Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005314.1 Hibiscus syriacus cultivar Beakdansim tig00012031_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: 113425
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8739 original size:36 final size:36
Alignment explanation
Indices: 8699--8783 Score: 170
Period size: 36 Copynumber: 2.4 Consensus size: 36
8689 GAAACATTTA
8699 CCAAACTTTGAAAAAAACATTTTCCAAAGTTGGTTG
1 CCAAACTTTGAAAAAAACATTTTCCAAAGTTGGTTG
8735 CCAAACTTTGAAAAAAACATTTTCCAAAGTTGGTTG
1 CCAAACTTTGAAAAAAACATTTTCCAAAGTTGGTTG
8771 CCAAACTTTGAAA
1 CCAAACTTTGAAA
8784 CTTTTAACAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (36 bp):
CCAAACTTTGAAAAAAACATTTTCCAAAGTTGGTTG
Found at i:12834 original size:16 final size:16
Alignment explanation
Indices: 12810--12843 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
12800 TATCGCCGAC
*
12810 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
12826 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
12842 CG
1 CG
12844 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:18887 original size:19 final size:20
Alignment explanation
Indices: 18863--18907 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
18853 CCCAGTCCTA
* *
18863 CAACAAT-CCCTTAACAAAT
1 CAACAATCCCCCTAACAAAC
18882 CAACAATCCCCCTAACAAAC
1 CAACAATCCCCCTAACAAAC
18902 CAACAA
1 CAACAA
18908 AGCCATCCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.49, C:0.38, G:0.00, T:0.13
Consensus pattern (20 bp):
CAACAATCCCCCTAACAAAC
Found at i:21298 original size:7 final size:7
Alignment explanation
Indices: 21286--21429 Score: 112
Period size: 7 Copynumber: 20.4 Consensus size: 7
21276 ATATTATAAA
21286 GTTTAGG
1 GTTTAGG
21293 GTTTAGG
1 GTTTAGG
21300 GTTTAGG
1 GTTTAGG
**
21307 GTTTATA
1 GTTTAGG
*
21314 GTTTA-T
1 GTTTAGG
* *
21320 GTGATAAG
1 GT-TTAGG
*
21328 ATTTAAGG
1 GTTT-AGG
* *
21336 TTTTAGA
1 GTTTAGG
21343 GTTTAGG
1 GTTTAGG
21350 GTTTAGG
1 GTTTAGG
21357 GTTTAGG
1 GTTTAGG
21364 GTTTAGG
1 GTTTAGG
21371 GTTTAGG
1 GTTTAGG
*
21378 GTTTAGA
1 GTTTAGG
* *
21385 TTTTAAG
1 GTTTAGG
*
21392 ATTTAGG
1 GTTTAGG
**
21399 GTTT-TT
1 GTTTAGG
21405 GTGTTAGG
1 GT-TTAGG
*
21413 GGTTAGG
1 GTTTAGG
21420 GTTTAGG
1 GTTTAGG
21427 GTT
1 GTT
21430 AAATATAAAA
Statistics
Matches: 107, Mismatches: 25, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
6 4 0.04
7 96 0.90
8 7 0.07
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (7 bp):
GTTTAGG
Found at i:21670 original size:20 final size:21
Alignment explanation
Indices: 21633--21672 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
21623 TTAACAATGT
*
21633 AAATTCTATATATTTTTAATA
1 AAATTCTATATATATTTAATA
*
21654 AAATTTTATA-ATATTTAAT
1 AAATTCTATATATATTTAAT
21673 TTGAATTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
AAATTCTATATATATTTAATA
Found at i:23044 original size:31 final size:31
Alignment explanation
Indices: 22984--23044 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
22974 GTTCGAGCAT
* * *
22984 TTTCGAGTTCGAGTCGAGTTTTAATATTTTC
1 TTTCGAGTTCGAGTCGAGCTTAAAAATTTTC
*
23015 TTTCGAGTTCGAGTTGAGCTTAAAAATTTT
1 TTTCGAGTTCGAGTCGAGCTTAAAAATTTT
23045 AGGCTCGCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.23, C:0.11, G:0.20, T:0.46
Consensus pattern (31 bp):
TTTCGAGTTCGAGTCGAGCTTAAAAATTTTC
Found at i:25834 original size:41 final size:41
Alignment explanation
Indices: 25709--25864 Score: 129
Period size: 42 Copynumber: 3.8 Consensus size: 41
25699 TAAACAACCA
** * * * * *
25709 TATTGCGGCGTTTTAGATATAAACGCCACTAATTTACCAATA
1 TATTGCGGCGTTTGGGCTATAAACGCCGCTAAATTA-CACTC
* *
25751 TATTGTGGCGTTTGTGG-TATAAACGCCGCTACATTAACACTC
1 TATTGCGGCGTTTG-GGCTATAAACGCCGCTAAATT-ACACTC
25793 TATTGCGGCGTTTGGGCTA-AAACGCCGCTAAATGT-CTACTC
1 TATTGCGGCGTTTGGGCTATAAACGCCGCTAAAT-TAC-ACTC
* ***
25834 TATTGCGACGTTTTTACTATAAACGCCGCTA
1 TATTGCGGCGTTTGGGCTATAAACGCCGCTA
25865 TTGATTAACC
Statistics
Matches: 94, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
40 1 0.01
41 34 0.36
42 57 0.61
43 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (41 bp):
TATTGCGGCGTTTGGGCTATAAACGCCGCTAAATTACACTC
Found at i:26882 original size:25 final size:25
Alignment explanation
Indices: 26848--26900 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
26838 AAACATTGCC
26848 ATTTATTATATGTAGTCTAAAAATA
1 ATTTATTATATGTAGTCTAAAAATA
26873 ATTTATTATATGTAGTCTAAAAATA
1 ATTTATTATATGTAGTCTAAAAATA
26898 ATT
1 ATT
26901 GATAAATTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (25 bp):
ATTTATTATATGTAGTCTAAAAATA
Found at i:30075 original size:42 final size:42
Alignment explanation
Indices: 30024--30125 Score: 111
Period size: 42 Copynumber: 2.5 Consensus size: 42
30014 CACGAAAGCT
30024 AATTTCGCAACAC-AGTTTCCGAATTCGCAACTCGAATTTGA
1 AATTTCGCAACACGAGTTTCCGAATTCGCAACTCGAATTTGA
* * *** * *
30065 CAATTTCGCAACACTAATTT-CTTTTTCGCAACTCGATTTTTA
1 -AATTTCGCAACACGAGTTTCCGAATTCGCAACTCGAATTTGA
30107 AA-TTCGCAACACGAGTTTC
1 AATTTCGCAACACGAGTTTC
30126 TTTTTTCGCA
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
40 14 0.28
41 2 0.04
42 30 0.60
43 4 0.08
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (42 bp):
AATTTCGCAACACGAGTTTCCGAATTCGCAACTCGAATTTGA
Found at i:30144 original size:41 final size:40
Alignment explanation
Indices: 30069--30157 Score: 117
Period size: 41 Copynumber: 2.2 Consensus size: 40
30059 ATTTGACAAT
* **
30069 TTCGCAACACTAATTTCTTTTTCGCAACTCGATTTT-TAAA
1 TTCGCAACACGAATTTCTTTTTCGCAACAAGATTTTCT-AA
*
30109 TTCGCAACACGAGTTTCTTTTTTCGCAACAAGATTTTCTAA
1 TTCGCAACACGAATTTC-TTTTTCGCAACAAGATTTTCTAA
30150 TTCGCAAC
1 TTCGCAAC
30158 GCGGGTTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
40 15 0.35
41 27 0.63
42 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.39
Consensus pattern (40 bp):
TTCGCAACACGAATTTCTTTTTCGCAACAAGATTTTCTAA
Found at i:30155 original size:20 final size:20
Alignment explanation
Indices: 30069--30157 Score: 72
Period size: 20 Copynumber: 4.4 Consensus size: 20
30059 ATTTGACAAT
* * **
30069 TTCGCAACACTAATTTCTTT
1 TTCGCAACACGATTTTCTAA
*
30089 TTCGCAACTCGATTTT-TAAA
1 TTCGCAACACGATTTTCT-AA
* **
30109 TTCGCAACACGAGTTTCTTTT
1 TTCGCAACACGATTTTC-TAA
*
30130 TTCGCAACAAGATTTTCTAA
1 TTCGCAACACGATTTTCTAA
30150 TTCGCAAC
1 TTCGCAAC
30158 GCGGGTTTAA
Statistics
Matches: 53, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
19 1 0.02
20 36 0.68
21 15 0.28
22 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.39
Consensus pattern (20 bp):
TTCGCAACACGATTTTCTAA
Found at i:30173 original size:20 final size:20
Alignment explanation
Indices: 30150--30217 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
30140 GATTTTCTAA
**
30150 TTCGCAACGCGGGTTTAAAT
1 TTCGCAACGCGAATTTAAAT
* ***
30170 TTCGCAACACGAATTTCGTT
1 TTCGCAACGCGAATTTAAAT
*
30190 TTTGCAACGCGAATTTAAAT
1 TTCGCAACGCGAATTTAAAT
30210 TTCGCAAC
1 TTCGCAAC
30218 TCAGCTTTTA
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (20 bp):
TTCGCAACGCGAATTTAAAT
Found at i:30215 original size:60 final size:61
Alignment explanation
Indices: 30103--30239 Score: 154
Period size: 60 Copynumber: 2.3 Consensus size: 61
30093 CAACTCGATT
* * * * * *
30103 TTTAAA-TTCGCAACACGAGTTTCTTTTTTCGCAACAAGATTTTCTAATTCGCAACGCGGG
1 TTTAAATTTCGCAACACGAATTTCGTTTTTCGCAACAAGAATTTCAAATTCGCAACGCAGC
** *
30163 TTTAAATTTCGCAACACGAATTTCGTTTTT-GCAACGCGAATTT-AAATTTCGCAACTCAGC
1 TTTAAATTTCGCAACACGAATTTCGTTTTTCGCAACAAGAATTTCAAA-TTCGCAACGCAGC
*
30223 TTTTAATTTCGCAACAC
1 TTTAAATTTCGCAACAC
30240 AAATGTTTTG
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
59 2 0.03
60 42 0.65
61 21 0.32
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (61 bp):
TTTAAATTTCGCAACACGAATTTCGTTTTTCGCAACAAGAATTTCAAATTCGCAACGCAGC
Found at i:37543 original size:27 final size:27
Alignment explanation
Indices: 37513--37610 Score: 79
Period size: 27 Copynumber: 3.4 Consensus size: 27
37503 TCAAATAATA
*
37513 CCCTGCTACCAAGTTTCTCGAACCATG
1 CCCTGCTACCAAGTTGCTCGAACCATG
*
37540 CCCTGTTACCCTAATCAAGTTGCTCGAACCATG
1 CCCTG-----CT-ACCAAGTTGCTCGAACCATG
* * * *
37573 TCTTGCTACCAAGTTGATCGAACTATG
1 CCCTGCTACCAAGTTGCTCGAACCATG
*
37600 CTCTGCTACCA
1 CCCTGCTACCA
37611 TGATACTACA
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
27 30 0.55
28 2 0.04
32 2 0.04
33 21 0.38
ACGTcount: A:0.23, C:0.33, G:0.15, T:0.29
Consensus pattern (27 bp):
CCCTGCTACCAAGTTGCTCGAACCATG
Found at i:37728 original size:27 final size:27
Alignment explanation
Indices: 37690--37741 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
37680 TTCGAGTGGC
*
37690 TAACAGGGCATGGTTCGAGAAACTTAG
1 TAACAGGGCATGATTCGAGAAACTTAG
* *
37717 TAACATGGCATGATTCGAGTAACTT
1 TAACAGGGCATGATTCGAGAAACTT
37742 TATCGAGGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (27 bp):
TAACAGGGCATGATTCGAGAAACTTAG
Found at i:37819 original size:27 final size:27
Alignment explanation
Indices: 37781--37834 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
37771 GTTTCAGGGC
**
37781 AGCAGGGCATGGTTTGAGCAACTTAAT
1 AGCAGGGCATGGTTCAAGCAACTTAAT
37808 AGCAGGGCATGGTTCAAGCAACTTAAT
1 AGCAGGGCATGGTTCAAGCAACTTAAT
37835 CAGGGTAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (27 bp):
AGCAGGGCATGGTTCAAGCAACTTAAT
Found at i:38233 original size:13 final size:12
Alignment explanation
Indices: 38215--38291 Score: 57
Period size: 13 Copynumber: 5.8 Consensus size: 12
38205 GATGCACTAC
38215 ATTTTTTTTTGTT
1 ATTTTTTTTT-TT
38228 ATTTTTGTTATTTT
1 ATTTTT-TT-TTTT
*
38242 -TGTTATTTTTATT
1 AT-TT-TTTTTTTT
38255 ATTTTTGTTTTTT
1 ATTTTT-TTTTTT
*
38268 ATTTTCTTTTGTT
1 ATTTT-TTTTTTT
38281 ATTTTCTTTTT
1 ATTTT-TTTTT
38292 CTTTTCCTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
12 2 0.04
13 37 0.70
14 10 0.19
15 4 0.08
ACGTcount: A:0.10, C:0.03, G:0.06, T:0.81
Consensus pattern (12 bp):
ATTTTTTTTTTT
Found at i:38234 original size:9 final size:9
Alignment explanation
Indices: 38220--38285 Score: 84
Period size: 9 Copynumber: 7.4 Consensus size: 9
38210 ACTACATTTT
38220 TTTTTGTTA
1 TTTTTGTTA
38229 TTTTTGTTA
1 TTTTTGTTA
38238 TTTTTGTTA
1 TTTTTGTTA
*
38247 TTTTTATTA
1 TTTTTGTTA
38256 TTTTTGTT-
1 TTTTTGTTA
38264 TTTTAT-TT-
1 TTTT-TGTTA
38272 TCTTTTGTTA
1 T-TTTTGTTA
38282 TTTT
1 TTTT
38286 CTTTTTCTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
8 8 0.16
9 42 0.82
10 1 0.02
ACGTcount: A:0.11, C:0.02, G:0.08, T:0.80
Consensus pattern (9 bp):
TTTTTGTTA
Found at i:38303 original size:13 final size:12
Alignment explanation
Indices: 38257--38304 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
38247 TTTTTATTAT
*
38257 TTTTGTTTTTTA
1 TTTTCTTTTTTA
38269 TTTTCTTTTGTTA
1 TTTTCTTTT-TTA
38282 TTTTCTTTTTCT-
1 TTTTCTTTTT-TA
*
38294 TTTCCTTTTTT
1 TTTTCTTTTTT
38305 TCGTTACATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 1 0.03
12 18 0.56
13 13 0.41
ACGTcount: A:0.04, C:0.10, G:0.04, T:0.81
Consensus pattern (12 bp):
TTTTCTTTTTTA
Found at i:39748 original size:38 final size:38
Alignment explanation
Indices: 39697--39772 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
39687 TGATTTACCC
39697 TTTTAATTTTTTTACCTTATAAACAGTATTTTGAAAAT
1 TTTTAATTTTTTTACCTTATAAACAGTATTTTGAAAAT
39735 TTTTAATTTTTTTACCTTATAAACAGTATTTTGAAAAT
1 TTTTAATTTTTTTACCTTATAAACAGTATTTTGAAAAT
39773 CGGACCGGAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (38 bp):
TTTTAATTTTTTTACCTTATAAACAGTATTTTGAAAAT
Found at i:39954 original size:23 final size:21
Alignment explanation
Indices: 39920--39969 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
39910 GATTCAACCT
*
39920 AATTTTTTTAT-TTTTTATTA
1 AATTTTTTGATATTTTTATTA
*
39940 AATATTTTTGATATTTTTATTT
1 AAT-TTTTTGATATTTTTATTA
39962 AATTTTTT
1 AATTTTTT
39970 AAATAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 3 0.12
21 12 0.46
22 11 0.42
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (21 bp):
AATTTTTTGATATTTTTATTA
Found at i:43998 original size:12 final size:12
Alignment explanation
Indices: 43983--44024 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
43973 TATTATCTGG
43983 TTTATAAATTTA
1 TTTATAAATTTA
*
43995 TTTATAAACTTA
1 TTTATAAATTTA
*
44007 TTTATAAATTCA
1 TTTATAAATTTA
44019 TTTATA
1 TTTATA
44025 TGATTCTCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (12 bp):
TTTATAAATTTA
Found at i:48778 original size:2 final size:2
Alignment explanation
Indices: 48766--48798 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
48756 AACTCTAATC
48766 AT AT AT CAT 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
48799 GACTTAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48993 original size:14 final size:14
Alignment explanation
Indices: 48958--48998 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
48948 CATCCAAATC
*
48958 CTAATATTATTTAA
1 CTAATATTATTTAT
48972 CT-ATATTATTTAT
1 CTAATATTATTTAT
*
48985 TTAATATTATTTAT
1 CTAATATTATTTAT
48999 AAATCAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (14 bp):
CTAATATTATTTAT
Found at i:60353 original size:20 final size:20
Alignment explanation
Indices: 60330--60377 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
60320 GGTTGGTAGC
60330 TGACAAAACCGATTGAAATT
1 TGACAAAACCGATTGAAATT
* **
60350 TGACAAAACTGATTTCAATT
1 TGACAAAACCGATTGAAATT
60370 TGACAAAA
1 TGACAAAA
60378 TCGGTAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (20 bp):
TGACAAAACCGATTGAAATT
Found at i:61692 original size:18 final size:18
Alignment explanation
Indices: 61666--61712 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
61656 GATACAGTTC
* *
61666 TTCTTAACCAAAACCTTT
1 TTCTCAACCAAAACCATT
* *
61684 TTCTCAACCAATATCATT
1 TTCTCAACCAAAACCATT
61702 TTCTCAACCAA
1 TTCTCAACCAA
61713 TGTTCTTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.34, C:0.30, G:0.00, T:0.36
Consensus pattern (18 bp):
TTCTCAACCAAAACCATT
Found at i:61713 original size:18 final size:18
Alignment explanation
Indices: 61682--61726 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
61672 ACCAAAACCT
61682 TTTTCTCAACCAAT-ATC
1 TTTTCTCAACCAATGATC
*
61699 ATTTTCTCAACCAATGTTC
1 -TTTTCTCAACCAATGATC
61718 TTTTCTCAA
1 TTTTCTCAA
61727 TTAAGGTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 23 0.92
19 2 0.08
ACGTcount: A:0.27, C:0.27, G:0.02, T:0.44
Consensus pattern (18 bp):
TTTTCTCAACCAATGATC
Found at i:65411 original size:6 final size:6
Alignment explanation
Indices: 65375--65455 Score: 83
Period size: 6 Copynumber: 13.2 Consensus size: 6
65365 TTGAGTTCCC
* * *
65375 TGTATA AGTATA AGTATA TGTATA TGTATA CGTATA CT-TATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA -TGTATA TGTATA
* *
65423 TGTATATA TATATA TGTATA TGCATA TGTATA T
1 TG--TATA TGTATA TGTATA TGTATA TGTATA T
65456 CTTCTTTATC
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
5 1 0.02
6 57 0.90
8 5 0.08
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.46
Consensus pattern (6 bp):
TGTATA
Found at i:65436 original size:14 final size:14
Alignment explanation
Indices: 65413--65443 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
65403 TACGTATACT
*
65413 TATATGTATATGTA
1 TATATATATATGTA
65427 TATATATATATGTA
1 TATATATATATGTA
65441 TAT
1 TAT
65444 GCATATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (14 bp):
TATATATATATGTA
Found at i:80633 original size:109 final size:108
Alignment explanation
Indices: 80443--80648 Score: 340
Period size: 109 Copynumber: 1.9 Consensus size: 108
80433 CATGACTTCT
* * *
80443 TTCATTGAGATTTACTATTTAAGAGACATTTACTTTGTATGATTTGTTATAGTATACAAGTCTTT
1 TTCATTGAGATTTACTATTTAAGAGACATTTACTTTGCATGATTTGTTATAATATACAAGTCTCT
80508 TGTTTGTAATAATGATTTAATCTAGATATCTCGTATATAGTGA
66 TGTTTGTAATAATGATTTAATCTAGATATCTCGTATATAGTGA
* **
80551 TTCATTGAGATTTACTATTTAAGATATTTTTGACTTTGCATGATTTGTTATAATATACAAGTCTC
1 TTCATTGAGATTTACTATTTAAGAGACATTT-ACTTTGCATGATTTGTTATAATATACAAGTCTC
*
80616 TTGTTTGTAATAGTGATTTAATCTAGATATCTC
65 TTGTTTGTAATAATGATTTAATCTAGATATCTC
80649 ATATTTATTA
Statistics
Matches: 90, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
108 28 0.31
109 62 0.69
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.47
Consensus pattern (108 bp):
TTCATTGAGATTTACTATTTAAGAGACATTTACTTTGCATGATTTGTTATAATATACAAGTCTCT
TGTTTGTAATAATGATTTAATCTAGATATCTCGTATATAGTGA
Found at i:91482 original size:30 final size:29
Alignment explanation
Indices: 91444--91502 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 29
91434 GAAACGCGAG
91444 TATATGACGACTGATCCCATCAACATATC
1 TATATGACGACTGATCCCATCAACATATC
91473 TATACTGACGACTGATCCCATCAACATATC
1 TATA-TGACGACTGATCCCATCAACATATC
91503 GTTTAAGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.34, C:0.29, G:0.10, T:0.27
Consensus pattern (29 bp):
TATATGACGACTGATCCCATCAACATATC
Found at i:92390 original size:10 final size:9
Alignment explanation
Indices: 92358--92394 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
92348 AAGATATAAT
92358 ATTTTTGAA
1 ATTTTTGAA
92367 ATTTTTGAA
1 ATTTTTGAA
92376 A-TTTTGATA
1 ATTTTTGA-A
92385 ATTTTTGAA
1 ATTTTTGAA
92394 A
1 A
92395 GATGTTCTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 6 0.23
9 14 0.54
10 6 0.23
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (9 bp):
ATTTTTGAA
Found at i:93443 original size:67 final size:69
Alignment explanation
Indices: 93362--93512 Score: 243
Period size: 67 Copynumber: 2.2 Consensus size: 69
93352 CCTAAATTTG
* * * *
93362 TTCGGTTCGATTAATAATTTTTAAATAAATTTTGGTTCGATTAATGGTTAAAG-AAAAAA-TTGG
1 TTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACGGTTAAAGAAAAAAAGTAGG
93425 TTAA
66 TTAA
93429 TTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACGGTTAAAGAAAAAAAGTAGG
1 TTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACGGTTAAAGAAAAAAAGTAGG
93494 TTAA
66 TTAA
*
93498 TTCGGCTCGGTTAAT
1 TTCGGTTCGGTTAAT
93513 CGAACCAAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
67 50 0.65
68 6 0.08
69 21 0.27
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.39
Consensus pattern (69 bp):
TTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACGGTTAAAGAAAAAAAGTAGG
TTAA
Found at i:97046 original size:23 final size:21
Alignment explanation
Indices: 97020--97061 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
97010 TATAAAAAAT
97020 TATTTTTCATTAAATATTTTTGA
1 TATTTTT-ATTAAAT-TTTTTGA
*
97043 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
97062 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 6 0.33
23 7 0.39
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGA
Found at i:107716 original size:26 final size:26
Alignment explanation
Indices: 107686--107744 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
107676 TTAACATAAA
* *
107686 CGGTTTTTTCCCGTCCACGTTTAATT
1 CGGTTTTTCCCCGTCCACATTTAATT
107712 CGGTTTTTCCCCGTCCACATTTAATT
1 CGGTTTTTCCCCGTCCACATTTAATT
*
107738 CGATTTT
1 CGGTTTT
107745 CTATTTTCCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.14, C:0.27, G:0.14, T:0.46
Consensus pattern (26 bp):
CGGTTTTTCCCCGTCCACATTTAATT
Found at i:108825 original size:11 final size:11
Alignment explanation
Indices: 108809--108859 Score: 93
Period size: 11 Copynumber: 4.6 Consensus size: 11
108799 AAAATTGGTG
108809 ATTTGAAATTA
1 ATTTGAAATTA
108820 ATTTGAAATTA
1 ATTTGAAATTA
108831 ATTTGAAATTA
1 ATTTGAAATTA
108842 ATTTGAAATTA
1 ATTTGAAATTA
*
108853 AATTGAA
1 ATTTGAA
108860 TAGAGTCACC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
11 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43
Consensus pattern (11 bp):
ATTTGAAATTA
Found at i:111967 original size:133 final size:132
Alignment explanation
Indices: 111728--112152 Score: 562
Period size: 133 Copynumber: 3.2 Consensus size: 132
111718 GTCCAAGGGT
* *
111728 GGATGACACGGCTCATACGTGATGAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTC
1 GGATGACACGACTCATACGTGATGAAGAGTTCTGGCCATCTTTAGG-AGGGTGATAACTCGGTTC
* * ** *
111793 CTACGTGATGAGGACAACTGGTTATCTAAGGGTGATACGGCTCCTACGTGATGAGGAGATCTGGT
65 CTACGTGATGAGGACGACTGGTTATCTAAGGTTGACGCGGCTCCTACGTGATGAGGAGGTCTGGT
111858 CGG
130 CGG
* * * ** *
111861 GGATGACACGATTCCTACGTGATGAGGACATCTGGCCATATTTAGGAGTGGTGATAACTCGGTTC
1 GGATGACACGACTCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAG-GGTGATAACTCGGTTC
* * * * *
111926 CTACGCGATGAGAACGGCTGGTTATCTACGGTTGACGCGGCTCCTACGTGATGAGGAGGTATGGT
65 CTACGTGATGAGGACGACTGGTTATCTAAGGTTGACGCGGCTCCTACGTGATGAGGAGGTCTGGT
*
111991 CAG
130 CGG
* * * *
111994 GGATGACACTACTCATACGCGATGAAGAGTTTTGGCCATCTTTAGGAAAGGTGATAACTCGGTTC
1 GGATGACACGACTCATACGTGATGAAGAGTTCTGGCCATCTTTAGG-AGGGTGATAACTCGGTTC
* *
112059 CTACGTGATGAGGACGACTGGTTATCTAAAGTTGACGTGGCTCCTACGTGATGAGGAGGTCTGGT
65 CTACGTGATGAGGACGACTGGTTATCTAAGGTTGACGCGGCTCCTACGTGATGAGGAGGTCTGGT
112124 CGAG
130 CG-G
** *
112128 GGATGACACGGTTCCTACGTGATGA
1 GGATGACACGACTCATACGTGATGA
112153 GGATGACCAT
Statistics
Matches: 247, Mismatches: 42, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
132 2 0.01
133 223 0.90
134 22 0.09
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (132 bp):
GGATGACACGACTCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAGGGTGATAACTCGGTTCC
TACGTGATGAGGACGACTGGTTATCTAAGGTTGACGCGGCTCCTACGTGATGAGGAGGTCTGGTC
GG
Found at i:112355 original size:65 final size:64
Alignment explanation
Indices: 112205--112396 Score: 226
Period size: 64 Copynumber: 3.0 Consensus size: 64
112195 AAAGATAATT
* * * *
112205 TGTTTCAAAAGAAACTGTCTCAAAAGAGACAAAACTCGTTTCAAGGGAAGCGACTCAAAGATGA
1 TGTTTCAAAGGAAACTGTCTCAAAAGAGACAAAATTCGTTTCAAGGGAAACGTCTCAAAGATGA
* * ** * *
112269 AGTTTTAAAGGAAACTGTCTCAAGCGAGACAAAATTTGTTTTTAAGGGAAAC-TCTCAAAGATCG
1 TGTTTCAAAGGAAACTGTCTCAAAAGAGACAAAATTCG-TTTCAAGGGAAACGTCTCAAAGAT-G
*
112333 G
64 A
* *
112334 TGTTTCATAGGAAACTGTCTCAAATGAGAC-AAATTCGTTTCAAGGGAAACGATCTCAAAGATG
1 TGTTTCAAAGGAAACTGTCTCAAAAGAGACAAAATTCGTTTCAAGGGAAACG-TCTCAAAGATG
112397 TTTGTTTGTT
Statistics
Matches: 106, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
63 12 0.11
64 47 0.44
65 47 0.44
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.25
Consensus pattern (64 bp):
TGTTTCAAAGGAAACTGTCTCAAAAGAGACAAAATTCGTTTCAAGGGAAACGTCTCAAAGATGA
Found at i:112403 original size:65 final size:66
Alignment explanation
Indices: 112192--112403 Score: 220
Period size: 65 Copynumber: 3.3 Consensus size: 66
112182 AAAAGACCGA
* * * *
112192 CTCAAAGATAATTTGTTTCAAAAGAAACTGTCTCAAAAGAGACAAAACTCGTTTCAAGGGAAGCG
1 CTCAAAGAT-AGTTGTTTCAAAGGAAACTGTCTCAAAAGAGACAAAATTCGTTTCAAGGGAAACG
112257 A-
65 AT
** * ** * *
112258 CTCAAAGAT-GAAGTTTTAAAGGAAACTGTCTCAAGCGAGACAAAATTTGTTTTTAAGGGAAAC-
1 CTCAAAGATAGTTGTTTCAAAGGAAACTGTCTCAAAAGAGACAAAATTCG-TTTCAAGGGAAACG
112321 -T
65 AT
* * * *
112322 CTCAAAGATCGGTGTTTCATAGGAAACTGTCTCAAATGAGAC-AAATTCGTTTCAAGGGAAACGA
1 CTCAAAGATAGTTGTTTCAAAGGAAACTGTCTCAAAAGAGACAAAATTCGTTTCAAGGGAAACGA
112386 T
66 T
112387 CTCAAAGAT-GTTTGTTT
1 CTCAAAGATAG-TTGTTT
112404 GTTTCAAAAC
Statistics
Matches: 120, Mismatches: 20, Indels: 13
0.78 0.13 0.08
Matches are distributed among these distances:
63 12 0.10
64 47 0.39
65 52 0.43
66 9 0.08
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (66 bp):
CTCAAAGATAGTTGTTTCAAAGGAAACTGTCTCAAAAGAGACAAAATTCGTTTCAAGGGAAACGA
T
Found at i:112647 original size:65 final size:66
Alignment explanation
Indices: 112543--112689 Score: 246
Period size: 65 Copynumber: 2.3 Consensus size: 66
112533 CGTTTTAAGT
*
112543 GAGACAAAATTTG-TTTCAAATGAAACAATCTCAAAGGTTGGTTTTTCATTA-AAATTGTCTCAA
1 GAGACAAAATTTGTTTTCAAATGAAACAATCTCAAAGGTTGATTTTTCATTAGAAA-TGTCTCAA
*
112606 GC
65 GA
112608 GAGACAAAATTTGTTTTCAAA-GAAACAATCTCAAAGGTTGATTTTTCATTAGAAATGTCTCAAG
1 GAGACAAAATTTGTTTTCAAATGAAACAATCTCAAAGGTTGATTTTTCATTAGAAATGTCTCAAG
112672 A
66 A
112673 GAGACAAAATTTGTTTT
1 GAGACAAAATTTGTTTT
112690 TAAGGGAATA
Statistics
Matches: 78, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
65 68 0.87
66 10 0.13
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (66 bp):
GAGACAAAATTTGTTTTCAAATGAAACAATCTCAAAGGTTGATTTTTCATTAGAAATGTCTCAAG
A
Found at i:113034 original size:91 final size:93
Alignment explanation
Indices: 112926--113117 Score: 345
Period size: 91 Copynumber: 2.1 Consensus size: 93
112916 TTGTCTCCGC
*
112926 GAGACGAATCAGCTTTGAAAATCTCAAGTGATATTAATTTTGTTT-AAGTACAAC-ACTTTGAAA
1 GAGACGAATCAGCTTTGAAAATCTCAA-TGATATTAATTTTGTTTCAAGTAAAACAACTTTGAAA
112989 TTTGTA-TATGAGGGAAAATGTCTCAAGT
65 TTTGTATTATGAGGGAAAATGTCTCAAGT
113017 GAGACGAATCAGCTTTGAAAATCTCAATGATATTAATTTTGTTTCAAGTAAAACAACTTTGAAAT
1 GAGACGAATCAGCTTTGAAAATCTCAATGATATTAATTTTGTTTCAAGTAAAACAACTTTGAAAT
113082 TTGTATTATGAGGGAAAATGTCTCAAGT
66 TTGTATTATGAGGGAAAATGTCTCAAGT
113110 GAGACGAA
1 GAGACGAA
113118 ATTTGTTTTG
Statistics
Matches: 97, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
90 17 0.18
91 35 0.36
92 15 0.15
93 30 0.31
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.33
Consensus pattern (93 bp):
GAGACGAATCAGCTTTGAAAATCTCAATGATATTAATTTTGTTTCAAGTAAAACAACTTTGAAAT
TTGTATTATGAGGGAAAATGTCTCAAGT
Found at i:113317 original size:34 final size:35
Alignment explanation
Indices: 113201--113393 Score: 130
Period size: 34 Copynumber: 5.5 Consensus size: 35
113191 CTCAAAGGAA
* ** *
113201 AAAAATGTCTCAAGCGAGATGAAGTTTGTTTT-AAG
1 AAAACTGTCTCAAGCGAGACAAAATTT-TTTTCAAG
* * *
113236 ATAAATTGTCTTAAGTGAGACAAAATTTGTTTTTCAAG
1 A-AAACTGTCTCAAGCGAGACAAAA-TT-TTTTTCAAG
113274 --AACTGTCTCAAGCGAGACAAAA-TTTTTTCAAG
1 AAAACTGTCTCAAGCGAGACAAAATTTTTTTCAAG
* * * *
113306 AAAACTGTCTCAAGCGAGATAAAAGTGTTTT-GAG
1 AAAACTGTCTCAAGCGAGACAAAATTTTTTTCAAG
** * **
113340 AAATTTGTCTC-AGCGAGACAAAGTTTATTTTTGAG
1 AAAACTGTCTCAAGCGAGACAAAATTT-TTTTCAAG
*
113375 AAAAC-GATCTCAAGTGAGA
1 AAAACTG-TCTCAAGCGAGA
113394 TCAACTTTGT
Statistics
Matches: 126, Mismatches: 21, Indels: 21
0.75 0.12 0.12
Matches are distributed among these distances:
32 9 0.07
33 12 0.10
34 37 0.29
35 35 0.28
36 23 0.18
37 6 0.05
38 4 0.03
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (35 bp):
AAAACTGTCTCAAGCGAGACAAAATTTTTTTCAAG
Done.