Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold337
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1638316
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.28
Warning! 264207 characters in sequence are not A, C, G, or T
File 6 of 5
Found at i:1220116 original size:4 final size:4
Alignment explanation
Indices: 1220109--1220163 Score: 74
Period size: 4 Copynumber: 13.8 Consensus size: 4
1220099 GTTTAAATAA
** * *
1220109 AAAT AAAT AAAT AAAT TGAT AAAT AAAT AAAT ACAT ACAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1220157 AAAT AAA
1 AAAT AAA
1220164 AATTATTCGG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:1220132 original size:16 final size:16
Alignment explanation
Indices: 1220102--1220163 Score: 74
Period size: 16 Copynumber: 4.0 Consensus size: 16
1220092 AATAAAAGTT
1220102 TAAATAAA-A-ATAAA
1 TAAATAAATACATAAA
**
1220116 TAAATAAATTGATAAA
1 TAAATAAATACATAAA
*
1220132 TAAATAAATACATACA
1 TAAATAAATACATAAA
*
1220148 TAAATAAATAAATAAA
1 TAAATAAATACATAAA
1220164 AATTATTCGG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
14 8 0.20
16 32 0.80
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (16 bp):
TAAATAAATACATAAA
Found at i:1220134 original size:20 final size:20
Alignment explanation
Indices: 1220109--1220163 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
1220099 GTTTAAATAA
**
1220109 AAATAAATAAATAAATTGAT
1 AAATAAATAAATAAATACAT
*
1220129 AAATAAATAAATACATACAT
1 AAATAAATAAATAAATACAT
1220149 AAATAAATAAATAAA
1 AAATAAATAAATAAA
1220164 AATTATTCGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (20 bp):
AAATAAATAAATAAATACAT
Found at i:1221892 original size:14 final size:14
Alignment explanation
Indices: 1221873--1221900 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1221863 AGCATTTTGC
1221873 CTTTGTGTACACAT
1 CTTTGTGTACACAT
1221887 CTTTGTGTACACAT
1 CTTTGTGTACACAT
1221901 TAAAAATAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.43
Consensus pattern (14 bp):
CTTTGTGTACACAT
Found at i:1239241 original size:49 final size:49
Alignment explanation
Indices: 1239169--1239317 Score: 262
Period size: 49 Copynumber: 3.0 Consensus size: 49
1239159 AGCAAGAAAA
* *
1239169 AACAAAATCTTCACAGGAAAATATCATTTTGCAAGAAGTCGAATGATGT
1 AACAAAATCTTCACAGGAAAATATCATTTTGCAAGAAGTTGAATGATAT
1239218 AACAAAATCTTCACAGGAAAATATCATTTTGCAAGAAGTTGAATGATAT
1 AACAAAATCTTCACAGGAAAATATCATTTTGCAAGAAGTTGAATGATAT
* *
1239267 AACACAATCTTCACAAGAAAATATCATTTTGCAAGAAGTTGAATGATAT
1 AACAAAATCTTCACAGGAAAATATCATTTTGCAAGAAGTTGAATGATAT
1239316 AA
1 AA
1239318 ATAAAGCACG
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 96 1.00
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.28
Consensus pattern (49 bp):
AACAAAATCTTCACAGGAAAATATCATTTTGCAAGAAGTTGAATGATAT
Found at i:1243304 original size:159 final size:158
Alignment explanation
Indices: 1243015--1243331 Score: 625
Period size: 159 Copynumber: 2.0 Consensus size: 158
1243005 AATCGGCTGT
1243015 CCACTAGCGCGGCATCTCCTCGGCCCGTGTTATGAAATTGTACACTCAACGTGGTGGGTTTGAAA
1 CCACTAGCGCGGCATCTCCTCGGCCCGTGTTATGAAATTGTACACTCAACGTGGTGGGTTTGAAA
1243080 TGTTTGCAGTTTGATAACTGAATTTTATTTTCCAACAAAAAAACTATTTCATGACATAGACAATA
66 TGTTTGCAGTTTGATAACTGAATTTTATTTTCCAACAAAAAAACTATTTCATGACATAGACAATA
1243145 TCACAAAGAACGCCCTTTTTTCAATGAC
131 TCACAAAGAACGCCCTTTTTTCAATGAC
1243173 NCCACTAGCGCGGCATCTCCTCGGCCCGTGTTATGAAATTGTACACTCAACGTGGTGGGTTTGAA
1 -CCACTAGCGCGGCATCTCCTCGGCCCGTGTTATGAAATTGTACACTCAACGTGGTGGGTTTGAA
1243238 ATGTTTGCAGTTTGATAACTGAATTTTATTTTCCAACAAAAAAACTATTTCATGACATAGACAAT
65 ATGTTTGCAGTTTGATAACTGAATTTTATTTTCCAACAAAAAAACTATTTCATGACATAGACAAT
1243303 ATCACAAAGAACGCCCTTTTTTCAATGAC
130 ATCACAAAGAACGCCCTTTTTTCAATGAC
1243332 AGTCATACTA
Statistics
Matches: 158, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
159 158 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (158 bp):
CCACTAGCGCGGCATCTCCTCGGCCCGTGTTATGAAATTGTACACTCAACGTGGTGGGTTTGAAA
TGTTTGCAGTTTGATAACTGAATTTTATTTTCCAACAAAAAAACTATTTCATGACATAGACAATA
TCACAAAGAACGCCCTTTTTTCAATGAC
Found at i:1253244 original size:83 final size:79
Alignment explanation
Indices: 1253157--1253326 Score: 202
Period size: 79 Copynumber: 2.1 Consensus size: 79
1253147 GGCTATAAAG
*
1253157 TGATTCTTATAATGG-AATAC-ACTCCAAACCGCTGTTGAAAAAAAATAGTTCAGTACTGGTTTC
1 TGATTCTTATAA-GGAAATACTAC-CCAAACCAC--TTG--AAAAAATAGTTCAGTACTGGTTTC
1253220 TTTCAA-ATGTGGTTGCAAAT
60 TTTCAATA-GTGGTTGCAAAT
* * * * *
1253240 TGATTCTTCTAAGGAAATACTACCCAAGCCACTTGAAATATTAGTTCAGTAGTGGTTTCTTTCAA
1 TGATTCTTATAAGGAAATACTACCCAAACCACTTGAAAAAATAGTTCAGTACTGGTTTCTTTCAA
1253305 TAGTGGTTGCAAAT
66 TAGTGGTTGCAAAT
1253319 TGATTCTT
1 TGATTCTT
1253327 TTTATGAAAT
Statistics
Matches: 78, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
79 47 0.60
80 1 0.01
81 3 0.04
82 2 0.03
83 23 0.29
84 2 0.03
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (79 bp):
TGATTCTTATAAGGAAATACTACCCAAACCACTTGAAAAAATAGTTCAGTACTGGTTTCTTTCAA
TAGTGGTTGCAAAT
Found at i:1270574 original size:2 final size:2
Alignment explanation
Indices: 1270567--1270606 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1270557 AATAAATGAT
1270567 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1270607 AATTTGCCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1271288 original size:2 final size:2
Alignment explanation
Indices: 1271281--1271343 Score: 108
Period size: 2 Copynumber: 31.5 Consensus size: 2
1271271 CAACAATAAT
* *
1271281 GA GA GA GA GA GA GG GA GA GA GA AA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1271323 GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA G
1271344 TATGCTCTTA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1275926 original size:4 final size:4
Alignment explanation
Indices: 1275917--1275960 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
1275907 CTTGTATTTG
* * * *
1275917 GAGA GAGA GACA GAGA GAGA GAGA GACA GATA GAGA GACA GAGA
1 GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA
1275961 CAGACAGACA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.50, C:0.07, G:0.41, T:0.02
Consensus pattern (4 bp):
GAGA
Found at i:1275933 original size:10 final size:10
Alignment explanation
Indices: 1275918--1275968 Score: 52
Period size: 10 Copynumber: 5.3 Consensus size: 10
1275908 TTGTATTTGG
1275918 AGAGAGAGAC
1 AGAGAGAGAC
1275928 AGAGAGAG--
1 AGAGAGAGAC
* *
1275936 AGAGAGACAG
1 AGAGAGAGAC
*
1275946 ATAGAGAGAC
1 AGAGAGAGAC
*
1275956 AGAGACAGAC
1 AGAGAGAGAC
1275966 AGA
1 AGA
1275969 CAGACAGACA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
8 7 0.21
10 26 0.79
ACGTcount: A:0.51, C:0.10, G:0.37, T:0.02
Consensus pattern (10 bp):
AGAGAGAGAC
Found at i:1275936 original size:14 final size:14
Alignment explanation
Indices: 1275917--1275972 Score: 67
Period size: 14 Copynumber: 4.0 Consensus size: 14
1275907 CTTGTATTTG
1275917 GAGAGAGAGACAGA
1 GAGAGAGAGACAGA
* *
1275931 GAGAGAGAGAGACA
1 GAGAGAGAGACAGA
*
1275945 GATAGAGAGACAGA
1 GAGAGAGAGACAGA
* *
1275959 GACAGACAGACAGA
1 GAGAGAGAGACAGA
1275973 CAGACAGACA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.50, C:0.11, G:0.38, T:0.02
Consensus pattern (14 bp):
GAGAGAGAGACAGA
Found at i:1275967 original size:4 final size:4
Alignment explanation
Indices: 1275924--1275990 Score: 75
Period size: 4 Copynumber: 17.2 Consensus size: 4
1275914 TTGGAGAGAG
* * * * *
1275924 AGAC AGAG AGAG AGAG AGAC AGAT AGAG AGAC AG-- AGAC AGAC AGAC
1 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC
1275970 AGAC AGAC AGAC AGAC AGAC A
1 AGAC AGAC AGAC AGAC AGAC A
1275991 CCGAAAGCCC
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
2 2 0.04
4 54 0.96
ACGTcount: A:0.51, C:0.16, G:0.31, T:0.01
Consensus pattern (4 bp):
AGAC
Found at i:1276034 original size:2 final size:2
Alignment explanation
Indices: 1276027--1276066 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1276017 AATTATATCT
*
1276027 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GG GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1276067 TGCGGACTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1277931 original size:11 final size:11
Alignment explanation
Indices: 1277915--1277983 Score: 57
Period size: 11 Copynumber: 6.3 Consensus size: 11
1277905 CCCATTTTTG
1277915 CGTTCGCTCAC
1 CGTTCGCTCAC
*
1277926 CGTTCGCTCAG
1 CGTTCGCTCAC
* *
1277937 CGTGCGTTCAC
1 CGTTCGCTCAC
* *
1277948 CGATCGCTCAG
1 CGTTCGCTCAC
** *
1277959 CGCGCGTTCAC
1 CGTTCGCTCAC
*
1277970 CGTTCGCCCAC
1 CGTTCGCTCAC
1277981 CGT
1 CGT
1277984 GTTAATCTTA
Statistics
Matches: 42, Mismatches: 16, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
11 42 1.00
ACGTcount: A:0.10, C:0.42, G:0.25, T:0.23
Consensus pattern (11 bp):
CGTTCGCTCAC
Found at i:1277947 original size:22 final size:22
Alignment explanation
Indices: 1277922--1277976 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1277912 TTGCGTTCGC
*
1277922 TCACCGTTCGCTCAGCGTGCGT
1 TCACCGTTCGCTCAGCGCGCGT
*
1277944 TCACCGATCGCTCAGCGCGCGT
1 TCACCGTTCGCTCAGCGCGCGT
1277966 TCACCGTTCGC
1 TCACCGTTCGC
1277977 CCACCGTGTT
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:0.11, C:0.40, G:0.25, T:0.24
Consensus pattern (22 bp):
TCACCGTTCGCTCAGCGCGCGT
Found at i:1278832 original size:21 final size:22
Alignment explanation
Indices: 1278806--1278855 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
1278796 GTAATTAACA
1278806 CGCATGTTCA-CACAAACAAGT
1 CGCATGTTCAGCACAAACAAGT
* *
1278827 CTCATG-TCAGCATAAACAAGT
1 CGCATGTTCAGCACAAACAAGT
1278848 CGCATGTT
1 CGCATGTT
1278856 GTCATAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 20 0.83
22 1 0.04
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (22 bp):
CGCATGTTCAGCACAAACAAGT
Found at i:1279644 original size:21 final size:22
Alignment explanation
Indices: 1279615--1279660 Score: 85
Period size: 21 Copynumber: 2.1 Consensus size: 22
1279605 TTCTGATAAA
1279615 TATAGTTTCACAATTGTGAAAC
1 TATAGTTTCACAATTGTGAAAC
1279637 TATA-TTTCACAATTGTGAAAC
1 TATAGTTTCACAATTGTGAAAC
1279658 TAT
1 TAT
1279661 GATTAACAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (22 bp):
TATAGTTTCACAATTGTGAAAC
Found at i:1279669 original size:21 final size:21
Alignment explanation
Indices: 1279624--1279669 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1279614 ATATAGTTTC
*
1279624 ACAATTGTGAAACTATATTTC
1 ACAATTGTGAAACTATATTTA
1279645 ACAATTGTGAAACTATGA-TTA
1 ACAATTGTGAAACTAT-ATTTA
1279666 ACAA
1 ACAA
1279670 CAATTAGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (21 bp):
ACAATTGTGAAACTATATTTA
Found at i:1279844 original size:20 final size:20
Alignment explanation
Indices: 1279776--1279851 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
1279766 GATATTCATT
1279776 CGTTAACTATAGTTTACAAC
1 CGTTAACTATAGTTTACAAC
*
1279796 CGTTTAA-TATAATTTTACAGA-
1 CG-TTAACTAT-AGTTTACA-AC
* **
1279817 TGAAAACTATAGTTTACAAC
1 CGTTAACTATAGTTTACAAC
1279837 CGTTAACTATAGTTT
1 CGTTAACTATAGTTT
1279852 GTCGTTCGTA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
19 1 0.02
20 26 0.60
21 15 0.35
22 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (20 bp):
CGTTAACTATAGTTTACAAC
Found at i:1279980 original size:25 final size:23
Alignment explanation
Indices: 1279952--1280015 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 23
1279942 GTTTGCCATA
1279952 GACATAATTATCTTGCACTGATGTT
1 GACATAATTATCTTGCAC--ATGTT
*
1279977 GACATAATGT-TTTTG--CATGTT
1 GACATAAT-TATCTTGCACATGTT
1279998 GACATAATTTATCTTGCA
1 GACATAA-TTATCTTGCA
1280016 TGTAGGGGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
21 13 0.41
22 5 0.16
23 1 0.03
25 12 0.38
26 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (23 bp):
GACATAATTATCTTGCACATGTT
Found at i:1279998 original size:21 final size:22
Alignment explanation
Indices: 1279972--1280018 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
1279962 TCTTGCACTG
1279972 ATGTTGACATAATGTT-T-TTGC
1 ATGTTGACATAAT-TTATCTTGC
1279993 ATGTTGACATAATTTATCTTGC
1 ATGTTGACATAATTTATCTTGC
1280015 ATGT
1 ATGT
1280019 AGGGGACAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 2 0.08
21 14 0.58
22 8 0.33
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.47
Consensus pattern (22 bp):
ATGTTGACATAATTTATCTTGC
Found at i:1280121 original size:21 final size:21
Alignment explanation
Indices: 1280095--1280151 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
1280085 ATGTTCTTGC
1280095 ATGTTGACATTATTTTATTAT
1 ATGTTGACATTATTTTATTAT
1280116 ATGTTGACATTATTTTATTAT
1 ATGTTGACATTATTTTATTAT
1280137 ATGTTGACATTATTT
1 ATGTTGACATTATTT
1280152 ATCTTTCACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.28, C:0.05, G:0.11, T:0.56
Consensus pattern (21 bp):
ATGTTGACATTATTTTATTAT
Found at i:1285560 original size:2 final size:2
Alignment explanation
Indices: 1285553--1285597 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1285543 AGTCTTTAGA
1285553 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1285595 TC T
1 TC T
1285598 GAATGAACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1295676 original size:48 final size:48
Alignment explanation
Indices: 1295533--1296049 Score: 800
Period size: 48 Copynumber: 10.6 Consensus size: 48
1295523 ACAAAACAAA
* * *
1295533 GCTAAATTAACCACAGTAGATAAATTGTAGCTTTAAATGTTTGGTGGT
1 GCTAAATTAACCACAGTAAATAAACTGTAGTTTTAAATGTTTGGTGGT
* * *
1295581 GCTAAATTAACCACAGTAATTGAACTGTTACAGTAGCTTTAAGTGTTTGGTGGT
1 GCTAAATTAACCACAGTAAATAAACTG-T--AGT---TTTAAATGTTTGGTGGT
* *
1295635 GCTAAATTGACCACAGTAAATGAACTGTAGTTTTAAATGTTTGGTGGT
1 GCTAAATTAACCACAGTAAATAAACTGTAGTTTTAAATGTTTGGTGGT
* *
1295683 GCTAAATTATCCACAGTAAATAAACTGTAGTTTTAAGTGTTTGGTGGT
1 GCTAAATTAACCACAGTAAATAAACTGTAGTTTTAAATGTTTGGTGGT
*
1295731 GCTAAATTAACCGCAGTAAATAAACTGTAGTTTTAAATGTTTGGTGGT
1 GCTAAATTAACCACAGTAAATAAACTGTAGTTTTAAATGTTTGGTGGT
* *
1295779 GCTAAATTAACCACAGTAAATGAACTGTAGTTTTTAATGTTTGGTGGT
1 GCTAAATTAACCACAGTAAATAAACTGTAGTTTTAAATGTTTGGTGGT
* *
1295827 GCTAAATTATCCACAGTAAATAAACTGTAGTTTTAAGTGTTTGGTGGT
1 GCTAAATTAACCACAGTAAATAAACTGTAGTTTTAAATGTTTGGTGGT
1295875 GCTAAATTAACCACAGTAAATAAACTGTAGTTTTAAATGTTTGGTGGT
1 GCTAAATTAACCACAGTAAATAAACTGTAGTTTTAAATGTTTGGTGGT
*
1295923 GCTAAATTAACCACAGTAAATGAACTGTAGTTTTAAATGTTTGGTGGT
1 GCTAAATTAACCACAGTAAATAAACTGTAGTTTTAAATGTTTGGTGGT
* *
1295971 GCTAAATTATCCACAGTAAATAAACTGTAGTTTTAAGTGTTTGGTGGT
1 GCTAAATTAACCACAGTAAATAAACTGTAGTTTTAAATGTTTGGTGGT
* *
1296019 GCTAAATTAACCGCTGTAAATAAACTGTAGT
1 GCTAAATTAACCACAGTAAATAAACTGTAGT
1296050 CTGGAGTTTG
Statistics
Matches: 431, Mismatches: 32, Indels: 12
0.91 0.07 0.03
Matches are distributed among these distances:
48 383 0.89
49 1 0.00
51 5 0.01
53 1 0.00
54 41 0.10
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (48 bp):
GCTAAATTAACCACAGTAAATAAACTGTAGTTTTAAATGTTTGGTGGT
Found at i:1296209 original size:2 final size:2
Alignment explanation
Indices: 1296202--1296245 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1296192 AATGGTAGGC
1296202 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 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
1296244 AG
1 AG
1296246 TAGCTGTCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1306796 original size:4 final size:4
Alignment explanation
Indices: 1306787--1306876 Score: 180
Period size: 4 Copynumber: 22.5 Consensus size: 4
1306777 AAATTACATT
1306787 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1306835 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TA
1306877 AAAAAACCCG
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 86 1.00
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (4 bp):
TAGA
Found at i:1310567 original size:17 final size:17
Alignment explanation
Indices: 1310541--1310576 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1310531 CTATTTGATC
*
1310541 AAGAATTATAGACCAGG
1 AAGAACTATAGACCAGG
1310558 AAGAACTATAGACCAGG
1 AAGAACTATAGACCAGG
1310575 AA
1 AA
1310577 CCGTCGCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.50, C:0.14, G:0.22, T:0.14
Consensus pattern (17 bp):
AAGAACTATAGACCAGG
Found at i:1337820 original size:2 final size:2
Alignment explanation
Indices: 1337813--1337849 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1337803 AATTAGGCCA
1337813 TC TC TC TC TC TC TC TC TC TC TC 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 T
1337850 AGATGTCCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1358559 original size:21 final size:21
Alignment explanation
Indices: 1358511--1358560 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1358501 TCTCTCACAG
*
1358511 GTTGCAGGAACTCTCGCATAC
1 GTTGCATGAACTCTCGCATAC
* *
1358532 GTTGCATGAGCTCTCGCATTC
1 GTTGCATGAACTCTCGCATAC
1358553 GTTGCATG
1 GTTGCATG
1358561 CGTTTTAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (21 bp):
GTTGCATGAACTCTCGCATAC
Found at i:1360534 original size:21 final size:21
Alignment explanation
Indices: 1360508--1360555 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1360498 CTTACACTCA
1360508 TGCAACAAATGCGAGAGCTCG
1 TGCAACAAATGCGAGAGCTCG
** * *
1360529 TGCAACCTATGCGAGAGTTTG
1 TGCAACAAATGCGAGAGCTCG
1360550 TGCAAC
1 TGCAAC
1360556 GTAGGAGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (21 bp):
TGCAACAAATGCGAGAGCTCG
Found at i:1369765 original size:20 final size:19
Alignment explanation
Indices: 1369723--1369765 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
1369713 AAATGCTTTG
*
1369723 TGTTTTTACATAAGTTTTG
1 TGTTTTTACATAAGTTTTC
1369742 TGTTTTTACAATTAA-TTTTC
1 TGTTTTTAC-A-TAAGTTTTC
1369762 TGTT
1 TGTT
1369766 GGATGAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
20 9 0.43
21 3 0.14
ACGTcount: A:0.21, C:0.07, G:0.12, T:0.60
Consensus pattern (19 bp):
TGTTTTTACATAAGTTTTC
Found at i:1381905 original size:36 final size:36
Alignment explanation
Indices: 1381864--1381935 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
1381854 ACTCGGGAGC
* *
1381864 TACGCTCCCTCGGGTCATTTTGACCACGCCCATCGG
1 TACGCTCCCTCGGGTCATTATGACCACACCCATCGG
*
1381900 TACGCTCCCTCGTGTCATTATGACCACACCCATCGG
1 TACGCTCCCTCGGGTCATTATGACCACACCCATCGG
1381936 GTACCTGCAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.17, C:0.39, G:0.19, T:0.25
Consensus pattern (36 bp):
TACGCTCCCTCGGGTCATTATGACCACACCCATCGG
Found at i:1384574 original size:59 final size:59
Alignment explanation
Indices: 1384473--1384605 Score: 178
Period size: 59 Copynumber: 2.2 Consensus size: 59
1384463 TACATATTAT
* *
1384473 AGTTTTTATTAATTAATTAAGATCTTCCGTTTCCAACGGAAGACCTTATAGTTTTTGTAC
1 AGTTTTTATT-ATTAATTAAGATCTTCCGTTTCCAACAGAAGACCTTATAGTTTTCGTAC
* *
1384533 AGTTTCTTATTATT-ATTAAGGTCTTCCGTTTCCAACAGAAGACCTTATTGTTTTCGTAC
1 AGTTT-TTATTATTAATTAAGATCTTCCGTTTCCAACAGAAGACCTTATAGTTTTCGTAC
* *
1384592 GGTTTAGTATTATT
1 AGTTT-TTATTATT
1384606 TTTTTTCCAA
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
59 52 0.80
60 8 0.12
61 5 0.08
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.45
Consensus pattern (59 bp):
AGTTTTTATTATTAATTAAGATCTTCCGTTTCCAACAGAAGACCTTATAGTTTTCGTAC
Found at i:1393503 original size:2 final size:2
Alignment explanation
Indices: 1393496--1393576 Score: 135
Period size: 2 Copynumber: 40.5 Consensus size: 2
1393486 TCAAAATTGC
1393496 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 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
* * *
1393538 AG AG AG AG AG AG AG AG AG AG AC AG AG AC AG AG AC AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1393577 CAGACAGACA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.04, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1393577 original size:6 final size:6
Alignment explanation
Indices: 1393500--1393658 Score: 105
Period size: 6 Copynumber: 26.8 Consensus size: 6
1393490 AATTGCAGAG
* * * * * * * *
1393500 AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG
1 AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC
* *
1393548 AGAGAG AGAGAC AGAGAC AGAGAC AGAGAC AGACAGAC AGACA- AGAGAC
1 AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC AG--AGAC AGAGAC AGAGAC
* * * *
1393597 AAAGAC AGAGA- AG-GAATT AGAGAC AGACA- AGAGAG AGAGA- AG-GAC
1 AGAGAC AGAGAC AGAG-A-C AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC
*
1393642 AGAGAC AGACAC AGAGA
1 AGAGAC AGAGAC AGAGA
1393659 GAAAGAGAGA
Statistics
Matches: 133, Mismatches: 10, Indels: 20
0.82 0.06 0.12
Matches are distributed among these distances:
4 3 0.02
5 15 0.11
6 105 0.79
7 3 0.02
8 7 0.05
ACGTcount: A:0.52, C:0.09, G:0.38, T:0.01
Consensus pattern (6 bp):
AGAGAC
Found at i:1393577 original size:12 final size:12
Alignment explanation
Indices: 1393496--1393670 Score: 126
Period size: 12 Copynumber: 14.6 Consensus size: 12
1393486 TCAAAATTGC
*
1393496 AGAGAGAGAGAG
1 AGAGAGAGACAG
*
1393508 AGAGAGAGAGAG
1 AGAGAGAGACAG
*
1393520 AGAGAGAGAGAG
1 AGAGAGAGACAG
*
1393532 AGAGAGAGAGAG
1 AGAGAGAGACAG
*
1393544 AGAGAGAGAGAG
1 AGAGAGAGACAG
*
1393556 AGACAGAGACAG
1 AGAGAGAGACAG
*
1393568 AGACAGAGACAG
1 AGAGAGAGACAG
* *
1393580 ACAGACAGACAAG
1 AGAGAGAGAC-AG
* *
1393593 AGACAAAGACAG
1 AGAGAGAGACAG
*
1393605 AGA-AG-GA-ATT
1 AGAGAGAGACA-G
*
1393615 AGAGACAGACAAG
1 AGAGAGAGAC-AG
1393628 AGAGAGAGA-AG
1 AGAGAGAGACAG
*
1393639 -GACAGAGACAG
1 AGAGAGAGACAG
* *
1393650 ACACAGAGAGAAAG
1 --AGAGAGAGACAG
1393664 AGAGAGA
1 AGAGAGA
1393671 AATAAAAAAA
Statistics
Matches: 135, Mismatches: 18, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
9 1 0.01
10 12 0.09
11 6 0.04
12 90 0.67
13 17 0.13
14 9 0.07
ACGTcount: A:0.52, C:0.09, G:0.38, T:0.01
Consensus pattern (12 bp):
AGAGAGAGACAG
Found at i:1394040 original size:2 final size:2
Alignment explanation
Indices: 1394033--1394091 Score: 91
Period size: 2 Copynumber: 29.5 Consensus size: 2
1394023 TCAAAATTGC
*
1394033 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AC
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* *
1394075 AG AG AC AG AG AC AG AG A
1 AG AG AG AG AG AG AG AG A
1394092 CAAGACAGAC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.05, G:0.44, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1394092 original size:6 final size:6
Alignment explanation
Indices: 1394032--1394178 Score: 101
Period size: 6 Copynumber: 25.0 Consensus size: 6
1394022 GTCAAAATTG
* * * * * *
1394032 CAGAGA GAGAGA GAGAGA GAGAGA GAGAGA GAGAGA GAGAGA CAGAGA
1 CAGAGA CAGAGA CAGAGA CAGAGA CAGAGA CAGAGA CAGAGA CAGAGA
* *
1394080 CAGAGA CAGAGA CA-AGA CAGACAGA CAGACA -AGAGA CAAAGA CAGAGA
1 CAGAGA CAGAGA CAGAGA CAG--AGA CAGAGA CAGAGA CAGAGA CAGAGA
* * * *
1394128 -AG-GAA TTAGAGA CAGACA -AGAGA GAGAGA -AG-GA CAGAGA CAGACA
1 CAGAG-A -CAGAGA CAGAGA CAGAGA CAGAGA CAGAGA CAGAGA CAGAGA
1394173 CAGAGA
1 CAGAGA
1394179 GAAAGAGAGA
Statistics
Matches: 119, Mismatches: 11, Indels: 22
0.78 0.07 0.14
Matches are distributed among these distances:
4 3 0.03
5 20 0.17
6 86 0.72
7 3 0.03
8 7 0.06
ACGTcount: A:0.52, C:0.12, G:0.35, T:0.01
Consensus pattern (6 bp):
CAGAGA
Found at i:1394121 original size:25 final size:25
Alignment explanation
Indices: 1394077--1394125 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1394067 AGAGAGACAG
*
1394077 AGACAGAGACAGAGACAAGACAGAC
1 AGACAGACACAGAGACAAGACAGAC
1394102 AGACAGACA-AGAGACAAAGACAGA
1 AGACAGACACAGAGAC-AAGACAGA
1394126 GAAGGAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.18, G:0.27, T:0.00
Consensus pattern (25 bp):
AGACAGACACAGAGACAAGACAGAC
Found at i:1395160 original size:26 final size:27
Alignment explanation
Indices: 1395130--1395198 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 27
1395120 ATGGTCGATA
* *
1395130 ACGATG-TGATGGTAATGTTGATGACG
1 ACGATGATGATGGTAATGATGACGACG
*
1395156 ACGATGATGTTATGGTGATGATGACGACG
1 ACGATGATG--ATGGTAATGATGACGACG
*
1395185 ATGATGATGATGGT
1 ACGATGATGATGGT
1395199 CACGTCGATG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 6 0.17
27 7 0.19
29 23 0.64
ACGTcount: A:0.28, C:0.07, G:0.35, T:0.30
Consensus pattern (27 bp):
ACGATGATGATGGTAATGATGACGACG
Found at i:1395194 original size:18 final size:18
Alignment explanation
Indices: 1395171--1395244 Score: 55
Period size: 18 Copynumber: 4.1 Consensus size: 18
1395161 GATGTTATGG
1395171 TGATGATGACGACGATGA
1 TGATGATGACGACGATGA
*
1395189 TGATGATGGTC-ACG-TCGA
1 TGATGAT-GACGACGAT-GA
*
1395207 TGATGATGAAGTA-GATGA
1 TGATGATGACG-ACGATGA
* * *
1395225 TTATGGTAACGACGATGA
1 TGATGATGACGACGATGA
1395243 TG
1 TG
1395245 TCTATTATGA
Statistics
Matches: 42, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
17 3 0.07
18 35 0.83
19 4 0.10
ACGTcount: A:0.31, C:0.09, G:0.32, T:0.27
Consensus pattern (18 bp):
TGATGATGACGACGATGA
Found at i:1395211 original size:33 final size:33
Alignment explanation
Indices: 1395172--1395244 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
1395162 ATGTTATGGT
* * *
1395172 GATGATGACGACG-ATGATGATGATGGTCACGTC
1 GATGATGACGAAGTA-GATGATGATGGTAACGAC
* *
1395205 GATGATGATGAAGTAGATGATTATGGTAACGAC
1 GATGATGACGAAGTAGATGATGATGGTAACGAC
1395238 GATGATG
1 GATGATG
1395245 TCTATTATGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 33 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.10, G:0.33, T:0.26
Consensus pattern (33 bp):
GATGATGACGAAGTAGATGATGATGGTAACGAC
Found at i:1396718 original size:2 final size:2
Alignment explanation
Indices: 1396711--1396746 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1396701 GTTAGGAAAT
1396711 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1396747 CTCAAAGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1400400 original size:1 final size:1
Alignment explanation
Indices: 1400365--1400390 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1400355 AATTTTGCCC
1400365 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
1400391 ACATTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1403079 original size:98 final size:99
Alignment explanation
Indices: 1402905--1403091 Score: 263
Period size: 98 Copynumber: 1.9 Consensus size: 99
1402895 GTAAGCCGTG
* *
1402905 ATGATGATTTAATTGTTTAAATATCAAAGTGAATAAGAATGTACCAAAATTAAATATATAGAAGC
1 ATGATGATTTAATTGTTT-AACATCAAAGTGAATAAGAATATACCAAAATTAAATATATAGAAGC
*
1402970 TGCCTGCCCATGTAAGCCGTGATAATTAGGATCGA
65 TGCCTGCCCATGGAAGCCGTGATAATTAGGATCGA
*
1403005 ATGATGATTTAATTGTTT-ACATCAAAGTGAATAAGAATATA-CAAAAGTTACATAGT-TAGAAG
1 ATGATGATTTAATTGTTTAACATCAAAGTGAATAAGAATATACCAAAA-TTAAATA-TATAGAAG
* * *
1403067 CTGCTTGTCCATGGAAGCTGTGATA
64 CTGCCTGCCCATGGAAGCCGTGATA
1403092 TGTAAAATTT
Statistics
Matches: 78, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
97 5 0.06
98 54 0.69
99 1 0.01
100 18 0.23
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (99 bp):
ATGATGATTTAATTGTTTAACATCAAAGTGAATAAGAATATACCAAAATTAAATATATAGAAGCT
GCCTGCCCATGGAAGCCGTGATAATTAGGATCGA
Found at i:1412067 original size:17 final size:17
Alignment explanation
Indices: 1412045--1412077 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1412035 TTTTCATGAA
1412045 AGTGACGGAGTTAGGGT
1 AGTGACGGAGTTAGGGT
*
1412062 AGTGACGTAGTTAGGG
1 AGTGACGGAGTTAGGG
1412078 GGCTATGCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.06, G:0.45, T:0.24
Consensus pattern (17 bp):
AGTGACGGAGTTAGGGT
Found at i:1422624 original size:27 final size:27
Alignment explanation
Indices: 1422567--1422634 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
1422557 CACTGCAGTT
* **
1422567 ACCTTGGATGTATCTATAGCTGCAAGG
1 ACCTTGGATGTATCTATAGCAGCAACA
*
1422594 ACCTTGGATGTATCTATAGCAGCCACA
1 ACCTTGGATGTATCTATAGCAGCAACA
*
1422621 ACCTTAGATGTATC
1 ACCTTGGATGTATC
1422635 CAGAGGTGAC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (27 bp):
ACCTTGGATGTATCTATAGCAGCAACA
Found at i:1424041 original size:27 final size:27
Alignment explanation
Indices: 1423984--1424051 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
1423974 CACTGCAGTT
* **
1423984 ACCTTGGATGTATCTATAGCTGCAAGG
1 ACCTTGGATGTATCTATAGCAGCAACA
*
1424011 ACCTTGGATGTATCTATAGCAGCCACA
1 ACCTTGGATGTATCTATAGCAGCAACA
*
1424038 ACCTTAGATGTATC
1 ACCTTGGATGTATC
1424052 CAGAGGTGAC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (27 bp):
ACCTTGGATGTATCTATAGCAGCAACA
Found at i:1429065 original size:2 final size:2
Alignment explanation
Indices: 1429052--1429107 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
1429042 AATTGCTGGT
*
1429052 TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1429094 TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC
1429108 GCAATCTCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1434366 original size:17 final size:18
Alignment explanation
Indices: 1434333--1434366 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1434323 CCTAGATTCA
*
1434333 TTATCAGCTATATAAAAG
1 TTATCAGCTATACAAAAG
1434351 TTATCAG-TATACAAAA
1 TTATCAGCTATACAAAA
1434367 TTTAGAAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (18 bp):
TTATCAGCTATACAAAAG
Found at i:1434627 original size:2 final size:2
Alignment explanation
Indices: 1434622--1434661 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1434612 ACACACACAC
1434622 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1434662 NATCAATGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1441175 original size:14 final size:14
Alignment explanation
Indices: 1441156--1441194 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
1441146 CATTCTGAAC
1441156 GATTTTGGTTTTGA
1 GATTTTGGTTTTGA
*
1441170 GATTTTGTTTTTGA
1 GATTTTGGTTTTGA
1441184 GA-TTTGGTTTT
1 GATTTTGGTTTT
1441195 AAGACTTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.13, C:0.00, G:0.26, T:0.62
Consensus pattern (14 bp):
GATTTTGGTTTTGA
Found at i:1443914 original size:2 final size:2
Alignment explanation
Indices: 1443907--1443937 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1443897 CAGATAACCC
1443907 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1443938 AGCCACGGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1444509 original size:82 final size:82
Alignment explanation
Indices: 1444409--1444572 Score: 301
Period size: 82 Copynumber: 2.0 Consensus size: 82
1444399 AAATTTACAA
*
1444409 CATGTGTCATGTTGTAAATTTTGTGTTTACACCCACCCAGTAAATTCAAAATTTACAACATGACA
1 CATGTGTCATGTTGTAAATTTTGTATTTACACCCACCCAGTAAATTCAAAATTTACAACATGACA
*
1444474 GATGCGTTGGAATGAAT
66 GATGCATTGGAATGAAT
*
1444491 CATGTGTCATGTTGTAAATTTTGTATTTACACCCATCCAGTAAATTCAAAATTTACAACATGACA
1 CATGTGTCATGTTGTAAATTTTGTATTTACACCCACCCAGTAAATTCAAAATTTACAACATGACA
1444556 GATGCATTGGAATGAAT
66 GATGCATTGGAATGAAT
1444573 ATAAATGTAA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (82 bp):
CATGTGTCATGTTGTAAATTTTGTATTTACACCCACCCAGTAAATTCAAAATTTACAACATGACA
GATGCATTGGAATGAAT
Found at i:1446255 original size:2 final size:2
Alignment explanation
Indices: 1446248--1446301 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1446238 GAGACAGTAC
1446248 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 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
1446290 AG AG AG AG AG AG
1 AG AG AG AG AG AG
1446302 TCCATCAATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1457086 original size:146 final size:146
Alignment explanation
Indices: 1456822--1457503 Score: 1130
Period size: 146 Copynumber: 4.7 Consensus size: 146
1456812 GTCTGTGCAA
1456822 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
*
1456887 TTATGACCTAAGGGTGTGTCATGACCTTTACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
*
1456952 AGAAAAAGTGCAAAAT
131 AGAAAAAATGCAAAAT
*
1456968 TCGTGTCCGGTCCATATCTCTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
*
1457033 TTATGACCTAAGGGTGTGTCATGACCTTTACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
*
1457098 AGAAAAAGTGCAAAAT
131 AGAAAAAATGCAAAAT
*
1457114 TCGTGTCCGGTCCATATCTTTCTTATTGG-GAAACATTGGAAGTTTTTACTTCACACAAAGATTG
1 TCGTGTCCGGTCCATATCTTTCTTA-TGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTG
*
1457178 CTTATGACCTACGGGTGTGTCATGACCTTGACCCAAGGTCA-T-----AAGGTCAAGGTCACTGG
65 CTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGG
1457237 CAGAAAAAATGCAAAAT
130 CAGAAAAAATGCAAAAT
* *
1457254 TTGTGTCCGGTCCATATCTTTCTTATGGGGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
* *
1457319 TTATGACCTAAGGGTGTGTCATGACCTTGACTCAAGGTCATTCGGGCAAGGTCAAGGTCACT-GA
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
*
1457383 AAAAAAAATGCAAAAT
131 AGAAAAAATGCAAAAT
* * *
1457399 TTGTGTCCGGTCCATATCTTTCTTATGGGGAAACATTGGAAGTTCTTACTTTACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
* *
1457464 TTATGA-TTAAAGGGTGTGTCATGACCTTGACGCAAGGTCA
66 TTATGACCT-AAGGGTGTGTCATGACCTTGACCCAAGGTCA
1457504 ATTGAGAAAG
Statistics
Matches: 512, Mismatches: 15, Indels: 19
0.94 0.03 0.03
Matches are distributed among these distances:
139 3 0.01
140 130 0.25
141 1 0.00
144 1 0.00
145 117 0.23
146 257 0.50
147 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (146 bp):
TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
AGAAAAAATGCAAAAT
Found at i:1457340 original size:286 final size:287
Alignment explanation
Indices: 1456822--1457508 Score: 1121
Period size: 286 Copynumber: 2.4 Consensus size: 287
1456812 GTCTGTGCAA
1456822 TCGTGTCCGGTCCATATCTTTCTTA-TGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTG
1 TCGTGTCCGGTCCATATCTTTCTTATTGG-GAAACATTGGAAGTTCTTACTTCACACAAAGATTG
*
1456886 CTTATGACCTAAGGGTGTGTCATGACCTTTACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGG
65 CTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATT---G-AAGGTCAAGGTCACTGG
*
1456951 CAGAAAAAGTGCAAAATTCGTGTCCGGTCCATATCTCTCTTATGGAGAAACATTGGAAGTTCTTA
126 CAGAAAAAATGCAAAATTCGTGTCCGGTCCATATCTCTCTTATGGAGAAACATTGGAAGTTCTTA
*
1457016 CTTCACACAAAGATTGCTTATGACCTAAGGGTGTGTCATGACCTTTACCCAAGGTCATTCGGGCA
191 CTTCACACAAAGATTGCTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCA
* * *
1457081 AGGTCAAGGTCACTGGCAGAAAAAGTGCAAAAT
256 AGGTCAAGGTCACT-GAAAAAAAAATGCAAAAT
*
1457114 TCGTGTCCGGTCCATATCTTTCTTATTGGGAAACATTGGAAGTTTTTACTTCACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATTGGGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
*
1457179 TTATGACCTACGGGTGTGTCATGACCTTGACCCAAGGTCA-T-AAGGTCAAGGTCACTGGCAGAA
66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTGAAGGTCAAGGTCACTGGCAGAA
* * *
1457242 AAAATGCAAAATTTGTGTCCGGTCCATATCTTTCTTATGGGGAAACATTGGAAGTTCTTACTTCA
131 AAAATGCAAAATTCGTGTCCGGTCCATATCTCTCTTATGGAGAAACATTGGAAGTTCTTACTTCA
*
1457307 CACAAAGATTGCTTATGACCTAAGGGTGTGTCATGACCTTGACTCAAGGTCATTCGGGCAAGGTC
196 CACAAAGATTGCTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTC
1457372 AAGGTCACTGAAAAAAAAATGCAAAAT
261 AAGGTCACTGAAAAAAAAATGCAAAAT
* * *
1457399 TTGTGTCCGGTCCATATCTTTCTTATGGGGAAACATTGGAAGTTCTTACTTTACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATTGGGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
* *
1457464 TTATGA-TTAAAGGGTGTGTCATGACCTTGACGCAAGGTCAATTGA
66 TTATGACCT-AAGGGTGTGTCATGACCTTGACCCAAGGTC-ATTGA
1457509 GAAAGTTCAA
Statistics
Matches: 371, Mismatches: 19, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
284 1 0.00
285 110 0.30
286 156 0.42
287 1 0.00
288 1 0.00
291 1 0.00
292 98 0.26
293 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (287 bp):
TCGTGTCCGGTCCATATCTTTCTTATTGGGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTGAAGGTCAAGGTCACTGGCAGAA
AAAATGCAAAATTCGTGTCCGGTCCATATCTCTCTTATGGAGAAACATTGGAAGTTCTTACTTCA
CACAAAGATTGCTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTC
AAGGTCACTGAAAAAAAAATGCAAAAT
Found at i:1460038 original size:77 final size:77
Alignment explanation
Indices: 1459911--1460068 Score: 235
Period size: 77 Copynumber: 2.1 Consensus size: 77
1459901 TTCATGATTG
* * *
1459911 TTTGCATTATTTTTCCCGTAACGTTGTAAACATAAAACTACTTACAGTGACGTCATAATGGTTAA
1 TTTGCATTATTTTCCCCGTAACGCTGTAAACATAAAACTACTGACAGTGACGTCATAATGGTTAA
1459976 ACGTCATAAATC
66 ACGTCATAAATC
** * *
1459988 TTTGCATTATTTTCCCCGTATTGCTGTAAACATAAAACTACTGACTGTGACTTCATAATGGTTAA
1 TTTGCATTATTTTCCCCGTAACGCTGTAAACATAAAACTACTGACAGTGACGTCATAATGGTTAA
* *
1460053 TCGTCATAGATC
66 ACGTCATAAATC
1460065 TTTG
1 TTTG
1460069 TGACGTCGCA
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
77 72 1.00
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.37
Consensus pattern (77 bp):
TTTGCATTATTTTCCCCGTAACGCTGTAAACATAAAACTACTGACAGTGACGTCATAATGGTTAA
ACGTCATAAATC
Found at i:1462672 original size:17 final size:17
Alignment explanation
Indices: 1462639--1462673 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1462629 CTAAGTAACA
*
1462639 TTATATAATTATACATG
1 TTATATAATCATACATG
*
1462656 TTATATAATCATGCATG
1 TTATATAATCATACATG
1462673 T
1 T
1462674 AAGAAACATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (17 bp):
TTATATAATCATACATG
Found at i:1463451 original size:14 final size:14
Alignment explanation
Indices: 1463328--1463739 Score: 148
Period size: 14 Copynumber: 28.4 Consensus size: 14
1463318 GAGAATGGAG
1463328 GGAGGGGAGAAAGAGA
1 GGAGGGGAG--AGAGA
1463344 GGGAGGGGAAGGAGAGA
1 -GGAGGGG-A-GAGAGA
*
1463361 GTGATGAGG-GAGAGA
1 G-GA-GGGGAGAGAGA
*
1463376 GGAGGGGAGAGAAA
1 GGAGGGGAGAGAGA
*
1463390 GAAGGGAGAGAGAGA
1 GGAGGG-GAGAGAGA
* * *
1463405 GCAGGGAAAAGAGA
1 GGAGGGGAGAGAGA
*
1463419 -GAGTAGGGAGAGAGG
1 GGAG--GGGAGAGAGA
*
1463434 GGAGGGGAGTGAGA
1 GGAGGGGAGAGAGA
*
1463448 GGAGGGGAGAAAGA
1 GGAGGGGAGAGAGA
*
1463462 GGGGGCGGA-AGAGA
1 GGAGG-GGAGAGAGA
* *
1463476 GG-GGGAGAAGGGAAA
1 GGAGGG-G-AGAGAGA
* *
1463491 AGAGAGGAGAGAGA
1 GGAGGGGAGAGAGA
* * *
1463505 -GAAGGTAGAGAGT
1 GGAGGGGAGAGAGA
**
1463518 GAGAATGGAG-G-GA
1 G-GAGGGGAGAGAGA
* *
1463531 GG-GGAGAAAGAGA
1 GGAGGGGAGAGAGA
1463544 GGGAGGGGAAGGAGAGA
1 -GGAGGGG-A-GAGAGA
*
1463561 GTGATGAGG-GAGAGA
1 G-GA-GGGGAGAGAGA
*
1463576 GGAGGGGAGAGAAA
1 GGAGGGGAGAGAGA
*
1463590 GAAGGGAGAGAGAGA
1 GGAGGG-GAGAGAGA
* * *
1463605 GCAGGGAAAAGAGA
1 GGAGGGGAGAGAGA
*
1463619 -GAGTAGGGAGAGAGG
1 GGAG--GGGAGAGAGA
*
1463634 GGAGGGGAGTGAGA
1 GGAGGGGAGAGAGA
*
1463648 GGAGGGGAGAAAGA
1 GGAGGGGAGAGAGA
*
1463662 GGGGGCGGA-AGAGA
1 GGAGG-GGAGAGAGA
* *
1463676 GG-GGGAGAAGGGAAAA
1 GGAGGG-G-AGAG-AGA
* *
1463692 GAGAAGGGATAGAG-
1 G-GAGGGGAGAGAGA
*
1463706 GTAGGGGAGAGAGA
1 GGAGGGGAGAGAGA
1463720 GGAGGGAGAGAGAGA
1 GGAGGG-GAGAGAGA
*
1463735 AGAGG
1 GGAGG
1463740 ATAGGCAAAG
Statistics
Matches: 291, Mismatches: 66, Indels: 78
0.67 0.15 0.18
Matches are distributed among these distances:
11 2 0.01
12 4 0.01
13 38 0.13
14 112 0.38
15 86 0.30
16 16 0.05
17 23 0.08
18 9 0.03
19 1 0.00
ACGTcount: A:0.39, C:0.01, G:0.57, T:0.03
Consensus pattern (14 bp):
GGAGGGGAGAGAGA
Found at i:1463638 original size:200 final size:200
Alignment explanation
Indices: 1463295--1463695 Score: 802
Period size: 200 Copynumber: 2.0 Consensus size: 200
1463285 AATATATTGC
1463295 AGGAGAGAGAGAAGGTAGAGAGTGAGAATGGAGGGAGGGGAGAAAGAGAGGGAGGGGAAGGAGAG
1 AGGAGAGAGAGAAGGTAGAGAGTGAGAATGGAGGGAGGGGAGAAAGAGAGGGAGGGGAAGGAGAG
1463360 AGTGATGAGGGAGAGAGGAGGGGAGAGAAAGAAGGGAGAGAGAGAGCAGGGAAAAGAGAGAGTAG
66 AGTGATGAGGGAGAGAGGAGGGGAGAGAAAGAAGGGAGAGAGAGAGCAGGGAAAAGAGAGAGTAG
1463425 GGAGAGAGGGGAGGGGAGTGAGAGGAGGGGAGAAAGAGGGGGCGGAAGAGAGGGGGAGAAGGGAA
131 GGAGAGAGGGGAGGGGAGTGAGAGGAGGGGAGAAAGAGGGGGCGGAAGAGAGGGGGAGAAGGGAA
1463490 AAGAG
196 AAGAG
1463495 AGGAGAGAGAGAAGGTAGAGAGTGAGAATGGAGGGAGGGGAGAAAGAGAGGGAGGGGAAGGAGAG
1 AGGAGAGAGAGAAGGTAGAGAGTGAGAATGGAGGGAGGGGAGAAAGAGAGGGAGGGGAAGGAGAG
1463560 AGTGATGAGGGAGAGAGGAGGGGAGAGAAAGAAGGGAGAGAGAGAGCAGGGAAAAGAGAGAGTAG
66 AGTGATGAGGGAGAGAGGAGGGGAGAGAAAGAAGGGAGAGAGAGAGCAGGGAAAAGAGAGAGTAG
1463625 GGAGAGAGGGGAGGGGAGTGAGAGGAGGGGAGAAAGAGGGGGCGGAAGAGAGGGGGAGAAGGGAA
131 GGAGAGAGGGGAGGGGAGTGAGAGGAGGGGAGAAAGAGGGGGCGGAAGAGAGGGGGAGAAGGGAA
1463690 AAGAG
196 AAGAG
1463695 A
1 A
1463696 AGGGATAGAG
Statistics
Matches: 201, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
200 201 1.00
ACGTcount: A:0.40, C:0.01, G:0.56, T:0.03
Consensus pattern (200 bp):
AGGAGAGAGAGAAGGTAGAGAGTGAGAATGGAGGGAGGGGAGAAAGAGAGGGAGGGGAAGGAGAG
AGTGATGAGGGAGAGAGGAGGGGAGAGAAAGAAGGGAGAGAGAGAGCAGGGAAAAGAGAGAGTAG
GGAGAGAGGGGAGGGGAGTGAGAGGAGGGGAGAAAGAGGGGGCGGAAGAGAGGGGGAGAAGGGAA
AAGAG
Found at i:1463871 original size:11 final size:11
Alignment explanation
Indices: 1463809--1463900 Score: 61
Period size: 10 Copynumber: 8.7 Consensus size: 11
1463799 ATAGAGTAAA
*
1463809 GAGAGAGGA-G
1 GAGAGAAGAGG
1463819 GAGA-AAGAGG
1 GAGAGAAGAGG
*
1463829 GA-AG-AGGGG
1 GAGAGAAGAGG
*
1463838 GAGTGATAGAGG
1 GAGAGA-AGAGG
1463850 G-GAGAAGAGG
1 GAGAGAAGAGG
*
1463860 GAGAGAATAGGG
1 GAGAGAAGA-GG
* *
1463872 GAGAGATGAGA
1 GAGAGAAGAGG
*
1463883 GAGAG-AGAGA
1 GAGAGAAGAGG
1463893 GAGAGAAG
1 GAGAGAAG
1463901 GGAAAAGAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
9 10 0.16
10 23 0.36
11 17 0.27
12 14 0.22
ACGTcount: A:0.42, C:0.00, G:0.53, T:0.04
Consensus pattern (11 bp):
GAGAGAAGAGG
Found at i:1463877 original size:23 final size:23
Alignment explanation
Indices: 1463829--1463888 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
1463819 GAGAAAGAGG
* *
1463829 GAAGAGGGGGAGTGATAGAGGGGA
1 GAAGAGGGAGAG-AATAGAGGGGA
1463853 GAAGAGGGAGAGAATAG-GGGAGA
1 GAAGAGGGAGAGAATAGAGGG-GA
* *
1463876 GATGAGAGAGAGA
1 GAAGAGGGAGAGA
1463889 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
22 3 0.10
23 17 0.55
24 11 0.35
ACGTcount: A:0.40, C:0.00, G:0.53, T:0.07
Consensus pattern (23 bp):
GAAGAGGGAGAGAATAGAGGGGA
Found at i:1463959 original size:11 final size:11
Alignment explanation
Indices: 1463922--1464251 Score: 89
Period size: 11 Copynumber: 29.9 Consensus size: 11
1463912 GAGATTAAAA
1463922 GAGAGAAGAGAGG
1 GAGAG-AGAG-GG
* * *
1463935 GAGGGATAGAG
1 GAGAGAGAGGG
1463946 GAGAGAGAGGG
1 GAGAGAGAGGG
**
1463957 GAGAGAGAAAG
1 GAGAGAGAGGG
*
1463968 GATAGAG-GGAG
1 GAGAGAGAGG-G
*
1463979 G-GTAGAGAGGAA
1 GAG-AGAGAGG-G
* *
1463991 GAAAGGGAGGG
1 GAGAGAGAGGG
* *
1464002 GAGGGAGAGAGT
1 GAGAGAGAG-GG
*
1464014 GATGATAGAGGG
1 GA-GAGAGAGGG
* *
1464026 AAGAGAAAGGG
1 GAGAGAGAGGG
*
1464037 AGGGAGAGAGGG
1 -GAGAGAGAGGG
*
1464049 GAGGGAGAGAGG
1 GAGAGAGAG-GG
*
1464061 G-GAGA-ATGG
1 GAGAGAGAGGG
*
1464070 GAGAGGGAGGG
1 GAGAGAGAGGG
1464081 GAGAGAGAGGAG
1 GAGAGAGAGG-G
*
1464093 G-GAGAGAAGGAA
1 GAGAGAG-AGG-G
*
1464105 GAGAGAAAGGG
1 GAGAGAGAGGG
*
1464116 GAAAGAGAAGGG
1 GAGAGAG-AGGG
*
1464128 AGAGAGAAAGGG
1 -GAGAGAGAGGG
* **
1464140 GAAAGAGAGAA
1 GAGAGAGAGGG
*
1464151 GA-AGAGAGGT
1 GAGAGAGAGGG
1464161 G-G-GAGAGGG
1 GAGAGAGAGGG
*
1464170 GAG-G-G-GAG
1 GAGAGAGAGGG
*
1464178 GAGAAAGAGGG
1 GAGAGAGAGGG
1464189 GAG-G-GAGGG
1 GAGAGAGAGGG
* * *
1464198 AGATAGAAAAGG
1 -GAGAGAGAGGG
*
1464210 G-G-GAGAGGA
1 GAGAGAGAGGG
* *
1464219 AAAAGAGAGGG
1 GAGAGAGAGGG
1464230 GCAG-GAGAGGG
1 G-AGAGAGAGGG
1464241 AGAGAGAGAGG
1 -GAGAGAGAGG
1464252 AGGTAGATAA
Statistics
Matches: 223, Mismatches: 66, Indels: 57
0.64 0.19 0.16
Matches are distributed among these distances:
8 5 0.02
9 20 0.09
10 16 0.07
11 106 0.48
12 58 0.26
13 18 0.08
ACGTcount: A:0.41, C:0.00, G:0.56, T:0.03
Consensus pattern (11 bp):
GAGAGAGAGGG
Found at i:1463974 original size:24 final size:23
Alignment explanation
Indices: 1463947--1464167 Score: 95
Period size: 24 Copynumber: 9.7 Consensus size: 23
1463937 GGGATAGAGG
1463947 AGAGAGAGGGGAGAGAGAAAGGA
1 AGAGAGAGGGGAGAGAGAAAGGA
* * *
1463970 TAGAGGGAGGGTAGAGAGGAA-GA
1 -AGAGAGAGGGGAGAGAGAAAGGA
* * *
1463993 A-AGGGAGGGGAGGGAGAGAGTGA
1 AGAGAGAGGGGAGAGAGAAAG-GA
* *
1464016 TGATAGA-GGGA-AGAGAAAGGGA
1 AGAGAGAGGGGAGAGAGAAA-GGA
* * *
1464038 GGGAGAGAGGGGAGGGAGAGAGG-
1 -AGAGAGAGGGGAGAGAGAAAGGA
* * * * *
1464061 GGAGA-ATGGGAGAG-GGAGGGG
1 AGAGAGAGGGGAGAGAGAAAGGA
1464082 AGAGAGAGGAGG-GAGAG-AAGGA
1 AGAGAGAGG-GGAGAGAGAAAGGA
* *
1464104 AGAGAGAAAGGGGAAAGAGAAGGGA
1 AGAGAG--AGGGGAGAGAGAAAGGA
* *
1464129 GAGAGAAAGGGGAAAGAGAGAA-GA
1 -AGAGAGAGGGGAGAGAGA-AAGGA
1464153 AGAGAG-GTGGGAGAG
1 AGAGAGAG-GGGAGAG
1464168 GGGAGGGGAG
Statistics
Matches: 148, Mismatches: 31, Indels: 37
0.69 0.14 0.17
Matches are distributed among these distances:
20 3 0.02
21 25 0.17
22 28 0.19
23 30 0.20
24 47 0.32
25 10 0.07
26 5 0.03
ACGTcount: A:0.42, C:0.00, G:0.55, T:0.03
Consensus pattern (23 bp):
AGAGAGAGGGGAGAGAGAAAGGA
Found at i:1464052 original size:13 final size:13
Alignment explanation
Indices: 1464034--1464099 Score: 73
Period size: 13 Copynumber: 4.9 Consensus size: 13
1464024 GGAAGAGAAA
1464034 GGGAGGGAGAGAG
1 GGGAGGGAGAGAG
1464047 GGGAGGGAGAGAG
1 GGGAGGGAGAGAG
1464060 GGGAGAATGG-GAGA-
1 GGGAG---GGAGAGAG
1464074 GGGAGGGGAGAGAG
1 GGGA-GGGAGAGAG
*
1464088 AGGAGGGAGAGA
1 GGGAGGGAGAGA
1464100 AGGAAGAGAG
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
12 2 0.04
13 30 0.65
14 7 0.15
15 5 0.11
16 2 0.04
ACGTcount: A:0.33, C:0.00, G:0.65, T:0.02
Consensus pattern (13 bp):
GGGAGGGAGAGAG
Found at i:1464052 original size:28 final size:26
Alignment explanation
Indices: 1464021--1464139 Score: 72
Period size: 26 Copynumber: 4.6 Consensus size: 26
1464011 AGTGATGATA
1464021 GAGGGAAGAGAAAGGGAGGGAGAGAGGG
1 GAGGG-AGAGAAAGGGAGGGAGAGA-GG
*
1464049 GAGGGAGAG-AGGGGAGAATGG-GAGAGG
1 GAGGGAGAGAAAGGGAG---GGAGAGAGG
* *
1464076 GAGGG-GAGAGAGAGGAGGGAGAGAAG
1 GAGGGAGAGAAAG-GGAGGGAGAGAGG
* **
1464102 GA-AGAGAGAAAGGG-GAAAGAGAAGG
1 GAGGGAGAGAAAGGGAGGGAGAG-AGG
1464127 GA--GAGAGAAAGGG
1 GAGGGAGAGAAAGGG
1464140 GAAAGAGAGA
Statistics
Matches: 74, Mismatches: 9, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
24 16 0.22
25 9 0.12
26 22 0.30
27 12 0.16
28 13 0.18
29 2 0.03
ACGTcount: A:0.41, C:0.00, G:0.58, T:0.01
Consensus pattern (26 bp):
GAGGGAGAGAAAGGGAGGGAGAGAGG
Found at i:1466483 original size:2 final size:2
Alignment explanation
Indices: 1466476--1466520 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1466466 ATATAGCCTA
1466476 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 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
1466518 AG A
1 AG A
1466521 ATAATCAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1487005 original size:2 final size:2
Alignment explanation
Indices: 1486998--1487022 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1486988 NNNNNNNNNN
1486998 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
1487023 AAATTTGATA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1489309 original size:12 final size:11
Alignment explanation
Indices: 1489279--1489309 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
1489269 GCTGCCACAC
1489279 CTTTTTCTAGT
1 CTTTTTCTAGT
1489290 CTTTTTCTAGT
1 CTTTTTCTAGT
1489301 CTTTCTTCT
1 CTTT-TTCT
1489310 CTCACAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.06, C:0.23, G:0.06, T:0.65
Consensus pattern (11 bp):
CTTTTTCTAGT
Found at i:1497914 original size:2 final size:2
Alignment explanation
Indices: 1497907--1497959 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1497897 ATATTTAAGA
1497907 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1497949 CT CT CT CT CT C
1 CT CT CT CT CT C
1497960 ATATCTGCTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1501464 original size:2 final size:2
Alignment explanation
Indices: 1501457--1501488 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1501447 NNNNNNNNNN
1501457 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1501489 TATTTGACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1521473 original size:9 final size:9
Alignment explanation
Indices: 1521455--1521493 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
1521445 TTTGTCGACT
*
1521455 TTCTTTTTC
1 TTCTTATTC
1521464 TTCTTATTC
1 TTCTTATTC
1521473 TTCTTATTC
1 TTCTTATTC
* *
1521482 TTATTCTTC
1 TTCTTATTC
1521491 TTC
1 TTC
1521494 ATCCAAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.08, C:0.23, G:0.00, T:0.69
Consensus pattern (9 bp):
TTCTTATTC
Found at i:1521473 original size:15 final size:15
Alignment explanation
Indices: 1521464--1521492 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1521454 TTTCTTTTTC
1521464 TTCTTATTCTTCTTA
1 TTCTTATTCTTCTTA
1521479 TTCTTATTCTTCTT
1 TTCTTATTCTTCTT
1521493 CATCCAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.21, G:0.00, T:0.69
Consensus pattern (15 bp):
TTCTTATTCTTCTTA
Found at i:1522203 original size:19 final size:17
Alignment explanation
Indices: 1522171--1522205 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
1522161 GTCCAGTTCA
1522171 ACCTTACCAAAATTTTG
1 ACCTTACCAAAATTTTG
1522188 ACCTTGACCTAAAATTTT
1 ACCTT-ACC-AAAATTTT
1522206 TATTTCAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.34, C:0.23, G:0.06, T:0.37
Consensus pattern (17 bp):
ACCTTACCAAAATTTTG
Found at i:1522334 original size:440 final size:440
Alignment explanation
Indices: 1521513--1522490 Score: 1591
Period size: 440 Copynumber: 2.2 Consensus size: 440
1521503 TGTCCAAGCC
* *
1521513 GTAACTTAAATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTGAGAAG
1 GTAACTTAGATACCTTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTGAGAAG
* * *
1521578 GAGTGCACGCCACCAAAATTTTTGACCTTGACCTATTTTCTTTTTCAAGGTCAAGCGTTTTATAA
66 GAGTGCACGCCACCAAAATTTTTGACCTTGACCTATTATCTTCTTCAAGGTCAAGCGTTTTAAAA
*** * * *
1521643 AAAATAGAGTTTGGACTATAACACAAGATTCCTTAAACATACAAACTTTTAACTTGTATCATAGA
131 AAAATAGAGTCCAGACCATAACACAAGACTCCTTAAACATACAAACTTTTAACTTGTATCATACA
* *
1521708 TAGATGGTATATAGTCCAGTTGAACCTAACCAAAATTTTTTACCTTGACCTTAAAATTTTATTTC
196 TAGATGGTATATAGTCCAGTTCAACCTAACCAAAATTTTTGACCTTGACCTTAAAATTTTATTTC
*
1521773 AAGGTCAAATCAGAAAAAACTTCATTGTTCACCTCCTAAAAATTCTTTGACAGAAGGACTTCAAA
261 AAGGTCAAATCAGAAAAAACTTCATTGTTCACCTCCTAAAAATTCTATGACAGAAGGACTTCAAA
*
1521838 CTTTACACAAAGAACAATTATAATACACTGAGGTGTACTATTGATTAATATTTGACCTTGACCTT
326 CTTTACACAAAGAACAATTATAATACACTGAGGTGTACTATTGATAAATATTTGACCTTGACCTT
* *
1521903 GTTTTACTCAAGGTCAACTTGAGAAAAAATAATTAAATTTTGTCTGGGTG
391 GTTTTACTCAAGGTCAAATTAAGAAAAAATAATTAAATTTTGTCTGGGTG
*
1521953 GTAACTTAGATACCTTTTGACATTAAGACTTCAAACTTGGAACGTAGGTAGATGGTATTGAGAAG
1 GTAACTTAGATACCTTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTGAGAAG
* * * *
1522018 AAGTGCACGCTATCAAACTTTTTGACCTTGACCTATTATCTTCTTCAAGGTCAAGCGTTTTAAAA
66 GAGTGCACGCCACCAAAATTTTTGACCTTGACCTATTATCTTCTTCAAGGTCAAGCGTTTTAAAA
* * *
1522083 AAAATATAGTCCAGACCATAACACAAGACTCCTTAATCATACAATCTTTTAACTTGTATCATACA
131 AAAATAGAGTCCAGACCATAACACAAGACTCCTTAAACATACAAACTTTTAACTTGTATCATACA
*
1522148 TAGATGGTATATAGTCCAGTTCAACCTTACCAAAA-TTTTGACCTTGACC-TAAAATTTTTATTT
196 TAGATGGTATATAGTCCAGTTCAACCTAACCAAAATTTTTGACCTTGACCTTAAAA-TTTTATTT
* * * *
1522211 CAAGGTCAAATTAGAAAAAAACTTCATTGTTCACCTCCTAAATATTCTATGGCGGAAGGACTTCA
260 CAAGGTCAAATCAG-AAAAAACTTCATTGTTCACCTCCTAAAAATTCTATGACAGAAGGACTTCA
* *
1522276 AACTTTACACAAAGAACAATTATAATACACTGAGGTTTTCTATTGATAAATATTTGACCTTGACC
324 AACTTTACACAAAGAACAATTATAATACACTGAGGTGTACTATTGATAAATATTTGACCTTGACC
1522341 TTGTTTTACTCAAGGTCAAATTAAGAAAAAATAATTAAATTTTGTCTGGGTG
389 TTGTTTTACTCAAGGTCAAATTAAGAAAAAATAATTAAATTTTGTCTGGGTG
* *
1522393 GTAACTTGGATACCTTTTGACATTAAGGCTTCAAACTTGGAACATAGGTAGATGGTATTGAGAAG
1 GTAACTTAGATACCTTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTGAGAAG
* * *
1522458 GAGTGCACGCCTCCATAATTTTTTACCTTGACC
66 GAGTGCACGCCACCAAAATTTTTGACCTTGACC
1522491 AATCTTGTGT
Statistics
Matches: 494, Mismatches: 42, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
438 5 0.01
439 34 0.07
440 455 0.92
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (440 bp):
GTAACTTAGATACCTTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTGAGAAG
GAGTGCACGCCACCAAAATTTTTGACCTTGACCTATTATCTTCTTCAAGGTCAAGCGTTTTAAAA
AAAATAGAGTCCAGACCATAACACAAGACTCCTTAAACATACAAACTTTTAACTTGTATCATACA
TAGATGGTATATAGTCCAGTTCAACCTAACCAAAATTTTTGACCTTGACCTTAAAATTTTATTTC
AAGGTCAAATCAGAAAAAACTTCATTGTTCACCTCCTAAAAATTCTATGACAGAAGGACTTCAAA
CTTTACACAAAGAACAATTATAATACACTGAGGTGTACTATTGATAAATATTTGACCTTGACCTT
GTTTTACTCAAGGTCAAATTAAGAAAAAATAATTAAATTTTGTCTGGGTG
Found at i:1528071 original size:24 final size:24
Alignment explanation
Indices: 1528039--1528234 Score: 293
Period size: 24 Copynumber: 7.8 Consensus size: 24
1528029 GATGAAACTG
1528039 TGTATAATCTGCCATCTTTAACCA
1 TGTATAATCTGCCATCTTTAACCA
1528063 TGTATAATCTGCCATCTTTAACCA
1 TGTATAATCTGCCATCTTTAACCA
1528087 TGTATAATCTGCCATCTTTAACCA
1 TGTATAATCTGCCATCTTTAACCA
*
1528111 TGTATAATCTGCCCTCTTTAACCA
1 TGTATAATCTGCCATCTTTAACCA
*
1528135 TGTATAATCTACCATCTTTAATTAACCA
1 TGTATAATCTGCCATC--T--TTAACCA
1528163 TGTATAATCTGCCATCTTTAACCA
1 TGTATAATCTGCCATCTTTAACCA
*
1528187 TGTATAATCTGCCCTCTTTAATTAACCA
1 TGTATAATCTGCCATC--T--TTAACCA
1528215 TGTATAATCTGCCATCTTTA
1 TGTATAATCTGCCATCTTTA
1528235 GGGCTACTCA
Statistics
Matches: 158, Mismatches: 6, Indels: 16
0.88 0.03 0.09
Matches are distributed among these distances:
24 110 0.70
26 4 0.03
28 44 0.28
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.39
Consensus pattern (24 bp):
TGTATAATCTGCCATCTTTAACCA
Found at i:1528182 original size:52 final size:52
Alignment explanation
Indices: 1528039--1528234 Score: 309
Period size: 52 Copynumber: 3.9 Consensus size: 52
1528029 GATGAAACTG
1528039 TGTATAATCTGCCATC--T--TTAACCATGTATAATCTGCCATCTTTAACCA
1 TGTATAATCTGCCATCTTTAATTAACCATGTATAATCTGCCATCTTTAACCA
*
1528087 TGTATAATCTGCCATC--T--TTAACCATGTATAATCTGCCCTCTTTAACCA
1 TGTATAATCTGCCATCTTTAATTAACCATGTATAATCTGCCATCTTTAACCA
*
1528135 TGTATAATCTACCATCTTTAATTAACCATGTATAATCTGCCATCTTTAACCA
1 TGTATAATCTGCCATCTTTAATTAACCATGTATAATCTGCCATCTTTAACCA
*
1528187 TGTATAATCTGCCCTCTTTAATTAACCATGTATAATCTGCCATCTTTA
1 TGTATAATCTGCCATCTTTAATTAACCATGTATAATCTGCCATCTTTA
1528235 GGGCTACTCA
Statistics
Matches: 139, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
48 62 0.45
50 1 0.01
52 76 0.55
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.39
Consensus pattern (52 bp):
TGTATAATCTGCCATCTTTAATTAACCATGTATAATCTGCCATCTTTAACCA
Found at i:1530212 original size:34 final size:34
Alignment explanation
Indices: 1530169--1530234 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
1530159 AAGCCTATAG
1530169 GGATTTTGCACTGAATCTTACAATTATTCATACA
1 GGATTTTGCACTGAATCTTACAATTATTCATACA
* *
1530203 GGATTTTGCACTGAATGTTACAATTTTTCATA
1 GGATTTTGCACTGAATCTTACAATTATTCATA
1530235 TAATCTGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (34 bp):
GGATTTTGCACTGAATCTTACAATTATTCATACA
Found at i:1532896 original size:30 final size:30
Alignment explanation
Indices: 1532859--1532944 Score: 129
Period size: 30 Copynumber: 2.9 Consensus size: 30
1532849 TTGAACTGCC
* *
1532859 GGTCAATAGACTGCGATCTATTAGGTCGCCA
1 GGTCAATAGACTGTGATCTATT-GGACGCCA
*
1532890 -GTCAATAGACTGTGATCTATTGGACGGCA
1 GGTCAATAGACTGTGATCTATTGGACGCCA
1532919 GGTCAATAGACTGTGATCTATTGGAC
1 GGTCAATAGACTGTGATCTATTGGAC
1532945 CGGCAACTTA
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
29 6 0.12
30 45 0.88
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.28
Consensus pattern (30 bp):
GGTCAATAGACTGTGATCTATTGGACGCCA
Found at i:1533544 original size:30 final size:30
Alignment explanation
Indices: 1533507--1533592 Score: 120
Period size: 30 Copynumber: 2.9 Consensus size: 30
1533497 TTGAACTGCC
* *
1533507 GGTCAATAGACTGCGATCTATTAGGCCGCCA
1 GGTCAATAGACTGTGATCTATT-GGACGCCA
* *
1533538 -GTCAATAGACTGTGATCTATTGGATGGCA
1 GGTCAATAGACTGTGATCTATTGGACGCCA
1533567 GGTCAATAGACTGTGATCTATTGGAC
1 GGTCAATAGACTGTGATCTATTGGAC
1533593 CGGCAACTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
29 5 0.10
30 44 0.90
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.28
Consensus pattern (30 bp):
GGTCAATAGACTGTGATCTATTGGACGCCA
Found at i:1534339 original size:136 final size:137
Alignment explanation
Indices: 1534096--1534725 Score: 761
Period size: 146 Copynumber: 4.5 Consensus size: 137
1534086 CACCCTTTAA
1534096 TCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCCCCATAAGAAAGATATGGACCGG
1 TCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCCCCATAAGAAAGATATGGACCGG
* * * * *
1534161 ACACGAATTTTGCATTTTTTTTGCCAGTGACCTTGCCCTTGCCCGAATGACCTTAGGTCAAGGTC
66 ACACGAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTC
*
1534226 ATG-AGA
131 ATGCAGG
1534232 TCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCCCCATAAGAAAGATATGGACCGG
1 TCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCCCCATAAGAAAGATATGGACCGG
*
1534297 ACACGAATTTTGCATTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTC
66 ACACGAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTC
1534362 ATGACACACCCTTAGG
131 ATG-------C--AGG
* *
1534378 TCATAAGCAATCTTTGTGTGAAGTAAAAACCTCCAATGTTT--CC-----------A--GACCGG
1 TCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCCCCATAAGAAAGATATGGACCGG
** * *
1534428 ACACGAATTTTGCACTTTTTCTTTCAGTGACCTTGACCTTGCCCGAATGACCTTGGGTCAAGATC
66 ACACGAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTC
1534493 ATGACACACCCTTAGG
131 ATG-------C--AGG
* *
1534509 TCATAAGCAATCTTTGTGTGAAGTAAGAACTTCAAATGTTTCTCCATAAGAAAGATATGGACCGG
1 TCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCCCCATAAGAAAGATATGGACCGG
1534574 ACACGAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTC
66 ACACGAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTC
1534639 ATGACACACCTTTAGG
131 ATG------C---AGG
*
1534655 TCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGG
1 TCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCCCCATAAGAAAGATATGGACCGG
1534720 ACACGA
66 ACACGA
1534726 TTGCACAGAC
Statistics
Matches: 443, Mismatches: 25, Indels: 42
0.87 0.05 0.08
Matches are distributed among these distances:
131 120 0.27
133 3 0.01
136 129 0.29
144 3 0.01
145 2 0.00
146 186 0.42
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (137 bp):
TCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCCCCATAAGAAAGATATGGACCGG
ACACGAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTC
ATGCAGG
Found at i:1534587 original size:277 final size:266
Alignment explanation
Indices: 1534155--1534696 Score: 870
Period size: 277 Copynumber: 2.0 Consensus size: 266
1534145 GAAAGATATG
*
1534155 GACCGGACACGAATTTTGCATTTTTTTTGCCAGTGACCTTGCCCTTGCCCGAATGACCTTAGGTC
1 GACCGGACACGAATTTTGCATTTTTTTT-CCAGTGACCTTGACCTTGCCCGAATGACCTTAGGTC
* *
1534220 AAGGTCATGAGATCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCCCCATAAGAAA
65 AAGATCATGAGATCATAAGCAATCTTTGTGTGAAGTAAGAACTTCAAATGTTTCCCCATAAGAAA
*
1534285 GATATGGACCGGACACGAATTTTGCATTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCT
130 GATATGGACCGGACACGAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCT
1534350 TGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAAAACCTCCAAT
195 TGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAAAACCTCCAAT
1534415 GTTTCCA
260 GTTTCCA
*
1534422 GACCGGACACGAATTTTGCACTTTTTCTTT-CAGTGACCTTGACCTTGCCCGAATGACCTTGGGT
1 GACCGGACACGAATTTTGCA-TTTTT-TTTCCAGTGACCTTGACCTTGCCCGAATGACCTTAGGT
*
1534486 CAAGATCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCAAATGTTTC
64 CAAGATCATG----------AGATCATAAGCAATCTTTGTGTGAAGTAAGAACTTCAAATGTTTC
*
1534551 TCCATAAGAAAGATATGGACCGGACACGAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGC
119 CCCATAAGAAAGATATGGACCGGACACGAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGC
*
1534616 CCAAATGACCTTGGGTCAAGGTCATGACACACCTTTAGGTCATAAGCAATCTTTGTGTGAAGTAA
184 CCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAA
* *
1534681 GAACTTCCAATGTTTC
249 AAACCTCCAATGTTTC
1534697 TCCATAAGAA
Statistics
Matches: 253, Mismatches: 10, Indels: 14
0.91 0.04 0.05
Matches are distributed among these distances:
267 61 0.24
268 5 0.02
269 3 0.01
277 184 0.73
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (266 bp):
GACCGGACACGAATTTTGCATTTTTTTTCCAGTGACCTTGACCTTGCCCGAATGACCTTAGGTCA
AGATCATGAGATCATAAGCAATCTTTGTGTGAAGTAAGAACTTCAAATGTTTCCCCATAAGAAAG
ATATGGACCGGACACGAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTT
GGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAAAACCTCCAATG
TTTCCA
Found at i:1534776 original size:8 final size:8
Alignment explanation
Indices: 1534730--1534780 Score: 57
Period size: 8 Copynumber: 6.4 Consensus size: 8
1534720 ACACGATTGC
*
1534730 ACAGACAG
1 ACAGACGG
* *
1534738 ACGGACAG
1 ACAGACGG
*
1534746 ACAGACAG
1 ACAGACGG
1534754 ACAGACGG
1 ACAGACGG
1534762 ACAGACGG
1 ACAGACGG
*
1534770 ACGGACGG
1 ACAGACGG
1534778 ACA
1 ACA
1534781 AGGTGATTCC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 38 1.00
ACGTcount: A:0.41, C:0.25, G:0.33, T:0.00
Consensus pattern (8 bp):
ACAGACGG
Found at i:1534779 original size:4 final size:4
Alignment explanation
Indices: 1534730--1534767 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
1534720 ACACGATTGC
* *
1534730 ACAG ACAG ACGG ACAG ACAG ACAG ACAG ACGG ACAG AC
1 ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG AC
1534768 GGACGGACGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.45, C:0.26, G:0.29, T:0.00
Consensus pattern (4 bp):
ACAG
Found at i:1537800 original size:36 final size:36
Alignment explanation
Indices: 1537753--1538370 Score: 1128
Period size: 36 Copynumber: 17.2 Consensus size: 36
1537743 CCTGCTCTCA
1537753 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
1 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
1537789 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
1 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
* *
1537825 TCAGACTGTGATAACATACCCTGGGCAGTGGTGAAG
1 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
*
1537861 TCAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
1 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
*
1537897 TAAGACTGTGATTACATACTCTGGGCAGTGGTGAAG
1 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
1537933 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
1 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
1537969 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
1 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
*
1538005 TCAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
1 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
* * *
1538041 TCAGACTGTGATTACATACCCTAGGCAGTGTTGAAG
1 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
1538077 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
1 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
*
1538113 TAAGACTGTGATTACATACCCTTGGCAGTGGTGAAG
1 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
1538149 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
1 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
1538185 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
1 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
* *
1538221 TAAGACTGTGATTACATACCCTGGGCAGTGATGGAG
1 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
*
1538257 TAAGACTGTGATTACATACTCTGGGCAGTGGTGAAG
1 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
1538293 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
1 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
1538329 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
1 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
1538365 TAAGAC
1 TAAGAC
1538371 CCTGGGCAGT
Statistics
Matches: 562, Mismatches: 20, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 562 1.00
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (36 bp):
TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
Found at i:1537944 original size:108 final size:108
Alignment explanation
Indices: 1537753--1538677 Score: 1608
Period size: 108 Copynumber: 8.7 Consensus size: 108
1537743 CCTGCTCTCA
1537753 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACATACCCTGGGCAGT
1 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACATACCCTGGGCAGT
* *
1537818 GGTGAAGTCAGACTGTGATAACATACCCTGGGCAGTGGTGAAG
66 GGTGAAGTAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
* *
1537861 TCAGACTGTGATTACATACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACATACTCTGGGCAGT
1 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACATACCCTGGGCAGT
1537926 GGTGAAGTAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
66 GGTGAAGTAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
*
1537969 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAGTCAGACTGTGATTACATACCCTGGGCAGT
1 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACATACCCTGGGCAGT
* * *
1538034 GGTGAAGTCAGACTGTGATTACATACCCTAGGCAGTGTTGAAG
66 GGTGAAGTAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
*
1538077 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACATACCCTTGGCAGT
1 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACATACCCTGGGCAGT
1538142 GGTGAAGTAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
66 GGTGAAGTAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
1538185 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACATACCCTGGGCAGT
1 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACATACCCTGGGCAGT
* * *
1538250 GATGGAGTAAGACTGTGATTACATACTCTGGGCAGTGGTGAAG
66 GGTGAAGTAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
1538293 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACATACCCTGGGCAGT
1 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACATACCCTGGGCAGT
1538358 GGTGAAGT-A-A----G-------ACCCTGGGCAGTGGTGAAG
66 GGTGAAGTAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
*
1538388 TAAGACTGTGATTACATACCCTGGGCAGTTGTGAAGTAAGACTGTGATTACATACCCAT-GGCAG
1 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACATACCC-TGGGCAG
*
1538452 TGATGAAGTAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
65 TGGTGAAGTAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
1538496 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACATACCCTGGGCAGT
1 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACATACCCTGGGCAGT
1538561 GGTGAAGTAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
66 GGTGAAGTAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
*
1538604 TAAGACTGTGATTACATACCCTGGGCAGTGATGAAGTAAGACTGTGATTACATACCCTGGGCAGT
1 TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACATACCCTGGGCAGT
1538669 GGTGAAGTA
66 GGTGAAGTA
1538678 CTGGATGGAC
Statistics
Matches: 775, Mismatches: 27, Indels: 30
0.93 0.03 0.04
Matches are distributed among these distances:
95 87 0.11
96 2 0.00
97 1 0.00
101 1 0.00
102 1 0.00
106 1 0.00
107 2 0.00
108 680 0.88
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (108 bp):
TAAGACTGTGATTACATACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACATACCCTGGGCAGT
GGTGAAGTAAGACTGTGATTACATACCCTGGGCAGTGGTGAAG
Found at i:1538372 original size:23 final size:23
Alignment explanation
Indices: 1538346--1538393 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1538336 GTGATTACAT
1538346 ACCCTGGGCAGTGGTGAAGTAAG
1 ACCCTGGGCAGTGGTGAAGTAAG
1538369 ACCCTGGGCAGTGGTGAAGTAAG
1 ACCCTGGGCAGTGGTGAAGTAAG
1538392 AC
1 AC
1538394 TGTGATTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.19, G:0.38, T:0.17
Consensus pattern (23 bp):
ACCCTGGGCAGTGGTGAAGTAAG
Found at i:1538402 original size:59 final size:59
Alignment explanation
Indices: 1538310--1538429 Score: 231
Period size: 59 Copynumber: 2.0 Consensus size: 59
1538300 GTGATTACAT
1538310 ACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACATACCCTGGGCAGTGGTGAAGTAAG
1 ACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACATACCCTGGGCAGTGGTGAAGTAAG
*
1538369 ACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACATACCCTGGGCAGTTGTGAAGTAAG
1 ACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACATACCCTGGGCAGTGGTGAAGTAAG
1538428 AC
1 AC
1538430 TGTGATTACA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.28, C:0.17, G:0.33, T:0.23
Consensus pattern (59 bp):
ACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACATACCCTGGGCAGTGGTGAAGTAAG
Found at i:1538416 original size:36 final size:36
Alignment explanation
Indices: 1538369--1538677 Score: 575
Period size: 36 Copynumber: 8.6 Consensus size: 36
1538359 GTGAAGTAAG
1538369 ACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACAT
1 ACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACAT
*
1538405 ACCCTGGGCAGTTGTGAAGTAAGACTGTGATTACAT
1 ACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACAT
*
1538441 ACCCAT-GGCAGTGATGAAGTAAGACTGTGATTACAT
1 ACCC-TGGGCAGTGGTGAAGTAAGACTGTGATTACAT
1538477 ACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACAT
1 ACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACAT
1538513 ACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACAT
1 ACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACAT
1538549 ACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACAT
1 ACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACAT
1538585 ACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACAT
1 ACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACAT
*
1538621 ACCCTGGGCAGTGATGAAGTAAGACTGTGATTACAT
1 ACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACAT
1538657 ACCCTGGGCAGTGGTGAAGTA
1 ACCCTGGGCAGTGGTGAAGTA
1538678 CTGGATGGAC
Statistics
Matches: 265, Mismatches: 6, Indels: 4
0.96 0.02 0.01
Matches are distributed among these distances:
35 1 0.00
36 263 0.99
37 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (36 bp):
ACCCTGGGCAGTGGTGAAGTAAGACTGTGATTACAT
Found at i:1540817 original size:16 final size:14
Alignment explanation
Indices: 1540785--1540813 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1540775 GTGGAGGGTT
1540785 TTTTCTATTGCTGA
1 TTTTCTATTGCTGA
1540799 TTTTCTATTGCTGA
1 TTTTCTATTGCTGA
1540813 T
1 T
1540814 ATTTATGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (14 bp):
TTTTCTATTGCTGA
Found at i:1544254 original size:40 final size:40
Alignment explanation
Indices: 1544199--1544317 Score: 220
Period size: 40 Copynumber: 3.0 Consensus size: 40
1544189 AAGTTATGTA
*
1544199 TACAGTGTATTGACGGGTACAAACACATCATCTCTTACCT
1 TACAGTATATTGACGGGTACAAACACATCATCTCTTACCT
1544239 TACAGTATATTGACGGGTACAAACACATCATCTCTTACCT
1 TACAGTATATTGACGGGTACAAACACATCATCTCTTACCT
*
1544279 TACAGTATATTGACTGGTACAAACACATCATCTCTTACC
1 TACAGTATATTGACGGGTACAAACACATCATCTCTTACC
1544318 GTTCCAATCG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 77 1.00
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.30
Consensus pattern (40 bp):
TACAGTATATTGACGGGTACAAACACATCATCTCTTACCT
Found at i:1550618 original size:22 final size:22
Alignment explanation
Indices: 1550590--1550664 Score: 89
Period size: 22 Copynumber: 3.4 Consensus size: 22
1550580 TTTTCTTGGT
*
1550590 GCGCCCCAAGTACA-ATTCACGA
1 GCGCCCCAAGTATATA-TCACGA
*
1550612 GCGCCCCAAGTGTATATCACGA
1 GCGCCCCAAGTATATATCACGA
* *
1550634 GCGCCCCAATTATATCTCACGA
1 GCGCCCCAAGTATATATCACGA
*
1550656 GCCCCCCAA
1 GCGCCCCAA
1550665 AAATGCAGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
22 45 0.98
23 1 0.02
ACGTcount: A:0.28, C:0.39, G:0.17, T:0.16
Consensus pattern (22 bp):
GCGCCCCAAGTATATATCACGA
Found at i:1552841 original size:18 final size:19
Alignment explanation
Indices: 1552820--1552887 Score: 57
Period size: 23 Copynumber: 3.4 Consensus size: 19
1552810 CTCTTGATTT
1552820 AGCTATT-TAGCTTGAAAA
1 AGCTATTATAGCTTGAAAA
* *
1552838 AGCTATATATAGCTTTATAA
1 AGCTAT-TATAGCTTGAAAA
*
1552858 AGCTATTCAAAATAGCTTGATAA
1 AGCTATT----ATAGCTTGAAAA
1552881 AGCTATT
1 AGCTATT
1552888 TATGTGCAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 6 0.15
19 2 0.05
20 15 0.37
23 18 0.44
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (19 bp):
AGCTATTATAGCTTGAAAA
Found at i:1553428 original size:18 final size:18
Alignment explanation
Indices: 1553404--1553445 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1553394 GCTTCTCTGA
1553404 ATAGCTTAATAAAGCTAT
1 ATAGCTTAATAAAGCTAT
* * *
1553422 TTAGCTTATTCAAGCTAT
1 ATAGCTTAATAAAGCTAT
1553440 ATAGCT
1 ATAGCT
1553446 AAATCTGGAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (18 bp):
ATAGCTTAATAAAGCTAT
Found at i:1559347 original size:21 final size:21
Alignment explanation
Indices: 1559321--1559416 Score: 165
Period size: 21 Copynumber: 4.6 Consensus size: 21
1559311 AAGGAGGTCA
*
1559321 CCGATCTTTGACTGATCGGGG
1 CCGATCATTGACTGATCGGGG
*
1559342 CCGATCTTTGACTGATCGGGG
1 CCGATCATTGACTGATCGGGG
1559363 CCGATCATTGACTGATCGGGG
1 CCGATCATTGACTGATCGGGG
*
1559384 CCGATCATTGACTGGTCGGGG
1 CCGATCATTGACTGATCGGGG
1559405 CCGATCATTGAC
1 CCGATCATTGAC
1559417 GGATTGAGGG
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 73 1.00
ACGTcount: A:0.17, C:0.25, G:0.32, T:0.26
Consensus pattern (21 bp):
CCGATCATTGACTGATCGGGG
Found at i:1575766 original size:17 final size:17
Alignment explanation
Indices: 1575744--1575851 Score: 216
Period size: 17 Copynumber: 6.4 Consensus size: 17
1575734 AGTTAGGTGT
1575744 GTGTACACGACAGTTAG
1 GTGTACACGACAGTTAG
1575761 GTGTACACGACAGTTAG
1 GTGTACACGACAGTTAG
1575778 GTGTACACGACAGTTAG
1 GTGTACACGACAGTTAG
1575795 GTGTACACGACAGTTAG
1 GTGTACACGACAGTTAG
1575812 GTGTACACGACAGTTAG
1 GTGTACACGACAGTTAG
1575829 GTGTACACGACAGTTAG
1 GTGTACACGACAGTTAG
1575846 GTGTAC
1 GTGTAC
1575852 CTCGATGCTG
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 91 1.00
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.24
Consensus pattern (17 bp):
GTGTACACGACAGTTAG
Found at i:1577166 original size:19 final size:17
Alignment explanation
Indices: 1577124--1577167 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1577114 AAAGTCTTCG
1577124 TTTTCATTGGTTCTCTA
1 TTTTCATTGGTTCTCTA
* *
1577141 ATTTCATTGGTCTTTCTTA
1 TTTTCATTGGT-TCTC-TA
1577160 TTTTCATT
1 TTTTCATT
1577168 ATCCTAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 10 0.45
18 3 0.14
19 9 0.41
ACGTcount: A:0.14, C:0.16, G:0.09, T:0.61
Consensus pattern (17 bp):
TTTTCATTGGTTCTCTA
Found at i:1580003 original size:87 final size:85
Alignment explanation
Indices: 1579856--1580057 Score: 377
Period size: 87 Copynumber: 2.4 Consensus size: 85
1579846 GATTGAATAG
1579856 ATAGAACGCAGTTCGCAATTCAAAATTTAGAATTCATATTTGGGGCCCGCTTGCCTATATGCAAT
1 ATAGAACGCAGTTCGCAATTCAAAATTTAGAATTCATATTTGGGGCCCGCTTGCCTATATGCAAT
1579921 TGAATAGTGAACTGCGTTCGAT
66 TGAATAGTGAACTGCGTTC--T
*
1579943 CTAGAACGCAGTTCGCAATTCAAAATTTAGAATTCATATTTGGGGCCCGCTTGCCTATATGCAAT
1 ATAGAACGCAGTTCGCAATTCAAAATTTAGAATTCATATTTGGGGCCCGCTTGCCTATATGCAAT
1580008 TGAATAGTGAACTGCGTTCT
66 TGAATAGTGAACTGCGTTCT
1580028 ATAGAACGCAGTTCGCAATTCAAAATTTAG
1 ATAGAACGCAGTTCGCAATTCAAAATTTAG
1580058 TGCGATTGAA
Statistics
Matches: 113, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
85 30 0.27
87 83 0.73
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (85 bp):
ATAGAACGCAGTTCGCAATTCAAAATTTAGAATTCATATTTGGGGCCCGCTTGCCTATATGCAAT
TGAATAGTGAACTGCGTTCT
Found at i:1580073 original size:56 final size:57
Alignment explanation
Indices: 1580006--1580115 Score: 195
Period size: 58 Copynumber: 1.9 Consensus size: 57
1579996 CCTATATGCA
1580006 ATTGAATAGTGAACTGCGTTCTA-TAGAACGCAGTTCGCAATTCAAAATTTAGTGCG
1 ATTGAATAGTGAACTGCGTTCTACTAGAACGCAGTTCGCAATTCAAAATTTAGTGCG
*
1580062 ATTGAATAGTGAACTGCGTTCTATCTAGAATGCAGTTCGCAATTCAAAATTTAG
1 ATTGAATAGTGAACTGCGTTCTA-CTAGAACGCAGTTCGCAATTCAAAATTTAG
1580116 AATTCATATT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
56 23 0.45
58 28 0.55
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (57 bp):
ATTGAATAGTGAACTGCGTTCTACTAGAACGCAGTTCGCAATTCAAAATTTAGTGCG
Found at i:1580244 original size:38 final size:38
Alignment explanation
Indices: 1580193--1580267 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
1580183 AGTTCGCAAT
1580193 TCAAAATTTAGTGCGATTGAATAGTGAACTGCGTTCTG
1 TCAAAATTTAGTGCGATTGAATAGTGAACTGCGTTCTG
*
1580231 TCAAAATTTAGTGCGATTGAATAGTGAACTGTGTTCT
1 TCAAAATTTAGTGCGATTGAATAGTGAACTGCGTTCT
1580268 ATCTAGAACG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.36
Consensus pattern (38 bp):
TCAAAATTTAGTGCGATTGAATAGTGAACTGCGTTCTG
Found at i:1580356 original size:184 final size:184
Alignment explanation
Indices: 1580047--1580387 Score: 646
Period size: 184 Copynumber: 1.9 Consensus size: 184
1580037 AGTTCGCAAT
*
1580047 TCAAAATTTAGTGCGATTGAATAGTGAACTGCGTTCTATCTAGAATGCAGTTCGCAATTCAAAAT
1 TCAAAATTTAGTGCGATTGAATAGTGAACTGCGTTCTATCTAGAACGCAGTTCGCAATTCAAAAT
1580112 TTAGAATTCATATTTGGGGCCCGCTTGCCTTATATGCAATTGAATAATGAACTGCGTTCTATCTA
66 TTAGAATTCATATTTGGGGCCCGCTTGCCTTATATGCAATTGAATAATGAACTGCGTTCTATCTA
1580177 GAACGCAGTTCGCAATTCAAAATTTAGTGCGATTGAATAGTGAACTGCGTTCTG
131 GAACGCAGTTCGCAATTCAAAATTTAGTGCGATTGAATAGTGAACTGCGTTCTG
* *
1580231 TCAAAATTTAGTGCGATTGAATAGTGAACTGTGTTCTATCTAGAACGCAGTTCGCAATTTAAAAT
1 TCAAAATTTAGTGCGATTGAATAGTGAACTGCGTTCTATCTAGAACGCAGTTCGCAATTCAAAAT
*
1580296 TTAGAATTTATATTTGGGGCCCGCTTGCCTTATATGCAATTGAATAATGAACTGCGTTCTATCTA
66 TTAGAATTCATATTTGGGGCCCGCTTGCCTTATATGCAATTGAATAATGAACTGCGTTCTATCTA
1580361 GAACGCAGTTCGCAATTCAAAATTTAG
131 GAACGCAGTTCGCAATTCAAAATTTAG
1580388 AATTCATATT
Statistics
Matches: 153, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
184 153 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Consensus pattern (184 bp):
TCAAAATTTAGTGCGATTGAATAGTGAACTGCGTTCTATCTAGAACGCAGTTCGCAATTCAAAAT
TTAGAATTCATATTTGGGGCCCGCTTGCCTTATATGCAATTGAATAATGAACTGCGTTCTATCTA
GAACGCAGTTCGCAATTCAAAATTTAGTGCGATTGAATAGTGAACTGCGTTCTG
Found at i:1580397 original size:88 final size:88
Alignment explanation
Indices: 1580062--1580401 Score: 425
Period size: 88 Copynumber: 3.8 Consensus size: 88
1580052 ATTTAGTGCG
* *
1580062 ATTGAATAGTGAACTGCGTTCTATCTAGAATGCAGTTCGCAATTCAAAATTTAGAATTCATATTT
1 ATTGAATAATGAACTGCGTTCTATCTAGAACGCAGTTCGCAATTCAAAATTTAGAATTCATATTT
1580127 GGGGCCCGCTTGCCTTATATGCA
66 GGGGCCCGCTTGCCTTATATGCA
*
1580150 ATTGAATAATGAACTGCGTTCTATCTAGAACGCAGTTCGCAATTCAAAATTTAG--TGCGATTGA
1 ATTGAATAATGAACTGCGTTCTATCTAGAACGCAGTTCGCAATTCAAAATTTAGAATTC-A-T-A
* * ** * * * *
1580213 ATAGTGAACTGCGTTCTGTCAAAATT-TAGTGCG
63 TTTG-GGGC-CCGCT-TG-C---CTTATA-TGCA
* * * *
1580246 ATTGAATAGTGAACTGTGTTCTATCTAGAACGCAGTTCGCAATTTAAAATTTAGAATTTATATTT
1 ATTGAATAATGAACTGCGTTCTATCTAGAACGCAGTTCGCAATTCAAAATTTAGAATTCATATTT
1580311 GGGGCCCGCTTGCCTTATATGCA
66 GGGGCCCGCTTGCCTTATATGCA
1580334 ATTGAATAATGAACTGCGTTCTATCTAGAACGCAGTTCGCAATTCAAAATTTAGAATTCATATTT
1 ATTGAATAATGAACTGCGTTCTATCTAGAACGCAGTTCGCAATTCAAAATTTAGAATTCATATTT
1580399 GGG
66 GGG
1580402 ACCTGAATTT
Statistics
Matches: 210, Mismatches: 28, Indels: 28
0.79 0.11 0.11
Matches are distributed among these distances:
86 2 0.01
87 1 0.00
88 122 0.58
89 5 0.02
90 2 0.01
91 4 0.02
92 4 0.02
93 4 0.02
94 2 0.01
95 5 0.02
96 57 0.27
97 1 0.00
98 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Consensus pattern (88 bp):
ATTGAATAATGAACTGCGTTCTATCTAGAACGCAGTTCGCAATTCAAAATTTAGAATTCATATTT
GGGGCCCGCTTGCCTTATATGCA
Found at i:1580909 original size:31 final size:31
Alignment explanation
Indices: 1580870--1580995 Score: 189
Period size: 31 Copynumber: 4.1 Consensus size: 31
1580860 CTGTGAATCT
*
1580870 TGCAAAGTTGCGTTAGCGCGACGGCGTGTTA
1 TGCAAAGTTGCGTTAGCGCGACGGCGTGTTG
* **
1580901 AGCAAAGTTGTTTTAGCGCGACGGCGTGTTG
1 TGCAAAGTTGCGTTAGCGCGACGGCGTGTTG
* *
1580932 TGCAAAGTTGTGTTAGTGCGACGGCGTGTTG
1 TGCAAAGTTGCGTTAGCGCGACGGCGTGTTG
*
1580963 TGCAAAGTTGCGTTAGCGCGACGGTGTGTTG
1 TGCAAAGTTGCGTTAGCGCGACGGCGTGTTG
1580994 TG
1 TG
1580996 TACATGTGTT
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 85 1.00
ACGTcount: A:0.17, C:0.16, G:0.37, T:0.29
Consensus pattern (31 bp):
TGCAAAGTTGCGTTAGCGCGACGGCGTGTTG
Found at i:1580960 original size:16 final size:15
Alignment explanation
Indices: 1580918--1580965 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1580908 TTGTTTTAGC
1580918 GCGACGGCGTGTTGT
1 GCGACGGCGTGTTGT
* * **
1580933 GCAAAGTTGTGTTAGT
1 GCGACGGCGTGTT-GT
1580949 GCGACGGCGTGTTGT
1 GCGACGGCGTGTTGT
1580964 GC
1 GC
1580966 AAAGTTGCGT
Statistics
Matches: 24, Mismatches: 8, Indels: 2
0.71 0.24 0.06
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.12, C:0.17, G:0.42, T:0.29
Consensus pattern (15 bp):
GCGACGGCGTGTTGT
Found at i:1581314 original size:88 final size:88
Alignment explanation
Indices: 1581188--1581474 Score: 511
Period size: 88 Copynumber: 3.3 Consensus size: 88
1581178 AACTGCGTTC
*
1581188 TAGAACGCAGTTCACTATTCAATTGCATATAAGGCAATCGGGCCCCAAATATAAATTCTAATTTT
1 TAGAACGCAGTTCACTATTCAATTGCATATAAGGCAATCGGGCCCCAAATATAAATTCTAAATTT
1581253 TGAATCGCGAACTGCATTCTAGA
66 TGAATCGCGAACTGCATTCTAGA
1581276 TAGAACGCAGTTCACTATTCAATTGCATATAAGGCAATCGGGCCCCAAATATAAATTCTAAATTT
1 TAGAACGCAGTTCACTATTCAATTGCATATAAGGCAATCGGGCCCCAAATATAAATTCTAAATTT
1581341 TGAATCGCGAACTGCATTCTAGA
66 TGAATCGCGAACTGCATTCTAGA
* * *
1581364 TAGAACGCAGTTCACTATTCAATTGCATATAAGGCAAGCGGGCCCCAAGTATGAATTCTAAATTT
1 TAGAACGCAGTTCACTATTCAATTGCATATAAGGCAATCGGGCCCCAAATATAAATTCTAAATTT
* * *
1581429 TGAATTGCGAACTGCGTTCTAGT
66 TGAATCGCGAACTGCATTCTAGA
1581452 TAGAACGCAGTTCACTATTCAAT
1 TAGAACGCAGTTCACTATTCAAT
1581475 CGCACTAAAT
Statistics
Matches: 192, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 192 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.29
Consensus pattern (88 bp):
TAGAACGCAGTTCACTATTCAATTGCATATAAGGCAATCGGGCCCCAAATATAAATTCTAAATTT
TGAATCGCGAACTGCATTCTAGA
Found at i:1581529 original size:55 final size:57
Alignment explanation
Indices: 1581421--1581529 Score: 195
Period size: 55 Copynumber: 1.9 Consensus size: 57
1581411 AGTATGAATT
1581421 CTAAATTTTGAATTGCGAACTGCGTTCTAGTTAGAACGCAGTTCACTATTCAATCGCA
1 CTAAATTTTGAATTGCGAACTGCGTTCTAG-TAGAACGCAGTTCACTATTCAATCGCA
1581479 CTAAA-TTTGAATTGCGAACTGCGTTCTA-TAGAACGCAGTTCACTATTCAAT
1 CTAAATTTTGAATTGCGAACTGCGTTCTAGTAGAACGCAGTTCACTATTCAAT
1581530 TGCATATAGG
Statistics
Matches: 51, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
55 23 0.45
57 23 0.45
58 5 0.10
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (57 bp):
CTAAATTTTGAATTGCGAACTGCGTTCTAGTAGAACGCAGTTCACTATTCAATCGCA
Found at i:1581629 original size:86 final size:86
Alignment explanation
Indices: 1581479--1581876 Score: 780
Period size: 86 Copynumber: 4.6 Consensus size: 86
1581469 TTCAATCGCA
1581479 CTAAA-TTTGAATTGCGAACTGCGTTCTATAGAACGCAGTTCACTATTCAATTGCATATAGGGCA
1 CTAAATTTTGAATTGCGAACTGCGTTCTATAGAACGCAGTTCACTATTCAATTGCATATAGGGCA
1581543 AGCGGGCCCCAAATATGAATT
66 AGCGGGCCCCAAATATGAATT
1581564 CTAAATTTTGAATTGCGAACTGCGTTCTATAGAACGCAGTTCACTATTCAATTGCATATAGGGCA
1 CTAAATTTTGAATTGCGAACTGCGTTCTATAGAACGCAGTTCACTATTCAATTGCATATAGGGCA
1581629 AGCGGGCCCCAAATATGAATT
66 AGCGGGCCCCAAATATGAATT
1581650 CTAAATTTTGAATTGCGAACTGCGTTCTATAGAACGCAGTTCACTATTCAATTGCATATAGGGCA
1 CTAAATTTTGAATTGCGAACTGCGTTCTATAGAACGCAGTTCACTATTCAATTGCATATAGGGCA
1581715 AGCGGGCCCCAAATATGAATT
66 AGCGGGCCCCAAATATGAATT
1581736 CTAAATTTTGAATTGCGAACTGCGTTCTATAGAACGCAGTTCACTATTCAATTGCATATAGGGCA
1 CTAAATTTTGAATTGCGAACTGCGTTCTATAGAACGCAGTTCACTATTCAATTGCATATAGGGCA
*
1581801 AGCGGGCCCCAAGTATGAATT
66 AGCGGGCCCCAAATATGAATT
1581822 CTAAATTTTGAATTGCGAACTGCGTTCTATAGAACGCAGTTCACTATTCAATTGC
1 CTAAATTTTGAATTGCGAACTGCGTTCTATAGAACGCAGTTCACTATTCAATTGC
1581877 GAACTGCGAA
Statistics
Matches: 311, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
85 5 0.02
86 306 0.98
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (86 bp):
CTAAATTTTGAATTGCGAACTGCGTTCTATAGAACGCAGTTCACTATTCAATTGCATATAGGGCA
AGCGGGCCCCAAATATGAATT
Found at i:1581678 original size:229 final size:229
Alignment explanation
Indices: 1581251--1581701 Score: 771
Period size: 229 Copynumber: 2.0 Consensus size: 229
1581241 AATTCTAATT
*
1581251 TTTGAATCGCGAACTGCATTCTAGATAGAACGCAGTTCACTATTCAATTGCATATAAGGCAATCG
1 TTTGAATCGCGAACTGCATTCTA-ATAGAACGCAGTTCACTATTCAATTGCATATAAGGCAAGCG
1581316 GGCCCCAAATATAAATTCTAAATTTTGAATCGCGAACTGCATTCTAGATAGAACGCAGTTCACTA
65 GGCCCCAAATATAAATTCTAAATTTTGAATCGCGAACTGCATTCTA-ATAGAACGCAGTTCACTA
*
1581381 TTCAATTGCATATAAGGCAAGCGGGCCCCAAGTATGAATTCTAAATTTTGAATTGCGAACTGCGT
129 TTCAATTGCATATAAGGCAAGCGGGCCCCAAATATGAATTCTAAATTTTGAATTGCGAACTGCGT
1581446 TCTAGTTAGAACGCAGTTCACTATTCAATCGCACTAAA
194 TCTA--TAGAACGCAGTTCACTATTCAATCGCACTAAA
* * *
1581484 TTTGAATTGCGAACTGCGTTCT-ATAGAACGCAGTTCACTATTCAATTGCATATAGGGCAAGCGG
1 TTTGAATCGCGAACTGCATTCTAATAGAACGCAGTTCACTATTCAATTGCATATAAGGCAAGCGG
* * *
1581548 GCCCCAAATATGAATTCTAAATTTTGAATTGCGAACTGCGTTCT-ATAGAACGCAGTTCACTATT
66 GCCCCAAATATAAATTCTAAATTTTGAATCGCGAACTGCATTCTAATAGAACGCAGTTCACTATT
*
1581612 CAATTGCATATAGGGCAAGCGGGCCCCAAATATGAATTCTAAATTTTGAATTGCGAACTGCGTTC
131 CAATTGCATATAAGGCAAGCGGGCCCCAAATATGAATTCTAAATTTTGAATTGCGAACTGCGTTC
1581677 TATAGAACGCAGTTCACTATTCAAT
196 TATAGAACGCAGTTCACTATTCAAT
1581702 TGCATATAGG
Statistics
Matches: 209, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
227 23 0.11
229 85 0.41
231 81 0.39
233 20 0.10
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.29
Consensus pattern (229 bp):
TTTGAATCGCGAACTGCATTCTAATAGAACGCAGTTCACTATTCAATTGCATATAAGGCAAGCGG
GCCCCAAATATAAATTCTAAATTTTGAATCGCGAACTGCATTCTAATAGAACGCAGTTCACTATT
CAATTGCATATAAGGCAAGCGGGCCCCAAATATGAATTCTAAATTTTGAATTGCGAACTGCGTTC
TATAGAACGCAGTTCACTATTCAATCGCACTAAA
Found at i:1602554 original size:32 final size:33
Alignment explanation
Indices: 1602488--1602564 Score: 122
Period size: 33 Copynumber: 2.4 Consensus size: 33
1602478 GATTTTGGTC
1602488 TCAATTTTCAACGTTGAAAAATGACCCCCCGGG
1 TCAATTTTCAACGTTGAAAAATGACCCCCCGGG
1602521 TCAATATTT-AACGTTGAAAAATGA-CCCCCGGG
1 TCAAT-TTTCAACGTTGAAAAATGACCCCCCGGG
*
1602553 TCCATTTTCAAC
1 TCAATTTTCAAC
1602565 CTGGGTCAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
31 3 0.07
32 15 0.37
33 20 0.49
34 3 0.07
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (33 bp):
TCAATTTTCAACGTTGAAAAATGACCCCCCGGG
Found at i:1609370 original size:19 final size:17
Alignment explanation
Indices: 1609346--1609382 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1609336 CACTAAGTGT
1609346 TTTAATTTGGAGAAAAAAA
1 TTTAA-TTGGA-AAAAAAA
1609365 TTTAATTGGAAAAAAAA
1 TTTAATTGGAAAAAAAA
1609382 T
1 T
1609383 CAAAATTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 5 0.28
19 5 0.28
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.32
Consensus pattern (17 bp):
TTTAATTGGAAAAAAAA
Found at i:1609379 original size:18 final size:19
Alignment explanation
Indices: 1609346--1609381 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1609336 CACTAAGTGT
*
1609346 TTTAATTTGGAGAAAAAAA
1 TTTAATTTGGAAAAAAAAA
1609365 TTTAA-TTGGAAAAAAAA
1 TTTAATTTGGAAAAAAAA
1609382 TCAAAATTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.56, C:0.00, G:0.14, T:0.31
Consensus pattern (19 bp):
TTTAATTTGGAAAAAAAAA
Found at i:1609525 original size:2 final size:2
Alignment explanation
Indices: 1609512--1609639 Score: 115
Period size: 2 Copynumber: 66.5 Consensus size: 2
1609502 TGAATTAACA
* * *
1609512 TC TC TC TT TC TC TC T- TG T- TC TC TC TC TC T- TC TC TC T- TG
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * *
1609550 T- TC TC TC TC TC TC TC TG TC TG TC TC TC TG TC TG TC TG TC TG
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
1609591 TC TC TGC -C TG TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC T-C TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1609633 TC TC TC T
1 TC TC TC T
1609640 NNNNNNNNNN
Statistics
Matches: 103, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
1 6 0.06
2 96 0.93
3 1 0.01
ACGTcount: A:0.00, C:0.40, G:0.08, T:0.52
Consensus pattern (2 bp):
TC
Done.