Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397254.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_30.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 15579451
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 73860 characters in sequence are not A, C, G, or T
File 23 of 32
Found at i:11662720 original size:3 final size:3
Alignment explanation
Indices: 11662712--11662742 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
11662702 TTATATGTGT
11662712 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
11662743 GAAACTGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:11664105 original size:153 final size:155
Alignment explanation
Indices: 11663820--11664107 Score: 406
Period size: 153 Copynumber: 1.8 Consensus size: 155
11663810 AATTTTGTTA
* *
11663820 CCCGTTTTACTTGTTTACACCATTATTTTTTTTTTAATTGAGGGGAGCGAAATTCGAACTTGCTC
1 CCCGTTTTACTTGTTTACACCATTATTTTTTTTTTAATTGAAGGGAGAGAAATTCGAACTTGCTC
* * *
11663885 TATATATAAGGGTTTATGTACTAACCAATAAGTTAAATGTCATCACTCATTTTACTTGTAAACTT
66 TATAGATAAGGG----TGTA-TAACCAATAAGTCAAATGTCATCACTCATTTTACTTGCAAACTT
11663950 GCTCTGAGGGGAGGGAGATTCGAACTTGCT
126 GCTCTGAGGGGAGGGAGATTCGAACTTGCT
*
11663980 CCCGTTTTACTTGTTTACACCATTATTATTTTTTTTAATTGAAGGGA-AGAAGATTTGAACTTGC
1 CCCGTTTTACTTGTTTACACCATTATT-TTTTTTTTAATTGAAGGGAGAGAA-ATTCGAACTTGC
*
11664044 TCTATAGAT-AGGG-GT-TTACCAATAAGTCAAATGTCATCAC-CTATTTTACTTGCAAACTTGC
64 TCTATAGATAAGGGTGTATAACCAATAAGTCAAATGTCATCACTC-ATTTTACTTGCAAACTTGC
11664105 TCT
128 TCT
11664108 ATAGGTAAAG
Statistics
Matches: 118, Mismatches: 7, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
152 1 0.01
153 44 0.37
155 2 0.02
160 34 0.29
161 37 0.31
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (155 bp):
CCCGTTTTACTTGTTTACACCATTATTTTTTTTTTAATTGAAGGGAGAGAAATTCGAACTTGCTC
TATAGATAAGGGTGTATAACCAATAAGTCAAATGTCATCACTCATTTTACTTGCAAACTTGCTCT
GAGGGGAGGGAGATTCGAACTTGCT
Found at i:11665780 original size:22 final size:22
Alignment explanation
Indices: 11665751--11665798 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
11665741 TTAGACTCTT
*
11665751 TTTC-AACGGATTATG-GGTTCA
1 TTTCTAACGGATT-TGAGGCTCA
11665772 TTTCTAACGGATTTGAGGCTCA
1 TTTCTAACGGATTTGAGGCTCA
11665794 TTTCT
1 TTTCT
11665799 GATGAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.42
Consensus pattern (22 bp):
TTTCTAACGGATTTGAGGCTCA
Found at i:11668907 original size:15 final size:15
Alignment explanation
Indices: 11668886--11668933 Score: 78
Period size: 15 Copynumber: 3.2 Consensus size: 15
11668876 TTTTCTCTTA
11668886 AAATTCTTTTGGAGG
1 AAATTCTTTTGGAGG
*
11668901 GAATTCTTTTGGAGG
1 AAATTCTTTTGGAGG
*
11668916 AAACTCTTTTGGAGG
1 AAATTCTTTTGGAGG
11668931 AAA
1 AAA
11668934 ATTGATTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.29, C:0.08, G:0.27, T:0.35
Consensus pattern (15 bp):
AAATTCTTTTGGAGG
Found at i:11670384 original size:31 final size:30
Alignment explanation
Indices: 11670327--11670384 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
11670317 AAAAAAGCTA
* *
11670327 TAAAAAAGATAAAATTATAAATATAATCAG
1 TAAAAAAGATAAAATTAAAAAAATAATCAG
11670357 TAAAAAA-ATTAAATATTAAAAAAATAAT
1 TAAAAAAGA-TAAA-ATTAAAAAAATAAT
11670385 AACAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 1 0.04
30 11 0.46
31 12 0.50
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (30 bp):
TAAAAAAGATAAAATTAAAAAAATAATCAG
Found at i:11670403 original size:12 final size:12
Alignment explanation
Indices: 11670374--11670415 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
11670364 ATTAAATATT
11670374 AAAAAAATAATA
1 AAAAAAATAATA
11670386 ACAAAAAA-AATA
1 A-AAAAAATAATA
*
11670398 GAAAAAAATTATA
1 -AAAAAAATAATA
11670411 AAAAA
1 AAAAA
11670416 CTAAATCTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.14
Consensus pattern (12 bp):
AAAAAAATAATA
Found at i:11670421 original size:25 final size:25
Alignment explanation
Indices: 11670359--11670421 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 25
11670349 ATAATCAGTA
*
11670359 AAAAAATTAAATATTAAAAAAATAAT
1 AAAAAA-TAAATATGAAAAAAATAAT
* *
11670385 AACAAAAAAAATA-GAAAAAAATTAT
1 AA-AAAATAAATATGAAAAAAATAAT
11670410 AAAAAACTAAAT
1 AAAAAA-TAAAT
11670422 CTCAATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
24 4 0.13
25 16 0.52
26 7 0.23
27 4 0.13
ACGTcount: A:0.75, C:0.03, G:0.02, T:0.21
Consensus pattern (25 bp):
AAAAAATAAATATGAAAAAAATAAT
Found at i:11683267 original size:27 final size:27
Alignment explanation
Indices: 11683236--11683291 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
11683226 ACAATAGCAT
11683236 TGAATCAAAGACA-AAGAACAGCAAATG
1 TGAATCAAAGACAGAAG-ACAGCAAATG
* *
11683263 TGAATCAAAGATAGAAGATAGCAAATG
1 TGAATCAAAGACAGAAGACAGCAAATG
11683290 TG
1 TG
11683292 CAAAATCTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.52, C:0.11, G:0.21, T:0.16
Consensus pattern (27 bp):
TGAATCAAAGACAGAAGACAGCAAATG
Found at i:11708651 original size:18 final size:17
Alignment explanation
Indices: 11708623--11708742 Score: 65
Period size: 18 Copynumber: 7.1 Consensus size: 17
11708613 TTTCCTGCAT
11708623 AATTGAAAAATACTA-AACA
1 AATT-AAAAATAC-AGAA-A
11708642 AATTAAAAATACAGAAA
1 AATTAAAAATACAGAAA
*
11708659 ATTTAAAAATACAACGAAA
1 AATTAAAAATAC-A-GAAA
* *
11708678 AATAAAAAATCCAG-AA
1 AATTAAAAATACAGAAA
*
11708694 GA-T-AAAAT--AGAAA
1 AATTAAAAATACAGAAA
* **
11708707 AAATAAAAATATTG-AA
1 AATTAAAAATACAGAAA
11708723 AATTAAAAAAATACAGAAA
1 AATT--AAAAATACAGAAA
11708742 A
1 A
11708743 TTGTAAAAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 22
0.71 0.10 0.20
Matches are distributed among these distances:
12 2 0.03
13 3 0.04
14 6 0.08
15 5 0.06
16 8 0.10
17 15 0.19
18 20 0.25
19 20 0.25
ACGTcount: A:0.68, C:0.07, G:0.07, T:0.18
Consensus pattern (17 bp):
AATTAAAAATACAGAAA
Found at i:11710868 original size:15 final size:16
Alignment explanation
Indices: 11710857--11710886 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11710847 CAAAAAAGTT
11710857 AAAAAG-AAAAAAATA
1 AAAAAGTAAAAAAATA
11710872 AAAAAGTAAAAAAAT
1 AAAAAGTAAAAAAAT
11710887 CATACATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (16 bp):
AAAAAGTAAAAAAATA
Found at i:11733090 original size:25 final size:27
Alignment explanation
Indices: 11733061--11733144 Score: 75
Period size: 28 Copynumber: 3.1 Consensus size: 27
11733051 AAGTCAAGCC
*
11733061 AAACAAGTTT-TC-AATTTAAATAAGA
1 AAACAAGTTTGTCTAATTTAAACAAGA
*
11733086 AAACATGTTTGTCTTAATTTAAACAAGA
1 AAACAAGTTTGTC-TAATTTAAACAAGA
* * *
11733114 AAATATGTTTTTCTTAATTTAAGACAA-A
1 AAACAAGTTTGTC-TAATTTAA-ACAAGA
11733142 AAA
1 AAA
11733145 TGATAAGAGA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
25 9 0.18
26 2 0.04
28 36 0.71
29 4 0.08
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (27 bp):
AAACAAGTTTGTCTAATTTAAACAAGA
Found at i:11733145 original size:28 final size:28
Alignment explanation
Indices: 11733073--11733145 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
11733063 ACAAGTTTTC
* *
11733073 AATTTAAATAAGAAAACATGTTTGTCTT
1 AATTTAAACAAGAAAATATGTTTGTCTT
*
11733101 AATTTAAACAAGAAAATATGTTTTTCTT
1 AATTTAAACAAGAAAATATGTTTGTCTT
11733129 AATTTAAGACAA-AAAAT
1 AATTTAA-ACAAGAAAAT
11733146 GATAAGAGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 37 0.90
29 4 0.10
ACGTcount: A:0.48, C:0.07, G:0.08, T:0.37
Consensus pattern (28 bp):
AATTTAAACAAGAAAATATGTTTGTCTT
Found at i:11746972 original size:7 final size:7
Alignment explanation
Indices: 11746960--11747034 Score: 60
Period size: 7 Copynumber: 10.3 Consensus size: 7
11746950 TGTTATAATT
11746960 AAAATAA
1 AAAATAA
*
11746967 AAAATATT
1 AAAATA-A
11746975 AAAATAA
1 AAAATAA
* *
11746982 AATATAT
1 AAAATAA
*
11746989 AATATAA
1 AAAATAA
*
11746996 AAATTAA
1 AAAATAA
*
11747003 AAATTAAA
1 AAAAT-AA
11747011 AAAATAA
1 AAAATAA
*
11747018 AATATAA
1 AAAATAA
11747025 AAAATTAA
1 AAAA-TAA
11747033 AA
1 AA
11747035 TTTATATAAT
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
7 38 0.69
8 17 0.31
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (7 bp):
AAAATAA
Found at i:11746975 original size:15 final size:15
Alignment explanation
Indices: 11746957--11747035 Score: 71
Period size: 15 Copynumber: 5.5 Consensus size: 15
11746947 TAATGTTATA
11746957 ATTAAAATAAAAAAT
1 ATTAAAATAAAAAAT
*
11746972 ATTAAAATAAAATAT
1 ATTAAAATAAAAAAT
*
11746987 A-TAATAT-AAAAAT
1 ATTAAAATAAAAAAT
*
11747000 -TAAAAATTAAAAAA-
1 ATTAAAA-TAAAAAAT
11747014 A-TAAAATATAAAAA-
1 ATTAAAATA-AAAAAT
11747028 ATTAAAAT
1 ATTAAAAT
11747036 TTATATAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
13 10 0.19
14 16 0.31
15 26 0.50
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
ATTAAAATAAAAAAT
Found at i:11747035 original size:36 final size:36
Alignment explanation
Indices: 11746956--11747036 Score: 101
Period size: 36 Copynumber: 2.3 Consensus size: 36
11746946 ATAATGTTAT
** *
11746956 AATTAAAA-TAAAAAATATTAAAATAAAATATATAA
1 AATTAAAATTAAAAAATAAAAAAATAAAATATAAAA
* * *
11746991 TATAAAAATTAAAAATTAAAAAAATAAAATATAAAA
1 AATTAAAATTAAAAAATAAAAAAATAAAATATAAAA
11747027 AATTAAAATT
1 AATTAAAATT
11747037 TATATAATAT
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
35 6 0.16
36 31 0.84
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (36 bp):
AATTAAAATTAAAAAATAAAAAAATAAAATATAAAA
Found at i:11747090 original size:15 final size:14
Alignment explanation
Indices: 11746963--11747086 Score: 63
Period size: 14 Copynumber: 8.6 Consensus size: 14
11746953 TATAATTAAA
*
11746963 ATAAAAAATATTAAA
1 ATAAAAAATA-TAAT
*
11746978 ATAAAATATATAAT
1 ATAAAAAATATAAT
* *
11746992 ATAAAAATTA-AAA
1 ATAAAAAATATAAT
*
11747005 ATTAAAAAAATAAAAT
1 A-T-AAAAAATATAAT
*
11747021 ATAAAAAATTAAAAT
1 ATAAAAAA-TATAAT
* * * *
11747036 TTATATAATATAGGT
1 ATAAAAAATATA-AT
* * *
11747051 AGAATAAAT-TAAA
1 ATAAAAAATATAAT
*
11747064 ATAAAATATATAAT
1 ATAAAAAATATAAT
11747078 ATAAAAAAT
1 ATAAAAAAT
11747087 TATATTAAAG
Statistics
Matches: 79, Mismatches: 24, Indels: 13
0.68 0.21 0.11
Matches are distributed among these distances:
13 9 0.11
14 34 0.43
15 33 0.42
16 3 0.04
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (14 bp):
ATAAAAAATATAAT
Found at i:11747114 original size:34 final size:32
Alignment explanation
Indices: 11747062--11747147 Score: 91
Period size: 33 Copynumber: 2.5 Consensus size: 32
11747052 GAATAAATTA
*
11747062 AAATAAAATATATAATATAAAAAATTATATTAAAG
1 AAATAAAATA-A-AATATAAAAAATTATAAT-AAG
* * *
11747097 AAATGAAAATAAAATATATAAGATTATAATAAT
1 AAAT-AAAATAAAATATAAAAAATTATAATAAG
11747130 AAATAAAAATAAAATATA
1 AAAT-AAAATAAAATATA
11747148 TGACATTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
33 19 0.42
34 15 0.33
35 5 0.11
36 6 0.13
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.29
Consensus pattern (32 bp):
AAATAAAATAAAATATAAAAAATTATAATAAG
Found at i:11748442 original size:20 final size:21
Alignment explanation
Indices: 11748395--11748475 Score: 57
Period size: 20 Copynumber: 4.1 Consensus size: 21
11748385 AAAAATATTT
* *
11748395 TATAATGTTATAATTAAAATA
1 TATAATATTATAAATAAAATA
* *
11748416 AAAAATATT-TAAATAAAATA
1 TATAATATTATAAATAAAATA
*
11748436 TATAATA-TAAAAATCAAAA-A
1 TATAATATTATAAAT-AAAATA
*
11748456 T-TAA-AATA-AAATAAAATA
1 TATAATATTATAAATAAAATA
11748474 TA
1 TA
11748476 AAAAATTAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
17 4 0.08
18 7 0.15
19 6 0.12
20 21 0.44
21 10 0.21
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (21 bp):
TATAATATTATAAATAAAATA
Found at i:11748463 original size:33 final size:32
Alignment explanation
Indices: 11748417--11748479 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 32
11748407 ATTAAAATAA
*
11748417 AAAATATTTAAATAAAATATATAATATAAAAATC
1 AAAATATTAAAATAAAATA-A-AATATAAAAATC
11748451 AAAA-ATTAAAATAAAATAAAATATAAAAA
1 AAAATATTAAAATAAAATAAAATATAAAAA
11748480 ATTAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 10 0.36
32 1 0.04
33 13 0.46
34 4 0.14
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (32 bp):
AAAATATTAAAATAAAATAAAATATAAAAATC
Found at i:11748497 original size:24 final size:25
Alignment explanation
Indices: 11748451--11748540 Score: 81
Period size: 25 Copynumber: 3.3 Consensus size: 25
11748441 TATAAAAATC
11748451 AAAAATTAAAATAAAATAAAATATA
1 AAAAATTAAAATAAAATAAAATATA
* * *
11748476 AAAAATTAAAATTTATATAATATAGGTAA
1 AAAAATTAAAA-TAAAATAAAATA--T-A
*
11748505 AATAAATTAAAATACAATATATAATATA
1 AA-AAATTAAAATA-AA-ATAAAATATA
11748533 AAAAATTA
1 AAAAATTA
11748541 TATTAAAGAA
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
25 11 0.22
26 9 0.18
27 6 0.12
28 4 0.08
29 5 0.10
30 10 0.20
31 6 0.12
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (25 bp):
AAAAATTAAAATAAAATAAAATATA
Found at i:11748566 original size:34 final size:33
Alignment explanation
Indices: 11748527--11748599 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
11748517 TACAATATAT
* *
11748527 AATATAAAAAATTATATTAAAGAAATGAAAATAA
1 AATATAAAAAATTATAAT-AAGAAATAAAAATAA
* * *
11748561 AATATATAAGATTATAATAATAAATAAAAATAA
1 AATATAAAAAATTATAATAAGAAATAAAAATAA
11748594 AATATA
1 AATATA
11748600 TGACATTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 19 0.56
34 15 0.44
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (33 bp):
AATATAAAAAATTATAATAAGAAATAAAAATAA
Found at i:11748853 original size:15 final size:15
Alignment explanation
Indices: 11748812--11748860 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
11748802 TAATGTTATT
*
11748812 TTACTTGCAATGACA
1 TTACTTGCAATCACA
11748827 TTGA-TTGCAATCACA
1 TT-ACTTGCAATCACA
*
11748842 TTACTTGTAATCACA
1 TTACTTGCAATCACA
11748857 TTAC
1 TTAC
11748861 ATTGTAAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 1 0.03
15 28 0.93
16 1 0.03
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (15 bp):
TTACTTGCAATCACA
Found at i:11758472 original size:17 final size:18
Alignment explanation
Indices: 11758427--11758472 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
11758417 AAAAAATGCC
11758427 TTCATTTTTTTCTCCTTT
1 TTCATTTTTTTCTCCTTT
*
11758445 TTCCATTTTTTGC-CC-TT
1 TT-CATTTTTTTCTCCTTT
11758462 TTCATTTTTTT
1 TTCATTTTTTT
11758473 TTGTTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 8 0.32
17 4 0.16
18 4 0.16
19 9 0.36
ACGTcount: A:0.07, C:0.22, G:0.02, T:0.70
Consensus pattern (18 bp):
TTCATTTTTTTCTCCTTT
Found at i:11765329 original size:17 final size:18
Alignment explanation
Indices: 11765297--11765330 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11765287 AACTAAAACT
*
11765297 ACTTCGCACAGAATAACC
1 ACTTCACACAGAATAACC
11765315 ACTTCACAC-GAATAAC
1 ACTTCACACAGAATAAC
11765331 AGTGAAAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.41, C:0.32, G:0.09, T:0.18
Consensus pattern (18 bp):
ACTTCACACAGAATAACC
Found at i:11765530 original size:29 final size:29
Alignment explanation
Indices: 11765487--11765542 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
11765477 TTTTTCCTTG
* *
11765487 TTCTCTTGTACCTGTTCACGTACAGCTTC
1 TTCTATTGTACCTGTTCACATACAGCTTC
* *
11765516 TTCTATTGTATCTGTTTACATACAGCT
1 TTCTATTGTACCTGTTCACATACAGCT
11765543 CATCTTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.18, C:0.25, G:0.12, T:0.45
Consensus pattern (29 bp):
TTCTATTGTACCTGTTCACATACAGCTTC
Found at i:11769957 original size:174 final size:174
Alignment explanation
Indices: 11769652--11769992 Score: 515
Period size: 174 Copynumber: 2.0 Consensus size: 174
11769642 GGTCTTCAAA
* * *
11769652 GAACTAGCCCAGTACTGGCTAATGAATCAAAAGAAGACCTTCCTGATCTGCTTCTACCATTTTCT
1 GAACTAACCCAGTACTGGCTAATGAATCAAAAGAAGACCTTCCTGATCTGCTTCTACCATTGTCC
* **
11769717 TTTTATGCGTTTGATGAATTGCTAAGTGGAGTGAACATTTTCTTGTTTTTCGTTTCAGATTATTT
66 TTTTATGCGTTGGATGAATTGCTAAGTGGAGTGAACATTTTCCAGTTTTTCGTTTCAGATTATTT
*
11769782 GATTTCTTGGATAC-ATATTTCCAAAATTTAAAACTTGTAGTCCC
131 GATTTCTAGGATACGA-ATTTCCAAAATTTAAAACTTGTAGTCCC
* * *
11769826 GAACTAACCCATTATTGGCTAATGAATCAAAAGAAGACCTTCTTGATCTGCTTCTACCATTGTCC
1 GAACTAACCCAGTACTGGCTAATGAATCAAAAGAAGACCTTCCTGATCTGCTTCTACCATTGTCC
* * **
11769891 TTTTATGTGTTGGATGGATTGCTAAGTGGAGTGAATGTTTTCCAGATTTTT-GTTTCAGATTATT
66 TTTTATGCGTTGGATGAATTGCTAAGTGGAGTGAACATTTTCCAG-TTTTTCGTTTCAGATTATT
*
11769955 TGATTTCTAGGGTACGAATTTCCAAAATTTAAAACTTG
130 TGATTTCTAGGATACGAATTTCCAAAATTTAAAACTTG
11769993 CTGTCCTGGA
Statistics
Matches: 150, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
174 144 0.96
175 6 0.04
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.39
Consensus pattern (174 bp):
GAACTAACCCAGTACTGGCTAATGAATCAAAAGAAGACCTTCCTGATCTGCTTCTACCATTGTCC
TTTTATGCGTTGGATGAATTGCTAAGTGGAGTGAACATTTTCCAGTTTTTCGTTTCAGATTATTT
GATTTCTAGGATACGAATTTCCAAAATTTAAAACTTGTAGTCCC
Found at i:11792121 original size:3 final size:3
Alignment explanation
Indices: 11792113--11792143 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
11792103 TGAAGGGGAT
*
11792113 AAG AAG AAG AAG AAG AAG AAA AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
11792144 GCATTGAGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:11801527 original size:21 final size:22
Alignment explanation
Indices: 11801495--11801535 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
11801485 TTATGTATAG
11801495 TTAAATTTAGA-TATAGATTAGA
1 TTAAATTTAGATTA-AGATTAGA
11801517 TTAAA-TTAGATTAAGATTA
1 TTAAATTTAGATTAAGATTA
11801536 AAATTTAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.41
Consensus pattern (22 bp):
TTAAATTTAGATTAAGATTAGA
Found at i:11801535 original size:16 final size:15
Alignment explanation
Indices: 11801508--11801537 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
11801498 AATTTAGATA
11801508 TAGATTAGATTAAAT
1 TAGATTAGATTAAAT
11801523 TAGATTAAGATTAAA
1 TAGATT-AGATTAAA
11801538 ATTTAATCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (15 bp):
TAGATTAGATTAAAT
Found at i:11801925 original size:93 final size:93
Alignment explanation
Indices: 11801756--11801934 Score: 204
Period size: 93 Copynumber: 1.9 Consensus size: 93
11801746 TAAGTTTTGG
* * *
11801756 TATTATTTTGTTTTCATTATCTTCAAGCTTCAAAAGGATTTCAATGATTGATCTATGATTTTTGA
1 TATTATTTTGTTTTCATTATCTTCAAGCTTCAAAAGAATTTCAATGATTGATCTATAATTTTAGA
* * *
11801821 TTTTAGCAAATCTGGTGAGTGTTGTTAT
66 TTGTAGCAAATCGGGTAAGTGTTGTTAT
* * *
11801849 TATTATTTTGTTTTCATTATC-TCTAAGC-TCTAAAAGAATTTCAAT-ATTTGGTTTTTAATTTC
1 TATTATTTTGTTTTCATTATCTTC-AAGCTTC-AAAAGAATTTCAATGA-TTGATCTATAATTT-
*
11801911 TAG-TTGTAGTAAATCGGGTAAGTG
62 TAGATTGTAGCAAATCGGGTAAGTG
11801935 ACTTGATATC
Statistics
Matches: 72, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
92 5 0.07
93 65 0.90
94 2 0.03
ACGTcount: A:0.27, C:0.09, G:0.16, T:0.48
Consensus pattern (93 bp):
TATTATTTTGTTTTCATTATCTTCAAGCTTCAAAAGAATTTCAATGATTGATCTATAATTTTAGA
TTGTAGCAAATCGGGTAAGTGTTGTTAT
Found at i:11806812 original size:25 final size:25
Alignment explanation
Indices: 11806783--11806838 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
11806773 GATCAGAAAA
*
11806783 AAATTTAATACTATTACTACAATAC
1 AAATTTAAGACTATTACTACAATAC
* * *
11806808 AAATTTGAGATTATTACTACTATAC
1 AAATTTAAGACTATTACTACAATAC
11806833 AAATTT
1 AAATTT
11806839 GAGATTTGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (25 bp):
AAATTTAAGACTATTACTACAATAC
Found at i:11806839 original size:25 final size:25
Alignment explanation
Indices: 11806794--11806844 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
11806784 AATTTAATAC
11806794 TATTACTACAATACAAATTTGAGAT
1 TATTACTACAATACAAATTTGAGAT
*
11806819 TATTACTACTATACAAATTTGAGAT
1 TATTACTACAATACAAATTTGAGAT
11806844 T
1 T
11806845 TGTTCAGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (25 bp):
TATTACTACAATACAAATTTGAGAT
Found at i:11814331 original size:33 final size:31
Alignment explanation
Indices: 11814294--11814469 Score: 109
Period size: 33 Copynumber: 5.7 Consensus size: 31
11814284 AAATAAAAAT
11814294 ATTAAAATAAAATATATAATATAA-AAATTAGAA
1 ATTAAAATAAAATA-A-AATATAAGAAATTA-AA
11814327 ATTAAAATAAAATAAAATATAAGAAATTAAA
1 ATTAAAATAAAATAAAATATAAGAAATTAAA
* * * * *
11814358 ATT-ATATAATAT-AAGTAAAAGATATTAAA
1 ATTAAAATAAAATAAAATATAAGAAATTAAA
* * *
11814387 A-TAAAAT---ATATAATATAAAAAATT-AT
1 ATTAAAATAAAATAAAATATAAGAAATTAAA
*
11814413 ATTAAAAAATAAAAATAAAATATATA-AAATTATA
1 ATT--AAAAT-AAAATAAAATATA-AGAAATTAAA
* *
11814447 ATAAGAAATGAAACTAAAATATA
1 ATTA-AAAT-AAAATAAAATATA
11814470 TAGCATTAAA
Statistics
Matches: 112, Mismatches: 18, Indels: 26
0.72 0.12 0.17
Matches are distributed among these distances:
26 4 0.04
27 10 0.09
28 1 0.01
29 23 0.21
30 7 0.06
31 12 0.11
32 8 0.07
33 44 0.39
34 3 0.03
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (31 bp):
ATTAAAATAAAATAAAATATAAGAAATTAAA
Found at i:11814470 original size:33 final size:33
Alignment explanation
Indices: 11814384--11814471 Score: 113
Period size: 33 Copynumber: 2.6 Consensus size: 33
11814374 AAAAGATATT
* * *
11814384 AAAATAAAATATATAATATAAAAAATTATATTAA
1 AAAATAAAA-ATAAAATATATAAAATTATAATAA
11814418 AAAATAAAAATAAAATATATAAAATTATAATAA
1 AAAATAAAAATAAAATATATAAAATTATAATAA
* * *
11814451 GAAATGAAACTAAAATATATA
1 AAAATAAAAATAAAATATATA
11814472 GCATTAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 39 0.81
34 9 0.19
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.28
Consensus pattern (33 bp):
AAAATAAAAATAAAATATATAAAATTATAATAA
Found at i:11824466 original size:2 final size:2
Alignment explanation
Indices: 11824459--11824486 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11824449 GATTTTCTTC
11824459 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
11824487 TTTAAAAATT
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:11833539 original size:31 final size:31
Alignment explanation
Indices: 11833501--11833563 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
11833491 CGATTGCCTA
11833501 TGTTTAATCACCATATATCTAAGGATAAGGT
1 TGTTTAATCACCATATATCTAAGGATAAGGT
11833532 TGTTTAATCACCATATATCTAAGGATAAGGT
1 TGTTTAATCACCATATATCTAAGGATAAGGT
11833563 T
1 T
11833564 CCTTTTCGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (31 bp):
TGTTTAATCACCATATATCTAAGGATAAGGT
Found at i:11834125 original size:15 final size:15
Alignment explanation
Indices: 11834092--11834132 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
11834082 AGCCAATTTT
11834092 CTCC-AAATA-TTCC
1 CTCCAAAATATTTCC
*
11834105 CCCCAAAATATTTCC
1 CTCCAAAATATTTCC
*
11834120 CTCCAAAACATTT
1 CTCCAAAATATTT
11834133 AGGAGGGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 3 0.13
14 5 0.22
15 15 0.65
ACGTcount: A:0.34, C:0.37, G:0.00, T:0.29
Consensus pattern (15 bp):
CTCCAAAATATTTCC
Found at i:11834401 original size:14 final size:15
Alignment explanation
Indices: 11834354--11834414 Score: 65
Period size: 14 Copynumber: 4.1 Consensus size: 15
11834344 GGGCCCCGAG
*
11834354 CCTGAGTGCTGCTCA
1 CCTGCGTGCTGCTCA
*
11834369 CCCATGC-TG-TGCCCA
1 -CC-TGCGTGCTGCTCA
11834384 CCTGCGTGCTG-TCA
1 CCTGCGTGCTGCTCA
11834398 CCTGCGTGCTGCTCA
1 CCTGCGTGCTGCTCA
11834413 CC
1 CC
11834415 CATGCTGTGC
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
13 3 0.08
14 17 0.45
15 12 0.32
16 4 0.11
17 2 0.05
ACGTcount: A:0.10, C:0.41, G:0.25, T:0.25
Consensus pattern (15 bp):
CCTGCGTGCTGCTCA
Found at i:11834495 original size:71 final size:69
Alignment explanation
Indices: 11834413--11834809 Score: 264
Period size: 71 Copynumber: 5.6 Consensus size: 69
11834403 GTGCTGCTCA
* * * *
11834413 CCCATGCTGTGCACCCATGCGTGCCGCGCACCCTTGCTGGGCCGACCGGCCCTGAGCCTGCGTAC
1 CCCATGTTGTGCGCCC-TGCGTGCCGCGCACCCCTGCTGGGCCGACCGGCCCCGAGCCTGCGT-C
*
11834478 CATGCG
64 CGTGCG
* ** * *
11834484 CCCATGTTGTGCGCCCTCGCGTGCCGCGCACCCCTGCTGGGTCG-GGGGCCCCGGGCCTACGT-C
1 CCCATGTTGTGCGCCCT-GCGTGCCGCGCACCCCTGCTGGGCCGACCGGCCCCGAGCCTGCGTCC
11834547 GTGCTAG
65 GTGC--G
* ** * * * * *
11834554 CCCATGCCATGTG-GGTCTGCGTGCCGCGCACCCTTGCTGGGCCGACGGGCCCTGTGCCTGAGTA
1 CCCATG--TTGTGCGCCCTGCGTGCCGCGCACCCCTGCTGGGCCGACCGGCCCCGAGCCTGCGT-
*
11834618 CCGTGTG
63 CCGTGCG
* * * *
11834625 TCCATGTTGTGTGCCCTTGCGTGCCGCGAACCCCTGCTGGGCCGA-CGACCCCGAGCCTGCGTCC
1 CCCATGTTGTGCGCCC-TGCGTGCCGCGCACCCCTGCTGGGCCGACCGGCCCCGAGCCTGCGTCC
*
11834689 TGCGCG
65 -GTGCG
*** ** ** * *** * *
11834695 CCCATGCCATGCGGGTCTGCGTGCCGTACACCCCTGCTGGGCTGGTTGGCCCCGGGCCTGAGTAC
1 CCCATGTTGTGC-GCCCTGCGTGCCGCGCACCCCTGCTGGGCCGACCGGCCCCGAGCCTGCGT-C
*
11834760 CGTGTG
64 CGTGCG
* * *
11834766 TCCATGCTATGTGC-CCCTGTGTGCCGCGCACCTCTGCTGGGCCG
1 CCCATG-T-TGTGCGCCCTGCGTGCCGCGCACCCCTGCTGGGCCG
11834810 GCGGCCTCGG
Statistics
Matches: 247, Mismatches: 63, Indels: 32
0.72 0.18 0.09
Matches are distributed among these distances:
68 4 0.02
69 6 0.02
70 92 0.37
71 132 0.53
72 6 0.02
73 7 0.03
ACGTcount: A:0.08, C:0.39, G:0.33, T:0.20
Consensus pattern (69 bp):
CCCATGTTGTGCGCCCTGCGTGCCGCGCACCCCTGCTGGGCCGACCGGCCCCGAGCCTGCGTCCG
TGCG
Found at i:11834677 original size:141 final size:141
Alignment explanation
Indices: 11834430--11834809 Score: 463
Period size: 141 Copynumber: 2.7 Consensus size: 141
11834420 TGTGCACCCA
* * * *
11834430 TGCGTGCCGCGCACCCTTGCTGGGCCGACCGGCCCTGAGCCTGCGTACCATGCGCCCATGTTGTG
1 TGCGTGCCGCGCACCCTTGCTGGGCCGACCGGCCCTGAGCCTGAGTACCGTGTGTCCATGTTGTG
* * * ** * * * *
11834495 CGCCCTCGCGTGCCGCGCACCCCTGCTGGGTCGGGGGCCCCGGGCCTACGTCGTGCTAGCCCATG
66 TGCCCTTGCGTGCCGCGCACCCCTGCTGGGCCGACGACCCCGAGCCTACGTCCTGCGAGCCCATG
*
11834560 CCATGTGGGTC
131 CCATGCGGGTC
* *
11834571 TGCGTGCCGCGCACCCTTGCTGGGCCGACGGGCCCTGTGCCTGAGTACCGTGTGTCCATGTTGTG
1 TGCGTGCCGCGCACCCTTGCTGGGCCGACCGGCCCTGAGCCTGAGTACCGTGTGTCCATGTTGTG
* * *
11834636 TGCCCTTGCGTGCCGCGAACCCCTGCTGGGCCGACGACCCCGAGCCTGCGTCCTGCGCGCCCATG
66 TGCCCTTGCGTGCCGCGCACCCCTGCTGGGCCGACGACCCCGAGCCTACGTCCTGCGAGCCCATG
11834701 CCATGCGGGTC
131 CCATGCGGGTC
** * * *** * * * *
11834712 TGCGTGCCGTACACCCCTGCTGGGCTGGTTGGCCCCGGGCCTGAGTACCGTGTGTCCATGCTATG
1 TGCGTGCCGCGCACCCTTGCTGGGCCGACCGGCCCTGAGCCTGAGTACCGTGTGTCCATGTTGTG
* * *
11834777 TGCCCCTGTGTGCCGCGCACCTCTGCTGGGCCG
66 TGCCCTTGCGTGCCGCGCACCCCTGCTGGGCCG
11834810 GCGGCCTCGG
Statistics
Matches: 205, Mismatches: 34, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
141 205 1.00
ACGTcount: A:0.08, C:0.38, G:0.34, T:0.20
Consensus pattern (141 bp):
TGCGTGCCGCGCACCCTTGCTGGGCCGACCGGCCCTGAGCCTGAGTACCGTGTGTCCATGTTGTG
TGCCCTTGCGTGCCGCGCACCCCTGCTGGGCCGACGACCCCGAGCCTACGTCCTGCGAGCCCATG
CCATGCGGGTC
Found at i:11842591 original size:28 final size:30
Alignment explanation
Indices: 11842537--11842592 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 30
11842527 ATCATTATTC
* * *
11842537 TTTTATTATATTTAATTTAAATTTTTATAT
1 TTTTATTATATTTAAGTCAAATATTTATAT
11842567 TTTTATT-T-TTTAAGTCAAATATTTAT
1 TTTTATTATATTTAAGTCAAATATTTAT
11842593 TATGATTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 15 0.65
29 1 0.04
30 7 0.30
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (30 bp):
TTTTATTATATTTAAGTCAAATATTTATAT
Found at i:11844521 original size:2 final size:2
Alignment explanation
Indices: 11844514--11844541 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11844504 GGATATTGGA
11844514 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
11844542 TGTCCTAGTT
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:11845458 original size:20 final size:20
Alignment explanation
Indices: 11845435--11845484 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
11845425 ATTTAAATGC
11845435 ATGTAAAAAAAATGCCTTTT
1 ATGTAAAAAAAATGCCTTTT
* *
11845455 ATGT-AAACAAATGCTTTTT
1 ATGTAAAAAAAATGCCTTTT
11845474 ATGTTAAAAAA
1 ATG-TAAAAAA
11845485 TAGGAAGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 16 0.64
20 5 0.20
21 4 0.16
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (20 bp):
ATGTAAAAAAAATGCCTTTT
Found at i:11846046 original size:34 final size:32
Alignment explanation
Indices: 11845974--11846060 Score: 86
Period size: 33 Copynumber: 2.6 Consensus size: 32
11845964 TTTAAATGTC
*
11845974 ATATATTTTATTTTGATTTACTATTATAATCTT
1 ATATATTTTATTTT-ATTTACTAATATAATCTT
*
11846007 ATATATTTTATTTTCATTT-CTGTAATATAATTTT
1 ATATATTTTATTTT-ATTTAC--TAATATAATCTT
*
11846041 TTATATTATATATTTTATTT
1 ATATATT-T-TATTTTATTT
11846061 TATTTTATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
32 1 0.02
33 18 0.39
34 16 0.35
35 5 0.11
36 6 0.13
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (32 bp):
ATATATTTTATTTTATTTACTAATATAATCTT
Found at i:11846113 original size:48 final size:49
Alignment explanation
Indices: 11846010--11846163 Score: 177
Period size: 48 Copynumber: 3.0 Consensus size: 49
11846000 TAATCTTATA
* * * * *
11846010 TATTTTATTTTCATTTCTGTAATATAATTTTTTATATTATATATTTTATTT
1 TATTTTATTTT-ATTTATATTATATAATATTTTAT-TTTTATATTTTATTT
11846061 TATTTTATTTTATTTATATTATATAA-ATTTTATTTTTATATTTTATTT
1 TATTTTATTTTATTTATATTATATAATATTTTATTTTTATATTTTATTT
*
11846109 TATTTTAATTT-TTTATTATTATATTATATATTTTATTTTAATATATTTTATTT
1 TATTTTATTTTATTTA-TATTATA-TA-ATATTTTATTTT--TATATTTTATTT
11846162 TA
1 TA
11846164 ATTATAAAAT
Statistics
Matches: 91, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
47 4 0.04
48 31 0.34
49 8 0.09
50 13 0.14
51 21 0.23
53 14 0.15
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.69
Consensus pattern (49 bp):
TATTTTATTTTATTTATATTATATAATATTTTATTTTTATATTTTATTT
Found at i:11846131 original size:53 final size:51
Alignment explanation
Indices: 11846038--11846163 Score: 166
Period size: 53 Copynumber: 2.4 Consensus size: 51
11846028 GTAATATAAT
11846038 TTTTTATATTATATATTTTATTTTATTTTATTTTATTTATATTATATAAATTTTA
1 TTTTTATATT-T-TATTTTATTTTATTTTATTTTATTTATATTATAT--ATTTTA
11846093 TTTTTATATTTTATTTTATTTTAATTTT-TTATTA-TTATATTATATATTTTA
1 TTTTTATATTTTATTTTATTTT-ATTTTATT-TTATTTATATTATATATTTTA
11846144 TTTTAATATATTTTATTTTA
1 TTTT--TATATTTTATTTTA
11846164 ATTATAAAAT
Statistics
Matches: 67, Mismatches: 0, Indels: 10
0.87 0.00 0.13
Matches are distributed among these distances:
51 10 0.15
53 38 0.57
54 9 0.13
55 10 0.15
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (51 bp):
TTTTTATATTTTATTTTATTTTATTTTATTTTATTTATATTATATATTTTA
Found at i:11846139 original size:38 final size:42
Alignment explanation
Indices: 11846041--11846148 Score: 112
Period size: 43 Copynumber: 2.5 Consensus size: 42
11846031 ATATAATTTT
*
11846041 TTATATTATATATTTTATTTTA-TTTTATTTTATTTATATTA
1 TTATATTATATATTTTATTTTATTTTTATATTATTTATATTA
* * * * *
11846082 TATAAATTTTATTTTTATATTTTA-TTTTATTTTAATTTTTTATTA
1 T-TATATTATATATTT-TATTTTATTTTTATATT-A-TTTATATTA
11846127 TTATATTATATATTTTATTTTA
1 TTATATTATATATTTTATTTTA
11846149 ATATATTTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
41 1 0.02
42 11 0.20
43 23 0.41
44 12 0.21
45 9 0.16
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (42 bp):
TTATATTATATATTTTATTTTATTTTTATATTATTTATATTA
Found at i:11846145 original size:5 final size:5
Alignment explanation
Indices: 11846051--11846163 Score: 90
Period size: 5 Copynumber: 22.4 Consensus size: 5
11846041 TTATATTATA
* * * *
11846051 TATTT TATTT TATTT TATTT TA-TT TATAT TATATA AATTT TA-TT T-TTA
1 TATTT TATTT TATTT TATTT TATTT TATTT TAT-TT TATTT TATTT TATTT
*
11846099 TATTT TATTT TATTT TAATTT T-TTAT TATTA TATTAT ATATTT TATTT
1 TATTT TATTT TATTT T-ATTT TATT-T TATTT TATT-T -TATTT TATTT
* *
11846147 TAATA TATTT TATTT TA
1 TATTT TATTT TATTT TA
11846164 ATTATAAAAT
Statistics
Matches: 85, Mismatches: 14, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
4 11 0.13
5 60 0.71
6 10 0.12
7 4 0.05
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (5 bp):
TATTT
Found at i:11846164 original size:48 final size:50
Alignment explanation
Indices: 11846011--11846166 Score: 160
Period size: 53 Copynumber: 3.1 Consensus size: 50
11846001 AATCTTATAT
* * * *
11846011 ATTTTATTTTCATTTCTGTAATATAATTTT-TTATATTATATATTTTATTTT-
1 ATTTTATTTT-ATTTATATTATATAATTTTATT-T-TAATATATTTTATTTTA
*
11846062 ATTTTATTTTATTTATATTATATAAATTTTATTTTTATATTTTATTTTATTTTA
1 ATTTTATTTTATTTATATTATAT-AATTTTA-TTTTA-A-TATATTTTATTTTA
11846116 ATTTT-TTATTA-TTATATTATAT-ATTTTATTTTAATATATTTTATTTTA
1 ATTTTATT-TTATTTATATTATATAATTTTATTTTAATATATTTTATTTTA
11846164 ATT
1 ATT
11846167 ATAAAATTAT
Statistics
Matches: 92, Mismatches: 6, Indels: 17
0.80 0.05 0.15
Matches are distributed among these distances:
48 16 0.17
49 1 0.01
50 15 0.16
51 23 0.25
52 2 0.02
53 27 0.29
54 8 0.09
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.69
Consensus pattern (50 bp):
ATTTTATTTTATTTATATTATATAATTTTATTTTAATATATTTTATTTTA
Found at i:11846306 original size:27 final size:26
Alignment explanation
Indices: 11846276--11846326 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
11846266 TGAACTGTAA
11846276 TTATATTA-ATATAATTACATTATAATT
1 TTATATTATA-ATAATT-CATTATAATT
*
11846303 TTATATTATAATAATTTATTATAA
1 TTATATTATAATAATTCATTATAA
11846327 AATAAGTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 7 0.32
27 14 0.64
28 1 0.05
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (26 bp):
TTATATTATAATAATTCATTATAATT
Found at i:11846593 original size:21 final size:21
Alignment explanation
Indices: 11846564--11846604 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
11846554 TTGCCTTCCA
*
11846564 TTTTAATTTTAATTTTAATGT
1 TTTTAATTTTAAATTTAATGT
*
11846585 TTTTTATTTTAAATTTAATG
1 TTTTAATTTTAAATTTAATG
11846605 CAACTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (21 bp):
TTTTAATTTTAAATTTAATGT
Found at i:11860508 original size:17 final size:17
Alignment explanation
Indices: 11860486--11860518 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
11860476 AATATTATTT
11860486 TTTTTC-TTTCTATTTTG
1 TTTTTCATTTC-ATTTTG
11860503 TTTTTCATTTCATTTT
1 TTTTTCATTTCATTTT
11860519 CTATTGTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.09, C:0.12, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTTTCATTTCATTTTG
Found at i:11862915 original size:22 final size:22
Alignment explanation
Indices: 11862864--11862915 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
11862854 TTTTTCACAC
* *
11862864 TATCTTTTTTTATTTGATTCAA
1 TATCTTTTTTGATTTGATTAAA
11862886 T-TCGTTTTCTTGATTT-ATTAAA
1 TATC-TTTT-TTGATTTGATTAAA
11862908 TATCTTTT
1 TATCTTTT
11862916 ATAGTAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 2 0.08
22 15 0.60
23 8 0.32
ACGTcount: A:0.21, C:0.10, G:0.06, T:0.63
Consensus pattern (22 bp):
TATCTTTTTTGATTTGATTAAA
Found at i:11865473 original size:19 final size:19
Alignment explanation
Indices: 11865451--11865488 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
11865441 GTCTTTCATT
* *
11865451 TTCTTTTTCCTTCTGTTTG
1 TTCTTCTTCCTTCTATTTG
11865470 TTCTTCTTCCTTCTATTTG
1 TTCTTCTTCCTTCTATTTG
11865489 CCTTTTTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.03, C:0.24, G:0.08, T:0.66
Consensus pattern (19 bp):
TTCTTCTTCCTTCTATTTG
Found at i:11874570 original size:32 final size:35
Alignment explanation
Indices: 11874525--11874612 Score: 101
Period size: 32 Copynumber: 2.6 Consensus size: 35
11874515 AAATTACATT
*
11874525 TTTAAGGATCAAGCATAACCTTT-ACA-AA-GCAC
1 TTTATGGATCAAGCATAACCTTTAACATAATGCAC
* **
11874557 TTTATGGATCAAGCACAACCTTTCAACATAATGCTT
1 TTTATGGATCAAGCATAACCTTT-AACATAATGCAC
*
11874593 TTTATGAATCAAGCATAACC
1 TTTATGGATCAAGCATAACC
11874613 ACTATACCCT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
32 21 0.46
34 3 0.07
35 2 0.04
36 20 0.43
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.30
Consensus pattern (35 bp):
TTTATGGATCAAGCATAACCTTTAACATAATGCAC
Found at i:11876643 original size:17 final size:17
Alignment explanation
Indices: 11876609--11876644 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
11876599 CAAAAGAGAG
11876609 ATAAACAAAAATTAGAA
1 ATAAACAAAAATTAGAA
11876626 ATAAAGCAAAAATT-GAA
1 ATAAA-CAAAAATTAGAA
11876643 AT
1 AT
11876645 TTCGAGAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.19
Consensus pattern (17 bp):
ATAAACAAAAATTAGAA
Found at i:11880030 original size:28 final size:29
Alignment explanation
Indices: 11879951--11880032 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 29
11879941 AAGATTAATG
11879951 TTTTAAA-AAAATTCAAACTTTTATTCTTT
1 TTTTAAATAAAA-TCAAACTTTTATTCTTT
* * * *
11879980 TATTACATATAATCAAATTTTTTATT-TTT
1 TTTTAAATAAAATCAAA-CTTTTATTCTTT
11880009 ATTTTAAATAAAAT-AAACTTTTAT
1 -TTTTAAATAAAATCAAACTTTTAT
11880033 AATTAATAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
28 6 0.14
29 16 0.38
30 20 0.48
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52
Consensus pattern (29 bp):
TTTTAAATAAAATCAAACTTTTATTCTTT
Found at i:11882242 original size:5 final size:5
Alignment explanation
Indices: 11882232--11882295 Score: 58
Period size: 5 Copynumber: 12.4 Consensus size: 5
11882222 ATGCTATAAT
* * * *
11882232 TAAAA TAAAA TACAT TAAAA TAAAA T-ATA TAATA TAAGAA TAAAAA TTAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAA-AA T-AAAA -TAAAA
11882284 TAAAA TAAAA TA
1 TAAAA TAAAA TA
11882296 TAAAAACTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
4 3 0.06
5 35 0.71
6 8 0.16
7 3 0.06
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (5 bp):
TAAAA
Found at i:11882476 original size:28 final size:27
Alignment explanation
Indices: 11882349--11882488 Score: 108
Period size: 29 Copynumber: 5.0 Consensus size: 27
11882339 CAAAATATAT
*
11882349 AATAT-AATATATTAAAAATAAAAATAA
1 AATATAAATATA-TAAAAATAATAATAA
* * *
11882376 AATATATAAGATTATAATAATAATGAAAAA
1 AATATA-AATA-TATAAAAATAAT-AATAA
*
11882406 AATATAAAGTCAT-TAAAAAT-ATATTTAA
1 AATATAAA-T-ATATAAAAATAATA-ATAA
11882434 AATATAATATTATATAAAAATTAATAATAA
1 AATATAA-A-TATATAAAAA-TAATAATAA
*
11882464 AATATAAATATATTAAAATAA-AATA
1 AATATAAATATATAAAAATAATAATA
11882489 TATGACATTA
Statistics
Matches: 91, Mismatches: 11, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
26 4 0.04
27 9 0.10
28 22 0.24
29 28 0.31
30 24 0.26
31 4 0.04
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (27 bp):
AATATAAATATATAAAAATAATAATAA
Found at i:11882479 original size:58 final size:58
Alignment explanation
Indices: 11882349--11882486 Score: 142
Period size: 58 Copynumber: 2.4 Consensus size: 58
11882339 CAAAATATAT
*
11882349 AATAT-AATATATTAAAAATAAAAATAAAATATATAAGATTATAATAATAATGAAAAA
1 AATATAAATATATTAAAAATAAAAATAAAATATATAAGATTATAAAAATAATGAAAAA
* * ** ** *
11882406 AATATAAAGT-CATTAAAAATATATTTAAAATATAATATTA-TATAAAAATTAAT-AATAA
1 AATATAAA-TATATTAAAAATAAAAATAAAATAT-ATAAGATTATAAAAA-TAATGAAAAA
11882464 AATATAAATATATT-AAAATAAAA
1 AATATAAATATATTAAAAATAAAA
11882487 TATATGACAT
Statistics
Matches: 65, Mismatches: 11, Indels: 10
0.76 0.13 0.12
Matches are distributed among these distances:
57 13 0.20
58 43 0.66
59 9 0.14
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (58 bp):
AATATAAATATATTAAAAATAAAAATAAAATATATAAGATTATAAAAATAATGAAAAA
Found at i:11882485 original size:21 final size:20
Alignment explanation
Indices: 11882445--11882490 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 20
11882435 ATATAATATT
11882445 ATATAAAAATTAATAATAAA
1 ATATAAAAATTAATAATAAA
11882465 ATATAAATATATTAA-AATAAA
1 ATATAAA-A-ATTAATAATAAA
11882486 ATATA
1 ATATA
11882491 TGACATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 7 0.29
21 12 0.50
22 5 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATATAAAAATTAATAATAAA
Found at i:11882502 original size:21 final size:21
Alignment explanation
Indices: 11882445--11882503 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 21
11882435 ATATAATATT
* *
11882445 ATATAA-AAATTAATAATAAA
1 ATATAATACATTAAAAATAAA
*
11882465 ATATAAATATATT-AAAATAAA
1 ATAT-AATACATTAAAAATAAA
11882486 ATAT-ATGACATTAAAAAT
1 ATATAAT-ACATTAAAAAT
11882504 TATTTAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 2 0.06
20 8 0.25
21 18 0.56
22 4 0.12
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (21 bp):
ATATAATACATTAAAAATAAA
Found at i:11885363 original size:19 final size:20
Alignment explanation
Indices: 11885335--11885399 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
11885325 TTTATTTTTT
*
11885335 AAATATTAATATTTTATTTA
1 AAATACTAATATTTTATTTA
* **
11885355 TAAT-CTAATCATTACATTATA
1 AAATACTAAT-ATTTTATT-TA
*
11885376 AAATATTAATATTTTATTTA
1 AAATACTAATATTTTATTTA
11885396 AAAT
1 AAAT
11885400 TAATGTTGTT
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
19 4 0.12
20 15 0.44
21 11 0.32
22 4 0.12
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATACTAATATTTTATTTA
Found at i:11885476 original size:27 final size:29
Alignment explanation
Indices: 11885411--11885476 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
11885401 AATGTTGTTA
* * *
11885411 TGATTATTTATTTTTAAATATTAATAATT
1 TGATAATTTATTTTAAAATATTAATAAAT
*
11885440 TTATAATTTA-TTTAAAATATTAA-AAAT
1 TGATAATTTATTTTAAAATATTAATAAAT
*
11885467 TGATACTTTA
1 TGATAATTTA
11885477 AATATTAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
27 11 0.35
28 12 0.39
29 8 0.26
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (29 bp):
TGATAATTTATTTTAAAATATTAATAAAT
Found at i:11885565 original size:72 final size:76
Alignment explanation
Indices: 11885484--11885641 Score: 220
Period size: 76 Copynumber: 2.1 Consensus size: 76
11885474 TTAAATATTA
* *
11885484 ATATTTTATTTATAATTTAATTGTTA-T-T-GTGATTGT-TTATT-TTT-ATTTTATTTTTTAAA
1 ATATTTTATTTATAATTTAATTGTTATTATGGTCATT-TATTATTGTTTAATTTTATCTTTT-AA
11885543 ATATTAATAATTT
64 ATATTAATAATTT
*
11885556 ATATTTTATTTATAATTTAATTGTTATTATGGTCATTTATTTTTGTTTAATTTTATCTTTTAAAT
1 ATATTTTATTTATAATTTAATTGTTATTATGGTCATTTATTATTGTTTAATTTTATCTTTTAAAT
11885621 ATTAATAATTT
66 ATTAATAATTT
*
11885632 ATTTTTTATT
1 ATATTTTATT
11885642 CAAAATATTA
Statistics
Matches: 76, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
72 26 0.34
73 1 0.01
74 2 0.03
75 9 0.12
76 27 0.36
77 11 0.14
ACGTcount: A:0.30, C:0.01, G:0.05, T:0.64
Consensus pattern (76 bp):
ATATTTTATTTATAATTTAATTGTTATTATGGTCATTTATTATTGTTTAATTTTATCTTTTAAAT
ATTAATAATTT
Found at i:11885584 original size:36 final size:37
Alignment explanation
Indices: 11885484--11885584 Score: 93
Period size: 36 Copynumber: 2.8 Consensus size: 37
11885474 TTAAATATTA
* *
11885484 ATATTTTATTTATAATTTAATTGTTATT-GTGATTGT
1 ATATTTTATTTATAATTTAATTGTTATTAATAATTGT
* ** **
11885520 TTATTTTTATTTTATTTTTTAA--AATATTAATAATT-T
1 ATA-TTTTA-TTTATAATTTAATTGTTATTAATAATTGT
11885556 ATATTTTATTTATAATTTAATTGTTATTA
1 ATATTTTATTTATAATTTAATTGTTATTA
11885585 TGGTCATTTA
Statistics
Matches: 48, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
34 10 0.21
35 5 0.10
36 14 0.29
37 9 0.19
38 10 0.21
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (37 bp):
ATATTTTATTTATAATTTAATTGTTATTAATAATTGT
Found at i:11885810 original size:27 final size:27
Alignment explanation
Indices: 11885773--11885824 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
11885763 GTATTTTATT
11885773 TTTAAAATATTAATAATTTATAATTGA
1 TTTAAAATATTAATAATTTATAATTGA
*
11885800 TTTAAAATATTAATAATTTGTAATT
1 TTTAAAATATTAATAATTTATAATT
11885825 TAAATATTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (27 bp):
TTTAAAATATTAATAATTTATAATTGA
Found at i:11885832 original size:22 final size:23
Alignment explanation
Indices: 11885799--11885842 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
11885789 TTTATAATTG
11885799 ATTTAAAATATTAATAATTTGTA
1 ATTTAAAATATTAATAATTTGTA
* *
11885822 ATTT-AAATATTACTATTTTGT
1 ATTTAAAATATTAATAATTTGT
11885843 TTATAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (23 bp):
ATTTAAAATATTAATAATTTGTA
Found at i:11885883 original size:160 final size:160
Alignment explanation
Indices: 11885605--11885908 Score: 396
Period size: 160 Copynumber: 1.9 Consensus size: 160
11885595 TTTTTGTTTA
** * *
11885605 ATTTTATCTTTTAAATATTAATAATTTATTTTTTATTCAAAATATTAATAATTAATCATTTAAAT
1 ATTTTATCTTTTAAATATTAATAATTTATAATTGATTCAAAATATTAATAATTAATAATTTAAAT
* **
11885670 ATTAATATCTTATTTAAAATTTAATCATTAATATTATAAAATACTGTTATTTTAATT-ATAATTT
66 ATTAATATCTTATTTAAAATTTAATCATTAAAATTATAAAATACTAATATTTT-ATTAATAATTT
* *
11885734 TAATGTTACTATGATTATTCGTAGTTATTGT
130 AAATATTACTATGATTATTCGTAGTTATTGT
* **
11885765 ATTTTAT-TTTTAAAATATTAATAATTTATAATTGATTTAAAATATTAATAATTTGTAATTTAAA
1 ATTTTATCTTTT-AAATATTAATAATTTATAATTGATTCAAAATATTAATAATTAATAATTTAAA
* * * * * * *
11885829 TATTACTATTTTGTTTATAATTTAATCATTAAAATTTTAAAGTATTAATATTTTATTAATAATTT
65 TATTAATATCTTATTTAAAATTTAATCATTAAAATTATAAAATACTAATATTTTATTAATAATTT
*
11885894 AAATATTATTATGAT
130 AAATATTACTATGAT
11885909 AAAACTATTA
Statistics
Matches: 122, Mismatches: 20, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
159 7 0.06
160 115 0.94
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (160 bp):
ATTTTATCTTTTAAATATTAATAATTTATAATTGATTCAAAATATTAATAATTAATAATTTAAAT
ATTAATATCTTATTTAAAATTTAATCATTAAAATTATAAAATACTAATATTTTATTAATAATTTA
AATATTACTATGATTATTCGTAGTTATTGT
Found at i:11897423 original size:22 final size:19
Alignment explanation
Indices: 11897396--11897439 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
11897386 TAAAATTAAT
11897396 TAAATACATAAAAAATTTAAAA
1 TAAATA-ATAAAAAA--TAAAA
*
11897418 TAAATATTAAAAAATAAAA
1 TAAATAATAAAAAATAAAA
11897437 TAA
1 TAA
11897440 GAGTCTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 8 0.38
21 7 0.33
22 6 0.29
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (19 bp):
TAAATAATAAAAAATAAAA
Found at i:11911614 original size:15 final size:15
Alignment explanation
Indices: 11911592--11911637 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
11911582 ACATTACAAT
11911592 GCAATGTGATTACAG
1 GCAATGTGATTACAG
* * *
11911607 GTAATGTGATTGCAA
1 GCAATGTGATTACAG
11911622 GCAATGTGATTACAG
1 GCAATGTGATTACAG
11911637 G
1 G
11911638 GAAAATAACA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.28
Consensus pattern (15 bp):
GCAATGTGATTACAG
Found at i:11911845 original size:60 final size:59
Alignment explanation
Indices: 11911772--11912109 Score: 305
Period size: 56 Copynumber: 5.8 Consensus size: 59
11911762 CTAATTATTA
**
11911772 AAATATAAGTTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTCTT
1 AAATATATTTTTAATATATTTATA-TTTTTATTATTAATTTTTATATAATATCATTTCTT
* *
11911832 AAATATATTTTTAATATCA--TATA-TTTTATT-TTTATTTATTATTATAATAT--TTT-AT
1 AAATATATTTTTAATAT-ATTTATATTTTTATTATTAATTT-TTA-TATAATATCATTTCTT
* *
11911887 -ATTTTATTTTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTT
1 AAATATATTTTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTT
* * * *
11911945 AAATATATTTTTAATGTCA--TATA-TTTTATT-TTTATTTATTATTGTAATAT--TTT-AT
1 AAATATATTTTTAATAT-ATTTATATTTTTATTATTAATTT-TTA-TATAATATCATTTCTT
* * *
11912000 -ATTTTATTTTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATT-TT
1 AAATATATTTTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCAT-TTCTT
* *
11912058 AAATATATTTTTAATATTATATTTTATTTATTTATTATTATAATTTTATATA
1 AAATATATTTTTAATA-TAT-TTATA-TT-TTTATTATTA-ATTTTTATATA
11912110 TTTTATTTTT
Statistics
Matches: 225, Mismatches: 26, Indels: 50
0.75 0.09 0.17
Matches are distributed among these distances:
53 2 0.01
54 27 0.12
55 25 0.11
56 37 0.16
57 36 0.16
58 23 0.10
59 30 0.13
60 19 0.08
61 5 0.02
62 2 0.01
63 9 0.04
64 10 0.04
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (59 bp):
AAATATATTTTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTT
Found at i:11911857 original size:29 final size:27
Alignment explanation
Indices: 11911781--11912158 Score: 166
Period size: 30 Copynumber: 13.5 Consensus size: 27
11911771 AAAATATAAG
*
11911781 TTTAATATATTTATATTTTTTATTATTAATT
1 TTTAATATA--TATATTTTTAATTA-T-ATT
*
11911812 TTT-ATATAATATCATTTCTTAAATATATT
1 TTTAATAT-ATAT-ATTT-TTAATTATATT
* *
11911841 TTTAATATCATATA-TTTTATTTTTATT
1 TTTAATAT-ATATATTTTTAATTATATT
* *
11911868 TATTATTATA-ATA-TTTTATATTTTATT
1 T-TTAATATATATATTTTTA-ATTATATT
11911895 TTTAATATATTTATATTTTT-ATTATTAATT
1 TTTAATATA--TATATTTTTAATTA-T-ATT
*
11911925 TTT-ATATAATATCATTTCTTAAATATATT
1 TTTAATAT-ATAT-ATTT-TTAATTATATT
* * *
11911954 TTTAATGTCATATA-TTTTATTTTTATT
1 TTTAATAT-ATATATTTTTAATTATATT
* * *
11911981 TATTATTGTA-ATA-TTTTATATTTTATT
1 T-TTAATATATATATTTTTA-ATTATATT
* *
11912008 TTTAATATATTTATATTTATATTATTAATT
1 TTTAATATATATATTTTTA-ATTA-T-ATT
*
11912038 TTT-ATATAATATCATATTTTAAATATATT
1 TTTAATAT-ATAT-AT-TTTTAATTATATT
11912067 TTTAATAT-TATA-TTTT-ATT-TATT
1 TTTAATATATATATTTTTAATTATATT
*
11912090 TATT-AT-TATA-ATTTTATATATTTTATT
1 T-TTAATATATATATTTT-TA-ATTATATT
11912117 TTTAATATATTTATATTTTT-ATTATTAATT
1 TTTAATATA--TATATTTTTAATTA-T-ATT
11912147 TTT-ATATA-ATAT
1 TTTAATATATATAT
11912159 CATTTCTAGA
Statistics
Matches: 278, Mismatches: 28, Indels: 87
0.71 0.07 0.22
Matches are distributed among these distances:
22 2 0.01
23 12 0.04
24 5 0.02
25 4 0.01
26 38 0.14
27 46 0.17
28 38 0.14
29 46 0.17
30 61 0.22
31 22 0.08
32 4 0.01
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.64
Consensus pattern (27 bp):
TTTAATATATATATTTTTAATTATATT
Found at i:11911861 original size:21 final size:21
Alignment explanation
Indices: 11911837--11911978 Score: 58
Period size: 25 Copynumber: 6.4 Consensus size: 21
11911827 TTCTTAAATA
11911837 TATTTTTAATATCATATATTT
1 TATTTTTAATATCATATATTT
*
11911858 TATTTTTATTTATTATTATAATATTT
1 TATTTTTA---A-TATCAT-ATATTT
* * *
11911884 TATATTTTATTTTTAATATATTT
1 TAT-TTTTA-ATATCATATATTT
*
11911907 ATATTTTTATTAT--TA-ATTT
1 -TATTTTTAATATCATATATTT
* * * *
11911926 T-TATATAATATCATTTCTTAAAT
1 TATTTTTAATATCATATATT---T
*
11911949 ATATTTTTAATGTCATATATTT
1 -TATTTTTAATATCATATATTT
11911971 TATTTTTA
1 TATTTTTA
11911979 TTTATTATTG
Statistics
Matches: 91, Mismatches: 15, Indels: 30
0.67 0.11 0.22
Matches are distributed among these distances:
17 7 0.08
18 1 0.01
19 5 0.05
20 4 0.04
21 16 0.18
22 4 0.04
23 12 0.13
24 9 0.10
25 19 0.21
26 9 0.10
27 5 0.05
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (21 bp):
TATTTTTAATATCATATATTT
Found at i:11911866 original size:6 final size:6
Alignment explanation
Indices: 11911855--11911929 Score: 53
Period size: 6 Copynumber: 12.0 Consensus size: 6
11911845 ATATCATATA
* * * *
11911855 TTTTAT TTTTAT TTATTAT TATAAT ATTTTAT ATTTTAT TTTTA- ATATAT
1 TTTTAT TTTTAT TT-TTAT TTTTAT -TTTTAT -TTTTAT TTTTAT TTTTAT
* *
11911905 TTATAT TTTTAT TATTAAT TTTTAT
1 TTTTAT TTTTAT T-TTTAT TTTTAT
11911930 ATAATATCAT
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
5 3 0.05
6 31 0.56
7 21 0.38
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTAT
Found at i:11911980 original size:113 final size:113
Alignment explanation
Indices: 11911781--11912165 Score: 674
Period size: 113 Copynumber: 3.4 Consensus size: 113
11911771 AAAATATAAG
11911781 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
1 TTTAATATATTTATA-TTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
11911846 TATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
65 TATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
11911895 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
1 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
* *
11911960 GTCATATATTTTATTTTTATTTATTATTGTAATATTTTATATTTTATT
66 ATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
*
11912008 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATT-TTAAATATATTTTTAA
1 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCAT-TTCTTAAATATATTTTTAA
11912072 TAT--TATATTTTA--TTTATTTATTATTATAAT-TTTATATATTTTATT
65 TATCATATATTTTATTTTTATTTATTATTATAATATTT-TATATTTTATT
11912117 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCT
1 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCT
11912166 AGACCTGTCA
Statistics
Matches: 262, Mismatches: 6, Indels: 11
0.94 0.02 0.04
Matches are distributed among these distances:
108 5 0.02
109 73 0.28
111 9 0.03
113 158 0.60
114 17 0.06
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.64
Consensus pattern (113 bp):
TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
ATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
Found at i:11911995 original size:21 final size:20
Alignment explanation
Indices: 11911971--11912153 Score: 92
Period size: 21 Copynumber: 8.5 Consensus size: 20
11911961 TCATATATTT
11911971 TATTTT-TATTTATTATTGTAA
1 TATTTTATATTTATT-TT-TAA
11911992 TATTTTATATTTTATTTTTAA
1 TATTTTATA-TTTATTTTTAA
11912013 TATATTTATATTTATATTATTAA
1 TAT-TTTATATTTAT-TT-TTAA
11912036 T-TTTTATATAATATCATATTTTAA
1 TATTTTATAT--T-T-AT-TTTTAA
* * * *
11912060 -A-TATATTTTTAATATT-A
1 TATTTTATATTTATTTTTAA
11912077 TATTTTATTTATTTATTATTATAA
1 TATTTTA--TATTTATT-TT-TAA
11912101 T-TTTATATATTTTATTTTTAA
1 TATTT-TATA-TTTATTTTTAA
*
11912122 TATATTTATATTTTTATTATTAA
1 TAT-TTTATA--TTTATTTTTAA
11912145 T-TTTTATAT
1 TATTTTATAT
11912154 AATATCATTT
Statistics
Matches: 131, Mismatches: 9, Indels: 46
0.70 0.05 0.25
Matches are distributed among these distances:
17 1 0.01
18 4 0.03
19 5 0.04
20 1 0.01
21 41 0.31
22 24 0.18
23 41 0.31
24 9 0.07
25 5 0.04
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.66
Consensus pattern (20 bp):
TATTTTATATTTATTTTTAA
Found at i:11912106 original size:8 final size:9
Alignment explanation
Indices: 11911963--11912142 Score: 59
Period size: 8 Copynumber: 20.8 Consensus size: 9
11911953 TTTTAATGTC
11911963 ATATATTTT
1 ATATATTTT
* *
11911972 ATTTTTATTT
1 ATATAT-TTT
*
11911982 AT-TATTGT
1 ATATATTTT
11911990 A-ATA-TTT
1 ATATATTTT
11911997 -TATATTTT
1 ATATATTTT
*
11912005 AT-T-TTTA
1 ATATATTTT
11912012 ATATATTTAT
1 ATATATTT-T
* *
11912022 ATTTATATT
1 ATATATTTT
11912031 AT-TAATTTT
1 ATAT-ATTTT
**
11912040 -TATATAAT
1 ATATATTTT
11912048 ATCATATTTT
1 AT-ATATTTT
11912058 AAATATATTTT
1 --ATATATTTT
*
11912069 -TA-ATATT
1 ATATATTTT
*
11912076 ATATTTTATTT
1 ATA-TAT-TTT
*
11912087 ATTTATTATT
1 ATATATT-TT
11912097 ATA-ATTTT
1 ATATATTTT
11912105 ATATATTTT
1 ATATATTTT
*
11912114 AT-T-TTTA
1 ATATATTTT
11912121 ATATA-TTT
1 ATATATTTT
11912129 ATAT-TTTT
1 ATATATTTT
11912137 AT-TATT
1 ATATATT
11912143 AATTTTTATA
Statistics
Matches: 125, Mismatches: 22, Indels: 49
0.64 0.11 0.25
Matches are distributed among these distances:
7 20 0.16
8 39 0.31
9 30 0.24
10 23 0.18
11 11 0.09
12 2 0.02
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.66
Consensus pattern (9 bp):
ATATATTTT
Found at i:11912154 original size:23 final size:24
Alignment explanation
Indices: 11911979--11912154 Score: 102
Period size: 23 Copynumber: 7.9 Consensus size: 24
11911969 TTTATTTTTA
11911979 TTTATTATTGTAATA-TTT-TATA-T
1 TTTATTA-T-TAATATTTTATATATT
* *
11912002 TTTATTTTTAATATATT-TATATT
1 TTTATTATTAATATTTTATATATT
*
11912025 TATATTATTAAT-TTTTATATA--
1 TTTATTATTAATATTTTATATATT
*
11912046 ---A-TA-TCATATTTTAAATATATT
1 TTTATTATTAATATTTT--ATATATT
* *
11912067 TTTAATATT-ATATTTTAT-T-TA
1 TTTATTATTAATATTTTATATATT
11912088 TTTATTATT-ATAATTTTATATA-T
1 TTTATTATTAAT-ATTTTATATATT
* *
11912111 TTTATTTTTAATATATT-TATATT
1 TTTATTATTAATATTTTATATATT
11912134 TTTATTATTAAT-TTTTATATA
1 TTTATTATTAATATTTTATATA
11912155 ATATCATTTC
Statistics
Matches: 121, Mismatches: 13, Indels: 38
0.70 0.08 0.22
Matches are distributed among these distances:
16 3 0.02
17 6 0.05
18 1 0.01
19 5 0.04
21 16 0.13
22 25 0.21
23 52 0.43
24 3 0.02
25 9 0.07
26 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.65
Consensus pattern (24 bp):
TTTATTATTAATATTTTATATATT
Found at i:11915363 original size:48 final size:49
Alignment explanation
Indices: 11915229--11915432 Score: 333
Period size: 49 Copynumber: 4.2 Consensus size: 49
11915219 CCTCCCACAG
11915229 TCCCACGAGTCCCGATTCCCCCCTGCGGCCCTGCCCGCCCCCCTCCGGC
1 TCCCACGAGTCCCGATTCCCCCCTGCGGCCCTGCCCGCCCCCCTCCGGC
* *
11915278 TCCCACGAGTCCCGGTTCCCCCCTGCGGCCCTG-CCG-CCCCCTCAGGC
1 TCCCACGAGTCCCGATTCCCCCCTGCGGCCCTGCCCGCCCCCCTCCGGC
* **
11915325 TCCCACGAGTCCCGGTTCCCCCCTGCATCCCTGCCCGCCCCCCTCCGGC
1 TCCCACGAGTCCCGATTCCCCCCTGCGGCCCTGCCCGCCCCCCTCCGGC
*
11915374 TCCCACGAGT-CCGATTCCCCCCTGCGGCCCTACCCGCCCCCCTCCGGC
1 TCCCACGAGTCCCGATTCCCCCCTGCGGCCCTGCCCGCCCCCCTCCGGC
11915422 TCCCACGAGTC
1 TCCCACGAGTC
11915433 TTTTGGGTGA
Statistics
Matches: 143, Mismatches: 9, Indels: 6
0.91 0.06 0.04
Matches are distributed among these distances:
47 41 0.29
48 50 0.35
49 52 0.36
ACGTcount: A:0.07, C:0.57, G:0.20, T:0.15
Consensus pattern (49 bp):
TCCCACGAGTCCCGATTCCCCCCTGCGGCCCTGCCCGCCCCCCTCCGGC
Found at i:11915367 original size:96 final size:97
Alignment explanation
Indices: 11915201--11915432 Score: 337
Period size: 96 Copynumber: 2.4 Consensus size: 97
11915191 TTGGGGAGTG
* * *
11915201 CCTGCGGCCCTACCC-CCCCCTCCCACAG-TCCCACGAGTCCCGATTCCCCCCTGCGGCCCTGCC
1 CCTGCGGCCCTACCCGCCCCC-CTCA-GGCTCCCACGAGTCCCGATTCCCCCCTGCAGCCCTGCC
*
11915264 CGCCCCCCTCCGGCTCCCACGAGTCCCGGTTCCCC
64 CGCCCCCCTCCGGCTCCCACGAGT-CCGATTCCCC
* * *
11915299 CCTGCGGCCCT-GCCG-CCCCCTCAGGCTCCCACGAGTCCCGGTTCCCCCCTGCATCCCTGCCCG
1 CCTGCGGCCCTACCCGCCCCCCTCAGGCTCCCACGAGTCCCGATTCCCCCCTGCAGCCCTGCCCG
11915362 CCCCCCTCCGGCTCCCACGAGTCCGATTCCCC
66 CCCCCCTCCGGCTCCCACGAGTCCGATTCCCC
*
11915394 CCTGCGGCCCTACCCGCCCCCCTCCGGCTCCCACGAGTC
1 CCTGCGGCCCTACCCGCCCCCCTCAGGCTCCCACGAGTC
11915433 TTTTGGGTGA
Statistics
Matches: 121, Mismatches: 9, Indels: 9
0.87 0.06 0.06
Matches are distributed among these distances:
95 21 0.17
96 62 0.51
97 27 0.22
98 11 0.09
ACGTcount: A:0.08, C:0.58, G:0.19, T:0.15
Consensus pattern (97 bp):
CCTGCGGCCCTACCCGCCCCCCTCAGGCTCCCACGAGTCCCGATTCCCCCCTGCAGCCCTGCCCG
CCCCCCTCCGGCTCCCACGAGTCCGATTCCCC
Found at i:11915728 original size:20 final size:20
Alignment explanation
Indices: 11915705--11915764 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 20
11915695 TCATATATTT
11915705 TATTTTAT-TTATTATTATAA
1 TATTTTATATT-TTATTATAA
*
11915725 TATTTTATATTTTATTTTAA
1 TATTTTATATTTTATTATAA
11915745 TATATTTATATTTATATTAT
1 TAT-TTTATATTT-TATTAT
11915765 TACTTTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 19 0.54
21 11 0.31
22 5 0.14
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTTTATATTTTATTATAA
Found at i:11915735 original size:27 final size:27
Alignment explanation
Indices: 11915697--11915852 Score: 107
Period size: 27 Copynumber: 5.7 Consensus size: 27
11915687 TTTTAATGTC
11915697 ATATATTT-TATTTTATTTATTATTATA
1 ATAT-TTTATATTTTATTTATTATTATA
11915724 ATATTTTATATTTTATTTTAATATATT-T-
1 ATATTTTATATTTTA-TTT-AT-TATTATA
11915752 ATA-TTTATATTATTACTTT-TTATATAATA
1 ATATTTTATATT-TTA-TTTATTAT-T-ATA
* *
11915781 CATATTTTA-AATATATTT-TTAATGTCAT-
1 -ATATTTTATATTTTATTTATT-AT-T-ATA
11915809 ATATTTTAT-TTTTATTTATTATTATA
1 ATATTTTATATTTTATTTATTATTATA
11915835 AT-TTTTATATTTTTATTT
1 ATATTTTATA-TTTTATTT
11915853 TATTTCTTTA
Statistics
Matches: 105, Mismatches: 7, Indels: 34
0.72 0.05 0.23
Matches are distributed among these distances:
25 11 0.10
26 8 0.08
27 43 0.41
28 20 0.19
29 10 0.10
30 9 0.09
31 4 0.04
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.65
Consensus pattern (27 bp):
ATATTTTATATTTTATTTATTATTATA
Found at i:11915773 original size:15 final size:14
Alignment explanation
Indices: 11915712--11915887 Score: 62
Period size: 13 Copynumber: 12.1 Consensus size: 14
11915702 TTTTATTTTA
*
11915712 TTTATTATTATAATAT
1 TTTA-TATTATTAT-T
11915728 TTTATATT-TTATT
1 TTTATATTATTATT
* *
11915741 TTAATA-TATTTATA
1 TTTATATTA-TTATT
11915755 TTTATATTATTACTT
1 TTTATATTATTA-TT
* *
11915770 TTTATATAATACATAT
1 TTTATATTAT-TAT-T
*
11915786 TTTAAATATATT-TT
1 TTTATAT-TATTATT
*
11915800 TAATGTCATATATTTTATT
1 T--T-T-ATAT-TATTATT
11915819 TTTAT-TTATTATT
1 TTTATATTATTATT
* * *
11915832 ATAAT-TTTTATATT
1 TTTATATTAT-TATT
* *
11915846 TTTATTTTATT-TC
1 TTTATATTATTATT
11915859 TTTATA-TATT-TT
1 TTTATATTATTATT
11915871 TTTATATTATATATT
1 TTTATATTAT-TATT
11915886 TT
1 TT
11915888 ATTTTAATTT
Statistics
Matches: 121, Mismatches: 22, Indels: 35
0.68 0.12 0.20
Matches are distributed among these distances:
12 12 0.10
13 27 0.22
14 27 0.22
15 27 0.22
16 14 0.12
17 4 0.03
18 7 0.06
19 3 0.02
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (14 bp):
TTTATATTATTATT
Found at i:11915844 original size:32 final size:34
Alignment explanation
Indices: 11915808--11915891 Score: 104
Period size: 32 Copynumber: 2.6 Consensus size: 34
11915798 TTTAATGTCA
11915808 TATATTTTAT-TTTTATTTA-TTAT-TATAATTTT
1 TATATTTTATATTTTATTTATTTATATAT-ATTTT
* *
11915840 TATATTTT-TATTTTATTTCTTTATATATTTTTT
1 TATATTTTATATTTTATTTATTTATATATATTTT
*
11915873 TATATTATATATTTTATTT
1 TATATTTTATATTTTATTT
11915892 TAATTTGTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
31 1 0.02
32 16 0.36
33 15 0.33
34 13 0.29
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.73
Consensus pattern (34 bp):
TATATTTTATATTTTATTTATTTATATATATTTT
Found at i:11915979 original size:13 final size:12
Alignment explanation
Indices: 11915698--11915990 Score: 75
Period size: 12 Copynumber: 24.0 Consensus size: 12
11915688 TTTAATGTCA
11915698 TATATTTTA-TT
1 TATATTTTATTT
11915709 T-TA-TTTATTAT
1 TATATTTTATT-T
*
11915720 TATA--ATATTT
1 TATATTTTATTT
11915730 TATATTTTATTT
1 TATATTTTATTT
11915742 TAATATATTTATATT
1 T-ATAT-TTTAT-TT
11915757 TATATTATTACTTT
1 TATATT-TTA-TTT
* * *
11915771 T-TA-TATAATA
1 TATATTTTATTT
* **
11915781 CATATTTTA-AA
1 TATATTTTATTT
*
11915792 TATATTTTTAATGTCA
1 TATA-TTTT-AT-T-T
11915808 TATATTTTATTT
1 TATATTTTATTT
11915820 T-TA-TTTATTAT
1 TATATTTTATT-T
* *
11915831 TATAATTT-TTA
1 TATATTTTATTT
11915842 TAT-TTTTATTT
1 TATATTTTATTT
*
11915853 TATTTCTTTATATAT
1 TATAT-TTTAT-T-T
11915868 T-T-TTTTATATT
1 TATATTTTAT-TT
11915879 ATATATTTTATTT
1 -TATATTTTATTT
*
11915892 TA-A-TTTGTTT
1 TATATTTTATTT
* *
11915902 TACCTATATTA-TA
1 TA--TATTTTATTT
* *
11915915 TAAATGTTAATTTT
1 TATAT-TTTA-TTT
11915929 TATATTTTATTT
1 TATATTTTATTT
*
11915941 TAT-TTTAATTT
1 TATATTTTATTT
11915952 T-TATTCTTATATT
1 TATATT-TTAT-TT
*
11915965 AATATTTTATTT
1 TATATTTTATTT
11915977 TAATATTTTTATTT
1 T-ATA-TTTTATTT
11915991 AATTATAATA
Statistics
Matches: 213, Mismatches: 28, Indels: 79
0.67 0.09 0.25
Matches are distributed among these distances:
9 4 0.02
10 27 0.13
11 41 0.19
12 45 0.21
13 37 0.17
14 44 0.21
15 10 0.05
16 5 0.02
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.66
Consensus pattern (12 bp):
TATATTTTATTT
Found at i:11915989 original size:6 final size:6
Alignment explanation
Indices: 11915924--11915990 Score: 55
Period size: 6 Copynumber: 10.7 Consensus size: 6
11915914 ATAAATGTTA
* * * *
11915924 ATTTTT ATATTTT A-TTTT ATTTTA ATTTTT ATTCTT ATATTA ATATTTT
1 ATTTTT AT-TTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT AT-TTTT
11915973 ATTTTAAT ATTTTT ATTT
1 ATTTT--T ATTTTT ATTT
11915991 AATTATAATA
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
5 5 0.10
6 28 0.58
7 9 0.19
8 6 0.12
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.72
Consensus pattern (6 bp):
ATTTTT
Found at i:11918985 original size:31 final size:34
Alignment explanation
Indices: 11918947--11919030 Score: 113
Period size: 35 Copynumber: 2.5 Consensus size: 34
11918937 TTCTTACTGT
*
11918947 ATTAAATAAAA-TTTA-T-AT-ATATATTTTTTAA
1 ATTAAATAAAATTTTATTAATAATA-ATTATTTAA
11918978 ATTAAATAAAATTTTATTAATAATAATTATTTAA
1 ATTAAATAAAATTTTATTAATAATAATTATTTAA
11919012 ATTTAAATAAAATTTTATT
1 A-TTAAATAAAATTTTATT
11919031 TATTGTTTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
31 11 0.23
32 4 0.09
33 1 0.02
34 11 0.23
35 20 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (34 bp):
ATTAAATAAAATTTTATTAATAATAATTATTTAA
Found at i:11919048 original size:5 final size:5
Alignment explanation
Indices: 11919040--11919104 Score: 54
Period size: 5 Copynumber: 14.2 Consensus size: 5
11919030 TTATTGTTTT
* *
11919040 ATATA ATATA ATATTA ATAAA ATAT- AT-TA ATAT- ATATT AT-TA A-ATA
1 ATATA ATATA ATA-TA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
11919086 ATATA ATAT- AT-TA ATATA A
1 ATATA ATATA ATATA ATATA A
11919105 GATGATAACA
Statistics
Matches: 49, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
3 2 0.04
4 17 0.35
5 25 0.51
6 5 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
ATATA
Found at i:11919080 original size:13 final size:14
Alignment explanation
Indices: 11919045--11919103 Score: 61
Period size: 13 Copynumber: 4.2 Consensus size: 14
11919035 GTTTTATATA
11919045 ATATA-ATATTAAT
1 ATATATATATTAAT
*
11919058 A-AAATATATTAAT
1 ATATATATATTAAT
11919071 ATATAT-TATTAAAT
1 ATATATATATT-AAT
11919085 AATATAATATATTAAT
1 -ATAT-ATATATTAAT
11919101 ATA
1 ATA
11919104 AGATGATAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
12 2 0.05
13 14 0.37
14 6 0.16
15 7 0.18
16 5 0.13
17 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATATATATTAAT
Found at i:11919089 original size:17 final size:18
Alignment explanation
Indices: 11919039--11919104 Score: 59
Period size: 18 Copynumber: 3.7 Consensus size: 18
11919029 TTTATTGTTT
11919039 TATA-TAATATAATATTAA
1 TATATTAATATAATA-TAA
* *
11919057 TAAAAT-ATATTAATAT-A
1 TATATTAATA-TAATATAA
11919074 TATTATTAA-ATAATATAA
1 TA-TATTAATATAATATAA
11919092 TATATTAATATAA
1 TATATTAATATAA
11919105 GATGATAACA
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
17 15 0.38
18 17 0.44
19 7 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATATTAATATAATATAA
Found at i:11919104 original size:13 final size:13
Alignment explanation
Indices: 11919039--11919104 Score: 57
Period size: 13 Copynumber: 5.0 Consensus size: 13
11919029 TTTATTGTTT
11919039 TATA-TAATAT-A
1 TATATTAATATAA
*
11919050 -ATATTAATAAAA
1 TATATTAATATAA
11919062 TATATTAATATATA
1 TATATTAATATA-A
*
11919076 TTATTAAATAATATAA
1 -TA-T-ATTAATATAA
11919092 TATATTAATATAA
1 TATATTAATATAA
11919105 GATGATAACA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
10 3 0.07
11 5 0.11
12 1 0.02
13 19 0.43
14 2 0.05
15 4 0.09
16 2 0.05
17 8 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TATATTAATATAA
Found at i:11922036 original size:29 final size:29
Alignment explanation
Indices: 11921986--11922042 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
11921976 TTGTATGGGT
**
11921986 AATAAGGCTTTCTTTGGTTAAAATAAAAG
1 AATAAGGCTTTCTTTGCATAAAATAAAAG
*
11922015 AATAAGGGCTTT-TTTGCATAAAGTAAAA
1 AATAA-GGCTTTCTTTGCATAAAATAAAA
11922043 TAGTTCAGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (29 bp):
AATAAGGCTTTCTTTGCATAAAATAAAAG
Found at i:11928912 original size:2 final size:2
Alignment explanation
Indices: 11928905--11928935 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11928895 GGCTAGAGTG
11928905 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
11928936 GNNNNNNNNN
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:11947462 original size:18 final size:18
Alignment explanation
Indices: 11947439--11947474 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
11947429 CTGAAGAACT
11947439 ACAATACCGTTTAAAAGA
1 ACAATACCGTTTAAAAGA
*
11947457 ACAATACCTTTTAAAAGA
1 ACAATACCGTTTAAAAGA
11947475 TGATTTTGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.50, C:0.17, G:0.08, T:0.25
Consensus pattern (18 bp):
ACAATACCGTTTAAAAGA
Found at i:11953443 original size:17 final size:17
Alignment explanation
Indices: 11953421--11953454 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
11953411 TCAAGATGAC
11953421 ATGTCAACATGTCACAT
1 ATGTCAACATGTCACAT
11953438 ATGTCAACATGTCACAT
1 ATGTCAACATGTCACAT
11953455 CGTGATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (17 bp):
ATGTCAACATGTCACAT
Found at i:11954393 original size:18 final size:18
Alignment explanation
Indices: 11954365--11954436 Score: 94
Period size: 18 Copynumber: 4.1 Consensus size: 18
11954355 TTTTTAAACA
*
11954365 ATTTAATATATGTACATAT
1 ATTT-ATATATATACATAT
11954384 ATTTATATATATACATAT
1 ATTTATATATATACATAT
* *
11954402 A--CATATATGTACATAT
1 ATTTATATATATACATAT
11954418 ATTTATATATATACATAT
1 ATTTATATATATACATAT
11954436 A
1 A
11954437 CATATATGTA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.30
18 28 0.61
19 4 0.09
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (18 bp):
ATTTATATATATACATAT
Found at i:11954396 original size:6 final size:6
Alignment explanation
Indices: 11954370--11954452 Score: 67
Period size: 6 Copynumber: 13.8 Consensus size: 6
11954360 AAACAATTTA
* * * * * * *
11954370 ATATAT GTACAT ATATTT ATATAT ATACAT ATACAT ATATGT ACATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* * * *
11954418 ATTTAT ATATAT ACATAT ACATAT ATGTAT ATATA
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATA
11954453 CACACATATT
Statistics
Matches: 59, Mismatches: 18, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (6 bp):
ATATAT
Found at i:11954408 original size:34 final size:34
Alignment explanation
Indices: 11954370--11954452 Score: 157
Period size: 34 Copynumber: 2.4 Consensus size: 34
11954360 AAACAATTTA
11954370 ATATATGTACATATATTTATATATATACATATAC
1 ATATATGTACATATATTTATATATATACATATAC
11954404 ATATATGTACATATATTTATATATATACATATAC
1 ATATATGTACATATATTTATATATATACATATAC
*
11954438 ATATATGTATATATA
1 ATATATGTACATATA
11954453 CACACATATT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (34 bp):
ATATATGTACATATATTTATATATATACATATAC
Found at i:11954425 original size:24 final size:24
Alignment explanation
Indices: 11954370--11954450 Score: 81
Period size: 24 Copynumber: 3.4 Consensus size: 24
11954360 AAACAATTTA
* * *
11954370 ATATATGTACATATATTTATATAT
1 ATATATATACATATATATACATAT
* *
11954394 ATACATATACATATATGTACATAT
1 ATATATATACATATATATACATAT
* * *
11954418 ATTTATATATATACATATACATAT
1 ATATATATACATATATATACATAT
*
11954442 ATGTATATA
1 ATATATATA
11954451 TACACACATA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (24 bp):
ATATATATACATATATATACATAT
Found at i:11954441 original size:16 final size:16
Alignment explanation
Indices: 11954388--11954454 Score: 80
Period size: 16 Copynumber: 4.1 Consensus size: 16
11954378 ACATATATTT
11954388 ATATATATACATATAC
1 ATATATATACATATAC
* *
11954404 ATATATGTACATATATTT
1 ATATATATACATATA--C
11954422 ATATATATACATATAC
1 ATATATATACATATAC
* *
11954438 ATATATGTATATATAC
1 ATATATATACATATAC
11954454 A
1 A
11954455 CACATATTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
16 29 0.67
18 14 0.33
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (16 bp):
ATATATATACATATAC
Found at i:11954442 original size:18 final size:18
Alignment explanation
Indices: 11954370--11954448 Score: 90
Period size: 18 Copynumber: 4.5 Consensus size: 18
11954360 AAACAATTTA
* *
11954370 ATATATGTACATATATTT
1 ATATATATACATATACTT
11954388 ATATATATACATATAC--
1 ATATATATACATATACTT
* *
11954404 ATATATGTACATATATTT
1 ATATATATACATATACTT
*
11954422 ATATATATACATATACAT
1 ATATATATACATATACTT
*
11954440 ATATGTATA
1 ATATATATA
11954449 TATACACACA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
16 14 0.27
18 37 0.73
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (18 bp):
ATATATATACATATACTT
Found at i:11959986 original size:17 final size:16
Alignment explanation
Indices: 11959955--11960001 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
11959945 GTTTCTTTAC
*
11959955 TCTTTTTTCTCTCTCT
1 TCTTTTTTCTTTCTCT
11959971 TCTTTTTCTCTTTCTCT
1 TCTTTTT-TCTTTCTCT
11959988 TCTCTTTTGTCTTT
1 TCT-TTTT-TCTTT
11960002 TTTTTTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 7 0.26
17 11 0.41
18 9 0.33
ACGTcount: A:0.00, C:0.28, G:0.02, T:0.70
Consensus pattern (16 bp):
TCTTTTTTCTTTCTCT
Found at i:11970082 original size:33 final size:32
Alignment explanation
Indices: 11970045--11970109 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
11970035 TAAGATAGAT
11970045 AATATTTTTTACA-AAATAATTTAAATAATAAAA
1 AATA-TTTTTA-ATAAATAATTTAAATAATAAAA
* *
11970078 AATATTTTTAATAATTTATTTAAATAATAAAA
1 AATATTTTTAATAAATAATTTAAATAATAAAA
11970110 GTTTTGAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 1 0.03
32 24 0.83
33 4 0.14
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (32 bp):
AATATTTTTAATAAATAATTTAAATAATAAAA
Found at i:11975729 original size:19 final size:19
Alignment explanation
Indices: 11975705--11975741 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
11975695 TGATTAATTA
11975705 TTATTAATTAAAATTTTAC
1 TTATTAATTAAAATTTTAC
* *
11975724 TTATTATTTTAAATTTTA
1 TTATTAATTAAAATTTTA
11975742 TAATACTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATTAATTAAAATTTTAC
Found at i:11977355 original size:15 final size:15
Alignment explanation
Indices: 11977331--11977364 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
11977321 ACTCCAAGGC
*
11977331 GATGACGAAGATGAA
1 GATGAAGAAGATGAA
11977346 GATGAAGAAGATGAA
1 GATGAAGAAGATGAA
11977361 GATG
1 GATG
11977365 GTAACGTCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.35, T:0.15
Consensus pattern (15 bp):
GATGAAGAAGATGAA
Found at i:11980727 original size:4 final size:4
Alignment explanation
Indices: 11980718--11980761 Score: 52
Period size: 4 Copynumber: 10.5 Consensus size: 4
11980708 GCCAAAAAGG
* *
11980718 AGAA AGAA AGAA AGAA AGAGA GGAA AGAA GGAA AGAA AGGAA AG
1 AGAA AGAA AGAA AGAA AGA-A AGAA AGAA AGAA AGAA A-GAA AG
11980762 GTTGCTGGTC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
4 27 0.79
5 7 0.21
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:11980745 original size:17 final size:17
Alignment explanation
Indices: 11980718--11980761 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
11980708 GCCAAAAAGG
11980718 AGAAA-GAAAGAAAGAA
1 AGAAAGGAAAGAAAGAA
* *
11980734 AGAGAGGAAAGAAGGAA
1 AGAAAGGAAAGAAAGAA
11980751 AGAAAGGAAAG
1 AGAAAGGAAAG
11980762 GTTGCTGGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 4 0.17
17 20 0.83
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (17 bp):
AGAAAGGAAAGAAAGAA
Found at i:11990289 original size:26 final size:26
Alignment explanation
Indices: 11990260--11990309 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
11990250 TTTAACCTTG
*
11990260 TTTGCTATTAGAGATTGTTTTCATAA
1 TTTGCTATTACAGATTGTTTTCATAA
11990286 TTTGCTATTACAGATTGTTTTCAT
1 TTTGCTATTACAGATTGTTTTCAT
11990310 GGATGGACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.52
Consensus pattern (26 bp):
TTTGCTATTACAGATTGTTTTCATAA
Found at i:11998430 original size:32 final size:32
Alignment explanation
Indices: 11998393--11998457 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
11998383 TGTATGGCTT
*
11998393 TTTAGGTTTTTGGCTGATCTACGCATTTTTTA
1 TTTAGGTTTTTGGCTGATCTACGCATTTCTTA
*
11998425 TTTAGGTTTTTGGCTGATCTGCGCATTTCTTA
1 TTTAGGTTTTTGGCTGATCTACGCATTTCTTA
11998457 T
1 T
11998458 CCAACACCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (32 bp):
TTTAGGTTTTTGGCTGATCTACGCATTTCTTA
Found at i:12001751 original size:2 final size:2
Alignment explanation
Indices: 12001744--12001769 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12001734 AAAAGCATGC
12001744 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
12001770 TGGACGTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12002788 original size:6 final size:6
Alignment explanation
Indices: 12002772--12002820 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
12002762 AGCTACAATT
* * * * *
12002772 TATATA AATATA TATATA TATATA TATTTA TTTATA TTTATA TTTATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
12002820 T
1 T
12002821 TTTTCTATGG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (6 bp):
TATATA
Found at i:12002798 original size:10 final size:10
Alignment explanation
Indices: 12002772--12002820 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
12002762 AGCTACAATT
*
12002772 TATATAAATA
1 TATATATATA
12002782 TATATATATA
1 TATATATATA
*
12002792 TATATATTTA
1 TATATATATA
* *
12002802 TTTATATTTA
1 TATATATATA
*
12002812 TATTTATAT
1 TATATATAT
12002821 TTTTCTATGG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TATATATATA
Found at i:12004809 original size:22 final size:22
Alignment explanation
Indices: 12004784--12004825 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
12004774 ATAAATTGGC
* *
12004784 ACTTGCAATGAAAGCTTGACTT
1 ACTTGAAATCAAAGCTTGACTT
*
12004806 ACTTGAAATCAAATCTTGAC
1 ACTTGAAATCAAAGCTTGAC
12004826 GTGTCAAGTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (22 bp):
ACTTGAAATCAAAGCTTGACTT
Found at i:12009647 original size:2 final size:2
Alignment explanation
Indices: 12009640--12009664 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12009630 ACAGCCGTAC
12009640 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
12009665 ATCTTTCTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12014934 original size:37 final size:37
Alignment explanation
Indices: 12014890--12014966 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
12014880 TGAGAAAAGA
12014890 AAACCAATTCAAAGGCAATCACCTCACATTGAAGAAC
1 AAACCAATTCAAAGGCAATCACCTCACATTGAAGAAC
12014927 AAACCAATTCAAAGGCAATCACCTCACATTGAAGAAC
1 AAACCAATTCAAAGGCAATCACCTCACATTGAAGAAC
12014964 AAA
1 AAA
12014967 AAAGAATATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.48, C:0.26, G:0.10, T:0.16
Consensus pattern (37 bp):
AAACCAATTCAAAGGCAATCACCTCACATTGAAGAAC
Found at i:12018655 original size:105 final size:105
Alignment explanation
Indices: 12018473--12018683 Score: 377
Period size: 105 Copynumber: 2.0 Consensus size: 105
12018463 AAAGTACCTT
12018473 TTCATTGACCTAGATATGAGAAACAATGGCAAAACCACAAGGAAACCAGCATGGAGAAATTTGAA
1 TTCATTGACCTAGATATGAGAAACAATGGCAAAACCACAAGGAAACCAGCATGGAGAAATTTGAA
12018538 ACATGTGAATAACATAAGAAATTGAGTTCTATGAAAATGA
66 ACATGTGAATAACATAAGAAATTGAGTTCTATGAAAATGA
* **
12018578 TTCATTGACCTAGATATGTGAAACAATGGCAAAACTGCAAGGAAACCAGCATGGAGAAATTTGAA
1 TTCATTGACCTAGATATGAGAAACAATGGCAAAACCACAAGGAAACCAGCATGGAGAAATTTGAA
* *
12018643 ACATGTGAATAACATACGAAATTGAGTTTTATGAAAATGA
66 ACATGTGAATAACATAAGAAATTGAGTTCTATGAAAATGA
12018683 T
1 T
12018684 ATTAATCTAC
Statistics
Matches: 101, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 101 1.00
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.24
Consensus pattern (105 bp):
TTCATTGACCTAGATATGAGAAACAATGGCAAAACCACAAGGAAACCAGCATGGAGAAATTTGAA
ACATGTGAATAACATAAGAAATTGAGTTCTATGAAAATGA
Found at i:12039518 original size:282 final size:281
Alignment explanation
Indices: 12039009--12039543 Score: 781
Period size: 282 Copynumber: 1.9 Consensus size: 281
12038999 GGGATCGAAC
* *
12039009 ATAAAAATCACTTCATTTAACCAATATTCTACACATTCCACATATAAATAATAACTTGATGTTTG
1 ATAAAAATCACTTCATTTAACCAATATTCTACACATTCCACATATAAACAATAACTTGATGTCTG
**
12039074 TCTCCAAAGAATACAAGACTAACAATGTTTCCATGGAATTCTTTCATTAGCATTTTTTGATAAAA
66 TCTCCAAAGAATACAAGACTAACAATAATTCCATGGAATTCTTTCATTAGCATTTTTTGATAAAA
** * * **
12039139 GACTTAAACACATGGGTACCACTTTTGAAAAGTCTGAATAAGGATGACATCTACCATTTTCTTAA
131 GACTTAAACACAAAGGCACCACTTTTGAAAAGTCTAAATAAGGATGACATCTACCATTTTCCCAA
* *
12039204 GTGCATGCCATCTTCTCCATAATTGGCCATTATTTTCCTTAATACAACAAGTTTAGCTGATACAA
196 GTGCATGCCATCTTCTCCATAATTGACCATTATTTTCCTTAATACAACAAGTCTAGCTGATACAA
12039269 GTTCCTCTATTATTCATTCCA
261 GTTCCTCTATTATTCATTCCA
* ** *
12039290 ATAATAAATCACTTCATTTAACCAATGTTCTACATGTTCCACATGTAAACAATAACTTGATGTCT
1 ATAA-AAATCACTTCATTTAACCAATATTCTACACATTCCACATATAAACAATAACTTGATGTCT
* * * * *
12039355 GTCTCCAAAGTAA-ACAAGACTAACAATAATTCCATTGAATTTTTTCCTTGGCATTTTTTTATAA
65 GTCTCCAAAG-AATACAAGACTAACAATAATTCCATGGAATTCTTTCATTAGCATTTTTTGATAA
* *
12039419 AGGACTTAAGCACAAAGGCACCACTTTT-AAAAGGTCTAAATAAGGATGACATC-AGCCATTTTC
129 AAGACTTAAACACAAAGGCACCACTTTTGAAAA-GTCTAAATAAGGATGACATCTA-CCATTTTC
*
12039482 CCAAGTGCATGCCATTTTCTCCATAATCT-ACCATTATTTTCCTTAATACAACAAGTCTAGCT
192 CCAAGTGCATGCCATCTTCTCCATAAT-TGACCATTATTTTCCTTAATACAACAAGTCTAGCT
12039544 AATAATTGGC
Statistics
Matches: 225, Mismatches: 24, Indels: 9
0.87 0.09 0.03
Matches are distributed among these distances:
281 9 0.04
282 213 0.95
283 3 0.01
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.34
Consensus pattern (281 bp):
ATAAAAATCACTTCATTTAACCAATATTCTACACATTCCACATATAAACAATAACTTGATGTCTG
TCTCCAAAGAATACAAGACTAACAATAATTCCATGGAATTCTTTCATTAGCATTTTTTGATAAAA
GACTTAAACACAAAGGCACCACTTTTGAAAAGTCTAAATAAGGATGACATCTACCATTTTCCCAA
GTGCATGCCATCTTCTCCATAATTGACCATTATTTTCCTTAATACAACAAGTCTAGCTGATACAA
GTTCCTCTATTATTCATTCCA
Found at i:12041468 original size:29 final size:30
Alignment explanation
Indices: 12041403--12041468 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
12041393 CCAGGCTTAA
* * *
12041403 AAAATTTATAATTTTTATGTCTTGTGTTTT
1 AAAATTTAAAAATTTTATGTCTTATGTTTT
*
12041433 AAAATTTAAAAATTTTAT-TCTTATTTTTT
1 AAAATTTAAAAATTTTATGTCTTATGTTTT
*
12041462 AAGATTT
1 AAAATTT
12041469 TTTTGTAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 15 0.48
30 16 0.52
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (30 bp):
AAAATTTAAAAATTTTATGTCTTATGTTTT
Found at i:12047299 original size:25 final size:25
Alignment explanation
Indices: 12047271--12047324 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
12047261 AAACAGGGAA
*
12047271 AAAGTATGCAGAGAAGCTTTAGAGG
1 AAAGCATGCAGAGAAGCTTTAGAGG
*
12047296 AAAGCATGTAGAGAAGCTTTAGAGG
1 AAAGCATGCAGAGAAGCTTTAGAGG
12047321 AAAG
1 AAAG
12047325 GCTTGGTGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.43, C:0.07, G:0.31, T:0.19
Consensus pattern (25 bp):
AAAGCATGCAGAGAAGCTTTAGAGG
Done.