Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006735.1 Hibiscus syriacus cultivar Beakdansim tig00016902_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: 77560
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:999 original size:24 final size:24
Alignment explanation
Indices: 972--1071 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
962 GATATCAAAA
*
972 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
996 ATCATAACAGAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
1020 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
1044 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
1068 ATCA
1 ATCA
1072 GATAAAATAT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:1071 original size:48 final size:48
Alignment explanation
Indices: 965--1073 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
955 AAACGGAGAT
* * * * *
965 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
1013 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
1061 ATCAGAAATCAGA
1 ATCAGAAATCAGA
1074 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:3550 original size:7 final size:7
Alignment explanation
Indices: 3538--3577 Score: 62
Period size: 7 Copynumber: 5.4 Consensus size: 7
3528 TGGTCAACTC
3538 CGGTCAA
1 CGGTCAA
3545 CGGTCAA
1 CGGTCAA
3552 CGGGTCAA
1 C-GGTCAA
3560 CGGTCAA
1 CGGTCAA
3567 CGGGTCAA
1 C-GGTCAA
3575 CGG
1 CGG
3578 GTCGGGTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 17 0.55
8 14 0.45
ACGTcount: A:0.25, C:0.28, G:0.35, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:3559 original size:8 final size:8
Alignment explanation
Indices: 3539--3593 Score: 75
Period size: 8 Copynumber: 7.5 Consensus size: 8
3529 GGTCAACTCC
3539 GGTCAAC-
1 GGTCAACG
3546 GGTCAACG
1 GGTCAACG
3554 GGTCAAC-
1 GGTCAACG
3561 GGTCAACG
1 GGTCAACG
3569 GGTCAACG
1 GGTCAACG
3577 GGT---CG
1 GGTCAACG
3582 GGTCAACG
1 GGTCAACG
3590 GGTC
1 GGTC
3594 GGGTCGGGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.12
7 14 0.33
8 24 0.56
ACGTcount: A:0.22, C:0.25, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:3559 original size:15 final size:15
Alignment explanation
Indices: 3539--3577 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
3529 GGTCAACTCC
3539 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
3554 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
3569 GGTCAACGG
1 GGTCAACGG
3578 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.36, T:0.13
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:3585 original size:13 final size:13
Alignment explanation
Indices: 3567--3598 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
3557 CAACGGTCAA
3567 CGGGTCAACGGGT
1 CGGGTCAACGGGT
3580 CGGGTCAACGGGT
1 CGGGTCAACGGGT
3593 CGGGTC
1 CGGGTC
3599 GGGTCAACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.25, G:0.47, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:3605 original size:31 final size:31
Alignment explanation
Indices: 3567--3646 Score: 135
Period size: 31 Copynumber: 2.6 Consensus size: 31
3557 CAACGGTCAA
3567 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
* *
3598 CGGGTCAACAGGTCGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
3629 CGGGT-AACGGGTCGGGTC
1 CGGGTCAACGGGTCGGGTC
3647 GGGTTGTGAC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 11 0.24
31 34 0.76
ACGTcount: A:0.15, C:0.21, G:0.47, T:0.16
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
Found at i:3611 original size:13 final size:13
Alignment explanation
Indices: 3595--3629 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
3585 CAACGGGTCG
3595 GGTCGGGTCAACA
1 GGTCGGGTCAACA
* *
3608 GGTCGGGTAAACG
1 GGTCGGGTCAACA
3621 GGTCGGGTC
1 GGTCGGGTC
3630 GGGTAACGGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.17, C:0.20, G:0.46, T:0.17
Consensus pattern (13 bp):
GGTCGGGTCAACA
Found at i:5817 original size:24 final size:24
Alignment explanation
Indices: 5790--5889 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
5780 GATATCAAAA
*
5790 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
5814 ATCATAACAGAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
5838 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
5862 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
5886 ATCA
1 ATCA
5890 GATAAAATAT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:5889 original size:48 final size:48
Alignment explanation
Indices: 5783--5891 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
5773 AAACGGAGAT
* * * * *
5783 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
5831 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
5879 ATCAGAAATCAGA
1 ATCAGAAATCAGA
5892 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:8386 original size:7 final size:7
Alignment explanation
Indices: 8374--8413 Score: 62
Period size: 7 Copynumber: 5.4 Consensus size: 7
8364 TGGTCAACTC
8374 CGGTCAA
1 CGGTCAA
8381 CGGTCAA
1 CGGTCAA
8388 CGGGTCAA
1 C-GGTCAA
8396 CGGTCAA
1 CGGTCAA
8403 CGGGTCAA
1 C-GGTCAA
8411 CGG
1 CGG
8414 GTCGGGTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 17 0.55
8 14 0.45
ACGTcount: A:0.25, C:0.28, G:0.35, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:8395 original size:8 final size:8
Alignment explanation
Indices: 8375--8429 Score: 75
Period size: 8 Copynumber: 7.5 Consensus size: 8
8365 GGTCAACTCC
8375 GGTCAAC-
1 GGTCAACG
8382 GGTCAACG
1 GGTCAACG
8390 GGTCAAC-
1 GGTCAACG
8397 GGTCAACG
1 GGTCAACG
8405 GGTCAACG
1 GGTCAACG
8413 GGT---CG
1 GGTCAACG
8418 GGTCAACG
1 GGTCAACG
8426 GGTC
1 GGTC
8430 GGGTCGGGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.12
7 14 0.33
8 24 0.56
ACGTcount: A:0.22, C:0.25, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:8395 original size:15 final size:15
Alignment explanation
Indices: 8375--8413 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
8365 GGTCAACTCC
8375 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
8390 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
8405 GGTCAACGG
1 GGTCAACGG
8414 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.36, T:0.13
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:8421 original size:13 final size:13
Alignment explanation
Indices: 8403--8434 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
8393 CAACGGTCAA
8403 CGGGTCAACGGGT
1 CGGGTCAACGGGT
8416 CGGGTCAACGGGT
1 CGGGTCAACGGGT
8429 CGGGTC
1 CGGGTC
8435 GGGTCAACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.25, G:0.47, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:8434 original size:18 final size:18
Alignment explanation
Indices: 8397--8487 Score: 93
Period size: 18 Copynumber: 5.2 Consensus size: 18
8387 ACGGGTCAAC
8397 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
8418 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
8436 GGTCAA-----CAGGTCG
1 GGTCAACGGGTCGGGTCG
*
8449 GGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
8467 GGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
8485 GGT
1 GGT
8488 TGTGACCGGT
Statistics
Matches: 62, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
13 11 0.18
18 40 0.65
21 11 0.18
ACGTcount: A:0.16, C:0.20, G:0.47, T:0.16
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:8441 original size:31 final size:31
Alignment explanation
Indices: 8403--8483 Score: 135
Period size: 31 Copynumber: 2.6 Consensus size: 31
8393 CAACGGTCAA
8403 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
* *
8434 CGGGTCAACAGGTCGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
*
8465 CGGGTAAACGGGTCGGGTC
1 CGGGTCAACGGGTCGGGTC
8484 GGGTTGTGAC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.16, C:0.21, G:0.47, T:0.16
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
Found at i:8482 original size:13 final size:13
Alignment explanation
Indices: 8429--8464 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
8419 GTCAACGGGT
*
8429 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
*
8442 CAGGTCGGGTAAA
1 CGGGTCGGGTAAA
8455 CGGGTCGGGT
1 CGGGTCGGGT
8465 CGGGTAAACG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.17, C:0.19, G:0.47, T:0.17
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:9467 original size:20 final size:20
Alignment explanation
Indices: 9442--9499 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
9432 ATTCATTTGA
9442 CTATCGCAACGCGAAAATGC
1 CTATCGCAACGCGAAAATGC
*
9462 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGC
*
9482 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
9500 CGCAATGCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGC
Found at i:9540 original size:19 final size:19
Alignment explanation
Indices: 9518--9571 Score: 108
Period size: 19 Copynumber: 2.8 Consensus size: 19
9508 AAAATGAAAA
9518 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
9537 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
9556 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
9572 TCGTTGCGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:9589 original size:33 final size:35
Alignment explanation
Indices: 9518--9600 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 35
9508 AAAATGAAAA
**
9518 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTC--TTCG-ATTGCGATTGCCATT
9556 TCGCATTGCGATTTTC-TCG-TTGCGATTGCCATT
1 TCGCATTGCGATTTTCTTCGATTGCGATTGCCATT
*
9589 TCGCGTTGCGAT
1 TCGCATTGCGAT
9601 AGTCTGTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
33 23 0.55
35 3 0.07
38 16 0.38
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.43
Consensus pattern (35 bp):
TCGCATTGCGATTTTCTTCGATTGCGATTGCCATT
Found at i:9707 original size:14 final size:14
Alignment explanation
Indices: 9688--9724 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
9678 CATCAATTAA
9688 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
9702 ACAAATCATCTTTT
1 ACAAATCAACATTT
9716 ACAAATCAA
1 ACAAATCAA
9725 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:11610 original size:20 final size:19
Alignment explanation
Indices: 11587--11654 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
11577 GAAACTTAAA
11587 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
11607 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
11627 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
11646 ATCGCAACG
1 ATCGCAACG
11655 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 14 0.34
20 26 0.63
21 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:11662 original size:14 final size:14
Alignment explanation
Indices: 11643--11699 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 14
11633 ATGCGAAATG
11643 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
11657 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
11673 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
11689 AAAATCGCAAC
1 AAAATCGCAAC
11700 ACGAAACACA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.49, C:0.26, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:11685 original size:32 final size:33
Alignment explanation
Indices: 11627--11705 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
11617 GGAAATGGCT
*
11627 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
11660 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
11692 ATCGCAACACGAAA
1 ATCGCAACGCGAAA
11706 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.48, C:0.24, G:0.18, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:11753 original size:14 final size:14
Alignment explanation
Indices: 11734--11791 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
11724 TTTCATTTCG
11734 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
11748 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
11764 CGCATTGCAATTTTGT
1 CG--TTGCGATTTTGT
11780 CGTTGCGATTTT
1 CGTTGCGATTTT
11792 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:11764 original size:32 final size:33
Alignment explanation
Indices: 11717--11807 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
11707 ACAAATCGCA
*
11717 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
11750 TTGCGA-TTTCATTTCGCATTGCAATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
11782 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
11808 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:11843 original size:20 final size:20
Alignment explanation
Indices: 11792--11835 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
11782 TTGCGATTTT
* *
11792 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGTGATAGC
*
11811 CATTTCCGCGTTGTGATAGT
1 CATTTCCGCGTTGTGATAGC
11831 CATTT
1 CATTT
11836 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (20 bp):
CATTTCCGCGTTGTGATAGC
Found at i:12354 original size:18 final size:18
Alignment explanation
Indices: 12328--12372 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
12318 GTCGATCAGA
* *
12328 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTAGGCGAGG
*
12346 TGATAGCTCTAGGCGAGG
1 TGATGGCTCTAGGCGAGG
12364 TGATGGCTC
1 TGATGGCTC
12373 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:13717 original size:20 final size:20
Alignment explanation
Indices: 13692--13729 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
13682 AATAGTTTCT
13692 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
13712 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
13730 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:14020 original size:22 final size:22
Alignment explanation
Indices: 13993--14036 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
13983 GATGGAGATA
13993 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
14015 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
14037 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:14249 original size:20 final size:20
Alignment explanation
Indices: 14224--14317 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
14214 GATTATGTAT
14224 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
14244 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
14264 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
14285 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
14305 TATCGCATTGCGA
1 TATCGCGTTGCGA
14318 TTTTCCCAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 45 0.73
21 12 0.19
22 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:14289 original size:41 final size:41
Alignment explanation
Indices: 14244--14321 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
14234 CGAAAGTCAG
* * *
14244 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTGTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTGTAT
* *
14285 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
14322 CCCAATTCGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTGTAT
Found at i:14318 original size:20 final size:19
Alignment explanation
Indices: 14204--14318 Score: 86
Period size: 20 Copynumber: 5.7 Consensus size: 19
14194 CGCTTTGAAA
*
14204 ATCGCATTGCGATTATGTATT
1 ATCGCATTGCGA-TA-GTAGT
* *
14225 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGT-AGT
* *
14245 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGT-AGT
* * * *
14265 ATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGA--TAGTAGT
14286 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGT-AGT
14306 ATCGCATTGCGAT
1 ATCGCATTGCGAT
14319 TTTCCCAATT
Statistics
Matches: 78, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
19 5 0.06
20 48 0.62
21 23 0.29
22 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (19 bp):
ATCGCATTGCGATAGTAGT
Found at i:14337 original size:41 final size:41
Alignment explanation
Indices: 14244--14339 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 41
14234 CGAAAGTCAG
* * * ** *
14244 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
* *
14285 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAA
14327 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
14340 TTACTTATTC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 43 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
Found at i:15160 original size:18 final size:18
Alignment explanation
Indices: 15137--15172 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
15127 AGTGTCTCCT
15137 GCACCCGATAATAGGGAG
1 GCACCCGATAATAGGGAG
*
15155 GCACCCGATATTAGGGAG
1 GCACCCGATAATAGGGAG
15173 CAGATCTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.22, G:0.33, T:0.14
Consensus pattern (18 bp):
GCACCCGATAATAGGGAG
Found at i:15379 original size:20 final size:20
Alignment explanation
Indices: 15354--15403 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
15344 CGCTATAGTT
*
15354 GGTAGCAACCCGACCAACCA
1 GGTAGCAACCCAACCAACCA
15374 GGTAGCAACCCAACCAACCA
1 GGTAGCAACCCAACCAACCA
15394 GGTAGCAACC
1 GGTAGCAACC
15404 AACTATAGCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.36, C:0.38, G:0.20, T:0.06
Consensus pattern (20 bp):
GGTAGCAACCCAACCAACCA
Found at i:25603 original size:17 final size:17
Alignment explanation
Indices: 25581--25618 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
25571 GTGCAAATAG
25581 CACTTTTCAATAATTGA
1 CACTTTTCAATAATTGA
25598 CACTTTTCAATAATTGA
1 CACTTTTCAATAATTGA
25615 CACT
1 CACT
25619 ATGTTATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.39
Consensus pattern (17 bp):
CACTTTTCAATAATTGA
Found at i:25739 original size:17 final size:17
Alignment explanation
Indices: 25700--25740 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
25690 CGCCTTTGAA
25700 ATTTTTAAATTCCTTTAT
1 ATTTTTAAATT-CTTTAT
25718 A-TTTTAAATT-TTTAT
1 ATTTTTAAATTCTTTAT
25733 GATTTTTA
1 -ATTTTTA
25741 TTTGTTTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 5 0.24
16 1 0.05
17 14 0.67
18 1 0.05
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (17 bp):
ATTTTTAAATTCTTTAT
Found at i:26757 original size:21 final size:19
Alignment explanation
Indices: 26728--26768 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
26718 CCTCAAAAAC
26728 ATTAATAAATTATTTCAAATT
1 ATTAATAAATTA--TCAAATT
*
26749 ATTATTAAATTATCAAATT
1 ATTAATAAATTATCAAATT
26768 A
1 A
26769 AAATATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
21 11 0.58
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTAATAAATTATCAAATT
Found at i:28437 original size:13 final size:13
Alignment explanation
Indices: 28405--28429 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28395 AATAAAATTT
28405 TATAATTGAATAA
1 TATAATTGAATAA
28418 TATAATTGAATA
1 TATAATTGAATA
28430 TTTGAATTTA
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:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (13 bp):
TATAATTGAATAA
Found at i:30209 original size:32 final size:32
Alignment explanation
Indices: 30167--30266 Score: 139
Period size: 33 Copynumber: 3.1 Consensus size: 32
30157 AAAATTTTTG
*
30167 AATTGTTACAAAATGATCATTGAGGTTTATCA
1 AATTGTTACAAAATGATCATTGAGATTTATCA
* * *
30199 AATTGCTACAAAATTATCATTGAAGTTTTATCA
1 AATTGTTACAAAATGATCATTG-AGATTTATCA
*
30232 AATTGTTACAAAATGATCATT-AAATTTATCA
1 AATTGTTACAAAATGATCATTGAGATTTATCA
30263 AATT
1 AATT
30267 TTTTCACTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
31 12 0.20
32 20 0.33
33 28 0.47
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (32 bp):
AATTGTTACAAAATGATCATTGAGATTTATCA
Found at i:30263 original size:31 final size:32
Alignment explanation
Indices: 30142--30266 Score: 146
Period size: 31 Copynumber: 3.9 Consensus size: 32
30132 TTCCAAAAAC
* * **
30142 TACAAAATGGTCATTAAAATTT-TTGAATTGT
1 TACAAAATGATCATTGAAATTTATCAAATTGT
** *
30173 TACAAAATGATCATTGAGGTTTATCAAATTGC
1 TACAAAATGATCATTGAAATTTATCAAATTGT
* *
30205 TACAAAATTATCATTGAAGTTTTATCAAATTGT
1 TACAAAATGATCATTGAA-ATTTATCAAATTGT
30238 TACAAAATGATCATT-AAATTTATCAAATT
1 TACAAAATGATCATTGAAATTTATCAAATT
30267 TTTTCACTTA
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
31 29 0.37
32 24 0.30
33 26 0.33
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (32 bp):
TACAAAATGATCATTGAAATTTATCAAATTGT
Found at i:33946 original size:106 final size:107
Alignment explanation
Indices: 33808--34006 Score: 346
Period size: 106 Copynumber: 1.9 Consensus size: 107
33798 TCCACGCATC
* *
33808 CCTCCTTTTCTACTGGGGGAAGGAGAAAAAGAAAATTCATCTAGCTTAGTTATTGGATAATGTGA
1 CCTCCTTTTCTACTGGGGGAAGGAGAAAAAGAAAATTCATCTAGCTTAGTTATTGGACAATATGA
33873 CTTTCTTTATGGGATTGTTCAAAAAAAAAAACACGTCGATGA
66 CTTTCTTTATGGGATTGTTCAAAAAAAAAAACACGTCGATGA
* *
33915 CCTCCTTTTCTACT-GGGGAAGGAGAAAAAGAAAATTCATCTGGCTTAGTTATTGGGCAATATGA
1 CCTCCTTTTCTACTGGGGGAAGGAGAAAAAGAAAATTCATCTAGCTTAGTTATTGGACAATATGA
*
33979 CTTTCTTTATGGGATTGTTCCAAAAAAA
66 CTTTCTTTATGGGATTGTTCAAAAAAAA
34007 TAGTCGAGGA
Statistics
Matches: 87, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
106 73 0.84
107 14 0.16
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.32
Consensus pattern (107 bp):
CCTCCTTTTCTACTGGGGGAAGGAGAAAAAGAAAATTCATCTAGCTTAGTTATTGGACAATATGA
CTTTCTTTATGGGATTGTTCAAAAAAAAAAACACGTCGATGA
Found at i:44548 original size:10 final size:10
Alignment explanation
Indices: 44535--44559 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
44525 TCCTACACAC
44535 ATATACATAT
1 ATATACATAT
44545 ATATACATAT
1 ATATACATAT
44555 ATATA
1 ATATA
44560 ATCTTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (10 bp):
ATATACATAT
Found at i:56268 original size:31 final size:31
Alignment explanation
Indices: 56211--56269 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
56201 AGTTGTATGG
**
56211 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATTTCAGTATTACAAAACTAAA
56242 ATTATTTAAATTTCAGTATTACAAAACT
1 ATTATTTAAATTTCAGTATTACAAAACT
56270 TTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTACAAAACTAAA
Found at i:70888 original size:17 final size:18
Alignment explanation
Indices: 70869--70927 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 18
70859 ATTTTTTAAA
70869 TAAAAATATTTAAAATA-
1 TAAAAATATTTAAAATAC
* *
70886 TAAAAATATTCAAAA-AG
1 TAAAAATATTTAAAATAC
* *
70903 TAAATATA-ATAAAATAC
1 TAAAAATATTTAAAATAC
70920 TAAAAATA
1 TAAAAATA
70928 AAAATTAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
16 5 0.15
17 29 0.85
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (18 bp):
TAAAAATATTTAAAATAC
Found at i:71001 original size:16 final size:16
Alignment explanation
Indices: 70980--71011 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
70970 TGAATTTAAC
70980 AATTTTTATTTTAAAT
1 AATTTTTATTTTAAAT
70996 AATTTTTATTTTAAAT
1 AATTTTTATTTTAAAT
71012 CTAAACGCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
AATTTTTATTTTAAAT
Found at i:72321 original size:60 final size:61
Alignment explanation
Indices: 72193--72356 Score: 165
Period size: 60 Copynumber: 2.7 Consensus size: 61
72183 TATAATTCTT
** * * * ** *
72193 ATTTTAAATTG-GTCCTTAAAATTTTAAATATTCTAATTTTATCCCTAAATTATGACTCTC
1 ATTTTAAATTGAACCCTTAAAATTTTAAATATTCCAATTTCATCCCTAAACTACAACCCTC
*
72253 ATTTTAAATT-AACCCTTAAACTTTTAAATATTCCAATTTCATCCCTAAACTACAACCCTC
1 ATTTTAAATTGAACCCTTAAAATTTTAAATATTCCAATTTCATCCCTAAACTACAACCCTC
** * * *
72313 -TTTCTAAATTGGTCCC-TAAAGTTTTGAATATTCCAAATTCATCC
1 ATTT-TAAATTGAACCCTTAAAATTTTAAATATTCCAATTTCATCC
72357 TCAAATTCAT
Statistics
Matches: 87, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
59 3 0.03
60 81 0.93
61 3 0.03
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.41
Consensus pattern (61 bp):
ATTTTAAATTGAACCCTTAAAATTTTAAATATTCCAATTTCATCCCTAAACTACAACCCTC
Found at i:74043 original size:20 final size:20
Alignment explanation
Indices: 74018--74062 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
74008 TGTGAATTGA
*
74018 ATTTTCTTCAATTACTACTT
1 ATTTTCTTCAATTACTACCT
74038 ATTTTCTTCAATTACTACCT
1 ATTTTCTTCAATTACTACCT
74058 ATTTT
1 ATTTT
74063 ATGATTATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTTCTTCAATTACTACCT
Found at i:76982 original size:17 final size:18
Alignment explanation
Indices: 76950--76983 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
76940 GAGTATGAAA
76950 AAGTCATTATATTGTCTT
1 AAGTCATTATATTGTCTT
76968 AAGTCATTA-ATTGTCT
1 AAGTCATTATATTGTCT
76984 AGTTTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (18 bp):
AAGTCATTATATTGTCTT
Done.