Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002881.1 Hibiscus syriacus cultivar Beakdansim tig00005939_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: 1746118
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 9
Found at i:631853 original size:27 final size:27
Alignment explanation
Indices: 631822--631878 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
631812 AATTATACTT
631822 ATAATATTAAATTTTATACTATAGCTA
1 ATAATATTAAATTTTATACTATAGCTA
631849 ATAATATTAAATTTTATACTATAGCTA
1 ATAATATTAAATTTTATACTATAGCTA
631876 ATA
1 ATA
631879 CTATGTTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.44
Consensus pattern (27 bp):
ATAATATTAAATTTTATACTATAGCTA
Found at i:636880 original size:21 final size:21
Alignment explanation
Indices: 636855--636898 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
636845 TTTTTAATAT
636855 TTTCTACCT-AAAATATTATTA
1 TTTCTA-CTGAAAATATTATTA
* *
636876 TTTCTATTGAAAATGTTATTA
1 TTTCTACTGAAAATATTATTA
636897 TT
1 TT
636899 GGACGCTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.52
Consensus pattern (21 bp):
TTTCTACTGAAAATATTATTA
Found at i:637969 original size:2 final size:2
Alignment explanation
Indices: 637962--637991 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
637952 TTTTAAATAG
637962 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
637992 CCATAAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:638847 original size:15 final size:13
Alignment explanation
Indices: 638815--638839 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
638805 GTTTATTATC
638815 ATTATTTGAAAAT
1 ATTATTTGAAAAT
638828 ATTATTTGAAAA
1 ATTATTTGAAAA
638840 AATATTATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
ATTATTTGAAAAT
Found at i:642400 original size:3 final size:3
Alignment explanation
Indices: 642392--642435 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
642382 TTCTGACTCA
* *
642392 TCG TCG TCG TCG TCG TCG TCG TCA TCA TCG TCG TCG TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
642436 CTGAGCAAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.05, C:0.34, G:0.27, T:0.34
Consensus pattern (3 bp):
TCG
Found at i:644513 original size:17 final size:18
Alignment explanation
Indices: 644493--644533 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
644483 GAATTATATT
644493 AGTAAAAT-ATTAAATAA
1 AGTAAAATAATTAAATAA
644510 AGTAAAATAATTAAATAA
1 AGTAAAATAATTAAATAA
*
644528 ATTAAA
1 AGTAAA
644534 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATAATTAAATAA
Found at i:644594 original size:10 final size:10
Alignment explanation
Indices: 644575--644605 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
644565 CTTAAATAGA
*
644575 GAGAGTATTT
1 GAGAGAATTT
644585 GAGAGAATTT
1 GAGAGAATTT
644595 GAGAGAATTT
1 GAGAGAATTT
644605 G
1 G
644606 GTGTGATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:648449 original size:24 final size:22
Alignment explanation
Indices: 648411--648472 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 22
648401 TTAAACTACG
* *
648411 TTTTTAGTATTTAAATAATT-AA
1 TTTTTATTTTTTAAA-AATTAAA
*
648433 TTTTTATCTGTTTTAAAACTTAAA
1 TTTTTAT-T-TTTTAAAAATTAAA
648457 TTTTTATTTTTTAAAA
1 TTTTTATTTTTTAAAA
648473 TAACACTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
22 14 0.41
23 5 0.15
24 15 0.44
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.58
Consensus pattern (22 bp):
TTTTTATTTTTTAAAAATTAAA
Found at i:650167 original size:192 final size:192
Alignment explanation
Indices: 649823--650194 Score: 437
Period size: 192 Copynumber: 1.9 Consensus size: 192
649813 GGGTATGTGT
* * * * * * *
649823 TTAACAGGTTTATGTTTAATTGTTAAAGTCTTTTCATGTGTTTGAAAGCTTTTTGGCGTATGAAT
1 TTAACAGGTTTATGTTTAATTGTTAAAGTCTTTTAATGTATTTGAAAGCTCTATAGAGTACGAAT
* * *
649888 CAAGTGATCTTAGTAGTTAAGGGATTGCTATTATTACTTGAGGTCCCGAATTCTAGCATCGCATA
66 CAAGTGACCTTAGTAGTTAAGGGATTGCTATTATTACTTGAAGTCCCGAATTCGAGCATCGCATA
* * ** ** *
649953 TATTGGAGTGTATGGGCGTTCACAGTCAAATGGTTGAGAA-TCTTTGAATAAATACTATGAGC
131 TAGTGAAACGTATGAACGTTCACAGTCAAATAGTTGA-AAGTCTTTGAATAAATACTATGAGC
* *
650015 TTAACACGG-TTATGTTTGATTTTTAAAGTCTTTTAATGTATTTGAAAGCTCTATAGAGTACGAA
1 TTAACA-GGTTTATGTTTAATTGTTAAAGTCTTTTAATGTATTTGAAAGCTCTATAGAGTACGAA
* *** *
650079 TCAAGTGACCTTAGTA-TATAAGGGATTG-TGATTATTCCTTGAAGTTTTGGATTCGAGCATCGC
65 TCAAGTGACCTTAGTAGT-TAAGGGATTGCT-ATTATTACTTGAAGTCCCGAATTCGAGCATCGC
* * *
650142 ATATAGTGAAACGTATGAACGTTCACTGTTAAATAGTTGAAAGTTTTTGAATA
128 ATATAGTGAAACGTATGAACGTTCACAGTCAAATAGTTGAAAGTCTTTGAATA
650195 TATTATATCC
Statistics
Matches: 149, Mismatches: 27, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
191 4 0.03
192 143 0.96
193 2 0.01
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.38
Consensus pattern (192 bp):
TTAACAGGTTTATGTTTAATTGTTAAAGTCTTTTAATGTATTTGAAAGCTCTATAGAGTACGAAT
CAAGTGACCTTAGTAGTTAAGGGATTGCTATTATTACTTGAAGTCCCGAATTCGAGCATCGCATA
TAGTGAAACGTATGAACGTTCACAGTCAAATAGTTGAAAGTCTTTGAATAAATACTATGAGC
Found at i:650307 original size:21 final size:20
Alignment explanation
Indices: 650270--650308 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
650260 TATTGTATCT
*
650270 TTTTATTTTGACTATCGATC
1 TTTTATTTTGACAATCGATC
*
650290 TTTTAGTTTTGTCAATCGA
1 TTTTA-TTTTGACAATCGA
650309 ACTATTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.21, C:0.13, G:0.13, T:0.54
Consensus pattern (20 bp):
TTTTATTTTGACAATCGATC
Found at i:650904 original size:29 final size:29
Alignment explanation
Indices: 650862--650919 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
650852 AAATCTCAAA
650862 GTTTAAGATTTCTAAGGAGAACAACACAC
1 GTTTAAGATTTCTAAGGAGAACAACACAC
650891 GTTTAAGATTTCTAAGGAGAACAACACAC
1 GTTTAAGATTTCTAAGGAGAACAACACAC
650920 TTTGTAAACG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.24
Consensus pattern (29 bp):
GTTTAAGATTTCTAAGGAGAACAACACAC
Found at i:654499 original size:21 final size:21
Alignment explanation
Indices: 654457--654509 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
654447 ATTCTGACTA
654457 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* ** *
654478 TCGCGTTGCGATTTTTCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
654499 TCGCAATGCGA
1 TCGCATTGCGA
654510 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:654524 original size:20 final size:20
Alignment explanation
Indices: 654499--654585 Score: 104
Period size: 20 Copynumber: 4.3 Consensus size: 20
654489 TTTTTCTAAT
654499 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
654519 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
654540 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
654560 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
654580 TCGCAA
1 TCGCAA
654586 CGAGATTCTG
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
19 1 0.02
20 39 0.71
21 15 0.27
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:654545 original size:41 final size:40
Alignment explanation
Indices: 654499--654585 Score: 129
Period size: 41 Copynumber: 2.1 Consensus size: 40
654489 TTTTTCTAAT
*
654499 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATCT-GAAAA
* * *
654540 TCGCAATGCGATTACGTAAATCGCAATGCGAATCTGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATCTGAAAA
654580 TCGCAA
1 TCGCAA
654586 CGAGATTCTG
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 10 0.24
41 32 0.76
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.22
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAACGCGAATCTGAAAA
Found at i:654595 original size:20 final size:20
Alignment explanation
Indices: 654514--654595 Score: 78
Period size: 20 Copynumber: 4.0 Consensus size: 20
654504 ATGCGAATAC
654514 GTAAATCGCAACGCGAATT-T
1 GTAAATCGCAACGCG-ATTCT
* *
654534 GGAAAATCGCAATGCGATTAC-
1 -GTAAATCGCAACGCGATT-CT
* *
654555 GTAAATCGCAATGCGAATCT
1 GTAAATCGCAACGCGATTCT
*
654575 GTAAATCGCAACGAGATTCT
1 GTAAATCGCAACGCGATTCT
654595 G
1 G
654596 ACTATCGCAA
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.02
20 37 0.73
21 13 0.25
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (20 bp):
GTAAATCGCAACGCGATTCT
Found at i:654625 original size:61 final size:60
Alignment explanation
Indices: 654491--654626 Score: 136
Period size: 61 Copynumber: 2.2 Consensus size: 60
654481 CGTTGCGATT
* * *
654491 TTTCTAATTCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAATCGCAATGCGA
1 TTTCAAATTCGCAATGCGAATACGTAAATCGCAACGAGAATTTGGAAAATCGCAATACGA
* **
654551 TTACGTAAA-TCGCAATGCGAAT-CTGTAAATCGCAACGAG-ATTCT-GACTATCGCAATACTGA
1 TTTC--AAATTCGCAATGCGAATAC-GTAAATCGCAACGAGAATT-TGGAAAATCGCAATAC-G-
654612 A
60 A
654613 TTTCAAATTCGCAA
1 TTTCAAATTCGCAA
654627 CTCGATTTCT
Statistics
Matches: 62, Mismatches: 7, Indels: 13
0.76 0.09 0.16
Matches are distributed among these distances:
60 21 0.34
61 35 0.56
62 6 0.10
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (60 bp):
TTTCAAATTCGCAATGCGAATACGTAAATCGCAACGAGAATTTGGAAAATCGCAATACGA
Found at i:655474 original size:24 final size:24
Alignment explanation
Indices: 655447--655500 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
655437 GTATTCGAAA
655447 TTTGATCTTGGTCAATACCCAGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
655471 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
655495 TTTGAT
1 TTTGAT
655501 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:657954 original size:20 final size:20
Alignment explanation
Indices: 657929--658017 Score: 117
Period size: 20 Copynumber: 4.5 Consensus size: 20
657919 CAACGCGGAA
657929 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
**
657949 ATCGCAACATGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* *
657969 ATCGCAATGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
*
657989 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
658009 ATCGCAACG
1 ATCGCAACG
658018 AGAGAATTGC
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 55 0.95
21 3 0.05
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:657988 original size:40 final size:40
Alignment explanation
Indices: 657929--658017 Score: 144
Period size: 40 Copynumber: 2.2 Consensus size: 40
657919 CAACGCGGAA
*
657929 ATCGCAACGCGAATATGACTATCGCAACATGGAAATGACT
1 ATCGCAACGCGAATATGACTATCGCAACACGGAAATGACT
*
657969 ATCGCAATGCGGAAT-TGACTATCGCAACACGGAAATGACT
1 ATCGCAACGC-GAATATGACTATCGCAACACGGAAATGACT
658009 ATCGCAACG
1 ATCGCAACG
658018 AGAGAATTGC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
40 41 0.91
41 4 0.09
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (40 bp):
ATCGCAACGCGAATATGACTATCGCAACACGGAAATGACT
Found at i:658077 original size:34 final size:33
Alignment explanation
Indices: 658000--658084 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 33
657990 TCGCAACACG
** *
658000 GAAATGACTATCGCAACGAGAGAATTGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
*
658033 GAAATGAAAATCGCAACGAGTGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
658066 GAAAATGAAAATCGCAACG
1 G-AAATGAAAATCGCAACG
658085 CGAAAATTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 30 0.64
34 17 0.36
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:658132 original size:33 final size:34
Alignment explanation
Indices: 658090--658158 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 34
658080 CAACGCGAAA
**
658090 ATTCACTCGTTGCGATTTTCATTT-CGCATTGCG
1 ATTCACTCGTTGCGATAGTCATTTCCGCATTGCG
* *
658123 ATTCTCTCGTTGCGATAGTCATTTCCGCGTTGCG
1 ATTCACTCGTTGCGATAGTCATTTCCGCATTGCG
658157 AT
1 AT
658159 AGTCTGTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 21 0.68
34 10 0.32
ACGTcount: A:0.14, C:0.25, G:0.20, T:0.41
Consensus pattern (34 bp):
ATTCACTCGTTGCGATAGTCATTTCCGCATTGCG
Found at i:658284 original size:14 final size:14
Alignment explanation
Indices: 658265--658301 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
658255 CATCAATTAA
658265 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
658279 ACAAATCATCTTTT
1 ACAAATCAACATTT
658293 ACAAATCAA
1 ACAAATCAA
658302 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:659682 original size:42 final size:42
Alignment explanation
Indices: 659603--659684 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
659593 CCTCTTCAAC
* * *
659603 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* *
659645 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGA
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGA
659685 ACTATGGCAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 31 0.91
43 3 0.09
ACGTcount: A:0.21, C:0.17, G:0.40, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:660198 original size:20 final size:20
Alignment explanation
Indices: 660175--660276 Score: 92
Period size: 20 Copynumber: 5.5 Consensus size: 20
660165 GAAACTTAAA
660175 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
660195 ATCGCAA--CG-AGA-GA--
1 ATCGCAACGCGAAAATGACT
* **
660209 ATCGCAATGCG-AAATGAAA
1 ATCGCAACGCGAAAATGACT
660228 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
660248 ATCGCAATGCGAATCTGACT
1 ATCGCAACGCGAAAATGACT
660268 ATCGCAACG
1 ATCGCAACG
660277 AGAGAATCGC
Statistics
Matches: 67, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
14 7 0.10
16 6 0.09
17 4 0.06
18 2 0.03
19 10 0.15
20 38 0.57
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:660349 original size:20 final size:20
Alignment explanation
Indices: 660321--660464 Score: 192
Period size: 20 Copynumber: 7.5 Consensus size: 20
660311 GATTCTTTCG
**
660321 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
660341 TTACGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
660361 TTGCAATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
660381 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
660401 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
660421 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
660435 TTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
660455 TTGCGATAGT
1 TTGCGATAGT
660465 AAACTATTCT
Statistics
Matches: 109, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
14 7 0.06
16 6 0.06
18 5 0.05
20 91 0.83
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:662386 original size:20 final size:20
Alignment explanation
Indices: 662339--662406 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
662329 GAAACTTTAA
* **
662339 ATCGCAACACAAAAATGAAA
1 ATCGCAACACGAAAATGACT
*
662359 ATCACAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* **
662379 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
662399 ATCGCAAC
1 ATCGCAAC
662407 GCAAGAATCG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.46, C:0.25, G:0.13, T:0.16
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:662477 original size:20 final size:20
Alignment explanation
Indices: 662452--662498 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
662442 GATTCTCTCG
662452 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
662472 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
662492 TTGCGAT
1 TTGCGAT
662499 TCACTCGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:663116 original size:20 final size:20
Alignment explanation
Indices: 663090--663221 Score: 174
Period size: 20 Copynumber: 6.5 Consensus size: 20
663080 ATAGTCAGAT
663090 TCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAA
* *
663110 TCACATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAA
*
663130 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAA
*
663150 TCACATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAA
* **
663170 TCGCATTGCGATTTTCCAAA
1 TCGCATTGCGATTTACGTAA
* *
663190 TTCGCGTTGCGATTTACGTAT
1 -TCGCATTGCGATTTACGTAA
663211 TCGCATTGCGA
1 TCGCATTGCGA
663222 ATTAGGAAAA
Statistics
Matches: 96, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
20 81 0.84
21 15 0.16
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAA
Found at i:663132 original size:40 final size:40
Alignment explanation
Indices: 663088--663221 Score: 196
Period size: 40 Copynumber: 3.3 Consensus size: 40
663078 CGATAGTCAG
663088 ATTCGCATTGCGATTTACGTAATCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGTAATCACATTGCGATTTACGT
*
663128 ATTCGCATTGCGATTTACGTATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGTAATCACATTGCGATTTACGT
* * ** * *
663168 AATCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGTAA-TCACATTGCGATTTACGT
663209 ATTCGCATTGCGA
1 ATTCGCATTGCGA
663222 ATTAGGAAAA
Statistics
Matches: 84, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
40 56 0.67
41 28 0.33
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCACATTGCGATTTACGT
Found at i:663163 original size:60 final size:61
Alignment explanation
Indices: 663088--663221 Score: 207
Period size: 61 Copynumber: 2.2 Consensus size: 61
663078 CGATAGTCAG
**
663088 ATTCGCATTGCGATTTACGTAATCACATTGCGA-TTTACGTATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGTAATCACATTGCGATTTTACAAATTCGCATTGCGATTTACGT
* * * *
663148 ATTCACATTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGTAATCACATTGCGATTTTACAAATTCGCATTGCGATTTACGT
663209 ATTCGCATTGCGA
1 ATTCGCATTGCGA
663222 ATTAGGAAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
60 31 0.47
61 35 0.53
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (61 bp):
ATTCGCATTGCGATTTACGTAATCACATTGCGATTTTACAAATTCGCATTGCGATTTACGT
Found at i:663263 original size:21 final size:21
Alignment explanation
Indices: 663211--663263 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
663201 ATTTACGTAT
*
663211 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
* * * *
663232 TCGTAACGCGAATTTGGGAAA
1 TCGCAATGCGAATTAGGAAAA
663253 TCGCAATGCGA
1 TCGCAATGCGA
663264 TAGTCAGAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:665780 original size:15 final size:16
Alignment explanation
Indices: 665760--665791 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
665750 ACACTCTATT
665760 GTGAA-GGGGAAGAGA
1 GTGAAGGGGGAAGAGA
665775 GTGAAGGGGGAAGAGA
1 GTGAAGGGGGAAGAGA
665791 G
1 G
665792 GGTTAACAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.38, C:0.00, G:0.56, T:0.06
Consensus pattern (16 bp):
GTGAAGGGGGAAGAGA
Found at i:666932 original size:43 final size:43
Alignment explanation
Indices: 666879--667091 Score: 257
Period size: 43 Copynumber: 4.9 Consensus size: 43
666869 TGGTAACAAA
*** * *
666879 AAACGCCGCAATAGGTAACGATATATAGCGGCGTTTGTCCAAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
* * *
666922 AAACGCCGCAATATGTGTTGATATTTGGCGGCATTTTTCCAAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
* * * *
666965 AAATGCCGCAATAGGTGTTGAGATTTAGCGGTGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
*
667008 AAACGCCGCAATAGGTGTTGAAATTTAGCGGCGTTTTTTTTCCAA-
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCG---TTTTTCCAAC
* *
667053 AAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTC
667092 TCACAAATAC
Statistics
Matches: 146, Mismatches: 21, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
42 6 0.04
43 101 0.69
45 31 0.21
46 8 0.05
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.30
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
Found at i:667133 original size:88 final size:89
Alignment explanation
Indices: 666955--667133 Score: 236
Period size: 88 Copynumber: 2.0 Consensus size: 89
666945 TTTGGCGGCA
* * * * *
666955 TTTTTCCAACAAATGCCGCAATAGGTGTTGAGATTTAGCGGTGTTTTTCCCACAAACGCCGCAAT
1 TTTTTCCAACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCACAAACACCGCAAA
* * *
667020 AGGTGTTGAAATTTAGCGGCGTTT
66 AGATGCTGAAATATAGCGGCGTTT
* *
667044 TTTTTCCAA-AAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCTCACAAATACCGCAAA
1 TTTTTCCAACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCACAAACACCGCAAA
**
667108 AGAT-CTGGTATATAGCGGCGTTT
66 AGATGCTGAAATATAGCGGCGTTT
667131 TTT
1 TTT
667134 AGAACAAACG
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
87 18 0.23
88 51 0.65
89 9 0.12
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.33
Consensus pattern (89 bp):
TTTTTCCAACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCACAAACACCGCAAA
AGATGCTGAAATATAGCGGCGTTT
Found at i:667328 original size:21 final size:21
Alignment explanation
Indices: 667302--667360 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
667292 ATTTTCCAAT
*
667302 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
* *
667323 AAACTTAAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAC
**
667344 AAAAATGAAATCCATAA
1 AAACTTGAAATCCATAA
667361 TAATAAATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.56, C:0.20, G:0.05, T:0.19
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:670452 original size:18 final size:18
Alignment explanation
Indices: 670431--670481 Score: 102
Period size: 18 Copynumber: 2.8 Consensus size: 18
670421 TTAATTAATT
670431 TTATGAAGCAAATTGGGA
1 TTATGAAGCAAATTGGGA
670449 TTATGAAGCAAATTGGGA
1 TTATGAAGCAAATTGGGA
670467 TTATGAAGCAAATTG
1 TTATGAAGCAAATTG
670482 ATTGTGTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.39, C:0.06, G:0.25, T:0.29
Consensus pattern (18 bp):
TTATGAAGCAAATTGGGA
Found at i:671023 original size:41 final size:41
Alignment explanation
Indices: 670911--671293 Score: 403
Period size: 41 Copynumber: 9.3 Consensus size: 41
670901 AGTCTATTAC
* * *
670911 AAACGCCACTAAAATACAAGTCTTTAGCGGCGTTTGTAAACA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATA-A
*
670953 CAAACGCCATTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
1 -AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * *
670995 AAATGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTTTAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * *
671036 AAACGCCACTAAAGTACGAGTCTATAGCGGTGTTTGTACAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* *
671077 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTCTAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* ** *
671118 AAACGCCACTAAAGTACGAGTCTATAGTAGCGTTTGTCTAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * * * * *
671159 AAATGCCACTAAAGTA-TAGTCTTTAGCGACGTTTTTTTAC
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * * * *
671199 AAACTCCACTAAAGTAC-ATTCTTTGGCGGCGTTTTTTATAC
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCG-TTTGTATAA
* * * * * *
671240 AAATGCCGCTAATGTAC-AATCTTTAGCGGCGTTTATTCTAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTT-GTATAA
*
671281 AAACGCCGCTAAA
1 AAACGCCACTAAA
671294 AATGCCGCTA
Statistics
Matches: 295, Mismatches: 42, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
40 44 0.15
41 214 0.73
42 1 0.00
43 36 0.12
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
Found at i:673424 original size:450 final size:453
Alignment explanation
Indices: 672576--673585 Score: 1850
Period size: 450 Copynumber: 2.2 Consensus size: 453
672566 TTAAAATTTA
*
672576 TTGGAGGTCGTACGAAGATGGGAAAATAATATCATGTGTGTCGCAAGATGTGTAGAAGATTGTCA
1 TTGGAGGTCGTAAGAAGATGGGAAAATAATATCATGTGTGTCGCAAGATGTGTAGAAGATTGTCA
* *
672641 ATATTGTTGTGTCGTTACACCATTGATCCATTTTGCTTTTGTTTAGTTTTAATTTTTTGATAGAG
66 ATATTGGTGTCTCGTTACACCATTGATCCATTTTGCTTTTGTTTAGTTTTAATTTTTTGATAGAG
*
672706 TGTTGAAGCAATTTGGTTTCCACCGTCTATTCCCTGAGTTCCAGACAATTATGACGCTTTTTACA
131 TGTTGAAGCAATTTGGTTTCCACCGTCTATTCCCCGAGTTCCAGACAATTATGACGCTTTTTACA
672771 TATTATAATATATAGATTGGATAAGCACACTGAGAATTGGATTGAGAAATATGCAAACTACATCA
196 -ATTAT-ATATATAGATTGGATAAGCACACTGAGAATTGGATTGAGAAATATGCAAACTACATCA
672836 ATTTTTTGAACAATAGAGCTTTACATTTGTCAACTTTTACTTTCTTTCAAGAGGTTGACTTTAAT
259 ATTTTTTGAACAATAGAGCTTTACATTTGTCAACTTTTACTTTCTTTCAAGAGGTTGACTTTAAT
672901 TTTAAAAATTCAGATTATCTTAATTATTATTGGAATAATGGAAATATGTCTTTGACAGTGATAAC
324 TTTAAAAATTCAGATTATCTTAATTATTATTGGAATAATGGAAATATGTCTTTGACAGTGATAAC
672966 AAAAAAGAGGCCATTTATACAATATATTATAATTACTAATAACCATCGTATCTCTGTTGTTTTTG
389 AAAAAAGAGGCCATTTATACAATATATTATAATTACTAATAACCATCGTATCTCTGTTGTTTTTG
*
673031 TTGGAGGTCGTAGGAAGATGGGAAAATAATATCATGTGTGTCGCAAGATGTGTAGAAGATTGTCA
1 TTGGAGGTCGTAAGAAGATGGGAAAATAATATCATGTGTGTCGCAAGATGTGTAGAAGATTGTCA
*
673096 ATATTGGTGTCTCGTAACACCATTGATCCATTTTGCTTTTGTTTAGTTTTAATTTTTTGATAGAG
66 ATATTGGTGTCTCGTTACACCATTGATCCATTTTGCTTTTGTTTAGTTTTAATTTTTTGATAGAG
673161 TGTTGAAGCAATTTGGTTTCCACCGTCTATTCCCCGAGTTCCAGACAATTATGACGCTTTTTAC-
131 TGTTGAAGCAATTTGGTTTCCACCGTCTATTCCCCGAGTTCCAGACAATTATGACGCTTTTTACA
673225 A-TAT-TATATAGATTGGATAAGCACACTGAGAATTGGATTGAGAAATATGCAAACTACATCAAT
196 ATTATATATATAGATTGGATAAGCACACTGAGAATTGGATTGAGAAATATGCAAACTACATCAAT
673288 TTTTTGAACAATAGAGCTTTACATTTGTCAACTTTTACTTTCTTTCAAGAGGTTGACTTTAATTT
261 TTTTTGAACAATAGAGCTTTACATTTGTCAACTTTTACTTTCTTTCAAGAGGTTGACTTTAATTT
* *
673353 TAAGAATTCAGATTATCTTAATTATTATTGGAATAATGGAAATATGTCTTTGACAGTGATAACAG
326 TAAAAATTCAGATTATCTTAATTATTATTGGAATAATGGAAATATGTCTTTGACAGTGATAACAA
*
673418 AAAAGAGGCCATTTATACAATATATTATAATTACTAATAACCATTGTATCTCTGTTGTTTTTG
391 AAAAGAGGCCATTTATACAATATATTATAATTACTAATAACCATCGTATCTCTGTTGTTTTTG
* *
673481 TTGGAAGTCGTAAGAAGATGAGAAAATAATATCA--TGTGTCGCAAGATGTGTAGAAGATTGTCA
1 TTGGAGGTCGTAAGAAGATGGGAAAATAATATCATGTGTGTCGCAAGATGTGTAGAAGATTGTCA
* *
673544 ATATTGGTGTCTCATTACACCATTGATCTATTTTGCTTTTGT
66 ATATTGGTGTCTCGTTACACCATTGATCCATTTTGCTTTTGT
673586 ATCTCTGTTG
Statistics
Matches: 541, Mismatches: 14, Indels: 7
0.96 0.02 0.01
Matches are distributed among these distances:
448 68 0.13
450 280 0.52
452 3 0.01
453 1 0.00
455 189 0.35
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (453 bp):
TTGGAGGTCGTAAGAAGATGGGAAAATAATATCATGTGTGTCGCAAGATGTGTAGAAGATTGTCA
ATATTGGTGTCTCGTTACACCATTGATCCATTTTGCTTTTGTTTAGTTTTAATTTTTTGATAGAG
TGTTGAAGCAATTTGGTTTCCACCGTCTATTCCCCGAGTTCCAGACAATTATGACGCTTTTTACA
ATTATATATATAGATTGGATAAGCACACTGAGAATTGGATTGAGAAATATGCAAACTACATCAAT
TTTTTGAACAATAGAGCTTTACATTTGTCAACTTTTACTTTCTTTCAAGAGGTTGACTTTAATTT
TAAAAATTCAGATTATCTTAATTATTATTGGAATAATGGAAATATGTCTTTGACAGTGATAACAA
AAAAGAGGCCATTTATACAATATATTATAATTACTAATAACCATCGTATCTCTGTTGTTTTTG
Found at i:674073 original size:23 final size:22
Alignment explanation
Indices: 674047--674089 Score: 77
Period size: 22 Copynumber: 1.9 Consensus size: 22
674037 ATAAATATTA
674047 AAAAAAAGGTTTTAAAAAAATTT
1 AAAAAAAGG-TTTAAAAAAATTT
674070 AAAAAAAGGTTTAAAAAAAT
1 AAAAAAAGGTTTAAAAAAAT
674090 AAAATCATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (22 bp):
AAAAAAAGGTTTAAAAAAATTT
Found at i:674088 original size:12 final size:12
Alignment explanation
Indices: 674047--674088 Score: 61
Period size: 10 Copynumber: 3.6 Consensus size: 12
674037 ATAAATATTA
674047 AAAAAAAGGTTTT
1 AAAAAAAGG-TTT
674060 AAAAAAA--TTT
1 AAAAAAAGGTTT
674070 AAAAAAAGGTTT
1 AAAAAAAGGTTT
674082 AAAAAAA
1 AAAAAAA
674089 TAAAATCATG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 10 0.37
12 10 0.37
13 7 0.26
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.24
Consensus pattern (12 bp):
AAAAAAAGGTTT
Found at i:675490 original size:16 final size:15
Alignment explanation
Indices: 675467--675513 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 15
675457 AATAAAATTA
675467 AATAAAATAAGT-AAT
1 AATAAAATAA-TAAAT
675482 AATATAAATAATAAAT
1 AATA-AAATAATAAAT
675498 AATAATATATAATAAA
1 AATAA-A-ATAATAAA
675514 AATTATATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 6 0.21
16 14 0.50
17 8 0.29
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (15 bp):
AATAAAATAATAAAT
Found at i:675500 original size:19 final size:19
Alignment explanation
Indices: 675472--675545 Score: 73
Period size: 19 Copynumber: 3.8 Consensus size: 19
675462 AATTAAATAA
*
675472 AATAAGTAATAATATAAAT
1 AATAAATAATAATATAAAT
675491 AATAAATAATAATATATAAT
1 AATAAATAATAATATA-AAT
675511 AA-AAATTATATAATACTAAA-
1 AATAAA-TA-ATAATA-TAAAT
*
675531 AATAAAAAAT-ATATA
1 AATAAATAATAATATA
675546 TTATACATTT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
17 2 0.04
18 3 0.06
19 20 0.42
20 10 0.21
21 11 0.23
22 2 0.04
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (19 bp):
AATAAATAATAATATAAAT
Found at i:675501 original size:10 final size:10
Alignment explanation
Indices: 675456--675516 Score: 58
Period size: 10 Copynumber: 6.4 Consensus size: 10
675446 ACCTGTTTAA
675456 AAATAA-AATT
1 AAATAATAA-T
675466 AAATAA-AAT
1 AAATAATAAT
*
675475 AAGTAATAAT
1 AAATAATAAT
*
675485 ATA-AATAAT
1 AAATAATAAT
675494 AAATAATAAT
1 AAATAATAAT
*
675504 ATATAATAA-
1 AAATAATAAT
675513 AAAT
1 AAAT
675517 TATATAATAC
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
9 17 0.40
10 26 0.60
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (10 bp):
AAATAATAAT
Found at i:675530 original size:17 final size:17
Alignment explanation
Indices: 675457--675535 Score: 74
Period size: 17 Copynumber: 4.6 Consensus size: 17
675447 CCTGTTTAAA
*
675457 AATAAAATTAA-ATAA-
1 AATAAAAATAATATAAT
*
675472 AATAAGTAATAATATAAAT
1 AATAA-AAATAATAT-AAT
675491 AATAAATAATAATAT-AT
1 AATAAA-AATAATATAAT
*
675508 AATAAAAATTATATAAT
1 AATAAAAATAATATAAT
*
675525 ACTAAAAATAA
1 AATAAAAATAA
675536 AAAATATATA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
15 5 0.10
16 11 0.21
17 21 0.40
18 2 0.04
19 13 0.25
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (17 bp):
AATAAAAATAATATAAT
Found at i:675531 original size:16 final size:14
Alignment explanation
Indices: 675480--675525 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
675470 AAAATAAGTA
* *
675480 ATAATATAAATAAT
1 ATAATAAAAATTAT
*
675494 A-AATAATAA-TAT
1 ATAATAAAAATTAT
675506 ATAATAAAAATTAT
1 ATAATAAAAATTAT
675520 ATAATA
1 ATAATA
675526 CTAAAAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 3 0.12
13 13 0.50
14 10 0.38
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATAATAAAAATTAT
Found at i:675575 original size:37 final size:36
Alignment explanation
Indices: 675533--675912 Score: 267
Period size: 37 Copynumber: 10.5 Consensus size: 36
675523 ATACTAAAAA
* * *
675533 TAAAAAATATATATTATACATTTTCAAAATCGT-TTT
1 TAAAAACTATATAATATACGTTTTCAAAAT-GTATTT
* *
675569 TAAAAAACTATATATTATACATTTTCAAAAT-TATTT
1 T-AAAAACTATATAATATACGTTTTCAAAATGTATTT
* * * *
675605 TAAAAA--ATTTATTATATGTTTTTAAAAT-TATTT
1 TAAAAACTATATAATATACGTTTTCAAAATGTATTT
* * * *
675638 TAAAAGCTATATACTATATGTTTTCAAAACCGT-TTT
1 TAAAAACTATATAATATACGTTTTCAAAA-TGTATTT
*
675674 TAAAAAACTATATAATATACGTTTTCAAAATGTGTTT
1 T-AAAAACTATATAATATACGTTTTCAAAATGTATTT
* *
675711 TCAAAACTATATAATATATGTTTTCAAAAACTGT-TTT
1 TAAAAACTATATAATATACGTTTTC-AAAA-TGTATTT
* * *
675748 TCAAAACTATATAATATACGTTTTAAAAAATGTGTTT
1 TAAAAACTATATAATATACGTTTT-CAAAATGTATTT
* * * *
675785 TCAAAATTATATAATATATGTTTT-TAAATCGTATTT
1 TAAAAACTATATAATATACGTTTTCAAAAT-GTATTT
* * ** *
675821 TCAAAACTATATTATATATATTTTCAAAAACCG-ATTT
1 TAAAAACTATATAATATACGTTTTC-AAAA-TGTATTT
* ** *
675858 CTAAAAATTATATGTTATACGTTTTTCAAAA-ATATTT
1 -TAAAAACTATATAATATACG-TTTTCAAAATGTATTT
* *
675895 TCAAAAATTATATTATAT
1 T-AAAAACTATATAATAT
675913 TATTATATAT
Statistics
Matches: 288, Mismatches: 36, Indels: 39
0.79 0.10 0.11
Matches are distributed among these distances:
33 28 0.10
35 28 0.10
36 63 0.22
37 139 0.48
38 25 0.09
39 5 0.02
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.44
Consensus pattern (36 bp):
TAAAAACTATATAATATACGTTTTCAAAATGTATTT
Found at i:675731 original size:73 final size:74
Alignment explanation
Indices: 675533--675849 Score: 293
Period size: 73 Copynumber: 4.4 Consensus size: 74
675523 ATACTAAAAA
* * * * **
675533 TAAAAAA-TATATATTATACATTTTCAAAATCGT-TTTTAAAAAACTATATATTATACATTTTCA
1 TAAAAAACTATATAATATACGTTTTCAAAAT-GTGTTTT-CAAAACTATATAATATATGTTTTCA
*
675596 AAA--TTATTT
64 AAACCGTATTT
* * * * *
675605 TAAAAAA-T-T-TATTATATGTTTTTAAAAT-TATTTT-AAAAGCTATATACTATATGTTTTCAA
1 TAAAAAACTATATAATATACGTTTTCAAAATGTGTTTTCAAAA-CTATATAATATATGTTTTCAA
675665 AACCGT-TTT
65 AACCGTATTT
675674 TAAAAAACTATATAATATACGTTTTCAAAATGTGTTTTCAAAACTATATAATATATGTTTTCAAA
1 TAAAAAACTATATAATATACGTTTTCAAAATGTGTTTTCAAAACTATATAATATATGTTTTC-AA
*
675739 AACTGT-TTT
65 AACCGTATTT
* * * *
675748 T-CAAAACTATATAATATACGTTTTAAAAAATGTGTTTTCAAAATTATATAATATATGTTTT-TA
1 TAAAAAACTATATAATATACGTTTT-CAAAATGTGTTTTCAAAACTATATAATATATGTTTTCAA
*
675811 AATCGTATTT
65 AACCGTATTT
* * **
675821 T-CAAAACTATATTATATATATTTTCAAAA
1 TAAAAAACTATATAATATACGTTTTCAAAA
675850 ACCGATTTCT
Statistics
Matches: 210, Mismatches: 23, Indels: 24
0.82 0.09 0.09
Matches are distributed among these distances:
67 4 0.02
68 21 0.10
69 14 0.07
70 18 0.09
71 2 0.01
72 33 0.16
73 69 0.33
74 49 0.23
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (74 bp):
TAAAAAACTATATAATATACGTTTTCAAAATGTGTTTTCAAAACTATATAATATATGTTTTCAAA
ACCGTATTT
Found at i:677269 original size:37 final size:37
Alignment explanation
Indices: 677194--677266 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 37
677184 TTTCCTCATA
*
677194 TTTCTTTATATATTTGATATTAAATTGCTTTTAAAAG
1 TTTCATTATATATTTGATATTAAATTGCTTTTAAAAG
* * *
677231 TTTCATTATATATTTGGTTATTGAGTTGCTTTTAAA
1 TTTCATTATATATTT-GATATTAAATTGCTTTTAAA
677267 GTTGGGATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 14 0.45
38 17 0.55
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.55
Consensus pattern (37 bp):
TTTCATTATATATTTGATATTAAATTGCTTTTAAAAG
Found at i:683735 original size:28 final size:28
Alignment explanation
Indices: 683702--683756 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
683692 GCTTCAAAAC
683702 ATGGATGAAGAAAATGAGAATCGGATGG
1 ATGGATGAAGAAAATGAGAATCGGATGG
683730 ATGGATGAAGAAAATGAGAATCGGATG
1 ATGGATGAAGAAAATGAGAATCGGATG
683757 TGCTTATGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.44, C:0.04, G:0.35, T:0.18
Consensus pattern (28 bp):
ATGGATGAAGAAAATGAGAATCGGATGG
Found at i:684466 original size:28 final size:28
Alignment explanation
Indices: 684386--684466 Score: 99
Period size: 29 Copynumber: 2.9 Consensus size: 28
684376 CTGTCAATTG
*
684386 TCACCACAAAACCTAACAATATCATCTA
1 TCACCACAAAACCTAACAATATCAACTA
* ****
684414 TCCCTCACGTGTCCTAACAATATCAACTA
1 TCAC-CACAAAACCTAACAATATCAACTA
684443 TCACCACAAAACCTAACAATATCA
1 TCACCACAAAACCTAACAATATCA
684467 GCTGATCAAA
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
28 19 0.46
29 22 0.54
ACGTcount: A:0.42, C:0.33, G:0.02, T:0.22
Consensus pattern (28 bp):
TCACCACAAAACCTAACAATATCAACTA
Found at i:684957 original size:16 final size:15
Alignment explanation
Indices: 684911--684957 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
684901 AATAAGCTCC
684911 AATCAATCTAAAACA
1 AATCAATCTAAAACA
*
684926 AATGCAAGCTAAAACA
1 AAT-CAATCTAAAACA
*
684942 AAGTCAATCTATAACA
1 AA-TCAATCTAAAACA
684958 TACTGGCAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 3 0.11
16 23 0.85
17 1 0.04
ACGTcount: A:0.55, C:0.19, G:0.06, T:0.19
Consensus pattern (15 bp):
AATCAATCTAAAACA
Found at i:685576 original size:13 final size:13
Alignment explanation
Indices: 685558--685614 Score: 55
Period size: 13 Copynumber: 4.4 Consensus size: 13
685548 GCCAACAACT
685558 ATATGCATGAACA
1 ATATGCATGAACA
685571 ATATGCA-GTAACA
1 ATATGCATG-AACA
*
685584 ATATGTAAT-AACA
1 ATATG-CATGAACA
* *
685597 GTATGCATGAAGA
1 ATATGCATGAACA
685610 ATATG
1 ATATG
685615 TATTACCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
12 3 0.09
13 31 0.89
14 1 0.03
ACGTcount: A:0.46, C:0.11, G:0.18, T:0.26
Consensus pattern (13 bp):
ATATGCATGAACA
Found at i:685596 original size:26 final size:26
Alignment explanation
Indices: 685567--685616 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
685557 TATATGCATG
685567 AACAATATGCA-GTAACAATATGTAAT
1 AACAATATGCATG-AACAATATGTAAT
* *
685593 AACAGTATGCATGAAGAATATGTA
1 AACAATATGCATGAACAATATGTA
685617 TTACCAAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 20 0.95
27 1 0.05
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.26
Consensus pattern (26 bp):
AACAATATGCATGAACAATATGTAAT
Found at i:686070 original size:65 final size:63
Alignment explanation
Indices: 685953--686160 Score: 208
Period size: 65 Copynumber: 3.2 Consensus size: 63
685943 TTTCAAAGTG
* * *
685953 ATGCAACGATGCACCAATCCATGCATCGATGCAC-CATGG-AATAAATTG-AACATCGAATGCAT
1 ATGCATCGATGCA-CAA-CCATGCATCGATGCACTCA-GGTTAT-TA-TGAAACATCGAATGCAT
686015 TTC
61 TTC
*
686018 ATGCATCGATGCACATACTATGCATCGATGCACTCAGAGTT-TTATGAAAACATCGAATGCATTT
1 ATGCATCGATGCACA-ACCATGCATCGATGCACTCAG-GTTATTATG-AAACATCGAATGCATTT
*
686082 G
63 C
* * * * *
686083 ATGCATCGATGTACCAGCCATGCATCGATGCACTCTGGTTATTTTGAAACATTGAATGCATTTC
1 ATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGTTATTATGAAACATCGAATGCATTTC
*
686147 ATGCATCGGTGCAC
1 ATGCATCGATGCAC
686161 TCTTAGTGCA
Statistics
Matches: 121, Mismatches: 14, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
63 3 0.02
64 49 0.40
65 67 0.55
66 2 0.02
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (63 bp):
ATGCATCGATGCACAACCATGCATCGATGCACTCAGGTTATTATGAAACATCGAATGCATTTC
Found at i:691855 original size:39 final size:38
Alignment explanation
Indices: 691812--691911 Score: 90
Period size: 30 Copynumber: 2.8 Consensus size: 38
691802 TCAGCAGGTT
691812 CTGGTTCATCAATTTTAGGTTCATTAATTTCTGGCTAAG
1 CTGGTTCATCAATTTT-GGTTCATTAATTTCTGGCTAAG
*
691851 CTGG-T--TC-----TGGTTCATTAATTTCTGGCTGAG
1 CTGGTTCATCAATTTTGGTTCATTAATTTCTGGCTAAG
* * *
691881 CTGGTTCATTAATTTCGGGTTCAGTAATTTC
1 CTGGTTCATCAATTT-TGGTTCATTAATTTC
691912 GGGTTGAACT
Statistics
Matches: 48, Mismatches: 4, Indels: 18
0.69 0.06 0.26
Matches are distributed among these distances:
30 25 0.52
31 2 0.04
33 1 0.02
36 2 0.04
38 1 0.02
39 17 0.35
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (38 bp):
CTGGTTCATCAATTTTGGTTCATTAATTTCTGGCTAAG
Found at i:691863 original size:30 final size:30
Alignment explanation
Indices: 691829--691887 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
691819 ATCAATTTTA
691829 GGTTCATTAATTTCTGGCTAAGCTGGTTCT
1 GGTTCATTAATTTCTGGCTAAGCTGGTTCT
*
691859 GGTTCATTAATTTCTGGCTGAGCTGGTTC
1 GGTTCATTAATTTCTGGCTAAGCTGGTTC
691888 ATTAATTTCG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.15, C:0.17, G:0.25, T:0.42
Consensus pattern (30 bp):
GGTTCATTAATTTCTGGCTAAGCTGGTTCT
Found at i:691903 original size:15 final size:15
Alignment explanation
Indices: 691883--691916 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
691873 TGGCTGAGCT
*
691883 GGTTCATTAATTTCG
1 GGTTCAGTAATTTCG
691898 GGTTCAGTAATTTCG
1 GGTTCAGTAATTTCG
691913 GGTT
1 GGTT
691917 GAACTGGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.12, G:0.26, T:0.44
Consensus pattern (15 bp):
GGTTCAGTAATTTCG
Found at i:691924 original size:69 final size:69
Alignment explanation
Indices: 691812--691941 Score: 181
Period size: 69 Copynumber: 1.9 Consensus size: 69
691802 TCAGCAGGTT
* * * *
691812 CTGGTTCATCAATTTTAGGTTCATTAATTTCTGGCTAAGCTGGTTCTGGTTCATTAATTTCTGGC
1 CTGGTTCATCAATTTCAGGTTCAGTAATTTCGGGCTAAGCTGGTTCTGCTTCATTAATTTCTGGC
691877 TGAG
66 TGAG
* * *
691881 CTGGTTCATTAATTTCGGGTTCAGTAATTTCGGGTTGAA-CTGGTTCTGCTTCATTAATTTC
1 CTGGTTCATCAATTTCAGGTTCAGTAATTTCGGGCT-AAGCTGGTTCTGCTTCATTAATTTC
691942 AGGTTCATTA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
69 51 0.96
70 2 0.04
ACGTcount: A:0.18, C:0.16, G:0.22, T:0.44
Consensus pattern (69 bp):
CTGGTTCATCAATTTCAGGTTCAGTAATTTCGGGCTAAGCTGGTTCTGCTTCATTAATTTCTGGC
TGAG
Found at i:692590 original size:15 final size:15
Alignment explanation
Indices: 692572--692600 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
692562 ATTCATACAC
692572 AACATATACATGCAT
1 AACATATACATGCAT
692587 AACATATACATGCA
1 AACATATACATGCA
692601 GTACTCACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.21, G:0.07, T:0.24
Consensus pattern (15 bp):
AACATATACATGCAT
Found at i:693167 original size:24 final size:24
Alignment explanation
Indices: 693132--693198 Score: 100
Period size: 24 Copynumber: 2.8 Consensus size: 24
693122 ACGGGGAGGT
693132 TGAAGG-TGAATGGGTTTTCTGCGA
1 TGAAGGCT-AATGGGTTTTCTGCGA
*
693156 TGAAGGCTAATGGGTTTTCTGCGG
1 TGAAGGCTAATGGGTTTTCTGCGA
*
693180 TGAAGGCGAATGGGTTTTC
1 TGAAGGCTAATGGGTTTTC
693199 AGACGAAATC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
24 39 0.98
25 1 0.03
ACGTcount: A:0.19, C:0.10, G:0.37, T:0.33
Consensus pattern (24 bp):
TGAAGGCTAATGGGTTTTCTGCGA
Found at i:693361 original size:88 final size:88
Alignment explanation
Indices: 693212--693385 Score: 312
Period size: 88 Copynumber: 2.0 Consensus size: 88
693202 CGAAATCTTT
*
693212 TGAAATCTCTCTAAAGTGCGAAGGATTTTTAGACGAGGAGGTTGAAGGCGAATGAGTTTTCTGCG
1 TGAAATCTCTCTAAAGTGCGAAGGATTTTCAGACGAGGAGGTTGAAGGCGAATGAGTTTTCTGCG
*
693277 ATGAAGGTGAATGGGTTTTCAGA
66 ATGAAGGCGAATGGGTTTTCAGA
*
693300 TGAAATCTCTCTAAAGTGCGAAGGATTTTCAGACGAGGAGGTTGAAGGCGAATGGGTTTTCTGCG
1 TGAAATCTCTCTAAAGTGCGAAGGATTTTCAGACGAGGAGGTTGAAGGCGAATGAGTTTTCTGCG
*
693365 ATGAAGGCGAATGTGTTTTCA
66 ATGAAGGCGAATGGGTTTTCA
693386 CTCTTTCAAC
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 82 1.00
ACGTcount: A:0.28, C:0.11, G:0.32, T:0.29
Consensus pattern (88 bp):
TGAAATCTCTCTAAAGTGCGAAGGATTTTCAGACGAGGAGGTTGAAGGCGAATGAGTTTTCTGCG
ATGAAGGCGAATGGGTTTTCAGA
Found at i:706987 original size:15 final size:15
Alignment explanation
Indices: 706950--706997 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
706940 TGTATGAATC
*
706950 AATATTAAAGT-CTA
1 AATATTAAAGTAATA
706964 AACTA-TAAAGTAATA
1 AA-TATTAAAGTAATA
*
706979 AATATTAAAATAATA
1 AATATTAAAGTAATA
706994 AATA
1 AATA
706998 GGTTTTGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
14 10 0.34
15 19 0.66
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (15 bp):
AATATTAAAGTAATA
Found at i:709169 original size:23 final size:23
Alignment explanation
Indices: 709143--709195 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
709133 ATTGTACCTA
709143 AGTGCCACGTAGAATTGCACCGG
1 AGTGCCACGTAGAATTGCACCGG
* *
709166 AGTGCCGCGTAGAATTGCACCGT
1 AGTGCCACGTAGAATTGCACCGG
709189 AGTGCCA
1 AGTGCCA
709196 TATAATAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.25, C:0.26, G:0.30, T:0.19
Consensus pattern (23 bp):
AGTGCCACGTAGAATTGCACCGG
Found at i:709330 original size:103 final size:103
Alignment explanation
Indices: 709211--709531 Score: 606
Period size: 103 Copynumber: 3.1 Consensus size: 103
709201 TAATGTCCAT
709211 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
709276 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
709314 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
709379 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
709417 AAAGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
709482 GACTTCACACATGTTCCAAAGAATACATATATGTCTCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
709520 AAGGACCACATA
1 AAGGACCACATA
709532 GACCCTCTAC
Statistics
Matches: 211, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 211 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:716186 original size:23 final size:23
Alignment explanation
Indices: 716155--716223 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
716145 CACCACAGCT
*
716155 CATATAATTGCACCTAAGTGCCA
1 CATAGAATTGCACCTAAGTGCCA
* *
716178 CGTAGAATTGCACC-AGAGTGCCG
1 CATAGAATTGCACCTA-AGTGCCA
716201 CATAGAATTGCACCGT-AGTGCCA
1 CATAGAATTGCACC-TAAGTGCCA
716224 TATAATAATG
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
22 1 0.03
23 37 0.97
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (23 bp):
CATAGAATTGCACCTAAGTGCCA
Found at i:716363 original size:103 final size:103
Alignment explanation
Indices: 716239--716559 Score: 561
Period size: 103 Copynumber: 3.1 Consensus size: 103
716229 TAATGTCCAT
*
716239 AAGGACCATATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
716304 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * *
716342 AAAGACCACATATCATTCCTTAAGAATCATATACGTATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
* *
716407 GACCTCACACATGTTCCAAAGAATACATATATGTCCTG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
716445 AAGGACCACATATCATTCCTTAATAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
* *
716510 GACTTTACACATGTTCCAAAGAATACATATATGTCTCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
716548 AAGGACCACATA
1 AAGGACCACATA
716560 GACCCTCTAC
Statistics
Matches: 204, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 204 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:717076 original size:19 final size:20
Alignment explanation
Indices: 717039--717076 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
717029 TTTTTCATTA
*
717039 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
717059 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
717077 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:719867 original size:2 final size:2
Alignment explanation
Indices: 719862--719888 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
719852 AGTAAACTCT
719862 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
719889 TATGTGCCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:720026 original size:23 final size:21
Alignment explanation
Indices: 720000--720064 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 21
719990 ATGTGAAATT
720000 TGTCCCGAATGACCTCATGTATA
1 TGTCCCGAA-GACCT-ATGTATA
*
720023 TGTCTCGAAGAACCTATGTATA
1 TGTCCCGAAG-ACCTATGTATA
*
720045 TGTTCCGAAGGACCTATGTA
1 TGTCCCGAA-GACCTATGTA
720065 ACCCTCGACT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 24 0.65
23 13 0.35
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.31
Consensus pattern (21 bp):
TGTCCCGAAGACCTATGTATA
Found at i:720692 original size:20 final size:20
Alignment explanation
Indices: 720667--720712 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
720657 CACTTGAGTA
*
720667 GTATCGGTACCCCTTCAATG
1 GTATCGCTACCCCTTCAATG
720687 GTATCGCTACCCCTTCAATG
1 GTATCGCTACCCCTTCAATG
720707 GTATCG
1 GTATCG
720713 ATACTTCCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (20 bp):
GTATCGCTACCCCTTCAATG
Found at i:724268 original size:23 final size:23
Alignment explanation
Indices: 724238--724305 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
724228 AATCTTATAT
724238 GGCACTACGGTGCATTTCTACGC
1 GGCACTACGGTGCATTTCTACGC
* *
724261 GGCACTACGGTGCAATTCTACGT
1 GGCACTACGGTGCATTTCTACGC
** *
724284 GGCACTTTGGTGCATTTATACG
1 GGCACTACGGTGCATTTCTACG
724306 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.29
Consensus pattern (23 bp):
GGCACTACGGTGCATTTCTACGC
Found at i:727277 original size:21 final size:21
Alignment explanation
Indices: 727251--727296 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
727241 GATTTCTGGG
* *
727251 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
727272 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
727293 CAAG
1 CAAG
727297 CGAATAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.15
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:727367 original size:23 final size:22
Alignment explanation
Indices: 727323--727367 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
727313 AATGTCATGG
*
727323 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
727345 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
727368 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:728712 original size:32 final size:31
Alignment explanation
Indices: 728670--728797 Score: 143
Period size: 31 Copynumber: 4.1 Consensus size: 31
728660 AGAGTCGAGG
728670 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* *
728701 TTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 -GTTTACCTATGTTC-TACGGA-ACATATGGACA
* *
728733 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* * * *
728764 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
728795 GTT
1 GTT
728798 ACCGAGGATC
Statistics
Matches: 80, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
31 53 0.66
32 27 0.34
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:728817 original size:30 final size:30
Alignment explanation
Indices: 728756--728852 Score: 113
Period size: 30 Copynumber: 3.2 Consensus size: 30
728746 CTAAGGAACA
* * ***
728756 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAG-TTACCGAGGATCTTTATGACC
728787 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
* *
728817 TCTGGATAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
*
728847 TCTGGA
1 TATGGA
728853 TAGGTCCTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
30 50 0.85
31 9 0.15
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGATCTTTATGACC
Found at i:728853 original size:30 final size:30
Alignment explanation
Indices: 728783--728855 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
728773 GGTTCTTCGG
* *
728783 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
728813 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
728843 GACCTCTGGATAG
1 GACCTCTGGATAG
728856 GTCCTTCGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:748562 original size:30 final size:31
Alignment explanation
Indices: 748526--748601 Score: 127
Period size: 31 Copynumber: 2.5 Consensus size: 31
748516 AAAAATTGAA
748526 AGTTTAGGTACTAAAACATAT-AAAACTAAT
1 AGTTTAGGTACTAAAACATATCAAAACTAAT
*
748556 AGTTTAGGTACTAAAACATATCAAAACTGAT
1 AGTTTAGGTACTAAAACATATCAAAACTAAT
*
748587 AGTTTAGGTATTAAA
1 AGTTTAGGTACTAAA
748602 CGTGTTAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
30 21 0.49
31 22 0.51
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.32
Consensus pattern (31 bp):
AGTTTAGGTACTAAAACATATCAAAACTAAT
Found at i:748589 original size:31 final size:30
Alignment explanation
Indices: 748517--748601 Score: 125
Period size: 30 Copynumber: 2.8 Consensus size: 30
748507 AAGTTTTGAA
* *
748517 AAAATTGAAAGTTTAGGTACTAAAACATAT
1 AAAACTGATAGTTTAGGTACTAAAACATAT
*
748547 AAAACTAATAGTTTAGGTACTAAAACATAT
1 AAAACTGATAGTTTAGGTACTAAAACATAT
*
748577 CAAAACTGATAGTTTAGGTATTAAA
1 -AAAACTGATAGTTTAGGTACTAAA
748602 CGTGTTAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 27 0.55
31 22 0.45
ACGTcount: A:0.48, C:0.08, G:0.13, T:0.31
Consensus pattern (30 bp):
AAAACTGATAGTTTAGGTACTAAAACATAT
Found at i:749525 original size:29 final size:30
Alignment explanation
Indices: 749466--749528 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
749456 CATAAAATTA
*
749466 GGTTGTTGATTTCTTCGTAAAATACTATTG
1 GGTTATTGATTTCTTCGTAAAATACTATTG
*
749496 GGTTATTGTTTTCTTCGT-AAATACTATTG
1 GGTTATTGATTTCTTCGTAAAATACTATTG
749525 GGTT
1 GGTT
749529 GTTGCAGCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 15 0.48
30 16 0.52
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.49
Consensus pattern (30 bp):
GGTTATTGATTTCTTCGTAAAATACTATTG
Found at i:749727 original size:2 final size:2
Alignment explanation
Indices: 749720--749754 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
749710 AAAAGAGTGT
749720 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
749755 TAATATTGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:751846 original size:19 final size:19
Alignment explanation
Indices: 751822--751908 Score: 75
Period size: 19 Copynumber: 4.2 Consensus size: 19
751812 GCGATTTTGA
751822 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
*
751841 AAAATGTGTTGCGAGAGTTT
1 AAAATGTGTTGCGATAG-TT
*
751861 GAAAAATGTGTTGTTGCGATAGTG
1 --AAAA--TG-TGTTGCGATAGTT
* *
751885 AAAACGTGTTGCTATAGTGT
1 AAAATGTGTTGCGATAGT-T
751905 AAAA
1 AAAA
751909 GATTCCCAAG
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
19 27 0.49
20 7 0.13
22 8 0.15
24 3 0.05
25 10 0.18
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.33
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTT
Found at i:751869 original size:22 final size:22
Alignment explanation
Indices: 751817--751873 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 22
751807 GCAACGCGAT
*
751817 TTTGAAAAATGTGTTGCGATAG
1 TTTGAAAAATGTGTTGCGAGAG
751839 -TT--AAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGAGAG
751858 TTTGAAAAATGTGTTG
1 TTTGAAAAATGTGTTG
751874 TTGCGATAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
19 16 0.52
20 2 0.06
21 2 0.06
22 11 0.35
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.37
Consensus pattern (22 bp):
TTTGAAAAATGTGTTGCGAGAG
Found at i:751888 original size:22 final size:21
Alignment explanation
Indices: 751819--751895 Score: 61
Period size: 22 Copynumber: 3.6 Consensus size: 21
751809 AACGCGATTT
*
751819 TGAAAAATG-TGTTGCGATAG
1 TGAAAAGTGTTGTTGCGATAG
* *
751839 TTAAAA-TG-TGTTGCGAGAG
1 TGAAAAGTGTTGTTGCGATAG
751858 TTTGAAAAATGTGTTGTTGCGATAG
1 --TG-AAAA-GTGTTGTTGCGATAG
751883 TGAAAACGTGTTG
1 TGAAAA-GTGTTG
751896 CTATAGTGTA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
19 12 0.26
20 5 0.11
21 1 0.02
22 14 0.30
23 2 0.04
24 2 0.04
25 10 0.22
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.34
Consensus pattern (21 bp):
TGAAAAGTGTTGTTGCGATAG
Found at i:752303 original size:40 final size:40
Alignment explanation
Indices: 752248--752430 Score: 172
Period size: 40 Copynumber: 4.5 Consensus size: 40
752238 TGAACTTGGC
* *
752248 CGCGAACTTGGACTATCGCAATGAATTTGGAAAATCGCAA
1 CGCGAACTTGGACTATCGCAACGAACTTGGAAAATCGCAA
* ** *
752288 CGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCGA
1 CGCGAACTTGGACTATCGCAAC--GAACTTGGAAAATCGCAA
* ** * **
752330 --CGAATTTGGAAAATCGCAACACGAACTTCGACTATCGCAA
1 CGCGAACTTGGACTATCGC-A-ACGAACTTGGAAAATCGCAA
* * * *
752370 CGTGAACTTCGACTATCGCAACGAATTTTGAAAATCGCAA
1 CGCGAACTTGGACTATCGCAACGAACTTGGAAAATCGCAA
752410 CGCGAACTTGGACTATCGCAA
1 CGCGAACTTGGACTATCGCAA
752431 AATCGCGTTG
Statistics
Matches: 114, Mismatches: 23, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
40 84 0.74
41 2 0.02
42 28 0.25
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.22
Consensus pattern (40 bp):
CGCGAACTTGGACTATCGCAACGAACTTGGAAAATCGCAA
Found at i:752307 original size:21 final size:21
Alignment explanation
Indices: 752281--752430 Score: 146
Period size: 21 Copynumber: 7.3 Consensus size: 21
752271 AATTTGGAAA
752281 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
752302 ATCGCAACGTGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
* * * **
752323 ATCGCGA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
*
752342 ATCGCAACACGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
752363 ATCGCAACGTGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * **
752384 ATCGCAA--CGAATTTTGAAA
1 ATCGCAACGCGAACTTCGACT
*
752403 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
752424 ATCGCAA
1 ATCGCAA
752431 AATCGCGTTG
Statistics
Matches: 102, Mismatches: 23, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
19 28 0.27
21 74 0.73
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:752346 original size:61 final size:61
Alignment explanation
Indices: 752251--752430 Score: 306
Period size: 61 Copynumber: 3.0 Consensus size: 61
752241 ACTTGGCCGC
*
752251 GAACTTGGACTATCGCAATGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGT
1 GAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGT
* *
752312 GAACTTGGACTATCGCGACGAATTTGGAAAATCGCAACACGAACTTCGACTATCGCAACGT
1 GAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGT
* * *
752373 GAACTTCGACTATCGCAACGAATTTTGAAAATCGCAACGCGAACTTGGACTATCGCAA
1 GAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAA
752431 AATCGCGTTG
Statistics
Matches: 111, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 111 1.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (61 bp):
GAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGT
Found at i:753695 original size:40 final size:41
Alignment explanation
Indices: 753600--753719 Score: 197
Period size: 40 Copynumber: 3.0 Consensus size: 41
753590 TGAAGGAAAT
* *
753600 TGTAGTTGTTGTTGAAGCAAATTTGTTTCTTATAATGTTGG
1 TGTAGTTGTTGTTGAAGGAAATTTGTTTCTTGTAATGTTGG
*
753641 TGTAGTTGTTGTTGAAGGAAATTTGTTTCTTGTAGTGTT-G
1 TGTAGTTGTTGTTGAAGGAAATTTGTTTCTTGTAATGTTGG
*
753681 TGTAGTTGTTGTTGAAGGAAGTTTGTTTCTTGTAATGTT
1 TGTAGTTGTTGTTGAAGGAAATTTGTTTCTTGTAATGTT
753720 TCTTATAATT
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
40 38 0.51
41 36 0.49
ACGTcount: A:0.19, C:0.03, G:0.28, T:0.50
Consensus pattern (41 bp):
TGTAGTTGTTGTTGAAGGAAATTTGTTTCTTGTAATGTTGG
Found at i:753771 original size:17 final size:17
Alignment explanation
Indices: 753749--753782 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
753739 AAAACCAACA
*
753749 GTTGAAGGAAATTTGTT
1 GTTGAAGAAAATTTGTT
753766 GTTGAAGAAAATTTGTT
1 GTTGAAGAAAATTTGTT
753783 TCATATATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.41
Consensus pattern (17 bp):
GTTGAAGAAAATTTGTT
Found at i:756021 original size:21 final size:21
Alignment explanation
Indices: 755997--756037 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
755987 ATATTTAATG
755997 AAAAAGATATCAATTGTTAAC
1 AAAAAGATATCAATTGTTAAC
*
756018 AAAAGGATATCAATTGTTAA
1 AAAAAGATATCAATTGTTAA
756038 AAGATACCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.29
Consensus pattern (21 bp):
AAAAAGATATCAATTGTTAAC
Found at i:760617 original size:30 final size:29
Alignment explanation
Indices: 760576--760645 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
760566 GGTGTTGACA
* *
760576 GTGGAGTTGAAGCAGGGGGAGCACAAAGAG
1 GTGGTGTTGAAGCA-GAGGAGCACAAAGAG
* *
760606 GTGGTGTTGAAGCAGAGGTGTACAAAGAG
1 GTGGTGTTGAAGCAGAGGAGCACAAAGAG
760635 GTGGTGTTGAA
1 GTGGTGTTGAA
760646 TCAATCCCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 23 0.64
30 13 0.36
ACGTcount: A:0.30, C:0.07, G:0.44, T:0.19
Consensus pattern (29 bp):
GTGGTGTTGAAGCAGAGGAGCACAAAGAG
Found at i:762959 original size:57 final size:57
Alignment explanation
Indices: 762894--763055 Score: 288
Period size: 57 Copynumber: 2.8 Consensus size: 57
762884 ACTTAAATAC
762894 ATCAATATAGTTAACAGTTAATAAACAAAATAATTTAATCAACATGCACCTAAAAAT
1 ATCAATATAGTTAACAGTTAATAAACAAAATAATTTAATCAACATGCACCTAAAAAT
* * *
762951 ATCAATATAGTTAACAGTTAATTACCAAAATAATTTAATCAACATGTACCTAAAAAT
1 ATCAATATAGTTAACAGTTAATAAACAAAATAATTTAATCAACATGCACCTAAAAAT
*
763008 ATCAATATAGTTAACATTTAATAAACAAAATAATTTAATCAACATGCA
1 ATCAATATAGTTAACAGTTAATAAACAAAATAATTTAATCAACATGCA
763056 ACAAAATAAA
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 98 1.00
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (57 bp):
ATCAATATAGTTAACAGTTAATAAACAAAATAATTTAATCAACATGCACCTAAAAAT
Found at i:762966 original size:29 final size:29
Alignment explanation
Indices: 762934--763024 Score: 80
Period size: 29 Copynumber: 3.2 Consensus size: 29
762924 TAATTTAATC
*
762934 AACATGCACCTAAAAATATCAATATAGTT
1 AACATGTACCTAAAAATATCAATATAGTT
** * * * *
762963 AACA-GTTAATTACCAAA-AT-AATTTAATC
1 AACATG-TACCTA-AAAATATCAATATAGTT
762991 AACATGTACCTAAAAATATCAATATAGTT
1 AACATGTACCTAAAAATATCAATATAGTT
763020 AACAT
1 AACAT
763025 TTAATAAACA
Statistics
Matches: 44, Mismatches: 13, Indels: 10
0.66 0.19 0.15
Matches are distributed among these distances:
27 3 0.07
28 17 0.39
29 21 0.48
30 3 0.07
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.30
Consensus pattern (29 bp):
AACATGTACCTAAAAATATCAATATAGTT
Found at i:763122 original size:29 final size:28
Alignment explanation
Indices: 763086--763142 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
763076 ATATTTTAAT
*
763086 AGTTAATAAACACCACCAAAAGAACCAAA
1 AGTTAATAAACAACACC-AAAGAACCAAA
*
763115 AGTTAATAAACAACACCAAATAACCAAA
1 AGTTAATAAACAACACCAAAGAACCAAA
763143 TAATCAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 10 0.38
29 16 0.62
ACGTcount: A:0.60, C:0.23, G:0.05, T:0.12
Consensus pattern (28 bp):
AGTTAATAAACAACACCAAAGAACCAAA
Found at i:771179 original size:31 final size:31
Alignment explanation
Indices: 771144--771202 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
771134 TACTTAAAAG
* * *
771144 AGTTTTGCAATGCTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
771175 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
771203 CCATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:771253 original size:22 final size:22
Alignment explanation
Indices: 771227--771326 Score: 164
Period size: 22 Copynumber: 4.5 Consensus size: 22
771217 TAATAAATTA
771227 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
771249 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
***
771271 TTTAAAATAAATTTTTCCATAT
1 TTTAAAATAAATCAATCCATAT
*
771293 TTTAAAATAAATCAATCTATAT
1 TTTAAAATAAATCAATCCATAT
771315 TTTAAAATAAAT
1 TTTAAAATAAAT
771327 TTTAAAATAG
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 71 1.00
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:771343 original size:11 final size:12
Alignment explanation
Indices: 771313--771352 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
771303 ATCAATCTAT
771313 ATTTTAAAATAA
1 ATTTTAAAATAA
*
771325 ATTTTAAAATAG
1 ATTTTAAAATAA
771337 A-TTT-AAAT-A
1 ATTTTAAAATAA
771346 ATTTTAA
1 ATTTTAA
771353 TTTCTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
9 1 0.04
10 7 0.29
11 4 0.17
12 12 0.50
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (12 bp):
ATTTTAAAATAA
Found at i:771346 original size:44 final size:44
Alignment explanation
Indices: 771249--771343 Score: 136
Period size: 44 Copynumber: 2.1 Consensus size: 44
771239 CAATCCATAT
*** *
771249 TTTAAAATAAATCAATCCATATTTTAAAATAAATTTTTCCATAT
1 TTTAAAATAAATCAATCCATATTTTAAAATAAATTTTAAAATAA
*
771293 TTTAAAATAAATCAATCTATATTTTAAAATAAATTTTAAAATAGA
1 TTTAAAATAAATCAATCCATATTTTAAAATAAATTTTAAAATA-A
771338 TTTAAA
1 TTTAAA
771344 TAATTTTAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 39 0.87
45 6 0.13
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.42
Consensus pattern (44 bp):
TTTAAAATAAATCAATCCATATTTTAAAATAAATTTTAAAATAA
Found at i:772273 original size:17 final size:18
Alignment explanation
Indices: 772235--772280 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
772225 GTTTCTGAGA
*
772235 GAATTGGAATCTGTGAAG
1 GAATTGGAATCTGTCAAG
*
772253 GAATTGGAATCTG-CCAG
1 GAATTGGAATCTGTCAAG
772270 GAATTGGAATC
1 GAATTGGAATC
772281 CAATTCCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (18 bp):
GAATTGGAATCTGTCAAG
Found at i:772945 original size:37 final size:37
Alignment explanation
Indices: 772850--772947 Score: 112
Period size: 38 Copynumber: 2.6 Consensus size: 37
772840 CCGGTTTTTT
*
772850 TCACACTT-AAAAACGAACCCGA-TCCGACCCGAATA
1 TCACACTTAAAAAACCAACCCGACTCCGACCCGAATA
* * *
772885 TCACACTTAAAAAACCCCGACCCGACT-CGACTCGAATG
1 TCACACTTAAAAAA--CCAACCCGACTCCGACCCGAATA
772923 TCACACTTAAAAAACACAACCCGAC
1 TCACACTTAAAAAAC-CAACCCGAC
772948 CCAAACAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
35 8 0.15
36 6 0.11
37 8 0.15
38 30 0.57
39 1 0.02
ACGTcount: A:0.40, C:0.36, G:0.10, T:0.14
Consensus pattern (37 bp):
TCACACTTAAAAAACCAACCCGACTCCGACCCGAATA
Found at i:775299 original size:25 final size:25
Alignment explanation
Indices: 775271--775327 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
775261 ATTGTTCATA
*
775271 AAATTCTAAGTAAAATCATGTTTCC
1 AAATTCTAAGAAAAATCATGTTTCC
775296 AAATTCTAAGAAAAATCATGTTTCC
1 AAATTCTAAGAAAAATCATGTTTCC
775321 AAATTCT
1 AAATTCT
775328 TTCTTTTGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.35
Consensus pattern (25 bp):
AAATTCTAAGAAAAATCATGTTTCC
Found at i:781248 original size:17 final size:19
Alignment explanation
Indices: 781212--781248 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
781202 TTAAATTTAA
*
781212 TTATAAATATTTATAATAT
1 TTATAAATATTTAAAATAT
781231 TTAT-AATA-TTAAAATAT
1 TTATAAATATTTAAAATAT
781248 T
1 T
781249 ATTCGATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTATAAATATTTAAAATAT
Found at i:781660 original size:259 final size:258
Alignment explanation
Indices: 781235--781717 Score: 754
Period size: 259 Copynumber: 1.9 Consensus size: 258
781225 TAATATTTAT
*
781235 AATATTAAAATATTATTCGATTTCAATTTAAGTGACTTTCTATAACCATATATACAATACAAATA
1 AATATTAAAATATTATTCGATTCCAATTTAAGTGACTTTCTATAACCATATATACAATACAAATA
* * *
781300 TATTTCTTCATATTTTTTCATGTTTGATATACATATATTATTACAAAGCCAAGAACTCAAGTCAA
66 TATTTATTCATATTTTTTCATATGTGATATACATATATTATTACAAAGCCAAGAACTCAAGTCAA
* *
781365 ACTTGAAAATAAATCCACTAGTTACTAAAAATTTTGATTTATTCGAATTGTATTTTACAACTCGA
131 ACTTGAAAATAAATCCACTAGTTACTAAAAATTTTGAGTTATTCGAATTGCATTTTACAACTCGA
* * *
781430 TTTGAATTTGAATTTTTTTTGAGTCGAGTCAATTTTTTGAGTTTTTATTTAAATTTAATTGTA
196 TTTAAATTTGAAATTTTTTCGAGTCGAGTCAATTTTTTGAGTTTTTATTTAAATTTAATTGTA
* ** * * *
781493 AATATTATAATATTATTTTATTCCAATTTAAGTGACTTTCTGTATTTA-TATATATATAATACAA
1 AATATTAAAATATTATTCGATTCCAATTTAAGTGACTTTC--TA-TAACCATATATACAATACAA
* *
781557 ATATATTTATTCATATTTTTTCATATGTGATATACATATATTA-TACAAAGCCAAGGACTCGAGT
63 ATATATTTATTCATATTTTTTCATATGTGATATACATATATTATTACAAAGCCAAGAACTCAAGT
* *
781621 CAAACTTGAAAATAAATCTACTAGTTACTAAAAATTTTGAGTTATTCGAGTTGCATTTTACAACT
128 CAAACTTGAAAATAAATCCACTAGTTACTAAAAATTTTGAGTTATTCGAATTGCATTTTACAACT
781686 CGATTTAAATTTGAAATTTTTTCGAGTCGAGT
193 CGATTTAAATTTGAAATTTTTTCGAGTCGAGT
781718 TTTTCAATTT
Statistics
Matches: 203, Mismatches: 19, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
258 36 0.18
259 109 0.54
260 56 0.28
261 2 0.01
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43
Consensus pattern (258 bp):
AATATTAAAATATTATTCGATTCCAATTTAAGTGACTTTCTATAACCATATATACAATACAAATA
TATTTATTCATATTTTTTCATATGTGATATACATATATTATTACAAAGCCAAGAACTCAAGTCAA
ACTTGAAAATAAATCCACTAGTTACTAAAAATTTTGAGTTATTCGAATTGCATTTTACAACTCGA
TTTAAATTTGAAATTTTTTCGAGTCGAGTCAATTTTTTGAGTTTTTATTTAAATTTAATTGTA
Found at i:794044 original size:39 final size:40
Alignment explanation
Indices: 793990--794067 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 40
793980 ACCTAGCCCA
* * *
793990 CAATTAAATTAATACTTGTAGAGAAGTA-GAAAGCTTGAG
1 CAATTAAATCAATACTTGTACAGAAGTACAAAAGCTTGAG
794029 CAATTAAATCAATACTTGTACAGAAGTACAAAAGCTTGA
1 CAATTAAATCAATACTTGTACAGAAGTACAAAAGCTTGA
794068 TAAACATCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 26 0.74
40 9 0.26
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.27
Consensus pattern (40 bp):
CAATTAAATCAATACTTGTACAGAAGTACAAAAGCTTGAG
Found at i:803067 original size:3 final size:3
Alignment explanation
Indices: 803059--803088 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
803049 TAATTTACTC
803059 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
803089 AGATGCAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:804463 original size:14 final size:14
Alignment explanation
Indices: 804446--804526 Score: 69
Period size: 14 Copynumber: 5.7 Consensus size: 14
804436 AATATATATG
804446 TATATATATATAAA
1 TATATATATATAAA
*
804460 TATAGGATATA-AAA
1 TATA-TATATATAAA
* *
804474 TAGATA-ATATAAG
1 TATATATATATAAA
804487 TATATATATATACAA
1 TATATATATATA-AA
804502 TACTA-ATTATATAAA
1 TA-TATA-TATATAAA
*
804517 TCTATATATA
1 TATATATATA
804527 GTCAAATTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
12 3 0.06
13 8 0.15
14 21 0.40
15 13 0.25
16 8 0.15
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.38
Consensus pattern (14 bp):
TATATATATATAAA
Found at i:804589 original size:22 final size:19
Alignment explanation
Indices: 804564--804605 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
804554 ATATATTTAT
804564 ATAAATAAAATAACATATGTAA
1 ATAAAT-AAATAA-ATAT-TAA
804586 ATAAATAAATAAATATTAA
1 ATAAATAAATAAATATTAA
804605 A
1 A
804606 AAAAAGAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 4 0.20
21 6 0.30
22 6 0.30
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (19 bp):
ATAAATAAATAAATATTAA
Found at i:812323 original size:21 final size:21
Alignment explanation
Indices: 812297--812336 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
812287 CCCCCTTTGA
*
812297 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
812318 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
812337 TGGGGTTCTG
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:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:815994 original size:106 final size:106
Alignment explanation
Indices: 815804--816560 Score: 845
Period size: 105 Copynumber: 7.3 Consensus size: 106
815794 TGTTCCGGGG
* * * * * ** * **
815804 CCAAAATCTTTCGCCGTGAAGTTAAAATTGACTCTGAAA-CCGGAAA--GTTTATTGACAGTCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG
* * * * * * **
815866 CCGTCCCTTCGTTGTGAAGTTGAAATTGTGCTATCTTAAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
815907 CTAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG
* * *
815972 TC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT
66 -CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * * * * *** * ** *
816013 GGCACGATATCCTCCGTTGTGGAGTTGAAA-TCGCGGGAGAAACT-AAAAAGTTGTTTATTGACA
1 --C-CAATATCCTTCGCTGTGAAGTTGAAATTGGC-TCTGAAATTGGGAAA-TTGTTTGTTGACA
* * * *
816076 ACCAGTC-GTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCGAGT
61 ACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
816122 CCAATATCCTTCG-T-T---G-TG-AA---G-T-TGAAATTGGGAAATTGTTTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG
*
816175 CGGTCCCTTCGTCGAGAAGTTGAACTTGCGTTGTCTGGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
816216 CCAATATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG
* *
816281 CGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTAGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * *
816322 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTT-ATTGTTAACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG
816386 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
816427 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGTCAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG
* *
816491 CGGTCCCTTCGTCGTGAAGTTGAACTAGCGTTATCTGGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
816532 CCAATATCCTCCACTGTGAAGTTGAAATT
1 CCAATATCCTTCGCTGTGAAGTTGAAATT
816561 TTGGACGTTT
Statistics
Matches: 571, Mismatches: 59, Indels: 46
0.84 0.09 0.07
Matches are distributed among these distances:
93 1 0.00
94 69 0.12
95 4 0.01
97 1 0.00
99 3 0.01
100 4 0.01
101 3 0.01
103 33 0.06
104 7 0.01
105 181 0.32
106 173 0.30
107 2 0.00
108 7 0.01
109 83 0.15
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (106 bp):
CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG
CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
Found at i:816468 original size:309 final size:311
Alignment explanation
Indices: 815863--816560 Score: 874
Period size: 309 Copynumber: 2.2 Consensus size: 311
815853 TATTGACAGT
* * * * * ** *
815863 CAGCCGTCCCTTCGTTGTGAAGTTGAAATTGTGCTATCTTAAGTCTAATATCCTTCGCTGTGAAG
1 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTGGAGTCCAATATCCTTCGCTGTGAAG
* *
815928 TTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTT
66 TTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGTCGTCCCTTCATCGTGAAGTT
* * * * * *
815993 GAACTTGTGTTGTCTCGAGTGGCACGATATCCTCCGTTGTGGAGTTGAAATCGCGGGAGAAACTA
131 GAACTTGCGTTGTCTAGAGT-GCACAATATCCTCCGCTGTGAAGTTGAAATCGCGGCAGAAACTA
* * * *
816058 AAAAGTTGTTTATTGACAACCAGTCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCGAGTC
195 AAAAGTTGATTATTAACAACCAGTCGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTCGAGTC
*
816123 CAATATCCTTCGTTGTGAAGTTGAAATTGGGAAATT-G-T-TTGTTGACAAC
260 CAATATCCTTCGCTGTGAAGTTGAAATTGGGAAATTGGTTGTTGTTGACAAC
* * *
816172 CAGCGGTCCCTTCGTCGAGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGAGAAG
1 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTGGAGTCCAATATCCTTCGCTGTGAAG
816237 TTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG-CGGTCCCTTCATCGTGAAGT
66 TTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGTC-GTCCCTTCATCGTGAAGT
* * * * *
816301 TGAACTTGCGTTGTCTAGAGT-C-CAATATCCTTCGCTGTGAAGTTGAAATTG-GCTCTGAAATT
130 TGAACTTGCGTTGTCTAGAGTGCACAATATCCTCCGCTGTGAAGTTGAAATCGCG-GCAGAAACT
*** * * *
816363 GGGAAGTT-ATTGTTAACAACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
194 AAAAAGTTGATTATTAACAACCAGTC-GTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTCGAG
*
816426 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGTCAAC
258 TCCAATATCCTTCGCTGTGAAGTTGAAATTGG----GAAATT--G--GTTGTTGTTGACAAC
* * *
816488 CAGCGGTCCCTTCGTCGTGAAGTTGAACTAGCGTTATCTGGAGTCCAATATCCTCCACTGTGAAG
1 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTGGAGTCCAATATCCTTCGCTGTGAAG
816553 TTGAAATT
66 TTGAAATT
816561 TTGGACGTTT
Statistics
Matches: 333, Mismatches: 42, Indels: 21
0.84 0.11 0.05
Matches are distributed among these distances:
304 1 0.00
305 78 0.23
306 34 0.10
307 1 0.00
308 1 0.00
309 139 0.42
314 1 0.00
315 1 0.00
316 77 0.23
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (311 bp):
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTGGAGTCCAATATCCTTCGCTGTGAAG
TTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGTCGTCCCTTCATCGTGAAGTT
GAACTTGCGTTGTCTAGAGTGCACAATATCCTCCGCTGTGAAGTTGAAATCGCGGCAGAAACTAA
AAAGTTGATTATTAACAACCAGTCGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTCGAGTCC
AATATCCTTCGCTGTGAAGTTGAAATTGGGAAATTGGTTGTTGTTGACAAC
Found at i:817342 original size:14 final size:14
Alignment explanation
Indices: 817320--817369 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
817310 CCCACCTTGT
817320 TTTCTTTCTTTTTC
1 TTTCTTTCTTTTTC
*
817334 TTTCGTTCTTTTTTC
1 TTTCTTTC-TTTTTC
817349 TCTT-TTTCTTTTTC
1 T-TTCTTTCTTTTTC
817363 TTT-TTTC
1 TTTCTTTC
817370 AATTTAGGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 6 0.19
14 14 0.44
15 10 0.31
16 2 0.06
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (14 bp):
TTTCTTTCTTTTTC
Found at i:817451 original size:61 final size:63
Alignment explanation
Indices: 817343--817463 Score: 158
Period size: 61 Copynumber: 2.0 Consensus size: 63
817333 CTTTCGTTCT
* * *
817343 TTTTTCTCTTTTTCTTTTTCTTTTTTCAATTTAGGGCGCCCTTTCGGGTTTTCACCCTAAACG
1 TTTTTCTCTTTTTCTCTTTCTTTTTTCAACTTAGGACGCCCTTTCGGGTTTTCACCCTAAACG
* * *
817406 TTTTTCTCTTTTT-TCTTT-TTTTTTCAACTTAGGATG-TCTTCTCGGGTTTTCATCCTAA
1 TTTTTCTCTTTTTCTCTTTCTTTTTTCAACTTAGGACGCCCTT-TCGGGTTTTCACCCTAA
817464 GCGAAGTATT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
60 3 0.06
61 31 0.61
62 4 0.08
63 13 0.25
ACGTcount: A:0.12, C:0.21, G:0.12, T:0.55
Consensus pattern (63 bp):
TTTTTCTCTTTTTCTCTTTCTTTTTTCAACTTAGGACGCCCTTTCGGGTTTTCACCCTAAACG
Found at i:828130 original size:15 final size:15
Alignment explanation
Indices: 828110--828149 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
828100 ATATATGTAT
828110 ATATATAAATATAGG
1 ATATATAAATATAGG
828125 ATATATAAATATAGG
1 ATATATAAATATAGG
828140 ATATA-AAATA
1 ATATATAAATA
828150 GATAATAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 5 0.20
15 20 0.80
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (15 bp):
ATATATAAATATAGG
Found at i:837267 original size:13 final size:13
Alignment explanation
Indices: 837249--837273 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
837239 TTAAATGCTA
837249 AAATTGAAAATTT
1 AAATTGAAAATTT
837262 AAATTGAAAATT
1 AAATTGAAAATT
837274 AAAAATTCGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
AAATTGAAAATTT
Found at i:837417 original size:9 final size:9
Alignment explanation
Indices: 837388--837436 Score: 64
Period size: 9 Copynumber: 5.4 Consensus size: 9
837378 AATTCAAGGG
837388 AAAATAAAT
1 AAAATAAAT
*
837397 AAATACAAAT
1 AAA-ATAAAT
837407 AAAATAAAT
1 AAAATAAAT
837416 -AAATAAAT
1 AAAATAAAT
*
837424 AAAATAAGT
1 AAAATAAAT
837433 AAAA
1 AAAA
837437 ACAAAATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
8 8 0.23
9 19 0.54
10 8 0.23
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (9 bp):
AAAATAAAT
Found at i:837429 original size:32 final size:33
Alignment explanation
Indices: 837389--837461 Score: 96
Period size: 32 Copynumber: 2.2 Consensus size: 33
837379 ATTCAAGGGA
* *
837389 AAAT-AAATAAATACAAATAAAATAAATAAAT-
1 AAATAAAATAAATAAAAACAAAATAAATAAATC
*
837420 AAATAAAATAAGTAAAAACAAAATAAATAAATC
1 AAATAAAATAAATAAAAACAAAATAAATAAATC
837453 AAATTAAAA
1 AAA-TAAAA
837462 AGTGTTAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 4 0.11
32 24 0.67
33 3 0.08
34 5 0.14
ACGTcount: A:0.74, C:0.04, G:0.01, T:0.21
Consensus pattern (33 bp):
AAATAAAATAAATAAAAACAAAATAAATAAATC
Found at i:837456 original size:5 final size:4
Alignment explanation
Indices: 837389--837456 Score: 59
Period size: 4 Copynumber: 16.0 Consensus size: 4
837379 ATTCAAGGGA
*
837389 AAAT AAAT AAAT ACAAAT AAAAT AAAT AAAT AAAT AAAAT AAGT AAA-
1 AAAT AAAT AAAT --AAAT -AAAT AAAT AAAT AAAT -AAAT AAAT AAAT
837436 AACA- AAAT AAAT AAAT CAAAT
1 AA-AT AAAT AAAT AAAT -AAAT
837457 TAAAAAGTGT
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
3 3 0.05
4 36 0.65
5 12 0.22
6 4 0.07
ACGTcount: A:0.74, C:0.04, G:0.01, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:837461 original size:19 final size:17
Alignment explanation
Indices: 837388--837461 Score: 80
Period size: 19 Copynumber: 4.2 Consensus size: 17
837378 AATTCAAGGG
837388 AAAATAAATAAATACAAAT
1 AAAATAAATAAAT--AAAT
837407 AAAATAAATAAATAAAT
1 AAAATAAATAAATAAAT
* *
837424 AAAATAAGT-AA-AAAC
1 AAAATAAATAAATAAAT
837439 AAAATAAATAAATCAAATT
1 AAAATAAATAAAT-AAA-T
837458 AAAA
1 AAAA
837462 AGTGTTAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
15 11 0.23
16 4 0.09
17 12 0.26
18 3 0.06
19 17 0.36
ACGTcount: A:0.74, C:0.04, G:0.01, T:0.20
Consensus pattern (17 bp):
AAAATAAATAAATAAAT
Found at i:838675 original size:4 final size:4
Alignment explanation
Indices: 838666--838723 Score: 50
Period size: 4 Copynumber: 14.0 Consensus size: 4
838656 TAATAATAAT
838666 AATA AATA AATA AATA AATA AAGGTA AATA AATTA AA-A TAA-A AATA
1 AATA AATA AATA AATA AATA AA--TA AATA AA-TA AATA -AATA AATA
838712 AACTA AA-A AATA
1 AA-TA AATA AATA
838724 TTTTCCAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
3 6 0.13
4 29 0.62
5 8 0.17
6 4 0.09
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.22
Consensus pattern (4 bp):
AATA
Found at i:838707 original size:14 final size:13
Alignment explanation
Indices: 838632--838723 Score: 56
Period size: 12 Copynumber: 7.4 Consensus size: 13
838622 CCTTGCAACA
838632 AAATGAAAAT-AA-
1 AAAT-AAAATAAAT
* *
838644 AAATAAAATGAGT
1 AAATAAAATAAAT
838657 -AATAATAAT-AAT
1 AAATAA-AATAAAT
838669 AAAT-AAATAAAT
1 AAATAAAATAAAT
*
838681 AAATAAAGGTAAAT
1 AAATAAA-ATAAAT
838695 AAATTAAAAT-AA-
1 AAA-TAAAATAAAT
*
838707 AAATAAACTAAA-
1 AAATAAAATAAAT
838719 AAATA
1 AAATA
838724 TTTTCCAAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
11 13 0.20
12 30 0.45
13 10 0.15
14 9 0.14
15 4 0.06
ACGTcount: A:0.71, C:0.01, G:0.05, T:0.23
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:838784 original size:36 final size:37
Alignment explanation
Indices: 838715--838813 Score: 130
Period size: 36 Copynumber: 2.7 Consensus size: 37
838705 AAAAATAAAC
* *
838715 TAAAAAATATTTTCCAAAAATCTATATAATATATATTTT
1 TAAAAAATATTTT-CAAAATTATATATAATATAT-TTTT
*
838754 T-AAAAATATTTT-AAAATTATATATTATATATTTTT
1 TAAAAAATATTTTCAAAATTATATATAATATATTTTT
*
838789 TAAAAAATGTTTTCAAAATTATATA
1 TAAAAAATATTTTCAAAATTATATA
838814 GTTTTCAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
35 5 0.09
36 26 0.48
37 11 0.20
38 11 0.20
39 1 0.02
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.46
Consensus pattern (37 bp):
TAAAAAATATTTTCAAAATTATATATAATATATTTTT
Done.