Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397254.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_30.0, 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: 15579451
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 73860 characters in sequence are not A, C, G, or T
File 12 of 32
Found at i:6364754 original size:18 final size:18
Alignment explanation
Indices: 6364731--6364776 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
6364721 AAATCATTGC
6364731 CAATATGATTAGTAAGTA
1 CAATATGATTAGTAAGTA
6364749 CAATATGATTAGTAAGTA
1 CAATATGATTAGTAAGTA
*
6364767 CAAGATGATT
1 CAATATGATT
6364777 TATAACTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (18 bp):
CAATATGATTAGTAAGTA
Found at i:6373002 original size:73 final size:73
Alignment explanation
Indices: 6372880--6373022 Score: 232
Period size: 73 Copynumber: 2.0 Consensus size: 73
6372870 AACTAGGAGC
* * * * **
6372880 AAAGTGAAATCAACAATTCTGACTTGAACATAGGAATAGGTCGTTTAGGTTTGTTTAAGGAGGAA
1 AAAGTGAAATCAACAATTCTGACTAGAACATAGGAATAAGTCATCTAGGTTTGTAGAAGGAGGAA
6372945 CTTTGAGG
66 CTTTGAGG
6372953 AAAGTGAAATCAACAATTCTGACTAGAACATAGGAATAAGTCATCTAGGTTTGTAGAAGGAGGAA
1 AAAGTGAAATCAACAATTCTGACTAGAACATAGGAATAAGTCATCTAGGTTTGTAGAAGGAGGAA
6373018 CTTTG
66 CTTTG
6373023 TAAAGTAAGA
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 64 1.00
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.28
Consensus pattern (73 bp):
AAAGTGAAATCAACAATTCTGACTAGAACATAGGAATAAGTCATCTAGGTTTGTAGAAGGAGGAA
CTTTGAGG
Found at i:6381496 original size:2 final size:2
Alignment explanation
Indices: 6381489--6381524 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
6381479 CAAGTAACAA
6381489 AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6381525 ATTTGATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6390681 original size:89 final size:89
Alignment explanation
Indices: 6390530--6390705 Score: 325
Period size: 89 Copynumber: 2.0 Consensus size: 89
6390520 CCTCTTACCA
*
6390530 CTTAAGTTGATACTTAACTTAATATAAGTTAGATTAATTGACTAATTGTAACGATCCAAATCCAA
1 CTTAAGTTGATACTTAACTTAATATAACTTAGATTAATTGACTAATTGTAACGATCCAAATCCAA
* *
6390595 CCACTGGCCTAGTAATTTTTTGAG
66 CCACTGACCTAGCAATTTTTTGAG
6390619 CTTAAGTTGATACTTAACTTAATATAACTTAGATTAATTGACTAATTGTAACGATCCAAATCCAA
1 CTTAAGTTGATACTTAACTTAATATAACTTAGATTAATTGACTAATTGTAACGATCCAAATCCAA
6390684 CCACTGACCTAGCAATTTTTTG
66 CCACTGACCTAGCAATTTTTTG
6390706 GGTTTAAACC
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
89 84 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (89 bp):
CTTAAGTTGATACTTAACTTAATATAACTTAGATTAATTGACTAATTGTAACGATCCAAATCCAA
CCACTGACCTAGCAATTTTTTGAG
Found at i:6390880 original size:20 final size:20
Alignment explanation
Indices: 6390855--6390893 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
6390845 GTCCTCATCA
6390855 AGGCCACACATCACATCCAC
1 AGGCCACACATCACATCCAC
*
6390875 AGGCCATACATCACATCCA
1 AGGCCACACATCACATCCA
6390894 AATCCTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.41, G:0.10, T:0.13
Consensus pattern (20 bp):
AGGCCACACATCACATCCAC
Found at i:6391194 original size:20 final size:20
Alignment explanation
Indices: 6391169--6391211 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
6391159 GTCCTCATCA
6391169 AGGCCACACATCACATCCAC
1 AGGCCACACATCACATCCAC
* *
6391189 AGGCCATACATCACATCTAC
1 AGGCCACACATCACATCCAC
6391209 AGG
1 AGG
6391212 ACCAAGATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.37, G:0.14, T:0.14
Consensus pattern (20 bp):
AGGCCACACATCACATCCAC
Found at i:6391280 original size:25 final size:24
Alignment explanation
Indices: 6391211--6391282 Score: 71
Period size: 25 Copynumber: 3.1 Consensus size: 24
6391201 ACATCTACAG
6391211 GACCAAGATCTCATTAGAG--C--
1 GACCAAGATCTCATTAGAGCACAT
* * *
6391231 GACCAAGATCTCATCACATCTACAT
1 GACCAAGATCTCATTAGAGC-ACAT
6391256 GACCAAGATCTCATTAGAGCAACAT
1 GACCAAGATCTCATTAGAGC-ACAT
6391281 GA
1 GA
6391283 AAGCTCACGT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
20 16 0.40
23 1 0.03
25 23 0.57
ACGTcount: A:0.38, C:0.26, G:0.15, T:0.21
Consensus pattern (24 bp):
GACCAAGATCTCATTAGAGCACAT
Found at i:6391668 original size:123 final size:124
Alignment explanation
Indices: 6391443--6391671 Score: 316
Period size: 123 Copynumber: 1.9 Consensus size: 124
6391433 GTCTTAACAA
* *
6391443 TCACATTCACATCAGATGTGGGATGTTAGGTATCACAATCACACCCACTCAAATCCTTAATGTCC
1 TCACATTCACATCAGATGTGAGATGTTAGGTATCACAATCACACCCACTCAAATACTTAATGTCC
*
6391508 TCATCAAGGCCACACATTACATCCATAGGACCAAGATCTCATTAGAGTAATGTGAAAGT
66 TCATCAAGGCCACACATCACATCCATAGGACCAAGATCTCATTAGAGTAATGTGAAAGT
* ** * * * *
6391567 TCACA-TCACATCAGATGTGAGATGTTGGGTATCACAATTTCATCCACTCAAATATTTGATGTTC
1 TCACATTCACATCAGATGTGAGATGTTAGGTATCACAATCACACCCACTCAAATACTTAATGTCC
* ** * *
6391631 TCATTAAGGTTACACATCACATTCATAGGATCAAGATCTCA
66 TCATCAAGGCCACACATCACATCCATAGGACCAAGATCTCA
6391672 ACAGAGCTTT
Statistics
Matches: 90, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
123 85 0.94
124 5 0.06
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (124 bp):
TCACATTCACATCAGATGTGAGATGTTAGGTATCACAATCACACCCACTCAAATACTTAATGTCC
TCATCAAGGCCACACATCACATCCATAGGACCAAGATCTCATTAGAGTAATGTGAAAGT
Found at i:6391769 original size:102 final size:102
Alignment explanation
Indices: 6391580--6391780 Score: 269
Period size: 102 Copynumber: 2.0 Consensus size: 102
6391570 CATCACATCA
** * * * * * *
6391580 GATGTGAGATGTTGGGTATCACAATTTCATCCACTCAAATATTTGATGTTCTCATTAAGGTTACA
1 GATGTGAGATGTTGGGTATCACAATCCCACCCACTCAAATACTTGATGTCCTCATCAAAGCTACA
*
6391645 CATCACATTCATAGGATCAAGATCTCAACAGAGCTTT
66 CATCACATCCATAGGATCAAGATCTCAACAGAGCTTT
* *
6391682 GATGTGAGATGTTGGGTATCACAATCCCACCCATTCAAATCCTTGATGTCCTCATCAAAGCTACA
1 GATGTGAGATGTTGGGTATCACAATCCCACCCACTCAAATACTTGATGTCCTCATCAAAGCTACA
* *
6391747 CATCACATCCATCGGA-CTAAGATCTCACCAGAGC
66 CATCACATCCATAGGATC-AAGATCTCAACAGAGC
6391781 AATGTGAAAG
Statistics
Matches: 85, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
101 1 0.01
102 84 0.99
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (102 bp):
GATGTGAGATGTTGGGTATCACAATCCCACCCACTCAAATACTTGATGTCCTCATCAAAGCTACA
CATCACATCCATAGGATCAAGATCTCAACAGAGCTTT
Found at i:6393521 original size:19 final size:20
Alignment explanation
Indices: 6393499--6393563 Score: 60
Period size: 24 Copynumber: 3.0 Consensus size: 20
6393489 TCATAATCTA
6393499 ATTATAATTAACTAA-TAAT
1 ATTATAATTAACTAACTAAT
* *
6393518 ATTATAATAGAACTCTAATTAGAT
1 ATTATAAT-TAA--CTAACTA-AT
6393542 ATTATAACTTAACTAACTAAT
1 ATTATAA-TTAACTAACTAAT
6393563 A
1 A
6393564 GTATTATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
19 8 0.22
20 2 0.05
21 3 0.08
22 10 0.27
23 2 0.05
24 11 0.30
25 1 0.03
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.38
Consensus pattern (20 bp):
ATTATAATTAACTAACTAAT
Found at i:6407131 original size:12 final size:12
Alignment explanation
Indices: 6407114--6407157 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
6407104 GTCAAACACC
6407114 AATAATAATTCT
1 AATAATAATTCT
**
6407126 AATAATAATAAT
1 AATAATAATTCT
6407138 AATAATAATTACT
1 AATAATAATT-CT
6407151 -ATAATAA
1 AATAATAA
6407158 CAACTCCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 26 0.96
13 1 0.04
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (12 bp):
AATAATAATTCT
Found at i:6422606 original size:2 final size:2
Alignment explanation
Indices: 6422599--6422628 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6422589 TTCCAAGGAA
6422599 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
6422629 CTTGCAAGCG
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:6432353 original size:20 final size:20
Alignment explanation
Indices: 6432328--6432367 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
6432318 TGAAAGGTTT
6432328 TTTATTATAATTATAAAATA
1 TTTATTATAATTATAAAATA
**
6432348 TTTATTATTTTTATAAAATA
1 TTTATTATAATTATAAAATA
6432368 AATTCAGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTATTATAATTATAAAATA
Found at i:6432925 original size:15 final size:13
Alignment explanation
Indices: 6432890--6432943 Score: 65
Period size: 13 Copynumber: 4.1 Consensus size: 13
6432880 AAAGATAAAA
6432890 TTTTTATTTA-AT
1 TTTTTATTTATAT
6432902 TTTTTATTTATAT
1 TTTTTATTTATAT
6432915 TATTATTATTTATAT
1 T-TT-TTATTTATAT
* *
6432930 TTTTAAATTATAT
1 TTTTTATTTATAT
6432943 T
1 T
6432944 CTATTTACTC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
12 10 0.27
13 12 0.32
14 4 0.11
15 11 0.30
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTATTTATAT
Found at i:6432948 original size:27 final size:27
Alignment explanation
Indices: 6432893--6432948 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
6432883 GATAAAATTT
* * *
6432893 TTATTTAATTTTTTATTTATATTATTA
1 TTATTTAATTTTTAAATTATATTACTA
6432920 TTATTTATATTTTTAAATTATATT-CTA
1 TTATTTA-ATTTTTAAATTATATTACTA
6432947 TT
1 TT
6432949 TACTCATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (27 bp):
TTATTTAATTTTTAAATTATATTACTA
Found at i:6433088 original size:15 final size:16
Alignment explanation
Indices: 6433070--6433103 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
6433060 TATTATGTGG
*
6433070 ATTTT-ATTTTTAATA
1 ATTTTAATTTTTAAAA
6433085 ATTTTAATTTTTAAAA
1 ATTTTAATTTTTAAAA
6433101 ATT
1 ATT
6433104 AAAAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTAATTTTTAAAA
Found at i:6437666 original size:27 final size:28
Alignment explanation
Indices: 6437636--6437704 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
6437626 ATATCAAATA
* * *
6437636 TTTATGTTGTGTTTCATCATG-TTCTCT
1 TTTATGTCGTGTTTCATCACGTTTATCT
* *
6437663 TTTATATCGTGTTTCATTACGTTTATCT
1 TTTATGTCGTGTTTCATCACGTTTATCT
6437691 TTTATGTCGTGTTT
1 TTTATGTCGTGTTT
6437705 TGTAATATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
27 17 0.49
28 18 0.51
ACGTcount: A:0.13, C:0.13, G:0.14, T:0.59
Consensus pattern (28 bp):
TTTATGTCGTGTTTCATCACGTTTATCT
Found at i:6446470 original size:31 final size:29
Alignment explanation
Indices: 6446433--6446503 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 29
6446423 ATATAAAATA
6446433 TTAATAATATTTAGTAATAATTATATTATAT
1 TTAATAATATTTAGTAA-AATTAT-TTATAT
* *
6446464 TTAATAATATTTATTTAAATTATTTATAT
1 TTAATAATATTTAGTAAAATTATTTATAT
*
6446493 ATAAT-ATATTT
1 TTAATAATATTT
6446504 TTTAAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 6 0.16
29 10 0.27
30 6 0.16
31 15 0.41
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (29 bp):
TTAATAATATTTAGTAAAATTATTTATAT
Found at i:6446473 original size:15 final size:14
Alignment explanation
Indices: 6446433--6446519 Score: 65
Period size: 15 Copynumber: 6.1 Consensus size: 14
6446423 ATATAAAATA
6446433 TTAATAATATTTAGT
1 TTAATAATATTTA-T
* *
6446448 AATAATTATATTATAT
1 -TTAATAATATT-TAT
6446464 TTAATAATATTTAT
1 TTAATAATATTTAT
*
6446478 TTAA-ATTATTTAT
1 TTAATAATATTTAT
6446491 ATATAAT-ATATTT-T
1 -T-TAATAATATTTAT
6446505 TTAA-AATATATTAT
1 TTAATAATAT-TTAT
6446519 T
1 T
6446520 AATGGTCATT
Statistics
Matches: 58, Mismatches: 6, Indels: 16
0.73 0.08 0.20
Matches are distributed among these distances:
12 7 0.12
13 11 0.19
14 11 0.19
15 17 0.29
16 10 0.17
17 2 0.03
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (14 bp):
TTAATAATATTTAT
Found at i:6446475 original size:10 final size:10
Alignment explanation
Indices: 6446429--6446476 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
6446419 TTATATATAA
6446429 AATA-TTAAT
1 AATATTTAAT
*
6446438 AATATTTAGT
1 AATATTTAAT
*
6446448 AATAATTATAT
1 AATATTTA-AT
*
6446459 TATATTTAAT
1 AATATTTAAT
6446469 AATATTTA
1 AATATTTA
6446477 TTTAAATTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
9 4 0.13
10 20 0.65
11 7 0.23
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (10 bp):
AATATTTAAT
Found at i:6446516 original size:29 final size:30
Alignment explanation
Indices: 6446430--6446516 Score: 85
Period size: 29 Copynumber: 3.0 Consensus size: 30
6446420 TATATATAAA
* *
6446430 ATAT-TAATAATATTTAGTAATAAT-TATATT
1 ATATATAATAATATTTATTTA-AATATAT-TT
*
6446460 ATATTTAATAATATTTATTTAAAT-TATTT
1 ATATATAATAATATTTATTTAAATATATTT
6446489 ATATATAAT-ATATTT-TTTAAAATATATT
1 ATATATAATAATATTTATTT-AAATATATT
6446517 ATTAATGGTC
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
27 3 0.06
28 10 0.20
29 14 0.27
30 10 0.20
31 14 0.27
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (30 bp):
ATATATAATAATATTTATTTAAATATATTT
Found at i:6451059 original size:111 final size:111
Alignment explanation
Indices: 6450865--6451077 Score: 390
Period size: 111 Copynumber: 1.9 Consensus size: 111
6450855 TTTCTTTGCC
* *
6450865 AATTTGGGGACGAAATTGAATATGTCAGTGGTATTTGTAATCTTTCAGTTTTATCTCTTAAATTG
1 AATTTGGGGACGAAATCGAATATGTCAGTGGTATTCGTAATCTTTCAGTTTTATCTCTTAAATTG
*
6450930 GATACGTCGAAGCAATGGTCATGGGCGTCTTACTCTATTATCTTTG
66 GATACGTCGAAGAAATGGTCATGGGCGTCTTACTCTATTATCTTTG
6450976 AATTTGGGGACGAAATCGAATATGTCAGTGGTATTCGTAATCTTTCAGTTTTATCTCTTAAATTG
1 AATTTGGGGACGAAATCGAATATGTCAGTGGTATTCGTAATCTTTCAGTTTTATCTCTTAAATTG
*
6451041 GATATGTCGAAGAAATGGTCATGGGCGTCTTACTCTA
66 GATACGTCGAAGAAATGGTCATGGGCGTCTTACTCTA
6451078 CACCTCTGGC
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 98 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (111 bp):
AATTTGGGGACGAAATCGAATATGTCAGTGGTATTCGTAATCTTTCAGTTTTATCTCTTAAATTG
GATACGTCGAAGAAATGGTCATGGGCGTCTTACTCTATTATCTTTG
Found at i:6464959 original size:21 final size:21
Alignment explanation
Indices: 6464917--6464960 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
6464907 TGTTGAGTCG
* *
6464917 TTAATCAATTTAATTAAATTT
1 TTAATCAATTAAATCAAATTT
* *
6464938 TTAATTAATTAAATCAATTTT
1 TTAATCAATTAAATCAAATTT
6464959 TT
1 TT
6464961 TTATAAATGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
TTAATCAATTAAATCAAATTT
Found at i:6478014 original size:21 final size:19
Alignment explanation
Indices: 6477976--6478016 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
6477966 TGATAATTTG
*
6477976 TATTATTTGATTTTTTTAT
1 TATTATTTGATGTTTTTAT
6477995 TATTAATTTGAATGTTTTTAT
1 TATT-ATTTG-ATGTTTTTAT
6478016 T
1 T
6478017 TTAGTATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 5 0.26
21 10 0.53
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.68
Consensus pattern (19 bp):
TATTATTTGATGTTTTTAT
Found at i:6486457 original size:16 final size:17
Alignment explanation
Indices: 6486436--6486468 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
6486426 NNNAAAAATT
6486436 AAAATT-TAAATATCTC
1 AAAATTATAAATATCTC
6486452 AAAATTAATAAATATCT
1 AAAATT-ATAAATATCT
6486469 TATCCATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAATTATAAATATCTC
Found at i:6488176 original size:15 final size:15
Alignment explanation
Indices: 6488156--6488189 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
6488146 CAGTTATGTG
* *
6488156 AATTTTATTTTTTAT
1 AATTTTAATTTTTAA
6488171 AATTTTAATTTTTAA
1 AATTTTAATTTTTAA
6488186 AATT
1 AATT
6488190 AATAAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
AATTTTAATTTTTAA
Found at i:6488469 original size:20 final size:23
Alignment explanation
Indices: 6488432--6488476 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
6488422 TATTTAATTA
6488432 TTTATATTTTATGTATTAT-AGT
1 TTTATATTTTATGTATTATAAGT
6488454 TTTATA-TTTA-GTATTATAAGT
1 TTTATATTTTATGTATTATAAGT
6488475 TT
1 TT
6488477 AAATAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.32
21 9 0.41
22 6 0.27
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (23 bp):
TTTATATTTTATGTATTATAAGT
Found at i:6489509 original size:347 final size:338
Alignment explanation
Indices: 6488851--6489561 Score: 870
Period size: 346 Copynumber: 2.1 Consensus size: 338
6488841 NNNNNNNNNN
* * * * *
6488851 TAATAATTTTATAAATTATAATTTTTGTAATGTTAACACAAAATAGAAAGTAAATATGTTTATGT
1 TAATAATTTTATAAGTTATAATTTTTATAATATTAACACAAAATAAAAAGTAAATATGTTTATAT
* * * ** * ** *
6488916 TTAAAATGTATATATATTAAAAGTATTTTAGTATATATATAATAGTAATTATATTTGTTATAAAC
66 TTAAAATATATATAAACTAAAAGTATTTTAACACATATATAATAGTAATTATATTCCTCATAAAC
* * *
6488981 AAACTCAATGTCTACAAAGTAATATATTAAAAAACATTACAAGTCAATTAATAATCAAAGTTTTA
131 AAACTCAATATATACAAAGTAATATATTAAAAAACATCACAAGTCAATTAATAATCAAAGTTTTA
* * * * * * *
6489046 TTAATTAATTTAATTAATTTTATGAGTTTATCCTTAATTACATGAAATTAAAAAAAATAATTAAG
196 TGAATCAATTTAATTAATTATATGAGTTTAGCCTTAATTACATAAAATTAAAAAAAATAACTAAA
* *
6489111 TTTCAAAACTATTATAATCTCACAACTTCTTTTTAGATTTATATATTATAAGTTCATATAAATAA
261 TTTCAAAACTATTATAATCTCACAACTTCTCTTTAGATTTATATATTATAAG-T--TATAAACAA
*
6489176 AGGTATATATACTGTAAT
323 AGGTATA-A-ACTATAAT
* * *
6489194 TAATAGTTTTATAAGTTATAATTTTTAT-ATATTAACATAAAATAAAAAGTAGATATGTTTATAT
1 TAATAATTTTATAAGTTATAATTTTTATAATATTAACACAAAATAAAAAGTAAATATGTTTATAT
*
6489258 TTAAAGTACATATATGTAAACTAAAAG-ATTTTAACACATATATAATAGTAATTATATTCCTCAT
66 TT-AA--A-ATATATATAAACTAAAAGTATTTTAACACATATATAATAGTAATTATATTCCTCAT
** * * * * * *
6489322 AAATGAACTTAATATATATAAAGTATATATATTAAAAGACATCACAAGTTAATTAATAATTATAG
127 AAACAAACTCAATATATACAAAGTA-ATATATTAAAAAACATCACAAGTCAATTAATAATCAAAG
* *
6489387 TTTTATGAATCAATTTAATTAATTATATGAGTTT-GCCTTTAATTGCATAAAATTTTAAAAAAAT
191 TTTTATGAATCAATTTAATTAATTATATGAGTTTAGCC-TTAATTACATAAAA-TTAAAAAAAAT
* * * *
6489451 AACTAAATTTCAAAACTATTCTAATTTCATAATTTCTCTTTAGATTTATATATTATAAGTTATAA
254 AACTAAATTTCAAAACTATTATAATCTCACAACTTCTCTTTAGATTTATATATTATAAGTTATAA
*
6489516 ACAAAGGTATAAATTATAAT
319 ACAAAGGTATAAACTATAAT
*
6489536 TAATAATTTTATAAGTTATATTTTTT
1 TAATAATTTTATAAGTTATAATTTTT
6489562 GTAAGTTTTG
Statistics
Matches: 313, Mismatches: 48, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
342 63 0.20
343 28 0.09
344 15 0.05
345 53 0.17
346 92 0.29
347 62 0.20
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.42
Consensus pattern (338 bp):
TAATAATTTTATAAGTTATAATTTTTATAATATTAACACAAAATAAAAAGTAAATATGTTTATAT
TTAAAATATATATAAACTAAAAGTATTTTAACACATATATAATAGTAATTATATTCCTCATAAAC
AAACTCAATATATACAAAGTAATATATTAAAAAACATCACAAGTCAATTAATAATCAAAGTTTTA
TGAATCAATTTAATTAATTATATGAGTTTAGCCTTAATTACATAAAATTAAAAAAAATAACTAAA
TTTCAAAACTATTATAATCTCACAACTTCTCTTTAGATTTATATATTATAAGTTATAAACAAAGG
TATAAACTATAAT
Found at i:6489781 original size:247 final size:246
Alignment explanation
Indices: 6489347--6489809 Score: 623
Period size: 247 Copynumber: 1.9 Consensus size: 246
6489337 ATATAAAGTA
*
6489347 TATATATTAAAAGACATCACAAGTTAATTAATAATTATAGTTTTATGAATCAATTTAATTAATTA
1 TATATATTAAAAGACATCACAAGTCAATTAATAATTATAGTTTTATGAATCAATTTAATTAA-TA
* *
6489412 TATGAGTTTGCCTTTAATTGCATAAAATTTTAAAAAAATAACTAAATTTCAAAACTATTCTAATT
65 TATAAGTTTGCCTTTAATTGCATAAAA-TTTAAAAAAATAACTAAATTCCAAAACTATTCTAATT
* ** *
6489477 TCATAATTTCTCTTTAGATTTATATATTATAAGTTATAAACAAAGGTATAAATTATAATTAATAA
129 TCAAAAGCTCTCTTTAGATATATATATTATAAGTTATAAACAAAGGTATAAATTATAATTAATAA
*
6489542 TTTTATAAGTTAT-ATTTTTTGTAAGTTTTGTAAATTAACACAATATATAAAC
194 TCTTATAAGTTATAATTTTTTGTAAGTTTTGTAAATTAACACAATATATAAAC
* *
6489594 TATATATTAAAAGACATTACAAGTCAATTAATAATTATAGTTTTATGAATTAATTTAATTAA-AT
1 TATATATTAAAAGACATCACAAGTCAATTAATAATTATAGTTTTATGAATCAATTTAATTAATAT
* ** * ** *
6489658 ATAATTTTTTC-TTAATTTCATAAAA-TTAAAAAAATAGTTAGATTCCAAAACTATTCTAATATT
66 ATAAGTTTGCCTTTAATTGCATAAAATTTAAAAAAATAACTAAATTCCAAAACTATTCTAAT-TT
* * *
6489721 -AAAAGCTCTTTTTA-AGTATATATATTATAAGTTTATATAAACAATGGTAAATATATTATAATT
130 CAAAAGCTCTCTTTAGA-TATATATATTATAAG--T-TATAAACAAAGGT--ATAAATTATAATT
6489784 AATAATCTTATAAGTTATAATTTTTT
189 AATAATCTTATAAGTTATAATTTTTT
6489810 TAATGTTAAT
Statistics
Matches: 188, Mismatches: 20, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
241 1 0.01
242 55 0.29
243 2 0.01
244 14 0.07
245 21 0.11
247 88 0.47
248 7 0.04
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (246 bp):
TATATATTAAAAGACATCACAAGTCAATTAATAATTATAGTTTTATGAATCAATTTAATTAATAT
ATAAGTTTGCCTTTAATTGCATAAAATTTAAAAAAATAACTAAATTCCAAAACTATTCTAATTTC
AAAAGCTCTCTTTAGATATATATATTATAAGTTATAAACAAAGGTATAAATTATAATTAATAATC
TTATAAGTTATAATTTTTTGTAAGTTTTGTAAATTAACACAATATATAAAC
Found at i:6505650 original size:246 final size:244
Alignment explanation
Indices: 6505179--6505662 Score: 776
Period size: 246 Copynumber: 2.0 Consensus size: 244
6505169 ATATTTGGTT
6505179 AGCAATACTTCGTGGCATGTCATCCTACAACACCAGTGTTCACCTGTCCATTCAACATTTCCAAG
1 AGCAATACTTCGTGGCATGTCATCCTACAACACCAGTGTTCACCTGTCCATTCAACATTTCCAAG
* * *
6505244 GTAGTAAAATTGTGCTCTAATGCACACTTTTGCAGTGAAAACTCAGATAAAAGATAAACAAGGGC
66 GCAGTAAAATTGTGCACTAATGCACACTTTTGCAGTGAAAACTCAAATAAAAGATAAACAAGGGC
* * *
6505309 CAATAGAAGGCAAGGTGAGGACACGAAAAAAGAATGGATATCTCTTTAATCAACAAATCTAAGCC
131 AAATAGAAGACAAGGCGAGGACACGAAAAAAGAATGGATATCTCTTTAATCAACAAATCTAAGCC
* *
6505374 TTGGTAAACTAATTGGACCATGTCATCTTTAGGAAAAAGATAAACCCTA
196 TTGGTAAACTAATAGGACCATATCATCTTTAGGAAAAAGATAAACCCTA
* *
6505423 AGCAATACTTCGTGGCATGTCATCCTACAGCACCAGTGTTCACCTGTCCATTCAACATTTCCATG
1 AGCAATACTTCGTGGCATGTCATCCTACAACACCAGTGTTCACCTGTCCATTCAACATTTCCAAG
* *
6505488 GCAGTAAACTTGTGCACTAATGCACACTTTTGCAGTGAACACACTCAAATTAAAGATAATA-AAG
66 GCAGTAAAATTGTGCACTAATGCACACTTTTGCAGTGAA-A-ACTCAAATAAAAGATAA-ACAAG
*
6505552 GGCAAATAGAAGACATA-GCGAGGACACGGAAAAAGAATGGATATCTCTTTAATCAACAAATCTA
128 GGCAAATAGAAGACA-AGGCGAGGACACGAAAAAAGAATGGATATCTCTTTAATCAACAAATCTA
*
6505616 AGCCTTGGTTAACTAATAGGA-CAGTATCATCTTTAGGAAAAAGATAA
192 AGCCTTGGTAAACTAATAGGACCA-TATCATCTTTAGGAAAAAGATAA
6505663 TAATAAAGAT
Statistics
Matches: 221, Mismatches: 14, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
244 99 0.45
245 3 0.01
246 117 0.53
247 2 0.01
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.25
Consensus pattern (244 bp):
AGCAATACTTCGTGGCATGTCATCCTACAACACCAGTGTTCACCTGTCCATTCAACATTTCCAAG
GCAGTAAAATTGTGCACTAATGCACACTTTTGCAGTGAAAACTCAAATAAAAGATAAACAAGGGC
AAATAGAAGACAAGGCGAGGACACGAAAAAAGAATGGATATCTCTTTAATCAACAAATCTAAGCC
TTGGTAAACTAATAGGACCATATCATCTTTAGGAAAAAGATAAACCCTA
Found at i:6510223 original size:2 final size:2
Alignment explanation
Indices: 6510216--6510245 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6510206 CTTCTTCCTG
6510216 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
6510246 CGGACTCTCT
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:6514898 original size:21 final size:23
Alignment explanation
Indices: 6514867--6514908 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
6514857 AAAAAACTCA
6514867 TAAATTTAAAT-AATTTTTATTT
1 TAAATTTAAATAAATTTTTATTT
6514889 TAAA-TTAAATAAATTTTTAT
1 TAAATTTAAATAAATTTTTAT
6514909 AATTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TAAATTTAAATAAATTTTTATTT
Found at i:6514921 original size:25 final size:21
Alignment explanation
Indices: 6514867--6514908 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6514857 AAAAAACTCA
*
6514867 TAAATTTAAATAATTTTTATT
1 TAAAATTAAATAATTTTTATT
*
6514888 TTAAATTAAATAAATTTTTAT
1 TAAAATTAAAT-AATTTTTAT
6514909 AATTAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TAAAATTAAATAATTTTTATT
Found at i:6515046 original size:36 final size:33
Alignment explanation
Indices: 6514956--6515033 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
6514946 TACATTAAAG
* * *
6514956 TGATATGTTAAAATATTATAATTGATGATGATA
1 TGATATATTAATATATTATAATTGATGATGACA
*
6514989 TTATATATTAATATATTATAATTGATGATGACA
1 TGATATATTAATATATTATAATTGATGATGACA
6515022 TGATATATTAAT
1 TGATATATTAAT
6515034 TTGATATAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.42, C:0.01, G:0.12, T:0.45
Consensus pattern (33 bp):
TGATATATTAATATATTATAATTGATGATGACA
Found at i:6515109 original size:15 final size:15
Alignment explanation
Indices: 6515089--6515118 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6515079 ATATACAATG
*
6515089 ATTAATAACATTTAA
1 ATTAATAACAATTAA
6515104 ATTAATAACAATTAA
1 ATTAATAACAATTAA
6515119 TCAATTATTA
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:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (15 bp):
ATTAATAACAATTAA
Found at i:6516652 original size:15 final size:15
Alignment explanation
Indices: 6516628--6516662 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
6516618 TTCTGCTGGC
*
6516628 TTCTTTGGCTCCTCT
1 TTCTTGGGCTCCTCT
*
6516643 TTCTTGGGCTCTTCT
1 TTCTTGGGCTCCTCT
6516658 TTCTT
1 TTCTT
6516663 CTTCTCTGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.29, G:0.14, T:0.57
Consensus pattern (15 bp):
TTCTTGGGCTCCTCT
Found at i:6518240 original size:42 final size:42
Alignment explanation
Indices: 6518193--6518288 Score: 183
Period size: 42 Copynumber: 2.3 Consensus size: 42
6518183 TCCCACCACT
*
6518193 TTTCCCTCCAAAGTTTTTAATTCAAAGTATTCCCCCAAAAGA
1 TTTCCCTCCAAAGTTTTCAATTCAAAGTATTCCCCCAAAAGA
6518235 TTTCCCTCCAAAGTTTTCAATTCAAAGTATTCCCCCAAAAGA
1 TTTCCCTCCAAAGTTTTCAATTCAAAGTATTCCCCCAAAAGA
6518277 TTTCCCTCCAAA
1 TTTCCCTCCAAA
6518289 ACATTTGGGA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.32, C:0.29, G:0.06, T:0.32
Consensus pattern (42 bp):
TTTCCCTCCAAAGTTTTCAATTCAAAGTATTCCCCCAAAAGA
Found at i:6518431 original size:35 final size:34
Alignment explanation
Indices: 6518375--6518440 Score: 96
Period size: 35 Copynumber: 1.9 Consensus size: 34
6518365 GGGCTGGCAC
*
6518375 CCTCTTGGCCTCTTGGCGGGTCCGGACTGTGTCA
1 CCTCTTGGCCTCCTGGCGGGTCCGGACTGTGTCA
* *
6518409 CCTCTTGGGCCTCCTGGTGGGTCTGGACTGTG
1 CCTCTT-GGCCTCCTGGCGGGTCCGGACTGTG
6518441 GCCGTGACAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 6 0.21
35 22 0.79
ACGTcount: A:0.05, C:0.30, G:0.35, T:0.30
Consensus pattern (34 bp):
CCTCTTGGCCTCCTGGCGGGTCCGGACTGTGTCA
Found at i:6525194 original size:27 final size:27
Alignment explanation
Indices: 6525164--6525218 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
6525154 CAATTTTGCC
*
6525164 TGATATTGCCTCAGACGTGATTGCTTA
1 TGATATTGCCACAGACGTGATTGCTTA
*
6525191 TGATATTGCCACAGATGTGATTGCTTA
1 TGATATTGCCACAGACGTGATTGCTTA
6525218 T
1 T
6525219 CTTTCTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (27 bp):
TGATATTGCCACAGACGTGATTGCTTA
Found at i:6533516 original size:7 final size:7
Alignment explanation
Indices: 6533504--6533529 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
6533494 CCTTCAGGGT
6533504 AAATTCA
1 AAATTCA
6533511 AAATTCA
1 AAATTCA
6533518 AAATTCA
1 AAATTCA
6533525 AAATT
1 AAATT
6533530 TGGCCTAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.31
Consensus pattern (7 bp):
AAATTCA
Found at i:6534907 original size:34 final size:34
Alignment explanation
Indices: 6534864--6534931 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
6534854 AGGATAAGAG
*
6534864 AACATTTTTGAAATTAAATATTCTCGGCAAACTT
1 AACATTTTTGAAATTAAATATGCTCGGCAAACTT
6534898 AACATTTTTGAAATTAAATATGCTCGGCAAACTT
1 AACATTTTTGAAATTAAATATGCTCGGCAAACTT
6534932 GTCGGTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (34 bp):
AACATTTTTGAAATTAAATATGCTCGGCAAACTT
Found at i:6542380 original size:22 final size:22
Alignment explanation
Indices: 6542355--6542401 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
6542345 TATAAAGGGA
6542355 TACAGTATGCTACCAAAAACAT
1 TACAGTATGCTACCAAAAACAT
6542377 TACAGTATGCTACCAAAAACAT
1 TACAGTATGCTACCAAAAACAT
6542399 TAC
1 TAC
6542402 TAGATGTGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.45, C:0.23, G:0.09, T:0.23
Consensus pattern (22 bp):
TACAGTATGCTACCAAAAACAT
Found at i:6563672 original size:15 final size:15
Alignment explanation
Indices: 6563637--6563665 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
6563627 TGCACGAGGT
6563637 ATTTCCTCTTCTTTC
1 ATTTCCTCTTCTTTC
6563652 ATTTCC-CTTCTTTC
1 ATTTCCTCTTCTTTC
6563666 CGTTTCCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.07, C:0.34, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTCCTCTTCTTTC
Found at i:6564603 original size:144 final size:144
Alignment explanation
Indices: 6564406--6564696 Score: 582
Period size: 144 Copynumber: 2.0 Consensus size: 144
6564396 CTAGGGCCTA
6564406 AGGTGCTTGTCTTAAACATCCTTATCTACTCTTTCATATTGTCTTTATTTTTCATTTGTTTGGTT
1 AGGTGCTTGTCTTAAACATCCTTATCTACTCTTTCATATTGTCTTTATTTTTCATTTGTTTGGTT
6564471 TCCTTAGATTTTTCTTTGTTTTATGGAGCAGGAGGTTGAGGAAGTGGGAGGTCTAGAAGAATTGG
66 TCCTTAGATTTTTCTTTGTTTTATGGAGCAGGAGGTTGAGGAAGTGGGAGGTCTAGAAGAATTGG
6564536 AGAAAGAGATCAAT
131 AGAAAGAGATCAAT
6564550 AGGTGCTTGTCTTAAACATCCTTATCTACTCTTTCATATTGTCTTTATTTTTCATTTGTTTGGTT
1 AGGTGCTTGTCTTAAACATCCTTATCTACTCTTTCATATTGTCTTTATTTTTCATTTGTTTGGTT
6564615 TCCTTAGATTTTTCTTTGTTTTATGGAGCAGGAGGTTGAGGAAGTGGGAGGTCTAGAAGAATTGG
66 TCCTTAGATTTTTCTTTGTTTTATGGAGCAGGAGGTTGAGGAAGTGGGAGGTCTAGAAGAATTGG
6564680 AGAAAGAGATCAAT
131 AGAAAGAGATCAAT
6564694 AGG
1 AGG
6564697 AGAATCAAAT
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
144 147 1.00
ACGTcount: A:0.24, C:0.12, G:0.23, T:0.41
Consensus pattern (144 bp):
AGGTGCTTGTCTTAAACATCCTTATCTACTCTTTCATATTGTCTTTATTTTTCATTTGTTTGGTT
TCCTTAGATTTTTCTTTGTTTTATGGAGCAGGAGGTTGAGGAAGTGGGAGGTCTAGAAGAATTGG
AGAAAGAGATCAAT
Found at i:6580478 original size:33 final size:33
Alignment explanation
Indices: 6580437--6580548 Score: 127
Period size: 33 Copynumber: 3.4 Consensus size: 33
6580427 TTCATGCCAT
*
6580437 GAATTCTGTCGCAGTGGTTGTTCTGAATCTTGT
1 GAATTCTGTCGCAGTGGTTGTTCTGAATCTTGA
* * *
6580470 GAATTCTGTTGCAATGGTTGTTCCGAATCTTGA
1 GAATTCTGTCGCAGTGGTTGTTCTGAATCTTGA
* * * *
6580503 AAACTCTGCCGTAGTGGTCT-TTCTGAATCTTGA
1 GAATTCTGTCGCAGTGGT-TGTTCTGAATCTTGA
*
6580536 GAATTTTGTCGCA
1 GAATTCTGTCGCA
6580549 CTGTCCGTGT
Statistics
Matches: 62, Mismatches: 16, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
33 61 0.98
34 1 0.02
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (33 bp):
GAATTCTGTCGCAGTGGTTGTTCTGAATCTTGA
Found at i:6610509 original size:24 final size:23
Alignment explanation
Indices: 6610478--6610541 Score: 94
Period size: 22 Copynumber: 2.8 Consensus size: 23
6610468 AATTAACTAC
*
6610478 TATAATCAAAAATAATTTTTTTT
1 TATAATCATAAATAATTTTTTTT
6610501 GTATAATCATAAATAA-TTTTTTT
1 -TATAATCATAAATAATTTTTTTT
*
6610524 AATAATCATAAATAATTT
1 TATAATCATAAATAATTT
6610542 AATAATGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
22 14 0.38
23 9 0.24
24 14 0.38
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (23 bp):
TATAATCATAAATAATTTTTTTT
Found at i:6610542 original size:18 final size:17
Alignment explanation
Indices: 6610521--6610556 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
6610511 AAATAATTTT
6610521 TTTAATAATCATAAATAA
1 TTTAATAATCA-AAATAA
*
6610539 TTTAATAATGAAAATAA
1 TTTAATAATCAAAATAA
6610556 T
1 T
6610557 CTCAATTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (17 bp):
TTTAATAATCAAAATAA
Found at i:6611452 original size:60 final size:61
Alignment explanation
Indices: 6611371--6611523 Score: 175
Period size: 60 Copynumber: 2.5 Consensus size: 61
6611361 TGGTGTGGAG
* * *
6611371 AGTTCCCACAAGTAAGTAAAAGGGGACCTAAAGCCTCAACTTTTATTTGGTGGCAT-GAGA
1 AGTTCCCACAAGTAGGTAAAAGGGGACCTAAAGCCTCAACTTATATTTAGTGGCATAGAGA
* * * * * * *
6611431 AGTTCTCACAAGTAGGTAAAAGAGAACTTAAAACCTCGACTTATATTTAGTGGCATAGGGA
1 AGTTCCCACAAGTAGGTAAAAGGGGACCTAAAGCCTCAACTTATATTTAGTGGCATAGAGA
* * *
6611492 A-TTCCCACGAGCAGGGAAAAGGGGACCTAAAG
1 AGTTCCCACAAGTAGGTAAAAGGGGACCTAAAG
6611524 TCTTGATTTA
Statistics
Matches: 74, Mismatches: 18, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
60 70 0.95
61 4 0.05
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (61 bp):
AGTTCCCACAAGTAGGTAAAAGGGGACCTAAAGCCTCAACTTATATTTAGTGGCATAGAGA
Found at i:6626417 original size:2 final size:2
Alignment explanation
Indices: 6626412--6626445 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
6626402 ATATATAGTA
*
6626412 TG TG TG TG TG -G TG TA TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
6626446 TATAAAGAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (2 bp):
TG
Found at i:6627665 original size:27 final size:27
Alignment explanation
Indices: 6627635--6627688 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
6627625 AATGAATTAG
6627635 GTAGATATAAGATTTA-TTTTCAAAAAA
1 GTAGATATAAGA-TTACTTTTCAAAAAA
6627662 GTAGATATAAGATTACTTTTCAAAAAA
1 GTAGATATAAGATTACTTTTCAAAAAA
6627689 AAAAAAGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 3 0.12
27 23 0.88
ACGTcount: A:0.48, C:0.06, G:0.11, T:0.35
Consensus pattern (27 bp):
GTAGATATAAGATTACTTTTCAAAAAA
Found at i:6628033 original size:31 final size:31
Alignment explanation
Indices: 6627997--6628061 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
6627987 TAGAGTGACA
6627997 TTGTTATCGTATCCCTATGCTATTCTTTAGC
1 TTGTTATCGTATCCCTATGCTATTCTTTAGC
6628028 TTGTTATCGTATCCCTATGCTATTCTTTAGC
1 TTGTTATCGTATCCCTATGCTATTCTTTAGC
6628059 TTG
1 TTG
6628062 AATATTAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.15, C:0.22, G:0.14, T:0.49
Consensus pattern (31 bp):
TTGTTATCGTATCCCTATGCTATTCTTTAGC
Found at i:6630773 original size:4 final size:4
Alignment explanation
Indices: 6630764--6630789 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
6630754 TAAACCAATA
6630764 TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TA
6630790 CGCATATGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:6636643 original size:17 final size:19
Alignment explanation
Indices: 6636618--6636658 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
6636608 AAAAAATTCT
6636618 AGAACAAAAAA-AAATAGAG
1 AGAA-AAAAAAGAAATAGAG
6636637 AGAAAAAAAAGAAATAGAG
1 AGAAAAAAAAGAAATAGAG
6636656 AGA
1 AGA
6636659 CTTGACTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.05
Consensus pattern (19 bp):
AGAAAAAAAAGAAATAGAG
Found at i:6655526 original size:21 final size:21
Alignment explanation
Indices: 6655502--6655541 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
6655492 TTTTTTAAAA
*
6655502 TTTAAAGAT-ATTTTTAATTTT
1 TTTAAA-ATGATTATTAATTTT
6655523 TTTAAAATGATTATTAATT
1 TTTAAAATGATTATTAATT
6655542 GAAGAAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
TTTAAAATGATTATTAATTTT
Found at i:6655657 original size:11 final size:11
Alignment explanation
Indices: 6655630--6655663 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 11
6655620 ATATAATCAC
6655630 ATTATATCTATTG
1 ATTATAT-TA-TG
6655643 ATTATATTATG
1 ATTATATTATG
6655654 ATTATATTAT
1 ATTATATTAT
6655664 AATTTCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 12 0.57
12 2 0.10
13 7 0.33
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (11 bp):
ATTATATTATG
Found at i:6666847 original size:15 final size:16
Alignment explanation
Indices: 6666819--6666856 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
6666809 ATTTAATATT
6666819 TTATAATATAATATAA
1 TTATAATATAATATAA
* *
6666835 TTATAA-ATGATATAG
1 TTATAATATAATATAA
6666850 TTATAAT
1 TTATAAT
6666857 TACAAGTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (16 bp):
TTATAATATAATATAA
Found at i:6666868 original size:21 final size:20
Alignment explanation
Indices: 6666821--6666871 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
6666811 TTAATATTTT
*
6666821 ATAATATAATATAATTATAA
1 ATAATATAATATAATTACAA
* *
6666841 ATGATATAGTTATAATTACAA
1 ATAATATA-ATATAATTACAA
*
6666862 GTAATATAAT
1 ATAATATAAT
6666872 TACAAAAAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (20 bp):
ATAATATAATATAATTACAA
Found at i:6692298 original size:6 final size:6
Alignment explanation
Indices: 6692287--6692313 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
6692277 GGATTTTCTC
6692287 TTCTTT TTCTTT TTCTTT TTCTTT TTC
1 TTCTTT TTCTTT TTCTTT TTCTTT TTC
6692314 CTCTATTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TTCTTT
Found at i:6699509 original size:17 final size:17
Alignment explanation
Indices: 6699483--6699515 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
6699473 TCTGCTCTGT
6699483 TTCTTTTCTTA-TATCC
1 TTCTTTTCTTAGTATCC
6699499 TTCTCTTTCTTAGTATC
1 TTCT-TTTCTTAGTATC
6699516 TAACCAACTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.12, C:0.24, G:0.03, T:0.61
Consensus pattern (17 bp):
TTCTTTTCTTAGTATCC
Found at i:6703386 original size:22 final size:22
Alignment explanation
Indices: 6703347--6703403 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
6703337 CACACCATAC
* **
6703347 TTAAAAATTAATCTCATAATAT
1 TTAAAAATTAGTAACATAATAT
*
6703369 TTAAAAATTAGTAACATAATGT
1 TTAAAAATTAGTAACATAATAT
*
6703391 CTAAAAATTAGTA
1 TTAAAAATTAGTA
6703404 TTGTAAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (22 bp):
TTAAAAATTAGTAACATAATAT
Found at i:6703723 original size:10 final size:10
Alignment explanation
Indices: 6703710--6703771 Score: 54
Period size: 11 Copynumber: 5.8 Consensus size: 10
6703700 TAATTTATCT
6703710 AAAATTATTAA
1 AAAATTATT-A
6703721 AAAATTATTA
1 AAAATTATTA
*
6703731 TCAAATTATACTA
1 -AAAATTAT--TA
6703744 AAAATTAATTA
1 AAAATT-ATTA
*
6703755 AAAATAATT-
1 AAAATTATTA
6703764 AAAATTAT
1 AAAATTAT
6703772 AATAAATAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
9 7 0.16
10 4 0.09
11 23 0.53
12 5 0.12
13 4 0.09
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (10 bp):
AAAATTATTA
Found at i:6708400 original size:2 final size:2
Alignment explanation
Indices: 6708393--6708417 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6708383 TACATATCAC
6708393 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6708418 CATGTATTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6711841 original size:26 final size:26
Alignment explanation
Indices: 6711803--6711857 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
6711793 CGAGTTAAGG
* *
6711803 TATCCATCCACTTTTAATAGTAAAAT
1 TATCCATCAACTTCTAATAGTAAAAT
* * *
6711829 TATCTATCAACTTCTAGTGGTAAAAT
1 TATCCATCAACTTCTAATAGTAAAAT
6711855 TAT
1 TAT
6711858 TCTTAAATTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.40
Consensus pattern (26 bp):
TATCCATCAACTTCTAATAGTAAAAT
Found at i:6712163 original size:54 final size:53
Alignment explanation
Indices: 6712045--6712175 Score: 149
Period size: 53 Copynumber: 2.4 Consensus size: 53
6712035 GATTGGACAG
* * * *
6712045 ATTTATAATTTTTTATTAGTAGCTCGTTTGTCAAATTTACTTTAGAGAATGAAA
1 ATTTATAA-TTTTTATTAATAGCTCATTTATCAAATTCACTTTAGAGAATGAAA
* *
6712099 ATTTATAATTTTTATTAATAGCTCATTTATCACATTCA-TTTCAGAGAATTG-AT
1 ATTTATAATTTTTATTAATAGCTCATTTATCAAATTCACTTT-AGAGAA-TGAAA
*
6712152 ATTTATGAATTTTCATTAATAGCT
1 ATTTAT-AATTTTTATTAATAGCT
6712176 ATATAATAAC
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
52 3 0.04
53 38 0.57
54 26 0.39
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.47
Consensus pattern (53 bp):
ATTTATAATTTTTATTAATAGCTCATTTATCAAATTCACTTTAGAGAATGAAA
Found at i:6714169 original size:22 final size:23
Alignment explanation
Indices: 6714143--6714201 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
6714133 TTTTTTTAAT
6714143 TATTTATTAAA-TTTAATTTATTA
1 TATTTATTAAATTTTAATTT-TTA
**
6714166 -ATTTAAAAAATTTTAATTTTTA
1 TATTTATTAAATTTTAATTTTTA
*
6714188 TATTT-TTAATTTTT
1 TATTTATTAAATTTT
6714202 CAATAAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
22 17 0.59
23 12 0.41
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TATTTATTAAATTTTAATTTTTA
Found at i:6716211 original size:51 final size:51
Alignment explanation
Indices: 6716155--6716257 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
6716145 ATGGAAGGCC
6716155 ACTCCCATGGAAAGGAGGAACCTGTGGCTTCAAAGATGATTGCATTGACGG
1 ACTCCCATGGAAAGGAGGAACCTGTGGCTTCAAAGATGATTGCATTGACGG
6716206 ACTCCCATGGAAAGGAGGAACCTGTGGCTTCAAAGATGATTGCATTGACGG
1 ACTCCCATGGAAAGGAGGAACCTGTGGCTTCAAAGATGATTGCATTGACGG
6716257 A
1 A
6716258 TAGCTTGCCA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.21
Consensus pattern (51 bp):
ACTCCCATGGAAAGGAGGAACCTGTGGCTTCAAAGATGATTGCATTGACGG
Found at i:6717908 original size:20 final size:21
Alignment explanation
Indices: 6717875--6717922 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
6717865 TAAAATATTT
*
6717875 ATTATTTAAATTTAATTATAA
1 ATTAATTAAATTTAATTATAA
* *
6717896 A-TAATTAATTTTAATTTTAA
1 ATTAATTAAATTTAATTATAA
6717916 ATTAATT
1 ATTAATT
6717923 TTTATAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTAATTAAATTTAATTATAA
Found at i:6731715 original size:2 final size:2
Alignment explanation
Indices: 6731708--6731739 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6731698 GCATGCTAGG
6731708 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
6731740 ACACACACAC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:6741067 original size:2 final size:2
Alignment explanation
Indices: 6741060--6741088 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6741050 AGGGGTAATC
6741060 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6741089 AATAACAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6748095 original size:22 final size:21
Alignment explanation
Indices: 6748069--6748111 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
6748059 GATTCTTATC
*
6748069 ATATATGTATTTATGTAGTTTT
1 ATATATGAATTTATGTA-TTTT
6748091 ATATATGAATTTATGTATTTT
1 ATATATGAATTTATGTATTTT
6748112 GTTGCAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (21 bp):
ATATATGAATTTATGTATTTT
Found at i:6762153 original size:13 final size:13
Alignment explanation
Indices: 6762135--6762159 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6762125 TTTTTTATTA
6762135 ATAAAAAATAATT
1 ATAAAAAATAATT
6762148 ATAAAAAATAAT
1 ATAAAAAATAAT
6762160 AAAAAATAAA
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
ATAAAAAATAATT
Found at i:6762296 original size:17 final size:18
Alignment explanation
Indices: 6762274--6762307 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
6762264 AAAATAAAGT
6762274 ATATATTTTGTA-AATTA
1 ATATATTTTGTATAATTA
6762291 ATATATTTTGTATAATT
1 ATATATTTTGTATAATT
6762308 TAAATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (18 bp):
ATATATTTTGTATAATTA
Found at i:6777703 original size:49 final size:50
Alignment explanation
Indices: 6777611--6777709 Score: 146
Period size: 49 Copynumber: 2.0 Consensus size: 50
6777601 AAATAACTAA
*
6777611 TCTCCAACAACCATTCATACCTTTGCTCTCAATGACCACTCTTTGATCTT
1 TCTCCAACAACCATTCATACCTTTGCTCTCAATGAACACTCTTTGATCTT
* * * *
6777661 TCTCCAGCAATCATTCATACC-TTGCTCTCAATGAACATTCTTTTATCTT
1 TCTCCAACAACCATTCATACCTTTGCTCTCAATGAACACTCTTTGATCTT
6777710 ACTCAGAACA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
49 25 0.57
50 19 0.43
ACGTcount: A:0.24, C:0.31, G:0.06, T:0.38
Consensus pattern (50 bp):
TCTCCAACAACCATTCATACCTTTGCTCTCAATGAACACTCTTTGATCTT
Found at i:6780274 original size:24 final size:25
Alignment explanation
Indices: 6780237--6780284 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
6780227 AATTAATATA
*
6780237 TAAATTTTATTTAAATAATAAAATT
1 TAAATTTTATTTAAATAAAAAAATT
*
6780262 TAAA-TTTATTTAATTAAAAAAAT
1 TAAATTTTATTTAAATAAAAAAAT
6780285 AATACTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TAAATTTTATTTAAATAAAAAAATT
Found at i:6780799 original size:21 final size:22
Alignment explanation
Indices: 6780756--6780796 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
6780746 TTAATTTTAT
*
6780756 TAATTATTACTTAAAATACAAG
1 TAATTATTACTTAAAAAACAAG
6780778 TAATT-TT-CTTAAAAAACAA
1 TAATTATTACTTAAAAAACAA
6780797 AGTCACTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 2 0.11
22 5 0.28
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (22 bp):
TAATTATTACTTAAAAAACAAG
Found at i:6830894 original size:36 final size:36
Alignment explanation
Indices: 6830847--6830916 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
6830837 GGGTATACTA
*
6830847 ACAAATGTGTTGTCAAAAAATTGTTTTGAACTAGCG
1 ACAAATGTGTTGTCAAAAAACTGTTTTGAACTAGCG
6830883 ACAAATGTGTTGTCAAAAAACTGTTTTGAACTAG
1 ACAAATGTGTTGTCAAAAAACTGTTTTGAACTAG
6830917 TGACGTTTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (36 bp):
ACAAATGTGTTGTCAAAAAACTGTTTTGAACTAGCG
Found at i:6845648 original size:13 final size:13
Alignment explanation
Indices: 6845630--6845654 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6845620 AATCCTAAAT
6845630 AAATAATTAAAAA
1 AAATAATTAAAAA
6845643 AAATAATTAAAA
1 AAATAATTAAAA
6845655 TCTTAAAAAA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAATTAAAAA
Found at i:6850604 original size:2 final size:2
Alignment explanation
Indices: 6850597--6850626 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6850587 GGAGTGGGAT
6850597 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
6850627 CGCACACTTT
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:6857450 original size:4 final size:4
Alignment explanation
Indices: 6857441--6857482 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
6857431 GAAGAAGAAG
* *
6857441 AAGA AAGA AAGA AAGA AAGA AAAA AATAA AAGA AA-A AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AA-GA AAGA AAGA AAGA AA
6857483 TGGCATGCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.09
4 27 0.79
5 4 0.12
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (4 bp):
AAGA
Found at i:6857456 original size:12 final size:11
Alignment explanation
Indices: 6857425--6857482 Score: 50
Period size: 11 Copynumber: 5.3 Consensus size: 11
6857415 ATAATAATAA
6857425 AAAGAAGAAGAAG
1 AAAGAA-AA-AAG
*
6857438 -AAGAAGAAAG
1 AAAGAAAAAAG
6857448 AAAGAAAGAAAG
1 AAAGAAA-AAAG
*
6857460 AAA-AAAATA-
1 AAAGAAAAAAG
6857469 AAAGAAAAAAG
1 AAAGAAAAAAG
6857480 AAA
1 AAA
6857483 TGGCATGCTA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
9 3 0.08
10 10 0.27
11 12 0.32
12 12 0.32
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.02
Consensus pattern (11 bp):
AAAGAAAAAAG
Found at i:6885586 original size:30 final size:29
Alignment explanation
Indices: 6885545--6885612 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 29
6885535 AAACAAATCA
* *
6885545 TTATATTTTTATTTTAAGTCAAATAAGTTT
1 TTAT-TTTTTATTTTAAATCAAATAAGTTG
6885575 TTATGTTTTTATTTTAAATCAAATAAGTTG
1 TTAT-TTTTTATTTTAAATCAAATAAGTTG
6885605 TTATTTTT
1 TTATTTTT
6885613 AATAATTGAC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 4 0.11
30 31 0.89
ACGTcount: A:0.31, C:0.03, G:0.07, T:0.59
Consensus pattern (29 bp):
TTATTTTTTATTTTAAATCAAATAAGTTG
Found at i:6889910 original size:17 final size:16
Alignment explanation
Indices: 6889888--6889921 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
6889878 GTGTCACTGA
6889888 TTTTTATTTTTGAGAAT
1 TTTTTATTTTTGA-AAT
6889905 TTTTTATTTTTGAAAT
1 TTTTTATTTTTGAAAT
6889921 T
1 T
6889922 CTATATCAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.68
Consensus pattern (16 bp):
TTTTTATTTTTGAAAT
Found at i:6894853 original size:30 final size:30
Alignment explanation
Indices: 6894817--6894878 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
6894807 GGGTCTGGTA
*
6894817 GGATTGGTGGCCAAATACCAGATTGGCTGG
1 GGATTGGTGGCCAAATACCAGACTGGCTGG
* *
6894847 GGATTGGTGGCCATATTCCAGACTGGCTGG
1 GGATTGGTGGCCAAATACCAGACTGGCTGG
6894877 GG
1 GG
6894879 GTGCTAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.19, C:0.18, G:0.39, T:0.24
Consensus pattern (30 bp):
GGATTGGTGGCCAAATACCAGACTGGCTGG
Found at i:6902935 original size:72 final size:72
Alignment explanation
Indices: 6902850--6903001 Score: 225
Period size: 72 Copynumber: 2.1 Consensus size: 72
6902840 AAACACCTTC
* *
6902850 ATCTTTCTGGCAATCAATTGAA-TGGGACAATCCCAGAAAGTCTTGGGCAACTTTCCAGCCTCAA
1 ATCTTTCTGGCAATCAATTGAACGGGGAC-ATCCCAGAAAGTCTTGGGCAACTTTCCAACCTCAA
*
6902914 GACTTTAG
65 CACTTTAG
* * * *
6902922 ATCTTTCTGGCAATCAATTGAACGGGGTCATCTCAGAAAGTCTTGGGCAACTTTGCAACCTCGAC
1 ATCTTTCTGGCAATCAATTGAACGGGGACATCCCAGAAAGTCTTGGGCAACTTTCCAACCTCAAC
6902987 ACTTTAG
66 ACTTTAG
6902994 ATCTTTCT
1 ATCTTTCT
6903002 TACAATTCAT
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
72 68 0.94
73 4 0.06
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (72 bp):
ATCTTTCTGGCAATCAATTGAACGGGGACATCCCAGAAAGTCTTGGGCAACTTTCCAACCTCAAC
ACTTTAG
Found at i:6910002 original size:20 final size:21
Alignment explanation
Indices: 6909961--6910003 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
6909951 CTTTCTTTTC
*
6909961 TTTTCTTTTTCTCTCTTTTTT
1 TTTTCTTTTTCTCTCTTATTT
*
6909982 TTTTCTTTTT-TGTCTTATTT
1 TTTTCTTTTTCTCTCTTATTT
6910002 TT
1 TT
6910004 ACTTTTGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.81
Consensus pattern (21 bp):
TTTTCTTTTTCTCTCTTATTT
Found at i:6915572 original size:12 final size:12
Alignment explanation
Indices: 6915555--6915677 Score: 122
Period size: 12 Copynumber: 10.2 Consensus size: 12
6915545 TGGACCTGCC
6915555 AAAGAAGAGAAG
1 AAAGAAGAGAAG
*
6915567 AAAGAAGAAAAG
1 AAAGAAGAGAAG
* *
6915579 AAAGAGGAAAAG
1 AAAGAAGAGAAG
* *
6915591 AAGGAGGAGAA-
1 AAAGAAGAGAAG
*
6915602 AAAGGAGGAGAAG
1 AAA-GAAGAGAAG
6915615 AAAGAAGAGAAG
1 AAAGAAGAGAAG
* *
6915627 AAAGAGGAAAAG
1 AAAGAAGAGAAG
* *
6915639 AAGGAAGAAAAG
1 AAAGAAGAGAAG
*
6915651 AAGGAAGAGAAG
1 AAAGAAGAGAAG
*
6915663 AAGGAAGAGAAG
1 AAAGAAGAGAAG
6915675 AAA
1 AAA
6915678 TGAAAAAGCC
Statistics
Matches: 97, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
11 2 0.02
12 92 0.95
13 3 0.03
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (12 bp):
AAAGAAGAGAAG
Found at i:6915616 original size:48 final size:48
Alignment explanation
Indices: 6915558--6915677 Score: 188
Period size: 48 Copynumber: 2.5 Consensus size: 48
6915548 ACCTGCCAAA
* *
6915558 GAAGAGAAGAAAGAAGAAAAGAAAGAGGAAAAGAAGGAGGAGAAA-AAG
1 GAAGAGAAGAAAGAAGAGAAGAAAGAGGAAAAGAAGGAAGA-AAAGAAG
*
6915606 GAGGAGAAGAAAGAAGAGAAGAAAGAGGAAAAGAAGGAAGAAAAGAAG
1 GAAGAGAAGAAAGAAGAGAAGAAAGAGGAAAAGAAGGAAGAAAAGAAG
*
6915654 GAAGAGAAGAAGGAAGAGAAGAAA
1 GAAGAGAAGAAAGAAGAGAAGAAA
6915678 TGAAAAAGCC
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
47 3 0.05
48 63 0.95
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (48 bp):
GAAGAGAAGAAAGAAGAGAAGAAAGAGGAAAAGAAGGAAGAAAAGAAG
Found at i:6915619 original size:60 final size:60
Alignment explanation
Indices: 6915555--6915677 Score: 192
Period size: 60 Copynumber: 2.0 Consensus size: 60
6915545 TGGACCTGCC
* * *
6915555 AAAGAAGAGAAGAAAGAAGAAAAGAAAGAGGAAAAGAAGGAGGAGAAAAAGGAGGAGAAG
1 AAAGAAGAGAAGAAAGAAGAAAAGAAAGAAGAAAAGAAGGAAGAGAAAAAGGAAGAGAAG
* * *
6915615 AAAGAAGAGAAGAAAGAGGAAAAGAAGGAAGAAAAGAAGGAAGAGAAGAAGGAAGAGAAG
1 AAAGAAGAGAAGAAAGAAGAAAAGAAAGAAGAAAAGAAGGAAGAGAAAAAGGAAGAGAAG
6915675 AAA
1 AAA
6915678 TGAAAAAGCC
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (60 bp):
AAAGAAGAGAAGAAAGAAGAAAAGAAAGAAGAAAAGAAGGAAGAGAAAAAGGAAGAGAAG
Found at i:6917528 original size:212 final size:210
Alignment explanation
Indices: 6917268--6917673 Score: 560
Period size: 212 Copynumber: 1.9 Consensus size: 210
6917258 TAATTGTATA
* * *
6917268 AATATATTATATATACATATATTTAATTTATACATAAGTATTACTATAATTTATAAAAAATTTTA
1 AATATATTATATATACATATATTTAATTTATACATAAGCATGACTATAACTTATAAAAAATTTTA
** * * * *
6917333 TTTATATAATTACACTTAATAACTTTATTAGTTATAACTTTAGATTATATTACATATTGTATATT
66 TTTATATAATTACACTTAATAACTTTATTAACTATAACCTTAGATTATATAACATATTCTATATA
* * * * *
6917398 ATTAGTTATCATTTATACAAACTTTAATATAAAACATTTTAGCGTATAATTTGTATCATTAATTC
131 ATTAGTTATCATTTATACAAACTTTAATATAAAACATTATAACATATAAGTTATATCATTAATTC
6917463 TATATATAATAAAAT
196 TATATATAATAAAAT
* * *
6917478 AATATATTATACATATTCATATATTTAATTTATATATAAGCATGACTATAACTTATAATAAATTT
1 AATATATTAT--ATATACATATATTTAATTTATACATAAGCATGACTATAACTTATAAAAAATTT
* * * * *
6917543 TATTTATATGATTACACTTAATAAGTTTATTAACTATCACCTTAGATTTTATAACATATTCTTTA
64 TATTTATATAATTACACTTAATAACTTTATTAACTATAACCTTAGATTATATAACATATTCTATA
* ** *
6917608 TAATTAGTTATTATTTATACAAACTTTGTTATAAAATATTATAACATATAAGTTATATCATTAAT
129 TAATTAGTTATCATTTATACAAACTTTAATATAAAACATTATAACATATAAGTTATATCATTAAT
6917673 T
194 T
6917674 TCATACATAT
Statistics
Matches: 168, Mismatches: 26, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
210 10 0.06
212 158 0.94
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.47
Consensus pattern (210 bp):
AATATATTATATATACATATATTTAATTTATACATAAGCATGACTATAACTTATAAAAAATTTTA
TTTATATAATTACACTTAATAACTTTATTAACTATAACCTTAGATTATATAACATATTCTATATA
ATTAGTTATCATTTATACAAACTTTAATATAAAACATTATAACATATAAGTTATATCATTAATTC
TATATATAATAAAAT
Found at i:6943505 original size:2 final size:2
Alignment explanation
Indices: 6943498--6943523 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6943488 TGTGTAACTG
6943498 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
6943524 ACTAACGTGT
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):
GA
Found at i:6955210 original size:33 final size:35
Alignment explanation
Indices: 6955164--6955239 Score: 111
Period size: 35 Copynumber: 2.2 Consensus size: 35
6955154 GAAACTTAGT
*
6955164 TCAATTA-GTTTTTTA-CTCTTTTCAAAGGCTAAC
1 TCAATTAGGTTTTTTATCTATTTTCAAAGGCTAAC
* *
6955197 TCAATTAGGTTTTTTATTTATTTTCAAAGGCTTAC
1 TCAATTAGGTTTTTTATCTATTTTCAAAGGCTAAC
6955232 TCAATTAG
1 TCAATTAG
6955240 TTCATGTACT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 7 0.18
34 8 0.21
35 23 0.61
ACGTcount: A:0.28, C:0.14, G:0.11, T:0.47
Consensus pattern (35 bp):
TCAATTAGGTTTTTTATCTATTTTCAAAGGCTAAC
Found at i:6973018 original size:18 final size:17
Alignment explanation
Indices: 6972990--6973025 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
6972980 TCAATTTGTG
6972990 ATTTTGATTAAAAAAAC
1 ATTTTGATTAAAAAAAC
*
6973007 ATTTTCGATTAAATAAAC
1 ATTTT-GATTAAAAAAAC
6973025 A
1 A
6973026 GTGTTTGTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.36
Consensus pattern (17 bp):
ATTTTGATTAAAAAAAC
Found at i:6974349 original size:2 final size:2
Alignment explanation
Indices: 6974342--6974379 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6974332 TTGTCTATGC
6974342 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
6974380 AAGTATTGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6975213 original size:14 final size:14
Alignment explanation
Indices: 6975179--6975218 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
6975169 TATTGCGGAT
* *
6975179 ATATATATGTATGC
1 ATATATATATATAC
*
6975193 ATTTATATATATAC
1 ATATATATATATAC
6975207 ATATATATATAT
1 ATATATATATAT
6975219 TCAAATATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (14 bp):
ATATATATATATAC
Found at i:6977730 original size:25 final size:25
Alignment explanation
Indices: 6977702--6977759 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
6977692 TAAATTTTTA
*
6977702 TTTTTATTATTTTTAATTAAATTGT
1 TTTTTATTATTTTTAATTAAATTAT
6977727 TTTTTATTATTTTTAATTAAATTAT
1 TTTTTATTATTTTTAATTAAATTAT
6977752 TTTTTATT
1 TTTTTATT
6977760 TTAAATCAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.71
Consensus pattern (25 bp):
TTTTTATTATTTTTAATTAAATTAT
Found at i:6977750 original size:15 final size:15
Alignment explanation
Indices: 6977707--6977755 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
6977697 TTTTATTTTT
6977707 ATTATTTTTAATTAA
1 ATTATTTTTAATTAA
*
6977722 ATT-GTTTT--TT--
1 ATTATTTTTAATTAA
6977732 ATTATTTTTAATTAA
1 ATTATTTTTAATTAA
6977747 ATTATTTTT
1 ATTATTTTT
6977756 TATTTTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
10 3 0.11
11 4 0.15
12 2 0.07
13 2 0.07
14 4 0.15
15 12 0.44
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
ATTATTTTTAATTAA
Found at i:6977761 original size:22 final size:23
Alignment explanation
Indices: 6977703--6977770 Score: 84
Period size: 25 Copynumber: 2.9 Consensus size: 23
6977693 AAATTTTTAT
*
6977703 TTTTATTATTTTTAATTAAATTGTT
1 TTTTATTATTTTTAATTAAA-T-TA
6977728 TTTTATTATTTTTAATTAAATTA
1 TTTTATTATTTTTAATTAAATTA
* *
6977751 TTTT-TTATTTTAAATCAAAT
1 TTTTATTATTTTTAATTAAAT
6977771 AAATTTTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
22 14 0.35
23 5 0.12
24 1 0.03
25 20 0.50
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (23 bp):
TTTTATTATTTTTAATTAAATTA
Found at i:6977777 original size:22 final size:22
Alignment explanation
Indices: 6977733--6977780 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
6977723 TTGTTTTTTA
* * * *
6977733 TTATTTTTAATTAAATTATTTT
1 TTATTTTAAATCAAATAAATTT
6977755 TTATTTTAAATCAAATAAATTT
1 TTATTTTAAATCAAATAAATTT
6977777 TTAT
1 TTAT
6977781 AATTAAATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATTTTAAATCAAATAAATTT
Found at i:6978073 original size:34 final size:35
Alignment explanation
Indices: 6978034--6978099 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
6978024 CGTGATATAA
* *
6978034 AATAATAAATA-TTATTTTAATT-AATATAAATGTT
1 AATAATAAAGAGTTA-TTTAATTCAAAATAAATGTT
6978068 AATAATAAAGAGTTATTTAATTCAAAATAAAT
1 AATAATAAAGAGTTATTTAATTCAAAATAAAT
6978100 ATATAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 17 0.61
35 11 0.39
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.41
Consensus pattern (35 bp):
AATAATAAAGAGTTATTTAATTCAAAATAAATGTT
Found at i:6978164 original size:21 final size:19
Alignment explanation
Indices: 6978130--6978169 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
6978120 ATATAAATTT
6978130 ATTTAAAATTTTTAAAATA
1 ATTTAAAATTTTTAAAATA
6978149 ATTTAAGAACTTTTTAAAATA
1 ATTTAA-AA-TTTTTAAAATA
6978170 TTATATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 2 0.11
21 11 0.58
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (19 bp):
ATTTAAAATTTTTAAAATA
Found at i:7022454 original size:38 final size:32
Alignment explanation
Indices: 7022369--7022435 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
7022359 AACATTTGAG
*
7022369 TATTTTGAGCATTCTTTGTCAAGTAGACATAT
1 TATTTTGAGTATTCTTTGTCAAGTAGACATAT
7022401 TATTTTGAGTATTCTTTGTCAAGTAGACATAT
1 TATTTTGAGTATTCTTTGTCAAGTAGACATAT
7022433 TAT
1 TAT
7022436 ATTCATTGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.46
Consensus pattern (32 bp):
TATTTTGAGTATTCTTTGTCAAGTAGACATAT
Found at i:7022611 original size:22 final size:22
Alignment explanation
Indices: 7022521--7022612 Score: 69
Period size: 22 Copynumber: 4.2 Consensus size: 22
7022511 GATTTGGTAG
* ** *
7022521 TTTTTAGGCATTGTGTGATCGA
1 TTTTTAGACATTGCATGATTGA
* *
7022543 TTTTTGGACATTGTATGATT-A
1 TTTTTAGACATTGCATGATTGA
* * * *
7022564 GTTTTTAAACATTGCATTACTAA
1 -TTTTTAGACATTGCATGATTGA
*
7022587 TTTTTAGATATTGCATGATTGA
1 TTTTTAGACATTGCATGATTGA
7022609 TTTT
1 TTTT
7022613 AAGTACGTGA
Statistics
Matches: 54, Mismatches: 14, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
21 1 0.02
22 52 0.96
23 1 0.02
ACGTcount: A:0.25, C:0.08, G:0.17, T:0.50
Consensus pattern (22 bp):
TTTTTAGACATTGCATGATTGA
Found at i:7022666 original size:23 final size:23
Alignment explanation
Indices: 7022620--7022685 Score: 91
Period size: 23 Copynumber: 2.9 Consensus size: 23
7022610 TTTAAGTACG
7022620 TGACTGGTT-G-ATAGGCATTGCA
1 TGACTGGTTAGTA-AGGCATTGCA
*
7022642 TGACTGGTTAGTAAGGTATTGCA
1 TGACTGGTTAGTAAGGCATTGCA
*
7022665 TGACTAGTTAGTAAGGCATTG
1 TGACTGGTTAGTAAGGCATTG
7022686 TGTGACTTAG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
22 9 0.23
23 29 0.74
24 1 0.03
ACGTcount: A:0.26, C:0.11, G:0.30, T:0.33
Consensus pattern (23 bp):
TGACTGGTTAGTAAGGCATTGCA
Found at i:7026306 original size:29 final size:29
Alignment explanation
Indices: 7026274--7026335 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
7026264 ATTTCACTAA
*
7026274 AAAAATAAAT-TTAAAATTTTAAGAAACTT
1 AAAAATAAATGTTAAAATTTTAA-AAAATT
**
7026303 AAAAATAAATGTTATTATTTTAAAAAATT
1 AAAAATAAATGTTAAAATTTTAAAAAATT
7026332 AAAA
1 AAAA
7026336 CTAATTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 19 0.66
30 10 0.34
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAAATAAATGTTAAAATTTTAAAAAATT
Found at i:7042700 original size:33 final size:34
Alignment explanation
Indices: 7042637--7042703 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
7042627 TGACTAAAGA
7042637 AAAAATTATTATAAAGATAAAATTTTAAAATTTT
1 AAAAATTATTATAAAGATAAAATTTTAAAATTTT
* *
7042671 AAAAATTA-TATATTAGA-AAATTTTTAAAATTTT
1 AAAAATTATTATA-AAGATAAAATTTTAAAATTTT
7042704 TGTAGAGACA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 19 0.63
34 11 0.37
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (34 bp):
AAAAATTATTATAAAGATAAAATTTTAAAATTTT
Found at i:7074306 original size:112 final size:114
Alignment explanation
Indices: 7074162--7074393 Score: 296
Period size: 112 Copynumber: 2.1 Consensus size: 114
7074152 TTTTTTAATC
*
7074162 TTTTAATTTTATTGTCATTAAAATTTTAAAATATTAATAATTTATTATTAAATTATTAATAT-GA
1 TTTTAATTTTATTGTCATTAAAATTTTAAAATATTAATAATTTATTATTAAATTATTAATATAAA
* * *
7074226 TTTTTTA-TTGCACTTTCTTTTTATTTTTTCTCTA-TTTATATTTTC-ATT
66 TTTTTTACTT-CAATTTCTTTTCACTTTTTCTCTATTTTA-ATTTTCTATT
* * *
7074274 TTTTAATTTCTATTTTCGTT-AAATATTT-AAATATTAATAATTTATTATTAAATTATTCATATA
1 TTTTAATTT-TATTGTCATTAAAAT-TTTAAAATATTAATAATTTATTATTAAATTATTAATATA
* *
7074337 AATTTTTTACTTTAATTTCTTTTCACTTTTTCTTTATTTTAATTTTCTATT
64 AATTTTTTACTTCAATTTCTTTTCACTTTTTCTCTATTTTAATTTTCTATT
*
7074388 TGTTAA
1 TTTTAA
7074394 GTTGTAATTA
Statistics
Matches: 104, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
112 46 0.44
113 44 0.42
114 14 0.13
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (114 bp):
TTTTAATTTTATTGTCATTAAAATTTTAAAATATTAATAATTTATTATTAAATTATTAATATAAA
TTTTTTACTTCAATTTCTTTTCACTTTTTCTCTATTTTAATTTTCTATT
Found at i:7074602 original size:17 final size:18
Alignment explanation
Indices: 7074580--7074615 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
7074570 AATTGTACTC
*
7074580 TCTCATCC-TTTATAAAT
1 TCTCATCCATGTATAAAT
7074597 TCTCATCCATGTATAAAT
1 TCTCATCCATGTATAAAT
7074615 T
1 T
7074616 TTGCTTGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.44
Consensus pattern (18 bp):
TCTCATCCATGTATAAAT
Found at i:7079492 original size:2 final size:2
Alignment explanation
Indices: 7079485--7079509 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7079475 TGGAAATGTC
7079485 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
7079510 GACGTATTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7080798 original size:19 final size:19
Alignment explanation
Indices: 7080770--7080806 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
7080760 TTAATTTAAA
*
7080770 ATATTCTCAAAAGCATAAG
1 ATATTCTCAAAAGAATAAG
*
7080789 ATATTTTCAAAAGAATAA
1 ATATTCTCAAAAGAATAA
7080807 AAAAATGCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (19 bp):
ATATTCTCAAAAGAATAAG
Found at i:7080811 original size:99 final size:96
Alignment explanation
Indices: 7080707--7080889 Score: 226
Period size: 99 Copynumber: 1.9 Consensus size: 96
7080697 TAGAGAACAG
* * * *
7080707 AAAAAATACTTTTATACTAAG-TCTAGC-AGTATAGGTTTGATAATTATTAATATTTAATTTAAA
1 AAAAAATACATTTATACTAAGCT-TAGCTA-TATAAGTTTGAAAAATATTAATATTTAATTTAAA
7080770 ATATTCTCAAAAGCATAAGATATTTTCAAAAGAATA
64 ATATT-TCAAAA--ATAAGATATTTTCAAAAGAATA
* ** *
7080806 AAAAAATGCATTTATGTTAAGCTTGGCTATATAAGTTTGAAAAATATTAATATTTAATTTAAAAT
1 AAAAAATACATTTATACTAAGCTTAGCTATATAAGTTTGAAAAATATTAATATTTAATTTAAAAT
*
7080871 ATTTTAAAAATAAGATATT
66 ATTTCAAAAATAAGATATT
7080890 AATATTTAAC
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
96 10 0.14
98 5 0.07
99 56 0.77
100 2 0.03
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.39
Consensus pattern (96 bp):
AAAAAATACATTTATACTAAGCTTAGCTATATAAGTTTGAAAAATATTAATATTTAATTTAAAAT
ATTTCAAAAATAAGATATTTTCAAAAGAATA
Found at i:7081189 original size:82 final size:82
Alignment explanation
Indices: 7081099--7081249 Score: 221
Period size: 82 Copynumber: 1.8 Consensus size: 82
7081089 TTTTTGATTA
* * * *
7081099 TTTATACAATTAATGAATGTACATATTTTTATAGCGTTATGATAAGGAAAGGATGAGATGGAAAT
1 TTTATACAATTAATGAATATACATATTTTTATAGCATTATGATAAAGAAACGATGAGATGGAAAT
7081164 TTTTTTGAAAATTAGAG
66 TTTTTTGAAAATTAGAG
** * * *
7081181 TTTATACAATTAATGAATATGGATGTTTTTGTAGTATTATGATAAAGAAACGATGAGATGGAAAT
1 TTTATACAATTAATGAATATACATATTTTTATAGCATTATGATAAAGAAACGATGAGATGGAAAT
7081246 TTTT
66 TTTT
7081250 GAAAGGTAGA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
82 60 1.00
ACGTcount: A:0.38, C:0.03, G:0.19, T:0.39
Consensus pattern (82 bp):
TTTATACAATTAATGAATATACATATTTTTATAGCATTATGATAAAGAAACGATGAGATGGAAAT
TTTTTTGAAAATTAGAG
Found at i:7082343 original size:16 final size:16
Alignment explanation
Indices: 7082322--7082354 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
7082312 CTTATGTAAG
7082322 CAAAAAAAAAAAAAAA
1 CAAAAAAAAAAAAAAA
*
7082338 CAAAAACAAAAAAAAA
1 CAAAAAAAAAAAAAAA
7082354 C
1 C
7082355 TCTTAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (16 bp):
CAAAAAAAAAAAAAAA
Found at i:7086858 original size:73 final size:73
Alignment explanation
Indices: 7086685--7086862 Score: 203
Period size: 73 Copynumber: 2.4 Consensus size: 73
7086675 CTTGTTGCAA
* * * * * ** *
7086685 CAAGAATGCAAGTTGACTGCACCAAGGAACAAGATAGAATTAAGCTCCCAAGTCAAAAACTTTCT
1 CAAGAATTCAAGTTGGCTGCAACGAGAAACAAGGCAGAATTAAGCTCCCAAGTCAAAAACTTTAT
* * **
7086750 CGTTGTAG
66 AGCTAAAG
* * *
7086758 CGAGAATTCAAGTTGGCTGCAATGAGAAACAAGGCAGAATTAAGCTCCCAAGTCAAAAAGTTTAT
1 CAAGAATTCAAGTTGGCTGCAACGAGAAACAAGGCAGAATTAAGCTCCCAAGTCAAAAACTTTAT
7086823 AGCTAAAG
66 AGCTAAAG
* *
7086831 CAAGAATTCAAGTTGGCTGTAGCGAGAAACAA
1 CAAGAATTCAAGTTGGCTGCAACGAGAAACAA
7086863 AGCAAAATGA
Statistics
Matches: 86, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
73 86 1.00
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (73 bp):
CAAGAATTCAAGTTGGCTGCAACGAGAAACAAGGCAGAATTAAGCTCCCAAGTCAAAAACTTTAT
AGCTAAAG
Found at i:7126915 original size:29 final size:30
Alignment explanation
Indices: 7126880--7126956 Score: 104
Period size: 29 Copynumber: 2.6 Consensus size: 30
7126870 AATTTATTTA
*
7126880 ATTAAAAATAAAAGTATAAG-GGTTTATTG
1 ATTAAAAATAAAAGTATAAGAGGTTGATTG
*
7126909 GTTAAAAATAAAAGTATAAGAGGTTGATTG
1 ATTAAAAATAAAAGTATAAGAGGTTGATTG
* *
7126939 AAT-ATAATAAAAGTATAA
1 ATTAAAAATAAAAGTATAA
7126957 AAACTTATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 33 0.79
30 9 0.21
ACGTcount: A:0.52, C:0.00, G:0.17, T:0.31
Consensus pattern (30 bp):
ATTAAAAATAAAAGTATAAGAGGTTGATTG
Found at i:7146040 original size:27 final size:27
Alignment explanation
Indices: 7146006--7146058 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
7145996 TTGACGAAAT
*
7146006 ATATAAAAATAAAATAGAATAATTATA
1 ATATAAAAATAAAATAAAATAATTATA
7146033 ATATAAAAATAAAATAAAATAATTAT
1 ATATAAAAATAAAATAAAATAATTAT
7146059 TATTTAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (27 bp):
ATATAAAAATAAAATAAAATAATTATA
Found at i:7146258 original size:19 final size:19
Alignment explanation
Indices: 7146208--7146287 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
7146198 TATATTTTTA
7146208 AAATATTAATAATTTTATAATTT
1 AAATATTAAT-A-TTT-T-ATTT
7146231 AAATATTAATATTTTATTT
1 AAATATTAATATTTTATTT
*
7146250 ATAAT-TTAATATTATTATTAA
1 A-AATATTAATATT-TTATT-T
7146271 AAATATTAATAATTTTA
1 AAATATTAAT-ATTTTA
7146288 ATTCATTTGC
Statistics
Matches: 51, Mismatches: 1, Indels: 12
0.80 0.02 0.19
Matches are distributed among these distances:
19 13 0.25
20 12 0.24
21 12 0.24
22 4 0.08
23 10 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AAATATTAATATTTTATTT
Found at i:7146533 original size:8 final size:8
Alignment explanation
Indices: 7146522--7146663 Score: 53
Period size: 8 Copynumber: 17.8 Consensus size: 8
7146512 TTTTATATTT
7146522 AATATTAA
1 AATATTAA
7146530 AATATTAA
1 AATATTAA
**
7146538 AAT-CCAA
1 AATATTAA
*
7146545 TATATTAA
1 AATATTAA
7146553 TAA-ATT-A
1 -AATATTAA
* *
7146560 ATTAATAA
1 AATATTAA
* * *
7146568 AACACTAT
1 AATATTAA
7146576 AATATTAA
1 AATATTAA
7146584 AATATTAA
1 AATATTAA
* *
7146592 TATTTTAA
1 AATATTAA
*
7146600 TCATATT--
1 -AATATTAA
7146607 AATATTAA
1 AATATTAA
7146615 TAATATTTAA
1 -AATA-TTAA
**
7146625 CTTATATAA
1 AATAT-TAA
7146634 AATATTAA
1 AATATTAA
* *
7146642 TATTTTAA
1 AATATTAA
7146650 AAT-TTATA
1 AATATTA-A
7146658 AATATT
1 AATATT
7146664 TTTTCTATTT
Statistics
Matches: 95, Mismatches: 27, Indels: 23
0.66 0.19 0.16
Matches are distributed among these distances:
6 6 0.06
7 10 0.11
8 56 0.59
9 19 0.20
10 4 0.04
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (8 bp):
AATATTAA
Found at i:7146608 original size:25 final size:24
Alignment explanation
Indices: 7146577--7146663 Score: 90
Period size: 25 Copynumber: 3.5 Consensus size: 24
7146567 AAACACTATA
7146577 ATATTAAAATATTAATATTTTAATC
1 ATATTAAAATATTAATATTTTAA-C
7146602 ATATT--AATATTAATAATATTTAAC
1 ATATTAAAATATTAAT-AT-TTTAAC
* *
7146626 TTATATAAAATATTAATATTTTAAA
1 ATAT-TAAAATATTAATATTTTAAC
7146651 AT-TTATAAATATT
1 ATATTA-AAATATT
7146664 TTTTCTATTT
Statistics
Matches: 53, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
23 11 0.21
24 14 0.26
25 17 0.32
26 2 0.04
27 9 0.17
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
ATATTAAAATATTAATATTTTAAC
Found at i:7157431 original size:16 final size:17
Alignment explanation
Indices: 7157400--7157432 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
7157390 AGATACAGTG
*
7157400 CTCTGGATGGATTCAAA
1 CTCTGGATGAATTCAAA
7157417 CTCTGGAT-AATTCAAA
1 CTCTGGATGAATTCAAA
7157433 GTTTGTATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (17 bp):
CTCTGGATGAATTCAAA
Found at i:7162824 original size:15 final size:16
Alignment explanation
Indices: 7162804--7162844 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
7162794 ACATCTATAC
7162804 ATTAATATTTAA-TAA
1 ATTAATATTTAATTAA
7162819 ATTAATATTTTAATTAA
1 ATTAATA-TTTAATTAA
7162836 A-TAATATTT
1 ATTAATATTT
7162845 TTAATCAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 10 0.42
16 10 0.42
17 4 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTAATATTTAATTAA
Done.