Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold47
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: 2157611
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 149227 characters in sequence are not A, C, G, or T
File 10 of 15
Found at i:1255356 original size:3 final size:3
Alignment explanation
Indices: 1255350--1255379 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1255340 TAATAATAAT
1255350 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1255380 GAAAACTTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1259102 original size:20 final size:20
Alignment explanation
Indices: 1259079--1259123 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1259069 AACCAAATGC
*
1259079 ATATTTTTATTAATAATTTA
1 ATATTTTTAATAATAATTTA
* * *
1259099 ATATATTTAATATTTATTTA
1 ATATTTTTAATAATAATTTA
1259119 ATATT
1 ATATT
1259124 AAAATATTTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATTTTTAATAATAATTTA
Found at i:1259185 original size:46 final size:48
Alignment explanation
Indices: 1259124--1259225 Score: 145
Period size: 46 Copynumber: 2.1 Consensus size: 48
1259114 ATTTAATATT
* * *
1259124 AAAATATTTTAAAATTTTATTTTAATTAATTAATTAATTAAAA-TT-AA
1 AAAATA-TTTAAAATTTTATTTAAATAAATTAATTAATAAAAATTTCAA
*
1259171 AAAATATTTAAAATTTTATTTAAATAAATTTATTAATAAAAATTTCAA
1 AAAATATTTAAAATTTTATTTAAATAAATTAATTAATAAAAATTTCAA
1259219 AAAATAT
1 AAAATAT
1259226 CAATTTAATC
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
46 32 0.65
47 8 0.16
48 9 0.18
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (48 bp):
AAAATATTTAAAATTTTATTTAAATAAATTAATTAATAAAAATTTCAA
Found at i:1264125 original size:8 final size:9
Alignment explanation
Indices: 1264097--1264155 Score: 59
Period size: 8 Copynumber: 6.6 Consensus size: 9
1264087 AATTGACTGA
1264097 AATTAAATT
1 AATTAAATT
1264106 AAATTAAATT
1 -AATTAAATT
1264116 AATT-AATT
1 AATTAAATT
1264124 AATT-AATT
1 AATTAAATT
* **
1264132 AATCAAAAG
1 AATTAAATT
1264141 AATTAAATT
1 AATTAAATT
1264150 CAATTA
1 -AATTA
1264156 TAATAAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
8 15 0.37
9 12 0.29
10 14 0.34
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (9 bp):
AATTAAATT
Found at i:1264845 original size:17 final size:16
Alignment explanation
Indices: 1264819--1264850 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1264809 CAAGTGTCCG
1264819 ATACAGTATATATCCC
1 ATACAGTATATATCCC
1264835 ATACAAGTATATATCC
1 ATAC-AGTATATATCC
1264851 GGACACTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.41, C:0.22, G:0.06, T:0.31
Consensus pattern (16 bp):
ATACAGTATATATCCC
Found at i:1269453 original size:23 final size:24
Alignment explanation
Indices: 1269427--1269483 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
1269417 TAAAAATTAT
**
1269427 TTTTATTAATT-AATATTTATATA
1 TTTTATTAATTAAATATAAATATA
1269450 TTTTA-TAATTAAATATAAATATA
1 TTTTATTAATTAAATATAAATATA
1269473 TTATT-TTAATT
1 TT-TTATTAATT
1269484 TAAAAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 5 0.17
23 17 0.59
24 7 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTTATTAATTAAATATAAATATA
Found at i:1270387 original size:17 final size:17
Alignment explanation
Indices: 1270367--1270425 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
1270357 TTATTATACT
1270367 TAAAAAATAAATTTAAA
1 TAAAAAATAAATTTAAA
**
1270384 TAAAAAATAAATTTATT
1 TAAAAAATAAATTTAAA
1270401 TAAAAAAATTAAACTTTAAA
1 T-AAAAAA-TAAA-TTTAAA
1270421 -AAAAA
1 TAAAAA
1270426 TTTTAAGCTC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 16 0.46
18 11 0.31
19 4 0.11
20 4 0.11
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAAAATAAATTTAAA
Found at i:1270774 original size:16 final size:15
Alignment explanation
Indices: 1270749--1270778 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1270739 ATTAATATTT
1270749 TAAATTAATTTAATC
1 TAAATTAATTTAATC
1270764 TAAATTTAATTTAAT
1 TAAA-TTAATTTAAT
1270779 TTATAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAATTAATTTAATC
Found at i:1272111 original size:15 final size:17
Alignment explanation
Indices: 1272080--1272116 Score: 60
Period size: 15 Copynumber: 2.3 Consensus size: 17
1272070 AGGTTTTTTT
1272080 TTTTTGCAAATAAAATA
1 TTTTTGCAAATAAAATA
1272097 TTTTTG-AAA-AAAATA
1 TTTTTGCAAATAAAATA
1272112 TTTTT
1 TTTTT
1272117 TGATTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 11 0.55
16 3 0.15
17 6 0.30
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (17 bp):
TTTTTGCAAATAAAATA
Found at i:1272116 original size:16 final size:17
Alignment explanation
Indices: 1272079--1272119 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
1272069 TAGGTTTTTT
1272079 TTTTTTGCAAATAAAATA
1 TTTTTTG-AAATAAAATA
1272097 -TTTTTGAAA-AAAATA
1 TTTTTTGAAATAAAATA
1272112 TTTTTTGA
1 TTTTTTGA
1272120 TTTTTTTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 6 0.27
16 10 0.45
17 6 0.27
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (17 bp):
TTTTTTGAAATAAAATA
Found at i:1272755 original size:18 final size:17
Alignment explanation
Indices: 1272721--1272775 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 17
1272711 CATTTAAATT
1272721 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
1272738 ATTTTAATATATTA-AT-A
1 ATTTT-ATAT-TTATATAA
*
1272755 A-TTTATA-TTATTTAA
1 ATTTTATATTTATATAA
1272770 ATTTTA
1 ATTTTA
1272776 AAAATTCACA
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
13 3 0.09
14 1 0.03
15 5 0.16
16 7 0.22
17 7 0.22
18 6 0.19
19 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:1272990 original size:12 final size:12
Alignment explanation
Indices: 1272967--1272996 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1272957 GTCTATATCC
1272967 ATATTA-TTTTT
1 ATATTATTTTTT
1272978 ATATTATTTTTT
1 ATATTATTTTTT
1272990 ATATTAT
1 ATATTAT
1272997 ATTATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.33
12 12 0.67
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
ATATTATTTTTT
Found at i:1273592 original size:29 final size:27
Alignment explanation
Indices: 1273540--1273612 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 27
1273530 CACGGCATAA
*
1273540 ACATAATAAAAAAATAATTAAAATATT
1 ACATAATAAAAAAATAATTAAAATATG
1273567 ACATAATACGAAAAAATAA-TATAAATATG
1 ACATAATA--AAAAAATAATTA-AAATATG
*
1273596 ACATAAATATAAAAATA
1 ACAT-AATAAAAAAATA
1273613 CGTTAAGATT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
27 8 0.20
28 9 0.22
29 19 0.47
30 4 0.10
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (27 bp):
ACATAATAAAAAAATAATTAAAATATG
Found at i:1273928 original size:2 final size:2
Alignment explanation
Indices: 1273923--1273950 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1273913 TATATATATA
1273923 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1273951 GAGTGAGGGG
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1277319 original size:29 final size:29
Alignment explanation
Indices: 1277238--1277334 Score: 74
Period size: 29 Copynumber: 3.2 Consensus size: 29
1277228 AAATAATAAA
*
1277238 AAATTATAAATTTTATCATTTTATTTTAATAA-
1 AAATTTTAAATTTTA--A-TTTATTTTAA-AAT
*
1277270 ATATTTTAATACTTTT-A-TTATTTTAAAAT
1 AAATTTTAA-A-TTTTAATTTATTTTAAAAT
** *
1277299 AAATTTTAAATTTTAATTTATACTAGAAT
1 AAATTTTAAATTTTAATTTATTTTAAAAT
1277328 AAATTTT
1 AAATTTT
1277335 TAACTTAAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
27 4 0.07
28 4 0.07
29 33 0.61
31 1 0.02
32 7 0.13
33 1 0.02
34 4 0.07
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (29 bp):
AAATTTTAAATTTTAATTTATTTTAAAAT
Found at i:1278656 original size:2 final size:2
Alignment explanation
Indices: 1278649--1278681 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1278639 CAAAATGCAA
1278649 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1278682 GTAATATGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1278922 original size:25 final size:24
Alignment explanation
Indices: 1278887--1278940 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
1278877 TTCTCATTTT
1278887 AAATTAGAT-AAGATAATATTAAATA
1 AAATTAGATAAAGATAATA-TAAA-A
* *
1278912 AAATTATATAAATATAATATAAAA
1 AAATTAGATAAAGATAATATAAAA
1278936 AAATT
1 AAATT
1278941 TAATATGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 6 0.23
25 12 0.46
26 8 0.31
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATTAGATAAAGATAATATAAAA
Found at i:1278987 original size:16 final size:16
Alignment explanation
Indices: 1278935--1279021 Score: 70
Period size: 16 Copynumber: 5.3 Consensus size: 16
1278925 ATAATATAAA
*
1278935 AAAATTTAATATGATAT
1 AAAATTT-ATATAATAT
* * * *
1278952 GAAAATATAAATATTTT
1 -AAAATTTATATAATAT
1278969 AAAATTTATATAATAT
1 AAAATTTATATAATAT
*
1278985 AAATTATTA-AT-ATATT
1 AAAAT-TTATATAATA-T
1279001 AAAATTTATATAATAT
1 AAAATTTATATAATAT
1279017 AAAAT
1 AAAAT
1279022 ATTTAAAACA
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
15 6 0.11
16 31 0.57
17 11 0.20
18 6 0.11
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
AAAATTTATATAATAT
Found at i:1279003 original size:32 final size:32
Alignment explanation
Indices: 1278916--1279024 Score: 130
Period size: 32 Copynumber: 3.3 Consensus size: 32
1278906 TAAATAAAAT
** *
1278916 TATATAAATA-TAATATAAAAAAATTTAATATGA
1 TATA-AAATATTAATATATTAAAATTT-ATATAA
* *
1278949 TATGAAAATATAAATATTTTAAAATTTATATAA
1 TAT-AAAATATTAATATATTAAAATTTATATAA
*
1278982 TATAAATTATTAATATATTAAAATTTATATAA
1 TATAAAATATTAATATATTAAAATTTATATAA
1279014 TATAAAATATT
1 TATAAAATATT
1279025 TAAAACATAA
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
32 36 0.55
33 16 0.25
34 13 0.20
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (32 bp):
TATAAAATATTAATATATTAAAATTTATATAA
Found at i:1279025 original size:18 final size:17
Alignment explanation
Indices: 1278925--1279039 Score: 64
Period size: 16 Copynumber: 6.8 Consensus size: 17
1278915 TTATATAAAT
*
1278925 ATAATATAAAAAAATTTA
1 ATAATAT-AAAATATTTA
*
1278943 ATATGATATGAAAATA-TAA
1 ATA--ATAT-AAAATATTTA
* *
1278962 AT-ATTTTAAA-ATTTA
1 ATAATATAAAATATTTA
*
1278977 TATAATATAAATTA-TTA
1 -ATAATATAAAATATTTA
*
1278994 AT-ATATTAAA-ATTTA
1 ATAATATAAAATATTTA
1279009 TATAATATAAAATATTTA
1 -ATAATATAAAATATTTA
*
1279027 A-AACATAAAATAT
1 ATAATATAAAATAT
1279040 AACTAAATAA
Statistics
Matches: 74, Mismatches: 13, Indels: 22
0.68 0.12 0.20
Matches are distributed among these distances:
14 2 0.03
15 14 0.19
16 20 0.27
17 16 0.22
18 9 0.12
19 4 0.05
20 9 0.12
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (17 bp):
ATAATATAAAATATTTA
Found at i:1279036 original size:32 final size:32
Alignment explanation
Indices: 1278935--1279037 Score: 102
Period size: 32 Copynumber: 3.2 Consensus size: 32
1278925 ATAATATAAA
* **
1278935 AAAATTTAATATGATATGAAAATA-TAAATATTTT
1 AAAATTT-ATATAATAT-AAAATATTAAA-ACATT
* * *
1278969 AAAATTTATATAATATAAATTATTAATATATT
1 AAAATTTATATAATATAAAATATTAAAACATT
1279001 AAAATTTATATAATATAAAATATTTAAAACA-T
1 AAAATTTATATAATATAAAATA-TTAAAACATT
1279033 AAAAT
1 AAAAT
1279038 ATAACTAAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
32 36 0.60
33 17 0.28
34 7 0.12
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (32 bp):
AAAATTTATATAATATAAAATATTAAAACATT
Found at i:1279071 original size:22 final size:24
Alignment explanation
Indices: 1279008--1279080 Score: 68
Period size: 23 Copynumber: 3.3 Consensus size: 24
1278998 ATTAAAATTT
*
1279008 ATATAATATAAA-ATATTTAAAAC
1 ATATAATATAAATATATATAAAAC
* *
1279031 ATAAAATATAACTA-A-ATAAAA-
1 ATATAATATAAATATATATAAAAC
*
1279052 A-ATAATATAAATATATAT-AAAT
1 ATATAATATAAATATATATAAAAC
1279074 ATATAAT
1 ATATAAT
1279081 TTTTCAAATC
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
20 10 0.25
21 5 0.12
22 8 0.20
23 16 0.40
24 1 0.03
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (24 bp):
ATATAATATAAATATATATAAAAC
Found at i:1279998 original size:18 final size:18
Alignment explanation
Indices: 1279972--1280007 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1279962 AAAATTTATT
*
1279972 TTATAAAATAATATTTTA
1 TTATAAAATAATAATTTA
*
1279990 TTATTAAATAATAATTTA
1 TTATAAAATAATAATTTA
1280008 AATTAAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTATAAAATAATAATTTA
Found at i:1280287 original size:13 final size:13
Alignment explanation
Indices: 1280256--1280305 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
1280246 AGTAAATCTA
1280256 ATAATAAATAA-AT
1 ATAATAAA-AATAT
*
1280269 ACAATAAAAATAT
1 ATAATAAAAATAT
1280282 ATAATATAAAATAT
1 ATAATA-AAAATAT
1280296 -TAA-AAAAATA
1 ATAATAAAAATA
1280306 ATACGAGCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 6 0.18
12 3 0.09
13 17 0.52
14 7 0.21
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (13 bp):
ATAATAAAAATAT
Found at i:1280871 original size:11 final size:11
Alignment explanation
Indices: 1280855--1280888 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
1280845 TTATTTTCCT
1280855 TTACCTAAGGC
1 TTACCTAAGGC
1280866 TTACCTAAGGC
1 TTACCTAAGGC
1280877 TTACCTAAGGC
1 TTACCTAAGGC
1280888 T
1 T
1280889 GGCTACACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (11 bp):
TTACCTAAGGC
Found at i:1281037 original size:15 final size:14
Alignment explanation
Indices: 1281016--1281054 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
1281006 AATATTTTTT
1281016 ATTAATTTAAATTA
1 ATTAATTTAAATTA
1281030 ATTTAATTTAAA-TA
1 A-TTAATTTAAATTA
1281044 ATT-ATTTAAAT
1 ATTAATTTAAAT
1281055 ATTAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 7 0.30
13 2 0.09
14 4 0.17
15 10 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTAATTTAAATTA
Found at i:1281046 original size:18 final size:18
Alignment explanation
Indices: 1281024--1281076 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
1281014 TTATTAATTT
1281024 AAATTAATTTAAT-TTAA
1 AAATTAATTTAATATTAA
1281041 ATAATT-ATTTAAATATTAA
1 A-AATTAATTT-AATATTAA
*
1281060 AAAATAATTTAATATTA
1 AAATTAATTTAATATTA
1281077 TTTTAATGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 5 0.16
18 17 0.55
19 9 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATTAATTTAATATTAA
Found at i:1281069 original size:19 final size:18
Alignment explanation
Indices: 1281028--1281076 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
1281018 TAATTTAAAT
*
1281028 TAATTTAAT-TTAAATAA
1 TAATTTAATATTAAAAAA
*
1281045 TTATTTAAATATTAAAAAA
1 TAATTT-AATATTAAAAAA
1281064 TAATTTAATATTA
1 TAATTTAATATTA
1281077 TTTTAATGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 5 0.19
18 10 0.37
19 12 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAATTTAATATTAAAAAA
Found at i:1281617 original size:16 final size:16
Alignment explanation
Indices: 1281598--1281642 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1281588 TTTGAACTCG
*
1281598 AAATGACTCGAATCTA
1 AAATGATTCGAATCTA
* * *
1281614 AAATGATTCAAACCTG
1 AAATGATTCGAATCTA
1281630 AAATGATTCGAAT
1 AAATGATTCGAAT
1281643 AATTAACTCG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (16 bp):
AAATGATTCGAATCTA
Found at i:1282889 original size:23 final size:23
Alignment explanation
Indices: 1282841--1282882 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
1282831 GATTTGATAG
*
1282841 TTTAAATAATTATTAAAAATTTA
1 TTTAAATAATTATAAAAAATTTA
1282864 TTTAAAT-ATTA-AAAAAATT
1 TTTAAATAATTATAAAAAATT
1282883 ATAATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 4 0.22
23 7 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTAAATAATTATAAAAAATTTA
Found at i:1282897 original size:23 final size:23
Alignment explanation
Indices: 1282871--1282915 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1282861 TTATTTAAAT
* *
1282871 ATTAAAAAAATTATAATTTTATA
1 ATTAAAAAAATAAAAATTTTATA
*
1282894 ATTAAATAAATAAAAATTTTAT
1 ATTAAAAAAATAAAAATTTTAT
1282916 TTTAATTAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTAAAAAAATAAAAATTTTATA
Found at i:1283196 original size:21 final size:21
Alignment explanation
Indices: 1283170--1283230 Score: 76
Period size: 19 Copynumber: 3.0 Consensus size: 21
1283160 TTAATATTAT
1283170 ATAAAAAATAATATAAATATA
1 ATAAAAAATAATATAAATATA
1283191 AT-AAAAAT-ATATAAATAT-
1 ATAAAAAATAATATAAATATA
*
1283209 ATAAAAAA-ATTATATAATATA
1 ATAAAAAATAATATA-AATATA
1283230 A
1 A
1283231 AATTTTAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
18 2 0.06
19 19 0.54
20 11 0.31
21 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAAAAAATAATATAAATATA
Found at i:1283202 original size:31 final size:28
Alignment explanation
Indices: 1283136--1283205 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
1283126 AACGGTAACG
* *
1283136 AATATAATAAAAAATAATTAAAATTTAAT
1 AATAT-ATAAAAAATAATTAAAATATAAA
*
1283165 ATTATATAAAAAATAATATAAATATAATAAA
1 AATATATAAAAAATAAT-TAAA-AT-ATAAA
1283196 AATATATAAA
1 AATATATAAA
1283206 TATATAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 12 0.35
29 8 0.24
30 2 0.06
31 12 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (28 bp):
AATATATAAAAAATAATTAAAATATAAA
Found at i:1283296 original size:21 final size:19
Alignment explanation
Indices: 1283272--1283315 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 19
1283262 ATAATATTTT
*
1283272 AAATATAATTATGATATATAA
1 AAATATAA-TAT-AAATATAA
1283293 AAATATAATATAAATATAA
1 AAATATAATATAAATATAA
1283312 AAAT
1 AAAT
1283316 TACCAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.50
20 3 0.14
21 8 0.36
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
AAATATAATATAAATATAA
Found at i:1283509 original size:2 final size:2
Alignment explanation
Indices: 1283502--1283531 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1283492 TATTATATTT
1283502 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1283532 AATTTGATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1284571 original size:17 final size:19
Alignment explanation
Indices: 1284535--1284581 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
1284525 AAATAATTTA
1284535 TAAATTTAAA--ATTAATT
1 TAAATTTAAATTATTAATT
1284552 T-AATTTAAATTATT-ATT
1 TAAATTTAAATTATTAATT
1284569 TAAATTT-AATTAT
1 TAAATTTAAATTAT
1284582 AATAATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 8 0.30
17 11 0.41
18 8 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TAAATTTAAATTATTAATT
Found at i:1284604 original size:22 final size:22
Alignment explanation
Indices: 1284569--1284610 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1284559 AATTATTATT
*
1284569 TAAATTTAATTATAATAATATA
1 TAAATTTAATTATAAAAATATA
1284591 TAAATATTAA-TATAAAAATA
1 TAAAT-TTAATTATAAAAATA
1284611 ATATGTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:1296332 original size:50 final size:50
Alignment explanation
Indices: 1296275--1296512 Score: 404
Period size: 50 Copynumber: 4.8 Consensus size: 50
1296265 GGTGGAAAGT
*
1296275 ACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCA
1 ACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTCTTCACCA
* *
1296325 ACCTTTGATAATAGAGGGAGGTGGCCATAATTGTTGATGATTCTTCACCA
1 ACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTCTTCACCA
1296375 ACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTCTTCACCA
1 ACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTCTTCACCA
*
1296425 ACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTCTTCATCA
1 ACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTCTTCACCA
* * **
1296475 ATCTTTGACAATGGAGAAAGGTGGCCATAATTGTTGAC
1 ACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGAC
1296513 TCTAAGTATA
Statistics
Matches: 178, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 178 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (50 bp):
ACCTTTGACAATAGAGGGAGGTGGCCATAATTGTTGACGATTCTTCACCA
Found at i:1304603 original size:14 final size:16
Alignment explanation
Indices: 1304572--1304618 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
1304562 AAAAAAAGTC
1304572 AAAA-GCAAAAGCACAA
1 AAAATGCAAAAGCA-AA
1304588 AAAATG-AAAAG-AAA
1 AAAATGCAAAAGCAAA
*
1304602 AAAGTGCAAAAGCAAA
1 AAAATGCAAAAGCAAA
1304618 A
1 A
1304619 TAAAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 7 0.26
15 6 0.22
16 13 0.48
17 1 0.04
ACGTcount: A:0.70, C:0.11, G:0.15, T:0.04
Consensus pattern (16 bp):
AAAATGCAAAAGCAAA
Found at i:1306107 original size:28 final size:27
Alignment explanation
Indices: 1305931--1306657 Score: 1033
Period size: 27 Copynumber: 26.6 Consensus size: 27
1305921 ACTGTGACCT
* ** *
1305931 CTTTAAAGTCCACAACTCTATGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1305958 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1305985 CTTTTAAGTCTACAATTCCGTGGCA-C
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1306011 CTTTTAAAGTCTACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* **
1306039 CTTTAAAGTCCACAACTCCGTGAAACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* **
1306066 CTTTAAAGTCCACAACTCCGTGAAACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
**
1306093 CTTTTAAAGTCCACAACTCTATGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
1306121 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
1306149 CTTTTTAAGTCCACAACTCCGTGGCACC
1 C-TTTTAAGTCCACAACTCCGTGGCACC
1306177 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
1306205 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1306232 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
1306260 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1306287 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1306314 CTTTTAAGTCTATAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1306341 CTTTTAAGTCCATAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1306368 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1306395 CTTTTAAGTCCATAATTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1306422 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1306449 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
1306477 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1306504 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
1306532 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1306559 CTTTTAAAGTCCACAACTCCGTGGCACT
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
1306587 CTTTTAAAGTCCACAACTCTGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* * * *
1306615 CTTTTAAGTTCACAGCTTCGTGGTACTC
1 CTTTTAAGTCCACAACTCCGTGGCAC-C
*
1306643 TTTTTAAGTCCACAA
1 CTTTTAAGTCCACAA
1306658 GGCGGTGGCA
Statistics
Matches: 642, Mismatches: 48, Indels: 19
0.91 0.07 0.03
Matches are distributed among these distances:
26 6 0.01
27 392 0.61
28 240 0.37
29 4 0.01
ACGTcount: A:0.24, C:0.32, G:0.14, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:1306741 original size:28 final size:28
Alignment explanation
Indices: 1306677--1307041 Score: 322
Period size: 28 Copynumber: 12.3 Consensus size: 28
1306667 ATTCCCTTCT
*
1306677 AAAGCCCACAAGTTAGTGGCACCATTTTC
1 AAAGCCCACAAGTCAGTGGCACCA-TTTC
* * *
1306706 AAAGCCCACAAGTTAGTGGCATCTTTTC
1 AAAGCCCACAAGTCAGTGGCACCATTTC
* *
1306734 AAAGCCCACAAGTCAGTGGCATCTTTTC
1 AAAGCCCACAAGTCAGTGGCACCATTTC
**
1306762 AAAGTCCACACAAGTTGGTGGCATCC-TTTC
1 AAAG-CC-CACAAGTCAGTGGCA-CCATTTC
1306792 AAAGCCCACAAGTCAGTGGCATCC-TTTC
1 AAAGCCCACAAGTCAGTGGCA-CCATTTC
* * *
1306820 AAAACCCACAAGTTAATGGCACCATTTC
1 AAAGCCCACAAGTCAGTGGCACCATTTC
1306848 AAAGCCCACAAGTCAGTGGCACCATTTC
1 AAAGCCCACAAGTCAGTGGCACCATTTC
*
1306876 AAAGCTCACACAAGTCGGTGGCACCATTTC
1 AAAGC-C-CACAAGTCAGTGGCACCATTTC
*
1306906 AAAGCCCACACAAGTCGGTGGCAACCCATTTC
1 AAAG-CC-CACAAGTCAGTGGC-A-CCATTTC
* * *
1306938 AAAGCCCACACAAGTCGGTGGTAACCTTTTTC
1 AAAG-CC-CACAAGTCAGTGG-CACC-ATTTC
*
1306970 AAAGCCCACACGAGTC-GATTGCAATCCATTTC
1 AAAGCCCACA--AGTCAG-TGGC-A-CCATTTC
* *
1307002 AAAGCCCACACGAGTCGGTGGCAACCCTTTTC
1 AAAGCCCACA--AGTCAGTGGC-A-CCATTTC
1307034 AAAGCCCA
1 AAAGCCCA
1307042 TACAAGTTGA
Statistics
Matches: 296, Mismatches: 23, Indels: 31
0.85 0.07 0.09
Matches are distributed among these distances:
27 2 0.01
28 107 0.36
29 27 0.09
30 66 0.22
31 8 0.03
32 83 0.28
33 3 0.01
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCACCATTTC
Found at i:1306810 original size:86 final size:88
Alignment explanation
Indices: 1306683--1307068 Score: 347
Period size: 86 Copynumber: 4.3 Consensus size: 88
1306673 TTCTAAAGCC
* * *
1306683 CACAAGTTAGTGGCACCATTTTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAGCCCACAAGTC
1 CACAAGTTGGTGGCACC-TTTTCAAAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACAAGTC
* * *
1306748 AGTGGC-A-TCTTTTCAAAGTCCA
65 AGTGGCAACCCATTTCAAAGCCCA
* * *
1306770 CACAAGTTGGTGGCATCC-TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAACCCACAAGTT
1 CACAAGTTGGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACAAGTC
*
1306834 AATGGC-A-CCATTTCAAAG-CC-
65 AGTGGCAACCCATTTCAAAGCCCA
** * * *
1306854 CACAAGTCAGTGGCACCATTTCAAAGCTCACACAAGTCGGTGGCACCATTTCAAAGCCCACACAA
1 CACAAGTTGGTGGCACCTTTTCAAAGC-C-CACAAGTCAGTGGCATCATTTCAAAG-CC-CACAA
*
1306919 GTCGGTGGCAACCCATTTCAAAGCCCA
62 GTCAGTGGCAACCCATTTCAAAGCCCA
* * *
1306946 CACAAGTCGGTGGTAACCTTTTTCAAAGCCCACACGAGTC-GATTGCAATCCATTTCAAAGCCCA
1 CACAAGTTGGTGG-CACC-TTTTCAAAGCCCACA--AGTCAG-TGGC-AT-CATTTCAAAGCCCA
* *
1307010 CACGAGTCGGTGGCAACCCTTTTCAAAGCCCA
59 CA--AGTCAGTGGCAACCCATTTCAAAGCCCA
* * *
1307042 TACAAGTTGATGGGAACCTCTTTCAAA
1 CACAAGTTGGT-GGCACCT-TTTCAAA
1307069 AGTCCACACT
Statistics
Matches: 252, Mismatches: 26, Indels: 33
0.81 0.08 0.11
Matches are distributed among these distances:
83 2 0.01
84 22 0.09
85 3 0.01
86 79 0.31
87 16 0.06
88 13 0.05
89 1 0.00
90 11 0.04
91 2 0.01
92 16 0.06
93 5 0.02
94 20 0.08
95 4 0.02
96 56 0.22
97 2 0.01
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (88 bp):
CACAAGTTGGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACAAGTCA
GTGGCAACCCATTTCAAAGCCCA
Found at i:1306828 original size:114 final size:114
Alignment explanation
Indices: 1306653--1307041 Score: 381
Period size: 114 Copynumber: 3.3 Consensus size: 114
1306643 TTTTTAAGTC
* * *
1306653 CACAAGGCGGTGGCATTCCCTTCTAAAGCCCACAAGTTAGTGGCACCATTTTCAAAGCCCACAAG
1 CACAAGTCGGTGGCA-TCCTTTC-AAAGCCCACAAGTCAGTGGCACCA-TTTCAAAGCCCACAAG
* * * * *
1306718 TTAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAG-TCCA
63 TTAATGGCACCATTTCAAAGCCCACAAGTCAGTGGCACCATTTCAAAGCT-CA
* *
1306770 CACAAGTTGGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAACCCACAAGTT
1 CACAAGTCGGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCA-CCATTTCAAAGCCCACAAGTT
1306834 AATGGCACCATTTCAAAGCCCACAAGTCAGTGGCACCATTTCAAAGCTCA
65 AATGGCACCATTTCAAAGCCCACAAGTCAGTGGCACCATTTCAAAGCTCA
*
1306884 CACAAGTCGGTGGCA-CCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACA
1 CACAAGTCGGTGGCATCC-TTTCAAAG-CC-CACAAGTCAGTGGC-A-CCATTTCAAAG-CC-CA
*** * * * *
1306948 CAAGTCGGTGGTAACCTTTTTCAAAGCCCACACGAGTC-GATTGCAATCCATTTCAAAGCCCA
59 CAAGTTAATGG-CACC-ATTTCAAAGCCCACA--AGTCAG-TGGC-A-CCATTTCAAAGCTCA
* *
1307010 CACGAGTCGGTGGCAACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGC-ATCC-TTTCAAAGCCCA
1307042 TACAAGTTGA
Statistics
Matches: 231, Mismatches: 23, Indels: 27
0.82 0.08 0.10
Matches are distributed among these distances:
113 2 0.01
114 82 0.35
115 23 0.10
116 21 0.09
117 16 0.07
118 7 0.03
119 2 0.01
120 10 0.04
121 3 0.01
122 14 0.06
123 1 0.00
124 7 0.03
125 1 0.00
126 29 0.13
127 3 0.01
128 10 0.04
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22
Consensus pattern (114 bp):
CACAAGTCGGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCATTTCAAAGCCCACAAGTTA
ATGGCACCATTTCAAAGCCCACAAGTCAGTGGCACCATTTCAAAGCTCA
Found at i:1306940 original size:32 final size:32
Alignment explanation
Indices: 1306730--1307132 Score: 310
Period size: 32 Copynumber: 13.2 Consensus size: 32
1306720 AGTGGCATCT
* * *
1306730 TTTCAAAG-CC-CACAAGTCAGTGGC-A-TCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* * *
1306758 TTTCAAAGTCCACACAAGTTGGTGGC-ATCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
1306788 TTTCAAAG-CC-CACAAGTCAGTGGC-ATCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* ***
1306816 TTTCAAA-ACC-CACAAGTTAATGGC-A-CCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
1306844 TTTCAAAG-CC-CACAAGTCAGTGGC-A-CCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
1306872 TTTCAAAGCTCACACAAGTCGGTGGC-A-CCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1306902 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* **
1306934 TTTCAAAGCCCACACAAGTCGGTGGTAACCTT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* * * *
1306966 TTTCAAAGCCCACACGAGTCGATTGCAATCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
1306998 TTTCAAAGCCCACACGAGTCGGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* * * *
1307030 TTTCAAAGCCCATACAAGTTGATGGGAACCTC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACC-CA
* ** *
1307062 TTTCAAAAGTCCACAC-TTTCGGTGGCAACCCT
1 TTTC-AAAGCCCACACAAGTCGGTGGCAACCCA
* * * * *
1307094 TTTAAAAGCCCACGCAAGTCAGTGGTAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1307126 TTTCAAA
1 TTTCAAA
1307133 TCACCATTTT
Statistics
Matches: 315, Mismatches: 46, Indels: 24
0.82 0.12 0.06
Matches are distributed among these distances:
27 2 0.01
28 79 0.25
29 5 0.02
30 63 0.20
31 12 0.04
32 144 0.46
33 10 0.03
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.23
Consensus pattern (32 bp):
TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
Found at i:1308365 original size:4 final size:4
Alignment explanation
Indices: 1308358--1308405 Score: 50
Period size: 4 Copynumber: 12.5 Consensus size: 4
1308348 AAAGTTAAGT
1308358 AAGA AAGA AAGA AAG- AAGA TGAA-A AAGA AAGA AAGA AA-A AA-A AAGA
1 AAGA AAGA AAGA AAGA AAGA --AAGA AAGA AAGA AAGA AAGA AAGA AAGA
1308404 AA
1 AA
1308406 AAAATATGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
3 11 0.28
4 25 0.64
5 1 0.03
6 2 0.05
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (4 bp):
AAGA
Found at i:1308386 original size:16 final size:14
Alignment explanation
Indices: 1308365--1308409 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
1308355 AGTAAGAAAG
1308365 AAAGAAAGAAGATGAA
1 AAAGAAAGAA-A-GAA
1308381 AAAGAAAGAAAGAA
1 AAAGAAAGAAAGAA
*
1308395 AAAAAAAGAAA-AA
1 AAAGAAAGAAAGAA
1308408 AA
1 AA
1308410 TATGAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 4 0.14
14 13 0.46
15 1 0.04
16 10 0.36
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (14 bp):
AAAGAAAGAAAGAA
Found at i:1308405 original size:24 final size:24
Alignment explanation
Indices: 1308358--1308407 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
1308348 AAAGTTAAGT
* * *
1308358 AAGAAAGAAAGAAAGAAGATGAAA
1 AAGAAAGAAAGAAAAAAAAAGAAA
1308382 AAGAAAGAAAGAAAAAAAAAGAAA
1 AAGAAAGAAAGAAAAAAAAAGAAA
1308406 AA
1 AA
1308408 AATATGAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (24 bp):
AAGAAAGAAAGAAAAAAAAAGAAA
Found at i:1311961 original size:16 final size:17
Alignment explanation
Indices: 1311931--1311962 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1311921 TTCAATAAAA
1311931 ATTTTATTTTATAAATT
1 ATTTTATTTTATAAATT
1311948 ATTTTATTTT-TAAAT
1 ATTTTATTTTATAAAT
1311963 GATGTATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTTTATTTTATAAATT
Found at i:1312079 original size:15 final size:16
Alignment explanation
Indices: 1312040--1312079 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1312030 ATTTCATTAA
1312040 TTAT-TTTTAGTTTTG
1 TTATATTTTAGTTTTG
1312055 TT-TCATTTTAGTTTT-
1 TTAT-ATTTTAGTTTTG
1312070 TTATATTTTA
1 TTATATTTTA
1312080 AATAATATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.05
15 10 0.45
16 11 0.50
ACGTcount: A:0.17, C:0.03, G:0.07, T:0.72
Consensus pattern (16 bp):
TTATATTTTAGTTTTG
Found at i:1312449 original size:6 final size:7
Alignment explanation
Indices: 1312432--1312460 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1312422 CTCTTTTTTT
1312432 AAAAAAG
1 AAAAAAG
1312439 AAAAAAG
1 AAAAAAG
1312446 AAAAAAG
1 AAAAAAG
1312453 AAAAAAG
1 AAAAAAG
1312460 A
1 A
1312461 GTTCGAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:1314069 original size:11 final size:11
Alignment explanation
Indices: 1314053--1314077 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1314043 TTTAAAAATA
1314053 AATAAATATTT
1 AATAAATATTT
1314064 AATAAATATTT
1 AATAAATATTT
1314075 AAT
1 AAT
1314078 TTAAAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AATAAATATTT
Found at i:1314934 original size:22 final size:22
Alignment explanation
Indices: 1314909--1314965 Score: 75
Period size: 21 Copynumber: 2.6 Consensus size: 22
1314899 AATAAATAAT
1314909 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
1314931 TA-TTTTATAATTAAATTTATA
1 TATTTTTATAATTAAATTTATA
1314952 TAATTTTT-TAATTA
1 T-ATTTTTATAATTA
1314966 TTAAATATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
21 14 0.44
22 14 0.44
23 4 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:1314938 original size:21 final size:22
Alignment explanation
Indices: 1314912--1314965 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
1314902 AAATAATTAT
1314912 TTTTAT-ATTAATATTTATAT-A
1 TTTTATAATTAA-ATTTATATAA
1314933 TTTTATAATTAAATTTATATAA
1 TTTTATAATTAAATTTATATAA
*
1314955 TTTTTTAATTA
1 TTTTATAATTA
1314966 TTAAATATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 14 0.47
22 16 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTTATAATTAAATTTATATAA
Found at i:1315564 original size:30 final size:32
Alignment explanation
Indices: 1315503--1315571 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
1315493 TCAGAAAGTG
*
1315503 AACTTTAATAATTATAATTTCATAGACATAAA
1 AACTTTAATAATTATAATTTCATACACATAAA
*
1315535 AACTTTCATAATTA-AA-TTCATTACA-ATAAA
1 AACTTTAATAATTATAATTTCA-TACACATAAA
1315565 AA-TTTAA
1 AACTTTAA
1315572 GAGCATACAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
29 4 0.12
30 11 0.33
31 5 0.15
32 13 0.39
ACGTcount: A:0.51, C:0.10, G:0.01, T:0.38
Consensus pattern (32 bp):
AACTTTAATAATTATAATTTCATACACATAAA
Found at i:1319073 original size:20 final size:21
Alignment explanation
Indices: 1319048--1319091 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1319038 ACGAATATGG
*
1319048 TTTTTATTATAAAATT-TATA
1 TTTTTATAATAAAATTATATA
*
1319068 TTTTTATAATATAATTATATA
1 TTTTTATAATAAAATTATATA
1319089 TTT
1 TTT
1319092 AGAATAATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTTATAATAAAATTATATA
Found at i:1319716 original size:16 final size:16
Alignment explanation
Indices: 1319695--1319741 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
1319685 GAAATTTTAA
1319695 AATATATTTATATTAT
1 AATATATTTATATTAT
1319711 AATATATTT-TAATTAT
1 AATATATTTAT-ATTAT
*
1319727 --TTTATTTATATTAT
1 AATATATTTATATTAT
1319741 A
1 A
1319742 TTCATACAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 11 0.41
15 2 0.07
16 14 0.52
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
AATATATTTATATTAT
Found at i:1321039 original size:20 final size:18
Alignment explanation
Indices: 1321010--1321050 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
1321000 GTGTATAATT
*
1321010 TTAAACTTTAACTTTATTAA
1 TTAAAATTTAA-TTT-TTAA
1321030 TTAAAATTTAATTTTTAA
1 TTAAAATTTAATTTTTAA
1321048 TTA
1 TTA
1321051 TATTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 3 0.15
20 10 0.50
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (18 bp):
TTAAAATTTAATTTTTAA
Found at i:1321040 original size:27 final size:26
Alignment explanation
Indices: 1321009--1321067 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
1320999 AGTGTATAAT
*
1321009 TTTAAACTTTAACTT-TATTAATTAAAA
1 TTTAAACTTTAA-TTATATTAA-AAAAA
**
1321036 TTTAATTTTTAATTATATTAAAAAAA
1 TTTAAACTTTAATTATATTAAAAAAA
1321062 TTTAAA
1 TTTAAA
1321068 ATAATTTTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 11 0.41
27 16 0.59
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.49
Consensus pattern (26 bp):
TTTAAACTTTAATTATATTAAAAAAA
Found at i:1326641 original size:16 final size:16
Alignment explanation
Indices: 1326622--1326652 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1326612 GTTTAATATA
*
1326622 TATTTATTATTTATTG
1 TATTTAATATTTATTG
1326638 TATTTAATATTTATT
1 TATTTAATATTTATT
1326653 TAAAGTTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TATTTAATATTTATTG
Found at i:1328741 original size:2 final size:2
Alignment explanation
Indices: 1328729--1328760 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1328719 TTGATATTTC
1328729 AT AT A- AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1328761 TCAAACAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1328923 original size:24 final size:24
Alignment explanation
Indices: 1328893--1328965 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 24
1328883 TTTTAATTTG
* *
1328893 AATTAATATATTTAAATTATTATTT
1 AATTAATAAATTTAAATTATT-TTA
*
1328918 AA-TAATAAAAATTAAAAATTATTTTA
1 AATTAAT--AAATT-TAAATTATTTTA
1328944 AATTAATAAATTTAAATTATTT
1 AATTAATAAATTTAAATTATTT
1328966 GAGTTAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
24 13 0.32
25 7 0.17
26 8 0.20
27 12 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AATTAATAAATTTAAATTATTTTA
Found at i:1332487 original size:17 final size:16
Alignment explanation
Indices: 1332438--1332497 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 16
1332428 ATTTAAATTC
1332438 ATATATTTAT-TTTAT
1 ATATATTTATGTTTAT
1332453 ATATATTTTGATATGTTTAT
1 ATATA--TT--TATGTTTAT
1332473 ATATATTTCATGTTTCAT
1 ATATATTT-ATGTTT-AT
1332491 AT-TATTT
1 ATATATTT
1332498 TTTTGTTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
15 5 0.13
16 1 0.03
17 13 0.34
18 6 0.16
19 3 0.08
20 10 0.26
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (16 bp):
ATATATTTATGTTTAT
Found at i:1333587 original size:15 final size:17
Alignment explanation
Indices: 1333567--1333611 Score: 58
Period size: 15 Copynumber: 2.7 Consensus size: 17
1333557 ATTTTCAGAA
1333567 TAAATTATTTA-A-ATT
1 TAAATTATTTATATATT
1333582 TAAATTATTTATATATT
1 TAAATTATTTATATATT
*
1333599 TATATTATATTAT
1 TAAATTAT-TTAT
1333612 TTATATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 11 0.42
16 1 0.04
17 10 0.38
18 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TAAATTATTTATATATT
Found at i:1333612 original size:14 final size:13
Alignment explanation
Indices: 1333586--1333631 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
1333576 TAAATTTAAA
1333586 TTAT-TTATATAT
1 TTATATTATATAT
1333598 TTATATTATATTAT
1 TTATATTATA-TAT
1333612 TTATA-TAT-TAT
1 TTATATTATATAT
*
1333623 GTATATTAT
1 TTATATTAT
1333632 GTTAATTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 7 0.23
12 7 0.23
13 8 0.27
14 8 0.27
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (13 bp):
TTATATTATATAT
Found at i:1333617 original size:9 final size:9
Alignment explanation
Indices: 1333579--1333631 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
1333569 AATTATTTAA
*
1333579 ATTTAAATT
1 ATTTATATT
1333588 ATTTATA-T
1 ATTTATATT
1333596 ATTTATATT
1 ATTTATATT
1333605 ATATTAT-TT
1 AT-TTATATT
1333614 A--TATATT
1 ATTTATATT
*
1333621 ATGTATATT
1 ATTTATATT
1333630 AT
1 AT
1333632 GTTAATTTCT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
6 3 0.08
7 3 0.08
8 8 0.21
9 20 0.53
10 4 0.11
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (9 bp):
ATTTATATT
Found at i:1334963 original size:24 final size:24
Alignment explanation
Indices: 1334931--1334978 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1334921 CCTCAATGAA
1334931 GTAGCAACCTAATTTTAGTGTACT
1 GTAGCAACCTAATTTTAGTGTACT
*
1334955 GTAGTAACCTAATTTTAGTGTACT
1 GTAGCAACCTAATTTTAGTGTACT
1334979 ATTATTTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.40
Consensus pattern (24 bp):
GTAGCAACCTAATTTTAGTGTACT
Found at i:1335715 original size:22 final size:22
Alignment explanation
Indices: 1335690--1335747 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 22
1335680 ATTAAATAAT
*
1335690 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTAAA
1335712 TA-TTTTATAATTAAATTTAAA
1 TATTTTTATAATTAAATTTAAA
*
1335733 TAATTTTTTTAATTA
1 T-ATTTTTATAATTA
1335748 TTAAACATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 13 0.42
22 8 0.26
23 10 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTAAA
Found at i:1340276 original size:11 final size:11
Alignment explanation
Indices: 1340230--1340280 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
1340220 TTTTAAAATA
1340230 TATATTTATAT
1 TATATTTATAT
*
1340241 TATA-ATATAT
1 TATATTTATAT
* *
1340251 TTTAGTTAT-T
1 TATATTTATAT
1340261 T-TATTTATAT
1 TATATTTATAT
1340271 TATATTTATA
1 TATATTTATA
1340281 CTACCGTGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 6 0.18
10 12 0.36
11 15 0.45
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1344586 original size:13 final size:13
Alignment explanation
Indices: 1344568--1344600 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1344558 TTTTTTAATT
1344568 TTATTAAATTATA
1 TTATTAAATTATA
*
1344581 TTATTAAATTTTA
1 TTATTAAATTATA
1344594 TTATTAA
1 TTATTAA
1344601 TAAATTAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TTATTAAATTATA
Found at i:1346237 original size:29 final size:29
Alignment explanation
Indices: 1346190--1346246 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1346180 ATGTTTAATC
*
1346190 TAATTCAAATCAAGTTAATATATATATTG
1 TAATTCAAATCAAGTTAATATAAATATTG
* *
1346219 TAATTTAAATCAA-TCTAATTTAAATATT
1 TAATTCAAATCAAGT-TAATATAAATATT
1346247 ATTTAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.44
Consensus pattern (29 bp):
TAATTCAAATCAAGTTAATATAAATATTG
Found at i:1354455 original size:23 final size:21
Alignment explanation
Indices: 1354422--1354464 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
1354412 ACATTTGCAG
1354422 AAAAAAATTAATAAGACCATT
1 AAAAAAATTAATAAGACCATT
*
1354443 AAAAAATATTTAATAATACCAT
1 AAAAAA-A-TTAATAAGACCAT
1354465 GTATTGGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 1 0.05
23 12 0.63
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.28
Consensus pattern (21 bp):
AAAAAAATTAATAAGACCATT
Found at i:1354671 original size:2 final size:2
Alignment explanation
Indices: 1354664--1354702 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1354654 ATTATACATT
* *
1354664 TA TA TA TA CA TA CA 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 T
1354703 GTATGTGTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1354673 original size:12 final size:12
Alignment explanation
Indices: 1354656--1354702 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
1354646 GAATTTAGAT
*
1354656 TATACATTTATA
1 TATACATATATA
*
1354668 TATACATACATA
1 TATACATATATA
*
1354680 TATATATATATA
1 TATACATATATA
*
1354692 TATATATATAT
1 TATACATATAT
1354703 GTATGTGTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (12 bp):
TATACATATATA
Found at i:1357176 original size:23 final size:23
Alignment explanation
Indices: 1357149--1357217 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
1357139 CTATTTATGT
1357149 AATAAAATAAAATTTTTATATTA
1 AATAAAATAAAATTTTTATATTA
* **
1357172 AATAAAA-AAATATATAAATATTA
1 AATAAAATAAA-ATTTTTATATTA
1357195 ATATAAAAT-AAATTTTTAATATT
1 A-ATAAAATAAAATTTTT-ATATT
1357218 TTTAATAGTA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
22 3 0.08
23 20 0.56
24 13 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
AATAAAATAAAATTTTTATATTA
Found at i:1360341 original size:33 final size:32
Alignment explanation
Indices: 1360299--1360365 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
1360289 TAACAGTGAC
* *
1360299 ATGACACTAATATACAAACGTGTCAAAATTTAT
1 ATGACACTAAT-TACAAACATATCAAAATTTAT
**
1360332 ATGACACTAATTAGTAACATATCAAAATTTAT
1 ATGACACTAATTACAAACATATCAAAATTTAT
1360364 AT
1 AT
1360366 AAACAAAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 19 0.63
33 11 0.37
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.33
Consensus pattern (32 bp):
ATGACACTAATTACAAACATATCAAAATTTAT
Found at i:1361401 original size:11 final size:10
Alignment explanation
Indices: 1361373--1361403 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
1361363 TTTTTATTTT
1361373 TTATTTTAAA
1 TTATTTTAAA
1361383 TTATTTTAAA
1 TTATTTTAAA
1361393 TTAATTTTAAA
1 TT-ATTTTAAA
1361404 AATAAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 12 0.60
11 8 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TTATTTTAAA
Found at i:1361577 original size:20 final size:20
Alignment explanation
Indices: 1361554--1361619 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
1361544 GACTTTCGAT
1361554 TTTTTTTATAGCTTTTTTGG
1 TTTTTTTATAGCTTTTTTGG
* *
1361574 TTTTTTTTGTCAGC-TTTTTGA
1 -TTTTTTTAT-AGCTTTTTTGG
* *
1361595 TTTTTTTCATA-TTTTTTTTG
1 TTTTTTT-ATAGCTTTTTTGG
1361615 TTTTT
1 TTTTT
1361620 AGTTTTTCAT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
20 18 0.50
21 15 0.42
22 3 0.08
ACGTcount: A:0.09, C:0.06, G:0.11, T:0.74
Consensus pattern (20 bp):
TTTTTTTATAGCTTTTTTGG
Found at i:1361577 original size:21 final size:21
Alignment explanation
Indices: 1361553--1361619 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
1361543 TGACTTTCGA
1361553 TTTTTTTTATAGCTTTTTTGG
1 TTTTTTTTATAGCTTTTTTGG
* *
1361574 TTTTTTTTGTCAGC-TTTTTGA
1 TTTTTTTTAT-AGCTTTTTTGG
* * *
1361595 TTTTTTTCATA-TTTTTTTTG
1 TTTTTTTTATAGCTTTTTTGG
1361615 TTTTT
1 TTTTT
1361620 AGTTTTTCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
20 11 0.30
21 23 0.62
22 3 0.08
ACGTcount: A:0.09, C:0.06, G:0.10, T:0.75
Consensus pattern (21 bp):
TTTTTTTTATAGCTTTTTTGG
Found at i:1361613 original size:35 final size:34
Alignment explanation
Indices: 1361574--1361648 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 34
1361564 GCTTTTTTGG
* *
1361574 TTTTTT-TTGTCAGCTTTTTGAT-TTTTTTCATATT
1 TTTTTTGTTTTCAG-TTTTTCATATTTTTT-ATATT
*
1361608 TTTTTTGTTTTTAGTTTTTCATAATTTTTTATATT
1 TTTTTTGTTTTCAGTTTTTCAT-ATTTTTTATATT
1361643 TTTTTT
1 TTTTTT
1361649 AAAATTTTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
34 13 0.37
35 16 0.46
36 6 0.17
ACGTcount: A:0.13, C:0.05, G:0.07, T:0.75
Consensus pattern (34 bp):
TTTTTTGTTTTCAGTTTTTCATATTTTTTATATT
Found at i:1361644 original size:25 final size:25
Alignment explanation
Indices: 1361597--1361644 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1361587 CTTTTTGATT
* *
1361597 TTTTTCATATTTTTTTTGTTTTTAG
1 TTTTTCATATTTTTTATGATTTTAG
1361622 TTTTTCATAATTTTTTAT-ATTTT
1 TTTTTCAT-ATTTTTTATGATTTT
1361645 TTTTAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 12 0.60
26 8 0.40
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.75
Consensus pattern (25 bp):
TTTTTCATATTTTTTATGATTTTAG
Found at i:1361838 original size:13 final size:13
Alignment explanation
Indices: 1361820--1361858 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
1361810 TATATATATT
1361820 TTATTTTATTATA
1 TTATTTTATTATA
1361833 TTATTTTATTA-A
1 TTATTTTATTATA
*
1361845 TTTTTTTAATTATA
1 TTATTTT-ATTATA
1361859 GTTAAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 7 0.30
13 15 0.65
14 1 0.04
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTATTTTATTATA
Found at i:1364953 original size:87 final size:90
Alignment explanation
Indices: 1364751--1365015 Score: 333
Period size: 87 Copynumber: 3.0 Consensus size: 90
1364741 TTTATCGTGT
* * * * * *
1364751 CATTAGTCAAATATTTTTTGACATTTCAGAAGGAATTTGATACCCTATGCA--TGTCACATATTT
1 CATTAGTCAAATATTTTATGTCATGTCAGAAGAAATTTGATACCCCATGCATCTGTCACATCTTT
* *
1364814 CAGGTTTCAAGATTAATTTTATTAGG
66 CGGGTTCCAAGA-TAATTTTATTAGG
* *
1364840 CATTAGTTAAATATTTTCTGTCATGTCAGAAGAAATTTGATACCCCATGCATCTGTCACATCTTT
1 CATTAGTCAAATATTTTATGTCATGTCAGAAGAAATTTGATACCCCATGCATCTGTCACATCTTT
*
1364905 TGGGTTCCAA-A-AA-TTTATTAGG
66 CGGGTTCCAAGATAATTTTATTAGG
* * * *
1364927 CATTAGTCAAATATTTTATGTTATGTCAGAAGAAATCTGATACCTCATGCATCTTTCACATCTTT
1 CATTAGTCAAATATTTTATGTCATGTCAGAAGAAATTTGATACCCCATGCATCTGTCACATCTTT
*
1364992 CGGGTTCTAAGATTAATTTTATTA
66 CGGGTTCCAAGA-TAATTTTATTA
1365016 AAACATATTA
Statistics
Matches: 152, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
87 76 0.50
88 3 0.02
89 45 0.30
90 3 0.02
91 25 0.16
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (90 bp):
CATTAGTCAAATATTTTATGTCATGTCAGAAGAAATTTGATACCCCATGCATCTGTCACATCTTT
CGGGTTCCAAGATAATTTTATTAGG
Found at i:1367458 original size:21 final size:21
Alignment explanation
Indices: 1367400--1367459 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 21
1367390 ACAACATAAA
* * *
1367400 TAAATTTCATCGTACTAAAAT
1 TAAATTTAATCATAATAAAAT
* * * *
1367421 TAAACTTAGTTACAATAAAAT
1 TAAATTTAATCATAATAAAAT
1367442 TAAATTTAATCATAATAA
1 TAAATTTAATCATAATAA
1367460 TGAATTACAA
Statistics
Matches: 28, Mismatches: 11, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.37
Consensus pattern (21 bp):
TAAATTTAATCATAATAAAAT
Found at i:1367479 original size:35 final size:36
Alignment explanation
Indices: 1367439--1367517 Score: 88
Period size: 41 Copynumber: 2.1 Consensus size: 36
1367429 GTTACAATAA
*
1367439 AATTAA-ATTTAATCATAATAATGAATTACAAAGCT
1 AATTAATATTTAATCATAATAATAAATTACAAAGCT
*
1367474 AATTAATTTTTTATTTAATCATAATAATAAATTATAAAGCT
1 AATTAA-----TATTTAATCATAATAATAAATTACAAAGCT
1367515 AAT
1 AAT
1367518 CATAAGAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
35 6 0.17
41 30 0.83
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (36 bp):
AATTAATATTTAATCATAATAATAAATTACAAAGCT
Found at i:1367572 original size:17 final size:17
Alignment explanation
Indices: 1367524--1367572 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
1367514 TAATCATAAG
*
1367524 AAAAAAAA-CAAAAAAC
1 AAAAAAAATAAAAAAAC
**
1367540 AAAAAAAATATCAAAAC
1 AAAAAAAATAAAAAAAC
1367557 AAAAAAAATAAAAAAA
1 AAAAAAAATAAAAAAA
1367573 AGTATATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 8 0.30
17 19 0.70
ACGTcount: A:0.86, C:0.08, G:0.00, T:0.06
Consensus pattern (17 bp):
AAAAAAAATAAAAAAAC
Found at i:1368266 original size:18 final size:18
Alignment explanation
Indices: 1368232--1368278 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
1368222 AAATTTAATC
1368232 ATAACAATAAATTATAAAA
1 ATAACAAT-AATTATAAAA
*
1368251 ATAACAATACTTATAAAA
1 ATAACAATAATTATAAAA
*
1368269 ATAAAAATAA
1 ATAACAATAA
1368279 AACATATCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (18 bp):
ATAACAATAATTATAAAA
Found at i:1368593 original size:35 final size:36
Alignment explanation
Indices: 1368554--1368629 Score: 106
Period size: 35 Copynumber: 2.2 Consensus size: 36
1368544 TTATATATAC
1368554 AAAAAAAAAAC-TA-G-AAAAAATCAAAAGCTATTG
1 AAAAAAAAAACTTATGAAAAAAATCAAAAGCTATTG
*
1368587 -AAAAAAAATCTTATGAAAAAAATCAAAAGCTATTG
1 AAAAAAAAAACTTATGAAAAAAATCAAAAGCTATTG
*
1368622 GAAAAAAA
1 AAAAAAAA
1368630 GCAATTCGGA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
32 9 0.24
33 2 0.05
34 1 0.03
35 19 0.50
36 7 0.18
ACGTcount: A:0.66, C:0.08, G:0.09, T:0.17
Consensus pattern (36 bp):
AAAAAAAAAACTTATGAAAAAAATCAAAAGCTATTG
Found at i:1369893 original size:20 final size:20
Alignment explanation
Indices: 1369868--1369921 Score: 92
Period size: 20 Copynumber: 2.7 Consensus size: 20
1369858 GTTACAAGCA
1369868 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATGT-ATC
1369888 ATGTATCGATACAATGTATC
1 ATGTATCGATACAATGTATC
1369908 ATGTATCGATACAA
1 ATGTATCGATACAA
1369922 ACAGTGGTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 32 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATGTATC
Found at i:1369976 original size:20 final size:20
Alignment explanation
Indices: 1369951--1370005 Score: 87
Period size: 19 Copynumber: 2.8 Consensus size: 20
1369941 TGCCAGTTTT
1369951 ATGTATCGATACAATTG-TCC
1 ATGTATCGATACAATTGAT-C
1369971 ATGTATCGATACAA-TGATC
1 ATGTATCGATACAATTGATC
1369990 ATGTATCGATACAATT
1 ATGTATCGATACAATT
1370006 ATCGATACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACAATTGATC
Found at i:1370785 original size:11 final size:10
Alignment explanation
Indices: 1370755--1370802 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 10
1370745 ATAAATTAGT
1370755 TTTAAATAAA
1 TTTAAATAAA
1370765 TTACTAAATAAA
1 TT--TAAATAAA
1370777 CTTTAAATAAA
1 -TTTAAATAAA
*
1370788 TCATAAATAAA
1 T-TTAAATAAA
1370799 TTTA
1 TTTA
1370803 TTCGTGAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
10 5 0.16
11 17 0.53
12 8 0.25
13 2 0.06
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (10 bp):
TTTAAATAAA
Found at i:1371106 original size:12 final size:12
Alignment explanation
Indices: 1371088--1371131 Score: 54
Period size: 11 Copynumber: 3.7 Consensus size: 12
1371078 TGGAACTATC
1371088 ATTTTTTTAA-A
1 ATTTTTTTAATA
1371099 ATTTTTTTAATA
1 ATTTTTTTAATA
* *
1371111 ATTTTTTAAAGTT
1 ATTTTTTTAA-TA
1371124 ATTTTTTT
1 ATTTTTTT
1371132 TGATATTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 10 0.36
12 10 0.36
13 8 0.29
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (12 bp):
ATTTTTTTAATA
Found at i:1371363 original size:13 final size:13
Alignment explanation
Indices: 1371345--1371370 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1371335 AATTTAATTT
1371345 TAATTAATTTTTA
1 TAATTAATTTTTA
1371358 TAATTAATTTTTA
1 TAATTAATTTTTA
1371371 AAAAATTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TAATTAATTTTTA
Found at i:1371462 original size:2 final size:2
Alignment explanation
Indices: 1371455--1371480 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1371445 CTTTGTGTAA
1371455 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
1371481 CATAATAATA
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:1373339 original size:16 final size:16
Alignment explanation
Indices: 1373305--1373354 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
1373295 CGTTATCATG
*
1373305 TAATATTTATATTAA-T
1 TAATATTTA-ATAAATT
1373321 TAATATTTAATAAATT
1 TAATATTTAATAAATT
*
1373337 TAAAATTTAATAATATT
1 TAATATTTAATAA-ATT
1373354 T
1 T
1373355 TTTATTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 4 0.13
16 22 0.73
17 4 0.13
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATATTTAATAAATT
Found at i:1373445 original size:13 final size:13
Alignment explanation
Indices: 1373429--1373485 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
1373419 GTTTATGATT
1373429 AATATTAAATATA
1 AATATTAAATATA
**
1373442 AATATTTTAT-TA
1 AATATTAAATATA
*
1373454 TAT-TTAAATAT-
1 AATATTAAATATA
*
1373465 -ATATTAAAAATA
1 AATATTAAATATA
1373477 AATATTAAA
1 AATATTAAA
1373486 AACATAAGAG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
10 2 0.06
11 11 0.32
12 5 0.15
13 16 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATATTAAATATA
Found at i:1374008 original size:3 final size:3
Alignment explanation
Indices: 1374000--1374034 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1373990 CTGAGCATTT
*
1374000 TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1374035 GAGCTGTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1374994 original size:21 final size:21
Alignment explanation
Indices: 1374970--1375010 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1374960 GTTGTAATTC
*
1374970 AAAATTTTATATTT-TTATTTA
1 AAAAATTTAT-TTTATTATTTA
1374991 AAAAATTTATTTTATTATTT
1 AAAAATTTATTTTATTATTT
1375011 TTAATAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
AAAAATTTATTTTATTATTTA
Found at i:1375044 original size:34 final size:33
Alignment explanation
Indices: 1375000--1375063 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
1374990 AAAAAATTTA
*
1375000 TTTTATTATTTTTAATAATAATTA-AAATAATAT
1 TTTTATTATTTTT-ATAATAAATATAAATAATAT
1375033 TTTTATATATTTTTATAATAAATATAAATAA
1 TTTTAT-TATTTTTATAATAAATATAAATAA
1375064 AAATATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 15 0.54
34 13 0.46
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
TTTTATTATTTTTATAATAAATATAAATAATAT
Found at i:1375640 original size:26 final size:25
Alignment explanation
Indices: 1375603--1375671 Score: 65
Period size: 26 Copynumber: 2.8 Consensus size: 25
1375593 TTAAATTAAT
1375603 TTAA-ATTT-AAATTTTATTATT-TA
1 TTAATATTTAAAATTTTATT-TTATA
*
1375626 TT-ATATTATTAAAATATTATTTTATA
1 TTAATA-T-TTAAAATTTTATTTTATA
1375652 TTAATATTTAAATATTTTAT
1 TTAATATTTAAA-ATTTTAT
1375672 AATAAATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
22 1 0.03
23 3 0.08
24 1 0.03
25 9 0.24
26 20 0.54
27 3 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TTAATATTTAAAATTTTATTTTATA
Found at i:1375682 original size:20 final size:21
Alignment explanation
Indices: 1375643--1375684 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1375633 ATTAAAATAT
*
1375643 TATTTTATATTAATATTTAAA
1 TATTTTATAATAATATTTAAA
1375664 TATTTTATAATAA-ATTTAAA
1 TATTTTATAATAATATTTAAA
1375684 T
1 T
1375685 TAAAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTTTATAATAATATTTAAA
Found at i:1377421 original size:15 final size:16
Alignment explanation
Indices: 1377387--1377425 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
1377377 TCGGATTAAG
*
1377387 TATTTATTATAAGTATA
1 TATTTAATATAAG-ATA
1377404 TATTTAATATAA-ATA
1 TATTTAATATAAGATA
1377419 TATTTAA
1 TATTTAA
1377426 ATTTTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.48
17 11 0.52
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
TATTTAATATAAGATA
Found at i:1377472 original size:26 final size:26
Alignment explanation
Indices: 1377397--1377477 Score: 81
Period size: 26 Copynumber: 3.0 Consensus size: 26
1377387 TATTTATTAT
* *
1377397 AAGTATATATTTAATATAAATATATTTA
1 AAGTTTATATTT-ATATAAATAT-TTAA
* * * * *
1377425 AATTTTAAATTTTTTTATATATTTAA
1 AAGTTTATATTTATATAAATATTTAA
1377451 AAGTTTATATTTATATAAATATTTAA
1 AAGTTTATATTTATATAAATATTTAA
1377477 A
1 A
1377478 TATATTTTAA
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
26 25 0.61
27 7 0.17
28 9 0.22
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (26 bp):
AAGTTTATATTTATATAAATATTTAA
Found at i:1377989 original size:30 final size:31
Alignment explanation
Indices: 1377932--1377989 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1377922 TTTTTCATTC
* *
1377932 TTATTTTTTATATTTATTTTATTTAAACTCT
1 TTATTTTTTATATATATTTTATATAAACTCT
1377963 TTATTTTTTA-A-ATATTTATATATAAAC
1 TTATTTTTTATATATATTT-TATATAAAC
1377990 ACATATATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.21
30 9 0.38
31 10 0.42
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (31 bp):
TTATTTTTTATATATATTTTATATAAACTCT
Found at i:1382770 original size:2 final size:2
Alignment explanation
Indices: 1382763--1382810 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
1382753 TTTTTAAATT
* *
1382763 TA TA TA TA TA TA TA TA TA TA T- TT TA TT TA TA TA TA T- TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1382802 TA TA T- TA TA
1 TA TA TA TA TA
1382811 ATTATATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
1 4 0.10
2 35 0.90
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (2 bp):
TA
Found at i:1382793 original size:23 final size:23
Alignment explanation
Indices: 1382761--1382817 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
1382751 AATTTTTAAA
*
1382761 TTTATATATATATA-TATATATAT
1 TTTATTTATATATATTAT-TATAT
1382784 TTTATTTATATATATTATTATAT
1 TTTATTTATATATATTATTATAT
* *
1382807 TATAATTATAT
1 TTTATTTATAT
1382818 TTAAAATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 27 0.90
24 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTATTTATATATATTATTATAT
Found at i:1382795 original size:17 final size:18
Alignment explanation
Indices: 1382767--1382916 Score: 73
Period size: 17 Copynumber: 9.1 Consensus size: 18
1382757 TAAATTTATA
1382767 TATATATATATATATATTT
1 TATAT-TATATATATATTT
*
1382786 TAT-TTATATATAT-TAT
1 TATATTATATATATATTT
1382802 TATATTATA-AT-TA---
1 TATATTATATATATATTT
1382815 TAT-TTA-A-A-ATATTT
1 TATATTATATATATATTT
* *
1382829 TATATT-TATGTAAATTT
1 TATATTATATATATATTT
* *
1382846 TAATATAAT-TA-ATAATT
1 T-ATATTATATATATATTT
* *
1382863 TATATTTTATATATATCT
1 TATATTATATATATATTT
1382881 TATATT-TATAT-TATTAT
1 TATATTATATATATATT-T
* *
1382898 T-TATGATATTTATATTT
1 TATATTATATATATATTT
1382915 TA
1 TA
1382917 ATAATTTTTT
Statistics
Matches: 99, Mismatches: 14, Indels: 37
0.66 0.09 0.25
Matches are distributed among these distances:
11 4 0.04
12 3 0.03
13 3 0.03
14 3 0.03
15 4 0.04
16 18 0.18
17 40 0.40
18 20 0.20
19 4 0.04
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (18 bp):
TATATTATATATATATTT
Found at i:1382895 original size:27 final size:26
Alignment explanation
Indices: 1382761--1382914 Score: 95
Period size: 27 Copynumber: 5.7 Consensus size: 26
1382751 AATTTTTAAA
* * *
1382761 TTTATATATATATATATATATATTTT
1 TTTATATATATTTATATTTATATTAT
1382787 ATTTATATATA-TTATTATATTATAATTAT
1 -TTTATATATATTTA-TAT-TTAT-ATTAT
* * *
1382816 ATTTA-AAATATTTTATATTTATGTAAAT
1 -TTTATATATA-TTTATATTTATAT-TAT
* *
1382844 TTTA-ATATAATTAATAATT-TA-TAT
1 TTTATATAT-ATTTATATTTATATTAT
1382868 TTTATATATATCTTATATTTATATTAT
1 TTTATATATAT-TTATATTTATATTAT
1382895 TATT-TATGATATTTATATTT
1 T-TTATAT-ATATTTATATTT
1382915 TAATAATTTT
Statistics
Matches: 101, Mismatches: 13, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
24 8 0.08
25 10 0.10
26 5 0.05
27 43 0.43
28 20 0.20
29 12 0.12
30 3 0.03
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (26 bp):
TTTATATATATTTATATTTATATTAT
Found at i:1382914 original size:6 final size:6
Alignment explanation
Indices: 1382755--1382901 Score: 57
Period size: 6 Copynumber: 25.8 Consensus size: 6
1382745 TTTTAAAATT
* * * *
1382755 TTTAAA TTTATA --TATA TATATA TATATA TTT-TA TTTATA TATAT-
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
* ** * **
1382799 TATTATA -TTATA ATTATA TTTA-A AATAT- TTTATA TTTATG TAAAT-
1 T-TTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
* * *
1382844 TTTA-A TATA-A TTAATAA TTTATA TTT-TA TATATA TCTTATA TTTATA
1 TTTATA TTTATA TTTAT-A TTTATA TTTATA TTTATA T-TTATA TTTATA
1382891 -TTATTA TTTAT
1 TTTA-TA TTTAT
1382902 GATATTTATA
Statistics
Matches: 106, Mismatches: 20, Indels: 30
0.68 0.13 0.19
Matches are distributed among these distances:
4 4 0.04
5 32 0.30
6 57 0.54
7 13 0.12
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.59
Consensus pattern (6 bp):
TTTATA
Found at i:1384547 original size:2 final size:2
Alignment explanation
Indices: 1384540--1384568 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1384530 ATTGTTTGTC
1384540 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 A
1384569 ATAGTGGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 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):
AT
Found at i:1385194 original size:32 final size:33
Alignment explanation
Indices: 1385134--1385204 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 33
1385124 AAAAATTTTG
*
1385134 AAATAACATTTATCTTCAATAATATTAAATTAA
1 AAATAACATTTATCCTCAATAATATTAAATTAA
* *
1385167 AAATAATATTTATCCT-ACTAATATTAAATTAA
1 AAATAACATTTATCCTCAATAATATTAAATTAA
1385199 AAATAA
1 AAATAA
1385205 AAAATTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
32 21 0.60
33 14 0.40
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (33 bp):
AAATAACATTTATCCTCAATAATATTAAATTAA
Found at i:1385772 original size:13 final size:14
Alignment explanation
Indices: 1385740--1385813 Score: 50
Period size: 13 Copynumber: 5.4 Consensus size: 14
1385730 TTAAAAATAA
1385740 TAATATTATAATTAT
1 TAAT-TTATAATTAT
1385755 T-ATTTATAATT-T
1 TAATTTATAATTAT
* *
1385767 TAATTTTTTATTAT
1 TAATTTATAATTAT
*
1385781 TAATATT-TATCTTAAT
1 TAAT-TTATA-ATT-AT
1385797 TAA-TTATAATTA-
1 TAATTTATAATTAT
1385809 TAATT
1 TAATT
1385814 ATTAAACTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 16
0.69 0.07 0.24
Matches are distributed among these distances:
12 5 0.11
13 18 0.38
14 12 0.26
15 7 0.15
16 5 0.11
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATTTATAATTAT
Found at i:1386269 original size:22 final size:22
Alignment explanation
Indices: 1386227--1386269 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1386217 ACAATTAAAA
*
1386227 TTTAAATAGTAATATATATATT
1 TTTAAATAGTAATATAAATATT
*
1386249 TTTAATTA-TAATCATAAATAT
1 TTTAAATAGTAAT-ATAAATAT
1386270 AATAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTAAATAGTAATATAAATATT
Found at i:1389135 original size:8 final size:8
Alignment explanation
Indices: 1389109--1389190 Score: 58
Period size: 8 Copynumber: 9.8 Consensus size: 8
1389099 GCTTATATTA
*
1389109 TTTATTTT
1 TTTAATTT
**
1389117 TTTAAAAT
1 TTTAATTT
1389125 TTTAATTT
1 TTTAATTT
1389133 TTTAA-TT
1 TTTAATTT
1389140 TTTAATTTT
1 TTTAA-TTT
*
1389149 TTTCTATTT
1 TTT-AATTT
1389158 TTTAATTT
1 TTTAATTT
*
1389166 TTAAAATTTT
1 TT-TAA-TTT
*
1389176 TCTTAATTA
1 T-TTAATTT
1389185 TTTAAT
1 TTTAAT
1389191 ATCAGGATAT
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
7 7 0.12
8 27 0.47
9 16 0.28
10 7 0.12
11 1 0.02
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (8 bp):
TTTAATTT
Found at i:1389150 original size:15 final size:16
Alignment explanation
Indices: 1389109--1389150 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
1389099 GCTTATATTA
*
1389109 TTTATTTTTTTAAAAT
1 TTTAATTTTTTAAAAT
*
1389125 TTTAATTTTTT-AATT
1 TTTAATTTTTTAAAAT
1389140 TTTAATTTTTT
1 TTTAATTTTTT
1389151 TCTATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTAATTTTTTAAAAT
Found at i:1389151 original size:18 final size:18
Alignment explanation
Indices: 1389130--1389167 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1389120 AAAATTTTAA
1389130 TTTTT-TAATTTTTAATT
1 TTTTTCTAATTTTTAATT
*
1389147 TTTTTCTATTTTTTAATT
1 TTTTTCTAATTTTTAATT
1389165 TTT
1 TTT
1389168 AAAATTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTCTAATTTTTAATT
Found at i:1389157 original size:25 final size:25
Alignment explanation
Indices: 1389115--1389178 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
1389105 ATTATTTATT
*
1389115 TTTTTAAAA-TTTT-AATTTTTTAA
1 TTTTTAAAATTTTTCTATTTTTTAA
**
1389138 TTTTTAATTTTTTTCTATTTTTTAA
1 TTTTTAAAATTTTTCTATTTTTTAA
1389163 TTTTTAAAATTTTTCT
1 TTTTTAAAATTTTTCT
1389179 TAATTATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 7 0.21
24 4 0.12
25 23 0.68
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (25 bp):
TTTTTAAAATTTTTCTATTTTTTAA
Found at i:1389581 original size:17 final size:17
Alignment explanation
Indices: 1389559--1389596 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1389549 TTATTATTAG
*
1389559 AAATTTAAATATTTAAT
1 AAATTTAAATATTTAAC
*
1389576 AAATTTAGATATTTAAC
1 AAATTTAAATATTTAAC
1389593 AAAT
1 AAAT
1389597 ATTACTATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (17 bp):
AAATTTAAATATTTAAC
Found at i:1391586 original size:22 final size:21
Alignment explanation
Indices: 1391544--1391586 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
1391534 AAAAAAATAT
*
1391544 TATTAAATAAATTTATATTAA
1 TATTAAATAAATTGATATTAA
1391565 TATTCAAATCAAATTGAT-TTAA
1 TATT-AAAT-AAATTGATATTAA
1391587 ATTTTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 8 0.42
23 7 0.37
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (21 bp):
TATTAAATAAATTGATATTAA
Found at i:1391697 original size:14 final size:14
Alignment explanation
Indices: 1391678--1391714 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1391668 GAACGTATGT
1391678 ATATATATATACAC
1 ATATATATATACAC
*
1391692 ATATATATATATAC
1 ATATATATATACAC
1391706 ATATATATA
1 ATATATATA
1391715 AAGAGATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATATATATACAC
Found at i:1391698 original size:16 final size:16
Alignment explanation
Indices: 1391677--1391714 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
1391667 AGAACGTATG
1391677 TATATATATATACACA
1 TATATATATATACACA
*
1391693 TATATATATATACATA
1 TATATATATATACACA
1391709 TATATA
1 TATATA
1391715 AAGAGATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (16 bp):
TATATATATATACACA
Done.