Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1761
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: 49320
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.35
Found at i:1103 original size:2 final size:2
Alignment explanation
Indices: 1096--1123 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1086 AAATGAAATA
1096 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
1124 GTATGTATGA
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:1327 original size:4 final size:4
Alignment explanation
Indices: 1318--1348 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1308 GCCAAAGAAT
1318 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1349 TGATTTTGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:1673 original size:8 final size:9
Alignment explanation
Indices: 1654--1683 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1644 ATATGATATA
1654 TTTAATTTT
1 TTTAATTTT
1663 TTTAATTTT
1 TTTAATTTT
*
1672 TTTTATTTT
1 TTTAATTTT
1681 TTT
1 TTT
1684 TATATATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTAATTTT
Found at i:1711 original size:24 final size:25
Alignment explanation
Indices: 1675--1725 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
1665 TAATTTTTTT
* *
1675 TATTTTTTTTATATATAAAAAT-TA
1 TATTTTATATATATATAAAAATGTA
*
1699 TATTTTATATATATTTAAAAATGTA
1 TATTTTATATATATATAAAAATGTA
1724 TA
1 TA
1726 AAATGTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
TATTTTATATATATATAAAAATGTA
Found at i:5517 original size:32 final size:32
Alignment explanation
Indices: 5481--5547 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
5471 CACAAGTAGG
* *
5481 TTAATTTTTT-TATATATTTAATATGATTATAT
1 TTAATTTTTTATATAAATTTAA-ATGATCATAT
5513 TTAATTTTTTATATAAATTTAAATGATCATAT
1 TTAATTTTTTATATAAATTTAAATGATCATAT
5545 TTA
1 TTA
5548 TATATAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 22 0.69
33 10 0.31
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.58
Consensus pattern (32 bp):
TTAATTTTTTATATAAATTTAAATGATCATAT
Found at i:7401 original size:11 final size:11
Alignment explanation
Indices: 7355--7455 Score: 63
Period size: 11 Copynumber: 9.7 Consensus size: 11
7345 ATGATACGAA
7355 AAATATA-TAT
1 AAATATATTAT
* *
7365 AAATTTAATAT
1 AAATATATTAT
*
7376 AAAAATATTAT
1 AAATATATTAT
*
7387 AAATATGTTAT
1 AAATATATTAT
7398 AAATA-A--AT
1 AAATATATTAT
*
7406 TAATATATTA-
1 AAATATATTAT
*
7416 AAATTTA-TAT
1 AAATATATTAT
*
7426 AATATAAATTAT
1 AA-ATATATTAT
* *
7438 TAATTTATTA-
1 AAATATATTAT
7448 AAATATAT
1 AAATATAT
7456 AATACATTAA
Statistics
Matches: 67, Mismatches: 17, Indels: 14
0.68 0.17 0.14
Matches are distributed among these distances:
8 6 0.09
9 3 0.04
10 19 0.28
11 35 0.52
12 4 0.06
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (11 bp):
AAATATATTAT
Found at i:7424 original size:37 final size:38
Alignment explanation
Indices: 7358--7430 Score: 98
Period size: 37 Copynumber: 1.9 Consensus size: 38
7348 ATACGAAAAA
*
7358 TATATATAAATTTAATATAAAAATATTATA-AATATGT
1 TATAAATAAATTTAATATAAAAATATTATATAATATGT
7395 TATAAATAAA-TTAATATATTAAAAT-TTATATAATAT
1 TATAAATAAATTTAATATA--AAAATATTATATAATAT
7431 AAATTATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 8 0.25
37 14 0.44
38 10 0.31
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (38 bp):
TATAAATAAATTTAATATAAAAATATTATATAATATGT
Found at i:7447 original size:32 final size:31
Alignment explanation
Indices: 7395--7459 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 31
7385 ATAAATATGT
7395 TATAAATAAATTAATATATTAAAATTTATATAA
1 TATAAATAAATTAATATATTAAAA--TATATAA
* *
7428 TATAAAT-TATTAATTTATTAAAATATATAA
1 TATAAATAAATTAATATATTAAAATATATAA
7458 TA
1 TA
7460 CATTAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 9 0.30
32 14 0.47
33 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (31 bp):
TATAAATAAATTAATATATTAAAATATATAA
Found at i:7464 original size:17 final size:17
Alignment explanation
Indices: 7372--7467 Score: 63
Period size: 16 Copynumber: 5.5 Consensus size: 17
7362 TATAAATTTA
*
7372 ATATAAAAATATTATAAAT
1 ATATTAAAATA-TAT-AAT
* *
7391 ATGTTATAAATAAATTAAT
1 ATATTA-AAATATA-TAAT
*
7410 ATATTAAAATTTAT-AT
1 ATATTAAAATATATAAT
*
7426 A-ATATAAATTAT-TAAT
1 ATAT-TAAAATATATAAT
*
7442 TTATTAAAATATATAAT
1 ATATTAAAATATATAAT
*
7459 ACATTAAAA
1 ATATTAAAA
7468 ATAAAAAAAT
Statistics
Matches: 59, Mismatches: 12, Indels: 14
0.69 0.14 0.16
Matches are distributed among these distances:
15 3 0.05
16 18 0.31
17 14 0.24
18 5 0.08
19 13 0.22
20 6 0.10
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (17 bp):
ATATTAAAATATATAAT
Found at i:8702 original size:22 final size:22
Alignment explanation
Indices: 8677--8719 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
8667 AAAAAAATTA
8677 TTTTAT-ATTAATATTCATATAT
1 TTTTATAATTAA-ATTCATATAT
*
8699 TTTTATAATTAAATTTATATA
1 TTTTATAATTAAATTCATATA
8720 AAAATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTATAATTAAATTCATATAT
Found at i:15898 original size:17 final size:17
Alignment explanation
Indices: 15876--15909 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
15866 TTAATATATT
15876 TTTTTATAA-TTTAATTA
1 TTTTTA-AATTTTAATTA
15893 TTTTTAAATTTTAATTA
1 TTTTTAAATTTTAATTA
15910 GAATTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTTAAATTTTAATTA
Found at i:28583 original size:23 final size:22
Alignment explanation
Indices: 28532--28584 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
28522 AATTATTTTT
* *
28532 ATAAT-ATTTATATATTTTATA
1 ATAATAATTTAAATATATTATA
*
28553 ATTA-AATTTAAATATATTATAA
1 ATAATAATTTAAATATATTAT-A
28575 ATAATAATTT
1 ATAATAATTT
28585 TATATTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 16 0.64
22 4 0.16
23 5 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATAATAATTTAAATATATTATA
Found at i:28833 original size:15 final size:15
Alignment explanation
Indices: 28810--28846 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
28800 ATTCGATAAG
*
28810 TTGAGTTAAATTATT
1 TTGAATTAAATTATT
28825 TTGAATTAAATTATT
1 TTGAATTAAATTATT
*
28840 TTAAATT
1 TTGAATT
28847 TTAAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (15 bp):
TTGAATTAAATTATT
Found at i:28904 original size:16 final size:15
Alignment explanation
Indices: 28880--28931 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
28870 GATTTAGATT
*
28880 ATTTCGAGTTCGGATC
1 ATTTAGAGTTCGG-TC
28896 ATTTAGAGTTCAGGTC
1 ATTTAGAGTTC-GGTC
28912 ATTTTA-AGTTCGGGTC
1 A-TTTAGAGTTC-GGTC
28928 ATTT
1 ATTT
28932 CGAATTCAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 3 0.09
16 23 0.72
17 6 0.19
ACGTcount: A:0.21, C:0.13, G:0.23, T:0.42
Consensus pattern (15 bp):
ATTTAGAGTTCGGTC
Found at i:29036 original size:53 final size:53
Alignment explanation
Indices: 28942--29044 Score: 127
Period size: 53 Copynumber: 1.9 Consensus size: 53
28932 CGAATTCAGA
* * ** * *
28942 TCAATTGGGTTTAATACTCGGGTTAATCGGGTTTGAGTCATTTTGGATTTGTG
1 TCAATTGGGTTTAACACTCGGGTTAATCGGATTCAAATCATTTTAGATTTGTG
*
28995 TCAATTGGGTTTAACATTC-GGTTAAATCGGATTCAAATCATTTTAGATTT
1 TCAATTGGGTTTAACACTCGGGTT-AATCGGATTCAAATCATTTTAGATTT
29045 AAGTTTAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
52 4 0.10
53 38 0.90
ACGTcount: A:0.24, C:0.11, G:0.22, T:0.43
Consensus pattern (53 bp):
TCAATTGGGTTTAACACTCGGGTTAATCGGATTCAAATCATTTTAGATTTGTG
Found at i:29601 original size:16 final size:16
Alignment explanation
Indices: 29580--29628 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
29570 GTTAATTATC
29580 CGAATCATTTC-AGATT
1 CGAATCATTTCAAG-TT
29596 CGAATCATTTCAAGTT
1 CGAATCATTTCAAGTT
*
29612 CGGATCATTTCAAGTT
1 CGAATCATTTCAAGTT
29628 C
1 C
29629 AAGATATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 29 0.94
17 2 0.06
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (16 bp):
CGAATCATTTCAAGTT
Found at i:29652 original size:16 final size:16
Alignment explanation
Indices: 29633--29676 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
29623 AAGTTCAAGA
*
29633 TATTTTGAGTTTAAAT
1 TATTTTGAATTTAAAT
*
29649 TATTTCGAATTTAAAT
1 TATTTTGAATTTAAAT
*
29665 TATTTTAAATTT
1 TATTTTGAATTT
29677 TGAATCAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.57
Consensus pattern (16 bp):
TATTTTGAATTTAAAT
Found at i:29739 original size:16 final size:15
Alignment explanation
Indices: 29718--29749 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
29708 TATTTTTATT
29718 AATTTAAATTAAATTA
1 AATTTAAATT-AATTA
29734 AATTTAAATTAATTA
1 AATTTAAATTAATTA
29749 A
1 A
29750 TTAATTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTTAAATTAATTA
Found at i:34773 original size:22 final size:23
Alignment explanation
Indices: 34730--34774 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
34720 ATTTAATTTA
*
34730 AAATAAATTAAATTAAATTATAT
1 AAATAAATTAAATAAAATTATAT
34753 AAAT-AATT-AATAAAATATATAT
1 AAATAAATTAAATAAAAT-TATAT
34775 TTTTAGTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 7 0.35
22 9 0.45
23 4 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AAATAAATTAAATAAAATTATAT
Found at i:35013 original size:44 final size:42
Alignment explanation
Indices: 34931--35017 Score: 102
Period size: 42 Copynumber: 2.0 Consensus size: 42
34921 CTCATTTTAA
* * * *
34931 ATTATTTATATTTATTATTTATAATTAATAATATATTTAAAT
1 ATTATTTATATATAATATTTAAAATTAATAATAAATTTAAAT
* *
34973 ATTATTTTTATATAATATTTAAATATTTATAATTAAATTTAAAT
1 ATTATTTATATATAATATTTAAA-ATTAATAA-TAAATTTAAAT
35017 A
1 A
35018 AAAATATTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
42 19 0.51
43 7 0.19
44 11 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (42 bp):
ATTATTTATATATAATATTTAAAATTAATAATAAATTTAAAT
Found at i:36162 original size:23 final size:23
Alignment explanation
Indices: 36102--36169 Score: 79
Period size: 23 Copynumber: 3.1 Consensus size: 23
36092 TTATGATTTA
* *
36102 ATTAATA-AAAAATTAT-TCAAT
1 ATTAATATAAAAAATATATAAAT
* *
36123 TTTAAT-TATAAAATATATAAAT
1 ATTAATATAAAAAATATATAAAT
36145 ATTAATATAAAAAATATATAAAT
1 ATTAATATAAAAAATATATAAAT
36168 AT
1 AT
36170 ATTAAACAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
21 12 0.32
22 9 0.24
23 17 0.45
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (23 bp):
ATTAATATAAAAAATATATAAAT
Found at i:37032 original size:18 final size:16
Alignment explanation
Indices: 36980--37032 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 16
36970 CACCATTAAG
36980 AATATAAAATTTATAT
1 AATATAAAATTTATAT
*
36996 AATAT--AACTTATAAT
1 AATATAAAATTTAT-AT
37011 AATATCAAAATTTATAT
1 AATAT-AAAATTTATAT
37028 GAATA
1 -AATA
37033 AATAATACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 6 0.20
15 7 0.23
16 5 0.17
17 2 0.07
18 10 0.33
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (16 bp):
AATATAAAATTTATAT
Found at i:37616 original size:3 final size:3
Alignment explanation
Indices: 37599--37651 Score: 74
Period size: 3 Copynumber: 17.7 Consensus size: 3
37589 AAATTTTAAA
37599 ATT ATTT ATT A-T ATT ATT ATT ATT A-T ATT ATT ACTT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
37644 ATT ATT AT
1 ATT ATT AT
37652 ATGATGAACA
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.09
3 36 0.78
4 6 0.13
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:37968 original size:13 final size:13
Alignment explanation
Indices: 37945--37978 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
37935 AAAGATTTGA
37945 TATATTTAATAATT
1 TATA-TTAATAATT
37959 TATATTAATAATT
1 TATATTAATAATT
37972 TATATTA
1 TATATTA
37979 TATTAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATATTAATAATT
Found at i:38180 original size:11 final size:11
Alignment explanation
Indices: 38087--38181 Score: 50
Period size: 11 Copynumber: 8.1 Consensus size: 11
38077 AAAGCTTTTT
38087 TATTATTCATTA
1 TATTATT-ATTA
**
38099 TATTATTAAAA
1 TATTATTATTA
*
38110 TATTATTTTTA
1 TATTATTATTA
*
38121 TATTAATATTTA
1 TATTATTA-TTA
*
38133 TATCTTATAATTA
1 TA--TTATTATTA
*
38146 AATT-TTATTAAAAA
1 TATTATTATT----A
38160 TATT-TTATTA
1 TATTATTATTA
38170 TATTATTATTA
1 TATTATTATTA
38181 T
1 T
38182 TATCTAATCG
Statistics
Matches: 63, Mismatches: 12, Indels: 17
0.68 0.13 0.18
Matches are distributed among these distances:
10 9 0.14
11 25 0.40
12 12 0.19
13 4 0.06
14 13 0.21
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (11 bp):
TATTATTATTA
Found at i:41973 original size:26 final size:25
Alignment explanation
Indices: 41939--41998 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
41929 AACAAATTTA
41939 ATTTA-TAATTT-ATTAAAAATTATT
1 ATTTATTAATTTAATT-AAAATTATT
* *
41963 TTTTAATTAATTTAATTTAAATTATT
1 ATTT-ATTAATTTAATTAAAATTATT
41989 ATTTATTAAT
1 ATTTATTAAT
41999 AATATATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 3 0.10
25 7 0.23
26 17 0.57
27 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
ATTTATTAATTTAATTAAAATTATT
Found at i:41982 original size:43 final size:44
Alignment explanation
Indices: 41933--42033 Score: 116
Period size: 43 Copynumber: 2.3 Consensus size: 44
41923 TTATTTAACA
* *
41933 AATTTAATTTATAATTTATTAAAAAT-TATTTTTTAATT-AATTT
1 AATTTAAATTATAATTTATTAAAAATATA-TATTTAATTAAATTT
* * *
41976 AATTTAAATTATTATTTATTAATAATATATATTTATTTAAATTT
1 AATTTAAATTATAATTTATTAAAAATATATATTTAATTAAATTT
*
42020 AATTATAAAATATA
1 AATT-TAAATTATA
42034 GATTAATATT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
43 30 0.62
44 11 0.23
45 7 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (44 bp):
AATTTAAATTATAATTTATTAAAAATATATATTTAATTAAATTT
Found at i:41992 original size:17 final size:17
Alignment explanation
Indices: 41934--42018 Score: 55
Period size: 15 Copynumber: 5.5 Consensus size: 17
41924 TATTTAACAA
*
41934 ATTTAATTTATA-ATTT
1 ATTTAAATTATATATTT
*
41950 A-TTAAA-AAT-TATTT
1 ATTTAAATTATATATTT
*
41964 -TTT-AATTA-AT-TTA
1 ATTTAAATTATATATTT
41977 ATTTAAATTAT-TATTT
1 ATTTAAATTATATATTT
*
41993 A-TTAATAATATATATTT
1 ATTTAA-ATTATATATTT
42010 ATTTAAATT
1 ATTTAAATT
42019 TAATTATAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 21
0.65 0.09 0.27
Matches are distributed among these distances:
13 4 0.08
14 13 0.25
15 14 0.27
16 8 0.16
17 8 0.16
18 4 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTAAATTATATATTT
Found at i:46244 original size:56 final size:56
Alignment explanation
Indices: 46170--46275 Score: 212
Period size: 56 Copynumber: 1.9 Consensus size: 56
46160 TGCTTGATTT
46170 CCAAAAATCACATAAACAACCAATTCACACAATATCAAACATATTTTGCATTGCGG
1 CCAAAAATCACATAAACAACCAATTCACACAATATCAAACATATTTTGCATTGCGG
46226 CCAAAAATCACATAAACAACCAATTCACACAATATCAAACATATTTTGCA
1 CCAAAAATCACATAAACAACCAATTCACACAATATCAAACATATTTTGCA
46276 CTGTGGGTTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.47, C:0.25, G:0.05, T:0.23
Consensus pattern (56 bp):
CCAAAAATCACATAAACAACCAATTCACACAATATCAAACATATTTTGCATTGCGG
Found at i:47832 original size:2 final size:2
Alignment explanation
Indices: 47825--47868 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
47815 AAAGATGAAG
*
47825 AT AT AT AT AT AT AT AT AT AT AT AT AT AA 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
47867 AT
1 AT
47869 TAATTTTCTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48881 original size:18 final size:19
Alignment explanation
Indices: 48844--48882 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
48834 TTATAATTTT
* *
48844 TTATTATTTTTTTTGTTAG
1 TTATTATTTTTTATGATAG
48863 TTATTA-TTTTTATGATAG
1 TTATTATTTTTTATGATAG
48881 TT
1 TT
48883 GCCAACATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (19 bp):
TTATTATTTTTTATGATAG
Done.