Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003781.1 Hibiscus syriacus cultivar Beakdansim tig00008095_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: 70594
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1498 original size:19 final size:21
Alignment explanation
Indices: 1455--1502 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1445 GTTCAGGTAT
*
1455 TGTTCATACGGTATTGTTCAC
1 TGTTCATACCGTATTGTTCAC
1476 TGTTCATACCGTATT-TT-AC
1 TGTTCATACCGTATTGTTCAC
1495 TGTTCATA
1 TGTTCATA
1503 AAATGTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 10 0.38
20 2 0.08
21 14 0.54
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.46
Consensus pattern (21 bp):
TGTTCATACCGTATTGTTCAC
Found at i:1857 original size:27 final size:29
Alignment explanation
Indices: 1810--1873 Score: 80
Period size: 27 Copynumber: 2.3 Consensus size: 29
1800 AATATACGAT
* *
1810 AAATCAGATGTCGGATAAGCA-TATTAAG
1 AAATCAGGTGTCGAATAAGCAGTATTAAG
*
1838 AAATCAGGTG-CGAATAAGCAGTATTCAG
1 AAATCAGGTGTCGAATAAGCAGTATTAAG
1866 -AATCAGGT
1 AAATCAGGT
1874 ATCATATCGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 17 0.53
28 15 0.47
ACGTcount: A:0.41, C:0.12, G:0.23, T:0.23
Consensus pattern (29 bp):
AAATCAGGTGTCGAATAAGCAGTATTAAG
Found at i:3263 original size:24 final size:24
Alignment explanation
Indices: 3231--3278 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
3221 GACAGCAAAT
3231 GCCTTCACCTTTCATGAGATGATC
1 GCCTTCACCTTTCATGAGATGATC
3255 GCCTTCACCTTTCATGAGATGATC
1 GCCTTCACCTTTCATGAGATGATC
3279 AGAGTATCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (24 bp):
GCCTTCACCTTTCATGAGATGATC
Found at i:5753 original size:21 final size:21
Alignment explanation
Indices: 5725--5764 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
5715 TTTGCCTTCC
5725 AAACAAAATAG-AATATTTAA
1 AAACAAAATAGAAATATTTAA
*
5745 AAACTAAAATCGAAATATTT
1 AAAC-AAAATAGAAATATTT
5765 TAGTTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 6 0.35
22 7 0.41
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.28
Consensus pattern (21 bp):
AAACAAAATAGAAATATTTAA
Found at i:11862 original size:20 final size:21
Alignment explanation
Indices: 11837--11888 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
11827 TTTTCCCAAT
11837 TCGCAATGCGAATAAGG-AAA
1 TCGCAATGCGAATAAGGAAAA
* **
11857 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGGAAAA
11878 TCGCAATGCGA
1 TCGCAATGCGA
11889 TACTGACTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.38, C:0.19, G:0.27, T:0.15
Consensus pattern (21 bp):
TCGCAATGCGAATAAGGAAAA
Found at i:11902 original size:20 final size:20
Alignment explanation
Indices: 11877--12011 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
11867 AATTGGGAAA
11877 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
11897 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
11917 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
11938 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
11958 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
11978 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
11998 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
12012 TTTCAAAGCG
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 4 0.04
20 66 0.69
21 24 0.25
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:11921 original size:61 final size:61
Alignment explanation
Indices: 11874--12005 Score: 183
Period size: 61 Copynumber: 2.2 Consensus size: 61
11864 GCGAATTGGG
* * * * *
11874 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
11935 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
11996 ATAATCGCAA
1 AAAATCGCAA
12006 TGCGATTTTC
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:12206 original size:22 final size:22
Alignment explanation
Indices: 12178--12221 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
12168 CACTCTCTCA
12178 CCCATCTCC-GACGAAATCCGTC
1 CCCATCTCCAG-CGAAATCCGTC
12200 CCCATCTCCAGCGAAATCCGTC
1 CCCATCTCCAGCGAAATCCGTC
12222 TATCTCCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCAGCGAAATCCGTC
Found at i:12228 original size:20 final size:21
Alignment explanation
Indices: 12178--12229 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
12168 CACTCTCTCA
12178 CCCATCTCC-GACGAAATCCGT
1 CCCATCTCCAG-CGAAATCCGT
12199 CCCCATCTCCAGCGAAATCCGT
1 -CCCATCTCCAGCGAAATCCGT
*
12221 -CTATCTCCA
1 CCCATCTCCA
12230 TCTCTCAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 8 0.29
22 19 0.68
23 1 0.04
ACGTcount: A:0.23, C:0.44, G:0.12, T:0.21
Consensus pattern (21 bp):
CCCATCTCCAGCGAAATCCGT
Found at i:12500 original size:20 final size:20
Alignment explanation
Indices: 12483--12520 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12473 CAATTTTCTC
12483 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
12503 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
12521 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:12711 original size:25 final size:24
Alignment explanation
Indices: 12657--12711 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
12647 TGTTTATTAT
* *
12657 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
12681 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
12707 TGTTT
1 TGTTT
12712 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:13859 original size:18 final size:18
Alignment explanation
Indices: 13838--13882 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
13828 CTCACTTCGG
*
13838 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
13856 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
13874 GAGCCATCA
1 GAGCCATCA
13883 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:14389 original size:20 final size:20
Alignment explanation
Indices: 14364--14409 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
14354 TAGTTTACTT
14364 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * **
14384 TCGCAACGCGGAAATGGTTA
1 TCGCAACACGAAAATGACTA
14404 TCGCAA
1 TCGCAA
14410 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:14438 original size:14 final size:14
Alignment explanation
Indices: 14419--14476 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
14409 ATGCGAAATG
14419 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
14433 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
14449 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
14465 AAAATCGCAACG
1 AAAATCGCAACG
14477 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:14461 original size:32 final size:33
Alignment explanation
Indices: 14403--14493 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
14393 GGAAATGGTT
14403 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
14436 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
14468 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
14494 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:14529 original size:14 final size:14
Alignment explanation
Indices: 14510--14568 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
14500 TTGTGTTTCG
14510 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
14524 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
14541 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
14557 CGTTGCGATTTT
1 CGTTGCGATTTT
14569 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:14542 original size:33 final size:33
Alignment explanation
Indices: 14505--14584 Score: 151
Period size: 33 Copynumber: 2.4 Consensus size: 33
14495 GCGATTTGTG
*
14505 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
14538 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
14571 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
14585 AGCCATTTCC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:14603 original size:20 final size:19
Alignment explanation
Indices: 14569--14624 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
14559 TTGCGATTTT
*
14569 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
14588 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
14608 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
14625 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:15840 original size:42 final size:42
Alignment explanation
Indices: 15764--15876 Score: 154
Period size: 42 Copynumber: 2.7 Consensus size: 42
15754 ATAAATGAAT
* *
15764 GATAGGAGTGGACTCTTGAGGGATGACAGTGGCCTCTTGAAC
1 GATAGGAGTGGACTCTTGAGGGATGACAGAGGCCTCTTCAAC
* * * * * *
15806 GGTGGGAGGGGACTCTCGAGGAATGATAGAGGCCTCTTCAAC
1 GATAGGAGTGGACTCTTGAGGGATGACAGAGGCCTCTTCAAC
15848 GATAGGAGTGGACTCTTGAGGGATGACAG
1 GATAGGAGTGGACTCTTGAGGGATGACAG
15877 GCGAGTCGGG
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.25, C:0.16, G:0.38, T:0.21
Consensus pattern (42 bp):
GATAGGAGTGGACTCTTGAGGGATGACAGAGGCCTCTTCAAC
Found at i:16267 original size:91 final size:90
Alignment explanation
Indices: 16095--16278 Score: 289
Period size: 91 Copynumber: 2.0 Consensus size: 90
16085 ATTTCAAACT
*
16095 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTAAAGAATACACAGTTTAGCA
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGT--AGAATAAACAGTTTAGCA
16160 GAATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
*
16187 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGT-TAATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTAGAATAAACAGTTTAGCA
**
16251 TTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
16278 T
1 T
16279 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
91 41 0.48
92 19 0.22
94 26 0.30
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTAGAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:18028 original size:19 final size:19
Alignment explanation
Indices: 17964--18095 Score: 130
Period size: 19 Copynumber: 7.1 Consensus size: 19
17954 TCTTTTGGTT
*
17964 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
17983 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
18003 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
** *
18023 GAAATGACTATCGCGA--C
1 GAAATGAAAATCGCAACGC
*
18040 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
18056 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
18075 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
18094 GA
1 GA
18096 TTTTGGTTTC
Statistics
Matches: 96, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
14 8 0.08
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 50 0.52
20 30 0.31
21 2 0.02
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:18088 original size:52 final size:53
Alignment explanation
Indices: 17989--18088 Score: 157
Period size: 52 Copynumber: 1.9 Consensus size: 53
17979 ACGAGATAAT
** **
17989 GAGAATCGCAACGCGGAAATGACTATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGGAAATGAAAATCGCAACGCGAAATGAAAATCGCGACGA
18042 GAGAATCGCAACGC-GAAATGAAAATCGCAACGCGAAATGAAAATCGC
1 GAGAATCGCAACGCGGAAATGAAAATCGCAACGCGAAATGAAAATCGC
18089 AATGCGATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
52 29 0.67
53 14 0.33
ACGTcount: A:0.40, C:0.23, G:0.25, T:0.12
Consensus pattern (53 bp):
GAGAATCGCAACGCGGAAATGAAAATCGCAACGCGAAATGAAAATCGCGACGA
Found at i:18118 original size:19 final size:19
Alignment explanation
Indices: 18091--18156 Score: 80
Period size: 18 Copynumber: 3.5 Consensus size: 19
18081 AAAATCGCAA
**
18091 TGCGATTTTGGTTTCGCG-
1 TGCGATTTTTATTTCGCGT
18109 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
18128 TGCGATAGTTATTTCTGCGT
1 TGCGATTTTTATTTC-GCGT
18148 TGCGATTTT
1 TGCGATTTT
18157 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
18 16 0.40
19 13 0.32
20 11 0.28
ACGTcount: A:0.11, C:0.15, G:0.26, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:18149 original size:20 final size:19
Alignment explanation
Indices: 18102--18153 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
18092 GCGATTTTGG
**
18102 TTTCGCG-TGCGATTTTTA
1 TTTCGCGTTGCGATAGTTA
18120 TTTCGCGTTGCGATAGTTA
1 TTTCGCGTTGCGATAGTTA
18139 TTTCTGCGTTGCGAT
1 TTTC-GCGTTGCGAT
18154 TTTCATTCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 7 0.23
19 13 0.43
20 10 0.33
ACGTcount: A:0.12, C:0.17, G:0.25, T:0.46
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTTA
Found at i:18861 original size:21 final size:21
Alignment explanation
Indices: 18821--18861 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
18811 ACTGTAGACC
**
18821 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
18842 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
18862 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:19355 original size:43 final size:43
Alignment explanation
Indices: 19289--19394 Score: 151
Period size: 43 Copynumber: 2.5 Consensus size: 43
19279 TCAGGCAGCA
* *
19289 CGAGCAGGGGAG-TAGACTAGATGAGTAGGGTTTCAAACTAGG
1 CGAGCAGGGGAGCAAGACTAGATGAGTAGGGGTTCAAACTAGG
* * *
19331 CGAGGAGGGGAGCAAGAGTAGATGAGTAGGGGTTCAAATTAGG
1 CGAGCAGGGGAGCAAGACTAGATGAGTAGGGGTTCAAACTAGG
*
19374 CGAGCAGGGGAGCAGGACTAG
1 CGAGCAGGGGAGCAAGACTAG
19395 GCTATTAACT
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 11 0.20
43 44 0.80
ACGTcount: A:0.31, C:0.11, G:0.42, T:0.15
Consensus pattern (43 bp):
CGAGCAGGGGAGCAAGACTAGATGAGTAGGGGTTCAAACTAGG
Found at i:32469 original size:41 final size:41
Alignment explanation
Indices: 32412--32491 Score: 160
Period size: 41 Copynumber: 2.0 Consensus size: 41
32402 ATACACTGTT
32412 TCATTTGTTTACAACGTACTGAGAATCTATAAGATGTCAAC
1 TCATTTGTTTACAACGTACTGAGAATCTATAAGATGTCAAC
32453 TCATTTGTTTACAACGTACTGAGAATCTATAAGATGTCA
1 TCATTTGTTTACAACGTACTGAGAATCTATAAGATGTCA
32492 GTTGACTGCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (41 bp):
TCATTTGTTTACAACGTACTGAGAATCTATAAGATGTCAAC
Found at i:34120 original size:29 final size:29
Alignment explanation
Indices: 34078--34140 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
34068 GATTTGCCTT
* * *
34078 GACTTGGACCCCCTTAGTCCTTCGACAAA
1 GACTTAGACCCCCTTAATCCTTCAACAAA
34107 GACTTAGACCCCCTTAATCCTTCAACAAA
1 GACTTAGACCCCCTTAATCCTTCAACAAA
34136 GACTT
1 GACTT
34141 GGATGACTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.29, C:0.33, G:0.13, T:0.25
Consensus pattern (29 bp):
GACTTAGACCCCCTTAATCCTTCAACAAA
Found at i:34854 original size:60 final size:57
Alignment explanation
Indices: 34677--34859 Score: 145
Period size: 60 Copynumber: 3.1 Consensus size: 57
34667 GTCCTTAAAT
* * * * * * *
34677 TATGACTCTAATTTTAAATTGTTCTCTAAATTTTTAAACGTTCCAATTTTATTTCTAAGC
1 TATGACTATCATTCTAAATTGTTC-CTAAA-TTTTAAACATTCCAATTTCA-TCCCAAGC
* * * *
34737 TATGGCTATCATTCTAAATTAG-TCATCAAAATTTTGAACATTTCAATTTCATCCCCAAGC
1 TATGACTATCATTCTAAATT-GTTC--CTAAATTTTAAACATTCCAATTTCAT-CCCAAGC
*
34797 TATGAC-ATTCATTCTAAATTGGTTCCTAAACTTATTAAACATTCCAATTTCATCCCAAAC
1 TATGACTA-TCATTCTAAATT-GTTCCTAAA-TT-TTAAACATTCCAATTTCATCCCAAGC
34857 TAT
1 TAT
34860 ACGTATATGC
Statistics
Matches: 99, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
59 6 0.06
60 68 0.69
61 25 0.25
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.41
Consensus pattern (57 bp):
TATGACTATCATTCTAAATTGTTCCTAAATTTTAAACATTCCAATTTCATCCCAAGC
Found at i:35112 original size:60 final size:57
Alignment explanation
Indices: 34981--35164 Score: 165
Period size: 60 Copynumber: 3.1 Consensus size: 57
34971 ATTTTGATGA
* *
34981 AATTGAGGATGAAATT-GAAATATTCAAAAGTTTAGGGACTAATTTAGAAAT-ATGATCAT
1 AATTTAGGATGAAATTAG-AATATTCAAAAGTTTA-GGACTAATTTAG-AATGA-GATTAT
* *
35040 AGTTTAGAGATGAAATTAGAATGTTCAAAAGTTTGAGGACTAATTTAGAATGAGATTTAT
1 AATTTAG-GATGAAATTAGAATATTCAAAAGTTT-AGGACTAATTTAGAATGAGA-TTAT
* * * * * * *
35100 AATTTAAGGATGAAACTAAAACATTTAAAAGTTTAAGAACCAATTTAAAATGAAGATTAT
1 AATTT-AGGATGAAATTAGAATATTCAAAAGTTT-AGGACTAATTTAGAATG-AGATTAT
35160 AATTT
1 AATTT
35165 GGAGACATAT
Statistics
Matches: 104, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
59 10 0.10
60 87 0.84
61 7 0.07
ACGTcount: A:0.45, C:0.05, G:0.17, T:0.33
Consensus pattern (57 bp):
AATTTAGGATGAAATTAGAATATTCAAAAGTTTAGGACTAATTTAGAATGAGATTAT
Found at i:42647 original size:70 final size:70
Alignment explanation
Indices: 42534--42674 Score: 237
Period size: 70 Copynumber: 2.0 Consensus size: 70
42524 TCTTAAGAAA
* *
42534 AGCCGATTATTAGAACTACAAAGTTTTTAACCAACACATTATGGGTAATGATGTTATAATTCACG
1 AGCCGATTATTAGAACTACAAAGTTTTTAACCAACACACTATGGGTAATGATGCTATAATTCACG
42599 GATAG
66 GATAG
* * *
42604 AGCCGGTTATTAGAACTATAGAGTTTTTAACCAACACACTATGGGTAATGATGCTATAATTCACG
1 AGCCGATTATTAGAACTACAAAGTTTTTAACCAACACACTATGGGTAATGATGCTATAATTCACG
42669 GATAG
66 GATAG
42674 A
1 A
42675 CAATAAGTTC
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 66 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (70 bp):
AGCCGATTATTAGAACTACAAAGTTTTTAACCAACACACTATGGGTAATGATGCTATAATTCACG
GATAG
Found at i:55373 original size:30 final size:30
Alignment explanation
Indices: 55312--55408 Score: 113
Period size: 30 Copynumber: 3.2 Consensus size: 30
55302 CTAAGGAACA
* * * * *
55312 TATGGACAATTTACCTAGGTTCTTCAGGACC
1 TATGGAC-AGTTACCGAGGATCTTTATGACC
55343 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
* *
55373 TCTGGATAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
*
55403 TCTGGA
1 TATGGA
55409 TAGGTCCTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
30 52 0.88
31 7 0.12
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGATCTTTATGACC
Found at i:55409 original size:30 final size:30
Alignment explanation
Indices: 55339--55411 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
55329 GGTTCTTCAG
* *
55339 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
55369 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
55399 GACCTCTGGATAG
1 GACCTCTGGATAG
55412 GTCCTTCGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:57510 original size:20 final size:20
Alignment explanation
Indices: 57477--57520 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
57467 AAAATGGTCC
* *
57477 AATTTCACATTCTAACATCA
1 AATTTAACACTCTAACATCA
*
57497 AATTTAACACTCTAACATTA
1 AATTTAACACTCTAACATCA
57517 AATT
1 AATT
57521 CTAGCTTAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.36
Consensus pattern (20 bp):
AATTTAACACTCTAACATCA
Found at i:61910 original size:22 final size:22
Alignment explanation
Indices: 61884--61966 Score: 82
Period size: 22 Copynumber: 3.8 Consensus size: 22
61874 TCAATACACG
*
61884 AAAGTG-CATTAGCACTGGTACT
1 AAAGTGAC-TTAGCACTGATACT
* *
61906 AAAGTGACTTAACACTGATACG
1 AAAGTGACTTAGCACTGATACT
*
61928 AAAGTGTAGTT-GCACTGATACT
1 AAAGTG-ACTTAGCACTGATACT
61950 AAAGT-ATCTTAGCACTG
1 AAAGTGA-CTTAGCACTG
61967 CTGTCATATA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
20 1 0.02
21 2 0.04
22 43 0.86
23 4 0.08
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (22 bp):
AAAGTGACTTAGCACTGATACT
Found at i:64779 original size:21 final size:22
Alignment explanation
Indices: 64731--64782 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
64721 ACGTATAATT
*
64731 ATAAATTAGTTAAAATTTTAAAG
1 ATAAATTAGTTAAAA-TTAAAAG
* *
64754 GTAAATTATTTAAAA-TAAAAG
1 ATAAATTAGTTAAAATTAAAAG
64775 ATAAATTA
1 ATAAATTA
64783 CATCAGTGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 12 0.48
23 13 0.52
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.37
Consensus pattern (22 bp):
ATAAATTAGTTAAAATTAAAAG
Found at i:65885 original size:21 final size:22
Alignment explanation
Indices: 65859--65904 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
65849 ATTGGTATCG
*
65859 TTTACCTTT-TATTTTAAATAA
1 TTTACCTTTAAATTTTAAATAA
*
65880 TTTACCTTTAAATTTTAACTAA
1 TTTACCTTTAAATTTTAAATAA
65902 TTT
1 TTT
65905 TTAACTATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTACCTTTAAATTTTAAATAA
Found at i:69272 original size:31 final size:31
Alignment explanation
Indices: 69237--69313 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
69227 TCAAAAAACA
*
69237 TAAGATATGATCACTTTTGTTTTTACTTAAT
1 TAAGATATGATCACTTTCGTTTTTACTTAAT
* *
69268 TAAGATATGACCACTTTCGTTTTTATTTAAT
1 TAAGATATGATCACTTTCGTTTTTACTTAAT
* *
69299 TAAGATGTGGTCACT
1 TAAGATATGATCACT
69314 CCCGAGTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.47
Consensus pattern (31 bp):
TAAGATATGATCACTTTCGTTTTTACTTAAT
Found at i:69676 original size:12 final size:13
Alignment explanation
Indices: 69650--69685 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
69640 CCGGTATCCA
69650 ATTTTATATTTTTT
1 ATTTTATA-TTTTT
69664 ATTTT-TATTTTT
1 ATTTTATATTTTT
69676 ATTTTATATT
1 ATTTTATATT
69686 AAATTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.48
13 6 0.29
14 5 0.24
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
ATTTTATATTTTT
Found at i:70120 original size:27 final size:24
Alignment explanation
Indices: 70050--70124 Score: 93
Period size: 27 Copynumber: 3.1 Consensus size: 24
70040 TAATTTTATA
*
70050 TATATTAACTTA--AAATAT-TTT
1 TATATTAACTTATTAAAAATATTT
70071 TATATTAACTTATTAAAAATATTT
1 TATATTAACTTATTAAAAATATTT
70095 TACTATTAACTTAATTTAAAAATATTT
1 TA-TATTAACTT-A-TTAAAAATATTT
70122 TAT
1 TAT
70125 TTATAATTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
21 12 0.26
23 5 0.11
24 5 0.11
25 9 0.19
26 2 0.04
27 14 0.30
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (24 bp):
TATATTAACTTATTAAAAATATTT
Found at i:70140 original size:27 final size:27
Alignment explanation
Indices: 70061--70123 Score: 96
Period size: 25 Copynumber: 2.4 Consensus size: 27
70051 ATATTAACTT
70061 AAAATATTTTTA-TATTAACTT-A-TTA
1 AAAATA-TTTTACTATTAACTTAATTTA
70086 AAAATATTTTACTATTAACTTAATTTA
1 AAAATATTTTACTATTAACTTAATTTA
70113 AAAATATTTTA
1 AAAATATTTTA
70124 TTTATAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
24 5 0.14
25 15 0.43
26 1 0.03
27 14 0.40
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (27 bp):
AAAATATTTTACTATTAACTTAATTTA
Done.