Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002685.1 Hibiscus syriacus cultivar Beakdansim tig00005549_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: 67374
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:2374 original size:21 final size:21
Alignment explanation
Indices: 2307--2384 Score: 77
Period size: 22 Copynumber: 3.7 Consensus size: 21
2297 CGGTGTTTGA
* * *
2307 GTGCATGAATGCACTGCA-TG
1 GTGCATGGATGCACTACAGAG
* **
2327 GTGCATCGATGCACTAGTGCAG
1 GTGCATGGATGCACTACAG-AG
*
2349 GTGCATGGATGCACTACAGGG
1 GTGCATGGATGCACTACAGAG
2370 GTGCATGGATGCACT
1 GTGCATGGATGCACT
2385 TTGACACCCT
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
20 13 0.28
21 16 0.35
22 17 0.37
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.23
Consensus pattern (21 bp):
GTGCATGGATGCACTACAGAG
Found at i:2484 original size:29 final size:28
Alignment explanation
Indices: 2452--2516 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 28
2442 GAAACCTTTT
2452 AAAACTTTGAATAAATTCAATT-AAGTCCA
1 AAAACTTTG--TAAATTCAATTCAAGTCCA
2481 AAAACATTTTGTAAATTCAATTCAAGTCCA
1 AAAAC--TTTGTAAATTCAATTCAAGTCCA
2511 AAAACT
1 AAAACT
2517 ATTTTGCCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
28 1 0.03
29 16 0.48
30 12 0.36
31 4 0.12
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (28 bp):
AAAACTTTGTAAATTCAATTCAAGTCCA
Found at i:2510 original size:30 final size:30
Alignment explanation
Indices: 2463--2522 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
2453 AAACTTTGAA
2463 TAAATTCAATTAAGTCCAAAAAC-ATTTTG
1 TAAATTCAATTAAGTCCAAAAACTATTTTG
2492 TAAATTCAATTCAAGTCCAAAAACTATTTTG
1 TAAATTCAATT-AAGTCCAAAAACTATTTTG
2523 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACTATTTTG
Found at i:2962 original size:21 final size:21
Alignment explanation
Indices: 2887--2963 Score: 59
Period size: 21 Copynumber: 3.7 Consensus size: 21
2877 CGCAAATCAG
2887 TTTCCAGAATCGCATTGCGAT
1 TTTCCAGAATCGCATTGCGAT
* * * *
2908 TCTT-GAAAATCGCAATGTGAT
1 T-TTCCAGAATCGCATTGCGAT
** *
2929 AGTACA-AATTCGCATTGCGAT
1 TTTCCAGAA-TCGCATTGCGAT
2950 TTTCCAGAATCGCA
1 TTTCCAGAATCGCA
2964 ACGCGAATAT
Statistics
Matches: 40, Mismatches: 12, Indels: 8
0.67 0.20 0.13
Matches are distributed among these distances:
20 3 0.08
21 33 0.82
22 4 0.10
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (21 bp):
TTTCCAGAATCGCATTGCGAT
Found at i:2982 original size:20 final size:20
Alignment explanation
Indices: 2957--3012 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
2947 GATTTTCCAG
*
2957 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACAT-ATA
2977 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAACATATA
2997 AATCGCAACGCGAACA
1 AATCGCAACGCGAACA
3013 ATCGCAAGCG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 1 0.03
20 33 0.97
ACGTcount: A:0.45, C:0.25, G:0.18, T:0.12
Consensus pattern (20 bp):
AATCGCAACGCGAACATATA
Found at i:3091 original size:41 final size:41
Alignment explanation
Indices: 3031--3226 Score: 329
Period size: 41 Copynumber: 4.8 Consensus size: 41
3021 CGATCTTACT
** * *
3031 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCATAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
* *
3072 ATCGCAATGACAATACGTAAAATTGCAACGCGTATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
3113 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
3154 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
*
3195 ATCGCAACGACAATACGTAAAATCACAACGCG
1 ATCGCAACGACAATACGTAAAATCGCAACGCG
3227 ATTTTTAAAG
Statistics
Matches: 146, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 146 1.00
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.18
Consensus pattern (41 bp):
ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:3213 original size:20 final size:20
Alignment explanation
Indices: 3069--3215 Score: 147
Period size: 20 Copynumber: 7.2 Consensus size: 20
3059 CGCGTATCCA
*
3069 TAAATCGCAATGACAATACG
1 TAAATCGCAACGACAATACG
* * *
3089 TAAAATTGCAACG-CGTATCCG
1 T-AAATCGCAACGAC-AATACG
3110 TAAATCGCAACGACAATACG
1 TAAATCGCAACGACAATACG
* *
3130 TAAAATCGCAACG-CGTATCCG
1 T-AAATCGCAACGAC-AATACG
3151 TAAATCGCAACGACAATACG
1 TAAATCGCAACGACAATACG
* *
3171 TAAAATCGCAACG-CGTATCCG
1 T-AAATCGCAACGAC-AATACG
3192 TAAATCGCAACGACAATACG
1 TAAATCGCAACGACAATACG
3212 TAAA
1 TAAA
3216 ATCACAACGC
Statistics
Matches: 103, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
20 54 0.52
21 49 0.48
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.18
Consensus pattern (20 bp):
TAAATCGCAACGACAATACG
Found at i:3786 original size:21 final size:20
Alignment explanation
Indices: 3760--3814 Score: 78
Period size: 18 Copynumber: 2.8 Consensus size: 20
3750 TTTGCAGAAG
3760 AATCGCAACGAGAGAAATGAA
1 AATCGCAACGAGAGAAATG-A
*
3781 AATCGCAAC--GCGAAATGA
1 AATCGCAACGAGAGAAATGA
3799 AATCGCAACGAGAGAA
1 AATCGCAACGAGAGAA
3815 TCGCAACGCG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 10 0.33
19 7 0.23
20 4 0.13
21 9 0.30
ACGTcount: A:0.49, C:0.18, G:0.24, T:0.09
Consensus pattern (20 bp):
AATCGCAACGAGAGAAATGA
Found at i:3797 original size:19 final size:18
Alignment explanation
Indices: 3773--3827 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
3763 CGCAACGAGA
3773 GAAATGAAAATCGCAACGC
1 GAAATG-AAATCGCAACGC
3792 GAAATGAAATCGCAA--C
1 GAAATGAAATCGCAACGC
*
3808 GAGA-G-AATCGCAACGC
1 GAAATGAAATCGCAACGC
3824 GAAA
1 GAAA
3828 ACCAAAATCG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
14 8 0.25
15 1 0.03
16 8 0.25
18 9 0.28
19 6 0.19
ACGTcount: A:0.47, C:0.20, G:0.24, T:0.09
Consensus pattern (18 bp):
GAAATGAAATCGCAACGC
Found at i:3873 original size:14 final size:14
Alignment explanation
Indices: 3854--3910 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 14
3844 GATTGTCATT
3854 TCGTTGCGATTCTC
1 TCGTTGCGATTCTC
3868 TCGTTGCGATTTTCATTTC
1 TCGTTGCGA--TTC---TC
*
3887 GCGTTGCGA-TCTC
1 TCGTTGCGATTCTC
3900 TCGTTGCGATT
1 TCGTTGCGATT
3911 TTCATTTCCG
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
13 10 0.29
14 10 0.29
16 5 0.14
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
TCGTTGCGATTCTC
Found at i:3923 original size:33 final size:32
Alignment explanation
Indices: 3840--3929 Score: 139
Period size: 32 Copynumber: 2.8 Consensus size: 32
3830 CAAAATCGCA
*
3840 TTGCGATTGTCATTT--CGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGA-TCTCTCG
3871 TTGCGATTTTCATTTCGCGTTGCGATCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATCTCTCG
3903 TTGCGATTTTCATTTCCGCGTTGCGAT
1 TTGCGATTTTCATTT-CGCGTTGCGAT
3930 AGTCATTCTC
Statistics
Matches: 55, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
31 14 0.25
32 22 0.40
33 19 0.35
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (32 bp):
TTGCGATTTTCATTTCGCGTTGCGATCTCTCG
Found at i:3926 original size:20 final size:21
Alignment explanation
Indices: 3896--3958 Score: 76
Period size: 20 Copynumber: 3.1 Consensus size: 21
3886 CGCGTTGCGA
*
3896 TCTCTCGTTGCGATTTTCATT
1 TCTCGCGTTGCGATTTTCATT
**
3917 TC-CGCGTTGCGATAGTCA-T
1 TCTCGCGTTGCGATTTTCATT
*
3936 TCTCTCGTTGCGATTTTCATT
1 TCTCGCGTTGCGATTTTCATT
3957 TC
1 TC
3959 AACCAAAAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 3 0.09
20 26 0.76
21 5 0.15
ACGTcount: A:0.11, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TCTCGCGTTGCGATTTTCATT
Found at i:5864 original size:93 final size:94
Alignment explanation
Indices: 5651--5874 Score: 344
Period size: 94 Copynumber: 2.4 Consensus size: 94
5641 TAGATTGCTT
* * * * *
5651 AGTAAATTTATTCGGTTGCTGCCAATACTACTAAATTGTTTATTCTTTAACACTATGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAGATAGT
*
5716 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTCTGTTTTGTCTTTTGGTTGA
*
5745 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAA-ATAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAGATAGT
5809 ATTTGT-TTCTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTCTGTTTTGTCTTTTGGTTG-A
* *
5838 AGTAAATTTGTTCGGTTGCTGCCAATTATGCTAAACT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACT
5875 AATACCCTGA
Statistics
Matches: 120, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
92 20 0.17
93 46 0.38
94 54 0.45
ACGTcount: A:0.24, C:0.13, G:0.17, T:0.46
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAGATAGT
ATTTGTCTTCTGTTTTGTCTTTTGGTTGA
Found at i:6011 original size:19 final size:19
Alignment explanation
Indices: 5971--6066 Score: 94
Period size: 19 Copynumber: 5.3 Consensus size: 19
5961 TAGTTTACTT
* *
5971 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
5991 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
6010 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
*
6024 TCGCAACGAGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
**
6043 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
6062 TCGCA
1 TCGCA
6067 TTGCGATTTT
Statistics
Matches: 63, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
14 10 0.16
15 1 0.02
16 1 0.02
17 2 0.03
18 1 0.02
19 36 0.57
20 12 0.19
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:6027 original size:14 final size:14
Alignment explanation
Indices: 6008--6034 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5998 GCGAAATGAA
6008 AATCGCAACGAGAG
1 AATCGCAACGAGAG
6022 AATCGCAACGAGA
1 AATCGCAACGAGA
6035 AATGAAAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.22, G:0.26, T:0.07
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:6084 original size:19 final size:19
Alignment explanation
Indices: 6062--6192 Score: 82
Period size: 19 Copynumber: 7.8 Consensus size: 19
6052 GAAACCAAAA
6062 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
6081 TCGCATTGTGA--TTC-TC
1 TCGCATTGCGATTTTCATT
6097 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
6114 TCGCATTGCGA--TTC-TG
1 TCGCATTGCGATTTTCATT
*
6130 TCG--TTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
*
6147 TCGCGTTGCG--TTTC---
1 TCGCATTGCGATTTTCATT
6161 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
6178 TCGCGA-TGCGATTTT
1 TCGC-ATTGCGATTTT
6193 AAGTTTCGTG
Statistics
Matches: 86, Mismatches: 8, Indels: 36
0.66 0.06 0.28
Matches are distributed among these distances:
12 5 0.06
14 18 0.21
16 13 0.15
17 20 0.23
19 30 0.35
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:6109 original size:33 final size:33
Alignment explanation
Indices: 6067--6190 Score: 182
Period size: 33 Copynumber: 3.8 Consensus size: 33
6057 CAAAATCGCA
*
6067 TTGCGATTTTCATTTCGCATTGTGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
6100 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* *
6133 TTGCGATTTTTATTTCGCGTTGCG-TT-TCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
6164 TTGCGATTTTCATTTCGCGA-TGCGATT
1 TTGCGATTTTCATTTCGC-ATTGCGATT
6191 TTAAGTTTCG
Statistics
Matches: 82, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
31 25 0.30
32 4 0.05
33 53 0.65
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:6180 original size:64 final size:66
Alignment explanation
Indices: 6067--6190 Score: 191
Period size: 64 Copynumber: 1.9 Consensus size: 66
6057 CAAAATCGCA
*
6067 TTGCGATTTTCATTTCGCATTGTGATTCTCTCGTTGCGATTTTCATTTCGC-ATTGCGATTCTGT
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCGA-TGCGATTCTGT
6131 CG
65 CG
* *
6133 TTGCGATTTTTATTTCGCGTTGCG-TT-TCTCGTTGCGATTTTCATTTCGCGATGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCGATGCGATT
6191 TTAAGTTTCG
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
64 30 0.56
65 3 0.06
66 21 0.39
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.48
Consensus pattern (66 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCGATGCGATTCTGTC
G
Found at i:6206 original size:19 final size:18
Alignment explanation
Indices: 6161--6207 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
6151 GTTGCGTTTC
*
6161 TCGT-TGCGATTTTCATT
1 TCGTGTGCGATTTTAATT
*
6178 TCGCGATGCGATTTTAAGTT
1 TCGTG-TGCGATTTTAA-TT
6198 TCGTGTGCGA
1 TCGTGTGCGA
6208 AAGTAACTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 3 0.12
19 15 0.62
20 6 0.25
ACGTcount: A:0.15, C:0.17, G:0.26, T:0.43
Consensus pattern (18 bp):
TCGTGTGCGATTTTAATT
Found at i:8057 original size:14 final size:14
Alignment explanation
Indices: 8038--8070 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
8028 ATTGTTTGAT
8038 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
8052 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
8066 TGATT
1 TGATT
8071 CAATAGTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.42
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:8127 original size:83 final size:84
Alignment explanation
Indices: 7979--8153 Score: 298
Period size: 83 Copynumber: 2.1 Consensus size: 84
7969 TGGTTGCAAT
** *
7979 AGTTGATTCAATAGTAGATGAGGAAATAATTCTTATTGCTTATTTTTTGATTGTTTGATTGATTT
1 AGTTGATTCAATAGTAGATGAGGAAATAATGATTATTGCTTATTTTTTGATTGTTTAATTGATTT
*
8044 GTAAAAGATGATTTGTAAA
66 GTAAAACATGATTTGTAAA
*
8063 AGTTGATTCAATAGTAGATGGGGAAATAA-GATTATTGCTTATTTTTTGATTGTTTAATTGATTT
1 AGTTGATTCAATAGTAGATGAGGAAATAATGATTATTGCTTATTTTTTGATTGTTTAATTGATTT
8127 GTAAAACATGATTTGTAAA
66 GTAAAACATGATTTGTAAA
8146 AGTTGATT
1 AGTTGATT
8154 TGTTTAATTG
Statistics
Matches: 86, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
83 58 0.67
84 28 0.33
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.45
Consensus pattern (84 bp):
AGTTGATTCAATAGTAGATGAGGAAATAATGATTATTGCTTATTTTTTGATTGTTTAATTGATTT
GTAAAACATGATTTGTAAA
Found at i:8140 original size:14 final size:14
Alignment explanation
Indices: 8121--8156 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
8111 ATTGTTTAAT
8121 TGATTTGTAAAACA
1 TGATTTGTAAAACA
**
8135 TGATTTGTAAAAGT
1 TGATTTGTAAAACA
8149 TGATTTGT
1 TGATTTGT
8157 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAACA
Found at i:8333 original size:52 final size:52
Alignment explanation
Indices: 8263--8373 Score: 204
Period size: 52 Copynumber: 2.1 Consensus size: 52
8253 AAAAATGACT
* *
8263 ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAGA
1 ATCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAA
8315 ATCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAA
8367 ATCGCAA
1 ATCGCAA
8374 CGAGAGAATC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 57 1.00
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAA
Found at i:8403 original size:33 final size:33
Alignment explanation
Indices: 8311--8406 Score: 174
Period size: 33 Copynumber: 2.9 Consensus size: 33
8301 AATGCGAAAT
*
8311 GAGAATCGCAATGCGAAATGAAAATCACAACGA
1 GAGAATCGCAATGCGAAATGAAAATCGCAACGA
8344 GAGAATCGCAATGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAATGCGAAATGAAAATCGCAACGA
*
8377 GAGAATCGCAATGTGAAATGAAAATCGCAA
1 GAGAATCGCAATGCGAAATGAAAATCGCAA
8407 TGCGAATTAG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.14
Consensus pattern (33 bp):
GAGAATCGCAATGCGAAATGAAAATCGCAACGA
Found at i:8443 original size:14 final size:14
Alignment explanation
Indices: 8424--8478 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
8414 TAGTTTCGCA
8424 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
8438 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
8455 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
8471 TTGCGATT
1 TTGCGATT
8479 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:8454 original size:33 final size:33
Alignment explanation
Indices: 8417--8546 Score: 172
Period size: 33 Copynumber: 3.8 Consensus size: 33
8407 TGCGAATTAG
8417 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
8450 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
* *
8483 TTTCGCATTACGATTTTCATTTCCGCGTTGCGATTTTCA
1 TTTCGCATTGCGA--TTC---T-CTCGTTGCGATTTTCA
*
8522 TTTCGCATTGCGA-TCTCTTGTTGCG
1 TTTCGCATTGCGATTCTCTCGTTGCG
8547 GTTGTAATTT
Statistics
Matches: 86, Mismatches: 5, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
32 7 0.08
33 46 0.53
35 3 0.03
36 2 0.02
38 1 0.01
39 27 0.31
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.45
Consensus pattern (33 bp):
TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
Found at i:8518 original size:20 final size:19
Alignment explanation
Indices: 8438--8535 Score: 125
Period size: 19 Copynumber: 5.4 Consensus size: 19
8428 GATTCTCTCG
8438 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
8457 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
8471 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
8490 TTACGATTTTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
8510 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
8529 TTGCGAT
1 TTGCGAT
8536 CTCTTGTTGC
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 7 0.10
19 30 0.45
20 17 0.25
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:8575 original size:72 final size:72
Alignment explanation
Indices: 8436--8575 Score: 192
Period size: 72 Copynumber: 1.9 Consensus size: 72
8426 GCGATTCTCT
* * **
8436 CGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTACGATTTTC
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATTTCGCATTACGATAGTC
8501 ATTTCCG
66 ATTTCCG
* * * *
8508 CGTTGCGATTTTCATTTCGCATTGCGA-TCTCTTGTTGCGGTTGTAATTTCCGCGTTGCGATAGT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATTT-CGCATTACGATAGT
8572 CATT
65 CATT
8576 AAGATGATTG
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
71 18 0.31
72 41 0.69
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (72 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATTTCGCATTACGATAGTC
ATTTCCG
Found at i:9220 original size:39 final size:39
Alignment explanation
Indices: 9177--9251 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
9167 GTAGCAGATG
**
9177 GGAAATGACTATCGCAATGCGAAATGAAAATCGCAATGC
1 GGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC
9216 GGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 GGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
9252 CGAGAGAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.45, C:0.16, G:0.23, T:0.16
Consensus pattern (39 bp):
GGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC
Found at i:9222 original size:20 final size:19
Alignment explanation
Indices: 9187--9251 Score: 121
Period size: 19 Copynumber: 3.4 Consensus size: 19
9177 GGAAATGACT
9187 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
9206 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
9226 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
9245 ATCGCAA
1 ATCGCAA
9252 CGAGAGAATC
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
19 26 0.58
20 19 0.42
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:9608 original size:18 final size:18
Alignment explanation
Indices: 9585--9621 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
9575 CGAAATTTAT
9585 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
9603 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
9621 A
1 A
9622 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:9891 original size:33 final size:34
Alignment explanation
Indices: 9831--9906 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 34
9821 TTCATTTCCG
* *
9831 CGTTACGATTTTCATATTCGCACTGCGATTTTCAT
1 CGTTGCGATTTTCATATTCGCACTGCGATTCTC-T
*
9866 -GTTGCGATTTTCAT-TTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATATTCGCACTGCGATTCTCT
9898 CGTTGCGAT
1 CGTTGCGAT
9907 AGTCATTAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 1 0.03
33 23 0.62
34 13 0.35
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATATTCGCACTGCGATTCTCT
Found at i:12424 original size:23 final size:24
Alignment explanation
Indices: 12382--12427 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
12372 CTGAAACATC
12382 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAT
*
12406 ATCAAAGTCCG-GTATTGACCAA
1 ATCAAAATCCGAGTATTGACCAA
12428 GATGAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAT
Found at i:13141 original size:20 final size:20
Alignment explanation
Indices: 13116--13236 Score: 206
Period size: 20 Copynumber: 6.0 Consensus size: 20
13106 AAATTTCAGT
*
13116 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACAGATTATC
*
13136 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTATC
13156 GTTGCGATTTACAGATTATC
1 GTTGCGATTTACAGATTATC
*
13176 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACAGATTATC
*
13196 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTATC
13216 GTTGCGATTTACAGATTATC
1 GTTGCGATTTACAGATTATC
13236 G
1 G
13237 CAACGAGAGA
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 94 1.00
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (20 bp):
GTTGCGATTTACAGATTATC
Found at i:13209 original size:60 final size:60
Alignment explanation
Indices: 13116--13236 Score: 242
Period size: 60 Copynumber: 2.0 Consensus size: 60
13106 AAATTTCAGT
13116 GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACAGATTATC
1 GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACAGATTATC
13176 GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACAGATTATC
1 GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACAGATTATC
13236 G
1 G
13237 CAACGAGAGA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (60 bp):
GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACAGATTATC
Found at i:13279 original size:14 final size:14
Alignment explanation
Indices: 13260--13287 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
13250 GCAATGCGAA
13260 ATGAAAATCGCAAC
1 ATGAAAATCGCAAC
13274 ATGAAAATCGCAAC
1 ATGAAAATCGCAAC
13288 GCGAATATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.21, G:0.14, T:0.14
Consensus pattern (14 bp):
ATGAAAATCGCAAC
Found at i:13297 original size:20 final size:20
Alignment explanation
Indices: 13274--13387 Score: 160
Period size: 20 Copynumber: 5.8 Consensus size: 20
13264 AAATCGCAAC
13274 ATGAAAATCGCAACGC-GAA
1 ATGAAAATCGCAACGCGGAA
13293 TATGAAAATCGCAACGCGGAA
1 -ATGAAAATCGCAACGCGGAA
* *
13314 ATGAAAATCGGAATGCGGAA
1 ATGAAAATCGCAACGCGGAA
*
13334 ATGAAAATCGCAATGCGGAA
1 ATGAAAATCGCAACGCGGAA
* *
13354 ATGAAAATCGCAATG-TGAA
1 ATGAAAATCGCAACGCGGAA
13373 ATGAAAATCGCAACG
1 ATGAAAATCGCAACG
13388 AGAGAATCGC
Statistics
Matches: 88, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
19 17 0.19
20 68 0.77
21 3 0.03
ACGTcount: A:0.46, C:0.16, G:0.24, T:0.15
Consensus pattern (20 bp):
ATGAAAATCGCAACGCGGAA
Found at i:13338 original size:40 final size:39
Alignment explanation
Indices: 13246--13387 Score: 188
Period size: 40 Copynumber: 3.7 Consensus size: 39
13236 GCAACGAGAG
13246 AATCGCAATGCGAAATGAAAATCGCAA--C----ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGCGGAAATGAA
*
13279 AATCGCAACGCGAATATGAAAATCGCAACGCGGAAATGAA
1 AATCGCAATGCGAA-ATGAAAATCGCAACGCGGAAATGAA
* *
13319 AATCGGAATGCGGAAATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAAAATCGCAACGCGGAAATGAA
*
13359 AATCGCAATGTGAAATGAAAATCGCAACG
1 AATCGCAATGCGAAATGAAAATCGCAACG
13388 AGAGAATCGC
Statistics
Matches: 94, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
33 13 0.14
34 13 0.14
36 1 0.01
39 17 0.18
40 47 0.50
41 3 0.03
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.15
Consensus pattern (39 bp):
AATCGCAATGCGAAATGAAAATCGCAACGCGGAAATGAA
Found at i:13545 original size:33 final size:33
Alignment explanation
Indices: 13468--13594 Score: 164
Period size: 33 Copynumber: 3.7 Consensus size: 33
13458 ATCATCGCAT
*
13468 GATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGC
1 GATTTTCATTTCGCATTGCGA--TT-ATCT-CG--TTGC
* * *
13507 GATTTTTATTTCGTATTGCGATTCTCTCGTTGC
1 GATTTTCATTTCGCATTGCGATTATCTCGTTGC
13540 GATTTTCATTTCGCATTGCGATTATCTCGTTGC
1 GATTTTCATTTCGCATTGCGATTATCTCGTTGC
13573 GATTTTCATTTCGCATTGCGAT
1 GATTTTCATTTCGCATTGCGAT
13595 AGTCATTTTT
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
33 56 0.69
35 2 0.02
36 2 0.02
37 2 0.02
39 19 0.23
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.47
Consensus pattern (33 bp):
GATTTTCATTTCGCATTGCGATTATCTCGTTGC
Found at i:13602 original size:19 final size:19
Alignment explanation
Indices: 13468--13594 Score: 139
Period size: 19 Copynumber: 7.2 Consensus size: 19
13458 ATCATCGCAT
13468 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
13487 GATTTTCATTTCCGCATTGC
1 GATTTTCATTT-CGCATTGC
* *
13507 GATTTTTATTTCGTATTGC
1 GATTTTCATTTCGCATTGC
*
13526 GA--TTC-TCTCG--TTGC
1 GATTTTCATTTCGCATTGC
13540 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
*
13559 GA--TT-ATCTCG--TTGC
1 GATTTTCATTTCGCATTGC
13573 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
13592 GAT
1 GAT
13595 AGTCATTTTT
Statistics
Matches: 90, Mismatches: 7, Indels: 22
0.76 0.06 0.18
Matches are distributed among these distances:
14 12 0.13
16 14 0.16
17 13 0.14
19 33 0.37
20 18 0.20
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.47
Consensus pattern (19 bp):
GATTTTCATTTCGCATTGC
Found at i:13719 original size:14 final size:13
Alignment explanation
Indices: 13700--13736 Score: 58
Period size: 12 Copynumber: 2.8 Consensus size: 13
13690 CATCAATTAA
13700 ACAAATCAACTTTT
1 ACAAATCAA-TTTT
13714 ACAAATC-ATTTT
1 ACAAATCAATTTT
13726 ACAAATCAATT
1 ACAAATCAATT
13737 AAACAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 11 0.50
13 4 0.18
14 7 0.32
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (13 bp):
ACAAATCAATTTT
Found at i:13788 original size:81 final size:83
Alignment explanation
Indices: 13703--13875 Score: 287
Period size: 84 Copynumber: 2.1 Consensus size: 83
13693 CAATTAAACA
***
13703 AATCAACTTTTACAAATCA-TTTTACAAATCAATTAAACAAT-AAAAAATAAGCAATAATTCTTA
1 AATCAACTTTTACAAATCACTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAAGAATTA
13766 TTTCCTCATCTACTATTG
66 TTTCCTCATCTACTATTG
13784 AATCAACTTTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAAGAATT
1 AATCAACTTTTACAAATCA-CTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAAGAATT
*
13849 ATTTTCTCATCTACTATTG
65 ATTTCCTCATCTACTATTG
13868 AATCAACT
1 AATCAACT
13876 ATTGCAGCCA
Statistics
Matches: 85, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
81 19 0.22
83 22 0.26
84 44 0.52
ACGTcount: A:0.45, C:0.17, G:0.03, T:0.35
Consensus pattern (83 bp):
AATCAACTTTTACAAATCACTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAAGAATTA
TTTCCTCATCTACTATTG
Found at i:13807 original size:14 final size:14
Alignment explanation
Indices: 13784--13817 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
13774 TCTACTATTG
13784 AATCAACTTTTACA
1 AATCAACTTTTACA
*
13798 AATCATCTTTTACA
1 AATCAACTTTTACA
13812 AATCAA
1 AATCAA
13818 TTAAACAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (14 bp):
AATCAACTTTTACA
Found at i:15728 original size:19 final size:19
Alignment explanation
Indices: 15672--15812 Score: 141
Period size: 19 Copynumber: 7.6 Consensus size: 19
15662 ATATTTACTT
* *
15672 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* **
15692 TCGCAACGTGAAAAATGACTA
1 TCGCAACGCG--AAATGAAAA
15713 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
15732 TCGCAACGAGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
15751 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
15770 TCGCAA--CG--A--AAAA
1 TCGCAACGCGAAATGAAAA
**
15783 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
15802 TCGCAACGCGA
1 TCGCAACGCGA
15813 TTATAGTTTC
Statistics
Matches: 103, Mismatches: 10, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
13 10 0.10
15 3 0.03
17 3 0.03
19 64 0.62
20 8 0.08
21 12 0.12
22 3 0.03
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:15786 original size:32 final size:34
Alignment explanation
Indices: 15712--15809 Score: 128
Period size: 32 Copynumber: 2.8 Consensus size: 34
15702 AAAAATGACT
15712 ATCGCAACGCGAAATGAAAATCGCAACGAGAAATGAAA
1 ATCGCAACGCGAAATGAAAATCGCAAC--G-AA-GAAA
15750 ATCGCAACGCGAAATGAAAATCGCAACG-A-AAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAAGAAA
**
15782 ATCGCAACGCGAAACCAAAATCGCAACG
1 ATCGCAACGCGAAATGAAAATCGCAACG
15810 CGATTATAGT
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
32 29 0.50
34 1 0.02
36 1 0.02
38 27 0.47
ACGTcount: A:0.48, C:0.23, G:0.19, T:0.09
Consensus pattern (34 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAAGAAA
Found at i:15831 original size:19 final size:19
Alignment explanation
Indices: 15809--15852 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
15799 AAATCGCAAC
15809 GCGATTATAGTTTCACGTT
1 GCGATTATAGTTTCACGTT
* * *
15828 GCGATTTTGGTTTCGCGTT
1 GCGATTATAGTTTCACGTT
*
15847 ACGATT
1 GCGATT
15853 TTGTCGTTGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.16, C:0.16, G:0.25, T:0.43
Consensus pattern (19 bp):
GCGATTATAGTTTCACGTT
Found at i:15853 original size:19 final size:19
Alignment explanation
Indices: 15818--15855 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
15808 CGCGATTATA
*
15818 GTTTCACGTTGCGATTTTG
1 GTTTCACGTTACGATTTTG
*
15837 GTTTCGCGTTACGATTTTG
1 GTTTCACGTTACGATTTTG
15856 TCGTTGCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.11, C:0.16, G:0.26, T:0.47
Consensus pattern (19 bp):
GTTTCACGTTACGATTTTG
Found at i:15866 original size:33 final size:33
Alignment explanation
Indices: 15824--15887 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
15814 TATAGTTTCA
**
15824 CGTTGCGATTTTGGTTTCGCGTTACGATTTTGT
1 CGTTGCGATTTTCATTTCGCGTTACGATTTTGT
*
15857 CGTTGCGATTTTCATTTCGCGTTGCGATTTT
1 CGTTGCGATTTTCATTTCGCGTTACGATTTT
15888 CATTTCTCGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.09, C:0.17, G:0.25, T:0.48
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTACGATTTTGT
Found at i:15881 original size:19 final size:19
Alignment explanation
Indices: 15857--15935 Score: 96
Period size: 19 Copynumber: 4.4 Consensus size: 19
15847 ACGATTTTGT
15857 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
15876 CGTTGCGATTTTCATTTCT
1 CGTTGCGATTTTCATTTCG
*
15895 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
*
15909 CGTTACGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
15928 CGTTGCGA
1 CGTTGCGA
15936 GAGTCATTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
19 35 0.69
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:15887 original size:52 final size:52
Alignment explanation
Indices: 15819--15935 Score: 162
Period size: 52 Copynumber: 2.2 Consensus size: 52
15809 GCGATTATAG
* ** * * *
15819 TTTCACGTTGCGATTTTGGTTTCGCGTTACGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCATTTCGCGTTACGATTCTCTCGTTACGATTTTCA
* *
15871 TTTCGCGTTGCGATTTTCATTTCTCGTTGCGATTCTCTCGTTACGATTTTCA
1 TTTCGCGTTGCGATTTTCATTTCGCGTTACGATTCTCTCGTTACGATTTTCA
15923 TTTCGCGTTGCGA
1 TTTCGCGTTGCGA
15936 GAGTCATTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 57 1.00
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (52 bp):
TTTCGCGTTGCGATTTTCATTTCGCGTTACGATTCTCTCGTTACGATTTTCA
Found at i:15943 original size:52 final size:52
Alignment explanation
Indices: 15838--15958 Score: 143
Period size: 52 Copynumber: 2.3 Consensus size: 52
15828 GCGATTTTGG
* * * * * ***
15838 TTTCGCGTTACGATTTTGTCGTTGCGATTTTCATTTCGCGTTGCGATTTTCA
1 TTTCTCGTTGCGATTCTCTCGTTACGATTTTCATTTCGCGTTGCGAGAGTCA
15890 TTTCTCGTTGCGATTCTCTCGTTACGATTTTCATTTCGCGTTGCGAGAGTCA
1 TTTCTCGTTGCGATTCTCTCGTTACGATTTTCATTTCGCGTTGCGAGAGTCA
*
15942 TTTTTCAGGTTGCGATT
1 TTTCTC--GTTGCGATT
15959 TTAAGTTTCG
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
52 49 0.84
54 9 0.16
ACGTcount: A:0.12, C:0.20, G:0.21, T:0.46
Consensus pattern (52 bp):
TTTCTCGTTGCGATTCTCTCGTTACGATTTTCATTTCGCGTTGCGAGAGTCA
Found at i:16311 original size:95 final size:94
Alignment explanation
Indices: 16030--16315 Score: 459
Period size: 93 Copynumber: 3.1 Consensus size: 94
16020 ATGGATTGCA
* * *
16030 TTAC-TTCAACCAAAAGACAAAACAAAGATAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
16094 TTAGCAGAATTAGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
16123 TTACTTCCAACCAAAAGACAAAACAAAGACAAATACT-ATTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
16187 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
16216 TTACTTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCATAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
16281 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
16311 TTACT
1 TTACT
16316 AAGCAATCTA
Statistics
Matches: 178, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
93 79 0.44
94 43 0.24
95 56 0.31
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:17952 original size:26 final size:25
Alignment explanation
Indices: 17901--17954 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
17891 ATACCAAGTT
* *
17901 AGATATACCAAAAACTACACTGTAA
1 AGATATACCAAAAACTAAACTATAA
17926 AGATATACCAAAAACAATAAAC-ATAA
1 AGATATACCAAAAAC--TAAACTATAA
17952 AGA
1 AGA
17955 GTAGTAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 15 0.60
26 6 0.24
27 4 0.16
ACGTcount: A:0.59, C:0.17, G:0.07, T:0.17
Consensus pattern (25 bp):
AGATATACCAAAAACTAAACTATAA
Found at i:18040 original size:20 final size:20
Alignment explanation
Indices: 18010--18154 Score: 130
Period size: 20 Copynumber: 7.7 Consensus size: 20
18000 TTTTGGTTGA
18010 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
** *
18030 AATGACTATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
18049 AAATGAAAATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
** *
18070 AATGACTATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
*
18089 AATGAAAATCGCAA--TGAG
1 AATGAAAATCGCAACGAGAG
*
18107 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
*
18122 AATGAAAATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
18141 AATGAAAATCGCAA
1 AATGAAAATCGCAA
18155 TGCGATTTTG
Statistics
Matches: 103, Mismatches: 13, Indels: 19
0.76 0.10 0.14
Matches are distributed among these distances:
14 8 0.08
16 4 0.04
17 4 0.04
19 40 0.39
20 46 0.45
21 1 0.01
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:18052 original size:40 final size:39
Alignment explanation
Indices: 18008--18159 Score: 201
Period size: 40 Copynumber: 4.1 Consensus size: 39
17998 TCTTTTGGTT
18008 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGC
18047 GGAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGC
*
18087 GAAATGAAAATCGCAA--TGAG-A-GA--ATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGC
* ** *
18120 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGC
18158 GA
1 GA
18160 TTTTGGTTTC
Statistics
Matches: 103, Mismatches: 3, Indels: 14
0.86 0.03 0.12
Matches are distributed among these distances:
33 26 0.25
35 5 0.05
36 3 0.03
37 3 0.03
38 11 0.11
39 16 0.16
40 39 0.38
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (39 bp):
GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGC
Found at i:18099 original size:19 final size:19
Alignment explanation
Indices: 18008--18159 Score: 161
Period size: 19 Copynumber: 8.1 Consensus size: 19
17998 TCTTTTGGTT
*
18008 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
**
18027 GAGAATGACTATCGCAACGC
1 GA-AATGAAAATCGCAACGC
*
18047 GGAAATGAAAATCGCAACGA
1 -GAAATGAAAATCGCAACGC
**
18067 GAGAATGACTATCGCAACGC
1 GA-AATGAAAATCGCAACGC
*
18087 GAAATGAAAATCGCAA--T
1 GAAATGAAAATCGCAACGC
*
18104 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
18120 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
18139 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
18158 GA
1 GA
18160 TTTTGGTTTC
Statistics
Matches: 109, Mismatches: 16, Indels: 16
0.77 0.11 0.11
Matches are distributed among these distances:
14 10 0.09
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 49 0.45
20 44 0.40
21 2 0.02
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:18133 original size:52 final size:53
Alignment explanation
Indices: 18056--18156 Score: 168
Period size: 52 Copynumber: 1.9 Consensus size: 53
18046 CGGAAATGAA
**
18056 AATCGCAACGAGAGAATGACTATCGCAACGCGAAATGAAAATCGCAATGAGAG
1 AATCGCAACGAGAGAATGAAAATCGCAACGCGAAATGAAAATCGCAATGAGAG
*
18109 AATCGCAACGCGA-AATGAAAATCGCAACGCGAAATGAAAATCGCAATG
1 AATCGCAACGAGAGAATGAAAATCGCAACGCGAAATGAAAATCGCAATG
18157 CGATTTTGGT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 33 0.73
53 12 0.27
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.13
Consensus pattern (53 bp):
AATCGCAACGAGAGAATGAAAATCGCAACGCGAAATGAAAATCGCAATGAGAG
Found at i:18239 original size:34 final size:35
Alignment explanation
Indices: 18201--18273 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
18191 CTATTTTCAT
*
18201 TTCTCTCGTTGTGATAGTCATTT-TCGCGTTGAGA
1 TTCTCTCGTTGCGATAGTCATTTCTCGCGTTGAGA
** * *
18235 TTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGA
1 TTCTCTCGTTGCGATAGTCATTTCTCGCGTTGAGA
18270 TTCT
1 TTCT
18274 TCTGCAAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
34 20 0.61
35 13 0.39
ACGTcount: A:0.11, C:0.22, G:0.19, T:0.48
Consensus pattern (35 bp):
TTCTCTCGTTGCGATAGTCATTTCTCGCGTTGAGA
Found at i:18491 original size:33 final size:31
Alignment explanation
Indices: 18445--18506 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
18435 AAATTACCAG
* * *
18445 TAAACTAATCAAAAGTTTCAATATGAAAAACC
1 TAAAATAATCAAAAATTTCAAAAT-AAAAACC
18477 TAAAATAATGCAAAAATTTCAAAATAAAAA
1 TAAAATAAT-CAAAAATTTCAAAATAAAAA
18507 TAATTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 13 0.50
33 13 0.50
ACGTcount: A:0.60, C:0.11, G:0.05, T:0.24
Consensus pattern (31 bp):
TAAAATAATCAAAAATTTCAAAATAAAAACC
Found at i:18836 original size:20 final size:20
Alignment explanation
Indices: 18811--18985 Score: 135
Period size: 20 Copynumber: 8.7 Consensus size: 20
18801 CTTTAAAAAT
18811 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
18831 CGCGTTGCGATTTTTCGTAT-
1 CGCGTTGCGA-TTTACGGATA
* * * *
18851 TGTCGTTGCGATTAACGTATT
1 CG-CGTTGCGATTTACGGATA
* * *
18872 CTCGTTGCGA-TAATCAGA-A
1 CGCGTTGCGATTTA-CGGATA
*
18891 TCGCGTTGCGATTTACGTAT-
1 -CGCGTTGCGATTTACGGATA
*
18911 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
18932 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
18952 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
18973 CGCGTTGCGATTT
1 CGCGTTGCGATTT
18986 TTACGAGTAC
Statistics
Matches: 122, Mismatches: 21, Indels: 24
0.73 0.13 0.14
Matches are distributed among these distances:
19 4 0.03
20 83 0.68
21 35 0.29
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:18878 original size:41 final size:39
Alignment explanation
Indices: 18808--19049 Score: 198
Period size: 41 Copynumber: 6.0 Consensus size: 39
18798 GCGCTTTAAA
* * *
18808 AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTTCG
1 AATCGCGTTGCGATTTACGTATTCTCGTTGCGA-TTTTCG
* * * **
18848 TATTGTCGTTGCGATTAACGTATTCTCGTTGCGATAATCAG
1 AATCG-CGTTGCGATTTACGTATTCTCGTTGCGATTTTC-G
* *
18889 AATCGCGTTGCGATTTACGTATTGTCGTTGCGATTTACG
1 AATCGCGTTGCGATTTACGTATTCTCGTTGCGATTTTCG
* * *
18928 GATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACG
1 AAT-CGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTTCG
* * **
18969 GATACGCGTTGCGATTTTTACG-AGTACTCGTTGCGATAGTCAG
1 AAT-CGCGTTGCGA--TTTACGTA-TTCTCGTTGCGATTTTC-G
** * *
19012 AATCGCGTTGCGATTTATATGTTCGCGTTGCGATTTTC
1 AATCGCGTTGCGATTTACGTATTCTCGTTGCGATTTTC
19050 ATATTCACTT
Statistics
Matches: 165, Mismatches: 29, Indels: 16
0.79 0.14 0.08
Matches are distributed among these distances:
39 3 0.02
40 61 0.37
41 69 0.42
42 29 0.18
43 3 0.02
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.38
Consensus pattern (39 bp):
AATCGCGTTGCGATTTACGTATTCTCGTTGCGATTTTCG
Found at i:18950 original size:81 final size:81
Alignment explanation
Indices: 18808--18963 Score: 201
Period size: 81 Copynumber: 1.9 Consensus size: 81
18798 GCGCTTTAAA
* * *
18808 AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTTCGTATTGTCGTTGCGATTAACGTATTC
1 AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATCGTCGTTGCGATTAACGTATTC
18873 TCGTTGCGATAATCAG
66 TCGTTGCGATAATCAG
* * *
18889 AATCGCGTTGCGATTTACGTAT-TGTCGTTGCGA-TTTACGGATACG-CGTTGCGATTTTACGTA
1 AATCGCGTTGCGATTTACGGATACG-CGTTGCGATTTTACGGAT-CGTCGTTGCGA-TTAACGTA
*
18951 TTGTCGTTGCGAT
63 TTCTCGTTGCGAT
18964 TTACGGATAC
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
80 16 0.25
81 49 0.75
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.38
Consensus pattern (81 bp):
AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATCGTCGTTGCGATTAACGTATTC
TCGTTGCGATAATCAG
Found at i:21697 original size:51 final size:51
Alignment explanation
Indices: 21640--21742 Score: 163
Period size: 51 Copynumber: 2.0 Consensus size: 51
21630 TATGAGTTGC
*
21640 CTCTCTTTATAAC-ATTTTTTTGTTGCAAAATGAGTTGCCTCATTCATTTAA
1 CTCTCTTTATAACGA-TTTTTTGTCGCAAAATGAGTTGCCTCATTCATTTAA
* *
21691 CTCTCTTTATAACGATTTTTTGTCGGAAAATGAGTTGCCTCATTCGTTTAA
1 CTCTCTTTATAACGATTTTTTGTCGCAAAATGAGTTGCCTCATTCATTTAA
21742 C
1 C
21743 GATTTCTTGT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
51 47 0.98
52 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.45
Consensus pattern (51 bp):
CTCTCTTTATAACGATTTTTTGTCGCAAAATGAGTTGCCTCATTCATTTAA
Found at i:31001 original size:123 final size:122
Alignment explanation
Indices: 30778--31129 Score: 323
Period size: 123 Copynumber: 2.8 Consensus size: 122
30768 GACCGTTAGG
* * * * * *
30778 CTCGGCCTCGATTCAAAATCATTGGTGAATGAATGACTTCTTCTCTCGTTTAAGACCAGCATCGT
1 CTCGGCCTTGGTTCAAAATCACTGGTGAATG-ATG---TCTTCTCTCCTTTAAGACCAACATCAT
* *
30843 CGCCAG-CATAAAACATTACGCTTGGCCTCGATTCAAAATCACTACCCACATAAGCCT-TTACA
62 CG-CAGCCAT-AGACATTACGCTTGGCCTCGGTTCAAAATCACTACCCACATAAG-CTGTTACA
30905 CTCGGCCTTGGTTCAAAATCACTGGTGAATGATGTCTTCTCTCCTTTAAGACCAACATCATCGTC
1 CTCGGCCTTGGTTCAAAATCACTGGTGAATGATGTCTTCTCTCCTTTAAGACCAACATCATCG-C
* ** **
30970 -GCCATAGACTGTTACGCTTGGCCTCGGTTCAAAATCACTACTGACATAAGCTGTTATG
65 AGCCATAGAC-ATTACGCTTGGCCTCGGTTCAAAATCACTACCCACATAAGCTGTTACA
* * * * * * * *
31028 CTTGGCCTTAGCTCAAAAGTACCACTAGTGAATGGTTTCTTATTTCCTTTAAGACCAACATCATC
1 CTCGGCCTTGGTTCAAAA-T--CACTGGTGAATGATGTCTTCTCTCCTTTAAGACCAACATCATC
** * * * *
31093 GCTTCCATAGGCCCTTACGCTTGGCCTTGGCTCAAAA
63 GCAGCCATA-GACATTACGCTTGGCCTCGGTTCAAAA
31130 ATATTTGGTG
Statistics
Matches: 190, Mismatches: 27, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
122 6 0.03
123 84 0.44
124 1 0.01
125 1 0.01
126 68 0.36
127 30 0.16
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (122 bp):
CTCGGCCTTGGTTCAAAATCACTGGTGAATGATGTCTTCTCTCCTTTAAGACCAACATCATCGCA
GCCATAGACATTACGCTTGGCCTCGGTTCAAAATCACTACCCACATAAGCTGTTACA
Found at i:31118 original size:126 final size:123
Alignment explanation
Indices: 30858--31129 Score: 314
Period size: 126 Copynumber: 2.2 Consensus size: 123
30848 GCATAAAACA
* * *
30858 TTACGCTTGGCCTCGATTCAAAATCACTACCCACATAAGCCTTTACACTCGGCCTTGGTTCAAAA
1 TTACGCTTGGCCTCGGTTCAAAATCACTACCCACATAAGCCTTTACACTCGGCCTTAGCTCAAAA
* * **
30923 TCACTGGTGAATGATGTCTTCTCTCCTTTAAGACCAACATCATCGTCGCCATAGACTG
66 TCACTAGTGAATGATGTCTTATCTCCTTTAAGACCAACATCATCGTCGCCATAGACCC
** ** *
30981 TTACGCTTGGCCTCGGTTCAAAATCACTACTGACATAAG-CTGTTATGCTTGGCCTTAGCTCAAA
1 TTACGCTTGGCCTCGGTTCAAAATCACTACCCACATAAGCCT-TTACACTCGGCCTTAGCTCAAA
* * * * *
31045 AGTACCACTAGTGAATGGTTTCTTATTTCCTTTAAGACCAACATCATCG-CTTCCATAGGCCC
65 A-T--CACTAGTGAATGATGTCTTATCTCCTTTAAGACCAACATCATCGTC-GCCATAGACCC
* *
31107 TTACGCTTGGCCTTGGCTCAAAA
1 TTACGCTTGGCCTCGGTTCAAAA
31130 ATATTTGGTG
Statistics
Matches: 125, Mismatches: 19, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
122 2 0.02
123 54 0.43
124 1 0.01
125 1 0.01
126 67 0.54
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.31
Consensus pattern (123 bp):
TTACGCTTGGCCTCGGTTCAAAATCACTACCCACATAAGCCTTTACACTCGGCCTTAGCTCAAAA
TCACTAGTGAATGATGTCTTATCTCCTTTAAGACCAACATCATCGTCGCCATAGACCC
Found at i:31210 original size:82 final size:82
Alignment explanation
Indices: 31055--31211 Score: 179
Period size: 82 Copynumber: 1.9 Consensus size: 82
31045 AGTACCACTA
* * * ** * *
31055 GTGAATGGTTTCTTATTTCCTTTAAGACCAACATCATCGCTTCCATAGGCCCTTACGCTTGGCCT
1 GTGAATGGCTTCTTATCTCATTTAAGACCAACATCATCGCCACCATAAGCCCTTACCCTTGGCCT
*
31120 TGGCTCAAAAATATTTG
66 CGGCTCAAAAATATTTG
* * *** *
31137 GTGAATGGCTTCTTCTCTCATTTAAGACCAACATCATTGCCACCATAAGTTGTTACCCTTGGTCT
1 GTGAATGGCTTCTTATCTCATTTAAGACCAACATCATCGCCACCATAAGCCCTTACCCTTGGCCT
*
31202 CGGTTCAAAA
66 CGGCTCAAAA
31212 TCACTACTGA
Statistics
Matches: 60, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
82 60 1.00
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (82 bp):
GTGAATGGCTTCTTATCTCATTTAAGACCAACATCATCGCCACCATAAGCCCTTACCCTTGGCCT
CGGCTCAAAAATATTTG
Found at i:31241 original size:42 final size:42
Alignment explanation
Indices: 31180--31259 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
31170 TCATTGCCAC
*
31180 CATAAGTTGTTACCCTTGGTCTCGGTTCAAAATCACTACTGA
1 CATAAGTTGTTACCCTTGGTCTCAGTTCAAAATCACTACTGA
*** * *
31222 CATAAGTTGTTATGTTTGGTCTTAGTTGAAAATCACTA
1 CATAAGTTGTTACCCTTGGTCTCAGTTCAAAATCACTA
31260 GTGAATGATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (42 bp):
CATAAGTTGTTACCCTTGGTCTCAGTTCAAAATCACTACTGA
Found at i:31379 original size:213 final size:207
Alignment explanation
Indices: 30939--31427 Score: 540
Period size: 213 Copynumber: 2.3 Consensus size: 207
30929 GTGAATGATG
* * * * * *
30939 TCTTCTCTCCTTTAAGACCAACATCATCGTCGCCAT-AGACTGTTACGCTTGGCCTCGGTTCAAA
1 TCTTCTCTCATGTAAGACCAACATCATTGCCACCATAAG-CTGTTACGCTTGGTCTCGGTTCAAA
*
31003 ATCACTACTGACATAAGCTGTTATGCTTGGCCTTAGCTCAAAAGTACCACTAGTGAATGGTTTCT
65 ATCACTACTGACATAAGCTGTTATGCTTGGCCTTAGCTCAAAAGTA-CACTAGTGAATGATTTCT
* * ** * *
31068 TATTTCCTTTAAGACCAACATCATCGCTTCCATAGGCCCTTACGCTTGGCCTTGGCTCAAAAATA
129 TATTTCCTTTAAGACCAACATCATAGCCTCCATAGGCCCTTAAACTTAGCCGTGGCTCAAAAATA
31133 TTTGGTGAATGGCT
194 TTTGGTGAATGGCT
* * *
31147 TCTTCTCTCATTTAAGACCAACATCATTGCCACCATAAGTTGTTACCCTTGGTCTCGGTTCAAAA
1 TCTTCTCTCATGTAAGACCAACATCATTGCCACCATAAGCTGTTACGCTTGGTCTCGGTTCAAAA
* * * * *
31212 TCACTACTGACATAAGTTGTTATGTTTGGTCTTAGTTGAAAA-T-CACTAGTGAATGATTTCTTC
66 TCACTACTGACATAAGCTGTTATGCTTGGCCTTAGCTCAAAAGTACACTAGTGAATGATTTCTT-
** *
31275 ACTCTTTTTGTCCTTTAAGACCAGA-ATCATAGCCTCCATAGGCGGTTAAACTTAGCCAGT-GTT
130 A------TT-TCCTTTAAGACCA-ACATCATAGCCTCCATAGGCCCTTAAACTTAGCC-GTGGCT
31338 CAAAAATCA-TTGGTGAATGGCT
186 CAAAAAT-ATTTGGTGAATGGCT
* * * * * * *
31360 TTTTTTTTCGTGTAAGACCAGCATCATTGCCACCATAAGCCGTTACGCTTGGTCTTGGTTCAAAA
1 TCTTCTCTCATGTAAGACCAACATCATTGCCACCATAAGCTGTTACGCTTGGTCTCGGTTCAAAA
31425 TCA
66 TCA
31428 TTAGTGTCGT
Statistics
Matches: 237, Mismatches: 32, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
205 18 0.08
206 1 0.00
207 1 0.00
208 92 0.39
209 2 0.01
212 2 0.01
213 118 0.50
214 3 0.01
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.34
Consensus pattern (207 bp):
TCTTCTCTCATGTAAGACCAACATCATTGCCACCATAAGCTGTTACGCTTGGTCTCGGTTCAAAA
TCACTACTGACATAAGCTGTTATGCTTGGCCTTAGCTCAAAAGTACACTAGTGAATGATTTCTTA
TTTCCTTTAAGACCAACATCATAGCCTCCATAGGCCCTTAAACTTAGCCGTGGCTCAAAAATATT
TGGTGAATGGCT
Found at i:33520 original size:3 final size:3
Alignment explanation
Indices: 33512--33633 Score: 217
Period size: 3 Copynumber: 40.7 Consensus size: 3
33502 TTAATATATT
*
33512 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
33560 TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
33608 TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
33634 TGGATAAAAA
Statistics
Matches: 113, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 113 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:34090 original size:112 final size:112
Alignment explanation
Indices: 33952--34154 Score: 345
Period size: 112 Copynumber: 1.8 Consensus size: 112
33942 GAATTATGCC
* * *
33952 AAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
34017 ATGAAC-TTCTCCGGAAAAGATAATCCATCAATTGATGGATTCAGGT
66 ATGAACTTTCTCCAGAAAAGATAATCCATCAATTGATGGATTCAGGT
34063 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAA-GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
34128 TATGAACTTTCTCTAGAAAAGATAATC
65 TATGAACTTTCTCCAGAAAAGATAATC
34155 TTTCAAATGA
Statistics
Matches: 85, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
111 4 0.05
112 64 0.75
113 17 0.20
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (112 bp):
AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCCAGAAAAGATAATCCATCAATTGATGGATTCAGGT
Found at i:34820 original size:83 final size:83
Alignment explanation
Indices: 34723--34960 Score: 406
Period size: 83 Copynumber: 2.9 Consensus size: 83
34713 TATACTTCTT
* *
34723 CAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCTAAATTCA
*
34788 ATGATTG-TTCTGTCCAAC
65 ATGATTGATTATGTCCAAC
*
34806 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAA
34871 TGATTGATTATGTCCAAC
66 TGATTGATTATGTCCAAC
*
34889 CAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCAAATTCATCTTCTAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT-GGCAAATTCATCTTCTAAATTCA
34954 ATGATTG
65 ATGATTG
34961 GACTAAGATA
Statistics
Matches: 147, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
82 27 0.18
83 91 0.62
84 29 0.20
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.28
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAA
TGATTGATTATGTCCAAC
Found at i:36113 original size:11 final size:11
Alignment explanation
Indices: 36082--36115 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
36072 CTTGACCCCC
*
36082 TTTCTTTTTCT
1 TTTCTTTTTTT
*
36093 TCTCTTTTTTT
1 TTTCTTTTTTT
36104 TTTCTTTTTTT
1 TTTCTTTTTTT
36115 T
1 T
36116 CCTATTCTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:46738 original size:13 final size:15
Alignment explanation
Indices: 46716--46752 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
46706 TTTGACATAA
46716 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
46728 AAATAAAATACTTGC
1 AAATAAAATACTTGC
46743 AAATAAAATA
1 AAATAAAATA
46753 AAACATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 2 0.09
15 10 0.45
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAAATACTTGC
Found at i:46791 original size:18 final size:17
Alignment explanation
Indices: 46743--46793 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
46733 AAATACTTGC
*
46743 AAATAAAATAAAACATAT
1 AAAT-AAATAAAAAATAT
*
46761 AAAT-ATTATAAAAATAAT
1 AAATAAATA-AAAAAT-AT
46779 AAATAAATAAAAAAT
1 AAATAAATAAAAAAT
46794 TTGAAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 3 0.11
17 5 0.19
18 16 0.59
19 3 0.11
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATAAATAAAAAATAT
Found at i:48979 original size:3 final size:3
Alignment explanation
Indices: 48971--49092 Score: 208
Period size: 3 Copynumber: 40.7 Consensus size: 3
48961 TTAATATATT
*
48971 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
49019 TAA TAA TAA TAA TAA TAA TAA TGA TAA TAG TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
49067 TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
49093 TGGATAAAAA
Statistics
Matches: 111, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 111 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:52278 original size:21 final size:21
Alignment explanation
Indices: 52253--52390 Score: 67
Period size: 21 Copynumber: 6.9 Consensus size: 21
52243 ATATAGAATT
52253 TGTCCCGAAGGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
*
52274 TGTCCCGAAAGACCAC-----
1 TGTCCCGAAGGACCACATAGA
** *
52290 --TCCTTAAGGACCACATACA
1 TGTCCCGAAGGACCACATAGA
* * * *
52309 TATTCC-AATGGACCAAATAGG
1 TGTCCCGAA-GGACCACATAGA
* * *
52330 TGTACCGAAGTACCACATATA
1 TGTCCCGAAGGACCACATAGA
* * ** *
52351 TGTTCCAAAGGATTACATATA
1 TGTCCCGAAGGACCACATAGA
52372 TGTCCCGAAGGACCACATA
1 TGTCCCGAAGGACCACATA
52391 AAACCCTCGA
Statistics
Matches: 84, Mismatches: 24, Indels: 18
0.67 0.19 0.14
Matches are distributed among these distances:
14 11 0.13
20 2 0.02
21 69 0.82
22 2 0.02
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATAGA
Found at i:57879 original size:27 final size:27
Alignment explanation
Indices: 57841--57897 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
57831 ATGGTTTTCG
* *
57841 TAAATCCGACATTAAATATTAATAAAT
1 TAAATCCGACATCAAACATTAATAAAT
*
57868 TAAATCCGACATCAAGCATTAATAAAT
1 TAAATCCGACATCAAACATTAATAAAT
57895 TAA
1 TAA
57898 TAAATTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (27 bp):
TAAATCCGACATCAAACATTAATAAAT
Found at i:59687 original size:15 final size:14
Alignment explanation
Indices: 59669--59698 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
59659 TGAACAATAT
59669 ATATGTATTTATAAA
1 ATATGTATTTA-AAA
59684 ATATGTATTTAAAA
1 ATATGTATTTAAAA
59698 A
1 A
59699 GCTATCCGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (14 bp):
ATATGTATTTAAAA
Found at i:59870 original size:38 final size:36
Alignment explanation
Indices: 59804--60117 Score: 139
Period size: 36 Copynumber: 8.8 Consensus size: 36
59794 TTTAAATATA
* *
59804 ATTTTTGAAAATATATAGTATATGTTTTGAAAACGT
1 ATTTTTGAAAACATATAATATATGTTTTGAAAACGT
59840 ATTTTTGAAAACATATAATATATAGTTTTTGAAAAC--
1 ATTTTTGAAAACATATAATATAT-G-TTTTGAAAACGT
59876 A----T------ATATAATATAGT-TTTTGAAAACGT
1 ATTTTTGAAAACATATAATATA-TGTTTTGAAAACGT
* *
59902 ATTTTTGAAAACATATAATATATAGTTTTTTAAAATG-
1 ATTTTTGAAAACATATAATATAT-G-TTTTGAAAACGT
* *
59939 A-TTTTGAAAACGTATAATATATAGTTTTTAAAACG-
1 ATTTTTGAAAACATATAATATAT-GTTTTGAAAACGT
* * * * *
59974 -GTTTTGTAAACGTATAATATATAATTTTTTTAAAACCG-
1 ATTTTTGAAAACATAT-A-ATAT-ATGTTTTGAAAA-CGT
* * * *
60012 -GTTTTGAAAACGTATAATATATGATTTTTTTAAAAATGGT
1 ATTTTTGAAAACATATAATATATG----TTTTGAAAA-CGT
* * *
60052 -TTTTGGAACACATTTATAATATA-GTTTTTAAAAGCGT
1 ATTTTTGAAAACA--TATAATATATGTTTTGAAAA-CGT
*
60089 ATTTTTAAAAACATATAATATATAGTTTT
1 ATTTTTGAAAACATATAATATAT-GTTTT
60118 TTAAAAATGT
Statistics
Matches: 222, Mismatches: 23, Indels: 64
0.72 0.07 0.21
Matches are distributed among these distances:
24 10 0.05
26 11 0.05
27 1 0.00
30 1 0.00
32 1 0.00
35 26 0.12
36 68 0.31
37 26 0.12
38 51 0.23
39 9 0.04
40 8 0.04
41 1 0.00
42 9 0.04
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (36 bp):
ATTTTTGAAAACATATAATATATGTTTTGAAAACGT
Found at i:59873 original size:24 final size:24
Alignment explanation
Indices: 59841--59899 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
59831 TGAAAACGTA
59841 TTTTTGAAAACATATA-ATATATAG
1 TTTTTGAAAACATATATA-ATATAG
59865 TTTTTGAAAACATATATAATATAG
1 TTTTTGAAAACATATATAATATAG
59889 TTTTTGAAAAC
1 TTTTTGAAAAC
59900 GTATTTTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 33 0.97
25 1 0.03
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.42
Consensus pattern (24 bp):
TTTTTGAAAACATATATAATATAG
Found at i:59902 original size:62 final size:61
Alignment explanation
Indices: 59799--59936 Score: 217
Period size: 62 Copynumber: 2.3 Consensus size: 61
59789 ATAATTTTAA
* *
59799 ATATAATTTTTG-AAAATATATAGTATATGTTTTGAAAACGTATTTTTGAAAACATATAAT
1 ATATAGTTTTTGAAAAATATATAATATATGTTTTGAAAACGTATTTTTGAAAACATATAAT
59859 ATATAGTTTTTGAAAACATATATAATATA-GTTTTTGAAAACGTATTTTTGAAAACATATAAT
1 ATATAGTTTTTGAAAA-ATATATAATATATG-TTTTGAAAACGTATTTTTGAAAACATATAAT
*
59921 ATATAGTTTTTTAAAA
1 ATATAGTTTTTGAAAA
59937 TGATTTTGAA
Statistics
Matches: 72, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
60 11 0.15
61 4 0.06
62 57 0.79
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.43
Consensus pattern (61 bp):
ATATAGTTTTTGAAAAATATATAATATATGTTTTGAAAACGTATTTTTGAAAACATATAAT
Found at i:59944 original size:36 final size:36
Alignment explanation
Indices: 59866--60170 Score: 242
Period size: 38 Copynumber: 8.1 Consensus size: 36
59856 AATATATAGT
*
59866 TTTTGAAAACATAT-ATAATATAGTTTTTGAAAACGTA
1 TTTTGAAAACATATAAT-ATATAGTTTTTTAAAACG-A
*
59903 TTTTTGAAAACATATAATATATAGTTTTTTAAAATGA
1 -TTTTGAAAACATATAATATATAGTTTTTTAAAACGA
* *
59940 TTTTGAAAACGTATAATATATAG-TTTTTAAAACGG
1 TTTTGAAAACATATAATATATAGTTTTTTAAAACGA
* * * *
59975 TTTTGTAAACGTATAATATATAATTTTTTTAAAACCGG
1 TTTTGAAAACATATAATATAT-AGTTTTTTAAAA-CGA
* * * *
60013 TTTTGAAAACGTATAATATATGATTTTTTTAAAAATGGT
1 TTTTGAAAACATATAATATAT-AGTTTTTT-AAAA-CGA
* *
60052 TTTTGGAACACAT-TTATAATATAG-TTTTTAAAAGCGTA
1 TTTT-GAAAACATATAAT-ATATAGTTTTTTAAAA-CG-A
* * *
60090 TTTTTAAAAACATATAATATATAGTTTTTTAAAAATGT
1 -TTTTGAAAACATATAATATATAGTTTTTT-AAAACGA
60128 TTTTGAAAACGTATATAATTTATATAGTTTCTTTGAAAA-GA
1 TTTTGAAAAC--ATATAA--TATATAGTTT-TTT-AAAACGA
60169 TT
1 TT
60171 GAAATATAAT
Statistics
Matches: 223, Mismatches: 27, Indels: 31
0.79 0.10 0.11
Matches are distributed among these distances:
35 30 0.13
36 23 0.10
37 24 0.11
38 78 0.35
39 34 0.15
40 14 0.06
41 13 0.06
42 7 0.03
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (36 bp):
TTTTGAAAACATATAATATATAGTTTTTTAAAACGA
Found at i:60243 original size:21 final size:21
Alignment explanation
Indices: 60195--60243 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
60185 ATACATATTA
*
60195 TTATTAGTATTTTATTTTTCGT
1 TTATTAATATTTTATTTTTC-T
60217 TT-TTAATATTTTATTTGTT-T
1 TTATTAATATTTTATTT-TTCT
60237 TTATTAA
1 TTATTAA
60244 CTTATCATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 3 0.12
21 17 0.71
22 4 0.17
ACGTcount: A:0.22, C:0.02, G:0.06, T:0.69
Consensus pattern (21 bp):
TTATTAATATTTTATTTTTCT
Found at i:63696 original size:25 final size:25
Alignment explanation
Indices: 63648--63697 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
63638 AGGGTAACTC
* *
63648 TTTTATGGGATTTACTGCAGTATGA
1 TTTTATGAGATTTACTGCACTATGA
*
63673 TTTTATGAGATTTACTGGACTATGA
1 TTTTATGAGATTTACTGCACTATGA
63698 CTTGTTTAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
TTTTATGAGATTTACTGCACTATGA
Done.