Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007383.1 Hibiscus syriacus cultivar Beakdansim tig00019839_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: 57431
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:518 original size:55 final size:56
Alignment explanation
Indices: 452--562 Score: 215
Period size: 55 Copynumber: 2.0 Consensus size: 56
442 TGCACTGTTT
452 CGTCATGGTTCCCTCAATCTTTTTCTATTTATTTGGAAG-ACATAGCCTCTTCGAC
1 CGTCATGGTTCCCTCAATCTTTTTCTATTTATTTGGAAGAACATAGCCTCTTCGAC
507 CGTCATGGTTCCCTCAATCTTTTTCTATTTATTTGGAAGAACATAGCCTCTTCGAC
1 CGTCATGGTTCCCTCAATCTTTTTCTATTTATTTGGAAGAACATAGCCTCTTCGAC
563 TGCAATAATC
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 39 0.71
56 16 0.29
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.40
Consensus pattern (56 bp):
CGTCATGGTTCCCTCAATCTTTTTCTATTTATTTGGAAGAACATAGCCTCTTCGAC
Found at i:1064 original size:21 final size:21
Alignment explanation
Indices: 1021--1065 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1011 TATCGCATTA
**
1021 CGATTTTCCAAATTCGCGTTG
1 CGATTTTCCAAATTCGCAATG
*
1042 CGATTTTCCTAATTCGCAATG
1 CGATTTTCCAAATTCGCAATG
1063 CGA
1 CGA
1066 ATACGTAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (21 bp):
CGATTTTCCAAATTCGCAATG
Found at i:1080 original size:20 final size:20
Alignment explanation
Indices: 1055--1161 Score: 117
Period size: 20 Copynumber: 5.3 Consensus size: 20
1045 TTTTCCTAAT
1055 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
1075 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
1096 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1116 TCGCAATGCGAATACGTGAA
1 TCGCAATGCGAATACGTAAA
* *
1136 TCACAACGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
1156 TCGCAA
1 TCGCAA
1162 CACGAATCTA
Statistics
Matches: 70, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
19 1 0.01
20 54 0.77
21 15 0.21
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1205 original size:20 final size:21
Alignment explanation
Indices: 1155--1217 Score: 80
Period size: 20 Copynumber: 3.1 Consensus size: 21
1145 GAATCTGTAA
1155 ATCGCAACACGA-A-TCT-ACT
1 ATCGCAA-ACGAGATTCTGACT
1174 ATCGCAAACGAGATTCTGACT
1 ATCGCAAACGAGATTCTGACT
*
1195 ATCGC-AACGAGATTGTGACT
1 ATCGCAAACGAGATTCTGACT
1215 ATC
1 ATC
1218 AATACTGAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
18 4 0.10
19 8 0.20
20 20 0.50
21 8 0.20
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.24
Consensus pattern (21 bp):
ATCGCAAACGAGATTCTGACT
Found at i:2085 original size:24 final size:24
Alignment explanation
Indices: 2053--2106 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2043 GTATTCAAAA
2053 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
2077 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2101 TTTGAT
1 TTTGAT
2107 GATTTTCAGA
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:4526 original size:20 final size:20
Alignment explanation
Indices: 4470--4577 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
4460 AACATTCATT
4470 TGACTATCGCAACGCGG-AA
1 TGACTATCGCAACGCGGAAA
4489 --A-T-T-GCAACGC-GAATA
1 TGACTATCGCAACGCGGAA-A
*
4504 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
*
4524 TGACTATCGCAACGCGGAAT
1 TGACTATCGCAACGCGGAAA
*
4544 TGACTATCGCAACGCGGGAA
1 TGACTATCGCAACGCGGAAA
*
4564 TGACTATTGCAACG
1 TGACTATCGCAACG
4578 AGAGAATCGT
Statistics
Matches: 75, Mismatches: 6, Indels: 15
0.78 0.06 0.16
Matches are distributed among these distances:
13 1 0.01
14 8 0.11
15 2 0.03
16 1 0.01
17 2 0.03
18 1 0.01
19 1 0.01
20 56 0.75
21 3 0.04
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.19
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:4609 original size:33 final size:34
Alignment explanation
Indices: 4572--4644 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 34
4562 AATGACTATT
* *
4572 GCAACGAGAGAATCGTAATGC-AAAATGAAAATC
1 GCAACGAGAGAATCGCAATACGAAAATGAAAATC
*
4605 GCAACGAGTGAATCGCAATACGAAAATGAAAATC
1 GCAACGAGAGAATCGCAATACGAAAATGAAAATC
4639 GCAACG
1 GCAACG
4645 CGAATTTAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
33 18 0.50
34 18 0.50
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (34 bp):
GCAACGAGAGAATCGCAATACGAAAATGAAAATC
Found at i:4720 original size:32 final size:33
Alignment explanation
Indices: 4665--4729 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
4655 TTCGCGTTAC
4665 GATTTTCATTTTCGCATTACGATTCTCTCGTTGT
1 GATTTTCA-TTTCGCATTACGATTCTCTCGTTGT
*
4699 GATTTTCA-TTCGCATTGCGATTCTCTCGTTG
1 GATTTTCATTTCGCATTACGATTCTCTCGTTG
4730 CGATAGTCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 22 0.73
34 8 0.27
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.48
Consensus pattern (33 bp):
GATTTTCATTTCGCATTACGATTCTCTCGTTGT
Found at i:4740 original size:32 final size:32
Alignment explanation
Indices: 4675--4740 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
4665 GATTTTCATT
* **
4675 TTCGCATTACGATTCTCTCGTTGTGATTTTCA
1 TTCGCATTACGATTCTCTCGTTGCGATAGTCA
*
4707 TTCGCATTGCGATTCTCTCGTTGCGATAGTCA
1 TTCGCATTACGATTCTCTCGTTGCGATAGTCA
4739 TT
1 TT
4741 TCCGCGTTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (32 bp):
TTCGCATTACGATTCTCTCGTTGCGATAGTCA
Found at i:4876 original size:14 final size:14
Alignment explanation
Indices: 4857--4893 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
4847 ACATCAATTA
4857 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
4871 ACAAATCATCTTTT
1 ACAAATCAACATTT
4885 ACAAATCAA
1 ACAAATCAA
4894 TTAAACATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:6935 original size:20 final size:20
Alignment explanation
Indices: 6847--6933 Score: 147
Period size: 20 Copynumber: 4.3 Consensus size: 20
6837 GAAACTTAAA
6847 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
6867 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
6887 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
6907 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
6927 ATCGCAA
1 ATCGCAA
6934 TGAGAGAATT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:6983 original size:20 final size:20
Alignment explanation
Indices: 6958--7102 Score: 93
Period size: 20 Copynumber: 7.9 Consensus size: 20
6948 TGCGATTTTC
6958 ATTTCGCATTGCGATAGTCA
1 ATTTCGCATTGCGATAGTCA
6978 ATTTCGCATTGCGATAGTCA
1 ATTTCGCATTGCGATAGTCA
* *
6998 TTTTCGCGTTGCGAT--T--
1 ATTTCGCATTGCGATAGTCA
* * **
7014 -TTGTTG--TTACGATTTTC-
1 ATT-TCGCATTGCGATAGTCA
7031 ATTTCGCATTGCGAT--TC-
1 ATTTCGCATTGCGATAGTCA
*
7048 -TCTCG--TTGCGATAGTCA
1 ATTTCGCATTGCGATAGTCA
* *
7065 TTTTCGCGTTGCGATAGTCA
1 ATTTCGCATTGCGATAGTCA
*
7085 TTTTCGCATTGCGATAGT
1 ATTTCGCATTGCGATAGT
7103 AAACTATTCT
Statistics
Matches: 103, Mismatches: 9, Indels: 26
0.75 0.07 0.19
Matches are distributed among these distances:
14 13 0.13
15 2 0.02
16 9 0.09
17 4 0.04
18 7 0.07
19 6 0.06
20 62 0.60
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.42
Consensus pattern (20 bp):
ATTTCGCATTGCGATAGTCA
Found at i:7066 original size:33 final size:34
Alignment explanation
Indices: 6986--7079 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 34
6976 CAATTTCGCA
* * *
6986 TTGCGATAGTCATTTTCGCGTTGCGATTTTGTTG
1 TTGCGATAGTCATTTTCGCGTTGCGATTCTCTCG
* ** *
7020 TTACGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTTCGCGTTGCGATTCTCTCG
7053 TTGCGATAGTCATTTTCGCGTTGCGAT
1 TTGCGATAGTCATTTTCGCGTTGCGAT
7080 AGTCATTTTC
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
33 26 0.54
34 22 0.46
ACGTcount: A:0.14, C:0.19, G:0.22, T:0.45
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCGTTGCGATTCTCTCG
Found at i:8993 original size:20 final size:20
Alignment explanation
Indices: 8968--9018 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
8958 TCTGAAACTT
8968 AAAATCGCAACACAAAAATG
1 AAAATCGCAACACAAAAATG
*
8988 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACAAAAATG
**
9008 ACTATCGCAAC
1 AAAATCGCAAC
9019 GAGAATTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.53, C:0.24, G:0.12, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACAAAAATG
Found at i:9451 original size:22 final size:22
Alignment explanation
Indices: 9389--9454 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
9379 TGACCGTGAA
* *
9389 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
* *
9411 TAATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
*
9433 TGATTTTGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
9455 GGATGTCGCC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.23, C:0.14, G:0.38, T:0.26
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:9673 original size:20 final size:20
Alignment explanation
Indices: 9650--9723 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
9640 CGATAGTCAG
*
9650 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* **
9670 ATTCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
9691 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
9711 ATTCGCATTGCGA
1 ATTCGCATTGCGA
9724 ATTAGGAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:9696 original size:21 final size:20
Alignment explanation
Indices: 9632--9723 Score: 78
Period size: 20 Copynumber: 4.5 Consensus size: 20
9622 GCTATGTAAA
* *
9632 TCGCATTGCGATAGT-CAGAT
1 TCGCATTGCGAT-TTACAAAT
* **
9652 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACAAAT
*
9672 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACAAAT
* **
9693 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACAAAT
9713 TCGCATTGCGA
1 TCGCATTGCGA
9724 ATTAGGAAAA
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
19 1 0.02
20 40 0.70
21 16 0.28
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACAAAT
Found at i:9702 original size:41 final size:40
Alignment explanation
Indices: 9632--9723 Score: 148
Period size: 41 Copynumber: 2.3 Consensus size: 40
9622 GCTATGTAAA
*
9632 TCGCATTGCGATAGTCAGATTCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATAGTCAAATTCGCGTTGCGATTTACGTAT
**
9672 TCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATAGT-CAAATTCGCGTTGCGATTTACGTAT
9713 TCGCATTGCGA
1 TCGCATTGCGA
9724 ATTAGGAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
40 13 0.27
41 35 0.73
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.36
Consensus pattern (40 bp):
TCGCATTGCGATAGTCAAATTCGCGTTGCGATTTACGTAT
Found at i:9744 original size:41 final size:41
Alignment explanation
Indices: 9658--9745 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 41
9648 AGATTCGCGT
* * * **
9658 TGCGATTTACGTATTCGCATTGCGATTTTCCAAATTCGCGT
1 TGCGATTTACGTATTCGCATTGCGAATTACCAAAATCGCAA
**
9699 TGCGATTTACGTATTCGCATTGCGAATTAGGAAAATCGCAA
1 TGCGATTTACGTATTCGCATTGCGAATTACCAAAATCGCAA
9740 TGCGAT
1 TGCGAT
9746 AGTCAGAATC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (41 bp):
TGCGATTTACGTATTCGCATTGCGAATTACCAAAATCGCAA
Found at i:10122 original size:32 final size:32
Alignment explanation
Indices: 10086--10147 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
10076 AGAAGTGGTG
*
10086 TTTAGGGTGTAGGTGGTGTTAACAAGGAGGGA
1 TTTAGAGTGTAGGTGGTGTTAACAAGGAGGGA
*
10118 TTTAGAGTGTAGGTGGTGTTAACGAGGAGG
1 TTTAGAGTGTAGGTGGTGTTAACAAGGAGG
10148 AAAACACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.24, C:0.03, G:0.44, T:0.29
Consensus pattern (32 bp):
TTTAGAGTGTAGGTGGTGTTAACAAGGAGGGA
Found at i:15520 original size:27 final size:28
Alignment explanation
Indices: 15452--15527 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 28
15442 ATAGATGGGT
* *
15452 TAAATTGGATTTTTTTAAAGTTCGAGGGC
1 TAAATT-GATTTTTTAAAAGTTCAAGGGC
*
15481 TAAATTGATTTTTTAAAAGTTCAAGGGG
1 TAAATTGATTTTTTAAAAGTTCAAGGGC
* *
15509 TTATTTGATTTTTATAAAA
1 TAAATTGATTTTT-TAAAA
15528 AATAAATTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
28 30 0.73
29 11 0.27
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.45
Consensus pattern (28 bp):
TAAATTGATTTTTTAAAAGTTCAAGGGC
Found at i:17084 original size:19 final size:20
Alignment explanation
Indices: 17035--17084 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
17025 TTATGCCAGT
*
17035 AGTATCGATACTGACCCTTG
1 AGTATCGATACTCACCCTTG
* *
17055 GGTATCAATACTCACCC-TG
1 AGTATCGATACTCACCCTTG
17074 AGTATCGATAC
1 AGTATCGATAC
17085 CAAAAATAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (20 bp):
AGTATCGATACTCACCCTTG
Found at i:20045 original size:136 final size:136
Alignment explanation
Indices: 19782--20064 Score: 444
Period size: 136 Copynumber: 2.1 Consensus size: 136
19772 GTCATAGGTG
19782 CATTTCGACATAATTTGTATATAAAAGTTATCGATCGATTTTGTTTAATGCATAATAGTGCATTT
1 CATTTCGACATAATTTG-ATATAAAAGTTATCGATCGATTTTGTTTAATGCATAATAGTGCATTT
* * *
19847 TCGTATCAGTACTATGTGTACTTTCGACACTAAATGTGCAATCATGGTATTCATAATGAGTTTGT
65 CCGTATCAGTACTATATGTACTTTCGACACTAAATGTGCAATCATGGAATTCATAATGAGTTTGT
19912 AAATTAC
130 AAATTAC
* *
19919 CATTTCGATATAATTATG-TATAAAAGTTATCGATCGATTTTGTTTAATGCATAATGGTGCATTT
1 CATTTCGACATAATT-TGATATAAAAGTTATCGATCGATTTTGTTTAATGCATAATAGTGCATTT
**
19983 CCGTATCAGTACTATATGTACTTTCGACACTATGTGTGC-ATCCATGGAATTCATAATGAGTTTG
65 CCGTATCAGTACTATATGTACTTTCGACACTAAATGTGCAAT-CATGGAATTCATAATGAGTTTG
* *
20047 TGAATTTC
129 TAAATTAC
20055 CATTTCGACA
1 CATTTCGACA
20065 CTTCTGTGTA
Statistics
Matches: 134, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
135 2 0.01
136 116 0.87
137 14 0.10
138 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (136 bp):
CATTTCGACATAATTTGATATAAAAGTTATCGATCGATTTTGTTTAATGCATAATAGTGCATTTC
CGTATCAGTACTATATGTACTTTCGACACTAAATGTGCAATCATGGAATTCATAATGAGTTTGTA
AATTAC
Found at i:26307 original size:17 final size:18
Alignment explanation
Indices: 26285--26324 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
26275 GGTACCATAG
26285 TATAGAA-GTATCGATAC
1 TATAGAAGGTATCGATAC
26302 TATAGAATGGGTATCGATAC
1 TATAGAA--GGTATCGATAC
26322 TAT
1 TAT
26325 TAAGACTGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
20 13 0.65
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.33
Consensus pattern (18 bp):
TATAGAAGGTATCGATAC
Found at i:27077 original size:138 final size:138
Alignment explanation
Indices: 26820--27070 Score: 405
Period size: 138 Copynumber: 1.8 Consensus size: 138
26810 ATTTGTATAC
*
26820 AAAAGTTATTGATTGATTTTGTTTAATGCATAATGGTGCATTTTCGTATCAGTACTATATGTACT
1 AAAAGTTATCGATTGATTTTGTTTAATGCATAATGGTGCATTTTCGTATCAGTACTATATGTACT
* * *
26885 TTCGACACTAAATGTGAAATCATAGTATTCATAATGCGTTTGTGAATTACCATTTTGATATACAA
66 TTCGACAATAAATGTGAAATCATAGAATTCATAATGAGTTTGTGAATTACCATTTTGATATACAA
26950 TTATGTAT
131 TTATGTAT
26958 AAAAGTTATCGATTGATTTTGTTTAATGCATAATGGTGCATTTTCGTATCAGTACTATATGTACT
1 AAAAGTTATCGATTGATTTTGTTTAATGCATAATGGTGCATTTTCGTATCAGTACTATATGTACT
* ** * *
27023 TTCGGCAATATGTGTG-CATCCATGGAATTCATAATGAGTTTGTGAATT
66 TTCGACAATAAATGTGAAAT-CATAGAATTCATAATGAGTTTGTGAATT
27071 TTCATTTCGG
Statistics
Matches: 103, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
137 2 0.02
138 101 0.98
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.41
Consensus pattern (138 bp):
AAAAGTTATCGATTGATTTTGTTTAATGCATAATGGTGCATTTTCGTATCAGTACTATATGTACT
TTCGACAATAAATGTGAAATCATAGAATTCATAATGAGTTTGTGAATTACCATTTTGATATACAA
TTATGTAT
Found at i:32415 original size:12 final size:12
Alignment explanation
Indices: 32398--32422 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32388 ATGATTTCTA
32398 TGAAGAAAGAAG
1 TGAAGAAAGAAG
32410 TGAAGAAAGAAG
1 TGAAGAAAGAAG
32422 T
1 T
32423 AGTATGGTAT
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:0.56, C:0.00, G:0.32, T:0.12
Consensus pattern (12 bp):
TGAAGAAAGAAG
Found at i:37069 original size:21 final size:21
Alignment explanation
Indices: 37045--37092 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
37035 TCCTACAGGC
*
37045 AGCCAAATACCTAGAATGGGT
1 AGCCAAATACCCAGAATGGGT
37066 AGCCAAATACCCAGAATGGGT
1 AGCCAAATACCCAGAATGGGT
37087 AGCCAA
1 AGCCAA
37093 CATAGTTCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.15
Consensus pattern (21 bp):
AGCCAAATACCCAGAATGGGT
Found at i:40376 original size:22 final size:21
Alignment explanation
Indices: 40345--40397 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 21
40335 TTATTCCAAG
40345 TTTA-TCTTTTTGAAATTCAA
1 TTTATTCTTTTTGAAATTCAA
40365 TTTATTCATTTTTGAAATTCAA
1 TTTATTC-TTTTTGAAATTCAA
40387 TTTATTCTTTT
1 TTTATTCTTTT
40398 ATATAAACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.13
21 6 0.19
22 21 0.68
ACGTcount: A:0.26, C:0.09, G:0.04, T:0.60
Consensus pattern (21 bp):
TTTATTCTTTTTGAAATTCAA
Found at i:40602 original size:20 final size:20
Alignment explanation
Indices: 40577--40624 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
40567 AATGTTTTAC
*
40577 GAACCAGTAATTATGGTGCT
1 GAACCAATAATTATGGTGCT
*
40597 GAACCAATAATTATGGTGTT
1 GAACCAATAATTATGGTGCT
40617 GAACCAAT
1 GAACCAAT
40625 GTTGCGATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (20 bp):
GAACCAATAATTATGGTGCT
Found at i:40976 original size:22 final size:22
Alignment explanation
Indices: 40949--41028 Score: 99
Period size: 22 Copynumber: 3.6 Consensus size: 22
40939 TACATTCTTT
*
40949 AAAGATGATATATTCTCTTTAC
1 AAAGATGATATATTCTCTTTTC
*
40971 AAAGATGATAGATTCT-TTCTTC
1 AAAGATGATATATTCTCTT-TTC
*
40993 AAAGATGATACATTCTCTTTTC
1 AAAGATGATATATTCTCTTTTC
* *
41015 AAAGAAGAAATATT
1 AAAGATGATATATT
41029 TATTGGATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.04
22 46 0.92
23 2 0.04
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (22 bp):
AAAGATGATATATTCTCTTTTC
Found at i:41731 original size:113 final size:112
Alignment explanation
Indices: 41383--41946 Score: 705
Period size: 112 Copynumber: 4.9 Consensus size: 112
41373 GCAAAGATTT
* * *
41383 GAATCCATCACTCAATGGATCAACATTTCCGGAGAAGTTCATAATGAGAAGAACTTATATGAAGA
1 GAATTCATCACTCAATGGATCAACATTTCCAGAGAAGTTCATAATGAGAAGAACTTATCTGAAGA
41448 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTCACTC
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTCACTC
* * *
41495 GAATTCATCACTCGATGGATCAGCATTTCCAGAGAAGTTTATAATGAGAAGAACTTATCTGAAGA
1 GAATTCATCACTCAATGGATCAACATTTCCAGAGAAGTTCATAATGAGAAGAACTTATCTGAAGA
*
41560 AGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTCACTC
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTCACTC
*
41607 GAATTCATCACTCAATGGATCAACATTTCCAGAGAAGTTCATAATGAGAAGAACTTATCTAAAGA
1 GAATTCATCACTCAATGGATCAACATTTCCAGAGAAGTTCATAATGAGAAGAACTTATCTGAAG-
* *
41672 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTGAACCTTTCGCTC
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTCACTC
* * * *
41720 GAATTCATCACTCGATGGATCAGCATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAA
1 GAATTCATCACTCAATGGATCAACATTTCCAGAG-A-AGTTCATAATGAGAAGAACTTATCTGAA
* *
41784 G-AGGAAGGAA-AAGTTCATAATGAGAAGAACTTATTCAACCTTTTGTA-T-
64 GAAGGAA-GAAGAAGTTCATAATGAGAAGAACTTGTTCAACC-TTT-CACTC
* * * *
41832 G-ACTCTATCACAGAAGGAGAT-ATATAGCATCAACAGTTCCAGA-AGTGTTCATAATGAGAAGA
1 GAATTC-ATCAC---------TCA-AT-GGATCAACATTTCCAGAGA-AGTTCATAATGAGAAGA
*
41894 ACTCATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
53 ACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
41947 GCCTTAATTC
Statistics
Matches: 400, Mismatches: 31, Indels: 34
0.86 0.07 0.07
Matches are distributed among these distances:
111 3 0.01
112 205 0.51
113 82 0.20
114 27 0.07
120 5 0.01
121 63 0.16
122 15 0.04
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.26
Consensus pattern (112 bp):
GAATTCATCACTCAATGGATCAACATTTCCAGAGAAGTTCATAATGAGAAGAACTTATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTCACTC
Found at i:41803 original size:225 final size:224
Alignment explanation
Indices: 41383--41826 Score: 732
Period size: 225 Copynumber: 2.0 Consensus size: 224
41373 GCAAAGATTT
* *
41383 GAATCCATCACTCAATGGATCAACATTTCCGGAGAAGTTCATAATGAGAAGAACTTATATGAAGA
1 GAATCCATCACTCAATGGATCAACATTTCCAGAGAAGTTCATAATGAGAAGAACTTATATAAAGA
41448 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTCACTCGAATTCATCACTCGATGG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTCACTCGAATTCATCACTCGATGG
* * *
41513 ATCAGCATTTCCAGAGAAGTTTATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAATTCATA
131 ATCAGCATTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATA
*
41578 ATGAGAAGAACTTGTTCAACCTTTCACTC
196 ATGAGAAGAACTTATTCAACCTTTCACTC
* *
41607 GAATTCATCACTCAATGGATCAACATTTCCAGAGAAGTTCATAATGAGAAGAACTTATCTAAAGA
1 GAATCCATCACTCAATGGATCAACATTTCCAGAGAAGTTCATAATGAGAAGAACTTATATAAAG-
* *
41672 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTGAACCTTTCGCTCGAATTCATCACTCGATG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTCACTCGAATTCATCACTCGATG
*
41737 GATCAGCATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGGAA-AAGTT
130 GATCAGCATTGCCAGAG-A-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA-GAAGAAATT
41799 CATAATGAGAAGAACTTATTCAACCTTT
192 CATAATGAGAAGAACTTATTCAACCTTT
41827 TGTATGACTC
Statistics
Matches: 205, Mismatches: 11, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
224 61 0.30
225 114 0.56
226 30 0.15
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (224 bp):
GAATCCATCACTCAATGGATCAACATTTCCAGAGAAGTTCATAATGAGAAGAACTTATATAAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTCACTCGAATTCATCACTCGATGG
ATCAGCATTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATA
ATGAGAAGAACTTATTCAACCTTTCACTC
Found at i:42327 original size:3 final size:3
Alignment explanation
Indices: 42304--42428 Score: 114
Period size: 3 Copynumber: 42.7 Consensus size: 3
42294 ATTTGTTTTT
* * *
42304 TTA TTT TTA TTT TTA -TA TTA TTA TTA ATA TTA TT- TTA TT- TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* * * * * * * *
42347 CTA TTA TTT TTA TTT TTA TTT TTA -TA TTA TTA ATA TTA ATA ATA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
42394 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
42429 TACATTACAT
Statistics
Matches: 99, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
2 7 0.07
3 92 0.93
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:42351 original size:23 final size:25
Alignment explanation
Indices: 42310--42384 Score: 77
Period size: 26 Copynumber: 3.1 Consensus size: 25
42300 TTTTTTATTT
*
42310 TTATTTTTATATTAT--TATTAATA
1 TTATTTTTATTTTATACTATTAATA
* *
42333 TTA-TTTTA-TTTATACTATTATTT
1 TTATTTTTATTTTATACTATTAATA
*
42356 TTATTTTTATTTTTATATTATTAATA
1 TTATTTTTA-TTTTATACTATTAATA
42382 TTA
1 TTA
42385 ATAATAATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
21 4 0.10
22 5 0.12
23 12 0.29
24 5 0.12
26 15 0.37
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (25 bp):
TTATTTTTATTTTATACTATTAATA
Found at i:43817 original size:21 final size:22
Alignment explanation
Indices: 43771--43815 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
43761 TCATTGTTTA
43771 TTTATAT-TTTAATTTTATATG
1 TTTATATATTTAATTTTATATG
43792 TTTATATATTTAATTATTAT-TG
1 TTTATATATTTAATT-TTATATG
43814 TT
1 TT
43816 ATTATTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.32
22 11 0.50
23 4 0.18
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTATATATTTAATTTTATATG
Found at i:44009 original size:146 final size:143
Alignment explanation
Indices: 43882--44188 Score: 367
Period size: 145 Copynumber: 2.1 Consensus size: 143
43872 TTTTATATAT
43882 TAAATAAAAATCCTA-TTTATAAAT-T-TAAT-TTTATATAAATTACTTT-TAAGAAAAATAATC
1 TAAATAAAAATCCTATTTTATAAATATATAATATTTATATAAATTA-TTTGT-AGAAAAAT-AT-
43942 ATATT-TTAATATTTATTTATTTTTTTAATATTAAGAAATGGACTGTCTTAAAGCACCTAGAAGT
62 -T-TTATTAATATTTATTTA-TTTTTTAATATTAAGAAATGGACTGTCTTAAAGCACCTAGAAGT
*
44006 TATTTTCTGATATTCTTAAA
124 TATTTACTGATATTCTTAAA
* * * * *
44026 TAAATAAATATCCTATTTTTATAAATAATATATTATTTATTTTAATTATTTGTAGAGAAATATTT
1 TAAATAAAAATCCTA-TTTTATAAAT-ATATAATATTTATATAAATTATTTGTAGAAAAATATTT
* *
44091 TATTAATATTTATTTATTTTTTAATATTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGTCATTT
64 TATTAATATTTATTTATTTTTTAATATTAAGAAATGGACTGTCTTAAAGCACCTAGAAGTTATTT
* *
44156 TCTGATATT-TCTAAG
129 ACTGATATTCT-TAAA
* *
44171 TAAATAAATATCTTATTT
1 TAAATAAAAATCCTATTT
44189 ACAAAAAATA
Statistics
Matches: 145, Mismatches: 9, Indels: 18
0.84 0.05 0.10
Matches are distributed among these distances:
144 18 0.12
145 75 0.52
146 24 0.17
148 3 0.02
149 13 0.09
150 12 0.08
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (143 bp):
TAAATAAAAATCCTATTTTATAAATATATAATATTTATATAAATTATTTGTAGAAAAATATTTTA
TTAATATTTATTTATTTTTTAATATTAAGAAATGGACTGTCTTAAAGCACCTAGAAGTTATTTAC
TGATATTCTTAAA
Found at i:44062 original size:20 final size:20
Alignment explanation
Indices: 44025--44063 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
44015 ATATTCTTAA
44025 ATAAATAAATATCCTATTTTT
1 ATAAATAAATAT-CTATTTTT
44046 ATAAATAATATAT-TATTT
1 ATAAATAA-ATATCTATTT
44064 ATTTTAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
ATAAATAAATATCTATTTTT
Found at i:44836 original size:79 final size:80
Alignment explanation
Indices: 44697--44849 Score: 227
Period size: 79 Copynumber: 1.9 Consensus size: 80
44687 CTTCCACTGG
* * * * *
44697 AAATATTGATCCACCTCTTTCTGTGATGGAATCGAGTGAAATGTTGAACAAGTTCATCTCATTAG
1 AAATATTGATCCACCTCCTTCTGTGATAGAATCAAGTCAAAGGTTGAACAAGTTCATCTCATTAG
44762 GAACTTCTTTATTGA
66 GAACTTCTTTATTGA
* * *
44777 AAATATTGATCCACCTCCTTCTGTGATAGAGTCAAG-CAAAGGTTGAACAAGTTCTTCTCATTAT
1 AAATATTGATCCACCTCCTTCTGTGATAGAATCAAGTCAAAGGTTGAACAAGTTCATCTCATTAG
44841 GAACTTCTT
66 GAACTTCTT
44850 CTCCCTCATT
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
79 33 0.51
80 32 0.49
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.35
Consensus pattern (80 bp):
AAATATTGATCCACCTCCTTCTGTGATAGAATCAAGTCAAAGGTTGAACAAGTTCATCTCATTAG
GAACTTCTTTATTGA
Found at i:44955 original size:118 final size:118
Alignment explanation
Indices: 44771--45019 Score: 338
Period size: 118 Copynumber: 2.1 Consensus size: 118
44761 GGAACTTCTT
* *
44771 TATTGAAAATATTGATCCACCTCCTTCTGTGATAGAGTCAAGCAAAGGTTGAACAAGTTCTTCTC
1 TATTGAAAATATTAATCCACCTCCTTCTGTGATAGACTCAAGCAAAGGTTGAACAAGTTCTTCTC
* ** *
44836 ATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTACAAACACTTC
66 ATTATGAACTTATTCTCCCTCATCAGATGAGTTATTCTCATTACAAACACTTC
* * * * *
44889 TATTGGAAATGTTAATCCACCTCCTTTTGTGATGGACTCGAA-CCAAGGTTGAACAAGTTCTTCT
1 TATTGAAAATATTAATCCACCTCCTTCTGTGATAGACTC-AAGCAAAGGTTGAACAAGTTCTTCT
* ** *
44953 CATTATGAACTTATTCTCTCTCATCAGATGAGTTATTCTCATTATGAACCCTTC
65 CATTATGAACTTATTCTCCCTCATCAGATGAGTTATTCTCATTACAAACACTTC
*
45007 CATTGAAAATATT
1 TATTGAAAATATT
45020 GGCTGATTTA
Statistics
Matches: 112, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
118 110 0.98
119 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.37
Consensus pattern (118 bp):
TATTGAAAATATTAATCCACCTCCTTCTGTGATAGACTCAAGCAAAGGTTGAACAAGTTCTTCTC
ATTATGAACTTATTCTCCCTCATCAGATGAGTTATTCTCATTACAAACACTTC
Found at i:46602 original size:54 final size:52
Alignment explanation
Indices: 46469--46854 Score: 262
Period size: 54 Copynumber: 7.0 Consensus size: 52
46459 AATTATCATT
* * * * * *
46469 AAGAAACCCATAAAAATTACGCTTAGTTTTTTTAAAAATTCATTGGAAGTAATCATC
1 AAGAAACCC-TGAAAA-TAGGCTTAGCTCTTTTAAAAATTCATT---TGTAAACATC
**
46526 AAGAAACCCCTGAAAATCAGGCTTAGCTCTTTTCCAAA-TCTATTTGTAAACATC
1 AAGAAA-CCCTGAAAAT-AGGCTTAGCTCTTTTAAAAATTC-ATTTGTAAACATC
* * * *
46580 AAGAAACTCCTAAAAAGTAGGCTTAACTCCTTTAAAAATTCATTTGAAAACATC
1 AAGAAAC-CCTGAAAA-TAGGCTTAGCTCTTTTAAAAATTCATTTGTAAACATC
*
46634 AAGAAACCCTTGAAAATTAGGCTTAGCT-TCTTTAAAAATTCATTAGAAGTAATA-ATC
1 AAGAAACCC-TGAAAA-TAGGCTTAGCTCT-TTTAAAAATTCATT---TGTAA-ACATC
* ** * *
46691 AAGAAACCCCTAAAAACTAGAATT--CTCTTCTTTAAAAATTTAATTTGAAAACATC
1 AAGAAA-CCCTGAAAA-TAGGCTTAGCTC-T-TTTAAAAA-TTCATTTGTAAACATC
** * *
46746 AAGAAACCCATGAAAATCAAACTTAGCTCCTTTAAAAATTTATTTGTAAACATC
1 AAGAAACCC-TGAAAAT-AGGCTTAGCTCTTTTAAAAATTCATTTGTAAACATC
* * *
46800 AAGAAACCCTTGAAAATCAGGCTTAGCT-TCTTTCAACATTCATTTGAAAACATC
1 AAGAAACCC-TGAAAAT-AGGCTTAGCTCT-TTTAAAAATTCATTTGTAAACATC
46854 A
1 A
46855 TATTGTTTGG
Statistics
Matches: 266, Mismatches: 41, Indels: 47
0.75 0.12 0.13
Matches are distributed among these distances:
53 3 0.01
54 150 0.56
55 34 0.13
56 3 0.01
57 64 0.24
58 12 0.05
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.30
Consensus pattern (52 bp):
AAGAAACCCTGAAAATAGGCTTAGCTCTTTTAAAAATTCATTTGTAAACATC
Found at i:46762 original size:112 final size:111
Alignment explanation
Indices: 46577--46785 Score: 292
Period size: 112 Copynumber: 1.9 Consensus size: 111
46567 ATTTGTAAAC
* * ** *
46577 ATCAAGAAACTCCTAAAAAGTAGGCTTAACTCCTTTAAAAATTCATTTGAAAACATCAAGAAACC
1 ATCAAGAAACCCCTAAAAACTAGAATTAACTCCTTTAAAAATTAATTTGAAAACATCAAGAAACC
* * ** *
46642 CTTGAAAATTAGGCTTAGCTTCTTTAAAAATTCATTAGAAGTAATA
66 CATGAAAATCAAACTTAGCTCCTTTAAAAATTCATTAGAAGTAATA
** *
46688 ATCAAGAAACCCCTAAAAACTAGAATTCTCTTCTTTAAAAATTTAATTTGAAAACATCAAGAAAC
1 ATCAAGAAACCCCTAAAAACTAGAATTAACTCCTTTAAAAA-TTAATTTGAAAACATCAAGAAAC
46753 CCATGAAAATCAAACTTAGCTCCTTTAAAAATT
65 CCATGAAAATCAAACTTAGCTCCTTTAAAAATT
46786 TATTTGTAAA
Statistics
Matches: 84, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
111 34 0.40
112 50 0.60
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.29
Consensus pattern (111 bp):
ATCAAGAAACCCCTAAAAACTAGAATTAACTCCTTTAAAAATTAATTTGAAAACATCAAGAAACC
CATGAAAATCAAACTTAGCTCCTTTAAAAATTCATTAGAAGTAATA
Found at i:46807 original size:166 final size:163
Alignment explanation
Indices: 46408--46843 Score: 468
Period size: 166 Copynumber: 2.6 Consensus size: 163
46398 AAGGACTCAT
* * * *
46408 CATCAAGAAACCTTTGAAAATCAAACTTGGCTTCC-TCAAAAATTCATTT-ACAATTATCATTAA
1 CATCAAGAAACC-CTGAAAATCAAACTTAGC-TCCTTTAAAAATTCATTTGA-AA--A-CATCAA
* * * * * * *
46471 GAAACCCATAAAAATTACGCTTAGTTTTTTTAAAAATTCATTGGAAGTAATCATCAAGAAACCCC
60 GAAACCCTTGAAAATTAGGCTTAGCTTCTTTAAAAATTCATTAGAAGTAATAATCAAGAAACCCC
* ** ** *
46536 TGAAAATCAGGCTTAGCTCTTTTCCAAATCTATTTGTAAA
125 TAAAAATCAGAATTA-CTCTTTTAAAAATCTATTTGAAAA
* ** *
46576 CATCAAGAAACTCCTAAAAAGT-AGGCTTAACTCCTTTAAAAATTCATTTGAAAACATCAAGAAA
1 CATCAAGAAAC-CCTGAAAA-TCAAACTTAGCTCCTTTAAAAATTCATTTGAAAACATCAAGAAA
46640 CCCTTGAAAATTAGGCTTAGCTTCTTTAAAAATTCATTAGAAGTAATAATCAAGAAACCCCTAAA
64 CCCTTGAAAATTAGGCTTAGCTTCTTTAAAAATTCATTAGAAGTAATAATCAAGAAACCCCTAAA
*
46705 AA-CTAGAATT-CTCTTCTTTAAAAATTTAATTTGAAAA
129 AATC-AGAATTACTC-T-TTTAAAAATCT-ATTTGAAAA
* *
46742 CATCAAGAAACCCATGAAAATCAAACTTAGCTCCTTTAAAAATTTATTTGTAAACATCAAGAAAC
1 CATCAAGAAACCC-TGAAAATCAAACTTAGCTCCTTTAAAAATTCATTTGAAAACATCAAGAAAC
* * *
46807 CCTTGAAAATCAGGCTTAGCTTCTTTCAACATTCATT
65 CCTTGAAAATTAGGCTTAGCTTCTTTAAAAATTCATT
46844 TGAAAACATC
Statistics
Matches: 227, Mismatches: 31, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
163 3 0.01
164 2 0.01
165 83 0.37
166 97 0.43
167 3 0.01
168 36 0.16
169 3 0.01
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (163 bp):
CATCAAGAAACCCTGAAAATCAAACTTAGCTCCTTTAAAAATTCATTTGAAAACATCAAGAAACC
CTTGAAAATTAGGCTTAGCTTCTTTAAAAATTCATTAGAAGTAATAATCAAGAAACCCCTAAAAA
TCAGAATTACTCTTTTAAAAATCTATTTGAAAA
Found at i:49453 original size:165 final size:165
Alignment explanation
Indices: 49181--49513 Score: 576
Period size: 165 Copynumber: 2.0 Consensus size: 165
49171 TTTCTCACTT
* * * *
49181 TATTTCATCATGACTTGCCTCTGTAAAAAAATCTGGATTGATGGCTTTCATTCTTGTAAACAGAT
1 TATTTCACCATGACTTGCCTCTGCAAAAAAATATGGATTGATGGCTTTCATTCTTGCAAACAGAT
49246 TTCCTTCACCTTGCCCCCAGGTGTGGAGGGTGATCCTTGGTTAGGGTTGAATCAAAAGGAAAATA
66 TTCCTTCACCTTGCCCCCAGGTGTGGAGGGTGATCCTTGGTTAGGGTTGAATCAAAAGGAAAATA
*
49311 CTATAGGCTCAAGTGGGGACAACGAGGGATATATA
131 CTATAGGATCAAGTGGGGACAACGAGGGATATATA
* * * *
49346 TATTTCACCATGACTTGCCTCTGCAATAAAATATGGATTGATGGTTTTCATTCTTGCAAGCATAT
1 TATTTCACCATGACTTGCCTCTGCAAAAAAATATGGATTGATGGCTTTCATTCTTGCAAACAGAT
*
49411 TTCCTTCACCTTGCCCCCAGGTGTGGAGGGTGATCTTTGGTTAGGGTTGAATCAAAAGGAAAATA
66 TTCCTTCACCTTGCCCCCAGGTGTGGAGGGTGATCCTTGGTTAGGGTTGAATCAAAAGGAAAATA
49476 CTATAGGATCAAGTGGGGACAACGAGGGATATATA
131 CTATAGGATCAAGTGGGGACAACGAGGGATATATA
49511 TAT
1 TAT
49514 ATTTGGTGAA
Statistics
Matches: 158, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
165 158 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (165 bp):
TATTTCACCATGACTTGCCTCTGCAAAAAAATATGGATTGATGGCTTTCATTCTTGCAAACAGAT
TTCCTTCACCTTGCCCCCAGGTGTGGAGGGTGATCCTTGGTTAGGGTTGAATCAAAAGGAAAATA
CTATAGGATCAAGTGGGGACAACGAGGGATATATA
Found at i:52819 original size:28 final size:29
Alignment explanation
Indices: 52779--52842 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
52769 ATTCTAATAA
*
52779 AAAGTTTAAGGA-CTAA-AATAAAAAAACT
1 AAAGTCTAAGGACCTAAGAATAAAAAAA-T
* **
52807 AAAGTCTAGGGACCTAAGTGTAAAAAAAT
1 AAAGTCTAAGGACCTAAGAATAAAAAAAT
52836 AAAGTCT
1 AAAGTCT
52843 TGGAACTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 10 0.33
29 12 0.40
30 8 0.27
ACGTcount: A:0.53, C:0.09, G:0.16, T:0.22
Consensus pattern (29 bp):
AAAGTCTAAGGACCTAAGAATAAAAAAAT
Found at i:52833 original size:29 final size:29
Alignment explanation
Indices: 52797--52859 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
52787 AGGACTAAAA
*
52797 TAAAAAAACTAAAGTCTAGGGACCTAAGTG
1 TAAAAAAA-TAAAGTCTAGGAACCTAAGTG
* *
52827 TAAAAAAATAAAGTCTTGGAACTTAAGTG
1 TAAAAAAATAAAGTCTAGGAACCTAAGTG
52856 TAAA
1 TAAA
52860 GAATCTAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 22 0.73
30 8 0.27
ACGTcount: A:0.49, C:0.10, G:0.17, T:0.24
Consensus pattern (29 bp):
TAAAAAAATAAAGTCTAGGAACCTAAGTG
Found at i:53416 original size:12 final size:14
Alignment explanation
Indices: 53390--53420 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
53380 CTAAATACCC
53390 TTTTTTCATTCTCT
1 TTTTTTCATTCTCT
53404 TTTTTTCATTCT-T
1 TTTTTTCATTCTCT
53417 TTTT
1 TTTT
53421 AGAGAGAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTTCATTCTCT
Found at i:54485 original size:45 final size:44
Alignment explanation
Indices: 54421--54533 Score: 129
Period size: 45 Copynumber: 2.5 Consensus size: 44
54411 CAATGCCAAC
*
54421 AATACATATCCATTGATTGAACCAAAAACTTTAATTAAACTAA-AT
1 AATACATAT-CATTGATTGAACCAAAAA-TTTAATTAAACTAACAA
** *
54466 AATACATATCATTTGATTGAACCTGAAATTTAATTAAATTAACTAA
1 AATACATATCA-TTGATTGAACCAAAAATTTAATTAAACTAAC-AA
54512 ACATACATATCAATTGATTGAA
1 A-ATACATATC-ATTGATTGAA
54534 ACTTTAGCGA
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
44 15 0.25
45 23 0.39
46 2 0.03
47 18 0.31
48 1 0.02
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (44 bp):
AATACATATCATTGATTGAACCAAAAATTTAATTAAACTAACAA
Found at i:54725 original size:17 final size:17
Alignment explanation
Indices: 54681--54725 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 17
54671 ATTTTGTTTG
* *
54681 ATATGATATTGATTCGA
1 ATATCATATTGATTCAA
54698 ATATC--ATTGATTCAA
1 ATATCATATTGATTCAA
54713 ATATCATATTGAT
1 ATATCATATTGAT
54726 GCAATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 14 0.58
17 10 0.42
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (17 bp):
ATATCATATTGATTCAA
Found at i:54841 original size:77 final size:77
Alignment explanation
Indices: 54760--54907 Score: 228
Period size: 77 Copynumber: 1.9 Consensus size: 77
54750 TTGATTATTT
* *
54760 AATATCATATTGATGCAATTAAAGGT-AAAAATATCATTTTGTTTGATATACTGA-TCATTTAGA
1 AATATCATATTGATGCAATTAAAAGTAAAAAATAT-AATTTGTTTGATATACTGAGTCATTTAGA
54823 ATTTAAATGATTCA
65 A-TTAAATGATTCA
* *
54837 AATATCATATTGATGCAATTAAAAGTAAAAAATATAATTTGTTTGATATGCTGAGTCCTTTAGAA
1 AATATCATATTGATGCAATTAAAAGTAAAAAATATAATTTGTTTGATATACTGAGTCATTTAGAA
54902 TTAAAT
66 TTAAAT
54908 TTTTATAAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
77 48 0.74
78 17 0.26
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.39
Consensus pattern (77 bp):
AATATCATATTGATGCAATTAAAAGTAAAAAATATAATTTGTTTGATATACTGAGTCATTTAGAA
TTAAATGATTCA
Done.