Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397264.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_130.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8132550
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 35170 characters in sequence are not A, C, G, or T
File 5 of 14
Found at i:1979893 original size:21 final size:21
Alignment explanation
Indices: 1979867--1979910 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1979857 ATTTTACTTG
1979867 ATTTAAAATAAAAATA-TAAAA
1 ATTT-AAATAAAAATAGTAAAA
* *
1979888 ATTTAATTAAATATAGTAAAA
1 ATTTAAATAAAAATAGTAAAA
1979909 AT
1 AT
1979911 AAAAATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
ATTTAAATAAAAATAGTAAAA
Found at i:1984888 original size:23 final size:25
Alignment explanation
Indices: 1984857--1984903 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
1984847 AAAATGAAAA
*
1984857 ATGTGCCAAG-AAAAT-TATTCATT
1 ATGTACCAAGAAAAATGTATTCATT
1984880 ATGTACCAAGAAAAATGTATTCAT
1 ATGTACCAAGAAAAATGTATTCAT
1984904 GCCAAAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.43
24 5 0.24
25 7 0.33
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.32
Consensus pattern (25 bp):
ATGTACCAAGAAAAATGTATTCATT
Found at i:1986037 original size:45 final size:45
Alignment explanation
Indices: 1985936--1986025 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
1985926 TTCTTTGAAA
* *
1985936 ACTACGGTATCTCTAGTGGGTTCATTTTATGGGTAGAAAAATCTT
1 ACTATGGTATCTCTAGTGGGTTCATCTTATGGGTAGAAAAATCTT
**
1985981 ACTATGGTATCTCTAGTGGGTTTGTCTTATGGGTAGAAAAATCTT
1 ACTATGGTATCTCTAGTGGGTTCATCTTATGGGTAGAAAAATCTT
1986026 CTTTGGGTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (45 bp):
ACTATGGTATCTCTAGTGGGTTCATCTTATGGGTAGAAAAATCTT
Found at i:1998012 original size:2 final size:2
Alignment explanation
Indices: 1998005--1998032 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1997995 TTATATGCAT
1998005 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1998033 GCAGAGAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2000009 original size:48 final size:48
Alignment explanation
Indices: 1999950--2000046 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
1999940 TGATAGCAAG
1999950 TTACAAATGGGTTTTGCGAACGCACACTTTTTAGTTAGTGATAATGGC
1 TTACAAATGGGTTTTGCGAACGCACACTTTTTAGTTAGTGATAATGGC
1999998 TTACAAATGGGTTTTGCGAACGCACACTTTTTAGTTAGTGATAATGGC
1 TTACAAATGGGTTTTGCGAACGCACACTTTTTAGTTAGTGATAATGGC
2000046 T
1 T
2000047 GCATCAGGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (48 bp):
TTACAAATGGGTTTTGCGAACGCACACTTTTTAGTTAGTGATAATGGC
Found at i:2002740 original size:147 final size:147
Alignment explanation
Indices: 2002473--2002776 Score: 572
Period size: 147 Copynumber: 2.1 Consensus size: 147
2002463 TGAACCTTGC
*
2002473 ATTTTATCATGCATCAACTATAAGAAAAATGTCCTGACCAGATAAACAATTGTTTCTGATTTTGG
1 ATTTTATCATGCATCAACTACAAGAAAAATGTCCTGACCAGATAAACAATTGTTTCTGATTTTGG
2002538 TGTAAAAGAATTTTGTCTTCTTTAAGGCAACTAAAATTATCTTGTACAAAGTCCAAACCCCATGA
66 TGTAAAAGAATTTTGTCTTCTTTAAGGCAACTAAAATTATCTTGTACAAAGTCCAAACCCCATGA
2002603 CCCTAATCAATAGCATT
131 CCCTAATCAATAGCATT
*
2002620 ATTTTATTATGCATCAACTACAAGAAAAATGTCCTGACCAGATAAACAATTGTTTCTGATTTTGG
1 ATTTTATCATGCATCAACTACAAGAAAAATGTCCTGACCAGATAAACAATTGTTTCTGATTTTGG
* *
2002685 TGTAAAAGAATTTTGTCTTCTTTAAGGCAACTAAAATTATCTTTTACGAAGTCCAAACCCCATGA
66 TGTAAAAGAATTTTGTCTTCTTTAAGGCAACTAAAATTATCTTGTACAAAGTCCAAACCCCATGA
2002750 CCCTAATCAATAGCATT
131 CCCTAATCAATAGCATT
2002767 ATTTTATCAT
1 ATTTTATCAT
2002777 AGACCATTGA
Statistics
Matches: 152, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
147 152 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.35
Consensus pattern (147 bp):
ATTTTATCATGCATCAACTACAAGAAAAATGTCCTGACCAGATAAACAATTGTTTCTGATTTTGG
TGTAAAAGAATTTTGTCTTCTTTAAGGCAACTAAAATTATCTTGTACAAAGTCCAAACCCCATGA
CCCTAATCAATAGCATT
Found at i:2002861 original size:2 final size:2
Alignment explanation
Indices: 2002854--2002887 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2002844 GGACAGGTAC
2002854 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2002888 GTCGCCAAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2004366 original size:2 final size:2
Alignment explanation
Indices: 2004359--2004390 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2004349 CACTGGGAGC
2004359 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
2004391 GAATGGCTAG
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):
AG
Found at i:2013106 original size:58 final size:58
Alignment explanation
Indices: 2013011--2013127 Score: 189
Period size: 58 Copynumber: 2.0 Consensus size: 58
2013001 AAAGTGGAAA
*
2013011 GGTGAAGACACAACCTCCAATAACATGAAATAGAAAACTACCACTAACAATAAAATAG
1 GGTGAAGACACAACCTCCAACAACATGAAATAGAAAACTACCACTAACAATAAAATAG
* * * *
2013069 GGTGGAGACACAACCTCCCACAACATGAAATGGAAAACTACCATTAACAATAAAATAG
1 GGTGAAGACACAACCTCCAACAACATGAAATAGAAAACTACCACTAACAATAAAATAG
2013127 G
1 G
2013128 AACCACAATG
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.49, C:0.21, G:0.15, T:0.15
Consensus pattern (58 bp):
GGTGAAGACACAACCTCCAACAACATGAAATAGAAAACTACCACTAACAATAAAATAG
Found at i:2015563 original size:40 final size:40
Alignment explanation
Indices: 2015508--2015588 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
2015498 TCTTTGGTCT
*
2015508 CTATTATATAGATATTTACTCACGCATCATACTTGTTTCA
1 CTATTATATAGATATTTACTCACCCATCATACTTGTTTCA
* * * * *
2015548 CTATTTTATGGATATTTACTCCCCCATGATCCTTGTTTCA
1 CTATTATATAGATATTTACTCACCCATCATACTTGTTTCA
2015588 C
1 C
2015589 AAGTAATTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.25, C:0.23, G:0.09, T:0.43
Consensus pattern (40 bp):
CTATTATATAGATATTTACTCACCCATCATACTTGTTTCA
Found at i:2020224 original size:17 final size:18
Alignment explanation
Indices: 2020202--2020237 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2020192 GTACAAAAAA
2020202 ATATTTATA-AAAAATAT
1 ATATTTATATAAAAATAT
*
2020219 ATATTTATATTAAAATAT
1 ATATTTATATAAAAATAT
2020237 A
1 A
2020238 ATGTAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATTTATATAAAAATAT
Found at i:2023040 original size:2 final size:2
Alignment explanation
Indices: 2023033--2023062 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2023023 ACCAGTAAAC
2023033 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2023063 AAGAATGTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2023470 original size:15 final size:15
Alignment explanation
Indices: 2023446--2023491 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
2023436 TCAAAATGTA
2023446 AAATAA-AATAATAT
1 AAATAATAATAATAT
2023460 AAATAATAATAATA-
1 AAATAATAATAATAT
*
2023474 ACAACAATAATAAT-T
1 A-AATAATAATAATAT
2023489 AAA
1 AAA
2023492 AAAACCTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 9 0.32
15 19 0.68
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATAATAATAATAT
Found at i:2027266 original size:24 final size:23
Alignment explanation
Indices: 2027204--2027279 Score: 70
Period size: 23 Copynumber: 3.3 Consensus size: 23
2027194 TTATATTATT
*
2027204 ATTTTTATATAAAATT-TTAAAA
1 ATTTTTAAATAAAATTATTAAAA
* *
2027226 ATTTATTAAA-ATAATTATTTAAA
1 ATTT-TTAAATAAAATTATTAAAA
2027249 ATTATTTAAATAAAATTA--AAATA
1 ATT-TTTAAATAAAATTATTAAA-A
2027272 ATTTTTAA
1 ATTTTTAA
2027280 TAAGTTGATA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
22 16 0.36
23 21 0.48
24 7 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTTTTAAATAAAATTATTAAAA
Found at i:2027275 original size:46 final size:45
Alignment explanation
Indices: 2027188--2027279 Score: 107
Period size: 46 Copynumber: 2.0 Consensus size: 45
2027178 TTTGGGCATG
** * *
2027188 AAATAATTATATTATTATTTTTATATAAAATTTTAAAAATTTATTA
1 AAATAATTATATTAAAATTTTTAAATAAAATTTAAAAAATTT-TTA
2027234 AAATAATTAT-TTAAAATTATTTAAATAAAA-TTAAAATAATTTTTA
1 AAATAATTATATTAAAATT-TTTAAATAAAATTTAAAA-AATTTTTA
2027279 A
1 A
2027280 TAAGTTGATA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
45 15 0.38
46 25 0.62
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (45 bp):
AAATAATTATATTAAAATTTTTAAATAAAATTTAAAAAATTTTTA
Found at i:2033094 original size:2 final size:2
Alignment explanation
Indices: 2033087--2033111 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2033077 GGTTGTTATG
2033087 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
2033112 ATACACATCC
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:2039856 original size:147 final size:153
Alignment explanation
Indices: 2039705--2040467 Score: 428
Period size: 153 Copynumber: 5.0 Consensus size: 153
2039695 TTCTATTCAT
* * * *
2039705 CCATCTGCACCAGGTAA-AGTGCCAAGCTTGACACTGCCTGCAACGTCGCCTTCAGAAACTACCC
1 CCATCTGCACCAGATAACA-TGCCAAGCTTGACACTGCCTGCAACATCACCTTCAGAAACCACCC
*
2039769 AACCATCGTTG-CT-T-A-A-TCCATC-TTCGTCCAACTCAAC-ATCAGGCTTGACACAACATGG
65 AACCATCGTTGCCTATAATAGTCCATCATTC-TCCAACTCAACGATCAAGCTTGACACAACATGG
2039827 AATGGCACCTATGGCTTCCTCTCCG
129 AATGGCACCTATGGCTTCCTCTCCG
* * * * ** *
2039852 CCATCTTCGCTAGATAACATGCCAAGCTTGACACTGCCTGCAACATCACCTTCTGCTACCAGCCA
1 CCATCTGCACCAGATAACATGCCAAGCTTGACACTGCCTGCAACATCACCTTCAGAAACCACCCA
* * *
2039917 ACCATCTTTGCCTACTAATAGTCCATCATTCTCCAATTCAACGATCAAGCTTGACACAACCTGGA
66 ACCATCGTTGCCTA-TAATAGTCCATCATTCTCCAACTCAACGATCAAGCTTGACACAACATGGA
* **
2039982 ATGGCACCTATGGCTTCGTCTCAA
130 ATGGCACCTATGGCTTCCTCTCCG
* ** * ** * **** *
2040006 CCATCATTGTCA--A-ACTCA-ATGCCAAGCTTGGGACTG-CTTCAATGTCGCCTTCTCCTACCG
1 CCATC--TG-CACCAGA-TAACATGCCAAGCTTGACACTGCCTGCAACATCACCTTCAGAAACCA
* * * * * * * * * *
2040066 GCCAACCATCATTACCTACAAATATTGCATCATTCTCCAACTCAAC-ACCAAGCTTGGCGCAACC
62 CCCAACCATCGTTGCCTA-TAATAGTCCATCATTCTCCAACTCAACGATCAAGCTTGACACAACA
* **
2040130 TGGAATGGCACCTTTGGCTTCCTCTCAA
126 TGGAATGGCACCTATGGCTTCCTCTCCG
* ** * ** * ****
2040158 CCATCATTGTTA--A-ACTCAAC--GCCAAGCTTGGGACTGCCTTCAATGTCGCCTTCTCCTACC
1 CCATC--TG-CACCAGA-T-AACATGCCAAGCTTGACACTGCCTGCAACATCACCTTCAGAAACC
* * *
2040218 AGCCAACCATCTTTGCCTACTAATAGTCCATCATTCTCCAATTCAACG-TCAAGCTTGACACAAC
61 ACCCAACCATCGTTGCCTA-TAATAGTCCATCATTCTCCAACTCAACGATCAAGCTTGACACAAC
* * **
2040282 CTGGAATGGCACCTATGGCTTCGTCTCAA
125 ATGGAATGGCACCTATGGCTTCCTCTCCG
** * ** * * **
2040311 CCATCATTGTCA--A-ACTCAAC--GCCAAGCTTGGGACTGCCTTCAATGTCGCCTTCTGCTACC
1 CCATC--TG-CACCAGA-T-AACATGCCAAGCTTGACACTGCCTGCAACATCACCTTCAGAAACC
* * * * * * *
2040371 AACCAACCATCTTTGCCCACAAATA-TCCATCGTTCTCCAACTCAAC-ACCAAGCTTGGCACAAC
61 ACCCAACCATCGTTGCCTA-TAATAGTCCATCATTCTCCAACTCAACGATCAAGCTTGACACAAC
* * * *
2040434 CTGGAATGCCACCTATGTCTTCCTCTCAG
125 ATGGAATGGCACCTATGGCTTCCTCTCCG
2040463 CCATC
1 CCATC
2040468 ATTATCAAAC
Statistics
Matches: 531, Mismatches: 67, Indels: 31
0.84 0.11 0.05
Matches are distributed among these distances:
147 61 0.11
148 3 0.01
150 1 0.00
151 1 0.00
152 136 0.26
153 258 0.49
154 66 0.12
155 3 0.01
156 1 0.00
157 1 0.00
ACGTcount: A:0.26, C:0.34, G:0.14, T:0.26
Consensus pattern (153 bp):
CCATCTGCACCAGATAACATGCCAAGCTTGACACTGCCTGCAACATCACCTTCAGAAACCACCCA
ACCATCGTTGCCTATAATAGTCCATCATTCTCCAACTCAACGATCAAGCTTGACACAACATGGAA
TGGCACCTATGGCTTCCTCTCCG
Found at i:2040184 original size:306 final size:304
Alignment explanation
Indices: 2039784--2041019 Score: 1078
Period size: 305 Copynumber: 4.1 Consensus size: 304
2039774 TCGTTGCTTA
* * * *
2039784 ATCCATCTTCGTCCAACTCAACATCAGGCTTGACACAACATGGAATGGCACCTATGGCTTCCTCT
1 ATCCATCTTC-TCCAACTCAACACCAAGCTTGGCACAACCTGGAATGGCACCTATGGCTTCCTCT
* * * *
2039849 CCGCCATC-TTCGCTAGA-T-AACATGCCAAGCTTGACACTGCCTGCAACATCACCTTCTGCTAC
65 CAGCCATCATT-GTTAAACTCAAC--GCCAAGCTTGACACTGCCTGCAACATCACCTTCTCCTAC
2039911 CAGCCAACCATCTTTGCCTACTAATAGTCCATCATTCTCCAATTCAACGATCAAGCTTGACACAA
127 CAGCCAACCATCTTTGCCTACTAATAGTCCATCATTCTCCAATTCAACG-TCAAGCTTGACACAA
*
2039976 CCTGGAATGGCACCTATGGCTTCGTCTCAACCATCATTGTCAAACTCAATGCCAAGCTTGGGACT
191 CCTGGAATGGCACCTATGGCTTCGTCTCAACCATCATTGTCAAACTCAACGCCAAGCTTGGGACT
** *
2040041 G-CTTCAATGTCGCCTTCTCCTACCGGCCAACCATCATTACCTACAAAT
256 GCCTTCAATGTCGCCTTCTCCTACCAACCAACCATCATTACCCACAAAT
* * *
2040089 ATTGCATCATTCTCCAACTCAACACCAAGCTTGGCGCAACCTGGAATGGCACCTTTGGCTTCCTC
1 A-TCCATC-TTCTCCAACTCAACACCAAGCTTGGCACAACCTGGAATGGCACCTATGGCTTCCTC
* ** * ** *
2040154 TCAACCATCATTGTTAAACTCAACGCCAAGCTTGGGACTGCCTTCAATGTCGCCTTCTCCTACCA
64 TCAGCCATCATTGTTAAACTCAACGCCAAGCTTGACACTGCCTGCAACATCACCTTCTCCTACCA
2040219 GCCAACCATCTTTGCCTACTAATAGTCCATCATTCTCCAATTCAACGTCAAGCTTGACACAACCT
129 GCCAACCATCTTTGCCTACTAATAGTCCATCATTCTCCAATTCAACGTCAAGCTTGACACAACCT
2040284 GGAATGGCACCTATGGCTTCGTCTCAACCATCATTGTCAAACTCAACGCCAAGCTTGGGACTGCC
194 GGAATGGCACCTATGGCTTCGTCTCAACCATCATTGTCAAACTCAACGCCAAGCTTGGGACTGCC
* * *
2040349 TTCAATGTCGCCTTCTGCTACCAACCAACCATCTTTGCCCACAAAT
259 TTCAATGTCGCCTTCTCCTACCAACCAACCATCATTACCCACAAAT
* *
2040395 ATCCATCGTTCTCCAACTCAACACCAAGCTTGGCACAACCTGGAATGCCACCTATGTCTTCCTCT
1 ATCCATC-TTCTCCAACTCAACACCAAGCTTGGCACAACCTGGAATGGCACCTATGGCTTCCTCT
* * ** * ***
2040460 CAGCCATCATTATCAAACTCAACGCCAAGCTTGACACAACCTGGAATGGCACCTATGGCTTCCT-
65 CAGCCATCATTGTTAAACTCAACGCCAAGCTTGACACTGCCTGCAACATCACCT-T--C-TCCTA
* * * * * *
2040524 CTCAGCC-ATCA-C--TGTCAATCTCAA-CG-CCAAGC-TTGGGACTGCC--TTCAATGTC--GC
126 C-CAGCCAACCATCTTTGCCTA-CT-AATAGTCC-ATCATT----CT-CCAATTCAACGTCAAG-
* * * * * * * ** *** * * * * *
2040578 CTT--CTGCTACCAGCCAAT--CATCTTTGCCCACAAAT-ATTCCATCGTTCTCCAACTCAACAC
181 CTTGAC-ACAACCTG-GAATGGCACCTATGGCTTCGTCTCA-ACCATCATTGTCAAACTCAACGC
* ** ** * * * * *
2040638 CAAGCTTGGCACAACCTGGAATGCCACCTATGT-CT----TCC--TC-TCA--A--C-C----
243 CAAGCTTGGGACTGCCTTCAATGTCGCCT-TCTCCTACCAACCAACCATCATTACCCACAAAT
* * * * *
2040684 AT-C--CTTATCAAACTCAACGCCAAGCTTGACACAACCTGGAATGGCACCAATGGCTTCCTCTC
1 ATCCATCTTCTCCAACTCAACACCAAGCTTGGCACAACCTGGAATGGCACCTATGGCTTCCTCTC
* * * * * ** * ** * *
2040746 AACCATCATTGTCAAATTCAACTCCAACCTTGGGACTGCCTTCAATGTCGCCTTCTGCTACCAGC
66 AGCCATCATTGTTAAACTCAACGCCAAGCTTGACACTGCCTGCAACATCACCTTCTCCTACCAGC
* * * * * *
2040811 CAACCATCTTTACCTACAAATAGCCCATCGTTCTCCAACTCAACGTCAAGCTTGACACCAACTTG
131 CAACCATCTTTGCCTACTAATAGTCCATCATTCTCCAATTCAACGTCAAGCTTGACA-CAACCTG
2040876 GAATGGCACCTATGGCTTCGTCTCAACCATCATTGTCAAACTCAACGCCAAGCTTGGGACTGCCT
195 GAATGGCACCTATGGCTTCGTCTCAACCATCATTGTCAAACTCAACGCCAAGCTTGGGACTGCCT
* * *
2040941 TCAATGTCGCCTTCTGCTACCAACCAACCATCTTTGCCCACAAAT
260 TCAATGTCGCCTTCTCCTACCAACCAACCATCATTACCCACAAAT
2040986 ATTCCATCGTTCTCCAACTCAACACCAAGCTTGG
1 A-TCCATC-TTCTCCAACTCAACACCAAGCTTGG
2041020 NNNNNNNNNN
Statistics
Matches: 726, Mismatches: 141, Indels: 126
0.73 0.14 0.13
Matches are distributed among these distances:
280 2 0.00
281 10 0.01
282 12 0.02
283 6 0.01
284 9 0.01
285 105 0.14
286 52 0.07
287 1 0.00
288 1 0.00
289 2 0.00
290 2 0.00
292 1 0.00
293 3 0.00
294 1 0.00
297 1 0.00
298 3 0.00
299 1 0.00
301 2 0.00
302 1 0.00
303 1 0.00
304 2 0.00
305 242 0.33
306 201 0.28
307 36 0.05
308 16 0.02
309 11 0.02
310 2 0.00
ACGTcount: A:0.26, C:0.34, G:0.14, T:0.26
Consensus pattern (304 bp):
ATCCATCTTCTCCAACTCAACACCAAGCTTGGCACAACCTGGAATGGCACCTATGGCTTCCTCTC
AGCCATCATTGTTAAACTCAACGCCAAGCTTGACACTGCCTGCAACATCACCTTCTCCTACCAGC
CAACCATCTTTGCCTACTAATAGTCCATCATTCTCCAATTCAACGTCAAGCTTGACACAACCTGG
AATGGCACCTATGGCTTCGTCTCAACCATCATTGTCAAACTCAACGCCAAGCTTGGGACTGCCTT
CAATGTCGCCTTCTCCTACCAACCAACCATCATTACCCACAAAT
Found at i:2040255 original size:153 final size:153
Alignment explanation
Indices: 2039785--2040492 Score: 953
Period size: 153 Copynumber: 4.6 Consensus size: 153
2039775 CGTTGCTTAA
* *
2039785 TCCATC-TTCGTCCAACTCAACATCAGGCTTGACACAACATGGAATGGCACCTATGGCTTCCTCT
1 TCCATCATTC-TCCAACTCAACATCAAGCTTGACACAACCTGGAATGGCACCTATGGCTTCCTCT
** * ** * ** * *
2039849 CCGCCATC-TTCG-CTAGA-T-AACATGCCAAGCTTGACACTGCCTGCAACATCACCTTCTGCTA
65 CAACCATCATT-GTC-AAACTCAAC--GCCAAGCTTGGGACTGCCTTCAATGTCGCCTTCTCCTA
*
2039910 CCAGCCAACCATCTTTGCCTACTAATAG
126 CCAGCCAACCATCTTTGCCTACAAATAG
* *
2039938 TCCATCATTCTCCAATTCAACGATCAAGCTTGACACAACCTGGAATGGCACCTATGGCTTCGTCT
1 TCCATCATTCTCCAACTCAAC-ATCAAGCTTGACACAACCTGGAATGGCACCTATGGCTTCCTCT
* *
2040003 CAACCATCATTGTCAAACTCAATGCCAAGCTTGGGACTG-CTTCAATGTCGCCTTCTCCTACCGG
65 CAACCATCATTGTCAAACTCAACGCCAAGCTTGGGACTGCCTTCAATGTCGCCTTCTCCTACCAG
* * *
2040067 CCAACCATCATTACCTACAAATAT
130 CCAACCATCTTTGCCTACAAATAG
* * * * *
2040091 TGCATCATTCTCCAACTCAACACCAAGCTTGGCGCAACCTGGAATGGCACCTTTGGCTTCCTCTC
1 TCCATCATTCTCCAACTCAACATCAAGCTTGACACAACCTGGAATGGCACCTATGGCTTCCTCTC
*
2040156 AACCATCATTGTTAAACTCAACGCCAAGCTTGGGACTGCCTTCAATGTCGCCTTCTCCTACCAGC
66 AACCATCATTGTCAAACTCAACGCCAAGCTTGGGACTGCCTTCAATGTCGCCTTCTCCTACCAGC
*
2040221 CAACCATCTTTGCCTACTAATAG
131 CAACCATCTTTGCCTACAAATAG
* * *
2040244 TCCATCATTCTCCAATTCAACGTCAAGCTTGACACAACCTGGAATGGCACCTATGGCTTCGTCTC
1 TCCATCATTCTCCAACTCAACATCAAGCTTGACACAACCTGGAATGGCACCTATGGCTTCCTCTC
* *
2040309 AACCATCATTGTCAAACTCAACGCCAAGCTTGGGACTGCCTTCAATGTCGCCTTCTGCTACCAAC
66 AACCATCATTGTCAAACTCAACGCCAAGCTTGGGACTGCCTTCAATGTCGCCTTCTCCTACCAGC
*
2040374 CAACCATCTTTGCCCACAAATA-
131 CAACCATCTTTGCCTACAAATAG
* * * * *
2040396 TCCATCGTTCTCCAACTCAACACCAAGCTTGGCACAACCTGGAATGCCACCTATGTCTTCCTCTC
1 TCCATCATTCTCCAACTCAACATCAAGCTTGACACAACCTGGAATGGCACCTATGGCTTCCTCTC
* *
2040461 AGCCATCATTATCAAACTCAACGCCAAGCTTG
66 AACCATCATTGTCAAACTCAACGCCAAGCTTG
2040493 ACACAACCTG
Statistics
Matches: 491, Mismatches: 57, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
152 162 0.33
153 257 0.52
154 66 0.13
155 4 0.01
156 2 0.00
ACGTcount: A:0.26, C:0.34, G:0.14, T:0.26
Consensus pattern (153 bp):
TCCATCATTCTCCAACTCAACATCAAGCTTGACACAACCTGGAATGGCACCTATGGCTTCCTCTC
AACCATCATTGTCAAACTCAACGCCAAGCTTGGGACTGCCTTCAATGTCGCCTTCTCCTACCAGC
CAACCATCTTTGCCTACAAATAG
Found at i:2040503 original size:66 final size:66
Alignment explanation
Indices: 2040409--2040558 Score: 237
Period size: 66 Copynumber: 2.3 Consensus size: 66
2040399 ATCGTTCTCC
* * * *
2040409 AACTCAACACCAAGCTTGGCACAACCTGGAATGCCACCTATGTCTTCCTCTCAGCCATCATTATC
1 AACTCAACGCCAAGCTTGACACAACCTGGAATGCCACCTATGGCTTCCTCTCAGCCATCACTATC
2040474 A
66 A
* *
2040475 AACTCAACGCCAAGCTTGACACAACCTGGAATGGCACCTATGGCTTCCTCTCAGCCATCACTGTC
1 AACTCAACGCCAAGCTTGACACAACCTGGAATGCCACCTATGGCTTCCTCTCAGCCATCACTATC
2040540 A
66 A
*
2040541 ATCTCAACGCCAAGCTTG
1 AACTCAACGCCAAGCTTG
2040559 GGACTGCCTT
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 77 1.00
ACGTcount: A:0.28, C:0.35, G:0.15, T:0.23
Consensus pattern (66 bp):
AACTCAACGCCAAGCTTGACACAACCTGGAATGCCACCTATGGCTTCCTCTCAGCCATCACTATC
A
Found at i:2040722 original size:66 final size:66
Alignment explanation
Indices: 2040628--2040777 Score: 210
Period size: 66 Copynumber: 2.3 Consensus size: 66
2040618 ATCGTTCTCC
* * * *
2040628 AACTCAACACCAAGCTTGGCACAACCTGGAATGCCACCTATGTCTTCCTCTCAACCATCCTTATC
1 AACTCAACACCAAGCTTGACACAACCTGGAATGCCACCAATGGCTTCCTCTCAACCATCATTATC
2040693 A
66 A
* * *
2040694 AACTCAACGCCAAGCTTGACACAACCTGGAATGGCACCAATGGCTTCCTCTCAACCATCATTGTC
1 AACTCAACACCAAGCTTGACACAACCTGGAATGCCACCAATGGCTTCCTCTCAACCATCATTATC
2040759 A
66 A
* * *
2040760 AATTCAACTCCAACCTTG
1 AACTCAACACCAAGCTTG
2040778 GGACTGCCTT
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 74 1.00
ACGTcount: A:0.30, C:0.35, G:0.12, T:0.23
Consensus pattern (66 bp):
AACTCAACACCAAGCTTGACACAACCTGGAATGCCACCAATGGCTTCCTCTCAACCATCATTATC
A
Found at i:2040724 original size:219 final size:218
Alignment explanation
Indices: 2040245--2040931 Score: 1097
Period size: 219 Copynumber: 3.1 Consensus size: 218
2040235 TACTAATAGT
* * * * *
2040245 CCATCATTCTCCAATTCAACGTCAAGCTTGACACAACCTGGAATGGCACCTATGGCTTCGTCTCA
1 CCATCATTATCAAACTCAACGCCAAGCTTGACACAACCTGGAATGGCACCTATGGCTTCCTCTCA
* *
2040310 ACCATCATTGTCAAACTCAACGCCAAGCTTGGGACTGCCTTCAATGTCGCCTTCTGCTACCAACC
66 ACCATCATTGTCAATCTCAACGCCAAGCTTGGGACTGCCTTCAATGTCGCCTTCTGCTACCAGCC
2040375 AACCATCTTTGCCCACAAATATCCATCGTTCTCCAACTCAACACCAAGCTTGGCACAACCTGGAA
131 AACCATCTTTGCCCACAAATATCCATCGTTCTCCAACTCAACACCAAGCTTGGCACAACCTGGAA
*
2040440 TGCCACCTATGTCTTCCTCTCAG
196 TGCCACCTATGTCTTCCTCTCAA
2040463 CCATCATTATCAAACTCAACGCCAAGCTTGACACAACCTGGAATGGCACCTATGGCTTCCTCTCA
1 CCATCATTATCAAACTCAACGCCAAGCTTGACACAACCTGGAATGGCACCTATGGCTTCCTCTCA
* *
2040528 GCCATCACTGTCAATCTCAACGCCAAGCTTGGGACTGCCTTCAATGTCGCCTTCTGCTACCAGCC
66 ACCATCATTGTCAATCTCAACGCCAAGCTTGGGACTGCCTTCAATGTCGCCTTCTGCTACCAGCC
*
2040593 AATCATCTTTGCCCACAAATATTCCATCGTTCTCCAACTCAACACCAAGCTTGGCACAACCTGGA
131 AACCATCTTTGCCCACAAATA-TCCATCGTTCTCCAACTCAACACCAAGCTTGGCACAACCTGGA
2040658 ATGCCACCTATGTCTTCCTCTCAA
195 ATGCCACCTATGTCTTCCTCTCAA
* *
2040682 CCATCCTTATCAAACTCAACGCCAAGCTTGACACAACCTGGAATGGCACCAATGGCTTCCTCTCA
1 CCATCATTATCAAACTCAACGCCAAGCTTGACACAACCTGGAATGGCACCTATGGCTTCCTCTCA
* *
2040747 ACCATCATTGTCAAAT-TCAACTCCAACCTTGGGACTGCCTTCAATGTCGCCTTCTGCTACCAGC
66 ACCATCATTGTC-AATCTCAACGCCAAGCTTGGGACTGCCTTCAATGTCGCCTTCTGCTACCAGC
* * * ** * *
2040811 CAACCATCTTTACCTACAAATAGCCCATCGTTCTCCAACTCAACGTCAAGCTTGACACCAACTTG
130 CAACCATCTTTGCCCACAAATA-TCCATCGTTCTCCAACTCAACACCAAGCTTGGCA-CAACCTG
* * *
2040876 GAATGGCACCTATGGCTTCGTCTCAA
193 GAATGCCACCTATGTCTTCCTCTCAA
*
2040902 CCATCATTGTCAAACTCAACGCCAAGCTTG
1 CCATCATTATCAAACTCAACGCCAAGCTTG
2040932 GGACTGCCTT
Statistics
Matches: 435, Mismatches: 31, Indels: 4
0.93 0.07 0.01
Matches are distributed among these distances:
218 141 0.32
219 234 0.54
220 60 0.14
ACGTcount: A:0.27, C:0.35, G:0.14, T:0.25
Consensus pattern (218 bp):
CCATCATTATCAAACTCAACGCCAAGCTTGACACAACCTGGAATGGCACCTATGGCTTCCTCTCA
ACCATCATTGTCAATCTCAACGCCAAGCTTGGGACTGCCTTCAATGTCGCCTTCTGCTACCAGCC
AACCATCTTTGCCCACAAATATCCATCGTTCTCCAACTCAACACCAAGCTTGGCACAACCTGGAA
TGCCACCTATGTCTTCCTCTCAA
Found at i:2040961 original size:154 final size:153
Alignment explanation
Indices: 2040694--2041018 Score: 524
Period size: 154 Copynumber: 2.1 Consensus size: 153
2040684 ATCCTTATCA
2040694 AACTCAACGCCAAGCTTGACACAACCTGGAATGGCACCAATGGCTTCCTCTCAACCATCATTGTC
1 AACTCAACGCCAAGCTTGACACAACCTGGAATGGCACCAATGGCTTCCTCTCAACCATCATTGTC
* * *
2040759 AAATTCAACTCCAACCTTGGGACTGCCTTCAATGTCGCCTTCTGCTACCAGCCAACCATCTTTAC
66 AAACTCAACGCCAACCTTGGGACTGCCTTCAATGTCGCCTTCTGCTACCAACCAACCATCTTTAC
*
2040824 CTACAAATAGCCCATCGTTCTCC
131 CCACAAATAGCCCATCGTTCTCC
* * * *
2040847 AACTCAACGTCAAGCTTGACACCAACTTGGAATGGCACCTATGGCTTCGTCTCAACCATCATTGT
1 AACTCAACGCCAAGCTTGACA-CAACCTGGAATGGCACCAATGGCTTCCTCTCAACCATCATTGT
* *
2040912 CAAACTCAACGCCAAGCTTGGGACTGCCTTCAATGTCGCCTTCTGCTACCAACCAACCATCTTTG
65 CAAACTCAACGCCAACCTTGGGACTGCCTTCAATGTCGCCTTCTGCTACCAACCAACCATCTTTA
**
2040977 CCCACAAATATTCCATCGTTCTCC
130 CCCACAAATAGCCCATCGTTCTCC
*
2041001 AACTCAACACCAAGCTTG
1 AACTCAACGCCAAGCTTG
2041019 GNNNNNNNNN
Statistics
Matches: 157, Mismatches: 14, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
153 20 0.13
154 137 0.87
ACGTcount: A:0.27, C:0.34, G:0.14, T:0.25
Consensus pattern (153 bp):
AACTCAACGCCAAGCTTGACACAACCTGGAATGGCACCAATGGCTTCCTCTCAACCATCATTGTC
AAACTCAACGCCAACCTTGGGACTGCCTTCAATGTCGCCTTCTGCTACCAACCAACCATCTTTAC
CCACAAATAGCCCATCGTTCTCC
Found at i:2042516 original size:36 final size:36
Alignment explanation
Indices: 2042437--2042516 Score: 117
Period size: 35 Copynumber: 2.2 Consensus size: 36
2042427 TATTCAAATA
* * *
2042437 ATAAAAAGATAGATTTCAAAGTGTTTTTCATATGCT
1 ATAAAAAAATAGATTTCAAAGTATTTTTCATAAGCT
*
2042473 ATAAAAAATTAGATTTC-AAGTATTTTTCATAAGCT
1 ATAAAAAAATAGATTTCAAAGTATTTTTCATAAGCT
2042508 ATAAAAAAA
1 ATAAAAAAA
2042517 GTGTTTTCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 24 0.62
36 15 0.38
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.36
Consensus pattern (36 bp):
ATAAAAAAATAGATTTCAAAGTATTTTTCATAAGCT
Found at i:2052491 original size:26 final size:26
Alignment explanation
Indices: 2052449--2052500 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
2052439 CTAGGAAACT
2052449 TGTGACATATCTCTAATGCTATTAGA
1 TGTGACATATCTCTAATGCTATTAGA
* *
2052475 TGTGACATATGTTTAATGCTATTAGA
1 TGTGACATATCTCTAATGCTATTAGA
2052501 GCTTCTCTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (26 bp):
TGTGACATATCTCTAATGCTATTAGA
Found at i:2059865 original size:3 final size:3
Alignment explanation
Indices: 2059859--2059896 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
2059849 TTTCTTCTTC
*
2059859 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT TTT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2059897 AGAAAGAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:2060112 original size:21 final size:22
Alignment explanation
Indices: 2060069--2060112 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
2060059 TCAAGAAAAT
* **
2060069 TTAAATAAATTTTTATTTTTAA
1 TTAAATAAATTTTTAATAATAA
2060091 TTAAATAAA-TTTTAATAATAA
1 TTAAATAAATTTTTAATAATAA
2060112 T
1 T
2060113 GATTAATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTAAATAAATTTTTAATAATAA
Found at i:2069816 original size:19 final size:19
Alignment explanation
Indices: 2069792--2069830 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2069782 AGTGTTCCCC
* *
2069792 TATGTACTTTGTTGGATCA
1 TATGTACTTTATGGGATCA
2069811 TATGTACTTTATGGGATCA
1 TATGTACTTTATGGGATCA
2069830 T
1 T
2069831 GTAATGGTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.10, G:0.21, T:0.46
Consensus pattern (19 bp):
TATGTACTTTATGGGATCA
Found at i:2102037 original size:12 final size:12
Alignment explanation
Indices: 2102020--2102053 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
2102010 TCTTAACAGA
2102020 ATTATTATTAAC
1 ATTATTATTAAC
2102032 ATTATTATTAAC
1 ATTATTATTAAC
*
2102044 ACTATTATTA
1 ATTATTATTA
2102054 TTTCTAGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTATTATTAAC
Found at i:2109946 original size:5 final size:5
Alignment explanation
Indices: 2109936--2109974 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
2109926 TTACCTTTCG
*
2109936 GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT AAAAT -AAAT
1 GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT
2109975 ATTTTCACTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
4 4 0.12
5 29 0.88
ACGTcount: A:0.64, C:0.00, G:0.15, T:0.21
Consensus pattern (5 bp):
GAAAT
Found at i:2131911 original size:6 final size:7
Alignment explanation
Indices: 2131897--2131923 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2131887 GTGTTTTCCA
2131897 TTTCTTT
1 TTTCTTT
2131904 TTTCTTT
1 TTTCTTT
2131911 TTTCTTT
1 TTTCTTT
2131918 TTTCTT
1 TTTCTT
2131924 ATATTTCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTCTTT
Found at i:2132155 original size:20 final size:21
Alignment explanation
Indices: 2132132--2132173 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2132122 TTCTTAGATT
* *
2132132 TAATTTTTAA-TTTTAATAAA
1 TAATTATTAAGTTATAATAAA
2132152 TAATTATTAAGTTATAATAAA
1 TAATTATTAAGTTATAATAAA
2132173 T
1 T
2132174 CGGACCCAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
TAATTATTAAGTTATAATAAA
Found at i:2133694 original size:29 final size:29
Alignment explanation
Indices: 2133661--2133731 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
2133651 GTTAATTATT
* **
2133661 AAATATAATATTTATTTGAATAAAAACAA
1 AAATATAAAATTTAAGTGAATAAAAACAA
* * *
2133690 AAATATAAAATTTAAGTGACTTAAAATAA
1 AAATATAAAATTTAAGTGAATAAAAACAA
2133719 AAATATAAAATTT
1 AAATATAAAATTT
2133732 TAATTAAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.34
Consensus pattern (29 bp):
AAATATAAAATTTAAGTGAATAAAAACAA
Found at i:2133746 original size:29 final size:29
Alignment explanation
Indices: 2133683--2133749 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
2133673 TATTTGAATA
* * *
2133683 AAAACAAAAATATAAAATTTAAGTGACTT
1 AAAATAAAAATATAAAATTTAAGTAAATT
*
2133712 AAAATAAAAATATAAAATTTTAATTAAATT
1 AAAATAAAAATATAAAA-TTTAAGTAAATT
*
2133742 -TAATAAAA
1 AAAATAAAA
2133750 GTAAAAAGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 23 0.72
30 9 0.28
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (29 bp):
AAAATAAAAATATAAAATTTAAGTAAATT
Found at i:2157247 original size:20 final size:19
Alignment explanation
Indices: 2157222--2157306 Score: 61
Period size: 20 Copynumber: 4.4 Consensus size: 19
2157212 AATATTTTAT
*
2157222 AATATTATAATTAAAATAAA
1 AATATTA-AAATAAAATAAA
*
2157242 AATATTAAAATAAAATATAT
1 AATATTAAAATAAAATA-AA
*
2157262 AATA-TAAGAATAAAA-ATTA
1 AATATTAA-AATAAAATA-AA
2157281 AA-A-TAAAATAAAATATAA
1 AATATTAAAATAAAATA-AA
*
2157299 AAAATTAA
1 AATATTAA
2157307 CATTTATATA
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
17 7 0.13
18 9 0.16
19 17 0.31
20 22 0.40
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.29
Consensus pattern (19 bp):
AATATTAAAATAAAATAAA
Found at i:2157278 original size:40 final size:40
Alignment explanation
Indices: 2157219--2157411 Score: 140
Period size: 40 Copynumber: 4.6 Consensus size: 40
2157209 AAAAATATTT
* * *
2157219 TATAATATTATAATTAAAATAAAAATATTAAAATAAAATA
1 TATAATATAATAATAAAAATAAAAAAATTAAAATAAAATA
* *
2157259 TATAATATAAGAATAAAAATTAAAATAAAATAAAATATAAA-A
1 TATAATATAATAATAAAAA-TAAAA-AAATTAAAATA-AAATA
* * * *
2157301 AATTAACATTTATATAATATAGATAAAACAAATTAAAATAAAATA
1 TA-T-A-ATATA-ATAATAAAAATAAAA-AAATTAAAATAAAATA
* * *
2157346 TATAATATAA-AA-AATATATTAAAGAAATAAAAATAAAATA
1 TATAATATAATAATAA-A-AATAAAAAAATTAAAATAAAATA
* *
2157386 TATAAAATTATAATAATAAATAAAAA
1 TATAATATAATAATAA-AAATAAAAA
2157412 TAAAATATAT
Statistics
Matches: 118, Mismatches: 23, Indels: 23
0.72 0.14 0.14
Matches are distributed among these distances:
39 1 0.01
40 42 0.36
41 18 0.15
42 19 0.16
43 5 0.04
44 5 0.04
45 21 0.18
46 7 0.06
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (40 bp):
TATAATATAATAATAAAAATAAAAAAATTAAAATAAAATA
Found at i:2157382 original size:55 final size:55
Alignment explanation
Indices: 2157275--2157383 Score: 125
Period size: 55 Copynumber: 2.0 Consensus size: 55
2157265 ATAAGAATAA
* * * *
2157275 AAATTAAAATAAAATAAAATATAAAAAATTAACATTTATATAATATAGATAAAAC
1 AAATTAAAATAAAATAAAATATAAAAAATTAACATTTAAAAAATAAAAATAAAAC
*
2157330 AAATTAAAATAAAATATATAATATAAAAAA-T-ATA-TTAAAGAAATAAAAATAAAA
1 AAATTAAAATAAAATA-A-AATATAAAAAATTAACATTTAAA-AAATAAAAATAAAA
2157384 TATATAAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
54 4 0.09
55 29 0.63
56 2 0.04
57 11 0.24
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (55 bp):
AAATTAAAATAAAATAAAATATAAAAAATTAACATTTAAAAAATAAAAATAAAAC
Found at i:2157386 original size:33 final size:33
Alignment explanation
Indices: 2157336--2157420 Score: 109
Period size: 33 Copynumber: 2.5 Consensus size: 33
2157326 AAACAAATTA
* *
2157336 AAATAAAATATATAATATAAAAAA-TATATTAAAG
1 AAATAAAA-ATAAAATATAAAAAATTATAAT-AAG
* *
2157370 AAATAAAAATAAAATATATAAAATTATAATAAT
1 AAATAAAAATAAAATATAAAAAATTATAATAAG
2157403 AAATAAAAATAAAATATA
1 AAATAAAAATAAAATATA
2157421 TGACATTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
33 33 0.72
34 13 0.28
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.28
Consensus pattern (33 bp):
AAATAAAAATAAAATATAAAAAATTATAATAAG
Found at i:2157548 original size:111 final size:113
Alignment explanation
Indices: 2157373--2157819 Score: 738
Period size: 106 Copynumber: 4.0 Consensus size: 113
2157363 ATTAAAGAAA
2157373 TAAAAATAAAATATATAAAATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATAT
1 TAAAAATAAAATATATAAAATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATAT
2157438 TTAA-AATATGATATTATATAAAAATTAATAATATAAATATAAA-ATAT
66 TTAAGAA-ATGATATTATATAAAAATTAATAATATAAATATAAATATAT
*
2157485 TAAAAATAAAATATA-AAATATTACAATAATAAAT-AAAATAAAATATATGACATTAAAAATATA
1 TAAAAATAAAATATATAAA-ATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATA
2157548 TTTAAGAAATGATATTATATAAAAATTAAT-A-AT--A-A-AAATATAT
65 TTTAAGAAATGATATTATATAAAAATTAATAATATAAATATAAATATAT
*
2157591 TAAAAATAAAATATATAAAATTATAATAATAAAT-AAAATAAAATATATGATATTAAAAATATA-
1 TAAAAATAAAATATATAAAATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATAT
*
2157654 TTAAAAATATGATATTATATAAAAATTAATAATATAAATATAAATATAT
66 TTAAGAA-ATGATATTATATAAAAATTAATAATATAAATATAAATATAT
*
2157703 TAAAAATAAAATATATAAAATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATAT
1 TAAAAATAAAATATATAAAATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATAT
*
2157768 TTAAGAAATGATATTATATAAAAATTAATAATAAAAATATAAATATAT
66 TTAAGAAATGATATTATATAAAAATTAATAATATAAATATAAATATAT
2157816 TAAA
1 TAAA
2157820 CTTATATTTT
Statistics
Matches: 316, Mismatches: 6, Indels: 25
0.91 0.02 0.07
Matches are distributed among these distances:
105 9 0.03
106 84 0.27
107 5 0.02
108 2 0.01
109 2 0.01
110 2 0.01
111 60 0.19
112 73 0.23
113 73 0.23
114 6 0.02
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.34
Consensus pattern (113 bp):
TAAAAATAAAATATATAAAATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATAT
TTAAGAAATGATATTATATAAAAATTAATAATATAAATATAAATATAT
Found at i:2157632 original size:32 final size:34
Alignment explanation
Indices: 2157597--2157740 Score: 88
Period size: 32 Copynumber: 4.1 Consensus size: 34
2157587 ATATTAAAAA
2157597 TAAAATATATAAAATTATAATAATA-AAT-AAAA
1 TAAAATATATAAAATTATAATAATATAATAAAAA
* * *
2157629 TAAAATATATGATATTA-AA-AATATATTAAAAA
1 TAAAATATATAAAATTATAATAATATAATAAAAA
* *
2157661 TATGATATTATATAAAAAT-TAATAATATAAATATAAATA
1 TA--A-AATATATAAAATTATAATAATAT-AATA-AAA-A
2157700 TATTAAA-A-ATAAAATATATAA-AATTATAATAATAAA
1 TA--AAATATATAAAAT-TATAATAA-TATAATAA-AAA
2157736 TAAAA
1 TAAAA
2157741 ATAAAATATA
Statistics
Matches: 87, Mismatches: 11, Indels: 26
0.70 0.09 0.21
Matches are distributed among these distances:
30 4 0.05
31 4 0.05
32 21 0.24
34 4 0.05
35 11 0.13
36 15 0.17
37 13 0.15
38 10 0.11
39 5 0.06
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (34 bp):
TAAAATATATAAAATTATAATAATATAATAAAAA
Found at i:2157655 original size:64 final size:63
Alignment explanation
Indices: 2157580--2157815 Score: 177
Period size: 59 Copynumber: 3.9 Consensus size: 63
2157570 AAATTAATAA
2157580 TAAAAATATATTAA-AAATAAAATATATAAAATTATAATAATAAATAAAATAAAATATATGATAT
1 TAAAAATATATTAAGAAATAAAATATATAAAA-TATAATAATAAATAAAAT-AAATATATGATAT
** * * *
2157644 TAAAAATATATTAA-AAATATGATAT-T---ATATAAAAATTAATAATATAAATATAAAT-ATAT
1 TAAAAATATATTAAGAAATAAAATATATAAAATATAATAATAAATAAAATAAATAT--ATGATAT
* *
2157703 TAAAAATA-A--AATATATAAAAT-TATAATAATA-AATAA-AAAT---A-AAATATATGATAT
1 TAAAAATATATTAAGAAATAAAATATATAA-AATATAATAATAAATAAAATAAATATATGATAT
* * *
2157757 TAAAAATATATTTAAGAAATGATATTATATAAAA-ATTAATAATAAA-AATATAAATATAT
1 TAAAAATATA-TTAAGAAAT-AAAATATATAAAATA-TAATAATAAATAAAATAAATATAT
2157816 TAAACTTATA
Statistics
Matches: 136, Mismatches: 14, Indels: 44
0.70 0.07 0.23
Matches are distributed among these distances:
53 2 0.01
54 12 0.09
55 7 0.05
56 4 0.03
57 7 0.05
58 13 0.10
59 35 0.26
60 17 0.12
61 6 0.04
63 2 0.01
64 31 0.23
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (63 bp):
TAAAAATATATTAAGAAATAAAATATATAAAATATAATAATAAATAAAATAAATATATGATAT
Found at i:2157699 original size:48 final size:46
Alignment explanation
Indices: 2157371--2157758 Score: 165
Period size: 48 Copynumber: 8.8 Consensus size: 46
2157361 ATATTAAAGA
* * * * * *
2157371 AATAA-AAATAAAATATA-TAAAATTATAATAATAAATAAAAATAA
1 AATAATAAATAAAATATATTAAAAATATGATATTATATAAAATTAT
* *
2157415 AATATATGACATTAAAAATATATTTAAAATATGATATTATATAAAAATTAAT
1 AATA-AT-A-AAT-AAAATATATTAAAAATATGATATTATAT-AAAATT-AT
* *
2157467 AAT-ATAAATATAAA-ATATTAAAAATA--A-AATATA-AAATATTAC
1 AATAATAAATA-AAATATATTAAAAATATGATATTATATAAA-ATTAT
* *
2157509 AATAATAAAT-AAA-ATA--AAATATATGACA-T-TA-AAAA-TAT
1 AATAATAAATAAAATATATTAAAAATATGATATTATATAAAATTAT
* * * * *
2157547 ATTTAAGAAATGATAT-TATATAAAAAT-T-A-A-TA-ATAAAAATAT
1 A-ATAATAAATAAAATATAT-TAAAAATATGATATTATATAAAATTAT
* * * * * *
2157589 ATTAA-AAATAAAATATA-TAAAATTATAATAATAAATAAAA-TAA
1 AATAATAAATAAAATATATTAAAAATATGATATTATATAAAATTAT
*
2157632 AATATATGATATTAAAAATATATTAAAAATATGATATTATATAAAAATTAAT
1 AATA-AT-A-AAT-AAAATATATTAAAAATATGATATTATAT-AAAATT-AT
*
2157684 AAT-ATAAATATAAATATATTAAAAATA--A-AATATATAAAATTAT
1 AATAATAAATA-AAATATATTAAAAATATGATATTATATAAAATTAT
*
2157727 AATAATAAATAAAA-ATA--AAATATATGATATTA
1 AATAATAAATAAAATATATTAAAAATATGATATTA
2157759 AAAATATATT
Statistics
Matches: 268, Mismatches: 33, Indels: 87
0.69 0.09 0.22
Matches are distributed among these distances:
38 3 0.01
39 20 0.07
40 26 0.10
41 20 0.07
42 18 0.07
43 32 0.12
44 29 0.11
45 8 0.03
46 2 0.01
47 16 0.06
48 33 0.12
49 25 0.09
50 22 0.08
51 6 0.02
52 8 0.03
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (46 bp):
AATAATAAATAAAATATATTAAAAATATGATATTATATAAAATTAT
Found at i:2157716 original size:14 final size:14
Alignment explanation
Indices: 2157456--2157749 Score: 79
Period size: 14 Copynumber: 21.0 Consensus size: 14
2157446 TGATATTATA
2157456 TAAAAATTAATAATA-
1 TAAAAA-TAA-AATAT
*
2157471 TAAATATAAAATAT
1 TAAAAATAAAATAT
2157485 TAAAAATAAAATA-
1 TAAAAATAAAATAT
*
2157498 TAAAATATTACAATA-
1 TAAAA-A-TAAAATAT
*
2157513 -ATAAATAAAATA-
1 TAAAAATAAAATAT
* ** *
2157525 -AAATATATGACAT
1 TAAAAATAAAATAT
*
2157538 TAAAAAT-ATAT-T
1 TAAAAATAAAATAT
* *
2157550 TAAGAAATGATATTAT
1 TAA-AAAT-AAAATAT
* *
2157566 ATAAAAAT-TAATAA
1 -TAAAAATAAAATAT
2157580 TAAAAAT---ATAT
1 TAAAAATAAAATAT
2157591 TAAAAATAAAATAT
1 TAAAAATAAAATAT
* *
2157605 ATAAAATTATAATA-
1 -TAAAAATAAAATAT
*
2157619 -ATAAATAAAATA-
1 TAAAAATAAAATAT
* **
2157631 -AAATATATGATAT
1 TAAAAATAAAATAT
2157644 TAAAAAT---ATAT
1 TAAAAATAAAATAT
*
2157655 TAAAAATATGATATTAT
1 TAAAAATA--A-AATAT
2157672 ATAAAAATTAATAATA-
1 -TAAAAA-TAA-AATAT
*
2157688 TAAATATAAATATAT
1 TAAAAATAAA-ATAT
2157703 TAAAAATAAAATAT
1 TAAAAATAAAATAT
*
2157717 ATAAAATTATAATAATAAA
1 -TAAAA--ATAA-AAT-AT
2157736 TAAAAATAAAATAT
1 TAAAAATAAAATAT
2157750 ATGATATTAA
Statistics
Matches: 212, Mismatches: 36, Indels: 63
0.68 0.12 0.20
Matches are distributed among these distances:
11 21 0.10
12 34 0.16
13 23 0.11
14 48 0.23
15 45 0.21
16 9 0.04
17 15 0.07
18 14 0.07
19 3 0.01
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.33
Consensus pattern (14 bp):
TAAAAATAAAATAT
Found at i:2157997 original size:15 final size:15
Alignment explanation
Indices: 2157969--2158022 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
2157959 TTTTTCCTGT
*
2157969 AATCACATTGCTTGC
1 AATCACATTACTTGC
*
2157984 AATCATATTACTTGC
1 AATCACATTACTTGC
* * *
2157999 AATCACGTTACCTGT
1 AATCACATTACTTGC
2158014 AATCACATT
1 AATCACATT
2158023 GCATTGTAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.35
Consensus pattern (15 bp):
AATCACATTACTTGC
Found at i:2167429 original size:67 final size:67
Alignment explanation
Indices: 2167321--2167455 Score: 155
Period size: 67 Copynumber: 2.0 Consensus size: 67
2167311 TGTTTGTATG
* * * * *
2167321 AAATATGAAAAATATTACATGATAATATTATTATACCATATAAACATA-TTAGATAATCATCTAT
1 AAATATAAAAAATATCACATAATAATACTATCATACCATATAAACA-AGTTAGATAATCATCTAT
2167385 TAT
65 TAT
* * * * * *
2167388 AAATATAAAAAATATCACATAATAGTACTATCATGCTATATAAATAAGTTAGATCATCATTTATT
1 AAATATAAAAAATATCACATAATAATACTATCATACCATATAAACAAGTTAGATAATCATCTATT
2167453 AT
66 AT
2167455 A
1 A
2167456 GTATATTGAT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
66 1 0.02
67 55 0.98
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (67 bp):
AAATATAAAAAATATCACATAATAATACTATCATACCATATAAACAAGTTAGATAATCATCTATT
AT
Found at i:2171881 original size:134 final size:130
Alignment explanation
Indices: 2171657--2171903 Score: 352
Period size: 134 Copynumber: 1.9 Consensus size: 130
2171647 ATGATTTACA
* * *
2171657 ATGCATAATATGAAAATTTAATGTTAATTTTTTTTACTTTATATTTATTTATTTAGTGAATCTAA
1 ATGCATAATATGAAAATCTAATGTTAATTTTTTTTACTTTATATCTATTTATTTAGTAAATCTAA
* * *
2171722 AAACTTATATAATTTTAAATTGTTAATGAAATTTTTTGTTATAATTTAGTCAAACACAATTTATG
66 AAACTTATATAAATTTAAATTGTTAATAAAATTTTATGTTATAATTTAGTCAAACACAATTTATG
* * * *
2171787 ATGCTTAATGTGAAAATCTAATGTTAATTTTTCTTTCTGCTTTATGTCTATTTATATTAGTAAAT
1 ATGCATAATATGAAAATCTAATGTTAA-TTTT-TTT-TACTTTATATCTATTTAT-TTAGTAAAT
2171852 CTGAAAAA-TTATATAAATTTAAATTGTTAATAAAATTTTATGTTATAATTTA
62 CT-AAAAACTTATATAAATTTAAATTGTTAATAAAATTTTATGTTATAATTTA
2171904 ATTTTATATT
Statistics
Matches: 102, Mismatches: 10, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
130 24 0.24
131 4 0.04
132 3 0.03
133 15 0.15
134 51 0.50
135 5 0.05
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.49
Consensus pattern (130 bp):
ATGCATAATATGAAAATCTAATGTTAATTTTTTTTACTTTATATCTATTTATTTAGTAAATCTAA
AAACTTATATAAATTTAAATTGTTAATAAAATTTTATGTTATAATTTAGTCAAACACAATTTATG
Found at i:2177519 original size:29 final size:29
Alignment explanation
Indices: 2177485--2177550 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
2177475 AAATTTCTGA
2177485 ATTATTTTAAAAAATTTAAAT-AAATTTTT
1 ATTATTTTAAAAAATTT-AATCAAATTTTT
* ** *
2177514 ATTATTCTATTAAGTTTAATCAAATTTTT
1 ATTATTTTAAAAAATTTAATCAAATTTTT
2177543 A-TATTTTA
1 ATTATTTTA
2177551 TTGAACTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 9 0.29
29 22 0.71
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.55
Consensus pattern (29 bp):
ATTATTTTAAAAAATTTAATCAAATTTTT
Found at i:2179348 original size:12 final size:12
Alignment explanation
Indices: 2179330--2179385 Score: 60
Period size: 12 Copynumber: 4.8 Consensus size: 12
2179320 GAATACCTTG
*
2179330 ATAAATTAATTT
1 ATAAATTAATAT
*
2179342 TTAAATTAATAT
1 ATAAATTAATAT
2179354 ATAAATTAATAT
1 ATAAATTAATAT
* *
2179366 AT-TATTAATTT
1 ATAAATTAATAT
*
2179377 ATCAATTAA
1 ATAAATTAA
2179386 GTAATATTTC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
11 9 0.24
12 28 0.76
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (12 bp):
ATAAATTAATAT
Found at i:2184198 original size:14 final size:14
Alignment explanation
Indices: 2184179--2184209 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2184169 AGTATTTTTT
2184179 TAAAAAAAATTAAA
1 TAAAAAAAATTAAA
2184193 TAAAAAAAATTAAA
1 TAAAAAAAATTAAA
2184207 TAA
1 TAA
2184210 TTAATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAAAAAAATTAAA
Found at i:2187314 original size:36 final size:36
Alignment explanation
Indices: 2187267--2187341 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
2187257 AGATCAGCAG
*
2187267 CAAAAGGATTGATGAAATCACTATCATCAATGTCAA
1 CAAAAGGATTGATGAAATCACTATCACCAATGTCAA
*
2187303 CAAAAGGATTGATGAAATCACTATCACCACTGTCAA
1 CAAAAGGATTGATGAAATCACTATCACCAATGTCAA
2187339 CAA
1 CAA
2187342 GATTTTGTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.23
Consensus pattern (36 bp):
CAAAAGGATTGATGAAATCACTATCACCAATGTCAA
Found at i:2202384 original size:28 final size:28
Alignment explanation
Indices: 2202306--2202387 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
2202296 AACAATAATA
* * *
2202306 TTTTTTTTTCAA-CACGGCATATAATAAT
1 TTTTTTTTT-AACCATGGCATGTAATAAC
***
2202334 TTTTTTTTTAACCATGATGTGTAATAAC
1 TTTTTTTTTAACCATGGCATGTAATAAC
2202362 TTTTTTTTTAACCATGGCATGTAATA
1 TTTTTTTTTAACCATGGCATGTAATA
2202388 TGTTTTTATA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 2 0.05
28 42 0.95
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.49
Consensus pattern (28 bp):
TTTTTTTTTAACCATGGCATGTAATAAC
Found at i:2202393 original size:28 final size:27
Alignment explanation
Indices: 2202301--2202394 Score: 91
Period size: 28 Copynumber: 3.4 Consensus size: 27
2202291 TGTGTAACAA
* * *
2202301 TAATATTTTTTTTTCAA-CACGGCATA
1 TAATATTTTTTTTTTAACCATGGCATG
***
2202327 TAATAATTTTTTTTTTAACCATGATGTG
1 TAAT-ATTTTTTTTTTAACCATGGCATG
*
2202355 TAATAACTTTTTTTTTAACCATGGCATG
1 TAAT-ATTTTTTTTTTAACCATGGCATG
*
2202383 TAATATGTTTTT
1 TAATATTTTTTT
2202395 ATACACGATA
Statistics
Matches: 54, Mismatches: 12, Indels: 3
0.78 0.17 0.04
Matches are distributed among these distances:
26 4 0.07
27 18 0.33
28 32 0.59
ACGTcount: A:0.29, C:0.11, G:0.10, T:0.51
Consensus pattern (27 bp):
TAATATTTTTTTTTTAACCATGGCATG
Found at i:2220299 original size:2 final size:2
Alignment explanation
Indices: 2220292--2220319 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2220282 AATTTAATCT
2220292 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2220320 GGATCCTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2225840 original size:48 final size:48
Alignment explanation
Indices: 2225785--2225939 Score: 166
Period size: 48 Copynumber: 3.2 Consensus size: 48
2225775 TTACTATAAA
* * * * *
2225785 TCTCCTCCACCACCTTCCCCATCCCCTCCACCACCATACTATTACAAG
1 TCTCCACCACCACCATCACCATCACCTCCACCACCTTACTATTACAAG
* * * * * *
2225833 TCTCCTCCACCACCATCTCCTTCACCACCTCCACCTTACTATTATAAG
1 TCTCCACCACCACCATCACCATCACCTCCACCACCTTACTATTACAAG
* * * * *
2225881 TCTCCACCACCACCCTCACCATCTCCTCTACCTCCTTACTACTACAAG
1 TCTCCACCACCACCATCACCATCACCTCCACCACCTTACTATTACAAG
2225929 TCTCCACCACC
1 TCTCCACCACC
2225940 TCCTCCACAT
Statistics
Matches: 88, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 88 1.00
ACGTcount: A:0.23, C:0.50, G:0.02, T:0.25
Consensus pattern (48 bp):
TCTCCACCACCACCATCACCATCACCTCCACCACCTTACTATTACAAG
Found at i:2227408 original size:36 final size:35
Alignment explanation
Indices: 2227337--2227409 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 35
2227327 ACCCGCTTAT
*
2227337 ATCTACAAATCACCACCTCCTCCACCACCAACATAC
1 ATCTACAAATCACCACCACCTCCACCACC-ACATAC
*
2227373 ATCTACAAGTCACCACCACCTCCATCCCACC-CATAC
1 ATCTACAAATCACCACCACCTCCA--CCACCACATAC
2227409 A
1 A
2227410 AGCCACCAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 28 0.85
38 5 0.15
ACGTcount: A:0.34, C:0.48, G:0.01, T:0.16
Consensus pattern (35 bp):
ATCTACAAATCACCACCACCTCCACCACCACATAC
Found at i:2227444 original size:72 final size:72
Alignment explanation
Indices: 2227360--2227605 Score: 211
Period size: 72 Copynumber: 3.4 Consensus size: 72
2227350 CACCTCCTCC
* *
2227360 ACCACCAACATACATCTACAAGTCACCACCACCTCCATCCCACCCATACAAGCCACCAACTGAGC
1 ACCACCACCATACATCTACAAATCACCACCACCTCCATCCCACCCATACAAGCCACCAACTGAGC
2227425 CACACAA
66 CACACAA
* * * * *
2227432 ACCACCACCATACTAT-TACAAATCTCCACCTCCACCATCACCCACCTACATTTATAAGTCACC-
1 ACCACCACCATAC-ATCTACAAATCACCACCACCTCCAT--CCCACC--CA--TACAAGCCACCA
* *
2227495 AC----CCCCACCA
59 ACTGAGCCACACAA
* * * * *
2227505 ACCCCCA-CTTACGTTTACAAATCACCACCACCTCCATCTCACCCATACAAGCCACCAACTGAGC
1 ACCACCACCATACATCTACAAATCACCACCACCTCCATCCCACCCATACAAGCCACCAACTGAGC
*
2227569 CATACAA
66 CACACAA
* *
2227576 ACCACCACCATAC-TACTACAAGTCCCCACC
1 ACCACCACCATACAT-CTACAAATCACCACC
2227606 TCNNNNNNNN
Statistics
Matches: 133, Mismatches: 26, Indels: 30
0.70 0.14 0.16
Matches are distributed among these distances:
66 9 0.07
67 2 0.02
68 2 0.02
70 5 0.04
71 13 0.10
72 69 0.52
73 14 0.11
74 6 0.05
76 2 0.02
77 2 0.02
78 9 0.07
ACGTcount: A:0.35, C:0.46, G:0.04, T:0.15
Consensus pattern (72 bp):
ACCACCACCATACATCTACAAATCACCACCACCTCCATCCCACCCATACAAGCCACCAACTGAGC
CACACAA
Found at i:2227497 original size:36 final size:36
Alignment explanation
Indices: 2227447--2227542 Score: 102
Period size: 36 Copynumber: 2.7 Consensus size: 36
2227437 CACCATACTA
* *
2227447 TTACAAATCTCCACCTCCACCATCACCCACCTACAT
1 TTACAAATCACCACCACCACCATCACCCACCTACAT
* * * * * * *
2227483 TTATAAGTCACCACCCCCACCAACCCCCACTTACGT
1 TTACAAATCACCACCACCACCATCACCCACCTACAT
*
2227519 TTACAAATCACCACCACCTCCATC
1 TTACAAATCACCACCACCACCATC
2227543 TCACCCATAC
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.30, C:0.47, G:0.02, T:0.21
Consensus pattern (36 bp):
TTACAAATCACCACCACCACCATCACCCACCTACAT
Found at i:2228397 original size:17 final size:17
Alignment explanation
Indices: 2228371--2228404 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2228361 CAGAATCGTC
*
2228371 TTTTTCTTTTCTCTTTT
1 TTTTTCTTTTCACTTTT
*
2228388 TTTTTTTTTTCACTTTT
1 TTTTTCTTTTCACTTTT
2228405 CTCTCTCCCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTCTTTTCACTTTT
Found at i:2235710 original size:21 final size:22
Alignment explanation
Indices: 2235669--2235718 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 22
2235659 TATAAAAATT
2235669 ATTTTTTATTATATTAAATTAA
1 ATTTTTTATTATATTAAATTAA
2235691 ATTTTTATATTTTTATATTAAATTAA
1 ATTTTT-TA---TTATATTAAATTAA
2235717 AT
1 AT
2235719 AAAATATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.25
23 2 0.08
26 16 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTTTTATTATATTAAATTAA
Found at i:2244780 original size:33 final size:33
Alignment explanation
Indices: 2244741--2244978 Score: 264
Period size: 33 Copynumber: 7.2 Consensus size: 33
2244731 AATATCTACA
*
2244741 GCCAACCTGGACAGCCAAGTGCTAATCCTTATG
1 GCCAACCTGCACAGCCAAGTGCTAATCCTTATG
* * *
2244774 GTCAACCTGGACAGCCAAGTGCTAATCCCTATG
1 GCCAACCTGCACAGCCAAGTGCTAATCCTTATG
* ** * * *
2244807 GCCAATCTGTGCAGCCAAGCGCCAATCCATATG
1 GCCAACCTGCACAGCCAAGTGCTAATCCTTATG
* * *
2244840 GCCAATCTGCACAGCCAAATGCTAGT-CTGTATG
1 GCCAACCTGCACAGCCAAGTGCTAATCCT-TATG
* * *
2244873 GCCAATCTGCACAGCCAAATGCTAATCCATATG
1 GCCAACCTGCACAGCCAAGTGCTAATCCTTATG
*
2244906 GCCAACCTGCACAACCAAGTGCTAATACC-TATG
1 GCCAACCTGCACAGCCAAGTGCTAAT-CCTTATG
* * *
2244939 GCCAACCTGTACAACCCAGTGCTAATCCTTATG
1 GCCAACCTGCACAGCCAAGTGCTAATCCTTATG
2244972 GCCAACC
1 GCCAACC
2244979 CACACAACCA
Statistics
Matches: 178, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
32 3 0.02
33 172 0.97
34 3 0.02
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (33 bp):
GCCAACCTGCACAGCCAAGTGCTAATCCTTATG
Found at i:2245761 original size:18 final size:18
Alignment explanation
Indices: 2245740--2245808 Score: 70
Period size: 17 Copynumber: 3.9 Consensus size: 18
2245730 GGGTTCTGGC
*
2245740 ATGGGTATGGGTATGGGT
1 ATGGGTATGGGGATGGGT
2245758 ATGGGTATGGGGATGGG-
1 ATGGGTATGGGGATGGGT
* ** *
2245775 GTGGGGGTGGGGATGGGG
1 ATGGGTATGGGGATGGGT
*
2245793 ATGGG-ATGGGAATGGG
1 ATGGGTATGGGGATGGG
2245809 AATGAGCGGT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
17 23 0.53
18 20 0.47
ACGTcount: A:0.16, C:0.00, G:0.61, T:0.23
Consensus pattern (18 bp):
ATGGGTATGGGGATGGGT
Found at i:2245785 original size:11 final size:11
Alignment explanation
Indices: 2245765--2245808 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
2245755 GGTATGGGTA
2245765 TGGGGATGGGG
1 TGGGGATGGGG
*
2245776 TGGGGGTGGGG
1 TGGGGATGGGG
*
2245787 ATGGGGATGGGA
1 -TGGGGATGGGG
*
2245799 TGGGAATGGG
1 TGGGGATGGG
2245809 AATGAGCGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.14, C:0.00, G:0.68, T:0.18
Consensus pattern (11 bp):
TGGGGATGGGG
Found at i:2245808 original size:23 final size:23
Alignment explanation
Indices: 2245740--2245808 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
2245730 GGGTTCTGGC
* * *
2245740 ATGGGTATGGGTATGGGTATGGGT
1 ATGGGGATGGG-ATGGGAATGGGG
* **
2245764 ATGGGGATGGGGTGGGGGTGGGG
1 ATGGGGATGGGATGGGAATGGGG
2245787 ATGGGGATGGGATGGGAATGGG
1 ATGGGGATGGGATGGGAATGGG
2245809 AATGAGCGGT
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
23 27 0.73
24 10 0.27
ACGTcount: A:0.16, C:0.00, G:0.61, T:0.23
Consensus pattern (23 bp):
ATGGGGATGGGATGGGAATGGGG
Found at i:2245812 original size:6 final size:6
Alignment explanation
Indices: 2245740--2245808 Score: 70
Period size: 6 Copynumber: 11.8 Consensus size: 6
2245730 GGGTTCTGGC
* * * * *
2245740 ATGGGT ATGGGT ATGGGT ATGGGT ATGGGG ATGGGG -TGGGG GTGGGG
1 ATGGGG ATGGGG ATGGGG ATGGGG ATGGGG ATGGGG ATGGGG ATGGGG
*
2245787 ATGGGG AT-GGG ATGGGA ATGGG
1 ATGGGG ATGGGG ATGGGG ATGGG
2245809 AATGAGCGGT
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
5 10 0.17
6 48 0.83
ACGTcount: A:0.16, C:0.00, G:0.61, T:0.23
Consensus pattern (6 bp):
ATGGGG
Found at i:2254153 original size:21 final size:21
Alignment explanation
Indices: 2254127--2254169 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2254117 TATTACACGT
*
2254127 CATGTACAAAAACATGTTACA
1 CATGTACAAAAACATGTGACA
*
2254148 CATGTACAAAAATATGTGACA
1 CATGTACAAAAACATGTGACA
2254169 C
1 C
2254170 GTCATGATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.23
Consensus pattern (21 bp):
CATGTACAAAAACATGTGACA
Found at i:2254398 original size:29 final size:30
Alignment explanation
Indices: 2254366--2254431 Score: 100
Period size: 29 Copynumber: 2.2 Consensus size: 30
2254356 ACACGTTATA
2254366 TTAAAAAAATATTATTATTACATA-C-TAT
1 TTAAAAAAATATTATTATTACATATCATAT
*
2254394 GTTAAAAAAATATTATTATTATATATCATAT
1 -TTAAAAAAATATTATTATTACATATCATAT
2254425 TTAAAAA
1 TTAAAAA
2254432 TATTTTTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 23 0.68
30 8 0.24
31 3 0.09
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (30 bp):
TTAAAAAAATATTATTATTACATATCATAT
Found at i:2259400 original size:4 final size:4
Alignment explanation
Indices: 2259391--2259425 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
2259381 AGCTATGGTT
2259391 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
2259426 AGGATCAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:2266013 original size:24 final size:25
Alignment explanation
Indices: 2265986--2266043 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
2265976 AAATGAAAAT
2265986 ATAAAAAATTATATTAATA-AA-TTA
1 ATAAAAAATT-TATTAATATAATTTA
*
2266010 ATAATAAA-TTATTAATATAATTTTA
1 ATAAAAAATTTATTAATATAA-TTTA
2266035 ATAAAAAAT
1 ATAAAAAAT
2266044 AAATTAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 8 0.29
23 3 0.11
24 7 0.25
25 10 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
ATAAAAAATTTATTAATATAATTTA
Found at i:2266035 original size:11 final size:11
Alignment explanation
Indices: 2265997--2266039 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
2265987 TAAAAAATTA
2265997 TATTAATAAAT
1 TATTAATAAAT
*
2266008 TAATAATAAAT
1 TATTAATAAAT
2266019 TATTAATATAAT
1 TATTAATA-AAT
2266031 T-TTAATAAA
1 TATTAATAAA
2266040 AAATAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 2 0.07
11 23 0.79
12 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TATTAATAAAT
Found at i:2266149 original size:21 final size:22
Alignment explanation
Indices: 2266109--2266149 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2266099 AAATATCATA
* *
2266109 TTAATATAATTAATATTAAACC
1 TTAATATAATTAACAATAAACC
2266131 TTAATAT-ATTAACAATAAA
1 TTAATATAATTAACAATAAA
2266150 TTATTAGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (22 bp):
TTAATATAATTAACAATAAACC
Found at i:2295782 original size:15 final size:16
Alignment explanation
Indices: 2295756--2295786 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2295746 GAGATGAATT
2295756 TTATGATATATATTTA
1 TTATGATATATATTTA
2295772 TTATG-TATATATTTA
1 TTATGATATATATTTA
2295787 AATATTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (16 bp):
TTATGATATATATTTA
Found at i:2301675 original size:22 final size:22
Alignment explanation
Indices: 2301628--2301678 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
2301618 ATAGACTTTA
2301628 TTTATATAATTATACTTAATAAT
1 TTTATATAATTATACTTAAT-AT
2301651 TTTAT-TAATTATCACCTTAAT-T
1 TTTATATAATTAT-A-CTTAATAT
2301673 TTTATA
1 TTTATA
2301679 ACATATTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
22 13 0.52
23 6 0.24
24 6 0.24
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTATATAATTATACTTAATAT
Found at i:2301725 original size:214 final size:214
Alignment explanation
Indices: 2301359--2301814 Score: 552
Period size: 214 Copynumber: 2.1 Consensus size: 214
2301349 GCATAAACAT
* * * * *
2301359 TATATATATATATATTTAATTTATCCTTAAGCATTACTATAACTTATAATATTTATTTATATGAT
1 TATATATACATATATTTAATTTATCATTAAGCAATACTACAACTTATAATATTTATTTATATAAT
***
2301424 TACACTAAATAACTTCATTAATTATTGTCTAAGTTTTTATAACATATTGTTTATAATTAATTATT
66 TACACTAAATAACTTCATTAATTATCACCTAAGTTTTTATAACATATTGTTTATAATTAATTATT
2301489 ATTTATATAAATTTGAATAT-A-AAA-TATTATAACATATGAA-TT-ATGTCATTAATTTCATAT
131 ATTTATATAAATTTGAATATAATAAACTATTATAACATAT-AAGTTGAT-TCATTAATTTC--AT
2301549 ATATATAATAAAG-TA-ATATTA
192 ATATATAATAAAGTTATATATTA
* * *
2301570 TATATATACATATATTTAAATTAT-ATATAAGCAATATTGCAACTTATAATAGACTTTATTTATA
1 TATATATACATATATTTAATTTATCAT-TAAGCAATACTACAACTTATAAT--A-TTTATTTATA
* * * * *
2301634 TAATTATACTTAATAATTTTATTAATTATCACCTTAA-TTTTTATAACATATTGTTTATAATTAG
62 TAATTACACTAAATAACTTCATTAATTATCACC-TAAGTTTTTATAACATATTGTTTATAATTAA
*
2301698 TTATTATTTATATAAATTTTGATATAAAAATTAAACTATTATAACATATAAGTTGATTCATTAAT
126 TTATTATTTATATAAA-TTTGA-AT-ATAA-TAAACTATTATAACATATAAGTTGATTCATTAAT
*
2301763 TTCATATATATAATAAAGTTATATTTTA
187 TTCATATATATAATAAAGTTATATATTA
* *
2301791 TATATATACGTTTATTTAATTTAT
1 TATATATACATATATTTAATTTAT
2301815 TCATAATTTG
Statistics
Matches: 208, Mismatches: 21, Indels: 22
0.83 0.08 0.09
Matches are distributed among these distances:
210 1 0.00
211 41 0.20
213 1 0.00
214 77 0.37
215 8 0.04
216 2 0.01
217 1 0.00
218 1 0.00
219 15 0.07
220 7 0.03
221 52 0.25
222 2 0.01
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.48
Consensus pattern (214 bp):
TATATATACATATATTTAATTTATCATTAAGCAATACTACAACTTATAATATTTATTTATATAAT
TACACTAAATAACTTCATTAATTATCACCTAAGTTTTTATAACATATTGTTTATAATTAATTATT
ATTTATATAAATTTGAATATAATAAACTATTATAACATATAAGTTGATTCATTAATTTCATATAT
ATAATAAAGTTATATATTA
Found at i:2302702 original size:141 final size:141
Alignment explanation
Indices: 2302507--2302773 Score: 498
Period size: 141 Copynumber: 1.9 Consensus size: 141
2302497 ATACTAAGAC
*
2302507 CTTGGCTTAACACAAGGAATCTTCGCAATAAAAGCGGGCAAACATTGAAGTGGTTTGGTTGGGTT
1 CTTGGCTTAACACAAGGAATCTTCGCAATAAAACCGGGCAAACATTGAAGTGGTTTGGTTGGGTT
2302572 TGGCTTCTGCACGTTGGGTTGTGGGTCCCAGCTTTAAAATTTTGAACCATTTTAAGAGCTTCCGT
66 TGGCTTCTGCACGTTGGGTTGTGGGTCCCAGCTTTAAAATTTTGAACCATTTTAAGAGCTTCCGT
2302637 GATAATAAGGA
131 GATAATAAGGA
*
2302648 CTTGGCTTAACACAAGGAATCTTCGTAATAAAACCGGGCAAACATTGAAGTGGTTTGGTTGGGTT
1 CTTGGCTTAACACAAGGAATCTTCGCAATAAAACCGGGCAAACATTGAAGTGGTTTGGTTGGGTT
* *
2302713 TGGCTTCTGGATGTTGGGTTGTGGGTCCCAGCTTTAAAATTTTGAACCATTTTAAGAGCTT
66 TGGCTTCTGCACGTTGGGTTGTGGGTCCCAGCTTTAAAATTTTGAACCATTTTAAGAGCTT
2302774 GTTAGGACAC
Statistics
Matches: 122, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
141 122 1.00
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (141 bp):
CTTGGCTTAACACAAGGAATCTTCGCAATAAAACCGGGCAAACATTGAAGTGGTTTGGTTGGGTT
TGGCTTCTGCACGTTGGGTTGTGGGTCCCAGCTTTAAAATTTTGAACCATTTTAAGAGCTTCCGT
GATAATAAGGA
Found at i:2305885 original size:2 final size:2
Alignment explanation
Indices: 2305878--2305909 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2305868 GGTTTGGTTA
2305878 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2305910 CTGTACTTAA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2313947 original size:2 final size:2
Alignment explanation
Indices: 2313940--2313965 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2313930 GCTAAATTAA
2313940 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
2313966 TTTCTATTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2316753 original size:36 final size:37
Alignment explanation
Indices: 2316681--2316754 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 37
2316671 CACTGTACGA
*
2316681 ATTTTCTTTGTTTAGGTTGAAGATGGTTTCATGATTG
1 ATTTTCTTTGTTTAGGTTGAAGATGGTTTCAAGATTG
*
2316718 ATTTTCTTTGTTTAGGTCT-CA-ATGGTTTCAAGATTG
1 ATTTTCTTTGTTTAGGT-TGAAGATGGTTTCAAGATTG
2316754 A
1 A
2316755 AGCATGACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 15 0.44
37 18 0.53
38 1 0.03
ACGTcount: A:0.20, C:0.08, G:0.22, T:0.50
Consensus pattern (37 bp):
ATTTTCTTTGTTTAGGTTGAAGATGGTTTCAAGATTG
Found at i:2318300 original size:6 final size:6
Alignment explanation
Indices: 2318289--2318319 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
2318279 ATTGTTGAAG
*
2318289 GCTCCA GCTCCA GCTCCA GCTCCA GCACCA G
1 GCTCCA GCTCCA GCTCCA GCTCCA GCTCCA G
2318320 AGACTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.48, G:0.19, T:0.13
Consensus pattern (6 bp):
GCTCCA
Found at i:2332475 original size:5 final size:6
Alignment explanation
Indices: 2332460--2332498 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
2332450 TCAAAGCCCC
2332460 AAAAAT AAAAAT AAAAAT AAAAAT -AAAAT -AAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
2332499 ACTAATAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 10 0.31
6 22 0.69
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:2332505 original size:16 final size:16
Alignment explanation
Indices: 2332460--2332498 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 16
2332450 TCAAAGCCCC
2332460 AAAAATAAAAATAAAAAT
1 AAAAAT-AAAAT-AAAAT
2332478 AAAAATAAAATAAAAT
1 AAAAATAAAATAAAAT
2332494 AAAAA
1 AAAAA
2332499 ACTAATAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 10 0.48
17 5 0.24
18 6 0.29
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (16 bp):
AAAAATAAAATAAAAT
Found at i:2334305 original size:38 final size:41
Alignment explanation
Indices: 2334263--2334344 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 41
2334253 TTTAGTAATA
*
2334263 ATTTATTTAGTTAATATATTTA-AAATTTT-TTAAA-TATT
1 ATTTATTTAATTAATATATTTATAAATTTTATTAAATTATT
* *
2334301 ATTTATTTAATTATTATTTTTATTAAATTTTATTAAATTATT
1 ATTTATTTAATTAATATATTTA-TAAATTTTATTAAATTATT
2334343 AT
1 AT
2334345 ATTTTTATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 19 0.51
40 7 0.19
41 5 0.14
42 6 0.16
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (41 bp):
ATTTATTTAATTAATATATTTATAAATTTTATTAAATTATT
Found at i:2334315 original size:15 final size:14
Alignment explanation
Indices: 2334287--2334321 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
2334277 TATATTTAAA
2334287 ATTTTTTAAATATT
1 ATTTTTTAAATATT
*
2334301 ATTTATTTAATTATT
1 ATTT-TTTAAATATT
2334316 ATTTTT
1 ATTTTT
2334322 ATTAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
ATTTTTTAAATATT
Found at i:2334333 original size:16 final size:18
Alignment explanation
Indices: 2334297--2334335 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
2334287 ATTTTTTAAA
*
2334297 TATTATTTATTTAATTAT
1 TATTATTTATTAAATTAT
2334315 TATT-TTTATTAAATT-T
1 TATTATTTATTAAATTAT
2334331 TATTA
1 TATTA
2334336 AATTATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 5 0.26
17 10 0.53
18 4 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTATTTATTAAATTAT
Found at i:2334358 original size:31 final size:33
Alignment explanation
Indices: 2334290--2334359 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 33
2334280 ATTTAAAATT
* *
2334290 TTTTAAATATTATTTATTTAATTATTATTTTTA
1 TTTTAAATATTATTAAATTAATTATTATTTTTA
*
2334323 --TTAAATTTTATTAAATT-ATTA-TATTTTTA
1 TTTTAAATATTATTAAATTAATTATTATTTTTA
2334352 TTTTAAAT
1 TTTTAAAT
2334360 CAAATAAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
29 8 0.25
30 4 0.12
31 20 0.62
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (33 bp):
TTTTAAATATTATTAAATTAATTATTATTTTTA
Found at i:2337713 original size:5 final size:5
Alignment explanation
Indices: 2337703--2337730 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2337693 AGAATCAAAG
2337703 TATTT TATTT TATTT TATTT TATTT TAT
1 TATTT TATTT TATTT TATTT TATTT TAT
2337731 ATTGTAGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:2337894 original size:25 final size:25
Alignment explanation
Indices: 2337866--2337922 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
2337856 AAAGGGGACT
2337866 TTTGGTTTGAACAAAACCCAAGTCA
1 TTTGGTTTGAACAAAACCCAAGTCA
2337891 TTTGGTTTGAACAAAACCCAAGTCA
1 TTTGGTTTGAACAAAACCCAAGTCA
2337916 TTTGGTT
1 TTTGGTT
2337923 CACTATTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (25 bp):
TTTGGTTTGAACAAAACCCAAGTCA
Found at i:2338055 original size:15 final size:15
Alignment explanation
Indices: 2338035--2338064 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2338025 CAACTTAGTC
*
2338035 GATGATTTTAACAGT
1 GATGATTTCAACAGT
2338050 GATGATTTCAACAGT
1 GATGATTTCAACAGT
2338065 TATTATGATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (15 bp):
GATGATTTCAACAGT
Found at i:2349499 original size:2 final size:2
Alignment explanation
Indices: 2349492--2349521 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2349482 TCCCATTGCA
2349492 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2349522 CATCTTTCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2354286 original size:25 final size:24
Alignment explanation
Indices: 2354225--2354287 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
2354215 ACTAAATTGA
2354225 ATAAA-ATTAAAATATTAAAAAAT
1 ATAAATATTAAAATATTAAAAAAT
**
2354248 -TAAATTAAAAAAATATTTAAAAAAT
1 ATAAA-TATTAAAATA-TTAAAAAAT
*
2354273 ATAAATATTTAAATA
1 ATAAATATTAAAATA
2354288 GATGATAGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
22 4 0.13
24 7 0.23
25 16 0.52
26 4 0.13
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
ATAAATATTAAAATATTAAAAAAT
Found at i:2355256 original size:15 final size:14
Alignment explanation
Indices: 2355220--2355256 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2355210 TTGATTTTAG
2355220 TTATGAAATTTTTT
1 TTATGAAATTTTTT
*
2355234 TTTTGAAATTTTTT
1 TTATGAAATTTTTT
2355248 TTATAGAAA
1 TTAT-GAAA
2355257 GAGAATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.59
Consensus pattern (14 bp):
TTATGAAATTTTTT
Found at i:2355451 original size:31 final size:32
Alignment explanation
Indices: 2355416--2355488 Score: 91
Period size: 30 Copynumber: 2.4 Consensus size: 32
2355406 TTTAAATATT
2355416 TTTAATTTAATCTCTGAATAATT-TA-ATTTTG
1 TTTAATTTAATCTCTGAAT-ATTATATATTTTG
*
2355447 TTTAATTTAA--TCTGTATATTATATATTTTG
1 TTTAATTTAATCTCTGAATATTATATATTTTG
*
2355477 TTCAATTTAATC
1 TTTAATTTAATC
2355489 ACTATGACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
28 3 0.08
29 8 0.22
30 15 0.42
31 10 0.28
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (32 bp):
TTTAATTTAATCTCTGAATATTATATATTTTG
Found at i:2368472 original size:15 final size:16
Alignment explanation
Indices: 2368444--2368488 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2368434 AATTTTTTAT
2368444 TATATTTAATTAAATA
1 TATATTTAATTAAATA
2368460 TATATTT-ATTAAATA
1 TATATTTAATTAAATA
*
2368475 AATTATTATAATTA
1 TA-TATT-TAATTA
2368489 TCAATTGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 9 0.36
16 11 0.44
17 1 0.04
18 4 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TATATTTAATTAAATA
Found at i:2388179 original size:21 final size:21
Alignment explanation
Indices: 2388149--2388196 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
2388139 GATACTCATT
*
2388149 GATTTTTCAGAATCTGCTTCA
1 GATTTATCAGAATCTGCTTCA
2388170 GATTTATCAGAATCTGCTTCA
1 GATTTATCAGAATCTGCTTCA
2388191 GATTTA
1 GATTTA
2388197 GTAATGTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.42
Consensus pattern (21 bp):
GATTTATCAGAATCTGCTTCA
Found at i:2389995 original size:27 final size:29
Alignment explanation
Indices: 2389965--2390043 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 29
2389955 AAACATTAAA
*
2389965 GTGTAATAA-AATA-TTTTTGAATATGAC
1 GTGTAATAATAATATTTTTTCAATATGAC
*
2389992 GTGTAACAATAATATTTTTTCAATATGAC
1 GTGTAATAATAATATTTTTTCAATATGAC
* * * *
2390021 GTATAATAACAACATATTTTCAA
1 GTGTAATAATAATATTTTTTCAA
2390044 CATGGTACGT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 8 0.19
28 4 0.09
29 31 0.72
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (29 bp):
GTGTAATAATAATATTTTTTCAATATGAC
Found at i:2390132 original size:26 final size:23
Alignment explanation
Indices: 2390089--2390160 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 23
2390079 ACAATAATTT
*
2390089 TTTTTTTCAACATGACGTGTAATAA
1 TTTTTTT-AACATAACGTGTAA-AA
*
2390114 CTTTTTTTAACCATAACGTGTAACA
1 -TTTTTTTAA-CATAACGTGTAAAA
*
2390139 TGTTTTTATACATAACGTGTAA
1 TTTTTTTA-ACATAACGTGTAA
2390161 CAACAATATT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
24 19 0.46
25 4 0.10
26 18 0.44
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (23 bp):
TTTTTTTAACATAACGTGTAAAA
Found at i:2390152 original size:24 final size:24
Alignment explanation
Indices: 2390117--2390162 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
2390107 GTAATAACTT
2390117 TTTTTAACCATAACGTGTAACATG
1 TTTTTAACCATAACGTGTAACATG
2390141 TTTTTATA-CATAACGTGTAACA
1 TTTTTA-ACCATAACGTGTAACA
2390163 ACAATATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (24 bp):
TTTTTAACCATAACGTGTAACATG
Found at i:2390197 original size:56 final size:56
Alignment explanation
Indices: 2390132--2390239 Score: 155
Period size: 56 Copynumber: 1.9 Consensus size: 56
2390122 AACCATAACG
*
2390132 TGTAACATGTTTTTATACATAACGTGTAACAACAATATTTGTTT-TTCAACATAGTA
1 TGTAACATGTTTTTATACATAACATGTAACAACAATATTT-TTTCTTCAACATAGTA
* * * *
2390188 TGTAGCATGTTTTTATATATAACATGTAACAATAGTATTTTTTCTTCAACAT
1 TGTAACATGTTTTTATACATAACATGTAACAACAATATTTTTTCTTCAACAT
2390240 GACACATAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
55 3 0.07
56 43 0.93
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (56 bp):
TGTAACATGTTTTTATACATAACATGTAACAACAATATTTTTTCTTCAACATAGTA
Found at i:2390385 original size:2 final size:2
Alignment explanation
Indices: 2390378--2390403 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2390368 AATATTCCAT
2390378 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2390404 GACATGGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2391495 original size:72 final size:73
Alignment explanation
Indices: 2391329--2391518 Score: 346
Period size: 72 Copynumber: 2.6 Consensus size: 73
2391319 TCTTCGCAAT
2391329 TTCTTCTCTACTTCCTTCTCTCTTTATAAAGACCCATCTTTACTCTCTCTACACCATTTCATAGA
1 TTCTTCTCTACTTCCTTCTCTCTTTATAAAGACCCATCTTTACTCTCTCTACACCATTTCATAGA
*
2391394 TTTACATT
66 TTTACATG
2391402 TTCTTCTCTACTTCCTTCTCTCTTTATAAAGACCCATCTTTACTCTCT-TACACCATTTCATAGA
1 TTCTTCTCTACTTCCTTCTCTCTTTATAAAGACCCATCTTTACTCTCTCTACACCATTTCATAGA
*
2391466 TTTGCATG
66 TTTACATG
*
2391474 TTCTTCTCTACTTCCTTCTCTCTTTATAAAGAGCCATCTTTACTC
1 TTCTTCTCTACTTCCTTCTCTCTTTATAAAGACCCATCTTTACTC
2391519 CATTTCAGAG
Statistics
Matches: 114, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
72 66 0.58
73 48 0.42
ACGTcount: A:0.21, C:0.30, G:0.04, T:0.45
Consensus pattern (73 bp):
TTCTTCTCTACTTCCTTCTCTCTTTATAAAGACCCATCTTTACTCTCTCTACACCATTTCATAGA
TTTACATG
Found at i:2400996 original size:3 final size:3
Alignment explanation
Indices: 2400982--2401059 Score: 93
Period size: 3 Copynumber: 26.0 Consensus size: 3
2400972 ATGTAGCAAG
* * * * * * *
2400982 TAT TAT TGT TAT TAT TAT TAT TAT TGT TGT TGT TGT TGT TAT TGT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2401030 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2401060 GTATAAAGGA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2405092 original size:2 final size:2
Alignment explanation
Indices: 2405085--2405119 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2405075 TTGAATCAGG
2405085 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2405120 NNNNNNNNNN
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2415040 original size:63 final size:63
Alignment explanation
Indices: 2414958--2415080 Score: 201
Period size: 63 Copynumber: 2.0 Consensus size: 63
2414948 AATCACCTTC
* *
2414958 AAATGTTCACTGAATATCCATGTCACATTCATGTTCAAAGAGCATAAAGAACATTTGTACTTA
1 AAATGTTCACTGAACATCCATGTCACATTCATGTTCAAAGACCATAAAGAACATTTGTACTTA
* * *
2415021 AAATGTTCATTGAACATCCATGTCATATTCATGTTCAGAGACCATAAAGAACATTTGTAC
1 AAATGTTCACTGAACATCCATGTCACATTCATGTTCAAAGACCATAAAGAACATTTGTAC
2415081 AAGGAAATAT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (63 bp):
AAATGTTCACTGAACATCCATGTCACATTCATGTTCAAAGACCATAAAGAACATTTGTACTTA
Found at i:2421769 original size:4 final size:4
Alignment explanation
Indices: 2421762--2421788 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2421752 ATATATATTA
2421762 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
2421789 ATGCTAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:2433647 original size:46 final size:48
Alignment explanation
Indices: 2433594--2433692 Score: 157
Period size: 46 Copynumber: 2.1 Consensus size: 48
2433584 AATAAAACCA
2433594 AACTTCCAAGTGATCCTTTAACTAACATAAAAAAT-A-ATCTGCATTT
1 AACTTCCAAGTGATCCTTTAACTAACATAAAAAATAATATCTGCATTT
* * *
2433640 AACTTCCAAGTGATCCTTTACCTGACATAAGAAATAATATCTGCATTT
1 AACTTCCAAGTGATCCTTTAACTAACATAAAAAATAATATCTGCATTT
2433688 AACTT
1 AACTT
2433693 AATGTCAAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
46 32 0.67
47 1 0.02
48 15 0.31
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.33
Consensus pattern (48 bp):
AACTTCCAAGTGATCCTTTAACTAACATAAAAAATAATATCTGCATTT
Found at i:2442402 original size:10 final size:10
Alignment explanation
Indices: 2442384--2442413 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
2442374 AAGAGAAAAC
2442384 GCGAGAAAGT
1 GCGAGAAAGT
2442394 GCGAGAAAGT
1 GCGAGAAAGT
2442404 GCGAGGAAAG
1 GCGA-GAAAG
2442414 AGAGGGGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.74
11 5 0.26
ACGTcount: A:0.40, C:0.10, G:0.43, T:0.07
Consensus pattern (10 bp):
GCGAGAAAGT
Found at i:2458931 original size:2 final size:2
Alignment explanation
Indices: 2458926--2458960 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2458916 CTCTCTCTCT
*
2458926 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AA AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2458961 AGCGCACATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.46, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2459762 original size:13 final size:13
Alignment explanation
Indices: 2459737--2459771 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
2459727 AATAGACTAA
*
2459737 AATT-ACTACAAT
1 AATTAACTATAAT
2459749 AATTAACTATAAT
1 AATTAACTATAAT
2459762 AATTAACTAT
1 AATTAACTAT
2459772 CTTCAAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.37
Consensus pattern (13 bp):
AATTAACTATAAT
Found at i:2461220 original size:2 final size:2
Alignment explanation
Indices: 2461213--2461247 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2461203 TTATAAACAG
*
2461213 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2461248 CCCAACTAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2463392 original size:14 final size:14
Alignment explanation
Indices: 2463370--2463403 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2463360 TAAATTATTT
2463370 GATAATTTTTAAAA
1 GATAATTTTTAAAA
*
2463384 GATATTTTTTAAAA
1 GATAATTTTTAAAA
*
2463398 AATAAT
1 GATAAT
2463404 ATTATAATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (14 bp):
GATAATTTTTAAAA
Found at i:2463473 original size:22 final size:23
Alignment explanation
Indices: 2463411--2463474 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 23
2463401 AATATTATAA
*
2463411 TTATATTTAATAGATGAAAATATTT
1 TTATATTTAA-AGA-AAAAATATTT
* * * *
2463436 TTAAAATAAAATAAAAAAT-TTT
1 TTATATTTAAAGAAAAAATATTT
2463458 TTATATTTAAAGAAAAA
1 TTATATTTAAAGAAAAA
2463475 CTCCTCATAA
Statistics
Matches: 30, Mismatches: 9, Indels: 3
0.71 0.21 0.07
Matches are distributed among these distances:
22 16 0.53
23 5 0.17
24 2 0.07
25 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (23 bp):
TTATATTTAAAGAAAAAATATTT
Found at i:2476619 original size:18 final size:18
Alignment explanation
Indices: 2476596--2476640 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
2476586 AAATGAAAGT
2476596 GCAAAGTAGATAAGCTAG
1 GCAAAGTAGATAAGCTAG
2476614 GCAAAGTAGATAAGCTAG
1 GCAAAGTAGATAAGCTAG
2476632 GCAAAGTAG
1 GCAAAGTAG
2476641 GAAGTAGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.44, C:0.11, G:0.29, T:0.16
Consensus pattern (18 bp):
GCAAAGTAGATAAGCTAG
Found at i:2481946 original size:2 final size:2
Alignment explanation
Indices: 2481941--2481978 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2481931 TGTGTGTGTG
*
2481941 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2481979 CACACTTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2490206 original size:174 final size:174
Alignment explanation
Indices: 2489878--2490226 Score: 441
Period size: 174 Copynumber: 2.0 Consensus size: 174
2489868 TACCATATTG
* *
2489878 ATACAATCTTCATGAGAGGTTACACCTTGTATTGTGTTTTAAAATCACAAGTCTCTCTACTTTGT
1 ATACAATCTTCATGAGAGGTAACACCTTGGATTGTGTTTTAAAATCACAAGTCTCTCTACTTTGT
* * * * ** *
2489943 ATTCTGAGAATCAGTGCTTTGTCAGAAGTACAACGGGTCTTGTGGTAATAGATTGTACCTATCGA
66 ATTCCGAGAATAAATGATTTGTCAGAACCACAACGGGTCTTGTGGTAATAGATTGTACCTATAGA
* * * *
2490008 AGTGTGTCGTGTTCAGATTGTCTGTTCCTAGGTAACTAAGCAAA
131 AGTGTCTCATGTTCAGACTGTCTGTTCCAAGGTAACTAAGCAAA
* * *
2490052 ATACAATTTTTATGATGAGGTAACACCTTGGATTGTGTTTTAAAATCACGAGTCTCTCTACTTTG
1 ATACAATCTTCATGA-GAGGTAACACCTTGGATTGTGTTTTAAAATCACAAGTCTCTCTACTTTG
** * * *
2490117 TATTCCGAGAATAAAT-ATTCTGTC-TTACCACAACGGGTCTTGTGGTGATAGATTGTAGCTGTA
65 TATTCCGAGAATAAATGATT-TGTCAGAACCACAACGGGTCTTGTGGTAATAGATTGTACCTATA
* * * *
2490180 TAAGTGTCTCATGTTCAGACTGTCTGTTTCAAGGTGATTAAGCAAA
129 GAAGTGTCTCATGTTCAGACTGTCTGTTCCAAGGTAACTAAGCAAA
2490226 A
1 A
2490227 GTTTGTCAGA
Statistics
Matches: 148, Mismatches: 25, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
174 85 0.57
175 63 0.43
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (174 bp):
ATACAATCTTCATGAGAGGTAACACCTTGGATTGTGTTTTAAAATCACAAGTCTCTCTACTTTGT
ATTCCGAGAATAAATGATTTGTCAGAACCACAACGGGTCTTGTGGTAATAGATTGTACCTATAGA
AGTGTCTCATGTTCAGACTGTCTGTTCCAAGGTAACTAAGCAAA
Found at i:2493765 original size:20 final size:21
Alignment explanation
Indices: 2493719--2493765 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
2493709 AATAATATGT
2493719 TATAAAAATTATAAAATAAAAG
1 TATAAAAATTATAAAAT-AAAG
*
2493741 -A-AAAAATTATAAAAT-TAG
1 TATAAAAATTATAAAATAAAG
2493759 TATAAAA
1 TATAAAA
2493766 CTAATGTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
18 2 0.09
19 1 0.05
20 18 0.82
21 1 0.05
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (21 bp):
TATAAAAATTATAAAATAAAG
Found at i:2495900 original size:23 final size:22
Alignment explanation
Indices: 2495874--2495916 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2495864 ATTATTTATT
*
2495874 CATTTTTAATTATTTTTTAAATA
1 CATTATTAATT-TTTTTTAAATA
*
2495897 CATTATTGATTTTTTTTAAA
1 CATTATTAATTTTTTTTAAA
2495917 ATGCAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (22 bp):
CATTATTAATTTTTTTTAAATA
Found at i:2501514 original size:20 final size:20
Alignment explanation
Indices: 2501448--2501594 Score: 101
Period size: 20 Copynumber: 7.3 Consensus size: 20
2501438 TATGACTATC
*
2501448 TATTTTATTTTTAAATATTAA
1 TATTTTA-TTTAAAATATTAA
* *
2501469 T-TATTTATTTTAAATAGTAA
1 TAT-TTTATTTAAAATATTAA
2501489 TA----ATTTAAAATATTAA
1 TATTTTATTTAAAATATTAA
* *
2501505 TATTTTATTTATAAT-TTAT
1 TATTTTATTTAAAATATTAA
**
2501524 TCATTAACATTTAAAATATTAA
1 T-ATT-TTATTTAAAATATTAA
*
2501546 TATTTTATTTATAAT-TTAAA
1 TATTTTATTTAAAATATT-AA
2501566 TATTATTATGATTAAAATATTAA
1 TATT-TTAT--TTAAAATATTAA
2501589 TATTTT
1 TATTTT
2501595 CAATTATTTT
Statistics
Matches: 99, Mismatches: 13, Indels: 27
0.71 0.09 0.19
Matches are distributed among these distances:
16 14 0.14
19 6 0.06
20 39 0.39
21 20 0.20
22 6 0.06
23 12 0.12
24 2 0.02
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (20 bp):
TATTTTATTTAAAATATTAA
Found at i:2501539 original size:41 final size:41
Alignment explanation
Indices: 2501469--2501594 Score: 150
Period size: 41 Copynumber: 3.0 Consensus size: 41
2501459 TAAATATTAA
* *
2501469 TTATTTAT--TTTAAATAGTAATAATTTAAAATATTAATATT
1 TTATTTATAATTTAAATATTAA-CATTTAAAATATTAATATT
*
2501509 TTATTTATAATTT-ATTCATTAACATTTAAAATATTAATATT
1 TTATTTATAATTTAAAT-ATTAACATTTAAAATATTAATATT
**
2501550 TTATTTATAATTTAAATATTATTATGATTAAAATATTAATATT
1 TTATTTATAATTTAAATATTAACAT--TTAAAATATTAATATT
2501593 TT
1 TT
2501595 CAATTATTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
40 8 0.11
41 39 0.53
42 9 0.12
43 18 0.24
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (41 bp):
TTATTTATAATTTAAATATTAACATTTAAAATATTAATATT
Found at i:2501797 original size:18 final size:19
Alignment explanation
Indices: 2501774--2501809 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2501764 TAAAATTTTA
2501774 ATAATTTAAT-AATTATGC
1 ATAATTTAATCAATTATGC
*
2501792 ATAATTTTATCAATTATG
1 ATAATTTAATCAATTATG
2501810 ATTTGGAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.47
Consensus pattern (19 bp):
ATAATTTAATCAATTATGC
Found at i:2503760 original size:33 final size:34
Alignment explanation
Indices: 2503711--2503779 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 34
2503701 CCCTCCAAAA
*
2503711 CATTTGGGAGGGAAAGCT-AAAGTTTCTAGAAGCT
1 CATTTGGGAAGGAAAGCTGAAAGTTTC-AGAAGCT
* *
2503745 CATTT-GGAAGGAAAGCTGAAATTTTCAGCAGCT
1 CATTTGGGAAGGAAAGCTGAAAGTTTCAGAAGCT
2503778 CA
1 CA
2503780 ATACATGGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 19 0.61
34 12 0.39
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.26
Consensus pattern (34 bp):
CATTTGGGAAGGAAAGCTGAAAGTTTCAGAAGCT
Found at i:2503980 original size:15 final size:15
Alignment explanation
Indices: 2503947--2504018 Score: 90
Period size: 15 Copynumber: 4.8 Consensus size: 15
2503937 CCGAGTCATT
* * *
2503947 CTGCGTGCCACGCAT
1 CTGCGTGCCGCGTAC
2503962 CTGCGTGCCGCGTAC
1 CTGCGTGCCGCGTAC
*
2503977 CTGCGTGACGCGTAC
1 CTGCGTGCCGCGTAC
*
2503992 CTGCATGCCGCGTAC
1 CTGCGTGCCGCGTAC
*
2504007 CTGCATGCCGCG
1 CTGCGTGCCGCG
2504019 CATTTGCATG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 51 1.00
ACGTcount: A:0.11, C:0.39, G:0.31, T:0.19
Consensus pattern (15 bp):
CTGCGTGCCGCGTAC
Done.