Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 4 of 97
Found at i:1436573 original size:19 final size:20
Alignment explanation
Indices: 1436539--1436577 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
1436529 TATACATAAT
1436539 ATTTAAAAAAGTATTTAAATC
1 ATTTAAAAAAG-ATTTAAATC
1436560 ATTTAAAAAA-ATTTAAAT
1 ATTTAAAAAAGATTTAAAT
1436578 AAATTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
21 10 0.56
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (20 bp):
ATTTAAAAAAGATTTAAATC
Found at i:1436726 original size:33 final size:33
Alignment explanation
Indices: 1436673--1436737 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
1436663 ATATGACACT
* *
1436673 TATTAACATATAACATTTAATAATTATATGATG
1 TATTAACATATAACAATTAATAATAATATGATG
* * *
1436706 TATTAACATATCATAATTAATTATAATATGAT
1 TATTAACATATAACAATTAATAATAATATGAT
1436738 CATGTCATGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (33 bp):
TATTAACATATAACAATTAATAATAATATGATG
Found at i:1446224 original size:25 final size:25
Alignment explanation
Indices: 1446173--1446228 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
1446163 TCAAAATATT
*
1446173 TTTA-ATTTAAAATTATCTTATTTA
1 TTTATATTTAAAATTATCTTATTAA
*
1446197 TTTATATTTAAAAATTATTTTA-TAA
1 TTTATATTT-AAAATTATCTTATTAA
1446222 TTT-TATT
1 TTTATATT
1446229 AAGTAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 8 0.29
25 9 0.32
26 11 0.39
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (25 bp):
TTTATATTTAAAATTATCTTATTAA
Found at i:1446226 original size:26 final size:24
Alignment explanation
Indices: 1446154--1446227 Score: 60
Period size: 25 Copynumber: 2.9 Consensus size: 24
1446144 ATTTGTATCA
**
1446154 TTAAAATTATCAAAATATTTT-TAAT
1 TTAAAATTATC-TTATATTTTAT-AT
*
1446179 TTAAAATTATCTTATTTATTTATAT
1 TTAAAATTATCTTATAT-TTTATAT
*
1446204 TTAAAAATTATTTTATAATTTTAT
1 TT-AAAATTATCTTAT-ATTTTAT
1446228 TAAGTAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
24 3 0.08
25 18 0.45
26 18 0.45
27 1 0.03
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (24 bp):
TTAAAATTATCTTATATTTTATAT
Found at i:1449520 original size:22 final size:21
Alignment explanation
Indices: 1449478--1449520 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1449468 ATAATACTTT
* **
1449478 AAAAATTTTAAAAAATTATTA
1 AAAAAATTTAAAAAAACATTA
1449499 AAAAAATTTAAATAAAACATTA
1 AAAAAATTTAAA-AAAACATTA
1449521 TTTTTAAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAAAATTTAAAAAAACATTA
Found at i:1449774 original size:21 final size:22
Alignment explanation
Indices: 1449732--1449793 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 22
1449722 TTGTTTTTTA
*
1449732 TAAATAATAATTAAAATTTAAT
1 TAAATAATAATTAAAATATAAT
1449754 TAAAT-ATAA-TAAAATAATAAT
1 TAAATAATAATTAAAAT-ATAAT
* *
1449775 TTATTAGATAATTTAAAAT
1 TAAATA-ATAA-TTAAAAT
1449794 TTTTATATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 6 0.19
21 11 0.34
22 5 0.16
23 4 0.12
25 6 0.19
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
TAAATAATAATTAAAATATAAT
Found at i:1455935 original size:19 final size:19
Alignment explanation
Indices: 1455907--1455943 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1455897 ACATCTATCT
*
1455907 TCTCTTTCTTTCCGTTCTC
1 TCTCTATCTTTCCGTTCTC
*
1455926 TCTCTATCTTTCCTTTCT
1 TCTCTATCTTTCCGTTCT
1455944 TTTTTGTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.03, C:0.35, G:0.03, T:0.59
Consensus pattern (19 bp):
TCTCTATCTTTCCGTTCTC
Found at i:1466430 original size:86 final size:87
Alignment explanation
Indices: 1466340--1466500 Score: 288
Period size: 89 Copynumber: 1.8 Consensus size: 87
1466330 ATATATACAG
*
1466340 AACACTGAGGAAACAGTTTAATTTCCTTC-TGAGATGTCAGCTTCTGTTATTAATTCGCTAGATA
1 AACACTAAGGAAACAGTTTAATTTCCTTCATGAGATGTCAGCTTCTGTTATTAATTCGCTAGATA
1466404 GTGACCCATATTATATATTTAT
66 GTGACCCATATTATATATTTAT
1466426 AACACTAAGGAAACAGTTTAATTTCCTTCTGATGAGATGTCAGCTTCTGTTATTAATTCGCTAGA
1 AACACTAAGGAAACAGTTTAATTTCCTTC--ATGAGATGTCAGCTTCTGTTATTAATTCGCTAGA
1466491 TAGTGACCCA
64 TAGTGACCCA
1466501 CATTTTTATA
Statistics
Matches: 71, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
86 28 0.39
89 43 0.61
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.36
Consensus pattern (87 bp):
AACACTAAGGAAACAGTTTAATTTCCTTCATGAGATGTCAGCTTCTGTTATTAATTCGCTAGATA
GTGACCCATATTATATATTTAT
Found at i:1469706 original size:2 final size:2
Alignment explanation
Indices: 1469701--1469727 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1469691 TGTGTGTGTG
1469701 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1469728 GTTTGGAGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1477084 original size:14 final size:13
Alignment explanation
Indices: 1477065--1477171 Score: 62
Period size: 14 Copynumber: 8.2 Consensus size: 13
1477055 TAACGTTATA
1477065 ATTAAAATAACAAT
1 ATTAAAATAA-AAT
1477079 ATTAAAATAAAAT
1 ATTAAAATAAAAT
*
1477092 ATATAATATAAAA-
1 AT-TAAAATAAAAT
1477105 A-TAAAA-AATTAA-
1 ATTAAAATAA--AAT
1477117 ATTAAAATAAAAT
1 ATTAAAATAAAAT
*
1477130 ATATAATATTAAAA-
1 AT-TAA-AATAAAAT
** * *
1477144 ATTGTATTAAAAA
1 ATTAAAATAAAAT
*
1477157 ATGAAAATAAAAT
1 ATTAAAATAAAAT
1477170 AT
1 AT
1477172 ATAAGATTAT
Statistics
Matches: 74, Mismatches: 10, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
10 2 0.03
11 4 0.05
12 12 0.16
13 24 0.32
14 26 0.35
15 6 0.08
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (13 bp):
ATTAAAATAAAAT
Found at i:1477116 original size:33 final size:33
Alignment explanation
Indices: 1477061--1477146 Score: 90
Period size: 32 Copynumber: 2.7 Consensus size: 33
1477051 TTTATAACGT
*
1477061 TATAAT-T-AAAATAACAATATTAAAATAAAATA
1 TATAATATAAAAATAA-AAAATTAAAATAAAATA
*
1477093 TATAATATAAAAATAAAAAATTAAATTAAAATA
1 TATAATATAAAAATAAAAAATTAAAATAAAATA
* *
1477126 -A-AATATATAATATTAAAAATT
1 TATAATATA-AAAATAAAAAATT
1477147 GTATTAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
31 6 0.13
32 18 0.38
33 16 0.34
34 7 0.15
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (33 bp):
TATAATATAAAAATAAAAAATTAAAATAAAATA
Found at i:1477195 original size:40 final size:39
Alignment explanation
Indices: 1477060--1477196 Score: 123
Period size: 40 Copynumber: 3.5 Consensus size: 39
1477050 TTTTATAACG
* *
1477060 TTATAATTAAAATAACAATATTAAAATAAAATATATAATA
1 TTATAATAAAAATAA-AAAATTAAAATAAAATATATAATA
* * **
1477100 TAAAAATAAAAA-ATTAAATTAAAATAAAATATATAATA
1 TTATAATAAAAATAAAAAATTAAAATAAAATATATAATA
* *** * * *
1477138 TTAAAAATTGTATTAAAAAATGAAAATAAAATATATAAGA
1 TT-ATAATAAAAATAAAAAATTAAAATAAAATATATAATA
1477178 TTATAATAAGAAATAAAAA
1 TTATAATAA-AAATAAAAA
1477197 TAAAACATAT
Statistics
Matches: 74, Mismatches: 20, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
38 23 0.31
39 11 0.15
40 40 0.54
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.31
Consensus pattern (39 bp):
TTATAATAAAAATAAAAAATTAAAATAAAATATATAATA
Found at i:1477445 original size:15 final size:15
Alignment explanation
Indices: 1477425--1477472 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
1477415 TTTTTCCTGC
1477425 AATCACATTGCTTGT
1 AATCACATTGCTTGT
* **
1477440 AATCACATTACTTAC
1 AATCACATTGCTTGT
1477455 AATCACATTGCATTGT
1 AATCACATTGC-TTGT
1477471 AA
1 AA
1477473 AGTACCAAAC
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
15 22 0.85
16 4 0.15
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.35
Consensus pattern (15 bp):
AATCACATTGCTTGT
Found at i:1481982 original size:144 final size:143
Alignment explanation
Indices: 1481719--1481978 Score: 371
Period size: 144 Copynumber: 1.8 Consensus size: 143
1481709 GAAGCAAAAT
* * ** * * *
1481719 GGGGCAAAATGCATTTTGGAAGTACTAGGATTGACCCCACGCTTCCAAGGGTTGATCTTTAAGCC
1 GGGGAAAAATGCATTATGGAAGTACTAGGATCAACCCCACCCTTCCAAGGGTTGATCTTAAACCC
* * *
1481784 TCCAGGATAGAAAATGCATTCTGTTTTAGACCAGGATCGACTCCCATCCTTTAAAGGGTGATCCA
66 TCCAAGATAGAAAATGCATTCTGTTTTAGACCAAGATCGACCCCCATCCTTTAAAGGGTGATCCA
1481849 AAAAGGTAGAATG
131 AAAAGGTAGAATG
* *
1481862 GGGGAAAAATGCATTATGGAAGTGCTAGGATCAATCCCTACCCTTCCAAGGGTTGATCCTTAAAC
1 GGGGAAAAATGCATTATGGAAGTACTAGGATCAA-CCCCACCCTTCCAAGGGTTGAT-CTTAAAC
*
1481927 CCT-CAAGATAGAAAATGCATTTTGTTTTAGACCAAGATCGACCCCCA-CCTTT
64 CCTCCAAGATAGAAAATGCATTCTGTTTTAGACCAAGATCGACCCCCATCCTTT
1481979 TAAACAGTCA
Statistics
Matches: 102, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
143 34 0.33
144 60 0.59
145 8 0.08
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (143 bp):
GGGGAAAAATGCATTATGGAAGTACTAGGATCAACCCCACCCTTCCAAGGGTTGATCTTAAACCC
TCCAAGATAGAAAATGCATTCTGTTTTAGACCAAGATCGACCCCCATCCTTTAAAGGGTGATCCA
AAAAGGTAGAATG
Found at i:1482682 original size:12 final size:12
Alignment explanation
Indices: 1482665--1482707 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1482655 GAAAATGTTT
1482665 TGAATGTATATA
1 TGAATGTATATA
*
1482677 TGAATGTAAATA
1 TGAATGTATATA
* *
1482689 TGAATATATGTA
1 TGAATGTATATA
*
1482701 TGTATGT
1 TGAATGT
1482708 TTTCATGGGG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.19, T:0.42
Consensus pattern (12 bp):
TGAATGTATATA
Found at i:1482852 original size:27 final size:27
Alignment explanation
Indices: 1482822--1482950 Score: 109
Period size: 27 Copynumber: 4.8 Consensus size: 27
1482812 TAATTGGACT
*
1482822 TTGTTAGGTGCCTTAATACCTTCGAAA
1 TTGTTAGGTGCCTTAACACCTTCGAAA
* * *
1482849 TTGTTAAGTGCCTTAACATCTTC--AG
1 TTGTTAGGTGCCTTAACACCTTCGAAA
* * * *
1482874 TCGTTCGGTGCCTTAACACCTTTGGATA
1 TTGTTAGGTGCCTTAACACC-TTCGAAA
* * * *
1482902 TTGTTAGGTGCCTTAGCATCTTTGGAA
1 TTGTTAGGTGCCTTAACACCTTCGAAA
* *
1482929 TGGTTAGGTGCCATAACACCTT
1 TTGTTAGGTGCCTTAACACCTT
1482951 TAGATTTGGT
Statistics
Matches: 77, Mismatches: 22, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
25 17 0.22
26 2 0.03
27 42 0.55
28 16 0.21
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (27 bp):
TTGTTAGGTGCCTTAACACCTTCGAAA
Found at i:1482924 original size:28 final size:27
Alignment explanation
Indices: 1482824--1482965 Score: 108
Period size: 27 Copynumber: 5.3 Consensus size: 27
1482814 ATTGGACTTT
* * * *
1482824 GTTAGGTGCCTTAATACCTTCGAAATT
1 GTTAGGTGCCTTAACACCTTTGGAATG
* * * * *
1482851 GTTAAGTGCCTTAACATC-TT-CAGTC
1 GTTAGGTGCCTTAACACCTTTGGAATG
* *
1482876 GTTCGGTGCCTTAACACCTTTGGATATT
1 GTTAGGTGCCTTAACACCTTTGGA-ATG
* *
1482904 GTTAGGTGCCTTAGCATCTTTGGAATG
1 GTTAGGTGCCTTAACACCTTTGGAATG
* * *
1482931 GTTAGGTGCCATAACACCTTTAGATTTG
1 GTTAGGTGCCTTAACACCTTTGGA-ATG
1482959 GTTAGGT
1 GTTAGGT
1482966 ATCGTAGCAC
Statistics
Matches: 89, Mismatches: 22, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
25 17 0.19
26 3 0.03
27 38 0.43
28 31 0.35
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (27 bp):
GTTAGGTGCCTTAACACCTTTGGAATG
Found at i:1482951 original size:27 final size:28
Alignment explanation
Indices: 1482880--1482983 Score: 111
Period size: 28 Copynumber: 3.8 Consensus size: 28
1482870 TCAGTCGTTC
*
1482880 GGTGCCTTAACACCTTTGGATATTGTTA
1 GGTGCCTTAACACCTTTGGATATGGTTA
* *
1482908 GGTGCCTTAGCATCTTTGGA-ATGGTTA
1 GGTGCCTTAACACCTTTGGATATGGTTA
* * *
1482935 GGTGCCATAACACCTTTAGATTTGGTTA
1 GGTGCCTTAACACCTTTGGATATGGTTA
** * *
1482963 GGTATCGTAGCACCTTTGGAT
1 GGTGCCTTAACACCTTTGGAT
1482984 TTTGGCCATG
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
27 22 0.35
28 40 0.65
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (28 bp):
GGTGCCTTAACACCTTTGGATATGGTTA
Found at i:1485256 original size:28 final size:28
Alignment explanation
Indices: 1485184--1485283 Score: 107
Period size: 28 Copynumber: 3.7 Consensus size: 28
1485174 GTAAGATACT
*
1485184 TTAGCACCTTTGGA--TTGCTAGGTGTC
1 TTAGCACCTTTGGATTTTGTTAGGTGTC
* * * *
1485210 TTAGCA-CTTTTGAATTTGTTAAGTGCC
1 TTAGCACCTTTGGATTTTGTTAGGTGTC
1485237 TTAGCACCTTTGGATTTTGTTAGGTGTC
1 TTAGCACCTTTGGATTTTGTTAGGTGTC
* * *
1485265 ATAACACCTTAGGATTTTG
1 TTAGCACCTTTGGATTTTG
1485284 GCCATGAGCC
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
25 6 0.10
26 6 0.10
27 15 0.25
28 33 0.55
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.42
Consensus pattern (28 bp):
TTAGCACCTTTGGATTTTGTTAGGTGTC
Found at i:1486249 original size:30 final size:30
Alignment explanation
Indices: 1486213--1486273 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
1486203 CACCTCACGA
1486213 ATATTTGGGGCTTACTAGAGGAGTTTTCTC
1 ATATTTGGGGCTTACTAGAGGAGTTTTCTC
1486243 ATATTTGGGGCTTACTAGAGGAGTTTTCTC
1 ATATTTGGGGCTTACTAGAGGAGTTTTCTC
1486273 A
1 A
1486274 AATATATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.26, T:0.39
Consensus pattern (30 bp):
ATATTTGGGGCTTACTAGAGGAGTTTTCTC
Found at i:1486486 original size:2 final size:2
Alignment explanation
Indices: 1486479--1486516 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1486469 CGCACGCACG
1486479 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1486517 TATATATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1489751 original size:35 final size:35
Alignment explanation
Indices: 1489709--1489815 Score: 205
Period size: 35 Copynumber: 3.1 Consensus size: 35
1489699 GGCTTTATGT
1489709 TTTACTTCCCTGTACTCCATATTTGGCTAATTGAC
1 TTTACTTCCCTGTACTCCATATTTGGCTAATTGAC
*
1489744 TTTACTTCTCTGTACTCCATATTTGGCTAATTGAC
1 TTTACTTCCCTGTACTCCATATTTGGCTAATTGAC
1489779 TTTACTTCCCTGTACTCCATATTTGGCTAATTGAC
1 TTTACTTCCCTGTACTCCATATTTGGCTAATTGAC
1489814 TT
1 TT
1489816 ACTGTTGAAG
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 70 1.00
ACGTcount: A:0.20, C:0.24, G:0.11, T:0.45
Consensus pattern (35 bp):
TTTACTTCCCTGTACTCCATATTTGGCTAATTGAC
Found at i:1489924 original size:27 final size:26
Alignment explanation
Indices: 1489886--1489938 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
1489876 CTCATTCGTG
1489886 AACAATAGAATAGT-TGATTAAGAAACT
1 AACAATAGAATAGTCT-ATTAA-AAACT
*
1489913 AACAGTAGAATAGTCTATTAAAAACT
1 AACAATAGAATAGTCTATTAAAAACT
1489939 TATACCAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 5 0.21
27 18 0.75
28 1 0.04
ACGTcount: A:0.51, C:0.09, G:0.13, T:0.26
Consensus pattern (26 bp):
AACAATAGAATAGTCTATTAAAAACT
Found at i:1497477 original size:32 final size:32
Alignment explanation
Indices: 1497440--1497501 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
1497430 CATTTTAAGA
1497440 AAATTCCATCAAAAGAAATAAAGAAAGCAAAT
1 AAATTCCATCAAAAGAAATAAAGAAAGCAAAT
*
1497472 AAATTCCGTCAAAAGAAATAAAGAAAGCAA
1 AAATTCCATCAAAAGAAATAAAGAAAGCAA
1497502 GAATCTGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.61, C:0.13, G:0.11, T:0.15
Consensus pattern (32 bp):
AAATTCCATCAAAAGAAATAAAGAAAGCAAAT
Found at i:1497916 original size:2 final size:2
Alignment explanation
Indices: 1497901--1497938 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1497891 AATAAATAAG
* *
1497901 AT AT AT GT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1497939 GTAAAACTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1497916 original size:10 final size:10
Alignment explanation
Indices: 1497896--1497938 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
1497886 TACTTAATAA
1497896 ATAAGATATAT
1 ATAA-ATATAT
*
1497907 GTAAATATAT
1 ATAAATATAT
*
1497917 ATATATATAT
1 ATAAATATAT
*
1497927 ATATATATAT
1 ATAAATATAT
1497937 AT
1 AT
1497939 GTAAAACTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 26 0.90
11 3 0.10
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (10 bp):
ATAAATATAT
Found at i:1511320 original size:72 final size:72
Alignment explanation
Indices: 1511171--1511321 Score: 178
Period size: 72 Copynumber: 2.1 Consensus size: 72
1511161 CAATTCTCTA
* * * * * * * **
1511171 AATGGATTCATTCCATTATATATTGGTAAACTATCTAGACTGACTTATCTCGATTTGTCTTTCAA
1 AATGGAATCATTCCATCAGATATCGGTAAACTATCTAGACTAACTTACCTCGACTTGTCTACCAA
1511236 TCATTTT
66 TCATTTT
* *
1511243 AATGGAATCATTCCATCAGATATCGGTAATCTATCTAGACTAACTTACCTCGGCTTGTCTACCAA
1 AATGGAATCATTCCATCAGATATCGGTAAACTATCTAGACTAACTTACCTCGACTTGTCTACCAA
*
1511308 TTATCTTT
66 TCAT-TTT
1511316 -ATGGAA
1 AATGGAA
1511322 ATATACCTTT
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
72 63 0.95
73 3 0.05
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (72 bp):
AATGGAATCATTCCATCAGATATCGGTAAACTATCTAGACTAACTTACCTCGACTTGTCTACCAA
TCATTTT
Found at i:1512029 original size:432 final size:432
Alignment explanation
Indices: 1511246--1512076 Score: 1213
Period size: 432 Copynumber: 1.9 Consensus size: 432
1511236 TCATTTTAAT
* * *
1511246 GGAATCATTCCATCAGATATCGGTAATCTATCTAGACTAACTTACCTCGGCTTGTCTACCAATTA
1 GGAACCATTCCATCAAATATCGGTAATCTATCTAGACTAACTTACCTCAGCTTGTCTACCAATTA
*
1511311 TCTTTATGGAAATATACCTTTTGAAATAGGAAAGTTAAGGTTTCTTTCTGAACTCTATCTACAAG
66 TCTTTATGGAAATATACCTTTTGAAATAGGAAAGTTAAGGTCTCTTTCTGAACTCTATCTACAAG
* *
1511376 AAAACATTCTGATAGGTTCAATCCCTCCTTCTATAGGAAACTTGACAAACTTGTTCTTTCTCTTC
131 AAAACATTCTGATAGGTTCAATCCCTCCTTCTATAGGAAACTTGACAAACTTATTCTTTCTCTAC
*
1511441 TTGTTCAACAACAAGCTCTCTAGTGCTATACCTCAACAAGTTGGAATGCTGAAGTCTCTATACAA
196 TTGTTCAACAACAAGCTCTCTAGTGCTATACCTCAACAAGTTGGAATGCTGAAATCTCTATACAA
* * * ** *
1511506 ATTTACACTCTCTGATAATAATCTAGTCGGTCCTCTCCCTAACTCTATTGGAAATTTAAGTAACT
261 ATTGACACTCTCTCAAAATAATCTAGTCGGTCCTCTCCCTAACTCTATTAAAAACTTAAGTAACT
* * * * *
1511571 TATCAGATCTTCGTCTTTTTAACAACAAAATTTCGGGTCTCATACCTCAAGAAATTGGAATGCTG
326 TATCAGATCTTCGCCTTATGAACAACAAAATTTCAGGACTCATACCTCAAGAAATTGGAATGCTG
*
1511636 AGGTCTCTTAATTGGCTTGATTTGTCTAACAATTCTCTCAAA
391 AGATCTCTTAATTGGCTTGATTTGTCTAACAATTCTCTCAAA
* * * * * *
1511678 GGAACCATTTCATCAAATATTGGTAA-CTTATCTAGACTGACTTACCTCAGCTTGTTTTCTAATT
1 GGAACCATTCCATCAAATATCGGTAATC-TATCTAGACTAACTTACCTCAGCTTGTCTACCAATT
* * * * **
1511742 ATTTTTGTGGAAATATACCTTTTGAAATAGGAGAGTTAAGGTCTCTTTCTGAGCTCTATCTGGAA
65 ATCTTTATGGAAATATACCTTTTGAAATAGGAAAGTTAAGGTCTCTTTCTGAACTCTATCTACAA
*
1511807 GAAAATATTCTGATAGGTTCAATCCCTCCTTCTATAGGAAACTTGACAAACTTATTCTTTCTCTA
130 GAAAACATTCTGATAGGTTCAATCCCTCCTTCTATAGGAAACTTGACAAACTTATTCTTTCTCTA
*
1511872 CTTGTTCAACAACAAGCTCTCTGGTGCTATACCTCAACAAGTTGGAATGCTGAAATCTCTGA-AT
195 CTTGTTCAACAACAAGCTCTCTAGTGCTATACCTCAACAAGTTGGAATGCTGAAATCTCT-ATA-
* * * * *
1511936 GAACTTGAC-CTCTCTCAAAATAATCT-GATTGGTTCTCTCCC-AATCTCTATTAAAAACTTAAT
258 CAAATTGACACTCTCTCAAAATAATCTAG-TCGGTCCTCTCCCTAA-CTCTATTAAAAACTTAAG
* * *
1511998 TAACTTATCATATTTTCGCCTTATGAACAACAAAATTTCAGGACTCATACCTCGAGAAATTGGAA
321 TAACTTATCAGATCTTCGCCTTATGAACAACAAAATTTCAGGACTCATACCTCAAGAAATTGGAA
1512063 TGCTGAGATCTCTT
386 TGCTGAGATCTCTT
1512077 CATCATCTTT
Statistics
Matches: 353, Mismatches: 41, Indels: 10
0.87 0.10 0.02
Matches are distributed among these distances:
431 4 0.01
432 342 0.97
433 7 0.02
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (432 bp):
GGAACCATTCCATCAAATATCGGTAATCTATCTAGACTAACTTACCTCAGCTTGTCTACCAATTA
TCTTTATGGAAATATACCTTTTGAAATAGGAAAGTTAAGGTCTCTTTCTGAACTCTATCTACAAG
AAAACATTCTGATAGGTTCAATCCCTCCTTCTATAGGAAACTTGACAAACTTATTCTTTCTCTAC
TTGTTCAACAACAAGCTCTCTAGTGCTATACCTCAACAAGTTGGAATGCTGAAATCTCTATACAA
ATTGACACTCTCTCAAAATAATCTAGTCGGTCCTCTCCCTAACTCTATTAAAAACTTAAGTAACT
TATCAGATCTTCGCCTTATGAACAACAAAATTTCAGGACTCATACCTCAAGAAATTGGAATGCTG
AGATCTCTTAATTGGCTTGATTTGTCTAACAATTCTCTCAAA
Found at i:1516630 original size:18 final size:18
Alignment explanation
Indices: 1516609--1516649 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1516599 ATTTATTGAA
* *
1516609 TATTTATTTTTTATTTTT
1 TATTTATTTTTAATTATT
*
1516627 TATTAATTTTTAATTATT
1 TATTTATTTTTAATTATT
1516645 TATTT
1 TATTT
1516650 CACTTGTCCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
TATTTATTTTTAATTATT
Found at i:1530158 original size:5 final size:5
Alignment explanation
Indices: 1530148--1530172 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1530138 ACTGAATGGG
1530148 GTTTT GTTTT GTTTT GTTTT GTTTT
1 GTTTT GTTTT GTTTT GTTTT GTTTT
1530173 ATCTGGCTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (5 bp):
GTTTT
Found at i:1556192 original size:3 final size:3
Alignment explanation
Indices: 1556180--1556235 Score: 58
Period size: 3 Copynumber: 18.7 Consensus size: 3
1556170 TTCTTCTTCT
* ** * * *
1556180 TCC TCT TCC TCC TCC AAC TCA TCG TCC TCC TCC TCC TCC TCC TCC GCC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC
1556228 TCC TCC TC
1 TCC TCC TC
1556236 TTCACCTTCT
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.05, C:0.59, G:0.04, T:0.32
Consensus pattern (3 bp):
TCC
Found at i:1556540 original size:2 final size:2
Alignment explanation
Indices: 1556533--1556587 Score: 62
Period size: 2 Copynumber: 29.0 Consensus size: 2
1556523 TTTAAAGGAA
* **
1556533 AG AG AG AG AG AG AG AG AG AG AG -G GG NT A- AG A- AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1556572 AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG
1556588 GGTATATGTG
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
1 3 0.06
2 44 0.94
ACGTcount: A:0.47, C:0.00, G:0.49, T:0.02
Consensus pattern (2 bp):
AG
Found at i:1557272 original size:17 final size:17
Alignment explanation
Indices: 1557242--1557275 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1557232 AGTTAATTAA
1557242 TTATTAATTATAAAATT
1 TTATTAATTATAAAATT
* *
1557259 TTATTTATTTTAAAATT
1 TTATTAATTATAAAATT
1557276 AAAATATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATTAATTATAAAATT
Found at i:1562964 original size:16 final size:16
Alignment explanation
Indices: 1562940--1562972 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1562930 TCGTCCGACA
*
1562940 TCTCTCTTTCTCTCTC
1 TCTCCCTTTCTCTCTC
1562956 TCTCCCTTTCTCTCTC
1 TCTCCCTTTCTCTCTC
1562972 T
1 T
1562973 GCTTCACGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (16 bp):
TCTCCCTTTCTCTCTC
Found at i:1579247 original size:21 final size:22
Alignment explanation
Indices: 1579221--1579263 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1579211 TAATTATTTG
1579221 TTATTTATATGAA-TATTTATT
1 TTATTTATATGAATTATTTATT
* *
1579242 TTATTTATTTTAATTATTTATT
1 TTATTTATATGAATTATTTATT
1579264 ATCATTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TTATTTATATGAATTATTTATT
Found at i:1594157 original size:30 final size:29
Alignment explanation
Indices: 1594085--1594186 Score: 104
Period size: 29 Copynumber: 3.6 Consensus size: 29
1594075 AGTTCGTAAG
* * *
1594085 TAATAATAATA--TTTTAAATATTAAAGTG
1 TAATAATAATATTTTTTTAATA-TAACGTA
* * *
1594113 TAATAA-AATA-TTTTTAAATATGATGTA
1 TAATAATAATATTTTTTTAATATAACGTA
*
1594140 TAATAATAATATTTTTTTAATATAACGTG
1 TAATAATAATATTTTTTTAATATAACGTA
1594169 TAATAATAATATTTTTTT
1 TAATAATAATATTTTTTT
1594187 TTTCAATACG
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
27 14 0.22
28 19 0.30
29 31 0.48
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.48
Consensus pattern (29 bp):
TAATAATAATATTTTTTTAATATAACGTA
Found at i:1594186 original size:29 final size:28
Alignment explanation
Indices: 1594084--1594184 Score: 125
Period size: 28 Copynumber: 3.6 Consensus size: 28
1594074 TAGTTCGTAA
1594084 GTAATAATAATA-TTTTAAATATTAAAGT
1 GTAATAATAATATTTTTAAATA-TAAAGT
* *
1594112 GTAATAA-AATATTTTTAAATATGATGT
1 GTAATAATAATATTTTTAAATATAAAGT
* * *
1594139 ATAATAATAATATTTTTTTAATATAACGT
1 GTAATAATAATA-TTTTTAAATATAAAGT
1594168 GTAATAATAATATTTTT
1 GTAATAATAATATTTTT
1594185 TTTTTCAATA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
27 14 0.22
28 25 0.40
29 24 0.38
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.47
Consensus pattern (28 bp):
GTAATAATAATATTTTTAAATATAAAGT
Found at i:1594202 original size:33 final size:32
Alignment explanation
Indices: 1594139--1594204 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
1594129 AATATGATGT
*
1594139 ATAATAATAATATTTTTTTAATATAACGTGTA
1 ATAATAATAATATTTTTTTAATACAACGTGTA
* * **
1594171 ATAATAATATTTTTTTTTTCAATACGGCGTGTA
1 ATAATAATAATATTTTTTT-AATACAACGTGTA
1594204 A
1 A
1594205 CAATTTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (32 bp):
ATAATAATAATATTTTTTTAATACAACGTGTA
Found at i:1594310 original size:54 final size:55
Alignment explanation
Indices: 1594207--1594312 Score: 142
Period size: 54 Copynumber: 1.9 Consensus size: 55
1594197 GCGTGTAACA
* * * *
1594207 ATTTTTTTTAATCATGACGTGTAACATATTTTTGTATATGATATATAATAATAAT
1 ATTTTTTTTAATCATAAAGTATAACATATTTTTGTATATAATATATAATAATAAT
* * *
1594262 ATTTTTTTTAAT-ATAAAGTATAACATATTTTTTTATATAATTTGTAATAAT
1 ATTTTTTTTAATCATAAAGTATAACATATTTTTGTATATAATATATAATAAT
1594313 TTAATCATGA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
54 32 0.73
55 12 0.27
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.52
Consensus pattern (55 bp):
ATTTTTTTTAATCATAAAGTATAACATATTTTTGTATATAATATATAATAATAAT
Found at i:1594311 original size:27 final size:26
Alignment explanation
Indices: 1594228--1594311 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 26
1594218 TCATGACGTG
* * *
1594228 TAACATATTTTTGTATATGATATATAA
1 TAACATATTTTTTTATATAAT-TGTAA
* *
1594255 TAATAATATTTTTTTTAATATAA-AGT-A
1 TAA-CATA-TTTTTTT-ATATAATTGTAA
1594282 TAACATATTTTTTTATATAATTTGTAA
1 TAACATATTTTTTTATATAA-TTGTAA
1594309 TAA
1 TAA
1594312 TTTAATCATG
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
24 6 0.14
25 7 0.16
26 5 0.11
27 11 0.25
28 4 0.09
29 6 0.14
30 5 0.11
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (26 bp):
TAACATATTTTTTTATATAATTGTAA
Found at i:1594352 original size:24 final size:24
Alignment explanation
Indices: 1594286--1594354 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 24
1594276 AAAGTATAAC
* * *
1594286 ATATTTTTTTATATAATTTGTAAT
1 ATATTTTTATACATAATATGTAAT
* *
1594310 A-A-TTTAAT-CATGATATGTAAT
1 ATATTTTTATACATAATATGTAAT
*
1594331 ATATTTTTATACATAATGTGTAAT
1 ATATTTTTATACATAATATGTAAT
1594355 TTTATAACGT
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
21 11 0.32
22 5 0.15
23 6 0.18
24 12 0.35
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.52
Consensus pattern (24 bp):
ATATTTTTATACATAATATGTAAT
Found at i:1598286 original size:120 final size:123
Alignment explanation
Indices: 1598141--1598394 Score: 415
Period size: 129 Copynumber: 2.0 Consensus size: 123
1598131 AGCTCCTCCA
*
1598141 CCACCACCTCCTCCTCCAATGCCACCTTTGAATGAAAATTTAGCTTCTGGATCTGCACCT-T-CT
1 CCACCACCTCCTCCTCCAATGCCACCTTTGAAGGAAAATTTAGCTTCTGGATCTGCACCTCTCCT
*
1598204 -CCACCTTCTCTTCATTCCAGGCAAGCAGCAAGTCCTGCAGCTTCATCATCGGCACCC
66 CCCACCTCCTCTTCATTCCAGGCAAGCAGCAAGTCCTGCAGCTTCATCATCGGCACCC
1598261 CCACCACCTCCTCCTCCAATGCCACCTTTGAAGGAAAATTTAGCTTCTGGATCTGCACCTCCTCC
1 CCACCACCTCCTCCTCCAATGCCACCTTTGAAGGAAAATTTAGCTTCTGGATCTGCACCT-CT--
1598326 ACCTCCACCACCTCCTCTTCATTCCAGGCAAGCAGCAAGTCCTGCAGCTTCATCATCGGCACCC
63 -CCT-C-CCACCTCCTCTTCATTCCAGGCAAGCAGCAAGTCCTGCAGCTTCATCATCGGCACCC
1598390 CCACC
1 CCACC
1598395 GCCACCGCCA
Statistics
Matches: 123, Mismatches: 2, Indels: 9
0.92 0.01 0.07
Matches are distributed among these distances:
120 59 0.48
122 1 0.01
126 2 0.02
129 61 0.50
ACGTcount: A:0.22, C:0.41, G:0.13, T:0.24
Consensus pattern (123 bp):
CCACCACCTCCTCCTCCAATGCCACCTTTGAAGGAAAATTTAGCTTCTGGATCTGCACCTCTCCT
CCCACCTCCTCTTCATTCCAGGCAAGCAGCAAGTCCTGCAGCTTCATCATCGGCACCC
Found at i:1598319 original size:60 final size:59
Alignment explanation
Indices: 1598141--1598331 Score: 147
Period size: 60 Copynumber: 3.2 Consensus size: 59
1598131 AGCTCCTCCA
1598141 CCACCACCTCCTCCTCCAATGCCACCTTTGAATGAAAATTTAGCTTCTGGATCTGCACCT
1 CCACCACCTCCTCCTCCAATGCCACCTTTGAA-GAAAATTTAGCTTCTGGATCTGCACCT
* * * * * * ** * * * * * * *
1598201 TCTCCACCTTCT-CTTC-ATTCCAGGC-AAGCAGCAAGTCCTGCAGCTTCAT-CATCGGCACCC
1 CCACCACCTCCTCCTCCAATGCCA-CCTTTGAAGAAAAT--T-TAGCTTC-TGGATCTGCACCT
1598261 CCACCACCTCCTCCTCCAATGCCACCTTTGAAGGAAAATTTAGCTTCTGGATCTGCACCT
1 CCACCACCTCCTCCTCCAATGCCACCTTTGAA-GAAAATTTAGCTTCTGGATCTGCACCT
*
1598321 CCTCCACCTCC
1 CCACCACCTCC
1598332 ACCACCTCCT
Statistics
Matches: 90, Mismatches: 31, Indels: 20
0.64 0.22 0.14
Matches are distributed among these distances:
57 4 0.04
58 7 0.08
59 6 0.07
60 56 0.62
61 6 0.07
62 7 0.08
63 4 0.04
ACGTcount: A:0.21, C:0.40, G:0.13, T:0.26
Consensus pattern (59 bp):
CCACCACCTCCTCCTCCAATGCCACCTTTGAAGAAAATTTAGCTTCTGGATCTGCACCT
Found at i:1608468 original size:45 final size:45
Alignment explanation
Indices: 1608404--1608566 Score: 200
Period size: 45 Copynumber: 3.6 Consensus size: 45
1608394 TGTACCAGAG
* *
1608404 GAGAAGCCTAACAAAGTTGTTGATGAAGAAAAGAAAATACCTGAA
1 GAGAAGCCTAACAAAGTTGTTAATGAAGAAAAGAAAATACATGAA
*
1608449 GAGAAGCCTGACAAAGTTGTTAATGAAGAAAAGAAAATACATGAA
1 GAGAAGCCTAACAAAGTTGTTAATGAAGAAAAGAAAATACATGAA
* * * ** ** *
1608494 GAAAAGCCTAAGAAAGCTGTTAATGAAGTGAAGAAGTTACAAGAA
1 GAGAAGCCTAACAAAGTTGTTAATGAAGAAAAGAAAATACATGAA
* * *
1608539 GATAAGCCTAGCAAAGTTGTCAATGAAG
1 GAGAAGCCTAACAAAGTTGTTAATGAAG
1608567 TGAAGAAACT
Statistics
Matches: 101, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 101 1.00
ACGTcount: A:0.48, C:0.10, G:0.23, T:0.18
Consensus pattern (45 bp):
GAGAAGCCTAACAAAGTTGTTAATGAAGAAAAGAAAATACATGAA
Found at i:1615519 original size:22 final size:22
Alignment explanation
Indices: 1615494--1615576 Score: 103
Period size: 22 Copynumber: 3.7 Consensus size: 22
1615484 CTAAAAAACG
*
1615494 AGTCACGCAATGCCTATCAATC
1 AGTCACGTAATGCCTATCAATC
* * *
1615516 AGTCATGTAATGTCATATCAACC
1 AGTCACGTAATG-CCTATCAATC
* *
1615539 AGTCACGTAATACCTAACAATC
1 AGTCACGTAATGCCTATCAATC
1615561 AGTCACGTAATGCCTA
1 AGTCACGTAATGCCTA
1615577 AAAATTAGTA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
22 32 0.64
23 18 0.36
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.25
Consensus pattern (22 bp):
AGTCACGTAATGCCTATCAATC
Found at i:1615623 original size:22 final size:22
Alignment explanation
Indices: 1615598--1615649 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1615588 TCCCATGTCT
*
1615598 AAAAACTAATTATACAATACCC
1 AAAAACTAATTACACAATACCC
* *
1615620 AAAAA-TCAATTACGCAATACCT
1 AAAAACT-AATTACACAATACCC
1615642 AAAAACTA
1 AAAAACTA
1615650 TTAAAACTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 1 0.04
22 23 0.92
23 1 0.04
ACGTcount: A:0.56, C:0.21, G:0.02, T:0.21
Consensus pattern (22 bp):
AAAAACTAATTACACAATACCC
Found at i:1617931 original size:129 final size:125
Alignment explanation
Indices: 1617565--1618266 Score: 764
Period size: 126 Copynumber: 5.5 Consensus size: 125
1617555 TATACGTATA
* * * * * *
1617565 TAATCAATTATTGAGAAA-AGCGAATGTTGAAGGAGTGAAATCGAACTTTGGGATATATTTGATG
1 TAATCAATTATTGA-AAAGA-AGAATGTCGAAGGAGTGAAACCGAACTTTGAGATATATTTAACG
*** * * * * * * * *
1617629 TACCAATAAAAGTAAGTGTGTCTATCTCCAACTCACTTTGATTGATAAAT-AACATAATGTT
64 TAATGACAAAAATATGTGTGTATATCTCCGATTCACTTTGATTGACAAATGAACATAACGTT
* * * *
1617690 TAATTAATTATTGGAAAAGAAGAATGTCGAAAGAGTATTGAAATCGAACTTTGGGATATATTTAA
1 TAATCAATTATT-GAAAAGAAGAATGTCG-AAG-G-AGTGAAACCGAACTTTGAGATATATTTAA
* * * * * *
1617755 CATAATGACAGAAATATGTATGTATATCTCCGATTTATTTTGATTGACAAATGAACATAACTTT
62 CGTAATGACAAAAATATGTGTGTATATCTCCGATTCACTTTGATTGACAAATGAACATAACGTT
* * *
1617819 TAATCAATTATTGAAGAAGAAGATTGTCGAAGGAGTGAAACCAAACTTTGAAATATATTTAACGT
1 TAATCAATTATTGAA-AAGAAGAATGTCGAAGGAGTGAAACCGAACTTTGAGATATATTTAACGT
* * **
1617884 AATGATAAAAATATGTGTGTGTATATCTCTGATTTCACTTTGATTGACAAATGAGTATAACGTT
65 AATGACAAAAATA--TGTGTGTATATCTCCGA-TTCACTTTGATTGACAAATGAACATAACGTT
* * *
1617948 TAATCAATTATTTAAAAAGAAGAATGTCGAAGCAAG-GAAACCGAACTTTGAAATATATTTAACG
1 TAATCAATTA-TTGAAAAGAAGAATGTCGAAG-GAGTGAAACCGAACTTTGAGATATATTTAACG
* *
1618012 TAATGACGAAAATATGTGTGTATATCTCCGATTCACTTTGATTGACAAATGAGCATAACGTT
64 TAATGACAAAAATATGTGTGTATATCTCCGATTCACTTTGATTGACAAATGAACATAACGTT
* * * * * *
1618074 TAATCAATTATTGAAAAAGAAAAATGTAGAAGTAGTGAAACCAAACTTTGAGATATATTTGACGC
1 TAATCAATTATTG-AAAAGAAGAATGTCGAAGGAGTGAAACCGAACTTTGAGATATATTTAACGT
* * * * *
1618139 AATAACAAAAGTATGTGTTTATATCTCCGATTCACTTTGA-TGACAAATGAAGAAAACGTT
65 AATGACAAAAATATGTGTGTATATCTCCGATTCACTTTGATTGACAAATGAACATAACGTT
* * * *
1618199 TAATCAATTATTAGAAAAGAAAAATGTCGAAGGAGTGAAACCGAACTCTGGGATATATTTGACGT
1 TAATCAATTATT-GAAAAGAAGAATGTCGAAGGAGTGAAACCGAACTTTGAGATATATTTAACGT
1618264 AAT
65 AAT
1618267 AATAAAGGTA
Statistics
Matches: 493, Mismatches: 69, Indels: 30
0.83 0.12 0.05
Matches are distributed among these distances:
125 102 0.21
126 161 0.33
127 18 0.04
128 84 0.17
129 122 0.25
130 6 0.01
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (125 bp):
TAATCAATTATTGAAAAGAAGAATGTCGAAGGAGTGAAACCGAACTTTGAGATATATTTAACGTA
ATGACAAAAATATGTGTGTATATCTCCGATTCACTTTGATTGACAAATGAACATAACGTT
Found at i:1618036 original size:255 final size:250
Alignment explanation
Indices: 1617565--1618354 Score: 775
Period size: 255 Copynumber: 3.1 Consensus size: 250
1617555 TATACGTATA
** * * * ** * *
1617565 TAATCAATTATTGAGAAAAG-CGAATGTTGAAGGAGTGAAATCGAACTTTGGGATATATTTGATG
1 TAATCAATTATTGA-AAAAGAAAAATGTAGAAGGAGTGAAACCAAACTTTGAAATATATTTAACG
* ** * * * * * * * * * * *
1617629 TACCAATAAAAGTAAGTGTGTCTATCTCCAACTCACTTTGATTGATAAATAACATAATGTTTAAT
65 CAATAACAAAAATATGTGTTTATATCTCCGATTCACTTTGATTGACAAATGAGATAACGTTTAAT
* ** * * *
1617694 TAATTATTGGAAAAGAAGAATGTCGAAAGAGTATTGAAATCGAACTTTGGGATATATTTAACATA
130 CAATTATTTAAAAAGAAGAATGTCG-AAGA--A-GGAAACCGAACTTTGGGATATATTTAACGTA
* * *
1617759 ATGACAGAAATATGTATGTATATCTCCGATTTATTTTGATTGACAAATGAACATAACTTT
191 ATGACAGAAATATGTATGTATATCTCCGATTCACTTTGATTGACAAATGAACATAACGTT
* * * * *
1617819 TAATCAATTATTGAAGAAGAAGATTGTCGAAGGAGTGAAACCAAACTTTGAAATATATTTAACGT
1 TAATCAATTATTGAAAAAGAAAAATGTAGAAGGAGTGAAACCAAACTTTGAAATATATTTAACGC
* * *
1617884 AATGATAAAAATATGTGTGTGTATATCTCTGATTTCACTTTGATTGACAAATGAGTATAACGTTT
66 AATAACAAAAATATGTGT-T-TATATCTCCGA-TTCACTTTGATTGACAAATGAG-ATAACGTTT
**
1617949 AATCAATTATTTAAAAAGAAGAATGTCGAAGCAAGGAAACCGAACTTTGAAATATATTTAACGTA
127 AATCAATTATTTAAAAAGAAGAATGTCGAAG-AAGGAAACCGAACTTTGGGATATATTTAACGTA
* *
1618014 ATGAC-GAAAATATGTGTGTATATCTCCGATTCACTTTGATTGACAAATGAGCATAACGTT
191 ATGACAG-AAATATGTATGTATATCTCCGATTCACTTTGATTGACAAATGAACATAACGTT
* * *
1618074 TAATCAATTATTGAAAAAGAAAAATGTAGAAGTAGTGAAACCAAACTTTGAGATATATTTGACGC
1 TAATCAATTATTGAAAAAGAAAAATGTAGAAGGAGTGAAACCAAACTTTGAAATATATTTAACGC
* *
1618139 AATAACAAAAGTATGTGTTTATATCTCCGATTCACTTTGA-TGACAAATGAAGAAAACGTTTAAT
66 AATAACAAAAATATGTGTTTATATCTCCGATTCACTTTGATTGACAAATG-AGATAACGTTTAAT
* * * *
1618203 CAATTA-TTAGAAAAGAAAAATGTCGAAGGAGTGAAACCGAACTCTGGGATATATTTGACGTAAT
130 CAATTATTTA-AAAAGAAGAATGTCGAAGAAG-GAAACCGAACTTTGGGATATATTTAACGTAAT
* * * ** * * * * *
1618267 -A-ATAAAGGTACGTGCATGCATGTATCTTTGACTCACCTTAATTGAAAAATAAACATAACGTT
193 GACAGAAA--TA--TGTATG--TATATCTCCGATTCACTTTGATTGACAAATGAACATAACGTT
*
1618329 TAATCAATTATT-AAAAAAAAAAATGT
1 TAATCAATTATTGAAAAAGAAAAATGT
1618355 TGACGCAACG
Statistics
Matches: 450, Mismatches: 69, Indels: 34
0.81 0.12 0.06
Matches are distributed among these distances:
249 3 0.01
250 6 0.01
251 73 0.16
252 12 0.03
253 18 0.04
254 78 0.17
255 196 0.44
256 9 0.02
257 21 0.05
258 34 0.08
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.32
Consensus pattern (250 bp):
TAATCAATTATTGAAAAAGAAAAATGTAGAAGGAGTGAAACCAAACTTTGAAATATATTTAACGC
AATAACAAAAATATGTGTTTATATCTCCGATTCACTTTGATTGACAAATGAGATAACGTTTAATC
AATTATTTAAAAAGAAGAATGTCGAAGAAGGAAACCGAACTTTGGGATATATTTAACGTAATGAC
AGAAATATGTATGTATATCTCCGATTCACTTTGATTGACAAATGAACATAACGTT
Found at i:1621173 original size:13 final size:13
Alignment explanation
Indices: 1621155--1621179 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1621145 GACTTAAATT
1621155 AACAAAAAAAAAA
1 AACAAAAAAAAAA
1621168 AACAAAAAAAAA
1 AACAAAAAAAAA
1621180 TATGTTGATG
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:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
AACAAAAAAAAAA
Found at i:1634295 original size:150 final size:150
Alignment explanation
Indices: 1633993--1634287 Score: 547
Period size: 150 Copynumber: 2.0 Consensus size: 150
1633983 TAAGCCTTTC
*
1633993 AATATTTCATTGAATAAAAGTTCGAAGTTACTTCAATTGTAACTCTCCAAACAGAGAACAAAAGA
1 AATATTTCATTGAATAAAAGTTCGAAGTTACTTCAATTGTAACTCTCAAAACAGAGAACAAAAGA
1634058 TTTTCTGGACAATAGTCCTATAGAACCTGTTAGCCCATAAGGACATGTACAGGGCTAACAGGTTC
66 TTTTCTGGACAATAGTCCTATAGAACCTGTTAGCCCATAAGGACATGTACAGGGCTAACAGGTTC
1634123 TATAGGACTTATGTCCAAAA
131 TATAGGACTTATGTCCAAAA
*
1634143 AATATTTCATTGAATAAAAGTTCGGAGTTACTTCAATTGTAACTCTCAAAACAGAGAACAAAAGA
1 AATATTTCATTGAATAAAAGTTCGAAGTTACTTCAATTGTAACTCTCAAAACAGAGAACAAAAGA
*
1634208 TTTTTTGGAC-ATAAGTCCTATAGAACCTGTTAGCCCATAAGGACATGTACAGGGCTAACAGGTT
66 TTTTCTGGACAAT-AGTCCTATAGAACCTGTTAGCCCATAAGGACATGTACAGGGCTAACAGGTT
1634272 CTATAGGACTTATGTC
130 CTATAGGACTTATGTC
1634288 TAGAAAATCT
Statistics
Matches: 141, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
149 2 0.01
150 139 0.99
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (150 bp):
AATATTTCATTGAATAAAAGTTCGAAGTTACTTCAATTGTAACTCTCAAAACAGAGAACAAAAGA
TTTTCTGGACAATAGTCCTATAGAACCTGTTAGCCCATAAGGACATGTACAGGGCTAACAGGTTC
TATAGGACTTATGTCCAAAA
Found at i:1639757 original size:19 final size:19
Alignment explanation
Indices: 1639735--1639807 Score: 60
Period size: 19 Copynumber: 3.8 Consensus size: 19
1639725 NNNTTTTTTT
* *
1639735 TTTTTTTTTTTTTTTTCAA
1 TTTTATTTTATTTTTTCAA
1639754 TTTTATTTTATTTTTTC-A
1 TTTTATTTTATTTTTTCAA
* **
1639772 -TATATTTTAAGTTTTCATAA
1 TTTTATTTTATTTTTTC--AA
*
1639792 TTTTTTTTTATTTTTT
1 TTTTATTTTATTTTTT
1639808 AAATCACCAA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
17 13 0.32
18 1 0.02
19 15 0.37
20 1 0.02
21 11 0.27
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.77
Consensus pattern (19 bp):
TTTTATTTTATTTTTTCAA
Found at i:1639777 original size:17 final size:17
Alignment explanation
Indices: 1639757--1639800 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
1639747 TTTTCAATTT
1639757 TATTTTATTTTTTCATA
1 TATTTTATTTTTTCATA
**
1639774 TATTTTAAGTTTTCATA
1 TATTTTATTTTTTCATA
1639791 -ATTTT-TTTTT
1 TATTTTATTTTT
1639801 ATTTTTTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 3 0.13
16 5 0.22
17 15 0.65
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (17 bp):
TATTTTATTTTTTCATA
Found at i:1639902 original size:15 final size:16
Alignment explanation
Indices: 1639882--1639916 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1639872 CTGTTATATG
*
1639882 AATTTT-ATTTTTAAT
1 AATTTTAATTTTTAAA
1639897 AATTTTAATTTTTAAA
1 AATTTTAATTTTTAAA
1639913 AATT
1 AATT
1639917 AAAAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
AATTTTAATTTTTAAA
Found at i:1640218 original size:16 final size:16
Alignment explanation
Indices: 1640199--1640233 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1640189 TATAATAAAA
*
1640199 TGAGAATATTGGATAT
1 TGAGAATATTAGATAT
1640215 TGAGAATATTAGATAT
1 TGAGAATATTAGATAT
1640231 TGA
1 TGA
1640234 CTATATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.37
Consensus pattern (16 bp):
TGAGAATATTAGATAT
Found at i:1640239 original size:16 final size:16
Alignment explanation
Indices: 1640203--1640241 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1640193 ATAAAATGAG
* *
1640203 AATATTGGATATTGAG
1 AATATTAGATATTGAC
1640219 AATATTAGATATTGAC
1 AATATTAGATATTGAC
*
1640235 TATATTA
1 AATATTA
1640242 ATTTTTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.41, C:0.03, G:0.15, T:0.41
Consensus pattern (16 bp):
AATATTAGATATTGAC
Found at i:1640768 original size:18 final size:18
Alignment explanation
Indices: 1640745--1640784 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1640735 ACATAGCTTA
*
1640745 TTATTTATATTATTTATT
1 TTATTTATATTATTTAAT
* *
1640763 TTATTTTTATTTTTTAAT
1 TTATTTATATTATTTAAT
1640781 TTAT
1 TTAT
1640785 CATATATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (18 bp):
TTATTTATATTATTTAAT
Found at i:1657698 original size:2 final size:2
Alignment explanation
Indices: 1657687--1657726 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
1657677 AAAATCATGG
1657687 TC TC -C TC TC TC TC TC TC TC -C TC ATC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC -TC TC TC TC TC TC TC TC T
1657727 TTTATCATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 31 0.89
3 2 0.06
ACGTcount: A:0.03, C:0.50, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:1658385 original size:2 final size:2
Alignment explanation
Indices: 1658380--1658404 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1658370 AANNNGAGAG
1658380 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
1658405 AATAAAATTT
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:1665250 original size:47 final size:47
Alignment explanation
Indices: 1665158--1665250 Score: 123
Period size: 47 Copynumber: 2.0 Consensus size: 47
1665148 ACATCTTTCT
* *
1665158 CACTTCAACAAGGGCCTAACTCCACTTTAATATCAACTATTACGATC
1 CACTTCAACAAAGGCCTAACTCCACTTTAATATCAACTATCACGATC
* * ** *
1665205 CACTTCAATAAAGGCTTAACTTTACTTTAATATCAACTGTCACGAT
1 CACTTCAACAAAGGCCTAACTCCACTTTAATATCAACTATCACGAT
1665251 TCACACTAAC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
47 39 1.00
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (47 bp):
CACTTCAACAAAGGCCTAACTCCACTTTAATATCAACTATCACGATC
Found at i:1671507 original size:17 final size:18
Alignment explanation
Indices: 1671477--1671510 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1671467 TAAATATTTT
*
1671477 TAAAAAATTAATTAAATA
1 TAAAAAAATAATTAAATA
1671495 TAAAAAAAT-ATTAAAT
1 TAAAAAAATAATTAAAT
1671511 CGATTAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAAAAATAATTAAATA
Found at i:1671672 original size:22 final size:22
Alignment explanation
Indices: 1671647--1671702 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
1671637 TTATGTATAA
1671647 ATTAAATACATATATATAAT-AT
1 ATTAAATACATATATAT-ATGAT
**
1671669 ATTACTTTAC-TATATATATGAT
1 ATTA-AATACATATATATATGAT
1671691 ATTAAATACATA
1 ATTAAATACATA
1671703 ACTTATATGT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
21 5 0.19
22 19 0.70
23 3 0.11
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (22 bp):
ATTAAATACATATATATATGAT
Found at i:1704142 original size:2 final size:2
Alignment explanation
Indices: 1704135--1704163 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1704125 AATGTTCTTT
1704135 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1704164 CTTTTTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1706076 original size:4 final size:4
Alignment explanation
Indices: 1706067--1706096 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
1706057 TCATGTTGTG
1706067 GATA GATA GATA GATA GATA GATA GATA GA
1 GATA GATA GATA GATA GATA GATA GATA GA
1706097 GGTTCTGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.27, T:0.23
Consensus pattern (4 bp):
GATA
Found at i:1717617 original size:13 final size:13
Alignment explanation
Indices: 1717599--1717624 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1717589 ATTATCAAGG
1717599 ACAATGTGAAACT
1 ACAATGTGAAACT
1717612 ACAATGTGAAACT
1 ACAATGTGAAACT
1717625 CAAGACATCT
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:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
ACAATGTGAAACT
Found at i:1718126 original size:2 final size:2
Alignment explanation
Indices: 1718119--1718143 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1718109 CAGAGTGAAA
1718119 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1718144 ATCTAGAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1719850 original size:138 final size:138
Alignment explanation
Indices: 1719602--1719877 Score: 489
Period size: 138 Copynumber: 2.0 Consensus size: 138
1719592 TGGTGTTCAA
* *
1719602 AAGAAGGGGAGAACTTCTTACATTCCTAACCTGCCTAGACAAATACATGCAAGCTCTATTTTCTT
1 AAGAAGGGGAGAACTTCTCACATTCCTAACCTGCCTAGACAAATACATGCAAGCTCAATTTTCTT
1719667 TCTTTCTTCCACACACGATTGTATGCCTTCTTTTGTGTTTGTACGATACAACCGTGTAATCATAA
66 TCTTTCTTCCACACACGATTGTATGCCTTCTTTTGTGTTTGTACGATACAACCGTGTAATCATAA
1719732 GCTGGCAT
131 GCTGGCAT
* *
1719740 AAGAAGGGGGGAACTTCTCACATTCCTAACCTGCCTAGATAAATACATGCAAGCTCAATTTTCTT
1 AAGAAGGGGAGAACTTCTCACATTCCTAACCTGCCTAGACAAATACATGCAAGCTCAATTTTCTT
* * *
1719805 TCTTTCTTCTATACACGATTGTATGCCTTCTTTTGTGTTTGTACGATACTACCGTGTAATCATAA
66 TCTTTCTTCCACACACGATTGTATGCCTTCTTTTGTGTTTGTACGATACAACCGTGTAATCATAA
1719870 GCTGGCAT
131 GCTGGCAT
1719878 GCAGAATCTG
Statistics
Matches: 131, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
138 131 1.00
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.35
Consensus pattern (138 bp):
AAGAAGGGGAGAACTTCTCACATTCCTAACCTGCCTAGACAAATACATGCAAGCTCAATTTTCTT
TCTTTCTTCCACACACGATTGTATGCCTTCTTTTGTGTTTGTACGATACAACCGTGTAATCATAA
GCTGGCAT
Found at i:1764806 original size:54 final size:54
Alignment explanation
Indices: 1764724--1764833 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
1764714 TTACTGTGGA
1764724 ATGAAATCAACGGCATCGGCCTGATGGCAACAGATGGGCCTTTCTCTTGTCTTC
1 ATGAAATCAACGGCATCGGCCTGATGGCAACAGATGGGCCTTTCTCTTGTCTTC
1764778 ATGAAATCAACGGCATCGGCCTGATGGCAACAGATGGGCCTTTCTCTTGTCTTC
1 ATGAAATCAACGGCATCGGCCTGATGGCAACAGATGGGCCTTTCTCTTGTCTTC
1764832 AT
1 AT
1764834 ATGGCAAGGG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.28
Consensus pattern (54 bp):
ATGAAATCAACGGCATCGGCCTGATGGCAACAGATGGGCCTTTCTCTTGTCTTC
Found at i:1780736 original size:20 final size:20
Alignment explanation
Indices: 1780711--1780749 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1780701 GGGGCTCGGG
* *
1780711 TTTGCGCTGGCAGGAGAGGT
1 TTTGCGCCGACAGGAGAGGT
1780731 TTTGCGCCGACAGGAGAGG
1 TTTGCGCCGACAGGAGAGG
1780750 AAGCCCGACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.44, T:0.21
Consensus pattern (20 bp):
TTTGCGCCGACAGGAGAGGT
Found at i:1780836 original size:71 final size:71
Alignment explanation
Indices: 1780744--1780935 Score: 258
Period size: 71 Copynumber: 2.7 Consensus size: 71
1780734 GCGCCGACAG
* * *
1780744 GAGAGGAAGCCCGACCGTCGCGCTACCAGATCTGGCGCAATGAAGAGAGGAGAGACACGCGATCG
1 GAGAGGAAGCCCGACCGTCGCGCCACCAGATCTGGCGCAAGGAAGAGAGGAGAGACACCCGATCG
1780809 GCGGTA
66 GCGGTA
* * * * * * * *
1780815 GAGAGTAAGCCCGACCCTCGCGCCACCAGATCTGACGTAGGGAAGAGAGGGGAGATACCCGATCT
1 GAGAGGAAGCCCGACCGTCGCGCCACCAGATCTGGCGCAAGGAAGAGAGGAGAGACACCCGATCG
1780880 GCGGTA
66 GCGGTA
* * *
1780886 GAGAGGAAGCCCGACCGTCGCGCCACCAGATCCGGAGCGAGGAAGAGAGG
1 GAGAGGAAGCCCGACCGTCGCGCCACCAGATCTGGCGCAAGGAAGAGAGG
1780936 GAGCTGTCGG
Statistics
Matches: 102, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
71 102 1.00
ACGTcount: A:0.28, C:0.27, G:0.36, T:0.09
Consensus pattern (71 bp):
GAGAGGAAGCCCGACCGTCGCGCCACCAGATCTGGCGCAAGGAAGAGAGGAGAGACACCCGATCG
GCGGTA
Found at i:1781898 original size:13 final size:12
Alignment explanation
Indices: 1781871--1781926 Score: 60
Period size: 13 Copynumber: 4.5 Consensus size: 12
1781861 ACATGACATT
1781871 AAATAAATAAAA
1 AAATAAATAAAA
*
1781883 AAATAACATTAAA
1 AAATAA-ATAAAA
1781896 AAATAAATAATAA
1 AAATAAATAA-AA
1781909 AAA-AAATCAAAA
1 AAATAAAT-AAAA
*
1781921 CAATAA
1 AAATAA
1781927 CTAATTTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
12 17 0.46
13 20 0.54
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (12 bp):
AAATAAATAAAA
Found at i:1781925 original size:25 final size:26
Alignment explanation
Indices: 1781871--1781931 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
1781861 ACATGACATT
*
1781871 AAATAAATAA-AAAAATAACATTAAA
1 AAATAAATAATAAAAATAACATCAAA
1781896 AAATAAATAATAAAAA-AA-ATCAAA
1 AAATAAATAATAAAAATAACATCAAA
*
1781920 ACAATAACTAAT
1 A-AATAAATAAT
1781932 TTAAAATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 6 0.19
25 21 0.66
26 5 0.16
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.20
Consensus pattern (26 bp):
AAATAAATAATAAAAATAACATCAAA
Found at i:1783923 original size:30 final size:30
Alignment explanation
Indices: 1783882--1783945 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
1783872 ATCCTCTTCA
1783882 TCATAATTTCTATGATCATTTTGAATCTCT
1 TCATAATTTCTATGATCATTTTGAATCTCT
*
1783912 TCATGATTTCTATGATCATTTTGAATCTCT
1 TCATAATTTCTATGATCATTTTGAATCTCT
1783942 TCAT
1 TCAT
1783946 TAACATCTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (30 bp):
TCATAATTTCTATGATCATTTTGAATCTCT
Found at i:1784765 original size:17 final size:18
Alignment explanation
Indices: 1784743--1784784 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
1784733 TTTTATTAAT
1784743 TATTTTTT-ATTTTTATA
1 TATTTTTTAATTTTTATA
1784760 TATTTTTTAATTTTTATA
1 TATTTTTTAATTTTTATA
1784778 TATTTTT
1 TATTTTT
1784785 AATATAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
TATTTTTTAATTTTTATA
Found at i:1784768 original size:11 final size:10
Alignment explanation
Indices: 1784750--1784789 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
1784740 AATTATTTTT
1784750 TATTTTTATA
1 TATTTTTATA
1784760 TATTTTT-TA
1 TATTTTTATA
1784769 -ATTTTTATA
1 TATTTTTATA
1784778 TATTTTTA-A
1 TATTTTTATA
1784787 TAT
1 TAT
1784790 AATTAATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 6 0.21
9 8 0.29
10 14 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TATTTTTATA
Found at i:1785753 original size:18 final size:16
Alignment explanation
Indices: 1785706--1785756 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 16
1785696 ACCAAATTAC
*
1785706 AAAAGTATTAGGTTG-
1 AAAATTATTAGGTTGA
*
1785721 AAAATT-TTGGGTTGA
1 AAAATTATTAGGTTGA
1785736 CAAAATTTATTAGGTTGA
1 -AAAA-TTATTAGGTTGA
1785754 AAA
1 AAA
1785757 TTTTTAGAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 7 0.24
15 5 0.17
16 4 0.14
17 5 0.17
18 8 0.28
ACGTcount: A:0.41, C:0.02, G:0.22, T:0.35
Consensus pattern (16 bp):
AAAATTATTAGGTTGA
Found at i:1785756 original size:16 final size:15
Alignment explanation
Indices: 1785713--1785763 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
1785703 TACAAAAGTA
1785713 TTAGGTTGAAAA-TT
1 TTAGGTTGAAAATTT
*
1785727 TTGGGTTGACAAAATTT
1 TTAGGTTG--AAAATTT
1785744 ATTAGGTTGAAAATTT
1 -TTAGGTTGAAAATTT
1785760 TTAG
1 TTAG
1785764 AGTGATAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 7 0.23
15 4 0.13
16 11 0.35
17 2 0.06
18 7 0.23
ACGTcount: A:0.33, C:0.02, G:0.22, T:0.43
Consensus pattern (15 bp):
TTAGGTTGAAAATTT
Found at i:1786221 original size:16 final size:14
Alignment explanation
Indices: 1786180--1786220 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1786170 TCTTTGGAGC
**
1786180 TTTTTTTTAAGCTT
1 TTTTTTTTAAAATT
1786194 TTTTTTTTAAAATT
1 TTTTTTTTAAAATT
1786208 TTGTTTTTTAAAA
1 TT-TTTTTTAAAA
1786221 AAAAATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 14 0.58
15 10 0.42
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68
Consensus pattern (14 bp):
TTTTTTTTAAAATT
Found at i:1813090 original size:122 final size:122
Alignment explanation
Indices: 1812939--1813183 Score: 490
Period size: 122 Copynumber: 2.0 Consensus size: 122
1812929 GAATACTTGA
1812939 TTCCATCCATAGAATACATTAAATGTAAAGCATGAAATAACACATTAAGACCCTCCATTAGAAAG
1 TTCCATCCATAGAATACATTAAATGTAAAGCATGAAATAACACATTAAGACCCTCCATTAGAAAG
1813004 GCTACCGTTGGGCAAGGATTGGAAGCCAAACCTCAGTTGCAGTATAACATAGCTTTT
66 GCTACCGTTGGGCAAGGATTGGAAGCCAAACCTCAGTTGCAGTATAACATAGCTTTT
1813061 TTCCATCCATAGAATACATTAAATGTAAAGCATGAAATAACACATTAAGACCCTCCATTAGAAAG
1 TTCCATCCATAGAATACATTAAATGTAAAGCATGAAATAACACATTAAGACCCTCCATTAGAAAG
1813126 GCTACCGTTGGGCAAGGATTGGAAGCCAAACCTCAGTTGCAGTATAACATAGCTTTT
66 GCTACCGTTGGGCAAGGATTGGAAGCCAAACCTCAGTTGCAGTATAACATAGCTTTT
1813183 T
1 T
1813184 GTTAGTATGA
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
122 123 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (122 bp):
TTCCATCCATAGAATACATTAAATGTAAAGCATGAAATAACACATTAAGACCCTCCATTAGAAAG
GCTACCGTTGGGCAAGGATTGGAAGCCAAACCTCAGTTGCAGTATAACATAGCTTTT
Found at i:1832924 original size:21 final size:21
Alignment explanation
Indices: 1832894--1832934 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1832884 ATTCATATAG
* *
1832894 TATTTTTAAATTTTAATTAAA
1 TATTTATAAAATTTAATTAAA
*
1832915 TATTTATAAAATTTAGTTAA
1 TATTTATAAAATTTAATTAA
1832935 CTTAACAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TATTTATAAAATTTAATTAAA
Found at i:1832939 original size:26 final size:25
Alignment explanation
Indices: 1832906--1832954 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
1832896 TTTTTAAATT
*
1832906 TTAATTAA-ATATTTATAAAATTTAG
1 TTAATTAACA-ATTAATAAAATTTAG
1832931 TTAACTTAACAATTAATAAAATTT
1 TTAA-TTAACAATTAATAAAATTT
1832955 GATATAGGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 4 0.19
26 16 0.76
27 1 0.05
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (25 bp):
TTAATTAACAATTAATAAAATTTAG
Found at i:1833404 original size:21 final size:21
Alignment explanation
Indices: 1833378--1833418 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1833368 ATCTCAATAA
* *
1833378 ATATTTTTTAATTTTAATTAG
1 ATATTTATAAATTTTAATTAG
1833399 ATATTTATAAATTTTAATTA
1 ATATTTATAAATTTTAATTA
1833419 TTTTATCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
ATATTTATAAATTTTAATTAG
Found at i:1833406 original size:93 final size:93
Alignment explanation
Indices: 1833147--1833406 Score: 351
Period size: 93 Copynumber: 2.8 Consensus size: 93
1833137 AAATTTGAGA
* * * *
1833147 ATTTAATGAG-TACTGTTTAAAATATCAAAATACAAATTTTGATAAATATTTATAAATTTTAATT
1 ATTTAATGAGTTA-TGTATAAAATATTAAAATACAAATTTTAATAAATATTTTTAAATTTTAATT
* *
1833211 AGATATTTAATTTGTAAAATCGAGTATGT
65 AGATATTTATTTTGTAAAATCAAGTATGT
* * * *
1833240 ATTTAATGAGTAATATATAAAATATTAAAATACAAATTTTAATAAATATTTTTAAATTTTGATTG
1 ATTTAATGAGTTATGTATAAAATATTAAAATACAAATTTTAATAAATATTTTTAAATTTTAATTA
*
1833305 GATGTTTATTTTGTAAAATCAAGTATGT
66 GATATTTATTTTGTAAAATCAAGTATGT
* ** * * *
1833333 ATTTAATGAGTTATGTCTAAAATATTAAAATATGAATCTCAATAAATATTTTTTAATTTTAATTA
1 ATTTAATGAGTTATGTATAAAATATTAAAATACAAATTTTAATAAATATTTTTAAATTTTAATTA
1833398 GATATTTAT
66 GATATTTAT
1833407 AAATTTTAAT
Statistics
Matches: 144, Mismatches: 22, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
93 143 0.99
94 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (93 bp):
ATTTAATGAGTTATGTATAAAATATTAAAATACAAATTTTAATAAATATTTTTAAATTTTAATTA
GATATTTATTTTGTAAAATCAAGTATGT
Found at i:1850715 original size:18 final size:18
Alignment explanation
Indices: 1850689--1850726 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1850679 AACGTCTGAG
*
1850689 TTGCTTTTTTATATATCA
1 TTGCCTTTTTATATATCA
1850707 TTGCCTTTTTATATATCA
1 TTGCCTTTTTATATATCA
1850725 TT
1 TT
1850727 ACTCCAATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.13, G:0.05, T:0.61
Consensus pattern (18 bp):
TTGCCTTTTTATATATCA
Found at i:1860751 original size:17 final size:15
Alignment explanation
Indices: 1860720--1860761 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
1860710 TTCAATAAAT
*
1860720 TTTTTA-TTATTATA
1 TTTTTATTTTTTATA
1860734 TTTAATTATTTTTTATA
1 TTT--TTATTTTTTATA
1860751 TTTTTATTTTT
1 TTTTTATTTTT
1860762 AATTAAATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 3 0.12
15 8 0.33
16 3 0.12
17 10 0.42
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTATTTTTTATA
Found at i:1860752 original size:25 final size:24
Alignment explanation
Indices: 1860719--1860766 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
1860709 TTTCAATAAA
1860719 TTTTTTATTATTATATTTAATTAT
1 TTTTTTATTATTATATTTAATTAT
* *
1860743 TTTTTATATTTTTATTTTTAATTA
1 TTTTT-TATTATTATATTTAATTA
1860767 AATAGTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTTTTATTATTATATTTAATTAT
Found at i:1860831 original size:30 final size:30
Alignment explanation
Indices: 1860797--1860854 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1860787 AATCATTAAG
*
1860797 TATAAAAATTTATTTGATTTAAAATAAATA
1 TATAAAAATTTATTTAATTTAAAATAAATA
**
1860827 TATAAATTTTTATTTAATTTAAAATAAA
1 TATAAAAATTTATTTAATTTAAAATAAA
1860855 AAACTTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (30 bp):
TATAAAAATTTATTTAATTTAAAATAAATA
Found at i:1860864 original size:19 final size:20
Alignment explanation
Indices: 1860840--1860877 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1860830 AAATTTTTAT
*
1860840 TTAATTTAAAATAA-AAAAC
1 TTAATTAAAAATAATAAAAC
1860859 TTAATTAAAAATAATAAAA
1 TTAATTAAAAATAATAAAA
1860878 ATTTAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (20 bp):
TTAATTAAAAATAATAAAAC
Found at i:1871276 original size:30 final size:28
Alignment explanation
Indices: 1871241--1871306 Score: 87
Period size: 30 Copynumber: 2.3 Consensus size: 28
1871231 AATTATTAAT
*
1871241 AATAAAAATTCATATAACTTAAAATAAAA
1 AATAAAAATTCATATAA-ATAAAATAAAA
* *
1871270 ATATAAAAATTCATTTAAATATAATAAAA
1 A-ATAAAAATTCATATAAATAAAATAAAA
1871299 AATAAAAA
1 AATAAAAA
1871307 AATTAACTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 7 0.21
29 11 0.33
30 15 0.45
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (28 bp):
AATAAAAATTCATATAAATAAAATAAAA
Found at i:1871345 original size:18 final size:18
Alignment explanation
Indices: 1871311--1871345 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1871301 TAAAAAAATT
* *
1871311 AACTTTTTTAAATTTTAA
1 AACTTTTTAAAAATTTAA
1871329 AACTTTTTAAAAATTTA
1 AACTTTTTAAAAATTTA
1871346 CCAAAAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (18 bp):
AACTTTTTAAAAATTTAA
Found at i:1885413 original size:60 final size:60
Alignment explanation
Indices: 1885341--1885464 Score: 239
Period size: 60 Copynumber: 2.1 Consensus size: 60
1885331 TGTCACCATA
*
1885341 TGAGGTTTCAGTTTTGGTAGTGATACAAAACTTACACCCTTATTTTGAGGAACAAAGATT
1 TGAGGTTTCAGTTTTGGTAGTGATACAAAACTTACACCCTTATTTTGAGGAACAAAGAAT
1885401 TGAGGTTTCAGTTTTGGTAGTGATACAAAACTTACACCCTTATTTTGAGGAACAAAGAAT
1 TGAGGTTTCAGTTTTGGTAGTGATACAAAACTTACACCCTTATTTTGAGGAACAAAGAAT
1885461 TGAG
1 TGAG
1885465 CTTAGCGGCA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (60 bp):
TGAGGTTTCAGTTTTGGTAGTGATACAAAACTTACACCCTTATTTTGAGGAACAAAGAAT
Found at i:1891919 original size:51 final size:51
Alignment explanation
Indices: 1891859--1891978 Score: 168
Period size: 51 Copynumber: 2.4 Consensus size: 51
1891849 GATAGAGTAT
* * *
1891859 ATTGATGTTCAAAAAAGTACATGTTCAGAAATAAGCAACATGGTAGTGTAA
1 ATTGATGTTCAAAAAAGTACATGTTCAGAAAAAAACAACATGGTAATGTAA
* * *
1891910 ATTGATGTTCGAAAAAGTATATGTTCAGAAAAAAACTACATGGTAATGTAA
1 ATTGATGTTCAAAAAAGTACATGTTCAGAAAAAAACAACATGGTAATGTAA
**
1891961 ATTGATGTTTTAAAAAGT
1 ATTGATGTTCAAAAAAGT
1891979 TTAATTATCC
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.43, C:0.07, G:0.18, T:0.31
Consensus pattern (51 bp):
ATTGATGTTCAAAAAAGTACATGTTCAGAAAAAAACAACATGGTAATGTAA
Found at i:1894305 original size:74 final size:75
Alignment explanation
Indices: 1894216--1894356 Score: 239
Period size: 75 Copynumber: 1.9 Consensus size: 75
1894206 AGAGGGTATG
* * *
1894216 TGATAGTTCGAGTGGTTCTT-ACCTAAAGAAAGTTTTTAATGGAATATAGTATTAGACATTGTTA
1 TGATAGTTCGAGTGGTTCTTAACCAAAAGAAAGTTTTTAATGGAATAAAATATTAGACATTGTTA
1894280 AGGTATATTT
66 AGGTATATTT
*
1894290 TGATAGTTCGAGTGGTTCTTAACCAAAAGAAATTTTTTAATGGAATAAAATATTAGACATTGTTA
1 TGATAGTTCGAGTGGTTCTTAACCAAAAGAAAGTTTTTAATGGAATAAAATATTAGACATTGTTA
1894355 AG
66 AG
1894357 TTAGATGCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
74 20 0.32
75 42 0.68
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.38
Consensus pattern (75 bp):
TGATAGTTCGAGTGGTTCTTAACCAAAAGAAAGTTTTTAATGGAATAAAATATTAGACATTGTTA
AGGTATATTT
Found at i:1906602 original size:28 final size:28
Alignment explanation
Indices: 1906562--1906620 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
1906552 AGGGGAGTCA
1906562 TGAATTGACTCATAAATCTTAAATTAAC
1 TGAATTGACTCATAAATCTTAAATTAAC
* * *
1906590 TGAATTGAGTCATTAATCTTACATTAAC
1 TGAATTGACTCATAAATCTTAAATTAAC
1906618 TGA
1 TGA
1906621 CATTATAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (28 bp):
TGAATTGACTCATAAATCTTAAATTAAC
Found at i:1906632 original size:24 final size:24
Alignment explanation
Indices: 1906573--1906639 Score: 64
Period size: 28 Copynumber: 2.6 Consensus size: 24
1906563 GAATTGACTC
*
1906573 ATAAATCTTAAATTAACTGAATTG
1 ATAAATCTTACATTAACTGAATTG
1906597 AGTCATTAATCTTACATTAACTGACATT-
1 A-T-A--AATCTTACATTAACTGA-ATTG
*
1906625 ATAAATCTCACATTA
1 ATAAATCTTACATTA
1906640 TCTAGGCATT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
24 12 0.33
25 1 0.03
26 2 0.06
27 1 0.03
28 17 0.47
29 3 0.08
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.37
Consensus pattern (24 bp):
ATAAATCTTACATTAACTGAATTG
Found at i:1920753 original size:18 final size:18
Alignment explanation
Indices: 1920730--1920774 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
1920720 CTAGATGATG
1920730 TTCTTCTTCCTCCTCCTC
1 TTCTTCTTCCTCCTCCTC
*
1920748 TTCTTCTTCCTCTTCCTC
1 TTCTTCTTCCTCCTCCTC
1920766 TTCTTCTTC
1 TTCTTCTTC
1920775 AATAGCGAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (18 bp):
TTCTTCTTCCTCCTCCTC
Found at i:1920755 original size:6 final size:6
Alignment explanation
Indices: 1920734--1920774 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
1920724 ATGATGTTCT
* * *
1920734 TCTTCC TCCTCC TCTTCT TCTTCC TCTTCC TCTTCT TCTTC
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTC
1920775 AATAGCGAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (6 bp):
TCTTCC
Found at i:1922107 original size:19 final size:19
Alignment explanation
Indices: 1922049--1922107 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 19
1922039 TATTATAATT
1922049 AATA-TTAATTAAATTATAAA
1 AATATTTAATTAAA-TAT-AA
*
1922069 ATATATTTGATTTAAA-ATAA
1 A-ATATTT-AATTAAATATAA
1922089 AATATTTAATTAAATATAA
1 AATATTTAATTAAATATAA
1922108 TAAAAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
18 6 0.18
19 10 0.30
20 4 0.12
21 5 0.15
22 2 0.06
23 6 0.18
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
AATATTTAATTAAATATAA
Found at i:1922777 original size:4 final size:4
Alignment explanation
Indices: 1922768--1922794 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1922758 CAGAATTATA
1922768 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
1922795 AAGGAATTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:1926386 original size:87 final size:87
Alignment explanation
Indices: 1926287--1926633 Score: 505
Period size: 87 Copynumber: 4.0 Consensus size: 87
1926277 GTTAAGCACA
* ** **
1926287 TTATTCATGTTCTTCTCACAGGACACTTTTGCAGCACTAGCAAGCTTTGCTTTCTTATGTGGCCT
1 TTATTCATGTTCTTGTCATTGGACACTTTCACAGCACTAGCAAGCTTTGCTTTCTTATGTGGCCT
1926352 CTCATCTACCTCACCTGAATCT
66 CTCATCTACCTCACCTGAATCT
* * *
1926374 TTTTTCATGTTCTTGTCATTGGACACTTTCACAGCACTAGCAAGCTTTGATTTCTTATGTGGCCC
1 TTATTCATGTTCTTGTCATTGGACACTTTCACAGCACTAGCAAGCTTTGCTTTCTTATGTGGCCT
1926439 CTCATCTACCTCACCTGAATCT
66 CTCATCTACCTCACCTGAATCT
* * * * *
1926461 TTATTCATGTTCTTGTCAGTGAACACTTTCACAGTACTATCAAGCTTTGCTTTCTTCTGTGGCCT
1 TTATTCATGTTCTTGTCATTGGACACTTTCACAGCACTAGCAAGCTTTGCTTTCTTATGTGGCCT
* *
1926526 CTCATGTACCTCACCTGAATCC
66 CTCATCTACCTCACCTGAATCT
* * * * *
1926548 TTATTCGTGTTCTTGTCATTGGACACTTTCACAGTACTATCAAGCTTTGCTTTCTTCTGTGACCT
1 TTATTCATGTTCTTGTCATTGGACACTTTCACAGCACTAGCAAGCTTTGCTTTCTTATGTGGCCT
*
1926613 CTGATCTACCTCACCTGAATC
66 CTCATCTACCTCACCTGAATC
1926634 CTTAGTTGAT
Statistics
Matches: 236, Mismatches: 24, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 236 1.00
ACGTcount: A:0.19, C:0.28, G:0.14, T:0.39
Consensus pattern (87 bp):
TTATTCATGTTCTTGTCATTGGACACTTTCACAGCACTAGCAAGCTTTGCTTTCTTATGTGGCCT
CTCATCTACCTCACCTGAATCT
Found at i:1929314 original size:17 final size:17
Alignment explanation
Indices: 1929271--1929325 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
1929261 CGTGTATGTT
*
1929271 ATTTATAATACAAAGTAAA
1 ATTTATAATACAAA--ATA
*
1929290 AATTATAATACAAAATA
1 ATTTATAATACAAAATA
1929307 ATTTATAATACAAGAATA
1 ATTTATAATACAA-AATA
1929325 A
1 A
1929326 AAGAATGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 14 0.44
18 5 0.16
19 13 0.41
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.31
Consensus pattern (17 bp):
ATTTATAATACAAAATA
Found at i:1931521 original size:24 final size:24
Alignment explanation
Indices: 1931483--1931536 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1931473 TATTAAAGTA
1931483 TATATATAATAGTAATTATATTACT
1 TATA-ATAATAGTAATTATATTACT
* *
1931508 TATAATAATTGTAATTATATTTCT
1 TATAATAATAGTAATTATATTACT
1931532 TATAA
1 TATAA
1931537 ATTAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (24 bp):
TATAATAATAGTAATTATATTACT
Found at i:1931550 original size:24 final size:23
Alignment explanation
Indices: 1931483--1931547 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 23
1931473 TATTAAAGTA
1931483 TATATATAATAGTAATTATATTACT
1 TATA-ATAATA-TAATTATATTACT
* *
1931508 TATAATAATTGTAATTATATTTCT
1 TATAATAA-TATAATTATATTACT
1931532 TATAAATTAATATAAT
1 TAT-AA-TAATATAAT
1931548 ATAAAAACTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 19 0.56
25 12 0.35
26 3 0.09
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (23 bp):
TATAATAATATAATTATATTACT
Found at i:1948483 original size:211 final size:211
Alignment explanation
Indices: 1948110--1948524 Score: 652
Period size: 211 Copynumber: 2.0 Consensus size: 211
1948100 TTTGTCTTAC
* * * * *
1948110 TCACTGTCGTAACTTTCATGTCAGTGTGCTGTTTACCTTGACAGAACCTTTAGGTGTGGAATCAA
1 TCACTGTCCTAACTTTCACGTCACTGTGCTGTTAACCTTGAAAGAACCTTTAGGTGTGGAATCAA
* *
1948175 CTGAAGGTGCTTTTTCACTTGGGCTACGTCAACAAAACAAATTTATGTGATGGTGCTGCTTTGCT
66 CTGAAGGTGCTATTTCACTTGGGCTACGTCAACAAAACAAATTTATGTGATGGTGCTGCTTTGCC
*
1948240 GTCAGGTATGACCACATTCCATTGCAGACATTTCTGGCACTTTCTTGCTAGTTCTGAGT-CCAGG
131 GTCAGGTATGACCACATTCCAATGCAGACATTTCTGGCACTTTCTTGCTAGTTCTGAGTCCCA-G
*
1948304 CAAACTTTGAGCTGTTG
195 CAAACCTTGAGCTGTTG
*
1948321 TCACTGTCCTAACTTTCACGTCACTGTGCTGTTAACCTTGAAAGAACCTTTAGGTGTGGAATGAA
1 TCACTGTCCTAACTTTCACGTCACTGTGCTGTTAACCTTGAAAGAACCTTTAGGTGTGGAATCAA
* * * * *
1948386 TTGATGTTGCTATTTCACTTGGGCTACTTCAACAAACCAAATTTATGTGATGGTGCTGCTTTGCC
66 CTGAAGGTGCTATTTCACTTGGGCTACGTCAACAAAACAAATTTATGTGATGGTGCTGCTTTGCC
* * *
1948451 GTCAGGTATGACCACATTCCAATGCTGACATTTCTGGCTCTTTCTTGCTAGTTTTGAGTCCCAGC
131 GTCAGGTATGACCACATTCCAATGCAGACATTTCTGGCACTTTCTTGCTAGTTCTGAGTCCCAGC
1948516 AAACCTTGA
196 AAACCTTGA
1948525 TTTTTGGTTA
Statistics
Matches: 185, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
211 182 0.98
212 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.35
Consensus pattern (211 bp):
TCACTGTCCTAACTTTCACGTCACTGTGCTGTTAACCTTGAAAGAACCTTTAGGTGTGGAATCAA
CTGAAGGTGCTATTTCACTTGGGCTACGTCAACAAAACAAATTTATGTGATGGTGCTGCTTTGCC
GTCAGGTATGACCACATTCCAATGCAGACATTTCTGGCACTTTCTTGCTAGTTCTGAGTCCCAGC
AAACCTTGAGCTGTTG
Found at i:1952976 original size:15 final size:16
Alignment explanation
Indices: 1952948--1952980 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1952938 GACTTCAACC
1952948 AAGGAGAAGCGAAGGG
1 AAGGAGAAGCGAAGGG
*
1952964 AAGG-GAAGGGAAGGG
1 AAGGAGAAGCGAAGGG
1952979 AA
1 AA
1952981 AGCCAAGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.45, C:0.03, G:0.52, T:0.00
Consensus pattern (16 bp):
AAGGAGAAGCGAAGGG
Found at i:1953088 original size:17 final size:17
Alignment explanation
Indices: 1953033--1953088 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
1953023 AGACTTTCGA
*
1953033 AGAGAAGAAACGGATCT
1 AGAGAAGAAACGGTTCT
*
1953050 AGAG-AGAAA-GAGTTCA
1 AGAGAAGAAACG-GTTCT
*
1953066 AGGAGAAGAAACGGTTTT
1 A-GAGAAGAAACGGTTCT
1953084 AGAGA
1 AGAGA
1953089 GAGGAAGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
15 1 0.03
16 9 0.29
17 11 0.35
18 9 0.29
19 1 0.03
ACGTcount: A:0.46, C:0.07, G:0.32, T:0.14
Consensus pattern (17 bp):
AGAGAAGAAACGGTTCT
Found at i:1954799 original size:212 final size:211
Alignment explanation
Indices: 1954432--1954845 Score: 738
Period size: 212 Copynumber: 2.0 Consensus size: 211
1954422 TTTATCTTAC
1954432 TCACTGTCGTAACTTTCATGTCAGTGTGCTGTTAACCTTGAAAGAACCTTTACGCATGGAATGAA
1 TCACTGTCGTAACTTTCATGTCAGTGTGCTGTTAACCTTGAAAGAACCTTTACGCATGGAATGAA
* * * *
1954497 TTGAAGGTGCTTTTTCACTTGGGCTACTTCAACAAAACAAATTTATGTGATGGTGCTGCTTTGCT
66 TTGAAGGTGCTCTTTCACTTGGGCTACTTCAACAAAACAAATTTATGTGACGGTGCTGCTTCGCC
*
1954562 GTCAGGTATGACCACATTTCATTGCTGACATTTCTGGCCCTTTCTTGCTAGTTTTGAGTCCCAGC
131 GTCAGGTATGACCACATTCCATTGCTGACATTTCTGGCCCTTTCTTGCTAGTTTTGAGTCCCAGC
1954627 AAACTTTGTGTTGTTG
196 AAACTTTGTGTTGTTG
* **
1954643 TCACTGTCGTAACTTTCATGTCAGTGTGCTGTTAACCTTGAAAGAAACCTTTAGGTGTGGAATGA
1 TCACTGTCGTAACTTTCATGTCAGTGTGCTGTTAACCTTGAAAG-AACCTTTACGCATGGAATGA
*
1954708 ATTGAAGGTGCTCTTTCACTTGGGCTACTTCAACAAACCAAATTTATGTGACGGTGCTGCTTCGC
65 ATTGAAGGTGCTCTTTCACTTGGGCTACTTCAACAAAACAAATTTATGTGACGGTGCTGCTTCGC
1954773 CGTCAGGTATGACCACATTCCATTGCTGACATTTCTGGCCCTTTCTTGCTAGTTTTGAGTCCCAG
130 CGTCAGGTATGACCACATTCCATTGCTGACATTTCTGGCCCTTTCTTGCTAGTTTTGAGTCCCAG
1954838 CAAACTTT
195 CAAACTTT
1954846 CAGTATTTGT
Statistics
Matches: 193, Mismatches: 9, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
211 44 0.23
212 149 0.77
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (211 bp):
TCACTGTCGTAACTTTCATGTCAGTGTGCTGTTAACCTTGAAAGAACCTTTACGCATGGAATGAA
TTGAAGGTGCTCTTTCACTTGGGCTACTTCAACAAAACAAATTTATGTGACGGTGCTGCTTCGCC
GTCAGGTATGACCACATTCCATTGCTGACATTTCTGGCCCTTTCTTGCTAGTTTTGAGTCCCAGC
AAACTTTGTGTTGTTG
Found at i:1963665 original size:77 final size:76
Alignment explanation
Indices: 1963513--1963664 Score: 288
Period size: 77 Copynumber: 2.0 Consensus size: 76
1963503 ATCTTGCTTA
1963513 CGATCTTTCCATTTTGTTGTTTCGATGAAGATTTATTAGGTTAAACAACTTTTTTTTTTTGAGGG
1 CGATCTTTCCATTTTGTTGTTTCGATGAAGATTTATTAGGTTAAACAACTTTTTTTTTTTGAGGG
1963578 GGGGGGGGGGG
66 GGGGGGGGGGG
1963589 NCGATCTTTCCATTTTGTTGTTTCGATGAAGATTTATTAGGTTAAACAAC-TTTTTTTTTTGAGG
1 -CGATCTTTCCATTTTGTTGTTTCGATGAAGATTTATTAGGTTAAACAACTTTTTTTTTTTGAGG
1963653 GGGGGGGGGGGG
65 GGGGGGGGGGGG
1963665 GGGAGGTAAG
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
76 26 0.35
77 49 0.65
ACGTcount: A:0.18, C:0.09, G:0.30, T:0.41
Consensus pattern (76 bp):
CGATCTTTCCATTTTGTTGTTTCGATGAAGATTTATTAGGTTAAACAACTTTTTTTTTTTGAGGG
GGGGGGGGGGG
Found at i:1965328 original size:24 final size:24
Alignment explanation
Indices: 1965301--1965350 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1965291 TTTACTGCTG
1965301 TTATGTTTTTTTATAGTATGTGCC
1 TTATGTTTTTTTATAGTATGTGCC
1965325 TTATGTTTTTTTATAGTATGTGCC
1 TTATGTTTTTTTATAGTATGTGCC
1965349 TT
1 TT
1965351 TTCTAACACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (24 bp):
TTATGTTTTTTTATAGTATGTGCC
Found at i:1967935 original size:16 final size:16
Alignment explanation
Indices: 1967914--1967944 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1967904 TTTGCTGGTC
1967914 TTGATTCTTCTTTTCA
1 TTGATTCTTCTTTTCA
1967930 TTGATTCTTCTTTTC
1 TTGATTCTTCTTTTC
1967945 TTCAAACATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.10, C:0.19, G:0.06, T:0.65
Consensus pattern (16 bp):
TTGATTCTTCTTTTCA
Found at i:1973152 original size:2 final size:2
Alignment explanation
Indices: 1973145--1973171 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1973135 TTAACCTTTT
1973145 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1973172 TTATGAACTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1978649 original size:6 final size:7
Alignment explanation
Indices: 1978634--1978658 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1978624 GACCATCCAG
1978634 TTTTATT
1 TTTTATT
1978641 TTTTATT
1 TTTTATT
1978648 TTTTATT
1 TTTTATT
1978655 TTTT
1 TTTT
1978659 TCCCATTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:1985007 original size:25 final size:25
Alignment explanation
Indices: 1984973--1985023 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1984963 CCTACAAATG
1984973 TGTATGGCATAAAACGTCCATAACT
1 TGTATGGCATAAAACGTCCATAACT
1984998 TGTATGGCATAAAACGTCCATAACT
1 TGTATGGCATAAAACGTCCATAACT
1985023 T
1 T
1985024 ATATTAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (25 bp):
TGTATGGCATAAAACGTCCATAACT
Found at i:2014063 original size:17 final size:16
Alignment explanation
Indices: 2014035--2014066 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2014025 CACATAATGA
2014035 TTAAATATATAAATAG
1 TTAAATATATAAATAG
2014051 TTAAATAATATAAATA
1 TTAAAT-ATATAAATA
2014067 AAAAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
TTAAATATATAAATAG
Found at i:2014198 original size:18 final size:18
Alignment explanation
Indices: 2014175--2014221 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
2014165 TGAGTTATAT
*
2014175 AAAAAAAAAGGTAAAGTA
1 AAAAAAAAAGATAAAGTA
2014193 AAAAAAAAAGATAAAGTA
1 AAAAAAAAAGATAAAGTA
* *
2014211 GAAAAGAAAGA
1 AAAAAAAAAGA
2014222 GAAAAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (18 bp):
AAAAAAAAAGATAAAGTA
Found at i:2016918 original size:51 final size:51
Alignment explanation
Indices: 2016822--2016938 Score: 141
Period size: 51 Copynumber: 2.3 Consensus size: 51
2016812 AAGAATAGTA
*
2016822 AACCCTTGTTGAAGTGAGAAAAATATCACAGTCTTCACGCAGAGGACAAT-
1 AACCCTTGTTGAAGTGAAAAAAATATCACAGTCTTCACGCAGAGGACAATG
* **
2016872 AGACCCTTGTTGAAGTGAAAAAAATATCAC-GATCCTTGA-GTGGAGGACAATG
1 A-ACCCTTGTTGAAGTGAAAAAAATATCACAG-T-CTTCACGCAGAGGACAATG
*
2016924 AACCCTTATTGAAGT
1 AACCCTTGTTGAAGT
2016939 AGGAAGATGT
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
50 2 0.03
51 51 0.88
52 5 0.09
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (51 bp):
AACCCTTGTTGAAGTGAAAAAAATATCACAGTCTTCACGCAGAGGACAATG
Found at i:2017365 original size:107 final size:107
Alignment explanation
Indices: 2017172--2017378 Score: 351
Period size: 107 Copynumber: 1.9 Consensus size: 107
2017162 TCTTTTCCAC
* *
2017172 TAAAACTCTAAGCATTAATATGAATTTAAACAATTTGTTTATTTTAACTTTTTCTGCTATTAAAC
1 TAAAACTCTAACCATTAATATGAATTTAAACAATTTGTTTATTTTAACTTTTTCTACTATTAAAC
** *
2017237 TGGTTTTCTTGAAACTGTAATTTTCACCATGTTAATTTCAAT
66 TGACTTTCTTGAAACTATAATTTTCACCATGTTAATTTCAAT
*
2017279 TAAAACTCTAACCATTAATATGAATTTAGACAATTTGTTTATTTTAACTTTTTCTACTATTAAAC
1 TAAAACTCTAACCATTAATATGAATTTAAACAATTTGTTTATTTTAACTTTTTCTACTATTAAAC
*
2017344 TGACTTTCTTGAAATTATAATTTTCACCATGTTAA
66 TGACTTTCTTGAAACTATAATTTTCACCATGTTAA
2017379 GTGAAATCTT
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
107 93 1.00
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (107 bp):
TAAAACTCTAACCATTAATATGAATTTAAACAATTTGTTTATTTTAACTTTTTCTACTATTAAAC
TGACTTTCTTGAAACTATAATTTTCACCATGTTAATTTCAAT
Found at i:2019671 original size:20 final size:21
Alignment explanation
Indices: 2019643--2019684 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
2019633 TTATTTAATT
2019643 TTAAATAAAAAT-ATAAAAAA
1 TTAAATAAAAATAATAAAAAA
* *
2019663 TTAATTAAATATAATAAAAAA
1 TTAAATAAAAATAATAAAAAA
2019684 T
1 T
2019685 AAAAATTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
TTAAATAAAAATAATAAAAAA
Found at i:2026918 original size:22 final size:23
Alignment explanation
Indices: 2026885--2026954 Score: 74
Period size: 22 Copynumber: 3.1 Consensus size: 23
2026875 ATAATTTTAA
*
2026885 TTAATT-TAATAATTTTATATAT
1 TTAATTATAATAATATTATATAT
*
2026907 TTAATTAT-ATAAGATTA-ATAAT
1 TTAATTATAATAATATTATAT-AT
*
2026929 TTAATTATCAATAATATTATTTAT
1 TTAATTAT-AATAATATTATATAT
2026953 TT
1 TT
2026955 TATATATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
21 2 0.05
22 23 0.59
23 1 0.03
24 12 0.31
25 1 0.03
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (23 bp):
TTAATTATAATAATATTATATAT
Found at i:2027065 original size:25 final size:25
Alignment explanation
Indices: 2026993--2027074 Score: 67
Period size: 25 Copynumber: 3.1 Consensus size: 25
2026983 TTATCAAATT
*
2026993 AATAATTTTAATTTATAAATTAAATCATAA
1 AATAATTTT-A-TTATAAA-AAAAT-A-AA
**
2027023 AATAATTTTATTATAAAATTATAAA
1 AATAATTTTATTATAAAAAAATAAA
*
2027048 AATAATTTT-TTTTGAAAAAAATAAA
1 AATAATTTTATTAT-AAAAAAATAAA
2027073 AA
1 AA
2027075 ATGGACTGAC
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
24 3 0.07
25 22 0.49
26 1 0.02
27 2 0.04
28 7 0.16
29 1 0.02
30 9 0.20
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (25 bp):
AATAATTTTATTATAAAAAAATAAA
Found at i:2034705 original size:28 final size:29
Alignment explanation
Indices: 2034650--2034705 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
2034640 ATATTTAATA
* * **
2034650 TTCTTGTTTTTTATATTTTAAATTTATTT
1 TTCTTATTTTTTATATGTTAAAAATATTT
2034679 TTCTTATTTTTT-TATGTTAAAAATATT
1 TTCTTATTTTTTATATGTTAAAAATATT
2034706 GAATATCTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.68
Consensus pattern (29 bp):
TTCTTATTTTTTATATGTTAAAAATATTT
Done.