Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2027
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: 87286
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:1433 original size:33 final size:33
Alignment explanation
Indices: 1396--1460 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
1386 AAAATGCCTG
* *
1396 AATGTATCGATACATTGAAAAATATATCGATAT
1 AATGTATCGACACAATGAAAAATATATCGATAT
* *
1429 AATGTATCGACACAATGAACAATGTATCGATA
1 AATGTATCGACACAATGAAAAATATATCGATA
1461 CAAATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (33 bp):
AATGTATCGACACAATGAAAAATATATCGATAT
Found at i:1526 original size:21 final size:21
Alignment explanation
Indices: 1500--1576 Score: 136
Period size: 21 Copynumber: 3.7 Consensus size: 21
1490 GTTGGGACCT
*
1500 TGTATCGATACATTAAGGGCA
1 TGTATCGACACATTAAGGGCA
1521 TGTATCGACACATTAAGGGCA
1 TGTATCGACACATTAAGGGCA
1542 TGTATCGACACATTAAGGGCA
1 TGTATCGACACATTAAGGGCA
*
1563 TGTATCGATACATT
1 TGTATCGACACATT
1577 TTGGCAAAAG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (21 bp):
TGTATCGACACATTAAGGGCA
Found at i:5099 original size:13 final size:13
Alignment explanation
Indices: 5081--5106 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5071 AATTTTTTTG
5081 TGTATCGATACAT
1 TGTATCGATACAT
5094 TGTATCGATACAT
1 TGTATCGATACAT
5107 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:6408 original size:19 final size:18
Alignment explanation
Indices: 6383--6434 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
6373 TGTATTTATG
6383 TTAT-TTTTAT-TATATAT
1 TTATATTTTATGTATAT-T
6400 TTATATTTTATGTATATT
1 TTATATTTTATGTATATT
*
6418 TTAATATCTTCATGTAT
1 TT-ATAT-TTTATGTAT
6435 TAATGTCATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 4 0.13
18 9 0.30
19 9 0.30
20 8 0.27
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (18 bp):
TTATATTTTATGTATATT
Found at i:7928 original size:19 final size:20
Alignment explanation
Indices: 7893--7938 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
7883 TCTTAATATT
7893 TTTATATATAATAAATTAAA
1 TTTATATATAATAAATTAAA
* *
7913 TTTATATAT-TTAAATTATA
1 TTTATATATAATAAATTAAA
7932 TTTATAT
1 TTTATAT
7939 TTTTTATCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTATATATAATAAATTAAA
Found at i:11278 original size:22 final size:23
Alignment explanation
Indices: 11228--11279 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
11218 GAACCACAAT
* *
11228 ATAATTTATAAAAAATATTTAAAT
1 ATAA-TTATAAAAAATATATAAAA
*
11252 TTAATTAT-AAAAATATATAAAA
1 ATAATTATAAAAAATATATAAAA
11274 ATAATT
1 ATAATT
11280 TTTTTAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 17 0.71
23 4 0.17
24 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
ATAATTATAAAAAATATATAAAA
Found at i:12212 original size:21 final size:21
Alignment explanation
Indices: 12174--12213 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
12164 TTGTTGTAGG
*
12174 TGATACAAGATTAAAGGAAAA
1 TGATACAAGATAAAAGGAAAA
12195 TGATACAAGA-AAAGAGGAA
1 TGATACAAGATAAA-AGGAA
12214 GGAAAAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.57, C:0.05, G:0.23, T:0.15
Consensus pattern (21 bp):
TGATACAAGATAAAAGGAAAA
Found at i:14679 original size:57 final size:57
Alignment explanation
Indices: 14611--14725 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 57
14601 AATTGTACTT
*
14611 AATTTTCAATAGGACCTCCGTTGACCCTATTACTGCCCTGCTCATAGGTCTAACTAG
1 AATTTTCAATAGGACCTCCGTTGACCCTATTACTGCCCTGCACATAGGTCTAACTAG
*
14668 AATTTTCAATAGGACCTCCGTTGACCCTATTACTGCCCTGCACATAGGTCTAAGTAG
1 AATTTTCAATAGGACCTCCGTTGACCCTATTACTGCCCTGCACATAGGTCTAACTAG
14725 A
1 A
14726 TTGTTTGTAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (57 bp):
AATTTTCAATAGGACCTCCGTTGACCCTATTACTGCCCTGCACATAGGTCTAACTAG
Found at i:17014 original size:23 final size:24
Alignment explanation
Indices: 16964--17016 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
16954 TATCAAAAAT
* **
16964 ATTATTTTGATCTCAAATAGCTCG
1 ATTATTTTGATCACAAATAGCTAA
*
16988 ATTATTTTG-TCACTAATAGCTAA
1 ATTATTTTGATCACAAATAGCTAA
17011 ATTATT
1 ATTATT
17017 CCGTTGCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.45
Consensus pattern (24 bp):
ATTATTTTGATCACAAATAGCTAA
Found at i:17764 original size:18 final size:18
Alignment explanation
Indices: 17737--17804 Score: 93
Period size: 18 Copynumber: 3.8 Consensus size: 18
17727 GTTTCTTAAT
*
17737 TTTGGTTTTATTTAATTA
1 TTTGATTTTATTTAATTA
*
17755 TTTGAGTTTATTTAATTA
1 TTTGATTTTATTTAATTA
*
17773 TTTAATTTTATTTAATTA
1 TTTGATTTTATTTAATTA
*
17791 ATTG-TTTTATTTAA
1 TTTGATTTTATTTAA
17805 CAAGATTAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
17 10 0.23
18 34 0.77
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (18 bp):
TTTGATTTTATTTAATTA
Found at i:17786 original size:22 final size:22
Alignment explanation
Indices: 17761--17802 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
17751 ATTATTTGAG
*
17761 TTTATTTAATTATTTAATTTTA
1 TTTAATTAATTATTTAATTTTA
* *
17783 TTTAATTAATTGTTTTATTT
1 TTTAATTAATTATTTAATTT
17803 AACAAGATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTAATTAATTATTTAATTTTA
Found at i:17814 original size:36 final size:36
Alignment explanation
Indices: 17742--17815 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 36
17732 TTAATTTTGG
* ** *
17742 TTTTATTTAATTATTTGAGTTTATTTAATTATTTAA
1 TTTTATTTAATTAATTGAGTTTATTTAACAAATTAA
*
17778 TTTTATTTAATTAATTG-TTTTATTTAACAAGATTAA
1 TTTTATTTAATTAATTGAGTTTATTTAACAA-ATTAA
17814 TT
1 TT
17816 ACTAATCTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 10 0.31
36 22 0.69
ACGTcount: A:0.32, C:0.01, G:0.05, T:0.61
Consensus pattern (36 bp):
TTTTATTTAATTAATTGAGTTTATTTAACAAATTAA
Found at i:20663 original size:90 final size:88
Alignment explanation
Indices: 20434--20681 Score: 239
Period size: 91 Copynumber: 2.8 Consensus size: 88
20424 AGTGGGGATG
* * *
20434 GAGTTTTCCTAAGGATAAAATTATACGAATGGTAAATTTGAAAATTTTTTA-ATAAAACGGGGGT
1 GAGTTTTCCTAAGGATAAAATTATACGAA-GGAAAATTTG--AATTTTTTAGA-AAAATGGGGTT
* *
20498 AGAATATCACCTTGAAGGAATGGGGAT
62 AGAATATCACCTCGAAGGAATGGAGAT
* * * * * * *
20525 GAGTATCCCCAAAGATAAAATTATACAAAGGAAAAATTTTGAAATTTTTAGAAAAATGGGGTTGG
1 GAGTTTTCCTAAGGATAAAATTATACGAAGG-AAAA-TTTGAATTTTTTAGAAAAATGGGGTTAG
* * *
20590 AGTATCCCCTCGAAGTAATGGAGAT
64 AATATCACCTCGAAGGAATGGAGAT
* * * *
20615 AGAGTTTTCCTAAGGATAAAATTATACGAAGGGAACATTTGAGTTTTTT-GTAAAATGAGGTTAG
1 -GAGTTTTCCTAAGGATAAAATTATACGAA-GGAAAATTTGAATTTTTTAGAAAAATGGGGTTAG
20679 AAT
64 AAT
20682 GTCCTCTCGG
Statistics
Matches: 125, Mismatches: 27, Indels: 12
0.76 0.16 0.07
Matches are distributed among these distances:
89 14 0.11
90 50 0.40
91 55 0.44
92 6 0.05
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.30
Consensus pattern (88 bp):
GAGTTTTCCTAAGGATAAAATTATACGAAGGAAAATTTGAATTTTTTAGAAAAATGGGGTTAGAA
TATCACCTCGAAGGAATGGAGAT
Found at i:23238 original size:18 final size:18
Alignment explanation
Indices: 23212--23248 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
23202 GCCAACACAA
*
23212 TGCTAAAAAATTCTGGAC
1 TGCTAAAAAATTCTAGAC
*
23230 TGCTTAAAAATTCTAGAC
1 TGCTAAAAAATTCTAGAC
23248 T
1 T
23249 ATTTAGGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (18 bp):
TGCTAAAAAATTCTAGAC
Found at i:23932 original size:11 final size:10
Alignment explanation
Indices: 23913--23976 Score: 51
Period size: 10 Copynumber: 6.6 Consensus size: 10
23903 TAGTTAGAAA
23913 TTCTTTTTTT
1 TTCTTTTTTT
*
23923 TCCTTTTTTT
1 TTCTTTTTTT
*
23933 TTC--TTTTC
1 TTCTTTTTTT
*
23941 TTCTTTATTT
1 TTCTTTTTTT
* * *
23951 TTCTCTATTC
1 TTCTTTTTTT
23961 TTCTTTTTTT
1 TTCTTTTTTT
*
23971 CTCTTT
1 TTCTTT
23977 GGTGAAAGAA
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
8 7 0.17
10 34 0.83
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:23951 original size:20 final size:19
Alignment explanation
Indices: 23925--23974 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
23915 CTTTTTTTTC
*
23925 CTTTTTTTT-TCTTTTCTT
1 CTTTTTTTTCTCTATTCTT
23943 CTTTATTTTTCTCTATTCTT
1 CTTT-TTTTTCTCTATTCTT
23963 C-TTTTTTTCTCT
1 CTTTTTTTTCTCT
23975 TTGGTGAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 13 0.45
19 7 0.24
20 9 0.31
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (19 bp):
CTTTTTTTTCTCTATTCTT
Found at i:28214 original size:21 final size:21
Alignment explanation
Indices: 28188--28246 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
28178 ATTTTTGTCT
*
28188 AAATGTATTGATACATTTGAG
1 AAATGTATCGATACATTTGAG
* *
28209 AAATGTATCGATACATGTGTG
1 AAATGTATCGATACATTTGAG
*
28230 -AATGTATCAATACATTT
1 AAATGTATCGATACATTT
28247 TTCAATGTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.37
Consensus pattern (21 bp):
AAATGTATCGATACATTTGAG
Found at i:28235 original size:20 final size:20
Alignment explanation
Indices: 28189--28266 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
28179 TTTTTGTCTA
* *
28189 AATGTATTGATACATTTGAG
1 AATGTATCGATACATTTGTG
*
28209 AAATGTATCGATACATGTGTG
1 -AATGTATCGATACATTTGTG
* * *
28230 AATGTATCAATACATTTTTC
1 AATGTATCGATACATTTGTG
*
28250 AATGTATCGATATATTT
1 AATGTATCGATACATTT
28267 TTTTGTGTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
20 31 0.65
21 17 0.35
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (20 bp):
AATGTATCGATACATTTGTG
Found at i:29221 original size:21 final size:20
Alignment explanation
Indices: 29197--29236 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
29187 TAGCCTTTGA
*
29197 TCATGCATTTTATACCATATT
1 TCATGCA-TTTATAACATATT
*
29218 TCATGTATTTATAACATAT
1 TCATGCATTTATAACATAT
29237 CCAACCTCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.47
Consensus pattern (20 bp):
TCATGCATTTATAACATATT
Found at i:38060 original size:20 final size:20
Alignment explanation
Indices: 38035--38157 Score: 102
Period size: 20 Copynumber: 5.6 Consensus size: 20
38025 TTTTAACTAG
*
38035 ATGTATCGATACTTTGAAAA
1 ATGTATCGATACATTGAAAA
38055 ATGTATCGATACATCTGGGTAAAAA
1 ATGTATCGATACAT-T--G--AAAA
*
38080 GATAGAATGTATCGATACATTGAAGA
1 -AT-G--T--ATCGATACATTGAAAA
* * *
38106 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTGAAAA
38126 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
38146 ATGTATCGATAC
1 ATGTATCGATAC
38158 TTCTGGGTAC
Statistics
Matches: 83, Mismatches: 9, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
20 54 0.65
21 1 0.01
22 1 0.01
23 1 0.01
24 1 0.01
25 6 0.07
26 5 0.06
27 1 0.01
28 1 0.01
29 1 0.01
30 1 0.01
31 10 0.12
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:39121 original size:28 final size:28
Alignment explanation
Indices: 39039--39776 Score: 758
Period size: 28 Copynumber: 25.5 Consensus size: 28
39029 CACCGATTCG
* * *
39039 TGTGGGCTTTGAAAAGAGTTACCACTGGCT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT
* *
39069 TGTGGGCTTTGAAAAGAGTGCCACTAACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
*
39098 TGTGGGCTTTGAAAGTGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
39126 TGTGGGCTTTAAAAGGGTGCCATTAATT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
39154 TGTGGGCTTTGAAAAGAGTGCCACTAACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
*
39183 TGTGGGCTTTAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
39211 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
39239 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
39268 TGTGGGCTTTGAAAGGTTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
**
39296 TGTGGGCTTTGAAAGTATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
39324 TGTGGGCTTTGGAAA-TGTGCCATTGACT
1 TGTGGGCTTT-GAAAGGGTGCCACTGACT
* *
39352 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* **
39380 TGTGGGCTTTGAAAAGAGTTGCCACCAACT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT
*
39410 CGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
39438 TGTGCGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
** *
39466 TGTGGGCTTTGAAAGTATGCCACTGACA
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
39494 TGTGGGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
39522 TGTGGACTTTGAAAAGATGCGACTGGCT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
39550 TGTGGGCTTTGAAAGGGTGCCACTGACTT
1 TGTGGGCTTTGAAAGGGTGCCACTGAC-T
* * **
39579 GTGTGGGATTTGAAATGGGTTGCAACCAACTT
1 -TGTGGGCTTTGAAA-GGG-TGCCACTGAC-T
* **
39611 GTGTGGGCTTTGAAATGGTTTGCCACCAACTT
1 -TGTGGGCTTTGAAA-GG-GTGCCACTGAC-T
**
39643 GTGTGGGCTTTGAAATGGGTTGCCACCAACTT
1 -TGTGGGCTTTGAAA-GGG-TGCCACTGAC-T
* *
39675 GTGTGGGCTTTGAAATGAGTTGCCACCGACTT
1 -TGTGGGCTTTGAAA-G-GGTGCCACTGAC-T
* *
39707 GTGTGGGCTTTGAAATGATGCCACTGACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
39736 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
39764 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
39777 GAGATGGACG
Statistics
Matches: 620, Mismatches: 75, Indels: 28
0.86 0.10 0.04
Matches are distributed among these distances:
27 4 0.01
28 359 0.58
29 83 0.13
30 60 0.10
31 3 0.00
32 110 0.18
33 1 0.00
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:39432 original size:170 final size:168
Alignment explanation
Indices: 39039--39776 Score: 816
Period size: 170 Copynumber: 4.2 Consensus size: 168
39029 CACCGATTCG
* * *
39039 TGTGGGCTTTGAAAAGAGTTACCACTGGCTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGG
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTAACTTGTGGG
* * ** * *
39104 CTTTGAAA-GTGTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCATTAATTTGTGGGCTTTGAAA
63 CTTTGAAAGGT-TGCCACTAACTTGTGGGCTTTGAAAGTATGCCACTAACTTGTGGGCTTTGAAA
* * *
39168 AGAGTGCCACTAACTTGTGGGCTTTAAAAGGGTGCCACTGACT
127 AGA-TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* *
39211 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTAACTTGTGGGCT
* *
39276 TTGAAAGGTTGCCACTAACTTGTGGGCTTTGAAAGTATGCCACTGACTTGTGGGCTTTGGAAATG
65 TTGAAAGGTTGCCACTAACTTGTGGGCTTTGAAAGTATGCCACTAACTTGTGGGCTTT-GAAAAG
* *
39341 -TGCCATTGACTTGTGGGCTTTGAAAGGATGCCACTAACT
129 ATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* ** * * * *
39380 TGTGGGCTTTGAAAAGAGTTGCCACCAACTCGTGGGCTTTGAAAGGGTGCCACTGACTTGTGCGC
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTAACTTGTGGGC
* * * * *
39445 TTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGTATGCCACTGACATGTGGGCTTTGAAAAG
64 TTTGAAAGGTTGCCACTAACTTGTGGGCTTTGAAAGTATGCCACTAACTTGTGGGCTTTGAAAAG
* * * *
39510 ATGCCACTGACTTGTGGACTTTGAAAAGATGCGACTGGCT
129 ATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
39550 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGTGGGATTTGAAATGGGTTGCAACCAACTTGTGT
1 TGTGGGCTTTGAAAGGGTGCCACTGAC-T-TGTGGGCTTTGAAA-GAG-TGCCACTAAC-T-TGT
* *
39615 GGGCTTTGAAATGGTTTGCCACCAACTTGTGTGGGCTTTGAAATGGGT-TGCCACCAACTTGTGT
60 GGGCTTTGAAA-GG-TTGCCACTAAC-T-TGTGGGCTTTGAAA---GTATGCCACTAAC-T-TGT
* * *
39679 GGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGATGCCACTGACT
116 GGGCTTTGAAA--AGATGCCACTGAC-T-TGTGGGCTTTGAAAGGATGCCACTGACT
39736 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAA
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAA
39777 GAGATGGACG
Statistics
Matches: 485, Mismatches: 57, Indels: 36
0.84 0.10 0.06
Matches are distributed among these distances:
168 9 0.02
169 55 0.11
170 231 0.48
171 34 0.07
172 18 0.04
173 1 0.00
174 13 0.03
175 1 0.00
176 8 0.02
177 1 0.00
178 14 0.03
180 8 0.02
181 2 0.00
182 14 0.03
184 23 0.05
185 2 0.00
186 51 0.11
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (168 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTAACTTGTGGGCTT
TGAAAGGTTGCCACTAACTTGTGGGCTTTGAAAGTATGCCACTAACTTGTGGGCTTTGAAAAGAT
GCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:39615 original size:32 final size:32
Alignment explanation
Indices: 39550--39776 Score: 276
Period size: 32 Copynumber: 7.4 Consensus size: 32
39540 GCGACTGGCT
**
39550 TGTGGGCTTTGAAA-GGG-TGCCACTGACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* *
39580 TGTGGGATTTGAAATGGGTTGCAACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
*
39612 TGTGGGCTTTGAAATGGTTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
39644 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* *
39676 TGTGGGCTTTGAAATGAGTTGCCACCGACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* **
39708 TGTGGGCTTTGAAAT--GATGCCACTGAC-T-
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
**
39736 TGTGGGCTTTGAAA-GGG-TGCCACTGAC-T-
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
39764 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
39777 GAGATGGACG
Statistics
Matches: 181, Mismatches: 12, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
28 38 0.21
29 2 0.01
30 23 0.13
31 3 0.02
32 115 0.64
ACGTcount: A:0.19, C:0.17, G:0.32, T:0.32
Consensus pattern (32 bp):
TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
Found at i:39680 original size:96 final size:90
Alignment explanation
Indices: 39001--39767 Score: 434
Period size: 85 Copynumber: 8.7 Consensus size: 90
38991 AAGTGCTATT
* * * * * *
39001 AACTTGTGTGAGCTTTGAAAAGAGTCGCCACCGATTCGTGTGGGCTTTGAAAAGAGTTACCACTG
1 AACTTGTGTGGGCTTTGAAATGA-T-GCCACC-A-ACTTGTGGGCTTTG-AAAG-GGTGCCACTG
* * * * *
39066 GC-T-TGTGGGCTTTGAAAAGAG-TGCCACT
60 ACTTGTGTGGGATTTGAAATGAGTTGCAACC
** * * *
39094 AAC-T-TGTGGGCTTTGAAAGTG-TGCCACTGACTTGTGGGCTTTAAAAGGGTGCCA-TTAATT-
1 AACTTGTGTGGGCTTTGAAA-TGATGCCACCAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
* * * *
39154 TGTGGGCTTTGAAAAGAG-TGCCACT
65 TGTGGGATTTGAAATGAGTTGCAACC
* * * ** *
39179 AAC-T-TGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGAC-T-T
1 AACTTGTGTGGGCTTTGAAATGATGCCACCAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGT
* * * *
39240 GTGGGCTTTGAAAAGAG-TGCCACT
66 GTGGGATTTGAAATGAGTTGCAACC
* * * * **
39264 GAC-T-TGTGGGCTTTGAAAGGTTGCCACTAACTTGTGGGCTTTGAAAGTATGCCACTGAC-T-T
1 AACTTGTGTGGGCTTTGAAATGATGCCACCAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGT
* * **
39325 GTGGGCTTTGGAAAT--G-TGCCATT
66 GTGGGATTT-GAAATGAGTTGCAACC
* * * * **
39348 GAC-T-TGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGAGTTGCCACCAAC-T
1 AACTTGTGTGGGCTTTGAAATGATGCCACCAACTTGTGGGCTTTG-AAAG-GGTGCCACTGACTT
* * * * *
39410 -CGTGGGCTTTGAAA-G-GGTGCCACT
64 GTGTGGGATTTGAAATGAGTTGCAACC
* * * ** ** *
39434 GAC-T-TGTGCGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGTATGCCACTGAC--AT
1 AACTTGTGTGGGCTTTGAAATGATGCCACCAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGT
* * * *
39495 GTGGGCTTTGAAA--AGATGCCACT
66 GTGGGATTTGAAATGAGTTGCAACC
* * * * ***
39518 GAC-T-TGTGGACTTTGAAAAGATGCGACTGGCTTGTGGGCTTTGAAAGGGTGCCACTGACTTGT
1 AACTTGTGTGGGCTTTGAAATGATGCCACCAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGT
*
39581 GTGGGATTTGAAATGGGTTGCAACC
66 GTGGGATTTGAAATGAGTTGCAACC
* **
39606 AACTTGTGTGGGCTTTGAAATGGTTTGCCACCAACTTGTGTGGGCTTTGAAATGGGTTGCCACCA
1 AACTTGTGTGGGCTTTGAAAT-G-ATGCCACCAAC-T-TGTGGGCTTTGAAA-GGG-TGCCACTG
* *
39671 ACTTGTGTGGGCTTTGAAATGAGTTGCCACC
60 ACTTGTGTGGGATTTGAAATGAGTTGCAACC
* **
39702 GACTTGTGTGGGCTTTGAAATGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGT
1 AACTTGTGTGGGCTTTGAAATGATGCCACCAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGT
39767 G
66 G
39768 GGCTTTGAAG
Statistics
Matches: 579, Mismatches: 72, Indels: 49
0.83 0.10 0.07
Matches are distributed among these distances:
84 133 0.23
85 183 0.32
86 87 0.15
87 11 0.02
88 8 0.01
89 6 0.01
90 27 0.05
91 17 0.03
92 22 0.04
93 5 0.01
94 22 0.04
95 4 0.01
96 54 0.09
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (90 bp):
AACTTGTGTGGGCTTTGAAATGATGCCACCAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGT
GTGGGATTTGAAATGAGTTGCAACC
Found at i:41037 original size:18 final size:18
Alignment explanation
Indices: 40992--41052 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
40982 TTGGACCTTT
* *
40992 TTTTTTTGCTATTTTTTC
1 TTTTTTTGTTATTTTTTG
*
41010 TTGGTTTTTTTTAATTTTTTG
1 TT--TTTTTGTT-ATTTTTTG
*
41031 TTTTTTTGTTTTTTTTTG
1 TTTTTTTGTTATTTTTTG
41049 TTTT
1 TTTT
41053 GGGTATAAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 13 0.37
19 7 0.20
20 6 0.17
21 9 0.26
ACGTcount: A:0.05, C:0.03, G:0.10, T:0.82
Consensus pattern (18 bp):
TTTTTTTGTTATTTTTTG
Found at i:41052 original size:25 final size:24
Alignment explanation
Indices: 40990--41052 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 24
40980 ATTTGGACCT
* *
40990 TTTTTTTTTGCTATTTTTTCTTGG
1 TTTTTTTTTGTTTTTTTTTCTTGG
** * *
41014 TTTTTTTTAATTTTTTGTTTTTTTG
1 TTTTTTTTTGTTTTTT-TTTCTTGG
41039 TTTTTTTTTGTTTT
1 TTTTTTTTTGTTTT
41053 GGGTATAAAG
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
24 12 0.40
25 18 0.60
ACGTcount: A:0.05, C:0.03, G:0.10, T:0.83
Consensus pattern (24 bp):
TTTTTTTTTGTTTTTTTTTCTTGG
Found at i:44042 original size:60 final size:60
Alignment explanation
Indices: 43949--44129 Score: 344
Period size: 60 Copynumber: 3.0 Consensus size: 60
43939 GCATGTCTTG
43949 ATATGACCAAGCAAATACATCTCGGTATTCTTGGAGTAAGTCAATCAGCTTAGTCCTAGT
1 ATATGACCAAGCAAATACATCTCGGTATTCTTGGAGTAAGTCAATCAGCTTAGTCCTAGT
*
44009 ATATGACCAAGCAAATACATCTCGGTATTCTTGGAGTAAGTGAATCAGCTTAGTCCTAGT
1 ATATGACCAAGCAAATACATCTCGGTATTCTTGGAGTAAGTCAATCAGCTTAGTCCTAGT
*
44069 ATATGACCAAGCAAATACATCTCGGTATTCTTGGAGTAAGTCAATCAGCTTAGCCCTAGT
1 ATATGACCAAGCAAATACATCTCGGTATTCTTGGAGTAAGTCAATCAGCTTAGTCCTAGT
44129 A
1 A
44130 GTCAATCTTA
Statistics
Matches: 118, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 118 1.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (60 bp):
ATATGACCAAGCAAATACATCTCGGTATTCTTGGAGTAAGTCAATCAGCTTAGTCCTAGT
Found at i:47812 original size:13 final size:13
Alignment explanation
Indices: 47794--47818 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47784 ATGTTGCACA
47794 GTATCGATACATT
1 GTATCGATACATT
47807 GTATCGATACAT
1 GTATCGATACAT
47819 GTTGCATTGT
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):
GTATCGATACATT
Found at i:47813 original size:33 final size:33
Alignment explanation
Indices: 47771--47836 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
47761 TACACATTTA
47771 ATTGTATCGATACATGTTGCACAGTATCGATAC
1 ATTGTATCGATACATGTTGCACAGTATCGATAC
**
47804 ATTGTATCGATACATGTTGCATTGTATCGATAC
1 ATTGTATCGATACATGTTGCACAGTATCGATAC
47837 TTGAAAAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (33 bp):
ATTGTATCGATACATGTTGCACAGTATCGATAC
Found at i:47927 original size:13 final size:13
Alignment explanation
Indices: 47909--47934 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
47899 TACACAAAGT
47909 ATGTATCGATACA
1 ATGTATCGATACA
47922 ATGTATCGATACA
1 ATGTATCGATACA
47935 CCATAAAATG
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:50936 original size:13 final size:13
Alignment explanation
Indices: 50918--50943 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
50908 ACACCAAAGT
50918 ATGTATCGATACA
1 ATGTATCGATACA
50931 ATGTATCGATACA
1 ATGTATCGATACA
50944 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:50941 original size:33 final size:33
Alignment explanation
Indices: 50899--50963 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
50889 TAGCCAAACT
* *
50899 TGTATCGATACAC-CAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAAT-TGTATCGATACAA
50932 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
50964 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:57148 original size:13 final size:13
Alignment explanation
Indices: 57130--57168 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
57120 ACATTTTTCT
57130 TTGTATCGATACA
1 TTGTATCGATACA
*
57143 TTGTATCGACACA
1 TTGTATCGATACA
*
57156 CTGTATCGATACA
1 TTGTATCGATACA
57169 GGGGGATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:59772 original size:13 final size:13
Alignment explanation
Indices: 59754--59779 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
59744 ACACCAAAGT
59754 ATGTATCGATACA
1 ATGTATCGATACA
59767 ATGTATCGATACA
1 ATGTATCGATACA
59780 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:59777 original size:33 final size:33
Alignment explanation
Indices: 59735--59799 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
59725 TAGCCAAACT
* *
59735 TGTATCGATACAC-CAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAAT-TGTATCGATACAA
59768 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
59800 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:67529 original size:20 final size:20
Alignment explanation
Indices: 67504--67628 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
67494 TTTTAACTAG
67504 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
67524 ATGTATCGATACATCTGGGTAAAAAGATAAA
1 ATGTATCGATACAT-T--G-----A-A-A-A
*
67555 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAAAA
* * *
67575 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTGAAAA
* * *
67595 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTGAAAA
67615 ATGTATCGATACAT
1 ATGTATCGATACAT
67629 CTAGGTACTT
Statistics
Matches: 89, Mismatches: 5, Indels: 22
0.77 0.04 0.19
Matches are distributed among these distances:
20 65 0.73
21 1 0.01
22 1 0.01
23 2 0.02
28 2 0.02
29 1 0.01
30 2 0.02
31 15 0.17
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:67608 original size:12 final size:12
Alignment explanation
Indices: 67575--67628 Score: 52
Period size: 12 Copynumber: 5.2 Consensus size: 12
67565 ACATTGAAGA
67575 ATGTATCGATAC
1 ATGTATCGATAC
67587 A--T-TC-ATAC
1 ATGTATCGATAC
67595 ATGTATCGATAC
1 ATGTATCGATAC
67607 A--T-TC-ATAC
1 ATGTATCGATAC
67615 ATGTATCGATAC
1 ATGTATCGATAC
67627 AT
1 AT
67629 CTAGGTACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 16
0.68 0.00 0.32
Matches are distributed among these distances:
8 10 0.29
9 4 0.12
10 4 0.12
11 4 0.12
12 12 0.35
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:68768 original size:2 final size:2
Alignment explanation
Indices: 68761--68791 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
68751 ACTAACTATC
68761 AT AT AT 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 AT AT AT A
68792 AACACAAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:69681 original size:166 final size:163
Alignment explanation
Indices: 69488--69924 Score: 420
Period size: 166 Copynumber: 2.6 Consensus size: 163
69478 AAATAATTTA
* * *
69488 AATTTTTCAAAACTGATTTAATATGAATTTAATGACAATATTAGATGAATTTTAAAAATTTTAAA
1 AATTTTTCAAAACTGATTT-ATATGAATTAAATGAAAATATTTGATGAATTTTAAAAATTTTAAA
* *
69553 CTAAGAAAAATCTTTCCTAAAAAAATTATGGAGAAGAAAACTTCGTTTTTCAAAAATAAAGAAAT
65 CT-AGAAAAATCTTTCCT-AAAAAATTATGGAGAAGAAAACTTCGTATTTCAAAAACAAAGAAAT
*
69618 TTCAAGGAAAAAACGAAAAACTCA-GAAAAATAAATG
128 TTCAAGGAAAAAACGAAAAACTCATGAAAAA-AAAGG
* *** * *
69654 AGTTTTTCAAAACTGATTTACTATGAATTAAATGATGTTATTTTATGAATATTAAAAATTTTAAA
1 AATTTTTCAAAACTGATTTA-TATGAATTAAATGAAAATATTTGATGAATTTTAAAAATTTTAAA
* * * * * * * **
69719 CCTAGAAAAATC--CCCTGAAAATATT-TACGAAATAGCAAACTTCGTATTTCGAAAACAGAGGG
65 -CTAGAAAAATCTTTCCT-AAAAAATTAT-GGAGA-AGAAAACTTCGTATTTCAAAAACAAAGAA
* * **
69781 ATTTCAATGAAAAAATGAAAAACTCATGAACTAAAAGG
126 ATTTCAAGGAAAAAACGAAAAACTCATGAAAAAAAAGG
** * * *
69819 AATTTTAAAAAACTAATTTA-ATGGTAATTAAATAAAAAATATTTGATAAATTTTAAAAATTTTA
1 AATTTTTCAAAACTGATTTATAT-G-AATTAAAT-GAAAATATTTGATGAATTTTAAAAATTTTA
*
69883 AA-TAGATGAAAATCTTTCC-AAAAAATTACGGAGAAGAAAACT
63 AACTAGA--AAAATCTTTCCTAAAAAATTATGGAGAAGAAAACT
69925 CTATATTTCG
Statistics
Matches: 216, Mismatches: 42, Indels: 27
0.76 0.15 0.09
Matches are distributed among these distances:
163 3 0.01
164 18 0.08
165 82 0.38
166 109 0.50
167 2 0.01
168 2 0.01
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (163 bp):
AATTTTTCAAAACTGATTTATATGAATTAAATGAAAATATTTGATGAATTTTAAAAATTTTAAAC
TAGAAAAATCTTTCCTAAAAAATTATGGAGAAGAAAACTTCGTATTTCAAAAACAAAGAAATTTC
AAGGAAAAAACGAAAAACTCATGAAAAAAAAGG
Found at i:78484 original size:21 final size:21
Alignment explanation
Indices: 78463--78501 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
78453 TTTAATGATA
78463 AATAA-AAATTAAAAATTTAT
1 AATAATAAATTAAAAATTTAT
**
78483 AATAATATTTTAAAAATTT
1 AATAATAAATTAAAAATTT
78502 TAGATTTTCA
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AATAATAAATTAAAAATTTAT
Found at i:78794 original size:18 final size:17
Alignment explanation
Indices: 78768--78807 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
78758 GATTATTGTC
* *
78768 TTTAATTTATTATTTTAT
1 TTTATTTTATT-TTTTAA
78786 TTTATTTTATTTTTTAA
1 TTTATTTTATTTTTTAA
78803 TTTAT
1 TTTAT
78808 GTTTGTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTATTTTATTTTTTAA
Found at i:79120 original size:148 final size:148
Alignment explanation
Indices: 78943--79238 Score: 380
Period size: 148 Copynumber: 2.0 Consensus size: 148
78933 GTCAATAAAC
* * *
78943 AAAGAATCCTTATAGTATTAAAGTAATTCTCACTTAATTAAAAACT-TAATTACGTAGGAATTAA
1 AAAGAATACTTATAATATTAAAGTAATTCTCACTTAATTAAAAA-TAGAATTACGTAGGAATTAA
* * * * * * * *
79007 AATTAAGATTTT-TTATCATAAAATAGATACTATAGTTTTTATTTTCATAAAACAATAAATGTTA
65 AACTAAGATTTTCTTCT-ATAAAATAAATACTACAATTGTTATTTTCAAAAAACAATAAATATTA
*
79071 AGTAATACTTTATTAACTAT
129 AATAATACTTTATTAACTAT
** * **
79091 AAAGAATACTTATAATATTAAAGTAATTCTCACTTAATTAGTAATAGAATTATGTATTAATTAAA
1 AAAGAATACTTATAATATTAAAGTAATTCTCACTTAATTAAAAATAGAATTACGTAGGAATTAAA
* *
79156 ACTAAGATTTTCTTCTATAAAATAAATATTACAATTGTTATTTTCAAAAAATAATAAATATTAAA
66 ACTAAGATTTTCTTCTATAAAATAAATACTACAATTGTTATTTTCAAAAAACAATAAATATTAAA
*
79221 TAATACTTTATTGACTAT
131 TAATACTTTATTAACTAT
79239 TATTCTTTGT
Statistics
Matches: 126, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
147 1 0.01
148 122 0.97
149 3 0.02
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.40
Consensus pattern (148 bp):
AAAGAATACTTATAATATTAAAGTAATTCTCACTTAATTAAAAATAGAATTACGTAGGAATTAAA
ACTAAGATTTTCTTCTATAAAATAAATACTACAATTGTTATTTTCAAAAAACAATAAATATTAAA
TAATACTTTATTAACTAT
Found at i:84471 original size:30 final size:30
Alignment explanation
Indices: 84395--84472 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 30
84385 TCGATACATT
* *
84395 GAAA-AATGTATCAATACATCTGGGTAAAA
1 GAAAGAATGTATCGATACATATGGGTAAAA
* *
84424 GACAGAATGTATCGATACATATGTGTAAAA
1 GAAAGAATGTATCGATACATATGGGTAAAA
*
84454 GAAAGAATGTATTGATACA
1 GAAAGAATGTATCGATACA
84473 CTGAAAAATG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 3 0.07
30 39 0.93
ACGTcount: A:0.46, C:0.09, G:0.19, T:0.26
Consensus pattern (30 bp):
GAAAGAATGTATCGATACATATGGGTAAAA
Found at i:84491 original size:20 final size:21
Alignment explanation
Indices: 84454--84492 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
84444 ATGTGTAAAA
**
84454 GAAAGAATGTATTGATACACT
1 GAAAGAATGTATCAATACACT
84475 GAAA-AATGTATCAATACA
1 GAAAGAATGTATCAATACA
84493 TCTAGGTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (21 bp):
GAAAGAATGTATCAATACACT
Done.