Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006279.1 Hibiscus syriacus cultivar Beakdansim tig00014990_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: 119148
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:5241 original size:18 final size:18
Alignment explanation
Indices: 5218--5252 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
5208 ACTGAATATT
5218 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
5236 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
5253 GATAATCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.23, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:9706 original size:64 final size:63
Alignment explanation
Indices: 9590--9730 Score: 151
Period size: 64 Copynumber: 2.2 Consensus size: 63
9580 CACGTTCAAT
* * *
9590 GTGCATCGATGCACTCTTTAAAGAAGAAACCTCGAATACAATTAGTGCATCGATACATAAGG-A
1 GTGCATCGATGCACCCTTTAAAGAAGAAACATCGAAGACAATTAGTGCATCGATACAT-AGGTA
* ** * * * *
9653 GTGCATCGATGCATCCCTTTAAA-ATGAAAACATCGAAGGTAATTTGTGTATCGATGCATGGGTA
1 GTGCATCGATGCA-CCCTTTAAAGAAG-AAACATCGAAGACAATTAGTGCATCGATACATAGGTA
9717 GTGCATCGATGCAC
1 GTGCATCGATGCAC
9731 ATGTTAAAGA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
63 18 0.28
64 47 0.72
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCACCCTTTAAAGAAGAAACATCGAAGACAATTAGTGCATCGATACATAGGTA
Found at i:10628 original size:18 final size:18
Alignment explanation
Indices: 10605--10682 Score: 113
Period size: 18 Copynumber: 4.3 Consensus size: 18
10595 GAGGTTCTAC
* *
10605 GTGGTCTTTCGGGATATA
1 GTGGTCATTCGGGACATA
10623 GTGGTCATTCGGGACATA
1 GTGGTCATTCGGGACATA
*
10641 ATGGTTC-TTCGGGACATA
1 GTGG-TCATTCGGGACATA
10659 GTGGTCATTCGGGACATA
1 GTGGTCATTCGGGACATA
10677 GTGGTC
1 GTGGTC
10683 CTAGGAGACA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
17 2 0.04
18 50 0.93
19 2 0.04
ACGTcount: A:0.19, C:0.15, G:0.33, T:0.32
Consensus pattern (18 bp):
GTGGTCATTCGGGACATA
Found at i:10692 original size:18 final size:18
Alignment explanation
Indices: 10615--10692 Score: 52
Period size: 18 Copynumber: 4.3 Consensus size: 18
10605 GTGGTCTTTC
* * *
10615 GGGATATAGTGGTCATTC
1 GGGACATAGTGGTCACTA
* * *
10633 GGGACATAATGGTTC-TTC
1 GGGACATAGTGG-TCACTA
* *
10651 GGGACATAGTGGTCATTC
1 GGGACATAGTGGTCACTA
10669 GGGACATAGTGGTC-CTA
1 GGGACATAGTGGTCACTA
10686 GGAGACA
1 GG-GACA
10693 AATTCTACGC
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
17 5 0.10
18 45 0.87
19 2 0.04
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.27
Consensus pattern (18 bp):
GGGACATAGTGGTCACTA
Found at i:14017 original size:20 final size:22
Alignment explanation
Indices: 13972--14029 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
13962 GCATGGGTAG
13972 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
13996 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
14016 TGCATCGATGCACT
1 TGCATCGATGCACT
14030 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:14863 original size:18 final size:18
Alignment explanation
Indices: 14840--14927 Score: 122
Period size: 18 Copynumber: 4.9 Consensus size: 18
14830 GAGGGTCTAC
**
14840 GTGGTCCTTCGACACATA
1 GTGGTCCTTCGGGACATA
*
14858 GTGGTCATTCGGGACATA
1 GTGGTCCTTCGGGACATA
* *
14876 ATGGTCCTTCGGGACACA
1 GTGGTCCTTCGGGACATA
14894 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
14912 GTGGTCCTACGGGACA
1 GTGGTCCTTCGGGACA
14928 AATTCTATGC
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 61 1.00
ACGTcount: A:0.20, C:0.24, G:0.31, T:0.25
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:19074 original size:13 final size:13
Alignment explanation
Indices: 19056--19093 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
19046 TCAGAGTCAA
*
19056 TGAGTTGACTTAG
1 TGAGTTGACTCAG
*
19069 TGAGTTGGCTCAG
1 TGAGTTGACTCAG
19082 TGAGTTGACTCA
1 TGAGTTGACTCA
19094 ACCGAGTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.21, C:0.13, G:0.32, T:0.34
Consensus pattern (13 bp):
TGAGTTGACTCAG
Found at i:20799 original size:30 final size:30
Alignment explanation
Indices: 20764--20851 Score: 115
Period size: 30 Copynumber: 2.9 Consensus size: 30
20754 AATGGATTTA
* *
20764 TTTAGTGACCAAATTATAAATTTGGTAAAG
1 TTTAGTGACCAAAATATAAATTTGGAAAAG
*
20794 TTTAGTGACCAAAGTATAAACTTT-GAAAAG
1 TTTAGTGACCAAAATATAAA-TTTGGAAAAG
* *
20824 TTTAGGGACCAAAATATAATTTTGGAAA
1 TTTAGTGACCAAAATATAAATTTGGAAA
20852 CATTACAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (30 bp):
TTTAGTGACCAAAATATAAATTTGGAAAAG
Found at i:32444 original size:3 final size:3
Alignment explanation
Indices: 32438--32549 Score: 172
Period size: 3 Copynumber: 37.7 Consensus size: 3
32428 TTAATATATT
32438 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * **
32485 TAA TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAA GGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
32533 TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
32550 TGGATAAAAA
Statistics
Matches: 98, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
2 2 0.02
3 96 0.98
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:32999 original size:113 final size:113
Alignment explanation
Indices: 32801--33565 Score: 1113
Period size: 113 Copynumber: 6.8 Consensus size: 113
32791 TCTTGATGAG
*
32801 TTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
*
32866 GCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
66 GCAATGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
32914 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
* * *
32979 GCAATGTTGATCCATCAAATGCTGAATTCAAGTAAAAGGTTGAACAAA
66 GCAATGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
* *
33027 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTT-CTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-CT
** * * * *
33091 GGCAAAAATAATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAA
65 GGCAATGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
* *
33140 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
* * * *** * * *
33205 GCACTGCTGATCCACCGGGTGATGAATTTAAGCAAAAAGTTGAACAAG
66 GCAATGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
* * *
33253 TTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAAATGAGTTCTTCTCATTATGAACTCTAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
* * * *
33317 GTAATGATGATCCATCAAATGATGAATTTAAGCAAAAAGTTGAACAAG
66 GCAATGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
*
33365 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTATCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
* * **
33430 GCAATGATAATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAA
66 GCAATGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
* * **
33478 TTCTTCTCATTATGAATTTCTTCTCCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
* **
33543 G-AATGTTGATCCATTGAATGATG
66 GCAATGATGATCCATCAAATGATG
33566 GATTTGAACT
Statistics
Matches: 594, Mismatches: 55, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
112 122 0.21
113 472 0.79
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
GCAATGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
Found at i:33997 original size:22 final size:22
Alignment explanation
Indices: 33972--34026 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
33962 GATAAAGCTT
* *
33972 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTAAAAAGAGAATCTA
*
33994 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
34016 TCATCTTTAAA
1 TCATCTTTAAA
34027 GAATGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAATCTA
Found at i:36854 original size:83 final size:83
Alignment explanation
Indices: 36714--36978 Score: 460
Period size: 83 Copynumber: 3.2 Consensus size: 83
36704 CTTATTTCTA
* *
36714 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCC-AACCAGATTAGATAACTCAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTG-CCAAACCAGATCAGATAACTCAA
36778 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
* *
36797 CTATGAACAAATTCATCTTCTAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
36862 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
36880 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
36945 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
36963 CTATGAGCACATTCAT
1 CTATGAGCAAATTCAT
36979 TTGTTCCATT
Statistics
Matches: 174, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
82 2 0.01
83 172 0.99
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.28
Consensus pattern (83 bp):
CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:39223 original size:6 final size:6
Alignment explanation
Indices: 39209--39253 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
39199 CTTTATTCGA
* *
39209 TTTTCC TTTTTC TTTTT- TTTTTC TTTTTC TTCTTC TTCTTTC TTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT-TTTC TTT
39254 GCTGGATGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
5 5 0.15
6 24 0.71
7 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:39234 original size:17 final size:19
Alignment explanation
Indices: 39209--39253 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
39199 CTTTATTCGA
*
39209 TTTTCCTTTTTCTT-TT-T
1 TTTTTCTTTTTCTTCTTCT
39226 TTTTTCTTTTTCTTCTTCT
1 TTTTTCTTTTTCTTCTTCT
*
39245 TCTTTCTTT
1 TTTTTCTTT
39254 GCTGGATGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 13 0.54
18 2 0.08
19 9 0.38
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTCTTTTTCTTCTTCT
Found at i:42553 original size:14 final size:14
Alignment explanation
Indices: 42519--42572 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
42509 TTGTGCAATA
* *
42519 CAAATGCAAAGATG
1 CAAATGTAAATATG
42533 CCAAATGTAAATATG
1 -CAAATGTAAATATG
*
42548 CAAATGTAAAAATG
1 CAAATGTAAATATG
*
42562 TAAATGTAAAT
1 CAAATGTAAAT
42573 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:46470 original size:3 final size:3
Alignment explanation
Indices: 46464--46564 Score: 148
Period size: 3 Copynumber: 33.7 Consensus size: 3
46454 TTAATATATT
* *
46464 TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* ** *
46512 TAA TAA TAA TAT TAA TAA TAA TAA GGA TAA TAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
46560 TAA TA
1 TAA TA
46565 TGGATAAAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 86 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:46976 original size:24 final size:23
Alignment explanation
Indices: 46948--47027 Score: 69
Period size: 24 Copynumber: 3.5 Consensus size: 23
46938 CACTTAACAA
46948 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCATCCC-TTGAATG
* *
46972 TGCATCGATTCATCACGTTG-A--
1 TGCATCGATGCATC-CCTTGAATG
*
46993 TGCACCGATGCA-CGCCTTGAATG
1 TGCATCGATGCATC-CCTTGAATG
*
47016 TGCATCCATGCA
1 TGCATCGATGCA
47028 CAGGGTCATG
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
20 5 0.11
21 11 0.25
23 11 0.25
24 16 0.36
25 1 0.02
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.29
Consensus pattern (23 bp):
TGCATCGATGCATCCCTTGAATG
Found at i:49752 original size:65 final size:64
Alignment explanation
Indices: 49683--49844 Score: 252
Period size: 65 Copynumber: 2.5 Consensus size: 64
49673 TGATTTAATT
* * *
49683 AAACATCGAATGTATTTGATGCATCGATGCACATACCATGCATCGATGCACTCAGGGTTTTATGA
1 AAACATCGAATGCATTTGATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTTTT-TCA
*
49748 AAACATCGAATGCATTTGATGCATCGATGCACATATCATGCATCGATGCACTCAGGCTTTTTCA
1 AAACATCGAATGCATTTGATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTTTTTCA
* *
49812 AAACATCGAATGCATTTTATGCATTCAATGCAC
1 AAACATCGAATGCATTTGATGCA-TCGATGCAC
49845 TCTTAGTGCA
Statistics
Matches: 90, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
64 24 0.27
65 66 0.73
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (64 bp):
AAACATCGAATGCATTTGATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTTTTTCA
Found at i:49860 original size:65 final size:65
Alignment explanation
Indices: 49683--49864 Score: 244
Period size: 65 Copynumber: 2.8 Consensus size: 65
49673 TGATTTAATT
* * *
49683 AAACATCGAATGTATTTGATGCATCGATGCACATAC-CATGCATCGATGCACTCAGGGTTTTATG
1 AAACATCGAATGCATTTGATGCATCGATGCACAT-CTCATGCATCGATGCACTCAGGCTTTTATC
49747 A
65 A
*
49748 AAACATCGAATGCATTTGATGCATCGATGCACATATCATGCATCGATGCACTCAGGCTTTT-TCA
1 AAACATCGAATGCATTTGATGCATCGATGCACATCTCATGCATCGATGCACTCAGGCTTTTATCA
* * * *
49812 AAACATCGAATGCATTTTATGCATTCAATGCAC-TCTTAGTGCACCGATGCACT
1 AAACATCGAATGCATTTGATGCA-TCGATGCACATCTCA-TGCATCGATGCACT
49865 GAGAGTCCAA
Statistics
Matches: 105, Mismatches: 9, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
64 27 0.26
65 78 0.74
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (65 bp):
AAACATCGAATGCATTTGATGCATCGATGCACATCTCATGCATCGATGCACTCAGGCTTTTATCA
Found at i:52943 original size:27 final size:27
Alignment explanation
Indices: 52883--52934 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
52873 AATGATGTCC
** *
52883 AAGGAAAAACTTCCTGAAATGCTCTAT
1 AAGGAAACGCTTCCTGAAACGCTCTAT
52910 AAGGAAACGCTTCCTGAAACGCTCT
1 AAGGAAACGCTTCCTGAAACGCTCT
52935 TTGAAGAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (27 bp):
AAGGAAACGCTTCCTGAAACGCTCTAT
Found at i:58555 original size:76 final size:75
Alignment explanation
Indices: 58464--58628 Score: 233
Period size: 76 Copynumber: 2.2 Consensus size: 75
58454 TTAAACTCAA
* *
58464 ATTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGT
1 ATTTAGGATATTATTTT-AACATTATATCTTTATCTTTGTATTTTAGTTTAAATAAG-TTTTAGT
58528 ATTTTAATTAAG
64 ATTTTAATTAAG
* * * *
58540 TTTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAAGTTTTAGTAT
1 ATTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAAGTTTTAGTAT
*
58605 TTTAATTAGG
66 TTTAATTAAG
*
58615 ATTTAGAATATTAT
1 ATTTAGGATATTAT
58629 ATTATTTTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
75 37 0.47
76 42 0.53
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.56
Consensus pattern (75 bp):
ATTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAAGTTTTAGTAT
TTTAATTAAG
Found at i:58814 original size:42 final size:43
Alignment explanation
Indices: 58753--58849 Score: 160
Period size: 43 Copynumber: 2.3 Consensus size: 43
58743 TAGAAACATA
*
58753 TCTCTCTCATTTGAGAATAAAATCTTC-TTTTTCCCTCTAGCTT
1 TCTCTCT-ATTTAAGAATAAAATCTTCTTTTTTCCCTCTAGCTT
*
58796 TCTCTCTATTTAAGAATAAAATCTTCTTTTTTCTCTCTAGCTT
1 TCTCTCTATTTAAGAATAAAATCTTCTTTTTTCCCTCTAGCTT
58839 TCTCTCTATTT
1 TCTCTCTATTT
58850 TTCGCATACT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
42 18 0.35
43 33 0.65
ACGTcount: A:0.21, C:0.24, G:0.05, T:0.51
Consensus pattern (43 bp):
TCTCTCTATTTAAGAATAAAATCTTCTTTTTTCCCTCTAGCTT
Found at i:59344 original size:21 final size:22
Alignment explanation
Indices: 59319--59359 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
59309 CTTTAATTTG
59319 TTTATTTAATTATT-TTTTTCT
1 TTTATTTAATTATTATTTTTCT
*
59340 TTTATTTAATTCTTATTTTT
1 TTTATTTAATTATTATTTTT
59360 TATTTTAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTATTTAATTATTATTTTTCT
Found at i:66897 original size:76 final size:76
Alignment explanation
Indices: 66776--66941 Score: 253
Period size: 76 Copynumber: 2.2 Consensus size: 76
66766 TTAAACTCAA
* *
66776 ATTTAGGATAATATTTTAAACATTATATTTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGT
1 ATTTAGGATATTATTTTAAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGT
66841 ATTTTAATTAAG
65 ATTTTAATTAAG
* * *
66853 ATTTAGGATATTATTTT-TATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTA
1 ATTTAGGATATTATTTTAAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTA
*
66917 TTTTAATTAGG
66 TTTTAATTAAG
*
66928 ATTTAGAATATTAT
1 ATTTAGGATATTAT
66942 ATTATTTTTT
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
75 31 0.38
76 35 0.43
77 16 0.20
ACGTcount: A:0.31, C:0.02, G:0.11, T:0.56
Consensus pattern (76 bp):
ATTTAGGATATTATTTTAAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTA
TTTTAATTAAG
Found at i:66927 original size:19 final size:19
Alignment explanation
Indices: 66899--66961 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
66889 TGTATTTTAG
*
66899 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
* *
66918 TTTAATTAGGATTTAGAAT
1 TTTAATTAGGTTTTAGTAT
* **
66937 ATTATATTATTTTTTAGGTAT
1 TTTA-ATTAGGTTTTA-GTAT
66958 TTTA
1 TTTA
66962 GTTTAAATAG
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 8 0.24
21 6 0.18
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.56
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:67614 original size:21 final size:22
Alignment explanation
Indices: 67589--67629 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
67579 CTTTAATTTG
67589 TTTATTTAATTATT-TTTTTCT
1 TTTATTTAATTATTATTTTTCT
*
67610 TTTATTTAATTCTTATTTTT
1 TTTATTTAATTATTATTTTT
67630 TATTTTAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTATTTAATTATTATTTTTCT
Found at i:72458 original size:21 final size:21
Alignment explanation
Indices: 72432--72485 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
72422 ACTACATATG
*
72432 TGCTTAAGAAATGCTAGATTT
1 TGCTTACGAAATGCTAGATTT
72453 TGCTTACGAAATGCTAGATTT
1 TGCTTACGAAATGCTAGATTT
72474 TGCTTACGAAAT
1 TGCTTACGAAAT
72486 ACGGATAACC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (21 bp):
TGCTTACGAAATGCTAGATTT
Found at i:74071 original size:24 final size:24
Alignment explanation
Indices: 74044--74159 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
74034 TTCTATTTGA
74044 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
74068 ATTCTGATCTGATA-TCTGACATAG
1 ATTCTGATCTGATACT-TGACATGG
*
74092 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
*
74116 ATTCTGATCTGATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGG
* * *
74140 ATTTTGATATTATACTTGAC
1 ATTCTGATCTGATACTTGAC
74160 CTGATTTATG
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
23 1 0.01
24 81 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:77339 original size:24 final size:24
Alignment explanation
Indices: 77311--77361 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
77301 AAATCATATC
77311 TAACGTTAAGTTTTAGTTTTATTT
1 TAACGTTAAGTTTTAGTTTTATTT
77335 TAACGTTAAGTTTTAGTTTTATTT
1 TAACGTTAAGTTTTAGTTTTATTT
77359 TAA
1 TAA
77362 TCATCTGTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.04, G:0.12, T:0.57
Consensus pattern (24 bp):
TAACGTTAAGTTTTAGTTTTATTT
Found at i:90300 original size:9 final size:9
Alignment explanation
Indices: 90261--90317 Score: 75
Period size: 9 Copynumber: 6.7 Consensus size: 9
90251 TCTGCAAAAA
*
90261 AAATTAATT
1 AAATTAAAT
90270 AAA-TAAA-
1 AAATTAAAT
*
90277 ATATTAAAT
1 AAATTAAAT
90286 -AATTAAAT
1 AAATTAAAT
90294 AAATTAAAT
1 AAATTAAAT
90303 AAATTAAAT
1 AAATTAAAT
90312 AAATTA
1 AAATTA
90318 CTAAATATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
7 2 0.05
8 14 0.33
9 26 0.62
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
AAATTAAAT
Found at i:90322 original size:26 final size:26
Alignment explanation
Indices: 90262--90331 Score: 67
Period size: 26 Copynumber: 2.8 Consensus size: 26
90252 CTGCAAAAAA
* *
90262 AATTAATTAAATA-AA-ATATTAAAT
1 AATTAAATAAATATAATAAATTAAAT
90286 AATTAAATAAAT-TAAATAAATTAAAT
1 AATTAAATAAATAT-AATAAATTAAAT
*
90312 AAATT-ACTAAATATAATAAA
1 -AATTAAATAAATATAATAAA
90332 ATATACCTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
24 11 0.29
25 2 0.05
26 20 0.53
27 5 0.13
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (26 bp):
AATTAAATAAATATAATAAATTAAAT
Found at i:96220 original size:19 final size:19
Alignment explanation
Indices: 96198--96234 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
96188 TATTATTTCA
96198 CCAGTATAAAATTAAATCT
1 CCAGTATAAAATTAAATCT
96217 CCAGTATAAAATTAAATC
1 CCAGTATAAAATTAAATC
96235 ACCAATGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.30
Consensus pattern (19 bp):
CCAGTATAAAATTAAATCT
Found at i:96247 original size:19 final size:19
Alignment explanation
Indices: 96195--96240 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
96185 ACTTATTATT
*
96195 TCACCAGTATAAAATTAAA
1 TCACCAATATAAAATTAAA
* *
96214 TCTCCAGTATAAAATTAAA
1 TCACCAATATAAAATTAAA
96233 TCACCAAT
1 TCACCAAT
96241 GTCAAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.48, C:0.20, G:0.04, T:0.28
Consensus pattern (19 bp):
TCACCAATATAAAATTAAA
Found at i:107362 original size:2 final size:2
Alignment explanation
Indices: 107357--107391 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
107347 CAATTACTTT
107357 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
107392 TAAGTATCGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:107619 original size:23 final size:24
Alignment explanation
Indices: 107579--107641 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 24
107569 ATATATTTCG
* * *
107579 CGAATATATAAGCGAACATGTTCA
1 CGAAAATATAAACAAACATGTTCA
*
107603 CGAACAT-TAAACAAACATGTTCA
1 CGAAAATATAAACAAACATGTTCA
107626 CGAAAATATAAACAAA
1 CGAAAATATAAACAAA
107642 TACTTTCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 20 0.59
24 14 0.41
ACGTcount: A:0.51, C:0.17, G:0.11, T:0.21
Consensus pattern (24 bp):
CGAAAATATAAACAAACATGTTCA
Found at i:108838 original size:20 final size:20
Alignment explanation
Indices: 108813--108884 Score: 144
Period size: 20 Copynumber: 3.6 Consensus size: 20
108803 TATTTGAAAA
108813 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
108833 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
108853 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
108873 TCGCGTTGCGAT
1 TCGCGTTGCGAT
108885 AGTCTACAGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.10, C:0.25, G:0.22, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:108904 original size:22 final size:21
Alignment explanation
Indices: 108876--108967 Score: 82
Period size: 22 Copynumber: 4.4 Consensus size: 21
108866 TTCCATTTCG
*
108876 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGAT-T
* * *
108898 CGTTGCGAT--TTTCCAAATT
1 CGTTGCGATAGTCTACAGATT
*
108917 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGAT-T
* *
108939 TGTTGCGATAGTTTACA-ATT
1 CGTTGCGATAGTCTACAGATT
108959 CGTTGCGAT
1 CGTTGCGAT
108968 GGCGGCGGCG
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
19 10 0.18
20 14 0.25
21 6 0.11
22 25 0.45
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGATT
Found at i:108931 original size:41 final size:40
Alignment explanation
Indices: 108856--108967 Score: 152
Period size: 41 Copynumber: 2.7 Consensus size: 40
108846 TTCCATTTCG
*
108856 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAATT--CGTTGCGATAGTCTACAGTTGT
108898 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCC-AATTCGTTGCGATAGTCTACAGTTGT
* *
108939 TGTTGCGATAGTTTACAATTCGTTGCGAT
1 CGTTGCGAT--TTTCCAATTCGTTGCGAT
108968 GGCGGCGGCG
Statistics
Matches: 64, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
41 30 0.47
42 27 0.42
43 7 0.11
ACGTcount: A:0.18, C:0.19, G:0.23, T:0.40
Consensus pattern (40 bp):
CGTTGCGATTTTCCAATTCGTTGCGATAGTCTACAGTTGT
Found at i:110042 original size:42 final size:41
Alignment explanation
Indices: 109994--110073 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 41
109984 AACTAATTTA
109994 GAAAATCGCAACGACAACTGT-AGACTATCGCAACGCGAAATG
1 GAAAATCGCAAC-ACAACTGTCA-ACTATCGCAACGCGAAATG
* * *
110036 GAAAATCGCAACACGATTTTCAACTATCGCAACGCGAA
1 GAAAATCGCAACACAACTGTCAACTATCGCAACGCGAA
110074 TTTGCGATAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 21 0.62
42 13 0.38
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.16
Consensus pattern (41 bp):
GAAAATCGCAACACAACTGTCAACTATCGCAACGCGAAATG
Found at i:118539 original size:15 final size:15
Alignment explanation
Indices: 118521--118554 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
118511 ATTATATAAA
118521 ATATAATGAATTATT
1 ATATAATGAATTATT
* *
118536 ATATTATGGATTATT
1 ATATAATGAATTATT
118551 ATAT
1 ATAT
118555 TTTGTATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (15 bp):
ATATAATGAATTATT
Found at i:118736 original size:15 final size:14
Alignment explanation
Indices: 118685--118740 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 14
118675 AACCGGGTAT
118685 CGGGTACCCGATTA
1 CGGGTACCCGATTA
*
118699 CGAGTACCCGCAAAATT-
1 CGGGTACCCG----ATTA
118716 CGGGTACCCGATTA
1 CGGGTACCCGATTA
118730 CCGGGTACCCG
1 -CGGGTACCCG
118741 TAATATCTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
13 3 0.09
14 9 0.26
15 10 0.29
17 9 0.26
18 3 0.09
ACGTcount: A:0.23, C:0.32, G:0.27, T:0.18
Consensus pattern (14 bp):
CGGGTACCCGATTA
Done.