Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003321.1 Hibiscus syriacus cultivar Beakdansim tig00006993_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: 59889
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:13848 original size:18 final size:18
Alignment explanation
Indices: 13825--13868 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
13815 CTATGGCACA
* *
13825 CTCTCTCTCTCTCACTTT
1 CTCTCTCACACTCACTTT
* *
13843 CTCTCTAACACTCTCTTT
1 CTCTCTCACACTCACTTT
13861 CTCTCTCA
1 CTCTCTCA
13869 TAGTTTTTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.11, C:0.43, G:0.00, T:0.45
Consensus pattern (18 bp):
CTCTCTCACACTCACTTT
Found at i:18053 original size:15 final size:15
Alignment explanation
Indices: 18025--18062 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
18015 CATTCCTATC
18025 AAAA-AAAA-AAAAG
1 AAAAGAAAATAAAAG
*
18038 AAAAGCAAATAAAAG
1 AAAAGAAAATAAAAG
18053 AAAAGAAAAT
1 AAAAGAAAAT
18063 GACATATGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 4 0.19
14 3 0.14
15 14 0.67
ACGTcount: A:0.82, C:0.03, G:0.11, T:0.05
Consensus pattern (15 bp):
AAAAGAAAATAAAAG
Found at i:18056 original size:20 final size:19
Alignment explanation
Indices: 18024--18061 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
18014 CCATTCCTAT
18024 CAAAAAAAAAAAAGAAAAG
1 CAAAAAAAAAAAAGAAAAG
*
18043 CAAATAAAAGAAAAGAAAA
1 CAAA-AAAAAAAAAGAAAA
18062 TGACATATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.82, C:0.05, G:0.11, T:0.03
Consensus pattern (19 bp):
CAAAAAAAAAAAAGAAAAG
Found at i:24872 original size:21 final size:21
Alignment explanation
Indices: 24843--24895 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
24833 ATTCTGACTA
24843 TCGCATTGCGATTTTCCGAAT
1 TCGCATTGCGATTTTCCGAAT
* *
24864 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCGAAT
*
24885 TCGCAATGCGA
1 TCGCATTGCGA
24896 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCGAAT
Found at i:24910 original size:20 final size:20
Alignment explanation
Indices: 24885--24937 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
24875 TTTTCCTAAT
24885 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
24905 TCGCAATGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
24925 TCGCAACGCGAAT
1 TCGCAATGCGAAT
24938 CTGACTATCG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:24947 original size:20 final size:20
Alignment explanation
Indices: 24924--25010 Score: 138
Period size: 20 Copynumber: 4.3 Consensus size: 20
24914 GAATACGTAA
* *
24924 ATCGCAACGCGAATCTGACT
1 ATCGCAACGAGATTCTGACT
24944 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
24964 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
* *
24984 ATTGCAACGCGATTCTGACT
1 ATCGCAACGAGATTCTGACT
25004 ATCGCAA
1 ATCGCAA
25011 TACTGAATTT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:25905 original size:24 final size:24
Alignment explanation
Indices: 25847--25893 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
25837 AGTCAGTTTT
*
25847 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
25871 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
25894 TCGGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:28337 original size:20 final size:20
Alignment explanation
Indices: 28312--28394 Score: 116
Period size: 20 Copynumber: 4.2 Consensus size: 20
28302 GACATTCATT
28312 TGACTATCGCAACGC-GAATA
1 TGACTATCGCAACGCGGAA-A
*
28332 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
*
28352 TGACTATCGCAACGCGGAAT
1 TGACTATCGCAACGCGGAAA
28372 TGACTATCGCAACGTC-GAAA
1 TGACTATCGCAACG-CGGAAA
28392 TGA
1 TGA
28395 TTTCGCGTTG
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
20 53 0.93
21 4 0.07
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:28457 original size:33 final size:34
Alignment explanation
Indices: 28400--28495 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 34
28390 AATGATTTCG
28400 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
*
28434 CGTTACGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
** *
28467 CGTTGCGATAGTCATTTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
28496 AGTCTGTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.54
34 26 0.46
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.44
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
Found at i:28620 original size:14 final size:14
Alignment explanation
Indices: 28601--28637 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
28591 CATCAATTAA
28601 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
28615 ACAAATCATCTTTT
1 ACAAATCAACATTT
28629 ACAAATCAA
1 ACAAATCAA
28638 TTAAACAATC
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:30104 original size:18 final size:20
Alignment explanation
Indices: 30081--30120 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
30071 CTCTTGAGGG
30081 ATGATA-GGA-GCCTCTTGA
1 ATGATAGGGAGGCCTCTTGA
30099 ATGATAGGGGAGGCCTCTTGA
1 ATGATA-GGGAGGCCTCTTGA
30120 A
1 A
30121 CGATGACAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
20 3 0.16
21 10 0.53
ACGTcount: A:0.28, C:0.15, G:0.33, T:0.25
Consensus pattern (20 bp):
ATGATAGGGAGGCCTCTTGA
Found at i:30624 original size:14 final size:14
Alignment explanation
Indices: 30607--30639 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
30597 TCTGAAACTT
30607 AAAATCGCAACGCG
1 AAAATCGCAACGCG
30621 AAAATCGCAACGCG
1 AAAATCGCAACGCG
30635 AAAAT
1 AAAAT
30640 GACTATCGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.48, C:0.24, G:0.18, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGCG
Found at i:30649 original size:20 final size:20
Alignment explanation
Indices: 30624--30732 Score: 164
Period size: 20 Copynumber: 5.5 Consensus size: 20
30614 CAACGCGAAA
**
30624 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAATTTGACT
* **
30644 ATCGCAAAGCGAAAATGACT
1 ATCGCAACGCGAATTTGACT
30664 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
30684 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
*
30704 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
30724 ATCGCAACG
1 ATCGCAACG
30733 AGAGAATCGC
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 83 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:30804 original size:20 final size:20
Alignment explanation
Indices: 30775--30933 Score: 94
Period size: 20 Copynumber: 8.6 Consensus size: 20
30765 GCGATTCTCT
* **
30775 CATTGGGATAGTCAAATTCG
1 CATTGCGATAGTCATTTTCG
30795 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
* *
30815 CATTACAATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
30835 CGTTGCGAT--T--TTATT-G
1 CATTGCGATAGTCATT-TTCG
* **
30851 --TTACGATTTTCA-TTTCG
1 CATTGCGATAGTCATTTTCG
*
30868 CATTGCGAT--TC--TCTCG
1 CATTGCGATAGTCATTTTCG
* *
30884 --TTGCGATAATCATTTTCA
1 CATTGCGATAGTCATTTTCG
*
30902 CGTTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
30922 CATTGCGATAGT
1 CATTGCGATAGT
30934 AAACTATTCT
Statistics
Matches: 109, Mismatches: 16, Indels: 28
0.71 0.10 0.18
Matches are distributed among these distances:
14 13 0.12
16 12 0.11
17 6 0.06
18 4 0.04
19 6 0.06
20 68 0.62
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (20 bp):
CATTGCGATAGTCATTTTCG
Found at i:32830 original size:20 final size:20
Alignment explanation
Indices: 32807--32896 Score: 101
Period size: 20 Copynumber: 4.5 Consensus size: 20
32797 TCTGAAACTT
32807 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
32827 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
32847 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** *
32867 ACTATCGCAACGC-AAAATG
1 AAAATCGCAACACGAAAATG
32886 AAAATCGCAAC
1 AAAATCGCAAC
32897 GACAGAATCG
Statistics
Matches: 61, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
19 13 0.21
20 48 0.79
ACGTcount: A:0.47, C:0.23, G:0.16, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:33229 original size:22 final size:22
Alignment explanation
Indices: 33204--33257 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
33194 GGACTGTGAA
*
33204 TGATTTCGCCGGAGATGGAGAC
1 TGATATCGCCGGAGATGGAGAC
* *
33226 TGATATCGTCGGAGATGGGGAC
1 TGATATCGCCGGAGATGGAGAC
* *
33248 AGATGTCGCC
1 TGATATCGCC
33258 TTAGAGAGTG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.22
Consensus pattern (22 bp):
TGATATCGCCGGAGATGGAGAC
Found at i:33465 original size:20 final size:20
Alignment explanation
Indices: 33424--33554 Score: 194
Period size: 20 Copynumber: 6.5 Consensus size: 20
33414 GCTATGTAAA
33424 TCGCATTGCGATTGT-CAG-AT
1 TCGCATTGCGATT-TAC-GTAT
*
33444 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
*
33464 TCGCATTACGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
33484 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
33504 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* *
33524 TCACATTGCGATTTACATAT
1 TCGCATTGCGATTTACGTAT
33544 TCGCATTGCGA
1 TCGCATTGCGA
33555 ATTAGGAAAA
Statistics
Matches: 102, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
19 2 0.02
20 100 0.98
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:33575 original size:21 final size:21
Alignment explanation
Indices: 33551--33596 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
33541 TATTCGCATT
33551 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
33572 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
33593 GCGA
1 GCGA
33597 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:35242 original size:20 final size:20
Alignment explanation
Indices: 35217--35272 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
35207 ACACAAACAG
35217 ATTTAAAGGGAAAACACAAT
1 ATTTAAAGGGAAAACACAAT
*
35237 ATTTAAAGGGAAAGCACAAT
1 ATTTAAAGGGAAAACACAAT
35257 ATTTAAA-GGAAAACAC
1 ATTTAAAGGGAAAACAC
35273 GTCAATTTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 8 0.24
20 26 0.76
ACGTcount: A:0.54, C:0.11, G:0.16, T:0.20
Consensus pattern (20 bp):
ATTTAAAGGGAAAACACAAT
Found at i:35986 original size:21 final size:21
Alignment explanation
Indices: 35962--36005 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
35952 AGCAAAATTG
35962 TGCATCGATGCACTGCTACAA
1 TGCATCGATGCACTGCTACAA
*
35983 TGCATCGATGCCCTGCTACAA
1 TGCATCGATGCACTGCTACAA
36004 TG
1 TG
36006 ACTTTCGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (21 bp):
TGCATCGATGCACTGCTACAA
Found at i:39024 original size:11 final size:11
Alignment explanation
Indices: 39008--39047 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
38998 GGGCGCCTGC
39008 AAAATAAAATA
1 AAAATAAAATA
39019 AAAATAAAATA
1 AAAATAAAATA
* *
39030 TAAATATAATA
1 AAAATAAAATA
*
39041 ATAATAA
1 AAAATAA
39048 TTATTATTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:39474 original size:84 final size:84
Alignment explanation
Indices: 39338--39516 Score: 259
Period size: 84 Copynumber: 2.1 Consensus size: 84
39328 AGCTGAATGA
* * *
39338 AATCGAACTCGTCAGGTCTTTGGTTGGCAGATAGCCCTTCTTGACTTAAGTTATGCTACAAATGA
1 AATCGAACTCG-AATGTCTTTGGTTGGCAAATAGCCCTTCTTGACTTAAGTTATGCTACAAATGA
*
39403 TGTGCCTTGGAGCTGAGCGT
65 GGTGCCTTGGAGCTGAGCGT
* * * * *
39423 AGTCGAACTCGAATGTCTTTGGTTGGCAAATAGCCCTTCTTGCCTTGAGTTATGTTGCAAATGAG
1 AATCGAACTCGAATGTCTTTGGTTGGCAAATAGCCCTTCTTGACTTAAGTTATGCTACAAATGAG
*
39488 GTGCCTTGGAGCTGAGTGT
66 GTGCCTTGGAGCTGAGCGT
39507 AATCGAACTC
1 AATCGAACTC
39517 AAAGGTTTGG
Statistics
Matches: 83, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
84 73 0.88
85 10 0.12
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (84 bp):
AATCGAACTCGAATGTCTTTGGTTGGCAAATAGCCCTTCTTGACTTAAGTTATGCTACAAATGAG
GTGCCTTGGAGCTGAGCGT
Found at i:39618 original size:37 final size:37
Alignment explanation
Indices: 39557--39670 Score: 111
Period size: 37 Copynumber: 3.0 Consensus size: 37
39547 CAAAGGTTTT
* *
39557 TTTTGTGTATCAAGAGAAACTGTCTCAAGGGAGAGAAAA
1 TTTTGT-T-TCAAAAGAAAATGTCTCAAGGGAGAGAAAA
** *
39596 TTTTGTTTCAAAAGAAAATGTCTCAAAAGAGACAAAA
1 TTTTGTTTCAAAAGAAAATGTCTCAAGGGAGAGAAAA
* * * *
39633 CTTAGTTCCGAAAGAAAACTGTCTCAAGGGAGACGAAA
1 TTTTGTTTCAAAAGAAAA-TGTCTCAAGGGAGA-GAAA
39671 TATGTTTCAA
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
37 39 0.64
38 13 0.21
39 9 0.15
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (37 bp):
TTTTGTTTCAAAAGAAAATGTCTCAAGGGAGAGAAAA
Found at i:39666 original size:38 final size:38
Alignment explanation
Indices: 39568--39666 Score: 119
Period size: 37 Copynumber: 2.6 Consensus size: 38
39558 TTTGTGTATC
* * * *
39568 AAGAGAAACTGTCTCAAGGGAGAGAAAATTTTGTTTCAA
1 AAGA-AAACTGTCTCAAGGGAGACAAAACTTAGTTCCAA
** *
39607 AAGAAAA-TGTCTCAAAAGAGACAAAACTTAGTTCCGA
1 AAGAAAACTGTCTCAAGGGAGACAAAACTTAGTTCCAA
39644 AAGAAAACTGTCTCAAGGGAGAC
1 AAGAAAACTGTCTCAAGGGAGAC
39667 GAAATATGTT
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
37 30 0.60
38 16 0.32
39 4 0.08
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.20
Consensus pattern (38 bp):
AAGAAAACTGTCTCAAGGGAGACAAAACTTAGTTCCAA
Found at i:39858 original size:144 final size:138
Alignment explanation
Indices: 39557--39947 Score: 507
Period size: 144 Copynumber: 2.8 Consensus size: 138
39547 CAAAGGTTTT
* * * * *
39557 TTTTGTGTATCAAGAGAAACTGTCTCAAGGGAGAGAAAATTTTGTTTCAAAAGAAAATGTCTCAA
1 TTTTGT-T-TCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGAGAAACTGTCTCAA
* *
39622 AAGAGACAAAACTTAGTTCCGAAAGAAAACTGTCTCAAGGGAGACGAAATATGTTTCAATGAAAA
63 GAGAGACAAAACTTAGTTCCAAAAG-AAACTGTCTCAAGGGAGACGAAATATGTTTCAATGAAAA
39687 CATATTCAAAGA
127 CATATTCAAAGA
39699 TTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGACAAAATTTGTTTCAAGAGAAACTGTCT
1 TTTTGTTTCAAGGGAAACTGTCTC-A-AGAG----AGACAAAATTTGTTTCAAGAGAAACTGTCT
* * * *
39764 CAAGAGAGACAGAACTTAGTTCCAAAAGAAGCTGTCTCAAGGGAGACGGAATTTGTTT-AATGTA
60 CAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATATGTTTCAATG-A
39828 AAACATATTCAAAGA
124 AAACATATTCAAAGA
* *
39843 TTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAG
1 TTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAG
* * * * *
39908 AGATAAAATTTA-TTTCAAGAGAAACTGTCTCAAGAGAGAC
66 AGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGAC
39948 AAAACTTTGT
Statistics
Matches: 222, Mismatches: 20, Indels: 19
0.85 0.08 0.07
Matches are distributed among these distances:
137 24 0.11
138 43 0.19
140 16 0.07
141 2 0.01
142 13 0.06
143 5 0.02
144 67 0.30
145 45 0.20
146 7 0.03
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (138 bp):
TTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAG
AGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATATGTTTCAATGAAAACATA
TTCAAAGA
Found at i:39895 original size:36 final size:36
Alignment explanation
Indices: 39848--39951 Score: 190
Period size: 36 Copynumber: 2.9 Consensus size: 36
39838 AAAGATTTTG
39848 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
*
39884 TTTCAAGGGAAACTGTCTCAAGAGAGATAAAATTTA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
*
39920 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
39952 CTTTGTTTTA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 65 1.00
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.24
Consensus pattern (36 bp):
TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
Found at i:42967 original size:16 final size:17
Alignment explanation
Indices: 42946--42984 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
42936 TAAATGATAC
42946 AAAAGATGAA-AAAAAT-
1 AAAAGAT-AACAAAAATG
42962 AAAAGATAACAAAAATG
1 AAAAGATAACAAAAATG
42979 AAAAGA
1 AAAAGA
42985 GATAGTGAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.10
16 13 0.62
17 6 0.29
ACGTcount: A:0.74, C:0.03, G:0.13, T:0.10
Consensus pattern (17 bp):
AAAAGATAACAAAAATG
Found at i:42969 original size:25 final size:25
Alignment explanation
Indices: 42934--42982 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
42924 ACCTCTTTTG
*
42934 AATAAATGAT-ACAAAAGATGAAAAA
1 AATAAAAGATAACAAAA-ATGAAAAA
42959 AATAAAAGATAACAAAAATGAAAA
1 AATAAAAGATAACAAAAATGAAAA
42983 GAGATAGTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.71, C:0.04, G:0.10, T:0.14
Consensus pattern (25 bp):
AATAAAAGATAACAAAAATGAAAAA
Found at i:44181 original size:13 final size:13
Alignment explanation
Indices: 44165--44189 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44155 TAATTATAAA
44165 ATAAAATTTTTAT
1 ATAAAATTTTTAT
44178 ATAAAATTTTTA
1 ATAAAATTTTTA
44190 ATTAATTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATAAAATTTTTAT
Found at i:44239 original size:186 final size:180
Alignment explanation
Indices: 43926--44298 Score: 586
Period size: 186 Copynumber: 2.0 Consensus size: 180
43916 ATAAAAATTA
* *
43926 AATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAAT
1 AATATTTTGTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAT
*
43991 TTTAGATAATTTTTTTAATTAATATTGATTTATGTTTAAAAATTATTGGATCTTAAATTATTAAT
66 TTTAGATAATTTTTTTAATTAATATTGATTTAGGTTTAAAAATTATTGGATCTTAAATTATTAAT
*
44056 TGGGTTTTAAATGGTTTGGGAT-AAGATCATATGTTATATATAATATATTT
131 TGGGTTTTAAATGGTTTGGGATGAA-ACCATATGTTATATATAATATATTT
44106 AATATTTTGTAATTCAAAAAAATAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAA
1 AATATTTTGTAATTC-AAAAAA-AGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAA
* * *
44171 TTTTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATT
64 ATTTTAGAT--AATTTTT--TTAATTAATATTGATTTAGGTTTAAAAATTATTGGATCTTAAATT
* *
44236 ATTAATTGGGTTTTAAATGGTTTGGGCTGAACCCATATGTTATATATAATATATTT
125 ATTAATTGGGTTTTAAATGGTTTGGGATGAAACCATATGTTATATATAATATATTT
*
44292 AAAATTT
1 AATATTT
44299 AAAATTTAAT
Statistics
Matches: 176, Mismatches: 10, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
180 14 0.08
181 6 0.03
182 48 0.27
184 7 0.04
186 99 0.56
187 2 0.01
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (180 bp):
AATATTTTGTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAT
TTTAGATAATTTTTTTAATTAATATTGATTTAGGTTTAAAAATTATTGGATCTTAAATTATTAAT
TGGGTTTTAAATGGTTTGGGATGAAACCATATGTTATATATAATATATTT
Found at i:46427 original size:31 final size:30
Alignment explanation
Indices: 46392--46475 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 30
46382 GGAGTACCTT
*
46392 GGGGCCTGC-GAGCCTACCCAAGACAATTCTC
1 GGGGCC-GCAGAGCCTACCCAAGA-AAATCTC
* * *
46423 GGGGCCACAAAGGCTTACCCAAGAAAATCTC
1 GGGGCCGCAGA-GCCTACCCAAGAAAATCTC
*
46454 AGGGCCGCAGAGCCTACCCAAG
1 GGGGCCGCAGAGCCTACCCAAG
46476 GCTCGACTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
30 11 0.26
31 21 0.49
32 11 0.26
ACGTcount: A:0.29, C:0.33, G:0.26, T:0.12
Consensus pattern (30 bp):
GGGGCCGCAGAGCCTACCCAAGAAAATCTC
Found at i:47470 original size:56 final size:56
Alignment explanation
Indices: 47384--47557 Score: 233
Period size: 56 Copynumber: 3.1 Consensus size: 56
47374 ACAGTCAACT
* * * *
47384 ATTACAAAAATAACACATTTTT-TAAATAATTACGAAAATATCACTTTTTCGAAATA
1 ATTACCAAAATATCAC-TTTTTCAAAATAATTACAAAAATATCACTTTTTCGAAATA
* *
47440 ATTACCAAAATATCACTTTTTCGAAATAATTACAAAAATATCACTTTTTCAAAATA
1 ATTACCAAAATATCACTTTTTCAAAATAATTACAAAAATATCACTTTTTCGAAATA
* * *
47496 ATTACCAAAATATCACTTTTTCAAAATAATTACCAAAATATTATTTTTTTCGAAATA
1 ATTACCAAAATATCACTTTTTCAAAATAATTACAAAAATATCA-CTTTTTCGAAATA
*
47553 TTTAC
1 ATTAC
47558 GAAACTAACA
Statistics
Matches: 105, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
55 5 0.05
56 85 0.81
57 15 0.14
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.38
Consensus pattern (56 bp):
ATTACCAAAATATCACTTTTTCAAAATAATTACAAAAATATCACTTTTTCGAAATA
Found at i:47495 original size:16 final size:16
Alignment explanation
Indices: 47474--47523 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
47464 AATAATTACA
47474 AAAATATCACTTTTTC
1 AAAATATCACTTTTTC
**
47490 AAAATA--A--TTACC
1 AAAATATCACTTTTTC
47502 AAAATATCACTTTTTC
1 AAAATATCACTTTTTC
47518 AAAATA
1 AAAATA
47524 ATTACCAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
12 9 0.35
14 2 0.08
16 15 0.58
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAATATCACTTTTTC
Found at i:47525 original size:84 final size:85
Alignment explanation
Indices: 47384--47568 Score: 266
Period size: 84 Copynumber: 2.2 Consensus size: 85
47374 ACAGTCAACT
* * *
47384 ATTACAAAAATAACACATTTTTTAAATAATTACGAAAATATCACTTTTTCGAAATAATTACCAAA
1 ATTACAAAAATAACACATTTTTAAAATAATTACCAAAATATCACTTTTTCAAAATAATTACCAAA
47449 ATATCA-CTTTTTCGAAATA
66 ATATCATCTTTTTCGAAATA
*
47468 ATTACAAAAATATCAC-TTTTTCAAAATAATTACCAAAATATCACTTTTTCAAAATAATTACCAA
1 ATTACAAAAATAACACATTTTT-AAAATAATTACCAAAATATCACTTTTTCAAAATAATTACCAA
* *
47532 AATATTATTTTTTTCGAAATA
65 AATATCATCTTTTTCGAAATA
* * *
47553 TTTACGAAACTAACAC
1 ATTACAAAAATAACAC
47569 CTTCTTAACA
Statistics
Matches: 89, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
83 5 0.06
84 60 0.67
85 24 0.27
ACGTcount: A:0.46, C:0.15, G:0.03, T:0.36
Consensus pattern (85 bp):
ATTACAAAAATAACACATTTTTAAAATAATTACCAAAATATCACTTTTTCAAAATAATTACCAAA
ATATCATCTTTTTCGAAATA
Found at i:47544 original size:28 final size:28
Alignment explanation
Indices: 47384--47536 Score: 227
Period size: 28 Copynumber: 5.5 Consensus size: 28
47374 ACAGTCAACT
* * *
47384 ATTACAAAAATAACACATTTTT-TAAATA
1 ATTACCAAAATATCAC-TTTTTCAAAATA
* *
47412 ATTACGAAAATATCACTTTTTCGAAATA
1 ATTACCAAAATATCACTTTTTCAAAATA
*
47440 ATTACCAAAATATCACTTTTTCGAAATA
1 ATTACCAAAATATCACTTTTTCAAAATA
*
47468 ATTACAAAAATATCACTTTTTCAAAATA
1 ATTACCAAAATATCACTTTTTCAAAATA
47496 ATTACCAAAATATCACTTTTTCAAAATA
1 ATTACCAAAATATCACTTTTTCAAAATA
47524 ATTACCAAAATAT
1 ATTACCAAAATAT
47537 TATTTTTTTC
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
27 5 0.04
28 112 0.96
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.35
Consensus pattern (28 bp):
ATTACCAAAATATCACTTTTTCAAAATA
Found at i:47584 original size:29 final size:29
Alignment explanation
Indices: 47549--47615 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
47539 TTTTTTTCGA
47549 AATATTTACGAAACTAACACCTTCTTAAC
1 AATATTTACGAAACTAACACCTTCTTAAC
* ** *
47578 AGTATTTACGAAACTAACATTTTTTTAAC
1 AATATTTACGAAACTAACACCTTCTTAAC
47607 AATATTTAC
1 AATATTTAC
47616 ATAACATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.37
Consensus pattern (29 bp):
AATATTTACGAAACTAACACCTTCTTAAC
Found at i:47626 original size:25 final size:25
Alignment explanation
Indices: 47592--47641 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
47582 TTTACGAAAC
47592 TAACATTTTTTTAACAATATTTACA
1 TAACATTTTTTTAACAATATTTACA
47617 TAACATTTTTTTAACAATATTTACA
1 TAACATTTTTTTAACAATATTTACA
47642 AAAATACCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (25 bp):
TAACATTTTTTTAACAATATTTACA
Found at i:48223 original size:20 final size:21
Alignment explanation
Indices: 48189--48239 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
48179 CTCCCACTTC
*
48189 ATTTTATCT-TAGTGCTAAT-
1 ATTTTATTTATAGTGCTAATA
*
48208 ATTTTATTTATAGTGCTATTA
1 ATTTTATTTATAGTGCTAATA
48229 ATTTT-TTTATA
1 ATTTTATTTATA
48240 TTATATTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 8 0.29
20 15 0.54
21 5 0.18
ACGTcount: A:0.27, C:0.06, G:0.08, T:0.59
Consensus pattern (21 bp):
ATTTTATTTATAGTGCTAATA
Found at i:56929 original size:19 final size:21
Alignment explanation
Indices: 56892--56934 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
56882 TAACTTTTTC
56892 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
56912 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
56932 TTT
1 TTT
56935 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:56940 original size:19 final size:20
Alignment explanation
Indices: 56891--56940 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
56881 TTAACTTTTT
*
56891 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
56911 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
56930 CTTTTACCTTT
1 CTTTTACCTTT
56941 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Done.