Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006972.1 Hibiscus syriacus cultivar Beakdansim tig00017957_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: 78377
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:12554 original size:27 final size:25
Alignment explanation
Indices: 12511--12597 Score: 115
Period size: 24 Copynumber: 3.4 Consensus size: 25
12501 AAATTGAACG
*
12511 ACCGGTTTTTTT-ACCGGATTAAAA
1 ACCGGTTTTTTTAACCGGATAAAAA
12535 ACCGGTTTTTTTCAAACCGGATAAAAA
1 ACCGGTTTTTTT--AACCGGATAAAAA
*
12562 ACCGG-TTTTTTATCCGGATAAAAA
1 ACCGGTTTTTTTAACCGGATAAAAA
12586 ACCAGGTTTTTT
1 ACC-GGTTTTTT
12598 AAAAAACCGG
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
24 27 0.48
25 2 0.04
26 11 0.20
27 16 0.29
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (25 bp):
ACCGGTTTTTTTAACCGGATAAAAA
Found at i:12601 original size:41 final size:40
Alignment explanation
Indices: 12556--12653 Score: 128
Period size: 40 Copynumber: 2.4 Consensus size: 40
12546 TCAAACCGGA
*
12556 TAAAAAACCGGTTTTTTATCCGGATAAAAAACCAGG-TT-TTT
1 TAAAAAACCGGTTTTTTAACC-GA-AAAAAACC-GGTTTATTT
*
12597 TAAAAAACCGGTTTTTTAACCGAAAAAATCCGGTTTATTT
1 TAAAAAACCGGTTTTTTAACCGAAAAAAACCGGTTTATTT
*
12637 TTAAAAACCGGTTTTTT
1 TAAAAAACCGGTTTTTT
12654 GCAAACCGAA
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
38 2 0.04
39 9 0.17
40 21 0.40
41 20 0.38
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (40 bp):
TAAAAAACCGGTTTTTTAACCGAAAAAAACCGGTTTATTT
Found at i:12602 original size:40 final size:40
Alignment explanation
Indices: 12556--12653 Score: 121
Period size: 41 Copynumber: 2.4 Consensus size: 40
12546 TCAAACCGGA
*
12556 TAAAAAACCGGTTTTTTATCCGGATAAAAAACCAGG-T-TTTT
1 TAAAAAACCGGTTTTTTAACC-GA-AAAAAACC-GGTTATTTT
*
12597 TAAAAAACCGGTTTTTTAACCGAAAAAATCCGGTTTATTTT
1 TAAAAAACCGGTTTTTTAACCGAAAAAAACCGG-TTATTTT
12638 T-AAAAACCGGTTTTTT
1 TAAAAAACCGGTTTTTT
12654 GCAAACCGAA
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
38 2 0.04
39 7 0.13
40 18 0.35
41 25 0.48
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (40 bp):
TAAAAAACCGGTTTTTTAACCGAAAAAAACCGGTTATTTT
Found at i:12609 original size:16 final size:17
Alignment explanation
Indices: 12580--12615 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
12570 TTTATCCGGA
12580 TAAAAAACCAGGTTTTT
1 TAAAAAACCAGGTTTTT
12597 TAAAAAACC-GGTTTTT
1 TAAAAAACCAGGTTTTT
12613 TAA
1 TAA
12616 CCGAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (17 bp):
TAAAAAACCAGGTTTTT
Found at i:12613 original size:18 final size:18
Alignment explanation
Indices: 12580--12653 Score: 55
Period size: 17 Copynumber: 3.9 Consensus size: 18
12570 TTTATCCGGA
12580 TAAAAAACCAGG--TTTTT
1 TAAAAAACC-GGTTTTTTT
*
12597 TAAAAAACCGGTTTTTTAACC
1 TAAAAAACCGGTTTTTT---T
*
12618 GAAAAAATCCGGTTTATTTT
1 TAAAAAA-CCGGTTT-TTTT
12638 T-AAAAACCGGTTTTTT
1 TAAAAAACCGGTTTTTT
12654 GCAAACCGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
16 2 0.04
17 12 0.26
18 11 0.24
19 5 0.11
21 6 0.13
22 7 0.15
23 3 0.07
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (18 bp):
TAAAAAACCGGTTTTTTT
Found at i:14505 original size:20 final size:21
Alignment explanation
Indices: 14482--14536 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
14472 CAAATTTCCT
14482 TTTCGCAACGCGAA-CTCCAA
1 TTTCGCAACGCGAATCTCCAA
*
14502 TTTCGCAACGC-AATTTCCAA
1 TTTCGCAACGCGAATCTCCAA
* *
14522 ATTCGCAAGGCGAAT
1 TTTCGCAACGCGAAT
14537 TTCTTTTTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.07
20 25 0.83
21 3 0.10
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (21 bp):
TTTCGCAACGCGAATCTCCAA
Found at i:18207 original size:20 final size:20
Alignment explanation
Indices: 18182--18263 Score: 74
Period size: 20 Copynumber: 4.1 Consensus size: 20
18172 GATTCGTAAC
18182 TCAAATTCGCAACGCAAAAA
1 TCAAATTCGCAACGCAAAAA
* *
18202 TCAAATTCGCAATGCGAAAA
1 TCAAATTCGCAACGCAAAAA
** **
18222 TCGTATTCGCAACGTGAAAA
1 TCAAATTCGCAACGCAAAAA
* ** *
18242 TAAAATTTTCAACACAAAAA
1 TCAAATTCGCAACGCAAAAA
18262 TC
1 TC
18264 GCAACGCGAA
Statistics
Matches: 47, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.46, C:0.21, G:0.11, T:0.22
Consensus pattern (20 bp):
TCAAATTCGCAACGCAAAAA
Found at i:19685 original size:21 final size:21
Alignment explanation
Indices: 19635--19685 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
19625 AGGTGGATCC
*
19635 TGAACGATAGAAGGGGCCTCT
1 TGAACGATGGAAGGGGCCTCT
* *
19656 TGAATGATGGAAGGGGCTTCT
1 TGAACGATGGAAGGGGCCTCT
19677 TGAACGATG
1 TGAACGATG
19686 ACAAGTGAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.14, G:0.35, T:0.24
Consensus pattern (21 bp):
TGAACGATGGAAGGGGCCTCT
Found at i:19733 original size:21 final size:21
Alignment explanation
Indices: 19694--19734 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
19684 TGACAAGTGA
*
19694 ATCCTGAATAATAGGAGGTGG
1 ATCCTGAACAATAGGAGGTGG
19715 ATCCTGAACAAT-GGTAGGTG
1 ATCCTGAACAATAGG-AGGTG
19735 AATCGGGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.32, C:0.12, G:0.32, T:0.24
Consensus pattern (21 bp):
ATCCTGAACAATAGGAGGTGG
Found at i:19945 original size:21 final size:21
Alignment explanation
Indices: 19921--19973 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
19911 TGCACCATTG
19921 TCATCACGTAAAGCACCGACC
1 TCATCACGTAAAGCACCGACC
*
19942 TCATTACGTAAAGCACCGACC
1 TCATCACGTAAAGCACCGACC
19963 TCATCACGTAA
1 TCATCACGTAA
19974 CTCCCCTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.34, C:0.34, G:0.13, T:0.19
Consensus pattern (21 bp):
TCATCACGTAAAGCACCGACC
Found at i:20252 original size:42 final size:42
Alignment explanation
Indices: 20105--20255 Score: 216
Period size: 42 Copynumber: 3.6 Consensus size: 42
20095 GTGATGAAAT
** * *
20105 AGGTGATGGCTCTCGGTGTC-GAGGT-GTAGAATCGGCTCTATC
1 AGGTGATGGCTCTCGGTGTCGGA-GTAG-AGAAGAGGCTCGATG
* *
20147 AGGTGATAGCTCTCGGTGTCGAAGTAGAGAAGAGGCTCGATG
1 AGGTGATGGCTCTCGGTGTCGGAGTAGAGAAGAGGCTCGATG
20189 AGGTGATGGCTCTCGGTGTCGGAGTAGAGAAGAGGCTCGATG
1 AGGTGATGGCTCTCGGTGTCGGAGTAGAGAAGAGGCTCGATG
20231 AGGTGATGGCTCTCGGTGTCGGAGT
1 AGGTGATGGCTCTCGGTGTCGGAGT
20256 GGGGGTGCTC
Statistics
Matches: 99, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
42 97 0.98
43 2 0.02
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.25
Consensus pattern (42 bp):
AGGTGATGGCTCTCGGTGTCGGAGTAGAGAAGAGGCTCGATG
Found at i:21810 original size:34 final size:35
Alignment explanation
Indices: 21759--21837 Score: 106
Period size: 34 Copynumber: 2.3 Consensus size: 35
21749 TTTATTCTTC
* * * *
21759 AAACTTAAATTCGCAACATGAAAATTGCAACTCGA
1 AAACTAAAATTCACAACACGAAAATTGCAACGCGA
*
21794 AAA-TAAAATTCACAACACGAAATTTGCAACGCGA
1 AAACTAAAATTCACAACACGAAAATTGCAACGCGA
21828 AAACTAAAAT
1 AAACTAAAAT
21838 CGCGTTGCGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
34 29 0.76
35 9 0.24
ACGTcount: A:0.51, C:0.19, G:0.10, T:0.20
Consensus pattern (35 bp):
AAACTAAAATTCACAACACGAAAATTGCAACGCGA
Found at i:21860 original size:20 final size:20
Alignment explanation
Indices: 21837--21905 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
21827 AAAACTAAAA
21837 TCGCGTTGCGAATTTCATTT
1 TCGCGTTGCGAATTTCATTT
* *
21857 TCGCATTGCGATTTTCA---
1 TCGCGTTGCGAATTTCATTT
21874 T---GTTGCGAATTTCATTT
1 TCGCGTTGCGAATTTCATTT
*
21891 TCGAGTTGCGAATTT
1 TCGCGTTGCGAATTT
21906 AAGATTCAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
14 11 0.28
17 2 0.05
20 26 0.67
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGAATTTCATTT
Found at i:22274 original size:22 final size:22
Alignment explanation
Indices: 22249--22296 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
22239 ATGGAGGGGG
* *
22249 GTCGCCGGA-TATGGGGATGGAT
1 GTCGCCGGAGAAT-GGGACGGAT
22271 GTCGCCGGAGAATGGGACGGAT
1 GTCGCCGGAGAATGGGACGGAT
22293 GTCG
1 GTCG
22297 TCGTAGAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.19, C:0.17, G:0.46, T:0.19
Consensus pattern (22 bp):
GTCGCCGGAGAATGGGACGGAT
Found at i:22499 original size:20 final size:20
Alignment explanation
Indices: 22476--22526 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
22466 CAAATTCGCA
22476 TTGCGAATTTGGAAACTGTG
1 TTGCGAATTTGGAAACTGTG
* ***
22496 TTGCGAAATTGGAGTTTGTG
1 TTGCGAATTTGGAAACTGTG
22516 TTGCGAATTTG
1 TTGCGAATTTG
22527 AGATCGCGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.22, C:0.08, G:0.31, T:0.39
Consensus pattern (20 bp):
TTGCGAATTTGGAAACTGTG
Found at i:33029 original size:25 final size:25
Alignment explanation
Indices: 32992--33080 Score: 70
Period size: 25 Copynumber: 3.3 Consensus size: 25
32982 ATTAATTTAT
* *
32992 TATTTATATTTAATAAAAAATATTA
1 TATTTTTAATTAATAAAAAATATTA
33017 TATTTTTAATTAAATAATAAAAATCTAGTTGA
1 TATTTTTAATT-AAT-A-AAAAA--TA-TT-A
* * *
33049 AATTTTTAATTAATAATAAATTTTA
1 TATTTTTAATTAATAAAAAATATTA
33074 TATTTTT
1 TATTTTT
33081 TTATTTTCAC
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
25 16 0.31
26 5 0.10
27 2 0.04
28 5 0.10
29 4 0.08
30 3 0.06
31 5 0.10
32 11 0.22
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (25 bp):
TATTTTTAATTAATAAAAAATATTA
Found at i:33229 original size:16 final size:16
Alignment explanation
Indices: 33190--33233 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
33180 AGTTATATCG
*
33190 CTAAATGATTATTAAA
1 CTAAATGATAATTAAA
33206 CTAGAATGA-AATTAAA
1 CTA-AATGATAATTAAA
33222 CCTAAATGATAA
1 -CTAAATGATAA
33234 GATTTACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (16 bp):
CTAAATGATAATTAAA
Found at i:39430 original size:13 final size:13
Alignment explanation
Indices: 39401--39438 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
39391 TTTTTGGGTG
**
39401 TTTTTTAAAATAA
1 TTTTTTAATTTAA
39414 -TTTTTAATTTAA
1 TTTTTTAATTTAA
39426 TTTTTTAATTTAA
1 TTTTTTAATTTAA
39439 ATAAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTTTAATTTAA
Found at i:39846 original size:21 final size:22
Alignment explanation
Indices: 39798--39855 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
39788 GAGCGTTACT
* *
39798 TAAAATGTTATTTTTTTCTACC
1 TAAAATGTTATATTTTGCTACC
39820 -ATAAATGTTA-ATTTTGCTACC
1 TA-AAATGTTATATTTTGCTACC
*
39841 TAAAATG-AATATTTT
1 TAAAATGTTATATTTT
39856 CGATATTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
20 1 0.03
21 20 0.67
22 9 0.30
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.48
Consensus pattern (22 bp):
TAAAATGTTATATTTTGCTACC
Found at i:41257 original size:26 final size:27
Alignment explanation
Indices: 41220--41273 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
41210 AGGGTTTTCA
* *
41220 AATTAC-ATAAAAACTAGAAAGCTGGG
1 AATTACAAAAAAAACTACAAAGCTGGG
41246 AATTACAAAAAAAACTACAAAGCTGGG
1 AATTACAAAAAAAACTACAAAGCTGGG
41273 A
1 A
41274 TTGAAAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.54, C:0.13, G:0.17, T:0.17
Consensus pattern (27 bp):
AATTACAAAAAAAACTACAAAGCTGGG
Found at i:42038 original size:19 final size:19
Alignment explanation
Indices: 42010--42076 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 19
42000 AATGTGATTT
42010 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
* * *
42029 TCCAAGTTCGCGTTACGATTTAT
1 TCCAAATT--CGTTGCGA--TAG
*
42052 TCCAAATTAGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
42071 TCCAAA
1 TCCAAA
42077 ATCGCAACGA
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
19 15 0.41
21 13 0.35
23 9 0.24
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (19 bp):
TCCAAATTCGTTGCGATAG
Found at i:42176 original size:6 final size:6
Alignment explanation
Indices: 42165--42191 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
42155 GACACGTATT
42165 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
42192 GACGGCGGCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:42952 original size:21 final size:21
Alignment explanation
Indices: 42897--43040 Score: 84
Period size: 21 Copynumber: 7.0 Consensus size: 21
42887 CGTTGCGATT
*
42897 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* *
42916 TTGGAATAAATAGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
42939 CTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* * *
42958 TTGTAATAAATCGCAACCCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
42981 TTGGACTATCGCAA--TGAAT
1 TTGGACTATCGCAACGCGAAC
**
43000 TTGGAAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
* *
43021 TTCGACTATCGCAATGCGAA
1 TTGGACTATCGCAACGCGAA
43041 TATGTAAATC
Statistics
Matches: 92, Mismatches: 23, Indels: 18
0.69 0.17 0.14
Matches are distributed among these distances:
19 29 0.32
21 45 0.49
23 18 0.20
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:42957 original size:42 final size:42
Alignment explanation
Indices: 42897--43034 Score: 208
Period size: 42 Copynumber: 3.3 Consensus size: 42
42887 CGTTGCGATT
*
42897 TTGGACTATCGCAACGAATTTGGAATAAATAGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* * *
42939 CTGGACTATCGCAACGAATTTGTAATAAATCGCAACCCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
*
42981 TTGGACTATCGCAATGAATTTGG-A-AAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
*
43021 TTCGACTATCGCAA
1 TTGGACTATCGCAA
43035 TGCGAATATG
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
40 28 0.32
41 1 0.01
42 58 0.67
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
Found at i:43020 original size:40 final size:41
Alignment explanation
Indices: 42897--43059 Score: 197
Period size: 42 Copynumber: 4.0 Consensus size: 41
42887 CGTTGCGATT
*
42897 TTGGACTATCGCAACGAATTTGGAATAAATAGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGG-ATAAATCGCAACGCGAAC
* * *
42939 CTGGACTATCGCAACGAATTTGTAATAAATCGCAACCCGAAC
1 TTGGACTATCGCAACGAATTTG-GATAAATCGCAACGCGAAC
*
42981 TTGGACTATCGCAATGAATTTGGA-AAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGATAAATCGCAACGCGAAC
* * *
43021 TTCGACTATCGCAATGCGAATAT-G-TAAATCGCAATGCGA
1 TTGGACTATCGCAA--CGAATTTGGATAAATCGCAACGCGA
43060 TAGTCGAAGT
Statistics
Matches: 105, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
40 28 0.27
41 15 0.14
42 62 0.59
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (41 bp):
TTGGACTATCGCAACGAATTTGGATAAATCGCAACGCGAAC
Found at i:48120 original size:2 final size:2
Alignment explanation
Indices: 48113--48138 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
48103 TTATATGTAC
48113 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
48139 CACGTAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:48993 original size:3 final size:3
Alignment explanation
Indices: 48985--49009 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
48975 ATATAAATAG
48985 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
49010 TATAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:50965 original size:4 final size:4
Alignment explanation
Indices: 50956--50982 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
50946 CACACTCACA
50956 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
50983 AGTTGACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:54989 original size:38 final size:38
Alignment explanation
Indices: 54929--55001 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
54919 AATAGTTCAT
*
54929 ATTTTCAATTATATATTAAAATAATATGTATTTATTGA
1 ATTTTCAATTATATATTAAAATAATATATATTTATTGA
*
54967 ATTTTCAATTATGTATGT-AAATAATATATATTTAT
1 ATTTTCAATTATATAT-TAAAATAATATATATTTAT
55002 ATCAATAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
38 31 0.97
39 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (38 bp):
ATTTTCAATTATATATTAAAATAATATATATTTATTGA
Found at i:56087 original size:2 final size:2
Alignment explanation
Indices: 56080--56113 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
56070 AGAAATTAAG
56080 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
56114 ATACTTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:62794 original size:20 final size:22
Alignment explanation
Indices: 62749--62806 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
62739 GCATGGGTAG
62749 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
62773 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
62793 TGCATCGATGCACT
1 TGCATCGATGCACT
62807 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:63570 original size:18 final size:18
Alignment explanation
Indices: 63542--63663 Score: 158
Period size: 18 Copynumber: 6.9 Consensus size: 18
63532 GAGGGTCTAC
*
63542 GTGGTCATTCGGGACATA
1 GTGGTCCTTCGGGACATA
* *
63560 ATGGTCCTTCGGGACACA
1 GTGGTCCTTCGGGACATA
63578 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
63596 GTGGTCCTTCGGG--ATA
1 GTGGTCCTTCGGGACATA
* * *
63612 ATGGTTCTTCGGGACACA
1 GTGGTCCTTCGGGACATA
*
63630 GTGGTCCTTCGAGACATA
1 GTGGTCCTTCGGGACATA
*
63648 GTGGTCCTACGGGACA
1 GTGGTCCTTCGGGACA
63664 AATTCTACAC
Statistics
Matches: 88, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
16 14 0.16
18 74 0.84
ACGTcount: A:0.20, C:0.22, G:0.32, T:0.26
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:63622 original size:52 final size:52
Alignment explanation
Indices: 63542--63661 Score: 186
Period size: 52 Copynumber: 2.3 Consensus size: 52
63532 GAGGGTCTAC
* *
63542 GTGGTCATTCGGGACATAATGGTCCTTCGGGACACAGTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGG--ATAATGGTCCTTCGGGACACAGTGGTCCTTCGAGACATA
*
63596 GTGGTCCTTCGGGATAATGGTTCTTCGGGACACAGTGGTCCTTCGAGACATA
1 GTGGTCCTTCGGGATAATGGTCCTTCGGGACACAGTGGTCCTTCGAGACATA
*
63648 GTGGTCCTACGGGA
1 GTGGTCCTTCGGGA
63662 CAAATTCTAC
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
52 50 0.81
54 12 0.19
ACGTcount: A:0.19, C:0.22, G:0.33, T:0.27
Consensus pattern (52 bp):
GTGGTCCTTCGGGATAATGGTCCTTCGGGACACAGTGGTCCTTCGAGACATA
Found at i:63924 original size:2 final size:2
Alignment explanation
Indices: 63919--63957 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
63909 ATATATGTTA
63919 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
63958 CAATGACTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:66954 original size:24 final size:24
Alignment explanation
Indices: 66927--66987 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
66917 GTATGGGTAG
* *
66927 TGCATCAATGCATATGTTAAAGAA
1 TGCATCGATGCACATGTTAAAGAA
*
66951 TGCATCGATGTACATGTTAAAGAA
1 TGCATCGATGCACATGTTAAAGAA
66975 TGCATCGATGCAC
1 TGCATCGATGCAC
66988 TTCAAGGGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (24 bp):
TGCATCGATGCACATGTTAAAGAA
Found at i:67383 original size:53 final size:53
Alignment explanation
Indices: 67320--67454 Score: 225
Period size: 53 Copynumber: 2.5 Consensus size: 53
67310 TCGAGGGTCT
* *
67320 ACGTGGTCCTTCGAGATATAGTGGTCCTTCGGGACATAATGGTCCTTCGGGAC
1 ACGTGGTCCTTCGGGACATAGTGGTCCTTCGGGACATAATGGTCCTTCGGGAC
* *
67373 ACGTGGTCCTTCGGGACATAATGGTCCTTCGGGACATAATGGTTCTTCGGGAC
1 ACGTGGTCCTTCGGGACATAGTGGTCCTTCGGGACATAATGGTCCTTCGGGAC
67426 ACAGTGGTCCTTCGGGACATAGTGGTCCT
1 AC-GTGGTCCTTCGGGACATAGTGGTCCT
67455 ATGGGATAAA
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 51 0.67
54 25 0.33
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.28
Consensus pattern (53 bp):
ACGTGGTCCTTCGGGACATAGTGGTCCTTCGGGACATAATGGTCCTTCGGGAC
Found at i:67460 original size:18 final size:18
Alignment explanation
Indices: 67322--67454 Score: 187
Period size: 18 Copynumber: 7.4 Consensus size: 18
67312 GAGGGTCTAC
* *
67322 GTGGTCCTTCGAGATATA
1 GTGGTCCTTCGGGACATA
67340 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
* *
67358 ATGGTCCTTCGGGACA-C
1 GTGGTCCTTCGGGACATA
67375 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
67393 ATGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
* * *
67411 ATGGTTCTTCGGGACACA
1 GTGGTCCTTCGGGACATA
67429 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
67447 GTGGTCCT
1 GTGGTCCT
67455 ATGGGATAAA
Statistics
Matches: 102, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
17 15 0.15
18 87 0.85
ACGTcount: A:0.18, C:0.23, G:0.31, T:0.29
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:72370 original size:15 final size:15
Alignment explanation
Indices: 72350--72382 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
72340 ACAATTTCTG
*
72350 TAAAATTATATTAAT
1 TAAAATTATATCAAT
72365 TAAAATTATATCAAT
1 TAAAATTATATCAAT
72380 TAA
1 TAA
72383 TATTTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAAATTATATCAAT
Found at i:74603 original size:15 final size:16
Alignment explanation
Indices: 74566--74605 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
74556 CAAAATTATA
*
74566 ATTTTATTTTTTAAGT
1 ATTTTATTTCTTAAGT
74582 ATTTTATTTCTTAA-T
1 ATTTTATTTCTTAAGT
*
74597 GTTTTATTT
1 ATTTTATTT
74606 TAAGATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.70
Consensus pattern (16 bp):
ATTTTATTTCTTAAGT
Done.