Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, 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: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 136 of 147
Found at i:24685476 original size:17 final size:16
Alignment explanation
Indices: 24685456--24685487 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
24685446 TATATAATTC
24685456 ACATATATATAATTTAT
1 ACATATATA-AATTTAT
24685473 ACATATATAAATTTA
1 ACATATATAAATTTA
24685488 GGTTAGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (16 bp):
ACATATATAAATTTAT
Found at i:24685478 original size:15 final size:15
Alignment explanation
Indices: 24685444--24685487 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
24685434 ATTTTTAATT
*
24685444 CATATATAATTCACA
1 CATATATAATTTACA
* *
24685459 TATATATAATTTATA
1 CATATATAATTTACA
24685474 CATATATAAATTTA
1 CATATAT-AATTTA
24685488 GGTTAGTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 18 0.75
16 6 0.25
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (15 bp):
CATATATAATTTACA
Found at i:24685779 original size:2 final size:2
Alignment explanation
Indices: 24685772--24685796 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
24685762 CTTGGAAAAC
24685772 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
24685797 GCTATCCCAA
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:24685920 original size:17 final size:16
Alignment explanation
Indices: 24685893--24685925 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
24685883 TTTTTCATGA
24685893 TCAATAAATAATTAAT
1 TCAATAAATAATTAAT
24685909 TCAATCAAATAATTAAT
1 TCAAT-AAATAATTAAT
24685926 GAAAATGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (16 bp):
TCAATAAATAATTAAT
Found at i:24695907 original size:23 final size:23
Alignment explanation
Indices: 24695881--24695928 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
24695871 CAAAACCTAG
*
24695881 ACAATTGAGTAAGCAGAGGCAAA
1 ACAATTGAGTAAACAGAGGCAAA
24695904 ACAATTGAGTAAACAGAGGCAAA
1 ACAATTGAGTAAACAGAGGCAAA
24695927 AC
1 AC
24695929 GTAGATAAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.50, C:0.15, G:0.23, T:0.12
Consensus pattern (23 bp):
ACAATTGAGTAAACAGAGGCAAA
Found at i:24697134 original size:13 final size:13
Alignment explanation
Indices: 24697116--24697140 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24697106 TTTGGTTTGG
24697116 TTAGAGAGAGAAA
1 TTAGAGAGAGAAA
24697129 TTAGAGAGAGAA
1 TTAGAGAGAGAA
24697141 TTATTTTGGT
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:0.52, C:0.00, G:0.32, T:0.16
Consensus pattern (13 bp):
TTAGAGAGAGAAA
Found at i:24697174 original size:21 final size:21
Alignment explanation
Indices: 24697150--24697192 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
24697140 ATTATTTTGG
* *
24697150 TTTTATAGAGAGAATATGAAT
1 TTTTAGAGAAAGAATATGAAT
*
24697171 TTTTAGAGAAAGAATATTAAT
1 TTTTAGAGAAAGAATATGAAT
24697192 T
1 T
24697193 GAGATGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (21 bp):
TTTTAGAGAAAGAATATGAAT
Found at i:24697813 original size:110 final size:110
Alignment explanation
Indices: 24697615--24697830 Score: 360
Period size: 110 Copynumber: 2.0 Consensus size: 110
24697605 TGTAGACAAA
*
24697615 CTGAGTTAAATTTAAATATGACAATTTTAAATGTAACACGATAATACGATATAAAAATGACATGA
1 CTGAGTTAAATTTAAATATGACAATTTTAAATGTAACACGATAATACGATATAAAAATAACATGA
*
24697680 AAAAATCATATGTGTTTAGCATAATAGTGTTTCATGTCTTACAGG
66 AAAAATCATATGTGTTTAACATAATAGTGTTTCATGTCTTACAGG
* * *
24697725 CTGAGTTAAATTTAAATATGATAATTTTAAATGTAACATGATAATACGATATGAAAATAACATGA
1 CTGAGTTAAATTTAAATATGACAATTTTAAATGTAACACGATAATACGATATAAAAATAACATGA
* * *
24697790 AAAAATCGTATGTTTTTAACATAATATTGTTTCATGTCTTA
66 AAAAATCATATGTGTTTAACATAATAGTGTTTCATGTCTTA
24697831 ATTATGTCAA
Statistics
Matches: 98, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
110 98 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (110 bp):
CTGAGTTAAATTTAAATATGACAATTTTAAATGTAACACGATAATACGATATAAAAATAACATGA
AAAAATCATATGTGTTTAACATAATAGTGTTTCATGTCTTACAGG
Found at i:24702796 original size:20 final size:20
Alignment explanation
Indices: 24702754--24702797 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
24702744 TATTTATATA
* *
24702754 TATTTAATAAATAAATTTTT
1 TATTAAATAAATAAATTTAT
24702774 TATTAAATAATATAAA-TTAT
1 TATTAAATAA-ATAAATTTAT
24702794 TATT
1 TATT
24702798 TTACATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TATTAAATAAATAAATTTAT
Found at i:24702910 original size:21 final size:21
Alignment explanation
Indices: 24702830--24702910 Score: 58
Period size: 21 Copynumber: 3.8 Consensus size: 21
24702820 ATTTTTATTG
*
24702830 AAAAATAAATATTAATATATTTA
1 AAAAATAAAT-TTAA-ATATTCA
* *
24702853 TAAAAAT-TATTTAAATATACA
1 -AAAAATAAATTTAAATATTCA
* **
24702874 AGATAA-AAATAAAAATATTCA
1 A-AAAATAAATTTAAATATTCA
24702895 AAAAATAAATTTAAAT
1 AAAAATAAATTTAAAT
24702911 TTAAATTTTT
Statistics
Matches: 43, Mismatches: 11, Indels: 9
0.68 0.17 0.14
Matches are distributed among these distances:
20 4 0.09
21 27 0.63
22 4 0.09
23 2 0.05
24 6 0.14
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.33
Consensus pattern (21 bp):
AAAAATAAATTTAAATATTCA
Found at i:24706829 original size:19 final size:19
Alignment explanation
Indices: 24706801--24706843 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
24706791 CTAAATGAAC
24706801 ATAT-TTTATAAGTAATAT
1 ATATATTTATAAGTAATAT
*
24706819 ATATATTTATAAGTATTAT
1 ATATATTTATAAGTAATAT
*
24706838 CTATAT
1 ATATAT
24706844 ATAATTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (19 bp):
ATATATTTATAAGTAATAT
Found at i:24707127 original size:16 final size:16
Alignment explanation
Indices: 24707106--24707148 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
24707096 TTGAATATAA
*
24707106 ATAAATAATTATTTTT
1 ATAAATAATTATTTAT
*
24707122 ATAAATTA-TATTTAT
1 ATAAATAATTATTTAT
*
24707137 ACAAATAATTAT
1 ATAAATAATTAT
24707149 AATCATTTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
ATAAATAATTATTTAT
Found at i:24707551 original size:2 final size:2
Alignment explanation
Indices: 24707544--24707574 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
24707534 TAGTTGAATA
*
24707544 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24707575 CCTAAATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:24707609 original size:22 final size:22
Alignment explanation
Indices: 24707558--24707684 Score: 66
Period size: 22 Copynumber: 5.9 Consensus size: 22
24707548 ATATATATAT
**
24707558 ATATATATATAT-TTATACCTA
1 ATATATATATATCTTATAAGTA
24707579 A-ATGA-ATATATCTTATAAGTA
1 ATAT-ATATATATCTTATAAGTA
*
24707600 ATATATATAT-TTTCTATAAGTA
1 ATATATATATATCT-TATAAGTA
* * * *
24707622 TTATGTATATATTCTTAT-ATTC
1 ATATATATATA-TCTTATAAGTA
* * * *
24707644 AGATATACATATTTTGTAAGTA
1 ATATATATATATCTTATAAGTA
* * *
24707666 ATATGTACACATCTTATAA
1 ATATATATATATCTTATAA
24707685 AAAAAACAAT
Statistics
Matches: 77, Mismatches: 21, Indels: 15
0.68 0.19 0.13
Matches are distributed among these distances:
20 8 0.10
21 17 0.22
22 47 0.61
23 3 0.04
24 2 0.03
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (22 bp):
ATATATATATATCTTATAAGTA
Found at i:24712402 original size:3 final size:3
Alignment explanation
Indices: 24712396--24712435 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
24712386 TGTGATTTAC
*
24712396 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATT ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
24712436 AATTATTAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:24712441 original size:8 final size:9
Alignment explanation
Indices: 24712396--24712441 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
24712386 TGTGATTTAC
*
24712396 ATAATAATA
1 ATAATAATT
*
24712405 ATAATAATA
1 ATAATAATT
*
24712414 ATAATAATA
1 ATAATAATT
24712423 ATAATAATT
1 ATAATAATT
24712432 ATAA-AATT
1 ATAATAATT
24712440 AT
1 AT
24712442 TAACGAAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
8 6 0.17
9 30 0.83
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
ATAATAATT
Found at i:24720230 original size:17 final size:17
Alignment explanation
Indices: 24720208--24720241 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
24720198 GTATGTAGCA
*
24720208 ACAGGCAGCAGCACTTG
1 ACAGGCAGCACCACTTG
24720225 ACAGGCAGCACCACTTG
1 ACAGGCAGCACCACTTG
24720242 CAATAACTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.32, G:0.26, T:0.12
Consensus pattern (17 bp):
ACAGGCAGCACCACTTG
Found at i:24720826 original size:94 final size:94
Alignment explanation
Indices: 24720661--24720837 Score: 318
Period size: 94 Copynumber: 1.9 Consensus size: 94
24720651 AACCTTAACA
* *
24720661 ATTCAGCCTCAAGATCAATTTATCTCTTGAGTTAGATCCAATTCTCAAACAAAAAGTCAAACTGA
1 ATTCAACCTCAAGATCAATTTATCTCTTGAGTTAGATCCAAATCTCAAACAAAAAGTCAAACTGA
24720726 GACAGTCTGTTTCAAAACAGATTCATATT
66 GACAGTCTGTTTCAAAACAGATTCATATT
*
24720755 ATTCAACCTCAAGATCAATTTATCTCTTGAGTTAGATCCAAATCTCAAATAAAAAGTCAAACTGA
1 ATTCAACCTCAAGATCAATTTATCTCTTGAGTTAGATCCAAATCTCAAACAAAAAGTCAAACTGA
*
24720820 GCCAGTCTGTTTCAAAAC
66 GACAGTCTGTTTCAAAAC
24720838 TTCACGCAAA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 79 1.00
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (94 bp):
ATTCAACCTCAAGATCAATTTATCTCTTGAGTTAGATCCAAATCTCAAACAAAAAGTCAAACTGA
GACAGTCTGTTTCAAAACAGATTCATATT
Found at i:24723831 original size:2 final size:2
Alignment explanation
Indices: 24723824--24723855 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
24723814 TCATGTTAAC
*
24723824 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24723856 GAACGTGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:24724284 original size:30 final size:29
Alignment explanation
Indices: 24724245--24724305 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 29
24724235 GATGATTGTG
*
24724245 AATTATATTTAATAATTTTAGATAAATATA
1 AATTATATTTAATAATTTTAAATAAAT-TA
*
24724275 AATTGTATTTAATAATTTTAAATAAATTA
1 AATTATATTTAATAATTTTAAATAAATTA
24724304 AA
1 AA
24724306 AATTAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (29 bp):
AATTATATTTAATAATTTTAAATAAATTA
Found at i:24726330 original size:16 final size:16
Alignment explanation
Indices: 24726309--24726339 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
24726299 TTTTAATATT
*
24726309 AATATAAAATTAAATA
1 AATATAAAATCAAATA
24726325 AATATAAAATCAAAT
1 AATATAAAATCAAAT
24726340 TTACTTAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
AATATAAAATCAAATA
Found at i:24727154 original size:12 final size:12
Alignment explanation
Indices: 24727137--24727161 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24727127 CCTATCACCA
24727137 CTTCATTCTTGT
1 CTTCATTCTTGT
24727149 CTTCATTCTTGT
1 CTTCATTCTTGT
24727161 C
1 C
24727162 CATTGCTGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.28, G:0.08, T:0.56
Consensus pattern (12 bp):
CTTCATTCTTGT
Found at i:24730832 original size:45 final size:45
Alignment explanation
Indices: 24730761--24730850 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
24730751 GCACAAGTTG
* * *
24730761 TGAACATTATAGATAAAGATTGGCTACCTTTTATAAACAATGCTA
1 TGAACATTATAGATAAAAATTAGCTACCTTTTACAAACAATGCTA
*
24730806 TGAACATTATATATAAAAATTAGCTACCTTTTACAAACAATGCTA
1 TGAACATTATAGATAAAAATTAGCTACCTTTTACAAACAATGCTA
24730851 CAATAGATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.33
Consensus pattern (45 bp):
TGAACATTATAGATAAAAATTAGCTACCTTTTACAAACAATGCTA
Found at i:24731791 original size:2 final size:2
Alignment explanation
Indices: 24731784--24731821 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
24731774 TCCTCCACAA
24731784 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
24731822 GCACAAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:24743907 original size:33 final size:28
Alignment explanation
Indices: 24743870--24743931 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 28
24743860 TCATAATTTG
24743870 ATTTTATTCGAATTAATTGATTAAATTAAATTA
1 ATTTTATT--AATTAATT-ATT--ATTAAATTA
24743903 ATTTTATTAATTAATTATTATTAAATTA
1 ATTTTATTAATTAATTATTATTAAATTA
24743931 A
1 A
24743932 GTTTGATCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
28 10 0.34
30 3 0.10
31 8 0.28
33 8 0.28
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (28 bp):
ATTTTATTAATTAATTATTATTAAATTA
Found at i:24743911 original size:14 final size:15
Alignment explanation
Indices: 24743880--24743931 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 15
24743870 ATTTTATTCG
24743880 AATTAATTGATTAAATTA
1 AATTAATT-ATT--ATTA
24743898 AATTAATT-TTATT-
1 AATTAATTATTATTA
24743911 AATTAATTATTATTA
1 AATTAATTATTATTA
24743926 AATTAA
1 AATTAA
24743932 GTTTGATCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 6 0.19
16 2 0.06
18 8 0.25
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
AATTAATTATTATTA
Found at i:24743960 original size:24 final size:26
Alignment explanation
Indices: 24743933--24743985 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
24743923 TTAAATTAAG
24743933 TTTGA-TCAATT-TAAAAATAATAAA
1 TTTGATTCAATTATAAAAATAATAAA
* *
24743957 TTTGATTTAATTAATAAAAATAATTAA
1 TTTGATTCAATT-ATAAAAATAATAAA
24743984 TT
1 TT
24743986 AATTTAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.21
25 5 0.21
27 14 0.58
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (26 bp):
TTTGATTCAATTATAAAAATAATAAA
Found at i:24743990 original size:26 final size:27
Alignment explanation
Indices: 24743944--24743997 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
24743934 TTGATCAATT
*
24743944 TAAAAATAATAAATTTGATTTAATTAA
1 TAAAAATAATAAATTTAATTTAATTAA
*
24743971 TAAAAATAATTAA-TTAATTTAATTAA
1 TAAAAATAATAAATTTAATTTAATTAA
24743997 T
1 T
24743998 TTAATTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 13 0.52
27 12 0.48
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (27 bp):
TAAAAATAATAAATTTAATTTAATTAA
Found at i:24764715 original size:13 final size:13
Alignment explanation
Indices: 24764697--24764723 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
24764687 GTATTTTGCC
24764697 AAAAAAAGAGAAA
1 AAAAAAAGAGAAA
24764710 AAAAAAAGAGAAA
1 AAAAAAAGAGAAA
24764723 A
1 A
24764724 TTAACAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAGAAA
Found at i:24764750 original size:19 final size:18
Alignment explanation
Indices: 24764726--24764774 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
24764716 AGAGAAAATT
*
24764726 AACAAATAAAAAAATAAAA
1 AACAAAGAAAAAAAT-AAA
* *
24764745 AACAAAGAAGAGAATAAA
1 AACAAAGAAAAAAATAAA
24764763 AACAAAGAAAAA
1 AACAAAGAAAAA
24764775 TAAAGAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.80, C:0.06, G:0.08, T:0.06
Consensus pattern (18 bp):
AACAAAGAAAAAAATAAA
Found at i:24764767 original size:37 final size:36
Alignment explanation
Indices: 24764697--24764785 Score: 94
Period size: 37 Copynumber: 2.4 Consensus size: 36
24764687 GTATTTTGCC
* *
24764697 AAAAAAAGAGAAAAAAAAAAGAGAAAATTAACAAAT
1 AAAAAAAGAGAAAAAAAAAAGAGAAAATAAACAAAG
*
24764733 AAAAAAATA-AAAAACAAAGAAGAGAATAA-AAACAAAG
1 AAAAAAAGAGAAAAA-AAA-AAGAGAA-AATAAACAAAG
24764770 AAAAATAA-AGAAAAAA
1 AAAAA-AAGAGAAAAAA
24764786 TAAGGAAAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
35 5 0.11
36 11 0.24
37 20 0.44
38 9 0.20
ACGTcount: A:0.80, C:0.03, G:0.10, T:0.07
Consensus pattern (36 bp):
AAAAAAAGAGAAAAAAAAAAGAGAAAATAAACAAAG
Found at i:24766040 original size:48 final size:49
Alignment explanation
Indices: 24765751--24766052 Score: 252
Period size: 49 Copynumber: 6.1 Consensus size: 49
24765741 TTTCAAATAG
* **
24765751 ATTTTAAAGTTTCCAAGCCTCTGTTTAGGGCAAGCCATTTTCAAACAAGA
1 ATTTTAAAGTTTCAAAGCCTCTGTTTAGGGGGAGCCATTTTCAAACAA-A
* * * * * ** * *
24765801 TTTTTTTTTAAGTTTTAAAGCAAT-TGTTTAAGAAGAGCTATTTTCAAACAAG
1 ---ATTTTAAAGTTTCAAAGC-CTCTGTTTAGGGGGAGCCATTTTCAAACAAA
** * * *
24765853 ATTTTAAAGTTTCAAAGTTTTTGTTTAGGGGGAGGCATTTTCAAATAAA
1 ATTTTAAAGTTTCAAAGCCTCTGTTTAGGGGGAGCCATTTTCAAACAAA
* * * * * *
24765902 ATTTTTATAAAGTTTCAAAGCTTTTGTTTAGGGGAAGTCATTTTTAAACAAG
1 A--TTT-TAAAGTTTCAAAGCCTCTGTTTAGGGGGAGCCATTTTCAAACAAA
* * *
24765954 ATTTTAAAGTTTTAAAGCCTCTGTTTAAGGAGG-G-CATTTTTAAACAAA
1 ATTTTAAAGTTTCAAAGCCTCTGTTT-AGGGGGAGCCATTTTCAAACAAA
*
24766002 ATTTT-AAGTTTCAAAGCCTCTATTTAGGGGGAGCCATTTTCAAACAAA
1 ATTTTAAAGTTTCAAAGCCTCTGTTTAGGGGGAGCCATTTTCAAACAAA
24766050 ATT
1 ATT
24766053 AAAAAAATAA
Statistics
Matches: 202, Mismatches: 39, Indels: 21
0.77 0.15 0.08
Matches are distributed among these distances:
46 5 0.02
47 19 0.09
48 35 0.17
49 56 0.28
50 7 0.03
51 3 0.01
52 40 0.20
53 36 0.18
54 1 0.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (49 bp):
ATTTTAAAGTTTCAAAGCCTCTGTTTAGGGGGAGCCATTTTCAAACAAA
Found at i:24768080 original size:21 final size:22
Alignment explanation
Indices: 24768043--24768083 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
24768033 GGTTCAAAGA
24768043 TTTTAAATATTTATTGGTTTTC
1 TTTTAAATATTTATTGGTTTTC
*
24768065 TTTTAAA-ATTTGTTGGTTT
1 TTTTAAATATTTATTGGTTT
24768084 AAGCTTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.22, C:0.02, G:0.12, T:0.63
Consensus pattern (22 bp):
TTTTAAATATTTATTGGTTTTC
Found at i:24769038 original size:18 final size:20
Alignment explanation
Indices: 24769015--24769054 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
24769005 ATAAAATTAG
24769015 AACAAAAT-TAAAACA-AAT
1 AACAAAATGTAAAACATAAT
*
24769033 AACAAAATGTATAACATAAT
1 AACAAAATGTAAAACATAAT
24769053 AA
1 AA
24769055 TAAGTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 6 0.32
20 5 0.26
ACGTcount: A:0.68, C:0.10, G:0.03, T:0.20
Consensus pattern (20 bp):
AACAAAATGTAAAACATAAT
Found at i:24771687 original size:22 final size:21
Alignment explanation
Indices: 24771641--24771687 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
24771631 TAATTTATTT
*
24771641 AAAGTTTTATAAAAAAACTAT
1 AAAGTTTTATAAAAAAACTAC
*
24771662 AAAGTTTTATAAAAAAAATTAC
1 AAAGTTTTAT-AAAAAAACTAC
24771684 AAAG
1 AAAG
24771688 ATACGAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (21 bp):
AAAGTTTTATAAAAAAACTAC
Found at i:24788505 original size:17 final size:20
Alignment explanation
Indices: 24788483--24788524 Score: 56
Period size: 17 Copynumber: 2.3 Consensus size: 20
24788473 AGTTTAATGA
24788483 AAAAATTA-ATAAT-ATA-T
1 AAAAATTATATAATGATATT
24788500 AAAAA-TATATAATGATATT
1 AAAAATTATATAATGATATT
24788519 AAAAAT
1 AAAAAT
24788525 ATCATTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.10
17 10 0.48
18 3 0.14
19 6 0.29
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
AAAAATTATATAATGATATT
Found at i:24788517 original size:20 final size:19
Alignment explanation
Indices: 24788489--24788526 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
24788479 ATGAAAAAAT
24788489 TAATAATATATAAAAATATA
1 TAATAATAT-TAAAAATATA
*
24788509 TAATGATATTAAAAATAT
1 TAATAATATTAAAAATAT
24788527 CATTTATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (19 bp):
TAATAATATTAAAAATATA
Found at i:24797116 original size:2 final size:2
Alignment explanation
Indices: 24797100--24797131 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
24797090 TCAACTGATG
24797100 GA GA G- GA GA -A GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
24797132 TATGATATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:24797529 original size:21 final size:21
Alignment explanation
Indices: 24797503--24797545 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
24797493 ATATACAAAA
*
24797503 ATATATAATTTTAAAAAAATT
1 ATATATAAATTTAAAAAAATT
*
24797524 ATATATAAATTTAATAAAATT
1 ATATATAAATTTAAAAAAATT
24797545 A
1 A
24797546 AAATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATATAAATTTAAAAAAATT
Found at i:24799329 original size:11 final size:12
Alignment explanation
Indices: 24799304--24799333 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
24799294 AAATGATAAT
24799304 TATTTTATATTA
1 TATTTTATATTA
24799316 TATTTTAT-TTA
1 TATTTTATATTA
24799327 TATTTTA
1 TATTTTA
24799334 AAAAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TATTTTATATTA
Found at i:24802105 original size:22 final size:21
Alignment explanation
Indices: 24802075--24802137 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
24802065 AGTTTATTTG
24802075 ATATT-AATTTTTTAAAATAA
1 ATATTAAATTTTTTAAAATAA
* ** *
24802095 TTATTTAAATTAATTAAATTAA
1 ATA-TTAAATTTTTTAAAATAA
24802117 ATATTAAATTTTATATAAAAT
1 ATATTAAATTTT-T-TAAAAT
24802138 TTTTTTGATT
Statistics
Matches: 31, Mismatches: 8, Indels: 5
0.70 0.18 0.11
Matches are distributed among these distances:
20 2 0.06
21 9 0.29
22 15 0.48
23 5 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATATTAAATTTTTTAAAATAA
Found at i:24802307 original size:29 final size:29
Alignment explanation
Indices: 24802261--24802325 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
24802251 TATTTTACTT
*
24802261 AAATAAATCTTTATATTTT-TATTACATCC
1 AAATAAATCTTTAAATTTTAT-TTACATCC
* *
24802290 AAATAAAT-TCTTAAATTTTATTTGCATTC
1 AAATAAATCT-TTAAATTTTATTTACATCC
24802319 AAATAAA
1 AAATAAA
24802326 ATTTTAACCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 1 0.03
29 29 0.94
30 1 0.03
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.45
Consensus pattern (29 bp):
AAATAAATCTTTAAATTTTATTTACATCC
Found at i:24802381 original size:30 final size:30
Alignment explanation
Indices: 24802319--24802383 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
24802309 ATTTGCATTC
* *
24802319 AAATAAAATTTTAACCATTAACTTGTATTT
1 AAATAAAATTTTAACCATTAACTTATACTT
*** *
24802349 AAATAAAATTTTAATGTTTAATTTATACTT
1 AAATAAAATTTTAACCATTAACTTATACTT
24802379 AAATA
1 AAATA
24802384 TATCTTTAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (30 bp):
AAATAAAATTTTAACCATTAACTTATACTT
Found at i:24802496 original size:29 final size:28
Alignment explanation
Indices: 24802438--24802498 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
24802428 AGATACAAAT
* **
24802438 TAAAAAATAAAATTTTATTTAAATGCAA
1 TAAAAAATAAAAATTTATTTAAATAAAA
24802466 TAAAAATATAAAAATTTATTTAAATAAAA
1 TAAAAA-ATAAAAATTTATTTAAATAAAA
24802495 TAAA
1 TAAA
24802499 TAATTCAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (28 bp):
TAAAAAATAAAAATTTATTTAAATAAAA
Found at i:24807688 original size:4 final size:4
Alignment explanation
Indices: 24807679--24807712 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
24807669 CATAATTGTC
*
24807679 TATT TATT TATT TATT TGTT TATTT TATT TATT T
1 TATT TATT TATT TATT TATT TA-TT TATT TATT T
24807713 TACTATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:24807700 original size:12 final size:13
Alignment explanation
Indices: 24807679--24807712 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
24807669 CATAATTGTC
24807679 TATTTATTTA-TT
1 TATTTATTTATTT
*
24807691 TATTTGTTTATTT
1 TATTTATTTATTT
24807704 TATTTATTT
1 TATTTATTT
24807713 TACTATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (13 bp):
TATTTATTTATTT
Found at i:24807978 original size:8 final size:7
Alignment explanation
Indices: 24807954--24807987 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
24807944 TCTTTTCCAA
24807954 AAAAATT
1 AAAAATT
24807961 AAAAATT
1 AAAAATT
24807968 AAAAA-T
1 AAAAATT
*
24807974 ATAAATT
1 AAAAATT
24807981 AAAAATT
1 AAAAATT
24807988 TGGGTGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AAAAATT
Found at i:24812147 original size:22 final size:21
Alignment explanation
Indices: 24812118--24812162 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
24812108 TTGCTTTTCA
24812118 ATGAAAAT-ATCCATATTTGAT
1 ATGAAAATGA-CCATATTTGAT
*
24812139 ATGATAAATGACCATATTTTAT
1 ATGA-AAATGACCATATTTGAT
24812161 AT
1 AT
24812163 TTTTTTACGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
22 16 0.76
23 1 0.05
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (21 bp):
ATGAAAATGACCATATTTGAT
Found at i:24812417 original size:10 final size:10
Alignment explanation
Indices: 24812379--24812420 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
24812369 TCTTAATGTG
*
24812379 GAAAAATAAA
1 GAAAAAAAAA
24812389 G-AAAAAAAA
1 GAAAAAAAAA
*
24812398 GGAAAAAAAA
1 GAAAAAAAAA
24812408 GAAAAAAAAA
1 GAAAAAAAAA
24812418 GAA
1 GAA
24812421 TGCATGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 8 0.28
10 21 0.72
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:24812418 original size:20 final size:20
Alignment explanation
Indices: 24812378--24812416 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
24812368 GTCTTAATGT
24812378 GGAAAAATAAAGAAAAAAAA
1 GGAAAAATAAAGAAAAAAAA
24812398 GGAAAAA-AAAGAAAAAAAA
1 GGAAAAATAAAGAAAAAAAA
24812417 AGAATGCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (20 bp):
GGAAAAATAAAGAAAAAAAA
Found at i:24813899 original size:22 final size:21
Alignment explanation
Indices: 24813852--24813921 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 21
24813842 ATAAGAAATT
* * *
24813852 ATTTGTAAGACCTCCAACCATG
1 ATTTGTAAGA-CTTCAAACATA
24813874 ATTTGTAAGACTTTCAAACATA
1 ATTTGTAAGAC-TTCAAACATA
* * *
24813896 ATTTTTAAAACCTCTAAACATA
1 ATTTGTAAGACTTC-AAACATA
24813918 ATTT
1 ATTT
24813922 TCAAGATCTC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 3 0.08
22 37 0.93
ACGTcount: A:0.39, C:0.19, G:0.07, T:0.36
Consensus pattern (21 bp):
ATTTGTAAGACTTCAAACATA
Found at i:24814792 original size:43 final size:43
Alignment explanation
Indices: 24814612--24814821 Score: 153
Period size: 43 Copynumber: 4.9 Consensus size: 43
24814602 AGTAAAAATA
* * * * *
24814612 TTTTTATATTTTTCAAAATGGTTGAA-CCTCTGTTAAAAAAAT-
1 TTTTTATATTTTTCAAAATTGTT-AAGCCTTTGTTGAGAAGATC
* * * * *
24814654 TTTTTATATTTTTCAAAATTTTTGATCTTTTGTTGAGATGAATC
1 TTTTTATATTTTTCAAAATTGTTAAGCCTTTGTTGAGAAG-ATC
* * * *
24814698 -TTTTATATTTTTCAAAAGTTGTTAAG-TTTTATT-AAAATGAAC
1 TTTTTATATTTTTCAAAA-TTGTTAAGCCTTTGTTGAGAA-GATC
* * *
24814740 CTTTAATA-TTTTCAAAAGTTGTTAAGCCTCTGTTGAGAAGATC
1 TTTTTATATTTTTCAAAA-TTGTTAAGCCTTTGTTGAGAAGATC
* * *
24814783 TTTTTATATTTTTAAAAATTATTAAGCCTTTGTTTAGAA
1 TTTTTATATTTTTCAAAATTGTTAAGCCTTTGTTGAGAA
24814822 TAACCTTTAT
Statistics
Matches: 131, Mismatches: 28, Indels: 17
0.74 0.16 0.10
Matches are distributed among these distances:
41 1 0.01
42 51 0.39
43 63 0.48
44 16 0.12
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.49
Consensus pattern (43 bp):
TTTTTATATTTTTCAAAATTGTTAAGCCTTTGTTGAGAAGATC
Found at i:24814827 original size:86 final size:86
Alignment explanation
Indices: 24814684--24814842 Score: 202
Period size: 86 Copynumber: 1.8 Consensus size: 86
24814674 TTTGATCTTT
* * *
24814684 TGTTGAGATGAATCTTTTATATTTTTCAAAAGTTGTTAAGTTTTATTAAAATGAACCTTTAATAT
1 TGTTGAGAAGAATCTTTTATATTTTTCAAAAATTATTAAGTTTTATTAAAATGAACCTTT-ATAT
24814749 T-TTCAAAAGTTGTTAAGCCTC
65 TGTTCAAAAGTTGTTAAGCCTC
*
24814770 TGTTGAGAAG-ATCTTTTTATATTTTT-AAAAATTATTAAGCCTTTGT-TTAGAAT-AACCTTTA
1 TGTTGAGAAGAATC-TTTTATATTTTTCAAAAATTATTAAG--TTT-TATTAAAATGAACCTTTA
24814831 TATTGTTCAAAA
62 TATTGTTCAAAA
24814843 AACCTGAGTT
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
85 19 0.30
86 35 0.55
87 9 0.14
88 1 0.02
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (86 bp):
TGTTGAGAAGAATCTTTTATATTTTTCAAAAATTATTAAGTTTTATTAAAATGAACCTTTATATT
GTTCAAAAGTTGTTAAGCCTC
Found at i:24814843 original size:43 final size:42
Alignment explanation
Indices: 24814699--24814843 Score: 125
Period size: 43 Copynumber: 3.4 Consensus size: 42
24814689 AGATGAATCT
* *
24814699 TTTATATTTTTCAAAAGTTGTTAAG--TTT-TATTAAAATGAACC
1 TTTATA-TTTTCAAAAATTGTTAAGCCTTTGT-TTAGAAT-AACC
* * * * * *
24814741 TTTAATATTTTCAAAAGTTGTTAAGCCTCTGTTGAGAAGATCTT
1 TTT-ATATTTTCAAAAATTGTTAAGCCTTTGTTTAGAATAAC-C
* *
24814785 TTTATATTTTTAAAAATTATTAAGCCTTTGTTTAGAATAACC
1 TTTATATTTTCAAAAATTGTTAAGCCTTTGTTTAGAATAACC
24814827 TTTATATTGTTCAAAAA
1 TTTATATT-TTCAAAAA
24814844 ACCTGAGTTT
Statistics
Matches: 82, Mismatches: 15, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
42 29 0.35
43 43 0.52
44 9 0.11
45 1 0.01
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (42 bp):
TTTATATTTTCAAAAATTGTTAAGCCTTTGTTTAGAATAACC
Found at i:24816512 original size:18 final size:20
Alignment explanation
Indices: 24816476--24816512 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
24816466 TCCATAGAGC
*
24816476 TTAACTATTAATTTTGTGAT
1 TTAACTATTAATTTGGTGAT
24816496 TTAACTA-T-ATTTGGTGA
1 TTAACTATTAATTTGGTGA
24816513 AGCTCCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 1 0.06
20 7 0.44
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (20 bp):
TTAACTATTAATTTGGTGAT
Found at i:24817232 original size:25 final size:25
Alignment explanation
Indices: 24817189--24817251 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
24817179 AATTAATGAA
* *
24817189 CAAATTGAATCAATAAAATTTAATT
1 CAAATTGAATTAATAAAATCTAATT
* *
24817214 TAAATTGAATT-ATATAAATCTCATT
1 CAAATTGAATTAATA-AAATCTAATT
*
24817239 CAAATTCAATTAA
1 CAAATTGAATTAA
24817252 ATTTTAAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
24 3 0.10
25 26 0.87
26 1 0.03
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (25 bp):
CAAATTGAATTAATAAAATCTAATT
Found at i:24822174 original size:10 final size:10
Alignment explanation
Indices: 24822161--24822194 Score: 52
Period size: 9 Copynumber: 3.4 Consensus size: 10
24822151 CTTAATGTGA
24822161 AAAAAAAAAG
1 AAAAAAAAAG
24822171 -AAAAAAAAG
1 AAAAAAAAAG
24822180 AAAAAAAAATG
1 AAAAAAAAA-G
24822191 AAAA
1 AAAA
24822195 TGCATGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.41
10 8 0.36
11 5 0.23
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:24823679 original size:22 final size:22
Alignment explanation
Indices: 24823632--24823749 Score: 76
Period size: 22 Copynumber: 5.4 Consensus size: 22
24823622 ATAAAAAATT
* *
24823632 ATTTGTAAGACCTCCAACCATG
1 ATTTGTAAGACCTCCAAACATA
*
24823654 ATTTGTAAGACCTCTAAACATA
1 ATTTGTAAGACCTCCAAACATA
* *****
24823676 ATTT-TCAAAACCTTTGGGCATA
1 ATTTGT-AAGACCTCCAAACATA
* * * *
24823698 ACTTATAAGACTTCCAGACATA
1 ATTTGTAAGACCTCCAAACATA
* * *
24823720 ATTTGTAAAACCTCCGAACATG
1 ATTTGTAAGACCTCCAAACATA
24823742 ATTTGTAA
1 ATTTGTAA
24823750 CATTTTCGAA
Statistics
Matches: 72, Mismatches: 22, Indels: 4
0.73 0.22 0.04
Matches are distributed among these distances:
21 1 0.01
22 70 0.97
23 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.31
Consensus pattern (22 bp):
ATTTGTAAGACCTCCAAACATA
Found at i:24824448 original size:44 final size:43
Alignment explanation
Indices: 24824396--24824630 Score: 172
Period size: 44 Copynumber: 5.4 Consensus size: 43
24824386 GTAAAAATAT
* *
24824396 TTTTATATTTTTCAAAAGTGATTGAACCTCTGTTAAAAGAAACC
1 TTTTATATTTTTCAAAAGTTATTGAACCTTTGTTAAAAG-AACC
* * * * * *
24824440 TTTTATATTTTTCAAAAGTTTTTGAGCTTTTGTTGAGATGAATC
1 TTTTATATTTTTCAAAAGTTATTGAACCTTTGTT-AAAAGAACC
* *
24824484 TTTTATATTTTTCAAAAGTTATT-AAGTCTTTATTAAAAGGAACC
1 TTTTATATTTTTCAAAAGTTATTGAA-CCTTTGTTAAAA-GAACC
* * * * ***
24824528 TTTAATA-TTTTCAAAAGTTATTAAACCTATGTTGAGAAGAGTT
1 TTTTATATTTTTCAAAAGTTATTGAACCTTTGTT-AAAAGAACC
** * *
24824571 TTTTATATTTTT-AAAAACTATT-AAGCCTTTGTTTAGAAGAACA
1 TTTTATATTTTTCAAAAGTTATTGAA-CCTTTG-TTAAAAGAACC
* *
24824614 TTTTATGTTGTTCAAAA
1 TTTTATATTTTTCAAAA
24824631 AGTATGAGTT
Statistics
Matches: 149, Mismatches: 33, Indels: 18
0.75 0.17 0.09
Matches are distributed among these distances:
42 2 0.01
43 60 0.40
44 84 0.56
45 3 0.02
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (43 bp):
TTTTATATTTTTCAAAAGTTATTGAACCTTTGTTAAAAGAACC
Found at i:24824628 original size:87 final size:85
Alignment explanation
Indices: 24824395--24824630 Score: 222
Period size: 87 Copynumber: 2.7 Consensus size: 85
24824385 AGTAAAAATA
* * *
24824395 TTTTTATATTTTTCAAAAGTGATTGAA-CCTCTGTTAAAAGAAACCTTTTATATTTTTCAAAAGT
1 TTTTTATATTTTTAAAAACT-ATT-AAGCCTTTGTTAAAAG-AACCTTTTATA-TTTTCAAAAGT
* * * * * *
24824459 TTTTGAGCTTTTGTTGAGATGAAT
62 TATTAAACCTATGTTGAGAAGAAT
* ** * * *
24824483 CTTTTATATTTTTCAAAAGTTATTAAGTCTTTATTAAAAGGAACCTTTAATATTTTCAAAAGTTA
1 TTTTTATATTTTT-AAAAACTATTAAGCCTTTGTTAAAA-GAACCTTTTATATTTTCAAAAGTTA
*
24824548 TTAAACCTATGTTGAGAAGAGT
64 TTAAACCTATGTTGAGAAGAAT
* * *
24824570 TTTTTATATTTTTAAAAACTATTAAGCCTTTGTTTAGAAGAACATTTTATGTTGTTCAAAA
1 TTTTTATATTTTTAAAAACTATTAAGCCTTTG-TTAAAAGAACCTTTTATATT-TTCAAAA
24824631 AGTATGAGTT
Statistics
Matches: 119, Mismatches: 24, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
86 26 0.22
87 54 0.45
88 34 0.29
89 5 0.04
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (85 bp):
TTTTTATATTTTTAAAAACTATTAAGCCTTTGTTAAAAGAACCTTTTATATTTTCAAAAGTTATT
AAACCTATGTTGAGAAGAAT
Found at i:24825338 original size:8 final size:8
Alignment explanation
Indices: 24825316--24825359 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
24825306 TTTATCATAA
*
24825316 TTGTCTAT
1 TTGTTTAT
*
24825324 TTATTTAT
1 TTGTTTAT
24825332 TTGTTTAT
1 TTGTTTAT
24825340 TTGTTTATT
1 TTGTTTA-T
*
24825349 TTATTTAT
1 TTGTTTAT
24825357 TTG
1 TTG
24825360 ACTATTTATG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
8 23 0.77
9 7 0.23
ACGTcount: A:0.16, C:0.02, G:0.09, T:0.73
Consensus pattern (8 bp):
TTGTTTAT
Found at i:24825899 original size:53 final size:53
Alignment explanation
Indices: 24825814--24825917 Score: 149
Period size: 53 Copynumber: 2.0 Consensus size: 53
24825804 AATAAGAAAA
* *
24825814 TATTTCTAAATTTAACTTAAATGATAGAAAATTTAGAAATTAAATTTGTAAGG
1 TATTTCTAAATTTAACTCAAATGATAGAAAATTTAGAAATAAAATTTGTAAGG
*
24825867 TATTTCTAAA-TTAAGCTCAAATGGTA-AGAAATTTAGAAATAAAATTTGTAA
1 TATTTCTAAATTTAA-CTCAAATGATAGA-AAATTTAGAAATAAAATTTGTAA
24825918 AAAGAAAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
52 5 0.11
53 41 0.89
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.38
Consensus pattern (53 bp):
TATTTCTAAATTTAACTCAAATGATAGAAAATTTAGAAATAAAATTTGTAAGG
Found at i:24827234 original size:18 final size:20
Alignment explanation
Indices: 24827198--24827234 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
24827188 TCCATAGAGC
*
24827198 TTAACTATTAATTTTGTGAT
1 TTAACTATTAATTTGGTGAT
24827218 TTAACTA-T-ATTTGGTGA
1 TTAACTATTAATTTGGTGA
24827235 AGCTCCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 1 0.06
20 7 0.44
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (20 bp):
TTAACTATTAATTTGGTGAT
Found at i:24827994 original size:26 final size:25
Alignment explanation
Indices: 24827940--24827995 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
24827930 TTAATGAACA
* *
24827940 AAATTGAATCAATAAAATTTAATTT
1 AAATTGAATCAATAAAATCTAATTC
* *
24827965 AAATTGAATTATATAAAATCTCATTC
1 AAATTGAATCA-ATAAAATCTAATTC
24827991 AAATT
1 AAATT
24827996 CAAATTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (25 bp):
AAATTGAATCAATAAAATCTAATTC
Found at i:24828281 original size:14 final size:14
Alignment explanation
Indices: 24828234--24828300 Score: 55
Period size: 15 Copynumber: 4.6 Consensus size: 14
24828224 AAAATTAACA
*
24828234 AATTTAATTCAAAT
1 AATTTAATTTAAAT
* *
24828248 AA-TAAATATAAATTT
1 AATTTAATTTAAA--T
*
24828263 AATTTAATTTAACT
1 AATTTAATTTAAAT
24828277 AATTTAATTTTAAAT
1 AATTTAA-TTTAAAT
*
24828292 AATTCAATT
1 AATTTAATT
24828301 CAAAATTAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
13 7 0.17
14 12 0.29
15 15 0.37
16 7 0.17
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.46
Consensus pattern (14 bp):
AATTTAATTTAAAT
Found at i:24838774 original size:20 final size:20
Alignment explanation
Indices: 24838747--24838786 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
24838737 TTTGTAAAAG
24838747 AAAAAAAAAGTTTGAATTTA
1 AAAAAAAAAGTTTGAATTTA
*
24838767 AAAGAAAAAATTTTGAATTT
1 AAA-AAAAAAGTTTGAATTT
24838787 TCTTATTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (20 bp):
AAAAAAAAAGTTTGAATTTA
Found at i:24842377 original size:16 final size:16
Alignment explanation
Indices: 24842356--24842395 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
24842346 CAGCAACCAA
* *
24842356 TTATTTTTATTTTTAG
1 TTATTTTTAATTTAAG
*
24842372 TTATTTTTAATTTAAT
1 TTATTTTTAATTTAAG
24842388 TTATTTTT
1 TTATTTTT
24842396 TCAGTCATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (16 bp):
TTATTTTTAATTTAAG
Found at i:24843869 original size:2 final size:2
Alignment explanation
Indices: 24843864--24843888 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
24843854 GGGTGTGTAA
24843864 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
24843889 GGGGAAGGAT
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:24845873 original size:8 final size:8
Alignment explanation
Indices: 24845852--24845881 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
24845842 TACCAAACAA
24845852 GCCCAAGT
1 GCCCAAGT
24845860 GCCCCAAGT
1 G-CCCAAGT
24845869 GCCCAAGT
1 GCCCAAGT
24845877 GCCCA
1 GCCCA
24845882 TCTTTGACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.23, C:0.43, G:0.23, T:0.10
Consensus pattern (8 bp):
GCCCAAGT
Found at i:24852024 original size:8 final size:9
Alignment explanation
Indices: 24851995--24852022 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
24851985 GAACAAGAAA
24851995 TTAATTTTT
1 TTAATTTTT
24852004 TTAATTTTT
1 TTAATTTTT
24852013 TTAATTTTT
1 TTAATTTTT
24852022 T
1 T
24852023 AAAAATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTAATTTTT
Found at i:24852520 original size:29 final size:29
Alignment explanation
Indices: 24852487--24852544 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
24852477 GAGTTCAAAT
* * *
24852487 TAAAAAT-TAAAGATTTATTTGAATAAAA
1 TAAAAATATAAAGACTAATTTAAATAAAA
24852515 TAAAAATATAAAGACTAATTTAAATAAAA
1 TAAAAATATAAAGACTAATTTAAATAAAA
24852544 T
1 T
24852545 GATAAAGTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAAAATATAAAGACTAATTTAAATAAAA
Found at i:24852539 original size:24 final size:24
Alignment explanation
Indices: 24852512--24852557 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
24852502 TATTTGAATA
24852512 AAATAAAAAT-ATAAAGACTAATTT
1 AAAT-AAAATGATAAAGACTAATTT
*
24852536 AAATAAAATGATAAAGTCTAAT
1 AAATAAAATGATAAAGACTAAT
24852558 GAGATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (24 bp):
AAATAAAATGATAAAGACTAATTT
Found at i:24853509 original size:13 final size:13
Alignment explanation
Indices: 24853491--24853518 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
24853481 TCAAATTTAT
24853491 AATAATCAAATAC
1 AATAATCAAATAC
24853504 AATAATCAAATAC
1 AATAATCAAATAC
24853517 AA
1 AA
24853519 AATTTAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.21
Consensus pattern (13 bp):
AATAATCAAATAC
Found at i:24855664 original size:2 final size:2
Alignment explanation
Indices: 24855657--24855685 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
24855647 AGGAGTTGTT
24855657 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
24855686 AAGGAGTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24860836 original size:17 final size:17
Alignment explanation
Indices: 24860811--24860850 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
24860801 TTTGAATGTT
24860811 AGAA-AAAAATAAATAAA
1 AGAAGAAAAAT-AATAAA
24860828 AGAAGAAAAATAATAAA
1 AGAAGAAAAATAATAAA
24860845 A-AAGAA
1 AGAAGAA
24860851 TTTTAACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.23
17 11 0.50
18 6 0.27
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (17 bp):
AGAAGAAAAATAATAAA
Found at i:24860847 original size:19 final size:17
Alignment explanation
Indices: 24860811--24860850 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
24860801 TTTGAATGTT
*
24860811 AGAAAAAAATAAATAAA
1 AGAAAAAAATAAAAAAA
24860828 AGAAGAAAAATAATAAAAA
1 AGAA-AAAAATAA-AAAAA
24860847 AGAA
1 AGAA
24860851 TTTTAACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 8 0.40
19 8 0.40
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (17 bp):
AGAAAAAAATAAAAAAA
Found at i:24861570 original size:2 final size:2
Alignment explanation
Indices: 24861563--24861593 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
24861553 TATTAACAAT
24861563 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
24861594 AGTGAACATC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24865427 original size:25 final size:23
Alignment explanation
Indices: 24865383--24865444 Score: 63
Period size: 26 Copynumber: 2.6 Consensus size: 23
24865373 TATTTTAGAG
* *
24865383 ATAAATAA-AAAAAGACATAAAT
1 ATAAATAATAAAAAGAAATAAAA
24865405 ATAAATAATAAAAAGTGAAATAAAA
1 ATAAATAATAAAAA--GAAATAAAA
*
24865430 ATTAAAAAATAAAAA
1 A-TAAATAATAAAAA
24865445 ATTATTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 8 0.24
23 5 0.15
25 8 0.24
26 12 0.36
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (23 bp):
ATAAATAATAAAAAGAAATAAAA
Found at i:24866207 original size:34 final size:35
Alignment explanation
Indices: 24866164--24866233 Score: 124
Period size: 34 Copynumber: 2.0 Consensus size: 35
24866154 GGACGTATCC
*
24866164 TGCACGCGATTTGAAAGGTCCAATC-TTAAAAACT
1 TGCACGCGATTAGAAAGGTCCAATCTTTAAAAACT
24866198 TGCACGCGATTAGAAAGGTCCAATCTTTAAAAACT
1 TGCACGCGATTAGAAAGGTCCAATCTTTAAAAACT
24866233 T
1 T
24866234 CTACTATATC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 24 0.71
35 10 0.29
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (35 bp):
TGCACGCGATTAGAAAGGTCCAATCTTTAAAAACT
Found at i:24874035 original size:21 final size:21
Alignment explanation
Indices: 24874009--24874053 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
24873999 ATAAAGTAAC
*
24874009 AATGATTAAAAGTTAAGAAA-A
1 AATGATTAAAAATTAA-AAATA
24874030 AATGATTAAAAATTAAAAATA
1 AATGATTAAAAATTAAAAATA
24874051 AAT
1 AAT
24874054 ATAAAGACGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (21 bp):
AATGATTAAAAATTAAAAATA
Found at i:24879179 original size:17 final size:17
Alignment explanation
Indices: 24879157--24879189 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
24879147 ACAACTTAAG
24879157 GTCATACTAATC-TCAAT
1 GTCATA-TAATCATCAAT
24879174 GTCATATAATCATCAA
1 GTCATATAATCATCAA
24879190 GCAATATACC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.33
Consensus pattern (17 bp):
GTCATATAATCATCAAT
Found at i:24881195 original size:14 final size:15
Alignment explanation
Indices: 24881176--24881209 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
24881166 CGCTTGTAGC
24881176 AAAAAATTTT-TTTA
1 AAAAAATTTTATTTA
24881190 AAAAAATTTTAATTTA
1 AAAAAATTTT-ATTTA
24881206 AAAA
1 AAAA
24881210 CTATGTAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
16 8 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAAAATTTTATTTA
Found at i:24891680 original size:25 final size:25
Alignment explanation
Indices: 24891652--24891699 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
24891642 ACATATTATT
*
24891652 TTTTTTTTATAAATGAAGTTATCAA
1 TTTTTTTTATAAATGAAATTATCAA
*
24891677 TTTTTTTTATAATTGAAATTATC
1 TTTTTTTTATAAATGAAATTATC
24891700 GAAATATGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.56
Consensus pattern (25 bp):
TTTTTTTTATAAATGAAATTATCAA
Found at i:24892290 original size:22 final size:24
Alignment explanation
Indices: 24892271--24892317 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
24892261 TAAAATTAAA
*
24892271 AATAATAACAAAAATCATTATAAC
1 AATAATAAAAAAAATCATTATAAC
* *
24892295 TATAATAAAAAAAAACTATTATA
1 AATAATAAAAAAAATC-ATTATA
24892318 TCGTCATTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.28
Consensus pattern (24 bp):
AATAATAAAAAAAATCATTATAAC
Found at i:24893353 original size:26 final size:26
Alignment explanation
Indices: 24893323--24893375 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
24893313 CTGTGTTTCT
24893323 AGCTACTCTTACTGCATCATTTTCCA
1 AGCTACTCTTACTGCATCATTTTCCA
24893349 AGCTACTCTTACTGCATCATTTTCCA
1 AGCTACTCTTACTGCATCATTTTCCA
24893375 A
1 A
24893376 CACTGTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.25, C:0.30, G:0.08, T:0.38
Consensus pattern (26 bp):
AGCTACTCTTACTGCATCATTTTCCA
Found at i:24895338 original size:24 final size:24
Alignment explanation
Indices: 24895304--24895352 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
24895294 AAGTGTAATT
*
24895304 GTGCTGCCATGACTGCTTCTTCCA
1 GTGCTGACATGACTGCTTCTTCCA
*
24895328 GTGCTGACATGACTGTTTCTTCCA
1 GTGCTGACATGACTGCTTCTTCCA
24895352 G
1 G
24895353 ATGAGTCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.14, C:0.29, G:0.22, T:0.35
Consensus pattern (24 bp):
GTGCTGACATGACTGCTTCTTCCA
Found at i:24901109 original size:26 final size:24
Alignment explanation
Indices: 24901059--24901130 Score: 81
Period size: 25 Copynumber: 2.9 Consensus size: 24
24901049 GGAAGTAAAA
* * *
24901059 TTTTTAGCCCTCATTGCTGACTTC
1 TTTTTAGCCTTCATTGCCGAATTC
24901083 TATTTTAGACCTTCATTGCCGAATTC
1 T-TTTTAG-CCTTCATTGCCGAATTC
*
24901109 TGTTTAGGCCTTCATTGCCGAA
1 TTTTTA-GCCTTCATTGCCGAA
24901131 CATTTTCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
24 1 0.02
25 24 0.59
26 16 0.39
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.42
Consensus pattern (24 bp):
TTTTTAGCCTTCATTGCCGAATTC
Found at i:24904798 original size:22 final size:22
Alignment explanation
Indices: 24904772--24904815 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
24904762 TGTATATTTA
*
24904772 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
24904794 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
24904816 GACAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:24907261 original size:20 final size:20
Alignment explanation
Indices: 24907225--24907262 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
24907215 CTAGATAAAT
*
24907225 AAAAGACTAAAATATAAAAA
1 AAAAGACTAAAAAATAAAAA
24907245 AAAAGA-TAAATAAATAAA
1 AAAAGACTAAA-AAATAAA
24907263 TAATACAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (20 bp):
AAAAGACTAAAAAATAAAAA
Found at i:24914055 original size:2 final size:2
Alignment explanation
Indices: 24914048--24914083 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
24914038 AACATTTTGC
*
24914048 AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24914084 TTGTAATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:24915383 original size:15 final size:14
Alignment explanation
Indices: 24915358--24915478 Score: 58
Period size: 15 Copynumber: 8.7 Consensus size: 14
24915348 GTTGTATGAG
24915358 ATATGATATAATTA
1 ATATGATATAATTA
24915372 ATATGTATATAATTA
1 ATATG-ATATAATTA
*
24915387 AT-T-AT-T--TAA
1 ATATGATATAATTA
*
24915396 ATATGATATAAATA
1 ATATGATATAATTA
* *
24915410 ATACGAATATATATAA
1 ATATG-ATATA-ATTA
* *
24915426 ATA-AATATGATTA
1 ATATGATATAATTA
*
24915439 ATACGAATATATATTA
1 ATATG-ATATA-ATTA
*
24915455 ATA-GACATAATTA
1 ATATGATATAATTA
*
24915468 ACATGAATATA
1 ATATG-ATATA
24915479 TATAAAAATA
Statistics
Matches: 80, Mismatches: 14, Indels: 25
0.67 0.12 0.21
Matches are distributed among these distances:
9 4 0.05
10 1 0.01
11 3 0.04
12 3 0.04
13 12 0.15
14 20 0.25
15 25 0.31
16 12 0.15
ACGTcount: A:0.52, C:0.03, G:0.07, T:0.38
Consensus pattern (14 bp):
ATATGATATAATTA
Found at i:24915440 original size:29 final size:28
Alignment explanation
Indices: 24915408--24915495 Score: 106
Period size: 29 Copynumber: 3.1 Consensus size: 28
24915398 ATGATATAAA
24915408 TAATACGAATATATATAAATAAATATGAT
1 TAATACGAATATATAT-AATAAATATGAT
* * *
24915437 TAATACGAATATATATTAATAGACATAAT
1 TAATACGAATATATA-TAATAAATATGAT
* *
24915466 TAACATGAATATATATAA-AAATATGAT
1 TAATACGAATATATATAATAAATATGAT
24915493 TAA
1 TAA
24915496 AATAATAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
27 9 0.18
28 3 0.06
29 37 0.74
30 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.34
Consensus pattern (28 bp):
TAATACGAATATATATAATAAATATGAT
Found at i:24915752 original size:11 final size:11
Alignment explanation
Indices: 24915730--24915759 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
24915720 TATATGACTA
24915730 ATATTAATATTT
1 ATATT-ATATTT
24915742 ATATTATATTT
1 ATATTATATTT
24915753 ATATTAT
1 ATATTAT
24915760 TAATATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
ATATTATATTT
Found at i:24916264 original size:21 final size:21
Alignment explanation
Indices: 24916240--24916284 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
24916230 GTAATAAAAT
*
24916240 ATTAAAATTTTAATTT-TGATA
1 ATTAAAATTTAAATTTAT-ATA
*
24916261 ATTAAAGTTTAAATTTATATA
1 ATTAAAATTTAAATTTATATA
24916282 ATT
1 ATT
24916285 CTAAATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (21 bp):
ATTAAAATTTAAATTTATATA
Found at i:24916492 original size:30 final size:30
Alignment explanation
Indices: 24916456--24916516 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
24916446 GACTTAGACT
24916456 TATACATAAGTT-GAATGGAATCAAATTTGA
1 TATACATAAGTTCG-ATGGAATCAAATTTGA
* * *
24916486 TATACATAGGTTCGATGGATTTAAATTTGA
1 TATACATAAGTTCGATGGAATCAAATTTGA
24916516 T
1 T
24916517 TAATTTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (30 bp):
TATACATAAGTTCGATGGAATCAAATTTGA
Found at i:24916826 original size:23 final size:23
Alignment explanation
Indices: 24916800--24916843 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
24916790 ACTAAAATTC
24916800 AATTAAAAATT-ATTAAATATTAT
1 AATTAAAAATTGATT-AATATTAT
* *
24916823 AATTTAAATTTGATTAATATT
1 AATTAAAAATTGATTAATATT
24916844 TATTTAATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.83
24 3 0.17
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
AATTAAAAATTGATTAATATTAT
Found at i:24931753 original size:2 final size:2
Alignment explanation
Indices: 24931746--24931780 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
24931736 CCTTTTAGTT
*
24931746 TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
24931781 CCTTTTCTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:24934364 original size:15 final size:13
Alignment explanation
Indices: 24934333--24934389 Score: 59
Period size: 12 Copynumber: 4.5 Consensus size: 13
24934323 TAAAAAATTA
24934333 CTAATAATAATA-
1 CTAATAATAATAT
*
24934345 ATAATAATAATATGT
1 CTAATAATAATA--T
24934360 CTAATAAT-ATAT
1 CTAATAATAATAT
24934372 CTAATAATAA-AT
1 CTAATAATAATAT
24934384 -TAATAA
1 CTAATAA
24934390 AATCATTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
11 6 0.15
12 22 0.56
13 1 0.03
14 3 0.08
15 7 0.18
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (13 bp):
CTAATAATAATAT
Found at i:24935388 original size:25 final size:25
Alignment explanation
Indices: 24935334--24935395 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 25
24935324 AAGTATAGTA
* *
24935334 ATTAAATCATTATATTTGATAAATT
1 ATTAAATAATTATATGTGATAAATT
* *
24935359 TTTAAATAATTTTATGTGAT-AATAT
1 ATTAAATAATTATATGTGATAAAT-T
*
24935384 ATTAAATTATTA
1 ATTAAATAATTA
24935396 AAAATAATTG
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
24 3 0.10
25 26 0.90
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (25 bp):
ATTAAATAATTATATGTGATAAATT
Found at i:24935599 original size:38 final size:38
Alignment explanation
Indices: 24935535--24935624 Score: 135
Period size: 38 Copynumber: 2.4 Consensus size: 38
24935525 TTATGGTTAA
24935535 AATCCAATCCATTTATCTATTCCTAAAAGGAAAGGAGT
1 AATCCAATCCATTTATCTATTCCTAAAAGGAAAGGAGT
* * * * *
24935573 AATCTAATACATTTATTTATTTCTAAAAGGAAGGGAGT
1 AATCCAATCCATTTATCTATTCCTAAAAGGAAAGGAGT
24935611 AATCCAATCCATTT
1 AATCCAATCCATTT
24935625 TGTACTGTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (38 bp):
AATCCAATCCATTTATCTATTCCTAAAAGGAAAGGAGT
Found at i:24938322 original size:82 final size:83
Alignment explanation
Indices: 24938183--24938447 Score: 343
Period size: 82 Copynumber: 3.0 Consensus size: 83
24938173 AGAAAACCAA
24938183 TGAAAACAAAGAAGAAAAAAAAACTGTGTTGAAAGTTCACATAAAAGATGTGCTATTAGGATTTT
1 TGAAAACAAAGAAGAAAAAAAAACTGTGTTGAAAGTTCACATAAAAGATGTGCTATTAGGATTTT
*
24938248 CAATTATTTGAAATGTTT
66 CAATTATTTGAAACGTTT
*
24938266 TGAAAACAAAGAAGAAAAAAAAA-TGTGTTGAAAGTTCACATAAAAGATGTGTTATTAGGATTTT
1 TGAAAACAAAGAAGAAAAAAAAACTGTGTTGAAAGTTCACATAAAAGATGTGCTATTAGGATTTT
24938330 CAATTATTTGAAACGTTTT
66 CAATTATTTGAAACG-TTT
* *
24938349 GAAGGACCAATGAAAACAAAGAAGAAAAAAAAAATAAATTGTGTTGAAAGTTCACATAAAGGATG
1 ----------TGAAAACAAAGAAG-AAAAAAAA----ACTGTGTTGAAAGTTCACATAAAAGATG
24938414 TGCTATTAGGATTTTCAATTATTTGAAACGTTT
51 TGCTATTAGGATTTTCAATTATTTGAAACGTTT
24938447 T
1 T
24938448 AAAGGTTAGG
Statistics
Matches: 161, Mismatches: 4, Indels: 29
0.83 0.02 0.15
Matches are distributed among these distances:
82 54 0.34
83 26 0.16
88 1 0.01
93 14 0.09
94 8 0.05
98 4 0.02
99 54 0.34
ACGTcount: A:0.45, C:0.07, G:0.17, T:0.31
Consensus pattern (83 bp):
TGAAAACAAAGAAGAAAAAAAAACTGTGTTGAAAGTTCACATAAAAGATGTGCTATTAGGATTTT
CAATTATTTGAAACGTTT
Found at i:24938371 original size:93 final size:96
Alignment explanation
Indices: 24938266--24938452 Score: 299
Period size: 99 Copynumber: 1.9 Consensus size: 96
24938256 TGAAATGTTT
*
24938266 TGAAAACAAAGAAG-AAAAAA-AAA-TGTGTTGAAAGTTCACATAAAAGATGTGTTATTAGGATT
1 TGAAAACAAAGAAGAAAAAAATAAATTGTGTTGAAAGTTCACATAAAAGATGTGCTATTAGGATT
*
24938328 TTCAATTATTTGAAACGTTTTGAAGGACCAA
66 TTCAATTATTTGAAACGTTTTAAAGGACCAA
*
24938359 TGAAAACAAAGAAGAAAAAAAAAATAAATTGTGTTGAAAGTTCACATAAAGGATGTGCTATTAGG
1 TGAAAACAAAGAAG---AAAAAAATAAATTGTGTTGAAAGTTCACATAAAAGATGTGCTATTAGG
24938424 ATTTTCAATTATTTGAAACGTTTTAAAGG
63 ATTTTCAATTATTTGAAACGTTTTAAAGG
24938453 TTAGGGAAAT
Statistics
Matches: 85, Mismatches: 3, Indels: 6
0.90 0.03 0.06
Matches are distributed among these distances:
93 14 0.16
97 6 0.07
98 3 0.04
99 62 0.73
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.29
Consensus pattern (96 bp):
TGAAAACAAAGAAGAAAAAAATAAATTGTGTTGAAAGTTCACATAAAAGATGTGCTATTAGGATT
TTCAATTATTTGAAACGTTTTAAAGGACCAA
Found at i:24940391 original size:23 final size:24
Alignment explanation
Indices: 24940365--24940413 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
24940355 AATTTGACAA
*
24940365 ATTAAATCAATCAATA-TATAATT
1 ATTAAATCAATAAATACTATAATT
*
24940388 ATTAAATTAATAAATACTATAATT
1 ATTAAATCAATAAATACTATAATT
24940412 AT
1 AT
24940414 AATTATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (24 bp):
ATTAAATCAATAAATACTATAATT
Found at i:24941894 original size:19 final size:20
Alignment explanation
Indices: 24941859--24941898 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
24941849 TAATTTGAAA
24941859 AATTAATTAAATCAATATAT
1 AATTAATTAAATCAATATAT
*
24941879 AATTAA-TAAATTAATATAT
1 AATTAATTAAATCAATATAT
24941898 A
1 A
24941899 CTATAATTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (20 bp):
AATTAATTAAATCAATATAT
Found at i:24943205 original size:12 final size:12
Alignment explanation
Indices: 24943181--24943226 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
24943171 ACTTTATTTC
*
24943181 AATTTTATCTCT
1 AATTTTCTCTCT
*
24943193 AAATTTCTCTCT
1 AATTTTCTCTCT
24943205 AATTTTCTCTCT
1 AATTTTCTCTCT
24943217 AATTTTCTCT
1 AATTTTCTCT
24943227 TTGCTTCGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.57
Consensus pattern (12 bp):
AATTTTCTCTCT
Found at i:24944684 original size:2 final size:2
Alignment explanation
Indices: 24944677--24944709 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
24944667 CTCACTTTTG
*
24944677 AT AT AT AT AA AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24944710 GAAGTTGTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24949239 original size:37 final size:37
Alignment explanation
Indices: 24949189--24949263 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
24949179 CTAATCACTA
*
24949189 GCCTTGTCCACAAGGTCTCTAGAAATTTCAAATTGGT
1 GCCTTGTCCACAAGGTATCTAGAAATTTCAAATTGGT
* * *
24949226 GCCTTTTCCACAAGTTATCTAGAAGTTTCAAATTGGT
1 GCCTTGTCCACAAGGTATCTAGAAATTTCAAATTGGT
24949263 G
1 G
24949264 TGAACCAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (37 bp):
GCCTTGTCCACAAGGTATCTAGAAATTTCAAATTGGT
Found at i:24967720 original size:4 final size:4
Alignment explanation
Indices: 24967711--24967759 Score: 53
Period size: 4 Copynumber: 12.2 Consensus size: 4
24967701 TACATGTGTG
* * * * *
24967711 TATA TATA TATA TATA TATA TATG TATG TATG TATG TATG TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
24967759 T
1 T
24967760 TTCTCGATCG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (4 bp):
TATA
Found at i:24972143 original size:24 final size:24
Alignment explanation
Indices: 24972087--24972143 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
24972077 TCACTTAATA
*
24972087 CACTTTTAATTCTAATTAAAAATT
1 CACTTTTAATTATAATTAAAAATT
* *** *
24972111 AAAAATTAATTATATTTAAAAATT
1 CACTTTTAATTATAATTAAAAATT
24972135 CACTTTTAA
1 CACTTTTAA
24972144 AGCACTATAT
Statistics
Matches: 23, Mismatches: 10, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (24 bp):
CACTTTTAATTATAATTAAAAATT
Found at i:24972945 original size:28 final size:28
Alignment explanation
Indices: 24972880--24972945 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 28
24972870 TAAAAATCTC
24972880 TAAATTATTTTGATTTACAATTATAATT
1 TAAATTATTTTGATTTACAATTATAATT
* *
24972908 TGAATAATTTTGATATTTA-AA-TA-AATT
1 TAAATTATTTTG--ATTTACAATTATAATT
24972935 TAAAATTATTT
1 T-AAATTATTT
24972946 AATTTATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
27 5 0.16
28 19 0.61
29 2 0.06
30 5 0.16
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (28 bp):
TAAATTATTTTGATTTACAATTATAATT
Found at i:24973026 original size:12 final size:12
Alignment explanation
Indices: 24973011--24973061 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
24973001 AATTATTCAC
*
24973011 ATAAATATTTAT
1 ATAAATATATAT
*
24973023 ATAAAT-TGTAAT
1 ATAAATATAT-AT
*
24973035 ATACATATATAT
1 ATAAATATATAT
*
24973047 ATATATATATAT
1 ATAAATATATAT
24973059 ATA
1 ATA
24973062 GGTGTCAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 2 0.06
12 29 0.88
13 2 0.06
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (12 bp):
ATAAATATATAT
Found at i:24975400 original size:23 final size:23
Alignment explanation
Indices: 24975370--24975422 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
24975360 TTTATTAAAA
*
24975370 AATTTTTTAATTAAAATTATAAT
1 AATTTTTTAATCAAAATTATAAT
**
24975393 AATTTTTTAATCGTAATTATAAT
1 AATTTTTTAATCAAAATTATAAT
24975416 AATTTTT
1 AATTTTT
24975423 ATTACATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
AATTTTTTAATCAAAATTATAAT
Found at i:24975578 original size:45 final size:45
Alignment explanation
Indices: 24975502--24975589 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 45
24975492 ACTTAGTGAG
*
24975502 TTCATTTTAATTTTTTTTTAAAAAATAATATTCAAGAAATTTAGGA
1 TTCATTTTAATTTTTTTTT-AAAAATAATATTCAAAAAATTTAGGA
24975548 TTCATTTTAAGTTTTTTTTT-AAAATAATATTCAAAAAATTTA
1 TTCATTTTAA-TTTTTTTTTAAAAATAATATTCAAAAAATTTA
24975590 AATTCTAAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
45 21 0.52
46 10 0.25
47 9 0.22
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (45 bp):
TTCATTTTAATTTTTTTTTAAAAATAATATTCAAAAAATTTAGGA
Found at i:24980184 original size:2 final size:2
Alignment explanation
Indices: 24980177--24980209 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
24980167 GATATCAATG
24980177 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24980210 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24980214 original size:2 final size:2
Alignment explanation
Indices: 24980209--24980233 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
24980199 ATATATATAT
24980209 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
24980234 CAGCACAAGA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:24986138 original size:32 final size:29
Alignment explanation
Indices: 24986077--24986145 Score: 84
Period size: 32 Copynumber: 2.3 Consensus size: 29
24986067 TTTAATGTAT
* *
24986077 TATTTAAATTTTAAAAATTTATAATATGA
1 TATTTAAATTATAAAAATTAATAATATGA
24986106 TATTTAAATTATAAATACATTAAATAATATGA
1 TATTTAAATTATAAA-A-ATT-AATAATATGA
*
24986138 TACTTAAA
1 TATTTAAA
24986146 AAATTATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 14 0.41
30 1 0.03
31 3 0.09
32 16 0.47
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (29 bp):
TATTTAAATTATAAAAATTAATAATATGA
Found at i:24986144 original size:16 final size:16
Alignment explanation
Indices: 24986097--24986145 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
24986087 TTAAAAATTT
*
24986097 ATAATATGATATTTAA
1 ATAATATGATACTTAA
* *
24986113 ATTATA-AATACATTAA
1 ATAATATGATAC-TTAA
24986129 ATAATATGATACTTAA
1 ATAATATGATACTTAA
24986145 A
1 A
24986146 AAATTATTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
15 3 0.12
16 19 0.73
17 4 0.15
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (16 bp):
ATAATATGATACTTAA
Found at i:24987335 original size:25 final size:26
Alignment explanation
Indices: 24987285--24987342 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
24987275 TAAGGTGTTT
*
24987285 TTTATATAAAAATATCTTAAATAATCA
1 TTTA-ATAAAAATATATTAAATAATCA
*
24987312 TTTAATAAAAATATATTATA-AATCA
1 TTTAATAAAAATATATTAAATAATCA
24987337 TTTAAT
1 TTTAAT
24987343 TTTTTATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 11 0.38
26 14 0.48
27 4 0.14
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (26 bp):
TTTAATAAAAATATATTAAATAATCA
Found at i:24993148 original size:34 final size:35
Alignment explanation
Indices: 24993100--24993180 Score: 101
Period size: 34 Copynumber: 2.3 Consensus size: 35
24993090 GGGAATCTAT
* *
24993100 TTTTTAAAAATTATAATATATTTTCGAAAATCAA-
1 TTTTTGAAATTTATAATATATTTTCGAAAATCAAG
* * *
24993134 TTTTTGAAATTTATATTATATTTTTGAAAATGAAG
1 TTTTTGAAATTTATAATATATTTTCGAAAATCAAG
24993169 TCTTTTGAAATT
1 T-TTTTGAAATT
24993181 AAATTTTCGA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 29 0.73
35 1 0.03
36 10 0.25
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (35 bp):
TTTTTGAAATTTATAATATATTTTCGAAAATCAAG
Found at i:24996096 original size:13 final size:14
Alignment explanation
Indices: 24996071--24996106 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
24996061 TAACTTGTCC
*
24996071 AAATAATAACAAAA
1 AAATAAAAACAAAA
24996085 AAA-AAAAACAAAA
1 AAATAAAAACAAAA
24996098 AAATAAAAA
1 AAATAAAAA
24996107 AGAAAGGGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.86, C:0.06, G:0.00, T:0.08
Consensus pattern (14 bp):
AAATAAAAACAAAA
Done.