Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017291.1 Corchorus olitorius cultivar O-4 contig17324, 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: 9657
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:1700 original size:28 final size:28
Alignment explanation
Indices: 1668--1794 Score: 152
Period size: 27 Copynumber: 4.6 Consensus size: 28
1658 AAGTGAACTT
* *
1668 AAAATGACCAAAATGCCCCCGGATATGC
1 AAAATGACCAAAATGCCCCTGGACATGC
*
1696 AAAATGGCCAAAATG-CCCTGGACATGC
1 AAAATGACCAAAATGCCCCTGGACATGC
* **
1723 AAAATGACCAAAATACCCCTGGATGTGC
1 AAAATGACCAAAATGCCCCTGGACATGC
* *
1751 -AAATGACTAAAATGCCCCTGAACATGC
1 AAAATGACCAAAATGCCCCTGGACATGC
*
1778 AAAA-GACTAAAATGCCC
1 AAAATGACCAAAATGCCC
1795 ACCTAGGTGG
Statistics
Matches: 85, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
27 58 0.68
28 27 0.32
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.16
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTGGACATGC
Found at i:1734 original size:55 final size:55
Alignment explanation
Indices: 1668--1794 Score: 168
Period size: 55 Copynumber: 2.3 Consensus size: 55
1658 AAGTGAACTT
* *
1668 AAAATGACCAAAATGCCCCCGGATATGCAAAATGGCCAAAATG-CCCTGGACATGC
1 AAAATGACCAAAATGCCCCCGGATATGC-AAATGACCAAAATGCCCCTGAACATGC
* * * *
1723 AAAATGACCAAAATACCCCTGGATGTGCAAATGACTAAAATGCCCCTGAACATGC
1 AAAATGACCAAAATGCCCCCGGATATGCAAATGACCAAAATGCCCCTGAACATGC
*
1778 AAAA-GACTAAAATGCCC
1 AAAATGACCAAAATGCCC
1795 ACCTAGGTGG
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
54 23 0.37
55 40 0.63
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.16
Consensus pattern (55 bp):
AAAATGACCAAAATGCCCCCGGATATGCAAATGACCAAAATGCCCCTGAACATGC
Found at i:2272 original size:31 final size:30
Alignment explanation
Indices: 2036--3155 Score: 1424
Period size: 30 Copynumber: 36.6 Consensus size: 30
2026 GAATGGATTT
*
2036 TCAAACAGGATTAAAACGAAGCAATGATCC
1 TCAAACAGGATTAAAATGAAGCAATGATCC
* * *
2066 TCAAACAAGATTAAAATAAAGCAATGATTC
1 TCAAACAGGATTAAAATGAAGCAATGATCC
* *
2096 TCAAACAGGATTAAAATGAAGCCATGGTCC
1 TCAAACAGGATTAAAATGAAGCAATGATCC
2126 TCAAACAGGATTAAAATGAAGCAATGATCC
1 TCAAACAGGATTAAAATGAAGCAATGATCC
2156 TCAAACAGGATTAAAATGAAGCAATGATCC
1 TCAAACAGGATTAAAATGAAGCAATGATCC
2186 TCAAACAGGATTAAAATGAAGCAATGATCC
1 TCAAACAGGATTAAAATGAAGCAATGATCC
*
2216 TCAAACAGGATTAAAATGAAGCAATGGTCC
1 TCAAACAGGATTAAAATGAAGCAATGATCC
* *
2246 TCAACCAGGATTAGAAATAAAGCAATGATCC
1 TCAAACAGGATTA-AAATGAAGCAATGATCC
* *
2277 TTAAACAGGATTAAAGTGAAGCAATGATCC
1 TCAAACAGGATTAAAATGAAGCAATGATCC
*
2307 TCAAACAGGATTAGAAATCAAGCAATGATCC
1 TCAAACAGGATTA-AAATGAAGCAATGATCC
2338 TCAAACAGGATTAGAAATAAAGCAATGATGCAATGATCC
1 TCAAACAGGATTA-AAAT---G--A--A-GCAATGATCC
* * *
2377 TCAAATAGGATTAGAAATCAAGCAATTATCC
1 TCAAACAGGATTA-AAATGAAGCAATGATCC
**
2408 TCAAACATAATTAAAATGAAGCAATGATCC
1 TCAAACAGGATTAAAATGAAGCAATGATCC
2438 TCAAACAGGATTAAAATGAAGCAATGATCC
1 TCAAACAGGATTAAAATGAAGCAATGATCC
* *
2468 TCGAACAGGATTAAAATGAAGCAATGGTCC
1 TCAAACAGGATTAAAATGAAGCAATGATCC
* *
2498 TCAACCAGGATTAGAAATAAAGCAATGATCC
1 TCAAACAGGATTA-AAATGAAGCAATGATCC
* * * *
2529 TTAAATAGGATTAACATAAAGCAATGATCC
1 TCAAACAGGATTAAAATGAAGCAATGATCC
* *
2559 TCAAACAGGATTAAAATAAAGCAACGATCC
1 TCAAACAGGATTAAAATGAAGCAATGATCC
* * *
2589 TCAACCAGGATTAAAATAAAGCAACGATCC
1 TCAAACAGGATTAAAATGAAGCAATGATCC
* * *
2619 TCAACCAGGATTAACATAAAGCAATGATCC
1 TCAAACAGGATTAAAATGAAGCAATGATCC
* *
2649 TCAAACAAGATTTAAAATAAAGCAATGATCC
1 TCAAACAGGA-TTAAAATGAAGCAATGATCC
* *
2680 T-AAATAGGATTTAAAATAAAGCAATGATCC
1 TCAAACAGGA-TTAAAATGAAGCAATGATCC
* * *
2710 TCGAACAGGATTTAAAATAAAGTAATGATCC
1 TCAAACAGGA-TTAAAATGAAGCAATGATCC
*
2741 TCAAACAGGATTAAAATGAAGTAATGATCC
1 TCAAACAGGATTAAAATGAAGCAATGATCC
* *
2771 TCAAATAGGATTAAAAATGAAGTAATGATCC
1 TCAAACAGGATT-AAAATGAAGCAATGATCC
* *
2802 TCAAACAGCATTAAAAATGAAGCCATGATCC
1 TCAAACAGGATT-AAAATGAAGCAATGATCC
2833 TCAAACAGGATTAAAATGAAGCAATGATCC
1 TCAAACAGGATTAAAATGAAGCAATGATCC
* *
2863 TCAGACAGGATTAAAA-GCAAAGCAAAGATCC
1 TCAAACAGGATTAAAATG--AAGCAATGATCC
2894 TCAAACAGGATTAAAATGAAGCAAAT-ATCC
1 TCAAACAGGATTAAAATGAAGC-AATGATCC
2924 TCAAACAGGATTGAAAATGAAGCAATGATCC
1 TCAAACAGGATT-AAAATGAAGCAATGATCC
* ** *
2955 TCACACAGGATTAAAACAAAGCAAAGATCC
1 TCAAACAGGATTAAAATGAAGCAATGATCC
*
2985 TCAAGCAGGATTAAAAATGAAGCACAT-ATCC
1 TCAAACAGGATT-AAAATGAAGCA-ATGATCC
3016 TCAAACAGGATTAAAAAATGAAGCAATGATCC
1 TCAAACAGGATT--AAAATGAAGCAATGATCC
* ** *
3048 TCACACAGGATTAAAACAAAGCAAAGATCC
1 TCAAACAGGATTAAAATGAAGCAATGATCC
*
3078 TCAAACAGGATTAAAAT-AGAGCAAAGATCC
1 TCAAACAGGATTAAAATGA-AGCAATGATCC
3108 TCAAACAGGATTAAAA-GCAAAGCAATGATCC
1 TCAAACAGGATTAAAATG--AAGCAATGATCC
3139 TCAAACAGGATTAAAAT
1 TCAAACAGGATTAAAAT
3156 AGAGCAAAGA
Statistics
Matches: 973, Mismatches: 88, Indels: 56
0.87 0.08 0.05
Matches are distributed among these distances:
29 2 0.00
30 591 0.61
31 319 0.33
32 31 0.03
34 1 0.00
36 1 0.00
38 1 0.00
39 27 0.03
ACGTcount: A:0.47, C:0.17, G:0.16, T:0.20
Consensus pattern (30 bp):
TCAAACAGGATTAAAATGAAGCAATGATCC
Found at i:2299 original size:61 final size:60
Alignment explanation
Indices: 2036--3155 Score: 1438
Period size: 61 Copynumber: 18.3 Consensus size: 60
2026 GAATGGATTT
* * *
2036 TCAAACAGGATTAAAACGAAGCAATGATCCTCAAACAAGATTAAAATAAAGCAATGATTC
1 TCAAACAGGATTAAAATGAAGCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCC
* * *
2096 TCAAACAGGATTAAAATGAAGCCATGGTCCTCAAACAGGATTAAAATGAAGCAATGATCC
1 TCAAACAGGATTAAAATGAAGCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCC
*
2156 TCAAACAGGATTAAAATGAAGCAATGATCCTCAAACAGGATTAAAATGAAGCAATGATCC
1 TCAAACAGGATTAAAATGAAGCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCC
* *
2216 TCAAACAGGATTAAAATGAAGCAATGGTCCTCAACCAGGATTAGAAATAAAGCAATGATCC
1 TCAAACAGGATTAAAATGAAGCAATGATCCTCAAACAGGATTA-AAATAAAGCAATGATCC
* * *
2277 TTAAACAGGATTAAAGTGAAGCAATGATCCTCAAACAGGATTAGAAATCAAGCAATGATCC
1 TCAAACAGGATTAAAATGAAGCAATGATCCTCAAACAGGATTA-AAATAAAGCAATGATCC
* *
2338 TCAAACAGGATTAGAAATAAAGCAATGATGCAATGATCCTCAAATAGGATTAGAAATCAAGCAAT
1 TCAAACAGGATTA-AAAT---G--A--A-GCAATGATCCTCAAACAGGATTA-AAATAAAGCAAT
*
2403 TATCC
56 GATCC
** *
2408 TCAAACATAATTAAAATGAAGCAATGATCCTCAAACAGGATTAAAATGAAGCAATGATCC
1 TCAAACAGGATTAAAATGAAGCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCC
* * *
2468 TCGAACAGGATTAAAATGAAGCAATGGTCCTCAACCAGGATTAGAAATAAAGCAATGATCC
1 TCAAACAGGATTAAAATGAAGCAATGATCCTCAAACAGGATTA-AAATAAAGCAATGATCC
* * * * *
2529 TTAAATAGGATTAACATAAAGCAATGATCCTCAAACAGGATTAAAATAAAGCAACGATCC
1 TCAAACAGGATTAAAATGAAGCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCC
* * * * *
2589 TCAACCAGGATTAAAATAAAGCAACGATCCTCAACCAGGATTAACATAAAGCAATGATCC
1 TCAAACAGGATTAAAATGAAGCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCC
* * *
2649 TCAAACAAGATTTAAAATAAAGCAATGATCCT-AAATAGGATTTAAAATAAAGCAATGATCC
1 TCAAACAGGA-TTAAAATGAAGCAATGATCCTCAAACAGGA-TTAAAATAAAGCAATGATCC
* * * * *
2710 TCGAACAGGATTTAAAATAAAGTAATGATCCTCAAACAGGATTAAAATGAAGTAATGATCC
1 TCAAACAGGA-TTAAAATGAAGCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCC
* * * * *
2771 TCAAATAGGATTAAAAATGAAGTAATGATCCTCAAACAGCATTAAAAATGAAGCCATGATCC
1 TCAAACAGGATT-AAAATGAAGCAATGATCCTCAAACAGGATT-AAAATAAAGCAATGATCC
* * *
2833 TCAAACAGGATTAAAATGAAGCAATGATCCTCAGACAGGATTAAAAGCAAAGCAAAGATCC
1 TCAAACAGGATTAAAATGAAGCAATGATCCTCAAACAGGATTAAAA-TAAAGCAATGATCC
*
2894 TCAAACAGGATTAAAATGAAGCAAAT-ATCCTCAAACAGGATTGAAAATGAAGCAATGATCC
1 TCAAACAGGATTAAAATGAAGC-AATGATCCTCAAACAGGATT-AAAATAAAGCAATGATCC
* ** * * *
2955 TCACACAGGATTAAAACAAAGCAAAGATCCTCAAGCAGGATTAAAAATGAAGCACAT-ATCC
1 TCAAACAGGATTAAAATGAAGCAATGATCCTCAAACAGGATT-AAAATAAAGCA-ATGATCC
* * *
3016 TCAAACAGGATTAAAAAATGAAGCAATGATCCTCACACAGGATTAAAACAAAGCAAAGATCC
1 TCAAACAGGATT--AAAATGAAGCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCC
* *
3078 TCAAACAGGATTAAAAT-AGAGCAAAGATCCTCAAACAGGATTAAAAGCAAAGCAATGATCC
1 TCAAACAGGATTAAAATGA-AGCAATGATCCTCAAACAGGATTAAAA-TAAAGCAATGATCC
3139 TCAAACAGGATTAAAAT
1 TCAAACAGGATTAAAAT
3156 AGAGCAAAGA
Statistics
Matches: 939, Mismatches: 95, Indels: 51
0.87 0.09 0.05
Matches are distributed among these distances:
59 1 0.00
60 326 0.35
61 456 0.49
62 72 0.08
63 25 0.03
64 1 0.00
65 1 0.00
66 1 0.00
67 1 0.00
69 5 0.01
70 50 0.05
ACGTcount: A:0.47, C:0.17, G:0.16, T:0.20
Consensus pattern (60 bp):
TCAAACAGGATTAAAATGAAGCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCC
Found at i:2387 original size:39 final size:39
Alignment explanation
Indices: 2328--2402 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
2318 TAGAAATCAA
2328 GCAATGATCCTCAAACAGGATTAGAAATAAAGCAATGAT
1 GCAATGATCCTCAAACAGGATTAGAAATAAAGCAATGAT
* *
2367 GCAATGATCCTCAAATAGGATTAGAAATCAAGCAAT
1 GCAATGATCCTCAAACAGGATTAGAAATAAAGCAAT
2403 TATCCTCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.45, C:0.16, G:0.17, T:0.21
Consensus pattern (39 bp):
GCAATGATCCTCAAACAGGATTAGAAATAAAGCAATGAT
Found at i:3446 original size:35 final size:35
Alignment explanation
Indices: 3341--3821 Score: 346
Period size: 35 Copynumber: 13.6 Consensus size: 35
3331 TAATTGTAAA
* *
3341 CCTGGATCCATTGAAATAAATTGAAGAAAAGATCGC
1 CCTGGATCAACTGAAATAAATTGAAG-AAAGATCGC
* * *
3377 CCTGGGTC-A--G--GTAAACTGAAGAAAAGATCGC
1 CCTGGATCAACTGAAATAAATTGAAG-AAAGATCGC
* * * *
3408 CCTGGATCAACTAAAATAACTTGCAGTAAGATCGC
1 CCTGGATCAACTGAAATAAATTGAAGAAAGATCGC
* *
3443 CCTGGATCAATTGAAATGAATTGAAGAAAG-TCCGC
1 CCTGGATCAACTGAAATAAATTGAAGAAAGAT-CGC
* * * * *
3478 CCTGGGTCAGCTGAAATAACTTGAAGAATGACCGC
1 CCTGGATCAACTGAAATAAATTGAAGAAAGATCGC
* * *
3513 CCTGGGTCAGCTAAAATAAATTGAACGAAAGATCGC
1 CCTGGATCAACTGAAATAAATTGAA-GAAAGATCGC
* *
3549 CCTGGATCGACTGAAATAAATTGAATAAAAGATCGC
1 CCTGGATCAACTGAAATAAATTGAA-GAAAGATCGC
* * * * * *
3585 CCTAGATCAACTGGAGTAAATTGAGGAGAGATCAC
1 CCTGGATCAACTGAAATAAATTGAAGAAAGATCGC
* * *
3620 CCTGGATCAACTGACATAAACTGAATG-AAGATCAC
1 CCTGGATCAACTGAAATAAATTGAA-GAAAGATCGC
* * * *
3655 CCTGGATCCATTGAAATAAAATGAAAAAAAAAGATCGC
1 CCTGGATCAACTGAAATAAATTG---AAGAAAGATCGC
* * * *
3693 CCTGGATCCATTGAAATAAAATGAAAAAAAAAAGATCGC
1 CCTGGATCAACTGAAATAAATTG----AAGAAAGATCGC
* *
3732 CCTGGATCAACTGGAATAAATTGAAGAAAGACCGC
1 CCTGGATCAACTGAAATAAATTGAAGAAAGATCGC
* * * * * * * * *
3767 CATGGGTCGATTGAAAAAAATTGACGGAGGACCGC
1 CCTGGATCAACTGAAATAAATTGAAGAAAGATCGC
*
3802 CCTGGGTCAACTGAAATAAA
1 CCTGGATCAACTGAAATAAA
3822 CTAAAGCATC
Statistics
Matches: 358, Mismatches: 73, Indels: 29
0.78 0.16 0.06
Matches are distributed among these distances:
31 26 0.07
32 1 0.00
33 1 0.00
34 1 0.00
35 190 0.53
36 73 0.20
38 32 0.09
39 34 0.09
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.20
Consensus pattern (35 bp):
CCTGGATCAACTGAAATAAATTGAAGAAAGATCGC
Found at i:3552 original size:106 final size:102
Alignment explanation
Indices: 3341--3790 Score: 307
Period size: 106 Copynumber: 4.2 Consensus size: 102
3331 TAATTGTAAA
* * *
3341 CCTGGATCCATTGAAATAAATTGAAGAAAAGATCGCCCTGGGTCAGGTAAACTGAAGAAAAGATC
1 CCTGGATCAATTGAAATAAATTGAAGAAAAGATCGCCCTGGGTCAGGAAAACTGAAGAAAAGACC
* * *
3406 GCCCTGGATCAACTAAAATAACTTGCAGTAAGATCGC
66 GCCCTGGATCAACTAAAATAAATTGAAGAAAGATCGC
*
3443 CCTGGATCAATTGAAATGAATTGAAG-AAAG-TCCGCCCTGGGTCAGCTGAAATAACTTGAAG-A
1 CCTGGATCAATTGAAATAAATTGAAGAAAAGAT-CGCCCTGGGTCAG--G-AA-AAC-TGAAGAA
* * *
3505 ATGACCGCCCTGGGTCAGCTAAAATAAATTGAACGAAAGATCGC
60 AAGACCGCCCTGGATCAACTAAAATAAATTGAA-GAAAGATCGC
* * * * * * * *
3549 CCTGGATCGACTGAAATAAATTGAATAAAAGATCGCCCTAGATCAACTGGAGTAAATTG-AGGAG
1 CCTGGATCAATTGAAATAAATTGAAGAAAAGATCGCCCTGGGTC-A--GGA--AAACTGAAGAAA
* * * * * *
3613 AGATCACCCTGGATCAACTGACATAAACTGAATG-AAGATCAC
61 AGACCGCCCTGGATCAACTAAAATAAATTGAA-GAAAGATCGC
* * * * * *
3655 CCTGGATCCATTGAAATAAAATGAAAAAAAAAGATCGCCCTGGATCCATTGAAATAAAATGAAAA
1 CCTGGATCAATTGAAATAAATTG--AAGAAAAGATCGCCCTGGGT-CA--G-GA-AAACTG---A
* * ** *
3720 AAAAAAGATCGCCCTGGATCAACTGGAATAAATTGAAGAAAGACCGC
56 AGAAAAGACCGCCCTGGATCAACTAAAATAAATTGAAGAAAGATCGC
* * * *
3767 CATGGGTCGATTGAAAAAAATTGA
1 CCTGGATCAATTGAAATAAATTGA
3791 CGGAGGACCG
Statistics
Matches: 274, Mismatches: 50, Indels: 40
0.75 0.14 0.11
Matches are distributed among these distances:
100 1 0.00
101 17 0.06
102 24 0.09
103 1 0.00
104 1 0.00
105 31 0.11
106 65 0.24
107 42 0.15
108 32 0.12
109 3 0.01
110 2 0.01
111 1 0.00
112 54 0.20
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.20
Consensus pattern (102 bp):
CCTGGATCAATTGAAATAAATTGAAGAAAAGATCGCCCTGGGTCAGGAAAACTGAAGAAAAGACC
GCCCTGGATCAACTAAAATAAATTGAAGAAAGATCGC
Found at i:3751 original size:39 final size:39
Alignment explanation
Indices: 3647--3739 Score: 170
Period size: 38 Copynumber: 2.4 Consensus size: 39
3637 AAACTGAATG
*
3647 AAGATCACCCTGGATCCATTGAAATAAAATG-AAAAAAA
1 AAGATCGCCCTGGATCCATTGAAATAAAATGAAAAAAAA
3685 AAGATCGCCCTGGATCCATTGAAATAAAATGAAAAAAAA
1 AAGATCGCCCTGGATCCATTGAAATAAAATGAAAAAAAA
3724 AAGATCGCCCTGGATC
1 AAGATCGCCCTGGATC
3740 AACTGGAATA
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
38 30 0.57
39 23 0.43
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.18
Consensus pattern (39 bp):
AAGATCGCCCTGGATCCATTGAAATAAAATGAAAAAAAA
Found at i:5092 original size:14 final size:13
Alignment explanation
Indices: 5058--5098 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
5048 AGCATCCTCA
* *
5058 TGAAAACAAATTT
1 TGAAAACCATTTT
5071 TGAAAACCATTTT
1 TGAAAACCATTTT
5084 TGAAAAACCATTTT
1 TG-AAAACCATTTT
5098 T
1 T
5099 TTGAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (13 bp):
TGAAAACCATTTT
Found at i:5113 original size:16 final size:16
Alignment explanation
Indices: 5068--5106 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
5058 TGAAAACAAA
5068 TTTTG-AAAACCA--T
1 TTTTGAAAAACCATTT
5081 TTTTGAAAAACCATTT
1 TTTTGAAAAACCATTT
5097 TTTTGAAAAA
1 TTTTGAAAAA
5107 ATCTTTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.22
14 7 0.30
16 11 0.48
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (16 bp):
TTTTGAAAAACCATTT
Found at i:5527 original size:2 final size:2
Alignment explanation
Indices: 5520--5544 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5510 GAACAGTAGA
5520 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
5545 CATAATGGAA
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:7998 original size:16 final size:16
Alignment explanation
Indices: 7973--8003 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7963 CAGATACTTA
7973 TGATGATTTGCATGAC
1 TGATGATTTGCATGAC
*
7989 TGATGCTTTGCATGA
1 TGATGATTTGCATGA
8004 ATGCATTCGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.39
Consensus pattern (16 bp):
TGATGATTTGCATGAC
Found at i:8278 original size:7 final size:7
Alignment explanation
Indices: 8266--8290 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
8256 CAAATGCACG
8266 TGAATGC
1 TGAATGC
8273 TGAATGC
1 TGAATGC
8280 TGAATGC
1 TGAATGC
8287 TGAA
1 TGAA
8291 ACAAGAACGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.28
Consensus pattern (7 bp):
TGAATGC
Done.