Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001603.1 Hibiscus syriacus cultivar Beakdansim tig00003187_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: 60764
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:2003 original size:3 final size:3
Alignment explanation
Indices: 1995--2033 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1985 TAATTGTTAG
1995 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2034 TTTGGTAGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:8856 original size:30 final size:30
Alignment explanation
Indices: 8749--8916 Score: 149
Period size: 30 Copynumber: 5.5 Consensus size: 30
8739 TAAGTATATG
* * * *
8749 AACTTACAAGGACCAAAATGGAGAAAAACATA
1 AACTTA-AAGGACTAAAATAGA-AAAAATAGA
* * * * *
8781 AACTTAAAGGACCAAAATAGTACATATAGG
1 AACTTAAAGGACTAAAATAGAAAAAATAGA
* *
8811 AA-TTGAAAAGTCTAAAATAGAAAAAATAGA
1 AACTT-AAAGGACTAAAATAGAAAAAATAGA
* * *
8841 AACTTAATGGACTAAAATAGTAAAAACAGA
1 AACTTAAAGGACTAAAATAGAAAAAATAGA
* * *
8871 CATTTAAAGGACTAAAATAGCAAAAATAGA
1 AACTTAAAGGACTAAAATAGAAAAAATAGA
8901 AACTTAAAGGACTAAA
1 AACTTAAAGGACTAAA
8917 CCACAAATAA
Statistics
Matches: 108, Mismatches: 26, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
29 2 0.02
30 85 0.79
31 15 0.14
32 6 0.06
ACGTcount: A:0.57, C:0.11, G:0.14, T:0.18
Consensus pattern (30 bp):
AACTTAAAGGACTAAAATAGAAAAAATAGA
Found at i:8913 original size:60 final size:60
Alignment explanation
Indices: 8780--8916 Score: 177
Period size: 60 Copynumber: 2.3 Consensus size: 60
8770 AGAAAAACAT
* * * * *
8780 AAACTTAAAGGACCAAAATAGTACATATAGGAATTGAAAAGTCTAAAATAGAAAAAATAG
1 AAACTTAAAGGACTAAAATAGTAAAAACAGGAATTGAAAAGACTAAAATAGAAAAAATAG
* * * *
8840 AAACTTAATGGACTAAAATAGTAAAAACA-GACATTTAAAGGACTAAAATAGCAAAAATAG
1 AAACTTAAAGGACTAAAATAGTAAAAACAGGA-ATTGAAAAGACTAAAATAGAAAAAATAG
8900 AAACTTAAAGGACTAAA
1 AAACTTAAAGGACTAAA
8917 CCACAAATAA
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
59 2 0.03
60 64 0.97
ACGTcount: A:0.57, C:0.09, G:0.14, T:0.20
Consensus pattern (60 bp):
AAACTTAAAGGACTAAAATAGTAAAAACAGGAATTGAAAAGACTAAAATAGAAAAAATAG
Found at i:10382 original size:12 final size:12
Alignment explanation
Indices: 10367--10394 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
10357 ATAACAATAA
10367 TAATAAATTAAT
1 TAATAAATTAAT
10379 TAATAAATTAAT
1 TAATAAATTAAT
10391 TAAT
1 TAAT
10395 TAATAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TAATAAATTAAT
Found at i:12164 original size:27 final size:28
Alignment explanation
Indices: 12133--12209 Score: 72
Period size: 28 Copynumber: 2.8 Consensus size: 28
12123 TAAAATTGCC
*
12133 ATAAAAAAGTAAAATTAAAG-TTAAACA
1 ATAAAAAAATAAAATTAAAGATTAAACA
*
12160 ATAAAATAAAATAAAA-TAAAGTATTAAATA
1 AT-AAA-AAAATAAAATTAAAG-ATTAAACA
12190 A-AAAAAACA-AAAATTAAAGA
1 ATAAAAAA-ATAAAATTAAAGA
12210 GGATTAAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
27 10 0.24
28 17 0.40
29 8 0.19
30 7 0.17
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (28 bp):
ATAAAAAAATAAAATTAAAGATTAAACA
Found at i:12218 original size:15 final size:15
Alignment explanation
Indices: 12200--12232 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
12190 AAAAAAACAA
12200 AAATT-AAAGAGGATT
1 AAATTGAAA-AGGATT
12215 AAATTGAAAAGGATT
1 AAATTGAAAAGGATT
12230 AAA
1 AAA
12233 AGATTAGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.58, C:0.00, G:0.18, T:0.24
Consensus pattern (15 bp):
AAATTGAAAAGGATT
Found at i:13776 original size:2 final size:2
Alignment explanation
Indices: 13744--14045 Score: 133
Period size: 2 Copynumber: 160.5 Consensus size: 2
13734 TAAATCCAAA
* * *
13744 AT AT AA AT A- AT AA AT AT AT GT ACT AT A- AT AT AT A- AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
* *
13783 AT AT AT -T AT AT AT AT AT ACT AT A- AT AT AT A- AC AT AA AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
*
13823 AT AT A- AT A- AT AT AT A- AT AT AT ACT -T AT AT A- AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
*
13861 AT AT A- AT AT A- AT AT AT AT AT AT AA AT ACT AT A- AT A- AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * *
13899 AT AT A- AT AT AT AT -T AT A- AC AT AT AT A- AT AC AT ACT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* * *
13938 A- AT AT ACT AT AT A- AC AT ACT AT AT AT TT AT AT ACT TT AT A-
1 AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT
* * * *
13978 AT AC ACT AT AT AA ACT AC AT A- AT AT AT A- AT AT AA AT A- AT AT
1 AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
14019 A- AT AT AT ACT AT AT A- AT AC AT A- AT AT A
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A
14046 ATAATTCCAG
Statistics
Matches: 226, Mismatches: 33, Indels: 82
0.66 0.10 0.24
Matches are distributed among these distances:
1 30 0.13
2 178 0.79
3 18 0.08
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:13777 original size:7 final size:7
Alignment explanation
Indices: 13767--14050 Score: 177
Period size: 7 Copynumber: 40.9 Consensus size: 7
13757 ATATATGTAC
13767 TATAATA
1 TATAATA
13774 TATAATA
1 TATAATA
13781 T-T-ATA
1 TATAATA
*
13786 TATTATA
1 TATAATA
13793 TATATATA
1 TATA-ATA
13801 CTATAATA
1 -TATAATA
*
13809 TATAACA
1 TATAATA
13816 TA-AATA
1 TATAATA
13822 TAT-ATA
1 TATAATA
13828 -ATAATA
1 TATAATA
13834 TATAATA
1 TATAATA
*
13841 TATACTTA
1 TATA-ATA
13849 TATAATA
1 TATAATA
*
13856 TAT-ACA
1 TATAATA
13862 TAT-A-A
1 TATAATA
13867 TATAATA
1 TATAATA
13874 TAT-ATA
1 TATAATA
13880 TATAA-A
1 TATAATA
13886 TACT-ATA
1 TA-TAATA
13893 -ATAATAA
1 TATAAT-A
13900 TATAATA
1 TATAATA
*
13907 TATATTA
1 TATAATA
13914 TA-ACATA
1 TATA-ATA
13921 TATAATA
1 TATAATA
* *
13928 CATACTA
1 TATAATA
*
13935 TTTAATA
1 TATAATA
13942 TACTATATAA
1 TA-TA-AT-A
* *
13952 CATACTA
1 TATAATA
*
13959 TATATTTA
1 TATA-ATA
* *
13967 TATACTT
1 TATAATA
13974 TATAATA
1 TATAATA
*
13981 CACT-ATA
1 TA-TAATA
13988 TA-AACTA
1 TATAA-TA
*
13995 CATAATA
1 TATAATA
14002 TATAATA
1 TATAATA
14009 TA-AATAA
1 TATAAT-A
14016 TATAATA
1 TATAATA
*
14023 TATACTA
1 TATAATA
14030 TATAATA
1 TATAATA
*
14037 CATAATA
1 TATAATA
14044 TAATAAT
1 T-ATAAT
14051 TCCAGACGCA
Statistics
Matches: 218, Mismatches: 30, Indels: 57
0.71 0.10 0.19
Matches are distributed among these distances:
5 11 0.05
6 38 0.17
7 121 0.56
8 38 0.17
9 8 0.04
10 2 0.01
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.41
Consensus pattern (7 bp):
TATAATA
Found at i:13778 original size:25 final size:25
Alignment explanation
Indices: 13750--14045 Score: 118
Period size: 25 Copynumber: 11.6 Consensus size: 25
13740 CAAAATATAA
*
13750 ATAATAAATATATGTACTATAATAT
1 ATAATAAATATATATACTATAATAT
*
13775 ATAAT--AT-TATATATTATATATAT
1 ATAATAAATATATATACTATA-ATAT
* *
13798 ATACTATAATATATA-ACATAAATATAT
1 ATAATA-AATATATATAC-TATA-ATAT
*
13825 ATAAT-AATATATAATA-TATACTTAT
1 ATAATAAATATAT-ATACTATA-ATAT
* * *
13850 ATAATATATACATATAATATAATAT
1 ATAATAAATATATATACTATAATAT
*
13875 AT-AT--ATATAAATACTATAATA-
1 ATAATAAATATATATACTATAATAT
13896 ATAATATAATATATAT--TATAACATAT
1 ATAATA-AATATATATACTAT-A-ATAT
* * * *
13922 ATAATACATACTATTTAATATACTAT
1 ATAATAAATA-TATATACTATAATAT
* * * *
13948 ATAACATACTATATATTTA-TATACTTT
1 AT-A-ATA-AATATATATACTATAATAT
* *
13975 ATAATACACTATATAAACTACATAATAT
1 ATAATA-AATATATATACT--ATAATAT
*
14003 ATAATATAAATAATATAATA-TATACTAT
1 AT-A-ATAAAT-ATAT-ATACTATAATAT
*
14031 ATAATACATA-ATATA
1 ATAATAAATATATATA
14046 ATAATTCCAG
Statistics
Matches: 210, Mismatches: 31, Indels: 62
0.69 0.10 0.20
Matches are distributed among these distances:
21 2 0.01
22 25 0.12
23 16 0.08
24 5 0.02
25 55 0.26
26 35 0.17
27 29 0.14
28 27 0.13
29 6 0.03
30 8 0.04
31 2 0.01
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.41
Consensus pattern (25 bp):
ATAATAAATATATATACTATAATAT
Found at i:13797 original size:35 final size:34
Alignment explanation
Indices: 13757--14050 Score: 152
Period size: 33 Copynumber: 8.7 Consensus size: 34
13747 TAAATAATAA
*
13757 ATATATGTACTATAATATATAATATTATATATTAT
1 ATATATATACTATAATATATAATATTATATA-TAT
* *
13792 ATATATATACTATAATATATAACA-TAAATATAT
1 ATATATATACTATAATATATAATATTATATATAT
*
13825 ATA-ATAATA-TATAATATAT-A-CTTATATAATAT
1 ATATAT-ATACTATAATATATAATATTATAT-ATAT
* * *
13857 ATACATATAATATAATATAT-ATA-TATAAATACT
1 ATATATATACTATAATATATAATATTATATATA-T
* * * *
13890 ATA-ATAATAATATAATATATATTATAACATATAT
1 ATATAT-ATACTATAATATATAATATTATATATAT
* **
13924 A-ATACATACTATTTAATATACTATATAACATACTATAT
1 ATATATATACTA--TAATATA-TA-ATATTATA-TATAT
* * * * *
13962 ATTTATATACT-TTATA-AT-ACACTATATAAACT
1 ATATATATACTATAATATATAATATTATATATA-T
* *
13994 ACATA-ATA-TATAATATA-AATAATATAATATAT
1 ATATATATACTATAATATATAATATTAT-ATATAT
14026 ACTATATAATAC-ATAATATAATAAT
1 A-TATAT-ATACTATAATAT-ATAAT
14051 TCCAGACGCA
Statistics
Matches: 200, Mismatches: 31, Indels: 54
0.70 0.11 0.19
Matches are distributed among these distances:
30 1 0.00
31 15 0.08
32 44 0.22
33 57 0.28
34 11 0.05
35 45 0.22
36 7 0.04
37 7 0.04
38 6 0.03
39 7 0.04
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.41
Consensus pattern (34 bp):
ATATATATACTATAATATATAATATTATATATAT
Found at i:13928 original size:40 final size:40
Alignment explanation
Indices: 13743--14048 Score: 173
Period size: 40 Copynumber: 7.6 Consensus size: 40
13733 ATAAATCCAA
* *
13743 AATATAAATAATAA-ATATAT-GTACTATAATATATAATAT
1 AATATATATAATAATATATATAATACTATAATA-ATAATAT
*
13782 --TATATAT--T-ATATATAT-ATACTATAATATATAACAT
1 AATATATATAATAATATATATAATACTATAATA-ATAATAT
13817 AAATATATATAATAATATATAATATATACT-TATATAAT-ATAT
1 -AATATATATAATAATATAT-ATA-ATACTATA-ATAATAATAT
13859 ACATATAATATAATATATATATATAAATACTATAATAATAATAT
1 A-ATAT-ATATAATA-ATATATAT-AATACTATAATAATAATAT
* * * *
13903 AATATATATTATAACATATATAATAC-ATACTATTTAATAT
1 AATATATATAATAATATATATAATACTATAATA-ATAATAT
* * * * * *
13943 ACTATATA-ACATACTATATAT-TTA-TATACTTTATAATAC
1 AATATATATA-ATAATATATATAATACTATA-ATAATAATAT
*
13982 ACTATATA-AACTACATAATATATAATA-TA-AATAAT-ATAAT
1 AATATATATAA-TA-AT-ATATATAATACTATAATAATAAT-AT
14022 ATATACTATATAATACATA-ATATAATA
1 A-ATA-TATATAATA-ATATATATAATA
14049 ATTCCAGACG
Statistics
Matches: 215, Mismatches: 23, Indels: 57
0.73 0.08 0.19
Matches are distributed among these distances:
34 1 0.00
35 24 0.11
37 6 0.03
38 8 0.04
39 28 0.13
40 43 0.20
41 24 0.11
42 29 0.13
43 30 0.14
44 22 0.10
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (40 bp):
AATATATATAATAATATATATAATACTATAATAATAATAT
Found at i:15818 original size:23 final size:26
Alignment explanation
Indices: 15759--15818 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 26
15749 CGTCTTTTAT
*
15759 TAATATTATTATATTATATAATCATA
1 TAATATTATTATATCATATAATCATA
** *
15785 TCGTATAATTATA-CATAT-AT-ATA
1 TAATATTATTATATCATATAATCATA
15808 TAATATTATTA
1 TAATATTATTA
15819 ATTTTATTCG
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
23 11 0.41
24 2 0.07
25 4 0.15
26 10 0.37
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (26 bp):
TAATATTATTATATCATATAATCATA
Found at i:17235 original size:2 final size:2
Alignment explanation
Indices: 17228--17258 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
17218 ACATTTTTAT
*
17228 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17259 TTCATTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:17274 original size:19 final size:21
Alignment explanation
Indices: 17250--17294 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
17240 TATATATATA
17250 TATTTATATTT-CATTTA-TT
1 TATTTATATTTCCATTTATTT
* *
17269 TATTTATTTTTCCTTTTATTT
1 TATTTATATTTCCATTTATTT
17290 TATTT
1 TATTT
17295 TTTTTCTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 10 0.45
20 5 0.23
21 7 0.32
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (21 bp):
TATTTATATTTCCATTTATTT
Found at i:27745 original size:9 final size:10
Alignment explanation
Indices: 27731--27777 Score: 53
Period size: 11 Copynumber: 4.6 Consensus size: 10
27721 AATAGAGAGG
27731 AAAAAAA-CA
1 AAAAAAAGCA
27740 AAAAAAAGCAA
1 AAAAAAAGC-A
27751 AAAAAAATG-A
1 AAAAAAA-GCA
27761 AGAAAAAAGCA
1 A-AAAAAAGCA
27772 AAAAAA
1 AAAAAA
27778 CGTTTAGGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
9 7 0.21
10 9 0.27
11 16 0.48
12 1 0.03
ACGTcount: A:0.83, C:0.06, G:0.09, T:0.02
Consensus pattern (10 bp):
AAAAAAAGCA
Found at i:27756 original size:22 final size:22
Alignment explanation
Indices: 27731--27777 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
27721 AATAGAGAGG
*
27731 AAAAAA-ACAAAAAAAAGCAAA
1 AAAAAATAAAAAAAAAAGCAAA
* *
27752 AAAAAATGAAGAAAAAAGCAAA
1 AAAAAATAAAAAAAAAAGCAAA
27774 AAAA
1 AAAA
27778 CGTTTAGGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.83, C:0.06, G:0.09, T:0.02
Consensus pattern (22 bp):
AAAAAATAAAAAAAAAAGCAAA
Found at i:27864 original size:45 final size:44
Alignment explanation
Indices: 27771--27865 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 44
27761 AGAAAAAAGC
*
27771 AAAAAAACGTTTAGGGTGAAAACCCGAAAGGGCGCCCTAGACAA
1 AAAAAAACGTTTAGGGTGAAAACCCGAAAGGGCGCCCTAAACAA
* *
27815 AAAAAACACGTTTAGGGTGAAAACCCGAAAGGGCGCCCTAAATAG
1 AAAAAA-ACGTTTAGGGTGAAAACCCGAAAGGGCGCCCTAAACAA
27860 AAAAAA
1 AAAAAA
27866 GAGAAAAAGA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
44 6 0.13
45 41 0.87
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (44 bp):
AAAAAAACGTTTAGGGTGAAAACCCGAAAGGGCGCCCTAAACAA
Found at i:29443 original size:105 final size:105
Alignment explanation
Indices: 28617--29424 Score: 1366
Period size: 105 Copynumber: 7.7 Consensus size: 105
28607 AGGTTTTACC
* *
28617 CAGAGCCAATTTCAATTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* **
28682 ACGAAGGGATCGCTGGTTGTCAACAGCCATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
28722 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAGCGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
28787 ACGAAGGGACCGCTGGTTGTCAACAACCATTTCTCGATTC
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
28827 CAGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCAAG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
28892 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
28932 CAGAGCCAGTTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
28997 ATGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* * *
29037 CAGAGCCAGTTTCAACTTCACAACGAATGACATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
29102 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
29142 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCATG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
29207 ACGAAGGGACCGCTGGTTGTCGACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
29247 CAGAGCCAATTTCAACTTCAAAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
29312 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* * * * * *
29352 CAGAGCCAATTTCAACTTCGCAACGAAGGATATTAGACTCGAGACAGCACAAGCTCAACTTCAC-
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
29416 AGCGAAGGG
66 A-CGAAGGG
29425 GCGGCTGACT
Statistics
Matches: 665, Mismatches: 37, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
104 1 0.00
105 664 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:31245 original size:12 final size:12
Alignment explanation
Indices: 31228--31275 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
31218 TTACGTTTCA
31228 TTATTATATATT
1 TTATTATATATT
31240 TTATTATTATATAT
1 TTATTA-TATAT-T
*
31254 ATATATATATATT
1 TTAT-TATATATT
*
31267 TGATTATAT
1 TTATTATAT
31276 TTTCTATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 11 0.37
13 8 0.27
14 9 0.30
15 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (12 bp):
TTATTATATATT
Found at i:31605 original size:2 final size:2
Alignment explanation
Indices: 31600--31644 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
31590 CATTTTTTAT
31600 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
31642 TA T
1 TA T
31645 TATTTCATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31682 original size:20 final size:20
Alignment explanation
Indices: 31659--31696 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31649 TCATTTATTA
31659 TTTA-TTTATTTATTTTTCCT
1 TTTATTTTATTT-TTTTTCCT
31679 TTTATTTTATTTTTTTTC
1 TTTATTTTATTTTTTTTC
31697 TACTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTATTTTATTTTTTTTCCT
Found at i:32166 original size:3 final size:3
Alignment explanation
Indices: 32158--32183 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
32148 GGTGCTCCCC
32158 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
32184 AGGTAAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:38600 original size:56 final size:56
Alignment explanation
Indices: 38514--38621 Score: 191
Period size: 56 Copynumber: 1.9 Consensus size: 56
38504 TGCTTTCATC
38514 TCTAATTACCAAGAAGTTGAATGATTAAAAGATGACCAAACACTTATCTACTGCCG
1 TCTAATTACCAAGAAGTTGAATGATTAAAAGATGACCAAACACTTATCTACTGCCG
*
38570 TCTAATTACCAAG-AGATTGAATGATTAAAAGATGACCAAACACTTATTTACT
1 TCTAATTACCAAGAAG-TTGAATGATTAAAAGATGACCAAACACTTATCTACT
38622 ACAGTAAATT
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
55 2 0.04
56 48 0.96
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.29
Consensus pattern (56 bp):
TCTAATTACCAAGAAGTTGAATGATTAAAAGATGACCAAACACTTATCTACTGCCG
Found at i:48216 original size:2 final size:2
Alignment explanation
Indices: 48209--48233 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
48199 TTGGTTTTTA
48209 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 A
48234 CACACACACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:50601 original size:30 final size:30
Alignment explanation
Indices: 50567--50657 Score: 155
Period size: 30 Copynumber: 3.0 Consensus size: 30
50557 CTTTTTCTGA
50567 CGTGTTCAACAATCAAGTGTCAGTCATAAT
1 CGTGTTCAACAATCAAGTGTCAGTCATAAT
*
50597 CGTGTTCAACAATCAAGTGTCAGTCATTAT
1 CGTGTTCAACAATCAAGTGTCAGTCATAAT
* *
50627 CGTGTTCAACAATCCAGTGTCAATCATAAT
1 CGTGTTCAACAATCAAGTGTCAGTCATAAT
50657 C
1 C
50658 ATGGGTTATA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (30 bp):
CGTGTTCAACAATCAAGTGTCAGTCATAAT
Found at i:51771 original size:10 final size:10
Alignment explanation
Indices: 51740--51773 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
51730 AAGTCTAATT
51740 TGAATGGTGA
1 TGAATGGTGA
*
51750 TGATTAGGTGA
1 TGAAT-GGTGA
51761 TGAATGGTGA
1 TGAATGGTGA
51771 TGA
1 TGA
51774 CATTCCAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.29, C:0.00, G:0.38, T:0.32
Consensus pattern (10 bp):
TGAATGGTGA
Found at i:51979 original size:3 final size:3
Alignment explanation
Indices: 51973--52055 Score: 166
Period size: 3 Copynumber: 27.7 Consensus size: 3
51963 TGATGATGAT
51973 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
52021 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
52056 GCGAGTGATT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:57677 original size:23 final size:23
Alignment explanation
Indices: 57648--57708 Score: 122
Period size: 23 Copynumber: 2.7 Consensus size: 23
57638 TCCCCTACAG
57648 GGGGAATCGGTTCCCATTCAAAT
1 GGGGAATCGGTTCCCATTCAAAT
57671 GGGGAATCGGTTCCCATTCAAAT
1 GGGGAATCGGTTCCCATTCAAAT
57694 GGGGAATCGGTTCCC
1 GGGGAATCGGTTCCC
57709 TTATGGGGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.25
Consensus pattern (23 bp):
GGGGAATCGGTTCCCATTCAAAT
Done.