Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002545.1 Hibiscus syriacus cultivar Beakdansim tig00005168_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: 59319
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2874 original size:16 final size:17
Alignment explanation
Indices: 2844--2879 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
2834 TTACTATGTT
2844 TCCTCTTCAATCGTTCA
1 TCCTCTTCAATCGTTCA
2861 TCCTCTTC-ATCGTTCA
1 TCCTCTTCAATCGTTCA
2877 TCC
1 TCC
2880 ATAGTTTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.14, C:0.39, G:0.06, T:0.42
Consensus pattern (17 bp):
TCCTCTTCAATCGTTCA
Found at i:9241 original size:134 final size:135
Alignment explanation
Indices: 9075--9318 Score: 357
Period size: 134 Copynumber: 1.8 Consensus size: 135
9065 ACTCAAATAT
* * *
9075 TAAGAATCCTTTTTTTCATGTAATACTCAAATTTC-TTTAGGTTCAATAGATTTCTCTCATTCAA
1 TAAGAATCCTTTTTTTCATGTAATACTAAAATTTCTTTTAGGTTCAATA-AATTCTCTAATTCAA
* *
9139 CCAATAATGAGAATAAATATATTCACTGTAAATGAACTGAAAACTTGCACCTCTGCCATCCAAAT
65 CCAATAATGAGAATAAATAGATTCACAGTAAATGAACTGAAAACTTGCACCTCTGCCATCCAAAT
9204 AAAAAA
130 AAAAAA
* * * *
9210 TAAGAGTCC-TTTTTTCATGTGATTCTAAAATTTCTTTTAGGTTCAATAAATTCTCTAATTCAGC
1 TAAGAATCCTTTTTTTCATGTAATACTAAAATTTCTTTTAGGTTCAATAAATTCTCTAATTCAAC
* * *
9274 CGATCATGAGAATAACTAGATTCACAGTAAATGAACTGAAAACTT
66 CAATAATGAGAATAAATAGATTCACAGTAAATGAACTGAAAACTT
9319 ACATGTGCTG
Statistics
Matches: 96, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
134 75 0.78
135 21 0.22
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (135 bp):
TAAGAATCCTTTTTTTCATGTAATACTAAAATTTCTTTTAGGTTCAATAAATTCTCTAATTCAAC
CAATAATGAGAATAAATAGATTCACAGTAAATGAACTGAAAACTTGCACCTCTGCCATCCAAATA
AAAAA
Found at i:15291 original size:149 final size:149
Alignment explanation
Indices: 15021--15473 Score: 897
Period size: 149 Copynumber: 3.0 Consensus size: 149
15011 CAAAGTGCCC
*
15021 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCAAAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
15086 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
15151 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
15170 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
15235 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
15300 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
15319 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
15384 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
15449 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
15468 CGTAGA
1 CGTAGA
15474 CCCTCGACTC
Statistics
Matches: 303, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
149 303 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCGAAGAACCG
Found at i:16989 original size:21 final size:21
Alignment explanation
Indices: 16965--17009 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
16955 TCTTGTTCGT
* *
16965 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
16986 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
17007 TTG
1 TTG
17010 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:20657 original size:9 final size:9
Alignment explanation
Indices: 20643--20676 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
20633 TAAGTAAAAT
20643 ATTAAATAA
1 ATTAAATAA
20652 ATTAAAT-A
1 ATTAAATAA
*
20660 CTTAAATAA
1 ATTAAATAA
20669 ATTAAATA
1 ATTAAATA
20677 CAAAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (9 bp):
ATTAAATAA
Found at i:20675 original size:17 final size:17
Alignment explanation
Indices: 20639--20677 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
20629 TAATTAAGTA
20639 AAATA-TTAAATAAATT
1 AAATACTTAAATAAATT
20655 AAATACTTAAATAAATT
1 AAATACTTAAATAAATT
20672 AAATAC
1 AAATAC
20678 AAAATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATACTTAAATAAATT
Found at i:23736 original size:75 final size:75
Alignment explanation
Indices: 23642--23786 Score: 193
Period size: 75 Copynumber: 1.9 Consensus size: 75
23632 ATATATACGA
* ** * * *
23642 GATATGATCATATTATACAA-GATAAAACTCTTTTAATTATACGTATATTTAGAATTGTTGGATA
1 GATAAGATCATATTATACAATG-TAAAACTCTTTTAATTATACACATATTTAGAACTATTAGATA
23706 AGTGAATATAT
65 AGTGAATATAT
* * *
23717 GATAAGATCCTATTATACAATGTAAAACTCTTTTAGTTTTACACATATTTAGAACTATTAGATAA
1 GATAAGATCATATTATACAATGTAAAACTCTTTTAATTATACACATATTTAGAACTATTAGATAA
23782 GTGAA
66 GTGAA
23787 AACAGACGGT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
75 59 0.98
76 1 0.02
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (75 bp):
GATAAGATCATATTATACAATGTAAAACTCTTTTAATTATACACATATTTAGAACTATTAGATAA
GTGAATATAT
Found at i:25092 original size:20 final size:21
Alignment explanation
Indices: 25067--25111 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
25057 AATAAATAAT
*
25067 AATATATTAATT-TTTTTATA
1 AATATATTAATTATTTTTAAA
*
25087 AATATATTATTTATTTTTAAA
1 AATATATTAATTATTTTTAAA
25108 AATA
1 AATA
25112 GTTGCATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AATATATTAATTATTTTTAAA
Found at i:28275 original size:24 final size:24
Alignment explanation
Indices: 28243--28290 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
28233 CTTTAGGGCT
28243 GGTATAGTTGTTTGCATATGGATA
1 GGTATAGTTGTTTGCATATGGATA
28267 GGTATAGTTGTTTGCATATGGATA
1 GGTATAGTTGTTTGCATATGGATA
28291 TTTGTTTGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.04, G:0.29, T:0.42
Consensus pattern (24 bp):
GGTATAGTTGTTTGCATATGGATA
Found at i:28688 original size:29 final size:29
Alignment explanation
Indices: 28645--28727 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
28635 CTCACCTAAC
28645 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
28675 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
28704 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
28728 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:32237 original size:15 final size:15
Alignment explanation
Indices: 32219--32254 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
32209 CATATCCTTA
32219 AGTTGCAGCTTGAGG
1 AGTTGCAGCTTGAGG
32234 AGTTGCAGCTTGAGG
1 AGTTGCAGCTTGAGG
32249 AGTTGC
1 AGTTGC
32255 TCAGTAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.19, C:0.14, G:0.39, T:0.28
Consensus pattern (15 bp):
AGTTGCAGCTTGAGG
Found at i:33464 original size:29 final size:29
Alignment explanation
Indices: 33428--33503 Score: 125
Period size: 29 Copynumber: 2.6 Consensus size: 29
33418 AACTAAATTG
33428 ATGTAAGCAATGACATCATTAATTAAATA
1 ATGTAAGCAATGACATCATTAATTAAATA
* *
33457 ATGTAAGCAATGACATCTTTAATTAAATG
1 ATGTAAGCAATGACATCATTAATTAAATA
*
33486 ATGTAAGTAATGACATCA
1 ATGTAAGCAATGACATCA
33504 ATTTAGTTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.32
Consensus pattern (29 bp):
ATGTAAGCAATGACATCATTAATTAAATA
Found at i:39145 original size:69 final size:69
Alignment explanation
Indices: 39046--39184 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 69
39036 ACAGAACTAG
39046 TATTTTTCGTGTTTGCATTTCCAATATATATTTACTTGTGCCTTTTCATTGATAACCTGTATCCA
1 TATTTTTCGTGTTTGCATTTCCAATATATATTTACTTGTGCCTTTTCATTGATAACCTGTATCCA
39111 TAGT
66 TAGT
*
39115 TATTTTTCGTGTTTGCATTTCCAATATATATTTACTTGTTCCTTTTCATTGATAACCTGTATCCA
1 TATTTTTCGTGTTTGCATTTCCAATATATATTTACTTGTGCCTTTTCATTGATAACCTGTATCCA
39180 TAGT
66 TAGT
39184 T
1 T
39185 GGTTTGCAGT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.22, C:0.17, G:0.11, T:0.50
Consensus pattern (69 bp):
TATTTTTCGTGTTTGCATTTCCAATATATATTTACTTGTGCCTTTTCATTGATAACCTGTATCCA
TAGT
Found at i:40524 original size:78 final size:80
Alignment explanation
Indices: 40366--40528 Score: 276
Period size: 78 Copynumber: 2.0 Consensus size: 80
40356 CGATGATATT
*
40366 AAATCTAATTCCAAGATAAATAAATGGTAGGAATAACAAAACGACCAAAGAAAATCCTAAAATAT
1 AAATCTAATTCCAAGATAAATAAATGGTAGGAACAACAAAAC-ACCAAAGAAAATCCTAAAATAT
40431 ATGCTAAAAAGTAGAA
65 ATGCTAAAAAGTAGAA
*
40447 AAATCTAATTCCAAGATAAATAAATGGTAGGAACAAC-AAA-ACCAAAGAAAATCCTAAAATGTA
1 AAATCTAATTCCAAGATAAATAAATGGTAGGAACAACAAAACACCAAAGAAAATCCTAAAATATA
*
40510 TGCTAAAAGGTAGAA
66 TGCTAAAAAGTAGAA
40525 AAAT
1 AAAT
40529 TGACATAAAA
Statistics
Matches: 79, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
78 40 0.51
80 3 0.04
81 36 0.46
ACGTcount: A:0.55, C:0.12, G:0.13, T:0.20
Consensus pattern (80 bp):
AAATCTAATTCCAAGATAAATAAATGGTAGGAACAACAAAACACCAAAGAAAATCCTAAAATATA
TGCTAAAAAGTAGAA
Found at i:44187 original size:32 final size:30
Alignment explanation
Indices: 44150--44219 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
44140 GTTAATTTAA
44150 ATTTTTAATATCATATTTGTATTCGTTTATTT
1 ATTTTTAA-A-CATATTTGTATTCGTTTATTT
** *
44182 ATTTTTAAAGGTATTTGTGTTCGTTTATTT
1 ATTTTTAAACATATTTGTATTCGTTTATTT
*
44212 ATTGTTAA
1 ATTTTTAA
44220 CGAATATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 25 0.74
31 1 0.03
32 8 0.24
ACGTcount: A:0.24, C:0.04, G:0.11, T:0.60
Consensus pattern (30 bp):
ATTTTTAAACATATTTGTATTCGTTTATTT
Found at i:44199 original size:30 final size:30
Alignment explanation
Indices: 44163--44219 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
44153 TTTAATATCA
*
44163 TATTTGTATTCGTTTATTTATTTTTAAAGG
1 TATTTGTATTCGTTTATTTATTGTTAAAGG
*
44193 TATTTGTGTTCGTTTATTTATTGTTAA
1 TATTTGTATTCGTTTATTTATTGTTAA
44220 CGAATATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.21, C:0.04, G:0.14, T:0.61
Consensus pattern (30 bp):
TATTTGTATTCGTTTATTTATTGTTAAAGG
Found at i:44932 original size:38 final size:38
Alignment explanation
Indices: 44881--44957 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
44871 TAAGGTAAGC
*
44881 ACGGAAGAATACATAAGGTATCGTATATTAATAGATCA
1 ACGGAAGAATACATAAGGTATCGGATATTAATAGATCA
* * *
44919 ACGGAAGATTACATGATGTATCGGATATTAATAGATCA
1 ACGGAAGAATACATAAGGTATCGGATATTAATAGATCA
44957 A
1 A
44958 ATATCGATAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.27
Consensus pattern (38 bp):
ACGGAAGAATACATAAGGTATCGGATATTAATAGATCA
Found at i:51814 original size:21 final size:19
Alignment explanation
Indices: 51761--51816 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 19
51751 TCATGTGTAT
51761 AATTTAAGATTTATATTTGA
1 AATTTAAGA-TTATATTTGA
51781 AGATTATAA-ATTAGTATTTAGA
1 A-ATT-TAAGATTA-TATTT-GA
51803 AATTTAAGATTATA
1 AATTTAAGATTATA
51817 AATGATCTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
20 9 0.29
21 16 0.52
22 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.45
Consensus pattern (19 bp):
AATTTAAGATTATATTTGA
Found at i:51819 original size:14 final size:14
Alignment explanation
Indices: 51761--51819 Score: 52
Period size: 14 Copynumber: 4.2 Consensus size: 14
51751 TCATGTGTAT
51761 AATTTAAGATT-TA
1 AATTTAAGATTATA
*
51774 TATTTGAAGATTATA
1 AATTT-AAGATTATA
*
51789 AA-TT-AGTATTTAGA
1 AATTTAAG-A-TTATA
51803 AATTTAAGATTATA
1 AATTTAAGATTATA
51817 AAT
1 AAT
51820 GATCTTATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 11
0.71 0.08 0.22
Matches are distributed among these distances:
12 2 0.06
13 5 0.14
14 21 0.58
15 6 0.17
16 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (14 bp):
AATTTAAGATTATA
Found at i:56137 original size:64 final size:61
Alignment explanation
Indices: 56067--56245 Score: 168
Period size: 64 Copynumber: 2.8 Consensus size: 61
56057 TTGGAACCTT
* *
56067 AGTGCATTGGTGCACTAAGAGTGCATTGATGCATCAAGTGCATTCGATGTT-TTA-AAATAGCC-
1 AGTGCATCGGTGCACT--G-GTGCATCGATGCATCAA-TGCATTCGATGTTCTTATAAA-AGCCT
56129 C
61 C
* *
56130 GAGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTCTTATAAAATCCT
1 -AGTGCATCGGTGCA---CTGGTGCATCGATGCATC-AATGCATTCGATGTTCTTATAAAAGCCT
56195 C
61 C
*
56196 AGTGCATCGGTGCA-TGGTGTGCATCGATGCATGGAATGCATTCGATGTTC
1 AGTGCATCGGTGCACT-G-GTGCATCGATGCAT-CAATGCATTCGATGTTC
56246 AATTTTATTC
Statistics
Matches: 99, Mismatches: 6, Indels: 21
0.79 0.05 0.17
Matches are distributed among these distances:
61 1 0.01
62 1 0.01
63 30 0.30
64 39 0.39
65 22 0.22
66 4 0.04
67 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (61 bp):
AGTGCATCGGTGCACTGGTGCATCGATGCATCAATGCATTCGATGTTCTTATAAAAGCCTC
Found at i:56219 original size:17 final size:17
Alignment explanation
Indices: 56197--56229 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
56187 AAAATCCTCA
*
56197 GTGCATCGGTGCATGGT
1 GTGCATCGATGCATGGT
56214 GTGCATCGATGCATGG
1 GTGCATCGATGCATGG
56230 AATGCATTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.18, G:0.39, T:0.27
Consensus pattern (17 bp):
GTGCATCGATGCATGGT
Found at i:56234 original size:63 final size:64
Alignment explanation
Indices: 56087--56245 Score: 193
Period size: 63 Copynumber: 2.5 Consensus size: 64
56077 TGCACTAAGA
* *
56087 GTGCATTGATGCATCAAGTGCATTCGATGTT-TTAAAATAGCCCGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCAT-AAATGCATTCGATGTTCTTAAAATAGCCCGAGTGCATCGATGCATGGCTG
* *
56151 GTGCATCGATGCATCAAATGCATTCGATGTTCTTATAAA-ATCCTC-AGTGCATCGGTGCATGG-
1 GTGCATCGATGCAT-AAATGCATTCGATGTTCTTA-AAATAGCC-CGAGTGCATCGATGCATGGC
56213 T-
63 TG
*
56214 GTGCATCGATGCATGGAATGCATTCGATGTTC
1 GTGCATCGATGCAT-AAATGCATTCGATGTTC
56246 AATTTTATTC
Statistics
Matches: 86, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
63 30 0.35
64 30 0.35
65 22 0.26
66 4 0.05
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATAAATGCATTCGATGTTCTTAAAATAGCCCGAGTGCATCGATGCATGGCTG
Found at i:56235 original size:17 final size:17
Alignment explanation
Indices: 56198--56242 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
56188 AAATCCTCAG
* **
56198 TGCATCGGTGCATGGTG
1 TGCATCGATGCATGGAA
56215 TGCATCGATGCATGGAA
1 TGCATCGATGCATGGAA
56232 TGCATTCGATG
1 TGCA-TCGATG
56243 TTCAATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 18 0.75
18 6 0.25
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (17 bp):
TGCATCGATGCATGGAA
Found at i:56678 original size:19 final size:19
Alignment explanation
Indices: 56656--56693 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
56646 TTTAAAAAAC
56656 ATTTCAACACTTAACATTT
1 ATTTCAACACTTAACATTT
56675 ATTTCAACACTTAACATTT
1 ATTTCAACACTTAACATTT
56694 CTCCCCCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTTCAACACTTAACATTT
Found at i:57412 original size:21 final size:21
Alignment explanation
Indices: 57378--57421 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
57368 GAGCCGAAGG
* *
57378 AGGAGGAGCACGAGAGGAGCT
1 AGGAGCAGCACGAGAGGAACT
*
57399 AGGAGCAGCTCGAGAGGAACT
1 AGGAGCAGCACGAGAGGAACT
57420 AG
1 AG
57422 TTCCCGGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.16, G:0.43, T:0.07
Consensus pattern (21 bp):
AGGAGCAGCACGAGAGGAACT
Done.