Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002965.1 Hibiscus syriacus cultivar Beakdansim tig00006133_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: 79633
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:5800 original size:15 final size:15
Alignment explanation
Indices: 5780--5816 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
5770 CTAGTATTTT
*
5780 CATCTTGCAGTAATG
1 CATCTTGAAGTAATG
5795 CATCTTGAAGTAATG
1 CATCTTGAAGTAATG
5810 CATCTTG
1 CATCTTG
5817 TGATCTTACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (15 bp):
CATCTTGAAGTAATG
Found at i:5993 original size:2 final size:2
Alignment explanation
Indices: 5986--6012 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5976 CTTACGCATT
5986 TA 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 TA T
6013 GTGTGTGTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6166 original size:17 final size:18
Alignment explanation
Indices: 6138--6171 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
6128 AAGTATAAGG
6138 ATTTATTTAAAAGTAATA
1 ATTTATTTAAAAGTAATA
*
6156 ATTTA-TTAAAATTAAT
1 ATTTATTTAAAAGTAAT
6172 TATAATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
ATTTATTTAAAAGTAATA
Found at i:6796 original size:18 final size:19
Alignment explanation
Indices: 6773--6813 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
6763 AAAGCAATGA
*
6773 TAAAAATAAATATC-AAAT
1 TAAAAATAAACATCAAAAT
*
6791 TAAAAATAAGCATCAAAAT
1 TAAAAATAAACATCAAAAT
6810 TAAA
1 TAAA
6814 TTAAGGATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.24
Consensus pattern (19 bp):
TAAAAATAAACATCAAAAT
Found at i:6818 original size:18 final size:18
Alignment explanation
Indices: 6787--6833 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
6777 AATAAATATC
6787 AAATTAAAAATAAGCATCA
1 AAATT-AAAATAAGCATCA
* *
6806 AAATTAAATTAAGGATCA
1 AAATTAAAATAAGCATCA
*
6824 ATATTAAAAT
1 AAATTAAAAT
6834 TTGCGTATCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.28
Consensus pattern (18 bp):
AAATTAAAATAAGCATCA
Found at i:9056 original size:18 final size:15
Alignment explanation
Indices: 9018--9077 Score: 56
Period size: 14 Copynumber: 4.1 Consensus size: 15
9008 AGTTTTTAAT
*
9018 ATTAAAAATGAAA-A
1 ATTAAAAATAAAATA
9032 A-T-AAAATAAAATA
1 ATTAAAAATAAAATA
9045 ATAGTAATAAATAAAA-A
1 AT--TAA-AAATAAAATA
9062 ATTAAAAATAAAATA
1 ATTAAAAATAAAATA
9077 A
1 A
9078 AAACATGGTA
Statistics
Matches: 38, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
12 8 0.21
13 3 0.08
14 9 0.24
15 5 0.13
16 1 0.03
17 4 0.11
18 8 0.21
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (15 bp):
ATTAAAAATAAAATA
Found at i:9060 original size:29 final size:31
Alignment explanation
Indices: 9014--9077 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 31
9004 TTATAGTTTT
* *
9014 TAATATTAAAAATGAAAAA-T-AAAATAAAA
1 TAATAGTAAAAATAAAAAATTAAAAATAAAA
9043 TAATAGTAATAAATAAAAAATTAAAAATAAAA
1 TAATAGTAA-AAATAAAAAATTAAAAATAAAA
9075 TAA
1 TAA
9078 AAACATGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 8 0.27
30 9 0.30
31 1 0.03
32 12 0.40
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (31 bp):
TAATAGTAAAAATAAAAAATTAAAAATAAAA
Found at i:9079 original size:18 final size:18
Alignment explanation
Indices: 9020--9080 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
9010 TTTTTAATAT
*
9020 TAAAAATGAAAAATAAAA
1 TAAAAATTAAAAATAAAA
* **
9038 TAAAATAATAGTAAT-AAA
1 TAAAA-ATTAAAAATAAAA
9056 TAAAAAATTAAAAATAAAA
1 T-AAAAATTAAAAATAAAA
9075 TAAAAA
1 TAAAAA
9081 CATGGTAAAG
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
18 20 0.61
19 13 0.39
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.21
Consensus pattern (18 bp):
TAAAAATTAAAAATAAAA
Found at i:11014 original size:19 final size:20
Alignment explanation
Indices: 10992--11034 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
10982 ATATTTACTT
10992 TTTAAAAAATAATTT-AATA
1 TTTAAAAAATAATTTAAATA
* * *
11011 TTTATAATATATTTTAAATA
1 TTTAAAAAATAATTTAAATA
11031 TTTA
1 TTTA
11035 TTTTAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTAAAAAATAATTTAAATA
Found at i:18196 original size:33 final size:33
Alignment explanation
Indices: 18140--18216 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 33
18130 AAATTTGAAA
18140 AACTATCAAAATGAATCAATTACAGTGAACTAC
1 AACTATCAAAATGAATCAATTACAGTGAACTAC
* * *
18173 AACTGTCAAAATGGAAT-ATTTACAGTGAACAAAC
1 AACTATCAAAAT-GAATCAATTACAGTGAAC-TAC
18207 AA-TATCAAAA
1 AACTATCAAAA
18217 ACACAAAACA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
33 30 0.79
34 8 0.21
ACGTcount: A:0.51, C:0.16, G:0.10, T:0.23
Consensus pattern (33 bp):
AACTATCAAAATGAATCAATTACAGTGAACTAC
Found at i:18751 original size:14 final size:14
Alignment explanation
Indices: 18727--18795 Score: 61
Period size: 14 Copynumber: 4.8 Consensus size: 14
18717 TTTTGATTTA
*
18727 AATCGAATGTAAAT
1 AATCAAATGTAAAT
*
18741 ACTCAAATGTAAAT
1 AATCAAATGTAAAT
18755 AAT-AAAT-TAAATTT
1 AATCAAATGTAAA--T
18769 AAAATCAAATGTAAAT
1 --AATCAAATGTAAAT
*
18785 AGTCAAATGTA
1 AATCAAATGTA
18796 TATTTCTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
12 4 0.09
13 4 0.09
14 25 0.56
16 4 0.09
17 4 0.09
18 4 0.09
ACGTcount: A:0.54, C:0.07, G:0.09, T:0.30
Consensus pattern (14 bp):
AATCAAATGTAAAT
Found at i:18931 original size:21 final size:21
Alignment explanation
Indices: 18905--18946 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
18895 CTTGCACTGG
18905 GAATTAGGGCCGG-TCACGGTC
1 GAATTA-GGCCGGTTCACGGTC
*
18926 GAATTAGGTCGGTTCACGGTC
1 GAATTAGGCCGGTTCACGGTC
18947 CGAAACTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
GAATTAGGCCGGTTCACGGTC
Found at i:19068 original size:29 final size:28
Alignment explanation
Indices: 19005--19069 Score: 71
Period size: 31 Copynumber: 2.3 Consensus size: 28
18995 TCATTGTTAA
19005 TTAAA-TAATTTTTTTTAAAAAAATATT
1 TTAAATTAATTTTTTTTAAAAAAATATT
* *
19032 TTATAATTAAGTTTTATTTTTAAAAGAT-TT
1 TTA-AATTAA-TTTT-TTTTAAAAAAATATT
19062 TTAAATTA
1 TTAAATTA
19070 TGTAAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 3 0.09
28 2 0.06
29 8 0.25
30 9 0.28
31 10 0.31
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (28 bp):
TTAAATTAATTTTTTTTAAAAAAATATT
Found at i:27473 original size:2 final size:2
Alignment explanation
Indices: 27435--27459 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27425 ACATCATGAA
27435 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 A
27460 ATTATAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28267 original size:2 final size:2
Alignment explanation
Indices: 28260--28294 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
28250 ATTTAAACTA
28260 AT AT AT AT 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 AT AT AT AT A
28295 AAATTACTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31178 original size:22 final size:21
Alignment explanation
Indices: 31137--31179 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
31127 AATCAACATA
31137 AATTTAAATTTGTTAGTTTAAT
1 AATTTAAATTTGTTA-TTTAAT
31159 AATTTGAAATATTGTT-TTTAA
1 AATTT-AAAT-TTGTTATTTAA
31180 AAAATGTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 10 0.53
23 4 0.21
24 5 0.26
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (21 bp):
AATTTAAATTTGTTATTTAAT
Found at i:33399 original size:22 final size:21
Alignment explanation
Indices: 33358--33400 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
33348 AATCAACATA
33358 AATTTAAATTTGTTAGTTTAAT
1 AATTTAAATTTGTTA-TTTAAT
33380 AATTTGAAATGTTGTT-TTTAA
1 AATTT-AAAT-TTGTTATTTAA
33401 AAAATGTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 10 0.53
23 4 0.21
24 5 0.26
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (21 bp):
AATTTAAATTTGTTATTTAAT
Found at i:39629 original size:31 final size:31
Alignment explanation
Indices: 39593--39652 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
39583 AACTTAAAAG
*
39593 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
39624 AGTTTTATAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
39653 CACACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:39701 original size:22 final size:22
Alignment explanation
Indices: 39675--40275 Score: 872
Period size: 22 Copynumber: 27.6 Consensus size: 22
39665 ATAATAAATT
* *
39675 TTTTAAAATAAATAAATTCATA
1 TTTTAAAATAAATCAATCCATA
39697 TTTT---A-AAAT--ATCCATA
1 TTTTAAAATAAATCAATCCATA
39713 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
39735 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
39757 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
39779 TTTTAAAATAAATCAATCCATG
1 TTTTAAAATAAATCAATCCATA
39801 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
39823 TTTTAAAATGAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
39845 TTTTAAAATGAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
39867 TTTTAAAGTAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
39889 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
39911 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
***
39933 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
*
39955 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
*** *
39977 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
*
39999 TTTTTAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
40021 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
*
40043 TTTTAAAGTAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
40065 TTTTAAAATAAATCAATCGATA
1 TTTTAAAATAAATCAATCCATA
***
40087 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
*
40109 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
* *** *
40131 TTTTAAAATAATTTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
40153 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
***
40175 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
40197 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
40219 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
40241 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
40263 TTTTAAAATAAAT
1 TTTTAAAATAAAT
40276 TTTAAAATAG
Statistics
Matches: 519, Mismatches: 54, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
16 10 0.02
18 4 0.01
19 2 0.00
20 4 0.01
22 499 0.96
ACGTcount: A:0.47, C:0.11, G:0.01, T:0.41
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:41737 original size:33 final size:33
Alignment explanation
Indices: 41681--41757 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 33
41671 AAATTAGAAA
41681 AACTATCAAAATGAATCAATTACAGTGAACTAC
1 AACTATCAAAATGAATCAATTACAGTGAACTAC
* * *
41714 AACTGTCAAAATGGAAT-ATTTACAGTGAACAAAC
1 AACTATCAAAAT-GAATCAATTACAGTGAAC-TAC
41748 AA-TATCAAAA
1 AACTATCAAAA
41758 ATACAAAACA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
33 30 0.79
34 8 0.21
ACGTcount: A:0.51, C:0.16, G:0.10, T:0.23
Consensus pattern (33 bp):
AACTATCAAAATGAATCAATTACAGTGAACTAC
Found at i:42290 original size:14 final size:14
Alignment explanation
Indices: 42266--42334 Score: 52
Period size: 14 Copynumber: 4.8 Consensus size: 14
42256 TTTTGATTTA
*
42266 AATCGAATGTAAAT
1 AATCAAATGTAAAT
*
42280 ACTCAAATGTAAAT
1 AATCAAATGTAAAT
42294 AAT-AAAT-TAAATTT
1 AATCAAATGTAAA--T
*
42308 AAAATCAAATATAAAT
1 --AATCAAATGTAAAT
*
42324 ACTCAAATGTA
1 AATCAAATGTA
42335 TATTTCTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
12 4 0.09
13 4 0.09
14 24 0.55
16 4 0.09
17 4 0.09
18 4 0.09
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (14 bp):
AATCAAATGTAAAT
Found at i:42471 original size:21 final size:21
Alignment explanation
Indices: 42445--42486 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
42435 CTTGCACTGG
42445 GAATTAGGGCCGG-TCACGGTC
1 GAATTA-GGCCGGTTCACGGTC
*
42466 GAATTAGGTCGGTTCACGGTC
1 GAATTAGGCCGGTTCACGGTC
42487 CGAAACTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
GAATTAGGCCGGTTCACGGTC
Found at i:46668 original size:18 final size:18
Alignment explanation
Indices: 46626--46670 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
46616 AAGAATATAA
*
46626 TGCTACACGTGCACATGC
1 TGCTACTCGTGCACATGC
46644 TGCTACTCGTGCACATGC
1 TGCTACTCGTGCACATGC
46662 TGCTACTCG
1 TGCTACTCG
46671 GTTCTTTCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.18, C:0.33, G:0.22, T:0.27
Consensus pattern (18 bp):
TGCTACTCGTGCACATGC
Found at i:51375 original size:22 final size:21
Alignment explanation
Indices: 51334--51376 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
51324 AATCAACATA
51334 AATTTAAATTTGTTAGTTTAAT
1 AATTTAAATTTGTTA-TTTAAT
51356 AATTTGAAATATTGTT-TTTAA
1 AATTT-AAAT-TTGTTATTTAA
51377 AAATGTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 10 0.53
23 4 0.21
24 5 0.26
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (21 bp):
AATTTAAATTTGTTATTTAAT
Found at i:53934 original size:63 final size:63
Alignment explanation
Indices: 53860--53987 Score: 188
Period size: 63 Copynumber: 2.0 Consensus size: 63
53850 AGTCCAAGAG
* *
53860 AATTTCCTTCTTTGAAGCATTTGGA-GTTGT-TCAGGTGTGAGATCAGCCAAGACTTCACTCTAC
1 AATTTCCTTCTTTGAAGCATTT-GATCTTATAT-AGGTGTGAGATCAGCCAAGACTTCACTCTAC
* *
53923 AATTTTCTTCTTTGAAGCATTTGATCTTATATGGGTGTGAGATCAGCCAAGACTTCACTCTAC
1 AATTTCCTTCTTTGAAGCATTTGATCTTATATAGGTGTGAGATCAGCCAAGACTTCACTCTAC
53986 AA
1 AA
53988 GGTAATTTGA
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
62 2 0.03
63 56 0.95
64 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.36
Consensus pattern (63 bp):
AATTTCCTTCTTTGAAGCATTTGATCTTATATAGGTGTGAGATCAGCCAAGACTTCACTCTAC
Found at i:58400 original size:15 final size:15
Alignment explanation
Indices: 58380--58416 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
58370 CTAGTATTTT
*
58380 CATCTTGCAGTAATG
1 CATCTTGAAGTAATG
58395 CATCTTGAAGTAATG
1 CATCTTGAAGTAATG
58410 CATCTTG
1 CATCTTG
58417 TGATCTTACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (15 bp):
CATCTTGAAGTAATG
Found at i:58593 original size:2 final size:2
Alignment explanation
Indices: 58586--58612 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
58576 CTTACGCATT
58586 TA 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 TA T
58613 GTGTGTGTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:58768 original size:17 final size:18
Alignment explanation
Indices: 58740--58773 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
58730 AAGTATAAGG
58740 ATTTATTTAAAAGTAATA
1 ATTTATTTAAAAGTAATA
*
58758 ATTTA-TTAAAATTAAT
1 ATTTATTTAAAAGTAAT
58774 TATAATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
ATTTATTTAAAAGTAATA
Found at i:59413 original size:19 final size:19
Alignment explanation
Indices: 59377--59437 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 19
59367 AAAGCAATGA
**
59377 TAAAAATAAATATC-AAAT
1 TAAAAATAAGCATCAAAAT
59395 TAAAAATAAGCATCAAAAT
1 TAAAAATAAGCATCAAAAT
* * * *
59414 TTAAATTAAGGATCAATAT
1 TAAAAATAAGCATCAAAAT
59433 TAAAA
1 TAAAA
59438 TTTGCGTATC
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
18 12 0.34
19 23 0.66
ACGTcount: A:0.61, C:0.07, G:0.05, T:0.28
Consensus pattern (19 bp):
TAAAAATAAGCATCAAAAT
Found at i:61659 original size:18 final size:15
Alignment explanation
Indices: 61637--61680 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 15
61627 AATGAAAAAT
61637 AAAATAAAATAATAGTA
1 AAAATAAAATAATA--A
61654 ATAAATAAAA-AATAA
1 A-AAATAAAATAATAA
61669 AAAATAAAATAA
1 AAAATAAAATAA
61681 AAACATGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 8 0.32
15 4 0.16
17 5 0.20
18 8 0.32
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.20
Consensus pattern (15 bp):
AAAATAAAATAATAA
Found at i:63620 original size:19 final size:20
Alignment explanation
Indices: 63598--63640 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
63588 ATATTTACTT
63598 TTTAAAAAATAATTT-AATA
1 TTTAAAAAATAATTTAAATA
* * *
63617 TTTATAATATATTTTAAATA
1 TTTAAAAAATAATTTAAATA
63637 TTTA
1 TTTA
63641 TTTTTAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTAAAAAATAATTTAAATA
Found at i:70771 original size:33 final size:33
Alignment explanation
Indices: 70729--70805 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 33
70719 TAAATTGAAA
70729 AACTATCAAAAT-GAATCAATTACAGTGAACTAC
1 AACTATCAAAATGGAAT-AATTACAGTGAACTAC
* * *
70762 AACTGTCAAAATGGAATATTTACAGTGAACAAAC
1 AACTATCAAAATGGAATAATTACAGTGAAC-TAC
70796 AA-TATCAAAA
1 AACTATCAAAA
70806 ACACAAAACA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
33 30 0.79
34 8 0.21
ACGTcount: A:0.51, C:0.16, G:0.10, T:0.23
Consensus pattern (33 bp):
AACTATCAAAATGGAATAATTACAGTGAACTAC
Found at i:71331 original size:14 final size:14
Alignment explanation
Indices: 71307--71375 Score: 61
Period size: 14 Copynumber: 4.8 Consensus size: 14
71297 TTTTGATTTA
*
71307 AATCGAATGTAAAT
1 AATCAAATGTAAAT
*
71321 ACTCAAATGTAAAT
1 AATCAAATGTAAAT
71335 AAT-AAAT-TAAATTT
1 AATCAAATGTAAA--T
71349 AAAATCAAATGTAAAT
1 --AATCAAATGTAAAT
*
71365 ACTCAAATGTA
1 AATCAAATGTA
71376 TATTTCTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
12 4 0.09
13 4 0.09
14 25 0.56
16 4 0.09
17 4 0.09
18 4 0.09
ACGTcount: A:0.54, C:0.09, G:0.07, T:0.30
Consensus pattern (14 bp):
AATCAAATGTAAAT
Done.