Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008202.1 Hibiscus syriacus cultivar Beakdansim tig00110822_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: 53961
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.30
Found at i:52 original size:13 final size:14
Alignment explanation
Indices: 34--64 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
24 AGTCAAAGAA
34 GGTCAACGGTC-AC
1 GGTCAACGGTCAAC
47 GGTCAACGGTCAAC
1 GGTCAACGGTCAAC
61 GGTC
1 GGTC
65 GGGTCGAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.23, C:0.29, G:0.32, T:0.16
Consensus pattern (14 bp):
GGTCAACGGTCAAC
Found at i:55 original size:7 final size:7
Alignment explanation
Indices: 34--64 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
24 AGTCAAAGAA
34 GGTCAAC
1 GGTCAAC
41 GGTC-AC
1 GGTCAAC
47 GGTCAAC
1 GGTCAAC
54 GGTCAAC
1 GGTCAAC
61 GGTC
1 GGTC
65 GGGTCGAGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.23, C:0.29, G:0.32, T:0.16
Consensus pattern (7 bp):
GGTCAAC
Found at i:77 original size:17 final size:17
Alignment explanation
Indices: 55--94 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
45 ACGGTCAACG
*
55 GTCAACGGTCGGGTCGA
1 GTCAACAGTCGGGTCGA
*
72 GTCAACAGTCGGGTCGG
1 GTCAACAGTCGGGTCGA
89 GTCAAC
1 GTCAAC
95 CCGGTTCAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.20, C:0.25, G:0.38, T:0.17
Consensus pattern (17 bp):
GTCAACAGTCGGGTCGA
Found at i:112 original size:19 final size:20
Alignment explanation
Indices: 88--158 Score: 92
Period size: 19 Copynumber: 3.6 Consensus size: 20
78 AGTCGGGTCG
*
88 GGTCAACCCGGTTCAG-ACC
1 GGTCAAACCGGTTCAGAACC
*
107 GGTCAAATCGGTTC-GAACC
1 GGTCAAACCGGTTCAGAACC
* *
126 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTCAGAACC
146 GGTCAAACCGGTT
1 GGTCAAACCGGTT
159 TTCCAGCAGC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
18 1 0.02
19 28 0.62
20 16 0.36
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.20
Consensus pattern (20 bp):
GGTCAAACCGGTTCAGAACC
Found at i:128 original size:10 final size:10
Alignment explanation
Indices: 90--158 Score: 63
Period size: 9 Copynumber: 7.1 Consensus size: 10
80 TCGGGTCGGG
*
90 TCAACCCGGT
1 TCAAACCGGT
*
100 TCAGACCGG-
1 TCAAACCGGT
*
109 TCAAATCGGT
1 TCAAACCGGT
*
119 TCGAACCGG-
1 TCAAACCGGT
128 TCAAACCGGT
1 TCAAACCGGT
*
138 TCAAAACTGG-
1 TC-AAACCGGT
148 TCAAACCGGT
1 TCAAACCGGT
158 T
1 T
159 TTCCAGCAGC
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
9 21 0.46
10 19 0.41
11 6 0.13
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:4552 original size:17 final size:17
Alignment explanation
Indices: 4530--4570 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
4520 TCTGAACCGG
*
4530 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
4547 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
4564 GTTGACC
1 GTTGACC
4571 GTTGACCGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:4584 original size:6 final size:7
Alignment explanation
Indices: 4560--4589 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
4550 GACCCGACCC
4560 GACCGTT
1 GACCGTT
4567 GACCGTT
1 GACCGTT
4574 GACCG-T
1 GACCGTT
4580 GACCGTT
1 GACCGTT
4587 GAC
1 GAC
4590 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:4584 original size:13 final size:14
Alignment explanation
Indices: 4560--4589 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
4550 GACCCGACCC
4560 GACCGTTGACCGTT
1 GACCGTTGACCGTT
4574 GACCG-TGACCGTT
1 GACCGTTGACCGTT
4587 GAC
1 GAC
4590 TTTCTTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (14 bp):
GACCGTTGACCGTT
Found at i:8415 original size:13 final size:14
Alignment explanation
Indices: 8397--8427 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
8387 AGTCAAAGAA
8397 GGTCAACGGTC-AC
1 GGTCAACGGTCAAC
8410 GGTCAACGGTCAAC
1 GGTCAACGGTCAAC
8424 GGTC
1 GGTC
8428 GGGTCGAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.23, C:0.29, G:0.32, T:0.16
Consensus pattern (14 bp):
GGTCAACGGTCAAC
Found at i:8418 original size:7 final size:7
Alignment explanation
Indices: 8397--8427 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
8387 AGTCAAAGAA
8397 GGTCAAC
1 GGTCAAC
8404 GGTC-AC
1 GGTCAAC
8410 GGTCAAC
1 GGTCAAC
8417 GGTCAAC
1 GGTCAAC
8424 GGTC
1 GGTC
8428 GGGTCGAGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.23, C:0.29, G:0.32, T:0.16
Consensus pattern (7 bp):
GGTCAAC
Found at i:8440 original size:17 final size:17
Alignment explanation
Indices: 8418--8457 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
8408 ACGGTCAACG
*
8418 GTCAACGGTCGGGTCGA
1 GTCAACAGTCGGGTCGA
*
8435 GTCAACAGTCGGGTCGG
1 GTCAACAGTCGGGTCGA
8452 GTCAAC
1 GTCAAC
8458 CCGGTTCAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.20, C:0.25, G:0.38, T:0.17
Consensus pattern (17 bp):
GTCAACAGTCGGGTCGA
Found at i:8475 original size:19 final size:20
Alignment explanation
Indices: 8451--8521 Score: 92
Period size: 19 Copynumber: 3.6 Consensus size: 20
8441 AGTCGGGTCG
*
8451 GGTCAACCCGGTTCAG-ACC
1 GGTCAAACCGGTTCAGAACC
*
8470 GGTCAAATCGGTTC-GAACC
1 GGTCAAACCGGTTCAGAACC
* *
8489 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTCAGAACC
8509 GGTCAAACCGGTT
1 GGTCAAACCGGTT
8522 TTCCAGCAGC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
18 1 0.02
19 28 0.62
20 16 0.36
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.20
Consensus pattern (20 bp):
GGTCAAACCGGTTCAGAACC
Found at i:8491 original size:10 final size:10
Alignment explanation
Indices: 8453--8521 Score: 63
Period size: 9 Copynumber: 7.1 Consensus size: 10
8443 TCGGGTCGGG
*
8453 TCAACCCGGT
1 TCAAACCGGT
*
8463 TCAGACCGG-
1 TCAAACCGGT
*
8472 TCAAATCGGT
1 TCAAACCGGT
*
8482 TCGAACCGG-
1 TCAAACCGGT
8491 TCAAACCGGT
1 TCAAACCGGT
*
8501 TCAAAACTGG-
1 TC-AAACCGGT
8511 TCAAACCGGT
1 TCAAACCGGT
8521 T
1 T
8522 TTCCAGCAGC
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
9 21 0.46
10 19 0.41
11 6 0.13
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:12969 original size:6 final size:7
Alignment explanation
Indices: 12952--12981 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
12942 GACCCGACCC
12952 GACCGTT
1 GACCGTT
12959 GACCG-T
1 GACCGTT
12965 GACCGTT
1 GACCGTT
12972 GACCGTT
1 GACCGTT
12979 GAC
1 GAC
12982 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:12970 original size:13 final size:13
Alignment explanation
Indices: 12952--12977 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12942 GACCCGACCC
12952 GACCGTTGACCGT
1 GACCGTTGACCGT
12965 GACCGTTGACCGT
1 GACCGTTGACCGT
12978 TGACTTTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:16841 original size:13 final size:13
Alignment explanation
Indices: 16823--16873 Score: 93
Period size: 13 Copynumber: 3.8 Consensus size: 13
16813 AGTCAAAGAA
16823 GGTCAACGGTCAC
1 GGTCAACGGTCAC
16836 GGTCAACGGTCAC
1 GGTCAACGGTCAC
16849 GGTCAACGGTCAAC
1 GGTCAACGGTC-AC
16863 GGTCAACGGTC
1 GGTCAACGGTC
16874 GGGTCGAGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 24 0.65
14 13 0.35
ACGTcount: A:0.24, C:0.29, G:0.31, T:0.16
Consensus pattern (13 bp):
GGTCAACGGTCAC
Found at i:16844 original size:7 final size:7
Alignment explanation
Indices: 16823--16873 Score: 88
Period size: 7 Copynumber: 7.6 Consensus size: 7
16813 AGTCAAAGAA
16823 GGTCAAC
1 GGTCAAC
16830 GGTC-AC
1 GGTCAAC
16836 GGTCAAC
1 GGTCAAC
16843 GGTC-AC
1 GGTCAAC
16849 GGTCAAC
1 GGTCAAC
16856 GGTCAAC
1 GGTCAAC
16863 GGTCAAC
1 GGTCAAC
16870 GGTC
1 GGTC
16874 GGGTCGAGTC
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
6 12 0.29
7 30 0.71
ACGTcount: A:0.24, C:0.29, G:0.31, T:0.16
Consensus pattern (7 bp):
GGTCAAC
Found at i:16857 original size:20 final size:21
Alignment explanation
Indices: 16823--16873 Score: 88
Period size: 20 Copynumber: 2.5 Consensus size: 21
16813 AGTCAAAGAA
16823 GGTCAACGGTC-ACGGTCAAC
1 GGTCAACGGTCAACGGTCAAC
16843 GGTC-ACGGTCAACGGTCAAC
1 GGTCAACGGTCAACGGTCAAC
16863 GGTCAACGGTC
1 GGTCAACGGTC
16874 GGGTCGAGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.21
20 17 0.59
21 6 0.21
ACGTcount: A:0.24, C:0.29, G:0.31, T:0.16
Consensus pattern (21 bp):
GGTCAACGGTCAACGGTCAAC
Found at i:16886 original size:17 final size:17
Alignment explanation
Indices: 16864--16903 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
16854 ACGGTCAACG
*
16864 GTCAACGGTCGGGTCGA
1 GTCAACAGTCGGGTCGA
*
16881 GTCAACAGTCGGGTCGG
1 GTCAACAGTCGGGTCGA
16898 GTCAAC
1 GTCAAC
16904 CCCGGTTCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.20, C:0.25, G:0.38, T:0.17
Consensus pattern (17 bp):
GTCAACAGTCGGGTCGA
Found at i:21369 original size:17 final size:17
Alignment explanation
Indices: 21347--21387 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
21337 TCTGAACCGG
*
21347 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
21364 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
21381 GTTGACC
1 GTTGACC
21388 GTTGACCGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:21389 original size:7 final size:7
Alignment explanation
Indices: 21377--21413 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
21367 GACCCGACCC
21377 GACCGTT
1 GACCGTT
21384 GACCGTT
1 GACCGTT
21391 GACCG-T
1 GACCGTT
21397 GACCGTT
1 GACCGTT
21404 GACCGTT
1 GACCGTT
21411 GAC
1 GAC
21414 TTTCTTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:21401 original size:13 final size:13
Alignment explanation
Indices: 21377--21409 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
21367 GACCCGACCC
21377 GACCGTTGACCGTT
1 GACCG-TGACCGTT
21391 GACCGTGACCGTT
1 GACCGTGACCGTT
21404 GACCGT
1 GACCGT
21410 TGACTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.24
Consensus pattern (13 bp):
GACCGTGACCGTT
Found at i:22837 original size:17 final size:17
Alignment explanation
Indices: 22799--22837 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
22789 GATAGTATAA
*
22799 TTTATTTATAATTTCAT
1 TTTATTTATAATATCAT
* *
22816 GTTATTTATAATATGAT
1 TTTATTTATAATATCAT
22833 TTTAT
1 TTTAT
22838 ATTGATGGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (17 bp):
TTTATTTATAATATCAT
Found at i:28615 original size:10 final size:10
Alignment explanation
Indices: 28586--28645 Score: 61
Period size: 10 Copynumber: 6.1 Consensus size: 10
28576 GCTGCTGGAA
28586 AACCGGTTTG
1 AACCGGTTTG
*
28596 -ACCAGTTTTG
1 AACC-GGTTTG
28606 AACCGGTTTG
1 AACCGGTTTG
*
28616 -ACCGGTCTG
1 AACCGGTTTG
*
28625 AACCGGTCTG
1 AACCGGTTTG
*
28635 AACCGGGTTG
1 AACCGGTTTG
28645 A
1 A
28646 CCCGACCCGA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
9 11 0.26
10 28 0.67
11 3 0.07
ACGTcount: A:0.20, C:0.23, G:0.30, T:0.27
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:28663 original size:17 final size:18
Alignment explanation
Indices: 28641--28683 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
28631 TCTGAACCGG
28641 GTTGACCCGACC-CGACC
1 GTTGACCCGACCGCGACC
*
28658 GTTGACCCGACCGTTGACC
1 GTTGACCCGACCG-CGACC
28677 GTTGACC
1 GTTGACC
28684 GTGACAGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.52
19 11 0.48
ACGTcount: A:0.16, C:0.40, G:0.26, T:0.19
Consensus pattern (18 bp):
GTTGACCCGACCGCGACC
Found at i:28666 original size:12 final size:12
Alignment explanation
Indices: 28649--28676 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
28639 GGGTTGACCC
28649 GACCCGACCGTT
1 GACCCGACCGTT
28661 GACCCGACCGTT
1 GACCCGACCGTT
28673 GACC
1 GACC
28677 GTTGACCGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.43, G:0.25, T:0.14
Consensus pattern (12 bp):
GACCCGACCGTT
Found at i:28676 original size:7 final size:7
Alignment explanation
Indices: 28654--28702 Score: 59
Period size: 7 Copynumber: 7.4 Consensus size: 7
28644 GACCCGACCC
28654 GACCGTT
1 GACCGTT
*
28661 GACC--C
1 GACCGTT
28666 GACCGTT
1 GACCGTT
28673 GACCGTT
1 GACCGTT
28680 GACCG-T
1 GACCGTT
*
28686 GACAGTT
1 GACCGTT
28693 GACCGTT
1 GACCGTT
28700 GAC
1 GAC
28703 TTTCTTTGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
5 4 0.11
6 5 0.14
7 26 0.74
ACGTcount: A:0.18, C:0.31, G:0.29, T:0.22
Consensus pattern (7 bp):
GACCGTT
Found at i:28695 original size:20 final size:19
Alignment explanation
Indices: 28654--28702 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
28644 GACCCGACCC
*
28654 GACCGTTGACCCGACCGTT
1 GACCGTTGACCCGACAGTT
*
28673 GACCGTTGACCGTGACAGTT
1 GACCGTTGACC-CGACAGTT
28693 GACCGTTGAC
1 GACCGTTGAC
28703 TTTCTTTGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.18, C:0.31, G:0.29, T:0.22
Consensus pattern (19 bp):
GACCGTTGACCCGACAGTT
Found at i:36901 original size:13 final size:14
Alignment explanation
Indices: 36883--36912 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
36873 GTCAAAGAAA
36883 GTCAACGGTC-ACG
1 GTCAACGGTCAACG
36896 GTCAACGGTCAACG
1 GTCAACGGTCAACG
36910 GTC
1 GTC
36913 GGGTCGGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:36903 original size:7 final size:7
Alignment explanation
Indices: 36883--36912 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
36873 GTCAAAGAAA
36883 GTCAACG
1 GTCAACG
36890 GTC-ACG
1 GTCAACG
36896 GTCAACG
1 GTCAACG
36903 GTCAACG
1 GTCAACG
36910 GTC
1 GTC
36913 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:36924 original size:17 final size:17
Alignment explanation
Indices: 36902--36942 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
36892 CACGGTCAAC
*
36902 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
36919 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
36936 GGTCAAC
1 GGTCAAC
36943 CCGGTTCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:36960 original size:19 final size:20
Alignment explanation
Indices: 36936--37006 Score: 101
Period size: 19 Copynumber: 3.6 Consensus size: 20
36926 AGTCGGGTCG
*
36936 GGTCAACCCGGTTCAG-ACC
1 GGTCAAACCGGTTCAGAACC
36955 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAGAACC
* *
36974 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTCAGAACC
36994 GGTCAAACCGGTT
1 GGTCAAACCGGTT
37007 TTCCAACAGC
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
18 1 0.02
19 30 0.64
20 16 0.34
ACGTcount: A:0.27, C:0.30, G:0.25, T:0.18
Consensus pattern (20 bp):
GGTCAAACCGGTTCAGAACC
Found at i:36973 original size:10 final size:10
Alignment explanation
Indices: 36938--37006 Score: 72
Period size: 9 Copynumber: 7.1 Consensus size: 10
36928 TCGGGTCGGG
*
36938 TCAACCCGGT
1 TCAAACCGGT
*
36948 TCAGACCGG-
1 TCAAACCGGT
36957 TCAAACCGGT
1 TCAAACCGGT
*
36967 TCGAACCGG-
1 TCAAACCGGT
36976 TCAAACCGGT
1 TCAAACCGGT
*
36986 TCAAAACTGG-
1 TC-AAACCGGT
36996 TCAAACCGGT
1 TCAAACCGGT
37006 T
1 T
37007 TTCCAACAGC
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 22 0.46
10 20 0.42
11 6 0.12
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:37877 original size:2 final size:2
Alignment explanation
Indices: 37870--37903 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
37860 AGCTCAGGTT
37870 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
37904 ACCCACCACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:41919 original size:15 final size:15
Alignment explanation
Indices: 41899--41927 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
41889 TCGCAGCCGC
41899 AGCAGCCTTCTTCTG
1 AGCAGCCTTCTTCTG
41914 AGCAGCCTTCTTCT
1 AGCAGCCTTCTTCT
41928 TGCTGGCGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.34, G:0.17, T:0.34
Consensus pattern (15 bp):
AGCAGCCTTCTTCTG
Found at i:44734 original size:5 final size:5
Alignment explanation
Indices: 44718--44753 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
44708 TTTCGCAAAG
* *
44718 ATAAA ATGAA ATAAA ATAAA ACAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
44754 ATGAAAAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (5 bp):
ATAAA
Found at i:44738 original size:15 final size:15
Alignment explanation
Indices: 44718--44759 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
44708 TTTCGCAAAG
44718 ATAAAATGAAATAAA
1 ATAAAATGAAATAAA
**
44733 ATAAAACAAAATAAA
1 ATAAAATGAAATAAA
44748 ATAAAAATGAAA
1 AT-AAAATGAAA
44760 AGAAGTAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (15 bp):
ATAAAATGAAATAAA
Found at i:45090 original size:30 final size:30
Alignment explanation
Indices: 45051--45220 Score: 114
Period size: 30 Copynumber: 5.7 Consensus size: 30
45041 AAATAGTAAT
*
45051 AACAGAAATTTACAGGACTAAAACAACAAA
1 AACAGAAATTTAAAGGACTAAAACAACAAA
* * * *
45081 AACGGAAATTTAAATGACTAAAATAATAAA
1 AACAGAAATTTAAAGGACTAAAACAACAAA
* * *
45111 AACAGAAAGTTAAAGGACTAAAA-TAGAAA
1 AACAGAAATTTAAAGGACTAAAACAACAAA
* * ** **
45140 AACATAATTTTAAATGG--TTGAACAGTAAA
1 AACAGAAATTTAAA-GGACTAAAACAACAAA
* * * * *
45169 AAAAGAAACTAAAAGGACTAAAACAATAAT
1 AACAGAAATTTAAAGGACTAAAACAACAAA
*
45199 TACA-AACATTTAAAGGACTAAA
1 AACAGAA-ATTTAAAGGACTAAA
45221 TAGTAAAAAT
Statistics
Matches: 104, Mismatches: 31, Indels: 10
0.72 0.21 0.07
Matches are distributed among these distances:
28 5 0.05
29 29 0.28
30 70 0.67
ACGTcount: A:0.59, C:0.10, G:0.12, T:0.19
Consensus pattern (30 bp):
AACAGAAATTTAAAGGACTAAAACAACAAA
Found at i:45152 original size:29 final size:30
Alignment explanation
Indices: 45051--45153 Score: 118
Period size: 30 Copynumber: 3.5 Consensus size: 30
45041 AAATAGTAAT
* * *
45051 AACAGAAATTTACAGGACTAAAACAACAAA
1 AACAGAAATTTAAAGGACTAAAATAAGAAA
* * *
45081 AACGGAAATTTAAATGACTAAAATAATAAA
1 AACAGAAATTTAAAGGACTAAAATAAGAAA
*
45111 AACAGAAAGTTAAAGGACTAAAAT-AGAAA
1 AACAGAAATTTAAAGGACTAAAATAAGAAA
* *
45140 AACATAATTTTAAA
1 AACAGAAATTTAAA
45154 TGGTTGAACA
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
29 15 0.25
30 46 0.75
ACGTcount: A:0.60, C:0.10, G:0.11, T:0.19
Consensus pattern (30 bp):
AACAGAAATTTAAAGGACTAAAATAAGAAA
Found at i:50307 original size:27 final size:27
Alignment explanation
Indices: 50270--50333 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
50260 TCTTCCCTTT
* *
50270 GCCGCCATCACCACCACCCCCGTTCTC
1 GCCGCCATCACCACCACCACCATTCTC
*
50297 GCCGCCATCACCGCCACCACCATTCTC
1 GCCGCCATCACCACCACCACCATTCTC
50324 GCCGCCATCA
1 GCCGCCATCA
50334 TTTTTGCCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.17, C:0.56, G:0.12, T:0.14
Consensus pattern (27 bp):
GCCGCCATCACCACCACCACCATTCTC
Done.