Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003607.1 Hibiscus syriacus cultivar Beakdansim tig00007626_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: 61419
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:104 original size:29 final size:30
Alignment explanation
Indices: 70--128 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
60 CATTCGTGAA
*
70 CGTTCGATATCCA-TTCATTATGTTCGTTT
1 CGTTCGATATCCACTCCATTATGTTCGTTT
* * *
99 CGTTCGGTATTCACTCCTTTATGTTCGTTT
1 CGTTCGATATCCACTCCATTATGTTCGTTT
129 GTTTAATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.14, C:0.22, G:0.15, T:0.49
Consensus pattern (30 bp):
CGTTCGATATCCACTCCATTATGTTCGTTT
Found at i:5852 original size:29 final size:29
Alignment explanation
Indices: 5812--5881 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
5802 GATTAAGATT
5812 AAAAAAATTTTAAG-TACACATTTTAATA
1 AAAAAAATTTTAAGATACACATTTTAATA
** *
5840 AAAAAAATCTTT-AGATACTTATTTTGATA
1 AAAAAAAT-TTTAAGATACACATTTTAATA
5869 AAAAAAATTTTAA
1 AAAAAAATTTTAA
5882 ACATTTTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 13 0.36
29 23 0.64
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.37
Consensus pattern (29 bp):
AAAAAAATTTTAAGATACACATTTTAATA
Found at i:8178 original size:30 final size:30
Alignment explanation
Indices: 8098--8180 Score: 85
Period size: 32 Copynumber: 2.7 Consensus size: 30
8088 ATAAGGAATG
*
8098 ATATGAACATGTGATATGTGAACATAAGAGA
1 ATATG-ACATGAGATATGTGAACATAAGAGA
* * * * *
8129 TTAAGTGATATGAGCTATGTGACCATATGAGA
1 AT-A-TGACATGAGATATGTGAACATAAGAGA
8161 ATATGACATGAGATATGTGA
1 ATATGACATGAGATATGTGA
8181 TATGTGAATT
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
30 15 0.37
31 2 0.05
32 22 0.54
33 2 0.05
ACGTcount: A:0.40, C:0.07, G:0.24, T:0.29
Consensus pattern (30 bp):
ATATGACATGAGATATGTGAACATAAGAGA
Found at i:8446 original size:18 final size:18
Alignment explanation
Indices: 8423--8457 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
8413 GTTCTTAAGG
*
8423 AGTGGTCCTTCGGGACAT
1 AGTGGTCCATCGGGACAT
8441 AGTGGTCCATCGGGACA
1 AGTGGTCCATCGGGACA
8458 AATTTCATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.23, G:0.34, T:0.23
Consensus pattern (18 bp):
AGTGGTCCATCGGGACAT
Found at i:9239 original size:32 final size:32
Alignment explanation
Indices: 9207--9329 Score: 88
Period size: 32 Copynumber: 3.8 Consensus size: 32
9197 ATATATATAT
* *
9207 ATATCATATCATCATCTTAAGTGACGTAATAT
1 ATATTATATCATCATCTTAAGTGACGTAATAC
* * * * * * *
9239 ATGTTATCTTATCAT-TATAAGTTATGTAGTGC
1 ATATTATATCATCATCT-TAAGTGACGTAATAC
* * * *
9271 ATATTACATCATTATCTTAAGTGAAGTATTAC
1 ATATTATATCATCATCTTAAGTGACGTAATAC
*
9303 ATATAATATCATCA-CGTTAAGTGACGT
1 ATATTATATCATCATC-TTAAGTGACGT
9330 GACATGTATC
Statistics
Matches: 66, Mismatches: 22, Indels: 6
0.70 0.23 0.06
Matches are distributed among these distances:
31 2 0.03
32 63 0.95
33 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (32 bp):
ATATTATATCATCATCTTAAGTGACGTAATAC
Found at i:10007 original size:2 final size:2
Alignment explanation
Indices: 10000--10030 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9990 TAAATGTAAT
10000 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 T
10031 TGAAATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10787 original size:19 final size:19
Alignment explanation
Indices: 10752--10788 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
10742 ATGACCAACA
* *
10752 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCAATCTCT
10771 AAATCGCAACGCAATCTC
1 AAATCGCAACGCAATCTC
10789 CATTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCAATCTCT
Found at i:10851 original size:21 final size:21
Alignment explanation
Indices: 10821--10886 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
10811 GATTCGCAAC
*
10821 GCGA-TTTTGATCATCGCATT
1 GCGATTTTTGATAATCGCATT
*
10841 GCGATTTTTGA-AATCCGCGTT
1 GCGATTTTTGATAAT-CGCATT
* *
10862 GCGATTTTAGATAATCGCAAT
1 GCGATTTTTGATAATCGCATT
10883 GCGA
1 GCGA
10887 ATATGTAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
20 6 0.16
21 29 0.76
22 3 0.08
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (21 bp):
GCGATTTTTGATAATCGCATT
Found at i:10941 original size:20 final size:20
Alignment explanation
Indices: 10916--10988 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
10906 ATAACACGTG
10916 ATCACAACGCGATTCTGACT
1 ATCACAACGCGATTCTGACT
10936 ATCACAACGCGATTCTGACT
1 ATCACAACGCGATTCTGACT
* *
10956 ATCGCAACGAGATTCTGACT
1 ATCACAACGCGATTCTGACT
*
10976 ATCGCAACGCGAT
1 ATCACAACGCGAT
10989 AATACGTGAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCACAACGCGATTCTGACT
Found at i:14106 original size:18 final size:18
Alignment explanation
Indices: 14083--14117 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
14073 AGCAAAAGGC
14083 AATCAAAATCGCAATCAA
1 AATCAAAATCGCAATCAA
*
14101 AATCAAAATCTCAATCA
1 AATCAAAATCGCAATCA
14118 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.23, G:0.03, T:0.20
Consensus pattern (18 bp):
AATCAAAATCGCAATCAA
Found at i:14320 original size:20 final size:20
Alignment explanation
Indices: 14295--14549 Score: 197
Period size: 20 Copynumber: 13.7 Consensus size: 20
14285 CACATTCATT
14295 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
* *
14315 TGACTATCGCAACGTGAATT
1 TGACTATCGCAACGCGAATA
* *
14335 TGAATATCGCAACG-G--GA
1 TGACTATCGCAACGCGAATA
* *
14352 T-A--ATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
*
14369 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
*
14389 TGACTATCGCAA--CG-AGA
1 TGACTATCGCAACGCGAATA
* * *
14406 T-A--ATCGCAATGCAAAAA
1 TGACTATCGCAACGCGAATA
*
14423 TGACTATCGCAACGCGAAAA
1 TGACTATCGCAACGCGAATA
*
14443 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
* *
14463 TGACTATCGC-AC-TG-AGA
1 TGACTATCGCAACGCGAATA
14480 T-A--ATCGCAACGCGAA-A
1 TGACTATCGCAACGCGAATA
*
14496 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
* * * *
14516 TGATTATCGTAACGGGAATT
1 TGACTATCGCAACGCGAATA
14536 TGACTATCGCAACG
1 TGACTATCGCAACG
14550 AGAAAATCGC
Statistics
Matches: 188, Mismatches: 28, Indels: 38
0.74 0.11 0.15
Matches are distributed among these distances:
14 20 0.11
15 3 0.02
16 7 0.04
17 12 0.06
18 5 0.03
19 16 0.09
20 125 0.66
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (20 bp):
TGACTATCGCAACGCGAATA
Found at i:14366 original size:54 final size:54
Alignment explanation
Indices: 14300--14456 Score: 242
Period size: 54 Copynumber: 2.9 Consensus size: 54
14290 TCATTTGACT
* * * * *
14300 ATCGCAACGCGAATATGACTATCGCAACGTGAATTTGAATATCGCAACGGGATA
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGAGATA
14354 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGAGATA
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGAGATA
* **
14408 ATCGCAATGCAAAAATGACTATCGCAACGCGAAAATGACTATCGCAACG
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACG
14457 CGAATTTGAC
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 95 1.00
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (54 bp):
ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGAGATA
Found at i:14412 original size:34 final size:34
Alignment explanation
Indices: 14374--14583 Score: 163
Period size: 34 Copynumber: 5.9 Consensus size: 34
14364 GAAAATGACT
14374 ATCGCAACGCGAATTTGACTATCGCAACGAGATA
1 ATCGCAACGCGAATTTGACTATCGCAACGAGATA
* * ** *
14408 ATCGCAATGCAAAAATGACTATCGCAACGCGAAAATGA
1 ATCGCAACGCGAATTTGACTATCGCAA--CG-AGAT-A
14446 CTATCGCAACGCGAATTTGACTATCGC-ACTGAGATA
1 --ATCGCAACGCGAATTTGACTATCGCAAC-GAGATA
* *
14482 ATCGCAACGCGAA-ATGACTATCGCAACGCGAATTTGATT
1 ATCGCAACGCGAATTTGACTATCGCAA--CG-A---GATA
* * *
14521 ATCGTAACGGGAATTTGACTATCGCAACGAGAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGAGATA
* * * *
14555 ATCGCAAAGTGTATTAGACTATCGCAACG
1 ATCGCAACGCGAATTTGACTATCGCAACG
14584 CGAATATGAT
Statistics
Matches: 139, Mismatches: 22, Indels: 30
0.73 0.12 0.16
Matches are distributed among these distances:
33 10 0.07
34 63 0.45
35 1 0.01
36 5 0.04
37 8 0.06
38 4 0.03
39 15 0.11
40 33 0.24
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.21
Consensus pattern (34 bp):
ATCGCAACGCGAATTTGACTATCGCAACGAGATA
Found at i:14432 original size:74 final size:73
Alignment explanation
Indices: 14295--14561 Score: 315
Period size: 74 Copynumber: 3.6 Consensus size: 73
14285 CACATTCATT
* * * * * ***
14295 TGACTATCGCAACGCGAATATGACTATCGCAACGTGA-ATTTGAATATCGCAACGGGA-TAATCG
1 TGACTATCGCAACGCGAATTTGACTATCGCAACGAGATAATCGCA-A-CGCAAAATGACT-ATCG
*
14358 CAATGCGAAAA
63 CAACGCGAAAA
*
14369 TGACTATCGCAACGCGAATTTGACTATCGCAACGAGATAATCGCAATGCAAAAATGACTATCGCA
1 TGACTATCGCAACGCGAATTTGACTATCGCAACGAGATAATCGCAACGC-AAAATGACTATCGCA
14434 ACGCGAAAA
65 ACGCGAAAA
*
14443 TGACTATCGCAACGCGAATTTGACTATCGC-ACTGAGATAATCGCAACGCGAAATGACTATCGCA
1 TGACTATCGCAACGCGAATTTGACTATCGCAAC-GAGATAATCGCAACGCAAAATGACTATCGCA
**
14507 ACGCGAATT
65 ACGCGAAAA
* * * *
14516 TGATTATCGTAACGGGAATTTGACTATCGCAACGAGAAAATCGCAA
1 TGACTATCGCAACGCGAATTTGACTATCGCAACGAGATAATCGCAA
14562 AGTGTATTAG
Statistics
Matches: 170, Mismatches: 18, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
73 64 0.38
74 101 0.59
75 5 0.03
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (73 bp):
TGACTATCGCAACGCGAATTTGACTATCGCAACGAGATAATCGCAACGCAAAATGACTATCGCAA
CGCGAAAA
Found at i:14723 original size:36 final size:34
Alignment explanation
Indices: 14683--14758 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 34
14673 TAAACTTTTA
*
14683 ATCAATTAAATAAGCACAAATAATAATTATTTACAC
1 ATCAATTAAATAA--ACAAATAAGAATTATTTACAC
14719 ATCAA-T---TAAACAAATAAGAATTATTTACAC
1 ATCAATTAAATAAACAAATAAGAATTATTTACAC
14749 ATCAATTAAA
1 ATCAATTAAA
14759 CAAATCAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
30 25 0.71
31 1 0.03
32 3 0.09
35 1 0.03
36 5 0.14
ACGTcount: A:0.54, C:0.13, G:0.03, T:0.30
Consensus pattern (34 bp):
ATCAATTAAATAAACAAATAAGAATTATTTACAC
Found at i:14732 original size:30 final size:30
Alignment explanation
Indices: 14698--14763 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
14688 TTAAATAAGC
*
14698 ACAAATAATAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
14728 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
14758 ACAAAT
1 ACAAAT
14764 CAACTCTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.55, C:0.14, G:0.02, T:0.30
Consensus pattern (30 bp):
ACAAATAAGAATTATTTACACATCAATTAA
Found at i:16062 original size:21 final size:21
Alignment explanation
Indices: 16036--16077 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
16026 GGTACTGGCC
16036 GGTAACTTATACGAAAGCCAA
1 GGTAACTTATACGAAAGCCAA
16057 GGTAACTTATACGAAAGCCAA
1 GGTAACTTATACGAAAGCCAA
16078 CAGTCATCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (21 bp):
GGTAACTTATACGAAAGCCAA
Found at i:16193 original size:21 final size:21
Alignment explanation
Indices: 16169--16271 Score: 91
Period size: 21 Copynumber: 4.9 Consensus size: 21
16159 TTGGGAGAGA
*
16169 CCTCTTCAACGATGACAGGGG
1 CCTCTTGAACGATGACAGGGG
* **
16190 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGACAGGGG
* ** * *
16211 ACTCTTGAGGGATGATAGAGG
1 CCTCTTGAACGATGACAGGGG
* *
16232 CCTCTTGAACGAT-AGGAGAGG
1 CCTCTTGAACGATGA-CAGGGG
16253 CCTCTTGAACGATGACAGG
1 CCTCTTGAACGATGACAGG
16272 TGAGTTGGGC
Statistics
Matches: 63, Mismatches: 17, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
20 1 0.02
21 61 0.97
22 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.35, T:0.20
Consensus pattern (21 bp):
CCTCTTGAACGATGACAGGGG
Found at i:16225 original size:42 final size:42
Alignment explanation
Indices: 16162--16271 Score: 123
Period size: 42 Copynumber: 2.6 Consensus size: 42
16152 TAGAATGTTG
* * *
16162 GGAGA-GACCTCTTCAACGATGACAGGGGCCTCTTGAACGGTG
1 GGAGAGGA-CTCTTGAACGATGACAGGGGCCTCTTGAACGATA
* ** * *
16204 GGAGGGGACTCTTGAGGGATGATAGAGGCCTCTTGAACGATA
1 GGAGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGATA
*
16246 GGAGAGGCCTCTTGAACGATGACAGG
1 GGAGAGGACTCTTGAACGATGACAGG
16272 TGAGTTGGGC
Statistics
Matches: 53, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
42 51 0.96
43 2 0.04
ACGTcount: A:0.25, C:0.19, G:0.36, T:0.19
Consensus pattern (42 bp):
GGAGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGATA
Found at i:16774 original size:20 final size:20
Alignment explanation
Indices: 16749--16789 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
16739 AATAGTTTCT
16749 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
16769 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
16789 G
1 G
16790 GAAATGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.24, G:0.12, T:0.15
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:16802 original size:20 final size:20
Alignment explanation
Indices: 16759--16885 Score: 85
Period size: 20 Copynumber: 6.4 Consensus size: 20
16749 GAAACTTAAA
* * **
16759 ATCGCAACACGAAACTTAAA
1 ATCGCAACACGAAAATGATT
*
16779 ATCGCAACACGGAAATGATT
1 ATCGCAACACGAAAATGATT
*
16799 ATCGCAACGCGAAAATGATT
1 ATCGCAACACGAAAATGATT
** ** *
16819 ATCGCAATGCGAATTTGACT
1 ATCGCAACACGAAAATGATT
* ** *
16839 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGATT
* *
16859 ATCGCAACGCG-AAATGACT
1 ATCGCAACACGAAAATGATT
*
16878 ATCACAAC
1 ATCGCAAC
16886 GAGAAAATCG
Statistics
Matches: 92, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
19 13 0.14
20 79 0.86
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (20 bp):
ATCGCAACACGAAAATGATT
Found at i:16823 original size:40 final size:39
Alignment explanation
Indices: 16779--16893 Score: 131
Period size: 40 Copynumber: 2.9 Consensus size: 39
16769 GAAACTTAAA
* * *
16779 ATCGCAACACGGAAATGATTATCGCAACGCGAAAATGATT
1 ATCGCAACGC-GAAATGACTATCGCAACGCGAAAATGACT
* * **
16819 ATCGCAATGCGAATTTGACTATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAA-ATGACTATCGCAACGCGAAAATGACT
* *
16859 ATCGCAACGCGAAATGACTATCACAACGAGAAAAT
1 ATCGCAACGCGAAATGACTATCGCAACGCGAAAAT
16894 CGCAACGCGA
Statistics
Matches: 61, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
39 20 0.33
40 41 0.67
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (39 bp):
ATCGCAACGCGAAATGACTATCGCAACGCGAAAATGACT
Found at i:16961 original size:20 final size:20
Alignment explanation
Indices: 16934--17109 Score: 126
Period size: 20 Copynumber: 9.4 Consensus size: 20
16924 ACTAAATTCA
16934 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* *
16954 CATTGCGAT--T-A---TCC
1 CGTTGCGATAGTCATTTTCG
* **
16968 CGTTACGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
16988 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTTCG
*
17008 CGTTGCGATAGTCGTTTTCG
1 CGTTGCGATAGTCATTTTCG
* *
17028 CATTGCGAT--T-A---TCC
1 CGTTGCGATAGTCATTTTCG
*
17042 CGTTGCGATAGTCAAATTT-G
1 CGTTGCGATAGTC-ATTTTCG
**
17062 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
17082 CGTTGCGATAATCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
17102 TGTTGCGA
1 CGTTGCGA
17110 CTATTCTTCT
Statistics
Matches: 121, Mismatches: 21, Indels: 28
0.71 0.12 0.16
Matches are distributed among these distances:
14 19 0.16
16 2 0.02
17 2 0.02
18 3 0.02
19 4 0.03
20 90 0.74
21 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:17082 original size:54 final size:53
Alignment explanation
Indices: 16988--17090 Score: 136
Period size: 54 Copynumber: 1.9 Consensus size: 53
16978 GTCAAATTCG
***
16988 CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCGTTTTCGCATTGCGATTATCC
1 CGTTGCGATAGTCATTT-CGCGTTGCGATAGTCAAATTCGCATTGCGATTATCC
*
17042 CGTTGCGATAGTCAAATTT-GCGTTGCGATAGTCAAATTCGCGTTGCGAT
1 CGTTGCGATAGTC--ATTTCGCGTTGCGATAGTCAAATTCGCATTGCGAT
17091 AATCATTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
54 39 0.91
56 4 0.09
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.35
Consensus pattern (53 bp):
CGTTGCGATAGTCATTTCGCGTTGCGATAGTCAAATTCGCATTGCGATTATCC
Found at i:17109 original size:74 final size:74
Alignment explanation
Indices: 16927--17101 Score: 280
Period size: 74 Copynumber: 2.4 Consensus size: 74
16917 ACACGAAACT
*
16927 AAATTCACGTTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTACGATAGTCAAATTCGCGTT
1 AAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTACGATAGTCAAATTCGCGTT
16992 GCGATAGTC
66 GCGATAGTC
* * * *
17001 -ATTTCCGCGTTGCGATAGTCGTTTTCGCATTGCGATTATCCCGTTGCGATAGTCAAATTTGCGT
1 AAATT-CGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTACGATAGTCAAATTCGCGT
17065 TGCGATAGTC
65 TGCGATAGTC
*
17075 AAATTCGCGTTGCGATAATCATTTTCG
1 AAATTCGCGTTGCGATAGTCATTTTCG
17102 TGTTGCGACT
Statistics
Matches: 91, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
73 3 0.03
74 85 0.93
75 3 0.03
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (74 bp):
AAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTACGATAGTCAAATTCGCGTT
GCGATAGTC
Found at i:19141 original size:20 final size:20
Alignment explanation
Indices: 19118--19173 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
19108 TCTGAAACTT
19118 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
19138 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
19158 ATTATCGCAACGCGAA
1 AAAATCGCAACACGAA
19174 TTTGACTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:19183 original size:20 final size:20
Alignment explanation
Indices: 19121--19189 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
19111 GAAACTTAAA
* **
19121 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
* *
19141 ATCGCAACACGAAAATGATT
1 ATCGCAACGCGAAAATGACT
**
19161 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
19181 ATCGCAACG
1 ATCGCAACG
19190 AGATAATCGC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:19604 original size:22 final size:22
Alignment explanation
Indices: 19550--19629 Score: 97
Period size: 22 Copynumber: 3.6 Consensus size: 22
19540 GATGGAGATA
* *
19550 GACGAATTTCACCGGAAATGGG
1 GACGGATTTCGCCGGAAATGGG
*
19572 GACGTATTTCGCCGGAAATGGG
1 GACGGATTTCGCCGGAAATGGG
* * *
19594 GACGGATTTCGTCAGAGATGGG
1 GACGGATTTCGCCGGAAATGGG
*
19616 GACGGATGTCGCCG
1 GACGGATTTCGCCG
19630 TAGAGAGTGA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.24, C:0.19, G:0.38, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAAATGGG
Found at i:19807 original size:20 final size:20
Alignment explanation
Indices: 19782--19866 Score: 143
Period size: 20 Copynumber: 4.2 Consensus size: 20
19772 TTATCGCAAC
*
19782 GCGATAGTCAGAATCTCGTT
1 GCGATAGTCAGAATCGCGTT
19802 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
*
19822 GCGATAGTCCGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
*
19842 GCGATAGTTAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
19862 GCGAT
1 GCGAT
19867 TTACATATTT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (20 bp):
GCGATAGTCAGAATCGCGTT
Found at i:19997 original size:19 final size:19
Alignment explanation
Indices: 19982--20047 Score: 123
Period size: 19 Copynumber: 3.5 Consensus size: 19
19972 GGAGATCGTG
19982 TTGCGATTTAGAGATCGCA
1 TTGCGATTTAGAGATCGCA
*
20001 TTGTGATTTAGAGATCGCA
1 TTGCGATTTAGAGATCGCA
20020 TTGCGATTTAGAGATCGCA
1 TTGCGATTTAGAGATCGCA
20039 TTGCGATTT
1 TTGCGATTT
20048 TGTTGGTCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 45 1.00
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (19 bp):
TTGCGATTTAGAGATCGCA
Found at i:20016 original size:38 final size:38
Alignment explanation
Indices: 19973--20047 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
19963 TGCGATAATG
** *
19973 GAGATCGTGTTGCGATTTAGAGATCGCATTGTGATTTA
1 GAGATCGCATTGCGATTTAGAGATCGCATTGCGATTTA
20011 GAGATCGCATTGCGATTTAGAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTTAGAGATCGCATTGCGATTT
20048 TGTTGGTCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.24, C:0.13, G:0.28, T:0.35
Consensus pattern (38 bp):
GAGATCGCATTGCGATTTAGAGATCGCATTGCGATTTA
Found at i:27355 original size:3 final size:3
Alignment explanation
Indices: 27344--27401 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
27334 TTTTTTCCCG
** *
27344 TTA TT- TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
27389 TTA TTTA TTA TTA
1 TTA -TTA TTA TTA
27402 CAATTTTTGC
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 5 0.11
3 37 0.82
4 3 0.07
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:27510 original size:25 final size:25
Alignment explanation
Indices: 27481--27605 Score: 225
Period size: 25 Copynumber: 5.0 Consensus size: 25
27471 CCAACAACCC
27481 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
27506 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
27531 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
27556 ATCAGATTAGGGTTTCAAACCCTAAA
1 ATCAGATTAGGGTTTCAAACCCT-AA
*
27582 ACCA-ATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
27606 TCCCCTACTC
Statistics
Matches: 98, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
24 2 0.02
25 91 0.93
26 5 0.05
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:29993 original size:16 final size:16
Alignment explanation
Indices: 29959--30001 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
29949 AACGTAGATC
*
29959 AAATTTTTGTCTTATA
1 AAATTTTTTTCTTATA
29975 AAATTATTTTTCTTA-A
1 AAATT-TTTTTCTTATA
29991 AAATTGTTTTT
1 AAATT-TTTTT
30002 AAAAGACGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.58
Consensus pattern (16 bp):
AAATTTTTTTCTTATA
Found at i:42224 original size:87 final size:90
Alignment explanation
Indices: 42058--42269 Score: 295
Period size: 89 Copynumber: 2.4 Consensus size: 90
42048 GTCATCCCCA
*
42058 GACCAGATCTCTTCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTA
1 GACCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTA
* **
42123 GGAACCGTGCTATCA-CCTTTAGAT
66 GGAACCGAGCTATCACCCTAAAGAT
* * *
42147 GGCCAGATCTCTTCATCACGTAAGAGCCGTGTCAACC-T-GATAACCAGTCGTCCTCATTACGTA
1 GACCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTA
*
42210 GGAACCGAGTTATCATCCCTAAAGAT
66 GGAACCGAGCTATCA-CCCTAAAGAT
* * *
42236 GACCAGATCTCCTCATCACGTAGGAGCCATGTCA
1 GACCAGATCTCTTCATCACGTAAGAGCCGTGTCA
42270 CCCTTAGACG
Statistics
Matches: 109, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
87 36 0.33
88 1 0.01
89 72 0.66
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (90 bp):
GACCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTA
GGAACCGAGCTATCACCCTAAAGAT
Found at i:42479 original size:3 final size:3
Alignment explanation
Indices: 42468--42525 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
42458 TTTTTTTCCG
** *
42468 TTA TT- TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
42513 TTA TTTA TTA TTA
1 TTA -TTA TTA TTA
42526 CAATTTTTGC
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 5 0.11
3 37 0.82
4 3 0.07
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:42634 original size:25 final size:25
Alignment explanation
Indices: 42605--42729 Score: 216
Period size: 25 Copynumber: 5.0 Consensus size: 25
42595 CCAACAACCC
42605 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
42630 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
42655 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
*
42680 ATCAGATTAGGGTTTTAAACCCTAAA
1 ATCAGATTAGGGTTTCAAACCCT-AA
*
42706 ACCA-ATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
42730 TCCCCTACTC
Statistics
Matches: 96, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
24 2 0.02
25 89 0.93
26 5 0.05
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:45117 original size:16 final size:16
Alignment explanation
Indices: 45083--45125 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
45073 AACGTAGATC
*
45083 AAATTTTTGTCTTATA
1 AAATTTTTTTCTTATA
45099 AAATTATTTTTCTTA-A
1 AAATT-TTTTTCTTATA
45115 AAATTGTTTTT
1 AAATT-TTTTT
45126 AAAAGACGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.58
Consensus pattern (16 bp):
AAATTTTTTTCTTATA
Found at i:47477 original size:51 final size:51
Alignment explanation
Indices: 47401--47501 Score: 166
Period size: 51 Copynumber: 2.0 Consensus size: 51
47391 AAGAACAAAT
*
47401 TAATTACTATCAATTTTTAAAGATAAGCTCGATTTGTTTTCAAGTTCACAC
1 TAATTACTATCAATTTTTAAAGATAAGCTCGATTTGTTATCAAGTTCACAC
* * *
47452 TAATTTCTATCATTTTTTAAAGATAATCTCGATTTGTTATCAAGTTCACA
1 TAATTACTATCAATTTTTAAAGATAAGCTCGATTTGTTATCAAGTTCACA
47502 ATTTGTTCGA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.44
Consensus pattern (51 bp):
TAATTACTATCAATTTTTAAAGATAAGCTCGATTTGTTATCAAGTTCACAC
Found at i:50390 original size:3 final size:3
Alignment explanation
Indices: 50382--50437 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
50372 TAATTTATTT
50382 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
50429 ATA ATA ATA
1 ATA ATA ATA
50438 TAGAGATAAG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:50446 original size:26 final size:26
Alignment explanation
Indices: 50384--50435 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
50374 ATTTATTTAT
50384 AATAATAATAATAATAATAATAATAA
1 AATAATAATAATAATAATAATAATAA
50410 AATAATAATAATAATAATAATAATAA
1 AATAATAATAATAATAATAATAATAA
50436 TATAGAGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (26 bp):
AATAATAATAATAATAATAATAATAA
Done.