Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008207.1 Hibiscus syriacus cultivar Beakdansim tig00110829_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: 135326
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:3997 original size:14 final size:15
Alignment explanation
Indices: 3958--3990 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
3948 GAAATGAAGA
3958 ATACAATATAC-AAAT
1 ATAC-ATATACGAAAT
3973 ATACATATACGAAAT
1 ATACATATACGAAAT
3988 ATA
1 ATA
3991 TTATACGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.58, C:0.12, G:0.03, T:0.27
Consensus pattern (15 bp):
ATACATATACGAAAT
Found at i:6032 original size:10 final size:10
Alignment explanation
Indices: 6017--6063 Score: 76
Period size: 10 Copynumber: 4.6 Consensus size: 10
6007 TGGAAGACTA
6017 AATTTATTTT
1 AATTTATTTT
6027 AATTTATTTT
1 AATTTATTTT
*
6037 AAATTATTTT
1 AATTTATTTT
6047 AATTTATTTTT
1 AATTTA-TTTT
6058 AATTTA
1 AATTTA
6064 ATATATTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
10 24 0.71
11 10 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
AATTTATTTT
Found at i:6355 original size:27 final size:30
Alignment explanation
Indices: 6315--6371 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
6305 TATCTCTTTA
*
6315 TTTATTTAACTTATT-GA-ATATTTTATTT
1 TTTATTTAACTTATTAAATATATTTTATTT
*
6343 TTTA-TTAATTTATTAAATATATTTTATTT
1 TTTATTTAACTTATTAAATATATTTTATTT
6372 ATCTTAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 9 0.36
28 5 0.20
29 11 0.44
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (30 bp):
TTTATTTAACTTATTAAATATATTTTATTT
Found at i:6489 original size:31 final size:33
Alignment explanation
Indices: 6453--6525 Score: 96
Period size: 31 Copynumber: 2.3 Consensus size: 33
6443 AATATATTTA
6453 AATATTTTACTATTAATTTAATATAAAA-ATAT
1 AATATTTTACTATTAATTTAATATAAAATATAT
* * * *
6485 -ATATTTTACTCTTATTTTTATTTAAAATATAT
1 AATATTTTACTATTAATTTAATATAAAATATAT
6517 AATATTTTA
1 AATATTTTA
6526 ATATATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 23 0.66
32 4 0.11
33 8 0.23
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (33 bp):
AATATTTTACTATTAATTTAATATAAAATATAT
Found at i:6766 original size:29 final size:29
Alignment explanation
Indices: 6677--6769 Score: 100
Period size: 29 Copynumber: 3.2 Consensus size: 29
6667 AGTGATGATG
* * *
6677 ATAAAATATATTT-TTGTATTAAAATAAAA
1 ATAAAATATATTTAAT-AATTAAAACAAAA
* *
6706 ACAAAATATATTTAATAAATAAATACAAAA
1 ATAAAATATATTTAATAATTAAA-ACAAAA
6736 ATAAAA-ATATTTAATAAGTTAAAACAAAA
1 ATAAAATATATTTAATAA-TTAAAACAAAA
6765 ATAAA
1 ATAAA
6770 TAGATAATTT
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
29 39 0.72
30 15 0.28
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.31
Consensus pattern (29 bp):
ATAAAATATATTTAATAATTAAAACAAAA
Found at i:7660 original size:21 final size:21
Alignment explanation
Indices: 7630--8116 Score: 325
Period size: 21 Copynumber: 23.0 Consensus size: 21
7620 GATTTACATA
*
7630 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
7651 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
7672 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
7695 TT--CGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
*
7716 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
7735 TTCGCGTTGCGTTTTATTCCAAA
1 TTCGCGTTGCG--ATAGTCCAAG
7758 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
**
7777 TT--CGTTGCGATAGTCGTAG
1 TTCGCGTTGCGATAGTCCAAG
* *
7796 TTCGTGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
* *
7819 TT--CGTAGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
7838 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
7861 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
7880 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
7903 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
7922 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
*
7945 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
*
7964 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
*
7987 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
8006 TTCGCGTTGCAATTTATTCCAAATTCG
1 TTCGCGTTGCGA--TAGTCC-AA---G
* *
8033 TTGCGCGTTGCGATTTATTCCAAA
1 TT-CGCGTTGCGA--TAGTCCAAG
8057 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
8076 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
8099 TT--CGTTGCGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
8117 AATCACAACG
Statistics
Matches: 376, Mismatches: 51, Indels: 80
0.74 0.10 0.16
Matches are distributed among these distances:
19 96 0.26
21 180 0.48
23 74 0.20
24 4 0.01
27 5 0.01
28 17 0.05
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:7682 original size:42 final size:41
Alignment explanation
Indices: 7630--8037 Score: 434
Period size: 42 Copynumber: 9.8 Consensus size: 41
7620 GATTTACATA
* * *
7630 TTCGCATTGCGA-TAGTCCAAGTTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTATTCCAAGTT--CGTTGCGATAGTCCAAG
* *
7672 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA-TTATTCCAAGTTCGTTGCGA--TAGTCCAAG
* * * * *
7716 TT--CGTTGCGA-TAGTCGAAGTTCGCGTTGCGTTTTATTCCAAA
1 TTCGCGTTGCGATTATTCCAAGTT--CGTTGCG--ATAGTCCAAG
* **
7758 TT--CGTTGCGA-TAGTCCAAGTTCGTTGCGATAGTCGTAG
1 TTCGCGTTGCGATTATTCCAAGTTCGTTGCGATAGTCCAAG
* * *
7796 TTCGTGTTGCGATTTATTCCAAGTTCGTAGCGATAGTCGAAG
1 TTCGCGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCCAAG
*
7838 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAG
1 TTCGCGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCCAAG
*
7880 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAG
1 TTCGCGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCCAAG
*
7922 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCCAAG
*
7964 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCCAAG
* *
8006 TTCGCGTTGCAATTTATTCCAAATTCGTTGCG
1 TTCGCGTTGCGA-TTATTCCAAGTTCGTTGCG
8038 CGTTGCGATT
Statistics
Matches: 326, Mismatches: 28, Indels: 24
0.86 0.07 0.06
Matches are distributed among these distances:
38 7 0.02
40 22 0.07
42 279 0.86
44 18 0.06
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (41 bp):
TTCGCGTTGCGATTATTCCAAGTTCGTTGCGATAGTCCAAG
Found at i:7956 original size:126 final size:126
Alignment explanation
Indices: 7655--8116 Score: 545
Period size: 126 Copynumber: 3.8 Consensus size: 126
7645 TCCAAGTTCG
* * *
7655 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAGTT--
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGA--TAGTCGAAGTTCG
* * * * * * *
7718 CGTTGCGA--TAGTCGAAGTTCGCGTTGCGTTTTATTCCAAATT--CGTTGCGA--TAGTCCAAG
64 CGTTGCGATTTATTCCAAGTT--CGTTGCG--ATAGTCCAAGTTCGCGTTGCGATTTATTCCAAA
7777 TT
125 TT
* * *
7779 CGTTGCGATAGTCGTAGTTCGTGTTGCGATTTATTCCAAGTTCGTAGCGATAGTCGAAGTTCGCG
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCG
*
7844 TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
66 TTGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
*
7905 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCG
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCG
* *
7970 TTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCAATTTATTCCAAA--
66 TTGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
* *
8029 --TT-CG-T--T----G--CGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCG
8082 TTGCGATTTATTCCAAGTTCGTTGCGATAGTCCAA
66 TTGCGATTTATTCCAAGTTCGTTGCGATAGTCCAA
8117 AATCACAACG
Statistics
Matches: 306, Mismatches: 24, Indels: 28
0.85 0.07 0.08
Matches are distributed among these distances:
112 78 0.25
114 1 0.00
118 1 0.00
120 1 0.00
121 2 0.01
122 20 0.07
124 69 0.23
126 134 0.44
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (126 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCG
TTGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:8048 original size:28 final size:28
Alignment explanation
Indices: 8008--8065 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
7998 AGTCGAAGTT
8008 CGCGTTGCAATTTATTCCAAATTCGTTG
1 CGCGTTGCAATTTATTCCAAATTCGTTG
*
8036 CGCGTTGCGATTTATTCCAAATTCGTTG
1 CGCGTTGCAATTTATTCCAAATTCGTTG
8064 CG
1 CG
8066 ATAGTCCAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (28 bp):
CGCGTTGCAATTTATTCCAAATTCGTTG
Found at i:8049 original size:70 final size:70
Alignment explanation
Indices: 7966--8107 Score: 248
Period size: 70 Copynumber: 2.0 Consensus size: 70
7956 AGTCGAAGTT
* *
7966 CGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCAATTTATTCCAAATT
1 CGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCAATTTATTCCAAATT
8031 CGTTG
66 CGTTG
* *
8036 CGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTT
1 CGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCAATTTATTCCAAATT
8101 CGTTG
66 CGTTG
8106 CG
1 CG
8108 ATAGTCCAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (70 bp):
CGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCAATTTATTCCAAATT
CGTTG
Found at i:8217 original size:6 final size:6
Alignment explanation
Indices: 8206--8244 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
8196 GACACGTATT
8206 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
8245 CGAGACGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.51, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:9035 original size:21 final size:20
Alignment explanation
Indices: 9010--9080 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 20
9000 ATTTTGGACT
9010 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAAT-A
* *
9031 ATCGCAACGCGAACTTCGACT-
1 ATCGCAA--CGAACTTGGAATA
*
9052 ATCGCAACGAACATGGAATTA
1 ATCGCAACGAACTTGGAA-TA
9073 ATCGCAAC
1 ATCGCAAC
9081 TATTGCAACG
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
19 8 0.20
20 1 0.02
21 22 0.54
23 10 0.24
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (20 bp):
ATCGCAACGAACTTGGAATA
Found at i:9099 original size:30 final size:28
Alignment explanation
Indices: 9049--9106 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 28
9039 GCGAACTTCG
9049 ACTATCGCAACGAACATGGAATTAATCGCA
1 ACTATCGCAACGAACATGGAA--AATCGCA
* **
9079 ACTATTGCAACGAATTTGGAAAATCGCA
1 ACTATCGCAACGAACATGGAAAATCGCA
9107 TTGCGATAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.28
30 18 0.72
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (28 bp):
ACTATCGCAACGAACATGGAAAATCGCA
Found at i:9131 original size:21 final size:21
Alignment explanation
Indices: 9102--9154 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
9092 ATTTGGAAAA
*
9102 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
9123 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
9144 TCGCGTTGCGA
1 TCGCGTTGCGA
9155 ATCTGGAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:12907 original size:41 final size:41
Alignment explanation
Indices: 12839--12937 Score: 101
Period size: 41 Copynumber: 2.4 Consensus size: 41
12829 AGGTTTTTAA
*
12839 CGGC-TTTTTTTAAAAACGCCGCAAAAGGTAATGAAATGTAG
1 CGGCGTTTTTTT-CAAACGCCGCAAAAGGTAATGAAATGTAG
* * * * *
12880 CGGCGTTTTTTTCAAACGTCGCTAAAGGTTATGATATTTAG
1 CGGCGTTTTTTTCAAACGCCGCAAAAGGTAATGAAATGTAG
* * *
12921 TGGTGTTTTCTTCAAAC
1 CGGCGTTTTTTTCAAAC
12938 ACCGTTATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
41 41 0.85
42 7 0.15
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.35
Consensus pattern (41 bp):
CGGCGTTTTTTTCAAACGCCGCAAAAGGTAATGAAATGTAG
Found at i:13279 original size:21 final size:21
Alignment explanation
Indices: 13255--13313 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
13245 ATTATCCAAT
*
13255 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
*
13276 AAACTTGAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAC
*
13297 AAACTTGAAATCTATAA
1 AAACTTGAAATCCATAA
13314 TAATAAATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.51, C:0.20, G:0.07, T:0.22
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:15975 original size:41 final size:41
Alignment explanation
Indices: 15930--16026 Score: 149
Period size: 41 Copynumber: 2.4 Consensus size: 41
15920 TAAATTGTGA
*
15930 CGTTTGTATAAAAACACCACTAAAATAATAGTCTTTAGCGG
1 CGTTTGTATAAAAACACCACTAAAATAAGAGTCTTTAGCGG
* * * *
15971 CGTTTGTATAAAAATACCACTAAATTACGAGTCTTTGGCGG
1 CGTTTGTATAAAAACACCACTAAAATAAGAGTCTTTAGCGG
16012 CGTTTGTATAAAAAC
1 CGTTTGTATAAAAAC
16027 TGTAACACCC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (41 bp):
CGTTTGTATAAAAACACCACTAAAATAAGAGTCTTTAGCGG
Found at i:16612 original size:17 final size:17
Alignment explanation
Indices: 16590--16622 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16580 TAACCATTTG
16590 TTTAATTTGCCCAGACT
1 TTTAATTTGCCCAGACT
*
16607 TTTAATTTGTCCAGAC
1 TTTAATTTGCCCAGAC
16623 GTATAATACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.42
Consensus pattern (17 bp):
TTTAATTTGCCCAGACT
Found at i:16756 original size:23 final size:22
Alignment explanation
Indices: 16699--16788 Score: 89
Period size: 21 Copynumber: 4.1 Consensus size: 22
16689 TCGTAATTTG
16699 CACCGAAGTGCCACATAATTGT
1 CACCGAAGTGCCACATAATTGT
* *
16721 C-CCGAAG-GACCACATAGGTTTT
1 CACCGAAGTG-CCACATA-ATTGT
*
16743 CACCGAAGTGCCACATATTTGT
1 CACCGAAGTGCCACATAATTGT
*
16765 C-CCGAAG-GACCGCATAATTGT
1 CACCGAAGTG-CCACATAATTGT
16786 CAC
1 CAC
16789 TGAGAACCAC
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
20 2 0.04
21 30 0.54
22 10 0.18
23 13 0.23
24 1 0.02
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (22 bp):
CACCGAAGTGCCACATAATTGT
Found at i:27899 original size:20 final size:20
Alignment explanation
Indices: 27874--27954 Score: 63
Period size: 20 Copynumber: 3.9 Consensus size: 20
27864 TTTTGGTGCA
*
27874 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
* *
27894 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATACCCCC-AT
* *
27915 GAAGGGGAACCGATCCCCCCAC
1 G-A-GGGAACCGATACCCCCAT
* * *
27937 AATGGAATCGATACCCCC
1 GAGGGAACCGATACCCCC
27955 CCTGGGGTTC
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
20 29 0.60
21 3 0.06
22 1 0.02
23 15 0.31
ACGTcount: A:0.27, C:0.35, G:0.23, T:0.15
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:33294 original size:21 final size:21
Alignment explanation
Indices: 33268--33309 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
33258 ATTTGAATAT
*
33268 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
33289 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
33310 CCCATTATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:35472 original size:21 final size:21
Alignment explanation
Indices: 35447--35569 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 21
35437 GTAATTTGCA
*
35447 CCGAAGTG-CCACATAATTGTC
1 CCGAAG-GACCACATAATTATC
*
35468 CCGAAGGACCACATAGGTT-TGC
1 CCGAAGGACCACATA-ATTAT-C
* * *
35490 ACCGAAGTG-TCACATATTTGTC
1 -CCGAAG-GACCACATAATTATC
*
35512 CCGAAGTACCACATAATTATC
1 CCGAAGGACCACATAATTATC
*
35533 CCGGAGGACCACATAATTATC
1 CCGAAGGACCACATAATTATC
*
35554 CCGGAGGACCACATAA
1 CCGAAGGACCACATAA
35570 AACCCTCGAC
Statistics
Matches: 86, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
20 1 0.01
21 65 0.76
22 6 0.07
23 13 0.15
24 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.21
Consensus pattern (21 bp):
CCGAAGGACCACATAATTATC
Found at i:35492 original size:44 final size:43
Alignment explanation
Indices: 35438--35569 Score: 153
Period size: 44 Copynumber: 3.1 Consensus size: 43
35428 CCACAGCTCG
35438 TAATTTGCACCGAAGTGCCACATAATTGTCCCGAAGGACCACA
1 TAATTTGCACCGAAGTGCCACATAATTGTCCCGAAGGACCACA
* * * *
35481 TAGGTTTGCACCGAAGTGTCACATATTTGTCCCGAAGTACCACA
1 TA-ATTTGCACCGAAGTGCCACATAATTGTCCCGAAGGACCACA
* * *
35525 TAATTAT-C-CCGGAG-GACCACATAATTATCCCGGAGGACCACA
1 TAATT-TGCACCGAAGTG-CCACATAATTGTCCCGAAGGACCACA
35567 TAA
1 TAA
35570 AACCCTCGAC
Statistics
Matches: 75, Mismatches: 11, Indels: 7
0.81 0.12 0.08
Matches are distributed among these distances:
41 1 0.01
42 29 0.39
43 5 0.07
44 40 0.53
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.23
Consensus pattern (43 bp):
TAATTTGCACCGAAGTGCCACATAATTGTCCCGAAGGACCACA
Found at i:36446 original size:20 final size:20
Alignment explanation
Indices: 36402--36479 Score: 72
Period size: 19 Copynumber: 3.9 Consensus size: 20
36392 TGTTTGCGTG
* * *
36402 GTATCGATACCATCCTT-CG
1 GTATCGATACTACCCTTACA
36421 GTATCGATACTACCCTTACA
1 GTATCGATACTACCCTTACA
*
36441 GTATCGATAC--CTCTTCAACAA
1 GTATCGATACTACCCTT--AC-A
36462 GTATCGATACTACCCTTA
1 GTATCGATACTACCCTTA
36480 ATAATTTCAC
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
18 4 0.08
19 15 0.31
20 13 0.27
21 12 0.25
23 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.12, T:0.31
Consensus pattern (20 bp):
GTATCGATACTACCCTTACA
Found at i:37299 original size:41 final size:40
Alignment explanation
Indices: 37239--37379 Score: 158
Period size: 40 Copynumber: 3.5 Consensus size: 40
37229 ATTGGGATGT
* * *
37239 TACAAAAACGTCACGAAAGTACGAGTATTTAACGGCGTTTG
1 TACAAAAATGCCACTAAAGTA-GAGTATTTAACGGCGTTTG
* * *
37280 TACAAAAATGCCACTAAAGTATAGTATTTAACGGTGTTTA
1 TACAAAAATGCCACTAAAGTAGAGTATTTAACGGCGTTTG
* *
37320 TATAAAAATGCCACTAAAGTATGAGTATTTATCGGCGTTTG
1 TACAAAAATGCCACTAAAGTA-GAGTATTTAACGGCGTTTG
*
37361 TTTA-AAAAATGCCGCTAAA
1 --TACAAAAATGCCACTAAA
37380 AATCCCTCTA
Statistics
Matches: 85, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
40 36 0.42
41 33 0.39
42 14 0.16
43 2 0.02
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (40 bp):
TACAAAAATGCCACTAAAGTAGAGTATTTAACGGCGTTTG
Found at i:37327 original size:40 final size:41
Alignment explanation
Indices: 37254--37379 Score: 173
Period size: 40 Copynumber: 3.1 Consensus size: 41
37244 AAACGTCACG
* *
37254 AAAGTACGAGTATTTAACGGCGTTTGTACAAAAATGCCACT
1 AAAGTATGAGTATTTAACGGCGTTTGTATAAAAATGCCACT
* *
37295 AAAGTAT-AGTATTTAACGGTGTTTATATAAAAATGCCACT
1 AAAGTATGAGTATTTAACGGCGTTTGTATAAAAATGCCACT
* * *
37335 AAAGTATGAGTATTTATCGGCGTTTGTTTAAAAAATGCCGCT
1 AAAGTATGAGTATTTAACGGCGTTTGTAT-AAAAATGCCACT
37377 AAA
1 AAA
37380 AATCCCTCTA
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
40 37 0.50
41 23 0.31
42 14 0.19
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (41 bp):
AAAGTATGAGTATTTAACGGCGTTTGTATAAAAATGCCACT
Found at i:37827 original size:31 final size:31
Alignment explanation
Indices: 37791--37868 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
37781 GTTTCAAAAG
* *
37791 TAATAAATTGGTCACTAATGTTATCGATTTA
1 TAATAAAATGGTCACTAACGTTATCGATTTA
* * *
37822 TAATAAAATAGTTACTAACGTTATTGATTTA
1 TAATAAAATGGTCACTAACGTTATCGATTTA
37853 TAATAAAATGGTCACT
1 TAATAAAATGGTCACT
37869 CTCCCATTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.40
Consensus pattern (31 bp):
TAATAAAATGGTCACTAACGTTATCGATTTA
Found at i:41589 original size:31 final size:31
Alignment explanation
Indices: 41523--41589 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
41513 GTAACGATAG
* * *
41523 AGTGATCATTTTGTTAGAAATCGATAACGTC
1 AGTGATCATTTTGTTACAAATAGATAAAGTC
* *
41554 AGTGATCATTTTGTTACAAATAGGTAAAGTT
1 AGTGATCATTTTGTTACAAATAGATAAAGTC
41585 AGTGA
1 AGTGA
41590 CTAATTTGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (31 bp):
AGTGATCATTTTGTTACAAATAGATAAAGTC
Found at i:46478 original size:2 final size:2
Alignment explanation
Indices: 46471--46533 Score: 108
Period size: 2 Copynumber: 31.5 Consensus size: 2
46461 CATTAGTTAG
46471 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
* *
46513 AT AT AT AC AT AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
46534 GGAATTTGTA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:47285 original size:31 final size:31
Alignment explanation
Indices: 47212--47298 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 31
47202 CTTTCGAGAT
* * **
47212 ATATGGACAGTATACCTATGTTCTAAGGAAC
1 ATATGGACAGTTTACCTAGGTTCTTTGGAAC
*
47243 ATATGGACAGTTTACCTAGGTTCTTTGGGAC
1 ATATGGACAGTTTACCTAGGTTCTTTGGAAC
* *
47274 CTATGGACAGTTT-CCGAGGTTCTTT
1 ATATGGACAGTTTACCTAGGTTCTTT
47299 ATGACCTCTG
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 11 0.22
31 38 0.78
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.34
Consensus pattern (31 bp):
ATATGGACAGTTTACCTAGGTTCTTTGGAAC
Found at i:47296 original size:30 final size:30
Alignment explanation
Indices: 47244--47339 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
47234 CTAAGGAACA
* *
47244 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAGTTT-CCGAGGTTCTTTGTGACC
*
47275 TATGGACAGTTTCCGAGGTTCTTTATGACC
1 TATGGACAGTTTCCGAGGTTCTTTGTGACC
* * * *
47305 TCTGGATAGTTACCG-GGGTCTTTGTGACC
1 TATGGACAGTTTCCGAGGTTCTTTGTGACC
*
47334 TCTGGA
1 TATGGA
47340 TAGGTCCTTC
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 18 0.32
30 27 0.47
31 12 0.21
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (30 bp):
TATGGACAGTTTCCGAGGTTCTTTGTGACC
Found at i:58705 original size:46 final size:45
Alignment explanation
Indices: 58606--58776 Score: 256
Period size: 46 Copynumber: 3.8 Consensus size: 45
58596 GATAAACTGG
* * **
58606 AAAATAAGCTTACTAGCTTATGGAAT-AATGACAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGT
58650 AAAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTAT-GGATTAAATGGTAAGTATATTGGT
* *
58696 AAAATAAGCTTACTAGCTTATGGGATTAAATGGTAAGTATTTTGGT
1 AAAATAAGCTTACGAGCTTAT-GGATTAAATGGTAAGTATATTGGT
58742 AAAATAAGCTTACGAGCTTATGGA-TAAATGGTAAG
1 AAAATAAGCTTACGAGCTTATGGATTAAATGGTAAG
58777 AGATTTTATC
Statistics
Matches: 118, Mismatches: 7, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
44 31 0.26
45 7 0.06
46 80 0.68
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.32
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGT
Found at i:59213 original size:33 final size:33
Alignment explanation
Indices: 59176--59241 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
59166 TACTGTAGTA
* *
59176 GTTACTGTAGCAGTGCATCGGTACACTGTTCAC
1 GTTACTGTAACAATGCATCGGTACACTGTTCAC
59209 GTTACTGTAACAATGCATCGGTACACTGTTCAC
1 GTTACTGTAACAATGCATCGGTACACTGTTCAC
59242 TGTTCATGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.30
Consensus pattern (33 bp):
GTTACTGTAACAATGCATCGGTACACTGTTCAC
Found at i:62624 original size:41 final size:41
Alignment explanation
Indices: 62563--62685 Score: 219
Period size: 41 Copynumber: 3.0 Consensus size: 41
62553 CCTAATAAAT
* *
62563 TAGTTGTTAATTCAAGGGAAGATGAAACTCCAAAAGTTCAC
1 TAGTTATTAATTCAATGGAAGATGAAACTCCAAAAGTTCAC
62604 TAGTTATTAATTCAATGGAAGATGAAACTCCAAAAGTTCAC
1 TAGTTATTAATTCAATGGAAGATGAAACTCCAAAAGTTCAC
*
62645 TAGTTATTAATTCAATGGAATATGAAACTCCAAAAGTTCAC
1 TAGTTATTAATTCAATGGAAGATGAAACTCCAAAAGTTCAC
62686 GTAGAATGAA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 79 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (41 bp):
TAGTTATTAATTCAATGGAAGATGAAACTCCAAAAGTTCAC
Found at i:64171 original size:21 final size:21
Alignment explanation
Indices: 64147--64214 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
64137 AATATGTAAA
64147 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
64168 TCGCGTTGCGATTTTGCAAAT
1 TCGCATTGCGATTTTCCAAAT
* * *
64189 TCACGTTGTGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
64210 TCGCA
1 TCGCA
64215 ACACGAATCT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:64235 original size:20 final size:20
Alignment explanation
Indices: 64210--64258 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
64200 TTTTCCAAAT
64210 TCGCAACACGAATCTATAAA
1 TCGCAACACGAATCTATAAA
* * *
64230 TCGCAACGCGAATTTGTAAA
1 TCGCAACACGAATCTATAAA
64250 TCGCAACAC
1 TCGCAACAC
64259 ATACGTCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.39, C:0.27, G:0.14, T:0.20
Consensus pattern (20 bp):
TCGCAACACGAATCTATAAA
Found at i:64273 original size:20 final size:20
Alignment explanation
Indices: 64250--64416 Score: 221
Period size: 20 Copynumber: 8.3 Consensus size: 20
64240 AATTTGTAAA
* *
64250 TCGCAACACATACGTCAAAT
1 TCGCAACACAAAAGTCAAAT
64270 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
64290 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
64310 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
64330 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* * *
64350 TCGCAACGCGATAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* **
64370 TCGTAACACGAATTTGT-AAA-
1 TCGCAACAC-AA-AAGTCAAAT
*
64390 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
64410 TCGCAAC
1 TCGCAAC
64417 GCGGAATTTC
Statistics
Matches: 130, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
18 2 0.02
19 4 0.03
20 117 0.90
21 4 0.03
22 3 0.02
ACGTcount: A:0.44, C:0.25, G:0.13, T:0.18
Consensus pattern (20 bp):
TCGCAACACAAAAGTCAAAT
Found at i:64417 original size:60 final size:60
Alignment explanation
Indices: 64250--64437 Score: 227
Period size: 60 Copynumber: 3.1 Consensus size: 60
64240 AATTTGTAAA
* * * *
64250 TCGCAACACATACGTCAAATTCGCAACACAAAAGTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAAAGTCAAAT
*
64310 TCGCAACACAAAAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAAAGTCAAAT
* ** * **
64370 TCGTAACACGAATTTGT-AAA-TCGCAACACAGAAGTCAAATTCGCAACGCGGAATTTCAAAT
1 TCGCAACAC-AA-AAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGC-GAAAGTCAAAT
*
64431 TTGCAAC
1 TCGCAAC
64438 TGAATTTCAA
Statistics
Matches: 111, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
60 91 0.82
61 18 0.16
62 2 0.02
ACGTcount: A:0.43, C:0.24, G:0.13, T:0.19
Consensus pattern (60 bp):
TCGCAACACAAAAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAAAGTCAAAT
Found at i:64456 original size:60 final size:60
Alignment explanation
Indices: 64205--64456 Score: 223
Period size: 60 Copynumber: 4.2 Consensus size: 60
64195 TGTGATTTTC
* * **
64205 CAAATTCGCAACAC-GAA-TCTATAAATCGCAACGCGAATTTGT-AAA-TCGCAACAC-ATACGT
1 CAAATTCGCAACACAAAAGTC-A-AATTCGCAACGCGAA--TGTCAAATTCGCAACACGA-ATTT
* * * * **
64265 CAAATTCGCAACACAAAAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACACAAAAGT
1 CAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAATGTCAAATTCGCAACACGAATTT
*
64325 CAAATTCGCAACACAAAAGTCAAATTCGCAACGCG-ATAGTCAAATTCGTAACACGAATTT
1 CAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAAT-GTCAAATTCGCAACACGAATTT
* * * * *
64385 GTAAA-TCGCAACACAGAAGTCAAATTCGCAACGCGGAATTTCAAATTTGCAAC-TGAATTT
1 -CAAATTCGCAACACAAAAGTCAAATTCGCAACGC-GAATGTCAAATTCGCAACACGAATTT
*
64445 CAAATTTGCAAC
1 CAAATTCGCAAC
64457 TAGATTTTTG
Statistics
Matches: 161, Mismatches: 21, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
58 2 0.01
59 7 0.04
60 129 0.80
61 19 0.12
62 4 0.02
ACGTcount: A:0.42, C:0.23, G:0.13, T:0.21
Consensus pattern (60 bp):
CAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAATGTCAAATTCGCAACACGAATTT
Found at i:64463 original size:19 final size:19
Alignment explanation
Indices: 64420--64457 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
64410 TCGCAACGCG
64420 GAATTTCAAATTTGCAACT
1 GAATTTCAAATTTGCAACT
64439 GAATTTCAAATTTGCAACT
1 GAATTTCAAATTTGCAACT
64458 AGATTTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (19 bp):
GAATTTCAAATTTGCAACT
Found at i:65448 original size:24 final size:24
Alignment explanation
Indices: 65421--65474 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
65411 GTATTCGAAA
65421 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
65445 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
65469 TTTGAT
1 TTTGAT
65475 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:67757 original size:18 final size:18
Alignment explanation
Indices: 67734--67769 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
67724 AAACAAAAGG
*
67734 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
67752 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
67770 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:68176 original size:20 final size:21
Alignment explanation
Indices: 68151--68214 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 21
68141 TTAACACTTA
*
68151 TTTCGCATTGCAAATTTGA-T
1 TTTCGCATTGCAAATTTGACC
* *
68171 TTTCGCGTTGCGAATTT-ACC
1 TTTCGCATTGCAAATTTGACC
*
68191 TTTCGCATTACAAATTTGTACC
1 TTTCGCATTGCAAATTTG-ACC
68213 TT
1 TT
68215 CAACAGGTCT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 1 0.03
20 29 0.83
22 5 0.14
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.44
Consensus pattern (21 bp):
TTTCGCATTGCAAATTTGACC
Found at i:68344 original size:66 final size:65
Alignment explanation
Indices: 68262--68437 Score: 257
Period size: 66 Copynumber: 2.6 Consensus size: 65
68252 AATTTAAAAC
68262 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATC-AATT
68327 A
65 A
* *
68328 AACAAATCAACTTTTACAAATCAATTAAACAAGC-AAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTA
68392 AACAAATCAACTTTCAATGTA-AAATTCAATTAAACAAGCAAAAAAA
1 AACAAATCAAC-TT---T-TACAAA-TCAATTAAACAAGCAAAAAAA
68438 GTATACCCCA
Statistics
Matches: 101, Mismatches: 2, Indels: 10
0.89 0.02 0.09
Matches are distributed among these distances:
64 16 0.16
65 25 0.25
66 34 0.34
68 4 0.04
69 16 0.16
70 6 0.06
ACGTcount: A:0.53, C:0.17, G:0.02, T:0.28
Consensus pattern (65 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTA
Found at i:69811 original size:21 final size:21
Alignment explanation
Indices: 69787--69885 Score: 85
Period size: 21 Copynumber: 4.7 Consensus size: 21
69777 GCGGATGGGA
*
69787 CCTCTTGAACGATGACAGGGG
1 CCTCTTGAACGATGAGAGGGG
* * * *
69808 CCTCTTGAAAGGTGGGATGGG
1 CCTCTTGAACGATGAGAGGGG
* *
69829 CATCTTCG-ATGATGAGAGGGG
1 CCTCTT-GAACGATGAGAGGGG
*
69850 CCTCTTGAACGAT-AGGAGGCG
1 CCTCTTGAACGATGA-GAGGGG
*
69871 CCTCTTGAATGATGA
1 CCTCTTGAACGATGA
69886 TAGATGCATC
Statistics
Matches: 60, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
20 2 0.03
21 56 0.93
22 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.23
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:69883 original size:42 final size:42
Alignment explanation
Indices: 69779--69885 Score: 119
Period size: 42 Copynumber: 2.5 Consensus size: 42
69769 CTTGAACGGC
* * *
69779 GGATGGGACCTCTTGAACGATGACAGGGGCCTCTTGAAAGGTG
1 GGATGGG-CCTCTTGAATGATGACAGGGGCCTCTTGAAAGATA
* * *
69822 GGATGGGCATCTTCG-ATGATGAGAGGGGCCTCTTGAACGATA
1 GGATGGGCCTCTT-GAATGATGACAGGGGCCTCTTGAAAGATA
69864 GGA-GGCGCCTCTTGAATGATGA
1 GGATGG-GCCTCTTGAATGATGA
69886 TAGATGCATC
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
41 3 0.06
42 43 0.80
43 8 0.15
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.22
Consensus pattern (42 bp):
GGATGGGCCTCTTGAATGATGACAGGGGCCTCTTGAAAGATA
Found at i:72489 original size:22 final size:22
Alignment explanation
Indices: 72434--72491 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
72424 GATGGAGATA
*
72434 GATGGATTTCGCCGGAGATGGG
1 GATGGATTTCGTCGGAGATGGG
*
72456 GACGGATTTCGTCGGAGATGGG
1 GATGGATTTCGTCGGAGATGGG
*
72478 GATGGATGTCGTCG
1 GATGGATTTCGTCG
72492 TAGAGAGTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.17, C:0.14, G:0.45, T:0.24
Consensus pattern (22 bp):
GATGGATTTCGTCGGAGATGGG
Found at i:72645 original size:20 final size:20
Alignment explanation
Indices: 72600--72746 Score: 156
Period size: 20 Copynumber: 7.3 Consensus size: 20
72590 TGTGTTTCGC
* *
72600 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTG-ACTTCTGT
*
72621 GTTGCGAATTTGACTTCTTT
1 GTTGCGAATTTGACTTCTGT
72641 GTTGCGAATTTGACTATC-GT
1 GTTGCGAATTTGACT-TCTGT
*
72661 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTCTGT
* *
72681 GTTGCGAATTTGACTTTTGG
1 GTTGCGAATTTGACTTCTGT
*
72701 GTTGC-AGATTTGACTATC-GC
1 GTTGCGA-ATTTGACT-TCTGT
*
72721 GTTTCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCTGT
*
72741 ATTGCG
1 GTTGCG
72747 GTTTACAAAT
Statistics
Matches: 108, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
19 4 0.04
20 88 0.81
21 16 0.15
ACGTcount: A:0.18, C:0.14, G:0.24, T:0.44
Consensus pattern (20 bp):
GTTGCGAATTTGACTTCTGT
Found at i:72686 original size:60 final size:60
Alignment explanation
Indices: 72596--72746 Score: 198
Period size: 60 Copynumber: 2.5 Consensus size: 60
72586 ATATTGTGTT
* * *
72596 TCGCGTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTTCTT-TGTTGC-GAATTTGACTA
1 TCGCGTTGCGAATTTG-ACTTCTGTGTTGCGAATTTGACTT-TTGGGTTGCAG-ATTTGACTA
* *
72657 TCGTGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTTTGGGTTGCAGATTTGACTA
1 TCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACTTTTGGGTTGCAGATTTGACTA
* *
72717 TCGCGTTTCGAATTTGACTTCTGTATTGCG
1 TCGCGTTGCGAATTTGACTTCTGTGTTGCG
72747 GTTTACAAAT
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
59 2 0.03
60 61 0.77
61 16 0.20
ACGTcount: A:0.18, C:0.15, G:0.25, T:0.43
Consensus pattern (60 bp):
TCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACTTTTGGGTTGCAGATTTGACTA
Found at i:72765 original size:60 final size:61
Alignment explanation
Indices: 72596--72774 Score: 161
Period size: 60 Copynumber: 3.0 Consensus size: 61
72586 ATATTGTGTT
* * * **
72596 TCGCGTTGCGAATTTGAAATTCAGTGTTGCGAATTTGAC-TTCTTTGTTGCG-AATTTGACTA
1 TCGCGTTGCGAATTTG-ACTTCTGTATTGCGAATTTGACATTC-GCGTTGCGAAATTTGACTA
* * * * * * *
72657 TCGTGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTTTGGGTTGC-AGATTTGACTA
1 TCGCGTTGCGAATTTGACTTCTGTATTGCGAATTTGACATTCGCGTTGCGAAATTTGACTA
* *
72717 TCGCGTTTCGAATTTGACTTCTGTATTGCG-GTTT-ACAAATTCGCGTTGCGAAATTTGA
1 TCGCGTTGCGAATTTGACTTCTGTATTGCGAATTTGAC--ATTCGCGTTGCGAAATTTGA
72775 AATTGGGTTG
Statistics
Matches: 96, Mismatches: 17, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
58 2 0.02
59 3 0.03
60 67 0.70
61 24 0.25
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.42
Consensus pattern (61 bp):
TCGCGTTGCGAATTTGACTTCTGTATTGCGAATTTGACATTCGCGTTGCGAAATTTGACTA
Found at i:72784 original size:20 final size:20
Alignment explanation
Indices: 72761--72814 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
72751 ACAAATTCGC
*
72761 GTTGCGAAATTTGAAATTGG
1 GTTGCGAAATTGGAAATTGG
72781 GTTGCGAAATTGGAAATTGG
1 GTTGCGAAATTGGAAATTGG
72801 GTTGCGAAATTGGA
1 GTTGCGAAATTGGA
72815 GTTCGCGTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.30, C:0.06, G:0.33, T:0.31
Consensus pattern (20 bp):
GTTGCGAAATTGGAAATTGG
Found at i:72824 original size:20 final size:19
Alignment explanation
Indices: 72754--72828 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 19
72744 GCGGTTTACA
*
72754 AATTCGCGTTGCGAAATTTGA
1 AATT-GCGTTGCGAAA-TTGG
*
72775 AATTGGGTTGCGAAATTGG
1 AATTGCGTTGCGAAATTGG
*
72794 AAATTGGGTTGCGAAATTGG
1 -AATTGCGTTGCGAAATTGG
*
72814 AGTTCGCGTTGCGAA
1 AATT-GCGTTGCGAA
72829 TTTGTTGGTC
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
19 6 0.12
20 38 0.79
21 4 0.08
ACGTcount: A:0.27, C:0.11, G:0.32, T:0.31
Consensus pattern (19 bp):
AATTGCGTTGCGAAATTGG
Found at i:76143 original size:25 final size:25
Alignment explanation
Indices: 76115--76185 Score: 72
Period size: 26 Copynumber: 2.8 Consensus size: 25
76105 GGAGGTTGTG
*
76115 ATTTGGGATTTAGAG-TTCGAGTATA
1 ATTTGGGATTTAG-GTTTAGAGTATA
* * *
76140 ATTTGAAGATTAAGGTTTAGGGTATA
1 ATTTG-GGATTTAGGTTTAGAGTATA
76166 ATTTGGGATTTAAGGTTTAG
1 ATTTGGGATTT-AGGTTTAG
76186 GTGTTTAGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
25 10 0.27
26 27 0.73
ACGTcount: A:0.30, C:0.01, G:0.28, T:0.41
Consensus pattern (25 bp):
ATTTGGGATTTAGGTTTAGAGTATA
Found at i:76164 original size:26 final size:26
Alignment explanation
Indices: 76135--76186 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
76125 TAGAGTTCGA
76135 GTATAATTTGAAGA-TTAAGGTTTAGG
1 GTATAATTTG-AGATTTAAGGTTTAGG
*
76161 GTATAATTTGGGATTTAAGGTTTAGG
1 GTATAATTTGAGATTTAAGGTTTAGG
76187 TGTTTAGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 2 0.08
26 22 0.92
ACGTcount: A:0.31, C:0.00, G:0.29, T:0.40
Consensus pattern (26 bp):
GTATAATTTGAGATTTAAGGTTTAGG
Found at i:79129 original size:43 final size:43
Alignment explanation
Indices: 79068--79174 Score: 205
Period size: 43 Copynumber: 2.5 Consensus size: 43
79058 TATTTTATAA
79068 AGCAAAAACATTCTGGAAAAATATATTTATTTATCGTTGTAAC
1 AGCAAAAACATTCTGGAAAAATATATTTATTTATCGTTGTAAC
79111 AGCAAAAACATTCTGGAAAAATATATTTATTTATCGTTGTAAC
1 AGCAAAAACATTCTGGAAAAATATATTTATTTATCGTTGTAAC
*
79154 AGCAAAAACATTCTGAAAAAA
1 AGCAAAAACATTCTGGAAAAA
79175 AAAACACATT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 63 1.00
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.31
Consensus pattern (43 bp):
AGCAAAAACATTCTGGAAAAATATATTTATTTATCGTTGTAAC
Found at i:79185 original size:19 final size:19
Alignment explanation
Indices: 79157--79212 Score: 89
Period size: 18 Copynumber: 3.0 Consensus size: 19
79147 TTGTAACAGC
79157 AAAA-ACATTCTGAAAAAA
1 AAAACACATTCTGAAAAAA
79175 AAAACACATTCTG-AAAAA
1 AAAACACATTCTGAAAAAA
79193 AAAACACATTCTGGAAAAAA
1 AAAACACATTCT-GAAAAAA
79213 CAAATTAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
18 21 0.60
19 9 0.26
20 5 0.14
ACGTcount: A:0.62, C:0.14, G:0.07, T:0.16
Consensus pattern (19 bp):
AAAACACATTCTGAAAAAA
Found at i:81129 original size:22 final size:22
Alignment explanation
Indices: 81104--81151 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
81094 ACAACACCAT
81104 CATACACCAAGTATGTCAATTA
1 CATACACCAAGTATGTCAATTA
*
81126 CATACATCAAGTATGTCAATTA
1 CATACACCAAGTATGTCAATTA
81148 CATA
1 CATA
81152 TATAGTGCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (22 bp):
CATACACCAAGTATGTCAATTA
Found at i:81960 original size:22 final size:22
Alignment explanation
Indices: 81935--81982 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
81925 ACAACACCAT
81935 CATACACCAAGTATGTCAATTA
1 CATACACCAAGTATGTCAATTA
*
81957 CATACATCAAGTATGTCAATTA
1 CATACACCAAGTATGTCAATTA
81979 CATA
1 CATA
81983 TATAGTGCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (22 bp):
CATACACCAAGTATGTCAATTA
Found at i:82792 original size:22 final size:22
Alignment explanation
Indices: 82767--82814 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
82757 ACAACACCAT
82767 CATACACCAAGTATGTCAATTA
1 CATACACCAAGTATGTCAATTA
*
82789 CATACATCAAGTATGTCAATTA
1 CATACACCAAGTATGTCAATTA
82811 CATA
1 CATA
82815 TATAGTGCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (22 bp):
CATACACCAAGTATGTCAATTA
Found at i:82801 original size:832 final size:832
Alignment explanation
Indices: 80759--83255 Score: 4987
Period size: 832 Copynumber: 3.0 Consensus size: 832
80749 TGCCTAACAT
80759 ACTTATCAATTAGAATATTCCAAAATATTCATTCACAACCTAATGTATGACAAATGAGAATGCAA
1 ACTTATCAATTAGAATATTCCAAAATATTCATTCACAACCTAATGTATGACAAATGAGAATGCAA
80824 GGTACGCAACAAGCACCTAAGTGCCGCAATGACGTATAGGTACTATGGTACACAACAACACTATG
66 GGTACGCAACAAGCACCTAAGTGCCGCAATGACGTATAGGTACTATGGTACACAACAACACTATG
80889 CTAACCATTTTCATAGTAGTAATCCTATATGACTACCATCCTTGCACACAAAGTGCCGAAAGTAC
131 CTAACCATTTTCATAGTAGTAATCCTATATGACTACCATCCTTGCACACAAAGTGCCGAAAGTAC
80954 GCAAAGGTACTAATATGATTATGCAACAAATGCATTTAAACAAAACCGATCAATAACCATCATGT
196 GCAAAGGTACTAATATGATTATGCAACAAATGCATTTAAACAAAACCGATCAATAACCATCATGT
81019 TCCAAGTATGTCAATTACATACATAGTGCTTCAGTATACAAAGTACTACTACAATACCATCTTAT
261 TCCAAGTATGTCAATTACATACATAGTGCTTCAGTATACAAAGTACTACTACAATACCATCTTAT
81084 TTATGGTATTACAACACCATCATACACCAAGTATGTCAATTACATACATCAAGTATGTCAATTAC
326 TTATGGTATTACAACACCATCATACACCAAGTATGTCAATTACATACATCAAGTATGTCAATTAC
81149 ATATATAGTGCTTCAGTACACAAAGTATTACTACAATACCATCGTATTTATGGTATTACAATTGC
391 ATATATAGTGCTTCAGTACACAAAGTATTACTACAATACCATCGTATTTATGGTATTACAATTGC
81214 ACATATGACTCTCAATGTACATACAATAGGCTCTAAAATCCAAATTGCAGGTTAAACATTTATTC
456 ACATATGACTCTCAATGTACATACAATAGGCTCTAAAATCCAAATTGCAGGTTAAACATTTATTC
81279 CAAACCTACAATAAATGATCATTTGTGTGGAACACATCCATTCGCTTTAGGGCAGTTCATACCCT
521 CAAACCTACAATAAATGATCATTTGTGTGGAACACATCCATTCGCTTTAGGGCAGTTCATACCCT
81344 AAAATCATTCGTAAAATCA-TTTCATAAACTTTATGAAAATATTTATATATCAAAACACATTCAA
586 AAAATCATTCGTAAAATCATTTTCATAAACTTTATGAAAATATTTATATATCAAAACACATTCAA
81408 AACATATTTAATAAGCACTCGAGGTTGACTTATCGCAAGTCGTCCTCATATCATATAAATACATA
651 AACATATTTAATAAGCACTCGAGGTTGACTTATCGCAAGTCGTCCTCATATCATATAAATACATA
81473 ATAAATGCACTCACCAGGTGTTCCTCACTATTATGCCTTACTGTCAATATCCAATTACTCTTAGA
716 ATAAATGCACTCACCAGGTGTTCCTCACTATTATGCCTTACTGTCAATATCCAATTACTCTTAGA
81538 CTTTTTCCTTGCCTTTCACTTTGCTTGTATCACGGTTTTGATCACGTTCTAC
781 CTTTTTCCTTGCCTTTCACTTTGCTTGTATCACGGTTTTGATCACGTTCTAC
81590 ACTTATCAATTAGAATATTCCAAAATATTCATTCACAACCTAATGTATGACAAATGAGAATGCAA
1 ACTTATCAATTAGAATATTCCAAAATATTCATTCACAACCTAATGTATGACAAATGAGAATGCAA
81655 GGTACGCAACAAGCACCTAAGTGCCGCAATGACGTATAGGTACTATGGTACACAACAACACTATG
66 GGTACGCAACAAGCACCTAAGTGCCGCAATGACGTATAGGTACTATGGTACACAACAACACTATG
81720 CTAACCATTTTCATAGTAGTAATCCTATATGACTACCATCCTTGCACACAAAGTGCCGAAAGTAC
131 CTAACCATTTTCATAGTAGTAATCCTATATGACTACCATCCTTGCACACAAAGTGCCGAAAGTAC
81785 GCAAAGGTACTAATATGATTATGCAACAAATGCATTTAAACAAAACCGATCAATAACCATCATGT
196 GCAAAGGTACTAATATGATTATGCAACAAATGCATTTAAACAAAACCGATCAATAACCATCATGT
81850 TCCAAGTATGTCAATTACATACATAGTGCTTCAGTATACAAAGTACTACTACAATACCATCTTAT
261 TCCAAGTATGTCAATTACATACATAGTGCTTCAGTATACAAAGTACTACTACAATACCATCTTAT
81915 TTATGGTATTACAACACCATCATACACCAAGTATGTCAATTACATACATCAAGTATGTCAATTAC
326 TTATGGTATTACAACACCATCATACACCAAGTATGTCAATTACATACATCAAGTATGTCAATTAC
81980 ATATATAGTGCTTCAGTACACAAAGTATTACTACAATACCATCGTATTTATGGTATTACAATTGC
391 ATATATAGTGCTTCAGTACACAAAGTATTACTACAATACCATCGTATTTATGGTATTACAATTGC
82045 ACATATGACTCTCAATGTACATACAATAGGCTCTAAAATCCAAATTGCAGGTTAAACATTTATTC
456 ACATATGACTCTCAATGTACATACAATAGGCTCTAAAATCCAAATTGCAGGTTAAACATTTATTC
82110 CAAACCTACAATAAATGATCATTTGTGTGGAACACATCCATTCGCTTTAGGGCAGTTCATACCCT
521 CAAACCTACAATAAATGATCATTTGTGTGGAACACATCCATTCGCTTTAGGGCAGTTCATACCCT
82175 AAAATCATTCGTAAAATCATTTTCATAAACTTTATGAAAATATTTATATATCAAAACACATTCAA
586 AAAATCATTCGTAAAATCATTTTCATAAACTTTATGAAAATATTTATATATCAAAACACATTCAA
82240 AACATATTTAATAAGCACTCGAGGTTGACTTATCGCAAGTCGTCCTCATATCATATAAATACATA
651 AACATATTTAATAAGCACTCGAGGTTGACTTATCGCAAGTCGTCCTCATATCATATAAATACATA
82305 ATAAATGCACTCACCAGGTGTTCCTCACTATTATGCCTTACTGTCAATATCCAATTACTCTTAGA
716 ATAAATGCACTCACCAGGTGTTCCTCACTATTATGCCTTACTGTCAATATCCAATTACTCTTAGA
82370 CTTTTTCCTTGCCTTTCACTTTGCTTGTATCACGGTTTTGATCACGTTCTAC
781 CTTTTTCCTTGCCTTTCACTTTGCTTGTATCACGGTTTTGATCACGTTCTAC
82422 ACTTATCAATTAGAATATTCCAAAATATTCATTCACAACCTAATGTATGACAAATGAGAATGCAA
1 ACTTATCAATTAGAATATTCCAAAATATTCATTCACAACCTAATGTATGACAAATGAGAATGCAA
82487 GGTACGCAACAAGCACCTAAGTGCCGCAATGACGTATAGGTACTATGGTACACAACAACACTATG
66 GGTACGCAACAAGCACCTAAGTGCCGCAATGACGTATAGGTACTATGGTACACAACAACACTATG
82552 CTAACCATTTTCATAGTAGTAATCCTATATGACTACCATCCTTGCACACAAAGTGCCGAAAGTAC
131 CTAACCATTTTCATAGTAGTAATCCTATATGACTACCATCCTTGCACACAAAGTGCCGAAAGTAC
82617 GCAAAGGTACTAATATGATTATGCAACAAATGCATTTAAACAAAACCGATCAATAACCATCATGT
196 GCAAAGGTACTAATATGATTATGCAACAAATGCATTTAAACAAAACCGATCAATAACCATCATGT
82682 TCCAAGTATGTCAATTACATACATAGTGCTTCAGTATACAAAGTACTACTACAATACCATCTTAT
261 TCCAAGTATGTCAATTACATACATAGTGCTTCAGTATACAAAGTACTACTACAATACCATCTTAT
82747 TTATGGTATTACAACACCATCATACACCAAGTATGTCAATTACATACATCAAGTATGTCAATTAC
326 TTATGGTATTACAACACCATCATACACCAAGTATGTCAATTACATACATCAAGTATGTCAATTAC
82812 ATATATAGTGCTTCAGTACACAAAGTATTACTACAATACCATCGTATTTATGGTATTACAATTGC
391 ATATATAGTGCTTCAGTACACAAAGTATTACTACAATACCATCGTATTTATGGTATTACAATTGC
82877 ACATATGACTCTCAATGTACATACAATAGGCTCTAAAATCCAAATTGCAGGTTAAACATTTATTC
456 ACATATGACTCTCAATGTACATACAATAGGCTCTAAAATCCAAATTGCAGGTTAAACATTTATTC
82942 CAAACCTACAATAAATGATCATTTGTGTGGAACACATCCATTCGCTTTAGGGCAGTTCATACCCT
521 CAAACCTACAATAAATGATCATTTGTGTGGAACACATCCATTCGCTTTAGGGCAGTTCATACCCT
83007 AAAATCATTCGTAAAATCATTTTCATAAACTTTATGAAAATATTTATATATCAAAACACATTCAA
586 AAAATCATTCGTAAAATCATTTTCATAAACTTTATGAAAATATTTATATATCAAAACACATTCAA
83072 AACATATTTAATAAGCACTCGAGGTTGACTTATCGCAAGTCGTCCTCATATCATATAAATACATA
651 AACATATTTAATAAGCACTCGAGGTTGACTTATCGCAAGTCGTCCTCATATCATATAAATACATA
83137 ATAAATGCACTCACCAGGTGTTCCTCACTATTATGCCTTACTGTCAATATCCAATTACTCTTAGA
716 ATAAATGCACTCACCAGGTGTTCCTCACTATTATGCCTTACTGTCAATATCCAATTACTCTTAGA
83202 CTTTTTCCTTGCCTTTCACTTTGCTTGTATCACGGTTTTGATCACGTTCTAC
781 CTTTTTCCTTGCCTTTCACTTTGCTTGTATCACGGTTTTGATCACGTTCTAC
83254 AC
1 AC
83256 AAGCATCCAT
Statistics
Matches: 1665, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
831 604 0.36
832 1061 0.64
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (832 bp):
ACTTATCAATTAGAATATTCCAAAATATTCATTCACAACCTAATGTATGACAAATGAGAATGCAA
GGTACGCAACAAGCACCTAAGTGCCGCAATGACGTATAGGTACTATGGTACACAACAACACTATG
CTAACCATTTTCATAGTAGTAATCCTATATGACTACCATCCTTGCACACAAAGTGCCGAAAGTAC
GCAAAGGTACTAATATGATTATGCAACAAATGCATTTAAACAAAACCGATCAATAACCATCATGT
TCCAAGTATGTCAATTACATACATAGTGCTTCAGTATACAAAGTACTACTACAATACCATCTTAT
TTATGGTATTACAACACCATCATACACCAAGTATGTCAATTACATACATCAAGTATGTCAATTAC
ATATATAGTGCTTCAGTACACAAAGTATTACTACAATACCATCGTATTTATGGTATTACAATTGC
ACATATGACTCTCAATGTACATACAATAGGCTCTAAAATCCAAATTGCAGGTTAAACATTTATTC
CAAACCTACAATAAATGATCATTTGTGTGGAACACATCCATTCGCTTTAGGGCAGTTCATACCCT
AAAATCATTCGTAAAATCATTTTCATAAACTTTATGAAAATATTTATATATCAAAACACATTCAA
AACATATTTAATAAGCACTCGAGGTTGACTTATCGCAAGTCGTCCTCATATCATATAAATACATA
ATAAATGCACTCACCAGGTGTTCCTCACTATTATGCCTTACTGTCAATATCCAATTACTCTTAGA
CTTTTTCCTTGCCTTTCACTTTGCTTGTATCACGGTTTTGATCACGTTCTAC
Found at i:83370 original size:11 final size:11
Alignment explanation
Indices: 83354--83379 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
83344 ATTATTTTCG
83354 AATTCTTCTAA
1 AATTCTTCTAA
83365 AATTCTTCTAA
1 AATTCTTCTAA
83376 AATT
1 AATT
83380 TTCCTTTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (11 bp):
AATTCTTCTAA
Found at i:92486 original size:22 final size:22
Alignment explanation
Indices: 92460--92538 Score: 92
Period size: 23 Copynumber: 3.7 Consensus size: 22
92450 TTGGTGCAGA
*
92460 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCTTGAAG
*
92482 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-TTGAAG
*
92505 GGGAACCGATTCCCCC-T--AG
1 GGGAACCGATACCCCCTTGAAG
*
92524 GGGAATCGATACCCC
1 GGGAACCGATACCCC
92539 ATTGGGGTTC
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
19 15 0.29
21 1 0.02
22 14 0.27
23 22 0.42
ACGTcount: A:0.24, C:0.32, G:0.27, T:0.18
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGAAG
Found at i:92502 original size:23 final size:23
Alignment explanation
Indices: 92460--92521 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
92450 TTGGTGCAGA
* *
92460 GGGAATCGATACCCCC-TTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
92482 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
92505 GGGAACCGATTCCCCCT
1 GGGAACCGATTCCCCCT
92522 AGGGGAATCG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
22 14 0.38
23 23 0.62
ACGTcount: A:0.23, C:0.32, G:0.26, T:0.19
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:92545 original size:19 final size:19
Alignment explanation
Indices: 92503--92545 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
92493 CCCCCTTTGA
* *
92503 AGGGGAACCGATTCCCCCT
1 AGGGGAACCGATACCCCAT
*
92522 AGGGGAATCGATACCCCAT
1 AGGGGAACCGATACCCCAT
*
92541 TGGGG
1 AGGGG
92546 TTCTGGTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.28, G:0.33, T:0.16
Consensus pattern (19 bp):
AGGGGAACCGATACCCCAT
Found at i:101073 original size:23 final size:23
Alignment explanation
Indices: 101047--101093 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
101037 CATTTTGCCC
101047 TTAATGAAACTTAATATTTACCT
1 TTAATGAAACTTAATATTTACCT
101070 TTAATGAAACTTAATATTTACCT
1 TTAATGAAACTTAATATTTACCT
101093 T
1 T
101094 AATACCAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.45
Consensus pattern (23 bp):
TTAATGAAACTTAATATTTACCT
Found at i:110385 original size:12 final size:12
Alignment explanation
Indices: 110356--110386 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
110346 CGGTTTTTTT
*
110356 ACCGGATAAAAA
1 ACCGGTTAAAAA
110368 ACCGGTTAAAAA
1 ACCGGTTAAAAA
110380 ACCGGTT
1 ACCGGTT
110387 TTTATCCGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.19, G:0.19, T:0.16
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:112713 original size:21 final size:21
Alignment explanation
Indices: 112689--112728 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
112679 TTTATTTTAT
112689 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
112710 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
112729 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:112776 original size:33 final size:33
Alignment explanation
Indices: 112723--112821 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
112713 TTTGTTTCAA
112723 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
112755 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
112788 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
112821 T
1 T
112822 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:112850 original size:13 final size:13
Alignment explanation
Indices: 112807--112861 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
112797 TTGGAAGTAT
112807 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
112820 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
112834 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
112847 TTAAGTATTTGAA
1 TTAAGTATTTCAA
112860 TT
1 TT
112862 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:113268 original size:15 final size:15
Alignment explanation
Indices: 113248--113294 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
113238 ATTAAAATCA
*
113248 GTTTTTTTATAACCG
1 GTTTTTTTAAAACCG
*
113263 GTTTTTTAAAAAAACCG
1 GTTTTTT--TAAAACCG
113280 GTTTTTTTAAAACCG
1 GTTTTTTTAAAACCG
113295 AAACCGGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 14 0.52
17 13 0.48
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.45
Consensus pattern (15 bp):
GTTTTTTTAAAACCG
Found at i:113303 original size:21 final size:18
Alignment explanation
Indices: 113258--113291 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
113248 GTTTTTTTAT
113258 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
113275 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
113292 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:113411 original size:15 final size:17
Alignment explanation
Indices: 113385--113416 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
113375 TTCTATGAGA
113385 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
113401 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
113417 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:125666 original size:27 final size:26
Alignment explanation
Indices: 125633--125699 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 26
125623 TACAAAACCG
*
125633 ATAAAAATATAATATTACA-AAATTATA
1 ATAAAAATATAATAATA-AGAAATTA-A
125660 ATAAAAATAT-ATAATAAGAAATTAA
1 ATAAAAATATAATAATAAGAAATTAA
*
125685 TTAAAAAATATAATA
1 AT-AAAAATATAATA
125700 GAGTTTGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
25 3 0.09
26 19 0.54
27 13 0.37
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (26 bp):
ATAAAAATATAATAATAAGAAATTAA
Found at i:125674 original size:13 final size:13
Alignment explanation
Indices: 125633--125699 Score: 61
Period size: 13 Copynumber: 5.2 Consensus size: 13
125623 TACAAAACCG
125633 ATAAAAATATAATA
1 ATAAAAATAT-ATA
*
125647 TTACAAAAT-TATA
1 ATA-AAAATATATA
125660 ATAAAAATATATA
1 ATAAAAATATATA
125673 ATAAGAAAT-TA-A
1 ATAA-AAATATATA
*
125685 TTAAAAA-ATATA
1 ATAAAAATATATA
125697 ATA
1 ATA
125700 GAGTTTGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
11 5 0.11
12 12 0.27
13 15 0.34
14 7 0.16
15 5 0.11
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (13 bp):
ATAAAAATATATA
Found at i:126192 original size:43 final size:42
Alignment explanation
Indices: 126101--126193 Score: 98
Period size: 43 Copynumber: 2.2 Consensus size: 42
126091 ATTAGGATGG
**
126101 AGATATATCCCTCCGTAGAAGATCCCAATAAAAAACAAGATGT
1 AGATAT-TCCCTCCGTAGAAGATCCCAATAAAAAACAAGACAT
* * * *
126144 GGATATTGCCCTCCGTAGAGGTTCCC-ATGCAAAAACAAGACAT
1 AGATATT-CCCTCCGTAGAAGATCCCAAT-AAAAAACAAGACAT
126187 AGATATT
1 AGATATT
126194 ACCTTTCATA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
42 3 0.07
43 38 0.93
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.23
Consensus pattern (42 bp):
AGATATTCCCTCCGTAGAAGATCCCAATAAAAAACAAGACAT
Found at i:133350 original size:15 final size:15
Alignment explanation
Indices: 133326--133355 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
133316 ATTAAGCTTC
133326 CTGTGATGCTATAAT
1 CTGTGATGCTATAAT
*
133341 CTGTGTTGCTATAAT
1 CTGTGATGCTATAAT
133356 GACTGACAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.13, G:0.20, T:0.43
Consensus pattern (15 bp):
CTGTGATGCTATAAT
Done.