Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005587.1 Hibiscus syriacus cultivar Beakdansim tig00012971_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: 72600
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Found at i:20118 original size:12 final size:12
Alignment explanation
Indices: 20101--20125 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20091 TGAAGCCTTT
20101 AAACCGAACCGA
1 AAACCGAACCGA
20113 AAACCGAACCGA
1 AAACCGAACCGA
20125 A
1 A
20126 CCGTTTTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.32, G:0.16, T:0.00
Consensus pattern (12 bp):
AAACCGAACCGA
Found at i:29682 original size:18 final size:18
Alignment explanation
Indices: 29659--29695 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
29649 TATAGTTTGT
29659 TGTTTTTT-TTCTTTTCTC
1 TGTTTTTTCTT-TTTTCTC
29677 TGTTTTTTCTTTTTTCTC
1 TGTTTTTTCTTTTTTCTC
29695 T
1 T
29696 TCGGTTCTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.78
Consensus pattern (18 bp):
TGTTTTTTCTTTTTTCTC
Found at i:30185 original size:3 final size:3
Alignment explanation
Indices: 30177--30272 Score: 120
Period size: 3 Copynumber: 32.0 Consensus size: 3
30167 TTAATATATT
* * * *
30177 TAA TAA TAA AAA AAA TAA TAA TAA TAA TAA TAA TAA AAA TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
30225 TAA TAA TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
30273 AATGGATAAA
Statistics
Matches: 79, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:30742 original size:114 final size:114
Alignment explanation
Indices: 30522--31314 Score: 1460
Period size: 114 Copynumber: 6.9 Consensus size: 114
30512 GCTCTTGATG
*
30522 AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-T
30587 TCCTCTGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
62 T-CTCTGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
*
30641 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
30706 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
66 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
30755 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
30820 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
66 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
30869 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
30934 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
66 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
30983 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
31048 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
66 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
31097 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
31162 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
66 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
*
31211 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-T
*
31276 TCTCTGGAAAAGAATGATCCATCAATTTGATGAATTCAA
62 TCTCTGGAAAAGAATGATCCATCAA-GTGATGAATTCAA
31315 ATCTTTGCTA
Statistics
Matches: 664, Mismatches: 5, Indels: 10
0.98 0.01 0.01
Matches are distributed among these distances:
114 545 0.82
115 2 0.00
116 20 0.03
117 21 0.03
118 26 0.04
119 50 0.08
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.36
Consensus pattern (114 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
Found at i:32001 original size:52 final size:52
Alignment explanation
Indices: 31952--32362 Score: 693
Period size: 52 Copynumber: 7.9 Consensus size: 52
31942 CTATCCAATT
* *
31952 AGATCAGATATCTCAAAGAACACTTCCAGAAAATGCTATGTTCTG-TCCAACC
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGAT-CAACC
*
32004 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGATCAACC
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGATCAACC
* *
32056 AGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATGTTATGATCAACC
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGATCAACC
*
32108 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGATCAACC
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGATCAACC
*
32160 AGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATGTTCTG-TCCAACC
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGAT-CAACC
32212 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCCAACC
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGAT-CAACC
*
32264 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGATCAACC
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGATCAACC
*
32316 AGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATGTTCTGAT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGAT
32363 GCTTTTCCAT
Statistics
Matches: 345, Mismatches: 11, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
51 1 0.00
52 342 0.99
53 2 0.01
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (52 bp):
AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGATCAACC
Found at i:33009 original size:16 final size:16
Alignment explanation
Indices: 32973--33010 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
32963 TGAATTTCCA
32973 AAAATAAATTGAATCT
1 AAAATAAATTGAATCT
*
32989 CAAATAAATTGAA-CTT
1 AAAATAAATTGAATC-T
33005 AAAATA
1 AAAATA
33011 GATAGAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 1 0.05
16 18 0.95
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.29
Consensus pattern (16 bp):
AAAATAAATTGAATCT
Found at i:33334 original size:1 final size:1
Alignment explanation
Indices: 33330--33377 Score: 60
Period size: 1 Copynumber: 48.0 Consensus size: 1
33320 TTGACCCCTC
* ** *
33330 TTTTTTCTTTTTTTTCCTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
33378 CTTCAAGCAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (1 bp):
T
Found at i:33354 original size:12 final size:11
Alignment explanation
Indices: 33330--33380 Score: 79
Period size: 11 Copynumber: 4.8 Consensus size: 11
33320 TTGACCCCTC
33330 TTTTTTC-TTT
1 TTTTTTCTTTT
*
33340 TTTTTCCTTTT
1 TTTTTTCTTTT
33351 TTTTTTCTTTT
1 TTTTTTCTTTT
33362 TTTTTT-TTTT
1 TTTTTTCTTTT
33372 TTTTTTCTT
1 TTTTTTCTT
33381 CAAGCATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
10 16 0.43
11 21 0.57
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:33356 original size:21 final size:21
Alignment explanation
Indices: 33330--33380 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
33320 TTGACCCCTC
33330 TTTTTTCTTTTTTTTCCTTTT
1 TTTTTTCTTTTTTTTCCTTTT
**
33351 TTTTTTCTTTTTTTTTTTTTT
1 TTTTTTCTTTTTTTTCCTTTT
33372 TTTTTTCTT
1 TTTTTTCTT
33381 CAAGCATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (21 bp):
TTTTTTCTTTTTTTTCCTTTT
Found at i:45672 original size:18 final size:18
Alignment explanation
Indices: 45649--45685 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
45639 TATAGTTTGT
45649 TGTTTTTT-TTCTTTTCTC
1 TGTTTTTTCTT-TTTTCTC
45667 TGTTTTTTCTTTTTTCTC
1 TGTTTTTTCTTTTTTCTC
45685 T
1 T
45686 TCGGTTCTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.78
Consensus pattern (18 bp):
TGTTTTTTCTTTTTTCTC
Found at i:46174 original size:3 final size:3
Alignment explanation
Indices: 46166--46258 Score: 114
Period size: 3 Copynumber: 31.0 Consensus size: 3
46156 TTAATATATT
* * * *
46166 TAA TAA TAA AAA AAA TAA TAA TAA TAA TAA TAA AAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
46214 TAA TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
46259 AATGGATAAA
Statistics
Matches: 76, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:46641 original size:30 final size:30
Alignment explanation
Indices: 46605--46694 Score: 180
Period size: 30 Copynumber: 3.0 Consensus size: 30
46595 TTTTCCCCCC
46605 GAACTTACTTTACCTCATCTGCTATTGGTT
1 GAACTTACTTTACCTCATCTGCTATTGGTT
46635 GAACTTACTTTACCTCATCTGCTATTGGTT
1 GAACTTACTTTACCTCATCTGCTATTGGTT
46665 GAACTTACTTTACCTCATCTGCTATTGGTT
1 GAACTTACTTTACCTCATCTGCTATTGGTT
46695 AACAATGCTC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.20, C:0.23, G:0.13, T:0.43
Consensus pattern (30 bp):
GAACTTACTTTACCTCATCTGCTATTGGTT
Found at i:48104 original size:6 final size:6
Alignment explanation
Indices: 48093--48121 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
48083 TATATTTAGA
48093 GAGAGG GAGAGG GAGAGG GAGAGG GAGAG
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAG
48122 AACTTACTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:48840 original size:20 final size:21
Alignment explanation
Indices: 48817--49099 Score: 120
Period size: 20 Copynumber: 14.0 Consensus size: 21
48807 ATACGAACTC
48817 CAAATTCGCAACAC-AATTTT
1 CAAATTCGCAACACGAATTTT
* *
48837 CAAATTCGCAACTC--AGTTT
1 CAAATTCGCAACACGAATTTT
*
48856 CTACAA-TCGCAACGCGAATTTT
1 C-A-AATTCGCAACACGAATTTT
* *
48878 ---TTCTCGCAACGCG-ATTTT
1 CAAAT-TCGCAACACGAATTTT
48896 CCAAATTCGCAACACGGAA-TTT
1 -CAAATTCGCAACAC-GAATTTT
48918 CAAATTCGCAACACGGAA-TTT
1 CAAATTCGCAACAC-GAATTTT
*
48939 CAAATTCGCAACTCG-ATTTAT
1 CAAATTCGCAACACGAATTT-T
* * *
48960 -GAATTCGTAACTCG-A-TTT
1 CAAATTCGCAACACGAATTTT
* *
48978 CTGAATTCGCAACGCGAA-TTT
1 C-AAATTCGCAACACGAATTTT
*** * *
48999 CTTTTTCCCAACAC-AAGTTT
1 CAAATTCGCAACACGAATTTT
*** * *
49019 CCTTTTCGTAACAAG-ATTTT
1 CAAATTCGCAACACGAATTTT
*
49039 CTAAA-TCGCAACGCGAATTTT
1 C-AAATTCGCAACACGAATTTT
**
49060 -ATTTTCGCAACACG-ATTTT
1 CAAATTCGCAACACGAATTTT
*
49079 CGAATTCGCAACACGAATTTT
1 CAAATTCGCAACACGAATTTT
49100 AATTTTGCAA
Statistics
Matches: 205, Mismatches: 34, Indels: 47
0.72 0.12 0.16
Matches are distributed among these distances:
18 6 0.03
19 26 0.13
20 103 0.50
21 60 0.29
22 9 0.04
23 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (21 bp):
CAAATTCGCAACACGAATTTT
Found at i:48929 original size:42 final size:41
Alignment explanation
Indices: 48797--49098 Score: 137
Period size: 40 Copynumber: 7.5 Consensus size: 41
48787 AAATGACCAA
* * *
48797 CAAATCCGCAATACGAA-CTCCAAATTCGCAACAC-AATTTT
1 CAAATTCGCAACACGAATTTCCAAATTCGCAACACGAA-TTT
* * * *
48837 CAAATTCGCAACTC-AGTTTCTACAA-TCGCAACGCGAATTT
1 CAAATTCGCAACACGAATTTCCA-AATTCGCAACACGAATTT
** * *
48877 --TTTCTCGCAACGCGATTTTCCAAATTCGCAACACGGAATTT
1 CAAAT-TCGCAACACGAATTTCCAAATTCGCAACAC-GAATTT
*
48918 CAAATTCGCAACACGGAATTT-CAAATTCGCAACTCG-ATTT
1 CAAATTCGCAACAC-GAATTTCCAAATTCGCAACACGAATTT
* * ** *
48958 -ATGAATTCGTAACTCG-ATTTCTGAATTCGCAACGCGAATTT
1 CA--AATTCGCAACACGAATTTCCAAATTCGCAACACGAATTT
*** * ** * * *
48999 CTTTTTCCCAACAC-AAGTTTCC-TTTTCGTAACAAGATTTT
1 CAAATTCGCAACACGAA-TTTCCAAATTCGCAACACGAATTT
* * ** *
49039 CTAAA-TCGCAACGCGAATTT-TATTTTCGCAACACGATTTT
1 C-AAATTCGCAACACGAATTTCCAAATTCGCAACACGAATTT
*
49079 CGAATTCGCAACACGAATTT
1 CAAATTCGCAACACGAATTT
49099 TAATTTTGCA
Statistics
Matches: 195, Mismatches: 46, Indels: 42
0.69 0.16 0.15
Matches are distributed among these distances:
38 1 0.01
39 18 0.09
40 118 0.61
41 31 0.16
42 21 0.11
43 6 0.03
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (41 bp):
CAAATTCGCAACACGAATTTCCAAATTCGCAACACGAATTT
Found at i:49065 original size:40 final size:41
Alignment explanation
Indices: 49021--49112 Score: 125
Period size: 40 Copynumber: 2.3 Consensus size: 41
49011 ACAAGTTTCC
* * *
49021 TTTTCGTAACAAGATTTTCTAAATCGCAACGCGAATTTT-A
1 TTTTCGCAACAAGATTTTCGAAATCGCAACACGAATTTTAA
* *
49061 TTTTCGCAACACGATTTTCGAATTCGCAACACGAATTTTAA
1 TTTTCGCAACAAGATTTTCGAAATCGCAACACGAATTTTAA
49102 TTTT-GCAACAA
1 TTTTCGCAACAA
49113 CTTTTATTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 40 0.89
41 5 0.11
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.36
Consensus pattern (41 bp):
TTTTCGCAACAAGATTTTCGAAATCGCAACACGAATTTTAA
Found at i:49109 original size:20 final size:20
Alignment explanation
Indices: 49046--49111 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
49036 TTTCTAAATC
*
49046 GCAACGCGAATTTT-ATTTT
1 GCAACACGAATTTTAATTTT
*
49065 CGCAACACG-ATTTTCGAA-TTC
1 -GCAACACGAATTTT--AATTTT
49086 GCAACACGAATTTTAATTTT
1 GCAACACGAATTTTAATTTT
49106 GCAACA
1 GCAACA
49112 ACTTTTATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
19 7 0.18
20 23 0.61
21 7 0.18
22 1 0.03
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (20 bp):
GCAACACGAATTTTAATTTT
Found at i:49110 original size:60 final size:60
Alignment explanation
Indices: 48821--49130 Score: 233
Period size: 60 Copynumber: 5.2 Consensus size: 60
48811 GAACTCCAAA
* * * *
48821 TTCGCAACACAATTTTCAAATTCGCAACTC-AGTTTCTACAATCGCAACGCGAATTTT-TT
1 TTCGCAACACGATTTTCAAATTCGCAACACGAATTTCTA-ATTCGCAACGCGAATTTTATT
* * * * * **
48880 CTCGCAACGCGATTTTCCAAATTCGCAACACGGAATTTCAAATTCGCAACACGGAATTTCAAA
1 TTCGCAACACGATTTT-CAAATTCGCAACAC-GAATTTCTAATTCGCAACGC-GAATTTTATT
* * * *
48943 TTCGCAACTCGATTTAT-GAATTCGTAACTCG-ATTTCTGAATTCGCAACGCGAATTTCT-TT
1 TTCGCAACACGATTT-TCAAATTCGCAACACGAATTTCT-AATTCGCAACGCGAATTT-TATT
* * * *** * * * *
49003 TTCCCAACACAAGTTTCCTTTTCGTAACAAGATTTTCTAAATCGCAACGCGAATTTTATT
1 TTCGCAACACGATTTTCAAATTCGCAACACGAATTTCTAATTCGCAACGCGAATTTTATT
* *
49063 TTCGCAACACGATTTTCGAATTCGCAACACGAATTT-TAATTTTGCAA--C-AACTTTTATT
1 TTCGCAACACGATTTTCAAATTCGCAACACGAATTTCTAA-TTCGCAACGCGAA-TTTTATT
49121 TTCGCAACAC
1 TTCGCAACAC
49131 AAATGTTTTG
Statistics
Matches: 195, Mismatches: 43, Indels: 27
0.74 0.16 0.10
Matches are distributed among these distances:
57 2 0.01
58 18 0.09
59 18 0.09
60 95 0.49
61 26 0.13
62 22 0.11
63 13 0.07
64 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (60 bp):
TTCGCAACACGATTTTCAAATTCGCAACACGAATTTCTAATTCGCAACGCGAATTTTATT
Found at i:49285 original size:14 final size:16
Alignment explanation
Indices: 49268--49304 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
49258 TCTCAATCTC
49268 TAATTTT-TTT-TACA
1 TAATTTTATTTCTACA
*
49282 TAATTTTATTTCTATA
1 TAATTTTATTTCTACA
49298 TAATTTT
1 TAATTTT
49305 CAATGATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 3 0.15
16 10 0.50
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (16 bp):
TAATTTTATTTCTACA
Found at i:52110 original size:55 final size:55
Alignment explanation
Indices: 52050--52571 Score: 603
Period size: 55 Copynumber: 9.5 Consensus size: 55
52040 GAGTCCATTT
*
52050 CCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAGCAAACGTGTCTGCTC
1 CCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGCTC
* * * *
52105 CCTATTCATTTAGGGAGTATAAGACTCGAACAATCTTCAGCAAACGTATCTGCTC
1 CCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGCTC
*
52160 CCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAGCAAACGTGTCTGCTC
1 CCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGCTC
* * * *
52215 CCTATTCATTTAGGGAGTATAAGACTCGAACAATCTTCAGCAAACGTGTATGCTC
1 CCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGCTC
* *
52270 CCTATTCGTTCAAGGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCCGCTC
1 CCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGCTC
* ** * * * * * *
52325 CCTATTCCTTCATAGAGTATAGGACTCGAACAATTTTTAACAAAACGGGTCCGCTT
1 CCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAAC-AAACGTGTCTGCTC
* * * * * * *
52381 CCTATTCCTTCAGAGAGTATAGGACTCCAACAATCTTCAACAAAATGGGTCTGCTT
1 CCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAAC-AAACGTGTCTGCTC
*
52437 CCTATTCGTTCAGGGAGTAT-AGAACTCGAACAATCTTCATA-AAACAG-GTCCGCTC
1 CCTATTCGTTCAGGGAGTATAAG-ACTCGAACAATCTTCA-ACAAAC-GTGTCTGCTC
* * * *
52492 TCTATTCCTTCAGAGAGTAT-AGAACTCG----ATCTTCAACAAACGTGTCCGCTC
1 CCTATTCGTTCAGGGAGTATAAG-ACTCGAACAATCTTCAACAAACGTGTCTGCTC
* *
52543 CCTATTAC-TTCAGAGAGTATAGGACTCGA
1 CCTATT-CGTTCAGGGAGTATAAGACTCGA
52572 TCTTCATAAA
Statistics
Matches: 417, Mismatches: 41, Indels: 21
0.87 0.09 0.04
Matches are distributed among these distances:
50 2 0.00
51 41 0.10
52 2 0.00
55 275 0.66
56 96 0.23
57 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.28
Consensus pattern (55 bp):
CCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGCTC
Found at i:53925 original size:8 final size:8
Alignment explanation
Indices: 53901--53979 Score: 51
Period size: 8 Copynumber: 10.2 Consensus size: 8
53891 ATTTATTTTC
53901 TTTTTC-T
1 TTTTTCTT
*
53908 TTTTT-AT
1 TTTTTCTT
53915 TTTTTCTT
1 TTTTTCTT
*
53923 TTTCTC-T
1 TTTTTCTT
*
53930 TTCTTCTT
1 TTTTTCTT
*
53938 TTTTAT-TA
1 TTTT-TCTT
*
53946 TTATT-TT
1 TTTTTCTT
*
53953 TTCTTCTT
1 TTTTTCTT
53961 TTTTTCTT
1 TTTTTCTT
53969 TTTTTCATT
1 TTTTTC-TT
53978 TT
1 TT
53980 CCATCATTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
7 22 0.39
8 29 0.52
9 5 0.09
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTCTT
Found at i:53930 original size:22 final size:21
Alignment explanation
Indices: 53887--53971 Score: 68
Period size: 23 Copynumber: 3.9 Consensus size: 21
53877 TGAACCCCCC
53887 TTTTATTTATTTTCTTTTTCTT
1 TTTTATTT-TTTTCTTTTTCTT
53909 TTTTA-TTTTTTCTTTTTCTCT
1 TTTTATTTTTTTCTTTTTCT-T
*
53930 TTCTTCTTTTTTAT-TATTATT-TT
1 TT-TTATTTTTT-TCT-TT-TTCTT
*
53953 TTCTTCTTTTTTTCTTTTT
1 TT-TTATTTTTTTCTTTTT
53972 TTCATTTTCC
Statistics
Matches: 55, Mismatches: 1, Indels: 15
0.77 0.01 0.21
Matches are distributed among these distances:
20 12 0.22
21 7 0.13
22 10 0.18
23 20 0.36
24 4 0.07
25 2 0.04
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTTATTTTTTTCTTTTTCTT
Found at i:53972 original size:7 final size:7
Alignment explanation
Indices: 53896--53972 Score: 68
Period size: 7 Copynumber: 10.6 Consensus size: 7
53886 CTTTTATTTA
53896 TTTTC-T
1 TTTTCTT
53902 TTTTCTT
1 TTTTCTT
*
53909 TTTTATT
1 TTTTCTT
53916 TTTTCTT
1 TTTTCTT
53923 TTTCTCTT
1 TTT-TCTT
*
53931 TCTTCTT
1 TTTTCTT
*
53938 TTTTATT
1 TTTTCTT
53945 ATTATT-TT
1 -TT-TTCTT
53953 TTCTTCTTT
1 TT-TTC-TT
53962 TTTTCTT
1 TTTTCTT
53969 TTTT
1 TTTT
53973 TCATTTTCCA
Statistics
Matches: 59, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
6 5 0.08
7 35 0.59
8 13 0.22
9 6 0.10
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTCTT
Found at i:53989 original size:17 final size:16
Alignment explanation
Indices: 53969--54021 Score: 65
Period size: 17 Copynumber: 3.3 Consensus size: 16
53959 TTTTTTTCTT
53969 TTTTTCATTTTCCATCA
1 TTTTTCATTTTCC-TCA
*
53986 TTTTTCATTTTTCTCA
1 TTTTTCATTTTCCTCA
54002 TTTTTC-TTCTT-CTCA
1 TTTTTCATT-TTCCTCA
54017 TTTTT
1 TTTTT
54022 ATTATTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
15 11 0.32
16 11 0.32
17 12 0.35
ACGTcount: A:0.11, C:0.21, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTCATTTTCCTCA
Found at i:54014 original size:15 final size:16
Alignment explanation
Indices: 53969--54021 Score: 65
Period size: 15 Copynumber: 3.3 Consensus size: 16
53959 TTTTTTTCTT
53969 TTTTTCATT-TTCCATCA
1 TTTTTCATTCTT-C-TCA
*
53986 TTTTTCATTTTTCTCA
1 TTTTTCATTCTTCTCA
54002 TTTTTC-TTCTTCTCA
1 TTTTTCATTCTTCTCA
54017 TTTTT
1 TTTTT
54022 ATTATTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
15 13 0.38
16 9 0.26
17 10 0.29
18 2 0.06
ACGTcount: A:0.11, C:0.21, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTCATTCTTCTCA
Found at i:54039 original size:19 final size:19
Alignment explanation
Indices: 54008--54052 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
53998 CTCATTTTTC
54008 TTCTTCTCATTTTTATTAT
1 TTCTTCTCATTTTTATTAT
* * *
54027 TTTTTCTCTTTTTTTTTAT
1 TTCTTCTCATTTTTATTAT
54046 TTCTTCT
1 TTCTTCT
54053 TCAAACGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.76
Consensus pattern (19 bp):
TTCTTCTCATTTTTATTAT
Found at i:58332 original size:15 final size:17
Alignment explanation
Indices: 58298--58335 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
58288 ACGAATTAAA
*
58298 AAATAAAAAATAGACTT
1 AAATAAAAAATAGACAT
58315 AAATAAAAAA-A-ACAT
1 AAATAAAAAATAGACAT
58330 AAATAA
1 AAATAA
58336 CAAGGGATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
16 1 0.05
17 10 0.50
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (17 bp):
AAATAAAAAATAGACAT
Found at i:60257 original size:3 final size:3
Alignment explanation
Indices: 60249--60279 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
60239 ATATAACCCT
*
60249 GAA GAA GAA GAA GAA GAA GAA TAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
60280 TCCCCAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:62359 original size:6 final size:6
Alignment explanation
Indices: 62348--62382 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
62338 AAGCAAAAGG
* *
62348 AAATCA AAATCA AAATCG CAATCA AAATCA AAATC
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATC
62383 CCAATCACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:62372 original size:18 final size:18
Alignment explanation
Indices: 62349--62394 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
62339 AGCAAAAGGA
*
62349 AATCAAAATCAAAATCGC
1 AATCAAAATCAAAATCCC
62367 AATCAAAATCAAAATCCC
1 AATCAAAATCAAAATCCC
*
62385 AATCACAATC
1 AATCAAAATC
62395 GGCTTCACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.54, C:0.26, G:0.02, T:0.17
Consensus pattern (18 bp):
AATCAAAATCAAAATCCC
Found at i:63941 original size:21 final size:21
Alignment explanation
Indices: 63912--63988 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
63902 GTGAATCGGG
* *
63912 CTATTGAACGGTGGGAGGAGC
1 CTATTGAACGATGAGAGGAGC
* *
63933 CTCTTGAACGATGAGAGGGGC
1 CTATTGAACGATGAGAGGAGC
*
63954 CTATTGAACGATAAGAGTG-GC
1 CTATTGAACGATGAGAG-GAGC
*
63975 CTTTTGAACGATGA
1 CTATTGAACGATGA
63989 CAGGTGAATC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
21 46 0.98
22 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.34, T:0.23
Consensus pattern (21 bp):
CTATTGAACGATGAGAGGAGC
Found at i:64423 original size:21 final size:21
Alignment explanation
Indices: 64399--64439 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
64389 GCCATCACAT
* *
64399 AAAGTACCGACCTCATCACGC
1 AAAGCACCAACCTCATCACGC
*
64420 AAAGCACTAACCTCATCACG
1 AAAGCACCAACCTCATCACG
64440 TAACTCCCCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.37, G:0.12, T:0.15
Consensus pattern (21 bp):
AAAGCACCAACCTCATCACGC
Found at i:64632 original size:42 final size:42
Alignment explanation
Indices: 64557--64655 Score: 153
Period size: 42 Copynumber: 2.4 Consensus size: 42
64547 GTGATGGAAT
* * * *
64557 AGGTGATGGCTCTCGTTGTGGAGGTGTATAATCGGCTCGATC
1 AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCGGCTCGATC
*
64599 AGGTGATGGCTCTGGGTGTCGAGCTGTAGAATCGGCTCGATC
1 AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCGGCTCGATC
64641 AGGTGATGGCTCTCG
1 AGGTGATGGCTCTCG
64656 AAGTGGGGGT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.16, C:0.18, G:0.37, T:0.28
Consensus pattern (42 bp):
AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCGGCTCGATC
Found at i:66533 original size:22 final size:22
Alignment explanation
Indices: 66503--66544 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
66493 TGGAGGTCGT
*
66503 CGGATATGGGGACAGATGTCAC
1 CGGAGATGGGGACAGATGTCAC
*
66525 CGGAGATGGGGACGGATGTC
1 CGGAGATGGGGACAGATGTC
66545 GCCGTAGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.17, G:0.43, T:0.17
Consensus pattern (22 bp):
CGGAGATGGGGACAGATGTCAC
Found at i:66673 original size:19 final size:20
Alignment explanation
Indices: 66651--66688 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
66641 AATATTGTGT
66651 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
66670 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
66689 TGCGCTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:66689 original size:19 final size:20
Alignment explanation
Indices: 66659--66701 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
66649 GTTTCGAATT
*
66659 CGAAAATAAAATTCGCGTTG
1 CGAAAATAAAATGCGCGTTG
*
66679 CGAAAAT-AAATGCGCTTTG
1 CGAAAATAAAATGCGCGTTG
66698 CGAA
1 CGAA
66702 TTTGACTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (20 bp):
CGAAAATAAAATGCGCGTTG
Found at i:71573 original size:29 final size:29
Alignment explanation
Indices: 71528--71596 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
71518 TATAATCCTA
*
71528 TAATTCTAATTACATTTAATTTTAA-TTT
1 TAATTATAATTACATTTAATTTTAACTTT
* *
71556 TAAATTATAATTATATTTAGTTTTAACTTT
1 T-AATTATAATTACATTTAATTTTAACTTT
71586 TAATTATAATT
1 TAATTATAATT
71597 CTTCTTAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.03
29 31 0.86
30 4 0.11
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (29 bp):
TAATTATAATTACATTTAATTTTAACTTT
Found at i:71574 original size:23 final size:23
Alignment explanation
Indices: 71548--71593 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
71538 TACATTTAAT
71548 TTTAATTTTAAATTATAATTATA
1 TTTAATTTTAAATTATAATTATA
* * *
71571 TTTAGTTTTAACTTTTAATTATA
1 TTTAATTTTAAATTATAATTATA
71594 ATTCTTCTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (23 bp):
TTTAATTTTAAATTATAATTATA
Done.