Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, 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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 150 of 190
Found at i:24283029 original size:7 final size:8
Alignment explanation
Indices: 24283010--24283067 Score: 59
Period size: 7 Copynumber: 7.4 Consensus size: 8
24283000 TAACAATACA
24283010 AAAATAAAT
1 AAAAT-AAT
24283019 AAAAT-AT
1 AAAATAAT
24283026 AAAATAAT
1 AAAATAAT
24283034 AATAATAAT
1 AA-AATAAT
24283043 -AAATAA-
1 AAAATAAT
**
24283049 ATTATAAT
1 AAAATAAT
24283057 AAAATAAT
1 AAAATAAT
24283065 AAA
1 AAA
24283068 TATATAACTA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
7 16 0.39
8 14 0.34
9 11 0.27
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (8 bp):
AAAATAAT
Found at i:24283085 original size:28 final size:28
Alignment explanation
Indices: 24282975--24283090 Score: 89
Period size: 28 Copynumber: 4.1 Consensus size: 28
24282965 TAAAAAAAAT
* * *
24282975 AATAACAAATATATAATTAGATAAATAAC
1 AATAATAAATAAATAA-TATATAAATAAC
* * *
24283004 AATACAAAAATAAATAAAATATAAAATAAT
1 AATA-ATAAATAAATAATATAT-AAATAAC
24283034 AATAAT-AATAAATAA-AT-TATAATAA-
1 AATAATAAATAAATAATATATA-AATAAC
*
24283059 AATAATAAATATATAACTATATAAATAA-
1 AATAATAAATAAATAA-TATATAAATAAC
24283087 AATA
1 AATA
24283091 CATATAAATA
Statistics
Matches: 73, Mismatches: 7, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
25 7 0.10
26 14 0.19
27 2 0.03
28 20 0.27
29 10 0.14
30 20 0.27
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.28
Consensus pattern (28 bp):
AATAATAAATAAATAATATATAAATAAC
Found at i:24283125 original size:4 final size:4
Alignment explanation
Indices: 24283118--24283184 Score: 57
Period size: 4 Copynumber: 16.8 Consensus size: 4
24283108 AAAGAAAAGA
* * * * *
24283118 AAAT AAAT AAAT AAAT AAAT AAAT ATAT ACAT ATAT TAAT ACAT AGTAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A--AAT
24283168 -AAT AAAT AAAT -AAT AAA
1 AAAT AAAT AAAT AAAT AAA
24283185 ATACATAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
3 6 0.12
4 43 0.84
6 2 0.04
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (4 bp):
AAAT
Found at i:24283507 original size:41 final size:41
Alignment explanation
Indices: 24283413--24283703 Score: 401
Period size: 41 Copynumber: 7.0 Consensus size: 41
24283403 TTTAACCAAA
* * * *
24283413 GCTCCTCTAAACAGAGGCTCAACTACTTTGAGAAACATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-TGAAA-ATAAATT
* *
24283456 GCTCCTCTAAACAGAGGCACCATGACTTTTGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAATAAATT
* *
24283497 GCTCCTCTAAACAGAGGTACCACGACTTTTGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAATAAATT
24283538 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTTG-AAAATAAATT
24283579 GCTCCTCTAAACAGAGGCACCACACGAC-TTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCA-C-CACGACTTTTG-AAAATAAATT
*
24283622 GCTCCTCTAAACAGAGGCACCACGAC-TTTCAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAA-TAAATT
24283663 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTTG-AAAATAAATT
24283704 ACTTCTTGAC
Statistics
Matches: 231, Mismatches: 12, Indels: 12
0.91 0.05 0.05
Matches are distributed among these distances:
40 8 0.03
41 148 0.64
42 10 0.04
43 65 0.28
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAATAAATT
Found at i:24283635 original size:125 final size:123
Alignment explanation
Indices: 24283413--24283703 Score: 458
Period size: 125 Copynumber: 2.3 Consensus size: 123
24283403 TTTAACCAAA
* * *
24283413 GCTCCTCTAAACAGAGGCTCAACTACTTTGAGAAACATAAATTGCTCCTCTAAACAGAGGCACCA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAA-ATAAATTGCTCCTCTAAACAGAGGCACCA
* * * **
24283478 TGACTTTTGAAAGTAAATTGCTCCTCTAAACAGAGGTACCACGACTTTTGAAAGTAAATT
64 CGACTTTTGAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTCAAAAGTAAATT
24283538 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCA-C-CA
24283603 CGAC-TTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTCAAAAGTAAATT
64 CGACTTTTG-AAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTCAAAAGTAAATT
24283663 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATT
24283704 ACTTCTTGAC
Statistics
Matches: 155, Mismatches: 8, Indels: 6
0.92 0.05 0.04
Matches are distributed among these distances:
123 26 0.17
124 8 0.05
125 121 0.78
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (123 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACG
ACTTTTGAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTCAAAAGTAAATT
Found at i:24283641 original size:84 final size:82
Alignment explanation
Indices: 24283413--24283703 Score: 442
Period size: 84 Copynumber: 3.5 Consensus size: 82
24283403 TTTAACCAAA
* * *
24283413 GCTCCTCTAAACAGAGGCTCAACTACTTTGAGAAACATAAATTGCTCCTCTAAACAGAGGCACCA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAA-ATAAATTGCTCCTCTAAACAGAGGCACCA
*
24283478 TGACTTTTG-AAAGTAAATT
64 CGAC-TTTGAAAAGTAAATT
* *
24283497 GCTCCTCTAAACAGAGGTACCACGACTTTTG-AAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCAC
*
24283561 GACTTTGAAAAATAAATT
65 GACTTTGAAAAGTAAATT
24283579 GCTCCTCTAAACAGAGGCACCACACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCA
1 GCTCCTCTAAACAGAGGCA-C-CACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCA
*
24283644 CGACTTTCAAAAGTAAATT
64 CGACTTTGAAAAGTAAATT
24283663 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATT
24283704 ACTTCTTGAC
Statistics
Matches: 191, Mismatches: 11, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
81 4 0.02
82 79 0.41
83 9 0.05
84 95 0.50
85 4 0.02
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (82 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACG
ACTTTGAAAAGTAAATT
Found at i:24284988 original size:9 final size:9
Alignment explanation
Indices: 24284976--24285006 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
24284966 CATTTTTTCA
24284976 TTTCTTTTT
1 TTTCTTTTT
24284985 TTTCTTTTTT
1 TTTC-TTTTT
24284995 TTTCTTTTT
1 TTTCTTTTT
24285004 TTT
1 TTT
24285007 TCACCATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:24284992 original size:19 final size:19
Alignment explanation
Indices: 24284970--24285006 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
24284960 TTTTTTCATT
24284970 TTTTCATTTCTTTTTTTTC
1 TTTTCATTTCTTTTTTTTC
**
24284989 TTTTTTTTTCTTTTTTTT
1 TTTTCATTTCTTTTTTTT
24285007 TCACCATTTT
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:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (19 bp):
TTTTCATTTCTTTTTTTTC
Found at i:24285003 original size:10 final size:10
Alignment explanation
Indices: 24284960--24285008 Score: 64
Period size: 10 Copynumber: 4.7 Consensus size: 10
24284950 TTTGAATCTC
24284960 TTTTTTCATTT
1 TTTTTTC-TTT
24284971 TTTCATTTC-TT
1 TTT--TTTCTTT
24284982 TTTTTTCTTT
1 TTTTTTCTTT
24284992 TTTTTTCTTT
1 TTTTTTCTTT
24285002 TTTTTTC
1 TTTTTTC
24285009 ACCATTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.11
10 19 0.54
11 8 0.23
13 4 0.11
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:24285024 original size:10 final size:10
Alignment explanation
Indices: 24284960--24285027 Score: 57
Period size: 10 Copynumber: 6.3 Consensus size: 10
24284950 TTTGAATCTC
24284960 TTTTTTCATTT
1 TTTTTTCA-TT
24284971 TTTCATTTC-TT
1 TTT--TTTCATT
*
24284982 TTTTTTCTTT
1 TTTTTTCATT
*
24284992 TTTTTTCTTT
1 TTTTTTCATT
24285002 TTTTTTCACCATT
1 TTTTTT---CATT
24285015 TTTTTTCATT
1 TTTTTTCATT
24285025 TTT
1 TTT
24285028 CATCCATTGT
Statistics
Matches: 50, Mismatches: 1, Indels: 13
0.78 0.02 0.20
Matches are distributed among these distances:
9 4 0.08
10 25 0.50
11 8 0.16
13 13 0.26
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTTCATT
Found at i:24289064 original size:62 final size:61
Alignment explanation
Indices: 24288932--24289156 Score: 271
Period size: 61 Copynumber: 3.7 Consensus size: 61
24288922 TCTTGCGTAG
* **
24288932 GGAAAATTGATACTTTCAACTTTTCC-CTAAAAA---TATTTTTCAAAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTC-AAAAATTTTTTTTTTTGAAAA-TTTGATTTTCAA
*
24288991 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTTTTGAAAATTT-ATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAA--TTTTTTTTTTTGAAAATTTGATTTTCAA
* * * * *
24289053 GGAAAATTGATACTTTCAACTTTTTCTCAAAAATATATTTTTTTGAAACTTTGATTTCCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTTTTTGAAAATTTGATTTTCAA
* **
24289114 AGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTTTT
24289157 GCTTTTTATT
Statistics
Matches: 144, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
59 31 0.22
60 17 0.12
61 44 0.31
62 39 0.27
63 3 0.02
64 10 0.07
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (61 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTTTTTGAAAATTTGATTTTCAA
Found at i:24289127 original size:61 final size:61
Alignment explanation
Indices: 24288932--24289147 Score: 287
Period size: 62 Copynumber: 3.6 Consensus size: 61
24288922 TCTTGCGTAG
* **
24288932 GGAAAATTGATACTTTCAACTTTTCC-CTAAAA-ATA-TTTTTCAAAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATATTTTTTTGAAAA-TTTGATTTTCAA
* * *
24288991 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTTTTGAAAATTT-ATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAA--TATATTTTTTTGAAAATTTGATTTTCAA
* * *
24289053 GGAAAATTGATACTTTCAACTTTTTCTCAAAAATATATTTTTTTGAAACTTTGATTTCCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATATTTTTTTGAAAATTTGATTTTCAA
*
24289114 AGAAAATTGATACTTTCAACTTTTCCTCAAAAAT
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAT
24289148 CCTTTTTTTG
Statistics
Matches: 137, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
59 26 0.19
60 21 0.15
61 38 0.28
62 39 0.28
63 4 0.03
64 9 0.07
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (61 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATATTTTTTTGAAAATTTGATTTTCAA
Found at i:24289154 original size:123 final size:121
Alignment explanation
Indices: 24288932--24289156 Score: 351
Period size: 123 Copynumber: 1.8 Consensus size: 121
24288922 TCTTGCGTAG
* * * *
24288932 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTCAAAAATTTTGATTTTCAAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCCAAAAAATATTTTTCAAAAACTTTGATTTCCAAAGAAAA
*
24288997 TTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTTTTGAAAATTTATTTTTAA
66 TTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTTTTTGAAAATTTATTTTTAA
* ***
24289053 GGAAAATTGATACTTTCAACTTTTTCTCAAAAATATATTTTTTTGAAACTTTGATTTCCAAAGAA
1 GGAAAATTGATACTTTCAAC-TTTTCCCAAAAA-ATATTTTTCAAAAACTTTGATTTCCAAAGAA
24289118 AATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTT
64 AATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTT
24289157 GCTTTTTATT
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
121 20 0.22
122 10 0.11
123 63 0.68
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (121 bp):
GGAAAATTGATACTTTCAACTTTTCCCAAAAAATATTTTTCAAAAACTTTGATTTCCAAAGAAAA
TTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTTTTTGAAAATTTATTTTTAA
Found at i:24289196 original size:22 final size:22
Alignment explanation
Indices: 24289171--24289212 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
24289161 TTTATTTAAA
24289171 GAAAATAGAATAAA-ATAAAAGT
1 GAAAATA-AATAAAGATAAAAGT
24289193 GAAAATAAATAAAGATAAAA
1 GAAAATAAATAAAGATAAAA
24289213 AATAAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.17
Consensus pattern (22 bp):
GAAAATAAATAAAGATAAAAGT
Found at i:24289214 original size:17 final size:16
Alignment explanation
Indices: 24289194--24289311 Score: 55
Period size: 17 Copynumber: 7.2 Consensus size: 16
24289184 AATAAAAGTG
24289194 AAAATAAATAAAGATAA
1 AAAATAAATAAA-ATAA
*
24289211 AAAATAAAGAAAAGTAA
1 AAAATAAATAAAA-TAA
24289228 AACAA-AAATAAAAATAA
1 AA-AATAAAT-AAAATAA
* *
24289245 GATAA-AGATAAAA-AA
1 -AAAATAAATAAAATAA
* * **
24289260 ATATTAAATGAATCTAA
1 AAAATAAAT-AAAATAA
**
24289277 CCTAATAAATAAAATAA
1 -AAAATAAATAAAATAA
*
24289294 TAAATAAAT-AAATAA
1 AAAATAAATAAAATAA
24289309 AAA
1 AAA
24289312 TTCTGAAAAA
Statistics
Matches: 78, Mismatches: 15, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
14 3 0.04
15 13 0.17
16 14 0.18
17 34 0.44
18 14 0.18
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.19
Consensus pattern (16 bp):
AAAATAAATAAAATAA
Found at i:24289257 original size:22 final size:21
Alignment explanation
Indices: 24289172--24289257 Score: 54
Period size: 21 Copynumber: 3.9 Consensus size: 21
24289162 TTATTTAAAG
*
24289172 AAAAT-AGAATAAAATAAAAGTG
1 AAAATAAG-ATAAAATAAAA-TA
24289194 AAAATAA-ATAAAGATAAAAAATA
1 AAAATAAGATAAA-AT--AAAATA
*
24289217 AAGAA-AAG-TAAAACAAAAATA
1 AA-AATAAGATAAAA-TAAAATA
24289238 AAAATAAGATAAAGATAAAA
1 AAAATAAGATAAA-ATAAAA
24289258 AAATATTAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 20
0.69 0.04 0.27
Matches are distributed among these distances:
20 2 0.04
21 16 0.31
22 16 0.31
23 11 0.22
24 6 0.12
ACGTcount: A:0.74, C:0.01, G:0.09, T:0.15
Consensus pattern (21 bp):
AAAATAAGATAAAATAAAATA
Found at i:24289760 original size:18 final size:19
Alignment explanation
Indices: 24289724--24289761 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
24289714 CTTGGATTCT
* *
24289724 TCACCGGAAACTTGGAAGG
1 TCACCGAAAACTTGCAAGG
24289743 TCACCGAAAACTT-CAAGG
1 TCACCGAAAACTTGCAAGG
24289761 T
1 T
24289762 TGGTTGGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18
Consensus pattern (19 bp):
TCACCGAAAACTTGCAAGG
Found at i:24290280 original size:4 final size:4
Alignment explanation
Indices: 24290258--24290449 Score: 52
Period size: 4 Copynumber: 48.2 Consensus size: 4
24290248 ATATAATTAG
*
24290258 ATAA ATAAA ATACA A-AA ATAA ATAA A-AT ATAA A-ATA AT-A AT-A AT-A
1 ATAA AT-AA ATA-A ATAA ATAA ATAA ATAA ATAA ATA-A ATAA ATAA ATAA
* * *
24290303 ATAA ATAA ATTATA ATAA A-ATA ATAA ATAT ATAA CTAT ATAA ATAAA
1 ATAA ATAA A-TA-A ATAA ATA-A ATAA ATAA ATAA ATAA ATAA AT-AA
* * *
24290350 ATACA TATAA AT-A TTAA CAGAA AGAA A-AGA A-AA A-AA AT-A ATAA
1 ATA-A -ATAA ATAA ATAA -ATAA ATAA ATA-A ATAA ATAA ATAA ATAA
* * * * * *
24290393 ATAA ATAA ATAA AGAT ATAC ATAT ATTA ATAC ATAGTA AT-A ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA--A ATAA ATAA ATAA
24290442 AT-A ATAA A
1 ATAA ATAA A
24290450 ATACATAAAA
Statistics
Matches: 144, Mismatches: 21, Indels: 46
0.68 0.10 0.22
Matches are distributed among these distances:
3 32 0.22
4 86 0.60
5 19 0.13
6 7 0.05
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:24290280 original size:17 final size:16
Alignment explanation
Indices: 24290258--24290331 Score: 78
Period size: 17 Copynumber: 4.4 Consensus size: 16
24290248 ATATAATTAG
24290258 ATAAATAAAATACAAAA
1 ATAAATAAAATA-AAAA
*
24290275 ATAAATAAAATATAAA
1 ATAAATAAAATAAAAA
*
24290291 AT-AATAATAATAATAA
1 ATAAATAA-AATAAAAA
*
24290307 ATAAATTATAATAAAATA
1 ATAAA-TAAAATAAAA-A
24290325 ATAAATA
1 ATAAATA
24290332 TATAACTATA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
15 5 0.10
16 13 0.27
17 22 0.46
18 8 0.17
ACGTcount: A:0.72, C:0.01, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAATAAAATAAAAA
Found at i:24290289 original size:7 final size:8
Alignment explanation
Indices: 24290261--24290329 Score: 65
Period size: 8 Copynumber: 8.8 Consensus size: 8
24290251 TAATTAGATA
24290261 AATAAAAT
1 AATAAAAT
24290269 ACA-AAAAT
1 A-ATAAAAT
24290277 AAATAAAAT
1 -AATAAAAT
24290286 -ATAAAAT
1 AATAAAAT
24290293 AATAATAAT
1 AATAA-AAT
24290302 AAT-AAAT
1 AATAAAAT
**
24290309 AA-ATTAT
1 AATAAAAT
24290316 AATAAAAT
1 AATAAAAT
24290324 AATAAA
1 AATAAA
24290330 TATATAACTA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
7 16 0.32
8 21 0.42
9 13 0.26
ACGTcount: A:0.72, C:0.01, G:0.00, T:0.26
Consensus pattern (8 bp):
AATAAAAT
Found at i:24290289 original size:28 final size:27
Alignment explanation
Indices: 24290258--24290352 Score: 95
Period size: 28 Copynumber: 3.4 Consensus size: 27
24290248 ATATAATTAG
24290258 ATAAATAAAATACAAAAATAAATAAAAT
1 ATAAATAAAATA-AAAAATAAATAAAAT
* *
24290286 ATAAAATAATAAT-AATAATAAATAAATT
1 AT-AAATAA-AATAAAAAATAAATAAAAT
* * *
24290314 AT-AATAAAATAATAAATATATAACTAT
1 ATAAATAAAATAAAAAATAAATAA-AAT
24290341 ATAAATAAAATA
1 ATAAATAAAATA
24290353 CATATAAATA
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
25 3 0.05
26 14 0.25
27 3 0.05
28 26 0.47
29 6 0.11
30 3 0.05
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.28
Consensus pattern (27 bp):
ATAAATAAAATAAAAAATAAATAAAAT
Found at i:24290301 original size:47 final size:46
Alignment explanation
Indices: 24290223--24290336 Score: 112
Period size: 47 Copynumber: 2.4 Consensus size: 46
24290213 AATTTATAGG
* *
24290223 ATAAAATAAA-AAAATAATAACAGATATATAATTAGATAAATAAA-ATA
1 ATAAAATAAATAAAAT-ATAAAAAATATATAA-TA-ATAAATAAATATA
24290270 CA-AAAATAAATAAAATATAAAATAATA-ATAATAATAAATAAATTATA
1 -ATAAAATAAATAAAATATAAAA-AATATATAATAATAAATAAA-TATA
24290317 ATAAAAT-AATAAATATATAA
1 ATAAAATAAATAAA-ATATAA
24290337 CTATATAAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
45 9 0.16
46 9 0.16
47 31 0.53
48 9 0.16
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (46 bp):
ATAAAATAAATAAAATATAAAAAATATATAATAATAAATAAATATA
Found at i:24290317 original size:14 final size:14
Alignment explanation
Indices: 24290274--24290321 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
24290264 AAAATACAAA
*
24290274 AATAAATAAAATAT
1 AATAAATAAATTAT
* *
24290288 AAAATAAT-AATAAT
1 AATA-AATAAATTAT
24290302 AATAAATAAATTAT
1 AATAAATAAATTAT
24290316 AATAAA
1 AATAAA
24290322 ATAATAAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
13 3 0.11
14 21 0.78
15 3 0.11
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AATAAATAAATTAT
Found at i:24290627 original size:33 final size:33
Alignment explanation
Indices: 24290590--24290652 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
24290580 AAGCAGAGGT
* *
24290590 CATGAAGCTTGAATGATTTATCTAAACAAAGGC
1 CATGAAACTTGAATGATTCATCTAAACAAAGGC
* *
24290623 CATGAAATTTGAATGATTCCTCTAAACAAA
1 CATGAAACTTGAATGATTCATCTAAACAAA
24290653 TGGCTTACAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (33 bp):
CATGAAACTTGAATGATTCATCTAAACAAAGGC
Found at i:24291540 original size:17 final size:18
Alignment explanation
Indices: 24291508--24291541 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
24291498 ATAACTCCCT
24291508 TTGATTATTTAAAAAAAA
1 TTGATTATTTAAAAAAAA
*
24291526 TTGATT-TTTATAAAAA
1 TTGATTATTTAAAAAAA
24291542 TTCTTTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
TTGATTATTTAAAAAAAA
Found at i:24292369 original size:14 final size:15
Alignment explanation
Indices: 24292304--24292382 Score: 63
Period size: 15 Copynumber: 5.3 Consensus size: 15
24292294 TAAAAATTAG
* *
24292304 AGTTTTGGGTTTTGG
1 AGTTTAGGGTTTTGA
* **
24292319 ATTTTAAAGTTTTGAA
1 AGTTTAGGGTTTTG-A
* * *
24292335 ATTTTATGGTTTTTA
1 AGTTTAGGGTTTTGA
24292350 AGTTTAGGGTTTTGA
1 AGTTTAGGGTTTTGA
24292365 A-TTTAGGGTTTTG-
1 AGTTTAGGGTTTTGA
24292378 AGTTT
1 AGTTT
24292383 TAAAGGTTTT
Statistics
Matches: 51, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
13 1 0.02
14 15 0.29
15 24 0.47
16 11 0.22
ACGTcount: A:0.20, C:0.00, G:0.25, T:0.54
Consensus pattern (15 bp):
AGTTTAGGGTTTTGA
Found at i:24292453 original size:17 final size:17
Alignment explanation
Indices: 24292431--24292465 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
24292421 TTAGGGCTTG
24292431 GATTTTAAGGTTTGGAA
1 GATTTTAAGGTTTGGAA
*
24292448 GATTTTAAGGTTTTGAA
1 GATTTTAAGGTTTGGAA
24292465 G
1 G
24292466 GTCTAAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.43
Consensus pattern (17 bp):
GATTTTAAGGTTTGGAA
Found at i:24292615 original size:22 final size:22
Alignment explanation
Indices: 24292589--24292632 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
24292579 AGGATTCTGA
*
24292589 TTTTAGAGTTTAAAGGGTTTAG
1 TTTTAGAGTTTAAAGGATTTAG
* *
24292611 TTTTAGGGTTTGAAGGATTTAG
1 TTTTAGAGTTTAAAGGATTTAG
24292633 GGTTTTAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (22 bp):
TTTTAGAGTTTAAAGGATTTAG
Found at i:24292652 original size:52 final size:52
Alignment explanation
Indices: 24292524--24292652 Score: 127
Period size: 52 Copynumber: 2.5 Consensus size: 52
24292514 TTTAGAAATC
* *
24292524 TTAGGGTTTCAAATTTTAGGGTTTAAAAGGCCTAGTTTTAGAGTTTTGAGTGT
1 TTAGGGTTT-TAATTTTAGGGTTTAAAAGGCCTAGTTTTAGAGGTTTGAGTGT
* * * * * **
24292577 TTAGGATTCTGATTTTAGAGTTTAAAGGGTTTAGTTTTAG-GGTTTGAAG-GAT
1 TTAGGGTTTTAATTTTAGGGTTTAAAAGGCCTAGTTTTAGAGGTTTG-AGTG-T
*
24292629 TTAGGGTTTTAATTTTTGGGTTTA
1 TTAGGGTTTTAATTTTAGGGTTTA
24292653 GAGTTTTAGA
Statistics
Matches: 60, Mismatches: 14, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
51 6 0.10
52 47 0.78
53 7 0.12
ACGTcount: A:0.23, C:0.03, G:0.27, T:0.47
Consensus pattern (52 bp):
TTAGGGTTTTAATTTTAGGGTTTAAAAGGCCTAGTTTTAGAGGTTTGAGTGT
Found at i:24294618 original size:22 final size:22
Alignment explanation
Indices: 24294566--24294626 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
24294556 AAATTTTTCT
* *
24294566 AAGAGGTTTTAAAGATTATGTC
1 AAGAGGTCTTAAAGATTATGCC
** *
24294588 TGGATGTCTTAAAGATTATGCC
1 AAGAGGTCTTAAAGATTATGCC
*
24294610 AAGAGGTCTTAATGATT
1 AAGAGGTCTTAAAGATT
24294627 TCAAAATCTT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36
Consensus pattern (22 bp):
AAGAGGTCTTAAAGATTATGCC
Found at i:24295220 original size:32 final size:32
Alignment explanation
Indices: 24295152--24295221 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
24295142 TGCCATGATG
* * *
24295152 CAAATGCAAATTTCTTTTCCATGATGCACATG
1 CAAATGCAAATTCCTTTTCCATGATGCAAATA
* *
24295184 CAAATGCAAATATCCTTTT-CATTATGTAAATA
1 CAAATGCAAAT-TCCTTTTCCATGATGCAAATA
24295216 CAAATG
1 CAAATG
24295222 TGAATGTCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 26 0.81
33 6 0.19
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (32 bp):
CAAATGCAAATTCCTTTTCCATGATGCAAATA
Found at i:24296727 original size:18 final size:18
Alignment explanation
Indices: 24296692--24296742 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
24296682 AGTACATGTC
24296692 TTTCTT-TTTTTTGCTCTTT
1 TTTCTTATTTTTT--TCTTT
24296711 TTTCTTATTTTTTTCTTT
1 TTTCTTATTTTTTTCTTT
*
24296729 TCTT-TAATTTTTTT
1 T-TTCTTATTTTTTT
24296743 TTATGAAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 15 0.52
19 8 0.28
20 6 0.21
ACGTcount: A:0.06, C:0.12, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTCTTATTTTTTTCTTT
Found at i:24303951 original size:15 final size:15
Alignment explanation
Indices: 24303927--24304009 Score: 60
Period size: 16 Copynumber: 5.4 Consensus size: 15
24303917 GGAATTTGGA
24303927 GTTTTGAAATTTTAAG
1 GTTTT-AAATTTTAAG
*
24303943 GTTTTAAATTTTTATG
1 GTTTTAAA-TTTTAAG
* **
24303959 GTTTTTAGGTTTAAG
1 GTTTTAAATTTTAAG
* *
24303974 GTTTTGAA-TTTAGG
1 GTTTTAAATTTTAAG
* *
24303988 GTTTTGAGTTTTAAGG
1 GTTTTAAATTTTAA-G
24304004 GTTTTA
1 GTTTTA
24304010 GGGTTTGGTT
Statistics
Matches: 53, Mismatches: 11, Indels: 6
0.76 0.16 0.09
Matches are distributed among these distances:
14 12 0.23
15 18 0.34
16 23 0.43
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (15 bp):
GTTTTAAATTTTAAG
Found at i:24304021 original size:13 final size:13
Alignment explanation
Indices: 24304003--24304060 Score: 53
Period size: 13 Copynumber: 4.1 Consensus size: 13
24303993 GAGTTTTAAG
24304003 GGTTTTAGGGTTT
1 GGTTTTAGGGTTT
24304016 GGTTTTAGGGTTT
1 GGTTTTAGGGTTT
* *
24304029 ACAGAGTTTTAAGGCTT
1 ---G-GTTTTAGGGTTT
24304046 GGATTTTAGGGTTT
1 GG-TTTTAGGGTTT
24304060 G
1 G
24304061 AAAGATTTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
13 14 0.39
14 11 0.31
16 1 0.03
17 10 0.28
ACGTcount: A:0.16, C:0.03, G:0.34, T:0.47
Consensus pattern (13 bp):
GGTTTTAGGGTTT
Found at i:24304037 original size:22 final size:23
Alignment explanation
Indices: 24303990--24304037 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
24303980 AATTTAGGGT
* *
24303990 TTTGAGTTTTAAGGGTTTTAGGG
1 TTTGAGTTTTAAGGGTTTCAGAG
24304013 TTTG-GTTTT-AGGGTTTACAGAG
1 TTTGAGTTTTAAGGGTTT-CAGAG
24304035 TTT
1 TTT
24304038 TAAGGCTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 7 0.32
22 11 0.50
23 4 0.18
ACGTcount: A:0.17, C:0.02, G:0.31, T:0.50
Consensus pattern (23 bp):
TTTGAGTTTTAAGGGTTTCAGAG
Found at i:24304181 original size:22 final size:22
Alignment explanation
Indices: 24304154--24304195 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
24304144 AGTTTCAAAC
*
24304154 TTTAGGGTTTGAAGGGTTTAGT
1 TTTAGGGTTTAAAGGGTTTAGT
*
24304176 TTTAGGGTTTAAATGGTTTA
1 TTTAGGGTTTAAAGGGTTTA
24304196 AGATTTCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (22 bp):
TTTAGGGTTTAAAGGGTTTAGT
Found at i:24304194 original size:31 final size:30
Alignment explanation
Indices: 24304159--24304256 Score: 90
Period size: 31 Copynumber: 3.2 Consensus size: 30
24304149 CAAACTTTAG
24304159 GGTTTGAAGGGTTTAGTTTTAGGGTTTAAAT
1 GGTTT-AAGGGTTTAGTTTTAGGGTTTAAAT
* * * *
24304190 GGTTTAA-GATTTCAATTTTAGAGTTTAAAG
1 GGTTTAAGGGTTT-AGTTTTAGGGTTTAAAT
* * **
24304220 GGTTTTAGGGTTTTGATTTTAGGGTTCGAAT
1 GGTTTAAGGGTTTAG-TTTTAGGGTTTAAAT
24304251 GGTTTA
1 GGTTTA
24304257 GTTTTAGGGT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 4 0.08
30 22 0.43
31 25 0.49
ACGTcount: A:0.23, C:0.02, G:0.29, T:0.46
Consensus pattern (30 bp):
GGTTTAAGGGTTTAGTTTTAGGGTTTAAAT
Found at i:24304276 original size:22 final size:23
Alignment explanation
Indices: 24304218--24304279 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
24304208 TAGAGTTTAA
* *
24304218 AGGGTTT-TAGGGTTTTGATTTT
1 AGGGTTTGAAGGGTTTAGATTTT
* *
24304240 AGGGTTCGAATGGTTTAG-TTTT
1 AGGGTTTGAAGGGTTTAGATTTT
*
24304262 AGGGTTTGGAGGGTTTAG
1 AGGGTTTGAAGGGTTTAG
24304280 GGTTTCGATT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
22 25 0.78
23 7 0.22
ACGTcount: A:0.16, C:0.02, G:0.37, T:0.45
Consensus pattern (23 bp):
AGGGTTTGAAGGGTTTAGATTTT
Found at i:24304277 original size:83 final size:81
Alignment explanation
Indices: 24304154--24304313 Score: 203
Period size: 83 Copynumber: 2.0 Consensus size: 81
24304144 AGTTTCAAAC
* * *
24304154 TTTAGGGTTTGAAGGGTTTAGTTTTAGGGTTTAAATGGTTTAAGATTTCAATTTTAGAGTTTAAA
1 TTTAGGGTTCGAAGGGTTTAGTTTTAGGGTTTAAAGGGTTTAAGATTTCAATTATAGAGTTT--A
24304219 GGGTTTTAGGGTTTTGAT
64 GGGTTTTAGGGTTTTGAT
* ** * * * * *
24304237 TTTAGGGTTCGAATGGTTTAGTTTTAGGGTTTGGAGGGTTTAGGGTTTCGATTATAGGGTTTGGG
1 TTTAGGGTTCGAAGGGTTTAGTTTTAGGGTTTAAAGGGTTTAAGATTTCAATTATAGAGTTTAGG
24304302 GTTTTAGGGTTT
66 GTTTTAGGGTTT
24304314 CAATTTTATG
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
81 14 0.21
83 52 0.79
ACGTcount: A:0.19, C:0.02, G:0.33, T:0.46
Consensus pattern (81 bp):
TTTAGGGTTCGAAGGGTTTAGTTTTAGGGTTTAAAGGGTTTAAGATTTCAATTATAGAGTTTAGG
GTTTTAGGGTTTTGAT
Found at i:24304499 original size:10 final size:10
Alignment explanation
Indices: 24304471--24304536 Score: 51
Period size: 10 Copynumber: 6.2 Consensus size: 10
24304461 ATTATAAAAA
*
24304471 TTATTATTAT
1 TTATTTTTAT
* *
24304481 TAATATTTAT
1 TTATTTTTAT
24304491 TTATTTTTATT
1 TTATTTTTA-T
*
24304502 ATTGTTTTATTAT
1 -TT-ATTT-TTAT
24304515 TTATTTTTAT
1 TTATTTTTAT
*
24304525 TTATTTATAT
1 TTATTTTTAT
24304535 TT
1 TT
24304537 TTTATAATTC
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
10 29 0.66
11 4 0.09
12 4 0.09
13 4 0.09
14 3 0.07
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.73
Consensus pattern (10 bp):
TTATTTTTAT
Found at i:24304504 original size:17 final size:17
Alignment explanation
Indices: 24304474--24304541 Score: 68
Period size: 17 Copynumber: 4.0 Consensus size: 17
24304464 ATAAAAATTA
* *
24304474 TTATTATTAATATTTAT
1 TTATTTTTATTATTTAT
24304491 TTATTTTTATTATTGT-T
1 TTATTTTTATTATT-TAT
24304508 TTATTATTTATT-TTTAT
1 TTATT-TTTATTATTTAT
* *
24304525 TTATTTATATTTTTTAT
1 TTATTTTTATTATTTAT
24304542 AATTCCCTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
16 6 0.14
17 31 0.70
18 7 0.16
ACGTcount: A:0.25, C:0.00, G:0.01, T:0.74
Consensus pattern (17 bp):
TTATTTTTATTATTTAT
Found at i:24304682 original size:13 final size:13
Alignment explanation
Indices: 24304666--24304713 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
24304656 CATTTTTTGG
*
24304666 TTATTTTTCTCTT
1 TTATTTTTTTCTT
*
24304679 TTATTTATTTTGTT
1 TTATTT-TTTTCTT
24304693 TTATTATTTTTCTT
1 TTATT-TTTTTCTT
24304707 ATTATTT
1 -TTATTT
24304714 AAAGAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 6 0.21
14 17 0.59
15 6 0.21
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (13 bp):
TTATTTTTTTCTT
Found at i:24311040 original size:16 final size:17
Alignment explanation
Indices: 24311011--24311044 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
24311001 ATTTTTAAGG
24311011 ATTTAATTTCAAAATCA
1 ATTTAATTTCAAAATCA
*
24311028 ATTT-ATTTTAAAATCA
1 ATTTAATTTCAAAATCA
24311044 A
1 A
24311045 ATCAAATCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTAATTTCAAAATCA
Found at i:24312253 original size:41 final size:42
Alignment explanation
Indices: 24312164--24312277 Score: 103
Period size: 41 Copynumber: 2.7 Consensus size: 42
24312154 TGTATTGCTT
* * *
24312164 TTATC-TTTTA-TTTAATTTTTACAT-ATTTTTATTATTTAT
1 TTATCATTTTATTTTATTTTTTGCATGATTTTTATTATTTAA
*
24312203 TTATCATTTTATTTTATTTTTTGCATGATTTTTATATCTTTAA
1 TTATCATTTTATTTTATTTTTTGCATGATTTTTAT-TATTTAA
*
24312246 TT-T-ATTTTCATGTAGTATTTATTTGCATGATT
1 TTATCATTTT-AT-T-TTATTT-TTTGCATGATT
24312278 CATTATTCGC
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
39 5 0.08
40 5 0.08
41 17 0.27
42 11 0.18
43 8 0.13
44 5 0.08
45 11 0.18
ACGTcount: A:0.24, C:0.06, G:0.05, T:0.65
Consensus pattern (42 bp):
TTATCATTTTATTTTATTTTTTGCATGATTTTTATTATTTAA
Found at i:24312371 original size:19 final size:19
Alignment explanation
Indices: 24312288--24312359 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
24312278 CATTATTCGC
24312288 ATTATTGCATGATTATTTAT
1 ATTATTGCATGATTA-TTAT
* *
24312308 ATTATTTGTATGATTAATAT
1 ATTA-TTGCATGATTATTAT
24312328 ATTATTGCATGATTATTAT
1 ATTATTGCATGATTATTAT
*
24312347 ATTATTGTATGAT
1 ATTATTGCATGAT
24312360 ATTTACATTA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
19 25 0.54
20 11 0.24
21 10 0.22
ACGTcount: A:0.32, C:0.03, G:0.11, T:0.54
Consensus pattern (19 bp):
ATTATTGCATGATTATTAT
Found at i:24316529 original size:10 final size:10
Alignment explanation
Indices: 24316515--24316569 Score: 58
Period size: 10 Copynumber: 5.4 Consensus size: 10
24316505 CAAAAGTAGA
24316515 AAAAAAAGAGG
1 AAAAAAA-AGG
*
24316526 AAAAAAAAAGA
1 -AAAAAAAAGG
*
24316537 AAAAAAAAAG
1 AAAAAAAAGG
*
24316547 AAAAAAAAAG
1 AAAAAAAAGG
24316557 -AAAAAAAGG
1 AAAAAAAAGG
24316566 AAAA
1 AAAA
24316570 TTTAAATTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
9 8 0.21
10 21 0.55
11 2 0.05
12 7 0.18
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGG
Found at i:24316529 original size:11 final size:10
Alignment explanation
Indices: 24316512--24316563 Score: 77
Period size: 10 Copynumber: 4.9 Consensus size: 10
24316502 AAGCAAAAGT
24316512 AGAAAAAAAA
1 AGAAAAAAAA
24316522 GAGGAAAAAAAA
1 -A-GAAAAAAAA
24316534 AGAAAAAAAAA
1 AG-AAAAAAAA
24316545 AGAAAAAAAA
1 AGAAAAAAAA
24316555 AGAAAAAAA
1 AGAAAAAAA
24316564 GGAAAATTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
10 18 0.46
11 12 0.31
12 9 0.23
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:24316530 original size:21 final size:22
Alignment explanation
Indices: 24316512--24316563 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
24316502 AAGCAAAAGT
* *
24316512 AGAAAAAAAAGAGGAAAAAAAA
1 AGAAAAAAAAAAGAAAAAAAAA
24316534 AGAAAAAAAAAAG-AAAAAAAA
1 AGAAAAAAAAAAGAAAAAAAAA
24316555 AGAAAAAAA
1 AGAAAAAAA
24316564 GGAAAATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (22 bp):
AGAAAAAAAAAAGAAAAAAAAA
Found at i:24316532 original size:13 final size:11
Alignment explanation
Indices: 24316512--24316563 Score: 79
Period size: 11 Copynumber: 4.8 Consensus size: 11
24316502 AAGCAAAAGT
*
24316512 AGAAAAAAAAG
1 AGAAAAAAAAA
*
24316523 AGGAAAAAAAA
1 AGAAAAAAAAA
24316534 AGAAAAAAAAA
1 AGAAAAAAAAA
24316545 AG-AAAAAAAA
1 AGAAAAAAAAA
24316555 AGAAAAAAA
1 AGAAAAAAA
24316564 GGAAAATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
10 10 0.27
11 27 0.73
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
AGAAAAAAAAA
Found at i:24316539 original size:9 final size:9
Alignment explanation
Indices: 24316468--24316569 Score: 52
Period size: 9 Copynumber: 11.4 Consensus size: 9
24316458 AGAGGTGTGC
24316468 AAAAAAAATG
1 AAAAAAAA-G
*
24316478 -AAAAAATG
1 AAAAAAAAG
24316486 AAAAACAAA-
1 AAAAA-AAAG
*
24316495 ACAAAACAAG
1 A-AAAAAAAG
* **
24316505 CAAAAGTAG
1 AAAAAAAAG
24316514 AAAAAAAAG
1 AAAAAAAAG
**
24316523 -AGGAAAA-
1 AAAAAAAAG
*
24316530 AAAAAGAA-
1 AAAAAAAAG
24316538 AAAAAAAAG
1 AAAAAAAAG
24316547 AAAAAAAAAG
1 -AAAAAAAAG
*
24316557 AAAAAAAGG
1 AAAAAAAAG
24316566 AAAA
1 AAAA
24316570 TTTAAATTGA
Statistics
Matches: 69, Mismatches: 16, Indels: 15
0.69 0.16 0.15
Matches are distributed among these distances:
8 17 0.25
9 37 0.54
10 15 0.22
ACGTcount: A:0.80, C:0.04, G:0.13, T:0.03
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:24324111 original size:16 final size:14
Alignment explanation
Indices: 24324081--24324116 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 14
24324071 ACGATGATTC
24324081 AAATTTAAAAATTT
1 AAATTTAAAAATTT
24324095 AAATTTGAAATAATTT
1 AAATTT-AAA-AATTT
24324111 AAATTT
1 AAATTT
24324117 TTTGACACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.30
15 3 0.15
16 11 0.55
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (14 bp):
AAATTTAAAAATTT
Found at i:24325288 original size:2 final size:2
Alignment explanation
Indices: 24325281--24325323 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
24325271 CTTTATCTTT
24325281 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
24325323 T
1 T
24325324 TATTTTAATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:24325785 original size:14 final size:15
Alignment explanation
Indices: 24325766--24325807 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
24325756 TATAATGTTA
*
24325766 AATTATAATTA-ATT
1 AATTATAATTATAAT
24325780 AATTAT-ATTATAAT
1 AATTATAATTATAAT
24325794 AATTATAAATTATA
1 AATTAT-AATTATA
24325808 TACTTTCAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 4 0.17
14 14 0.58
16 6 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTATAATTATAAT
Found at i:24326363 original size:2 final size:2
Alignment explanation
Indices: 24326356--24326391 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
24326346 TTTTACACTG
24326356 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24326392 TGAAATGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24326549 original size:3 final size:3
Alignment explanation
Indices: 24326541--24326585 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
24326531 TAGTGCAAAC
24326541 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
24326586 TTGTAATTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:24329127 original size:22 final size:25
Alignment explanation
Indices: 24329081--24329127 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 25
24329071 CAGACTTTAA
*
24329081 AAATTTTACTGATAATATATGAAAT
1 AAATTTTACTGATAATATATCAAAT
24329106 AAATTTTA-T-AT-ATATATCAAAT
1 AAATTTTACTGATAATATATCAAAT
24329128 CTGATAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 10 0.48
23 2 0.10
24 1 0.05
25 8 0.38
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (25 bp):
AAATTTTACTGATAATATATCAAAT
Found at i:24329623 original size:3 final size:3
Alignment explanation
Indices: 24329617--24329652 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
24329607 AAATGCAAAC
24329617 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
24329653 TGATATCCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:24330578 original size:31 final size:33
Alignment explanation
Indices: 24330524--24330584 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
24330514 ATATTTTATA
*
24330524 TTTTCGTATTAATACATATTAT-AATATACGAT
1 TTTTCGTATTAAAACATATTATAAATATACGAT
24330556 TTTTCGTA-TAAAACATGA-TATAAATATAC
1 TTTTCGTATTAAAACAT-ATTATAAATATAC
24330585 AAATTATCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 10 0.38
32 16 0.62
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.43
Consensus pattern (33 bp):
TTTTCGTATTAAAACATATTATAAATATACGAT
Found at i:24330958 original size:31 final size:31
Alignment explanation
Indices: 24330923--24330986 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 31
24330913 ATTATATAAA
* * * *
24330923 TAATCCTTGTATTTACATAAGATTTGAAATT
1 TAATCCTTATACTTACACAAAATTTGAAATT
* *
24330954 TAATCTTTATACTTACACAAAATTTTAAATT
1 TAATCCTTATACTTACACAAAATTTGAAATT
24330985 TA
1 TA
24330987 GTTCTTCTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (31 bp):
TAATCCTTATACTTACACAAAATTTGAAATT
Found at i:24331178 original size:16 final size:14
Alignment explanation
Indices: 24331097--24331194 Score: 69
Period size: 14 Copynumber: 6.9 Consensus size: 14
24331087 ATATATTACT
*
24331097 TTTAATTTTATATAA
1 TTTAATATTA-ATAA
24331112 -TTAATTATTAATAA
1 TTTAA-TATTAATAA
* *
24331126 TATCATATTAATAA
1 TTTAATATTAATAA
* *
24331140 TATTATTATT-ATCA
1 T-TTAATATTAATAA
*
24331154 -TTGATATTAATCAA
1 TTTAATATTAAT-AA
24331168 TTATAATATTAATAA
1 TT-TAATATTAATAA
24331183 TTTAA-ATTAATA
1 TTTAATATTAATA
24331195 TATCAAAGCT
Statistics
Matches: 65, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
12 6 0.09
13 9 0.14
14 25 0.38
15 16 0.25
16 9 0.14
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (14 bp):
TTTAATATTAATAA
Found at i:24332070 original size:13 final size:13
Alignment explanation
Indices: 24332047--24332085 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
24332037 TAGATTTTTC
*
24332047 AATATTATGATAG
1 AATATTGTGATAG
*
24332060 AGTATTGTGATAG
1 AATATTGTGATAG
*
24332073 AATATTGTAATAG
1 AATATTGTGATAG
24332086 TATTTAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (13 bp):
AATATTGTGATAG
Found at i:24332194 original size:30 final size:31
Alignment explanation
Indices: 24332158--24332234 Score: 95
Period size: 29 Copynumber: 2.5 Consensus size: 31
24332148 TATTAGATGG
*
24332158 GCTAAATTTCAAATTTCATACGAGTACAA-A
1 GCTAAATTTCAAATTTCATACGAATACAAGA
**
24332188 GCTAAA-TTCAAATTTTGTACGAATACAAGA
1 GCTAAATTTCAAATTTCATACGAATACAAGA
* *
24332218 ACTACATTTCAAATTTC
1 GCTAAATTTCAAATTTC
24332235 GTATAAGTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
29 19 0.49
30 11 0.28
31 9 0.23
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (31 bp):
GCTAAATTTCAAATTTCATACGAATACAAGA
Found at i:24332399 original size:20 final size:20
Alignment explanation
Indices: 24332342--24332390 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
24332332 CACGTCCATA
24332342 AAATCAATGCCCATGTCATC
1 AAATCAATGCCCATGTCATC
24332362 AAATCAATGCCCATGTCATC
1 AAATCAATGCCCATGTCATC
24332382 AAATCAATG
1 AAATCAATG
24332391 GTCAAGTCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.39, C:0.27, G:0.10, T:0.24
Consensus pattern (20 bp):
AAATCAATGCCCATGTCATC
Found at i:24337521 original size:20 final size:20
Alignment explanation
Indices: 24337496--24337534 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
24337486 TGACACTTGC
24337496 AAAATAATAAGAATGATATA
1 AAAATAATAAGAATGATATA
*
24337516 AAAATAATAAGCATGATAT
1 AAAATAATAAGAATGATAT
24337535 TAAATGTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.10, T:0.26
Consensus pattern (20 bp):
AAAATAATAAGAATGATATA
Found at i:24341543 original size:12 final size:12
Alignment explanation
Indices: 24341502--24341550 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
24341492 TATTAAAAGT
*
24341502 TTTATTACTATTA
1 TTTATTA-TTTTA
* *
24341515 TTTATTAATCT-
1 TTTATTATTTTA
24341526 TTTATTATTTTA
1 TTTATTATTTTA
24341538 TTTATTATTTTA
1 TTTATTATTTTA
24341550 T
1 T
24341551 AATTCCCCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
11 9 0.30
12 14 0.47
13 7 0.23
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:24341642 original size:14 final size:14
Alignment explanation
Indices: 24341623--24341656 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
24341613 AGGGATTTGA
*
24341623 AATTTTCATTTTCT
1 AATTTTAATTTTCT
*
24341637 AATTTTAATTTTTT
1 AATTTTAATTTTCT
24341651 AATTTT
1 AATTTT
24341657 TTTAAACATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (14 bp):
AATTTTAATTTTCT
Found at i:24341790 original size:23 final size:23
Alignment explanation
Indices: 24341732--24341791 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 23
24341722 GATCATTGCT
* *
24341732 TATTACTATT-TTA-TATTATTC
1 TATTATTATTATTATTATTATTA
24341753 TA-TATGTA-TATTTATTATTATTA
1 TATTAT-TATTA-TTATTATTATTA
24341776 TATTATTATTATTATT
1 TATTATTATTATTATT
24341792 TAAAATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
20 3 0.10
21 4 0.13
22 3 0.10
23 16 0.52
24 5 0.16
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (23 bp):
TATTATTATTATTATTATTATTA
Found at i:24343314 original size:20 final size:20
Alignment explanation
Indices: 24343285--24343322 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
24343275 CCCTTCCCCA
24343285 CCCCACCCCACCCAATCCTT
1 CCCCACCCCACCCAATCCTT
*
24343305 CCCCATCCCACCCAATCC
1 CCCCACCCCACCCAATCC
24343323 CTCCTCACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.66, G:0.00, T:0.13
Consensus pattern (20 bp):
CCCCACCCCACCCAATCCTT
Found at i:24343314 original size:25 final size:26
Alignment explanation
Indices: 24343257--24343317 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 26
24343247 CAGCCCCCAA
* *
24343257 CACCTCACCACACCAAATCCCTTCCC
1 CACCCCACCCCACCAAATCCCTTCCC
*
24343283 CACCCCACCCCACCCAAT-CCTTCCC
1 CACCCCACCCCACCAAATCCCTTCCC
*
24343308 CATCCCACCC
1 CACCCCACCC
24343318 AATCCCTCCT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 16 0.52
26 15 0.48
ACGTcount: A:0.23, C:0.64, G:0.00, T:0.13
Consensus pattern (26 bp):
CACCCCACCCCACCAAATCCCTTCCC
Found at i:24344988 original size:3 final size:3
Alignment explanation
Indices: 24344980--24345030 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
24344970 CCTTTTCTTA
*
24344980 TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
24345028 TAT
1 TAT
24345031 ATTCACTATA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:24345427 original size:34 final size:35
Alignment explanation
Indices: 24345369--24345437 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 35
24345359 ATTATAAAAC
24345369 CCTTTTTTCTTTGCTTTTTAGTTTTTTTTGTTTTG
1 CCTTTTTTCTTTGCTTTTTAGTTTTTTTTGTTTTG
* *
24345404 CCTTTTTATTTTTG-TTTTT-GTTTTTTTTTTTTTG
1 CCTTTTT-TCTTTGCTTTTTAGTTTTTTTTGTTTTG
24345438 AGTTTTTAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 14 0.45
35 12 0.39
36 5 0.16
ACGTcount: A:0.03, C:0.09, G:0.10, T:0.78
Consensus pattern (35 bp):
CCTTTTTTCTTTGCTTTTTAGTTTTTTTTGTTTTG
Found at i:24345428 original size:19 final size:18
Alignment explanation
Indices: 24345390--24345433 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
24345380 TGCTTTTTAG
24345390 TTTTTTTTGTTTTGCCTT
1 TTTTTTTTGTTTTGCCTT
24345408 TTTATTTTTGTTTTTG--TT
1 TTT-TTTTTG-TTTTGCCTT
24345426 TTTTTTTT
1 TTTTTTTT
24345434 TTTGAGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 5 0.21
18 8 0.33
19 6 0.25
20 5 0.21
ACGTcount: A:0.02, C:0.05, G:0.09, T:0.84
Consensus pattern (18 bp):
TTTTTTTTGTTTTGCCTT
Found at i:24345434 original size:19 final size:19
Alignment explanation
Indices: 24345390--24345437 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
24345380 TGCTTTTTAG
24345390 TTTTTTTTGTTTTGCCTTT
1 TTTTTTTTGTTTTGCCTTT
* **
24345409 TTATTTTTGTTTTTGTTTTT
1 TTTTTTTTG-TTTTGCCTTT
24345429 TTTTTTTTG
1 TTTTTTTTG
24345438 AGTTTTTAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.02, C:0.04, G:0.10, T:0.83
Consensus pattern (19 bp):
TTTTTTTTGTTTTGCCTTT
Found at i:24345444 original size:34 final size:36
Alignment explanation
Indices: 24345370--24345445 Score: 95
Period size: 34 Copynumber: 2.2 Consensus size: 36
24345360 TTATAAAACC
* *
24345370 CTTTTT-TCTTTGCTTTTTAGTTTTTTTTGTTTTGC
1 CTTTTTATTTTTGCTTTTTAGTTTTTTTTGTTTTGA
*
24345405 CTTTTTATTTTTG-TTTTT-GTTTTTTTTTTTTTGA
1 CTTTTTATTTTTGCTTTTTAGTTTTTTTTGTTTTGA
*
24345439 GTTTTTA
1 CTTTTTA
24345446 AGGTTCGAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 20 0.56
35 11 0.31
36 5 0.14
ACGTcount: A:0.05, C:0.07, G:0.11, T:0.78
Consensus pattern (36 bp):
CTTTTTATTTTTGCTTTTTAGTTTTTTTTGTTTTGA
Found at i:24345678 original size:36 final size:34
Alignment explanation
Indices: 24345575--24345687 Score: 113
Period size: 35 Copynumber: 3.2 Consensus size: 34
24345565 AATTGTAAGT
24345575 AAAA-AAAAATGATTAGGACAATACCACAAGTCA
1 AAAATAAAAATGATTAGGACAATACCACAAGTCA
* * **
24345608 AAAATAAAGAATGGTT-GGAACGATACTGCAAGTCA
1 AAAATAAA-AATGATTAGG-ACAATACCACAAGTCA
* *
24345643 AGTAATTAAAAATGATTAAGACAATACCACAAGTCAA
1 A--AAATAAAAATGATTAGGACAATACCACAAGTC-A
24345680 AAAATAAA
1 AAAATAAA
24345688 GAACGATCGA
Statistics
Matches: 62, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
33 4 0.06
34 5 0.08
35 26 0.42
36 18 0.29
37 9 0.15
ACGTcount: A:0.55, C:0.12, G:0.14, T:0.19
Consensus pattern (34 bp):
AAAATAAAAATGATTAGGACAATACCACAAGTCA
Found at i:24345718 original size:107 final size:107
Alignment explanation
Indices: 24345607--24345833 Score: 249
Period size: 107 Copynumber: 2.1 Consensus size: 107
24345597 ACCACAAGTC
** * * * * * * *
24345607 AAAAATAAAGAATGGTTGGAACGATACTGCAAGTCAAGTAATTAAAAATGATTAAGACAATACCA
1 AAAAATAAAGAATGACTGAAACAACACTGCAAGTCAA-AAATAAAAAATGATCAAGACAACACCA
* *
24345672 CAAGTCAAAAAATAAAGAACGATC-GAGATAACAACGTAAATCA
65 CAAGTCAAAAAATAAAGAACGATCAG-GACAACAACATAAATCA
* * * * *
24345715 AAAAATAAAAAATGACTGAAATAACACTGCAAGTCAAAAATAAAAAATGATCAGGACAACATCAT
1 AAAAATAAAGAATGACTGAAACAACACTGCAAGTCAAAAATAAAAAATGATCAAGACAACACCAC
* * * *
24345780 AAGTTAAAAAATAAAGAATGATCAGGACAACACCATAAGTCA
66 AAGTCAAAAAATAAAGAACGATCAGGACAACAACATAAATCA
24345822 AAAAATAAAGAA
1 AAAAATAAAGAA
24345834 CGATCAAGAT
Statistics
Matches: 97, Mismatches: 21, Indels: 3
0.80 0.17 0.02
Matches are distributed among these distances:
107 66 0.68
108 31 0.32
ACGTcount: A:0.56, C:0.13, G:0.14, T:0.17
Consensus pattern (107 bp):
AAAAATAAAGAATGACTGAAACAACACTGCAAGTCAAAAATAAAAAATGATCAAGACAACACCAC
AAGTCAAAAAATAAAGAACGATCAGGACAACAACATAAATCA
Found at i:24345723 original size:36 final size:35
Alignment explanation
Indices: 24345673--24345853 Score: 150
Period size: 36 Copynumber: 5.1 Consensus size: 35
24345663 ACAATACCAC
*
24345673 AAGTCAAAAAATAAAGAACGATCGAGATAACAACGT
1 AAGTCAAAAAATAAAGAATGATC-AGATAACAACGT
* * * * *
24345709 AAATCAAAAAATAAAAAATGACTGAAATAAC-ACTGC
1 AAGTCAAAAAATAAAGAATGA-TCAGATAACAAC-GT
* * * *
24345745 AAGTC-AAAAATAAAAAATGATCAGGACAACATCAT
1 AAGTCAAAAAATAAAGAATGATCA-GATAACAACGT
* * * *
24345780 AAGTTAAAAAATAAAGAATGATCAGGACAACACCAT
1 AAGTCAAAAAATAAAGAATGATCA-GATAACAACGT
* *
24345816 AAGTCAAAAAATAAAGAACGATCAAGATAACACCGT
1 AAGTCAAAAAATAAAGAATGATC-AGATAACAACGT
24345852 AA
1 AA
24345854 ATTATAAATA
Statistics
Matches: 119, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
34 2 0.02
35 25 0.21
36 90 0.76
37 2 0.02
ACGTcount: A:0.57, C:0.14, G:0.13, T:0.15
Consensus pattern (35 bp):
AAGTCAAAAAATAAAGAATGATCAGATAACAACGT
Found at i:24345724 original size:71 final size:70
Alignment explanation
Indices: 24345575--24345855 Score: 196
Period size: 71 Copynumber: 4.0 Consensus size: 70
24345565 AATTGTAAGT
* * * * *
24345575 AAAA-AAAAATGATTAGGACAATACCACAAGTCAAAAATAAAGAATGGTTG-G--AACGATACTG
1 AAAATAAAAATGATTAAGACAACACCACAAGTCAAAAATAAAGAACGATCGAGATAAC-A-AC-G
* *
24345636 CAAGTCAA
63 TAAATCAA
* * *
24345644 GTAATTAAAAATGATTAAGACAATACCACAAGTCAAAAAATAAAGAACGATCGAGATAACAACGT
1 -AAAATAAAAATGATTAAGACAACACCACAAGTC-AAAAATAAAGAACGATCGAGATAACAACGT
24345709 AAATCAA
64 AAATCAA
* * ** * * * * *
24345716 AAAATAAAAAATGACTGAA-ATAACACTGCAAGTCAAAAATAAAAAATGATC-AGGACAACATCA
1 AAAAT-AAAAATGA-TTAAGACAACACCACAAGTCAAAAATAAAGAACGATCGA-GATAACAACG
* *
24345779 TAAGTTAA
63 TAAATCAA
* * * * *
24345787 AAAATAAAGAATGATCAGGACAACACCATAAGTCAAAAAATAAAGAACGATCAAGATAACACCGT
1 AAAATAAA-AATGATTAAGACAACACCACAAGTC-AAAAATAAAGAACGATCGAGATAACAACGT
24345852 AAAT
64 AAAT
24345856 TATAAATAAA
Statistics
Matches: 165, Mismatches: 34, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
70 8 0.05
71 79 0.48
72 67 0.41
73 7 0.04
74 1 0.01
75 3 0.02
ACGTcount: A:0.56, C:0.14, G:0.14, T:0.17
Consensus pattern (70 bp):
AAAATAAAAATGATTAAGACAACACCACAAGTCAAAAATAAAGAACGATCGAGATAACAACGTAA
ATCAA
Found at i:24345789 original size:35 final size:34
Alignment explanation
Indices: 24345745--24346399 Score: 269
Period size: 35 Copynumber: 18.6 Consensus size: 34
24345735 ATAACACTGC
* *
24345745 AAGTCAAAAATAAAAAATGATCAGGACAACATCAT
1 AAGTCAAAAATAAAGAATGA-CAGGACAACACCAT
*
24345780 AAGTTAAAAAATAAAGAATGATCAGGACAACACCAT
1 AAG-TCAAAAATAAAGAATGA-CAGGACAACACCAT
* * * *
24345816 AAGTCAAAAAATAAAGAACGATCAAGATAACACCGT
1 AAGTC-AAAAATAAAGAATGA-CAGGACAACACCAT
* * * * **
24345852 AAATTATAAATAAAGAATAACTAGGACAACACTGT
1 AAGTCAAAAATAAAGAATGAC-AGGACAACACCAT
* * * **
24345887 AAGTCAAGTAATAAAGAATGACTGGGACAATACCGC
1 AAGTCAA-AAATAAAGAATGAC-AGGACAACACCAT
* * * **
24345923 GAGTCAAAAAATAAAGAATAACTGGGACAACGTCAT
1 AAGTC-AAAAATAAAGAATGAC-AGGACAACACCAT
* * **
24345959 ATGTCAAAAATATAA-AATAACTAGGACAACACTGT
1 AAGTCAAAAATA-AAGAATGAC-AGGACAACACCAT
* * ** ** * ***
24345994 AAATCAAAAAATAAAAAACAATTGAGATAACACTGC
1 AAGTC-AAAAATAAAGAATGACAG-GACAACACCAT
** * * *
24346030 AAGTCAAAAATAAAGAGCGACTGAAACAACATCAT
1 AAGTCAAAAATAAAGAATGACAG-GACAACACCAT
*
24346065 AAGTCAAAAATAAAAAATGATC-GAGACAACACCAT
1 AAGTCAAAAATAAAGAATGA-CAG-GACAACACCAT
* * * *
24346100 -AG--AAAAATAAAGAATGACCAAGATAACATCAC
1 AAGTCAAAAATAAAGAATGA-CAGGACAACACCAT
* * *
24346132 AAGTCAAAAATAAA-AGATGACCCGGATAACATCAT
1 AAGTCAAAAATAAAGA-ATGA-CAGGACAACACCAT
* * * * *
24346167 AAGTCAAAAATAAAAAACGACTAAGACAACACTAC
1 AAGTCAAAAATAAAGAATGAC-AGGACAACACCAT
* * * **
24346202 AAGTCAAAAATAAAGAATGACTGAGATAACATCGC
1 AAGTCAAAAATAAAGAATGACAG-GACAACACCAT
* * * *
24346237 AAGTTAAAAAATAAAAGAATGACTGTGATAACATCAT
1 AAG-TCAAAAAT-AAAGAATGACAG-GACAACACCAT
* * * * * *
24346274 AACTAAAAAATAAAGGATAACCAAGACAACACCAC
1 AAGTCAAAAATAAAGAATGA-CAGGACAACACCAT
* * * *
24346309 AAGTTAAAAATAACGAATGACTGAGACAACACCGT
1 AAGTCAAAAATAAAGAATGACAG-GACAACACCAT
* * * * *
24346344 AAGTTAGAAAATAAAAAATGATTAGGATAACACCGT
1 AAGTCA-AAAATAAAGAATGA-CAGGACAACACCAT
* *
24346380 AAGTTAAAAAATAAAAAATG
1 AAG-TCAAAAATAAAGAATG
24346400 CTAATATGAG
Statistics
Matches: 481, Mismatches: 114, Indels: 49
0.75 0.18 0.08
Matches are distributed among these distances:
32 23 0.05
33 2 0.00
34 6 0.01
35 229 0.48
36 193 0.40
37 28 0.06
ACGTcount: A:0.55, C:0.15, G:0.14, T:0.17
Consensus pattern (34 bp):
AAGTCAAAAATAAAGAATGACAGGACAACACCAT
Found at i:24345863 original size:71 final size:71
Alignment explanation
Indices: 24345649--24345883 Score: 208
Period size: 71 Copynumber: 3.3 Consensus size: 71
24345639 GTCAAGTAAT
* * * *
24345649 TAAA-AATGATTAAGACAATACCACAAGTCAAAAAATAAAGAACGATCGAGATAACAACGTAAAT
1 TAAAGAATGATCAGGACAACACCACAAGTCAAAAAATAAAGAACGATCAAGATAACAACGTAAAT
*
24345713 CAAAAAA
66 -TAAAAA
* * * * ** * * * * * * *
24345720 TAAAAAATGA-CTGAAATAACACTGCAAGTC-AAAAATAAAAAATGATCAGGACAACATCATAAG
1 TAAAGAATGATCAG-GACAACACCACAAGTCAAAAAATAAAGAACGATCAAGATAACAACGTAAA
24345783 TTAAAAAA
65 TT-AAAAA
* *
24345791 TAAAGAATGATCAGGACAACACCATAAGTCAAAAAATAAAGAACGATCAAGATAACACCGTAAAT
1 TAAAGAATGATCAGGACAACACCACAAGTCAAAAAATAAAGAACGATCAAGATAACAACGTAAAT
*
24345856 TATAAA
66 TAAAAA
*
24345862 TAAAGAAT-AACTAGGACAACAC
1 TAAAGAATGATC-AGGACAACAC
24345884 TGTAAGTCAA
Statistics
Matches: 125, Mismatches: 33, Indels: 12
0.74 0.19 0.07
Matches are distributed among these distances:
70 2 0.02
71 77 0.62
72 46 0.37
ACGTcount: A:0.57, C:0.14, G:0.12, T:0.17
Consensus pattern (71 bp):
TAAAGAATGATCAGGACAACACCACAAGTCAAAAAATAAAGAACGATCAAGATAACAACGTAAAT
TAAAAA
Found at i:24345890 original size:71 final size:71
Alignment explanation
Indices: 24345673--24345904 Score: 227
Period size: 71 Copynumber: 3.3 Consensus size: 71
24345663 ACAATACCAC
* * * * *
24345673 AAGTCAAAAAATAAAGAACGATCGAGATAACAACGTAAATCAAAAAATAAAAAATGACT-GAAAT
1 AAGTCAAAAAATAAAGAACGATCAAGATAACAACGTAAAT-TAAAAATAAAGAATGACTAG-GAC
*
24345737 AACACTGC
64 AACACTGT
* * * * * * *
24345745 AAGTC-AAAAATAAAAAATGATCAGGACAACATCATAAGTTAAAAAATAAAGAATGA-TCAGGAC
1 AAGTCAAAAAATAAAGAACGATCAAGATAACAACGTAAATT-AAAAATAAAGAATGACT-AGGAC
**
24345808 AACACCAT
64 AACACTGT
* * *
24345816 AAGTCAAAAAATAAAGAACGATCAAGATAACACCGTAAATTATAAATAAAGAATAACTAGGACAA
1 AAGTCAAAAAATAAAGAACGATCAAGATAACAACGTAAATTAAAAATAAAGAATGACTAGGACAA
24345881 CACTGT
66 CACTGT
**
24345887 AAGTCAAGTAATAAAGAA
1 AAGTCAAAAAATAAAGAA
24345905 TGACTGGGAC
Statistics
Matches: 127, Mismatches: 28, Indels: 11
0.77 0.17 0.07
Matches are distributed among these distances:
70 1 0.01
71 91 0.72
72 35 0.28
ACGTcount: A:0.57, C:0.13, G:0.13, T:0.17
Consensus pattern (71 bp):
AAGTCAAAAAATAAAGAACGATCAAGATAACAACGTAAATTAAAAATAAAGAATGACTAGGACAA
CACTGT
Found at i:24345903 original size:36 final size:35
Alignment explanation
Indices: 24345737--24346045 Score: 164
Period size: 36 Copynumber: 8.7 Consensus size: 35
24345727 TGACTGAAAT
* * *
24345737 AACACTGCAAGTCAAAAATAAAAAATGA-TCAGGAC
1 AACACTGTAAGTCAAAAATAAAGAATAACT-AGGAC
* * *
24345772 AACA-TCATAAGTTAAAAAATAAAGAATGA-TCAGGAC
1 AACACT-GTAAG-TCAAAAATAAAGAATAACT-AGGAC
** ** * *
24345808 AACACCATAAGTCAAAAAATAAAGAACGA-TCAAGAT
1 AACACTGTAAGTC-AAAAATAAAGAATAACT-AGGAC
* * * *
24345844 AACACCGTAAATTATAAATAAAGAATAACTAGGAC
1 AACACTGTAAGTCAAAAATAAAGAATAACTAGGAC
* * *
24345879 AACACTGTAAGTCAAGTAATAAAGAATGACTGGGAC
1 AACACTGTAAGTCAA-AAATAAAGAATAACTAGGAC
* * ** *
24345915 AATACCGCGAGTCAAAAAATAAAGAATAACTGGGAC
1 AACACTGTAAGTC-AAAAATAAAGAATAACTAGGAC
* * *
24345951 AAC-GTCATATGTCAAAAATATAA-AATAACTAGGAC
1 AACACT-GTAAGTCAAAAATA-AAGAATAACTAGGAC
* * * * *
24345986 AACACTGTAAATCAAAAAATAAAAAACAA-TTGAGAT
1 AACACTGTAAGTC-AAAAATAAAGAATAACTAG-GAC
*
24346022 AACACTGCAAGTCAAAAATAAAGA
1 AACACTGTAAGTCAAAAATAAAGA
24346046 GCGACTGAAA
Statistics
Matches: 213, Mismatches: 48, Indels: 26
0.74 0.17 0.09
Matches are distributed among these distances:
34 1 0.00
35 73 0.34
36 137 0.64
37 2 0.01
ACGTcount: A:0.54, C:0.15, G:0.14, T:0.17
Consensus pattern (35 bp):
AACACTGTAAGTCAAAAATAAAGAATAACTAGGAC
Found at i:24346304 original size:107 final size:106
Alignment explanation
Indices: 24345650--24346398 Score: 402
Period size: 107 Copynumber: 7.1 Consensus size: 106
24345640 TCAAGTAATT
* * * * * * * * *
24345650 AAAAATGATTAAGACAATACCACAAGTCAAAAAATAAAGAACGA-TCGAGATAACAACGTAAATC
1 AAAAATAACTAAGACAACACTACAAGTC-AAAAATAAAGAATGACT-GAGATAACACCGCAAGTT
* * *
24345714 AAAAAATAAAA-AATGACT-GA-AATAACACTGCAAGTCAAAAATA
64 AAAAAATAAAAGAATGACTGGACAACATCA-T--AAGTAAAAAATA
* * * * * * **
24345757 AAAAATGA-TCAGGACAACA-TCATAAGTTAAAAAATAAAGAATGA-TCAGGACAACACCATAAG
1 AAAAATAACT-AAGACAACACT-ACAAG-TCAAAAATAAAGAATGACTGA-GATAACACCGCAAG
* * ** * * * * * *
24345819 TCAAAAAAT-AAAGAACGATCAAGATAACACCGTAAATTATAAATA
62 TTAAAAAATAAAAGAATGA-CTGGACAACATCATAAGTAAAAAATA
* * ** * * * * * *
24345864 AAGAATAACTAGGACAACACTGTAAGTCAAGTAATAAAGAATGACTGGGACAATACCGCGAGTCA
1 AAAAATAACTAAGACAACACTACAAGTCAA-AAATAAAGAATGACTGAGATAACACCGCAAGTTA
* * * *
24345929 AAAAAT-AAAGAATAACTGGGACAACGTCATATGTCAAAAATA
65 AAAAATAAAAGAATGACT-GGACAACATCATAAGTAAAAAATA
* * ** * * ** * * *
24345971 TAAAATAACTAGGACAACACTGTAAATCAAAAAATAAAAAACAATTGAGATAACACTGCAAG-TC
1 AAAAATAACTAAGACAACACTACAAGTC-AAAAATAAAGAATGACTGAGATAACACCGCAAGTTA
** * *
24346035 AAAAAT-AAAGAGCGACTGAAACAACATCATAAGTCAAAAATA
65 AAAAATAAAAGAATGACTG-GACAACATCATAAGTAAAAAATA
* * ** * *
24346077 AAAAATGA-TCGAGACAACAC--CATAG--AAAAATAAAGAATGACCAAGATAACATCACAAG-T
1 AAAAATAACT-AAGACAACACTACA-AGTCAAAAATAAAGAATGACTGAGATAACACCGCAAGTT
* * * *
24346136 CAAAAATAAAAG-ATGACCCGGATAACATCATAAGTCAAAAATA
64 AAAAAATAAAAGAATGA-CTGGACAACATCATAAGTAAAAAATA
** *
24346179 AAAAACGACTAAGACAACACTACAAGTCAAAAATAAAGAATGACTGAGATAACATCGCAAGTTAA
1 AAAAATAACTAAGACAACACTACAAGTCAAAAATAAAGAATGACTGAGATAACACCGCAAGTTAA
* *
24346244 AAAATAAAAGAATGACTGTGATAACATCATAACTAAAAAATA
66 AAAATAAAAGAATGACTG-GACAACATCATAAGTAAAAAATA
** * * * * * * *
24346286 AAGGATAACCAAGACAACACCACAAGTTAAAAATAACGAATGACTGAGACAACACCGTAAGTTAG
1 AAAAATAACTAAGACAACACTACAAGTCAAAAATAAAGAATGACTGAGATAACACCGCAAGTTAA
* * * *
24346351 AAAATAAAA-AATGATTAGGATAACACCGTAAGTTAAAAAATA
66 AAAATAAAAGAATGACT-GGACAACATCATAAG-TAAAAAATA
24346393 AAAAAT
1 AAAAAT
24346399 GCTAATATGA
Statistics
Matches: 503, Mismatches: 110, Indels: 58
0.75 0.16 0.09
Matches are distributed among these distances:
102 71 0.14
103 9 0.02
104 3 0.01
105 33 0.07
106 88 0.17
107 285 0.57
108 7 0.01
109 3 0.01
110 4 0.01
ACGTcount: A:0.55, C:0.15, G:0.13, T:0.17
Consensus pattern (106 bp):
AAAAATAACTAAGACAACACTACAAGTCAAAAATAAAGAATGACTGAGATAACACCGCAAGTTAA
AAAATAAAAGAATGACTGGACAACATCATAAGTAAAAAATA
Found at i:24346318 original size:142 final size:140
Alignment explanation
Indices: 24346029--24346399 Score: 362
Period size: 142 Copynumber: 2.6 Consensus size: 140
24346019 GATAACACTG
* *
24346029 CAAGTCAAAAATAAAGAGCGACTGAA-ACAACA-TCATAAGTCAAAAATAAAAAATGATCGAGAC
1 CAAGTCAAAAATAAAGAACGACT-AAGACAACACT-ATAAGTCAAAAATAAAAAATGAT-GAGAT
* * *
24346092 AACAC-C-A--TAGAAAAAT-AAAGAATGACCAAGATAACATCACAAGTCAAAAATAAAAGATGA
63 AACACGCAAGTTA-AAAAATAAAAGAATGACCAAGATAACATCACAACTAAAAAATAAAAGATAA
** * *
24346152 CCCGGATAACATCA
127 CCAAGACAACACCA
* * * *
24346166 TAAGTCAAAAATAAAAAACGACTAAGACAACACTACAAGTCAAAAATAAAGAATGACTGAGATAA
1 CAAGTCAAAAATAAAGAACGACTAAGACAACACTATAAGTCAAAAATAAAAAATGA-TGAGATAA
*** * *
24346231 CATCGCAAGTTAAAAAATAAAAGAATGACTGTGATAACATCATAACTAAAAAATAAAGGATAACC
65 CA-CGCAAGTTAAAAAATAAAAGAATGACCAAGATAACATCACAACTAAAAAATAAAAGATAACC
24346296 AAGACAACACCA
129 AAGACAACACCA
* * * * ** * *
24346308 CAAGTTAAAAATAACGAATGACTGAGACAACACCGTAAGTTAGAAAATAAAAAATGATTAGGATA
1 CAAGTCAAAAATAAAGAACGACTAAGACAACACTATAAGTCA-AAAATAAAAAATGATGA-GATA
*
24346373 ACACCGTAAGTTAAAAAATAAAA-AATG
64 ACA-CGCAAGTTAAAAAATAAAAGAATG
24346400 CTAATATGAG
Statistics
Matches: 191, Mismatches: 32, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
136 2 0.01
137 54 0.28
138 3 0.02
139 1 0.01
140 1 0.01
141 6 0.03
142 86 0.45
143 38 0.20
ACGTcount: A:0.56, C:0.15, G:0.13, T:0.16
Consensus pattern (140 bp):
CAAGTCAAAAATAAAGAACGACTAAGACAACACTATAAGTCAAAAATAAAAAATGATGAGATAAC
ACGCAAGTTAAAAAATAAAAGAATGACCAAGATAACATCACAACTAAAAAATAAAAGATAACCAA
GACAACACCA
Found at i:24346591 original size:33 final size:33
Alignment explanation
Indices: 24346484--24346709 Score: 151
Period size: 32 Copynumber: 7.0 Consensus size: 33
24346474 TAGGCTTACA
* * *
24346484 TGCCAACTAAATTGGGCTTAAATTTTCATAGAAG
1 TGCCAACTAAATTAGGCTTAAATTTTCATTG-GG
* **
24346518 T--CAAGTAAATTA-GCTTAAATCTTT-ATTGAA
1 TGCCAACTAAATTAGGCTTAAAT-TTTCATTGGG
* * **
24346548 TGCTAGCTAAATTAGGCTTAAAACTTCATTGGG
1 TGCCAACTAAATTAGGCTTAAATTTTCATTGGG
* *
24346581 TGCCAACTAAATT-GGATTTAAATTTTCATTAGG
1 TGCCAACTAAATTAGG-CTTAAATTTTCATTGGG
* * * *
24346614 TGCCAGCTAAACT-GGGTTTAATTTTCATTGGG
1 TGCCAACTAAATTAGGCTTAAATTTTCATTGGG
* * * *
24346646 TGTCAACTAAACTAGGTTTAAA-TTTCATTAGG
1 TGCCAACTAAATTAGGCTTAAATTTTCATTGGG
*** * *
24346678 TATTAGCTAATTTAGGCTTAAATTTTCATTGG
1 TGCCAACTAAATTAGGCTTAAATTTTCATTGG
24346710 ACACTAGCTA
Statistics
Matches: 150, Mismatches: 34, Indels: 17
0.75 0.17 0.08
Matches are distributed among these distances:
30 2 0.01
31 11 0.07
32 74 0.49
33 62 0.41
34 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (33 bp):
TGCCAACTAAATTAGGCTTAAATTTTCATTGGG
Found at i:24346702 original size:65 final size:66
Alignment explanation
Indices: 24346550--24346709 Score: 191
Period size: 65 Copynumber: 2.5 Consensus size: 66
24346540 TTATTGAATG
** *
24346550 CTAGCTAAATTAGGCTTAAAACTTCATTGGGTGCCAACTAAATTGGATTTAAATTTTCATTAGGT
1 CTAGCTAAATTAGGCTTAAATTTTCATTGGGTGCCAACTAAATAGGATTTAAATTTTCATTAGGT
*
24346615 G
66 A
* * * * *
24346616 CCAGCTAAACT-GGGTTTAATTTTCATTGGGTGTCAACTAAACTAGG-TTTAAA-TTTCATTAGG
1 CTAGCTAAATTAGGCTTAAATTTTCATTGGGTGCCAACTAAA-TAGGATTTAAATTTTCATTAGG
24346678 TA
65 TA
* *
24346680 TTAGCTAATTTAGGCTTAAATTTTCATTGG
1 CTAGCTAAATTAGGCTTAAATTTTCATTGG
24346710 ACACTAGCTA
Statistics
Matches: 77, Mismatches: 15, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
64 18 0.23
65 47 0.61
66 12 0.16
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (66 bp):
CTAGCTAAATTAGGCTTAAATTTTCATTGGGTGCCAACTAAATAGGATTTAAATTTTCATTAGGT
A
Found at i:24347421 original size:20 final size:20
Alignment explanation
Indices: 24347372--24347425 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 20
24347362 TTCTCAGTTC
*
24347372 CTTCTTTCTTTTTTTTTTTG
1 CTTCTATCTTTTTTTTTTTG
*
24347392 C-T-TAT-TTTTTTTATTTTT
1 CTTCTATCTTTTTTT-TTTTG
24347410 CTTCTATCTTTTTTTT
1 CTTCTATCTTTTTTTT
24347426 GCTGATTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
17 7 0.25
18 7 0.25
19 2 0.07
20 5 0.18
21 7 0.25
ACGTcount: A:0.06, C:0.13, G:0.02, T:0.80
Consensus pattern (20 bp):
CTTCTATCTTTTTTTTTTTG
Found at i:24350318 original size:178 final size:176
Alignment explanation
Indices: 24350018--24350412 Score: 634
Period size: 178 Copynumber: 2.2 Consensus size: 176
24350008 CTTGTGTAGG
* *
24350018 GAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGGAAATTTCGATTTTTAAGGAAAA
1 GAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTC-ATTTCTAAGGAAAA
* **
24350082 TTGATACTTTCAACTTTTCTTCAAAAATCTTTTTTTTGAAAATTTATTTTTAAGGAAAATTGATA
65 TTGATACTTTCAACTTTTCCTCAAAAATCCCTTTTTTGAAAATTTATTTTTAAGGAAAATTGATA
*
24350147 CTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAAATTTTGATTT-TCAAA
130 CTTTCAACTTTTCCCCAAAAATA-TTTTTTTGAAAA-TTT-ATTTCT-AAA
*
24350197 GAAAATTGATACTTTCAATTTTTCCCCAAAAATATTTTTTTGAAAATTT-ATTTCTAAGGAAAAT
1 GAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTCATTTCTAAGGAAAAT
24350261 TGATACTTTCAACTTTTCCTCAAAAATCCCTTTTTTGAAAATTTATTTTTAAGGAAAATTGATAC
66 TGATACTTTCAACTTTTCCTCAAAAATCCCTTTTTTGAAAATTTATTTTTAAGGAAAATTGATAC
* *
24350326 TTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTATTTCTAAG
131 TTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTCTAAA
*
24350372 GAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTT
1 GAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTT
24350413 TTGATTTAAA
Statistics
Matches: 203, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
175 45 0.22
176 4 0.02
177 11 0.05
178 97 0.48
179 33 0.16
180 13 0.06
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (176 bp):
GAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTCATTTCTAAGGAAAAT
TGATACTTTCAACTTTTCCTCAAAAATCCCTTTTTTGAAAATTTATTTTTAAGGAAAATTGATAC
TTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTCTAAA
Found at i:24350412 original size:59 final size:58
Alignment explanation
Indices: 24350017--24350412 Score: 587
Period size: 59 Copynumber: 6.7 Consensus size: 58
24350007 TCTTGTGTAG
*
24350017 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGGAAATTTCGATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTT--ATTTTTAA
** *
24350076 GGAAAATTGATACTTTCAACTTTTCTTCAAAAATCTTTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAAT-ATTTTTTTGAAAATTTATTTTTAA
* *
24350135 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTTGAAAA-TTT-ATTTTTAA
* * *
24350196 AGAAAATTGATACTTTCAATTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTAA
* **
24350254 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCCTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAAT-ATTTTTTTGAAAATTTATTTTTAA
* *
24350313 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTAA
*
24350371 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTT
24350413 TTGATTTAAA
Statistics
Matches: 305, Mismatches: 26, Indels: 13
0.89 0.08 0.04
Matches are distributed among these distances:
58 98 0.32
59 140 0.46
60 15 0.05
61 52 0.17
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.45
Consensus pattern (58 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTAA
Found at i:24350474 original size:21 final size:21
Alignment explanation
Indices: 24350421--24350497 Score: 59
Period size: 21 Copynumber: 3.5 Consensus size: 21
24350411 TTTTGATTTA
* *
24350421 AAAAATACAAAACAAAATAAAAGT
1 AAAAATA-AAAA-AAAGTAAAA-C
*
24350445 AAAAGTAAATAAAGAAG-AAAA-
1 AAAAATAAA-AAA-AAGTAAAAC
*
24350466 AAAAATAAAGAAAAGTAAAAC
1 AAAAATAAAAAAAAGTAAAAC
24350487 AAAAATAAAAA
1 AAAAATAAAAA
24350498 TAGGATAAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
19 3 0.07
20 6 0.14
21 18 0.41
23 7 0.16
24 10 0.23
ACGTcount: A:0.78, C:0.04, G:0.08, T:0.10
Consensus pattern (21 bp):
AAAAATAAAAAAAAGTAAAAC
Found at i:24350563 original size:25 final size:26
Alignment explanation
Indices: 24350535--24350583 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
24350525 AATATAATCT
*
24350535 AATAAATAAAAAAAT-AAAAAAAACA
1 AATAAACAAAAAAATGAAAAAAAACA
*
24350560 AATAAACAAATAAATGAAAAAAAA
1 AATAAACAAAAAAATGAAAAAAAA
24350584 AAAACCTGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.82, C:0.04, G:0.02, T:0.12
Consensus pattern (26 bp):
AATAAACAAAAAAATGAAAAAAAACA
Found at i:24351455 original size:21 final size:22
Alignment explanation
Indices: 24351431--24351475 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
24351421 AAAACTAGAT
24351431 AATTA-GAAAAGATAAATAAAA
1 AATTATGAAAAGATAAATAAAA
* *
24351452 AATTATTATAAGATAAATAAAA
1 AATTATGAAAAGATAAATAAAA
24351474 AA
1 AA
24351476 GAAATAACAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (22 bp):
AATTATGAAAAGATAAATAAAA
Found at i:24351488 original size:22 final size:22
Alignment explanation
Indices: 24351439--24351481 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
24351429 ATAATTAGAA
** *
24351439 AAGATAAATAAAAAATTATTAT
1 AAGATAAATAAAAAAGAAATAT
24351461 AAGATAAATAAAAAAGAAATA
1 AAGATAAATAAAAAAGAAATA
24351482 ACAGATATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (22 bp):
AAGATAAATAAAAAAGAAATAT
Found at i:24351527 original size:17 final size:18
Alignment explanation
Indices: 24351498--24351536 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
24351488 ATATAATTAG
24351498 ATAAATAAAAATACAAAA
1 ATAAATAAAAATACAAAA
*
24351516 ATAAAT-AAAATATAAAA
1 ATAAATAAAAATACAAAA
24351533 ATAA
1 ATAA
24351537 TAATATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (18 bp):
ATAAATAAAAATACAAAA
Found at i:24351543 original size:14 final size:14
Alignment explanation
Indices: 24351518--24351558 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
24351508 ATACAAAAAT
24351518 AAATAA-AATATAA
1 AAATAATAATATAA
24351531 AAATAATAATATAA
1 AAATAATAATATAA
*
24351545 TAATAATAAATATA
1 AAATAAT-AATATA
24351559 TAACTATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 6 0.24
14 13 0.52
15 6 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAATAATAATATAA
Found at i:24351547 original size:17 final size:17
Alignment explanation
Indices: 24351512--24351575 Score: 51
Period size: 17 Copynumber: 3.6 Consensus size: 17
24351502 ATAAAAATAC
*
24351512 AAAAATAAATAAAAT-AT
1 AAAAAT-AATAATATAAT
24351529 AAAAATAATAATATAAT
1 AAAAATAATAATATAAT
*
24351546 AATAATAA-ATATATAACT
1 AAAAATAATA-ATATAA-T
24351564 ATATAAATAATA
1 A-A-AAATAATA
24351576 TACATATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
16 8 0.21
17 21 0.55
18 2 0.05
19 1 0.03
20 5 0.13
21 1 0.03
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAAATAATAATATAAT
Found at i:24351561 original size:14 final size:14
Alignment explanation
Indices: 24351532--24351669 Score: 58
Period size: 14 Copynumber: 9.5 Consensus size: 14
24351522 AAAATATAAA
24351532 AATAAT-AATATAAT
1 AATAATAAATAT-AT
24351546 AATAATAAATATAT
1 AATAATAAATATAT
24351560 AACTATATAAATAATAT
1 AA-TA-ATAAAT-ATAT
*
24351577 ACAT-ATAAATCTATTCT
1 A-ATAATAAA--TA-TAT
*
24351594 AAATAATTAAAAATA-
1 -AATAA-TAAATATAT
24351609 AATAAATAAATATA-
1 AAT-AATAAATATAT
* *
24351623 GAT-ATACATATATT
1 AATAATAAATATA-T
24351637 AATACAT-AATA-AT
1 AATA-ATAAATATAT
*
24351650 AATAATAAATACAT
1 AATAATAAATATAT
24351664 AA-AATA
1 AATAATA
24351670 TAAAAGAAAA
Statistics
Matches: 98, Mismatches: 8, Indels: 37
0.69 0.06 0.26
Matches are distributed among these distances:
12 10 0.10
13 13 0.13
14 29 0.30
15 17 0.17
16 10 0.10
17 12 0.12
18 3 0.03
19 4 0.04
ACGTcount: A:0.61, C:0.05, G:0.01, T:0.33
Consensus pattern (14 bp):
AATAATAAATATAT
Found at i:24351576 original size:17 final size:17
Alignment explanation
Indices: 24351535--24351586 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
24351525 ATATAAAAAT
24351535 AATAATATAA-TAATAATA
1 AATAATATAACT-AT-ATA
24351553 AAT-ATATAACTATATA
1 AATAATATAACTATATA
24351569 AATAATAT-AC-ATATA
1 AATAATATAACTATATA
24351584 AAT
1 AAT
24351587 CTATTCTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
15 8 0.25
16 8 0.25
17 12 0.38
18 4 0.12
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (17 bp):
AATAATATAACTATATA
Found at i:24351584 original size:15 final size:16
Alignment explanation
Indices: 24351538--24351586 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
24351528 TAAAAATAAT
24351538 AATATAATAA-TA-ATA
1 AATAT-ATAACTATATA
24351553 AATATATAACTATATA
1 AATATATAACTATATA
24351569 AATA-ATATAC-ATATA
1 AATATATA-ACTATATA
24351584 AAT
1 AAT
24351587 CTATTCTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
14 4 0.13
15 18 0.58
16 9 0.29
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (16 bp):
AATATATAACTATATA
Found at i:24351856 original size:1 final size:1
Alignment explanation
Indices: 24351850--24351910 Score: 68
Period size: 1 Copynumber: 61.0 Consensus size: 1
24351840 CTCAACATCA
* * ** * *
24351850 TTTTTTTTGTTTTTTTTTATTTTTTTTTTTTTTTTTGATTTTTTTTGTTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
24351911 CTTAACCAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.03, C:0.00, G:0.07, T:0.90
Consensus pattern (1 bp):
T
Found at i:24351873 original size:19 final size:20
Alignment explanation
Indices: 24351849--24351903 Score: 96
Period size: 19 Copynumber: 2.9 Consensus size: 20
24351839 ACTCAACATC
24351849 ATTTTTTTTGTTTTTTTTT-
1 ATTTTTTTTGTTTTTTTTTG
24351868 ATTTTTTTT-TTTTTTTTTG
1 ATTTTTTTTGTTTTTTTTTG
24351887 ATTTTTTTTGTTTTTTT
1 ATTTTTTTTGTTTTTTT
24351904 GTTTTTTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
18 9 0.26
19 18 0.53
20 7 0.21
ACGTcount: A:0.05, C:0.00, G:0.05, T:0.89
Consensus pattern (20 bp):
ATTTTTTTTGTTTTTTTTTG
Found at i:24351891 original size:28 final size:28
Alignment explanation
Indices: 24351850--24351910 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
24351840 CTCAACATCA
* *
24351850 TTTTTTTTGTTTTTTTTTATTTTTTTTT
1 TTTTTTTTGATTTTTTTTATTTTTTTGT
*
24351878 TTTTTTTTGATTTTTTTTGTTTTTTTGT
1 TTTTTTTTGATTTTTTTTATTTTTTTGT
24351906 TTTTT
1 TTTTT
24351911 CTTAACCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.03, C:0.00, G:0.07, T:0.90
Consensus pattern (28 bp):
TTTTTTTTGATTTTTTTTATTTTTTTGT
Found at i:24351910 original size:10 final size:10
Alignment explanation
Indices: 24351850--24351903 Score: 76
Period size: 10 Copynumber: 5.6 Consensus size: 10
24351840 CTCAACATCA
24351850 TTTTTTTTGT
1 TTTTTTTTGT
*
24351860 TTTTTTTT-A
1 TTTTTTTTGT
24351869 TTTTTTTT-T
1 TTTTTTTTGT
*
24351878 TTTTTTTTGA
1 TTTTTTTTGT
24351888 TTTTTTTTGT
1 TTTTTTTTGT
24351898 TTTTTT
1 TTTTTT
24351904 GTTTTTTCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
9 16 0.41
10 23 0.59
ACGTcount: A:0.04, C:0.00, G:0.06, T:0.91
Consensus pattern (10 bp):
TTTTTTTTGT
Found at i:24352094 original size:42 final size:41
Alignment explanation
Indices: 24351921--24352260 Score: 520
Period size: 42 Copynumber: 8.1 Consensus size: 41
24351911 CTTAACCAAA
* * * *
24351921 GCTCCTCTAAACAGAGGCTCAACAACTTTGAGAAACATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAA-GTAAATT
24351964 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
24352005 GCTCCTCTAAACAGAGGCACCACGACTTTG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* *
24352045 GGTCCTCTAAACAGAGGTACCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATT
* *
24352087 GCTCCTCTAAACAGAGGCACGACGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
24352128 GCTCCTCTAAACAGAGGTACCACGACTTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTT-GAAAAGTAAATT
*
24352171 GCTCCTTTAAACAGAGGCACCACGACTTTGAAAATGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAA-GTAAATT
24352213 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATT
24352255 GCTCCT
1 GCTCCT
24352261 TGACAATCAT
Statistics
Matches: 275, Mismatches: 16, Indels: 13
0.90 0.05 0.04
Matches are distributed among these distances:
40 37 0.13
41 77 0.28
42 93 0.34
43 68 0.25
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.24
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
Found at i:24353502 original size:23 final size:22
Alignment explanation
Indices: 24353471--24353532 Score: 67
Period size: 20 Copynumber: 2.9 Consensus size: 22
24353461 AATTTGAATC
*
24353471 TCTTTTTTCATTTTTTCATTTTT
1 TCTTCTTTCATTTTTTC-TTTTT
*
24353494 TCTTCTTTC-TTTCTT-TTTTT
1 TCTTCTTTCATTTTTTCTTTTT
*
24353514 TCTTCTTT-TTTTTTTCTTT
1 TCTTCTTTCATTTTTTCTTT
24353533 GTTTTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 18 0.53
21 3 0.09
22 5 0.15
23 8 0.24
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (22 bp):
TCTTCTTTCATTTTTTCTTTTT
Found at i:24353507 original size:8 final size:7
Alignment explanation
Indices: 24353471--24353542 Score: 69
Period size: 7 Copynumber: 10.1 Consensus size: 7
24353461 AATTTGAATC
24353471 TCTTTTT
1 TCTTTTT
24353478 TCATTTTT
1 TC-TTTTT
24353486 TCATTTTT
1 TC-TTTTT
*
24353494 TCTTCTT
1 TCTTTTT
*
24353501 TCTTTCT
1 TCTTTTT
24353508 T-TTTTT
1 TCTTTTT
24353514 TCTTCTTT
1 TCTT-TTT
24353522 T-TTTTT
1 TCTTTTT
24353528 TCTTTGTT
1 TCTTT-TT
24353536 T-TTTTT
1 TCTTTTT
24353542 T
1 T
24353543 TTCATCTATT
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
6 12 0.21
7 22 0.39
8 22 0.39
ACGTcount: A:0.03, C:0.14, G:0.01, T:0.82
Consensus pattern (7 bp):
TCTTTTT
Found at i:24353508 original size:11 final size:10
Alignment explanation
Indices: 24353489--24353545 Score: 57
Period size: 11 Copynumber: 5.7 Consensus size: 10
24353479 CATTTTTTCA
24353489 TTTTTTCTTC
1 TTTTTTCTTC
24353499 TTTCTTTCTT-
1 TTT-TTTCTTC
24353509 TTTTTTCTTC
1 TTTTTTCTTC
*
24353519 TTTTTTTTTTC
1 -TTTTTTCTTC
24353530 TTTGTTT-TT-
1 TTT-TTTCTTC
24353539 TTTTTTC
1 TTTTTTC
24353546 ATCTATTGTT
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
8 3 0.07
9 9 0.22
10 11 0.27
11 18 0.44
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (10 bp):
TTTTTTCTTC
Found at i:24353521 original size:12 final size:12
Alignment explanation
Indices: 24353499--24353538 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
24353489 TTTTTTCTTC
24353499 TTTCTTTCTTTTT
1 TTTC-TTCTTTTT
24353512 TTTCTTCTTTTT
1 TTTCTTCTTTTT
24353524 TTT-TTCTTTGTT
1 TTTCTTCTTT-TT
24353536 TTT
1 TTT
24353539 TTTTTTCATC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 6 0.23
12 16 0.62
13 4 0.15
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (12 bp):
TTTCTTCTTTTT
Found at i:24353529 original size:27 final size:28
Alignment explanation
Indices: 24353481--24353541 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
24353471 TCTTTTTTCA
24353481 TTTTTTCATTTTTTCTTCTTTCTTTCTT
1 TTTTTTCATTTTTTCTTCTTTCTTTCTT
* *
24353509 TTTTTTC-TTCTTTT-TTTTTTCTTTGTT
1 TTTTTTCATT-TTTTCTTCTTTCTTTCTT
24353536 TTTTTT
1 TTTTTT
24353542 TTTCATCTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 19 0.63
28 11 0.37
ACGTcount: A:0.02, C:0.13, G:0.02, T:0.84
Consensus pattern (28 bp):
TTTTTTCATTTTTTCTTCTTTCTTTCTT
Found at i:24353555 original size:20 final size:17
Alignment explanation
Indices: 24353489--24353544 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
24353479 CATTTTTTCA
* *
24353489 TTTTTTCTTCTTTCTTT
1 TTTTTTTTTCTTTGTTT
* *
24353506 CTTTTTTTTC--T-TCT
1 TTTTTTTTTCTTTGTTT
24353520 TTTTTTTTTCTTTGTTT
1 TTTTTTTTTCTTTGTTT
24353537 TTTTTTTT
1 TTTTTTTT
24353545 CATCTATTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
14 11 0.35
15 1 0.03
16 1 0.03
17 18 0.58
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.86
Consensus pattern (17 bp):
TTTTTTTTTCTTTGTTT
Found at i:24357508 original size:59 final size:59
Alignment explanation
Indices: 24357411--24357559 Score: 237
Period size: 61 Copynumber: 2.5 Consensus size: 59
24357401 ATTGTTCTTG
*
24357411 TTTAGGGAAAATTGATACTTTCAACTTTTTCCCAAAAAT-ATTTTTTGGAAATTTTGATT
1 TTTAAGGAAAATTGATACTTTCAAC-TTTTCCCAAAAATCATTTTTTGGAAATTTTGATT
*
24357470 TTTAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTTGGAAATTTTGATT
1 TTTAAGGAAAATTGATACTTTCAACTTTTCC-CAAAAAT-CATTTTTTGGAAATTTTGATT
*
24357531 TTCAAGGAAAATTGATACTTTCAACTTTT
1 TTTAAGGAAAATTGATACTTTCAACTTTT
24357560 TTGAGGAAAA
Statistics
Matches: 84, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
58 6 0.07
59 31 0.37
61 47 0.56
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (59 bp):
TTTAAGGAAAATTGATACTTTCAACTTTTCCCAAAAATCATTTTTTGGAAATTTTGATT
Found at i:24361811 original size:15 final size:15
Alignment explanation
Indices: 24361772--24361812 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
24361762 TTTTGTAAGT
*
24361772 GTAATGAATGAGAAT
1 GTAATGAATGAGAAC
*
24361787 GCAATGAATGAGAAC
1 GTAATGAATGAGAAC
*
24361802 GTAATCAATGA
1 GTAATGAATGA
24361813 AAAATGCATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.46, C:0.07, G:0.24, T:0.22
Consensus pattern (15 bp):
GTAATGAATGAGAAC
Found at i:24363497 original size:9 final size:10
Alignment explanation
Indices: 24363483--24363528 Score: 51
Period size: 9 Copynumber: 4.5 Consensus size: 10
24363473 AGGAGTCTTT
24363483 TGTATT-TTA
1 TGTATTATTA
24363492 TGTATTTATTA
1 TGTA-TTATTA
24363503 T-TATTATTA
1 TGTATTATTA
24363512 TGTATTAATATA
1 TGTATT-AT-TA
24363524 TGTAT
1 TGTAT
24363529 ATCTGTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
9 11 0.34
10 8 0.25
11 6 0.19
12 7 0.22
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (10 bp):
TGTATTATTA
Found at i:24363514 original size:20 final size:20
Alignment explanation
Indices: 24363485--24363553 Score: 63
Period size: 19 Copynumber: 3.5 Consensus size: 20
24363475 GAGTCTTTTG
24363485 TATT-TTATGTATTTATTAT
1 TATTATTATGTATTTATTAT
*
24363504 TATTATTATGTA-TTAATA-
1 TATTATTATGTATTTATTAT
*
24363522 TATGTATATCTGTATTTATTTAT
1 TAT-TAT-TATGTATTTA-TTAT
*
24363545 TTTTATTAT
1 TATTATTAT
24363554 TTAGAATAGA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
18 3 0.08
19 12 0.31
20 12 0.31
21 5 0.13
22 5 0.13
23 2 0.05
ACGTcount: A:0.29, C:0.01, G:0.06, T:0.64
Consensus pattern (20 bp):
TATTATTATGTATTTATTAT
Found at i:24363556 original size:17 final size:17
Alignment explanation
Indices: 24363534--24363653 Score: 54
Period size: 17 Copynumber: 6.8 Consensus size: 17
24363524 TGTATATCTG
24363534 TATTTATTTATTTTTAT
1 TATTTATTTATTTTTAT
** *
24363551 TATTTAGAATAGATTTATAT
1 TATTT---ATTTATTTTTAT
*
24363571 GTATATTATTTATATAGTTAT
1 -TAT-TTATTTAT-T-TTTAT
24363592 ATATTTA-TTATTATATTAT
1 -TATTTATTTATT-T-TTAT
24363611 TA-TTA-TTATTTTTA-
1 TATTTATTTATTTTTAT
*
24363625 TATTTTATTTATTTTT-G
1 TA-TTTATTTATTTTTAT
24363642 TATTT-TTTATTT
1 TATTTATTTATTT
24363654 ATCTAATTAT
Statistics
Matches: 82, Mismatches: 9, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
14 2 0.02
15 10 0.12
16 7 0.09
17 23 0.28
18 4 0.05
19 12 0.15
20 13 0.16
21 9 0.11
22 2 0.02
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (17 bp):
TATTTATTTATTTTTAT
Found at i:24363570 original size:40 final size:39
Alignment explanation
Indices: 24363490--24363583 Score: 102
Period size: 40 Copynumber: 2.4 Consensus size: 39
24363480 TTTTGTATTT
* *
24363490 TATGTATTTA-TTATTATTATTATGTATTAATATATGTA
1 TATGTATTTATTTATTATTATTATGTATGAATAGATGTA
* * *
24363528 TATCTGTATTTATTTATTTTTATTATTTA-GAATAGATTTA
1 TA--TGTATTTATTTATTATTATTATGTATGAATAGATGTA
24363568 TATGTATATTATTTAT
1 TATGTAT-TTATTTAT
24363584 ATAGTTATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
38 7 0.15
39 8 0.17
40 18 0.38
41 14 0.30
ACGTcount: A:0.32, C:0.01, G:0.07, T:0.60
Consensus pattern (39 bp):
TATGTATTTATTTATTATTATTATGTATGAATAGATGTA
Found at i:24363581 original size:15 final size:15
Alignment explanation
Indices: 24363563--24363611 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 15
24363553 TTTAGAATAG
24363563 ATTTATATGTATATT
1 ATTTATATGTATATT
24363578 ATTTATATAGT-TATAT
1 ATTTATAT-GTATAT-T
24363594 ATTTATTAT-TATATT
1 ATTTA-TATGTATATT
24363609 ATT
1 ATT
24363612 ATTATTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 16 0.53
16 11 0.37
17 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (15 bp):
ATTTATATGTATATT
Found at i:24363591 original size:23 final size:22
Alignment explanation
Indices: 24363565--24363627 Score: 60
Period size: 23 Copynumber: 2.9 Consensus size: 22
24363555 TAGAATAGAT
*
24363565 TTATATGTATATTATTTATATAG
1 TTATATATATATTA-TTATATAG
*
24363588 TTATATATTTATTATTATATTA-
1 TTATATATATATTATTATA-TAG
*
24363610 TTAT-TAT-TATTTTTATAT
1 TTATATATATATTATTATAT
24363628 TTTATTTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 1 0.03
20 9 0.25
21 3 0.08
22 9 0.25
23 14 0.39
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (22 bp):
TTATATATATATTATTATATAG
Found at i:24364042 original size:25 final size:25
Alignment explanation
Indices: 24363989--24364042 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
24363979 CTGGGAGTGA
* *
24363989 GAAAAAATTTTTAGAAGTTTTTGGT
1 GAAAAAATTTTTAGAAATTTCTGGT
*
24364014 GAAAAAATTTTTTGGAAATTTCTGG-
1 GAAAAAA-TTTTTAGAAATTTCTGGT
24364039 GAAA
1 GAAA
24364043 TTTCCAGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.39, C:0.02, G:0.20, T:0.39
Consensus pattern (25 bp):
GAAAAAATTTTTAGAAATTTCTGGT
Found at i:24364580 original size:25 final size:24
Alignment explanation
Indices: 24364545--24364591 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
24364535 TCTAGGTTTT
*
24364545 TTTTTTCATTTATTTGTTTATTTG
1 TTTTTTCATTTATTTATTTATTTG
*
24364569 TTTTTTCTATTTTTTTATTTATT
1 TTTTTTC-ATTTATTTATTTATT
24364592 AGATTAGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.79
Consensus pattern (24 bp):
TTTTTTCATTTATTTATTTATTTG
Done.