Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003265.1 Hibiscus syriacus cultivar Beakdansim tig00006862_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: 52213
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:8285 original size:20 final size:20
Alignment explanation
Indices: 8262--8306 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
8252 TTGGCCATTA
*
8262 ACTTTGATCATTAACCGTTT
1 ACTTTGACCATTAACCGTTT
*
8282 ACTTTGACCATTGACCGTTT
1 ACTTTGACCATTAACCGTTT
8302 ACTTT
1 ACTTT
8307 TTGTTGACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.44
Consensus pattern (20 bp):
ACTTTGACCATTAACCGTTT
Found at i:17653 original size:40 final size:38
Alignment explanation
Indices: 17600--17675 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 38
17590 ATTAGTTCCT
17600 AAATAAAATAATAATAAAATAATCAAACTAAAAATCTG
1 AAATAAAATAATAATAAAATAATCAAACTAAAAATCTG
*
17638 AAATAAGAAGTAATAATAAAATAATCAAACTAGAAATC
1 AAATAA-AA-TAATAATAAAATAATCAAACTAAAAATC
17676 ATAAATCTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 6 0.17
39 2 0.06
40 27 0.77
ACGTcount: A:0.64, C:0.08, G:0.05, T:0.22
Consensus pattern (38 bp):
AAATAAAATAATAATAAAATAATCAAACTAAAAATCTG
Found at i:19211 original size:15 final size:15
Alignment explanation
Indices: 19188--19219 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
19178 ACTATTATGA
*
19188 CAAATTTAATTTTGT
1 CAAAATTAATTTTGT
19203 CAAAATTAATTTTGT
1 CAAAATTAATTTTGT
19218 CA
1 CA
19220 CTATTGGTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (15 bp):
CAAAATTAATTTTGT
Found at i:19736 original size:14 final size:14
Alignment explanation
Indices: 19717--19756 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
19707 ATGTTTTAAT
19717 TATATTGACAAAAA
1 TATATTGACAAAAA
* *
19731 TATATTGTCACAAA
1 TATATTGACAAAAA
*
19745 TATAGTGACAAA
1 TATATTGACAAA
19757 TTTTGTTACT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (14 bp):
TATATTGACAAAAA
Found at i:20233 original size:138 final size:138
Alignment explanation
Indices: 19984--20249 Score: 383
Period size: 138 Copynumber: 1.9 Consensus size: 138
19974 TTATCACATC
19984 AAATAATAAAATTTAAGTTTTTTGTAATAAATTATTTTTGTACTTATATATTTAATCATTATGAA
1 AAATAATAAAATTTAAGTTTTTTGTAATAAATTATTTTTGTACTTATATATTTAATCATTATGAA
* *
20049 AACAAAATACTATCAGAACCATTCTCCCTATTTTTTACTGTAAAAAATGTTATATAGTAACAAAA
66 AACAAAATACTATCAGAAACATTCTCCCTACTTTTTACTGTAAAAAATGTTATATAGTAACAAAA
20114 TATATTGT
131 TATATTGT
*
20122 AAATAATAAAATTTAAGTTTTTTGTAATAAATTATTTTTGTAGTTATATATTTTAATCATTATGA
1 AAATAATAAAATTTAAGTTTTTTGTAATAAATTATTTTTGTACTTATATA-TTTAATCATTATGA
** ** * * ** * *
20187 AAAC-TTATTTTATTAGAAATAGTTCTCCCTACTTTTTGGTG-CAAAAATGTTATATAGTGACAA
65 AAACAAAATACTATCAGAAACA-TTCTCCCTACTTTTTACTGTAAAAAATGTTATATAGTAACAA
20250 GTTTTGTAAC
Statistics
Matches: 113, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
138 79 0.70
139 34 0.30
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (138 bp):
AAATAATAAAATTTAAGTTTTTTGTAATAAATTATTTTTGTACTTATATATTTAATCATTATGAA
AACAAAATACTATCAGAAACATTCTCCCTACTTTTTACTGTAAAAAATGTTATATAGTAACAAAA
TATATTGT
Found at i:20334 original size:26 final size:27
Alignment explanation
Indices: 20296--20346 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
20286 AAATTATCAC
*
20296 AACAAAAATTTC-ATTTTTTTTAAATT
1 AACAAAAATTTCAATTTTTTATAAATT
20322 AACAAAAGA-TTCAATTTTTTATAAA
1 AACAAAA-ATTTCAATTTTTTATAAA
20347 AAAAATTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (27 bp):
AACAAAAATTTCAATTTTTTATAAATT
Found at i:20449 original size:2 final size:2
Alignment explanation
Indices: 20444--20490 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
20434 TTTTCTGATA
*
20444 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20486 AT AT A
1 AT AT A
20491 ATTAAATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:24156 original size:2 final size:2
Alignment explanation
Indices: 24151--24216 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
24141 AGAAATGAAG
24151 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
24193 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
24217 TATTACCTCT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28033 original size:20 final size:20
Alignment explanation
Indices: 28008--28048 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
27998 TACCCCTTAC
28008 CAACCAATTAGGGATGGGCA
1 CAACCAATTAGGGATGGGCA
28028 CAACCAATTAGGGATGGGCA
1 CAACCAATTAGGGATGGGCA
28048 C
1 C
28049 GGGACGAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.22, G:0.29, T:0.15
Consensus pattern (20 bp):
CAACCAATTAGGGATGGGCA
Found at i:28294 original size:15 final size:15
Alignment explanation
Indices: 28215--28300 Score: 56
Period size: 15 Copynumber: 6.0 Consensus size: 15
28205 GAGTATATTA
28215 ATATTTTA-AATAAT
1 ATATTTTATAATAAT
*
28229 ATATTTTATACTAAT
1 ATATTTTATAATAAT
* *
28244 ATA-ATTATAATTAT
1 ATATTTTATAATAAT
* * **
28258 TTATTATATTTTAA-
1 ATATTTTATAATAAT
28272 ATGA--TTATAATAAT
1 AT-ATTTTATAATAAT
*
28286 ATATTTTATGATAAT
1 ATATTTTATAATAAT
28301 TTTAATTTTT
Statistics
Matches: 51, Mismatches: 15, Indels: 11
0.66 0.19 0.14
Matches are distributed among these distances:
13 7 0.14
14 21 0.41
15 23 0.45
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (15 bp):
ATATTTTATAATAAT
Found at i:31353 original size:45 final size:45
Alignment explanation
Indices: 31262--31443 Score: 258
Period size: 45 Copynumber: 4.1 Consensus size: 45
31252 GTAAGCATGC
* *
31262 AAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTGTATTGATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTTTATTGATA
*
31306 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTTTATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTTTATTGATA
* * * *
31351 AAATAAGCTTACGAGCTCATGAAATAAATGGTAAGTTTGTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTTTATTGATA
* * * *
31396 TAATAAGCTTACGAGCTTATGGAATAAAGGGTAAATATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTTTATTGATA
31441 AAA
1 AAA
31444 AAATGTTTTA
Statistics
Matches: 122, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
44 25 0.20
45 97 0.80
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTTTATTGATA
Found at i:33356 original size:5 final size:5
Alignment explanation
Indices: 33348--33372 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
33338 TTTATTTAAT
33348 TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG
33373 AATGTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (5 bp):
TTATG
Found at i:34345 original size:17 final size:18
Alignment explanation
Indices: 34323--34356 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
34313 TTAAGCTAAC
*
34323 AAATTAA-GAAGAAAATT
1 AAATTAATGAAAAAAATT
34340 AAATTAATGAAAAAAAT
1 AAATTAATGAAAAAAAT
34357 AAACGGATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.24
Consensus pattern (18 bp):
AAATTAATGAAAAAAATT
Found at i:36303 original size:20 final size:19
Alignment explanation
Indices: 36266--36325 Score: 68
Period size: 20 Copynumber: 3.2 Consensus size: 19
36256 TGTTTTCTAA
36266 AAATTATAAAAAAATTATT
1 AAATTATAAAAAAATTATT
* *
36285 AAATTATTAAAATATTTATT
1 AAATTA-TAAAAAAATTATT
**
36305 AAATTA-AATTAAATTATT
1 AAATTATAAAAAAATTATT
36323 AAA
1 AAA
36326 AATAATCATT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 11 0.32
19 6 0.18
20 17 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATTATAAAAAAATTATT
Found at i:37422 original size:2 final size:2
Alignment explanation
Indices: 37415--37449 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
37405 AACGAAGTAA
*
37415 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
37450 ATAAGGATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:37646 original size:11 final size:11
Alignment explanation
Indices: 37630--37663 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
37620 GACTAGTATG
37630 AAAATAATAAT
1 AAAATAATAAT
37641 AAAATAATAATT
1 AAAATAATAA-T
*
37653 AAAGTAATAAT
1 AAAATAATAAT
37664 TTAAACATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:37660 original size:12 final size:12
Alignment explanation
Indices: 37630--37664 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
37620 GACTAGTATG
37630 AAAATAATAA-T
1 AAAATAATAATT
37641 AAAATAATAATT
1 AAAATAATAATT
*
37653 AAAGTAATAATT
1 AAAATAATAATT
37665 TAAACATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (12 bp):
AAAATAATAATT
Found at i:38005 original size:21 final size:22
Alignment explanation
Indices: 37970--38011 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
37960 GATCTCCACT
*
37970 ATTGCAAATTCGCGTTGCGATA
1 ATTGCAAAATCGCGTTGCGATA
37992 ATTG-AAAATCGCGTTGCGAT
1 ATTGCAAAATCGCGTTGCGAT
38012 TTTCCAGTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.31
Consensus pattern (22 bp):
ATTGCAAAATCGCGTTGCGATA
Found at i:38106 original size:22 final size:22
Alignment explanation
Indices: 38066--38110 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
38056 TCCAAATTCG
* *
38066 TAGTCTACAGTTATTGTTGCGA
1 TAGTCTACAGCTATCGTTGCGA
*
38088 TAGTCTACAGCTGTCGTTGCGA
1 TAGTCTACAGCTATCGTTGCGA
38110 T
1 T
38111 TTTCCAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (22 bp):
TAGTCTACAGCTATCGTTGCGA
Found at i:38235 original size:6 final size:6
Alignment explanation
Indices: 38224--38278 Score: 96
Period size: 6 Copynumber: 9.5 Consensus size: 6
38214 GAAACGTATT
38224 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
38271 ACC-CG ACC
1 ACCACG ACC
38279 CGAGACGAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.20
6 39 0.80
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:38775 original size:5 final size:5
Alignment explanation
Indices: 38765--38791 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
38755 CCGCCACCGC
38765 CGTCT CGTCT CGTCT CGTCT CGTCT CG
1 CGTCT CGTCT CGTCT CGTCT CGTCT CG
38792 GGTCGGGTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.41, G:0.22, T:0.37
Consensus pattern (5 bp):
CGTCT
Found at i:38957 original size:22 final size:22
Alignment explanation
Indices: 38929--39105 Score: 167
Period size: 22 Copynumber: 8.4 Consensus size: 22
38919 AATTTGAAAA
38929 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
38951 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
38973 ATCGCAAC-A-AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
38992 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
**
39014 ATCGCAACG-CGAACTG--GAAA
1 ATCGCAACGAC-AACTGTAGACT
39034 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* **
39056 ATCACAACG-CGAACTG--GAAA
1 ATCGCAACGAC-AACTGTAGACT
*
39076 ATCGCAACGAC-ATTGTAGACT
1 ATCGCAACGACAACTGTAGACT
39097 ATCGCAACG
1 ATCGCAACG
39106 CGAAATGGAA
Statistics
Matches: 124, Mismatches: 20, Indels: 23
0.74 0.12 0.14
Matches are distributed among these distances:
19 15 0.12
20 29 0.23
21 18 0.15
22 62 0.50
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.17
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:39039 original size:20 final size:20
Alignment explanation
Indices: 38986--39148 Score: 127
Period size: 20 Copynumber: 7.9 Consensus size: 20
38976 GCAACAAATT
38986 TGGAAAATCGCAACGAC-AAC
1 TGGAAAATCGCAACG-CGAAC
**
39006 TGTAGACTATCGCAACGCGAAC
1 TG--GAAAATCGCAACGCGAAC
39028 TGGAAAATCGCAACGAC-AAC
1 TGGAAAATCGCAACG-CGAAC
** *
39048 TGTAGACTATCACAACGCGAAC
1 TG--GAAAATCGCAACGCGAAC
*
39070 TGGAAAATCGCAA--CGACAT
1 TGGAAAATCGCAACGCGA-AC
** *
39089 TGTAGACTATCGCAACGCGAAA
1 TG--GAAAATCGCAACGCGAAC
*
39111 TGGAAAATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGAAC
39131 TGGAAAATCGCAACGCGA
1 TGGAAAATCGCAACGCGA
39149 TTTTCAACTA
Statistics
Matches: 115, Mismatches: 16, Indels: 24
0.74 0.10 0.15
Matches are distributed among these distances:
18 3 0.03
19 3 0.03
20 60 0.52
21 12 0.10
22 34 0.30
23 3 0.03
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.14
Consensus pattern (20 bp):
TGGAAAATCGCAACGCGAAC
Found at i:39045 original size:42 final size:42
Alignment explanation
Indices: 38951--39125 Score: 266
Period size: 41 Copynumber: 4.2 Consensus size: 42
38941 ACTGTAGACT
* * *
38951 ATCGCAACAACAACTGTAGACTATCGCAA--CAAATTTGGAAA
1 ATCGCAACGACAACTGTAGACTATCGCAACGCGAA-CTGGAAA
38992 ATCGCAACGACAACTGTAGACTATCGCAACGCGAACTGGAAA
1 ATCGCAACGACAACTGTAGACTATCGCAACGCGAACTGGAAA
*
39034 ATCGCAACGACAACTGTAGACTATCACAACGCGAACTGGAAA
1 ATCGCAACGACAACTGTAGACTATCGCAACGCGAACTGGAAA
* *
39076 ATCGCAACGAC-ATTGTAGACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGACAACTGTAGACTATCGCAACGCGAACTGGAAA
39117 ATCGCAACG
1 ATCGCAACG
39126 CGAAATGGAA
Statistics
Matches: 125, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
41 64 0.51
42 58 0.46
43 3 0.02
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.16
Consensus pattern (42 bp):
ATCGCAACGACAACTGTAGACTATCGCAACGCGAACTGGAAA
Found at i:39049 original size:83 final size:82
Alignment explanation
Indices: 38951--39125 Score: 262
Period size: 83 Copynumber: 2.1 Consensus size: 82
38941 ACTGTAGACT
* * *
38951 ATCGCAACAACAACTGTAGACTATCGCAA-CAAATTTGGAAAATCGCAACGACAACTGTAGACTA
1 ATCGCAACGACAACTGTAGACTATCACAACCAAA-CTGGAAAATCGCAACGAC-ACTGTAGACTA
*
39015 TCGCAACGCGAACTGGAAA
64 TCGCAACGCGAAATGGAAA
* *
39034 ATCGCAACGACAACTGTAGACTATCACAACGCGAACTGGAAAATCGCAACGACATTGTAGACTAT
1 ATCGCAACGACAACTGTAGACTATCACAAC-CAAACTGGAAAATCGCAACGACACTGTAGACTAT
39099 CGCAACGCGAAATGGAAA
65 CGCAACGCGAAATGGAAA
39117 ATCGCAACG
1 ATCGCAACG
39126 CGAAATGGAA
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
83 64 0.76
84 17 0.20
85 3 0.04
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.16
Consensus pattern (82 bp):
ATCGCAACGACAACTGTAGACTATCACAACCAAACTGGAAAATCGCAACGACACTGTAGACTATC
GCAACGCGAAATGGAAA
Found at i:40473 original size:3 final size:3
Alignment explanation
Indices: 40465--40518 Score: 83
Period size: 3 Copynumber: 18.3 Consensus size: 3
40455 ATTTATTTAG
* *
40465 TAA TAA TAA T-A TAA TAA TAA TAA TAC TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
40512 TAA TAA T
1 TAA TAA T
40519 TTTAAAATGA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:40784 original size:45 final size:45
Alignment explanation
Indices: 40692--40920 Score: 361
Period size: 45 Copynumber: 5.1 Consensus size: 45
40682 GAGGTCTTAT
* * *
40692 CATCTTGCACTGAAGGTCTTACAGATGA-CCGAAGGCTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
40736 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
* *
40781 CATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGATAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
* * *
40826 CATCATGCACTAAAGGGCTTATAGATGACCCGAAGGCTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
*
40871 CATCATACACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
*
40916 AATCA
1 CATCA
40921 AAAAGCTCCC
Statistics
Matches: 169, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
44 26 0.15
45 143 0.85
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (45 bp):
CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
Found at i:40950 original size:76 final size:74
Alignment explanation
Indices: 40854--40996 Score: 207
Period size: 76 Copynumber: 1.9 Consensus size: 74
40844 TTATAGATGA
40854 CCCGAAGGCTTTGAAAACATCATACACTGAAGGGCTTACA-GATGACCCGAAGGTTTTGAAAAAA
1 CCCGAAGGCTTTGAAAACATCATACACTGAAGGGCTTA-AGGATGACCCGAAGGTTTTGAAAAAA
40918 TCAAAAAGCT
65 TCAAAAAGCT
* * * * *
40928 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTAAGGATGACCCGAAGGTTTTGAAAAC
1 CCCGAAGGC--TTTGAAAACATCATACACTGAAGGGCTTAAGGATGACCCGAAGGTTTTGAAAAA
40993 ATCA
64 ATCA
40997 TGCACTGTAG
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
74 9 0.15
75 1 0.02
76 51 0.84
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (74 bp):
CCCGAAGGCTTTGAAAACATCATACACTGAAGGGCTTAAGGATGACCCGAAGGTTTTGAAAAAAT
CAAAAAGCT
Found at i:40994 original size:45 final size:45
Alignment explanation
Indices: 40928--41041 Score: 176
Period size: 45 Copynumber: 2.5 Consensus size: 45
40918 TCAAAAAGCT
*
40928 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTA-AGGATGA
1 CCCGAAGG--TTTTGAAAACATCATGCACTGTAGGTCTTACA-GATGA
40975 CCCGAAGGTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGA
*
41020 CCCGAAGGCTTTGAAAACATCA
1 CCCGAAGGTTTTGAAAACATCA
41042 AAAAGCTTCC
Statistics
Matches: 64, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
45 55 0.86
46 1 0.02
47 8 0.12
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGA
Found at i:41033 original size:121 final size:121
Alignment explanation
Indices: 40809--41238 Score: 596
Period size: 121 Copynumber: 3.6 Consensus size: 121
40799 TTACAGATGA
* *
40809 CCCGAAGG--TTTTGATAACATCATGCACTAAAGGGCTTATAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTAAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
* * * * *
40872 ATCATACACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAAATCAAAAAGCT
66 ATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
* ** * *
40928 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTA-AGGATGACCCGAAGGTTTTGAAAA
1 CCCGAAGGCTTTTTGAAAACATCATGCACTAAAGGGCTTACA-GATGACCCGAAGGCTTTGAAAA
*
40992 CATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
65 CATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
* * ** * * ** *
41049 TCCGAAGGCTTTTTGAAAACATCCTTTACTATAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTAAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
* *
41114 ATCATGCACTGTATGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAATCT
66 ATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
* *
41170 CCCAAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTAAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
41235 ATCA
66 ATCA
41239 AAAAGCTCCT
Statistics
Matches: 277, Mismatches: 30, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
119 8 0.03
120 1 0.00
121 268 0.97
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (121 bp):
CCCGAAGGCTTTTTGAAAACATCATGCACTAAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
ATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
Found at i:41063 original size:76 final size:74
Alignment explanation
Indices: 40976--41117 Score: 203
Period size: 76 Copynumber: 1.9 Consensus size: 74
40966 TAAGGATGAC
*
40976 CCGAAGGTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATC
1 CCGAAGGTTTTGAAAACATCATGCACTATAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATC
41041 AAAAAGCTT
66 AAAAAGCTT
* ** ** *
41050 CCGAAGGCTTTTTGAAAACATCCTTTACTATAGGTCTTATGGATGACCCGAAGGTTTTGAAAACA
1 CCGAAGG--TTTTGAAAACATCATGCACTATAGGTCTTACAGATGACCCGAAGGCTTTGAAAACA
41115 TCA
64 TCA
41118 TGCACTGTAT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
74 7 0.12
76 52 0.88
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (74 bp):
CCGAAGGTTTTGAAAACATCATGCACTATAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATC
AAAAAGCTT
Found at i:41116 original size:45 final size:45
Alignment explanation
Indices: 41050--41162 Score: 127
Period size: 45 Copynumber: 2.5 Consensus size: 45
41040 CAAAAAGCTT
* ** * **
41050 CCGAAGGCTTTTTGAAAACATCCTTTACTATAGGTCTTATGGATGAC
1 CCGAAGG--TTTTGAAAACATCATGCACTATAGGACTTACAGATGAC
* *
41097 CCGAAGGTTTTGAAAACATCATGCACTGTATGACTTACAGATGAC
1 CCGAAGGTTTTGAAAACATCATGCACTATAGGACTTACAGATGAC
*
41142 CCGAAGGCTTTGAAAACATCA
1 CCGAAGGTTTTGAAAACATCA
41163 AAAATCTCCC
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
45 50 0.88
47 7 0.12
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.28
Consensus pattern (45 bp):
CCGAAGGTTTTGAAAACATCATGCACTATAGGACTTACAGATGAC
Found at i:41230 original size:76 final size:76
Alignment explanation
Indices: 41104--41314 Score: 323
Period size: 76 Copynumber: 2.8 Consensus size: 76
41094 GACCCGAAGG
* *
41104 TTTTGAAAACATCATGCACTGTATGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAATC
1 TTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
41169 TCCCAAAGGCT
66 TCCCAAAGGCT
* *
41180 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
1 TTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
**
41245 TCCTGAAGGCT
66 TCCCAAAGGCT
* * ** *
41256 TTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCA
1 TTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCA
41315 TGCATTGTAG
Statistics
Matches: 123, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
76 123 1.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.26
Consensus pattern (76 bp):
TTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
TCCCAAAGGCT
Found at i:42039 original size:22 final size:22
Alignment explanation
Indices: 42004--42077 Score: 112
Period size: 22 Copynumber: 3.4 Consensus size: 22
41994 AAAGCTTATT
*
42004 TTTGAAAAGAGAATCTATCATC
1 TTTGAAGAGAGAATCTATCATC
*
42026 TTTAAAGAGAGAATCTATCATC
1 TTTGAAGAGAGAATCTATCATC
* *
42048 TTTGAAGAGGGAATCTAACATC
1 TTTGAAGAGAGAATCTATCATC
42070 TTTGAAGA
1 TTTGAAGA
42078 ATGTAGATGT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (22 bp):
TTTGAAGAGAGAATCTATCATC
Found at i:43761 original size:75 final size:75
Alignment explanation
Indices: 43666--43805 Score: 219
Period size: 75 Copynumber: 1.9 Consensus size: 75
43656 AATATAGACA
*
43666 TTCAAAATGCGCCAATATTCC-AATTTCTGATTGAAATGGACTTTCAGCATGCCCCAACATTTGT
1 TTCAAAATGCGCCAATATTCCTAA-TTATGATTGAAATGGACTTTCAGCATGCCCCAACATTTGT
43730 TGATACAAACG
65 TGATACAAACG
* * * *
43741 TTCAAAATGCGTCAATATTCCTGATTATGATTGAAATGGGCTTTGAGCATGCCCCAACATTTGTT
1 TTCAAAATGCGCCAATATTCCTAATTATGATTGAAATGGACTTTCAGCATGCCCCAACATTTGTT
43806 TTTTTTGTTG
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
75 58 0.98
76 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (75 bp):
TTCAAAATGCGCCAATATTCCTAATTATGATTGAAATGGACTTTCAGCATGCCCCAACATTTGTT
GATACAAACG
Found at i:51699 original size:11 final size:11
Alignment explanation
Indices: 51683--51716 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
51673 GACTAGTATG
51683 AAAATAATAAT
1 AAAATAATAAT
51694 AAAATAATAATT
1 AAAATAATAA-T
*
51706 AAAGTAATAAT
1 AAAATAATAAT
51717 TTAAACATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:51713 original size:12 final size:12
Alignment explanation
Indices: 51683--51717 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
51673 GACTAGTATG
51683 AAAATAATAA-T
1 AAAATAATAATT
51694 AAAATAATAATT
1 AAAATAATAATT
*
51706 AAAGTAATAATT
1 AAAATAATAATT
51718 TAAACATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (12 bp):
AAAATAATAATT
Done.