Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006949.1 Hibiscus syriacus cultivar Beakdansim tig00017856_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: 55788
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:1027 original size:19 final size:20
Alignment explanation
Indices: 986--1057 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
976 GACATGGGAT
986 AATCGGTA-CCCCTGGGAGGG
1 AATCGGTACCCCCTGGG-GGG
* *
1006 AATCTGT-TCCCCTGGGGGG
1 AATCGGTACCCCCTGGGGGG
1025 AATCGGTACCCCCTGGGGGG
1 AATCGGTACCCCCTGGGGGG
1045 AAT--GTACCCCCTG
1 AATCGGTACCCCCTG
1058 AACAATTTGA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
18 10 0.21
19 9 0.19
20 28 0.60
ACGTcount: A:0.17, C:0.29, G:0.35, T:0.19
Consensus pattern (20 bp):
AATCGGTACCCCCTGGGGGG
Found at i:13138 original size:2 final size:2
Alignment explanation
Indices: 13133--13159 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13123 AAAAAAGAAA
13133 AT 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 AT A
13160 AATGTTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19440 original size:25 final size:26
Alignment explanation
Indices: 19391--19442 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
19381 ACATATTTAC
* *
19391 ATTTAATTTATATTATTTTCCATGTT
1 ATTTAATTTATATAATTTTACATGTT
*
19417 ATTTAATTTATA-AATTTTAGATGTT
1 ATTTAATTTATATAATTTTACATGTT
19442 A
1 A
19443 AAATCATGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.58
Consensus pattern (26 bp):
ATTTAATTTATATAATTTTACATGTT
Found at i:20660 original size:40 final size:40
Alignment explanation
Indices: 20605--20687 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
20595 TAAAGAAATT
20605 TTTCCAAGCTTTAAATTAGCCCTTTTATCTCTTTATCCGC
1 TTTCCAAGCTTTAAATTAGCCCTTTTATCTCTTTATCCGC
20645 TTTCCAAGCTTTAAATTAGCCCTTTTATCTCTTTATCCGC
1 TTTCCAAGCTTTAAATTAGCCCTTTTATCTCTTTATCCGC
20685 TTT
1 TTT
20688 AGTAATACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.19, C:0.27, G:0.07, T:0.47
Consensus pattern (40 bp):
TTTCCAAGCTTTAAATTAGCCCTTTTATCTCTTTATCCGC
Found at i:25910 original size:26 final size:24
Alignment explanation
Indices: 25825--25915 Score: 71
Period size: 25 Copynumber: 3.7 Consensus size: 24
25815 AAAAAAGTCC
* *
25825 TACAAATTTAACAAAATAAAGTAAG
1 TACAAA-TTAAAAAAATAAAGTAAA
* *
25850 TATTAAATGAAAAATAATAAA--AAA
1 TA-CAAATTAAAAA-AATAAAGTAAA
25874 TTAC-AATTAAACAAAATAAAGTAAA
1 -TACAAATTAAA-AAAATAAAGTAAA
25899 TACAAATATAAAAAAAT
1 TACAAAT-TAAAAAAAT
25916 CTATCGATGT
Statistics
Matches: 52, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
23 12 0.23
24 7 0.13
25 20 0.38
26 13 0.25
ACGTcount: A:0.66, C:0.05, G:0.04, T:0.24
Consensus pattern (24 bp):
TACAAATTAAAAAAATAAAGTAAA
Found at i:28114 original size:17 final size:18
Alignment explanation
Indices: 28094--28134 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
28084 GAATTATATT
28094 AGTAAAAT-ATTAAATAA
1 AGTAAAATAATTAAATAA
28111 AGTAAAATAATTAAATAA
1 AGTAAAATAATTAAATAA
*
28129 ATTAAA
1 AGTAAA
28135 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATAATTAAATAA
Found at i:29101 original size:21 final size:21
Alignment explanation
Indices: 29075--29171 Score: 142
Period size: 21 Copynumber: 4.7 Consensus size: 21
29065 GCGAATAAGT
29075 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
29096 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
29117 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
29137 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
29158 AAATCGCAATGCGA
1 AAATCGCAACGCGA
29172 TACTGACTAT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
20 16 0.24
21 50 0.76
ACGTcount: A:0.40, C:0.19, G:0.26, T:0.15
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:29202 original size:41 final size:41
Alignment explanation
Indices: 29157--29234 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
29147 GCGAATTGGG
* * *
29157 AAAATCGCAATGCGATACTGACTATCGTAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAATGCGATAATAA
* *
29198 AAAATCGCAACGAGATACTTACTTTCGCAATGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAATGCGATA
29235 CTGTCTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAATGCGATAATAA
Found at i:29203 original size:62 final size:61
Alignment explanation
Indices: 29058--29209 Score: 191
Period size: 62 Copynumber: 2.5 Consensus size: 61
29048 TTTTCCCAAT
* *
29058 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGAAAATCGCAACGCGAATTGGGAAAATCGCAACGCGAACT-GGAAAA
* * **
29120 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCGCAATGCGATACT-GACTA
1 TCGCAATGCGAATAAGAAAATCGCAACGCGAATTGGGAAAATCGCAACGCGA-ACTGGAAAA
*
29181 TCGTAATGCGATAATAA-AAAATCGCAACG
1 TCGCAATGCG--AATAAGAAAATCGCAACG
29210 AGATACTTAC
Statistics
Matches: 81, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
61 12 0.15
62 62 0.77
63 7 0.09
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.18
Consensus pattern (61 bp):
TCGCAATGCGAATAAGAAAATCGCAACGCGAATTGGGAAAATCGCAACGCGAACTGGAAAA
Found at i:29227 original size:20 final size:20
Alignment explanation
Indices: 29202--29254 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
29192 TAATAAAAAA
*
29202 TCGCAACGAGATACT-TACTT
1 TCGCAACGCGATACTGT-CTT
*
29222 TCGCAATGCGATACTGTCTT
1 TCGCAACGCGATACTGTCTT
29242 TCGCAACGCGATA
1 TCGCAACGCGATA
29255 ATACATAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGATACTGTCTT
Found at i:29470 original size:22 final size:22
Alignment explanation
Indices: 29442--29485 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
29432 CACTCTCTCA
29442 CCCATCTCC-GACGAAATCCGTC
1 CCCATCTCCAG-CGAAATCCGTC
29464 CCCATCTCCAGCGAAATCCGTC
1 CCCATCTCCAGCGAAATCCGTC
29486 TATCTAAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCAGCGAAATCCGTC
Found at i:29739 original size:20 final size:20
Alignment explanation
Indices: 29716--29753 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29706 TTAGTTTCTC
29716 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
29736 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
29754 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:31094 original size:18 final size:18
Alignment explanation
Indices: 31073--31117 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
31063 TCCACTTCGG
*
31073 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
31091 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
31109 GAGCCATCA
1 GAGCCATCA
31118 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:31644 original size:19 final size:20
Alignment explanation
Indices: 31590--31656 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
31580 TAGTTTACTT
* *
31590 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
31610 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
31630 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
31649 TCGCAACG
1 TCGCAACG
31657 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:31664 original size:14 final size:14
Alignment explanation
Indices: 31645--31702 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
31635 ATGCGAAATG
31645 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
31659 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
*
31675 ATGAAATCACAACGAC
1 A--AAATCGCAACGAC
31691 AAAATCGCAACG
1 AAAATCGCAACG
31703 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.50, C:0.24, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:31671 original size:33 final size:33
Alignment explanation
Indices: 31629--31719 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
31619 GGAAATGGCT
31629 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
31662 ATCGCAATGCGAAATG-AAATCACAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
31694 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
31720 TGCGATTTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:31776 original size:19 final size:19
Alignment explanation
Indices: 31750--31816 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
31740 GCGATTTTGT
**
31750 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
31769 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
31789 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
31808 CGTTGCGAT
1 CGTTGCGAT
31817 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:31796 original size:20 final size:19
Alignment explanation
Indices: 31762--31816 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
31752 TTGCGATTTT
*
31762 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
31781 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
31801 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
31817 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:33852 original size:33 final size:33
Alignment explanation
Indices: 33807--33924 Score: 137
Period size: 33 Copynumber: 3.4 Consensus size: 33
33797 AAAACAGACT
* ***
33807 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
* *
33840 ATCGCAATGCGAAATGAAAATCGCAATGCGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
33873 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAA
33911 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
33925 ATCGCAATGC
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
33 53 0.74
35 1 0.01
38 18 0.25
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:33858 original size:19 final size:19
Alignment explanation
Indices: 33836--33969 Score: 163
Period size: 19 Copynumber: 7.8 Consensus size: 19
33826 ATCGCAACGA
33836 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
33855 GAAAATCGCAATGC-----
1 GAAAATCGCAATGCGAAAT
33869 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
33888 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
33907 GAAAATCGCAATGC-----
1 GAAAATCGCAATGCGAAAT
33921 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
33940 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
33954 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
33970 TTTTCATTTC
Statistics
Matches: 102, Mismatches: 0, Indels: 28
0.78 0.00 0.22
Matches are distributed among these distances:
14 39 0.38
15 1 0.01
16 2 0.02
17 2 0.02
19 58 0.57
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:33892 original size:52 final size:52
Alignment explanation
Indices: 33836--33969 Score: 233
Period size: 52 Copynumber: 2.7 Consensus size: 52
33826 ATCGCAACGA
33836 GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAAATCGCAATGCGAAAT
33888 GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAAATCGCAATGCGAAAT
33940 GAAAATCGCAA--CG--A-GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGAAATGAAAATCGCAATGCGA
33970 TTTTCATTTC
Statistics
Matches: 82, Mismatches: 0, Indels: 5
0.94 0.00 0.06
Matches are distributed among these distances:
47 16 0.20
48 1 0.01
50 2 0.02
52 63 0.77
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (52 bp):
GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAAATCGCAATGCGAAAT
Found at i:33925 original size:33 final size:33
Alignment explanation
Indices: 33888--33969 Score: 146
Period size: 33 Copynumber: 2.5 Consensus size: 33
33878 AATGCGAAAT
* *
33888 GAAAATCGCAATGCGAAATGAAAATCGCAATGC
1 GAAAATCGCAATGCGAAATGAAAATCGCAACGA
33921 GAAAATCGCAATGCGAAATGAAAATCGCAACGA
1 GAAAATCGCAATGCGAAATGAAAATCGCAACGA
33954 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
33970 TTTTCATTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (33 bp):
GAAAATCGCAATGCGAAATGAAAATCGCAACGA
Found at i:34030 original size:20 final size:20
Alignment explanation
Indices: 33988--34044 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
33978 TCGCATTGCG
*
33988 ATTTTCTCGTTGCGATA-CC
1 ATTTTCGCGTTGCGATAGCC
34007 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
34027 ATTTTCGCGTTTCGATAG
1 ATTTTCGCGTTGCGATAG
34045 TCAAATGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 16 0.46
20 19 0.54
ACGTcount: A:0.16, C:0.23, G:0.21, T:0.40
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:35131 original size:24 final size:24
Alignment explanation
Indices: 35104--35157 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
35094 GTATTCGAAA
* *
35104 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
35128 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
35152 TTTGAT
1 TTTGAT
35158 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:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:37668 original size:19 final size:19
Alignment explanation
Indices: 37646--37776 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
37636 GGAAATTACT
37646 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
37665 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
37679 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
37698 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
37712 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
37731 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
37745 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
37764 ATCGCAACGCGAA
1 ATCGCAATGCGAA
37777 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:37688 original size:33 final size:33
Alignment explanation
Indices: 37646--37772 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
37636 GGAAATTACT
37646 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
37679 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
37711 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
37745 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
37773 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:37753 original size:66 final size:66
Alignment explanation
Indices: 37647--37779 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
37637 GAAATTACTA
*
37647 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
37712 T
66 T
*
37713 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
37778 T
66 T
37779 T
1 T
37780 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:37794 original size:19 final size:19
Alignment explanation
Indices: 37772--37813 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
37762 AAATCGCAAC
37772 GCGAATTTAATTTCGCGTT
1 GCGAATTTAATTTCGCGTT
* *
37791 GCGATTTTCATTTCGCGTT
1 GCGAATTTAATTTCGCGTT
37810 GCGA
1 GCGA
37814 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (19 bp):
GCGAATTTAATTTCGCGTT
Found at i:37814 original size:19 final size:19
Alignment explanation
Indices: 37781--37847 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
37771 CGCGAATTTA
37781 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
37800 ATTTCGCGTTGCGA--TTC
1 ATTTCGCGTTGCGATTTTC
*
37817 ---TCTCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
*
37833 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
37848 AGTACTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 10 0.25
16 3 0.08
17 3 0.08
19 24 0.60
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:37973 original size:14 final size:14
Alignment explanation
Indices: 37954--38004 Score: 84
Period size: 14 Copynumber: 3.6 Consensus size: 14
37944 CATCAATTAA
37954 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
37968 ACAAATCACCTTTT
1 ACAAATCAACTTTT
*
37982 ACAAATCACCTTTT
1 ACAAATCAACTTTT
37996 ACAAATCAA
1 ACAAATCAA
38005 TTAAACAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.43, C:0.25, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:39459 original size:41 final size:40
Alignment explanation
Indices: 39398--39478 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
39388 CGATGACAGT
* * *
39398 GGCCTCTTGAACGGTGGGAGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGA-GGACTCTCGAGGAATGATAGG
* *
39439 GGCCTCTTCAACGATAGGAGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGACTCTCGAGGAATGATAGG
39479 CGAGTCGGGC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
40 19 0.54
41 16 0.46
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.21
Consensus pattern (40 bp):
GGCCTCTTCAACGATAGGAGGACTCTCGAGGAATGATAGG
Found at i:39475 original size:40 final size:41
Alignment explanation
Indices: 39389--39478 Score: 110
Period size: 41 Copynumber: 2.2 Consensus size: 41
39379 CCTCTTCAAC
* * * * *
39389 GATGACAGTGGCCTCTTGAACGGTGGGAGGGACTCTCGAGG
1 GATGATAGGGGCCTCTTCAACGATAGGAGGGACTCTCGAGG
* *
39430 AATGATAGGGGCCTCTTCAACGATAGGA-GGACTCTTGAGG
1 GATGATAGGGGCCTCTTCAACGATAGGAGGGACTCTCGAGG
39470 GATGATAGG
1 GATGATAGG
39479 CGAGTCGGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
40 19 0.46
41 22 0.54
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.21
Consensus pattern (41 bp):
GATGATAGGGGCCTCTTCAACGATAGGAGGGACTCTCGAGG
Found at i:41505 original size:20 final size:19
Alignment explanation
Indices: 41474--41534 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
41464 TCTTTTGGTT
41474 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
41493 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
41514 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
41533 GA
1 GA
41535 GAATCGCAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.11
20 29 0.83
21 2 0.06
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:41556 original size:33 final size:33
Alignment explanation
Indices: 41499--41594 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 33
41489 ACGAGATAAT
*
41499 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
41533 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* *
41566 GACAATCGCAACGCGAAATGA-AATCGCAA
1 GAGAATCGCAACGCGAAATGACTATCGCAA
41595 TGCGATTTGG
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
32 6 0.11
33 37 0.65
34 14 0.25
ACGTcount: A:0.40, C:0.25, G:0.24, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:41629 original size:19 final size:19
Alignment explanation
Indices: 41605--41674 Score: 69
Period size: 19 Copynumber: 3.9 Consensus size: 19
41595 TGCGATTTGG
41605 TTTCGCGTTGCGATTTTTA
1 TTTCGCGTTGCGATTTTTA
41624 TTTCGCGTTGCGA---TTA
1 TTTCGCGTTGCGATTTTTA
* **
41640 --TCTCGTTGCGATAGTTA
1 TTTCGCGTTGCGATTTTTA
41657 TTTCCGCGTTGCGATTTT
1 TTT-CGCGTTGCGATTTT
41675 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
14 10 0.24
16 3 0.07
17 3 0.07
19 14 0.34
20 11 0.27
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTTA
Found at i:42191 original size:20 final size:20
Alignment explanation
Indices: 42166--42279 Score: 120
Period size: 20 Copynumber: 5.7 Consensus size: 20
42156 CGCTATGTAA
* *
42166 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
42186 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
42206 ATCCCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
42227 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
42247 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
42267 ATCGCATTGCGAT
1 ATCGCATTGCGAT
42280 TTTCCCAATT
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
20 67 0.84
21 13 0.16
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:42268 original size:61 final size:61
Alignment explanation
Indices: 42166--42282 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
42156 CGCTATGTAA
* * *
42166 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAAGTAAGTATCCCGTTGCGATTTTTTATT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGAAAGTAAGTATCCCATTGCGATTTTTTATT
* * * *
42227 ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGAAAGTAAGTATCCCATTGCGATTTT
42283 CCCAATTCGC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTCAGTATCGCATTGCGAAAGTAAGTATCCCATTGCGATTTTTTATT
Found at i:42297 original size:21 final size:21
Alignment explanation
Indices: 42268--42360 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
42258 ATAGTCAGTA
42268 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
42289 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
42309 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
42330 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
42350 TCGCATTGCGA
1 TCGCATTGCGA
42361 ATTGAGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:42298 original size:41 final size:41
Alignment explanation
Indices: 42268--42360 Score: 150
Period size: 41 Copynumber: 2.3 Consensus size: 41
42258 ATAGTCAGTA
* *
42268 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
* *
42309 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
42350 TCGCATTGCGA
1 TCGCATTGCGA
42361 ATTGAGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:42298 original size:61 final size:61
Alignment explanation
Indices: 42166--42300 Score: 164
Period size: 61 Copynumber: 2.2 Consensus size: 61
42156 CGCTATGTAA
* * * ** *
42166 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAAGTAAGTATCCCGTTGCGATTTTTTATT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGAAAGTAAGTATCCCATTGCGATTTTCCAAT
* * * *
42227 ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGAAAGTAAGTATCCCATTGCGATTTT-CCAAT
42289 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
42301 TTACTTATTC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
61 60 0.97
62 2 0.03
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTCAGTATCGCATTGCGAAAGTAAGTATCCCATTGCGATTTTCCAAT
Found at i:49461 original size:6 final size:6
Alignment explanation
Indices: 49452--50334 Score: 1655
Period size: 6 Copynumber: 148.8 Consensus size: 6
49442 TACAAGTGTA
*
49452 TATTTA TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
1 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
49500 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
1 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
49548 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
1 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
49596 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
1 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
49644 TA-TT- TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
1 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
49690 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TA-TTG TATTTG
1 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
49737 TATTTG TATTTG TATTTG TATTTG --TTTG TATTTG TATTTG TATTTG
1 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
49783 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
1 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
49831 TATTTG TATTTG TATTTG TATTTG TA-TTG TATTTG TATTTG TATTTG
1 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
49878 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
1 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
49926 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
1 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
49974 TATTTG TATTTTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
1 TATTTG TA--TTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
50024 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
1 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
50072 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
1 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
50120 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
1 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
50168 TATTTG TATTTG TA-TTG TATTTG TATTTG TATTTG TA-TTG TA-TT-
1 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
50212 TATTTG TA-TTG TATTTG TATTTG TA-TTG TATTTG TATTTG TATTTG
1 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
50258 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
1 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
50306 TATTTG TATTTG TATTTG TATTTG TATTT
1 TATTTG TATTTG TATTTG TATTTG TATTT
50335 ACAGTCCAAG
Statistics
Matches: 863, Mismatches: 1, Indels: 26
0.97 0.00 0.03
Matches are distributed among these distances:
4 8 0.01
5 38 0.04
6 811 0.94
8 6 0.01
ACGTcount: A:0.17, C:0.00, G:0.16, T:0.67
Consensus pattern (6 bp):
TATTTG
Found at i:52137 original size:2 final size:2
Alignment explanation
Indices: 52130--52177 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
52120 TTCGAACAAT
52130 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
52172 TA TA TA
1 TA TA TA
52178 AAGCATGATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53324 original size:2 final size:2
Alignment explanation
Indices: 53317--53344 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
53307 AAATAAATAA
53317 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53345 TACTTTTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.