Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009344.1 Hibiscus syriacus cultivar Beakdansim tig00113124_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: 4287485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 24 of 24
Found at i:4266039 original size:24 final size:24
Alignment explanation
Indices: 4266007--4266054 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
4265997 TATATATGAT
4266007 TAGGGTATTGATTGGTGGAGCCAG
1 TAGGGTATTGATTGGTGGAGCCAG
4266031 TAGGGTATTGATTGGTGGAGCCAG
1 TAGGGTATTGATTGGTGGAGCCAG
4266055 AGACAGACGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.08, G:0.42, T:0.29
Consensus pattern (24 bp):
TAGGGTATTGATTGGTGGAGCCAG
Found at i:4266201 original size:22 final size:22
Alignment explanation
Indices: 4266154--4266204 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
4266144 CGAAACATAT
**
4266154 TTTTAAAAAGAAATACATATTT
1 TTTTAAAAAGAAATACATATAA
*
4266176 TTTTAAAAA-AAATATATGATAA
1 TTTTAAAAAGAAATACAT-ATAA
4266198 TTTTAAA
1 TTTTAAA
4266205 TTTTTATAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (22 bp):
TTTTAAAAAGAAATACATATAA
Found at i:4266712 original size:25 final size:25
Alignment explanation
Indices: 4266673--4266737 Score: 87
Period size: 24 Copynumber: 2.6 Consensus size: 25
4266663 AAAAAAATAT
* *
4266673 ATAATGTAACATTTTTATCATTTTA
1 ATAATATAATATTTTTATCATTTTA
* *
4266698 ATAAT-TAGTATTTTTGTCATTTTA
1 ATAATATAATATTTTTATCATTTTA
4266722 ATAATATAATATTTTT
1 ATAATATAATATTTTT
4266738 TAGATTATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 21 0.60
25 14 0.40
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (25 bp):
ATAATATAATATTTTTATCATTTTA
Found at i:4267816 original size:3 final size:3
Alignment explanation
Indices: 4267808--4267888 Score: 144
Period size: 3 Copynumber: 27.0 Consensus size: 3
4267798 TTTTTATCCA
*
4267808 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
4267856 TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4267889 AATATATATA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:4269270 original size:18 final size:19
Alignment explanation
Indices: 4269234--4269273 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
4269224 GTAGTATTTG
**
4269234 TATTTTTATTATTGTTAAA
1 TATTTTTATTATTCATAAA
4269253 TATTTTTA-TATTCATAAA
1 TATTTTTATTATTCATAAA
4269271 TAT
1 TAT
4269274 AATAAATAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (19 bp):
TATTTTTATTATTCATAAA
Found at i:4269997 original size:18 final size:17
Alignment explanation
Indices: 4269974--4270024 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
4269964 TTCTTTTCAA
4269974 ATTTTTTATTTATTTAT
1 ATTTTTTATTTATTTAT
*
4269991 -TATTTTTATAATATTTAT
1 AT-TTTTTAT-TTATTTAT
*
4270009 ATGTTTTATTTTATTT
1 ATTTTTTA-TTTATTT
4270025 GCAATTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
16 1 0.04
17 7 0.26
18 17 0.63
19 2 0.07
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (17 bp):
ATTTTTTATTTATTTAT
Found at i:4270034 original size:15 final size:13
Alignment explanation
Indices: 4270014--4270051 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
4270004 TTTATATGTT
4270014 TTATTTTATTTGCAA
1 TTATTTTATTT-C-A
4270029 TTATTTTATTTCA
1 TTATTTTATTTCA
4270042 TTA-TTTATTT
1 TTATTTTATTT
4270052 TGTCAGAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.30
13 4 0.17
14 1 0.04
15 11 0.48
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (13 bp):
TTATTTTATTTCA
Found at i:4280629 original size:11 final size:11
Alignment explanation
Indices: 4280605--4280653 Score: 62
Period size: 12 Copynumber: 4.3 Consensus size: 11
4280595 ATTATGCTTG
4280605 AAGAAAAAAGAA
1 AAGAAAAAA-AA
4280617 AAGAAAAAAAA
1 AAGAAAAAAAA
4280628 AAGAGAAAAAAA
1 AAGA-AAAAAAA
* *
4280640 AAGAGAGAAAA
1 AAGAAAAAAAA
4280651 AAG
1 AAG
4280654 GGGGGTCAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
11 14 0.41
12 20 0.59
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:4280636 original size:23 final size:23
Alignment explanation
Indices: 4280605--4280653 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
4280595 ATTATGCTTG
*
4280605 AAGAAAAAAGAAAAGAAAAAAAA
1 AAGAAAAAAAAAAAGAAAAAAAA
* * *
4280628 AAGAGAAAAAAAAAGAGAGAAAA
1 AAGAAAAAAAAAAAGAAAAAAAA
4280651 AAG
1 AAG
4280654 GGGGGTCAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (23 bp):
AAGAAAAAAAAAAAGAAAAAAAA
Found at i:4280641 original size:14 final size:14
Alignment explanation
Indices: 4280608--4280652 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
4280598 ATGCTTGAAG
*
4280608 AAAAAAGAAA-AG-
1 AAAAAAAAAAGAGA
4280620 AAAAAAAAAAGAGA
1 AAAAAAAAAAGAGA
*
4280634 AAAAAAAAGAGAGA
1 AAAAAAAAAAGAGA
4280648 AAAAA
1 AAAAA
4280653 GGGGGGTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 9 0.31
13 2 0.07
14 18 0.62
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAGAGA
Found at i:4280980 original size:16 final size:16
Alignment explanation
Indices: 4280961--4281000 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
4280951 ATACAATTAT
4280961 ATTTATTTCAAG-TTCA
1 ATTTATTT-AAGATTCA
*
4280977 ATTTATTTGAGATTCA
1 ATTTATTTAAGATTCA
4280993 ATTTATTT
1 ATTTATTT
4281001 TCGAAAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.09
16 20 0.91
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (16 bp):
ATTTATTTAAGATTCA
Found at i:4281947 original size:83 final size:83
Alignment explanation
Indices: 4281801--4282098 Score: 515
Period size: 83 Copynumber: 3.6 Consensus size: 83
4281791 TGTGCTCAAC
* * * * * * * *
4281801 AGCATCTTCTAGAAGTGTTCTTTGATTTATCTGATCTGGTTAGACAGAACCAATCAATAAATTTA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAATCATTGAATTTG
4281866 GAAGATGAATTTGCCAAT
66 GAAGATGAATTTGCCAAT
4281884 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAATCATTGAATTTG
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAATCATTGAATTTG
4281949 GAAGATGAATTTGCCAAT
66 GAAGATGAATTTGCCAAT
4281967 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAATCATTGAATTTG
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAATCATTGAATTTG
4282032 GAAGATGAATTTGCCAAT
66 GAAGATGAATTTGCCAAT
*
4282050 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAA
4282099 CCAAGCATCT
Statistics
Matches: 206, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 206 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (83 bp):
AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAATCATTGAATTTG
GAAGATGAATTTGCCAAT
Found at i:4282128 original size:52 final size:52
Alignment explanation
Indices: 4282050--4282154 Score: 194
Period size: 52 Copynumber: 2.0 Consensus size: 52
4282040 ATTTGCCAAT
4282050 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAACCA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAACCA
4282102 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCA
4282154 A
1 A
4282155 TCATTGAATT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
52 48 0.92
53 4 0.08
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (52 bp):
AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCA
Found at i:4282262 original size:219 final size:218
Alignment explanation
Indices: 4281884--4282325 Score: 787
Period size: 219 Copynumber: 2.0 Consensus size: 218
4281874 ATTTGCCAAT
*
4281884 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAATCATTGAATTTG
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAACCAATCATTGAATTTG
* *
4281949 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAG
66 GAAGATGAAGTTGCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAG
4282014 AATCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
131 AATCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
* *
4282079 TCTGATCTGGTTGGACAGAACCA
196 TATGATCTGATTGGACAGAACCA
*
4282102 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAACCAATCATTGAATTT
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GATTGGACAGAACCAATCATTGAATTT
4282166 GGAAGATGAAGTTGCTCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGAC
65 GGAAGATGAAGTTGC-CAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGAC
*
4282231 AGAATCAATCATTGAATTTGGAAGATGAATTTGCCGATAGCATCTTCTGGAAGTGTTCTTTGAGT
129 AGAATCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
*
4282296 TATATGATCTGATTGGACAGAATCA
194 TATATGATCTGATTGGACAGAACCA
4282321 AGCAT
1 AGCAT
4282326 TGAGTTTAGA
Statistics
Matches: 214, Mismatches: 8, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
218 70 0.33
219 144 0.67
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.36
Consensus pattern (218 bp):
AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAACCAATCATTGAATTTG
GAAGATGAAGTTGCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAG
AATCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
TATGATCTGATTGGACAGAACCA
Found at i:4282307 original size:83 final size:83
Alignment explanation
Indices: 4282102--4282553 Score: 762
Period size: 83 Copynumber: 5.4 Consensus size: 83
4282092 GACAGAACCA
* * *
4282102 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAACCAATCATTGAATTT
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GATTGGACAGAATCAAGCATTGAATTT
*
4282166 GGAAGATGAAGTTGCTCAAT
65 GGAAGATGAATTTGC-CAAT
* *
4282186 AACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAATCATTGAATTTG
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATTTG
*
4282251 GAAGATGAATTTGCCGAT
66 GAAGATGAATTTGCCAAT
* * *
4282269 AGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATCTGATTGGACAGAATCAAGCATTGAGTTTA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATTTG
4282334 GAAGATGAATTTGCCAAT
66 GAAGATGAATTTGCCAAT
* *
4282352 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAGTTTA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATTTG
4282417 GAAGATGAATTTGCCAAT
66 GAAGATGAATTTGCCAAT
4282435 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATTTG
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATTTG
4282500 GAAGATGAATTTGCCAAT
66 GAAGATGAATTTGCCAAT
*
4282518 AGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATC
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
4282554 AGAAGAAGTG
Statistics
Matches: 352, Mismatches: 15, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
83 283 0.80
84 69 0.20
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (83 bp):
AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATTTG
GAAGATGAATTTGCCAAT
Found at i:4282346 original size:302 final size:301
Alignment explanation
Indices: 4281801--4282408 Score: 1063
Period size: 302 Copynumber: 2.0 Consensus size: 301
4281791 TGTGCTCAAC
*
4281801 AGCATCTTCTAGAAGTGTTCTTTGATTTATCTGATCTGGTTAGACAGAACCAATCAATAAATTTA
1 AGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCAATAAATTTA
* *
4281866 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAG
66 GAAGATGAAGTTGCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAG
4281931 AATCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
131 AATCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
* * *
4281996 TCTGATCTGATTGGACAGAATCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTG
196 TATGATCTGATTGGACAGAATCAAGCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTG
*
4282061 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCA
261 GAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAACCA
* * * * * *
4282102 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTG
1 AGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCAATAAATTTA
4282167 GAAGATGAAGTTGCTCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACA
66 GAAGATGAAGTTGC-CAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACA
*
4282232 GAATCAATCATTGAATTTGGAAGATGAATTTGCCGATAGCATCTTCTGGAAGTGTTCTTTGAGTT
130 GAATCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTT
*
4282297 ATATGATCTGATTGGACAGAATCAAGCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCT
195 ATATGATCTGATTGGACAGAATCAAGCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCT
*
4282362 GGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCA
260 GGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAACCA
4282404 AGCAT
1 AGCAT
4282409 TGAGTTTAGA
Statistics
Matches: 290, Mismatches: 16, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
301 71 0.24
302 219 0.76
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.36
Consensus pattern (301 bp):
AGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCAATAAATTTA
GAAGATGAAGTTGCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAG
AATCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
TATGATCTGATTGGACAGAATCAAGCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTG
GAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAACCA
Found at i:4283423 original size:113 final size:113
Alignment explanation
Indices: 4283110--4283888 Score: 1314
Period size: 113 Copynumber: 7.0 Consensus size: 113
4283100 CAAAGATTCA
4283110 AATCCATCATTTGATGGACCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGACCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
4283175 AGGAAGAAGAAGTTCATAATGAGAAGAA-TTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
4283222 AAT-CATCATTTGATGGACCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGACCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
4283286 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
4283334 AATCCATCATTTGATGGACCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGACCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
4283399 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
*
4283447 AATCCATCATTTGATGGACCAGATTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGACCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
4283512 AGGAAGAGGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
4283560 AATCCATCATTTGA-GAGACCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCATTTGATG-GACCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
4283624 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
*
4283673 AATCCATCATTTGA-GAGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCATTTGATG-GACCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
4283737 AA-GAAGGAAGAAGAATTCATAATGAGAAGAATTTGTTCAACCCTTTACCTG
65 AAGGAA-GAAGAAG--TTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
*
4283788 AATCCATCATTTGA-GAGATCAGC-TTTCCAGAG-AAGTTCATAATGAGAA-AA--C-TCTGAAG
1 AATCCATCATTTGATG-GACCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * * *
4283846 AAGAAAGAAGAAGTTCATAATAAGAAG-ACTTGTTCAACTTTTT
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
4283889 GCATAATTCT
Statistics
Matches: 647, Mismatches: 13, Indels: 20
0.95 0.02 0.03
Matches are distributed among these distances:
106 13 0.02
107 13 0.02
109 16 0.02
110 3 0.00
111 89 0.14
112 31 0.05
113 415 0.64
114 9 0.01
115 58 0.09
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.27
Consensus pattern (113 bp):
AATCCATCATTTGATGGACCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
Found at i:4284208 original size:3 final size:3
Alignment explanation
Indices: 4284200--4284282 Score: 127
Period size: 3 Copynumber: 28.7 Consensus size: 3
4284190 TTTTTATCCA
*
4284200 TAT TAT TAT TAT TAT TAT TA- TAT TAT TAC TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
4284246 TAT TAT TAT TAT TAT TAT CAT T-T TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
4284283 AATATATATT
Statistics
Matches: 73, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
2 6 0.08
3 67 0.92
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:4284232 original size:23 final size:23
Alignment explanation
Indices: 4284201--4284282 Score: 123
Period size: 23 Copynumber: 3.6 Consensus size: 23
4284191 TTTTATCCAT
4284201 ATTATTATTATTATTAT-TATATT
1 ATTATTATTATTATTATAT-TATT
*
4284224 ATTACTATTATTATTATATTATT
1 ATTATTATTATTATTATATTATT
4284247 ATTATTATTATTATTATCATT-TT
1 ATTATTATTATTATTAT-ATTATT
4284270 ATTATTATTATTA
1 ATTATTATTATTA
4284283 AATATATATT
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
23 51 0.93
24 4 0.07
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (23 bp):
ATTATTATTATTATTATATTATT
Found at i:4284293 original size:20 final size:20
Alignment explanation
Indices: 4284199--4284280 Score: 130
Period size: 20 Copynumber: 4.1 Consensus size: 20
4284189 ATTTTTATCC
4284199 ATATTATTATTATTATTATT
1 ATATTATTATTATTATTATT
*
4284219 ATATTATTACTATTATTATT
1 ATATTATTATTATTATTATT
4284239 ATATTATTATTATTATTATT
1 ATATTATTATTATTATTATT
*
4284259 ATTATCATT-TTATTATTATT
1 A-TATTATTATTATTATTATT
4284279 AT
1 AT
4284281 TAAATATATA
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
19 1 0.02
20 51 0.88
21 6 0.10
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
ATATTATTATTATTATTATT
Found at i:4285298 original size:29 final size:29
Alignment explanation
Indices: 4285265--4285321 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
4285255 TCACTAATTA
4285265 AATTTATAATAT-TTTTAATTCAGTCTTCG
1 AATTT-TAATATCTTTTAATTCAGTCTTCG
* * *
4285294 AATTTTAATTTCTTTTATTTTAGTCTTC
1 AATTTTAATATCTTTTAATTCAGTCTTC
4285322 ATATTAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.26, C:0.11, G:0.05, T:0.58
Consensus pattern (29 bp):
AATTTTAATATCTTTTAATTCAGTCTTCG
Found at i:4286647 original size:54 final size:51
Alignment explanation
Indices: 4286493--4286651 Score: 211
Period size: 50 Copynumber: 3.1 Consensus size: 51
4286483 TTCATACTAC
*
4286493 AAAAAAT-TAGCACTTAACACATACTTA-GACTGGTGTAAGTGAATAAAAT
1 AAAAAATGTAGTACTTAACACATACTTACGACTGGTGTAAGTGAATAAAAT
*
4286542 AAATAAGTGTA-TCACTTAACACATAC-TAC-ACTGGTGTAAGTGAATAAAAT
1 AAA-AAATGTAGT-ACTTAACACATACTTACGACTGGTGTAAGTGAATAAAAT
*
4286592 AAAAAATGTAGTACTTAACACATACTTACACTGACTGGTGTAAGTAAATAAAAT
1 AAAAAATGTAGTACTTAACACATACTT--AC-GACTGGTGTAAGTGAATAAAAT
4286646 AAAAAA
1 AAAAAA
4286652 ATGCAACACT
Statistics
Matches: 96, Mismatches: 4, Indels: 15
0.83 0.03 0.13
Matches are distributed among these distances:
49 22 0.23
50 31 0.32
51 15 0.16
52 2 0.02
54 26 0.27
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (51 bp):
AAAAAATGTAGTACTTAACACATACTTACGACTGGTGTAAGTGAATAAAAT
Found at i:4287376 original size:21 final size:20
Alignment explanation
Indices: 4287307--4287447 Score: 75
Period size: 21 Copynumber: 6.8 Consensus size: 20
4287297 AAATGACCAA
***
4287307 CAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
4287327 CAGAATCGCAAATCAGTTTTT
1 CAAAATCGCAACGC-GATTTT
4287348 CCAAAATCGCAACGCGATTCTT
1 -CAAAATCGCAACGCGATT-TT
* * * *
4287370 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
4287391 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
4287411 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
4287432 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
4287448 ACACATAAAT
Statistics
Matches: 88, Mismatches: 28, Indels: 10
0.70 0.22 0.08
Matches are distributed among these distances:
20 26 0.30
21 49 0.56
22 13 0.15
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:4287440 original size:20 final size:20
Alignment explanation
Indices: 4287415--4287484 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
4287405 GATTTTCCAG
* *
4287415 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
4287435 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
4287455 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
4287475 AATCGCAACG
1 AATCGCAACG
4287485 T
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
19 1 0.02
20 41 0.93
21 2 0.05
ACGTcount: A:0.40, C:0.27, G:0.19, T:0.14
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Done.