Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008857.1 Hibiscus syriacus cultivar Beakdansim tig00112079_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: 530231
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 3 of 3
Found at i:342697 original size:16 final size:16
Alignment explanation
Indices: 342676--342707 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
342666 TTACTATTCA
342676 CGTGAATAATGAATTT
1 CGTGAATAATGAATTT
*
342692 CGTGAATAGTGAATTT
1 CGTGAATAATGAATTT
342708 TTGTCGGCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (16 bp):
CGTGAATAATGAATTT
Found at i:349615 original size:33 final size:33
Alignment explanation
Indices: 349568--349631 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
349558 ACAAACATTA
*
349568 CGAATCTAATAAACTCGAATAAGGAGACCATAT
1 CGAATCTAACAAACTCGAATAAGGAGACCATAT
*
349601 CGAATGTAACAAACTCGAATAAGGAGACCAT
1 CGAATCTAACAAACTCGAATAAGGAGACCAT
349632 CTTCATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.19
Consensus pattern (33 bp):
CGAATCTAACAAACTCGAATAAGGAGACCATAT
Found at i:350011 original size:23 final size:21
Alignment explanation
Indices: 349972--350015 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
349962 TTCGAGGGAC
*
349972 TCGACTCATACTTAAAAATTAA
1 TCGACTAATAC-TAAAAATTAA
349994 TCGACTAATTACTAAAAATTAA
1 TCGACTAA-TACTAAAAATTAA
350016 ATTTTCAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.32
Consensus pattern (21 bp):
TCGACTAATACTAAAAATTAA
Found at i:353953 original size:49 final size:50
Alignment explanation
Indices: 353858--353955 Score: 121
Period size: 49 Copynumber: 2.0 Consensus size: 50
353848 GGTCGTGCCT
*
353858 TACCTTTAATTCTGACATAATTATATATAGTGCGGAGCAGAGACCGCGCTA
1 TACCTTTAA-TCTGACATAATTATATATAGCGCGGAGCAGAGACCGCGCTA
* *
353909 TACCTTTAA-CTGATATAATTATATA-AGACGCGGTGCA-AGTACCGCGC
1 TACCTTTAATCTGACATAATTATATATAG-CGCGGAGCAGAG-ACCGCGC
353956 CTTGTATAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
48 4 0.10
49 29 0.69
51 9 0.21
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (50 bp):
TACCTTTAATCTGACATAATTATATATAGCGCGGAGCAGAGACCGCGCTA
Found at i:357606 original size:35 final size:34
Alignment explanation
Indices: 357521--357607 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
357511 AAAATAATTT
*
357521 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* * *
357555 TAAAGGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAA-TACAACAAAATTACAATAA--G-TATTAAATGG
357593 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
357608 ACTGAAATAC
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
34 4 0.09
35 24 0.56
36 1 0.02
37 3 0.07
38 11 0.26
ACGTcount: A:0.54, C:0.10, G:0.09, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:359947 original size:17 final size:18
Alignment explanation
Indices: 359906--359944 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
359896 ATTATATAAG
359906 TAAAATA-TTAAATAAAT
1 TAAAATACTTAAATAAAT
359923 TAAAATACTTAAATAAAT
1 TAAAATACTTAAATAAAT
359941 TAAA
1 TAAA
359945 TACAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAATACTTAAATAAAT
Found at i:360026 original size:10 final size:10
Alignment explanation
Indices: 359998--360032 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
359988 ATATAAGAGT
*
359998 ATTTGAGAGA
1 ATTTGAGATA
*
360008 AGTTGAGATA
1 ATTTGAGATA
360018 ATTTGAGATA
1 ATTTGAGATA
360028 ATTTG
1 ATTTG
360033 GTGTGCTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (10 bp):
ATTTGAGATA
Found at i:360714 original size:21 final size:21
Alignment explanation
Indices: 360685--360736 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
360675 ATTCTGACTA
360685 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
360706 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
360727 TCGCAATGCG
1 TCGCATTGCG
360737 CATACATAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:360785 original size:20 final size:20
Alignment explanation
Indices: 360727--360792 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
360717 TTTTCCTAAT
* * *
360727 TCGCAATGCGCATACATAAA
1 TCGCAATACGAATACGTAAA
* *
360747 TCGCAATGCGATTACGTAAA
1 TCGCAATACGAATACGTAAA
360767 TCGCAATACGAAT-CTGTAAA
1 TCGCAATACGAATAC-GTAAA
360787 TCGCAA
1 TCGCAA
360793 CGAGATTCTG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 1 0.03
20 39 0.98
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.23
Consensus pattern (20 bp):
TCGCAATACGAATACGTAAA
Found at i:360802 original size:20 final size:20
Alignment explanation
Indices: 360743--360802 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
360733 TGCGCATACA
* *
360743 TAAATCGCAATGCGATTAC-G
1 TAAATCGCAACGAGATT-CTG
360763 TAAATCGCAATACGA-A-TCTG
1 TAAATCGC-A-ACGAGATTCTG
360783 TAAATCGCAACGAGATTCTG
1 TAAATCGCAACGAGATTCTG
360803 ACTATCGCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
18 4 0.12
19 3 0.09
20 22 0.67
21 2 0.06
22 2 0.06
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (20 bp):
TAAATCGCAACGAGATTCTG
Found at i:361698 original size:24 final size:24
Alignment explanation
Indices: 361647--361700 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
361637 GTATTCGAAA
*
361647 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
361671 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
361695 TTTGAT
1 TTTGAT
361701 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:364206 original size:19 final size:19
Alignment explanation
Indices: 364179--364284 Score: 107
Period size: 19 Copynumber: 5.8 Consensus size: 19
364169 GCAACGAGAG
364179 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
364198 AATCCCAATGC-AACATGAA
1 AATCGCAATGCGAA-ATGAA
364217 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
364236 AAGCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
*
364250 AATCGCAATGCAAAAATGAA
1 AATCGCAATGC-GAAATGAA
*
364270 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
364285 CTAATTTTGC
Statistics
Matches: 70, Mismatches: 9, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
14 7 0.10
16 4 0.06
17 2 0.03
18 5 0.07
19 40 0.57
20 12 0.17
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:365890 original size:42 final size:42
Alignment explanation
Indices: 365830--365926 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
365820 CGTGTGAATC
* * * *
365830 GGCCTCTAGAATGTTGGGA-GGGACCTCTTCAACGATGACAGT
1 GGCCTCTTGAACGGTGGGAGGGGA-CTCTTCAACGATGACAGG
* ** *
365872 GGCCTCTTGAACGGTGGGAGGGGACTCTTGAGGGATGATAGG
1 GGCCTCTTGAACGGTGGGAGGGGACTCTTCAACGATGACAGG
365914 GGCCTCTTGAACG
1 GGCCTCTTGAACG
365927 ATAGGGGAGG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 42 0.91
43 4 0.09
ACGTcount: A:0.21, C:0.20, G:0.37, T:0.23
Consensus pattern (42 bp):
GGCCTCTTGAACGGTGGGAGGGGACTCTTCAACGATGACAGG
Found at i:366490 original size:33 final size:33
Alignment explanation
Indices: 366430--366513 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 33
366420 TCTGAAACTT
** * *
366430 AAAATCGCAACGCGAAAATGACTATCGCAACGAG
1 AAAATCGCAACGCG-AAATGAAAATCGCAACAAC
* *
366464 AGAATCGCAATGCGAAATGAAAATCGCAACAAC
1 AAAATCGCAACGCGAAATGAAAATCGCAACAAC
366497 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
366514 ATGACTATCG
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
33 30 0.71
34 12 0.29
ACGTcount: A:0.48, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACAAC
Found at i:366525 original size:20 final size:20
Alignment explanation
Indices: 366500--366548 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
366490 CAACAACAAA
366500 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
366520 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
366540 ATCGCAACG
1 ATCGCAACG
366549 AGAGAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:366612 original size:34 final size:34
Alignment explanation
Indices: 366572--366693 Score: 145
Period size: 34 Copynumber: 3.4 Consensus size: 34
366562 GCGATTTTTA
*
366572 TTTCGCATTGCGATTCTTTCGTTGCGATAGTCAA
1 TTTCGCATTGCGATTCTTTCGTTGCGATAGTCAT
* *
366606 ATTCGCATTGCGATAGTTATTTTCGCATTGCGATAGTCAT
1 TTTCGCATTGCG--A-TT-CTTTCG--TTGCGATAGTCAT
*
366646 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAT
1 TTTCGCATTGCGATTCTTTCGTTGCGATAGTCAT
*
366680 TTTCGCGTTGCGAT
1 TTTCGCATTGCGAT
366694 AGTCATTTTC
Statistics
Matches: 75, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
34 37 0.49
36 5 0.07
37 4 0.05
38 6 0.08
40 23 0.31
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.41
Consensus pattern (34 bp):
TTTCGCATTGCGATTCTTTCGTTGCGATAGTCAT
Found at i:366618 original size:20 final size:20
Alignment explanation
Indices: 366593--366716 Score: 152
Period size: 20 Copynumber: 6.5 Consensus size: 20
366583 GATTCTTTCG
**
366593 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
366613 TTGCGATAGTTATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
366633 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
366653 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
366667 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
366687 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
366707 ATGCGATAGT
1 TTGCGATAGT
366717 AAAATGTTCT
Statistics
Matches: 90, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.08
16 6 0.07
18 6 0.07
20 71 0.79
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:366675 original size:74 final size:74
Alignment explanation
Indices: 366555--366716 Score: 236
Period size: 74 Copynumber: 2.2 Consensus size: 74
366545 AACGAGAGAA
** * *
366555 TCGCAATGCGATTTTTA-TTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAATTCGCATTGCGA
1 TCGCAATGCGATAGTCATTTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGA
*
366619 TAGTTATTT
66 TAGTCATTT
* ** *
366628 TCGCATTGCGATAGTCATTTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCGTTGCGA
1 TCGCAATGCGATAGTCATTTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGA
366693 TAGTCATTT
66 TAGTCATTT
366702 TCGCAATGCGATAGT
1 TCGCAATGCGATAGT
366717 AAAATGTTCT
Statistics
Matches: 78, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
73 13 0.17
74 65 0.83
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (74 bp):
TCGCAATGCGATAGTCATTTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGA
TAGTCATTT
Found at i:368638 original size:20 final size:20
Alignment explanation
Indices: 368613--368667 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
368603 GCAAAACTTT
368613 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
368633 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
** *
368653 CTATCGCAACGCGAA
1 AAATCGCAACACGAA
368668 TTTGACTATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.11
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:368673 original size:20 final size:20
Alignment explanation
Indices: 368615--368684 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
368605 AAAACTTTAA
* **
368615 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
*
368635 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
368655 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
*
368675 ATCGTAACGC
1 ATCGCAACGC
368685 AAGAATCGCA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:369311 original size:20 final size:20
Alignment explanation
Indices: 369286--369379 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
369276 GCGCTATGTA
369286 AATCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
369306 AATCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
* * **
369326 ATTCGCATTGCGATTTTCCA
1 AATCGCATTGCGATTTACGT
*
369346 AATTCGCGTTGCGATTTACGT
1 AA-TCGCATTGCGATTTACGT
*
369367 ATTCGCATTGCGA
1 AATCGCATTGCGA
369380 ATTAGGAAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
20 47 0.76
21 15 0.24
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.36
Consensus pattern (20 bp):
AATCGCATTGCGATTTACGT
Found at i:369367 original size:41 final size:40
Alignment explanation
Indices: 369288--369379 Score: 139
Period size: 41 Copynumber: 2.3 Consensus size: 40
369278 GCTATGTAAA
**
369288 TCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACCAAATCGCATTGCGATTTACGTAT
* *
369328 TCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACCAAA-TCGCATTGCGATTTACGTAT
369369 TCGCATTGCGA
1 TCGCATTGCGA
369380 ATTAGGAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
40 17 0.36
41 30 0.64
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.37
Consensus pattern (40 bp):
TCGCATTGCGATTTACCAAATCGCATTGCGATTTACGTAT
Found at i:369401 original size:21 final size:21
Alignment explanation
Indices: 369377--369416 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
369367 ATTCGCATTG
369377 CGAATTAGGAAAATCGCAACC
1 CGAATTAGGAAAATCGCAACC
* *
369398 CGAATTTGGGAAATCGCAA
1 CGAATTAGGAAAATCGCAA
369417 TGCGATAGTC
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:0.40, C:0.20, G:0.23, T:0.17
Consensus pattern (21 bp):
CGAATTAGGAAAATCGCAACC
Found at i:373996 original size:14 final size:14
Alignment explanation
Indices: 373979--374006 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
373969 TATAGATCTA
373979 TGGATTCGGATGAT
1 TGGATTCGGATGAT
373993 TGGATTCGGATGAT
1 TGGATTCGGATGAT
374007 CCATAATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.36, T:0.36
Consensus pattern (14 bp):
TGGATTCGGATGAT
Found at i:375244 original size:16 final size:16
Alignment explanation
Indices: 375214--375259 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
375204 TTGAATTTTT
375214 AGTATCCGAAAATTTCA
1 AGTA-CCGAAAATTTCA
*
375231 AGTACCGAACATTTCA
1 AGTACCGAAAATTTCA
*
375247 GGTACTCGAAAAT
1 AGTAC-CGAAAAT
375260 GTGAGTATCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (16 bp):
AGTACCGAAAATTTCA
Found at i:386587 original size:63 final size:63
Alignment explanation
Indices: 386483--386629 Score: 206
Period size: 63 Copynumber: 2.3 Consensus size: 63
386473 CTCCCTCCTA
* *
386483 TCTCTCTC-CCGCTCCCTCTCTAGCTCACGATCACTCCCGTGCCTCCTCGACCTACTACTGCT
1 TCTCTCTCTCCGATCCCTCTCTAGCTCACGATCAATCCCGTGCCTCCTCGACCTACTACTGCT
* * ** *
386545 TCTCTCTCTCCGATCTCTCTCTATCTCACGATCAATTTCGTGCCTTCTCGACCTACTACTGCT
1 TCTCTCTCTCCGATCCCTCTCTAGCTCACGATCAATCCCGTGCCTCCTCGACCTACTACTGCT
**
386608 TCTCTCTCTCCTCTCCCTCTCT
1 TCTCTCTCTCCGATCCCTCTCT
386630 TTCTCTTTAT
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
62 8 0.11
63 66 0.89
ACGTcount: A:0.11, C:0.45, G:0.09, T:0.35
Consensus pattern (63 bp):
TCTCTCTCTCCGATCCCTCTCTAGCTCACGATCAATCCCGTGCCTCCTCGACCTACTACTGCT
Found at i:387222 original size:24 final size:25
Alignment explanation
Indices: 387174--387223 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
387164 AAAGATTTAA
* *
387174 AATTATCATATTTTTTCACCTAAAT
1 AATTATAATATTTTTTCACCAAAAT
*
387199 AATTATAATATTTTTT-ATCAAAAT
1 AATTATAATATTTTTTCACCAAAAT
387223 A
1 A
387224 GATATCTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (25 bp):
AATTATAATATTTTTTCACCAAAAT
Found at i:387560 original size:20 final size:20
Alignment explanation
Indices: 387513--387583 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
387503 GTGATTTTCC
*
387513 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGATTAT
*
387533 GTA-AATCGCAATGCGATTAT
1 G-ACTATCGCAATGCGATTAT
* *
387553 GACTATCGCAACGCGATTCT
1 GACTATCGCAATGCGATTAT
*
387573 GACTGTCGCAA
1 GACTATCGCAA
387584 CACTGAATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
19 1 0.02
20 41 0.95
21 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (20 bp):
GACTATCGCAATGCGATTAT
Found at i:388423 original size:24 final size:24
Alignment explanation
Indices: 388391--388444 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
388381 GTATTCGAAA
388391 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
388415 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
388439 TTTGAT
1 TTTGAT
388445 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:390706 original size:12 final size:12
Alignment explanation
Indices: 390691--390720 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
390681 AAGAAAAAGG
390691 CAATCAAAATCA
1 CAATCAAAATCA
*
390703 CAATCAAAATCC
1 CAATCAAAATCA
390715 CAATCA
1 CAATCA
390721 CAACCGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.30, G:0.00, T:0.17
Consensus pattern (12 bp):
CAATCAAAATCA
Found at i:391032 original size:140 final size:140
Alignment explanation
Indices: 390780--391045 Score: 496
Period size: 140 Copynumber: 1.9 Consensus size: 140
390770 AAACGTTGTA
390780 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATATATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATATATTAGTAACTTGAGTTTGAACATTGCTA
* *
390845 TGATCTGTTTAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
390910 TATGTGTATT
131 TATGTGTATT
* *
390920 TTATGTGTAAACTTTTAACATTTTCAGTTTGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATATATTAGTAACTTGAGTTTGAACATTGCTA
390985 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGA
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGA
391046 TTATCGCAAC
Statistics
Matches: 122, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 122 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATATATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:391045 original size:20 final size:20
Alignment explanation
Indices: 391020--391357 Score: 323
Period size: 20 Copynumber: 17.7 Consensus size: 20
391010 TTACACATTC
*
391020 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
391040 ATTTGATTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
* *
391059 A----A-AATCGAAACGCGA
1 ATTTGACTATCGCAACGCGA
*
391074 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
* *
391094 ATATGGCTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
391114 ATTTGTCTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
391134 ATTTGACTATCGCAACGCG-
1 ATTTGACTATCGCAACGCGA
391153 ATTTGACTAT--CAACGCGA
1 ATTTGACTATCGCAACGCGA
* **
391171 ATTTGTCTATCGCAATACGA
1 ATTTGACTATCGCAACGCGA
* *
391191 ATTTGACTATCGCAATG-GCT
1 ATTTGACTATCGCAACGCG-A
391211 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
391231 ATTTGACTATCACAACGGGA
1 ATTTGACTATCGCAACGCGA
*
391251 ATTTGAGTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
391271 ATTTGATTATCGCAACGTGT
1 ATTTGACTATCGCAACGCGA
*
391291 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
391311 A----A--ATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
*
391325 ATTAGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
391345 A-TTGACTTTCGCA
1 ATTTGACTATCGCA
391358 TTGCGATTTT
Statistics
Matches: 261, Mismatches: 40, Indels: 35
0.78 0.12 0.10
Matches are distributed among these distances:
14 18 0.07
15 3 0.01
16 1 0.00
17 7 0.03
18 10 0.04
19 24 0.09
20 197 0.75
21 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:391375 original size:20 final size:20
Alignment explanation
Indices: 391350--391388 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
391340 CGCGAATTGA
391350 CTTTCGCATTGCGATTTTGT
1 CTTTCGCATTGCGATTTTGT
391370 CTTTCGCATTGCGATTTTG
1 CTTTCGCATTGCGATTTTG
391389 AGTTTAGCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.21, G:0.21, T:0.49
Consensus pattern (20 bp):
CTTTCGCATTGCGATTTTGT
Found at i:391401 original size:20 final size:20
Alignment explanation
Indices: 391346--391403 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
391336 GCAACGCGAA
*
391346 TTGACTTTCGCATTGCGATT
1 TTGACTTTAGCATTGCGATT
* *
391366 TTGTCTTTCGCATTGCGATT
1 TTGACTTTAGCATTGCGATT
* *
391386 TTGAGTTTAGCGTTGCGA
1 TTGACTTTAGCATTGCGA
391404 AAGTGTACCT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.14, C:0.17, G:0.24, T:0.45
Consensus pattern (20 bp):
TTGACTTTAGCATTGCGATT
Found at i:393058 original size:42 final size:42
Alignment explanation
Indices: 392979--393071 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
392969 CCTCTTCAAC
* * *
392979 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
393021 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
393063 GATGACAGG
1 GATGACAGG
393072 TGAGTCAGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:393572 original size:18 final size:19
Alignment explanation
Indices: 393549--393593 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
393539 GAAACTTAAA
393549 ATCGCAACACG-AATGACT
1 ATCGCAACACGAAATGACT
*
393567 ATCGCAACGCGAAAATGACT
1 ATCGCAACACG-AAATGACT
393587 ATCGCAA
1 ATCGCAA
393594 TGCGATTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 10 0.42
20 14 0.58
ACGTcount: A:0.40, C:0.27, G:0.18, T:0.16
Consensus pattern (19 bp):
ATCGCAACACGAAATGACT
Found at i:393585 original size:20 final size:20
Alignment explanation
Indices: 393560--393598 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
393550 TCGCAACACG
393560 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
*
393580 AATGACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
393599 TTTTCATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:393653 original size:20 final size:20
Alignment explanation
Indices: 393624--393691 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
393614 GCGATTCTTT
* **
393624 CGTTGTGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
393644 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
393664 CGTTGCGATAGTCATTTTTG
1 CGTTGCGATAGTCATTTTCG
393684 CGTTGCGA
1 CGTTGCGA
393692 AAGTAAACTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:395455 original size:20 final size:20
Alignment explanation
Indices: 395432--395495 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
395422 AAACTTAAAT
395432 TCGCAACACGAAAATGAAAA
1 TCGCAACACGAAAATGAAAA
**
395452 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGAAAA
* *
395472 TCGCAACGCGAAACT-AAAA
1 TCGCAACACGAAAATGAAAA
395491 TCGCA
1 TCGCA
395496 TTGCGATTCT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
19 7 0.18
20 31 0.82
ACGTcount: A:0.47, C:0.25, G:0.16, T:0.12
Consensus pattern (20 bp):
TCGCAACACGAAAATGAAAA
Found at i:395908 original size:22 final size:22
Alignment explanation
Indices: 395881--395923 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
395871 GAGATAGACG
395881 GATTTCGTCGGAGATGGGGACT
1 GATTTCGTCGGAGATGGGGACT
395903 GATTTCGTCGGAGATGGGGAC
1 GATTTCGTCGGAGATGGGGAC
395924 GGATGTCGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.14, G:0.42, T:0.26
Consensus pattern (22 bp):
GATTTCGTCGGAGATGGGGACT
Found at i:396128 original size:20 final size:20
Alignment explanation
Indices: 396098--396191 Score: 116
Period size: 20 Copynumber: 4.7 Consensus size: 20
396088 GCGCTTTGAA
*
396098 AATCGCATTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
** *
396118 CTTCGCGTTGCGACAGTCAG
1 AATCGCGTTGCGATAGTCAG
396138 AATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
396158 AATCGTGTTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
* *
396178 ACTCGCATTGCGAT
1 AATCGCGTTGCGAT
396192 TTACATATTC
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:398029 original size:4 final size:4
Alignment explanation
Indices: 398022--398092 Score: 51
Period size: 4 Copynumber: 17.2 Consensus size: 4
398012 TATATATATA
*
398022 TATT TATT TATT TA-T TATT TACTAT T-CT TATT TATTT TATT TATT T-TT
1 TATT TATT TATT TATT TATT TA-T-T TATT TATT TA-TT TATT TATT TATT
398070 CT-TCT TATT TATTT TATT TATT T
1 -TAT-T TATT TA-TT TATT TATT T
398093 TTCTTCTTAC
Statistics
Matches: 56, Mismatches: 2, Indels: 18
0.74 0.03 0.24
Matches are distributed among these distances:
3 7 0.12
4 36 0.64
5 11 0.20
6 2 0.04
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:398074 original size:25 final size:25
Alignment explanation
Indices: 398022--398110 Score: 117
Period size: 25 Copynumber: 3.4 Consensus size: 25
398012 TATATATATA
398022 TATTTA-TTTATTTATTATTTACTATTCT
1 TATTTATTTTATTTATT-TTT-C--TTCT
398050 TATTTATTTTATTTATTTTTCTTCT
1 TATTTATTTTATTTATTTTTCTTCT
398075 TATTTATTTTATTTATTTTTCTTCT
1 TATTTATTTTATTTATTTTTCTTCT
*
398100 TACTATATTTT
1 TA-TTTATTTT
398111 TTTGTATATA
Statistics
Matches: 58, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
25 31 0.53
26 7 0.12
27 1 0.02
28 9 0.16
29 10 0.17
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (25 bp):
TATTTATTTTATTTATTTTTCTTCT
Found at i:398237 original size:15 final size:16
Alignment explanation
Indices: 398210--398246 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
398200 GTTTTATTTG
398210 TTATTTGTTATTTAT-T
1 TTATTTGTTATTT-TCT
398226 TTATTT-TTATTTTCT
1 TTATTTGTTATTTTCT
398241 TTATTT
1 TTATTT
398247 ATCCCCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 1 0.05
15 13 0.65
16 6 0.30
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (16 bp):
TTATTTGTTATTTTCT
Found at i:398317 original size:48 final size:46
Alignment explanation
Indices: 398265--398366 Score: 109
Period size: 48 Copynumber: 2.2 Consensus size: 46
398255 TTATTTTGTA
*
398265 TTATTTT-TATATATTTATTATTATTT-TCTCTCTTGATTTTATCTTATT
1 TTATTTTGTATATATTT-TTA-TATTTGTCTCTATT-ATTTTAT-TTATT
* *
398313 TTATTTATGTATATGTTTTTATATTTGTCTCTATTTTTTTATTTATT
1 TTATTT-TGTATATATTTTTATATTTGTCTCTATTATTTTATTTATT
*
398360 TCATTTT
1 TTATTTT
398367 CTCCATATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
46 1 0.02
47 10 0.21
48 17 0.36
49 11 0.23
50 8 0.17
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.70
Consensus pattern (46 bp):
TTATTTTGTATATATTTTTATATTTGTCTCTATTATTTTATTTATT
Found at i:398447 original size:14 final size:14
Alignment explanation
Indices: 398391--398459 Score: 52
Period size: 15 Copynumber: 4.6 Consensus size: 14
398381 TAATTATGCC
*
398391 ATTTAATTTT-TTT
1 ATTTTATTTTCTTT
*
398404 ATCTTTATTATTTGTTT
1 AT-TTTA-T-TTTCTTT
398421 CATTTT-TTCTTCTTT
1 -ATTTTATT-TTCTTT
398436 ATTTTATTTTCTTT
1 ATTTTATTTTCTTT
398450 ATTTTTATTT
1 A-TTTTATTT
398460 ATTTTACCCG
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
13 2 0.04
14 16 0.35
15 17 0.37
16 3 0.07
17 6 0.13
18 2 0.04
ACGTcount: A:0.16, C:0.07, G:0.01, T:0.75
Consensus pattern (14 bp):
ATTTTATTTTCTTT
Found at i:399058 original size:28 final size:28
Alignment explanation
Indices: 399013--399066 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
399003 TTGGTTCACT
* *
399013 GAAAACGTTTTCCGGAAAATG-AAATCTG
1 GAAAACGTTTTACAG-AAATGTAAATCTG
*
399041 GAAAATGTTTTACAGAAATGTAAATC
1 GAAAACGTTTTACAGAAATGTAAATC
399067 ATTTTCCAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.28
Consensus pattern (28 bp):
GAAAACGTTTTACAGAAATGTAAATCTG
Found at i:399248 original size:17 final size:17
Alignment explanation
Indices: 399226--399264 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
399216 AAGGTTCATT
*
399226 TTTTATATATAAT-TATA
1 TTTTATA-AAAATCTATA
399243 TTTTATAAAAATCTATA
1 TTTTATAAAAATCTATA
399260 TTTTA
1 TTTTA
399265 GATAATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTATAAAAATCTATA
Found at i:402393 original size:23 final size:23
Alignment explanation
Indices: 402367--402411 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
402357 CACCACAGCT
* *
402367 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATACACCGAAGTGCCG
* *
402390 CGTAGAATTACACCGTAGTGCC
1 CGTAGAAATACACCGAAGTGCC
402412 ATATAATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCG
Found at i:404244 original size:21 final size:21
Alignment explanation
Indices: 404220--404264 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
404210 TTTTGTTCGT
* *
404220 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
404241 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
404262 TTG
1 TTG
404265 CCCAGAAATC
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:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:407569 original size:23 final size:23
Alignment explanation
Indices: 407543--407587 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
407533 CACCACAGCT
*
407543 CGTATAAATACACCGAAGTGCCG
1 CGTAGAAATACACCGAAGTGCCG
* * *
407566 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATACACCGAAGTGCC
407588 ATATAATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCG
Found at i:409418 original size:21 final size:21
Alignment explanation
Indices: 409394--409438 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
409384 TTTTGTTCGT
* *
409394 TTGAAGGGGAATCGGTTCCCC
1 TTGAAGGGGAACCGATTCCCC
* *
409415 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGAACCGATTCCCC
409436 TTG
1 TTG
409439 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGAACCGATTCCCC
Found at i:429375 original size:21 final size:20
Alignment explanation
Indices: 429337--429375 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
429327 TCTGCTGAAA
*
429337 CTCCACCTGTTTGGAGTATG
1 CTCCACCTGTTCGGAGTATG
429357 CTCCACCTGTTGCGGAGTA
1 CTCCACCTGTT-CGGAGTA
429376 CTACTTGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.15, C:0.28, G:0.26, T:0.31
Consensus pattern (20 bp):
CTCCACCTGTTCGGAGTATG
Found at i:432001 original size:30 final size:30
Alignment explanation
Indices: 431967--432037 Score: 133
Period size: 30 Copynumber: 2.4 Consensus size: 30
431957 TTTGCTAGTG
431967 TTCCAGCTTTTCAACTGCTCTGCATGTGAT
1 TTCCAGCTTTTCAACTGCTCTGCATGTGAT
*
431997 TTCCATCTTTTCAACTGCTCTGCATGTGAT
1 TTCCAGCTTTTCAACTGCTCTGCATGTGAT
432027 TTCCAGCTTTT
1 TTCCAGCTTTT
432038 TCAATTATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.15, C:0.27, G:0.14, T:0.44
Consensus pattern (30 bp):
TTCCAGCTTTTCAACTGCTCTGCATGTGAT
Found at i:432100 original size:24 final size:24
Alignment explanation
Indices: 432068--432115 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
432058 CAAAGGAAAA
432068 AAATGCATGTTTCCTTCTTATTAT
1 AAATGCATGTTTCCTTCTTATTAT
432092 AAATGCATGTTTCCTTCTTATTAT
1 AAATGCATGTTTCCTTCTTATTAT
432116 TCCACACACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (24 bp):
AAATGCATGTTTCCTTCTTATTAT
Found at i:435671 original size:27 final size:29
Alignment explanation
Indices: 435635--435700 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 29
435625 TTTTTTACTC
435635 AATTTAATTTCAAATTTAAAT-TTATAA-TA
1 AATTT-ATTTCAAA-TTAAATATTATAATTA
* *
435664 AA-TTATTTTAAATTACATATTATAATTA
1 AATTTATTTCAAATTAAATATTATAATTA
435692 AATTTATTT
1 AATTTATTT
435701 TCTTATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 5 0.16
27 13 0.41
28 6 0.19
29 8 0.25
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (29 bp):
AATTTATTTCAAATTAAATATTATAATTA
Found at i:448917 original size:35 final size:35
Alignment explanation
Indices: 448877--448947 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
448867 AGAACGAAAC
*
448877 CTAAGAAAGGGATCGGGCCGGAATGATGATGAAGA
1 CTAAGAAAGGGATCGGGCCGGAATGAGGATGAAGA
448912 CTAAGAAAGGGATCGGGCCGGAATGAGGATGAAGA
1 CTAAGAAAGGGATCGGGCCGGAATGAGGATGAAGA
448947 C
1 C
448948 GAGTGCTGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.13, G:0.38, T:0.13
Consensus pattern (35 bp):
CTAAGAAAGGGATCGGGCCGGAATGAGGATGAAGA
Found at i:452076 original size:16 final size:16
Alignment explanation
Indices: 452055--452114 Score: 93
Period size: 16 Copynumber: 3.8 Consensus size: 16
452045 TAATAAATAA
452055 ACGAACATAAACAAAC
1 ACGAACATAAACAAAC
452071 ACGAACATAAACAAAC
1 ACGAACATAAACAAAC
**
452087 ACGAACATAAATGAAC
1 ACGAACATAAACAAAC
*
452103 ACAAACATAAAC
1 ACGAACATAAAC
452115 GGACATAAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.62, C:0.23, G:0.07, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACAAAC
Found at i:452102 original size:26 final size:26
Alignment explanation
Indices: 452073--452123 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
452063 AAACAAACAC
*
452073 GAACATAAACA-AACACGAACATAAAT
1 GAACACAAACATAA-ACGAACATAAAT
*
452099 GAACACAAACATAAACGGACATAAA
1 GAACACAAACATAAACGAACATAAA
452124 CGTTGGAGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.61, C:0.20, G:0.10, T:0.10
Consensus pattern (26 bp):
GAACACAAACATAAACGAACATAAAT
Found at i:452364 original size:12 final size:11
Alignment explanation
Indices: 452327--452372 Score: 65
Period size: 11 Copynumber: 4.1 Consensus size: 11
452317 CTCGAGTTCA
452327 ATTCAAGCTCG
1 ATTCAAGCTCG
*
452338 ATTCAAGCCCG
1 ATTCAAGCTCG
*
452349 ATTCTGAGCTCG
1 ATTC-AAGCTCG
452361 ATTCAAGCTCG
1 ATTCAAGCTCG
452372 A
1 A
452373 CATTGCCCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 21 0.70
12 9 0.30
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (11 bp):
ATTCAAGCTCG
Found at i:453258 original size:14 final size:14
Alignment explanation
Indices: 453240--453272 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
453230 GAATGAACAT
453240 AAACGAACATAACC
1 AAACGAACATAACC
*
453254 GAACGAACATAACC
1 AAACGAACATAACC
453268 AAACG
1 AAACG
453273 TTCACGAACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.55, C:0.27, G:0.12, T:0.06
Consensus pattern (14 bp):
AAACGAACATAACC
Found at i:458331 original size:25 final size:25
Alignment explanation
Indices: 458303--458360 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
458293 GCTCCCCTAT
458303 GTTTCTATCCTTGGTGAAGGAGATC
1 GTTTCTATCCTTGGTGAAGGAGATC
458328 GTTTCTATCCTTGGTGAAGGAGATC
1 GTTTCTATCCTTGGTGAAGGAGATC
458353 GTTTCTAT
1 GTTTCTAT
458361 AATGGAAGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.19, C:0.16, G:0.26, T:0.40
Consensus pattern (25 bp):
GTTTCTATCCTTGGTGAAGGAGATC
Found at i:470046 original size:2 final size:2
Alignment explanation
Indices: 470041--470077 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
470031 ATAAAAAATA
470041 AT AT AT 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 AT AT AT A
470078 CTCTAAAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:470160 original size:38 final size:36
Alignment explanation
Indices: 470154--470410 Score: 237
Period size: 36 Copynumber: 6.7 Consensus size: 36
470144 CTATATTATA
*
470154 TATATATATATATATATATTCAAAATGTTTTCAAAATC
1 TATAT-TATATATATATATTCAAAATGTTTT-AAAAAC
* *
470192 TATATAATATATATATTTTCAAAATGTTTTAAAAAC
1 TATATTATATATATATATTCAAAATGTTTTAAAAAC
*
470228 TATA-TATTATATATATGTTACGAAAATGTTTTAAAAAC
1 TATATTA-TATATATATATT-C-AAAATGTTTTAAAAAC
*
470266 TATAATATATATATATATATATATATATATCAAAATGTTTTAAAAAT
1 ---------TATAT-TATATATATATAT-TCAAAATGTTTTAAAAAC
*
470313 TATATAATATATATATATTCAAAATGTTTTAAAAAC
1 TATATTATATATATATATTCAAAATGTTTTAAAAAC
* * * *
470349 TATATAATATATGTATGTTTTCAAAATGTTTTAAAAAA
1 TATAT--TATATATATATATTCAAAATGTTTTAAAAAC
* *
470387 TATATAATATATATATTTTCAAAA
1 TATATTATATATATATATTCAAAA
470411 AATGATTTTT
Statistics
Matches: 185, Mismatches: 17, Indels: 36
0.78 0.07 0.15
Matches are distributed among these distances:
35 1 0.01
36 58 0.31
37 36 0.19
38 57 0.31
47 19 0.10
48 11 0.06
49 3 0.02
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (36 bp):
TATATTATATATATATATTCAAAATGTTTTAAAAAC
Found at i:470243 original size:47 final size:45
Alignment explanation
Indices: 470192--470402 Score: 164
Period size: 38 Copynumber: 5.1 Consensus size: 45
470182 TTTCAAAATC
470192 TATATAATATATATATTTTCAAAATGTTTTAAAAAC--TATATAT-
1 TATATAATATATATA-TTTCAAAATGTTTTAAAAACTATATATATA
*
470235 TATAT-ATATGT-TA---CGAAAATGTTTTAAAAACTATAATATATA
1 TATATAATATATATATTTC-AAAATGTTTTAAAAACTAT-ATATATA
*
470277 TATATATATATATATATATCAAAATGTTTT--AAA--A-AT-TATA
1 TATATA-ATATATATATTTCAAAATGTTTTAAAAACTATATATATA
470317 TA-AT-ATATATATA-TTCAAAATGTTTTAAAAAC----TATATA
1 TATATAATATATATATTTCAAAATGTTTTAAAAACTATATATATA
* * *
470355 -ATAT-ATGTATGT-TTTCAAAATGTTTTAAAAAATATATAATATA
1 TATATAATATATATATTTCAAAATGTTTTAAAAACTATAT-ATATA
470398 TATAT
1 TATAT
470403 TTTCAAAAAA
Statistics
Matches: 139, Mismatches: 6, Indels: 45
0.73 0.03 0.24
Matches are distributed among these distances:
36 12 0.09
37 12 0.09
38 49 0.35
39 2 0.01
40 7 0.05
41 10 0.07
42 11 0.08
43 11 0.08
44 9 0.06
45 5 0.04
47 10 0.07
48 1 0.01
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (45 bp):
TATATAATATATATATTTCAAAATGTTTTAAAAACTATATATATA
Found at i:470269 original size:121 final size:121
Alignment explanation
Indices: 470127--470402 Score: 430
Period size: 121 Copynumber: 2.3 Consensus size: 121
470117 CTATATATTA
*
470127 AAAATGTTTTCAAAAAACTATATTATATATATATATATATATATAT-TCAAAATGTTTTCAAAAT
1 AAAATGTTTT--AAAAACTATATTATATATATATATATATATATATATCAAAATGTTTTAAAAAT
* *
470191 CTATATAATATATATATTTTCAAAATGTTTTAAAAACTATATATTATATATATG-TTAC
64 -TATATAATATATATATATTCAAAATGTTTTAAAAACTATATAATATATATATGTTTAC
*
470249 GAAAATGTTTTAAAAACTATAATATATATATATATATATATATATATCAAAATGTTTTAAAAATT
1 -AAAATGTTTTAAAAACTATATTATATATATATATATATATATATATCAAAATGTTTTAAAAATT
* *
470314 ATATAATATATATATATTCAAAATGTTTTAAAAACTATATAATATATGTATGTTTTC
65 ATATAATATATATATATTCAAAATGTTTTAAAAACTATATAATATATATATGTTTAC
* *
470371 AAAATGTTTTAAAAAATATATAATATATATAT
1 AAAATGTTTTAAAAACTATATTATATATATAT
470403 TTTCAAAAAA
Statistics
Matches: 142, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
121 112 0.79
122 20 0.14
123 10 0.07
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (121 bp):
AAAATGTTTTAAAAACTATATTATATATATATATATATATATATATCAAAATGTTTTAAAAATTA
TATAATATATATATATTCAAAATGTTTTAAAAACTATATAATATATATATGTTTAC
Found at i:470277 original size:2 final size:2
Alignment explanation
Indices: 470266--470295 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
470256 TTTTAAAAAC
470266 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
470296 CAAAATGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:474195 original size:38 final size:40
Alignment explanation
Indices: 474139--474220 Score: 132
Period size: 38 Copynumber: 2.1 Consensus size: 40
474129 TAAGAAATGA
*
474139 TAAAATATACAGTGATAAAAATATTTATACA-TTTTACACT
1 TAAAATATA-AGTGATAAAAATATTTATACACTTTTACAAT
474179 TAAAATAT-AGTGATAAAAATATTTATACACTTTTACAAT
1 TAAAATATAAGTGATAAAAATATTTATACACTTTTACAAT
474218 TAA
1 TAA
474221 TATTTATGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
38 21 0.52
39 11 0.28
40 8 0.20
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.38
Consensus pattern (40 bp):
TAAAATATAAGTGATAAAAATATTTATACACTTTTACAAT
Found at i:476239 original size:23 final size:24
Alignment explanation
Indices: 476213--476263 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
476203 AATATTTGTT
*
476213 ATTTCAAA-TTCATATAAAATATA
1 ATTTCAAACCTCATATAAAATATA
* * *
476236 ATTTTAAACCTGATATAAGATATA
1 ATTTCAAACCTCATATAAAATATA
476260 ATTT
1 ATTT
476264 AAGAAATGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (24 bp):
ATTTCAAACCTCATATAAAATATA
Found at i:476281 original size:23 final size:24
Alignment explanation
Indices: 476224--476282 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
476214 TTTCAAATTC
**
476224 ATATAAAATATAATTTTAAACCTG
1 ATATAAAATATAATTTTAAAAATG
*
476248 ATATAAGATATAA-TTTAAGAAATG
1 ATATAAAATATAATTTTAA-AAATG
476272 ATA-AAAATATA
1 ATATAAAATATA
476283 CAGTGATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 12 0.40
24 18 0.60
ACGTcount: A:0.56, C:0.03, G:0.07, T:0.34
Consensus pattern (24 bp):
ATATAAAATATAATTTTAAAAATG
Found at i:476779 original size:16 final size:16
Alignment explanation
Indices: 476758--476803 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
476748 TTACCCGACC
* *
476758 TGTTTTCAACCTGACT
1 TGTTTTTAACCTGACA
*
476774 TGTTTTTAACCTCACA
1 TGTTTTTAACCTGACA
476790 TGTTTTTAACCTGA
1 TGTTTTTAACCTGA
476804 TCTGATATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.46
Consensus pattern (16 bp):
TGTTTTTAACCTGACA
Found at i:477060 original size:23 final size:23
Alignment explanation
Indices: 477032--477096 Score: 130
Period size: 23 Copynumber: 2.8 Consensus size: 23
477022 AAAATTAAAA
477032 ATAGTTTAATTTATATAAATTAT
1 ATAGTTTAATTTATATAAATTAT
477055 ATAGTTTAATTTATATAAATTAT
1 ATAGTTTAATTTATATAAATTAT
477078 ATAGTTTAATTTATATAAA
1 ATAGTTTAATTTATATAAA
477097 GAAAAAATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.51
Consensus pattern (23 bp):
ATAGTTTAATTTATATAAATTAT
Found at i:477070 original size:14 final size:14
Alignment explanation
Indices: 477032--477094 Score: 56
Period size: 14 Copynumber: 5.2 Consensus size: 14
477022 AAAATTAAAA
477032 ATAGTTTAATTTAT
1 ATAGTTTAATTTAT
477046 ATA----AA-TTAT
1 ATAGTTTAATTTAT
477055 ATAGTTTAATTTAT
1 ATAGTTTAATTTAT
477069 ATA----AA-TTAT
1 ATAGTTTAATTTAT
477078 ATAGTTTAATTTAT
1 ATAGTTTAATTTAT
477092 ATA
1 ATA
477095 AAGAAAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 20
0.66 0.00 0.34
Matches are distributed among these distances:
9 14 0.36
10 4 0.10
13 4 0.10
14 17 0.44
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (14 bp):
ATAGTTTAATTTAT
Found at i:477267 original size:7 final size:6
Alignment explanation
Indices: 477255--477306 Score: 50
Period size: 7 Copynumber: 7.8 Consensus size: 6
477245 ATTATATTAG
*
477255 GGTTTA GGATTTA GTGTTTA TGGTTTA GGATTA GGGTTTA GAGTTTA GGTTT
1 GGTTTA GG-TTTA G-GTTTA -GGTTTA GGTTTA -GGTTTA G-GTTTA GGTTT
477307 TTATAATTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
6 12 0.31
7 25 0.64
8 2 0.05
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.48
Consensus pattern (6 bp):
GGTTTA
Found at i:477273 original size:14 final size:12
Alignment explanation
Indices: 477255--477306 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 12
477245 ATTATATTAG
477255 GGTTTAGGATTTA
1 GGTTTAGG-TTTA
477268 GTGTTTATGGTTTA
1 G-GTTTA-GGTTTA
*
477282 GGATTAGGGTTTA
1 GGTTTA-GGTTTA
477295 GAGTTTAGGTTT
1 G-GTTTAGGTTT
477307 TTATAATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 17 0.52
14 14 0.42
15 2 0.06
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.48
Consensus pattern (12 bp):
GGTTTAGGTTTA
Found at i:477293 original size:20 final size:20
Alignment explanation
Indices: 477255--477303 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
477245 ATTATATTAG
*
477255 GGTTTAGGATTTAGTGTTTA
1 GGTTTAGGATTTAGGGTTTA
477275 TGGTTTAGGA-TTAGGGTTTA
1 -GGTTTAGGATTTAGGGTTTA
477295 GAGTTTAGG
1 G-GTTTAGG
477304 TTTTTATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 1 0.04
20 16 0.62
21 9 0.35
ACGTcount: A:0.20, C:0.00, G:0.35, T:0.45
Consensus pattern (20 bp):
GGTTTAGGATTTAGGGTTTA
Found at i:477399 original size:15 final size:15
Alignment explanation
Indices: 477379--477415 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
477369 TAATTTACTT
477379 TATATAGTTTATATA
1 TATATAGTTTATATA
477394 TATATAGTTTATATA
1 TATATAGTTTATATA
477409 TACTATA
1 TA-TATA
477416 CATGGTTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:478061 original size:25 final size:26
Alignment explanation
Indices: 478019--478067 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
478009 TTGATCTAGC
* *
478019 TGGTTTATATATATATA-TATATACA
1 TGGTTTATACATACATATTATATACA
478044 TGGTTTATACATACATATTATATA
1 TGGTTTATACATACATATTATATA
478068 AAATTATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (26 bp):
TGGTTTATACATACATATTATATACA
Found at i:478520 original size:2 final size:2
Alignment explanation
Indices: 478509--478703 Score: 153
Period size: 2 Copynumber: 101.0 Consensus size: 2
478499 ATAGTGTTTC
478509 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
478550 TC TA TA GA T- TA CT- TA TA T- TA GT- TA TA CA TA CA TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* *
478590 TA TA TA -A TA TA -A T- TA T- TA TA AA CTA TA T- TT TA TA TA GT-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA
* * * * * *
478628 TT TA TA TA TA GTT TA TA TA CA TA CA TA CA TA TC TA TA -A TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
478670 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
478704 GAAAATTAAA
Statistics
Matches: 154, Mismatches: 22, Indels: 34
0.73 0.10 0.16
Matches are distributed among these distances:
1 12 0.08
2 137 0.89
3 5 0.03
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:478928 original size:12 final size:12
Alignment explanation
Indices: 478911--478935 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
478901 AAAATTTATA
478911 TTCCCTCTAAAT
1 TTCCCTCTAAAT
478923 TTCCCTCTAAAT
1 TTCCCTCTAAAT
478935 T
1 T
478936 CTCAATTTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (12 bp):
TTCCCTCTAAAT
Found at i:479115 original size:15 final size:14
Alignment explanation
Indices: 479095--479218 Score: 88
Period size: 15 Copynumber: 9.1 Consensus size: 14
479085 ACATACTTTT
479095 TATAGTTTATACATA
1 TATAGTTTATA-ATA
*
479110 TATAGTTTA-CATA
1 TATAGTTTATAATA
479123 TATAG-TT-T-ATA
1 TATAGTTTATAATA
479134 TATAGTTCATATAA-A
1 TATAGTT--TATAATA
* *
479149 CATAATTTAT-ATA
1 TATAGTTTATAATA
*
479162 TATAGCTTATAATTA
1 TATAGTTTATAA-TA
479177 TATAGTTTATAATA
1 TATAGTTTATAATA
479191 TAAATAGTTTAT-ATA
1 T--ATAGTTTATAATA
479206 TA-A-TTTAT-ATA
1 TATAGTTTATAATA
479217 TA
1 TA
479219 AACTTGTATT
Statistics
Matches: 91, Mismatches: 7, Indels: 26
0.73 0.06 0.21
Matches are distributed among these distances:
11 18 0.20
12 5 0.05
13 20 0.22
14 5 0.05
15 33 0.36
16 10 0.11
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.48
Consensus pattern (14 bp):
TATAGTTTATAATA
Found at i:479120 original size:13 final size:13
Alignment explanation
Indices: 479104--479140 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
479094 TTATAGTTTA
479104 TACATATATAGTT
1 TACATATATAGTT
479117 TACATATATAGTT
1 TACATATATAGTT
479130 T--ATATATAGTT
1 TACATATATAGTT
479141 CATATAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 10 0.42
13 14 0.58
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (13 bp):
TACATATATAGTT
Found at i:479146 original size:13 final size:12
Alignment explanation
Indices: 479107--479218 Score: 59
Period size: 11 Copynumber: 8.6 Consensus size: 12
479097 TAGTTTATAC
*
479107 ATATATAGTTTAC
1 ATATATAG-TTAT
479120 ATATATAGTT-T
1 ATATATAGTTAT
479131 ATATATAGTTCAT
1 ATATATAGTT-AT
* *
479144 ATAAACATAATTTAT
1 AT--ATAT-AGTTAT
479159 ATATATAGCTTAT
1 ATATATAG-TTAT
479172 AATTATATAGTTTAT
1 -A-TATATAG-TTAT
479187 AATATAAATAGTT-T
1 -ATAT--ATAGTTAT
*
479201 ATATATAATT-T
1 ATATATAGTTAT
479212 ATATATA
1 ATATATA
479219 AACTTGTATT
Statistics
Matches: 82, Mismatches: 7, Indels: 22
0.74 0.06 0.20
Matches are distributed among these distances:
11 23 0.28
12 3 0.04
13 22 0.27
14 5 0.06
15 22 0.27
16 7 0.09
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (12 bp):
ATATATAGTTAT
Found at i:479185 original size:28 final size:27
Alignment explanation
Indices: 479095--479218 Score: 82
Period size: 26 Copynumber: 4.6 Consensus size: 27
479085 ACATACTTTT
479095 TATAGTTTATACATATATAG-TT-TACATA
1 TATAGTTTAT--ATATATAGCTTATA-ATA
* *
479123 TATAGTTTATATATAGT-TCATATAA-A
1 TATAGTTTATATATA-TAGCTTATAATA
* *
479149 CATAATTTATATATATAGCTTATAATTA
1 TATAGTTTATATATATAGCTTATAA-TA
479177 TATAGTTTATAATATAAATAG-TT-T-ATA
1 TATAGTTTAT-ATAT--ATAGCTTATAATA
*
479204 TATAATTTATATATA
1 TATAGTTTATATATA
479219 AACTTGTATT
Statistics
Matches: 78, Mismatches: 9, Indels: 22
0.72 0.08 0.20
Matches are distributed among these distances:
24 1 0.01
25 1 0.01
26 29 0.37
27 14 0.18
28 22 0.28
29 5 0.06
30 2 0.03
31 4 0.05
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.48
Consensus pattern (27 bp):
TATAGTTTATATATATAGCTTATAATA
Found at i:479192 original size:20 final size:19
Alignment explanation
Indices: 479169--479216 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 19
479159 ATATATAGCT
479169 TATAATTATATAGTTTATA
1 TATAATTATATAGTTTATA
*
479188 -AT-A-TAAATAGTTTATA
1 TATAATTATATAGTTTATA
479204 TATAATTTATATA
1 TATAA-TTATATA
479217 TAAACTTGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 7
0.72 0.06 0.22
Matches are distributed among these distances:
16 12 0.52
17 3 0.13
18 3 0.13
20 5 0.22
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (19 bp):
TATAATTATATAGTTTATA
Found at i:479205 original size:27 final size:28
Alignment explanation
Indices: 479150--479235 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 28
479140 TCATATAAAC
* *
479150 ATAATTTATATATATAGCT--TATAATTAT
1 ATAATTTATATATA-AACTAGTATTA-TAT
*
479178 ATAGTTTATAATATAAA-TAGT-TTATAT
1 ATAATTTAT-ATATAAACTAGTATTATAT
*
479205 ATAATTTATATATAAACTTGTATTATAT
1 ATAATTTATATATAAACTAGTATTATAT
479233 ATA
1 ATA
479236 CTATATTTTC
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
26 7 0.15
27 15 0.31
28 20 0.42
29 6 0.12
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (28 bp):
ATAATTTATATATAAACTAGTATTATAT
Found at i:484255 original size:31 final size:31
Alignment explanation
Indices: 484217--484312 Score: 165
Period size: 31 Copynumber: 3.1 Consensus size: 31
484207 GAATAGAAAG
484217 TTTGATTGACAACACTTCAATTGTTATGTGA
1 TTTGATTGACAACACTTCAATTGTTATGTGA
484248 TTTGATTGACAACACTTCAATTGTTATGTGA
1 TTTGATTGACAACACTTCAATTGTTATGTGA
* * *
484279 TTTGATTGACAACACTTAAATAGTTAAGTGA
1 TTTGATTGACAACACTTCAATTGTTATGTGA
484310 TTT
1 TTT
484313 AATTAATAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.42
Consensus pattern (31 bp):
TTTGATTGACAACACTTCAATTGTTATGTGA
Found at i:485561 original size:17 final size:17
Alignment explanation
Indices: 485539--485571 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
485529 TTAATGGTGT
485539 TGTTGTTACC-TCCTCTA
1 TGTTG-TACCATCCTCTA
485556 TGTTGTACCATCCTCT
1 TGTTGTACCATCCTCT
485572 TTGAAGTGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.12, C:0.30, G:0.12, T:0.45
Consensus pattern (17 bp):
TGTTGTACCATCCTCTA
Found at i:487752 original size:2 final size:2
Alignment explanation
Indices: 487745--487772 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
487735 TACTTGATTC
487745 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
487773 TATTTTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:490960 original size:32 final size:32
Alignment explanation
Indices: 490924--490996 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
490914 TTGATACATG
* *
490924 TATTGATATATGTATCAGTACT-CTAAGAACAA
1 TATTGATATAGGTATAAGTACTAC-AAGAACAA
*
490956 TATTGATATGGGTATAAGTACTACAAGAACAA
1 TATTGATATAGGTATAAGTACTACAAGAACAA
*
490988 TATCGATAT
1 TATTGATAT
490997 TGTCATCCTG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
32 35 0.97
33 1 0.03
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (32 bp):
TATTGATATAGGTATAAGTACTACAAGAACAA
Found at i:494594 original size:20 final size:20
Alignment explanation
Indices: 494569--494616 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
494559 GCATTTTCAG
* *
494569 AACTTTGAAGAAAGTTTTTA
1 AACTTTGAAGAAAATTTTAA
494589 AACTTTTG-AGAAAATTTTAA
1 AAC-TTTGAAGAAAATTTTAA
494609 AACTTTGA
1 AACTTTGA
494617 TAAAACTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 4 0.17
20 16 0.67
21 4 0.17
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40
Consensus pattern (20 bp):
AACTTTGAAGAAAATTTTAA
Found at i:494596 original size:21 final size:20
Alignment explanation
Indices: 494572--494632 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
494562 TTTTCAGAAC
* *
494572 TTTGAAGAAAGTTTTTAAACT
1 TTTG-AGAAAATTTTAAAACT
494593 TTTGAGAAAATTTTAAAAC-
1 TTTGAGAAAATTTTAAAACT
* *
494612 TTTGATAAAACTTTTGAAACT
1 TTTGAGAAAA-TTTTAAAACT
494633 CTTACTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 9 0.26
20 21 0.62
21 4 0.12
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (20 bp):
TTTGAGAAAATTTTAAAACT
Found at i:494745 original size:21 final size:21
Alignment explanation
Indices: 494691--494745 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
494681 TTATGGGTGC
* **
494691 AAAGGTTCGAAACTTTTTGTA
1 AAAGTTTCGAAACTTTTAATA
*
494712 AAA-TTTTGAAACTTTTAATA
1 AAAGTTTCGAAACTTTTAATA
494732 AAAGTTTCGAAACT
1 AAAGTTTCGAAACT
494746 CCTACTAAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (21 bp):
AAAGTTTCGAAACTTTTAATA
Found at i:499975 original size:24 final size:24
Alignment explanation
Indices: 499942--499994 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
499932 AGGCGGATAT
*
499942 TCAGGGGTCTCGGAATGGTGCAGA
1 TCAGGGGTCTCGGAACGGTGCAGA
* *
499966 TCAGGTGTCTCGGAACGGTGCTGA
1 TCAGGGGTCTCGGAACGGTGCAGA
499990 TCAGG
1 TCAGG
499995 AGTCGGGTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.40, T:0.23
Consensus pattern (24 bp):
TCAGGGGTCTCGGAACGGTGCAGA
Found at i:501246 original size:21 final size:20
Alignment explanation
Indices: 501204--501248 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
501194 TGAAGAAATG
*
501204 AGAGAAAAAATAAAAGCTAA
1 AGAGAAAAAATAAAAGATAA
* *
501224 AGAGAAAAAATTAAGGATGAA
1 AGAGAAAAAATAAAAGAT-AA
501245 AGAG
1 AGAG
501249 GAAAGAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.64, C:0.02, G:0.22, T:0.11
Consensus pattern (20 bp):
AGAGAAAAAATAAAAGATAA
Found at i:509565 original size:18 final size:19
Alignment explanation
Indices: 509537--509575 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
509527 TCTCTTATTT
*
509537 TTTACTTTAATTGCTTTTA
1 TTTACTTTAATCGCTTTTA
*
509556 TTTA-TTTAATCGTTTTTA
1 TTTACTTTAATCGCTTTTA
509574 TT
1 TT
509576 ACTACTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.21, C:0.08, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTACTTTAATCGCTTTTA
Found at i:514459 original size:64 final size:63
Alignment explanation
Indices: 514391--514620 Score: 219
Period size: 64 Copynumber: 3.6 Consensus size: 63
514381 TTGGAACACT
* ***
514391 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGAC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGAC
** * **
514455 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGAC
* * * * * **
514519 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCA
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATAGA
*
514583 T
63 C
* * *
514584 TGATGCATCGATGCATGTACTGATGCATCGGTGCATG
1 TGATGCATCGATGCATGGAGTG-TGCATCGATGCATG
514621 CCTTTGAATA
Statistics
Matches: 136, Mismatches: 25, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
63 4 0.03
64 68 0.50
65 64 0.47
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (63 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGAC
Found at i:514543 original size:19 final size:19
Alignment explanation
Indices: 514519--514569 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
514509 GAAAATATTC
514519 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
514538 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
514557 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
514570 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:514545 original size:65 final size:65
Alignment explanation
Indices: 514412--514571 Score: 216
Period size: 65 Copynumber: 2.5 Consensus size: 65
514402 TGCACCAAGT
* ***
514412 GTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGACTGATGCATCGATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGACAGATGCATCGATGCATGGAGA
* **
514476 GTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGACAGA-TGCATCGATGCATGGAG
514540 A
65 A
* *
514541 GTGCATCGGTGCATGGAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
514572 CAATTAATTC
Statistics
Matches: 84, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 37 0.44
65 47 0.56
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGACAGATGCATCGATGCATGGAGA
Found at i:514611 original size:65 final size:63
Alignment explanation
Indices: 514413--514620 Score: 210
Period size: 65 Copynumber: 3.2 Consensus size: 63
514403 GCACCAAGTG
** *
514413 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGACTGATGCATCGATGCATGGCTTG-
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATTCA-TGATGCATCGATGCATGAC-TGA
*
514477 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGA--
1 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAA-ATTCATGA-TGCATCGATGCAT-GACT
514539 GA
62 GA
* * * *
514541 GTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCATTGATGCATCGATGCATGTACT
1 -TGCATCGATGCATGAAATGCATTCGATGTTTGAA-AAATTCA-TGATGCATCGATGCATG-ACT
514605 GA
62 GA
*
514607 TGCATCGGTGCATG
1 TGCATCGATGCATG
514621 CCTTTGAATA
Statistics
Matches: 123, Mismatches: 9, Indels: 23
0.79 0.06 0.15
Matches are distributed among these distances:
63 11 0.09
64 44 0.36
65 62 0.50
66 6 0.05
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (63 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATTCATGATGCATCGATGCATGACTGA
Found at i:514812 original size:20 final size:21
Alignment explanation
Indices: 514789--514828 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
514779 GAATCGAATA
514789 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
514809 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
514829 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:523049 original size:64 final size:65
Alignment explanation
Indices: 522981--523161 Score: 172
Period size: 64 Copynumber: 2.8 Consensus size: 65
522971 TTGGAACACT
*
522981 TGATGCATC-AGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGC
1 TGATGCATCGA-TGCACCAAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAATAGC
523044 C
65 C
***** **
523045 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTC
1 TGATGCATCGATGCACCAAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAATAGCC
* *** * **
523109 AGAGTGCATCGATGCATGGAGAGTGCATC-AGTGCATGGAATGCATTCGATGTT
1 TGA-TGCATCGATGCACCAAGTGTGCATCGA-TGCATCAAATGCATTCGATGTT
523162 CAATTAATTC
Statistics
Matches: 99, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
64 52 0.53
65 47 0.47
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.29
Consensus pattern (65 bp):
TGATGCATCGATGCACCAAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAATAGCC
Found at i:523133 original size:19 final size:19
Alignment explanation
Indices: 523109--523159 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
523099 GAAAATATTC
523109 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
523128 AGAGTGCATC-AGTGCATGG
1 AGAGTGCATCGA-TGCATGG
523147 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
523160 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.27, C:0.16, G:0.33, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:523135 original size:65 final size:65
Alignment explanation
Indices: 523002--523161 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 65
522992 TGCACCAAGT
* ***
523002 GTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGATGCATCGATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
* **
523066 GTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGA-TGCATCGATGCATGGAG
523130 A
65 A
*
523131 GTGCATC-AGTGCATGGAATGCATTCGATGTT
1 GTGCATCGA-TGCATGAAATGCATTCGATGTT
523162 CAATTAATTC
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 38 0.45
65 46 0.55
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
Found at i:523401 original size:20 final size:21
Alignment explanation
Indices: 523378--523417 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
523368 GAATCGAATA
523378 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
523398 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
523418 AACTTAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Done.