Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007768.1 Hibiscus syriacus cultivar Beakdansim tig00110044_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2539099
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 11
Found at i:1427776 original size:65 final size:65
Alignment explanation
Indices: 1427653--1428058 Score: 296
Period size: 65 Copynumber: 6.1 Consensus size: 65
1427643 TTTGTCTCTC
* ** *
1427653 TTGAGATA-TTTTCTCTTAAAACAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATC
1 TTGA-ATATTTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTAAAACAAAATC
1427717 T
65 T
* **
1427718 TTGAATATGTTTTC-CTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATAT
1 TTGAATAT-TTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTAAAACAAA-A-
1427782 TGTCTCT
63 ----TCT
* * *
1427789 CTTGAGACA-TTTTCTCTT--AA-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
1 -TTGA-ATATTTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTAAAACAAAAT
1427850 CT
64 CT
* * * *
1427852 TTGAATCTGTTTTC-CTTGAAACAAATTTCGTCTCCCTGGAGACAG-TTCCTTTTAAAACAAATT
1 TTGAATAT-TTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCC-CTTAAAACAAA--
*
1427915 TTGTCTCT
62 ----ATCT
* * * *
1427923 CTTGAGACA-TTTTCTCTT---AGAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
1 -TTGA-ATATTTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTAAAACAAAAT
1427984 CT
64 CT
* * * * * **
1427986 TTGAATCTATTTCCCTTGAAACAAGTTTTGTCTCCCTTGAGACAATTTTTCTTGAAACACAAAAT
1 TTGAATATTTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTT-AAA-ACAAAAT
1428051 CT
64 CT
1428053 TTGAAT
1 TTGAAT
1428059 TTATTTCCAT
Statistics
Matches: 267, Mismatches: 41, Indels: 64
0.72 0.11 0.17
Matches are distributed among these distances:
61 2 0.01
62 18 0.07
63 11 0.04
64 9 0.03
65 100 0.37
66 8 0.03
67 15 0.06
68 1 0.00
69 64 0.24
70 6 0.02
71 16 0.06
72 14 0.05
73 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (65 bp):
TTGAATATTTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTAAAACAAAATCT
Found at i:1427787 original size:36 final size:34
Alignment explanation
Indices: 1427561--1427847 Score: 214
Period size: 36 Copynumber: 8.2 Consensus size: 34
1427551 AATTTACTCA
* *
1427561 AAACAAAGTTTTGTCTCTTTTGAGACAATTTCTCTT
1 AAACAAA--TTTGTCTCTCTTGAGACAGTTTCTCTT
* * *
1427597 AAAACAAATTTTGTCTCTCTTGAGATAATTTCTCGTAA
1 -AAACAAA-TTTGTCTCTCTTGAGACAGTTTCTC-T-T
* *
1427635 AAACAAATTTTGTCTCTCTTGAGATATTTTCTCTT
1 AAACAAA-TTTGTCTCTCTTGAGACAGTTTCTCTT
* *
1427670 AAAACAAATTTTGTCTATCTTGAGACAGTTTCCCTT
1 -AAACAAA-TTTGTCTCTCTTGAGACAGTTTCTCTT
* *
1427706 GAAACAAA-----ATCT-TTGA-ATATGTTT-TCCTT
1 -AAACAAATTTGTCTCTCTTGAGACA-GTTTCT-CTT
* *
1427735 GAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTT
1 -AAACAAATTT-GTCTCTCTTGAGACAGTTTCTCTT
*
1427771 AAAACAAATATTGTCTCTCTTGAGACATTTTCTCTT
1 -AAACAAAT-TTGTCTCTCTTGAGACAGTTTCTCTT
* *
1427807 AAA-AATTTTGTCTCTCTTGAGACAGTTTCCCTT
1 AAACAAATTTGTCTCTCTTGAGACAGTTTCTCTT
1427840 GAAACAAA
1 -AAACAAA
1427848 ATCTTTGAAT
Statistics
Matches: 207, Mismatches: 26, Indels: 36
0.77 0.10 0.13
Matches are distributed among these distances:
28 2 0.01
29 19 0.09
30 2 0.01
33 24 0.12
34 6 0.03
35 7 0.03
36 102 0.49
37 45 0.22
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (34 bp):
AAACAAATTTGTCTCTCTTGAGACAGTTTCTCTT
Found at i:1427847 original size:134 final size:134
Alignment explanation
Indices: 1427589--1428029 Score: 675
Period size: 134 Copynumber: 3.3 Consensus size: 134
1427579 TTTGAGACAA
* * * * * * *
1427589 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGATAATTTCTCGTAAAAACAAATTTTGTCTCTCT
1 TTTC-CTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCT-TTTAAAACAAATTTTGTCTCTCT
* *
1427654 TGAGATATTTTCTCTTAAAACAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTT
64 TGAGACATTTTCTCTT--AA-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTT
*
1427719 TGAATATGT
126 TGAATCTGT
*
1427728 TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATATTGTCTCTCTTG
1 TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTG
1427793 AGACATTTTCTCTTAAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAAT
66 AGACATTTTCTCTTAAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAAT
1427858 CTGT
131 CTGT
* *
1427862 TTTCCTTGAAACAAATTTCGTCTCCCTGGAGACAGTTCCTTTTAAAACAAATTTTGTCTCTCTTG
1 TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTG
*
1427927 AGACATTTTCTCTTAGAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAAT
66 AGACATTTTCTCTTAAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAAT
*
1427992 CTAT
131 CTGT
* * *
1427996 TTCCCTTGAAACAAGTTTTGTCTCCCTTGAGACA
1 TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACA
1428030 ATTTTTCTTG
Statistics
Matches: 282, Mismatches: 20, Indels: 5
0.92 0.07 0.02
Matches are distributed among these distances:
134 210 0.74
135 2 0.01
137 35 0.12
138 31 0.11
139 4 0.01
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (134 bp):
TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTG
AGACATTTTCTCTTAAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAAT
CTGT
Found at i:1427952 original size:33 final size:32
Alignment explanation
Indices: 1427910--1427977 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
1427900 CTTTTAAAAC
* *
1427910 AAATTTTGTCTCTCTTGAGACATTTTCTCTTAG
1 AAATTTTGTCTCTCTTGAGACAGTTTCCCTT-G
1427943 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1427975 AAA
1 AAA
1427978 CAAAATCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 4 0.12
33 29 0.88
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (32 bp):
AAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:1429865 original size:12 final size:12
Alignment explanation
Indices: 1429848--1429883 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1429838 TTTTCCTTTG
1429848 ATTTGTTTATTT
1 ATTTGTTTATTT
1429860 ATTTGTTTATTTT
1 ATTTGTTTA-TTT
*
1429873 ATTTTTTTATT
1 ATTTGTTTATT
1429884 GTTTTTACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.78
Consensus pattern (12 bp):
ATTTGTTTATTT
Found at i:1429889 original size:17 final size:17
Alignment explanation
Indices: 1429869--1429931 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
1429859 TATTTGTTTA
1429869 TTTTATTTTTTTATTGT
1 TTTTATTTTTTTATTGT
1429886 TTTTACTTTTTCCTT-TTG-
1 TTTTA-TTTTT--TTATTGT
* *
1429904 ATTTATTTTTTTATTAT
1 TTTTATTTTTTTATTGT
*
1429921 TTTCATTTTTT
1 TTTTATTTTTT
1429932 ACGTTTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
15 2 0.05
16 2 0.05
17 19 0.51
18 9 0.24
19 3 0.08
20 2 0.05
ACGTcount: A:0.13, C:0.06, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTTATTTTTTTATTGT
Found at i:1429890 original size:9 final size:8
Alignment explanation
Indices: 1429848--1429944 Score: 61
Period size: 8 Copynumber: 11.5 Consensus size: 8
1429838 TTTTCCTTTG
*
1429848 ATTTGTTT
1 ATTTTTTT
*
1429856 ATTTATTT
1 ATTTTTTT
*
1429864 GTTTATTTT
1 ATTT-TTTT
1429873 ATTTTTTT
1 ATTTTTTT
1429881 ATTGTTTTT
1 ATT-TTTTT
* *
1429890 ACTTTTTC
1 ATTTTTTT
*
1429898 CTTTTGATTT
1 ATTTT--TTT
1429908 ATTTTTTT
1 ATTTTTTT
*
1429916 ATTATTTTC
1 ATT-TTTTT
1429925 A-TTTTTT
1 ATTTTTTT
*
1429932 ACGTTTTTT
1 A-TTTTTTT
1429941 ATTT
1 ATTT
1429945 GATTTATTTA
Statistics
Matches: 69, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
7 5 0.07
8 33 0.48
9 25 0.36
10 6 0.09
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.75
Consensus pattern (8 bp):
ATTTTTTT
Found at i:1429923 original size:27 final size:27
Alignment explanation
Indices: 1429878--1429929 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1429868 ATTTTATTTT
*
1429878 TTTATTGTTTTTACTTTTTCCTTTTGA
1 TTTATTGTTTTTACTTTTTCATTTTGA
*
1429905 TTTATT-TTTTTATTATTTTCATTTT
1 TTTATTGTTTTTACT-TTTTCATTTT
1429930 TTACGTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.13, C:0.08, G:0.04, T:0.75
Consensus pattern (27 bp):
TTTATTGTTTTTACTTTTTCATTTTGA
Found at i:1429946 original size:42 final size:43
Alignment explanation
Indices: 1429853--1429954 Score: 115
Period size: 42 Copynumber: 2.4 Consensus size: 43
1429843 CTTTGATTTG
* *
1429853 TTTATTT-ATTTGTTTATTTTATTTTTTTATTGTTTTTACTTT
1 TTTATTTGATTTATTTATTTTATTTTTTCATTGTTTTTACTTT
1429895 TTCCT-TTTGATTTATTT-TTTTATTATTTTCA-T-TTTTTACGTTT
1 TT--TATTTGATTTATTTATTTTATT-TTTTCATTGTTTTTAC-TTT
1429938 TTTATTTGATTTATTTA
1 TTTATTTGATTTATTTA
1429955 ATATTTTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
41 1 0.02
42 21 0.41
43 16 0.31
44 13 0.25
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.75
Consensus pattern (43 bp):
TTTATTTGATTTATTTATTTTATTTTTTCATTGTTTTTACTTT
Found at i:1437083 original size:7 final size:7
Alignment explanation
Indices: 1437073--1437146 Score: 78
Period size: 7 Copynumber: 10.7 Consensus size: 7
1437063 AAATCCTACT
1437073 CTAAACC
1 CTAAACC
1437080 CTAAACC
1 CTAAACC
*
1437087 CTAAACT
1 CTAAACC
1437094 CTAAACC
1 CTAAACC
*
1437101 CTAAATC
1 CTAAACC
*
1437108 TTAAACC
1 CTAAACC
*
1437115 CTAAAAC
1 CTAAACC
* *
1437122 TTAAATC
1 CTAAACC
*
1437129 ATAAACC
1 CTAAACC
1437136 CT-AACC
1 CTAAACC
1437142 CTAAA
1 CTAAA
1437147 AACATTATTT
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
6 6 0.11
7 48 0.89
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.22
Consensus pattern (7 bp):
CTAAACC
Found at i:1437094 original size:21 final size:21
Alignment explanation
Indices: 1437073--1437146 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
1437063 AAATCCTACT
* * *
1437073 CTAAACCCTAAACCCTAAACT
1 CTAAACCCTAAATCATAAACC
*
1437094 CTAAACCCTAAATCTTAAACC
1 CTAAACCCTAAATCATAAACC
* *
1437115 CTAAAACTTAAATCATAAACC
1 CTAAACCCTAAATCATAAACC
1437136 CT-AACCCTAAA
1 CTAAACCCTAAA
1437147 AACATTATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 7 0.16
21 38 0.84
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.22
Consensus pattern (21 bp):
CTAAACCCTAAATCATAAACC
Found at i:1447048 original size:59 final size:60
Alignment explanation
Indices: 1446954--1447080 Score: 177
Period size: 59 Copynumber: 2.1 Consensus size: 60
1446944 TTTAGAATTC
* * *
1446954 CAATTTCATCCACAAATTATTACTTTTATTGTAAATTAGTCCCTA-AAATTTTAAATATTT
1 CAATTTCATCCACAAACTATGACTTTTATTCTAAATTAGTCCCTATAAATTTT-AATATTT
* * *
1447014 TAATTTCATCTACAAACTATGA-TTTTATTCTAAATTAGTCTCTATAAATTTTAATATTT
1 CAATTTCATCCACAAACTATGACTTTTATTCTAAATTAGTCCCTATAAATTTTAATATTT
1447073 CAATTTCA
1 CAATTTCA
1447081 CCTCAAATCA
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
59 34 0.58
60 25 0.42
ACGTcount: A:0.36, C:0.14, G:0.03, T:0.46
Consensus pattern (60 bp):
CAATTTCATCCACAAACTATGACTTTTATTCTAAATTAGTCCCTATAAATTTTAATATTT
Found at i:1448133 original size:22 final size:22
Alignment explanation
Indices: 1448105--1448166 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 22
1448095 GAGATAATTA
1448105 CAATAAAACTCATATTTTT-TT
1 CAATAAAACTCATATTTTTATT
*
1448126 CAATTAAA-TCCATATTTTTATT
1 CAATAAAACT-CATATTTTTATT
*
1448148 GAATAAAACT-AT-TTTTTAT
1 CAATAAAACTCATATTTTTAT
1448167 AAAAATATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
20 8 0.23
21 18 0.51
22 8 0.23
23 1 0.03
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (22 bp):
CAATAAAACTCATATTTTTATT
Found at i:1450501 original size:21 final size:20
Alignment explanation
Indices: 1450439--1450507 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 20
1450429 CGTTCGTCGG
1450439 TATTTTTTATTGTT-TTTTTTT
1 TATTTTTT-TT-TTCTTTTTTT
* * *
1450460 TATTTTTTTATATCATATTTT
1 TATTTTTTT-TTTCTTTTTTT
1450481 TATTTTTTTTTTCTTGTTTTT
1 TATTTTTTTTTTCTT-TTTTT
*
1450502 AATTTT
1 TATTTT
1450508 CAGTAAGTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
20 6 0.16
21 32 0.84
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.80
Consensus pattern (20 bp):
TATTTTTTTTTTCTTTTTTT
Found at i:1452688 original size:31 final size:28
Alignment explanation
Indices: 1452620--1452690 Score: 72
Period size: 31 Copynumber: 2.4 Consensus size: 28
1452610 TATATAAACC
* *
1452620 AAGACTTATTTGAATATGAGAAAAATTT
1 AAGACTTATTTAAATATGAGAAAAATTA
1452648 AAGAGCTTATTTAAATAAATTGAG-AAAATGTA
1 AAGA-CTTATTTAAAT--A-TGAGAAAAAT-TA
1452680 AAGACTTATTT
1 AAGACTTATTT
1452691 GATATATTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
28 4 0.11
29 10 0.28
31 13 0.36
32 9 0.25
ACGTcount: A:0.46, C:0.04, G:0.14, T:0.35
Consensus pattern (28 bp):
AAGACTTATTTAAATATGAGAAAAATTA
Found at i:1456307 original size:21 final size:21
Alignment explanation
Indices: 1456283--1456327 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1456273 AATTTACGTG
1456283 TTTAGTATTTAAA-TTATTAGT
1 TTTAGTATTTAAACTT-TTAGT
*
1456304 TTTAGTGTTTAAACTTTTAGT
1 TTTAGTATTTAAACTTTTAGT
1456325 TTT
1 TTT
1456328 TTCAAAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.27, C:0.02, G:0.11, T:0.60
Consensus pattern (21 bp):
TTTAGTATTTAAACTTTTAGT
Found at i:1460064 original size:3 final size:3
Alignment explanation
Indices: 1460056--1460093 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1460046 ACTTTATTTA
1460056 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1460094 ACTACATCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1461737 original size:101 final size:101
Alignment explanation
Indices: 1461560--1461752 Score: 341
Period size: 101 Copynumber: 1.9 Consensus size: 101
1461550 TGAAGTAAAG
1461560 TTTTCATTTATATTAACCAAACATGTTTTCTAATTTTCAAAAAATTGAAAATGAAAACTATTTTC
1 TTTTCATTTATATTAACCAAACATGTTTTCTAATTTTCAAAAAATTGAAAATGAAAACTATTTTC
1461625 TGAAAACAAAAACAGAAAATAAAAATAAATTCAATT
66 TGAAAACAAAAACAGAAAATAAAAATAAATTCAATT
* *
1461661 TTTTCATTTATATTAACCAAACATGTTTTCTAATTTTTAAAAAATTGAAAATGAAAACTATTTTT
1 TTTTCATTTATATTAACCAAACATGTTTTCTAATTTTCAAAAAATTGAAAATGAAAACTATTTTC
* * *
1461726 TGAAAATAAAAATAGAAAATGAAAATA
66 TGAAAACAAAAACAGAAAATAAAAATA
1461753 GAAAATATTT
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
101 87 1.00
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.36
Consensus pattern (101 bp):
TTTTCATTTATATTAACCAAACATGTTTTCTAATTTTCAAAAAATTGAAAATGAAAACTATTTTC
TGAAAACAAAAACAGAAAATAAAAATAAATTCAATT
Found at i:1461745 original size:13 final size:13
Alignment explanation
Indices: 1461727--1461759 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1461717 ACTATTTTTT
1461727 GAAAATAAAAATA
1 GAAAATAAAAATA
*
1461740 GAAAATGAAAATA
1 GAAAATAAAAATA
1461753 GAAAATA
1 GAAAATA
1461760 TTTTCTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (13 bp):
GAAAATAAAAATA
Found at i:1461756 original size:7 final size:7
Alignment explanation
Indices: 1461727--1461759 Score: 52
Period size: 6 Copynumber: 5.0 Consensus size: 7
1461717 ACTATTTTTT
1461727 GAAAATA
1 GAAAATA
1461734 -AAAATA
1 GAAAATA
1461740 GAAAAT-
1 GAAAATA
1461746 GAAAATA
1 GAAAATA
1461753 GAAAATA
1 GAAAATA
1461760 TTTTCTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 12 0.50
7 12 0.50
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (7 bp):
GAAAATA
Found at i:1465497 original size:21 final size:21
Alignment explanation
Indices: 1465464--1465520 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
1465454 GTTAATATCG
* * *
1465464 AAAATATTCATTTTAGGTGACA
1 AAAATAAT-ATTTTAGGTAAAA
* *
1465486 AAATTAATATTTTCGGTAAAA
1 AAAATAATATTTTAGGTAAAA
1465507 AAAATAATATTTTA
1 AAAATAATATTTTA
1465521 AATAACACTC
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 22 0.79
22 6 0.21
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.39
Consensus pattern (21 bp):
AAAATAATATTTTAGGTAAAA
Found at i:1466010 original size:13 final size:13
Alignment explanation
Indices: 1465988--1466029 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1465978 ACGTAGAAAT
*
1465988 TAAATGAATATAA
1 TAAATAAATATAA
1466001 TAAATAAATATAA
1 TAAATAAATATAA
*
1466014 TAATATTAAT-TAA
1 TAA-ATAAATATAA
1466027 TAA
1 TAA
1466030 TATTAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 21 0.81
14 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (13 bp):
TAAATAAATATAA
Found at i:1466049 original size:13 final size:13
Alignment explanation
Indices: 1465998--1466038 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1465988 TAAATGAATA
*
1465998 TAATAA-ATAAAT
1 TAATAATATTAAT
1466010 ATAATAATATTAAT
1 -TAATAATATTAAT
1466024 TAATAATATTAAT
1 TAATAATATTAAT
1466037 TA
1 TA
1466039 TTAAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 21 0.81
14 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TAATAATATTAAT
Found at i:1466469 original size:4 final size:4
Alignment explanation
Indices: 1466460--1466485 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1466450 ATATTTTTAC
1466460 TATT TATT TATT TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TA
1466486 GTCTATTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:1467961 original size:20 final size:22
Alignment explanation
Indices: 1467936--1467975 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1467926 TGTTGTATAT
1467936 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
1467956 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
1467976 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:1468111 original size:20 final size:20
Alignment explanation
Indices: 1468086--1468160 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 20
1468076 TTGCAGCCTT
*
1468086 GATGCATGGATGCATGGCAG
1 GATGCATCGATGCATGGCAG
**
1468106 GATGCATCGATGCATGGCCTT
1 GATGCATCGATGCATGG-CAG
* * ** *
1468127 AATACATCGATGCACAGAAG
1 GATGCATCGATGCATGGCAG
1468147 GATGCATCGATGCA
1 GATGCATCGATGCA
1468161 CTAATTGAAT
Statistics
Matches: 42, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 28 0.67
21 14 0.33
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.21
Consensus pattern (20 bp):
GATGCATCGATGCATGGCAG
Found at i:1468251 original size:21 final size:20
Alignment explanation
Indices: 1468183--1468280 Score: 99
Period size: 21 Copynumber: 4.7 Consensus size: 20
1468173 GGTGTTTGAG
* *
1468183 TGCATGGATGTACTGCATGA
1 TGCATGGATGCACTGCAGGA
*
1468203 TGCATCGATGCACTAGTGCAGG-
1 TGCATGGATGCAC---TGCAGGA
1468225 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCA-GGA
*
1468246 TGCATGGATGCACTGTAGGGA
1 TGCATGGATGCACTGCA-GGA
*
1468267 TGCATGTATGCACT
1 TGCATGGATGCACT
1468281 TTGACACCCT
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.06
20 13 0.19
21 33 0.49
22 12 0.18
23 5 0.07
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26
Consensus pattern (20 bp):
TGCATGGATGCACTGCAGGA
Found at i:1468271 original size:42 final size:41
Alignment explanation
Indices: 1468182--1468280 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 41
1468172 CGGTGTTTGA
* *
1468182 GTGCATGGATGTACTGCATGATGCATCGATGCACTAGTGCAG
1 GTGCATGGATGCACTGCAGGATGCATCGATGCACTAGTG-AG
*
1468224 GTGCATGGATGCACTGCAGGGATGCATGGATGCACT-GT-AGG
1 GTGCATGGATGCACTGCA-GGATGCATCGATGCACTAGTGA-G
*
1468265 GATGCATGTATGCACT
1 G-TGCATGGATGCACT
1468281 TTGACACCCT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
40 1 0.02
41 2 0.04
42 32 0.64
43 15 0.30
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.25
Consensus pattern (41 bp):
GTGCATGGATGCACTGCAGGATGCATCGATGCACTAGTGAG
Found at i:1468407 original size:30 final size:30
Alignment explanation
Indices: 1468360--1468419 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1468350 AAACTTTGAA
1468360 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
*
1468389 TAAATTTAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
1468420 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 11 0.39
31 7 0.25
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:1469650 original size:23 final size:23
Alignment explanation
Indices: 1469606--1469651 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1469596 TAAATCAAGA
* *
1469606 TTTTCTTTTTCAAAACTTTAAAT
1 TTTTATTTTTCAAAACTCTAAAT
* *
1469629 TTTTATTTTTGAAAGCTCTAAAT
1 TTTTATTTTTCAAAACTCTAAAT
1469652 CCTTTTTCAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.11, G:0.04, T:0.54
Consensus pattern (23 bp):
TTTTATTTTTCAAAACTCTAAAT
Found at i:1469698 original size:19 final size:20
Alignment explanation
Indices: 1469655--1469702 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1469645 TCTAAATCCT
*
1469655 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
1469675 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
1469694 TTTTCAAAA
1 TTTTCAAAA
1469703 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:1470871 original size:20 final size:22
Alignment explanation
Indices: 1470846--1470885 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1470836 TGTTGTATAT
1470846 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
1470866 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
1470886 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:1471050 original size:41 final size:41
Alignment explanation
Indices: 1470991--1471070 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
1470981 AGCCGTTGCA
*
1470991 GCCTTGATGCATGTATGCA-TGACAGGATGCATCAATGCATG
1 GCCTTGATGCATGTATGCACAGA-AGGATGCATCAATGCATG
*
1471032 GCCTTGATGCATCG-ATGCACAGAAGGATGCATCGATGCA
1 GCCTTGATGCAT-GTATGCACAGAAGGATGCATCAATGCA
1471071 CTAATTGCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 32 0.91
42 3 0.09
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (41 bp):
GCCTTGATGCATGTATGCACAGAAGGATGCATCAATGCATG
Found at i:1471162 original size:21 final size:21
Alignment explanation
Indices: 1471093--1471211 Score: 145
Period size: 21 Copynumber: 5.7 Consensus size: 21
1471083 GGTGTTTGAG
1471093 TGCATGGATGCACTGCAT-GA
1 TGCATGGATGCACTGCATGGA
*
1471113 TGCATCGATGCACTAGTGCA-GG-
1 TGCATGGATGCAC---TGCATGGA
* *
1471135 TGTATGGATACACTGCATGGA
1 TGCATGGATGCACTGCATGGA
*
1471156 TGCATGGATGCACTGCAAGGA
1 TGCATGGATGCACTGCATGGA
*
1471177 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCATGGA
1471198 TGCATGGATGCACT
1 TGCATGGATGCACT
1471212 TTGACACCCT
Statistics
Matches: 85, Mismatches: 8, Indels: 11
0.82 0.08 0.11
Matches are distributed among these distances:
19 4 0.05
20 14 0.16
21 52 0.61
22 10 0.12
23 5 0.06
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (21 bp):
TGCATGGATGCACTGCATGGA
Found at i:1471323 original size:29 final size:31
Alignment explanation
Indices: 1471291--1471350 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
1471281 AAACTTTGAA
*
1471291 TAAATTCAA-TTAAGACC-AAAAACATTTTG
1 TAAATTCAAGTCAAGACCAAAAAACATTTTG
*
1471320 TAAATTCAAGTCAAGTCCAAAAAACATTTTG
1 TAAATTCAAGTCAAGACCAAAAAACATTTTG
1471351 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 9 0.33
30 6 0.22
31 12 0.44
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.30
Consensus pattern (31 bp):
TAAATTCAAGTCAAGACCAAAAAACATTTTG
Found at i:1475052 original size:5 final size:5
Alignment explanation
Indices: 1475042--1475094 Score: 106
Period size: 5 Copynumber: 10.6 Consensus size: 5
1475032 TACTTTCTAC
1475042 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1475092 TAA
1 TAA
1475095 AAATTTTGGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 48 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:1476068 original size:16 final size:17
Alignment explanation
Indices: 1476032--1476068 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1476022 TTTACGTTCA
1476032 ATTTAAAAAATATATTT
1 ATTTAAAAAATATATTT
*
1476049 -TTTAAATAATAT-TTT
1 ATTTAAAAAATATATTT
1476064 ATTTA
1 ATTTA
1476069 TCAAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 3 0.17
16 15 0.83
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTAAAAAATATATTT
Found at i:1480203 original size:31 final size:28
Alignment explanation
Indices: 1480138--1480251 Score: 108
Period size: 29 Copynumber: 3.9 Consensus size: 28
1480128 AAAATAGATT
1480138 TATTAATATTTATAATAATATAAATATAA
1 TATT-ATATTTATAATAATATAAATATAA
*
1480167 TATTATATTTTTAATATTATATAAA-ATAA
1 TATTATATTTATAATA--ATATAAATATAA
*
1480196 TCAATTATA-TTATAATAATATAAGATATTA
1 T--ATTATATTTATAATAATATAA-ATATAA
*
1480226 TATTTTTATTT-TAATAATATATAATA
1 TA-TTATATTTATAATAATATA-AATA
1480252 ATTTTTTTTA
Statistics
Matches: 72, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
28 18 0.25
29 27 0.38
30 21 0.29
31 6 0.08
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (28 bp):
TATTATATTTATAATAATATAAATATAA
Found at i:1480247 original size:24 final size:23
Alignment explanation
Indices: 1480215--1480261 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
1480205 TTATAATAAT
* *
1480215 ATAAGATATTATATTTTTATTTTA
1 ATAAGATATAATAATTTT-TTTTA
*
1480239 ATAATATATAATAATTTTTTTTA
1 ATAAGATATAATAATTTTTTTTA
1480262 TTTAATAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
ATAAGATATAATAATTTTTTTTA
Found at i:1480260 original size:29 final size:28
Alignment explanation
Indices: 1480144--1480270 Score: 77
Period size: 29 Copynumber: 4.4 Consensus size: 28
1480134 GATTTATTAA
*
1480144 TATTTATAATAATATAA-ATATA-ATATTA
1 TATTT-TAATAATATAAGATATATAT-TTT
* * *
1480172 TATTTTTAATATTATATAAAATA-ATCAATTA
1 TA-TTTTAATA--ATATAAGATATAT-ATTTT
*
1480203 TATTATAATAATATAAGATATTATATTTT
1 TATTTTAATAATATAAGATA-TATATTTT
1480232 TATTTTAATAATATATA-ATA-AT-TTTT
1 TATTTTAATAATATA-AGATATATATTTT
*
1480258 TTTATTTAATAAT
1 TAT-TTTAATAAT
1480271 GAATAATTTT
Statistics
Matches: 82, Mismatches: 7, Indels: 21
0.75 0.06 0.19
Matches are distributed among these distances:
26 6 0.07
27 11 0.13
28 16 0.20
29 23 0.28
30 17 0.21
31 8 0.10
32 1 0.01
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (28 bp):
TATTTTAATAATATAAGATATATATTTT
Found at i:1480267 original size:24 final size:24
Alignment explanation
Indices: 1480240--1480286 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1480230 TTTATTTTAA
*
1480240 TAATATAT-AATAATTTTTTTTATT
1 TAATA-ATGAATAATTTTATTTATT
1480264 TAATAATGAATAATTTTATTTAT
1 TAATAATGAATAATTTTATTTAT
1480287 ATATTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TAATAATGAATAATTTTATTTATT
Found at i:1480403 original size:9 final size:9
Alignment explanation
Indices: 1480389--1480427 Score: 50
Period size: 7 Copynumber: 4.8 Consensus size: 9
1480379 TAAATAATAT
1480389 TATTTATTA
1 TATTTATTA
1480398 TATTTA-T-
1 TATTTATTA
1480405 TATTTATTA
1 TATTTATTA
1480414 TATTTA--A
1 TATTTATTA
1480421 TATTTAT
1 TATTTAT
1480428 AATAAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
7 13 0.48
8 2 0.07
9 12 0.44
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TATTTATTA
Found at i:1480407 original size:16 final size:16
Alignment explanation
Indices: 1480386--1480427 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
1480376 TGATAAATAA
1480386 TATTATTTATTATATT
1 TATTATTTATTATATT
1480402 TATTATTTATTATATT
1 TATTATTTATTATATT
*
1480418 TAATATTTAT
1 TATTATTTAT
1480428 AATAAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTATTTATTATATT
Found at i:1480565 original size:29 final size:30
Alignment explanation
Indices: 1480527--1480596 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
1480517 TCCAGAAATA
1480527 TAATTCATTTTCCAG-AATTCAAATTCCAG
1 TAATTCATTTTCCAGTAATTCAAATTCCAG
*
1480556 TAATTTATTTTCCAGTAATTCAAATTCCAG
1 TAATTCATTTTCCAGTAATTCAAATTCCAG
1480586 TAATTCATTTT
1 TAATTCATTTT
1480597 TTTGAAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 14 0.37
30 24 0.63
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (30 bp):
TAATTCATTTTCCAGTAATTCAAATTCCAG
Found at i:1480568 original size:15 final size:15
Alignment explanation
Indices: 1480527--1480596 Score: 88
Period size: 15 Copynumber: 4.7 Consensus size: 15
1480517 TCCAGAAATA
1480527 TAATTCATTTTCCAG
1 TAATTCATTTTCCAG
**
1480542 -AATTCAAATTCCAG
1 TAATTCATTTTCCAG
*
1480556 TAATTTATTTTCCAG
1 TAATTCATTTTCCAG
**
1480571 TAATTCAAATTCCAG
1 TAATTCATTTTCCAG
1480586 TAATTCATTTT
1 TAATTCATTTT
1480597 TTTGAAAAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
14 12 0.27
15 32 0.73
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (15 bp):
TAATTCATTTTCCAG
Found at i:1481095 original size:31 final size:29
Alignment explanation
Indices: 1481009--1481104 Score: 79
Period size: 31 Copynumber: 3.2 Consensus size: 29
1480999 TGAACGAGGC
*
1481009 ACTAAAATGAAATAAAAACTAAACTTTAAAT
1 ACTAAAAT-AAAT-AAAACTAAAGTTTAAAT
** * *
1481040 -CTAATTTTAA-AAAATTAAAAGTTTAAAT
1 ACTAAAATAAATAAAACT-AAAGTTTAAAT
*
1481068 ACTAAAATAAATTAAAACTAATAGTTTAGAT
1 ACTAAAATAAA-TAAAACTAA-AGTTTAAAT
1481099 ACTAAA
1 ACTAAA
1481105 TACATAATTT
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
27 5 0.10
28 10 0.20
29 9 0.18
30 7 0.14
31 19 0.38
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.31
Consensus pattern (29 bp):
ACTAAAATAAATAAAACTAAAGTTTAAAT
Found at i:1481410 original size:18 final size:18
Alignment explanation
Indices: 1481389--1481433 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1481379 TCAGTGGTCC
1481389 TTCGGGACATAGTGATCA
1 TTCGGGACATAGTGATCA
* * *
1481407 TTCGGGATATAGTGGTCC
1 TTCGGGACATAGTGATCA
1481425 TTCGGGACA
1 TTCGGGACA
1481434 AATATTCAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (18 bp):
TTCGGGACATAGTGATCA
Found at i:1484558 original size:19 final size:19
Alignment explanation
Indices: 1484534--1484595 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
1484524 ATTTTTCATT
*
1484534 AAAAAATTGAACTGAACCA
1 AAAAAATTGAACCGAACCA
**
1484553 AAAAAATTGAACCG--TTA
1 AAAAAATTGAACCGAACCA
*
1484570 AAAAAATCGAACCGAACCA
1 AAAAAATTGAACCGAACCA
1484589 AAAAAAT
1 AAAAAAT
1484596 CAATTTCACA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 14 0.40
19 21 0.60
ACGTcount: A:0.60, C:0.16, G:0.10, T:0.15
Consensus pattern (19 bp):
AAAAAATTGAACCGAACCA
Found at i:1485691 original size:17 final size:17
Alignment explanation
Indices: 1485669--1485702 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1485659 GAAAATGCCC
1485669 CAAAATTTGTAAATCTT
1 CAAAATTTGTAAATCTT
1485686 CAAAATTTGTAAATCTT
1 CAAAATTTGTAAATCTT
1485703 GATTCAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (17 bp):
CAAAATTTGTAAATCTT
Found at i:1494876 original size:21 final size:21
Alignment explanation
Indices: 1494850--1494890 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1494840 AAACAAGAGG
1494850 CTTTTT-TTCTTTCTTTTCTTC
1 CTTTTTCTT-TTTCTTTTCTTC
1494871 CTTTTTCTTTTTCTTTTCTT
1 CTTTTTCTTTTTCTTTTCTT
1494891 TTTTCTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (21 bp):
CTTTTTCTTTTTCTTTTCTTC
Found at i:1495998 original size:20 final size:21
Alignment explanation
Indices: 1495975--1496014 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1495965 TCGCTCTTTA
* *
1495975 TTTC-CTCCCTTTTCCTCTCG
1 TTTCTCTCACTTTCCCTCTCG
1495995 TTTCTCTCACTTTCCCTCTC
1 TTTCTCTCACTTTCCCTCTC
1496015 CCAACGACCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.03, C:0.45, G:0.03, T:0.50
Consensus pattern (21 bp):
TTTCTCTCACTTTCCCTCTCG
Found at i:1499467 original size:28 final size:28
Alignment explanation
Indices: 1499427--1499485 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
1499417 GTCCCTGAGT
1499427 CAAGCCACCTTTCCACTTCCAACACCAA
1 CAAGCCACCTTTCCACTTCCAACACCAA
1499455 CAAGCCACCTTTCCACTTCCAACACCAA
1 CAAGCCACCTTTCCACTTCCAACACCAA
1499483 CAA
1 CAA
1499486 CCCAAGTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.34, C:0.46, G:0.03, T:0.17
Consensus pattern (28 bp):
CAAGCCACCTTTCCACTTCCAACACCAA
Found at i:1500917 original size:169 final size:169
Alignment explanation
Indices: 1500638--1500977 Score: 662
Period size: 169 Copynumber: 2.0 Consensus size: 169
1500628 CCATAGTGAA
*
1500638 AATAATCTATATCCTTTTTCTCATAGAATGATCACTTTGGTTGCCAAACCTGAAGAGATCGATTC
1 AATAATCTATATCCTTTTTCTCATAGAATGATCACTTTGGTTGCCAAACCTGAAGAGATCGATCC
1500703 TCTATTCATAGGAGTCAATTCTTTGGTACTTAGAATTGATAAACTGGCTCAACAATCATAAGTAA
66 TCTATTCATAGGAGTCAATTCTTTGGTACTTAGAATTGATAAACTGGCTCAACAATCATAAGTAA
1500768 TCGATCATTATTTGAACAGAATAATTCCTTTGGCTTGAG
131 TCGATCATTATTTGAACAGAATAATTCCTTTGGCTTGAG
1500807 AATAATCTATATCCTTTTTCTCATAGAATGATCACTTTGGTTGCCAAACCTGAAGAGATCGATCC
1 AATAATCTATATCCTTTTTCTCATAGAATGATCACTTTGGTTGCCAAACCTGAAGAGATCGATCC
*
1500872 TCTATTCATAGGAGTCAATTCTTTGGTACTTAGATTTGATAAACTGGCTCAACAATCATAAGTAA
66 TCTATTCATAGGAGTCAATTCTTTGGTACTTAGAATTGATAAACTGGCTCAACAATCATAAGTAA
1500937 TCGATCATTATTTGAACAGAATAATTCCTTTGGCTTGAG
131 TCGATCATTATTTGAACAGAATAATTCCTTTGGCTTGAG
1500976 AA
1 AA
1500978 GCAGAAGAAT
Statistics
Matches: 169, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
169 169 1.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.35
Consensus pattern (169 bp):
AATAATCTATATCCTTTTTCTCATAGAATGATCACTTTGGTTGCCAAACCTGAAGAGATCGATCC
TCTATTCATAGGAGTCAATTCTTTGGTACTTAGAATTGATAAACTGGCTCAACAATCATAAGTAA
TCGATCATTATTTGAACAGAATAATTCCTTTGGCTTGAG
Found at i:1501260 original size:16 final size:16
Alignment explanation
Indices: 1501221--1501265 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1501211 AGAGTGGTAG
*
1501221 ATTAAATTCTTCAAGC
1 ATTAAATTCTTCAAAC
*
1501237 ATTCAATT-TTCAAAC
1 ATTAAATTCTTCAAAC
1501252 ATTTAAATTCTTCA
1 A-TTAAATTCTTCA
1501266 TCTCTTGCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 7 0.29
16 13 0.54
17 4 0.17
ACGTcount: A:0.38, C:0.18, G:0.02, T:0.42
Consensus pattern (16 bp):
ATTAAATTCTTCAAAC
Found at i:1508323 original size:34 final size:34
Alignment explanation
Indices: 1508259--1508324 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
1508249 ATATTGAACC
*
1508259 CTAAATCATAAACTTAAACCATATAGCTTAAATA
1 CTAAATCATAAACTTAAACCATATACCTTAAATA
*
1508293 CTAAATCATAAATCTTAAACCCTA-ACCTTAAA
1 CTAAATCATAAA-CTTAAACCATATACCTTAAA
1508325 AAGAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 19 0.66
35 10 0.34
ACGTcount: A:0.48, C:0.21, G:0.02, T:0.29
Consensus pattern (34 bp):
CTAAATCATAAACTTAAACCATATACCTTAAATA
Found at i:1510051 original size:30 final size:30
Alignment explanation
Indices: 1509987--1510273 Score: 297
Period size: 30 Copynumber: 9.6 Consensus size: 30
1509977 GATATAATAT
* * **
1509987 CATGCAGATGTCAAAAC-GGGAATTTATCC
1 CATGCAAATGTCAGAACGGGGAATAAATCC
* * *
1510016 CATGCAAATGTCAGATCGGAGAATAAATCT
1 CATGCAAATGTCAGAACGGGGAATAAATCC
* * ** *
1510046 CATGCAAATATCAGAACAGGGAATTTATCT
1 CATGCAAATGTCAGAACGGGGAATAAATCC
* * * **
1510076 CATGCAGATGTTAGAATGGGGAATTTATCC
1 CATGCAAATGTCAGAACGGGGAATAAATCC
* *
1510106 CATGCAAATGTCAGAATGGGGAATAAATCT
1 CATGCAAATGTCAGAACGGGGAATAAATCC
* **
1510136 CATGCAAATGTCAGAACGAGGAATTTATCC
1 CATGCAAATGTCAGAACGGGGAATAAATCC
* *
1510166 CATGCATATGTCAGAATGGGGAATAAATCC
1 CATGCAAATGTCAGAACGGGGAATAAATCC
* * *
1510196 CATGTAGATGTCAGAACGGGAAATAAATCC
1 CATGCAAATGTCAGAACGGGGAATAAATCC
* *
1510226 CATGCAGATGTCAGAACGGGGAATAAATCA
1 CATGCAAATGTCAGAACGGGGAATAAATCC
*
1510256 CATGCAAATATCAGAACG
1 CATGCAAATGTCAGAACG
1510274 AGGATTATGC
Statistics
Matches: 214, Mismatches: 43, Indels: 1
0.83 0.17 0.00
Matches are distributed among these distances:
29 14 0.07
30 200 0.93
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (30 bp):
CATGCAAATGTCAGAACGGGGAATAAATCC
Found at i:1510138 original size:90 final size:89
Alignment explanation
Indices: 1509986--1510245 Score: 344
Period size: 90 Copynumber: 2.9 Consensus size: 89
1509976 AGATATAATA
** *
1509986 TCATGCAGATGTCA-AAACGGGAATTTATCCCATGCAAATGTCAG-ATCGGAGAATAAATCTCAT
1 TCATGCAGATGTCAGAATGGGGAATTTATCCCATGCAAATGTCAGAAT-GGGGAATAAATCTCAT
*
1510049 GCAAATATCAGAACAGGGAATTTATC
65 GCAAATGTCAGAAC-GGGAATTTATC
*
1510075 TCATGCAGATGTTAGAATGGGGAATTTATCCCATGCAAATGTCAGAATGGGGAATAAATCTCATG
1 TCATGCAGATGTCAGAATGGGGAATTTATCCCATGCAAATGTCAGAATGGGGAATAAATCTCATG
1510140 CAAATGTCAGAACGAGGAATTTATC
66 CAAATGTCAGAACG-GGAATTTATC
* * ** * * * * *
1510165 CCATGCATATGTCAGAATGGGGAATAAATCCCATGTAGATGTCAGAACGGGAAATAAATCCCATG
1 TCATGCAGATGTCAGAATGGGGAATTTATCCCATGCAAATGTCAGAATGGGGAATAAATCTCATG
*
1510230 CAGATGTCAGAACGGG
66 CAAATGTCAGAACGGG
1510246 GAATAAATCA
Statistics
Matches: 152, Mismatches: 16, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
89 16 0.11
90 134 0.88
91 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.24
Consensus pattern (89 bp):
TCATGCAGATGTCAGAATGGGGAATTTATCCCATGCAAATGTCAGAATGGGGAATAAATCTCATG
CAAATGTCAGAACGGGAATTTATC
Found at i:1510372 original size:2 final size:2
Alignment explanation
Indices: 1510365--1510389 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1510355 CATAAGTCAA
1510365 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
1510390 ATTAGATCAC
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:1510630 original size:17 final size:17
Alignment explanation
Indices: 1510604--1510645 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
1510594 TTTAAAAAAA
*
1510604 ATTTAAAATATTATTAT
1 ATTTATAATATTATTAT
1510621 ATTTATAATATTATTAT
1 ATTTATAATATTATTAT
1510638 ATTTATAA
1 ATTTATAA
1510646 AAAACCTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTATAATATTATTAT
Found at i:1510961 original size:18 final size:19
Alignment explanation
Indices: 1510935--1510972 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1510925 TTTTCAAAGT
*
1510935 TTTGGG-TTTATTTCAAAA
1 TTTGGGTTTTATTTAAAAA
*
1510953 TTTGTGTTTTATTTAAAAA
1 TTTGGGTTTTATTTAAAAA
1510972 T
1 T
1510973 ATATATATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.29, C:0.03, G:0.13, T:0.55
Consensus pattern (19 bp):
TTTGGGTTTTATTTAAAAA
Found at i:1527428 original size:18 final size:18
Alignment explanation
Indices: 1527405--1527466 Score: 124
Period size: 18 Copynumber: 3.4 Consensus size: 18
1527395 ACATTGCCAA
1527405 TAATCTTATTCCCGCCGG
1 TAATCTTATTCCCGCCGG
1527423 TAATCTTATTCCCGCCGG
1 TAATCTTATTCCCGCCGG
1527441 TAATCTTATTCCCGCCGG
1 TAATCTTATTCCCGCCGG
1527459 TAATCTTA
1 TAATCTTA
1527467 CATTTCTTGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.19, C:0.31, G:0.15, T:0.35
Consensus pattern (18 bp):
TAATCTTATTCCCGCCGG
Found at i:1533604 original size:3 final size:3
Alignment explanation
Indices: 1533596--1533626 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1533586 TTTTTCTACC
1533596 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1533627 CTTTTAATTT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1534476 original size:3 final size:3
Alignment explanation
Indices: 1534470--1534517 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
1534460 ATGATGTGGC
1534470 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1534518 TAAAAATAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1535483 original size:21 final size:22
Alignment explanation
Indices: 1535446--1535491 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
1535436 AATTGTTAGT
*
1535446 ATTTAATTTATTCATTGA-TTA
1 ATTTAATTTAATCATTGAGTTA
1535467 ATTTAATTTAAAT-ATTGAGTTA
1 ATTTAATTT-AATCATTGAGTTA
1535489 ATT
1 ATT
1535492 GTATCATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (22 bp):
ATTTAATTTAATCATTGAGTTA
Found at i:1535589 original size:59 final size:60
Alignment explanation
Indices: 1535507--1535664 Score: 169
Period size: 60 Copynumber: 2.6 Consensus size: 60
1535497 ATATTTCCTC
* * *
1535507 AAACTTTGACCCTCA-TCTCAAATTAGACCTTAAA-TTTTAAACATTCTAATTTCATCCCA
1 AAACTATGACTCTCATTCT-AAATTAGACCTTAAACTTTTAAACATTCCAATTTCATCCCA
* * * * *
1535566 AAATTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCATCCCC
1 AAACTATGACTCTCATTCTAAATTAGACCTTAAACTTTTAAACATTCCAATTTCATCCCA
* * * *
1535626 AAACTGTGAATATCATTCTAAATTAG-TCTCTAAACTTTT
1 AAACTATGACTCTCATTCTAAATTAGACCT-TAAACTTTT
1535665 GCATCTTCAC
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
59 28 0.34
60 55 0.66
ACGTcount: A:0.34, C:0.22, G:0.05, T:0.39
Consensus pattern (60 bp):
AAACTATGACTCTCATTCTAAATTAGACCTTAAACTTTTAAACATTCCAATTTCATCCCA
Found at i:1535642 original size:60 final size:60
Alignment explanation
Indices: 1535526--1535665 Score: 176
Period size: 60 Copynumber: 2.4 Consensus size: 60
1535516 CCCTCATCTC
* * * * * *
1535526 AAATTAGACCTTAAA-TTTTAAACATTCTAATTTCATCCCAAAATTATGACTCTCATTCT
1 AAATTAGTCCTTAAACTTTTGAACATTCCAATTTCATCCCAAAACTATGAATATCATTCT
* * *
1535585 AAATTAGTCCTTAAACTTTTGAATATTCCAATTTCATCCCCAAACTGTGAATATCATTCT
1 AAATTAGTCCTTAAACTTTTGAACATTCCAATTTCATCCCAAAACTATGAATATCATTCT
1535645 AAATTAGT-CTCTAAACTTTTG
1 AAATTAGTCCT-TAAACTTTTG
1535666 CATCTTCACT
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
59 16 0.23
60 54 0.77
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.39
Consensus pattern (60 bp):
AAATTAGTCCTTAAACTTTTGAACATTCCAATTTCATCCCAAAACTATGAATATCATTCT
Found at i:1536550 original size:23 final size:23
Alignment explanation
Indices: 1536520--1536589 Score: 85
Period size: 23 Copynumber: 3.1 Consensus size: 23
1536510 GTGGGCTAAT
1536520 TTAATTTGTCATACACTGTGACA
1 TTAATTTGTCATACACTGTGACA
1536543 TTAATTTGTCACGTGA-AC-GT-A-A
1 TTAATTTGTCA--T-ACACTGTGACA
1536565 TTAATTTGTCATACACTGTGACA
1 TTAATTTGTCATACACTGTGACA
1536588 TT
1 TT
1536590 TGTCGGAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
19 1 0.03
20 3 0.08
21 2 0.05
22 13 0.32
23 15 0.38
24 2 0.05
25 3 0.08
26 1 0.03
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (23 bp):
TTAATTTGTCATACACTGTGACA
Found at i:1546138 original size:29 final size:29
Alignment explanation
Indices: 1546096--1546155 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
1546086 ACAGTATTGG
1546096 TTGTAGGTCGCCATGCACTCCGGGCGACC
1 TTGTAGGTCGCCATGCACTCCGGGCGACC
*
1546125 TTGTAGGTCGCCATGCACTCCTGGCGACC
1 TTGTAGGTCGCCATGCACTCCGGGCGACC
1546154 TT
1 TT
1546156 CGCCATGCAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.13, C:0.33, G:0.28, T:0.25
Consensus pattern (29 bp):
TTGTAGGTCGCCATGCACTCCGGGCGACC
Found at i:1546162 original size:23 final size:23
Alignment explanation
Indices: 1546132--1546177 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
1546122 ACCTTGTAGG
1546132 TCGCCATGCACTCCT-GGCGACCT
1 TCGCCATGCACT-CTGGGCGACCT
1546155 TCGCCATGCACTCTGGGCGACCT
1 TCGCCATGCACTCTGGGCGACCT
1546178 ACCCTTGCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.13, C:0.41, G:0.24, T:0.22
Consensus pattern (23 bp):
TCGCCATGCACTCTGGGCGACCT
Found at i:1546269 original size:29 final size:29
Alignment explanation
Indices: 1546236--1546291 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1546226 TCCCAACACA
* *
1546236 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGAGACCTTG
1546265 TAGGTCGCCATGCACTCCGGGAGACCT
1 TAGGTCGCCATGCACTCCGGGAGACCT
1546292 ACTCTCGCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.14, C:0.36, G:0.30, T:0.20
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGAGACCTTG
Found at i:1546344 original size:23 final size:23
Alignment explanation
Indices: 1546317--1546368 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
1546307 CCCTCAGATT
1546317 CCCTCGCATAGCTCGCTCGGATG
1 CCCTCGCATAGCTCGCTCGGATG
*
1546340 CCCTCGCATAGCTCGTTCGGATG
1 CCCTCGCATAGCTCGCTCGGATG
*
1546363 GCCTCG
1 CCCTCG
1546369 GTCGGATGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.12, C:0.38, G:0.27, T:0.23
Consensus pattern (23 bp):
CCCTCGCATAGCTCGCTCGGATG
Found at i:1546373 original size:14 final size:14
Alignment explanation
Indices: 1546351--1546381 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1546341 CCTCGCATAG
*
1546351 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
1546365 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
1546379 CTC
1 CTC
1546382 ATATGCACAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.06, C:0.32, G:0.35, T:0.26
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:1551690 original size:2 final size:2
Alignment explanation
Indices: 1551683--1551738 Score: 68
Period size: 2 Copynumber: 30.5 Consensus size: 2
1551673 ATCTCAAACT
*
1551683 TA TA TA TA TA TA TA TA TA -A TA T- TA TA TA -A TA TC T- TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1551720 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
1551739 GAAAGACGTG
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
1 5 0.10
2 43 0.90
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1553457 original size:2 final size:2
Alignment explanation
Indices: 1553368--1553440 Score: 75
Period size: 2 Copynumber: 39.0 Consensus size: 2
1553358 TAAAATAATT
* *
1553368 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA AA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1553409 -A TA -A CA -A T- TA TA TA TA CA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1553441 ATTGGACCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
1 5 0.08
2 57 0.92
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1562672 original size:2 final size:2
Alignment explanation
Indices: 1562661--1562707 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1562651 ACTTAAACAG
1562661 TA TA TA -A TA TA 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 TA TA TA TA TA TA
1562702 TA TA TA
1 TA TA TA
1562708 ACACATTGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1563169 original size:22 final size:22
Alignment explanation
Indices: 1563144--1563197 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
1563134 ACCCTAAATT
* *
1563144 ATAAATCCTAAATCATAATCCC
1 ATAAACCCTAAATCATAAACCC
1563166 AT-AACCTCTAAATCATAAACCC
1 ATAAACC-CTAAATCATAAACCC
1563188 -TAAACCCTAA
1 ATAAACCCTAA
1563198 TTTATAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 8 0.29
22 20 0.71
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (22 bp):
ATAAACCCTAAATCATAAACCC
Found at i:1570918 original size:20 final size:20
Alignment explanation
Indices: 1570882--1570919 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1570872 ATCCGATTCT
**
1570882 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1570902 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1570920 GTGAATCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1571732 original size:20 final size:20
Alignment explanation
Indices: 1571707--1571744 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1571697 ATGGACCATC
*
1571707 CATATCATGTCATGTTATGT
1 CATATCATATCATGTTATGT
1571727 CATATCATATCATGTTAT
1 CATATCATATCATGTTAT
1571745 CATCTTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.45
Consensus pattern (20 bp):
CATATCATATCATGTTATGT
Found at i:1572876 original size:16 final size:16
Alignment explanation
Indices: 1572793--1572879 Score: 111
Period size: 16 Copynumber: 5.4 Consensus size: 16
1572783 GGTATTACCC
1572793 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
1572809 GACATGTTTTCAACCT
1 GACCTGTTTTCAACCT
* * * *
1572825 GACTTATTTTTAACTT
1 GACCTGTTTTCAACCT
*
1572841 GACATGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
1572857 GACCTGTTTTTAACCT
1 GACCTGTTTTCAACCT
1572873 GACCTGT
1 GACCTGT
1572880 AAATGATCCA
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 60 1.00
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.41
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:1573170 original size:14 final size:14
Alignment explanation
Indices: 1573148--1573194 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
1573138 TGTAAAGGAA
*
1573148 AATTAATATAGTTT
1 AATTTATATAGTTT
1573162 AATTTATATA----
1 AATTTATATAGTTT
1573172 AA-TTATATAGTTT
1 AATTTATATAGTTT
1573185 AATTTATATA
1 AATTTATATA
1573195 AAGACAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:1573181 original size:23 final size:24
Alignment explanation
Indices: 1573147--1573196 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
1573137 ATGTAAAGGA
1573147 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
1573171 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
1573194 AAA
1 AAA
1573197 GACAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:1573376 original size:14 final size:14
Alignment explanation
Indices: 1573359--1573429 Score: 63
Period size: 14 Copynumber: 5.1 Consensus size: 14
1573349 TCCATTTAAA
1573359 TTAGGGTTTATGGT
1 TTAGGGTTTATGGT
*
1573373 TTAGTGTTTATGGT
1 TTAGGGTTTATGGT
** **
1573387 TTAAAGTTTA-GAA
1 TTAGGGTTTATGGT
*
1573400 TTAGGGTTTATGAT
1 TTAGGGTTTATGGT
* *
1573414 TTAGGATTTAGGGT
1 TTAGGGTTTATGGT
1573428 TT
1 TT
1573430 CTATAAACTA
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
13 9 0.20
14 36 0.80
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (14 bp):
TTAGGGTTTATGGT
Found at i:1573429 original size:41 final size:40
Alignment explanation
Indices: 1573353--1573429 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 40
1573343 TGTTAGTCCA
* *
1573353 TTTAAATTAGGGTTTATGGTTTAGTGTTTATGGTTTAAAG
1 TTTAAATTAGGGTTTATGATTTAGTGTTTAGGGTTTAAAG
1573393 TTTAGAATTAGGGTTTATGATTTAG-GATTTAGGGTTT
1 TTTA-AATTAGGGTTTATGATTTAGTG-TTTAGGGTTT
1573430 CTATAAACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
40 5 0.15
41 28 0.85
ACGTcount: A:0.25, C:0.00, G:0.26, T:0.49
Consensus pattern (40 bp):
TTTAAATTAGGGTTTATGATTTAGTGTTTAGGGTTTAAAG
Found at i:1574441 original size:63 final size:64
Alignment explanation
Indices: 1574304--1574442 Score: 192
Period size: 64 Copynumber: 2.2 Consensus size: 64
1574294 GAACTGAAAA
*
1574304 TGACCCGACCTGAACCCGATCTGGATCTGGTGTCAAATCAACCTGAAAATAACCCGAACTGATT
1 TGACCCGACCTGAACCCGATCTGGATCTGGTGTCAAATCAACCTGAAAATAACCCGAACCGATT
* * * * *
1574368 TGACCTGACCTGAACCCGATCTGGATCTGGTG-CAAATCAACCT-AAATTGACCTGTATCCGATT
1 TGACCCGACCTGAACCCGATCTGGATCTGGTGTCAAATCAACCTGAAAATAACCCG-AACCGATT
*
1574431 TTACCCGACCTG
1 TGACCCGACCTG
1574443 CCAAGATCCG
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
62 8 0.12
63 27 0.41
64 31 0.47
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (64 bp):
TGACCCGACCTGAACCCGATCTGGATCTGGTGTCAAATCAACCTGAAAATAACCCGAACCGATT
Found at i:1576601 original size:22 final size:23
Alignment explanation
Indices: 1576563--1576607 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
1576553 ATTCTGTTTG
*
1576563 GGGTGTTATTTGTGTAAA-ATTT
1 GGGTGTTATTTGAGTAAATATTT
1576585 GGGTGTTAGTTT-AGTAAATATTT
1 GGGTGTTA-TTTGAGTAAATATTT
1576608 ACAGAATGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (23 bp):
GGGTGTTATTTGAGTAAATATTT
Found at i:1579134 original size:24 final size:23
Alignment explanation
Indices: 1579107--1579162 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
1579097 AAATATTTTA
1579107 TCTGATTTTCGACTTGAATTATGT
1 TCTGATTTT-GACTTGAATTATGT
** *
1579131 TCTGATACATGACTTGAATTCTGT
1 TCTGAT-TTTGACTTGAATTATGT
1579155 TCTGATTT
1 TCTGATTT
1579163 CTGATCTGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.48
Consensus pattern (23 bp):
TCTGATTTTGACTTGAATTATGT
Found at i:1580306 original size:2 final size:2
Alignment explanation
Indices: 1580301--1580328 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1580291 TTATTTTTAA
1580301 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
1580329 GGTTTAAATA
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:1584520 original size:115 final size:114
Alignment explanation
Indices: 1584293--1584580 Score: 294
Period size: 115 Copynumber: 2.5 Consensus size: 114
1584283 TCAGCTCATT
* * * *
1584293 CTTAAATGATCAATTTTAGTTCGTTTTAATACTTAAATTTTGATTTTTTTTTAAAATCATATGCA
1 CTTAAATTATCAATTTTGGTTCATTTTAATACTTAAATTTT-A-TTTTTTTT-AAATTATATGCA
* * *
1584358 ACCTTTAGTATTTGTTTCATATACTACTATAATTCTTTTATCACGTTTTATA
63 ACCTTTAGTATTTGATTCATATAATACTATAATTCTTTTATCACGTTTAATA
* * * *
1584410 TTTCAATTATCAGTTTTGG-TCATTTTAATACTTAAACTTTTATTTTTTTTAAATTATACT-TAA
1 CTTAAATTATCAATTTTGGTTCATTTTAATACTTAAA-TTTTATTTTTTTTAAATTATA-TGCAA
* * * * *
1584473 CTTTTAGTTTTTGATTCATTTTAATACTCTAATGT-TTTTATCGCGTTTAATA
64 CCTTTAGTATTTGATTCA-TATAATACTATAAT-TCTTTTATCACGTTTAATA
* * * * *
1584525 CTTAAATTATCAATTTTGGTTCTTTTTAGTATTTAAATTTTTAATTTTTTAAAATT
1 CTTAAATTATCAATTTTGGTTCATTTTAATACTTAAA-TTTTATTTTTTTTAAATT
1584581 TAACCTTAAG
Statistics
Matches: 141, Mismatches: 25, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
114 24 0.17
115 51 0.36
116 48 0.34
117 18 0.13
ACGTcount: A:0.29, C:0.10, G:0.07, T:0.55
Consensus pattern (114 bp):
CTTAAATTATCAATTTTGGTTCATTTTAATACTTAAATTTTATTTTTTTTAAATTATATGCAACC
TTTAGTATTTGATTCATATAATACTATAATTCTTTTATCACGTTTAATA
Found at i:1586359 original size:13 final size:13
Alignment explanation
Indices: 1586341--1586367 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1586331 CATAGTTAAA
1586341 CAGTCTTCATATG
1 CAGTCTTCATATG
1586354 CAGTCTTCATATG
1 CAGTCTTCATATG
1586367 C
1 C
1586368 GATTCTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:1609897 original size:18 final size:18
Alignment explanation
Indices: 1609872--1609967 Score: 120
Period size: 18 Copynumber: 5.3 Consensus size: 18
1609862 AGCAGAAGAC
1609872 ACCTAAAGGATCAGCCAA
1 ACCTAAAGGATCAGCCAA
* *
1609890 ATCTAAAGGATCAACCAA
1 ACCTAAAGGATCAGCCAA
* *
1609908 ACCTGAAGGATCAGACAA
1 ACCTAAAGGATCAGCCAA
* * *
1609926 ATCTAAAGGATCAACAAA
1 ACCTAAAGGATCAGCCAA
*
1609944 ACCTGAAGGATCAGCCAA
1 ACCTAAAGGATCAGCCAA
1609962 ACCTAA
1 ACCTAA
1609968 GCGACAAACT
Statistics
Matches: 62, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 62 1.00
ACGTcount: A:0.47, C:0.24, G:0.16, T:0.14
Consensus pattern (18 bp):
ACCTAAAGGATCAGCCAA
Found at i:1609927 original size:36 final size:36
Alignment explanation
Indices: 1609872--1609967 Score: 156
Period size: 36 Copynumber: 2.7 Consensus size: 36
1609862 AGCAGAAGAC
* *
1609872 ACCTAAAGGATCAGCCAAATCTAAAGGATCAACCAA
1 ACCTGAAGGATCAGCCAAATCTAAAGGATCAACAAA
*
1609908 ACCTGAAGGATCAGACAAATCTAAAGGATCAACAAA
1 ACCTGAAGGATCAGCCAAATCTAAAGGATCAACAAA
*
1609944 ACCTGAAGGATCAGCCAAACCTAA
1 ACCTGAAGGATCAGCCAAATCTAA
1609968 GCGACAAACT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.47, C:0.24, G:0.16, T:0.14
Consensus pattern (36 bp):
ACCTGAAGGATCAGCCAAATCTAAAGGATCAACAAA
Found at i:1615860 original size:14 final size:14
Alignment explanation
Indices: 1615841--1615869 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1615831 AGAAAAAATG
1615841 TCACAATTGTCTTT
1 TCACAATTGTCTTT
1615855 TCACAATTGTCTTT
1 TCACAATTGTCTTT
1615869 T
1 T
1615870 TGGATCAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.52
Consensus pattern (14 bp):
TCACAATTGTCTTT
Found at i:1618469 original size:31 final size:31
Alignment explanation
Indices: 1618405--1618471 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
1618395 TTTAGTATTT
*
1618405 AAATTATTATTTTTGTTTCGTTTTGATGCCC
1 AAATTATTATTTTTGTTTCGTTTGGATGCCC
* * *
1618436 AAATTA-TACTTTTTGTTTTGTTTGGGTGTCC
1 AAATTATTA-TTTTTGTTTCGTTTGGATGCCC
1618467 AAATT
1 AAATT
1618472 CCGTACTTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.21, C:0.10, G:0.15, T:0.54
Consensus pattern (31 bp):
AAATTATTATTTTTGTTTCGTTTGGATGCCC
Found at i:1621083 original size:21 final size:21
Alignment explanation
Indices: 1621022--1621089 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
1621012 TCAATAGTAG
* *
1621022 TAATATGGCGGTCCACGATGT
1 TAATGTGGCGGTCCACGGTGT
*
1621043 TGATGTGGCGGTCCACGGTGT
1 TAATGTGGCGGTCCACGGTGT
* *
1621064 TAATGTGGCCGTCCATGGTGAT
1 TAATGTGGCGGTCCACGGTG-T
1621086 TAAT
1 TAAT
1621090 AATTTAACCG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
21 35 0.88
22 5 0.12
ACGTcount: A:0.19, C:0.18, G:0.32, T:0.31
Consensus pattern (21 bp):
TAATGTGGCGGTCCACGGTGT
Found at i:1623469 original size:92 final size:91
Alignment explanation
Indices: 1623314--1623489 Score: 253
Period size: 92 Copynumber: 1.9 Consensus size: 91
1623304 TCGTCTCTTG
* * *
1623314 TCATTTAAAAATATACATCAAGAGATATAAATTTGATACGACCCACCTCATGTCCATCTCTACCC
1 TCATTTAAAAATATACATCAAGAGATATAAATCTAATACGACCCACCTCATGTCCATCCCTACCC
1623379 TACCCATAGACCAGTATTGTTTTCATT
66 TA-CCATAGACCAGTATTGTTTTCATT
* * * *
1623406 TCATTTAAAAATATACATCAAGAGATATAAATCTAATCCGATCCGCCTCGTGTCCATCCCTACCC
1 TCATTTAAAAATATACATCAAGAGATATAAATCTAATACGACCCACCTCATGTCCATCCCTACCC
* * *
1623471 TATCATGGACCAGTTTTGT
66 TACCATAGACCAGTATTGT
1623490 CAACTTAAGG
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
91 14 0.19
92 60 0.81
ACGTcount: A:0.32, C:0.26, G:0.10, T:0.32
Consensus pattern (91 bp):
TCATTTAAAAATATACATCAAGAGATATAAATCTAATACGACCCACCTCATGTCCATCCCTACCC
TACCATAGACCAGTATTGTTTTCATT
Found at i:1628629 original size:23 final size:23
Alignment explanation
Indices: 1628599--1628646 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
1628589 AATATATAAT
*
1628599 ATTAATCATTCTATCAGTTGAAA
1 ATTAATCATTCTACCAGTTGAAA
*
1628622 ATTAATCATTTTACCAGTTGAAA
1 ATTAATCATTCTACCAGTTGAAA
1628645 AT
1 AT
1628647 ATACAGCTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (23 bp):
ATTAATCATTCTACCAGTTGAAA
Found at i:1629148 original size:22 final size:24
Alignment explanation
Indices: 1629122--1629166 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
1629112 TAAACTTTAA
1629122 ATTAAAATTTAA-AAAA-ACTAAC
1 ATTAAAATTTAATAAAATACTAAC
*
1629144 ATTAAATTTTAATAAAATACTAA
1 ATTAAAATTTAATAAAATACTAA
1629167 AATGAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
23 4 0.20
24 5 0.25
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (24 bp):
ATTAAAATTTAATAAAATACTAAC
Found at i:1629184 original size:35 final size:34
Alignment explanation
Indices: 1629109--1629215 Score: 94
Period size: 34 Copynumber: 3.1 Consensus size: 34
1629099 TCGTTTTAGT
* * *
1629109 AATTAAACTTTAAATTAAAAT-TTAAAAAAACT-AA
1 AATTAAA-TTTTAAGTAAAATACTAAAAAAA-TAAA
*
1629143 CATTAAATTTTAA-TAAAATACTAAAATGAAATAAA
1 AATTAAATTTTAAGTAAAATACTAAAA--AAATAAA
* **
1629178 AATTAAATTTTAAGTATAATTTTAAAAAAATAAA
1 AATTAAATTTTAAGTAAAATACTAAAAAAATAAA
1629212 AATT
1 AATT
1629216 TGAATATTAA
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
32 6 0.10
33 10 0.16
34 18 0.30
35 17 0.28
36 10 0.16
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (34 bp):
AATTAAATTTTAAGTAAAATACTAAAAAAATAAA
Found at i:1631298 original size:144 final size:150
Alignment explanation
Indices: 1631106--1631527 Score: 493
Period size: 144 Copynumber: 2.8 Consensus size: 150
1631096 TTGTCGGCAT
* *
1631106 CGTTGTTGGCAATCCTCGAACCTCCTCTGGGGATCTTCGGGGCTCGATTCATGGCGGCCGCGGCC
1 CGTTGTTGGCATTCCTTGAACCTCCTCTGGGGATCTTCGGGGCTCGATTCATGGCGGCCGCGGCC
* ** * *
1631171 TCTCCCTTCTTGTTGTTCTCTCTGATCCCCGAATTCTCTCTGGCATTGTTGTTGGCATTGA-GA-
66 TCTCCCTTCTTGTTGCTCTCTCTGATCCCCGAATTCTCTCCAGCACTGTTGTTCGCATT-ATGAC
*
1631234 T-TG-TTGTCTTTGT-CC-T-
130 TCTGTTTGTCCTTGTACCGTA
* * * *
1631250 TGTTGTTGGCATTCCTTGAACCTCCTCTGAGGATCTTCGGGGCACGATTCATGGCGGACGCGGCC
1 CGTTGTTGGCATTCCTTGAACCTCCTCTGGGGATCTTCGGGGCTCGATTCATGGCGGCCGCGGCC
* *
1631315 TCTCCCTTCTTGTTGCTCTCTCTGATCCTCGAATTCTCTCCAGCACTGTTGTTCGTATTATGACT
66 TCTCCCTTCTTGTTGCTCTCTCTGATCCCCGAATTCTCTCCAGCACTGTTGTTCGCATTATGACT
1631380 GCTGTTTTTGTCCTTGTACCGTA
131 -CTG--TTTGTCCTTGTACCGTA
* * **
1631403 CCGTTGTTGGCATTCCTTGAACCTCCTCTGGGGATC-TCGGGGGCTCGATTCATGGTGGCTGCAA
1 -CGTTGTTGGCATTCCTTGAACCTCCTCTGGGGATCTTC-GGGGCTCGATTCATGGCGGCCGCGG
* * * ** * *
1631467 CCTCTCCCTTCTTCTTGCTCCCTTTGATCTTCGAGTTCTCTCC-GACACTCTTGTTCGCATT
64 CCTCTCCCTTCTTGTTGCTCTCTCTGATCCCCGAATTCTCTCCAG-CACTGTTGTTCGCATT
1631528 GCAAGTGTAG
Statistics
Matches: 236, Mismatches: 29, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
143 1 0.00
144 113 0.48
145 1 0.00
147 2 0.01
150 9 0.04
151 2 0.01
152 1 0.00
153 3 0.01
154 104 0.44
ACGTcount: A:0.11, C:0.29, G:0.23, T:0.37
Consensus pattern (150 bp):
CGTTGTTGGCATTCCTTGAACCTCCTCTGGGGATCTTCGGGGCTCGATTCATGGCGGCCGCGGCC
TCTCCCTTCTTGTTGCTCTCTCTGATCCCCGAATTCTCTCCAGCACTGTTGTTCGCATTATGACT
CTGTTTGTCCTTGTACCGTA
Found at i:1632312 original size:28 final size:28
Alignment explanation
Indices: 1632271--1632336 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
1632261 GCCGGACGAG
* *
1632271 TTAAAATATTTATTTT-AGGCATCAAATT
1 TTAAAAAATATATTTTGAGGCATCAAA-T
* **
1632299 TTAAAAAATATATTTTGATGTGTCAAAT
1 TTAAAAAATATATTTTGAGGCATCAAAT
1632327 TTAAAAAATA
1 TTAAAAAATA
1632337 CACTTTTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 25 0.78
29 7 0.22
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (28 bp):
TTAAAAAATATATTTTGAGGCATCAAAT
Found at i:1632354 original size:30 final size:28
Alignment explanation
Indices: 1632292--1632359 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 28
1632282 ATTTTAGGCA
* * *
1632292 TCAAATTTTAAAAAATATATTTTGATGTG
1 TCAAA-TTTAAAAAATACATTTTAAGGTG
1632321 TCAAATTTAAAAAATACACTTTTAAAGGTG
1 TCAAATTTAAAAAATACA-TTTT-AAGGTG
*
1632351 TCAAGTTTA
1 TCAAATTTA
1632360 TAAATTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 12 0.36
29 9 0.27
30 12 0.36
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (28 bp):
TCAAATTTAAAAAATACATTTTAAGGTG
Found at i:1632566 original size:14 final size:14
Alignment explanation
Indices: 1632534--1632569 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1632524 GTTATGTTTG
*
1632534 TTTATGTTCGTTCG
1 TTTATGTTCGTTCA
*
1632548 GTTATGTTCGTTCA
1 TTTATGTTCGTTCA
1632562 TTTATGTT
1 TTTATGTT
1632570 TAACCCAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.58
Consensus pattern (14 bp):
TTTATGTTCGTTCA
Found at i:1633494 original size:16 final size:16
Alignment explanation
Indices: 1633469--1633535 Score: 75
Period size: 16 Copynumber: 4.3 Consensus size: 16
1633459 GTCTCTAACG
1633469 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
* * **
1633485 TTTATATTCGTTTTTG
1 TTTATGTTCGTGTTCA
*
1633501 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
1633517 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
1633531 TTTAT
1 TTTAT
1633536 TAAATGAACG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
14 5 0.12
15 2 0.05
16 36 0.84
ACGTcount: A:0.12, C:0.09, G:0.16, T:0.63
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:1633509 original size:32 final size:32
Alignment explanation
Indices: 1633468--1633529 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
1633458 GGTCTCTAAC
1633468 GTTTATGTTCGTGTTCATTTATATTCGTTTTT
1 GTTTATGTTCGTGTTCATTTATATTCGTTTTT
* *
1633500 GTTTATGTTCGTGTTCGTTTATGTTCGTTT
1 GTTTATGTTCGTGTTCATTTATATTCGTTT
1633530 ATTTATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.61
Consensus pattern (32 bp):
GTTTATGTTCGTGTTCATTTATATTCGTTTTT
Found at i:1633620 original size:16 final size:16
Alignment explanation
Indices: 1633599--1633631 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1633589 AAAAAATATT
1633599 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1633615 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1633631 T
1 T
1633632 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1638932 original size:18 final size:18
Alignment explanation
Indices: 1638909--1638958 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
1638899 AACCTATTCT
*
1638909 GGAGTAATCACTAGGTCG
1 GGAGTAATCACTAGGCCG
* *
1638927 GGAGTAGTCGCTAGGCCG
1 GGAGTAATCACTAGGCCG
*
1638945 GGAGAAATCACTAG
1 GGAGTAATCACTAG
1638959 ACCTATTGCC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.28, C:0.18, G:0.36, T:0.18
Consensus pattern (18 bp):
GGAGTAATCACTAGGCCG
Found at i:1641558 original size:5 final size:5
Alignment explanation
Indices: 1641550--1641575 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1641540 ATAAAATTTC
1641550 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
1641576 ATATATGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:1641731 original size:32 final size:33
Alignment explanation
Indices: 1641695--1641769 Score: 100
Period size: 32 Copynumber: 2.3 Consensus size: 33
1641685 AACCCTAAAC
*
1641695 CCGACCCAAATCCAG-TTTTTTTTTAAAAAAAT
1 CCGACCCAAATCCAGATTTTTTTTAAAAAAAAT
* *
1641727 CCGACCC-GATCCCGATTTTTTTTAAAAAAAAT
1 CCGACCCAAATCCAGATTTTTTTTAAAAAAAAT
*
1641759 CCGACCTAAAT
1 CCGACCCAAAT
1641770 ATCAAAATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
31 5 0.14
32 29 0.81
33 2 0.06
ACGTcount: A:0.36, C:0.25, G:0.08, T:0.31
Consensus pattern (33 bp):
CCGACCCAAATCCAGATTTTTTTTAAAAAAAAT
Found at i:1647683 original size:19 final size:21
Alignment explanation
Indices: 1647659--1647699 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1647649 ATATTCTTTT
1647659 AATAATT-TAAA-ATATAATA
1 AATAATTATAAATATATAATA
*
1647678 AATAATTATAAATATATTATA
1 AATAATTATAAATATATAATA
1647699 A
1 A
1647700 TAAACATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AATAATTATAAATATATAATA
Found at i:1647692 original size:42 final size:39
Alignment explanation
Indices: 1647601--1647695 Score: 129
Period size: 42 Copynumber: 2.4 Consensus size: 39
1647591 TTTTTATATT
* *
1647601 ATTA-AAATATATTCTTTAATTATTAAAATATAAAAATT
1 ATTATAAATATATTCTTTAATAATTAAAATATAAAAATA
1647639 ATTATATAATATATTCTTTTAATAATTTAAAATATAATAAATA
1 ATTATA-AATATATTC-TTTAATAA-TTAAAATATAA-AAATA
1647682 ATTATAAATATATT
1 ATTATAAATATATT
1647696 ATAATAAACA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
38 4 0.08
39 1 0.02
40 9 0.18
41 7 0.14
42 19 0.38
43 10 0.20
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (39 bp):
ATTATAAATATATTCTTTAATAATTAAAATATAAAAATA
Found at i:1648787 original size:21 final size:20
Alignment explanation
Indices: 1648737--1648788 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
1648727 GACCAACAAA
*
1648737 ATCGCAATGCGATTTCTAAT
1 ATCGCAACGCGATTTCTAAT
*
1648757 -TCGTAACGCGATTT-TCAACT
1 ATCGCAACGCGATTTCT-AA-T
1648777 ATCGCAACGCGA
1 ATCGCAACGCGA
1648789 ATTTGCGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 1 0.04
19 14 0.54
20 1 0.04
21 10 0.38
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (20 bp):
ATCGCAACGCGATTTCTAAT
Found at i:1649799 original size:29 final size:29
Alignment explanation
Indices: 1649766--1649831 Score: 123
Period size: 29 Copynumber: 2.3 Consensus size: 29
1649756 ATTAAGTCTA
1649766 CCGACTATCAAAAGCTACAAAATGGTCAT
1 CCGACTATCAAAAGCTACAAAATGGTCAT
*
1649795 CCGACTATCAAAAGTTACAAAATGGTCAT
1 CCGACTATCAAAAGCTACAAAATGGTCAT
1649824 CCGACTAT
1 CCGACTAT
1649832 TCATTATGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.23
Consensus pattern (29 bp):
CCGACTATCAAAAGCTACAAAATGGTCAT
Found at i:1661709 original size:22 final size:22
Alignment explanation
Indices: 1661681--1661934 Score: 330
Period size: 22 Copynumber: 11.6 Consensus size: 22
1661671 ATAATAATTT
1661681 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
1661703 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
*
1661725 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
**
1661747 TTTTAAAATAAAT-TTTCCATA
1 TTTTAAAATAAATCAATCCATA
*
1661768 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
* **
1661790 TTTTAAAACAAATCAATTTATA
1 TTTTAAAATAAATCAATCCATA
* ***
1661812 TTTTAAAATAATTTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
*
1661834 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
1661856 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* *** *
1661878 TTTTAAAATAATTTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
*
1661900 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
1661922 TTTTAAAATAAAT
1 TTTTAAAATAAAT
1661935 TTTAAAATAG
Statistics
Matches: 198, Mismatches: 33, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
21 18 0.09
22 180 0.91
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:1661751 original size:66 final size:66
Alignment explanation
Indices: 1661681--1661934 Score: 404
Period size: 66 Copynumber: 3.9 Consensus size: 66
1661671 ATAATAATTT
***
1661681 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT-TCATATTTTAAAATAAATCAATTCA
1 TTTTAAAATAAATTTTTCCATATTTTAAAATAAATCAATCT-ATATTTTAAAATAAATCAATTCA
1661745 TA
65 TA
* *
1661747 TTTTAAAATAAA-TTTTCCATATTTTAAAATAAATCAATCTATATTTTAAAACAAATCAATTTAT
1 TTTTAAAATAAATTTTTCCATATTTTAAAATAAATCAATCTATATTTTAAAATAAATCAATTCAT
1661811 A
66 A
* *
1661812 TTTTAAAATAATTTTTTCCATATTTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCAT
1 TTTTAAAATAAATTTTTCCATATTTTAAAATAAATCAATCTATATTTTAAAATAAATCAATTCAT
1661877 A
66 A
* *
1661878 TTTTAAAATAATTTTTTTCATATTTTAAAATAAATCAATCTATATTTTAAAATAAAT
1 TTTTAAAATAAATTTTTCCATATTTTAAAATAAATCAATCTATATTTTAAAATAAAT
1661935 TTTAAAATAG
Statistics
Matches: 176, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
65 57 0.32
66 119 0.68
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (66 bp):
TTTTAAAATAAATTTTTCCATATTTTAAAATAAATCAATCTATATTTTAAAATAAATCAATTCAT
A
Found at i:1666463 original size:10 final size:10
Alignment explanation
Indices: 1666450--1666479 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1666440 TTATTTTTTT
1666450 ATTATTATTA
1 ATTATTATTA
1666460 ATTATTATTA
1 ATTATTATTA
*
1666470 ACTATTATTA
1 ATTATTATTA
1666480 TTAATTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (10 bp):
ATTATTATTA
Found at i:1666464 original size:13 final size:14
Alignment explanation
Indices: 1666448--1666485 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
1666438 TTTTATTTTT
1666448 TTATTATT-ATTAA
1 TTATTATTAATTAA
*
1666461 TTATTATTAACT-A
1 TTATTATTAATTAA
1666474 TTATTATTAATT
1 TTATTATTAATT
1666486 TTACATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 20 0.91
14 2 0.09
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (14 bp):
TTATTATTAATTAA
Found at i:1679907 original size:8 final size:8
Alignment explanation
Indices: 1679894--1679931 Score: 76
Period size: 8 Copynumber: 4.8 Consensus size: 8
1679884 TACACTTAAA
1679894 AAAAAATC
1 AAAAAATC
1679902 AAAAAATC
1 AAAAAATC
1679910 AAAAAATC
1 AAAAAATC
1679918 AAAAAATC
1 AAAAAATC
1679926 AAAAAA
1 AAAAAA
1679932 AAAAATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.79, C:0.11, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAAATC
Found at i:1679945 original size:7 final size:7
Alignment explanation
Indices: 1679894--1679947 Score: 65
Period size: 8 Copynumber: 7.4 Consensus size: 7
1679884 TACACTTAAA
1679894 AAAAAAT
1 AAAAAAT
1679901 CAAAAAAT
1 -AAAAAAT
1679909 CAAAAAAT
1 -AAAAAAT
1679917 CAAAAAAT
1 -AAAAAAT
*
1679925 CAAAAA-
1 AAAAAAT
1679931 AAAAAAT
1 AAAAAAT
1679938 AAAAAAT
1 AAAAAAT
1679945 AAA
1 AAA
1679948 TAAAGGAGGG
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
6 5 0.12
7 15 0.35
8 23 0.53
ACGTcount: A:0.81, C:0.07, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:1681118 original size:141 final size:141
Alignment explanation
Indices: 1680900--1681170 Score: 402
Period size: 141 Copynumber: 1.9 Consensus size: 141
1680890 AACATCAGCT
1680900 GACCAGATCTCCTCATCACGTAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTA
1 GACCAGATCTCCTCATCACGTAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTA
* ** *
1680965 GGAACCGAGTTATCACCCTTCCTAAAGATGGCCAGAGTTCTTCATCATGTATGAACCATGTCATC
66 GGAACCGAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAACCATGTCATC
1681030 TACCCTTAGAC
131 TACCCTTAGAC
* * **
1681041 GACCAGA-CTTCCTCATCACGTAGGAGCCGTGTCAACCTTA-GATAATTAGCCGTCCTCATCACG
1 GACCAGATC-TCCTCATCACGTAGGAG-AGTGTCAACATTAGGATAACCAGCCGTCCTCATCACG
* * * *
1681104 TAGGAACCGAGTTATCACCCTTCTTAAAGATGACCAGAACTCTTCATCGCGTATGAGCCGTGTCA
64 TAGGAACCGAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAACCATGTCA
1681169 TC
129 TC
1681171 CCTTGACCAG
Statistics
Matches: 116, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
140 1 0.01
141 104 0.90
142 11 0.09
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (141 bp):
GACCAGATCTCCTCATCACGTAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTA
GGAACCGAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAACCATGTCATC
TACCCTTAGAC
Found at i:1681435 original size:13 final size:13
Alignment explanation
Indices: 1681417--1681441 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1681407 ATTTTTTTTT
1681417 TATTATTATTAAC
1 TATTATTATTAAC
1681430 TATTATTATTAA
1 TATTATTATTAA
1681442 TTTTACATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTATTATTAAC
Done.