Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008864.1 Hibiscus syriacus cultivar Beakdansim tig00112098_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: 59533
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:1254 original size:5 final size:5
Alignment explanation
Indices: 1244--1294 Score: 65
Period size: 5 Copynumber: 10.8 Consensus size: 5
1234 AAAATAATAA
1244 AAAAG AAAAG AAAAG -AAA- AAAAG AAAAG -AAAG AAAA- AAAAG AAAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG -AAAAG
1291 AAAA
1 AAAA
1295 AGAGGGGTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
4 14 0.34
5 22 0.54
6 5 0.12
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1263 original size:18 final size:19
Alignment explanation
Indices: 1242--1294 Score: 83
Period size: 18 Copynumber: 2.8 Consensus size: 19
1232 AAAAAATAAT
1242 AAAAAAGAAAAGAAAAG-A
1 AAAAAAGAAAAGAAAAGAA
1260 AAAAAAGAAAAG-AAAGAA
1 AAAAAAGAAAAGAAAAGAA
1278 AAAAAAGAAAAAGAAAA
1 AAAAAAG-AAAAGAAAA
1295 AGAGGGGTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.12
18 20 0.62
19 5 0.16
20 3 0.09
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (19 bp):
AAAAAAGAAAAGAAAAGAA
Found at i:1265 original size:13 final size:13
Alignment explanation
Indices: 1230--1289 Score: 68
Period size: 13 Copynumber: 4.5 Consensus size: 13
1220 TATGCTTAAT
*
1230 GAAAAAAATAATAA
1 GAAAAAAAGAA-AA
*
1244 AAAAGAAAAGAAAA
1 GAAA-AAAAGAAAA
1258 GAAAAAAAGAAAA
1 GAAAAAAAGAAAA
1271 GAAAGAAAA-AAAA
1 GAAA-AAAAGAAAA
1284 GAAAAA
1 GAAAAA
1290 GAAAAAGAGG
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
12 2 0.05
13 21 0.51
14 12 0.29
15 6 0.15
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.03
Consensus pattern (13 bp):
GAAAAAAAGAAAA
Found at i:1294 original size:13 final size:12
Alignment explanation
Indices: 1230--1297 Score: 64
Period size: 13 Copynumber: 5.2 Consensus size: 12
1220 TATGCTTAAT
1230 GAAAAAAATAATAA
1 GAAAAAAA-AA-AA
*
1244 AAAAGAAAAGAAAA
1 GAAA-AAAA-AAAA
1258 GAAAAAAAGAAAA
1 GAAAAAAA-AAAA
1271 GAAAGAAAAAAAA
1 GAAA-AAAAAAAA
*
1284 GAAAAAGAAAAA
1 GAAAAAAAAAAA
1296 GA
1 GA
1298 GGGGTCAAGG
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
12 9 0.19
13 21 0.44
14 12 0.25
15 6 0.12
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (12 bp):
GAAAAAAAAAAA
Found at i:2572 original size:83 final size:83
Alignment explanation
Indices: 2433--2824 Score: 624
Period size: 83 Copynumber: 4.7 Consensus size: 83
2423 ACATTAGCTG
*
2433 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
2498 AAACCAATCATTGAATTT
66 AAACCAATCATTGAATTT
*
2516 GAAAGATGAATGTGCTCATAGCATCTTCTGTAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
* *
2581 AAACCAGTTATTGAATTT
66 AAACCAATCATTGAATTT
*
2599 GGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGGT
1 -GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGT
*
2664 AAAACTAATCATTGAATTT
65 AAAACCAATCATTGAATTT
* * *
2683 GGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
2748 AAACCAATCATTGAATTT
66 AAACCAATCATTGAATTT
* * *
2766 GAAAGAAAT-AAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
1 GAAAG--ATGAATGTG-CTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
2825 AATTTGGTTT
Statistics
Matches: 284, Mismatches: 20, Indels: 7
0.91 0.06 0.02
Matches are distributed among these distances:
83 161 0.57
84 82 0.29
85 3 0.01
86 38 0.13
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (83 bp):
GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
AAACCAATCATTGAATTT
Found at i:2707 original size:167 final size:167
Alignment explanation
Indices: 2431--2824 Score: 639
Period size: 167 Copynumber: 2.3 Consensus size: 167
2421 AAACATTAGC
2431 TGGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGG
1 TGGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGG
* * *
2496 TAAAACCAATCATTGAATTTGAAAGATGAATGTGCTCATAGCATCTTCTGTAAGTGTTCTTTGAG
66 TAAAACCAATCATTGAATTTGAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTATTCTTTGAG
* *
2561 TTATCTGATCTGGTTTGGTAAAACCAGTTATTGAATT
131 TTATCTGATCTGGTTTGGTAAAACCAATCATTGAATT
2598 TGGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGG
1 TGGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGG
* *
2663 TAAAACTAATCATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTATTCTTTGAG
66 TAAAACCAATCATTGAATTTGAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTATTCTTTGAG
2728 TTATCTGATCTGGTTTGGTAAAACCAATCATTGAATT
131 TTATCTGATCTGGTTTGGTAAAACCAATCATTGAATT
* * * *
2765 T-GAAAGAAAT-AAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
1 TGGAAAG--ATGAATGTG-CTC-ATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCT
2825 AATTTGGTTT
Statistics
Matches: 212, Mismatches: 11, Indels: 6
0.93 0.05 0.03
Matches are distributed among these distances:
166 5 0.02
167 165 0.78
168 4 0.02
169 38 0.18
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.36
Consensus pattern (167 bp):
TGGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGG
TAAAACCAATCATTGAATTTGAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTATTCTTTGAG
TTATCTGATCTGGTTTGGTAAAACCAATCATTGAATT
Found at i:3950 original size:226 final size:221
Alignment explanation
Indices: 3553--4207 Score: 849
Period size: 226 Copynumber: 3.0 Consensus size: 221
3543 GCAAAGATTT
*
3553 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAG-AGTTCATAATGAGAAGAACTCATCT-AAG
* *
3618 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTTGATG
64 AAGGA-GAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTGATG
* * * *
3683 GATTATCTTTTCCAGTTCG-AGTTCATAATGAGAATAACTCATCTGAAGAAGGAAGAAGAAGTTC
128 GATCAACTTTTCCAG--AGAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTC
3747 ATAATGAGAAGAATTTGTTCAACCTTTTGCTC
190 ATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* ** *
3779 AAATCCATCACTTGATGGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATTTAAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAG-AAGAGTTCATAATGAGAAGAACTCATCT-AAG
3844 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTGATG
64 AAGG-AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTGATG
*
3909 GATCAACTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCA
128 GATCAACTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCA
* *
3974 TAATGAGAAGAATTTGTTCAGCTTTTTGCTC
191 TAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * *
4005 AAATCCATCACTTGATGGATCAACTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCT----
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGA-AGAGTTCATAATGAGAAGAACTCATCTAAGA
* * *
4066 ----GAAG-A----ATAATGAGAATAATTTGTTCAGCTTTTTGCTCAAATCCATCACTTGATGGG
65 AGGAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTGATGGA
** *
4122 TCAGTTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATC---AGGAGAAGAAGAAGTTCATAAT
130 TCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAAT
** *
4184 GAGAAGAGCTTATTCAACCTTTTG
195 GAGAAGAATTTGTTCAACCTTTTG
4208 AATGACTCTA
Statistics
Matches: 390, Mismatches: 34, Indels: 30
0.86 0.07 0.07
Matches are distributed among these distances:
206 37 0.09
207 3 0.01
210 25 0.06
211 60 0.15
215 1 0.00
216 4 0.01
224 1 0.00
226 257 0.66
227 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.31
Consensus pattern (221 bp):
AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTAAGAA
GGAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTGATGGAT
CAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATG
AGAAGAATTTGTTCAACCTTTTGCTC
Found at i:4072 original size:113 final size:113
Alignment explanation
Indices: 3553--4071 Score: 813
Period size: 113 Copynumber: 4.6 Consensus size: 113
3543 GCAAAGATTT
* *
3553 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
3618 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * **** *
3666 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAATAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
3731 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * **** * *
3779 AAATCCATCACTTGATGGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATTTAAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
3844 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
3892 AAATCCATCACTTGATGGATCAACTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
3957 AATGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAGCTTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
4005 AAATCCATCACTTGATGGATCAACTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
4070 AA
66 AA
4072 TAATGAGAAT
Statistics
Matches: 380, Mismatches: 26, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
113 380 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (113 bp):
AAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:4107 original size:98 final size:97
Alignment explanation
Indices: 3973--4161 Score: 324
Period size: 98 Copynumber: 1.9 Consensus size: 97
3963 GAAGAAGTTC
*
3973 ATAATGAGAAGAATTTGTTCAGCTTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCTAGA
1 ATAATGAGAAGAATTTGTTCAGCTTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGA
4038 GAAAGTTCATAATGAGAAGAACTCATCTGAAGA
66 G-AAGTTCATAATGAGAAGAACTCATCTGAAGA
* * **
4071 ATAATGAGAATAATTTGTTCAGCTTTTTGCTCAAATCCATCACTTGATGGGTCAGTTTTTCCAGA
1 ATAATGAGAAGAATTTGTTCAGCTTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGA
4136 GAAGTTCATAATGAGAAGAACTCATC
66 GAAGTTCATAATGAGAAGAACTCATC
4162 AGGAGAAGAA
Statistics
Matches: 86, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
97 25 0.29
98 61 0.71
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (97 bp):
ATAATGAGAAGAATTTGTTCAGCTTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGA
GAAGTTCATAATGAGAAGAACTCATCTGAAGA
Found at i:4190 original size:17 final size:17
Alignment explanation
Indices: 4135--4190 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
4125 GTTTTTCCAG
4135 AGAAGTTCATAATGAGA
1 AGAAGTTCATAATGAGA
*
4152 AGAA-CTCATCAGGA-GAAGA
1 AGAAGTTCAT-A--ATG-AGA
4171 AGAAGTTCATAATGAGA
1 AGAAGTTCATAATGAGA
4188 AGA
1 AGA
4191 GCTTATTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
16 4 0.13
17 12 0.39
18 2 0.06
19 9 0.29
20 4 0.13
ACGTcount: A:0.48, C:0.09, G:0.25, T:0.18
Consensus pattern (17 bp):
AGAAGTTCATAATGAGA
Found at i:4445 original size:3 final size:3
Alignment explanation
Indices: 4437--4511 Score: 82
Period size: 3 Copynumber: 25.3 Consensus size: 3
4427 ATGTTATTTA
* * * *
4437 TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT TAT AAT TAT AAT TAT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
4485 AAT TAT TAT TA- TAT TA- TAT ATAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT T
4512 TAATATTACA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
2 4 0.07
3 54 0.89
4 3 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:4459 original size:15 final size:15
Alignment explanation
Indices: 4441--4496 Score: 94
Period size: 15 Copynumber: 3.7 Consensus size: 15
4431 TATTTATATT
4441 ATTATTATTATTATA
1 ATTATTATTATTATA
4456 ATTATTATTATTATA
1 ATTATTATTATTATA
* *
4471 ATTATAATTATAATA
1 ATTATTATTATTATA
4486 ATTATTATTAT
1 ATTATTATTAT
4497 ATTATATATA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTATTATTATTATA
Found at i:4497 original size:15 final size:15
Alignment explanation
Indices: 4441--4516 Score: 91
Period size: 15 Copynumber: 5.0 Consensus size: 15
4431 TATTTATATT
*
4441 ATTATTATTATTATA
1 ATTATTATTATAATA
*
4456 ATTATTATTATTATA
1 ATTATTATTATAATA
*
4471 ATTATAATTATAATA
1 ATTATTATTATAATA
*
4486 ATTATTATTATATTA
1 ATTATTATTATAATA
4501 TATATATTATT-TAATA
1 -AT-TATTATTATAATA
4517 TTACAAGCCC
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
15 41 0.76
16 6 0.11
17 7 0.13
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTATTATTATAATA
Found at i:17986 original size:29 final size:30
Alignment explanation
Indices: 17953--18010 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
17943 CCTTTGGTTT
17953 TAGTTTAGTATCTAACGTTT-ATTTCGTTC
1 TAGTTTAGTATCTAACGTTTCATTTCGTTC
* * **
17982 TAGTTTGGTGTCTAATTTTTCATTTCGTT
1 TAGTTTAGTATCTAACGTTTCATTTCGTT
18011 ACTCATTTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.17, C:0.12, G:0.16, T:0.55
Consensus pattern (30 bp):
TAGTTTAGTATCTAACGTTTCATTTCGTTC
Found at i:24873 original size:10 final size:10
Alignment explanation
Indices: 24858--24901 Score: 61
Period size: 10 Copynumber: 4.1 Consensus size: 10
24848 TTTTTTGTGT
24858 TGTTCGTTTA
1 TGTTCGTTTA
24868 TGTTCGTTTA
1 TGTTCGTTTA
24878 TTGAGTTCGTTTA
1 -T--GTTCGTTTA
24891 TGTTCGTTTA
1 TGTTCGTTTA
24901 T
1 T
24902 TGTTTTCGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 20 0.65
11 1 0.03
12 1 0.03
13 9 0.29
ACGTcount: A:0.11, C:0.09, G:0.20, T:0.59
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:24885 original size:13 final size:12
Alignment explanation
Indices: 24859--24915 Score: 59
Period size: 13 Copynumber: 4.9 Consensus size: 12
24849 TTTTTGTGTT
24859 GTTCGTTTA-T-
1 GTTCGTTTATTG
24869 GTTCGTTTATTG
1 GTTCGTTTATTG
24881 AGTTCGTTTA-T-
1 -GTTCGTTTATTG
24892 GTTCGTTTATTG
1 GTTCGTTTATTG
*
24904 TTTTCGTTTATT
1 -GTTCGTTTATT
24916 TATTAAATGA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
10 18 0.45
11 2 0.05
12 1 0.03
13 19 0.47
ACGTcount: A:0.11, C:0.09, G:0.19, T:0.61
Consensus pattern (12 bp):
GTTCGTTTATTG
Found at i:24887 original size:23 final size:23
Alignment explanation
Indices: 24859--24914 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
24849 TTTTTGTGTT
24859 GTTCGTTTATGTTCGTTTATTGA
1 GTTCGTTTATGTTCGTTTATTGA
*
24882 GTTCGTTTATGTTCGTTTATTGT
1 GTTCGTTTATGTTCGTTTATTGA
*
24905 TTTCGTTTAT
1 GTTCGTTTAT
24915 TTATTAAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.11, C:0.09, G:0.20, T:0.61
Consensus pattern (23 bp):
GTTCGTTTATGTTCGTTTATTGA
Found at i:33887 original size:20 final size:19
Alignment explanation
Indices: 33851--33889 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
33841 TTTGGGAAAA
**
33851 ATCGGTTTTTTTTAACCGG
1 ATCGGTTTTTTAAAACCGG
33870 ATCGGATTTTTTAAAACCGG
1 ATCGG-TTTTTTAAAACCGG
33890 TTATTTTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (19 bp):
ATCGGTTTTTTAAAACCGG
Found at i:36284 original size:21 final size:21
Alignment explanation
Indices: 36260--36299 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
36250 TTTATTTTAT
36260 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
36281 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
36300 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:36347 original size:33 final size:33
Alignment explanation
Indices: 36294--36392 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
36284 TTTGTTTCAA
36294 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
36326 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
36359 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
36392 T
1 T
36393 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:36421 original size:13 final size:13
Alignment explanation
Indices: 36378--36432 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
36368 TTGGAAGTAT
36378 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
36391 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
36405 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
36418 TTAAGTATTTGAA
1 TTAAGTATTTCAA
36431 TT
1 TT
36433 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:36654 original size:21 final size:21
Alignment explanation
Indices: 36628--36684 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
36618 TGGAGCGTGG
*
36628 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
36649 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
36670 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
36685 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:37021 original size:15 final size:17
Alignment explanation
Indices: 36995--37026 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
36985 CTCATAGAGA
36995 AAAAACCGGATC-GGAT
1 AAAAACCGGATCTGGAT
37011 AAAAACC-GATCTGGAT
1 AAAAACCGGATCTGGAT
37027 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.16
Consensus pattern (17 bp):
AAAAACCGGATCTGGAT
Found at i:44327 original size:14 final size:14
Alignment explanation
Indices: 44308--44334 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44298 CTTTGACCCA
44308 AATATATATGCATT
1 AATATATATGCATT
44322 AATATATATGCAT
1 AATATATATGCAT
44335 GCTTTTACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (14 bp):
AATATATATGCATT
Found at i:44482 original size:2 final size:2
Alignment explanation
Indices: 44475--44505 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
44465 TGTTGAGCAT
44475 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 T
44506 TGAACATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45014 original size:33 final size:33
Alignment explanation
Indices: 44970--45081 Score: 179
Period size: 33 Copynumber: 3.4 Consensus size: 33
44960 TGTTTTTGTT
*
44970 TCCATGCATCATGCCATACGTCACATGCATAGA
1 TCCATCCATCATGCCATACGTCACATGCATAGA
* *
45003 TTCATCCATCATGTCATACGTCACATGCATAGA
1 TCCATCCATCATGCCATACGTCACATGCATAGA
* *
45036 TCCATCCATCATGCCACACGTTACATGCATAGA
1 TCCATCCATCATGCCATACGTCACATGCATAGA
45069 TCCATCCATCATG
1 TCCATCCATCATG
45082 ACTTGTTTAT
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 72 1.00
ACGTcount: A:0.29, C:0.31, G:0.12, T:0.27
Consensus pattern (33 bp):
TCCATCCATCATGCCATACGTCACATGCATAGA
Found at i:48126 original size:55 final size:54
Alignment explanation
Indices: 48035--48192 Score: 178
Period size: 55 Copynumber: 2.9 Consensus size: 54
48025 ATATTCGGAA
* * *
48035 AACGAGCTCGCTCCCTCATTT-TTAGGGAGTATAGAACTCGAACAATTTTCTG-C
1 AACGAGTTCACTCCCTC-TTTCTTAGGGAGTATAGAACTCGAACAATCTTCTGTC
*
48088 GAACGAGTTCACTCCCTCTTTCTTCGGGGAGTATAGAACTCGAACAATCTTCTGTC
1 -AACGAGTTCACTCCCTCTTTCTT-AGGGAGTATAGAACTCGAACAATCTTCTGTC
* ** * * *
48144 AACGGGTTCGTTCCCTCTTTCTTAGGGAGTA-GGAACTTGAAGAATCTTC
1 AACGAGTTCACTCCCTCTTTCTTAGGGAGTATAGAACTCGAACAATCTTC
48193 ATCAATCGTG
Statistics
Matches: 90, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
53 18 0.20
54 24 0.27
55 47 0.52
56 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (54 bp):
AACGAGTTCACTCCCTCTTTCTTAGGGAGTATAGAACTCGAACAATCTTCTGTC
Found at i:48247 original size:55 final size:55
Alignment explanation
Indices: 48186--48688 Score: 692
Period size: 55 Copynumber: 9.1 Consensus size: 55
48176 GAACTTGAAG
* *
48186 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACCCAAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACTCGAAC
* * * * *
48241 AATCTTCAACAAATCTTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCCAAAC
1 AATCTTCATC-AATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACTCGAAC
* * *
48297 AATCTTCATCAATCGTGTCTGCTCCCCA-TTCCTTCATAGAGTATAAGACTTGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCC-TCAGAGAGTATAAGACTCGAAC
* *
48352 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCGCAGAGAGTGTAAGACTCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACTCGAAC
48407 AATCTTCATCAATCGTGTCTGCTCCCTATTT-CTGCAGAGAGTATAAGACTCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCT-CAGAGAGTATAAGACTCGAAC
* * *
48462 AATTTTCAACAATCGTGTCTGCT-CCTCA-TTCCTTCAGAGAGTACAAGACTCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCT-ATTTCC-TCAGAGAGTATAAGACTCGAAC
* *
48517 AATCTTCATCCATCGTGTCTGCTCCATATTT-CTGCAGAGAGTATAAGACTCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCT-CAGAGAGTATAAGACTCGAAC
* * **
48572 AATTTTCAACAATCGTGTCTGCTCCCTATTTTTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACTCGAAC
* * * *
48627 AATCTTCAACAATCGCGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGATC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACTCGAAC
48682 AATCTTC
1 AATCTTC
48689 GATTATCGTT
Statistics
Matches: 402, Mismatches: 35, Indels: 22
0.88 0.08 0.05
Matches are distributed among these distances:
54 10 0.02
55 330 0.82
56 62 0.15
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.31
Consensus pattern (55 bp):
AATCTTCATCAATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACTCGAAC
Found at i:48497 original size:165 final size:164
Alignment explanation
Indices: 48186--48688 Score: 772
Period size: 165 Copynumber: 3.0 Consensus size: 164
48176 GAACTTGAAG
* * *
48186 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACCCAAACAATCTTCAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCGCAGAGAGTATAAGACTCGAACAATCTTCAAC
* * * *
48251 AAATCTTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCCAAACAATCTTCATCAATCGTGTC
66 -AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTC
* *
48316 TGCTCCCCATTCCTTCATAGAGTATAAGACTTGAAC
130 TGCT-CCCATTCCTTCAGAGAGTATAAGACTCGAAC
* *
48352 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCGCAGAGAGTGTAAGACTCGAACAATCTTCATC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCGCAGAGAGTATAAGACTCGAACAATCTTCAAC
* *
48417 AATCGTGTCTGCTCCCTATTTCTGCAGAGAGTATAAGACTCGAACAATTTTCAACAATCGTGTCT
66 AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
*
48482 GCTCCTCATTCCTTCAGAGAGTACAAGACTCGAAC
131 GCTCC-CATTCCTTCAGAGAGTATAAGACTCGAAC
* * * *
48517 AATCTTCATCCATCGTGTCTGCTCCATATTTCTGCAGAGAGTATAAGACTCGAACAATTTTCAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCGCAGAGAGTATAAGACTCGAACAATCTTCAAC
* *
48582 AATCGTGTCTGCTCCCTATTTTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCT
66 AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
* *
48647 GCTCCCTATTTCTTCAGAGAGTATAAGACTCGATC
131 GCTCCC-ATTCCTTCAGAGAGTATAAGACTCGAAC
48682 AATCTTC
1 AATCTTC
48689 GATTATCGTT
Statistics
Matches: 308, Mismatches: 27, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
164 3 0.01
165 245 0.80
166 60 0.19
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.31
Consensus pattern (164 bp):
AATCTTCATCAATCGTGTCTGCTCCCTATTTCCGCAGAGAGTATAAGACTCGAACAATCTTCAAC
AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
GCTCCCATTCCTTCAGAGAGTATAAGACTCGAAC
Found at i:49740 original size:8 final size:8
Alignment explanation
Indices: 49690--49740 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
49680 GAACCCTTCT
49690 TTTTTTCCA
1 TTTTTT-CA
*
49699 TTTTTCCA
1 TTTTTTCA
*
49707 TTTTTTTA
1 TTTTTTCA
*
49715 TTTTTTTA
1 TTTTTTCA
49723 -TTTTTC-
1 TTTTTTCA
49729 TTTTTTCA
1 TTTTTTCA
49737 TTTT
1 TTTT
49741 CACTCATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
7 11 0.31
8 20 0.56
9 5 0.14
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTTCA
Done.