Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002390.1 Hibiscus syriacus cultivar Beakdansim tig00004889_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: 111349
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:8741 original size:14 final size:13
Alignment explanation
Indices: 8697--8760 Score: 65
Period size: 14 Copynumber: 4.6 Consensus size: 13
8687 ACAATTCAGA
*
8697 AAATTAAAAGCTGG
1 AAATTAAAGGCT-G
*
8711 AATTTAAAGGACTG
1 AAATTAAAGG-CTG
*
8725 AAATGTAAATGCTG
1 AAAT-TAAAGGCTG
8739 AAATTTAAAGGCTG
1 AAA-TTAAAGGCTG
8753 AAATTAAA
1 AAATTAAA
8761 ATAACATAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
13 5 0.12
14 29 0.69
15 8 0.19
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.27
Consensus pattern (13 bp):
AAATTAAAGGCTG
Found at i:8754 original size:28 final size:28
Alignment explanation
Indices: 8697--8761 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 28
8687 ACAATTCAGA
*
8697 AAATTAAAAGCTGGAATTTAAAGGACTG
1 AAATTAAAAGCTGAAATTTAAAGGACTG
*
8725 AAATGTAAATGCTGAAATTTAAAGG-CTG
1 AAAT-TAAAAGCTGAAATTTAAAGGACTG
8753 AAATTAAAA
1 AAATTAAAA
8762 TAACATAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 4 0.12
28 11 0.33
29 18 0.55
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.26
Consensus pattern (28 bp):
AAATTAAAAGCTGAAATTTAAAGGACTG
Found at i:8762 original size:28 final size:29
Alignment explanation
Indices: 8697--8762 Score: 93
Period size: 28 Copynumber: 2.3 Consensus size: 29
8687 ACAATTCAGA
*
8697 AAATTAAAA-GCTGGAATTTAAAGGACTG
1 AAATTAAAATGCTGAAATTTAAAGGACTG
8725 AAATGT-AAATGCTGAAATTTAAAGG-CTG
1 AAAT-TAAAATGCTGAAATTTAAAGGACTG
8753 AAATTAAAAT
1 AAATTAAAAT
8763 AACATAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
27 1 0.03
28 18 0.53
29 15 0.44
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.27
Consensus pattern (29 bp):
AAATTAAAATGCTGAAATTTAAAGGACTG
Found at i:21564 original size:24 final size:22
Alignment explanation
Indices: 21513--21564 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 22
21503 TTTTTCGAAT
21513 ATAATTAAAATTCTAAAAAAAA
1 ATAATTAAAATTCTAAAAAAAA
* *
21535 ATTAATTAAACATTTTAAAAATATA
1 A-TAATTAAA-ATTCTAAAAA-AAA
21560 ATAAT
1 ATAAT
21565 AATAATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 1 0.04
23 8 0.32
24 13 0.52
25 3 0.12
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (22 bp):
ATAATTAAAATTCTAAAAAAAA
Found at i:27256 original size:17 final size:17
Alignment explanation
Indices: 27216--27257 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
27206 TTAATGCATC
27216 AATAATGAAATCATACG
1 AATAATGAAATCATACG
*
27233 AATTAAT-AAATTATATCG
1 AA-TAATGAAATCATA-CG
27251 AATAATG
1 AATAATG
27258 GACTAATGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (17 bp):
AATAATGAAATCATACG
Found at i:28771 original size:5 final size:5
Alignment explanation
Indices: 28757--28789 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
28747 ATAAAGTCAT
28757 AATT- AATTA AATTA AATTA AATTA AATTA AATT
1 AATTA AATTA AATTA AATTA AATTA AATTA AATT
28790 TTGTCCTCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
AATTA
Found at i:30438 original size:6 final size:6
Alignment explanation
Indices: 30427--30470 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
30417 CGCTCAACAT
30427 TATCCC TATCCC TATCCC TATCCC TATCCC TATCCC TATCCC TA
1 TATCCC TATCCC TATCCC TATCCC TATCCC TATCCC TATCCC TA
30471 ATCCATCCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.18, C:0.48, G:0.00, T:0.34
Consensus pattern (6 bp):
TATCCC
Found at i:31958 original size:2 final size:2
Alignment explanation
Indices: 31951--32010 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
31941 TTATCTCTAA
31951 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
31993 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
32011 GGGTCGGGTC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33365 original size:17 final size:19
Alignment explanation
Indices: 33339--33380 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
33329 TAAATTATCA
*
33339 AAATTTATTA-TT-ATAAT
1 AAATTAATTATTTGATAAT
33356 AAATTAATTATTTGATAAT
1 AAATTAATTATTTGATAAT
33375 -AATTAA
1 AAATTAA
33381 GGGACCTCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 8 0.36
19 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
AAATTAATTATTTGATAAT
Found at i:38576 original size:17 final size:17
Alignment explanation
Indices: 38554--38588 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
38544 TCTTCTCCAA
38554 AAGAATGGCTAAATATT
1 AAGAATGGCTAAATATT
38571 AAGAATGGCTAAATATT
1 AAGAATGGCTAAATATT
38588 A
1 A
38589 TTGTTGATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.06, G:0.17, T:0.29
Consensus pattern (17 bp):
AAGAATGGCTAAATATT
Found at i:39202 original size:22 final size:21
Alignment explanation
Indices: 39177--39218 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
39167 GGATTCTACC
39177 TAAAAATCAC-AAAATATATATA
1 TAAAAAT-ACTAAAATA-ATATA
39199 TAAAAATACTAAAATAATAT
1 TAAAAATACTAAAATAATAT
39219 CATTTGATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAAATACTAAAATAATATA
Found at i:48818 original size:16 final size:13
Alignment explanation
Indices: 48784--48810 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
48774 TGAATAAAAT
48784 TAATTATATATTA
1 TAATTATATATTA
48797 TAATTATATATTA
1 TAATTATATATTA
48810 T
1 T
48811 TTAAATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAATTATATATTA
Found at i:48820 original size:20 final size:21
Alignment explanation
Indices: 48797--48840 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
48787 TTATATATTA
*
48797 TAATTATATATTAT-TTAAAT
1 TAATTATAAATTATCTTAAAT
*
48817 TAATTATAAATTATCTTTAAT
1 TAATTATAAATTATCTTAAAT
48838 TAA
1 TAA
48841 AAAATATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TAATTATAAATTATCTTAAAT
Found at i:48853 original size:27 final size:29
Alignment explanation
Indices: 48789--48855 Score: 70
Period size: 27 Copynumber: 2.4 Consensus size: 29
48779 AAAATTAATT
* *
48789 ATATATTATAATTATATATTATTTAAATTA
1 ATATATTA-AATTATATATTAATTAAATAA
*
48819 AT-TA-TAAATTATCT-TTAATTAAA-AA
1 ATATATTAAATTATATATTAATTAAATAA
48844 ATATATTAAATT
1 ATATATTAAATT
48856 TTAAAAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
25 3 0.09
26 10 0.31
27 13 0.41
28 2 0.06
29 2 0.06
30 2 0.06
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (29 bp):
ATATATTAAATTATATATTAATTAAATAA
Found at i:48891 original size:16 final size:17
Alignment explanation
Indices: 48870--48901 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
48860 AAAATTTAAA
48870 AAAAATTAATT-AATTC
1 AAAAATTAATTGAATTC
48886 AAAAATTAATTGAATT
1 AAAAATTAATTGAATT
48902 AATCGAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
AAAAATTAATTGAATTC
Found at i:51660 original size:21 final size:23
Alignment explanation
Indices: 51636--51681 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
51626 ATGTTTTAAT
* *
51636 TTTTATTTTA-TT-TTTCAAAAA
1 TTTTATTATACTTGTTTAAAAAA
51657 TTTTATTATACTTGTTTAAAAAA
1 TTTTATTATACTTGTTTAAAAAA
51680 TT
1 TT
51682 AAAATTGATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.43
22 2 0.10
23 10 0.48
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (23 bp):
TTTTATTATACTTGTTTAAAAAA
Found at i:54775 original size:5 final size:5
Alignment explanation
Indices: 54765--54795 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
54755 TGACTTAGAA
*
54765 ACCCG ACCCG ATCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG ACCCG A
54796 AATAATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.23, C:0.55, G:0.19, T:0.03
Consensus pattern (5 bp):
ACCCG
Found at i:71709 original size:25 final size:24
Alignment explanation
Indices: 71681--71727 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
71671 AATTTAACGA
71681 ATATAAAAATAAAAAAATATATTAT
1 ATATAAAAAT-AAAAAATATATTAT
**
71706 ATATATGAATAAAAAATATATT
1 ATATAAAAATAAAAAATATATT
71728 CACATAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (24 bp):
ATATAAAAATAAAAAATATATTAT
Found at i:76034 original size:17 final size:16
Alignment explanation
Indices: 76009--76052 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
75999 ATTTTTAATA
76009 AAAATTATAAAAAATT
1 AAAATTATAAAAAATT
* *
76025 AAAATATATAATAATTT
1 AAAAT-TATAAAAAATT
*
76042 AAAATTTTAAA
1 AAAATTATAAA
76053 CACGATTGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAATTATAAAAAATT
Found at i:78598 original size:20 final size:20
Alignment explanation
Indices: 78575--78634 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
78565 TCCAATTTCA
* *
78575 CAACGCGAATAGGTAAATCG
1 CAACGCAAATATGTAAATCG
78595 CAACG-ATAATATGTAAATCG
1 CAACGCA-AATATGTAAATCG
*
78615 CAACGCAAATTTGTAAATCG
1 CAACGCAAATATGTAAATCG
78635 TAACACAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 34 0.97
21 1 0.03
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (20 bp):
CAACGCAAATATGTAAATCG
Found at i:78743 original size:20 final size:20
Alignment explanation
Indices: 78718--78756 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
78708 GAATTCGGGC
*
78718 GGAATTAGCGTTGCGAATTA
1 GGAATTAGCGTCGCGAATTA
78738 GGAATTAGCGTCGCGAATT
1 GGAATTAGCGTCGCGAATT
78757 TGAAATTTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.13, G:0.31, T:0.28
Consensus pattern (20 bp):
GGAATTAGCGTCGCGAATTA
Found at i:78763 original size:20 final size:20
Alignment explanation
Indices: 78720--78763 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
78710 ATTCGGGCGG
* *
78720 AATTAGCGTTGCGAATTAGG
1 AATTAGCGTCGCGAATTAGA
*
78740 AATTAGCGTCGCGAATTTGA
1 AATTAGCGTCGCGAATTAGA
78760 AATT
1 AATT
78764 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (20 bp):
AATTAGCGTCGCGAATTAGA
Found at i:81321 original size:35 final size:35
Alignment explanation
Indices: 81275--81351 Score: 154
Period size: 35 Copynumber: 2.2 Consensus size: 35
81265 TTAGGAAAGG
81275 CATGTTTTCTTTTTTCATTATTATTAAAGGGAAGA
1 CATGTTTTCTTTTTTCATTATTATTAAAGGGAAGA
81310 CATGTTTTCTTTTTTCATTATTATTAAAGGGAAGA
1 CATGTTTTCTTTTTTCATTATTATTAAAGGGAAGA
81345 CATGTTT
1 CATGTTT
81352 ATATCCATGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.27, C:0.09, G:0.14, T:0.49
Consensus pattern (35 bp):
CATGTTTTCTTTTTTCATTATTATTAAAGGGAAGA
Found at i:94296 original size:20 final size:20
Alignment explanation
Indices: 94273--94339 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
94263 GTTTTCAGAT
*
94273 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTCTGACTA
* * * *
94293 TCGCAATGCGAATGTGTA-AA
1 TCGCAACGCGATTCTG-ACTA
94313 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
94333 TCGCAAC
1 TCGCAAC
94340 ACTGAATTTC
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 1 0.03
20 35 0.95
21 1 0.03
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:94693 original size:20 final size:20
Alignment explanation
Indices: 94668--94712 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
94658 TTACAATATA
*
94668 TGCGATTTTGACTTTCGCAT
1 TGCGATTTTGACTTTAGCAT
* *
94688 TGCGATTTTGAGTTTAGCGT
1 TGCGATTTTGACTTTAGCAT
94708 TGCGA
1 TGCGA
94713 ATGTGTACCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.16, G:0.27, T:0.42
Consensus pattern (20 bp):
TGCGATTTTGACTTTAGCAT
Found at i:96018 original size:21 final size:21
Alignment explanation
Indices: 95994--96068 Score: 52
Period size: 21 Copynumber: 3.7 Consensus size: 21
95984 GTGACAGAAT
95994 AGGTGATGGCTCTCGTTGTAG
1 AGGTGATGGCTCTCGTTGTAG
* * * *
96015 AGGTGTATAG-TATGGTTG-ATC
1 AGGTG-ATGGCTCTCGTTGTA-G
*
96036 AGGTGATGGCTCT-G-GGT-G
1 AGGTGATGGCTCTCGTTGTAG
96054 AGGTGATGGCTCTCG
1 AGGTGATGGCTCTCG
96069 AAGTGGAGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
18 13 0.32
19 2 0.05
20 5 0.12
21 18 0.44
22 3 0.07
ACGTcount: A:0.16, C:0.12, G:0.40, T:0.32
Consensus pattern (21 bp):
AGGTGATGGCTCTCGTTGTAG
Found at i:97841 original size:22 final size:21
Alignment explanation
Indices: 97807--97870 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 21
97797 TCTGAGAGAT
97807 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
*
97827 GGAGATGATGACGGATTTCGTC
1 GGAGATGA-GACGGATTTCGCC
* *
97849 GGAGATGGGACGGATGTCGCC
1 GGAGATGAGACGGATTTCGCC
97870 G
1 G
97871 TAGAGAGTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 6 0.16
21 13 0.34
22 19 0.50
ACGTcount: A:0.22, C:0.17, G:0.41, T:0.20
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:98091 original size:19 final size:19
Alignment explanation
Indices: 98067--98103 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
98057 TACGATACTG
*
98067 GAGATCATATTGCGATTTA
1 GAGATCATATTACGATTTA
*
98086 GAGATCGTATTACGATTT
1 GAGATCATATTACGATTT
98104 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.38
Consensus pattern (19 bp):
GAGATCATATTACGATTTA
Found at i:100622 original size:26 final size:26
Alignment explanation
Indices: 100592--100643 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
100582 CAAACAAAAT
100592 AGAAGACACAAGCAACCAAGGAAGCA
1 AGAAGACACAAGCAACCAAGGAAGCA
100618 AGAAGACACAAGCAACCAAGGAAGCA
1 AGAAGACACAAGCAACCAAGGAAGCA
100644 GGGAAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.54, C:0.23, G:0.23, T:0.00
Consensus pattern (26 bp):
AGAAGACACAAGCAACCAAGGAAGCA
Found at i:100747 original size:30 final size:30
Alignment explanation
Indices: 100711--100767 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
100701 CCACCAAGAG
100711 CTTTCTTCAGCTTCTTAATGAGAGGCAGAA
1 CTTTCTTCAGCTTCTTAATGAGAGGCAGAA
100741 CTTTCTTCAGCTTCTTAATGAGAGGCA
1 CTTTCTTCAGCTTCTTAATGAGAGGCA
100768 TTGAGGAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (30 bp):
CTTTCTTCAGCTTCTTAATGAGAGGCAGAA
Found at i:102638 original size:44 final size:44
Alignment explanation
Indices: 102572--102659 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
102562 AATTCATTTT
102572 AAGATGGAAATTGTTAGCCTGATTCAAAGTCATTATGGCATAAA
1 AAGATGGAAATTGTTAGCCTGATTCAAAGTCATTATGGCATAAA
*
102616 AAGATGGAAATTGTTAGTCTGATTCAAAGTCATTATGGCATAAA
1 AAGATGGAAATTGTTAGCCTGATTCAAAGTCATTATGGCATAAA
102660 TTAATTAAGA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (44 bp):
AAGATGGAAATTGTTAGCCTGATTCAAAGTCATTATGGCATAAA
Found at i:103245 original size:22 final size:22
Alignment explanation
Indices: 103218--103273 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
103208 TTTTAAAGTT
*
103218 TTTAAAGTTTAATTAATATTAG
1 TTTAAAGTTTAAATAATATTAG
* * *
103240 TTTAAATTTTTAAATCATATTCG
1 TTTAAA-GTTTAAATAATATTAG
*
103263 TTTAATGTTTA
1 TTTAAAGTTTA
103274 CAAACCAACA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
22 10 0.37
23 17 0.63
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.54
Consensus pattern (22 bp):
TTTAAAGTTTAAATAATATTAG
Done.