Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007066.1 Hibiscus syriacus cultivar Beakdansim tig00018355_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: 60868
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:5342 original size:6 final size:6
Alignment explanation
Indices: 5331--5378 Score: 96
Period size: 6 Copynumber: 8.0 Consensus size: 6
5321 TGGTATGGTT
5331 CAATGC CAATGC CAATGC CAATGC CAATGC CAATGC CAATGC CAATGC
1 CAATGC CAATGC CAATGC CAATGC CAATGC CAATGC CAATGC CAATGC
5379 AAAGTTGCTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.33, C:0.33, G:0.17, T:0.17
Consensus pattern (6 bp):
CAATGC
Found at i:8569 original size:36 final size:36
Alignment explanation
Indices: 8529--8598 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
8519 TCCTATAAAT
*
8529 ATACATATCCTCTAAATTAAGTCGAATTTTATACTC
1 ATACATATCCTCTAAATTAAGTCGAATGTTATACTC
* *
8565 ATACATATCTTTTAAATTAAGTCGAATGTTATAC
1 ATACATATCCTCTAAATTAAGTCGAATGTTATAC
8599 ACTGAATGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.40
Consensus pattern (36 bp):
ATACATATCCTCTAAATTAAGTCGAATGTTATACTC
Found at i:10308 original size:20 final size:20
Alignment explanation
Indices: 10279--10316 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
10269 AAGGTTCAAG
10279 TATCGATACTGGATGAACAA
1 TATCGATACTGGATGAACAA
*
10299 TATCGTTACTGGATGAAC
1 TATCGATACTGGATGAAC
10317 TAGGATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (20 bp):
TATCGATACTGGATGAACAA
Found at i:16200 original size:3 final size:3
Alignment explanation
Indices: 16183--16225 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
16173 TATTATCATT
16183 ATA A-A ATA TATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
16226 AGTATTGTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:17935 original size:3 final size:3
Alignment explanation
Indices: 17927--17959 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
17917 AAAATTTAAT
17927 TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
17960 CGGACGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:19103 original size:15 final size:15
Alignment explanation
Indices: 19085--19126 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
19075 AAATATATTT
19085 TTTC-TTAATAAAACA
1 TTTCATTAATAAAA-A
*
19100 TTTCATTTATAAAAA
1 TTTCATTAATAAAAA
*
19115 TATCATTAATAA
1 TTTCATTAATAA
19127 GTTATTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.43
Consensus pattern (15 bp):
TTTCATTAATAAAAA
Found at i:19322 original size:13 final size:13
Alignment explanation
Indices: 19304--19336 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
19294 AATAGTTAAA
19304 TTTTAAAC-TGCAC
1 TTTTAAACAT-CAC
19317 TTTTAAACATCAC
1 TTTTAAACATCAC
19330 TTTTAAA
1 TTTTAAA
19337 AGTTATTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 18 0.95
14 1 0.05
ACGTcount: A:0.36, C:0.18, G:0.03, T:0.42
Consensus pattern (13 bp):
TTTTAAACATCAC
Found at i:22022 original size:2 final size:2
Alignment explanation
Indices: 22015--22063 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
22005 TTTGGTACAT
22015 TA TA TA TA TA TA TA TA TA 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
22057 TA TA TA T
1 TA TA TA T
22064 CATCCCTTCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:23236 original size:33 final size:33
Alignment explanation
Indices: 23199--23267 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
23189 AAAAATATCC
23199 TATAAAGTAACTAATAATAAAAAATTAAATAAA
1 TATAAAGTAACTAATAATAAAAAATTAAATAAA
** * * * *
23232 TATAATTTAACTAATATTAACAAATTATATATA
1 TATAAAGTAACTAATAATAAAAAATTAAATAAA
23265 TAT
1 TAT
23268 GCGTATAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.36
Consensus pattern (33 bp):
TATAAAGTAACTAATAATAAAAAATTAAATAAA
Found at i:24990 original size:18 final size:18
Alignment explanation
Indices: 24967--25011 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
24957 AGTAGCTAAA
24967 CGGGTCGGGTCTTGTAAC
1 CGGGTCGGGTCTTGTAAC
24985 CGGGTCGGGTCTTGTAAC
1 CGGGTCGGGTCTTGTAAC
*
25003 CGAGTCGGG
1 CGGGTCGGG
25012 ATCCGGGTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.11, C:0.22, G:0.42, T:0.24
Consensus pattern (18 bp):
CGGGTCGGGTCTTGTAAC
Found at i:25127 original size:3 final size:3
Alignment explanation
Indices: 25119--25149 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
25109 GGCATGCATA
25119 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
25150 TTTATATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:25495 original size:24 final size:24
Alignment explanation
Indices: 25463--25511 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
25453 TTACTGATGA
25463 CCCGAAGGATTTAATCATCTTGCT
1 CCCGAAGGATTTAATCATCTTGCT
25487 CCCGAAGGATTTAATCATCTTGCT
1 CCCGAAGGATTTAATCATCTTGCT
25511 C
1 C
25512 GAAAGACTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (24 bp):
CCCGAAGGATTTAATCATCTTGCT
Found at i:25529 original size:66 final size:66
Alignment explanation
Indices: 25421--25552 Score: 201
Period size: 66 Copynumber: 2.0 Consensus size: 66
25411 CTTAAGATGG
* * **
25421 CCCGAAGGACTTAATCATCATGTTTGAAAGACTTACTGATGACCCGAAGGATTTAATCATCTTGC
1 CCCGAAGGACTTAATCATCATGCTCGAAAGACTTACAAATGACCCGAAGGATTTAATCATCTTGC
25486 T
66 T
* * *
25487 CCCGAAGGATTTAATCATCTTGCTCGAAAGACTTACAAATGACCCGAATGATTTAATCATCTTGC
1 CCCGAAGGACTTAATCATCATGCTCGAAAGACTTACAAATGACCCGAAGGATTTAATCATCTTGC
25552 T
66 T
25553 TGAAAGACTT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (66 bp):
CCCGAAGGACTTAATCATCATGCTCGAAAGACTTACAAATGACCCGAAGGATTTAATCATCTTGC
T
Found at i:25655 original size:42 final size:42
Alignment explanation
Indices: 25487--25653 Score: 226
Period size: 42 Copynumber: 4.0 Consensus size: 42
25477 TCATCTTGCT
*
25487 CCCGAAGGATTTAATCATCTTGCTCGAAAGACTTACAAATGA
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACAAATGA
* * *
25529 CCCGAATGATTTAATCATCTTGCTTGAAAGACTTACAAATGA
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACAAATGA
* * ** *
25571 CCCGAAGGATTTAATCATCAAGCTCAAAAGACTTACTGATGG
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACAAATGA
* * *
25613 CCCGAAGGATTTCATCATCATGCTCGAAATACTTACTAATG
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACAAATG
25654 GCATTTACTG
Statistics
Matches: 110, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 110 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.28
Consensus pattern (42 bp):
CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACAAATGA
Found at i:25771 original size:42 final size:42
Alignment explanation
Indices: 25712--26032 Score: 196
Period size: 42 Copynumber: 7.8 Consensus size: 42
25702 ATTACCCAAA
* *
25712 ATCATCATGATCAAAAGACTTACTGATGTCCCGAAGGACTTC
1 ATCATCATGCTCGAAAGACTTACTGATGTCCCGAAGGACTTC
**
25754 ATCATCATGCTCGAAAGACTTACTGATG----GATTTG-CTTC
1 ATCATCATGCTCGAAAGACTTACTGATGTCCCGA-AGGACTTC
* * ** * *
25792 A-CTACTCTTCGGT-G-AAGACTTACAAAT-TACCCGAAGGATTTA
1 ATC-A-TCAT-GCTCGAAAGACTTACTGATGT-CCCGAAGGACTTC
*
25834 ATCATCATGCTCGAAAGACTTATTGATAG-CCCGAAGGACTTC
1 ATCATCATGCTCGAAAGACTTACTGAT-GTCCCGAAGGACTTC
* **
25876 CTCATCATGCTCGAAAGACTTACTGATGT----ATTTG-CTTC
1 ATCATCATGCTCGAAAGACTTACTGATGTCCCGA-AGGACTTC
* * * * *
25914 A-CTACTCTTCGGT-G-AAGGCTTA-TAAAT-TACCCGAAGGATTTC
1 ATC-A-TCAT-GCTCGAAAGACTTACT-GATGT-CCCGAAGGACTTC
* * *
25956 ATCATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTA
1 ATCATCATGCTCGAAAGACTTACTGATGTCCCGAAGGACTTC
25998 ATCATCATGCTCGAAAGACTTACTGATGTCCCGAA
1 ATCATCATGCTCGAAAGACTTACTGATGTCCCGAA
26033 TAACTTATAA
Statistics
Matches: 209, Mismatches: 38, Indels: 64
0.67 0.12 0.21
Matches are distributed among these distances:
37 4 0.02
38 34 0.16
39 10 0.05
40 8 0.04
41 11 0.05
42 139 0.67
43 3 0.01
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (42 bp):
ATCATCATGCTCGAAAGACTTACTGATGTCCCGAAGGACTTC
Found at i:25895 original size:22 final size:22
Alignment explanation
Indices: 25835--25899 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
25825 AAGGATTTAA
*
25835 TCATCATGCTCGAAAGACTTAT
1 TCATCATGCTCGAAAGACTTAC
* * * *
25857 TGAT-A-GCCCGAAGGACTTCC
1 TCATCATGCTCGAAAGACTTAC
25877 TCATCATGCTCGAAAGACTTAC
1 TCATCATGCTCGAAAGACTTAC
25899 T
1 T
25900 GATGTATTTG
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
20 14 0.44
21 2 0.06
22 16 0.50
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (22 bp):
TCATCATGCTCGAAAGACTTAC
Found at i:26026 original size:122 final size:121
Alignment explanation
Indices: 25658--26025 Score: 543
Period size: 122 Copynumber: 3.1 Consensus size: 121
25648 CTAATGGCAT
* * *
25658 TTACTGATGGATTTGTTTCACTACTCTTCGGTTAATGCTTACAAATTACCC-AA--A---ATCAT
1 TTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCCGAAGGATTTATCAT
* * *
25717 CATGATCAAAAGACTTACTGATGTCCCGAAGGACTTCATCATCATGCTCGAAAGAC
66 CATGCTCGAAAGACTTACTGATGACCCGAAGGACTTCATCATCATGCTCGAAAGAC
*
25773 TTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGACTTACAAATTACCCGAAGGATTTAATCA
1 TTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCCGAAGGATTT-ATCA
* *
25838 TCATGCTCGAAAGACTTATTGAT-AGCCCGAAGGACTTCCTCATCATGCTCGAAAGAC
65 TCATGCTCGAAAGACTTACTGATGA-CCCGAAGGACTTCATCATCATGCTCGAAAGAC
* *
25895 TTACTGATGTATTTGCTTCACTACTCTTCGGTGAAGGCTTATAAATTACCCGAAGGATTTCATCA
1 TTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCCGAAGGATTT-ATCA
* *
25960 TCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTAATCATCATGCTCGAAAGAC
65 TCATGCTCGAAAGACTTACTGATGACCCGAAGGACTTCATCATCATGCTCGAAAGAC
26017 TTACTGATG
1 TTACTGATG
26026 TCCCGAATAA
Statistics
Matches: 227, Mismatches: 17, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
115 47 0.21
116 2 0.01
118 1 0.00
122 176 0.78
123 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (121 bp):
TTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCCGAAGGATTTATCAT
CATGCTCGAAAGACTTACTGATGACCCGAAGGACTTCATCATCATGCTCGAAAGAC
Found at i:26247 original size:42 final size:41
Alignment explanation
Indices: 26166--26266 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 41
26156 AGGTCTTATG
* * * *
26166 GATGGCCCGAAGGACTTATCATCCTGCTCAAAAGGCTTACA
1 GATGACCCGAAGGACTTAACATCATGCTCAAAAGACTTACA
* * *
26207 GATGACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGACTT-AACATCATGCTCAAAAGACTTACA
26249 GATGACCCGAAGGACTTA
1 GATGACCCGAAGGACTTA
26267 CCAATTTTAG
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 16 0.31
42 35 0.69
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.22
Consensus pattern (41 bp):
GATGACCCGAAGGACTTAACATCATGCTCAAAAGACTTACA
Found at i:26264 original size:20 final size:20
Alignment explanation
Indices: 26197--26267 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
26187 TCCTGCTCAA
*
26197 AAGG-CTTACAGATGACCCG
1 AAGGACTTACTGATGACCCG
* * *
26216 AAGGATTTAAACATCATG-CTCG
1 AAGGACTT--AC-TGATGACCCG
*
26238 AAAGACTTACTGATGACCCG
1 AAGGACTTACTGATGACCCG
26258 AAGGACTTAC
1 AAGGACTTAC
26268 CAATTTTAGA
Statistics
Matches: 38, Mismatches: 9, Indels: 9
0.68 0.16 0.16
Matches are distributed among these distances:
19 8 0.21
20 16 0.42
22 11 0.29
23 3 0.08
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (20 bp):
AAGGACTTACTGATGACCCG
Found at i:32348 original size:6 final size:6
Alignment explanation
Indices: 32336--32371 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
32326 AAAAAATAAG
* *
32336 AATGCA GATGCA GATGCA AATGCA AATGCA AATGCA
1 AATGCA AATGCA AATGCA AATGCA AATGCA AATGCA
32372 CGAGGTGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.17
Consensus pattern (6 bp):
AATGCA
Found at i:34589 original size:33 final size:33
Alignment explanation
Indices: 34552--34620 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
34542 AAAAATATCC
34552 TATAAAGTAACTAATAATAAAAAATTAAATAAA
1 TATAAAGTAACTAATAATAAAAAATTAAATAAA
** * * * *
34585 TATAATTTAACTAATATTAACAAATTATATATA
1 TATAAAGTAACTAATAATAAAAAATTAAATAAA
34618 TAT
1 TAT
34621 GCGTATAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.36
Consensus pattern (33 bp):
TATAAAGTAACTAATAATAAAAAATTAAATAAA
Found at i:36345 original size:18 final size:18
Alignment explanation
Indices: 36322--36366 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
36312 AGTAGCTAAA
36322 CGGGTCGGGTCTTGTAAC
1 CGGGTCGGGTCTTGTAAC
36340 CGGGTCGGGTCTTGTAAC
1 CGGGTCGGGTCTTGTAAC
*
36358 CGAGTCGGG
1 CGGGTCGGG
36367 ATCCGGGTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.11, C:0.22, G:0.42, T:0.24
Consensus pattern (18 bp):
CGGGTCGGGTCTTGTAAC
Found at i:38381 original size:47 final size:47
Alignment explanation
Indices: 38320--38771 Score: 584
Period size: 47 Copynumber: 9.6 Consensus size: 47
38310 TAATTTTCAC
* * *
38320 TTATGGTATCCTTTCCTGCCTTATTGCATCCGTTCATGCATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAG
* * *
38367 TTATGGCATCCTTTCATGCCTTAATACATCCATTCATGTATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAG
* * * * * *
38414 TTATGGCATCCTTTCATGCCTTAATGTATACGTTCCTTCATTTTCAA
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAG
* *
38461 TTATGGCATCCTTTCATGCCATAATGCATTCGTTCATGCATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAG
*
38508 TTATGGCATCCTTTCATGCCTTAATAG-ATCCATTCATGCATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAAT-GCATCCGTTCATGCATTTTTAG
* * * *
38555 TTATGACATCCTTTCATGCCTTAATGCACCCATTCAAT-AATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTC-ATGCATTTTTAG
* *
38602 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTCAA
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAG
**
38649 TTATGGCATCCTTTCATGCCTTAATGCATCAATTCATGCATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAG
* * * * *
38696 TTATGGCATCTTTTCATGCCTTAATGAATCCGTTCATTCATTTTCAT
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAG
* * *
38743 TTATGGAATTCTTTCATGCCAATAATGCA
1 TTATGGCATCCTTTCATGCC-TTAATGCA
38772 CCATATGCAT
Statistics
Matches: 350, Mismatches: 50, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
46 3 0.01
47 338 0.97
48 9 0.03
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (47 bp):
TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAG
Found at i:38382 original size:27 final size:27
Alignment explanation
Indices: 38340--38432 Score: 83
Period size: 27 Copynumber: 3.7 Consensus size: 27
38330 CTTTCCTGCC
* *
38340 TTATTGCATCCGTTCATGCATTTTTAG
1 TTATGGCATCCTTTCATGCATTTTTAG
*
38367 TTATGGCATCCTTTCATGC---CTTA-
1 TTATGGCATCCTTTCATGCATTTTTAG
* * *
38390 --AT-ACATCCATTCATGTATTTTTAG
1 TTATGGCATCCTTTCATGCATTTTTAG
38414 TTATGGCATCCTTTCATGC
1 TTATGGCATCCTTTCATGC
38433 CTTAATGTAT
Statistics
Matches: 49, Mismatches: 10, Indels: 14
0.67 0.14 0.19
Matches are distributed among these distances:
20 11 0.22
21 2 0.04
23 3 0.06
24 3 0.06
26 2 0.04
27 28 0.57
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.45
Consensus pattern (27 bp):
TTATGGCATCCTTTCATGCATTTTTAG
Found at i:38566 original size:141 final size:141
Alignment explanation
Indices: 38312--38771 Score: 652
Period size: 141 Copynumber: 3.3 Consensus size: 141
38302 TTATTCGTTA
* * * * *
38312 ATTTTCACTTATGGTATCCTTTCCTGCCTTATTGCATCCGTTCATGCATTTTTAGTTATGGCATC
1 ATTTTCAATTATGGCATCCTTTCATGCCATAATGCATCCGTTCATGCATTTTTAGTTATGGCATC
* * *
38377 CTTTCATGCCTTAATACATCCATTCATGTATTTTTAGTTATGGCATCCTTTCATGCCTTAATGTA
66 CTTTCATGCCTTAATAGATCCATTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGAA
* *
38442 TACGTTCCTTC
131 TCCGTTCATTC
*
38453 ATTTTCAATTATGGCATCCTTTCATGCCATAATGCATTCGTTCATGCATTTTTAGTTATGGCATC
1 ATTTTCAATTATGGCATCCTTTCATGCCATAATGCATCCGTTCATGCATTTTTAGTTATGGCATC
* *
38518 CTTTCATGCCTTAATAGATCCATTCATGCATTTTTAGTTATGACATCCTTTCATGCCTTAATGCA
66 CTTTCATGCCTTAATAGATCCATTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGAA
* * * *
38583 CCCATTCAATA
131 TCCGTTCATTC
* * * * *
38594 ATTTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTCAATTATGGCATC
1 ATTTTCAATTATGGCATCCTTTCATGCCATAATGCATCCGTTCATGCATTTTTAGTTATGGCATC
* *
38659 CTTTCATGCCTTAAT-GCATCAATTCATGCATTTTTAGTTATGGCATCTTTTCATGCCTTAATGA
66 CTTTCATGCCTTAATAG-ATCCATTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGA
38723 ATCCGTTCATTC
130 ATCCGTTCATTC
* * *
38735 ATTTTCATTTATGGAATTCTTTCATGCCAATAATGCA
1 ATTTTCAATTATGGCATCCTTTCATGCC-ATAATGCA
38772 CCATATGCAT
Statistics
Matches: 282, Mismatches: 35, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
140 1 0.00
141 274 0.97
142 7 0.02
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (141 bp):
ATTTTCAATTATGGCATCCTTTCATGCCATAATGCATCCGTTCATGCATTTTTAGTTATGGCATC
CTTTCATGCCTTAATAGATCCATTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGAA
TCCGTTCATTC
Found at i:38632 original size:20 final size:20
Alignment explanation
Indices: 38607--38678 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 20
38597 TTTAGTTATG
38607 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
* *
38627 GCATCCGTTCATGCATTTTCAATTAT
1 GCATCCTTTCATGC--CTT--A--AT
38653 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
38674 GCATC
1 GCATC
38679 AATTCATGCA
Statistics
Matches: 41, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
20 18 0.44
21 2 0.05
22 2 0.05
23 1 0.02
24 1 0.02
25 2 0.05
26 2 0.05
27 13 0.32
ACGTcount: A:0.21, C:0.28, G:0.12, T:0.39
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:38900 original size:45 final size:45
Alignment explanation
Indices: 38799--38906 Score: 162
Period size: 45 Copynumber: 2.4 Consensus size: 45
38789 TTATATCAAG
* *
38799 AATGCACCCATATGCATTTCAGCTATGTCATCCTTTCATGCCAAT
1 AATGCACCCATATGCATTTCAGCTATGGCATCCTTTCAAGCCAAT
**
38844 AATTTACCCATATGCATTTCAGCTATGGCATCCTTTCAAGCCAAT
1 AATGCACCCATATGCATTTCAGCTATGGCATCCTTTCAAGCCAAT
* *
38889 AATGCATCCATATACATT
1 AATGCACCCATATGCATT
38907 ATTCTTTTAT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.33
Consensus pattern (45 bp):
AATGCACCCATATGCATTTCAGCTATGGCATCCTTTCAAGCCAAT
Found at i:43461 original size:29 final size:29
Alignment explanation
Indices: 43374--43443 Score: 131
Period size: 29 Copynumber: 2.4 Consensus size: 29
43364 TCCATTATTA
*
43374 TTTTACTCAACAGTTTTTGACCTTTCATC
1 TTTTACTCAACAGTTTTTGACCTTTTATC
43403 TTTTACTCAACAGTTTTTGACCTTTTATC
1 TTTTACTCAACAGTTTTTGACCTTTTATC
43432 TTTTACTCAACA
1 TTTTACTCAACA
43444 TTGTTTAACT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.23, C:0.23, G:0.06, T:0.49
Consensus pattern (29 bp):
TTTTACTCAACAGTTTTTGACCTTTTATC
Found at i:43996 original size:47 final size:47
Alignment explanation
Indices: 43921--44360 Score: 648
Period size: 47 Copynumber: 9.4 Consensus size: 47
43911 TAATTTTCAC
*
43921 TTATGGCATCCTTT-ATTGCCTTATTGCATCCGTTCATGCATTTTTAG
1 TTATGGCATCCTTTCA-TGCCTTAATGCATCCGTTCATGCATTTTTAG
* **
43968 TTATGGTATCCTTTCATGAATTAATGCATCCGTTCATGCATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAG
* * * *
44015 TTATGGCATCATTTCATGCCTTAATGCATCTGTTCATGCATTTTCAA
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAG
* *
44062 TTACGGTATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAG
44109 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAG
* *
44156 TTATGGCATCCTTTCATGCCTTAATGCATCCATTCATGCATTTTTAA
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAG
** * *
44203 TTATGAAATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTCAA
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAG
* *
44250 TTATGGCATCCTTTCATTCCTTAATGCATTCGTTCATGCATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAG
* * * * *
44297 TTATAGCATCATTTCATGCCTTAATGCATCCGTCCATGCATTTTCAA
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAG
*
44344 TTATGGCATTCTTTCAT
1 TTATGGCATCCTTTCAT
44361 TCCAATAATG
Statistics
Matches: 351, Mismatches: 41, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
47 350 1.00
48 1 0.00
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.43
Consensus pattern (47 bp):
TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAG
Found at i:44097 original size:20 final size:20
Alignment explanation
Indices: 44069--44241 Score: 85
Period size: 20 Copynumber: 7.6 Consensus size: 20
44059 CAATTACGGT
44069 ATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCCTTAATGC
* *
44089 ATCCGTTCATGCATTTTTAGTTATGGC
1 ATCCTTTCATGC---CTTA---AT-GC
44116 ATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCCTTAATGC
* *
44136 ATCCGTTCATGCATTTTTAGTTATGGC
1 ATCCTTTCATGC---CTTA---AT-GC
44163 ATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCCTTAATGC
* * *
44183 ATCCATTCATGCATTTTTAATTATGAA
1 ATCCTTTCATGC---CTT-A--ATG-C
44210 ATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCCTTAATGC
*
44230 ATCCGTTCATGC
1 ATCCTTTCATGC
44242 ATTTTCAATT
Statistics
Matches: 117, Mismatches: 15, Indels: 42
0.67 0.09 0.24
Matches are distributed among these distances:
20 48 0.41
21 7 0.06
23 9 0.08
24 9 0.08
26 7 0.06
27 37 0.32
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.42
Consensus pattern (20 bp):
ATCCTTTCATGCCTTAATGC
Found at i:44389 original size:34 final size:34
Alignment explanation
Indices: 44351--44418 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
44341 CAATTATGGC
*
44351 ATTCTTTCAT-TCCAATAATGCACCCATATGCATT
1 ATTCTTTCATGT-CAAGAATGCACCCATATGCATT
* * *
44385 ATTCTTTTATGTCGAGAATGCACTCATATGCATT
1 ATTCTTTCATGTCAAGAATGCACCCATATGCATT
44419 CAGCTATGGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 28 0.97
35 1 0.03
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.40
Consensus pattern (34 bp):
ATTCTTTCATGTCAAGAATGCACCCATATGCATT
Found at i:44436 original size:78 final size:79
Alignment explanation
Indices: 44345--44551 Score: 301
Period size: 78 Copynumber: 2.6 Consensus size: 79
44335 CATTTTCAAT
* * * *
44345 TATGGCATTCTTTCATTCCAATAATGCACCCATATGCATTATTCTTTTATG-TCGAGAATGCACT
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCT-AAGAATGCACC
*
44409 CATATGCA-TTCAGC
65 CATATCCATTTCAGC
* *
44423 TATGGCATCCTTTCATGCCAATAATGCACCCATGTGAATTATTCTTTTATGCTAAGAATGCACCC
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCTAAGAATGCACCC
44488 ATATCCATTTCAGC
66 ATATCCATTTCAGC
* * *
44502 TATGTCATCTTTTCATGCCAATAATGCACCTATATGCATTATTCTTTTAT
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTAT
44552 TCATTCATTC
Statistics
Matches: 115, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
78 63 0.55
79 52 0.45
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (79 bp):
TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCTAAGAATGCACCC
ATATCCATTTCAGC
Found at i:45004 original size:22 final size:20
Alignment explanation
Indices: 44955--45006 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
44945 AAGCTCAATA
*
44955 GTATCGATACTACTACCTTG
1 GTATCGATACTACTAACTTG
* *
44975 GTACCGATACTTCTATACTATG
1 GTATCGATACTACTA-ACT-TG
44997 GTATCGATAC
1 GTATCGATAC
45007 CCCATTTTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 13 0.50
21 2 0.08
22 11 0.42
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (20 bp):
GTATCGATACTACTAACTTG
Found at i:45032 original size:18 final size:19
Alignment explanation
Indices: 44995--45032 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
44985 TTCTATACTA
*
44995 TGGTATCGATACCCCATTT
1 TGGTATCGATACCACATTT
45014 TGGTATCGATA-CACATTT
1 TGGTATCGATACCACATTT
45032 T
1 T
45033 AGGTTTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (19 bp):
TGGTATCGATACCACATTT
Found at i:45158 original size:94 final size:96
Alignment explanation
Indices: 44968--45175 Score: 253
Period size: 94 Copynumber: 2.2 Consensus size: 96
44958 TCGATACTAC
* * * * ***
44968 TACCTTGGTACCGATACT-TCTATACTATGGTATCGATACCCCATTTTGGTATCGATACACATTT
1 TACCATGGTATCGATACTATCTATACTATAGTACCGATACCCCATTCCAGTATCGATACACATTT
* * * *
45032 TAGGTTTGATATTGCCTGGTATTGATACCCT
66 TAGATTCGATATTGCCTGATATCGATACCCT
*
45063 TACCATGGTATGGATACTATC-ATACTATAGTACCGATACCCC-TTCCAGTATCGATAC-CAATT
1 TACCATGGTATCGATACTATCTATACTATAGTACCGATACCCCATTCCAGTATCGATACAC-ATT
* *
45125 TTAGATTCGATGTTTCCTGATATCGATACCCT
65 TTAGATTCGATATTGCCTGATATCGATACCCT
45157 TACCATGGTATCGATACTA
1 TACCATGGTATCGATACTA
45176 CCTCATCGAT
Statistics
Matches: 96, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
93 1 0.01
94 59 0.61
95 34 0.35
96 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (96 bp):
TACCATGGTATCGATACTATCTATACTATAGTACCGATACCCCATTCCAGTATCGATACACATTT
TAGATTCGATATTGCCTGATATCGATACCCT
Found at i:53955 original size:23 final size:22
Alignment explanation
Indices: 53908--53961 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
53898 AACATCAAAA
*
53908 TTAAAAAATACAAAAATTCAAT
1 TTAAAAAATACAAAAAATCAAT
*
53930 TTAAAAATTCACAAAAAAT-AATT
1 TTAAAAAAT-ACAAAAAATCAA-T
53953 TTAAAAAAT
1 TTAAAAAAT
53962 TACCTTGCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.37
23 17 0.63
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (22 bp):
TTAAAAAATACAAAAAATCAAT
Found at i:56061 original size:25 final size:26
Alignment explanation
Indices: 56013--56064 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
56003 ACAAAATTAT
* **
56013 TTTTGGATTTTTTTATTTTTATTAAA
1 TTTTGAATTTTTTTATTTAAATTAAA
56039 TTTTGAATTTTTTTA-TTAAATTAAA
1 TTTTGAATTTTTTTATTTAAATTAAA
56064 T
1 T
56065 GGCAGAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (26 bp):
TTTTGAATTTTTTTATTTAAATTAAA
Found at i:56185 original size:18 final size:18
Alignment explanation
Indices: 56158--56208 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
56148 TGTAAAAAAC
56158 CAAA-AATAAAATATTTA
1 CAAATAATAAAATATTTA
*
56175 CAAATAATAAAAAATTTA
1 CAAATAATAAAATATTTA
* *
56193 GAAGT-ATAAAATATTT
1 CAAATAATAAAATATTT
56209 TTTAAATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (18 bp):
CAAATAATAAAATATTTA
Done.