Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1737
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: 38482
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Found at i:6242 original size:10 final size:10
Alignment explanation
Indices: 6221--6278 Score: 52
Period size: 9 Copynumber: 6.0 Consensus size: 10
6211 TTTTATACAA
6221 ATTTTTAT-T
1 ATTTTTATAT
6230 ATTTTTATAT
1 ATTTTTATAT
*
6240 ATTTATAT-T
1 ATTTTTATAT
*
6249 A-TATTATAT
1 ATTTTTATAT
6258 ATTTTT-TAATT
1 ATTTTTAT-A-T
6269 ATTTTTATAT
1 ATTTTTATAT
6279 TATATAAACT
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
8 4 0.10
9 13 0.33
10 13 0.33
11 8 0.21
12 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
ATTTTTATAT
Found at i:6765 original size:18 final size:19
Alignment explanation
Indices: 6744--6876 Score: 84
Period size: 20 Copynumber: 6.9 Consensus size: 19
6734 TGGATATAAA
* *
6744 ATAAAATT-TTAATATGAT
1 ATAAAATTATAAATATTAT
6762 ATAAAAATTAATTAAAATATTAT
1 AT-AAAATT-A-T-AAATATTAT
6785 ATAAAAATTATAAATATTAT
1 AT-AAAATTATAAATATTAT
6805 ATAAATATT-TAAATATATAT
1 ATAAA-ATTATAAATAT-TAT
*
6825 ATATAAATT-T--ATATAAT
1 ATA-AAATTATAAATATTAT
*
6842 AT-AAATTATTAAT-TTAT
1 ATAAAATTATAAATATTAT
6859 -TAAAATATATATAATATT
1 ATAAAAT-TATA-AATATT
6877 TTAAATATAA
Statistics
Matches: 95, Mismatches: 5, Indels: 28
0.74 0.04 0.22
Matches are distributed among these distances:
15 5 0.05
16 2 0.02
17 11 0.12
18 11 0.12
19 19 0.20
20 26 0.27
21 3 0.03
22 2 0.02
23 16 0.17
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (19 bp):
ATAAAATTATAAATATTAT
Found at i:6774 original size:23 final size:23
Alignment explanation
Indices: 6754--6809 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
6744 ATAAAATTTT
6754 AATATGATATAAAAATTAATTAA
1 AATATGATATAAAAATTAATTAA
*
6777 AATATTATATAAAAATT-A-T-A
1 AATATGATATAAAAATTAATTAA
*
6797 AATATTATATAAA
1 AATATGATATAAA
6810 TATTTAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 14 0.44
21 1 0.03
22 1 0.03
23 16 0.50
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
AATATGATATAAAAATTAATTAA
Found at i:6794 original size:11 final size:11
Alignment explanation
Indices: 6760--6809 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
6750 TTTTAATATG
6760 ATATAAAAATT
1 ATATAAAAATT
6771 A-ATTAAAATATT
1 ATA-TAAAA-ATT
6783 ATATAAAAA-T
1 ATATAAAAATT
*
6793 -TATAAATATT
1 ATATAAAAATT
6803 ATATAAA
1 ATATAAA
6810 TATTTAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
9 7 0.21
10 3 0.09
11 13 0.39
12 9 0.27
13 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
ATATAAAAATT
Found at i:6801 original size:20 final size:20
Alignment explanation
Indices: 6754--6843 Score: 92
Period size: 20 Copynumber: 4.2 Consensus size: 20
6744 ATAAAATTTT
*
6754 AATATGATATAAAAATTAATTAA
1 AATATTATATAAAAATT-A-T-A
6777 AATATTATATAAAAATTATA
1 AATATTATATAAAAATTATA
*
6797 AATATTATATAAATATT-TA
1 AATATTATATAAAAATTATA
*
6816 AATATATATATATAAATTTATA
1 AATAT-TATATA-AAAATTATA
6838 TAATAT
1 -AATAT
6844 AAATTATTAA
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
19 7 0.12
20 23 0.39
21 5 0.08
22 3 0.05
23 21 0.36
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (20 bp):
AATATTATATAAAAATTATA
Found at i:6826 original size:14 final size:14
Alignment explanation
Indices: 6776--6847 Score: 60
Period size: 14 Copynumber: 5.3 Consensus size: 14
6766 AAATTAATTA
*
6776 AAATAT-TATATAA
1 AAATATATATATAT
*
6789 AAAT-TATAAATAT
1 AAATATATATATAT
* * *
6802 -TATATAAATATTT
1 AAATATATATATAT
6815 AAATATATATATAT
1 AAATATATATATAT
*
6829 AAATTTATATAATAT
1 AAATATATAT-ATAT
6844 AAAT
1 AAAT
6848 TATTAATTTA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
12 3 0.07
13 15 0.33
14 19 0.42
15 8 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATATATATATAT
Found at i:6842 original size:23 final size:22
Alignment explanation
Indices: 6778--6893 Score: 83
Period size: 20 Copynumber: 5.6 Consensus size: 22
6768 ATTAATTAAA
**
6778 ATAT-TATATAAAAATTATAA-
1 ATATATATATAAATTTTATAAT
6798 ATAT-TATATAAATATTTA-AAT
1 ATATATATATAAAT-TTTATAAT
6819 ATATATATATAAATTTATATAAT
1 ATATATATATAAATTT-TATAAT
* *
6842 ATAAAT-TATTAA-TTTATTAA-
1 ATATATATATAAATTTTA-TAAT
6862 A-ATATATATAATATTTTA-AAT
1 ATATATATATAA-ATTTTATAAT
6883 ATA-AT-TATAAA
1 ATATATATATAAA
6894 ATATAAAAAT
Statistics
Matches: 79, Mismatches: 6, Indels: 23
0.73 0.06 0.21
Matches are distributed among these distances:
19 4 0.05
20 28 0.35
21 18 0.23
22 21 0.27
23 8 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATATATATATAAATTTTATAAT
Found at i:7405 original size:15 final size:15
Alignment explanation
Indices: 7385--7416 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
7375 ATCATGGTAG
*
7385 TTTTTTAATTTTTAA
1 TTTTTTAATCTTTAA
7400 TTTTTTAATCTTTAA
1 TTTTTTAATCTTTAA
7415 TT
1 TT
7417 AAATTGGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTTAATCTTTAA
Found at i:7724 original size:29 final size:28
Alignment explanation
Indices: 7686--7752 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
7676 ATTAAATATT
*
7686 TTAAACATAATTAT-AATATGATAAAATA
1 TTAAATATAATTATAAATAT-ATAAAATA
*
7714 TATAAATATAA-TATAAATATATAAATTA
1 T-TAAATATAATTATAAATATATAAAATA
*
7742 TTAAATTTAAT
1 TTAAATATAAT
7753 CTCACATAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 8 0.24
28 12 0.36
29 13 0.39
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (28 bp):
TTAAATATAATTATAAATATATAAAATA
Found at i:7733 original size:19 final size:18
Alignment explanation
Indices: 7700--7739 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
7690 ACATAATTAT
*
7700 AATATGATAAAATATATA
1 AATATAATAAAATATATA
7718 AATATAATATAAATATATA
1 AATATAATA-AAATATATA
7737 AAT
1 AAT
7740 TATTAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
AATATAATAAAATATATA
Found at i:8112 original size:17 final size:17
Alignment explanation
Indices: 8084--8134 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
8074 CATATATCTT
8084 TTAAATATATTAATAAAA
1 TTAAA-ATATTAATAAAA
8102 TTAAAATATTAATTAAAA
1 TTAAAATATTAA-TAAAA
* *
8120 ATAAAATAATAATAA
1 TTAAAATATTAATAA
8135 TCTCTTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 10 0.33
18 20 0.67
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAATATTAATAAAA
Found at i:9252 original size:40 final size:39
Alignment explanation
Indices: 9169--9244 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 39
9159 AAATTAGATT
*
9169 AATTTGAAAATTTATATTATTATTTAAAATATTAATAAAA
1 AATTTGAAAATATATATTATTATTT-AAATATTAATAAAA
* *
9209 AATTTTAAAATATATATT-TTATATT-AATATTTATAA
1 AATTTGAAAATATATATTATTAT-TTAAATATTAATAA
9245 TTAAAATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 10 0.31
39 4 0.12
40 18 0.56
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (39 bp):
AATTTGAAAATATATATTATTATTTAAATATTAATAAAA
Found at i:10025 original size:22 final size:22
Alignment explanation
Indices: 10000--10041 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
9990 TTATTTTTAT
10000 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
10022 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
10042 ATTTTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:10889 original size:7 final size:7
Alignment explanation
Indices: 10877--10921 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
10867 GAAAAAAAAG
10877 ATTTTAA
1 ATTTTAA
10884 ATTTTAA
1 ATTTTAA
10891 ATTTTAA
1 ATTTTAA
*
10898 ATTTATTA
1 ATTT-TAA
*
10906 ATTATTAT
1 ATT-TTAA
10914 ATTTTAA
1 ATTTTAA
10921 A
1 A
10922 AATAATTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
7 22 0.69
8 9 0.28
9 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
ATTTTAA
Found at i:11191 original size:31 final size:31
Alignment explanation
Indices: 11156--11221 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
11146 CATATATTTA
11156 TATAAATTTTAATACATTAATCAT-TTTATAT
1 TATAAATTTTAATACATTAAT-ATATTTATAT
* *
11187 TATAAATTTTAATATATTTATATATTTATAT
1 TATAAATTTTAATACATTAATATATTTATAT
11218 TATA
1 TATA
11222 TTTTGTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (31 bp):
TATAAATTTTAATACATTAATATATTTATAT
Found at i:11674 original size:22 final size:20
Alignment explanation
Indices: 11645--11703 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
11635 AAAAAAACTG
*
11645 TCATTTATTTTTTTCTTTATT
1 TCATTTA-TTTTTTCATTATT
11666 TCATATTATTTTTTCATTATT
1 TCAT-TTATTTTTTCATTATT
* *
11687 TAATTT-TTTTTGCATTA
1 TCATTTATTTTTTCATTA
11704 ATTAAAAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.29
20 2 0.06
21 19 0.56
22 3 0.09
ACGTcount: A:0.20, C:0.08, G:0.02, T:0.69
Consensus pattern (20 bp):
TCATTTATTTTTTCATTATT
Found at i:11696 original size:19 final size:19
Alignment explanation
Indices: 11652--11708 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
11642 CTGTCATTTA
*
11652 TTTTTTTCTTTATTTCATATT
1 TTTTTTTCATTATTT-A-ATT
*
11673 ATTTTTTCATTATTTAATT
1 TTTTTTTCATTATTTAATT
* *
11692 TTTTTTGCATTAATTAA
1 TTTTTTTCATTATTTAA
11709 AAAACATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 17 0.55
20 1 0.03
21 13 0.42
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTTTTTCATTATTTAATT
Found at i:12324 original size:13 final size:13
Alignment explanation
Indices: 12306--12394 Score: 61
Period size: 13 Copynumber: 5.9 Consensus size: 13
12296 CATAAAGTGT
12306 TGTATCGATACAA
1 TGTATCGATACAA
12319 TGTATCGATACATAA
1 TGTATCGATAC--AA
12334 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
12351 TGTATCGATACATAA
1 TGTATCGATAC--AA
12366 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
*
12383 TGTATTGATACA
1 TGTATCGATACA
12395 TAAGTTTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 24
0.72 0.01 0.27
Matches are distributed among these distances:
13 33 0.52
15 4 0.06
17 4 0.06
19 22 0.35
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:12341 original size:32 final size:32
Alignment explanation
Indices: 12286--12415 Score: 233
Period size: 32 Copynumber: 4.0 Consensus size: 32
12276 TTCAACGATT
12286 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
12319 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
12351 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
12383 TGTATTGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
12415 T
1 T
12416 TTAAGCTACT
Statistics
Matches: 95, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
32 82 0.86
33 13 0.14
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:12474 original size:13 final size:13
Alignment explanation
Indices: 12456--12480 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12446 ATTACTCAAA
12456 TGTATCGATACAT
1 TGTATCGATACAT
12469 TGTATCGATACA
1 TGTATCGATACA
12481 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:16019 original size:21 final size:21
Alignment explanation
Indices: 15999--16037 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
15989 TTAAAAAAAT
15999 TTAATAT-ATTTTAAATTAAA
1 TTAATATAATTTTAAATTAAA
* *
16019 TTATTTTAATTTTAAATTA
1 TTAATATAATTTTAAATTA
16038 TCTTGAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAATATAATTTTAAATTAAA
Found at i:16034 original size:16 final size:15
Alignment explanation
Indices: 15995--16038 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
15985 GATGTTAAAA
*
15995 AAATTTAATATATTTT
1 AAATTAAAT-TATTTT
16011 AAATTAAATTATTTT
1 AAATTAAATTATTTT
*
16026 AATTTTAAATTAT
1 AA-ATTAAATTAT
16039 CTTGAATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AAATTAAATTATTTT
Found at i:16397 original size:5 final size:5
Alignment explanation
Indices: 16367--16395 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
16357 AAATCTATGC
16367 CTTTT CTTTT CTTTT CTTTT CTTTT -TTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
16396 TTCAATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
CTTTT
Found at i:17135 original size:15 final size:14
Alignment explanation
Indices: 17117--17179 Score: 54
Period size: 15 Copynumber: 4.2 Consensus size: 14
17107 TTGAAAAAAT
17117 TTTAAAATGTTTTAA
1 TTTAAAAT-TTTTAA
*
17132 TTTAAATTATTTTAAA
1 TTTAAA--ATTTTTAA
*
17148 TTTAAATATTTTAAA
1 TTTAAA-ATTTTTAA
* *
17163 TTTTAATTTTTTAA
1 TTTAAAATTTTTAA
17177 TTT
1 TTT
17180 TGATGATATA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
14 9 0.21
15 20 0.48
16 11 0.26
17 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
TTTAAAATTTTTAA
Found at i:17956 original size:26 final size:27
Alignment explanation
Indices: 17923--17973 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
17913 TTTATTTTTT
*
17923 ATATAATATAATTAATTAAA-ATATAA
1 ATATAATATAATTAAATAAACATATAA
*
17949 ATATAATATGATTAAATAAACATAT
1 ATATAATATAATTAAATAAACATAT
17974 TTAATTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (27 bp):
ATATAATATAATTAAATAAACATATAA
Found at i:17973 original size:21 final size:21
Alignment explanation
Indices: 17922--17964 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
17912 GTTTATTTTT
17922 TATATAATATAATTAATTAAAA
1 TATA-AATATAATTAATTAAAA
*
17944 TATAAATATAATATGATTAAA
1 TATAAATATAAT-TAATTAAA
17965 TAAACATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
TATAAATATAATTAATTAAAA
Found at i:18372 original size:19 final size:19
Alignment explanation
Indices: 18348--18384 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
18338 TAAATAATAA
18348 TATTTTTACTAATAAAAAT
1 TATTTTTACTAATAAAAAT
* *
18367 TATTTTTATTATTAAAAA
1 TATTTTTACTAATAAAAA
18385 GATATTATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTTTTACTAATAAAAAT
Found at i:19334 original size:35 final size:35
Alignment explanation
Indices: 19284--19394 Score: 134
Period size: 35 Copynumber: 3.1 Consensus size: 35
19274 TATATGATAA
*
19284 ATAATTAAAAATATATTTATATGAAATAATAAAAT
1 ATAATTAAAATTATATTTATATGAAATAATAAAAT
* *
19319 ATAAATAAAATTATATTTATGTCGAATAATAATTAAAA-
1 ATAATTAAAATTATATTTATAT-G-A-AATAA-TAAAAT
* *
19357 ATTATTAAAATTATATTTATATTAAATAATAAAAT
1 ATAATTAAAATTATATTTATATGAAATAATAAAAT
19392 ATA
1 ATA
19395 CATATATTCG
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
34 5 0.08
35 26 0.41
36 2 0.03
37 1 0.02
38 24 0.38
39 5 0.08
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.40
Consensus pattern (35 bp):
ATAATTAAAATTATATTTATATGAAATAATAAAAT
Found at i:19385 original size:38 final size:36
Alignment explanation
Indices: 19282--19390 Score: 121
Period size: 38 Copynumber: 3.0 Consensus size: 36
19272 TATATATGAT
* *
19282 AAATAATTAAAAATATATTTATATGAAATAAT-AAA
1 AAATAATTAAAATTATATTTATATCAAATAATAAAA
* * * *
19317 ATATAAATAAAATTATATTTATGTCGAATAATAATTAA
1 AAATAATTAAAATTATATTTATATCAAATAATAA--AA
* *
19355 AAATTATTAAAATTATATTTATATTAAATAATAAAA
1 AAATAATTAAAATTATATTTATATCAAATAATAAAA
19391 TATACATATA
Statistics
Matches: 59, Mismatches: 12, Indels: 5
0.78 0.16 0.07
Matches are distributed among these distances:
35 26 0.44
36 3 0.05
38 30 0.51
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.39
Consensus pattern (36 bp):
AAATAATTAAAATTATATTTATATCAAATAATAAAA
Found at i:19425 original size:25 final size:22
Alignment explanation
Indices: 19363--19432 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
19353 AAAAATTATT
19363 AAAATTATATTTATATTAAATA
1 AAAATTATATTTATATTAAATA
* ** *
19385 ATAAAATATACATATATTCGGAAGTA
1 A-AAATTATATTTATATT---AAATA
19411 AAAATTATATTTATATTAAATA
1 AAAATTATATTTATATTAAATA
19433 TTATTTATAT
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
22 5 0.14
23 13 0.36
25 13 0.36
26 5 0.14
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.40
Consensus pattern (22 bp):
AAAATTATATTTATATTAAATA
Found at i:19435 original size:18 final size:16
Alignment explanation
Indices: 19418--19465 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
19408 GTAAAAATTA
*
19418 TATTTATATTAAATAT
1 TATTTATATTAAAAAT
19434 TATTTATATTAAAATAT
1 TATTTATATTAAAA-AT
* *
19451 AATTTA-ATAAAAAAT
1 TATTTATATTAAAAAT
19466 AAAAAATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 2 0.07
16 19 0.68
17 7 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATTTATATTAAAAAT
Found at i:19437 original size:16 final size:17
Alignment explanation
Indices: 19418--19456 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
19408 GTAAAAATTA
19418 TATTTATATT-AAATAT
1 TATTTATATTAAAATAT
19434 TATTTATATTAAAATAT
1 TATTTATATTAAAATAT
*
19451 AATTTA
1 TATTTA
19457 ATAAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATTTATATTAAAATAT
Found at i:19917 original size:2 final size:2
Alignment explanation
Indices: 19910--19938 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19900 GAAAAAGCAA
19910 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
19939 AATAAACAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20566 original size:13 final size:13
Alignment explanation
Indices: 20550--20594 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
20540 TTTAAATAAT
*
20550 TTTTTATTTTTTA
1 TTTTTATTATTTA
20563 TTTTTATTATTTA
1 TTTTTATTATTTA
*
20576 -TTTAATTATTTA
1 TTTTTATTATTTA
20588 CTTTTTA
1 -TTTTTA
20595 ATTCGTTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 11 0.41
13 12 0.44
14 4 0.15
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTATTATTTA
Found at i:21784 original size:21 final size:19
Alignment explanation
Indices: 21758--21802 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
21748 ATATATAAAT
*
21758 ATTTATTTATGTTTAATATAA
1 ATTTATTAAT-TTT-ATATAA
*
21779 ATTTATTAATTTTTTATAA
1 ATTTATTAATTTTATATAA
21798 ATTTA
1 ATTTA
21803 AAGTATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 10 0.45
20 3 0.14
21 9 0.41
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTATTAATTTTATATAA
Found at i:22299 original size:18 final size:18
Alignment explanation
Indices: 22273--22315 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
22263 AACAGTAGTG
* *
22273 ATAATAAAATAAATTATA
1 ATAAAAAAATAAATGATA
*
22291 GTAAAAAAATAAATGATA
1 ATAAAAAAATAAATGATA
22309 ATAAAAA
1 ATAAAAA
22316 TATTACATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (18 bp):
ATAAAAAAATAAATGATA
Found at i:22471 original size:18 final size:20
Alignment explanation
Indices: 22428--22478 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
22418 ACACTTTAAA
22428 TAAAATTATATAATAATTAT
1 TAAAATTATATAATAATTAT
*
22448 TAAAAATATATAAATAA-T-T
1 TAAAATTATAT-AATAATTAT
22467 TAAAATTA-ATAA
1 TAAAATTATATAA
22479 CTTTTAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 2 0.07
18 2 0.07
19 8 0.29
20 11 0.39
21 5 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAAATTATATAATAATTAT
Found at i:24057 original size:99 final size:100
Alignment explanation
Indices: 23936--24115 Score: 254
Period size: 99 Copynumber: 1.8 Consensus size: 100
23926 TTGAATCAAG
* * ** *** * * *
23936 TCAACTCCGACCTAGGTATGAAAATATAAATTTTTTCGGGTTATAACTCGGACCATGCAAAGGTG
1 TCAACTCAGACCTAAGTATGAAAATATAAAAATTTTCAAATTATAACCCAGACCATGCAAAGGTA
24001 AGCAAA-TTTTTGGTTAAAACTAGTTCAAATCCAA
66 AGCAAATTTTTTGGTTAAAACTAGTTCAAATCCAA
*
24035 TCAACTCAGACTTAAGTATGAAAATATAAAAATTTTCAAATTATAACCCAGACCATGCAAAGGTA
1 TCAACTCAGACCTAAGTATGAAAATATAAAAATTTTCAAATTATAACCCAGACCATGCAAAGGTA
24100 AGCAAATTTTTTGGTT
66 AGCAAATTTTTTGGTT
24116 TAAGCTGATA
Statistics
Matches: 69, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
99 60 0.87
100 9 0.13
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (100 bp):
TCAACTCAGACCTAAGTATGAAAATATAAAAATTTTCAAATTATAACCCAGACCATGCAAAGGTA
AGCAAATTTTTTGGTTAAAACTAGTTCAAATCCAA
Found at i:33015 original size:20 final size:20
Alignment explanation
Indices: 32978--33015 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
32968 ATATTTTAAT
*
32978 TAAATTTAATTATTAAATTA
1 TAAATTTAATTATAAAATTA
32998 TAAATATTAA-TATAAAAT
1 TAAAT-TTAATTATAAAAT
33016 AATTTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAATTTAATTATAAAATTA
Found at i:33045 original size:48 final size:46
Alignment explanation
Indices: 32956--33047 Score: 109
Period size: 48 Copynumber: 2.0 Consensus size: 46
32946 AATTATTATT
*
32956 TATTAATTAAAAATATTTTAATTAAATTTAATTATTAAATTATAAA
1 TATTAATTAAAAATATTTTAATTAAATTTAATTAATAAATTATAAA
33002 TATTAA-TATAAAATAATTTTTAA-TAAATTTTAAATTAAT-AATTATA
1 TATTAATTA-AAAAT-A-TTTTAATTAAA-TTT-AATTAATAAATTATA
33048 TTGATTCATC
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
45 2 0.05
46 11 0.28
47 5 0.12
48 16 0.40
49 6 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (46 bp):
TATTAATTAAAAATATTTTAATTAAATTTAATTAATAAATTATAAA
Found at i:33185 original size:11 final size:11
Alignment explanation
Indices: 33168--33207 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
33158 TTTTAACATG
33168 GAAAAAGTAAAA
1 GAAAAAG-AAAA
33180 -AAAAAGAAAA
1 GAAAAAGAAAA
33190 GAAAAAGAAAA
1 GAAAAAGAAAA
33201 CGAAAAA
1 -GAAAAA
33208 TATATAGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 4 0.15
11 16 0.62
12 6 0.23
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.03
Consensus pattern (11 bp):
GAAAAAGAAAA
Found at i:33348 original size:18 final size:16
Alignment explanation
Indices: 33319--33353 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
33309 CAAATATTTT
33319 TAAAAAATATTAAAAA
1 TAAAAAATATTAAAAA
33335 TAAAAAATTAATTAAAAA
1 TAAAAAA-T-ATTAAAAA
33353 T
1 T
33354 TTAAACATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 1 0.06
18 9 0.53
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
TAAAAAATATTAAAAA
Found at i:33731 original size:23 final size:22
Alignment explanation
Indices: 33703--33766 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 22
33693 AATTAAAAAT
33703 ATATTTTTATTTTTTATTTATAA
1 ATATTTTTATTTTTTATTTAT-A
* * *
33726 ATATTTTTATAATTTAATGTATA
1 ATATTTTTAT-TTTTTATTTATA
33749 AT-TTTTTATTATTTTATT
1 ATATTTTTATT-TTTTATT
33767 GATTAAATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
22 12 0.36
23 13 0.39
24 8 0.24
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
ATATTTTTATTTTTTATTTATA
Found at i:34098 original size:21 final size:20
Alignment explanation
Indices: 34068--34118 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
34058 TCTTCCCTAC
* *
34068 TTTTTC-TCTCCTTTCTTTCT
1 TTTTTCTTCTCCCTCCTTT-T
34088 TTTTTCTTCTCCCTCCTTTT
1 TTTTTCTTCTCCCTCCTTTT
34108 TTTCTTCTTCT
1 TTT-TTCTTCT
34119 TTTTTTCCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTTCTTCTCCCTCCTTTT
Found at i:35078 original size:15 final size:15
Alignment explanation
Indices: 35058--35092 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
35048 ATATTATATC
35058 ATTTTTAAAAATAAT
1 ATTTTTAAAAATAAT
* *
35073 ATTTTTAAGATTAAT
1 ATTTTTAAAAATAAT
35088 ATTTT
1 ATTTT
35093 ATATTTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
ATTTTTAAAAATAAT
Found at i:35339 original size:24 final size:22
Alignment explanation
Indices: 35307--35357 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
35297 TAAAATATTA
*
35307 AAATATAAAAGATAAATTATTAAT
1 AAATATAAAA-ATAAA-TATAAAT
* *
35331 AAATTTAAAAATTAATATAAAT
1 AAATATAAAAATAAATATAAAT
35353 AAATA
1 AAATA
35358 GACAATAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 10 0.43
23 4 0.17
24 9 0.39
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
AAATATAAAAATAAATATAAAT
Found at i:36867 original size:21 final size:19
Alignment explanation
Indices: 36851--36887 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
36841 AATTTAATTT
36851 TTATT-TAAATACTTTTAA
1 TTATTATAAATACTTTTAA
*
36869 TTATTATATATACTTTTAA
1 TTATTATAAATACTTTTAA
36888 ACTGAATTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATTATAAATACTTTTAA
Found at i:37088 original size:22 final size:23
Alignment explanation
Indices: 37036--37088 Score: 56
Period size: 25 Copynumber: 2.3 Consensus size: 23
37026 TTTATATTTG
37036 AATAAAATATATTTTAATATTAT
1 AATAAAATATATTTTAATATTAT
*
37059 ATAGTAAAA-ATATTATTATTATTA-
1 A-A-TAAAATATATT-TTAATATTAT
37083 AATAAA
1 AATAAA
37089 TAATTACATA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
22 4 0.15
23 2 0.08
24 7 0.27
25 13 0.50
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
AATAAAATATATTTTAATATTAT
Found at i:37693 original size:15 final size:15
Alignment explanation
Indices: 37654--37695 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
37644 TTTTTATATT
37654 TTAAATAAATTTTAA
1 TTAAATAAATTTTAA
** *
37669 TTCTAT-AATTTTAC
1 TTAAATAAATTTTAA
37683 TTAAATAAATTTT
1 TTAAATAAATTTT
37696 TATCATAATA
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (15 bp):
TTAAATAAATTTTAA
Done.