Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008510.1 Hibiscus syriacus cultivar Beakdansim tig00111365_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: 178315
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:1441 original size:14 final size:14
Alignment explanation
Indices: 1422--1449 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1412 ATACTATATA
1422 TTTCCATCACCATC
1 TTTCCATCACCATC
1436 TTTCCATCACCATC
1 TTTCCATCACCATC
1450 CTCCATCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.00, T:0.36
Consensus pattern (14 bp):
TTTCCATCACCATC
Found at i:1644 original size:15 final size:15
Alignment explanation
Indices: 1626--1668 Score: 86
Period size: 15 Copynumber: 2.9 Consensus size: 15
1616 TTTCCATTTC
1626 CATTTCCTTTCTTAT
1 CATTTCCTTTCTTAT
1641 CATTTCCTTTCTTAT
1 CATTTCCTTTCTTAT
1656 CATTTCCTTTCTT
1 CATTTCCTTTCTT
1669 CTTCCATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (15 bp):
CATTTCCTTTCTTAT
Found at i:10103 original size:14 final size:13
Alignment explanation
Indices: 10086--10135 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
10076 GTGCAAAAAG
10086 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
10100 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
10113 ATAAG-AAAAG--A
1 A-AAGAAAAAGAAA
10124 AAAGAAAAAGAA
1 AAAGAAAAAGAA
10136 TTCAAAAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:16165 original size:24 final size:21
Alignment explanation
Indices: 16131--16173 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
16121 TCTACAAGAT
*
16131 ATGTCCTTTGACATTTCAAATG
1 ATGTCCTTTGA-AATTCAAATG
16153 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
16174 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAATG
Found at i:18665 original size:24 final size:21
Alignment explanation
Indices: 18631--18673 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
18621 TCTACAAGAT
*
18631 ATGTCCTTTGACATTTCAAATG
1 ATGTCCTTTGA-AATTCAAATG
18653 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
18674 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAATG
Found at i:21164 original size:24 final size:21
Alignment explanation
Indices: 21130--21172 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
21120 TCTACAAGAT
*
21130 ATGTCCTTTGACATTTCAAATG
1 ATGTCCTTTGA-AATTCAAATG
21152 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
21173 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAATG
Found at i:23117 original size:11 final size:11
Alignment explanation
Indices: 23101--23126 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
23091 ATTGGCGTGC
23101 AAAGCAAAAGA
1 AAAGCAAAAGA
23112 AAAGCAAAAGA
1 AAAGCAAAAGA
23123 AAAG
1 AAAG
23127 ACTCCTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.08, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAGCAAAAGA
Found at i:23181 original size:19 final size:18
Alignment explanation
Indices: 23150--23211 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
23140 AATTGGAGTG
23150 CAAAAAGAA-AGAAAAAGA
1 CAAAAAGAAGAGAAAAA-A
*
23168 CAAAAAGAAGAGAAAAAT
1 CAAAAAGAAGAGAAAAAA
*
23186 CAGAAAAGAAGAAAAGAAAA
1 CA-AAAAGAAGAGAA-AAAA
23206 GCAAAA
1 -CAAAA
23212 GAATTCAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 11 0.30
19 18 0.49
20 6 0.16
21 2 0.05
ACGTcount: A:0.74, C:0.06, G:0.18, T:0.02
Consensus pattern (18 bp):
CAAAAAGAAGAGAAAAAA
Found at i:27865 original size:35 final size:37
Alignment explanation
Indices: 27797--27876 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
27787 ATACTATTTC
**
27797 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCCACCATTATCACGCCTATAT
* *
27834 CATCACCATAGTCCA-CCACCA-TATCATGCCTATAT
1 CATCACCATAATCCATCCACCATTATCACGCCTATAT
27869 CATCACCA
1 CATCACCA
27877 AATTCTCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 21 0.54
36 4 0.10
37 14 0.36
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCCACCATTATCACGCCTATAT
Found at i:31012 original size:19 final size:21
Alignment explanation
Indices: 30988--31039 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
30978 CGGCCAAGAG
*
30988 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
31007 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
31028 CATGTATTTTCA
1 CATGTATTTTCA
31040 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:31788 original size:8 final size:8
Alignment explanation
Indices: 31777--31820 Score: 54
Period size: 8 Copynumber: 5.2 Consensus size: 8
31767 GAGAAAAATC
31777 AGAAAAGA
1 AGAAAAGA
31785 AGAAAAGA
1 AGAAAAGA
31793 AGAAAAGAAA
1 AGAAAAG--A
31803 AGAAAAGA
1 AGAAAAGA
31811 A-AAAGAGA
1 AGAAA-AGA
31819 AG
1 AG
31821 TTCAAAAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
7 3 0.09
8 21 0.66
10 8 0.25
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:31790 original size:16 final size:16
Alignment explanation
Indices: 31777--31820 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 16
31767 GAGAAAAATC
31777 AGAAAAGAAGAAAAGA
1 AGAAAAGAAGAAAAGA
31793 AGAAAAGAAAAGAAAAGA
1 AGAAAAG--AAGAAAAGA
31811 A-AAAGAGAAG
1 AGAAA-AGAAG
31821 TTCAAAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 10 0.40
17 3 0.12
18 12 0.48
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (16 bp):
AGAAAAGAAGAAAAGA
Found at i:31800 original size:13 final size:13
Alignment explanation
Indices: 31777--31811 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
31767 GAGAAAAATC
31777 AGAAAAGAAGAAA
1 AGAAAAGAAGAAA
31790 AGAAGAA-AAGAAA
1 AGAA-AAGAAGAAA
31803 AGAAAAGAA
1 AGAAAAGAA
31812 AAAGAGAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.10
13 16 0.80
14 2 0.10
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AGAAAAGAAGAAA
Found at i:34307 original size:30 final size:31
Alignment explanation
Indices: 34255--34314 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
34245 CTTAGCTTTA
**
34255 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
34285 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
34315 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:35247 original size:19 final size:20
Alignment explanation
Indices: 35223--35270 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
35213 CGGCCAAGAG
35223 CATGTATCTTCA-TT-AAAAT
1 CATGTAT-TTCATTTAAAAAT
*
35242 CATGTATTTTATTTAAAAAT
1 CATGTATTTCATTTAAAAAT
35262 CATGTATTT
1 CATGTATTT
35271 TCAAAGGGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 3 0.12
19 9 0.35
20 14 0.54
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.48
Consensus pattern (20 bp):
CATGTATTTCATTTAAAAAT
Found at i:36021 original size:8 final size:8
Alignment explanation
Indices: 35992--36050 Score: 50
Period size: 8 Copynumber: 7.0 Consensus size: 8
35982 TTGGAGTGCA
35992 AAAAGAAG
1 AAAAGAAG
*
36000 AAAA-AATC
1 AAAAGAA-G
36008 AGAAAGAAG
1 A-AAAGAAG
36017 AAAAGAAG
1 AAAAGAAG
36025 AAAAGAAAAG
1 AAAAG--AAG
36035 AAAAGAA-
1 AAAAGAAG
36042 AAAGAGAAG
1 AAA-AGAAG
36051 TTCAAAAAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
7 5 0.12
8 23 0.55
9 4 0.10
10 10 0.24
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (8 bp):
AAAAGAAG
Found at i:36036 original size:25 final size:25
Alignment explanation
Indices: 35991--36050 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
35981 ATTGGAGTGC
*
35991 AAAAAGAAGAAAAAATCAG-AAAGA
1 AAAAAGAAGAAAAAATAAGAAAAGA
36015 AGAAAAGAAGAAAAGAA-AAGAAAAGA
1 A-AAAAGAAGAAAA-AATAAGAAAAGA
36041 AAAAGAGAAG
1 AAAA-AGAAG
36051 TTCAAAAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
24 1 0.03
25 17 0.55
26 13 0.42
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (25 bp):
AAAAAGAAGAAAAAATAAGAAAAGA
Found at i:39290 original size:19 final size:21
Alignment explanation
Indices: 39266--39317 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
39256 CGGCCAAGAG
*
39266 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
39285 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
39306 CATGTATTTTCA
1 CATGTATTTTCA
39318 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:39670 original size:164 final size:165
Alignment explanation
Indices: 39400--39728 Score: 619
Period size: 164 Copynumber: 2.0 Consensus size: 165
39390 CTAGTGCATT
39400 TCATTTGTAATGATCTCATCTCTTATATAAACATACTCTGTGAGTTAATTTCTCTTCAAAGTTCT
1 TCATTTGTAATGATCTCATCTCTTATATAAACATACTCTGTGAGTTAATTTCTCTTCAAAGTTCT
39465 TTGTGAACTTTATCGATTAAGCAAGTATAATTTATATACTTGTGGCGTCATTC-TTCCAACTTGA
66 TTGTGAACTTTATCGATTAAGCAAGTATAATTTATATACTTGTGGCGTCATTCTTTCCAACTTGA
39529 TTCCTAAATTCCTAGATTATTATCTAGT-GGTTGA
131 TTCCTAAATTCCTAGATTATTATCTAGTGGGTTGA
39563 TCATTTGTAATGATCTCATCTCTTATATAAAACATACTCTTGTGAGTTAATTTCTC-TCAAAGTT
1 TCATTTGTAATGATCTCATCTCTTATAT-AAACATACTC-TGTGAGTTAATTTCTCTTCAAAGTT
39627 CTTTGTGAACTTTATCGATTAAGCAAGTATAATTTATATACTTGTGGCGTCATTCTTTCCAACTT
64 CTTTGTGAACTTTATCGATTAAGCAAGTATAATTTATATACTTGTGGCGTCATTCTTTCCAACTT
39692 GATTCCTAAATTCCTAGATTATTATCTAGTGGGTTGA
129 GATTCCTAAATTCCTAGATTATTATCTAGTGGGTTGA
39729 AGACACTATC
Statistics
Matches: 162, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
163 28 0.17
164 73 0.45
165 55 0.34
166 6 0.04
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (165 bp):
TCATTTGTAATGATCTCATCTCTTATATAAACATACTCTGTGAGTTAATTTCTCTTCAAAGTTCT
TTGTGAACTTTATCGATTAAGCAAGTATAATTTATATACTTGTGGCGTCATTCTTTCCAACTTGA
TTCCTAAATTCCTAGATTATTATCTAGTGGGTTGA
Found at i:41876 original size:19 final size:20
Alignment explanation
Indices: 41852--41891 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
41842 GTTATTGTTG
41852 CCCATCTTG-AATCATAACA
1 CCCATCTTGAAATCATAACA
41871 CCCATCTTGAAATCATAACA
1 CCCATCTTGAAATCATAACA
41891 C
1 C
41892 TCAAAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.38, C:0.33, G:0.05, T:0.25
Consensus pattern (20 bp):
CCCATCTTGAAATCATAACA
Found at i:42821 original size:10 final size:11
Alignment explanation
Indices: 42772--42828 Score: 73
Period size: 11 Copynumber: 5.4 Consensus size: 11
42762 AATTTTGGAA
*
42772 TTTTTTGGCTT
1 TTTTTTTGCTT
*
42783 TTTTTTAGCTT
1 TTTTTTTGCTT
*
42794 TTTTTTTGTTT
1 TTTTTTTGCTT
42805 TTTTTTTG-TT
1 TTTTTTTGCTT
42815 TTTTTTTG-TT
1 TTTTTTTGCTT
42825 TTTT
1 TTTT
42829 GAAAAAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
10 16 0.37
11 27 0.63
ACGTcount: A:0.02, C:0.04, G:0.11, T:0.84
Consensus pattern (11 bp):
TTTTTTTGCTT
Found at i:44377 original size:6 final size:6
Alignment explanation
Indices: 44366--44390 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
44356 AGATGGTTGA
44366 TATGGT TATGGT TATGGT TATGGT T
1 TATGGT TATGGT TATGGT TATGGT T
44391 TATGAAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (6 bp):
TATGGT
Found at i:51440 original size:12 final size:12
Alignment explanation
Indices: 51425--51453 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
51415 CTTTTTTTTG
51425 TTTTTTTGCCTT
1 TTTTTTTGCCTT
51437 TTTTTTTGCCTT
1 TTTTTTTGCCTT
51449 TTTTT
1 TTTTT
51454 GTTTTTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTTTTGCCTT
Found at i:51458 original size:20 final size:19
Alignment explanation
Indices: 51400--51461 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
51390 GTTTTTGAAA
* * *
51400 TTTTGGCTTTTTTGGCTTT
1 TTTTTGCTTTTTTTGTTTT
51419 TTTTTG-TTTTTTTGCCTTTT
1 TTTTTGCTTTTTTTG--TTTT
51439 TTTTTGCCTTTTTTTGTTTT
1 TTTTTG-CTTTTTTTGTTTT
51459 TTT
1 TTT
51462 GAAAAAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
18 7 0.19
19 5 0.14
20 16 0.44
22 8 0.22
ACGTcount: A:0.00, C:0.10, G:0.13, T:0.77
Consensus pattern (19 bp):
TTTTTGCTTTTTTTGTTTT
Found at i:53733 original size:14 final size:14
Alignment explanation
Indices: 53714--53743 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
53704 GTGCTTCAAC
*
53714 TTCTTTTTTTTCTT
1 TTCTTTTTCTTCTT
53728 TTCTTTTTCTTCTT
1 TTCTTTTTCTTCTT
53742 TT
1 TT
53744 GAGTGCTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTCTTTTTCTTCTT
Found at i:53786 original size:28 final size:29
Alignment explanation
Indices: 53725--53786 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 29
53715 TCTTTTTTTT
* *
53725 CTTTTCTTTTTCTTCTTTTGAGTGCTGGA
1 CTTTTCTTTCTCTTCTTTTGAGTGCTGCA
* *
53754 TTTTTCTTTCT-TTCTTTTGAGTGCTTCA
1 CTTTTCTTTCTCTTCTTTTGAGTGCTGCA
53782 CTTTT
1 CTTTT
53787 TTTTTCTGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.06, C:0.18, G:0.13, T:0.63
Consensus pattern (29 bp):
CTTTTCTTTCTCTTCTTTTGAGTGCTGCA
Found at i:53786 original size:29 final size:29
Alignment explanation
Indices: 53726--53793 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
53716 CTTTTTTTTC
* *
53726 TTTTCTTTTTCTTCTTTTGAGTGCTGGAT
1 TTTTCTTTCTCTTCTTTTGAGTGCTGCAT
*
53755 TTTTCTTTCT-TTCTTTTGAGTGCTTCACT
1 TTTTCTTTCTCTTCTTTTGAGTGCTGCA-T
*
53784 TTTTTTTTCT
1 TTTTCTTTCT
53794 GATTTTTCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 15 0.44
29 19 0.56
ACGTcount: A:0.06, C:0.16, G:0.12, T:0.66
Consensus pattern (29 bp):
TTTTCTTTCTCTTCTTTTGAGTGCTGCAT
Found at i:56594 original size:19 final size:20
Alignment explanation
Indices: 56570--56613 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
56560 TATCCTTTCT
56570 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
56589 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
56609 -TATTT
1 TTATTT
56614 TTATCCCCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.20, C:0.14, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:59371 original size:19 final size:20
Alignment explanation
Indices: 59330--59380 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
59320 GAAACCCCTT
*
59330 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
59350 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
59369 TGAAGATACATG
1 TGAAAATACATG
59381 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:60330 original size:30 final size:31
Alignment explanation
Indices: 60290--60349 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
60280 ACATTCTTCC
**
60290 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
60321 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
60350 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:64143 original size:12 final size:12
Alignment explanation
Indices: 64126--64187 Score: 61
Period size: 12 Copynumber: 5.1 Consensus size: 12
64116 CATCTTCATT
* *
64126 TCATCATCAACA
1 TCATCAACACCA
*
64138 TCATCAACATCCT
1 TCATCAACA-CCA
*
64151 TCATCAAGACCA
1 TCATCAACACCA
*
64163 TCATCAAGACCA
1 TCATCAACACCA
*
64175 TCATCAAGACCA
1 TCATCAACACCA
64187 T
1 T
64188 AATTCCACAG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
12 35 0.80
13 9 0.20
ACGTcount: A:0.39, C:0.34, G:0.05, T:0.23
Consensus pattern (12 bp):
TCATCAACACCA
Found at i:64183 original size:24 final size:25
Alignment explanation
Indices: 64136--64187 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
64126 TCATCATCAA
*
64136 CATCATCAACATCCTTCATCAAGAC
1 CATCATCAACATCCATCATCAAGAC
*
64161 CATCATCAAGA-CCATCATCAAGAC
1 CATCATCAACATCCATCATCAAGAC
64185 CAT
1 CAT
64188 AATTCCACAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 15 0.60
25 10 0.40
ACGTcount: A:0.38, C:0.35, G:0.06, T:0.21
Consensus pattern (25 bp):
CATCATCAACATCCATCATCAAGAC
Found at i:64672 original size:8 final size:8
Alignment explanation
Indices: 64661--64704 Score: 54
Period size: 8 Copynumber: 5.2 Consensus size: 8
64651 GAGAAAAATC
64661 AGAAAAGA
1 AGAAAAGA
64669 AGAAAAGA
1 AGAAAAGA
64677 AGAAAAGAAA
1 AGAAAAG--A
64687 AGAAAAGA
1 AGAAAAGA
64695 A-AAAGAGA
1 AGAAA-AGA
64703 AG
1 AG
64705 TTCAAAAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
7 3 0.09
8 21 0.66
10 8 0.25
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:64674 original size:16 final size:16
Alignment explanation
Indices: 64661--64704 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 16
64651 GAGAAAAATC
64661 AGAAAAGAAGAAAAGA
1 AGAAAAGAAGAAAAGA
64677 AGAAAAGAAAAGAAAAGA
1 AGAAAAG--AAGAAAAGA
64695 A-AAAGAGAAG
1 AGAAA-AGAAG
64705 TTCAAAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 10 0.40
17 3 0.12
18 12 0.48
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (16 bp):
AGAAAAGAAGAAAAGA
Found at i:64684 original size:13 final size:13
Alignment explanation
Indices: 64661--64695 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
64651 GAGAAAAATC
64661 AGAAAAGAAGAAA
1 AGAAAAGAAGAAA
64674 AGAAGAA-AAGAAA
1 AGAA-AAGAAGAAA
64687 AGAAAAGAA
1 AGAAAAGAA
64696 AAAGAGAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.10
13 16 0.80
14 2 0.10
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AGAAAAGAAGAAA
Found at i:72987 original size:18 final size:19
Alignment explanation
Indices: 72966--73010 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
72956 ACTTCTCTTT
72966 TTCTTTTCT-TTTCTTT-TC
1 TTCTTTTCTATTT-TTTCTC
72984 TTCTTTTCTGATTTTTTCTC
1 TTCTTTTCT-ATTTTTTCTC
73004 TTCTTTT
1 TTCTTTT
73011 TGCACTCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.38
19 3 0.12
20 12 0.50
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (19 bp):
TTCTTTTCTATTTTTTCTC
Found at i:76121 original size:12 final size:12
Alignment explanation
Indices: 76089--76128 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
76079 TCATCATCAA
*
76089 CATCATCAACATC
1 CATCATCAAGA-C
*
76102 CTTCATCAAGAC
1 CATCATCAAGAC
76114 CATCATCAAGAC
1 CATCATCAAGAC
76126 CAT
1 CAT
76129 AATTCCGCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 15 0.62
13 9 0.38
ACGTcount: A:0.38, C:0.35, G:0.05, T:0.23
Consensus pattern (12 bp):
CATCATCAAGAC
Found at i:76370 original size:13 final size:13
Alignment explanation
Indices: 76357--76404 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 13
76347 TTTGAACTTC
76357 TCTTTT-TC-TTT
1 TCTTTTCTCTTTT
76368 TCTTTTCTCTTTT
1 TCTTTTCTCTTTT
76381 TCTTTTCTTCTTTTCT
1 TCTTTTC-TC-TTT-T
76397 TCTTTTCT
1 TCTTTTCT
76405 TATTTCCTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 6 0.19
12 2 0.06
13 10 0.31
14 2 0.06
15 4 0.12
16 8 0.25
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TCTTTTCTCTTTT
Found at i:76391 original size:8 final size:8
Alignment explanation
Indices: 76367--76405 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
76357 TCTTTTTCTT
76367 TTCTTTTC
1 TTCTTTTC
76375 -TC-TTT-
1 TTCTTTTC
76380 TTCTTTTC
1 TTCTTTTC
76388 TTCTTTTC
1 TTCTTTTC
76396 TTCTTTTC
1 TTCTTTTC
76404 TT
1 TT
76406 ATTTCCTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
6 5 0.18
7 5 0.18
8 18 0.64
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (8 bp):
TTCTTTTC
Found at i:76405 original size:13 final size:13
Alignment explanation
Indices: 76362--76397 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
76352 ACTTCTCTTT
76362 TTCTTTTCTTTTC
1 TTCTTTTCTTTTC
76375 -TCTTTTTCTTTTC
1 TTC-TTTTCTTTTC
76388 TTCTTTTCTT
1 TTCTTTTCTT
76398 CTTTTCTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 2 0.10
13 17 0.81
14 2 0.10
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (13 bp):
TTCTTTTCTTTTC
Found at i:77186 original size:19 final size:20
Alignment explanation
Indices: 77139--77189 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
77129 GAAACCCCTT
*
77139 TGAAAATACATGATTTTGGA
1 TGAAAATACATGATTTTGAA
77159 TGAAAATACATGATTTT-AA
1 TGAAAATACATGATTTTGAA
*
77178 TGAAGATACATG
1 TGAAAATACATG
77190 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTGAA
Found at i:78139 original size:30 final size:31
Alignment explanation
Indices: 78099--78158 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
78089 ACATGCTGCC
**
78099 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
78130 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
78159 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:80166 original size:5 final size:5
Alignment explanation
Indices: 80156--80216 Score: 51
Period size: 5 Copynumber: 12.6 Consensus size: 5
80146 CTCTTTTGAA
*
80156 TTTCT TTTCT TTTC- -TTCT TTTCT TAT-T TTT-T TTTCT TATT-T TTGTCTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T-TTCT TT-TC-T
80204 TTTCT TTTCT TTT
1 TTTCT TTTCT TTT
80217 TGCACTCTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
3 3 0.06
4 8 0.17
5 29 0.62
6 4 0.09
7 3 0.06
ACGTcount: A:0.03, C:0.15, G:0.02, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:80173 original size:13 final size:12
Alignment explanation
Indices: 80156--80217 Score: 65
Period size: 13 Copynumber: 5.2 Consensus size: 12
80146 CTCTTTTGAA
80156 TTTCTTTTCTTT
1 TTTCTTTTCTTT
80168 TCTTCTTTTCTTAT
1 T-TTCTTTTCTT-T
* *
80182 TTTTTTTTCTTA
1 TTTCTTTTCTTT
*
80194 TTT-TTGTC-TT
1 TTTCTTTTCTTT
80204 TTTCTTTTCTTT
1 TTTCTTTTCTTT
80216 TT
1 TT
80218 GCACTCTAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
10 4 0.10
11 8 0.20
12 8 0.20
13 19 0.46
14 2 0.05
ACGTcount: A:0.03, C:0.15, G:0.02, T:0.81
Consensus pattern (12 bp):
TTTCTTTTCTTT
Found at i:84552 original size:13 final size:13
Alignment explanation
Indices: 84534--84558 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
84524 ATTTGTAACT
84534 CATAACATGAACC
1 CATAACATGAACC
84547 CATAACATGAAC
1 CATAACATGAAC
84559 ATGCACGGCA
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:0.28, G:0.08, T:0.16
Consensus pattern (13 bp):
CATAACATGAACC
Found at i:88257 original size:18 final size:18
Alignment explanation
Indices: 88236--88298 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
88226 ATTGGAGTAC
88236 AAAAGAA-AAGAAAAGATA
1 AAAAGAAGAAGAAAAGA-A
88254 AAAAGAAGAA-AAAAGAA
1 AAAAGAAGAAGAAAAGAA
*
88271 AAGAAAAAGAAGAAAAGTCAA
1 AA-AAGAAGAAGAAAAG--AA
88292 AAAAGAA
1 AAAAGAA
88299 AGCAAGCAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
17 3 0.08
18 20 0.53
19 7 0.18
20 4 0.11
21 4 0.11
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (18 bp):
AAAAGAAGAAGAAAAGAA
Found at i:88267 original size:23 final size:21
Alignment explanation
Indices: 88241--88286 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 21
88231 AGTACAAAAG
88241 AAAAGAAAAGATAAAAAGAAGAA
1 AAAAGAAAAG--AAAAAGAAGAA
88264 AAAAGAAAAGAAAAAGAAGAA
1 AAAAGAAAAGAAAAAGAAGAA
88285 AA
1 AA
88287 GTCAAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 13 0.57
23 10 0.43
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (21 bp):
AAAAGAAAAGAAAAAGAAGAA
Found at i:88293 original size:28 final size:28
Alignment explanation
Indices: 88236--88299 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
88226 ATTGGAGTAC
*
88236 AAAAGAAAAGAAAAGATAAAAAGAAGAA
1 AAAAGAAAAGAAAAGATAAAAAGAACAA
*
88264 AAAAGAAAAGAAAAAGA-AGAAAAG-TCAA
1 AAAAGAAAAG-AAAAGATA-AAAAGAACAA
88292 AAAAGAAA
1 AAAAGAAA
88300 GCAAGCAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 21 0.66
29 11 0.34
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (28 bp):
AAAAGAAAAGAAAAGATAAAAAGAACAA
Found at i:88297 original size:14 final size:13
Alignment explanation
Indices: 88241--88299 Score: 61
Period size: 14 Copynumber: 4.6 Consensus size: 13
88231 AGTACAAAAG
*
88241 AAAAGAAAAGATA
1 AAAAGAAAAGAAA
88254 AAAAG--AAG-AA
1 AAAAGAAAAGAAA
88264 AAAAGAAAAGAAA
1 AAAAGAAAAGAAA
*
88277 AAGAAGAAAAGTCAA
1 AA-AAGAAAAG-AAA
88292 AAAAGAAA
1 AAAAGAAA
88300 GCAAGCAAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
10 6 0.15
11 3 0.08
12 3 0.08
13 9 0.23
14 14 0.36
15 4 0.10
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (13 bp):
AAAAGAAAAGAAA
Found at i:90888 original size:13 final size:13
Alignment explanation
Indices: 90870--90905 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
90860 ACGTCTATAT
90870 CATCACCATAGTC
1 CATCACCATAGTC
90883 CATCACCATAGTC
1 CATCACCATAGTC
90896 CATCACCATA
1 CATCACCATA
90906 TCACGCCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.39, G:0.06, T:0.22
Consensus pattern (13 bp):
CATCACCATAGTC
Found at i:90922 original size:48 final size:50
Alignment explanation
Indices: 90831--90925 Score: 149
Period size: 48 Copynumber: 1.9 Consensus size: 50
90821 AGATACTATT
* *
90831 TCCATCACCATAATCCATCTTCCATTATCACGTCTATATCATCACCATAG
1 TCCATCACCATAATCCATCTACCATTATCACGCCTATATCATCACCATAG
*
90881 TCCATCACCATAGTCCATC-ACCA-TATCACGCCTATATCATCACCA
1 TCCATCACCATAATCCATCTACCATTATCACGCCTATATCATCACCA
90926 AATTCTCAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
48 21 0.50
49 3 0.07
50 18 0.43
ACGTcount: A:0.31, C:0.37, G:0.04, T:0.28
Consensus pattern (50 bp):
TCCATCACCATAATCCATCTACCATTATCACGCCTATATCATCACCATAG
Found at i:91405 original size:14 final size:15
Alignment explanation
Indices: 91371--91417 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
91361 AATTTGGAGT
91371 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
91386 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
91400 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
91417 G
1 G
91418 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:96658 original size:35 final size:37
Alignment explanation
Indices: 96589--96668 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
96579 ATACTATTTC
*
96589 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
96626 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
96661 CATCACCA
1 CATCACCA
96669 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:103500 original size:35 final size:37
Alignment explanation
Indices: 103430--103510 Score: 130
Period size: 35 Copynumber: 2.2 Consensus size: 37
103420 GATACTATTT
*
103430 TCATCACCATAATCCATCTTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCTACCATTATCACGCCTATA
*
103467 TCATCACCATAGTCCATC-ACCA-TATCACGCCTATA
1 TCATCACCATAATCCATCTACCATTATCACGCCTATA
103502 TCATCACCA
1 TCATCACCA
103511 AATTCTCAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.52
36 3 0.07
37 17 0.40
ACGTcount: A:0.31, C:0.37, G:0.04, T:0.28
Consensus pattern (37 bp):
TCATCACCATAATCCATCTACCATTATCACGCCTATA
Found at i:104233 original size:18 final size:20
Alignment explanation
Indices: 104207--104243 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
104197 AGTGGAAGGT
*
104207 GAAGCCCT-AGTGGTCAAAA
1 GAAGCCCTAAGTGCTCAAAA
104226 GAAG-CCTAAGTGCTCAAA
1 GAAGCCCTAAGTGCTCAAA
104244 TGGTAGAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 3 0.19
19 13 0.81
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (20 bp):
GAAGCCCTAAGTGCTCAAAA
Found at i:107970 original size:8 final size:8
Alignment explanation
Indices: 107959--107983 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
107949 GAGAAAAATC
107959 AGAAAAGA
1 AGAAAAGA
107967 AGAAAAGA
1 AGAAAAGA
107975 AGAAAAGA
1 AGAAAAGA
107983 A
1 A
107984 AAGAAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:114444 original size:13 final size:13
Alignment explanation
Indices: 114426--114450 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
114416 ATTTGTAGCT
114426 CATAACATGAACC
1 CATAACATGAACC
114439 CATAACATGAAC
1 CATAACATGAAC
114451 ATGCATGGAA
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:0.28, G:0.08, T:0.16
Consensus pattern (13 bp):
CATAACATGAACC
Found at i:123005 original size:30 final size:30
Alignment explanation
Indices: 122971--123043 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
122961 TCAATGTCTC
*
122971 CCAAATGTTCCACTAAGCTCTATATATCTT
1 CCAAATGCTCCACTAAGCTCTATATATCTT
* *
123001 CCAAATGCTCCACTAAGCTGTATATGTCTT
1 CCAAATGCTCCACTAAGCTCTATATATCTT
*
123031 CCAAGTGCTCCAC
1 CCAAATGCTCCAC
123044 GAAGTTGTCC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.27, C:0.30, G:0.11, T:0.32
Consensus pattern (30 bp):
CCAAATGCTCCACTAAGCTCTATATATCTT
Found at i:124167 original size:24 final size:24
Alignment explanation
Indices: 124140--124185 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
124130 CTCTTCAAGG
124140 GTCACGTCCGTTAAGCCTTTATGA
1 GTCACGTCCGTTAAGCCTTTATGA
*
124164 GTCACGTCCTTTAAGCCTTTAT
1 GTCACGTCCGTTAAGCCTTTAT
124186 AAATCACCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (24 bp):
GTCACGTCCGTTAAGCCTTTATGA
Found at i:124192 original size:24 final size:24
Alignment explanation
Indices: 124141--124192 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
124131 TCTTCAAGGG
* *
124141 TCACGTCCGTTAAGCCTTTATGAG
1 TCACGTCCGTTAAGCCTTTATAAA
*
124165 TCACGTCCTTTAAGCCTTTATAAA
1 TCACGTCCGTTAAGCCTTTATAAA
124189 TCAC
1 TCAC
124193 CCCTCTTGGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.25, C:0.27, G:0.13, T:0.35
Consensus pattern (24 bp):
TCACGTCCGTTAAGCCTTTATAAA
Found at i:126066 original size:33 final size:36
Alignment explanation
Indices: 125991--126067 Score: 106
Period size: 37 Copynumber: 2.2 Consensus size: 36
125981 TACTATTTCT
*
125991 ATCACCATAATCCATCTTCCATTATCACGCCTATATC
1 ATCACCATAATCCATCTACCATTATCACGCC-ATATC
*
126028 ATCACCATAGTCCATC-ACCA-TATCACGCC-TATC
1 ATCACCATAATCCATCTACCATTATCACGCCATATC
126061 ATCACCA
1 ATCACCA
126068 AATTCTCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
33 11 0.29
35 9 0.24
36 3 0.08
37 15 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.27
Consensus pattern (36 bp):
ATCACCATAATCCATCTACCATTATCACGCCATATC
Found at i:129957 original size:20 final size:21
Alignment explanation
Indices: 129926--129981 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
129916 ATTGGAGTGC
*
129926 AAAAAGAAAGAAAAGA-CA-A
1 AAAAAAAAAGAAAAGATCAGA
129945 AAAAAAAAGAGAAAA-ATCAGA
1 AAAAAAAA-AGAAAAGATCAGA
*
129966 AAAAGAAAAGAAAAGA
1 AAAAAAAAAGAAAAGA
129982 AAAGATTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 8 0.26
20 14 0.45
21 9 0.29
ACGTcount: A:0.79, C:0.04, G:0.16, T:0.02
Consensus pattern (21 bp):
AAAAAAAAAGAAAAGATCAGA
Found at i:138547 original size:35 final size:37
Alignment explanation
Indices: 138478--138557 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
138468 ATACTATTTC
*
138478 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
* *
138515 CATCACCATAGTCCATC-ACTA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
138550 CATCACCA
1 CATCACCA
138558 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 22 0.55
36 2 0.05
37 16 0.40
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:149492 original size:27 final size:27
Alignment explanation
Indices: 149439--149493 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
149429 CTTGTTTTCT
* *
149439 TGCACATTTAGGTACATTGGAGTATGA
1 TGCACATTGAGGTACATTGGAGGATGA
*
149466 TGCACATTGAGGTAGC-TTGGTGGATGA
1 TGCACATTGAGGTA-CATTGGAGGATGA
149493 T
1 T
149494 TTGGACGACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.25, C:0.11, G:0.31, T:0.33
Consensus pattern (27 bp):
TGCACATTGAGGTACATTGGAGGATGA
Found at i:163873 original size:22 final size:23
Alignment explanation
Indices: 163845--163896 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
163835 ATTTATAAGT
163845 TGGTGATAATATAGGCGTGAT-A
1 TGGTGATAATATAGGCGTGATAA
* *
163867 TGGTGATGATATAGGTGTGATAA
1 TGGTGATAATATAGGCGTGATAA
163890 TGGTGAT
1 TGGTGAT
163897 GGACTATGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.29, C:0.02, G:0.35, T:0.35
Consensus pattern (23 bp):
TGGTGATAATATAGGCGTGATAA
Found at i:163905 original size:36 final size:36
Alignment explanation
Indices: 163865--163936 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
163855 ATAGGCGTGA
* * *
163865 TATGGTGATGATATAGGTGTGATAATGGTGATGGAC
1 TATGGCGATGATAAAGGCGTGATAATGGTGATGGAC
*
163901 TATGGCGATGATAAAGGCGTGATGATGGTGATGGAC
1 TATGGCGATGATAAAGGCGTGATAATGGTGATGGAC
163937 ATATTGTATC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.28, C:0.06, G:0.38, T:0.29
Consensus pattern (36 bp):
TATGGCGATGATAAAGGCGTGATAATGGTGATGGAC
Found at i:168010 original size:24 final size:24
Alignment explanation
Indices: 167966--168012 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
167956 ATAAAGAACC
*
167966 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
167990 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
168013 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:171314 original size:19 final size:20
Alignment explanation
Indices: 171292--171335 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
171282 GAGAAAAGGT
171292 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
171311 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
171331 AAAAG
1 AAAAG
171336 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Done.