Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009267.1 Hibiscus syriacus cultivar Beakdansim tig00112925_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: 1725308
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 10
Found at i:1414800 original size:20 final size:21
Alignment explanation
Indices: 1414756--1414807 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1414746 ATAGTCAGTA
*
1414756 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
1414777 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
1414797 TCGCATTGCGA
1 TCGCATTGCGA
1414808 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:1415022 original size:12 final size:12
Alignment explanation
Indices: 1415003--1415036 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1414993 CTCTCTGGCG
1415003 ACATCCGTTCCT
1 ACATCCGTTCCT
*
1415015 ATATCCGTTCCT
1 ACATCCGTTCCT
1415027 ACATCC-TTCC
1 ACATCCGTTCC
1415037 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:1415620 original size:24 final size:24
Alignment explanation
Indices: 1415593--1415646 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1415583 GTATTCGAAA
*
1415593 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
1415617 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
1415641 TTTGAT
1 TTTGAT
1415647 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:1418146 original size:19 final size:19
Alignment explanation
Indices: 1418124--1418182 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
1418114 GGAAATTACT
1418124 ATCGCAATACGAAATGAAA
1 ATCGCAATACGAAATGAAA
*
1418143 ATCGC-A-ACG---TGAGA
1 ATCGCAATACGAAATGAAA
*
1418157 ATCGCAATGCGAAATGAAA
1 ATCGCAATACGAAATGAAA
1418176 ATCGCAA
1 ATCGCAA
1418183 CGCTAATTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 9 0.28
15 1 0.03
16 2 0.06
17 3 0.09
18 1 0.03
19 16 0.50
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.15
Consensus pattern (19 bp):
ATCGCAATACGAAATGAAA
Found at i:1418170 original size:33 final size:33
Alignment explanation
Indices: 1418124--1418246 Score: 169
Period size: 33 Copynumber: 3.7 Consensus size: 33
1418114 GGAAATTACT
*
1418124 ATCGCAATACGAAATGAAAATCGCAACGTGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGTGAGA
1418157 ATCGCAATGCGAAATGAAAATCGCAACGCT-A-A
1 ATCGCAATGCGAAATGAAAATCGCAACG-TGAGA
* * * *
1418189 TTTCACAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGTGAGA
1418223 ATCGCAATGCGAAATGAAAATCGC
1 ATCGCAATGCGAAATGAAAATCGC
1418247 GACGCGAATT
Statistics
Matches: 79, Mismatches: 7, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
32 1 0.01
33 76 0.96
34 2 0.03
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGTGAGA
Found at i:1418239 original size:66 final size:66
Alignment explanation
Indices: 1418128--1418257 Score: 215
Period size: 66 Copynumber: 2.0 Consensus size: 66
1418118 ATTACTATCG
* *
1418128 CAATACGAAATGAAAATCGCAACGTGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAATTTC
1 CAATACGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTC
1418193 A
66 A
* * *
1418194 CAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCGACGCGAATTT
1 CAATACGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1418258 AATTTCGCGT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (66 bp):
CAATACGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTC
A
Found at i:1418282 original size:14 final size:14
Alignment explanation
Indices: 1418265--1418321 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1418255 TTTAATTTCG
1418265 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1418279 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1418298 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1418312 CGTTGCGATT
1 CGTTGCGATT
1418322 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1418301 original size:33 final size:33
Alignment explanation
Indices: 1418250--1418339 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
1418240 AAATCGCGAC
* *
1418250 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1418283 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
1418316 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
1418340 AGTACTTTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.43
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:1418303 original size:19 final size:19
Alignment explanation
Indices: 1418279--1418339 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
1418269 GCGATTCTCT
1418279 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1418298 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
1418312 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1418331 CATTGCGAT
1 CGTTGCGAT
1418340 AGTACTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 18 0.53
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1418465 original size:14 final size:14
Alignment explanation
Indices: 1418446--1418482 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1418436 CATCAATTAA
1418446 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1418460 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1418474 ACAAATCAA
1 ACAAATCAA
1418483 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1419879 original size:21 final size:21
Alignment explanation
Indices: 1419855--1419965 Score: 55
Period size: 21 Copynumber: 5.3 Consensus size: 21
1419845 GTGGGAGGGA
1419855 CCTCTTCAACGATGACAGTGG
1 CCTCTTCAACGATGACAGTGG
* * ** *
1419876 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTCAACGATGACAGTGG
* * * * *
1419897 ACTC-TCGAGGAATGATAGGGG
1 CCTCTTCAACG-ATGACAGTGG
*
1419918 CCTCTTCAACGAT-AGGAGTGG
1 CCTCTTCAACGATGA-CAGTGG
* * **
1419939 ACTCTTGAGGGATGACAGTGG
1 CCTCTTCAACGATGACAGTGG
1419960 CCTCTT
1 CCTCTT
1419966 GAACTGTGGG
Statistics
Matches: 63, Mismatches: 23, Indels: 8
0.67 0.24 0.09
Matches are distributed among these distances:
20 4 0.06
21 54 0.86
22 5 0.08
ACGTcount: A:0.22, C:0.22, G:0.33, T:0.23
Consensus pattern (21 bp):
CCTCTTCAACGATGACAGTGG
Found at i:1419894 original size:42 final size:41
Alignment explanation
Indices: 1419835--1420040 Score: 164
Period size: 42 Copynumber: 4.9 Consensus size: 41
1419825 ATGAATCGGG
* *
1419835 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * *
1419877 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * *
1419919 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAGTGGC
* * * *
1419961 CTCTTGAACTGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * *
1420003 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAG
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAG
1420041 GCGAGTCGGG
Statistics
Matches: 126, Mismatches: 30, Indels: 16
0.73 0.17 0.09
Matches are distributed among these distances:
41 9 0.07
42 106 0.84
43 11 0.09
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:1419976 original size:84 final size:84
Alignment explanation
Indices: 1419865--1420040 Score: 343
Period size: 84 Copynumber: 2.1 Consensus size: 84
1419855 CCTCTTCAAC
1419865 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1419930 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
*
1419949 GATGACAGTGGCCTCTTGAACTGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1420014 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
1420033 GATGACAG
1 GATGACAG
1420041 GCGAGTCGGG
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 91 1.00
ACGTcount: A:0.23, C:0.18, G:0.38, T:0.22
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:1420436 original size:91 final size:90
Alignment explanation
Indices: 1420259--1420443 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
1420249 ATTTCAAACT
*
1420259 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
1420324 AGAATTGGCAGCAACCAAATAAATTTAC
63 AGAATTGGCAGCAACCAAATAAATTTAC
1420352 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
* *
1420416 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCAAATAAATTTAC
1420443 T
1 T
1420444 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 41 0.47
93 19 0.22
95 27 0.31
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCAAATAAATTTAC
Found at i:1422153 original size:20 final size:19
Alignment explanation
Indices: 1422122--1422253 Score: 130
Period size: 19 Copynumber: 7.1 Consensus size: 19
1422112 TCTTTTGGTT
*
1422122 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
1422141 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1422161 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
* *
1422179 G--A-GAGAATCGCAACGT
1 GAAATGAAAATCGCAACGC
**
1422195 GAAATGACTATCGCAACGC
1 GAAATGAAAATCGCAACGC
1422214 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1422233 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1422252 GA
1 GA
1422254 TTTTGGTTTC
Statistics
Matches: 93, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
14 9 0.10
15 1 0.01
16 1 0.01
17 1 0.01
18 2 0.02
19 50 0.54
20 27 0.29
21 2 0.02
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1422204 original size:33 final size:34
Alignment explanation
Indices: 1422147--1422212 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 34
1422137 ACGAGATAAT
1422147 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
*
1422181 GAGAATCGCAACG-TGAAATGACTATCGCAACG
1 GAGAATCGCAACGCGGAAATGACTATCGCAACG
1422213 CGAAATGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 18 0.58
34 13 0.42
ACGTcount: A:0.38, C:0.23, G:0.26, T:0.14
Consensus pattern (34 bp):
GAGAATCGCAACGCGGAAATGACTATCGCAACGA
Found at i:1422282 original size:19 final size:19
Alignment explanation
Indices: 1422249--1422293 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1422239 AAAATCGCAA
*
1422249 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
1422268 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
1422287 TGCGATT
1 TGCGATT
1422294 CTCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:1422896 original size:20 final size:20
Alignment explanation
Indices: 1422847--1422886 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1422837 GCGCTATGTA
*
1422847 AATCGCGTTGCGAAAGTCAG
1 AATCACGTTGCGAAAGTCAG
1422867 AATCACGTTGCGAAAGTCAG
1 AATCACGTTGCGAAAGTCAG
1422887 TAACTCGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.20
Consensus pattern (20 bp):
AATCACGTTGCGAAAGTCAG
Found at i:1422933 original size:20 final size:20
Alignment explanation
Indices: 1422908--1422961 Score: 92
Period size: 20 Copynumber: 2.7 Consensus size: 20
1422898 GATTTTGTAT
1422908 TATCGCATTGCGATAGT-AA
1 TATCGCATTGCGATAGTCAA
1422927 GTATCGCATTGCGATAGTCAA
1 -TATCGCATTGCGATAGTCAA
1422948 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1422962 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 31 0.94
21 2 0.06
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTCAA
Found at i:1423877 original size:23 final size:26
Alignment explanation
Indices: 1423835--1423885 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
1423825 ATAATTATGA
*
1423835 TTATAATAATCTTTAAAATC-TAAAT
1 TTATAATAATCTTCAAAATCTTAAAT
1423860 TTATAA-AAT-TTCAAAATCTTAAAT
1 TTATAATAATCTTCAAAATCTTAAAT
1423884 TT
1 TT
1423886 CAAAATCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 8 0.33
24 10 0.42
25 6 0.25
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (26 bp):
TTATAATAATCTTCAAAATCTTAAAT
Found at i:1426679 original size:130 final size:129
Alignment explanation
Indices: 1426545--1427132 Score: 514
Period size: 130 Copynumber: 4.6 Consensus size: 129
1426535 AAGACTACAT
* * * **
1426545 AACAAGTTAATTTCAGTGAGTTACCCTAGATGTTAATATTAAATGCTTTCTTTGATGACATACAT
1 AACAAGTTAATTTCAGTGAATTACCTTTGATGTTAATATTGGATGCTTTCTTTGATGACATACAT
* * *
1426610 ACATCTCAGAGTCCAAAAGAGATGTAATATCCAAATTCAAAATTATGTCGA-AATTAGGACTGCA
66 ACCTCTCAGAGT-TAAAAGAGATGTAACATCCAAATTCAAAATTATGTC-ATAATTAGGACTGCA
1426674 A
129 A
* * * *
1426675 AACAAGTTAATTTCAGTGAATTGCC-TT--TGTTAATATTGTATGTTTTCTTTGATGACGA-ACG
1 AACAAGTTAATTTCAGTGAATTACCTTTGATGTTAATATTGGATGCTTTCTTTGATGAC-ATACA
* * * * *
1426736 TACCTCTCAGAGTTTAAAAAAGTTGTAACATCCAAATTCAACATTGTGTCATAGTTAGGACTGCA
65 TACCTCTCAGAG-TTAAAAGAGATGTAACATCCAAATTCAAAATTATGTCATAATTAGGACTGCA
*
1426801 T
129 A
* * * * * **
1426802 GACAAGTTAATTTTAGTGAATTACCTTTGATATGAATATTGGATGCTTACTTTGATGATGTACAT
1 AACAAGTTAATTTCAGTGAATTACCTTTGATGTTAATATTGGATGCTTTCTTTGATGACATACAT
* ** * * *** * * **** *
1426867 ACCTCAT-AAAGTTTGAAGTGGGTGTAACATCCAAATTCTGTAGTGTGTTGCGATCAGGACTGCA
66 ACCTC-TCAGAGTTAAAAG-AGATGTAACATCCAAATTCAAAATTATGTCATAATTAGGACTGCA
*
1426931 T
129 A
* * * ** * *
1426932 AACAAGTTAATTTCAGTGAGTTACTTTTGATGTGAATATCAGATGCTTTCTTTGATAACATACGT
1 AACAAGTTAATTTCAGTGAATTACCTTTGATGTTAATATTGGATGCTTTCTTTGATGACATACAT
* * * *
1426997 AACTCTCAGGGTTAAAA-A-A-GTAACATCCAAATTCAGTAA-TATGTCATAATTAGAACTAG-A
66 ACCTCTCAGAGTTAAAAGAGATGTAACATCCAAATTCA-AAATTATGTCATAATTAGGACT-GCA
1427057 A
129 A
* * * * *
1427058 AACAAGTTAATATCAATGAATTGCCTTTGATGTTATTATTGGATGCTTGCTTTGATGACATACAT
1 AACAAGTTAATTTCAGTGAATTACCTTTGATGTTAATATTGGATGCTTTCTTTGATGACATACAT
1427123 ACCTCTCAGA
66 ACCTCTCAGA
1427133 TGTTGAAGTG
Statistics
Matches: 359, Mismatches: 87, Indels: 28
0.76 0.18 0.06
Matches are distributed among these distances:
126 89 0.25
127 105 0.29
128 4 0.01
129 6 0.02
130 154 0.43
131 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (129 bp):
AACAAGTTAATTTCAGTGAATTACCTTTGATGTTAATATTGGATGCTTTCTTTGATGACATACAT
ACCTCTCAGAGTTAAAAGAGATGTAACATCCAAATTCAAAATTATGTCATAATTAGGACTGCAA
Found at i:1427113 original size:256 final size:255
Alignment explanation
Indices: 1426665--1427159 Score: 581
Period size: 256 Copynumber: 1.9 Consensus size: 255
1426655 TGTCGAAATT
* * * *
1426665 AGGACTGCAAAACAAGTTAATTTCAGTGAATTGCCTTTGTTAATATTGTATGTTTTCTTTGATGA
1 AGGACTGCAAAACAAGTTAATTTCAGTGAATTACCTTTGTTAATATAGTATGCTTTCTTTGATAA
* * * * * *
1426730 CGAACGTACCTCTCAGAGTTTAAAAAAGTTGTAACATCCAAATTCAACATTGTGTCATAGTTAGG
66 CGAACGTAACTCTCAGAGGTTAAAAAA--TGTAACATCCAAATTCAACAATATGTCATAATTAGA
** * * *
1426795 ACTGCATGACAAGTTAATTTTAGTGAATTACCTTTGATATGAATATTGGATGCTTACTTTGATGA
129 ACTGCAAAACAAGTTAATATCAATGAATTACCTTTGATATGAATATTGGATGCTTACTTTGATGA
** *
1426860 TGTACATACCTCATAA-A-GTTTGAAGTGGGTGTAACATCCAAATTCTGTAGTGTGTTGCGATC
194 CATACATACCTC-TAAGATG-TTGAAGTGGGTCTAACATCCAAATTCTGTAGTGTGTTGCGATC
* * *
1426922 AGGACTGCATAACAAGTTAATTTCAGTGAGTTACTTTTGATGTGAATATCAG-ATGCTTTCTTTG
1 AGGACTGCAAAACAAGTTAATTTCAGTGAATTACCTTTG-T-T-AATAT-AGTATGCTTTCTTTG
**
1426986 ATAAC-ATACGTAACTCTCAG-GGTTAAAAAA-GTAACATCCAAATTCAGTAATATGTCATAATT
62 ATAACGA-ACGTAACTCTCAGAGGTTAAAAAATGTAACATCCAAATTCAACAATATGTCATAATT
* * * * *
1427048 AGAACTAG-AAAACAAGTTAATATCAATGAATTGCCTTTGATGTTATTATTGGATGCTTGCTTTG
126 AGAACT-GCAAAACAAGTTAATATCAATGAATTACCTTTGATATGAATATTGGATGCTTACTTTG
* *
1427112 ATGACATACATACCTCTCAGATGTTGAAGTGGGTCTAACATCTAAATT
190 ATGACATACATACCTCTAAGATGTTGAAGTGGGTCTAACATCCAAATT
1427160 TTGCAATGTG
Statistics
Matches: 200, Mismatches: 30, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
255 2 0.01
256 116 0.58
257 37 0.19
258 1 0.00
259 11 0.05
260 32 0.16
261 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (255 bp):
AGGACTGCAAAACAAGTTAATTTCAGTGAATTACCTTTGTTAATATAGTATGCTTTCTTTGATAA
CGAACGTAACTCTCAGAGGTTAAAAAATGTAACATCCAAATTCAACAATATGTCATAATTAGAAC
TGCAAAACAAGTTAATATCAATGAATTACCTTTGATATGAATATTGGATGCTTACTTTGATGACA
TACATACCTCTAAGATGTTGAAGTGGGTCTAACATCCAAATTCTGTAGTGTGTTGCGATC
Found at i:1427320 original size:128 final size:128
Alignment explanation
Indices: 1427087--1427321 Score: 303
Period size: 128 Copynumber: 1.8 Consensus size: 128
1427077 ATTGCCTTTG
* *
1427087 ATGTTATTATTGGATGCTTGCTTTGATGACATACATACCTCTCAGATGTTGAAGTGGGTCTAACA
1 ATGTTAATATTGAATGCTTGCTTTGATGACATACATACCTCTCAGATGTTGAAGTGGGTCTAACA
* * **
1427152 TCTAAATTTTGCAATGTGTTACAATTAGAACTACACAACAAAATAATTTAGTGAGTTGATTTA
66 TATAAATTCTGCAATGTACTACAATTAGAACTACACAACAAAATAATTTAGTGAGTTGATTTA
* * * *
1427215 ATGTTAATATTGAATGCTTGCTTTGATGACATGCATACCTCTTATA-GTTTAATGTGGGTGC-AA
1 ATGTTAATATTGAATGCTTGCTTTGATGACATACATACCTCTCAGATGTTGAA-GTGGGT-CTAA
* * * * *
1427278 CATATAAATTCTGTAATGTACTGCAATTAGGATTACATAACAAA
64 CATATAAATTCTGCAATGTACTACAATTAGAACTACACAACAAA
1427322 TTTTATTAGG
Statistics
Matches: 90, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
127 5 0.06
128 84 0.93
129 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (128 bp):
ATGTTAATATTGAATGCTTGCTTTGATGACATACATACCTCTCAGATGTTGAAGTGGGTCTAACA
TATAAATTCTGCAATGTACTACAATTAGAACTACACAACAAAATAATTTAGTGAGTTGATTTA
Found at i:1430594 original size:20 final size:20
Alignment explanation
Indices: 1430565--1430616 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1430555 ACTTAAGGGA
1430565 TGTACCGATACCCTGTAGAG
1 TGTACCGATACCCTGTAGAG
*
1430585 TGTACTGATACCCTGTAGAG
1 TGTACCGATACCCTGTAGAG
1430605 TGTACCGATACC
1 TGTACCGATACC
1430617 TATGTTAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (20 bp):
TGTACCGATACCCTGTAGAG
Found at i:1431766 original size:32 final size:31
Alignment explanation
Indices: 1431694--1431813 Score: 127
Period size: 32 Copynumber: 3.9 Consensus size: 31
1431684 GAGTCGAGGG
* * * *
1431694 TTACCTATGTCTTTCGAGACATATGGATAGT
1 TTACCTATGTCCTTCGGGACATATGGACAGA
1431725 TTACCTATGTCCTTCGGGACATATGGACACGA
1 TTACCTATGTCCTTCGGGACATATGGACA-GA
**
1431757 TTACCTATGTCCTTTAGGACATATGGAC--A
1 TTACCTATGTCCTTCGGGACATATGGACAGA
* **
1431786 TCTACCTATGTTCTTCGAAACATATGGA
1 T-TACCTATGTCCTTCGGGACATATGGA
1431814 TAGGTCCTTC
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
29 2 0.03
30 21 0.28
31 26 0.34
32 27 0.36
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (31 bp):
TTACCTATGTCCTTCGGGACATATGGACAGA
Found at i:1433712 original size:20 final size:20
Alignment explanation
Indices: 1433684--1433785 Score: 143
Period size: 20 Copynumber: 5.0 Consensus size: 20
1433674 TAAATTGTAG
*
1433684 CACATAAGTCAAATTCGCAA
1 CACAGAAGTCAAATTCGCAA
1433704 CACAGAAGTCAAATTCGCAA
1 CACAGAAGTCAAATTCGCAA
*
1433724 CACAGAAGTCAAAATCGCAA
1 CACAGAAGTCAAATTCGCAA
*
1433744 AACAGAAGTCAAATTCGCAA
1 CACAGAAGTCAAATTCGCAA
*
1433764 CAC-GAAATTTCAAATTCGCAA
1 CACAG-AA-GTCAAATTCGCAA
1433785 C
1 C
1433786 CCGAATTTAT
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
19 1 0.01
20 60 0.81
21 13 0.18
ACGTcount: A:0.46, C:0.25, G:0.13, T:0.17
Consensus pattern (20 bp):
CACAGAAGTCAAATTCGCAA
Found at i:1433859 original size:40 final size:40
Alignment explanation
Indices: 1433803--1433905 Score: 125
Period size: 40 Copynumber: 2.6 Consensus size: 40
1433793 TATTTTTCAT
** *
1433803 ACACAAATTTCCTTTTCGCAACAAGATTTTCTAAATCGCA
1 ACACAAATTTTATTTTCGCAACAAGATTTTCGAAATCGCA
* * ** *
1433843 ACACGAATTTTGTTTTCGCAACTCGATTTTCGAATTCGCA
1 ACACAAATTTTATTTTCGCAACAAGATTTTCGAAATCGCA
*
1433883 ACACAAATTTTAATTTCGCAACA
1 ACACAAATTTTATTTTCGCAACA
1433906 GCTTTTATTT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.34
Consensus pattern (40 bp):
ACACAAATTTTATTTTCGCAACAAGATTTTCGAAATCGCA
Found at i:1433861 original size:20 final size:20
Alignment explanation
Indices: 1433838--1433905 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
1433828 ATTTTCTAAA
*
1433838 TCGCAACACGAATTTTGTTT
1 TCGCAACACGAATTTTGATT
* *
1433858 TCGCAACTCG-ATTTTCGAAT
1 TCGCAACACGAATTTT-GATT
* *
1433878 TCGCAACACAAATTTTAATT
1 TCGCAACACGAATTTTGATT
1433898 TCGCAACA
1 TCGCAACA
1433906 GCTTTTATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 5 0.13
20 29 0.74
21 5 0.13
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.34
Consensus pattern (20 bp):
TCGCAACACGAATTTTGATT
Found at i:1434081 original size:14 final size:15
Alignment explanation
Indices: 1434062--1434099 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1434052 TCACCATCTC
1434062 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
1434076 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1434092 TAATTTTT
1 TAATTTTT
1434100 CAATGATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1434710 original size:12 final size:12
Alignment explanation
Indices: 1434689--1434722 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1434679 ACCACATTTC
*
1434689 CAATACCAAACA
1 CAATATCAAACA
1434701 CAATATCAAACA
1 CAATATCAAACA
*
1434713 CAATCTCAAA
1 CAATATCAAA
1434723 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1435060 original size:3 final size:3
Alignment explanation
Indices: 1435052--1435079 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1435042 ATATAACCCT
1435052 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1435080 TCCCCGGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1437442 original size:20 final size:20
Alignment explanation
Indices: 1437419--1437526 Score: 86
Period size: 20 Copynumber: 5.8 Consensus size: 20
1437409 AAATCGCAAC
1437419 GCGAATTTGACTTTCGCGTT
1 GCGAATTTGACTTTCGCGTT
1437439 GCG-A-TT---TTT-GC-TT
1 GCGAATTTGACTTTCGCGTT
*
1437452 GCGAATTTGATTTTCGCGTT
1 GCGAATTTGACTTTCGCGTT
** **
1437472 GTAAATTTGACTTTCAAGTT
1 GCGAATTTGACTTTCGCGTT
* ***
1437492 GCGAATTTGACTATCGCAAC
1 GCGAATTTGACTTTCGCGTT
1437512 GCGAATTTGACTTTC
1 GCGAATTTGACTTTC
1437527 CCATTACGAA
Statistics
Matches: 67, Mismatches: 14, Indels: 14
0.71 0.15 0.15
Matches are distributed among these distances:
13 5 0.07
14 3 0.04
15 5 0.07
18 5 0.07
19 3 0.04
20 46 0.69
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (20 bp):
GCGAATTTGACTTTCGCGTT
Found at i:1439034 original size:21 final size:21
Alignment explanation
Indices: 1439010--1439101 Score: 141
Period size: 21 Copynumber: 4.4 Consensus size: 21
1439000 GTGAATCGGG
* *
1439010 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
1439031 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
1439052 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
*
1439073 CTCTTGAACGA-CATGAGGGGC
1 CTCTTGAACGATGA-GAGGGGC
1439094 CTCTTGAA
1 CTCTTGAA
1439102 TAATGACAGG
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
20 1 0.01
21 66 0.99
ACGTcount: A:0.22, C:0.21, G:0.37, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:1439260 original size:4 final size:4
Alignment explanation
Indices: 1439251--1439276 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1439241 GGGCCGCTAA
1439251 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
1439277 TGTCGAAAAA
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1439523 original size:21 final size:21
Alignment explanation
Indices: 1439499--1439548 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1439489 ACCATTATCG
* *
1439499 TCACGTAAAGTACTGACCTCA
1 TCACGTAAAGCACTGACCACA
**
1439520 TCACACAAAGCACTGACCACA
1 TCACGTAAAGCACTGACCACA
1439541 TCACGTAA
1 TCACGTAA
1439549 CTCCACTAAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.32, G:0.12, T:0.18
Consensus pattern (21 bp):
TCACGTAAAGCACTGACCACA
Found at i:1439743 original size:42 final size:42
Alignment explanation
Indices: 1439665--1439760 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
1439655 GATGGTATAG
* * * * * *
1439665 GTGATGGCTCTCGTTGTGGAGGTGTATAATCGGCTCGAT-TA
1 GTGATGGCTCTCGGTGTCGAGCTGTAGAATCAGCTCGATCAA
*
1439706 GTTGATGGCTCTGGGTGTCGAGCTGTAGAATCAGCTCGATCAA
1 G-TGATGGCTCTCGGTGTCGAGCTGTAGAATCAGCTCGATCAA
1439749 GTGATGGCTCTC
1 GTGATGGCTCTC
1439761 AAAGTGGGGG
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
41 1 0.02
42 42 0.93
43 2 0.04
ACGTcount: A:0.18, C:0.18, G:0.33, T:0.31
Consensus pattern (42 bp):
GTGATGGCTCTCGGTGTCGAGCTGTAGAATCAGCTCGATCAA
Found at i:1441218 original size:20 final size:20
Alignment explanation
Indices: 1441195--1441247 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1441185 AAACTTAAAT
*
1441195 TCGCAACACGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
1441215 TCGCAATGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
1441235 TCGCAACGCGAAA
1 TCGCAACGCGAAA
1441248 CCAAAATCAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.49, C:0.21, G:0.19, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:1441289 original size:20 final size:20
Alignment explanation
Indices: 1441264--1441302 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1441254 TCACGTTGCG
1441264 ATTTTCGTGTTGCGAATTTC
1 ATTTTCGTGTTGCGAATTTC
1441284 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTGCGAATTT
1441303 AAGTTTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.13, G:0.21, T:0.51
Consensus pattern (20 bp):
ATTTTCGTGTTGCGAATTTC
Found at i:1441309 original size:20 final size:20
Alignment explanation
Indices: 1441266--1441309 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1441256 ACGTTGCGAT
* *
1441266 TTTCGTGTTGCGAATTTCAT
1 TTTCGTGTTGCGAATTTAAG
1441286 TTTCGTGTTGCGAATTTAAG
1 TTTCGTGTTGCGAATTTAAG
1441306 TTTC
1 TTTC
1441310 AAAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGTGTTGCGAATTTAAG
Found at i:1441652 original size:22 final size:22
Alignment explanation
Indices: 1441627--1441681 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1441617 ATAGAGGGGG
*
1441627 GTCGCCGGATATGGGGACGGAT
1 GTCGCCGGAGATGGGGACGGAT
*
1441649 GTCGCTGGAGATGGGGACGGAT
1 GTCGCCGGAGATGGGGACGGAT
1441671 GTCGCCGGAGA
1 GTCGCCGGAGA
1441682 GAGTGAGAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.18, C:0.18, G:0.47, T:0.16
Consensus pattern (22 bp):
GTCGCCGGAGATGGGGACGGAT
Found at i:1441829 original size:20 final size:20
Alignment explanation
Indices: 1441804--1441873 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
1441794 TAAAATTCGC
1441804 GTTGCGATTTTGACTTCTGT
1 GTTGCGATTTTGACTTCTGT
1441824 GTTGCGATTTTGACTTCTGT
1 GTTGCGATTTTGACTTCTGT
* * *
1441844 GTTACGAATTTGACTTCTAT
1 GTTGCGATTTTGACTTCTGT
*
1441864 GTTGGGATTT
1 GTTGCGATTT
1441874 ACATATTCGC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.14, C:0.13, G:0.24, T:0.49
Consensus pattern (20 bp):
GTTGCGATTTTGACTTCTGT
Found at i:1441892 original size:40 final size:39
Alignment explanation
Indices: 1441797--1441896 Score: 110
Period size: 40 Copynumber: 2.5 Consensus size: 39
1441787 TCGAAAATAA
* * **
1441797 AATTCGCGTTGCGATTTTGACTTCTGTGTTGCGATTTTG
1 AATTCGCGTTGCGAATTTGACTTCTATGTTGCGATTTAC
* * * *
1441836 ACTTCTGTGTTACGAATTTGACTTCTATGTTGGGATTTAC
1 AATTC-GCGTTGCGAATTTGACTTCTATGTTGCGATTTAC
1441876 ATATTCGCGTTGCGAATTTGA
1 A-ATTCGCGTTGCGAATTTGA
1441897 AACCTGTGTT
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
39 4 0.08
40 41 0.85
41 3 0.06
ACGTcount: A:0.18, C:0.15, G:0.23, T:0.44
Consensus pattern (39 bp):
AATTCGCGTTGCGAATTTGACTTCTATGTTGCGATTTAC
Found at i:1445698 original size:21 final size:21
Alignment explanation
Indices: 1445668--1445708 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1445658 AAATGTTAAA
* *
1445668 AAATATTAATGTTTTAGGTAG
1 AAATAATAATATTTTAGGTAG
1445689 AAATAATAATATTTTAGGTA
1 AAATAATAATATTTTAGGTA
1445709 ATATTTTACT
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:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (21 bp):
AAATAATAATATTTTAGGTAG
Found at i:1448966 original size:15 final size:16
Alignment explanation
Indices: 1448926--1448970 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
1448916 TAAATTTAAT
1448926 AAATATCATA-TA-AA
1 AAATATCATATTATAA
1448940 AATATATCATATTATAA
1 AA-ATATCATATTATAA
1448957 AAATAT-ATATTATA
1 AAATATCATATTATA
1448971 CATAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 2 0.07
15 16 0.57
16 6 0.21
17 4 0.14
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATATCATATTATAA
Found at i:1451023 original size:22 final size:22
Alignment explanation
Indices: 1450995--1451040 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
1450985 TTATATGTAA
1450995 GAATAATATCATTTTAAGACAT
1 GAATAATATCATTTTAAGACAT
1451017 GAATAATATCATTTTAAGACAT
1 GAATAATATCATTTTAAGACAT
1451039 GA
1 GA
1451041 CAAACCTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.35
Consensus pattern (22 bp):
GAATAATATCATTTTAAGACAT
Found at i:1454548 original size:21 final size:21
Alignment explanation
Indices: 1454522--1454562 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1454512 AGGGCAGGCG
*
1454522 TTGCACGCATTATCGGAGCAC
1 TTGCACACATTATCGGAGCAC
*
1454543 TTGCACACATTATTGGAGCA
1 TTGCACACATTATCGGAGCA
1454563 TGCATCGTTG
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:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (21 bp):
TTGCACACATTATCGGAGCAC
Found at i:1458241 original size:201 final size:198
Alignment explanation
Indices: 1457864--1458583 Score: 910
Period size: 200 Copynumber: 3.6 Consensus size: 198
1457854 ACCTAAATAT
* *
1457864 GTGTCGATACATTTTCTAAAAGTATCGATCCAAAAAAATATCGAAACCAATAATTATAATGTAAT
1 GTGTCGATACATTTTTTAAAAGTATCGATCC-AAAAAACATCGAAACCAATAATTATAATGTAAT
* * * * * * *
1457929 AGGTAAATTAACAATGTAACCAGTATAAATATACCGGTTAATTAGAAAACATGTCAACATAATGT
65 AGGTAAATTTACAATGTAACCGGTATAAATATACCGTTTTATGAGAAAATAGGTC-ACATAATGT
** *
1457994 ATCGACACTTATGGAATTTGTGTCGATACTTATTGTCCAGAATGAATGCCCAAACGAGGTGCACA
129 ATCGACACTTATTAAATTTGTGTCGATACTT-TTTTCCAGAATGAATGCCCAAACGAGGTGCACA
1458059 CATAAA
193 CATAAA
*
1458065 GTGTCGATACATTTTTTAAAAGTATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAATA
1 GTGTCGATACATTTTTTAAAAGTATCGATCCAAAAAACATCGAAACCAATAATTATAATGTAATA
*
1458130 GGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAAAATAGGTCAGCATAAAGT
66 GGTAAATTTACAATGTAACCGGTATAAATATACCG-TTTTATGAGAAAATAGGTCA-CATAATGT
* * *
1458195 ATCGACACTTGTTAAATTTGTGTCGATACATTTTTTCCATAATGAATG-CCAAACGGGGTGCACA
129 ATCGACACTTATTAAATTTGTGTCGATAC-TTTTTTCCAGAATGAATGCCCAAACGAGGTGCACA
*
1458259 CATAGA
193 CATAAA
* * * * * *
1458265 GTGTCGATACATTTATTAAAAGTATTGATCCCAAAAACATCGAAACCGATAATTACAATGTGATA
1 GTGTCGATACATTTTTTAAAAGTATCGATCCAAAAAACATCGAAACCAATAATTATAATGTAATA
* * * *
1458330 GGTAAATTTACAATGTACCCGATATAAACATACCGGTTTTATGAGAAAATAGGTCTAAATAATGT
66 GGTAAATTTACAATGTAACCGGTATAAATATACC-GTTTTATGAGAAAATAGGTC-ACATAATGT
* ** * *
1458395 ATCGACACTTTTTACGTTTGTGTCGATACGTTTTTCCAGAATGAATGCCC-AACGAGGTGCACGC
129 ATCGACACTTATTAAATTTGTGTCGATACTTTTTTCCAGAATGAATGCCCAAACGAGGTGCACAC
1458459 ATAAA
194 ATAAA
* * * * * *
1458464 GTGTCGGTACA---TTTAAAATTGTATTGATCAAAAAAATATCGAAACCGATAATTATAATGTAT
1 GTGTCGATACATTTTTTAAAA--GTATCGATCCAAAAAACATCGAAACCAATAATTATAATGTAA
* * * * *
1458526 TAGGTAAATTTACAATGTTACCGGTATAAATATATCGGTTTACTTAGAAAATATGTCA
64 TAGGTAAATTTACAATGTAACCGGTATAAATATACCGTTTTA-TGAGAAAATAGGTCA
1458584 ATATAAGCGC
Statistics
Matches: 458, Mismatches: 52, Indels: 22
0.86 0.10 0.04
Matches are distributed among these distances:
196 6 0.01
197 6 0.01
198 79 0.17
199 42 0.09
200 230 0.50
201 93 0.20
202 2 0.00
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (198 bp):
GTGTCGATACATTTTTTAAAAGTATCGATCCAAAAAACATCGAAACCAATAATTATAATGTAATA
GGTAAATTTACAATGTAACCGGTATAAATATACCGTTTTATGAGAAAATAGGTCACATAATGTAT
CGACACTTATTAAATTTGTGTCGATACTTTTTTCCAGAATGAATGCCCAAACGAGGTGCACACAT
AAA
Found at i:1458631 original size:23 final size:23
Alignment explanation
Indices: 1458575--1458631 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
1458565 TTACTTAGAA
*
1458575 AATATGTCAATATAAGCGCTACCT
1 AATATGT-TATATAAGCGCTACCT
* **
1458599 ATTACATTATATAAGCGCTACCT
1 AATATGTTATATAAGCGCTACCT
1458622 AATATGTTAT
1 AATATGTTAT
1458632 TGAACTTGAT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.35
Consensus pattern (23 bp):
AATATGTTATATAAGCGCTACCT
Found at i:1458679 original size:87 final size:87
Alignment explanation
Indices: 1458584--1458746 Score: 299
Period size: 87 Copynumber: 1.9 Consensus size: 87
1458574 AAATATGTCA
1458584 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGAACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGAACTTGATAATATTT
*
1458649 TCGGTTAAATGCCTATTTTATT
66 CCGGTTAAATGCCTATTTTATT
* *
1458671 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATTTGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGAACTTGATAATATTT
1458736 CCGGTTAAATG
66 CCGGTTAAATG
1458747 ATATAACATA
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.40
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGAACTTGATAATATTT
CCGGTTAAATGCCTATTTTATT
Found at i:1458686 original size:23 final size:23
Alignment explanation
Indices: 1458660--1458718 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
1458650 CGGTTAAATG
1458660 CCTATTTTATTATATAAGCGCTA
1 CCTATTTTATTATATAAGCGCTA
**
1458683 CCTATTACATTATATAAGCGCTA
1 CCTATTTTATTATATAAGCGCTA
* *
1458706 CCTAATTTGTTAT
1 CCTATTTTATTAT
1458719 TGTACTTGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (23 bp):
CCTATTTTATTATATAAGCGCTA
Found at i:1461393 original size:2 final size:2
Alignment explanation
Indices: 1461386--1461418 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1461376 TAAATATTAC
1461386 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1461419 TATGTTAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1464676 original size:13 final size:13
Alignment explanation
Indices: 1464658--1464695 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1464648 GTCCGACCCT
1464658 ACCCGACCCGTTG
1 ACCCGACCCGTTG
**
1464671 ACCCGACTTGTTG
1 ACCCGACCCGTTG
1464684 ACCCGACCCGTT
1 ACCCGACCCGTT
1464696 AACCGTTTAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.16, C:0.42, G:0.21, T:0.21
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:1475366 original size:50 final size:49
Alignment explanation
Indices: 1475302--1475422 Score: 161
Period size: 50 Copynumber: 2.4 Consensus size: 49
1475292 ATTTAACGCA
*
1475302 CAACACTAACTTACACCAGTGTAAGTTAGTTATTTCATTTACTAAACTAT
1 CAACACTAACTTACA-CAGTGTAAGTTAGTCATTTCATTTACTAAACTAT
* ** *
1475352 CAACACTAATTTACATTGGTATAAGTTAGTCATTTCATTTACTAAACTAT
1 CAACACTAACTTACA-CAGTGTAAGTTAGTCATTTCATTTACTAAACTAT
* *
1475402 CAATACTGACTTACACAGTGT
1 CAACACTAACTTACACAGTGT
1475423 TATCATAGCT
Statistics
Matches: 59, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
49 3 0.05
50 56 0.95
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (49 bp):
CAACACTAACTTACACAGTGTAAGTTAGTCATTTCATTTACTAAACTAT
Found at i:1480540 original size:25 final size:25
Alignment explanation
Indices: 1480506--1480564 Score: 91
Period size: 25 Copynumber: 2.3 Consensus size: 25
1480496 CAAAGAGAGA
1480506 AAAATGAGACAATGGAAAATCATAGC
1 AAAA-GAGACAATGGAAAATCATAGC
*
1480532 AAAAGAGACCATGGAAAATCATAGC
1 AAAAGAGACAATGGAAAATCATAGC
*
1480557 AAATGAGA
1 AAAAGAGA
1480565 TAATCTAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 27 0.87
26 4 0.13
ACGTcount: A:0.54, C:0.12, G:0.20, T:0.14
Consensus pattern (25 bp):
AAAAGAGACAATGGAAAATCATAGC
Found at i:1481873 original size:20 final size:19
Alignment explanation
Indices: 1481820--1481874 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
1481810 TTCCATATTC
*
1481820 TTCCACACTCTTCCATAAGG
1 TTCCACACTC-TCCACAAGG
*
1481840 ATCCACACTACTCCACAAGG
1 TTCCACACT-CTCCACAAGG
1481860 TTCCACACATCTCCA
1 TTCCACAC-TCTCCA
1481875 GAATATTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 28 0.93
21 2 0.07
ACGTcount: A:0.29, C:0.40, G:0.07, T:0.24
Consensus pattern (19 bp):
TTCCACACTCTCCACAAGG
Found at i:1486036 original size:2 final size:2
Alignment explanation
Indices: 1486029--1486061 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1486019 GAAGACATTC
1486029 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1486062 GAACAAATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1491137 original size:20 final size:20
Alignment explanation
Indices: 1491112--1491242 Score: 95
Period size: 20 Copynumber: 6.5 Consensus size: 20
1491102 GGGAAAATCA
1491112 CAATGCGATACTGACTATCG
1 CAATGCGATACTGACTATCG
*
1491132 CAATGCGATACTTACTATCG
1 CAATGCGATACTGACTATCG
* *
1491152 CAATGCGATAAT-ACAAAATCG
1 CAATGCGATACTGAC--TATCG
* * *
1491173 CAACGAGATACTGACTTTCG
1 CAATGCGATACTGACTATCG
* * * *
1491193 CAACGTGATTCTGACTTTCG
1 CAATGCGATACTGACTATCG
* * *
1491213 CAACGTGATAAT-ACATAATCG
1 CAATGCGATACTGAC-T-ATCG
1491234 CAATGCGAT
1 CAATGCGAT
1491243 TTTCAAAGCG
Statistics
Matches: 91, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
19 4 0.04
20 62 0.68
21 23 0.25
22 2 0.02
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.26
Consensus pattern (20 bp):
CAATGCGATACTGACTATCG
Found at i:1491170 original size:61 final size:61
Alignment explanation
Indices: 1491105--1491242 Score: 168
Period size: 61 Copynumber: 2.3 Consensus size: 61
1491095 GCGAATTGGG
* * * *
1491105 AAAATCACAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * * * * *
1491166 AAAATCGCAACGAGATACTGACTTTCGCAACGTGATTCTGACTTTCGCAACGTGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
1491227 ATAATCGCAATGCGAT
1 AAAATCGCAATGCGAT
1491243 TTTCAAAGCG
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (61 bp):
AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:1491779 original size:20 final size:20
Alignment explanation
Indices: 1491740--1491798 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
1491730 GCGATTCTCT
**
1491740 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
1491760 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* * **
1491780 TGTTGAGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
1491799 AGAAACTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1493128 original size:18 final size:18
Alignment explanation
Indices: 1493107--1493151 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1493097 TCCACTTTGG
*
1493107 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1493125 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1493143 GAGCCATCA
1 GAGCCATCA
1493152 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1493687 original size:19 final size:20
Alignment explanation
Indices: 1493644--1493688 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1493634 AGCAACACGA
1493644 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
1493664 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
1493683 AAATGA
1 AAATGA
1493689 AAATCACAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:1493707 original size:14 final size:14
Alignment explanation
Indices: 1493688--1493745 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1493678 ATGCGAAATG
*
1493688 AAAATCACAACGAC
1 AAAATCGCAACGAC
*
1493702 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1493718 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1493734 AAAATCGCAACG
1 AAAATCGCAACG
1493746 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.50, C:0.24, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1493731 original size:32 final size:33
Alignment explanation
Indices: 1493672--1493762 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1493662 GGAAATGGCT
*
1493672 ATCGCAATGCGAAATGAAAATCACAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1493705 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1493737 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1493763 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1493756 original size:19 final size:19
Alignment explanation
Indices: 1493672--1493767 Score: 79
Period size: 19 Copynumber: 5.6 Consensus size: 19
1493662 GGAAATGGCT
1493672 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1493691 ATCACAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
1493705 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
1493723 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
1493737 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1493756 ATCGCAATGCGA
1 ATCGCAATGCGA
1493768 TTTGTGTTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 22
0.67 0.08 0.25
Matches are distributed among these distances:
14 19 0.32
15 1 0.02
16 6 0.10
17 2 0.03
18 11 0.19
19 20 0.34
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1493800 original size:14 final size:14
Alignment explanation
Indices: 1493781--1493836 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
1493771 GTGTTTCACA
1493781 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
1493795 TTGCGATTTCATTTCG
1 TTGCGATTT--TGTCG
1493811 CATTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
*
1493827 ATGCGATTTT
1 TTGCGATTTT
1493837 CATTTCGCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 18 0.51
16 8 0.23
18 9 0.26
ACGTcount: A:0.12, C:0.16, G:0.23, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:1493843 original size:33 final size:33
Alignment explanation
Indices: 1493774--1493885 Score: 181
Period size: 33 Copynumber: 3.4 Consensus size: 33
1493764 GCGATTTGTG
*
1493774 TTTCACATTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
1493806 TTTCGCATTGCGATTTTGTCGATGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
* *
1493839 TTTCGCATTGTGATTTTATCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1493872 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1493886 AGCCATTTCC
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
32 25 0.34
33 48 0.66
ACGTcount: A:0.15, C:0.18, G:0.20, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1493855 original size:19 final size:19
Alignment explanation
Indices: 1493795--1493928 Score: 92
Period size: 20 Copynumber: 7.5 Consensus size: 19
1493785 GATTTTGTCG
1493795 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1493813 TTGCGA-TTT--TGTCG-A
1 TTGCGATTTTCATTTCGCA
1493828 -TGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1493846 TTGTGATTTT-A--TCG--
1 TTGCGATTTTCATTTCGCA
1493860 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*** *
1493879 TTGCGATAGCCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
** *
1493899 TTGCGATAGTCATTTTCGCG
1 TTGCGATTTTCA-TTTCGCA
1493919 TTGCGATTTT
1 TTGCGATTTT
1493929 AAGTTTCGTG
Statistics
Matches: 93, Mismatches: 11, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
14 14 0.15
15 5 0.05
16 7 0.08
17 7 0.08
18 11 0.12
19 20 0.22
20 26 0.28
21 3 0.03
ACGTcount: A:0.15, C:0.19, G:0.21, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1493869 original size:14 final size:14
Alignment explanation
Indices: 1493781--1493869 Score: 52
Period size: 14 Copynumber: 5.7 Consensus size: 14
1493771 GTGTTTCACA
*
1493781 TTGCGATTTTGTCG
1 TTGCGATTTTATCG
*
1493795 TTGCGATTTCATTTCG
1 TTGCGATTT--TATCG
*
1493811 CATTGCGATTTTGTCG
1 --TTGCGATTTTATCG
*
1493827 ATGCGATTTTCATTTCG
1 TTGCGATTTT-A--TCG
*
1493844 CATTGTGATTTTATCG
1 --TTGCGATTTTATCG
1493860 TTGCGATTTT
1 TTGCGATTTT
1493870 CATTTCGCAT
Statistics
Matches: 59, Mismatches: 7, Indels: 18
0.70 0.08 0.21
Matches are distributed among these distances:
14 27 0.46
16 11 0.19
17 3 0.05
18 10 0.17
19 8 0.14
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.49
Consensus pattern (14 bp):
TTGCGATTTTATCG
Found at i:1494387 original size:41 final size:42
Alignment explanation
Indices: 1494291--1494378 Score: 124
Period size: 41 Copynumber: 2.1 Consensus size: 42
1494281 GACTCACCTG
* *
1494291 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
* * *
1494333 TCCTCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
1494374 TCATC
1 TCATC
1494379 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 22 0.55
42 18 0.45
ACGTcount: A:0.22, C:0.43, G:0.15, T:0.20
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
Found at i:1495813 original size:14 final size:14
Alignment explanation
Indices: 1495794--1495829 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1495784 ATTGTTTAAT
1495794 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1495808 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1495822 TGATTTGT
1 TGATTTGT
1495830 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1495990 original size:19 final size:19
Alignment explanation
Indices: 1495966--1496033 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
1495956 ATCGCAACGA
1495966 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1495985 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1496004 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
1496018 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
1496034 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1496051 original size:19 final size:19
Alignment explanation
Indices: 1496023--1496110 Score: 78
Period size: 19 Copynumber: 4.8 Consensus size: 19
1496013 AACGAGAAAA
*
1496023 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1496042 TCGCATTGCGGTTTTC---
1 TCGCATTGCGATTTTCATT
* ***
1496058 TAG--TTGCGATAGCCATTT
1 TCGCATTGCGATTTTCA-TT
1496076 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1496095 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
1496111 TCGTTGCGAT
Statistics
Matches: 52, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
14 7 0.13
16 2 0.04
18 2 0.04
19 32 0.62
20 9 0.17
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1496084 original size:20 final size:20
Alignment explanation
Indices: 1496061--1496140 Score: 59
Period size: 19 Copynumber: 4.3 Consensus size: 20
1496051 GGTTTTCTAG
1496061 TTGCGATAGCCATTTTCGCA
1 TTGCGATAGCCATTTTCGCA
***
1496081 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGCCATTTTCGCA
1496100 TTGCGAT-----TTTCTCG--
1 TTGCGATAGCCATTT-TCGCA
*
1496114 TTGCGATAGCCATTTTCGCG
1 TTGCGATAGCCATTTTCGCA
1496134 TTGCGAT
1 TTGCGAT
1496141 TTCCCCGTTG
Statistics
Matches: 48, Mismatches: 3, Indels: 18
0.70 0.04 0.26
Matches are distributed among these distances:
14 7 0.15
15 2 0.04
16 3 0.06
18 3 0.06
19 17 0.35
20 16 0.33
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.41
Consensus pattern (20 bp):
TTGCGATAGCCATTTTCGCA
Found at i:1496087 original size:53 final size:53
Alignment explanation
Indices: 1496023--1496142 Score: 204
Period size: 53 Copynumber: 2.3 Consensus size: 53
1496013 AACGAGAAAA
* *
1496023 TCGCAATGCGATTTTCATTTCGCATTGCGGTTTTCTAGTTGCGATAGCCATTT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTAGTTGCGATAGCCATTT
*
1496076 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAGCCATTT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTAGTTGCGATAGCCATTT
*
1496129 TCGCGTTGCGATTT
1 TCGCATTGCGATTT
1496143 CCCCGTTGCG
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 63 1.00
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.42
Consensus pattern (53 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTAGTTGCGATAGCCATTT
Found at i:1496379 original size:20 final size:20
Alignment explanation
Indices: 1496354--1496403 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1496344 TTGAAGATGA
1496354 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
1496374 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
1496394 TTGCGATTTT
1 TTGCGATTTT
1496404 GTATTATCTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:1496456 original size:21 final size:21
Alignment explanation
Indices: 1496430--1496502 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
1496420 ATAGTCAGTA
1496430 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
1496451 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* * **
1496472 TCGCATTACGA-TTTACTTAT
1 TCGCATTGCGATTTTCCAAAT
1496492 TCGCATTGCGA
1 TCGCATTGCGA
1496503 ATTAGGAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 16 0.34
21 31 0.66
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:1496718 original size:12 final size:12
Alignment explanation
Indices: 1496699--1496732 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1496689 CTCTCCGGCG
1496699 ACATCCGTTCCT
1 ACATCCGTTCCT
*
1496711 ATATCCGTTCCT
1 ACATCCGTTCCT
1496723 ACATCC-TTCC
1 ACATCCGTTCC
1496733 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:1497308 original size:24 final size:24
Alignment explanation
Indices: 1497281--1497334 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1497271 GTATTCGAAA
*
1497281 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
1497305 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
1497329 TTTGAT
1 TTTGAT
1497335 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:1497526 original size:12 final size:12
Alignment explanation
Indices: 1497509--1497533 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1497499 ATATAATCCT
1497509 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1497521 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1497533 G
1 G
1497534 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1499823 original size:19 final size:19
Alignment explanation
Indices: 1499801--1499859 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
1499791 GGAAATTACT
1499801 ATCGCAATACGAAATGAAA
1 ATCGCAATACGAAATGAAA
*
1499820 ATCGC-A-ACG--A-GAGA
1 ATCGCAATACGAAATGAAA
*
1499834 ATCGCAATGCGAAATGAAA
1 ATCGCAATACGAAATGAAA
1499853 ATCGCAA
1 ATCGCAA
1499860 CGCTAATTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 8 0.25
15 2 0.06
16 2 0.06
17 3 0.09
18 2 0.06
19 15 0.47
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (19 bp):
ATCGCAATACGAAATGAAA
Found at i:1499847 original size:33 final size:33
Alignment explanation
Indices: 1499801--1499922 Score: 176
Period size: 33 Copynumber: 3.7 Consensus size: 33
1499791 GGAAATTACT
*
1499801 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
1499834 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1499866 TTTCGCAATGCGAAATG-AAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1499899 ATCGCAATGCGAAATGAAAATCGC
1 ATCGCAATGCGAAATGAAAATCGC
1499923 GACGCGAATT
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
32 27 0.35
33 51 0.65
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1499892 original size:32 final size:32
Alignment explanation
Indices: 1499802--1499965 Score: 165
Period size: 33 Copynumber: 5.0 Consensus size: 32
1499792 GAAATTACTA
* * *
1499802 TCGCAATACGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGCGAAATGAAAATCGCAACGCGA-AT
*
1499835 TCGCAATGCGAAATGAAAATCGCAACGCTAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAA-T
*
1499868 TCGCAATGCGAAATG-AAATCGCAACGAGGGAA-
1 TCGCAATGCGAAATGAAAATCGCAAC--GCGAAT
*
1499900 TCGCAATGCGAAATGAAAATCGCGACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAAT
* *
1499932 T--TAATTTCGCGAAATGAAAATCGCGACGCGAAT
1 TCGCAA--T-GCGAAATGAAAATCGCAACGCGAAT
1499965 T
1 T
1499966 TAATTTCGCG
Statistics
Matches: 114, Mismatches: 9, Indels: 16
0.82 0.06 0.12
Matches are distributed among these distances:
30 2 0.02
31 4 0.04
32 28 0.25
33 77 0.68
34 3 0.03
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.18
Consensus pattern (32 bp):
TCGCAATGCGAAATGAAAATCGCAACGCGAAT
Found at i:1499907 original size:65 final size:66
Alignment explanation
Indices: 1499802--1499933 Score: 221
Period size: 65 Copynumber: 2.0 Consensus size: 66
1499792 GAAATTACTA
*
1499802 TCGCAATACGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATACGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1499867 T
66 T
* * *
1499868 TCGCAATGCGAAATG-AAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCGACGCGAAT
1 TCGCAATACGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1499932 T
66 T
1499933 T
1 T
1499934 AATTTCGCGA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
65 48 0.77
66 14 0.23
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATACGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:1499941 original size:19 final size:19
Alignment explanation
Indices: 1499919--1499975 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 19
1499909 GAAATGAAAA
1499919 TCGCGACGCGAATTTAATT
1 TCGCGACGCGAATTTAATT
* **
1499938 TCGCGA----AA-TGAAAA
1 TCGCGACGCGAATTTAATT
1499952 TCGCGACGCGAATTTAATT
1 TCGCGACGCGAATTTAATT
1499971 TCGCG
1 TCGCG
1499976 TTGCGATTCT
Statistics
Matches: 27, Mismatches: 6, Indels: 10
0.63 0.14 0.23
Matches are distributed among these distances:
14 9 0.33
15 2 0.07
18 2 0.07
19 14 0.52
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (19 bp):
TCGCGACGCGAATTTAATT
Found at i:1499944 original size:33 final size:33
Alignment explanation
Indices: 1499907--1499975 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
1499897 GAATCGCAAT
1499907 GCGAAATGAAAATCGCGACGCGAATTTAATTTC
1 GCGAAATGAAAATCGCGACGCGAATTTAATTTC
1499940 GCGAAATGAAAATCGCGACGCGAATTTAATTTC
1 GCGAAATGAAAATCGCGACGCGAATTTAATTTC
1499973 GCG
1 GCG
1499976 TTGCGATTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (33 bp):
GCGAAATGAAAATCGCGACGCGAATTTAATTTC
Found at i:1499944 original size:65 final size:64
Alignment explanation
Indices: 1499805--1499955 Score: 207
Period size: 65 Copynumber: 2.3 Consensus size: 64
1499795 ATTACTATCG
* *
1499805 CAATACGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAATTT
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
* *
1499869 CGCAATGCGAAATG-AAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCGACGCGAATT
1 --CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATT
1499933 T
64 T
1499934 -AATTTCGCGAAATGAAAATCGC
1 CAA--T-GCGAAATGAAAATCGC
1499956 GACGCGAATT
Statistics
Matches: 77, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
62 2 0.03
64 1 0.01
65 56 0.73
66 18 0.23
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (64 bp):
CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
Found at i:1500011 original size:18 final size:18
Alignment explanation
Indices: 1499963--1500045 Score: 76
Period size: 18 Copynumber: 5.1 Consensus size: 18
1499953 CGCGACGCGA
*
1499963 ATTTAATTTCGCGTTGCG
1 ATTTCATTTCGCGTTGCG
*
1499981 A-TTC---TCTCGTTGCG
1 ATTTCATTTCGCGTTGCG
1499995 ATTTCATTTCGCGTTGCG
1 ATTTCATTTCGCGTTGCG
1500013 ATTTC---T--CGTTGCG
1 ATTTCATTTCGCGTTGCG
*
1500026 ATTTCATTTCGCATTGCG
1 ATTTCATTTCGCGTTGCG
1500044 AT
1 AT
1500046 AGTACTTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
13 12 0.23
14 10 0.19
15 4 0.08
16 1 0.02
17 2 0.04
18 23 0.44
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (18 bp):
ATTTCATTTCGCGTTGCG
Found at i:1500022 original size:13 final size:13
Alignment explanation
Indices: 1499968--1500030 Score: 63
Period size: 13 Copynumber: 4.4 Consensus size: 13
1499958 CGCGAATTTA
*
1499968 ATTTCGCGTTGCG
1 ATTTCTCGTTGCG
1499981 ATTCTCTCGTTGCG
1 ATT-TCTCGTTGCG
1499995 ATTTCATTTCGCGTTGCG
1 ATTTC---T--CGTTGCG
1500013 ATTTCTCGTTGCG
1 ATTTCTCGTTGCG
1500026 ATTTC
1 ATTTC
1500031 ATTTCGCATT
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
13 17 0.40
14 12 0.28
15 1 0.02
16 1 0.02
18 12 0.28
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.44
Consensus pattern (13 bp):
ATTTCTCGTTGCG
Found at i:1500023 original size:31 final size:32
Alignment explanation
Indices: 1499963--1500045 Score: 141
Period size: 31 Copynumber: 2.6 Consensus size: 32
1499953 CGCGACGCGA
*
1499963 ATTTAATTTCGCGTTGCGATTCTCTCGTTGCG
1 ATTTCATTTCGCGTTGCGATTCTCTCGTTGCG
1499995 ATTTCATTTCGCGTTGCGATT-TCTCGTTGCG
1 ATTTCATTTCGCGTTGCGATTCTCTCGTTGCG
*
1500026 ATTTCATTTCGCATTGCGAT
1 ATTTCATTTCGCGTTGCGAT
1500046 AGTACTTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
31 29 0.59
32 20 0.41
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (32 bp):
ATTTCATTTCGCGTTGCGATTCTCTCGTTGCG
Found at i:1500170 original size:14 final size:14
Alignment explanation
Indices: 1500151--1500186 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1500141 ACATCAATAA
1500151 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1500165 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1500179 AC-AATCAA
1 ACAAATCAA
1500187 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1501560 original size:21 final size:21
Alignment explanation
Indices: 1501536--1501651 Score: 56
Period size: 21 Copynumber: 5.5 Consensus size: 21
1501526 GTGGGAGGGA
1501536 CCTCTTCAACGATGACAGTGG
1 CCTCTTCAACGATGACAGTGG
* * ** *
1501557 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTCAACGATGACAGTGG
* * * * *
1501578 ACTC-TCGAGGAATGATAGGGG
1 CCTCTTCAACG-ATGACAGTGG
*
1501599 CCTCTTCAACGAT-AGGAGTGG
1 CCTCTTCAACGATGA-CAGTGG
* * **
1501620 ACTCTTGAGGGATGACAGTGG
1 CCTCTTCAACGATGACAGTGG
*
1501641 CCTCTTGAACG
1 CCTCTTCAACG
1501652 GTGGGAGGGG
Statistics
Matches: 66, Mismatches: 25, Indels: 8
0.67 0.25 0.08
Matches are distributed among these distances:
20 4 0.06
21 57 0.86
22 5 0.08
ACGTcount: A:0.22, C:0.22, G:0.34, T:0.22
Consensus pattern (21 bp):
CCTCTTCAACGATGACAGTGG
Found at i:1501575 original size:42 final size:41
Alignment explanation
Indices: 1501516--1501666 Score: 151
Period size: 42 Copynumber: 3.6 Consensus size: 41
1501506 GTGAATCGGG
** *
1501516 CTCTTGAATTGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * *
1501558 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * *
1501600 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAGTGGC
1501642 CTCTTGAACGGTGGGAGGGGACTCT
1 CTCTTGAACGGTGGGA-GGGACTCT
1501667 CGAGGAATGA
Statistics
Matches: 87, Mismatches: 17, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
41 5 0.06
42 74 0.85
43 8 0.09
ACGTcount: A:0.21, C:0.19, G:0.36, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:1501657 original size:84 final size:81
Alignment explanation
Indices: 1501546--1501718 Score: 310
Period size: 84 Copynumber: 2.1 Consensus size: 81
1501536 CCTCTTCAAC
1501546 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGG-C-CTTCAACGA
*
1501611 TAGGAGTGGACTCTTGAGG
64 TAAG-GTGGACTCTTGAGG
1501630 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTTCAACGATA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTTCAACGATA
1501695 AGGTGGACTCTTGAGG
66 AGGTGGACTCTTGAGG
1501711 GATGACAG
1 GATGACAG
1501719 GCGAGTCGGG
Statistics
Matches: 88, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
81 22 0.25
82 12 0.14
83 1 0.01
84 53 0.60
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.21
Consensus pattern (81 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTTCAACGATA
AGGTGGACTCTTGAGG
Found at i:1501666 original size:21 final size:21
Alignment explanation
Indices: 1501558--1501666 Score: 53
Period size: 21 Copynumber: 5.2 Consensus size: 21
1501548 TGACAGTGGC
1501558 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
* ** *
1501579 CTCTCG-A-GGAATGATAGGGGC
1 CTCTTGAACGG--TGGGAGGGGA
* * * *
1501600 CTCTTCAACGATAGGAGTGGA
1 CTCTTGAACGGTGGGAGGGGA
* ** * *
1501621 CTCTTG-AGGGATGACAGTGGC
1 CTCTTGAACGG-TGGGAGGGGA
1501642 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1501663 CTCT
1 CTCT
1501667 CGAGGAATGA
Statistics
Matches: 58, Mismatches: 24, Indels: 12
0.62 0.26 0.13
Matches are distributed among these distances:
19 2 0.03
20 3 0.05
21 48 0.83
22 4 0.07
23 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.39, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1501685 original size:42 final size:42
Alignment explanation
Indices: 1501555--1501685 Score: 190
Period size: 42 Copynumber: 3.1 Consensus size: 42
1501545 CGATGACAGT
1501555 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
* * * * * * * *
1501597 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGT
1 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1501639 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1501681 GGCCT
1 GGCCT
1501686 TCAACGATAA
Statistics
Matches: 73, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.21, C:0.18, G:0.40, T:0.21
Consensus pattern (42 bp):
GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
Found at i:1502096 original size:90 final size:85
Alignment explanation
Indices: 1501931--1502109 Score: 227
Period size: 90 Copynumber: 2.0 Consensus size: 85
1501921 ATTTCAAACT
*
1501931 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAAT
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAAT
*
1501996 TGGCAGCAACCAAATAAATTTAC
63 TGACAGCAACCAAATAAATTTAC
1502019 TTCAACCAAAAGACAAAACAAAAAGAC-AATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTT---A
*
1502082 GTATTGACAGCAACCGAATAAATTTAC
61 --ATTGACAGCAACCAAATAAATTTAC
1502109 T
1 T
1502110 AAGCAATCTA
Statistics
Matches: 81, Mismatches: 3, Indels: 12
0.84 0.03 0.12
Matches are distributed among these distances:
85 11 0.14
88 20 0.25
89 20 0.25
90 30 0.37
ACGTcount: A:0.48, C:0.19, G:0.11, T:0.22
Consensus pattern (85 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAATTGA
CAGCAACCAAATAAATTTAC
Found at i:1503768 original size:20 final size:19
Alignment explanation
Indices: 1503737--1503891 Score: 99
Period size: 19 Copynumber: 8.8 Consensus size: 19
1503727 TCTTTTGGTT
1503737 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
1503756 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
1503777 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1503796 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
1503810 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
1503829 G--A-G--AATCGCAACGCA
1 GAAATGAAAATCGCAACG-A
1503844 -AAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1503862 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
1503876 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1503892 TGCGATTTTG
Statistics
Matches: 106, Mismatches: 11, Indels: 38
0.68 0.07 0.25
Matches are distributed among these distances:
14 30 0.28
15 1 0.01
16 6 0.06
17 6 0.06
18 1 0.01
19 31 0.29
20 29 0.27
21 2 0.02
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1503805 original size:14 final size:14
Alignment explanation
Indices: 1503786--1503874 Score: 70
Period size: 14 Copynumber: 5.6 Consensus size: 14
1503776 GGAAATGACT
1503786 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
1503800 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
1503817 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
*
1503833 ATCGCAACGCAAAATGAAA
1 ATCGCAACG----A-GAGA
1503852 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
1503866 ATCGCAACG
1 ATCGCAACG
1503875 CGAAATGAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
14 28 0.46
15 1 0.02
16 6 0.10
17 6 0.10
18 1 0.02
19 19 0.31
ACGTcount: A:0.43, C:0.24, G:0.24, T:0.10
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:1503819 original size:33 final size:33
Alignment explanation
Indices: 1503762--1503891 Score: 206
Period size: 33 Copynumber: 3.9 Consensus size: 33
1503752 ACGAGATAAT
**
1503762 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGAAAATCGCAACGA
**
1503796 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
*
1503829 GAGAATCGCAACGCAAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
1503862 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGAAAATCGCAA
1503892 TGCGATTTTG
Statistics
Matches: 92, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
33 78 0.85
34 14 0.15
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:1503925 original size:19 final size:19
Alignment explanation
Indices: 1503892--1503936 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1503882 AAAATCGCAA
*
1503892 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
1503911 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
1503930 TGCGATT
1 TGCGATT
1503937 CTCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:1504519 original size:20 final size:20
Alignment explanation
Indices: 1504491--1504543 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1504481 GCGCTATGTA
1504491 AATCACGTTGCGAAAGTCAG
1 AATCACGTTGCGAAAGTCAG
* *
1504511 AATCGCGTTGTGAAAGTCAG
1 AATCACGTTGCGAAAGTCAG
* *
1504531 TATCTCGTTGCGA
1 AATCACGTTGCGA
1504544 TTTTGTATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.26
Consensus pattern (20 bp):
AATCACGTTGCGAAAGTCAG
Found at i:1504577 original size:20 final size:20
Alignment explanation
Indices: 1504552--1504605 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1504542 GATTTTGTAT
1504552 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
1504572 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1504592 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1504606 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1504624 original size:61 final size:61
Alignment explanation
Indices: 1504496--1504626 Score: 138
Period size: 61 Copynumber: 2.1 Consensus size: 61
1504486 ATGTAAATCA
* * * * * * ** *
1504496 CGTTGCGAAAGTCAGAATCGCGTTGTGAAAGTCAGTATCTCGTTGCGATTTTGTATTATCG
1 CGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCG
* * *
1504557 CATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT-TCG
1 CGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAATATCG
1504618 CGTTGCGAT
1 CGTTGCGAT
1504627 TTACTTATTC
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
61 54 0.96
62 2 0.04
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (61 bp):
CGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCG
Found at i:1505526 original size:23 final size:26
Alignment explanation
Indices: 1505484--1505534 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
1505474 ATAATTATGA
*
1505484 TTATAATAATCTTTAAAATC-TAAAT
1 TTATAATAATCTTCAAAATCTTAAAT
1505509 TTATAA-AAT-TTCAAAATCTTAAAT
1 TTATAATAATCTTCAAAATCTTAAAT
1505533 TT
1 TT
1505535 CAAAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 8 0.33
24 10 0.42
25 6 0.25
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (26 bp):
TTATAATAATCTTCAAAATCTTAAAT
Found at i:1506058 original size:20 final size:21
Alignment explanation
Indices: 1506033--1506125 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
1506023 TTTTCCCAAT
*
1506033 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1506053 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
1506074 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1506094 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1506115 TCGCAATGCGA
1 TCGCAATGCGA
1506126 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1506078 original size:41 final size:41
Alignment explanation
Indices: 1506033--1506125 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
1506023 TTTTCCCAAT
1506033 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1506074 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1506115 TCGCAATGCGA
1 TCGCAATGCGA
1506126 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1506138 original size:41 final size:41
Alignment explanation
Indices: 1506052--1506186 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
1506042 GAATAAGTAA
** *
1506052 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
1506093 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * * *
1506134 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTGACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
1506175 TTCGCAACGCGA
1 ATCGCAACGCGA
1506187 TTCTGACTTT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
40 5 0.06
41 73 0.91
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:1506204 original size:20 final size:20
Alignment explanation
Indices: 1506156--1506208 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1506146 TAATACAAAA
* *
1506156 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
1506176 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
1506196 TCGCAACGCGATT
1 TCGCAACGCGATT
1506209 TACATAGCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:1506788 original size:19 final size:18
Alignment explanation
Indices: 1506726--1506791 Score: 87
Period size: 19 Copynumber: 3.5 Consensus size: 18
1506716 TTCGAGAATG
1506726 AAAATCGCAACGCGGAAAT
1 AAAATCGCAACGC-GAAAT
*
1506745 AACTATCGCAACGCGAAAT
1 AA-AATCGCAACGCGAAAT
*
1506764 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAA-T
1506783 AAAATCGCA
1 AAAATCGCA
1506792 TTGCGATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
18 14 0.33
19 18 0.43
20 10 0.24
ACGTcount: A:0.47, C:0.26, G:0.17, T:0.11
Consensus pattern (18 bp):
AAAATCGCAACGCGAAAT
Found at i:1506835 original size:20 final size:19
Alignment explanation
Indices: 1506787--1506952 Score: 127
Period size: 20 Copynumber: 9.1 Consensus size: 19
1506777 GAAACCAAAA
*
1506787 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1506806 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1506825 TCGCGGTTGCGATTTTAATT
1 TCGC-GTTGCGATTTTCATT
*
1506845 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
1506861 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1506878 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
1506892 TCTCGTTGTGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1506911 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1506931 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1506951 TC
1 TC
1506953 AACCAAAAGA
Statistics
Matches: 117, Mismatches: 17, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
14 19 0.16
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 41 0.35
20 48 0.41
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1506868 original size:39 final size:39
Alignment explanation
Indices: 1506792--1506868 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
1506782 CAAAATCGCA
* * *
1506792 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCGG
1 TTGCGATTTTAATTTCGCGTTGCGATTGTCATGTCGCGG
1506831 TTGCGATTTTAATTTCGCGTTGCGATTGTC-TGGTCGCG
1 TTGCGATTTTAATTTCGCGTTGCGATTGTCAT-GTCGCG
1506869 ATAGTCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 1 0.03
39 33 0.97
ACGTcount: A:0.10, C:0.19, G:0.26, T:0.44
Consensus pattern (39 bp):
TTGCGATTTTAATTTCGCGTTGCGATTGTCATGTCGCGG
Found at i:1506922 original size:34 final size:33
Alignment explanation
Indices: 1506842--1506927 Score: 127
Period size: 33 Copynumber: 2.6 Consensus size: 33
1506832 TGCGATTTTA
* *
1506842 ATTTCGCGTTGCGATTGTCTGGTCGCGATAGTC
1 ATTTCGCGTTGCGATTCTCTCGTCGCGATAGTC
* *
1506875 ATTTCGCGTTGCGATTCTCTCGTTGTGATAGTC
1 ATTTCGCGTTGCGATTCTCTCGTCGCGATAGTC
1506908 ATTTCCGCGTTGCGATTCTC
1 ATTT-CGCGTTGCGATTCTC
1506928 ATTATCTCGT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
33 33 0.69
34 15 0.31
ACGTcount: A:0.12, C:0.23, G:0.26, T:0.40
Consensus pattern (33 bp):
ATTTCGCGTTGCGATTCTCTCGTCGCGATAGTC
Found at i:1509028 original size:42 final size:42
Alignment explanation
Indices: 1508948--1509070 Score: 106
Period size: 42 Copynumber: 2.9 Consensus size: 42
1508938 GCCCGACTCG
* * * * * * *
1508948 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGACC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGACC
*
1508990 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGACC
* * * *
1509032 ACTGTTA-TCGTCGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCCTCCCACCATTCAAGAG
1509071 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 5 0.07
42 60 0.90
43 2 0.03
ACGTcount: A:0.24, C:0.37, G:0.16, T:0.23
Consensus pattern (42 bp):
CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGACC
Found at i:1510445 original size:14 final size:14
Alignment explanation
Indices: 1510426--1510461 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1510416 ATTGTTTAAT
1510426 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1510440 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1510454 TGATTTGT
1 TGATTTGT
1510462 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1510662 original size:19 final size:19
Alignment explanation
Indices: 1510640--1510790 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
1510630 CGAAATTAAA
1510640 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1510659 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1510674 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
1510692 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
1510706 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1510725 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1510740 -TCTCGTTGCGATTTTCAA
1 TTCGCGTTGCGATTTTCAT
* ** *
1510758 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1510777 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1510791 GGACATTAAG
Statistics
Matches: 94, Mismatches: 22, Indels: 31
0.64 0.15 0.21
Matches are distributed among these distances:
14 28 0.30
16 6 0.06
17 6 0.06
19 44 0.47
20 10 0.11
ACGTcount: A:0.16, C:0.23, G:0.21, T:0.41
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1510686 original size:33 final size:32
Alignment explanation
Indices: 1510644--1510770 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
1510634 ATTAAATTCG
1510644 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
1510677 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
1510710 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
1510743 CGTTGCGATTTTCAATTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1510771 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.42
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1510733 original size:66 final size:66
Alignment explanation
Indices: 1510637--1510769 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
1510627 ACACGAAATT
* *
1510637 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCAATTCGCATTGC
1510702 G
66 G
*
1510703 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAATTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCAATTCGCATTGC
1510768 G
66 G
1510769 A
1 A
1510770 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCAATTCGCATTGC
G
Found at i:1513080 original size:12 final size:12
Alignment explanation
Indices: 1513063--1513087 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1513053 TCTTCGGGGA
1513063 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1513075 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1513087 C
1 C
1513088 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1513296 original size:24 final size:24
Alignment explanation
Indices: 1513262--1513316 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
1513252 CTGAAACATC
*
1513262 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAT
* *
1513286 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAT
1513310 AT-AAAAT
1 ATCAAAAT
1513317 TTCGAATACT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.25
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAT
Found at i:1514399 original size:20 final size:20
Alignment explanation
Indices: 1514374--1514431 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
1514364 ATTCATTTGA
1514374 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1514394 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
1514414 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
1514432 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Done.