Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007984.1 Hibiscus syriacus cultivar Beakdansim tig00110429_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 12923621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 65
Found at i:3745835 original size:64 final size:64
Alignment explanation
Indices: 3745748--3745968 Score: 218
Period size: 64 Copynumber: 3.5 Consensus size: 64
3745738 TAATGAAGGT
* * * * * *
3745748 ATGCATCGATGTACTACTGATGCATCGGTGCA-TAAAATGTATTCGTTGTTGT-ATTATTACTGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACT-AAATGCATTCGATGTT-TCATTATTAATGG
3745811 G
64 G
* * *
3745812 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACTAAATGCATTCGATGTTTCATTATTAATGGG
* * * **
3745876 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACTAAATGCATTCGATGT-TTCATTATTAATGGG
**
3745939 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
3745969 ACACCTTCAA
Statistics
Matches: 134, Mismatches: 17, Indels: 12
0.82 0.10 0.07
Matches are distributed among these distances:
63 4 0.03
64 124 0.93
65 6 0.04
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACTAAATGCATTCGATGTTTCATTATTAATGGG
Found at i:3748985 original size:2 final size:2
Alignment explanation
Indices: 3748978--3749007 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3748968 GATATAACAT
3748978 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
3749008 ACATATACAT
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:3749487 original size:30 final size:30
Alignment explanation
Indices: 3749421--3749513 Score: 125
Period size: 30 Copynumber: 3.1 Consensus size: 30
3749411 GAAGGACCTA
* * *
3749421 TCCAGAGGTCAAAAAGA-CCCCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
3749450 TCCAGAGGTCATAAAGATCCTCAGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
* *
3749480 TCTAGAGGTCATAAATATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
3749510 TCCA
1 TCCA
3749514 TAAGGACCAC
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 16 0.29
30 39 0.71
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:3750523 original size:64 final size:64
Alignment explanation
Indices: 3750436--3750656 Score: 227
Period size: 64 Copynumber: 3.5 Consensus size: 64
3750426 TAATGAGGGT
* * * * *
3750436 ATGCATCAATGCACTACTGATGCATCGGTGCA-TAAAATGTATTCGATGTTGT-ATTATTACTGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACT-AAATGCATTCGATGTT-TCATTATTAATGG
3750499 G
64 G
* * *
3750500 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACTAAATGCATTCGATGTTTCATTATTAATGGG
* * * **
3750564 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACTAAATGCATTCGATGT-TTCATTATTAATGGG
**
3750627 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
3750657 ACACCTTCAA
Statistics
Matches: 135, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
63 4 0.03
64 125 0.93
65 6 0.04
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACTAAATGCATTCGATGTTTCATTATTAATGGG
Found at i:3752072 original size:27 final size:28
Alignment explanation
Indices: 3752014--3752072 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
3752004 TGGCCCAATT
* *
3752014 TTTTTAATACTTATTATTAGAGATCTAT
1 TTTTTAATACTTATTATTAGAGATATAC
* *
3752042 TTTTTAATA-TTATTATTAGGGGTATAC
1 TTTTTAATACTTATTATTAGAGATATAC
3752069 TTTT
1 TTTT
3752073 AAAATTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 18 0.67
28 9 0.33
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.56
Consensus pattern (28 bp):
TTTTTAATACTTATTATTAGAGATATAC
Found at i:3752255 original size:72 final size:71
Alignment explanation
Indices: 3752148--3752281 Score: 175
Period size: 72 Copynumber: 1.9 Consensus size: 71
3752138 AGAGGTTGAA
* * * *
3752148 TTTTTAAATACTTATTATTATGAGCATACTCTTAAAATTTACTTCTTTT-AATATTTATTATTAG
1 TTTTTAAATACTTATTATTATAAGCATACTCTTAAAAATTA-TT-TTTTCAACACTTATTATTAG
3752212 GGACTTAT
64 GGACTTAT
3752220 TTTTTAAATACTTATTATTATTAAGC-TA-TCTTTAAAAATTATTTTTTCAACACTTATTATTA
1 TTTTTAAATACTTATTATTA-TAAGCATACTC-TTAAAAATTATTTTTTCAACACTTATTATTA
3752282 TGAACCATTA
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
70 4 0.07
71 16 0.29
72 31 0.56
73 4 0.07
ACGTcount: A:0.34, C:0.10, G:0.04, T:0.52
Consensus pattern (71 bp):
TTTTTAAATACTTATTATTATAAGCATACTCTTAAAAATTATTTTTTCAACACTTATTATTAGGG
ACTTAT
Found at i:3759196 original size:44 final size:43
Alignment explanation
Indices: 3759148--3759369 Score: 239
Period size: 44 Copynumber: 5.1 Consensus size: 43
3759138 GATTTTACAT
* * *
3759148 CGTTTTTAGGATACAAACGTCGCTAAAACTCTGGTATATAGCGG
1 CGTTTTTAGAATACAAACGCCGCTAAAA-TATGGTATATAGCGG
* * * * * * *
3759192 CGTTTTCAGTATATAAACGCCGCTAAATGTCTGGTATACATCGG
1 CGTTTTTAGAATACAAACGCCGCTAAA-ATATGGTATATAGCGG
*
3759236 CGTTTTTAGAATACAAACGCCGCT-AAATATGGTATATAGAGG
1 CGTTTTTAGAATACAAACGCCGCTAAAATATGGTATATAGCGG
* * *
3759278 CGTTTTTAGAATACAAACGCCGCTAAATATATGATATATAACGT
1 CGTTTTTAGAATACAAACGCCGCTAAA-ATATGGTATATAGCGG
* * * *
3759322 CGTTTTTAGGATACAAACGCCGCTAAATGTTTGGTATATAGCGA
1 CGTTTTTAGAATACAAACGCCGCTAAA-ATATGGTATATAGCGG
3759366 CGTT
1 CGTT
3759370 GGTATTCTAA
Statistics
Matches: 150, Mismatches: 25, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
42 35 0.23
43 4 0.03
44 111 0.74
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (43 bp):
CGTTTTTAGAATACAAACGCCGCTAAAATATGGTATATAGCGG
Found at i:3759298 original size:86 final size:86
Alignment explanation
Indices: 3759148--3759349 Score: 269
Period size: 86 Copynumber: 2.3 Consensus size: 86
3759138 GATTTTACAT
* * * * *
3759148 CGTTTTTAGGATACAAACGTCGCTAAAACTCTGGTATATAGCGGCGTTTTCAGTATATAAACGCC
1 CGTTTTTAGGATACAAACGCCGCT-AAA-TATGGTATATAGAGGCGTTTTCAGAATACAAACGCC
* * * *
3759213 GCTAAATGTCTGGTATACATCGG
64 GCTAAATATATGATATACAACGG
* *
3759236 CGTTTTTAGAATACAAACGCCGCTAAATATGGTATATAGAGGCGTTTTTAGAATACAAACGCCGC
1 CGTTTTTAGGATACAAACGCCGCTAAATATGGTATATAGAGGCGTTTTCAGAATACAAACGCCGC
* *
3759301 TAAATATATGATATATAACGT
66 TAAATATATGATATACAACGG
3759322 CGTTTTTAGGATACAAACGCCGCTAAAT
1 CGTTTTTAGGATACAAACGCCGCTAAAT
3759350 GTTTGGTATA
Statistics
Matches: 100, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
86 75 0.75
87 3 0.03
88 22 0.22
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (86 bp):
CGTTTTTAGGATACAAACGCCGCTAAATATGGTATATAGAGGCGTTTTCAGAATACAAACGCCGC
TAAATATATGATATACAACGG
Found at i:3759388 original size:130 final size:130
Alignment explanation
Indices: 3759148--3759392 Score: 294
Period size: 130 Copynumber: 1.9 Consensus size: 130
3759138 GATTTTACAT
* * * * * * *
3759148 CGTTTTTAGGATACAAACGTCGCTAAAACTCTGGTATATAGCGGCGTTTTCAGTATATAAACGCC
1 CGTTTTTAGAATACAAACGCCGCTAAAACTATGATATATAACGGCGTTTTCAGGATACAAACGCC
* * ** *
3759213 GCTAAATGTCTGGTATACATCGGCGTTTTTAGAATACAAACGCCGCTAAATATGGTATATAGAGG
66 GCTAAATGTCTGGTATACAGCGACGTTGGTAGAATAAAAACGCCGCTAAATATGGTATATAGAGG
* *
3759278 CGTTTTTAGAATACAAACGCCGCTAAATA-TATGATATATAACGTCGTTTTTAGGATACAAACGC
1 CGTTTTTAGAATACAAACGCCGCTAAA-ACTATGATATATAACGGCGTTTTCAGGATACAAACGC
* * *** *
3759342 CGCTAAATGTTTGGTATATAGCGACGTTGGTATTCTAAAAATGCCGCTAAA
65 CGCTAAATGTCTGGTATACAGCGACGTTGGTAGAATAAAAACGCCGCTAAA
3759393 GGTTAATATA
Statistics
Matches: 94, Mismatches: 20, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
130 93 0.99
131 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (130 bp):
CGTTTTTAGAATACAAACGCCGCTAAAACTATGATATATAACGGCGTTTTCAGGATACAAACGCC
GCTAAATGTCTGGTATACAGCGACGTTGGTAGAATAAAAACGCCGCTAAATATGGTATATAGAGG
Found at i:3763771 original size:28 final size:28
Alignment explanation
Indices: 3763738--3763796 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
3763728 AGAGAACTTC
* *
3763738 TTTCCATTAGCCAACTACTTCGAACATG
1 TTTCCATTAACCAACCACTTCGAACATG
3763766 TTTCCATTAACCAACCACTTCGAACATG
1 TTTCCATTAACCAACCACTTCGAACATG
3763794 TTT
1 TTT
3763797 GTGCAGCACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (28 bp):
TTTCCATTAACCAACCACTTCGAACATG
Found at i:3768892 original size:42 final size:43
Alignment explanation
Indices: 3768801--3768975 Score: 109
Period size: 42 Copynumber: 4.2 Consensus size: 43
3768791 ACATACTATT
* * * * *
3768801 GCGGCGTTTA--TTACAAAACACCTCTAAATTACAACTCTATTA
1 GCGGCGTTTATGTTA-AAAACGCCACTAAAGTACAACTATTTTA
* *
3768843 -CGACGTTTATGTTAAAAATGCCACTAAAGTACAACT-TTTTA
1 GCGGCGTTTATGTTAAAAACGCCACTAAAGTACAACTATTTTA
* * *
3768884 GCGGCG-TT-TGGTAACAAACGCCACTAAATTA-AGAGTATTTT-
1 GCGGCGTTTATGTTAA-AAACGCCACTAAAGTACA-ACTATTTTA
* * ** *
3768925 GCAGCGTTTGAT-TAAAAAACGCCACTAAAGTATTACT-CTTTA
1 GCGGCGTTT-ATGTTAAAAACGCCACTAAAGTACAACTATTTTA
3768967 GCGGCGTTT
1 GCGGCGTTT
3768976 TTGGATACAA
Statistics
Matches: 103, Mismatches: 19, Indels: 22
0.72 0.13 0.15
Matches are distributed among these distances:
40 6 0.06
41 38 0.37
42 53 0.51
43 5 0.05
44 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31
Consensus pattern (43 bp):
GCGGCGTTTATGTTAAAAACGCCACTAAAGTACAACTATTTTA
Found at i:3771607 original size:21 final size:21
Alignment explanation
Indices: 3771565--3771607 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3771555 TTTCTGAGCT
* *
3771565 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
3771586 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
3771607 A
1 A
3771608 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:3771660 original size:20 final size:20
Alignment explanation
Indices: 3771635--3771672 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3771625 GAATGCTAGA
*
3771635 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
3771655 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
3771673 TAAAAAAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:3772647 original size:103 final size:103
Alignment explanation
Indices: 3772422--3772639 Score: 393
Period size: 103 Copynumber: 2.1 Consensus size: 103
3772412 GTCGAGGGTC
3772422 TATGTGGTCCTTCGGGACATATATAAATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATAAATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
3772487 TTGATCCTTGTCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTAGTCATATGTATATGATTCTTAAGGAATGA
**
3772525 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATAAATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
3772590 TTGATCCCTAGT-ATATGTATATGATTCTTAAGGAATGA
66 TTGAT-CCTAGTCATATGTATATGATTCTTAAGGAATGA
3772628 TATGTGGTCCTT
1 TATGTGGTCCTT
3772640 ATGGACATTA
Statistics
Matches: 111, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
103 106 0.95
104 5 0.05
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATAAATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTAGTCATATGTATATGATTCTTAAGGAATGA
Found at i:3772689 original size:23 final size:23
Alignment explanation
Indices: 3772655--3772721 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 23
3772645 CATTATTATA
** *
3772655 TGGCACTACGGTGTAATTCTACG
1 TGGCACTACGGTACAATTATACG
* *
3772678 TGGCACTCCGGTACAATTATATG
1 TGGCACTACGGTACAATTATACG
* * *
3772701 TGGCACTTCAGTGCAATTATA
1 TGGCACTACGGTACAATTATA
3772722 TGAGCTGTGG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.31
Consensus pattern (23 bp):
TGGCACTACGGTACAATTATACG
Found at i:3772722 original size:23 final size:23
Alignment explanation
Indices: 3772677--3772723 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3772667 GTAATTCTAC
*
3772677 GTGGCACTCCGGTACAATTATAT
1 GTGGCACTCCAGTACAATTATAT
* *
3772700 GTGGCACTTCAGTGCAATTATAT
1 GTGGCACTCCAGTACAATTATAT
3772723 G
1 G
3772724 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (23 bp):
GTGGCACTCCAGTACAATTATAT
Found at i:3775099 original size:2 final size:2
Alignment explanation
Indices: 3775092--3775142 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
3775082 GATACAATTG
3775092 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3775134 TA TA TA TA T
1 TA TA TA TA T
3775143 CTGATCATAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3777378 original size:20 final size:20
Alignment explanation
Indices: 3777353--3777390 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3777343 GAATGCTAGA
*
3777353 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
3777373 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
3777391 TAAAAAAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:3778333 original size:103 final size:103
Alignment explanation
Indices: 3778153--3778362 Score: 357
Period size: 103 Copynumber: 2.0 Consensus size: 103
3778143 AGGGTCTATG
* *
3778153 TGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTTTGGTGAGACACATACTTGA
1 TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
* *
3778218 TCCTTGGCATATGTATATGATTCTTAAGGAATGATATA
66 TCCCTAGCATATGTATATGATTCTTAAGGAATGATATA
*
3778256 TGGTCCTTCGGGACATATATGTATTCTTTGGAGCATGTGTGAAGTCTGGTGAGACACATACTTGA
1 TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
* *
3778321 TCCCTAGTATATGTATATGATTCTTAAGGAATGATATG
66 TCCCTAGCATATGTATATGATTCTTAAGGAATGATATA
3778359 TGGT
1 TGGT
3778363 TCTTATGGAC
Statistics
Matches: 100, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 100 1.00
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.37
Consensus pattern (103 bp):
TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
TCCCTAGCATATGTATATGATTCTTAAGGAATGATATA
Found at i:3778417 original size:23 final size:23
Alignment explanation
Indices: 3778391--3778450 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
3778381 ATGGCACTAT
* *
3778391 GGTGTAATTCTATGCGACACTCC
1 GGTGCAATTATATGCGACACTCC
* * *
3778414 GGTGCAATTATATGTGGCACTTC
1 GGTGCAATTATATGCGACACTCC
3778437 GGTGCAATTATATG
1 GGTGCAATTATATG
3778451 AGATGTGGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (23 bp):
GGTGCAATTATATGCGACACTCC
Found at i:3780918 original size:24 final size:24
Alignment explanation
Indices: 3780885--3780942 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
3780875 AGGCGGATAT
* * *
3780885 TCAGGGGTCTCAGAACGGTGTGGA
1 TCAGGAGTCTCAGAACGGTATAGA
*
3780909 TCAGGAGTCTCTGAACGGTATAGA
1 TCAGGAGTCTCAGAACGGTATAGA
3780933 TCAGGAGTCT
1 TCAGGAGTCT
3780943 GGTCATCAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.24, C:0.17, G:0.34, T:0.24
Consensus pattern (24 bp):
TCAGGAGTCTCAGAACGGTATAGA
Found at i:3782190 original size:20 final size:21
Alignment explanation
Indices: 3782159--3782210 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
3782149 ATATGAGAGA
*
3782159 GAAAGAGTAAAAGTTAA-AAT
1 GAAAGAGAAAAAGTTAAGAAT
* *
3782179 GAAATAGAAAAAGTTAAGGAT
1 GAAAGAGAAAAAGTTAAGAAT
3782200 GAAAGAGAAAA
1 GAAAGAGAAAA
3782211 TAAAAAGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (21 bp):
GAAAGAGAAAAAGTTAAGAAT
Found at i:3793600 original size:16 final size:16
Alignment explanation
Indices: 3793560--3793600 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
3793550 TCCCTCGGGA
3793560 GTAAGGTGCAACTGAC
1 GTAAGGTGCAACTGAC
*
3793576 ATAAGGTGCAACTGAC
1 GTAAGGTGCAACTGAC
*
3793592 GTAATGTGC
1 GTAAGGTGC
3793601 TGAGAGTCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (16 bp):
GTAAGGTGCAACTGAC
Found at i:3795284 original size:18 final size:19
Alignment explanation
Indices: 3795239--3795288 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
3795229 CCCCTATGGG
*
3795239 GAGTATCGATACTCTACCCT
1 GAGTATCGATACTC-ACCAT
*
3795259 GGGTATCGATACTC-CCAT
1 GAGTATCGATACTCACCAT
3795277 GAGTATCGATAC
1 GAGTATCGATAC
3795289 CAAAATCAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 14 0.52
20 13 0.48
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (19 bp):
GAGTATCGATACTCACCAT
Found at i:3797775 original size:24 final size:23
Alignment explanation
Indices: 3797745--3797797 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 23
3797735 AACTATTTAT
3797745 AATATTTTAAAAATTATTAATTAA
1 AATATTTTAAAAATT-TTAATTAA
* * *
3797769 TATATTTTAAATATTTTTATTAA
1 AATATTTTAAAAATTTTAATTAA
3797792 AATATT
1 AATATT
3797798 ATTAGATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
AATATTTTAAAAATTTTAATTAA
Found at i:3797826 original size:20 final size:20
Alignment explanation
Indices: 3797803--3797841 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3797793 ATATTATTAG
3797803 ATAATATCTTAATATATTTT
1 ATAATATCTTAATATATTTT
* *
3797823 ATAATATTTTCATATATTT
1 ATAATATCTTAATATATTT
3797842 AAAATAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (20 bp):
ATAATATCTTAATATATTTT
Found at i:3798018 original size:23 final size:23
Alignment explanation
Indices: 3797985--3798040 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 23
3797975 ATTATAATAT
3797985 TATATTATTAAGA-ATATTAATAAA
1 TATATT-TTAA-ATATATTAATAAA
* *
3798009 TATATTTTAAATATTTTAATAAT
1 TATATTTTAAATATATTAATAAA
3798032 TACTATTTT
1 TA-TATTTT
3798041 GATTAAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 1 0.04
23 15 0.54
24 12 0.43
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TATATTTTAAATATATTAATAAA
Found at i:3798323 original size:7 final size:7
Alignment explanation
Indices: 3798307--3798335 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
3798297 AGTAAGAAAG
3798307 TTTTAAT
1 TTTTAAT
3798314 TTTT-AT
1 TTTTAAT
3798320 TTTTAAT
1 TTTTAAT
3798327 TTTTAAT
1 TTTTAAT
3798334 TT
1 TT
3798336 AGATTGGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTAAT
Found at i:3798325 original size:13 final size:13
Alignment explanation
Indices: 3798307--3798331 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3798297 AGTAAGAAAG
3798307 TTTTAATTTTTAT
1 TTTTAATTTTTAT
3798320 TTTTAATTTTTA
1 TTTTAATTTTTA
3798332 ATTTAGATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTAATTTTTAT
Found at i:3799668 original size:25 final size:25
Alignment explanation
Indices: 3799603--3799662 Score: 120
Period size: 25 Copynumber: 2.4 Consensus size: 25
3799593 AACATTGATT
3799603 GAATAATTGATTTTTTTCTGACATA
1 GAATAATTGATTTTTTTCTGACATA
3799628 GAATAATTGATTTTTTTCTGACATA
1 GAATAATTGATTTTTTTCTGACATA
3799653 GAATAATTGA
1 GAATAATTGA
3799663 GGTTTTAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.45
Consensus pattern (25 bp):
GAATAATTGATTTTTTTCTGACATA
Found at i:3799923 original size:2 final size:2
Alignment explanation
Indices: 3799916--3799949 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
3799906 GTCATTAATA
* *
3799916 AT AT AT AT AT AT AT AT AT AT AT AT CT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3799950 CTTGCAGACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3801640 original size:29 final size:29
Alignment explanation
Indices: 3801605--3801688 Score: 114
Period size: 29 Copynumber: 2.9 Consensus size: 29
3801595 CCCCAACATA
* **
3801605 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCCAGCGACCTTG
*
3801634 TAGGTCGCCATGCACTCCCAGTGACCTTG
1 TAGGTCGCCATGCACTCCCAGCGACCTTG
* *
3801663 TAGGTCGCCATGCACGCCCGGCGACC
1 TAGGTCGCCATGCACTCCCAGCGACC
3801689 AACGTTGTGA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.14, C:0.38, G:0.29, T:0.19
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCTTG
Found at i:3801756 original size:43 final size:43
Alignment explanation
Indices: 3801695--3801821 Score: 236
Period size: 43 Copynumber: 3.0 Consensus size: 43
3801685 GACCAACGTT
3801695 GTGATTCCAGCTGCTGCTCTGCTTTGGTGCTTTGCATGGGCCA
1 GTGATTCCAGCTGCTGCTCTGCTTTGGTGCTTTGCATGGGCCA
* *
3801738 GTGATTCCAGCTACTGCTCTGCTTTGGTTCTTTGCATGGGCCA
1 GTGATTCCAGCTGCTGCTCTGCTTTGGTGCTTTGCATGGGCCA
3801781 GTGATTCCAGCTGCTGCTCTGCTTTGGTGCTTTGCATGGGC
1 GTGATTCCAGCTGCTGCTCTGCTTTGGTGCTTTGCATGGGC
3801822 AATGCACATG
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 80 1.00
ACGTcount: A:0.09, C:0.25, G:0.29, T:0.36
Consensus pattern (43 bp):
GTGATTCCAGCTGCTGCTCTGCTTTGGTGCTTTGCATGGGCCA
Found at i:3801933 original size:23 final size:23
Alignment explanation
Indices: 3801907--3801970 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
3801897 TGAATTTAGC
* *
3801907 TGCATTATTACAGTCGTTATTGT
1 TGCATTATTGCAGTCCTTATTGT
*
3801930 TGCATTATTGCAGCCCTTATTGT
1 TGCATTATTGCAGTCCTTATTGT
3801953 TGCATTATTGCAGTCCTT
1 TGCATTATTGCAGTCCTT
3801971 CAGCTCACTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.45
Consensus pattern (23 bp):
TGCATTATTGCAGTCCTTATTGT
Found at i:3802214 original size:39 final size:39
Alignment explanation
Indices: 3802171--3802279 Score: 143
Period size: 39 Copynumber: 2.8 Consensus size: 39
3802161 TTATTATTTT
** *
3802171 AAATTATTAGTTTCTTAGTTTA-TGGTTTAAGGTAAAACA
1 AAATT-TTAGTTAATTAGTTTAGTAGTTTAAGGTAAAACA
3802210 AAATTTTAGTTAATTAG-TTAGTTAGTTTAAGGTAAAACA
1 AAATTTTAGTTAATTAGTTTAG-TAGTTTAAGGTAAAACA
3802249 AAATTTTAGTTAATTAGTTT-GTTAGTTTAAG
1 AAATTTTAGTTAATTAGTTTAG-TAGTTTAAG
3802280 TTTTATTATT
Statistics
Matches: 64, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
37 3 0.05
38 10 0.16
39 49 0.77
40 2 0.03
ACGTcount: A:0.37, C:0.03, G:0.16, T:0.45
Consensus pattern (39 bp):
AAATTTTAGTTAATTAGTTTAGTAGTTTAAGGTAAAACA
Found at i:3802401 original size:28 final size:27
Alignment explanation
Indices: 3802362--3802414 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
3802352 ATATTAAAAA
3802362 AATAATTAATTAGTGTGTTAGTTAGTCT
1 AATAATTAATTAGTGTG-TAGTTAGTCT
* *
3802390 AATATTTAATTAGTTTGTAGTTAGT
1 AATAATTAATTAGTGTGTAGTTAGT
3802415 TAAATAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (27 bp):
AATAATTAATTAGTGTGTAGTTAGTCT
Found at i:3802420 original size:27 final size:29
Alignment explanation
Indices: 3802361--3802425 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
3802351 TATATTAAAA
3802361 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
* *
3802390 -AATATTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
3802416 AAATAGTTAA
1 AAATAATTAA
3802426 GTTATATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.03
27 16 0.50
28 15 0.47
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (29 bp):
AAATAATTAATTAGTGTGTTAGTTAGTCT
Found at i:3802908 original size:29 final size:30
Alignment explanation
Indices: 3802853--3802948 Score: 124
Period size: 30 Copynumber: 3.2 Consensus size: 30
3802843 TTTAGTTAAT
*
3802853 TAGTTTTTTAGTAGTAAA-TTATAATTAAA-AA
1 TAGTTTATTAGT--TAAAGTTAT-ATTAAAGAA
* *
3802884 TCGTTTATTAGTTTAAGTTATATTAAAGAA
1 TAGTTTATTAGTTAAAGTTATATTAAAGAA
3802914 TAGTTTATTAGTTAAAGTTATATTAAAGAA
1 TAGTTTATTAGTTAAAGTTATATTAAAGAA
3802944 TAGTT
1 TAGTT
3802949 AAAGTTATAT
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
29 9 0.16
30 39 0.67
31 10 0.17
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.46
Consensus pattern (30 bp):
TAGTTTATTAGTTAAAGTTATATTAAAGAA
Found at i:3802917 original size:22 final size:22
Alignment explanation
Indices: 3802892--3802972 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 22
3802882 AATCGTTTAT
3802892 TAGTTTAAGTTATATTAAAGAA
1 TAGTTTAAGTTATATTAAAGAA
3802914 TAGTTTATTAGTTAAAGTTATATTAAAGAA
1 TAG-----T--TTA-AGTTATATTAAAGAA
* *
3802944 TAGTTAAAGTTATATTAAAGGA
1 TAGTTTAAGTTATATTAAAGAA
3802966 TAGTTTA
1 TAGTTTA
3802973 TTAGTTGTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
22 23 0.48
23 2 0.04
25 1 0.02
27 1 0.02
29 3 0.06
30 18 0.38
ACGTcount: A:0.43, C:0.00, G:0.15, T:0.42
Consensus pattern (22 bp):
TAGTTTAAGTTATATTAAAGAA
Found at i:3802922 original size:15 final size:16
Alignment explanation
Indices: 3802899--3802949 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 16
3802889 TATTAGTTTA
3802899 AGTTATATTAAAGAAT
1 AGTTATATTAAAGAAT
***
3802915 AGTT-TATTAGTTAA-
1 AGTTATATTAAAGAAT
3802929 AGTTATATTAAAGAAT
1 AGTTATATTAAAGAAT
3802945 AGTTA
1 AGTTA
3802950 AAGTTATATT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
14 4 0.15
15 14 0.52
16 9 0.33
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (16 bp):
AGTTATATTAAAGAAT
Found at i:3802941 original size:11 final size:11
Alignment explanation
Indices: 3802925--3802963 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
3802915 AGTTTATTAG
3802925 TTAAAGTTATA
1 TTAAAGTTATA
*
3802936 TTAAAG-AATA
1 TTAAAGTTATA
3802946 GTTAAAGTTATA
1 -TTAAAGTTATA
3802958 TTAAAG
1 TTAAAG
3802964 GATAGTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (11 bp):
TTAAAGTTATA
Found at i:3803314 original size:20 final size:20
Alignment explanation
Indices: 3803289--3803355 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
3803279 AATTCGTAAT
3803289 GCGAATAAGTAAATCGCAAC
1 GCGAATAAGTAAATCGCAAC
** * *
3803309 GCGAATTGGGAAAATCGCAAT
1 GCGAA-TAAGTAAATCGCAAC
3803330 GCGAATAAGTAAATCGCAAC
1 GCGAATAAGTAAATCGCAAC
3803350 GCGAAT
1 GCGAAT
3803356 TGGGAAAATC
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (20 bp):
GCGAATAAGTAAATCGCAAC
Found at i:3803325 original size:21 final size:21
Alignment explanation
Indices: 3803299--3803374 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
3803289 GCGAATAAGT
3803299 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
3803320 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
3803340 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
3803361 AAATCGCAATGCGA
1 AAATCGCAACGCGA
3803375 TACTGACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:3803388 original size:20 final size:20
Alignment explanation
Indices: 3803363--3803497 Score: 146
Period size: 20 Copynumber: 6.7 Consensus size: 20
3803353 AATTGGGAAA
*
3803363 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
3803383 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
3803403 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
3803424 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
3803444 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
3803464 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
3803484 TTCGCAACGCGATA
1 ATCGCAACGCGATA
3803498 ATACATAATC
Statistics
Matches: 101, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
19 2 0.02
20 84 0.83
21 13 0.13
22 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:3803389 original size:41 final size:41
Alignment explanation
Indices: 3803286--3803374 Score: 178
Period size: 41 Copynumber: 2.2 Consensus size: 41
3803276 CCCAATTCGT
3803286 AATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCGC
1 AATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCGC
3803327 AATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCGC
1 AATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCGC
3803368 AATGCGA
1 AATGCGA
3803375 TACTGACTAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.42, C:0.17, G:0.25, T:0.17
Consensus pattern (41 bp):
AATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCGC
Found at i:3803407 original size:61 final size:61
Alignment explanation
Indices: 3803360--3803476 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
3803350 GCGAATTGGG
* * * *
3803360 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
3803421 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
3803477 TCTGACTTTC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:3803713 original size:22 final size:22
Alignment explanation
Indices: 3803685--3803728 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3803675 CACTCTCTCA
*
3803685 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
*
3803707 CCCATCTCCGGCAAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
3803729 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACAAAATCCGTC
Found at i:3804221 original size:25 final size:24
Alignment explanation
Indices: 3804167--3804221 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
3804157 TGTTTATTAT
* *
3804167 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
3804191 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
3804217 TGTTT
1 TGTTT
3804222 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:3805371 original size:18 final size:18
Alignment explanation
Indices: 3805350--3805394 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
3805340 TCCACTTCGG
*
3805350 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
3805368 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
3805386 GAGCCATCA
1 GAGCCATCA
3805395 TCTGATTGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:3805930 original size:19 final size:20
Alignment explanation
Indices: 3805876--3805921 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
3805866 TAGTTTACTT
* *
3805876 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
3805896 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
3805916 TCGCAA
1 TCGCAA
3805922 TGTGAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:3805937 original size:19 final size:19
Alignment explanation
Indices: 3805915--3805996 Score: 95
Period size: 19 Copynumber: 4.6 Consensus size: 19
3805905 GGAAATGGCT
*
3805915 ATCGCAATGTGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3805934 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
3805948 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
3805966 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3805985 ATCGCAATGCGA
1 ATCGCAATGCGA
3805997 TTTGTGTTTC
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 1 0.02
18 18 0.35
19 20 0.38
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3806027 original size:14 final size:14
Alignment explanation
Indices: 3806008--3806065 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
3805998 TTGTGTTTCG
3806008 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
3806022 CGTTGCGATTTCACT-T
1 CGTTGCGATTT---TGT
3806038 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
3806054 CGTTGCGATTTT
1 CGTTGCGATTTT
3806066 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 2 0.05
17 1 0.03
18 11 0.29
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:3806043 original size:32 final size:33
Alignment explanation
Indices: 3806004--3806081 Score: 131
Period size: 32 Copynumber: 2.4 Consensus size: 33
3805994 CGATTTGTGT
3806004 TTCGCGTTGCGATTTTGTCGTTGCGA-TTTCAC
1 TTCGCGTTGCGATTTTGTCGTTGCGATTTTCAC
*
3806036 TTCGCGTTGCGATTTTGTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTGTCGTTGCGATTTTCAC
*
3806069 TTCGCATTGCGAT
1 TTCGCGTTGCGAT
3806082 AGCCATTTCC
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
32 26 0.60
33 17 0.40
ACGTcount: A:0.10, C:0.21, G:0.24, T:0.45
Consensus pattern (33 bp):
TTCGCGTTGCGATTTTGTCGTTGCGATTTTCAC
Found at i:3806100 original size:20 final size:20
Alignment explanation
Indices: 3806075--3806121 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
3806065 TCATTTCGCA
3806075 TTGCGATAGCCATTTCCACG
1 TTGCGATAGCCATTTCCACG
* * *
3806095 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGCCATTTCCACG
3806115 TTGCGAT
1 TTGCGAT
3806122 TTTAAGTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCACG
Found at i:3808008 original size:14 final size:14
Alignment explanation
Indices: 3807989--3808024 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3807979 ATTGTTTAAT
3807989 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
3808003 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
3808017 TGATTTGT
1 TGATTTGT
3808025 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3808150 original size:14 final size:14
Alignment explanation
Indices: 3808131--3808184 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
3808121 TGAAATGGCT
3808131 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
3808145 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
3808164 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
3808178 ATCGCAA
1 ATCGCAA
3808185 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:3808202 original size:33 final size:33
Alignment explanation
Indices: 3808112--3808189 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
3808102 AAAACAGACT
* ***
3808112 ATCGCAATGTGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
3808145 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
3808178 ATCGCAATGCGA
1 ATCGCAATGCGA
3808190 TTTTCATTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:3808233 original size:20 final size:20
Alignment explanation
Indices: 3808208--3808285 Score: 147
Period size: 20 Copynumber: 3.9 Consensus size: 20
3808198 TCGCATTGCG
*
3808208 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
3808228 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
3808248 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
3808268 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
3808286 TCAAATGAAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.37
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:3809358 original size:24 final size:24
Alignment explanation
Indices: 3809331--3809378 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
3809321 TAGTCAGTAT
*
3809331 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATATTGGTCAATAC
*
3809355 TCGAACTTTGATATTGGTCAATAC
1 TCGAAATTTGATATTGGTCAATAC
3809379 ACGGATTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (24 bp):
TCGAAATTTGATATTGGTCAATAC
Found at i:3809388 original size:24 final size:24
Alignment explanation
Indices: 3809332--3809390 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
3809322 AGTCAGTATT
* * *
3809332 CGAAATTTGATCTTGGTCAATACT
1 CGAACTTTGATATTGGTCAATACA
3809356 CGAACTTTGATATTGGTCAATACA
1 CGAACTTTGATATTGGTCAATACA
* *
3809380 CGGATTTTGAT
1 CGAACTTTGAT
3809391 GACGTTTCAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (24 bp):
CGAACTTTGATATTGGTCAATACA
Found at i:3809582 original size:12 final size:12
Alignment explanation
Indices: 3809565--3809589 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3809555 ATATAATCCT
3809565 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3809577 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3809589 G
1 G
3809590 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3811901 original size:33 final size:33
Alignment explanation
Indices: 3811859--3811985 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
3811849 GGAAATTACT
3811859 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
3811892 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
3811924 TTTCACAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
3811958 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
3811986 CGAATTTAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:3811969 original size:66 final size:66
Alignment explanation
Indices: 3811863--3811992 Score: 242
Period size: 66 Copynumber: 2.0 Consensus size: 66
3811853 ATTACTATCG
*
3811863 CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAATTTC
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTC
3811928 A
66 A
*
3811929 CAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
3811993 AATTTCGCGT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (66 bp):
CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTC
A
Found at i:3812187 original size:14 final size:14
Alignment explanation
Indices: 3812168--3812204 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3812158 CATCAATTAA
3812168 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3812182 ACAAATCACCTTTT
1 ACAAATCAACTTTT
3812196 ACAAATCAA
1 ACAAATCAA
3812205 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3813608 original size:21 final size:21
Alignment explanation
Indices: 3813542--3813608 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
3813532 GTGAATCGGG
*
3813542 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
3813562 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
3813584 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
3813605 CTCT
1 CTCT
3813609 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:3813627 original size:42 final size:41
Alignment explanation
Indices: 3813542--3813663 Score: 111
Period size: 42 Copynumber: 2.9 Consensus size: 41
3813532 GTGAATCGGG
* * * *
3813542 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
3813584 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
3813626 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAG
3813664 ACGAGTCGGG
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 56 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:3815692 original size:20 final size:19
Alignment explanation
Indices: 3815661--3815721 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
3815651 TCTTTTGGTT
3815661 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
3815680 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
3815701 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
3815720 GA
1 GA
3815722 GAATCGCAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.11
20 29 0.83
21 2 0.06
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:3815743 original size:33 final size:33
Alignment explanation
Indices: 3815686--3815773 Score: 149
Period size: 33 Copynumber: 2.6 Consensus size: 33
3815676 ACGAGATAAT
*
3815686 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
3815720 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
3815753 GAGAATCGCAACGCGAAATGA
1 GAGAATCGCAACGCGAAATGA
3815774 AAATTGCAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
33 38 0.73
34 14 0.27
ACGTcount: A:0.39, C:0.24, G:0.26, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:3815805 original size:19 final size:19
Alignment explanation
Indices: 3815783--3815827 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
3815773 AAAATTGCAA
*
3815783 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
3815802 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
3815821 TGCGATT
1 TGCGATT
3815828 CTCTCATTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.07, C:0.16, G:0.24, T:0.53
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:3816442 original size:41 final size:41
Alignment explanation
Indices: 3816380--3816541 Score: 135
Period size: 41 Copynumber: 3.8 Consensus size: 41
3816370 CGCTATGTAA
* * * *
3816380 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTGTATT
* * * ***
3816421 ATCGCATTGCGATAGTAAGTATCGCAAATACGAATGGCGCTATGT
1 ATCGCATTGCGAAAGTAAGTATCGC-ATTGCG-ATTTTG-TAT-T
* * * *
3816466 AAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 --ATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTGTATT
*
3816509 ATCGCATTGCGATAGTAAGTATCGCATTGCGAT
1 ATCGCATTGCGAAAGTAAGTATCGCATTGCGAT
3816542 AGTCAGTATC
Statistics
Matches: 90, Mismatches: 25, Indels: 12
0.71 0.20 0.09
Matches are distributed among these distances:
41 49 0.54
42 3 0.03
43 4 0.04
44 6 0.07
45 4 0.04
46 3 0.03
47 21 0.23
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.33
Consensus pattern (41 bp):
ATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTGTATT
Found at i:3816490 original size:47 final size:46
Alignment explanation
Indices: 3816359--3816490 Score: 130
Period size: 41 Copynumber: 3.0 Consensus size: 46
3816349 AATACGCGTT
*
3816359 AATACGAATGGCGCTATGTAAATCGCGTTGCGAAAGTCAGTATCTC
1 AATACGAATGGCGCTATGTAAATCGCGTTGCGAAAGTCAGTATCGC
** * *** * * *
3816405 GTTGCG-ATTTTG-TAT-T--ATCGCATTGCGATAGTAAGTATCGC
1 AATACGAATGGCGCTATGTAAATCGCGTTGCGAAAGTCAGTATCGC
3816446 AAATACGAATGGCGCTATGTAAATCGCGTTGCGAAAGTCAGTATC
1 -AATACGAATGGCGCTATGTAAATCGCGTTGCGAAAGTCAGTATC
3816491 TCGTTGCGAT
Statistics
Matches: 61, Mismatches: 19, Indels: 11
0.67 0.21 0.12
Matches are distributed among these distances:
41 21 0.34
42 3 0.05
43 4 0.07
44 6 0.10
45 4 0.07
46 3 0.05
47 20 0.33
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (46 bp):
AATACGAATGGCGCTATGTAAATCGCGTTGCGAAAGTCAGTATCGC
Found at i:3816508 original size:88 final size:88
Alignment explanation
Indices: 3816359--3816534 Score: 352
Period size: 88 Copynumber: 2.0 Consensus size: 88
3816349 AATACGCGTT
3816359 AATACGAATGGCGCTATGTAAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTATC
1 AATACGAATGGCGCTATGTAAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTATC
3816424 GCATTGCGATAGTAAGTATCGCA
66 GCATTGCGATAGTAAGTATCGCA
3816447 AATACGAATGGCGCTATGTAAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTATC
1 AATACGAATGGCGCTATGTAAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTATC
3816512 GCATTGCGATAGTAAGTATCGCA
66 GCATTGCGATAGTAAGTATCGCA
3816535 TTGCGATAGT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (88 bp):
AATACGAATGGCGCTATGTAAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTATC
GCATTGCGATAGTAAGTATCGCA
Found at i:3816533 original size:20 final size:20
Alignment explanation
Indices: 3816508--3816561 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
3816498 GATTTTGTAT
3816508 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
3816528 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
3816548 TATCGCATTGCGAT
1 TATCGCATTGCGAT
3816562 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:3816580 original size:61 final size:61
Alignment explanation
Indices: 3816468--3816582 Score: 142
Period size: 61 Copynumber: 1.9 Consensus size: 61
3816458 CGCTATGTAA
* * * ** *
3816468 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGCATTGCGATAGTAAGT
* *
3816529 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAATATCGCATTGCGAT
3816583 TTACATATTC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
61 43 0.96
62 2 0.04
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGCATTGCGATAGTAAGT
Found at i:3816672 original size:21 final size:21
Alignment explanation
Indices: 3816632--3816672 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3816622 ACTGTATACC
**
3816632 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
3816653 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
3816673 GCAAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:3819021 original size:59 final size:56
Alignment explanation
Indices: 3818958--3819078 Score: 179
Period size: 59 Copynumber: 2.1 Consensus size: 56
3818948 TATTATAATT
* *
3818958 TCATTACTAGTAATCATTAGTAAATCATTAATATCAAATAATTAAATATTAATAATAAA
1 TCATTACTAATAATAATTAGTAAATCATTAATATCAAATAATTAAATATT--TAA-AAA
* *
3819017 TCATTATTAATAATAATTAGTAAATCATTAGTATCAAATAATTAAATATTTAAAAA
1 TCATTACTAATAATAATTAGTAAATCATTAATATCAAATAATTAAATATTTAAAAA
3819073 TCATTA
1 TCATTA
3819079 ATAAATTTGA
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
56 9 0.16
57 3 0.05
59 46 0.79
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.39
Consensus pattern (56 bp):
TCATTACTAATAATAATTAGTAAATCATTAATATCAAATAATTAAATATTTAAAAA
Found at i:3819022 original size:21 final size:21
Alignment explanation
Indices: 3818978--3819046 Score: 59
Period size: 21 Copynumber: 3.1 Consensus size: 21
3818968 TAATCATTAG
*
3818978 TAAATCATTAAT-ATCAAATAAT
1 TAAAT-ATTAATAAT-AAATCAT
3819000 TAAATATTAATAATAAATCAT
1 TAAATATTAATAATAAATCAT
* *
3819021 TATTAATAATAATTAGTAAATCAT
1 TA--AATATTAA-TAATAAATCAT
3819045 TA
1 TA
3819047 GTATCAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
21 14 0.35
22 7 0.17
23 7 0.17
24 12 0.30
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (21 bp):
TAAATATTAATAATAAATCAT
Found at i:3819025 original size:24 final size:24
Alignment explanation
Indices: 3818969--3819046 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 24
3818959 CATTACTAGT
*
3818969 AATCATTAGTAAATCATTAAT-ATCA
1 AATCATTATTAAAT-ATTAATAAT-A
3818994 AAT-A--ATTAAATATTAATAATA
1 AATCATTATTAAATATTAATAATA
* *
3819015 AATCATTATT-AATAATAATTAGTA
1 AATCATTATTAAATATTAA-TAATA
3819039 AATCATTA
1 AATCATTA
3819047 GTATCAAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
21 10 0.22
22 9 0.20
23 7 0.16
24 16 0.36
25 3 0.07
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (24 bp):
AATCATTATTAAATATTAATAATA
Found at i:3819184 original size:14 final size:13
Alignment explanation
Indices: 3819161--3819433 Score: 152
Period size: 14 Copynumber: 20.9 Consensus size: 13
3819151 ATTAGTAATA
3819161 ATTATTAAATCATT
1 ATTA-TAAATCATT
3819175 ATTATAAAATCATT
1 ATTAT-AAATCATT
*
3819189 A--CTAAATCATT
1 ATTATAAATCATT
*
3819200 A-T-TAAATCATC
1 ATTATAAATCATT
* *
3819211 ACTAGTAGATCATT
1 ATTA-TAAATCATT
*
3819225 ATTAT-AATGATT
1 ATTATAAATCATT
3819237 ATTATTAAATCATT
1 ATTA-TAAATCATT
3819251 A-T-T--ATCATT
1 ATTATAAATCATT
3819260 ATTATTAAATCATT
1 ATTA-TAAATCATT
*
3819274 ATTAT-AATGATT
1 ATTATAAATCATT
3819286 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
3819300 ATTAT-AATGATT
1 ATTATAAATCATT
3819312 ATTATAAAATCATT
1 ATTAT-AAATCATT
3819326 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
*
3819345 AAATATTAAAGTCATT
1 -ATTA-TAAA-TCATT
3819361 A-T-TAAATCATT
1 ATTATAAATCATT
*
3819372 ATTAT-AATGATT
1 ATTATAAATCATT
3819384 ATTACTAAATCA-T
1 ATTA-TAAATCATT
3819397 -TTATTAAATCATAAT
1 ATTA-TAAATCAT--T
3819412 ATTA-AAATCATT
1 ATTATAAATCATT
3819424 A--ATAAATCAT
1 ATTATAAATCAT
3819434 CAAATCATTA
Statistics
Matches: 209, Mismatches: 17, Indels: 69
0.71 0.06 0.23
Matches are distributed among these distances:
9 7 0.03
10 2 0.01
11 32 0.15
12 60 0.29
13 10 0.05
14 69 0.33
15 7 0.03
16 10 0.05
18 1 0.00
19 10 0.05
20 1 0.00
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (13 bp):
ATTATAAATCATT
Found at i:3819253 original size:26 final size:26
Alignment explanation
Indices: 3819161--3819424 Score: 216
Period size: 26 Copynumber: 10.6 Consensus size: 26
3819151 ATTAGTAATA
* *
3819161 ATTATTAAATCATTATTATAA-AATC
1 ATTATTAAATCATTATTATAATGATT
* * *
3819186 ATTACTAAATCATTATTA-AATCATC
1 ATTATTAAATCATTATTATAATGATT
* * *
3819211 ACTAGTAGATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATGATT
*
3819237 ATTATTAAATCATTA-T-T-ATCATT
1 ATTATTAAATCATTATTATAATGATT
3819260 ATTATTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATGATT
*
3819286 ATTACTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATGATT
* * * *
3819312 ATTATAAAATCATTACTA-AATCATCAA
1 ATTATTAAATCATTATTATAATGAT--T
* *
3819339 ATCATT-AA--A-TATTA-AA-G-TC
1 ATTATTAAATCATTATTATAATGATT
3819358 ATTATTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATGATT
* *
3819384 ATTACTAAATCATTTATTA-AATCA-T
1 ATTATTAAATCA-TTATTATAATGATT
*
3819409 AATATTAAAATCATTA
1 ATTATT-AAATCATTA
3819425 ATAAATCATC
Statistics
Matches: 194, Mismatches: 29, Indels: 32
0.76 0.11 0.13
Matches are distributed among these distances:
19 5 0.03
20 2 0.01
21 1 0.01
22 1 0.01
23 31 0.16
24 7 0.04
25 51 0.26
26 86 0.44
27 10 0.05
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.44
Consensus pattern (26 bp):
ATTATTAAATCATTATTATAATGATT
Found at i:3819275 original size:49 final size:50
Alignment explanation
Indices: 3819161--3819326 Score: 210
Period size: 49 Copynumber: 3.3 Consensus size: 50
3819151 ATTAGTAATA
* * *
3819161 ATTATTAAATCATTATTATAA-AATCATTACTAAATCATTATTAAATCATC
1 ATTATTAAATCATTATTATAATGATTATTACTAAATCATTATT-AATCATT
* * * *
3819211 ACTAGTAGATCATTATTATAATGATTATTATTAAATCATTATT-ATCATT
1 ATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTAATCATT
*
3819260 ATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATGATTATTACTAAATCATTA-T-TAATCATT
*
3819312 ATTATAAAATCATTA
1 ATTATTAAATCATTA
3819327 CTAAATCATC
Statistics
Matches: 99, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
49 42 0.42
50 19 0.19
51 19 0.19
52 19 0.19
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.45
Consensus pattern (50 bp):
ATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTAATCATT
Found at i:3819373 original size:98 final size:98
Alignment explanation
Indices: 3819161--3819474 Score: 363
Period size: 98 Copynumber: 3.2 Consensus size: 98
3819151 ATTAGTAATA
* * * * *
3819161 ATTATTAAATCATTATTATAA-AATCATTACTAAATCA-TTATTAAATCATCACTAGT-AGATCA
1 ATTATTAAATCATTATTATAATGATTATTACTAAATCATTTATTAAATCAT-AATATTAAAATCA
* * * * * *
3819223 TTATTATAATGAT--TATTATTAAATCATTATTATCATT
65 TTAATA-AATCATCAAATCATTAAAT-ATTA--A-AATC
* *
3819260 ATTATTAAATCATTATTATAATGATTATTACTAAATCA-TTATTATAATGATTAT-TATAAAATC
1 ATTATTAAATCATTATTATAATGATTATTACTAAATCATTTATTA-AATCATAATAT-TAAAATC
* *
3819323 ATTACTAAATCATCAAATCATTAAATATTAAAGTC
64 ATTAATAAATCATCAAATCATTAAATATTAAAATC
3819358 ATTATTAAATCATTATTATAATGATTATTACTAAATCATTTATTAAATCATAATATTAAAATCAT
1 ATTATTAAATCATTATTATAATGATTATTACTAAATCATTTATTAAATCATAATATTAAAATCAT
3819423 TAATAAATCATCAAATCATTAAATATTAAAATC
66 TAATAAATCATCAAATCATTAAATATTAAAATC
*
3819456 ATTATTAAATCATTTTTAT
1 ATTATTAAATCATTATTAT
3819475 GGTTAATTGA
Statistics
Matches: 188, Mismatches: 19, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
98 104 0.55
99 29 0.15
100 27 0.14
101 19 0.10
102 9 0.05
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (98 bp):
ATTATTAAATCATTATTATAATGATTATTACTAAATCATTTATTAAATCATAATATTAAAATCAT
TAATAAATCATCAAATCATTAAATATTAAAATC
Found at i:3819451 original size:35 final size:33
Alignment explanation
Indices: 3819402--3819468 Score: 107
Period size: 35 Copynumber: 2.0 Consensus size: 33
3819392 ATCATTTATT
3819402 AAATCATAATATTAAAATCATTAATAAATCATC
1 AAATCATAATATTAAAATCATTAATAAATCATC
*
3819435 AAATCATTAAATATTAAAATCATTATTAAATCAT
1 AAATCA-T-AATATTAAAATCATTAATAAATCAT
3819469 TTTTATGGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 6 0.19
34 1 0.03
35 24 0.77
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (33 bp):
AAATCATAATATTAAAATCATTAATAAATCATC
Found at i:3819454 original size:8 final size:9
Alignment explanation
Indices: 3819412--3819469 Score: 50
Period size: 8 Copynumber: 6.3 Consensus size: 9
3819402 AAATCATAAT
3819412 ATTAAAATC
1 ATTAAAATC
3819421 ATTAATAAATC
1 ATT-A-AAATC
*
3819432 A-TCAAATC
1 ATTAAAATC
3819440 ATT-AAAT-
1 ATTAAAATC
3819447 ATTAAAATC
1 ATTAAAATC
3819456 ATTATTAAATC
1 ATTA--AAATC
3819467 ATT
1 ATT
3819470 TTTATGGTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
7 3 0.07
8 14 0.34
9 8 0.20
10 2 0.05
11 14 0.34
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (9 bp):
ATTAAAATC
Found at i:3819454 original size:16 final size:16
Alignment explanation
Indices: 3819398--3819459 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
3819388 CTAAATCATT
3819398 TATT-AAATCA-T-AA
1 TATTAAAATCATTAAA
3819411 TATTAAAATCATTAATA
1 TATTAAAATCATTAA-A
* *
3819428 AATCATCAAATCATTAAA
1 TAT--TAAAATCATTAAA
3819446 TATTAAAATCATTA
1 TATTAAAATCATTA
3819460 TTAAATCATT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
13 4 0.10
14 6 0.15
15 1 0.03
16 11 0.28
17 3 0.08
18 3 0.08
19 11 0.28
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (16 bp):
TATTAAAATCATTAAA
Found at i:3819462 original size:19 final size:19
Alignment explanation
Indices: 3819409--3819465 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
3819399 ATTAAATCAT
*
3819409 AATATTAAAATCATTAATA
1 AATATTAAAATCATTATTA
*
3819428 AATCA-TCAAATC---ATTA
1 AAT-ATTAAAATCATTATTA
3819444 AATATTAAAATCATTATTA
1 AATATTAAAATCATTATTA
3819463 AAT
1 AAT
3819466 CATTTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
15 1 0.03
16 12 0.40
19 16 0.53
20 1 0.03
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (19 bp):
AATATTAAAATCATTATTA
Found at i:3820107 original size:28 final size:30
Alignment explanation
Indices: 3820059--3820121 Score: 112
Period size: 28 Copynumber: 2.2 Consensus size: 30
3820049 AATTTTTATA
3820059 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
3820089 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
3820117 TAATA
1 TAATA
3820122 ATTTATTCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 26 0.79
29 1 0.03
30 6 0.18
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:3820519 original size:23 final size:23
Alignment explanation
Indices: 3820492--3820551 Score: 120
Period size: 23 Copynumber: 2.6 Consensus size: 23
3820482 TGCAATAATG
3820492 CAGCTATGGATGCAGGAATCTCC
1 CAGCTATGGATGCAGGAATCTCC
3820515 CAGCTATGGATGCAGGAATCTCC
1 CAGCTATGGATGCAGGAATCTCC
3820538 CAGCTATGGATGCA
1 CAGCTATGGATGCA
3820552 ACGTATGCAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.22
Consensus pattern (23 bp):
CAGCTATGGATGCAGGAATCTCC
Found at i:3820726 original size:32 final size:32
Alignment explanation
Indices: 3820683--3820747 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
3820673 GGATATGCAC
*
3820683 TGCTCCCTGGATAGCTCGCACTCACTCCTTGG
1 TGCTCCATGGATAGCTCGCACTCACTCCTTGG
*
3820715 TGCTCCATGGATAGTTCGCACTCACTCCTTGG
1 TGCTCCATGGATAGCTCGCACTCACTCCTTGG
3820747 T
1 T
3820748 CGCCCGGAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.14, C:0.34, G:0.22, T:0.31
Consensus pattern (32 bp):
TGCTCCATGGATAGCTCGCACTCACTCCTTGG
Found at i:3820781 original size:29 final size:29
Alignment explanation
Indices: 3820739--3820798 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
3820729 TTCGCACTCA
3820739 CTCCTTGGTCGCCCGGAGTGCATGGCGAC
1 CTCCTTGGTCGCCCGGAGTGCATGGCGAC
*
3820768 CTCCTTGGTTGCCCGGAGTGCATGGCGAC
1 CTCCTTGGTCGCCCGGAGTGCATGGCGAC
3820797 CT
1 CT
3820799 ACGGCTTCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.10, C:0.33, G:0.33, T:0.23
Consensus pattern (29 bp):
CTCCTTGGTCGCCCGGAGTGCATGGCGAC
Found at i:3821461 original size:15 final size:14
Alignment explanation
Indices: 3821443--3821477 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
3821433 TTTCATATTT
3821443 ATATTTTTCTAAATA
1 ATATTTTT-TAAATA
3821458 ATA-TTTTTAAATA
1 ATATTTTTTAAATA
3821471 ATATTTT
1 ATATTTT
3821478 ATTTTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 9 0.47
14 7 0.37
15 3 0.16
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (14 bp):
ATATTTTTTAAATA
Found at i:3821470 original size:13 final size:14
Alignment explanation
Indices: 3821447--3821477 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
3821437 ATATTTATAT
3821447 TTTTCTAAATAATA
1 TTTTCTAAATAATA
3821461 TTTT-TAAATAATA
1 TTTTCTAAATAATA
3821474 TTTT
1 TTTT
3821478 ATTTTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTTCTAAATAATA
Found at i:3824111 original size:23 final size:23
Alignment explanation
Indices: 3824084--3824127 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
3824074 AACACAATTT
*
3824084 ACTTTGCCGA-GACATTTCCATCC
1 ACTTTGCC-ACGACATATCCATCC
3824107 ACTTTGCCACGACATATCCAT
1 ACTTTGCCACGACATATCCAT
3824128 TAGCTACCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.25, C:0.34, G:0.11, T:0.30
Consensus pattern (23 bp):
ACTTTGCCACGACATATCCATCC
Found at i:3836179 original size:20 final size:20
Alignment explanation
Indices: 3836143--3836181 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3836133 TCTAAATCAT
* *
3836143 TTTTCAAAATTTTATTTTGA
1 TTTTCAAAATATAATTTTGA
3836163 TTTTCAAAATATAATTTTG
1 TTTTCAAAATATAATTTTG
3836182 CATTCACAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTTCAAAATATAATTTTGA
Found at i:3845195 original size:21 final size:22
Alignment explanation
Indices: 3845169--3845293 Score: 93
Period size: 21 Copynumber: 5.8 Consensus size: 22
3845159 ATAATTTGCA
3845169 CCGAAGTG-CCACATAATTGTC
1 CCGAAGTGACCACATAATTGTC
* *
3845190 CCGAAG-GACCACATAGGTTTGTA
1 CCGAAGTGACCACATA--ATTGTC
* *
3845213 TCGAAGT-ACCACATAGGTT-TGC
1 CCGAAGTGACCACATA-ATTGT-C
* *
3845235 ACCGAAGT-ACCACATATTTTTC
1 -CCGAAGTGACCACATAATTGTC
*
3845257 CCGAA-TGACCACATAATTATC
1 CCGAAGTGACCACATAATTGTC
3845278 CCGAAG-GACCACATAA
1 CCGAAGTGACCACATAA
3845294 AACCCTCAAC
Statistics
Matches: 86, Mismatches: 9, Indels: 18
0.76 0.08 0.16
Matches are distributed among these distances:
20 2 0.02
21 46 0.53
22 6 0.07
23 32 0.37
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (22 bp):
CCGAAGTGACCACATAATTGTC
Found at i:3845217 original size:23 final size:23
Alignment explanation
Indices: 3845163--3845250 Score: 101
Period size: 23 Copynumber: 3.9 Consensus size: 23
3845153 TAACTCATAA
*
3845163 TTTGCACCGAAGTGCCACATA--
1 TTTGCACCGAAGTACCACATAGG
* *
3845184 ATTGTC-CCGAAGGACCACATAGG
1 TTTG-CACCGAAGTACCACATAGG
* *
3845207 TTTGTATCGAAGTACCACATAGG
1 TTTGCACCGAAGTACCACATAGG
3845230 TTTGCACCGAAGTACCACATA
1 TTTGCACCGAAGTACCACATA
3845251 TTTTTCCCGA
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
21 16 0.30
22 1 0.02
23 37 0.69
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (23 bp):
TTTGCACCGAAGTACCACATAGG
Found at i:3851468 original size:22 final size:23
Alignment explanation
Indices: 3851441--3851500 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
3851431 ATAATTTTCC
3851441 CCAAAG-ACCACATAGGTTTACA
1 CCAAAGTACCACATAGGTTTACA
* *
3851463 CCAAAGTGCCACATAGGTTTGCA
1 CCAAAGTACCACATAGGTTTACA
* *
3851486 CCGAAGTGCCACATA
1 CCAAAGTACCACATA
3851501 TATGTCCCGA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 6 0.18
23 28 0.82
ACGTcount: A:0.35, C:0.28, G:0.18, T:0.18
Consensus pattern (23 bp):
CCAAAGTACCACATAGGTTTACA
Found at i:3851476 original size:23 final size:23
Alignment explanation
Indices: 3851448--3851500 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
3851438 TCCCCAAAGA
3851448 CCACATAGGTTTACACCAAAGTG
1 CCACATAGGTTTACACCAAAGTG
* *
3851471 CCACATAGGTTTGCACCGAAGTG
1 CCACATAGGTTTACACCAAAGTG
3851494 CCACATA
1 CCACATA
3851501 TATGTCCCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (23 bp):
CCACATAGGTTTACACCAAAGTG
Found at i:3851512 original size:21 final size:21
Alignment explanation
Indices: 3851486--3851532 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
3851476 TAGGTTTGCA
3851486 CCGAAGTG-CCACAT-ATATGTC
1 CCGAAG-GACCACATAAT-TGTC
3851507 CCGAAGGACCACATAATTGTC
1 CCGAAGGACCACATAATTGTC
3851528 CCGAA
1 CCGAA
3851533 ATAAAACCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.04
21 21 0.88
22 2 0.08
ACGTcount: A:0.32, C:0.30, G:0.19, T:0.19
Consensus pattern (21 bp):
CCGAAGGACCACATAATTGTC
Found at i:3852097 original size:19 final size:19
Alignment explanation
Indices: 3852059--3852097 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3852049 CATGCCTAGA
* *
3852059 AGTATCGGTACTACCTTAC
1 AGTATCGATACTACCCTAC
*
3852078 AGTATCGATACTTCCCTAC
1 AGTATCGATACTACCCTAC
3852097 A
1 A
3852098 AGGGTATCGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.31
Consensus pattern (19 bp):
AGTATCGATACTACCCTAC
Found at i:3854425 original size:30 final size:31
Alignment explanation
Indices: 3854378--3854458 Score: 130
Period size: 31 Copynumber: 2.7 Consensus size: 31
3854368 AAATTTATTT
3854378 GGACCAATTTT-TAATTTTGAGAAAGTT-GG
1 GGACCAATTTTGTAATTTTGAGAAAGTTAGG
3854407 GGACCAATTTTGTAATTTTGAGAAAGTTAGG
1 GGACCAATTTTGTAATTTTGAGAAAGTTAGG
* *
3854438 GAACCAATTTGGTAATTTTGA
1 GGACCAATTTTGTAATTTTGA
3854459 AAAATTAAGG
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 11 0.23
30 16 0.33
31 21 0.44
ACGTcount: A:0.32, C:0.07, G:0.23, T:0.37
Consensus pattern (31 bp):
GGACCAATTTTGTAATTTTGAGAAAGTTAGG
Found at i:3856207 original size:18 final size:18
Alignment explanation
Indices: 3856151--3856207 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
3856141 TGCATTGGGC
* *
3856151 TATGAACTTGAAAATAAGC
1 TATGAATTTG-AAATAAGT
* *
3856170 TATGAATCTAAAATTAAGT
1 TATGAATTTGAAA-TAAGT
3856189 TATGAATTTGAAATAAGT
1 TATGAATTTGAAATAAGT
3856207 T
1 T
3856208 TTGAGTCTGG
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 9 0.29
19 22 0.71
ACGTcount: A:0.46, C:0.05, G:0.14, T:0.35
Consensus pattern (18 bp):
TATGAATTTGAAATAAGT
Found at i:3856220 original size:19 final size:19
Alignment explanation
Indices: 3856162--3856240 Score: 54
Period size: 19 Copynumber: 4.2 Consensus size: 19
3856152 ATGAACTTGA
* * *
3856162 AAATAAGCTATGAATCT-A
1 AAATAAGTTCTGAATCTGG
* *
3856180 AAATTAAGTTATGAAT-TTG
1 AAA-TAAGTTCTGAATCTGG
* *
3856199 AAATAAGTTTTGAGTCTGG
1 AAATAAGTTCTGAATCTGG
* *
3856218 AAACAAGTTCTGAATCTGA
1 AAATAAGTTCTGAATCTGG
3856237 AAAT
1 AAAT
3856241 GAATTCTAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
18 14 0.29
19 34 0.71
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.33
Consensus pattern (19 bp):
AAATAAGTTCTGAATCTGG
Found at i:3856285 original size:13 final size:13
Alignment explanation
Indices: 3856267--3856303 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
3856257 AAGTACATAT
3856267 TATGAAAATGAAA
1 TATGAAAATGAAA
*
3856280 TATGAAAGTGAAA
1 TATGAAAATGAAA
*
3856293 GATGAAAATGA
1 TATGAAAATGA
3856304 GATAATAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.22, T:0.22
Consensus pattern (13 bp):
TATGAAAATGAAA
Found at i:3862923 original size:95 final size:96
Alignment explanation
Indices: 3862744--3862931 Score: 245
Period size: 95 Copynumber: 2.0 Consensus size: 96
3862734 AGGATAAAAT
* * *
3862744 TTCTTTTAGAATGGGGAGAGAGTTGTTATACCCCAATTTAGGGGCCAAAATTTTATTTTGTGAAA
1 TTCTTTTAGAAGGGGGAGAGAGTTGTTATACCCCAATTTAGAGGCCAAAAATTTATTTTGTGAAA
* * *
3862809 TCGATAATCAATTTGTATC-TTTTAAAACAA
66 TCGATAACCAAATTATATCTTTTTAAAACAA
* * *
3862839 TTCTTTTA-AAGGTGGGAGAGAGTTGTTATACCCTAATTTAGATGTCAAAAATTTATTTTGTGAA
1 TTCTTTTAGAAGG-GGGAGAGAGTTGTTATACCCCAATTTAGAGGCCAAAAATTTATTTTGTGAA
* * *
3862903 ATTGGTGACCAAATTATATCTTTTTAAAA
65 ATCGATAACCAAATTATATCTTTTTAAAA
3862932 ATTTTAATCA
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
94 3 0.04
95 68 0.86
96 8 0.10
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (96 bp):
TTCTTTTAGAAGGGGGAGAGAGTTGTTATACCCCAATTTAGAGGCCAAAAATTTATTTTGTGAAA
TCGATAACCAAATTATATCTTTTTAAAACAA
Found at i:3863958 original size:20 final size:19
Alignment explanation
Indices: 3863933--3863985 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
3863923 TGATTCAATC
*
3863933 AGTATCGATACCGAAAGGGG
1 AGTATCGATACC-AAAGGGA
*
3863953 AGTATCAATACCAAAGGGA
1 AGTATCGATACCAAAGGGA
3863972 AGGTATCGATACCA
1 A-GTATCGATACCA
3863986 TTTCGAAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 7 0.24
20 22 0.76
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (19 bp):
AGTATCGATACCAAAGGGA
Found at i:3864075 original size:20 final size:21
Alignment explanation
Indices: 3864009--3864079 Score: 78
Period size: 22 Copynumber: 3.5 Consensus size: 21
3863999 TGCAAAAATG
3864009 GTATCGATACCATA-TCAT--A
1 GTATCGATACCATAGT-ATGGA
*
3864028 GTATCGGTACCATAGTATGGTA
1 GTATCGATACCATAGTATGG-A
*
3864050 GTATCGATACCATGGTATGG-
1 GTATCGATACCATAGTATGGA
3864070 GTATCGATAC
1 GTATCGATAC
3864080 TAAGGGGCCA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
19 15 0.33
20 11 0.24
22 19 0.42
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.31
Consensus pattern (21 bp):
GTATCGATACCATAGTATGGA
Found at i:3864562 original size:55 final size:55
Alignment explanation
Indices: 3864408--3864950 Score: 681
Period size: 55 Copynumber: 9.9 Consensus size: 55
3864398 ACCAAATAGG
* * * *
3864408 CACTATATGTGCAAATCCACGGAATTCATCATGAGTTAATGAATAACTGTACAGG
1 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGA
* *
3864463 CA-TGATGTGTGC-AA-CCTATGGAATTCATCATGAGTTGATGAATAACAGTACAGA
1 CACT-ATGTGTGCAAATCC-ACGGAATTCATCATGAGTTGATGAATAACCGTACAGA
* *
3864517 CACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACC-TACAGG
1 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGA
* *
3864571 CACTATGTGTGCAGATCCACGGAATTCATCATGAGTTGATGAATAATCGTACA-A
1 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGA
* * ** *
3864625 GCACTCTGTGTGCAAATCCGCATAATTCATTATGAGTTGATGAATAACCGTACAGA
1 -CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGA
* * *
3864681 CACTATGTGTGCAAATCCACGAAATTCATCGTGAGTTGATGAATAACCATACATG-
1 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACA-GA
* *
3864736 CACTATGTGTGCAAATCCATGGAATTTATCATGAGTTGATGAATAACCGTACAGA
1 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGA
* * * *
3864791 CACTATATGTGCAAATTCACGGAATTCATCATGAGTTGTTGAATAACCGTACAGG
1 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGA
* * * *
3864846 TACTATGTGTGAAAATCCACTGAATTCATCATGAGTTGATGAATAACCGTATAGGA
1 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACA-GA
* * * *
3864902 -ACGATGTGTGC-AACCCACAGAATTCATCATGCGTTGATGAACT-ACCGTA
1 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAA-TAACCGTA
3864951 TAGGTACTAC
Statistics
Matches: 425, Mismatches: 51, Indels: 25
0.85 0.10 0.05
Matches are distributed among these distances:
53 2 0.00
54 130 0.31
55 288 0.68
56 5 0.01
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (55 bp):
CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGA
Found at i:3865285 original size:21 final size:21
Alignment explanation
Indices: 3865209--3865286 Score: 57
Period size: 21 Copynumber: 3.6 Consensus size: 21
3865199 GCAATGCATG
3865209 ATGATGTATAAAAGGCATGAA
1 ATGATGTATAAAAGGCATGAA
* * * ** *
3865230 AGGATGCCATAAATGAAATGTATT
1 ATGATG-TATAAAAGGCATG-A-A
* *
3865254 ATGGTCTATAAAAGGCATGAA
1 ATGATGTATAAAAGGCATGAA
3865275 ATGATGTATAAA
1 ATGATGTATAAA
3865287 CGAAATTAAT
Statistics
Matches: 38, Mismatches: 16, Indels: 6
0.63 0.27 0.10
Matches are distributed among these distances:
21 15 0.39
22 10 0.26
23 10 0.26
24 3 0.08
ACGTcount: A:0.45, C:0.06, G:0.22, T:0.27
Consensus pattern (21 bp):
ATGATGTATAAAAGGCATGAA
Found at i:3869614 original size:20 final size:20
Alignment explanation
Indices: 3869589--3869660 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
3869579 GATTCAATTG
*
3869589 GTATCGATATCGAAAGGGAA
1 GTATCGATATCAAAAGGGAA
* *
3869609 GTATCGATACCAAAAGGGGA
1 GTATCGATATCAAAAGGGAA
*
3869629 GTATCGATACCAAAA-GGAA
1 GTATCGATATCAAAAGGGAA
3869648 GGTATCGATATCA
1 -GTATCGATATCA
3869661 TTTCGAAACA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 3 0.07
20 43 0.93
ACGTcount: A:0.40, C:0.14, G:0.26, T:0.19
Consensus pattern (20 bp):
GTATCGATATCAAAAGGGAA
Found at i:3869708 original size:19 final size:19
Alignment explanation
Indices: 3869684--3869737 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 19
3869674 TGCAAAAATG
3869684 GTATCGATACCATATCATA
1 GTATCGATACCATATCATA
* *
3869703 GTATCGGTACCATAGTATGATA
1 GTATCGATACC--A-TATCATA
3869725 GTATCGATACCAT
1 GTATCGATACCAT
3869738 GGTTTGGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 11 0.38
20 1 0.03
21 1 0.03
22 16 0.55
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (19 bp):
GTATCGATACCATATCATA
Found at i:3870048 original size:22 final size:21
Alignment explanation
Indices: 3870014--3870054 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
3870004 TGTGTAACTA
3870014 TATGTTGTATTAATCATATAAG
1 TATGTTGTATTAAT-ATATAAG
3870036 TATGATTGT-TTAATATATA
1 TATG-TTGTATTAATATATA
3870055 TGTGGTGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 9 0.50
23 4 0.22
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (21 bp):
TATGTTGTATTAATATATAAG
Found at i:3870242 original size:55 final size:55
Alignment explanation
Indices: 3870072--3870607 Score: 767
Period size: 55 Copynumber: 9.8 Consensus size: 55
3870062 ATTACCAAAT
* * ** *
3870072 AGGCATTATATGTGCAAATCCACATAATTCATAATGAGTTGATGAATAACCGTAC
1 AGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTAC
* * * * *
3870127 ATGTACGATGTGTGC-AACCCACAGAATTCATCATGAGTTGATGAATAACCGTAC
1 AGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTAC
* * *
3870181 ATGCACTATGTGTGCAAATCCACGTAATTCATCATGAGTTGATGAATAACCGTGC
1 AGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTAC
*
3870236 AGGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCGTAC
1 AGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTAC
* * * *
3870291 ATGCACTATGTGTGCAAATCCA-TGAAAT--TCATGAGTTGATGAATAACCATAC
1 AGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTAC
* *
3870343 ATGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGAAGAATAACCGTAC
1 AGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTAC
*
3870398 ATGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTAC
1 AGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTAC
* * *
3870453 AGACACTATATGTGCAAATTCACGGAATTCATCATGAGTTGATGAATAACCGTAC
1 AGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTAC
* *
3870508 AGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAATCGTAA
1 AGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTAC
* * * *
3870563 AGGCACGATGTATGC-AACCCACGGAATTCATCATGAGTTAATGAA
1 AGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAA
3870608 CTACTGTATA
Statistics
Matches: 437, Mismatches: 40, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
52 45 0.10
53 4 0.01
54 80 0.18
55 308 0.70
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.27
Consensus pattern (55 bp):
AGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTAC
Found at i:3870484 original size:217 final size:218
Alignment explanation
Indices: 3870072--3870601 Score: 794
Period size: 217 Copynumber: 2.4 Consensus size: 218
3870062 ATTACCAAAT
* * ** * * *
3870072 AGGCATTATATGTGCAAATCCACATAATTCATAATGAGTTGATGAATAACCGTACATGTACGATG
1 AGGCACTATGTGTGCAAATCCACGGAAAT-ATCATGAGTTGATGAATAACCGTACATGCACGATG
* *
3870137 TGTGCAACCCACAGAATTCATCATGAGTTGATGAATAACCGTACATGCACTATGTGTGCAAATCC
65 TGTGCAACCCACGGAATTCATCATGAGTTGAAGAATAACCGTACATGCACTATGTGTGCAAATCC
* * * *
3870202 ACGTAATTCATCATGAGTTGATGAATAACCGTGCAGGCACTATGTGTGCAAATCCACGAAATTCA
130 ACGGAATTCATCATGAGTTGATGAATAACCGTACAGACACTATATGTGCAAATCCACGAAATTCA
3870267 TCATGAGTTGATGAATAACCGTAC
195 TCATGAGTTGATGAATAACCGTAC
* * * *
3870291 ATGCACTATGTGTGCAAATCCA-TGAAAT-TCATGAGTTGATGAATAACCATACATGCACTATGT
1 AGGCACTATGTGTGCAAATCCACGGAAATATCATGAGTTGATGAATAACCGTACATGCACGATGT
*
3870354 GTGCAAATCCACGGAATTCATCATGAGTTGAAGAATAACCGTACATGCACTATGTGTGCAAATCC
66 GTGC-AACCCACGGAATTCATCATGAGTTGAAGAATAACCGTACATGCACTATGTGTGCAAATCC
* *
3870419 ACGGAATTCATCATGAGTTGATGAATAACCGTACAGACACTATATGTGCAAATTCACGGAATTCA
130 ACGGAATTCATCATGAGTTGATGAATAACCGTACAGACACTATATGTGCAAATCCACGAAATTCA
3870484 TCATGAGTTGATGAATAACCGTAC
195 TCATGAGTTGATGAATAACCGTAC
* * * *
3870508 AGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAATCGTAAAGGCACGATG
1 AGGCACTATGTGTGCAAATCCACGGAAAT-ATCATGAGTTGATGAATAACCGTACATGCACGATG
*
3870573 TATGCAACCCACGGAATTCATCATGAGTT
65 TGTGCAACCCACGGAATTCATCATGAGTT
3870602 AATGAACTAC
Statistics
Matches: 278, Mismatches: 29, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
216 35 0.13
217 161 0.58
218 7 0.03
219 42 0.15
220 33 0.12
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (218 bp):
AGGCACTATGTGTGCAAATCCACGGAAATATCATGAGTTGATGAATAACCGTACATGCACGATGT
GTGCAACCCACGGAATTCATCATGAGTTGAAGAATAACCGTACATGCACTATGTGTGCAAATCCA
CGGAATTCATCATGAGTTGATGAATAACCGTACAGACACTATATGTGCAAATCCACGAAATTCAT
CATGAGTTGATGAATAACCGTAC
Found at i:3870846 original size:23 final size:23
Alignment explanation
Indices: 3870820--3870891 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
3870810 GCAATGCATA
3870820 ATGTGTATAAAAGGCATGAAATG
1 ATGTGTATAAAAGGCATGAAATG
* * ** * *
3870843 ATGT-CATAAATGAAATG-TATC
1 ATGTGTATAAAAGGCATGAAATG
*
3870864 ATGGTGTATAAAAGGCATGAAAGG
1 AT-GTGTATAAAAGGCATGAAATG
3870888 ATGT
1 ATGT
3870892 ATAAACGAAA
Statistics
Matches: 33, Mismatches: 13, Indels: 6
0.63 0.25 0.12
Matches are distributed among these distances:
21 4 0.12
22 11 0.33
23 15 0.45
24 3 0.09
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (23 bp):
ATGTGTATAAAAGGCATGAAATG
Found at i:3870893 original size:21 final size:21
Alignment explanation
Indices: 3870823--3870896 Score: 60
Period size: 21 Copynumber: 3.4 Consensus size: 21
3870813 ATGCATAATG
*
3870823 TGTATAAAAGGCATGAAATGA
1 TGTATAAAAGGCATGAAAGGA
* ** *
3870844 TGTCATAAATGAAATGTATCATGG-
1 TGT-ATAAAAGGCATG-A--AAGGA
3870868 TGTATAAAAGGCATGAAAGGA
1 TGTATAAAAGGCATGAAAGGA
3870889 TGTATAAA
1 TGTATAAA
3870897 CGAAATTAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 10
0.67 0.16 0.17
Matches are distributed among these distances:
20 3 0.08
21 11 0.28
22 10 0.26
23 10 0.26
24 3 0.08
25 2 0.05
ACGTcount: A:0.45, C:0.05, G:0.23, T:0.27
Consensus pattern (21 bp):
TGTATAAAAGGCATGAAAGGA
Found at i:3872253 original size:37 final size:38
Alignment explanation
Indices: 3872193--3872264 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 38
3872183 CCAATTTTCT
3872193 AAAACTAAAAAAAAACTATTTTTTGAAAATCAAACCAG
1 AAAACTAAAAAAAAACTATTTTTTGAAAATCAAACCAG
*
3872231 AAAA-TAAAAAAATATA-TATTTTTT-AGAATCAAAC
1 AAAACTAAAAAAA-A-ACTATTTTTTGAAAATCAAAC
3872265 GGAATTAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
37 17 0.55
38 13 0.42
39 1 0.03
ACGTcount: A:0.58, C:0.10, G:0.04, T:0.28
Consensus pattern (38 bp):
AAAACTAAAAAAAAACTATTTTTTGAAAATCAAACCAG
Found at i:3873018 original size:15 final size:15
Alignment explanation
Indices: 3872998--3873037 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
3872988 TGAACTAAAT
3872998 TAGTCCAGTCGAGCA
1 TAGTCCAGTCGAGCA
3873013 TAGTCCAGTCGAGCA
1 TAGTCCAGTCGAGCA
* *
3873028 GAGTCAAGTC
1 TAGTCCAGTC
3873038 AATCGACCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.28, C:0.25, G:0.28, T:0.20
Consensus pattern (15 bp):
TAGTCCAGTCGAGCA
Found at i:3875795 original size:31 final size:31
Alignment explanation
Indices: 3875730--3875829 Score: 119
Period size: 31 Copynumber: 3.2 Consensus size: 31
3875720 GGTCCCGAGA
* * * * *
3875730 GCCTACCTAGGAAAGTTACTCAAGGCCACGGG
1 GCCTACCCAAGAAAGAT-CTCAGGGCCACAGG
*
3875762 GCCTACCCAAGAAAGATCTTAGGGCCACAGG
1 GCCTACCCAAGAAAGATCTCAGGGCCACAGG
* *
3875793 GCCTACCCAAGAAAGATCTCAGGGCCTCAGA
1 GCCTACCCAAGAAAGATCTCAGGGCCACAGG
3875824 GCCTAC
1 GCCTAC
3875830 TCAAAGGTAT
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
31 45 0.76
32 14 0.24
ACGTcount: A:0.30, C:0.31, G:0.25, T:0.14
Consensus pattern (31 bp):
GCCTACCCAAGAAAGATCTCAGGGCCACAGG
Found at i:3876244 original size:943 final size:942
Alignment explanation
Indices: 3874419--3877262 Score: 5204
Period size: 943 Copynumber: 3.0 Consensus size: 942
3874409 TTGGGAAGCT
*
3874419 CAGTAATACAATACTACTTGTTGATGATACAAGACATGCAAATAAATGGAAATCCATATAATTTC
1 CAGTAATACAATACTACTTGTTGATGCTACAAGACATGCAAATAAATGGAAATCCATATAATTTC
*
3874484 CTTATTGAATCAGACGTATACTGGTTTTCGGGATAATCAGGGGTCCCACTGGTAGTTCATCGAAT
66 CTTATTGAATCAGACGTATACTGGTTTTCGGGATAATCTGGGGTCCCACTGGTAGTTCATCGAAT
* *
3874549 AGAAGCCATGAAGATCTCAGTTCATAGGAAGCATTCATAGCATCATGTTTTCAAGAGGTCAAATA
131 AGAAGCCATGAAGATCTCAGTTCATAGGAAGCATTCATAGTATCATGTTTTCAGGAGGTCAAATA
* *
3874614 GGATGTCTAGTGTGTTCCAATCAAAACCAGTGAAAAGATATAAGTCTTTTAAAACCATAGTGGAA
196 GGATGTCTAGTGTGTTCCAATCAAAACCAGTGAAAAGATATAAATCTTTTAAAACCATAGCGGAA
*
3874679 CCCTCCAACCAAACTCCAGTACGCAGTTCCCCAGAACTGCATCCGTAAGGCTTACCCTAAGCACA
261 CCCTCCAACCAAACTCCATTACGCAGTTCCCCAGAACTGCATCCGTAAGGCTTACCCTAAGCACA
3874744 CAGCAAAGGGAGCCAACCTAAGGGTATGCCTTGGGTCCCGAGAGCCTACCTAGGAAAGTTACTCA
326 CAGCAAAGGGAGCCAACCTAAGGGTATGCCTTGGGTCCCGAGAGCCTACCTAGGAAAGTTACTCA
* * *
3874809 GGGCCATGGGGCCTACCCAAGAAAGATCTTGGGGCCACAAGGCCTACCCAAGAAAGATCTCAAGG
391 GGGCCACGGGGCCTACCCAAGAAAGATCTTGGGGCCACAGGGCCTACCCAAGAAAGATCTCAGGG
3874874 CCTCAGAGCCTACTCAAAGGTATCCTTAGGTCCGTAAGGATTTACCAGCTGGATCAGGGTTGTAC
456 CCTCAGAGCCTACTCAAAGGTATCCTTAGGTCCGTAAGGATTTACCAGCTGGATCAGGGTTGTAC
* *
3874939 CTCCATACTCCAAAATCCTACCCATATAAAAATCCAGTAAAAATCAGTTTTAGCCGTAAATCATA
521 CTCCATACTCCAAAATCCTACCCATATAAAAATCTAGTAAAAATCAGTTTTAGCCGTAAATCGTA
*
3875004 ATATATGGATCATGATCCAGTAATATGTCATAACCGTGATAATGAAATAGATCGTATAACTTATT
586 ATATATGGATCTTGATCCAGTAATATGTCATAACCGTGATAATGAAATAGATCGTATAACTTATT
*
3875069 TCCACCTGTACACCATAAGTAGTTCCATGATTAACCCAAGGGAGTGCCTTGGGGCCAGAAAGCCT
651 TCCACCTGTACACCATAAGTAGTTCCATGATTAACCCAAGGGAGTGCCTT-GGGCCTGAAAGCCT
* *
3875134 ACCCAATGATCACCTTAGGTCCGTAAGTATTTACTAGCTTGATCAGATATGTACCTCCAGTCTAC
715 ACCCAATGATCACCTTAGGTCCGTAAGGATTTACCAGCTTGATCAGATATGTACCTCCAGTCTAC
*
3875199 CCATATAATATCCCAATAAAACAGTTCAAGTATAACTAGTGAAAACATAAAACCATAGTTCATAA
780 CCATATAATATCCCAATAAAACAGTTCGAGTATAACTAGTGAAAACATAAAACCATAGTTCATAA
3875264 ACCAATAATTTCCATGATTCCATAAATCAAGAACAATTCATATTCTTCGATGATAACTGTAATCG
845 ACCAATAATTTCCATGATTCCATAAATCAAGAACAATTCATATTCTTCGATGATAACTGTAATCG
3875329 GAGATCACATATCATGTTGTCATGGTTCATAAA
910 GAGATCACATATCATGTTGTCATGGTTCATAAA
*
3875362 CAGTAATACAATACTACTTGTTGATGCTACAAGACATGCAAATAAATGGAAATCTATATAATTTC
1 CAGTAATACAATACTACTTGTTGATGCTACAAGACATGCAAATAAATGGAAATCCATATAATTTC
*
3875427 CTTATTGAATCAGACGTATACTAGTTTTCGGGATAATCTGGGGTCCCACTGGTAGTTCATCGAAT
66 CTTATTGAATCAGACGTATACTGGTTTTCGGGATAATCTGGGGTCCCACTGGTAGTTCATCGAAT
*
3875492 AGAAGCCATGAAGATCTCAGCTCATAGGAAGCATTCATAGTATCATGTTTTCAGGAGGTCAAATA
131 AGAAGCCATGAAGATCTCAGTTCATAGGAAGCATTCATAGTATCATGTTTTCAGGAGGTCAAATA
*
3875557 GGATGTCTAGTGTGTTCCAATCAAAACCAGTGAAAAGATATAAATCTTTTAAAACCATAGCGAAA
196 GGATGTCTAGTGTGTTCCAATCAAAACCAGTGAAAAGATATAAATCTTTTAAAACCATAGCGGAA
* * *
3875622 CCCTTCAACCAAACTCCATTACGCAGTTCCCCAGAACTGCGTCCGTAAGGCTTACCCTAAGCACG
261 CCCTCCAACCAAACTCCATTACGCAGTTCCCCAGAACTGCATCCGTAAGGCTTACCCTAAGCACA
**
3875687 CAGCAAAGAAAGCCAACCTAAGGGTATGCCTTGGGTCCCGAGAGCCTACCTAGGAAAGTTACTCA
326 CAGCAAAGGGAGCCAACCTAAGGGTATGCCTTGGGTCCCGAGAGCCTACCTAGGAAAGTTACTCA
* *
3875752 AGGCCACGGGGCCTACCCAAGAAAGATCTTAGGGCCACAGGGCCTACCCAAGAAAGATCTCAGGG
391 GGGCCACGGGGCCTACCCAAGAAAGATCTTGGGGCCACAGGGCCTACCCAAGAAAGATCTCAGGG
*
3875817 CCTCAGAGCCTACTCAAAGGTATCCTTAGGCCCGTAAGGATTTACCAGCTGGATCAGGGTTGTAC
456 CCTCAGAGCCTACTCAAAGGTATCCTTAGGTCCGTAAGGATTTACCAGCTGGATCAGGGTTGTAC
*
3875882 CACCATACTCCAAAATCCTACCCATATAAAAATCTAGTAAAAATCAGTTTTAGCCGTAAATCGTA
521 CTCCATACTCCAAAATCCTACCCATATAAAAATCTAGTAAAAATCAGTTTTAGCCGTAAATCGTA
3875947 ATATATGGATCTTGATCCAGTAATATGTCATAACCGTGATAATGAAATAGATCGTATAACTTATT
586 ATATATGGATCTTGATCCAGTAATATGTCATAACCGTGATAATGAAATAGATCGTATAACTTATT
3876012 TCCACCTGTACACCATAAGTAGTTCCATGATTAACCCAAGGGAGTGCCTTGAGGCCTGAAAGCCT
651 TCCACCTGTACACCATAAGTAGTTCCATGATTAACCCAAGGGAGTGCCTTG-GGCCTGAAAGCCT
*
3876077 ACCCAATGATCTCCTTAGGTCCGTAAGGATTTACCAGCTTGATCAGATATGTACCTCCAGTCTAC
715 ACCCAATGATCACCTTAGGTCCGTAAGGATTTACCAGCTTGATCAGATATGTACCTCCAGTCTAC
*
3876142 CCATATAATATCCCAATAAAACAGTTTGAGTATAACTAGTGAAAACATAAAACCATAGTTCATAA
780 CCATATAATATCCCAATAAAACAGTTCGAGTATAACTAGTGAAAACATAAAACCATAGTTCATAA
*
3876207 ACTAATAATTTCCATGATTCCATAAATCAAGAACAATTCATATTCTTCGATGATAACTGTAATCG
845 ACCAATAATTTCCATGATTCCATAAATCAAGAACAATTCATATTCTTCGATGATAACTGTAATCG
3876272 GAGATCACATATCATGTTGTCATGGTTCATAAA
910 GAGATCACATATCATGTTGTCATGGTTCATAAA
3876305 CAGTAATACAATACTACTTGTTGATGCTACAAGACATGCAAATAAATGGAAATCCATATAATTTC
1 CAGTAATACAATACTACTTGTTGATGCTACAAGACATGCAAATAAATGGAAATCCATATAATTTC
*
3876370 CTTATTGAATCAGACATATACTGGTTTTCGGGATAATCTGGGGTCCCACTGGTAGTTCATCGAAT
66 CTTATTGAATCAGACGTATACTGGTTTTCGGGATAATCTGGGGTCCCACTGGTAGTTCATCGAAT
3876435 AGAAGCCATGAAGATCTCAGTTCATAGGAAGCATTCATAGTATCATGTTTTCAGGAGGTCAAATA
131 AGAAGCCATGAAGATCTCAGTTCATAGGAAGCATTCATAGTATCATGTTTTCAGGAGGTCAAATA
3876500 GGATGTCTAGTGTGTTCCAATCAAAACCAGTGAAAAGATATAAATCTTTTAAAACCATAGCGGAA
196 GGATGTCTAGTGTGTTCCAATCAAAACCAGTGAAAAGATATAAATCTTTTAAAACCATAGCGGAA
* *
3876565 CCCTCCAACCAAACTCCATTACGTAGTTCCCCAAAACTGCATCCGTAAGGCTTACCCTAAGCACA
261 CCCTCCAACCAAACTCCATTACGCAGTTCCCCAGAACTGCATCCGTAAGGCTTACCCTAAGCACA
*
3876630 CAGCAAAGGGAGCCAACCTAAGGGTATGCCTTGGGTCCCGAGAGCCTACCTGGGAAAGTTACTCA
326 CAGCAAAGGGAGCCAACCTAAGGGTATGCCTTGGGTCCCGAGAGCCTACCTAGGAAAGTTACTCA
* *
3876695 GGGCCACGGGGCCTACCCAAGAAAGATCTTGGGGCCACAGAGCCTACCCAAGAAAGATCTTAGGG
391 GGGCCACGGGGCCTACCCAAGAAAGATCTTGGGGCCACAGGGCCTACCCAAGAAAGATCTCAGGG
*
3876760 CCTCAGAGCCTACTCAAAGGTATACTTAGGTCCGTAAGGATTTACCAGCTGGATCAGGGTTGTAC
456 CCTCAGAGCCTACTCAAAGGTATCCTTAGGTCCGTAAGGATTTACCAGCTGGATCAGGGTTGTAC
*
3876825 CTCCATACTCCAAAATCCTACCTATATAAAAATCTAGTAAAAATCAGTTTTAGCCGTAAATCGTA
521 CTCCATACTCCAAAATCCTACCCATATAAAAATCTAGTAAAAATCAGTTTTAGCCGTAAATCGTA
* *
3876890 ATATATGGATCTTGATCTAGTAATATGTCATAACCGTGATAATGAAATAGATCATATAACTTATT
586 ATATATGGATCTTGATCCAGTAATATGTCATAACCGTGATAATGAAATAGATCGTATAACTTATT
* *
3876955 TCCACCTGTACACCATAAGTAGCTCCATGATTAACCTAAGGGAGTGCCTTGGGACCTGAAAGCCT
651 TCCACCTGTACACCATAAGTAGTTCCATGATTAACCCAAGGGAGTGCCTTGGG-CCTGAAAGCCT
*
3877020 ACCCAATGATCACCTTAGGTCCGTAAGGATTTATCAGCTTGATCAGATATGTACCTCCAGTCTAC
715 ACCCAATGATCACCTTAGGTCCGTAAGGATTTACCAGCTTGATCAGATATGTACCTCCAGTCTAC
* *
3877085 CCATATAATATCTCAATAAAATAGTTCGAGTATAACTAGTGAAAACATAAAACCATAGTTCATAA
780 CCATATAATATCCCAATAAAACAGTTCGAGTATAACTAGTGAAAACATAAAACCATAGTTCATAA
3877150 ACCAATAATTTCCATGATTCCATAAATCAAGAACAATTCATATTCTTCGATGATAACTGTAATCG
845 ACCAATAATTTCCATGATTCCATAAATCAAGAACAATTCATATTCTTCGATGATAACTGTAATCG
*
3877215 GAGATCATATATCATGTTGTCATGGTTCATAAA
910 GAGATCACATATCATGTTGTCATGGTTCATAAA
3877248 CAGTAA-ATCAATACT
1 CAGTAATA-CAATACT
3877263 TTCGTTAAAA
Statistics
Matches: 1833, Mismatches: 65, Indels: 6
0.96 0.03 0.00
Matches are distributed among these distances:
942 4 0.00
943 1829 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (942 bp):
CAGTAATACAATACTACTTGTTGATGCTACAAGACATGCAAATAAATGGAAATCCATATAATTTC
CTTATTGAATCAGACGTATACTGGTTTTCGGGATAATCTGGGGTCCCACTGGTAGTTCATCGAAT
AGAAGCCATGAAGATCTCAGTTCATAGGAAGCATTCATAGTATCATGTTTTCAGGAGGTCAAATA
GGATGTCTAGTGTGTTCCAATCAAAACCAGTGAAAAGATATAAATCTTTTAAAACCATAGCGGAA
CCCTCCAACCAAACTCCATTACGCAGTTCCCCAGAACTGCATCCGTAAGGCTTACCCTAAGCACA
CAGCAAAGGGAGCCAACCTAAGGGTATGCCTTGGGTCCCGAGAGCCTACCTAGGAAAGTTACTCA
GGGCCACGGGGCCTACCCAAGAAAGATCTTGGGGCCACAGGGCCTACCCAAGAAAGATCTCAGGG
CCTCAGAGCCTACTCAAAGGTATCCTTAGGTCCGTAAGGATTTACCAGCTGGATCAGGGTTGTAC
CTCCATACTCCAAAATCCTACCCATATAAAAATCTAGTAAAAATCAGTTTTAGCCGTAAATCGTA
ATATATGGATCTTGATCCAGTAATATGTCATAACCGTGATAATGAAATAGATCGTATAACTTATT
TCCACCTGTACACCATAAGTAGTTCCATGATTAACCCAAGGGAGTGCCTTGGGCCTGAAAGCCTA
CCCAATGATCACCTTAGGTCCGTAAGGATTTACCAGCTTGATCAGATATGTACCTCCAGTCTACC
CATATAATATCCCAATAAAACAGTTCGAGTATAACTAGTGAAAACATAAAACCATAGTTCATAAA
CCAATAATTTCCATGATTCCATAAATCAAGAACAATTCATATTCTTCGATGATAACTGTAATCGG
AGATCACATATCATGTTGTCATGGTTCATAAA
Done.