Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000802.1 Hibiscus syriacus cultivar Beakdansim tig00001557_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 85488
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:3693 original size:23 final size:23
Alignment explanation
Indices: 3651--3742 Score: 121
Period size: 23 Copynumber: 4.0 Consensus size: 23
3641 CACCACAGCT
* * *
3651 CGTATAATTGCATCGAAGTGCCA
1 CGTAGAATTGCACCGTAGTGCCA
* * *
3674 CATAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGTAGTGCCA
*
3697 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAATTGCACCGTAGTGCCA
3720 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGTAGTGCCA
3743 TATAATAATG
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGTAGTGCCA
Found at i:4420 original size:19 final size:19
Alignment explanation
Indices: 4396--4483 Score: 158
Period size: 19 Copynumber: 4.6 Consensus size: 19
4386 TTTAATGGGG
*
4396 TGCATCGATGCACACCTTA
1 TGCATCGATGCACTCCTTA
4415 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
*
4434 TGCATCGATGCACTCTTTA
1 TGCATCGATGCACTCCTTA
4453 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
4472 TGCATCGATGCA
1 TGCATCGATGCA
4484 TCGATGGCAT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 66 1.00
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.31
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:10673 original size:23 final size:23
Alignment explanation
Indices: 10647--10715 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
10637 CACCACAGCT
*
10647 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
10670 CGTAGAATTGCACC-AGAGTGCCG
1 CGTAGAATTGCACCGA-AGTGCCA
*
10693 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
10716 TATAATAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.03
23 39 0.98
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:11403 original size:27 final size:27
Alignment explanation
Indices: 11371--11434 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
11361 TTTAATGGGG
*
11371 TGCATCGATGCACTCCTTATGCATTGA
1 TGCATCGATGCACTCCTTATGCATCGA
11398 TGCATCGATGCACTCCTTATGCATCGA
1 TGCATCGATGCACTCCTTATGCATCGA
11425 TGCATCGATG
1 TGCATCGATG
11435 ACATTCGGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (27 bp):
TGCATCGATGCACTCCTTATGCATCGA
Found at i:14137 original size:21 final size:21
Alignment explanation
Indices: 14100--14141 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
14090 GTGAAGACAA
14100 CAATCTTTAATCAATTAAGGT
1 CAATCTTTAATCAATTAAGGT
*
14121 CAATCCTTTATTC-ATTAAGGT
1 CAAT-CTTTAATCAATTAAGGT
14142 TTTTTGGTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (21 bp):
CAATCTTTAATCAATTAAGGT
Found at i:15591 original size:44 final size:44
Alignment explanation
Indices: 15541--15640 Score: 191
Period size: 44 Copynumber: 2.3 Consensus size: 44
15531 CCTTAAGGAA
*
15541 GGTATCGATACCATTTTTGAATGAGAATTACAGAATACAAAATG
1 GGTATCGATACCATTTTTGAACGAGAATTACAGAATACAAAATG
15585 GGTATCGATACCATTTTTGAACGAGAATTACAGAATACAAAATG
1 GGTATCGATACCATTTTTGAACGAGAATTACAGAATACAAAATG
15629 GGTATCGATACC
1 GGTATCGATACC
15641 TAGGCATGGT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (44 bp):
GGTATCGATACCATTTTTGAACGAGAATTACAGAATACAAAATG
Found at i:16958 original size:31 final size:30
Alignment explanation
Indices: 16887--16982 Score: 111
Period size: 31 Copynumber: 3.1 Consensus size: 30
16877 AGAGTAGAGA
* *
16887 GTTACCTATGTCTTTCGGGACAAATGGACATG
1 GTTACCTATTTCTTT-GGGACATATGGACA-G
*
16919 ATTACCTATATTCTTTGGGACATATGGACAG
1 GTTACCTAT-TTCTTTGGGACATATGGACAG
* *
16950 GTTACCTATGTTCTTCGGGACATATGGATAG
1 GTTACCTAT-TTCTTTGGGACATATGGACAG
16981 GT
1 GT
16983 CCTCCGGGAC
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
31 30 0.54
32 21 0.38
33 5 0.09
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (30 bp):
GTTACCTATTTCTTTGGGACATATGGACAG
Found at i:18927 original size:30 final size:32
Alignment explanation
Indices: 18866--18929 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
18856 GATCTTCCCT
*
18866 TAGTTTCTCTCGAACACTAAGGATCTTTTACC
1 TAGTTTCTCTCGAACACTAAGGATATTTTACC
18898 TAGTTTCTCTCGAACACTAA-G-TATTTTACC
1 TAGTTTCTCTCGAACACTAAGGATATTTTACC
18928 TA
1 TA
18930 AGAAATGGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 10 0.32
31 1 0.03
32 20 0.65
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (32 bp):
TAGTTTCTCTCGAACACTAAGGATATTTTACC
Found at i:23472 original size:66 final size:66
Alignment explanation
Indices: 23366--23498 Score: 169
Period size: 66 Copynumber: 2.0 Consensus size: 66
23356 TGTTGAAAAA
* * * * *
23366 GGGCACTTTTACAAGCATGGGGCGCTAGGTTATTGCTCCCAAGACAATGCGTTATGGGACAATGG
1 GGGCAATTTTACAAACATGGGACGCTAGGTTATTGCTCCCAAGACAAGGAGTTATGGGACAATGG
23431 C
66 C
* * * *
23432 GGGCAATTTTATAAACATGGGACGCTCGGTGT-TTGCTCCCAAGACAAGGAGTTATGGGTCTATG
1 GGGCAATTTTACAAACATGGGACGCTAGGT-TATTGCTCCCAAGACAAGGAGTTATGGGACAATG
23496 GC
65 GC
23498 G
1 G
23499 CACGCTTGTC
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
66 56 0.98
67 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.26
Consensus pattern (66 bp):
GGGCAATTTTACAAACATGGGACGCTAGGTTATTGCTCCCAAGACAAGGAGTTATGGGACAATGG
C
Found at i:26729 original size:3 final size:3
Alignment explanation
Indices: 26723--26765 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
26713 CATTTGCTTA
*
26723 TAT TATT TAT TAT TAT TAT TAT TA- TGT TA- TAT TAT TAT TAT TA
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
26766 AATAATAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 3 0.09
3 29 0.83
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:26744 original size:16 final size:15
Alignment explanation
Indices: 26723--26765 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
26713 CATTTGCTTA
26723 TATTATTTATTATTAT
1 TATTATTTATTA-TAT
*
26739 TATTATTATGTTATAT
1 TATTATT-TATTATAT
26755 TATTA-TTATTA
1 TATTATTTATTA
26766 AATAATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 4 0.17
15 1 0.04
16 15 0.62
17 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTATTTATTATAT
Found at i:26747 original size:19 final size:19
Alignment explanation
Indices: 26723--26765 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
26713 CATTTGCTTA
26723 TATTAT-TTATTATTATTAT
1 TATTATGTTA-TATTATTAT
26742 TATTATGTTATATTATTAT
1 TATTATGTTATATTATTAT
26761 TATTA
1 TATTA
26766 AATAATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 20 0.87
20 3 0.13
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TATTATGTTATATTATTAT
Found at i:33845 original size:160 final size:160
Alignment explanation
Indices: 33581--33905 Score: 650
Period size: 160 Copynumber: 2.0 Consensus size: 160
33571 ATGGGAAACC
33581 TCATGACACTCCAATGAGCTCTTCAACAAAGCTTGACTTAGATGAAGGAGGTAAATGTGTAGATG
1 TCATGACACTCCAATGAGCTCTTCAACAAAGCTTGACTTAGATGAAGGAGGTAAATGTGTAGATG
33646 TTAAATTATATAGGTCAATGATTGGCTCTTTGCTTTATCTAACTGCAAGTAGACCGGACATTATG
66 TTAAATTATATAGGTCAATGATTGGCTCTTTGCTTTATCTAACTGCAAGTAGACCGGACATTATG
33711 TTTAGTGTTTGCTTATGTGCTAGATTTCAA
131 TTTAGTGTTTGCTTATGTGCTAGATTTCAA
33741 TCATGACACTCCAATGAGCTCTTCAACAAAGCTTGACTTAGATGAAGGAGGTAAATGTGTAGATG
1 TCATGACACTCCAATGAGCTCTTCAACAAAGCTTGACTTAGATGAAGGAGGTAAATGTGTAGATG
33806 TTAAATTATATAGGTCAATGATTGGCTCTTTGCTTTATCTAACTGCAAGTAGACCGGACATTATG
66 TTAAATTATATAGGTCAATGATTGGCTCTTTGCTTTATCTAACTGCAAGTAGACCGGACATTATG
33871 TTTAGTGTTTGCTTATGTGCTAGATTTCAA
131 TTTAGTGTTTGCTTATGTGCTAGATTTCAA
33901 TCATG
1 TCATG
33906 TCCTAAGGAA
Statistics
Matches: 165, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
160 165 1.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (160 bp):
TCATGACACTCCAATGAGCTCTTCAACAAAGCTTGACTTAGATGAAGGAGGTAAATGTGTAGATG
TTAAATTATATAGGTCAATGATTGGCTCTTTGCTTTATCTAACTGCAAGTAGACCGGACATTATG
TTTAGTGTTTGCTTATGTGCTAGATTTCAA
Found at i:38452 original size:17 final size:17
Alignment explanation
Indices: 38430--38464 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
38420 ACCTACCTAA
38430 CTCAAAAAGGTCAATGG
1 CTCAAAAAGGTCAATGG
38447 CTCAAAAAGGTCAATGG
1 CTCAAAAAGGTCAATGG
38464 C
1 C
38465 GACTCCCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.17
Consensus pattern (17 bp):
CTCAAAAAGGTCAATGG
Found at i:40474 original size:23 final size:25
Alignment explanation
Indices: 40440--40499 Score: 79
Period size: 23 Copynumber: 2.5 Consensus size: 25
40430 GCTTTTATGA
* **
40440 TAGGATAATAAATTTATAGTATTT-
1 TAGGATGATAAATTTATAAAATTTC
40464 TAGGA-GATAAATTTATAAAATTTC
1 TAGGATGATAAATTTATAAAATTTC
40488 TAGGATGATAAA
1 TAGGATGATAAA
40500 AATAGATTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 15 0.48
24 10 0.32
25 6 0.19
ACGTcount: A:0.45, C:0.02, G:0.15, T:0.38
Consensus pattern (25 bp):
TAGGATGATAAATTTATAAAATTTC
Found at i:45850 original size:34 final size:34
Alignment explanation
Indices: 45806--45873 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
45796 AATAGGAATT
*
45806 ACAACTTCTCTC-GATCTAACAAGAAGAAAACAATG
1 ACAACTTCTCTCTGA--TAAAAAGAAGAAAACAATG
45841 ACAA-TTCTCTCTTGATAAAAAGAAGAAAACAAT
1 ACAACTTCTCTC-TGATAAAAAGAAGAAAACAAT
45874 TCTCAAGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 24 0.80
35 4 0.13
36 2 0.07
ACGTcount: A:0.49, C:0.19, G:0.10, T:0.22
Consensus pattern (34 bp):
ACAACTTCTCTCTGATAAAAAGAAGAAAACAATG
Found at i:58526 original size:23 final size:24
Alignment explanation
Indices: 58500--58552 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
58490 ATATTTTACA
*
58500 TTAAGAG-ATAAATTTATAAAATT
1 TTAAGAGAATAAATTTATAAAACT
* *
58523 TTAAGGGAATGAATTTATAAAACT
1 TTAAGAGAATAAATTTATAAAACT
58547 TTAAGA
1 TTAAGA
58553 AACAAAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (24 bp):
TTAAGAGAATAAATTTATAAAACT
Found at i:58791 original size:2 final size:2
Alignment explanation
Indices: 58745--58779 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
58735 TATTAATAGA
58745 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
58780 ACTAAAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:59722 original size:21 final size:21
Alignment explanation
Indices: 59681--59723 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
59671 GCTCCGTCGT
*
59681 CTCCTCTTCCGCCAACTCCTC
1 CTCCTCTTCCGCCAACGCCTC
*
59702 CTCCTGTTCCGCC-ACGGCCTC
1 CTCCTCTTCCGCCAAC-GCCTC
59723 C
1 C
59724 AACTTCCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.07, C:0.56, G:0.12, T:0.26
Consensus pattern (21 bp):
CTCCTCTTCCGCCAACGCCTC
Found at i:64855 original size:12 final size:12
Alignment explanation
Indices: 64838--64868 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
64828 TTTCCACTTT
64838 CATATTCATTTA
1 CATATTCATTTA
*
64850 CATATTCATTTT
1 CATATTCATTTA
64862 CATATTC
1 CATATTC
64869 CATGTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.19, G:0.00, T:0.52
Consensus pattern (12 bp):
CATATTCATTTA
Found at i:64927 original size:19 final size:20
Alignment explanation
Indices: 64903--64948 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
64893 ATTTCATAAT
64903 TTATTTTCT-GAATCAGAAC
1 TTATTTTCTAGAATCAGAAC
* *
64922 TTA-TTTCTAGATTCATAAC
1 TTATTTTCTAGAATCAGAAC
64941 TTATTTTC
1 TTATTTTC
64949 ATACTCATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 14 0.61
20 4 0.17
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50
Consensus pattern (20 bp):
TTATTTTCTAGAATCAGAAC
Found at i:64956 original size:19 final size:19
Alignment explanation
Indices: 64921--64987 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
64911 TGAATCAGAA
* *
64921 CTTA-TTTCTAGATTCATAA
1 CTTATTTTC-AGACTCATAG
*
64940 CTTATTTTCATACTCATAG
1 CTTATTTTCAGACTCATAG
* * *
64959 CTTACTGTCAGATTCATAG
1 CTTATTTTCAGACTCATAG
64978 CTTATTTTCA
1 CTTATTTTCA
64988 AATTCATATC
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
19 34 0.89
20 4 0.11
ACGTcount: A:0.27, C:0.19, G:0.07, T:0.46
Consensus pattern (19 bp):
CTTATTTTCAGACTCATAG
Found at i:64992 original size:19 final size:19
Alignment explanation
Indices: 64932--64995 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
64922 TTATTTCTAG
* *
64932 ATTCATAACTTATTTTCAT
1 ATTCATAGCTTATTTTCAA
* * * *
64951 ACTCATAGCTTACTGTCAG
1 ATTCATAGCTTATTTTCAA
64970 ATTCATAGCTTATTTTCAA
1 ATTCATAGCTTATTTTCAA
64989 ATTCATA
1 ATTCATA
64996 TCCCAATGCA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (19 bp):
ATTCATAGCTTATTTTCAA
Found at i:68348 original size:7 final size:6
Alignment explanation
Indices: 68331--68384 Score: 54
Period size: 6 Copynumber: 8.2 Consensus size: 6
68321 TAATTAAAAT
*
68331 AATAAA AATAACA AATAAAA AATAAA ACAGTAAA AACATAA AATAAA AATAAA
1 AATAAA AATAA-A AAT-AAA AATAAA A-A-TAAA AATA-AA AATAAA AATAAA
68384 A
1 A
68385 TATGAGGACC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
6 19 0.46
7 15 0.37
8 7 0.17
ACGTcount: A:0.78, C:0.06, G:0.02, T:0.15
Consensus pattern (6 bp):
AATAAA
Found at i:70319 original size:25 final size:24
Alignment explanation
Indices: 70265--70319 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
70255 TTTACAGTTG
*
70265 TAAAATCAATTCAAACATTATATT
1 TAAAATCAATTCAAACAATATATT
*
70289 TCAAATCAGAGTTCAAACAAT-TATT
1 TAAAATCA-A-TTCAAACAATATATT
70314 TAAAAT
1 TAAAAT
70320 AGTTGTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 7 0.27
25 10 0.38
26 9 0.35
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (24 bp):
TAAAATCAATTCAAACAATATATT
Found at i:72694 original size:42 final size:41
Alignment explanation
Indices: 72565--72694 Score: 111
Period size: 42 Copynumber: 3.1 Consensus size: 41
72555 ATATTGAAAA
* * ** *
72565 CATCATGCTCGAAGGTCTTATGGATGGCCCGAAGGTCTTAT
1 CATCATGCTCGAAAGACTTATAAATGGCCCGAAGGACTTAT
* * * * *
72606 CATCTTGTTC-AGAAGACTTATAAATGGTCCGAAGGAGTTAAG
1 CATCATGCTCGA-AAGACTTATAAATGGCCCGAAGGACTT-AT
*
72648 CATCATGCTCGAAAGACTTACT-AATGGCCCGAAGAACTTACT
1 CATCATGCTCGAAAGACTTA-TAAATGGCCCGAAGGACTTA-T
72690 CATCA
1 CATCA
72695 AGAAAATCTT
Statistics
Matches: 68, Mismatches: 16, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
40 1 0.01
41 29 0.43
42 36 0.53
43 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (41 bp):
CATCATGCTCGAAAGACTTATAAATGGCCCGAAGGACTTAT
Found at i:72945 original size:20 final size:20
Alignment explanation
Indices: 72889--72952 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
72879 ACACTTATAA
72889 ATGGCCCGAAGGACTTAAGCATC
1 ATGGCCCGAAGGACTT-A-C-TC
* * *
72912 AT-GCTCGAAAGACTTACTG
1 ATGGCCCGAAGGACTTACTC
72931 ATGGCCCGAAGGACTTACTC
1 ATGGCCCGAAGGACTTACTC
72951 AT
1 AT
72953 CAAGAAAACC
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
19 3 0.09
20 17 0.50
21 1 0.03
22 11 0.32
23 2 0.06
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (20 bp):
ATGGCCCGAAGGACTTACTC
Found at i:72954 original size:42 final size:41
Alignment explanation
Indices: 72841--72954 Score: 131
Period size: 42 Copynumber: 2.7 Consensus size: 41
72831 GCCTTAAGGT
* ** *
72841 CTTATGGATGGCCCGAAGGTTTTATCATCTTGCTCGAAACA
1 CTTATAGATGGCCCGAAGGACTTATCATCATGCTCGAAACA
* * *
72882 CTTATAAATGGCCCGAAGGACTTAAGCATCATGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTT-ATCATCATGCTCGAAACA
72924 CTTACT-GATGGCCCGAAGGACTTACTCATCA
1 CTTA-TAGATGGCCCGAAGGACTTA-TCATCA
72955 AGAAAACCTT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
41 20 0.33
42 40 0.66
43 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTATCATCATGCTCGAAACA
Found at i:73122 original size:261 final size:260
Alignment explanation
Indices: 72519--73294 Score: 1209
Period size: 261 Copynumber: 3.0 Consensus size: 260
72509 ATACATTGTT
* * *
72519 GATTCAACTCCATATGTTATGAATCGAGTA-TAAAAAATATTGAAAACATCATGCTCGAAGGTCT
1 GATTCAACTCCATATGTGATGAATCGAGTACT-AGAAATGTTGAAAACATCATGCTCGAAGGTCT
* * * *
72583 TATGGATGGCCCGAAGGTCTTATCATCTTGTTCAGAAGACTTATAAATGGTCCGAAGGAGTTAAG
65 TATGGATGGCCCGAAGGTTTTATCATCTTGCTCA-AAGACTTATAAATGGCCCGAAGGACTTAAG
* * *
72648 CATCATGCTCGAAAGACTTACTAATGGCCCGAAGAACTTACTCATCAAGAAAATCTTGAAAATCA
129 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTCATCAAGAAAACCTTGAAAATCA
* *
72713 AGCTTAGTTTCTTA-AAAAATTCTTTTGAAAATATCATGTTGTTTGGGTAACATTCCCCCACATC
194 AGCTTAGTTTCTTATAAAAATTCTTTTGAAAATATCATGTTGTTTGGGTAACGTGCCCCCACATC
72777 AA
259 AA
* * *
72779 GATTCAATTCCATATGTGATGAATCGAGTACCAGAAATGTTGAAAACATCATGC-CTTAAGGTCT
1 GATTCAACTCCATATGTGATGAATCGAGTACTAGAAATGTTGAAAACATCATGCTC-GAAGGTCT
*
72843 TATGGATGGCCCGAAGGTTTTATCATCTTGCTCGAAACACTTATAAATGGCCCGAAGGACTTAAG
65 TATGGATGGCCCGAAGGTTTTATCATCTTGCTC-AAAGACTTATAAATGGCCCGAAGGACTTAAG
*
72908 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTCATCAAGAAAACCTTAAAAATCA
129 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTCATCAAGAAAACCTTGAAAATCA
*
72973 AGCTTAGTTCCTTATAAAAATTCTTTTGAAAATATCATGTTGTTTGGGTAACGTGCCCCCACATC
194 AGCTTAGTTTCTTATAAAAATTCTTTTGAAAATATCATGTTGTTTGGGTAACGTGCCCCCACATC
73038 AA
259 AA
* * *
73040 GATTCAACTCTATATGTGATGAATCGAGTACTGGAAATGTTGAAAACTTCCA-GCTCGAAGGTCT
1 GATTCAACTCCATATGTGATGAATCGAGTACTAGAAATGTTGAAAACAT-CATGCTCGAAGGTCT
* * ** * *
73104 TATAGATGGCCTGAAGGTTTTATCATCTTGCTCAAAAGACTTATAAATTACTCGAATGACTTAAG
65 TATGGATGGCCCGAAGGTTTTATCATCTTGCTC-AAAGACTTATAAATGGCCCGAAGGACTTAAG
* *
73169 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTGATCAATAAAACCTTGAAAATCA
129 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTCATCAAGAAAACCTTGAAAATCA
73234 AGCTTAGTTTCTTATAAAAATTCTTTTGAAAATATCATGTTGTTTGGGTAACGTGCCCCCA
194 AGCTTAGTTTCTTATAAAAATTCTTTTGAAAATATCATGTTGTTTGGGTAACGTGCCCCCA
73295 TGTCAAAGTA
Statistics
Matches: 474, Mismatches: 36, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
259 1 0.00
260 187 0.39
261 283 0.60
262 3 0.01
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (260 bp):
GATTCAACTCCATATGTGATGAATCGAGTACTAGAAATGTTGAAAACATCATGCTCGAAGGTCTT
ATGGATGGCCCGAAGGTTTTATCATCTTGCTCAAAGACTTATAAATGGCCCGAAGGACTTAAGCA
TCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTCATCAAGAAAACCTTGAAAATCAAG
CTTAGTTTCTTATAAAAATTCTTTTGAAAATATCATGTTGTTTGGGTAACGTGCCCCCACATCAA
Found at i:75212 original size:15 final size:14
Alignment explanation
Indices: 75194--75300 Score: 85
Period size: 15 Copynumber: 7.1 Consensus size: 14
75184 TTTCTCTCCC
75194 TTTTTTCTCTTTTCT
1 TTTTTTCTCTTTT-T
75209 TTTTTTCTCTTTTTT
1 TTTTTTCTC-TTTTT
75224 TCTTTTTCTCTCTTTT
1 T-TTTTTCTCT-TTTT
*
75240 TTCTTTCT-TTCTTT
1 TTTTTTCTCTT-TTT
75254 CTTTCTTTCTCTTTTT
1 -TTT-TTTCTCTTTTT
75270 TATTTCTT-TCTTTTAT
1 T-TTT-TTCTCTTTT-T
75286 ATTTTTTC-CTTTTT
1 -TTTTTTCTCTTTTT
75300 T
1 T
75301 CTATATCTTT
Statistics
Matches: 78, Mismatches: 2, Indels: 26
0.74 0.02 0.25
Matches are distributed among these distances:
13 2 0.03
14 5 0.06
15 35 0.45
16 33 0.42
17 3 0.04
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTTCTCTTTTT
Found at i:75214 original size:8 final size:8
Alignment explanation
Indices: 75193--75302 Score: 80
Period size: 8 Copynumber: 13.2 Consensus size: 8
75183 TTTTCTCTCC
75193 CTTTTTTCT
1 CTTTTTT-T
*
75202 CTTTTCTT
1 CTTTTTTT
*
75210 -TTTTTCT
1 CTTTTTTT
75217 CTTTTTTT
1 CTTTTTTT
*
75225 CTTTTTCT
1 CTTTTTTT
75233 CTCTTTTTT
1 CT-TTTTTT
*
75242 CTTTCTTT
1 CTTTTTTT
*
75250 CTTTCTTT
1 CTTTTTTT
75258 CTTTCTCTTT
1 CTTT-T-TTT
*
75268 -TTTATTT
1 CTTTTTTT
75275 CTTTCTTTT
1 CTTT-TTTT
*
75284 ATATTTTTT
1 CT-TTTTTT
*
75293 CCTTTTTT
1 CTTTTTTT
75301 CT
1 CT
75303 ATATCTTTTC
Statistics
Matches: 80, Mismatches: 14, Indels: 15
0.73 0.13 0.14
Matches are distributed among these distances:
7 8 0.10
8 43 0.54
9 24 0.30
10 5 0.06
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (8 bp):
CTTTTTTT
Found at i:75222 original size:16 final size:15
Alignment explanation
Indices: 75194--75300 Score: 94
Period size: 16 Copynumber: 7.0 Consensus size: 15
75184 TTTCTCTCCC
*
75194 TTTTTTCTCTTTTCT
1 TTTTTTCTCTTTTTT
75209 TTTTTTCTCTTTTTT
1 TTTTTTCTCTTTTTT
*
75224 TCTTTTTCTCTCTTTT
1 T-TTTTTCTCTTTTTT
*
75240 TTCTTTCT-TTCTTTCT
1 TTTTTTCTCTT-TTT-T
*
75256 TTCTTTCTCTTTTTT
1 TTTTTTCTCTTTTTT
* *
75271 ATTTCTTTCT-TTTATA
1 -TTT-TTTCTCTTTTTT
75287 TTTTTTC-CTTTTTT
1 TTTTTTCTCTTTTTT
75301 CTATATCTTT
Statistics
Matches: 76, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
14 9 0.12
15 28 0.37
16 32 0.42
17 7 0.09
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTTCTCTTTTTT
Found at i:75254 original size:29 final size:29
Alignment explanation
Indices: 75195--75282 Score: 106
Period size: 29 Copynumber: 3.0 Consensus size: 29
75185 TTCTCTCCCT
* * *
75195 TTTTTCTCTTTTCTTTTTTTCTCTTTTTTTC
1 TTTTTCTCTCTT-TTTTATT-TCTTTCTTTC
*
75226 TTTTTCTCTCTTTTTTCTTTCTTTCTTTC
1 TTTTTCTCTCTTTTTTATTTCTTTCTTTC
75255 TTTCTT-TCTCTTTTTTATTTCTTTCTTT
1 TTT-TTCTCTCTTTTTTATTTCTTTCTTT
75283 TATATTTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
29 33 0.63
30 8 0.15
31 11 0.21
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.78
Consensus pattern (29 bp):
TTTTTCTCTCTTTTTTATTTCTTTCTTTC
Found at i:75276 original size:44 final size:41
Alignment explanation
Indices: 75169--75322 Score: 127
Period size: 44 Copynumber: 3.6 Consensus size: 41
75159 ATTTGATCAG
* * *
75169 TTTTCTTTCTTCTTT-TTTCTCTCCCTTTTTTCTCTTTTCTTT
1 TTTTCTTTCTT-TTTCTTTTTCTCTCTTTTTTCTTTTTTC-TT
75211 TTTTCTCTT-TTTTTCTTTTTCTCTCTTTTTTCTTTCTTTCTT
1 TTTTCT-TTCTTTTTCTTTTTCTCTCTTTTTTCTTT-TTTCTT
* * *
75253 TCTTTCTTTCTCTTTT-TTATTTCTTTCTTTTATATTTTTTCCTT
1 T-TTTCTTTCT-TTTTCTT-TTTCTCTCTTTTTTCTTTTTT-CTT
75297 TTTTCTATATC-TTTTCTTATTTCTCT
1 TTTTCT-T-TCTTTTTCTT-TTTCTCT
75323 TTGTGTTATC
Statistics
Matches: 94, Mismatches: 7, Indels: 20
0.78 0.06 0.17
Matches are distributed among these distances:
41 3 0.03
42 30 0.32
43 26 0.28
44 33 0.35
45 2 0.02
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (41 bp):
TTTTCTTTCTTTTTCTTTTTCTCTCTTTTTTCTTTTTTCTT
Found at i:75290 original size:21 final size:21
Alignment explanation
Indices: 75234--75304 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
75224 TCTTTTTCTC
* *
75234 TCTTT-TTTCT-TTCTTTCTT
1 TCTTTCTTTCTATTTTTTATT
*
75253 TCTTTCTTTCTCTTTTTTATT
1 TCTTTCTTTCTATTTTTTATT
*
75274 TCTTTCTTT-TATATTTT-TT
1 TCTTTCTTTCTATTTTTTATT
*
75293 CCTTT-TTTCTAT
1 TCTTTCTTTCTAT
75305 ATCTTTTCTT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
18 3 0.07
19 14 0.32
20 11 0.25
21 16 0.36
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (21 bp):
TCTTTCTTTCTATTTTTTATT
Found at i:75291 original size:69 final size:69
Alignment explanation
Indices: 75169--75299 Score: 160
Period size: 69 Copynumber: 1.9 Consensus size: 69
75159 ATTTGATCAG
* * * *
75169 TTTTCTTTCTTCTTTTTTCTCTCCCTTTTTTCTCTTTTCTTTTTTTCTCTTTTTTTCTTTTTCTC
1 TTTTCTTTCTTCTTTTTTCTCTCCCTTTTTTCTCATTTCTTTTTTTATATTTTTTCCTTTTTCTC
75234 TCTT
66 TCTT
* *
75238 TTTTCTTTCTTTCTTTCTTTCTTTCTC-TTTTT-T-ATTTCTTTCTTTTATATTTTTTCCTTTTT
1 TTTTCTTTC-TTCTTT-TTTCTCTCCCTTTTTTCTCATTTCTTT-TTTTATATTTTTTCCTTTTT
75300 TCTATATCTT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
68 7 0.13
69 27 0.51
70 11 0.21
71 8 0.15
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.76
Consensus pattern (69 bp):
TTTTCTTTCTTCTTTTTTCTCTCCCTTTTTTCTCATTTCTTTTTTTATATTTTTTCCTTTTTCTC
TCTT
Found at i:75298 original size:29 final size:30
Alignment explanation
Indices: 75194--75300 Score: 87
Period size: 31 Copynumber: 3.5 Consensus size: 30
75184 TTTCTCTCCC
* *
75194 TTTTTTCTCTTTTCTTTT-TTTCTCTT-TTTT
1 TTTTTTCTCTTTT-TTTTCTTTCT-TTCTATA
* * *
75224 TCTTTTTCTCTCTTTTTTCTTTCTTTCTTTC
1 T-TTTTTCTCTTTTTTTTCTTTCTTTCTATA
75255 TTTCTTTCTCTTTTTTATTTCTTTCTTT-TATA
1 TTT-TTTCTC-TTTTT-TTTCTTTCTTTCTATA
75287 TTTTTTC-CTTTTTT
1 TTTTTTCTCTTTTTT
75301 CTATATCTTT
Statistics
Matches: 66, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
28 1 0.02
29 5 0.08
30 10 0.15
31 30 0.45
32 9 0.14
33 11 0.17
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.79
Consensus pattern (30 bp):
TTTTTTCTCTTTTTTTTCTTTCTTTCTATA
Found at i:79335 original size:51 final size:50
Alignment explanation
Indices: 79265--79382 Score: 150
Period size: 51 Copynumber: 2.3 Consensus size: 50
79255 AAATAAAATA
* *
79265 AAATAAAA-TGACTAAAATGCAAAAAAATAAAATT-TAGTAACTAAATCAG
1 AAATAAAAGTGACAAAAATGC-AAAAAATAAAATTACAGTAACTAAATCAG
* *
79314 AAATAAAGAGTGACAAAAATGCAAAAATTAAAATTACAGTAACTAAATGAG
1 AAATAAA-AGTGACAAAAATGCAAAAAATAAAATTACAGTAACTAAATCAG
*
79365 AAACTAACAGTGACAAAA
1 AAA-TAAAAGTGACAAAA
79383 TTAAAATAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
49 7 0.12
50 13 0.22
51 37 0.62
52 3 0.05
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.19
Consensus pattern (50 bp):
AAATAAAAGTGACAAAAATGCAAAAAATAAAATTACAGTAACTAAATCAG
Found at i:80105 original size:30 final size:30
Alignment explanation
Indices: 80069--80127 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
80059 AAAAAATAAA
80069 TATTCTTTTTTACTGATATTTAAAACCGAT
1 TATTCTTTTTTACTGATATTTAAAACCGAT
*
80099 TATTCTTTTTTATTGATATTTAAAACCGA
1 TATTCTTTTTTACTGATATTTAAAACCGA
80128 AGACAGTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.51
Consensus pattern (30 bp):
TATTCTTTTTTACTGATATTTAAAACCGAT
Done.