Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003761.1 Hibiscus syriacus cultivar Beakdansim tig00008060_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: 73734
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:4054 original size:19 final size:19
Alignment explanation
Indices: 4032--4068 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4022 TAGTGTTCAA
*
4032 GTATTTGAATTATGTTTTG
1 GTATTTGAACTATGTTTTG
4051 GTATTTGAACTATGTTTT
1 GTATTTGAACTATGTTTT
4069 CTTATGTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.03, G:0.19, T:0.57
Consensus pattern (19 bp):
GTATTTGAACTATGTTTTG
Found at i:5961 original size:12 final size:12
Alignment explanation
Indices: 5944--5978 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
5934 TTGAACCCAA
5944 AATTAATCGAAT
1 AATTAATCGAAT
5956 AATTAATCGAAT
1 AATTAATCGAAT
5968 AATTAATCGAA
1 AATTAATCGAA
5979 AAAAATCAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (12 bp):
AATTAATCGAAT
Found at i:14817 original size:29 final size:29
Alignment explanation
Indices: 14772--14829 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
14762 GTGTTGGTCG
* *
14772 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATACCTTCCCGGCGACCTAC
* *
14801 TAGGTCGCCATATCTTCCCGGCGAGCTAC
1 TAGGTCGCCATACCTTCCCGGCGACCTAC
14830 AAGAGATTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.16, C:0.36, G:0.26, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATACCTTCCCGGCGACCTAC
Found at i:14938 original size:33 final size:33
Alignment explanation
Indices: 14886--14958 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
14876 GGCCATCCGA
* * *
14886 CCGAGGCCATCTGAACGAGCAATGCGAAGGCAT
1 CCGAGGGCAACTGAACGAGCAATGCGAAGGAAT
* * *
14919 CCGAGGGCAACTGAGCGAGCTATGCGAGGGAAT
1 CCGAGGGCAACTGAACGAGCAATGCGAAGGAAT
14952 CCGAGGG
1 CCGAGGG
14959 AAGCCGAGCG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.27, C:0.25, G:0.37, T:0.11
Consensus pattern (33 bp):
CCGAGGGCAACTGAACGAGCAATGCGAAGGAAT
Found at i:14968 original size:33 final size:33
Alignment explanation
Indices: 14901--14970 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
14891 GCCATCTGAA
* *
14901 CGAGCAATGCGAAGGCATCCGAGGGCAACTGAG
1 CGAGCAATGCGAAGGAATCCGAGGGCAACCGAG
* *
14934 CGAGCTATGCGAGGGAATCCGAGGG-AAGCCGAG
1 CGAGCAATGCGAAGGAATCCGAGGGCAA-CCGAG
14967 CGAG
1 CGAG
14971 GGTAGGTCGC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 2 0.06
33 30 0.94
ACGTcount: A:0.29, C:0.23, G:0.40, T:0.09
Consensus pattern (33 bp):
CGAGCAATGCGAAGGAATCCGAGGGCAACCGAG
Found at i:15007 original size:29 final size:29
Alignment explanation
Indices: 14974--15030 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
14964 GAGCGAGGGT
14974 AGGTCGCCCGGAGGGCATGGCGACCTATA
1 AGGTCGCCCGGAGGGCATGGCGACCTATA
15003 AGGTCGCCCGGAGGGCATGGCGACCTAT
1 AGGTCGCCCGGAGGGCATGGCGACCTAT
15031 GTGTTGGGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.19, C:0.28, G:0.39, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTATA
Found at i:15075 original size:12 final size:12
Alignment explanation
Indices: 15058--15082 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15048 TGCCATGCAA
15058 CACGTTCATTCT
1 CACGTTCATTCT
15070 CACGTTCATTCT
1 CACGTTCATTCT
15082 C
1 C
15083 TCTGTTTGAG
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:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (12 bp):
CACGTTCATTCT
Found at i:15362 original size:2 final size:2
Alignment explanation
Indices: 15355--15381 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
15345 GTGTTTTTCA
15355 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
15382 AAGATAAACT
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:21257 original size:25 final size:24
Alignment explanation
Indices: 21224--21270 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
21214 CATTCATCAT
21224 ATAACACATATATCACTATATCAAAA
1 ATAACACATATATCA-T-TATCAAAA
21250 ATAA-ACATATATCATTATCAA
1 ATAACACATATATCATTATCAA
21271 CGCGTTTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 6 0.29
24 1 0.05
25 10 0.48
26 4 0.19
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (24 bp):
ATAACACATATATCATTATCAAAA
Found at i:21686 original size:32 final size:32
Alignment explanation
Indices: 21571--21691 Score: 122
Period size: 31 Copynumber: 3.8 Consensus size: 32
21561 TCGACAACTA
* * * *
21571 TCCATAGGTCCCGAAGAACCTAGGTAAAT-TG
1 TCCATATGTTCCGAAGAACATAGGTAATTCTG
** *
21602 TCCATATGTTCCTTAGAACATAGGT-ATACTG
1 TCCATATGTTCCGAAGAACATAGGTAATTCTG
**
21633 TCCATATGTCTCAAAAG-ACATAGGTAATTCTG
1 TCCATATGT-TCCGAAGAACATAGGTAATTCTG
*
21665 TCCATATGTTCCGTAGAACATAGGTAA
1 TCCATATGTTCCGAAGAACATAGGTAA
21692 ACCCTCGACT
Statistics
Matches: 72, Mismatches: 14, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
30 1 0.01
31 43 0.60
32 28 0.39
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (32 bp):
TCCATATGTTCCGAAGAACATAGGTAATTCTG
Found at i:23275 original size:34 final size:32
Alignment explanation
Indices: 23222--23291 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
23212 CCTTACAAAC
*
23222 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
23254 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
23288 TCCC
1 TCCC
23292 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:23534 original size:21 final size:21
Alignment explanation
Indices: 23506--23545 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
23496 AGTCGTATAT
23506 AGCCTTTGGGGATG-TTTTGG
1 AGCCTTTGGGGATGATTTTGG
23526 AGCCGTTTGGGGATGATTTT
1 AGCC-TTTGGGGATGATTTT
23546 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 10 0.56
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.38, T:0.40
Consensus pattern (21 bp):
AGCCTTTGGGGATGATTTTGG
Found at i:23599 original size:21 final size:21
Alignment explanation
Indices: 23573--23613 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
23563 CCCAGAATAG
*
23573 AGGGAATCGGTACACCTTCAA
1 AGGGAATCGATACACCTTCAA
*
23594 AGGGAATCGATACCCCTTCA
1 AGGGAATCGATACACCTTCA
23614 TAATATTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.27, G:0.22, T:0.20
Consensus pattern (21 bp):
AGGGAATCGATACACCTTCAA
Found at i:23739 original size:23 final size:23
Alignment explanation
Indices: 23707--23751 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
23697 AAAACCTGCA
* *
23707 GGGGGTATCTGTACCCCCTGGGG
1 GGGGGAATCTATACCCCCTGGGG
23730 GGGGGAATCTATACCCCCTGGG
1 GGGGGAATCTATACCCCCTGGG
23752 CAATCTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.13, C:0.27, G:0.40, T:0.20
Consensus pattern (23 bp):
GGGGGAATCTATACCCCCTGGGG
Found at i:23862 original size:29 final size:29
Alignment explanation
Indices: 23841--23898 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
23831 AAACTTTGAA
23841 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
23870 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
23899 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:23888 original size:30 final size:30
Alignment explanation
Indices: 23841--23900 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
23831 AAACTTTGAA
23841 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
23870 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
23901 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:24200 original size:19 final size:20
Alignment explanation
Indices: 24161--24200 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
24151 AAAACCTGCA
*
24161 GGGGGTATCTGCCCCCTGGG
1 GGGGGTATCTGCACCCTGGG
*
24181 GGGGGTATCTGTACCC-GGG
1 GGGGGTATCTGCACCCTGGG
24200 G
1 G
24201 TATCTGTACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.07, C:0.25, G:0.47, T:0.20
Consensus pattern (20 bp):
GGGGGTATCTGCACCCTGGG
Found at i:24202 original size:15 final size:15
Alignment explanation
Indices: 24182--24211 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
24172 CCCCCTGGGG
24182 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
24197 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
24212 CCTTGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:24232 original size:36 final size:35
Alignment explanation
Indices: 24162--24232 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 35
24152 AAACCTGCAG
* *
24162 GGGGTATCTGCCCCCTGGGGGGGGTATCTGTACCC
1 GGGGTATCTGCCCCCTGGGGGGGGAATCTATACCC
*
24197 GGGGTATCTGTACCCCCT-TGGGGGGAATCTATACCC
1 GGGGTATCTG--CCCCCTGGGGGGGGAATCTATACCC
24233 CCTAGGCAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 10 0.32
36 15 0.48
37 6 0.19
ACGTcount: A:0.13, C:0.28, G:0.35, T:0.24
Consensus pattern (35 bp):
GGGGTATCTGCCCCCTGGGGGGGGAATCTATACCC
Found at i:24360 original size:29 final size:31
Alignment explanation
Indices: 24328--24387 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
24318 AAACTTTGAA
24328 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
24357 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
24388 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:26211 original size:64 final size:62
Alignment explanation
Indices: 26143--26320 Score: 191
Period size: 64 Copynumber: 2.8 Consensus size: 62
26133 GGGACACTTA
*
26143 GTGCATCGGTGCACTAAGGATGCATCGATGCATAAAATGCATTCGATGTTTGAAAA-ATAGCCTG
1 GTGCATCGATGCA-T-AGGATGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAT-GCC-G
26207 -
62 C
* * *
26207 GTGCATCGATGCATTGCTTG-TGCATCGATGCATCAAATGCATTCGATGTTTGAAAATATTCCGC
1 GTGCATCGATGCATAG---GATGCATCGATGCATAAAATGCATTCGATGTTTGAAAATATGCCGC
* * *
26271 GTGCATCGATGCATGGAGAGTGCATCGGTGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATAG-GA-TGCATCGATGCATAAAATGCATTCGATGTT
26321 CAATTAAATC
Statistics
Matches: 99, Mismatches: 8, Indels: 14
0.82 0.07 0.12
Matches are distributed among these distances:
62 2 0.02
63 2 0.02
64 92 0.93
65 3 0.03
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (62 bp):
GTGCATCGATGCATAGGATGCATCGATGCATAAAATGCATTCGATGTTTGAAAATATGCCGC
Found at i:26339 original size:64 final size:61
Alignment explanation
Indices: 26163--26350 Score: 180
Period size: 64 Copynumber: 2.9 Consensus size: 61
26153 GCACTAAGGA
* * * ***
26163 TGCATCGATGCATAAAATGCATTCGATGTTTGAAAAATAGCCTGGTGCATCGATGCATTGCTTG
1 TGCATCGATGCATAAAATGCATTCGATG-TTCAAAAAT--CATGGTGCATCGATGCATGGAGAG
* * *
26227 TGCATCGATGCATCAAATGCATTCGATGTTTGAAAATATTC-CGCGTGCATCGATGCATGGAGAG
1 TGCATCGATGCATAAAATGCATTCGATG-TTCAAAA-A-TCATG-GTGCATCGATGCATGGAGAG
* *
26291 TGCATCGGTGCATGAAATGCATTCGATGTTCAATTAAATCATAGGTGCATCGATGCATGG
1 TGCATCGATGCATAAAATGCATTCGATGTTCAA--AAATCAT-GGTGCATCGATGCATGG
26351 TTTGATGCAT
Statistics
Matches: 107, Mismatches: 10, Indels: 14
0.82 0.08 0.11
Matches are distributed among these distances:
63 7 0.07
64 95 0.89
65 4 0.04
66 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (61 bp):
TGCATCGATGCATAAAATGCATTCGATGTTCAAAAATCATGGTGCATCGATGCATGGAGAG
Found at i:31778 original size:22 final size:21
Alignment explanation
Indices: 31736--31775 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
31726 GAGTTTGTTT
*
31736 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
31757 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
31776 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:34801 original size:34 final size:32
Alignment explanation
Indices: 34748--34817 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 32
34738 CCTTACAAAC
*
34748 TCCCTAGTTTTTCCGGGCTAAGCTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAGCTAGAACCTT
34780 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAGCTAGAACCTT
34814 TCCC
1 TCCC
34818 CTTTACAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 7 0.20
33 5 0.14
34 23 0.66
ACGTcount: A:0.20, C:0.31, G:0.17, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAGCTAGAACCTT
Found at i:35123 original size:21 final size:21
Alignment explanation
Indices: 35099--35141 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
35089 CCCAGAATAG
*
35099 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
35120 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
35141 A
1 A
35142 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:35204 original size:22 final size:22
Alignment explanation
Indices: 35177--35220 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
35167 CTGTTGAACA
35177 GGGGGGAATCGGTACCCCCTGG
1 GGGGGGAATCGGTACCCCCTGG
35199 GGGGGGAATCGGTACCCCCTGG
1 GGGGGGAATCGGTACCCCCTGG
35221 ACATTATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.14, C:0.27, G:0.45, T:0.14
Consensus pattern (22 bp):
GGGGGGAATCGGTACCCCCTGG
Found at i:35279 original size:21 final size:21
Alignment explanation
Indices: 35254--35332 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
35244 AAAACCTGCA
35254 GGGGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
*
35275 GGGGGTATCTATA--CCC---
1 GGGGGTATCTGTACCCCCTGG
35291 -GGGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
* *
35311 GGGGGAATCTCTACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
35332 G
1 G
35333 CAATCTTGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
15 11 0.23
17 3 0.06
19 3 0.06
21 31 0.65
ACGTcount: A:0.13, C:0.29, G:0.35, T:0.23
Consensus pattern (21 bp):
GGGGGTATCTGTACCCCCTGG
Found at i:35296 original size:15 final size:15
Alignment explanation
Indices: 35276--35305 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35266 ACCCCCTGGG
35276 GGGGTATCTATACCC
1 GGGGTATCTATACCC
*
35291 GGGGTATCTGTACCC
1 GGGGTATCTATACCC
35306 CCTGGGGGGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.27, G:0.30, T:0.27
Consensus pattern (15 bp):
GGGGTATCTATACCC
Found at i:35302 original size:36 final size:36
Alignment explanation
Indices: 35255--35326 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
35245 AAACCTGCAG
*
35255 GGGGTATCTGTACCCCCTGGGGGGGTATCTATACCC
1 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
*
35291 GGGGTATCTGTACCCCCTGGGGGGGAATCTCTACCC
1 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
35327 CCTGGGCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.14, C:0.29, G:0.33, T:0.24
Consensus pattern (36 bp):
GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
Found at i:35454 original size:29 final size:31
Alignment explanation
Indices: 35422--35481 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
35412 AAACTTTGAA
35422 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
35451 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
35482 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:37701 original size:11 final size:11
Alignment explanation
Indices: 37672--37705 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
37662 ATATTTTTAA
* *
37672 ATTTTTTATGT
1 ATTTTTTTTTT
37683 ATTTTTTTTTT
1 ATTTTTTTTTT
37694 ATTTTTTTTTT
1 ATTTTTTTTTT
37705 A
1 A
37706 CCTTTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (11 bp):
ATTTTTTTTTT
Found at i:38707 original size:2 final size:2
Alignment explanation
Indices: 38700--38724 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38690 ATTAATTAAT
38700 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
38725 CTTAATGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45544 original size:35 final size:36
Alignment explanation
Indices: 45505--45596 Score: 109
Period size: 35 Copynumber: 2.6 Consensus size: 36
45495 AAAACATCTG
*
45505 ATATATGTAAATATCTAATAACTATAATATC-TGAT
1 ATATATGTAAATATCTAATAACTATAATAGCTTGAT
* * * *
45540 ATATATGTAAATATCTTATAATTGTAATCGCTTGAT
1 ATATATGTAAATATCTAATAACTATAATAGCTTGAT
*
45576 AT-T-TGTAAATATCTGATAACT
1 ATATATGTAAATATCTAATAACT
45597 GTAAACATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
34 16 0.33
35 27 0.55
36 6 0.12
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (36 bp):
ATATATGTAAATATCTAATAACTATAATAGCTTGAT
Found at i:45565 original size:17 final size:17
Alignment explanation
Indices: 45500--45601 Score: 75
Period size: 17 Copynumber: 5.9 Consensus size: 17
45490 ACTGCAAAAC
45500 ATCTGAT-ATATGTAAAT
1 ATCTGATAAT-TGTAAAT
* * *
45517 ATCTAATAACTAT-AAT
1 ATCTGATAATTGTAAAT
45533 ATCTGATATATATGTAAAT
1 ATCTGATA-AT-TGTAAAT
*
45552 ATCTTATAATTGT-AAT
1 ATCTGATAATTGTAAAT
** *
45568 CGCTTGATATTTGTAAAT
1 ATC-TGATAATTGTAAAT
*
45586 ATCTGATAACTGTAAA
1 ATCTGATAATTGTAAA
45602 CATTTAAAAT
Statistics
Matches: 64, Mismatches: 15, Indels: 12
0.70 0.16 0.13
Matches are distributed among these distances:
16 14 0.22
17 31 0.48
18 9 0.14
19 10 0.16
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (17 bp):
ATCTGATAATTGTAAAT
Found at i:51698 original size:32 final size:32
Alignment explanation
Indices: 51626--51714 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 32
51616 GAAAGACCTA
** * *
51626 TCCATATGTTTCGAAGAACATAGGT-A-ACTG
1 TCCATATGTCCCGAAGGACATAGGTAATATTG
* *
51656 TCCATTTGTCCCGAAGGACATATGTAATATTG
1 TCCATATGTCCCGAAGGACATAGGTAATATTG
*
51688 TCCATATGTCCCGAATGACATAGGTAA
1 TCCATATGTCCCGAAGGACATAGGTAA
51715 CCCTCGACTC
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
30 20 0.42
31 1 0.02
32 27 0.56
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (32 bp):
TCCATATGTCCCGAAGGACATAGGTAATATTG
Found at i:52679 original size:20 final size:20
Alignment explanation
Indices: 52654--52727 Score: 64
Period size: 18 Copynumber: 3.6 Consensus size: 20
52644 CCTTTGAAGA
52654 GGTATCGGTACCCACTATAG
1 GGTATCGGTACCCACTATAG
52674 GGTATCGGTACTACC-CTAGCTGAG
1 GGTATCGGTAC--CCACTA--T-AG
* *
52698 GGTATCGATACCTAC-AT-G
1 GGTATCGGTACCCACTATAG
52716 GGTATCGGTACC
1 GGTATCGGTACC
52728 AAAATTTCAT
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
18 12 0.27
20 12 0.27
21 3 0.07
22 4 0.09
23 2 0.04
24 12 0.27
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.26
Consensus pattern (20 bp):
GGTATCGGTACCCACTATAG
Found at i:56323 original size:18 final size:19
Alignment explanation
Indices: 56297--56332 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
56287 AATTTCGGTT
56297 AAATAAAAGGAAA-AAGGA
1 AAATAAAAGGAAAGAAGGA
*
56315 AAATGAAAGGAAAGAAGG
1 AAATAAAAGGAAAGAAGG
56333 GGTGTTTCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.67, C:0.00, G:0.28, T:0.06
Consensus pattern (19 bp):
AAATAAAAGGAAAGAAGGA
Done.