Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_148
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: 164322
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:3778 original size:13 final size:13
Alignment explanation
Indices: 3760--3790 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3750 ACCGTATGCA
3760 TTTTTTTC-ATTT
1 TTTTTTTCGATTT
3772 TTTTTTTCGATTT
1 TTTTTTTCGATTT
3785 TTTTTT
1 TTTTTT
3791 GAATCTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.06, C:0.06, G:0.03, T:0.84
Consensus pattern (13 bp):
TTTTTTTCGATTT
Found at i:5759 original size:9 final size:9
Alignment explanation
Indices: 5747--5781 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
5737 ATTCAAAAAA
5747 ATTATTTTT
1 ATTATTTTT
5756 ATTA-TTTT
1 ATTATTTTT
5764 ATTATTTTT
1 ATTATTTTT
5773 ATTATTTTT
1 ATTATTTTT
5782 TTGTAACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
ATTATTTTT
Found at i:5769 original size:17 final size:17
Alignment explanation
Indices: 5747--5780 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5737 ATTCAAAAAA
5747 ATTATTTTTATTATTTT
1 ATTATTTTTATTATTTT
5764 ATTATTTTTATTATTTT
1 ATTATTTTTATTATTTT
5781 TTTGTAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTATTTTTATTATTTT
Found at i:5856 original size:12 final size:12
Alignment explanation
Indices: 5839--5863 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5829 GGAGAAGTAT
5839 AAAAGAAAAAAA
1 AAAAGAAAAAAA
5851 AAAAGAAAAAAA
1 AAAAGAAAAAAA
5863 A
1 A
5864 GCAAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAAA
Found at i:5857 original size:23 final size:22
Alignment explanation
Indices: 5819--5874 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
5809 TTTTGTAATT
* *
5819 GAAAAAAAAAGGAGAAGTATAAAA
1 GAAAAAAAAAGAAGAA--AAAAAA
5843 GAAAAAAAAA-AAGAAAAAAAA
1 GAAAAAAAAAGAAGAAAAAAAA
*
5864 GCAAAAAAAAG
1 GAAAAAAAAAG
5875 TGTTAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 14 0.50
23 4 0.14
24 10 0.36
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.04
Consensus pattern (22 bp):
GAAAAAAAAAGAAGAAAAAAAA
Found at i:5911 original size:15 final size:15
Alignment explanation
Indices: 5879--5914 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
5869 AAAAAGTGTT
**
5879 AAAAAATCGAAGTTA
1 AAAAAATCGAAGAGA
5894 AAAAAATCGAAGAGA
1 AAAAAATCGAAGAGA
5909 AAAAAA
1 AAAAAA
5915 AAGTGCTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.69, C:0.06, G:0.14, T:0.11
Consensus pattern (15 bp):
AAAAAATCGAAGAGA
Found at i:16720 original size:15 final size:14
Alignment explanation
Indices: 16684--16738 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 14
16674 TCTATTGATC
16684 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
16698 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
16712 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
*
16727 GAAAGAAAAGAA
1 GAGA-AAAAGAA
16739 TAAGGAGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 16 0.47
15 18 0.53
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:21301 original size:23 final size:23
Alignment explanation
Indices: 21258--21301 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
21248 GTGAAAAAGA
* *
21258 AATTGAAGAAAGAAGAGAAAATG
1 AATTGAAAAAAGAAGACAAAATG
21281 AATTAGAAAAAAGAA-ACAAAA
1 AATT-GAAAAAAGAAGACAAAA
21302 GAAAAAGACG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 9 0.50
24 9 0.50
ACGTcount: A:0.68, C:0.02, G:0.18, T:0.11
Consensus pattern (23 bp):
AATTGAAAAAAGAAGACAAAATG
Found at i:32018 original size:14 final size:13
Alignment explanation
Indices: 31956--32017 Score: 97
Period size: 13 Copynumber: 4.7 Consensus size: 13
31946 TTATAGATTC
31956 AAAAAAAATCGAA
1 AAAAAAAATCGAA
31969 AAAAAAAATCGAA
1 AAAAAAAATCGAA
*
31982 AAAAAAAATTGAA
1 AAAAAAAATCGAA
*
31995 AAAAAAAATTTGAA
1 AAAAAAAA-TCGAA
32009 AAAAAAAAT
1 AAAAAAAAT
32018 TGCATACGGT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
13 34 0.72
14 13 0.28
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.13
Consensus pattern (13 bp):
AAAAAAAATCGAA
Found at i:34289 original size:17 final size:18
Alignment explanation
Indices: 34250--34291 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
34240 AAGAAGAAAA
34250 ACAAAA-AGATGAGTGAT
1 ACAAAAGAGATGAGTGAT
*
34267 AAAAAAGAGA-GAGTGAT
1 ACAAAAGAGATGAGTGAT
*
34284 TCAAAAGA
1 ACAAAAGA
34292 AAAAGAAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (18 bp):
ACAAAAGAGATGAGTGAT
Found at i:37384 original size:20 final size:20
Alignment explanation
Indices: 37338--37384 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
37328 AGCTCGTTTC
*
37338 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
37358 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
37378 CAGCTCA
1 CAGCTCA
37385 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:38953 original size:22 final size:22
Alignment explanation
Indices: 38928--38972 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
38918 AGAAGTGAGC
*
38928 AAAAAAAGAAAAAAAAGTAAAA
1 AAAAAAACAAAAAAAAGTAAAA
* *
38950 AAAAGAACAAAAAAAAGTGAAA
1 AAAAAAACAAAAAAAAGTAAAA
38972 A
1 A
38973 GTCTTGTGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.82, C:0.02, G:0.11, T:0.04
Consensus pattern (22 bp):
AAAAAAACAAAAAAAAGTAAAA
Found at i:38972 original size:10 final size:9
Alignment explanation
Indices: 38928--38963 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
38918 AGAAGTGAGC
38928 AAAAAAAGA
1 AAAAAAAGA
38937 AAAAAAAGTA
1 AAAAAAAG-A
38947 AAAAAAAGA
1 AAAAAAAGA
38956 ACAAAAAA
1 A-AAAAAA
38964 AAGTGAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 10 0.40
10 15 0.60
ACGTcount: A:0.86, C:0.03, G:0.08, T:0.03
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:40069 original size:48 final size:47
Alignment explanation
Indices: 39990--40095 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
39980 GAGTGTCATG
*
39990 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
40038 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
40086 GAAAAAGAAA
1 GAAAAAGAAA
40096 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:41813 original size:20 final size:20
Alignment explanation
Indices: 41767--41813 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
41757 AGCTCGTTTC
*
41767 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
41787 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
41807 CAGCTCA
1 CAGCTCA
41814 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:45299 original size:22 final size:22
Alignment explanation
Indices: 45269--45312 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
45259 TTTGGTATTT
45269 GGGAATTGGTAAGAAATGGTAA
1 GGGAATTGGTAAGAAATGGTAA
* *
45291 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTAAGAAATGGTAA
45313 TGGTTCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.02, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTAAGAAATGGTAA
Found at i:52845 original size:14 final size:14
Alignment explanation
Indices: 52818--52851 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
52808 TATAAAAATT
52818 TAAACTAAATAAAA
1 TAAACTAAATAAAA
52832 TAAA-TAAATAAAAA
1 TAAACTAAAT-AAAA
52846 TAAACT
1 TAAACT
52852 TTACAACTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.28
14 12 0.67
15 1 0.06
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAACTAAATAAAA
Found at i:54262 original size:18 final size:18
Alignment explanation
Indices: 54241--54279 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
54231 TTTCTTCAAC
*
54241 TTCTATTTCAAATTTCTT
1 TTCTATTTCAAATTCCTT
* *
54259 TTCTGTTTCACATTCCTT
1 TTCTATTTCAAATTCCTT
54277 TTC
1 TTC
54280 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.15, C:0.23, G:0.03, T:0.59
Consensus pattern (18 bp):
TTCTATTTCAAATTCCTT
Found at i:59788 original size:18 final size:18
Alignment explanation
Indices: 59732--59791 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
59722 AGTGCGAGCG
59732 AGAAAAAGAAATCAAAAGAAA
1 AGAAAAAGAAATC--AA-AAA
* **
59753 AGAAAAAGAGATTGAAAA
1 AGAAAAAGAAATCAAAAA
59771 AGAAAAAGAAATCAAAAA
1 AGAAAAAGAAATCAAAAA
59789 AGA
1 AGA
59792 GAGTGAGGTC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 21 0.64
19 1 0.03
21 11 0.33
ACGTcount: A:0.73, C:0.03, G:0.17, T:0.07
Consensus pattern (18 bp):
AGAAAAAGAAATCAAAAA
Found at i:62021 original size:16 final size:16
Alignment explanation
Indices: 61983--62013 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
61973 GTATGGGAGT
61983 ATACATGAATGGTTGA
1 ATACATGAATGGTTGA
61999 ATACATGAATGGTTG
1 ATACATGAATGGTTG
62014 GATTCATGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.32
Consensus pattern (16 bp):
ATACATGAATGGTTGA
Found at i:66749 original size:79 final size:81
Alignment explanation
Indices: 66613--66795 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
66603 TCGAATGATG
* *
66613 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
66677 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * * **
66692 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
66754 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
66772 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
66796 TGAACGAGTA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 59 0.66
80 30 0.33
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:66804 original size:40 final size:39
Alignment explanation
Indices: 66614--66797 Score: 212
Period size: 40 Copynumber: 4.6 Consensus size: 39
66604 CGAATGATGT
* * * *
66614 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-AA
* *
66654 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA-A
*
66694 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
66732 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
66773 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
66798 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:66819 original size:79 final size:79
Alignment explanation
Indices: 66666--66820 Score: 208
Period size: 79 Copynumber: 2.0 Consensus size: 79
66656 GGACTAAGAT
* **
66666 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
66731 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* *
66745 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
*
66808 TACATCC-GGTTAA
63 TAAATCCGGGTTAA
66821 ATTCTGAAGG
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
78 2 0.03
79 41 0.61
80 24 0.36
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:77097 original size:20 final size:20
Alignment explanation
Indices: 77051--77097 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
77041 AGCTCGTTTC
*
77051 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
77071 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
77091 CAGCTCA
1 CAGCTCA
77098 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:78630 original size:14 final size:14
Alignment explanation
Indices: 78613--78664 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
78603 AAAAAAAGTG
78613 AAAAAAATTGAGCA
1 AAAAAAATTGAGCA
** *
78627 AAAAAAAAAGAAAGAA
1 AAAAAAATTG--AGCA
*
78643 AAAAAAAGTGAGCA
1 AAAAAAATTGAGCA
78657 AAAAAAAT
1 AAAAAAAT
78665 CAAGTTAAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
14 18 0.62
16 11 0.38
ACGTcount: A:0.75, C:0.04, G:0.13, T:0.08
Consensus pattern (14 bp):
AAAAAAATTGAGCA
Found at i:80357 original size:30 final size:30
Alignment explanation
Indices: 80323--80419 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
80313 TAAACTAAAA
*
80323 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
80353 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
80383 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
80412 ATGAGCTA
1 -TGAGCTA
80420 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:82651 original size:6 final size:6
Alignment explanation
Indices: 82635--82684 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
82625 TTTCTTTTTA
*
82635 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
82684 T
1 T
82685 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:82667 original size:37 final size:37
Alignment explanation
Indices: 82624--82694 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
82614 CTTGCCTCTC
82624 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
82661 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
82695 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:82695 original size:16 final size:16
Alignment explanation
Indices: 82620--82680 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
82610 GCCTCTTGCC
*
82620 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
82636 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
82652 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
82668 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
82681 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:83548 original size:11 final size:11
Alignment explanation
Indices: 83541--83583 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
83531 ATTTTTTGAT
83541 TTTTTTTTTAA
1 TTTTTTTTTAA
*
83552 TTTTTTTTTCGA
1 TTTTTTTTT-AA
*
83564 TTTTTTTTCAA
1 TTTTTTTTTAA
83575 TTTTTTTTT
1 TTTTTTTTT
83584 CAAATTTCCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.12, C:0.05, G:0.02, T:0.81
Consensus pattern (11 bp):
TTTTTTTTTAA
Found at i:83549 original size:12 final size:12
Alignment explanation
Indices: 83532--83571 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
83522 TATACTTCGA
83532 TTTTTTGATTTT
1 TTTTTTGATTTT
*
83544 TTTTTTAATTTT
1 TTTTTTGATTTT
*
83556 TTTTTCGATTTT
1 TTTTTTGATTTT
83568 TTTT
1 TTTT
83572 CAATTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.10, C:0.03, G:0.05, T:0.82
Consensus pattern (12 bp):
TTTTTTGATTTT
Found at i:83558 original size:23 final size:23
Alignment explanation
Indices: 83532--83584 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
83522 TATACTTCGA
*
83532 TTTTTT-GATTTTTTTTTTAATTT
1 TTTTTTCGA-TTTTTTTTCAATTT
83555 TTTTTTCGATTTTTTTTCAATTT
1 TTTTTTCGATTTTTTTTCAATTT
83578 TTTTTTC
1 TTTTTTC
83585 AAATTTCCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 26 0.93
24 2 0.07
ACGTcount: A:0.11, C:0.06, G:0.04, T:0.79
Consensus pattern (23 bp):
TTTTTTCGATTTTTTTTCAATTT
Found at i:83579 original size:12 final size:12
Alignment explanation
Indices: 83539--83586 Score: 71
Period size: 12 Copynumber: 4.1 Consensus size: 12
83529 CGATTTTTTG
*
83539 ATTTTTTTTTTA
1 ATTTTTTTTTCA
*
83551 ATTTTTTTTTCG
1 ATTTTTTTTTCA
83563 A-TTTTTTTTCA
1 ATTTTTTTTTCA
83574 ATTTTTTTTTCA
1 ATTTTTTTTTCA
83586 A
1 A
83587 ATTTCCTCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
11 10 0.31
12 22 0.69
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (12 bp):
ATTTTTTTTTCA
Found at i:85287 original size:30 final size:30
Alignment explanation
Indices: 85253--85349 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
85243 TAAACTAAAA
*
85253 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* * * * * * *
85283 TGAGCTGAGACTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
*
85313 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
85342 ATGAGCTA
1 -TGAGCTA
85350 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
29 1 0.02
30 49 0.98
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
Found at i:86451 original size:48 final size:47
Alignment explanation
Indices: 86374--86477 Score: 131
Period size: 48 Copynumber: 2.2 Consensus size: 47
86364 AGTATCATGG
*
86374 AAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATCGA
1 AAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATCGA
* *
86422 AAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATTGA
1 AAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATCGA
86470 AAAAGAAA
1 AAAAGAAA
86478 GAAAAGACAA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 38 0.76
49 8 0.16
50 4 0.08
ACGTcount: A:0.60, C:0.02, G:0.24, T:0.14
Consensus pattern (47 bp):
AAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATCGA
Found at i:88195 original size:20 final size:20
Alignment explanation
Indices: 88149--88195 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
88139 AGCTCGTTTC
*
88149 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
88169 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
88189 CAGCTCA
1 CAGCTCA
88196 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:94877 original size:4 final size:4
Alignment explanation
Indices: 94868--94899 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
94858 TTAAACTAAG
94868 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
94900 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:96305 original size:23 final size:22
Alignment explanation
Indices: 96253--96305 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
96243 TCCACGTCTT
*
96253 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
96275 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
96298 TTTCTTTT
1 TTTCTTTT
96306 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:100135 original size:23 final size:22
Alignment explanation
Indices: 100083--100135 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
100073 TCCACGTCTT
*
100083 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
100105 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
100128 TTTCTTTT
1 TTTCTTTT
100136 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:106524 original size:13 final size:14
Alignment explanation
Indices: 106478--106530 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 14
106468 AAAAAAATCC
106478 GAAAAAAAAAAGTT
1 GAAAAAAAAAAGTT
106492 -AAAAAAAAAAGTTT
1 GAAAAAAAAAAG-TT
106506 CG-AAAAAAAAA-TT
1 -GAAAAAAAAAAGTT
106519 GCAAAAAAAAAA
1 G-AAAAAAAAAA
106531 ATTGCATACG
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
12 1 0.03
13 13 0.38
14 11 0.32
15 9 0.26
ACGTcount: A:0.74, C:0.04, G:0.09, T:0.13
Consensus pattern (14 bp):
GAAAAAAAAAAGTT
Found at i:106530 original size:15 final size:15
Alignment explanation
Indices: 106466--106536 Score: 60
Period size: 15 Copynumber: 4.9 Consensus size: 15
106456 CGTAGCTTCG
*
106466 AAAAAAAAA-TCCGAA
1 AAAAAAAAATTGC-AA
*
106481 AAAAAAAAGTT--AA
1 AAAAAAAAATTGCAA
* * *
106494 AAAAAAAAGTTTC-G
1 AAAAAAAAATTGCAA
106508 AAAAAAAAATTGCAA
1 AAAAAAAAATTGCAA
106523 AAAAAAAAATTGCA
1 AAAAAAAAATTGCA
106537 TACGGTCTAG
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
13 13 0.28
14 11 0.23
15 22 0.47
16 1 0.02
ACGTcount: A:0.70, C:0.07, G:0.08, T:0.14
Consensus pattern (15 bp):
AAAAAAAAATTGCAA
Found at i:108816 original size:24 final size:25
Alignment explanation
Indices: 108789--108842 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
108779 ATGAGTGATA
*
108789 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
108813 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
108837 AAAAAA
1 AAAAAA
108843 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:109931 original size:15 final size:15
Alignment explanation
Indices: 109896--109968 Score: 80
Period size: 15 Copynumber: 5.1 Consensus size: 15
109886 AAATCGTAGC
*
109896 TTCGAAAAAAAAAAG
1 TTCGAAAAAAAAAAT
*
109911 TT--AAAAAAAAAGT
1 TTCGAAAAAAAAAAT
*
109924 TTCGAAAAAAAAAAA
1 TTCGAAAAAAAAAAT
*
109939 TCCGAAAAAAAAAAT
1 TTCGAAAAAAAAAAT
*
109954 TGC-AAAAAAAAAAT
1 TTCGAAAAAAAAAAT
109968 T
1 T
109969 GCATACGGTC
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
13 11 0.22
14 12 0.24
15 26 0.53
ACGTcount: A:0.68, C:0.07, G:0.08, T:0.16
Consensus pattern (15 bp):
TTCGAAAAAAAAAAT
Found at i:109946 original size:14 final size:14
Alignment explanation
Indices: 109929--109967 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
109919 AAAGTTTCGA
109929 AAAAAAAAAATC-C
1 AAAAAAAAAATCGC
*
109942 GAAAAAAAAAATTGC
1 -AAAAAAAAAATCGC
109957 AAAAAAAAAAT
1 AAAAAAAAAAT
109968 TGCATACGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 22 0.96
15 1 0.04
ACGTcount: A:0.77, C:0.08, G:0.05, T:0.10
Consensus pattern (14 bp):
AAAAAAAAAATCGC
Found at i:109946 original size:28 final size:28
Alignment explanation
Indices: 109896--109966 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
109886 AAATCGTAGC
* *
109896 TTCGAAAAAAAAAAGTTAAAAAAAAAGT
1 TTCGAAAAAAAAAAATCAAAAAAAAAGT
*
109924 TTCGAAAAAAAAAAATCCGAAAAAAAAAAT
1 TTCGAAAAAAAAAAAT-C-AAAAAAAAAGT
*
109954 TGC-AAAAAAAAAA
1 TTCGAAAAAAAAAA
109967 TTGCATACGG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 15 0.41
29 10 0.27
30 12 0.32
ACGTcount: A:0.70, C:0.07, G:0.08, T:0.14
Consensus pattern (28 bp):
TTCGAAAAAAAAAAATCAAAAAAAAAGT
Found at i:114768 original size:41 final size:40
Alignment explanation
Indices: 114708--114788 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 40
114698 AGACTTTTCA
*
114708 CTTTTTTTTAAACTTGATTTTTTTTTGCTCACCTTTTTTTTT
1 CTTTTTTTTAAACTCGATTTTTTTTTG-TCA-CTTTTTTTTT
114750 CTTTTTTTT-AACTCGATTTTTTTTTGTCACTTTTTTTTT
1 CTTTTTTTTAAACTCGATTTTTTTTTGTCACTTTTTTTTT
114789 GAATTTTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
39 10 0.26
40 3 0.08
41 16 0.42
42 9 0.24
ACGTcount: A:0.11, C:0.14, G:0.05, T:0.70
Consensus pattern (40 bp):
CTTTTTTTTAAACTCGATTTTTTTTTGTCACTTTTTTTTT
Found at i:114796 original size:41 final size:42
Alignment explanation
Indices: 114709--114816 Score: 125
Period size: 41 Copynumber: 2.6 Consensus size: 42
114699 GACTTTTCAC
* *
114709 TTTTTTTTAAACTTGATTTTTTTTTGCTCACCTTTTTTTTTC
1 TTTTTTTTAAACTCGATTTTTTTTTGCTCACCTTTTTTTTTA
114751 TTTTTTTT-AACTCGATTTTTTTTTG-TCA-CTTTTTTTTTGAA
1 TTTTTTTTAAACTCGATTTTTTTTTGCTCACCTTTTTTTTT--A
* *
114792 TTTTTTTTCAA-TCAAATTTTTTTTT
1 TTTTTTTTAAACTC-GATTTTTTTTT
114817 TCGAAATTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 8
0.84 0.04 0.11
Matches are distributed among these distances:
39 10 0.17
40 3 0.05
41 26 0.44
42 20 0.34
ACGTcount: A:0.15, C:0.11, G:0.05, T:0.69
Consensus pattern (42 bp):
TTTTTTTTAAACTCGATTTTTTTTTGCTCACCTTTTTTTTTA
Found at i:114823 original size:15 final size:15
Alignment explanation
Indices: 114780--114829 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
114770 TTTTTGTCAC
114780 TTTTTTTTT-G-AAT
1 TTTTTTTTTCGAAAT
*
114793 TTTTTTTCAATC-AAAT
1 TTTTTTT--TTCGAAAT
114809 TTTTTTTTTCGAAAT
1 TTTTTTTTTCGAAAT
114824 TTTTTT
1 TTTTTT
114830 GATTTTTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
13 7 0.23
14 2 0.07
15 11 0.37
16 10 0.33
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.70
Consensus pattern (15 bp):
TTTTTTTTTCGAAAT
Found at i:115429 original size:14 final size:13
Alignment explanation
Indices: 115410--115449 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
115400 AAAGGAGAAG
115410 AAATTCAGAAAAAA
1 AAATTC-GAAAAAA
115424 AAATTC-AAAAAA
1 AAATTCGAAAAAA
115436 AAA-TCGAAAAAA
1 AAATTCGAAAAAA
115448 AA
1 AA
115450 GGAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.08
12 17 0.68
14 6 0.24
ACGTcount: A:0.75, C:0.07, G:0.05, T:0.12
Consensus pattern (13 bp):
AAATTCGAAAAAA
Found at i:115435 original size:12 final size:12
Alignment explanation
Indices: 115417--115477 Score: 58
Period size: 11 Copynumber: 5.2 Consensus size: 12
115407 AAGAAATTCA
115417 GAAAAAAAAATTC
1 GAAAAAAAAA-TC
115430 -AAAAAAAAATC
1 GAAAAAAAAATC
*
115441 G-AAAAAAAA-G
1 GAAAAAAAAATC
115451 GAAAAAAAAAGT-
1 GAAAAAAAAA-TC
115463 GACAAAAAAAATC
1 GA-AAAAAAAATC
115476 GA
1 GA
115478 GTTAAAAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
10 1 0.02
11 18 0.44
12 12 0.29
13 10 0.24
ACGTcount: A:0.74, C:0.07, G:0.11, T:0.08
Consensus pattern (12 bp):
GAAAAAAAAATC
Found at i:116519 original size:18 final size:18
Alignment explanation
Indices: 116493--116595 Score: 73
Period size: 18 Copynumber: 5.6 Consensus size: 18
116483 AAATTGAAAG
*
116493 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
116511 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
* *
116529 AAAAGAAAAAGAAATCAA
1 AAAAGAAAAAGAAAACGA
** *
116547 AAAAGTGAGAGAAAA-GA
1 AAAAGAAAAAGAAAACGA
* *
116564 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
116585 AAAAGAAAAAG
1 AAAAGAAAAAG
116596 CGAAAAAAGA
Statistics
Matches: 64, Mismatches: 17, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
17 5 0.08
18 40 0.62
19 12 0.19
20 1 0.02
21 6 0.09
ACGTcount: A:0.72, C:0.04, G:0.17, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:116521 original size:6 final size:6
Alignment explanation
Indices: 116489--116595 Score: 58
Period size: 6 Copynumber: 17.7 Consensus size: 6
116479 AGAGAAATTG
* * ** *
116489 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * * *
116536 AAAGAA ATCA-AA AAAGTG AGAG-A AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
116586 AAAGAA AAAG
1 AAAGAA AAAG
116596 CGAAAAAAGA
Statistics
Matches: 74, Mismatches: 21, Indels: 13
0.69 0.19 0.12
Matches are distributed among these distances:
5 7 0.09
6 55 0.74
7 8 0.11
8 4 0.05
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:116575 original size:14 final size:14
Alignment explanation
Indices: 116555--116593 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
116545 AAAAAAGTGA
116555 GAGAAAAGAAAA-T
1 GAGAAAAGAAAATT
116568 GAAGAAAAGAAAATT
1 G-AGAAAAGAAAATT
116583 GA-AAAAGAAAA
1 GAGAAAAGAAAA
116594 AGCGAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 10 0.42
14 12 0.50
15 2 0.08
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.08
Consensus pattern (14 bp):
GAGAAAAGAAAATT
Found at i:119080 original size:20 final size:18
Alignment explanation
Indices: 119035--119081 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 18
119025 TTTTTCTAGA
119035 AAGTTCATGTCTTAATTT
1 AAGTTCATGTCTTAATTT
*
119053 AGGTTCAT-TACTTAATCATT
1 AAGTTCATGT-CTTAAT--TT
119073 AAGTTCATG
1 AAGTTCATG
119082 AATGGACTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 1 0.04
18 13 0.57
20 9 0.39
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.45
Consensus pattern (18 bp):
AAGTTCATGTCTTAATTT
Found at i:131909 original size:13 final size:12
Alignment explanation
Indices: 131893--132011 Score: 79
Period size: 12 Copynumber: 10.0 Consensus size: 12
131883 TTTTTTCGCT
131893 TTTTCTTTTTCAA
1 TTTTCTTTTTC-A
131906 TTTTCTTTTCTTCA
1 TTTTC-TTT-TTCA
131920 TTTTCTTTTTC-
1 TTTTCTTTTTCA
* *
131931 TTTCACTTTTTGA
1 TTT-TCTTTTTCA
131944 -TTTCTTTTTC-
1 TTTTCTTTTTCA
** *
131954 TTTTGCAATTTCT
1 TTTT-CTTTTTCA
*
131967 TTTTCTTTTTCG
1 TTTTCTTTTTCA
*
131979 TTTTCTTTTT-G
1 TTTTCTTTTTCA
131990 TTTTC--TTTCA
1 TTTTCTTTTTCA
*
132000 ATTTCTTTTTCA
1 TTTTCTTTTTCA
132012 ATCTCTTTCT
Statistics
Matches: 85, Mismatches: 11, Indels: 21
0.73 0.09 0.18
Matches are distributed among these distances:
9 3 0.04
10 4 0.05
11 18 0.21
12 36 0.42
13 12 0.14
14 9 0.11
15 3 0.04
ACGTcount: A:0.08, C:0.17, G:0.03, T:0.71
Consensus pattern (12 bp):
TTTTCTTTTTCA
Found at i:131922 original size:14 final size:14
Alignment explanation
Indices: 131893--131929 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
131883 TTTTTTCGCT
131893 TTTTC-TTTTTCAA
1 TTTTCTTTTTTCAA
131906 TTTTCTTTTCTTC-A
1 TTTTCTTTT-TTCAA
131920 TTTTCTTTTT
1 TTTTCTTTTT
131930 CTTTCACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.27
14 13 0.59
15 3 0.14
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTCTTTTTTCAA
Found at i:131929 original size:15 final size:15
Alignment explanation
Indices: 131893--131932 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
131883 TTTTTTCGCT
131893 TTTTCTTTTTC--AA
1 TTTTCTTTTTCTTAA
*
131906 TTTTC-TTTTCTTCA
1 TTTTCTTTTTCTTAA
131920 TTTTCTTTTTCTT
1 TTTTCTTTTTCTT
131933 TCACTTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
12 5 0.22
13 5 0.22
14 6 0.26
15 7 0.30
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTCTTTTTCTTAA
Found at i:131988 original size:18 final size:18
Alignment explanation
Indices: 131891--131993 Score: 91
Period size: 18 Copynumber: 5.6 Consensus size: 18
131881 TCTTTTTTCG
131891 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTC-ATTTT
* *
131910 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCATTTT
** *
131930 CTTTCACTTTTTGA-TTT
1 CTTTTTCTTTTTCATTTT
* *
131947 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCATTTT
*
131965 CTTTTTCTTTTTCGTTTT
1 CTTTTTCTTTTTCATTTT
*
131983 CTTTTTGTTTT
1 CTTTTTCTTTT
131994 CTTTCAATTT
Statistics
Matches: 66, Mismatches: 15, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
17 13 0.20
18 33 0.50
19 4 0.06
20 8 0.12
21 8 0.12
ACGTcount: A:0.07, C:0.17, G:0.04, T:0.73
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:132010 original size:6 final size:6
Alignment explanation
Indices: 131891--131997 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
131881 TCTTTTTTCG
* * **
131891 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTTTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
131942 -GATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
131989 -GTTTT CTTT
1 CTTTTT CTTT
131998 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 23, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
5 7 0.09
6 55 0.74
7 9 0.12
8 3 0.04
ACGTcount: A:0.07, C:0.17, G:0.04, T:0.73
Consensus pattern (6 bp):
CTTTTT
Found at i:135048 original size:30 final size:30
Alignment explanation
Indices: 135014--135095 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 30
135004 TTTGAAAAGA
*
135014 AAAAAGAAAAAGAAAATGAAA-ATGAGATTG
1 AAAAAGAAAAAGAAAA-GAAATATGAGAGTG
* * *
135044 AAAAAGAGAACGAAAAGAAATTTGAGAGTG
1 AAAAAGAAAAAGAAAAGAAATATGAGAGTG
* *
135074 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAAAG-AAAAGAAAT
135096 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 4 0.09
30 30 0.70
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (30 bp):
AAAAAGAAAAAGAAAAGAAATATGAGAGTG
Found at i:135068 original size:24 final size:24
Alignment explanation
Indices: 135019--135065 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
135009 AAAGAAAAAA
* *
135019 GAAAAAGAAAATGAAAATGAGATT
1 GAAAAAGAAAACGAAAATGAAATT
*
135043 GAAAAAGAGAACGAAAA-GAAATT
1 GAAAAAGAAAACGAAAATGAAATT
135066 TGAGAGTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.64, C:0.02, G:0.21, T:0.13
Consensus pattern (24 bp):
GAAAAAGAAAACGAAAATGAAATT
Found at i:137210 original size:30 final size:29
Alignment explanation
Indices: 137176--137268 Score: 84
Period size: 30 Copynumber: 3.2 Consensus size: 29
137166 AGCTCACTCC
137176 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ATTCAGCTCACGAGCTAAACCT
* * * * *
137206 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAA-TTCAGCTCACGAGCTAAACCT
* *
137236 CAGCTCAA--C-GCTCACGAGCTAAAGCT
1 TAGCTCAATTCAGCTCACGAGCTAAACCT
137262 TAGCTCA
1 TAGCTCA
137269 TTTTAGTTTA
Statistics
Matches: 49, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
26 17 0.35
27 1 0.02
29 1 0.02
30 30 0.61
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (29 bp):
TAGCTCAATTCAGCTCACGAGCTAAACCT
Found at i:141609 original size:30 final size:30
Alignment explanation
Indices: 141533--141618 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 30
141523 TTCAACTCAC
*
141533 GAGCTAAACCTTAGCTCAACTTCAGCTTAG
1 GAGCTAAACCTTAGCTCAACTTTAGCTTAG
* *
141563 GAG-TATAATCTCAGCTCAACTTTAGCTTAAG
1 GAGCTA-AACCTTAGCTCAACTTTAGCTT-AG
* *
141594 G-GCTAAAGCTTAGCTC-ATTTTAGCT
1 GAGCTAAACCTTAGCTCAACTTTAGCT
141619 CAAACCCAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
29 10 0.21
30 32 0.68
31 5 0.11
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.31
Consensus pattern (30 bp):
GAGCTAAACCTTAGCTCAACTTTAGCTTAG
Found at i:146405 original size:11 final size:11
Alignment explanation
Indices: 146389--146418 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
146379 TGAAATTTTC
146389 AATGTAATTGT
1 AATGTAATTGT
146400 AATGTAATTGT
1 AATGTAATTGT
146411 AATGTAAT
1 AATGTAAT
146419 GTAGGGTGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (11 bp):
AATGTAATTGT
Found at i:148607 original size:23 final size:22
Alignment explanation
Indices: 148555--148607 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
148545 TCCACGTCTT
*
148555 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
148577 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
148600 TTTCTTTT
1 TTTCTTTT
148608 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:149772 original size:7 final size:7
Alignment explanation
Indices: 149760--149789 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
149750 ATTCAAATGA
149760 TCAAAAG
1 TCAAAAG
149767 TCAAAAG
1 TCAAAAG
149774 TCAAAAG
1 TCAAAAG
149781 TCAAAAG
1 TCAAAAG
149788 TC
1 TC
149790 CTTTACAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.53, C:0.17, G:0.13, T:0.17
Consensus pattern (7 bp):
TCAAAAG
Found at i:150592 original size:20 final size:19
Alignment explanation
Indices: 150552--150612 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 19
150542 ACCAATAAAA
150552 TAAATGAGCT-GAATTGTAGC
1 TAAATGAGCTCG-ATTG-AGC
150572 TAAATTGAGCTCGATTGAGC
1 TAAA-TGAGCTCGATTGAGC
150592 TGAAATGAGCTC-ATTTGAGC
1 T-AAATGAGCTCGA-TTGAGC
150612 T
1 T
150613 GGTCGGAGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
19 1 0.03
20 22 0.59
21 13 0.35
22 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (19 bp):
TAAATGAGCTCGATTGAGC
Found at i:154341 original size:7 final size:7
Alignment explanation
Indices: 154329--154365 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
154319 ATTCAAATGA
154329 TCAAAAG
1 TCAAAAG
154336 TCAAAAG
1 TCAAAAG
154343 TCAAAAG
1 TCAAAAG
154350 TCAAAAG
1 TCAAAAG
154357 TCAAAAG
1 TCAAAAG
154364 TC
1 TC
154366 CCTTACAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.54, C:0.16, G:0.14, T:0.16
Consensus pattern (7 bp):
TCAAAAG
Found at i:155176 original size:20 final size:19
Alignment explanation
Indices: 155136--155196 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 19
155126 ACCAATAAAA
155136 TAAATGAGCT-GAATTGTAGC
1 TAAATGAGCTCG-ATTG-AGC
155156 TAAATTGAGCTCGATTGAGC
1 TAAA-TGAGCTCGATTGAGC
155176 TGAAATGAGCTC-ATTTGAGC
1 T-AAATGAGCTCGA-TTGAGC
155196 T
1 T
155197 GGTCGGAGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
19 1 0.03
20 22 0.59
21 13 0.35
22 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (19 bp):
TAAATGAGCTCGATTGAGC
Found at i:156256 original size:18 final size:18
Alignment explanation
Indices: 156230--156334 Score: 75
Period size: 18 Copynumber: 5.6 Consensus size: 18
156220 AAATTGAAAG
*
156230 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
156248 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
*
156266 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAAACGA
** * *
156284 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
156302 AAATGAAGAAAAGAAAATTGAA
1 AAAAG-A-AAAAGAAAA-CG-A
156324 AAAAGAAAAAG
1 AAAAGAAAAAG
156335 CGAAAAAAGA
Statistics
Matches: 66, Mismatches: 17, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
18 47 0.71
20 12 0.18
21 2 0.03
22 5 0.08
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:156258 original size:6 final size:6
Alignment explanation
Indices: 156226--156334 Score: 67
Period size: 6 Copynumber: 17.7 Consensus size: 6
156216 AAAGAAATTG
* * ** *
156226 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
156273 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AG-AA
156325 AAAGAA AAAG
1 AAAGAA AAAG
156335 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 24, Indels: 9
0.69 0.22 0.08
Matches are distributed among these distances:
5 3 0.04
6 60 0.80
7 4 0.05
8 8 0.11
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:156315 original size:14 final size:14
Alignment explanation
Indices: 156295--156352 Score: 66
Period size: 15 Copynumber: 4.1 Consensus size: 14
156285 AAAGTGAGAG
156295 AAAAAGAAAA-TGA
1 AAAAAGAAAATTGA
156308 AGAAAAGAAAATTGA
1 A-AAAAGAAAATTGA
**
156323 AAAAAGAAAAAGCGA
1 AAAAAG-AAAATTGA
156338 AAAAAG-AAATTGA
1 AAAAAGAAAATTGA
156351 AA
1 AA
156353 GAGAGCTTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
13 8 0.21
14 14 0.37
15 16 0.42
ACGTcount: A:0.72, C:0.02, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAAAGAAAATTGA
Found at i:156333 original size:15 final size:13
Alignment explanation
Indices: 156295--156352 Score: 62
Period size: 14 Copynumber: 4.2 Consensus size: 13
156285 AAAGTGAGAG
156295 AAAAAGAAAATGA
1 AAAAAGAAAATGA
156308 AGAAAAGAAAATTGA
1 A-AAAAGAAAA-TGA
*
156323 AAAAAGAAAAAGCGA
1 AAAAAG-AAAA-TGA
*
156338 AAAAAGAAATTGA
1 AAAAAGAAAATGA
156351 AA
1 AA
156353 GAGAGCTTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
13 5 0.13
14 17 0.45
15 16 0.42
ACGTcount: A:0.72, C:0.02, G:0.17, T:0.09
Consensus pattern (13 bp):
AAAAAGAAAATGA
Found at i:156386 original size:33 final size:33
Alignment explanation
Indices: 156349--156411 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
156339 AAAAGAAATT
156349 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
156382 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
156412 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:158206 original size:20 final size:20
Alignment explanation
Indices: 158183--158236 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
158173 AGTTTTTCCC
*
158183 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
158203 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
158223 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
158237 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:158218 original size:30 final size:30
Alignment explanation
Indices: 158183--158255 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 30
158173 AGTTTTTCCC
158183 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
158213 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
158243 AGCTCGTTTGAGC
1 AGCTCGTTTGAGC
158256 GTGGCTTAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 35 0.90
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:158246 original size:20 final size:20
Alignment explanation
Indices: 158183--158247 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
158173 AGTTTTTCCC
* * * *
158183 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
158203 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
158222 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
158243 AGCTC
1 AGCTC
158248 GTTTGAGCGT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:159915 original size:14 final size:14
Alignment explanation
Indices: 159868--159915 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
159858 AAAAAAATTA
159868 AAAAAAAAGAAGTG
1 AAAAAAAAGAAGTG
*
159882 ACAAAAAAATCG-AGTT
1 A-AAAAAAA--GAAGTG
159898 AAAAAAAAGAAGTG
1 AAAAAAAAGAAGTG
159912 AAAA
1 AAAA
159916 GTCTTGCGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 1 0.04
14 8 0.29
15 14 0.50
16 4 0.14
17 1 0.04
ACGTcount: A:0.69, C:0.04, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAAAAAAGAAGTG
Found at i:160958 original size:6 final size:6
Alignment explanation
Indices: 160933--161041 Score: 65
Period size: 6 Copynumber: 17.3 Consensus size: 6
160923 GAAAGAAAAC
* * ** * **
160933 AAAAGA AAACGA AGAAGA AAAAGA AATTGC AAAAGA AAAAGA AATCGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
* * * * *
160981 AAAAGT GAGAGA AAAAGA AAATGAA GAAAAGA AAATTGA AAAAGA AAAAGCGA
1 AAAAGA AAAAGA AAAAGA AAAAG-A -AAAAGA AAA-AGA AAAAGA AAAA--GA
161034 AAAAGA AA
1 AAAAGA AA
161042 TTGAAAGAGA
Statistics
Matches: 74, Mismatches: 24, Indels: 10
0.69 0.22 0.09
Matches are distributed among these distances:
6 57 0.77
7 7 0.09
8 10 0.14
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.06
Consensus pattern (6 bp):
AAAAGA
Found at i:160984 original size:18 final size:18
Alignment explanation
Indices: 160911--160985 Score: 78
Period size: 18 Copynumber: 4.1 Consensus size: 18
160901 GAAAGAGATT
*
160911 GAAAAAGAAATTGAAAGAA
1 GAAAAAGAAATCGAAA-AA
* * *
160930 AACAAAAGAAAACGAAGAA
1 GA-AAAAGAAATCGAAAAA
* *
160949 GAAAAAGAAATTGCAAAA
1 GAAAAAGAAATCGAAAAA
160967 GAAAAAGAAATCGAAAAA
1 GAAAAAGAAATCGAAAAA
160985 G
1 G
160986 TGAGAGAAAA
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
18 29 0.66
19 4 0.09
20 11 0.25
ACGTcount: A:0.69, C:0.05, G:0.19, T:0.07
Consensus pattern (18 bp):
GAAAAAGAAATCGAAAAA
Found at i:161012 original size:14 final size:13
Alignment explanation
Indices: 160991--161047 Score: 55
Period size: 14 Copynumber: 4.3 Consensus size: 13
160981 AAAAGTGAGA
160991 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
161003 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
**
161018 GAAAAAGAAAAAGC
1 GAAAAAG-AAAATT
161032 GAAAAAG-AAATT
1 GAAAAAGAAAATT
161044 GAAA
1 GAAA
161048 GAGAGCTTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
12 8 0.22
13 6 0.16
14 21 0.57
15 2 0.05
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:161105 original size:33 final size:33
Alignment explanation
Indices: 161044--161106 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
161034 AAAAGAAATT
161044 GAAAGAGAGCTTGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGCTTGAAAAGAAATCAAGTGAAAAA
*
161077 GAAAGAGAG-TCTGTAAAAGAAA-CGAGTGAA
1 GAAAGAGAGCT-TG-AAAAGAAATCAAGTGAA
161107 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 1 0.04
33 18 0.67
34 8 0.30
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGCTTGAAAAGAAATCAAGTGAAAAA
Found at i:162894 original size:20 final size:20
Alignment explanation
Indices: 162871--162924 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
162861 AGTTTTTCCC
*
162871 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
162891 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
162911 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
162925 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:162906 original size:30 final size:30
Alignment explanation
Indices: 162871--162944 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
162861 AGTTTTTCCC
162871 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
162901 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
162931 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
162945 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:162934 original size:20 final size:20
Alignment explanation
Indices: 162871--162935 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
162861 AGTTTTTCCC
* * * *
162871 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
162891 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
162910 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
162931 AGCTC
1 AGCTC
162936 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Done.