Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007560.1 Hibiscus syriacus cultivar Beakdansim tig00021374_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: 95717
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:7006 original size:18 final size:20
Alignment explanation
Indices: 6958--7007 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 20
6948 TTTAATATAC
6958 TTATTTT-TTAAA-AATTGA
1 TTATTTTATTAAATAATTGA
6976 TTA-TTTATCTAAATAA-T-A
1 TTATTTTAT-TAAATAATTGA
6994 TTATTTTATTAAAT
1 TTATTTTATTAAAT
7008 TTTTTAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
17 3 0.11
18 13 0.46
19 10 0.36
20 2 0.07
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTATTTTATTAAATAATTGA
Found at i:9155 original size:21 final size:20
Alignment explanation
Indices: 9118--9166 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
9108 AATAACTCAA
*
9118 ACAT-AATAAATAAACTGTT
1 ACATCAATAAATAAACTGTC
*
9137 ACATCAATAACATTAACTGTC
1 ACATCAATAA-ATAAACTGTC
9158 ACATCAATA
1 ACATCAATA
9167 CCAGATAGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 4 0.15
20 5 0.19
21 17 0.65
ACGTcount: A:0.49, C:0.18, G:0.04, T:0.29
Consensus pattern (20 bp):
ACATCAATAAATAAACTGTC
Found at i:12212 original size:32 final size:32
Alignment explanation
Indices: 12163--12232 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
12153 GATCTGTTTG
* *
12163 ATTTAAGTCCCTAAGCTGGTAATTTTCGTTCA
1 ATTTTAGTCCCTAAGCTGGTAATTCTCGTTCA
* *
12195 ATTTTAGTCCCTCAGCTGGTAATTCTCGTTTA
1 ATTTTAGTCCCTAAGCTGGTAATTCTCGTTCA
12227 ATTTTA
1 ATTTTA
12233 ATCCTTCGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.44
Consensus pattern (32 bp):
ATTTTAGTCCCTAAGCTGGTAATTCTCGTTCA
Found at i:12945 original size:46 final size:46
Alignment explanation
Indices: 12828--12964 Score: 181
Period size: 45 Copynumber: 3.0 Consensus size: 46
12818 CTCAAACTCG
* * *
12828 AGACTTTAAAGAATAGCAATAA--TTTTTTACTACTGAGGTGATTT
1 AGACTTTAAAGAATAACAATAATTTTTTTTACTACCGAGATGATTT
* * * *
12872 AAACTTCAAAGAATAACAAT-ATTTTTTTTACTACCGAAATAATTT
1 AGACTTTAAAGAATAACAATAATTTTTTTTACTACCGAGATGATTT
*
12917 AGACTTTAAAGAATAACAATAATTTTTTTTATTACCGAGATGATTT
1 AGACTTTAAAGAATAACAATAATTTTTTTTACTACCGAGATGATTT
12963 AG
1 AG
12965 TTCGTGCTGG
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
43 1 0.01
44 17 0.22
45 36 0.46
46 24 0.31
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (46 bp):
AGACTTTAAAGAATAACAATAATTTTTTTTACTACCGAGATGATTT
Found at i:20515 original size:2 final size:2
Alignment explanation
Indices: 20508--20532 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20498 CATGAGTTAG
20508 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
20533 GGAATTGGTA
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:21263 original size:22 final size:22
Alignment explanation
Indices: 21238--21315 Score: 113
Period size: 22 Copynumber: 3.5 Consensus size: 22
21228 GGGTATATTA
*
21238 GTCCTTCGGGATGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
21260 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
* *
21282 ATCCTTCGGGACGTATCTAGTG
1 GTCCTTCGGGACGTATCCAGTG
21304 G-CCTTTCGGGAC
1 GTCC-TTCGGGAC
21316 ATAATAGTCC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 2 0.04
22 49 0.96
ACGTcount: A:0.14, C:0.26, G:0.31, T:0.29
Consensus pattern (22 bp):
GTCCTTCGGGACGTATCCAGTG
Found at i:25945 original size:26 final size:26
Alignment explanation
Indices: 25911--25970 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
25901 AAGCTGGGAC
*
25911 TTTTGCCCTCCATACCTGCTCCTTCT
1 TTTTTCCCTCCATACCTGCTCCTTCT
25937 TTTTTCCCTCCATACCTGCTCCTTCT
1 TTTTTCCCTCCATACCTGCTCCTTCT
25963 TTTTTCCC
1 TTTTTCCC
25971 ATATGACATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.07, C:0.42, G:0.05, T:0.47
Consensus pattern (26 bp):
TTTTTCCCTCCATACCTGCTCCTTCT
Found at i:27448 original size:23 final size:23
Alignment explanation
Indices: 27403--27448 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
27393 CTGAATGATT
* **
27403 CAGTGTTGAATGATTCAGTAAAA
1 CAGTGCTGAATGATTCAACAAAA
27426 CAGTGCTGAATGATTCAACAAAA
1 CAGTGCTGAATGATTCAACAAAA
27449 TAATACATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (23 bp):
CAGTGCTGAATGATTCAACAAAA
Found at i:29940 original size:29 final size:27
Alignment explanation
Indices: 29892--29954 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 27
29882 ATTTGCTAAT
** *
29892 TTTATTTTATTGTTTAAATTTCATTTA
1 TTTATTTTATTGTTTAAATTAAATATA
*
29919 TTTATTTTGGTTGATTTAAATTAAATATA
1 TTTATTTT-ATTG-TTTAAATTAAATATA
29948 TTTATTT
1 TTTATTT
29955 AAATTTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 8 0.27
28 3 0.10
29 19 0.63
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.63
Consensus pattern (27 bp):
TTTATTTTATTGTTTAAATTAAATATA
Found at i:37919 original size:21 final size:21
Alignment explanation
Indices: 37890--37942 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
37880 ATTCTGACTA
37890 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
37911 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
37932 TCGCAATGCGA
1 TCGCATTGCGA
37943 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:38320 original size:15 final size:15
Alignment explanation
Indices: 38297--38347 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
38287 CGCCCCGCAT
* *
38297 CCGCACCGCATCCAC
1 CCGCCCCGCATCCGC
38312 CCGCCCCGCATCCGC
1 CCGCCCCGCATCCGC
* *
38327 CCTCCCCACATCCGC
1 CCGCCCCGCATCCGC
38342 CCGCCC
1 CCGCCC
38348 AACTAAATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.12, C:0.67, G:0.14, T:0.08
Consensus pattern (15 bp):
CCGCCCCGCATCCGC
Found at i:39445 original size:22 final size:22
Alignment explanation
Indices: 39420--39481 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
39410 GGCGACATCC
39420 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
39442 GTCCCCA----CGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
** *
39460 GTTTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
39482 TTCACGGTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
18 15 0.48
22 16 0.52
ACGTcount: A:0.26, C:0.37, G:0.16, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:39840 original size:19 final size:20
Alignment explanation
Indices: 39816--39865 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
39806 GCGATTCTGT
39816 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCG
**
39835 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
39855 TGTTGCGATTT
1 CGTTGCGATTT
39866 AAAGTTTCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.46
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:41759 original size:20 final size:20
Alignment explanation
Indices: 41734--41857 Score: 161
Period size: 20 Copynumber: 6.5 Consensus size: 20
41724 AGAATAGTTT
41734 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
41754 ACTATCACAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
41774 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
41790 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
41808 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
41828 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
41848 ACTATCGCAA
1 ACTATCGCAA
41858 CGAAAGAATC
Statistics
Matches: 91, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
14 7 0.08
16 4 0.04
17 4 0.04
18 4 0.04
20 72 0.79
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:41808 original size:34 final size:34
Alignment explanation
Indices: 41765--41878 Score: 147
Period size: 34 Copynumber: 3.2 Consensus size: 34
41755 CTATCACAAC
*
41765 GCGAAAATGACTATCGCAACGAGAGAATCGCAAT
1 GCGAAAATGACTATCGCAACGAAAGAATCGCAAT
41799 GCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAAT
1 GCGAAAATGACTATCGCAA--CG-AAA-GA--ATCGCAAT
**
41839 GCGAATTTGACTATCGCAACGAAAGAATCGCAAT
1 GCGAAAATGACTATCGCAACGAAAGAATCGCAAT
41873 GCGAAA
1 GCGAAA
41879 TGAAAATCGC
Statistics
Matches: 70, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
34 32 0.46
36 4 0.06
37 5 0.07
38 4 0.06
40 25 0.36
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (34 bp):
GCGAAAATGACTATCGCAACGAAAGAATCGCAAT
Found at i:41855 original size:74 final size:73
Alignment explanation
Indices: 41734--41895 Score: 243
Period size: 74 Copynumber: 2.2 Consensus size: 73
41724 AGAATAGTTT
*
41734 ACTATCGCAATGCGAAAATGACTATCACAACGCGAAAATGACTATCGCAACGAGAGAATCGCAAT
1 ACTATCGCAATGCGAAAATGACTATCACAACGCGAAAATGACTATCGCAACGAAAGAATCGCAAT
41799 GCGAAAATG
66 GCG-AAATG
* * **
41808 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAATTTGACTATCGCAACGAAAGAATCGCAAT
1 ACTATCGCAATGCGAAAATGACTATCACAACGCGAAAATGACTATCGCAACGAAAGAATCGCAAT
41873 GCGAAATG
66 GCGAAATG
** *
41881 AAAATCGCATTGCGA
1 ACTATCGCAATGCGA
41896 TTCTCTCGTT
Statistics
Matches: 80, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
73 17 0.21
74 63 0.79
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.19
Consensus pattern (73 bp):
ACTATCGCAATGCGAAAATGACTATCACAACGCGAAAATGACTATCGCAACGAAAGAATCGCAAT
GCGAAATG
Found at i:41929 original size:20 final size:20
Alignment explanation
Indices: 41904--41970 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
41894 GATTCTCTCG
*
41904 TTGCGATAGTCAAATTCGTA
1 TTGCGATAGTCAAATTCGCA
**
41924 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
41944 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
41964 TTGCGAT
1 TTGCGAT
41971 TTTGTTGTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:42035 original size:34 final size:34
Alignment explanation
Indices: 41885--42038 Score: 148
Period size: 34 Copynumber: 4.4 Consensus size: 34
41875 GAAATGAAAA
**
41885 TCGCATTGCGATTCTCTCGTTGCGATAGTCAAAT
1 TCGCATTGCGATTCTCTCGTTGCGATAGTCATTT
* *
41919 TCGTATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
1 TCGCATTGCGAT--TC--TCTCG--TTGCGATAGTCATTT
* * * * **
41959 TCGCGTTGCGATTTTGTTGTTGCGATTTTCA-TT
1 TCGCATTGCGATTCTCTCGTTGCGATAGTCATTT
41992 TCGCATTGCGATTCTCTCGTTGCGATAGTCATTT
1 TCGCATTGCGATTCTCTCGTTGCGATAGTCATTT
*
42026 TCGCGTTGCGATT
1 TCGCATTGCGATT
42039 TTAAGTTTCA
Statistics
Matches: 95, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
33 27 0.28
34 35 0.37
36 5 0.05
38 5 0.05
40 23 0.24
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.42
Consensus pattern (34 bp):
TCGCATTGCGATTCTCTCGTTGCGATAGTCATTT
Found at i:42562 original size:18 final size:19
Alignment explanation
Indices: 42523--42564 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
42513 CTCACCTGCC
42523 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
42544 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
42562 ATC
1 ATC
42565 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:44206 original size:34 final size:33
Alignment explanation
Indices: 44118--44211 Score: 125
Period size: 33 Copynumber: 2.8 Consensus size: 33
44108 AAAACAGACT
* ** *
44118 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACAAGAGA
*
44152 ATCGCAATGCGAAATGAAAATCGCAACAAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACAAGAGA
44185 ATCGCAATGCGAAAATGAAAATCGCAA
1 ATCGCAATGCG-AAATGAAAATCGCAA
44212 TGCGAAACTA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.56
34 24 0.44
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACAAGAGA
Found at i:44209 original size:20 final size:19
Alignment explanation
Indices: 44151--44218 Score: 83
Period size: 20 Copynumber: 3.8 Consensus size: 19
44141 GCAACGAGAG
44151 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
44170 AATCGCAA--C-AAGTG--
1 AATCGCAATGCGAAATGAA
44184 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
44204 AATCGCAATGCGAAA
1 AATCGCAATGCGAAA
44219 CTAATTTCGC
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
14 8 0.20
16 5 0.12
17 1 0.02
18 4 0.10
19 11 0.27
20 12 0.29
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:44248 original size:20 final size:20
Alignment explanation
Indices: 44223--44350 Score: 117
Period size: 20 Copynumber: 6.7 Consensus size: 20
44213 GCGAAACTAA
**
44223 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
*
44243 TTTCGCATTGCGAT--TC--
1 TTTCGCGTTGCGATAGTCAT
*
44259 TCTC--GTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* *
44277 TTCCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAT
*
44297 TTCCGCGTTGCGATAGTC-T
1 TTTCGCGTTGCGATAGTCAT
*
44316 TTTCCGTGTTGCGATAGTCAT
1 TTT-CGCGTTGCGATAGTCAT
*
44337 ATTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
44351 TTCCGCGTTG
Statistics
Matches: 89, Mismatches: 11, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
14 7 0.08
16 5 0.06
18 4 0.04
19 2 0.02
20 68 0.76
21 3 0.03
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.40
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:44320 original size:40 final size:40
Alignment explanation
Indices: 44262--44350 Score: 144
Period size: 40 Copynumber: 2.2 Consensus size: 40
44252 GCGATTCTCT
44262 CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCA-ATTCCG
1 CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCATATT-CG
* *
44302 CGTTGCGATAGTCTTTTCCGTGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTCG
44342 CGTTGCGAT
1 CGTTGCGAT
44351 TTCCGCGTTG
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
40 43 0.93
41 3 0.07
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.36
Consensus pattern (40 bp):
CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTCG
Found at i:46809 original size:24 final size:24
Alignment explanation
Indices: 46775--46828 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
46765 CTGAAAAATC
46775 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
46799 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
46823 ATCAAA
1 ATCAAA
46829 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:46842 original size:24 final size:24
Alignment explanation
Indices: 46775--46842 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
46765 CTGAAAAATC
* * *
46775 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
46799 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
46823 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
46843 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:47700 original size:20 final size:20
Alignment explanation
Indices: 47677--47772 Score: 81
Period size: 20 Copynumber: 4.8 Consensus size: 20
47667 TTGCGATAGT
* *
47677 CAGAATCTCGTTGCGATTTA
1 CAGAATCGCATTGCGATTTA
*
47697 CAGATTCGCATTGCGATTTA
1 CAGAATCGCATTGCGATTTA
* *
47717 C-GTATTCACATTGCGATTTA
1 CAG-AATCGCATTGCGATTTA
*
47737 C-GTATTCGCATTGCGATTTA
1 CAG-AATCGCATTGCGATTTA
*
47757 C-GTATTCGCATTGCGA
1 CAG-AATCGCATTGCGA
47773 ATTAGGAAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
19 1 0.01
20 69 0.99
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (20 bp):
CAGAATCGCATTGCGATTTA
Found at i:47731 original size:40 final size:40
Alignment explanation
Indices: 47687--47772 Score: 147
Period size: 40 Copynumber: 2.1 Consensus size: 40
47677 CAGAATCTCG
47687 TTGCGATTTACAG-ATTCGCATTGCGATTTACGTATTCACA
1 TTGCGATTTAC-GTATTCGCATTGCGATTTACGTATTCACA
*
47727 TTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCATTGCGATTTACGTATTCACA
47767 TTGCGA
1 TTGCGA
47773 ATTAGGAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
39 1 0.02
40 43 0.98
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (40 bp):
TTGCGATTTACGTATTCGCATTGCGATTTACGTATTCACA
Found at i:47795 original size:21 final size:21
Alignment explanation
Indices: 47769--47814 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
47759 TATTCGCATT
47769 GCGAATTAGGAAAATCACAAC
1 GCGAATTAGGAAAATCACAAC
* * * *
47790 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCACAAC
47811 GCGA
1 GCGA
47815 TAGTCATAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCACAAC
Found at i:49266 original size:30 final size:31
Alignment explanation
Indices: 49232--49291 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 31
49222 AAGTAATATT
49232 AGATA-TTTTTATAGGTATTAGATACTGTAG
1 AGATATTTTTTATAGGTATTAGATACTGTAG
49262 AGATATTTTTTTATAGGTATTAGATACTGT
1 AGATA-TTTTTTATAGGTATTAGATACTGT
49292 TGTCAAACCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 5 0.18
32 23 0.82
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.47
Consensus pattern (31 bp):
AGATATTTTTTATAGGTATTAGATACTGTAG
Found at i:49938 original size:13 final size:14
Alignment explanation
Indices: 49915--49945 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
49905 ATATCTAATC
49915 TTAATTAATAAATA
1 TTAATTAATAAATA
49929 TTAA-TAATAAATA
1 TTAATTAATAAATA
49942 TTAA
1 TTAA
49946 CCTACTGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTAATTAATAAATA
Found at i:64905 original size:28 final size:31
Alignment explanation
Indices: 64840--64906 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
64830 ATTTTTCTTG
64840 CATAGATTTACTTTCATTCTTTTGAAGGAAA
1 CATAGATTTACTTTCATTCTTTTGAAGGAAA
* **
64871 CACAGATTTACTTT-ATT-TTTTG-ATTAAA
1 CATAGATTTACTTTCATTCTTTTGAAGGAAA
64899 CATAGATT
1 CATAGATT
64907 AGGATGAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 11 0.34
29 5 0.16
30 3 0.09
31 13 0.41
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (31 bp):
CATAGATTTACTTTCATTCTTTTGAAGGAAA
Found at i:64934 original size:49 final size:49
Alignment explanation
Indices: 64862--64955 Score: 170
Period size: 49 Copynumber: 1.9 Consensus size: 49
64852 TTCATTCTTT
64862 TGAAGGAAACACAGATTTACTTTATTTTTTGATTAAACATAGATTAGGA
1 TGAAGGAAACACAGATTTACTTTATTTTTTGATTAAACATAGATTAGGA
* *
64911 TGAAGGATACACAGATTTGCTTTATTTTTTGATTAAACATAGATT
1 TGAAGGAAACACAGATTTACTTTATTTTTTGATTAAACATAGATT
64956 TACTTTAAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (49 bp):
TGAAGGAAACACAGATTTACTTTATTTTTTGATTAAACATAGATTAGGA
Found at i:74264 original size:14 final size:15
Alignment explanation
Indices: 74234--74266 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
74224 AATAGAATAA
74234 ATAAATAAATATTAT
1 ATAAATAAATATTAT
*
74249 ATAAATATAT-TTAT
1 ATAAATAAATATTAT
74263 ATAA
1 ATAA
74267 CTTAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAAATAAATATTAT
Found at i:74354 original size:15 final size:14
Alignment explanation
Indices: 74324--74383 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 14
74314 TATCAAACGT
74324 AATAATAAAA-TAA
1 AATAATAAAATTAA
74337 AATAATAATAATTAA
1 AATAATAA-AATTAA
74352 AATGAA-AGAAATTAA
1 AAT-AATA-AAATTAA
*
74367 AAGTAATAATATTAA
1 AA-TAATAAAATTAA
74382 AA
1 AA
74384 ACTAATGGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
13 8 0.20
14 2 0.05
15 25 0.62
16 5 0.12
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (14 bp):
AATAATAAAATTAA
Found at i:75136 original size:11 final size:11
Alignment explanation
Indices: 75120--75144 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
75110 GAACTTTTGA
75120 TTCCACGGTGG
1 TTCCACGGTGG
75131 TTCCACGGTGG
1 TTCCACGGTGG
75142 TTC
1 TTC
75145 GGCAGCTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.28, G:0.32, T:0.32
Consensus pattern (11 bp):
TTCCACGGTGG
Found at i:75743 original size:3 final size:3
Alignment explanation
Indices: 75730--75798 Score: 59
Period size: 3 Copynumber: 23.0 Consensus size: 3
75720 TATATATATT
* * * * *
75730 TAA TAAA TAA TAA TAA TAA -CA TTA TTA TAA TAA TAA TAA TAT TTA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
75775 TAA TAA TAA TTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
75799 ACGAAAAATT
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
2 1 0.02
3 49 0.92
4 3 0.06
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:75779 original size:15 final size:15
Alignment explanation
Indices: 75757--75798 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
75747 AACATTATTA
75757 TAATAATAATAATATT
1 TAATAATAATAAT-TT
75773 T-ATAATAATAATTT
1 TAATAATAATAATTT
75787 TAATAATAATAA
1 TAATAATAATAA
75799 ACGAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.12
15 21 0.84
16 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAATAATAATAATTT
Found at i:76230 original size:76 final size:76
Alignment explanation
Indices: 75946--76203 Score: 489
Period size: 76 Copynumber: 3.4 Consensus size: 76
75936 GAGGTCTTAA
* *
75946 AAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
76011 AGGCTTTTTGG
66 AGGCTTTTTGG
*
76022 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
76087 AGGCTTTTTGG
66 AGGCTTTTTGG
76098 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
76163 AGGCTTTTTGG
66 AGGCTTTTTGG
76174 AAACATCATGCACTGCAGGACTTACAGATG
1 AAACATCATGCACTGCAGGACTTACAGATG
76204 TAGGAAATAG
Statistics
Matches: 179, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 179 1.00
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.22
Consensus pattern (76 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:79283 original size:114 final size:114
Alignment explanation
Indices: 79083--79308 Score: 371
Period size: 114 Copynumber: 2.0 Consensus size: 114
79073 ACAATCATGC
* * * *
79083 AATTCATCTTTCAATTCTAATGATTGGTTCTGGGGTTCCTACCAAACCAGATCATATAACTCAAA
1 AATTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
*
79148 GAACACTTCCAGAAGATGCTATTAGGTCTCCTTATTTCTGCTATGAGCA
66 GAACACTTCCAGAAGATGCTATTAGGTCTCCTTATTTCTACTATGAGCA
* * *
79197 AATTCATTTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
1 AATTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
*
79262 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAG
66 GAACACTTCCAGAAGATGCTATTAGGTCTCCTTATTTCTACTATGAG
79309 AACGTGGCAC
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 103 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (114 bp):
AATTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGCTATTAGGTCTCCTTATTTCTACTATGAGCA
Found at i:81447 original size:7 final size:7
Alignment explanation
Indices: 81435--81479 Score: 56
Period size: 7 Copynumber: 6.4 Consensus size: 7
81425 TTTCTCCTTT
81435 TTTTTTC
1 TTTTTTC
81442 TTTTTTC
1 TTTTTTC
*
81449 TTTTTGC
1 TTTTTTC
*
81456 TTTTCT-
1 TTTTTTC
81462 TTTTTTC
1 TTTTTTC
81469 TTTCTTTC
1 TTT-TTTC
81477 TTT
1 TTT
81480 ATTTTTTCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
6 5 0.16
7 20 0.62
8 7 0.22
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (7 bp):
TTTTTTC
Found at i:81447 original size:8 final size:8
Alignment explanation
Indices: 81434--81503 Score: 50
Period size: 8 Copynumber: 7.9 Consensus size: 8
81424 ATTTCTCCTT
81434 TTTTTTTC
1 TTTTTTTC
*
81442 TTTTTTCTT
1 TTTTTT-TC
81451 TTTGCTTTTC
1 TTT--TTTTC
81461 TTTTTTTC
1 TTTTTTTC
*
81469 TTTCTTTCTT
1 TTT-TTT-TC
81479 TATTTTTTC
1 T-TTTTTTC
*
81488 TTTTTGTTG
1 TTTTT-TTC
81497 TTTTTTT
1 TTTTTTT
81504 TCAAGTATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
8 20 0.40
9 16 0.32
10 9 0.18
11 5 0.10
ACGTcount: A:0.01, C:0.11, G:0.04, T:0.83
Consensus pattern (8 bp):
TTTTTTTC
Found at i:81452 original size:12 final size:12
Alignment explanation
Indices: 81432--81491 Score: 52
Period size: 13 Copynumber: 4.8 Consensus size: 12
81422 CAATTTCTCC
81432 TTTTT-TTTTCT
1 TTTTTCTTTTCT
81443 TTTTTCTTTTTGCT
1 TTTTTC-TTTT-CT
*
81457 TTTCTTTTTTTCT
1 TTT-TTCTTTTCT
*
81470 TTCTTTC-TTTAT
1 TT-TTTCTTTTCT
81482 TTTTTCTTTT
1 TTTTTCTTTT
81492 TGTTGTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
11 9 0.22
12 9 0.22
13 10 0.25
14 10 0.25
15 2 0.05
ACGTcount: A:0.02, C:0.13, G:0.02, T:0.83
Consensus pattern (12 bp):
TTTTTCTTTTCT
Found at i:81459 original size:20 final size:19
Alignment explanation
Indices: 81432--81505 Score: 73
Period size: 19 Copynumber: 3.9 Consensus size: 19
81422 CAATTTCTCC
81432 TTTT-TTTTTCTTTTTTCT
1 TTTTGTTTTTCTTTTTTCT
*
81450 TTTTGCTTTTCTTTTTTTCT
1 TTTTGTTTTTC-TTTTTTCT
* *
81470 TTCTT-TCTTTATTTTTTCT
1 TT-TTGTTTTTCTTTTTTCT
*
81489 TTTTGTTGTT-TTTTTTC
1 TTTTGTTTTTCTTTTTTC
81506 AAGTATAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
18 13 0.28
19 18 0.39
20 13 0.28
21 2 0.04
ACGTcount: A:0.01, C:0.12, G:0.04, T:0.82
Consensus pattern (19 bp):
TTTTGTTTTTCTTTTTTCT
Found at i:81469 original size:27 final size:26
Alignment explanation
Indices: 81434--81502 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 26
81424 ATTTCTCCTT
81434 TTTTTTTCTTTTTTCTTT-TTGCTTTTC
1 TTTTTTTCTTTTTTCTTTATT--TTTTC
81461 TTTTTTTCTTTCTTTCTTTATTTTTTC
1 TTTTTTTCTTT-TTTCTTTATTTTTTC
*
81488 TTTTTGTTGTTTTTT
1 TTTTT-TTCTTTTTT
81503 TTCAAGTATA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
27 24 0.63
28 12 0.32
29 2 0.05
ACGTcount: A:0.01, C:0.12, G:0.04, T:0.83
Consensus pattern (26 bp):
TTTTTTTCTTTTTTCTTTATTTTTTC
Found at i:88802 original size:3 final size:3
Alignment explanation
Indices: 88794--88865 Score: 101
Period size: 3 Copynumber: 24.0 Consensus size: 3
88784 TATATATATT
*
88794 TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TTAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
**
88839 TAA TAA TAA TAA TTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
88866 ACGAAAAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
2 2 0.03
3 56 0.92
4 3 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Done.