Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001786.1 Hibiscus syriacus cultivar Beakdansim tig00003605_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: 49924
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1716 original size:29 final size:29
Alignment explanation
Indices: 1654--1718 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 29
1644 TAATATCCCA
*
1654 AAATTTTGAAAGTTTAGGGGATAAAGTAT
1 AAATTTTGAAAGTTTAGGGGATAAAATAT
1683 AAATTTTAGAAAAGTTTA-GGGA-AAAATA-
1 AAATTTT-G-AAAGTTTAGGGGATAAAATAT
1711 ATAATTTT
1 A-AATTTT
1719 CAAAATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
28 1 0.03
29 18 0.56
30 5 0.16
31 8 0.25
ACGTcount: A:0.46, C:0.00, G:0.18, T:0.35
Consensus pattern (29 bp):
AAATTTTGAAAGTTTAGGGGATAAAATAT
Found at i:2903 original size:19 final size:20
Alignment explanation
Indices: 2860--2904 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2850 GACTATGTTG
*
2860 GAAATTAATGTTAGAGTGCT
1 GAAATTAATGTTAGAATGCT
*
2880 GAAATTGATGTTAGAATG-T
1 GAAATTAATGTTAGAATGCT
2899 GAAATT
1 GAAATT
2905 TGGTCATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (20 bp):
GAAATTAATGTTAGAATGCT
Found at i:4433 original size:30 final size:30
Alignment explanation
Indices: 4397--4455 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
4387 TGTGGATTGG
4397 CACTGTAGTGTGTAAGGACACTTAGTGCAA
1 CACTGTAGTGTGTAAGGACACTTAGTGCAA
4427 CACTGTAGTGTGTAAGGACACTTAGTGCA
1 CACTGTAGTGTGTAAGGACACTTAGTGCA
4456 TATGGTAAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (30 bp):
CACTGTAGTGTGTAAGGACACTTAGTGCAA
Found at i:4935 original size:15 final size:16
Alignment explanation
Indices: 4915--4947 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4905 GTATGCAAAT
4915 TATT-AATATAGTTAG
1 TATTAAATATAGTTAG
*
4930 TATTAAATATGGTTAG
1 TATTAAATATAGTTAG
4946 TA
1 TA
4948 GTATGAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.45
Consensus pattern (16 bp):
TATTAAATATAGTTAG
Found at i:7696 original size:6 final size:6
Alignment explanation
Indices: 7685--7710 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
7675 AGGCTTTGCC
7685 TATTCA TATTCA TATTCA TATTCA TA
1 TATTCA TATTCA TATTCA TATTCA TA
7711 ACCAAATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (6 bp):
TATTCA
Found at i:8395 original size:76 final size:76
Alignment explanation
Indices: 8262--8415 Score: 236
Period size: 76 Copynumber: 2.0 Consensus size: 76
8252 TCCGATCGAA
* *
8262 TCGAGTCGAAATTTTGAGTTATTCGAGTTGACGACTCTTATTTTACAACTCGAAGTTGACTTTAA
1 TCGAGTCAAAATTTTGAGTTATTCGAGTTGACGACTCTTATTTTACAACCCGAAGTTGACTTTAA
*
8327 TTTTTTTCAAG
66 ATTTTTTCAAG
* ** *
8338 TCGAGTCAAAATTTTGAGTTATTTGAGTTGACGGGTCTTATTTTACAACCCGGAGTTGACTTTAA
1 TCGAGTCAAAATTTTGAGTTATTCGAGTTGACGACTCTTATTTTACAACCCGAAGTTGACTTTAA
*
8403 ATTTTTTCGAG
66 ATTTTTTCAAG
8414 TC
1 TC
8416 AAGTTGAGTT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
76 70 1.00
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (76 bp):
TCGAGTCAAAATTTTGAGTTATTCGAGTTGACGACTCTTATTTTACAACCCGAAGTTGACTTTAA
ATTTTTTCAAG
Found at i:11904 original size:76 final size:77
Alignment explanation
Indices: 11778--11930 Score: 254
Period size: 76 Copynumber: 2.0 Consensus size: 77
11768 GGTAACAGTC
*
11778 TCTCTTATATAATTACCCTCATCGTAAGAATCTTCTGCAACGTTTTACTCATTCAATAATTATGA
1 TCTCTAATATAATTACCCTCATCGTAAGAATCTTCTGCAACGTTTTACTCATTCAATAATTATGA
11843 TCAT-CAGCATG
66 TCATCCAGCATG
* * *
11854 TCTCTAATATAATTATCCTCGTCTTAAGAATCTTCTGCAACGTTTTACTCATTCAATAATTATGA
1 TCTCTAATATAATTACCCTCATCGTAAGAATCTTCTGCAACGTTTTACTCATTCAATAATTATGA
*
11919 TTATCCAGCATG
66 TCATCCAGCATG
11931 ATTATATACA
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
76 64 0.90
77 7 0.10
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (77 bp):
TCTCTAATATAATTACCCTCATCGTAAGAATCTTCTGCAACGTTTTACTCATTCAATAATTATGA
TCATCCAGCATG
Found at i:14417 original size:12 final size:12
Alignment explanation
Indices: 14401--14430 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
14391 AAACACAATA
14401 ACACACCCACAC
1 ACACACCCACAC
*
14413 CCACACCCACAC
1 ACACACCCACAC
14425 ACACAC
1 ACACAC
14431 ACATATATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.40, C:0.60, G:0.00, T:0.00
Consensus pattern (12 bp):
ACACACCCACAC
Found at i:14455 original size:2 final size:2
Alignment explanation
Indices: 14450--14492 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
14440 TATATATATA
* *
14450 TG TG TG TG TG TG TG TG TG TG GG TG TG TG TG TG TG AG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
14492 T
1 T
14493 TATTGTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.02, C:0.00, G:0.51, T:0.47
Consensus pattern (2 bp):
TG
Found at i:14574 original size:14 final size:14
Alignment explanation
Indices: 14555--14585 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
14545 GTCTACTGTG
14555 TATGTATGTATGTA
1 TATGTATGTATGTA
14569 TATGTATGTATGTA
1 TATGTATGTATGTA
14583 TAT
1 TAT
14586 ACCTGCTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (14 bp):
TATGTATGTATGTA
Found at i:17846 original size:21 final size:21
Alignment explanation
Indices: 17820--17890 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
17810 TCCAAGTTAC
*
17820 CCGCGACGGCCGCAATAGCGT
1 CCGCGACGACCGCAATAGCGT
*
17841 CCGCGACGACCGCAATAAC-T
1 CCGCGACGACCGCAATAGCGT
* *
17861 CCCGCGACGACCACAATAGCGC
1 -CCGCGACGACCGCAATAGCGT
17883 CCGCGACG
1 CCGCGACG
17891 GCCGTAATCA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
20 1 0.02
21 42 0.98
ACGTcount: A:0.24, C:0.42, G:0.27, T:0.07
Consensus pattern (21 bp):
CCGCGACGACCGCAATAGCGT
Found at i:23381 original size:21 final size:21
Alignment explanation
Indices: 23355--23410 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
23345 TGGGCTTGAT
*
23355 AGTATCGATACTACTGTTCAC
1 AGTATCGATAATACTGTTCAC
*
23376 AGTATCGATAATACTGTTCAT
1 AGTATCGATAATACTGTTCAC
*
23397 GGTATCGATAATAC
1 AGTATCGATAATAC
23411 AGTAGCAGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (21 bp):
AGTATCGATAATACTGTTCAC
Found at i:23510 original size:20 final size:20
Alignment explanation
Indices: 23485--23530 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
23475 TCGATACTAA
*
23485 TGTTCACATAGTATCGGTAC
1 TGTTCACACAGTATCGGTAC
* *
23505 TGTTCATACAGTATTGGTAC
1 TGTTCACACAGTATCGGTAC
*
23525 TATTCA
1 TGTTCA
23531 TACAATACGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTTCACACAGTATCGGTAC
Found at i:23531 original size:20 final size:20
Alignment explanation
Indices: 23494--23534 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
23484 ATGTTCACAT
*
23494 AGTATCGGTACTGTTCATAC
1 AGTATCGGTACTATTCATAC
*
23514 AGTATTGGTACTATTCATAC
1 AGTATCGGTACTATTCATAC
23534 A
1 A
23535 ATACGATACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (20 bp):
AGTATCGGTACTATTCATAC
Found at i:24308 original size:8 final size:8
Alignment explanation
Indices: 24295--24379 Score: 75
Period size: 8 Copynumber: 10.6 Consensus size: 8
24285 ATGATCCACC
24295 AAAAAAAG
1 AAAAAAAG
24303 AAAAAAA-
1 AAAAAAAG
24310 AAAGAAAA-
1 AAA-AAAAG
* *
24318 AAAAGAGG
1 AAAAAAAG
24326 AAAATAAAG
1 AAAA-AAAG
*
24335 AAAGAAAG
1 AAAAAAAG
*
24343 AAAGAAAG
1 AAAAAAAG
*
24351 AAAGAAAG
1 AAAAAAAG
*
24359 AAAGAAAG
1 AAAAAAAG
*
24367 AAAGAAAG
1 AAAAAAAG
24375 AAAAA
1 AAAAA
24380 GAGTTGTTTG
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
7 5 0.07
8 58 0.85
9 5 0.07
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (8 bp):
AAAAAAAG
Found at i:24312 original size:12 final size:12
Alignment explanation
Indices: 24295--24379 Score: 95
Period size: 12 Copynumber: 7.2 Consensus size: 12
24285 ATGATCCACC
24295 AAAA-AAAGAAA
1 AAAAGAAAGAAA
24306 AAAA-AAAGAAA
1 AAAAGAAAGAAA
*
24317 AAAA-AGAGGAAA
1 AAAAGA-AAGAAA
24329 ATAAAGAAAGAAA
1 A-AAAGAAAGAAA
*
24342 GAAAGAAAGAAA
1 AAAAGAAAGAAA
*
24354 GAAAGAAAGAAA
1 AAAAGAAAGAAA
*
24366 GAAAGAAAGAAA
1 AAAAGAAAGAAA
24378 AA
1 AA
24380 GAGTTGTTTG
Statistics
Matches: 67, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
11 16 0.24
12 42 0.63
13 8 0.12
14 1 0.01
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (12 bp):
AAAAGAAAGAAA
Found at i:24338 original size:4 final size:4
Alignment explanation
Indices: 24331--24377 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
24321 AGAGGAAAAT
24331 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
24378 AAGAGTTGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:25769 original size:52 final size:52
Alignment explanation
Indices: 25707--25835 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
25697 ATCTAGACAA
* *
25707 AAGGGTATCTCTCGATGCTCTTACAATGGCAAGACATGTTTTACCAAAACCC
1 AAGGCTATCTCTCGATGCTCTTACAATGCCAAGACATGTTTTACCAAAACCC
*
25759 AAGGCTATCTCTTGATGCTCTTACAATGCCAAGACATGTTTTACCAAAACCC
1 AAGGCTATCTCTCGATGCTCTTACAATGCCAAGACATGTTTTACCAAAACCC
25811 AAGGCTATCTCTCGATGCTCTTACA
1 AAGGCTATCTCTCGATGCTCTTACA
25836 GTGCTAAGGT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (52 bp):
AAGGCTATCTCTCGATGCTCTTACAATGCCAAGACATGTTTTACCAAAACCC
Found at i:27992 original size:30 final size:30
Alignment explanation
Indices: 27957--28052 Score: 147
Period size: 30 Copynumber: 3.2 Consensus size: 30
27947 GTTGGTTGTA
* *
27957 CTGGGATTGGTGTTGGACTAGTAGCTGCTG
1 CTGGGACTGGTGCTGGACTAGTAGCTGCTG
* * *
27987 TTGGGACTGGTGCTGGACTAGTAGTTACTG
1 CTGGGACTGGTGCTGGACTAGTAGCTGCTG
28017 CTGGGACTGGTGCTGGACTAGTAGCTGCTG
1 CTGGGACTGGTGCTGGACTAGTAGCTGCTG
28047 CTGGGA
1 CTGGGA
28053 ATGGCAATAT
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.15, C:0.16, G:0.40, T:0.30
Consensus pattern (30 bp):
CTGGGACTGGTGCTGGACTAGTAGCTGCTG
Found at i:39783 original size:15 final size:15
Alignment explanation
Indices: 39765--39839 Score: 68
Period size: 15 Copynumber: 5.2 Consensus size: 15
39755 GTGAAATTCT
39765 AATTATTTAAATAAA
1 AATTATTTAAATAAA
*
39780 AATTATTTATATAAA
1 AATTATTTAAATAAA
**
39795 AATTCA--TCGAT-AA
1 AATT-ATTTAAATAAA
*
39808 TA-TATTTAAATAAA
1 AATTATTTAAATAAA
*
39822 AATTATTTATATAAA
1 AATTATTTAAATAAA
39837 AAT
1 AAT
39840 CATCGATAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
11 1 0.02
12 1 0.02
13 6 0.13
14 6 0.13
15 32 0.68
16 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (15 bp):
AATTATTTAAATAAA
Found at i:39815 original size:42 final size:41
Alignment explanation
Indices: 39764--39850 Score: 158
Period size: 42 Copynumber: 2.1 Consensus size: 41
39754 AGTGAAATTC
39764 TAAT-TATTTAAATAAAAATTATTTATATAAAAATTCATCGA
1 TAATATATTTAAATAAAAATTATTTATATAAAAA-TCATCGA
39805 TAATATATTTAAATAAAAATTATTTATATAAAAATCATCGA
1 TAATATATTTAAATAAAAATTATTTATATAAAAATCATCGA
39846 TAATA
1 TAATA
39851 CATTATTGTA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
41 16 0.36
42 29 0.64
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (41 bp):
TAATATATTTAAATAAAAATTATTTATATAAAAATCATCGA
Found at i:44153 original size:95 final size:95
Alignment explanation
Indices: 43990--44186 Score: 385
Period size: 95 Copynumber: 2.1 Consensus size: 95
43980 TTTTTCATAA
43990 TATTTTTGTGTCACCTTACTCTTTTCTTTTGATTTTTGTTTAACCAGTGACGTCATCAATTTCAA
1 TATTTTTGTGTCACCTTACTCTTTTCTTTTGATTTTTGTTTAACCAGTGACGTCATCAATTTCAA
*
44055 TATTAGTTGTCGACCTCTAATTATTATTAT
66 TATTAGTTGTCGACCTCCAATTATTATTAT
44085 TATTTTTGTGTCACCTTACTCTTTTCTTTTGATTTTTGTTTAACCAGTGACGTCATCAATTTCAA
1 TATTTTTGTGTCACCTTACTCTTTTCTTTTGATTTTTGTTTAACCAGTGACGTCATCAATTTCAA
44150 TATTAGTTGTCGACCTCCAATTATTATTAT
66 TATTAGTTGTCGACCTCCAATTATTATTAT
44180 TATTTTT
1 TATTTTT
44187 CTTGTTCTTT
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 101 1.00
ACGTcount: A:0.22, C:0.17, G:0.10, T:0.51
Consensus pattern (95 bp):
TATTTTTGTGTCACCTTACTCTTTTCTTTTGATTTTTGTTTAACCAGTGACGTCATCAATTTCAA
TATTAGTTGTCGACCTCCAATTATTATTAT
Found at i:45568 original size:45 final size:45
Alignment explanation
Indices: 45517--46036 Score: 697
Period size: 45 Copynumber: 11.6 Consensus size: 45
45507 TTATGCTGAA
* * *
45517 AATGCACCCATATGCATT-TTAGC-TATGGCATCCTTTCGTGCCAAT
1 AATGCACCCATATGCATTATT--CTTTTGGCATCCTTTCATGCCGAT
* *
45562 AATGCACACATATGCATTATTCTTTTGGCATCCTTTCATGCCAAT
1 AATGCACCCATATGCATTATTCTTTTGGCATCCTTTCATGCCGAT
* * * *
45607 AACGCACCCATATGGATTATACTTTTGGCATCCTTTAATGCCGAT
1 AATGCACCCATATGCATTATTCTTTTGGCATCCTTTCATGCCGAT
* * **
45652 AATTCACCCATATACATTATTCTTTTGGCATCCTTTCATATCGAT
1 AATGCACCCATATGCATTATTCTTTTGGCATCCTTTCATGCCGAT
*
45697 AATGCACCCATATGCATTATTCTTTTGGCATCCTTTCATGCTGAT
1 AATGCACCCATATGCATTATTCTTTTGGCATCCTTTCATGCCGAT
* * ** *
45742 AATACACTCATATGCATTATTCTTTTAACATCTTTTCATGCCGAT
1 AATGCACCCATATGCATTATTCTTTTGGCATCCTTTCATGCCGAT
45787 AATGCACCCATATGCATTATTCTTTTGGCATCCTTTCATGCCGAT
1 AATGCACCCATATGCATTATTCTTTTGGCATCCTTTCATGCCGAT
* *
45832 AATGCACCCATATGCATTATTCTTTTGGCATTCTTTCATGTCGAT
1 AATGCACCCATATGCATTATTCTTTTGGCATCCTTTCATGCCGAT
* **
45877 AATGCA--CACATGCATTATTCTTTTTCCATCCTTTCATGCCGAT
1 AATGCACCCATATGCATTATTCTTTTGGCATCCTTTCATGCCGAT
* *
45920 AATGCACCCATAAGCATTATTCTTTTGGCATCTTTTCATGCCGAT
1 AATGCACCCATATGCATTATTCTTTTGGCATCCTTTCATGCCGAT
* * * *
45965 AATCCACCCATATGCATTATTCTTTTGACATTCTTTCATGGCGAT
1 AATGCACCCATATGCATTATTCTTTTGGCATCCTTTCATGCCGAT
* * *
46010 AATTCAGCCATATGCATTATTATTTTG
1 AATGCACCCATATGCATTATTCTTTTG
46037 TTCATTTGTT
Statistics
Matches: 417, Mismatches: 54, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
43 38 0.09
44 1 0.00
45 376 0.90
46 2 0.00
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.39
Consensus pattern (45 bp):
AATGCACCCATATGCATTATTCTTTTGGCATCCTTTCATGCCGAT
Found at i:47342 original size:9 final size:9
Alignment explanation
Indices: 47328--47355 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
47318 ACTAAATCTT
47328 AAATTTTCA
1 AAATTTTCA
47337 AAATTTTCA
1 AAATTTTCA
47346 AAATTTTCA
1 AAATTTTCA
47355 A
1 A
47356 TATAGTCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (9 bp):
AAATTTTCA
Found at i:48883 original size:84 final size:84
Alignment explanation
Indices: 48668--48900 Score: 283
Period size: 84 Copynumber: 2.8 Consensus size: 84
48658 AGCCTATTAT
* * * *
48668 AGCATAACTTAAGGCGAGAAGAGTTATATGTCAACAAAACCTTCGAGTTCGATTACATTTAG-T-
1 AGCATAACTCAAGGCGAGAAG-GTTATCTGTCAACAAAACCTTCGAGTTCGATTCCATTCAGCTC
* *
48731 ACAGGGCATATCAAATTTAT
65 ACAGGGAATATCAAATTTAC
* * * * * * *
48751 AGAATATCTCAAGGTGACAGGGGTTATCTATCAACCAAAACCTTCGAGTTTGATTCCATTCAGCT
1 AGCATAACTCAAGGCGAGA-AGGTTATCTGTCAA-CAAAACCTTCGAGTTCGATTCCATTCAGCT
48816 CA-AGGGAATATCAAATTTAC
64 CACAGGGAATATCAAATTTAC
*
48836 AGCATAGCTCAAGGCGAGAAGGTATATCTGTCAACAAAACCTTCGAGTTCGATTCCATTCAGCTC
1 AGCATAACTCAAGGCGAGAAGGT-TATCTGTCAACAAAACCTTCGAGTTCGATTCCATTCAGCTC
48901 GATGACAGCG
Statistics
Matches: 125, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
83 24 0.19
84 59 0.47
85 41 0.33
86 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (84 bp):
AGCATAACTCAAGGCGAGAAGGTTATCTGTCAACAAAACCTTCGAGTTCGATTCCATTCAGCTCA
CAGGGAATATCAAATTTAC
Done.