Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002742.1 Hibiscus syriacus cultivar Beakdansim tig00005652_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: 59701
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:831 original size:35 final size:35
Alignment explanation
Indices: 792--858 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
782 TTGAAAGTTC
*
792 ATTTCGTAGTTTGCTAGTTGTTAATTGTTTTATCA
1 ATTTCGTAGTTTGCTAGTTATTAATTGTTTTATCA
827 ATTTCGTAGTTTGCTAGTTATTAATTGTTTTA
1 ATTTCGTAGTTTGCTAGTTATTAATTGTTTTA
859 AGTGTTAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.21, C:0.07, G:0.16, T:0.55
Consensus pattern (35 bp):
ATTTCGTAGTTTGCTAGTTATTAATTGTTTTATCA
Found at i:2529 original size:39 final size:39
Alignment explanation
Indices: 2485--2587 Score: 152
Period size: 39 Copynumber: 2.6 Consensus size: 39
2475 ACAGCAACCC
*
2485 CCTCCTCCCTCAACTTCACCACCCCCGCCAACGGCAGCA
1 CCTCCTCCCTCAACTTCACCACCCCCGCCAACAGCAGCA
** **
2524 CCTCCTCCCTCAACTTCACCACCTACTTCAACAGCAGCA
1 CCTCCTCCCTCAACTTCACCACCCCCGCCAACAGCAGCA
*
2563 CCTCCACCCTCAACTTCACCACCCC
1 CCTCCTCCCTCAACTTCACCACCCC
2588 TTCAACAGCA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.22, C:0.55, G:0.06, T:0.17
Consensus pattern (39 bp):
CCTCCTCCCTCAACTTCACCACCCCCGCCAACAGCAGCA
Found at i:2537 original size:21 final size:21
Alignment explanation
Indices: 2463--2576 Score: 60
Period size: 18 Copynumber: 5.7 Consensus size: 21
2453 CACCACTGCT
* * *
2463 CCTCCACCCTCAACAGCAACCC
1 CCTCCTCCCTCAACAGC-AGCA
** *
2485 CCTCCTCCCTCAACTTCACCA
1 CCTCCTCCCTCAACAGCAGCA
* *
2506 CC-CC-CGC-CAACGGCAGCA
1 CCTCCTCCCTCAACAGCAGCA
** *
2524 CCTCCTCCCTCAACTTCACCA
1 CCTCCTCCCTCAACAGCAGCA
*
2545 CCTACT---TCAACAGCAGCA
1 CCTCCTCCCTCAACAGCAGCA
*
2563 CCTCCACCCTCAAC
1 CCTCCTCCCTCAAC
2577 TTCACCACCC
Statistics
Matches: 68, Mismatches: 18, Indels: 13
0.69 0.18 0.13
Matches are distributed among these distances:
18 23 0.34
19 4 0.06
20 4 0.06
21 23 0.34
22 14 0.21
ACGTcount: A:0.24, C:0.55, G:0.06, T:0.15
Consensus pattern (21 bp):
CCTCCTCCCTCAACAGCAGCA
Found at i:2585 original size:21 final size:21
Alignment explanation
Indices: 2463--2585 Score: 78
Period size: 21 Copynumber: 6.1 Consensus size: 21
2453 CACCACTGCT
* *
2463 CCTCCACCCTCAACAGCAACCC
1 CCTCCACCCTCAACTGC-ACCA
* *
2485 CCTCCTCCCTCAACTTCACCA
1 CCTCCACCCTCAACTGCACCA
* * *
2506 CC-CC-CGC-CAACGGCAGCA
1 CCTCCACCCTCAACTGCACCA
* *
2524 CCTCCTCCCTCAACTTCACCA
1 CCTCCACCCTCAACTGCACCA
* * *
2545 CCT--A-CTTCAACAGCAGCA
1 CCTCCACCCTCAACTGCACCA
*
2563 CCTCCACCCTCAACTTCACCA
1 CCTCCACCCTCAACTGCACCA
2584 CC
1 CC
2586 CCTTCAACAG
Statistics
Matches: 74, Mismatches: 21, Indels: 13
0.69 0.19 0.12
Matches are distributed among these distances:
18 23 0.31
19 4 0.05
20 5 0.07
21 28 0.38
22 14 0.19
ACGTcount: A:0.24, C:0.55, G:0.06, T:0.15
Consensus pattern (21 bp):
CCTCCACCCTCAACTGCACCA
Found at i:3571 original size:20 final size:20
Alignment explanation
Indices: 3548--3602 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
3538 GCAATGCGAA
3548 TTCCAATTTCGCAACCCAGT
1 TTCCAATTTCGCAACCCAGT
3568 TTCCAATTTCGCAACCCAGT
1 TTCCAATTTCGCAACCCAGT
3588 TTCCAATTTCGCAAC
1 TTCCAATTTCGCAAC
3603 GTGAATATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.25, C:0.35, G:0.09, T:0.31
Consensus pattern (20 bp):
TTCCAATTTCGCAACCCAGT
Found at i:4603 original size:24 final size:24
Alignment explanation
Indices: 4576--4622 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
4566 AGTCAGTATT
4576 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATCTTGGTCAATACC
*
4600 CGAACTTTGATCTTGGTCAATAC
1 CGAAATTTGATCTTGGTCAATAC
4623 TCGATTTTGA
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):
CGAAATTTGATCTTGGTCAATACC
Found at i:6722 original size:18 final size:18
Alignment explanation
Indices: 6701--6736 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
6691 CAAGCAAAAG
*
6701 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
6719 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
6737 CAACCGGCTT
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:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:7045 original size:20 final size:20
Alignment explanation
Indices: 7020--7070 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
7010 ATGTTACGAT
*
7020 CAACGCGAAAGTCAAATTTG
1 CAACGCGAAAGTCAAATTCG
*
7040 CAACGCAAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
*
7060 CAACGTGAAAG
1 CAACGCGAAAG
7071 CGTTGCGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.43, C:0.22, G:0.20, T:0.16
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCG
Found at i:7188 original size:14 final size:13
Alignment explanation
Indices: 7169--7218 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
7159 AATCAATTAA
7169 ACATTATTGTGGGT
1 ACATTATT-TGGGT
*
7183 ACATTATTT--GA
1 ACATTATTTGGGT
*
7194 ACATTGTTATGGGT
1 ACATTATT-TGGGT
7208 ACATTATTTGG
1 ACATTATTTGG
7219 AAAAATAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
11 8 0.28
12 1 0.03
13 4 0.14
14 16 0.55
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (13 bp):
ACATTATTTGGGT
Found at i:7196 original size:25 final size:25
Alignment explanation
Indices: 7168--7217 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
7158 AAATCAATTA
*
7168 AACATTATTGTGGGTACATTATTTG
1 AACATTATTATGGGTACATTATTTG
*
7193 AACATTGTTATGGGTACATTATTTG
1 AACATTATTATGGGTACATTATTTG
7218 GAAAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.44
Consensus pattern (25 bp):
AACATTATTATGGGTACATTATTTG
Found at i:7623 original size:18 final size:18
Alignment explanation
Indices: 7602--7648 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
7592 GTAATTGGAG
7602 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
7620 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
7638 TATCAATTTAA
1 TTTGAATTTAA
7649 CCTTGATGTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.49
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:7646 original size:24 final size:24
Alignment explanation
Indices: 7594--7646 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
7584 TTTCATATGT
* *
7594 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
7618 AATTTGAGTTTGAATTTCAATATC
1 AATTTGAGTTTGAATTTAAATATC
7642 AATTT
1 AATTT
7647 AACCTTGATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:7654 original size:24 final size:24
Alignment explanation
Indices: 7603--7654 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
7593 TAATTGGAGT
* * **
7603 TTGAATTTAAATTTCAATTTGAGT
1 TTGAATTTAAATATCAATTTAACC
*
7627 TTGAATTTCAATATCAATTTAACC
1 TTGAATTTAAATATCAATTTAACC
7651 TTGA
1 TTGA
7655 TGTTGTATGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.46
Consensus pattern (24 bp):
TTGAATTTAAATATCAATTTAACC
Found at i:9289 original size:21 final size:21
Alignment explanation
Indices: 9265--9359 Score: 106
Period size: 21 Copynumber: 4.6 Consensus size: 21
9255 GGCGGGACCA
* *
9265 CTTGAACGATGACAGGGGCCT
1 CTTGAATGATGAGAGGGGCCT
* *
9286 CTTGAATGGTGAGAGGGGCTT
1 CTTGAATGATGAGAGGGGCCT
9307 CTTCG-ATGATGAGAGGGGCCT
1 CTT-GAATGATGAGAGGGGCCT
*
9328 -TTGAACGAT-AGGAGGGGCCT
1 CTTGAATGATGA-GAGGGGCCT
9348 CTTGAATGATGA
1 CTTGAATGATGA
9360 TAGGTGCATC
Statistics
Matches: 61, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
19 2 0.03
20 15 0.25
21 42 0.69
22 2 0.03
ACGTcount: A:0.23, C:0.16, G:0.37, T:0.24
Consensus pattern (21 bp):
CTTGAATGATGAGAGGGGCCT
Found at i:9344 original size:41 final size:42
Alignment explanation
Indices: 9265--9359 Score: 106
Period size: 41 Copynumber: 2.3 Consensus size: 42
9255 GGCGGGACCA
* * * *
9265 CTTGAACGATGACAGGGGCCTCTTGAATGGTGAGAGGGGCTT
1 CTTGAATGATGACAGGGGCCTCTTGAACGATGAGAGGGGCCT
*
9307 CTTCG-ATGATGAGAGGGGCCT-TTGAACGAT-AGGAGGGGCCT
1 CTT-GAATGATGACAGGGGCCTCTTGAACGATGA-GAGGGGCCT
9348 CTTGAATGATGA
1 CTTGAATGATGA
9360 TAGGTGCATC
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
40 2 0.04
41 25 0.56
42 17 0.38
43 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.37, T:0.24
Consensus pattern (42 bp):
CTTGAATGATGACAGGGGCCTCTTGAACGATGAGAGGGGCCT
Found at i:11515 original size:20 final size:20
Alignment explanation
Indices: 11492--11542 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
11482 AGAAGTTTCT
*
11492 GAAACTTAAATTCACAACGC
1 GAAACTAAAATTCACAACGC
* * *
11512 GAAAATAAAAATCGCAACGC
1 GAAACTAAAATTCACAACGC
11532 GAAACTAAAAT
1 GAAACTAAAAT
11543 CGCTTTGCGA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.53, C:0.20, G:0.12, T:0.16
Consensus pattern (20 bp):
GAAACTAAAATTCACAACGC
Found at i:11875 original size:22 final size:22
Alignment explanation
Indices: 11845--11892 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
11835 GATGGAGATA
*
11845 GACGGATTTCGTCGGAAATGGG
1 GACGAATTTCGTCGGAAATGGG
*
11867 GACGAATTTCGTCGGAGATGGG
1 GACGAATTTCGTCGGAAATGGG
11889 GACG
1 GACG
11893 GATGTAGCCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.23, C:0.15, G:0.42, T:0.21
Consensus pattern (22 bp):
GACGAATTTCGTCGGAAATGGG
Found at i:12047 original size:20 final size:19
Alignment explanation
Indices: 12022--12166 Score: 109
Period size: 20 Copynumber: 7.3 Consensus size: 19
12012 CGTGTAAAAC
12022 ATTTGACTGTCGCGTTGCGA
1 ATTTGACT-TCGCGTTGCGA
* *
12042 ATTTGACTTCTGTGTTACG-
1 ATTTGACTTC-GCGTTGCGA
12061 ATTT-ACAAATTCGCGTTGCGA
1 ATTTGAC---TTCGCGTTGCGA
*
12082 ATTTGACTATCGCTTTGCGA
1 ATTTGACT-TCGCGTTGCGA
*
12102 ATTTGACTTCTGTGTTGCG-
1 ATTTGACTTC-GCGTTGCGA
*
12121 ATTT-ACAAATTCGCGTTACGA
1 ATTTGAC---TTCGCGTTGCGA
*
12142 ATTTGACTTTCGCATTGCGA
1 ATTTGAC-TTCGCGTTGCGA
12162 ATTTG
1 ATTTG
12167 GAAAAGCGCA
Statistics
Matches: 100, Mismatches: 12, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
18 4 0.04
19 13 0.13
20 65 0.65
21 14 0.14
22 4 0.04
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (19 bp):
ATTTGACTTCGCGTTGCGA
Found at i:12101 original size:60 final size:60
Alignment explanation
Indices: 12022--12166 Score: 236
Period size: 60 Copynumber: 2.4 Consensus size: 60
12012 CGTGTAAAAC
* * *
12022 ATTTGACTGTCGCGTTGCGAATTTGACTTCTGTGTTACGATTTACAAATTCGCGTTGCGA
1 ATTTGACTATCGCATTGCGAATTTGACTTCTGTGTTACGATTTACAAATTCGCGTTACGA
* *
12082 ATTTGACTATCGCTTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTACGA
1 ATTTGACTATCGCATTGCGAATTTGACTTCTGTGTTACGATTTACAAATTCGCGTTACGA
*
12142 ATTTGACTTTCGCATTGCGAATTTG
1 ATTTGACTATCGCATTGCGAATTTG
12167 GAAAAGCGCA
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 79 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (60 bp):
ATTTGACTATCGCATTGCGAATTTGACTTCTGTGTTACGATTTACAAATTCGCGTTACGA
Found at i:12243 original size:20 final size:19
Alignment explanation
Indices: 12192--12262 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
12182 AATTACATAT
12192 TCGCGTTGCGAAATTGGAA
1 TCGCGTTGCGAAATTGGAA
* * *
12211 ACTGGGTTACGAAATTGGAA
1 TC-GCGTTGCGAAATTGGAA
*
12231 TTCGCGTTGCG-AATTTGAGA
1 -TCGCGTTGCGAAATTGGA-A
12251 TCGCGTTGCGAA
1 TCGCGTTGCGAA
12263 TTTGTTGGTC
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
19 17 0.41
20 23 0.56
21 1 0.02
ACGTcount: A:0.25, C:0.15, G:0.31, T:0.28
Consensus pattern (19 bp):
TCGCGTTGCGAAATTGGAA
Found at i:14684 original size:12 final size:12
Alignment explanation
Indices: 14655--14728 Score: 57
Period size: 12 Copynumber: 6.2 Consensus size: 12
14645 AATTATTAAC
14655 ATATTTAA-AAT
1 ATATTTAATAAT
*
14666 ATATTTATTAAT
1 ATATTTAATAAT
*
14678 ATTTTTAATAAT
1 ATATTTAATAAT
*
14690 ATAATATAATAAT
1 AT-ATTTAATAAT
14703 A-A--TAATAAT
1 ATATTTAATAAT
*
14712 AATATTTCTATAAT
1 -ATATTT-AATAAT
14726 ATA
1 ATA
14729 CTCAATTATA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
9 7 0.14
10 1 0.02
11 9 0.18
12 15 0.30
13 13 0.26
14 5 0.10
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATTTAATAAT
Found at i:14684 original size:23 final size:23
Alignment explanation
Indices: 14637--14694 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
14627 CATTTTAATA
14637 AAAATATTAATTATTAACATATTT
1 AAAATA-TAATTATTAACATATTT
* * *
14661 AAAATATATTTATTAATATTTTT
1 AAAATATAATTATTAACATATTT
14684 AATAATATAAT
1 AA-AATATAAT
14695 ATAATAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 16 0.55
24 13 0.45
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAATATAATTATTAACATATTT
Found at i:14701 original size:3 final size:3
Alignment explanation
Indices: 14683--14715 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
14673 TTAATATTTT
14683 TAA TAA T-A TAA T-A TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
14716 TTTCTATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:14924 original size:21 final size:24
Alignment explanation
Indices: 14900--14946 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 24
14890 TAAAAATTCC
14900 TTAAAATAT-ATTT-AT-TAATTT
1 TTAAAATATAATTTAATATAATTT
*
14921 TTAAAATTTAATTTAATATAATTT
1 TTAAAATATAATTTAATATAATTT
14945 TT
1 TT
14947 TTATTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 4 0.18
23 2 0.09
24 8 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTAAAATATAATTTAATATAATTT
Found at i:19591 original size:2 final size:2
Alignment explanation
Indices: 19584--19609 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19574 GTCATAAATC
19584 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
19610 GTAGATTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22612 original size:43 final size:46
Alignment explanation
Indices: 22564--22675 Score: 158
Period size: 47 Copynumber: 2.5 Consensus size: 46
22554 GGTAAGTATG
22564 AAAATAAGCTTACGAGCTTATG-AA-T-AATGGCAAGTATATTGAT
1 AAAATAAGCTTACGAGCTTATGAAATTAAATGGCAAGTATATTGAT
* * *
22607 AAAATAAGCTTACGAGCTTATGAAATTTAAATGGTAAGTATTTTGGT
1 AAAATAAGCTTACGAGCTTATGAAA-TTAAATGGCAAGTATATTGAT
*
22654 AAAATAAGCTTACAAGCTTATG
1 AAAATAAGCTTACGAGCTTATG
22676 GGATAAATGG
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
43 22 0.36
44 2 0.03
46 1 0.02
47 36 0.59
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (46 bp):
AAAATAAGCTTACGAGCTTATGAAATTAAATGGCAAGTATATTGAT
Found at i:28104 original size:10 final size:9
Alignment explanation
Indices: 28069--28158 Score: 72
Period size: 10 Copynumber: 9.3 Consensus size: 9
28059 GCTGCTGGAA
*
28069 ACCGGTTTA
1 ACCGGTTTG
*
28078 ACCGGTTTTCA
1 ACCGG-TTT-G
28089 ACCGGTTCTG
1 ACCGGTT-TG
28099 ACCGGTTTG
1 ACCGGTTTG
*
28108 ACCGGTTTCA
1 ACCGGTTT-G
*
28118 ACCGGTTCG
1 ACCGGTTTG
28127 AACCGGTTTG
1 -ACCGGTTTG
*
28137 ACCGGTCTG
1 ACCGGTTTG
*
28146 AATCGGTTTG
1 -ACCGGTTTG
28156 ACC
1 ACC
28159 TGTCTGACCC
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
9 25 0.38
10 34 0.52
11 7 0.11
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:28113 original size:19 final size:19
Alignment explanation
Indices: 28070--28167 Score: 69
Period size: 19 Copynumber: 5.1 Consensus size: 19
28060 CTGCTGGAAA
* * *
28070 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
28090 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
*
28109 CCGGTTTCAACCGGTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
28129 CCGGTTTGACCGG-TCTGAA
1 CCGGTTTGACCGGTTCTG-A
* *
28148 TCGGTTTGACCTG-TCTGA
1 CCGGTTTGACCGGTTCTGA
28166 CC
1 CC
28168 CGACCCGACC
Statistics
Matches: 66, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
18 5 0.08
19 38 0.58
20 15 0.23
21 8 0.12
ACGTcount: A:0.15, C:0.28, G:0.27, T:0.31
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:28131 original size:29 final size:30
Alignment explanation
Indices: 28068--28142 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
28058 GGCTGCTGGA
*
28068 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
28099 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
28127 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
28143 CTGAATCGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 1 0.02
29 28 0.67
30 13 0.31
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:28185 original size:17 final size:17
Alignment explanation
Indices: 28163--28218 Score: 103
Period size: 17 Copynumber: 3.3 Consensus size: 17
28153 TTGACCTGTC
28163 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
*
28180 TGACCCGACCCGACTGT
1 TGACCCGACCCGACCGT
28197 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
28214 TGACC
1 TGACC
28219 GTTGACCGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.18, C:0.45, G:0.23, T:0.14
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:35464 original size:17 final size:17
Alignment explanation
Indices: 35442--35480 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
35432 TTGACCGGTC
35442 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
35459 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
35476 TGACC
1 TGACC
35481 GTTGACCGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:41546 original size:16 final size:16
Alignment explanation
Indices: 41513--41558 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
41503 GTTGTGGTTA
*
41513 AAATAAAAAATAAGAATT
1 AAAT-AAAAA-AATAATT
41531 AAATAAAAAAATAATT
1 AAATAAAAAAATAATT
*
41547 AAATAAACAAAT
1 AAATAAAAAAAT
41559 TAAAGAGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 17 0.65
17 5 0.19
18 4 0.15
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (16 bp):
AAATAAAAAAATAATT
Found at i:42218 original size:66 final size:68
Alignment explanation
Indices: 42147--42325 Score: 220
Period size: 66 Copynumber: 2.7 Consensus size: 68
42137 TAAAACATCT
* * ** *
42147 TAAATCCTAATTAAAACACTTAAAA-CTATCTAAACTAAAATACCTAAAAAAAAT-AATATAATA
1 TAAATCCTAATTAAAATACTTAAAACCTATTTAAACTAAAATACAGAAAAAAAATAAAAATAATA
*
42210 TTC
66 TCC
* * *
42213 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAGATAAAGATAAAATATAAAAATAAT
1 TAAATCCTAATTAAAATACTTAAAACCTATTTAAACTAAA-ATACAGAAAAAAAATAAAAATAAT
42277 ATCC
65 ATCC
* * *
42281 TAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACA
1 TAAATCCTAATTAAAATACTTAAAACCTATTTAAACTAAAATACA
42326 AAGATAAAAT
Statistics
Matches: 96, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
65 5 0.05
66 31 0.32
67 10 0.10
68 31 0.32
69 19 0.20
ACGTcount: A:0.57, C:0.13, G:0.01, T:0.28
Consensus pattern (68 bp):
TAAATCCTAATTAAAATACTTAAAACCTATTTAAACTAAAATACAGAAAAAAAATAAAAATAATA
TCC
Found at i:44141 original size:29 final size:29
Alignment explanation
Indices: 44108--44177 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
44098 TTGACACTTT
44108 AGTTTCTGTTATTT-TATTT-TAGTCATTTA
1 AGTTTCTGTT-TTTCTATTTAT-GTCATTTA
44137 AGTTT-TGTTTTTGCTATTTATGTCATTTA
1 AGTTTCTGTTTTT-CTATTTATGTCATTTA
*
44166 AATTTCTGTTTT
1 AGTTTCTGTTTT
44178 AGCTATCTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
27 3 0.08
28 4 0.11
29 22 0.61
30 7 0.19
ACGTcount: A:0.19, C:0.07, G:0.11, T:0.63
Consensus pattern (29 bp):
AGTTTCTGTTTTTCTATTTATGTCATTTA
Found at i:44183 original size:30 final size:29
Alignment explanation
Indices: 44125--44188 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
44115 GTTATTTTAT
* *
44125 TTTA-GTCATTTAAGTTTTGTTTTTGCTA
1 TTTATGTCATTTAAATTTTGTTTTAGCTA
44153 TTTATGTCATTTAAATTTCTGTTTTAGCTA
1 TTTATGTCATTTAAATTT-TGTTTTAGCTA
44183 TCTTAT
1 T-TTAT
44189 CCTTTTGAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 4 0.13
29 12 0.39
30 11 0.35
31 4 0.13
ACGTcount: A:0.20, C:0.09, G:0.11, T:0.59
Consensus pattern (29 bp):
TTTATGTCATTTAAATTTTGTTTTAGCTA
Found at i:45438 original size:17 final size:17
Alignment explanation
Indices: 45416--45458 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
45406 AATACATCTT
45416 TGTGGGTAGAAAGCATG
1 TGTGGGTAGAAAGCATG
45433 TGTGGGTAGAAAGCATG
1 TGTGGGTAGAAAGCATG
*
45450 TTTGGGTAG
1 TGTGGGTAG
45459 GACTACTATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.26, C:0.05, G:0.42, T:0.28
Consensus pattern (17 bp):
TGTGGGTAGAAAGCATG
Found at i:47023 original size:10 final size:11
Alignment explanation
Indices: 46998--47024 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
46988 TATCATGTTA
46998 AAAAAACAAAC
1 AAAAAACAAAC
47009 AAAAAACAAAC
1 AAAAAACAAAC
47020 AAAAA
1 AAAAA
47025 TCAATCAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAACAAAC
Found at i:50528 original size:24 final size:24
Alignment explanation
Indices: 50484--50530 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
50474 ATAAAGAACC
*
50484 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
50508 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
50531 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:58388 original size:23 final size:24
Alignment explanation
Indices: 58362--58438 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 24
58352 TTTGAAATTA
58362 TAAAAT-TTTAAAAAATGTAAAAT
1 TAAAATATTTAAAAAATGTAAAAT
*
58385 T-AAATCA-TTAATAAAA-ATAAAA-
1 TAAAAT-ATTTAA-AAAATGTAAAAT
58407 TAAAATATTTAAACAATATG-AAAATT
1 TAAAATATTTAAA-AA-ATGTAAAA-T
58433 TAAAAT
1 TAAAAT
58439 TTCTATGATG
Statistics
Matches: 42, Mismatches: 2, Indels: 17
0.69 0.03 0.28
Matches are distributed among these distances:
22 7 0.17
23 20 0.48
24 9 0.21
26 6 0.14
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (24 bp):
TAAAATATTTAAAAAATGTAAAAT
Done.