Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold66
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: 4623749
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 850 characters in sequence are not A, C, G, or T
File 7 of 26
Found at i:1196319 original size:24 final size:24
Alignment explanation
Indices: 1196292--1196337 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1196282 ATTAAAAATA
*
1196292 ATATAA-ATAAATATTTTAAATTTT
1 ATATAATATAAAT-TATTAAATTTT
1196316 ATATAATATAAATTATTAAATT
1 ATATAATATAAATTATTAAATT
1196338 ATTAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
ATATAATATAAATTATTAAATTTT
Found at i:1196326 original size:58 final size:59
Alignment explanation
Indices: 1196256--1196371 Score: 141
Period size: 56 Copynumber: 2.0 Consensus size: 59
1196246 AATGAGATGA
*
1196256 TTATATTATATAAAATGTAATATAA-TATTAAAAATAATAT-AA-AT-AAATATTTTAAATT
1 TTATATAATAT-AAAT-TAATA-AATTATTAAAAATAATATAAATATAAAATATTTTAAATT
* * *
1196314 TTATATAATATAAATTATTAAATTATTAAAATTTATATAAATATAAAATATTTTAAAT
1 TTATATAATATAAATTAATAAATTATTAAAAATAATATAAATATAAAATATTTTAAAT
1196372 ATAATTATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
55 2 0.04
56 17 0.34
57 6 0.12
58 12 0.24
59 13 0.26
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (59 bp):
TTATATAATATAAATTAATAAATTATTAAAAATAATATAAATATAAAATATTTTAAATT
Found at i:1196820 original size:2 final size:2
Alignment explanation
Indices: 1196813--1196868 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1196803 ACGTATTTGA
1196813 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1196855 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1196869 GGACGATGTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1200152 original size:2 final size:2
Alignment explanation
Indices: 1200145--1200172 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1200135 AAAATTAGCA
1200145 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
1200173 GTTGTTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1202584 original size:22 final size:24
Alignment explanation
Indices: 1202556--1202612 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 24
1202546 GTTGTTTTTA
*
1202556 TTATTATTA-TGTTGTAGTTGTTG
1 TTATTATTATTGTTGTAATTGTTG
1202579 -TATTATTATATTGTTGTAATTGTTG
1 TTATTA-T-TATTGTTGTAATTGTTG
1202604 TTATTATTA
1 TTATTATTA
1202613 ACATATTGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 5 0.17
23 1 0.03
24 4 0.14
25 14 0.48
26 5 0.17
ACGTcount: A:0.23, C:0.00, G:0.16, T:0.61
Consensus pattern (24 bp):
TTATTATTATTGTTGTAATTGTTG
Found at i:1202886 original size:21 final size:21
Alignment explanation
Indices: 1202860--1202902 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1202850 GCCGCCAGAT
1202860 ATCAATATGTTAAAAAAATAA
1 ATCAATATGTTAAAAAAATAA
* * *
1202881 ATCAATTTGTTAAGACAATAA
1 ATCAATATGTTAAAAAAATAA
1202902 A
1 A
1202903 GAAATGGAAG
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:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
ATCAATATGTTAAAAAAATAA
Found at i:1202971 original size:2 final size:2
Alignment explanation
Indices: 1202966--1202998 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1202956 TATATGTATA
1202966 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1202999 TTTAAGATTC
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1213947 original size:2 final size:2
Alignment explanation
Indices: 1213935--1213964 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1213925 ATGTATTTCA
*
1213935 AT AT AT GT 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
1213965 GGATGTTGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1214581 original size:18 final size:19
Alignment explanation
Indices: 1214544--1214588 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1214534 TTTATATATT
1214544 AATAATA-T-ATAAATTTA
1 AATAATATTAATAAATTTA
*
1214561 AATATTATTAATAAA-TTA
1 AATAATATTAATAAATTTA
1214579 AATAATATTA
1 AATAATATTA
1214589 TTTTATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.25
18 13 0.54
19 5 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATAATATTAATAAATTTA
Found at i:1215960 original size:41 final size:41
Alignment explanation
Indices: 1215915--1215995 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
1215905 AATAATCTGC
* * * *
1215915 AAACAAATTGTTTTAAAAAGATTGGCGATGTATGGTGTTAT
1 AAACAAATTGTTTCAAAAAGATTGGCAACGTAAGGTGTTAT
* *
1215956 AAACAATTTGTTTCCAAAAGATTGGCAACGTAAGGTGTTA
1 AAACAAATTGTTTCAAAAAGATTGGCAACGTAAGGTGTTA
1215996 AGGTTTAGGG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (41 bp):
AAACAAATTGTTTCAAAAAGATTGGCAACGTAAGGTGTTAT
Found at i:1217654 original size:30 final size:29
Alignment explanation
Indices: 1217618--1217697 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 29
1217608 AAGGGCATAT
*
1217618 TGATTAAATTATTATTGATTTTTAAATAAA
1 TGATTAAA-TATTATTGATTTTAAAATAAA
* *
1217648 TTATTAAAATATTATT-AATTTAAAATAAA
1 TGATT-AAATATTATTGATTTTAAAATAAA
1217677 TGATTAGAATATTATTG-TTTT
1 TGATTA-AATATTATTGATTTT
1217698 GATTGGCAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
28 1 0.02
29 27 0.64
30 11 0.26
31 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (29 bp):
TGATTAAATATTATTGATTTTAAAATAAA
Found at i:1217870 original size:16 final size:14
Alignment explanation
Indices: 1217849--1217882 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
1217839 CATTAACTGT
1217849 TATTATTATAATATTA
1 TATTATTAT-AT-TTA
1217865 TATTATTATATTTA
1 TATTATTATATTTA
1217879 TATT
1 TATT
1217883 TTTTAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 2 0.11
16 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTATTATATTTA
Found at i:1217914 original size:19 final size:19
Alignment explanation
Indices: 1217890--1217930 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1217880 ATTTTTTAAA
*
1217890 ATTAATAGAAG-ATTATATT
1 ATTAATAAAAGTA-TATATT
1217909 ATTAATAAAAGTATATATT
1 ATTAATAAAAGTATATATT
1217928 ATT
1 ATT
1217931 TTAAATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (19 bp):
ATTAATAAAAGTATATATT
Found at i:1218094 original size:20 final size:21
Alignment explanation
Indices: 1218057--1218098 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1218047 TAAGATTATA
**
1218057 TTAAAATAAAATTTATAATAT
1 TTAAAATAAAATAAATAATAT
1218078 TTAAAATAAAA-AAATAATAT
1 TTAAAATAAAATAAATAATAT
1218098 T
1 T
1218099 CGTAACATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TTAAAATAAAATAAATAATAT
Found at i:1223695 original size:2 final size:2
Alignment explanation
Indices: 1223688--1223728 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1223678 CTGTTTCGAG
1223688 TA TA TA TA TA TA TA TA TA TA 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 TA TA TA T
1223729 CGAATTTGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1228731 original size:9 final size:9
Alignment explanation
Indices: 1228717--1228754 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
1228707 CTCAATCTGC
1228717 TCTTCCTCT
1 TCTTCCTCT
1228726 TCTTCCTCT
1 TCTTCCTCT
*
1228735 TCTTCCTCC
1 TCTTCCTCT
1228744 TCTTCCTCT
1 TCTTCCTCT
1228753 TC
1 TC
1228755 CTCCAAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (9 bp):
TCTTCCTCT
Found at i:1228755 original size:15 final size:15
Alignment explanation
Indices: 1228698--1228758 Score: 58
Period size: 15 Copynumber: 4.3 Consensus size: 15
1228688 CATCCTCTAA
*
1228698 CTCCTCTTCCTCAAT-
1 CTCCTCTTCCTC-TTC
*
1228713 CTGCTCTTCCTCTTC
1 CTCCTCTTCCTCTTC
*
1228728 TTCCTC-T--TCTTC
1 CTCCTCTTCCTCTTC
1228740 CTCCTCTTCCTCTTC
1 CTCCTCTTCCTCTTC
1228755 CTCC
1 CTCC
1228759 AAATCACCCC
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
12 10 0.27
13 1 0.03
14 2 0.05
15 24 0.65
ACGTcount: A:0.03, C:0.49, G:0.02, T:0.46
Consensus pattern (15 bp):
CTCCTCTTCCTCTTC
Found at i:1234063 original size:3 final size:3
Alignment explanation
Indices: 1234057--1234087 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1234047 TATAATACAT
1234057 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1234088 AGTCTACAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1234588 original size:16 final size:16
Alignment explanation
Indices: 1234563--1234595 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1234553 AATTTTAATT
1234563 AATTTTTT-AATATTA
1 AATTTTTTAAATATTA
1234578 AATTATTTTAAATATTA
1 AATT-TTTTAAATATTA
1234595 A
1 A
1234596 TAAAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 4 0.25
17 8 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AATTTTTTAAATATTA
Found at i:1234935 original size:5 final size:5
Alignment explanation
Indices: 1234908--1235068 Score: 50
Period size: 5 Copynumber: 32.2 Consensus size: 5
1234898 CACATCATTG
* * * *
1234908 ATAT- ATATA ATAATA TTAT- ATATA ATATAA AAATA ATTAAA ATTTA
1 ATATA ATATA AT-ATA ATATA ATATA ATAT-A ATATA A-TATA ATATA
* * *
1234954 ATATAA TATATA ATATA ATATA A-A-A ATATA TATATAA ATATC TTAAA
1 ATAT-A -ATATA ATATA ATATA ATATA ATATA -ATAT-A ATATA ATATA
* * * * * * * *
1235001 AT-TT TTATA ATATA A-ATT AT-TA ATATA TTAAA ATAAA ATATC TTA-A
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
*
1235047 ATATA ATTAAA ATATA ATATA A
1 ATATA A-TATA ATATA ATATA A
1235069 AATATATTTT
Statistics
Matches: 111, Mismatches: 30, Indels: 31
0.65 0.17 0.18
Matches are distributed among these distances:
3 2 0.02
4 18 0.16
5 61 0.55
6 25 0.23
7 5 0.05
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:1234937 original size:17 final size:17
Alignment explanation
Indices: 1234908--1234974 Score: 57
Period size: 17 Copynumber: 3.9 Consensus size: 17
1234898 CACATCATTG
1234908 ATATAT-ATAATAATATT
1 ATATATAAT-ATAATATT
* *
1234925 ATATATAATATAAAAAT
1 ATATATAATATAATATT
* * *
1234942 A-ATTAAAATTTAATATA
1 ATA-TATAATATAATATT
1234959 ATATATAATATAATAT
1 ATATATAATATAATAT
1234975 AAAAATATAT
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
16 1 0.03
17 34 0.89
18 3 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATATAATATAATATT
Found at i:1234992 original size:12 final size:12
Alignment explanation
Indices: 1234953--1234994 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
1234943 ATTAAAATTT
1234953 AATATA-ATATA
1 AATATATATATA
*
1234964 TAATATAATATAAA
1 -AATAT-ATATATA
1234978 AATATATATATA
1 AATATATATATA
1234990 AATAT
1 AATAT
1234995 CTTAAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 16 0.62
13 6 0.23
14 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AATATATATATA
Found at i:1235518 original size:19 final size:19
Alignment explanation
Indices: 1235494--1235530 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1235484 TATTAAAATA
* *
1235494 AAATAATTTTTTATATTTT
1 AAATAATTATTTAAATTTT
1235513 AAATAATTATTTAAATTT
1 AAATAATTATTTAAATTT
1235531 AAGTAAAAAA
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
AAATAATTATTTAAATTTT
Found at i:1236019 original size:2 final size:2
Alignment explanation
Indices: 1236006--1236041 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1235996 TATCATCTAC
*
1236006 AT AT AC 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
1236042 GCCGAGATGT
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:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1236841 original size:18 final size:17
Alignment explanation
Indices: 1236820--1236889 Score: 67
Period size: 18 Copynumber: 4.2 Consensus size: 17
1236810 AAAATTATTA
1236820 TAATAATAAAATTAAAAT
1 TAATAATAAAA-TAAAAT
* *
1236838 TAATAATAAGATATATAT
1 TAATAATAAAATA-AAAT
1236856 TAAT-ATAAAAT--AA-
1 TAATAATAAAATAAAAT
1236869 TAATAATAAAATAAAAAT
1 TAATAATAAAAT-AAAAT
1236887 TAA
1 TAA
1236890 AAATTAAAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
13 4 0.10
14 8 0.19
17 10 0.24
18 20 0.48
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (17 bp):
TAATAATAAAATAAAAT
Found at i:1236963 original size:21 final size:21
Alignment explanation
Indices: 1236915--1236963 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
1236905 ACGTAAAAAT
* * *
1236915 ATATTAATTAATTATTTTTAT
1 ATATAAATTAATAATTTTTAC
*
1236936 GTATAAATTAATAATTTTTAC
1 ATATAAATTAATAATTTTTAC
*
1236957 ATTTAAA
1 ATATAAA
1236964 ATTTTAATAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (21 bp):
ATATAAATTAATAATTTTTAC
Found at i:1236996 original size:12 final size:12
Alignment explanation
Indices: 1236976--1237033 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
1236966 TTTAATAACT
1236976 ATTATTTTATATA
1 ATTA-TTTATATA
* *
1236989 TTTATTTAGATA
1 ATTATTTATATA
* *
1237001 ATTAATTTTTAAA
1 ATT-ATTTATATA
1237014 ATTATTTATA-A
1 ATTATTTATATA
1237025 ATTATTTAT
1 ATTATTTAT
1237034 TTTATTGAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
11 10 0.27
12 15 0.41
13 12 0.32
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (12 bp):
ATTATTTATATA
Found at i:1237067 original size:19 final size:18
Alignment explanation
Indices: 1237014--1237072 Score: 70
Period size: 17 Copynumber: 3.3 Consensus size: 18
1237004 AATTTTTAAA
1237014 ATTATTTATA-AATTATTT
1 ATTA-TTATAGAATTATTT
*
1237032 ATT-TTATTGAATT-TTT
1 ATTATTATAGAATTATTT
1237048 ATTATTATAGAATATATTT
1 ATTATTATAGAAT-TATTT
1237067 ATTATT
1 ATTATT
1237073 TATTATATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
16 10 0.29
17 12 0.34
18 4 0.11
19 9 0.26
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
ATTATTATAGAATTATTT
Found at i:1237075 original size:23 final size:21
Alignment explanation
Indices: 1237042--1237084 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
1237032 ATTTTATTGA
1237042 ATTTTTATTATTATAGAATAT
1 ATTTTTATTATTATAGAATAT
*
1237063 ATTTATTATTTATTATATAATA
1 ATTT-TTA-TTATTATAGAATA
1237085 ATTAATTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 3 0.16
23 12 0.63
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
ATTTTTATTATTATAGAATAT
Found at i:1237117 original size:25 final size:24
Alignment explanation
Indices: 1237047--1237117 Score: 65
Period size: 27 Copynumber: 2.8 Consensus size: 24
1237037 ATTGAATTTT
*
1237047 TATTAT-TATAGAATATATTTATTA
1 TATTATATATA-AAAATATTTATTA
*
1237071 T-TTATTATATAATAATTAATTTCATTA
1 TATTA-TATATAA-AAAT-ATTT-ATTA
1237098 TATTATATATAAAAATATTT
1 TATTATATATAAAAATATTT
1237118 TGCAAAAACC
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
23 3 0.08
24 3 0.08
25 10 0.26
26 7 0.18
27 12 0.32
28 3 0.08
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (24 bp):
TATTATATATAAAAATATTTATTA
Found at i:1237357 original size:28 final size:27
Alignment explanation
Indices: 1237325--1237396 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 27
1237315 TATTATTTTG
1237325 TATTATATTTTAATTTAT-ATCATGTATA
1 TATTATATTTTAATTTATCAT-AT-TATA
* *
1237353 TATTAT-TTTTATATCGTATCATATTTTA
1 TATTATATTTTA-AT-TTATCATATTATA
1237381 TATTATATTTTAATTT
1 TATTATATTTTAATTT
1237397 TTTTAATGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
27 6 0.16
28 19 0.51
29 10 0.27
30 2 0.05
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (27 bp):
TATTATATTTTAATTTATCATATTATA
Found at i:1239557 original size:21 final size:21
Alignment explanation
Indices: 1239488--1239605 Score: 73
Period size: 20 Copynumber: 5.5 Consensus size: 21
1239478 AAGTACAATG
* *
1239488 ATAATAATAAAAAAATCA-TAAG
1 ATAAT-ATAAAATAAT-ATTAAT
1239510 ATAATA-AAAATAATATTAAT
1 ATAATATAAAATAATATTAAT
1239530 ATAATATAAAA-AATATTAA-
1 ATAATATAAAATAATATTAAT
** *
1239549 ATTTTATATAAATATATAATAAT
1 ATAATATA-AAATA-ATATTAAT
* * *
1239572 TTAAATATACATATAATATAAAAT
1 AT-AATATA-AAATAATAT-TAAT
1239596 ATAATATAAA
1 ATAATATAAA
1239606 TCACAAAATT
Statistics
Matches: 74, Mismatches: 14, Indels: 16
0.71 0.13 0.15
Matches are distributed among these distances:
19 7 0.09
20 27 0.36
21 6 0.08
22 12 0.16
23 10 0.14
24 12 0.16
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.35
Consensus pattern (21 bp):
ATAATATAAAATAATATTAAT
Found at i:1239596 original size:27 final size:27
Alignment explanation
Indices: 1239524--1239596 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 27
1239514 TAAAAATAAT
1239524 ATTA-ATATAATATAAAA-AATATTAA
1 ATTACATATAATATAAAATAATATTAA
** *
1239549 ATTTTATATAAATATATAATAAT-TTAA
1 ATTACATAT-AATATAAAATAATATTAA
1239576 ATATACATATAATATAAAATA
1 AT-TACATATAATATAAAATA
1239597 TAATATAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
25 3 0.08
26 4 0.10
27 24 0.62
28 8 0.21
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (27 bp):
ATTACATATAATATAAAATAATATTAA
Found at i:1240648 original size:30 final size:30
Alignment explanation
Indices: 1240592--1240648 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
1240582 TAGAATCTAA
**
1240592 AAATTATTAAAATATAATTTTTTAAAAGAT
1 AAATTATTAAAATATAATTTAATAAAAGAT
*
1240622 AAATTAATTAAATTA-AATTTAATAAAA
1 AAATT-ATTAAAATATAATTTAATAAAA
1240649 TTTTAATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 15 0.65
31 8 0.35
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (30 bp):
AAATTATTAAAATATAATTTAATAAAAGAT
Found at i:1249167 original size:97 final size:97
Alignment explanation
Indices: 1249001--1249191 Score: 382
Period size: 97 Copynumber: 2.0 Consensus size: 97
1248991 CCGTATCTGA
1249001 TAATCACGTCCAAGTCTTAGTAACAGAGCATCAAACCATGAAGCAGCGATGAACATGACCAACTA
1 TAATCACGTCCAAGTCTTAGTAACAGAGCATCAAACCATGAAGCAGCGATGAACATGACCAACTA
1249066 ATAAACCCTAAAGTCAAAATTCCGGGCCTTAG
66 ATAAACCCTAAAGTCAAAATTCCGGGCCTTAG
1249098 TAATCACGTCCAAGTCTTAGTAACAGAGCATCAAACCATGAAGCAGCGATGAACATGACCAACTA
1 TAATCACGTCCAAGTCTTAGTAACAGAGCATCAAACCATGAAGCAGCGATGAACATGACCAACTA
1249163 ATAAACCCTAAAGTCAAAATTCCGGGCCT
66 ATAAACCCTAAAGTCAAAATTCCGGGCCT
1249192 AAACTTTTGG
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 94 1.00
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.19
Consensus pattern (97 bp):
TAATCACGTCCAAGTCTTAGTAACAGAGCATCAAACCATGAAGCAGCGATGAACATGACCAACTA
ATAAACCCTAAAGTCAAAATTCCGGGCCTTAG
Found at i:1256104 original size:25 final size:24
Alignment explanation
Indices: 1256070--1256123 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
1256060 ATTACCAAAT
* *
1256070 ATATTTTTTAATTTATAATAATAAA
1 ATATTATTTAAATT-TAATAATAAA
*
1256095 ATATTATTTAAATTTAATTATAAA
1 ATATTATTTAAATTTAATAATAAA
1256119 A-ATTA
1 ATATTA
1256124 ATATTTTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 4 0.15
24 10 0.38
25 12 0.46
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
ATATTATTTAAATTTAATAATAAA
Found at i:1256117 original size:27 final size:25
Alignment explanation
Indices: 1256070--1256134 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 25
1256060 ATTACCAAAT
1256070 ATATT-TTTTAATTTATAATAATAAA
1 ATATTATTTTAATTTATAATAA-AAA
* *
1256095 ATATTATTTAAATTTAATTATAAAAA
1 ATATTATTTTAATTT-ATAATAAAAA
* *
1256121 TTAATATTTTAATT
1 ATATTATTTTAATT
1256135 CGTAATATCA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
25 5 0.15
26 22 0.67
27 6 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATATTATTTTAATTTATAATAAAAA
Found at i:1265431 original size:19 final size:19
Alignment explanation
Indices: 1265404--1265472 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 19
1265394 TTTTTTTTTC
*
1265404 TTTTCAAATTATTATAATA
1 TTTTTAAATTATTATAATA
* * *
1265423 TTTTTAAATTAATCTGAAGA
1 TTTTTAAATTATTAT-AATA
1265443 -TTTTAAATATGATTA-AATA
1 TTTTTAAAT-T-ATTATAATA
*
1265462 TTTATAAATTA
1 TTTTTAAATTA
1265473 AAAAAATTTA
Statistics
Matches: 38, Mismatches: 8, Indels: 9
0.69 0.15 0.16
Matches are distributed among these distances:
18 1 0.03
19 24 0.63
20 11 0.29
21 2 0.05
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.49
Consensus pattern (19 bp):
TTTTTAAATTATTATAATA
Found at i:1266138 original size:19 final size:19
Alignment explanation
Indices: 1266116--1266153 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1266106 AATAATTAAA
1266116 TTTAAATAAAATATATTAT
1 TTTAAATAAAATATATTAT
* *
1266135 TTTAATTAAAATTTATTAT
1 TTTAAATAAAATATATTAT
1266154 CCTAACTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTAAATAAAATATATTAT
Found at i:1266207 original size:23 final size:24
Alignment explanation
Indices: 1266181--1266227 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1266171 AACTCAAAAT
*
1266181 AATAAAATT-AATACTTAAATTTA
1 AATAAAATTAAATAATTAAATTTA
1266204 AATAAAATTAAATAATTAAATTTA
1 AATAAAATTAAATAATTAAATTTA
1266228 TTAAATTAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
AATAAAATTAAATAATTAAATTTA
Found at i:1266555 original size:27 final size:26
Alignment explanation
Indices: 1266523--1266583 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
1266513 AAATTTAATA
*
1266523 ATTTATATTATATTTATAAA-TTTTTT
1 ATTTATATTATATTTA-AAAGATTTTT
*
1266549 ATATTATATTTTATTTAAAAGATTTTT
1 AT-TTATATTATATTTAAAAGATTTTT
1266576 ATTTATAT
1 ATTTATAT
1266584 AAATTTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 11 0.35
27 20 0.65
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (26 bp):
ATTTATATTATATTTAAAAGATTTTT
Found at i:1266615 original size:32 final size:33
Alignment explanation
Indices: 1266573--1266648 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 33
1266563 TTAAAAGATT
* *
1266573 TTTAT-TTATATAAATTTTAATATATTAATA-A
1 TTTATATTATATAAAATTTAAAATATTAATATA
*
1266604 TTTATATTATATAAAATTTAAAATATTTATATA
1 TTTATATTATATAAAATTTAAAATATTAATATA
1266637 TTTATATTATAT
1 TTTATATTATAT
1266649 TTTTATATCA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 5 0.12
32 22 0.55
33 13 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
TTTATATTATATAAAATTTAAAATATTAATATA
Found at i:1266636 original size:27 final size:27
Alignment explanation
Indices: 1266525--1266643 Score: 71
Period size: 27 Copynumber: 4.2 Consensus size: 27
1266515 ATTTAATAAT
* * *
1266525 TTATATTATATTTATAAAT-TTTTTATA
1 TTATATAAAATTTA-AAATATTTATATA
*** * *
1266552 TTATATTTTATTTAAAAGATTTTTAT-
1 TTATATAAAATTTAAAATATTTATATA
* *
1266578 TTATATAAATTTTAATATATTAATAATTTATA
1 TTATATAAAATTTAAAATATT--T-A--TATA
1266610 TTATATAAAATTTAAAATATTTATATA
1 TTATATAAAATTTAAAATATTTATATA
1266637 TTTATAT
1 -TTATAT
1266644 TATATTTTTA
Statistics
Matches: 73, Mismatches: 11, Indels: 15
0.74 0.11 0.15
Matches are distributed among these distances:
26 18 0.25
27 24 0.33
28 7 0.10
29 1 0.01
30 1 0.01
31 3 0.04
32 19 0.26
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (27 bp):
TTATATAAAATTTAAAATATTTATATA
Found at i:1267008 original size:35 final size:35
Alignment explanation
Indices: 1266960--1267067 Score: 101
Period size: 35 Copynumber: 2.9 Consensus size: 35
1266950 TGGAATCAAG
*
1266960 TAATATAAATATATAATAATAATTAAAATATATTA-
1 TAATATAATTATATAA-AATAATTAAAATATATTAT
* * *
1266995 TAATATAATTATATTAAAATTTATATAATATAAATTAT
1 TAATATAATTATA-TAAAA-TAAT-TAAAATATATTAT
*
1267033 TAATATAAAATTATATAAATATAATTATAATATAT
1 TAATAT--AATTATATAAA-ATAATTAAAATATAT
1267068 AAAAAATGTA
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
35 14 0.24
36 6 0.10
37 10 0.17
38 13 0.22
39 7 0.12
40 8 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (35 bp):
TAATATAATTATATAAAATAATTAAAATATATTAT
Found at i:1267294 original size:23 final size:24
Alignment explanation
Indices: 1267272--1267372 Score: 83
Period size: 23 Copynumber: 4.4 Consensus size: 24
1267262 ATTTGAATTA
1267272 ATTT-AATTTAATAA-AAATTATT
1 ATTTAAATTTAATAATAAATTATT
1267294 ATTTAAATATTAA-AATAAATT-TT
1 ATTTAAAT-TTAATAATAAATTATT
*
1267317 ATTTAAATTTAATTATAAA--A-T
1 ATTTAAATTTAATAATAAATTATT
* *
1267338 ATATAAATATTAAT-ATAAAATAATT
1 ATTTAAAT-TTAATAAT-AAATTATT
*
1267363 TTTTAAATTT
1 ATTTAAATTT
1267373 TTTAATATTT
Statistics
Matches: 65, Mismatches: 4, Indels: 18
0.75 0.05 0.21
Matches are distributed among these distances:
21 10 0.15
22 16 0.25
23 20 0.31
24 12 0.18
25 7 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATTTAAATTTAATAATAAATTATT
Found at i:1267354 original size:21 final size:21
Alignment explanation
Indices: 1267297--1267359 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
1267287 AATTATTATT
* * *
1267297 TAAATATTAAAATAAATTTTATT
1 TAAATATTAATATAAA--ATATA
1267320 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TATAAAATATA
1267341 TAAATATTAATATAAAATA
1 TAAATATTAATATAAAATA
1267360 ATTTTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
21 17 0.49
22 8 0.23
23 10 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:1267428 original size:18 final size:19
Alignment explanation
Indices: 1267407--1267445 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1267397 AGATATCATA
1267407 TTAAATTAAA-TTTAAATT
1 TTAAATTAAATTTTAAATT
*
1267425 TTAACTTAAATTTTAAATT
1 TTAAATTAAATTTTAAATT
1267444 TT
1 TT
1267446 TTATACTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (19 bp):
TTAAATTAAATTTTAAATT
Found at i:1268647 original size:10 final size:10
Alignment explanation
Indices: 1268605--1268686 Score: 64
Period size: 10 Copynumber: 8.5 Consensus size: 10
1268595 CAACACATTC
1268605 AAATTAATAT
1 AAATTAATAT
* *
1268615 TAACTAATAT
1 AAATTAATAT
* *
1268625 TAATCAATA-
1 AAATTAATAT
*
1268634 AAATTATTAT
1 AAATTAATAT
1268644 AAATTAATAT
1 AAATTAATAT
1268654 AAA--AATA-
1 AAATTAATAT
*
1268661 AAAATAATAT
1 AAATTAATAT
1268671 AATATTAATAT
1 AA-ATTAATAT
*
1268682 TAATT
1 AAATT
1268687 TTATTTTATT
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
7 3 0.05
8 4 0.07
9 10 0.18
10 32 0.56
11 8 0.14
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (10 bp):
AAATTAATAT
Found at i:1269313 original size:23 final size:23
Alignment explanation
Indices: 1269287--1269338 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
1269277 AATTAATATG
1269287 TTAAATGAAATAA-AATATAAATA
1 TTAAAT-AAATAATAATATAAATA
* * *
1269310 TTAAATTAATAATATTTTAAATA
1 TTAAATAAATAATAATATAAATA
1269333 TTAAAT
1 TTAAAT
1269339 TAAAATCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.20
23 20 0.80
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
TTAAATAAATAATAATATAAATA
Found at i:1269353 original size:23 final size:23
Alignment explanation
Indices: 1269304--1269353 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1269294 AAATAAAATA
***
1269304 TAAATATTAAATTAATAATATTT
1 TAAATATTAAATTAATAATAAAC
1269327 TAAATATTAAATTAA-AATCAAAC
1 TAAATATTAAATTAATAAT-AAAC
1269350 TAAA
1 TAAA
1269354 ATATATGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (23 bp):
TAAATATTAAATTAATAATAAAC
Found at i:1270572 original size:13 final size:14
Alignment explanation
Indices: 1270550--1270614 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 14
1270540 AATTAAAAAC
1270550 AAAATAATATAATA
1 AAAATAATATAATA
1270564 AAAAT-ATATAAT-
1 AAAATAATATAATA
** * * *
1270576 -ATTTATTATATTT
1 AAAATAATATAATA
1270589 AAAATAA-A-AATA
1 AAAATAATATAATA
1270601 AAAATAATATAATA
1 AAAATAATATAATA
1270615 TAAGCATATT
Statistics
Matches: 37, Mismatches: 9, Indels: 10
0.66 0.16 0.18
Matches are distributed among these distances:
11 2 0.05
12 14 0.38
13 9 0.24
14 12 0.32
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AAAATAATATAATA
Found at i:1270614 original size:51 final size:52
Alignment explanation
Indices: 1270497--1270614 Score: 170
Period size: 51 Copynumber: 2.3 Consensus size: 52
1270487 AAAAAAATTT
* * *
1270497 AAAAAATATTATAAT-TAACTATAATAATATTTATTATATTTAAAATTAAAA
1 AAAAAATAATATAATAAAAATATAATAATATTTATTATATTTAAAATTAAAA
*
1270548 ACAAAATAATATAATAAAAATAT-ATAATATTTATTATATTTAAAA-TAAAA
1 AAAAAATAATATAATAAAAATATAATAATATTTATTATATTTAAAATTAAAA
1270598 ATAAAAATAATATAATA
1 A-AAAAATAATATAATA
1270615 TAAGCATATT
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
50 6 0.10
51 49 0.82
52 5 0.08
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (52 bp):
AAAAAATAATATAATAAAAATATAATAATATTTATTATATTTAAAATTAAAA
Found at i:1271254 original size:10 final size:9
Alignment explanation
Indices: 1271224--1271307 Score: 52
Period size: 8 Copynumber: 9.6 Consensus size: 9
1271214 AGATTAGTAG
1271224 TATAAAATAA
1 TATAAAAT-A
*
1271234 TATTCAAATA
1 TA-TAAAATA
*
1271244 TCTTAAAATA
1 T-ATAAAATA
1271254 TAT-AAA-A
1 TATAAAATA
*
1271261 TATAAATTA
1 TATAAAATA
*
1271270 T-TAATATA
1 TATAAAATA
*
1271278 -ATAAAATT
1 TATAAAATA
*
1271286 TATATAAT-
1 TATAAAATA
1271294 TATAAAATA
1 TATAAAATA
1271303 TATAA
1 TATAA
1271308 TAAAATATAT
Statistics
Matches: 56, Mismatches: 11, Indels: 15
0.68 0.13 0.18
Matches are distributed among these distances:
7 4 0.07
8 22 0.39
9 14 0.25
10 11 0.20
11 5 0.09
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.39
Consensus pattern (9 bp):
TATAAAATA
Found at i:1271309 original size:34 final size:32
Alignment explanation
Indices: 1271247--1271314 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 32
1271237 TCAAATATCT
* *
1271247 TAAAATATATAAAATATAAATTATTAATATAA
1 TAAAATATATAAAATATAAAATATTAATAAAA
* *
1271279 TAAAATTTATATAATTATAAAATATATAATAAAA
1 TAAAATATATA-AAATATAAAATAT-TAATAAAA
1271313 TA
1 TA
1271315 TATGACAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 10 0.33
33 11 0.37
34 9 0.30
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (32 bp):
TAAAATATATAAAATATAAAATATTAATAAAA
Found at i:1274647 original size:143 final size:143
Alignment explanation
Indices: 1274384--1274671 Score: 450
Period size: 143 Copynumber: 2.0 Consensus size: 143
1274374 TGGCATTATG
*
1274384 ACAAATCTTTTTTAAGAAATTCTTTTCATCCCAATGACAAAACTTAAGATTTCTGCTATCAAGCT
1 ACAAACCTTTTTTAAGAAATTCTTTTCATCCCAATGACAAAACTTAAGATTTCTGCTATCAAGCT
* * * *
1274449 TTTTTCTTGCCTAAAGTTCGTCCCTTCGCTTCTTAGTCTTCAGCTTTATCCTCAAGTAGTCTTTG
66 TTTTTCCTGCCTAAAGTTCCTCCCTTCGCTTCTTAGTCCTCAGCTTTATCCTCAAGGAGTCTTTG
* *
1274514 ACCAAGTTAATTA
131 AACAAGATAATTA
* *
1274527 ACAAACCTTTTTTAAGAAATTCTTTTCATCCTAATGACAAAACTTAAGATTTCTGCTATCAAGTT
1 ACAAACCTTTTTTAAGAAATTCTTTTCATCCCAATGACAAAACTTAAGATTTCTGCTATCAAGCT
* * * *
1274592 TTTTTCCTGCCTAAGGTTCCTCCCTTTGCTTCTTAGTCCTCAGGTTTATCTTCAAGGAGTCTTTG
66 TTTTTCCTGCCTAAAGTTCCTCCCTTCGCTTCTTAGTCCTCAGCTTTATCCTCAAGGAGTCTTTG
*
1274657 AATAAGATAATTA
131 AACAAGATAATTA
1274670 AC
1 AC
1274672 TTAATCATCA
Statistics
Matches: 131, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
143 131 1.00
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.40
Consensus pattern (143 bp):
ACAAACCTTTTTTAAGAAATTCTTTTCATCCCAATGACAAAACTTAAGATTTCTGCTATCAAGCT
TTTTTCCTGCCTAAAGTTCCTCCCTTCGCTTCTTAGTCCTCAGCTTTATCCTCAAGGAGTCTTTG
AACAAGATAATTA
Found at i:1274927 original size:21 final size:21
Alignment explanation
Indices: 1274901--1274943 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1274891 AAGGCTTCCC
1274901 TCTTTAGAGAGAGGTAGATAT
1 TCTTTAGAGAGAGGTAGATAT
1274922 TCTTTAGAGAGAGGTAGATAT
1 TCTTTAGAGAGAGGTAGATAT
1274943 T
1 T
1274944 GATAAGTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.35
Consensus pattern (21 bp):
TCTTTAGAGAGAGGTAGATAT
Found at i:1278069 original size:134 final size:134
Alignment explanation
Indices: 1277829--1278099 Score: 463
Period size: 134 Copynumber: 2.0 Consensus size: 134
1277819 AAAAAGAAAA
*
1277829 ACAAATACTAGCAGGAAATGGTGCAAATGATTTAGCACAGCTTTCTTTAATGACCTTCAAGTTGT
1 ACAAATACCAGCAGGAAATGGTGCAAATGATTTAGCACAGCTTTCTTTAATGACCTTCAAGTTGT
* * *
1277894 CTGAAACGATCGCAGATCCATCAGCAGCAATTCCCCAGAAAAGCTTAACCCCCTTCATCTGCCCT
66 CTGAAACGACCACAGATCCATCAGCAGCAATTCCCCAGAAAAGCTTAACCCCCTTCATCTGCACT
*
1277959 TTGC
131 CTGC
*
1277963 ACAAATACCAGCAGGAAATGGTGCAAATGATTTAGCATAGCTTTCTTTAATGACCTTCAAGTTGT
1 ACAAATACCAGCAGGAAATGGTGCAAATGATTTAGCACAGCTTTCTTTAATGACCTTCAAGTTGT
*
1278028 CTGAAAC-AGCCACAGATCCATCAGCAGCAATTCCCCCGAAAAGCTTAACCCCCTTCATCTGCAC
66 CTGAAACGA-CCACAGATCCATCAGCAGCAATTCCCCAGAAAAGCTTAACCCCCTTCATCTGCAC
1278092 TCTGC
130 TCTGC
1278097 ACA
1 ACA
1278100 CCAGTAAATT
Statistics
Matches: 129, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
133 1 0.01
134 128 0.99
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (134 bp):
ACAAATACCAGCAGGAAATGGTGCAAATGATTTAGCACAGCTTTCTTTAATGACCTTCAAGTTGT
CTGAAACGACCACAGATCCATCAGCAGCAATTCCCCAGAAAAGCTTAACCCCCTTCATCTGCACT
CTGC
Found at i:1278488 original size:21 final size:21
Alignment explanation
Indices: 1278448--1278488 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1278438 ATCCAAACCC
* * *
1278448 AAAAACTTTAAATCAGAAAAT
1 AAAAACTTAAAACCAAAAAAT
1278469 AAAAACTTAAAACCAAAAAA
1 AAAAACTTAAAACCAAAAAA
1278489 AAGGGTTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.68, C:0.12, G:0.02, T:0.17
Consensus pattern (21 bp):
AAAAACTTAAAACCAAAAAAT
Found at i:1279305 original size:2 final size:2
Alignment explanation
Indices: 1279298--1279328 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1279288 AACATTTCTT
*
1279298 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 T
1279329 TTCCTTCTCC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1280283 original size:21 final size:21
Alignment explanation
Indices: 1280259--1280299 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1280249 TATTTTTATT
1280259 TAAA-TTTAATTATAAAATATA
1 TAAATTTTAA-TATAAAATATA
1280280 TAAATTTTAATATAAAATAT
1 TAAATTTTAATATAAAATAT
1280300 TTTTAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAATTTTAATATAAAATATA
Found at i:1281146 original size:2 final size:2
Alignment explanation
Indices: 1281139--1281179 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1281129 ACATCTTTTA
1281139 AT AT AT AT 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 AT AT AT AT A
1281180 AAGTATGCAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1282916 original size:19 final size:18
Alignment explanation
Indices: 1282884--1282929 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
1282874 TTTAATATTT
1282884 TATTTTAAAATAAA-AATA
1 TATTTTAAAATAAATAA-A
*
1282902 TATTATTAAACTAAATAAA
1 TATT-TTAAAATAAATAAA
1282921 TATTTTAAA
1 TATTTTAAA
1282930 TAATTCTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 9 0.36
19 14 0.56
20 2 0.08
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
TATTTTAAAATAAATAAA
Found at i:1289868 original size:10 final size:10
Alignment explanation
Indices: 1289818--1289875 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
1289808 AATTTAAAAT
*
1289818 TTTATTTAAA
1 TTTATTTAAG
1289828 TTTATTTATA-
1 TTTATTTA-AG
*
1289838 TTTATAAATAAG
1 TTTAT--TTAAG
1289850 -TTATTTAAG
1 TTTATTTAAG
1289859 TTTATTTAAG
1 TTTATTTAAG
1289869 -TTATTTA
1 TTTATTTA
1289876 TATTATTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
9 11 0.27
10 22 0.54
11 6 0.15
12 2 0.05
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (10 bp):
TTTATTTAAG
Found at i:1289883 original size:9 final size:9
Alignment explanation
Indices: 1289846--1289875 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
1289836 TATTTATAAA
1289846 TAAGTTATT
1 TAAGTTATT
1289855 TAAGTTTATT
1 TAAG-TTATT
1289865 TAAGTTATT
1 TAAGTTATT
1289874 TA
1 TA
1289876 TATTATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (9 bp):
TAAGTTATT
Found at i:1289915 original size:26 final size:27
Alignment explanation
Indices: 1289875--1289934 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 27
1289865 TAAGTTATTT
* * *
1289875 ATATTATTTTTAATTTAATTTTTAA-A
1 ATATAATTTTAAATTTAATCTTTAATA
1289901 ATATAATTTTAAATTTAATCTTTAATA
1 ATATAATTTTAAATTTAATCTTTAATA
*
1289928 ATTTAAT
1 ATATAAT
1289935 AATTTTTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 22 0.76
27 7 0.24
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (27 bp):
ATATAATTTTAAATTTAATCTTTAATA
Found at i:1290297 original size:19 final size:18
Alignment explanation
Indices: 1290273--1290309 Score: 65
Period size: 18 Copynumber: 2.0 Consensus size: 18
1290263 ATTTAAATTC
1290273 TTTTAAATATTAAATAGAT
1 TTTTAAAT-TTAAATAGAT
1290292 TTTTAAATTTAAATAGAT
1 TTTTAAATTTAAATAGAT
1290310 AATTTGCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (18 bp):
TTTTAAATTTAAATAGAT
Found at i:1290876 original size:3 final size:3
Alignment explanation
Indices: 1290868--1290907 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1290858 AACAGAGAGA
1290868 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1290908 TGGTATCAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1291655 original size:3 final size:3
Alignment explanation
Indices: 1291647--1291687 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1291637 ATATGCTATT
1291647 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1291688 TAAGTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1292521 original size:21 final size:21
Alignment explanation
Indices: 1292489--1292529 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1292479 AAAAATATTA
*
1292489 ATATTTTAATAAATTTAAATT
1 ATATTTTAATAAATATAAATT
1292510 ATATATTT-ATAAATATAAAT
1 ATAT-TTTAATAAATATAAAT
1292530 AACTTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATATTTTAATAAATATAAATT
Found at i:1294619 original size:149 final size:148
Alignment explanation
Indices: 1294344--1294641 Score: 420
Period size: 149 Copynumber: 2.0 Consensus size: 148
1294334 AAGAGATACT
* * *
1294344 ATACATTTCTTTGTGGTTCCTTAAAGGGTGAGGGTACTAAAAGTAGCTAATACCTATGTTGCTCT
1 ATACATTTCCTTGTGGTTCCTTAAAGGATGAGGGTACTAAAAGGAGCTAATACCTATGTTGCTCT
* * * *
1294409 GACTTTTCATTTTTCTTGAAAAACTTGTGTCCAACACTCATGTTCAACCTATATTTGGACAATGG
66 GACTTTTCATTTTTCTTCAAAAACTCGTGTCCAACACTCATATCCAACCTATATTTGGACAATGG
*
1294474 TATTGGTATGGGGATATG
131 TATTAGTATGGGGATATG
* *
1294492 ATACATTTCCTTGTGGTTGCTTAAACAGGATGAGGGTCCTAAAAGGAGCTAATACCTATGTTGCT
1 ATACATTTCCTTGTGGTTCCTT-AA-AGGATGAGGGTACTAAAAGGAGCTAATACCTATGTTGCT
** * * *
1294557 CTGAC-TTTCATTTTTCTTCAAGTA-TCCGTGTCCAATACTCATATCCGAGCTATATTTGGACAA
64 CTGACTTTTCATTTTTCTTCAAAAACT-CGTGTCCAACACTCATATCCAACCTATATTTGGACAA
1294620 TGGTATTAGTATGGGGATATG
128 TGGTATTAGTATGGGGATATG
1294641 A
1 A
1294642 CCCTCCAAGG
Statistics
Matches: 132, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
148 21 0.16
149 70 0.53
150 41 0.31
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (148 bp):
ATACATTTCCTTGTGGTTCCTTAAAGGATGAGGGTACTAAAAGGAGCTAATACCTATGTTGCTCT
GACTTTTCATTTTTCTTCAAAAACTCGTGTCCAACACTCATATCCAACCTATATTTGGACAATGG
TATTAGTATGGGGATATG
Found at i:1297018 original size:15 final size:15
Alignment explanation
Indices: 1296998--1297027 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1296988 TCATCTCAGT
1296998 GGTCCGAGTATTTTC
1 GGTCCGAGTATTTTC
1297013 GGTCCGAGTATTTTC
1 GGTCCGAGTATTTTC
1297028 TACTTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.20, G:0.27, T:0.40
Consensus pattern (15 bp):
GGTCCGAGTATTTTC
Found at i:1305111 original size:21 final size:21
Alignment explanation
Indices: 1305067--1305119 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1305057 GTATCTTTGA
* *
1305067 ATGAAATAATGCATTGGTTGG
1 ATGAAAAAATGCATTGGTTAG
* **
1305088 ATGAAAGAATGCATTTTTTAG
1 ATGAAAAAATGCATTGGTTAG
1305109 ATGAAAAAATG
1 ATGAAAAAATG
1305120 TAACTTTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.42, C:0.04, G:0.23, T:0.32
Consensus pattern (21 bp):
ATGAAAAAATGCATTGGTTAG
Found at i:1305692 original size:24 final size:24
Alignment explanation
Indices: 1305660--1305707 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1305650 ACATTTCAAA
1305660 CTGCAATGTATAAAGAAACAACAG
1 CTGCAATGTATAAAGAAACAACAG
1305684 CTGCAATGTATAAAGAAACAACAG
1 CTGCAATGTATAAAGAAACAACAG
1305708 ATTGCTGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.17
Consensus pattern (24 bp):
CTGCAATGTATAAAGAAACAACAG
Found at i:1308268 original size:20 final size:20
Alignment explanation
Indices: 1308240--1308278 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1308230 TTTTTTTTTG
**
1308240 GGGGGGGGGGGGGGGGTGGC
1 GGGGGGGGGAAGGGGGTGGC
*
1308260 GGGGTGGGGAAGGGGGTGG
1 GGGGGGGGGAAGGGGGTGG
1308279 TTTGGGTTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.05, C:0.03, G:0.85, T:0.08
Consensus pattern (20 bp):
GGGGGGGGGAAGGGGGTGGC
Found at i:1308852 original size:18 final size:19
Alignment explanation
Indices: 1308831--1308879 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
1308821 TATATAAATA
1308831 TTAATATAAAAATAAT-TT
1 TTAATATAAAAATAATATT
**
1308849 TTAATATATTAATAATATT
1 TTAATATAAAAATAATATT
1308868 TTAATAATAAAA
1 TTAAT-ATAAAA
1308880 TAAACTAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 14 0.56
19 7 0.28
20 4 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTAATATAAAAATAATATT
Found at i:1309045 original size:2 final size:2
Alignment explanation
Indices: 1309038--1309062 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1309028 TTAGATTTAG
1309038 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
1309063 GTAATTATAA
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:1314224 original size:12 final size:12
Alignment explanation
Indices: 1314203--1314268 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 12
1314193 TAATAAAAAT
*
1314203 TATTAGTTTAAA
1 TATTATTTTAAA
1314215 TATTATTTTAAA
1 TATTATTTTAAA
* *
1314227 -AATA-TATAAA
1 TATTATTTTAAA
* *
1314237 TATTAATATAAA
1 TATTATTTTAAA
*
1314249 TAATATTTT-AA
1 TATTATTTTAAA
1314260 TATT-TTTTA
1 TATTATTTTA
1314269 CTTAAATATA
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
10 9 0.21
11 11 0.26
12 23 0.53
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (12 bp):
TATTATTTTAAA
Found at i:1314261 original size:23 final size:22
Alignment explanation
Indices: 1314211--1314263 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1314201 ATTATTAGTT
* *
1314211 TAAATATTATTTTAAAAATATA
1 TAAATATTAATATAAAAATATA
*
1314233 TAAATATTAATATAAATAATATT
1 TAAATATTAATATAAA-AATATA
*
1314256 TTAATATT
1 TAAATATT
1314264 TTTTACTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:1317670 original size:17 final size:16
Alignment explanation
Indices: 1317650--1317748 Score: 67
Period size: 14 Copynumber: 6.8 Consensus size: 16
1317640 AAATTTTAAA
1317650 ATATAATATATAATAT
1 ATATAATATATAATAT
*
1317666 GATATAATA-ATTA-AT
1 -ATATAATATATAATAT
1317681 ATA-AATATATAATA-
1 ATATAATATATAATAT
* *
1317695 ATTTAA-ATAAAAT-T
1 ATATAATATATAATAT
* *
1317709 ATATTATATA-AAAAT
1 ATATAATATATAATAT
1317724 A-ATAA-ATATAATAT
1 ATATAATATATAATAT
1317738 A-A-AATATATAA
1 ATATAATATATAA
1317749 ATTTTTAAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
13 9 0.14
14 35 0.54
15 10 0.15
16 3 0.05
17 8 0.12
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (16 bp):
ATATAATATATAATAT
Found at i:1317690 original size:20 final size:20
Alignment explanation
Indices: 1317657--1317748 Score: 74
Period size: 20 Copynumber: 4.7 Consensus size: 20
1317647 AAAATATAAT
1317657 ATATAATATGATATAATAATTA
1 ATATAA-AT-ATATAATAATTA
1317679 ATATAAATATATAATAATTTA
1 ATATAAATATATAATAA-TTA
1317700 A-ATAAA-AT-T-AT-ATT-
1 ATATAAATATATAATAATTA
1317714 ATATAAA-A-ATAATAAATATA
1 ATATAAATATATAAT-AAT-TA
1317734 ATATAAAATATATAA
1 ATAT-AAATATATAA
1317749 ATTTTTAAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 21
0.74 0.00 0.26
Matches are distributed among these distances:
14 1 0.02
15 9 0.15
16 3 0.05
17 2 0.03
18 3 0.05
19 3 0.05
20 18 0.31
21 9 0.15
22 7 0.12
23 4 0.07
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (20 bp):
ATATAAATATATAATAATTA
Found at i:1317701 original size:16 final size:18
Alignment explanation
Indices: 1317648--1317745 Score: 71
Period size: 17 Copynumber: 5.4 Consensus size: 18
1317638 AAAAATTTTA
1317648 AAATATAAT-ATATAATAT
1 AAATATAATAAT-TAATAT
*
1317666 -GATATAATAATTAATAT
1 AAATATAATAATTAATAT
*
1317683 AAATAT-ATAA-TAATTT
1 AAATATAATAATTAATAT
*
1317699 AAATAAAATTATATT-ATAT
1 AAATATAA-TA-ATTAATAT
*
1317718 AAAAATAATAAATATAATAT
1 AAATATAAT-AAT-TAATAT
1317738 AAAATATA
1 -AAATATA
1317746 TAAATTTTTA
Statistics
Matches: 62, Mismatches: 8, Indels: 17
0.71 0.09 0.20
Matches are distributed among these distances:
16 10 0.16
17 18 0.29
18 11 0.18
19 12 0.19
20 5 0.08
21 6 0.10
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (18 bp):
AAATATAATAATTAATAT
Found at i:1317749 original size:20 final size:20
Alignment explanation
Indices: 1317626--1317750 Score: 84
Period size: 22 Copynumber: 6.2 Consensus size: 20
1317616 TTATATTAAA
* *
1317626 AAATATAATATAAAAAATTTT
1 AAATATAATATAAAATA-TAT
*
1317647 AAAATATAATATATAATATGAT
1 -AAATATAATATAAAATAT-AT
1317669 ATAATAATTAATAT-AAATATAT
1 A-AAT-A-TAATATAAAATATAT
*
1317691 AATAATTTAA-ATAAAAT-TAT
1 -A-AATATAATATAAAATATAT
*
1317711 -ATTAT-ATA-AAAATA-AT
1 AAATATAATATAAAATATAT
1317727 AAATATAATATAAAATATAT
1 AAATATAATATAAAATATAT
1317747 AAAT
1 AAAT
1317751 TTTTAAAATT
Statistics
Matches: 83, Mismatches: 8, Indels: 26
0.71 0.07 0.22
Matches are distributed among these distances:
16 8 0.10
17 8 0.10
18 3 0.04
19 6 0.07
20 11 0.13
21 9 0.11
22 21 0.25
23 11 0.13
24 6 0.07
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.38
Consensus pattern (20 bp):
AAATATAATATAAAATATAT
Found at i:1317895 original size:22 final size:22
Alignment explanation
Indices: 1317870--1317939 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 22
1317860 TATAATTTGG
1317870 ATAAATTAATAATTTATTTTAT
1 ATAAATTAATAATTTATTTTAT
* *
1317892 ATAAATT-TTAATATATATTTAT
1 ATAAATTAATAATTTAT-TTTAT
*
1317914 ATTAATATTAAT-ATTAAATTTTAT
1 A-TAA-ATTAATAATT-TATTTTAT
1317938 AT
1 AT
1317940 TATAATATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
21 7 0.18
22 13 0.34
23 4 0.11
24 11 0.29
25 3 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATAAATTAATAATTTATTTTAT
Found at i:1317939 original size:18 final size:19
Alignment explanation
Indices: 1317912--1317959 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
1317902 ATATATATTT
* *
1317912 ATATTAATATTAATATTAA
1 ATATTTATATTAATAATAA
*
1317931 AT-TTTATATT-ATAATAT
1 ATATTTATATTAATAATAA
1317948 ATATTTATATTA
1 ATATTTATATTA
1317960 TTCCTTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 7 0.29
18 15 0.62
19 2 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATATTTATATTAATAATAA
Found at i:1333578 original size:27 final size:26
Alignment explanation
Indices: 1333525--1333611 Score: 70
Period size: 26 Copynumber: 3.2 Consensus size: 26
1333515 TTTTTATAAA
**
1333525 TAAAAAATAAATTTATATATTTTTAT
1 TAAAAAATAAATTTATATATTCATAT
1333551 TAAAAAATAAATTTATAT-TTAACATAT
1 TAAAAAATAAATTTATATATT--CATAT
*
1333578 TAATTAATATATAAATTTAAATATT-ATTAT
1 TAA--AA-A-ATAAATTTATATATTCA-TAT
1333608 TAAA
1 TAAA
1333612 TTACATTATT
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
25 2 0.04
26 18 0.36
27 6 0.12
28 1 0.02
29 3 0.06
30 7 0.14
31 11 0.22
32 2 0.04
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (26 bp):
TAAAAAATAAATTTATATATTCATAT
Found at i:1334495 original size:21 final size:20
Alignment explanation
Indices: 1334458--1334524 Score: 68
Period size: 19 Copynumber: 3.4 Consensus size: 20
1334448 TTAATAAATG
*
1334458 AAACTTTTTA-TTTTTTAAA
1 AAACTATTTATTTTTTTAAA
1334477 AAACTATTTATTTTCTTTAAA
1 AAACTATTTATTTT-TTTAAA
*
1334498 AAA--ATTCATTTTTTTCATAA
1 AAACTATTTATTTTTTT-A-AA
1334518 AAACTAT
1 AAACTAT
1334525 CTGTACATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
18 3 0.08
19 18 0.45
20 8 0.20
21 9 0.22
22 2 0.05
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (20 bp):
AAACTATTTATTTTTTTAAA
Found at i:1334679 original size:11 final size:11
Alignment explanation
Indices: 1334657--1334715 Score: 55
Period size: 12 Copynumber: 5.0 Consensus size: 11
1334647 TAACATGTTA
1334657 TATTTATTATAT
1 TATTT-TTATAT
1334669 TATTTTTATAT
1 TATTTTTATAT
**
1334680 TATTAAATATAT
1 TATT-TTTATAT
*
1334692 TATATTTATATT
1 TATTTTTATA-T
1334704 ATATTTTTATAT
1 -TATTTTTATAT
1334716 AATATTTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
11 14 0.37
12 15 0.39
13 9 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTTTTATAT
Found at i:1334683 original size:23 final size:23
Alignment explanation
Indices: 1334657--1334723 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
1334647 TAACATGTTA
*
1334657 TATTTATTATATTATTTTTATAT
1 TATTTATTATATTATATTTATAT
* *
1334680 TATTAAATATATTATATTTATAT
1 TATTTATTATATTATATTTATAT
* *
1334703 TATATTTTTATATAATATTTA
1 TAT-TTATTATATTATATTTA
1334724 AAATTATTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 23 0.64
24 13 0.36
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TATTTATTATATTATATTTATAT
Found at i:1335078 original size:29 final size:29
Alignment explanation
Indices: 1335044--1335193 Score: 91
Period size: 29 Copynumber: 5.1 Consensus size: 29
1335034 AATAAATTTA
1335044 ATAATTTATATTT-ATGTATTTTAT-TTTTT
1 ATAA-TTATATTTAAT-TATTTTATATTTTT
1335073 ATAATTATATTTAAATTATTTTATATTTTT
1 ATAATTATATTT-AATTATTTTATATTTTT
* * *
1335103 ATATATTA-A-TAAATTAATTTTAAAATTTT
1 ATA-ATTATATTTAATT-ATTTTATATTTTT
* *
1335132 ATAAATT-T-TTATAAAT-TTTTATATATTT
1 AT-AATTATATT-TAATTATTTTATATTTTT
* *
1335160 AT-ATTATTTTTATATTATATTTAATATTATT
1 ATAATTATATTTA-ATTAT-TTT-ATATTTTT
1335191 ATA
1 ATA
1335194 TATGTAGTAA
Statistics
Matches: 94, Mismatches: 11, Indels: 29
0.70 0.08 0.22
Matches are distributed among these distances:
26 3 0.03
27 3 0.03
28 27 0.29
29 31 0.33
30 18 0.19
31 12 0.13
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (29 bp):
ATAATTATATTTAATTATTTTATATTTTT
Found at i:1335107 original size:10 final size:10
Alignment explanation
Indices: 1335094--1335196 Score: 70
Period size: 10 Copynumber: 10.5 Consensus size: 10
1335084 TAAATTATTT
1335094 TATATTTTTA
1 TATATTTTTA
**
1335104 TATATTAATA
1 TATATTTTTA
* *
1335114 AATTAATTTTA
1 TA-TATTTTTA
*
1335125 -AAAT-TTTA
1 TATATTTTTA
*
1335133 TAAATTTTTA
1 TATATTTTTA
*
1335143 TAAATTTTTA
1 TATATTTTTA
*
1335153 TATATTTATA
1 TATATTTTTA
1335163 T-TATTTTTA
1 TATATTTTTA
*
1335172 TATTATATTTA
1 TA-TATTTTTA
*
1335183 -ATATTATTA
1 TATATTTTTA
1335192 TATAT
1 TATAT
1335197 GTAGTAACTG
Statistics
Matches: 73, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
8 4 0.05
9 19 0.26
10 38 0.52
11 12 0.16
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TATATTTTTA
Found at i:1335173 original size:11 final size:11
Alignment explanation
Indices: 1335136--1335190 Score: 55
Period size: 11 Copynumber: 5.3 Consensus size: 11
1335126 AATTTTATAA
*
1335136 ATTTTTATA-A
1 ATTTTTATATT
1335146 ATTTTTATA-T
1 ATTTTTATATT
1335156 A--TTTATATT
1 ATTTTTATATT
1335165 ATTTTTATATT
1 ATTTTTATATT
*
1335176 ATATTTAATATT
1 AT-TTTTATATT
1335188 ATT
1 ATT
1335191 ATATATGTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
8 6 0.15
9 2 0.05
10 10 0.26
11 11 0.28
12 10 0.26
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTTTATATT
Found at i:1335195 original size:22 final size:22
Alignment explanation
Indices: 1335039--1335196 Score: 64
Period size: 22 Copynumber: 7.9 Consensus size: 22
1335029 GTCTTAATAA
*
1335039 ATTTA-ATAATTTATAT-TTATGT
1 ATTTATATTATTTATATATTA--T
*
1335061 ATTT-TATTTTTTATA-ATTAT
1 ATTTATATTATTTATATATTAT
*
1335081 ATTTAAATTATTT-TATA-T-T
1 ATTTATATTATTTATATATTAT
* *
1335100 -TTTATA-TATTAATAAATTA-
1 ATTTATATTATTTATATATTAT
** *
1335119 ATTT-TAAAATTT-TATA-AAT
1 ATTTATATTATTTATATATTAT
* *
1335138 TTTTATA-AATTT-T-TA-TAT
1 ATTTATATTATTTATATATTAT
*
1335156 ATTTATATTATTTTTATATTAT
1 ATTTATATTATTTATATATTAT
1335178 ATTTAATATTA-TTATATAT
1 ATTT-ATATTATTTATATAT
1335197 GTAGTAACTG
Statistics
Matches: 104, Mismatches: 16, Indels: 32
0.68 0.11 0.21
Matches are distributed among these distances:
17 4 0.04
18 19 0.18
19 20 0.19
20 17 0.16
21 9 0.09
22 29 0.28
23 6 0.06
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (22 bp):
ATTTATATTATTTATATATTAT
Found at i:1335446 original size:16 final size:16
Alignment explanation
Indices: 1335425--1335547 Score: 69
Period size: 16 Copynumber: 7.8 Consensus size: 16
1335415 ATTATTAAAG
1335425 TATAATATATAATAAT
1 TATAATATATAATAAT
*
1335441 TATAATATAAAATAA-
1 TATAATATATAATAAT
*
1335456 TATAATATAAATATATAT
1 TATAATATATA-ATA-AT
* * *
1335474 TTTAA-ATTTTAT-AT
1 TATAATATATAATAAT
1335488 TATAA-ATTATTAATATAT
1 TATAATA-TA-TAATA-AT
* * *
1335506 TAAAATTTAT-ATAAA
1 TATAATATATAATAAT
*
1335521 TATAAT-TATAATAAA
1 TATAATATATAATAAT
*
1335536 TAAAATATATAA
1 TATAATATATAA
1335548 ATATTATATC
Statistics
Matches: 84, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
14 10 0.12
15 28 0.33
16 30 0.36
17 4 0.05
18 12 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TATAATATATAATAAT
Found at i:1335504 original size:18 final size:21
Alignment explanation
Indices: 1335483--1335531 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 21
1335473 TTTTAAATTT
1335483 TATATTATAAA-TTAT-T-AA
1 TATATTATAAATTTATATAAA
1335501 TATATTA-AAATTTATATAAA
1 TATATTATAAATTTATATAAA
1335521 TATAATTATAA
1 TAT-ATTATAA
1335532 TAAATAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.12
18 11 0.42
19 1 0.04
20 5 0.19
21 4 0.15
22 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TATATTATAAATTTATATAAA
Found at i:1335549 original size:69 final size:69
Alignment explanation
Indices: 1335414--1335556 Score: 154
Period size: 71 Copynumber: 2.0 Consensus size: 69
1335404 TTTTAAGTCT
1335414 TATTATTAAAGTATAATATATAATAATTATAATATAAAATAATATAATATAAATATATATTTTAA
1 TATTATTAAAGTATAATATATAATAATTATAATATAAAATAATATAATATAAATATATA--TTAA
*
1335479 ATTTTA
64 ATATTA
*
1335485 TATTA-TAAATTATTAATATATTAA-AATT-T-ATATAAATATAATTATAATAAATAAA-ATATA
1 TATTATTAAAGTA-TAATATA-TAATAATTATAATATAAA-ATAA-TATAAT--ATAAATATATA
1335545 -TAAATATTA
60 TTAAATATTA
1335554 TAT
1 TAT
1335557 CAATCATTAT
Statistics
Matches: 64, Mismatches: 2, Indels: 14
0.80 0.03 0.17
Matches are distributed among these distances:
69 18 0.28
70 11 0.17
71 22 0.34
72 8 0.12
73 5 0.08
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.45
Consensus pattern (69 bp):
TATTATTAAAGTATAATATATAATAATTATAATATAAAATAATATAATATAAATATATATTAAAT
ATTA
Found at i:1341269 original size:2 final size:2
Alignment explanation
Indices: 1341264--1341308 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
1341254 TTGTTTGACA
* * * *
1341264 AT AT AT AT AT AT AT AT GT AT AT AT AG GT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1341306 AT A
1 AT A
1341309 GTTTTACTTG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1341279 original size:10 final size:10
Alignment explanation
Indices: 1341264--1341308 Score: 72
Period size: 10 Copynumber: 4.5 Consensus size: 10
1341254 TTGTTTGACA
*
1341264 ATATATATAT
1 ATATATGTAT
1341274 ATATATGTAT
1 ATATATGTAT
*
1341284 ATATAGGTAT
1 ATATATGTAT
1341294 ATATATGTAT
1 ATATATGTAT
1341304 ATATA
1 ATATA
1341309 GTTTTACTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (10 bp):
ATATATGTAT
Found at i:1349857 original size:2 final size:2
Alignment explanation
Indices: 1349846--1349889 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1349836 CAGTCCCTTC
1349846 CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1349887 CT C
1 CT C
1349890 ACGCGAATCT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1350488 original size:25 final size:24
Alignment explanation
Indices: 1350443--1350503 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
1350433 TTAAAATATA
*
1350443 ATTATTTTATTTTTTTAATAAATC
1 ATTATTTTATTTTTGTAATAAATC
1350467 ATTATTTT-TTTCTTGTACATAAAT-
1 ATTATTTTATTT-TTGTA-ATAAATC
**
1350491 AAAATTTTATTTT
1 ATTATTTTATTTT
1350504 ATAATTAGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 3 0.10
24 19 0.61
25 9 0.29
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.61
Consensus pattern (24 bp):
ATTATTTTATTTTTGTAATAAATC
Found at i:1350885 original size:14 final size:14
Alignment explanation
Indices: 1350854--1350905 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
1350844 GTTAATACTT
*
1350854 TTAAAGTATAAAAA
1 TTAAAATATAAAAA
* *
1350868 TTAAAATATTAAAT
1 TTAAAATATAAAAA
1350882 TTAATAATATAAAAA
1 TTAA-AATATAAAAA
1350897 TTAAAATAT
1 TTAAAATAT
1350906 TTTTTTAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (14 bp):
TTAAAATATAAAAA
Found at i:1351720 original size:18 final size:19
Alignment explanation
Indices: 1351680--1351728 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
1351670 ATTTCCATTG
*
1351680 AAATTTATTAATTTTGTGTGT
1 AAATTTATT--TTTTGTGAGT
1351701 AAATTTATTTTTT-TGAGT
1 AAATTTATTTTTTGTGAGT
*
1351719 AAATATATTT
1 AAATTTATTT
1351729 ATGAATTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 13 0.50
19 4 0.15
21 9 0.35
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (19 bp):
AAATTTATTTTTTGTGAGT
Found at i:1351802 original size:19 final size:19
Alignment explanation
Indices: 1351778--1351817 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1351768 TTAAATTAAT
*
1351778 TTTAAAATTTATATTAT-TA
1 TTTAAAA-TAATATTATATA
1351797 TTTAAAATAATATTATATA
1 TTTAAAATAATATTATATA
1351816 TT
1 TT
1351818 ATTTTTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTAAAATAATATTATATA
Found at i:1351809 original size:18 final size:20
Alignment explanation
Indices: 1351767--1351817 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 20
1351757 TTAAATTTTG
1351767 ATTAA-ATTA-AT-TTTAAA
1 ATTAATATTATATATTTAAA
*
1351784 ATTTATATTAT-TATTTAAA
1 ATTAATATTATATATTTAAA
1351803 A-TAATATTATATATT
1 ATTAATATTATATATT
1351818 ATTTTTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 4 0.14
18 13 0.46
19 11 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTAATATTATATATTTAAA
Found at i:1352462 original size:3 final size:3
Alignment explanation
Indices: 1352454--1352479 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1352444 TATTTTTTAT
1352454 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1352480 TTCTTATTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1352833 original size:19 final size:19
Alignment explanation
Indices: 1352809--1352850 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1352799 ATATAGATAT
1352809 TTTTAAATAAA-TAAATAAA
1 TTTTAAA-AAATTAAATAAA
*
1352828 TTTTAAAAAATTAAATATA
1 TTTTAAAAAATTAAATAAA
1352847 TTTT
1 TTTT
1352851 TTATTTGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTTTAAAAAATTAAATAAA
Found at i:1353747 original size:2 final size:2
Alignment explanation
Indices: 1353742--1353777 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1353732 TATATGTCAA
*
1353742 AT AT AT AC 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
1353778 GTTGGAAGAA
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:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1354375 original size:2 final size:2
Alignment explanation
Indices: 1354368--1354393 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1354358 AATTCACGAA
1354368 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
1354394 GTACGATCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1355426 original size:28 final size:29
Alignment explanation
Indices: 1355395--1355458 Score: 87
Period size: 27 Copynumber: 2.3 Consensus size: 29
1355385 AAAATTTAAA
* *
1355395 TTATTATTTAAATATTAATAAATAT-TTT
1 TTATTATTTAAATATAAATAAAAATATTT
*
1355423 TTA-TAATTAAATATAAATAAAAATATTT
1 TTATTATTTAAATATAAATAAAAATATTT
1355451 TTATTATT
1 TTATTATT
1355459 AAACAATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 18 0.60
28 9 0.30
29 3 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
TTATTATTTAAATATAAATAAAAATATTT
Found at i:1355460 original size:28 final size:27
Alignment explanation
Indices: 1355395--1355461 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 27
1355385 AAAATTTAAA
* *
1355395 TTATTATTTAAATATTAATAAATATTTT
1 TTATTA-TTAAATATAAATAAAAATTTT
*
1355423 TTATAATTAAATATAAATAAAAATATTT
1 TTATTATTAAATATAAATAAAAAT-TTT
1355451 TTATTATTAAA
1 TTATTATTAAA
1355462 CAATAATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 16 0.47
28 18 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
TTATTATTAAATATAAATAAAAATTTT
Found at i:1360493 original size:17 final size:17
Alignment explanation
Indices: 1360452--1360493 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1360442 AAATTAAGTA
1360452 ATTAATTTTGTAATTAT
1 ATTAATTTTGTAATTAT
*
1360469 ATTGATTTT-TAATTTAT
1 ATTAATTTTGTAA-TTAT
*
1360486 TTTAATTT
1 ATTAATTT
1360494 ATTTGATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (17 bp):
ATTAATTTTGTAATTAT
Found at i:1361488 original size:21 final size:23
Alignment explanation
Indices: 1361463--1361506 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1361453 TATGTTCTTT
1361463 TTATTT-AAAA-TAAATTAATTA
1 TTATTTAAAAACTAAATTAATTA
1361484 TTATTTAAAAACTAAATTAATTA
1 TTATTTAAAAACTAAATTAATTA
1361507 AATGACGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 6 0.29
22 4 0.19
23 11 0.52
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
TTATTTAAAAACTAAATTAATTA
Found at i:1374281 original size:23 final size:22
Alignment explanation
Indices: 1374255--1374337 Score: 53
Period size: 23 Copynumber: 3.5 Consensus size: 22
1374245 CAATTTTTTT
1374255 TATATTTTTTATTTAAAAATTAA
1 TATATTTTTTATTT-AAAATTAA
* *
1374278 TATAAATTTATTTTATATTAATATTTA
1 TAT--A-TT-TTTTAT-TTAAAATTAA
*
1374305 TATA-TTTTTATTATTAAATTTAA
1 TATATTTTTTA-T-TTAAAATTAA
1374328 -ATATTTTTTA
1 TATATTTTTTA
1374338 ATTTGAATTG
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
22 8 0.17
23 19 0.40
25 2 0.04
26 2 0.04
27 15 0.31
28 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TATATTTTTTATTTAAAATTAA
Found at i:1374297 original size:21 final size:20
Alignment explanation
Indices: 1374273--1374326 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 20
1374263 TTATTTAAAA
1374273 ATTAATATAAATTTATTTTAT
1 ATTAATATAAATTTATTTT-T
** *
1374294 ATTAATATTTATATATTTTT
1 ATTAATATAAATTTATTTTT
1374314 ATT-AT-TAAATTTA
1 ATTAATATAAATTTA
1374327 AATATTTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
18 5 0.19
19 2 0.07
20 4 0.15
21 16 0.59
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTAATATAAATTTATTTTT
Found at i:1374325 original size:22 final size:22
Alignment explanation
Indices: 1374288--1374335 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1374278 TATAAATTTA
*
1374288 TTTTATATTAATATTTATATAT
1 TTTTATATTAATATTTAAATAT
1374310 TTTTATTATTAA-ATTTAAATAT
1 TTTTA-TATTAATATTTAAATAT
1374332 TTTT
1 TTTT
1374336 TAATTTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTTATATTAATATTTAAATAT
Found at i:1377589 original size:16 final size:15
Alignment explanation
Indices: 1377557--1377595 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1377547 TATTTTTTAT
*
1377557 AATTAAAATTATAAAA
1 AATTAAAATTA-CAAA
*
1377573 AATTAAAATTACCAA
1 AATTAAAATTACAAA
1377588 AATTAAAA
1 AATTAAAA
1377596 AATTAATACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (15 bp):
AATTAAAATTACAAA
Found at i:1377924 original size:18 final size:18
Alignment explanation
Indices: 1377878--1377924 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
1377868 AATTATCATA
*
1377878 AAAATAATATAAAAATAT
1 AAAATTATATAAAAATAT
* *
1377896 ATAATTATATAAATATATT
1 AAAATTATATAAAAATA-T
1377915 AAAATT-TATA
1 AAAATTATATA
1377925 TGAATAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATTATATAAAAATAT
Found at i:1378059 original size:15 final size:17
Alignment explanation
Indices: 1378030--1378074 Score: 60
Period size: 15 Copynumber: 2.8 Consensus size: 17
1378020 TAAAATTTTT
1378030 TTAAATATATAAATAAA
1 TTAAATATATAAATAAA
*
1378047 TTAAATAT-T-AATATA
1 TTAAATATATAAATAAA
1378062 TTAAATATA-AAAT
1 TTAAATATATAAAT
1378075 TTTATCTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 13 0.52
16 4 0.16
17 8 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAATATATAAATAAA
Found at i:1378277 original size:2 final size:2
Alignment explanation
Indices: 1378270--1378306 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1378260 TGGCACCCAA
1378270 AT AT 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 AT AT A
1378307 ATAATTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1385397 original size:23 final size:22
Alignment explanation
Indices: 1385371--1385431 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
1385361 TAATTAAGGT
*
1385371 TTTTAATTTAAGTTTAGATGAG
1 TTTTAATTTAAGTTTAAATGAG
* *
1385393 CTTTTAGTTTAGGTTTAAATGAG
1 -TTTTAATTTAAGTTTAAATGAG
* *
1385416 TTTAAATTTAAATTTA
1 TTTTAATTTAAGTTTA
1385432 TATTTTATTA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 12 0.39
23 19 0.61
ACGTcount: A:0.33, C:0.02, G:0.15, T:0.51
Consensus pattern (22 bp):
TTTTAATTTAAGTTTAAATGAG
Found at i:1385572 original size:14 final size:14
Alignment explanation
Indices: 1385553--1385590 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
1385543 ATCAAAACTT
1385553 AAATTAAATT-AATC
1 AAATT-AATTAAATC
1385567 AAATTAATTAAATC
1 AAATTAATTAAATC
1385581 AAATTTAATT
1 AAA-TTAATT
1385591 TATTTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.18
14 12 0.55
15 6 0.27
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATTAATTAAATC
Done.