Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009001.1 Hibiscus syriacus cultivar Beakdansim tig00112383_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: 4740655
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 24
Found at i:4228536 original size:15 final size:16
Alignment explanation
Indices: 4228518--4228557 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
4228508 ATTTTGCTTA
4228518 TCTTTTTTTTCT-TTT
1 TCTTTTTTTTCTCTTT
*
4228533 TCTTTTTTTTTTCTTT
1 TCTTTTTTTTCTCTTT
*
4228549 TGTTTTTTT
1 TCTTTTTTT
4228558 ATGAAAGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.88
Consensus pattern (16 bp):
TCTTTTTTTTCTCTTT
Found at i:4233358 original size:12 final size:12
Alignment explanation
Indices: 4233341--4233374 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
4233331 GAAAATAAAG
4233341 AAAACTTAATGT
1 AAAACTTAATGT
*
4233353 AAAACTTGATGT
1 AAAACTTAATGT
4233365 AAAAC-TAATG
1 AAAACTTAATG
4233375 ACCCTAGCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (12 bp):
AAAACTTAATGT
Found at i:4233800 original size:18 final size:18
Alignment explanation
Indices: 4233777--4233815 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
4233767 ACCTAATCCA
4233777 CAAAATACATAATATAAT
1 CAAAATACATAATATAAT
* *
4233795 CAAAATCCATAATTTAAT
1 CAAAATACATAATATAAT
4233813 CAA
1 CAA
4233816 TTTTAGTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.28
Consensus pattern (18 bp):
CAAAATACATAATATAAT
Found at i:4242240 original size:13 final size:13
Alignment explanation
Indices: 4242222--4242256 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
4242212 TGAATTGAAA
4242222 GAAAGGAAAAGAG
1 GAAAGGAAAAGAG
4242235 GAAAGGAAAAGAG
1 GAAAGGAAAAGAG
4242248 GAAAGGAAA
1 GAAAGGAAA
4242257 TGTCGTGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (13 bp):
GAAAGGAAAAGAG
Found at i:4251003 original size:18 final size:18
Alignment explanation
Indices: 4250980--4251017 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
4250970 GAAATCCACC
*
4250980 AGCCCGCTAAAGCAGAAG
1 AGCCCGCGAAAGCAGAAG
*
4250998 AGCCCGCGGAAGCAGAAG
1 AGCCCGCGAAAGCAGAAG
4251016 AG
1 AG
4251018 TCTGCTGACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.37, C:0.26, G:0.34, T:0.03
Consensus pattern (18 bp):
AGCCCGCGAAAGCAGAAG
Found at i:4254662 original size:24 final size:25
Alignment explanation
Indices: 4254630--4254680 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 25
4254620 CAAATCCAAT
4254630 CCGATCCAAAAAA-ATAACCGAAAA
1 CCGATCCAAAAAACATAACCGAAAA
4254654 CCGATCCAAAAAACCGATAACCGAAAA
1 CCGATCCAAAAAA-C-ATAACCGAAAA
4254681 AAACCGAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 13 0.54
27 11 0.46
ACGTcount: A:0.55, C:0.27, G:0.10, T:0.08
Consensus pattern (25 bp):
CCGATCCAAAAAACATAACCGAAAA
Found at i:4254670 original size:20 final size:17
Alignment explanation
Indices: 4254639--4254689 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 17
4254629 TCCGATCCAA
4254639 AAAAATAACCGAAAACCG
1 AAAAA-AACCGAAAACCG
*
4254657 ATCCAAAAAACCGATAACCG
1 A---AAAAAACCGAAAACCG
4254677 AAAAAAACCGAAA
1 AAAAAAACCGAAA
4254690 CTGATTTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
17 11 0.39
18 1 0.04
20 12 0.43
21 4 0.14
ACGTcount: A:0.61, C:0.24, G:0.10, T:0.06
Consensus pattern (17 bp):
AAAAAAACCGAAAACCG
Found at i:4256027 original size:13 final size:13
Alignment explanation
Indices: 4256009--4256033 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4255999 TTCCAATGGC
4256009 AGGATCATGCTAA
1 AGGATCATGCTAA
4256022 AGGATCATGCTA
1 AGGATCATGCTA
4256034 TATTACATGA
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:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (13 bp):
AGGATCATGCTAA
Found at i:4267775 original size:79 final size:78
Alignment explanation
Indices: 4267687--4267843 Score: 296
Period size: 79 Copynumber: 2.0 Consensus size: 78
4267677 AAATACGATC
4267687 ATATATTGTTGAATTGTGTTTGTTATAAAATTTTTAGTCAAAAACGTATTTATGAACAGTAAAAT
1 ATATATTGTTGAATTGTGTTTGTTATAAAATTTTTAGTCAAAAACGTATTTATGAACAGTAAAAT
4267752 ACGGTATGAACAG
66 ACGGTATGAACAG
4267765 ATATATTTGTTGAATTGTGTTTGTTATAAAATTTTTAGTCAAAAACGTATTTATGAACAGTAAAA
1 ATATA-TTGTTGAATTGTGTTTGTTATAAAATTTTTAGTCAAAAACGTATTTATGAACAGTAAAA
*
4267830 TATGGTATGAACAG
65 TACGGTATGAACAG
4267844 TGTCGTATGA
Statistics
Matches: 77, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
78 5 0.06
79 72 0.94
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (78 bp):
ATATATTGTTGAATTGTGTTTGTTATAAAATTTTTAGTCAAAAACGTATTTATGAACAGTAAAAT
ACGGTATGAACAG
Found at i:4267951 original size:21 final size:21
Alignment explanation
Indices: 4267925--4267967 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
4267915 TACAAATAGG
4267925 GTACCGATACCCTGCTACAGT
1 GTACCGATACCCTGCTACAGT
4267946 GTACCGATACCCTGCTACAGT
1 GTACCGATACCCTGCTACAGT
4267967 G
1 G
4267968 CTGCTACAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.33, G:0.21, T:0.23
Consensus pattern (21 bp):
GTACCGATACCCTGCTACAGT
Found at i:4267973 original size:11 final size:11
Alignment explanation
Indices: 4267957--4267991 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
4267947 TACCGATACC
*
4267957 CTGCTACAGTG
1 CTGCTACAGTA
4267968 CTGCTACAGTA
1 CTGCTACAGTA
4267979 CTGCTACAGTA
1 CTGCTACAGTA
4267990 CT
1 CT
4267992 TCCGTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (11 bp):
CTGCTACAGTA
Found at i:4276684 original size:21 final size:21
Alignment explanation
Indices: 4276658--4276697 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4276648 CCCCCTTTGA
*
4276658 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
4276679 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
4276698 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:4281510 original size:14 final size:14
Alignment explanation
Indices: 4281491--4281521 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
4281481 AGAGTTCTGA
4281491 GTGATGTCCAATAC
1 GTGATGTCCAATAC
4281505 GTGATGTCCAATAC
1 GTGATGTCCAATAC
4281519 GTG
1 GTG
4281522 CCCACTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (14 bp):
GTGATGTCCAATAC
Found at i:4284584 original size:33 final size:34
Alignment explanation
Indices: 4284547--4284612 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
4284537 ATTTGGCAAG
*
4284547 TTGGAAAATTCATC-TTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTTGGTAGGTGGCCAACTTA
*
4284580 TTGGAAAATTCGTCTTTGGTAGGTGGCCAACTT
1 TTGGAAAATTCATCTTTGGTAGGTGGCCAACTT
4284613 TGCACATGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 13 0.43
34 17 0.57
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (34 bp):
TTGGAAAATTCATCTTTGGTAGGTGGCCAACTTA
Found at i:4295131 original size:31 final size:31
Alignment explanation
Indices: 4295093--4295152 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
4295083 AGATATATTG
4295093 TTTTTATTGTTTAAAAAACTTTTA-AAAATAA
1 TTTTTATTGTTTAAAAAA-TTTTACAAAATAA
* *
4295124 TTTTTATTGTTTGATAAATTTTACAAAAT
1 TTTTTATTGTTTAAAAAATTTTACAAAAT
4295153 TTATTTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (31 bp):
TTTTTATTGTTTAAAAAATTTTACAAAATAA
Found at i:4295160 original size:30 final size:30
Alignment explanation
Indices: 4295093--4295161 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
4295083 AGATATATTG
4295093 TTTTTATTGTTTAAAAAACTTTTAAAAATAA
1 TTTTTATTGTTTAAAAAACTTTTAAAAAT-A
* *
4295124 TTTTTATTGTTTGATAAA-TTTTACAAAAT-
1 TTTTTATTGTTTAAAAAACTTTTA-AAAATA
4295153 TTATTTATT
1 TT-TTTATT
4295162 ATAAATGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 2 0.06
30 11 0.32
31 21 0.62
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (30 bp):
TTTTTATTGTTTAAAAAACTTTTAAAAATA
Found at i:4295372 original size:23 final size:24
Alignment explanation
Indices: 4295336--4295402 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 24
4295326 AATAATTTCT
*
4295336 TTATTAAATATAATATTAAATAATA
1 TTATTTAAT-TAATATTAAATAATA
* *
4295361 TT-TTT-ATGTAATAATAAGTAATA
1 TTATTTAAT-TAATATTAAATAATA
4295384 TTAATTTAATTAATATTAA
1 TT-ATTTAATTAATATTAA
4295403 GATTTTCTAC
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
23 17 0.50
24 2 0.06
25 13 0.38
26 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (24 bp):
TTATTTAATTAATATTAAATAATA
Found at i:4296198 original size:10 final size:9
Alignment explanation
Indices: 4296184--4296217 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
4296174 AAATAGTTTT
4296184 TAAAAAAAA
1 TAAAAAAAA
*
4296193 TTAAAAAAA
1 TAAAAAAAA
4296202 TAAAATAAAA
1 TAAAA-AAAA
4296212 TAAAAA
1 TAAAAA
4296218 TCGATGGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:4297447 original size:18 final size:21
Alignment explanation
Indices: 4297424--4297464 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
4297414 GACACCATGT
4297424 AAAATATT-T-AA-AAATAAA
1 AAAATATTATAAACAAATAAA
4297442 AAAATATTATAAACAAATAAA
1 AAAATATTATAAACAAATAAA
4297463 AA
1 AA
4297465 TAAATAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
19 1 0.05
20 2 0.10
21 9 0.45
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAATATTATAAACAAATAAA
Found at i:4299818 original size:30 final size:30
Alignment explanation
Indices: 4299782--4299850 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
4299772 CCTTTTCCTC
*
4299782 TAAACCTCAGTTTCGCTATCTGTTTGACCT
1 TAAACCTCAGTTTCGCTATCTGTTCGACCT
4299812 TAAACCTCAGTTTCGCTATCTGTTCGACCT
1 TAAACCTCAGTTTCGCTATCTGTTCGACCT
4299842 TAAACCTCA
1 TAAACCTCA
4299851 CACATTATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.23, C:0.29, G:0.12, T:0.36
Consensus pattern (30 bp):
TAAACCTCAGTTTCGCTATCTGTTCGACCT
Found at i:4306155 original size:20 final size:20
Alignment explanation
Indices: 4306130--4306167 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4306120 AGTTAAATTT
*
4306130 GATTTAATTTCAAAATTTTA
1 GATTTAATTTAAAAATTTTA
4306150 GATTTAATTTAAAAATTT
1 GATTTAATTTAAAAATTT
4306168 ATGAGTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (20 bp):
GATTTAATTTAAAAATTTTA
Found at i:4306168 original size:19 final size:20
Alignment explanation
Indices: 4306124--4306168 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
4306114 AAGTATAGTT
4306124 AAATTT-GATTTAATTTCAA
1 AAATTTAGATTTAATTTCAA
*
4306143 AATTTTAGATTTAATTT-AA
1 AAATTTAGATTTAATTTCAA
4306162 AAATTTA
1 AAATTTA
4306169 TGAGTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (20 bp):
AAATTTAGATTTAATTTCAA
Found at i:4306369 original size:36 final size:35
Alignment explanation
Indices: 4306319--4306389 Score: 83
Period size: 35 Copynumber: 2.0 Consensus size: 35
4306309 ATATATAATC
*
4306319 ATATAATGTAGTTTTTGAACATAC-TTTTT-AAAACAT
1 ATATAATATAG-TTTTGAA-A-ACATTTTTGAAAACAT
*
4306355 ATATAATATGGTTTTGAAAACATTTTTGAAAACAT
1 ATATAATATAGTTTTGAAAACATTTTTGAAAACAT
4306390 TTTTGAAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
33 2 0.06
34 6 0.19
35 14 0.45
36 9 0.29
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (35 bp):
ATATAATATAGTTTTGAAAACATTTTTGAAAACAT
Found at i:4306374 original size:23 final size:23
Alignment explanation
Indices: 4306343--4306424 Score: 67
Period size: 23 Copynumber: 3.5 Consensus size: 23
4306333 TTGAACATAC
* *
4306343 TTTTTAAAACATATATAATATGG
1 TTTTGAAAACATATATAATATGA
* * **
4306366 TTTTGAAAACATTTTTGAA-AACA
1 TTTTGAAAACATATAT-AATATGA
*
4306389 TTTTTGAAAACGTATATAATATGA
1 -TTTTGAAAACATATATAATATGA
*
4306413 TTTTAAAAACAT
1 TTTTGAAAACAT
4306425 TTTTGAAAAC
Statistics
Matches: 43, Mismatches: 13, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
23 26 0.60
24 17 0.40
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (23 bp):
TTTTGAAAACATATATAATATGA
Found at i:4306383 original size:12 final size:12
Alignment explanation
Indices: 4306366--4306399 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
4306356 TATAATATGG
4306366 TTTTGAAAACAT
1 TTTTGAAAACAT
4306378 TTTTGAAAACAT
1 TTTTGAAAACAT
4306390 TTTTGAAAAC
1 TTTTGAAAAC
4306400 GTATATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (12 bp):
TTTTGAAAACAT
Found at i:4306399 original size:47 final size:45
Alignment explanation
Indices: 4306330--4306434 Score: 147
Period size: 47 Copynumber: 2.2 Consensus size: 45
4306320 TATAATGTAG
* *
4306330 TTTTTGAACATACTTTTTAAAACATATATAATATGGTTTTGAAAACA
1 TTTTTGAA-A-ACTTTTTAAAACATATATAATATGATTTTAAAAACA
*
4306377 TTTTTGAAAACATTTTTGAAAACGTATATAATATGATTTTAAAAACA
1 TTTTTGAAAAC-TTTTT-AAAACATATATAATATGATTTTAAAAACA
4306424 TTTTTGAAAAC
1 TTTTTGAAAAC
4306435 GTATAATATA
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
45 2 0.04
46 6 0.11
47 45 0.85
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.42
Consensus pattern (45 bp):
TTTTTGAAAACTTTTTAAAACATATATAATATGATTTTAAAAACA
Found at i:4306422 original size:35 final size:35
Alignment explanation
Indices: 4306378--4306456 Score: 133
Period size: 35 Copynumber: 2.3 Consensus size: 35
4306368 TTGAAAACAT
4306378 TTTTGAAAACATTTTTGAAAACGTAT-ATAATATGA
1 TTTTGAAAACATTTTTGAAAACGTATAAT-ATATGA
*
4306413 TTTTAAAAACATTTTTGAAAACGTATAATATATGA
1 TTTTGAAAACATTTTTGAAAACGTATAATATATGA
4306448 TTTTGAAAA
1 TTTTGAAAA
4306457 TGTATAATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 39 0.95
36 2 0.05
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (35 bp):
TTTTGAAAACATTTTTGAAAACGTATAATATATGA
Found at i:4306454 original size:23 final size:24
Alignment explanation
Indices: 4306425--4306481 Score: 89
Period size: 23 Copynumber: 2.4 Consensus size: 24
4306415 TTAAAAACAT
4306425 TTTTGAAAACGTATAATATAT-GA
1 TTTTGAAAACGTATAATATATGGA
* *
4306448 TTTTGAAAATGTATAATATATGGT
1 TTTTGAAAACGTATAATATATGGA
4306472 TTTTGAAAAC
1 TTTTGAAAAC
4306482 ATATTTTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 20 0.67
24 10 0.33
ACGTcount: A:0.40, C:0.04, G:0.14, T:0.42
Consensus pattern (24 bp):
TTTTGAAAACGTATAATATATGGA
Found at i:4306497 original size:61 final size:58
Alignment explanation
Indices: 4306390--4306517 Score: 168
Period size: 61 Copynumber: 2.2 Consensus size: 58
4306380 TTGAAAACAT
4306390 TTTTGAAAACGTATATAATATGATTTTAAAAACATTTTTGAAAACGTATAATATATGA
1 TTTTGAAAACGTATATAATATGATTTTAAAAACATTTTTGAAAACGTATAATATATGA
* * * *
4306448 TTTTGAAAATGTATA-ATATATGGTTTTTGAAAACATATTTTTGAAAACGTATAATATATGG
1 TTTTGAAAACGTATATA-ATAT-GATTTT-AAAA-ACATTTTTGAAAACGTATAATATATGA
*
4306509 TTTTAAAAA
1 TTTTGAAAA
4306518 AACAGTTTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
57 1 0.02
58 18 0.30
59 5 0.08
60 4 0.07
61 33 0.54
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.41
Consensus pattern (58 bp):
TTTTGAAAACGTATATAATATGATTTTAAAAACATTTTTGAAAACGTATAATATATGA
Found at i:4306527 original size:38 final size:39
Alignment explanation
Indices: 4306448--4306521 Score: 114
Period size: 38 Copynumber: 1.9 Consensus size: 39
4306438 TAATATATGA
* **
4306448 TTTTGAAAATGTATAATATATGGTTTT-TGAAAACATAT
1 TTTTGAAAACGTATAATATATGGTTTTAAAAAAACATAT
4306486 TTTTGAAAACGTATAATATATGGTTTTAAAAAAACA
1 TTTTGAAAACGTATAATATATGGTTTTAAAAAAACA
4306522 GTTTTTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 26 0.81
39 6 0.19
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.41
Consensus pattern (39 bp):
TTTTGAAAACGTATAATATATGGTTTTAAAAAAACATAT
Found at i:4306534 original size:39 final size:39
Alignment explanation
Indices: 4306453--4306554 Score: 102
Period size: 39 Copynumber: 2.6 Consensus size: 39
4306443 TATGATTTTG
* ** **
4306453 AAAATGTATAATATATGGTTTT-TGAAAACATATTTTTG
1 AAAACGTATAATATATGGTTTTAAAAAAACATATTTTAA
4306491 AAAACGTATAATATATGGTTTTAAAAAAACAGT-TTTTAA
1 AAAACGTATAATATATGGTTTTAAAAAAACA-TATTTTAA
* *
4306530 AAAACATAT-ATAATATAGTTTTAAA
1 AAAACGTATAAT-ATATGGTTTTAAA
4306555 TATATATATA
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
38 23 0.43
39 30 0.56
40 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.10, T:0.39
Consensus pattern (39 bp):
AAAACGTATAATATATGGTTTTAAAAAAACATATTTTAA
Found at i:4306656 original size:22 final size:22
Alignment explanation
Indices: 4306608--4306656 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
4306598 TATATATAAT
*
4306608 ATATATAGTTTTTGAAAACATA
1 ATATATAGTTTGTGAAAACATA
* * *
4306630 TTATATAGTTTGTGGAAATATA
1 ATATATAGTTTGTGAAAACATA
4306652 ATATA
1 ATATA
4306657 CATATGTTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (22 bp):
ATATATAGTTTGTGAAAACATA
Found at i:4306699 original size:19 final size:19
Alignment explanation
Indices: 4306677--4306739 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
4306667 ATAGTTTTTA
4306677 TTATTATTTATATTATTAT
1 TTATTATTTATATTATTAT
4306696 TTATTATTT-TA-TATTTAT
1 TTATTATTTATATTA-TTAT
* *
4306714 TATATTAGGTTATATTTTTAT
1 T-TATTA-TTTATATTATTAT
4306735 TTATT
1 TTATT
4306740 TTATTTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
17 2 0.05
18 7 0.19
19 14 0.38
20 6 0.16
21 7 0.19
22 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (19 bp):
TTATTATTTATATTATTAT
Found at i:4306712 original size:14 final size:13
Alignment explanation
Indices: 4306674--4306744 Score: 69
Period size: 12 Copynumber: 5.6 Consensus size: 13
4306664 TATATAGTTT
4306674 TTATTATTATTTA
1 TTATTATTATTTA
4306687 -TATTATTATTTA
1 TTATTATTATTTA
*
4306699 TTATTTTATATTTA
1 TTATTAT-TATTTA
*
4306713 TTA-TATTAGGTTA
1 TTATTATTA-TTTA
*
4306726 -TATTTTTATTTA
1 TTATTATTATTTA
4306738 TT-TTATT
1 TTATTATT
4306745 TTATTTTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
12 23 0.49
13 15 0.32
14 9 0.19
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (13 bp):
TTATTATTATTTA
Found at i:4310906 original size:12 final size:12
Alignment explanation
Indices: 4310891--4310928 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
4310881 GTTATTTAAA
4310891 CGGGTATTGGGC
1 CGGGTATTGGGC
*
4310903 CGGGTATTGGGT
1 CGGGTATTGGGC
*
4310915 CGAGTATTGGGC
1 CGGGTATTGGGC
4310927 CG
1 CG
4310929 AGAATCGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.11, C:0.16, G:0.47, T:0.26
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:4310938 original size:24 final size:24
Alignment explanation
Indices: 4310894--4310945 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
4310884 ATTTAAACGG
* * *
4310894 GTATTGGGCCGGGTATTGGGTCGA
1 GTATTGGGCCGAGAATCGGGTCGA
*
4310918 GTATTGGGCCGAGAATCGGGTCGG
1 GTATTGGGCCGAGAATCGGGTCGA
4310942 GTAT
1 GTAT
4310946 ATATATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.15, C:0.13, G:0.44, T:0.27
Consensus pattern (24 bp):
GTATTGGGCCGAGAATCGGGTCGA
Found at i:4311096 original size:13 final size:13
Alignment explanation
Indices: 4311051--4311099 Score: 73
Period size: 13 Copynumber: 3.8 Consensus size: 13
4311041 TTTAATATTT
*
4311051 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
*
4311063 ATCGGGGAGGGTA
1 ATCGGGGCGGGTA
4311076 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
4311089 ATCGGGGCGGG
1 ATCGGGGCGGG
4311100 GATTACCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
12 10 0.30
13 23 0.70
ACGTcount: A:0.14, C:0.14, G:0.55, T:0.16
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:4311341 original size:32 final size:32
Alignment explanation
Indices: 4311305--4311367 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
4311295 TTAATCATAC
*
4311305 TATTTATTTT-TATTTAAGATATTTAATTTTTT
1 TATTT-TTTTATAATTAAGATATTTAATTTTTT
*
4311337 TATTTTTTTATAATTAAGATCTTTAATTTTT
1 TATTTTTTTATAATTAAGATATTTAATTTTT
4311368 GTAATTTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 4 0.14
32 24 0.86
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.67
Consensus pattern (32 bp):
TATTTTTTTATAATTAAGATATTTAATTTTTT
Found at i:4311353 original size:23 final size:22
Alignment explanation
Indices: 4311327--4311389 Score: 54
Period size: 24 Copynumber: 2.8 Consensus size: 22
4311317 TTTAAGATAT
* *
4311327 TTAATTTTTTTATTTTTTTATAA
1 TTAAATTTTTTATTTTTGTA-AA
* * *
4311350 TTAAGATCTTTAATTTTTGTAAT
1 TTAA-ATTTTTTATTTTTGTAAA
*
4311373 TTAACTTTTTTATTTTT
1 TTAAATTTTTTATTTTT
4311390 ATAATTGAGA
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
22 10 0.32
23 9 0.29
24 12 0.39
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.68
Consensus pattern (22 bp):
TTAAATTTTTTATTTTTGTAAA
Found at i:4311372 original size:22 final size:22
Alignment explanation
Indices: 4311341--4311415 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
4311331 TTTTTTTATT
4311341 TTTTTATAATTAAGATCTTTAA
1 TTTTTATAATTAAGATCTTTAA
* * * *
4311363 TTTTTGTAATTTAA-CTTTTTTA
1 TTTTTATAA-TTAAGATCTTTAA
*
4311385 TTTTTATAATTGAGA-CTTCTAA
1 TTTTTATAATTAAGATCTT-TAA
4311407 TTTTT-TAAT
1 TTTTTATAAT
4311416 CACACTTTTT
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
21 9 0.22
22 28 0.68
23 4 0.10
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.60
Consensus pattern (22 bp):
TTTTTATAATTAAGATCTTTAA
Found at i:4311402 original size:23 final size:23
Alignment explanation
Indices: 4311332--4311402 Score: 65
Period size: 22 Copynumber: 3.1 Consensus size: 23
4311322 GATATTTAAT
4311332 TTTTTTATTTTTTTATAATTAAGA-
1 TTTTTTA--TTTTTATAATTAAGAC
* * * *
4311356 TCTTTAATTTTTGTAATTTA-AC
1 TTTTTTATTTTTATAATTAAGAC
*
4311378 TTTTTTATTTTTATAATTGAGAC
1 TTTTTTATTTTTATAATTAAGAC
4311401 TT
1 TT
4311403 CTAATTTTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
21 1 0.03
22 27 0.73
23 4 0.11
24 5 0.14
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.63
Consensus pattern (23 bp):
TTTTTTATTTTTATAATTAAGAC
Found at i:4311438 original size:87 final size:86
Alignment explanation
Indices: 4311342--4311785 Score: 288
Period size: 87 Copynumber: 5.1 Consensus size: 86
4311332 TTTTTTATTT
* * * * * *
4311342 TTTTATAATTAAGATCTTTAATTTTTGTAATTTAACTTTTTTATTTTTATAATTGAGACTTCTAA
1 TTTTATAATTAAGA-CTCTAATTTTTTTAATATCACTTTTTTATATTTATAATTGAGACGTCTAA
4311407 TTTTTTAATCA-CACTTTTTA-
65 TTTTTTAATCATCACTTTTTAC
* * * * *
4311427 TTATTCATAATTGAA-CCCCTAATTTTTTTAATATCAC-TTTTTATATTTATATTTGAGGCGGCT
1 TT-TT-ATAATT-AAGACTCTAATTTTTTTAATATCACTTTTTTATATTTATAATTGAGACGTCT
*
4311490 AATAATTTTAAT-ATCACTTTTTAC
63 AAT-TTTTTAATCATCACTTTTTAC
* **
4311514 TTTTATAATTGAAGACTCTAATTTTTTTCAATCTCA-TTTTTTACCTTTATAATTGAGACGGT-T
1 TTTTATAATT-AAGACTCTAATTTTTTT-AATATCACTTTTTTATATTTATAATTGAGAC-GTCT
* * *
4311577 AATTTTTTTAATC-TTACATTCTA-
63 AA-TTTTTTAATCATCACTTTTTAC
** * * * * * *
4311600 TATTTATAATTGAATCCCCTAATTATTTTCAATCTCAC-TTTTTATTTTTATAATTGAGGCATCT
1 T-TTTATAATT-AAGACTCTAATT-TTTTTAATATCACTTTTTTATATTTATAATTGAGACGTCT
* *
4311664 ACTTTTTTCACTTCAATTCCACTTTTTA-
63 AATTTTTT-A-ATC-A-T-CACTTTTTAC
* * * * * *
4311692 TATTTATAATTAAAGCCACT-ATTTTTTTAATCTCAC-TTTTTATATTTATAATCGAGAC-ACTT
1 T-TTTATAATT-AAGACTCTAATTTTTTTAATATCACTTTTTTATATTTATAATTGAGACGTCTA
*
4311754 ATATTTTTAATC-TCATTTTTTAC
64 AT-TTTTTAATCATCACTTTTTAC
4311777 TTTTATAAT
1 TTTTATAAT
4311786 CGAGGTTCTT
Statistics
Matches: 286, Mismatches: 49, Indels: 49
0.74 0.13 0.13
Matches are distributed among these distances:
84 16 0.06
85 38 0.13
86 56 0.20
87 97 0.34
88 12 0.04
89 4 0.01
90 36 0.13
91 4 0.01
92 23 0.08
ACGTcount: A:0.29, C:0.13, G:0.05, T:0.53
Consensus pattern (86 bp):
TTTTATAATTAAGACTCTAATTTTTTTAATATCACTTTTTTATATTTATAATTGAGACGTCTAAT
TTTTTAATCATCACTTTTTAC
Found at i:4311670 original size:130 final size:129
Alignment explanation
Indices: 4311379--4311808 Score: 345
Period size: 130 Copynumber: 3.3 Consensus size: 129
4311369 TAATTTAACT
* * *
4311379 TTTTTATTTTTATAATTGAGACTTCTAATTTTTT-AATCACACTTTTTATTATTCATAATTGAAC
1 TTTTTATTTTTATAATTGAGGCATCTAATTTTTTCAATCACACTTTTTACTATTCATAATTGAAC
* * * * **
4311443 CCCTAATTTTTTTAATATCACTTTTTATATTTATATTTGAGGCGGCTAATAATTTTAATATCAC
66 CCCTAATTTTTTTAATATCACATTCTATATTTATAATTGAAGCCCCTAATAATTTTAATATCAC
* * * *
4311507 TTTTTACTTTTATAATTGAAG-ACTCTAATTTTTTTCAATCTCATTTTTTACCT-TT-ATAATTG
1 TTTTTATTTTTATAATTGAGGCA-TCTAA-TTTTTTCAATCACACTTTTTA-CTATTCATAATTG
*** * * * * *
4311569 AGACGGTTAATTTTTTTAATCTTACATTCTATATTTATAATTGAATCCCCTAATTATTTTCAATC
63 A-ACCCCTAATTTTTTTAATATCACATTCTATATTTATAATTGAAGCCCCTAATAATTTT-AATA
4311634 TCAC
126 TCAC
* * *
4311638 TTTTTATTTTTATAATTGAGGCATCTACTTTTTTCACTTCAATTCCACTTTTTA-TATTTATAAT
1 TTTTTATTTTTATAATTGAGGCATCTAATTTTTTCA-ATC-A---CACTTTTTACTATTCATAAT
* * * * * * * * * *
4311702 TAAAGCCACT-ATTTTTTTAATCTCACTTTTTATATTTATAATCG-AGACACTTATATTTTTAAT
61 TGAA-CCCCTAATTTTTTTAATATCACATTCTATATTTATAATTGAAGCCCCTAATAATTTTAAT
* *
4311765 CTCAT
125 ATCAC
* * *
4311770 TTTTTACTTTTATAATCGAGG-TTCTTAATTTTTTCAATC
1 TTTTTATTTTTATAATTGAGGCATC-TAATTTTTTCAATC
4311809 TCAATCGGTA
Statistics
Matches: 239, Mismatches: 47, Indels: 29
0.76 0.15 0.09
Matches are distributed among these distances:
128 23 0.10
129 14 0.06
130 67 0.28
131 37 0.15
132 37 0.15
133 11 0.05
134 33 0.14
135 17 0.07
ACGTcount: A:0.28, C:0.14, G:0.06, T:0.52
Consensus pattern (129 bp):
TTTTTATTTTTATAATTGAGGCATCTAATTTTTTCAATCACACTTTTTACTATTCATAATTGAAC
CCCTAATTTTTTTAATATCACATTCTATATTTATAATTGAAGCCCCTAATAATTTTAATATCAC
Found at i:4311718 original size:48 final size:48
Alignment explanation
Indices: 4311627--4311743 Score: 133
Period size: 48 Copynumber: 2.6 Consensus size: 48
4311617 CCTAATTATT
* * *
4311627 TTCAATCTCACTTTTTATTTTTATAATTGAGGCATCTACTTTTTTCAC
1 TTCAATCTCACTTTTTATATTTATAATTAAGCCATCTACTTTTTTCAC
4311675 TTCAAT-TCCACTTTTTATATTTATAATTAAAGCCA-CTA--TTTTT---
1 TTCAATCT-CACTTTTTATATTTATAATT-AAGCCATCTACTTTTTTCAC
4311718 TT-AATCTCACTTTTTATATTTATAAT
1 TTCAATCTCACTTTTTATATTTATAAT
4311744 CGAGACACTT
Statistics
Matches: 63, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
42 22 0.35
43 3 0.05
46 5 0.08
47 1 0.02
48 28 0.44
49 4 0.06
ACGTcount: A:0.27, C:0.16, G:0.03, T:0.53
Consensus pattern (48 bp):
TTCAATCTCACTTTTTATATTTATAATTAAGCCATCTACTTTTTTCAC
Found at i:4311729 original size:42 final size:43
Alignment explanation
Indices: 4311360--4311785 Score: 287
Period size: 43 Copynumber: 9.8 Consensus size: 43
4311350 TTAAGATCTT
* * * * **
4311360 TAATTTTTGTAATTTAACTTTTTTATTTTTATAATTG-AGACTTC
1 TAATTTTTTTAATCTCAC-TTTTTATATTTATAATTGAAG-CCAC
* * *
4311404 TAA-TTTTTTAATCACACTTTTTATTATTCATAATTGAA-CCCC
1 TAATTTTTTTAATCTCACTTTTTA-TATTTATAATTGAAGCCAC
* * * **
4311446 TAATTTTTTTAATATCACTTTTTATATTTATATTTGAGGCGGC
1 TAATTTTTTTAATCTCACTTTTTATATTTATAATTGAAGCCAC
** * * *
4311489 TAATAATTTTAATATCACTTTTTACT-TTTATAATTGAAGACTC
1 TAATTTTTTTAATCTCACTTTTTA-TATTTATAATTGAAGCCAC
* ** ***
4311532 TAATTTTTTTCAATCTCATTTTTTACCTTTATAATTG-AGACGGT
1 TAATTTTTTT-AATCTCACTTTTTATATTTATAATTGAAG-CCAC
* * * * *
4311576 TAATTTTTTTAATCTTACATTCTATATTTATAATTGAATCCCC
1 TAATTTTTTTAATCTCACTTTTTATATTTATAATTGAAGCCAC
* * *
4311619 TAATTATTTTCAATCTCACTTTTTATTTTTATAATTG-AGGCATC
1 TAATT-TTTTTAATCTCACTTTTTATATTTATAATTGAAGCCA-C
* *
4311663 TACTTTTTTCACTTCAAT-TCCACTTTTTATATTTATAATTAAAGCCAC
1 TA-ATTTTT---TT-AATCT-CACTTTTTATATTTATAATTGAAGCCAC
* *
4311711 T-ATTTTTTTAATCTCACTTTTTATATTTATAATCG-AGACAC
1 TAATTTTTTTAATCTCACTTTTTATATTTATAATTGAAGCCAC
* * *
4311752 TTATATTTTTAATCTCATTTTTTACT-TTTATAAT
1 TAATTTTTTTAATCTCACTTTTTA-TATTTATAAT
4311786 CGAGGTTCTT
Statistics
Matches: 301, Mismatches: 60, Indels: 44
0.74 0.15 0.11
Matches are distributed among these distances:
41 6 0.02
42 72 0.24
43 116 0.39
44 70 0.23
45 2 0.01
46 5 0.02
47 2 0.01
48 24 0.08
49 4 0.01
ACGTcount: A:0.29, C:0.14, G:0.05, T:0.53
Consensus pattern (43 bp):
TAATTTTTTTAATCTCACTTTTTATATTTATAATTGAAGCCAC
Found at i:4312291 original size:15 final size:15
Alignment explanation
Indices: 4312271--4312358 Score: 97
Period size: 15 Copynumber: 5.5 Consensus size: 15
4312261 TAATAAGGTT
4312271 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
4312286 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
4312301 ATTTATTATAAAATATAGA
1 ATTTATT-TTAAA-AT--A
4312320 TTTATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
4312338 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
4312352 ATTTATT
1 ATTTATT
4312359 AGTATGGATT
Statistics
Matches: 64, Mismatches: 2, Indels: 15
0.79 0.02 0.19
Matches are distributed among these distances:
14 12 0.19
15 31 0.48
16 4 0.06
17 2 0.03
18 1 0.02
19 1 0.02
20 2 0.03
21 4 0.06
22 7 0.11
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:4312376 original size:32 final size:32
Alignment explanation
Indices: 4312338--4312691 Score: 290
Period size: 32 Copynumber: 12.4 Consensus size: 32
4312328 TTTTAAAATA
4312338 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
4312370 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
4312392 ATTTATTTTAAATAATTTATTAGTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
4312424 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
4312446 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
* * *
4312478 ATTTATTTTAAATAATTTATTAATGTAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
4312510 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
4312532 ATTTATTTTAAATAATTTATTAGTATGGATTA
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
4312564 ATTTATTTTAAATAATTTATTTGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
* * * *
4312596 ATTGA-TTT--AT--TTTA-AAATATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
* *
4312622 ATTTA--TT--AT--TGTAGTT-GTATGAATTG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTG
4312648 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
4312680 ATTTATTTTAAA
1 ATTTATTTTAAA
4312692 ATATGGATTG
Statistics
Matches: 260, Mismatches: 23, Indels: 78
0.72 0.06 0.22
Matches are distributed among these distances:
22 39 0.15
23 12 0.05
25 10 0.04
26 33 0.13
27 4 0.02
28 11 0.04
29 5 0.02
30 2 0.01
31 17 0.07
32 127 0.49
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:4312377 original size:22 final size:22
Alignment explanation
Indices: 4312361--4312403 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
4312351 AATTTATTAG
4312361 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
4312383 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
4312404 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:4312410 original size:54 final size:54
Alignment explanation
Indices: 4312338--4312489 Score: 295
Period size: 54 Copynumber: 2.8 Consensus size: 54
4312328 TTTTAAAATA
4312338 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
4312392 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
4312446 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
4312490 TAATTTATTA
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 96 1.00
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:4312433 original size:86 final size:86
Alignment explanation
Indices: 4312383--4312723 Score: 482
Period size: 86 Copynumber: 4.0 Consensus size: 86
4312373 TATTTTAAAA
4312383 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGAT
*
4312448 TTATTTTAAATAATTTATTAG
66 TGATTTTAAATAATTTATTAG
* *
4312469 TATGGATTGATTTATTTTAAATAATTTATTAATGTAGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGAT
*
4312534 TTATTTTAAATAATTTATTAG
66 TGATTTTAAATAATTTATTAG
* *
4312555 TATGGATTAATTTATTTTAAATAATTTATTTGTATGGATTGATTGATTTATTTTAAAATAT--A-
1 TATGGATTGATTTATTTTAAATAATTTATTAGTAT--A--GATTGATTTATTTTAAAATATGGAT
*
4312617 -GATTGA-TTT--ATTATTGTAGTT-G
62 TGATTGATTTTAAATAATT-TA-TTAG
* *
4312639 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGAT
*
4312704 TTATTTTAAATAATTTATTA
66 TGATTTTAAATAATTTATTA
4312724 TTGTAGTTGT
Statistics
Matches: 227, Mismatches: 14, Indels: 28
0.84 0.05 0.10
Matches are distributed among these distances:
80 21 0.09
82 1 0.00
83 5 0.02
84 40 0.18
85 10 0.04
86 122 0.54
87 5 0.02
88 2 0.01
90 21 0.09
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (86 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGAT
TGATTTTAAATAATTTATTAG
Found at i:4312527 original size:54 final size:54
Alignment explanation
Indices: 4312469--4312723 Score: 244
Period size: 54 Copynumber: 4.6 Consensus size: 54
4312459 AATTTATTAG
*
4312469 TATGGATTGATTTATTTTAAATAATTTATTAATGTAGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAATATAGATTGATTTATTTTAAAA
* * *
4312523 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTAATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAATATAGATTGATTTATTTTAAAA
** ** * * * * ***
4312576 TAATTTATTTGTATGGATTGATTGATTTATTT-TAAAATATAGATTGATTTATTATTGTAGTTG
1 T-ATGGA-TTG-ATTTATT--TTAAATAATTTAT-TAATATAGATTGATTTA-T-TT-TA-AAA
* * *
4312639 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAATATAGATTGATTTATTTTAAAA
4312693 TATGGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTA
4312724 TTGTAGTTGT
Statistics
Matches: 157, Mismatches: 32, Indels: 24
0.74 0.15 0.11
Matches are distributed among these distances:
53 4 0.03
54 79 0.50
55 5 0.03
56 7 0.04
57 2 0.01
58 43 0.27
59 2 0.01
60 7 0.04
61 4 0.03
62 3 0.02
63 1 0.01
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAATATAGATTGATTTATTTTAAAA
Found at i:4312551 original size:14 final size:14
Alignment explanation
Indices: 4312532--4312585 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
4312522 ATATGGATTG
4312532 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
4312546 ATTTATTAGTATGGATTA
1 ATTTATT--T-T-AAATA
4312564 ATTTATTTTAAATA
1 ATTTATTTTAAATA
4312578 ATTTATTT
1 ATTTATTT
4312586 GTATGGATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 18 0.56
15 1 0.03
16 2 0.06
17 1 0.03
18 10 0.31
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:4312696 original size:22 final size:22
Alignment explanation
Indices: 4312671--4312713 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
4312661 AATTTATTAG
4312671 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
4312693 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
4312714 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:4312795 original size:31 final size:31
Alignment explanation
Indices: 4312738--4312796 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
4312728 AGTTGTATGG
* *
4312738 ATTATTTAAATTTCAGTATTATAAAACTAAA
1 ATTATTTAAATCTCAGTATTACAAAACTAAA
*
4312769 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTACAAAACT
4312797 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTACAAAACTAAA
Found at i:4313783 original size:154 final size:154
Alignment explanation
Indices: 4313542--4313882 Score: 477
Period size: 157 Copynumber: 2.2 Consensus size: 154
4313532 ATGCTTTCAC
** * * * *
4313542 TATTTCTTCAATTCCTCCTTCATTTTAAGTCTATTTTCACCAAATTTGAATCGCATGCTCCTAAA
1 TATTTCTTCAATTTGTCATTTATTTTAAGTCTATTTTCACCAAATTTGAATCACATCCTCCTAAA
* ** *
4313607 CCATAGTAGAATACATGTGTACTTTCAATTTCTCTTTTTGAT-ATTTTTTTATTTTTCAATTTAG
66 CCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAAAATTTTTATTTGTCAATTTAG
*
4313671 TCTTTCAATTTTTCATAATCTCCT
131 TCCTTCAATTTTTCATAATCTCCT
* * * *
4313695 TATTTCTTCAATTTGTCATTTATTTTAAGTCTTTTTTTTACCAAATTTGAGTCACATCCTTCTAA
1 TATTTCTTCAATTTGTCATTTATTTTAAGTC-TATTTTCACCAAATTTGAATCACATCCTCCTAA
*
4313760 ATCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAAAAAATTTTTATTTGTCAATT
65 ACCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGAT--AAAATTTTTATTTGTCAATT
4313825 TAGTCCTTCAATTTTTCATAATCTCCT
128 TAGTCCTTCAATTTTTCATAATCTCCT
* * *
4313852 TATTCCATCAATTTGTGATTTATTTTAAGTC
1 TATTTCTTCAATTTGTCATTTATTTTAAGTC
4313883 CCTTTTACCT
Statistics
Matches: 165, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
153 27 0.16
154 68 0.41
157 70 0.42
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49
Consensus pattern (154 bp):
TATTTCTTCAATTTGTCATTTATTTTAAGTCTATTTTCACCAAATTTGAATCACATCCTCCTAAA
CCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAAAATTTTTATTTGTCAATTTAG
TCCTTCAATTTTTCATAATCTCCT
Found at i:4313956 original size:157 final size:156
Alignment explanation
Indices: 4313563--4313946 Score: 395
Period size: 157 Copynumber: 2.5 Consensus size: 156
4313553 TTCCTCCTTC
* * * * * * * * *
4313563 ATTTTAAGTCT-ATTTTCACCAAATTTGAATCGCATGCTCCTAAACCATAGTAGAATACATGTGT
1 ATTTTAAGTCTCCTTTT-ACCAAATTTAAACCACATCCTTCTAAATCATAATAGAAAACATGTGT
* * ** * *
4313627 ACTTTCAATTTCTCTTTTTGAT---ATTTTTTTATTTTTCAATTTAGTCTTTCAATTTTTCATAA
65 AATTTCAATTCCTCTTTTTGATAAAAAATTTTTATTTGTCAATTTAGTCCTTCAATTTTTCATAA
* *
4313689 TCTCCTTATTTCTTCAATTTGTCATTT
130 TCTCCTTATTCCATCAATTTGTCATTT
** * ** * *
4313716 ATTTTAAGTCTTTTTTTTACCAAATTTGAGTCACATCCTTCTAAATCATAGTAGAATACATGTGT
1 ATTTTAAGTC-TCCTTTTACCAAATTTAAACCACATCCTTCTAAATCATAATAGAAAACATGTGT
*
4313781 ACTTTCAATTCCTCTTTTTGATAAAAAATTTTTATTTGTCAATTTAGTCCTTCAATTTTTCATAA
65 AATTTCAATTCCTCTTTTTGATAAAAAATTTTTATTTGTCAATTTAGTCCTTCAATTTTTCATAA
*
4313846 TCTCCTTATTCCATCAATTTGTGATTT
130 TCTCCTTATTCCATCAATTTGTCATTT
* * * * *
4313873 ATTTTAAGTC-CCTTTTACCTAATTTTAAACCACATGC-TC-ATATACTATAATAGAAAACCTTT
1 ATTTTAAGTCTCCTTTTACC-AAATTTAAACCACATCCTTCTAAAT-C-ATAATAGAAAACATGT
4313935 GTAATTTCAATT
63 GTAATTTCAATT
4313947 TTTATTTTTT
Statistics
Matches: 196, Mismatches: 27, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
153 10 0.05
154 67 0.34
155 14 0.07
156 35 0.18
157 70 0.36
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.47
Consensus pattern (156 bp):
ATTTTAAGTCTCCTTTTACCAAATTTAAACCACATCCTTCTAAATCATAATAGAAAACATGTGTA
ATTTCAATTCCTCTTTTTGATAAAAAATTTTTATTTGTCAATTTAGTCCTTCAATTTTTCATAAT
CTCCTTATTCCATCAATTTGTCATTT
Found at i:4317903 original size:43 final size:43
Alignment explanation
Indices: 4317855--4318106 Score: 346
Period size: 43 Copynumber: 5.9 Consensus size: 43
4317845 TGATAACAAA
* * *
4317855 AAACGCCGCAAAAGGTCGAGATATATAGCGACATTTTTGGAAC
1 AAACGCCGCAAAAGGTCGAGATTTATAGCGGCGTTTTTGGAAC
* *
4317898 AAACGCCGTAAAAGGTCGAGATCTATAGCGGCGTTTTTGGATA-
1 AAACGCCGCAAAAGGTCGAGATTTATAGCGGCGTTTTTGGA-AC
* * *
4317941 AAACGCCGCAAAAGGTCAAGATTTATAGCAGCGTTTTTGGAAA
1 AAACGCCGCAAAAGGTCGAGATTTATAGCGGCGTTTTTGGAAC
** *
4317984 AAATACCGCAAAAGGTCGAGATCTATAGCGGCG-TTTTGGAAC
1 AAACGCCGCAAAAGGTCGAGATTTATAGCGGCGTTTTTGGAAC
** * *
4318026 AAACGATGCTAAAGGTCAAGATTTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCGAGATTTATAGCGGCGTTTTTGGAAC
4318069 AAACGCCGCAAAAGGTCGAGATTTATAGCGGCGTTTTT
1 AAACGCCGCAAAAGGTCGAGATTTATAGCGGCGTTTTT
4318107 CTATACAAAC
Statistics
Matches: 181, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
42 35 0.19
43 145 0.80
44 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.24
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCGAGATTTATAGCGGCGTTTTTGGAAC
Found at i:4318061 original size:85 final size:85
Alignment explanation
Indices: 4317854--4318105 Score: 353
Period size: 85 Copynumber: 3.0 Consensus size: 85
4317844 TTGATAACAA
* * * * * *
4317854 AAAACGCCGCAAAAGGTCGAGATATATAGCGACATTTTTGGAACAAACGCCGTAAAAGGTCGAGA
1 AAAACGACGCAAAAGGTCAAGATTTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCGAGA
4317919 TCTATAGCGGCGTTTTTGGAT
66 TCTATAGCGGCG-TTTTGGAT
* * * **
4317940 AAAACGCCGCAAAAGGTCAAGATTTATAGCAGCGTTTTTGGAAAAAATACCGCAAAAGGTCGAGA
1 AAAACGACGCAAAAGGTCAAGATTTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCGAGA
4318005 TCTATAGCGGCGTTTTGGA-
66 TCTATAGCGGCGTTTTGGAT
* *
4318024 ACAAACGATGCTAAAGGTCAAGATTTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCGAG
1 A-AAACGACGCAAAAGGTCAAGATTTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCGAG
*
4318089 ATTTATAGCGGCGTTTT
65 ATCTATAGCGGCGTTTT
4318106 TCTATACAAA
Statistics
Matches: 148, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
84 1 0.01
85 79 0.53
86 68 0.46
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (85 bp):
AAAACGACGCAAAAGGTCAAGATTTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCGAGA
TCTATAGCGGCGTTTTGGAT
Found at i:4318081 original size:128 final size:129
Alignment explanation
Indices: 4317860--4318106 Score: 374
Period size: 128 Copynumber: 1.9 Consensus size: 129
4317850 ACAAAAAACG
* * *
4317860 CCGCAAAAGGTCGAGATATATAGCGACATTTTTGGAACAAACGCCGTAAAAGGTCGAGATCTATA
1 CCGCAAAAGGTCGAGATATATAGCGACAGTTTTGGAACAAACGACGTAAAAGGTCAAGATCTATA
4317925 GCGGCGTTTTTGGATAAAACGCCGCAAAAGGTCAAGATTTATAGCAGCGTTTTTGGAAAAAATA
66 GCGGCGTTTTTGGATAAAACGCCGCAAAAGGTCAAGATTTATAGCAGCGTTTTTGGAAAAAATA
* * * *
4317989 CCGCAAAAGGTCGAGATCTATAGCGGC-GTTTTGGAACAAACGATGCT-AAAGGTCAAGATTTAT
1 CCGCAAAAGGTCGAGATATATAGCGACAGTTTTGGAACAAACGACG-TAAAAGGTCAAGATCTAT
* *
4318052 AGCGGCGTTTTTGGA-ACAAACGCCGCAAAAGGTCGAGATTTATAGCGGCGTTTTT
65 AGCGGCGTTTTTGGATA-AAACGCCGCAAAAGGTCAAGATTTATAGCAGCGTTTTT
4318107 CTATACAAAC
Statistics
Matches: 107, Mismatches: 9, Indels: 5
0.88 0.07 0.04
Matches are distributed among these distances:
127 1 0.01
128 80 0.75
129 26 0.24
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.25
Consensus pattern (129 bp):
CCGCAAAAGGTCGAGATATATAGCGACAGTTTTGGAACAAACGACGTAAAAGGTCAAGATCTATA
GCGGCGTTTTTGGATAAAACGCCGCAAAAGGTCAAGATTTATAGCAGCGTTTTTGGAAAAAATA
Found at i:4318265 original size:21 final size:21
Alignment explanation
Indices: 4318241--4318301 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
4318231 TAATTAAGAC
4318241 ACAAACTTGAAATCCATAACA
1 ACAAACTTGAAATCCATAACA
*
4318262 ACAAACTTGAAATCCGTAACA
1 ACAAACTTGAAATCCATAACA
*
4318283 AGAAACTTGAAATCCATAA
1 ACAAACTTGAAATCCATAA
4318302 TAATAAATCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.51, C:0.21, G:0.08, T:0.20
Consensus pattern (21 bp):
ACAAACTTGAAATCCATAACA
Found at i:4322254 original size:42 final size:43
Alignment explanation
Indices: 4322148--4322262 Score: 130
Period size: 42 Copynumber: 2.7 Consensus size: 43
4322138 AATGGTTAAA
* * **
4322148 CGCCAATAAAGTACTAGGTTTTAGCGGCG--TTTGTCTAAAAT
1 CGCCACTAAAGTATTAGGTTTTAGCGGCGTTTTTGAATAAAAT
* *
4322189 CGTCACTAAAGTATGA-GTATTTAGCGGCGTTTTTGAATAAAAT
1 CGCCACTAAAGTATTAGGT-TTTAGCGGCGTTTTTGAATAAAAT
*
4322232 -GCCTCTAAAGTATTAGGTTTTAGCGGCGTTT
1 CGCCACTAAAGTATTAGGTTTTAGCGGCGTTT
4322263 ATTTAAAAAC
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
40 2 0.03
41 22 0.36
42 25 0.41
43 12 0.20
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.35
Consensus pattern (43 bp):
CGCCACTAAAGTATTAGGTTTTAGCGGCGTTTTTGAATAAAAT
Found at i:4322345 original size:41 final size:41
Alignment explanation
Indices: 4322290--4322600 Score: 201
Period size: 41 Copynumber: 7.6 Consensus size: 41
4322280 TATATATACC
* * * *
4322290 CTATTGCGGTGTTTGTTTAAAAACGCAACTAAAGAACGATT
1 CTATAGCGGCGTTTGTTTAAAAACGCCACTAAAGTACGATT
* * *
4322331 CTATGGCGGCGTTTGTTTACAAACGCCACTAAAGTACAAGTT
1 CTATAGCGGCGTTTGTTTAAAAACGCCACTAAAGTACGA-TT
* * *
4322373 -T-TAGCGGCGTTT-TTGCATAAAACGCCTCTAAAGTACTAGGTT
1 CTATAGCGGCGTTTGTT-TA-AAAACGCCACTAAAGTAC--GATT
* * * * **
4322415 -T-TAGCGGCGTTTATCTAAAAATGCCAC-AATA-TATGTACC
1 CTATAGCGGCGTTTGTTTAAAAACGCCACTAA-AGTACG-ATT
* *
4322454 CTATTGCGGCGTTTGTTTAAAAACGCCACTAAAGAACGATT
1 CTATAGCGGCGTTTGTTTAAAAACGCCACTAAAGTACGATT
* * * * *
4322495 TTATGGCGGCGTTTTTTTAAAAATGCCACTAAAGTAC-TTAT
1 CTATAGCGGCGTTTGTTTAAAAACGCCACTAAAGTACGAT-T
* * * **
4322536 CTTTAGCGGCGCTTATCGAATAAACGCCACTAAAGTACGAGTT
1 CTATAGCGGCGTTTGTTTAA-AAACGCCACTAAAGTACGA-TT
*
4322579 -T-TAGCGGCGTTTGTTGAAAAAC
1 CTATAGCGGCGTTTGTTTAAAAAC
4322601 ACCGTTAACG
Statistics
Matches: 208, Mismatches: 46, Indels: 33
0.72 0.16 0.11
Matches are distributed among these distances:
38 1 0.00
39 2 0.01
40 21 0.10
41 143 0.69
42 38 0.18
43 2 0.01
44 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (41 bp):
CTATAGCGGCGTTTGTTTAAAAACGCCACTAAAGTACGATT
Found at i:4322395 original size:82 final size:78
Alignment explanation
Indices: 4322254--4322531 Score: 220
Period size: 82 Copynumber: 3.4 Consensus size: 78
4322244 TTAGGTTTTA
* * * * * *
4322254 GCGGCGTTTATTTAAAAACGCAACGATATATA-TACCCTATTGCGGTGTTTGTTTAAAAACGCAA
1 GCGGCGTTTATTTAAAAATGCCAC--TA-A-AGTACACTATTGCGGCGTTTGTTCAAAAACGCCA
4322318 CTAAAGAACGATTCTATG
62 CTAAAGAACGATT-TATG
* * * * * *
4322336 GCGGCGTTTGTTTACAAACGCCACTAAAGTACAAGTTTTAGCGGCGTTT-TTGCATAAAACGCCT
1 GCGGCGTTTATTTAAAAATGCCACTAAAGTAC-ACTATT-GCGGCGTTTGTT-CA-AAAACGCCA
* * *
4322400 CTAAAGTACTAGGTTT-TA
62 CTAAAGAAC--GATTTATG
* * * *
4322418 GCGGCGTTTATCTAAAAATGCCACAATATATGTACCCTATTGCGGCGTTTGTTTAAAAACGCCAC
1 GCGGCGTTTATTTAAAAATGCCAC--TA-AAGTACACTATTGCGGCGTTTGTTCAAAAACGCCAC
4322483 TAAAGAACGATTTTATG
63 TAAAGAACGA-TTTATG
*
4322500 GCGGCGTTTTTTTAAAAATGCCACTAAAGTAC
1 GCGGCGTTTATTTAAAAATGCCACTAAAGTAC
4322532 TTATCTTTAG
Statistics
Matches: 154, Mismatches: 29, Indels: 29
0.73 0.14 0.14
Matches are distributed among these distances:
78 1 0.01
79 9 0.06
80 10 0.06
81 12 0.08
82 96 0.62
83 11 0.07
84 10 0.06
85 5 0.03
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (78 bp):
GCGGCGTTTATTTAAAAATGCCACTAAAGTACACTATTGCGGCGTTTGTTCAAAAACGCCACTAA
AGAACGATTTATG
Found at i:4322435 original size:123 final size:122
Alignment explanation
Indices: 4322307--4322600 Score: 296
Period size: 123 Copynumber: 2.4 Consensus size: 122
4322297 GGTGTTTGTT
* * * * *
4322307 TAAAAACGCAACTAAAGAACGATTCTATGGCGGCGTTTGTTTACAAACGCCACTAAAGTACAAGT
1 TAAAAACGCCACTAAAGTACGATTCTATAGCGGCGTTTGTTTAAAAACGCCACTAAAGAACAA-T
* *
4322372 TTTA-GCGGCGTTTTTGCATAAAACGCCTCTAAAGTAC-TAGGT-TTTAGCGGCGTTTATC
65 TTTAGGCGGCGTTTTTGCA-AAAACGCCACTAAAGTACTTA--TCTTTAGCGGCGCTTATC
* * ** * *
4322430 TAAAAATGCCAC-AATA-TATGTACCCTATTGCGGCGTTTGTTTAAAAACGCCACTAAAGAACGA
1 TAAAAACGCCACTAA-AGTACG-ATTCTATAGCGGCGTTTGTTTAAAAACGCCACTAAAGAACAA
** *
4322493 TTTTATGGCGGCGTTTTTTTAAAAATGCCACTAAAGTACTTATCTTTAGCGGCGCTTATC
64 TTTTA-GGCGGCGTTTTTGCAAAAACGCCACTAAAGTACTTATCTTTAGCGGCGCTTATC
* *
4322553 GAATAAACGCCACTAAAGTACGAGTT-T-TAGCGGCGTTTGTTGAAAAAC
1 TAA-AAACGCCACTAAAGTACGA-TTCTATAGCGGCGTTTGTTTAAAAAC
4322601 ACCGTTAACG
Statistics
Matches: 139, Mismatches: 22, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
122 10 0.07
123 99 0.71
124 25 0.18
125 5 0.04
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (122 bp):
TAAAAACGCCACTAAAGTACGATTCTATAGCGGCGTTTGTTTAAAAACGCCACTAAAGAACAATT
TTAGGCGGCGTTTTTGCAAAAACGCCACTAAAGTACTTATCTTTAGCGGCGCTTATC
Found at i:4322456 original size:164 final size:164
Alignment explanation
Indices: 4322171--4322590 Score: 560
Period size: 164 Copynumber: 2.6 Consensus size: 164
4322161 CTAGGTTTTA
* * ** *
4322171 GCGGCGTTTGTCTAAAATCGTCACTAAAGTATGAGTATTTAGCGGCGTTTTTGAATAAAATGCCT
1 GCGGCGTTTGTTTAAAA-CGCCACTAAAGTACAAGTATTTAGCGGCGTTTTTGAATAAAACGCCT
* * * *
4322236 CTAAAGTATTAGGTTTTAGCGGCGTTTATTTAAAAACGCAACGATATATATACCCTATTGCGGTG
65 CTAAAGTACTAGGTTTTAGCGGCGTTTATCTAAAAACGCAACAATATATATACCCTATTGCGGCG
4322301 TTTGTTTAAAAACGCAACTAAAGAACGATTCTATG
130 TTTGTTTAAAAACGCAACTAAAGAACGATTCTATG
*
4322336 GCGGCGTTTGTTTACAAACGCCACTAAAGTACAAGT-TTTAGCGGCGTTTTTGCATAAAACGCCT
1 GCGGCGTTTGTTTA-AAACGCCACTAAAGTACAAGTATTTAGCGGCGTTTTTGAATAAAACGCCT
* * *
4322400 CTAAAGTACTAGGTTTTAGCGGCGTTTATCTAAAAATGCCACAATATATGTACCCTATTGCGGCG
65 CTAAAGTACTAGGTTTTAGCGGCGTTTATCTAAAAACGCAACAATATATATACCCTATTGCGGCG
* *
4322465 TTTGTTTAAAAACGCCACTAAAGAACGATTTTATG
130 TTTGTTTAAAAACGCAACTAAAGAACGATTCTATG
* * * * * *
4322500 GCGGCGTTTTTTTAAAAATGCCACTAAAGTACTTA-TCTTTAGCGGCGCTTATCGAAT-AAACGC
1 GCGGCGTTTGTTT-AAAACGCCACTAAAGTAC-AAGTATTTAGCGGCG-TTTTTGAATAAAACGC
* *
4322563 CACTAAAGTACGA-GTTTTAGCGGCGTTT
63 CTCTAAAGTACTAGGTTTTAGCGGCGTTT
4322591 GTTGAAAAAC
Statistics
Matches: 227, Mismatches: 23, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
164 161 0.71
165 57 0.25
166 9 0.04
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (164 bp):
GCGGCGTTTGTTTAAAACGCCACTAAAGTACAAGTATTTAGCGGCGTTTTTGAATAAAACGCCTC
TAAAGTACTAGGTTTTAGCGGCGTTTATCTAAAAACGCAACAATATATATACCCTATTGCGGCGT
TTGTTTAAAAACGCAACTAAAGAACGATTCTATG
Found at i:4331793 original size:22 final size:22
Alignment explanation
Indices: 4331767--4331816 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
4331757 CATGATCCGA
4331767 ATCCGATCCGAAATAACTGGAT
1 ATCCGATCCGAAATAACTGGAT
*
4331789 TTCCGATCCGAAATAACTGGAT
1 ATCCGATCCGAAATAACTGGAT
4331811 ATCCGA
1 ATCCGA
4331817 ATACATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (22 bp):
ATCCGATCCGAAATAACTGGAT
Found at i:4332263 original size:16 final size:17
Alignment explanation
Indices: 4332239--4332276 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
4332229 TTTAAATTAA
*
4332239 ATATAAGATATAAATT-
1 ATATTAGATATAAATTG
*
4332255 ATATTAGATCTAAATTG
1 ATATTAGATATAAATTG
4332272 ATATT
1 ATATT
4332277 TAAGAAGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (17 bp):
ATATTAGATATAAATTG
Found at i:4334584 original size:11 final size:11
Alignment explanation
Indices: 4334568--4334597 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4334558 ACATCAAATT
4334568 AGTTAGGTGAA
1 AGTTAGGTGAA
*
4334579 AGTTAGGTGAG
1 AGTTAGGTGAA
4334590 AGTTAGGT
1 AGTTAGGT
4334598 ATGTGTCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.40, T:0.30
Consensus pattern (11 bp):
AGTTAGGTGAA
Found at i:4336730 original size:11 final size:11
Alignment explanation
Indices: 4336714--4336756 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
4336704 ACATCAAATT
4336714 AGTTAGGTGAA
1 AGTTAGGTGAA
4336725 AGTTAGGTATGAA
1 AGTTAGG--TGAA
* *
4336738 ATTTAGGTGAG
1 AGTTAGGTGAA
4336749 AGTTAGGT
1 AGTTAGGT
4336757 ATGTGTCTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 17 0.63
13 10 0.37
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.33
Consensus pattern (11 bp):
AGTTAGGTGAA
Found at i:4338503 original size:18 final size:18
Alignment explanation
Indices: 4338479--4338563 Score: 98
Period size: 18 Copynumber: 4.7 Consensus size: 18
4338469 TTGGACATTT
*
4338479 CAGAAAATTCAGCCACCG
1 CAGAAAATTCAGCCATCG
* * *
4338497 TAGAAAATTCAGTCATTG
1 CAGAAAATTCAGCCATCG
*
4338515 CAGAAAATTCAGCCAACG
1 CAGAAAATTCAGCCATCG
* * *
4338533 TAGAAAATTCAGTCATTG
1 CAGAAAATTCAGCCATCG
4338551 CAGAAAATTCAGC
1 CAGAAAATTCAGC
4338564 TACCTTCAAT
Statistics
Matches: 53, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 53 1.00
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.21
Consensus pattern (18 bp):
CAGAAAATTCAGCCATCG
Found at i:4338526 original size:36 final size:36
Alignment explanation
Indices: 4338474--4338563 Score: 162
Period size: 36 Copynumber: 2.5 Consensus size: 36
4338464 CTTCCTTGGA
* *
4338474 CATTTCAGAAAATTCAGCCACCGTAGAAAATTCAGT
1 CATTGCAGAAAATTCAGCCAACGTAGAAAATTCAGT
4338510 CATTGCAGAAAATTCAGCCAACGTAGAAAATTCAGT
1 CATTGCAGAAAATTCAGCCAACGTAGAAAATTCAGT
4338546 CATTGCAGAAAATTCAGC
1 CATTGCAGAAAATTCAGC
4338564 TACCTTCAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (36 bp):
CATTGCAGAAAATTCAGCCAACGTAGAAAATTCAGT
Found at i:4343457 original size:26 final size:25
Alignment explanation
Indices: 4343391--4343450 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 25
4343381 TATGGCATTG
*
4343391 AATATTTATTTATATTATTATCGTT
1 AATATTTATTTATATTATTATAGTT
4343416 AATATTATATTTTTATATTTATTATAGTT
1 AATATT-TA--TTTATA-TTATTATAGTT
4343445 AATATT
1 AATATT
4343451 ACTTTATTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 6 0.20
26 2 0.07
28 6 0.20
29 16 0.53
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (25 bp):
AATATTTATTTATATTATTATAGTT
Found at i:4343660 original size:19 final size:20
Alignment explanation
Indices: 4343636--4343684 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
4343626 CTTAAGCCAC
*
4343636 TATTAATTTATATT-ATCAT
1 TATTAATTTATATTAATAAT
* *
4343655 TATTAAATTAAATTAATAAT
1 TATTAATTTATATTAATAAT
4343675 TA-TAATTTAT
1 TATTAATTTAT
4343685 CTAAATACTA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
TATTAATTTATATTAATAAT
Found at i:4343706 original size:17 final size:17
Alignment explanation
Indices: 4343680--4343714 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
4343670 ATAATTATAA
4343680 TTTATCTAAATACTATT
1 TTTATCTAAATACTATT
*
4343697 TTTATTTAAATACTATT
1 TTTATCTAAATACTATT
4343714 T
1 T
4343715 AAAATTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTATCTAAATACTATT
Found at i:4344526 original size:20 final size:20
Alignment explanation
Indices: 4344501--4344550 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
4344491 CATCTGGTAT
*
4344501 TATCGATACTACCTTGAGAG
1 TATCGATACTACCTAGAGAG
4344521 TATCGATACTACCTAGAGAG
1 TATCGATACTACCTAGAGAG
*
4344541 TATCAATACT
1 TATCGATACT
4344551 TCTCTTACCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (20 bp):
TATCGATACTACCTAGAGAG
Found at i:4357946 original size:29 final size:29
Alignment explanation
Indices: 4357904--4357992 Score: 178
Period size: 29 Copynumber: 3.1 Consensus size: 29
4357894 CTACAGTGGT
4357904 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
4357933 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
4357962 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
4357991 CT
1 CT
4357993 GTGTGTATTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.13, C:0.31, G:0.37, T:0.18
Consensus pattern (29 bp):
CTTGGAGGTCGCCATGGCATCCGGGCGAC
Found at i:4358122 original size:15 final size:15
Alignment explanation
Indices: 4358082--4358261 Score: 137
Period size: 15 Copynumber: 11.1 Consensus size: 15
4358072 AACATGGGAC
4358082 GTGGGAATGCATGGGG
1 GTGGGAATGCAT-GGG
* *
4358098 GAGGGGATGCATGGG
1 GTGGGAATGCATGGG
4358113 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
* *
4358128 G-GAGGGATCAACATGGG
1 GTG-GGAAT--GCATGGG
4358145 ATGTGGGAATGCATGGGG
1 --GTGGGAATGCAT-GGG
* *
4358163 GAGGGGATGCATGGG
1 GTGGGAATGCATGGG
4358178 ACGTGGGAATGCATGGG
1 --GTGGGAATGCATGGG
4358195 GTGGGAATGCATGGGG
1 GTGGGAATGCAT-GGG
* * *
4358211 GAGGGGATGGTGCATTGGAC
1 G-TGGGA--ATGCA-TGG-G
4358231 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
4358246 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
4358261 G
1 G
4358262 AGGGGATGGT
Statistics
Matches: 131, Mismatches: 18, Indels: 31
0.73 0.10 0.17
Matches are distributed among these distances:
14 1 0.01
15 52 0.40
16 27 0.21
17 30 0.23
18 3 0.02
19 15 0.11
20 3 0.02
ACGTcount: A:0.21, C:0.08, G:0.53, T:0.18
Consensus pattern (15 bp):
GTGGGAATGCATGGG
Found at i:4358142 original size:65 final size:66
Alignment explanation
Indices: 4358069--4358195 Score: 229
Period size: 65 Copynumber: 1.9 Consensus size: 66
4358059 GATGCATGCA
4358069 ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGG-GTGGGAATGCATGGGGGAGG
1 ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGAGTGGGAATGCATGGGGGAGG
4358133 G
66 G
*
4358134 ATCAACATGGGATGTGGGAATGCATGGGGGAGGGGATGCATGGGACGTGGGAATGCATGGGG
1 ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGA-GTGGGAATGCATGGGG
4358196 TGGGAATGCA
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
65 43 0.73
67 16 0.27
ACGTcount: A:0.24, C:0.09, G:0.50, T:0.17
Consensus pattern (66 bp):
ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGAGTGGGAATGCATGGGGGAGG
G
Found at i:4358190 original size:82 final size:83
Alignment explanation
Indices: 4358084--4358260 Score: 234
Period size: 82 Copynumber: 2.2 Consensus size: 83
4358074 CATGGGACGT
* * *
4358084 GGGAATGCATGGG-GGAGGGGATGCATGGGGTGGGAATGCATGGGGGA-GGGAT-CAACATGGGA
1 GGGAATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGCAACATGGGA
*
4358146 TGTGGGAATGCATGGGGGA
66 CGTGGGAATGCAT-GGGGA
* *** *
4358165 GGGGATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGGTGCATTGGA
1 GGGAATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGCAACATGGGA
*
4358230 CGTGGGAATGCATGGGGT
66 CGTGGGAATGCATGGGGA
4358248 GGGAATGCATGGG
1 GGGAATGCATGGG
4358261 GAGGGGATGG
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
81 12 0.15
82 31 0.38
83 21 0.26
84 18 0.22
ACGTcount: A:0.21, C:0.08, G:0.53, T:0.18
Consensus pattern (83 bp):
GGGAATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGCAACATGGGA
CGTGGGAATGCATGGGGA
Found at i:4358246 original size:51 final size:51
Alignment explanation
Indices: 4358147--4358271 Score: 213
Period size: 51 Copynumber: 2.5 Consensus size: 51
4358137 AACATGGGAT
4358147 GTGGGAATGCATGGGGGAGGGGA---TGCATGGGACGTGGGAATGCATGGG
1 GTGGGAATGCATGGGGGAGGGGATGGTGCATGGGACGTGGGAATGCATGGG
*
4358195 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
1 GTGGGAATGCATGGGGGAGGGGATGGTGCATGGGACGTGGGAATGCATGGG
4358246 GTGGGAATGCAT-GGGGAGGGGATGGT
1 GTGGGAATGCATGGGGGAGGGGATGGT
4358272 CACGGTGGTC
Statistics
Matches: 73, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
48 23 0.32
50 14 0.19
51 36 0.49
ACGTcount: A:0.20, C:0.07, G:0.54, T:0.18
Consensus pattern (51 bp):
GTGGGAATGCATGGGGGAGGGGATGGTGCATGGGACGTGGGAATGCATGGG
Found at i:4358353 original size:32 final size:32
Alignment explanation
Indices: 4358312--4358375 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
4358302 AAGGTCCTGC
4358312 TGCATGCATGCGTTGCATCATAGCTCATAGCT
1 TGCATGCATGCGTTGCATCATAGCTCATAGCT
4358344 TGCATGCATGCGTTGCATCATAGCTCATAGCT
1 TGCATGCATGCGTTGCATCATAGCTCATAGCT
4358376 CAGAGATTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (32 bp):
TGCATGCATGCGTTGCATCATAGCTCATAGCT
Found at i:4358731 original size:21 final size:21
Alignment explanation
Indices: 4358683--4358731 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
4358673 ACTAAAATCT
*
4358683 AGTTAATTAGTTTGTTAGTATA
1 AGTT-ATTAGTTTGTAAGTATA
* *
4358705 AATTATTAGTTTGTAAGTTTA
1 AGTTATTAGTTTGTAAGTATA
4358726 AGTTAT
1 AGTTAT
4358732 ATTATATTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (21 bp):
AGTTATTAGTTTGTAAGTATA
Found at i:4358741 original size:28 final size:30
Alignment explanation
Indices: 4358708--4358770 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 30
4358698 TAGTATAAAT
*
4358708 TATTAGTTTGTAAGTTTAAG-T-TATATTA
1 TATTAGTTTATAAGTTTAAGTTATATATTA
*
4358736 TATTAGTTTATTAGTTTAAGTTATATATTA
1 TATTAGTTTATAAGTTTAAGTTATATATTA
4358766 TATTA
1 TATTA
4358771 TATAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 18 0.58
29 1 0.03
30 12 0.39
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (30 bp):
TATTAGTTTATAAGTTTAAGTTATATATTA
Found at i:4359280 original size:16 final size:16
Alignment explanation
Indices: 4359256--4359313 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
4359246 GATAATTTCC
*
4359256 GTTTTAAAAATATTGT
1 GTTTAAAAAATATTGT
*
4359272 GTTTAAAAATATTTAGTGTT
1 GTTTAAAAA-A--TATTG-T
*
4359292 GTTTAAAAAATATTTT
1 GTTTAAAAAATATTGT
4359308 GTTTAA
1 GTTTAA
4359314 TTTACATTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 15 0.44
17 4 0.12
19 5 0.15
20 10 0.29
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (16 bp):
GTTTAAAAAATATTGT
Found at i:4359603 original size:26 final size:25
Alignment explanation
Indices: 4359574--4359632 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
4359564 AAATCATATT
*
4359574 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
4359600 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
4359626 ATTATTA
1 ATTATTA
4359633 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:4362540 original size:26 final size:26
Alignment explanation
Indices: 4362511--4362980 Score: 351
Period size: 26 Copynumber: 19.0 Consensus size: 26
4362501 TTTGATGATT
4362511 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
4362537 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* *
4362563 TAATAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* *
4362585 TA--AAT-ATTTAATGAACAAAT-ATT-
1 TAGTAATGATTTGAT-AA-TAATCATTA
4362608 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
4362634 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
4362660 TAATAATGATTT-ATTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** * * *
4362686 TAAAAATGATTTAATAATGAATTA-AA
1 TAGTAATGATTTGATAAT-AATCATTA
* *
4362712 TATTTAATGATTTG------ATGATT-
1 TA-GTAATGATTTGATAATAATCATTA
4362732 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
4362758 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* *
4362784 TAATAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
4362806 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
*
4362830 TAGTAATTATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
4362856 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* * *
4362882 TAATAATGA-TT--TAGTAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
4362904 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
*
4362928 TAGTAATTATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* * *
4362954 TAGTAATTATTTGATACTAATTATTA
1 TAGTAATGATTTGATAATAATCATTA
4362980 T
1 T
4362981 TAATAAGGAT
Statistics
Matches: 368, Mismatches: 36, Indels: 80
0.76 0.07 0.17
Matches are distributed among these distances:
19 13 0.04
20 20 0.05
22 9 0.02
23 38 0.10
24 24 0.07
25 32 0.09
26 207 0.56
27 25 0.07
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.45
Consensus pattern (26 bp):
TAGTAATGATTTGATAATAATCATTA
Found at i:4362648 original size:97 final size:98
Alignment explanation
Indices: 4362456--4362677 Score: 383
Period size: 97 Copynumber: 2.3 Consensus size: 98
4362446 ATGTATTTAT
* ****
4362456 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGAACAAATGATTTAGTAATGAT
4362521 TTGATAATAATCATTATAGTAATGATTTGATAA
66 TTGATAATAATCATTATAGTAATGATTTGATAA
4362554 TAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGAACAAAT-ATTTAGTAATGAT
1 TAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGAACAAATGATTTAGTAATGAT
4362618 TTGATAATAATCATTATAGTAATGATTTGATAA
66 TTGATAATAATCATTATAGTAATGATTTGATAA
*
4362651 TAATCATTATAATAATGATTTATTAAT
1 TAATCATTATAATAATGATTTAATAAT
4362678 AATCATTATA
Statistics
Matches: 118, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
97 72 0.61
98 46 0.39
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (98 bp):
TAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGAACAAATGATTTAGTAATGAT
TTGATAATAATCATTATAGTAATGATTTGATAA
Found at i:4362803 original size:98 final size:98
Alignment explanation
Indices: 4362634--4362993 Score: 605
Period size: 98 Copynumber: 3.7 Consensus size: 98
4362624 ATAATCATTA
* *
4362634 TAGTAATGATTTGATAATAATCATTATAATAATGATTT-ATTAATAATCATTATAAAAATGATTT
1 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGA-TAATAATCATTATAATAATGATTT
*
4362698 AATAATGAATTAAATATTTAATGATTTGATGATT
65 AATAATGATTTAAATATTTAATGATTTGATGATT
4362732 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
4362797 ATAATGATTTAAATATTTAATGATTTGATGATT
66 ATAATGATTTAAATATTTAATGATTTGATGATT
*
4362830 TAGTAATTATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
*
4362895 GTAATGATTTAAATATTTAATGATTTGATGATT
66 ATAATGATTTAAATATTTAATGATTTGATGATT
* * * * *
4362928 TAGTAATTATTTGATAATAATCATTATAGTAATTATTTGATACTAATTATTATTAATAAGGATTT
1 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTA-TAATAATGATTT
4362993 A
65 A
4362994 TTGTTAATAT
Statistics
Matches: 251, Mismatches: 9, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
98 238 0.95
99 13 0.05
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.45
Consensus pattern (98 bp):
TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
ATAATGATTTAAATATTTAATGATTTGATGATT
Found at i:4362860 original size:124 final size:120
Alignment explanation
Indices: 4362511--4362893 Score: 447
Period size: 124 Copynumber: 3.1 Consensus size: 120
4362501 TTTGATGATT
* * *
4362511 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATA-ATAATGATTT
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATAAT-ATTAAATATAATGA-TT
*
4362575 AATAATGATTTA-AATATTTAATGAACAAATATTTAGTAATGATTTGATAATAATCATTA
64 --TAATGATTTATAATATTTAATGAA-TAATATTTAGTAATGATTTGATAATAATCATTA
*
4362634 TAGTAATGATTTGATAATAATCATTATAATAATGATTTATTAATAATCATTATAA-A-AATGATT
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATAAT-ATTA-AATATAATGA-T
* * *
4362697 TAATAATGAATTA-AATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTA
63 T--TAATGATTTATAATATTTAATGA-ATAAT-ATTTAGTAATGATTTGATAATAATCATTA
*
4362758 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATGAT-TTAAATATTTAATGATT
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATAATATTAAATA--TAATGATT
* *
4362822 TGATGATTTAGTAATTATTTGAT-AATAATCATTATAGTAATGATTTGATAATAATCATTA
64 TAATGATTTA-TAA-TATTTAATGAATAAT-ATT-TAGTAATGATTTGATAATAATCATTA
*
4362882 TAATAATGATTT
1 TAGTAATGATTT
4362894 AGTAATGATT
Statistics
Matches: 232, Mismatches: 17, Indels: 21
0.86 0.06 0.08
Matches are distributed among these distances:
121 2 0.01
122 12 0.05
123 88 0.38
124 118 0.51
125 12 0.05
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.44
Consensus pattern (120 bp):
TAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATAATATTAAATATAATGATTTA
ATGATTTATAATATTTAATGAATAATATTTAGTAATGATTTGATAATAATCATTA
Found at i:4362886 original size:12 final size:12
Alignment explanation
Indices: 4362843--4362888 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
4362833 TAATTATTTG
4362843 ATAATAATCATT
1 ATAATAATCATT
* *
4362855 ATAGTAATGATTT
1 ATAATAATCA-TT
4362868 GATAATAATCATT
1 -ATAATAATCATT
4362881 ATAATAAT
1 ATAATAAT
4362889 GATTTAGTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 16 0.57
13 4 0.14
14 8 0.29
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (12 bp):
ATAATAATCATT
Found at i:4362976 original size:14 final size:14
Alignment explanation
Indices: 4362931--4362978 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
4362921 GATGATTTAG
4362931 TAATTATTTGATAA
1 TAATTATTTGATAA
* *
4362945 TAATCA-TT-ATAG
1 TAATTATTTGATAA
*
4362957 TAATTATTTGATAC
1 TAATTATTTGATAA
4362971 TAATTATT
1 TAATTATT
4362979 ATTAATAAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 8 0.29
13 4 0.14
14 16 0.57
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (14 bp):
TAATTATTTGATAA
Found at i:4363077 original size:17 final size:17
Alignment explanation
Indices: 4363052--4363084 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4363042 ACTAAATATC
*
4363052 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
4363069 TAATGATTTGATACTA
1 TAATGATTTGATACTA
4363085 AAAATCATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:4365523 original size:45 final size:47
Alignment explanation
Indices: 4365447--4365537 Score: 134
Period size: 45 Copynumber: 2.0 Consensus size: 47
4365437 CAACAAACAA
4365447 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTC
1 ATATAACTTAACTATTTAACTAACACAAACTAATT-AATAATTTTTTC
* *
4365495 ATATAAC-TAACTA-TTAAC-AATACAAACTAATTAATTATTTTTT
1 ATATAACTTAACTATTTAACTAACACAAACTAATTAATAATTTTTT
4365538 AACTATATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 10 0.24
45 13 0.32
46 5 0.12
47 6 0.15
48 7 0.17
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (47 bp):
ATATAACTTAACTATTTAACTAACACAAACTAATTAATAATTTTTTC
Found at i:4365606 original size:41 final size:40
Alignment explanation
Indices: 4365468--4365606 Score: 111
Period size: 41 Copynumber: 3.3 Consensus size: 40
4365458 CTATTTAACT
* * *
4365468 AACACAAACTAATTAAATAATTTTTTCA-TATAACTAACTATT
1 AACATAAACTAATTAAAT-ATTTTTTAACTAT-A-TAACTATA
*
4365510 AACAATACAAACTAATTAATTATTTTTTAACTATATAACTATCA
1 AAC-AT--AAACTAATTAAATATTTTTTAACTATATAACTAT-A
* * *
4365554 AACATATACTAATTAAATATTTTTTAATTTATGTATACTAT-
1 AACATAAACTAATTAAATATTTTTTAA-CTATATA-ACTATA
*
4365595 AACTTAAACTAA
1 AACATAAACTAA
4365607 CAATCATATA
Statistics
Matches: 80, Mismatches: 10, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
41 30 0.38
42 8 0.10
43 15 0.19
44 12 0.15
45 15 0.19
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.40
Consensus pattern (40 bp):
AACATAAACTAATTAAATATTTTTTAACTATATAACTATA
Found at i:4365769 original size:17 final size:16
Alignment explanation
Indices: 4365770--4365801 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
4365760 CCCTTTCTTT
4365770 CTTTCTTTCCTTTCTCC
1 CTTTCTTT-CTTTCTCC
4365787 CTTTCTTTCTTTCTC
1 CTTTCTTTCTTTCTC
4365802 GGCTGCAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (16 bp):
CTTTCTTTCTTTCTCC
Found at i:4365771 original size:4 final size:4
Alignment explanation
Indices: 4365743--4365800 Score: 53
Period size: 4 Copynumber: 14.0 Consensus size: 4
4365733 TTTCGAATTC
* ** **
4365743 TTCT TACT TTCCT TTCT CCCT TTCT TTCT TTCT TTCCT TTCT CCCT TTCT
1 TTCT TTCT TT-CT TTCT TTCT TTCT TTCT TTCT TT-CT TTCT TTCT TTCT
4365793 TTCT TTCT
1 TTCT TTCT
4365801 CGGCTGCAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
4 34 0.81
5 8 0.19
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (4 bp):
TTCT
Found at i:4365777 original size:25 final size:25
Alignment explanation
Indices: 4365743--4365800 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
4365733 TTTCGAATTC
*
4365743 TTCTTACTTTCCTTTCTCCCTTTCT
1 TTCTTTCTTTCCTTTCTCCCTTTCT
4365768 TTCTTTCTTTCCTTTCTCCCTTTCT
1 TTCTTTCTTTCCTTTCTCCCTTTCT
4365793 TTCTTTCT
1 TTCTTTCT
4365801 CGGCTGCAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (25 bp):
TTCTTTCTTTCCTTTCTCCCTTTCT
Found at i:4365890 original size:25 final size:25
Alignment explanation
Indices: 4365862--4365913 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
4365852 TTTCTTTTAT
*
4365862 AACCGGCTGCCTCAATTATTTCACC
1 AACCGACTGCCTCAATTATTTCACC
*
4365887 AACCGACTGCCTTAATTATTTCACC
1 AACCGACTGCCTCAATTATTTCACC
4365912 AA
1 AA
4365914 TAATTGTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.33, G:0.10, T:0.29
Consensus pattern (25 bp):
AACCGACTGCCTCAATTATTTCACC
Found at i:4366081 original size:26 final size:23
Alignment explanation
Indices: 4366024--4366083 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
4366014 ACACGTGAAG
4366024 GAATGGATGATGGGGCTGCATGT
1 GAATGGATGATGGGGCTGCATGT
4366047 GAATGGATGATGGGGCTGCATGT
1 GAATGGATGATGGGGCTGCATGT
*
4366070 GAATGGACGATGGG
1 GAATGGATGATGGG
4366084 AATGGCGCCG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.08, G:0.45, T:0.23
Consensus pattern (23 bp):
GAATGGATGATGGGGCTGCATGT
Found at i:4366122 original size:29 final size:29
Alignment explanation
Indices: 4366089--4366197 Score: 175
Period size: 29 Copynumber: 3.8 Consensus size: 29
4366079 ATGGGAATGG
4366089 CGCCGGGACTACATGGCGACCTATAAGGT
1 CGCCGGGACTACATGGCGACCTATAAGGT
4366118 CGCCGGGACTACATGGCGACCTATAAGGT
1 CGCCGGGACTACATGGCGACCTATAAGGT
*
4366147 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTATAAGGT
* *
4366176 CGCCTAGG-CTGCATGGCGACCT
1 CGCC-GGGACTACATGGCGACCT
4366198 CTCTCCTATT
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
29 74 0.97
30 2 0.03
ACGTcount: A:0.22, C:0.30, G:0.31, T:0.17
Consensus pattern (29 bp):
CGCCGGGACTACATGGCGACCTATAAGGT
Found at i:4366229 original size:19 final size:19
Alignment explanation
Indices: 4366205--4366242 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
4366195 CCTCTCTCCT
4366205 ATTCCACTGCATGGCCACC
1 ATTCCACTGCATGGCCACC
4366224 ATTCCACTGCATGGCCACC
1 ATTCCACTGCATGGCCACC
4366243 TCGCATGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.42, G:0.16, T:0.21
Consensus pattern (19 bp):
ATTCCACTGCATGGCCACC
Found at i:4366370 original size:55 final size:55
Alignment explanation
Indices: 4366305--4366415 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
4366295 GAACGACCTC
4366305 TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
1 TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
4366360 TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
1 TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
4366415 T
1 T
4366416 GGGGACCTCG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.16, C:0.34, G:0.22, T:0.28
Consensus pattern (55 bp):
TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
Found at i:4366392 original size:139 final size:139
Alignment explanation
Indices: 4366224--4366499 Score: 552
Period size: 139 Copynumber: 2.0 Consensus size: 139
4366214 CATGGCCACC
4366224 ATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCGCA
1 ATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCGCA
4366289 TGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCG
66 TGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCG
4366354 TATGCATCT
131 TATGCATCT
4366363 ATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCGCA
1 ATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCGCA
4366428 TGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCG
66 TGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCG
4366493 TATGCAT
131 TATGCAT
4366500 GGGGAGAACC
Statistics
Matches: 137, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
139 137 1.00
ACGTcount: A:0.17, C:0.33, G:0.25, T:0.24
Consensus pattern (139 bp):
ATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCGCA
TGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCG
TATGCATCT
Found at i:4366397 original size:27 final size:27
Alignment explanation
Indices: 4366312--4366397 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
4366302 CTCTCTATTC
4366312 CACTGCATGGCCACCTCGCATGGCTCG
1 CACTGCATGGCCACCTCGCATGGCTCG
* * * * ***
4366339 CACTCGTATGG-CTCGTATGCATCTATTC-
1 CACT-GCATGGCCACCT-CGCAT-GGCTCG
4366367 CACTGCATGGCCACCTCGCATGGCTCG
1 CACTGCATGGCCACCTCGCATGGCTCG
4366394 CACT
1 CACT
4366398 CGTATGGCTC
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
26 2 0.05
27 20 0.50
28 16 0.40
29 2 0.05
ACGTcount: A:0.16, C:0.37, G:0.22, T:0.24
Consensus pattern (27 bp):
CACTGCATGGCCACCTCGCATGGCTCG
Found at i:4366424 original size:41 final size:41
Alignment explanation
Indices: 4366370--4366501 Score: 119
Period size: 41 Copynumber: 3.2 Consensus size: 41
4366360 TCTATTCCAC
4366370 TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
** *** * *
4366411 TGCATGGGGACCTCGCATGGGGAGAACGACCTCTCTAT---TC-CA
1 TGCATGGCCACCTCGCATGGCTCG--C-A-CTC-GTATGGCTCGTA
4366453 CTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 -TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
4366495 TGCATGG
1 TGCATGG
4366502 GGAGAACCAG
Statistics
Matches: 67, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
38 3 0.04
39 3 0.04
40 1 0.01
41 29 0.43
42 2 0.03
43 22 0.33
44 1 0.01
45 3 0.04
46 3 0.04
ACGTcount: A:0.17, C:0.32, G:0.28, T:0.23
Consensus pattern (41 bp):
TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
Found at i:4367862 original size:17 final size:18
Alignment explanation
Indices: 4367825--4367863 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
4367815 TGACAGATCT
*
4367825 AAAAGTAGGGTAAATTAA
1 AAAAATAGGGTAAATTAA
4367843 AAAAATAGGGTAAATTAA
1 AAAAATAGGGTAAATTAA
4367861 AAA
1 AAA
4367864 TTTTATCACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.18, T:0.21
Consensus pattern (18 bp):
AAAAATAGGGTAAATTAA
Found at i:4369221 original size:25 final size:25
Alignment explanation
Indices: 4369183--4369282 Score: 103
Period size: 25 Copynumber: 4.0 Consensus size: 25
4369173 TGCCATATAG
**
4369183 ATTTGTCCCGAAGGACCACGTAGAA
1 ATTTGTCCTAAAGGACCACGTAGAA
* * ** *
4369208 ATTTATCCTAAAGGATCGTGTATAA
1 ATTTGTCCTAAAGGACCACGTAGAA
*
4369233 ATTTGTCCCAAAGGACCACGTAGAA
1 ATTTGTCCTAAAGGACCACGTAGAA
*
4369258 ATTTGT-CTCGAAGGACCACGTAGAA
1 ATTTGTCCT-AAAGGACCACGTAGAA
4369283 CCCTCGACTC
Statistics
Matches: 59, Mismatches: 15, Indels: 2
0.78 0.20 0.03
Matches are distributed among these distances:
24 1 0.02
25 58 0.98
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (25 bp):
ATTTGTCCTAAAGGACCACGTAGAA
Found at i:4369645 original size:13 final size:11
Alignment explanation
Indices: 4369617--4369660 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
4369607 ATTTCATGTC
*
4369617 AAATTTCATAA
1 AAATATCATAA
4369628 AAATATCATATCA
1 AAATATCATA--A
4369641 AAATATCATAA
1 AAATATCATAA
4369652 AAATATCAT
1 AAATATCAT
4369661 GTCATAATCC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 19 0.63
13 11 0.37
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATATCATAA
Found at i:4370243 original size:2 final size:2
Alignment explanation
Indices: 4370236--4370280 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
4370226 TCATAAATTT
*
4370236 TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4370278 TA T
1 TA T
4370281 TGTAGATTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4372724 original size:18 final size:18
Alignment explanation
Indices: 4372701--4372735 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
4372691 ATGTTGCCTA
4372701 AATCATATTAGAAGTTAT
1 AATCATATTAGAAGTTAT
4372719 AATCATATTAGAAGTTA
1 AATCATATTAGAAGTTA
4372736 GAAAAAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (18 bp):
AATCATATTAGAAGTTAT
Found at i:4373813 original size:15 final size:15
Alignment explanation
Indices: 4373790--4373824 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
4373780 TTTTGACATT
*
4373790 TTCTT-GACGTTTTC
1 TTCTTAGACGTTGTC
4373804 TTCTTAGACGTTGTC
1 TTCTTAGACGTTGTC
4373819 TTCTTA
1 TTCTTA
4373825 CCCCATGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.11, C:0.20, G:0.14, T:0.54
Consensus pattern (15 bp):
TTCTTAGACGTTGTC
Found at i:4373820 original size:26 final size:26
Alignment explanation
Indices: 4373770--4373820 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
4373760 TCCTTCTTTA
* * *
4373770 ACGTTTTCTTTTTTGACATTTTCTTG
1 ACGTTTTCTTCTTAGACATTGTCTTG
*
4373796 ACGTTTTCTTCTTAGACGTTGTCTT
1 ACGTTTTCTTCTTAGACATTGTCTT
4373821 CTTACCCCAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.12, C:0.18, G:0.14, T:0.57
Consensus pattern (26 bp):
ACGTTTTCTTCTTAGACATTGTCTTG
Found at i:4375211 original size:21 final size:21
Alignment explanation
Indices: 4375185--4375229 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4375175 GATTTCTGGG
* *
4375185 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
4375206 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
4375227 CAA
1 CAA
4375230 ACGAACAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:4375772 original size:2 final size:2
Alignment explanation
Indices: 4375765--4375804 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4375755 GAACATGTGA
4375765 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4375805 CTAAGAGAAG
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):
AT
Found at i:4376367 original size:31 final size:31
Alignment explanation
Indices: 4376244--4376355 Score: 188
Period size: 31 Copynumber: 3.6 Consensus size: 31
4376234 AGGGTCGAGG
*
4376244 GTTTACCTATGTTCTTCAGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4376275 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
4376306 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
4376337 GATTACCTAGGTTCTTCGG
1 GTTTACCTATGTTCTTCGG
4376356 AATCTATGGA
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 76 1.00
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:4379410 original size:21 final size:21
Alignment explanation
Indices: 4379384--4379428 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4379374 GATTTCTGGG
* *
4379384 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
4379405 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
4379426 CAA
1 CAA
4379429 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:4379968 original size:2 final size:2
Alignment explanation
Indices: 4379961--4379992 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4379951 GAACATGTGA
4379961 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
4379993 CTAAGAGAAG
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:4380470 original size:31 final size:31
Alignment explanation
Indices: 4380432--4380541 Score: 150
Period size: 31 Copynumber: 3.5 Consensus size: 31
4380422 AGGGTCGAGG
4380432 GTTTACCTATGTTCTTCAGGACATATGGACT
1 GTTTACCTATGTTCTTCAGGACATATGGACT
* *
4380463 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCAGGACATATGGACT
* *
4380494 GTTTACCTATGTCCTT-TGAGACATATGGACT
1 GTTTACCTATGTTCTTCAG-GACATATGGACT
* *
4380525 GATTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
4380542 GGAATCTATG
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
30 1 0.01
31 68 0.99
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCAGGACATATGGACT
Found at i:4380552 original size:31 final size:31
Alignment explanation
Indices: 4380432--4380556 Score: 148
Period size: 31 Copynumber: 4.0 Consensus size: 31
4380422 AGGGTCGAGG
4380432 GTTTACCTATGTTCTTCAGG-ACATATGGACT
1 GTTTACCTATGTTCTTC-GGAACATATGGACT
* *
4380463 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
4380494 GTTTACCTATGTCCTT-TGAGACATATGGACT
1 GTTTACCTATGTTCTTCGGA-ACATATGGACT
* *
4380525 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
4380556 G
1 G
4380557 GTCCTTCGGG
Statistics
Matches: 81, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
30 3 0.04
31 75 0.93
32 3 0.04
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:4380552 original size:62 final size:62
Alignment explanation
Indices: 4380432--4380553 Score: 167
Period size: 62 Copynumber: 2.0 Consensus size: 62
4380422 AGGGTCGAGG
* * * *
4380432 GTTTACCTATGTTCTTCAGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTCCTTCAGGACATATGGACTGATTACCTAGGTTCTTCGGAACATATGGATT
*
4380494 GTTTACCTATGTCCTT-TGAGACATATGGACTGATTACCTAGGTTCTTCGGAATC-TATGGA
1 GTTTACCTATGTCCTTCAG-GACATATGGACTGATTACCTAGGTTCTTCGGAA-CATATGGA
4380554 CTGGTCCTTC
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
61 1 0.02
62 51 0.96
63 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (62 bp):
GTTTACCTATGTCCTTCAGGACATATGGACTGATTACCTAGGTTCTTCGGAACATATGGATT
Done.