Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000791.1 Hibiscus syriacus cultivar Beakdansim tig00001533_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: 68363
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:4218 original size:20 final size:21
Alignment explanation
Indices: 4167--4305 Score: 146
Period size: 20 Copynumber: 6.9 Consensus size: 21
4157 AATTCGCATA
4167 CGAA-TACGTAAATCGCAATG
1 CGAATTACGTAAATCGCAATG
*
4187 CGAATTAGGTAAATCGCAATG
1 CGAATTACGTAAATCGCAATG
*
4208 CG-ATTACGTAAATTGCAATG
1 CGAATTACGTAAATCGCAATG
* *
4228 TGAATTAGGTAAATCGCAATG
1 CGAATTACGTAAATCGCAATG
* * *
4249 CGAATTGCGT-ATTCGCATTG
1 CGAATTACGTAAATCGCAATG
* *
4269 CGATTTACGT-AATCGCATTG
1 CGAATTACGTAAATCGCAATG
*
4289 CGATTTA-GT-AATCGCAA
1 CGAATTACGTAAATCGCAA
4306 CGAGATTCTG
Statistics
Matches: 102, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
19 9 0.09
20 53 0.52
21 40 0.39
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.29
Consensus pattern (21 bp):
CGAATTACGTAAATCGCAATG
Found at i:4226 original size:41 final size:41
Alignment explanation
Indices: 4171--4293 Score: 144
Period size: 41 Copynumber: 3.0 Consensus size: 41
4161 CGCATACGAA
*
4171 TACGTAAATCGCAATGCGAATTAGGTAAATCGCAATGCGAT
1 TACGTAAATTGCAATGCGAATTAGGTAAATCGCAATGCGAT
*
4212 TACGTAAATTGCAATGTGAATTAGGTAAATCGCAATGCGAAT
1 TACGTAAATTGCAATGCGAATTAGGTAAATCGCAATGCG-AT
* * * * *
4254 TGCGT--ATTCGCATTGCGATTTACGT-AATCGCATTGCGAT
1 TACGTAAATT-GCAATGCGAATTAGGTAAATCGCAATGCGAT
4293 T
1 T
4294 TAGTAATCGC
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
39 3 0.04
40 14 0.19
41 49 0.68
42 6 0.08
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (41 bp):
TACGTAAATTGCAATGCGAATTAGGTAAATCGCAATGCGAT
Found at i:4301 original size:19 final size:20
Alignment explanation
Indices: 4117--4304 Score: 105
Period size: 21 Copynumber: 9.3 Consensus size: 20
4107 GATTCTGACT
* **
4117 ATCGCATTGCGATTTCCCAA
1 ATCGCATTGCGATTTACGTA
* * *
4137 ATTCGCGTTGCGATTTTCCTA
1 A-TCGCATTGCGATTTACGTA
* *
4158 ATTCGCA-TACGA-ATACGTAA
1 A-TCGCATTGCGATTTACGT-A
* * *
4178 ATCGCAATGCGAATTAGGTAA
1 ATCGCATTGCGATTTACGT-A
*
4199 ATCGCAATGCGA-TTACGTAA
1 ATCGCATTGCGATTTACGT-A
* * * * *
4219 ATTGCAATGTGAATTAGGTAA
1 ATCGCATTGCGATTTACGT-A
* * *
4240 ATCGCAATGCGAATTGCGTA
1 ATCGCATTGCGATTTACGTA
*
4260 TTCGCATTGCGATTTACGTA
1 ATCGCATTGCGATTTACGTA
4280 ATCGCATTGCGATTTA-GTA
1 ATCGCATTGCGATTTACGTA
4299 ATCGCA
1 ATCGCA
4305 ACGAGATTCT
Statistics
Matches: 139, Mismatches: 24, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
19 17 0.12
20 60 0.43
21 62 0.45
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (20 bp):
ATCGCATTGCGATTTACGTA
Found at i:4312 original size:19 final size:20
Alignment explanation
Indices: 4270--4312 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
4260 TTCGCATTGC
** *
4270 GATTTACGTAATCGCATTGC
1 GATTTACGTAATCGCAACGA
4290 GATTTA-GTAATCGCAACGA
1 GATTTACGTAATCGCAACGA
4309 GATT
1 GATT
4313 CTGACTATCG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (20 bp):
GATTTACGTAATCGCAACGA
Found at i:6491 original size:30 final size:30
Alignment explanation
Indices: 6455--6562 Score: 139
Period size: 30 Copynumber: 3.6 Consensus size: 30
6445 TACAAGAATG
6455 AAAATCGCAACGA-AATCGCAATGCGAAAT
1 AAAATCGCAACGAGAATCGCAATGCGAAAT
6484 AAAAATCGCAACGAGAGAATCGCAATGCG-AAT
1 -AAAATCGCAAC--GAGAATCGCAATGCGAAAT
* *
6516 GAAATCGCAACGAGAATCGCAAAGCGAAAT
1 AAAATCGCAACGAGAATCGCAATGCGAAAT
* *
6546 GAAATCGCAACGCGAAT
1 AAAATCGCAACGAGAAT
6563 TTAGTTTCGC
Statistics
Matches: 71, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
29 14 0.20
30 30 0.42
31 10 0.14
32 5 0.07
33 12 0.17
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.12
Consensus pattern (30 bp):
AAAATCGCAACGAGAATCGCAATGCGAAAT
Found at i:6506 original size:14 final size:16
Alignment explanation
Indices: 6486--6530 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
6476 TGCGAAATAA
6486 AAATCGCAACGAGA-G
1 AAATCGCAACGAGATG
6501 -AATCGCAATGCGA-ATG
1 AAATCGCAA--CGAGATG
6517 AAATCGCAACGAGA
1 AAATCGCAACGAGA
6531 ATCGCAAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
14 8 0.32
15 4 0.16
16 5 0.20
17 8 0.32
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (16 bp):
AAATCGCAACGAGATG
Found at i:6523 original size:17 final size:16
Alignment explanation
Indices: 6466--6562 Score: 64
Period size: 17 Copynumber: 6.0 Consensus size: 16
6456 AAATCGCAAC
6466 GAAATCGCAATGCGAAAT
1 GAAATCGCAA-GCG-AAT
*
6484 AAAAATCGCAA-CG-A-
1 -GAAATCGCAAGCGAAT
6498 GAGAATCGCAATGCGAAT
1 GA-AATCGCAA-GCGAAT
6516 GAAATCGCAA-CG-A-
1 GAAATCGCAAGCGAAT
6529 G-AATCGCAAAGCGAAAT
1 GAAATCGC-AAGCG-AAT
6546 GAAATCGCAACGCGAAT
1 GAAATCGCAA-GCGAAT
6563 TTAGTTTCGC
Statistics
Matches: 64, Mismatches: 2, Indels: 26
0.70 0.02 0.28
Matches are distributed among these distances:
12 6 0.09
13 4 0.06
14 11 0.17
15 3 0.05
16 3 0.05
17 17 0.27
18 11 0.17
19 9 0.14
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (16 bp):
GAAATCGCAAGCGAAT
Found at i:6767 original size:14 final size:14
Alignment explanation
Indices: 6734--6769 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
6724 CATCAATTAA
6734 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
6748 AC-AATCATCTTTT
1 ACAAATCAACTTTT
6761 ACAAATCAA
1 ACAAATCAA
6770 TTAACAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:8171 original size:21 final size:21
Alignment explanation
Indices: 8105--8171 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
8095 GTGAATCGGG
*
8105 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
8125 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
8147 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
8168 CTCT
1 CTCT
8172 CGATGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:8685 original size:20 final size:19
Alignment explanation
Indices: 8624--8717 Score: 107
Period size: 19 Copynumber: 4.8 Consensus size: 19
8614 TCTGGAACTT
*
8624 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
** *
8645 ACTATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAATG
*
8664 AAAATCGCAACGAGAGAATG
1 AAAATCGCAACGCGA-AATG
*
8684 AAAATCGCAACGCGAAACG
1 AAAATCGCAACGCGAAATG
8703 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
8718 TTATAGTTTC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
19 34 0.55
20 18 0.29
21 10 0.16
ACGTcount: A:0.47, C:0.20, G:0.21, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:8693 original size:39 final size:40
Alignment explanation
Indices: 8624--8714 Score: 121
Period size: 39 Copynumber: 2.3 Consensus size: 40
8614 TCTGGAACTT
* ** * *
8624 AAAATCGCAACGTGAAAAATGACTATCGCAATGCGAAATG
1 AAAATCGCAACGAGAAAAATGAAAATCGCAACGCGAAACG
*
8664 AAAATCGCAACGAG-AGAATGAAAATCGCAACGCGAAACG
1 AAAATCGCAACGAGAAAAATGAAAATCGCAACGCGAAACG
8703 AAAATCGCAACG
1 AAAATCGCAACG
8715 CGATTATAGT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
39 32 0.71
40 13 0.29
ACGTcount: A:0.47, C:0.20, G:0.21, T:0.12
Consensus pattern (40 bp):
AAAATCGCAACGAGAAAAATGAAAATCGCAACGCGAAACG
Found at i:8748 original size:20 final size:20
Alignment explanation
Indices: 8723--8760 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
8713 CGCGATTATA
*
8723 GTTTCGCGTTGCGATTTTTG
1 GTTTCGAGTTGCGATTTTTG
8743 GTTTCGAGTTGCGATTTT
1 GTTTCGAGTTGCGATTTT
8761 GCGTTGTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.13, G:0.29, T:0.50
Consensus pattern (20 bp):
GTTTCGAGTTGCGATTTTTG
Found at i:8824 original size:20 final size:20
Alignment explanation
Indices: 8769--8828 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
8759 TTGCGTTGTG
8769 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
* * *
8789 GTT-TCGCATT--GATTTTC
1 ATTCTCTCGTTGCGATTTTC
8806 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
8826 ATT
1 ATT
8829 TTAACCAAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
17 9 0.29
18 5 0.16
19 5 0.16
20 12 0.39
ACGTcount: A:0.12, C:0.22, G:0.15, T:0.52
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:9077 original size:90 final size:92
Alignment explanation
Indices: 8920--9174 Score: 453
Period size: 94 Copynumber: 2.8 Consensus size: 92
8910 ATGGATTGCA
* *
8920 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
8984 TTAGCAGAATTGGCAGC-A-AACAAAT
66 TTAGCAGAATTGGCAGCAACAACAAAT
9009 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
9074 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAA-C-AACAAAT
9103 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
9168 TTAGCAG
66 TTAGCAG
9175 TAAATTTACT
Statistics
Matches: 159, Mismatches: 2, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
89 4 0.03
90 75 0.47
91 1 0.01
94 79 0.50
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (92 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACAACAAAT
Found at i:10955 original size:14 final size:14
Alignment explanation
Indices: 10936--10992 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
10926 TTGAAATGAA
10936 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
10950 AATCGCAAAGCGAAATTAA
1 AATCGC-AA-CG--A-GAG
10969 AATCGCAACGAGAG
1 AATCGCAACGAGAG
10983 AATCGCAACG
1 AATCGCAACG
10993 CGAAATGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 17 0.50
15 3 0.09
16 2 0.06
17 2 0.06
18 3 0.09
19 7 0.21
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:10971 original size:33 final size:33
Alignment explanation
Indices: 10928--11009 Score: 146
Period size: 33 Copynumber: 2.5 Consensus size: 33
10918 TCTTTTGGTT
10928 GAAATGAAAATCGCAACGAGAGAATCGCAAAGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAAAGC
* *
10961 GAAATTAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAAAGC
10994 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
11010 TGCGATTTTG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.49, C:0.18, G:0.22, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAAAGC
Found at i:11007 original size:19 final size:18
Alignment explanation
Indices: 10928--11014 Score: 64
Period size: 19 Copynumber: 5.1 Consensus size: 18
10918 TCTTTTGGTT
10928 GAAATGAAAATCGCAA-C
1 GAAATGAAAATCGCAAGC
*
10945 G--A-GAGAATCGCAAAGC
1 GAAATGAAAATCGC-AAGC
*
10961 GAAATTAAAATCGCAA-C
1 GAAATGAAAATCGCAAGC
*
10978 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAA-GC
10994 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAA-GC
11013 GA
1 GA
11015 TTTTGGTTTC
Statistics
Matches: 53, Mismatches: 7, Indels: 18
0.68 0.09 0.23
Matches are distributed among these distances:
14 17 0.32
15 4 0.08
16 4 0.08
17 3 0.06
18 4 0.08
19 21 0.40
ACGTcount: A:0.47, C:0.18, G:0.23, T:0.11
Consensus pattern (18 bp):
GAAATGAAAATCGCAAGC
Found at i:11073 original size:20 final size:20
Alignment explanation
Indices: 11021--11098 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
11011 GCGATTTTGG
*
11021 TTTCGCGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTCAT
**
11041 TTCTC-TCGTTGCGATAGTCAT
1 TT-TCGT-GTTGCGATTTTCAT
11062 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTCAT
*
11082 TTTCATGTTGCGATTTT
1 TTTCGTGTTGCGATTTT
11099 AAGTTTAGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
20 32 0.65
21 17 0.35
ACGTcount: A:0.12, C:0.18, G:0.19, T:0.51
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTCAT
Found at i:11730 original size:21 final size:21
Alignment explanation
Indices: 11705--11760 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
11695 TGCGATACGT
*
11705 AAATCGTAATGCGAATTAGGA
1 AAATCGCAATGCGAATTAGGA
* * *
11726 AAATCGCAACGCGAATTTGGG
1 AAATCGCAATGCGAATTAGGA
11747 AAATCGCAATGCGA
1 AAATCGCAATGCGA
11761 TAGTCAGAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (21 bp):
AAATCGCAATGCGAATTAGGA
Found at i:16697 original size:17 final size:18
Alignment explanation
Indices: 16675--16710 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
16665 GTGCACTAAG
16675 AGTGCA-TCGATGTATCA
1 AGTGCATTCGATGTATCA
*
16692 AGTGCATTCGATGTTTCA
1 AGTGCATTCGATGTATCA
16710 A
1 A
16711 AATAGCCAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (18 bp):
AGTGCATTCGATGTATCA
Found at i:16726 original size:64 final size:62
Alignment explanation
Indices: 16656--16836 Score: 179
Period size: 65 Copynumber: 2.8 Consensus size: 62
16646 TTGGACCCTT
* * * *
16656 AGTGCATTGGTGCACTAAGAGTGCATCGATGTATCAAGTGCATTCGATGTTTCA-AAATAGCCAG
1 AGTGCATCGGTGCACT--GAGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-AGCCAC
** * *
16720 AGTGCATCAATGCATGGCTG-GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCT
1 AGTGCATCGGTGCA---CTGAGTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAGCCA
16784 C
62 C
16785 AGTGCATCGGTGCA-TGGTAGGTGCATCGATGCATCAAATGCATTCGATGTTT
1 AGTGCATCGGTGCACT-G-A-GTGCATCGATGCATCAAATGCATTCGATGTTT
16837 AATTTAATTC
Statistics
Matches: 98, Mismatches: 10, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
61 1 0.01
62 1 0.01
64 41 0.42
65 50 0.51
66 3 0.03
67 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (62 bp):
AGTGCATCGGTGCACTGAGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAAGCCAC
Found at i:16873 original size:65 final size:63
Alignment explanation
Indices: 16676--16885 Score: 226
Period size: 65 Copynumber: 3.3 Consensus size: 63
16666 TGCACTAAGA
* * * ** * *
16676 GTGCATCGATGTATCAAGTGCATTCGATGTTTCAAAAT-AGCCAGAGTGCATCAATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTT-AATATAATTCAG-GTGCATCGATGCATGGTTG
* * * *
16740 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCA-GTGCATCGGTGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTAATATAAT--TCAGGTGCATCGATGCATGGTT
16804 G
63 G
*
16805 GTGCATCGATGCATCAAATGCATTCGATGTTTAATTTAATTCATGGTGCATCGATGCATGGATTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTAATATAATTCA-GGTGCATCGATGCATGG-TTG
*
16870 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
16886 CTCTGAAAAA
Statistics
Matches: 122, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
62 3 0.02
64 52 0.43
65 65 0.53
67 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTAATATAATTCAGGTGCATCGATGCATGGTTG
Found at i:25468 original size:18 final size:17
Alignment explanation
Indices: 25414--25462 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 17
25404 TTGGACCCTT
*
25414 AGTGCATCGATGCACTAA
1 AGTGCATCGATGCA-TCA
25432 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
25450 AGTGCATTCGATG
1 AGTGCA-TCGATG
25463 TTTCAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 6 0.21
18 8 0.29
19 14 0.50
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:25521 original size:65 final size:64
Alignment explanation
Indices: 25437--25623 Score: 197
Period size: 65 Copynumber: 2.9 Consensus size: 64
25427 ACTAAGAGTG
*
25437 CATCGATGCATCAAGTGCATTCGATGTTTCAAAATATTCCAGAGTGCATCGATGCATG-ACTGGT
1 CATCGATGCATCAAATGCATTCGATGTTTCAAAATATTCCAGAGTGCATCGATGCATGTA-T-GT
25501 A
64 A
** *
25502 CATCGATGCATCAAATGCATTCGATGTTTTCATAAA-A-TCCTCAGTGCATCGGTGCATGGTATG
1 CATCGATGCATCAAATGCATTCGATG-TTTCA-AAATATTCCAGAGTGCATCGATGCAT-GTATG
*
25565 TT
63 TA
* **
25567 CATCGATGCATGAAATGCATTCGATG-TTCAATTTAATT-CATG-GTGCATCGATGCATG
1 CATCGATGCATCAAATGCATTCGATGTTTCAAAAT-ATTCCA-GAGTGCATCGATGCATG
25624 GATTGGTGCA
Statistics
Matches: 103, Mismatches: 11, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
62 1 0.01
63 5 0.05
64 15 0.15
65 70 0.68
66 8 0.08
67 4 0.04
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (64 bp):
CATCGATGCATCAAATGCATTCGATGTTTCAAAATATTCCAGAGTGCATCGATGCATGTATGTA
Found at i:25642 original size:65 final size:64
Alignment explanation
Indices: 25437--25644 Score: 189
Period size: 65 Copynumber: 3.2 Consensus size: 64
25427 ACTAAGAGTG
* *
25437 CATCGATGCATCAAGTGCATTCGATGTTTCA-AAATAT-TCCAGAGTGCATCGATGCAT-GACTG
1 CATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCT-C--AGTGCATCGATGCATGGATTG
25499 GTA
62 GTA
*
25502 CATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGG-TAT-G
1 CATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGAT-TGG
*
25565 TT
63 TA
* **
25567 CATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGATTGG
1 CATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGGATTGG
*
25630 TG
63 TA
25632 CATC-AGTGCATCA
1 CATCGA-TGCATCA
25645 CTCTGAAAAA
Statistics
Matches: 121, Mismatches: 10, Indels: 24
0.78 0.06 0.15
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 22 0.18
65 79 0.65
66 9 0.07
67 4 0.03
68 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (64 bp):
CATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGATTGGTA
Found at i:38637 original size:23 final size:23
Alignment explanation
Indices: 38607--38651 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
38597 TATTCAAAGG
38607 GTAAATTACACTCTTACTCACTA
1 GTAAATTACACTCTTACTCACTA
*
38630 GTAAATTATACTCTTACTCACT
1 GTAAATTACACTCTTACTCACT
38652 GAACTTTAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.38
Consensus pattern (23 bp):
GTAAATTACACTCTTACTCACTA
Found at i:40282 original size:16 final size:16
Alignment explanation
Indices: 40261--40341 Score: 65
Period size: 16 Copynumber: 4.9 Consensus size: 16
40251 TTAACTGTAT
40261 ATAATAAATAAATATA
1 ATAATAAATAAATATA
*
40277 ATAAT-AATAATTAATA
1 ATAATAAATAAAT-ATA
* * *
40293 TTAATTATTAAATATA
1 ATAATAAATAAATATA
*
40309 ATAAATAATTAAAATATA
1 AT-AATAAAT-AAATATA
* *
40327 ATGATATATAAATAT
1 ATAATAAATAAATAT
40342 TGTAATTAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
15 6 0.12
16 22 0.42
17 15 0.29
18 9 0.17
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (16 bp):
ATAATAAATAAATATA
Found at i:44159 original size:21 final size:20
Alignment explanation
Indices: 44073--44230 Score: 88
Period size: 21 Copynumber: 7.8 Consensus size: 20
44063 AAATGACCAA
**
44073 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
44092 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
44112 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
44132 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
44153 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
44174 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
*
44194 CCAAAATCGCAACGCGAATATT
1 -CAAAATCGCAACGCG-ATTTT
44216 -AAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
44231 ACACATAAAT
Statistics
Matches: 105, Mismatches: 27, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
19 17 0.16
20 40 0.38
21 44 0.42
22 4 0.04
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:44221 original size:20 final size:20
Alignment explanation
Indices: 44133--44249 Score: 78
Period size: 20 Copynumber: 5.7 Consensus size: 20
44123 ATCAGTTTCC
* *
44133 AAAATCGCAACGCGATTCTT
1 AAAATCGCAACGCGAATATT
* *
44153 GAAAATCGCAATGCG-ATAGT
1 -AAAATCGCAACGCGAATATT
** *
44173 ACAAATTCGCATTGCG-ATTTT
1 A-AAA-TCGCAACGCGAATATT
44194 CCAAAATCGCAACGCGAATATT
1 --AAAATCGCAACGCGAATATT
* *
44216 AAAATCGCAACGCGAACA-C
1 AAAATCGCAACGCGAATATT
44235 ATAAATCGCAACGCG
1 A-AAATCGCAACGCG
44250 TATCCGTAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 13
0.76 0.12 0.13
Matches are distributed among these distances:
19 2 0.03
20 35 0.45
21 33 0.42
22 7 0.09
23 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGAATATT
Found at i:44259 original size:20 final size:20
Alignment explanation
Indices: 44217--44426 Score: 228
Period size: 20 Copynumber: 10.5 Consensus size: 20
44207 GCGAATATTA
* *
44217 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
44237 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
44257 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
44277 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
44297 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
44317 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
44337 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
44357 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
44377 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
44397 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
44417 AAATCACAAC
1 AAATCGCAAC
44427 ACTGAAATTT
Statistics
Matches: 162, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
19 1 0.01
20 159 0.98
21 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:45148 original size:24 final size:24
Alignment explanation
Indices: 45109--45155 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
45099 AAATTTGGTC
45109 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
45133 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
45156 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:45347 original size:12 final size:12
Alignment explanation
Indices: 45330--45354 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45320 ATATAATCCT
45330 GAAGAAGAAAAA
1 GAAGAAGAAAAA
45342 GAAGAAGAAAAA
1 GAAGAAGAAAAA
45354 G
1 G
45355 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:47699 original size:34 final size:33
Alignment explanation
Indices: 47631--47771 Score: 239
Period size: 33 Copynumber: 4.2 Consensus size: 33
47621 CGGAAATTAC
47631 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
* *
47664 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGA-GAGAATCGCAATGC-GAAATGAA
47698 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
47731 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
47764 AATCGCAA
1 AATCGCAA
47772 TGCGAAATGA
Statistics
Matches: 101, Mismatches: 4, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
32 1 0.01
33 70 0.69
34 29 0.29
35 1 0.01
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (33 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:47720 original size:67 final size:67
Alignment explanation
Indices: 47612--47771 Score: 243
Period size: 67 Copynumber: 2.4 Consensus size: 67
47602 GCATTTGACT
** * *
47612 ATCGCAACACGGAAATTACAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAAC-ATG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACGA-G
47676 AAA
65 AAA
*
47679 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACGAGA
*
47744 GA
66 AA
47746 ATCGCAATGC-GAAATGAAAATCGCAA
1 ATCGCAATGCGGAAATGAAAATCGCAA
47772 TGCGAAATGA
Statistics
Matches: 86, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
66 16 0.19
67 69 0.80
68 1 0.01
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.13
Consensus pattern (67 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACGAGA
AA
Found at i:47776 original size:52 final size:52
Alignment explanation
Indices: 47631--47823 Score: 242
Period size: 52 Copynumber: 3.8 Consensus size: 52
47621 CGGAAATTAC
*
47631 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* * *
47678 AATCGCAATGCG-GA-AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAA--CGAGAGAATCG-CAATGCGAAATGA-A-AATCGCAATGCGAAATGAA
47731 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
47783 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAA
47824 CGAGAGAATC
Statistics
Matches: 125, Mismatches: 7, Indels: 23
0.81 0.05 0.15
Matches are distributed among these distances:
46 7 0.06
47 15 0.12
48 9 0.07
49 2 0.02
50 1 0.01
51 2 0.02
52 62 0.50
53 20 0.16
54 7 0.06
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:47799 original size:85 final size:86
Alignment explanation
Indices: 47673--47845 Score: 339
Period size: 85 Copynumber: 2.0 Consensus size: 86
47663 AAATCCCAAC
47673 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
47738 ACGAGAGAATCGCAATGCGAA
66 ACGAGAGAATCGCAATGCGAA
47759 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
47823 ACGAGAGAATCGCAATGCGAA
66 ACGAGAGAATCGCAATGCGAA
47844 AT
1 AT
47846 TATAAACGCA
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
85 71 0.82
86 16 0.18
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (86 bp):
ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
ACGAGAGAATCGCAATGCGAA
Found at i:47801 original size:33 final size:33
Alignment explanation
Indices: 47764--47845 Score: 164
Period size: 33 Copynumber: 2.5 Consensus size: 33
47754 GCGAAATGAA
47764 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
47797 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
47830 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
47846 TATAAACGCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:47909 original size:52 final size:52
Alignment explanation
Indices: 47852--47966 Score: 214
Period size: 52 Copynumber: 2.2 Consensus size: 52
47842 AAATTATAAA
47852 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCA-TT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATTT
47904 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT
47956 CGCATTGCGAT
1 CGCATTGCGAT
47967 AGTCATTTTT
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
51 16 0.26
52 46 0.74
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (52 bp):
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT
Found at i:47974 original size:19 final size:19
Alignment explanation
Indices: 47870--47966 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
47860 GATTCTCTCG
47870 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
47890 TTGCGATTTTCA-TTCGCA
1 TTGCGATTTTCATTTCGCA
*
47908 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
47922 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
47941 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
47960 TTGCGAT
1 TTGCGAT
47967 AGTCATTTTT
Statistics
Matches: 69, Mismatches: 2, Indels: 13
0.82 0.02 0.15
Matches are distributed among these distances:
14 6 0.09
16 9 0.13
17 4 0.06
18 10 0.14
19 28 0.41
20 12 0.17
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:48091 original size:14 final size:14
Alignment explanation
Indices: 48072--48108 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
48062 CATCAATTAC
48072 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
48086 ACAAATCATCTTTT
1 ACAAATCAACTTTT
48100 ACAAATCAA
1 ACAAATCAA
48109 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:50115 original size:33 final size:33
Alignment explanation
Indices: 50064--50156 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
50054 GCGAAACCAA
*
50064 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
* *
50097 AATTGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
50130 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
50157 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:50135 original size:14 final size:14
Alignment explanation
Indices: 50083--50139 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
50073 GCGAAATGAA
*
50083 AATCGCAACGACAG
1 AATCGCAACGAAAG
*
50097 AATTGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
50114 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
50130 AATCGCAACG
1 AATCGCAACG
50140 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 17 0.49
16 5 0.14
17 6 0.17
19 7 0.20
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:50154 original size:19 final size:19
Alignment explanation
Indices: 50027--50161 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
50017 TAGTTTACTT
* *
50027 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
50047 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
50066 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
50085 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
* *
50099 TTGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
50118 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
50132 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
50151 TCGCAATGCGA
1 TCGCAACGCGA
50162 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:50173 original size:19 final size:19
Alignment explanation
Indices: 50157--50271 Score: 132
Period size: 19 Copynumber: 6.3 Consensus size: 19
50147 AAAATCGCAA
50157 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
50176 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
*
50190 TACGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
**
50209 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
50228 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
50247 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
50267 TGCGA
1 TGCGA
50272 AAGTAAACTA
Statistics
Matches: 80, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 53 0.66
20 13 0.16
ACGTcount: A:0.10, C:0.17, G:0.28, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:50478 original size:93 final size:93
Alignment explanation
Indices: 50319--50602 Score: 550
Period size: 93 Copynumber: 3.1 Consensus size: 93
50309 ATGGATTGCA
50319 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
50384 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
50412 TTACTTTCAACCAAAAGACAAAACAAAGACAAATCCTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
50477 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
50505 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
50570 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
50598 TTACT
1 TTACT
50603 AAGCAATCTA
Statistics
Matches: 188, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 188 1.00
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:52340 original size:19 final size:19
Alignment explanation
Indices: 52316--52399 Score: 106
Period size: 19 Copynumber: 4.7 Consensus size: 19
52306 GCAACGAGAG
*
52316 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
52335 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
52354 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
52368 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
52387 AATCGCAATGCGA
1 AATCGCAACGCGA
52400 TTTTGGTTTC
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 40 0.71
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:52412 original size:52 final size:52
Alignment explanation
Indices: 52294--52399 Score: 194
Period size: 52 Copynumber: 2.0 Consensus size: 52
52284 TCTTTTGGTT
*
52294 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGACAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
*
52346 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
52398 GA
1 GA
52400 TTTTGGTTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (52 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:52432 original size:14 final size:14
Alignment explanation
Indices: 52413--52467 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
52403 TGGTTTCGCA
52413 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
52427 TTGCGATTTTCATTTCGCG
1 TTGCGA--TTC---TCTCG
52446 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
52460 TTGCGATT
1 TTGCGATT
52468 TTCATTTCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:52443 original size:33 final size:33
Alignment explanation
Indices: 52395--52475 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
52385 AAAATCGCAA
**
52395 TGCGATTTTGGTTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
52428 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
52461 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
52476 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.10, C:0.22, G:0.21, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:52478 original size:21 final size:21
Alignment explanation
Indices: 52452--52527 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
52442 CGCGTTGCGA
52452 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
52473 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
52493 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
52514 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
52528 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:52508 original size:41 final size:41
Alignment explanation
Indices: 52451--52528 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
52441 TCGCGTTGCG
*
52451 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
52492 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
52529 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:52648 original size:33 final size:33
Alignment explanation
Indices: 52606--52676 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
52596 AATACTAACT
*
52606 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
52639 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
52672 TGAAA
1 TGAAA
52677 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:52911 original size:22 final size:22
Alignment explanation
Indices: 52859--52913 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
52849 TGGTTGTGAG
**
52859 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
52881 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
52903 GGATTTCTTCG
1 GGATTTCTTCG
52914 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:53085 original size:20 final size:20
Alignment explanation
Indices: 53060--53253 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
53050 CTTTAAATAT
53060 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
53080 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
53102 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
53121 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
53141 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
53161 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
53181 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
53201 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
53221 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
53241 CGCGTTGCGATTT
1 CGCGTTGCGATTT
53254 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:53247 original size:60 final size:60
Alignment explanation
Indices: 53060--53253 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
53050 CTTTAAATAT
**
53060 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
53121 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
53181 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
53241 CGCGTTGCGATTT
1 CGCGTTGCGATTT
53254 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:53270 original size:21 final size:21
Alignment explanation
Indices: 53240--53323 Score: 71
Period size: 21 Copynumber: 4.0 Consensus size: 21
53230 ATTTTCATAT
*
53240 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
53261 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
53282 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
53303 TCGCGTTGCGATTTTTGGAAA
1 TCGCATTGCGA-TTTTGGAAA
53324 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
20 1 0.02
21 39 0.83
22 5 0.11
23 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:53313 original size:42 final size:42
Alignment explanation
Indices: 53220--53318 Score: 98
Period size: 42 Copynumber: 2.4 Consensus size: 42
53210 ATTTATGTGT
* *
53220 TCGCGTTGCG-ATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTTCATATTCGCATTGCGATTTTGCAAAA
**
53261 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTT-TCA-TATTCGCATTGCGATTTTGCAA-AA
*
53303 TCGCGTTGCGATTTTT
1 TCGCGTTGCGAATTTT
53319 GGAAACTGAT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
41 11 0.23
42 33 0.70
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.38
Consensus pattern (42 bp):
TCGCGTTGCGAATTTTCATATTCGCATTGCGATTTTGCAAAA
Found at i:57858 original size:23 final size:23
Alignment explanation
Indices: 57827--57877 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
57817 ACCTATGAAT
*
57827 TTTAATTTTAATTCAATTTAATC
1 TTTATTTTTAATTCAATTTAATC
* ** *
57850 TTTATTTTTTATTTTATTTAATT
1 TTTATTTTTAATTCAATTTAATC
57873 TTTAT
1 TTTAT
57878 GATTTGGTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTATTTTTAATTCAATTTAATC
Found at i:61718 original size:2 final size:2
Alignment explanation
Indices: 61711--61787 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
61701 CTTAAACAAA
61711 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
61753 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
61788 CCTACCTAGC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.