Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004215.1 Hibiscus syriacus cultivar Beakdansim tig00009232_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: 64801
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:3562 original size:23 final size:23
Alignment explanation
Indices: 3507--3573 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
3497 TATACATTTC
* * *
3507 ATAT-ATATTTAAAATACAGTTA
1 ATATAATATTTAAAATAAAATAA
*
3529 ATATAAGATTTAAAATAAAATAA
1 ATATAATATTTAAAATAAAATAA
* *
3552 ATTTAATATTTTAAAATTAAAT
1 ATATAATA-TTTAAAATAAAAT
3574 TGAATATGTA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 4 0.11
23 20 0.56
24 12 0.33
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.40
Consensus pattern (23 bp):
ATATAATATTTAAAATAAAATAA
Found at i:3574 original size:20 final size:19
Alignment explanation
Indices: 3544--3613 Score: 95
Period size: 20 Copynumber: 3.6 Consensus size: 19
3534 AGATTTAAAA
3544 TAAAATAAATTTAATATTT
1 TAAAATAAATTTAATATTT
* *
3563 TAAAATTAAATTGAATATGTA
1 TAAAA-TAAATTTAATAT-TT
3584 TAAAATAAATTTAATATTT
1 TAAAATAAATTTAATATTT
*
3603 TGAAATAAATT
1 TAAAATAAATT
3614 AAAATTAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
19 16 0.36
20 22 0.50
21 6 0.14
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (19 bp):
TAAAATAAATTTAATATTT
Found at i:5786 original size:83 final size:82
Alignment explanation
Indices: 5655--5815 Score: 286
Period size: 83 Copynumber: 2.0 Consensus size: 82
5645 TAAGACATAA
**
5655 AAGAAGAATTATTGAAGGGACCAAATAAGTTCCTCAAGCCAAATTCTCGGCATCTTCACTTGCTC
1 AAGAAGAATTATTGAAGGGAAAAAATAAGTTCCTCAAGCCAAATTCTCGGCATCTTCACTTGCTC
5720 TCAGCATCATATAAAAG
66 TCAGCATCATATAAAAG
*
5737 AAGAATAATTATTGAAGGGATAAAAATAAGTTCCTCAAGCCAAATTCTCGGCATCTTCACTTGCT
1 AAGAAGAATTATTGAAGGGA-AAAAATAAGTTCCTCAAGCCAAATTCTCGGCATCTTCACTTGCT
5802 CTCAGCATCATATA
65 CTCAGCATCATATA
5816 GATCCCCCTG
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
82 19 0.25
83 56 0.75
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (82 bp):
AAGAAGAATTATTGAAGGGAAAAAATAAGTTCCTCAAGCCAAATTCTCGGCATCTTCACTTGCTC
TCAGCATCATATAAAAG
Found at i:8046 original size:29 final size:30
Alignment explanation
Indices: 8014--8085 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
8004 AAATTTTTGG
* * *
8014 TTAGTGACCAAAATATAACTTTTG-AAAGT
1 TTAGTGACCAAAATATAAATTTAGAAAAGC
* *
8043 TTAGTGATCAAAGTATAAATTTAGAAAAGC
1 TTAGTGACCAAAATATAAATTTAGAAAAGC
*
8073 TTAGAGACCAAAA
1 TTAGTGACCAAAA
8086 ATGTAATTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 20 0.59
30 14 0.41
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (30 bp):
TTAGTGACCAAAATATAAATTTAGAAAAGC
Found at i:10634 original size:18 final size:18
Alignment explanation
Indices: 10613--10649 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
10603 TATACATTGG
10613 GCTATGAATATGAAATGA
1 GCTATGAATATGAAATGA
10631 GCTATGAATATGAAATGA
1 GCTATGAATATGAAATGA
10649 G
1 G
10650 TTATAAATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.05, G:0.24, T:0.27
Consensus pattern (18 bp):
GCTATGAATATGAAATGA
Found at i:11771 original size:26 final size:25
Alignment explanation
Indices: 11742--11792 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
11732 AGTAATATAG
11742 ATAAAGTGAGATA-AAACATAAATTTC
1 ATAAAGT-A-ATATAAACATAAATTTC
*
11768 ATAAAGTATTATAAACATAAATTTC
1 ATAAAGTAATATAAACATAAATTTC
11793 TAGTTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 2 0.09
25 14 0.61
26 7 0.30
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (25 bp):
ATAAAGTAATATAAACATAAATTTC
Found at i:25325 original size:21 final size:21
Alignment explanation
Indices: 25276--25326 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
25266 TATGACTATT
25276 GCAATGCGATTTTCCAATTTC
1 GCAATGCGATTTTCCAATTTC
***
25297 GTGTTGCGATTTTCCCAA-TTC
1 GCAATGCGATTTT-CCAATTTC
25318 GCAATGCGA
1 GCAATGCGA
25327 ATTTGGAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.35
Consensus pattern (21 bp):
GCAATGCGATTTTCCAATTTC
Found at i:25340 original size:21 final size:21
Alignment explanation
Indices: 25316--25368 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
25306 TTTTCCCAAT
25316 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
25337 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
*
25358 TCGCAACGCGA
1 TCGCAATGCGA
25369 TACTAACTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:25382 original size:20 final size:20
Alignment explanation
Indices: 25357--25471 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
25347 AATTTGGAAA
25357 ATCGCAACGCGATACTAACT
1 ATCGCAACGCGATACTAACT
* * **
25377 ATCGCAACGTGATAATACAAA
1 ATCGCAACGCGATACTA-ACT
*
25398 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTAACT
* *
25418 TTCGCAACGCGATAGTTAA-T
1 ATCGCAACGCGATA-CTAACT
* *
25438 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTAACT
* *
25458 TTCGCAACGAGATA
1 ATCGCAACGCGATA
25472 ATACATAATC
Statistics
Matches: 77, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
19 2 0.03
20 58 0.75
21 17 0.22
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTAACT
Found at i:25454 original size:40 final size:41
Alignment explanation
Indices: 25354--25491 Score: 179
Period size: 41 Copynumber: 3.4 Consensus size: 41
25344 GCGAATTTGG
* * *
25354 AAAATCGCAACGCGATACTAACTATCGCAACGTGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGAGATAATAC
* * *
25395 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAGT-T
1 AAAATCGCAACGCGATACTGACTTTCGCAACGAGATAATAC
**
25435 AATTTCGCAACGCGATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGAGATAATAC
* *
25476 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
25492 TTTCAAAGCG
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
40 35 0.43
41 47 0.57
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGAGATAATAC
Found at i:25999 original size:20 final size:20
Alignment explanation
Indices: 25950--26008 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
25940 TTTATTCTCT
* **
25950 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
25970 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
25990 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
26009 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:27353 original size:18 final size:18
Alignment explanation
Indices: 27327--27374 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
27317 TCCACTTCGG
27327 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
27345 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
27363 GAGCCATCACCT
1 GAGCCATCACCT
27375 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:27977 original size:19 final size:18
Alignment explanation
Indices: 27955--28045 Score: 81
Period size: 19 Copynumber: 5.3 Consensus size: 18
27945 GGAAACGGCT
27955 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
27974 ATCGCAA-C--AA-CAAA
1 ATCGCAAGCGAAATGAAA
27988 ATCGCAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
28007 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATGAAA
28021 ATCGCAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
28040 ATCGCA
1 ATCGCA
28046 TTATGTCGTT
Statistics
Matches: 58, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 20 0.34
15 3 0.05
16 3 0.05
17 3 0.05
18 3 0.05
19 26 0.45
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:28000 original size:33 final size:33
Alignment explanation
Indices: 27955--28045 Score: 164
Period size: 33 Copynumber: 2.8 Consensus size: 33
27945 GGAAACGGCT
*
27955 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACAACAAA
*
27988 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACAACAAA
28021 ATCGCAACGCGAAATGAAAATCGCA
1 ATCGCAACGCGAAATGAAAATCGCA
28046 TTATGTCGTT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACAACAAA
Found at i:28029 original size:14 final size:14
Alignment explanation
Indices: 27971--28029 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
27961 ATGCGAAATG
*
27971 AAAATCGCAACAAC
1 AAAATCGCAACGAC
*
27985 AAAATCGCAACGCGAAATG
1 AAAATCGCAA--CG--A-C
28004 AAAATCGCAACGAC
1 AAAATCGCAACGAC
28018 AAAATCGCAACG
1 AAAATCGCAACG
28030 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 22 0.59
15 1 0.03
16 1 0.03
17 2 0.05
18 1 0.03
19 10 0.27
ACGTcount: A:0.51, C:0.25, G:0.15, T:0.08
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:28098 original size:20 final size:20
Alignment explanation
Indices: 28073--28118 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
28063 TCATTTTGCA
28073 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* *
28093 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGCCATTTCCGCG
28113 TTGCGA
1 TTGCGA
28119 AAGTAAGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.24, G:0.26, T:0.35
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:28129 original size:20 final size:20
Alignment explanation
Indices: 28089--28144 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
28079 TAGCCATTTC
* * *
28089 CGCGTTGCGATAGTCATTTT
1 CGCGTTGCGAAAGTAAGTTT
28109 CGCGTTGCGAAAGTAAGTTT
1 CGCGTTGCGAAAGTAAGTTT
*
28129 CGTGTTGCGAAAGTAA
1 CGCGTTGCGAAAGTAA
28145 ACTATTCTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (20 bp):
CGCGTTGCGAAAGTAAGTTT
Found at i:28519 original size:21 final size:21
Alignment explanation
Indices: 28493--28563 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
28483 CTGTCATCCC
28493 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCCAATCGT
* * **
28514 TCAAGAGGCCCCTATC-ATCCC
1 TCAAGAGTCCCCT-CCAATCGT
* *
28535 TCAAGAGTCCCCCCCCAACCGT
1 TCAAGAGT-CCCCTCCAATCGT
28557 TCAAGAG
1 TCAAGAG
28564 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 10, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
21 23 0.62
22 14 0.38
ACGTcount: A:0.25, C:0.41, G:0.15, T:0.18
Consensus pattern (21 bp):
TCAAGAGTCCCCTCCAATCGT
Found at i:28575 original size:43 final size:42
Alignment explanation
Indices: 28483--28575 Score: 141
Period size: 43 Copynumber: 2.2 Consensus size: 42
28473 CCCGACTCAC
* * *
28483 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCA
*
28525 CTATCATCCCTCAAGAGTCCCCCCCCAACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGT-CCCCCCCAACCGTTCAAGAGGCCA
28568 CTGTCATC
1 CTGTCATC
28576 GTTGAAGAGG
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 17 0.38
43 28 0.62
ACGTcount: A:0.23, C:0.42, G:0.15, T:0.20
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCA
Found at i:30020 original size:14 final size:14
Alignment explanation
Indices: 29986--30024 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
29976 TTGATTGTTT
29986 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
30000 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
30014 TGTTGATTTGT
1 AATTGATTTGT
30025 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:30257 original size:20 final size:20
Alignment explanation
Indices: 30227--30302 Score: 125
Period size: 20 Copynumber: 3.8 Consensus size: 20
30217 TCGCATTACA
*
30227 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
30247 CTTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
30267 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGCC
30287 ATTTTCGCGTTGCGAT
1 ATTTTCGCGTTGCGAT
30303 TTCCCCGCTG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.13, C:0.24, G:0.24, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:30551 original size:20 final size:20
Alignment explanation
Indices: 30526--30618 Score: 116
Period size: 20 Copynumber: 4.7 Consensus size: 20
30516 CATTTAAAAA
* *
30526 TCGCAACGCGATACTTACTT
1 TCGCAACGAGATACTGACTT
*
30546 TCGCAACGCGATACTGACTT
1 TCGCAACGAGATACTGACTT
*
30566 TCGCAAC-ATGATTCTGACTT
1 TCGCAACGA-GATACTGACTT
* *
30586 TCGCAACGAGATTCTGACTA
1 TCGCAACGAGATACTGACTT
30606 TCGCAACGAGATA
1 TCGCAACGAGATA
30619 ATACAGAATC
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
20 65 0.98
21 1 0.02
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (20 bp):
TCGCAACGAGATACTGACTT
Found at i:30783 original size:12 final size:12
Alignment explanation
Indices: 30764--30797 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
30754 CTCTCCGGCG
30764 ACATCCGTTCCT
1 ACATCCGTTCCT
*
30776 ATATCCGTTCCT
1 ACATCCGTTCCT
30788 ACATCC-TTCC
1 ACATCCGTTCC
30798 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:31380 original size:24 final size:24
Alignment explanation
Indices: 31353--31406 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
31343 GTATTCAAAA
*
31353 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
31377 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
31401 TTTGAT
1 TTTGAT
31407 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:31598 original size:12 final size:12
Alignment explanation
Indices: 31581--31605 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31571 ATATAATCCC
31581 GAAGAAGAAAAA
1 GAAGAAGAAAAA
31593 GAAGAAGAAAAA
1 GAAGAAGAAAAA
31605 G
1 G
31606 TCCCTGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:33955 original size:19 final size:18
Alignment explanation
Indices: 33933--34024 Score: 74
Period size: 19 Copynumber: 5.4 Consensus size: 18
33923 AGAAATTACT
33933 ATCGCAATGCGAAATGAAA
1 ATCGCAAT-CGAAATGAAA
*
33952 ATCGCAA-CG--A-GAGA
1 ATCGCAATCGAAATGAAA
*
33966 ATCGCAATACAAAATGAAA
1 ATCGCAAT-CGAAATGAAA
*
33985 ATCGCAA-CG--A-GAGA
1 ATCGCAATCGAAATGAAA
33999 ATCGCAATGCGAAATGAAA
1 ATCGCAAT-CGAAATGAAA
34018 ATCGCAA
1 ATCGCAA
34025 CTAGGGAATC
Statistics
Matches: 57, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 20 0.35
15 2 0.04
16 3 0.05
17 3 0.05
18 2 0.04
19 27 0.47
ACGTcount: A:0.48, C:0.18, G:0.21, T:0.13
Consensus pattern (18 bp):
ATCGCAATCGAAATGAAA
Found at i:33981 original size:33 final size:33
Alignment explanation
Indices: 33933--34059 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
33923 AGAAATTACT
*
33933 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
*
33966 ATCGCAATACAAAATGAAAATCGCAACGAGAGA
1 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
* * *
33999 ATCGCAATGCGAAATGAAAATCGCAACTAGGGA
1 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
34032 ATCGCAA-AGCGAAATGAAAATCGCAACG
1 ATCGCAATA-CGAAATGAAAATCGCAACG
34060 CGAATTTAGT
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
33 85 1.00
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAATACGAAATGAAAATCGCAACGAGAGA
Found at i:34062 original size:19 final size:18
Alignment explanation
Indices: 33933--34063 Score: 70
Period size: 19 Copynumber: 7.7 Consensus size: 18
33923 AGAAATTACT
33933 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
33952 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
* *
33966 ATCGCAATACAAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
33985 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
33999 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
* **
34018 ATCGCAA-C--TA-GGGA
1 ATCGCAAGCGAAATGAAA
34032 ATCGCAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
34051 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
34064 TTTAGTTTCG
Statistics
Matches: 84, Mismatches: 12, Indels: 32
0.66 0.09 0.25
Matches are distributed among these distances:
14 27 0.32
15 5 0.06
16 4 0.05
17 4 0.05
18 5 0.06
19 39 0.46
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:34091 original size:14 final size:14
Alignment explanation
Indices: 34074--34130 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
34064 TTTAGTTTCG
34074 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
34088 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
34107 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
34121 CGTTGCGATT
1 CGTTGCGATT
34131 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:34111 original size:33 final size:33
Alignment explanation
Indices: 34069--34148 Score: 151
Period size: 33 Copynumber: 2.4 Consensus size: 33
34059 GCGAATTTAG
34069 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
34102 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
*
34135 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
34149 AGTCATTTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
Found at i:34112 original size:19 final size:19
Alignment explanation
Indices: 34088--34148 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
34078 GCGATTCTCT
34088 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
34107 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
34121 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
34140 CATTGCGAT
1 CGTTGCGAT
34149 AGTCATTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 18 0.53
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:34281 original size:14 final size:14
Alignment explanation
Indices: 34255--34291 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
34245 CATCAATTAA
34255 ACAAATCAACTTTT
1 ACAAATCAACTTTT
* *
34269 ACATATCACCTTTT
1 ACAAATCAACTTTT
34283 ACAAATCAA
1 ACAAATCAA
34292 TTAAACAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.24, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:35708 original size:21 final size:21
Alignment explanation
Indices: 35642--35708 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
35632 GTGAATCGGG
*
35642 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
35662 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
35684 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
35705 CTCT
1 CTCT
35709 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:36159 original size:91 final size:90
Alignment explanation
Indices: 35982--36166 Score: 264
Period size: 91 Copynumber: 2.0 Consensus size: 90
35972 ATTTCAAACT
* *
35982 TTCAACCAAAATACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
*
36047 AGAATTGGCAGCAACCAAATAAATTTAC
63 AGAATTGGCAGCAACCAAATAAACTTAC
*
36075 TTCAACCAAAAGACAAAACAAAAAGACAAATATTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
* *
36139 GTATTGGCAGCAACCGAATAAACTTAC
64 GAATTGGCAGCAACCAAATAAACTTAC
36166 T
1 T
36167 AAGCAATCTA
Statistics
Matches: 84, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
91 40 0.48
93 18 0.21
95 26 0.31
ACGTcount: A:0.48, C:0.19, G:0.11, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCAAATAAACTTAC
Found at i:37889 original size:20 final size:19
Alignment explanation
Indices: 37862--37950 Score: 89
Period size: 20 Copynumber: 4.8 Consensus size: 19
37852 TCTTTTGGTT
37862 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
37881 GATAATGAAAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
37902 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
37921 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
37935 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
37951 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
14 10 0.18
16 2 0.04
17 2 0.04
19 11 0.19
20 30 0.53
21 2 0.04
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:38004 original size:33 final size:33
Alignment explanation
Indices: 37951--38022 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
37941 AAAATCGCAA
** * *
37951 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTAATTTCACGTTGCAATTATCTCGT
*
37984 TGCGATTTTAATTTCACGTTGCAATTCTCTCGT
1 TGCGATTTTAATTTCACGTTGCAATTATCTCGT
38017 TGCGAT
1 TGCGAT
38023 AGTTATTTCC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.14, C:0.19, G:0.22, T:0.44
Consensus pattern (33 bp):
TGCGATTTTAATTTCACGTTGCAATTATCTCGT
Found at i:38031 original size:33 final size:33
Alignment explanation
Indices: 37962--38031 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
37952 GCGATTTTGG
* * *
37962 TTTCGCGTTGCGATTATCTCGTTGCGATTTTAA
1 TTTCACGTTGCAATTATCTCGTTGCGATGTTAA
*
37995 TTTCACGTTGCAATTCTCTCGTTGCGATAGTT-A
1 TTTCACGTTGCAATTATCTCGTTGCGAT-GTTAA
38028 TTTC
1 TTTC
38032 CGCGTTGCGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 30 0.94
34 2 0.06
ACGTcount: A:0.16, C:0.20, G:0.19, T:0.46
Consensus pattern (33 bp):
TTTCACGTTGCAATTATCTCGTTGCGATGTTAA
Found at i:38619 original size:21 final size:21
Alignment explanation
Indices: 38593--38666 Score: 98
Period size: 20 Copynumber: 3.6 Consensus size: 21
38583 CGATAGTAAG
*
38593 ATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTACCTA
*
38614 ATTCGCATTGCGATTTACTTA
1 ATTCGCATTGCGATTTACCTA
* *
38635 A-TCGCGTTGCGATTTACGT-
1 ATTCGCATTGCGATTTACCTA
38654 ATTCGCATTGCGA
1 ATTCGCATTGCGA
38667 ATTATGAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
19 1 0.02
20 26 0.55
21 20 0.43
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (21 bp):
ATTCGCATTGCGATTTACCTA
Found at i:38687 original size:21 final size:21
Alignment explanation
Indices: 38663--38718 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
38653 TATTCGCATT
*
38663 GCGAATTATGAAAATCGCAAC
1 GCGAATTAAGAAAATCGCAAC
* *
38684 GCGAA-TAAGTAAATCGCAAT
1 GCGAATTAAGAAAATCGCAAC
*
38704 GCGAATTAGGAAAAT
1 GCGAATTAAGAAAAT
38719 TGCATTGCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.20
Consensus pattern (21 bp):
GCGAATTAAGAAAATCGCAAC
Found at i:38783 original size:21 final size:21
Alignment explanation
Indices: 38656--38811 Score: 104
Period size: 21 Copynumber: 7.5 Consensus size: 21
38646 ATTTACGTAT
*
38656 TCGCATTGCGAATTATGAAAA
1 TCGCATTGCGAATTAGGAAAA
** * *
38677 TCGCAACGCGAA-TAAGTAAA
1 TCGCATTGCGAATTAGGAAAA
*
38697 TCGCAATGCGAATTAGGAAAA
1 TCGCATTGCGAATTAGGAAAA
* * **
38718 TTGCATTGCG-A-TAGTCAGTA
1 TCGCATTGCGAATTAG-GAAAA
* *** *
38738 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGAATTAGGAAAA
*
38759 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATTAGGAAAA
**
38780 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCG-AATTAGGAAAA
38801 TCGCATTGCGA
1 TCGCATTGCGA
38812 TTGTCATAAT
Statistics
Matches: 102, Mismatches: 28, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 3 0.03
20 30 0.29
21 64 0.63
22 5 0.05
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (21 bp):
TCGCATTGCGAATTAGGAAAA
Found at i:38824 original size:20 final size:20
Alignment explanation
Indices: 38573--38831 Score: 66
Period size: 20 Copynumber: 12.7 Consensus size: 20
38563 ACGCTATGTA
* * *
38573 AATCGCATTGCGATAGTAAG
1 AATCGCATTGCGATTGTCAT
* * *
38593 ATTCGCATTGCGATTTTCCT
1 AATCGCATTGCGATTGTCAT
*
38613 AATTCGCATTGCGATT-TACTT
1 AA-TCGCATTGCGATTGT-CAT
* *
38634 AATCGCGTTGCGATT-TACGT
1 AATCGCATTGCGATTGT-CAT
* * * *
38654 ATTCGCATTGCGAATTATGAA
1 AATCGCATTGCG-ATTGTCAT
** *
38675 AATCGCAACGCGAATAAGT-A-
1 AATCGCATTGCG-AT-TGTCAT
* * *
38695 AATCGCAATGCGAATTAG-GAA
1 AATCGCATTGCG-ATT-GTCAT
* *
38716 AATTGCATTGCGATAGTCAGT
1 AATCGCATTGCGATTGTCA-T
*
38737 -ATCGCATTGCGATTTTCCA-
1 AATCGCATTGCGATTGT-CAT
** *
38756 AATTCGCATTGCGAATTGGGAA
1 AA-TCGCATTGCG-ATTGTCAT
** * *
38778 AATCGCAACGCGAAATTG-GAA
1 AATCGCATTGCG--ATTGTCAT
38799 AATCGCATTGCGATTGTCAT
1 AATCGCATTGCGATTGTCAT
*
38819 AATCGCGTTGCGA
1 AATCGCATTGCGA
38832 ATCTGGAAAC
Statistics
Matches: 182, Mismatches: 40, Indels: 34
0.71 0.16 0.13
Matches are distributed among these distances:
19 5 0.03
20 88 0.48
21 77 0.42
22 12 0.07
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (20 bp):
AATCGCATTGCGATTGTCAT
Found at i:57066 original size:29 final size:28
Alignment explanation
Indices: 57034--57223 Score: 145
Period size: 29 Copynumber: 6.6 Consensus size: 28
57024 AAGTTTAAAC
57034 TTTTTAGAATTTACAATAAAGTA-AAAATA
1 TTTTTA-AA-TTACAATAAAGTACAAAATA
* * * *
57063 TTTTATAAATTATAATAAAG--GATAATT
1 TTTT-TAAATTACAATAAAGTACAAAATA
*
57090 TTTTTAAAATTACAATAAAGTACAAAACAA
1 TTTTT-AAATTACAATAAAGTACAAAA-TA
* * *
57120 TTTATATATTACAATAAAGTACAAAACAA
1 TTTTTAAATTACAATAAAGTACAAAA-TA
*
57149 TTTATAAATTACAATAAAGTACAAAACTA
1 TTTTTAAATTACAATAAAGTACAAAA-TA
* * * * *
57178 TTTATAAATTAAAATAAAGGATAAAGT-
1 TTTTTAAATTACAATAAAGTACAAAATA
*
57205 TTTTATAAATTATAATAAA
1 TTTT-TAAATTACAATAAA
57224 AGGAGACAAA
Statistics
Matches: 136, Mismatches: 18, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
26 1 0.01
27 24 0.18
28 24 0.18
29 81 0.60
30 6 0.04
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (28 bp):
TTTTTAAATTACAATAAAGTACAAAATA
Found at i:57240 original size:30 final size:29
Alignment explanation
Indices: 57149--57253 Score: 97
Period size: 29 Copynumber: 3.6 Consensus size: 29
57139 TACAAAACAA
* * * *
57149 TTTATAAATTACAAT-AAAGTACAAAACTA
1 TTTATAAATTAAAATAAAAGGAGAAAA-TT
* *
57178 TTTATAAATTAAAAT-AAAGGATAAAGTT
1 TTTATAAATTAAAATAAAAGGAGAAAATT
*
57206 TTTATAAATTATAATAAAAGGAGACAAATT
1 TTTATAAATTAAAATAAAAGGAGA-AAATT
* *
57236 TTTATAAAATACAATAAA
1 TTTATAAATTAAAATAAA
57254 TTTAGCATAA
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
28 15 0.23
29 29 0.45
30 20 0.31
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (29 bp):
TTTATAAATTAAAATAAAAGGAGAAAATT
Found at i:59137 original size:55 final size:54
Alignment explanation
Indices: 59107--59535 Score: 660
Period size: 55 Copynumber: 7.8 Consensus size: 54
59097 CCCACTACCA
* *
59107 ATACGGAAATTCATAAACTTATTATGAATTTCTAAGTTTTGCACACACAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAG-TTTGCACACAAAGTGCCC
* * *
59162 ATATGGAAATTCATAAACTTATTGTGAATTTCTTAGTTTTGCACACAAAGAGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAG-TTTGCACACAAAGTGCCC
* *
59217 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTACACGCAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAG-TTTGCACACAAAGTGCCC
*
59272 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGGACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAG-TTTGCACACAAAGTGCCC
*
59327 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGGACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAG-TTTGCACACAAAGTGCCC
* *
59382 ATACGAAAATTCATAAACTTATTATAAATTTCTTAGTTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAG-TTTGCACACAAAGTGCCC
** *
59437 ATACAAAAATTCATAAACTTATTATGAATTTCTTAGTGTTGCACACAAAGTTCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGT-TTGCACACAAAGTGCCC
*
59492 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTACACA
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTGCACA
59536 TAGTGTCATT
Statistics
Matches: 351, Mismatches: 22, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
54 7 0.02
55 344 0.98
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (54 bp):
ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACAAAGTGCCC
Done.