Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397260.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_51.0, 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: 10072460
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 70252 characters in sequence are not A, C, G, or T
File 9 of 20
Found at i:3241969 original size:2 final size:2
Alignment explanation
Indices: 3241962--3241988 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3241952 TGCATGTTGC
3241962 AT 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 AT A
3241989 AAAGAATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3243389 original size:3 final size:3
Alignment explanation
Indices: 3243381--3243412 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
3243371 ATCATCTTCT
3243381 ATA ATA ATA ATA ATA ATAA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA A
3243413 AAGATCGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:3243404 original size:13 final size:13
Alignment explanation
Indices: 3243381--3243413 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
3243371 ATCATCTTCT
3243381 ATAAT-AATAATA
1 ATAATAAATAATA
3243393 ATAATAAATAATA
1 ATAATAAATAATA
3243406 ATAATAAA
1 ATAATAAA
3243414 AGATCGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
ATAATAAATAATA
Found at i:3256478 original size:30 final size:30
Alignment explanation
Indices: 3256419--3256479 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
3256409 TAAATTTATG
**
3256419 TATTTTCATTTTGAGCTAAATAAGTTTTTA
1 TATTTTCATTTTGAGCTAAATAAACTTTTA
* *
3256449 TATTTTTATTTTGAGTTAAATAAACTTTTA
1 TATTTTCATTTTGAGCTAAATAAACTTTTA
3256479 T
1 T
3256480 GATTAATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.05, G:0.08, T:0.56
Consensus pattern (30 bp):
TATTTTCATTTTGAGCTAAATAAACTTTTA
Found at i:3279228 original size:15 final size:15
Alignment explanation
Indices: 3279208--3279237 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3279198 TCCTTCAATT
3279208 TCCTTATCCCTCTTA
1 TCCTTATCCCTCTTA
3279223 TCCTTATCCCTCTTA
1 TCCTTATCCCTCTTA
3279238 AACTTTGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.40, G:0.00, T:0.47
Consensus pattern (15 bp):
TCCTTATCCCTCTTA
Found at i:3293819 original size:24 final size:25
Alignment explanation
Indices: 3293792--3293849 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
3293782 TAAAAAATAT
* * *
3293792 AAAAATATTATTTTTTTAA-TTTTA
1 AAAAATATTATTATATAAACTTTTA
*
3293816 AAAATTATTATTATATAAACTTTTA
1 AAAAATATTATTATATAAACTTTTA
3293841 AAAAA-ATTA
1 AAAAATATTA
3293850 AAAAAAATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 19 0.68
25 9 0.32
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (25 bp):
AAAAATATTATTATATAAACTTTTA
Found at i:3300960 original size:27 final size:27
Alignment explanation
Indices: 3300930--3300986 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
3300920 CTTAAGAGAT
* *
3300930 AAAGAATCATGCTAATAATGTATTGTG
1 AAAGAATCATACTAATAACGTATTGTG
** *
3300957 AAAGAATTGTACTGATAACGTATTGTG
1 AAAGAATCATACTAATAACGTATTGTG
3300984 AAA
1 AAA
3300987 TATAACCTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (27 bp):
AAAGAATCATACTAATAACGTATTGTG
Found at i:3311426 original size:49 final size:49
Alignment explanation
Indices: 3311350--3311443 Score: 152
Period size: 49 Copynumber: 1.9 Consensus size: 49
3311340 AGAGTAGGAA
*
3311350 CTAAGGATTACAGTTTATTAAAAGGAAGGCTTTATTGGTTAAGCATGAG
1 CTAAGGATTACAGTTTATTAAAAGGAAGACTTTATTGGTTAAGCATGAG
* * *
3311399 CTAAGGATTATAGTTTATTAAATGGAAGATTTTATTGGTTAAGCA
1 CTAAGGATTACAGTTTATTAAAAGGAAGACTTTATTGGTTAAGCA
3311444 CCTTTGCCAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.35, C:0.06, G:0.22, T:0.36
Consensus pattern (49 bp):
CTAAGGATTACAGTTTATTAAAAGGAAGACTTTATTGGTTAAGCATGAG
Found at i:3317518 original size:3 final size:3
Alignment explanation
Indices: 3317512--3317536 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3317502 GCTGCTGCTG
3317512 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
3317537 GAGCAAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:3321136 original size:13 final size:13
Alignment explanation
Indices: 3321118--3321142 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3321108 ATTCAATGAC
3321118 AAAAACAAAAAAG
1 AAAAACAAAAAAG
3321131 AAAAACAAAAAA
1 AAAAACAAAAAA
3321143 TGCATAAAGC
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:0.88, C:0.08, G:0.04, T:0.00
Consensus pattern (13 bp):
AAAAACAAAAAAG
Found at i:3324060 original size:15 final size:15
Alignment explanation
Indices: 3324042--3324089 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
3324032 TATTGCAAGA
*
3324042 AATGTGATTGTTGAG
1 AATGTGATTGTTAAG
**
3324057 AATGTGATTACTAAG
1 AATGTGATTGTTAAG
*
3324072 AATGTGACTGTTAAG
1 AATGTGATTGTTAAG
3324087 AAT
1 AAT
3324090 ATAACTTTGC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.35
Consensus pattern (15 bp):
AATGTGATTGTTAAG
Found at i:3328714 original size:12 final size:11
Alignment explanation
Indices: 3328698--3328740 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
3328688 CTAAACACCC
3328698 TAAACACTATA
1 TAAACACTATA
3328709 TGAAACACTATA
1 T-AAACACTATA
*
3328721 TAAACACAATA
1 TAAACACTATA
3328732 TAAA-ACTAT
1 TAAACACTAT
3328741 GAGACAGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 4 0.14
11 14 0.48
12 11 0.38
ACGTcount: A:0.56, C:0.16, G:0.02, T:0.26
Consensus pattern (11 bp):
TAAACACTATA
Found at i:3328725 original size:32 final size:32
Alignment explanation
Indices: 3328667--3328727 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
3328657 ATTCAACTTG
*
3328667 AAACACTATATAAACACTACCCTAAACACCCT
1 AAACACTATATAAACACTACCATAAACACCCT
*
3328699 AAACACTATATGAAACACTA-TATAAACAC
1 AAACACTATAT-AAACACTACCATAAACAC
3328728 AATATAAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 18 0.69
33 8 0.31
ACGTcount: A:0.51, C:0.28, G:0.02, T:0.20
Consensus pattern (32 bp):
AAACACTATATAAACACTACCATAAACACCCT
Found at i:3328727 original size:23 final size:22
Alignment explanation
Indices: 3328667--3328740 Score: 64
Period size: 21 Copynumber: 3.4 Consensus size: 22
3328657 ATTCAACTTG
**
3328667 AAACACTATATAAACACTACCCT
1 AAACACTATATAAACACTA-TAT
**
3328690 AAACAC--CCTAAACACTATAT
1 AAACACTATATAAACACTATAT
*
3328710 GAAACACTATATAAACACAATAT
1 -AAACACTATATAAACACTATAT
3328733 AAA-ACTAT
1 AAACACTAT
3328741 GAGACAGTGT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
20 1 0.02
21 20 0.49
22 3 0.07
23 17 0.41
ACGTcount: A:0.53, C:0.24, G:0.01, T:0.22
Consensus pattern (22 bp):
AAACACTATATAAACACTATAT
Found at i:3330389 original size:17 final size:19
Alignment explanation
Indices: 3330367--3330405 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
3330357 AGTGTTCATC
3330367 AGCTTGT-GCATCTG-CAT
1 AGCTTGTAGCATCTGACAT
*
3330384 AGCTTGTAGGATCTGACAT
1 AGCTTGTAGCATCTGACAT
3330403 AGC
1 AGC
3330406 CTAATTACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 6 0.32
19 6 0.32
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.31
Consensus pattern (19 bp):
AGCTTGTAGCATCTGACAT
Found at i:3339359 original size:23 final size:24
Alignment explanation
Indices: 3339333--3339381 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
3339323 ACTAAAAGGT
*
3339333 TGTGTTTATTG-TGCTTT-AATAGA
1 TGTGTCTATTGTTG-TTTCAATAGA
3339356 TGTGTCTATTGTTGTTTCAATAGA
1 TGTGTCTATTGTTGTTTCAATAGA
3339380 TG
1 TG
3339382 AATCTGTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.20, C:0.06, G:0.22, T:0.51
Consensus pattern (24 bp):
TGTGTCTATTGTTGTTTCAATAGA
Found at i:3344427 original size:3 final size:3
Alignment explanation
Indices: 3344419--3344447 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3344409 TCATTGAACA
3344419 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3344448 ATAAATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3344462 original size:9 final size:10
Alignment explanation
Indices: 3344418--3344459 Score: 56
Period size: 9 Copynumber: 4.6 Consensus size: 10
3344408 TTCATTGAAC
3344418 AAATAATAAT
1 AAATAATAAT
3344428 -AATAATAAT
1 AAATAATAAT
3344437 -AATAATAAT
1 AAATAATAAT
3344446 AAAT-A-AAT
1 AAATAATAAT
3344454 AAATAA
1 AAATAA
3344460 AATTTTAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 7 0.23
9 20 0.67
10 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AAATAATAAT
Found at i:3350251 original size:17 final size:20
Alignment explanation
Indices: 3350215--3350255 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3350205 TTAGACATTT
3350215 TTCATCAAAAGTGATTATTA
1 TTCATCAAAAGTGATTATTA
* *
3350235 TTCATCAAAGGTTATTATTA
1 TTCATCAAAAGTGATTATTA
3350255 T
1 T
3350256 CTTTGGGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.44
Consensus pattern (20 bp):
TTCATCAAAAGTGATTATTA
Found at i:3351735 original size:17 final size:17
Alignment explanation
Indices: 3351715--3351749 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3351705 AAACATGGTA
*
3351715 TTTTT-TTATAAGATAT
1 TTTTTATTAAAAGATAT
3351731 TTTTTATTAAAAGATAT
1 TTTTTATTAAAAGATAT
3351748 TT
1 TT
3351750 AAATCTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (17 bp):
TTTTTATTAAAAGATAT
Found at i:3353245 original size:60 final size:59
Alignment explanation
Indices: 3353147--3353273 Score: 175
Period size: 60 Copynumber: 2.2 Consensus size: 59
3353137 AATTAGTCTT
* *
3353147 AATGTGAATTTGCTATCATACAATATATATTATATTTTGTCTCTTGATTTATTAAATCG
1 AATGTGAATTTGCTATCATACAATATATATTATATTTTGTCTATTAATTTATTAAATCG
** * * *
3353206 CAATGTGAATTTGCTATCATGTAATCTATATTGTGTTTTGTCTATTAATTTATTAAATCG
1 -AATGTGAATTTGCTATCATACAATATATATTATATTTTGTCTATTAATTTATTAAATCG
3353266 AAT-TGAAT
1 AATGTGAAT
3353274 ATGTAAATAT
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
58 5 0.08
59 3 0.05
60 52 0.87
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.47
Consensus pattern (59 bp):
AATGTGAATTTGCTATCATACAATATATATTATATTTTGTCTATTAATTTATTAAATCG
Found at i:3362144 original size:21 final size:19
Alignment explanation
Indices: 3362109--3362152 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 19
3362099 TGTTTGGTTG
*
3362109 AAAAGAAAAAGCAAACAAT
1 AAAAGAAAAAGCAAACAAA
3362128 AAAAGACAAAAGTCAAACAAA
1 AAAAGA-AAAAG-CAAACAAA
3362149 AAAA
1 AAAA
3362153 ATCTTAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.27
20 5 0.23
21 11 0.50
ACGTcount: A:0.75, C:0.11, G:0.09, T:0.05
Consensus pattern (19 bp):
AAAAGAAAAAGCAAACAAA
Found at i:3362468 original size:3 final size:3
Alignment explanation
Indices: 3362460--3362491 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3362450 CAATCACCTG
3362460 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
3362492 TATGAGTAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:3362833 original size:3 final size:3
Alignment explanation
Indices: 3362827--3362852 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3362817 AAGAAGAAGA
3362827 AGG AGG AGG AGG AGG AGG AGG AGG AG
1 AGG AGG AGG AGG AGG AGG AGG AGG AG
3362853 AAGATAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:3368970 original size:19 final size:19
Alignment explanation
Indices: 3368942--3368989 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
3368932 GATGTAATTG
3368942 AAGAGAAATTGGTGAATAC
1 AAGAGAAATTGGTGAATAC
*
3368961 AAGAGGAATTGGTGAATAC
1 AAGAGAAATTGGTGAATAC
3368980 AAGAGAAATT
1 AAGAGAAATT
3368990 TTTGATTAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.48, C:0.04, G:0.27, T:0.21
Consensus pattern (19 bp):
AAGAGAAATTGGTGAATAC
Found at i:3369506 original size:14 final size:14
Alignment explanation
Indices: 3369487--3369516 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3369477 ATATAAACCC
*
3369487 TAATAAAATTTTTT
1 TAATAAAATTTATT
3369501 TAATAAAATTTATT
1 TAATAAAATTTATT
3369515 TA
1 TA
3369517 TCTGAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAATAAAATTTATT
Found at i:3370164 original size:40 final size:39
Alignment explanation
Indices: 3370080--3370192 Score: 109
Period size: 40 Copynumber: 2.7 Consensus size: 39
3370070 TGTTACACAC
* * *
3370080 CATATACAAAAATATGTTATACGTCATGGTTAGGTCACGT
1 CATATACAAAAACATGTTACACGTCATGATTAGGT-ACGT
* *
3370120 CATATACAAAAACATGTGACACGTCATGATTAGGTTGTTACATAT
1 CATATACAAAAACATGTTACACGTCATGATTA-G--G-TAC--GT
*
3370165 CATGTACAAAAACATGTTACACGTCATG
1 CATATACAAAAACATGTTACACGTCATG
3370193 TTGAAAAACA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
40 28 0.47
41 1 0.02
43 3 0.05
44 1 0.02
45 27 0.45
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (39 bp):
CATATACAAAAACATGTTACACGTCATGATTAGGTACGT
Found at i:3370191 original size:24 final size:24
Alignment explanation
Indices: 3370155--3370202 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3370145 ATGATTAGGT
*
3370155 TGTTACATATCATGTACAAAAACA
1 TGTTACACATCATGTACAAAAACA
* **
3370179 TGTTACACGTCATGTTGAAAAACA
1 TGTTACACATCATGTACAAAAACA
3370203 AATACTGTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (24 bp):
TGTTACACATCATGTACAAAAACA
Found at i:3370245 original size:29 final size:29
Alignment explanation
Indices: 3370170--3370263 Score: 100
Period size: 32 Copynumber: 3.1 Consensus size: 29
3370160 CATATCATGT
*
3370170 ACAAAAACATGTTACACGTCATGTTGAAAA
1 ACAAATAC-TGTTACACGTCATGTTGAAAA
3370200 ACAAATACTGTTATTACACGTCATGTTGAAAA
1 ACAAATACTG---TTACACGTCATGTTGAAAA
* * *
3370232 A-ATATTACTGTTACACGTCATATTCAAAA
1 ACA-AATACTGTTACACGTCATGTTGAAAA
3370261 ACA
1 ACA
3370264 TTTTATTACA
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
29 20 0.36
30 8 0.15
31 1 0.02
32 26 0.47
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.29
Consensus pattern (29 bp):
ACAAATACTGTTACACGTCATGTTGAAAA
Found at i:3370392 original size:11 final size:11
Alignment explanation
Indices: 3370378--3370407 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
3370368 CCAATTAAAG
3370378 TGTTTCTAACA
1 TGTTTCTAACA
3370389 TGTTTCTAACA
1 TGTTTCTAACA
3370400 TGTTTCTA
1 TGTTTCTA
3370408 TAAATCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.50
Consensus pattern (11 bp):
TGTTTCTAACA
Found at i:3375150 original size:27 final size:27
Alignment explanation
Indices: 3375108--3375172 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
3375098 TACAAGTAAG
* *
3375108 TGGATACATTTTCCCACC-ATAAATAGA
1 TGGATACCTTTACCCACCGA-AAATAGA
*
3375135 TGGATACCTTTACCCACCGAAAGTAGA
1 TGGATACCTTTACCCACCGAAAATAGA
3375162 TGGATA-CTTTA
1 TGGATACCTTTA
3375173 TCGACTAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.15
27 28 0.82
28 1 0.03
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (27 bp):
TGGATACCTTTACCCACCGAAAATAGA
Found at i:3394343 original size:12 final size:13
Alignment explanation
Indices: 3394320--3394348 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3394310 AGGGCCATCC
3394320 CTTTCTCATTTTT
1 CTTTCTCATTTTT
3394333 CTTTC-CATTTTT
1 CTTTCTCATTTTT
3394345 CTTT
1 CTTT
3394349 TGTTTGTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.69
Consensus pattern (13 bp):
CTTTCTCATTTTT
Found at i:3394725 original size:17 final size:18
Alignment explanation
Indices: 3394700--3394737 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
3394690 AAGATACATG
* *
3394700 TAAACAAGAAT-TTTACA
1 TAAAAAAGAATATTGACA
3394717 TAAAAAAGAATATTGACA
1 TAAAAAAGAATATTGACA
3394735 TAA
1 TAA
3394738 TCATAACCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.26
Consensus pattern (18 bp):
TAAAAAAGAATATTGACA
Found at i:3395489 original size:2 final size:2
Alignment explanation
Indices: 3395482--3395513 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3395472 GTTAAAAAGA
3395482 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
3395514 GAGCCCTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3398361 original size:40 final size:40
Alignment explanation
Indices: 3398306--3398386 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
3398296 CTGTCTTTTA
*
3398306 AAATTTTCTTTTATAAGACTTATAACATGTATGAGAGACC
1 AAATTTTCTTTTATAAGACTTATAACATGAATGAGAGACC
*
3398346 AAATTTTCTTTTATAAGACTTGTAACATGAATGAGAGACC
1 AAATTTTCTTTTATAAGACTTATAACATGAATGAGAGACC
3398386 A
1 A
3398387 TCTGCCAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (40 bp):
AAATTTTCTTTTATAAGACTTATAACATGAATGAGAGACC
Found at i:3398901 original size:53 final size:53
Alignment explanation
Indices: 3398842--3398950 Score: 218
Period size: 53 Copynumber: 2.1 Consensus size: 53
3398832 TGAATAATAA
3398842 TTAAACCTAAAGGTCCTATTTATAATATTATAGGCCCACATCTTAATAAAACT
1 TTAAACCTAAAGGTCCTATTTATAATATTATAGGCCCACATCTTAATAAAACT
3398895 TTAAACCTAAAGGTCCTATTTATAATATTATAGGCCCACATCTTAATAAAACT
1 TTAAACCTAAAGGTCCTATTTATAATATTATAGGCCCACATCTTAATAAAACT
3398948 TTA
1 TTA
3398951 CTTTTAGTTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.35
Consensus pattern (53 bp):
TTAAACCTAAAGGTCCTATTTATAATATTATAGGCCCACATCTTAATAAAACT
Found at i:3406329 original size:35 final size:36
Alignment explanation
Indices: 3406256--3406340 Score: 100
Period size: 36 Copynumber: 2.4 Consensus size: 36
3406246 AGGATTAGTT
* *
3406256 GTAACCTTCACAACATGCCTTTTACCAAGATCATGC
1 GTAACTTTCACAACATGCCTTTTACCAAGATCAAGC
* * *
3406292 GTAACTTTCATAACATGCTTTTTACC-ATATCAAGC
1 GTAACTTTCACAACATGCCTTTTACCAAGATCAAGC
*
3406327 GTAATCTTTAACAA
1 GTAA-CTTTCACAA
3406341 GAATGTATAC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
35 11 0.27
36 30 0.73
ACGTcount: A:0.33, C:0.25, G:0.09, T:0.33
Consensus pattern (36 bp):
GTAACTTTCACAACATGCCTTTTACCAAGATCAAGC
Found at i:3408280 original size:23 final size:24
Alignment explanation
Indices: 3408254--3408303 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
3408244 TCAATGTCTT
3408254 TTTTTGCA-TCTTGCCACCAATCC
1 TTTTTGCAGTCTTGCCACCAATCC
* *
3408277 TTTTTGTATGTCTTGCCACCCATCC
1 TTTTTGCA-GTCTTGCCACCAATCC
3408302 TT
1 TT
3408304 CTTCATCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 7 0.30
25 16 0.70
ACGTcount: A:0.14, C:0.32, G:0.10, T:0.44
Consensus pattern (24 bp):
TTTTTGCAGTCTTGCCACCAATCC
Found at i:3411041 original size:22 final size:22
Alignment explanation
Indices: 3410998--3411042 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3410988 AAAGATCATT
* *
3410998 AACTAGTTACACAATGTCTAAA
1 AACTAGTCACACAATCTCTAAA
3411020 AACTAGTCACACAATACT-TAAA
1 AACTAGTCACACAAT-CTCTAAA
3411042 A
1 A
3411043 CCCATGTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.49, C:0.20, G:0.07, T:0.24
Consensus pattern (22 bp):
AACTAGTCACACAATCTCTAAA
Found at i:3411115 original size:22 final size:22
Alignment explanation
Indices: 3411086--3411168 Score: 87
Period size: 22 Copynumber: 3.8 Consensus size: 22
3411076 CATACTTAAG
*
3411086 TCACATAATACCTAAAAACCAA
1 TCACATAATGCCTAAAAACCAA
* * *
3411108 TCATATAATGTCTAAAAACTAA
1 TCACATAATGCCTAAAAACCAA
* *
3411130 TCACATAATGCCTGAAAACTAGA
1 TCACATAATGCCTAAAAACCA-A
*
3411153 -CACATAATGCTTAAAA
1 TCACATAATGCCTAAAA
3411169 TGCATTCTTG
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
22 50 0.98
23 1 0.02
ACGTcount: A:0.49, C:0.20, G:0.06, T:0.24
Consensus pattern (22 bp):
TCACATAATGCCTAAAAACCAA
Found at i:3411231 original size:16 final size:16
Alignment explanation
Indices: 3411179--3411222 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
3411169 TGCATTCTTG
3411179 CAATGCCTAAGTCACA
1 CAATGCCTAAGTCACA
3411195 CAATGCCTAAGTCACA
1 CAATGCCTAAGTCACA
3411211 CAATGCCTAAGT
1 CAATGCCTAAGT
3411223 TGCGCAATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.36, C:0.30, G:0.14, T:0.20
Consensus pattern (16 bp):
CAATGCCTAAGTCACA
Found at i:3416237 original size:161 final size:155
Alignment explanation
Indices: 3415873--3416295 Score: 519
Period size: 161 Copynumber: 2.7 Consensus size: 155
3415863 TATATGTAAA
* * *
3415873 AAAAATTGAATAATTAATGAATAAAACTTT-CTCAATTCATTACTTGGATAACTAGTATGACGTG
1 AAAAATTGAATAATTAATGAATAAAACTTTCCT-AGTTCAATACTTGGATAAC-AGTAGGACGTG
** *
3415937 TCAATAGGGATTGGATTTCTAT-GCACAATATTAAAAATGTGTGAAGAATGAAGCATGTGTATTA
64 TCAATAGGGATTGGATTTCT-TCGCACAATATTAAAAATGTGCAAAGAATGAAGCATGTGTACTA
* * *
3416001 TTATGAAGATGCTAGATGCTGGCAGGAT
128 TTATAAAGATGCTAGAAGCTGGAAGGAT
* * * *
3416029 AAAATATTGAATAATTAATAAATAAAACTTTCTTAGTTCAATACTTGGATAAGCAGTAGGATGTA
1 AAAA-ATTGAATAATTAATGAATAAAACTTTCCTAGTTCAATACTTGGATAA-CAGTAGGACGTG
*
3416094 TCAATAGGGATTGGATTTCTTCGCACAATATTAAAATTGTGCAAAGAATGAAGCATGCATGTGTA
64 TCAATAGGGATTGGATTTCTTCGCACAATATTAAAAATGTGCAAAGAATG-A--A-GCATGTGTA
*
3416159 CTATTATAAAGGTGCTAGAAGCTGGAA-GAGT
125 CTATTATAAAGATGCTAGAAGCTGGAAGGA-T
*
3416190 GAAAAATTGAATAATTAATGAATAAAACTTTCCTAGTTCAATACTTGGATAACCAGTAGGAGGTG
1 -AAAAATTGAATAATTAATGAATAAAACTTTCCTAGTTCAATACTTGGATAA-CAGTAGGACGTG
* * * * * *
3416255 CCAATAGAGATTTGATTTCTTCGCATAGTATCAAAAATGTG
64 TCAATAGGGATTGGATTTCTTCGCACAATATTAAAAATGTG
3416296 TGATGATTGA
Statistics
Matches: 230, Mismatches: 27, Indels: 15
0.85 0.10 0.06
Matches are distributed among these distances:
156 5 0.02
157 94 0.41
158 3 0.01
160 3 0.01
161 121 0.53
162 4 0.02
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (155 bp):
AAAAATTGAATAATTAATGAATAAAACTTTCCTAGTTCAATACTTGGATAACAGTAGGACGTGTC
AATAGGGATTGGATTTCTTCGCACAATATTAAAAATGTGCAAAGAATGAAGCATGTGTACTATTA
TAAAGATGCTAGAAGCTGGAAGGAT
Found at i:3420315 original size:144 final size:144
Alignment explanation
Indices: 3420013--3420328 Score: 368
Period size: 144 Copynumber: 2.2 Consensus size: 144
3420003 AATGCAAAGT
* * *
3420013 TAGATGCTGCACATCTATCGATAGATAGCCAACCAGGAACCACATTAAAGGACATTGACTTGAAT
1 TAGATGCTACACATCTATCGATAAATAGCCAACCAGGAACCACATTAAAGGACATTGACTTAAAT
* * * *
3420078 TAATCGGTACATACACAGTATCTATAGATAAATAGGCACTTGAAAATGATTGCAAAGGACCGTGC
66 TAATCGATACATACACAGTATCTATAGATAAATAGACACCTGAAAATGATTGCAAAGGACCATGC
3420143 CATGCATCTATCAA
131 CATGCATCTATCAA
** * * * *
3420157 TAGATG-TGTGACATCTATTGATAAATAGCCAACTAGGAACCATATTAAAGGATATTGACTTAAA
1 TAGATGCT-ACACATCTATCGATAAATAGCCAACCAGGAACCACATTAAAGGACATTGACTTAAA
* ** * * *
3420221 TCT-ATCTATACATACATGGTATCTATCGATAGATTGACACCTGAAAATGATTG-AAGAGGACCA
65 T-TAATCGATACATACACAGTATCTATAGATAAATAGACACCTGAAAATGATTGCAA-AGGACCA
* * *
3420284 TGCCTTGCATTTATCCA
128 TGCCATGCATCTATCAA
* *
3420301 TAGATGCTACACATCTATCAATAGATAG
1 TAGATGCTACACATCTATCGATAAATAG
3420329 TCACCTGAGG
Statistics
Matches: 142, Mismatches: 26, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
143 3 0.02
144 137 0.96
145 2 0.01
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (144 bp):
TAGATGCTACACATCTATCGATAAATAGCCAACCAGGAACCACATTAAAGGACATTGACTTAAAT
TAATCGATACATACACAGTATCTATAGATAAATAGACACCTGAAAATGATTGCAAAGGACCATGC
CATGCATCTATCAA
Found at i:3420591 original size:14 final size:14
Alignment explanation
Indices: 3420569--3420598 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3420559 TGCTCGATAA
3420569 GAACATTATGCATG
1 GAACATTATGCATG
*
3420583 GAACTTTATGCATG
1 GAACATTATGCATG
3420597 GA
1 GA
3420599 CATGCCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.30
Consensus pattern (14 bp):
GAACATTATGCATG
Found at i:3422748 original size:26 final size:25
Alignment explanation
Indices: 3422695--3422817 Score: 70
Period size: 27 Copynumber: 4.7 Consensus size: 25
3422685 TAGCAAAACG
** *
3422695 TTTGAACATGGCATGTAGAAATTTTT
1 TTTGAACATGGTGTGTAGAAA-ATTT
3422721 TTTGAACATGGTGTGTAGAAAATGTT
1 TTTGAACATGGTGTGTAGAAAAT-TT
* * * * *
3422747 TTCTTAAAATGGCT-TGTCGCATACTATT
1 TT-TGAACATGG-TGTGTAG-AAAAT-TT
*
3422775 TTTGAACATGATGTGTAGGAAAATTAT
1 TTTGAACATGGTGTGTA-GAAAATT-T
*
3422802 TTTGCACAT-GTGTGTA
1 TTTGAACATGGTGTGTA
3422818 ACATCTTTTT
Statistics
Matches: 73, Mismatches: 17, Indels: 14
0.70 0.16 0.13
Matches are distributed among these distances:
25 1 0.01
26 31 0.42
27 32 0.44
28 9 0.12
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (25 bp):
TTTGAACATGGTGTGTAGAAAATTT
Found at i:3427387 original size:15 final size:15
Alignment explanation
Indices: 3427369--3427399 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3427359 ATTTAATTAC
*
3427369 AAGTAATGTGATTGT
1 AAGTAATATGATTGT
3427384 AAGTAATATGATTGT
1 AAGTAATATGATTGT
3427399 A
1 A
3427400 GGAAATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.23, T:0.39
Consensus pattern (15 bp):
AAGTAATATGATTGT
Found at i:3429862 original size:12 final size:12
Alignment explanation
Indices: 3429845--3429870 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3429835 CTAAGTAGAA
3429845 AAAAATATATTT
1 AAAAATATATTT
3429857 AAAAATATATTT
1 AAAAATATATTT
3429869 AA
1 AA
3429871 TCACAAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAAAATATATTT
Found at i:3437581 original size:28 final size:28
Alignment explanation
Indices: 3437541--3437645 Score: 111
Period size: 28 Copynumber: 3.7 Consensus size: 28
3437531 TAATGCATTG
3437541 TCAAGGTTCAAGCATAACCATTACCTTT
1 TCAAGGTTCAAGCATAACCATTACCTTT
* * *
3437569 TCAAGGATCAAGCATAACTATTGCCTTT
1 TCAAGGTTCAAGCATAACCATTACCTTT
* * * * *
3437597 TAAAAGTTCAACCACAACCTTTATGCCTTT
1 TCAAGGTTCAAGCATAACCATTA--CCTTT
*
3437627 TCAAGGTTCAATCATAACC
1 TCAAGGTTCAAGCATAACC
3437646 TCTAAACACT
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
28 40 0.67
30 20 0.33
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.31
Consensus pattern (28 bp):
TCAAGGTTCAAGCATAACCATTACCTTT
Found at i:3437625 original size:30 final size:30
Alignment explanation
Indices: 3437590--3437646 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
3437580 GCATAACTAT
3437590 TGCCTTTTAAAAGTTCAACCACAACCTTTA
1 TGCCTTTTAAAAGTTCAACCACAACCTTTA
* * * *
3437620 TGCCTTTTCAAGGTTCAATCATAACCT
1 TGCCTTTTAAAAGTTCAACCACAACCT
3437647 CTAAACACTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (30 bp):
TGCCTTTTAAAAGTTCAACCACAACCTTTA
Found at i:3438711 original size:23 final size:23
Alignment explanation
Indices: 3438678--3438722 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3438668 ATCATTTTGA
*
3438678 AAACTTTAAGACAACCACTTTCG
1 AAACTTCAAGACAACCACTTTCG
* *
3438701 AAACTTCAAGATAACCATTTTC
1 AAACTTCAAGACAACCACTTTC
3438723 AAAATCATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.24, G:0.07, T:0.29
Consensus pattern (23 bp):
AAACTTCAAGACAACCACTTTCG
Found at i:3438781 original size:20 final size:21
Alignment explanation
Indices: 3438756--3438794 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3438746 AAATCTTTTG
3438756 AGGT-AAATTTTCAAACCTCT
1 AGGTAAAATTTTCAAACCTCT
3438776 AGGTAAAATTTTCAAACCT
1 AGGTAAAATTTTCAAACCT
3438795 TCAAGTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (21 bp):
AGGTAAAATTTTCAAACCTCT
Found at i:3438802 original size:21 final size:21
Alignment explanation
Indices: 3438760--3438803 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3438750 CTTTTGAGGT
*
3438760 AAATTTTCAAACCTCTAGGTA
1 AAATTTTCAAACCTCTAAGTA
3438781 AAATTTTCAAACCT-TCAAGTA
1 AAATTTTCAAACCTCT-AAGTA
3438802 AA
1 AA
3438804 TCTTGCCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (21 bp):
AAATTTTCAAACCTCTAAGTA
Found at i:3438858 original size:22 final size:22
Alignment explanation
Indices: 3438833--3438901 Score: 111
Period size: 22 Copynumber: 3.1 Consensus size: 22
3438823 TATTGTTTTT
* *
3438833 AAATCCTTTAGGTACTTCTTTC
1 AAATCTTTTAGGTACATCTTTC
3438855 AAATCTTTTAGGTACATCTTTC
1 AAATCTTTTAGGTACATCTTTC
*
3438877 AAATCTTTTAGGTGCATCTTTC
1 AAATCTTTTAGGTACATCTTTC
3438899 AAA
1 AAA
3438902 ACCTCCAGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.28, C:0.19, G:0.10, T:0.43
Consensus pattern (22 bp):
AAATCTTTTAGGTACATCTTTC
Found at i:3447217 original size:21 final size:21
Alignment explanation
Indices: 3447187--3447227 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
3447177 CTAAGGTAGG
3447187 GATTTAGCTCAT-TATTGAAA
1 GATTTAGCTCATATATTGAAA
*
3447207 GATTTGAGCTCTTATATTGAA
1 GATTT-AGCTCATATATTGAA
3447228 TTGGGTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 7 0.39
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (21 bp):
GATTTAGCTCATATATTGAAA
Found at i:3456588 original size:19 final size:20
Alignment explanation
Indices: 3456564--3456602 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
3456554 AAGTGAGTTA
*
3456564 TTTTAATTTTA-TGTTATTT
1 TTTTAATTTGATTGTTATTT
3456583 TTTTAATTTGATTGTTATTT
1 TTTTAATTTGATTGTTATTT
3456603 ATTAGTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.72
Consensus pattern (20 bp):
TTTTAATTTGATTGTTATTT
Found at i:3457964 original size:17 final size:18
Alignment explanation
Indices: 3457934--3457967 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3457924 TGAATTTAGT
*
3457934 TATTTTTGAGAAGCTAGA
1 TATTTTCGAGAAGCTAGA
3457952 TATTTTCGA-AAGCTAG
1 TATTTTCGAGAAGCTAG
3457968 GAAATAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (18 bp):
TATTTTCGAGAAGCTAGA
Found at i:3460109 original size:17 final size:16
Alignment explanation
Indices: 3460077--3460116 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
3460067 TTTTTTCATT
3460077 AGGTTTTTTCTTAAAA
1 AGGTTTTTTCTTAAAA
3460093 AGGTTTTTTCTTAAAA
1 AGGTTTTTTCTTAAAA
3460109 A-GTTTTTT
1 AGGTTTTTT
3460117 AACAAGGTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 7 0.29
16 17 0.71
ACGTcount: A:0.28, C:0.05, G:0.12, T:0.55
Consensus pattern (16 bp):
AGGTTTTTTCTTAAAA
Found at i:3476385 original size:87 final size:87
Alignment explanation
Indices: 3476287--3476561 Score: 489
Period size: 87 Copynumber: 3.1 Consensus size: 87
3476277 ATTCTTTAAT
*
3476287 AATATAAATTTTTAAATAAAATATACATTTATCATATTAATTTATTAATTAAAAAATAAAAAAAT
1 AATATAAATTTTTAAATAAAATATACATTTATCATATTAATTTATTAATTAAAAATTAAAAAAAT
3476352 TTATCATTTTAAAATTAAAGGG
66 TTATCATTTTAAAATTAAAGGG
3476374 AATATAAATTTTTAAATAAAATATACATTTATCATATTAATTTATTAATTAAAAATTAAAAAAAT
1 AATATAAATTTTTAAATAAAATATACATTTATCATATTAATTTATTAATTAAAAATTAAAAAAAT
3476439 TTATCATTTTAAAATTAAAGGG
66 TTATCATTTTAAAATTAAAGGG
* *
3476461 AATATAAATTTTTACATAAAATATACATTTATCATATTAATTTAATAATTAAAAATTAAAAAACA
1 AATATAAATTTTTAAATAAAATATACATTTATCATATTAATTTATTAATTAAAAATTAAAAAA-A
3476526 TTTATCATTTTAAAATTAAAGGGG
65 TTTATCATTTTAAAATTAAA-GGG
*
3476550 AAT-TCAATTTTT
1 AATATAAATTTTT
3476562 GCAGTATTTT
Statistics
Matches: 182, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
87 147 0.81
88 29 0.16
89 6 0.03
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (87 bp):
AATATAAATTTTTAAATAAAATATACATTTATCATATTAATTTATTAATTAAAAATTAAAAAAAT
TTATCATTTTAAAATTAAAGGG
Found at i:3476500 original size:44 final size:43
Alignment explanation
Indices: 3476287--3476500 Score: 120
Period size: 43 Copynumber: 4.9 Consensus size: 43
3476277 ATTCTTTAAT
**
3476287 AATATAAATTTTTAAATAAAATATACATTTATCATATTAATTTA-TT
1 AATATAAATTTTT-AATAAAATATACATTTATCATATTAA---AGGG
*** * * * *
3476333 AAT-TAAA-AAATAAAAAAATTTATCATTT-TAAAATTAAAGGG
1 AATATAAATTTTTAATAAAATATA-CATTTATCATATTAAAGGG
**
3476374 AATATAAATTTTTAAATAAAATATACATTTATCATATTAATTTA-TT
1 AATATAAATTTTT-AATAAAATATACATTTATCATATTAA---AGGG
** * * * *
3476420 AAT-TAAA-AATTAAAAAAATTTATCATTT-TAAAATTAAAGGG
1 AATATAAATTTTTAATAAAATATA-CATTTATCATATTAAAGGG
3476461 AATATAAATTTTTACATAAAATATACATTTATCATATTAA
1 AATATAAATTTTTA-ATAAAATATACATTTATCATATTAA
3476501 TTTAATAATT
Statistics
Matches: 121, Mismatches: 32, Indels: 32
0.65 0.17 0.17
Matches are distributed among these distances:
40 2 0.02
41 6 0.05
42 8 0.07
43 46 0.38
44 44 0.36
45 8 0.07
46 6 0.05
47 1 0.01
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (43 bp):
AATATAAATTTTTAATAAAATATACATTTATCATATTAAAGGG
Found at i:3476837 original size:26 final size:26
Alignment explanation
Indices: 3476807--3476891 Score: 136
Period size: 26 Copynumber: 3.3 Consensus size: 26
3476797 ACTAGTATCG
3476807 TATCGTATTAT-CCGATATGTATCACA
1 TATCGTATTATACC-ATATGTATCACA
*
3476833 TATCGTATTATATCATATGTATCACA
1 TATCGTATTATACCATATGTATCACA
*
3476859 TATCGTATTATACCATACGTATCACA
1 TATCGTATTATACCATATGTATCACA
3476885 TATCGTA
1 TATCGTA
3476892 CGATAATGAT
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
26 54 0.98
27 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (26 bp):
TATCGTATTATACCATATGTATCACA
Found at i:3480002 original size:61 final size:61
Alignment explanation
Indices: 3479907--3480080 Score: 297
Period size: 55 Copynumber: 3.0 Consensus size: 61
3479897 CTCGTTGGTC
3479907 ACACATTTTATTTTCCCTATATGACAATGAATGGAGGATGAGTTAGATTGGGAGTTGTTTT
1 ACACATTTTATTTTCCCTATATGACAATGAATGGAGGATGAGTTAGATTGGGAGTTGTTTT
3479968 ACACATTTTATTTTCCCTATATGACAATGAATGGAGGATGAGTTAGATT----G--GTTTT
1 ACACATTTTATTTTCCCTATATGACAATGAATGGAGGATGAGTTAGATTGGGAGTTGTTTT
*
3480023 ACACATTTTATTTTCTCTATATGACAATGAATGGAGGATGAGTTAGATTGGGAGTTGT
1 ACACATTTTATTTTCCCTATATGACAATGAATGGAGGATGAGTTAGATTGGGAGTTGT
3480081 ACACGTTGAT
Statistics
Matches: 106, Mismatches: 1, Indels: 12
0.89 0.01 0.10
Matches are distributed among these distances:
55 53 0.50
57 1 0.01
59 1 0.01
61 51 0.48
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (61 bp):
ACACATTTTATTTTCCCTATATGACAATGAATGGAGGATGAGTTAGATTGGGAGTTGTTTT
Found at i:3483466 original size:17 final size:16
Alignment explanation
Indices: 3483433--3483475 Score: 54
Period size: 15 Copynumber: 2.7 Consensus size: 16
3483423 TAAAACTTTT
3483433 ATAAATTAAT-ACTCA
1 ATAAATTAATAACTCA
3483448 ATAAATTAATAATCTCA
1 ATAAATTAATAA-CTCA
3483465 ATTAAA-TAATA
1 A-TAAATTAATA
3483476 TTTTTGATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 10 0.40
16 1 0.04
17 10 0.40
18 4 0.16
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAAATTAATAACTCA
Found at i:3485106 original size:2 final size:2
Alignment explanation
Indices: 3485101--3485131 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3485091 TCTCTGGATC
3485101 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
3485132 GCACACACAC
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:3492338 original size:2 final size:2
Alignment explanation
Indices: 3492333--3492357 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3492323 TATATATATA
3492333 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
3492358 TGATGAAAAG
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3499279 original size:16 final size:17
Alignment explanation
Indices: 3499255--3499291 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
3499245 AATTTTACAT
*
3499255 AATATTTAAAT-ATATA
1 AATAGTTAAATAATATA
3499271 AATAGTTAAATAATATA
1 AATAGTTAAATAATATA
3499288 AATA
1 AATA
3499292 AAAAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
AATAGTTAAATAATATA
Found at i:3499486 original size:6 final size:6
Alignment explanation
Indices: 3499448--3499501 Score: 65
Period size: 6 Copynumber: 9.2 Consensus size: 6
3499438 CAAAAGAACA
* * * *
3499448 AAAGA- AAAAAG AAAGAT AAAAAG AAAGAG AAAGAG AAAGAG AGAGAG
1 AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG
3499495 AAAGAG A
1 AAAGAG A
3499502 TGCGAATAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
5 4 0.10
6 36 0.90
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (6 bp):
AAAGAG
Found at i:3508130 original size:15 final size:15
Alignment explanation
Indices: 3508112--3508145 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3508102 AGCTTTTTCC
*
3508112 TCTTTCTCCTTTCTT
1 TCTTTCTCCTTCCTT
*
3508127 TCTTTCTTCTTCCTT
1 TCTTTCTCCTTCCTT
3508142 TCTT
1 TCTT
3508146 CTTTTTCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (15 bp):
TCTTTCTCCTTCCTT
Found at i:3508136 original size:11 final size:11
Alignment explanation
Indices: 3508122--3508163 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
3508112 TCTTTCTCCT
*
3508122 TTCTTTCTTTC
1 TTCTTCCTTTC
3508133 TTCTTCCTTTC
1 TTCTTCCTTTC
3508144 TTCTT--TTTC
1 TTCTTCCTTTC
3508153 TTCTTCCTTTC
1 TTCTTCCTTTC
3508164 CAAGTCGATC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 9 0.32
11 19 0.68
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (11 bp):
TTCTTCCTTTC
Found at i:3508154 original size:20 final size:19
Alignment explanation
Indices: 3508118--3508163 Score: 74
Period size: 20 Copynumber: 2.4 Consensus size: 19
3508108 TTCCTCTTTC
3508118 TCCTTTCTTTCTTTCTTCT
1 TCCTTTCTTTCTTTCTTCT
*
3508137 TCCTTTCTTCTTTTTCTTCT
1 TCCTTTCTT-TCTTTCTTCT
3508157 TCCTTTC
1 TCCTTTC
3508164 CAAGTCGATC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (19 bp):
TCCTTTCTTTCTTTCTTCT
Found at i:3509596 original size:24 final size:23
Alignment explanation
Indices: 3509547--3509596 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
3509537 CTCCAATGCC
* * * *
3509547 TTTTTTTTTTGACATTAAACTCA
1 TTTTTTTTTTGAAAATAAAATAA
3509570 TTTTTTATTTTGAAAATAAAATAA
1 TTTTTT-TTTTGAAAATAAAATAA
3509594 TTT
1 TTT
3509597 CGTTTGCTAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (23 bp):
TTTTTTTTTTGAAAATAAAATAA
Found at i:3510307 original size:2 final size:2
Alignment explanation
Indices: 3510300--3510332 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3510290 AATATTCAAG
3510300 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3510333 TTCCCGATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3518162 original size:20 final size:22
Alignment explanation
Indices: 3518137--3518180 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
3518127 GGGCTTTCTT
3518137 TTCTAATGTTCTTA-A-CCTTG
1 TTCTAATGTTCTTATAGCCTTG
*
3518157 TTCTAATGTTGTTATAGCCTTG
1 TTCTAATGTTCTTATAGCCTTG
3518179 TT
1 TT
3518181 TGCCTTCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 1 0.05
22 7 0.33
ACGTcount: A:0.18, C:0.16, G:0.14, T:0.52
Consensus pattern (22 bp):
TTCTAATGTTCTTATAGCCTTG
Found at i:3529562 original size:22 final size:22
Alignment explanation
Indices: 3529490--3529664 Score: 167
Period size: 22 Copynumber: 7.9 Consensus size: 22
3529480 TCAATCATGT
* * *
3529490 TGTTACACGTAATTTTCAGAAAA
1 TGTTACATGTCATGTTCA-AAAA
*
3529513 TGTTACATGTCATGTTTAAAAAA
1 TGTTACATGTCATG-TTCAAAAA
*
3529536 TGTTACACGTCATGTTCAAAAA
1 TGTTACATGTCATGTTCAAAAA
* * *
3529558 CGTTACATG-CAAGTTTAAAAAA
1 TGTTACATGTCATG-TTCAAAAA
3529580 TGTTACATGTCATGTTCAAAAA
1 TGTTACATGTCATGTTCAAAAA
* *
3529602 TGTTACATGT-AAGTTCAAAAT
1 TGTTACATGTCATGTTCAAAAA
* *
3529623 TGTTACATGCCATATTCACAACAA
1 TGTTACATGTCATGTTCA-AA-AA
*
3529647 -GTTACATGCCATGTTCAA
1 TGTTACATGTCATGTTCAA
3529665 TAAAAATGTT
Statistics
Matches: 126, Mismatches: 20, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
21 21 0.17
22 52 0.41
23 49 0.39
24 4 0.03
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (22 bp):
TGTTACATGTCATGTTCAAAAA
Found at i:3531592 original size:27 final size:27
Alignment explanation
Indices: 3531530--3531597 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
3531520 NATGAAAATT
*
3531530 TATTAATTAATCAAGATATTATTTAATC
1 TATTAATTAAT-AAGATATTATTTAATA
* **
3531558 TATAAATTAATAATTTATTAATTT-ATA
1 TATTAATTAATAAGATATT-ATTTAATA
3531585 TATTAATTAATAA
1 TATTAATTAATAA
3531598 AAAAATTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 20 0.59
28 14 0.41
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (27 bp):
TATTAATTAATAAGATATTATTTAATA
Found at i:3543626 original size:26 final size:26
Alignment explanation
Indices: 3543573--3543629 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 26
3543563 AAGTTATATA
*
3543573 TTTTAAATGATATAAGTTATATGTTT
1 TTTTAAATGATACAAGTTATATGTTT
*
3543599 TTTTAAATAGATGCAAGTTATATGTTT
1 TTTTAAAT-GATACAAGTTATATGTTT
3543626 TTTT
1 TTTT
3543630 TTATATAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.54
Consensus pattern (26 bp):
TTTTAAATGATACAAGTTATATGTTT
Found at i:3544531 original size:47 final size:47
Alignment explanation
Indices: 3544462--3544563 Score: 145
Period size: 47 Copynumber: 2.2 Consensus size: 47
3544452 GATAGCAATA
* *
3544462 AGGGTT-AGGTTCGGATAATAAATTATAAAAATATTT-GCGTAGTTGT
1 AGGGTTCAGATTCGGATAATAAATTATAAAAATATTTAG-GTAATTGT
* *
3544508 AGGGTTCAGATTCGGATAGTAAATTTTAAAAATATTTAGGTAATTGT
1 AGGGTTCAGATTCGGATAATAAATTATAAAAATATTTAGGTAATTGT
3544555 AGGGTTCAG
1 AGGGTTCAG
3544564 GTACCTTACT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
46 6 0.12
47 43 0.86
48 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (47 bp):
AGGGTTCAGATTCGGATAATAAATTATAAAAATATTTAGGTAATTGT
Found at i:3546717 original size:21 final size:22
Alignment explanation
Indices: 3546692--3546733 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
3546682 TTCCTCACCA
*
3546692 AAATATTCAAAAT-AATAAATT
1 AAATATACAAAATAAATAAATT
*
3546713 AAATATACATAATAAATAAAT
1 AAATATACAAAATAAATAAAT
3546734 AATAAACATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (22 bp):
AAATATACAAAATAAATAAATT
Found at i:3553228 original size:21 final size:21
Alignment explanation
Indices: 3553202--3553261 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
3553192 ATTAAAATTG
3553202 TTTGAATGATCTTTG-AGCTTA
1 TTTGAATGATCTTTGAAG-TTA
* *
3553223 TTTGAATGATTTTTGAAGTTG
1 TTTGAATGATCTTTGAAGTTA
*
3553244 TTTGAATGAGTTTTTGAA
1 TTTGAATGA-TCTTTGAA
3553262 CTTAATTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
21 25 0.71
22 10 0.29
ACGTcount: A:0.25, C:0.03, G:0.22, T:0.50
Consensus pattern (21 bp):
TTTGAATGATCTTTGAAGTTA
Found at i:3553458 original size:21 final size:21
Alignment explanation
Indices: 3553434--3553480 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
3553424 CCATGTGAAA
3553434 AGTTTCAAAATTG-TATGAATG
1 AGTTTCAAAATTGCT-TGAATG
**
3553455 AGTTTTGAAATTGCTTGAATG
1 AGTTTCAAAATTGCTTGAATG
3553476 AGTTT
1 AGTTT
3553481 TGAACTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.32, C:0.04, G:0.21, T:0.43
Consensus pattern (21 bp):
AGTTTCAAAATTGCTTGAATG
Found at i:3553481 original size:21 final size:21
Alignment explanation
Indices: 3553441--3553523 Score: 96
Period size: 21 Copynumber: 4.0 Consensus size: 21
3553431 AAAAGTTTCA
*
3553441 AAATTGTATGAATGAGTTTTG
1 AAATTGTTTGAATGAGTTTTG
*
3553462 AAATTGCTTGAATGAGTTTTG
1 AAATTGTTTGAATGAGTTTTG
*
3553483 AACTTGTTTGAAT-AGGTTTTG
1 AAATTGTTTGAATGA-GTTTTG
* * *
3553504 AACTTGTTTAAATAAGTTTT
1 AAATTGTTTGAATGAGTTTT
3553524 AAACAACTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
20 1 0.02
21 53 0.96
22 1 0.02
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.46
Consensus pattern (21 bp):
AAATTGTTTGAATGAGTTTTG
Found at i:3557224 original size:20 final size:20
Alignment explanation
Indices: 3557199--3557238 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3557189 AAATCAACAG
3557199 GCAGATGAATCAAACTTGGT
1 GCAGATGAATCAAACTTGGT
3557219 GCAGATGAATCAAACTTGGT
1 GCAGATGAATCAAACTTGGT
3557239 CTACGTTGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (20 bp):
GCAGATGAATCAAACTTGGT
Found at i:3562412 original size:30 final size:31
Alignment explanation
Indices: 3562357--3562430 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 31
3562347 TTTCTTTAAC
* * *
3562357 TCAAAATAAAAGTACAAAAATTTATTT-AGT
1 TCAAAATAAAAATACAAAAACTTATTTGACT
* *
3562387 TCAAAATAAAAATATAAAGACTTATTTGACT
1 TCAAAATAAAAATACAAAAACTTATTTGACT
3562418 T-AAAATAAAAATA
1 TCAAAATAAAAATA
3562431 GACAAACATA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
30 35 0.92
31 3 0.08
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.31
Consensus pattern (31 bp):
TCAAAATAAAAATACAAAAACTTATTTGACT
Found at i:3564359 original size:15 final size:16
Alignment explanation
Indices: 3564341--3564370 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3564331 CTATTATGTG
3564341 GATTTT-ATTTTTAAT
1 GATTTTAATTTTTAAT
3564356 GATTTTAATTTTTAA
1 GATTTTAATTTTTAA
3564371 AAATTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (16 bp):
GATTTTAATTTTTAAT
Found at i:3565224 original size:14 final size:14
Alignment explanation
Indices: 3565205--3565232 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3565195 TTCCCATAAA
3565205 AAATCACATCATCG
1 AAATCACATCATCG
3565219 AAATCACATCATCG
1 AAATCACATCATCG
3565233 GGACTAACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.29, G:0.07, T:0.21
Consensus pattern (14 bp):
AAATCACATCATCG
Found at i:3565842 original size:3 final size:3
Alignment explanation
Indices: 3565834--3565874 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
3565824 TCTCTTGCAT
*
3565834 TTA TTA TTA TTA TTA TTA TTA -TA TTTA TTA TTA TCA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TT
3565875 TCATTATTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.88
4 2 0.06
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:3570535 original size:23 final size:23
Alignment explanation
Indices: 3570509--3570588 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 23
3570499 TAACCTTATT
3570509 AACCAGTCATGCAATGACCTATC
1 AACCAGTCATGCAATGACCTATC
***
3570532 AACCAGTCACAAAATGACCTATC
1 AACCAGTCATGCAATGACCTATC
* * * *
3570555 AACCAATAAAGCATTGACCTATC
1 AACCAGTCATGCAATGACCTATC
*
3570578 AACTAGTCATG
1 AACCAGTCATG
3570589 TACTGCCAAA
Statistics
Matches: 44, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.40, C:0.28, G:0.11, T:0.21
Consensus pattern (23 bp):
AACCAGTCATGCAATGACCTATC
Found at i:3573272 original size:33 final size:33
Alignment explanation
Indices: 3573199--3573279 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 33
3573189 ATCATACCAT
* * *
3573199 ATTAACATATTATATCATTATAAATTATGATAC
1 ATTAACATATCACATCATCATAAATTATGATAC
* * *
3573232 ATCAACATATCACATCATCATCAATTATGATAT
1 ATTAACATATCACATCATCATAAATTATGATAC
* *
3573265 GTTAACATACCACAT
1 ATTAACATATCACAT
3573280 TAGTGTTACG
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.43, C:0.17, G:0.04, T:0.36
Consensus pattern (33 bp):
ATTAACATATCACATCATCATAAATTATGATAC
Found at i:3573389 original size:28 final size:28
Alignment explanation
Indices: 3573357--3573427 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
3573347 TTTGGTTCAA
3573357 AATAAAAGTATAAAGCTTGATTAAACAT
1 AATAAAAGTATAAAGCTTGATTAAACAT
* * **
3573385 AATAAAAATATAAAGCTTGATTAGATGT
1 AATAAAAGTATAAAGCTTGATTAAACAT
*
3573413 AATAAAAGTACAAAG
1 AATAAAAGTATAAAG
3573428 GGTTATTTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.55, C:0.06, G:0.13, T:0.27
Consensus pattern (28 bp):
AATAAAAGTATAAAGCTTGATTAAACAT
Found at i:3581847 original size:2 final size:2
Alignment explanation
Indices: 3581840--3581879 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3581830 GCTAATTTAT
3581840 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3581880 GAACCTCAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3583487 original size:2 final size:2
Alignment explanation
Indices: 3583480--3583522 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
3583470 AGGTGGCGGG
*
3583480 AT AT AT AT AT AT AT AT AT AT AT AT AC 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
3583522 A
1 A
3583523 AATAGCTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3584402 original size:15 final size:16
Alignment explanation
Indices: 3584382--3584414 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3584372 AAAATCATAT
*
3584382 ATTTTTA-TATTATAA
1 ATTTTTACTATGATAA
3584397 ATTTTTACTATGATAA
1 ATTTTTACTATGATAA
3584413 AT
1 AT
3584415 CTTGAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (16 bp):
ATTTTTACTATGATAA
Found at i:3586085 original size:39 final size:39
Alignment explanation
Indices: 3586022--3586294 Score: 276
Period size: 39 Copynumber: 7.0 Consensus size: 39
3586012 GATTTCATCT
* ** * *
3586022 CATTCATAAATCAATATTTTTCATATAAATAAAACAAAA
1 CATTCATAAATCAATCTTCATCATATGAATAAACCAAAA
* *
3586061 CATTCATAAATCAATCATCATCATATAAATAAACCAAAA
1 CATTCATAAATCAATCTTCATCATATGAATAAACCAAAA
** * ** **
3586100 CATTTGTAAGTCAATCTTTGTCATATGAATAAATTAAAA
1 CATTCATAAATCAATCTTCATCATATGAATAAACCAAAA
* *
3586139 CATTCATAAATCAATCTTCATCATTTGAATAAATCAAAA
1 CATTCATAAATCAATCTTCATCATATGAATAAACCAAAA
* * *
3586178 CATTTATAAATCAATCTTTATCATCTGAATAAACCAAAA
1 CATTCATAAATCAATCTTCATCATATGAATAAACCAAAA
** * * *
3586217 TTTTCGTAAATCATTCTTCATCGTATGAATAAACCAAAA
1 CATTCATAAATCAATCTTCATCATATGAATAAACCAAAA
* * * * * *
3586256 TATTCACAAGTCGATTTTCATCATATGAACAAACCAAAA
1 CATTCATAAATCAATCTTCATCATATGAATAAACCAAAA
3586295 TAAAAAATAA
Statistics
Matches: 192, Mismatches: 42, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 192 1.00
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (39 bp):
CATTCATAAATCAATCTTCATCATATGAATAAACCAAAA
Found at i:3592334 original size:22 final size:22
Alignment explanation
Indices: 3592306--3592357 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
3592296 GTAGACTATC
* * *
3592306 TAAAACCTTCATGTTCATTTTG
1 TAAAACCTCCAGGTACATTTTG
*
3592328 TAAAACCTCCAGGTAGATTTTG
1 TAAAACCTCCAGGTACATTTTG
3592350 TAAAACCT
1 TAAAACCT
3592358 GAATACAACT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (22 bp):
TAAAACCTCCAGGTACATTTTG
Found at i:3593954 original size:19 final size:20
Alignment explanation
Indices: 3593934--3594011 Score: 72
Period size: 22 Copynumber: 3.8 Consensus size: 20
3593924 TCCAACTTTT
3593934 AATA-AAATATTAATATTTTA
1 AATATAAATATTAATA-TTTA
*
3593954 ACATATTAATATTAA-ATTATA
1 A-ATATAAATATTAATATT-TA
*
3593975 AATA-AAATATTACTATTTA
1 AATATAAATATTAATATTTA
3593994 AATTATAAATTATTAATA
1 AA-TATAAA-TATTAATA
3594012 AAATAACTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
19 11 0.23
20 11 0.23
21 10 0.21
22 15 0.32
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
AATATAAATATTAATATTTA
Found at i:3594105 original size:22 final size:21
Alignment explanation
Indices: 3594066--3594118 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
3594056 ATTTCATTTA
*
3594066 AATTATATATCAAATATTAAT
1 AATTAAATATCAAATATTAAT
*
3594087 AATTAAATCATCAATTATTAAT
1 AATTAAAT-ATCAAATATTAAT
*
3594109 ATTTTAAATA
1 A-ATTAAATA
3594119 AATTATCAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.26
22 14 0.52
23 6 0.22
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTAAATATCAAATATTAAT
Found at i:3594126 original size:27 final size:27
Alignment explanation
Indices: 3594090--3594250 Score: 118
Period size: 27 Copynumber: 5.9 Consensus size: 27
3594080 TATTAATAAT
*
3594090 TAAATCATCAATTATTAATATTTTAAA
1 TAAATTATCAATTATTAATATTTTAAA
*
3594117 TAAATTATCAATTATTAATATTTAAAAA
1 TAAATTATCAATTATTAATATTT-TAAA
*
3594145 TAAAAATTAATC-A-TAATAATA-TTTAAA
1 T--AAATT-ATCAATTATTAATATTTTAAA
*
3594172 TTAAA-TA--AAATATTAATATTTTAAAA
1 -TAAATTATCAATTATTAATATTTT-AAA
* * *
3594198 TATTAATGATTAAATTATTAATATTTGAAA
1 TA--AATTA-TCAATTATTAATATTTTAAA
**
3594228 TAAACAATCAATTATTAATATTT
1 TAAATTATCAATTATTAATATTT
3594251 AAAAACAAAA
Statistics
Matches: 108, Mismatches: 11, Indels: 30
0.72 0.07 0.20
Matches are distributed among these distances:
23 1 0.01
24 8 0.07
25 6 0.06
26 6 0.06
27 42 0.39
28 11 0.10
29 7 0.06
30 11 0.10
31 16 0.15
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (27 bp):
TAAATTATCAATTATTAATATTTTAAA
Found at i:3594196 original size:16 final size:16
Alignment explanation
Indices: 3594177--3594223 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
3594167 TTAAATTAAA
3594177 TAAAATATTAATATTT
1 TAAAATATTAATATTT
3594193 TAAAATATTAATGA--T
1 TAAAATATTAAT-ATTT
*
3594208 TAAATTATTAATATTT
1 TAAAATATTAATATTT
3594224 GAAATAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 1 0.04
15 12 0.44
16 13 0.48
17 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
TAAAATATTAATATTT
Found at i:3594231 original size:111 final size:115
Alignment explanation
Indices: 3594099--3594342 Score: 302
Period size: 122 Copynumber: 2.1 Consensus size: 115
3594089 TTAAATCATC
* **
3594099 AATTATTAATATTTTAAATAAATTATCAATTATTAATATTT-AA-AAA-T-AAA-AATTAATCAT
1 AATTATTAATATTTGAAATAAACAATCAATTATTAATATTTAAATAAAGTAAAATAATTAATCAT
*
3594159 AATAATATTTAAATTAAATAAAATATTAATATTTTAAAATATTAATGA-TT
66 AATAATATTTAAATTAAAT-AAATATTAATATTTTAAAATATTAACGACTT
3594209 AAATTATTAATATTTGAAATAAACAATCAATTATTAATATTTAAAAACAAAATAAAGTAAAATAA
1 -AATTATTAATATTTGAAATAAACAATCAATTATTAATATTT-------AAATAAAGTAAAATAA
* *
3594274 TTTATCATAATAATATTTAAATTAAATAAATATTAATATTTTAATATATTAACGACTT
58 TTAATCATAATAATATTTAAATTAAATAAATATTAATATTTTAAAATATTAACGACTT
*
3594332 AATTATAAATA
1 AATTATTAATA
3594343 CATATTAATA
Statistics
Matches: 113, Mismatches: 7, Indels: 15
0.84 0.05 0.11
Matches are distributed among these distances:
111 38 0.34
119 2 0.02
120 3 0.03
121 1 0.01
122 39 0.35
123 30 0.27
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (115 bp):
AATTATTAATATTTGAAATAAACAATCAATTATTAATATTTAAATAAAGTAAAATAATTAATCAT
AATAATATTTAAATTAAATAAATATTAATATTTTAAAATATTAACGACTT
Found at i:3594263 original size:84 final size:79
Alignment explanation
Indices: 3594102--3594264 Score: 177
Period size: 84 Copynumber: 2.0 Consensus size: 79
3594092 AATCATCAAT
* * *
3594102 TATTAATATTTTAAATAAATTATCAATTATTAATATTTAAAAATAAAAATTAATCATAATAATAT
1 TATTAATATTTTAAATAAATGATAAATTATTAATATTTAAAAATAAAAATCAAT-ATAATAATAT
**
3594167 TTAAATTAAATAAAA
65 TTAAACAAAATAAAA
* *
3594182 TATTAATATTTTAAAATATTAATGATTAAATTATTAATATTT-GAAATAAACAATCAAT-TATTA
1 TATTAATATTTT-AAATA--AATGA-TAAATTATTAATATTTAAAAATAAA-AATCAATATAATA
3594245 ATATTTAAAAACAAAATAAA
61 ATATTT--AAACAAAATAAA
3594265 GTAAAATAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
80 12 0.17
81 5 0.07
82 10 0.14
83 11 0.16
84 31 0.45
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.40
Consensus pattern (79 bp):
TATTAATATTTTAAATAAATGATAAATTATTAATATTTAAAAATAAAAATCAATATAATAATATT
TAAACAAAATAAAA
Found at i:3594352 original size:64 final size:63
Alignment explanation
Indices: 3594279--3594445 Score: 171
Period size: 64 Copynumber: 2.6 Consensus size: 63
3594269 AATAATTTAT
*
3594279 CATAATAATATTTAAATTAAATAAATATTAATATTTTAATATATTAACGACTT-AATTATAAAT-
1 CATATTAATATTTAAATTAAAT--ATATTAATATTTTAATATATTAACGA-TTAAATTATAAATG
3594342 A
63 A
* * *
3594343 CATATTAATATTTAAATGGTCAAT-TATTAATATTTTAAAATATTAATGATTAAATTATAAATGA
1 CATATTAATATTTAAAT--TAAATATATTAATATTTTAATATATTAACGATTAAATTATAAATGA
* * * *
3594407 AATATTTATATTTAAA-TGATTAGTTATTAATATTTTAAT
1 CATATTAATATTTAAATTAAATA--TATTAATATTTTAAT
3594446 TAAATTCTAG
Statistics
Matches: 87, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
61 3 0.03
62 2 0.02
63 33 0.38
64 45 0.52
66 4 0.05
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (63 bp):
CATATTAATATTTAAATTAAATATATTAATATTTTAATATATTAACGATTAAATTATAAATGA
Found at i:3594378 original size:63 final size:64
Alignment explanation
Indices: 3594304--3594445 Score: 198
Period size: 64 Copynumber: 2.2 Consensus size: 64
3594294 ATTAAATAAA
* *
3594304 TATTAATATTTTAATATATTAACGACTT-AATTATAAAT-ACATATTAATATTTAAATGGTCAAT
1 TATTAATATTTTAATATATTAACGA-TTAAATTATAAATGAAATATTAATATTTAAATGATCAAT
* * * * *
3594367 TATTAATATTTTAAAATATTAATGATTAAATTATAAATGAAATATTTATATTTAAATGATTAGT
1 TATTAATATTTTAATATATTAACGATTAAATTATAAATGAAATATTAATATTTAAATGATCAAT
3594431 TATTAATATTTTAAT
1 TATTAATATTTTAAT
3594446 TAAATTCTAG
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
62 2 0.03
63 33 0.48
64 34 0.49
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (64 bp):
TATTAATATTTTAATATATTAACGATTAAATTATAAATGAAATATTAATATTTAAATGATCAAT
Found at i:3594439 original size:22 final size:22
Alignment explanation
Indices: 3594345--3594441 Score: 87
Period size: 22 Copynumber: 4.5 Consensus size: 22
3594335 TATAAATACA
* *
3594345 TATTAATATTTAAATGGTCAAT
1 TATTAATATTTAAATGATTAAT
3594367 TATTAATATTTTAAAAT-ATTAAT
1 TATTAATA-TTT-AAATGATTAAT
*
3594390 GATTAA-ATTATAAATGA--AA-
1 TATTAATATT-TAAATGATTAAT
* *
3594409 TATTTATATTTAAATGATTAGT
1 TATTAATATTTAAATGATTAAT
3594431 TATTAATATTT
1 TATTAATATTT
3594442 TAATTAAATT
Statistics
Matches: 60, Mismatches: 7, Indels: 16
0.72 0.08 0.19
Matches are distributed among these distances:
19 11 0.18
20 5 0.08
21 7 0.12
22 21 0.35
23 12 0.20
24 4 0.07
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.48
Consensus pattern (22 bp):
TATTAATATTTAAATGATTAAT
Found at i:3594646 original size:16 final size:16
Alignment explanation
Indices: 3594625--3594655 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3594615 AATAATTATT
3594625 TTATTTTACTCTCATC
1 TTATTTTACTCTCATC
*
3594641 TTATTTTATTCTCAT
1 TTATTTTACTCTCAT
3594656 ATAATAATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATTTTACTCTCATC
Found at i:3595000 original size:9 final size:9
Alignment explanation
Indices: 3594986--3595016 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3594976 TTTAGTATTT
3594986 AATATAAAA
1 AATATAAAA
3594995 AATATAAAA
1 AATATAAAA
*
3595004 AATATAATA
1 AATATAAAA
3595013 AATA
1 AATA
3595017 GATTAGTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (9 bp):
AATATAAAA
Found at i:3596648 original size:23 final size:22
Alignment explanation
Indices: 3596614--3596684 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
3596604 AATTTAAAGA
3596614 TTTTATAA-AATATTACCCGAAGG
1 TTTTA-AAGAATA-TACCCGAAGG
**
3596637 TTTTAAAGAATATACTTGAAGG
1 TTTTAAAGAATATACCCGAAGG
* * * *
3596659 TTTTGAAGATTACACCCAAAGG
1 TTTTAAAGAATATACCCGAAGG
3596681 TTTT
1 TTTT
3596685 CAATATTGTA
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
22 30 0.77
23 9 0.23
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (22 bp):
TTTTAAAGAATATACCCGAAGG
Found at i:3596835 original size:23 final size:21
Alignment explanation
Indices: 3596821--3596877 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
3596811 TGATTATGGT
*
3596821 TACTTGAAGGTTTTGATAATG
1 TACTTAAAGGTTTTGATAATG
*
3596842 TACTTAAAGGTTTTCA-AGATTG
1 TACTTAAAGGTTTTGATA-A-TG
*
3596864 TACTCAAAGGTTTT
1 TACTTAAAGGTTTT
3596878 CAATATTGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.03
21 15 0.48
22 15 0.48
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (21 bp):
TACTTAAAGGTTTTGATAATG
Found at i:3596899 original size:22 final size:22
Alignment explanation
Indices: 3596840--3596888 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
3596830 GTTTTGATAA
*
3596840 TGTACTTAAAGGTTTTCAAGAT
1 TGTACTCAAAGGTTTTCAAGAT
*
3596862 TGTACTCAAAGGTTTTCAATAT
1 TGTACTCAAAGGTTTTCAAGAT
3596884 TGTAC
1 TGTAC
3596889 CTGGAAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (22 bp):
TGTACTCAAAGGTTTTCAAGAT
Found at i:3599445 original size:23 final size:22
Alignment explanation
Indices: 3599410--3599453 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
3599400 CTAGAAGCAT
*
3599410 AAAGAACAAAAAATAAATAAAAC
1 AAAGAACAAAAAA-AAACAAAAC
* *
3599433 AAAGCACACAAAAAAACAAAA
1 AAAGAACAAAAAAAAACAAAA
3599454 AAAAAAGGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.77, C:0.14, G:0.05, T:0.05
Consensus pattern (22 bp):
AAAGAACAAAAAAAAACAAAAC
Found at i:3602908 original size:52 final size:53
Alignment explanation
Indices: 3602821--3602933 Score: 158
Period size: 53 Copynumber: 2.2 Consensus size: 53
3602811 ATTTTAAAAT
* * *
3602821 TTTTATAACAACTTTTATTTTTTTGAAATTTTATAATTTTG-CACTACAATAA
1 TTTTATAACAACCTTTATTTTTTAGAAATTATATAATTTTGCCACTACAATAA
* *
3602873 TTTTATAACATACCTTTATTTTTTAG-AATTATATAATTTTGCCTCTATAATAA
1 TTTTATAACA-ACCTTTATTTTTTAGAAATTATATAATTTTGCCACTACAATAA
3602926 TTTTATAA
1 TTTTATAA
3602934 TTTTGCCCCT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
52 24 0.44
53 30 0.56
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.52
Consensus pattern (53 bp):
TTTTATAACAACCTTTATTTTTTAGAAATTATATAATTTTGCCACTACAATAA
Found at i:3605188 original size:27 final size:27
Alignment explanation
Indices: 3605122--3605282 Score: 100
Period size: 27 Copynumber: 6.0 Consensus size: 27
3605112 GTTCCAAGCC
*
3605122 AAGGGTATTCCAAGCTG--GAAGTGCCT
1 AAGGGTGTTCCAAGC-GCAGAAGTGCCT
* * *
3605148 AA-AGTGTTCTAAGCGCAGAAATGCCT
1 AAGGGTGTTCCAAGCGCAGAAGTGCCT
* *
3605174 AAGGGTGTTCCAAGCG-TGAA-TGCGT
1 AAGGGTGTTCCAAGCGCAGAAGTGCCT
* * *
3605199 CCAGGGATGTTCCAAGC-CTAGAAGCGCCC
1 -AAGGG-TGTTCCAAGCGC-AGAAGTGCCT
* * * *
3605228 AAGGGTGTTTCTAGCGCAGAAGCGCCC
1 AAGGGTGTTCCAAGCGCAGAAGTGCCT
* * *
3605255 AAGGGTGTTTCTAGCGCAGAAGCGCCT
1 AAGGGTGTTCCAAGCGCAGAAGTGCCT
3605282 A
1 A
3605283 GGGGCGTTTC
Statistics
Matches: 109, Mismatches: 17, Indels: 17
0.76 0.12 0.12
Matches are distributed among these distances:
24 1 0.01
25 13 0.12
26 19 0.17
27 66 0.61
28 8 0.07
29 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.20
Consensus pattern (27 bp):
AAGGGTGTTCCAAGCGCAGAAGTGCCT
Found at i:3605291 original size:27 final size:27
Alignment explanation
Indices: 3605218--3605304 Score: 138
Period size: 27 Copynumber: 3.2 Consensus size: 27
3605208 TTCCAAGCCT
3605218 AGAAGCGCCCAAGGGTGTTTCTAGCGC
1 AGAAGCGCCCAAGGGTGTTTCTAGCGC
3605245 AGAAGCGCCCAAGGGTGTTTCTAGCGC
1 AGAAGCGCCCAAGGGTGTTTCTAGCGC
* * * *
3605272 AGAAGCGCCTAGGGGCGTTTCTAGTGC
1 AGAAGCGCCCAAGGGTGTTTCTAGCGC
3605299 AGAAGC
1 AGAAGC
3605305 ACTTAGGACG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.23, C:0.24, G:0.34, T:0.18
Consensus pattern (27 bp):
AGAAGCGCCCAAGGGTGTTTCTAGCGC
Found at i:3605370 original size:27 final size:27
Alignment explanation
Indices: 3605336--3605410 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
3605326 AAAGCACCCA
*
3605336 AGGG-TGTTTCAAGCGCAGAAGAGCTC
1 AGGGATGTTTCAAGCGCAGAAGAGCGC
* *
3605362 AGGGATGTTTCAAGCACAGAAGTGCGC
1 AGGGATGTTTCAAGCGCAGAAGAGCGC
* *
3605389 AGGAATG-TTCTAAGCGTAGAAG
1 AGGGATGTTTC-AAGCGCAGAAG
3605411 CACCCAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
26 7 0.17
27 34 0.83
ACGTcount: A:0.31, C:0.16, G:0.33, T:0.20
Consensus pattern (27 bp):
AGGGATGTTTCAAGCGCAGAAGAGCGC
Found at i:3605410 original size:107 final size:107
Alignment explanation
Indices: 3605220--3605413 Score: 232
Period size: 107 Copynumber: 1.8 Consensus size: 107
3605210 CCAAGCCTAG
* * * * *
3605220 AAGCGCCCAAGGGTGTTTCTAGCGCAGAAGCGCCCAAGGGTGTTTCTAGCGCAGAAGCGCCTAGG
1 AAGCACCCAAGGGTGTTTCAAGCGCAGAAGAGCCCAAGGGTGTTTCAAGCACAGAAGCGCCTAGG
** *
3605285 GGCGTTTCTAGTGCAGAAGCACTTAGGACGTTCCAAGTACAA
66 AACGTTTCTAGCGCAGAAGCACTTAGGACGTTCCAAGTACAA
* *
3605327 AAGCACCCAAGGGTGTTTCAAGCGCAGAAGAGCTC-AGGGATGTTTCAAGCACAGAAGTGCGC-A
1 AAGCACCCAAGGGTGTTTCAAGCGCAGAAGAGCCCAAGGG-TGTTTCAAGCACAGAAGCGC-CTA
* *
3605390 GGAATG-TTCTAAGCGTAGAAGCAC
64 GGAACGTTTCT-AGCGCAGAAGCAC
3605414 CCAAAAAGCA
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
106 8 0.11
107 63 0.88
108 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.30, T:0.19
Consensus pattern (107 bp):
AAGCACCCAAGGGTGTTTCAAGCGCAGAAGAGCCCAAGGGTGTTTCAAGCACAGAAGCGCCTAGG
AACGTTTCTAGCGCAGAAGCACTTAGGACGTTCCAAGTACAA
Found at i:3608878 original size:15 final size:15
Alignment explanation
Indices: 3608860--3608897 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
3608850 AATATTTTAT
3608860 TATTTTT-AAAATAAA
1 TATTTTTCAAAA-AAA
3608875 TATTTTATCAAAAAAA
1 TATTTT-TCAAAAAAA
3608891 TATTTTT
1 TATTTTT
3608898 TATTAAACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.33
16 10 0.48
17 4 0.19
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTTTTCAAAAAAA
Found at i:3610554 original size:10 final size:10
Alignment explanation
Indices: 3610539--3610602 Score: 67
Period size: 10 Copynumber: 6.2 Consensus size: 10
3610529 ATAATTTTAT
3610539 TTTTTATTAA
1 TTTTTATTAA
*
3610549 TTTTTA-AAA
1 TTTTTATTAA
*
3610558 TTATTATTATA
1 TTTTTATTA-A
3610569 TAATTTTATTAA
1 T--TTTTATTAA
*
3610581 TTTTTTTTAA
1 TTTTTATTAA
3610591 TTTTTATTAA
1 TTTTTATTAA
3610601 TT
1 TT
3610603 ATAAAAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
9 7 0.16
10 26 0.59
11 2 0.05
12 2 0.05
13 7 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTTATTAA
Found at i:3628517 original size:2 final size:2
Alignment explanation
Indices: 3628512--3628539 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3628502 TGTGTGTGTG
3628512 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3628540 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3628544 original size:2 final size:2
Alignment explanation
Indices: 3628539--3628570 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3628529 ATATATATAT
3628539 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3628571 GTAGGTAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3629205 original size:15 final size:16
Alignment explanation
Indices: 3629174--3629208 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3629164 ATAATTTTTT
*
3629174 AATTTTTAAAAATTAA
1 AATTATTAAAAATTAA
3629190 AATTATTAAAAA-TAA
1 AATTATTAAAAATTAA
3629205 AATT
1 AATT
3629209 CATATAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATTATTAAAAATTAA
Found at i:3629495 original size:10 final size:9
Alignment explanation
Indices: 3629450--3629500 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
3629440 ATGGATAGTG
*
3629450 AAATTTAAA
1 AAATTAAAA
3629459 AAATTAAAA
1 AAATTAAAA
3629468 AAATT-AAA
1 AAATTAAAA
* *
3629476 AATTTGAATA
1 AAATT-AAAA
3629486 AAATTAAATA
1 AAATTAAA-A
3629496 AAATT
1 AAATT
3629501 TGTAAAATCA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
8 7 0.21
9 15 0.44
10 12 0.35
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (9 bp):
AAATTAAAA
Found at i:3629530 original size:15 final size:17
Alignment explanation
Indices: 3629510--3629543 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
3629500 TTGTAAAATC
3629510 ATTATATT-ATT-TTTA
1 ATTATATTAATTATTTA
3629525 ATTATATTAATTATTTA
1 ATTATATTAATTATTTA
3629542 AT
1 AT
3629544 AAAAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 3 0.18
17 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTATATTAATTATTTA
Done.