Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2729
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: 41574
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:3769 original size:20 final size:20
Alignment explanation
Indices: 3746--3818 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3736 ACAATTCAAA
3746 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
3766 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
3787 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
3807 GTATCGATACAT
1 GTATCGATACAT
3819 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:3790 original size:21 final size:21
Alignment explanation
Indices: 3764--3839 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
3754 ACATGTTGCA
3764 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
3785 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
3805 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
3826 TTGTATCGATACAT
1 ATGTATCGATACAT
3840 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:3797 original size:41 final size:41
Alignment explanation
Indices: 3746--3839 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
3736 ACAATTCAAA
*
3746 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
3787 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
3828 GTATCGATACAT
1 GTATCGATACAT
3840 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:3896 original size:13 final size:13
Alignment explanation
Indices: 3878--3903 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3868 TACAGCAAGT
3878 ATGTATCGATACA
1 ATGTATCGATACA
3891 ATGTATCGATACA
1 ATGTATCGATACA
3904 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4424 original size:34 final size:35
Alignment explanation
Indices: 4361--4427 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
4351 CTAAGTGATT
4361 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
4397 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
4428 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:5560 original size:21 final size:21
Alignment explanation
Indices: 5535--5586 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
5525 ATGATGATGA
*
5535 TGATGAAGATCATCAAGAGGT
1 TGATGAAAATCATCAAGAGGT
5556 TGATGAAAATCATCAAGAGGT
1 TGATGAAAATCATCAAGAGGT
5577 TGATGAAAAT
1 TGATGAAAAT
5587 GAAGAAATAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.42, C:0.08, G:0.25, T:0.25
Consensus pattern (21 bp):
TGATGAAAATCATCAAGAGGT
Found at i:7524 original size:13 final size:13
Alignment explanation
Indices: 7506--7530 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7496 TTTTCCAGAT
7506 TGTATCGATACAA
1 TGTATCGATACAA
7519 TGTATCGATACA
1 TGTATCGATACA
7531 TTGCTTCAGT
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:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:8713 original size:23 final size:23
Alignment explanation
Indices: 8683--8729 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
8673 GTGCAAATAA
8683 ATTTTGATATGAATTACTTGATT
1 ATTTTGATATGAATTACTTGATT
8706 ATTTTGATATGAATTACTTGATT
1 ATTTTGATATGAATTACTTGATT
8729 A
1 A
8730 AGGGGGAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.04, G:0.13, T:0.51
Consensus pattern (23 bp):
ATTTTGATATGAATTACTTGATT
Found at i:9388 original size:20 final size:20
Alignment explanation
Indices: 9365--9437 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
9355 ACAATTCAAA
9365 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
9385 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
9406 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
9426 GTATCGATACAT
1 GTATCGATACAT
9438 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:9409 original size:21 final size:21
Alignment explanation
Indices: 9383--9458 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
9373 ACATGTTGCA
9383 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
9404 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
9424 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
9445 TTGTATCGATACAT
1 ATGTATCGATACAT
9459 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:9416 original size:41 final size:41
Alignment explanation
Indices: 9365--9458 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
9355 ACAATTCAAA
*
9365 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
9406 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
9447 GTATCGATACAT
1 GTATCGATACAT
9459 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:9515 original size:13 final size:13
Alignment explanation
Indices: 9497--9522 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9487 TACAGCAAGT
9497 ATGTATCGATACA
1 ATGTATCGATACA
9510 ATGTATCGATACA
1 ATGTATCGATACA
9523 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:10043 original size:34 final size:35
Alignment explanation
Indices: 9980--10046 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
9970 CTAAGTGATT
9980 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
10016 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
10047 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:10333 original size:13 final size:13
Alignment explanation
Indices: 10315--10345 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
10305 ACAATTCATC
10315 ATGTATCGATACA
1 ATGTATCGATACA
10328 ATGTATCGATACA
1 ATGTATCGATACA
*
10341 TTGTA
1 ATGTA
10346 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:10339 original size:33 final size:33
Alignment explanation
Indices: 10297--10361 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
10287 TGAGCTCACA
* *
10297 GTATTGATACAATT-CATCATGTATCGATACAAT
1 GTATCGATAC-ATTGCACCATGTATCGATACAAT
*
10330 GTATCGATACATTGTACCATGTATCGATACAA
1 GTATCGATACATTGCACCATGTATCGATACAA
10362 ACAGTGGTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 3 0.11
33 25 0.89
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (33 bp):
GTATCGATACATTGCACCATGTATCGATACAAT
Found at i:11063 original size:22 final size:22
Alignment explanation
Indices: 11029--11070 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
11019 AGATAAACAT
*
11029 ATTTTTCCACCTTTATCAAAAC
1 ATTTCTCCACCTTTATCAAAAC
*
11051 ATTTCTCCTCCTTTATCAAA
1 ATTTCTCCACCTTTATCAAA
11071 TCTTTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTCTCCACCTTTATCAAAAC
Found at i:15691 original size:13 final size:13
Alignment explanation
Indices: 15673--15721 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
15663 CATGGGACAA
15673 TGTATCGATACAT
1 TGTATCGATACAT
15686 TGTATCGATACA-
1 TGTATCGATACAT
15698 TG-AT-GA-A-AT
1 TGTATCGATACAT
15707 TGTATCGATACAT
1 TGTATCGATACAT
15720 TG
1 TG
15722 CTTGTAACGG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
8 1 0.03
9 3 0.10
10 4 0.13
11 4 0.13
12 3 0.10
13 16 0.52
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:15694 original size:33 final size:34
Alignment explanation
Indices: 15652--15721 Score: 108
Period size: 33 Copynumber: 2.1 Consensus size: 34
15642 CTACCACTGT
15652 TTGTATCGATACATG-GGACAA-TGTATCGATACA
1 TTGTATCGATACATGAGGA-AATTGTATCGATACA
*
15685 TTGTATCGATACATGATGAAATTGTATCGATACA
1 TTGTATCGATACATGAGGAAATTGTATCGATACA
15719 TTG
1 TTG
15722 CTTGTAACGG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 17 0.50
34 17 0.50
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (34 bp):
TTGTATCGATACATGAGGAAATTGTATCGATACA
Found at i:19871 original size:52 final size:52
Alignment explanation
Indices: 19791--19919 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
19781 CGAAATATGA
19791 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
* *
19843 AAATTTGCCTGCATGTATCGATATATTTTGTAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
19895 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
19920 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
Found at i:19930 original size:52 final size:52
Alignment explanation
Indices: 19791--19939 Score: 230
Period size: 52 Copynumber: 2.9 Consensus size: 52
19781 CGAAATATGA
*
19791 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTGATAGTGTATCGATACATCTGGGC
*
19843 AAATTTGCCTGCATGTATCGATATATTTTG-TAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTTGATAGTGTATCGATACATCTGGGC
**
19895 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTTGAT-AGTGTATCGATACA
19940 ATGTATCGAT
Statistics
Matches: 89, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
50 1 0.01
51 1 0.01
52 84 0.94
53 3 0.03
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTGATAGTGTATCGATACATCTGGGC
Found at i:19946 original size:13 final size:13
Alignment explanation
Indices: 19928--19952 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19918 CAAAGATCAG
19928 TGTATCGATACAA
1 TGTATCGATACAA
19941 TGTATCGATACA
1 TGTATCGATACA
19953 TTTGAGTAAT
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:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:20019 original size:19 final size:18
Alignment explanation
Indices: 19995--20088 Score: 73
Period size: 19 Copynumber: 5.6 Consensus size: 18
19985 TAGCTTAAAT
19995 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
20014 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
20027 TGTATCGGTACAACACTTA
1 TGTATCGATACAA-ACTTA
20046 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
20059 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
20079 TGTATCGATA
1 TGTATCGATA
20089 TAAATCATTG
Statistics
Matches: 60, Mismatches: 2, Indels: 25
0.69 0.02 0.29
Matches are distributed among these distances:
13 21 0.35
14 2 0.03
16 4 0.07
18 1 0.02
19 22 0.37
20 10 0.17
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:20032 original size:13 final size:13
Alignment explanation
Indices: 20014--20070 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
20004 ACAAAACTTA
20014 TGTATCGATACAT
1 TGTATCGATACAT
*
20027 TGTATCGGTACAACACTT
1 TGTATC-G-A-TACA--T
20045 ATGTATCGATACAT
1 -TGTATCGATACAT
20059 TGTATCGATACA
1 TGTATCGATACA
20071 ACACTTTATG
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 18 0.50
14 2 0.06
15 1 0.03
16 6 0.17
17 1 0.03
18 2 0.06
19 6 0.17
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:20039 original size:32 final size:32
Alignment explanation
Indices: 19993--20088 Score: 165
Period size: 32 Copynumber: 3.0 Consensus size: 32
19983 AGTAGCTTAA
*
19993 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
*
20025 ATTGTATCGGTACAACACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
20057 ATTGTATCGATACAACACTTTATGTATCGATA
1 ATTGTATCGATACAACAC-TTATGTATCGATA
20089 TAAATCATTG
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
32 47 0.78
33 13 0.22
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (32 bp):
ATTGTATCGATACAACACTTATGTATCGATAC
Found at i:21001 original size:3 final size:3
Alignment explanation
Indices: 20993--21017 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20983 TGAAGAGGAA
20993 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
21018 GTGACTCGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:32820 original size:20 final size:20
Alignment explanation
Indices: 32795--32848 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
32785 ATTACAAGCA
* *
32795 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATGCACC
*
32815 ATGTATCGATACAATGGACC
1 ATGTATCGATACAATGCACC
32835 ATGTATCGATACAA
1 ATGTATCGATACAA
32849 ACAGTGGTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACAATGCACC
Found at i:35076 original size:18 final size:19
Alignment explanation
Indices: 35036--35076 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
35026 AGTTTTTTGT
* *
35036 AAATTTTTGATATTACAAG
1 AAATTTTTGAAATTAAAAG
35055 -AATTTTT-AAATTAAAAG
1 AAATTTTTGAAATTAAAAG
35072 AAATT
1 AAATT
35077 AGACCTTAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.41
Consensus pattern (19 bp):
AAATTTTTGAAATTAAAAG
Found at i:35125 original size:3 final size:3
Alignment explanation
Indices: 35108--35170 Score: 51
Period size: 3 Copynumber: 20.7 Consensus size: 3
35098 CAAAGTATTT
* *
35108 GAA GAA GCAA G-A GAA GAA GAAA GAA GAA GAAA CAA GAA -AA AAA G-A
1 GAA GAA G-AA GAA GAA GAA G-AA GAA GAA G-AA GAA GAA GAA GAA GAA
35153 GAA GAA GACA GAA GAA GA
1 GAA GAA GA-A GAA GAA GA
35171 TATTAATAAG
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
2 6 0.12
3 33 0.66
4 11 0.22
ACGTcount: A:0.67, C:0.05, G:0.29, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:35134 original size:10 final size:10
Alignment explanation
Indices: 35108--35170 Score: 55
Period size: 10 Copynumber: 6.5 Consensus size: 10
35098 CAAAGTATTT
35108 GAAGAAGCAAGA
1 GAAGAAG-AA-A
35120 GAAGAAGAAA
1 GAAGAAGAAA
35130 GAAGAAGAAA
1 GAAGAAGAAA
*
35140 CAAGAA-AAA
1 GAAGAAGAAA
35149 -AAG-AG-AA
1 GAAGAAGAAA
35156 GAAGACAG-AA
1 GAAGA-AGAAA
35166 GAAGA
1 GAAGA
35171 TATTAATAAG
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
7 3 0.07
8 6 0.13
9 3 0.07
10 25 0.54
11 2 0.04
12 7 0.15
ACGTcount: A:0.67, C:0.05, G:0.29, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAA
Found at i:35186 original size:33 final size:33
Alignment explanation
Indices: 35112--35198 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 33
35102 GTATTTGAAG
35112 AAGCAAGAGAAGAAGAAAGAAGAAGAAACAAGA
1 AAGCAAGAGAAGAAGAAAGAAGAAGAAACAAGA
** * ** *
35145 AAAAAAGAGAAGAAGACAGAAGAAGATATTAA-T
1 AAGCAAGAGAAGAAGAAAGAAGAAGA-AACAAGA
*
35178 AAGCAAGAGAAGAAAAAAGAA
1 AAGCAAGAGAAGAAGAAAGAA
35199 AATATAAGCA
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
33 40 0.93
34 3 0.07
ACGTcount: A:0.67, C:0.05, G:0.24, T:0.05
Consensus pattern (33 bp):
AAGCAAGAGAAGAAGAAAGAAGAAGAAACAAGA
Found at i:38440 original size:20 final size:21
Alignment explanation
Indices: 38398--38505 Score: 75
Period size: 21 Copynumber: 5.3 Consensus size: 21
38388 AGTTGAATTT
*
38398 TTTTCGTCCAACAAGTACATC
1 TTTTCATCCAACAAGTACATC
**
38419 TTTTCATCCAA-AAGTATGTC
1 TTTTCATCCAACAAGTACATC
* * *
38439 TTTTCATCTAACGAGTGCATC
1 TTTTCATCCAACAAGTACATC
* * *
38460 TATTT-ATCCAAAAAATATATC
1 T-TTTCATCCAACAAGTACATC
38481 ATTTT-ATCC-A-AA-TACATC
1 -TTTTCATCCAACAAGTACATC
38499 TTTTCAT
1 TTTTCAT
38506 GAAGGATAGT
Statistics
Matches: 68, Mismatches: 15, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
17 4 0.06
18 7 0.10
19 2 0.03
20 18 0.26
21 33 0.49
22 4 0.06
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.40
Consensus pattern (21 bp):
TTTTCATCCAACAAGTACATC
Found at i:39607 original size:16 final size:16
Alignment explanation
Indices: 39586--39618 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
39576 AATTAATCAA
39586 ATATT-ATCATTTATTC
1 ATATTAATCATTT-TTC
39602 ATATTAATCATTTTTC
1 ATATTAATCATTTTTC
39618 A
1 A
39619 AAAATTCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (16 bp):
ATATTAATCATTTTTC
Found at i:40307 original size:12 final size:12
Alignment explanation
Indices: 40290--40337 Score: 71
Period size: 12 Copynumber: 4.0 Consensus size: 12
40280 CGGTTCAACT
40290 AAAAAAA-AGAA
1 AAAAAAAGAGAA
40301 AAAAAAAGAGAA
1 AAAAAAAGAGAA
*
40313 AAAAAAGGAGAA
1 AAAAAAAGAGAA
40325 AAAAAAGAGAGAA
1 AAAAAA-AGAGAA
40338 GAAATAGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
11 7 0.21
12 21 0.64
13 5 0.15
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAGAA
Found at i:40326 original size:23 final size:21
Alignment explanation
Indices: 40290--40334 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 21
40280 CGGTTCAACT
40290 AAAAAAAAGAAAAAAAAAGAG
1 AAAAAAAAGAAAAAAAAAGAG
40311 AAAAAAAAGGAGAAAAAAAAGAG
1 AAAAAAAA-GA-AAAAAAAAGAG
40334 A
1 A
40335 GAAGAAATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 8 0.36
22 2 0.09
23 12 0.55
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (21 bp):
AAAAAAAAGAAAAAAAAAGAG
Found at i:40334 original size:11 final size:11
Alignment explanation
Indices: 40290--40334 Score: 74
Period size: 11 Copynumber: 4.1 Consensus size: 11
40280 CGGTTCAACT
40290 AAAAAAAAGA-
1 AAAAAAAAGAG
40300 AAAAAAAAGAG
1 AAAAAAAAGAG
40311 AAAAAAAAGGAG
1 AAAAAAAA-GAG
40323 AAAAAAAAGAG
1 AAAAAAAAGAG
40334 A
1 A
40335 GAAGAAATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.30
11 12 0.36
12 11 0.33
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAG
Done.