Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000399.1 Hibiscus syriacus cultivar Beakdansim tig00000732_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: 63564
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:3251 original size:65 final size:65
Alignment explanation
Indices: 3114--3273 Score: 200
Period size: 65 Copynumber: 2.5 Consensus size: 65
3104 TGCAGTAAGA
* * * * *
3114 GTGCATCGATGCATGAAGTGCATTCAATG-TTTCAAAATAGCCTGAGTGTATCGATGCATGTCTT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGATGCATGTCAT
* * *
3178 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTGAGTGCATCGATGTATGGT-
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATAGCCTGAGTGCATCGATGCAT-GTC
3241 AT
64 AT
*
3243 GTGTATCGATGCATAAAATGCATTCGATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
3274 CAATTTATTC
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 26 0.31
65 53 0.63
66 5 0.06
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.34
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGATGCATGTCAT
Found at i:10248 original size:17 final size:16
Alignment explanation
Indices: 10207--10248 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
10197 AAATACCTTT
10207 TAAAATAATTTTAAGA
1 TAAAATAATTTTAAGA
10223 -AAAATAATTTTAAAAGA
1 TAAAATAATTTT--AAGA
10240 TAAAA-AATT
1 TAAAATAATT
10249 GATTTGCGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 11 0.48
17 8 0.35
18 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (16 bp):
TAAAATAATTTTAAGA
Found at i:13074 original size:22 final size:23
Alignment explanation
Indices: 13048--13099 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
13038 CGGGATGGAT
*
13048 CTTTGTAAATGGG-TCGGGTTTA
1 CTTTGTAAATGGGCCCGGGTTTA
*
13070 CTTTGTAATTGGGCCCGGGTTTA
1 CTTTGTAAATGGGCCCGGGTTTA
*
13093 ATTTGTA
1 CTTTGTA
13100 GTTGGACTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 12 0.46
23 14 0.54
ACGTcount: A:0.17, C:0.12, G:0.29, T:0.42
Consensus pattern (23 bp):
CTTTGTAAATGGGCCCGGGTTTA
Found at i:13147 original size:3 final size:3
Alignment explanation
Indices: 13141--13180 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
13131 AATTATTATT
* *
13141 TAA TAA TAA TAA TAA TAA TAT TAA TGA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
13181 TGGGATGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:13164 original size:21 final size:20
Alignment explanation
Indices: 13121--13181 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 20
13111 CTTGTAAATA
* *
13121 AATAATAGATAATTATTATTT
1 AATAATA-ATAATAATAATTT
13142 AATAATAATAATAATAATATT
1 AATAATAATAATAATAAT-TT
*
13163 AATGATAATAATAATAATT
1 AATAATAATAATAATAATT
13182 GGGATGAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 26 0.72
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (20 bp):
AATAATAATAATAATAATTT
Found at i:14258 original size:20 final size:19
Alignment explanation
Indices: 14209--14262 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
14199 ATTCTTCATA
14209 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
14228 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
14249 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
14263 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:24772 original size:30 final size:30
Alignment explanation
Indices: 24733--24800 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
24723 TGATCATGAA
* * *
24733 TCTTATATACTTACTTTTTGAGTTCTATTT
1 TCTTTTATACTCACTTTTTGAGTTCTAGTT
24763 TCTTTTATACTCACTTTTTGAGTTCTAGTT
1 TCTTTTATACTCACTTTTTGAGTTCTAGTT
24793 TCTTTTAT
1 TCTTTTAT
24801 GAATCTTAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.18, C:0.15, G:0.07, T:0.60
Consensus pattern (30 bp):
TCTTTTATACTCACTTTTTGAGTTCTAGTT
Found at i:34797 original size:60 final size:60
Alignment explanation
Indices: 34684--34811 Score: 170
Period size: 60 Copynumber: 2.1 Consensus size: 60
34674 AGTATATGCA
* * *
34684 CATAGTTTGTGATGAAATTGGAATATTTAAAAAGTTTGGAGACCAATTTAGAATCAAT-GT
1 CATAGTTTGGGATGAAATTGAAATATTTAAAAAGTTTGAAGACCAATTTAGAAT-AATAGT
** *
34744 CATAGTTTGGGGATGAAATTGAAATATTTAAAAA-TTTGAAGATTAATTTAGAATGATAGT
1 CATAGTTT-GGGATGAAATTGAAATATTTAAAAAGTTTGAAGACCAATTTAGAATAATAGT
34804 CATAGTTT
1 CATAGTTT
34812 AAAGATGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
59 2 0.03
60 35 0.58
61 23 0.38
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.37
Consensus pattern (60 bp):
CATAGTTTGGGATGAAATTGAAATATTTAAAAAGTTTGAAGACCAATTTAGAATAATAGT
Found at i:34819 original size:60 final size:60
Alignment explanation
Indices: 34694--34839 Score: 163
Period size: 60 Copynumber: 2.4 Consensus size: 60
34684 CATAGTTTGT
* * ***
34694 GATGAAATTGGAATATTTAAAAAGTTTGGAGACCAATTTAGAATCAATGTCATAGTTTGGG
1 GATGAAATTGAAATATTTAAAAA-TTTGAAGACCAATTTAGAATCAATGTCATAGTTTAAA
** *
34755 GATGAAATTGAAATATTTAAAAATTTGAAGATTAATTTAGAAT-GATAGTCATAGTTTAAA
1 GATGAAATTGAAATATTTAAAAATTTGAAGACCAATTTAGAATCAAT-GTCATAGTTTAAA
*
34815 GATGAAATT-AGAATA-TAAAAAATTT
1 GATGAAATTGA-AATATTTAAAAATTT
34840 AGGGTATAAT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
59 12 0.16
60 40 0.54
61 22 0.30
ACGTcount: A:0.45, C:0.03, G:0.18, T:0.34
Consensus pattern (60 bp):
GATGAAATTGAAATATTTAAAAATTTGAAGACCAATTTAGAATCAATGTCATAGTTTAAA
Found at i:35125 original size:23 final size:23
Alignment explanation
Indices: 35099--35189 Score: 94
Period size: 23 Copynumber: 3.9 Consensus size: 23
35089 ACAAACGGAT
*
35099 ATAAACGAACATAAATGAACACA
1 ATAAACGAACATAAATGAACAAA
* *
35122 ATAAACGAACACAAAAGAA-AGAA
1 ATAAACGAACATAAATGAACA-AA
* *
35145 CGTAAACGAACATAAACGAACAAA
1 -ATAAACGAACATAAATGAACAAA
* *
35169 ACAAATGAACATAAATGAACA
1 ATAAACGAACATAAATGAACA
35190 TAAACCACAA
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
22 1 0.02
23 35 0.64
24 18 0.33
25 1 0.02
ACGTcount: A:0.63, C:0.16, G:0.11, T:0.10
Consensus pattern (23 bp):
ATAAACGAACATAAATGAACAAA
Found at i:35205 original size:33 final size:33
Alignment explanation
Indices: 35122--35194 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
35112 AATGAACACA
* *
35122 ATAAACGAACACAAA-AGAAAGAACGTAAACGAAC
1 ATAAACGAACA-AAACA-AATGAACATAAACGAAC
*
35156 ATAAACGAACAAAACAAATGAACATAAATGAAC
1 ATAAACGAACAAAACAAATGAACATAAACGAAC
35189 ATAAAC
1 ATAAAC
35195 CACAACAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
33 23 0.66
34 12 0.34
ACGTcount: A:0.63, C:0.16, G:0.11, T:0.10
Consensus pattern (33 bp):
ATAAACGAACAAAACAAATGAACATAAACGAAC
Found at i:35397 original size:14 final size:15
Alignment explanation
Indices: 35372--35408 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
35362 CTAGAGAGAT
35372 TGAACTAAACATAAA
1 TGAACTAAACATAAA
35387 TGAAC-AAACATAAA
1 TGAACTAAACATAAA
35401 TGAA-TAAA
1 TGAACTAAA
35409 AGTAAACGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.62, C:0.11, G:0.08, T:0.19
Consensus pattern (15 bp):
TGAACTAAACATAAA
Found at i:35438 original size:24 final size:24
Alignment explanation
Indices: 35406--35470 Score: 89
Period size: 24 Copynumber: 2.7 Consensus size: 24
35396 ATAAATGAAT
35406 AAAAGTAAACGAACGA-AAACAAAC
1 AAAAGTAAACGAAC-ATAAACAAAC
*
35430 AAAAGTAAACGAACATAAACGAAC
1 AAAAGTAAACGAACATAAACAAAC
35454 AAACA-TAAACGAACATA
1 AAA-AGTAAACGAACATA
35471 TTATCGAACG
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
23 1 0.03
24 36 0.95
25 1 0.03
ACGTcount: A:0.65, C:0.17, G:0.11, T:0.08
Consensus pattern (24 bp):
AAAAGTAAACGAACATAAACAAAC
Found at i:35458 original size:14 final size:14
Alignment explanation
Indices: 35441--35468 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
35431 AAAGTAAACG
35441 AACATAAACGAACA
1 AACATAAACGAACA
35455 AACATAAACGAACA
1 AACATAAACGAACA
35469 TATTATCGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.21, G:0.07, T:0.07
Consensus pattern (14 bp):
AACATAAACGAACA
Found at i:35995 original size:28 final size:28
Alignment explanation
Indices: 35936--36003 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
35926 GATAATCTTT
* * *
35936 AAATATTAAAAAATAGATAAATTTTCAT
1 AAATATTAAAAAATACATAAATTTACAG
*
35964 AAATTATTAAAAAA-ACATAAATTTAGAG
1 AAA-TATTAAAAAATACATAAATTTACAG
35992 AAATATATAAAA
1 AAATAT-TAAAA
36004 TTCCCATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
27 3 0.09
28 21 0.62
29 10 0.29
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (28 bp):
AAATATTAAAAAATACATAAATTTACAG
Found at i:36963 original size:21 final size:21
Alignment explanation
Indices: 36926--36966 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
36916 ACCCTAAACA
36926 TAAATTTTCAAAATTAATCCT
1 TAAATTTTCAAAATTAATCCT
*
36947 TAAACTTTTC-AACTTAATCC
1 TAAA-TTTTCAAAATTAATCC
36967 AATTTAACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAATTTTCAAAATTAATCCT
Found at i:37836 original size:47 final size:47
Alignment explanation
Indices: 37767--37868 Score: 168
Period size: 47 Copynumber: 2.2 Consensus size: 47
37757 GTGAGCAAAT
37767 CAAATAATCTAACAGGCTGTTTCACTACATAATTCTGATTATATCGG
1 CAAATAATCTAACAGGCTGTTTCACTACATAATTCTGATTATATCGG
** * *
37814 CAAATAATCTTGCAGGTTGTTTCACTATATAATTCTGATTATATCGG
1 CAAATAATCTAACAGGCTGTTTCACTACATAATTCTGATTATATCGG
37861 CAAATAAT
1 CAAATAAT
37869 TTTTTATCAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (47 bp):
CAAATAATCTAACAGGCTGTTTCACTACATAATTCTGATTATATCGG
Found at i:39709 original size:90 final size:90
Alignment explanation
Indices: 39602--39775 Score: 339
Period size: 90 Copynumber: 1.9 Consensus size: 90
39592 TCAGTGACTA
39602 AAATAGAAACAAAATAAAATTTGAAAAAAAAATACTTGGAACATTCATTTCAGTGACCAAAATGA
1 AAATAGAAACAAAATAAAATTTGAAAAAAAAATACTTGGAACATTCATTTCAGTGACCAAAATGA
*
39667 AAGTTTACAATTTCCGAGGAATACG
66 AAGTTTACAATTTACGAGGAATACG
39692 AAATAGAAACAAAATAAAATTTGAAAAAAAAATACTTGGAACATTCATTTCAGTGACCAAAATGA
1 AAATAGAAACAAAATAAAATTTGAAAAAAAAATACTTGGAACATTCATTTCAGTGACCAAAATGA
39757 AAGTTTACAATTTACGAGG
66 AAGTTTACAATTTACGAGG
39776 GATGCGGGAA
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 83 1.00
ACGTcount: A:0.51, C:0.11, G:0.13, T:0.25
Consensus pattern (90 bp):
AAATAGAAACAAAATAAAATTTGAAAAAAAAATACTTGGAACATTCATTTCAGTGACCAAAATGA
AAGTTTACAATTTACGAGGAATACG
Found at i:41004 original size:15 final size:15
Alignment explanation
Indices: 40972--41021 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
40962 ATTGTTTAGT
40972 GTTTAGGGATT-A-AA
1 GTTTA-GGATTCATAA
40986 GTTTAGGATTCATAA
1 GTTTAGGATTCATAA
41001 GTTTAGGATTCATAA
1 GTTTAGGATTCATAA
*
41016 TTTTAG
1 GTTTAG
41022 AATTAGGGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
13 5 0.15
14 6 0.18
15 22 0.67
ACGTcount: A:0.32, C:0.04, G:0.22, T:0.42
Consensus pattern (15 bp):
GTTTAGGATTCATAA
Found at i:41243 original size:19 final size:20
Alignment explanation
Indices: 41219--41269 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
41209 AAAGATGTTT
*
41219 TATGAATAGTACT-ATATTG
1 TATGAATAGTACTGATACTG
41238 TATGAATAGTACTGATACTG
1 TATGAATAGTACTGATACTG
* *
41258 TTTAAATAGTAC
1 TATGAATAGTAC
41270 CGTGAATAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (20 bp):
TATGAATAGTACTGATACTG
Found at i:42002 original size:22 final size:22
Alignment explanation
Indices: 41976--42058 Score: 130
Period size: 22 Copynumber: 3.8 Consensus size: 22
41966 GGCATGTGAA
*
41976 ATTTGTCCCGAATGACCTATGT
1 ATTTGTCCCGAAGGACCTATGT
*
41998 ATTTGTCCCGAATGACCTATGT
1 ATTTGTCCCGAAGGACCTATGT
*
42020 ATTTGTCCCGAAGGACCTTTGT
1 ATTTGTCCCGAAGGACCTATGT
*
42042 ATATGTCCCGAAGGACC
1 ATTTGTCCCGAAGGACC
42059 GCATAGACCC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (22 bp):
ATTTGTCCCGAAGGACCTATGT
Found at i:43827 original size:21 final size:21
Alignment explanation
Indices: 43801--43841 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
43791 GAATGTTATA
43801 GTTTAT-GATTTAGGGTTTAAT
1 GTTTATAG-TTTAGGGTTTAAT
43822 GTTTATAGTTTAGGGTTTAA
1 GTTTATAGTTTAGGGTTTAA
43842 GGTTAGGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (21 bp):
GTTTATAGTTTAGGGTTTAAT
Found at i:45532 original size:19 final size:19
Alignment explanation
Indices: 45504--45564 Score: 95
Period size: 19 Copynumber: 3.2 Consensus size: 19
45494 ACGATTTTGA
* *
45504 AAAATATGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTG
45523 AAAATGTGTTGCGATAGTG
1 AAAATGTGTTGCGATAGTG
*
45542 AAAAAGTGTTGCGATAGTG
1 AAAATGTGTTGCGATAGTG
45561 AAAA
1 AAAA
45565 ATCCAAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.30
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTG
Found at i:46020 original size:21 final size:20
Alignment explanation
Indices: 45994--46220 Score: 122
Period size: 21 Copynumber: 11.1 Consensus size: 20
45984 ATTTTGGAAA
*
45994 ATCGCAACGTGAACTTAGACT
1 ATCGCAACG-GAACTTGGACT
* **
46015 ATCGCAAC-GAATTTGGAAA
1 ATCGCAACGGAACTTGGACT
*
46034 ATCGCAACGCGAACTTCGACT
1 ATCGCAACG-GAACTTGGACT
* **
46055 ATCGCAAC-GAATTTGGAAA
1 ATCGCAACGGAACTTGGACT
* *
46074 ATCGGAACATGAACTTGGACT
1 ATCGCAAC-GGAACTTGGACT
* *
46095 ATCGCAAC-GAATTTGGAAAATCGC
1 ATCGCAACGGAACTTGG---A-C-T
*
46119 AACGCAACGTGAACTTGGACT
1 ATCGCAACG-GAACTTGGACT
* * **
46140 ATCACAAC-GAATTTGGAAA
1 ATCGCAACGGAACTTGGACT
* *
46159 ATTGCAACGCGAACTTCGACT
1 ATCGCAACG-GAACTTGGACT
*
46180 ATCGCAACGTGAACTTGGATT
1 ATCGCAACG-GAACTTGGACT
* *
46201 ATTGCAAC-GAATTTGGACT
1 ATCGCAACGGAACTTGGACT
46220 A
1 A
46221 ACGTAAATTT
Statistics
Matches: 153, Mismatches: 40, Indels: 28
0.69 0.18 0.13
Matches are distributed among these distances:
19 60 0.39
21 75 0.49
22 2 0.01
23 2 0.01
24 7 0.05
26 7 0.05
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (20 bp):
ATCGCAACGGAACTTGGACT
Found at i:46039 original size:19 final size:19
Alignment explanation
Indices: 45986--46122 Score: 112
Period size: 19 Copynumber: 6.9 Consensus size: 19
45976 TCATTGCGAT
45986 TTTGGAAAATCGCAACGTGAA
1 TTTGGAAAATCGCAAC--GAA
* * **
46007 CTTAGACTATCGCAACGAA
1 TTTGGAAAATCGCAACGAA
46026 TTTGGAAAATCGCAACGCGAA
1 TTTGGAAAATCGCAA--CGAA
* * **
46047 CTTCGACTATCGCAACGAA
1 TTTGGAAAATCGCAACGAA
*
46066 TTTGGAAAATCGGAACATGAA
1 TTTGGAAAATCGCAAC--GAA
* **
46087 CTTGGACTATCGCAACGAA
1 TTTGGAAAATCGCAACGAA
46106 TTTGGAAAATCGCAACG
1 TTTGGAAAATCGCAACG
46123 CAACGTGAAC
Statistics
Matches: 88, Mismatches: 24, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
19 46 0.52
21 42 0.48
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.22
Consensus pattern (19 bp):
TTTGGAAAATCGCAACGAA
Found at i:46041 original size:40 final size:40
Alignment explanation
Indices: 45986--46188 Score: 280
Period size: 40 Copynumber: 5.0 Consensus size: 40
45976 TCATTGCGAT
*
45986 TTTGGAAAATCGCAACGTGAACTTAGACTATCGCAACGAA
1 TTTGGAAAATCGCAACGTGAACTTCGACTATCGCAACGAA
*
46026 TTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAA
1 TTTGGAAAATCGCAACGTGAACTTCGACTATCGCAACGAA
* * *
46066 TTTGGAAAATCGGAACATGAACTTGGACTATCGCAACGAA
1 TTTGGAAAATCGCAACGTGAACTTCGACTATCGCAACGAA
* *
46106 TTTGGAAAATCGCAACGCAACGTGAACTTGGACTATCACAACGAA
1 TTTGGAAAAT-----CGCAACGTGAACTTCGACTATCGCAACGAA
* *
46151 TTTGGAAAATTGCAACGCGAACTTCGACTATCGCAACG
1 TTTGGAAAATCGCAACGTGAACTTCGACTATCGCAACG
46189 TGAACTTGGA
Statistics
Matches: 145, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
40 108 0.74
45 37 0.26
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (40 bp):
TTTGGAAAATCGCAACGTGAACTTCGACTATCGCAACGAA
Found at i:46217 original size:125 final size:121
Alignment explanation
Indices: 45996--46245 Score: 331
Period size: 125 Copynumber: 2.0 Consensus size: 121
45986 TTTGGAAAAT
*
45996 CGCAACGTGAACTTAGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCA
1 CGCAACGTGAACTTAGACTATCACAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCA
* * * *
46061 ACGAATTTGGAAAATCGGAACATGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAA
66 ACGAACTTGGAAAATCGCAACA-GAACTTGGACTAACG-AA--AATTTGGAAAATCACAA
* *
46121 CGCAACGTGAACTTGGACTATCACAACGAATTTGGAAAATTGCAACGCGAACTTCGACTATCGCA
1 CGCAACGTGAACTTAGACTATCACAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCA
** * * *
46186 ACGTGAACTTGGATTATTGCAAC-GAATTTGGACTAACGTAAATTTGGAAAATCACAA
66 AC--GAACTTGGAAAATCGCAACAGAACTTGGACTAACGAAAATTTGGAAAATCACAA
46243 CGC
1 CGC
46246 GAACTTGGAC
Statistics
Matches: 111, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
122 19 0.17
124 1 0.01
125 77 0.69
127 14 0.13
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (121 bp):
CGCAACGTGAACTTAGACTATCACAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCA
ACGAACTTGGAAAATCGCAACAGAACTTGGACTAACGAAAATTTGGAAAATCACAA
Found at i:46220 original size:40 final size:39
Alignment explanation
Indices: 45987--46220 Score: 164
Period size: 40 Copynumber: 5.7 Consensus size: 39
45977 CATTGCGATT
* * * * *
45987 TTGGAAAATCGCAACGTGAACTTAGACTATCGCAACGAAT
1 TTGGAAAATTGCAAC-CGAACTTGGACTATCACAACGAAC
* * * *
46027 TTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAAT
1 TTGGAAAATTGCAAC-CGAACTTGGACTATCACAACGAAC
* * * * *
46067 TTGGAAAATCGGAACATGAACTTGGACTATCGCAACGAAT
1 TTGGAAAATTGCAAC-CGAACTTGGACTATCACAACGAAC
* *
46107 TTGGAAAATCGCAACGCAACGTGAACTTGGACTATCACAACGAAT
1 TTGGAAAATTGCAA--C--C--GAACTTGGACTATCACAACGAAC
* *
46152 TTGGAAAATTGCAACGCGAACTTCGACTATCGCAACGTGAAC
1 TTGGAAAATTGCAAC-CGAACTTGGACTATCACAAC--GAAC
** *
46194 TTGGATTATTGCAA-CGAATTTGGACTA
1 TTGGAAAATTGCAACCGAACTTGGACTA
46221 ACGTAAATTT
Statistics
Matches: 169, Mismatches: 18, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
40 115 0.68
42 17 0.10
43 2 0.01
45 35 0.21
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (39 bp):
TTGGAAAATTGCAACCGAACTTGGACTATCACAACGAAC
Found at i:47454 original size:22 final size:21
Alignment explanation
Indices: 47429--47469 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
47419 ATATAAAAAT
47429 TATTTTTATTAAATATTTTTGG
1 TATTTTTATTAAAT-TTTTTGG
*
47451 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
47470 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGG
Found at i:61493 original size:26 final size:26
Alignment explanation
Indices: 61440--61531 Score: 168
Period size: 26 Copynumber: 3.6 Consensus size: 26
61430 TATCAAGTTC
*
61440 AACTCGAACTCGAAATA-AATATTGA
1 AACTTGAACTCGAAATATAATATTGA
61465 AACTTGAACTCGAAATATAATATTGA
1 AACTTGAACTCGAAATATAATATTGA
61491 AACTTGAACTCGAAATATAATATTGA
1 AACTTGAACTCGAAATATAATATTGA
61517 AACTTGAACTCGAAA
1 AACTTGAACTCGAAA
61532 AGGCTTGAAC
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
25 16 0.25
26 49 0.75
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (26 bp):
AACTTGAACTCGAAATATAATATTGA
Done.