Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007733.1 Hibiscus syriacus cultivar Beakdansim tig00109987_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: 1979160
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:1957344 original size:19 final size:20
Alignment explanation
Indices: 1957290--1957345 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
1957280 TAGTTTACTT
* *
1957290 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1957310 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
*
1957330 TCGCAATGC-GAAATGA
1 TCGCAACGCGGAAATGA
1957346 AAATCGTAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1957364 original size:14 final size:14
Alignment explanation
Indices: 1957345--1957433 Score: 79
Period size: 14 Copynumber: 5.8 Consensus size: 14
1957335 ATGCGAAATG
*
1957345 AAAATCGTAACGAC
1 AAAATCGCAACGAC
*
1957359 AAAATCGCAACGCGAAAT
1 AAAATCGCAA--CG--AC
1957377 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1957391 AAAATCGCAACGCTAA
1 AAAATCGCAACG--AC
1957407 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1957423 AAAATCGCAAC
1 AAAATCGCAAC
1957434 ACGAAACACA
Statistics
Matches: 62, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
14 32 0.52
16 8 0.13
18 22 0.35
ACGTcount: A:0.49, C:0.25, G:0.15, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1957382 original size:18 final size:18
Alignment explanation
Indices: 1957359--1957420 Score: 69
Period size: 18 Copynumber: 3.7 Consensus size: 18
1957349 TCGTAACGAC
1957359 AAAATCGCAACGCGAAAT
1 AAAATCGCAACGCGAAAT
*
1957377 AAAATCGCAA--CG--AC
1 AAAATCGCAACGCGAAAT
*
1957391 AAAATCGCAACGCTAAAT
1 AAAATCGCAACGCGAAAT
*
1957409 GAAATCGCAACG
1 AAAATCGCAACG
1957421 ACAAAATCGC
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 11 0.31
16 3 0.08
18 22 0.61
ACGTcount: A:0.48, C:0.24, G:0.16, T:0.11
Consensus pattern (18 bp):
AAAATCGCAACGCGAAAT
Found at i:1957389 original size:32 final size:32
Alignment explanation
Indices: 1957329--1957450 Score: 172
Period size: 32 Copynumber: 3.8 Consensus size: 32
1957319 GGAAATGGCT
* *
1957329 ATCGCAATGCGAAATGAAAATCGTAACGACAAA
1 ATCGCAACGCGAAAT-AAAATCGCAACGACAAA
1957362 ATCGCAACGCGAAATAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATAAAATCGCAACGACAAA
* *
1957394 ATCGCAACGCTAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATAAAATCGCAACGACAAA
* *
1957426 ATCGCAACACGAAACACAAATCGCA
1 ATCGCAACGCGAAATA-AAATCGCA
1957451 TTGCGATTTT
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
32 58 0.73
33 22 0.28
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.11
Consensus pattern (32 bp):
ATCGCAACGCGAAATAAAATCGCAACGACAAA
Found at i:1957468 original size:19 final size:19
Alignment explanation
Indices: 1957446--1957599 Score: 105
Period size: 19 Copynumber: 8.6 Consensus size: 19
1957436 GAAACACAAA
*
1957446 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1957465 TCGCGTTGTGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
1957481 T--CGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
*
1957497 TCGCGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
1957513 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* ***
1957530 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGATTTTCATT
**
1957549 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
*
1957569 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1957589 TCGTGTTGCGA
1 TCGCGTTGCGA
1957600 AAGTAAACTA
Statistics
Matches: 107, Mismatches: 17, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
14 18 0.17
15 3 0.03
16 6 0.06
17 2 0.02
18 14 0.13
19 35 0.33
20 29 0.27
ACGTcount: A:0.13, C:0.19, G:0.24, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1957491 original size:14 final size:14
Alignment explanation
Indices: 1957468--1957525 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1957458 TTTCATTTCG
*
1957468 CGTTGTGATTTTGT
1 CGTTGCGATTTTGT
*
1957482 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1957498 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1957514 CGTTGCGATTTT
1 CGTTGCGATTTT
1957526 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 22 0.59
16 4 0.11
18 11 0.30
ACGTcount: A:0.09, C:0.16, G:0.26, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1957532 original size:33 final size:33
Alignment explanation
Indices: 1957451--1957541 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1957441 ACAAATCGCA
*
1957451 TTGCGATTTTCATTTCGCGTTGTGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1957484 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
1957516 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
1957542 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:1957560 original size:20 final size:19
Alignment explanation
Indices: 1957526--1957580 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
1957516 TTGCGATTTT
*
1957526 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1957545 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
1957565 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
1957581 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1959623 original size:19 final size:19
Alignment explanation
Indices: 1959601--1959668 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
1959591 ATCGCAACGA
1959601 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1959620 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1959639 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
1959653 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
1959669 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1959712 original size:20 final size:20
Alignment explanation
Indices: 1959687--1959743 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
1959677 TCGCATTGCG
*
1959687 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAACC
1959707 ATTTTCGCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAACC
*
1959727 ATTTTCGCATTGCGATA
1 ATTTTCGCGTTGCGATA
1959744 GTCAAATGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAACC
Found at i:1960130 original size:14 final size:14
Alignment explanation
Indices: 1960111--1960146 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1960101 ATTGTTTAAT
1960111 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1960125 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1960139 TGATTTGT
1 TGATTTGT
1960147 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1961448 original size:24 final size:24
Alignment explanation
Indices: 1961397--1961450 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1961387 GTATTCAAAA
* * *
1961397 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGAAC
*
1961421 TTTGATATTGGTCAATACACGAAT
1 TTTGATATTGGTCAATACACGAAC
1961445 TTTGAT
1 TTTGAT
1961451 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGAAC
Found at i:1961642 original size:12 final size:12
Alignment explanation
Indices: 1961625--1961649 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1961615 ATATAATCCT
1961625 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1961637 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1961649 G
1 G
1961650 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1963980 original size:14 final size:14
Alignment explanation
Indices: 1963961--1964048 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
1963951 GCGAAATGAA
1963961 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1963975 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
1963994 AATCGCAACGAGGG
1 AATCGCAACGAGAG
*
1964008 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
1964027 AATCGCAACGAGGG
1 AATCGCAACGAGAG
1964041 AATCGCAA
1 AATCGCAA
1964049 TGCGAAATGA
Statistics
Matches: 57, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
14 26 0.46
15 2 0.04
16 4 0.07
17 4 0.07
18 2 0.04
19 19 0.33
ACGTcount: A:0.43, C:0.19, G:0.26, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1963985 original size:33 final size:33
Alignment explanation
Indices: 1963943--1964069 Score: 245
Period size: 33 Copynumber: 3.8 Consensus size: 33
1963933 GGAAATTACT
*
1963943 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1963976 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1964009 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1964042 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1964070 CGAATTTAAT
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
33 93 1.00
ACGTcount: A:0.43, C:0.19, G:0.25, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
Found at i:1964091 original size:19 final size:20
Alignment explanation
Indices: 1964069--1964111 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1964059 AAATCGCAAC
1964069 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
1964088 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
1964108 GCGA
1 GCGA
1964112 TTCCCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:1964271 original size:14 final size:14
Alignment explanation
Indices: 1964252--1964288 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1964242 CATCAATTAA
1964252 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1964266 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1964280 ACAAATCAA
1 ACAAATCAA
1964289 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1965712 original size:21 final size:21
Alignment explanation
Indices: 1965646--1965712 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1965636 GTGAATCGGG
*
1965646 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1965666 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1965688 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1965709 CTCT
1 CTCT
1965713 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1965731 original size:42 final size:41
Alignment explanation
Indices: 1965646--1965768 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1965636 GTGAATCGGG
* * * * *
1965646 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
1965688 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
1965730 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
1965769 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:1967809 original size:20 final size:19
Alignment explanation
Indices: 1967764--1967904 Score: 86
Period size: 19 Copynumber: 7.8 Consensus size: 19
1967754 TCTTTTGGTT
1967764 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* * *
1967783 GATAATGAGAATTGCAACGCG
1 GA-AATGAAAATCGCAACG-A
** *
1967804 GAAATGACTATCGCAATGA
1 GAAATGAAAATCGCAACGA
*
1967823 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** *
1967837 GAAATGACTATCGCGACGA
1 GAAATGAAAATCGCAACGA
*
1967856 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
1967870 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
1967889 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1967905 TGCGATTTTG
Statistics
Matches: 93, Mismatches: 17, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
14 18 0.19
16 4 0.04
17 4 0.04
19 39 0.42
20 26 0.28
21 2 0.02
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1967846 original size:33 final size:33
Alignment explanation
Indices: 1967789--1967887 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
1967779 ACGAGATAAT
* *
1967789 GAGAATTGCAACGCGGAAATGACTATCGCAATGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
1967823 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
1967856 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
1967888 CGAAATGAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 46 0.78
34 13 0.22
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.13
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:1967881 original size:19 final size:19
Alignment explanation
Indices: 1967859--1967909 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
1967849 GCGACGAGAG
1967859 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
1967878 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1967897 AATCGCAATGCGA
1 AATCGCAACGCGA
1967910 TTTTGGTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1967938 original size:19 final size:19
Alignment explanation
Indices: 1967905--1967971 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
1967895 AAAATCGCAA
**
1967905 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
1967924 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
** *
1967943 TGCGATAGTTATTTCCGCTT
1 TGCGATTTTTATTT-CGCGT
1967963 TGCGATTTT
1 TGCGATTTT
1967972 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 29 0.73
20 11 0.28
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.49
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:1968557 original size:40 final size:41
Alignment explanation
Indices: 1968513--1968606 Score: 111
Period size: 40 Copynumber: 2.3 Consensus size: 41
1968503 CGAAAGTCAG
* * *
1968513 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TAT
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTAA
* * *
1968553 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCTAA
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTT-CTAA
1968595 T-TCGCGTTGCGA
1 TATCGCGTTGCGA
1968607 TTTACTTATT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
40 32 0.71
41 10 0.22
42 3 0.07
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (41 bp):
TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTAA
Found at i:1968586 original size:20 final size:20
Alignment explanation
Indices: 1968494--1968586 Score: 96
Period size: 20 Copynumber: 4.7 Consensus size: 20
1968484 CGCTAAGTAA
*
1968494 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
1968514 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
1968534 ATCTCGTTGCGATTTTTATT
1 ATCGCGTTGCGATAGTCAGT
*
1968554 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
1968574 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
1968587 TTTCCTAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:1968619 original size:20 final size:21
Alignment explanation
Indices: 1968575--1968626 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1968565 ATAGTCAGTA
*
1968575 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTACTAAT
* *
1968596 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACTAAT
1968616 TCGCATTGCGA
1 TCGCATTGCGA
1968627 ATTGGGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTACTAAT
Found at i:1969746 original size:20 final size:22
Alignment explanation
Indices: 1969705--1969745 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1969695 TATAAAAAAT
1969705 TATTTTTATTAAATATTTTTTA
1 TATTTTTATTAAATATTTTTTA
*
1969727 TATTTTTATTTAAT-TTTTT
1 TATTTTTATTAAATATTTTT
1969746 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (22 bp):
TATTTTTATTAAATATTTTTTA
Found at i:1971923 original size:16 final size:16
Alignment explanation
Indices: 1971902--1971981 Score: 115
Period size: 16 Copynumber: 5.0 Consensus size: 16
1971892 ATAAACGAAT
1971902 ATAAACGAACACAAAC
1 ATAAACGAACACAAAC
*
1971918 ATAAACGATCACAAAC
1 ATAAACGAACACAAAC
*
1971934 ATAAACGAACACGAAC
1 ATAAACGAACACAAAC
* *
1971950 ATAAATGAACACGAAC
1 ATAAACGAACACAAAC
*
1971966 ATAAACGAACATAAAC
1 ATAAACGAACACAAAC
1971982 GTTGGAGACC
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 57 1.00
ACGTcount: A:0.59, C:0.23, G:0.09, T:0.10
Consensus pattern (16 bp):
ATAAACGAACACAAAC
Found at i:1973070 original size:24 final size:24
Alignment explanation
Indices: 1973043--1973104 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
1973033 ATAAATGAAT
1973043 GAACATAAATGAACATAACCGAAC
1 GAACATAAATGAACATAACCGAAC
*
1973067 GAACATAAACGAACATAACCGAAC
1 GAACATAAATGAACATAACCGAAC
* *
1973091 AAACGTAAATGAAC
1 GAACATAAATGAAC
1973105 GAACGAGACA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.55, C:0.21, G:0.13, T:0.11
Consensus pattern (24 bp):
GAACATAAATGAACATAACCGAAC
Found at i:1973490 original size:18 final size:19
Alignment explanation
Indices: 1973451--1973497 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
1973441 ATTTTTCAAG
**
1973451 TAAAA-ATAATAAATTTTA
1 TAAAATATAATAAATAATA
1973469 TAAAATATAATAAATAAT-
1 TAAAATATAATAAATAATA
*
1973487 TAAAATTTAAT
1 TAAAATATAAT
1973498 TGTGTTAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAATATAATAAATAATA
Found at i:1974826 original size:39 final size:40
Alignment explanation
Indices: 1974741--1974826 Score: 99
Period size: 39 Copynumber: 2.2 Consensus size: 40
1974731 TGCACTCCTG
* *
1974741 GAATCTTCTCTATTTGCCTGAAGACGTCATGCACTCGTTA
1 GAATCTTCTCTATTTACCTGAAGACGTCATGCAATCGTTA
*
1974781 G-GTCTTCT-TCATTTACCTGAAGACG-CGATGCAATCG-TA
1 GAATCTTCTCT-ATTTACCTGAAGACGTC-ATGCAATCGTTA
1974819 GAATCTTC
1 GAATCTTC
1974827 ATATTTAACT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
38 5 0.13
39 33 0.85
40 1 0.03
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (40 bp):
GAATCTTCTCTATTTACCTGAAGACGTCATGCAATCGTTA
Found at i:1978502 original size:2 final size:2
Alignment explanation
Indices: 1978491--1978525 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1978481 AAACTGACCA
1978491 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1978526 CTACACTACT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1978661 original size:7 final size:7
Alignment explanation
Indices: 1978651--1978689 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
1978641 TTTTAAACCC
1978651 TAAATCA
1 TAAATCA
*
1978658 TAAATCT
1 TAAATCA
1978665 TAAATCA
1 TAAATCA
1978672 TAAA-CA
1 TAAATCA
1978678 TAAATCA
1 TAAATCA
1978685 TAAAT
1 TAAAT
1978690 TTAAACCCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (7 bp):
TAAATCA
Found at i:1978681 original size:20 final size:21
Alignment explanation
Indices: 1978651--1978689 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1978641 TTTTAAACCC
*
1978651 TAAATCATAAATCTTAAATCA
1 TAAATCATAAATCATAAATCA
1978672 TAAA-CATAAATCATAAAT
1 TAAATCATAAATCATAAAT
1978690 TTAAACCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (21 bp):
TAAATCATAAATCATAAATCA
Found at i:1978683 original size:13 final size:14
Alignment explanation
Indices: 1978651--1978689 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
1978641 TTTTAAACCC
*
1978651 TAAATCATAAATCT
1 TAAATCATAAATCA
1978665 TAAATCATAAA-CA
1 TAAATCATAAATCA
1978678 TAAATCATAAAT
1 TAAATCATAAAT
1978690 TTAAACCCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAATCATAAATCA
Found at i:1978694 original size:13 final size:13
Alignment explanation
Indices: 1978651--1978694 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
1978641 TTTTAAACCC
1978651 TAAATCATAAATCT
1 TAAATCATAAAT-T
**
1978665 TAAATCATAAACA
1 TAAATCATAAATT
1978678 TAAATCATAAATT
1 TAAATCATAAATT
1978691 TAAA
1 TAAA
1978695 CCCTAATCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAATCATAAATT
Done.