Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003277.1 Hibiscus syriacus cultivar Beakdansim tig00006891_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: 103313
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:5701 original size:20 final size:20
Alignment explanation
Indices: 5676--5715 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5666 TTGAGGGGCC
5676 ATTTTCACTGCAAAAACCTT
1 ATTTTCACTGCAAAAACCTT
5696 ATTTTCACTGCAAAAACCTT
1 ATTTTCACTGCAAAAACCTT
5716 TTTAACATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (20 bp):
ATTTTCACTGCAAAAACCTT
Found at i:20621 original size:16 final size:17
Alignment explanation
Indices: 20602--20638 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
20592 ATTAAACACA
20602 TATTTTA-TTATTTTAT
1 TATTTTATTTATTTTAT
*
20618 TA-TTTATTTATTTTTT
1 TATTTTATTTATTTTAT
20634 TATTT
1 TATTT
20639 CATGTTTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 4 0.22
16 12 0.67
17 2 0.11
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
TATTTTATTTATTTTAT
Found at i:21757 original size:2 final size:2
Alignment explanation
Indices: 21750--21777 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21740 CCTATTATTA
21750 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
21778 TTAATTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21971 original size:3 final size:3
Alignment explanation
Indices: 21965--22007 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
21955 ATTCTTCTCT
21965 TTA TTA TTA TT- TATA TTA TTA TTA -TA TATA TTA TTA TTA TTA T
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA T-TA TTA TTA TTA TTA T
22008 ATATGTTACT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 3 0.08
3 29 0.81
4 4 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:21983 original size:15 final size:15
Alignment explanation
Indices: 21965--22011 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
21955 ATTCTTCTCT
21965 TTATTATTATTTATA
1 TTATTATTATTTATA
*
21980 TTATTATTATATATA
1 TTATTATTATTTATA
21995 TTATTATTATTATATA
1 TTATTATTATT-TATA
22011 T
1 T
22012 GTTACTAACC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 24 0.83
16 5 0.17
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTATTATTATTTATA
Found at i:22000 original size:12 final size:13
Alignment explanation
Indices: 21966--22007 Score: 63
Period size: 12 Copynumber: 3.5 Consensus size: 13
21956 TTCTTCTCTT
21966 TATTATTATT-TA
1 TATTATTATTATA
21978 TATTATTATTATA
1 TATTATTATTATA
21991 TA-TATTATTAT-
1 TATTATTATTATA
22002 TATTAT
1 TATTAT
22008 ATATGTTACT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.07
12 22 0.79
13 4 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTATTATTATA
Found at i:22008 original size:18 final size:17
Alignment explanation
Indices: 21965--22011 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
21955 ATTCTTCTCT
21965 TTATTATTAT-T-TATA
1 TTATTATTATATATATA
21980 TTATTATTATATATATTA
1 TTATTATTATATATA-TA
21998 TTATTATTATATAT
1 TTATTATTATATAT
22012 GTTACTAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
15 10 0.34
16 1 0.03
17 2 0.07
18 16 0.55
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATTATTATATATATA
Found at i:23474 original size:20 final size:21
Alignment explanation
Indices: 23438--23476 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
23428 TTCCTTTACC
23438 ATTTATTTTTTATTATTTTTT
1 ATTTATTTTTTATTATTTTTT
23459 ATTT-TTTTTT-TCTATTTT
1 ATTTATTTTTTAT-TATTTT
23477 ACTAACCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.06
20 12 0.71
21 4 0.24
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (21 bp):
ATTTATTTTTTATTATTTTTT
Found at i:32926 original size:10 final size:10
Alignment explanation
Indices: 32911--32941 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
32901 CTAAGTTGAA
32911 AAAAAAAAAG
1 AAAAAAAAAG
32921 AAAAAAAAAG
1 AAAAAAAAAG
*
32931 AAAAGAAAAG
1 AAAAAAAAAG
32941 A
1 A
32942 GAAGAACGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:32947 original size:15 final size:15
Alignment explanation
Indices: 32909--32939 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
32899 TCCTAAGTTG
32909 AAAAAAA-AAAAGAA
1 AAAAAAAGAAAAGAA
32923 AAAAAAAGAAAAGAA
1 AAAAAAAGAAAAGAA
32938 AA
1 AA
32940 GAGAAGAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAAGAA
Found at i:33010 original size:21 final size:21
Alignment explanation
Indices: 32986--33031 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
32976 CCTAAATTGA
32986 GAAAAGA-AAAAAGAAAAAGAG
1 GAAAAGAGAAAAA-AAAAAGAG
* *
33007 GAAAAGAGAATAAAAGAAGAG
1 GAAAAGAGAAAAAAAAAAGAG
33028 GAAA
1 GAAA
33032 TAAGGTGGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (21 bp):
GAAAAGAGAAAAAAAAAAGAG
Found at i:33967 original size:105 final size:105
Alignment explanation
Indices: 33785--34562 Score: 1286
Period size: 105 Copynumber: 7.4 Consensus size: 105
33775 AGGTTTTACC
33785 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
33850 ACGAAGGGACCGCTAGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
33890 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
33955 ACGAAGGGACCGCTGGTTGTCAACAAATATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
33995 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
34060 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCGATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
34100 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
34165 ACGAAGGGACCGCTGGTTGTCAACAAATATTTCTCAATGT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
34205 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
34270 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* ***
34310 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
** ** *
34375 ACGAAGGGACCGCTGACTGTCAACCGACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
* * * *
34416 CAAGAGCCAATTTCAACTTCACAACGAATGATACTGGACTCCGGACAACACAAGTTCAACTTCAC
1 C-AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
* * * * *
34481 GACGAAGGGACCGTTAGTTGTCAACAAATAATTTCCCAATTC
65 GACGAAGGGACCGCTGGTTGTCAACAAA-CATTTCTCAATTT
* * *
34523 CAGAACCAATTTCAACTTCACAGCGGAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
34563 GGAGCAATAC
Statistics
Matches: 629, Mismatches: 41, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
105 495 0.79
106 45 0.07
107 89 0.14
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:35088 original size:15 final size:15
Alignment explanation
Indices: 35068--35100 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
35058 AAACACATAT
35068 TTTA-TTATTTTATTA
1 TTTATTTATTTT-TTA
35083 TTTATTTATTTTTTA
1 TTTATTTATTTTTTA
35098 TTT
1 TTT
35101 CATGTTTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTATTTATTTTTTA
Found at i:36423 original size:3 final size:3
Alignment explanation
Indices: 36417--36459 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
36407 TTTCTTCTCT
36417 TTA TTA TTA TT- TATA TTA TTA TTA TT- TATA TTA TTA TTA TTA T
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA T-TA TTA TTA TTA TTA T
36460 ATATGTTACT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 2 0.06
3 32 0.89
4 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:36437 original size:15 final size:15
Alignment explanation
Indices: 36417--36463 Score: 85
Period size: 15 Copynumber: 3.1 Consensus size: 15
36407 TTTCTTCTCT
36417 TTATTATTATTTATA
1 TTATTATTATTTATA
36432 TTATTATTATTTATA
1 TTATTATTATTTATA
36447 TTATTATTATTATATA
1 TTATTATTATT-TATA
36463 T
1 T
36464 GTTACTAACC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 26 0.84
16 5 0.16
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATTATTATTTATA
Found at i:38308 original size:3 final size:3
Alignment explanation
Indices: 38300--38326 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
38290 ATCACTACAA
38300 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
38327 CTATGACGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:51668 original size:2 final size:2
Alignment explanation
Indices: 51663--51733 Score: 133
Period size: 2 Copynumber: 35.0 Consensus size: 2
51653 TTTTAATTTT
51663 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
51705 TA TA TA TA TA TA TA TA TA TA TA TGA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
51734 ATTACTTAAA
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 66 0.97
3 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:56757 original size:8 final size:8
Alignment explanation
Indices: 56729--56818 Score: 78
Period size: 9 Copynumber: 10.9 Consensus size: 8
56719 TATGCTTGAA
56729 GAAAAAAT
1 GAAAAAAT
**
56737 GAATGAAT
1 GAAAAAAT
56745 G-AAAAAT
1 GAAAAAAT
*
56752 GAAAAAAAAGA
1 G--AAAAAA-T
56763 GAAAAAAT
1 GAAAAAAT
56771 G-AAAAA-
1 GAAAAAAT
56777 GAAAAAAT
1 GAAAAAAT
56785 GGAAAAAAT
1 -GAAAAAAT
56794 GAAAAAAAT
1 G-AAAAAAT
56803 GAAAAAAT
1 GAAAAAAT
56811 GAAGAAAA
1 GAA-AAAA
56819 AAAAAAAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
6 1 0.01
7 15 0.22
8 19 0.28
9 26 0.39
10 5 0.07
11 1 0.01
ACGTcount: A:0.73, C:0.00, G:0.17, T:0.10
Consensus pattern (8 bp):
GAAAAAAT
Found at i:56791 original size:32 final size:33
Alignment explanation
Indices: 56728--56808 Score: 96
Period size: 32 Copynumber: 2.5 Consensus size: 33
56718 CTATGCTTGA
*
56728 AGAAAAAATGAATGAATGAAAAATGAAAAAAAA-G
1 AGAAAAAATGAA--AAAGAAAAATGAAAAAAAATG
*
56762 AGAAAAAATGAAAAAGAAAAAATG-GAAAAAATG
1 AGAAAAAATGAAAAAG-AAAAATGAAAAAAAATG
56795 A-AAAAAATGAAAAA
1 AGAAAAAATGAAAAA
56809 ATGAAGAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
32 22 0.51
33 9 0.21
34 12 0.28
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.10
Consensus pattern (33 bp):
AGAAAAAATGAAAAAGAAAAATGAAAAAAAATG
Found at i:57940 original size:105 final size:105
Alignment explanation
Indices: 57752--58054 Score: 417
Period size: 105 Copynumber: 2.8 Consensus size: 105
57742 AACTATAATT
57752 CACCCCAGAAGGAGGTGAATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAA
1 CACCCCAGAAGGAGGTGAATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAA
* * *
57817 GAGAAGGTTCGTAATGAGAAGATCCTATTTCTTTCAAATC
66 GAGAAGGTTCGTAATGAGAAGAACATATTCCTTTCAAATC
** * * * *
57857 CACCGTAGAAGGAGGTGAACCAACATTTCCAAAAGAGTTCATAATGAGAAGAACTCGTCTTAAAG
1 CACCCCAGAAGGAGGTGAATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAA
* *
57922 GAGAAGGTTCGTAATGAGAAGAACATGTTCCTTTCAAATT
66 GAGAAGGTTCGTAATGAGAAGAACATATTCCTTTCAAATC
* * * *
57962 CACCCCAGAATGAGGTGAATCAACATTTCCAGAAGAGTTCATAATAAGAAGAACTCATCCAACAA
1 CACCCCAGAAGGAGGTGAATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCC--TAA
* *
58027 AAGGAGAGAAGTTCATAATGAGAAGAAC
64 AA-GAGA-AGGTTCGTAATGAGAAGAAC
58055 TTGTTCAACC
Statistics
Matches: 171, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
105 146 0.85
107 3 0.02
108 4 0.02
109 18 0.11
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (105 bp):
CACCCCAGAAGGAGGTGAATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAA
GAGAAGGTTCGTAATGAGAAGAACATATTCCTTTCAAATC
Found at i:61515 original size:117 final size:116
Alignment explanation
Indices: 61346--61637 Score: 469
Period size: 117 Copynumber: 2.5 Consensus size: 116
61336 TTTCACAAAA
* * *
61346 CATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACGAAGCCAAGGAGCCTGCATTAAT
1 CATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCAC-AAGCAAAGGAGCCTGCAGTAAT
*
61411 AACATCTCCATCCAGTCACTTCC-ATCACTACAATGTGTAGGTTCCCCAGAAC
65 AACATCCCCATCCAGTCAC-TCCAATCACTACAATGTGTAGGTTCCCCAGAAC
*
61463 CATACACCCACCTGCACACCAGTAAGGACTTATCCTGAGCACACAGCAAAGGAGCCTGCAGTAAT
1 CATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACA-AGCAAAGGAGCCTGCAGTAAT
* *
61528 AACTTCCCCATCCAGTCACTCCAATCACTACAATGTGTAGGTTCCGCAGAAC
65 AACATCCCCATCCAGTCACTCCAATCACTACAATGTGTAGGTTCCCCAGAAC
*
61580 CATGCACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACATAGCAAAGGAGCCTG
1 CATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACA-AGCAAAGGAGCCTG
61638 AAATACTTCC
Statistics
Matches: 163, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
116 4 0.02
117 159 0.98
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (116 bp):
CATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACAAGCAAAGGAGCCTGCAGTAATA
ACATCCCCATCCAGTCACTCCAATCACTACAATGTGTAGGTTCCCCAGAAC
Found at i:62984 original size:30 final size:29
Alignment explanation
Indices: 62948--63045 Score: 115
Period size: 29 Copynumber: 3.3 Consensus size: 29
62938 CATTTTACAG
* *
62948 AAATAGCACTCTTTTTTAAAATAATTCCCA
1 AAATAGCAC-CTTTTTCAAATTAATTCCCA
* *
62978 AAATAGCACATTTTTCGAATTAATTCCCA
1 AAATAGCACCTTTTTCAAATTAATTCCCA
* **
63007 AAATAACACCCATTTCAAATTAATTCCCA
1 AAATAGCACCTTTTTCAAATTAATTCCCA
*
63036 AACTAGCACC
1 AAATAGCACC
63046 CATTTACAGT
Statistics
Matches: 57, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
29 48 0.84
30 9 0.16
ACGTcount: A:0.41, C:0.24, G:0.04, T:0.31
Consensus pattern (29 bp):
AAATAGCACCTTTTTCAAATTAATTCCCA
Found at i:63838 original size:2 final size:2
Alignment explanation
Indices: 63831--63865 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
63821 AAATTACAAT
63831 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
63866 TCAAATTTTC
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:69372 original size:25 final size:25
Alignment explanation
Indices: 69344--69396 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
69334 ACACCCACCT
69344 GCACACCAGTAAGGACTTATCCTGA
1 GCACACCAGTAAGGACTTATCCTGA
69369 GCACACCAGTAAGGACTTATCCTGA
1 GCACACCAGTAAGGACTTATCCTGA
69394 GCA
1 GCA
69397 TACAGCAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.32, C:0.28, G:0.21, T:0.19
Consensus pattern (25 bp):
GCACACCAGTAAGGACTTATCCTGA
Found at i:69483 original size:142 final size:142
Alignment explanation
Indices: 69227--69503 Score: 432
Period size: 142 Copynumber: 2.0 Consensus size: 142
69217 ACACCCACCT
** *
69227 GCACACCAATAAGGACTTACCCTAAGCACGAAGCCGAGGAGCCTGCAATAATAACGTCTCCATCC
1 GCACACCAATAAGGACTTACCCTAAGCACGAAGCAAAGGAGCCTGCAATAATAACGTCCCCATCC
69292 AGTCACTTCCATCACTACAATGTGTAGGTTCCCCAGAACCATACACCCACCTGCACACCAGTAAG
66 AGTCACTTCCATCACTACAATGTGTAGGTTCCCCAGAACCATACACCCACCTGCACACCAGTAAG
69357 GACTTATCCTGA
131 GACTTATCCTGA
* * * * * *
69369 GCACACCAGTAAGGACTTATCCTGAGCA-TACAGCAAAGGAGCCTGCAGTAATAACTTCCCCATC
1 GCACACCAATAAGGACTTACCCTAAGCACGA-AGCAAAGGAGCCTGCAATAATAACGTCCCCATC
*
69433 CAGTCAC-TCCAATCACTACAATGTGTAGGTTCCCCAGAACCATGCACCCACCTGCACACCAGTA
65 CAGTCACTTCC-ATCACTACAATGTGTAGGTTCCCCAGAACCATACACCCACCTGCACACCAGTA
69497 AGGACTT
129 AGGACTT
69504 TAACTGAGCA
Statistics
Matches: 123, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
141 4 0.03
142 119 0.97
ACGTcount: A:0.31, C:0.33, G:0.17, T:0.19
Consensus pattern (142 bp):
GCACACCAATAAGGACTTACCCTAAGCACGAAGCAAAGGAGCCTGCAATAATAACGTCCCCATCC
AGTCACTTCCATCACTACAATGTGTAGGTTCCCCAGAACCATACACCCACCTGCACACCAGTAAG
GACTTATCCTGA
Found at i:70504 original size:28 final size:28
Alignment explanation
Indices: 70424--70577 Score: 184
Period size: 28 Copynumber: 5.4 Consensus size: 28
70414 CCATTTTACA
* * * *
70424 AAAATAGCACCCTTTTTAAAATAATTACC
1 AAAATAGCA-CCATTTCAAATTAATTCCC
* *
70453 AAAATAGTA-CATTTTTCGAATTAATTCCC
1 AAAATAGCACCA--TTTCAAATTAATTCCC
*
70482 AAAGTAGCACCATTTCAAATTAATTCCC
1 AAAATAGCACCATTTCAAATTAATTCCC
70510 AAAATAGCACCATTTCAAATTAATTCCC
1 AAAATAGCACCATTTCAAATTAATTCCC
* *
70538 AAAATAGCACCCATTTCGAATTAATTCTC
1 AAAATAGCA-CCATTTCAAATTAATTCCC
70567 AAAATAGCACC
1 AAAATAGCACC
70578 TGGTCAACGG
Statistics
Matches: 109, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
27 1 0.01
28 53 0.49
29 53 0.49
30 2 0.02
ACGTcount: A:0.42, C:0.23, G:0.06, T:0.30
Consensus pattern (28 bp):
AAAATAGCACCATTTCAAATTAATTCCC
Found at i:70552 original size:57 final size:58
Alignment explanation
Indices: 70424--70577 Score: 197
Period size: 57 Copynumber: 2.7 Consensus size: 58
70414 CCATTTTACA
* * * * * *
70424 AAAATAGCACCCTTTTTAAAATAATTACCAAAATAGTA-CATTTTTCGAATTAATTCCC
1 AAAATAGCACCCATTTCAAATTAATTCCCAAAATAGCACCA-TTTTCAAATTAATTCCC
*
70482 AAAGTAGCA-CCATTTCAAATTAATTCCCAAAATAGCACCA-TTTCAAATTAATTCCC
1 AAAATAGCACCCATTTCAAATTAATTCCCAAAATAGCACCATTTTCAAATTAATTCCC
* *
70538 AAAATAGCACCCATTTCGAATTAATTCTCAAAATAGCACC
1 AAAATAGCACCCATTTCAAATTAATTCCCAAAATAGCACC
70578 TGGTCAACGG
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
56 23 0.27
57 51 0.61
58 10 0.12
ACGTcount: A:0.42, C:0.23, G:0.06, T:0.30
Consensus pattern (58 bp):
AAAATAGCACCCATTTCAAATTAATTCCCAAAATAGCACCATTTTCAAATTAATTCCC
Found at i:71329 original size:2 final size:2
Alignment explanation
Indices: 71322--71354 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
71312 AAATTACAAT
71322 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
71355 CAAATTTCCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:72566 original size:31 final size:31
Alignment explanation
Indices: 72509--72576 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
72499 TTTTATAGTA
* *
72509 TTTAGATAAATTTATTAATAAATTTATTATCT
1 TTTA-ATAAATTTAATAATAAATTTATAATCT
* *
72541 TTTAATAAATTTAATAAGT-ATTTTATAATTT
1 TTTAATAAATTTAATAA-TAAATTTATAATCT
72572 TTTAA
1 TTTAA
72577 ACTTTATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
31 26 0.84
32 5 0.16
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (31 bp):
TTTAATAAATTTAATAATAAATTTATAATCT
Found at i:73335 original size:31 final size:30
Alignment explanation
Indices: 73300--73386 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
73290 TCAACAAAGT
73300 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAAATTATAAAATA-TTATTAAATTTA
* *
73331 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAA-TATTATTAAATTTA
* *
73362 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAAT-ATTATTA
73387 TATTATCAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 44 0.92
32 3 0.06
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (30 bp):
TTAAAAAATTATAAAATATTATTAAATTTA
Found at i:73822 original size:20 final size:20
Alignment explanation
Indices: 73797--73845 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
73787 TTTATTTCCT
73797 TTTATTTT-TTATATTACATC
1 TTTATTTTCTTATATTA-ATC
*
73817 TTTATTTTCTTATATTAATT
1 TTTATTTTCTTATATTAATC
73837 TTTATTTTC
1 TTTATTTTC
73846 AATAAATCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 19 0.70
21 8 0.30
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTATTTTCTTATATTAATC
Done.