Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006779.1 Hibiscus syriacus cultivar Beakdansim tig00017173_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: 58615
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Found at i:900 original size:21 final size:21
Alignment explanation
Indices: 870--944 Score: 60
Period size: 21 Copynumber: 3.6 Consensus size: 21
860 AAAGGAAGGA
*
870 ATCGACCCTTTTCATCGAGAG
1 ATCGATCCTTTTCATCGAGAG
** ** *
891 ATCGATCCTTTTTGTAAAGGG
1 ATCGATCCTTTTCATCGAGAG
* * *
912 ATCGATCATTTTCCTCGAGTG
1 ATCGATCCTTTTCATCGAGAG
*
933 ATTGATCCTTTT
1 ATCGATCCTTTT
945 GTAAAGTGAT
Statistics
Matches: 40, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (21 bp):
ATCGATCCTTTTCATCGAGAG
Found at i:916 original size:42 final size:41
Alignment explanation
Indices: 865--955 Score: 110
Period size: 42 Copynumber: 2.2 Consensus size: 41
855 CCTATAAAGG
* *
865 AAGGAATCGACCCTTTTCATCGAGAGATCGATCCTTTTTGTA
1 AAGGGATCGACCATTTTCATCGAGAGATCGATCC-TTTTGTA
* * * *
907 AAGGGATCGATCATTTTCCTCGAGTGATTGATCCTTTTGTA
1 AAGGGATCGACCATTTTCATCGAGAGATCGATCCTTTTGTA
*
948 AAGTGATC
1 AAGGGATC
956 AATCCCAAAC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 14 0.33
42 28 0.67
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (41 bp):
AAGGGATCGACCATTTTCATCGAGAGATCGATCCTTTTGTA
Found at i:1008 original size:20 final size:20
Alignment explanation
Indices: 976--1033 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
966 TTTCTAGAAT
*
976 CCAAAGGATCAATCCTTTTA
1 CCAAGGGATCAATCCTTTTA
996 -CAAGGGTATCAATCCTTTTA
1 CCAAGGG-ATCAATCCTTTTA
*
1016 CCAAGGGATCGATCCTTT
1 CCAAGGGATCAATCCTTT
1034 GAGCAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.15
20 23 0.68
21 6 0.18
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (20 bp):
CCAAGGGATCAATCCTTTTA
Found at i:2733 original size:29 final size:29
Alignment explanation
Indices: 2691--2750 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
2681 GAAGAGACAA
2691 GTGGTTTGAATTAGAGATGGATTTAGAGG
1 GTGGTTTGAATTAGAGATGGATTTAGAGG
2720 GTGGTTTGAATTAGAGATGGATTTAGAGG
1 GTGGTTTGAATTAGAGATGGATTTAGAGG
2749 GT
1 GT
2751 TGGATGCGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.27, C:0.00, G:0.38, T:0.35
Consensus pattern (29 bp):
GTGGTTTGAATTAGAGATGGATTTAGAGG
Found at i:4944 original size:14 final size:14
Alignment explanation
Indices: 4927--4962 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
4917 TTATCAGTAT
*
4927 TTTTATTTTTATGC
1 TTTTATATTTATGC
4941 TTTTATATTTATGC
1 TTTTATATTTATGC
4955 TTTTATAT
1 TTTTATAT
4963 AACATCTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (14 bp):
TTTTATATTTATGC
Found at i:5895 original size:82 final size:81
Alignment explanation
Indices: 5737--5898 Score: 211
Period size: 81 Copynumber: 2.0 Consensus size: 81
5727 TTTAGCTGCG
* *
5737 TTTTACCAACAAACGCCGCGATAAAGAGTACTTTAGCGGCGTTTTAGACAAATGCCTCAATAGGG
1 TTTTACCAACAAACGCCGCGATAAAGAGTACTTTAACGGCGTTTTAGACAAATACCTCAATAGGG
**
5802 TTACTTTATAGTGGCA
66 TTACTCAATAGTGGCA
* * * *
5818 TTTTTCCAACAAACGCCGCGATAAAGAGTAGTTTAATGGCATTTTTAGACAAATACCAT-AATAG
1 TTTTACCAACAAACGCCGCGATAAAGAGTACTTTAACGGC-GTTTTAGACAAATACC-TCAATAG
5882 GGTT-CATCAATAGTGGC
64 GGTTAC-TCAATAGTGGC
5899 GTTTGTTATA
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
81 37 0.53
82 32 0.46
83 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (81 bp):
TTTTACCAACAAACGCCGCGATAAAGAGTACTTTAACGGCGTTTTAGACAAATACCTCAATAGGG
TTACTCAATAGTGGCA
Found at i:6339 original size:22 final size:22
Alignment explanation
Indices: 6311--6359 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
6301 GTGTTTTACT
6311 GCTTTCGAATAGAAAAATAATA
1 GCTTTCGAATAGAAAAATAATA
*
6333 GCTTTCGAATAGGAAAATAATA
1 GCTTTCGAATAGAAAAATAATA
6355 GCTTT
1 GCTTT
6360 TGAAAACGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.31
Consensus pattern (22 bp):
GCTTTCGAATAGAAAAATAATA
Found at i:17003 original size:42 final size:43
Alignment explanation
Indices: 16906--17036 Score: 138
Period size: 43 Copynumber: 3.1 Consensus size: 43
16896 CTGCAGTGTT
* *** *
16906 TTTGTATCAAAAAATGCTACTATATACCATAGCTTTTGCGGCG
1 TTTGTATAAAAAAATGCCGTTATATACCAGAGCTTTTGCGGCG
* * * *
16949 TTTATCT-GAAAAATGCCGTTATATACAAGAGCTTTTGCGGCG
1 TTTGTATAAAAAAATGCCGTTATATACCAGAGCTTTTGCGGCG
** * *
16991 TTTGTATAAAAAAATATCGTTATATACCAGACCTATTGCGGCG
1 TTTGTATAAAAAAATGCCGTTATATACCAGAGCTTTTGCGGCG
17034 TTT
1 TTT
17037 TTATCCCTAA
Statistics
Matches: 71, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
42 34 0.48
43 37 0.52
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Consensus pattern (43 bp):
TTTGTATAAAAAAATGCCGTTATATACCAGAGCTTTTGCGGCG
Found at i:21180 original size:3 final size:3
Alignment explanation
Indices: 21174--21216 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
21164 AATAATAATA
21174 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
21217 ATGTTAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:27362 original size:30 final size:30
Alignment explanation
Indices: 27326--27382 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
27316 AAAAAATTCT
27326 TCATTTATAAAGCATTACCAATAATATACA
1 TCATTTATAAAGCATTACCAATAATATACA
*
27356 TCATTTATAACGCATTACCAATAATAT
1 TCATTTATAAAGCATTACCAATAATAT
27383 GCATTCATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.44, C:0.18, G:0.04, T:0.35
Consensus pattern (30 bp):
TCATTTATAAAGCATTACCAATAATATACA
Found at i:34424 original size:9 final size:9
Alignment explanation
Indices: 34410--34496 Score: 60
Period size: 8 Copynumber: 10.0 Consensus size: 9
34400 TATTACATTT
34410 GAAAAAGAA
1 GAAAAAGAA
*
34419 GAAAAATAA
1 GAAAAAGAA
34428 GAAAAAAGTAA
1 G-AAAAAG-AA
*
34439 -AAAAGAAAA
1 GAAAA-AGAA
*
34448 GAAAAA-AG
1 GAAAAAGAA
*
34456 GAAAAGGAA
1 GAAAAAGAA
34465 -AAAAAGAA
1 GAAAAAGAA
34473 -AAAAAGAA
1 GAAAAAGAA
*
34481 -AAAAAG-G
1 GAAAAAGAA
34488 GAAAAAGAA
1 GAAAAAGAA
34497 AAATAAATAA
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
8 33 0.53
9 17 0.27
10 10 0.16
11 2 0.03
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (9 bp):
GAAAAAGAA
Found at i:34432 original size:8 final size:7
Alignment explanation
Indices: 34421--34499 Score: 63
Period size: 8 Copynumber: 10.7 Consensus size: 7
34411 AAAAAGAAGA
34421 AAAATAAG
1 AAAA-AAG
34429 AAAAAAG
1 AAAAAAG
34436 TAAAAAAG
1 -AAAAAAG
34444 --AAAAG
1 AAAAAAG
34449 AAAAAAG
1 AAAAAAG
* *
34456 GAAAAGG
1 AAAAAAG
34463 AAAAAAAG
1 -AAAAAAG
34471 AAAAAAAG
1 -AAAAAAG
34479 AAAAAAAGG
1 -AAAAAA-G
*
34488 GAAAAAG
1 AAAAAAG
34495 AAAAA
1 AAAAA
34500 TAAATAAATG
Statistics
Matches: 60, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
5 5 0.08
7 18 0.30
8 36 0.60
9 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:34460 original size:27 final size:25
Alignment explanation
Indices: 34411--34499 Score: 81
Period size: 27 Copynumber: 3.4 Consensus size: 25
34401 ATTACATTTG
* *
34411 AAAAAGAAGAAAAATAAGAAAAAAGTA
1 AAAAAGAA-AAAAAAAAG-AAAAAGAA
*
34438 AAAAAGAAAAGAAAAAAGGAAAAGGAA
1 AAAAAGAAAA-AAAAAA-GAAAAAGAA
* **
34465 AAAAAGAAAAAAAGAA-AAAAAGGG
1 AAAAAGAAAAAAAAAAGAAAAAGAA
34489 AAAAAGAAAAA
1 AAAAAGAAAAA
34500 TAAATAAATG
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
24 16 0.30
26 7 0.13
27 29 0.55
28 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (25 bp):
AAAAAGAAAAAAAAAAGAAAAAGAA
Found at i:35707 original size:137 final size:136
Alignment explanation
Indices: 35458--35886 Score: 497
Period size: 137 Copynumber: 3.1 Consensus size: 136
35448 ATTTTCAATC
* *
35458 GACCAGATCTCCTCATCACATAGGAGCAGTGTCAACCTTAGATAACCAAACTTCCTCATCACGTA
1 GACCAGATCTCCTCATCACGTAGGAGCATTGTCAACCTTAGATAACC-AACTTCCTCATCACGTA
* * *
35523 GGAACCATGTTATCT-TCTTTATCCCTAAAGATGGCCAGTCATTCTCATCACATAGGAATCATAT
65 GGAACCATGTTATCTCT-TTTATCCCTAAAGATGGCCAGCCGTCCTCATCACATAGGAATCATAT
*
35587 CATCCATT
129 CATCCACT
* * ** *
35595 GACCAGATCTCCTCATCACGTAGGAGCATTGTCAACTTTAAATAGTCAGACTTCCTCATCATGTA
1 GACCAGATCTCCTCATCACGTAGGAGCATTGTCAACCTTAGATAACCA-ACTTCCTCATCACGTA
* * * * *
35660 GGAACTATGTTATCTCTTTTATCCCTAAAGATGGCCAGCCGTCCTCATTACGTAGGAATCGTGTC
65 GGAACCATGTTATCTCTTTTATCCCTAAAGATGGCCAGCCGTCCTCATCACATAGGAATCATATC
35725 ATCCACT
130 ATCCACT
* * * *
35732 GA-CAGATCTCCTCATCAAGTAGGAGC-TGCGTCAACCTTAGATAACCAACCGTCCTCATCACAT
1 GACCAGATCTCCTCATCACGTAGGAGCAT-TGTCAACCTTAGATAACCAA-CTTCCTCATCACGT
* * * * * *
35795 AGGAACCCTGTTATCACCATTTATCCCTAAAGATGGCCAACCGTCCTCATCATATAGGAA-CTGT
64 AGGAACCATGTTATC-TCTTTTATCCCTAAAGATGGCCAGCCGTCCTCATCACATAGGAATC-AT
* * *
35859 GTCATCTACC
127 ATCATCCACT
*
35869 GACCATATCTCCTCATCA
1 GACCAGATCTCCTCATCA
35887 TATAGGAGTC
Statistics
Matches: 249, Mismatches: 36, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
135 2 0.01
136 63 0.25
137 169 0.68
138 15 0.06
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (136 bp):
GACCAGATCTCCTCATCACGTAGGAGCATTGTCAACCTTAGATAACCAACTTCCTCATCACGTAG
GAACCATGTTATCTCTTTTATCCCTAAAGATGGCCAGCCGTCCTCATCACATAGGAATCATATCA
TCCACT
Found at i:35946 original size:138 final size:136
Alignment explanation
Indices: 35461--35963 Score: 416
Period size: 137 Copynumber: 3.7 Consensus size: 136
35451 TTCAATCGAC
* ** * *
35461 CAGATCTCCTCATCACA-TAGGAGCAGTGTCAACCTTAGATAACCAA-ACTTCCTCATCACGTAG
1 CAGATCTCCTCATCA-AGTAGGAGCTGCCTCAACATTAGATAACCAACA-TTCCTCATCATGTAG
* * * ** * * * *
35524 GAACCATGTTATCTTC-TTTATCCCTAAAGATGGCCAGTCATTCTCATCACATAGGAATCATATC
64 GAACTACGTTATC-CCATTTATCCCTAAAGATGGCCAACCGTCCTCATCACATAGGAATCGTGTC
**
35588 ATCCATTGA
128 ATCCACCGA
* * * **
35597 CCAGATCTCCTCATCACGTAGGAGCATTG--TCAACTTTAAATAGTCAGAC-TTCCTCATCATGT
1 -CAGATCTCCTCATCAAGTAGGAGC--TGCCTCAACATTAGATAACCA-ACATTCCTCATCATGT
* * * * * *
35659 AGGAACTATGTTATCTCTTTTATCCCTAAAGATGGCCAGCCGTCCTCATTACGTAGGAATCGTGT
62 AGGAACTACGTTATCCCATTTATCCCTAAAGATGGCCAACCGTCCTCATCACATAGGAATCGTGT
*
35724 CATCCACTGA
127 CATCCACCGA
* * ** **
35734 CAGATCTCCTCATCAAGTAGGAGCTGCGTCAACCTTAGATAACCAACCGTCCTCATCACATAGGA
1 CAGATCTCCTCATCAAGTAGGAGCTGCCTCAACATTAGATAACCAACATTCCTCATCATGTAGGA
* *
35799 AC-CCTGTTATCACCATTTATCCCTAAAGATGGCCAACCGTCCTCATCATATAGGAA-CTGTGTC
66 ACTAC-GTTATC-CCATTTATCCCTAAAGATGGCCAACCGTCCTCATCACATAGGAATC-GTGTC
*
35862 ATCTACCGA
128 ATCCACCGA
* * * *
35871 CCATATCTCCTCATCATA-TAGGAG-TCGCCTTATCATTAGATAGCCATA-ATTCCTCATCATGT
1 -CAGATCTCCTCATCA-AGTAGGAGCT-GCCTCAACATTAGATAACCA-ACATTCCTCATCATGT
*
35933 AGGAACTGCGTTATCTCCATTTATCCCTAAA
62 AGGAACTACGTTATC-CCATTTATCCCTAAA
35964 TCGGCCAGAA
Statistics
Matches: 303, Mismatches: 46, Indels: 33
0.79 0.12 0.09
Matches are distributed among these distances:
134 2 0.01
135 2 0.01
136 61 0.20
137 161 0.53
138 73 0.24
139 4 0.01
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.29
Consensus pattern (136 bp):
CAGATCTCCTCATCAAGTAGGAGCTGCCTCAACATTAGATAACCAACATTCCTCATCATGTAGGA
ACTACGTTATCCCATTTATCCCTAAAGATGGCCAACCGTCCTCATCACATAGGAATCGTGTCATC
CACCGA
Found at i:35949 original size:274 final size:273
Alignment explanation
Indices: 35461--35963 Score: 638
Period size: 274 Copynumber: 1.8 Consensus size: 273
35451 TTCAATCGAC
* * *
35461 CAGATCTCCTCATCACATAGGAGCAGTGTCAACCTTAGATAACCAAACTTCCTCATCACGTAGGA
1 CAGATCTCCTCATCACATAGGAGCAGCGTCAACCTTAGATAACCAAACGTCCTCATCACATAGGA
** ** *
35526 ACCATGTTATCTTCTTTATCCCTAAAGATGGCCAGTCATTCTCATCACATAGGAATCATATCATC
66 ACCATGTTATCACCTTTATCCCTAAAGATGGCCAACCATCCTCATCACATAGGAATCATATCATC
** * * * *
35591 CATTGACCAGATCTCCTCATCACGTAGGAGCATTGTCAACTTTAAATAGTCAGACTTCCTCATCA
131 CACCGACCAGATCTCCTCATCACATAGGAGCATTATCAAC-TTAAATAGCCAGAATTCCTCATCA
* *
35656 TGTAGGAACTATGTTATCT-CTTTTATCCCTAAAGATGGCCAGCCGTCCTCATTACGTAGGAATC
195 TGTAGGAACTACGTTATCTCCATTTATCCCTAAAGATGGCCAGCCGTCCTCATTACGTAGGAATC
35720 GTGTCATCCACTGA
260 GTGTCATCCACTGA
* *
35734 CAGATCTCCTCATCA-AGTAGGAGCTGCGTCAACCTTAGATAACCAACCGTCCTCATCACATAGG
1 CAGATCTCCTCATCACA-TAGGAGCAGCGTCAACCTTAGATAACCAAACGTCCTCATCACATAGG
* * * * *
35798 AACCCTGTTATCACCATTTATCCCTAAAGATGGCCAACCGTCCTCATCATATAGGAA-CTGTGTC
65 AACCATGTTATCACC-TTTATCCCTAAAGATGGCCAACCATCCTCATCACATAGGAATC-ATATC
* * * * * *
35862 ATCTACCGACCATATCTCCTCATCATATAGGAGTCGCCTTATC-A-TTAGATAGCCATAATTCCT
128 ATCCACCGACCAGATCTCCTCATCACATAGGA---GCATTATCAACTTAAATAGCCAGAATTCCT
*
35925 CATCATGTAGGAACTGCGTTATCTCCATTTATCCCTAAA
190 CATCATGTAGGAACTACGTTATCTCCATTTATCCCTAAA
35964 TCGGCCAGAA
Statistics
Matches: 193, Mismatches: 30, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
272 1 0.01
273 70 0.36
274 102 0.53
275 13 0.07
276 1 0.01
277 6 0.03
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.29
Consensus pattern (273 bp):
CAGATCTCCTCATCACATAGGAGCAGCGTCAACCTTAGATAACCAAACGTCCTCATCACATAGGA
ACCATGTTATCACCTTTATCCCTAAAGATGGCCAACCATCCTCATCACATAGGAATCATATCATC
CACCGACCAGATCTCCTCATCACATAGGAGCATTATCAACTTAAATAGCCAGAATTCCTCATCAT
GTAGGAACTACGTTATCTCCATTTATCCCTAAAGATGGCCAGCCGTCCTCATTACGTAGGAATCG
TGTCATCCACTGA
Found at i:36211 original size:3 final size:3
Alignment explanation
Indices: 36203--36279 Score: 88
Period size: 3 Copynumber: 26.0 Consensus size: 3
36193 CCGGGTGTAA
* *
36203 ATT ATT ATT ATT ATT ATT ATT ATGA ATT ATT ATT AGT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT
*
36249 GTT ATT ATT AGTT -TT ATT -TT ATT -TT ATT ATT
1 ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT
36280 TTAATTAAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
2 6 0.10
3 53 0.84
4 4 0.06
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:36233 original size:22 final size:22
Alignment explanation
Indices: 36206--36266 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
36196 GGTGTAAATT
*
36206 ATTATTATTATTATTATTATGA
1 ATTATTATTAGTATTATTATGA
36228 ATTATTATTAGTATTATTATTG-
1 ATTATTATTAGTATTATTA-TGA
*
36250 -TTATTATTAGTTTTATT
1 ATTATTATTAGTATTATT
36267 TTATTTTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 16 0.44
22 18 0.50
23 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (22 bp):
ATTATTATTAGTATTATTATGA
Found at i:38005 original size:2 final size:2
Alignment explanation
Indices: 38000--38025 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
37990 TTTTATGAAT
38000 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
38026 CTTAATAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38303 original size:16 final size:15
Alignment explanation
Indices: 38282--38333 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 15
38272 AAAATCATTA
38282 TATTTTCATTTTATTT
1 TATTTTCA-TTTATTT
38298 TATTTT-ATTTATTT
1 TATTTTCATTTATTT
*
38312 TCGTTTTTCA-TTATTT
1 T--ATTTTCATTTATTT
38328 TATTTT
1 TATTTT
38334 TTTATAATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 12 0.39
15 1 0.03
16 17 0.55
17 1 0.03
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (15 bp):
TATTTTCATTTATTT
Found at i:38310 original size:25 final size:25
Alignment explanation
Indices: 38282--38336 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
38272 AAAATCATTA
*
38282 TATTTTCATTTTAT-TTTATTTTATT
1 TATTTTCATTTT-TCATTATTTTATT
*
38307 TATTTTCGTTTTTCATTATTTTATT
1 TATTTTCATTTTTCATTATTTTATT
38332 T-TTTT
1 TATTTT
38337 ATAATGTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 5 0.19
25 22 0.81
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.76
Consensus pattern (25 bp):
TATTTTCATTTTTCATTATTTTATT
Found at i:39118 original size:27 final size:27
Alignment explanation
Indices: 39081--39133 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
39071 GGATCGATGT
*
39081 TCCTCCTCTTTCGAACTTAATCTATGC
1 TCCTCCTCTTTCGAACTTAAACTATGC
39108 TCCTCCTCTTTCGAACTTAAACTATG
1 TCCTCCTCTTTCGAACTTAAACTATG
39134 TTAAACATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.21, C:0.32, G:0.08, T:0.40
Consensus pattern (27 bp):
TCCTCCTCTTTCGAACTTAAACTATGC
Found at i:44551 original size:65 final size:63
Alignment explanation
Indices: 44474--44634 Score: 207
Period size: 65 Copynumber: 2.5 Consensus size: 63
44464 GGAATAAATT
** *
44474 AAACATCGAATGCATTTCATGCATCGATGCACATATTATGCATCGATGCACTCGGAGT-TTTATG
1 AAACATCGAATGCATTTCATGCATCGATGCACA-ACCATGCATCGATGCACTCGGACTATTT-TG
* * * **
44538 AAAACATCGAATGCATTTGATACATCGATGTACCAACCATGCATCGATGCACTTTGACTATTTTG
1 -AAACATCGAATGCATTTCATGCATCGATGCA-CAACCATGCATCGATGCACTCGGACTATTTTG
44603 AAACATCGAATGCATTTCATGCATCGATGCAC
1 AAACATCGAATGCATTTCATGCATCGATGCAC
44635 TCTTAGTGCA
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
63 1 0.01
64 28 0.34
65 49 0.59
66 5 0.06
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.30
Consensus pattern (63 bp):
AAACATCGAATGCATTTCATGCATCGATGCACAACCATGCATCGATGCACTCGGACTATTTTG
Found at i:50467 original size:20 final size:20
Alignment explanation
Indices: 50438--50489 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
50428 ACCATAAAGG
50438 TGCATCGATGCACAAGGCCA
1 TGCATCGATGCACAAGGCCA
*
50458 TGCATTGATGCACAAGGCCA
1 TGCATCGATGCACAAGGCCA
50478 TGCATCGATGCA
1 TGCATCGATGCA
50490 TCCATCGGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.29, C:0.27, G:0.25, T:0.19
Consensus pattern (20 bp):
TGCATCGATGCACAAGGCCA
Found at i:52052 original size:21 final size:21
Alignment explanation
Indices: 52010--52053 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
52000 ACCCCGGGAG
* *
52010 CTAGTTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
52031 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
52052 CT
1 CT
52054 CCTCCGACAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.39, G:0.16, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:52433 original size:29 final size:28
Alignment explanation
Indices: 52401--52458 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
52391 GGATGTTTAA
52401 ATTTGATGGTTGT-TGGATGTTTTGAACTT
1 ATTTG-TGGTTGTATGGAT-TTTTGAACTT
* *
52430 ATTTGTTGTTTTATGGATTTTTGAACTT
1 ATTTGTGGTTGTATGGATTTTTGAACTT
52458 A
1 A
52459 ATATTTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.55
Consensus pattern (28 bp):
ATTTGTGGTTGTATGGATTTTTGAACTT
Found at i:52647 original size:2 final size:2
Alignment explanation
Indices: 52642--52676 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
52632 AAGCTCTCTC
52642 TA TA TA TA 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 TA TA TA TA T
52677 CAGTTGGCTA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:53303 original size:45 final size:46
Alignment explanation
Indices: 53190--53314 Score: 155
Period size: 46 Copynumber: 2.7 Consensus size: 46
53180 GAATAAATTG
* * *
53190 AACAGCGAATGCATTTCATGCATCGATGCACTCAGAGTTTTATGAA
1 AACATCGAATGCATTTCATGCATCGATGCACTCTGACTTTTATGAA
* *
53236 AACATCGAATGCATTTGATGCATCGATGCACTCTGCCTATTT-TG-A
1 AACATCGAATGCATTTCATGCATCGATGCACTCTGACT-TTTATGAA
* * *
53281 AACATCGACTGCATTTCTTGCATCGGTGCACTCT
1 AACATCGAATGCATTTCATGCATCGATGCACTCT
53315 TAGTGCACCG
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
45 31 0.45
46 35 0.51
47 3 0.04
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.31
Consensus pattern (46 bp):
AACATCGAATGCATTTCATGCATCGATGCACTCTGACTTTTATGAA
Found at i:56412 original size:93 final size:92
Alignment explanation
Indices: 56065--56409 Score: 352
Period size: 93 Copynumber: 3.7 Consensus size: 92
56055 CATTTGCTGC
* * * * *
56065 CCCAGACCCTCCTCCCCCATGAGCACATCATCTCTTGGATCCTCCGGCTCCATGGGGATATTATG
1 CCCAGACCCTCCTCCCCCATGAGCTCATCATCCCTTGGATCCTCCGGCTTCATGGGGACATCATG
*
56130 TTCCAGAGGTGAACTGGGCTCATCTTG
66 TTCCAGAGGTGAAATGGGCTCATCTTG
* * * * *
56157 TCCCAGACCCTTCTTCCCCATGAGCTCATCATCACC-TAGATCCTCCGGCTTCGTGGGGACATTA
1 -CCCAGACCCTCCTCCCCCATGAGCTCATCATC-CCTTGGATCCTCCGGCTTCATGGGGACATCA
*
56221 TGTTCCAGAGGTGAAATAGGCTCATCTTG
64 TGTTCCAGAGGTGAAATGGGCTCATCTTG
* * ** * ** * * *
56250 CCCTAGACCCTCTTTCCCCATGAGCTCATCATCCCCCGGACCCTCTTGCTTAATGGGGAGATCAA
1 CCC-AGACCCTCCTCCCCCATGAGCTCATCATCCCTTGGATCCTCCGGCTTCATGGGGACATCAT
* * * *
56315 G-TCCTAGATGTTAATTGGGCTCATCGTG
65 GTTCC-AGAGGTGAAATGGGCTCATCTTG
* * * * *
56343 CACCAAACACTCCTCCCCCATGAGCTTATCATCCCTTGGATCCTCTGGCTTCATGTGGACATCAT
1 C-CCAGACCCTCCTCCCCCATGAGCTCATCATCCCTTGGATCCTCCGGCTTCATGGGGACATCAT
56408 GT
65 GT
56410 CCTGCATGTG
Statistics
Matches: 206, Mismatches: 40, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
92 8 0.04
93 195 0.95
94 3 0.01
ACGTcount: A:0.20, C:0.33, G:0.20, T:0.28
Consensus pattern (92 bp):
CCCAGACCCTCCTCCCCCATGAGCTCATCATCCCTTGGATCCTCCGGCTTCATGGGGACATCATG
TTCCAGAGGTGAAATGGGCTCATCTTG
Done.