Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008339.1 Hibiscus syriacus cultivar Beakdansim tig00111061_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: 1048908
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 7
Found at i:621742 original size:18 final size:18
Alignment explanation
Indices: 621719--621754 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
621709 ATTTACAATA
*
621719 TTATTTTATTATTACTTT
1 TTATTTAATTATTACTTT
*
621737 TTATTTAATTATTGCTTT
1 TTATTTAATTATTACTTT
621755 AATTATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.06, G:0.03, T:0.69
Consensus pattern (18 bp):
TTATTTAATTATTACTTT
Found at i:623820 original size:22 final size:22
Alignment explanation
Indices: 623792--623840 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
623782 ATCTCTTTCA
623792 TTATAAGCCATAGATGGATAAG
1 TTATAAGCCATAGATGGATAAG
623814 TTATAAGCCATAGATGGATAAG
1 TTATAAGCCATAGATGGATAAG
623836 TTATA
1 TTATA
623841 GGCACAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.31
Consensus pattern (22 bp):
TTATAAGCCATAGATGGATAAG
Found at i:627840 original size:44 final size:43
Alignment explanation
Indices: 627715--627905 Score: 188
Period size: 44 Copynumber: 4.4 Consensus size: 43
627705 ATTCTGTGTT
* * * * * *
627715 ATTTAGCAGTGTTTGTA-ATAAAAAAGTCGCAATACACCATAC
1 ATTTAGCGGTGTTTGTATCTAAAAACGCCGCAATATACCAGAC
* * * * *
627757 ATTTAGCGGGGTTTGTAACAAAAAACGCCACAATATACCATAC
1 ATTTAGCGGTGTTTGTATCTAAAAACGCCGCAATATACCAGAC
*
627800 ATTTAGCGGTGTTTGTATCCTAAAAACGCCGCTATATACCAGAC
1 ATTTAGCGGTGTTTGTAT-CTAAAAACGCCGCAATATACCAGAC
* * * *
627844 ATTTAGCGGTTTTTGTATTCTAAAAATGCCGCTATATATCAGAC
1 ATTTAGCGGTGTTTGTA-TCTAAAAACGCCGCAATATACCAGAC
*
627888 CTTTAGCGGCT-TTTGTAT
1 ATTTAGCGG-TGTTTGTAT
627906 AAAAAAGGCG
Statistics
Matches: 127, Mismatches: 18, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
42 15 0.12
43 36 0.28
44 74 0.58
45 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (43 bp):
ATTTAGCGGTGTTTGTATCTAAAAACGCCGCAATATACCAGAC
Found at i:628049 original size:43 final size:42
Alignment explanation
Indices: 627926--628051 Score: 126
Period size: 43 Copynumber: 3.0 Consensus size: 42
627916 TCGTGAAATC
* *
627926 TCAACACCTATTGCGGCGTTTGTGGGAAAAATGCTGCTAAACA
1 TCAACACCTATTGCGGCGTTTGTGGGAAAAACGCCGCT-AACA
* ** ** * *
627969 TCAACACCTATTGCGGTGTTTGTAAGTCAAACACCGCTAACTT
1 TCAACACCTATTGCGGCGTTTGTGGGAAAAACGCCGCTAAC-A
* * *
628012 TCAACACCTATTGTGGCATTTGTGGGGAAAACGCCGCTAA
1 TCAACACCTATTGCGGCGTTTGTGGGAAAAACGCCGCTAA
628052 ATATCAAAAC
Statistics
Matches: 65, Mismatches: 17, Indels: 2
0.77 0.20 0.02
Matches are distributed among these distances:
42 3 0.05
43 62 0.95
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (42 bp):
TCAACACCTATTGCGGCGTTTGTGGGAAAAACGCCGCTAACA
Found at i:639537 original size:17 final size:18
Alignment explanation
Indices: 639496--639534 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
639486 ATTATATAAG
639496 TAAAATA-TTAAATAAAT
1 TAAAATACTTAAATAAAT
639513 TAAAATACTTAAATAAAT
1 TAAAATACTTAAATAAAT
639531 TAAA
1 TAAA
639535 TACAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAATACTTAAATAAAT
Found at i:639596 original size:10 final size:10
Alignment explanation
Indices: 639590--639622 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
639580 ATAAGAGTAT
*
639590 TTGAGAGAAG
1 TTGAGAGAAA
639600 TTGAGAGAAA
1 TTGAGAGAAA
639610 TTGAGAGAAA
1 TTGAGAGAAA
639620 TTG
1 TTG
639623 GTGTGATGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.33, T:0.24
Consensus pattern (10 bp):
TTGAGAGAAA
Found at i:640013 original size:8 final size:8
Alignment explanation
Indices: 640000--640030 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
639990 AGAGACTTGA
640000 GGGGAGAG
1 GGGGAGAG
640008 GGGGAGAG
1 GGGGAGAG
640016 GGGGAG-G
1 GGGGAGAG
640023 GGGGAGAG
1 GGGGAGAG
640031 AGAGAGAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.23, C:0.00, G:0.77, T:0.00
Consensus pattern (8 bp):
GGGGAGAG
Found at i:640018 original size:15 final size:15
Alignment explanation
Indices: 640000--640030 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
639990 AGAGACTTGA
640000 GGGGAGAGGGGGAGAG
1 GGGGAG-GGGGGAGAG
640016 GGGGAGGGGGGAGAG
1 GGGGAGGGGGGAGAG
640031 AGAGAGAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.23, C:0.00, G:0.77, T:0.00
Consensus pattern (15 bp):
GGGGAGGGGGGAGAG
Found at i:641460 original size:31 final size:31
Alignment explanation
Indices: 641424--641528 Score: 142
Period size: 31 Copynumber: 3.4 Consensus size: 31
641414 TCAAAAAACA
641424 TAAGTTTTAGTCACTTACGTTATTGTTTTAT
1 TAAGTTTTAGTCACTTACGTTATTGTTTTAT
* *
641455 TAAGTTTT-GATCACTTACGTTATCGTTTCAT
1 TAAGTTTTAG-TCACTTACGTTATTGTTTTAT
* *
641486 TAAGTTTGA-TCACTTACATTATTGTTTTAT
1 TAAGTTTTAGTCACTTACGTTATTGTTTTAT
*
641516 TAAGTTTTGGTCA
1 TAAGTTTTAGTCA
641529 TTCGGACATT
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
30 26 0.41
31 37 0.59
ACGTcount: A:0.24, C:0.11, G:0.13, T:0.51
Consensus pattern (31 bp):
TAAGTTTTAGTCACTTACGTTATTGTTTTAT
Found at i:641496 original size:30 final size:30
Alignment explanation
Indices: 641424--641522 Score: 144
Period size: 30 Copynumber: 3.2 Consensus size: 30
641414 TCAAAAAACA
*
641424 TAAGTTTTAGTCACTTACGTTATTGTTTTAT
1 TAAGTTTGA-TCACTTACGTTATTGTTTTAT
* *
641455 TAAGTTTTGATCACTTACGTTATCGTTTCAT
1 TAAG-TTTGATCACTTACGTTATTGTTTTAT
*
641486 TAAGTTTGATCACTTACATTATTGTTTTAT
1 TAAGTTTGATCACTTACGTTATTGTTTTAT
641516 TAAGTTT
1 TAAGTTT
641523 TGGTCATTCG
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
30 30 0.49
31 27 0.44
32 4 0.07
ACGTcount: A:0.24, C:0.11, G:0.12, T:0.53
Consensus pattern (30 bp):
TAAGTTTGATCACTTACGTTATTGTTTTAT
Found at i:645813 original size:31 final size:32
Alignment explanation
Indices: 645718--645841 Score: 187
Period size: 32 Copynumber: 3.9 Consensus size: 32
645708 GAGTCTAGGG
* * *
645718 TTACCTATGACTTTCGGGACATATGAACAAGA
1 TTACCTATGTCTTTCGGGACATATGGACAGGA
* *
645750 TTACCTATGTCTTTTGGGACATATGGATAGGA
1 TTACCTATGTCTTTCGGGACATATGGACAGGA
*
645782 TTACCTATGTCTTTCGGG-CATATAGACAGGA
1 TTACCTATGTCTTTCGGGACATATGGACAGGA
645813 TTACCTATGTCTTTCGGGACATATGGACA
1 TTACCTATGTCTTTCGGGACATATGGACA
645842 ACTACCTATG
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
31 29 0.35
32 53 0.65
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (32 bp):
TTACCTATGTCTTTCGGGACATATGGACAGGA
Found at i:645822 original size:63 final size:64
Alignment explanation
Indices: 645713--645839 Score: 195
Period size: 63 Copynumber: 2.0 Consensus size: 64
645703 GACAAGAGTC
* *
645713 TAGGGTTACCTATGACTTTCGGGACATATGAACAAGATTACCTATGTCTTTTGGGACATATGGA
1 TAGGATTACCTATGACTTTCGGGACATATGAACAAGATTACCTATGTCTTTCGGGACATATGGA
* *
645777 TAGGATTACCTATGTCTTTCGGG-CATAT-AGACAGGATTACCTATGTCTTTCGGGACATATGGA
1 TAGGATTACCTATGACTTTCGGGACATATGA-ACAAGATTACCTATGTCTTTCGGGACATATGGA
645840 CAACTACCTA
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
62 1 0.02
63 36 0.62
64 21 0.36
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.33
Consensus pattern (64 bp):
TAGGATTACCTATGACTTTCGGGACATATGAACAAGATTACCTATGTCTTTCGGGACATATGGA
Found at i:646480 original size:19 final size:19
Alignment explanation
Indices: 646456--646504 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
646446 ATATTCACAG
*
646456 TACTATTTATACAATATAA
1 TACTATTCATACAATATAA
*
646475 TACTATTCATACAATATAG
1 TACTATTCATACAATATAA
646494 TACTATTCATA
1 TACTATTCATA
646505 AAAACGGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (19 bp):
TACTATTCATACAATATAA
Found at i:657430 original size:20 final size:21
Alignment explanation
Indices: 657391--657430 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
657381 GAAGTTTTAA
* *
657391 GATCATCAATTTATTTTTGAT
1 GATCATCAATTAACTTTTGAT
657412 GATCATC-ATTAACTTTTGA
1 GATCATCAATTAACTTTTGA
657431 AAGTAAGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.47
Consensus pattern (21 bp):
GATCATCAATTAACTTTTGAT
Found at i:657582 original size:22 final size:21
Alignment explanation
Indices: 657540--657579 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
657530 AAGACTATTT
657540 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
657561 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
657580 ATAAAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:664759 original size:29 final size:29
Alignment explanation
Indices: 664711--664820 Score: 123
Period size: 29 Copynumber: 3.8 Consensus size: 29
664701 GAGGCCATAA
* * *
664711 TCCCCATCCTAATTTTGCATGGGATTTAT
1 TCCCCGTCCTGATTCTGCATGGGATTTAT
** * *
664740 TCCATGTCCTGATTCCGCATGAGATTTAT
1 TCCCCGTCCTGATTCTGCATGGGATTTAT
* * *
664769 TCCCCGTCCTGATTCTGTATGGG-CTTAG
1 TCCCCGTCCTGATTCTGCATGGGATTTAT
664797 TCCCCGTCCTGATTCTGCATGGGA
1 TCCCCGTCCTGATTCTGCATGGGA
664821 CTTCGTTCCT
Statistics
Matches: 65, Mismatches: 15, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
28 25 0.38
29 40 0.62
ACGTcount: A:0.16, C:0.27, G:0.20, T:0.36
Consensus pattern (29 bp):
TCCCCGTCCTGATTCTGCATGGGATTTAT
Found at i:672432 original size:3 final size:3
Alignment explanation
Indices: 672424--672450 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
672414 TTATTTTAGA
672424 TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
672451 CTCCTCAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:676769 original size:20 final size:20
Alignment explanation
Indices: 676744--676785 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
676734 CTGTAATTTA
*
676744 GATGTTAGAATGTTG-AATTC
1 GATGTTAAAATG-TGAAATTC
676764 GATGTTAAAATGTGAAATTC
1 GATGTTAAAATGTGAAATTC
676784 GA
1 GA
676786 CTAATTTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.36
Consensus pattern (20 bp):
GATGTTAAAATGTGAAATTC
Found at i:677308 original size:19 final size:19
Alignment explanation
Indices: 677284--677321 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
677274 ATTGGAATCA
677284 AATATT-AAACTATTGATTT
1 AATATTGAAA-TATTGATTT
*
677303 AATATTGAAATGTTGATTT
1 AATATTGAAATATTGATTT
677322 TGGACTAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.47
Consensus pattern (19 bp):
AATATTGAAATATTGATTT
Found at i:678178 original size:20 final size:20
Alignment explanation
Indices: 678138--678177 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
678128 CAGGAAAATA
*
678138 AGTTTTTAGTGGCGTTTTTT
1 AGTTTTTAGCGGCGTTTTTT
678158 AGTTTTATAGCGGCGTTTTT
1 AGTTTT-TAGCGGCGTTTTT
678178 AAGTGTCGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.12, C:0.07, G:0.25, T:0.55
Consensus pattern (20 bp):
AGTTTTTAGCGGCGTTTTTT
Found at i:678334 original size:42 final size:42
Alignment explanation
Indices: 678281--678409 Score: 154
Period size: 42 Copynumber: 3.1 Consensus size: 42
678271 TAGCGGCGTT
*
678281 TTTTG-CCACAAACGCCGCTAATTCTCTTATTTTTAGTAGCG
1 TTTTGACCACAAACGCCGCTAATTCTCTTATTTTTAGTGGCG
* * * *
678322 TTTTGACCACAAATGCCTCTAATTCTCTTATCTTTAGTGGCA
1 TTTTGACCACAAACGCCGCTAATTCTCTTATTTTTAGTGGCG
* * *
678364 TTTAT-AGCCACAAACGCCGCTAATTTTATTGTTTTTAGTGGCG
1 TTT-TGA-CCACAAACGCCGCTAATTCTCTTATTTTTAGTGGCG
678407 TTT
1 TTT
678410 GTAATACAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
41 5 0.07
42 35 0.48
43 33 0.45
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (42 bp):
TTTTGACCACAAACGCCGCTAATTCTCTTATTTTTAGTGGCG
Found at i:678463 original size:44 final size:43
Alignment explanation
Indices: 678356--678463 Score: 96
Period size: 44 Copynumber: 2.5 Consensus size: 43
678346 CTCTTATCTT
* * * *
678356 TAGTGGCATTTATAGCCAC-AAACGCCGCTAATTTTATTGTTTT
1 TAGTGGCATTTATA-CAACAAAACGCCACTAATATTATTGTTTG
* *
678399 TAGTGGCGTTTGTA-ATACAAAACGCCACTATATATTA-TGATTTG
1 TAGTGGCATTTATACA-ACAAAACGCCACTA-ATATTATTG-TTTG
*
678443 TAGTGGCATTTTTACAACAAA
1 TAGTGGCATTTATACAACAAA
678464 TGCCGCTATT
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
42 2 0.04
43 24 0.46
44 25 0.48
45 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.37
Consensus pattern (43 bp):
TAGTGGCATTTATACAACAAAACGCCACTAATATTATTGTTTG
Found at i:682376 original size:41 final size:41
Alignment explanation
Indices: 682315--682535 Score: 236
Period size: 41 Copynumber: 5.4 Consensus size: 41
682305 TTCTAAACAC
682315 AAAA-GCCACTAAAG-ACGAGTCTATAGCGGCGTTTGTATA
1 AAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATA
** * * * *
682354 AAAACGCCACTACTGTACGAGTCTATCGCGACGTTTATACA
1 AAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATA
* ** * *
682395 AAAATGCCACTAAAGTATAAGCCTATAGCGGCGTGTTTGTAAAA
1 AAAACGCCACTAAAGTACGAGTCTATAGCGGC--GTTTGT-ATA
682439 ACAAACGCCACTAAAGTACGAGTCTATAGC-G-G-TTGTATA
1 A-AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATA
* *
682478 TAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTTGTGTA
1 AAAACGCCACTAAAGTACGAGTCTATAGCGGCG-TTTGTATA
*
682520 AAAACGTCACTAAAGT
1 AAAACGCCACTAAAGT
682536 TACCATTTGT
Statistics
Matches: 147, Mismatches: 25, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
38 28 0.19
39 7 0.05
40 13 0.09
41 46 0.31
42 20 0.14
43 5 0.03
44 4 0.03
45 24 0.16
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (41 bp):
AAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATA
Found at i:682510 original size:83 final size:84
Alignment explanation
Indices: 682315--682697 Score: 312
Period size: 81 Copynumber: 4.5 Consensus size: 84
682305 TTCTAAACAC
* **
682315 AAAA-GCCACTAAAG-ACGAGTCTATAGCGGC--GTTTGT-ATAA-AAACGCCACTACTGTACGA
1 AAAACGCCACTAAAGTACGAGTCTATAGCGGCGTGTTTGTAAAAACAAACGCCACTAAAGTACGA
*
682374 GTCTATCGCGACGTTTATACA
66 GTCTATAGCGA-GTTTATA-A
* ** *
682395 AAAATGCCACTAAAGTATAAGCCTATAGCGGCGTGTTTGTAAAAACAAACGCCACTAAAGTACGA
1 AAAACGCCACTAAAGTACGAGTCTATAGCGGCGTGTTTGTAAAAACAAACGCCACTAAAGTACGA
682460 GTCTATAGCG-GTTGTAT-A
66 GTCTATAGCGAGTT-TATAA
* ** * *
682478 TAAACGCCACTAAAGTACGAGTCTATAGCGGCGT-TTTGT-GTAA-AAACGTCACTAAAGTTACC
1 AAAACGCCACTAAAGTACGAGTCTATAGCGGCGTGTTTGTAAAAACAAACGCCACTAAAG-TACG
*
682540 ATTTGTGGCGTTTGAAATGCGACGTTTATACA
65 A---GT--C---T-ATA-GCGA-GTTTATA-A
* ** *
682572 AAAATGCCACTAAAGTATAAGCCTATAGCGGC--GTTTGTAAAAACAAACGCCACTAAAGTACGA
1 AAAACGCCACTAAAGTACGAGTCTATAGCGGCGTGTTTGTAAAAACAAACGCCACTAAAGTACGA
682635 GTCTATAGCG-GTTGTAT-A
66 GTCTATAGCGAGTT-TATAA
* *
682653 TAAACGCCACTAAAGTACGAGTCTATAGCGGCAT-TTTGTATAAAA
1 AAAACGCCACTAAAGTACGAGTCTATAGCGGCGTGTTTGTA-AAAA
682698 ACGTCGCTAA
Statistics
Matches: 242, Mismatches: 32, Indels: 55
0.74 0.10 0.17
Matches are distributed among these distances:
80 17 0.07
81 44 0.18
82 27 0.11
83 37 0.15
84 14 0.06
85 8 0.03
86 28 0.12
89 2 0.01
90 2 0.01
91 5 0.02
92 3 0.01
93 8 0.03
94 34 0.14
95 13 0.05
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (84 bp):
AAAACGCCACTAAAGTACGAGTCTATAGCGGCGTGTTTGTAAAAACAAACGCCACTAAAGTACGA
GTCTATAGCGAGTTTATAA
Found at i:682674 original size:175 final size:176
Alignment explanation
Indices: 682381--682733 Score: 654
Period size: 175 Copynumber: 2.0 Consensus size: 176
682371 CGAGTCTATC
682381 GCGACGTTTATACAAAAATGCCACTAAAGTATAAGCCTATAGCGGCGTGTTTGTAAAAACAAACG
1 GCGACGTTTATACAAAAATGCCACTAAAGTATAAGCCTATAGCGGCG-GTTTGTAAAAACAAACG
*
682446 CCACTAAAGTACGAGTCTATAGCGGTTGTATATAAACGCCACTAAAGTACGAGTCTATAGCGGCG
65 CCACTAAAGTACGAGTCTATAGCGGTTGTATATAAACGCCACTAAAGTACGAGTCTATAGCGGCA
*
682511 TTTTGTGTAAAAACGTCACTAAAGTTACCATTTGTGGCGTTTGAAAT
130 TTTTGTATAAAAACGTCACTAAAGTTACCATTTGTGGCGTTTGAAAT
682558 GCGACGTTTATACAAAAATGCCACTAAAGTATAAGCCTATAGCGGC-GTTTGTAAAAACAAACGC
1 GCGACGTTTATACAAAAATGCCACTAAAGTATAAGCCTATAGCGGCGGTTTGTAAAAACAAACGC
682622 CACTAAAGTACGAGTCTATAGCGGTTGTATATAAACGCCACTAAAGTACGAGTCTATAGCGGCAT
66 CACTAAAGTACGAGTCTATAGCGGTTGTATATAAACGCCACTAAAGTACGAGTCTATAGCGGCAT
* *
682687 TTTGTATAAAAACGTCGCTAAAGTTACCATTTGTGGTGTTTGAAAT
131 TTTGTATAAAAACGTCACTAAAGTTACCATTTGTGGCGTTTGAAAT
682733 G
1 G
682734 TAAACGCCGC
Statistics
Matches: 172, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
175 126 0.73
177 46 0.27
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (176 bp):
GCGACGTTTATACAAAAATGCCACTAAAGTATAAGCCTATAGCGGCGGTTTGTAAAAACAAACGC
CACTAAAGTACGAGTCTATAGCGGTTGTATATAAACGCCACTAAAGTACGAGTCTATAGCGGCAT
TTTGTATAAAAACGTCACTAAAGTTACCATTTGTGGCGTTTGAAAT
Found at i:682708 original size:42 final size:38
Alignment explanation
Indices: 682571--682710 Score: 127
Period size: 38 Copynumber: 3.4 Consensus size: 38
682561 ACGTTTATAC
* ** * *
682571 AAAAATGCCACTAAAGTATAAGCCTATAGCGGCGTTTGTAAA
1 AAAAACGCCACTAAAGTACGAGTCTATAGC-G-G-TTGT-AT
682613 AACAAACGCCACTAAAGTACGAGTCTATAGCGGTTGTAT
1 AA-AAACGCCACTAAAGTACGAGTCTATAGCGGTTGTAT
*
682652 ATAAACGCCACTAAAGTACGAGTCTATAGCGGCATTTTGTAT
1 AAAAACGCCACTAAAGTACGAGTCTATAGCGG----TTGTAT
* *
682694 AAAAACGTCGCTAAAGT
1 AAAAACGCCACTAAAGT
682711 TACCATTTGT
Statistics
Matches: 84, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
38 30 0.36
39 2 0.02
40 4 0.05
41 1 0.01
42 23 0.27
43 24 0.29
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (38 bp):
AAAAACGCCACTAAAGTACGAGTCTATAGCGGTTGTAT
Found at i:683373 original size:17 final size:17
Alignment explanation
Indices: 683319--683373 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
683309 GTCATAAAAC
*
683319 AAAAGTAAAATATACAGT
1 AAAAG-AAATTATACAGT
*
683337 AAGAGAAATAGTATA-A-T
1 AAAAGAAAT--TATACAGT
683354 AAAAGAAATTATACAGT
1 AAAAGAAATTATACAGT
683371 AAA
1 AAA
683374 GGAATCATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
15 4 0.13
16 1 0.03
17 16 0.53
18 5 0.17
19 4 0.13
ACGTcount: A:0.62, C:0.04, G:0.13, T:0.22
Consensus pattern (17 bp):
AAAAGAAATTATACAGT
Found at i:683441 original size:34 final size:34
Alignment explanation
Indices: 683365--683488 Score: 98
Period size: 34 Copynumber: 3.6 Consensus size: 34
683355 AAAGAAATTA
*
683365 TACAGT-AAAGGAATC-ATCACA-GAAAAAGGAACAG
1 TACAGTGAAAGGAA-CGAT-ACAGGAAAAA-GAATAG
*
683399 TACGGTGAAAGGAACGATACAGGAAAAAGAATAG
1 TACAGTGAAAGGAACGATACAGGAAAAAGAATAG
*
683433 TACAGTGAAAGGATTA-G-TACAGGAAAAAGAGTAAG
1 TACAGTGAAAGGA--ACGATACAGGAAAAAGAAT-AG
* *
683468 TATA-TGAAAAGAAACGATACA
1 TACAGTG-AAAGGAACGATACA
683489 AGTTTAATTA
Statistics
Matches: 75, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
33 1 0.01
34 43 0.57
35 30 0.40
36 1 0.01
ACGTcount: A:0.52, C:0.10, G:0.24, T:0.15
Consensus pattern (34 bp):
TACAGTGAAAGGAACGATACAGGAAAAAGAATAG
Found at i:683443 original size:16 final size:16
Alignment explanation
Indices: 683389--683458 Score: 52
Period size: 17 Copynumber: 4.2 Consensus size: 16
683379 CATCACAGAA
* *
683389 AAAGGAACAGTACGGTG
1 AAAGGAATAGTACAG-G
*
683406 AAAGGAA-CGATACAGG
1 AAAGGAATAG-TACAGG
*
683422 AAAAAGAATAGTACAGTG
1 -AAAGGAATAGTACAG-G
*
683440 AAAGGATTAGTACAGG
1 AAAGGAATAGTACAGG
683456 AAA
1 AAA
683459 AAGAGTAAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
16 6 0.14
17 35 0.81
18 2 0.05
ACGTcount: A:0.50, C:0.09, G:0.29, T:0.13
Consensus pattern (16 bp):
AAAGGAATAGTACAGG
Found at i:688754 original size:21 final size:23
Alignment explanation
Indices: 688712--688768 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 23
688702 CTATATACAA
688712 TATCGATACTACTTAGTTTAGTAG
1 TATCGATACTACTTAG-TTAGTAG
*
688736 TATCGATACT-CTTAG-TAGTGG
1 TATCGATACTACTTAGTTAGTAG
*
688757 TACCGATACTAC
1 TATCGATACTAC
688769 CTTTTCGGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 14 0.47
22 1 0.03
23 5 0.17
24 10 0.33
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (23 bp):
TATCGATACTACTTAGTTAGTAG
Found at i:689647 original size:81 final size:81
Alignment explanation
Indices: 689467--690121 Score: 1053
Period size: 81 Copynumber: 8.1 Consensus size: 81
689457 TTAATCATTC
* * *
689467 AATCTTTTACTCAAAGGCATTTAGACTTTCATTTAACTTGCAATATTGGCACCTTTC--ACAAAT
1 AATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACCTTTCTGCCAAAT
689530 GCACAGCTAGGCAATT
66 GCACAGCTAGGCAATT
* * *
689546 AATCTTTTACTCAAAGGCATTTATCCTTTCATCTAACTTGCAATATTGGCACATTTCTACCAAAT
1 AATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACCTTTCTGCCAAAT
* *
689611 GCATAGGTAGGCAATT
66 GCACAGCTAGGCAATT
* * *
689627 AATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGTAATATTGGCACATTTATGCCAAAT
1 AATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACCTTTCTGCCAAAT
689692 GCACAGCTAGGCAATT
66 GCACAGCTAGGCAATT
** *
689708 AATCTTTTACTCAAAGGCATTTAGTATTGCATCTAACTTGCAATATTGGCACCTTTCTGCCAAAT
1 AATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACCTTTCTGCCAAAT
**
689773 GCACAATTAGGCAATT
66 GCACAGCTAGGCAATT
* * *
689789 AATCTTTTACTTAAAGGCATTTAGCCTTTCATCTAACTTGCATTATTGGCACCTTTCTTCCAAAT
1 AATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACCTTTCTGCCAAAT
689854 GCACAGCTAGGCAATT
66 GCACAGCTAGGCAATT
* *
689870 AATCCTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACCTTTCTACCAAAT
1 AATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACCTTTCTGCCAAAT
*
689935 GCACAACTAGGCAATT
66 GCACAGCTAGGCAATT
689951 AATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACCTTTCTGCCAAAT
1 AATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACCTTTCTGCCAAAT
690016 GCACAGCTAGGCAATT
66 GCACAGCTAGGCAATT
* * *
690032 AATCTTTTACTCGAAGGCATTTAGTCTTGCATCTAACTTGCAATATTGGCACCTTTCTGCCAAAT
1 AATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACCTTTCTGCCAAAT
**
690097 GCACAATTAGGCAATT
66 GCACAGCTAGGCAATT
690113 AATCTTTTA
1 AATCTTTTA
690122 TTTTAAAACA
Statistics
Matches: 532, Mismatches: 42, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
79 53 0.10
81 479 0.90
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (81 bp):
AATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACCTTTCTGCCAAAT
GCACAGCTAGGCAATT
Found at i:690650 original size:22 final size:22
Alignment explanation
Indices: 690594--690651 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 22
690584 CATTTTGGAT
* * * *
690594 CTATGGTATCGATACTTTTCTC
1 CTATGGTACCGATACTTCTATA
*
690616 CTA--GTACCAATACTTCTATA
1 CTATGGTACCGATACTTCTATA
690636 CTATGGTACCGATACT
1 CTATGGTACCGATACT
690652 CCGTTTAGTA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
20 15 0.54
22 13 0.46
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (22 bp):
CTATGGTACCGATACTTCTATA
Found at i:690698 original size:94 final size:94
Alignment explanation
Indices: 690531--690708 Score: 243
Period size: 94 Copynumber: 1.9 Consensus size: 94
690521 CATGGTATCG
* * * *
690531 ATACTTCTATAATGTGGTATCGATACTCCCTTTCAGTATCGATACCATTTCTACATTTTGGATCT
1 ATACTTCTATAATATGGTACCGATACTCCCTTTCAGTATCGATACCATTTCTACATTCTGGATCC
*
690596 ATGGTATCGATACTTTTCTCCTAGTACCA
66 ATGATATCGATACTTTTCTCCTAGTACCA
* * **
690625 ATACTTCTATACTATGGTACCGATACTCCGTTT-AGTATCGATACCATTT-TGGTATTCTGGAAT
1 ATACTTCTATAATATGGTACCGATACTCCCTTTCAGTATCGATACCATTTCT-ACATTCTGG-AT
690688 CCATGATATCGATACTTTTCT
64 CCATGATATCGATACTTTTCT
690709 TTTTGGTATT
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
92 1 0.01
93 22 0.30
94 50 0.68
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.40
Consensus pattern (94 bp):
ATACTTCTATAATATGGTACCGATACTCCCTTTCAGTATCGATACCATTTCTACATTCTGGATCC
ATGATATCGATACTTTTCTCCTAGTACCA
Found at i:693487 original size:24 final size:24
Alignment explanation
Indices: 693455--693508 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
693445 CGCTTGATTA
* *
693455 TATGATCGTTTATATTTATTCATT
1 TATGTTCGTTTATATTCATTCATT
* *
693479 TATGTTCGTTTATGTTCGTTCATT
1 TATGTTCGTTTATATTCATTCATT
693503 TATGTT
1 TATGTT
693509 TAAAACAGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.19, C:0.09, G:0.13, T:0.59
Consensus pattern (24 bp):
TATGTTCGTTTATATTCATTCATT
Found at i:693804 original size:10 final size:10
Alignment explanation
Indices: 693764--693857 Score: 53
Period size: 10 Copynumber: 8.1 Consensus size: 10
693754 TTTATTGTGT
693764 TGTTCGTTTA
1 TGTTCGTTTA
693774 TGTTCTCGTTTA
1 TG-T-TCGTTTA
693786 TTGTGTTCGTTTA
1 ---TGTTCGTTTA
*
693799 TGTTCGTTCGTTCG
1 TGTTCG-T--TT-A
693813 TGTTCGTTTA
1 TGTTCGTTTA
*
693823 TGTTCGTTCGTTCG
1 TGTTCG-T--TT-A
693837 TGTTCGTTTA
1 TGTTCGTTTA
693847 TGTTCGTTTA
1 TGTTCGTTTA
693857 T
1 T
693858 TTATTAAATT
Statistics
Matches: 67, Mismatches: 4, Indels: 26
0.69 0.04 0.27
Matches are distributed among these distances:
10 25 0.37
11 7 0.10
12 7 0.10
13 13 0.19
14 13 0.19
15 2 0.03
ACGTcount: A:0.06, C:0.14, G:0.22, T:0.57
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:693809 original size:14 final size:13
Alignment explanation
Indices: 693761--693850 Score: 70
Period size: 13 Copynumber: 7.3 Consensus size: 13
693751 TTTTTTATTG
693761 TGTTGTTCGTTTA
1 TGTTGTTCGTTTA
*
693774 TGTT-CTCGTTTA
1 TGTTGTTCGTTTA
693786 T-TGTGTTCGTTTA
1 TGT-TGTTCGTTTA
693799 TGTTCGTTCG-TT-
1 TGTT-GTTCGTTTA
*
693811 CG-TGTTCGTTTA
1 TGTTGTTCGTTTA
693823 TGTTCGTTCG-TT-
1 TGTT-GTTCGTTTA
*
693835 CG-TGTTCGTTTA
1 TGTTGTTCGTTTA
693847 TGTT
1 TGTT
693851 CGTTTATTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 22
0.68 0.07 0.25
Matches are distributed among these distances:
10 10 0.17
11 7 0.12
12 13 0.22
13 19 0.32
14 11 0.18
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (13 bp):
TGTTGTTCGTTTA
Found at i:693820 original size:24 final size:24
Alignment explanation
Indices: 693764--693854 Score: 139
Period size: 24 Copynumber: 3.8 Consensus size: 24
693754 TTTATTGTGT
**
693764 TGTTCGTTTATGTTCTCGTTTATT-G
1 TGTTCGTTTATG-T-TCGTTCGTTCG
693789 TGTTCGTTTATGTTCGTTCGTTCG
1 TGTTCGTTTATGTTCGTTCGTTCG
693813 TGTTCGTTTATGTTCGTTCGTTCG
1 TGTTCGTTTATGTTCGTTCGTTCG
693837 TGTTCGTTTATGTTCGTT
1 TGTTCGTTTATGTTCGTT
693855 TATTTATTAA
Statistics
Matches: 63, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
23 7 0.11
24 44 0.70
25 12 0.19
ACGTcount: A:0.05, C:0.14, G:0.23, T:0.57
Consensus pattern (24 bp):
TGTTCGTTTATGTTCGTTCGTTCG
Found at i:693943 original size:16 final size:16
Alignment explanation
Indices: 693922--693952 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
693912 AAAAAAAATT
693922 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
693938 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
693953 ATTTATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:697735 original size:81 final size:81
Alignment explanation
Indices: 697595--698171 Score: 822
Period size: 81 Copynumber: 7.1 Consensus size: 81
697585 TGTTAATCAT
* * *
697595 TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTAGCACCTTTCTGTCAA
1 TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACATTTCTGCCAA
* *
697660 ATGTACAGCTAGGTAA
66 ATGCACAGCTAGGCAA
697676 TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACATTTCTGCCAA
1 TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACATTTCTGCCAA
697741 ATGCACAGCTAGGCAA
66 ATGCACAGCTAGGCAA
* *
697757 TTAATCTTTTACTCAAA-GCATTTAGCCTTTCATCTAACTTGCAATATTGGTACCTTTCTGCCAA
1 TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACATTTCTGCCAA
697821 ATGCACAGCTAGGCAA
66 ATGCACAGCTAGGCAA
* *
697837 TTAATCTTTTACTCAAAGGCATTTAGCATTTCATCTAACTTGCAATATTGGCACATTTCTCCCAA
1 TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACATTTCTGCCAA
*
697902 ATGCACATCTAGGCAA
66 ATGCACAGCTAGGCAA
* * *
697918 CTAATCTTTTACTCAAAGGCATTTGGCCTTTCATCTAACTTGCAATATTGGCACCTTTCTGCCAA
1 TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACATTTCTGCCAA
*
697983 ATGCATAGCTAGGCAA
66 ATGCACAGCTAGGCAA
* * * * * **
697999 TTAATCTTTTACTTAAAGGTATTTAACCTTTAATCTAAC-TG-ACATGATTGACACATTTCTATC
1 TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCA-AT-ATTGGCACATTTCTGCC
*
698062 AAATGCACATCTAGGCAA
64 AAATGCACAGCTAGGCAA
* * * *
698080 TTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAAC-TG-ACATGATTGACACATTTCTGTC
1 TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCA-AT-ATTGGCACATTTCTGCC
* *
698143 AAATGCGCAACTAGGCAA
64 AAATGCACAGCTAGGCAA
*
698161 ATAATCTTTTA
1 TTAATCTTTTA
698172 TTTTAAAACG
Statistics
Matches: 456, Mismatches: 37, Indels: 6
0.91 0.07 0.01
Matches are distributed among these distances:
79 1 0.00
80 82 0.18
81 373 0.82
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (81 bp):
TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACATTTCTGCCAA
ATGCACAGCTAGGCAA
Found at i:701306 original size:137 final size:140
Alignment explanation
Indices: 701159--701408 Score: 321
Period size: 137 Copynumber: 1.8 Consensus size: 140
701149 CTCAAGACAG
* * *
701159 TTTCCTTTGAAACACAAG-CTTTAAAATCATTTCACTCAAAAGAAATCTTATCTCGCCTGA-GAT
1 TTTCCCTTGAAAC-CAAGACTTTAAAATCATTTCACCCAAAAGAAATCTTATCT-GACTGATGAT
* *
701222 T-TTTTT-CTCAAAAAAAAATTT-GTCTCACTTGATATTGTTTTTCTTAAGAATAGATTTCGTCT
64 TGTTTTTACTCAAAAAAAAATTTAGTCTCACTTGAGATTGTTTCTCTTAAGAATAGATTTCGTCT
701284 CACGCGAGATAA
129 CACGCGAGATAA
* ** * * *
701296 TTTCCCTTGAAACCTAGACTTTATGATCATTTCACCCAAAAGAAATTTTATCTTACTTATGATTG
1 TTTCCCTTGAAACCAAGACTTTAAAATCATTTCACCCAAAAGAAATCTTATCTGACTGATGATTG
* * *
701361 TTTTTACTTAAAAGAAAATTTAGTTTCACTTGAGATTGTTTCTCTTAA
66 TTTTTACTCAAAAAAAAATTTAGTCTCACTTGAGATTGTTTCTCTTAA
701409 AACAAAAACT
Statistics
Matches: 94, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
136 6 0.06
137 47 0.50
138 5 0.05
139 13 0.14
140 23 0.24
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.40
Consensus pattern (140 bp):
TTTCCCTTGAAACCAAGACTTTAAAATCATTTCACCCAAAAGAAATCTTATCTGACTGATGATTG
TTTTTACTCAAAAAAAAATTTAGTCTCACTTGAGATTGTTTCTCTTAAGAATAGATTTCGTCTCA
CGCGAGATAA
Found at i:701533 original size:36 final size:36
Alignment explanation
Indices: 701450--701647 Score: 272
Period size: 36 Copynumber: 5.5 Consensus size: 36
701440 CAAAATTTTA
* *
701450 TCTCACTTGAGATTTTTTTTCTTGAAAACAAAATTCG
1 TCTCACTTGAGATTGTTTTTCTT-AAAACAAATTTCG
* ** *
701487 TCTCACTTGAGATTATTTTTCTTAAAATGAATTTTG
1 TCTCACTTGAGATTGTTTTTCTTAAAACAAATTTCG
* *
701523 TCTCACTTGAGATTGTTTTTCTTAAAA-AAATGTCA
1 TCTCACTTGAGATTGTTTTTCTTAAAACAAATTTCG
*
701558 TCTCACTTGAGATTGTTTTTCTTAAAGCAAATTTCG
1 TCTCACTTGAGATTGTTTTTCTTAAAACAAATTTCG
* *
701594 TCTCACGTGAGATTGTTTTTCTTAAATCAAATTTCG
1 TCTCACTTGAGATTGTTTTTCTTAAAACAAATTTCG
*
701630 TCTTACTTGAGATTGTTT
1 TCTCACTTGAGATTGTTT
701648 CCTTTGAAAT
Statistics
Matches: 143, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
35 30 0.21
36 91 0.64
37 22 0.15
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.46
Consensus pattern (36 bp):
TCTCACTTGAGATTGTTTTTCTTAAAACAAATTTCG
Found at i:701591 original size:71 final size:71
Alignment explanation
Indices: 701437--701647 Score: 271
Period size: 71 Copynumber: 2.9 Consensus size: 71
701427 GTCTCACTTG
* * *
701437 AAACAAAATTTTATCTCACTTGAGATTTTTTTTCTTGAAAACAAAATTCGTCTCACTTGAGATTA
1 AAAC-AAATTTTGTCTCACTTGAGATTGTTTTTCTT--AAACAAAATTCGTCTCACTTGAGATTG
701502 TTTTTCTTA
63 TTTTTCTTA
** *
701511 AAATGAATTTTGTCTCACTTGAGATTGTTTTTCTTAAA-AAAATGTCATCTCACTTGAGATTGTT
1 AAACAAATTTTGTCTCACTTGAGATTGTTTTTCTTAAACAAAAT-TCGTCTCACTTGAGATTGTT
701575 TTTCTTA
65 TTTCTTA
* * * * *
701582 AAGCAAATTTCGTCTCACGTGAGATTGTTTTTCTTAAATCAAATTTCGTCTTACTTGAGATTGTT
1 AAACAAATTTTGTCTCACTTGAGATTGTTTTTCTTAAA-CAAAATTCGTCTCACTTGAGATTGTT
701647 T
65 T
701648 CCTTTGAAAT
Statistics
Matches: 120, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
70 5 0.04
71 61 0.51
72 19 0.16
73 32 0.27
74 3 0.03
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (71 bp):
AAACAAATTTTGTCTCACTTGAGATTGTTTTTCTTAAACAAAATTCGTCTCACTTGAGATTGTTT
TTCTTA
Found at i:701619 original size:107 final size:108
Alignment explanation
Indices: 701449--701647 Score: 303
Period size: 107 Copynumber: 1.9 Consensus size: 108
701439 ACAAAATTTT
* *
701449 ATCTCACTTGAGATTTTTTTTCTTGAAAACAAAATTCGTCTCACTTGAGATTATTTTTCTTAAAA
1 ATCTCACTTGAGATTGTTTTTCTTGAAAACAAAATTCGTCTCACGTGAGATTATTTTTCTT-AAA
* *
701514 T-GAATTTTGTCTCACTTGAGATTGTTTTTCTTAAAAAAATGTC
65 TCAAATTTCGTCTCACTTGAGATTGTTTTTCTTAAAAAAATGTC
* * *
701557 ATCTCACTTGAGATTGTTTTTCTT-AAAGCAAATTTCGTCTCACGTGAGATTGTTTTTCTTAAAT
1 ATCTCACTTGAGATTGTTTTTCTTGAAAACAAAATTCGTCTCACGTGAGATTATTTTTCTTAAAT
*
701621 CAAATTTCGTCTTACTTGAGATTGTTT
66 CAAATTTCGTCTCACTTGAGATTGTTT
701648 CCTTTGAAAT
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
106 4 0.05
107 55 0.67
108 23 0.28
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.46
Consensus pattern (108 bp):
ATCTCACTTGAGATTGTTTTTCTTGAAAACAAAATTCGTCTCACGTGAGATTATTTTTCTTAAAT
CAAATTTCGTCTCACTTGAGATTGTTTTTCTTAAAAAAATGTC
Found at i:705509 original size:16 final size:15
Alignment explanation
Indices: 705477--705513 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
705467 AAACTTGTTA
705477 ATAATAAAATCTATT
1 ATAATAAAATCTATT
*
705492 ATAATAATAATTTATT
1 ATAATAA-AATCTATT
705508 ATAATA
1 ATAATA
705514 TGATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAATAAAATCTATT
Found at i:713156 original size:3 final size:3
Alignment explanation
Indices: 713148--713172 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
713138 TAGCATAGAG
713148 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
713173 AACCCTATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:722793 original size:21 final size:20
Alignment explanation
Indices: 722753--722797 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
722743 CCTTCCATTT
*
722753 ATAACTACAAAATAAATTAA
1 ATAAATACAAAATAAATTAA
722773 ATAAATACTAAAA-AAATTTAA
1 ATAAATAC-AAAATAAA-TTAA
722794 ATAA
1 ATAA
722798 TTAAATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (20 bp):
ATAAATACAAAATAAATTAA
Found at i:722804 original size:29 final size:30
Alignment explanation
Indices: 722762--722818 Score: 107
Period size: 29 Copynumber: 1.9 Consensus size: 30
722752 TATAACTACA
722762 AAATAAATTAAATAAATACTAAAAAAATTT
1 AAATAAATTAAATAAATACTAAAAAAATTT
722792 AAAT-AATTAAATAAATACTAAAAAAAT
1 AAATAAATTAAATAAATACTAAAAAAAT
722819 AAATATAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 23 0.85
30 4 0.15
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (30 bp):
AAATAAATTAAATAAATACTAAAAAAATTT
Found at i:722820 original size:15 final size:14
Alignment explanation
Indices: 722771--722839 Score: 59
Period size: 15 Copynumber: 4.7 Consensus size: 14
722761 AAAATAAATT
722771 AAATAAATACTAAAA
1 AAATAAATA-TAAAA
* **
722786 AAATTTAA-ATAATT
1 AAA-TAAATATAAAA
722800 AAATAAATACTAAAA
1 AAATAAATA-TAAAA
*
722815 AAATAAATATAATA
1 AAATAAATATAAAA
722829 AAATATAATAT
1 AAATA-AATAT
722840 TACCTTCTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
13 3 0.07
14 16 0.37
15 21 0.49
16 3 0.07
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (14 bp):
AAATAAATATAAAA
Found at i:722826 original size:29 final size:30
Alignment explanation
Indices: 722762--722838 Score: 106
Period size: 29 Copynumber: 2.6 Consensus size: 30
722752 TATAACTACA
722762 AAATA-AATTAAATAAATACTAAAAAAATT
1 AAATATAATTAAATAAATACTAAAAAAATT
*
722791 TAA-ATAATTAAATAAATACTAAAAAAA-T
1 AAATATAATTAAATAAATACTAAAAAAATT
*
722819 AAATATAATAAAATATAATA
1 AAATATAATTAAATA-AATA
722839 TTACCTTCTA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 4 0.10
29 34 0.81
30 4 0.10
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (30 bp):
AAATATAATTAAATAAATACTAAAAAAATT
Found at i:723182 original size:51 final size:51
Alignment explanation
Indices: 723033--723185 Score: 195
Period size: 50 Copynumber: 3.0 Consensus size: 51
723023 GGCTGATGCA
* * * *
723033 CCGCGCCTTACCCCACG-TGCACCACATCAACGTAAGGTGCAGTGCATGGG
1 CCGCGCCTTACCTCACGTTGCATCACATCAGCGTAAGGCGCAGTGCATGGG
* *
723083 CCACGCCTTACCTCACGTGGCATC-CATCAGCGTAAGGCGCAGTGCATGGG
1 CCGCGCCTTACCTCACGTTGCATCACATCAGCGTAAGGCGCAGTGCATGGG
* * *
723133 TCGCGCCTTACCTCACGTTGCGTCACATCAGTGTAAGGCGC-GATGCATGGG
1 CCGCGCCTTACCTCACGTTGCATCACATCAGCGTAAGGCGCAG-TGCATGGG
723184 CC
1 CC
723186 ACACTTTTTG
Statistics
Matches: 88, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
50 60 0.68
51 28 0.32
ACGTcount: A:0.20, C:0.34, G:0.27, T:0.19
Consensus pattern (51 bp):
CCGCGCCTTACCTCACGTTGCATCACATCAGCGTAAGGCGCAGTGCATGGG
Found at i:723604 original size:40 final size:39
Alignment explanation
Indices: 723559--723649 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 39
723549 ACAAGTTTCC
* *
723559 TTTTCGCAACAAGATTTTCTAATTAGC-ACACGAATTTTGT
1 TTTTCGCAACAAGATTTTCGAATTAGCAACACGAA-TTT-A
** * *
723599 TTTTCGCAACTCGATTTTCGAATTCGCAATACGAATTTA
1 TTTTCGCAACAAGATTTTCGAATTAGCAACACGAATTTA
723638 TTTTCGCAACAA
1 TTTTCGCAACAA
723650 CTTTTATTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
39 10 0.24
40 26 0.62
41 6 0.14
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (39 bp):
TTTTCGCAACAAGATTTTCGAATTAGCAACACGAATTTA
Found at i:723823 original size:14 final size:15
Alignment explanation
Indices: 723804--723841 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
723794 TCCCCGTCTC
723804 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
723818 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
723834 TAATTTTT
1 TAATTTTT
723842 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:724449 original size:12 final size:12
Alignment explanation
Indices: 724428--724461 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
724418 ACCACATTTC
*
724428 CAATACCAAACA
1 CAATATCAAACA
724440 CAATATCAAACA
1 CAATATCAAACA
*
724452 CAATCTCAAA
1 CAATATCAAA
724462 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:727448 original size:15 final size:15
Alignment explanation
Indices: 727430--727462 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
727420 CTTGAAACTT
727430 AAATTCGCAACATGA
1 AAATTCGCAACATGA
*
727445 AAA-TCGCAACTTGA
1 AAATTCGCAACATGA
727459 AAAT
1 AAAT
727463 GAAATTCGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
14 13 0.81
15 3 0.19
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.21
Consensus pattern (15 bp):
AAATTCGCAACATGA
Found at i:727511 original size:14 final size:14
Alignment explanation
Indices: 727492--727519 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
727482 CTAAAATCGC
727492 GTTGCGAATTTCAT
1 GTTGCGAATTTCAT
727506 GTTGCGAATTTCAT
1 GTTGCGAATTTCAT
727520 TTTCGTGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.43
Consensus pattern (14 bp):
GTTGCGAATTTCAT
Found at i:727543 original size:20 final size:20
Alignment explanation
Indices: 727500--727544 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
727490 GCGTTGCGAA
* *
727500 TTTCATGTTGCGAATTTCAT
1 TTTCATGTTGCGAATTTAAG
*
727520 TTTCGTGTTGCGAATTTAAG
1 TTTCATGTTGCGAATTTAAG
727540 TTTCA
1 TTTCA
727545 AAACCTACTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.13, G:0.18, T:0.49
Consensus pattern (20 bp):
TTTCATGTTGCGAATTTAAG
Found at i:727916 original size:22 final size:22
Alignment explanation
Indices: 727868--727918 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
727858 ATGGAGGAGA
* * *
727868 GTCGCCGGATATGGGGACGGAT
1 GTCGTCGGAGATGGAGACGGAT
727890 GTCGTCGGAGATGGAGACGGAT
1 GTCGTCGGAGATGGAGACGGAT
727912 GTCGTCG
1 GTCGTCG
727919 TAGAGAGTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.18, C:0.18, G:0.45, T:0.20
Consensus pattern (22 bp):
GTCGTCGGAGATGGAGACGGAT
Found at i:728030 original size:20 final size:20
Alignment explanation
Indices: 728005--728045 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
727995 CTGTTTATAA
728005 TTGTGTTACGAAATTAATAT
1 TTGTGTTACGAAATTAATAT
728025 TTGTGTTACGAAATTAATAT
1 TTGTGTTACGAAATTAATAT
728045 T
1 T
728046 CGAGTTTCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.46
Consensus pattern (20 bp):
TTGTGTTACGAAATTAATAT
Found at i:728056 original size:20 final size:20
Alignment explanation
Indices: 728009--728056 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
727999 TTATAATTGT
* *
728009 GTTACGAAATTAATATTTGT
1 GTTACGAAATTAATATTCGA
728029 GTTACGAAATTAATATTCGA
1 GTTACGAAATTAATATTCGA
*
728049 GTTTCGAA
1 GTTACGAA
728057 TTCGAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (20 bp):
GTTACGAAATTAATATTCGA
Found at i:734399 original size:28 final size:29
Alignment explanation
Indices: 734327--734399 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
734317 TTGGTAATAG
* *
734327 TTTTTTTTTCTATAT-TGTTTCTCTGTTT
1 TTTTTTTTTCTATCTCTGTCTCTCTGTTT
* *
734355 TTTCTTTTTCCGA-CTCTGTCTCTCT-TTT
1 TTT-TTTTTTCTATCTCTGTCTCTCTGTTT
734383 TTTTTTTTTCTATCTCT
1 TTTTTTTTTCTATCTCT
734400 TTTGTCTCTG
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
27 7 0.19
28 14 0.39
29 15 0.42
ACGTcount: A:0.05, C:0.19, G:0.05, T:0.70
Consensus pattern (29 bp):
TTTTTTTTTCTATCTCTGTCTCTCTGTTT
Found at i:734840 original size:24 final size:24
Alignment explanation
Indices: 734812--734874 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 24
734802 TTTGGGCTTG
734812 TAATATTAAATAATA-TATTAATAA
1 TAATATTAAATAATATTATT-ATAA
* * *
734836 TAATAATAATTATTATTATTATAA
1 TAATATTAAATAATATTATTATAA
734860 TAATAATATAAATAA
1 TAAT-AT-TAAATAA
734875 AATAAAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
24 20 0.67
25 5 0.17
26 5 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TAATATTAAATAATATTATTATAA
Found at i:735397 original size:116 final size:116
Alignment explanation
Indices: 735191--735756 Score: 867
Period size: 116 Copynumber: 4.9 Consensus size: 116
735181 TAGAATTATG
* * *
735191 CAAAAAGTTGAACAAGTTCTTTTTATTATGAACTTCTTCTTCCTTTTTCAGATGACGAGTTCTTC
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
* * *
735256 TCATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAA
66 TCATTATGAACTCTACCTGGAAAAGCTGATCCATCAAATGATGAATTCAAA
735307 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
* * * *
735372 TCATTATGAACTCTACCTGGTAATGTTGATCTATCAAATGATGAATTCAAA
66 TCATTATGAACTCTACCTGGAAAAGCTGATCCATCAAATGATGAATTCAAA
735423 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTC
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
*
735485 TCATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAA
66 TCATTATGAACTCTAC-CTGGAAAAGCTGATCCATCAAATGATGAATTCAAA
*
735536 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGACGAGTTCTTC
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
**
735601 TCATTATGAACTCTACCTGGAAAAGCTGATCCATCAAATGATGAATTCAGG
66 TCATTATGAACTCTACCTGGAAAAGCTGATCCATCAAATGATGAATTCAAA
* * *
735652 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT---GAGTTCTTC
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
** * * * *
735714 TCATTATGAACTCTTTCTGGAAAATCTAATTCATCAAGTGATG
66 TCATTATGAACTCTACCTGGAAAAGCTGATCCATCAAATGATG
735757 GATTTGAATC
Statistics
Matches: 421, Mismatches: 24, Indels: 13
0.92 0.05 0.03
Matches are distributed among these distances:
112 2 0.00
113 150 0.36
116 267 0.63
117 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (116 bp):
CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
TCATTATGAACTCTACCTGGAAAAGCTGATCCATCAAATGATGAATTCAAA
Found at i:735595 original size:229 final size:230
Alignment explanation
Indices: 735191--735756 Score: 895
Period size: 229 Copynumber: 2.5 Consensus size: 230
735181 TAGAATTATG
* * *
735191 CAAAAAGTTGAACAAGTTCTTTTTATTATGAACTTCTTCTTCCTTTTTCAGATGACGAGTTCTTC
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTC
* * * *
735256 TCATTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAAC
63 TCATTATGAACTCTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAAC
*
735320 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTC
128 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGACGAGTTCTTCTCATTATGAACTC
* * * *
735385 TACCTGGTAATGTTGATCTATCAAATGATGAATTCAAA
193 TACCTGGAAAAGCTGATCCATCAAATGATGAATTCAAA
735423 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
735488 TTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAG
66 TTATGAACTCTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAG
735552 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGACGAGTTCTTCTCATTATGAACTCTAC
131 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGACGAGTTCTTCTCATTATGAACTCTAC
**
735617 CTGGAAAAGCTGATCCATCAAATGATGAATTCAGG
196 CTGGAAAAGCTGATCCATCAAATGATGAATTCAAA
* * *
735652 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * *
735717 TTATGAACTCTT-TCTGGAAAATCTAATTCATCAAGTGATG
66 TTATGAACTCTTCTCTGGAAAAGCTGATCCATCAAATGATG
735757 GATTTGAATC
Statistics
Matches: 311, Mismatches: 21, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
228 2 0.01
229 257 0.83
230 2 0.01
232 50 0.16
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (230 bp):
CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAG
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGACGAGTTCTTCTCATTATGAACTCTAC
CTGGAAAAGCTGATCCATCAAATGATGAATTCAAA
Found at i:736769 original size:164 final size:165
Alignment explanation
Indices: 736484--736942 Score: 830
Period size: 164 Copynumber: 2.8 Consensus size: 165
736474 GTAGTTCCTA
*
736484 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCA-ATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
736549 ATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATA
65 ATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATA
736614 AACACATTCATCTTCCAAATTCAATGATTGGTTCTG
130 AACACATTCATCTTCCAAATTCAATGATTGGTTCTG
736650 CCAAACCAGATC-ATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAA
1 CCAAACCAGATCAATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAA
*
736714 TTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
66 TTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATAA
736779 ACACATTCATCTTCCAAATTCAATGATTGGTTCTG
131 ACACATTCATCTTCCAAATTCAATGATTGGTTCTG
* * * * *
736814 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTTATCTTCTAA
1 CCAAACCAGATCA-ATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
736879 ATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
65 ATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
736943 TGGCCAATTC
Statistics
Matches: 284, Mismatches: 7, Indels: 4
0.96 0.02 0.01
Matches are distributed among these distances:
164 162 0.57
166 122 0.43
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (165 bp):
CCAAACCAGATCAATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAA
TTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATAA
ACACATTCATCTTCCAAATTCAATGATTGGTTCTG
Found at i:736957 original size:83 final size:83
Alignment explanation
Indices: 736484--736942 Score: 841
Period size: 83 Copynumber: 5.6 Consensus size: 83
736474 GTAGTTCCTA
*
736484 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
736549 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
*
736567 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATAAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
736632 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
736650 CCAAACCAGATC--ATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
736713 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
736731 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
736796 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* * * * *
736814 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTTATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
736879 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
736897 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
736943 TGGCCAATTC
Statistics
Matches: 366, Mismatches: 8, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
81 80 0.22
83 286 0.78
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
ATTCAATGATTGGTTCTG
Found at i:738109 original size:8 final size:8
Alignment explanation
Indices: 738096--738175 Score: 101
Period size: 8 Copynumber: 10.1 Consensus size: 8
738086 TTGACCCCCC
738096 TTTTTTCT
1 TTTTTTCT
738104 TTTTTT-T
1 TTTTTTCT
* *
738111 CTCTTT-T
1 TTTTTTCT
*
738118 TTTTTCCT
1 TTTTTTCT
*
738126 TTTTCTCT
1 TTTTTTCT
738134 TTTTTTCT
1 TTTTTTCT
738142 TTTTTTCT
1 TTTTTTCT
738150 TTTTTTCT
1 TTTTTTCT
738158 TTTTTTCT
1 TTTTTTCT
738166 TTCTTTTCT
1 TT-TTTTCT
738175 T
1 T
738176 CAAGCATAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
7 9 0.15
8 46 0.74
9 7 0.11
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTTCT
Found at i:750534 original size:27 final size:28
Alignment explanation
Indices: 750462--750534 Score: 69
Period size: 27 Copynumber: 2.6 Consensus size: 28
750452 TTGGTAATAG
* * *
750462 TTTTTTTTTTCTATAT-TGTTTCTCTGT
1 TTTTTTTTTTCTATCTCTGTCTCTCTGC
***
750489 TTTTTCTTTTTCCGGCTCTGTCTCTCT-C
1 TTTTT-TTTTTCTATCTCTGTCTCTCTGC
750517 TTTTTTTTTTCTATCTCT
1 TTTTTTTTTTCTATCTCT
750535 TTTGTCTCTG
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
27 15 0.43
28 12 0.34
29 8 0.23
ACGTcount: A:0.04, C:0.21, G:0.07, T:0.68
Consensus pattern (28 bp):
TTTTTTTTTTCTATCTCTGTCTCTCTGC
Found at i:750958 original size:12 final size:11
Alignment explanation
Indices: 750941--751012 Score: 67
Period size: 12 Copynumber: 6.3 Consensus size: 11
750931 TTTGGGCTTG
750941 TAAT-ATTAAA
1 TAATAATTAAA
750951 TAATATATT-AA
1 TAATA-ATTAAA
*
750962 TAATAATAATAA
1 TAATAATTA-AA
*
750974 TTATAATTATAA
1 TAATAATTA-AA
750986 TAATAATTATAA
1 TAATAATTA-AA
750998 TAATAATATAAA
1 TAATAAT-TAAA
751010 TAA
1 TAA
751013 AATAAAAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
10 6 0.11
11 7 0.13
12 38 0.72
13 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TAATAATTAAA
Found at i:750965 original size:3 final size:3
Alignment explanation
Indices: 750949--751017 Score: 72
Period size: 3 Copynumber: 23.7 Consensus size: 3
750939 TGTAATATTA
* * * *
750949 AAT AAT -AT ATT AAT AAT AAT AAT AAT TAT AAT TAT AAT AAT AAT TAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
750996 AAT AAT AAT -AT AAAT AA- AAT AA
1 AAT AAT AAT AAT -AAT AAT AAT AA
751018 AAAATGAAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
2 6 0.11
3 46 0.85
4 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:751738 original size:35 final size:35
Alignment explanation
Indices: 751663--751802 Score: 158
Period size: 35 Copynumber: 4.0 Consensus size: 35
751653 AAAAGATGAA
* ** *
751663 CACTTGAATCGAAAGT-ACGACACCTCCTTCCGTT
1 CACTTGAATCGAAAGTGTCGATGCTTCCTTCCGTT
* *
751697 CGACTTGAATCGAAAGTGTCGATGTTTTCTTCCGTT
1 C-ACTTGAATCGAAAGTGTCGATGCTTCCTTCCGTT
* *
751733 CACTTGAATCGAAAGCGTCGATGCTTCCTTTCGTT
1 CACTTGAATCGAAAGTGTCGATGCTTCCTTCCGTT
* * *
751768 CACTTAAATCGAAAGTGCCGATGC-TCCTTTCGTT
1 CACTTGAATCGAAAGTGTCGATGCTTCCTTCCGTT
751802 C
1 C
751803 TTCTTATTCA
Statistics
Matches: 91, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
34 12 0.13
35 66 0.73
36 13 0.14
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (35 bp):
CACTTGAATCGAAAGTGTCGATGCTTCCTTCCGTT
Found at i:760862 original size:18 final size:17
Alignment explanation
Indices: 760839--760872 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
760829 CAGTCTGTAT
760839 TATTTTAATGATTTTATA
1 TATTTTAAT-ATTTTATA
*
760857 TATTTTGATATTTTAT
1 TATTTTAATATTTTAT
760873 TTAATTATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TATTTTAATATTTTATA
Found at i:761805 original size:138 final size:137
Alignment explanation
Indices: 761501--761849 Score: 504
Period size: 138 Copynumber: 2.5 Consensus size: 137
761491 AATCTAGTAA
*
761501 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCGGACGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCGGATGAGTTCTTCTCATTAT
* *
761566 GAACTCTTCCATTGAAAATGTTGATCCTCAAGTGAGGTATCGCTGATTCAACTCCATATGTGATG
66 GAA--CTTCCATTGAAAATGTTGATCCTCAAGTGAGGTATCGCTAATTCAACTCCATAGGTGATG
761631 AATCAAGGC
129 AATCAAGGC
* * *
761640 AATGTTGAACAAGTTTTTCTCATTATGAACTTCTTCTTGCTCTTCGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCGGATGAGTTCTTCTCATTAT
* * * *
761705 GAACTTCC-TCTGGAAATGTTGATCCATCGAGTGAGGTGTCTCTAATTCAACTCCATAGGTGATG
66 GAACTTCCAT-TGAAAATGTTGATCC-TCAAGTGAGGTATCGCTAATTCAACTCCATAGGTGATG
761769 AATCAA-GC
129 AATCAAGGC
* * * *
761777 TAAGGTCGAACAAATTCTTCTCATTATGAACTTATTCTTCCTCTTCAGATGAGTTCTTCTCATTA
1 -AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCGGATGAGTTCTTCTCATTA
*
761842 TCAACTTC
65 TGAACTTC
761850 TTTCAGAAAT
Statistics
Matches: 189, Mismatches: 18, Indels: 7
0.88 0.08 0.03
Matches are distributed among these distances:
136 1 0.01
137 21 0.11
138 103 0.54
139 64 0.34
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (137 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCGGATGAGTTCTTCTCATTAT
GAACTTCCATTGAAAATGTTGATCCTCAAGTGAGGTATCGCTAATTCAACTCCATAGGTGATGAA
TCAAGGC
Found at i:762228 original size:17 final size:17
Alignment explanation
Indices: 762208--762249 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
762198 TGTTTCATTC
*
762208 TCTTTGCTGAG-TCTTTA
1 TCTTTGCTGAGAT-TTCA
762225 TCTTTGCTGAGATTTCA
1 TCTTTGCTGAGATTTCA
762242 TCTTTGCT
1 TCTTTGCT
762250 CTTTGCTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 22 0.96
18 1 0.04
ACGTcount: A:0.12, C:0.19, G:0.17, T:0.52
Consensus pattern (17 bp):
TCTTTGCTGAGATTTCA
Found at i:762262 original size:24 final size:22
Alignment explanation
Indices: 762225--762275 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 22
762215 TGAGTCTTTA
762225 TCTTTGCTGAGATTTCATCTTTGC
1 TCTTTGCTGAGATTTCA-C-TTGC
*
762249 TCTTTGCTTG-GATTTGACTTGC
1 TCTTTGC-TGAGATTTCACTTGC
762271 TCTTT
1 TCTTT
762276 TCATAGACTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 9 0.36
23 1 0.04
24 13 0.52
25 2 0.08
ACGTcount: A:0.10, C:0.20, G:0.18, T:0.53
Consensus pattern (22 bp):
TCTTTGCTGAGATTTCACTTGC
Found at i:762987 original size:15 final size:15
Alignment explanation
Indices: 762927--762987 Score: 88
Period size: 15 Copynumber: 3.9 Consensus size: 15
762917 TTGACCCCCT
762927 TTTTCTATTTTCTTTTC
1 TTTTCT-TTTT-TTTTC
762944 TTCTTC-TTTTTTTTC
1 TT-TTCTTTTTTTTTC
762959 TTTTCTTTTTTTTTC
1 TTTTCTTTTTTTTTC
762974 TTTTCTTTTTTTTT
1 TTTTCTTTTTTTTT
762988 TCTTCTTCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.07
15 30 0.71
16 4 0.10
17 2 0.05
18 3 0.07
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTCTTTTTTTTTC
Found at i:762987 original size:20 final size:20
Alignment explanation
Indices: 762934--762994 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
762924 CCTTTTTCTA
*
762934 TTTTCTTTTCTTCTTCTTTT-
1 TTTTCTTTTCTT-TTTTTTTC
762954 TTTTCTTTTCTTTTTTTTTC
1 TTTTCTTTTCTTTTTTTTTC
*
762974 TTTTCTTTT-TTTTTTCTTC
1 TTTTCTTTTCTTTTTTTTTC
762993 TT
1 TT
762995 CAAGCATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 17 0.45
20 21 0.55
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTTCTTTTCTTTTTTTTTC
Found at i:762988 original size:5 final size:5
Alignment explanation
Indices: 762934--762986 Score: 74
Period size: 5 Copynumber: 10.8 Consensus size: 5
762924 CCTTTTTCTA
*
762934 TTTTC TTTTC TTCTTC TTTT- TTTTC TTTTC TTTTT TTTTC TTTTC TTTT-
1 TTTTC TTTTC TT-TTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
762983 TTTT
1 TTTT
762987 TTCTTCTTCA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
4 8 0.18
5 31 0.70
6 5 0.11
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (5 bp):
TTTTC
Found at i:770704 original size:18 final size:18
Alignment explanation
Indices: 770681--770840 Score: 221
Period size: 18 Copynumber: 8.9 Consensus size: 18
770671 GAGGGTCTAT
*
770681 GTGGTCCTTCGAGACATA
1 GTGGTCCTTCGGGACATA
*
770699 GTGGTCATTCGGGACATA
1 GTGGTCCTTCGGGACATA
* * *
770717 ATTGTCCTTCGGGACACA
1 GTGGTCCTTCGGGACATA
770735 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
* *
770753 ATGGTCCTTCGGAACATA
1 GTGGTCCTTCGGGACATA
*
770771 GTGGTTCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
* *
770789 ATGGTCCTTCGGGACACA
1 GTGGTCCTTCGGGACATA
770807 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
770825 GTGGTCCTACGGGACA
1 GTGGTCCTTCGGGACA
770841 AATTCTACGC
Statistics
Matches: 122, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 122 1.00
ACGTcount: A:0.21, C:0.23, G:0.30, T:0.27
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:771095 original size:2 final size:2
Alignment explanation
Indices: 771088--771119 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
771078 ATGTACATGA
771088 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
771120 GAATGAATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:787101 original size:22 final size:21
Alignment explanation
Indices: 787058--787123 Score: 62
Period size: 22 Copynumber: 3.1 Consensus size: 21
787048 AAATTTTATG
* *
787058 TAATTTAAATGTATTTTATTAA
1 TAATTT-AATTTATATTATTAA
*
787080 TAATTTAATTTTATATTCTTAA
1 TAATTTAA-TTTATATTATTAA
* *
787102 -AATTTTATTTATATTTTTAA
1 TAATTTAATTTATATTATTAA
787122 TA
1 TA
787124 TAATTTCTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
20 12 0.32
21 9 0.24
22 16 0.43
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TAATTTAATTTATATTATTAA
Found at i:787110 original size:33 final size:33
Alignment explanation
Indices: 787070--787142 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
787060 ATTTAAATGT
* *
787070 ATTTTATTAATA-ATTTAATTTTATATTCTTAAA
1 ATTTTATTAATATATTTAATATAAT-TTCTTAAA
* *
787103 ATTTTATTTATATTTTTAATATAATTTCTTAAA
1 ATTTTATTAATATATTTAATATAATTTCTTAAA
*
787136 AATTTAT
1 ATTTTAT
787143 AATTATAAGC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 25 0.74
34 9 0.26
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (33 bp):
ATTTTATTAATATATTTAATATAATTTCTTAAA
Found at i:790395 original size:14 final size:14
Alignment explanation
Indices: 790370--790424 Score: 67
Period size: 14 Copynumber: 3.9 Consensus size: 14
790360 GGATCGACGG
790370 GTCAGGTCAACCGA
1 GTCAGGTCAACCGA
* *
790384 GTTAGGTTAACCGA
1 GTCAGGTCAACCGA
*
790398 GTCGGGTCAACCGA
1 GTCAGGTCAACCGA
790412 GTC-GGATCAACCG
1 GTCAGG-TCAACCG
790425 GGTCGGGTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
13 2 0.06
14 33 0.94
ACGTcount: A:0.25, C:0.25, G:0.31, T:0.18
Consensus pattern (14 bp):
GTCAGGTCAACCGA
Found at i:790423 original size:28 final size:28
Alignment explanation
Indices: 790374--790432 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
790364 CGACGGGTCA
*
790374 GGTCAACCGAGTTAGGTTAACCGAGTCG
1 GGTCAACCGAGTTAGGTCAACCGAGTCG
* *
790402 GGTCAACCGAG-TCGGATCAACCGGGTCG
1 GGTCAACCGAGTTAGG-TCAACCGAGTCG
790430 GGT
1 GGT
790433 ATTTTTGCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 3 0.11
28 24 0.89
ACGTcount: A:0.22, C:0.24, G:0.36, T:0.19
Consensus pattern (28 bp):
GGTCAACCGAGTTAGGTCAACCGAGTCG
Found at i:790429 original size:14 final size:14
Alignment explanation
Indices: 790392--790430 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
790382 GAGTTAGGTT
*
790392 AACCGAGTCGGGTC
1 AACCGAGTCGGATC
790406 AACCGAGTCGGATC
1 AACCGAGTCGGATC
*
790420 AACCGGGTCGG
1 AACCGAGTCGG
790431 GTATTTTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.23, C:0.28, G:0.36, T:0.13
Consensus pattern (14 bp):
AACCGAGTCGGATC
Found at i:803895 original size:3 final size:3
Alignment explanation
Indices: 803801--803884 Score: 118
Period size: 3 Copynumber: 28.0 Consensus size: 3
803791 AATTTTTCGT
* *
803801 TTA TTA TTA TTA -AA TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA TTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
803849 TTA TTA TTA TTA TTA TTA TATA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
803885 AATAATTATT
Statistics
Matches: 73, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
2 3 0.04
3 64 0.88
4 6 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:805666 original size:136 final size:138
Alignment explanation
Indices: 805316--805683 Score: 616
Period size: 138 Copynumber: 2.7 Consensus size: 138
805306 ACATTTTTAA
805316 TATTTATTTTATTTATTAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGTTCTTTTTTG
1 TATTTA-TTTATTTATTAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGTTCTTTTTTG
805381 ATATTCATAAATAAATAAATATCCTATTTTTATAAATTATATATTAATTATTTTTAGAAAAAATG
65 ATATTCATAAATAAATAAATATCCTATTTTTATAAATTATATATTAATTATTTTTAGAAAAAATG
805446 TTTTTTAGT
130 TTTTTTAGT
*
805455 TATTTATTTATTTATTAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGTTCTTTTTTTA
1 TATTTATTTATTTATTAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGTTCTTTTTTGA
*
805520 TATTCATAAATAAATAAATATCCTGTTTTTATAAATTATATATTAATTATTTTTAGAAAAAAT-T
66 TATTCATAAATAAATAAATATCCTATTTTTATAAATTATATATTAATTATTTTTAGAAAAAATGT
805584 TTTTTAGT
131 TTTTTAGT
* * * *
805592 TATTTATTTATTT-TTAATATCGAAGAAAGGAGCTGTCTTAAAGCACCTAGAAG-CCATTTTCTG
1 TATTTATTTATTTATTAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGTTC-TTTTTTG
** *
805655 ATATTTTTAAATAAATAAATATCTTATTT
65 ATATTCATAAATAAATAAATATCCTATTT
805684 ATACATATTA
Statistics
Matches: 217, Mismatches: 11, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
135 1 0.00
136 68 0.31
137 22 0.10
138 120 0.55
139 6 0.03
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.45
Consensus pattern (138 bp):
TATTTATTTATTTATTAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGTTCTTTTTTGA
TATTCATAAATAAATAAATATCCTATTTTTATAAATTATATATTAATTATTTTTAGAAAAAATGT
TTTTTAGT
Found at i:806237 original size:26 final size:28
Alignment explanation
Indices: 806184--806240 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
806174 TTTCAAATTT
**
806184 TTTATATATACTTATTATTTTTATAGTA
1 TTTATATATACTTATTATTTGCATAGTA
806212 TTTATATATA-TTATTATTTGCA-AGTA
1 TTTATATATACTTATTATTTGCATAGTA
806238 TTT
1 TTT
806241 TCATTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 7 0.26
27 10 0.37
28 10 0.37
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.60
Consensus pattern (28 bp):
TTTATATATACTTATTATTTGCATAGTA
Found at i:808284 original size:21 final size:22
Alignment explanation
Indices: 808259--808304 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
808249 GAGTAACACC
808259 TTTTCATATATGCA-TTTTCAT
1 TTTTCATATATGCATTTTTCAT
* *
808280 TTTTCATCTTTGCATTTTTCAT
1 TTTTCATATATGCATTTTTCAT
808302 TTT
1 TTT
808305 GCATTCATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.17, C:0.15, G:0.04, T:0.63
Consensus pattern (22 bp):
TTTTCATATATGCATTTTTCAT
Found at i:808297 original size:15 final size:14
Alignment explanation
Indices: 808271--808309 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
808261 TTCATATATG
808271 CATTTT-CATTTTT
1 CATTTTGCATTTTT
808284 CATCTTTGCATTTTT
1 CAT-TTTGCATTTTT
808299 CATTTTGCATT
1 CATTTTGCATT
808310 CATACTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 3 0.12
14 11 0.46
15 10 0.42
ACGTcount: A:0.15, C:0.18, G:0.05, T:0.62
Consensus pattern (14 bp):
CATTTTGCATTTTT
Found at i:811229 original size:21 final size:18
Alignment explanation
Indices: 811190--811226 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
811180 TCTTATACTC
811190 ATCCAGCAAAGAAAAAAA
1 ATCCAGCAAAGAAAAAAA
811208 ATCCAGCAAAGAAAAAAA
1 ATCCAGCAAAGAAAAAAA
811226 A
1 A
811227 AAAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.68, C:0.16, G:0.11, T:0.05
Consensus pattern (18 bp):
ATCCAGCAAAGAAAAAAA
Found at i:811261 original size:1 final size:1
Alignment explanation
Indices: 811219--811243 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
811209 TCCAGCAAAG
811219 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
811244 TAGATGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:811268 original size:16 final size:18
Alignment explanation
Indices: 811239--811277 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
811229 AAAAAAAAAA
*
811239 AAAAATAGATGAAAAAGG
1 AAAAATAGATGAAAAACG
811257 AAAAAT-GA-GAAAAACG
1 AAAAATAGATGAAAAACG
811273 AAAAA
1 AAAAA
811278 AAAAGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 2 0.10
18 6 0.30
ACGTcount: A:0.72, C:0.03, G:0.18, T:0.08
Consensus pattern (18 bp):
AAAAATAGATGAAAAACG
Found at i:811277 original size:17 final size:16
Alignment explanation
Indices: 811232--811293 Score: 61
Period size: 17 Copynumber: 3.7 Consensus size: 16
811222 AAAAAAAAAA
*
811232 AAAAAAAAAAAATAGATG
1 AAAAAGAAAAAAT-GA-G
*
811250 AAAAAGGAAAAATGAG
1 AAAAAGAAAAAATGAG
**
811266 AAAAACGAAAAAAAAAG
1 AAAAA-GAAAAAATGAG
811283 AAAAAGAAAAA
1 AAAAAGAAAAA
811294 GGGGAGAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
16 12 0.32
17 15 0.39
18 11 0.29
ACGTcount: A:0.79, C:0.02, G:0.15, T:0.05
Consensus pattern (16 bp):
AAAAAGAAAAAATGAG
Found at i:813764 original size:31 final size:31
Alignment explanation
Indices: 813726--813788 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
813716 GCACATATAA
* * *
813726 AATCTGTCAACTTTGCAATTGATGAATTCAG
1 AATCTGTCAAATCTACAATTGATGAATTCAG
813757 AATCTGTCAAATCTACAATTGATGAATTCAG
1 AATCTGTCAAATCTACAATTGATGAATTCAG
813788 A
1 A
813789 CTACATCTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (31 bp):
AATCTGTCAAATCTACAATTGATGAATTCAG
Found at i:816236 original size:22 final size:22
Alignment explanation
Indices: 816211--816287 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
816201 ATCTACATTC
*
816211 TTCAAAGATGATATATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
816233 TTCAAAGATGAAAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
816255 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
816277 TTCAAAGATGA
1 TTCAAAGATGA
816288 AAGCTTTATG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:817113 original size:165 final size:166
Alignment explanation
Indices: 816802--817125 Score: 508
Period size: 165 Copynumber: 2.0 Consensus size: 166
816792 AAAATGAGCA
*
816802 TTATCTTCAGATTGGGTCATGTTACCCAATCAACATGTTATTTCAAAAAACAGGATGAGAAAACG
1 TTATCTTCAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAACA-GATGAGAAAACG
* ** *
816867 ATTTTCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTT
65 ATTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTAAAAAGTAAGAAAACGATTTT
* * *
816932 CTTAGTTTTTTTACTTAGTAAACTATTTCTAACAGCC
130 CATAGTTCTCTTACTTAGTAAACTATTTCTAACAGCC
* ** *
816969 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTTGAAAAATA-ATGAGAAAACGA
1 TTATCTTCAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAACAGATGAGAAAACGA
817033 TTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATGAAATTGTTAAAAAGTAAGAAAACGATTTT
66 TTTCCATAGTTTCTCATTCAATCTTTTCT-AAAATGAAATTGTTAAAAAGTAAGAAAACGATTTT
817098 CATAG-TCTCTTACTTAGTAAACTATTTC
130 CATAGTTCTCTTACTTAGTAAACTATTTC
817126 CCACATCTGT
Statistics
Matches: 144, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
165 59 0.41
166 38 0.26
167 47 0.33
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (166 bp):
TTATCTTCAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAACAGATGAGAAAACGA
TTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTAAAAAGTAAGAAAACGATTTTC
ATAGTTCTCTTACTTAGTAAACTATTTCTAACAGCC
Found at i:817571 original size:76 final size:76
Alignment explanation
Indices: 817129--817537 Score: 759
Period size: 76 Copynumber: 5.4 Consensus size: 76
817119 CTATTTCCCA
*
817129 CATCTGTAAGTCCTGCAGTGCATGATGTTTCTAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
817193 AGCCTTCGGGT
66 AGCCTTAGGGT
817204 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
817268 AAGCCTTAGGGT
65 AAGCCTTAGGGT
817280 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
817345 AGCCTTAGGGT
66 AGCCTTAGGGT
*
817356 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
817421 AACCTTAGGGT
66 AGCCTTAGGGT
817432 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
817497 AGCCTTAGGGT
66 AGCCTTAGGGT
817508 CATCTGTAAGTCCTGCAGTGCATGATGTTT
1 CATCTGTAAGTCCTGCAGTGCATGATGTTT
817538 TTAAGACCTC
Statistics
Matches: 326, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
75 62 0.19
76 264 0.81
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:817785 original size:3 final size:3
Alignment explanation
Indices: 817690--817774 Score: 100
Period size: 3 Copynumber: 28.0 Consensus size: 3
817680 AATTTTTCGT
* * **
817690 TTA TTA TTA TAA ATA TTA TTA TTA TTA TTA TTA TTA TTA AAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
817738 TTA TTA TTAA ATA TTA TTA TATA TTA -TA TTA TTA TTA
1 TTA TTA TT-A TTA TTA TTA T-TA TTA TTA TTA TTA TTA
817775 AATAATTATT
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
2 2 0.03
3 62 0.90
4 5 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:818980 original size:20 final size:21
Alignment explanation
Indices: 818933--818984 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
818923 TAATATTTTG
* *
818933 AATTATTATCTTTATTTTTAAT
1 AATT-TTATATTTAGTTTTAAT
818955 AA-TTTATATTTAGTTTT-AT
1 AATTTTATATTTAGTTTTAAT
818974 AATTTTA-ATTT
1 AATTTTATATTT
818985 CTTTTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 8 0.30
20 16 0.59
21 1 0.04
22 2 0.07
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (21 bp):
AATTTTATATTTAGTTTTAAT
Found at i:818984 original size:19 final size:20
Alignment explanation
Indices: 818938--818978 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
818928 TTTTGAATTA
* *
818938 TTATCTTTATTTTTAATAAT
1 TTATATTTAGTTTTAATAAT
818958 TTATATTTAGTTTT-ATAAT
1 TTATATTTAGTTTTAATAAT
818977 TT
1 TT
818979 TAATTTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (20 bp):
TTATATTTAGTTTTAATAAT
Found at i:819427 original size:139 final size:138
Alignment explanation
Indices: 819177--819543 Score: 608
Period size: 139 Copynumber: 2.6 Consensus size: 138
819167 ACATTTTTAA
819177 TATTTATTTTATTTATTAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGTTCTTTTTTG
1 TATTTA-TTTATTTATTAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGTTCTTTTTTG
*
819242 ATATTCATAAATAAATAAATATCATGTTTTTATAAATTATATATTAATTATTTTTAGAAAAAATG
65 ATATTCATAAATAAATAAATATCTTGTTTTTATAAATTATATATTAATTATTTTTAGAAAAAATG
819307 TTTTTTAGT
130 TTTTTTAGT
* *
819316 TATTTATTTATTTATTAATATCAAAGAAAAGAGCTGTCTTAAAGCACATAGAAGTTCTTTTTTTT
1 TATTTATTTATTTATTAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGTTC-TTTTTTG
819381 ATATTCATAAATAAATAAATATCTTGTTTTTATAAATTATATATTAATTATTTTTAGAAAAAATG
65 ATATTCATAAATAAATAAATATCTTGTTTTTATAAATTATATATTAATTATTTTTAGAAAAAATG
819446 TTTTTTAGT
130 TTTTTTAGT
* * * * ** *
819455 TATTTATTTATTTTTTAATATCGAAGAAAGGAGCTGTCTTAAAGTACCTAGAAGCCCTTTTCTGA
1 TATTTATTTATTTATTAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGTTCTTTTTTGA
**
819520 TATTTTTAAATAAATAAATATCTT
66 TATTCATAAATAAATAAATATCTT
819544 ATTTATACAT
Statistics
Matches: 213, Mismatches: 14, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
138 78 0.37
139 135 0.63
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.46
Consensus pattern (138 bp):
TATTTATTTATTTATTAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGTTCTTTTTTGA
TATTCATAAATAAATAAATATCTTGTTTTTATAAATTATATATTAATTATTTTTAGAAAAAATGT
TTTTTAGT
Found at i:819615 original size:15 final size:16
Alignment explanation
Indices: 819575--819615 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
819565 TTCTTAAGAT
*
819575 TATTTGAAATAACATA
1 TATTTGAATTAACATA
819591 -ATTATGAATTAA-ATA
1 TATT-TGAATTAACATA
819606 TATTTGAATT
1 TATTTGAATT
819616 CTTAAATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.44
Consensus pattern (16 bp):
TATTTGAATTAACATA
Found at i:823674 original size:55 final size:55
Alignment explanation
Indices: 823586--824271 Score: 831
Period size: 55 Copynumber: 12.5 Consensus size: 55
823576 CAAATGACGA
* * *
823586 GTCCGCTCCCTATT-CTTCAGGGAGTATA-AGACTCGAACAATCTTCAGTAAACGT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAATAAACGG
* * * * *
823640 GTCTGCTCCCTATTCGTTCAGGGAGTATA-AGACTCGAACAATATTC-ATAAA-AG
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAATAAACGG
* * * * *
823693 GTTCGCTCCCTATTCGTTCAGGGAGTATAAAACTCGAACAATCTTC-ATAAAATGG
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAAT-AAACGG
* *
823748 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGG
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAACGG
* *
823803 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGG
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAACGG
* * * * * *
823858 GTTCACTCCCTATTCATTCAGGGAGTATAGAACTCAAAAAATCTTC-ATAAAACGG
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAAT-AAACGG
* * *
823913 GTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGG
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAACGG
* * *
823968 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCAAACAATCTTC-ATAAAATGG
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAAT-AAACGG
*
824023 GTCCG-TACTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAACGG
1 GTCCGCT-CCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAACGG
* * * *
824078 GTCCTCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAATGG
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAACGG
* * *
824133 GTCCGCTCCCTATT-CTATCAGAGAGTATAGAACTCAAACAATCTTCAA-CAATGG
1 GTCCGCTCCCTATTCCT-TCAGAGAGTATAGAACTCGAACAATCTTCAATAAACGG
* * * *
824187 GTCCGCTCCTTATT-TTATCAGAGAGTATAGACCTCGAACAATCTTCAACAAACGG
1 GTCCGCTCCCTATTCCT-TCAGAGAGTATAGAACTCGAACAATCTTCAATAAACGG
824242 GTCCGCTCCCTATT-CTATCAGAGAGTATAG
1 GTCCGCTCCCTATTCCT-TCAGAGAGTATAG
824272 GACTTGATCT
Statistics
Matches: 564, Mismatches: 55, Indels: 25
0.88 0.09 0.04
Matches are distributed among these distances:
53 43 0.08
54 75 0.13
55 441 0.78
56 5 0.01
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (55 bp):
GTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAACGG
Found at i:824348 original size:37 final size:38
Alignment explanation
Indices: 824289--824360 Score: 119
Period size: 37 Copynumber: 1.9 Consensus size: 38
824279 TCTTCATAAA
* *
824289 ATGAGTTTTCTTCACTACTCTTCCGTGAATGCTTATAT
1 ATGAGTTTGCTTCACTACTCTTCCGTGAAGGCTTATAT
824327 ATGA-TTTGCTTCACTACTCTTCCGTGAAGGCTTA
1 ATGAGTTTGCTTCACTACTCTTCCGTGAAGGCTTA
824361 AGATTAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
37 28 0.88
38 4 0.12
ACGTcount: A:0.21, C:0.22, G:0.15, T:0.42
Consensus pattern (38 bp):
ATGAGTTTGCTTCACTACTCTTCCGTGAAGGCTTATAT
Found at i:824644 original size:12 final size:12
Alignment explanation
Indices: 824629--824654 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
824619 TCATGCAATT
824629 ATGGATGCCATG
1 ATGGATGCCATG
824641 ATGGATGCCATG
1 ATGGATGCCATG
824653 AT
1 AT
824655 CCTATTTACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (12 bp):
ATGGATGCCATG
Found at i:825738 original size:18 final size:19
Alignment explanation
Indices: 825717--825758 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
825707 TATTTTTCTC
*
825717 TTTTCTTTC-CTTTTCATT
1 TTTTCTATCACTTTTCATT
*
825735 TTTTC-ATCATTTTTCATT
1 TTTTCTATCACTTTTCATT
825753 TTTTCT
1 TTTTCT
825759 CATTTTTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.10, C:0.19, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTCTATCACTTTTCATT
Found at i:825754 original size:16 final size:15
Alignment explanation
Indices: 825734--825868 Score: 56
Period size: 14 Copynumber: 9.1 Consensus size: 15
825724 TCCTTTTCAT
825734 TTTTTCATCATTTTTC
1 TTTTTC-TCATTTTTC
825750 ATTTTTTCTCATTTTTC
1 --TTTTTCTCATTTTTC
* *
825767 -TTTTCT--TCTAT-
1 TTTTTCTCATTTTTC
825778 TTTTTCTCATTTTT-
1 TTTTTCTCATTTTTC
* *
825792 TTCTTCT-TTTTTTC
1 TTTTTCTCATTTTTC
*
825806 ATTTTCTTC-TTTTT-
1 TTTTTC-TCATTTTTC
** *
825820 TTCTTTCATTTTTTTTA
1 TT-TTTC-TCATTTTTC
825837 TTTTTCTC-TTTTTC
1 TTTTTCTCATTTTTC
825851 TTTTT-TCCATTTCTTC
1 TTTTTCT-CATTT-TTC
825867 TT
1 TT
825869 CAAGCGAAAT
Statistics
Matches: 92, Mismatches: 13, Indels: 26
0.70 0.10 0.20
Matches are distributed among these distances:
12 9 0.10
13 6 0.07
14 31 0.34
15 15 0.16
16 14 0.15
17 11 0.12
18 6 0.07
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTTCTCATTTTTC
Found at i:825761 original size:28 final size:28
Alignment explanation
Indices: 825730--825849 Score: 99
Period size: 28 Copynumber: 4.3 Consensus size: 28
825720 TCTTTCCTTT
*
825730 TCATTTTTTCATCATTTTTCATTTTTTC
1 TCATTTTTTCTTCATTTTTCATTTTTTC
*
825758 TCA-TTTTTCTT--TTCTTCTATTTTTTC
1 TCATTTTTTCTTCATTTTTC-ATTTTTTC
*
825784 TCATTTTTTTCTTCTTTTTTTCATTTTCTTC
1 TCA-TTTTTTCTTC-ATTTTTCATTTT-TTC
**
825815 T--TTTTTTCTTTCATTTTTTTTATTTTTC
1 TCATTTTTTC-TTCATTTTTCAT-TTTTTC
825843 TC-TTTTT
1 TCATTTTT
825850 CTTTTTTCCA
Statistics
Matches: 76, Mismatches: 6, Indels: 19
0.75 0.06 0.19
Matches are distributed among these distances:
25 5 0.07
26 11 0.14
27 7 0.09
28 28 0.37
29 11 0.14
30 5 0.07
31 9 0.12
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (28 bp):
TCATTTTTTCTTCATTTTTCATTTTTTC
Found at i:825765 original size:17 final size:17
Alignment explanation
Indices: 825727--825781 Score: 78
Period size: 17 Copynumber: 3.2 Consensus size: 17
825717 TTTTCTTTCC
825727 TTTTCATTTTTTCATCAT
1 TTTTCATTTTTTC-TCAT
825745 TTTTCATTTTTTCTCAT
1 TTTTCATTTTTTCTCAT
825762 TTTTC-TTTTCTTCT-AT
1 TTTTCATTTT-TTCTCAT
825778 TTTT
1 TTTT
825782 TCTCATTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.28
17 13 0.36
18 13 0.36
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTCATTTTTTCTCAT
Found at i:825782 original size:17 final size:17
Alignment explanation
Indices: 825692--825849 Score: 77
Period size: 17 Copynumber: 9.3 Consensus size: 17
825682 GTTTTTCCAT
*
825692 TTTTTTTCCATTTTC-TA
1 TTTTTTT-CATTTTCTTC
*
825709 TTTTTCTC-TTTTCTT-
1 TTTTTTTCATTTTCTTC
**
825724 TCCTTTTCATTTT-TTC
1 TTTTTTTCATTTTCTTC
*
825740 ATCATTTTTCATTTT-TTC
1 -T-TTTTTTCATTTTCTTC
*
825758 TCATTTTTC-TTTTCTTC
1 T-TTTTTTCATTTTCTTC
825775 TATTTTTTCTCATTTTTTTCTTC
1 --TTTTTT-TCA---TTTTCTTC
825798 TTTTTTTCATTTTCTTC
1 TTTTTTTCATTTTCTTC
*
825815 TTTTTTTC--TTTCAT-
1 TTTTTTTCATTTTCTTC
825829 TTTTTTT-ATTTT-TCTC
1 TTTTTTTCATTTTCT-TC
825845 TTTTT
1 TTTTT
825850 CTTTTTTCCA
Statistics
Matches: 115, Mismatches: 9, Indels: 35
0.72 0.06 0.22
Matches are distributed among these distances:
14 7 0.06
15 21 0.18
16 15 0.13
17 35 0.30
18 17 0.15
19 3 0.03
20 3 0.03
21 6 0.05
23 8 0.07
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTTTCATTTTCTTC
Found at i:825795 original size:20 final size:19
Alignment explanation
Indices: 825767--825849 Score: 80
Period size: 20 Copynumber: 4.3 Consensus size: 19
825757 CTCATTTTTC
*
825767 TTTTCTTCTATTTTTTCTCA
1 TTTTTTTCT-TTTTTTCTCA
*
825787 TTTTTTTCTTCTTTTTTTCA
1 TTTTTTTCTT-TTTTTCTCA
*
825807 TTTTCTTCTTTTTTTCTTTCA
1 TTTTTTTCTTTTTTTC--TCA
*
825828 TTTTTTT-TATTTTTCTC-
1 TTTTTTTCTTTTTTTCTCA
825845 TTTTT
1 TTTTT
825850 CTTTTTTCCA
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
17 5 0.09
18 2 0.04
19 6 0.11
20 32 0.59
21 9 0.17
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTTTTCTTTTTTTCTCA
Found at i:825833 original size:12 final size:11
Alignment explanation
Indices: 825767--825846 Score: 59
Period size: 11 Copynumber: 7.6 Consensus size: 11
825757 CTCATTTTTC
825767 TTTTCTTCTATT
1 TTTTCTTC-ATT
825779 TTTTC-TCATTT
1 TTTTCTTCA-TT
825790 TTTTCTTC--T
1 TTTTCTTCATT
825799 TTTT-TTCA--
1 TTTTCTTCATT
*
825807 TTTTCTTCTTT
1 TTTTCTTCATT
825818 TTTTCTTTCATT
1 TTTTC-TTCATT
825830 TTTT-TT-ATT
1 TTTTCTTCATT
825839 TTTCTCTT
1 TTT-TCTT
825847 TTTCTTTTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 19
0.73 0.03 0.24
Matches are distributed among these distances:
8 7 0.12
9 14 0.25
10 4 0.07
11 16 0.28
12 16 0.28
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTCTTCATT
Found at i:825841 original size:39 final size:38
Alignment explanation
Indices: 825761--825856 Score: 110
Period size: 39 Copynumber: 2.5 Consensus size: 38
825751 TTTTTTCTCA
*
825761 TTTTTCTTTTCTTCTATTTTTTCTCATTTTTTTCTTCTT
1 TTTTTCTTTTCTTCT-TTTTTTCTCATTTTTTTCTTATT
825800 TTTTTCATTTTCTTCTTTTTTTCTTTCA-TTTTTT-TTATT
1 TTTTTC-TTTTCTTCTTTTTTTC--TCATTTTTTTCTTATT
*
825839 TTTCTC-TTT-TTCTTTTTT
1 TTTTTCTTTTCTTCTTTTTT
825857 CCATTTCTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
36 9 0.17
37 3 0.06
39 22 0.42
40 15 0.29
41 3 0.06
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (38 bp):
TTTTTCTTTTCTTCTTTTTTTCTCATTTTTTTCTTATT
Found at i:825849 original size:9 final size:9
Alignment explanation
Indices: 825733--825849 Score: 57
Period size: 9 Copynumber: 12.6 Consensus size: 9
825723 TTCCTTTTCA
825733 TTTTTTCATC
1 TTTTTTC-TC
* *
825743 ATTTTTC-A
1 TTTTTTCTC
825751 TTTTTTCTC
1 TTTTTTCTC
*
825760 ATTTTTCT-
1 TTTTTTCTC
* *
825768 TTTCTTCTA
1 TTTTTTCTC
825777 TTTTTTCTC
1 TTTTTTCTC
825786 ATTTTTTTCTTC
1 --TTTTTTC-TC
825798 TTTTTT-TC
1 TTTTTTCTC
825806 ATTTTCTTCT-
1 -TTTT-TTCTC
825816 TTTTTTCTTTC
1 TTTTTTC--TC
825827 ATTTTTT-T-
1 -TTTTTTCTC
825835 TATTTTTCTC
1 T-TTTTTCTC
825845 TTTTT
1 TTTTT
825850 CTTTTTTCCA
Statistics
Matches: 83, Mismatches: 9, Indels: 31
0.67 0.07 0.25
Matches are distributed among these distances:
7 1 0.01
8 22 0.27
9 28 0.34
10 16 0.19
11 8 0.10
12 8 0.10
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTTTCTC
Found at i:825850 original size:28 final size:28
Alignment explanation
Indices: 825744--825853 Score: 102
Period size: 30 Copynumber: 3.9 Consensus size: 28
825734 TTTTTCATCA
*
825744 TTTTTCATTTTTTCTC--ATT-TTTCTT
1 TTTTTCATTTTTTCTCTTTTTCTTTCTT
* *
825769 TTCTTCTATTTTTTCTCATTTTTTTCTTCTT
1 TTTTTC-ATTTTTTCTC-TTTTTCT-TTCTT
*
825800 TTTTTCATTTTCTTCTTTTTTTCTTTCATT
1 TTTTTCATTTT-TTCTCTTTTTCTTTC-TT
*
825830 TTTTTTA-TTTTTCTCTTTTTCTTT
1 TTTTTCATTTTTTCTCTTTTTCTTT
825854 TTTCCATTTC
Statistics
Matches: 70, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
25 5 0.07
26 10 0.14
28 13 0.19
29 8 0.11
30 20 0.29
31 14 0.20
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.77
Consensus pattern (28 bp):
TTTTTCATTTTTTCTCTTTTTCTTTCTT
Found at i:831091 original size:30 final size:30
Alignment explanation
Indices: 831020--831079 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
831010 ACAATTTAAG
831020 GCAAAATGTTTTTGGACTGGAATTGAATTT
1 GCAAAATGTTTTTGGACTGGAATTGAATTT
* *
831050 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTGGAATTGAATTT
831080 ATTCAAAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.05, G:0.22, T:0.43
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTGGAATTGAATTT
Found at i:831300 original size:20 final size:21
Alignment explanation
Indices: 831259--831313 Score: 94
Period size: 20 Copynumber: 2.7 Consensus size: 21
831249 ATGCAATTAG
831259 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
831280 TGCATCGATGCATCC-TGCCA
1 TGCATCGATGCATCCTTGCCA
*
831300 TGCATCCATGCATC
1 TGCATCGATGCATC
831314 AAGGCTGCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 18 0.55
21 15 0.45
ACGTcount: A:0.20, C:0.35, G:0.18, T:0.27
Consensus pattern (21 bp):
TGCATCGATGCATCCTTGCCA
Found at i:832631 original size:19 final size:20
Alignment explanation
Indices: 832607--832654 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
832597 AATGATTTTC
*
832607 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
832626 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
832646 TTTTGAAAA
1 TTTTGAAAA
832655 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:833999 original size:30 final size:30
Alignment explanation
Indices: 833930--833987 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
833920 AATTTAAGGT
833930 AAAATGTTTTTGGACTGGAATTGAATTTGC
1 AAAATGTTTTTGGACTGGAATTGAATTTGC
* *
833960 AAAATGTTTTTGGATTTGAATTGAATTT
1 AAAATGTTTTTGGACTGGAATTGAATTT
833988 ATTCAAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.03, G:0.21, T:0.45
Consensus pattern (30 bp):
AAAATGTTTTTGGACTGGAATTGAATTTGC
Found at i:834187 original size:20 final size:21
Alignment explanation
Indices: 834146--834200 Score: 94
Period size: 20 Copynumber: 2.7 Consensus size: 21
834136 ATGCAATTAG
834146 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
834167 TGCATCGATGCATCC-TGCCA
1 TGCATCGATGCATCCTTGCCA
*
834187 TGCATCCATGCATC
1 TGCATCGATGCATC
834201 AAGGCTGCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 18 0.55
21 15 0.45
ACGTcount: A:0.20, C:0.35, G:0.18, T:0.27
Consensus pattern (21 bp):
TGCATCGATGCATCCTTGCCA
Done.