Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007934.1 Hibiscus syriacus cultivar Beakdansim tig00110344_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: 290973
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:184587 original size:24 final size:24
Alignment explanation
Indices: 184554--184606 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
184544 ACATACACAT
*
184554 TTCTCGCCCTAATTCTTCCTCGTG
1 TTCTCACCCTAATTCTTCCTCGTG
*
184578 TTCTCACCCTAATTCTTCCTCGTT
1 TTCTCACCCTAATTCTTCCTCGTG
184602 TTCTC
1 TTCTC
184607 TCCCATCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.09, C:0.38, G:0.08, T:0.45
Consensus pattern (24 bp):
TTCTCACCCTAATTCTTCCTCGTG
Found at i:187051 original size:14 final size:15
Alignment explanation
Indices: 187032--187066 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
187022 TTATAATCGC
*
187032 AAAATATTATTA-AA
1 AAAATATTATAATAA
187046 AAAATATTATAATAA
1 AAAATATTATAATAA
187061 AAAATA
1 AAAATA
187067 ATGTGTAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAATATTATAATAA
Found at i:187229 original size:2 final size:2
Alignment explanation
Indices: 187222--187263 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
187212 CATAAAAACT
187222 TA TA TA TA TA TA TA TA TA -A 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
187263 T
1 T
187264 GTTAAGACTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:201492 original size:21 final size:21
Alignment explanation
Indices: 201466--201507 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
201456 TCAGAATGGG
*
201466 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
201487 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
201508 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:201676 original size:29 final size:31
Alignment explanation
Indices: 201629--201690 Score: 92
Period size: 29 Copynumber: 2.0 Consensus size: 31
201619 AATTATTTTT
*
201629 ATAAATTTTGAATACATTCAATT-AAGTCCAA
1 ATAAATTTTG-ATAAATTCAATTCAAGTCCAA
201660 ATAAATTTTG-TAAATTCAATTCAAGTCCAA
1 ATAAATTTTGATAAATTCAATTCAAGTCCAA
201690 A
1 A
201691 AACCATTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 10 0.34
30 9 0.31
31 10 0.34
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.35
Consensus pattern (31 bp):
ATAAATTTTGATAAATTCAATTCAAGTCCAA
Found at i:204219 original size:21 final size:21
Alignment explanation
Indices: 204193--204234 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
204183 TCAGAATGGG
*
204193 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
204214 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
204235 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:204382 original size:19 final size:19
Alignment explanation
Indices: 204340--204407 Score: 91
Period size: 19 Copynumber: 3.5 Consensus size: 19
204330 GAGCCTCGGG
* * *
204340 TTACTGTGTCAAACAGTGAT
1 TTACTGT-TCAAATAGTAAA
204360 TTACTGTTCAAATAGTAAA
1 TTACTGTTCAAATAGTAAA
204379 TTACTGTTCAAATAGTAAA
1 TTACTGTTCAAATAGTAAA
*
204398 TTACTATTCA
1 TTACTGTTCA
204408 TAAAAACATT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 37 0.84
20 7 0.16
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (19 bp):
TTACTGTTCAAATAGTAAA
Found at i:204507 original size:29 final size:31
Alignment explanation
Indices: 204461--204521 Score: 90
Period size: 29 Copynumber: 2.0 Consensus size: 31
204451 ATTATTTTTG
*
204461 TAAATTTTGAATACATTCAATT-AAGTCCAAA
1 TAAATTTTG-ATAAATTCAATTCAAGTCCAAA
204492 TAAATTTTG-TAAATTCAATTCAAGTCCAAA
1 TAAATTTTGATAAATTCAATTCAAGTCCAAA
204522 AACCATTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 10 0.36
30 9 0.32
31 9 0.32
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (31 bp):
TAAATTTTGATAAATTCAATTCAAGTCCAAA
Found at i:210369 original size:2 final size:2
Alignment explanation
Indices: 210362--210392 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
210352 GTATACCGTG
210362 TA TA TA TA TA TA TA -A 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
210393 GGGTCATGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:210380 original size:15 final size:15
Alignment explanation
Indices: 210362--210390 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
210352 GTATACCGTG
210362 TATATATATATATAA
1 TATATATATATATAA
210377 TATATATATATATA
1 TATATATATATATA
210391 TAGGGTCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATATATATATATAA
Found at i:220283 original size:19 final size:21
Alignment explanation
Indices: 220246--220284 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
220236 AAACAAGATA
220246 AAGATAAATCCTAAATTAAAG
1 AAGATAAATCCTAAATTAAAG
220267 AAGA-AAATCCT-AATTAAA
1 AAGATAAATCCTAAATTAAA
220285 ATACTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 7 0.39
21 4 0.22
ACGTcount: A:0.59, C:0.10, G:0.08, T:0.23
Consensus pattern (21 bp):
AAGATAAATCCTAAATTAAAG
Found at i:221603 original size:52 final size:51
Alignment explanation
Indices: 221533--221671 Score: 179
Period size: 52 Copynumber: 2.7 Consensus size: 51
221523 ATTAAACGAG
* * * * *
221533 GCATGGGCAGCAGTTGCATTAAGGCAACTTTTCATGCATGCAGCATGCCTCT
1 GCATGGGCAACA-ATGCATTAAGGCAACTTTGCATGCATGCAACATGCCTCA
*
221585 GCATGGGCAACAACTGCATTAAGGCAGCTTTGCATGCATGCAACATGCCTCA
1 GCATGGGCAACAA-TGCATTAAGGCAACTTTGCATGCATGCAACATGCCTCA
* *
221637 GCATAGGCAACAGATGCATTAAGGCATCTTTGCAT
1 GCATGGGCAACA-ATGCATTAAGGCAACTTTGCAT
221672 TCATCATGCG
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
52 76 0.99
53 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (51 bp):
GCATGGGCAACAATGCATTAAGGCAACTTTGCATGCATGCAACATGCCTCA
Found at i:224380 original size:15 final size:15
Alignment explanation
Indices: 224362--224404 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 15
224352 AAAAACGTCT
224362 TTTTAA-AAAAATTAA
1 TTTTAAGAAAAA-TAA
224377 TTTTAAGAAAAATAA
1 TTTTAAGAAAAATAA
224392 TTTTAAGACAAAA
1 TTTTAAGA-AAAA
224405 AAAAAGCTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (15 bp):
TTTTAAGAAAAATAA
Found at i:226713 original size:50 final size:50
Alignment explanation
Indices: 226653--226752 Score: 157
Period size: 50 Copynumber: 2.0 Consensus size: 50
226643 GAATGTGATC
* *
226653 CATACTCAATCGTGAAACACGATTGGGTTGA-AATTTGAATACTTTATCTT
1 CATACTCAATCATGAAACACGATTGAGTT-ACAATTTGAATACTTTATCTT
*
226703 CATACTCAATCATGAAACACGATTGAGTTACTATTTGAATACTTTATCTT
1 CATACTCAATCATGAAACACGATTGAGTTACAATTTGAATACTTTATCTT
226753 TATAATAAAC
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
49 1 0.02
50 45 0.98
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (50 bp):
CATACTCAATCATGAAACACGATTGAGTTACAATTTGAATACTTTATCTT
Found at i:236913 original size:4 final size:4
Alignment explanation
Indices: 236906--238932 Score: 3107
Period size: 4 Copynumber: 508.8 Consensus size: 4
236896 CCAACCATCT
236906 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
236954 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * *
237002 TACA CACA CACA CACA CACA CACA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
237050 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
237098 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
237146 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
237194 CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT- -ATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
237240 CATA CATA CATA CATA CAT- -ATA CATA CATA CATA C--A CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
237284 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
237332 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
237380 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
237428 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
237476 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
237524 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
237572 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
237620 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
237668 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
237716 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
237764 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
237812 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
237860 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * *
237908 CATA CATA CATA CATA CATA CATA CACA CATA C--A CACA CACA CACA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * * * * * * *
237954 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * * * * * * *
238002 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * * * * * * *
238050 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * * * * * * *
238098 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * * * * * * *
238146 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * * * * * * *
238194 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * * * * * * *
238242 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * *
238290 CACA CACA CACA CACA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
238338 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
238386 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
238434 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
238482 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
238530 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
238578 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
238626 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
238674 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
238722 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
238770 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
238818 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
238866 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
238914 CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CAT
238933 CACTCGAGAA
Statistics
Matches: 2008, Mismatches: 7, Indels: 16
0.99 0.00 0.01
Matches are distributed among these distances:
2 8 0.00
4 2000 1.00
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (4 bp):
CATA
Found at i:237010 original size:2 final size:2
Alignment explanation
Indices: 237003--237027 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
236993 ACATACATAT
237003 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
237028 TACATACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:237944 original size:2 final size:2
Alignment explanation
Indices: 237931--238307 Score: 745
Period size: 2 Copynumber: 188.5 Consensus size: 2
237921 ATACATACAT
*
237931 AC AC AC AT AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
237973 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
238015 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
238057 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
238099 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
238141 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
238183 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
238225 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
238267 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
238308 TACATACATA
Statistics
Matches: 373, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
2 373 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:239356 original size:22 final size:22
Alignment explanation
Indices: 239326--239380 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
239316 CGAGCTCCTC
*
239326 TAATTTTTTAAATT-TAAAAAT
1 TAATTTTTTAAATTAAAAAAAT
**
239347 TATATTTTTTGCATTAAAAAAAT
1 TA-ATTTTTTAAATTAAAAAAAT
239370 TAATTTTTTAA
1 TAATTTTTTAA
239381 TAAACTCGTC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 2 0.07
22 17 0.63
23 8 0.30
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TAATTTTTTAAATTAAAAAAAT
Found at i:252902 original size:18 final size:18
Alignment explanation
Indices: 252879--252931 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
252869 TTGACCGGTT
252879 CCGACCCGTCCCGTTGAC
1 CCGACCCGTCCCGTTGAC
* **
252897 CCGACCAGTTTCGTTGAC
1 CCGACCCGTCCCGTTGAC
*
252915 CCGACCCGACCCGTTGA
1 CCGACCCGTCCCGTTGA
252932 TCGTTGATCG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.43, G:0.23, T:0.19
Consensus pattern (18 bp):
CCGACCCGTCCCGTTGAC
Found at i:253030 original size:23 final size:24
Alignment explanation
Indices: 253003--253048 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
252993 CAAAAATAGT
*
253003 GCTATTTTTGTAATTTTT-AAAAG
1 GCTATTTTCGTAATTTTTGAAAAG
253026 GCTATTTTCGTAATTTTTGAAAA
1 GCTATTTTCGTAATTTTTGAAAA
253049 AAATGACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (24 bp):
GCTATTTTCGTAATTTTTGAAAAG
Found at i:253124 original size:29 final size:30
Alignment explanation
Indices: 253068--253125 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
253058 TTTAGTAAAT
**
253068 ATTTTGAAAATGGTACTATATTGGTAATTA
1 ATTTTGAAAATGGTACTATATTCATAATTA
* *
253098 ATTTT-AAAATGGTGCTATTTTCATAATT
1 ATTTTGAAAATGGTACTATATTCATAATT
253126 TTATTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47
Consensus pattern (30 bp):
ATTTTGAAAATGGTACTATATTCATAATTA
Found at i:263091 original size:21 final size:21
Alignment explanation
Indices: 263049--263091 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
263039 TTTCTGGGCT
* *
263049 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
263070 AGGGGAATTGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
263091 A
1 A
263092 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:263143 original size:20 final size:20
Alignment explanation
Indices: 263118--263155 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
263108 GAATGCTAGA
*
263118 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
263138 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
263156 TATAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:264887 original size:31 final size:31
Alignment explanation
Indices: 264849--264925 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
264839 GAGTCGAGGG
* * *
264849 TTACCTATGTTCTTCGGGACATATGGATTGT
1 TTACCTATGTTCTTCCGGACATATGGACTGA
*
264880 TTACCTATGTTTTTCCGGACATATGGACTGA
1 TTACCTATGTTCTTCCGGACATATGGACTGA
* *
264911 TTAACTAGGTTCTTC
1 TTACCTATGTTCTTC
264926 AAAATCTATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (31 bp):
TTACCTATGTTCTTCCGGACATATGGACTGA
Found at i:267493 original size:16 final size:16
Alignment explanation
Indices: 267472--267504 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
267462 TTAATTAAGG
267472 TTGGAAATGAATCAAT
1 TTGGAAATGAATCAAT
267488 TTGGAAATGAATCAAT
1 TTGGAAATGAATCAAT
267504 T
1 T
267505 ATATAATTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (16 bp):
TTGGAAATGAATCAAT
Found at i:270204 original size:31 final size:31
Alignment explanation
Indices: 270166--270242 Score: 136
Period size: 31 Copynumber: 2.5 Consensus size: 31
270156 GAGTCGAGGG
*
270166 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGA
270197 TTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGA
*
270228 TTACCTAGGTTCTTC
1 TTACCTATGTTCTTC
270243 AGAATCTATG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGA
Found at i:270253 original size:31 final size:31
Alignment explanation
Indices: 270166--270257 Score: 105
Period size: 31 Copynumber: 3.0 Consensus size: 31
270156 GAGTCGAGGG
* * * *
270166 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTAGGTTCTTCAGAACATATGGACTGA
* * *
270197 TTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTAGGTTCTTCAGAACATATGGACTGA
270228 TTACCTAGGTTCTTCAGAATC-TATGGACTG
1 TTACCTAGGTTCTTCAGAA-CATATGGACTG
270258 GTCTTTCGGG
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
31 55 0.98
32 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
TTACCTAGGTTCTTCAGAACATATGGACTGA
Found at i:273003 original size:3 final size:3
Alignment explanation
Indices: 272988--273089 Score: 132
Period size: 3 Copynumber: 34.0 Consensus size: 3
272978 TTTATCCATT
* * * * *
272988 TTA TTA ATA TTA TTA TTA ATA TTA TTC TTA TCA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
273036 TCA TTA TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
273084 TTA TTA
1 TTA TTA
273090 AATATATTAA
Statistics
Matches: 83, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 83 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:273527 original size:1 final size:1
Alignment explanation
Indices: 273521--273545 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
273511 CACCCACCTG
273521 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
273546 GAAGGGAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:285862 original size:20 final size:23
Alignment explanation
Indices: 285837--285894 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
285827 TATTATGCTT
285837 GAAGAAAAA-AAAA-AAAAAA-A
1 GAAGAAAAAGAAAAGAAAAAAGA
285857 GAAGAAAATAGAAAATGAAAAAAGA
1 GAAGAAAA-AGAAAA-GAAAAAAGA
285882 GAAGAAAAAGAAA
1 GAAGAAAAAGAAA
285895 GGGGGTCAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.24
21 1 0.03
22 4 0.12
24 11 0.33
25 9 0.27
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.03
Consensus pattern (23 bp):
GAAGAAAAAGAAAAGAAAAAAGA
Found at i:286899 original size:52 final size:52
Alignment explanation
Indices: 286821--287274 Score: 765
Period size: 52 Copynumber: 8.8 Consensus size: 52
286811 TATGTGCTCA
286821 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GATCAGAAC
286873 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GATCAGAAC
286925 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCAGAAC
286977 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GATCAGAAC
* *
287029 ATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCAGAAC
* *
287081 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTTGATCATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCAGAAC
* *
287133 ATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCAGAAC
287185 ATAGCATCTTCTGGAAGTGTTC-TTGAGTTATCTGATCTGGTTGGA-CAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GATCAGAAC
* *
287236 ATAGCATTTTCTGGAAGTGTTCTTTGAGATATCTGATCT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
287275 AATTGGATAG
Statistics
Matches: 387, Mismatches: 10, Indels: 10
0.95 0.02 0.02
Matches are distributed among these distances:
51 50 0.13
52 335 0.87
53 2 0.01
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.39
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCAGAAC
Found at i:288271 original size:113 final size:113
Alignment explanation
Indices: 287912--288572 Score: 1105
Period size: 113 Copynumber: 5.8 Consensus size: 113
287902 CAAAGATTCA
* * *
287912 AATTCATCACTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATTG
1 AATTCATCACTTGATGGATCAACATTACCAGA-GAA-AGTTCATAATGAGAAGAACTCATC--TG
*
287977 AAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
62 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
*
288029 AATTCATCACTTGATGGATCAACATTACCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCACTTGATGGATCAACATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
288094 AGGAAG-A-AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
* * *
288140 AATTCATCACTTGATGGATCATCGTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCACTTGATGGATCAACATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
288205 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
*
288253 AATTCATCACTTGATGGATCAACATTACCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCACTTGATGGATCAACATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
288318 AGGAAGAAGAAGTTCAT-ATGAGAAGAACTTGTTCAACCTTTTGCTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
* * *
288365 AATTCATCACTTGATGGATCATCGTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCACTTGATGGATCAACATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
288430 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
* *
288478 AATTCATCAGTTGATGGATCAACACTACCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATTCATCACTTGATGGATCAACATTACCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAG
*
288542 AAGGAAGAAAAAGTTCATAATGAGAAGAACT
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACT
288573 CATCAAGAGC
Statistics
Matches: 515, Mismatches: 25, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
111 106 0.21
112 111 0.22
113 243 0.47
115 22 0.04
116 3 0.01
117 30 0.06
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (113 bp):
AATTCATCACTTGATGGATCAACATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
Found at i:288456 original size:225 final size:225
Alignment explanation
Indices: 287912--288572 Score: 1175
Period size: 225 Copynumber: 2.9 Consensus size: 225
287902 CAAAGATTCA
* *
287912 AATTCATCACTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATTG
1 AATTCATCACTTGATGGATCATCGTTTCCAGA-GAA-AGTTCATAATGAGAAGAACTCATC--TG
*
287977 AAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTG
62 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTG
288042 ATGGATCAACATTACCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-AAAGTT
127 ATGGATCAACATTACCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAGTT
288106 CATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
192 CATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
288140 AATTCATCACTTGATGGATCATCGTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCACTTGATGGATCATCGTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
288205 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGG
288270 ATCAACATTACCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
131 ATCAACATTACCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA-AAGTTCAT
288335 -ATGAGAAGAACTTGTTCAACCTTTTGCTTG
195 AATGAGAAGAACTTGTTCAACCTTTTGCTTG
288365 AATTCATCACTTGATGGATCATCGTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCACTTGATGGATCATCGTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
288430 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCAGTTGATGG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGG
* *
288495 ATCAACACTACCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCA
131 ATCAACATTACCAGAG-AAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-AAAAGTTCA
288559 TAATGAGAAGAACT
194 TAATGAGAAGAACT
288573 CATCAAGAGC
Statistics
Matches: 421, Mismatches: 7, Indels: 12
0.96 0.02 0.03
Matches are distributed among these distances:
224 125 0.30
225 217 0.52
226 45 0.11
227 3 0.01
228 31 0.07
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (225 bp):
AATTCATCACTTGATGGATCATCGTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGG
ATCAACATTACCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTTGCTTG
Found at i:288832 original size:3 final size:3
Alignment explanation
Indices: 288817--288916 Score: 123
Period size: 3 Copynumber: 34.0 Consensus size: 3
288807 TTTATCCATT
* * * * *
288817 TTA TTA ATA TTA TTA -TA ATA TTA TTC TTA TCA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
288864 TCA TTA TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
288911 TTA TTA
1 TTA TTA
288917 AATATTAAAT
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
2 4 0.05
3 78 0.95
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:290005 original size:28 final size:29
Alignment explanation
Indices: 289956--290010 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
289946 GTCACTAAAC
289956 TGAATTTATAATATTTTAA-TTTAGTCTT
1 TGAATTTATAATATTTTAATTTTAGTCTT
* *
289984 TGAATTT-TAATTTTATTCATTTTAGTC
1 TGAATTTATAATATT-TTAATTTTAGTC
290011 CTTTTATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 6 0.26
28 10 0.43
29 7 0.30
ACGTcount: A:0.29, C:0.05, G:0.07, T:0.58
Consensus pattern (29 bp):
TGAATTTATAATATTTTAATTTTAGTCTT
Found at i:290335 original size:22 final size:20
Alignment explanation
Indices: 290294--290338 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
290284 ATAGAATTAT
**
290294 TATTTTATTATATTGTTAAA
1 TATTTTATTATATTCATAAA
290314 TATTTTGATATATATTCATAAA
1 TATTTT-AT-TATATTCATAAA
290336 TAT
1 TAT
290339 ATATAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 2 0.10
22 13 0.62
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
TATTTTATTATATTCATAAA
Done.