Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005818.1 Hibiscus syriacus cultivar Beakdansim tig00013635_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: 142730
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1586 original size:23 final size:24
Alignment explanation
Indices: 1535--1592 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
1525 CTTATAGTTT
* *
1535 TTAAAATTTTATTTTAAAATAAAA
1 TTAAAATTATATTTAAAAATAAAA
* *
1559 ATAAAATTATATTTAAAAAT-ACA
1 TTAAAATTATATTTAAAAATAAAA
*
1582 TTAAAAATATA
1 TTAAAATTATA
1593 AAAACCCCTA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 11 0.39
24 17 0.61
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
TTAAAATTATATTTAAAAATAAAA
Found at i:14481 original size:27 final size:27
Alignment explanation
Indices: 14429--14527 Score: 117
Period size: 32 Copynumber: 3.4 Consensus size: 27
14419 TTCGGGTCTG
* *
14429 TCGGGTAGGGTTTCTTTAAGTTTGATAT
1 TCGGGTCGGGTTT-TTTAAGTGTGATAT
*
14457 TCGGGTCGAGTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTAAGTGTGATAT
14484 ACGGGTCGGGTCGGGTTTTTTAAGTGTGATAT
1 -----TCGGGTCGGGTTTTTTAAGTGTGATAT
14516 TCGGGTCGGGTT
1 TCGGGTCGGGTT
14528 CGAGTTTAGG
Statistics
Matches: 62, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
27 25 0.40
28 11 0.18
32 26 0.42
ACGTcount: A:0.15, C:0.09, G:0.34, T:0.41
Consensus pattern (27 bp):
TCGGGTCGGGTTTTTTAAGTGTGATAT
Found at i:14493 original size:32 final size:32
Alignment explanation
Indices: 14457--14534 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 32
14447 AGTTTGATAT
14457 TCGGGTCGAGTTTTTTAAGTGTGATATACGGG
1 TCGGGTCGAGTTTTTTAAGTGTGATATACGGG
* *
14489 TCGGGTCGGGTTTTTTAAGTGTGATATTCGGG
1 TCGGGTCGAGTTTTTTAAGTGTGATATACGGG
14521 TCGGGTTCGAGTTT
1 TCGGG-TCGAGTTT
14535 AGGGTGAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
32 35 0.83
33 7 0.17
ACGTcount: A:0.14, C:0.10, G:0.36, T:0.40
Consensus pattern (32 bp):
TCGGGTCGAGTTTTTTAAGTGTGATATACGGG
Found at i:15094 original size:15 final size:15
Alignment explanation
Indices: 15071--15104 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
15061 AGATTTAAGA
* *
15071 TTCAGATTTCATTTC
1 TTCAAATTTCAATTC
15086 TTCAAATTTCAATTC
1 TTCAAATTTCAATTC
15101 TTCA
1 TTCA
15105 GAGATTCCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.21, G:0.03, T:0.50
Consensus pattern (15 bp):
TTCAAATTTCAATTC
Found at i:19362 original size:17 final size:16
Alignment explanation
Indices: 19336--19367 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
19326 TTGCTTTGTG
19336 GTGCTTTTTTTCATTT
1 GTGCTTTTTTTCATTT
19352 GTGCTTTTTTTCATTT
1 GTGCTTTTTTTCATTT
19368 CGTTCACTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.12, G:0.12, T:0.69
Consensus pattern (16 bp):
GTGCTTTTTTTCATTT
Found at i:22310 original size:23 final size:23
Alignment explanation
Indices: 22212--22310 Score: 101
Period size: 23 Copynumber: 4.3 Consensus size: 23
22202 ATAAACTAAT
* *
22212 ATAAACAAACGTAAACGAACACAA
1 ATAAACGAACATAAACGAACAC-A
* * *
22236 ATGAATGAACATAAACGAACATA
1 ATAAACGAACATAAACGAACACA
* *
22259 ATAAAAGAACATAATCGAACACA
1 ATAAACGAACATAAACGAACACA
*
22282 ATAAACGAACATAAACAAACCACA
1 ATAAACGAACATAAACGAA-CACA
22306 A-AAAC
1 ATAAAC
22311 ACAAAAAACA
Statistics
Matches: 62, Mismatches: 12, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
23 40 0.65
24 22 0.35
ACGTcount: A:0.62, C:0.19, G:0.08, T:0.11
Consensus pattern (23 bp):
ATAAACGAACATAAACGAACACA
Found at i:22937 original size:2 final size:2
Alignment explanation
Indices: 22930--22974 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
22920 ATTCAGAGGT
22930 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
22972 TA T
1 TA T
22975 TACAATACAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:24373 original size:29 final size:29
Alignment explanation
Indices: 24316--24411 Score: 140
Period size: 29 Copynumber: 3.3 Consensus size: 29
24306 TGCCTATTTT
* * *
24316 AATTAATTCCCAAAATAGCA-CCTTTTCG
1 AATTAATTCCTAAAGTAGCACCCATTTCG
* *
24344 AATAAATTCCTAAAGTAGTACCCATTTCG
1 AATTAATTCCTAAAGTAGCACCCATTTCG
24373 AATTAATTCCTAAAGTAGCACCCATTTCG
1 AATTAATTCCTAAAGTAGCACCCATTTCG
24402 AATTAATTCC
1 AATTAATTCC
24412 CAAAATATCA
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
28 16 0.27
29 44 0.73
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.32
Consensus pattern (29 bp):
AATTAATTCCTAAAGTAGCACCCATTTCG
Found at i:24423 original size:29 final size:29
Alignment explanation
Indices: 24316--24424 Score: 139
Period size: 29 Copynumber: 3.8 Consensus size: 29
24306 TGCCTATTTT
*
24316 AATTAATTCCCAAAATAGCA-CCTTTTCG
1 AATTAATTCCCAAAATAGCACCCATTTCG
* * * *
24344 AATAAATTCCTAAAGTAGTACCCATTTCG
1 AATTAATTCCCAAAATAGCACCCATTTCG
* *
24373 AATTAATTCCTAAAGTAGCACCCATTTCG
1 AATTAATTCCCAAAATAGCACCCATTTCG
*
24402 AATTAATTCCCAAAATATCACCC
1 AATTAATTCCCAAAATAGCACCC
24425 GATCAACGGT
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
28 16 0.23
29 54 0.77
ACGTcount: A:0.38, C:0.25, G:0.07, T:0.30
Consensus pattern (29 bp):
AATTAATTCCCAAAATAGCACCCATTTCG
Found at i:24459 original size:13 final size:13
Alignment explanation
Indices: 24441--24481 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
24431 CGGTCAACGA
24441 TCAACGGGTCGGG
1 TCAACGGGTCGGG
*
24454 TCAACGAGTCGGG
1 TCAACGGGTCGGG
24467 TCAACGGGTCGGG
1 TCAACGGGTCGGG
24480 TC
1 TC
24482 GGAACCGGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (13 bp):
TCAACGGGTCGGG
Found at i:30465 original size:14 final size:13
Alignment explanation
Indices: 30430--30472 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
30420 ACAGTGTATA
* *
30430 AAAATATTTTAAT
1 AAAATATTTCAGT
30443 AAAATATTTCAGT
1 AAAATATTTCAGT
*
30456 AAAATCATTTCATT
1 AAAAT-ATTTCAGT
30470 AAA
1 AAA
30473 CATGTTTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 16 0.62
14 10 0.38
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (13 bp):
AAAATATTTCAGT
Found at i:30745 original size:14 final size:15
Alignment explanation
Indices: 30710--30742 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
30700 CCGAAATACA
30710 GAAATCAGATATCAG
1 GAAATCAGATATCAG
30725 GAAATCA-ATATTCAG
1 GAAATCAGATA-TCAG
30740 GAA
1 GAA
30743 TCACGTATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.21
Consensus pattern (15 bp):
GAAATCAGATATCAG
Found at i:36594 original size:29 final size:29
Alignment explanation
Indices: 36538--36595 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
36528 ATAATTAGAT
* *
36538 ATAATTTATATATACTCTTAATTTATAAA
1 ATAATTTATATATAATCTTAATTAATAAA
*
36567 ATAATTTTTATATAATC-TAATATAATAAA
1 ATAATTTATATATAATCTTAAT-TAATAAA
36596 TGGGATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (29 bp):
ATAATTTATATATAATCTTAATTAATAAA
Found at i:64461 original size:29 final size:29
Alignment explanation
Indices: 64407--64462 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
64397 AATGAAAATC
*
64407 AAATTAAATATAATAAATTAACATTTTTT
1 AAATTAAATATAATAAATAAACATTTTTT
* *
64436 AAATTATAATA-AATTAATAAATATTTT
1 AAATTA-AATATAATAAATAAACATTTT
64463 ATATATAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 19 0.83
30 4 0.17
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (29 bp):
AAATTAAATATAATAAATAAACATTTTTT
Found at i:66437 original size:52 final size:54
Alignment explanation
Indices: 66358--66464 Score: 148
Period size: 52 Copynumber: 2.0 Consensus size: 54
66348 TTATAATATT
* *
66358 CTTGTGATTAGTTGTAATTCCCAAACTCTAGGCTAGTCTCCTA-TT-TATGTGC
1 CTTGTAATTAGTTGTAATTCCCAAACTCGAGGCTAGTCTCCTATTTCTATGTGC
* *
66410 CTTGTAATTAGTTGTAA-TCCCTTAACTCGAGGCTAGTTTCCTATTTCTATGTGC
1 CTTGTAATTAGTTGTAATTCCC-AAACTCGAGGCTAGTCTCCTATTTCTATGTGC
66464 C
1 C
66465 CCATCTTGTG
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
51 4 0.08
52 34 0.71
53 2 0.04
54 8 0.17
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.41
Consensus pattern (54 bp):
CTTGTAATTAGTTGTAATTCCCAAACTCGAGGCTAGTCTCCTATTTCTATGTGC
Found at i:71017 original size:52 final size:54
Alignment explanation
Indices: 70939--71045 Score: 155
Period size: 52 Copynumber: 2.0 Consensus size: 54
70929 TTATAATATT
* * * *
70939 CTTGTGATTAGTTGTAATTCCCTAACTCTAGGCTAGTCTCCTA-TT-TATGTGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAAGCTAGTCTCATATTTCTATGTGC
*
70991 CTTGTAATTAGTTGTAATCCCCTAACTCTAAGCTAGTTTCATATTTCTATGTGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAAGCTAGTCTCATATTTCTATGTGC
71045 C
1 C
71046 CCATCTTGTG
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
52 38 0.79
53 2 0.04
54 8 0.17
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.42
Consensus pattern (54 bp):
CTTGTAATTAGTTGTAATCCCCTAACTCTAAGCTAGTCTCATATTTCTATGTGC
Found at i:71178 original size:14 final size:14
Alignment explanation
Indices: 71161--71200 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
71151 TAAATGGGAG
*
71161 TATTTTTATTGAAA
1 TATTTTTATTAAAA
*
71175 TATTATTATTAAAA
1 TATTTTTATTAAAA
71189 TATTTTTTATTA
1 TA-TTTTTATTA
71201 TATAAATCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (14 bp):
TATTTTTATTAAAA
Found at i:72837 original size:18 final size:19
Alignment explanation
Indices: 72815--72861 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
72805 CTTGAAATAG
72815 ATAAAATCAATAAA-ATAA
1 ATAAAATCAATAAATATAA
*
72833 GTAAAAAT-AATAAATATAA
1 AT-AAAATCAATAAATATAA
*
72852 AAAAAATCAA
1 ATAAAATCAA
72862 GTTTTGAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
ATAAAATCAATAAATATAA
Found at i:78224 original size:24 final size:24
Alignment explanation
Indices: 78192--78245 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
78182 TGAATAAACT
78192 GCAGCAGCAGCAACAACAACAACA
1 GCAGCAGCAGCAACAACAACAACA
*
78216 GCAGCAGCAGCATCAACAACAACA
1 GCAGCAGCAGCAACAACAACAACA
78240 GCAGCA
1 GCAGCA
78246 TTATAAACTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.46, C:0.33, G:0.19, T:0.02
Consensus pattern (24 bp):
GCAGCAGCAGCAACAACAACAACA
Found at i:80330 original size:20 final size:20
Alignment explanation
Indices: 80294--80331 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
80284 ATCCTATTCC
**
80294 CTGATAATCTTTTATTCCCA
1 CTGATAATCTTACATTCCCA
80314 CTGATAATCTTACATTCC
1 CTGATAATCTTACATTCC
80332 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.42
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCA
Found at i:81571 original size:29 final size:29
Alignment explanation
Indices: 81529--81588 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
81519 TCTTCTAATC
81529 TTCTCTTATAGGAATCATAGAATCTTTCA
1 TTCTCTTATAGGAATCATAGAATCTTTCA
81558 TTCTCTTATAGGAATCATAGAATCTTTCA
1 TTCTCTTATAGGAATCATAGAATCTTTCA
81587 TT
1 TT
81589 AGTACAAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.43
Consensus pattern (29 bp):
TTCTCTTATAGGAATCATAGAATCTTTCA
Found at i:100770 original size:15 final size:15
Alignment explanation
Indices: 100746--100825 Score: 108
Period size: 15 Copynumber: 5.4 Consensus size: 15
100736 TTCCAGAAAA
100746 AATTACTGGAATTTG
1 AATTACTGGAATTTG
*
100761 AATTATTGGAATTTG
1 AATTACTGGAATTTG
**
100776 AATTACTGGAAAATG
1 AATTACTGGAATTTG
100791 AATTACTGGAATTTG
1 AATTACTGGAATTTG
**
100806 AATT-CTGGAAAATG
1 AATTACTGGAATTTG
100820 AATTAC
1 AATTAC
100826 ATTTCTGTAA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
14 12 0.21
15 44 0.79
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.36
Consensus pattern (15 bp):
AATTACTGGAATTTG
Found at i:100823 original size:29 final size:30
Alignment explanation
Indices: 100746--100825 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
100736 TTCCAGAAAA
** *
100746 AATTACTGGAATTTGAATTATTGGAATTTG
1 AATTACTGGAAAATGAATTACTGGAATTTG
100776 AATTACTGGAAAATGAATTACTGGAATTTG
1 AATTACTGGAAAATGAATTACTGGAATTTG
100806 AATT-CTGGAAAATGAATTAC
1 AATTACTGGAAAATGAATTAC
100826 ATTTCTGTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 16 0.34
30 31 0.66
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.36
Consensus pattern (30 bp):
AATTACTGGAAAATGAATTACTGGAATTTG
Found at i:100831 original size:20 final size:20
Alignment explanation
Indices: 100808--100876 Score: 129
Period size: 20 Copynumber: 3.5 Consensus size: 20
100798 GGAATTTGAA
100808 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
100828 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
100848 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
100868 TTCTGGAAA
1 TTCTGGAAA
100877 CATCTGGAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:101066 original size:28 final size:29
Alignment explanation
Indices: 101034--101088 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
101024 TTTACTAAAT
* *
101034 ATTATTGAATATATAAATAA-TATTATTC
1 ATTATTAAATATATAAAAAATTATTATTC
101062 ATTATTAAATATATAAAAAATTATTAT
1 ATTATTAAATATATAAAAAATTATTAT
101089 ATATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (29 bp):
ATTATTAAATATATAAAAAATTATTATTC
Found at i:101084 original size:19 final size:19
Alignment explanation
Indices: 101062--101098 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
101052 AATATTATTC
101062 ATTATTAAATATATAAAAA
1 ATTATTAAATATATAAAAA
* *
101081 ATTATTATATATTTAAAA
1 ATTATTAAATATATAAAA
101099 TAAAATATAA
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATTATTAAATATATAAAAA
Found at i:101099 original size:28 final size:28
Alignment explanation
Indices: 101034--101111 Score: 83
Period size: 28 Copynumber: 2.8 Consensus size: 28
101024 TTTACTAAAT
*
101034 ATTATTGAATATATAAATAATATTATTC
1 ATTATTAAATATATAAATAATATTATTC
101062 ATTATTAAATATATAAA-AA-ATTATT-
1 ATTATTAAATATATAAATAATATTATTC
*
101087 ATATATTTAAA-ATAAAATATAATAT
1 AT-TA-TTAAATATATAA-ATAATAT
101112 CTTATATTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
25 2 0.05
26 13 0.30
27 8 0.19
28 18 0.42
29 2 0.05
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (28 bp):
ATTATTAAATATATAAATAATATTATTC
Found at i:101128 original size:20 final size:20
Alignment explanation
Indices: 101103--101183 Score: 71
Period size: 20 Copynumber: 4.0 Consensus size: 20
101093 TTAAAATAAA
*
101103 ATATAATATCTTATATTATT
1 ATATAATATATTATATTATT
101123 ATATAATTGATATTATATAATATT
1 ATATAA-T-ATATTATAT--TATT
*
101147 A-AAAATATATTTATATTATT
1 ATATAATATA-TTATATTATT
101167 ATA-AATATA--ATATTATT
1 ATATAATATATTATATTATT
101184 TTAGTTTAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
17 8 0.15
20 17 0.32
21 5 0.09
22 15 0.28
23 3 0.06
24 5 0.09
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (20 bp):
ATATAATATATTATATTATT
Found at i:101182 original size:22 final size:22
Alignment explanation
Indices: 101101--101182 Score: 80
Period size: 22 Copynumber: 3.6 Consensus size: 22
101091 ATTTAAAATA
101101 AAATATAATATCTTATATTATTAT
1 AAATATAATA--TTATATTATTAT
* *
101125 ATAAT-TGATATTATATAATATTAA
1 A-AATATAATATTATAT--TATTAT
101149 AAATAT-AT-TTATATTATTAT
1 AAATATAATATTATATTATTAT
101169 AAATATAATATTAT
1 AAATATAATATTAT
101183 TTTAGTTTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
20 11 0.22
21 2 0.04
22 16 0.33
23 5 0.10
24 12 0.24
25 3 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (22 bp):
AAATATAATATTATATTATTAT
Found at i:101437 original size:42 final size:40
Alignment explanation
Indices: 101368--101470 Score: 149
Period size: 38 Copynumber: 2.6 Consensus size: 40
101358 ATGAATTACA
*
101368 TTCCGGAAAACGAATTACGTG--AAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAAAACACGGGAAAACATT
101406 TTCCGGAAAACGAATTACGTGAACACAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAA-A-AACACGGGAAAACATT
*
101448 TTCCGG-AAATGAATTACGTGAAA
1 TTCCGGAAAACGAATTACGTGAAA
101471 TAAACACAAG
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
38 21 0.36
40 1 0.02
41 16 0.27
42 21 0.36
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.19
Consensus pattern (40 bp):
TTCCGGAAAACGAATTACGTGAAAAACACGGGAAAACATT
Found at i:103776 original size:40 final size:40
Alignment explanation
Indices: 103721--103802 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
103711 GGACGACGTC
103721 GGTGCATACTGGAATATAACATAGAGTTGGGTAAAATGAA
1 GGTGCATACTGGAATATAACATAGAGTTGGGTAAAATGAA
103761 GGTGCATACTGGAATATAACATAGAGTTGGGTAAAATGAA
1 GGTGCATACTGGAATATAACATAGAGTTGGGTAAAATGAA
103801 GG
1 GG
103803 ATGACAAAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.39, C:0.07, G:0.29, T:0.24
Consensus pattern (40 bp):
GGTGCATACTGGAATATAACATAGAGTTGGGTAAAATGAA
Found at i:106314 original size:3 final size:3
Alignment explanation
Indices: 106306--106351 Score: 83
Period size: 3 Copynumber: 15.0 Consensus size: 3
106296 ATAATTCTAC
106306 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT
106352 GGTATATATT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:107668 original size:20 final size:20
Alignment explanation
Indices: 107640--107703 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 20
107630 CTAATCTTTA
*
107640 ATTACGTATATAATTTATGC
1 ATTATGTATATAATTTATGC
107660 ATTATGTATATAA-TTA--C
1 ATTATGTATATAATTTATGC
107677 -----GTATATAATTTATGC
1 ATTATGTATATAATTTATGC
107692 ATTATGTATATA
1 ATTATGTATATA
107704 TAATTTTTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 16
0.67 0.02 0.31
Matches are distributed among these distances:
12 8 0.23
13 3 0.09
15 1 0.03
17 1 0.03
19 3 0.09
20 19 0.54
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (20 bp):
ATTATGTATATAATTTATGC
Found at i:107674 original size:32 final size:32
Alignment explanation
Indices: 107638--107703 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
107628 TTCTAATCTT
107638 TAATTACGTATATAATTTATGCATTATGTATA
1 TAATTACGTATATAATTTATGCATTATGTATA
107670 TAATTACGTATATAATTTATGCATTATGTATA
1 TAATTACGTATATAATTTATGCATTATGTATA
107702 TA
1 TA
107704 TAATTTTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (32 bp):
TAATTACGTATATAATTTATGCATTATGTATA
Found at i:107760 original size:14 final size:14
Alignment explanation
Indices: 107742--107803 Score: 97
Period size: 14 Copynumber: 4.4 Consensus size: 14
107732 TACATTTATA
107742 ATTTTACAATTAAT
1 ATTTTACAATTAAT
*
107756 TTTTTACAATTAAT
1 ATTTTACAATTAAT
*
107770 ATTTTATAATTAAT
1 ATTTTACAATTAAT
*
107784 TTTTTACAATTAAT
1 ATTTTACAATTAAT
107798 ATTTTA
1 ATTTTA
107804 ATAACATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 42 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTTTACAATTAAT
Found at i:107762 original size:28 final size:28
Alignment explanation
Indices: 107742--107803 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
107732 TACATTTATA
107742 ATTTTACAATTAATTTTTTACAATTAAT
1 ATTTTACAATTAATTTTTTACAATTAAT
*
107770 ATTTTATAATTAATTTTTTACAATTAAT
1 ATTTTACAATTAATTTTTTACAATTAAT
107798 ATTTTA
1 ATTTTA
107804 ATAACATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (28 bp):
ATTTTACAATTAATTTTTTACAATTAAT
Found at i:109882 original size:23 final size:24
Alignment explanation
Indices: 109856--109910 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 24
109846 AGTTAAGAGT
*
109856 AATTAAATTAAGA-ATAATTTAAA
1 AATTAAATTAAGATATAAATTAAA
*
109879 AATTAAA--AATATATAAATTAAA
1 AATTAAATTAAGATATAAATTAAA
109901 AATATAAATT
1 AAT-TAAATT
109911 TTAGTGACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 3 0.12
22 12 0.46
23 11 0.42
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
AATTAAATTAAGATATAAATTAAA
Found at i:109910 original size:13 final size:15
Alignment explanation
Indices: 109878--109906 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
109868 AATAATTTAA
109878 AAATTAAAAATATAT
1 AAATTAAAAATATAT
109893 AAATTAAAAATATA
1 AAATTAAAAATATA
109907 AATTTTAGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATTAAAAATATAT
Found at i:114839 original size:2 final size:2
Alignment explanation
Indices: 114832--114871 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
114822 ATCATATACA
*
114832 AT AT AT AT AT AT AT AT AT AT CT 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 AT AT
114872 TTTTCCGTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:115688 original size:20 final size:21
Alignment explanation
Indices: 115641--115689 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
115631 GTATGTTTAA
**
115641 TAATTAATATAATATTTTGTT
1 TAATTAATATAATACGTTGTT
*
115662 TAA-TAATATAGTACGTT-TT
1 TAATTAATATAATACGTTGTT
115681 TAATTAATA
1 TAATTAATA
115690 ATTTGAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 5 0.21
20 16 0.67
21 3 0.12
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (21 bp):
TAATTAATATAATACGTTGTT
Found at i:116144 original size:4 final size:4
Alignment explanation
Indices: 116135--116244 Score: 67
Period size: 4 Copynumber: 25.8 Consensus size: 4
116125 GGAGGTAATT
* * *
116135 TTTA TTTA TTTA TTTA CTTTGAA TTTT TTTA TTTA TGTA TTCA TTTA TTTCGA
1 TTTA TTTA TTTA TTTA -TTT--A TTTA TTTA TTTA TTTA TTTA TTTA TTT--A
* * * * * * *
116188 ATAA ATTA GTGA TTTA TTTA TTTA TTTA TTTCAA ATAA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT--A TTTA TTTA TTTA TTTA
116238 TTTA TTT
1 TTTA TTT
116245 GAAGGGGTAT
Statistics
Matches: 82, Mismatches: 17, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
4 71 0.87
5 3 0.04
6 7 0.09
7 1 0.01
ACGTcount: A:0.28, C:0.04, G:0.05, T:0.64
Consensus pattern (4 bp):
TTTA
Found at i:116215 original size:34 final size:34
Alignment explanation
Indices: 116165--116244 Score: 106
Period size: 34 Copynumber: 2.4 Consensus size: 34
116155 GAATTTTTTT
* * *
116165 ATTTATGTATTCATTTATTTCGAATAAATTAGTG
1 ATTTATTTATTTATTTATTTCAAATAAATTAGTG
* * *
116199 ATTTATTTATTTATTTATTTCAAATAATTTATTT
1 ATTTATTTATTTATTTATTTCAAATAAATTAGTG
116233 ATTTATTTATTT
1 ATTTATTTATTT
116245 GAAGGGGTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.31, C:0.04, G:0.05, T:0.60
Consensus pattern (34 bp):
ATTTATTTATTTATTTATTTCAAATAAATTAGTG
Found at i:120054 original size:21 final size:23
Alignment explanation
Indices: 120003--120064 Score: 83
Period size: 21 Copynumber: 2.7 Consensus size: 23
119993 GAATGTTAAA
*
120003 ATGGTATCGATACTACTTAGTGT
1 ATGGTACCGATACTACTTAGTGT
*
120026 AGTAGTACCGATACT-CTTAGT-T
1 A-TGGTACCGATACTACTTAGTGT
120048 ATGGTACCGATACTACT
1 ATGGTACCGATACTACT
120065 CCTTTTGTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 12 0.35
22 4 0.12
23 7 0.21
24 11 0.32
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.35
Consensus pattern (23 bp):
ATGGTACCGATACTACTTAGTGT
Found at i:137181 original size:18 final size:19
Alignment explanation
Indices: 137160--137195 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
137150 ATTTAAAAGA
137160 AAACAC-AAATTTTGAAAT
1 AAACACAAAATTTTGAAAT
*
137178 AAACCCAAAATTTTGAAA
1 AAACACAAAATTTTGAAA
137196 ACATTCATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.56, C:0.14, G:0.06, T:0.25
Consensus pattern (19 bp):
AAACACAAAATTTTGAAAT
Found at i:137721 original size:28 final size:28
Alignment explanation
Indices: 137680--137745 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
137670 TTGAATTACG
* *
137680 AAATGAAACGTTAGGCACCAAACT-AGAAT
1 AAAT-AAACATTAGACACCAAACTGA-AAT
*
137709 AAATAAACATTAGACACTAAACTGAAAT
1 AAATAAACATTAGACACCAAACTGAAAT
137737 AAA-AAACAT
1 AAATAAACAT
137746 ACATTTGATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 6 0.18
28 22 0.67
29 5 0.15
ACGTcount: A:0.56, C:0.15, G:0.11, T:0.18
Consensus pattern (28 bp):
AAATAAACATTAGACACCAAACTGAAAT
Done.