Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004299.1 Hibiscus syriacus cultivar Beakdansim tig00009430_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: 57054
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:11083 original size:15 final size:15
Alignment explanation
Indices: 11065--11100 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
11055 AACACCTACA
*
11065 ACATCAGACAAATTC
1 ACATCAAACAAATTC
11080 ACATCAAACAAATTC
1 ACATCAAACAAATTC
11095 ACATCA
1 ACATCA
11101 TCAGAGTAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.50, C:0.28, G:0.03, T:0.19
Consensus pattern (15 bp):
ACATCAAACAAATTC
Found at i:12908 original size:19 final size:19
Alignment explanation
Indices: 12873--12911 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
12863 ATGTAAAATA
12873 TATCTATATAATTTTTTTG
1 TATCTATATAATTTTTTTG
*
12892 TATC-ATATAGTTATTTTTG
1 TATCTATATAATT-TTTTTG
12911 T
1 T
12912 TAGATTTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.26, C:0.05, G:0.08, T:0.62
Consensus pattern (19 bp):
TATCTATATAATTTTTTTG
Found at i:14269 original size:13 final size:13
Alignment explanation
Indices: 14251--14275 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14241 TCGCTACAAG
14251 CCATTTTATTAAA
1 CCATTTTATTAAA
14264 CCATTTTATTAA
1 CCATTTTATTAA
14276 TGTTGTTTGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (13 bp):
CCATTTTATTAAA
Found at i:14437 original size:50 final size:51
Alignment explanation
Indices: 14357--14456 Score: 175
Period size: 50 Copynumber: 2.0 Consensus size: 51
14347 ATAAATATAT
14357 GCCTCTCGAACAAGAAATTGGTGATGTTGAAGGTATTCATAAATCTTTGAC
1 GCCTCTCGAACAAGAAATTGGTGATGTTGAAGGTATTCATAAATCTTTGAC
* *
14408 GCCTCTCGTACAGGAAA-TGGTGATGTTGAAGGTATTCATAAATCTTTGA
1 GCCTCTCGAACAAGAAATTGGTGATGTTGAAGGTATTCATAAATCTTTGA
14457 TTGAGTCACT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
50 32 0.68
51 15 0.32
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (51 bp):
GCCTCTCGAACAAGAAATTGGTGATGTTGAAGGTATTCATAAATCTTTGAC
Found at i:16279 original size:3 final size:3
Alignment explanation
Indices: 16273--16319 Score: 85
Period size: 3 Copynumber: 15.3 Consensus size: 3
16263 AATATAATAA
16273 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT
16319 A
1 A
16320 CAAACCGGGC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:17597 original size:2 final size:2
Alignment explanation
Indices: 17590--17643 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
17580 TAAATATGTA
17590 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
17632 TT AT AT AT AT AT
1 AT AT AT AT AT AT
17644 CTTATAAACG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:18131 original size:76 final size:76
Alignment explanation
Indices: 18005--18187 Score: 269
Period size: 76 Copynumber: 2.4 Consensus size: 76
17995 TATCGTTGCA
* * * * *
18005 TATTCATTTCACTGGTGTAAGTCGATATTAAGTTTTACTGCAGGAATTATGTGATAAATTGAGTG
1 TATTCATTTCACTTGTGTAAGTCAATGTTAAATTTCACTGCAGGAATTATGTGATAAATTGAGTG
18070 CTGAAATTACC
66 CTGAAATTACC
* *
18081 TATTCATTTCACTTGTGTAAGTCAATGTTAAATTTCACTGCAGGAATTATGTGATAAGTTTAGTG
1 TATTCATTTCACTTGTGTAAGTCAATGTTAAATTTCACTGCAGGAATTATGTGATAAATTGAGTG
* *
18146 CTGGAATTACG
66 CTGAAATTACC
18157 TATTCATTTCAC-TGATGTAAGTCAATGTTAA
1 TATTCATTTCACTTG-TGTAAGTCAATGTTAA
18188 GGTTCAAAGT
Statistics
Matches: 97, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
75 2 0.02
76 95 0.98
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (76 bp):
TATTCATTTCACTTGTGTAAGTCAATGTTAAATTTCACTGCAGGAATTATGTGATAAATTGAGTG
CTGAAATTACC
Found at i:18226 original size:58 final size:58
Alignment explanation
Indices: 18136--18246 Score: 195
Period size: 58 Copynumber: 1.9 Consensus size: 58
18126 ATTATGTGAT
18136 AAGTTTAGTGCTGGAATTACGTATTCATTTCACTGATGTAAGTCAATGTTAAGGTTCA
1 AAGTTTAGTGCTGGAATTACGTATTCATTTCACTGATGTAAGTCAATGTTAAGGTTCA
* * *
18194 AAGTTTAGTGTTGGAGTTACTTATTCATTTCACTGATGTAAGTCAATGTTAAG
1 AAGTTTAGTGCTGGAATTACGTATTCATTTCACTGATGTAAGTCAATGTTAAG
18247 TTTCGCTGCT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.40
Consensus pattern (58 bp):
AAGTTTAGTGCTGGAATTACGTATTCATTTCACTGATGTAAGTCAATGTTAAGGTTCA
Found at i:18431 original size:76 final size:76
Alignment explanation
Indices: 18305--18782 Score: 510
Period size: 76 Copynumber: 6.3 Consensus size: 76
18295 CATTTTACTG
* * * * * * *
18305 GTTAAATTTCATTGCTAGAATTAGGTGATAAGTTTAGTG-TCGGAACTACGTATTCATTTCACTA
1 GTTAAGTTTCACTGCTGGAATTATGTGATAAGTTTAGTGCT-AGAATTACGTATTCATTTCACTG
18369 GTGTAAGTCAAT
65 GTGTAAGTCAAT
* * * **
18381 GTTAAATTTCATTGCTGGAATTATGTGATAAGTTTAGTGCTGGAATTACGTATTCATTTCTTTGG
1 GTTAAGTTTCACTGCTGGAATTATGTGATAAGTTTAGTGCTAGAATTACGTATTCATTTCACTGG
*
18446 TGTAAGTTAAT
66 TGTAAGTCAAT
* *** ** * * *
18457 GTTAAGTTTAACCATTGGAATTATGTGATAAGTTTAACGTTGGAATTACGTATTCATTTCACTGA
1 GTTAAGTTTCACTGCTGGAATTATGTGATAAGTTTAGTGCTAGAATTACGTATTCATTTCACTGG
* *
18522 TATAAGTCAAA
66 TGTAAGTCAAT
** ** *
18533 GTTAAGTTTCACTATTTAAATTACGTGATAAGTTTAGTGCTAGAATTACGTATTCATTTCACTGG
1 GTTAAGTTTCACTGCTGGAATTATGTGATAAGTTTAGTGCTAGAATTACGTATTCATTTCACTGG
18598 TGTAAGTCAAT
66 TGTAAGTCAAT
* * * * * *
18609 GTTAAGTTTCACTGCTGAAATCATGT-ATTAAGTTTAGTGCTAGAATCACATATTCATTTAACTA
1 GTTAAGTTTCACTGCTGGAATTATGTGA-TAAGTTTAGTGCTAGAATTACGTATTCATTTCACTG
* *
18673 CTATAAGTCAAT
65 GTGTAAGTCAAT
* * * * * *
18685 GTTAAGTTTCACTTCTGAAATCATGTCATAAGTTTATTGCTAGAATTACGTATTTATTTCACTGG
1 GTTAAGTTTCACTGCTGGAATTATGTGATAAGTTTAGTGCTAGAATTACGTATTCATTTCACTGG
*
18750 TGTAAGTTAAT
66 TGTAAGTCAAT
* *
18761 GTTATGTTTCACTGCTAGAATT
1 GTTAAGTTTCACTGCTGGAATT
18783 CTGATGTGTT
Statistics
Matches: 339, Mismatches: 60, Indels: 6
0.84 0.15 0.01
Matches are distributed among these distances:
75 1 0.00
76 336 0.99
77 2 0.01
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (76 bp):
GTTAAGTTTCACTGCTGGAATTATGTGATAAGTTTAGTGCTAGAATTACGTATTCATTTCACTGG
TGTAAGTCAAT
Found at i:19119 original size:69 final size:69
Alignment explanation
Indices: 18985--19156 Score: 177
Period size: 69 Copynumber: 2.5 Consensus size: 69
18975 GGAGGCTCGT
* * * *
18985 AGGATTAGAGTGACTCGCAAGGGAGGACCTAATCATGATTTTTCTGGATGACTCGCACGAAAGTC
1 AGGATTAGAGTGACTTGCACGGGAGCACCTAATCATAATTTTTCTGGATGACTCGCACGAAAGTC
19050 CAGA
66 CAGA
* * * * *
19054 AGGATTAGAGTGACTTACACGGGAGCACCTAATCATAATTATTTC-GGGTGACTTGGATC-AGAG
1 AGGATTAGAGTGACTTGCACGGGAGCACCTAATCATAATT-TTTCTGGATGACTCGCA-CGAAAG
**
19117 TCCCTA
64 TCCAGA
* * **
19123 AAGATTAGAGTGACTTGTACGAAAGCACCTAATC
1 AGGATTAGAGTGACTTGCACGGGAGCACCTAATC
19157 GTTTTGGTCG
Statistics
Matches: 85, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
69 80 0.94
70 5 0.06
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (69 bp):
AGGATTAGAGTGACTTGCACGGGAGCACCTAATCATAATTTTTCTGGATGACTCGCACGAAAGTC
CAGA
Found at i:20107 original size:76 final size:76
Alignment explanation
Indices: 19981--20716 Score: 843
Period size: 76 Copynumber: 9.6 Consensus size: 76
19971 CGGAATACTG
* * * * * * *
19981 GTTAAATTTCACTACTAGAATTAGGTGATAAGTTTAGTG-TCGGAACTACGTATTCATTTCACTA
1 GTTAAGTTTCACTGCTGGAATTATGTGATAAGTTTAGTGCT-AGAATTACGTATTCATTTCACTG
20045 GTGTAAGTCAAT
65 GTGTAAGTCAAT
* * * **
20057 GTTAAATTTCATTGCTGGAATTATGTGATAAGTTTAGTGCTGGAATTACGTATTCATTTCTTTGG
1 GTTAAGTTTCACTGCTGGAATTATGTGATAAGTTTAGTGCTAGAATTACGTATTCATTTCACTGG
*
20122 TGTAAGTTAAT
66 TGTAAGTCAAT
** ** * *
20133 GTTAAGTTTCACTATTGGAATTATGTGATAAGTTTAACGTTGGAATTACGTATTCATTTCACTGG
1 GTTAAGTTTCACTGCTGGAATTATGTGATAAGTTTAGTGCTAGAATTACGTATTCATTTCACTGG
* *
20198 TATAAGTAAAT
66 TGTAAGTCAAT
** ** * *
20209 GTTAAGTTTCACTATTTAAATTACGTGATAAGATTAGTGCTAGAATTACGTATTCATTTCACTGG
1 GTTAAGTTTCACTGCTGGAATTATGTGATAAGTTTAGTGCTAGAATTACGTATTCATTTCACTGG
20274 TGTAAGTCAAT
66 TGTAAGTCAAT
* * *
20285 GTTAAGTTTCACTGCTGAAATCATGT-ATTAAGTTTAGTGCTAGAATCACGTATTCATTTCACTG
1 GTTAAGTTTCACTGCTGGAATTATGTGA-TAAGTTTAGTGCTAGAATTACGTATTCATTTCACTG
*
20349 GTGTAAGTCGAT
65 GTGTAAGTCAAT
* * * * * *
20361 ATTAAGTTTTACTGCAT-GAATTATGTGATAAATTTAGTGCTGGAATTACCTATTCATTTCACTT
1 GTTAAGTTTCACTGC-TGGAATTATGTGATAAGTTTAGTGCTAGAATTACGTATTCATTTCACTG
20425 GTGTAAGTCAAT
65 GTGTAAGTCAAT
* * *
20437 GTTAAATTTCACTGCGGGAATTATGTGATAAGTTTAGTGCTAGAATTACATATTCATTTCACTGG
1 GTTAAGTTTCACTGCTGGAATTATGTGATAAGTTTAGTGCTAGAATTACGTATTCATTTCACTGG
20502 TGTAAGTCAAT
66 TGTAAGTCAAT
* * * * * * *
20513 GTTAAGTTTCACTACTGAAATCATGT-ATTAAGTTTAGTTCTAGAATCACATATTCATTTCACTA
1 GTTAAGTTTCACTGCTGGAATTATGTGA-TAAGTTTAGTGCTAGAATTACGTATTCATTTCACTG
*
20577 CTGTAAGTCAAT
65 GTGTAAGTCAAT
* * * * * *
20589 GTTAAGTTTCACTTCTGAAATCATGTCATAAGTTTAGTGCTAGAATTACGTATTCATTTGACTAG
1 GTTAAGTTTCACTGCTGGAATTATGTGATAAGTTTAGTGCTAGAATTACGTATTCATTTCACTGG
*
20654 TGTAAGTTAAT
66 TGTAAGTCAAT
* * *
20665 GTTATGTTTCACTGCTAGAATTCTGATGTGTTTAA-TTTAGTGCTAGAATTAC
1 GTTAAGTTTCACTGCTGGAA-T-T-ATGTG-ATAAGTTTAGTGCTAGAATTAC
20717 CTGTTAATGT
Statistics
Matches: 570, Mismatches: 79, Indels: 19
0.85 0.12 0.03
Matches are distributed among these distances:
75 2 0.00
76 539 0.95
77 5 0.01
79 21 0.04
80 3 0.01
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (76 bp):
GTTAAGTTTCACTGCTGGAATTATGTGATAAGTTTAGTGCTAGAATTACGTATTCATTTCACTGG
TGTAAGTCAAT
Found at i:20331 original size:25 final size:26
Alignment explanation
Indices: 20286--20348 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
20276 TAAGTCAATG
*
20286 TTAAGTTTCACTGCTGAAATCATGTA
1 TTAAGTTTCACTGCTGAAATCACGTA
*
20312 TTAAGTTT-AGTGCT-AGAATCACGTA
1 TTAAGTTTCACTGCTGA-AATCACGTA
*
20337 TTCA-TTTCACTG
1 TTAAGTTTCACTG
20349 GTGTAAGTCG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
24 4 0.13
25 19 0.61
26 8 0.26
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (26 bp):
TTAAGTTTCACTGCTGAAATCACGTA
Found at i:20543 original size:26 final size:26
Alignment explanation
Indices: 20514--20623 Score: 79
Period size: 26 Copynumber: 4.3 Consensus size: 26
20504 TAAGTCAATG
20514 TTAAGTTTCACTACTGAAATCATGTA
1 TTAAGTTTCACTACTGAAATCATGTA
* * **
20540 TTAAGTTT-AGTTCT-AGAATCACATA
1 TTAAGTTTCACTACTGA-AATCATGTA
* *
20565 TTCA-TTTCACTACTGTAAGTCAATG--
1 TTAAGTTTCACTACTG-AAATC-ATGTA
*
20590 TTAAGTTTCACTTCTGAAATCATGTCA
1 TTAAGTTTCACTACTGAAATCATGT-A
20617 -TAAGTTT
1 TTAAGTTT
20624 AGTGCTAGAA
Statistics
Matches: 62, Mismatches: 13, Indels: 18
0.67 0.14 0.19
Matches are distributed among these distances:
24 7 0.11
25 25 0.40
26 28 0.45
27 2 0.03
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (26 bp):
TTAAGTTTCACTACTGAAATCATGTA
Found at i:20962 original size:69 final size:68
Alignment explanation
Indices: 20889--21122 Score: 224
Period size: 69 Copynumber: 3.4 Consensus size: 68
20879 GGAGGCTCGT
* *
20889 AGGATTAGAGTGACTCGCAAGGGATG-ACCTAATCGTGATT-TTTCTGGGTGACTCGCACGAAAG
1 AGGATTAGAGTGACTCACAAGGGA-GCACCTAATCGTAATTATTTCTGGGTGACTCGCACG-AAG
20952 TCCAGA
64 TCC-GA
* * * * * *
20958 AGGATTAGAGTGACTTACACGGGAGCACCTAATCATAATTATTTCT-GGTGACTTGGATCGGAGT
1 AGGATTAGAGTGACTCACAAGGGAGCACCTAATCGTAATTATTTCTGGGTGACTCGCA-CGAAGT
*
21022 CCCTA
65 -CCGA
*** * ** * *
21027 AGGATTAGAGTGACTTGTACGAAAGCACCTAATCGTAATTATTTC-GGTTGACTCGCACAGGAAC
1 AGGATTAGAGTGACTCACAAGGGAGCACCTAATCGTAATTATTTCTGGGTGACTCGCAC--GAAG
21091 TCCGA
64 TCCGA
21096 AGGATTAGAGTGACTCACAAGGGAGCA
1 AGGATTAGAGTGACTCACAAGGGAGCA
21123 TATTATCGTA
Statistics
Matches: 132, Mismatches: 26, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
68 2 0.02
69 118 0.89
70 12 0.09
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.25
Consensus pattern (68 bp):
AGGATTAGAGTGACTCACAAGGGAGCACCTAATCGTAATTATTTCTGGGTGACTCGCACGAAGTC
CGA
Found at i:21131 original size:69 final size:68
Alignment explanation
Indices: 20867--21132 Score: 200
Period size: 69 Copynumber: 3.9 Consensus size: 68
20857 AGTATTCCGA
* * * * *
20867 GTGACTCGCACAGGAGGCT-CGTAGGATTAGAGTGACTCGCAAGGGATG-ACCTAATCGTGATT-
1 GTGACTCGCAC-GGA-ACTCCGAAGGATTAGAGTGACTCACAAGGGA-GCACATAATCGTAATTA
20929 TTTCTGG
63 TTTCT-G
* * * * * *
20936 GTGACTCGCACGAAAGTCCAGAAGGATTAGAGTGACTTACACGGGAGCACCTAATCATAATTATT
1 GTGACTCGCACGGAACTCC-GAAGGATTAGAGTGACTCACAAGGGAGCACATAATCGTAATTATT
21001 TCTG
65 TCTG
* * * * *** * ** *
21005 GTGACTTGGATCGG-AGTCCCTAAGGATTAGAGTGACTTGTACGAAAGCACCTAATCGTAATTAT
1 GTGACTCGCA-CGGAACT-CCGAAGGATTAGAGTGACTCACAAGGGAGCACATAATCGTAATTAT
21069 TTC-G
64 TTCTG
* *
21073 GTTGACTCGCACAGGAACTCCGAAGGATTAGAGTGACTCACAAGGGAGCATATTATCGTA
1 G-TGACTCGCAC-GGAACTCCGAAGGATTAGAGTGACTCACAAGGGAGCACATAATCGTA
21133 TTTGCTACCA
Statistics
Matches: 157, Mismatches: 31, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
67 1 0.01
68 7 0.04
69 138 0.88
70 11 0.07
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.26
Consensus pattern (68 bp):
GTGACTCGCACGGAACTCCGAAGGATTAGAGTGACTCACAAGGGAGCACATAATCGTAATTATTT
CTG
Found at i:23332 original size:24 final size:25
Alignment explanation
Indices: 23284--23337 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
23274 AATCATCGTT
*
23284 ATCATATATCAGTGAAAACCAAT-A
1 ATCATATATCAGTCAAAACCAATAA
*
23308 ATCATATATCAGTCATAATCC-ATAA
1 ATCATATATCAGTCA-AAACCAATAA
23333 ATCAT
1 ATCAT
23338 CACCAGTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 16 0.62
25 10 0.38
ACGTcount: A:0.46, C:0.19, G:0.06, T:0.30
Consensus pattern (25 bp):
ATCATATATCAGTCAAAACCAATAA
Found at i:24660 original size:26 final size:26
Alignment explanation
Indices: 24629--24690 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
24619 TCAATGTTTT
* * *
24629 TCCATTCATTTCAAAGCTTGCGGTTA
1 TCCATTCATTTCAAAGATTGAGGATA
24655 TCCATTCATTTCAAAGATTGAGGATA
1 TCCATTCATTTCAAAGATTGAGGATA
24681 TCCATTCATT
1 TCCATTCATT
24691 CCTGGGCTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (26 bp):
TCCATTCATTTCAAAGATTGAGGATA
Found at i:49312 original size:19 final size:19
Alignment explanation
Indices: 49277--49315 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
49267 ATGTAAAATA
49277 TATCTATATAATTTTTTTG
1 TATCTATATAATTTTTTTG
*
49296 TATC-ATATAGTTATTTTTG
1 TATCTATATAATT-TTTTTG
49315 T
1 T
49316 TAGATTTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.26, C:0.05, G:0.08, T:0.62
Consensus pattern (19 bp):
TATCTATATAATTTTTTTG
Found at i:50682 original size:13 final size:13
Alignment explanation
Indices: 50664--50691 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
50654 TATTCGCTAC
50664 AAGCCATTTTATT
1 AAGCCATTTTATT
50677 AAGCCATTTTATT
1 AAGCCATTTTATT
50690 AA
1 AA
50692 TATTGTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (13 bp):
AAGCCATTTTATT
Found at i:50859 original size:50 final size:51
Alignment explanation
Indices: 50771--50873 Score: 190
Period size: 50 Copynumber: 2.0 Consensus size: 51
50761 CGATAAATAT
50771 ATGCCTCTCGAACAAGAAATTGGTGATGTTGAAGGTATTCATAAATCTTTG
1 ATGCCTCTCGAACAAGAAATTGGTGATGTTGAAGGTATTCATAAATCTTTG
*
50822 ATGCCTCTCGTACAAGAAA-TGGTGATGTTGAAGGTATTCATAAATCTTTG
1 ATGCCTCTCGAACAAGAAATTGGTGATGTTGAAGGTATTCATAAATCTTTG
50872 AT
1 AT
50874 TGAGTCACTT
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 33 0.65
51 18 0.35
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (51 bp):
ATGCCTCTCGAACAAGAAATTGGTGATGTTGAAGGTATTCATAAATCTTTG
Found at i:52645 original size:3 final size:3
Alignment explanation
Indices: 52633--52702 Score: 97
Period size: 3 Copynumber: 23.3 Consensus size: 3
52623 TTCAAACGTC
* * *
52633 ATT A-T ATT ATT ATT ATA ATAA AAT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT
52678 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
52703 CAAACTGGGC
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.03
3 57 0.93
4 2 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:54607 original size:76 final size:76
Alignment explanation
Indices: 54481--54663 Score: 260
Period size: 76 Copynumber: 2.4 Consensus size: 76
54471 TATCGTTGCA
* * * * *
54481 TATTCATTTCACTGGTGTAAGTCAATATTAAGTTTTACTGCAGGAATTATGTGATAAATTGACTG
1 TATTCATTTCACTTGTGTAAGTCAATGTTAAATTTCACTGCAAGAATTATGTGATAAATTGACTG
54546 CTGAAATTACC
66 CTGAAATTACC
* * *
54557 TATTCATTTCACTTGTGTAAGTCAATGTTAAATTTCACTGCAAGAATTATGTGATAAGTTTAGTG
1 TATTCATTTCACTTGTGTAAGTCAATGTTAAATTTCACTGCAAGAATTATGTGATAAATTGACTG
* *
54622 CTGGAATTACG
66 CTGAAATTACC
54633 TATTCATTTCAC-TGATGTAAGTCAATGTTAA
1 TATTCATTTCACTTG-TGTAAGTCAATGTTAA
54664 GCTTCAAAGT
Statistics
Matches: 96, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
75 2 0.02
76 94 0.98
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (76 bp):
TATTCATTTCACTTGTGTAAGTCAATGTTAAATTTCACTGCAAGAATTATGTGATAAATTGACTG
CTGAAATTACC
Found at i:54702 original size:58 final size:58
Alignment explanation
Indices: 54612--54780 Score: 311
Period size: 58 Copynumber: 2.9 Consensus size: 58
54602 ATTATGTGAT
* * *
54612 AAGTTTAGTGCTGGAATTACGTATTCATTTCACTGATGTAAGTCAATGTTAAGCTTCA
1 AAGTTTAGTGTTGGAGTTACTTATTCATTTCACTGATGTAAGTCAATGTTAAGCTTCA
54670 AAGTTTAGTGTTGGAGTTACTTATTCATTTCACTGATGTAAGTCAATGTTAAGCTTCA
1 AAGTTTAGTGTTGGAGTTACTTATTCATTTCACTGATGTAAGTCAATGTTAAGCTTCA
54728 AAGTTTAGTGTTGGAGTTACTTATTCATTTCACTGATGTAAGTCAATGTTAAG
1 AAGTTTAGTGTTGGAGTTACTTATTCATTTCACTGATGTAAGTCAATGTTAAG
54781 TTTCGCTGCT
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 108 1.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (58 bp):
AAGTTTAGTGTTGGAGTTACTTATTCATTTCACTGATGTAAGTCAATGTTAAGCTTCA
Found at i:54965 original size:76 final size:76
Alignment explanation
Indices: 54839--55316 Score: 496
Period size: 76 Copynumber: 6.3 Consensus size: 76
54829 CATTTTACTG
* * * * * * *
54839 GTTAAATTTCATTGCTAGAATTAGGTGATAAGTTTAGTG-TCGGAACTACGTATTCATTTCACTA
1 GTTAAGTTTCACTGCTGGAATTATGTGATAAGTTTAGTGCT-AGAATTACGTATTCATTTCACTG
54903 GTGTAAGTCAAT
65 GTGTAAGTCAAT
* * * * **
54915 GTTAAATTTCATTGCTGGAATTATGTGATATGTTTAGTGCTGGAATTACGTATTCATTTCTTTGG
1 GTTAAGTTTCACTGCTGGAATTATGTGATAAGTTTAGTGCTAGAATTACGTATTCATTTCACTGG
54980 TGTAAG-CTAAT
66 TGTAAGTC-AAT
** * * * *
54991 GTTAAGTTTCACTATTGGAATTATGTGATAAGTTTAACT-TTGGAATTATGTATTCATTTCACTG
1 GTTAAGTTTCACTGCTGGAATTATGTGATAAGTTT-AGTGCTAGAATTACGTATTCATTTCACTG
*
55055 GTATAAGTCAAT
65 GTGTAAGTCAAT
** ** *
55067 GTTAAGTTTCACTATTTAAATTACGTGATAAGTTTAGTGCTAGAATTACGTATTCATTTCACTGG
1 GTTAAGTTTCACTGCTGGAATTATGTGATAAGTTTAGTGCTAGAATTACGTATTCATTTCACTGG
55132 TGTAAGTCAAT
66 TGTAAGTCAAT
* * * * * * *
55143 GTTAAGTTTCACTGCTGAAATCATAT-ATTAAGTTTAGTGCTAGAATCACATATTCATTTAACTA
1 GTTAAGTTTCACTGCTGGAATTATGTGA-TAAGTTTAGTGCTAGAATTACGTATTCATTTCACTG
* *
55207 CTATAAGTCAAT
65 GTGTAAGTCAAT
* * * * * *
55219 GTTAAGTTTCACTTCTGAAATCATCTCATAAGTTTAGTGCTAGAATTACATATTCATTTCACTGG
1 GTTAAGTTTCACTGCTGGAATTATGTGATAAGTTTAGTGCTAGAATTACGTATTCATTTCACTGG
* *
55284 TGAAAGTTAAT
66 TGTAAGTCAAT
* *
55295 GTTATGTTTCACTGCTAGAATT
1 GTTAAGTTTCACTGCTGGAATT
55317 CTGATGTGTT
Statistics
Matches: 343, Mismatches: 52, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
75 4 0.01
76 334 0.97
77 5 0.01
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (76 bp):
GTTAAGTTTCACTGCTGGAATTATGTGATAAGTTTAGTGCTAGAATTACGTATTCATTTCACTGG
TGTAAGTCAAT
Found at i:55036 original size:25 final size:26
Alignment explanation
Indices: 54993--55041 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
54983 AAGCTAATGT
*
54993 TAAGTTTCACTATTGGAATTATGTGA
1 TAAGTTTAACTATTGGAATTATGTGA
55019 TAAGTTTAACT-TTGGAATTATGT
1 TAAGTTTAACTATTGGAATTATGT
55042 ATTCATTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.31, C:0.06, G:0.18, T:0.45
Consensus pattern (26 bp):
TAAGTTTAACTATTGGAATTATGTGA
Found at i:55189 original size:25 final size:26
Alignment explanation
Indices: 55144--55241 Score: 71
Period size: 25 Copynumber: 3.8 Consensus size: 26
55134 TAAGTCAATG
*
55144 TTAAGTTTCACTGCTGAAATCATATA
1 TTAAGTTTCACTGCTGAAATCACATA
*
55170 TTAAGTTT-AGTGCT-AGAATCACATA
1 TTAAGTTTCACTGCTGA-AATCACATA
* * * *
55195 TTCA-TTTAACTACT-ATAAGTCA-ATG
1 TTAAGTTTCACTGCTGA-AA-TCACATA
*
55220 TTAAGTTTCACTTCTGAAATCA
1 TTAAGTTTCACTGCTGAAATCA
55242 TCTCATAAGT
Statistics
Matches: 57, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
24 4 0.07
25 31 0.54
26 21 0.37
27 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (26 bp):
TTAAGTTTCACTGCTGAAATCACATA
Found at i:55592 original size:69 final size:69
Alignment explanation
Indices: 55519--55752 Score: 215
Period size: 69 Copynumber: 3.4 Consensus size: 69
55509 GGAGGCTCGT
* * * *
55519 AGGATTAGAGTGACTCGCAAGGGAGGACCTAATCGTGATT-TTTCTGGGTGACTCGCA-CGAAAG
1 AGGATTAGAGTGACTCACAAGGGAGCACCTAATCATAATTATTTC-GGGTGACTCGCATCG-AAG
55582 TCCAGA
64 TCCAGA
* * * * *
55588 AGGATTAGAGTGACTTACACGGGAGCACCTAATCATAATTATTTCGGGTGACTTGGATCGGAGTC
1 AGGATTAGAGTGACTCACAAGGGAGCACCTAATCATAATTATTTCGGGTGACTCGCATCGAAGTC
**
55653 CCTA
66 CAGA
* * * ** * * * * *
55657 AGGATTAGAGTGACTTATACGAAAGCACCCAAACATAATTATTTTGGTTGACTCGCA-CAGGAAC
1 AGGATTAGAGTGACTCACAAGGGAGCACCTAATCATAATTATTTCGGGTGACTCGCATC--GAAG
55721 TCC-GA
64 TCCAGA
55726 AGGATTAGAGTGACTCACAAGGGAGCA
1 AGGATTAGAGTGACTCACAAGGGAGCA
55753 TATTATCGTA
Statistics
Matches: 133, Mismatches: 28, Indels: 8
0.79 0.17 0.05
Matches are distributed among these distances:
68 1 0.01
69 121 0.91
70 11 0.08
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (69 bp):
AGGATTAGAGTGACTCACAAGGGAGCACCTAATCATAATTATTTCGGGTGACTCGCATCGAAGTC
CAGA
Done.