Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001162.1 Hibiscus syriacus cultivar Beakdansim tig00002317_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: 1560963
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 9
Found at i:408076 original size:30 final size:30
Alignment explanation
Indices: 408036--408092 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
408026 TTGGTACTTT
408036 ATATACATATATA-AACTATAAAGTATAAGC
1 ATATACATATATATAA-TATAAAGTATAAGC
*
408066 ATATATATATATATAATATAAAGTATA
1 ATATACATATATATAATATAAAGTATA
408093 TAATATAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (30 bp):
ATATACATATATATAATATAAAGTATAAGC
Found at i:408092 original size:14 final size:14
Alignment explanation
Indices: 408075--408108 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
408065 CATATATATA
408075 TATATAATATAAAG
1 TATATAATATAAAG
408089 TATATAATATAAAG
1 TATATAATATAAAG
408103 TA-ATAA
1 TATATAA
408109 AGTGTTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (14 bp):
TATATAATATAAAG
Found at i:411654 original size:21 final size:21
Alignment explanation
Indices: 411630--411699 Score: 122
Period size: 21 Copynumber: 3.3 Consensus size: 21
411620 CCTGCGACAG
411630 CCGCAATAGCGTCCGCGATGA
1 CCGCAATAGCGTCCGCGATGA
411651 CCGCAATAGCGTCCGCGATGA
1 CCGCAATAGCGTCCGCGATGA
* *
411672 CCGCAATAGCGCCCGCGACGA
1 CCGCAATAGCGTCCGCGATGA
411693 CCGCAAT
1 CCGCAAT
411700 CACGGTAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.24, C:0.37, G:0.27, T:0.11
Consensus pattern (21 bp):
CCGCAATAGCGTCCGCGATGA
Found at i:414532 original size:18 final size:18
Alignment explanation
Indices: 414509--414548 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
414499 CGTACGTGTC
*
414509 ATTTTAATAAAAATATTA
1 ATTTTAATAAAAATATAA
*
414527 ATTTTAATTAAAATATAA
1 ATTTTAATAAAAATATAA
414545 ATTT
1 ATTT
414549 GTGGTCTGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTTTAATAAAAATATAA
Found at i:417054 original size:21 final size:20
Alignment explanation
Indices: 417008--417059 Score: 86
Period size: 20 Copynumber: 2.5 Consensus size: 20
416998 ACAACACGCG
*
417008 CAAAACTTAAGGGACAAAAT
1 CAAAACTTAAAGGACAAAAT
417028 CAAAACTTAAAGGACAAAAT
1 CAAAACTTAAAGGACAAAAT
417048 CAGAAACTTAAA
1 CA-AAACTTAAA
417060 AGATTCAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 21 0.70
21 9 0.30
ACGTcount: A:0.58, C:0.15, G:0.12, T:0.15
Consensus pattern (20 bp):
CAAAACTTAAAGGACAAAAT
Found at i:419850 original size:23 final size:20
Alignment explanation
Indices: 419808--419859 Score: 52
Period size: 23 Copynumber: 2.5 Consensus size: 20
419798 ATTTTAAACC
*
419808 AAAAT-AAACACCCAAACAA
1 AAAATCAAACACACAAACAA
419827 ACAAATCAAACACACAAATCCAA
1 A-AAATCAAACACACAAA--CAA
419850 AACAATCAAA
1 AA-AATCAAA
419860 ATATTTTAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 1 0.04
20 4 0.15
21 10 0.37
22 1 0.04
23 11 0.41
ACGTcount: A:0.65, C:0.27, G:0.00, T:0.08
Consensus pattern (20 bp):
AAAATCAAACACACAAACAA
Found at i:421880 original size:20 final size:19
Alignment explanation
Indices: 421834--421888 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
421824 CATTCAAAGA
*
421834 GGGTATCGATACACGTTGAAG
1 GGGTATCGATAC-C-TAGAAG
*
421855 GAGTATCGATACCTAGCAAG
1 GGGTATCGATACCTAG-AAG
*
421875 GGGTATCAATACCT
1 GGGTATCGATACCT
421889 GTTTTAGGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 2 0.07
20 16 0.55
21 11 0.38
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (19 bp):
GGGTATCGATACCTAGAAG
Found at i:427702 original size:73 final size:74
Alignment explanation
Indices: 427595--427766 Score: 224
Period size: 73 Copynumber: 2.4 Consensus size: 74
427585 GTTAAATGAC
* * * * *
427595 TAGGGGTATCGGTACCTCTA--AGAGGTATCGGTACCCATTGGGCATTCTATTTTTCTTAGAGCC
1 TAGGGGTATCGATACC-CTATGAGGGGCATCAGTACCCATTGGGCATTCTATTTTTCTCAGAGCC
427658 AAAATTGGCA
65 AAAATTGGCA
* * *
427668 TA-GGGTATCGATACCCTATGAGGGGCATCAGTACCCATTTGGCATTCTGTTTTTCTCGGAGCCA
1 TAGGGGTATCGATACCCTATGAGGGGCATCAGTACCCATTGGGCATTCTATTTTTCTCAGAGCCA
427732 AAATTGGCA
66 AAATTGGCA
* *
427741 TAGGGGTATCGGTACCTTATGAGGGG
1 TAGGGGTATCGATACCCTATGAGGGG
427767 TATCGATACC
Statistics
Matches: 86, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
71 3 0.03
72 12 0.14
73 50 0.58
74 21 0.24
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.30
Consensus pattern (74 bp):
TAGGGGTATCGATACCCTATGAGGGGCATCAGTACCCATTGGGCATTCTATTTTTCTCAGAGCCA
AAATTGGCA
Found at i:430727 original size:2 final size:2
Alignment explanation
Indices: 430720--430744 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
430710 AGGCATGTAA
430720 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
430745 GGTCTCCAGG
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:431405 original size:19 final size:18
Alignment explanation
Indices: 431364--431406 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
431354 TTAGAACTAC
431364 TTTTA-GATGTTTCAATG
1 TTTTATGATGTTTCAATG
*
431381 TATTTATGATGTTTTAATTG
1 T-TTTATGATGTTTCAA-TG
431401 TTTTAT
1 TTTTAT
431407 CTCACCTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 4 0.18
19 14 0.64
20 3 0.14
ACGTcount: A:0.23, C:0.02, G:0.14, T:0.60
Consensus pattern (18 bp):
TTTTATGATGTTTCAATG
Found at i:431647 original size:21 final size:20
Alignment explanation
Indices: 431617--431657 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
431607 TATCGGATTT
431617 GTTTAAATGGTCTGTAATAG
1 GTTTAAATGGTCTGTAATAG
431637 GTTTAAAATGGTCTGTAATAG
1 GTTT-AAATGGTCTGTAATAG
431658 TAAACTAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.39
Consensus pattern (20 bp):
GTTTAAATGGTCTGTAATAG
Found at i:431864 original size:23 final size:22
Alignment explanation
Indices: 431829--431871 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
431819 TTATGGTTTT
* *
431829 GTTGTTAATGAAATAGTTTTAAA
1 GTTGATAAAGAAATA-TTTTAAA
431852 GTTGATAAAGAAATATTTTA
1 GTTGATAAAGAAATATTTTA
431872 TAATGGAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (22 bp):
GTTGATAAAGAAATATTTTAAA
Found at i:434343 original size:131 final size:130
Alignment explanation
Indices: 434150--434596 Score: 524
Period size: 131 Copynumber: 3.4 Consensus size: 130
434140 ATAGATTTTT
* * *
434150 GAAGATCAAATCTG-AAAAGAGATATGCTCCT-CTGCTCTTCAGGGTATATCAGATCT-AGAAAC
1 GAAGATCAAATATGAAAAAGGGATATGCT-CTGCTGCTCTTCAGGGTAGATCAGATCTGA-AAAC
* * *
434212 ATTGATTCATTCCACTACTCTTCAGGGAAGATTGAATTGAAGTAGATTTGTTCCACTGCTCCTTA
64 ATTGATTCATTCCACTACTCTTCAGGGAAGATTGAATTGAGGTAGATTTGTTCCACTACTCCTCA
434277 GG
129 GG
* * * *
434279 GAAGATCAAATATGAAAAAAGGGATTTGCTCTGCTTCTCTTTAGGGTAGATCAGATTTGAAAACA
1 GAAGATCAAATATG-AAAAAGGGATATGCTCTGCTGCTCTTCAGGGTAGATCAGATCTGAAAACA
* * * * * * *
434344 TTAATTCACTCAACTACACTTCAGGGAAGATTTAATCGAGGTAGATTTGTTCCACTACTGCTCAG
65 TTGATTCATTCCACTACTCTTCAGGGAAGATTGAATTGAGGTAGATTTGTTCCACTACTCCTCAG
434409 G
130 G
* * * * * * * *
434410 GAAAATCAAATCTGAAAAAGGGATTTGCTTTGTTGGTCTTTAGGGTAGATCAGATCTGAAAATAT
1 GAAGATCAAATATGAAAAAGGGATATGCTCTGCTGCTCTTCAGGGTAGATCAGATCTGAAAACAT
* * *
434475 TGATTCATTCCAC-AGCTTTTCAGGGAAGATTGAATTGAGGAAGACTTGTTCCACTACTCCTCAG
66 TGATTCATTCCACTA-CTCTTCAGGGAAGATTGAATTGAGGTAGATTTGTTCCACTACTCCTCAG
434539 G
130 G
** * *
434540 GAAGATCAAATATAGAAAAAGGGGATATGCTCCACTGCTCTTCAGGGCATATCAGAT
1 GAAGATCAAATAT-GAAAAA-GGGATATGCTCTGCTGCTCTTCAGGGTAGATCAGAT
434597 TTGGAAACGT
Statistics
Matches: 265, Mismatches: 46, Indels: 11
0.82 0.14 0.03
Matches are distributed among these distances:
129 14 0.05
130 111 0.42
131 112 0.42
132 28 0.11
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (130 bp):
GAAGATCAAATATGAAAAAGGGATATGCTCTGCTGCTCTTCAGGGTAGATCAGATCTGAAAACAT
TGATTCATTCCACTACTCTTCAGGGAAGATTGAATTGAGGTAGATTTGTTCCACTACTCCTCAGG
Found at i:435960 original size:1 final size:1
Alignment explanation
Indices: 435954--436002 Score: 53
Period size: 1 Copynumber: 49.0 Consensus size: 1
435944 TTATTTATTC
* * * * *
435954 TTTTTTTTGTTTTTTTTTGTTTTTTTTTGTTTTTTGTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
436003 CATTTTCATT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (1 bp):
T
Found at i:435968 original size:7 final size:7
Alignment explanation
Indices: 435956--436002 Score: 71
Period size: 7 Copynumber: 6.9 Consensus size: 7
435946 ATTTATTCTT
435956 TTTTTTG
1 TTTTTTG
435963 TTTTTT-
1 TTTTTTG
435969 TTTGTTT-
1 TTT-TTTG
435976 TTTTTTG
1 TTTTTTG
435983 TTTTTTG
1 TTTTTTG
435990 TTTTTTG
1 TTTTTTG
435997 TTTTTT
1 TTTTTT
436003 CATTTTCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
6 6 0.16
7 32 0.84
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (7 bp):
TTTTTTG
Found at i:435969 original size:10 final size:10
Alignment explanation
Indices: 435954--436002 Score: 73
Period size: 10 Copynumber: 4.8 Consensus size: 10
435944 TTATTTATTC
435954 TTTTTTTTGT
1 TTTTTTTTGT
435964 TTTTTTTTGT
1 TTTTTTTTGT
435974 TTTTTTTTGT
1 TTTTTTTTGT
435984 TTTTTGTTT-T
1 TTTTT-TTTGT
435994 TTGTTTTTT
1 TT-TTTTTT
436003 CATTTTCATT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
10 31 0.84
11 6 0.16
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (10 bp):
TTTTTTTTGT
Found at i:436008 original size:20 final size:18
Alignment explanation
Indices: 435956--436002 Score: 71
Period size: 17 Copynumber: 2.7 Consensus size: 18
435946 ATTTATTCTT
435956 TTTTTTG-TTTTTTTTTG
1 TTTTTTGTTTTTTTTTTG
*
435973 TTTTTT-TTTGTTTTTTG
1 TTTTTTGTTTTTTTTTTG
435990 TTTTTTGTTTTTT
1 TTTTTTGTTTTTT
436003 CATTTTCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 21 0.81
18 5 0.19
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (18 bp):
TTTTTTGTTTTTTTTTTG
Found at i:436035 original size:10 final size:10
Alignment explanation
Indices: 436020--436077 Score: 57
Period size: 10 Copynumber: 5.9 Consensus size: 10
436010 ATTTTCATTA
436020 TTTCTTTTCC
1 TTTCTTTTCC
436030 TTTC-TTT-C
1 TTTCTTTTCC
*
436038 TTTCTTTTCT
1 TTTCTTTTCC
*
436048 TTTCTTTTTC
1 TTTCTTTTCC
*
436058 ATTCTTCTTCC
1 TTTCTT-TTCC
*
436069 TTTTTTTTC
1 TTTCTTTTC
436078 TTCAGGAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
8 5 0.13
9 6 0.16
10 20 0.53
11 7 0.18
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTCTTTTCC
Found at i:436041 original size:18 final size:18
Alignment explanation
Indices: 436020--436054 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
436010 ATTTTCATTA
436020 TTTCTTTTCCTTTCTTTC
1 TTTCTTTTCCTTTCTTTC
*
436038 TTTCTTTTCTTTTCTTT
1 TTTCTTTTCCTTTCTTT
436055 TTCATTCTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTCTTTTCCTTTCTTTC
Found at i:436066 original size:18 final size:18
Alignment explanation
Indices: 436000--436051 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
435990 TTTTTTGTTT
436000 TTTCATTTTCATTTTCATTA
1 TTTC-TTTTC-TTTTCATTA
* * *
436020 TTTCTTTTCCTTTCTTTC
1 TTTCTTTTCTTTTCATTA
436038 TTTCTTTTCTTTTC
1 TTTCTTTTCTTTTC
436052 TTTTTCATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 19 0.68
19 5 0.18
20 4 0.14
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTCTTTTCTTTTCATTA
Found at i:440019 original size:12 final size:12
Alignment explanation
Indices: 440008--440078 Score: 52
Period size: 12 Copynumber: 5.9 Consensus size: 12
439998 GATACATATA
*
440008 CATATACGTATA
1 CATATACGTATG
* *
440020 TATATGCGTATG
1 CATATACGTATG
**
440032 TGTATACGTATG
1 CATATACGTATG
*
440044 CATATGCGTATG
1 CATATACGTATG
**
440056 CATACGCGTATG
1 CATATACGTATG
* *
440068 CGTATGCGTAT
1 CATATACGTAT
440079 CTATATGTGT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 48 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (12 bp):
CATATACGTATG
Found at i:440031 original size:6 final size:6
Alignment explanation
Indices: 440022--440078 Score: 69
Period size: 6 Copynumber: 9.5 Consensus size: 6
440012 TACGTATATA
* * * * *
440022 TATGCG TATGTG TATACG TATGCA TATGCG TATGCA TACGCG TATGCG
1 TATGCG TATGCG TATGCG TATGCG TATGCG TATGCG TATGCG TATGCG
440070 TATGCG TAT
1 TATGCG TAT
440079 CTATATGTGT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (6 bp):
TATGCG
Found at i:440036 original size:18 final size:18
Alignment explanation
Indices: 440014--440072 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
440004 TATACATATA
440014 CGTATATATATGCGTATG
1 CGTATATATATGCGTATG
* ** *
440032 TGTATACGTATGCATATG
1 CGTATATATATGCGTATG
** *
440050 CGTATGCATACGCGTATG
1 CGTATATATATGCGTATG
440068 CGTAT
1 CGTAT
440073 GCGTATCTAT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (18 bp):
CGTATATATATGCGTATG
Found at i:440042 original size:24 final size:24
Alignment explanation
Indices: 440010--440055 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
440000 TACATATACA
*
440010 TATACGTATATATATGCGTATGTG
1 TATACGTATACATATGCGTATGTG
*
440034 TATACGTATGCATATGCGTATG
1 TATACGTATACATATGCGTATG
440056 CATACGCGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (24 bp):
TATACGTATACATATGCGTATGTG
Found at i:440085 original size:12 final size:12
Alignment explanation
Indices: 440021--440091 Score: 72
Period size: 12 Copynumber: 5.9 Consensus size: 12
440011 ATACGTATAT
*
440021 ATATGCGTATGT
1 ATATGCGTATGC
* *
440033 GTATACGTATGC
1 ATATGCGTATGC
440045 ATATGCGTATGC
1 ATATGCGTATGC
*
440057 ATACGCGTATGC
1 ATATGCGTATGC
*
440069 GTATGCGTAT-C
1 ATATGCGTATGC
*
440080 TATATGTGTATG
1 -ATATGCGTATG
440092 TGTATGTATA
Statistics
Matches: 47, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
11 1 0.02
12 46 0.98
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.37
Consensus pattern (12 bp):
ATATGCGTATGC
Found at i:440091 original size:6 final size:6
Alignment explanation
Indices: 440063--440372 Score: 224
Period size: 6 Copynumber: 51.7 Consensus size: 6
440053 ATGCATACGC
* * * * * * *
440063 GTATGC GTATGC GTATCT ATATGT GTATGT GTATGT ATATCT GTATCT
1 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
* * * * *
440111 ATATGT GTATCT GTATGT GTATGT GCATGT GTATCT GTATGT GCATGT
1 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
* * * * * * *
440159 GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT GTATGT GCATGT
1 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
* * * * * *
440207 ATATGG GTATAT TTATGT GCATGT GTATGT GCATGT GTATGT GTATGT
1 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
* * * * * * * *
440255 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
* * * * * * * *
440303 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
* * *
440351 GTATAT GTATAT GTATAT GTAT
1 GTATGT GTATGT GTATGT GTAT
440373 ATATATACAT
Statistics
Matches: 270, Mismatches: 34, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 270 1.00
ACGTcount: A:0.25, C:0.06, G:0.24, T:0.46
Consensus pattern (6 bp):
GTATGT
Found at i:440373 original size:6 final size:6
Alignment explanation
Indices: 440242--440379 Score: 249
Period size: 6 Copynumber: 23.0 Consensus size: 6
440232 TATGTGCATG
* *
440242 TGTATG TGTATG TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
440290 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
*
440338 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TATATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
440380 CATATACATA
Statistics
Matches: 130, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 130 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
TGTATA
Found at i:440384 original size:6 final size:6
Alignment explanation
Indices: 440370--442732 Score: 4064
Period size: 6 Copynumber: 397.3 Consensus size: 6
440360 TATGTATATG
*
440370 TATATA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
*
440418 TATACA TATACA TATACA TATACA TATAC- -ATACA TATACA CATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
* * *
440464 TATACA CATACA TATACA CATACA TATAC- -ATACA TATACA TATGCA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
*
440510 TATACA TATGCA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
440558 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
* *
440606 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TACATA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
* *
440654 TATATA CATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
440702 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
440750 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
440798 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
440846 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
440894 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TA-ACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
440941 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
440989 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
441037 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
441085 TATACA TATAC- -ATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
441131 TATACA TATACA TATAC- -ATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
441177 TACATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 T--ATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
441227 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
441275 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
441323 TATACA TATACA TATACA TATACA TATACA TATACA TATAC- -ATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
441369 TATACA TATAC- -ATACA TATACA TATAC- -ATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
441413 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
441461 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
441509 TATACA TATACA TATAC- -ATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
441555 TATACA TATACA TATACA TATAC- -ATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
441601 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
441649 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
*
441697 TATACA TATGCA TATACA TATAC- -ATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
441743 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
441791 TATACA TATACA TATACA TATACA TATACA TATACA TATAC- -ATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
441837 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
441885 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
441933 TATAC- -ATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
*
441979 TATACA TATACA TATACA TATACA TATACATA TATACA TATACA TATGCA
1 TATACA TATACA TATACA TATACA TATAC--A TATACA TATACA TATACA
* *
442029 TATATGCA TATGCA TATGCA TATTATGCA TATACA TATACA TATACA TACATACA
1 TATA--CA TATACA TATACA TA-TA--CA TATACA TATACA TATACA T--ATACA
* * *
442084 TATACA TATACA TATACA TATACA TATACA TACATGCA TATGC- -ATGCA
1 TATACA TATACA TATACA TATACA TATACA T--ATACA TATACA TATACA
* * * * * *
442132 TATGCA TATGCA TATGCA TATGCA TATGCA TATGC- -ATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
442178 TATACA TATACA TATAC- -ATACA TATAC- -ATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
442222 TATACA TATACA TATACA TATACATA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATAC--A TATACA TATACA TATACA TATACA
442272 TATACA TATACA TATACA TATACA TATACATA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATAC--A TATACA TATACA TATACA
* * *
442322 TATACA TACATA CATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
442370 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
442418 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
*
442466 TATACA TATACA TATACA TATACA TATACA TATACA CATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
442514 TATACA TATAC- -ATACA TATACA TATACA TATACA TATAC- -ATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
442558 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
442606 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
442654 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
442702 TATACA TATACA TATACA TATACA TAT-CA TA
1 TATACA TATACA TATACA TATACA TATACA TA
442733 AATAGAGAGT
Statistics
Matches: 2270, Mismatches: 33, Indels: 109
0.94 0.01 0.05
Matches are distributed among these distances:
4 71 0.03
5 9 0.00
6 2143 0.94
7 1 0.00
8 42 0.02
9 4 0.00
ACGTcount: A:0.49, C:0.17, G:0.01, T:0.33
Consensus pattern (6 bp):
TATACA
Found at i:446676 original size:19 final size:20
Alignment explanation
Indices: 446634--446680 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
446624 CTAAATCATT
*
446634 TTTCAAAATTTCATTTTGAT
1 TTTCAAAATTTCATTTTGAC
446654 TTTCAAAA-TTCATTTTTG-C
1 TTTCAAAATTTCA-TTTTGAC
446673 TTTCAAAA
1 TTTCAAAA
446681 GAAAATCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.32, C:0.13, G:0.04, T:0.51
Consensus pattern (20 bp):
TTTCAAAATTTCATTTTGAC
Found at i:450619 original size:10 final size:11
Alignment explanation
Indices: 450604--450636 Score: 52
Period size: 10 Copynumber: 3.2 Consensus size: 11
450594 TAAATAGTGC
450604 AATGAAAA-AA
1 AATGAAAACAA
450614 AATGAAAACAA
1 AATGAAAACAA
450625 AAT-AAAACAA
1 AATGAAAACAA
450635 AA
1 AA
450637 AGACAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 17 0.77
11 5 0.23
ACGTcount: A:0.79, C:0.06, G:0.06, T:0.09
Consensus pattern (11 bp):
AATGAAAACAA
Found at i:455089 original size:81 final size:83
Alignment explanation
Indices: 454932--455091 Score: 225
Period size: 81 Copynumber: 1.9 Consensus size: 83
454922 ATGTTCAACG
* * * *
454932 AATGTCTGTAAGGTTTATGTAACATCTTTAACTCGTATTTCGAGATGTATATGTGTTATGGGTTT
1 AATGTCTGTAAGGTTTATGTAACATCTTTAA--C-TATTTCGAGATGTATACGGGTTATAGGTGT
**
454997 TGTAATGGTCAGATCCCAGAC
63 TACAATGGTCAGATCCCAGAC
455018 AATGTCTGTAAGGTTTATGTAACATCTTT-A-TATTTCGAGATGTATACGGGTTATAGGTGTTAC
1 AATGTCTGTAAGGTTTATGTAACATCTTTAACTATTTCGAGATGTATACGGGTTATAGGTGTTAC
455081 AATGGTCAGAT
66 AATGGTCAGAT
455092 TTAGACGACA
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
81 38 0.56
85 1 0.01
86 29 0.43
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (83 bp):
AATGTCTGTAAGGTTTATGTAACATCTTTAACTATTTCGAGATGTATACGGGTTATAGGTGTTAC
AATGGTCAGATCCCAGAC
Found at i:459410 original size:16 final size:17
Alignment explanation
Indices: 459385--459420 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
459375 ACCCGACCCG
*
459385 ATTATTTTATATTT-AT
1 ATTATATTATATTTAAT
459401 ATTATATTATATTTAAT
1 ATTATATTATATTTAAT
459418 ATT
1 ATT
459421 TTATGAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTATATTATATTTAAT
Found at i:459553 original size:16 final size:14
Alignment explanation
Indices: 459519--459549 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
459509 ATAATAAATA
*
459519 ATTAAAAATATATT
1 ATTAAAAACATATT
459533 ATTAAAAACATATT
1 ATTAAAAACATATT
459547 ATT
1 ATT
459550 TTAATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (14 bp):
ATTAAAAACATATT
Found at i:475952 original size:20 final size:20
Alignment explanation
Indices: 475927--475977 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
475917 ACGTGAGAAG
475927 CAGATTTATCTCACCGAGGC
1 CAGATTTATCTCACCGAGGC
**
475947 CAGATTTATCTCGTCGAGGC
1 CAGATTTATCTCACCGAGGC
475967 CAGATTTATCT
1 CAGATTTATCT
475978 GAAGAAGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (20 bp):
CAGATTTATCTCACCGAGGC
Found at i:484574 original size:144 final size:144
Alignment explanation
Indices: 484314--484602 Score: 490
Period size: 144 Copynumber: 2.0 Consensus size: 144
484304 GGAGGAAATA
* *
484314 GAGAATGATGATTGTAATATTAGAGTATTAGATGTCACAAGTATTGCCTGAAATTTGAGAATGTT
1 GAGAATGATGATTGTAATATGAGAGTATCAGATGTCACAAGTATTGCCTGAAATTTGAGAATGTT
* * * * *
484379 GTGTCAAAGAACAAAAATATTATGTGTTTGTCATTTATGTTTCTAGGCTTTAATTATGTCTTTTA
66 GTGCCAAAGAACAAAAACATTATGTGTTTGTCATTTATGTTTCTAGACTTTAATTATATATTTTA
484444 TTATGGTGTTTTAT
131 TTATGGTGTTTTAT
*
484458 GAGAATGATGATTGTAATACTGA-AGTATCAGATGTCACAAGTATTGCCTGAAATTTTAGAATGT
1 GAGAATGATGATTGTAATA-TGAGAGTATCAGATGTCACAAGTATTGCCTGAAATTTGAGAATGT
484522 TGTGCCAAAGAACAAAAACATTATGTGTTTGTCATTTATGTTTCTAGACTTTAATTATATATTTT
65 TGTGCCAAAGAACAAAAACATTATGTGTTTGTCATTTATGTTTCTAGACTTTAATTATATATTTT
484587 ATTATGGTGTTTTAT
130 ATTATGGTGTTTTAT
484602 G
1 G
484603 TACTTTAAGA
Statistics
Matches: 136, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
144 134 0.99
145 2 0.01
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (144 bp):
GAGAATGATGATTGTAATATGAGAGTATCAGATGTCACAAGTATTGCCTGAAATTTGAGAATGTT
GTGCCAAAGAACAAAAACATTATGTGTTTGTCATTTATGTTTCTAGACTTTAATTATATATTTTA
TTATGGTGTTTTAT
Found at i:487095 original size:21 final size:20
Alignment explanation
Indices: 487071--487115 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
487061 AAAATGAAAG
*
487071 TTTAGGTACTAAAACGGATAA
1 TTTAGGTA-TAAAACGCATAA
* *
487092 TTTATGTATTAAACGCATAA
1 TTTAGGTATAAAACGCATAA
487112 TTTA
1 TTTA
487116 TCCATAATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (20 bp):
TTTAGGTATAAAACGCATAA
Found at i:488450 original size:19 final size:19
Alignment explanation
Indices: 488428--488496 Score: 122
Period size: 19 Copynumber: 3.7 Consensus size: 19
488418 GAGTATTTGG
488428 CGACCTATGGAGCACTTGA
1 CGACCTATGGAGCACTTGA
*
488447 CGACCTATGGAGCACTTGG
1 CGACCTATGGAGCACTTGA
488466 CGACCTATGGAGCACTTGA
1 CGACCTATGGAGCACTTGA
488485 CGA-CTATGGAGC
1 CGACCTATGGAGC
488497 TACAACAGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
18 9 0.19
19 39 0.81
ACGTcount: A:0.25, C:0.26, G:0.29, T:0.20
Consensus pattern (19 bp):
CGACCTATGGAGCACTTGA
Found at i:488475 original size:38 final size:37
Alignment explanation
Indices: 488424--488496 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 37
488414 TAAGGAGTAT
488424 TTGGCGACCTATGGAGCACTTGACGACCTATGGAGCAC
1 TTGGCGACCTATGGAGCACTTGACGA-CTATGGAGCAC
488462 TTGGCGACCTATGGAGCACTTGACGACTATGGAGC
1 TTGGCGACCTATGGAGCACTTGACGACTATGGAGC
488497 TACAACAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 9 0.26
38 26 0.74
ACGTcount: A:0.23, C:0.25, G:0.30, T:0.22
Consensus pattern (37 bp):
TTGGCGACCTATGGAGCACTTGACGACTATGGAGCAC
Found at i:488579 original size:19 final size:18
Alignment explanation
Indices: 488552--488607 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
488542 TGTCACAATA
*
488552 AACACTTGACGACCTATTG
1 AACATTTGACGACCTA-TG
*
488571 AACATTTGACGACTTATG
1 AACATTTGACGACCTATG
* **
488589 TACATTTGATAACCTATG
1 AACATTTGACGACCTATG
488607 A
1 A
488608 GATCACGGTA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
18 16 0.53
19 14 0.47
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (18 bp):
AACATTTGACGACCTATG
Found at i:488595 original size:18 final size:19
Alignment explanation
Indices: 488552--488597 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
488542 TGTCACAATA
*
488552 AACACTTGACGACCTATTG
1 AACATTTGACGACCTATTG
*
488571 AACATTTGACGACTTA-TG
1 AACATTTGACGACCTATTG
*
488589 TACATTTGA
1 AACATTTGA
488598 TAACCTATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (19 bp):
AACATTTGACGACCTATTG
Found at i:496847 original size:2 final size:2
Alignment explanation
Indices: 496842--496894 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
496832 TAATATTCTA
496842 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
496884 A- AT -T AT AT AT A
1 AT AT AT AT AT AT A
496895 ATTTTTTATC
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 47 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:496939 original size:2 final size:2
Alignment explanation
Indices: 496932--496962 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
496922 TTAATACCAT
496932 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
496963 TAGTGTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:496981 original size:10 final size:10
Alignment explanation
Indices: 496968--497008 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
496958 TATATTAGTG
*
496968 TTTTTTATTC
1 TTTTTTATTA
*
496978 TTTTTTACTA
1 TTTTTTATTA
496988 TTTATTTATTA
1 TTT-TTTATTA
496999 TTTTTTATTA
1 TTTTTTATTA
497009 AATACTATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 18 0.67
11 9 0.33
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTTATTA
Found at i:497019 original size:2 final size:2
Alignment explanation
Indices: 497014--497038 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
497004 TATTAAATAC
497014 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 T
497039 TACCTAACAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:497288 original size:26 final size:25
Alignment explanation
Indices: 497243--497326 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 25
497233 ATATTTTTAT
*
497243 TTTTTCATTATTATTATTATTATTTTG
1 TTTTTCA-T-TTATTTTTATTATTTTG
* *
497270 TTTTTCATTTAATTTTTATTCTTTTT
1 TTTTTCATTT-ATTTTTATTATTTTG
* * *
497296 TTTTATTATTTCTTTTTATTTTATTTG
1 TTTT-TCATTTATTTTTATTAT-TTTG
497323 TTTT
1 TTTT
497327 CGTAATTTAG
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
25 2 0.04
26 26 0.55
27 19 0.40
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (25 bp):
TTTTTCATTTATTTTTATTATTTTG
Found at i:497298 original size:13 final size:13
Alignment explanation
Indices: 497282--497315 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
497272 TTTCATTTAA
* *
497282 TTTTTATTCTTTT
1 TTTTTATTATTTC
497295 TTTTTATTATTTC
1 TTTTTATTATTTC
497308 TTTTTATT
1 TTTTTATT
497316 TTATTTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTATTATTTC
Found at i:498056 original size:23 final size:24
Alignment explanation
Indices: 498030--498097 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
498020 CAAATCAAAT
498030 AAAATAAAAGAAGAAA-AA-AATG-A
1 AAAATAAAA-AA-AAATAATAATGAA
*
498053 AAAACAAAAAAAAATAATAATGAA
1 AAAATAAAAAAAAATAATAATGAA
*
498077 AAAATAAAAAAATATATATAA
1 AAAATAAAAAAAAATA-ATAA
498098 CTATTAGGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
21 3 0.08
22 4 0.11
23 12 0.32
24 15 0.39
25 4 0.11
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.15
Consensus pattern (24 bp):
AAAATAAAAAAAAATAATAATGAA
Found at i:498079 original size:24 final size:24
Alignment explanation
Indices: 498048--498094 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
498038 AGAAGAAAAA
498048 AATGAAAAACAAAAAAAAATA-AT
1 AATGAAAAACAAAAAAAAATATAT
*
498071 AATGAAAAA-ATAAAAAAATATAT
1 AATGAAAAACAAAAAAAAATATAT
498094 A
1 A
498095 TAACTATTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.17
Consensus pattern (24 bp):
AATGAAAAACAAAAAAAAATATAT
Found at i:498280 original size:2 final size:2
Alignment explanation
Indices: 498275--498314 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
498265 AAGGTAAGGA
498275 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
498315 GTATTTAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:498323 original size:12 final size:11
Alignment explanation
Indices: 498274--498347 Score: 67
Period size: 12 Copynumber: 6.4 Consensus size: 11
498264 AAAGGTAAGG
498274 AATATATATAT
1 AATATATATAT
498285 ATATATATATAT
1 A-ATATATATAT
498297 ATATATATATAT
1 A-ATATATATAT
*
498309 AATATAGTATTT
1 AATATA-TATAT
* *
498321 AATAAATAAAT
1 AATATATATAT
* *
498332 AAATAAATAAAT
1 -AATATATATAT
498344 AATA
1 AATA
498348 GTAAAAAAGA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
11 13 0.23
12 43 0.77
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (11 bp):
AATATATATAT
Found at i:498328 original size:4 final size:4
Alignment explanation
Indices: 498321--498345 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
498311 TATAGTATTT
498321 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
498346 TAGTAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:498484 original size:13 final size:12
Alignment explanation
Indices: 498408--498489 Score: 53
Period size: 12 Copynumber: 6.7 Consensus size: 12
498398 ATAAAAAAAG
498408 AAAA-AAATAAT
1 AAAATAAATAAT
*
498419 GATAATAAATAA-
1 -AAAATAAATAAT
498431 ATAAATAAATATATT
1 A-AAATAAATA-A-T
* * *
498446 AGAAT-ATTAGT
1 AAAATAAATAAT
*
498457 AAAACAAATAAT
1 AAAATAAATAAT
498469 AAAATAAATGAAT
1 AAAATAAAT-AAT
498482 AAAATAAA
1 AAAATAAA
498490 ATATACATAC
Statistics
Matches: 53, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
11 5 0.09
12 23 0.43
13 21 0.40
14 3 0.06
15 1 0.02
ACGTcount: A:0.68, C:0.01, G:0.05, T:0.26
Consensus pattern (12 bp):
AAAATAAATAAT
Found at i:500453 original size:79 final size:83
Alignment explanation
Indices: 500290--500520 Score: 262
Period size: 80 Copynumber: 2.9 Consensus size: 83
500280 TTGCGGCAAG
* *** * *
500290 TATGCTCTTGAGCTGAATACGATCGATCTCGAAAGTTTGTTGACAGACAA--CCTTCTCGCCTTT
1 TATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTGTTGACAGA-AAGCCCTTCTCGCC-TT
*
500353 GAGTTATGCTGTAAATTTGA
64 GAGCTATGCTGTAAATTTGA
*
500373 TATGCCCTTGAGCT-AATGTAATC-AACTTG-AGGTTTGTTGACA-AAAGCCCTTCTCGCCTTGA
1 TATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTGTTGACAGAAAGCCCTTCTCGCCTTGA
500434 GCTATGCTGTAAATTTGA
66 GCTATGCTGTAAATTTGA
* * * * * *
500452 TATGTCTTTGAGCTGAGTGTAATCGAACTCGAAGG-TT-TTGACATATAGCCCTTCTCGCCTGGA
1 TATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTGTTGACAGAAAGCCCTTCTCGCCTTGA
500515 GCTATG
66 GCTATG
500521 TTGCAATAGG
Statistics
Matches: 128, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
78 2 0.02
79 34 0.27
80 36 0.28
81 34 0.27
82 9 0.07
83 13 0.10
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (83 bp):
TATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTGTTGACAGAAAGCCCTTCTCGCCTTGA
GCTATGCTGTAAATTTGA
Found at i:516744 original size:26 final size:24
Alignment explanation
Indices: 516715--516786 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
516705 AATGTCCAAC
516715 AAATTTAACAAAATAAAGTAAGTATT
1 AAATTTAACAAAATAAAGTAA--ATT
*
516741 AAA-TGAGA-AATAATAAA--AAATT
1 AAATTTA-ACAA-AATAAAGTAAATT
516763 ACAATTTAACAAAATAAAGTAAAT
1 A-AATTTAACAAAATAAAGTAAAT
516787 ACAAATATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 9 0.24
24 6 0.16
25 8 0.22
26 10 0.27
ACGTcount: A:0.62, C:0.04, G:0.07, T:0.26
Consensus pattern (24 bp):
AAATTTAACAAAATAAAGTAAATT
Found at i:517480 original size:24 final size:24
Alignment explanation
Indices: 517460--517506 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
517450 AAATTTGTTC
517460 TTGGTCAATACCCGGACTTTGATA
1 TTGGTCAATACCCGGACTTTGATA
* *
517484 TTGGTCAATACTCGGATTTTGAT
1 TTGGTCAATACCCGGACTTTGAT
517507 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATACCCGGACTTTGATA
Found at i:517697 original size:12 final size:12
Alignment explanation
Indices: 517680--517716 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
517670 ATATAATCCT
517680 GAAGAAGAAAAA
1 GAAGAAGAAAAA
517692 GAAGAAGAAAAA
1 GAAGAAGAAAAA
517704 GAAGAAGAAAAA
1 GAAGAAGAAAAA
517716 G
1 G
517717 TCCCCGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:520041 original size:33 final size:33
Alignment explanation
Indices: 519999--520125 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
519989 GGAAATTACT
519999 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
***
520032 ATCGCAATGCGAAATGAAAATCGCAACTCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
520064 TTTCACAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
520098 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
520126 CGAATTTAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
32 1 0.01
33 79 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:520132 original size:66 final size:66
Alignment explanation
Indices: 520003--520132 Score: 233
Period size: 66 Copynumber: 2.0 Consensus size: 66
519993 ATTACTATCG
* *
520003 CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACTCTAATTTC
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTC
520068 A
66 A
*
520069 CAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
520133 AATTTCGCGT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.17
Consensus pattern (66 bp):
CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTC
A
Found at i:520157 original size:14 final size:14
Alignment explanation
Indices: 520140--520196 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
520130 TTTAATTTCG
520140 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
520154 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
520173 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
520187 CGTTGCGATT
1 CGTTGCGATT
520197 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:520176 original size:33 final size:33
Alignment explanation
Indices: 520125--520215 Score: 155
Period size: 33 Copynumber: 2.8 Consensus size: 33
520115 AAATCGCAAC
* *
520125 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
520158 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
520191 GCGATTTTCATTTCGCATTGCGATT
1 GCGATTTTCATTTCGCGTTGCGATT
520216 GTACTTTTTG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:520178 original size:19 final size:19
Alignment explanation
Indices: 520154--520215 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
520144 GCGATTCTCT
520154 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
520173 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
520187 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
520206 CATTGCGATT
1 CGTTGCGATT
520216 GTACTTTTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 19 0.54
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:520340 original size:14 final size:14
Alignment explanation
Indices: 520321--520357 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
520311 CATCAATTAA
520321 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
520335 ACAAATCACCTTTT
1 ACAAATCAACTTTT
520349 ACAAATCAA
1 ACAAATCAA
520358 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:521777 original size:21 final size:21
Alignment explanation
Indices: 521711--521777 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
521701 GTGAATCGGG
*
521711 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
521731 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
521753 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
521774 CTCT
1 CTCT
521778 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:521796 original size:42 final size:41
Alignment explanation
Indices: 521711--521831 Score: 109
Period size: 42 Copynumber: 2.9 Consensus size: 41
521701 GTGAATCGGG
* * * *
521711 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
521753 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
521795 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACA
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACA
521832 TGCGAGTCGG
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 55 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:522206 original size:91 final size:91
Alignment explanation
Indices: 522051--522233 Score: 257
Period size: 91 Copynumber: 2.0 Consensus size: 91
522041 ATTTCAAACT
*
522051 TTCAACCAAAAGACAAACAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAG
1 TTCAACCAAAAGACAAACAAGACAAATACTAACTTCACAGTATTAAAGAATACACAGTTTAGCAG
*
522116 AATTGGCAGCAACCGAATAAATTTAC
66 AATTGGCAGCAACCAAATAAATTTAC
* *
522142 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTTACAGTATT-AATAA-ACA-A-TTTA
1 TTCAACCAAAAGAC-AAAC---AAGACAAATACTAACTTCACAGTATTAAAGAATACACAGTTTA
*
522203 GCAGTATTGGCAGCAACCAAATAAATTTAC
62 GCAGAATTGGCAGCAACCAAATAAATTTAC
522233 T
1 T
522234 AAGCAATCTA
Statistics
Matches: 83, Mismatches: 5, Indels: 8
0.86 0.05 0.08
Matches are distributed among these distances:
91 47 0.57
92 5 0.06
93 3 0.04
94 4 0.05
95 24 0.29
ACGTcount: A:0.48, C:0.19, G:0.11, T:0.22
Consensus pattern (91 bp):
TTCAACCAAAAGACAAACAAGACAAATACTAACTTCACAGTATTAAAGAATACACAGTTTAGCAG
AATTGGCAGCAACCAAATAAATTTAC
Found at i:524001 original size:33 final size:33
Alignment explanation
Indices: 523944--524078 Score: 153
Period size: 33 Copynumber: 3.9 Consensus size: 33
523934 ACGAGATAAT
**
523944 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGAAAATCGCAACGA
* **
523978 GAGAATCACAACGCGAAATGACTATCGCAACGCGAAA
1 GAGAATCGCAACGCGAAATGAAAATCGCAA--CG--A
* *
524015 TGAAAATCGCAACGCGAAATGAAAATTGCAACGA
1 -GAGAATCGCAACGCGAAATGAAAATCGCAACGA
524049 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGAAAATCGCAA
524079 TGCGATTTTG
Statistics
Matches: 88, Mismatches: 8, Indels: 11
0.82 0.07 0.10
Matches are distributed among these distances:
33 44 0.50
34 14 0.16
35 2 0.02
36 2 0.02
37 1 0.01
38 25 0.28
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:524010 original size:19 final size:19
Alignment explanation
Indices: 523919--524083 Score: 125
Period size: 19 Copynumber: 9.1 Consensus size: 19
523909 TCTTTTGGTT
* *
523919 GAAATGAAAATCGCAACGA
1 GAAATGACAATCGCAACGC
*
523938 GATAATGAGAATCGCAACGC
1 GA-AATGACAATCGCAACGC
*
523958 GGAAATGACTATCGCAA--C
1 -GAAATGACAATCGCAACGC
* *
523976 G--A-GAGAATCACAACGC
1 GAAATGACAATCGCAACGC
*
523992 GAAATGACTATCGCAACGC
1 GAAATGACAATCGCAACGC
*
524011 GAAATGAAAATCGCAACGC
1 GAAATGACAATCGCAACGC
* *
524030 GAAATGAAAATTGCAA--C
1 GAAATGACAATCGCAACGC
*
524047 G--A-GAGAATCGCAACGC
1 GAAATGACAATCGCAACGC
* *
524063 GAAATGAAAATCGCAATGC
1 GAAATGACAATCGCAACGC
524082 GA
1 GA
524084 TTTTGGTTTC
Statistics
Matches: 117, Mismatches: 17, Indels: 24
0.74 0.11 0.15
Matches are distributed among these distances:
14 17 0.15
15 2 0.02
16 4 0.03
17 3 0.03
18 3 0.03
19 59 0.50
20 27 0.23
21 2 0.02
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGACAATCGCAACGC
Found at i:524112 original size:19 final size:19
Alignment explanation
Indices: 524079--524123 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
524069 AAAATCGCAA
*
524079 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
524098 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
524117 TGCGATT
1 TGCGATT
524124 CTCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:524719 original size:20 final size:20
Alignment explanation
Indices: 524696--524772 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
524686 CGATAGTAAG
*
524696 ATTCGCATTGCAATTTACGT
1 ATTCGCATTGCAATTTACCT
* * *
524716 ATTCGCGTTGCGATTTTCCT
1 ATTCGCATTGCAATTTACCT
* *
524736 AATTCGCATTGCGATTTACTT
1 -ATTCGCATTGCAATTTACCT
*
524757 ATTCGTATTGCGAATT
1 ATTCGCATTGC-AATT
524773 GGGAAAATCA
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
20 26 0.57
21 20 0.43
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (20 bp):
ATTCGCATTGCAATTTACCT
Found at i:524824 original size:20 final size:20
Alignment explanation
Indices: 524799--524873 Score: 73
Period size: 20 Copynumber: 3.7 Consensus size: 20
524789 GAAATTGAAA
524799 AATCGCATTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAT
* * *
524819 AATCGCGTTGCGAATTAG-GAA
1 AATCGCATTGCG-A-TAGTCAT
*
524840 AATTGCATTGCGATAGTCAGT
1 AATCGCATTGCGATAGTCA-T
524861 -ATCGCATTGCGAT
1 AATCGCATTGCGAT
524874 TTTCCAAATT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
19 3 0.07
20 25 0.58
21 12 0.28
22 3 0.07
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.29
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAT
Found at i:524889 original size:41 final size:42
Alignment explanation
Indices: 524796--524894 Score: 105
Period size: 41 Copynumber: 2.4 Consensus size: 42
524786 TGCGAAATTG
* * *
524796 AAAAATCGCATTGCGATAGTCATAATCGCGTTGCGAATTAGG
1 AAAATTCGCATTGCGATAGTCATAATCGCATTGCGAATTAGC
**
524838 AAAATT-GCATTGCGATAGTCAGT-ATCGCATTGCG-ATTTTC
1 AAAATTCGCATTGCGATAGTCA-TAATCGCATTGCGAATTAGC
* *
524878 CAAATTCGCATTACGAT
1 AAAATTCGCATTGCGAT
524895 TTACTTATTC
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
40 8 0.17
41 34 0.71
42 6 0.12
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (42 bp):
AAAATTCGCATTGCGATAGTCATAATCGCATTGCGAATTAGC
Found at i:524960 original size:144 final size:144
Alignment explanation
Indices: 524718--524977 Score: 493
Period size: 144 Copynumber: 1.8 Consensus size: 144
524708 ATTTACGTAT
* * *
524718 TCGCGTTGCGATTTTCCTAATTCGCATTGCGATTTACTTATTCGTATTGCGAATTGGGAAAATCA
1 TCGCATTGCGATTTTCCAAATTCGCATTACGATTTACTTATTCGTATTGCGAATTGGGAAAATCA
524783 CAATGCGAAATTGAAAAATCGCATTGCGATAGTCATAATCGCGTTGCGAATTAGGAAAATTGCAT
66 CAATGCGAAATTGAAAAATCGCATTGCGATAGTCATAATCGCGTTGCGAATTAGGAAAATTGCAT
524848 TGCGATAGTCAGTA
131 TGCGATAGTCAGTA
524862 TCGCATTGCGATTTTCCAAATTCGCATTACGATTTACTTATTCGTATTGCGAATTGGGAAAATCA
1 TCGCATTGCGATTTTCCAAATTCGCATTACGATTTACTTATTCGTATTGCGAATTGGGAAAATCA
524927 CAATGCGAAATTGAAAAATCGCATTGCGATAGTCATAATCGCGTTGCGAAT
66 CAATGCGAAATTGAAAAATCGCATTGCGATAGTCATAATCGCGTTGCGAAT
524978 CTGTAAACTG
Statistics
Matches: 113, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
144 113 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Consensus pattern (144 bp):
TCGCATTGCGATTTTCCAAATTCGCATTACGATTTACTTATTCGTATTGCGAATTGGGAAAATCA
CAATGCGAAATTGAAAAATCGCATTGCGATAGTCATAATCGCGTTGCGAATTAGGAAAATTGCAT
TGCGATAGTCAGTA
Found at i:537834 original size:60 final size:60
Alignment explanation
Indices: 537734--537846 Score: 154
Period size: 60 Copynumber: 1.9 Consensus size: 60
537724 TATGGTTTTT
*
537734 ATTTTAAATTAGTCCCTAAACTTTTAAATATACCAATTTCATCCTTAAACTATGACTATA
1 ATTTTAAATTAGTCCCTAAACTTTTAAATATACCAATTTCATCCTCAAACTATGACTATA
** * *** *
537794 ATTTTAAATTAGTCTTTAAACTTTTCAATATTTTATTTTCATCCTCAAACTAT
1 ATTTTAAATTAGTCCCTAAACTTTTAAATATACCAATTTCATCCTCAAACTAT
537847 TTTCTTCATT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.35, C:0.17, G:0.03, T:0.45
Consensus pattern (60 bp):
ATTTTAAATTAGTCCCTAAACTTTTAAATATACCAATTTCATCCTCAAACTATGACTATA
Found at i:542076 original size:59 final size:59
Alignment explanation
Indices: 542007--542118 Score: 181
Period size: 59 Copynumber: 1.9 Consensus size: 59
541997 ACAAGGAAGG
*
542007 AAATCATACTAATGGTATGGA-TTTTCACATAGGGCATTTCATGTGCTAAAATGGTAACA
1 AAATCATACTAATGGTATGGATTTTTCA-ATAGGGCACTTCATGTGCTAAAATGGTAACA
* *
542066 AAATCATACTAATGGTATGGATTTTTGAATAGGGCACTTCTTGTGCTAAAATG
1 AAATCATACTAATGGTATGGATTTTTCAATAGGGCACTTCATGTGCTAAAATG
542119 AAAGGGGAAG
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
59 44 0.90
60 5 0.10
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (59 bp):
AAATCATACTAATGGTATGGATTTTTCAATAGGGCACTTCATGTGCTAAAATGGTAACA
Found at i:542301 original size:17 final size:18
Alignment explanation
Indices: 542279--542317 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
542269 AGATTATAGT
542279 ATATTCATTGGA-ATTAA
1 ATATTCATTGGAGATTAA
*
542296 ATATTCCTTGGAGATTAA
1 ATATTCATTGGAGATTAA
542314 ATAT
1 ATAT
542318 CAGAATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (18 bp):
ATATTCATTGGAGATTAA
Found at i:551013 original size:36 final size:36
Alignment explanation
Indices: 550966--551111 Score: 240
Period size: 36 Copynumber: 4.1 Consensus size: 36
550956 ACATGCTTAA
*
550966 TCTTCAGCTTTTTCCTTCATCTTTGCTCAGTGAATT
1 TCTTCAGCTTTTTCCTTCAGCTTTGCTCAGTGAATT
* *
551002 TCTTCAGCTTTTTCCTTCAACTTTGCTCAGTAAATT
1 TCTTCAGCTTTTTCCTTCAGCTTTGCTCAGTGAATT
551038 TCTTCAGCTTTTTCCTTCAGCTTTGCTCAGTGAA-T
1 TCTTCAGCTTTTTCCTTCAGCTTTGCTCAGTGAATT
* *
551073 TCTTCAACTTTTTTCTTCAGCTTTGCTCAGTGAATT
1 TCTTCAGCTTTTTCCTTCAGCTTTGCTCAGTGAATT
551109 TCT
1 TCT
551112 CATCCTTTAC
Statistics
Matches: 103, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
35 33 0.32
36 70 0.68
ACGTcount: A:0.16, C:0.25, G:0.11, T:0.49
Consensus pattern (36 bp):
TCTTCAGCTTTTTCCTTCAGCTTTGCTCAGTGAATT
Found at i:554493 original size:16 final size:16
Alignment explanation
Indices: 554472--554507 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
554462 AATTGGTTGT
554472 ACCACCTGATGGCTGA
1 ACCACCTGATGGCTGA
*
554488 ACCACCTGATGGTTGA
1 ACCACCTGATGGCTGA
554504 ACCA
1 ACCA
554508 TACAGGCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.31, G:0.22, T:0.19
Consensus pattern (16 bp):
ACCACCTGATGGCTGA
Found at i:558774 original size:6 final size:6
Alignment explanation
Indices: 558763--558795 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
558753 AATTTATAGT
558763 AAAATA AAAATA AAAAT- AAAATA AAAACTA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAA-TA AAA
558796 CGATTATCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 5 0.20
6 15 0.60
7 5 0.20
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:558780 original size:12 final size:12
Alignment explanation
Indices: 558763--558795 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
558753 AATTTATAGT
558763 AAAATAAAAATA
1 AAAATAAAAATA
558775 AAAAT-AAAATA
1 AAAATAAAAATA
558786 AAAACTAAAA
1 AAAA-TAAAA
558796 CGATTATCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.53
12 6 0.32
13 3 0.16
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAATAAAAATA
Found at i:558784 original size:17 final size:18
Alignment explanation
Indices: 558762--558795 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
558752 TAATTTATAG
558762 TAAAATAAAAA-TAAAAA
1 TAAAATAAAAACTAAAAA
558779 TAAAATAAAAACTAAAA
1 TAAAATAAAAACTAAAA
558796 CGATTATCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (18 bp):
TAAAATAAAAACTAAAAA
Found at i:559951 original size:10 final size:10
Alignment explanation
Indices: 559938--559989 Score: 54
Period size: 10 Copynumber: 5.2 Consensus size: 10
559928 ATTTATCATA
*
559938 AATAATATGT
1 AATAATATAT
559948 AATAATATAT
1 AATAATATAT
*
559958 AAT-GTATAT
1 AATAATATAT
559967 ATATAATGATAT
1 A-ATAAT-ATAT
559979 AAT-ATATAT
1 AATAATATAT
559988 AA
1 AA
559990 ACACTACAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
9 12 0.33
10 16 0.44
11 3 0.08
12 5 0.14
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (10 bp):
AATAATATAT
Found at i:559968 original size:13 final size:15
Alignment explanation
Indices: 559949--559986 Score: 62
Period size: 13 Copynumber: 2.7 Consensus size: 15
559939 ATAATATGTA
559949 ATAATATATAATG-T
1 ATAATATATAATGAT
559963 AT-ATATATAATGAT
1 ATAATATATAATGAT
559977 ATAATATATA
1 ATAATATATA
559987 TAAACACTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 10 0.45
14 5 0.23
15 7 0.32
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (15 bp):
ATAATATATAATGAT
Found at i:560123 original size:25 final size:24
Alignment explanation
Indices: 560087--560141 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
560077 TATAGTATGC
560087 ATATAT-TATATA-ATATA-AACATA
1 ATATATATATATACA-ATACAA-ATA
560110 ATATATATACTATACAATACAAATA
1 ATATATATA-TATACAATACAAATA
560135 ATATATA
1 ATATATA
560142 GTCATTATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 6 0.21
24 2 0.07
25 17 0.61
26 3 0.11
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.36
Consensus pattern (24 bp):
ATATATATATATACAATACAAATA
Found at i:560128 original size:27 final size:25
Alignment explanation
Indices: 560087--560141 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 25
560077 TATAGTATGC
* *
560087 ATATATTATATAATATAAACATAATAT
1 ATATACTATACAATA-AAA-ATAATAT
*
560114 ATATACTATACAATACAAATAATAT
1 ATATACTATACAATAAAAATAATAT
560139 ATA
1 ATA
560142 GTCATTATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 10 0.40
26 2 0.08
27 13 0.52
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.36
Consensus pattern (25 bp):
ATATACTATACAATAAAAATAATAT
Found at i:560189 original size:16 final size:16
Alignment explanation
Indices: 560158--560191 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
560148 ATACTATATA
*
560158 ATATAAATAGACTAAT
1 ATATAAATAGAATAAT
*
560174 ATATAAATATAATAAT
1 ATATAAATAGAATAAT
560190 AT
1 AT
560192 TATGCAAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (16 bp):
ATATAAATAGAATAAT
Found at i:561186 original size:2 final size:2
Alignment explanation
Indices: 561179--561224 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
561169 ATAATCGTGC
561179 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
561221 AT AT
1 AT AT
561225 TGAAGAGGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:561710 original size:15 final size:15
Alignment explanation
Indices: 561690--561728 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
561680 GTTTACTTTA
*
561690 GAATGATTAAGCGTT
1 GAATGATTAAACGTT
*
561705 GAATGATTTAAATGTT
1 GAATGA-TTAAACGTT
561721 GAATGATT
1 GAATGATT
561729 CAGAGGCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (15 bp):
GAATGATTAAACGTT
Found at i:561839 original size:23 final size:23
Alignment explanation
Indices: 561809--561872 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
561799 TACTTTGATG
*
561809 CTGAATCATTCAGCACTGTTTTA
1 CTGAATCAGTCAGCACTGTTTTA
*
561832 CTGAATCAGTCAGCACTGTTTTG
1 CTGAATCAGTCAGCACTGTTTTA
*
561855 TTGAATCAGTCAGCACTG
1 CTGAATCAGTCAGCACTG
561873 AATCATTTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (23 bp):
CTGAATCAGTCAGCACTGTTTTA
Found at i:563409 original size:5 final size:5
Alignment explanation
Indices: 563399--563426 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
563389 CTGGCTATGC
563399 TCTGT TCTGT TCTGT TCTGT TCTGT TCT
1 TCTGT TCTGT TCTGT TCTGT TCTGT TCT
563427 TTAACTGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.21, G:0.18, T:0.61
Consensus pattern (5 bp):
TCTGT
Found at i:564723 original size:24 final size:24
Alignment explanation
Indices: 564675--564720 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
564665 AAACACCACC
*
564675 AAATACATTCAACATATAAAAATA
1 AAATACATTCAACATAGAAAAATA
*
564699 AAATA-ATTCAA-ATAGACAAATA
1 AAATACATTCAACATAGAAAAATA
564721 TAATGACAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 9 0.45
23 6 0.30
24 5 0.25
ACGTcount: A:0.63, C:0.11, G:0.02, T:0.24
Consensus pattern (24 bp):
AAATACATTCAACATAGAAAAATA
Found at i:568180 original size:23 final size:24
Alignment explanation
Indices: 568146--568192 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
568136 AAATCTTATA
*
568146 TGGCACTACGGTGC-ATTTCTACG
1 TGGCACTACGGTGCAATTTATACG
*
568169 TGGCACTTCGGTGCAATTTATACG
1 TGGCACTACGGTGCAATTTATACG
568193 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (24 bp):
TGGCACTACGGTGCAATTTATACG
Found at i:568887 original size:12 final size:12
Alignment explanation
Indices: 568847--568879 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
568837 ATTTTCACTT
568847 TTCATGGTATTG
1 TTCATGGTATTG
*
568859 TTCATAGTATTG
1 TTCATGGTATTG
568871 TTCATGGTA
1 TTCATGGTA
568880 CTATTCATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.21, C:0.09, G:0.21, T:0.48
Consensus pattern (12 bp):
TTCATGGTATTG
Found at i:573844 original size:39 final size:39
Alignment explanation
Indices: 573739--573849 Score: 168
Period size: 39 Copynumber: 2.8 Consensus size: 39
573729 GTGCACGACA
* * *
573739 TCTTCAGGCAAAATAGGAAGATTCCAAACTTACCTAGCG
1 TCTTCAGGCAAAATAGGAAGACTCCAAGCTTACATAGCG
573778 TCTTCAGGCAAAATAGGAAGACTCCAAGCTTACATAGCG
1 TCTTCAGGCAAAATAGGAAGACTCCAAGCTTACATAGCG
* * *
573817 TCTTCAGGAAAAATAGGAAGACGCCAAGTTTAC
1 TCTTCAGGCAAAATAGGAAGACTCCAAGCTTAC
573850 CTGGCATCTT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 66 1.00
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (39 bp):
TCTTCAGGCAAAATAGGAAGACTCCAAGCTTACATAGCG
Found at i:574766 original size:27 final size:29
Alignment explanation
Indices: 574712--574776 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
574702 AATTCGAAGT
*
574712 AATAA-ATTTAATCATTATTATAATATAAT
1 AATAATATTTAATCATTATTAT-ATATAAA
*
574741 CATAATATTTAATCATTATT-T-TATAAA
1 AATAATATTTAATCATTATTATATATAAA
574768 AATAATATT
1 AATAATATT
574777 GTTAATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 13 0.41
29 5 0.16
30 14 0.44
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (29 bp):
AATAATATTTAATCATTATTATATATAAA
Found at i:575027 original size:31 final size:32
Alignment explanation
Indices: 574993--575054 Score: 115
Period size: 33 Copynumber: 1.9 Consensus size: 32
574983 TAAAAATATT
574993 AAAAATATTATTAATATATTTACATTTTTATAA
1 AAAAATATTATTAATATATTTACATTTTTAT-A
575026 AAAAATATTATTAATATATTTACATTTTT
1 AAAAATATTATTAATATATTTACATTTTT
575055 TGAAACTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (32 bp):
AAAAATATTATTAATATATTTACATTTTTATA
Found at i:577912 original size:27 final size:27
Alignment explanation
Indices: 577874--577962 Score: 160
Period size: 27 Copynumber: 3.3 Consensus size: 27
577864 TATTTTAATG
577874 AATGTGATTAATATCAATAGTTGAATT
1 AATGTGATTAATATCAATAGTTGAATT
577901 AATGTGATTAATATCAATAGTTGAATT
1 AATGTGATTAATATCAATAGTTGAATT
* *
577928 AATGTGATTAATATCAATATTTGAATG
1 AATGTGATTAATATCAATAGTTGAATT
577955 AATGTGAT
1 AATGTGAT
577963 GGATATTAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.40, C:0.03, G:0.16, T:0.40
Consensus pattern (27 bp):
AATGTGATTAATATCAATAGTTGAATT
Found at i:588021 original size:104 final size:105
Alignment explanation
Indices: 587887--588078 Score: 232
Period size: 104 Copynumber: 1.8 Consensus size: 105
587877 AAAAATATAA
* ** *
587887 TTTAAACTAAACTTACCAAACTACTCAAATACT-ACTTAATATATAAAATCAAAATAATAGT-CT
1 TTTAAACTAAACTTACCAAACCACGAAAATA-TAACTTAATATATAAAAT-AAAATAATA-TAAT
587950 AATAAT-TA-TTAT-TTAAAATAAAAATAAAAATTACACAAAAT
63 -ATAATATATTTATATTAAAATAAAAATAAAAATTACACAAAAT
* * * * *
587991 TTTAAATTAAACTTACTAAACCACGAAAATATAATTTAATCTATACAATAAAATAATATAATATA
1 TTTAAACTAAACTTACCAAACCACGAAAATATAACTTAATATATAAAATAAAATAATATAATATA
588056 ATATATTTATATTAAAATAAAAA
66 ATATATTTATATTAAAATAAAAA
588079 AAATAAAATT
Statistics
Matches: 74, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
102 6 0.08
103 13 0.18
104 43 0.58
105 12 0.16
ACGTcount: A:0.55, C:0.10, G:0.01, T:0.33
Consensus pattern (105 bp):
TTTAAACTAAACTTACCAAACCACGAAAATATAACTTAATATATAAAATAAAATAATATAATATA
ATATATTTATATTAAAATAAAAATAAAAATTACACAAAAT
Found at i:588311 original size:25 final size:25
Alignment explanation
Indices: 588269--588316 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
588259 CTTACATGCA
* *
588269 TTATTGGTGCACAATAATGGCACTG
1 TTATTAGTGCACAATAATAGCACTG
* *
588294 TTATTAGTGCCCAGTAATAGCAC
1 TTATTAGTGCACAATAATAGCAC
588317 CATGATTTGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (25 bp):
TTATTAGTGCACAATAATAGCACTG
Found at i:589482 original size:16 final size:14
Alignment explanation
Indices: 589438--589483 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
589428 ATATACTCAT
589438 AATTATTTT-TAT-
1 AATTATTTTATATA
589450 AA-TATTTTATATA
1 AATTATTTTATATA
589463 AATTATTTTATTATTA
1 AATTATTTTA-TA-TA
589479 AATTA
1 AATTA
589484 GATATAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 6 0.21
12 5 0.17
13 2 0.07
14 7 0.24
15 2 0.07
16 7 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
AATTATTTTATATA
Found at i:597159 original size:3 final size:3
Alignment explanation
Indices: 597153--597268 Score: 146
Period size: 3 Copynumber: 37.7 Consensus size: 3
597143 TCATTTAAAT
* *
597153 TTA TTA TTA TTGA -AA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
597198 TTA TTAA TTA TAA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TATA
1 TTA TT-A TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
597246 TTA TTA TTA TTA -TA TTTA TTA TT
1 TTA TTA TTA TTA TTA -TTA TTA TT
597269 TAATAAATAA
Statistics
Matches: 100, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
2 3 0.03
3 85 0.85
4 12 0.12
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:597710 original size:13 final size:14
Alignment explanation
Indices: 597685--597711 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
597675 CAGACGACAG
597685 AGAACGAAAAAAAC
1 AGAACGAAAAAAAC
597699 AGAACGAAAAAAA
1 AGAACGAAAAAAA
597712 AACAGAGGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.11, G:0.15, T:0.00
Consensus pattern (14 bp):
AGAACGAAAAAAAC
Found at i:599310 original size:20 final size:21
Alignment explanation
Indices: 599287--599338 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
599277 AGAAATTAAA
599287 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
599307 AATTCTTTTCTTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
599329 -ATT-ATTTATT
1 AATTCATTTATT
599339 ATTTTATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:604010 original size:15 final size:15
Alignment explanation
Indices: 603990--604028 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
603980 CTCATCCAGC
* *
603990 AAAGAAAGAAGAAAA
1 AAAGAAAAAAAAAAA
604005 AAAGAAAAAAAAAAA
1 AAAGAAAAAAAAAAA
604020 AAAGGAAAA
1 AAA-GAAAA
604029 TTGAATCAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAAAAAA
Found at i:606476 original size:92 final size:92
Alignment explanation
Indices: 606319--606549 Score: 453
Period size: 92 Copynumber: 2.5 Consensus size: 92
606309 AAATAAGGAG
*
606319 GCTCATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGGAATTACAGAAC
1 GCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGGAATTACAGAAC
606384 CAATCATTGAATTTAGAAGATGAATGT
66 CAATCATTGAATTTAGAAGATGAATGT
606411 GCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGGAATTACAGAAC
1 GCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGGAATTACAGAAC
606476 CAATCATTGAATTTAGAAGATGAATGT
66 CAATCATTGAATTTAGAAGATGAATGT
606503 GCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1 GCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
606550 ATACAGAACC
Statistics
Matches: 138, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 138 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (92 bp):
GCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGGAATTACAGAAC
CAATCATTGAATTTAGAAGATGAATGT
Found at i:608306 original size:22 final size:22
Alignment explanation
Indices: 608238--608317 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 22
608228 TACATCTGCA
* *
608238 CTTTTTAAAGATAATAGATTCT
1 CTTTTCAAAGATGATAGATTCT
** * * * *
608260 CACTTCAGAGATGACAAATTTT
1 CTTTTCAAAGATGATAGATTCT
*
608282 CTTTTTAAAGATGATAGATTCT
1 CTTTTCAAAGATGATAGATTCT
*
608304 CTTTTCAAAAATGA
1 CTTTTCAAAGATGA
608318 AAGCTTTATG
Statistics
Matches: 41, Mismatches: 17, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.40
Consensus pattern (22 bp):
CTTTTCAAAGATGATAGATTCT
Found at i:608957 original size:76 final size:76
Alignment explanation
Indices: 608831--609544 Score: 1329
Period size: 76 Copynumber: 9.4 Consensus size: 76
608821 CTATTTCTCA
*
608831 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
608896 ATCCTTCGGGT
66 ATCCTTCGGGT
608907 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
608972 ATCCTTCGGGT
66 ATCCTTCGGGT
*
608983 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
609048 AACCTTCGGGT
66 ATCCTTCGGGT
*
609059 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
609124 AACCTTCGGGT
66 ATCCTTCGGGT
609135 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
609200 AGCCTTCGGGT
66 ATCCTTCGGGT
609211 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
609276 AGCCTTCGGGT
66 ATCCTTCGGGT
609287 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
609352 AGCCTTCGGGT
66 ATCCTTCGGGT
*
609363 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
609428 ATCCTTCGGGT
66 ATCCTTCGGGT
609439 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
609504 ATCCTTAGGGT
66 ATCCTTCGGGT
*
609515 CATCTGTAAGCCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTT
609545 TCAACATTTC
Statistics
Matches: 628, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 628 1.00
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
ATCCTTCGGGT
Found at i:609683 original size:3 final size:3
Alignment explanation
Indices: 609677--609796 Score: 133
Period size: 3 Copynumber: 40.7 Consensus size: 3
609667 TCATTTAAAT
* *
609677 TTA TTA TTA TTGA -AA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
609722 TTA TTA -TA TAA TTA -TA TTA TTTA TTA TTA TTA TTA TTA -TA ATA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
*
609765 TTA ATA TTA -TA TTA TTA TATA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TT
609797 TAATAAATAA
Statistics
Matches: 100, Mismatches: 9, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
2 9 0.09
3 84 0.84
4 7 0.07
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:609746 original size:38 final size:34
Alignment explanation
Indices: 609677--609796 Score: 134
Period size: 38 Copynumber: 3.2 Consensus size: 34
609667 TCATTTAAAT
609677 TTATTATTATTGAAATTATTATTATTATTATTAGTATTA
1 TTATTATTATT--AA-TATTA-TATTATTATTA-TATTA
609716 TTATTATTATTATATAATTATATTATTTATTATTATTA
1 TTATTATTATTA-AT-ATTATATTA-TTATTA-TATTA
609754 TTATTATAATATTAATATTATATTATTA-TATATTA
1 TTATTAT--TATTAATATTATATTATTATTATATTA
609789 TTATTATT
1 TTATTATT
609797 TAATAAATAA
Statistics
Matches: 75, Mismatches: 1, Indels: 16
0.82 0.01 0.17
Matches are distributed among these distances:
33 1 0.01
35 12 0.16
36 2 0.03
37 10 0.13
38 32 0.43
39 13 0.17
40 5 0.07
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (34 bp):
TTATTATTATTAATATTATATTATTATTATATTA
Found at i:610229 original size:13 final size:13
Alignment explanation
Indices: 610211--610235 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
610201 CAGACGGCAG
610211 AGAACGAAAAAAC
1 AGAACGAAAAAAC
610224 AGAACGAAAAAA
1 AGAACGAAAAAA
610236 AACAGAGGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.12, G:0.16, T:0.00
Consensus pattern (13 bp):
AGAACGAAAAAAC
Found at i:611231 original size:35 final size:35
Alignment explanation
Indices: 611156--611231 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 35
611146 TAACTTAATT
* * *
611156 TTTATTATTTTAATATATTTTCAATCATTACTTTA
1 TTTATTATTTTAATATATTATAAATCATTACATTA
* * *
611191 ATTATTGTTTTACTATATTATAAAT-ATATACATTA
1 TTTATTATTTTAATATATTATAAATCAT-TACATTA
611226 TTTATT
1 TTTATT
611232 TAACAATGTT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
34 2 0.06
35 31 0.94
ACGTcount: A:0.34, C:0.07, G:0.01, T:0.58
Consensus pattern (35 bp):
TTTATTATTTTAATATATTATAAATCATTACATTA
Found at i:615239 original size:11 final size:11
Alignment explanation
Indices: 615223--615252 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
615213 CTCCAAAACA
*
615223 TTTCAAAATCT
1 TTTCAAAACCT
615234 TTTCAAAACCT
1 TTTCAAAACCT
615245 TTTCAAAA
1 TTTCAAAA
615253 GAAATCCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (11 bp):
TTTCAAAACCT
Found at i:615452 original size:10 final size:10
Alignment explanation
Indices: 615437--615484 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
615427 CTTTCAATTC
615437 TTTTATTATT
1 TTTTATTATT
615447 TTTTATTATT
1 TTTTATTATT
615457 TTATT-TTATT
1 TT-TTATTATT
* *
615467 TTATATCATT
1 TTTTATTATT
*
615477 GTTTATTA
1 TTTTATTA
615485 ATGTTTGCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
9 1 0.03
10 28 0.90
11 2 0.06
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (10 bp):
TTTTATTATT
Found at i:616964 original size:13 final size:14
Alignment explanation
Indices: 616916--616990 Score: 50
Period size: 13 Copynumber: 5.5 Consensus size: 14
616906 AATTCTTTTG
*
616916 TTGCA-TTTACATT
1 TTGCATTTTGCATT
*
616929 TTGCATTTTGTA-T
1 TTGCATTTTGCATT
**
616942 TCACATTTTGCATT
1 TTGCATTTTGCATT
616956 TTGCA-TTTGCA-T
1 TTGCATTTTGCATT
**
616968 AAGCATATTTGCATCT
1 TTGCAT-TTTGCAT-T
616984 TTGCATT
1 TTGCATT
616991 AGCATCTAAA
Statistics
Matches: 45, Mismatches: 11, Indels: 10
0.68 0.17 0.15
Matches are distributed among these distances:
12 4 0.09
13 21 0.47
14 14 0.31
15 1 0.02
16 5 0.11
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (14 bp):
TTGCATTTTGCATT
Found at i:618369 original size:13 final size:11
Alignment explanation
Indices: 618349--618470 Score: 115
Period size: 11 Copynumber: 10.8 Consensus size: 11
618339 AAACACACAC
618349 AAAAAGAAAGTA
1 AAAAAGAAAG-A
618361 AAAACAGAAAAGA
1 AAAA-AG-AAAGA
*
618374 GAAAAACAAAAGA
1 -AAAAA-GAAAGA
*
618387 AAAAAGAAAAA
1 AAAAAGAAAGA
618398 AAAAAGAAA-A
1 AAAAAGAAAGA
618408 AAGAAA-AAAGA
1 AA-AAAGAAAGA
618419 AAAAAGAAAGA
1 AAAAAGAAAGA
*
618430 AGAAAG-AAGA
1 AAAAAGAAAGA
*
618440 AAGAAGAAAGA
1 AAAAAGAAAGA
*
618451 AAGAAGAAAGA
1 AAAAAGAAAGA
*
618462 AAGAAGAAA
1 AAAAAGAAA
618471 ATAGACAGAT
Statistics
Matches: 96, Mismatches: 6, Indels: 17
0.81 0.05 0.14
Matches are distributed among these distances:
10 17 0.18
11 53 0.55
12 9 0.09
13 9 0.09
14 8 0.08
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.01
Consensus pattern (11 bp):
AAAAAGAAAGA
Found at i:618376 original size:7 final size:7
Alignment explanation
Indices: 618368--618471 Score: 108
Period size: 7 Copynumber: 15.3 Consensus size: 7
618358 GTAAAAACAG
*
618368 AAAAGAG
1 AAAAGAA
*
618375 AAAA-AC
1 AAAAGAA
618381 AAAAGAA
1 AAAAGAA
618388 AAAAG--
1 AAAAGAA
618393 AAAA-AA
1 AAAAGAA
618399 AAAAGAA
1 AAAAGAA
618406 AAAAGAA
1 AAAAGAA
618413 AAAAGAA
1 AAAAGAA
618420 AAAAGAA
1 AAAAGAA
*
618427 AGAAGAA
1 AAAAGAA
*
618434 AGAAGAA
1 AAAAGAA
*
618441 AGAAGAA
1 AAAAGAA
618448 AGAAAGAA
1 A-AAAGAA
*
618456 GAAAGAA
1 AAAAGAA
*
618463 AGAAGAA
1 AAAAGAA
618470 AA
1 AA
618472 TAGACAGATC
Statistics
Matches: 84, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
5 4 0.05
6 9 0.11
7 66 0.79
8 5 0.06
ACGTcount: A:0.80, C:0.01, G:0.19, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:618387 original size:18 final size:18
Alignment explanation
Indices: 618349--618471 Score: 113
Period size: 18 Copynumber: 6.6 Consensus size: 18
618339 AAACACACAC
*
618349 AAAAAGAAAGTAAAAACAGA
1 AAAAAGAAA--AAAAAAAGA
* *
618369 AAAGAGAAAAACAAAAGA
1 AAAAAGAAAAAAAAAAGA
618387 AAAAAGAAAAAAAAAAGA
1 AAAAAGAAAAAAAAAAGA
618405 AAAAAGAAAAAAGAAAA-A
1 AAAAAGAAAAAA-AAAAGA
*
618423 AGAAAGAAGAAAGAAGAAAGA
1 AAAAAGAA-AAA-AA-AAAGA
* * *
618444 AGAAAGAAAGAAGAAAGA
1 AAAAAGAAAAAAAAAAGA
*
618462 AAGAAGAAAA
1 AAAAAGAAAA
618472 TAGACAGATC
Statistics
Matches: 87, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
18 55 0.63
19 9 0.10
20 14 0.16
21 9 0.10
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.01
Consensus pattern (18 bp):
AAAAAGAAAAAAAAAAGA
Found at i:618389 original size:25 final size:25
Alignment explanation
Indices: 618355--618471 Score: 114
Period size: 25 Copynumber: 4.6 Consensus size: 25
618345 ACACAAAAAG
*
618355 AAAGTAAAAACAGAAAAGAGAAAA-ACA
1 AAAG-AAAAA-AGAAAA-AGAAAAGAAA
*
618382 AAAGAAAAAAGAAAAAAAAAAGAAA
1 AAAGAAAAAAGAAAAAGAAAAGAAA
*
618407 AAAGAAAAAAGAAAAA-AGAAAGAAG
1 AAAGAAAAAAGAAAAAGA-AAAGAAA
* *
618432 AAAGAAGAAAGAAGAAAG-AAAGAAG
1 AAAGAAAAAAGAA-AAAGAAAAGAAA
*
618457 AAAGAAAGAAGAAAA
1 AAAGAAAAAAGAAAA
618472 TAGACAGATC
Statistics
Matches: 80, Mismatches: 6, Indels: 11
0.82 0.06 0.11
Matches are distributed among these distances:
24 8 0.10
25 60 0.75
26 8 0.10
27 4 0.05
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.01
Consensus pattern (25 bp):
AAAGAAAAAAGAAAAAGAAAAGAAA
Found at i:620543 original size:54 final size:54
Alignment explanation
Indices: 620415--620615 Score: 303
Period size: 54 Copynumber: 3.7 Consensus size: 54
620405 TATTTTTATT
* *
620415 AGTTTTTAAAGAAGCTAAGTCTGATTTTCAGAAGTTTCATGATGATTTTCAAGTG
1 AGTTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCATGATGA-TTTCAAATG
* * *
620470 AGTTTTTAAAGAAACTAAGTCTGGTTTTCAGAAGTTTCTTGATGATTTCAAATA
1 AGTTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCATGATGATTTCAAATG
* * *
620524 AGTTTTCAACGAAACTAAGTTTGATTTTCAGAAGTTTCATGATGATTTCAAATG
1 AGTTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCATGATGATTTCAAATG
* *
620578 AGTTTTTAAAGAAACTAAGTCTGATTTTTATAAGTTTC
1 AGTTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTC
620616 TTGACACTTT
Statistics
Matches: 130, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
54 88 0.68
55 42 0.32
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (54 bp):
AGTTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCATGATGATTTCAAATG
Found at i:620639 original size:24 final size:24
Alignment explanation
Indices: 620612--620662 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
620602 TTTTTATAAG
620612 TTTCTTGACACTTTTCAAATGTGT
1 TTTCTTGACACTTTTCAAATGTGT
*
620636 TTTCTTGACGCTTTTCAAATGTGT
1 TTTCTTGACACTTTTCAAATGTGT
620660 TTT
1 TTT
620663 AAAGAAACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.18, C:0.16, G:0.14, T:0.53
Consensus pattern (24 bp):
TTTCTTGACACTTTTCAAATGTGT
Found at i:620779 original size:54 final size:53
Alignment explanation
Indices: 620689--620856 Score: 182
Period size: 54 Copynumber: 3.2 Consensus size: 53
620679 ATTTTCGAAA
* **
620689 GTTTCTTTATTTTTCTTAAATGAACGTTCAAAGAAATTAAGCCTAATTTTTAGGG
1 GTTTCTTGATTTTTC--AAATGAATTTTCAAAGAAATTAAGCCTAATTTTTAGGG
* ** *
620744 GTTTCTTGATGTTTTCAAATGAATTTTCAAAGAAATTAAGCATGGTTTTCAGGG
1 GTTTCTTGAT-TTTTCAAATGAATTTTCAAAGAAATTAAGCCTAATTTTTAGGG
* * **
620798 GTTTCTTGATTTTTCGAAT---TTTTGAAAGAAGCTAAGCCTAA-TTTTAGGG
1 GTTTCTTGATTTTTCAAATGAATTTTCAAAGAAATTAAGCCTAATTTTTAGGG
620847 GTTTCTTGAT
1 GTTTCTTGAT
620857 AACTGTAAAT
Statistics
Matches: 97, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
49 17 0.18
50 16 0.16
53 8 0.08
54 42 0.43
55 9 0.09
56 5 0.05
ACGTcount: A:0.28, C:0.10, G:0.18, T:0.43
Consensus pattern (53 bp):
GTTTCTTGATTTTTCAAATGAATTTTCAAAGAAATTAAGCCTAATTTTTAGGG
Done.