Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007376.1 Hibiscus syriacus cultivar Beakdansim tig00019804_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: 80113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:125 original size:15 final size:15
Alignment explanation
Indices: 105--138 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
95 CGAAGTATCA
105 GAAGTCGGCAAGAGG
1 GAAGTCGGCAAGAGG
120 GAAGTCGGCAAGAGG
1 GAAGTCGGCAAGAGG
135 GAAG
1 GAAG
139 AATTGATTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.35, C:0.12, G:0.47, T:0.06
Consensus pattern (15 bp):
GAAGTCGGCAAGAGG
Found at i:1998 original size:119 final size:116
Alignment explanation
Indices: 1789--2025 Score: 447
Period size: 119 Copynumber: 2.0 Consensus size: 116
1779 CCAAAATTCA
1789 TCAATGGCTTATATGCACAATTTTCAACCACCACAGTTTTTACATATCAACATTAGGTGAAACCG
1 TCAATGGCTTATATGCACAATTTTCAACCACCACAGTTTTTACATATCAACATTAGGTGAAACCG
1854 CCTAATCAACAATAAAATACCTTTTTTCGATGACGATCCTGGTAGCTTATAT
66 CCTAATCAACAATAAAATACCTTTTTTCGATGACGATCCTGGTAGC-TATAT
1906 TCAATGGCTTATATGCACAATTTTCAACCACCACAGTTTTTACATACATCAACATTAGGTGAAAC
1 TCAATGGCTTATATGCACAATTTTCAACCACCACAGTTTTTACAT--ATCAACATTAGGTGAAAC
1971 CGCCTAATCAACAATAAAATACCTTTTTTCGATGACGATCCTGGTAGCTATAT
64 CGCCTAATCAACAATAAAATACCTTTTTTCGATGACGATCCTGGTAGCTATAT
2024 TC
1 TC
2026 TAAAGGAACC
Statistics
Matches: 118, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
117 45 0.38
118 7 0.06
119 66 0.56
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.32
Consensus pattern (116 bp):
TCAATGGCTTATATGCACAATTTTCAACCACCACAGTTTTTACATATCAACATTAGGTGAAACCG
CCTAATCAACAATAAAATACCTTTTTTCGATGACGATCCTGGTAGCTATAT
Found at i:5548 original size:22 final size:21
Alignment explanation
Indices: 5505--5548 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
5495 TCTCTGTTTT
* *
5505 CTCCATGTTTCTCTGTCTCTC
1 CTCCATATTTCTCTGTCACTC
*
5526 CTCCATATTGTCTCTTTCACTC
1 CTCCATATT-TCTCTGTCACTC
5548 C
1 C
5549 AGGACCACAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.09, C:0.39, G:0.07, T:0.45
Consensus pattern (21 bp):
CTCCATATTTCTCTGTCACTC
Found at i:10409 original size:60 final size:59
Alignment explanation
Indices: 10299--10410 Score: 143
Period size: 60 Copynumber: 1.9 Consensus size: 59
10289 ATGGTCTCCC
* * *
10299 AACTATAGGTATTGTTTTATTAAGTCCCTAAACTACTAAAGGTTAGAAAATGGTCCTTT
1 AACTATAGGTATTATTTTATTAAGTCCCTAAACTACTAAAAGTTACAAAATGGTCCTTT
* * * * *
10358 AACTATAGAGTGTTATTTTGTTGAGTCCCTCAACTATTAAAAGTTACAAAATG
1 AACTATAG-GTATTATTTTATTAAGTCCCTAAACTACTAAAAGTTACAAAATG
10411 ATCATCCGCC
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
59 8 0.18
60 36 0.82
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (59 bp):
AACTATAGGTATTATTTTATTAAGTCCCTAAACTACTAAAAGTTACAAAATGGTCCTTT
Found at i:15754 original size:21 final size:20
Alignment explanation
Indices: 15728--15800 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 20
15718 AAAACAAGGA
* * *
15728 AGGGATCGATCCTTTATTTAG
1 AGGGATCGATCATTT-TCTCG
*
15749 AGGGATCAATCATTTTCTCG
1 AGGGATCGATCATTTTCTCG
*
15769 AGGGATTGATCATTTCTCTCG
1 AGGGATCGATCATTT-TCTCG
15790 AGGGATCGATC
1 AGGGATCGATC
15801 CATTGCACAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 16 0.36
21 28 0.64
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (20 bp):
AGGGATCGATCATTTTCTCG
Found at i:15773 original size:20 final size:21
Alignment explanation
Indices: 15748--15796 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
15738 CCTTTATTTA
15748 GAGGGATCAATCATTT-TCTC
1 GAGGGATCAATCATTTCTCTC
**
15768 GAGGGATTGATCATTTCTCTC
1 GAGGGATCAATCATTTCTCTC
15789 GAGGGATC
1 GAGGGATC
15797 GATCCATTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (21 bp):
GAGGGATCAATCATTTCTCTC
Found at i:15867 original size:21 final size:21
Alignment explanation
Indices: 15843--15901 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
15833 TTCGGTCGAG
15843 GGATCGATCCTTTTTGGTAAA
1 GGATCGATCCTTTTTGGTAAA
**** *
15864 GGATCGATCCTTTCCCCTAAG
1 GGATCGATCCTTTTTGGTAAA
15885 GGATCGATCCTTTTTGG
1 GGATCGATCCTTTTTGG
15902 AAAAAATCAC
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.19, C:0.22, G:0.24, T:0.36
Consensus pattern (21 bp):
GGATCGATCCTTTTTGGTAAA
Found at i:17340 original size:16 final size:17
Alignment explanation
Indices: 17307--17340 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
17297 CTTTCTATTT
*
17307 TTATTTTATATTTTAAA
1 TTATTTTATATATTAAA
17324 TTATTTT-TATATTAAA
1 TTATTTTATATATTAAA
17340 T
1 T
17341 AATACATCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTTATATATTAAA
Found at i:19633 original size:85 final size:85
Alignment explanation
Indices: 19481--19766 Score: 332
Period size: 84 Copynumber: 3.4 Consensus size: 85
19471 AGGGCCCTCT
* *
19481 ATTATAAAGATAGAAAGTGAGTTTGAAAAAACTTAG-GGCCTCAATTATAAAGGTAAAAAGTGAG
1 ATTATAAAGGTAGAAAGTGAGATTGAAAAAACTTAGAGGCCTCAATTATAAAGGTAAAAAGTGAG
*
19545 ATT-AAAAATTAACGGCTTCA
66 ATTAAAAAATTAA-GGCATCA
* * * *
19565 ATTATAAAGGTAGAAAGTGAGATTGAAAAAACTTAGAGGCCTCAATCATAATGGTAAAAAATGTG
1 ATTATAAAGGTAGAAAGTGAGATTGAAAAAACTTAGAGGCCTCAATTATAAAGGTAAAAAGTGAG
*
19630 ATTAAAAAAATTAGAGGCCTCA
66 ATT-AAAAAATTA-AGGCATCA
* * * * *
19652 ATTATAAAGGTAAAAAGTGTGATT-AAAAAA-TTAGAGGCATCAATTACAAAGATAAAAAGTGAG
1 ATTATAAAGGTAGAAAGTGAGATTGAAAAAACTTAGAGGCCTCAATTATAAAGGTAAAAAGTGAG
* *
19715 ATTGAAAAATTAAGGGCATCG
66 ATTAAAAAATTAA-GGCATCA
*
19736 ATTAGAAAGGTA-AAAGAT-AGAATTGAAAAAA
1 ATTATAAAGGTAGAAAG-TGAG-ATTGAAAAAA
19767 AAATAAAGAC
Statistics
Matches: 173, Mismatches: 21, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
83 6 0.03
84 62 0.36
85 62 0.36
86 6 0.03
87 36 0.21
88 1 0.01
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.24
Consensus pattern (85 bp):
ATTATAAAGGTAGAAAGTGAGATTGAAAAAACTTAGAGGCCTCAATTATAAAGGTAAAAAGTGAG
ATTAAAAAATTAAGGCATCA
Found at i:19696 original size:42 final size:43
Alignment explanation
Indices: 19463--19766 Score: 304
Period size: 43 Copynumber: 7.1 Consensus size: 43
19453 TTATGAAATT
* * * * *
19463 AAAAAACTAG-GGCCCTCTATTATAAAGATAGAAAGTGAGTTTG
1 AAAAAATTAGAGG-CCTCAATTATAAAGGTAAAAAGTGAGATTG
19506 AAAAAACTTAG-GGCCTCAATTATAAAGGTAAAAAGTGAGATT-
1 AAAAAA-TTAGAGGCCTCAATTATAAAGGTAAAAAGTGAGATTG
* *
19548 -AAAAATTA-ACGGCTTCAATTATAAAGGTAGAAAGTGAGATTG
1 AAAAAATTAGA-GGCCTCAATTATAAAGGTAAAAAGTGAGATTG
* * * * *
19590 AAAAAACTTAGAGGCCTCAATCATAATGGTAAAAAATGTGATTA
1 AAAAAA-TTAGAGGCCTCAATTATAAAGGTAAAAAGTGAGATTG
*
19634 AAAAAATTAGAGGCCTCAATTATAAAGGTAAAAAGTGTGATT-
1 AAAAAATTAGAGGCCTCAATTATAAAGGTAAAAAGTGAGATTG
* * *
19676 AAAAAATTAGAGGCATCAATTACAAAGATAAAAAGTGAGATTG
1 AAAAAATTAGAGGCCTCAATTATAAAGGTAAAAAGTGAGATTG
* * *
19719 -AAAAATTA-AGGGCATCGATTAGAAAGGT-AAAAGAT-AGAATTG
1 AAAAAATTAGA-GGCCTCAATTATAAAGGTAAAAAG-TGAG-ATTG
19761 AAAAAA
1 AAAAAA
19767 AAATAAAGAC
Statistics
Matches: 225, Mismatches: 24, Indels: 24
0.82 0.09 0.09
Matches are distributed among these distances:
40 3 0.01
41 42 0.19
42 66 0.29
43 74 0.33
44 39 0.17
45 1 0.00
ACGTcount: A:0.49, C:0.08, G:0.19, T:0.24
Consensus pattern (43 bp):
AAAAAATTAGAGGCCTCAATTATAAAGGTAAAAAGTGAGATTG
Found at i:19787 original size:129 final size:128
Alignment explanation
Indices: 19519--19795 Score: 303
Period size: 129 Copynumber: 2.2 Consensus size: 128
19509 AAACTTAGGG
* * * *
19519 CCTCAATTATAAAGGTAAAAAGTGAGATTAAAAATTAACGGCTTCAATTATAAAGGTAGAAAGTG
1 CCTCAATTATAAAGGTAAAAAGTGAGATTAAAAATTAACGGCATCAATTACAAAGATAAAAAGTG
* * * * * * *
19584 AGATTGAAAAAACTTAGAGGCCTCAATCATAATGGTAAAAAATGTGATTAAAAAAATTAGAGG
66 AGATTGAAAAAACTTAGAGGCATCAATCAGAAAGGTAAAAAATGTAATTAAAAAAAATAAAGA
*
19647 CCTCAATTATAAAGGTAAAAAGTGTGATTAAAAAATTAGA-GGCATCAATTACAAAGATAAAAAG
1 CCTCAATTATAAAGGTAAAAAGTGAGATT-AAAAATTA-ACGGCATCAATTACAAAGATAAAAAG
* * *
19711 TGAGATTG-AAAAA-TTA-AGGGCATCGATTAGAAAGGTAAAAGATAG-AATTGAAAAAAAAATA
64 TGAGATTGAAAAAACTTAGA-GGCATCAATCAGAAAGGTAAAAAAT-GTAATT--AAAAAAAATA
19772 AAGA
125 AAGA
* * *
19776 CTTTAATTATAAAGATAAAA
1 CCTCAATTATAAAGGTAAAA
19796 GACAAGATTA
Statistics
Matches: 125, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
126 1 0.01
127 25 0.20
128 34 0.27
129 64 0.51
130 1 0.01
ACGTcount: A:0.51, C:0.07, G:0.18, T:0.24
Consensus pattern (128 bp):
CCTCAATTATAAAGGTAAAAAGTGAGATTAAAAATTAACGGCATCAATTACAAAGATAAAAAGTG
AGATTGAAAAAACTTAGAGGCATCAATCAGAAAGGTAAAAAATGTAATTAAAAAAAATAAAGA
Found at i:25603 original size:36 final size:35
Alignment explanation
Indices: 25554--25626 Score: 101
Period size: 36 Copynumber: 2.1 Consensus size: 35
25544 TACGTTTATG
* *
25554 TTCATTTCTTTATTTTAGAATATGTTCATGTTTGA
1 TTCATTTCGTTATTTTAGAATATGTTCATGTTCGA
* *
25589 TTCATGTTCGTTATTTTTGAATATGTTCGTGTTCGA
1 TTCAT-TTCGTTATTTTAGAATATGTTCATGTTCGA
25625 TT
1 TT
25627 TGTTTAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
35 5 0.15
36 28 0.85
ACGTcount: A:0.19, C:0.10, G:0.15, T:0.56
Consensus pattern (35 bp):
TTCATTTCGTTATTTTAGAATATGTTCATGTTCGA
Found at i:25616 original size:19 final size:19
Alignment explanation
Indices: 25563--25618 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
25553 GTTCATTTCT
*
25563 TTATTTTAGAATATGTTC-
1 TTATTTTTGAATATGTTCG
* *
25581 --ATGTTTGATTCATGTTCG
1 TTATTTTTGAAT-ATGTTCG
25599 TTATTTTTGAATATGTTCG
1 TTATTTTTGAATATGTTCG
25618 T
1 T
25619 GTTCGATTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
16 7 0.24
17 6 0.21
19 8 0.28
20 8 0.28
ACGTcount: A:0.21, C:0.07, G:0.16, T:0.55
Consensus pattern (19 bp):
TTATTTTTGAATATGTTCG
Found at i:27469 original size:2 final size:2
Alignment explanation
Indices: 27464--27520 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
27454 AATGTAAAAT
* *
27464 TA TA TA TA TA TA CA TA CA 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
27506 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
27521 TATTTTATGA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:33428 original size:57 final size:56
Alignment explanation
Indices: 33367--33503 Score: 143
Period size: 59 Copynumber: 2.4 Consensus size: 56
33357 TTGAAATATG
* *
33367 AATATATAAAATATATTAAAATAATACGAATATATATTTTAAAATATATTCACTTAA
1 AATATATAAATTATA-TAAAATAATACGAATATATATTTTAAAATATATTAACTTAA
** * * *
33424 AATAT-TTTATTATTATACGAATAAAATATGAATATATTTTTTAAAATATATTAACTTAA
1 AATATATAAATTA-TATA--AA-ATAATACGAATATATATTTTAAAATATATTAACTTAA
*
33483 AA-ATACAAATTATATAAAATA
1 AATATATAAATTATATAAAATA
33504 TATTTTTAAT
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
55 2 0.03
56 8 0.12
57 7 0.11
58 8 0.12
59 39 0.61
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (56 bp):
AATATATAAATTATATAAAATAATACGAATATATATTTTAAAATATATTAACTTAA
Found at i:33520 original size:74 final size:72
Alignment explanation
Indices: 33420--33668 Score: 252
Period size: 74 Copynumber: 3.4 Consensus size: 72
33410 ATATATTCAC
* *
33420 TTAAAATATTTTATTATTATACGAATAAAATATGAATATATTTTTTAAAATATATTAACTTAAAA
1 TTAAAATATTTT-TTA--ATACGAATATAATACGAATATATTTTTTAAAATATATTAACTTAAAA
33485 ATACAAATTA
63 ATACAAATTA
* * *
33495 TATAAAATATATTTTTAATACGAATATAATACAAATATATATTTCAAAATATATTAACTT-AAAA
1 T-TAAAATAT-TTTTTAATACGAATATAATACGAATATATTTTTTAAAATATATTAACTTAAAAA
**
33559 T--ATTTTA
64 TACAAATTA
** ** * * * *
33566 TTATTATATGAATATAATATGAGTATAATACGAATATATATATTTTTATAATATATTAACTTAAA
1 TTAAAATAT-TTTTTAATACGAATATAATACG-A-ATATAT-TTTTTAAAATATATTAACTTAAA
33631 AATACAAATTA
62 AATACAAATTA
33642 TGTAAAATATTTTTTAATACGAATATA
1 T-TAAAATATTTTTTAATACGAATATA
33669 TATTTTTTAA
Statistics
Matches: 137, Mismatches: 28, Indels: 17
0.75 0.15 0.09
Matches are distributed among these distances:
70 22 0.16
71 6 0.04
72 6 0.04
73 22 0.16
74 43 0.31
75 1 0.01
76 28 0.20
77 9 0.07
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (72 bp):
TTAAAATATTTTTTAATACGAATATAATACGAATATATTTTTTAAAATATATTAACTTAAAAATA
CAAATTA
Found at i:33524 original size:133 final size:140
Alignment explanation
Indices: 33455--33709 Score: 353
Period size: 147 Copynumber: 1.8 Consensus size: 140
33445 TAAAATATGA
33455 ATATAT-TTTTTAAAATATATTAACTTAAAAATACAAATTATATAAAATATATTTTTAATACGAA
1 ATATATATTTTTAAAATATATTAACTTAAAAATACAAATTATATAAAATAT-TTTTTAATACG-A
* *
33519 TATAATACAAATATATATTTCAAAATATATTAACTTAAAATATTTTATTATTATATGAATATAAT
64 -ATAATAC-AATATATATTTTAAAATATATTAACTTAAAATATTTTATTATTATACGAATATAAT
33584 ATGAGTATAATACGAAT
127 A-GAG-ATAATA-GAAT
* *
33601 ATATATATTTTTATAATATATTAACTTAAAAATACAAATTATGTAAAATATTTTTTAATACGAAT
1 ATATATATTTTTAAAATATATTAACTTAAAAATACAAATTATATAAAATATTTTTTAATACGAAT
*
33666 -AT---ATAT-T-TTTTAAGATATATTAACTTAAAATATTTTATTATTAT
66 AATACAATATATATTTTAAAATATATTAACTTAAAATATTTTATTATTAT
33710 TTTAATATAT
Statistics
Matches: 104, Mismatches: 4, Indels: 11
0.87 0.03 0.09
Matches are distributed among these distances:
137 35 0.34
138 1 0.01
139 4 0.04
143 2 0.02
144 2 0.02
145 1 0.01
146 17 0.16
147 42 0.40
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (140 bp):
ATATATATTTTTAAAATATATTAACTTAAAAATACAAATTATATAAAATATTTTTTAATACGAAT
AATACAATATATATTTTAAAATATATTAACTTAAAATATTTTATTATTATACGAATATAATAGAG
ATAATAGAAT
Found at i:33708 original size:21 final size:22
Alignment explanation
Indices: 33683--33729 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
33673 TTTTAAGATA
33683 TATTAACTTAAAATATTTTAT-
1 TATTAACTTAAAATATTTTATG
** *
33704 TATTATTTTAATATATTTTATG
1 TATTAACTTAAAATATTTTATG
33726 TATT
1 TATT
33730 CATATATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
TATTAACTTAAAATATTTTATG
Found at i:45166 original size:21 final size:21
Alignment explanation
Indices: 45142--45185 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
45132 TGGTATAAAA
*
45142 TTATCTAAAATATTATTATTT
1 TTATCTAAAATATTAATATTT
*
45163 TTATTTAAAATATTAATATTT
1 TTATCTAAAATATTAATATTT
45184 TT
1 TT
45186 TAATATTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATCTAAAATATTAATATTT
Found at i:48889 original size:104 final size:104
Alignment explanation
Indices: 48707--48940 Score: 326
Period size: 104 Copynumber: 2.2 Consensus size: 104
48697 AAAGTCGTCG
* * *
48707 GGATGTCTTGGCGACCTATGGAAGTTTCAACTAAAAGTCTAATTACTGATATAGATAATCACTGT
1 GGATGACTTGGCGACCTATGGAGGTTTCAACTAAAAGCCTAATTACTGATATAGATAATCACTGT
* *
48772 TACTTATGGGAAATAAAGGAAACCAATGCTTGAACGTTC
66 TACTTATGAGAAATAAAGAAAACCAATGCTTGAACGTTC
* * * *
48811 GGATGACTTGGTGACCTATGGAGGTTTCGACTAAAAGCCTAATTACCT-ATTTAGGTAATCACTG
1 GGATGACTTGGCGACCTATGGAGGTTTCAACTAAAAGCCTAATTA-CTGATATAGATAATCACTG
* *
48875 TTACTTATGAGAAATATAGAAAACCAATGCTTGAACGTTT
65 TTACTTATGAGAAATAAAGAAAACCAATGCTTGAACGTTC
* * *
48915 GGAGGACTTGACGACCTATGAAGGTT
1 GGATGACTTGGCGACCTATGGAGGTT
48941 GCCTAGAGGA
Statistics
Matches: 114, Mismatches: 15, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
104 112 0.98
105 2 0.02
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (104 bp):
GGATGACTTGGCGACCTATGGAGGTTTCAACTAAAAGCCTAATTACTGATATAGATAATCACTGT
TACTTATGAGAAATAAAGAAAACCAATGCTTGAACGTTC
Found at i:49590 original size:24 final size:24
Alignment explanation
Indices: 49552--49597 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
49542 AATTATTTTT
*
49552 TTATTTTTTTAAAAATA-AAAATA
1 TTATTTTTTAAAAAATATAAAATA
49575 TTATTTTTTAATAAAATATAAAA
1 TTATTTTTTAA-AAAATATAAAA
49598 AAACTTAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 6 0.30
25 4 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TTATTTTTTAAAAAATATAAAATA
Found at i:52453 original size:2 final size:2
Alignment explanation
Indices: 52448--52482 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
52438 AAAATGCCAT
52448 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52483 CAGGGTTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:53651 original size:14 final size:14
Alignment explanation
Indices: 53631--53676 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
53621 ACAAAGGACT
53631 TGTTCGTTCATTTA
1 TGTTCGTTCATTTA
* *
53645 CGTTCGTT--TATA
1 TGTTCGTTCATTTA
53657 TGTTCGTTCATTTA
1 TGTTCGTTCATTTA
53671 TGTTCG
1 TGTTCG
53677 AACAGAGGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 10 0.38
14 16 0.62
ACGTcount: A:0.13, C:0.15, G:0.17, T:0.54
Consensus pattern (14 bp):
TGTTCGTTCATTTA
Found at i:53962 original size:14 final size:13
Alignment explanation
Indices: 53934--53969 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
53924 TGTTTTTTGT
53934 GTTTGTGTTGTTC
1 GTTTGTGTTGTTC
*
53947 GTTTATGTTCGTTC
1 GTTTGTGTT-GTTC
53961 GTTTGTGTT
1 GTTTGTGTT
53970 TGTTTACGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.03, C:0.08, G:0.28, T:0.61
Consensus pattern (13 bp):
GTTTGTGTTGTTC
Found at i:54536 original size:2 final size:2
Alignment explanation
Indices: 54529--54553 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54519 TATCTGATTC
54529 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
54554 ATTTAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:64405 original size:25 final size:23
Alignment explanation
Indices: 64331--64413 Score: 87
Period size: 23 Copynumber: 3.5 Consensus size: 23
64321 ATAAACAAAA
* *
64331 ATAATGGTAAAAGAAAATGTGTT
1 ATAAAGGTAAAAGAAAATGTGTC
* *
64354 ATAAA-GTCAAAGAAAAACGTGTC
1 ATAAAGGTAAAAG-AAAATGTGTC
64377 ATAAAGGTAAAAGAAGAAGTGTGTC
1 ATAAAGGTAAAAGAA-AA-TGTGTC
*
64402 ATAAAGATAAAA
1 ATAAAGGTAAAA
64414 TTATTAAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
22 6 0.12
23 19 0.39
24 8 0.16
25 16 0.33
ACGTcount: A:0.53, C:0.05, G:0.20, T:0.22
Consensus pattern (23 bp):
ATAAAGGTAAAAGAAAATGTGTC
Found at i:64872 original size:507 final size:501
Alignment explanation
Indices: 64029--65039 Score: 1808
Period size: 507 Copynumber: 2.0 Consensus size: 501
64019 TAAGATCATA
64029 TAAGGAAAAAGTAAAAATAAAATAAAAAAATAACCAAATAAACAAGGATAAAAAAGGTAGATACA
1 TAAGGAAAAAGTAAAAATAAAATAAAAAAATAACCAAATAAACAAGGATAAAAAAGGTAGATACA
64094 AATAAATGTGATCACATCGAAAAACAAACCACAAAAAGGGATGAAGCTATTGAAAAACACCAGCA
66 AATAAATGTGATCACATCGAAAAACAAACCACAAAAAGGGATGAAGCTATTGAAAAACACCAGCA
*
64159 AATCGTAAATCAGAATTGAGCGATATGAAAATACTAGCCGCGAACGCAAATCGCATATTCAAATC
131 AATCGTAAATCAGAATTGAGCGACATGAAAATACTAGCCGCGAACGCAAATCGCATATTCAAATC
64224 CAATATGATGATCCAAAGTATGGAAGATTAACATGATAACAAACAAAACATTATCTTTATTAGGC
196 CAATATGATGATCCAAAGTATGGAAGATTAACATGATAACAAACAAAACATTATCTTTATTAGGC
* ** *
64289 GTGACGATGTCAAATTCAATCCAGAAAAAATGATAAACAAAAATAATGGTAAAAGAAAATGTGTT
261 GTGACGATGTCAAATTCAACCCAGAAAAAATGATAAACAAAAATAACAGTAAAAGAAAATATGTT
*
64354 ATAAAGTCAAAGAAAAACGTGTCATAAAGGTAAAAGAAGAAGTGTGTCATAAAGATAAAATTATT
326 ATAAAGTCAAAGAAAAACGTGTCATAAAGGTAAAAGAAGAAGTGTGTCATAAAGATAAAATTATA
*
64419 AAAAATAAAAAATAAAAAATGATAGAATAAAACAAATGAAAAA-AATGAATATTGGCGATCGGTG
391 AAAAATAAAAAAT----AAT-AT--AATAAAACAAATGAAAAACAATGAATATTAGCGATCGGTG
* *
64483 ATCAATACCAAAATTAGAGTTACCGCCGATCACAAATATGAAAGAAAATAACC
449 ATCAATACCAAAATTAGAGTTACCGCCGATCACAAAGATAAAAGAAAATAACC
64536 TAAGGAAAAAGTAAAAATAAAATAAAAAAATAACCAAATAAACAAGGATAAAAAAGGTAGATACA
1 TAAGGAAAAAGTAAAAATAAAATAAAAAAATAACCAAATAAACAAGGATAAAAAAGGTAGATACA
*
64601 AATAAATGTGATCACATCGAAAAACAAACCACAAAAAGGGATGAAGCTATTGAAAGACACCAGCA
66 AATAAATGTGATCACATCGAAAAACAAACCACAAAAAGGGATGAAGCTATTGAAAAACACCAGCA
*
64666 AATCGTAAATCAGAATTGAGCGACATGAAAATACTAGCCGCGAATGCAAATCGCATATTCAAATC
131 AATCGTAAATCAGAATTGAGCGACATGAAAATACTAGCCGCGAACGCAAATCGCATATTCAAATC
*
64731 CAATATGATGATCCAAAGTATGGAAGATTAACATGATAACAAATAAAACATTATCTTTATTAGGC
196 CAATATGATGATCCAAAGTATGGAAGATTAACATGATAACAAACAAAACATTATCTTTATTAGGC
64796 GTGACGATGTCAAATTCAACCCAGAAAAAATGATAAACAAAAATAACAGTAAAAGAAAATATGTT
261 GTGACGATGTCAAATTCAACCCAGAAAAAATGATAAACAAAAATAACAGTAAAAGAAAATATGTT
* *
64861 ATAAAGTCAAAGAAAAACGTGTCATAAAGGTAGAAGAAGACGTGTGTCATAAAGATAAAATTATA
326 ATAAAGTCAAAGAAAAACGTGTCATAAAGGTAAAAGAAGAAGTGTGTCATAAAGATAAAATTATA
*
64926 AAAAATTAAAAATAATATAATAAAACAAATGAAAAACAATGAATATTAGCGATCGGTGATCAATA
391 AAAAATAAAAAATAATATAATAAAACAAATGAAAAACAATGAATATTAGCGATCGGTGATCAATA
*
64991 CCAAAATTAGAGTTACCGTCGATCACAAAGATAAAAGAAAATAACC
456 CCAAAATTAGAGTTACCGCCGATCACAAAGATAAAAGAAAATAACC
65037 TAA
1 TAA
65040 CGACATCTAA
Statistics
Matches: 487, Mismatches: 16, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
500 18 0.04
501 73 0.15
502 2 0.00
503 3 0.01
507 391 0.80
ACGTcount: A:0.52, C:0.12, G:0.15, T:0.20
Consensus pattern (501 bp):
TAAGGAAAAAGTAAAAATAAAATAAAAAAATAACCAAATAAACAAGGATAAAAAAGGTAGATACA
AATAAATGTGATCACATCGAAAAACAAACCACAAAAAGGGATGAAGCTATTGAAAAACACCAGCA
AATCGTAAATCAGAATTGAGCGACATGAAAATACTAGCCGCGAACGCAAATCGCATATTCAAATC
CAATATGATGATCCAAAGTATGGAAGATTAACATGATAACAAACAAAACATTATCTTTATTAGGC
GTGACGATGTCAAATTCAACCCAGAAAAAATGATAAACAAAAATAACAGTAAAAGAAAATATGTT
ATAAAGTCAAAGAAAAACGTGTCATAAAGGTAAAAGAAGAAGTGTGTCATAAAGATAAAATTATA
AAAAATAAAAAATAATATAATAAAACAAATGAAAAACAATGAATATTAGCGATCGGTGATCAATA
CCAAAATTAGAGTTACCGCCGATCACAAAGATAAAAGAAAATAACC
Found at i:69861 original size:59 final size:59
Alignment explanation
Indices: 69727--69866 Score: 163
Period size: 59 Copynumber: 2.4 Consensus size: 59
69717 AGGACCAACA
* * * * **
69727 TAGAATGAGGTTCATAATTTTGGGATGAAATTGGAATTTTTAAAAGGTCAGAGAACAAAT
1 TAGAATGAGGATCAT-AGTTTGGGATGAAATTGAAATGTCCAAAAGGTCAGAGAACAAAT
** * * *
69787 TAGAATGAAAATCATAGTTTGGGATGAAATTGAAATGTCCAAAAGTTTAGAGATCAAAT
1 TAGAATGAGGATCATAGTTTGGGATGAAATTGAAATGTCCAAAAGGTCAGAGAACAAAT
*
69846 TAGAATGAGGGTCATAGTTTG
1 TAGAATGAGGATCATAGTTTG
69867 AGGAGTATAG
Statistics
Matches: 66, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
59 54 0.82
60 12 0.18
ACGTcount: A:0.40, C:0.06, G:0.24, T:0.31
Consensus pattern (59 bp):
TAGAATGAGGATCATAGTTTGGGATGAAATTGAAATGTCCAAAAGGTCAGAGAACAAAT
Found at i:70986 original size:78 final size:78
Alignment explanation
Indices: 70897--71054 Score: 316
Period size: 78 Copynumber: 2.0 Consensus size: 78
70887 AACTTGTACC
70897 ATTCACAGTGTCACATTTGAATCTTGGACATTGTTTACAACATTTAACACTTCATACCGTTAAAT
1 ATTCACAGTGTCACATTTGAATCTTGGACATTGTTTACAACATTTAACACTTCATACCGTTAAAT
70962 CAATTAGTGATTG
66 CAATTAGTGATTG
70975 ATTCACAGTGTCACATTTGAATCTTGGACATTGTTTACAACATTTAACACTTCATACCGTTAAAT
1 ATTCACAGTGTCACATTTGAATCTTGGACATTGTTTACAACATTTAACACTTCATACCGTTAAAT
71040 CAATTAGTGATTG
66 CAATTAGTGATTG
71053 AT
1 AT
71055 GAGGAAGACA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (78 bp):
ATTCACAGTGTCACATTTGAATCTTGGACATTGTTTACAACATTTAACACTTCATACCGTTAAAT
CAATTAGTGATTG
Found at i:73562 original size:246 final size:246
Alignment explanation
Indices: 73128--73620 Score: 862
Period size: 246 Copynumber: 2.0 Consensus size: 246
73118 TGCTTTGACC
*
73128 TATCCGTTTGAAATTGCATGCTTATCTTAATCCGGGGCGGCCTCGACCTCTCTGCTCTGGAGCTT
1 TATCCGTTTGAAATTGCATGCTTATCTTAATCCGGGGCAGCCTCGACCTCTCTGCTCTGGAGCTT
*
73193 TAACTTGAGTGAAACTGAATTCATTGAGATTCTTGGTGTTGATTTAGAGAATTTGTTTCGAGCCT
66 TAACTTGAGTGAAACTGAATTCATTGAGAGTCTTGGTGTTGATTTAGAGAATTTGTTTCGAGCCT
73258 ACTTGTTATTGACACCAGGCGAGGCAAGGTGTGGCTATAGAAACTTACATATATAATTGTATATA
131 ACTTGTTATTGACACCAGGCGAGGCAAGGTGTGGCTATAGAAACTTACATATATAATTGTATATA
*
73323 CATGAGTTTTTGTATTCATGAGAGAGTTTTGGTGTTGATTCAGAGAACTTG
196 CATGAGTTCTTGTATTCATGAGAGAGTTTTGGTGTTGATTCAGAGAACTTG
* *
73374 TATCCGTTTGATATTGCATGCTTATTTTAATCCGGGGCAGCCTCGACCTCTCTGC-CGTGGAGCT
1 TATCCGTTTGAAATTGCATGCTTATCTTAATCCGGGGCAGCCTCGACCTCTCTGCTC-TGGAGCT
*
73438 TTAACTTGAGTGAAACTGAATTCATTGAGAGTCTTGGTGTTTATTTAGAGAATTTGTTTCGAGCC
65 TTAACTTGAGTGAAACTGAATTCATTGAGAGTCTTGGTGTTGATTTAGAGAATTTGTTTCGAGCC
* * * * *
73503 TACTTGTTGTTGACTCCAGGCGAGGCAAGGTGTGGCTATTGAAACTTATATGTATAATTGTATAT
130 TACTTGTTATTGACACCAGGCGAGGCAAGGTGTGGCTATAGAAACTTACATATATAATTGTATAT
*
73568 ACATGAGTTCTTGTATTCATGAGAGAGTTTTGGTGTTGATTCAGAGAGCTTG
195 ACATGAGTTCTTGTATTCATGAGAGAGTTTTGGTGTTGATTCAGAGAACTTG
73620 T
1 T
73621 GTCGAGCCTA
Statistics
Matches: 234, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
245 1 0.00
246 233 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (246 bp):
TATCCGTTTGAAATTGCATGCTTATCTTAATCCGGGGCAGCCTCGACCTCTCTGCTCTGGAGCTT
TAACTTGAGTGAAACTGAATTCATTGAGAGTCTTGGTGTTGATTTAGAGAATTTGTTTCGAGCCT
ACTTGTTATTGACACCAGGCGAGGCAAGGTGTGGCTATAGAAACTTACATATATAATTGTATATA
CATGAGTTCTTGTATTCATGAGAGAGTTTTGGTGTTGATTCAGAGAACTTG
Found at i:74548 original size:15 final size:16
Alignment explanation
Indices: 74520--74549 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
74510 AGAACTGTGA
74520 CAACATATGTTTTTGC
1 CAACATATGTTTTTGC
74536 CAACATA-GTTTTTG
1 CAACATATGTTTTTG
74550 AAATGCACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (16 bp):
CAACATATGTTTTTGC
Found at i:75151 original size:62 final size:61
Alignment explanation
Indices: 75065--75184 Score: 141
Period size: 62 Copynumber: 2.0 Consensus size: 61
75055 AAAATATTTG
* * * * *
75065 TTCTTTTTAACTTTGAATATTAAAAATAATTATATATTTGTGTATATTTTAAATTAAAATAA
1 TTCTATTTAACTTTGAATAGTAAAAAGAATTATATATTT-TGAATATTTCAAATTAAAATAA
* * * * *
75127 TTCTATTTAAGTTTGAATGGTAAAAAGAGTTTTATCTTTTGAATATTTCAAATTAAAA
1 TTCTATTTAACTTTGAATAGTAAAAAGAATTATATATTTTGAATATTTCAAATTAAAA
75185 AATATCGTTA
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
61 17 0.35
62 31 0.65
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.47
Consensus pattern (61 bp):
TTCTATTTAACTTTGAATAGTAAAAAGAATTATATATTTTGAATATTTCAAATTAAAATAA
Done.