Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007776.1 Hibiscus syriacus cultivar Beakdansim tig00110057_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: 2207776
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 11
Found at i:430095 original size:29 final size:29
Alignment explanation
Indices: 430037--430104 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 29
430027 ATATTTCTAA
* *
430037 ATAAATAAATATTTTATTTATAAATATAT
1 ATAAATAAATATTTTACTTAAAAATATAT
430066 ATAAATTAATATATTTT-CTTAAAAAT-TAT
1 ATAAA-TAA-ATATTTTACTTAAAAATATAT
430095 AGT-AATAAAT
1 A-TAAATAAAT
430105 TTGAGATAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
27 2 0.06
28 3 0.09
29 11 0.32
30 11 0.32
31 7 0.21
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (29 bp):
ATAAATAAATATTTTACTTAAAAATATAT
Found at i:432679 original size:17 final size:18
Alignment explanation
Indices: 432646--432679 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
432636 GACGTTTTTG
*
432646 TACTTTGTTTTATAATTT
1 TACTTTGTTTTAAAATTT
432664 TACTTT-TTTTAAAATT
1 TACTTTGTTTTAAAATT
432680 GTGGCAAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (18 bp):
TACTTTGTTTTAAAATTT
Found at i:435716 original size:3 final size:3
Alignment explanation
Indices: 435708--435738 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
435698 CTTAATTTAT
435708 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
435739 ATGCTTCGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:446405 original size:28 final size:28
Alignment explanation
Indices: 446373--446429 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
446363 CCGTCATTGC
446373 TTTCAAGCACTGCCTCAATGATATAATA
1 TTTCAAGCACTGCCTCAATGATATAATA
* ** *
446401 TTTCAAGCATTGGTTCGATGATATAATA
1 TTTCAAGCACTGCCTCAATGATATAATA
446429 T
1 T
446430 AAATGAAGTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (28 bp):
TTTCAAGCACTGCCTCAATGATATAATA
Found at i:450347 original size:28 final size:28
Alignment explanation
Indices: 450286--450339 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
450276 ATGATTGAGC
*
450286 ACCTCCATGCATCAATCTAGAAACTGAA
1 ACCTCAATGCATCAATCTAGAAACTGAA
450314 ACCTCAATGCATCAATCTAGAAACTG
1 ACCTCAATGCATCAATCTAGAAACTG
450340 GCAACTCAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.39, C:0.28, G:0.11, T:0.22
Consensus pattern (28 bp):
ACCTCAATGCATCAATCTAGAAACTGAA
Found at i:455788 original size:18 final size:18
Alignment explanation
Indices: 455755--455794 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
455745 TATAATGAAA
455755 AAAATAAAAAAGCAAAGAG
1 AAAATAAAAAAGCAAAG-G
455774 AAAATAAAAAA-CAAAGG
1 AAAATAAAAAAGCAAAGG
455791 AAAA
1 AAAA
455795 AGTGAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 5 0.24
18 5 0.24
19 11 0.52
ACGTcount: A:0.78, C:0.05, G:0.12, T:0.05
Consensus pattern (18 bp):
AAAATAAAAAAGCAAAGG
Found at i:456886 original size:32 final size:32
Alignment explanation
Indices: 456850--456996 Score: 154
Period size: 32 Copynumber: 4.6 Consensus size: 32
456840 CAATGGGGAT
*
456850 ATCTTTGAATATTCAACATCAAATGTTGGGGC
1 ATCTTTGAAGATTCAACATCAAATGTTGGGGC
* * *
456882 ATCTTTAAAGATTCAATATCAAATG-TGGGCC
1 ATCTTTGAAGATTCAACATCAAATGTTGGGGC
* *
456913 ATCTTTGAAGATTCAACGTCAAATGTTGGGGG
1 ATCTTTGAAGATTCAACATCAAATGTTGGGGC
* * * * *
456945 ATATTT-ACAGATTCAACATCCATTATTGAGGC
1 ATCTTTGA-AGATTCAACATCAAATGTTGGGGC
**
456977 ATCTTTGGGGATTCAACATC
1 ATCTTTGAAGATTCAACATC
456997 CTGATGCGAA
Statistics
Matches: 93, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
31 28 0.30
32 65 0.70
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Consensus pattern (32 bp):
ATCTTTGAAGATTCAACATCAAATGTTGGGGC
Found at i:457489 original size:60 final size:59
Alignment explanation
Indices: 457378--457745 Score: 312
Period size: 60 Copynumber: 6.0 Consensus size: 59
457368 GTTTTCAAGA
* *
457378 TTGGATTTCAACTTCACAACGAAGGATATACAACTCAAAGCTAATTTGGTGAAGCAATAC
1 TTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGC-AATTCGGTGAAGCAATAC
* * * * * *
457438 TTGGATTTCAACTTTACAACGAATGATATCTAACTTAAAGTCAATTCGGTGAAGTAGTAC
1 TTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAG-CAATTCGGTGAAGCAATAC
* ** * * *
457498 TTGGATTTTAACTTCTTAGCGAAGGATATCCAACTCAAAGCAGATTTGGTGAAGCACA-AGA
1 TTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCA-ATTCGGTGAAGCA-ATA-C
* * * * *
457559 TTGGATTTTAACTTCACAACGAAGGATATCCAACTCAAAACTGATTCGGTGAAACTTAACAAGC
1 TTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGC-AATTCGGTGAAGC--AA-TA-C
* * * * *
457623 TTGGATTTCAACTTCA-AACGAATGACATCCAACTCAAAACCAATTTGGTGAAACTTACACAATA
1 TTGGATTTCAACTTCACAACGAAGGATATCCAACTC-AAAGCAATTCGGTG--A---A-GCAATA
457687 -
59 C
* *
457687 TTGGA-TTCAACTTCACAACGAACGATATCCAACTGAAAGTCAATTCGGTGAAGCAATAC
1 TTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAG-CAATTCGGTGAAGCAATAC
457746 AACTTCAAAT
Statistics
Matches: 248, Mismatches: 41, Indels: 39
0.76 0.12 0.12
Matches are distributed among these distances:
58 5 0.02
59 3 0.01
60 94 0.38
61 48 0.19
62 2 0.01
63 38 0.15
64 51 0.21
65 1 0.00
66 1 0.00
67 2 0.01
68 1 0.00
69 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.27
Consensus pattern (59 bp):
TTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCAATTCGGTGAAGCAATAC
Found at i:457692 original size:64 final size:65
Alignment explanation
Indices: 457552--457793 Score: 258
Period size: 64 Copynumber: 3.7 Consensus size: 65
457542 TTTGGTGAAG
* * * **
457552 CACAAGATTGGATTTTAACTTCACAACGAAGGATATCCAACTCAAAACTGATTCGGTGAAACTTA
1 CACAAGATTGGATTTCAACTTCACAACGAATGACATCCAACTCAAAACCAATTCGGTGAAACTTA
* *
457617 -ACAAGCTTGGATTTCAACTTCA-AACGAATGACATCCAACTCAAAACCAATTTGGTGAAACTTA
1 CACAAGATTGGATTTCAACTTCACAACGAATGACATCCAACTCAAAACCAATTCGGTGAAACTTA
* * * * ** * *
457680 CACAATATTGGA-TTCAACTTCACAACGAACGATATCCAACTGAAAGTCAATTCGGTGAAGCAAT
1 CACAAGATTGGATTTCAACTTCACAACGAATGACATCCAACTCAAAACCAATTCGGTGAAAC-TT
457744 A
65 A
* *
457745 CAACTTCAA-ATTGGATTTCAACTTCGCAACGAATGACATCCAATTCAAA
1 C-A---CAAGATTGGATTTCAACTTCACAACGAATGACATCCAACTCAAA
457794 GCTCAACTTC
Statistics
Matches: 147, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
63 46 0.31
64 60 0.41
65 3 0.02
66 1 0.01
68 6 0.04
69 31 0.21
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (65 bp):
CACAAGATTGGATTTCAACTTCACAACGAATGACATCCAACTCAAAACCAATTCGGTGAAACTTA
Found at i:458553 original size:65 final size:62
Alignment explanation
Indices: 458438--458592 Score: 204
Period size: 63 Copynumber: 2.5 Consensus size: 62
458428 CACTCACCAT
* * *
458438 ATCGAATGCATTTTATGCATTGATGCACTACCATGCATCGATACACTCAGG-TTTTATGAAAAAC
1 ATCGAATGCATTTTATGCATCGATGCACGACCATGCATCGATACACTCAGGCTTGT-TG--AAAC
* * *
458502 ATTGATTGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCAGGCTTGTTGAAAC
1 ATCGAATGCATTTTATGCATCGATGCAC-GACCATGCATCGATACACTCAGGCTTGTTGAAAC
*
458565 ATCGAATGCATTTTATGCATCTATGCAC
1 ATCGAATGCATTTTATGCATCGATGCAC
458593 TCTTAGTGCA
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
63 29 0.36
64 25 0.31
65 23 0.29
66 3 0.04
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (62 bp):
ATCGAATGCATTTTATGCATCGATGCACGACCATGCATCGATACACTCAGGCTTGTTGAAAC
Found at i:458608 original size:63 final size:62
Alignment explanation
Indices: 458438--458612 Score: 185
Period size: 63 Copynumber: 2.7 Consensus size: 62
458428 CACTCACCAT
* *
458438 ATCGAATGCATTTTATGCAT-TGATGCACTACCATGCATCGATACACTCAGGTTTTATGAAAAAC
1 ATCGAATGCATTTTATGCATCT-ATGCACT-CCATGCATCGATGCACTCAGGTTGTATG-AAAAC
* * * *
458502 ATTGATTGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCAGGCTTGT-TG-AAAC
1 ATCGAATGCATTTTATGCATCTATGCAC--TCCATGCATCGATGCACTCAGG-TTGTATGAAAAC
* *
458565 ATCGAATGCATTTTATGCATCTATGCACTCTTAGTGCACCGATGCACT
1 ATCGAATGCATTTTATGCATCTATGCACTC-CA-TGCATCGATGCACT
458613 AAGTGTTCCA
Statistics
Matches: 93, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
61 1 0.01
62 1 0.01
63 42 0.45
64 24 0.26
65 22 0.24
66 3 0.03
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (62 bp):
ATCGAATGCATTTTATGCATCTATGCACTCCATGCATCGATGCACTCAGGTTGTATGAAAAC
Found at i:467209 original size:65 final size:63
Alignment explanation
Indices: 467116--467238 Score: 185
Period size: 63 Copynumber: 1.9 Consensus size: 63
467106 AATGCATTTT
* *
467116 ATGCATCGATACACTTAGGTTTTATGAAAAACATCGAATGCATTTTATGCATCGATGCACAGACC
1 ATGCATCGATACACTCAGGTTGTATG--AAACATCGAATGCATTTTATGCATCGATGCACAGACC
*
467181 ATGCATCGATGCACTCAGGCTTGT-TGAAACATCGAATGCATTTTATGCATCGATGCAC
1 ATGCATCGATACACTCAGG-TTGTATGAAACATCGAATGCATTTTATGCATCGATGCAC
467239 TCTTAGTGCA
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
63 32 0.59
65 19 0.35
66 3 0.06
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (63 bp):
ATGCATCGATACACTCAGGTTGTATGAAACATCGAATGCATTTTATGCATCGATGCACAGACC
Found at i:468463 original size:40 final size:40
Alignment explanation
Indices: 468361--468475 Score: 178
Period size: 40 Copynumber: 2.9 Consensus size: 40
468351 AGCGATGTCA
* *
468361 ACTA-GTCATCCTCATCACGTAGAAACCATGTCATCCCTCG
1 ACTAGGTC-TCCTCATCACGTAGGAACCGTGTCATCCCTCG
*
468401 ACTAGGTCTCCCCATCACGTAGGAACCGTGTCATCCCTCG
1 ACTAGGTCTCCTCATCACGTAGGAACCGTGTCATCCCTCG
*
468441 ACTAGGTCTCCTCATCACGTAGGAACTGTGTCATC
1 ACTAGGTCTCCTCATCACGTAGGAACCGTGTCATC
468476 ATCCTTTAGA
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
40 66 0.96
41 3 0.04
ACGTcount: A:0.23, C:0.34, G:0.17, T:0.25
Consensus pattern (40 bp):
ACTAGGTCTCCTCATCACGTAGGAACCGTGTCATCCCTCG
Found at i:469798 original size:30 final size:29
Alignment explanation
Indices: 469732--469800 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 29
469722 CTAATTTTGA
* *
469732 CACTTAAGTTTCTGTTATTTTATTTTAGT
1 CACTTAAGTTTCTGTTATTCTATTTTAAT
469761 CACTTAAGTTTCTGGTT-TTGCTATTTTAAT
1 CACTTAAGTTTCT-GTTATT-CTATTTTAAT
469791 C-CTTTAAGTT
1 CAC-TTAAGTT
469801 AATGTTTTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 16 0.46
30 19 0.54
ACGTcount: A:0.20, C:0.13, G:0.12, T:0.55
Consensus pattern (29 bp):
CACTTAAGTTTCTGTTATTCTATTTTAAT
Found at i:471001 original size:16 final size:16
Alignment explanation
Indices: 470980--471011 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
470970 ATATAACGCT
470980 TTGTTACTAGAAATGC
1 TTGTTACTAGAAATGC
470996 TTGTTACTAGAAATGC
1 TTGTTACTAGAAATGC
471012 CACAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (16 bp):
TTGTTACTAGAAATGC
Found at i:475263 original size:29 final size:29
Alignment explanation
Indices: 475226--475302 Score: 100
Period size: 29 Copynumber: 2.7 Consensus size: 29
475216 TTTAATTGAT
475226 TTTTTTACTAAGTTTGAGGGTCTAAATAA
1 TTTTTTACTAAGTTTGAGGGTCTAAATAA
* *
475255 TTTTTTACTATGTTTGAGGGTCTAATTAA
1 TTTTTTACTAAGTTTGAGGGTCTAAATAA
** **
475284 TGGTTTAGAAAGTTTGAGG
1 TTTTTTACTAAGTTTGAGG
475303 ACTTATTTCA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.27, C:0.05, G:0.22, T:0.45
Consensus pattern (29 bp):
TTTTTTACTAAGTTTGAGGGTCTAAATAA
Found at i:475961 original size:19 final size:20
Alignment explanation
Indices: 475921--475961 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
475911 GAGAGGAATG
*
475921 TGATGATGTTTTGCAAGATT
1 TGATGATGTTTAGCAAGATT
*
475941 TGATGATG-TTAGCAGGATT
1 TGATGATGTTTAGCAAGATT
475960 TG
1 TG
475962 GAGATGAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.24, C:0.05, G:0.29, T:0.41
Consensus pattern (20 bp):
TGATGATGTTTAGCAAGATT
Found at i:480864 original size:90 final size:90
Alignment explanation
Indices: 480758--480930 Score: 301
Period size: 90 Copynumber: 1.9 Consensus size: 90
480748 AATCTCGAAT
* * * *
480758 AATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTGATATGATTAGGG
1 AATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTAGGG
480823 TAACTTGGATATAAAAGGATTATTA
66 TAACTTGGATATAAAAGGATTATTA
480848 AATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTAGGG
1 AATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTAGGG
*
480913 TAACTTGGCTATAAAAGG
66 TAACTTGGATATAAAAGG
480931 GTGTGTTAGG
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 78 1.00
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (90 bp):
AATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTAGGG
TAACTTGGATATAAAAGGATTATTA
Found at i:490045 original size:10 final size:10
Alignment explanation
Indices: 490016--490058 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
490006 TGCTTTCTCT
*
490016 TTGATTCTCTC
1 TTGATTCT-TG
490027 TTGATTCTTG
1 TTGATTCTTG
490037 TTGATTCTTG
1 TTGATTCTTG
*
490047 TTGATTGTTG
1 TTGATTCTTG
490057 TT
1 TT
490059 TCTTGTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.09, C:0.12, G:0.19, T:0.60
Consensus pattern (10 bp):
TTGATTCTTG
Found at i:490054 original size:17 final size:16
Alignment explanation
Indices: 490034--490069 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
490024 CTCTTGATTC
490034 TTGTTGATTCTTGTTGA
1 TTGTTGATTCTTGTT-A
*
490051 TTGTTGTTTCTTGTTA
1 TTGTTGATTCTTGTTA
490067 TTG
1 TTG
490070 ATCAATGGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.08, C:0.06, G:0.22, T:0.64
Consensus pattern (16 bp):
TTGTTGATTCTTGTTA
Found at i:490362 original size:64 final size:64
Alignment explanation
Indices: 490291--490439 Score: 178
Period size: 64 Copynumber: 2.3 Consensus size: 64
490281 AAGAGTGTAA
* * * * * *
490291 CGATGCATAAATATGC-TTCGATGTTTTGA-AAAAGCTTGGGTGCATCGATGCATGGCTTGTGCA
1 CGATGCAT-AATATGCATTCGATGTTTTCATAAAAACCTGAGTGCATCGATGAATGG-TAGTGCA
490354 T
64 T
* *
490355 CGGTGCATTGA-ATGCATTCGATGTTTTCATAAAAACCTGAGTGCATCGATGAATGGTAGTGCAT
1 CGATGCA-TAATATGCATTCGATGTTTTCATAAAAACCTGAGTGCATCGATGAATGGTAGTGCAT
490419 CGATGCATAATATGCATTCGA
1 CGATGCATAATATGCATTCGA
490440 AATGGTGAGT
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
63 6 0.08
64 42 0.59
65 23 0.32
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.32
Consensus pattern (64 bp):
CGATGCATAATATGCATTCGATGTTTTCATAAAAACCTGAGTGCATCGATGAATGGTAGTGCAT
Found at i:491148 original size:13 final size:14
Alignment explanation
Indices: 491130--491158 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
491120 GATCGAACAC
491130 TTAAATTTT-AATT
1 TTAAATTTTAAATT
491143 TTAAATTTTAAATT
1 TTAAATTTTAAATT
491157 TT
1 TT
491159 TTAAATTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTAAATTTTAAATT
Found at i:491149 original size:7 final size:7
Alignment explanation
Indices: 491130--491158 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
491120 GATCGAACAC
491130 TTAAATT
1 TTAAATT
491137 TT-AATT
1 TTAAATT
491143 TTAAATT
1 TTAAATT
491150 TTAAATT
1 TTAAATT
491157 TT
1 TT
491159 TTAAATTAAG
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TTAAATT
Found at i:493923 original size:23 final size:23
Alignment explanation
Indices: 493867--493910 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
493857 AATAAAGACT
493867 ATGCTGAATGAAACAACAAAACA
1 ATGCTGAATGAAACAACAAAACA
493890 ATGCTGAATGAAACAACAAAA
1 ATGCTGAATGAAACAACAAAA
493911 TATTGCTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.57, C:0.16, G:0.14, T:0.14
Consensus pattern (23 bp):
ATGCTGAATGAAACAACAAAACA
Found at i:493930 original size:23 final size:23
Alignment explanation
Indices: 493867--493923 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
493857 AATAAAGACT
*
493867 ATGCTGAATGAAACAACAAAACA
1 ATGCTAAATGAAACAACAAAACA
* *
493890 ATGCTGAATGAAACAACAAAATA
1 ATGCTAAATGAAACAACAAAACA
*
493913 TTGCTAAATGA
1 ATGCTAAATGA
493924 TTCAACATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.53, C:0.14, G:0.14, T:0.19
Consensus pattern (23 bp):
ATGCTAAATGAAACAACAAAACA
Found at i:509725 original size:3 final size:3
Alignment explanation
Indices: 509719--509751 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
509709 ACATTATTAT
509719 TAA TAA TAA -AA T-A TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
509752 TCCCGGACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:510029 original size:54 final size:53
Alignment explanation
Indices: 509933--510521 Score: 439
Period size: 54 Copynumber: 10.9 Consensus size: 53
509923 CGAAAAACAT
* * * * * *
509933 GTTCACTCCCTATTCCTTCAGGAAGTA-GAAACTCGAACAATCTTTTGCCTACGG
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATGGAACTCGAAC-ATCTTTT-CTTACGG
* * * * ** *
509987 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTTGAAAATCTTCTGCAAATGG
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATGGAACTCGAACATCTT-TTCTTACGG
* * * * * *** *
510041 GTTCACTCCCTCTTTCTTAAGGGAGTATAGAACTCTAAGATCTTTTGAAAACGT
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATGGAACTCGAACATCTTTT-CTTACGG
* * * * * * **
510095 G-TCTGCTCCCTATTCCTTTAGAGAGTAT-GAGACTCGAACAT-TCTTC-AACAATC
1 GTTC-GCTCCCTCTTTCTTCAGGGAGTATGGA-ACTCGAACATCTTTTCTTAC--GG
* * * * * * *
510148 GTGTCTACTCCCTATTCCTTCAGAGAGTAT-AAGACTCGAACATATTCTCTTACGG
1 GT-TC-GCTCCCTCTTTCTTCAGGGAGTATGGA-ACTCGAACATCTTTTCTTACGG
* *
510203 GTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATATTCTTCTTACGG
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATGGAACTCGAACATCTT-TTCTTACGG
*
510257 GTTCGCTCCCTCATTC-TCTAGGGAGTATGGAACTC-AAGCATCTTCTTCTTACGG
1 GTTCGCTCCCTCTTTCTTC-AGGGAGTATGGAACTCGAA-CATCTT-TTCTTACGG
* * *
510311 GTTCGCTCCCTCTTTC-TCTAGGGAGTATGGAACTCAAACATATTCTTCTTACAG
1 GTTCGCTCCCTCTTTCTTC-AGGGAGTATGGAACTCGAACATCTT-TTCTTACGG
* *
510365 GTTCGCTCCCTTTTTC-TCTAGGGAGTATGGAACTCGAATATCTTCTTCTTACGG
1 GTTCGCTCCCTCTTTCTTC-AGGGAGTATGGAACTCGAACATCTT-TTCTTACGG
*
510419 GTTCGCTCCCTCTTTC-TCTAGGGAGTATGGAGA-TCGAACATCTTTTTCTTATGG
1 GTTCGCTCCCTCTTTCTTC-AGGGAGTATGGA-ACTCGAACATC-TTTTCTTACGG
* *
510473 GCTCGTTCCCTCTTTC-TCTAGGGAGTATGGAACTCGAACATCTTGTTCT
1 GTTCGCTCCCTCTTTCTTC-AGGGAGTATGGAACTCGAACATCTT-TTCT
510522 GCTTTACTAC
Statistics
Matches: 452, Mismatches: 63, Indels: 40
0.81 0.11 0.07
Matches are distributed among these distances:
51 3 0.01
53 47 0.10
54 345 0.76
55 52 0.12
56 3 0.01
57 2 0.00
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.35
Consensus pattern (53 bp):
GTTCGCTCCCTCTTTCTTCAGGGAGTATGGAACTCGAACATCTTTTCTTACGG
Found at i:510485 original size:162 final size:161
Alignment explanation
Indices: 510181--510513 Score: 526
Period size: 162 Copynumber: 2.1 Consensus size: 161
510171 AGAGTATAAG
* *
510181 ACTCGAACATATTCTCTTACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATAT
1 ACTCGAACATATTCTCTTACAGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATAT
510246 TCTTCTTACGGGTTCGCTCCCTCATTCTCTAGGGAGTATGGAACTCAAGCATCTTCTTCTTACGG
66 TCTTCTTACGGGTTCGCTCCCTCATTCTCTAGGGAGTATGGAACTCAAGCATCTTCTTCTTACGG
*
510311 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
131 GCTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * * *
510342 ACTCAAACATATTCTTCTTACAGGTTCGCTCCCTTTTTCTCTAGGGAGTATGGAACTCGAATATC
1 ACTCGAACATATTC-TCTTACAGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATA
* *
510407 TTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAGA-TCGAA-CATCTTTTTCTTA
65 TTCTTCTTACGGGTTCGCTCCCTCATTCTCTAGGGAGTATGGA-ACTC-AAGCATCTTCTTCTTA
* *
510470 TGGGCTCGTTCCCTCTTTCTCTAGGGAGTATGGA
128 CGGGCTCGCTCCCTCTTTCTCTAGGGAGTATGGA
510504 ACTCGAACAT
1 ACTCGAACAT
510514 CTTGTTCTGC
Statistics
Matches: 157, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
161 13 0.08
162 141 0.90
163 3 0.02
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.36
Consensus pattern (161 bp):
ACTCGAACATATTCTCTTACAGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATAT
TCTTCTTACGGGTTCGCTCCCTCATTCTCTAGGGAGTATGGAACTCAAGCATCTTCTTCTTACGG
GCTCGCTCCCTCTTTCTCTAGGGAGTATGGA
Found at i:510594 original size:37 final size:37
Alignment explanation
Indices: 510521--510600 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 37
510511 CATCTTGTTC
* * * *
510521 TGCTTTACTACTTTCTTGTGAAGACTTCTAGATGATT
1 TGCTTCACTACTCTCTCGTGAAGACTTCAAGATGATT
*
510558 TGCTTCACTACTCTCTCGTGAAGACTT-AAGTTTGATT
1 TGCTTCACTACTCTCTCGTGAAGACTTCAAG-ATGATT
510595 TGCTTC
1 TGCTTC
510601 GAAGGTCGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 2 0.05
37 35 0.95
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.44
Consensus pattern (37 bp):
TGCTTCACTACTCTCTCGTGAAGACTTCAAGATGATT
Found at i:510953 original size:37 final size:36
Alignment explanation
Indices: 510912--510984 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
510902 TTCTGAGAAT
510912 GCTTAAAAAGGATATGCTTCACTACTCTTTGGTGAAG
1 GCTTAAAAAGG-TATGCTTCACTACTCTTTGGTGAAG
* * *
510949 GCTTAAGATGGTTTGCTTCACTACTCTTTGGTGAAG
1 GCTTAAAAAGGTATGCTTCACTACTCTTTGGTGAAG
510985 ACTTGGCTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 24 0.73
37 9 0.27
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (36 bp):
GCTTAAAAAGGTATGCTTCACTACTCTTTGGTGAAG
Found at i:512378 original size:124 final size:124
Alignment explanation
Indices: 512218--512442 Score: 353
Period size: 124 Copynumber: 1.8 Consensus size: 124
512208 TGATACGGGC
* * * *
512218 CTTCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATTCTCAAAGCCTTCTTGGTCTGAATCTT
1 CTTCAAAATGACCCAACACCTCAAATTGTAAGGCTCATTCTCAAAGCCTTCTTCGTCCGAATCAT
* **
512283 GTCATTTCATCATGATGTG-GGTTCAGTCATGCCCCAATATAATCTTTTACTGTACAGGT
66 GTCATCTCAAAATGATG-GAGGTTCAGTCATGCCCCAATATAATCTTTTACTGTACAGGT
* *
512342 CTTCAAAATGACCCAACACCTCAAATTGTAAGGCTCATTCTCAATGTCTTCTTCGTCCGAATCAT
1 CTTCAAAATGACCCAACACCTCAAATTGTAAGGCTCATTCTCAAAGCCTTCTTCGTCCGAATCAT
512407 GTCATCTCAAAATGATGGAGGTTCAGTCATGCCCCA
66 GTCATCTCAAAATGATGGAGGTTCAGTCATGCCCCA
512443 GTGTAGGTAT
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
123 1 0.01
124 90 0.99
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (124 bp):
CTTCAAAATGACCCAACACCTCAAATTGTAAGGCTCATTCTCAAAGCCTTCTTCGTCCGAATCAT
GTCATCTCAAAATGATGGAGGTTCAGTCATGCCCCAATATAATCTTTTACTGTACAGGT
Found at i:515843 original size:72 final size:72
Alignment explanation
Indices: 515720--515870 Score: 230
Period size: 72 Copynumber: 2.1 Consensus size: 72
515710 CCCCTAACAG
* * * *
515720 GTTCTTGATCAGTTGCTATCATCACATTGGTTGCACCACTAATATTAAGATTCTCACTCGAAGTC
1 GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTAAGATTCTCACCCAAAGTC
*
515785 TTCATCT
66 TTCATAT
* *
515792 GTTCTTGATCATTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCAAAGTC
1 GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTAAGATTCTCACCCAAAGTC
515857 TTCATAT
66 TTCATAT
*
515864 TTTCTTG
1 GTTCTTG
515871 TGTAATAGGG
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.38
Consensus pattern (72 bp):
GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTAAGATTCTCACCCAAAGTC
TTCATAT
Found at i:516625 original size:55 final size:55
Alignment explanation
Indices: 516554--516661 Score: 171
Period size: 55 Copynumber: 2.0 Consensus size: 55
516544 TGTGGATCAG
* * *
516554 TCTTCAATCAGTTTCAAATTTCTCCATTCATTGGATGTCCTTCTTCATGAATCCT
1 TCTTCAATCAGGTTCAAATTTCTCCATTCATCGGATGTCCTGCTTCATGAATCCT
* *
516609 TCTTCAGTCAGGTTCAAATTTCTTCATTCATCGGATGTCCTGCTTCATGAATC
1 TCTTCAATCAGGTTCAAATTTCTCCATTCATCGGATGTCCTGCTTCATGAATC
516662 ATCTGAACGC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.21, C:0.25, G:0.12, T:0.42
Consensus pattern (55 bp):
TCTTCAATCAGGTTCAAATTTCTCCATTCATCGGATGTCCTGCTTCATGAATCCT
Found at i:517029 original size:47 final size:47
Alignment explanation
Indices: 516964--517097 Score: 171
Period size: 47 Copynumber: 2.8 Consensus size: 47
516954 CTTGTCATTC
* * * * * * *
516964 ACAAAAAATCCTAACCGCATGATATCTAATTCGCATGCTTGTTCGAGAA
1 ACAATAAA-CCTAACCGCATGATTTCTAGTTCGCATACATGCTC-AAAA
*
517013 A-AATAAACCTAGCCGCATGATTTCTAGTTCGCATACATGCTCAAAA
1 ACAATAAACCTAACCGCATGATTTCTAGTTCGCATACATGCTCAAAA
517059 ACAATAAACCTAACCGCATGATTTCTAGTTCGCATACAT
1 ACAATAAACCTAACCGCATGATTTCTAGTTCGCATACAT
517098 TTATTCAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
46 4 0.05
47 65 0.87
48 5 0.07
49 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.27
Consensus pattern (47 bp):
ACAATAAACCTAACCGCATGATTTCTAGTTCGCATACATGCTCAAAA
Found at i:521142 original size:3 final size:3
Alignment explanation
Indices: 521136--521168 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
521126 ACATTATTAT
521136 TAA TAA TAA -AA T-A TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
521169 TCCCGGACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:522155 original size:13 final size:13
Alignment explanation
Indices: 522129--522171 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
522119 ATGAAATGTA
*
522129 AAAGTGAATG-TG
1 AAAGTGAAAGATG
522141 AAAGTGAAAGATG
1 AAAGTGAAAGATG
* *
522154 AAAATGAAATATG
1 AAAGTGAAAGATG
522167 AAAGT
1 AAAGT
522172 TTTGTATTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
12 9 0.35
13 17 0.65
ACGTcount: A:0.53, C:0.00, G:0.26, T:0.21
Consensus pattern (13 bp):
AAAGTGAAAGATG
Found at i:522161 original size:19 final size:20
Alignment explanation
Indices: 522113--522163 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
522103 CGTACAAATT
522113 ATGAAAATGAAATGTAAAAG
1 ATGAAAATGAAATGTAAAAG
** *
522133 -TGAATGTGAAA-GTGAAAG
1 ATGAAAATGAAATGTAAAAG
522151 ATGAAAATGAAAT
1 ATGAAAATGAAAT
522164 ATGAAAGTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.55, C:0.00, G:0.24, T:0.22
Consensus pattern (20 bp):
ATGAAAATGAAATGTAAAAG
Found at i:523110 original size:83 final size:85
Alignment explanation
Indices: 523000--523167 Score: 286
Period size: 89 Copynumber: 2.0 Consensus size: 85
522990 AAAATTTACC
523000 AATTTCCCCTCAATTAAAAAATTGCATTTAT-A-AAAAAAAATATTTAACCTCTGTTATAATAAA
1 AATTTCCCCTCAATTAAAAAATTGCATTTATAATAAAAAAAATATTTAACCTCTGTTATAATAAA
523063 TTCCTAGTTTTACCTCTACT
66 TTCCTAGTTTTACCTCTACT
523083 AATTTCCCCTCAATTAAAAAATTGCATTTATAAAAAATAAAAAAAATATTTAACCTCTGTTATAA
1 AATTTCCCCTCAATTAAAAAATTGCATTTAT----AATAAAAAAAATATTTAACCTCTGTTATAA
523148 TAAATTCCTAGTTTTACCTC
62 TAAATTCCTAGTTTTACCTC
523168 GACTGAAATC
Statistics
Matches: 79, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
83 31 0.39
88 1 0.01
89 47 0.59
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.38
Consensus pattern (85 bp):
AATTTCCCCTCAATTAAAAAATTGCATTTATAATAAAAAAAATATTTAACCTCTGTTATAATAAA
TTCCTAGTTTTACCTCTACT
Found at i:528646 original size:13 final size:13
Alignment explanation
Indices: 528625--528681 Score: 62
Period size: 13 Copynumber: 4.5 Consensus size: 13
528615 TACGGATTAC
* *
528625 GAAAATGAAATGT
1 GAAAGTGAAATAT
528638 GAAAGTG-AATAT
1 GAAAGTGAAATAT
*
528650 GAAAGTGAAAGAT
1 GAAAGTGAAATAT
* *
528663 GAAACTGAGATAT
1 GAAAGTGAAATAT
528676 GAAAGT
1 GAAAGT
528682 TTTGTATTGT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
12 11 0.31
13 25 0.69
ACGTcount: A:0.51, C:0.02, G:0.26, T:0.21
Consensus pattern (13 bp):
GAAAGTGAAATAT
Found at i:528653 original size:19 final size:19
Alignment explanation
Indices: 528629--528665 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
528619 GATTACGAAA
528629 ATGAAATGTGAAAG-TGAAT
1 ATGAAA-GTGAAAGATGAAT
528648 ATGAAAGTGAAAGATGAA
1 ATGAAAGTGAAAGATGAA
528666 ACTGAGATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.51, C:0.00, G:0.27, T:0.22
Consensus pattern (19 bp):
ATGAAAGTGAAAGATGAAT
Found at i:528756 original size:39 final size:39
Alignment explanation
Indices: 528711--528793 Score: 123
Period size: 39 Copynumber: 2.1 Consensus size: 39
528701 AAAAAGAATA
*
528711 TGATATGACTATTATGCATGATATTGTTTATCAT-GTCTT
1 TGATATGACTATTATGCATGATATTGTTTAGCATGGT-TT
**
528750 TGATATGACTATTATTTATGATATTGTTTAGCATGGTTT
1 TGATATGACTATTATGCATGATATTGTTTAGCATGGTTT
528789 TGATA
1 TGATA
528794 AAATCATGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
39 38 0.95
40 2 0.05
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.49
Consensus pattern (39 bp):
TGATATGACTATTATGCATGATATTGTTTAGCATGGTTT
Found at i:532894 original size:50 final size:50
Alignment explanation
Indices: 532831--532938 Score: 198
Period size: 50 Copynumber: 2.2 Consensus size: 50
532821 TATGTTCAAG
* *
532831 AACAAACTCATGTATGAGTTCGTTTATTGATTCGTTTATTTATGTTGATT
1 AACAAGCTAATGTATGAGTTCGTTTATTGATTCGTTTATTTATGTTGATT
532881 AACAAGCTAATGTATGAGTTCGTTTATTGATTCGTTTATTTATGTTGATT
1 AACAAGCTAATGTATGAGTTCGTTTATTGATTCGTTTATTTATGTTGATT
532931 AACAAGCT
1 AACAAGCT
532939 CGTTTAGAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.45
Consensus pattern (50 bp):
AACAAGCTAATGTATGAGTTCGTTTATTGATTCGTTTATTTATGTTGATT
Found at i:539998 original size:9 final size:9
Alignment explanation
Indices: 539984--540011 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
539974 TATATTTTGT
539984 TTTTGCTTA
1 TTTTGCTTA
539993 TTTTGCTTA
1 TTTTGCTTA
540002 TTTTGCTTA
1 TTTTGCTTA
540011 T
1 T
540012 GAATGCTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.68
Consensus pattern (9 bp):
TTTTGCTTA
Found at i:545581 original size:64 final size:65
Alignment explanation
Indices: 545468--545610 Score: 168
Period size: 64 Copynumber: 2.2 Consensus size: 65
545458 TGCACTAAGA
* *
545468 GTGCATCGATGCATAAAATGTATTCAATGTTTCAAAATAGCCAGAGTGCATCGATGCATGG-TAT
1 GTGCATCGATGCATAAAATGCATTCAATGTCTCAAAATAGCCAGAGTGCATCGATGCATGGAT-T
545532 -
65 G
* ** *
545532 GTGCATCGATGCATAAAATGCATTCGATG-CTCAATTTAATCCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATAAAATGCATTCAATGTCTCAAAAT-AGCCA-GAGTGCATCGATGCATGGAT
545595 TG
64 TG
*
545597 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
545611 CACTTTGAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
63 5 0.07
64 48 0.71
65 15 0.22
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCAATGTCTCAAAATAGCCAGAGTGCATCGATGCATGGATTG
Found at i:546075 original size:2 final size:2
Alignment explanation
Indices: 546063--546093 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
546053 GTCAATTGAT
*
546063 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
546094 CTTAAGCTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 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):
TA
Found at i:547341 original size:42 final size:43
Alignment explanation
Indices: 547248--547341 Score: 111
Period size: 42 Copynumber: 2.2 Consensus size: 43
547238 GACCTTGTGC
**
547248 ATCGATGCACATTAAAGGCATGCATCGGTGCACCTTATGGTGT
1 ATCGATGCACATTAAAGGCATGCATCGACGCACCTTATGGTGT
* * * *
547291 ATCAATGCACATTCAAGG-ATGCGTCGACGCACTGTTA-GGTGT
1 ATCGATGCACATTAAAGGCATGCATCGACGCAC-CTTATGGTGT
547333 ATCGATGCA
1 ATCGATGCA
547342 TTAAGTACAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
42 24 0.56
43 19 0.44
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.27
Consensus pattern (43 bp):
ATCGATGCACATTAAAGGCATGCATCGACGCACCTTATGGTGT
Found at i:555378 original size:6 final size:6
Alignment explanation
Indices: 555367--555399 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
555357 TTATTTTCTC
*
555367 TTTTAT TTTTAT TTTTAT TCTTAT TTTT-T TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
555400 GTAGATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:555378 original size:18 final size:18
Alignment explanation
Indices: 555355--555399 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
555345 TAAATAATAA
*
555355 TTTTATTTTCTCTT-TTAT
1 TTTTATTTT-TATTCTTAT
555373 TTTTATTTTTATTCTTAT
1 TTTTATTTTTATTCTTAT
555391 TTTT-TTTTT
1 TTTTATTTTT
555400 GTAGATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTATTTTTATTCTTAT
Found at i:570312 original size:41 final size:41
Alignment explanation
Indices: 570258--570338 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 41
570248 CGGAACCCAA
* *
570258 TTTCCAATTTCGCAACGCGAATATGTAAATCGCAATGCGAT
1 TTTCCAAATTCGCAACGCGAATATGTAAATCGCAACGCGAT
* *
570299 TTTCCAAATTCGCAATGCGAATCTGTAAATCGCAACGCGA
1 TTTCCAAATTCGCAACGCGAATATGTAAATCGCAACGCGA
570339 ATTTGTAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.27
Consensus pattern (41 bp):
TTTCCAAATTCGCAACGCGAATATGTAAATCGCAACGCGAT
Found at i:570383 original size:20 final size:20
Alignment explanation
Indices: 570203--570489 Score: 180
Period size: 20 Copynumber: 14.3 Consensus size: 20
570193 AAATTACCAA
* *
570203 CAAATTCGCAATGCGAT-CT
1 CAAATTCGCAACGCGATAGT
*
570222 CAAATTCGCAACGCGA-ACT
1 CAAATTCGCAACGCGATAGT
* * * * *
570241 CCAATTTCGGAACCCAAT-TT
1 -CAAATTCGCAACGCGATAGT
*
570261 CCAATTTCGCAACGCGAATATGT
1 -CAAATTCGCAACGCG-ATA-GT
* **
570284 -AAA-TCGCAATGCGATTTT
1 CAAATTCGCAACGCGATAGT
* *
570302 CCAAATTCGCAATGCGAATCTGT
1 -CAAATTCGCAACGCG-AT-AGT
*
570325 -AAA-TCGCAACGCGAATTTGT
1 CAAATTCGCAACGCG-A-TAGT
* *
570345 -AAA-TCTCAACACAGA-AGT
1 CAAATTCGCAACGC-GATAGT
570363 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGATAGT
* * *
570383 CAAATTCGCAACACAAAAGT
1 CAAATTCGCAACGCGATAGT
*** *
570403 CAAATTCGCAACATAAAAGT
1 CAAATTCGCAACGCGATAGT
*
570423 CAAATTCGCAACGTGATAGT
1 CAAATTCGCAACGCGATAGT
*
570443 CAAATTCGCAACGCGGTAGT
1 CAAATTCGCAACGCGATAGT
570463 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGATAGT
570483 CAAATTC
1 CAAATTC
570490 CTCTACCAAA
Statistics
Matches: 221, Mismatches: 31, Indels: 31
0.78 0.11 0.11
Matches are distributed among these distances:
18 3 0.01
19 24 0.11
20 170 0.77
21 19 0.09
22 2 0.01
23 3 0.01
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.23
Consensus pattern (20 bp):
CAAATTCGCAACGCGATAGT
Found at i:571125 original size:65 final size:65
Alignment explanation
Indices: 571009--571152 Score: 245
Period size: 66 Copynumber: 2.2 Consensus size: 65
570999 ATTTCAAAAC
571009 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATC-AATT
571074 A
65 A
* **
571075 AACAAATCAACTTTTACAAATCAATTAAACAAGC-AAAAAATAATTCTTATTTCCTTATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTA
571139 AACAAATCAACTTT
1 AACAAATCAACTTT
571153 CAATGTAAAA
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
64 19 0.25
65 22 0.29
66 34 0.45
ACGTcount: A:0.51, C:0.17, G:0.01, T:0.31
Consensus pattern (65 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTA
Found at i:572535 original size:21 final size:21
Alignment explanation
Indices: 572473--572564 Score: 62
Period size: 21 Copynumber: 4.4 Consensus size: 21
572463 ATGAATCGGG
* * * *
572473 CTCTTGAACGGTGGGTGGGAC
1 CTCTTGAACAGTGAGAGGGGC
* *
572494 CTCTTGAAC-GATGACATGGGC
1 CTCTTGAACAG-TGAGAGGGGC
*
572515 CTCTTGAACAGTGGGAGGGGC
1 CTCTTGAACAGTGAGAGGGGC
* **
572536 TTCTTCGATGA-TGAGAGGGGC
1 CTCTT-GAACAGTGAGAGGGGC
572557 CTCTTGAA
1 CTCTTGAA
572565 TGATAGGAGG
Statistics
Matches: 54, Mismatches: 14, Indels: 7
0.72 0.19 0.09
Matches are distributed among these distances:
20 3 0.06
21 47 0.87
22 4 0.07
ACGTcount: A:0.20, C:0.20, G:0.36, T:0.25
Consensus pattern (21 bp):
CTCTTGAACAGTGAGAGGGGC
Found at i:572567 original size:21 final size:21
Alignment explanation
Indices: 572493--572591 Score: 87
Period size: 21 Copynumber: 4.7 Consensus size: 21
572483 GTGGGTGGGA
* * *
572493 CCTCTTGAACGATGACATGGG
1 CCTCTTGAATGATGAGAGGGG
* *
572514 CCTCTTGAA-CAGTGGGAGGGG
1 CCTCTTGAATGA-TGAGAGGGG
*
572535 CTTCTTCG-ATGATGAGAGGGG
1 CCTCTT-GAATGATGAGAGGGG
*
572556 CCTCTTGAATGAT-AGGAGGTG
1 CCTCTTGAATGATGA-GAGGGG
572577 CCTCTTGAATGATGA
1 CCTCTTGAATGATGA
572592 TAGGTGCATC
Statistics
Matches: 63, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
20 3 0.05
21 57 0.90
22 3 0.05
ACGTcount: A:0.22, C:0.18, G:0.33, T:0.26
Consensus pattern (21 bp):
CCTCTTGAATGATGAGAGGGG
Found at i:572574 original size:42 final size:42
Alignment explanation
Indices: 572473--572591 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
572463 ATGAATCGGG
* * * * * * *
572473 CTCTTGAACGGTGGGTGGGACCTCTTGAACGATGACATGGGC
1 CTCTTGAACAGTAGGAGGGGCCTCTTGAATGATGAGAGGGGC
* *
572515 CTCTTGAACAGTGGGAGGGGCTTCTTCG-ATGATGAGAGGGGC
1 CTCTTGAACAGTAGGAGGGGCCTCTT-GAATGATGAGAGGGGC
* *
572557 CTCTTGAA-TGATAGGAGGTGCCTCTTGAATGATGA
1 CTCTTGAACAG-TAGGAGGGGCCTCTTGAATGATGA
572592 TAGGTGCATC
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
41 2 0.03
42 60 0.95
43 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.35, T:0.26
Consensus pattern (42 bp):
CTCTTGAACAGTAGGAGGGGCCTCTTGAATGATGAGAGGGGC
Found at i:572596 original size:21 final size:21
Alignment explanation
Indices: 572543--572598 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
572533 GGCTTCTTCG
*
572543 ATGATGAGAGGGGCCTCTTGA
1 ATGATGAGAGGTGCCTCTTGA
572564 ATGAT-AGGAGGTGCCTCTTGA
1 ATGATGA-GAGGTGCCTCTTGA
*
572585 ATGATGATAGGTGC
1 ATGATGAGAGGTGC
572599 ATCGGGCTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.25, C:0.12, G:0.36, T:0.27
Consensus pattern (21 bp):
ATGATGAGAGGTGCCTCTTGA
Found at i:575307 original size:20 final size:20
Alignment explanation
Indices: 575282--575356 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
575272 GTGTTTTGCA
575282 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
***
575302 TTGCGAATTTGACTTTTATG
1 TTGCGAATTTGACTTTCGCG
* *
575322 TTGCGAATTTGGCTATCGCG
1 TTGCGAATTTGACTTTCGCG
575342 TTGCGAATTTGACTT
1 TTGCGAATTTGACTT
575357 CTGTGTTGCG
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.17, C:0.16, G:0.24, T:0.43
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGCG
Found at i:575326 original size:40 final size:40
Alignment explanation
Indices: 575282--575367 Score: 136
Period size: 40 Copynumber: 2.1 Consensus size: 40
575272 GTGTTTTGCA
* *
575282 TTGCGAATTTGACTTTCGCGTTGCGAATTTGACTTTTATG
1 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTATG
* *
575322 TTGCGAATTTGGCTATCGCGTTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTATG
575362 TTGCGA
1 TTGCGA
575368 TTTACAGATT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.16, C:0.16, G:0.26, T:0.42
Consensus pattern (40 bp):
TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTATG
Found at i:575364 original size:20 final size:20
Alignment explanation
Indices: 575282--575367 Score: 95
Period size: 20 Copynumber: 4.3 Consensus size: 20
575272 GTGTTTTGCA
575282 TTGCGAATTTGACTT-TCGCG
1 TTGCGAATTTGACTTCT-GCG
* **
575302 TTGCGAATTTGACTTTTATG
1 TTGCGAATTTGACTTCTGCG
*
575322 TTGCGAATTTGGCTATC-GCG
1 TTGCGAATTTGACT-TCTGCG
*
575342 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGCG
575362 TTGCGA
1 TTGCGA
575368 TTTACAGATT
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
19 2 0.04
20 51 0.93
21 2 0.04
ACGTcount: A:0.16, C:0.16, G:0.26, T:0.42
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGCG
Found at i:575405 original size:20 final size:20
Alignment explanation
Indices: 575361--575407 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
575351 TGACTTCTGT
575361 GTTGCGATTTACAGATTCAC
1 GTTGCGATTTACAGATTCAC
* * **
575381 TTTGCGATTTATAGATTTGC
1 GTTGCGATTTACAGATTCAC
575401 GTTGCGA
1 GTTGCGA
575408 ATTTGGAAAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.40
Consensus pattern (20 bp):
GTTGCGATTTACAGATTCAC
Found at i:578350 original size:3 final size:3
Alignment explanation
Indices: 578274--578337 Score: 87
Period size: 3 Copynumber: 21.7 Consensus size: 3
578264 TTCATTTGAA
*
578274 TAT TAT T-T ATAT TAT TAT AAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
578319 TAT TAT TGT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
578338 ATAAATATTA
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
2 3 0.05
3 51 0.93
4 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:579561 original size:25 final size:25
Alignment explanation
Indices: 579491--579561 Score: 62
Period size: 25 Copynumber: 2.9 Consensus size: 25
579481 AGTCATTAAC
*
579491 TTTAAATTAT-TA-GTTTATTA-TT
1 TTTAATTTATATATGTTTATTATTT
*
579513 TTTAATTTCATTTAT-TTTAGTTATTGT
1 TTTAATTT-ATATATGTTTA-TTATT-T
579540 TTTAATTT-TATATGTTTATTAT
1 TTTAATTTATATATGTTTATTAT
579562 CAATATATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
22 7 0.17
23 2 0.05
24 6 0.15
25 11 0.28
26 5 0.12
27 9 0.22
ACGTcount: A:0.27, C:0.01, G:0.06, T:0.66
Consensus pattern (25 bp):
TTTAATTTATATATGTTTATTATTT
Found at i:580316 original size:20 final size:20
Alignment explanation
Indices: 580291--580330 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
580281 TTAGAAATTT
580291 AAAATTCATATAT-TTTATTA
1 AAAATT-ATATATATTTATTA
580311 AAAATTATATATATTTATTA
1 AAAATTATATATATTTATTA
580331 TTTTCATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
AAAATTATATATATTTATTA
Found at i:580360 original size:20 final size:21
Alignment explanation
Indices: 580326--580375 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
580316 TATATATATT
580326 TATTATTTTCATAAT-ATTTA
1 TATTATTTTCATAATGATTTA
*
580346 TATTATTTT-ATTAATGTTTTA
1 TATTATTTTCA-TAATGATTTA
*
580367 TTTTATTTT
1 TATTATTTT
580376 TCAAGTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 1 0.04
20 13 0.50
21 12 0.46
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (21 bp):
TATTATTTTCATAATGATTTA
Found at i:583674 original size:15 final size:15
Alignment explanation
Indices: 583654--583685 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
583644 GATCAATACC
583654 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
583669 TTTTGCATACATTCA
1 TTTTGCATACATGCA
583684 TT
1 TT
583686 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:586900 original size:11 final size:11
Alignment explanation
Indices: 586884--586913 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
586874 GAGCTAAAAC
586884 TGGGAAAGGTT
1 TGGGAAAGGTT
586895 TGGGAAAGGTT
1 TGGGAAAGGTT
586906 TGGGAAAG
1 TGGGAAAG
586914 AATCTTCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (11 bp):
TGGGAAAGGTT
Found at i:592278 original size:113 final size:112
Alignment explanation
Indices: 592076--592524 Score: 596
Period size: 113 Copynumber: 4.0 Consensus size: 112
592066 GCAAAGATTC
* * * *
592076 AAATCCATCATTCAATGGATCAACATTTCCAGAAGAGTTCGTAATGAGAAGAACTCATCTGAAGA
1 AAATTCATCATTCGATGGATCAACATTTCCAGTAGAGTTCATAATGAGAAGAACTCATCTGAAGA
*
592141 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTT
* * *
592188 GAATTCATCATTCGATGGATCAGCATTTCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATTCATCATTCGATGGATCAACATTTCCA-GTAGAGTTCATAATGAGAAGAACTCATCTGAAG
*
592253 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTT
* * ** * * * *
592301 AAATTCATCACTCGGTGGATCAGTAGTGCCATTTAGAGTTCATAATGAGAACAACTCATCTGAAG
1 AAATTCATCATTCGATGGATCAACATTTCCA-GTAGAGTTCATAATGAGAAGAACTCATCTGAAG
* * * * *
592366 AAGAAAGAAGAAATTCATAATGATAAGAAATTGTTCAACCTTTTACTT
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTT
* *
592414 AAATTCATCACTT-GATGGATCAACTTTTCCAAAG-AAAGTTCATAATGAGAAGAACTCATCTGA
1 AAATTCATCA-TTCGATGGATCAACATTTCC--AGTAGAGTTCATAATGAGAAGAACTCATCTGA
* * *
592477 AGAAGGAAGAAGAAGTTCATAATAAGAAGAGCTTGTTCGACCTTTTGC
63 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
592525 ATGACTCTAT
Statistics
Matches: 290, Mismatches: 43, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
112 27 0.09
113 261 0.90
114 1 0.00
115 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (112 bp):
AAATTCATCATTCGATGGATCAACATTTCCAGTAGAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTT
Found at i:592933 original size:3 final size:3
Alignment explanation
Indices: 592862--592920 Score: 84
Period size: 3 Copynumber: 19.7 Consensus size: 3
592852 TTCATTTGAA
*
592862 TAT TAT T-T ATAT TAT TAT TAT TAT AAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
592907 TTT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
592921 ATAAATATTA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 1 0.02
3 48 0.96
4 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:595748 original size:23 final size:22
Alignment explanation
Indices: 595722--595769 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
595712 CAAAAATTTC
595722 AAATTTCAGCTTAATTACAAAAA
1 AAATTT-AGCTTAATTACAAAAA
*
595745 AAA-TTGGCTTAATTACAAAAA
1 AAATTTAGCTTAATTACAAAAA
595766 AAAT
1 AAAT
595770 CCAAACTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 18 0.78
22 2 0.09
23 3 0.13
ACGTcount: A:0.54, C:0.10, G:0.06, T:0.29
Consensus pattern (22 bp):
AAATTTAGCTTAATTACAAAAA
Found at i:595756 original size:21 final size:21
Alignment explanation
Indices: 595730--595769 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
595720 TCAAATTTCA
595730 GCTTAATTACAAAAAAAATTG
1 GCTTAATTACAAAAAAAATTG
595751 GCTTAATTACAAAAAAAAT
1 GCTTAATTACAAAAAAAAT
595770 CCAAACTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (21 bp):
GCTTAATTACAAAAAAAATTG
Found at i:596991 original size:20 final size:20
Alignment explanation
Indices: 596966--597004 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
596956 TTGATTAATG
596966 ATTTTTATT-CTCAAATGAAT
1 ATTTTT-TTACTCAAATGAAT
596986 ATTTTTTTACTCAAATGAA
1 ATTTTTTTACTCAAATGAA
597005 ACGAATGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (20 bp):
ATTTTTTTACTCAAATGAAT
Found at i:599855 original size:3 final size:3
Alignment explanation
Indices: 599801--599835 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
599791 CTCTTCTGTA
599801 ATT ATT GATT ATT ATT ATT ATT ATT ATT ATT -TT AT
1 ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
599836 AAAAAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:604324 original size:81 final size:81
Alignment explanation
Indices: 604225--604790 Score: 891
Period size: 81 Copynumber: 7.0 Consensus size: 81
604215 CACAGCTAAT
* * * *
604225 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGATACATTTTTAC
1 CCATTATTCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTAC
604290 CAATTGCACAGTTAGA
66 CAATTGCACAGTTAGA
* * * *
604306 CCCTTATTCTTTTACTCAACGGTACTTAACCGTTCATCCAACTCGCATAATTGGTACCTTTATAC
1 CCATTATTCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTAC
* *
604371 CAATTGCATAGTTAGG
66 CAATTGCACAGTTAGA
* *
604387 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCTTCTAACTGGCATAATTGGTACCTTTCTAC
1 CCATTATTCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTAC
*
604452 CAATTGCACAGTTAGT
66 CAATTGCACAGTTAGA
** * * *
604468 CCATTATTCTTTTACTCAACAATACTCAATCGTTCATCTAACTGGCATAATTGATACCTTTCTAC
1 CCATTATTCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTAC
*
604533 AAATTGCACAGTTAGA
66 CAATTGCACAGTTAGA
604549 CCATTATTCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTAC
1 CCATTATTCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTAC
*
604614 CAATTGCA-ATGTTAGG
66 CAATTGCACA-GTTAGA
* * *
604630 CCATTATTCTTTTACTCAACGGTACTTAATCGTTCATCTAACTGGCATAATCGGTACCTTTATAC
1 CCATTATTCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTAC
*
604695 CAATTGCATAGTTAGA
66 CAATTGCACAGTTAGA
*
604711 CCATTATTCTTTTACTCAACGGTACTTAATCGTTCATCTAACTGGCATAATTGGTACCTTTCTAC
1 CCATTATTCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTAC
604776 CAATTGCACAGTTAG
66 CAATTGCACAGTTAG
604791 GCCTCAAAGG
Statistics
Matches: 443, Mismatches: 40, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
80 1 0.00
81 441 1.00
82 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (81 bp):
CCATTATTCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTAC
CAATTGCACAGTTAGA
Found at i:604841 original size:68 final size:68
Alignment explanation
Indices: 604743--605195 Score: 595
Period size: 68 Copynumber: 6.8 Consensus size: 68
604733 TACTTAATCG
* ** * **
604743 TTCATCTAACTGGCATAATTGGTACCTTTCTACCA-ATTGCACAGTTAGGCCTCAAAGGCACTTA
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATA-TGCACAGTTAGGCCTCAAAGGCACTTA
*
604807 GTCT
65 GCCT
* * *
604811 TTTATCTAACTGGCATAAATGACACATTTCTGTCATATGCACAGTTAGGCCTCAAAGGTACTTAA
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATATGCACAGTTAGGCCTCAAAGGCACTTAG
*
604876 CAT
66 CCT
* * * * *
604879 TTCATCTAACTGACATAAATGACACATTTCTATCATATCCACAGTTAGGCCTCAATGACACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATATGCACAGTTAGGCCTCAAAGGCACTTAG
604944 CCT
66 CCT
*
604947 TTCATCTAACTGGCATAAATGACACATTTATGTCATATG--C----A--CCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATATGCACAGTTAGGCCTCAAAGGCACTTAG
605004 CCT
66 CCT
* * *
605007 TTCATCTAACTAGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCATCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATATGCACAGTTAGGCCTCAAAGGCACTTAG
605072 CCT
66 CCT
* * *
605075 TTCATCTAACTGGAATAAATGACACCTTTCTGTTATATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATATGCACAGTTAGGCCTCAAAGGCACTTAG
605140 CCT
66 CCT
*
605143 TT-ACTCTAACTGGCATAAATGACAC-CTTCTGTCATATGCACAGTTAGGCCTCA
1 TTCA-TCTAACTGGCATAAATGACACATTTCTGTCATATGCACAGTTAGGCCTCA
605196 TGATCTTTTA
Statistics
Matches: 338, Mismatches: 37, Indels: 21
0.85 0.09 0.05
Matches are distributed among these distances:
60 53 0.16
62 2 0.01
66 2 0.01
67 27 0.08
68 253 0.75
69 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACATTTCTGTCATATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:605126 original size:196 final size:195
Alignment explanation
Indices: 604792--605183 Score: 599
Period size: 196 Copynumber: 2.0 Consensus size: 195
604782 CACAGTTAGG
* * *
604792 CCTCAAAGGCACTTAGTCTTTTATCTAACTGGCATAAATGACACATTTCTGTCATATGCACAGTT
1 CCTCAAAGGCACTTAGCCTTTCATCTAACTAGCATAAATGACACATTTCTGTCATATGCACAGTT
* *
604857 AGGCCTCAAAGGTACTTAACATTTCATCTAACTGACATAAATGACACATTTCTATCATATCCACA
66 AGGCATCAAAGGCACTTAACATTTCATCTAACTGACATAAATGACACATTTCTATCATATCCACA
* *
604922 GTTAGGCCTCAATGACACTTAGCCTTT-CATCTAACTGGCATAAATGACACATTTATGTCATATG
131 GTTAGGCCTCAAAGACACTTAGCCTTTAC-TCTAACTGGCATAAATGACAC-CTTATGTCATATG
604986 CA
194 CA
*
604988 CCTCAAAGGCACTTAGCCTTTCATCTAACTAGCATAAATGACACCTTTCTGTCATATGCACAGTT
1 CCTCAAAGGCACTTAGCCTTTCATCTAACTAGCATAAATGACACATTTCTGTCATATGCACAGTT
* * * * * *
605053 AGGCATCAAAGGCACTTAGCCTTTCATCTAACTGGA-ATAAATGACACCTTTCTGTTATATGCAC
66 AGGCATCAAAGGCACTTAACATTTCATCTAACT-GACATAAATGACACATTTCTATCATATCCAC
* *
605117 AGTTAGGCCTCAAAGGCACTTAGCCTTTACTCTAACTGGCATAAATGACACCTTCTGTCATATGC
130 AGTTAGGCCTCAAAGACACTTAGCCTTTACTCTAACTGGCATAAATGACACCTTATGTCATATGC
605182 A
195 A
605183 C
1 C
605184 AGTTAGGCCT
Statistics
Matches: 178, Mismatches: 16, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
195 14 0.08
196 161 0.90
197 3 0.02
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.31
Consensus pattern (195 bp):
CCTCAAAGGCACTTAGCCTTTCATCTAACTAGCATAAATGACACATTTCTGTCATATGCACAGTT
AGGCATCAAAGGCACTTAACATTTCATCTAACTGACATAAATGACACATTTCTATCATATCCACA
GTTAGGCCTCAAAGACACTTAGCCTTTACTCTAACTGGCATAAATGACACCTTATGTCATATGCA
Found at i:605695 original size:59 final size:58
Alignment explanation
Indices: 605564--605736 Score: 231
Period size: 59 Copynumber: 3.0 Consensus size: 58
605554 TATATTTATC
* *
605564 ATACGGAAATTCATACACTTAGTATGAATTTCTTATCCTTTAGCACACAAGGTACCCA
1 ATACAGAAATTCATACACTTAGTATGAATTTCTTATCATTTAGCACACAAGGTACCCA
* * * *
605622 ATTCAGAAATTCATACACTTAGTATGAATTTCTTATGATGTTAGCACACGAA-GTGCCCT
1 ATACAGAAATTCATACACTTAGTATGAATTTCTTATCAT-TTAGCACAC-AAGGTACCCA
* * * *
605681 ATACAGAAATTCATACACTTAGTATGAATTTCTTAACATTTTGCACAAAATGTACC
1 ATACAGAAATTCATACACTTAGTATGAATTTCTTATCATTTAGCACACAAGGTACC
605737 ATTTGGTAAT
Statistics
Matches: 100, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
57 2 0.02
58 46 0.46
59 50 0.50
60 2 0.02
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (58 bp):
ATACAGAAATTCATACACTTAGTATGAATTTCTTATCATTTAGCACACAAGGTACCCA
Found at i:606256 original size:100 final size:95
Alignment explanation
Indices: 606077--606259 Score: 231
Period size: 100 Copynumber: 1.9 Consensus size: 95
606067 TACCAGGTAC
* * *
606077 CGATACTTCTATACTATGGTATCGATACCCCATTCTGATATCGATACCAAAATTAAGTTTAATAT
1 CGATACTACTATACTATGGTATCGATACCCCATTATGATATCGATACCAAAATTAAGTTCAATAT
*
606142 TTCATGGTATCGATACCCTCACCATGGGAT
66 TGCATGGTATCGATACCCTCACCATGGGAT
* * *
606172 CGATACTACTATACTATGGTATTGATACCCCCTATAGTATCGATATCGATACCGAAATTAGGTTC
1 CGATACTACTATACTATGGTATCGATA-CCCC-AT--TAT-GATATCGATACCAAAATTAAGTTC
* * *
606237 GATGTTGCTTGGTATCGATACCC
61 AATATTGCATGGTATCGATACCC
606260 CTTATTATGG
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
95 25 0.34
96 4 0.05
97 2 0.03
99 2 0.03
100 40 0.55
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (95 bp):
CGATACTACTATACTATGGTATCGATACCCCATTATGATATCGATACCAAAATTAAGTTCAATAT
TGCATGGTATCGATACCCTCACCATGGGAT
Found at i:613593 original size:61 final size:61
Alignment explanation
Indices: 613501--613618 Score: 164
Period size: 61 Copynumber: 1.9 Consensus size: 61
613491 TGCACTAAGC
* * * *
613501 TTACCCTCTATTGCTAATCCAGATATTACACATAAGGTCGTGCCCACCACCTACACTAGGT
1 TTACACTCTAGTGCTAATCCAAATATGACACATAAGGTCGTGCCCACCACCTACACTAGGT
* * * *
613562 TTACACTCTAGTGCTAATTCAAATATGACACATAAGGTTGTGCCCACTACCTGCACT
1 TTACACTCTAGTGCTAATCCAAATATGACACATAAGGTCGTGCCCACCACCTACACT
613619 TAGTGCCCTT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (61 bp):
TTACACTCTAGTGCTAATCCAAATATGACACATAAGGTCGTGCCCACCACCTACACTAGGT
Found at i:615075 original size:19 final size:19
Alignment explanation
Indices: 615051--615096 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
615041 AAAAATAATC
615051 CAATTTCACATCCTAACTT
1 CAATTTCACATCCTAACTT
615070 CAATTTCACATCCTAACTT
1 CAATTTCACATCCTAACTT
615089 CAATTTCA
1 CAATTTCA
615097 ACACTCCAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (19 bp):
CAATTTCACATCCTAACTT
Found at i:618910 original size:22 final size:22
Alignment explanation
Indices: 618857--618903 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
618847 TTCCTCAGAA
618857 AGACATCTTCCCTTTAATTGGG
1 AGACATCTTCCCTTTAATTGGG
*
618879 AGACATCTTCCCTTTAGTTGGG
1 AGACATCTTCCCTTTAATTGGG
618901 AGA
1 AGA
618904 AGTCTTCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.34
Consensus pattern (22 bp):
AGACATCTTCCCTTTAATTGGG
Found at i:619045 original size:19 final size:19
Alignment explanation
Indices: 619021--619066 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
619011 CATATTTAAT
619021 TACATATGATACAAATGA-A
1 TACATATGATACAAAT-ATA
**
619040 TACATAACATACAAATATA
1 TACATATGATACAAATATA
619059 TACATATG
1 TACATATG
619067 GTTTGAAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 1 0.05
19 21 0.95
ACGTcount: A:0.52, C:0.13, G:0.07, T:0.28
Consensus pattern (19 bp):
TACATATGATACAAATATA
Found at i:619212 original size:30 final size:28
Alignment explanation
Indices: 619178--619276 Score: 99
Period size: 30 Copynumber: 3.3 Consensus size: 28
619168 ATGACCAAAT
*
619178 TAGCAAAAAAGGAAACTTAAGGGACTAAAA
1 TAGCAAAAAA--AAATTTAAGGGACTAAAA
**
619208 TAGCATAAATAAAAATTTAAAAGACTAAAA
1 TAGCA-AAA-AAAAATTTAAGGGACTAAAA
*
619238 TAGTAAAAATAAAAATTTAAGGGACTAAAA
1 TAG-CAAAA-AAAAATTTAAGGGACTAAAA
*
619268 TTGCAAAAA
1 TAGCAAAAA
619277 TAGAATCTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
28 1 0.02
29 4 0.07
30 47 0.81
31 4 0.07
32 2 0.03
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (28 bp):
TAGCAAAAAAAAATTTAAGGGACTAAAA
Found at i:619246 original size:60 final size:60
Alignment explanation
Indices: 619190--619302 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
619180 GCAAAAAAGG
*
619190 AAACTTAAGGGACTAAAATAGCATAAATAAAAAT-TTAAAAGACTAAAATAGTAAAAATAA
1 AAACTTAAGGGACTAAAATAGCAAAAAT-AAAATCTTAAAAGACTAAAATAGTAAAAATAA
* * * *
619250 AAATTTAAGGGACTAAAATTGCAAAAATAGAATCTTAAAAGGCTAAAA-AGTAA
1 AAACTTAAGGGACTAAAATAGCAAAAATAAAATCTTAAAAGACTAAAATAGTAA
619303 TTACAAATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
59 9 0.19
60 38 0.81
ACGTcount: A:0.58, C:0.07, G:0.12, T:0.22
Consensus pattern (60 bp):
AAACTTAAGGGACTAAAATAGCAAAAATAAAATCTTAAAAGACTAAAATAGTAAAAATAA
Found at i:619277 original size:30 final size:30
Alignment explanation
Indices: 619194--619278 Score: 125
Period size: 30 Copynumber: 2.8 Consensus size: 30
619184 AAAAGGAAAC
*
619194 TTAAGGGACTAAAATAGCATAAATAAAAAT
1 TTAAGGGACTAAAATAGCAAAAATAAAAAT
** *
619224 TTAAAAGACTAAAATAGTAAAAATAAAAAT
1 TTAAGGGACTAAAATAGCAAAAATAAAAAT
*
619254 TTAAGGGACTAAAATTGCAAAAATA
1 TTAAGGGACTAAAATAGCAAAAATA
619279 GAATCTTAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.24
Consensus pattern (30 bp):
TTAAGGGACTAAAATAGCAAAAATAAAAAT
Found at i:619296 original size:30 final size:30
Alignment explanation
Indices: 619202--619297 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
619192 ACTTAAGGGA
* *
619202 CTAAAATAGCATAAATAAAAATTTAAAAGA
1 CTAAAATAGCAAAAATAAAAATTTAAAAGG
* *
619232 CTAAAATAGTAAAAATAAAAATTT-AAGGG
1 CTAAAATAGCAAAAATAAAAATTTAAAAGG
* *
619261 ACTAAAATTGCAAAAAT-AGAATCTTAAAAGG
1 -CTAAAATAGCAAAAATAAAAAT-TTAAAAGG
619292 CTAAAA
1 CTAAAA
619298 AGTAATTACA
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
29 7 0.13
30 44 0.80
31 4 0.07
ACGTcount: A:0.59, C:0.07, G:0.10, T:0.23
Consensus pattern (30 bp):
CTAAAATAGCAAAAATAAAAATTTAAAAGG
Found at i:621743 original size:19 final size:19
Alignment explanation
Indices: 621719--621762 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
621709 ACAGCCACGA
621719 GTGCATCGATGCATGGTCT
1 GTGCATCGATGCATGGTCT
621738 GTGCATCGATGCATGGTCT
1 GTGCATCGATGCATGGTCT
621757 GTGCAT
1 GTGCAT
621763 TGGTACGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.16, C:0.20, G:0.32, T:0.32
Consensus pattern (19 bp):
GTGCATCGATGCATGGTCT
Found at i:630609 original size:19 final size:20
Alignment explanation
Indices: 630569--630614 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
630559 AAGCTCTAAA
*
630569 TCATTCTTCAAGATTTCATTT
1 TCATT-TTCAAGATTCCATTT
*
630590 TGATTTTCAAGA-TCCATTT
1 TCATTTTCAAGATTCCATTT
630609 TCATTT
1 TCATTT
630615 CTAGAAGAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 11 0.50
20 7 0.32
21 4 0.18
ACGTcount: A:0.24, C:0.17, G:0.07, T:0.52
Consensus pattern (20 bp):
TCATTTTCAAGATTCCATTT
Found at i:632149 original size:65 final size:65
Alignment explanation
Indices: 632055--632208 Score: 195
Period size: 65 Copynumber: 2.4 Consensus size: 65
632045 GTACACTAGG
* * * * * *
632055 TGTGCATCGGTACACTAATTACATTCGATGTTTCCAA-AGAGCCATGAGTGCATCAATGCATGG-
1 TGTGCATCGGTACACAAAATGCATCCGATGTTT-CAATAAAGCCAAGAGTGCATCAATGCATGGC
632118 T
65 T
** *
632119 CTGTGCATCGGTACACAAAATGCATCCGATGTTTCAATAAATTCAAGAGTGCATCGATGCATGGC
1 -TGTGCATCGGTACACAAAATGCATCCGATGTTTCAATAAAGCCAAGAGTGCATCAATGCATGGC
632184 T
65 T
632185 TGTGCATCGGTACACAAAATGCAT
1 TGTGCATCGGTACACAAAATGCAT
632209 TCGAAATGGG
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
64 3 0.04
65 74 0.95
66 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (65 bp):
TGTGCATCGGTACACAAAATGCATCCGATGTTTCAATAAAGCCAAGAGTGCATCAATGCATGGCT
Found at i:632865 original size:63 final size:60
Alignment explanation
Indices: 632766--632884 Score: 166
Period size: 63 Copynumber: 1.9 Consensus size: 60
632756 TTGTTTTAAG
* **
632766 AGAAACTGTCTCAAGAGACAAAATTCGTTTCCAAAGAAACGGACTCAAAGATTTTTCAAA
1 AGAAACTGTCTCAAGAGACAAAATTCGTTACCAAAGAAACAAACTCAAAGATTTTTCAAA
* *
632826 AGAAATTGTCTCAAAAGAGACAAAATTTTGTTACCAAAGAAACAAACTCAAAGATTTTT
1 AGAAACTGTCTC--AAGAGACAAAA-TTCGTTACCAAAGAAACAAACTCAAAGATTTTT
632885 TTTCATTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
60 11 0.22
62 11 0.22
63 29 0.57
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.25
Consensus pattern (60 bp):
AGAAACTGTCTCAAGAGACAAAATTCGTTACCAAAGAAACAAACTCAAAGATTTTTCAAA
Found at i:633035 original size:36 final size:36
Alignment explanation
Indices: 632966--633034 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
632956 TTGCTCAAGA
*
632966 AAATTGTCTCATGAGAGACAAAACTTTTGTTTTTAG
1 AAATTGTCTCAAGAGAGACAAAACTTTTGTTTTTAG
* * *
633002 AAATTGTCTCAAGCGAGACGACAC-TTTGTTTTT
1 AAATTGTCTCAAGAGAGACAAAACTTTTGTTTTT
633035 TTAAGAAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 9 0.31
36 20 0.69
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.38
Consensus pattern (36 bp):
AAATTGTCTCAAGAGAGACAAAACTTTTGTTTTTAG
Found at i:634445 original size:2 final size:2
Alignment explanation
Indices: 634405--634437 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
634395 ATTGTATACT
*
634405 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
634438 GGTATATAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:640328 original size:12 final size:12
Alignment explanation
Indices: 640311--640344 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
640301 TTGTAAATGC
640311 ACATGACGTTGG
1 ACATGACGTTGG
640323 ACATGACGTTGG
1 ACATGACGTTGG
640335 ACATGACGTT
1 ACATGACGTT
640345 AGAGAACCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.26
Consensus pattern (12 bp):
ACATGACGTTGG
Found at i:642377 original size:21 final size:22
Alignment explanation
Indices: 642353--642407 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
642343 CCCCTTGCTA
642353 TGTATCGATACA-CCTTAAATG
1 TGTATCGATACATCCTTAAATG
* * *
642374 TGTACCGATATATTCCTTGAATG
1 TGTATCGATACA-TCCTTAAATG
642397 TGTATCGATAC
1 TGTATCGATAC
642408 CCCTCACGGG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 10 0.37
23 17 0.63
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.36
Consensus pattern (22 bp):
TGTATCGATACATCCTTAAATG
Found at i:643070 original size:12 final size:12
Alignment explanation
Indices: 643053--643077 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
643043 TCTAGTCGGT
643053 CAAACGGACCTC
1 CAAACGGACCTC
643065 CAAACGGACCTC
1 CAAACGGACCTC
643077 C
1 C
643078 TATTCCACTC
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:0.32, C:0.44, G:0.16, T:0.08
Consensus pattern (12 bp):
CAAACGGACCTC
Found at i:643472 original size:15 final size:15
Alignment explanation
Indices: 643452--643481 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
643442 CTAGGATATT
*
643452 TGGTTTAGATAACGA
1 TGGTTTAGACAACGA
643467 TGGTTTAGACAACGA
1 TGGTTTAGACAACGA
643482 AAGAGAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.30
Consensus pattern (15 bp):
TGGTTTAGACAACGA
Found at i:644816 original size:19 final size:20
Alignment explanation
Indices: 644774--644816 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
644764 AATAAAGTAT
* *
644774 TATTGAATTTTAAGATTTTA
1 TATTCAATTTTAAGATTATA
644794 TATTCAATTTTAA-ATTATA
1 TATTCAATTTTAAGATTATA
644813 TATT
1 TATT
644817 TGATTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (20 bp):
TATTCAATTTTAAGATTATA
Found at i:647353 original size:30 final size:30
Alignment explanation
Indices: 647309--647432 Score: 105
Period size: 30 Copynumber: 4.2 Consensus size: 30
647299 AAATAATAAC
* *
647309 TTAAAGGACCAAAATAGCAAAAAAGAAAAA
1 TTAAAGGACTAAAATAGCAAAAAAGAAAAT
* *
647339 TTAAGGGACTAAAATAGC--ATAA-AAAAT
1 TTAAAGGACTAAAATAGCAAAAAAGAAAAT
* *
647366 TTAAAGGACTAAAATAGTAAAAATAG-ACAT
1 TTAAAGGACTAAAATAGCAAAAA-AGAAAAT
* * * *
647396 TTAAGGGACTAAAATTGTAAAAAA-AGAAT
1 TTAAAGGACTAAAATAGCAAAAAAGAAAAT
647425 CTTAAAGG
1 -TTAAAGG
647433 GGTGAACATT
Statistics
Matches: 75, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
27 20 0.27
28 3 0.04
29 5 0.07
30 47 0.63
ACGTcount: A:0.57, C:0.07, G:0.15, T:0.20
Consensus pattern (30 bp):
TTAAAGGACTAAAATAGCAAAAAAGAAAAT
Found at i:647420 original size:57 final size:57
Alignment explanation
Indices: 647309--647420 Score: 145
Period size: 57 Copynumber: 2.0 Consensus size: 57
647299 AAATAATAAC
*
647309 TTAAAGGACCAAAATAGCAAAAAAGAAAAATTAAGGGACTAAAATAGCATAAAAAAT
1 TTAAAGGACCAAAATAGCAAAAAAGAAAAATTAAGGGACTAAAATAGCAAAAAAAAT
* * * * * *
647366 TTAAAGGACTAAAATAGTAAAAATAG-ACATTTAAGGGACTAAAATTGTAAAAAAA
1 TTAAAGGACCAAAATAGCAAAAA-AGAAAAATTAAGGGACTAAAATAGCAAAAAAA
647421 GAATCTTAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
57 45 0.96
58 2 0.04
ACGTcount: A:0.59, C:0.07, G:0.14, T:0.20
Consensus pattern (57 bp):
TTAAAGGACCAAAATAGCAAAAAAGAAAAATTAAGGGACTAAAATAGCAAAAAAAAT
Found at i:649331 original size:15 final size:15
Alignment explanation
Indices: 649311--649341 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
649301 TTTTGCACAC
649311 CCCTACTTTTACCCA
1 CCCTACTTTTACCCA
649326 CCCTACTTTTACCCA
1 CCCTACTTTTACCCA
649341 C
1 C
649342 TTCTGATAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.48, G:0.00, T:0.32
Consensus pattern (15 bp):
CCCTACTTTTACCCA
Found at i:653353 original size:43 final size:44
Alignment explanation
Indices: 653292--653377 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 44
653282 ATAGTTTTTT
*
653292 TATAATGATTGTTTGTATGTTATTATGTA-TTAATACACACATA
1 TATAATGATTGTTTGTATGTTATTATGTAGTTAACACACACATA
653335 TATAATGATTGTTTGTATGTTATTATGTAGTTAACACACACAT
1 TATAATGATTGTTTGTATGTTATTATGTAGTTAACACACACAT
653378 TTATTAATAA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
43 29 0.71
44 12 0.29
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (44 bp):
TATAATGATTGTTTGTATGTTATTATGTAGTTAACACACACATA
Found at i:654523 original size:25 final size:25
Alignment explanation
Indices: 654489--654536 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
654479 GTTAGGGATG
* *
654489 AATTTTTAAAATTTTAAGAGGAATA
1 AATTTATAAAATTTAAAGAGGAATA
654514 AATTTATAAAATTTAAAGAGGAA
1 AATTTATAAAATTTAAAGAGGAA
654537 AAACATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.35
Consensus pattern (25 bp):
AATTTATAAAATTTAAAGAGGAATA
Found at i:660270 original size:38 final size:39
Alignment explanation
Indices: 660182--660274 Score: 179
Period size: 39 Copynumber: 2.4 Consensus size: 39
660172 TGTTTTTCAC
660182 GTTGTAATAATAGTTTAGCTTAGCTTAGCTGGAAAGAAG
1 GTTGTAATAATAGTTTAGCTTAGCTTAGCTGGAAAGAAG
660221 GTTGTAATAATAGTTTAGCTTAGCTTAGCTGGAAAG-AG
1 GTTGTAATAATAGTTTAGCTTAGCTTAGCTGGAAAGAAG
660259 GTTGTAATAATAGTTT
1 GTTGTAATAATAGTTT
660275 TATTTCTTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 18 0.33
39 36 0.67
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.37
Consensus pattern (39 bp):
GTTGTAATAATAGTTTAGCTTAGCTTAGCTGGAAAGAAG
Found at i:660578 original size:58 final size:59
Alignment explanation
Indices: 660493--660614 Score: 142
Period size: 58 Copynumber: 2.1 Consensus size: 59
660483 TAAAATGCAT
* * *
660493 AAATGATCTTTGACTATAGGATATTGTTTTATTAAGTC-CCT-ACTATTAAAATTTATA
1 AAATGATCTTCGACTATAGGATATTGTTTTATTAAGTCACCTGACTATTAAAAGTTACA
* * * *
660550 AAATGATTCTTCGACTATAGAGA-GTTGTTTTGTTGAGTCACTTGACTATTAAAAGTTACA
1 AAATGA-TCTTCGACTATAG-GATATTGTTTTATTAAGTCACCTGACTATTAAAAGTTACA
660610 AAATG
1 AAATG
660615 GTCACTTGAC
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
57 6 0.11
58 25 0.46
59 4 0.07
60 19 0.35
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (59 bp):
AAATGATCTTCGACTATAGGATATTGTTTTATTAAGTCACCTGACTATTAAAAGTTACA
Found at i:668318 original size:18 final size:18
Alignment explanation
Indices: 668297--668341 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
668287 CTCAAGTGCA
668297 CTGATATCGCTATCAAAT
1 CTGATATCGCTATCAAAT
668315 CTGATATCGCTATCAAAT
1 CTGATATCGCTATCAAAT
668333 CTGATATCG
1 CTGATATCG
668342 ACTTTCGACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.33
Consensus pattern (18 bp):
CTGATATCGCTATCAAAT
Found at i:670206 original size:19 final size:19
Alignment explanation
Indices: 670164--670228 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 19
670154 ATTCATTCTC
*
670164 AATTCAAAACTT-ATTTCCA
1 AATTCATAACTTAATTT-CA
670183 AATTCATAACTTAATTTCA
1 AATTCATAACTTAATTTCA
* *
670202 TATTCATAGA-TTAGTTTCA
1 AATTCATA-ACTTAATTTCA
670221 AATTCATA
1 AATTCATA
670229 TCCCAATGCA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
19 35 0.88
20 5 0.12
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.42
Consensus pattern (19 bp):
AATTCATAACTTAATTTCA
Found at i:698621 original size:75 final size:75
Alignment explanation
Indices: 698542--698682 Score: 237
Period size: 75 Copynumber: 1.9 Consensus size: 75
698532 CCCTGCATAA
*
698542 GGTATCGATATCCTGCTGTGTAAAATTCAAATATTTCGACCGTTATGAGATGGGGGTATCGATAC
1 GGTATCGATATCCTGCTGTGTAAAATTCAAAAATTTCGACCGTTATGAGATGGGGGTATCGATAC
698607 CTCCTGGGGG
66 CTCCTGGGGG
* * * *
698617 GGTATCGGTATCCTGCTGTGTAAAATTCAAAAATTTTGATCGTTATGAGATGGGGGTATCGGTAC
1 GGTATCGATATCCTGCTGTGTAAAATTCAAAAATTTCGACCGTTATGAGATGGGGGTATCGATAC
698682 C
66 C
698683 CTCCGAGCAA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 61 1.00
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.32
Consensus pattern (75 bp):
GGTATCGATATCCTGCTGTGTAAAATTCAAAAATTTCGACCGTTATGAGATGGGGGTATCGATAC
CTCCTGGGGG
Found at i:699141 original size:28 final size:27
Alignment explanation
Indices: 699089--699141 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
699079 AAGTTTTGAA
*
699089 AAATTACTCCCCTTATACTTTAAAAAT
1 AAATTACTCCCCTTATACTTAAAAAAT
699116 AAATTACTCCCCCTTA-ATCTTAAAAA
1 AAATTACT-CCCCTTATA-CTTAAAAA
699142 CTCTTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.42, C:0.25, G:0.00, T:0.34
Consensus pattern (27 bp):
AAATTACTCCCCTTATACTTAAAAAAT
Found at i:702705 original size:17 final size:17
Alignment explanation
Indices: 702683--702722 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
702673 TATCATCAAC
702683 ATAAATTTGAACTACTA
1 ATAAATTTGAACTACTA
702700 ATAAATTTGAACTACTA
1 ATAAATTTGAACTACTA
702717 ATAAAT
1 ATAAAT
702723 CTTTACCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.35
Consensus pattern (17 bp):
ATAAATTTGAACTACTA
Found at i:708987 original size:2 final size:2
Alignment explanation
Indices: 708980--709004 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
708970 TAAACTCTTT
708980 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
709005 CCAATCTCAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:710958 original size:27 final size:27
Alignment explanation
Indices: 710928--711009 Score: 155
Period size: 27 Copynumber: 3.0 Consensus size: 27
710918 ATTGAGGTTA
710928 CTTAGGTTATTTAGTAGTCAAGTCTAT
1 CTTAGGTTATTTAGTAGTCAAGTCTAT
710955 CTTAGGTTATTTAGTAGTCAAGTCTAT
1 CTTAGGTTATTTAGTAGTCAAGTCTAT
*
710982 ATTAGGTTATTTAGTAGTCAAGTCTAT
1 CTTAGGTTATTTAGTAGTCAAGTCTAT
711009 C
1 C
711010 CCCGTCACTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.44
Consensus pattern (27 bp):
CTTAGGTTATTTAGTAGTCAAGTCTAT
Found at i:712155 original size:23 final size:24
Alignment explanation
Indices: 712114--712159 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
712104 ACCGGTCAAA
*
712114 GTCAAAGGTCAGCGGGTTGACTCC
1 GTCAAAGGTCAGCGAGTTGACTCC
*
712138 GTCAAA-GTCATCGAGTTGACTC
1 GTCAAAGGTCAGCGAGTTGACTC
712160 TATAACTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (24 bp):
GTCAAAGGTCAGCGAGTTGACTCC
Found at i:713173 original size:16 final size:16
Alignment explanation
Indices: 713152--713183 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
713142 GAGACTACAA
713152 AAGAATTATATCTCAC
1 AAGAATTATATCTCAC
713168 AAGAATTATATCTCAC
1 AAGAATTATATCTCAC
713184 CAAAATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (16 bp):
AAGAATTATATCTCAC
Found at i:713467 original size:11 final size:11
Alignment explanation
Indices: 713453--713477 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
713443 TAATATATGG
713453 TTTTGAAAACA
1 TTTTGAAAACA
713464 TTTTGAAAACA
1 TTTTGAAAACA
713475 TTT
1 TTT
713478 ATATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:713494 original size:38 final size:36
Alignment explanation
Indices: 713347--713823 Score: 451
Period size: 38 Copynumber: 13.1 Consensus size: 36
713337 ATAGCTTGTG
* * *
713347 AAAATATTTTGACAAA--ATATAATATATAATTTTCA
1 AAAACATTTTGAAAAATTATATAATATATAGTTTT-A
* * * * *
713382 GAAAACGATTTTTTAAAATTTATATATTATATGGTTTTTG
1 -AAAAC-A-TTTTGAAAAATTATATAATATATAG-TTTTA
* * * *
713422 AAAATATTTT-TAAAATATATATAATATATGGTTTTG
1 AAAACATTTTGAAAAAT-TATATAATATATAGTTTTA
* *
713458 AAAACATTTTGAAAACATTTATATATTATATAGTTTTT
1 AAAACATTTTGAAAA-A-TTATATAATATATAGTTTTA
* *
713496 AAAACATTTTGAAAACTTATATAATATATAGTTTTT
1 AAAACATTTTGAAAAATTATATAATATATAGTTTTA
* * *
713532 AAAACATTTTGAAAACTTATATAGTATATAGTTTTTT
1 AAAACATTTTGAAAAATTATATAATATATAG-TTTTA
713569 AAAACATTTTTGAAAAATTATATAATATATAGTTTTA
1 AAAACA-TTTTGAAAAATTATATAATATATAGTTTTA
*
713606 AAAATATTTTTTGAAAAATTATATAATATATAGTTTTA
1 AAAACA--TTTTGAAAAATTATATAATATATAGTTTTA
713644 AAAACATTTTTTGAAAAAATTATATAATATATAGTTTTA
1 AAAACA--TTTTG-AAAAATTATATAATATATAGTTTTA
*
713683 AAAACATTTTTGGAAAAATTATATAATATAAAGTTTTA
1 AAAACA-TTTT-GAAAAATTATATAATATATAGTTTTA
*
713721 AAAACATTTTTTGAAAACTTATAT-A-ATAT--TTTT-
1 AAAACA--TTTTGAAAAATTATATAATATATAGTTTTA
* *
713754 AAAACATTTTG-AAAACTATATAATATATAGTTTTG
1 AAAACATTTTGAAAAATTATATAATATATAGTTTTA
**
713789 AAAAC-TTTTTTAAAA--A-ATAATATATAG-TTTA
1 AAAACATTTTGAAAAATTATATAATATATAGTTTTA
713820 AAAA
1 AAAA
713824 TTATTTTTGA
Statistics
Matches: 388, Mismatches: 32, Indels: 47
0.83 0.07 0.10
Matches are distributed among these distances:
30 8 0.02
31 13 0.03
32 15 0.04
33 7 0.02
34 12 0.03
35 9 0.02
36 74 0.19
37 42 0.11
38 152 0.39
39 42 0.11
40 10 0.03
41 4 0.01
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (36 bp):
AAAACATTTTGAAAAATTATATAATATATAGTTTTA
Found at i:713855 original size:3 final size:3
Alignment explanation
Indices: 713842--713892 Score: 61
Period size: 3 Copynumber: 17.3 Consensus size: 3
713832 GAAGTATATA
* *
713842 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT T-T TCT TTT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
713886 TAT TAT T
1 TAT TAT T
713893 TTCTTTTTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 4 0.09
3 36 0.84
4 3 0.07
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:713909 original size:15 final size:14
Alignment explanation
Indices: 713855--713902 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
713845 TATATTATTA
* *
713855 TTATTATTATTATTA
1 TTATTATT-TTCTTT
713870 TTATTTATTTTCTTT
1 TTA-TTATTTTCTTT
713885 TTATTATTTTCTTT
1 TTATTATTTTCTTT
713899 TTAT
1 TTAT
713903 GTTTTTTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 15 0.50
15 10 0.33
16 5 0.17
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (14 bp):
TTATTATTTTCTTT
Found at i:714720 original size:2 final size:2
Alignment explanation
Indices: 714713--714742 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
714703 GGCTTAAGTG
714713 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
714743 CACAACCAAA
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:716094 original size:4 final size:4
Alignment explanation
Indices: 716051--716076 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
716041 TGACTTATTC
716051 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
716077 TAAAATTTTA
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:716101 original size:16 final size:16
Alignment explanation
Indices: 716051--716101 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
716041 TGACTTATTC
*
716051 TTATTTATTT-ATTTAT
1 TTATTTATTTAAATT-T
*
716067 TTATTTATTTTAAAATT
1 TTATTTA-TTTAAATTT
*
716084 TTATTTATTTAACTTT
1 TTATTTATTTAAATTT
716100 TT
1 TT
716102 CCTTTCTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 16 0.55
17 11 0.38
18 2 0.07
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATTTATTTAAATTT
Found at i:716123 original size:8 final size:8
Alignment explanation
Indices: 716110--716192 Score: 64
Period size: 8 Copynumber: 10.0 Consensus size: 8
716100 TTCCTTTCTA
716110 TTTTATTT
1 TTTTATTT
716118 TTTTATTT
1 TTTTATTT
716126 TTTTATTT
1 TTTTATTT
716134 TTATT-TTT
1 TT-TTATTT
716142 TTATTATCTGT
1 TT-TTAT-T-T
*
716153 TTTGA-TT
1 TTTTATTT
*
716160 TATTATTT
1 TTTTATTT
*
716168 TCTTATTT
1 TTTTATTT
716176 TTTT-TTAT
1 TTTTATT-T
716184 TATTTATTT
1 T-TTTATTT
716193 ACTATTTAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
7 6 0.10
8 41 0.66
9 7 0.11
10 5 0.08
11 3 0.05
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (8 bp):
TTTTATTT
Found at i:716132 original size:21 final size:21
Alignment explanation
Indices: 716108--716193 Score: 70
Period size: 21 Copynumber: 4.1 Consensus size: 21
716098 TTTTCCTTTC
716108 TATTTTATTTTTTTATTTTTT
1 TATTTTATTTTTTTATTTTTT
* *
716129 TATTTTTATTTTTTTATTATCTG
1 TA-TTTTATTTTTTTATT-TTTT
* * *
716152 T-TTTGA-TTTATTATTTTCT
1 TATTTTATTTTTTTATTTTTT
*
716171 TATTTT-TTTTTATTATTTATT
1 TATTTTATTTTT-TTATTTTTT
716192 TA
1 TA
716194 CTATTTAATC
Statistics
Matches: 49, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
19 2 0.04
20 14 0.29
21 15 0.31
22 15 0.31
23 3 0.06
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.78
Consensus pattern (21 bp):
TATTTTATTTTTTTATTTTTT
Done.