Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001424.1 Hibiscus syriacus cultivar Beakdansim tig00002763_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: 72261
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:5441 original size:28 final size:28
Alignment explanation
Indices: 5388--5441 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
5378 GTTTATCAAT
* *
5388 AACTTTAGTTATTAAATATAACGTTTGA
1 AACTTTAGTAATTAAATATAAAGTTTGA
5416 AACTTTAGTAATTAAA-ATAAAAGTTT
1 AACTTTAGTAATTAAATAT-AAAGTTT
5442 ACAAAACTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 2 0.09
28 21 0.91
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (28 bp):
AACTTTAGTAATTAAATATAAAGTTTGA
Found at i:17386 original size:25 final size:24
Alignment explanation
Indices: 17349--17401 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
17339 TATTATGGTA
17349 TAAAAAAATTAAAACTTC-AAGTAT
1 TAAAAAAATTAAAA-TTCTAAGTAT
*
17373 TAAAATAAATTAAAATTCTAAGTTT
1 TAAAA-AAATTAAAATTCTAAGTAT
17398 TAAA
1 TAAA
17402 GATCAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.34
Consensus pattern (24 bp):
TAAAAAAATTAAAATTCTAAGTAT
Found at i:21791 original size:103 final size:103
Alignment explanation
Indices: 21611--21800 Score: 285
Period size: 103 Copynumber: 1.8 Consensus size: 103
21601 TAATAACCGA
* ** * *
21611 TAGAAGCTAAGTTGTACTGGTACACAACCAGTATCGATATTGGCATATAACACTGGATTACTGGT
1 TAGAAGCTAAGATGTACTGGTACACAAAAAGTATCGATACTGGCATATAACACTGGATTACGGGT
21676 TACTTCCAATGTATCGATACCTTTAATGTATAGATACC
66 TACTTCCAATGTATCGATACCTTTAATGTATAGATACC
*
21714 TAGAAGCTAAGATGTA-TCGGTACACAAAAAGTATCGATACTGGCATATAACACTGTATTACGGG
1 TAGAAGCTAAGATGTACT-GGTACACAAAAAGTATCGATACTGGCATATAACACTGGATTACGGG
*
21778 TTACATT-CGATGTATCGATACCT
65 TTAC-TTCCAATGTATCGATACCT
21801 AGAAGCTAAA
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
102 1 0.01
103 75 0.96
104 2 0.03
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (103 bp):
TAGAAGCTAAGATGTACTGGTACACAAAAAGTATCGATACTGGCATATAACACTGGATTACGGGT
TACTTCCAATGTATCGATACCTTTAATGTATAGATACC
Found at i:21802 original size:86 final size:86
Alignment explanation
Indices: 21700--21886 Score: 259
Period size: 86 Copynumber: 2.2 Consensus size: 86
21690 CGATACCTTT
* * *
21700 AATGTATAGATACCTAGAAGCTAAGA-TGTATCGGTACACAAAAAGTATCGATACTGGCATATAA
1 AATGTATCGATACCTAGAAGCTAA-ACTGTACCGGTACACAAAAAGTATCGATACTGACATATAA
* * *
21764 CACTGTATTACGGGTTACATTC
65 CACTATATTACGAGTTACATCC
* * *
21786 GATGTATCGATACCTAGAAGCTAAACTGTACCGGTACACTAGAAGTATCGATACTGACATATAAC
1 AATGTATCGATACCTAGAAGCTAAACTGTACCGGTACACAAAAAGTATCGATACTGACATATAAC
*
21851 ACTATATTATGAGTTACATCC
66 ACTATATTACGAGTTACATCC
*
21872 AATATATCGATACCT
1 AATGTATCGATACCT
21887 TTAATGAATT
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
85 1 0.01
86 87 0.99
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (86 bp):
AATGTATCGATACCTAGAAGCTAAACTGTACCGGTACACAAAAAGTATCGATACTGACATATAAC
ACTATATTACGAGTTACATCC
Found at i:22485 original size:18 final size:18
Alignment explanation
Indices: 22462--22496 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
22452 GCCTATGGTG
*
22462 CATCGTCTTCATCATCAA
1 CATCGTCCTCATCATCAA
*
22480 CATCGTCCTCGTCATCA
1 CATCGTCCTCATCATCA
22497 TATTGAATGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.37, G:0.09, T:0.31
Consensus pattern (18 bp):
CATCGTCCTCATCATCAA
Found at i:23066 original size:37 final size:37
Alignment explanation
Indices: 23010--23113 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
23000 CTTTTCGTCC
* * *
23010 TACTAGGATTCAAACTCCTAAAAATAGGATATAATTT
1 TACTATGATTCAAACTCCTAAAAATAGGATAGAATTA
*
23047 TGA-TATGATTCAAACTCCTAAAAATAGGATAGAGTTA
1 T-ACTATGATTCAAACTCCTAAAAATAGGATAGAATTA
* * *
23084 TACTATTATTTAAACTCCTAAAGATAGGAT
1 TACTATGATTCAAACTCCTAAAAATAGGAT
23114 CCACAAGCAT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
36 1 0.02
37 56 0.97
38 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (37 bp):
TACTATGATTCAAACTCCTAAAAATAGGATAGAATTA
Found at i:23742 original size:29 final size:29
Alignment explanation
Indices: 23710--23794 Score: 68
Period size: 29 Copynumber: 2.9 Consensus size: 29
23700 TGATTACTAT
*
23710 TTTTTTAGTTAATATTATATGTATATTTA-
1 TTTTTTA-TTAATATTATATATATATTTAG
* *
23739 TTTTTCATTTAT-TTATTATTATATATTTAG
1 TTTTTTATTAATATTA-TA-TATATATTTAG
* * *
23769 TATTTTATT-ATATTATACATACATTT
1 TTTTTTATTAATATTATATATATATTT
23795 TTATATTTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
27 3 0.07
28 13 0.29
29 19 0.42
30 10 0.22
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.62
Consensus pattern (29 bp):
TTTTTTATTAATATTATATATATATTTAG
Found at i:23798 original size:19 final size:19
Alignment explanation
Indices: 23776--23822 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
23766 TAGTATTTTA
23776 TTATATTATACATACATTT
1 TTATATTATACATACATTT
* * *
23795 TTATATTTTATATATATTT
1 TTATATTATACATACATTT
*
23814 TTTTATTAT
1 TTATATTAT
23823 TTTATTTATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATATTATACATACATTT
Found at i:23805 original size:21 final size:22
Alignment explanation
Indices: 23771--23827 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
23761 ATATTTAGTA
*
23771 TTTTATTATATTATACATACAT
1 TTTTATTATTTTATACATACAT
* **
23793 TTTTA-TATTTTATATATATTT
1 TTTTATTATTTTATACATACAT
23814 TTTTATTATTTTAT
1 TTTTATTATTTTAT
23828 TTATACTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTATTATTTTATACATACAT
Found at i:23839 original size:21 final size:21
Alignment explanation
Indices: 23748--23841 Score: 73
Period size: 22 Copynumber: 4.4 Consensus size: 21
23738 ATTTTTCATT
* * *
23748 TATTTATTATTATATATTTAG
1 TATTTATTATTTTATATATAC
* *
23769 TATTTTATTATATTATACATAC
1 TA-TTTATTATTTTATATATAC
* *
23791 -ATTTTTATATTTTATATATATT
1 TATTTAT-TATTTTATATATA-C
* *
23813 TTTTTATTATTTTATTTATAC
1 TATTTATTATTTTATATATAC
23834 TATTTATT
1 TATTTATT
23842 TTCATTATTT
Statistics
Matches: 55, Mismatches: 14, Indels: 8
0.71 0.18 0.10
Matches are distributed among these distances:
20 4 0.07
21 21 0.38
22 26 0.47
23 4 0.07
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (21 bp):
TATTTATTATTTTATATATAC
Found at i:23848 original size:27 final size:24
Alignment explanation
Indices: 23792--23857 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 24
23782 TATACATACA
23792 TTTTTA-TATTTTA--TATATATT
1 TTTTTATTATTTTATTTATATATT
23813 TTTTTATTATTTTATTTATACTATT
1 TTTTTATTATTTTATTTATA-TATT
*
23838 TATTTTCATTATTTTTTTTA
1 T-TTTT-ATTATTTTATTTA
23858 GTTTCTTTGC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
21 6 0.16
22 7 0.18
24 4 0.11
25 5 0.13
26 4 0.11
27 12 0.32
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTTTATTATTTTATTTATATATT
Found at i:23850 original size:13 final size:11
Alignment explanation
Indices: 23792--23855 Score: 51
Period size: 12 Copynumber: 5.5 Consensus size: 11
23782 TATACATACA
23792 TTTTTA-TA-T
1 TTTTTATTATT
*
23801 TTTATATATATT
1 TTTTTAT-TATT
23813 TTTTTATTATT
1 TTTTTATTATT
23824 TTATTTATACTATT
1 TT-TTTAT--TATT
23838 TATTTTCATTATT
1 T-TTTT-ATTATT
23851 TTTTT
1 TTTTT
23856 TAGTTTCTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
9 5 0.11
11 8 0.18
12 16 0.36
13 5 0.11
14 8 0.18
15 3 0.07
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTTTATTATT
Found at i:23856 original size:13 final size:12
Alignment explanation
Indices: 23800--23857 Score: 53
Period size: 14 Copynumber: 4.4 Consensus size: 12
23790 CATTTTTATA
23800 TTTTATATATATTT
1 TTTTAT-TAT-TTT
23814 TTTTATTATTTT
1 TTTTATTATTTT
*
23826 ATTTATACTATTTAT
1 -TTT-TATTATTT-T
*
23841 TTTCATTATTTT
1 TTTTATTATTTT
23853 TTTTA
1 TTTTA
23858 GTTTCTTTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
12 8 0.22
13 12 0.32
14 16 0.43
15 1 0.03
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTTATTATTTT
Found at i:28309 original size:16 final size:16
Alignment explanation
Indices: 28290--28354 Score: 73
Period size: 15 Copynumber: 4.2 Consensus size: 16
28280 CAAAAAGGGC
28290 AAAAACAAAAAAGAAA
1 AAAAACAAAAAAGAAA
*
28306 AAAAGCAAAAAAG-AA
1 AAAAACAAAAAAGAAA
*
28321 GAAAACAAAAAA-AAGA
1 AAAAACAAAAAAGAA-A
*
28337 AAGAAC-AAAAAGAAA
1 AAAAACAAAAAAGAAA
28352 AAA
1 AAA
28355 GAAAAAGGGA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
15 21 0.52
16 19 0.47
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (16 bp):
AAAAACAAAAAAGAAA
Found at i:28330 original size:21 final size:19
Alignment explanation
Indices: 28303--28357 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
28293 AACAAAAAAG
28303 AAAAAAAGCAAAAAAGAAG-
1 AAAAAAAG-AAAAAAGAAGA
*
28322 AAAACAA-AAAAAAGAAAGA
1 AAAAAAAGAAAAAAG-AAGA
*
28341 ACAAAAAGAAAAAAGAA
1 AAAAAAAGAAAAAAGAA
28358 AAAGGGACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 7 0.23
18 3 0.10
19 13 0.43
20 7 0.23
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (19 bp):
AAAAAAAGAAAAAAGAAGA
Found at i:28346 original size:13 final size:13
Alignment explanation
Indices: 28290--28361 Score: 54
Period size: 13 Copynumber: 4.9 Consensus size: 13
28280 CAAAAAGGGC
28290 AAAAACAAAAAAGAA
1 AAAAAC-AAAAAG-A
28305 AAAAAGCAAAAAAGA
1 AAAAA-C-AAAAAGA
28320 AGAAAACAAAAAAAAGA
1 A-AAAAC---AAAAAGA
*
28337 AAGAACAAAAAGA
1 AAAAACAAAAAGA
*
28350 AAAAAGAAAAAG
1 AAAAACAAAAAG
28362 GGACAAAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
13 17 0.34
15 8 0.16
16 16 0.32
17 9 0.18
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAACAAAAAGA
Found at i:28357 original size:16 final size:14
Alignment explanation
Indices: 28290--28354 Score: 67
Period size: 16 Copynumber: 4.2 Consensus size: 14
28280 CAAAAAGGGC
28290 AAAAACAAAAAAGAA
1 AAAAACAAAAAA-AA
28305 AAAAAGCAAAAAAGAA
1 AAAAA-CAAAAAA-AA
*
28321 GAAAACAAAAAAAA
1 AAAAACAAAAAAAA
28335 GAAAGAACAAAAAGAAA
1 -AAA-AACAAAAA-AAA
28352 AAA
1 AAA
28355 GAAAAAGGGA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 2 0.05
15 14 0.32
16 25 0.57
17 3 0.07
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAACAAAAAAAA
Found at i:28360 original size:8 final size:8
Alignment explanation
Indices: 28296--28360 Score: 60
Period size: 9 Copynumber: 7.5 Consensus size: 8
28286 GGGCAAAAAC
28296 AAAAAAGA
1 AAAAAAGA
28304 AAAAAAGCAA
1 AAAAAAG--A
28314 AAAAGAAGA
1 AAAA-AAGA
*
28323 AAACAAAAA
1 AAA-AAAGA
28332 AAAGAAAGA
1 AAA-AAAGA
28341 ACAAAAAG-
1 A-AAAAAGA
28349 AAAAAAGA
1 AAAAAAGA
28357 AAAA
1 AAAA
28361 GGGACAAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
7 6 0.12
8 12 0.25
9 19 0.40
10 8 0.17
11 3 0.06
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:30088 original size:106 final size:106
Alignment explanation
Indices: 29958--31445 Score: 2377
Period size: 106 Copynumber: 14.0 Consensus size: 106
29948 ATATCGTGCC
* * * * *
29958 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-AGACTGGTTGTCAACAAATAACTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCC
* *
30022 CAATTTCAGAGCCAATTTCAACTTCACAGCAAAGAATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
30064 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
30129 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
30170 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTTTCAATAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
30235 AATTTCAGAGCTAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
30276 ACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
30341 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
30382 AATCCAGACAACGCAAGTTCAACTTCACGACGAAAGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
30447 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
30488 ACTCAAGATAACGCAAGTTCAACTTCAAGACAAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
30553 AATTTCAAAGCCAATTTCAACTTCACAGTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
30594 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTAGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
30659 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
30700 ACTCCAGACATCGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
30765 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATAATGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
30806 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
30871 AATTTCGGAGCCAATTTTAACTTCACAACGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
30912 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
30977 AATTTCGGAGCCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
31018 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
31083 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
31124 ACTCCAGACAACGCAAGTTCAACTTCAAGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
31189 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
31230 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
31295 AATTTCGGAGCCAATTTTAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
31336 ACTCGAGACAACACAAGTTCAACTTCACAACAAAGGGACGGTTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
31401 GATTCCAGAGCCAATTTTAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
31442 ACTC
1 ACTC
31446 GGAACAATGC
Statistics
Matches: 1289, Mismatches: 91, Indels: 4
0.93 0.07 0.00
Matches are distributed among these distances:
106 1288 1.00
107 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:32283 original size:37 final size:37
Alignment explanation
Indices: 32193--32296 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 37
32183 CCTTTTCGTC
*
32193 CTACTAGGATTCAAACTCCTAAAAATAGGATATAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
32230 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
32267 CTACTATTATTTAAACTCCTAAAGATAGGA
1 CTACTAGGATTCAAACTCCTAAAAATAGGA
32297 ACCACAAGCA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:32950 original size:11 final size:11
Alignment explanation
Indices: 32936--33043 Score: 64
Period size: 11 Copynumber: 9.8 Consensus size: 11
32926 ATTATATGTA
*
32936 TATTTATTTTT
1 TATTTATTTAT
32947 TATTTATTTAT
1 TATTTATTTAT
32958 TA-TTA-TTAT
1 TATTTATTTAT
* *
32967 TA-CTATTTAG
1 TATTTATTTAT
32977 TATTTTATTATAT
1 TA-TTTATT-TAT
** **
32990 TATACATAAAT
1 TATTTATTTAT
*
33001 T-TTTATATAT
1 TATTTATTTAT
33011 ATATTT-TTTAT
1 -TATTTATTTAT
33022 TATTTATTTAT
1 TATTTATTTAT
33033 ACTATTTATTT
1 --TATTTATTT
33044 TCATTATATT
Statistics
Matches: 75, Mismatches: 13, Indels: 16
0.72 0.12 0.15
Matches are distributed among these distances:
9 8 0.11
10 19 0.25
11 25 0.33
12 10 0.13
13 13 0.17
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.66
Consensus pattern (11 bp):
TATTTATTTAT
Found at i:32974 original size:30 final size:31
Alignment explanation
Indices: 32906--32992 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 31
32896 TATTTCTATG
*
32906 ATTACTATTTTTTAGTTAATATTA-TATGTAT
1 ATTACTATTTTTTAGTTTAT-TTATTATGTAT
32937 ATT--TATTTTTTA-TTTATTTATTAT-TATT
1 ATTACTATTTTTTAGTTTATTTATTATGTA-T
** *
32965 ATTACTATTTAGTATTTTATTATATTAT
1 ATTACTATTTTTTAGTTTATT-TATTAT
32993 ACATAAATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
27 5 0.11
28 11 0.23
29 9 0.19
30 7 0.15
31 9 0.19
32 6 0.13
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.64
Consensus pattern (31 bp):
ATTACTATTTTTTAGTTTATTTATTATGTAT
Found at i:33057 original size:26 final size:26
Alignment explanation
Indices: 32999--33057 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
32989 TTATACATAA
*
32999 ATTTTTATATATATATTTTTTATTAT
1 ATTTTTATATATATATTTTTCATTAT
*
33025 -TTATTTATACTATTTA-TTTTCATTAT
1 ATT-TTTATA-TATATATTTTTCATTAT
33051 ATTTTTA
1 ATTTTTA
33058 GTTTCTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
25 2 0.07
26 19 0.68
27 7 0.25
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (26 bp):
ATTTTTATATATATATTTTTCATTAT
Found at i:39219 original size:23 final size:23
Alignment explanation
Indices: 39161--39219 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
39151 TAGCACTTTG
*
39161 GTGCATTTCTACGCGGCAGTACA
1 GTGCATTTCTACGCGGCACTACA
* * *
39184 GTGCAATTCTACGTGGCACTTCA
1 GTGCATTTCTACGCGGCACTACA
*
39207 GTGCATTTATACG
1 GTGCATTTCTACG
39220 AGCTGTGGTG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.31
Consensus pattern (23 bp):
GTGCATTTCTACGCGGCACTACA
Found at i:39387 original size:39 final size:37
Alignment explanation
Indices: 39327--39407 Score: 85
Period size: 39 Copynumber: 2.1 Consensus size: 37
39317 AATGTATGTA
*
39327 ATATATGTATATGATGTGTGATATGAAT-TGTATGACATG
1 ATATATGTATATGATGAGTGAT-TGAATCTGT-T-ACATG
* *
39366 ATATATGTGTGAT-ATGAGTGATTGCATCTGTTACATG
1 ATATATGTAT-ATGATGAGTGATTGAATCTGTTACATG
39403 ATATA
1 ATATA
39408 CATGAATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
37 10 0.27
38 5 0.14
39 20 0.54
40 2 0.05
ACGTcount: A:0.32, C:0.05, G:0.22, T:0.41
Consensus pattern (37 bp):
ATATATGTATATGATGAGTGATTGAATCTGTTACATG
Found at i:43529 original size:2 final size:2
Alignment explanation
Indices: 43524--43549 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
43514 TATATATATA
43524 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
43550 AACATAAGAT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:45959 original size:45 final size:46
Alignment explanation
Indices: 45899--46003 Score: 149
Period size: 45 Copynumber: 2.3 Consensus size: 46
45889 TGCGCTAAGT
* * * *
45899 GTGCATCAATGCATAAAATGCATTCGATGTTTTGAAT-AAGCCTAA
1 GTGCATCGATGCATAAAATGCAATCGATGTTTTCAATAAAACCTAA
* *
45944 GTGCATCGATGCATAAAATGCAATCGATGTTTTCATTAAAACCTGA
1 GTGCATCGATGCATAAAATGCAATCGATGTTTTCAATAAAACCTAA
45990 GTGCATCGATGCAT
1 GTGCATCGATGCAT
46004 GGAGAGTGCA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 33 0.62
46 20 0.38
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30
Consensus pattern (46 bp):
GTGCATCGATGCATAAAATGCAATCGATGTTTTCAATAAAACCTAA
Found at i:46075 original size:20 final size:20
Alignment explanation
Indices: 46050--46087 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
46040 CAATTTATTC
46050 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
46070 ATTGGTGCATCGATGCAT
1 ATTGGTGCATCGATGCAT
46088 TCCTTTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:55581 original size:2 final size:2
Alignment explanation
Indices: 55576--55613 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
55566 ATTATGAATA
55576 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
55614 GACTAATACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58893 original size:15 final size:16
Alignment explanation
Indices: 58874--58910 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
58864 ATTTATAAAA
58874 AAATAATATATAATTT
1 AAATAATATATAATTT
*
58890 -AATAA-ATATCATTT
1 AAATAATATATAATTT
58904 AAATAAT
1 AAATAAT
58911 TAAATAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 4
0.78 0.04 0.17
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATAATATATAATTT
Found at i:58935 original size:31 final size:31
Alignment explanation
Indices: 58874--58943 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 31
58864 ATTTATAAAA
* * **
58874 AAATAA-TATATAATTTAATAAATATCATTT
1 AAATAATTAAATAATCTAATAAATAAAATTT
*
58904 AAATAATTAAATAATCTAATTAATAAAATTT
1 AAATAATTAAATAATCTAATAAATAAAATTT
*
58935 AGAT-ATTAA
1 AAATAATTAA
58944 CAATCAAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 11 0.33
31 22 0.67
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (31 bp):
AAATAATTAAATAATCTAATAAATAAAATTT
Found at i:66842 original size:20 final size:22
Alignment explanation
Indices: 66814--66857 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
66804 GCAGCAAGTG
*
66814 CATTAGAAAAAG-AGGGGAAAA
1 CATTAGAAAAAGAAAGGGAAAA
*
66835 CATT-GAAACAGAAAGGGAAAA
1 CATTAGAAAAAGAAAGGGAAAA
66856 CA
1 CA
66858 AGAGGATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.57, C:0.09, G:0.25, T:0.09
Consensus pattern (22 bp):
CATTAGAAAAAGAAAGGGAAAA
Found at i:68941 original size:112 final size:111
Alignment explanation
Indices: 68749--69305 Score: 756
Period size: 112 Copynumber: 5.0 Consensus size: 111
68739 TTGTCGGTTT
* * *
68749 GTGTCGATACTTTATAAAA--TATTGATCCATAATAATATAACAAGTAAACAAATGACAAAAACC
1 GTGTCGATACTTTATAAAATGTATCGATCCATAACAATATAACAGGTAAA-AAATGAC-AAAACC
*
68812 AGTCTAT-AATGACAAAACAGGTAAAAGCGCTACCGGATATATTGAAA
64 GGTCTATAAATGACAAAACAGGTAAAAGCGCTACCGGATATATTGAAA
* * * *
68859 GTGTTGATACTTTATAAAAATGTATCTATCCATAACAATATAACATGTAAAAAATGACAAAATCG
1 GTGTCGATACTTTAT-AAAATGTATCGATCCATAACAATATAACAGGTAAAAAATGACAAAACCG
* *
68924 GTCTATAAATGACAAAACAAGTAAAA-CGCTACTGG--ATATTGAAA
65 GTCTATAAATGACAAAACAGGTAAAAGCGCTACCGGATATATTGAAA
68968 GTGTCGATACTTTATAAAATGTATCGATCCATAACAATATAACAGGTAAAATAATGACAAAACCG
1 GTGTCGATACTTTATAAAATGTATCGATCCATAACAATATAACAGGTAAAA-AATGACAAAACCG
*
69033 GTCTATTAATGACAAAACAGGT-AAAGCGCTACCGGATATATTGAAA
65 GTCTATAAATGACAAAACAGGTAAAAGCGCTACCGGATATATTGAAA
* *
69079 GTGTCGATACTTTATAAAAATGTATCGAT-CTTAATAATATAACAGGTAAAAAAAATGACAAAAC
1 GTGTCGATACTTTAT-AAAATGTATCGATCCATAACAATATAACAGGT--AAAAAATGACAAAAC
* * *
69143 CGGTCTATAAATGACAAAACATGT-AAAGCGCTACCGGATATGTTGATA
63 CGGTCTATAAATGACAAAACAGGTAAAAGCGCTACCGGATATATTGAAA
* * *
69191 GTGTCGATATTTTATAAAATGTATCGATCTATAACAATAAAACAGGTAAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAATGTATCGATCCATAACAATATAACAGGT--AAAAAATGACAAAACC
* * * *
69256 GGTCTATAAATGACAAAACAGGTAAAA-TGCTACCAGATATGTTGATA
64 GGTCTATAAATGACAAAACAGGTAAAAGCGCTACCGGATATATTGAAA
69303 GTG
1 GTG
69306 ATACTTATTA
Statistics
Matches: 404, Mismatches: 30, Indels: 24
0.88 0.07 0.05
Matches are distributed among these distances:
108 37 0.09
109 63 0.16
110 14 0.03
111 76 0.19
112 182 0.45
113 32 0.08
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (111 bp):
GTGTCGATACTTTATAAAATGTATCGATCCATAACAATATAACAGGTAAAAAATGACAAAACCGG
TCTATAAATGACAAAACAGGTAAAAGCGCTACCGGATATATTGAAA
Found at i:69134 original size:221 final size:220
Alignment explanation
Indices: 68749--69305 Score: 791
Period size: 221 Copynumber: 2.5 Consensus size: 220
68739 TTGTCGGTTT
* * *
68749 GTGTCGATACTTTATAAAA--TATTGATCCATAATAATATAACAAGTAAACAAATGACAAAAACC
1 GTGTCGATACTTTATAAAATGTATCGATCCATAACAATATAACAGGTAAA-AAATGAC-AAAACC
* *
68812 AGTCTA-TAATGACAAAACAGGTAAAAGCGCTACCGGATATATTGAAAGTGTTGATACTTTATAA
64 GGTCTATTAATGACAAAACAGGT-AAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAA
* * *
68876 AAATGTATCTATCCATAACAATATAACATGTAAAAAATGACAAAATCGGTCTATAAATGACAAAA
128 AAATGTATCGATCCATAACAATATAACAGGTAAAAAATGACAAAACCGGTCTATAAATGACAAAA
*
68941 CAAGTAAAACGCTACTGGATA-TTGAAA
193 CAAGTAAAACGCTACCGGATAGTTGAAA
68968 GTGTCGATACTTTATAAAATGTATCGATCCATAACAATATAACAGGTAAAATAATGACAAAACCG
1 GTGTCGATACTTTATAAAATGTATCGATCCATAACAATATAACAGGTAAAA-AATGACAAAACCG
69033 GTCTATTAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAA
65 GTCTATTAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAA
* *
69098 ATGTATCGAT-CTTAATAATATAACAGGTAAAAAAAATGACAAAACCGGTCTATAAATGACAAAA
130 ATGTATCGATCCATAACAATATAACAGGT--AAAAAATGACAAAACCGGTCTATAAATGACAAAA
* * *
69162 CATGTAAAGCGCTACCGGATATGTTGATA
193 CAAGTAAAACGCTACCGGATA-GTTGAAA
* * *
69191 GTGTCGATATTTTATAAAATGTATCGATCTATAACAATAAAACAGGTAAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAATGTATCGATCCATAACAATATAACAGGT--AAAAAATGACAAAACC
* ** * * *
69256 GGTCTATAAATGACAAAACAGGTAAAATGCTACCAGATATGTTGATAGTG
64 GGTCTATTAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG
69306 ATACTTATTA
Statistics
Matches: 305, Mismatches: 23, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
219 34 0.11
220 63 0.21
221 99 0.32
223 49 0.16
224 56 0.18
225 4 0.01
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (220 bp):
GTGTCGATACTTTATAAAATGTATCGATCCATAACAATATAACAGGTAAAAAATGACAAAACCGG
TCTATTAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAA
TGTATCGATCCATAACAATATAACAGGTAAAAAATGACAAAACCGGTCTATAAATGACAAAACAA
GTAAAACGCTACCGGATAGTTGAAA
Found at i:69537 original size:178 final size:175
Alignment explanation
Indices: 69190--69634 Score: 553
Period size: 178 Copynumber: 2.5 Consensus size: 175
69180 ATATGTTGAT
* * * * *
69190 AGTGTCGATATTTTATAAAATGTATCGATCTATAACAATAA-AACAGGTAAAAAAAATGACAAAA
1 AGTGTCGATACTTTAAAAAATGTATCGATCCATAACAATAATAACAAGT--AAAATATGACAAAA
* **
69254 CCGGTCTATAAATGACAAAACAGGTAAAATGCTACCAGATATGTTGATAGTGATACTTATTATAA
64 TCGGTCTCGAAATGACAAAAC-GGTAAAATGCTACCAGATATGTTGATAGTGATACTTATTATAA
*
69319 GTACGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCG-CTAATAA
128 GTACGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGTC-AATAA
* *
69367 AGTGTCGATACTTTAAAAAATGTATCGATCCAT-ATAATAATAACATGT-AAATATGACAAAATC
1 AGTGTCGATACTTTAAAAAATGTATCGATCCATAACAATAATAACAAGTAAAATATGACAAAATC
* * * *
69430 GGTCTCGAAATGA-AAAATCGGTAAAGA-GCTATCGGATATGTTGATACTGTCGATAATTTTTTA
66 GGTCTCGAAATGACAAAA-CGGTAAA-ATGCTACCAGATATGTTGATA--GT-GAT-ACTTATTA
*
69493 TAAGTATCGATACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGTCAATAA
125 TAAGTA-CGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGTCAATAA
*
69545 AGTGTCAATACTTTATAAAAATGTATCGATCCATAACAAT-ATAACAAGTAAAAATATGACAAAA
1 AGTGTCGATACTTTA-AAAAATGTATCGATCCATAACAATAATAACAAGT-AAAATATGACAAAA
*
69609 TCGATCTCGAAATGACAAAACCGGTA
64 TCGGTCTCGAAATGACAAAA-CGGTA
69635 GTAAAAAAGT
Statistics
Matches: 234, Mismatches: 20, Indels: 23
0.84 0.07 0.08
Matches are distributed among these distances:
173 27 0.12
174 26 0.11
175 2 0.01
176 9 0.04
177 48 0.21
178 55 0.24
179 27 0.12
180 4 0.02
181 27 0.12
182 9 0.04
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.29
Consensus pattern (175 bp):
AGTGTCGATACTTTAAAAAATGTATCGATCCATAACAATAATAACAAGTAAAATATGACAAAATC
GGTCTCGAAATGACAAAACGGTAAAATGCTACCAGATATGTTGATAGTGATACTTATTATAAGTA
CGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGTCAATAA
Found at i:71345 original size:30 final size:29
Alignment explanation
Indices: 71310--71378 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 29
71300 TATGAAAGTG
*
71310 TTATTAAATTAATCAAGAATTATAAAATAA
1 TTATTAAATT-ATCAAAAATTATAAAATAA
*
71340 TTATTAAAATTATCAAAAATTATAAATTAA
1 TTATT-AAATTATCAAAAATTATAAAATAA
*
71370 -TACTAAATT
1 TTATTAAATT
71379 TGTTAAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.14
29 3 0.09
30 22 0.63
31 5 0.14
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.39
Consensus pattern (29 bp):
TTATTAAATTATCAAAAATTATAAAATAA
Done.