTCTT 58.249 52.632 5.73 0.00 0.00 2.52
636 646 4.496670 GTGTATCACGCGCCTTCT 57.503 55.556 5.73 0.00 0.00 2.85
720 734 1.933853 GAATCACGTGGTATGCTGTCC 59.066 52.381 17.00 0.00 0.00 4.02
775 789 4.188702 CGGAAAACGGCGATGGTA 57.811 55.556 16.62 0.00 39.42 3.25
884 898 9.793259 ACCAGAAGAACTAATTGAATGTTCTAA 57.207 29.630 10.21 0.00 46.39 2.10
898 912 3.492656 GCACACACTCACCAGAAGAACTA 60.493 47.826 0.00 0.00 0.00 2.24
902 916 0.106708 GGCACACACTCACCAGAAGA 59.893 55.000 0.00 0.00 0.00 2.87
938 952 1.546773 CCACGAGGGAAAATGGGTGAA 60.547 52.381 0.00 0.00 40.01 3.18
955 969 9.087424 GGATCAAGAAAATAAAGCATAAACCAC 57.913 33.333 0.00 0.00 0.00 4.16
1025 1052 0.473755 TGCAGGCTCTGGAAACTTCA 59.526 50.000 4.65 0.00 31.21 3.02
1080 1107 2.052690 CCCGACGACCTCTGTCCAT 61.053 63.158 0.00 0.00 38.32 3.41
1084 1111 1.304217 ACATCCCGACGACCTCTGT 60.304 57.895 0.00 0.00 0.00 3.41
1104 1131 0.321671 TCTCCTTGGCCTTCTCAACG 59.678 55.000 3.32 0.00 0.00 4.10
1128 1155 1.377725 ATCAGGCTTGTCCTTGGCG 60.378 57.895 0.00 0.00 44.75 5.69
1129 1156 1.941999 GCATCAGGCTTGTCCTTGGC 61.942 60.000 0.00 0.00 44.75 4.52
1130 1157 2.187073 GCATCAGGCTTGTCCTTGG 58.813 57.895 0.00 0.00 44.75 3.61
1166 1193 0.108992 GGTGACCAACGCATCGACTA 60.109 55.000 0.00 0.00 0.00 2.59
1182 1209 1.303282 GGGCCTTAAGTCCTGGGTG 59.697 63.158 0.84 0.00 0.00 4.61
1219 1246 3.650369 GGTGTCGGCAACAACGAT 58.350 55.556 0.00 0.00 42.82 3.73
1223 1250 1.071814 GTAGGGGTGTCGGCAACAA 59.928 57.895 7.66 0.00 40.31 2.83
1294 1321 5.353678 GCCTGATGTGCCAGATATCTTTATC 59.646 44.000 1.33 3.96 36.29 1.75
1310 1337 0.403271 AGAAAGTGCCTGCCTGATGT 59.597 50.000 0.00 0.00 0.00 3.06
1315 1342 1.143684 TCAAAGAGAAAGTGCCTGCCT 59.856 47.619 0.00 0.00 0.00 4.75
1318 1345 5.248640 TCCTTATCAAAGAGAAAGTGCCTG 58.751 41.667 0.00 0.00 34.37 4.85
1320 1347 6.765915 ATTCCTTATCAAAGAGAAAGTGCC 57.234 37.500 0.00 0.00 34.37 5.01
1333 1360 4.828939 CCAGCATGCCTTTATTCCTTATCA 59.171 41.667 15.66 0.00 31.97 2.15
1352 1392 1.170919 ATGATTCGCTCATGCCCAGC 61.171 55.000 0.20 0.00 43.15 4.85
1398 1438 2.234896 ATGCCCAACATGTCATGGAA 57.765 45.000 16.72 4.92 39.12 3.53
1407 1447 6.739286 GCAATTATACATGTCATGCCCAACAT 60.739 38.462 12.91 0.00 40.66 2.71
1416 1456 5.407691 CAGAGAGCGCAATTATACATGTCAT 59.592 40.000 11.47 0.00 0.00 3.06
1417 1457 4.746611 CAGAGAGCGCAATTATACATGTCA 59.253 41.667 11.47 0.00 0.00 3.58
1418 1458 4.747108 ACAGAGAGCGCAATTATACATGTC 59.253 41.667 11.47 0.00 0.00 3.06
1419 1459 4.697514 ACAGAGAGCGCAATTATACATGT 58.302 39.130 11.47 2.69 0.00 3.21
1420 1460 5.663795 AACAGAGAGCGCAATTATACATG 57.336 39.130 11.47 0.00 0.00 3.21
1421 1461 5.817296 TGAAACAGAGAGCGCAATTATACAT 59.183 36.000 11.47 0.00 0.00 2.29
1422 1462 5.175127 TGAAACAGAGAGCGCAATTATACA 58.825 37.500 11.47 0.00 0.00 2.29
1423 1463 5.718649 TGAAACAGAGAGCGCAATTATAC 57.281 39.130 11.47 0.00 0.00 1.47
1424 1464 6.283694 AGATGAAACAGAGAGCGCAATTATA 58.716 36.000 11.47 0.00 0.00 0.98
1425 1465 5.121811 AGATGAAACAGAGAGCGCAATTAT 58.878 37.500 11.47 0.00 0.00 1.28
1426 1466 4.507710 AGATGAAACAGAGAGCGCAATTA 58.492 39.130 11.47 0.00 0.00 1.40
1427 1467 3.341823 AGATGAAACAGAGAGCGCAATT 58.658 40.909 11.47 0.00 0.00 2.32
1428 1468 2.983229 AGATGAAACAGAGAGCGCAAT 58.017 42.857 11.47 0.00 0.00 3.56
1429 1469 2.462456 AGATGAAACAGAGAGCGCAA 57.538 45.000 11.47 0.00 0.00 4.85
1430 1470 2.755103 TCTAGATGAAACAGAGAGCGCA 59.245 45.455 11.47 0.00 0.00 6.09
1431 1471 3.428746 TCTAGATGAAACAGAGAGCGC 57.571 47.619 0.00 0.00 0.00 5.92
1432 1472 6.734137 AGTAATCTAGATGAAACAGAGAGCG 58.266 40.000 5.86 0.00 0.00 5.03
1433 1473 7.940850 AGAGTAATCTAGATGAAACAGAGAGC 58.059 38.462 5.86 0.00 0.00 4.09
1440 1480 9.902196 GCCTAGTAAGAGTAATCTAGATGAAAC 57.098 37.037 5.86 5.58 33.81 2.78
1441 1481 9.642343 TGCCTAGTAAGAGTAATCTAGATGAAA 57.358 33.333 5.86 0.00 33.81 2.69
1442 1482 9.290988 CTGCCTAGTAAGAGTAATCTAGATGAA 57.709 37.037 5.86 0.00 33.81 2.57
1443 1483 7.885922 CCTGCCTAGTAAGAGTAATCTAGATGA 59.114 40.741 5.86 0.00 33.81 2.92
1444 1484 7.122055 CCCTGCCTAGTAAGAGTAATCTAGATG 59.878 44.444 5.86 0.00 33.81 2.90
1445 1485 7.018751 TCCCTGCCTAGTAAGAGTAATCTAGAT 59.981 40.741 0.00 0.00 33.81 1.98
1446 1486 6.332103 TCCCTGCCTAGTAAGAGTAATCTAGA 59.668 42.308 0.00 0.00 33.81 2.43
1447 1487 6.544650 TCCCTGCCTAGTAAGAGTAATCTAG 58.455 44.000 0.00 0.00 0.00 2.43
1448 1488 6.526056 TCCCTGCCTAGTAAGAGTAATCTA 57.474 41.667 0.00 0.00 0.00 1.98
1449 1489 5.405063 TCCCTGCCTAGTAAGAGTAATCT 57.595 43.478 0.00 0.00 0.00 2.40
1450 1490 6.042208 ACATTCCCTGCCTAGTAAGAGTAATC 59.958 42.308 0.00 0.00 0.00 1.75
1451 1491 5.905913 ACATTCCCTGCCTAGTAAGAGTAAT 59.094 40.000 0.00 0.00 0.00 1.89
1452 1492 5.128827 CACATTCCCTGCCTAGTAAGAGTAA 59.871 44.000 0.00 0.00 0.00 2.24
1453 1493 4.649674 CACATTCCCTGCCTAGTAAGAGTA 59.350 45.833 0.00 0.00 0.00 2.59
1454 1494 3.452627 CACATTCCCTGCCTAGTAAGAGT 59.547 47.826 0.00 0.00 0.00 3.24
1455 1495 3.742640 GCACATTCCCTGCCTAGTAAGAG 60.743 52.174 0.00 0.00 0.00 2.85
1456 1496 2.170607 GCACATTCCCTGCCTAGTAAGA 59.829 50.000 0.00 0.00 0.00 2.10
1457 1497 2.565841 GCACATTCCCTGCCTAGTAAG 58.434 52.381 0.00 0.00 0.00 2.34
1458 1498 2.710096 GCACATTCCCTGCCTAGTAA 57.290 50.000 0.00 0.00 0.00 2.24
1465 1505 1.754234 ATTCGGGCACATTCCCTGC 60.754 57.895 0.00 0.00 44.30 4.85
1466 1506 2.008268 GCATTCGGGCACATTCCCTG 62.008 60.000 0.00 0.00 44.30 4.45
1467 1507 1.754234 GCATTCGGGCACATTCCCT 60.754 57.895 0.00 0.00 44.30 4.20
1468 1508 1.728490 GAGCATTCGGGCACATTCCC 61.728 60.000 0.00 0.00 43.02 3.97
1469 1509 1.729881 GAGCATTCGGGCACATTCC 59.270 57.895 0.00 0.00 35.83 3.01
1470 1510 1.353103 CGAGCATTCGGGCACATTC 59.647 57.895 0.00 0.00 43.05 2.67
1471 1511 3.501396 CGAGCATTCGGGCACATT 58.499 55.556 0.00 0.00 43.05 2.71
1479 1519 1.148157 CTAGCACCACCGAGCATTCG 61.148 60.000 0.00 0.00 46.29 3.34
1480 1520 0.108138 ACTAGCACCACCGAGCATTC 60.108 55.000 0.00 0.00 0.00 2.67
1481 1521 1.191535 TACTAGCACCACCGAGCATT 58.808 50.000 0.00 0.00 0.00 3.56
1482 1522 1.414158 ATACTAGCACCACCGAGCAT 58.586 50.000 0.00 0.00 0.00 3.79
1483 1523 1.191535 AATACTAGCACCACCGAGCA 58.808 50.000 0.00 0.00 0.00 4.26
1484 1524 2.202566 GAAATACTAGCACCACCGAGC 58.797 52.381 0.00 0.00 0.00 5.03
1485 1525 3.520290 TGAAATACTAGCACCACCGAG 57.480 47.619 0.00 0.00 0.00 4.63
1486 1526 3.196901 ACATGAAATACTAGCACCACCGA 59.803 43.478 0.00 0.00 0.00 4.69
1487 1527 3.531538 ACATGAAATACTAGCACCACCG 58.468 45.455 0.00 0.00 0.00 4.94
1488 1528 4.438744 GCAACATGAAATACTAGCACCACC 60.439 45.833 0.00 0.00 0.00 4.61
1489 1529 4.662145 GCAACATGAAATACTAGCACCAC 58.338 43.478 0.00 0.00 0.00 4.16
1490 1530 3.373748 CGCAACATGAAATACTAGCACCA 59.626 43.478 0.00 0.00 0.00 4.17
1506 1546 4.092816 GTCGAAAAGAAAAACTCGCAACA 58.907 39.130 0.00 0.00 0.00 3.33
1525 1565 4.273480 ACTCACAACTTGAAATTCCTGTCG 59.727 41.667 0.00 0.00 32.21 4.35
1580 1620 2.830104 ACGATAAATGACCGGCTAACC 58.170 47.619 0.00 0.00 0.00 2.85
1581 1621 5.119743 GGAATACGATAAATGACCGGCTAAC 59.880 44.000 0.00 0.00 0.00 2.34
1582 1622 5.232463 GGAATACGATAAATGACCGGCTAA 58.768 41.667 0.00 0.00 0.00 3.09
1583 1623 4.322198 GGGAATACGATAAATGACCGGCTA 60.322 45.833 0.00 0.00 0.00 3.93
1584 1624 3.556423 GGGAATACGATAAATGACCGGCT 60.556 47.826 0.00 0.00 0.00 5.52
1585 1625 2.740447 GGGAATACGATAAATGACCGGC 59.260 50.000 0.00 0.00 0.00 6.13
1586 1626 4.267349 AGGGAATACGATAAATGACCGG 57.733 45.455 0.00 0.00 0.00 5.28
1587 1627 6.263516 TCTAGGGAATACGATAAATGACCG 57.736 41.667 0.00 0.00 0.00 4.79
1588 1628 6.100668 GCTCTAGGGAATACGATAAATGACC 58.899 44.000 0.00 0.00 0.00 4.02
1589 1629 6.688578 TGCTCTAGGGAATACGATAAATGAC 58.311 40.000 0.00 0.00 0.00 3.06
1590 1630 6.911250 TGCTCTAGGGAATACGATAAATGA 57.089 37.500 0.00 0.00 0.00 2.57
1591 1631 7.441157 TGTTTGCTCTAGGGAATACGATAAATG 59.559 37.037 0.00 0.00 0.00 2.32
1592 1632 7.506114 TGTTTGCTCTAGGGAATACGATAAAT 58.494 34.615 0.00 0.00 0.00 1.40
1593 1633 6.880484 TGTTTGCTCTAGGGAATACGATAAA 58.120 36.000 0.00 0.00 0.00 1.40
1594 1634 6.474140 TGTTTGCTCTAGGGAATACGATAA 57.526 37.500 0.00 0.00 0.00 1.75
1595 1635 6.295123 GGATGTTTGCTCTAGGGAATACGATA 60.295 42.308 0.00 0.00 0.00 2.92
1596 1636 5.511545 GGATGTTTGCTCTAGGGAATACGAT 60.512 44.000 0.00 0.00 0.00 3.73
1597 1637 4.202223 GGATGTTTGCTCTAGGGAATACGA 60.202 45.833 0.00 0.00 0.00 3.43
1598 1638 4.058817 GGATGTTTGCTCTAGGGAATACG 58.941 47.826 0.00 0.00 0.00 3.06
1599 1639 5.036117 TGGATGTTTGCTCTAGGGAATAC 57.964 43.478 0.00 0.00 0.00 1.89
1600 1640 5.708736 TTGGATGTTTGCTCTAGGGAATA 57.291 39.130 0.00 0.00 0.00 1.75
1601 1641 4.591321 TTGGATGTTTGCTCTAGGGAAT 57.409 40.909 0.00 0.00 0.00 3.01
1602 1642 4.380843 TTTGGATGTTTGCTCTAGGGAA 57.619 40.909 0.00 0.00 0.00 3.97
1603 1643 4.380843 TTTTGGATGTTTGCTCTAGGGA 57.619 40.909 0.00 0.00 0.00 4.20
1604 1644 4.766891 TCTTTTTGGATGTTTGCTCTAGGG 59.233 41.667 0.00 0.00 0.00 3.53
1605 1645 5.617751 CGTCTTTTTGGATGTTTGCTCTAGG 60.618 44.000 0.00 0.00 0.00 3.02
1606 1646 5.179368 TCGTCTTTTTGGATGTTTGCTCTAG 59.821 40.000 0.00 0.00 0.00 2.43
1607 1647 5.049680 GTCGTCTTTTTGGATGTTTGCTCTA 60.050 40.000 0.00 0.00 0.00 2.43
1608 1648 3.882888 TCGTCTTTTTGGATGTTTGCTCT 59.117 39.130 0.00 0.00 0.00 4.09
1609 1649 3.975035 GTCGTCTTTTTGGATGTTTGCTC 59.025 43.478 0.00 0.00 0.00 4.26
1610 1650 3.380004 TGTCGTCTTTTTGGATGTTTGCT 59.620 39.130 0.00 0.00 0.00 3.91
1611 1651 3.701241 TGTCGTCTTTTTGGATGTTTGC 58.299 40.909 0.00 0.00 0.00 3.68
1612 1652 5.098893 TGTTGTCGTCTTTTTGGATGTTTG 58.901 37.500 0.00 0.00 0.00 2.93
1613 1653 5.317733 TGTTGTCGTCTTTTTGGATGTTT 57.682 34.783 0.00 0.00 0.00 2.83
1614 1654 4.974368 TGTTGTCGTCTTTTTGGATGTT 57.026 36.364 0.00 0.00 0.00 2.71
1615 1655 4.156922 TGTTGTTGTCGTCTTTTTGGATGT 59.843 37.500 0.00 0.00 0.00 3.06
1616 1656 4.667262 TGTTGTTGTCGTCTTTTTGGATG 58.333 39.130 0.00 0.00 0.00 3.51
1617 1657 4.974368 TGTTGTTGTCGTCTTTTTGGAT 57.026 36.364 0.00 0.00 0.00 3.41
1618 1658 4.456222 TCTTGTTGTTGTCGTCTTTTTGGA 59.544 37.500 0.00 0.00 0.00 3.53
1619 1659 4.728534 TCTTGTTGTTGTCGTCTTTTTGG 58.271 39.130 0.00 0.00 0.00 3.28
1620 1660 4.793216 CCTCTTGTTGTTGTCGTCTTTTTG 59.207 41.667 0.00 0.00 0.00 2.44
1621 1661 4.142469 CCCTCTTGTTGTTGTCGTCTTTTT 60.142 41.667 0.00 0.00 0.00 1.94
1622 1662 3.377172 CCCTCTTGTTGTTGTCGTCTTTT 59.623 43.478 0.00 0.00 0.00 2.27
1623 1663 2.943033 CCCTCTTGTTGTTGTCGTCTTT 59.057 45.455 0.00 0.00 0.00 2.52
1624 1664 2.169769 TCCCTCTTGTTGTTGTCGTCTT 59.830 45.455 0.00 0.00 0.00 3.01
1625 1665 1.760613 TCCCTCTTGTTGTTGTCGTCT 59.239 47.619 0.00 0.00 0.00 4.18
1626 1666 2.234300 TCCCTCTTGTTGTTGTCGTC 57.766 50.000 0.00 0.00 0.00 4.20
1627 1667 2.930826 ATCCCTCTTGTTGTTGTCGT 57.069 45.000 0.00 0.00 0.00 4.34
1628 1668 8.833231 ATATATTATCCCTCTTGTTGTTGTCG 57.167 34.615 0.00 0.00 0.00 4.35
1662 1702 5.865085 AGTAGTGACCAATTTGTGCTTAGA 58.135 37.500 0.00 0.00 0.00 2.10
1699 1739 5.186215 TCGAGATTTAGGGTGACACATAACA 59.814 40.000 8.08 0.00 0.00 2.41
1708 1748 3.055385 CCCTTGTTCGAGATTTAGGGTGA 60.055 47.826 10.38 0.00 38.00 4.02
1756 1796 4.037684 CCGACGATGGTACTAGGATTTCTT 59.962 45.833 0.00 0.00 0.00 2.52
1770 1810 2.933495 TCTTTGAGTACCGACGATGG 57.067 50.000 0.00 0.00 0.00 3.51
1771 1811 2.599082 GCTTCTTTGAGTACCGACGATG 59.401 50.000 0.00 0.00 0.00 3.84
1775 1815 4.329256 GGTTATGCTTCTTTGAGTACCGAC 59.671 45.833 0.00 0.00 0.00 4.79
1791 1831 3.181501 TGCAACAGATAAAGCGGTTATGC 60.182 43.478 0.00 4.14 32.26 3.14
1809 1849 9.926158 AGTGATAAAACATCATTATTTGTGCAA 57.074 25.926 0.00 0.00 0.00 4.08
1824 1864 9.515020 GAAAGTTCATGTGAAAGTGATAAAACA 57.485 29.630 0.00 0.00 35.58 2.83
1825 1865 9.515020 TGAAAGTTCATGTGAAAGTGATAAAAC 57.485 29.630 0.00 0.00 35.58 2.43
1828 1868 8.902806 AGTTGAAAGTTCATGTGAAAGTGATAA 58.097 29.630 0.00 0.00 37.00 1.75
1856 1896 7.012327 GCATGCCTATCACATTAAAGTTACAGA 59.988 37.037 6.36 0.00 0.00 3.41
1892 1932 2.331451 GCACAAAAAGAGCCGCGT 59.669 55.556 4.92 0.00 0.00 6.01
1897 1937 8.047395 TTGTCAATGTTTGGCACAAAAAGAGC 62.047 38.462 0.00 0.00 46.32 4.09
1958 1999 1.270947 TGCTACGTTTTCCCCGAATGT 60.271 47.619 0.00 0.00 0.00 2.71
1965 2006 5.735892 GTCGATATTTTTGCTACGTTTTCCC 59.264 40.000 0.00 0.00 0.00 3.97
1967 2008 7.013529 AGTGTCGATATTTTTGCTACGTTTTC 58.986 34.615 0.00 0.00 0.00 2.29
1972 2013 4.565166 TGGAGTGTCGATATTTTTGCTACG 59.435 41.667 0.00 0.00 0.00 3.51
1975 2016 5.957842 TTTGGAGTGTCGATATTTTTGCT 57.042 34.783 0.00 0.00 0.00 3.91
1983 2024 3.055458 TGCAGGATTTTGGAGTGTCGATA 60.055 43.478 0.00 0.00 0.00 2.92
1986 2027 1.522668 TGCAGGATTTTGGAGTGTCG 58.477 50.000 0.00 0.00 0.00 4.35
1987 2028 3.319122 ACTTTGCAGGATTTTGGAGTGTC 59.681 43.478 0.00 0.00 0.00 3.67
1988 2029 3.299503 ACTTTGCAGGATTTTGGAGTGT 58.700 40.909 0.00 0.00 0.00 3.55
1989 2030 3.305608 GGACTTTGCAGGATTTTGGAGTG 60.306 47.826 0.00 0.00 0.00 3.51
1990 2031 2.893489 GGACTTTGCAGGATTTTGGAGT 59.107 45.455 0.00 0.00 0.00 3.85
2000 2044 4.498682 GCAGCATATAAAGGACTTTGCAGG 60.499 45.833 7.53 1.89 34.23 4.85
2005 2049 6.796785 AATTGGCAGCATATAAAGGACTTT 57.203 33.333 2.57 2.57 36.63 2.66
2007 2051 7.006509 ACATAATTGGCAGCATATAAAGGACT 58.993 34.615 0.00 0.00 0.00 3.85
2015 2059 6.736110 AGGAAAACATAATTGGCAGCATAT 57.264 33.333 0.00 0.00 0.00 1.78
2080 2128 0.538287 GAAGCCCACTGCAACTCCTT 60.538 55.000 0.00 0.00 44.83 3.36
2129 2177 5.028549 TGAAGGAAGCATACTTGATCTCC 57.971 43.478 0.00 0.00 35.82 3.71
2130 2178 6.991531 AGATTGAAGGAAGCATACTTGATCTC 59.008 38.462 0.00 0.00 35.82 2.75
2153 2201 2.750166 TGACGGTTGTTGCTTTTTCAGA 59.250 40.909 0.00 0.00 0.00 3.27
2162 2210 0.526739 GGTTTGGTGACGGTTGTTGC 60.527 55.000 0.00 0.00 0.00 4.17
2166 2214 4.258543 ACTATATGGTTTGGTGACGGTTG 58.741 43.478 0.00 0.00 0.00 3.77
2167 2215 4.563140 ACTATATGGTTTGGTGACGGTT 57.437 40.909 0.00 0.00 0.00 4.44
2169 2217 6.764085 TCATAAACTATATGGTTTGGTGACGG 59.236 38.462 23.14 8.00 39.39 4.79
2171 2219 7.279313 ACGTCATAAACTATATGGTTTGGTGAC 59.721 37.037 29.89 29.89 43.17 3.67
2196 2245 1.957668 ACCCAGTTGAAACGGTGTAC 58.042 50.000 0.00 0.00 0.00 2.90
2210 2259 5.513267 GGATTCTAATACCTAGCCAACCCAG 60.513 48.000 0.00 0.00 0.00 4.45
2214 2263 8.154856 TGTTATGGATTCTAATACCTAGCCAAC 58.845 37.037 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.