Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001084.1 Hibiscus syriacus cultivar Beakdansim tig00002145_pilon, whole genome shotgun sequence
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: 72197
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:498 original size:3 final size:3
Alignment explanation
Indices: 490--517 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
480 ATATAACACT
490 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
518 TCCCTGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3927 original size:20 final size:20
Alignment explanation
Indices: 3902--3994 Score: 100
Period size: 20 Copynumber: 4.8 Consensus size: 20
3892 AGTAGTTTCT
*
3902 GAAAATTAAATTCGCAACGC
1 GAAAATTAAAATCGCAACGC
3922 GAAAATTAAAATCGC-ACGC
1 GAAAATTAAAATCGCAACGC
* * * *
3941 AAAAATGAAAATCCCAACGA
1 GAAAATTAAAATCGCAACGC
* *
3961 GAAAATGAAAATCACAACGC
1 GAAAATTAAAATCGCAACGC
*
3981 -AAAACTAAAATCGC
1 GAAAATTAAAATCGC
3995 GTTGCGATTT
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
19 27 0.44
20 34 0.56
ACGTcount: A:0.53, C:0.20, G:0.13, T:0.14
Consensus pattern (20 bp):
GAAAATTAAAATCGCAACGC
Found at i:3959 original size:39 final size:39
Alignment explanation
Indices: 3916--3992 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
3906 ATTAAATTCG
* * *
3916 CAACGCGAAAATTAAAATCGC-ACGCAAAAATGAAAATCC
1 CAACGAGAAAATGAAAATCACAACGCAAAAAT-AAAATCC
*
3955 CAACGAGAAAATGAAAATCACAACGCAAAACTAAAATC
1 CAACGAGAAAATGAAAATCACAACGCAAAAATAAAATC
3993 GCGTTGCGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 24 0.73
40 9 0.27
ACGTcount: A:0.55, C:0.22, G:0.12, T:0.12
Consensus pattern (39 bp):
CAACGAGAAAATGAAAATCACAACGCAAAAATAAAATCC
Found at i:4066 original size:20 final size:20
Alignment explanation
Indices: 4027--4066 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
4017 TGCAATTTTG
* * *
4027 GTGTTGCGATTTTCATTTTC
1 GTGTTGCGAATTTAAGTTTC
4047 GTGTTGCGAATTTAAGTTTC
1 GTGTTGCGAATTTAAGTTTC
4067 AAAAACTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.23, T:0.50
Consensus pattern (20 bp):
GTGTTGCGAATTTAAGTTTC
Found at i:4425 original size:22 final size:22
Alignment explanation
Indices: 4399--4449 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
4389 GATTGAGATA
4399 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
4421 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
4443 GACGGAT
1 GACGGAT
4450 GTCGCCGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.20, C:0.14, G:0.45, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:4629 original size:20 final size:20
Alignment explanation
Indices: 4604--4674 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
4594 TAAACGCGCT
*
4604 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGAG
4624 TTGCGAATTTGACTTCTGAG
1 TTGCGAATTTGACTTCTGAG
* * *
4644 TTGCGACATTGGAGTTC-GCG
1 TTGCGA-ATTTGACTTCTGAG
4664 TTGCGAATTTG
1 TTGCGAATTTG
4675 TTGGTCATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
19 4 0.09
20 33 0.73
21 8 0.18
ACGTcount: A:0.17, C:0.15, G:0.28, T:0.39
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGAG
Found at i:14225 original size:17 final size:18
Alignment explanation
Indices: 14184--14222 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
14174 ATTATATAAG
14184 TAAAATA-TTAAATAAAT
1 TAAAATACTTAAATAAAT
14201 TAAAATACTTAAATAAAT
1 TAAAATACTTAAATAAAT
14219 TAAA
1 TAAA
14223 TACAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAATACTTAAATAAAT
Found at i:14778 original size:20 final size:20
Alignment explanation
Indices: 14753--14795 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
14743 AATCACAACC
14753 CATACATCCCAATTTGGAAA
1 CATACATCCCAATTTGGAAA
14773 CATACATCCCAATTTGGAAA
1 CATACATCCCAATTTGGAAA
14793 CAT
1 CAT
14796 TTATTGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.40, C:0.26, G:0.09, T:0.26
Consensus pattern (20 bp):
CATACATCCCAATTTGGAAA
Found at i:15134 original size:14 final size:14
Alignment explanation
Indices: 15115--15146 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
15105 TTGTACATCC
15115 ATATTATTTTTATA
1 ATATTATTTTTATA
15129 ATATTATTTTTATA
1 ATATTATTTTTATA
15143 ATAT
1 ATAT
15147 ATATATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATATTATTTTTATA
Found at i:15150 original size:2 final size:2
Alignment explanation
Indices: 15139--15187 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
15129 ATATTATTTT
15139 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15180 TA TA TA TA
1 TA TA TA TA
15188 ATTGTAAGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:16133 original size:132 final size:130
Alignment explanation
Indices: 15803--16170 Score: 470
Period size: 131 Copynumber: 2.8 Consensus size: 130
15793 CGATATTGAG
* * * * * * *
15803 AATAGTAATATCTTTTCATTTCGGTCGGAGTAATAAATGATTGCTTTAATGCATGAAAGTGTATT
1 AATAGTAATATATTTTTATTTCGATTGGGGTAATAAATGATTGTTTTAATGCACGAAAG-GTATT
* * * * * *
15868 TATTTTCGATTGGAAATAATTTGATATTGTTGTTTTC-TTTCGAATTAATACTGATTTTTAAGAC
65 TATTCTCGATT-GAAATAATTAGATATTATTGTTTTCACTTCGAATCAATACTGAATTTTAAGAC
15932 GA
129 GA
* * **
15934 AATAGTAATATATCTTTATTTCAATTGGGGTAATAAATGATTGTTTTAATGCTGGAAAGGTAATT
1 AATAGTAATATATTTTTATTTCGATTGGGGTAATAAATGATTGTTTTAATGCACGAAAGGT-ATT
* * *
15999 TATTCTCGATTAGAAATAATTAGATATTATTGTTTTCACTT-GAATCGATATTGAATTTTAAGAT
65 TATTCTCGATT-GAAATAATTAGATATTATTGTTTTCACTTCGAATCAATACTGAATTTTAAGAC
16063 GA
129 GA
*
16065 AATAGTAATATTTTTTTTATTTCGATTGGGGTAATAAATGATTGTTTTAATGCACGAAAGGTCAT
1 AATAGTAATA-TATTTTTATTTCGATTGGGGTAATAAATGATTGTTTTAATGCACGAAAGGT-AT
16130 TTATTCTCGATTGAAAATAATTAGATATTATTGTTTTCACT
64 TTATTCTCGATTG-AAATAATTAGATATTATTGTTTTCACT
16171 CTTAAAATTA
Statistics
Matches: 207, Mismatches: 26, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
130 2 0.01
131 116 0.56
132 89 0.43
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (130 bp):
AATAGTAATATATTTTTATTTCGATTGGGGTAATAAATGATTGTTTTAATGCACGAAAGGTATTT
ATTCTCGATTGAAATAATTAGATATTATTGTTTTCACTTCGAATCAATACTGAATTTTAAGACGA
Found at i:18675 original size:3 final size:3
Alignment explanation
Indices: 18667--18735 Score: 54
Period size: 3 Copynumber: 23.3 Consensus size: 3
18657 TCGAGTTTTA
* * * *
18667 TAT TAT TAT TAT TAT T-T AAC TAT TAT TGT TAT TATT TAT TTT TAAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT T-AT
*
18713 TAT T-T TA- TAT TAT TTT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
18736 TATTTCTGTA
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
2 5 0.10
3 41 0.80
4 5 0.10
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:18692 original size:20 final size:20
Alignment explanation
Indices: 18667--18704 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
18657 TCGAGTTTTA
18667 TATTATTATTATTATTTAAC
1 TATTATTATTATTATTTAAC
*
18687 TATTATTGTTATTATTTA
1 TATTATTATTATTATTTA
18705 TTTTTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (20 bp):
TATTATTATTATTATTTAAC
Found at i:18724 original size:33 final size:33
Alignment explanation
Indices: 18664--18740 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 33
18654 TGTTCGAGTT
*
18664 TTATATTATTATTATTATTTAACTATTATTGTTA
1 TTAT-TTATTTTTATTATTTAACTATTATTGTTA
* *
18698 TTATTTATTTTTAATTATTTTA-TATTATTTTTA
1 TTATTTATTTTT-ATTATTTAACTATTATTGTTA
18731 TTATTTATTT
1 TTATTTATTT
18741 CTGTAGGCCT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
33 27 0.69
34 12 0.31
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.69
Consensus pattern (33 bp):
TTATTTATTTTTATTATTTAACTATTATTGTTA
Found at i:18736 original size:9 final size:9
Alignment explanation
Indices: 18702--18736 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 9
18692 TTGTTATTAT
18702 TTATTTTTAA
1 TTATTTTT-A
18712 TTATTTTATA
1 TTATTTT-TA
18722 TTATTTTTA
1 TTATTTTTA
18731 TTATTT
1 TTATTT
18737 ATTTCTGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 8 0.33
10 15 0.62
11 1 0.04
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
TTATTTTTA
Found at i:24908 original size:21 final size:21
Alignment explanation
Indices: 24870--24909 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
24860 CCCCCTTTGA
*
24870 AGGGGAACCGATCCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
* *
24891 AGGGGAATCGATATCCCCC
1 AGGGGAACCGATACCCCCC
24910 TGGGGTTTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:29432 original size:10 final size:11
Alignment explanation
Indices: 29404--29536 Score: 97
Period size: 10 Copynumber: 12.3 Consensus size: 11
29394 CACACACACA
29404 TATATATATAT
1 TATATATATAT
29415 TACT-T-TATA-
1 TA-TATATATAT
29424 T-TATAT-TAT
1 TATATATATAT
*
29433 TA-AGTATATTT
1 TATA-TATATAT
29444 TATACCTATTATAT
1 TATA--TA-TATAT
* *
29458 TATGTTTAT-T
1 TATATATATAT
29468 TCATATATATA-
1 T-ATATATATAT
29479 TATATATATA-
1 TATATATATAT
29489 TATATATATA-
1 TATATATATAT
29499 TATATATATAT
1 TATATATATAT
29510 ATATATATATAT
1 -TATATATATAT
29522 ATATATATATAT
1 -TATATATATAT
29534 TAT
1 TAT
29537 TTTATATGCA
Statistics
Matches: 101, Mismatches: 7, Indels: 28
0.74 0.05 0.21
Matches are distributed among these distances:
7 1 0.01
8 3 0.03
9 4 0.04
10 38 0.38
11 20 0.20
12 26 0.26
13 2 0.02
14 7 0.07
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (11 bp):
TATATATATAT
Found at i:29477 original size:2 final size:2
Alignment explanation
Indices: 29470--29695 Score: 160
Period size: 2 Copynumber: 115.0 Consensus size: 2
29460 TGTTTATTTC
29470 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* **
29512 AT AT AT AT AT AT AT AT AT AT AT -T AT -T TT AT AT GC AT AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * * * * * ** * * * * * * ** **
29553 AC GT TT AC CT TT CC ACG AT AC CT A- AG AC GT -T AT AT GC GC AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
29594 -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
29635 AT AT AT AT AT AT AT AT AT AT AT AA AT GT -T AT AT -T AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29675 CAT AT AT AT AT AT AT AT AT AT
1 -AT AT AT AT AT AT AT AT AT AT
29696 GTGTGTGTGT
Statistics
Matches: 179, Mismatches: 35, Indels: 20
0.76 0.15 0.09
Matches are distributed among these distances:
1 7 0.04
2 168 0.94
3 4 0.02
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:29732 original size:16 final size:16
Alignment explanation
Indices: 29692--29738 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
29682 ATATATATAT
29692 ATATG-TGTGTGTGT-
1 ATATGTTGTGTGTGTA
* *
29706 GTGTGTGTGTGTGTGTA
1 ATATGT-TGTGTGTGTA
29723 ATATGTTGTGTGTGTA
1 ATATGTTGTGTGTGTA
29739 TATTTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 3 0.12
16 19 0.73
17 4 0.15
ACGTcount: A:0.13, C:0.00, G:0.38, T:0.49
Consensus pattern (16 bp):
ATATGTTGTGTGTGTA
Found at i:29737 original size:2 final size:2
Alignment explanation
Indices: 29695--29721 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29685 TATATATATA
29695 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
29722 AATATGTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:31763 original size:23 final size:27
Alignment explanation
Indices: 31712--31762 Score: 72
Period size: 24 Copynumber: 2.0 Consensus size: 27
31702 TCATTTCATT
*
31712 ATATATATATATTAATATTTTTGAAAA
1 ATATATATATATTAATATTTTAGAAAA
31739 ATATA-ATATA-TAAT-TTTTAGAAAA
1 ATATATATATATTAATATTTTAGAAAA
31763 TGATTTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 9 0.39
25 4 0.17
26 5 0.22
27 5 0.22
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (27 bp):
ATATATATATATTAATATTTTAGAAAA
Found at i:31769 original size:37 final size:36
Alignment explanation
Indices: 31728--31973 Score: 142
Period size: 36 Copynumber: 6.7 Consensus size: 36
31718 ATATATTAAT
31728 ATTTTTGAAAAATATAATATATAATTTTTAGAAAATG
1 ATTTTTGAAAAATATAATATATAATTTTT-GAAAATG
* *
31765 ATTTTTGAAAACATATAATATAT--TGTTTAAAAATCG
1 ATTTTTGAAAA-ATATAATATATAATTTTTGAAAAT-G
* * *
31801 --GTTTAAAAAATAT-ATATTATACAGTTTTG-AAATG
1 ATTTTTGAAAAATATAATA-TATA-ATTTTTGAAAATG
*
31835 ATTTTTGAAAAAATATATATTATATAA--TTTGCAAATG
1 ATTTTTG-AAAAATATA-A-TATATAATTTTTGAAAATG
* *
31872 ATTTTTGAAAAAAAAATATATATAATATATAGTTTTGAAAA-C
1 ATTTTTG----AAAAATATA-AT-ATATA-ATTTTTGAAAATG
*
31914 A-TTTTG-AAAATATATATAATATATAGTTTTGAAAAT-
1 ATTTTTGAAAAATATA-AT-ATATA-ATTTTTGAAAATG
31950 ATTTTTTG-AAAATAT-ATATATAAT
1 A-TTTTTGAAAAATATAATATATAAT
31974 ATATAGTTTT
Statistics
Matches: 174, Mismatches: 12, Indels: 49
0.74 0.05 0.21
Matches are distributed among these distances:
32 3 0.02
33 7 0.04
34 9 0.05
35 14 0.08
36 47 0.27
37 31 0.18
38 24 0.14
39 6 0.03
40 19 0.11
41 6 0.03
42 1 0.01
43 7 0.04
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (36 bp):
ATTTTTGAAAAATATAATATATAATTTTTGAAAATG
Found at i:31884 original size:38 final size:37
Alignment explanation
Indices: 31728--32105 Score: 201
Period size: 37 Copynumber: 9.8 Consensus size: 37
31718 ATATATTAAT
*
31728 ATTTTTG-AAAAATATA-A-TATATAATTTTTAGAAAATG
1 ATTTTTGAAAAAATATATATTATAT-AGTTTT-G-AAATG
* * **
31765 ATTTTTGAAAACATATA-A-TATATTGTTTAAAAATCG
1 ATTTTTGAAAAAATATATATTATATAGTTTTGAAAT-G
* *
31801 --GTTT-AAAAAATATATATTATACAGTTTTGAAATG
1 ATTTTTGAAAAAATATATATTATATAGTTTTGAAATG
*
31835 ATTTTTGAAAAAATATATATTATATA-ATTTGCAAATG
1 ATTTTTGAAAAAATATATATTATATAGTTTTG-AAATG
**
31872 ATTTTTGAAAAAAAAATATATATAATATATAGTTTTGAAAAC
1 ATTTTTG---AAAAAATATATAT--TATATAGTTTTGAAATG
* *
31914 A-TTTTGAAAATATATATAATATATAGTTTTGAAAAT-
1 ATTTTTGAAAAAATATATATTATATAGTTTTG-AAATG
*
31950 ATTTTTTGAAAATATATATATAATATATAGTTTTGAAAACATTTTG
1 A-TTTTTGAAAA-A-ATATATATTATATAGTTTTG--AA-A---TG
** * *
31996 AAAATATTTTTTGAAAAATATATAATATATAGTTTATTAAAAT-
1 -----ATTTTTGAAAAAATATATATTATATAG-TT-TTGAAATG
* *
32039 ATTTTT-AAAAAGTATATATAATATAGTTTTTGAAAATG
1 ATTTTTGAAAAAATATATATTATATAG-TTTTG-AAATG
* *
32077 TTTTTTGAAAACATATA-A-TATATAGTTTT
1 ATTTTTGAAAAAATATATATTATATAGTTTT
32106 TAAAATATTT
Statistics
Matches: 273, Mismatches: 33, Indels: 71
0.72 0.09 0.19
Matches are distributed among these distances:
33 9 0.03
34 5 0.02
35 16 0.06
36 27 0.10
37 72 0.26
38 46 0.17
39 8 0.03
40 33 0.12
41 8 0.03
42 11 0.04
43 4 0.01
44 1 0.00
45 1 0.00
47 1 0.00
48 17 0.06
49 3 0.01
50 10 0.04
51 1 0.00
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (37 bp):
ATTTTTGAAAAAATATATATTATATAGTTTTGAAATG
Found at i:31954 original size:11 final size:11
Alignment explanation
Indices: 31904--32005 Score: 55
Period size: 11 Copynumber: 8.4 Consensus size: 11
31894 TAATATATAG
*
31904 TTTTGAAAACA
1 TTTTGAAAATA
31915 TTTTGAAAATA
1 TTTTGAAAATA
*
31926 TATAT-AATATATA
1 T-TTTGAA-A-ATA
31939 GTTTTGAAAATA
1 -TTTTGAAAATA
31951 TTTTTTGAAAATA
1 --TTTTGAAAATA
31964 TATATAT-AATATATA
1 T-T-T-TGAA-A-ATA
*
31979 GTTTTGAAAACA
1 -TTTTGAAAATA
31991 TTTTGAAAATA
1 TTTTGAAAATA
32002 TTTT
1 TTTT
32006 TTGAAAAATA
Statistics
Matches: 72, Mismatches: 6, Indels: 26
0.69 0.06 0.25
Matches are distributed among these distances:
11 28 0.39
12 9 0.12
13 22 0.31
14 8 0.11
15 4 0.06
16 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (11 bp):
TTTTGAAAATA
Found at i:31973 original size:76 final size:76
Alignment explanation
Indices: 31805--32002 Score: 251
Period size: 76 Copynumber: 2.6 Consensus size: 76
31795 AAATCGGTTT
* ** * * *
31805 AAAAAATATATAT--TATACAGTTTTGAAATGATTTTTGAAAAAATATATATTATATAATTTGCA
1 AAAAAATATATATAATATATAGTTTTGAAAACA-TTTTGAAAATATATATAATATATAATTTGAA
31868 AATGATTTTTGAAA
65 AATGATTTTTG--A
*
31882 AAAAAATATATATAATATATAGTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTGAA
1 AAAAAATATATATAATATATAGTTTTGAAAACATTTTGAAAATATATATAATATATA-ATTTGAA
31947 AAT-ATTTTTTG-
65 AATGA-TTTTTGA
*
31958 AAAATATATATATAATATATAGTTTTGAAAACATTTTGAAAATAT
1 AAAAAATATATATAATATATAGTTTTGAAAACATTTTGAAAATAT
32003 TTTTTGAAAA
Statistics
Matches: 109, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
76 44 0.40
77 13 0.12
78 23 0.21
79 29 0.27
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (76 bp):
AAAAAATATATATAATATATAGTTTTGAAAACATTTTGAAAATATATATAATATATAATTTGAAA
ATGATTTTTGA
Found at i:32000 original size:51 final size:49
Alignment explanation
Indices: 31940--32048 Score: 157
Period size: 48 Copynumber: 2.2 Consensus size: 49
31930 TAATATATAG
31940 TTTTGAAAATATTTTTTGAAAATATATATATAATATATAGTTT-TGAAAACA
1 TTTTGAAAATATTTTTTG-AAA-A-ATATATAATATATAGTTTATGAAAACA
* *
31991 TTTTGAAAATATTTTTTGAAAAATATATAATATATAGTTTATTAAAATA
1 TTTTGAAAATATTTTTTGAAAAATATATAATATATAGTTTATGAAAACA
*
32040 TTTTTAAAA
1 TTTTGAAAA
32049 AGTATATATA
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
48 18 0.33
49 15 0.28
50 3 0.06
51 18 0.33
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.47
Consensus pattern (49 bp):
TTTTGAAAATATTTTTTGAAAAATATATAATATATAGTTTATGAAAACA
Found at i:32016 original size:14 final size:13
Alignment explanation
Indices: 31940--32012 Score: 62
Period size: 13 Copynumber: 5.7 Consensus size: 13
31930 TAATATATAG
31940 TTTTGAAAATATT
1 TTTTGAAAATATT
31953 TTTTGAAAATATAT
1 TTTTGAAAATAT-T
* * * *
31967 ATAT-AATATATAG
1 TTTTGAAAATAT-T
*
31980 TTTTGAAAACA--
1 TTTTGAAAATATT
31991 TTTTGAAAATATT
1 TTTTGAAAATATT
32004 TTTTGAAAA
1 TTTTGAAAA
32013 ATATATAATA
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
11 10 0.21
13 30 0.64
14 7 0.15
ACGTcount: A:0.44, C:0.01, G:0.08, T:0.47
Consensus pattern (13 bp):
TTTTGAAAATATT
Found at i:32038 original size:76 final size:75
Alignment explanation
Indices: 31882--32113 Score: 169
Period size: 76 Copynumber: 3.1 Consensus size: 75
31872 ATTTTTGAAA
* * * * *
31882 AAAAAATATATATAATATATAGTTTTGAAAACATTTTGAAAATA-TATAT-AATATATAGTTTTG
1 AAAATATATATATAATATATAGTTTTGAAAACATTTTGAAAATATTTTTTGAA-AAATA--TAT-
*
31945 AA-A-ATATTTTTT
62 AATATATAGTTTTT
*
31957 GAAA-ATATATATATAATATATAGTTTTGAAAACATTTTGAAAATATTTTTTGAAAAATATATAA
1 AAAATATA--TATATAATATATAGTTTTGAAAACATTTTGAAAATATTTTTTGAAAAATATATAA
32021 TATATAGTTTATT
64 TATATAGTTT-TT
* * * * ** * *
32034 AAAATATTTTTA-AAAAGTATA--TAT-AATATAGTTTTTGAAAATGTTTTTTG-AAAACATATA
1 AAAATATATATATAATA-TATAGTTTTGAA-A-ACATTTTGAAAATATTTTTTGAAAAATATATA
32094 ATATATAGTTTTT
63 ATATATAGTTTTT
32107 AAAATAT
1 AAAATAT
32114 TTTATTTTCG
Statistics
Matches: 131, Mismatches: 15, Indels: 24
0.77 0.09 0.14
Matches are distributed among these distances:
73 11 0.08
74 28 0.21
75 27 0.21
76 49 0.37
77 12 0.09
78 4 0.03
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.44
Consensus pattern (75 bp):
AAAATATATATATAATATATAGTTTTGAAAACATTTTGAAAATATTTTTTGAAAAATATATAATA
TATAGTTTTT
Found at i:32087 original size:88 final size:88
Alignment explanation
Indices: 31915--32074 Score: 240
Period size: 88 Copynumber: 1.8 Consensus size: 88
31905 TTTGAAAACA
31915 TTTTGAAAATATATATAATATATAGTTTTGAAAATATTTTTTGAAAATATATATATAATATATAG
1 TTTTGAAAATATATATAATATATAGTTTTGAAAATATTTTTTGAAAATATATATATAATATATA-
31980 TTTTGAAAACATTTTGAAAATATT
65 TTTTGAAAACATTTTGAAAATATT
*
32004 TTTTGAAAA-ATATATAATATATAGTTTATTAAAATA-TTTTT-AAAA-AGTATATATAATATAG
1 TTTTGAAAATATATATAATATATAGTTT-TGAAAATATTTTTTGAAAATA-TATATATAATATA-
32065 T-TTTTGAAAA
63 TATTTTGAAAA
32075 TGTTTTTTGA
Statistics
Matches: 67, Mismatches: 1, Indels: 9
0.87 0.01 0.12
Matches are distributed among these distances:
86 10 0.15
87 17 0.25
88 24 0.36
89 16 0.24
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.46
Consensus pattern (88 bp):
TTTTGAAAATATATATAATATATAGTTTTGAAAATATTTTTTGAAAATATATATATAATATATAT
TTTGAAAACATTTTGAAAATATT
Found at i:33203 original size:5 final size:5
Alignment explanation
Indices: 33193--33530 Score: 73
Period size: 5 Copynumber: 65.6 Consensus size: 5
33183 CAAATGGAAT
* * * ** *
33193 AAATA AAATA AGATA AGA-A AAA-A AGATA AGGTA AAGATA AAA-A AAGT-
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AA-ATA AAATA AAATA
* * *
33240 AAATA AAAT- AAATA AAAT- AAATA AAA-A TAA-A AAATA AACAGA ATAAAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AA-ATA A-AATA
* * *
33288 AAATA AACATA AAGAAA TAAATA AAGATA AAGAAA AAATAA AAATA AAAGA
1 AAATA AA-ATA AA-ATA -AAATA AA-ATA AA-ATA AAAT-A AAATA AAATA
* * *
33339 AAAT- AAAT- AAAGA AAATA ACAA-A CGAAA-A ATAATA AAGT- CAATGA
1 AAATA AAATA AAATA AAATA A-AATA --AAATA A-AATA AAATA AAAT-A
*** *
33384 AAATA ATAA-A AAATA AATATGA TGGTA AAATA AATTA AAATA AAATA
1 AAATA A-AATA AAATA AA-AT-A AAATA AAATA AAATA AAATA AAATA
* *
33431 AAATA ACAAAA GAAATAA AAATA AAACA AAA-A AAAGT- -AATGA AAATA
1 AAATA A-AATA -AAAT-A AAATA AAATA AAATA AAA-TA AAAT-A AAATA
* * * *
33478 ACAGA AACA-C AAATA AAATGA TAAGAAA AAATA AAATA AAAGTA AGAATA
1 AAATA AA-ATA AAATA AAAT-A -AA-ATA AAATA AAATA AAA-TA A-AATA
33528 AAA
1 AAA
33531 ATAATATATA
Statistics
Matches: 249, Mismatches: 44, Indels: 80
0.67 0.12 0.21
Matches are distributed among these distances:
3 1 0.00
4 45 0.18
5 119 0.48
6 71 0.29
7 12 0.05
8 1 0.00
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.16
Consensus pattern (5 bp):
AAATA
Found at i:33250 original size:18 final size:17
Alignment explanation
Indices: 33150--33349 Score: 126
Period size: 18 Copynumber: 11.3 Consensus size: 17
33140 TAATGAAAAT
33150 ATAAAATAAAGAAAATACA
1 ATAAAATAAA-AAAATA-A
*
33169 ATAAAGA-AAAAAAACAA
1 ATAAA-ATAAAAAAATAA
**
33186 ATGGAATAAATAAAATAA
1 ATAAAATAAA-AAAATAA
*
33204 GATAAGAA-AAAAAGATAA
1 -ATAA-AATAAAAAAATAA
*
33222 GGTAAAGATAAAAAAAGTAA
1 -ATAAA-ATAAAAAAA-TAA
33242 ATAAAATAAATAAAATAA
1 ATAAAATAAA-AAAATAA
33260 ATAAAA-ATAAAAAATAA
1 ATAAAATA-AAAAAATAA
* *
33277 ACAGAATAAAAAAAT--
1 ATAAAATAAAAAAATAA
* *
33292 A-AACATAAAGAAATAA
1 ATAAAATAAAAAAATAA
*
33308 ATAAAGATAAAGAAA-AA
1 ATAAA-ATAAAAAAATAA
33325 ATAAAAATAAAAGAAAATAA
1 AT-AAAAT-AAA-AAAATAA
33345 ATAAA
1 ATAAA
33350 GAAAATAACA
Statistics
Matches: 145, Mismatches: 17, Indels: 38
0.73 0.09 0.19
Matches are distributed among these distances:
14 10 0.07
15 1 0.01
16 2 0.01
17 35 0.24
18 54 0.37
19 33 0.23
20 10 0.07
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (17 bp):
ATAAAATAAAAAAATAA
Found at i:33252 original size:4 final size:4
Alignment explanation
Indices: 33229--33349 Score: 60
Period size: 4 Copynumber: 30.2 Consensus size: 4
33219 TAAGGTAAAG
*
33229 ATAA AAAA AGTAA ATAAA ATAA ATAAA ATAA AT-A A-AA ATAA A-AA ATAA
1 ATAA ATAA A-TAA AT-AA ATAA AT-AA ATAA ATAA ATAA ATAA ATAA ATAA
* * * *
33277 ACAGA ATAA AAAA ATAAA CATAA AGAA ATAA ATAAA GATAA AGAA A-AA
1 ATA-A ATAA ATAA AT-AA -ATAA ATAA ATAA AT-AA -ATAA ATAA ATAA
*
33325 AT-A A-AA ATAA A-AG A-AA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
33350 GAAAATAACA
Statistics
Matches: 91, Mismatches: 11, Indels: 30
0.69 0.08 0.23
Matches are distributed among these distances:
3 18 0.20
4 47 0.52
5 22 0.24
6 4 0.04
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.16
Consensus pattern (4 bp):
ATAA
Found at i:33285 original size:35 final size:33
Alignment explanation
Indices: 33232--33357 Score: 100
Period size: 31 Copynumber: 3.8 Consensus size: 33
33222 GGTAAAGATA
*
33232 AAAAAAGTAAATAAAATAAATAAAATAAATAAAAAT
1 AAAAAA-TAAA-AGAATAAA-AAAATAAATAAAAAT
* * *
33268 AAAAAATAAACAGAATAAAAAAATAAACATAAAG
1 AAAAAATAAA-AGAATAAAAAAATAAATAAAAAT
*
33302 AAATAAAT-AAAG-ATAAAGAAA-AAATAAAAAT
1 AAA-AAATAAAAGAATAAAAAAATAAATAAAAAT
*
33333 AAAAGAA-AATA-AATAAAGAAAATAA
1 AAAA-AATAAAAGAATAAA-AAAATAA
33358 CAAACGAAAA
Statistics
Matches: 73, Mismatches: 11, Indels: 15
0.74 0.11 0.15
Matches are distributed among these distances:
30 1 0.01
31 19 0.26
32 11 0.15
33 4 0.05
34 17 0.23
35 15 0.21
36 6 0.08
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.15
Consensus pattern (33 bp):
AAAAAATAAAAGAATAAAAAAATAAATAAAAAT
Found at i:33367 original size:13 final size:13
Alignment explanation
Indices: 33153--33357 Score: 87
Period size: 13 Copynumber: 16.2 Consensus size: 13
33143 TGAAAATATA
33153 AAATAAAGAAAAT
1 AAATAAAGAAAAT
33166 ACAATAAAG--AA-
1 A-AATAAAGAAAAT
*
33177 AAA-AAA-CAAAT
1 AAATAAAGAAAAT
* *
33188 GGAATAAATAAAAT
1 -AAATAAAGAAAAT
*
33202 AAGAT-AAGAAAAA
1 AA-ATAAAGAAAAT
*
33215 AAGATAAGGTAAAGAT
1 AA-ATAAAG-AAA-AT
* *
33231 AAAAAAAGTAAAT
1 AAATAAAGAAAAT
*
33244 AAAATAAATAAAAT
1 -AAATAAAGAAAAT
*
33258 AAATAAA-AATAAA
1 AAATAAAGAA-AAT
* *
33271 AAATAAACAGAAT
1 AAATAAAGAAAAT
*
33284 AAA-AAA-ATAA-
1 AAATAAAGAAAAT
*
33294 ACATAAAG-AAAT
1 AAATAAAGAAAAT
*
33306 AAATAAAGATAAAG
1 AAATAAAGA-AAAT
*
33320 AAA-AAATAAAA-
1 AAATAAAGAAAAT
*
33331 ATA-AAAGAAAAT
1 AAATAAAGAAAAT
33343 AAATAAAGAAAAT
1 AAATAAAGAAAAT
33356 AA
1 AA
33358 CAAACGAAAA
Statistics
Matches: 146, Mismatches: 25, Indels: 42
0.69 0.12 0.20
Matches are distributed among these distances:
9 3 0.02
10 6 0.04
11 18 0.12
12 21 0.14
13 54 0.37
14 34 0.23
15 7 0.05
16 3 0.02
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (13 bp):
AAATAAAGAAAAT
Found at i:33400 original size:7 final size:8
Alignment explanation
Indices: 33241--33400 Score: 54
Period size: 9 Copynumber: 19.8 Consensus size: 8
33231 AAAAAAAGTA
33241 AATAAAAT
1 AATAAAAT
33249 AAATAAAAT
1 -AATAAAAT
33258 AA-ATAAA-
1 AATA-AAAT
33265 AATAAAA-
1 AATAAAAT
*
33272 AATAAACAG
1 AATAAA-AT
*
33281 AATAAAAA
1 AATAAAAT
33289 AATAAACAT
1 AATAAA-AT
33298 AA-AGAAAT
1 AATA-AAAT
33306 AAATAAAGAT
1 -AATAAA-AT
*
33316 AA-AGAAAA
1 AATA-AAAT
33324 AATAAAAAT
1 AAT-AAAAT
33333 AA-AAGAA-
1 AATAA-AAT
33340 AAT-AAAT
1 AATAAAAT
*
33347 AAAGAAAAT
1 -AATAAAAT
* *
33356 AA-CAAAC
1 AATAAAAT
*
33363 GA-AAAAT
1 AATAAAAT
*
33370 AATAAAGT
1 AATAAAAT
33378 CAATGAAAAT
1 -AAT-AAAAT
33388 AATAAAA-
1 AATAAAAT
33395 AATAAA
1 AATAAA
33401 TATGATGGTA
Statistics
Matches: 118, Mismatches: 13, Indels: 42
0.68 0.08 0.24
Matches are distributed among these distances:
6 2 0.02
7 31 0.26
8 35 0.30
9 42 0.36
10 8 0.07
ACGTcount: A:0.76, C:0.03, G:0.06, T:0.16
Consensus pattern (8 bp):
AATAAAAT
Found at i:33475 original size:24 final size:23
Alignment explanation
Indices: 33421--33478 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
33411 AAATAAATTA
* *
33421 AAAT-AAAATAAAATAACAAAAG
1 AAATAAAAATAAAAAAAAAAAAG
33443 AAATAAAAATAAAACAAAAAAAAG
1 AAATAAAAATAAAA-AAAAAAAAG
* *
33467 TAATGAAAATAA
1 AAATAAAAATAA
33479 CAGAAACACA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 4 0.13
23 9 0.30
24 17 0.57
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.14
Consensus pattern (23 bp):
AAATAAAAATAAAAAAAAAAAAG
Found at i:33534 original size:23 final size:23
Alignment explanation
Indices: 33488--33530 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
33478 ACAGAAACAC
33488 AAATAAAATGATAAGAAAAAATA
1 AAATAAAATGATAAGAAAAAATA
33511 AAATAAAA-G-TAAGAATAAAA
1 AAATAAAATGATAAGAA-AAAA
33531 ATAATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 5 0.26
23 8 0.42
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.16
Consensus pattern (23 bp):
AAATAAAATGATAAGAAAAAATA
Found at i:33567 original size:15 final size:15
Alignment explanation
Indices: 33549--33588 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 15
33539 TATAATTGTA
33549 ATAATAATAATGATG
1 ATAATAATAATGATG
33564 ATAATAA-AA--ATG
1 ATAATAATAATGATG
*
33576 AAAATAATAATGA
1 ATAATAATAATGA
33589 AACGAACCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
12 9 0.43
13 2 0.10
14 2 0.10
15 8 0.38
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (15 bp):
ATAATAATAATGATG
Found at i:33635 original size:2 final size:2
Alignment explanation
Indices: 33630--33662 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
33620 ATAAAAATAA
33630 AT 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 AT A
33663 AAAAGAAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35205 original size:85 final size:85
Alignment explanation
Indices: 35062--36568 Score: 1722
Period size: 85 Copynumber: 17.8 Consensus size: 85
35052 GTCATCAAGA
* * * * ** * * *
35062 TGAATGGAATCGAACTCGATA-ATTTTTGCTGACAGATAGCTTTTCTCGACTTAAGCTATGTTGT
1 TGAATGTAATCGAACTCGA-AGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGT
* * * *
35126 GAATTTGACATGCCCTTCAGC
65 AAATTTGATATGCCTTTGAGC
* * * * *
35147 TGAATGTAATCGAGCTCGAAGGTATTTGTTGACAGATAACCCTTCTCACCTTGAGCTATACTGTA
1 TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTA
* *
35212 AATTTAATATGCCTTTGAGT
66 AATTTGATATGCCTTTGAGC
* * * * * * * * *
35232 TGAATGTAATCAAACTTGGAGGTCTTTGCTGACAGATAACCCTTCTTGCCTTAAGTTATGTTGTA
1 TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTA
*
35297 AATTGGATATGCCTTTGAGC
66 AATTTGATATGCCTTTGAGC
* * * * *
35317 TGAATGTAATCGAAATCAGAA-GTCTTTATTGACAAATAGTCATTCTCGCCTTGAGCTATGCTGT
1 TGAATGTAATCGAACTC-GAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGT
* *
35381 AAATTTGATGTGTCTTTGAGC
65 AAATTTGATATGCCTTTGAGC
* * * * * * *
35402 TGAATGTAATCAAACTCGAAGGTCTTGGTTGACAGATAACCATTCTCACCTTGAGTTATGTTGTA
1 TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTA
* * * *
35467 GATTTGATGTGCCTTTTAGT
66 AATTTGATATGCCTTTGAGC
* * * * * * *
35487 TGAGTGTAATCGAACTCGAAGATCTTGGTTGACAGATAGTCCTTCTCGTCTTGAGCTAAGCTGCA
1 TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTA
* *
35552 AATTTGATGTGCATTTGAGC
66 AATTTGATATGCCTTTGAGC
* * * * **
35572 TGAGTGTAATCAAACTCGAAGGACTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTACA
1 TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTA
*
35637 AATTTGATGTGCCTTTGAGC
66 AATTTGATATGCCTTTGAGC
* * * * *
35657 TGAGTGTAATCGAACTCGAAGGTCTTGGTTGATAGATAGCCCTTATCGCCTTGAGCTATGCTATA
1 TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTA
* *
35722 AATTTAATGTGCCTTTGAGC
66 AATTTGATATGCCTTTGAGC
* * * * * * **
35742 TGAGTGTAATCGAACTCGAAGGACTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGTTGCG
1 TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTA
35807 AATTTGATATGCCTTTGAGC
66 AATTTGATATGCCTTTGAGC
* * * *
35827 TGAGTGTAATCGAACTGGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATACTGT
1 TGAATGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGT
*
35892 AAATTTGATTTGCCTTTGAGC
65 AAATTTGATATGCCTTTGAGC
* *
35913 TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTTGCCTTGAGCTATGCTATA
1 TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTA
**
35978 AATTTGATATGTTTTTGAGC
66 AATTTGATATGCCTTTGAGC
* * * *
35998 TGAATGTAATTGAACTCAAAGGT-TTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGT
1 TGAATGTAATCGAACTCGAAGGTCTTT-GTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGT
*
36062 AAATTTGATAGGCCTTTGAGC
65 AAATTTGATATGCCTTTGAGC
* *
36083 T-AAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCATTTTCGCCTTGAGCTATGCTGT
1 TGAA-TGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGT
**
36147 AAGGTTGATATGCCTTTGAGC
65 AAATTTGATATGCCTTTGAGC
** *
36168 TGAGCGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTA
1 TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTA
36233 AA--T-ATA--CCTTTGAGC
66 AATTTGATATGCCTTTGAGC
* * *
36248 TGAATGTAATCGAACTCGAAGGTCTTTTGTTGACATATAACCCTTCTCACCTTGAGCTATGCTGT
1 TGAATGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGT
* *
36313 AAATTTGATGTGCCTTTGAGT
65 AAATTTGATATGCCTTTGAGC
* * * * * * **
36334 TGAGTGT-ATCGAACTCGAAGGTCTTGGTTGGCAGATAACCCTTCTCACCTTGAGTTATGCTGGG
1 TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTA
36398 AATTTGATATGCCTTTGAGC
66 AATTTGATATGCCTTTGAGC
* * * * *
36418 T-AAGTGTAATCGAACTCAAAAGTATTTTGTTGACAGATAGCCCTTCTCGCCTTGACCTATGCTA
1 TGAA-TGTAATCGAACTCGAAGGT-CTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTG
*
36482 TAAATTTGATGTGCCTTTGAGC
64 TAAATTTGATATGCCTTTGAGC
* * * * * * * *
36504 TTAATATAATCAAAATCGAATGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTATGTTGTA
1 TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTA
36569 CTAGGTTTGT
Statistics
Matches: 1216, Mismatches: 188, Indels: 36
0.84 0.13 0.03
Matches are distributed among these distances:
80 31 0.03
81 39 0.03
82 3 0.00
83 3 0.00
84 68 0.06
85 908 0.75
86 162 0.13
87 2 0.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (85 bp):
TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTA
AATTTGATATGCCTTTGAGC
Found at i:37741 original size:94 final size:96
Alignment explanation
Indices: 37555--37753 Score: 267
Period size: 94 Copynumber: 2.1 Consensus size: 96
37545 GGACAGCTCA
* * * *
37555 ATATATAAACACCTTTATCAGGTTAGCTAAATATTATCCATAAAGTTAGTGCGTTTAACCAATTG
1 ATATATAATCACCTTTATCAGGCTAGCCAAATATTATCCATAAAGTTAGGGCGTTTAACCAATTG
* *
37620 CCTTAAAGGGATAACTCAAGCTTTATTGTAT
66 CCTTAAAGGGACAACTAAAGCTTTATTGTAT
* * * *
37651 AT-TATAATCACCTTTATCAGGCTAGCCGAATCTTATCCATAAAG-TCGGGCGTTTAACTAATTG
1 ATATATAATCACCTTTATCAGGCTAGCCAAATATTATCCATAAAGTTAGGGCGTTTAACCAATTG
* * *
37714 CTTTAGAGGGACAGCTAAAGCTTTATTGTAT
66 CCTTAAAGGGACAACTAAAGCTTTATTGTAT
37745 ATATATAAT
1 ATATATAAT
37754 ATTATAACCT
Statistics
Matches: 89, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
94 44 0.49
95 43 0.48
96 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (96 bp):
ATATATAATCACCTTTATCAGGCTAGCCAAATATTATCCATAAAGTTAGGGCGTTTAACCAATTG
CCTTAAAGGGACAACTAAAGCTTTATTGTAT
Found at i:41693 original size:14 final size:13
Alignment explanation
Indices: 41675--41802 Score: 50
Period size: 14 Copynumber: 9.2 Consensus size: 13
41665 AAACAAATGG
41675 AATAAATAAAATA
1 AATAAATAAAATA
41688 ATATAAGA-AAAA-A
1 A-ATAA-ATAAAATA
41701 AATATAAGGTAAAGATA
1 AATA-AA--TAAA-ATA
41718 AA-AAAGT-AAATAA
1 AATAAA-TAAAAT-A
*
41731 AACAAATAAAATAA
1 AATAAATAAAAT-A
*
41745 AGATAAAGAAAAATA
1 A-ATAAA-TAAAATA
*
41760 AATAAATAAACAGA
1 AATAAATAAA-ATA
*
41774 ATAAAAATAAACATA
1 A-ATAAATAAA-ATA
*
41789 AAGAAAT-AAATA
1 AATAAATAAAATA
41801 AA
1 AA
41803 GATAAAGAAA
Statistics
Matches: 93, Mismatches: 7, Indels: 31
0.71 0.05 0.24
Matches are distributed among these distances:
12 11 0.12
13 15 0.16
14 33 0.35
15 24 0.26
16 7 0.08
17 3 0.03
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.17
Consensus pattern (13 bp):
AATAAATAAAATA
Found at i:41766 original size:38 final size:38
Alignment explanation
Indices: 41678--41802 Score: 118
Period size: 38 Copynumber: 3.3 Consensus size: 38
41668 CAAATGGAAT
* *
41678 AAATAAAATAATATAAGA-AAA-AAAATATAAGGTAAAGATA
1 AAAT-AAATAA-ATAAAACAAATAAAATA-AAGATAAAGA-A
*
41718 AAA-AAGTAAATAAAACAAATAAAATAAAGATAAAGAA
1 AAATAAATAAATAAAACAAATAAAATAAAGATAAAGAA
*
41755 AAATAAATAAAT-AAACAGAATAAAAATAAACATAAAG--
1 AAATAAATAAATAAAACA-AAT-AAAATAAAGATAAAGAA
41792 AAATAAATAAA
1 AAATAAATAAA
41803 GATAAAGAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
37 25 0.33
38 27 0.36
39 20 0.27
40 3 0.04
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.17
Consensus pattern (38 bp):
AAATAAATAAATAAAACAAATAAAATAAAGATAAAGAA
Found at i:41784 original size:33 final size:33
Alignment explanation
Indices: 41740--41802 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
41730 AAACAAATAA
* * *
41740 AATAAAGATAAAGAAAAATAAATAAATAAACAG
1 AATAAAAATAAACAAAAAGAAATAAATAAACAG
*
41773 AATAAAAATAAACATAAAGAAATAAATAAA
1 AATAAAAATAAACAAAAAGAAATAAATAAA
41803 GATAAAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.16
Consensus pattern (33 bp):
AATAAAAATAAACAAAAAGAAATAAATAAACAG
Found at i:41824 original size:6 final size:6
Alignment explanation
Indices: 41815--41853 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
41805 TAAAGAAAAA
* *
41815 AAATAC AAATAC AAATAC AAACAC AAATAC AAACAC AAA
1 AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC AAA
41854 CGCAAACGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.69, C:0.21, G:0.00, T:0.10
Consensus pattern (6 bp):
AAATAC
Found at i:41824 original size:29 final size:30
Alignment explanation
Indices: 41710--41825 Score: 84
Period size: 29 Copynumber: 3.9 Consensus size: 30
41700 AAATATAAGG
*
41710 TAAAGATAAAAAAGTAA-ATAAAACAAATAAAA
1 TAAAGATAAAAAA--AACATAATACAAAT-AAA
* *
41742 TAAAGATAAAGAAAA-ATAA-ATAAATAAA
1 TAAAGATAAAAAAAACATAATACAAATAAA
* * *
41770 CAGA-ATAAAAATAAACATAA-AGAAATAAA
1 TAAAGATAAAAA-AAACATAATACAAATAAA
41799 TAAAGATAAAGAAAAA-A-AATACAAATA
1 TAAAGATAAA-AAAAACATAATACAAATA
41826 CAAATACAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
27 6 0.09
28 10 0.14
29 26 0.37
30 14 0.20
31 2 0.03
32 12 0.17
ACGTcount: A:0.74, C:0.03, G:0.07, T:0.16
Consensus pattern (30 bp):
TAAAGATAAAAAAAACATAATACAAATAAA
Found at i:41832 original size:12 final size:12
Alignment explanation
Indices: 41815--42074 Score: 151
Period size: 12 Copynumber: 21.7 Consensus size: 12
41805 TAAAGAAAAA
*
41815 AAATACAAATAC
1 AAATACAAACAC
41827 AAATACAAACAC
1 AAATACAAACAC
41839 AAATACAAACAC
1 AAATACAAACAC
** *
41851 AAACGCAAACGC
1 AAATACAAACAC
** *
41863 AAACGCAAACGC
1 AAATACAAACAC
** *
41875 AAACGCAAACGC
1 AAATACAAACAC
** *
41887 AAACGCAAACGC
1 AAATACAAACAC
** *
41899 AAACGCAAACGC
1 AAATACAAACAC
** *
41911 AAACGCAAACGC
1 AAATACAAACAC
** *
41923 AAACGCAAACGC
1 AAATACAAACAC
** *
41935 AAACGCAAACGC
1 AAATACAAACAC
** *
41947 AAACGCAAACGC
1 AAATACAAACAC
**
41959 AAACGCAAACAC
1 AAATACAAACAC
*
41971 AAATACAAATAC
1 AAATACAAACAC
* **
41983 AAATGCAAATGC
1 AAATACAAACAC
* *
41995 AAATGCAAATAC
1 AAATACAAACAC
*
42007 AAATACAAATAC
1 AAATACAAACAC
*
42019 AAATACAAATAC
1 AAATACAAACAC
*
42031 AAATACAAATAC
1 AAATACAAACAC
*
42043 AAATACAAATAC
1 AAATACAAACAC
*
42055 AAATACAAATAC
1 AAATACAAACAC
42067 AAATACAA
1 AAATACAA
42075 CAAAACAAAA
Statistics
Matches: 236, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 236 1.00
ACGTcount: A:0.58, C:0.25, G:0.08, T:0.08
Consensus pattern (12 bp):
AAATACAAACAC
Found at i:41854 original size:6 final size:6
Alignment explanation
Indices: 41819--42085 Score: 135
Period size: 6 Copynumber: 45.0 Consensus size: 6
41809 GAAAAAAAAT
* * * * *
41819 ACAAAT ACAAAT ACAAAC ACAAAT ACAAAC ACAAAC GCAAAC GCAAAC
1 ACAAAC ACAAAC ACAAAC ACAAAC ACAAAC ACAAAC ACAAAC ACAAAC
* * * * * * * *
41867 GCAAAC GCAAAC GCAAAC GCAAAC GCAAAC GCAAAC GCAAAC GCAAAC
1 ACAAAC ACAAAC ACAAAC ACAAAC ACAAAC ACAAAC ACAAAC ACAAAC
* * * * * * * *
41915 GCAAAC GCAAAC GCAAAC GCAAAC GCAAAC GCAAAC GCAAAC GCAAAC
1 ACAAAC ACAAAC ACAAAC ACAAAC ACAAAC ACAAAC ACAAAC ACAAAC
* * * * * * * * * * *
41963 GCAAAC ACAAAT ACAAAT ACAAAT GCAAAT GCAAAT GCAAAT ACAAAT
1 ACAAAC ACAAAC ACAAAC ACAAAC ACAAAC ACAAAC ACAAAC ACAAAC
* * * * * * * *
42011 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
1 ACAAAC ACAAAC ACAAAC ACAAAC ACAAAC ACAAAC ACAAAC ACAAAC
* *
42059 ACAAAT ACAAAT AC-AAC A-AAAC A-AAAC
1 ACAAAC ACAAAC ACAAAC ACAAAC ACAAAC
42086 GAAAATAACA
Statistics
Matches: 251, Mismatches: 9, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
5 11 0.04
6 240 0.96
ACGTcount: A:0.59, C:0.25, G:0.08, T:0.07
Consensus pattern (6 bp):
ACAAAC
Found at i:42117 original size:6 final size:6
Alignment explanation
Indices: 41964--42074 Score: 186
Period size: 6 Copynumber: 18.5 Consensus size: 6
41954 AACGCAAACG
* * * *
41964 CAAACA CAAATA CAAATA CAAATG CAAATG CAAATG CAAATA CAAATA
1 CAAATA CAAATA CAAATA CAAATA CAAATA CAAATA CAAATA CAAATA
42012 CAAATA CAAATA CAAATA CAAATA CAAATA CAAATA CAAATA CAAATA
1 CAAATA CAAATA CAAATA CAAATA CAAATA CAAATA CAAATA CAAATA
42060 CAAATA CAAATA CAA
1 CAAATA CAAATA CAA
42075 CAAAACAAAA
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 102 1.00
ACGTcount: A:0.64, C:0.18, G:0.03, T:0.15
Consensus pattern (6 bp):
CAAATA
Found at i:42188 original size:23 final size:22
Alignment explanation
Indices: 42162--42233 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 22
42152 ACGAAATAAC
*
42162 AAAAGAAAT-AAAAATAAAAGCAA
1 AAAAGAAATGAAAAA-AAAAAC-A
*
42185 AAAAGTAATGAAAAAAAAAACA
1 AAAAGAAATGAAAAAAAAAACA
*
42207 AAAAGAAAATGAAAAGAAAAAATA
1 AAAAG-AAATGAAAA-AAAAAACA
42231 AAA
1 AAA
42234 TAAAATAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
22 6 0.14
23 21 0.50
24 15 0.36
ACGTcount: A:0.79, C:0.03, G:0.10, T:0.08
Consensus pattern (22 bp):
AAAAGAAATGAAAAAAAAAACA
Found at i:42243 original size:28 final size:27
Alignment explanation
Indices: 42194--42254 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
42184 AAAAAGTAAT
42194 GAAAAAAAAAACAAAAAGAAAATGAAAA
1 GAAAAAAAAAACAAAAAGAAAAT-AAAA
* *
42222 GAAAAAATAAAA-TAAAATAAAATAAAA
1 GAAAAAA-AAAACAAAAAGAAAATAAAA
*
42249 TAAAAA
1 GAAAAA
42255 TAATATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 9 0.31
28 16 0.55
29 4 0.14
ACGTcount: A:0.82, C:0.02, G:0.07, T:0.10
Consensus pattern (27 bp):
GAAAAAAAAAACAAAAAGAAAATAAAA
Found at i:42250 original size:20 final size:21
Alignment explanation
Indices: 42225--42293 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 21
42215 ATGAAAAGAA
42225 AAAATAAAATA-AAATAAAAT
1 AAAATAAAATATAAATAAAAT
*
42245 AAAATAAAA-AT-AATATATAT
1 AAAATAAAATATAAATA-AAAT
*
42265 ATAATAATAATAATAAATGAATAAT
1 AAAATAA-AAT-ATAAAT-AA-AAT
42290 AAAA
1 AAAA
42294 GGAACCCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
19 5 0.14
20 18 0.49
21 2 0.05
23 2 0.05
24 4 0.11
25 6 0.16
ACGTcount: A:0.72, C:0.00, G:0.01, T:0.26
Consensus pattern (21 bp):
AAAATAAAATATAAATAAAAT
Found at i:42273 original size:17 final size:16
Alignment explanation
Indices: 42231--42291 Score: 63
Period size: 17 Copynumber: 3.8 Consensus size: 16
42221 AGAAAAAATA
42231 AAATAA-AATAA-AAT
1 AAATAATAATAATAAT
*
42245 AAAATAAAAATAATATAT
1 -AAATAATAATAATA-AT
*
42263 ATATAATAATAATAAT
1 AAATAATAATAATAAT
42279 AAATGAATAATAA
1 AAAT-AATAATAA
42292 AAGGAACCCA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
15 6 0.15
16 10 0.26
17 21 0.54
18 2 0.05
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (16 bp):
AAATAATAATAATAAT
Found at i:42339 original size:2 final size:2
Alignment explanation
Indices: 42334--42396 Score: 78
Period size: 2 Copynumber: 32.5 Consensus size: 2
42324 TAAAAAAACA
*
42334 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AG A- AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
*
42375 AA AT A- AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
42397 AAAAGGACTA
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
1 3 0.05
2 51 0.93
3 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (2 bp):
AT
Found at i:43969 original size:12 final size:12
Alignment explanation
Indices: 43937--43979 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
43927 TAATCTTAGC
43937 ATTCTTTTTATT
1 ATTCTTTTTATT
*
43949 ATTTTTTTTATT
1 ATTCTTTTTATT
*
43961 ATTCATTTT-TT
1 ATTCTTTTTATT
*
43972 CTTCTTTT
1 ATTCTTTT
43980 AATTTTAGCA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 8 0.31
12 18 0.69
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (12 bp):
ATTCTTTTTATT
Found at i:44031 original size:6 final size:5
Alignment explanation
Indices: 44000--44242 Score: 103
Period size: 5 Copynumber: 46.6 Consensus size: 5
43990 TGTTTTCAAG
*
44000 TTTAT TTTAT TTTAT TTTAT TATTATT TTTAT TTGT-T TTATGT TTTAT
1 TTTAT TTTAT TTTAT TTTAT T-TTA-T TTTAT TT-TAT TT-TAT TTTAT
* *
44048 GTTT-T TTTACT TCTTAT TAT-T TTTAT TTT-T TTTACT TTTAAAGT TTAACAT
1 -TTTAT TTTA-T T-TTAT TTTAT TTTAT TTTAT TTTA-T TTT--A-T TT--TAT
* * * *
44099 TTT-T TTTAT TTTTT CCTTTGA- TTTAT TTAAT ATT-T TTTAT TTTGTT
1 TTTAT TTTAT TTTAT --TTT-AT TTTAT TTTAT TTTAT TTTAT TTT-AT
* *
44145 TTTATT TTTAT GTTAT GTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT-T
1 TTTA-T TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
* * * *
44195 CTTTGAT TGT-T TTTAT TTTTT TGTTAT TTT-T ATT-T TTTAA TTTAT
1 -TTT-AT TTTAT TTTAT TTTAT T-TTAT TTTAT TTTAT TTTAT TTTAT
44240 TTT
1 TTT
44243 TTCCTTTGAT
Statistics
Matches: 184, Mismatches: 25, Indels: 58
0.69 0.09 0.22
Matches are distributed among these distances:
4 28 0.15
5 103 0.56
6 36 0.20
7 12 0.07
8 5 0.03
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.75
Consensus pattern (5 bp):
TTTAT
Found at i:44037 original size:43 final size:42
Alignment explanation
Indices: 43990--44081 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
43980 AATTTTAGCA
*
43990 TGTTTTCAAG-TTTAT-TTTATTTTATTTTATTATTATTTTTATT
1 TGTTTT-AAGTTTTATGTTT-TTTTA-CTTATTATTATTTTTATT
* *
44033 TGTTTTATGTTTTATGTTTTTTTACTTCTTATTATTTTTATT
1 TGTTTTAAGTTTTATGTTTTTTTACTTATTATTATTTTTATT
*
44075 TTTTTTA
1 TGTTTTA
44082 CTTTTAAAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
42 24 0.56
43 16 0.37
44 3 0.07
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.74
Consensus pattern (42 bp):
TGTTTTAAGTTTTATGTTTTTTTACTTATTATTATTTTTATT
Found at i:44038 original size:9 final size:8
Alignment explanation
Indices: 44009--44242 Score: 64
Period size: 9 Copynumber: 27.5 Consensus size: 8
43999 GTTTATTTTA
44009 TTTTATTT
1 TTTTATTT
*
44017 TATTATTAT
1 TTTTATT-T
44026 TTTTATTT
1 TTTTATTT
44034 GTTTTATGTT
1 -TTTTAT-TT
* *
44044 TTATGTTT
1 TTTTATTT
*
44052 TTTTA-CT
1 TTTTATTT
*
44059 TCTTATTAT
1 TTTTATT-T
44068 TTTTATTTT
1 TTTTA-TTT
*
44077 TTTTACTT
1 TTTTATTT
** *
44085 TTAAAGTT
1 TTTTATTT
***
44093 TAACATTT
1 TTTTATTT
*
44101 TTTT-TAT
1 TTTTATTT
**
44108 TTTT-TCC
1 TTTTATTT
*
44115 TTTGATTT
1 TTTTATTT
*
44123 ATTTAATATT
1 -TTTTAT-TT
44133 TTTTATTT
1 TTTTATTT
44141 TGTTT-TTAT
1 T-TTTATT-T
44150 TTTTATGTT
1 TTTTAT-TT
*
44159 ATGTTATTTT
1 -TTTTA-TTT
44169 ATTTTATTTT
1 -TTTTA-TTT
44179 ATTTTATTT
1 -TTTTATTT
*
44188 TATTT-TTC
1 T-TTTATTT
*
44196 TTTGATTGT
1 TTTTATT-T
44205 TTTTATTT
1 TTTTATTT
*
44213 TTTTGTTAT
1 TTTTATT-T
44222 TTTTATTT
1 TTTTATTT
*
44230 TTTAATTT
1 TTTTATTT
44238 ATTTT
1 -TTTT
44243 TTCCTTTGAT
Statistics
Matches: 168, Mismatches: 38, Indels: 39
0.69 0.16 0.16
Matches are distributed among these distances:
7 17 0.10
8 55 0.33
9 67 0.40
10 28 0.17
11 1 0.01
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.75
Consensus pattern (8 bp):
TTTTATTT
Found at i:44054 original size:16 final size:15
Alignment explanation
Indices: 44004--44077 Score: 53
Period size: 16 Copynumber: 4.7 Consensus size: 15
43994 TTCAAGTTTA
*
44004 TTTTA-TTTTATTTTA
1 TTTTATTTTTA-TTTG
44019 TTATTATTTTTATTTG
1 TT-TTATTTTTATTTG
*
44035 TTTTATGTTTTATGTTT
1 TTTTAT-TTTTAT-TTG
*
44052 TTTTACTTCTTATTAT-
1 TTTTA-TTTTTATT-TG
44068 TTTTATTTTT
1 TTTTATTTTT
44078 TTTACTTTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
15 10 0.20
16 20 0.41
17 18 0.37
18 1 0.02
ACGTcount: A:0.16, C:0.03, G:0.04, T:0.77
Consensus pattern (15 bp):
TTTTATTTTTATTTG
Found at i:44142 original size:24 final size:25
Alignment explanation
Indices: 44105--44151 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
44095 ACATTTTTTT
*
44105 TATTTTTTCCTTTG-ATTTATTTAA
1 TATTTTTTACTTTGTATTTATTTAA
* *
44129 TATTTTTTATTTTGTTTTTATTT
1 TATTTTTTACTTTGTATTTATTT
44152 TTATGTTATG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.74
Consensus pattern (25 bp):
TATTTTTTACTTTGTATTTATTTAA
Found at i:44254 original size:25 final size:24
Alignment explanation
Indices: 44180--44261 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 24
44170 TTTTATTTTA
*
44180 TTTTATTTTA-TTTTTCTTTGATT
1 TTTTAATTTATTTTTTCTTTGATT
* * *
44203 GTTTTTATTT-TTTTGTTATTTTTATT
1 -TTTTAATTTATTTT-TT-CTTTGATT
44229 TTTTAATTTATTTTTTCCTTTGATT
1 TTTTAATTTATTTTTT-CTTTGATT
44254 TATTTAAT
1 T-TTTAAT
44262 ATTTATTTCT
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
24 10 0.22
25 19 0.42
26 16 0.36
ACGTcount: A:0.16, C:0.04, G:0.05, T:0.76
Consensus pattern (24 bp):
TTTTAATTTATTTTTTCTTTGATT
Found at i:46791 original size:28 final size:27
Alignment explanation
Indices: 46769--46844 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 27
46759 GAAATCAAAG
46769 ATAAAATAGTA-AGTAAAAAAAATAAATA
1 ATAAAATA-TATA-TAAAAAAAATAAATA
*
46797 ATAAAATATATAT-AAAAAAAGAAA-A
1 ATAAAATATATATAAAAAAAATAAATA
* *
46822 AGAAAATA-A-ATAAAACAAATAAA
1 ATAAAATATATATAAAAAAAATAAA
46845 CAAAATAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
23 2 0.05
24 10 0.24
25 8 0.19
26 10 0.24
27 3 0.07
28 9 0.21
ACGTcount: A:0.75, C:0.01, G:0.05, T:0.18
Consensus pattern (27 bp):
ATAAAATATATATAAAAAAAATAAATA
Found at i:46802 original size:14 final size:13
Alignment explanation
Indices: 46782--46849 Score: 52
Period size: 13 Copynumber: 5.4 Consensus size: 13
46772 AAATAGTAAG
46782 TAAAAAAAATAAA
1 TAAAAAAAATAAA
* *
46795 T-AATAAAATATA
1 TAAAAAAAATAAA
*
46807 TATAAAAAAA-GAA
1 TA-AAAAAAATAAA
*
46820 -AAAGAAAATAAA
1 TAAAAAAAATAAA
*
46832 TAAAACAAATAAA
1 TAAAAAAAATAAA
*
46845 CAAAA
1 TAAAA
46850 TAATAATAAC
Statistics
Matches: 41, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
11 6 0.15
12 13 0.32
13 16 0.39
14 6 0.15
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (13 bp):
TAAAAAAAATAAA
Found at i:46827 original size:25 final size:24
Alignment explanation
Indices: 46784--46836 Score: 63
Period size: 26 Copynumber: 2.2 Consensus size: 24
46774 ATAGTAAGTA
* *
46784 AAAAAAATAAATAATAAAATATATAT
1 AAAAAAAGAAATAAGAAAATA-A-AT
46810 AAAAAAAGAAA-AAGAAAATAAAT
1 AAAAAAAGAAATAAGAAAATAAAT
46833 AAAA
1 AAAA
46837 CAAATAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.24
24 1 0.04
25 8 0.32
26 10 0.40
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (24 bp):
AAAAAAAGAAATAAGAAAATAAAT
Found at i:47236 original size:25 final size:23
Alignment explanation
Indices: 47192--47274 Score: 84
Period size: 24 Copynumber: 3.6 Consensus size: 23
47182 TATAACAACA
47192 ATAATATCAA-AAAAAATATATAAT
1 ATAATAT-AATAAAAAATATAT-AT
*
47216 ATAATGATAATAAAAAATATAGA-
1 ATAAT-ATAATAAAAAATATATAT
47239 A-AAT-TAATAGAAAAATATATAT
1 ATAATATAATA-AAAAATATATAT
*
47261 ATAATATTATAAAA
1 ATAATATAATAAAA
47275 TATAGCACTT
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
20 5 0.10
21 10 0.20
22 4 0.08
23 7 0.14
24 12 0.24
25 12 0.24
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (23 bp):
ATAATATAATAAAAAATATATAT
Found at i:47274 original size:21 final size:21
Alignment explanation
Indices: 47204--47278 Score: 60
Period size: 23 Copynumber: 3.4 Consensus size: 21
47194 AATATCAAAA
*
47204 AAAATATATAATATAATGATAAT
1 AAAATATAT-ATATAAT-ATTAT
* * * * *
47227 AAAAAATATAGAAAATTAATAGA
1 AAAATATATATATAA-TATTA-T
47250 AAAATATATATATAATATTAT
1 AAAATATATATATAATATTAT
47271 AAAATATA
1 AAAATATA
47279 GCACTTAAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 6
0.70 0.20 0.11
Matches are distributed among these distances:
21 8 0.21
22 10 0.26
23 21 0.54
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (21 bp):
AAAATATATATATAATATTAT
Found at i:47447 original size:33 final size:30
Alignment explanation
Indices: 47371--47449 Score: 81
Period size: 30 Copynumber: 2.6 Consensus size: 30
47361 TATATATAAC
* *
47371 AAAATAAATAAT-ATAAAAAAATACAAGTA
1 AAAATAAATAATAATAAAAAAAGAAAAGTA
* *
47400 ATAATACAAGAATAATAAAAAAAGAGAAAGTA
1 AAAATA-AATAATAATAAAAAAAGA-AAAGTA
*
47432 AAAA-ATATAATAATAAAA
1 AAAATAAATAATAATAAAA
47450 TATAAAAATA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
29 5 0.12
30 16 0.40
31 11 0.28
32 8 0.20
ACGTcount: A:0.72, C:0.03, G:0.06, T:0.19
Consensus pattern (30 bp):
AAAATAAATAATAATAAAAAAAGAAAAGTA
Found at i:47512 original size:12 final size:12
Alignment explanation
Indices: 47490--47534 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
47480 GAATAAAAGG
47490 AAAATATAATAGT
1 AAAA-ATAATAGT
*
47503 AAAAATAATAAT
1 AAAAATAATAGT
*
47515 AAATATAATAGT
1 AAAAATAATAGT
*
47527 AATAATAA
1 AAAAATAA
47535 AAATACAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
AAAAATAATAGT
Found at i:47518 original size:24 final size:24
Alignment explanation
Indices: 47491--47539 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
47481 AATAAAAGGA
*
47491 AAATATAATAGTAAAAATAATAAT
1 AAATATAATAGTAAAAATAAAAAT
*
47515 AAATATAATAGTAATAATAAAAAT
1 AAATATAATAGTAAAAATAAAAAT
47539 A
1 A
47540 CAAAGAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (24 bp):
AAATATAATAGTAAAAATAAAAAT
Found at i:48147 original size:37 final size:37
Alignment explanation
Indices: 48106--48197 Score: 139
Period size: 37 Copynumber: 2.5 Consensus size: 37
48096 GTGCTTGTGG
* * *
48106 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCATAGCAAAACTCT
* *
48143 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCATAGCAAAACTCT
48180 ATCCTATTTTTAGGAGTT
1 ATCCTATTTTTAGGAGTT
48198 GGATATCCTT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCATAGCAAAACTCT
Found at i:48735 original size:106 final size:106
Alignment explanation
Indices: 48417--49898 Score: 2172
Period size: 106 Copynumber: 14.0 Consensus size: 106
48407 AAATTGTTCT
* * * ** * *
48417 GAGTCCAGTATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
* * *
48481 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTT-CTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC-GTTGTCTG
* * * *
48523 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * * * * *
48582 TCAGCCGCCCCTTCGTCTTGAAGTTGAGCTTGTGTTATCT-
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
48622 TATGTCCAAGATCATTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
1 GA-GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
* * *
48687 ACCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGTGTTGTCTT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
48729 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
48794 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* ** *
48835 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTTAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
48900 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
48941 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
49006 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
49047 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGCAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
49112 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
49153 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
49218 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
49259 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
49324 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCCTTTTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
49365 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGACATTGAGAAGTTGTTTGTTGAAAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
49430 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
49471 GAGTCCAATATCCTTCGCTGTAAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGAAAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
49536 CCAGCGATCCCTTCGTCGTGAAGCTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
49577 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTAGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
49642 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
49683 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
49748 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
49789 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * *
49854 CCAGCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
49895 GAGT
1 GAGT
49899 GGCACGATAT
Statistics
Matches: 1250, Mismatches: 116, Indels: 20
0.90 0.08 0.01
Matches are distributed among these distances:
99 1 0.00
100 78 0.06
101 3 0.00
102 4 0.00
104 3 0.00
105 3 0.00
106 1156 0.92
107 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:50834 original size:22 final size:22
Alignment explanation
Indices: 50808--50884 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
50798 TTGTGTTTGG
*
50808 TCAAAGGTTTGGCATTTGACGC
1 TCAAAGGTTTGGCATTTGATGC
*
50830 TCAAAGGTTTAGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
50852 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
50874 TCAAAGGTTTG
1 TCAAAGGTTTG
50885 ATGGGGTAGC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:51522 original size:7 final size:7
Alignment explanation
Indices: 51490--51564 Score: 55
Period size: 7 Copynumber: 10.7 Consensus size: 7
51480 TTTTTGTCCC
51490 TTTTTC-
1 TTTTTCT
**
51496 TTTTTGA
1 TTTTTCT
*
51503 TTTTTGT
1 TTTTTCT
*
51510 TCTTTCT
1 TTTTTCT
51517 TTTTTCT
1 TTTTTCT
*
51524 TTTGT-T
1 TTTTTCT
*
51530 TTCTTCT
1 TTTTTCT
51537 TTTTTGCT
1 TTTTT-CT
51545 TCTTTTCT
1 T-TTTTCT
*
51553 TTTTTGT
1 TTTTTCT
51560 TTTTT
1 TTTTT
51565 TTCTTTCTGT
Statistics
Matches: 55, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
6 9 0.16
7 36 0.65
8 6 0.11
9 4 0.07
ACGTcount: A:0.01, C:0.12, G:0.07, T:0.80
Consensus pattern (7 bp):
TTTTTCT
Found at i:51526 original size:20 final size:20
Alignment explanation
Indices: 51492--51566 Score: 59
Period size: 20 Copynumber: 3.8 Consensus size: 20
51482 TTTGTCCCTT
**
51492 TTTCTTTTTGATTTTTGTTC
1 TTTCTTTTTTCTTTTTGTTC
*
51512 TTTCTTTTTTC-TTTTGTTT
1 TTTCTTTTTTCTTTTTGTTC
*
51531 TCTTCTTTTTTGCTTCTT-TTC
1 T-TTCTTTTTT-CTTTTTGTTC
51552 TTT-TTTGTTT-TTTTT
1 TTTCTTT-TTTCTTTTT
51567 CTTTCTGTTC
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
18 4 0.09
19 11 0.24
20 23 0.51
21 4 0.09
22 3 0.07
ACGTcount: A:0.01, C:0.12, G:0.07, T:0.80
Consensus pattern (20 bp):
TTTCTTTTTTCTTTTTGTTC
Found at i:51554 original size:16 final size:15
Alignment explanation
Indices: 51513--51570 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 15
51503 TTTTTGTTCT
51513 TTCTTTT-TTCTTTTG
1 TTCTTTTCTT-TTTTG
51528 TT-TTCTTCTTTTTTG
1 TTCTT-TTCTTTTTTG
51543 CTTCTTTTCTTTTTTG
1 -TTCTTTTCTTTTTTG
*
51559 TTTTTTTTCTTT
1 -TTCTTTTCTTT
51571 CTGTTCTGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
14 2 0.05
15 9 0.24
16 24 0.65
17 2 0.05
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (15 bp):
TTCTTTTCTTTTTTG
Found at i:51556 original size:35 final size:34
Alignment explanation
Indices: 51503--51569 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 34
51493 TTCTTTTTGA
51503 TTTTTGTTCTTTCTTTTTTCT-TTTGTTTTCTTCT
1 TTTTTGTTCTTTCTTTTTT-TGTTTGTTTTCTTCT
*
51537 TTTTTGCTTCTTT-TCTTTTTTGTTTTTTTTCTT
1 TTTTTG-TTCTTTCT-TTTTTTGTTTGTTTTCTT
51570 TCTGTTCTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 8 0.28
35 21 0.72
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (34 bp):
TTTTTGTTCTTTCTTTTTTTGTTTGTTTTCTTCT
Found at i:56200 original size:12 final size:12
Alignment explanation
Indices: 56183--56210 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
56173 TATATATATA
56183 AAAAAGAAAAAG
1 AAAAAGAAAAAG
56195 AAAAAGAAAAAG
1 AAAAAGAAAAAG
56207 AAAA
1 AAAA
56211 TAAATAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:56844 original size:24 final size:27
Alignment explanation
Indices: 56817--56870 Score: 78
Period size: 24 Copynumber: 2.1 Consensus size: 27
56807 AAAGAGAAAG
56817 TAAAAAAATATA-ATA-ATAA-AAAAA
1 TAAAAAAATATACATATATAATAAAAA
*
56841 TAAAAAAATATACATATATAATATAAA
1 TAAAAAAATATACATATATAATAAAAA
56868 TAA
1 TAA
56871 GTAGAATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 12 0.46
25 3 0.12
26 4 0.15
27 7 0.27
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (27 bp):
TAAAAAAATATACATATATAATAAAAA
Found at i:56850 original size:16 final size:16
Alignment explanation
Indices: 56761--56850 Score: 56
Period size: 16 Copynumber: 5.2 Consensus size: 16
56751 ATATATATAT
* *
56761 ATAACAAAAT-AAATA
1 ATAAAAAAATAAAAAA
56776 ATATAAAAAATAATACAAGA
1 ATA-AAAAAATAA-A-AA-A
*
56796 ATAATAAAAAGAAAGAGAA
1 ATAA-AAAAATAAA-A-AA
* *
56815 AGTAAAAAAATATAATA
1 A-TAAAAAAATAAAAAA
56832 ATAAAAAAATAAAAAA
1 ATAAAAAAATAAAAAA
56848 ATA
1 ATA
56851 TACATATATA
Statistics
Matches: 58, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
15 3 0.05
16 22 0.38
17 3 0.05
18 2 0.03
19 13 0.22
20 15 0.26
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.18
Consensus pattern (16 bp):
ATAAAAAAATAAAAAA
Found at i:65386 original size:30 final size:30
Alignment explanation
Indices: 65238--65369 Score: 239
Period size: 30 Copynumber: 4.4 Consensus size: 30
65228 TCCGAAGGAC
65238 CTATCCAGA-GTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
65267 CTATCCAGAGGTCATAAAGATCTTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
65297 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
65327 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
65357 CTATCCATAGGTC
1 CTATCCAGAGGTC
65370 CCGAAGAACC
Statistics
Matches: 99, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
29 9 0.09
30 90 0.91
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:65386 original size:60 final size:60
Alignment explanation
Indices: 65238--65394 Score: 226
Period size: 60 Copynumber: 2.6 Consensus size: 60
65228 TCCGAAGGAC
* *
65238 CTATCCAGA-GTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCTTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
*
65297 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
* * * * *
65357 CTATCCATAGGTCCCGAAGAACCTAGGTAAACTATCCA
1 CTATCCAGAGGTCACAAAGATCCTCGGT-AACTATCCA
65395 TATATCCTTA
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
59 9 0.10
60 71 0.80
61 9 0.10
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (60 bp):
CTATCCAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:65627 original size:4 final size:4
Alignment explanation
Indices: 65618--65658 Score: 68
Period size: 4 Copynumber: 10.8 Consensus size: 4
65608 TTCATATAAC
65618 CATA CATA CATA CATA CATA CATA CATA CAT- -ATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT
65659 GTCATCATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
4 33 0.94
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (4 bp):
CATA
Found at i:70017 original size:30 final size:30
Alignment explanation
Indices: 69981--70078 Score: 142
Period size: 30 Copynumber: 3.2 Consensus size: 30
69971 TTCCGAGGAC
69981 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
70011 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* * * * *
70041 CTATCCATAGGTCCTGAAGAACCTAGGTAAA
1 CTATCCAGAGGTCATAAAGATCCTCGGT-AA
70072 CTATCCA
1 CTATCCA
70079 TATGTTCCTT
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
30 53 0.85
31 9 0.15
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:70093 original size:31 final size:32
Alignment explanation
Indices: 70039--70114 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 32
70029 GATCCTCGGT
* *
70039 AACTATCCATA-GGTCCTGAAGAACCTAGGTA
1 AACTATCCATATGTTCCTGAAGAACATAGGTA
*
70070 AACTATCCATATGTTCCT-TAGAACATAGGTA
1 AACTATCCATATGTTCCTGAAGAACATAGGTA
* *
70101 TACTGTCCATATGT
1 AACTATCCATATGT
70115 CTCGAAAGAC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 34 0.87
32 5 0.13
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (32 bp):
AACTATCCATATGTTCCTGAAGAACATAGGTA
Found at i:71347 original size:20 final size:20
Alignment explanation
Indices: 71318--71357 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
71308 CATTGATGCA
71318 TCGGTACACAATGAATGTGC
1 TCGGTACACAATGAATGTGC
*
71338 TCGGTGCACAATGAATGTGC
1 TCGGTACACAATGAATGTGC
71358 ATCGATGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (20 bp):
TCGGTACACAATGAATGTGC
Done.