Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008062.1 Hibiscus syriacus cultivar Beakdansim tig00110557_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: 2089609
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 9
Found at i:1777902 original size:64 final size:63
Alignment explanation
Indices: 1777768--1777929 Score: 204
Period size: 64 Copynumber: 2.5 Consensus size: 63
1777758 TTATTGTTGG
* *
1777768 GATGCATCGATGCACTCCTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAATGG
1 GATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCGATGTTTCACTATTAATGA
* *
1777832 GATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTCTTTA-TTTTAAAAT
1 GATGCATCGATGCACTACTTATGCATCGATGCACG-ATTGCATTCGATGT-TTCACTATT--AAT
1777896 -A
62 GA
**
1777897 G-TGCATCGATGCACTACCAATGCATCGATGCAC
1 GATGCATCGATGCACTACTTATGCATCGATGCAC
1777930 ATTCATATAA
Statistics
Matches: 88, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
63 2 0.02
64 79 0.90
65 4 0.05
66 3 0.03
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (63 bp):
GATGCATCGATGCACTACTTATGCATCGATGCACGATTGCATTCGATGTTTCACTATTAATGA
Found at i:1784133 original size:15 final size:15
Alignment explanation
Indices: 1784110--1784142 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1784100 CGTAGGACTC
1784110 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
1784125 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
1784140 CTA
1 CTA
1784143 TTATACCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.33, G:0.21, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:1784269 original size:29 final size:29
Alignment explanation
Indices: 1784227--1784300 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
1784217 TTTCATATGT
1784227 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1784255 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1784284 TCATGTAGCTCATGTCA
1 TCATGTAGCTCATGTCA
1784301 CTTCATATCA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.16
29 38 0.84
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:1784333 original size:12 final size:12
Alignment explanation
Indices: 1784316--1784361 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
1784306 TATCATGTTC
*
1784316 TCATATCACAGG
1 TCATATCACAGA
*
1784328 TCATATCACATA
1 TCATATCACAGA
*
1784340 TCATATCACATA
1 TCATATCACAGA
*
1784352 ACATATCACA
1 TCATATCACA
1784362 TGAACATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.41, C:0.26, G:0.04, T:0.28
Consensus pattern (12 bp):
TCATATCACAGA
Found at i:1784362 original size:12 final size:12
Alignment explanation
Indices: 1784329--1784370 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
1784319 TATCACAGGT
*
1784329 CATATCACATAT
1 CATATCACATAA
1784341 CATATCACATAA
1 CATATCACATAA
1784353 CATATCACATGAA
1 CATATCACAT-AA
1784366 CATAT
1 CATAT
1784371 ATATATCTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 21 0.75
13 7 0.25
ACGTcount: A:0.45, C:0.24, G:0.02, T:0.29
Consensus pattern (12 bp):
CATATCACATAA
Found at i:1784779 original size:64 final size:64
Alignment explanation
Indices: 1784671--1784847 Score: 198
Period size: 64 Copynumber: 2.8 Consensus size: 64
1784661 TAATGAAAGT
* * * ** * * **
1784671 ATGCATCGATGCACTACTGATGCATCGGTGCATC-AAAGGTATTCGATGTAGT-ATTATTGTTGG
1 ATGCATCGATGCACTACTTATACATCGATGCA-CGAATTGCATTCGATGT-GTCACTATTAATGG
1784734 G
64 G
* *
1784735 ATGCATCGATGCACTCCTTATACATCGATGCACCG-ATTGCATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATACATCGATGCA-CGAATTGCATTCGATGTGTCACTATTAATGGG
*
1784799 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT
1 ATGCATCGATGCACTACTTATACATCGATGCACGAATTGCATTCGATGT
1784848 CTTTATTTTA
Statistics
Matches: 96, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
63 3 0.03
64 93 0.97
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATACATCGATGCACGAATTGCATTCGATGTGTCACTATTAATGGG
Found at i:1784868 original size:64 final size:63
Alignment explanation
Indices: 1784671--1784895 Score: 197
Period size: 64 Copynumber: 3.5 Consensus size: 63
1784661 TAATGAAAGT
* * * ** * * * ** *
1784671 ATGCATCGATGCACTACTGATGCATCGGTGCATCAAAGGTATTCGATGTAGT-ATTATTGTTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCGATGT-TTCACTATTAATGAG
* * *
1784735 ATGCATCGATGCACTCCTTATACATCGATGCACCGATTGCATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCGATGTTTCACTATTAATGAG
* *
1784799 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTCTTTA-TTTTAAAAT-
1 ATGCATCGATGCACTACTTATGCATCGATGCACG-ATTGCATTCGATGT-TTCACTATT--AATG
1784862 AG
62 AG
**
1784864 -TGCATCGATGCACTACCAATGCATCGATGCAC
1 ATGCATCGATGCACTACTTATGCATCGATGCAC
1784896 ATTCATATAA
Statistics
Matches: 136, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
63 3 0.02
64 126 0.93
65 4 0.03
66 3 0.02
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGATTGCATTCGATGTTTCACTATTAATGAG
Found at i:1788285 original size:36 final size:36
Alignment explanation
Indices: 1788245--1788347 Score: 188
Period size: 36 Copynumber: 2.9 Consensus size: 36
1788235 ACGGTGCTGG
1788245 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
1 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
* *
1788281 ACATTGATACACGAATGTACCAAAGCTGAAATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
1788317 ACATTGATACACGAATGTACCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
1788348 ATACTCAACT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 64 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.22
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATAGGATA
Found at i:1799596 original size:3 final size:3
Alignment explanation
Indices: 1799590--1799614 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1799580 ACACAACAAC
1799590 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
1799615 CAAGCTTTTT
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:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1799984 original size:38 final size:38
Alignment explanation
Indices: 1799933--1800009 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
1799923 CATGCCTATT
1799933 TTCTCGCAAGTTAGCTAATTATTTTATATTATTAATAA
1 TTCTCGCAAGTTAGCTAATTATTTTATATTATTAATAA
*
1799971 TTCTCGCATGTTAGCTAATTATTTTATATTATTAATAA
1 TTCTCGCAAGTTAGCTAATTATTTTATATTATTAATAA
1800009 T
1 T
1800010 AATTCTATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.10, G:0.08, T:0.49
Consensus pattern (38 bp):
TTCTCGCAAGTTAGCTAATTATTTTATATTATTAATAA
Found at i:1807720 original size:13 final size:13
Alignment explanation
Indices: 1807699--1807728 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1807689 GTTTTTTAAT
*
1807699 TTTTTTTATTTTC
1 TTTTGTTATTTTC
1807712 TTTTGTTATTTTC
1 TTTTGTTATTTTC
1807725 TTTT
1 TTTT
1807729 TTTGTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.03, T:0.83
Consensus pattern (13 bp):
TTTTGTTATTTTC
Found at i:1807780 original size:22 final size:21
Alignment explanation
Indices: 1807734--1807781 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
1807724 CTTTTTTTGT
* *
1807734 TAATTTGTAGAATAAATATTT
1 TAATTTGGAGAATAAATATTA
1807755 TAATTTGGAGAATTAAA-ATATA
1 TAATTTGGAGAA-TAAATAT-TA
1807777 TAATT
1 TAATT
1807782 ATGTAACTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (21 bp):
TAATTTGGAGAATAAATATTA
Found at i:1820450 original size:79 final size:79
Alignment explanation
Indices: 1820299--1820451 Score: 182
Period size: 79 Copynumber: 1.9 Consensus size: 79
1820289 TTAATATAAA
* * * * * *
1820299 CCGGTAAAAAATTACTTAAAACATTATTATTTCTACCGATTTTTTATTATTGGGCGCTTTACCGG
1 CCGGTAAAAAACTACCTAAAACATTATTATTTCTACCGATTTTATATTATTGGGCACTTTACAGA
***
1820364 TTTTATTAACATAT
66 AAATATTAACATAT
* * *
1820378 CCGGTAAAATACTACCTAAAATATTATT-TTTCTTCCGATTTTGATATTATTGGGCACTTTACAG
1 CCGGTAAAAAACTACCTAAAACATTATTATTTCTACCGATTTT-ATATTATTGGGCACTTTACAG
1820442 AAAATATTAA
65 AAAATATTAA
1820452 AAAATATTAA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
78 13 0.21
79 48 0.79
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (79 bp):
CCGGTAAAAAACTACCTAAAACATTATTATTTCTACCGATTTTATATTATTGGGCACTTTACAGA
AAATATTAACATAT
Found at i:1820476 original size:21 final size:21
Alignment explanation
Indices: 1820451--1820490 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1820441 GAAAATATTA
*
1820451 AAAAATATTAATATTTTAAAT
1 AAAAATAATAATATTTTAAAT
1820472 AAAAATAATAATATTTTAA
1 AAAAATAATAATATTTTAA
1820491 GTAATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAAATAATAATATTTTAAAT
Found at i:1826619 original size:23 final size:22
Alignment explanation
Indices: 1826584--1826632 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
1826574 ATGATGTGCC
* *
1826584 AAAAATGATATGAGATAACAAA
1 AAAAATGATATGAAAGAACAAA
1826606 TAAAAATG-TCATGAAAGAACAAA
1 -AAAAATGAT-ATGAAAGAACAAA
1826629 AAAA
1 AAAA
1826633 TCATATTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.16
Consensus pattern (22 bp):
AAAAATGATATGAAAGAACAAA
Found at i:1829760 original size:18 final size:18
Alignment explanation
Indices: 1829737--1829773 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1829727 CCCAATTAAT
* *
1829737 TTTATGTTTGTTTGTTTG
1 TTTATGTTCGTTCGTTTG
1829755 TTTATGTTCGTTCGTTTG
1 TTTATGTTCGTTCGTTTG
1829773 T
1 T
1829774 GTTTGTTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.05, C:0.05, G:0.22, T:0.68
Consensus pattern (18 bp):
TTTATGTTCGTTCGTTTG
Found at i:1830993 original size:2 final size:2
Alignment explanation
Indices: 1830986--1831019 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1830976 CACACTCACA
1830986 AT 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 AT
1831020 CCGACTTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1831435 original size:43 final size:43
Alignment explanation
Indices: 1831386--1831483 Score: 126
Period size: 43 Copynumber: 2.3 Consensus size: 43
1831376 TGAGAACAAA
* *
1831386 AAACGCCGCAATAGGTCAATATCTATTA-CGACGTTTTTTGAAC
1 AAACGCCGCAAAAGGTCAATATCTA-TAGCGACGTTTTTGGAAC
* * *
1831429 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAT
1 AAACGCCGCAAAAGGTCAATATCTATAGCGACGTTTTTGGAAC
*
1831472 AAACGTCGCAAA
1 AAACGCCGCAAA
1831484 TATATAGCCG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
42 2 0.04
43 46 0.96
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCAATATCTATAGCGACGTTTTTGGAAC
Found at i:1831520 original size:56 final size:57
Alignment explanation
Indices: 1831433--1831545 Score: 176
Period size: 56 Copynumber: 2.0 Consensus size: 57
1831423 TTGAACAAAC
* *
1831433 GCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGA-ATAAACGTCGCAAATATATA
1 GCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAA-ATATA
*
1831490 GCCGCAAAATGTC-ATATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAATATA
1 GCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAATATA
1831546 AGACCTATAC
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
56 28 0.54
57 24 0.46
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (57 bp):
GCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAATATA
Found at i:1831592 original size:42 final size:43
Alignment explanation
Indices: 1831514--1831596 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 43
1831504 TATCTATAGC
* *
1831514 GGCGTTTTTGGATACAAACGCCGCAAAATATAAGACCTATACT
1 GGCGTTTTTAGATACAAACGCCGCAAAAGATAAGACCTATACT
* * *
1831557 GGCGTTTTTAGA-ACAAACGCCGTAAAAGGTCAGACCTATA
1 GGCGTTTTTAGATACAAACGCCGCAAAAGATAAGACCTATA
1831597 GTGCCAACAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
42 24 0.69
43 11 0.31
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (43 bp):
GGCGTTTTTAGATACAAACGCCGCAAAAGATAAGACCTATACT
Found at i:1835328 original size:125 final size:125
Alignment explanation
Indices: 1834983--1835384 Score: 558
Period size: 125 Copynumber: 3.2 Consensus size: 125
1834973 TTGTAAACTT
* * *
1834983 GCGGCGTTTGTAAACACAAACGCCTCTATAGTACAAGTGTATAGCGACGTTTGAATAAAAACGCT
1 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAGCGACGTTTGTATAAAAACGCC
*
1835048 ACTAAAGTACGAGTCTTTAGCAGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTA
66 ACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTA
* * * ** * *
1835108 GCGACGTTTGTAAACACAAAATGCCACTAAAGTACGCGTCTTTAGCGGA-GTTTGTATAAAAACG
1 GCGGCGTTTGTAAACAC-AAACGCCACTATAGTACAAGTGTATAGC-GACGTTTGTATAAAAACG
* * * *
1835172 CCACTAAAGTATGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAATTATGAGTGTTTA
64 CCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTA
* * *
1835234 GCGGCGTTTGTAAACACAAACGCCACTATAGTACATGTGTATAACGACGTTTGTATAAAAGCGCC
1 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAGCGACGTTTGTATAAAAACGCC
* * * *
1835299 ACTAAAGTACAAGTATATAGCGGCGTTTGTATAAAAATACCACTAAATTACGAGTCTTTA
66 ACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTA
*
1835359 GCGGCGTTTGTATA-A-AAACGCCACTA
1 GCGGCGTTTGTAAACACAAACGCCACTA
1835385 AAGTGTTACT
Statistics
Matches: 241, Mismatches: 33, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
123 11 0.05
124 3 0.01
125 118 0.49
126 107 0.44
127 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (125 bp):
GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAGCGACGTTTGTATAAAAACGCC
ACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTA
Found at i:1835398 original size:41 final size:41
Alignment explanation
Indices: 1834983--1835426 Score: 433
Period size: 41 Copynumber: 10.6 Consensus size: 41
1834973 TTGTAAACTT
* * * * * *
1834983 GCGGCGTTTGTAAACACAAACGCCTCTATAGTACAAGTGTATA
1 GCGGCGTTTGTATA-A-AAACGCCACTAAAGTACGAGTCTTTA
* * *
1835026 GCGACGTTTGAATAAAAACGCTACTAAAGTACGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * *
1835067 GCAGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * *
1835108 GCGACGTTTGTAAACACAAAATGCCACTAAAGTACGCGTCTTTA
1 GCGGCGTTTGT--ATA-AAAACGCCACTAAAGTACGAGTCTTTA
* *
1835152 GCGGAGTTTGTATAAAAACGCCACTAAAGTATGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * *
1835193 GCGGCGTTTGTATAAAAACGCCACTAAATTATGAGTGTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * *
1835234 GCGGCGTTTGTAAACACAAACGCCACTATAGTAC-ATGTGTATA
1 GCGGCGTTTGTATA-A-AAACGCCACTAAAGTACGA-GTCTTTA
* * * * * *
1835277 ACGACGTTTGTATAAAAGCGCCACTAAAGTACAAGTATATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
** *
1835318 GCGGCGTTTGTATAAAAATACCACTAAATTACGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
*** * *
1835359 GCGGCGTTTGTATAAAAACGCCACTAAAGTGTTACTCTTTT
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
1835400 GCGGCGTTTGT-TGAAAAAACGCCACTA
1 GCGGCGTTTGTAT--AAAAACGCCACTA
1835427 TCGATGAACC
Statistics
Matches: 335, Mismatches: 57, Indels: 19
0.82 0.14 0.05
Matches are distributed among these distances:
40 1 0.00
41 236 0.70
42 20 0.06
43 44 0.13
44 34 0.10
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (41 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
Found at i:1835406 original size:166 final size:165
Alignment explanation
Indices: 1835024--1835427 Score: 445
Period size: 166 Copynumber: 2.4 Consensus size: 165
1835014 TACAAGTGTA
* * * * * * * *
1835024 TAGCGACGTTTGAATAAAAACGCTACTAAAGTACGAGTCTTTAGCAGCGTTTG-TATAAAAATGC
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTATGACTCTTTAGCGGCGTTTGTTAAAAAAACGC
* * * * * * ** ** * *
1835088 CACTAAATTACGA-GTCTTTAGCGACGTTTGTAAACACAAAATGCCACTAAAGTACGCGTCTTTA
66 CACTATAGTAC-ATGTGTATAACGACGTTTGT--ATA-AAAGCGCCACTAAAGTACAAGTATATA
* *
1835152 GCGGAGTTTGTATAAAAACGCCACTAAAGTATGAGTCTT
127 GCGGAGTTTGTATAAAAACACCACTAAAGTACGAGTCTT
* * *
1835191 TAGCGGCGTTTGTATAAAAACGCCACTAAATTATGAGTGTTTAGCGGCGTTTG-TAAACACAAAC
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTATGACTCTTTAGCGGCGTTTGTTAAA-A-AAAC
1835255 GCCACTATAGTACATGTGTATAACGACGTTTGTATAAAAGCGCCACTAAAGTACAAGTATATAGC
64 GCCACTATAGTACATGTGTATAACGACGTTTGTATAAAAGCGCCACTAAAGTACAAGTATATAGC
* * *
1835320 GGCGTTTGTATAAAAATACCACTAAATTACGAGTCTT
129 GGAGTTTGTATAAAAACACCACTAAAGTACGAGTCTT
* * * *
1835357 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTGTTACTCTTTTGCGGCGTTTGTTGAAAAAACGC
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTATGACTCTTTAGCGGCGTTTGTTAAAAAAACGC
1835422 CACTAT
66 CACTAT
1835428 CGATGAACCT
Statistics
Matches: 200, Mismatches: 33, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
165 12 0.06
166 103 0.51
167 54 0.27
168 2 0.01
169 29 0.14
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29
Consensus pattern (165 bp):
TAGCGGCGTTTGTATAAAAACGCCACTAAAGTATGACTCTTTAGCGGCGTTTGTTAAAAAAACGC
CACTATAGTACATGTGTATAACGACGTTTGTATAAAAGCGCCACTAAAGTACAAGTATATAGCGG
AGTTTGTATAAAAACACCACTAAAGTACGAGTCTT
Found at i:1835499 original size:251 final size:250
Alignment explanation
Indices: 1834983--1835475 Score: 638
Period size: 251 Copynumber: 2.0 Consensus size: 250
1834973 TTGTAAACTT
* * *
1834983 GCGGCGTTTGTAAACACAAACGCCTCTATAGTACAAGTGTATAGCGACGTTTGAATAAAAACGCT
1 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGACGTTTGAATAAAAACGCC
* * * *
1835048 ACTAAAGTACGAGTCTTTAGCAGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCGAC
66 ACTAAAGTACAAGTATATAGCAGCGTTTGTATAAAAATACCACTAAATTACGAGTCTTTAGCGAC
* *
1835113 GTTTGTAAACACAAAATGCCACTAAAGTACGCGTCTTTAGCGGAGTTTGTATAAAAACGCCACTA
131 GTTTGT-AACACAAAACGCCACTAAAGTACACGTCTTTAGCGGAGTTTGTATAAAAACGCCACTA
** **
1835178 AAGTATGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAATTATGAGTGTTTA
195 AAGTATGAACCTTTAGCGGCGTTTGTATAAAAACGCCACTAAATTACCAGTGTTTA
* * *
1835234 GCGGCGTTTGTAAACACAAACGCCACTATAGTACATGTGTATAACGACGTTTGTATAAAAGCGCC
1 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGACGTTTGAATAAAAACGCC
* *
1835299 ACTAAAGTACAAGTATATAGCGGCGTTTGTATAAAAATACCACTAAATTACGAGTCTTTAGCGGC
66 ACTAAAGTACAAGTATATAGCAGCGTTTGTATAAAAATACCACTAAATTACGAGTCTTTAGCGAC
* ** * *
1835364 GTTTGT-ATA-AAAACGCCACTAAAGTGTTAC-TCTTTTGCGGCGTTTGT-TGAAAAAACGCCAC
131 GTTTGTAACACAAAACGCCACTAAAGT-ACACGTCTTTAGCGGAGTTTGTAT--AAAAACGCCAC
** * **
1835425 TATCG-ATGAACCTATT-GCGGCGTTTTTATAAAAACGCTGCTAAAGTTACCA
193 TAAAGTATGAACCT-TTAGCGGCGTTTGTATAAAAACGCCACTAAA-TTACCA
1835476 TTTTGTGGCG
Statistics
Matches: 209, Mismatches: 28, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
247 1 0.00
248 61 0.29
249 23 0.11
251 124 0.59
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (250 bp):
GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGACGTTTGAATAAAAACGCC
ACTAAAGTACAAGTATATAGCAGCGTTTGTATAAAAATACCACTAAATTACGAGTCTTTAGCGAC
GTTTGTAACACAAAACGCCACTAAAGTACACGTCTTTAGCGGAGTTTGTATAAAAACGCCACTAA
AGTATGAACCTTTAGCGGCGTTTGTATAAAAACGCCACTAAATTACCAGTGTTTA
Found at i:1835689 original size:14 final size:14
Alignment explanation
Indices: 1835642--1835681 Score: 62
Period size: 15 Copynumber: 2.8 Consensus size: 14
1835632 AAATATATTG
*
1835642 ATATTTAAAATAAT
1 ATATTTATAATAAT
1835656 ATATTTTATAATAAT
1 ATA-TTTATAATAAT
1835671 ATATTTATAAT
1 ATATTTATAAT
1835682 TATTTATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATTTATAATAAT
Found at i:1835725 original size:31 final size:30
Alignment explanation
Indices: 1835649--1835756 Score: 95
Period size: 31 Copynumber: 3.7 Consensus size: 30
1835639 TTGATATTTA
*
1835649 AAATAATATATTTTATAATA-AT-AT-ATT
1 AAATAATATATTTTATAATATTTAATAATT
* * *
1835676 -TATAAT-TA-TTTATTATATTTAA-ACTGCT
1 AAATAATATATTTTATAATATTTAATAAT--T
1835704 AAATAATATATTTTATAATATTTTAATAATT
1 AAATAATATATTTTATAATA-TTTAATAATT
1835735 AAATAATATATTTTAATAATAT
1 AAATAATATATTTT-ATAATAT
1835757 AAAAATTCTT
Statistics
Matches: 63, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
24 8 0.13
25 3 0.05
26 7 0.11
28 1 0.02
29 5 0.08
30 2 0.03
31 24 0.38
32 11 0.17
33 2 0.03
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (30 bp):
AAATAATATATTTTATAATATTTAATAATT
Found at i:1837232 original size:58 final size:58
Alignment explanation
Indices: 1837167--1837292 Score: 207
Period size: 58 Copynumber: 2.2 Consensus size: 58
1837157 GGCAAGATTG
* * *
1837167 AAGAAACTTGGACCACAAGTAATTGGATTTCGTATCTGCCAGTTAGAGTTTATATAGA
1 AAGAAACTTGGACCACAAGTAATTGAATTTCGTACCTGCCAGTTAGAGTTCATATAGA
**
1837225 AAGAAACTTGGATTACAAGTAATTGAATTTCGTACCTGCCAGTTAGAGTTCATATAGA
1 AAGAAACTTGGACCACAAGTAATTGAATTTCGTACCTGCCAGTTAGAGTTCATATAGA
1837283 AAGAAACTTG
1 AAGAAACTTG
1837293 CTTCCAATGT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 63 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (58 bp):
AAGAAACTTGGACCACAAGTAATTGAATTTCGTACCTGCCAGTTAGAGTTCATATAGA
Found at i:1842069 original size:111 final size:111
Alignment explanation
Indices: 1841671--1842229 Score: 672
Period size: 111 Copynumber: 5.0 Consensus size: 111
1841661 AGAGGGGCTT
* **
1841671 CTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGAGTTGTGCCTTGAGTGTATGACTGCTCATATC
1 CTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACTTGTGCCTTGAGCATATGACTGCTCATATC
* * *
1841736 GAGGTGATCCTATGTTTGATATAGTTCCGTTTGCATGAAAATTATGCTG
66 GAGGTGATCCCATGTTTGATACAGTTCCATTTGCATGAAAATT-T--TG
* * * * *
1841785 CTGCTGCTGAACCAGCTGGCCACTCCAGGCAGGACTTGTGCCTTGATCACATGTCTGCTCATAAC
1 CTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACTTGTGCCTTGAGCATATGACTGCTCATATC
* * *
1841850 GAGGTGATCCCATGCTTGATACAGTT-CATTGGCATGAAAATTCTGCG
66 GAGGTGATCCCATGTTTGATACAGTTCCATTTGCATGAAAATT-T-TG
* ** * * * * *
1841897 ACTGGTGCTGAACCAGCTGGCCGCTCCAGGCAGGACTTGTGCCTTGAGAACATGTCTGCTCACAG
1 -CTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACTTGTGCCTTGAGCATATGACTGCTCATAT
*
1841962 AGAGGTGATCCCATGTTTGATACAGTTCCATTTGCATGAAAATTTTG
65 CGAGGTGATCCCATGTTTGATACAGTTCCATTTGCATGAAAATTTTG
* * * * *
1842009 CTGCTGCTGAACCATCTGTCCATTCCAGGAAGGACCTGTGCCTTGAGCATATGACTGCTCACATC
1 CTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACTTGTGCCTTGAGCATATGACTGCTCATATC
* * * * *
1842074 CAGGTGATCCCATGTTTGGTACAATTCCATTTGCAGGAAAATTATG
66 GAGGTGATCCCATGTTTGATACAGTTCCATTTGCATGAAAATTTTG
** * * *
1842120 CTGCTGCTGAACCATTTGGCCATTCCAGGCA-GACCTGTACCTTGAGCATATGACGGCTCATATC
1 CTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACTTGTGCCTTGAGCATATGACTGCTCATATC
** * *
1842184 GAGGCAATCCCGTGTTTGGTACAGTTCCATTTGCATGAAAATTTTG
66 GAGGTGATCCCATGTTTGATACAGTTCCATTTGCATGAAAATTTTG
1842230 TTGTTGTTGC
Statistics
Matches: 387, Mismatches: 56, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
110 69 0.18
111 122 0.32
112 2 0.01
113 99 0.26
114 95 0.25
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.29
Consensus pattern (111 bp):
CTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACTTGTGCCTTGAGCATATGACTGCTCATATC
GAGGTGATCCCATGTTTGATACAGTTCCATTTGCATGAAAATTTTG
Found at i:1843609 original size:124 final size:123
Alignment explanation
Indices: 1843376--1843613 Score: 305
Period size: 124 Copynumber: 1.9 Consensus size: 123
1843366 CATGTGCTGG
* * * *
1843376 AAAAACATGATGTTTAAATTGAAAAACTGGCTCACATAATGATGGATTAAGCATTTAGAACCAAA
1 AAAAACATGAAGTTTAAACTGAAAAACTGGCTCACATAATGATAGATTAAGCATTTACAACCAAA
* * * *
1843441 TTATTACACATATGTCAGATATATCAAGAGTTGAGTAGCCACTTTAAATAGAGCGGGA
66 TTATTACACAAATGTCAGATATATCAAGACTTAAGTAGCAACTTTAAATAGAGCGGGA
* * * * * *
1843499 AAAAATATGAAGTTTACACTGAAGAACTGGCTCACATACTGATAGATTTGAGCATTTACTACCAA
1 AAAAACATGAAGTTTAAACTGAAAAACTGGCTCACATAATGATAGA-TTAAGCATTTACAACCAA
* * * *
1843564 ATTATTACATAAATGTCAGTTATATCAAGACTTAAGTGGTAACTTTAAAT
65 ATTATTACACAAATGTCAGATATATCAAGACTTAAGTAGCAACTTTAAAT
1843614 CACTTAATGA
Statistics
Matches: 96, Mismatches: 18, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
123 39 0.41
124 57 0.59
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (123 bp):
AAAAACATGAAGTTTAAACTGAAAAACTGGCTCACATAATGATAGATTAAGCATTTACAACCAAA
TTATTACACAAATGTCAGATATATCAAGACTTAAGTAGCAACTTTAAATAGAGCGGGA
Found at i:1852540 original size:16 final size:18
Alignment explanation
Indices: 1852509--1852542 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1852499 TTTACGAAAG
1852509 CTTTTTTCAACATTAGCT
1 CTTTTTTCAACATTAGCT
1852527 CTTTTTT-AAC-TTAGCT
1 CTTTTTTCAACATTAGCT
1852543 GGACAATGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 3 0.19
18 7 0.44
ACGTcount: A:0.21, C:0.21, G:0.06, T:0.53
Consensus pattern (18 bp):
CTTTTTTCAACATTAGCT
Found at i:1855155 original size:98 final size:98
Alignment explanation
Indices: 1854986--1855172 Score: 374
Period size: 98 Copynumber: 1.9 Consensus size: 98
1854976 ATGGAGTATC
1854986 TCCAAATCTGCCAACCCACATCAAGCAAGTAAATTTGTAAGCAACCCTATTTATCCTAGTACTTG
1 TCCAAATCTGCCAACCCACATCAAGCAAGTAAATTTGTAAGCAACCCTATTTATCCTAGTACTTG
1855051 AAGTGCAGGCACACAGGGTAGCAACCCTATTTA
66 AAGTGCAGGCACACAGGGTAGCAACCCTATTTA
1855084 TCCAAATCTGCCAACCCACATCAAGCAAGTAAATTTGTAAGCAACCCTATTTATCCTAGTACTTG
1 TCCAAATCTGCCAACCCACATCAAGCAAGTAAATTTGTAAGCAACCCTATTTATCCTAGTACTTG
1855149 AAGTGCAGGCACACAGGGTAGCAA
66 AAGTGCAGGCACACAGGGTAGCAA
1855173 AACAACAAAA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 89 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (98 bp):
TCCAAATCTGCCAACCCACATCAAGCAAGTAAATTTGTAAGCAACCCTATTTATCCTAGTACTTG
AAGTGCAGGCACACAGGGTAGCAACCCTATTTA
Found at i:1868932 original size:9 final size:9
Alignment explanation
Indices: 1868918--1868943 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1868908 TTTGGTAAAA
1868918 AATAAAATT
1 AATAAAATT
1868927 AATAAAATT
1 AATAAAATT
1868936 AATAAAAT
1 AATAAAAT
1868944 ATCATCCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AATAAAATT
Found at i:1870802 original size:175 final size:177
Alignment explanation
Indices: 1870494--1870841 Score: 583
Period size: 175 Copynumber: 2.0 Consensus size: 177
1870484 CTTTTATTTT
*
1870494 TTTTCTTTTTTGGTTGTAATCTCGTTCCAAGGCTTTGTATTGATTAATCTGGATCAACCCGGATT
1 TTTTCTTTTTTGGTTGCAATCTCGTTCCAAGGCTTTGTATTGATTAATCTGGATCAACCCGGATT
* ** *
1870559 ATACACCTAATTTTGGTGGGTGAGTCTCCCGACGGGGATTTTCTGCATACACAATGACTCGAACC
66 ATACACCTAACTTTGGTGGGTGAGTCTCCCGACGAAGATTTTCTGCATACACAATAACTCGAACC
* * *
1870624 TGAGACAATACTTAAACGATATCAAACTGCTTACTATTTAAACAAAC
131 TGAGACAATAATTAAACGATATAAAACTGCTTACTACTTAAACAAAC
*
1870671 TTTT-TTTTTT-GTTGCAATCTCGTTCCAAGGCTTTGTCTTGATTAATCTGGATCAACCCGGATT
1 TTTTCTTTTTTGGTTGCAATCTCGTTCCAAGGCTTTGTATTGATTAATCTGGATCAACCCGGATT
*
1870734 ATACACCTGACTTTGGTGGGTGAGTCTCCCGACGAAGATTTTCTGCATACACAATAACTCGAACC
66 ATACACCTAACTTTGGTGGGTGAGTCTCCCGACGAAGATTTTCTGCATACACAATAACTCGAACC
*
1870799 TGAGACATTAATTAAACGATATAAAACTGCTTACTACTTAAAC
131 TGAGACAATAATTAAACGATATAAAACTGCTTACTACTTAAAC
1870842 TTATTTGATA
Statistics
Matches: 160, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
175 150 0.94
176 6 0.04
177 4 0.03
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (177 bp):
TTTTCTTTTTTGGTTGCAATCTCGTTCCAAGGCTTTGTATTGATTAATCTGGATCAACCCGGATT
ATACACCTAACTTTGGTGGGTGAGTCTCCCGACGAAGATTTTCTGCATACACAATAACTCGAACC
TGAGACAATAATTAAACGATATAAAACTGCTTACTACTTAAACAAAC
Found at i:1875916 original size:182 final size:183
Alignment explanation
Indices: 1875668--1876055 Score: 604
Period size: 182 Copynumber: 2.1 Consensus size: 183
1875658 AACCGAAATT
*
1875668 AAATATTAAATATATTATATATAACATATAGACTCAGCCCAAACCATTTAAAACTCAATTAATAA
1 AAATATTAAATATA-T-TATATAACATATAGACTAAGCCCAAACCATTTAAAACTCAATTAATAA
* * *
1875733 TTTAAGATCTAATAACTTTTAAACCTAAATCAATATTAATTAATTTA-AAATTTTATAT-AAAAT
64 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAAATAA-TTAGAAAATTTATATGAAAAT
*
1875796 TTTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTT-AATTAAA
128 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTTGAATTAAA
* * *
1875852 AAATATTAAATATATTATATAACATATGGGCTAAGCCTAAACCATTTAAAACTCAATTAATAATT
1 AAATATTAAATATATTATATAACATATAGACTAAGCCCAAACCATTTAAAACTCAATTAATAATT
* *
1875917 TAAGATCCAATAACTTTTAAACCTAAATCAATATTAAATAATTAGAAAATTTATCTGAAATTTTT
66 TAAGATCCAATAACTTTTAAACCTAAATCAATATTAAATAATTAGAAAATTTATATGAAAATTTT
1875982 ATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTTGAATTAAA
131 ATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTTGAATTAAA
* *
1876035 AAATATTTAAT-TTTTATATAA
1 AAATATTAAATATATTATATAA
1876056 ATTATAAAAT
Statistics
Matches: 189, Mismatches: 12, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
181 3 0.02
182 110 0.58
183 62 0.33
184 14 0.07
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (183 bp):
AAATATTAAATATATTATATAACATATAGACTAAGCCCAAACCATTTAAAACTCAATTAATAATT
TAAGATCCAATAACTTTTAAACCTAAATCAATATTAAATAATTAGAAAATTTATATGAAAATTTT
ATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTTGAATTAAA
Found at i:1878645 original size:36 final size:36
Alignment explanation
Indices: 1878612--1878679 Score: 104
Period size: 35 Copynumber: 1.9 Consensus size: 36
1878602 TACAAATTGT
1878612 AAAATATTTATA-AATTTTCTTTA-AAAATTAAATTC
1 AAAATATTTATATAATTTT-TTTACAAAATTAAATTC
*
1878647 ATAATATTTATATAATTTTTTTACAAAATTAAA
1 AAAATATTTATATAATTTTTTTACAAAATTAAA
1878680 AATATAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
35 15 0.50
36 15 0.50
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (36 bp):
AAAATATTTATATAATTTTTTTACAAAATTAAATTC
Found at i:1887789 original size:60 final size:60
Alignment explanation
Indices: 1887713--1887860 Score: 161
Period size: 60 Copynumber: 2.5 Consensus size: 60
1887703 TTTCATTTTG
* * *
1887713 AATTAGTCATTAAACTTTTGAATATTCCAATTTCATGCTCAAACCATGACTCTTATTCTA
1 AATTAGTCCTTAAACTTTTGAATATTCCAATTTCATACTCAAACCATGACCCTTATTCTA
* * ** * * * * *
1887773 ATTTAGTCCTTGAACTTTAAAACATTCTAATTTCATACTTAAACTATGACCCTTCTTCTA
1 AATTAGTCCTTAAACTTTTGAATATTCCAATTTCATACTCAAACCATGACCCTTATTCTA
* * *
1887833 AATTGGTCCCTAAACTATTGAATATTCC
1 AATTAGTCCTTAAACTTTTGAATATTCC
1887861 GCTTTCATCC
Statistics
Matches: 67, Mismatches: 21, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
60 67 1.00
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.40
Consensus pattern (60 bp):
AATTAGTCCTTAAACTTTTGAATATTCCAATTTCATACTCAAACCATGACCCTTATTCTA
Found at i:1893212 original size:69 final size:66
Alignment explanation
Indices: 1893064--1893250 Score: 261
Period size: 69 Copynumber: 2.8 Consensus size: 66
1893054 CGCCGTGAAC
** * * *
1893064 GTCGGAAAGGGCGGAG-TACATGTGAACACCGGGAAAGGAAAGCCAGGTGGTGGCACTCACGTGA
1 GTCGGAAAGGGCGGAGTTGGA-GTGAACACCGGGAAAGGAAAGCCAGGCGGCGGCACTCACGTAA
1893128 AT
65 AT
1893130 GTCGGAAAGGGCGGAGTTGGAGTGAACACCGGGAAAGGAAAGCCAGGGGGCGGCGGCACTCACGT
1 GTCGGAAAGGGCGGAGTTGGAGTGAACACCGGGAAAGGAAAGCCA---GGCGGCGGCACTCACGT
1893195 AAAT
63 AAAT
* *
1893199 GTCGGAAAGGGCGGAGTTGGAGTGAACACCGGGAAA-AAAAACCAGGCGGCGG
1 GTCGGAAAGGGCGGAGTTGGAGTGAACACCGGGAAAGGAAAGCCAGGCGGCGG
1893251 TGGCAGTCAT
Statistics
Matches: 110, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
65 8 0.07
66 40 0.36
67 2 0.02
68 6 0.05
69 54 0.49
ACGTcount: A:0.30, C:0.18, G:0.41, T:0.11
Consensus pattern (66 bp):
GTCGGAAAGGGCGGAGTTGGAGTGAACACCGGGAAAGGAAAGCCAGGCGGCGGCACTCACGTAAA
T
Found at i:1895557 original size:41 final size:41
Alignment explanation
Indices: 1895495--1895576 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
1895485 AACTGAAAAT
*
1895495 CGGTTGTTTTACGGGAACTTGATGCTGTACAATCTGAGGAC
1 CGGTTGTTTTACGGGAACTTGAAGCTGTACAATCTGAGGAC
1895536 CGGTTGTTTTAC-GGAACCTTGAAGCTGTACAATCTGAGGAC
1 CGGTTGTTTTACGGGAA-CTTGAAGCTGTACAATCTGAGGAC
1895577 TTTGCACCGT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 4 0.10
41 35 0.90
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.30
Consensus pattern (41 bp):
CGGTTGTTTTACGGGAACTTGAAGCTGTACAATCTGAGGAC
Found at i:1895930 original size:21 final size:22
Alignment explanation
Indices: 1895895--1895936 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1895885 TTTATTATTA
*
1895895 TTTTAATTATAAAATTAATTTT
1 TTTTAATTATAAAATAAATTTT
*
1895917 TTTTAA-TATTAAATAAATTT
1 TTTTAATTATAAAATAAATTT
1895937 CAAATTGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTAATTATAAAATAAATTTT
Found at i:1900894 original size:13 final size:13
Alignment explanation
Indices: 1900876--1900901 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1900866 CGTTTGTCAT
1900876 CAATTTAACAAAA
1 CAATTTAACAAAA
1900889 CAATTTAACAAAA
1 CAATTTAACAAAA
1900902 ATAAAAGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (13 bp):
CAATTTAACAAAA
Found at i:1902566 original size:20 final size:21
Alignment explanation
Indices: 1902541--1902581 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1902531 CTTTACCCCT
1902541 TATTTTA-ATATTG-TAGTAAA
1 TATTTTATA-ATTGATAGTAAA
1902561 TATTTTATAATTGATAGTAAA
1 TATTTTATAATTGATAGTAAA
1902582 ATTAAATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (21 bp):
TATTTTATAATTGATAGTAAA
Found at i:1910289 original size:21 final size:22
Alignment explanation
Indices: 1910265--1910317 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
1910255 TAGAAATATT
* *
1910265 TATTTTAAG-TAGTAAAATTAA
1 TATTTTAAGATAGAAAAAATAA
*
1910286 TATTTT-CGATAGAAAAAATAA
1 TATTTTAAGATAGAAAAAATAA
1910307 TATTTT-AGATA
1 TATTTTAAGATA
1910318 ACGCTATACA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (22 bp):
TATTTTAAGATAGAAAAAATAA
Found at i:1914784 original size:18 final size:19
Alignment explanation
Indices: 1914749--1914785 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1914739 CACGAAATGT
1914749 AAGATTATCAGTGGGAATAA
1 AAGATTATCAG-GGGAATAA
1914769 AAGATTATCA-GGGAATA
1 AAGATTATCAGGGGAATA
1914786 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.05, G:0.24, T:0.24
Consensus pattern (19 bp):
AAGATTATCAGGGGAATAA
Found at i:1915506 original size:13 final size:13
Alignment explanation
Indices: 1915488--1915512 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1915478 TTAATTGCAT
1915488 AACGTCACTACCA
1 AACGTCACTACCA
1915501 AACGTCACTACC
1 AACGTCACTACC
1915513 TGCAAAACTT
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:0.36, C:0.40, G:0.08, T:0.16
Consensus pattern (13 bp):
AACGTCACTACCA
Found at i:1917228 original size:25 final size:25
Alignment explanation
Indices: 1917196--1917246 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1917186 AGTAACAAAT
1917196 AACCTAAATCCCAAAATAATTCTCA
1 AACCTAAATCCCAAAATAATTCTCA
1917221 AACCTAAATCCCAAAATAATTCTCA
1 AACCTAAATCCCAAAATAATTCTCA
1917246 A
1 A
1917247 CCACCCATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (25 bp):
AACCTAAATCCCAAAATAATTCTCA
Found at i:1927193 original size:15 final size:16
Alignment explanation
Indices: 1927167--1927197 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1927157 ACGTAAAGAG
1927167 TTATTATTTTAAAACA
1 TTATTATTTTAAAACA
1927183 TTATT-TTTTAAAACA
1 TTATTATTTTAAAACA
1927198 AGCTCATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATTATTTTAAAACA
Found at i:1931190 original size:13 final size:13
Alignment explanation
Indices: 1931172--1931196 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1931162 AAATGGTTGA
1931172 GAATATTTAAAAC
1 GAATATTTAAAAC
1931185 GAATATTTAAAA
1 GAATATTTAAAA
1931197 TATGTATAAG
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:0.04, G:0.08, T:0.32
Consensus pattern (13 bp):
GAATATTTAAAAC
Found at i:1931346 original size:2 final size:2
Alignment explanation
Indices: 1931339--1931369 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1931329 TGATGAATGC
1931339 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1931370 ATTAGTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1931676 original size:32 final size:32
Alignment explanation
Indices: 1931635--1931701 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
1931625 CAAGGATCAC
*
1931635 TTTGTAATAGTTAAATAAAATTTAATGATTAT
1 TTTGTAATAGTTAAATAAAATTTAATGACTAT
** * *
1931667 TTTGTAATAGTTTGATGAAGTTTAATGACTAT
1 TTTGTAATAGTTAAATAAAATTTAATGACTAT
1931699 TTT
1 TTT
1931702 ATAACTTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.36, C:0.01, G:0.13, T:0.49
Consensus pattern (32 bp):
TTTGTAATAGTTAAATAAAATTTAATGACTAT
Found at i:1932885 original size:2 final size:2
Alignment explanation
Indices: 1932878--1932943 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
1932868 TAGACCCGTA
1932878 AT AT AT AT AT 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 AT AT AT AT AT
1932920 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
1932944 CTATTCTATA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1934194 original size:25 final size:25
Alignment explanation
Indices: 1934160--1934210 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1934150 TACCTAAGAG
1934160 TTCCAAACTCCCAGCAAAGTTTGTA
1 TTCCAAACTCCCAGCAAAGTTTGTA
1934185 TTCCAAACTCCCAGCAAAGTTTGTA
1 TTCCAAACTCCCAGCAAAGTTTGTA
1934210 T
1 T
1934211 CTATGATATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.29
Consensus pattern (25 bp):
TTCCAAACTCCCAGCAAAGTTTGTA
Found at i:1940866 original size:35 final size:35
Alignment explanation
Indices: 1940822--1940895 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 35
1940812 CATAATCCTT
*
1940822 AATTTCATTTTAAACCCCAAATTCCAAAATAATTC
1 AATTACATTTTAAACCCCAAATTCCAAAATAATTC
* * *
1940857 AATTACATTTTAAACCCTAAATTCTAAAATATTTC
1 AATTACATTTTAAACCCCAAATTCCAAAATAATTC
1940892 AATT
1 AATT
1940896 TAGGGTTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.43, C:0.19, G:0.00, T:0.38
Consensus pattern (35 bp):
AATTACATTTTAAACCCCAAATTCCAAAATAATTC
Found at i:1940931 original size:35 final size:35
Alignment explanation
Indices: 1940892--1940959 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
1940882 AAAATATTTC
* *
1940892 AATTTAGGGTTTATAATATAATTAAAGTATTTTGG
1 AATTTAGGATTTAGAATATAATTAAAGTATTTTGG
* * *
1940927 AATTTAGGATTTAGAATGTAATTGAAGTGTTTT
1 AATTTAGGATTTAGAATATAATTAAAGTATTTT
1940960 TGGAGCTTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (35 bp):
AATTTAGGATTTAGAATATAATTAAAGTATTTTGG
Found at i:1942223 original size:29 final size:30
Alignment explanation
Indices: 1942152--1942211 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1942142 CAATTTAAGG
1942152 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
1942183 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
1942212 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1942349 original size:22 final size:21
Alignment explanation
Indices: 1942301--1942343 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1942291 TTCAAGATTG
* *
1942301 CCCAGGGGGTATAGATTCCCC
1 CCCAGGGGGTACAGATACCCC
1942322 CCCAGGGGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
1942343 C
1 C
1942344 TGCAGGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.37, G:0.28, T:0.14
Consensus pattern (21 bp):
CCCAGGGGGTACAGATACCCC
Found at i:1942460 original size:21 final size:21
Alignment explanation
Indices: 1942434--1942476 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1942424 ATTTGAATAT
*
1942434 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1942455 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1942476 T
1 T
1942477 CTATTTTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:1945715 original size:29 final size:30
Alignment explanation
Indices: 1945644--1945703 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1945634 CAATTTAAGG
1945644 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
1945675 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
1945704 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1945821 original size:21 final size:21
Alignment explanation
Indices: 1945796--1945835 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1945786 AAGATTGCCC
* *
1945796 AGGGGGTATAGATTCCCCCCT
1 AGGGGGTACAGATACCCCCCT
1945817 AGGGGGTACAGATACCCCC
1 AGGGGGTACAGATACCCCC
1945836 TGCAGGTTTT
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:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (21 bp):
AGGGGGTACAGATACCCCCCT
Found at i:1945951 original size:21 final size:21
Alignment explanation
Indices: 1945926--1945966 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1945916 ATTTGAATAT
1945926 TATGAAGGGGTATCGATTCCA
1 TATGAAGGGGTATCGATTCCA
1945947 TATGAAGGGGTATCGATTCC
1 TATGAAGGGGTATCGATTCC
1945967 CTCTATTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTATCGATTCCA
Found at i:1946025 original size:21 final size:21
Alignment explanation
Indices: 1945996--1946035 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1945986 TTTGAGTATA
1945996 AAAATCATCCCCAAACGGCTCC
1 AAAATCAT-CCCAAACGGCTCC
*
1946018 AAAA-CATCCCTAACGGCT
1 AAAATCATCCCAAACGGCT
1946036 ATATACGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 3 0.18
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCAAACGGCTCC
Found at i:1949200 original size:16 final size:17
Alignment explanation
Indices: 1949179--1949212 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1949169 TTTTTTTATT
*
1949179 ATTTAATATA-AAAATA
1 ATTTAAAATATAAAATA
1949195 ATTTAAAATATAAAATA
1 ATTTAAAATATAAAATA
1949212 A
1 A
1949213 AACCCAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTTAAAATATAAAATA
Found at i:1949428 original size:16 final size:17
Alignment explanation
Indices: 1949393--1949425 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1949383 AAATATTATT
1949393 TTATTATTTATTTTAAA
1 TTATTATTTATTTTAAA
1949410 TTATT-TTTATATTTAA
1 TTATTATTTAT-TTTAA
1949426 TTACAGTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTATTTATTTTAAA
Found at i:1954655 original size:20 final size:20
Alignment explanation
Indices: 1954630--1954675 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1954620 TATATAATCA
* *
1954630 CAACGCGATTTTGATTATCG
1 CAACGCGATTCTGACTATCG
*
1954650 CAACGCGATTCTGACTGTCG
1 CAACGCGATTCTGACTATCG
1954670 CAACGC
1 CAACGC
1954676 TGAATTTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (20 bp):
CAACGCGATTCTGACTATCG
Found at i:1955523 original size:24 final size:24
Alignment explanation
Indices: 1955491--1955544 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1955481 GTATTCAAAA
1955491 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1955515 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1955539 TTTGAT
1 TTTGAT
1955545 GATGTTTCAG
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:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1955763 original size:14 final size:14
Alignment explanation
Indices: 1955734--1955770 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1955724 AGAAAAAGAA
1955734 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
1955749 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
1955763 GAAGAAAA
1 GAAGAAAA
1955771 TGCCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:1958088 original size:135 final size:138
Alignment explanation
Indices: 1957880--1958157 Score: 490
Period size: 135 Copynumber: 2.0 Consensus size: 138
1957870 GCAAACGTTG
1957880 TATTATCTGTATTTTATGTGTAAACTATTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATCTGTATTTTATGTGTAAACTATTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1957945 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTG-A-A-CAACGCG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATACCAACGCG
1958007 AATTTGAC
131 AATTTGAC
* *
1958015 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATCTGTATTTTATGTGTAAACTATTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
1958080 TTGAACATTGCTATGATCTGTTCAGTTGTTATCATTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATA-C-CAACG
1958145 CGAATTTGAC
129 CGAATTTGAC
1958155 TAT
1 TAT
1958158 CGCAACACGA
Statistics
Matches: 135, Mismatches: 3, Indels: 5
0.94 0.02 0.03
Matches are distributed among these distances:
135 115 0.85
136 1 0.01
137 1 0.01
140 18 0.13
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.43
Consensus pattern (138 bp):
TATTATCTGTATTTTATGTGTAAACTATTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATACCAACGCG
AATTTGAC
Found at i:1958153 original size:20 final size:20
Alignment explanation
Indices: 1958128--1958273 Score: 162
Period size: 20 Copynumber: 7.7 Consensus size: 20
1958118 TTACACATTC
*
1958128 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1958148 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
1958168 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
1958188 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
*
1958208 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
1958228 A----A--ATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
*
1958242 ATTAGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1958262 A-TTGACTTTCGC
1 ATTTGACTATCGC
1958274 GTTGCGATTT
Statistics
Matches: 106, Mismatches: 14, Indels: 13
0.80 0.11 0.10
Matches are distributed among these distances:
14 10 0.09
16 1 0.01
18 1 0.01
19 9 0.08
20 85 0.80
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:1958326 original size:20 final size:20
Alignment explanation
Indices: 1958263--1958340 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
1958253 GCAACGCGAA
*
1958263 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCATTGCGATT
* *
1958283 TTGGCTTTCGCATTACGATT
1 TTGACTTTCGCATTGCGATT
1958303 TTGACTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
* * *
1958323 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCATTGCGA
1958341 AAGTGTACCT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.14, C:0.18, G:0.24, T:0.44
Consensus pattern (20 bp):
TTGACTTTCGCATTGCGATT
Found at i:1958497 original size:63 final size:65
Alignment explanation
Indices: 1958414--1958549 Score: 240
Period size: 63 Copynumber: 2.1 Consensus size: 65
1958404 TTTATATTTC
*
1958414 AATCAATTAAATAAGCACAAATAAGAATTATTTACACAT-AA-ATTAAACAAAGCAACTTTTACA
1 AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATATTAAACAAAGCAACTTTTACA
*
1958477 AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATATTAAACAAATCAACTTTTACA
1 AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATATTAAACAAAGCAACTTTTACA
1958542 AATCAATT
1 AATCAATT
1958550 TTACAAATCA
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
63 38 0.55
64 2 0.03
65 29 0.42
ACGTcount: A:0.53, C:0.15, G:0.04, T:0.28
Consensus pattern (65 bp):
AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATATTAAACAAAGCAACTTTTACA
Found at i:1958541 original size:29 final size:27
Alignment explanation
Indices: 1958507--1958560 Score: 72
Period size: 29 Copynumber: 1.9 Consensus size: 27
1958497 ATAAGAATTA
*
1958507 TTTACACATCAATATTAAACAAATCAACT
1 TTTACAAATCAAT-TT-AACAAATCAACT
*
1958536 TTTACAAATCAATTTTACAAATCAA
1 TTTACAAATCAATTTAACAAATCAA
1958561 TTAAACAAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 9 0.39
28 2 0.09
29 12 0.52
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.33
Consensus pattern (27 bp):
TTTACAAATCAATTTAACAAATCAACT
Found at i:1958553 original size:13 final size:13
Alignment explanation
Indices: 1958525--1958562 Score: 67
Period size: 13 Copynumber: 2.8 Consensus size: 13
1958515 TCAATATTAA
1958525 ACAAATCAACTTTT
1 ACAAATCAA-TTTT
1958539 ACAAATCAATTTT
1 ACAAATCAATTTT
1958552 ACAAATCAATT
1 ACAAATCAATT
1958563 AAACAAGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 15 0.62
14 9 0.38
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.34
Consensus pattern (13 bp):
ACAAATCAATTTT
Found at i:1958568 original size:13 final size:13
Alignment explanation
Indices: 1958520--1958568 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
1958510 ACACATCAAT
1958520 ATTAAACAAATCA
1 ATTAAACAAATCA
**
1958533 ACTTTTACAAATCA
1 A-TTAAACAAATCA
**
1958547 ATTTTACAAATCA
1 ATTAAACAAATCA
1958560 ATTAAACAA
1 ATTAAACAA
1958569 GCAAAAAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
13 20 0.65
14 11 0.35
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (13 bp):
ATTAAACAAATCA
Found at i:1959969 original size:21 final size:21
Alignment explanation
Indices: 1959945--1960018 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
1959935 GGGAGGGACA
*
1959945 TCTTCAACGATGATAGGGGCC
1 TCTTGAACGATGATAGGGGCC
* ** *
1959966 TCTTGAACAATGGGAGGGGAC
1 TCTTGAACGATGATAGGGGCC
**
1959987 TCTTGAGGGATGATAGGGGCC
1 TCTTGAACGATGATAGGGGCC
1960008 TCTTGAACGAT
1 TCTTGAACGAT
1960019 AGGAGATGCC
Statistics
Matches: 40, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.24, C:0.18, G:0.34, T:0.24
Consensus pattern (21 bp):
TCTTGAACGATGATAGGGGCC
Found at i:1959971 original size:42 final size:42
Alignment explanation
Indices: 1959934--1960015 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
1959924 TCTTGAATGG
1959934 TGGGA-GGGACATCTTCAACGATGATAGGGGCCTCTTGAACAA
1 TGGGAGGGGAC-TCTTCAACGATGATAGGGGCCTCTTGAACAA
* **
1959976 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAAC
1 TGGGAGGGGACTCTTCAACGATGATAGGGGCCTCTTGAAC
1960016 GATAGGAGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 31 0.86
43 5 0.14
ACGTcount: A:0.24, C:0.17, G:0.37, T:0.22
Consensus pattern (42 bp):
TGGGAGGGGACTCTTCAACGATGATAGGGGCCTCTTGAACAA
Found at i:1960041 original size:42 final size:42
Alignment explanation
Indices: 1959936--1960041 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 42
1959926 TTGAATGGTG
* *
1959936 GGAG-GGACATCTTCAACGATGATAGGGGCCTCTTGAACAATG
1 GGAGAGGAC-TCTTAAACGATGATAGGGGCCTCTTGAACAATA
* * ** *
1959978 GGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGATA
1 GGAGAGGACTCTTAAACGATGATAGGGGCCTCTTGAACAATA
* *
1960020 GGAGATGCCTCTTAAACGATGA
1 GGAGAGGACTCTTAAACGATGA
1960042 CAGGTGAGTC
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 48 0.92
43 4 0.08
ACGTcount: A:0.27, C:0.17, G:0.34, T:0.22
Consensus pattern (42 bp):
GGAGAGGACTCTTAAACGATGATAGGGGCCTCTTGAACAATA
Found at i:1960551 original size:19 final size:20
Alignment explanation
Indices: 1960515--1960557 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
1960505 AATAGTTTCT
*
1960515 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCACAACAC
*
1960535 GAAACTT-AAATCACAACGC
1 GAAACTTAAAATCACAACAC
1960554 GAAA
1 GAAA
1960558 ATGACTATCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.51, C:0.23, G:0.12, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAATCACAACAC
Found at i:1960573 original size:20 final size:20
Alignment explanation
Indices: 1960548--1960612 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
1960538 ACTTAAATCA
1960548 CAACGCGAAAATGACTATCG
1 CAACGCGAAAATGACTATCG
*
1960568 CAACGCGGAAATGACTATCG
1 CAACGCGAAAATGACTATCG
**
1960588 CAACGCGAATTTGACTATCG
1 CAACGCGAAAATGACTATCG
1960608 CAACG
1 CAACG
1960613 GGATAATCGC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (20 bp):
CAACGCGAAAATGACTATCG
Found at i:1960715 original size:32 final size:34
Alignment explanation
Indices: 1960660--1960757 Score: 128
Period size: 32 Copynumber: 2.9 Consensus size: 34
1960650 AATAAATTCG
1960660 CGTTGCGATAGTCATTTTCGCATTGCGATTTTCA
1 CGTTGCGATAGTCATTTTCGCATTGCGATTTTCA
* * * * *
1960694 CGTTGCGAT-TTTA-TTTCGCATTGCAATTATCC
1 CGTTGCGATAGTCATTTTCGCATTGCGATTTTCA
*
1960726 CGTTGCGATAGTCATTTTCGCGTTGCGATTTT
1 CGTTGCGATAGTCATTTTCGCATTGCGATTTT
1960758 AAGTTTCGTG
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
32 25 0.48
33 4 0.08
34 23 0.44
ACGTcount: A:0.16, C:0.20, G:0.20, T:0.43
Consensus pattern (34 bp):
CGTTGCGATAGTCATTTTCGCATTGCGATTTTCA
Found at i:1962737 original size:20 final size:20
Alignment explanation
Indices: 1962645--1962737 Score: 71
Period size: 20 Copynumber: 4.7 Consensus size: 20
1962635 CTGAAACTTT
1962645 TATCGCAACACGAAAATGAA
1 TATCGCAACACGAAAATGAA
* * * *
1962665 AATTGCAACACAAAAATGAC
1 TATCGCAACACGAAAATGAA
** *
1962685 TATCGCAATGCG-AATTGAA
1 TATCGCAACACGAAAATGAA
* * * *
1962704 AATCGTAATACGAAAATGAC
1 TATCGCAACACGAAAATGAA
*
1962724 TATCGCAACGCGAA
1 TATCGCAACACGAA
1962738 TTAAACTATC
Statistics
Matches: 52, Mismatches: 20, Indels: 2
0.70 0.27 0.03
Matches are distributed among these distances:
19 14 0.27
20 38 0.73
ACGTcount: A:0.46, C:0.19, G:0.16, T:0.18
Consensus pattern (20 bp):
TATCGCAACACGAAAATGAA
Found at i:1963083 original size:22 final size:22
Alignment explanation
Indices: 1963055--1963111 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
1963045 GATGGATATA
1963055 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1963077 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1963099 GACGGATGTCGCC
1 GACGGATTTCGCC
1963112 TTAGAGAGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.18, C:0.19, G:0.44, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1965080 original size:8 final size:8
Alignment explanation
Indices: 1965067--1965091 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1965057 AATCAGTTAT
1965067 ATTATTAA
1 ATTATTAA
1965075 ATTATTAA
1 ATTATTAA
1965083 ATTATTAA
1 ATTATTAA
1965091 A
1 A
1965092 CCATTAATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATTATTAA
Found at i:1966438 original size:260 final size:267
Alignment explanation
Indices: 1965926--1966455 Score: 887
Period size: 260 Copynumber: 2.0 Consensus size: 267
1965916 ACATAAAATC
* *
1965926 ATGTGTCCGTCCTGTAAACCTTACATATGGAAAAAAAAATAATAATAAAAACATAATTTTTTTTG
1 ATGTGTCCGTCCTGTAAACCTTACATATGGAAAAAAAAATAATAAAAAAAAAATAATTTTTTTTG
1965991 TTAATATGGGGTAAATACAAGATAATATTTGTTCATAGATAACTCTCTATCATTTGACATTGAAC
66 TTAATATGGGGTAAATACAAGATAATATTTGTTCATAGATAACTCTCTATCATTTGACATTGAAC
* *
1966056 GTTTACGCCTCTAATATTTCTGGTACTTAAACTCAGAATCTTAAAGAATAACAATAATTCTTTTA
131 GTTTACGCCTCTAATATTTCTGGTACTCAAACTCAGAATCTCAAAGAATAACAATAATTCTTTTA
* * *
1966121 TTACTGAGCTCGTATAAAGGGATTGAAGAAGAGGAAGAGGGCAGGTGGGATTTTCAAACGGTTTA
196 TTACCGAGCTCGTATAAAGGGATTGAAGAAGAGGAAGAGAGCAGGTGGGACTTTCAAACGGTTTA
1966186 AGCCGTT
261 AGCCGTT
1966193 ATGTGTCCGTCCTGTAAACCTTACATATGGAAAAATAAAATAATAAAAAAAAAATAA-TTTTTTT
1 ATGTGTCCGTCCTGTAAACCTTACATATGGAAAAA-AAAATAATAAAAAAAAAATAATTTTTTTT
* * **
1966257 GTTAATATGGGGTAAATATAAGATAATA-TTGTTTATAGATAACTC-C-ATCATTTGTTATTGAA
65 GTTAATATGGGGTAAATACAAGATAATATTTGTTCATAGATAACTCTCTATCATTTGACATTGAA
*
1966319 CGTTTACGCCTCTAATA-TT-TGGTACTCGAACTCA-AATCTCAAA-AATAACAATAATTCTTTT
130 CGTTTACGCCTCTAATATTTCTGGTACTCAAACTCAGAATCTCAAAGAATAACAATAATTCTTTT
1966380 ATTACCGAGCTCGTATAAAGGGATTGAAGAAGAGGAAGAGAGCAGGTGGGACTTTCAAACGGTTT
195 ATTACCGAGCTCGTATAAAGGGATTGAAGAAGAGGAAGAGAGCAGGTGGGACTTTCAAACGGTTT
1966445 AAGCCGTT
260 AAGCCGTT
1966453 ATG
1 ATG
1966456 GGTTAGGAGC
Statistics
Matches: 250, Mismatches: 12, Indels: 9
0.92 0.04 0.03
Matches are distributed among these distances:
260 91 0.36
261 8 0.03
262 13 0.05
263 2 0.01
264 31 0.12
265 1 0.00
266 16 0.06
267 69 0.28
268 19 0.08
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (267 bp):
ATGTGTCCGTCCTGTAAACCTTACATATGGAAAAAAAAATAATAAAAAAAAAATAATTTTTTTTG
TTAATATGGGGTAAATACAAGATAATATTTGTTCATAGATAACTCTCTATCATTTGACATTGAAC
GTTTACGCCTCTAATATTTCTGGTACTCAAACTCAGAATCTCAAAGAATAACAATAATTCTTTTA
TTACCGAGCTCGTATAAAGGGATTGAAGAAGAGGAAGAGAGCAGGTGGGACTTTCAAACGGTTTA
AGCCGTT
Found at i:1970662 original size:2 final size:2
Alignment explanation
Indices: 1970655--1970692 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1970645 AGTGATTGAA
1970655 AT AT AT 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 AT AT AT
1970693 TGATTAGGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1974719 original size:29 final size:29
Alignment explanation
Indices: 1974677--1974749 Score: 130
Period size: 29 Copynumber: 2.6 Consensus size: 29
1974667 AGGAGAATAC
1974677 GAGTTTGTTTGTCTCGTGGAATATATTTT
1 GAGTTTGTTTGTCTCGTGGAATATATTTT
1974706 GAGTTTGTTTGTCTCGTGGAATATATTTT
1 GAGTTTGTTTGTCTCGTGGAATATATTTT
*
1974735 GAATTTGTTT-TCTCG
1 GAGTTTGTTTGTCTCG
1974750 GAAAGTTTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 5 0.12
29 38 0.88
ACGTcount: A:0.16, C:0.08, G:0.23, T:0.52
Consensus pattern (29 bp):
GAGTTTGTTTGTCTCGTGGAATATATTTT
Found at i:1975115 original size:31 final size:31
Alignment explanation
Indices: 1975071--1975155 Score: 127
Period size: 31 Copynumber: 2.8 Consensus size: 31
1975061 TTGAAGAAAA
* *
1975071 AAAATGAAT-GTTTAGGTATTAAATCAGACC
1 AAAATTAATAGTTTAAGTATTAAATCAGACC
* *
1975101 AAAATTAATAGTTTATGTATTAAATCATACC
1 AAAATTAATAGTTTAAGTATTAAATCAGACC
1975132 AAAATTAATAGTTTAAGTATTAAA
1 AAAATTAATAGTTTAAGTATTAAA
1975156 CGTGTTATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 8 0.16
31 42 0.84
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.35
Consensus pattern (31 bp):
AAAATTAATAGTTTAAGTATTAAATCAGACC
Found at i:1980725 original size:35 final size:35
Alignment explanation
Indices: 1980679--1980748 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
1980669 GGGCACATTA
1980679 CATAGCTAGTCATCCATGTGTAACTTGTATTCCGT
1 CATAGCTAGTCATCCATGTGTAACTTGTATTCCGT
1980714 CATAGCTAGTCATCCATGTGTAACTTGTATTCCGT
1 CATAGCTAGTCATCCATGTGTAACTTGTATTCCGT
1980749 TTTTCCTTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (35 bp):
CATAGCTAGTCATCCATGTGTAACTTGTATTCCGT
Found at i:1982944 original size:2 final size:2
Alignment explanation
Indices: 1982939--1982964 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1982929 TAAAAAAATC
1982939 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
1982965 GGATGGTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1984207 original size:19 final size:19
Alignment explanation
Indices: 1984183--1984220 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1984173 CATATACTCA
1984183 CCATGCAGACGAGCCATAC
1 CCATGCAGACGAGCCATAC
1984202 CCATGCAGACGAGCCATAC
1 CCATGCAGACGAGCCATAC
1984221 AAGCCATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.37, G:0.21, T:0.11
Consensus pattern (19 bp):
CCATGCAGACGAGCCATAC
Found at i:1984278 original size:31 final size:32
Alignment explanation
Indices: 1984235--1984304 Score: 106
Period size: 31 Copynumber: 2.2 Consensus size: 32
1984225 CATATACTCA
* *
1984235 CCATGCAGACGAGCCAGCCAACGGAGAGGTCG
1 CCATGCAAACGAGCCAGCCAACAGAGAGGTCG
*
1984267 -CATGCAAACGAGCCAGCCAATAGAGAGGTCG
1 CCATGCAAACGAGCCAGCCAACAGAGAGGTCG
1984298 CCATGCA
1 CCATGCA
1984305 GTCTGGGAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 28 0.82
32 6 0.18
ACGTcount: A:0.31, C:0.30, G:0.30, T:0.09
Consensus pattern (32 bp):
CCATGCAAACGAGCCAGCCAACAGAGAGGTCG
Found at i:1984333 original size:26 final size:29
Alignment explanation
Indices: 1984292--1984380 Score: 112
Period size: 29 Copynumber: 3.2 Consensus size: 29
1984282 GCCAATAGAG
* **
1984292 AGGTCGCCATGCAGTCTGGGAGACC-T-T
1 AGGTCGCCATGTAGTCCCGGAGACCTTGT
*
1984319 -GGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGAGACCTTGT
*
1984347 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGAGACCTTGT
1984376 AGGTC
1 AGGTC
1984381 CCCCGGCGTC
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
26 20 0.36
27 1 0.02
28 1 0.02
29 33 0.60
ACGTcount: A:0.15, C:0.29, G:0.33, T:0.24
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGAGACCTTGT
Found at i:1984358 original size:29 final size:29
Alignment explanation
Indices: 1984319--1984380 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
1984309 GGGAGACCTT
1984319 GGTCGCCATGTAGTCCCGGCGACCTTGTA
1 GGTCGCCATGTAGTCCCGGCGACCTTGTA
1984348 GGTCGCCATGTAGTCCCGGCGACCTTGTA
1 GGTCGCCATGTAGTCCCGGCGACCTTGTA
1984377 GGTC
1 GGTC
1984381 CCCCGGCGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.13, C:0.31, G:0.32, T:0.24
Consensus pattern (29 bp):
GGTCGCCATGTAGTCCCGGCGACCTTGTA
Found at i:1984480 original size:48 final size:47
Alignment explanation
Indices: 1984409--1984521 Score: 155
Period size: 48 Copynumber: 2.4 Consensus size: 47
1984399 CCCGAGACCA
1984409 TGCATG-C-ACATGCA-GCCAAATAACTTCACGTGCTCCTG-CCCCGC
1 TGCATGCCTACATGCATGCCAAATAACTTCACGTGCT-CTGCCCCCGC
*
1984453 TGCATGCCTGCATGCATGCCAAGATAACTTCACGTGCTCTGCTCCCCGC
1 TGCATGCCTACATGCATGCCAA-ATAACTTCACGTGCTCTGC-CCCCGC
1984502 TGCATGCCTACA-GCATGCCA
1 TGCATGCCTACATGCATGCCA
1984522 TGTGATCCTA
Statistics
Matches: 61, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
44 6 0.10
45 1 0.02
46 6 0.10
47 8 0.13
48 23 0.38
49 17 0.28
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.22
Consensus pattern (47 bp):
TGCATGCCTACATGCATGCCAAATAACTTCACGTGCTCTGCCCCCGC
Found at i:1984942 original size:46 final size:47
Alignment explanation
Indices: 1984877--1984966 Score: 139
Period size: 46 Copynumber: 1.9 Consensus size: 47
1984867 TTATATAGTT
*
1984877 AAAAAATAATTAATTAG-TTTGTTTTGTTAATAGTT-AGTTATATAAA
1 AAAAAATAATTAATTAGTTTTG-TTAGTTAATAGTTAAGTTATATAAA
*
1984923 AAAAAATTATTAATTAGTTTTGTTAGTTAATAGTTAAGTTATAT
1 AAAAAATAATTAATTAGTTTTGTTAGTTAATAGTTAAGTTATAT
1984967 TGTTTGTGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
46 28 0.70
47 12 0.30
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (47 bp):
AAAAAATAATTAATTAGTTTTGTTAGTTAATAGTTAAGTTATATAAA
Found at i:1984944 original size:42 final size:41
Alignment explanation
Indices: 1984837--1984947 Score: 107
Period size: 43 Copynumber: 2.6 Consensus size: 41
1984827 TACATAAATT
* *
1984837 AAAATTATTTAATTAGTATATGTTTGATAGTTATATAGTTAAAAA
1 AAAATTA-TTAATTAGT-TTTG-TTAATAGTTATATAG-TAAAAA
* * *
1984882 ATAATTAATTAGTTTGTTTTGTTAATAGTTAGTTATA-TAAAAA
1 AAAATT-ATTAATTAGTTTTGTTAATAGTTA--TATAGTAAAAA
1984925 AAAATTATTAATTAGTTTTGTTA
1 AAAATTATTAATTAGTTTTGTTA
1984948 GTTAATAGTT
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
42 15 0.27
43 20 0.36
44 3 0.05
45 16 0.29
46 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (41 bp):
AAAATTATTAATTAGTTTTGTTAATAGTTATATAGTAAAAA
Found at i:1984958 original size:42 final size:43
Alignment explanation
Indices: 1984837--1984947 Score: 104
Period size: 42 Copynumber: 2.6 Consensus size: 43
1984827 TACATAAATT
* *
1984837 AAAATTATTTAATTAGTATATGTT--T-GATAGTTATATAGTTAAAA
1 AAAATTAATTAATTAGT-TTTGTTAATAGATAGTTATATA---AAAA
* * *
1984881 AATAATTAATTAGTTTGTTTTGTTAATAGTTAGTTATATAAAAA
1 AA-AATTAATTAATTAGTTTTGTTAATAGATAGTTATATAAAAA
1984925 AAAATT-ATTAATTAGTTTTGTTA
1 AAAATTAATTAATTAGTTTTGTTA
1984948 GTTAATAGTT
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
42 15 0.27
43 4 0.07
44 13 0.23
45 12 0.21
46 1 0.02
47 11 0.20
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (43 bp):
AAAATTAATTAATTAGTTTTGTTAATAGATAGTTATATAAAAA
Found at i:1985079 original size:32 final size:33
Alignment explanation
Indices: 1985004--1985084 Score: 107
Period size: 32 Copynumber: 2.5 Consensus size: 33
1984994 TTAGTTAGTA
*
1985004 AGTTTATTAG-TAGTATATTATAATGAAAAAAT
1 AGTTTATTAGTTAGTTTATTATAATGAAAAAAT
1985036 AGTTTATTAGTTAGTTTAGTTAT-AT-AAAAAAT
1 AGTTTATTAGTTAGTTTA-TTATAATGAAAAAAT
*
1985068 ATTTTATTAGTT-GTTTA
1 AGTTTATTAGTTAGTTTA
1985085 AGGGTTTGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
31 5 0.11
32 28 0.62
33 8 0.18
34 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (33 bp):
AGTTTATTAGTTAGTTTATTATAATGAAAAAAT
Found at i:1985161 original size:15 final size:14
Alignment explanation
Indices: 1985141--1985171 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
1985131 AGTTATTAGT
1985141 TTATTATATTATAAG
1 TTATTATATTA-AAG
1985156 TTATTATATTAAAG
1 TTATTATATTAAAG
1985170 TT
1 TT
1985172 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:1985662 original size:14 final size:14
Alignment explanation
Indices: 1985643--1985687 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
1985633 TTAATTTATA
1985643 TTCGTTTACGTTCG
1 TTCGTTTACGTTCG
* *
1985657 TTCGTTTACATCCG
1 TTCGTTTACGTTCG
* *
1985671 TTCGTTCATGTTCG
1 TTCGTTTACGTTCG
1985685 TTC
1 TTC
1985688 ATTTGTATTC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.09, C:0.24, G:0.18, T:0.49
Consensus pattern (14 bp):
TTCGTTTACGTTCG
Found at i:1985799 original size:29 final size:29
Alignment explanation
Indices: 1985757--1985814 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1985747 CGAACACGAA
1985757 CAAGAATTTTTTTTCGTTTATGTTCGTGT
1 CAAGAATTTTTTTTCGTTTATGTTCGTGT
1985786 CAAGAATTTTTTTTCGTTTATGTTCGTGT
1 CAAGAATTTTTTTTCGTTTATGTTCGTGT
1985815 TTATTCATTT
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:0.17, C:0.10, G:0.17, T:0.55
Consensus pattern (29 bp):
CAAGAATTTTTTTTCGTTTATGTTCGTGT
Found at i:1986733 original size:19 final size:19
Alignment explanation
Indices: 1986709--1986747 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1986699 AGCGAAAGCC
1986709 CTTATTTTTGTTTATTTCA
1 CTTATTTTTGTTTATTTCA
1986728 CTTATTTTTGTTTATTTCA
1 CTTATTTTTGTTTATTTCA
1986747 C
1 C
1986748 CGTACAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.05, T:0.67
Consensus pattern (19 bp):
CTTATTTTTGTTTATTTCA
Found at i:1988411 original size:27 final size:27
Alignment explanation
Indices: 1988358--1988412 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
1988348 ATATTCATAC
*
1988358 AAAATTTTATATAGAATAAATACAAAT
1 AAAATTTTAAATAGAATAAATACAAAT
* *
1988385 AAAATTTTAAAATATAATTAATA-AAAT
1 AAAATTTT-AAATAGAATAAATACAAAT
1988412 A
1 A
1988413 GATAATTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (27 bp):
AAAATTTTAAATAGAATAAATACAAAT
Found at i:1988419 original size:16 final size:17
Alignment explanation
Indices: 1988398--1988429 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1988388 ATTTTAAAAT
1988398 ATAATTAA-TAAAATAG
1 ATAATTAATTAAAATAG
1988414 ATAATTAATTAAAATA
1 ATAATTAATTAAAATA
1988430 AATCTAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
ATAATTAATTAAAATAG
Found at i:1999033 original size:21 final size:21
Alignment explanation
Indices: 1999007--1999051 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1998997 AAATTACACA
*
1999007 TTTAGTATCTAAATTATTAGT
1 TTTAGTATCTAAATTATTAAT
* *
1999028 TTTAGTGTCTAAATTTTTAAT
1 TTTAGTATCTAAATTATTAAT
1999049 TTT
1 TTT
1999052 TAAAAAATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.04, G:0.09, T:0.58
Consensus pattern (21 bp):
TTTAGTATCTAAATTATTAAT
Found at i:2003137 original size:17 final size:17
Alignment explanation
Indices: 2003115--2003148 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2003105 ATAATTATAT
2003115 AAATATTATTTA-ATAAA
1 AAATA-TATTTACATAAA
2003132 AAATATATTTACATAAA
1 AAATATATTTACATAAA
2003149 TATATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATATATTTACATAAA
Found at i:2003151 original size:31 final size:29
Alignment explanation
Indices: 2003095--2003169 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 29
2003085 TTAATAATTC
*
2003095 TAAATAAATAATAATTATATAAATATTATTTAA
1 TAAA-AAAT-ATAATTACATAAATA-TA-TTAA
*
2003128 TAAAAAATATATTTACATAAATATATTAA
1 TAAAAAATATAATTACATAAATATATTAA
*
2003157 TATAAAATATAAT
1 TAAAAAATATAAT
2003170 AACTATTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 15 0.39
30 2 0.05
31 13 0.34
32 4 0.11
33 4 0.11
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (29 bp):
TAAAAAATATAATTACATAAATATATTAA
Found at i:2003169 original size:12 final size:14
Alignment explanation
Indices: 2003098--2003170 Score: 53
Period size: 14 Copynumber: 5.1 Consensus size: 14
2003088 ATAATTCTAA
2003098 ATAAATAATAATT-AT
1 ATAAAT-AT-ATTAAT
2003113 ATAAATATTATTTAAT
1 ATAAATA-TA-TTAAT
* * *
2003129 AAAAAATATATTTAC
1 -ATAAATATATTAAT
2003144 ATAAATATATTAAT
1 ATAAATATATTAAT
2003158 ATAAA-ATA-TAAT
1 ATAAATATATTAAT
2003170 A
1 A
2003171 ACTATTTAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
12 5 0.10
13 3 0.06
14 18 0.38
15 12 0.25
16 4 0.08
17 6 0.12
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (14 bp):
ATAAATATATTAAT
Found at i:2006501 original size:61 final size:61
Alignment explanation
Indices: 2006379--2006494 Score: 169
Period size: 62 Copynumber: 1.9 Consensus size: 61
2006369 ACAAAAATAG
* ** *
2006379 ACTAAAACTGATAATTAAGTATTAAATGATAAATACGTAGTTTACAGTTATACCTAAAAAA
1 ACTAAAACTGATAATTAAATATTAAATGATAAATACGTAGTTTACAAATACACCTAAAAAA
* *
2006440 ACTAAAACTGATAATTTAAATTTTAAATGATAAATGCGTAGTTTACAAATACACC
1 ACTAAAACTGATAA-TTAAATATTAAATGATAAATACGTAGTTTACAAATACACC
2006495 CCAAAAATAC
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
61 14 0.29
62 34 0.71
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.32
Consensus pattern (61 bp):
ACTAAAACTGATAATTAAATATTAAATGATAAATACGTAGTTTACAAATACACCTAAAAAA
Found at i:2006501 original size:62 final size:61
Alignment explanation
Indices: 2006370--2006501 Score: 165
Period size: 62 Copynumber: 2.1 Consensus size: 61
2006360 AGTATAGGTA
* ** *
2006370 CAAAAATAGACTAAAACTGATAATTAAGTATTAAATGATAAATACGTAGTTTACAGTTATACC
1 CAAAAA-A-ACTAAAACTGATAATTAAATATTAAATGATAAATACGTAGTTTACAAATACACC
* * *
2006433 TAAAAAAACTAAAACTGATAATTTAAATTTTAAATGATAAATGCGTAGTTTACAAATACACC
1 CAAAAAAACTAAAACTGATAA-TTAAATATTAAATGATAAATACGTAGTTTACAAATACACC
*
2006495 CCAAAAA
1 CAAAAAA
2006502 TACATATATA
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
61 14 0.24
62 40 0.68
63 5 0.08
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29
Consensus pattern (61 bp):
CAAAAAAACTAAAACTGATAATTAAATATTAAATGATAAATACGTAGTTTACAAATACACC
Found at i:2006512 original size:2 final size:2
Alignment explanation
Indices: 2006505--2006559 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
2006495 CCAAAAATAC
2006505 AT AT AT AT AT 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 AT AT AT AT AT
2006547 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
2006560 CAACAAGACT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2007079 original size:29 final size:30
Alignment explanation
Indices: 2007028--2007084 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
2007018 GAAAATGGTG
*
2007028 AATACTTTCAGGCATCTATTTTGATCAAAA
1 AATACTTTCAGGCACCTATTTTGATCAAAA
*
2007058 AATACTTT-AGGTACCTATTTTGATCAA
1 AATACTTTCAGGCACCTATTTTGATCAA
2007085 CAAGATAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.39
Consensus pattern (30 bp):
AATACTTTCAGGCACCTATTTTGATCAAAA
Found at i:2016853 original size:2 final size:2
Alignment explanation
Indices: 2016846--2016877 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2016836 TCCGGTAAAC
*
2016846 AG AG AG AG AG AG AG AG AG AG AG AG AC AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2016878 TTTGATTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2017961 original size:7 final size:7
Alignment explanation
Indices: 2017949--2017982 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
2017939 TTTGAATTAA
2017949 TATTATT
1 TATTATT
2017956 TATTATT
1 TATTATT
2017963 TATTATT
1 TATTATT
2017970 T-TTATT
1 TATTATT
2017976 T-TTATT
1 TATTATT
2017982 T
1 T
2017983 TTGTATTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 12 0.44
7 15 0.56
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TATTATT
Found at i:2017983 original size:5 final size:6
Alignment explanation
Indices: 2017951--2017984 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
2017941 TGAATTAATA
2017951 TTATTT ATTATTT ATTATTT TTATTT TTATTT TT
1 TTATTT -TTATTT -TTATTT TTATTT TTATTT TT
2017985 GTATTGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 14 0.52
7 13 0.48
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (6 bp):
TTATTT
Found at i:2018517 original size:23 final size:22
Alignment explanation
Indices: 2018491--2018563 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 22
2018481 ATCATATACA
2018491 TATATAGATATATTAATATTATT
1 TATATA-ATATATTAATATTATT
* *
2018514 TATATAATAATATAAATAATATT
1 TATATAAT-ATATTAATATTATT
* *
2018537 T-TTTACTATATATTAATATTGTT
1 TATATA--ATATATTAATATTATT
2018560 TATA
1 TATA
2018564 ATATAAATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
22 5 0.13
23 31 0.79
24 3 0.08
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (22 bp):
TATATAATATATTAATATTATT
Found at i:2018575 original size:20 final size:20
Alignment explanation
Indices: 2018520--2018572 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
2018510 TATTTATATA
2018520 ATAATATAAATAATATTTTT
1 ATAATATAAATAATATTTTT
* *
2018540 -TACTATATATTAATATTGTTT
1 ATAATATA-AATAATATT-TTT
2018561 ATAATATAAATA
1 ATAATATAAATA
2018573 TATAATAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
19 6 0.23
20 8 0.31
21 6 0.23
22 6 0.23
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
ATAATATAAATAATATTTTT
Found at i:2033758 original size:2 final size:2
Alignment explanation
Indices: 2033751--2033783 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2033741 ACTTTAATTA
2033751 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
2033784 ATGGAAGGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2042986 original size:18 final size:18
Alignment explanation
Indices: 2042963--2043000 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2042953 TTTGAATTTT
2042963 TGCCCGATCAAAAGATGA
1 TGCCCGATCAAAAGATGA
2042981 TGCCCGATCAAAAGATGA
1 TGCCCGATCAAAAGATGA
2042999 TG
1 TG
2043001 GCGACTGACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (18 bp):
TGCCCGATCAAAAGATGA
Found at i:2044571 original size:20 final size:20
Alignment explanation
Indices: 2044546--2044589 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2044536 CCTTGATGTT
2044546 GGCAGAACAGAAGAACTCTC
1 GGCAGAACAGAAGAACTCTC
***
2044566 GGCAGATTTGAAGAACTCTC
1 GGCAGAACAGAAGAACTCTC
2044586 GGCA
1 GGCA
2044590 TCTCGGCATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.23, G:0.27, T:0.16
Consensus pattern (20 bp):
GGCAGAACAGAAGAACTCTC
Found at i:2044593 original size:28 final size:28
Alignment explanation
Indices: 2044562--2044616 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
2044552 ACAGAAGAAC
2044562 TCTCGGCAGATTTGAAGAACTCTCGGCA
1 TCTCGGCAGATTTGAAGAACTCTCGGCA
*
2044590 TCTCGGCATATTTGAAGAACTCTCGGC
1 TCTCGGCAGATTTGAAGAACTCTCGGC
2044617 GAACCTGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (28 bp):
TCTCGGCAGATTTGAAGAACTCTCGGCA
Found at i:2046642 original size:80 final size:80
Alignment explanation
Indices: 2046507--2046714 Score: 326
Period size: 80 Copynumber: 2.5 Consensus size: 80
2046497 GCCATGGACT
* *
2046507 ATGTCATGCCAAACCTTGCTGACATGTATGAATCAGTAAGCAAGCTACTGATTTCAAGATAATCT
1 ATGTCATGCCAAACCTTGCTAACATG--TGAATCAGTAAGCAAGCTACTGATTTCAAGATAATCC
2046572 AATTAGTATGGTAGACC
64 AATTAGTATGGTAGACC
*
2046589 ATGTCAAGCCAAACCTTGCTAACATGTGAATCAGTAAGCAAGCTACTGATTTCAAGATAATCCAA
1 ATGTCATGCCAAACCTTGCTAACATGTGAATCAGTAAGCAAGCTACTGATTTCAAGATAATCCAA
2046654 TTAGTATGGTAGACC
66 TTAGTATGGTAGACC
** *
2046669 ATGTCATGCCAAACCTACCTAACATGTAGTAATCAGCAAGCAAGCT
1 ATGTCATGCCAAACCTTGCTAACATGT-G-AATCAGTAAGCAAGCT
2046715 GTACACCATA
Statistics
Matches: 117, Mismatches: 7, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
80 77 0.66
81 1 0.01
82 39 0.33
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (80 bp):
ATGTCATGCCAAACCTTGCTAACATGTGAATCAGTAAGCAAGCTACTGATTTCAAGATAATCCAA
TTAGTATGGTAGACC
Done.