Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006301.1 Hibiscus syriacus cultivar Beakdansim tig00015059_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: 116299
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Found at i:1726 original size:29 final size:30
Alignment explanation
Indices: 1668--1737 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 30
1658 AACAGTCTCT
* *
1668 AAACTTTTAAAATATTTGTATTTTAGTCATC
1 AAACTTTT-AAATATTTGTATTATAATCATC
*
1699 AAACTTTTAAA-ATTTGTATTATAATCATT
1 AAACTTTTAAATATTTGTATTATAATCATC
1728 AAACTTTTAA
1 AAACTTTTAA
1738 TTTATTTTAG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 25 0.69
30 3 0.08
31 8 0.22
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (30 bp):
AAACTTTTAAATATTTGTATTATAATCATC
Found at i:1996 original size:55 final size:55
Alignment explanation
Indices: 1900--2011 Score: 143
Period size: 55 Copynumber: 2.0 Consensus size: 55
1890 AAGAAGGTTG
* * * *
1900 TAGAACGTAATCACTTATCCAAACTAAAATATTATTATAACATTGACAAACATAA
1 TAGAACCTAACCACTTATCCAAACTAAAATATTATCATAACATTGACAAAAATAA
* * * * *
1955 TAGAACCTAACCATTTATCCAAGCTAAGATGTTATCGTAACATTGACAAAAATAA
1 TAGAACCTAACCACTTATCCAAACTAAAATATTATCATAACATTGACAAAAATAA
2010 TA
1 TA
2012 TTTATATTAA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.46, C:0.17, G:0.08, T:0.29
Consensus pattern (55 bp):
TAGAACCTAACCACTTATCCAAACTAAAATATTATCATAACATTGACAAAAATAA
Found at i:4058 original size:18 final size:19
Alignment explanation
Indices: 4013--4058 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
4003 ATATCCGTTA
4013 ATTTAGATT-TTTATTAAT
1 ATTTAGATTATTTATTAAT
*
4031 ATTTATATTATTT-TTAAT
1 ATTTAGATTATTTATTAAT
4049 -TTGTAGATTA
1 ATT-TAGATTA
4059 AATTGTATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 2 0.08
18 19 0.79
19 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.61
Consensus pattern (19 bp):
ATTTAGATTATTTATTAAT
Found at i:9455 original size:15 final size:15
Alignment explanation
Indices: 9435--9468 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
9425 TATTTCTAAA
* *
9435 ATTTCTCTTTTCAAT
1 ATTTCTATTTACAAT
9450 ATTTCTATTTACAAT
1 ATTTCTATTTACAAT
9465 ATTT
1 ATTT
9469 TTTGGCAAAA
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:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTCTATTTACAAT
Found at i:11938 original size:25 final size:26
Alignment explanation
Indices: 11910--11964 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
11900 GAGCTGCTCA
* *
11910 CGAGCTTCAGTTCA-GGATTTCGAGT
1 CGAGCTCCAGTTCATAGATTTCGAGT
* *
11935 CGAGCTCCATTTCATAGTTTTCGAGT
1 CGAGCTCCAGTTCATAGATTTCGAGT
11961 CGAG
1 CGAG
11965 TCGAGCTCAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (26 bp):
CGAGCTCCAGTTCATAGATTTCGAGT
Found at i:15156 original size:16 final size:16
Alignment explanation
Indices: 15121--15158 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
15111 GTTGACCTTA
15121 AAATTTAAAGGTTGCTC
1 AAATTTAAA-GTTGCTC
15138 AAATTTAAA-TTGACTC
1 AAATTTAAAGTTG-CTC
15154 AAATT
1 AAATT
15159 GACCCGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 3 0.15
16 8 0.40
17 9 0.45
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (16 bp):
AAATTTAAAGTTGCTC
Found at i:15878 original size:77 final size:77
Alignment explanation
Indices: 15785--15952 Score: 327
Period size: 77 Copynumber: 2.2 Consensus size: 77
15775 TTAAATAAAT
15785 AATTTGTGAGCCACTAATGCTCGGGTGTTAAGTTGTCAATCTGCTTCAATTTTCTTGCAAAGACA
1 AATTTGTGAGCCACTAATGCTCGGGTGTTAAGTTGTCAATCTGCTTCAATTTTCTTGCAAAGACA
15850 ACTAAATCAACC
66 ACTAAATCAACC
*
15862 AATTTGTGAGCCACTAATGCTCGGGTGTTAAGTTGTCAATCTGCTTCAATTTTCTTGCAAAGCCA
1 AATTTGTGAGCCACTAATGCTCGGGTGTTAAGTTGTCAATCTGCTTCAATTTTCTTGCAAAGACA
15927 ACTAAATCAACC
66 ACTAAATCAACC
15939 AATTTGTGAGCCAC
1 AATTTGTGAGCCAC
15953 ATTGCTTGCT
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 90 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.32
Consensus pattern (77 bp):
AATTTGTGAGCCACTAATGCTCGGGTGTTAAGTTGTCAATCTGCTTCAATTTTCTTGCAAAGACA
ACTAAATCAACC
Found at i:17550 original size:17 final size:17
Alignment explanation
Indices: 17530--17565 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
17520 AGGTCAACGA
*
17530 TCAACGGTCGGGTCGGG
1 TCAACGGACGGGTCGGG
17547 TCAACGGACGGGTCGGG
1 TCAACGGACGGGTCGGG
17564 TC
1 TC
17566 GGGTCAGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.25, G:0.44, T:0.17
Consensus pattern (17 bp):
TCAACGGACGGGTCGGG
Found at i:26778 original size:18 final size:18
Alignment explanation
Indices: 26755--26796 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
26745 ACCCATAGTA
26755 AAAATCCCGTAAAATTTT
1 AAAATCCCGTAAAATTTT
* *
26773 AAAATCTCTTAAAATTTT
1 AAAATCCCGTAAAATTTT
26791 AAAATC
1 AAAATC
26797 TTTTAAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (18 bp):
AAAATCCCGTAAAATTTT
Found at i:26784 original size:10 final size:9
Alignment explanation
Indices: 26764--26805 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 9
26754 AAAAATCCCG
26764 TAAAAT-TT
1 TAAAATCTT
26772 TAAAATCTCT
1 TAAAATCT-T
26782 TAAAAT-TT
1 TAAAATCTT
26790 TAAAATCTTT
1 TAAAATC-TT
26800 TAAAAT
1 TAAAAT
26806 GTGTATAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 13 0.43
9 2 0.07
10 15 0.50
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (9 bp):
TAAAATCTT
Found at i:26797 original size:18 final size:18
Alignment explanation
Indices: 26764--26805 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
26754 AAAAATCCCG
26764 TAAAATTTTAAAATCTCT
1 TAAAATTTTAAAATCTCT
*
26782 TAAAATTTTAAAATCTTT
1 TAAAATTTTAAAATCTCT
26800 TAAAAT
1 TAAAAT
26806 GTGTATAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAAATTTTAAAATCTCT
Found at i:28804 original size:30 final size:30
Alignment explanation
Indices: 28770--28863 Score: 107
Period size: 30 Copynumber: 3.1 Consensus size: 30
28760 ATAGGAGAAA
* *
28770 ATGAATATGTGATATGTGAAAGTGAATTAT
1 ATGAAAATGTGATATGTGAAAGTGAACTAT
* * * * *
28800 ATGAAAATGTGTTACGTGCAAGTGAACCAC
1 ATGAAAATGTGATATGTGAAAGTGAACTAT
28830 ATGATTAAATGTGATATGTGAAAGTGAACTAT
1 ATGA--AAATGTGATATGTGAAAGTGAACTAT
28862 AT
1 AT
28864 ATATATGAAT
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
30 27 0.54
32 23 0.46
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.32
Consensus pattern (30 bp):
ATGAAAATGTGATATGTGAAAGTGAACTAT
Found at i:29231 original size:15 final size:15
Alignment explanation
Indices: 29211--29240 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29201 GTGAATGATA
*
29211 TAATAAGAAGCTATG
1 TAATAAGAAGATATG
29226 TAATAAGAAGATATG
1 TAATAAGAAGATATG
29241 GGTTTATGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.03, G:0.20, T:0.27
Consensus pattern (15 bp):
TAATAAGAAGATATG
Found at i:29640 original size:31 final size:31
Alignment explanation
Indices: 29538--29691 Score: 127
Period size: 32 Copynumber: 4.9 Consensus size: 31
29528 GTCGAGGGTT
* * * **
29538 TACCTATGTTCTACGGAAAATATGGACAAAA
1 TACCTATGTTCTTCGGGACATATGGACATTA
*
29569 TTACCTATG-TCTTTCGGGACATATGAACA-TA
1 -TACCTATGTTC-TTCGGGACATATGGACATTA
29600 GTTACCTATG-TCTTTCGGGACATATGGACATTA
1 --TACCTATGTTC-TTCGGGACATATGGACATTA
** *
29633 TACCTATGTTCTAAGGAACATATGGACAATT-
1 TACCTATGTTCTTCGGGACATATGGAC-ATTA
* *
29664 TACCTAGGTTCTTCGGGACCTATGGACA
1 TACCTATGTTCTTCGGGACATATGGACA
29692 GTTGCCGAGG
Statistics
Matches: 103, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
30 1 0.01
31 46 0.45
32 54 0.52
33 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (31 bp):
TACCTATGTTCTTCGGGACATATGGACATTA
Found at i:33189 original size:2 final size:2
Alignment explanation
Indices: 33182--33209 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
33172 ATATGTGATA
33182 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
33210 GAACATAAGT
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):
AT
Found at i:33367 original size:15 final size:15
Alignment explanation
Indices: 33347--33376 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
33337 GTGAATGATA
*
33347 TAATAAGAAGCTATG
1 TAATAAGAAGATATG
33362 TAATAAGAAGATATG
1 TAATAAGAAGATATG
33377 GGTTTATGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.03, G:0.20, T:0.27
Consensus pattern (15 bp):
TAATAAGAAGATATG
Found at i:33723 original size:32 final size:32
Alignment explanation
Indices: 33682--33786 Score: 133
Period size: 32 Copynumber: 3.3 Consensus size: 32
33672 AGTCGAGGGT
*
33682 TTACCTATGT-TCTACGGAACATATGGACAGAA
1 TTACCTATGTCT-TACGGGACATATGGACAGAA
* * *
33714 TTACCTATGTCTTTCGGGACATATGGATAAAA
1 TTACCTATGTCTTACGGGACATATGGACAGAA
* *
33746 TTACCTATGTCTTTCGGGACATATGGACAGTA
1 TTACCTATGTCTTACGGGACATATGGACAGAA
33778 -TACCTATGT
1 TTACCTATGT
33787 TCTAAGGTGT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
31 9 0.14
32 55 0.85
33 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (32 bp):
TTACCTATGTCTTACGGGACATATGGACAGAA
Found at i:35166 original size:24 final size:24
Alignment explanation
Indices: 35134--35190 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
35124 AAACCACGTA
35134 GATATGATTTATGAGAGTATAAGT
1 GATATGATTTATGAGAGTATAAGT
*
35158 GATAAGATTTATGAGAGTATAAGT
1 GATATGATTTATGAGAGTATAAGT
35182 GATATGATT
1 GATATGATT
35191 GCAAGATTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.37
Consensus pattern (24 bp):
GATATGATTTATGAGAGTATAAGT
Found at i:35474 original size:18 final size:18
Alignment explanation
Indices: 35451--35524 Score: 58
Period size: 18 Copynumber: 3.9 Consensus size: 18
35441 GTTTTTAAGG
*
35451 AGTGGTCCTTCGAGACAT
1 AGTGGTCATTCGAGACAT
* *
35469 AGTGGTCATTCGGGATAAAT
1 AGTGGTCATTC--GAGACAT
* * *
35489 CAGTGGTCCTTTGGGACAT
1 -AGTGGTCATTCGAGACAT
*
35508 AGTGGTCATTCGGGACA
1 AGTGGTCATTCGAGACA
35525 AATATACAGT
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
18 25 0.58
19 4 0.09
20 5 0.12
21 9 0.21
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (18 bp):
AGTGGTCATTCGAGACAT
Found at i:35495 original size:21 final size:19
Alignment explanation
Indices: 35467--35528 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 19
35457 CCTTCGAGAC
35467 ATAGTGGTCATTCGGGATAA
1 ATAGTGGTCATTCGGGA-AA
* * *
35487 ATCAGTGGTCCTTTGGG-AC
1 AT-AGTGGTCATTCGGGAAA
35506 ATAGTGGTCATTCGGGACAA
1 ATAGTGGTCATTCGGGA-AA
35526 ATA
1 ATA
35529 TACAGTGCCC
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
18 12 0.36
19 3 0.09
20 6 0.18
21 12 0.36
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (19 bp):
ATAGTGGTCATTCGGGAAA
Found at i:35507 original size:39 final size:39
Alignment explanation
Indices: 35451--35527 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
35441 GTTTTTAAGG
*
35451 AGTGGTCCTTCGAGACATAGTGGTCATTCGGGATAAATC
1 AGTGGTCCTTCGAGACATAGTGGTCATTCGGGACAAATC
* *
35490 AGTGGTCCTTTGGGACATAGTGGTCATTCGGGACAAAT
1 AGTGGTCCTTCGAGACATAGTGGTCATTCGGGACAAAT
35528 ATACAGTGCC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.29
Consensus pattern (39 bp):
AGTGGTCCTTCGAGACATAGTGGTCATTCGGGACAAATC
Found at i:40718 original size:12 final size:12
Alignment explanation
Indices: 40701--40736 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
40691 AATGTGCATC
40701 GATGCATTAAGG
1 GATGCATTAAGG
40713 GATGCATTAAGG
1 GATGCATTAAGG
*
40725 GAAGCATTAAGG
1 GATGCATTAAGG
40737 AAATTAGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.36, C:0.08, G:0.33, T:0.22
Consensus pattern (12 bp):
GATGCATTAAGG
Found at i:41028 original size:25 final size:24
Alignment explanation
Indices: 40970--41028 Score: 57
Period size: 25 Copynumber: 2.3 Consensus size: 24
40960 ATAGGTCTAG
*
40970 ATTCAATATTTTGATACATGATGAC
1 ATTC-ATATTATGATACATGATGAC
*
40995 ATTTTATATTATGATACATGACATGA-
1 A-TTCATATTATGATACATG--ATGAC
41021 ATTCATAT
1 ATTCATAT
41029 CATATGCATT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
25 21 0.75
26 3 0.11
27 4 0.14
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.42
Consensus pattern (24 bp):
ATTCATATTATGATACATGATGAC
Found at i:41381 original size:23 final size:23
Alignment explanation
Indices: 41347--41390 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
41337 ACATATTATT
41347 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
41370 TGGCACTTCGGTGCATTTCTA
1 TGGCACTACGGTGCAATTCTA
41391 TGCGGTCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:41433 original size:24 final size:24
Alignment explanation
Indices: 41361--41435 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
41351 ACTACGGTGC
* *
41361 AATTCTACGTGGCACTTCGGTGC-
1 AATTCTACGTGGTACTTCGATGCA
* * * * *
41384 ATTTCTATGCGGTCCTTC-AGGACA
1 AATTCTACGTGGTACTTCGATG-CA
41408 AATTCTACGTGGTACTTCGATGCA
1 AATTCTACGTGGTACTTCGATGCA
41432 AATT
1 AATT
41436 TATATGAGTT
Statistics
Matches: 37, Mismatches: 12, Indels: 5
0.69 0.22 0.09
Matches are distributed among these distances:
22 1 0.03
23 14 0.38
24 20 0.54
25 2 0.05
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (24 bp):
AATTCTACGTGGTACTTCGATGCA
Found at i:45033 original size:64 final size:64
Alignment explanation
Indices: 44947--45107 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 64
44937 ATTGTTTAAG
* * ** *
44947 ATGCATCGATGCACATGCAGTGCATCGATGCAT-GATTTTAAATAGAAAACATCGAATAGGA-TT
1 ATGCATCGATGCACAAGCAGTGCATCGATGCATCCACATTAAATA-AAAACATCGAAT-GCATTT
45010 T
64 T
* * *
45011 ATGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAAAAACATCGAATGCATTTT
1 ATGCATCGATGCACAAGCAGTGCATCGATGCATCCACATTAAATAAAAACATCGAATGCATTTT
* *
45075 ATGCACCGATGCACAAGTAGTGCATCGATGCAT
1 ATGCATCGATGCACAAGCAGTGCATCGATGCAT
45108 ACATTCATTG
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
63 2 0.02
64 75 0.89
65 7 0.08
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (64 bp):
ATGCATCGATGCACAAGCAGTGCATCGATGCATCCACATTAAATAAAAACATCGAATGCATTTT
Found at i:45738 original size:30 final size:30
Alignment explanation
Indices: 45702--45765 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
45692 AAGGAACATA
* *
45702 TGGATAGTTCCCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* * *
45732 TGGATAGTTACCGGGGTTCTTTGTAACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
45762 TGGA
1 TGGA
45766 CAGGTCCTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.19, C:0.20, G:0.27, T:0.34
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:49196 original size:64 final size:64
Alignment explanation
Indices: 49110--49270 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 64
49100 ATTGTTTAAG
* * ** *
49110 ATGCATCGATGCACATGCAGTGCATCGATGCAT-GATTTTAAATAGAAAACATCGAATAGGA-TT
1 ATGCATCGATGCACAAGCAGTGCATCGATGCATCCACATTAAATA-AAAACATCGAAT-GCATTT
49173 T
64 T
* * *
49174 ATGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAAAAACATCGAATGCATTTT
1 ATGCATCGATGCACAAGCAGTGCATCGATGCATCCACATTAAATAAAAACATCGAATGCATTTT
* *
49238 ATGCACCGATGCACAAGTAGTGCATCGATGCAT
1 ATGCATCGATGCACAAGCAGTGCATCGATGCAT
49271 ACATTCATTG
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
63 2 0.02
64 75 0.89
65 7 0.08
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (64 bp):
ATGCATCGATGCACAAGCAGTGCATCGATGCATCCACATTAAATAAAAACATCGAATGCATTTT
Found at i:49911 original size:30 final size:30
Alignment explanation
Indices: 49875--49938 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
49865 AAGGAACATA
* *
49875 TGGATAGTTGCCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* * *
49905 TGGATAGTTACCGGGGTTCTTTGTAACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
49935 TGGA
1 TGGA
49939 CAGGTCCTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:54645 original size:25 final size:24
Alignment explanation
Indices: 54590--54648 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 24
54580 ATAAGTCTAG
*
54590 ATTCAATATTTTGATACATGATGAC
1 ATTC-ATATTATGATACATGATGAC
54615 ATTTCATATTATGATACATGACATGA-
1 A-TTCATATTATGATACATG--ATGAC
54641 ATTCATAT
1 ATTCATAT
54649 CATATGCATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 22 0.73
26 4 0.13
27 4 0.13
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (24 bp):
ATTCATATTATGATACATGATGAC
Found at i:55039 original size:24 final size:24
Alignment explanation
Indices: 54968--55055 Score: 85
Period size: 23 Copynumber: 3.8 Consensus size: 24
54958 CATATTATAC
*
54968 GGCACTACGGTGC-AATTCTACGT
1 GGCACTTCGGTGCAAATTCTACGT
* * *
54991 GGCACTTTGGCGC-ATTTCTACGT
1 GGCACTTCGGTGCAAATTCTACGT
*
55014 GGTC-CTTCGG-GACAAATTCTATGT
1 GG-CACTTCGGTG-CAAATTCTACGT
55038 GGCACTTCGGTGCAAATT
1 GGCACTTCGGTGCAAATT
55056 TATACGAGCT
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
22 1 0.02
23 28 0.53
24 23 0.43
25 1 0.02
ACGTcount: A:0.19, C:0.24, G:0.26, T:0.31
Consensus pattern (24 bp):
GGCACTTCGGTGCAAATTCTACGT
Found at i:58221 original size:34 final size:28
Alignment explanation
Indices: 58133--58195 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
58123 TATACTCGCG
58133 TTTAGCCCAATTCACGTTTTATGTGCAT
1 TTTAGCCCAATTCACGTTTTATGTGCAT
58161 TTTAGCCCAATTCACGTTTTATGTGCAT
1 TTTAGCCCAATTCACGTTTTATGTGCAT
58189 TTTAGCC
1 TTTAGCC
58196 ATAGCCCAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.43
Consensus pattern (28 bp):
TTTAGCCCAATTCACGTTTTATGTGCAT
Found at i:58244 original size:35 final size:34
Alignment explanation
Indices: 58163--58250 Score: 106
Period size: 34 Copynumber: 2.6 Consensus size: 34
58153 ATGTGCATTT
***
58163 TAGCCCAATTCACGTTTTATGTGCATTTTAGCCA
1 TAGCCCAATTCACGTTTTATGTGCATGAAAGCCA
* *
58197 TAGCCCAATTCACGTTTTATGTGCACTGAAATCTGA
1 TAGCCCAATTCACGTTTTATGTGCA-TGAAAGC-CA
58233 -AGCCCAATTCACGTTTTA
1 TAGCCCAATTCACGTTTTA
58251 ATTTGATTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
34 25 0.53
35 21 0.45
36 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (34 bp):
TAGCCCAATTCACGTTTTATGTGCATGAAAGCCA
Found at i:64496 original size:3 final size:3
Alignment explanation
Indices: 64483--64544 Score: 56
Period size: 3 Copynumber: 20.7 Consensus size: 3
64473 GTAATATGTA
** *
64483 AAT AA- AAT AAT AAT AAT AAT GCT AAT AAT AAT AATT AA- AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
*
64527 GAT AAT AAT AAT ATAT AA
1 AAT AAT AAT AAT A-AT AA
64545 AAAAGACCCG
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
2 4 0.09
3 37 0.79
4 6 0.13
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:64545 original size:24 final size:23
Alignment explanation
Indices: 64483--64546 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 23
64473 GTAATATGTA
* *
64483 AATAA-AATAATAATAATAATGCT
1 AATAATAATAATAA-AATAACGAT
64506 AATAATAATAATTAAAATAACGAT
1 AATAATAATAA-TAAAATAACGAT
64530 AATAATAATATATAAAA
1 AATAATAATA-ATAAAA
64547 AAGACCCGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
23 5 0.14
24 27 0.75
25 4 0.11
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (23 bp):
AATAATAATAATAAAATAACGAT
Found at i:64909 original size:46 final size:46
Alignment explanation
Indices: 64859--65038 Score: 182
Period size: 46 Copynumber: 4.1 Consensus size: 46
64849 AGTTCTGGCC
64859 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTT
1 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTT
* * * * * *
64905 ATCT-ATGGT--TGACACGGCTCATACGTGATGAAGA-GATCTGG--
1 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTT
* * * **
64946 -TCT---GGGGATGACACGGTTCCTACATGATGAGGACGGCTGGCC
1 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTT
64988 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTT
1 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTT
65034 ATCTA
1 ATCTA
65039 TGGTTGACAC
Statistics
Matches: 107, Mismatches: 17, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
38 2 0.02
40 28 0.26
41 1 0.01
42 1 0.01
43 28 0.26
45 4 0.04
46 43 0.40
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.26
Consensus pattern (46 bp):
ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTT
Found at i:64957 original size:129 final size:128
Alignment explanation
Indices: 64687--65120 Score: 602
Period size: 129 Copynumber: 3.3 Consensus size: 128
64677 TGTGTGTTGG
* * * * * * * *
64687 TGGGGACGACACTGCTCATACGTGATGAAGAGGTCTGGTCGTCTAAGGGTGGATGATAACTCAGT
1 TGGGGATGACACGGCTCATACATGATGAAGA-GTCTGGCCATCTAA---AGG-TGATAACACGGT
* *
64752 TCCTACGTGATGAGGACGACTGGTTATCTA-GGGTGACACGGCTCATACGTGATGAAGAGATCTG
61 TCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTG
64816 GTC
126 GTC
*
64819 -GGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCC
1 TGGGG-ATGACACGGCTCATACATGATGAAGAG-TCTGGCCATCTAAAGGTGATAACACGGTTCC
64883 TACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTC
64 TACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTC
* * * *
64948 TGGGGATGACACGGTTCCTACATGATGAGGACGGCTGGCCATCTAAAGGTGATAACACGGTTCCT
1 TGGGGATGACACGGCTCATACATGATGAAGA-GTCTGGCCATCTAAAGGTGATAACACGGTTCCT
65013 ACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTC
65 ACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTC
* * * *
65077 TGGGGATGACACGGTTCCTACATGATGAGGACGGCTGGCCATCT
1 TGGGGATGACACGGCTCATACATGATGAAGA-GTCTGGCCATCT
65121 TTAGGAGTTA
Statistics
Matches: 283, Mismatches: 14, Indels: 13
0.91 0.05 0.04
Matches are distributed among these distances:
128 39 0.14
129 199 0.70
130 5 0.02
131 5 0.02
132 35 0.12
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (128 bp):
TGGGGATGACACGGCTCATACATGATGAAGAGTCTGGCCATCTAAAGGTGATAACACGGTTCCTA
CGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTC
Found at i:64974 original size:40 final size:40
Alignment explanation
Indices: 64777--65104 Score: 180
Period size: 40 Copynumber: 7.8 Consensus size: 40
64767 ACGACTGGTT
*
64777 ATCTAGGG-TGACACGGCTCATACGTGATGAAGAGATCTGG
1 ATCTGGGGATGACACGGCTCATACGTGATGAAGAG-TCTGG
64817 -TC-GGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGG
1 ATCTGGGG-ATGACACGGCTCATACGTGATGAAGAG-TCTGG
* * * * * *
64857 CCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGG
1 --ATCT---GGGGATGACACGGCTCATACGTGATGAAGA-GTCTGG
** *
64903 TTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGG
1 --ATCTGGGGATGACACGGCTCATACGTGATGAAGAG-TCTGG
* * * * *
64946 -TCTGGGGATGACACGGTTCCTACATGATGAGGACGGCTGG
1 ATCTGGGGATGACACGGCTCATACGTGATGAAGA-GTCTGG
* * * * * *
64986 CCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGG
1 --ATCT---GGGGATGACACGGCTCATACGTGATGAAGA-GTCTGG
** *
65032 TTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGG
1 --ATCTGGGGATGACACGGCTCATACGTGATGAAGAG-TCTGG
* * *
65075 -TCTGGGGATGACACGGTTCCTACATGATGA
1 ATCTGGGGATGACACGGCTCATACGTGATGA
65105 GGACGGCTGG
Statistics
Matches: 222, Mismatches: 47, Indels: 38
0.72 0.15 0.12
Matches are distributed among these distances:
38 3 0.01
39 2 0.01
40 85 0.38
41 1 0.00
42 2 0.01
43 57 0.26
46 68 0.31
47 4 0.02
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (40 bp):
ATCTGGGGATGACACGGCTCATACGTGATGAAGAGTCTGG
Found at i:64992 original size:83 final size:85
Alignment explanation
Indices: 64825--64992 Score: 232
Period size: 83 Copynumber: 2.0 Consensus size: 85
64815 GGTCGGGGAA
* * *
64825 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGG-C-TCT--AGGGGATAACACGGTTCCTACATGA
**
64890 TGAGGACGGCTGGTTATCTATGGT
62 TGAGGACGGCTGGCCATCTATGGT
*
64914 TGACACGGCTCATACGTGATGAAGAGATCTGG-TCT-GGGGATGACACGGTTCCTACATGATGAG
1 TGACACGGCTCATACGTGATGAAGAGATCTGGCTCTAGGGGATAACACGGTTCCTACATGATGAG
64977 GACGGCTGGCCATCTA
66 GACGGCTGGCCATCTA
64993 AAGGTGATAA
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
83 39 0.53
86 3 0.04
89 31 0.42
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.25
Consensus pattern (85 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGCTCTAGGGGATAACACGGTTCCTACATGATGAG
GACGGCTGGCCATCTATGGT
Found at i:65173 original size:28 final size:28
Alignment explanation
Indices: 65153--65214 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
65143 AAACCAAATT
65153 AAAGATTTGTTTCAAAAGAAACAAACCC
1 AAAGATTTGTTTCAAAAGAAACAAACCC
* *
65181 AAAGATTTGTTTCAAGAA-AAATAAACTC
1 AAAGATTTGTTTCAA-AAGAAACAAACCC
65209 AAAGAT
1 AAAGAT
65215 GATATTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 29 0.94
29 2 0.06
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.24
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAAACCC
Found at i:65995 original size:28 final size:27
Alignment explanation
Indices: 65964--66023 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 27
65954 ATGATTTTCA
*
65964 AAAGAAATTGTCCCAAAGAAACAGACTC
1 AAAGAAATTGTCCAAAAGAAACA-ACTC
** * *
65992 AAAGATTTTTTTCAAAAGAAACAACTC
1 AAAGAAATTGTCCAAAAGAAACAACTC
66019 AAAGA
1 AAAGA
66024 TTTTTATTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 9 0.33
28 18 0.67
ACGTcount: A:0.52, C:0.17, G:0.12, T:0.20
Consensus pattern (27 bp):
AAAGAAATTGTCCAAAAGAAACAACTC
Found at i:66018 original size:27 final size:28
Alignment explanation
Indices: 65978--66069 Score: 132
Period size: 28 Copynumber: 3.3 Consensus size: 28
65968 AAATTGTCCC
65978 AAAGAAACAGACTCAAAGATTTTTTTCA
1 AAAGAAACAGACTCAAAGATTTTTTTCA
66006 AAAGAAACA-ACTCAAAGATTTTTATTCA
1 AAAGAAACAGACTCAAAGATTTTT-TTCA
* * *
66034 AAAGGAACAGACTCAAAGATTTATCTCA
1 AAAGAAACAGACTCAAAGATTTTTTTCA
*
66062 AGAGAAAC
1 AAAGAAAC
66070 TGTCTCCAGA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
27 14 0.25
28 30 0.53
29 13 0.23
ACGTcount: A:0.49, C:0.15, G:0.12, T:0.24
Consensus pattern (28 bp):
AAAGAAACAGACTCAAAGATTTTTTTCA
Found at i:66028 original size:28 final size:29
Alignment explanation
Indices: 65978--66055 Score: 133
Period size: 28 Copynumber: 2.8 Consensus size: 29
65968 AAATTGTCCC
65978 AAAGAAACAGACTCAAAGATTTTT-TTCA
1 AAAGAAACAGACTCAAAGATTTTTATTCA
66006 AAAGAAACA-ACTCAAAGATTTTTATTCA
1 AAAGAAACAGACTCAAAGATTTTTATTCA
*
66034 AAAGGAACAGACTCAAAGATTT
1 AAAGAAACAGACTCAAAGATTT
66056 ATCTCAAGAG
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
27 14 0.30
28 21 0.45
29 12 0.26
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.26
Consensus pattern (29 bp):
AAAGAAACAGACTCAAAGATTTTTATTCA
Found at i:66454 original size:35 final size:35
Alignment explanation
Indices: 66364--66468 Score: 140
Period size: 35 Copynumber: 3.0 Consensus size: 35
66354 TATCTCAAAG
* *
66364 GAAAAATGTCTCAAGCGAGACGAAATTTGTTTTGA
1 GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTTA
* *
66399 -AAGAAATTGTCTTAAACGAGACAAAATTTGTTTTTA
1 GAA-AAA-TGTCTCAAGCGAGACAAAATTTGTTTTTA
*
66435 GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTT
1 GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTT
66469 CAAAAGAAGA
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
34 2 0.03
35 29 0.48
36 27 0.45
37 2 0.03
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.32
Consensus pattern (35 bp):
GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTTA
Found at i:70489 original size:32 final size:32
Alignment explanation
Indices: 70453--70514 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
70443 TGAAAAAAAG
* *
70453 ACACAAACAACAGAAAATAAATAAGTTAGTGC
1 ACACAAACAAAAGAAAAGAAATAAGTTAGTGC
* *
70485 ACACAAAGAAAAGAAAAGAAATTAGTTAGT
1 ACACAAACAAAAGAAAAGAAATAAGTTAGT
70515 ACAGGTAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.58, C:0.11, G:0.15, T:0.16
Consensus pattern (32 bp):
ACACAAACAAAAGAAAAGAAATAAGTTAGTGC
Found at i:73446 original size:11 final size:10
Alignment explanation
Indices: 73425--73454 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
73415 CGAATGGGTA
73425 TTTTTTCTTT
1 TTTTTTCTTT
73435 TTTTTTCTTT
1 TTTTTTCTTT
73445 TTTTTT-TTT
1 TTTTTTCTTT
73454 T
1 T
73455 GGTTCTCACC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.20
10 16 0.80
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:73977 original size:3 final size:3
Alignment explanation
Indices: 73964--74025 Score: 56
Period size: 3 Copynumber: 20.7 Consensus size: 3
73954 GTAATATGTA
** *
73964 AAT AA- AAT AAT AAT AAT AAT GCT AAT AAT AAT AATT AA- AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
*
74008 GAT AAT AAT AAT ATAT AA
1 AAT AAT AAT AAT A-AT AA
74026 AAAAGACCCG
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
2 4 0.09
3 37 0.79
4 6 0.13
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:74026 original size:24 final size:23
Alignment explanation
Indices: 73964--74027 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 23
73954 GTAATATGTA
* *
73964 AATAA-AATAATAATAATAATGCT
1 AATAATAATAATAA-AATAACGAT
73987 AATAATAATAATTAAAATAACGAT
1 AATAATAATAA-TAAAATAACGAT
74011 AATAATAATATATAAAA
1 AATAATAATA-ATAAAA
74028 AAGACCCGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
23 5 0.14
24 27 0.75
25 4 0.11
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (23 bp):
AATAATAATAATAAAATAACGAT
Found at i:78031 original size:13 final size:13
Alignment explanation
Indices: 78000--78038 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
77990 AATACGACGA
78000 TTTTATT-TTTAT
1 TTTTATTATTTAT
78012 TTTTATTATTT-T
1 TTTTATTATTTAT
78024 TCTTTATTATTTAT
1 T-TTTATTATTTAT
78038 T
1 T
78039 AAGATATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 9 0.38
13 13 0.54
14 2 0.08
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTATTATTTAT
Found at i:79340 original size:29 final size:29
Alignment explanation
Indices: 79307--79381 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
79297 AACCCAACCA
**
79307 TAGGTCGCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
* * *
79336 TAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
*
79365 GAGGTCGCCATGCACTC
1 TAGGTCGCCATGCACTC
79382 GGGGCGACCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.15
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCAAC
Found at i:79387 original size:29 final size:29
Alignment explanation
Indices: 79308--79395 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
79298 ACCCAACCAT
* * ****
79308 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
79337 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
* **
79366 AGGTCGCCATGCACTCGGGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
79395 A
1 A
79396 TTCATGCATG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.20, C:0.38, G:0.31, T:0.11
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAAGG
Found at i:79643 original size:29 final size:29
Alignment explanation
Indices: 79610--79694 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
79600 AGCAGGGGAT
* * **
79610 GTCGCCGCGAGTGCATGGCGACCTCCTTG
1 GTCGCCGGGAGTGCATGGCGACCTACGAG
* *
79639 GTCGCCGGGCGTGCATGGCGACCTAGGAG
1 GTCGCCGGGAGTGCATGGCGACCTACGAG
*
79668 GTCGCTGGGAGTGCATGGCGACCTACG
1 GTCGCCGGGAGTGCATGGCGACCTACG
79695 GCCACTGTTG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.13, C:0.29, G:0.40, T:0.18
Consensus pattern (29 bp):
GTCGCCGGGAGTGCATGGCGACCTACGAG
Found at i:81839 original size:15 final size:15
Alignment explanation
Indices: 81790--81838 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
81780 GGTATTTAGT
*
81790 GGGCAGGCGGATGTG
1 GGGCAGGCGGATGCG
*
81805 GGGCAGGCGGATGCA
1 GGGCAGGCGGATGCG
*
81820 GGGCGGGCGGATGCG
1 GGGCAGGCGGATGCG
81835 GGGC
1 GGGC
81839 GAGTAAGGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.12, C:0.18, G:0.61, T:0.08
Consensus pattern (15 bp):
GGGCAGGCGGATGCG
Found at i:82877 original size:3 final size:3
Alignment explanation
Indices: 82869--82937 Score: 95
Period size: 3 Copynumber: 22.7 Consensus size: 3
82859 GTAATTTTTG
**
82869 TAA TAA TAAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TTG
1 TAA TAA T-AA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
82916 TAA T-A TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
82938 TATAGTCTCG
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
2 2 0.03
3 51 0.86
4 6 0.10
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:83918 original size:31 final size:30
Alignment explanation
Indices: 83865--83932 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
83855 TTTTATTAAT
*
83865 AATTTATTTTTGTCATTTTAAAATATTAAAA
1 AATTTATTTTTGTCATTCTAAAAT-TTAAAA
* * *
83896 AATTTATTTTATTTC-TTCTAAAATTTTATA
1 AATTTATTTT-TGTCATTCTAAAATTTAAAA
83926 AATTTAT
1 AATTTAT
83933 CTTCTTTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 11 0.34
31 18 0.56
32 3 0.09
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.56
Consensus pattern (30 bp):
AATTTATTTTTGTCATTCTAAAATTTAAAA
Found at i:89222 original size:22 final size:21
Alignment explanation
Indices: 89197--89239 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
89187 TATAATTAAT
89197 TTAACAAAACCAA-ATAAAAAAA
1 TTAACAAAA--AAGATAAAAAAA
*
89219 TTAATAAAAAAGATAAAAAAA
1 TTAACAAAAAAGATAAAAAAA
89240 GTAATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 2 0.11
21 9 0.47
22 8 0.42
ACGTcount: A:0.74, C:0.07, G:0.02, T:0.16
Consensus pattern (21 bp):
TTAACAAAAAAGATAAAAAAA
Found at i:102162 original size:44 final size:43
Alignment explanation
Indices: 102050--102163 Score: 151
Period size: 44 Copynumber: 2.7 Consensus size: 43
102040 ATTATGTGTT
*
102050 ATTTAGCGGCGTTTGTA-A-AAAAACACTGCAATATACCATAC
1 ATTTAGCGGCGTTTGTATACAAAAACGCTGCAATATACCATAC
* * *
102091 ATTTAGCGGCGTTTGTATACTAGAAACGTTGCAATATACTATAC
1 ATTTAGCGGCGTTTGTATAC-AAAAACGCTGCAATATACCATAC
*
102135 ATTTAGCGGCGTTTTTATACAATAAACGC
1 ATTTAGCGGCGTTTGTATACAA-AAACGC
102164 CGCTAATTCT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
41 17 0.27
42 1 0.02
43 1 0.02
44 43 0.69
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Consensus pattern (43 bp):
ATTTAGCGGCGTTTGTATACAAAAACGCTGCAATATACCATAC
Found at i:102378 original size:42 final size:43
Alignment explanation
Indices: 102328--102438 Score: 131
Period size: 42 Copynumber: 2.6 Consensus size: 43
102318 ATTTTTAAGT
102328 AAAACGCCGCTAAATCTCAACACCTACTGC-G-GTATTTTCCT-A
1 AAAACGCCGCTAAATCTCAACACCTACTGCGGCGTA-TTT-CTGA
*
102370 AAAACGCCGCTAAA-CATCAACACCTATTGCGGCGTATTTCTGA
1 AAAACGCCGCTAAATC-TCAACACCTACTGCGGCGTATTTCTGA
* **
102413 CAAACGCCGCTAAATAACAACACCTA
1 AAAACGCCGCTAAATCTCAACACCTA
102439 TTGTCAAACG
Statistics
Matches: 60, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
41 1 0.02
42 29 0.48
43 27 0.45
44 3 0.05
ACGTcount: A:0.35, C:0.31, G:0.13, T:0.22
Consensus pattern (43 bp):
AAAACGCCGCTAAATCTCAACACCTACTGCGGCGTATTTCTGA
Found at i:102434 original size:43 final size:42
Alignment explanation
Indices: 102328--102441 Score: 142
Period size: 43 Copynumber: 2.7 Consensus size: 42
102318 ATTTTTAAGT
* *
102328 AAAACGCCGCTAAATCTCAACACCTACTGCGGTATTTTCCTA
1 AAAACGCCGCTAAATATCAACACCTATTGCGGTATTTTCCTA
*
102370 AAAACGCCGCTAAACATCAACACCTATTGCGGCGTA-TTT-CTGA
1 AAAACGCCGCTAAATATCAACACCTATTGC-G-GTATTTTCCT-A
* *
102413 CAAACGCCGCTAAATAACAACACCTATTG
1 AAAACGCCGCTAAATATCAACACCTATTG
102442 TCAAACGCCG
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
42 29 0.46
43 31 0.49
44 3 0.05
ACGTcount: A:0.34, C:0.30, G:0.13, T:0.23
Consensus pattern (42 bp):
AAAACGCCGCTAAATATCAACACCTATTGCGGTATTTTCCTA
Found at i:103053 original size:32 final size:32
Alignment explanation
Indices: 102987--103057 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
102977 TTTATGTGAT
* * **
102987 AAATGTTTTTAATTATTTGATAATAAATGCTC
1 AAATATTTTTAATTATTTAATAATAAACACTC
*
103019 AAATATTTTTAATTATTTAATAATAAACATTC
1 AAATATTTTTAATTATTTAATAATAAACACTC
103051 AAATATT
1 AAATATT
103058 CTTACAGATG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (32 bp):
AAATATTTTTAATTATTTAATAATAAACACTC
Done.