Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008539.1 Hibiscus syriacus cultivar Beakdansim tig00111427_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: 6067759
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 31 of 31
Found at i:6028671 original size:20 final size:20
Alignment explanation
Indices: 6028623--6028688 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
6028613 AATAGTTTCT
** *
6028623 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
6028643 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
** *
6028663 GAATTTGACTATCGCAACGA
1 GAAAATGACTATCGCAACGC
6028683 GAAAAT
1 GAAAAT
6028689 CGCAACGCGA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.45, C:0.20, G:0.18, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:6028952 original size:22 final size:22
Alignment explanation
Indices: 6028925--6028968 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
6028915 GATGGAGATA
6028925 GACGGATTTCACCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
**
6028947 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
6028969 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCACCGGAGATGGG
Found at i:6029290 original size:20 final size:20
Alignment explanation
Indices: 6029156--6029289 Score: 153
Period size: 20 Copynumber: 6.7 Consensus size: 20
6029146 GATTATGTAT
6029156 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
6029176 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
6029196 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
6029216 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* * ** *
6029236 TATCTCGTTTCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
6029257 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
6029277 TATCGCATTGCGA
1 TATCGCGTTGCGA
6029290 TTTTCCCAAT
Statistics
Matches: 98, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
19 3 0.03
20 82 0.84
21 11 0.11
22 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:6029308 original size:21 final size:21
Alignment explanation
Indices: 6029279--6029371 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
6029269 ATAGTCAGTA
6029279 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
6029300 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
6029320 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
6029341 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
6029361 TCGCATTGCGA
1 TCGCATTGCGA
6029372 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:6029309 original size:41 final size:41
Alignment explanation
Indices: 6029279--6029371 Score: 150
Period size: 41 Copynumber: 2.3 Consensus size: 41
6029269 ATAGTCAGTA
* *
6029279 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
* *
6029320 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
6029361 TCGCATTGCGA
1 TCGCATTGCGA
6029372 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:6036173 original size:6 final size:6
Alignment explanation
Indices: 6036135--6036169 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
6036125 CTATTGCGAA
*
6036135 AGAGAT AGAGAT AGAGAT AGAGAT AGAGAG AGAGA
1 AGAGAT AGAGAT AGAGAT AGAGAT AGAGAT AGAGA
6036170 GAGAATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.51, C:0.00, G:0.37, T:0.11
Consensus pattern (6 bp):
AGAGAT
Found at i:6036511 original size:18 final size:17
Alignment explanation
Indices: 6036478--6036512 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
6036468 ATGTATGAGC
*
6036478 ATAAAATTAAATTAATA
1 ATAAAATTAAAATAATA
6036495 ATAAAATGTAAAATAATA
1 ATAAAAT-TAAAATAATA
6036513 TTTAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (17 bp):
ATAAAATTAAAATAATA
Found at i:6039836 original size:23 final size:23
Alignment explanation
Indices: 6039779--6039854 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
6039769 TTTTTAATAA
*
6039779 TAAAAAAATTCTTTAACAT-TCAAT
1 TAAAAAAATTCTTTAAAATAT--AT
* *
6039803 CCAAAACAATTCTTTAAAATATAT
1 -TAAAAAAATTCTTTAAAATATAT
* * *
6039827 TAAAAAAATTATTTAATATATGT
1 TAAAAAAATTCTTTAAAATATAT
6039850 TAAAA
1 TAAAA
6039855 GACATTTTCT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
23 23 0.55
24 2 0.05
25 16 0.38
26 1 0.02
ACGTcount: A:0.53, C:0.09, G:0.01, T:0.37
Consensus pattern (23 bp):
TAAAAAAATTCTTTAAAATATAT
Found at i:6039915 original size:22 final size:22
Alignment explanation
Indices: 6039899--6040000 Score: 74
Period size: 22 Copynumber: 4.8 Consensus size: 22
6039889 TATTTATCTA
6039899 AATTATTTAAATTATTTTTAAT
1 AATTATTTAAATTATTTTTAAT
* * *
6039921 AATTATTTAAATTGAATATTACT
1 AATTATTTAAATT-ATTTTTAAT
* *
6039944 TATT-TTT-AATAACTATTTT-A-
1 AATTATTTAAATTA-T-TTTTAAT
6039964 AATTATTTAAATTATTTTTAAT
1 AATTATTTAAATTATTTTTAAT
*
6039986 --TTATCTAAATT-TTTT
1 AATTATTTAAATTATTTT
6040001 ATATTTTTCT
Statistics
Matches: 62, Mismatches: 11, Indels: 17
0.69 0.12 0.19
Matches are distributed among these distances:
19 4 0.06
20 18 0.29
21 8 0.13
22 23 0.37
23 9 0.15
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (22 bp):
AATTATTTAAATTATTTTTAAT
Found at i:6040006 original size:19 final size:17
Alignment explanation
Indices: 6039978--6040017 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
6039968 ATTTAAATTA
6039978 TTTTTAATTTATCTAAAT
1 TTTTTAATTTATCT-AAT
*
6039996 TTTTTATATTTTTCTAAT
1 TTTTTA-ATTTATCTAAT
6040014 TTTT
1 TTTT
6040018 AATAATTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTTAATTTATCTAAT
Found at i:6040353 original size:82 final size:83
Alignment explanation
Indices: 6040181--6040585 Score: 440
Period size: 82 Copynumber: 4.9 Consensus size: 83
6040171 ATAAAATGGT
* *
6040181 AACTTTAGCGGCGTTTCTT-TACAAATGCCGTAATAGGGTTCAACTATAGTGGCATTGTTTT-GA
1 AACTTTAGCGGCGTTT-TTATACAAATGCCGTAATAGGGTTCACCTATAGTGGCATT-TTTTCAA
* * * **
6040244 CAAATGCCGTAACAGAGAAG
64 TAAACGCCGCAACAGATTAG
* * * *
6040264 TACTTTAGCGGCATTTTTATACAAATGCCGTAATA-GGTCCATCTATAGTGGCATTTTTTCAATA
1 AACTTTAGCGGCGTTTTTATACAAATGCCGTAATAGGGTTCACCTATAGTGGCATTTTTTCAATA
6040328 AACGCCGCAACAGATTAG
66 AACGCCGCAACAGATTAG
* * * * * *** *
6040346 TACTTTAGTGGTGTTTTTATATAAACGCTACAATAGGGTTCACCTATAGTGGCATTTTAT-AATA
1 AACTTTAGCGGCGTTTTTATACAAATGCCGTAATAGGGTTCACCTATAGTGGCATTTTTTCAATA
* *
6040410 AACACCGCAACAAATTAG
66 AACGCCGCAACAGATTAG
*** *
6040428 AACTTTAGCCATGTTTTTATACAAATGCCGTAATAGGGTTCACCTATAGTGGCATTTTGTCAATA
1 AACTTTAGCGGCGTTTTTATACAAATGCCGTAATAGGGTTCACCTATAGTGGCATTTTTTCAATA
* * *
6040493 AACACCACAACATATTAG
66 AACGCCGCAACAGATTAG
*** * * * *
6040511 AACTTTAGCGGCGTTTTTATACAAACATCGCAATAGTGTTTACCTATAGTTGCATTTTTTCAATA
1 AACTTTAGCGGCGTTTTTATACAAATGCCGTAATAGGGTTCACCTATAGTGGCATTTTTTCAATA
6040576 AACGCCGCAA
66 AACGCCGCAA
6040586 TTGTTTGAAC
Statistics
Matches: 270, Mismatches: 48, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
81 4 0.01
82 133 0.49
83 133 0.49
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (83 bp):
AACTTTAGCGGCGTTTTTATACAAATGCCGTAATAGGGTTCACCTATAGTGGCATTTTTTCAATA
AACGCCGCAACAGATTAG
Found at i:6040477 original size:165 final size:165
Alignment explanation
Indices: 6040277--6040585 Score: 433
Period size: 165 Copynumber: 1.9 Consensus size: 165
6040267 TTTAGCGGCA
* * * *
6040277 TTTTTATACAAATGCCGTAATAGGTCCATCTATAGTGGCATTTTTTCAATAAACGCCGCAACAGA
1 TTTTTATACAAATGCCGTAATAGGTCCACCTATAGTGGCATTTTGTCAATAAACACCACAACAGA
* * * * *
6040342 TTAGTACTTTAGTGGTGTTTTTATATAAAC-GCTACAATAGGGTTCACCTATAGTGGCATTTTAT
66 TTAGAACTTTAGCGGCGTTTTTATACAAACATC-ACAATAGGGTTCACCTATAGTGGCATTTTAT
6040406 -AATAAACACCGCAACAAATTAGAACTTTAGCCATG
130 CAATAAACACCGCAACAAATTAGAACTTTAGCCATG
* *
6040441 TTTTTATACAAATGCCGTAATAGGGTTCACCTATAGTGGCATTTTGTCAATAAACACCACAACAT
1 TTTTTATACAAATGCCGTAATA-GGTCCACCTATAGTGGCATTTTGTCAATAAACACCACAACAG
* * * * *
6040506 ATTAGAACTTTAGCGGCGTTTTTATACAAACATCGCAATAGTGTTTACCTATAGTTGCATTTTTT
65 ATTAGAACTTTAGCGGCGTTTTTATACAAACATCACAATAGGGTTCACCTATAGTGGCATTTTAT
*
6040571 CAATAAACGCCGCAA
130 CAATAAACACCGCAA
6040586 TTGTTTGAAC
Statistics
Matches: 125, Mismatches: 17, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
164 22 0.18
165 89 0.71
166 14 0.11
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (165 bp):
TTTTTATACAAATGCCGTAATAGGTCCACCTATAGTGGCATTTTGTCAATAAACACCACAACAGA
TTAGAACTTTAGCGGCGTTTTTATACAAACATCACAATAGGGTTCACCTATAGTGGCATTTTATC
AATAAACACCGCAACAAATTAGAACTTTAGCCATG
Found at i:6041216 original size:15 final size:15
Alignment explanation
Indices: 6041196--6041228 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
6041186 CTATGTAGAT
6041196 TGTGTTTTGAAGAAC
1 TGTGTTTTGAAGAAC
6041211 TGTGTTTTGAAGAAC
1 TGTGTTTTGAAGAAC
6041226 TGT
1 TGT
6041229 ATTGTGGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.06, G:0.27, T:0.42
Consensus pattern (15 bp):
TGTGTTTTGAAGAAC
Found at i:6043205 original size:194 final size:195
Alignment explanation
Indices: 6042846--6043206 Score: 427
Period size: 194 Copynumber: 1.9 Consensus size: 195
6042836 GTGTTTTGCT
* * ** * * *
6042846 ACAATATCTTTTTCGTCACATATATAAGTTGATTTTAATGCATTATTTGTGATGATATAAATTAT
1 ACAATATCTCTTTCGTCACA-ATATAAGTTGATTTTAATACATTATCCGTCACGATATAAATCAT
** *
6042911 CAATAACGAAATCTTATTTAATTTAGTGACGTAACCAACTGTCACAGAATATAAATTATAAAGTG
65 CAATAACGAAATCTTACATAATTTAGTGACATAACCAACTGTCACAGAATATAAATTATAAAGTG
* * * *
6042976 ACGTTATGCATAAACGTTATTCATAATATTATTAGGTAACATTTATATTATGTCACTAAAAATGT
130 ACGTTATACATAAACGTCATCCATAATACTATTAGGTAACATTTATATTATGTCACTAAAAATGT
6043041 G
195 G
* * *
6043042 ACAATATCTCTTTCTTCAC-ATATAGGTTGATTTTAATATATTATCCGTCACGATATAAATCATC
1 ACAATATCTCTTTCGTCACAATATAAGTTGATTTTAATACATTATCCGTCACGATATAAATCATC
* * ** ** ** * *
6043106 AATAATGAAATTTTACATAATTTAGTGACATAATTAGTTGTCATTGAATATTAATTATATAGTGA
66 AATAACGAAATCTTACATAATTTAGTGACATAACCAACTGTCACAGAATATAAATTATAAAGTGA
* * **
6043171 CGTTATATATAAATGTCATCCATGCTACTATTAGGT
131 CGTTATACATAAACGTCATCCATAATACTATTAGGT
6043207 GACTATATAC
Statistics
Matches: 134, Mismatches: 31, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
194 117 0.87
196 17 0.13
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (195 bp):
ACAATATCTCTTTCGTCACAATATAAGTTGATTTTAATACATTATCCGTCACGATATAAATCATC
AATAACGAAATCTTACATAATTTAGTGACATAACCAACTGTCACAGAATATAAATTATAAAGTGA
CGTTATACATAAACGTCATCCATAATACTATTAGGTAACATTTATATTATGTCACTAAAAATGTG
Found at i:6043945 original size:2 final size:2
Alignment explanation
Indices: 6043938--6044003 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
6043928 ACTTCTGTAA
6043938 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6043980 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
6044004 CAAAATGGTG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6049106 original size:21 final size:21
Alignment explanation
Indices: 6049077--6049116 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
6049067 TTTGAGCAGA
6049077 AAAATCATCTCCAAACGGCTCC
1 AAAATCATC-CCAAACGGCTCC
*
6049099 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCAAACGGCT
6049117 ATATACGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 4 0.24
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCAAACGGCTCC
Found at i:6049370 original size:34 final size:32
Alignment explanation
Indices: 6049331--6049400 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
6049321 TTTTGTAAAG
*
6049331 GGGAAATGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAATGTTCTAGCTTATCCCG-G-AAAAACTA
*
6049365 GGGAAATGTTCTAGTTTATCCCGGAAAAACTA
1 GGGAAATGTTCTAGCTTATCCCGGAAAAACTA
6049397 GGGA
1 GGGA
6049401 GTTGTAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (32 bp):
GGGAAATGTTCTAGCTTATCCCGGAAAAACTA
Found at i:6051271 original size:18 final size:18
Alignment explanation
Indices: 6051243--6051301 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 18
6051233 CAACAATTGG
6051243 TAACAAATTGATATCTTTT
1 TAAC-AATTGATATCTTTT
*
6051262 TAACAATTGATATTATTTTGT
1 TAACAATTGATA-T-CTTT-T
6051283 TAACAATTGATATCTTTT
1 TAACAATTGATATCTTTT
6051301 T
1 T
6051302 CATTAAACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
18 10 0.29
19 8 0.23
20 4 0.11
21 13 0.37
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51
Consensus pattern (18 bp):
TAACAATTGATATCTTTT
Found at i:6051445 original size:29 final size:28
Alignment explanation
Indices: 6051413--6051471 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 28
6051403 AATTTAAGGC
6051413 AAAATGATTTTTGGACTTGAATTGAATTTAA
1 AAAATG-TTTTTGGACTT-AATTGAATTT-A
6051444 AAAATGTTTTTGGACTTAATTGAATTTA
1 AAAATGTTTTTGGACTTAATTGAATTTA
6051472 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 1 0.04
29 10 0.36
30 11 0.39
31 6 0.21
ACGTcount: A:0.37, C:0.03, G:0.15, T:0.44
Consensus pattern (28 bp):
AAAATGTTTTTGGACTTAATTGAATTTA
Found at i:6051482 original size:29 final size:30
Alignment explanation
Indices: 6051413--6051471 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
6051403 AATTTAAGGC
6051413 AAAATGATTTTTGGACTTGAATTGAATTTAA
1 AAAATG-TTTTTGGACTTGAATTGAATTTAA
6051444 AAAATGTTTTTGGACTT-AATTGAATTTA
1 AAAATGTTTTTGGACTTGAATTGAATTTA
6051472 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.37, C:0.03, G:0.15, T:0.44
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAA
Found at i:6051740 original size:21 final size:21
Alignment explanation
Indices: 6051708--6051748 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6051698 TTTGAATTTA
*
6051708 ATGAAGGAGTACTGATACCCT
1 ATGAAGGAGTACCGATACCCT
6051729 ATGATAGG-GTACCGATACCC
1 ATGA-AGGAGTACCGATACCC
6051749 CCTATTATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (21 bp):
ATGAAGGAGTACCGATACCCT
Found at i:6052476 original size:2 final size:2
Alignment explanation
Indices: 6052469--6052529 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
6052459 AAAACTTTTG
6052469 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
6052511 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
6052530 CAAAATGGCG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6056105 original size:60 final size:59
Alignment explanation
Indices: 6055961--6056108 Score: 149
Period size: 60 Copynumber: 2.5 Consensus size: 59
6055951 TCAATTGATC
* *
6055961 CTTAAACTTTTGAATGTTCCAATTTTATTACCAAATAATGACCCACATTCTAAATTAGCG
1 CTTAAACTTTTGAATATTCCAATTTCATTA-CAAATAATGACCCACATTCTAAATTAGCG
* * * * * * *
6056021 CTTAAATTTTTTAACATTCTAATTTCATT-CATAAGCT-ATGACCCTCTTTCTAAATTAG-T
1 CTTAAACTTTTGAATATTCCAATTTCATTACA-AA--TAATGACCCACATTCTAAATTAGCG
6056080 CTCTAAACTTTTGAATATTCCAATTTCAT
1 CT-TAAACTTTTGAATATTCCAATTTCAT
6056109 CCAAATATGT
Statistics
Matches: 71, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
58 2 0.03
59 4 0.06
60 64 0.90
61 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (59 bp):
CTTAAACTTTTGAATATTCCAATTTCATTACAAATAATGACCCACATTCTAAATTAGCG
Found at i:6056314 original size:29 final size:29
Alignment explanation
Indices: 6056281--6056384 Score: 86
Period size: 30 Copynumber: 3.5 Consensus size: 29
6056271 TGAAAGTCAT
* *
6056281 AGTTTGGGGATGAAATTGGAATGTTCAAA
1 AGTTTAGGGATGAAATTGGAATGTTTAAA
* * * *
6056310 AGTTT-GAGGACT-AATTTAGAATGATTTTTAT
1 AGTTTAG-GGA-TGAAATTGGAATG--TTTAAA
6056341 AGTTTAGGGATGAAATTGGAGATGTTTAAA
1 AGTTTAGGGATGAAATTGGA-ATGTTTAAA
*
6056371 AGTTTAGTGATGAA
1 AGTTTAGGGATGAA
6056385 TTTAAAATGA
Statistics
Matches: 58, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
28 1 0.02
29 17 0.29
30 19 0.33
31 17 0.29
32 4 0.07
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.37
Consensus pattern (29 bp):
AGTTTAGGGATGAAATTGGAATGTTTAAA
Found at i:6056343 original size:60 final size:58
Alignment explanation
Indices: 6056219--6056375 Score: 190
Period size: 60 Copynumber: 2.6 Consensus size: 58
6056209 TAGTATATAC
* *
6056219 TTATAGTTTGGGATGAAATTGGAATGTTTAAAGTGTGGAGACCAATTTAGAATGAAAG
1 TTATAGTTTGGGATGAAATTGGAATGTTAAAAGTTTGGAGACCAATTTAGAATGAAAG
* * ***
6056277 TCATAGTTTGGGGATGAAATTGGAATGTTCAAAAGTTT-GAGGACTAATTTAGAATGATTT
1 TTATAGTTT-GGGATGAAATTGGAATGTT-AAAAGTTTGGA-GACCAATTTAGAATGAAAG
6056337 TTATAGTTTAGGGATGAAATTGGAGATGTTTAAAAGTTT
1 TTATAGTTT-GGGATGAAATTGGA-ATG-TTAAAAGTTT
6056376 AGTGATGAAT
Statistics
Matches: 85, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
58 8 0.09
59 21 0.25
60 43 0.51
61 11 0.13
62 2 0.02
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.36
Consensus pattern (58 bp):
TTATAGTTTGGGATGAAATTGGAATGTTAAAAGTTTGGAGACCAATTTAGAATGAAAG
Found at i:6056394 original size:61 final size:57
Alignment explanation
Indices: 6056219--6056394 Score: 183
Period size: 60 Copynumber: 2.9 Consensus size: 57
6056209 TAGTATATAC
* * *
6056219 TTATAGTTTGGGATGAAATTGGAATGTTT-AAAGTGTGGAGACCAATTTAGAATGAAAG
1 TTATAGTTTGGGATGAAATTGGAATGTTTAAAAGTTTAG-GA-TAATTTAGAATGAAAG
* * ***
6056277 TCATAGTTTGGGGATGAAATTGGAATGTTCAAAAGTTTGAGGACTAATTTAGAATGATTT
1 TTATAGTTT-GGGATGAAATTGGAATGTTTAAAAGTTT-AGGA-TAATTTAGAATGAAAG
*
6056337 TTATAGTTTAGGGATGAAATTGGAGATGTTTAAAAGTTTAGTGATGAATTTAAAATGA
1 TTATAGTTT-GGGATGAAATTGGA-ATGTTTAAAAGTTTAG-GAT-AATTTAGAATGA
6056395 GGTTCATACT
Statistics
Matches: 100, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
58 8 0.08
59 19 0.19
60 46 0.46
61 27 0.27
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.36
Consensus pattern (57 bp):
TTATAGTTTGGGATGAAATTGGAATGTTTAAAAGTTTAGGATAATTTAGAATGAAAG
Found at i:6057106 original size:2 final size:2
Alignment explanation
Indices: 6057099--6057170 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
6057089 ATCAGCATGA
6057099 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6057141 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
6057171 TAGTCAATAT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6063551 original size:13 final size:13
Alignment explanation
Indices: 6063533--6063571 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
6063523 GTCATAAATC
6063533 TATGACGCGCATT
1 TATGACGCGCATT
*
6063546 TATGACACGCATT
1 TATGACGCGCATT
*
6063559 TATGACGCTCATT
1 TATGACGCGCATT
6063572 GCGCGTCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:6063686 original size:85 final size:85
Alignment explanation
Indices: 6063543--6063710 Score: 266
Period size: 85 Copynumber: 2.0 Consensus size: 85
6063533 TATGACGCGC
*
6063543 ATTTATGACACGCATTTATGACGCTCATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAGATGA
1 ATTTATGACACGCATTTATGACGCTCATTGCGCGTCATTGAAGCCACCGTCATAAATGAAGATGA
* *
6063608 CACACATTTGTGTTTCATAA
66 CACACATTCGTGTGTCATAA
* * *
6063628 ATTTATTACACGCATTTATGAC-TTACATTGCGTGTCATTGAAGCCACCGTCATAAATGAAGATG
1 ATTTATGACACGCATTTATGACGCT-CATTGCGCGTCATTGAAGCCACCGTCATAAATGAAGATG
6063692 ACACACATTCGTGTGTCAT
65 ACACACATTCGTGTGTCAT
6063711 GATTGTATTT
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
84 1 0.01
85 75 0.99
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (85 bp):
ATTTATGACACGCATTTATGACGCTCATTGCGCGTCATTGAAGCCACCGTCATAAATGAAGATGA
CACACATTCGTGTGTCATAA
Found at i:6063735 original size:2 final size:2
Alignment explanation
Indices: 6063728--6063754 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6063718 TTTCGTAAAT
6063728 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
6063755 TGTAGATTGA
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
Done.