Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008844.1 Hibiscus syriacus cultivar Beakdansim tig00112051_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: 694789
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
File 2 of 2
Found at i:330839 original size:82 final size:82
Alignment explanation
Indices: 330753--330960 Score: 245
Period size: 82 Copynumber: 2.5 Consensus size: 82
330743 AGCATGCTAA
* ** * *
330753 AATTCACCATTCGATTCAATTCAATCATGAAAACATACAATAGTTTATCATTCAACTTGGTTTGA
1 AATTCACCATTCAATTCAATTCAATCATGGCAACATACAATAGTTAATCATTCAACTTGGTTCGA
*
330818 TCACAATATAATGCAAC
66 TCACAATAGAATGCAAC
* * * * *
330835 AATTCACCATTCAATTGAATTGAATCAAGGCAACATATAATAGTTAATCATTCAACTTTGTTCGA
1 AATTCACCATTCAATTCAATTCAATCATGGCAACATACAATAGTTAATCATTCAACTTGGTTCGA
*** * *
330900 TCATGGTAGATTGCAAT
66 TCACAATAGAATGCAAC
* * *
330917 AATTCAACATTCAATTCAATTCCATCATGGCAGCATACAATAGT
1 AATTCACCATTCAATTCAATTCAATCATGGCAACATACAATAGT
330961 GTTGGGACCG
Statistics
Matches: 103, Mismatches: 23, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
82 103 1.00
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.33
Consensus pattern (82 bp):
AATTCACCATTCAATTCAATTCAATCATGGCAACATACAATAGTTAATCATTCAACTTGGTTCGA
TCACAATAGAATGCAAC
Found at i:339789 original size:65 final size:64
Alignment explanation
Indices: 339654--339789 Score: 157
Period size: 65 Copynumber: 2.1 Consensus size: 64
339644 ACACCCCATT
* * * *
339654 TCGAATGCATTTTATGCACCGACACACAGCCATGCATCGATGCAGTCTAGATTTTATTTAAACA
1 TCGAATGCATTTTATGCACCGACACACAGCCATGCACCGATGCACTCTAGATTGTATTGAAACA
** * * *
339718 TCGAATGCATTTTATGCACCGATGCACATGCTATGCACCGATGCACTCCTGGCTTGT-TTGAAAC
1 TCGAATGCATTTTATGCACCGACACACA-GCCATGCACCGATGCACT-CTAGATTGTATTGAAAC
339782 A
64 A
*
339783 TTGAATG
1 TCGAATG
339790 TAATAAGTGT
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
64 26 0.43
65 28 0.47
66 6 0.10
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (64 bp):
TCGAATGCATTTTATGCACCGACACACAGCCATGCACCGATGCACTCTAGATTGTATTGAAACA
Found at i:356409 original size:41 final size:41
Alignment explanation
Indices: 356364--356672 Score: 196
Period size: 41 Copynumber: 7.5 Consensus size: 41
356354 TGATCTTGGC
* *
356364 AGCATGCAATAGTTCATCATTCAACTTGATTCAATCATTGT
1 AGCATGCAATAATTCATCATTCAACTTGATTCAATCATGGT
* * *
356405 AGCATGCAATAATTCACCATTCAA-TTCAATTCAATCATGGC
1 AGCATGCAATAATTCATCATTCAACTT-GATTCAATCATGGT
* * * ** *
356446 AACATACAATAGTTCATCATTCAACTTGATTTGATCATGTT
1 AGCATGCAATAATTCATCATTCAACTTGATTCAATCATGGT
* * * *
356487 ATCATGCAATAATTCA-CTATTCAA-TTCAATTCAATCAAGGC
1 AGCATGCAATAATTCATC-ATTCAACTT-GATTCAATCATGGT
* ** * ** *
356528 ATCATATAATAATTCATCATTGAACTTGATTTGATCATCGT
1 AGCATGCAATAATTCATCATTCAACTTGATTCAATCATGGT
* * * * ** * * *
356569 AGCAGGCAATAATTCACCATTCGA-TTCAATTCCTTTATAGC
1 AGCATGCAATAATTCATCATTCAACTT-GATTCAATCATGGT
* * * * * *
356610 AGTATTCAA-AAGTTAATCATTCAACTTTATTCGATCACGGT
1 AGCATGCAATAA-TTCATCATTCAACTTGATTCAATCATGGT
*
356651 AGCATGCAATAATTCACCATTC
1 AGCATGCAATAATTCATCATTC
356673 GATTCAATTC
Statistics
Matches: 195, Mismatches: 63, Indels: 20
0.70 0.23 0.07
Matches are distributed among these distances:
40 9 0.05
41 177 0.91
42 9 0.05
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (41 bp):
AGCATGCAATAATTCATCATTCAACTTGATTCAATCATGGT
Found at i:356483 original size:82 final size:82
Alignment explanation
Indices: 356360--356729 Score: 420
Period size: 82 Copynumber: 4.5 Consensus size: 82
356350 AGTTTGATCT
* * **
356360 TGGCAGCATGCAATAGTTCATCATTCAACTTGATTCAATCATTGTAGCATGCAATAATTCACCAT
1 TGGCAACATACAATAGTTCATCATTCAACTTGATTTGATCATTGTAGCATGCAATAATTCACCAT
356425 TCAATTCAATTCAATCA
66 TCAATTCAATTCAATCA
* *
356442 TGGCAACATACAATAGTTCATCATTCAACTTGATTTGATCA-TGTTATCATGCAATAATTCACTA
1 TGGCAACATACAATAGTTCATCATTCAACTTGATTTGATCATTG-TAGCATGCAATAATTCACCA
356506 TTCAATTCAATTCAATCA
65 TTCAATTCAATTCAATCA
* * * * * * *
356524 AGGCATCATATAATAATTCATCATTGAACTTGATTTGATCATCGTAGCAGGCAATAATTCACCAT
1 TGGCAACATACAATAGTTCATCATTCAACTTGATTTGATCATTGTAGCATGCAATAATTCACCAT
* ** *
356589 TCGATTCAATTCCTTTA
66 TCAATTCAATTCAATCA
* ** * * * * * **
356606 TAGCAGTATTCAAAAGTTAATCATTCAACTTTATTCGATCACGGTAGCATGCAATAATTCACCAT
1 TGGCAACATACAATAGTTCATCATTCAACTTGATTTGATCATTGTAGCATGCAATAATTCACCAT
*
356671 TCGATTCAATTCAATCA
66 TCAATTCAATTCAATCA
* * * *
356688 AGGCAATAGATAATAGTTCATCATTCAACTTGAATTT-ATCAT
1 TGGCAACATACAATAGTTCATCATTCAACTTG-ATTTGATCAT
356730 GGCAGCAAGC
Statistics
Matches: 237, Mismatches: 48, Indels: 6
0.81 0.16 0.02
Matches are distributed among these distances:
81 2 0.01
82 231 0.97
83 4 0.02
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.35
Consensus pattern (82 bp):
TGGCAACATACAATAGTTCATCATTCAACTTGATTTGATCATTGTAGCATGCAATAATTCACCAT
TCAATTCAATTCAATCA
Found at i:356580 original size:164 final size:163
Alignment explanation
Indices: 356371--356729 Score: 468
Period size: 164 Copynumber: 2.2 Consensus size: 163
356361 GGCAGCATGC
* * *
356371 AATAGTTCATCATTCAACTTGATTCAATCATTGTAGCATGCAATAATTCACCATTCAATTCAATT
1 AATAGTTCATCATTCAACTTGATT-TATCATCGTAGCAGGCAATAATTCACCATTCAATTCAATT
* * * * * * *
356436 CAATCATGGCAACATACAATAGTTCATCATTCAACTTGATTTGATCATGTTATCATGCAATAATT
65 CAATCATAGCAACATACAAAAGTTAATCATTCAACTTGATTCGATCACGGTAGCATGCAATAATT
* *
356501 CACTATTCAATTCAATTCAATCAAGGC-ATCATAT
130 CACCATTCAATTCAATTCAATCAAGGCAAT-AGAT
* * *
356535 AATAATTCATCATTGAACTTGATTTGATCATCGTAGCAGGCAATAATTCACCATTCGATTCAATT
1 AATAGTTCATCATTCAACTTGATTT-ATCATCGTAGCAGGCAATAATTCACCATTCAATTCAATT
** * ** * *
356600 CCTTTATAGCAGTATTCAAAAGTTAATCATTCAACTTTATTCGATCACGGTAGCATGCAATAATT
65 CAATCATAGCAACATACAAAAGTTAATCATTCAACTTGATTCGATCACGGTAGCATGCAATAATT
*
356665 CACCATTCGATTCAATTCAATCAAGGCAATAGAT
130 CACCATTCAATTCAATTCAATCAAGGCAATAGAT
356699 AATAGTTCATCATTCAACTTGAATTTATCAT
1 AATAGTTCATCATTCAACTTG-ATTTATCAT
356730 GGCAGCAAGC
Statistics
Matches: 167, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
164 161 0.96
165 6 0.04
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.35
Consensus pattern (163 bp):
AATAGTTCATCATTCAACTTGATTTATCATCGTAGCAGGCAATAATTCACCATTCAATTCAATTC
AATCATAGCAACATACAAAAGTTAATCATTCAACTTGATTCGATCACGGTAGCATGCAATAATTC
ACCATTCAATTCAATTCAATCAAGGCAATAGAT
Found at i:361899 original size:47 final size:45
Alignment explanation
Indices: 361800--361924 Score: 146
Period size: 47 Copynumber: 2.8 Consensus size: 45
361790 GTAAGTATGC
* **
361800 AAATAAGCTTACGAGCTTAT-GAAT-AACGACAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGATA
* *
361843 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGTTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATTGATA
* * *
361890 AAATAAGCTTAAGAGCATATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
361925 AGATTTTATA
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
43 20 0.29
44 3 0.04
45 11 0.16
46 1 0.01
47 35 0.50
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGATA
Found at i:363953 original size:13 final size:13
Alignment explanation
Indices: 363915--363974 Score: 50
Period size: 13 Copynumber: 4.3 Consensus size: 13
363905 AAGTGAAATC
363915 ATCAATAAA-TGAT
1 ATCAA-AAAGTGAT
363928 ATCAGAAAAGTGAT
1 ATCA-AAAAGTGAT
*
363942 ATCAACAAGTGAAAT
1 ATCAAAAAGTG--AT
*
363957 CATCAATAAGTGAT
1 -ATCAAAAAGTGAT
363971 ATCA
1 ATCA
363975 TAAATGGTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
13 17 0.43
14 11 0.28
15 2 0.05
16 10 0.25
ACGTcount: A:0.50, C:0.12, G:0.13, T:0.25
Consensus pattern (13 bp):
ATCAAAAAGTGAT
Found at i:363967 original size:16 final size:16
Alignment explanation
Indices: 363905--363975 Score: 62
Period size: 16 Copynumber: 4.8 Consensus size: 16
363895 ATTGTTGAAA
363905 AAGTGAAATCATCAAT
1 AAGTGAAATCATCAAT
* * *
363921 AAATGATATCA-GAA-
1 AAGTGAAATCATCAAT
*
363935 AAGTG--AT-ATCAAC
1 AAGTGAAATCATCAAT
363948 AAGTGAAATCATCAAT
1 AAGTGAAATCATCAAT
*
363964 AAGTGATATCAT
1 AAGTGAAATCAT
363976 AAATGGTTGC
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
11 1 0.02
12 4 0.09
13 5 0.12
14 4 0.09
15 4 0.09
16 25 0.58
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.25
Consensus pattern (16 bp):
AAGTGAAATCATCAAT
Found at i:366959 original size:20 final size:20
Alignment explanation
Indices: 366934--366971 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
366924 TTTCATAGAG
366934 AGTTTTAAAATTCGAGGATT
1 AGTTTTAAAATTCGAGGATT
366954 AGTTTTAAAATTCGAGGA
1 AGTTTTAAAATTCGAGGA
366972 CGAATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (20 bp):
AGTTTTAAAATTCGAGGATT
Found at i:366979 original size:20 final size:20
Alignment explanation
Indices: 366936--366980 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
366926 TCATAGAGAG
** *
366936 TTTTAAAATTCGAGGATTAG
1 TTTTAAAATTCGAGGACGAA
366956 TTTTAAAATTCGAGGACGAA
1 TTTTAAAATTCGAGGACGAA
366976 TTTTA
1 TTTTA
366981 TTAAGGAGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.40
Consensus pattern (20 bp):
TTTTAAAATTCGAGGACGAA
Found at i:369179 original size:47 final size:45
Alignment explanation
Indices: 369084--369208 Score: 146
Period size: 47 Copynumber: 2.8 Consensus size: 45
369074 GTAAGTATGC
* * *
369084 AAATAAGCTTACAAGCTTAT-GAAT-AATGGCAAATATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGATA
* * *
369127 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTGTTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATTGATA
* *
369174 AAATAAGCTTAAGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
369209 AGATTTTATA
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
43 19 0.27
44 3 0.04
45 11 0.16
46 1 0.01
47 36 0.51
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGATA
Found at i:385555 original size:10 final size:10
Alignment explanation
Indices: 385540--385569 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
385530 CGGGATCTTA
385540 TTTTCAATTT
1 TTTTCAATTT
385550 TTTTCAATTT
1 TTTTCAATTT
385560 TTTTCAATTT
1 TTTTCAATTT
385570 AGCTTCAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTCAATTT
Found at i:396920 original size:4 final size:4
Alignment explanation
Indices: 396906--396936 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
396896 CATTATCCGT
396906 TTTA TTTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TT
396937 GTAGGAATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:400721 original size:16 final size:17
Alignment explanation
Indices: 400700--400734 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
400690 TTACTATTCA
400700 CGTGAATAGTG-AATTT
1 CGTGAATAGTGAAATTT
400716 CGTGAATAGTGAAATTT
1 CGTGAATAGTGAAATTT
400733 CG
1 CG
400735 GTCGGCGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:401502 original size:15 final size:16
Alignment explanation
Indices: 401484--401516 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
401474 GTGGCAGATC
401484 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
*
401499 AAAATCTAGAACGGGA
1 AAAATCCAGAACGGGA
401515 AA
1 AA
401517 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:406747 original size:23 final size:25
Alignment explanation
Indices: 406706--406753 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
406696 TTCTTTTAAT
*
406706 TATATGATTTAATAATATAATATAA
1 TATATGATTTAATAATATAACATAA
*
406731 TATAT-ATTT-ATATTATAACATAA
1 TATATGATTTAATAATATAACATAA
406754 ATCAAACTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 12 0.57
24 4 0.19
25 5 0.24
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (25 bp):
TATATGATTTAATAATATAACATAA
Found at i:411656 original size:22 final size:22
Alignment explanation
Indices: 411631--411682 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
411621 GTTTGGACTT
411631 CAATTTGGAGTTGATCTTTGAG
1 CAATTTGGAGTTGATCTTTGAG
411653 CAATTTGGAGTTGATCTTTGAG
1 CAATTTGGAGTTGATCTTTGAG
411675 CAATTTGG
1 CAATTTGG
411683 CTCGACTCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.23, C:0.10, G:0.27, T:0.40
Consensus pattern (22 bp):
CAATTTGGAGTTGATCTTTGAG
Found at i:422971 original size:88 final size:90
Alignment explanation
Indices: 422868--423078 Score: 293
Period size: 88 Copynumber: 2.4 Consensus size: 90
422858 TCATGAACCT
* * *
422868 TTATGCATTTTCATTTGTGGCATCATTTCATGCCAATAATGCATCATTATGCATTTTCATTTATA
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCAATAATGCACCATTATGCATTTT-ATTTATA
* *
422933 GAAT-TTTCATGCC-A-ATTGCAAAG
65 GAATATGTCATGCCGATAATGCAAAG
* * *
422956 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTATTTATGG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCAATAATGCACCATTATGCATTTTATTTATAG
**
423021 AATCATGTCATGCCGATAATGCACCG
66 AAT-ATGTCATGCCGATAATGCAAAG
423047 TTATGCATTTTCATTTATGGCATCCTTTCATG
1 TTATGCATTTTCATTTATGGCATCCTTTCATG
423079 GTGATATGCA
Statistics
Matches: 109, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
87 10 0.09
88 52 0.48
89 8 0.07
90 1 0.01
91 38 0.35
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (90 bp):
TTATGCATTTTCATTTATGGCATCCTTTCATGCCAATAATGCACCATTATGCATTTTATTTATAG
AATATGTCATGCCGATAATGCAAAG
Found at i:423032 original size:45 final size:46
Alignment explanation
Indices: 422868--423129 Score: 329
Period size: 45 Copynumber: 5.8 Consensus size: 46
422858 TCATGAACCT
* * * * *
422868 TTATGCATTTTCATTTGTGGCATCATTTCATGCCAATAATGCATCA
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
* * * **
422914 TTATGCATTTTCATTTATAGAAT--TTTCATGCC-A-ATTGCAAAG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
422956 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
* * *
423002 TTATGCATTTT-ATTTATGGAATCATGTCATGCCGATAATGCACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
**
423047 TTATGCATTTTCATTTATGGCATCCTTTCATGGTGAT-ATGCACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
* *
423092 TTATGGATTTTCATTGATGGCATCCTTTCATGCCGATA
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATA
423130 CATCATTATG
Statistics
Matches: 186, Mismatches: 24, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
42 26 0.14
43 1 0.01
44 18 0.10
45 84 0.45
46 57 0.31
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (46 bp):
TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
Found at i:423073 original size:91 final size:91
Alignment explanation
Indices: 422868--423129 Score: 336
Period size: 91 Copynumber: 2.9 Consensus size: 91
422858 TCATGAACCT
* * * * * *
422868 TTATGCATTTTCATTTGTGGCATCATTTCATGCCAATAATGCATCATTATGCATTTTCATTTATA
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTTATG
*
422933 GAAT-TTTCATGCC-A-ATTGCAAAG
66 GAATCTTTCATGCCGATAATGCAAAG
422956 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTT-ATTTATG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTTATG
* **
423020 GAATCATGTCATGCCGATAATGCACCG
66 GAATC-TTTCATGCCGATAATGCAAAG
** * *
423047 TTATGCATTTTCATTTATGGCATCCTTTCATGGTGAT-ATGCACCGTTATGGATTTTCATTGATG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTTATG
*
423111 GCATCCTTTCATGCCGATA
66 GAAT-CTTTCATGCCGATA
423130 CATCATTATG
Statistics
Matches: 152, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
87 10 0.07
88 52 0.34
89 8 0.05
90 19 0.12
91 62 0.41
92 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (91 bp):
TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTTATG
GAATCTTTCATGCCGATAATGCAAAG
Found at i:433546 original size:23 final size:23
Alignment explanation
Indices: 433514--433557 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
433504 AAGCAGTTAA
* *
433514 AAAACTATGAAACCCTAATAATG
1 AAAACCATGAAACCATAATAATG
433537 AAAACCATGAAACCATAATAA
1 AAAACCATGAAACCATAATAA
433558 AACCAAACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.57, C:0.18, G:0.07, T:0.18
Consensus pattern (23 bp):
AAAACCATGAAACCATAATAATG
Found at i:436571 original size:26 final size:25
Alignment explanation
Indices: 436536--436617 Score: 78
Period size: 26 Copynumber: 3.1 Consensus size: 25
436526 CCATTTCATG
*
436536 TTATTATTATATATTATCATATTATA
1 TTATTGTTATATATTAT-ATATTATA
*
436562 TTATTGTTATATATTAT-TTTTATA
1 TTATTGTTATATATTATATATTATA
436586 TTATGTGGTGTAGTAT-TTATAATATTATA
1 TTAT-T-GT-TA-TATATTAT-ATATTATA
436615 TTA
1 TTA
436618 ATTATTTAGA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
24 10 0.21
25 1 0.02
26 18 0.38
27 6 0.13
28 3 0.06
29 9 0.19
ACGTcount: A:0.33, C:0.01, G:0.07, T:0.59
Consensus pattern (25 bp):
TTATTGTTATATATTATATATTATA
Found at i:436574 original size:13 final size:12
Alignment explanation
Indices: 436536--436589 Score: 56
Period size: 13 Copynumber: 4.3 Consensus size: 12
436526 CCATTTCATG
436536 TTATTATTATATA
1 TTATT-TTATATA
**
436549 TTATCATATTATA
1 TTATTTTA-TATA
436562 TTATTGTTATATA
1 TTATT-TTATATA
436575 TTATTTT-TATA
1 TTATTTTATATA
436586 TTAT
1 TTAT
436590 GTGGTGTAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
11 8 0.23
12 4 0.11
13 21 0.60
14 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (12 bp):
TTATTTTATATA
Found at i:436636 original size:22 final size:21
Alignment explanation
Indices: 436599--436640 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
436589 TGTGGTGTAG
*
436599 TATTTATAATATTATATTAAT
1 TATTTAGAATATTATATTAAT
436620 TATTTAGAATTATTATATTAA
1 TATTTAGAA-TATTATATTAA
436641 ATAAATGTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TATTTAGAATATTATATTAAT
Found at i:453502 original size:45 final size:45
Alignment explanation
Indices: 453442--453535 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 45
453432 TTTTATACGC
* * **
453442 CATTTCCATTTTGGCATCCTTTCATGCCTTTTATACGCTATTATA
1 CATTTCCATTTTGGCATCATTTCATGCATTTTATAAACTATTATA
*
453487 CATTT-CATTTATGGCATCATTTCATGCATTTTATAAATTATTATA
1 CATTTCCATTT-TGGCATCATTTCATGCATTTTATAAACTATTATA
453532 CATT
1 CATT
453536 GTTGTACATC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 5 0.12
45 38 0.88
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.48
Consensus pattern (45 bp):
CATTTCCATTTTGGCATCATTTCATGCATTTTATAAACTATTATA
Found at i:454071 original size:59 final size:59
Alignment explanation
Indices: 454008--454698 Score: 1035
Period size: 59 Copynumber: 11.7 Consensus size: 59
453998 CTCAATACAT
*
454008 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCAAACGAAGTGCCCTATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
* **
454067 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCAGACGAAGTGCCCTATA-TA
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
* * *
454125 AAATTCATACACTTAGTATGAATTTCTTAACACTTTAGCACATGAAGTGCCCTATATGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
* * *
454184 AAATTCATACACTTAGTATGAATTTCTTAACACTTTAGCACATGAAGTGCCCTATATGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
* * * *
454243 AAATTCATACACTTCGTATGAATTTCTTAATATTTTAGCACATGAAGTGCCCTATACAG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
* * * * * *
454302 AAACTCATTCACTTAGTATGAATTTCATAATATTTTAGCACTCGAAATGCCCTATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
*
454361 AAATTCATACACTTATTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
* * *
454420 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCTCTATACGA
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
* * *
454479 AAATTCATACACTTATTATAAATTTCTTAACATTTTAGCGCACGAAGTGCCCTATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
* * *
454538 AAATTCTTACACTTAGTTTGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATATGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
* * * * *
454597 AAATTCTTACACTTAGTTTAAATTTCTTAACTTTTTAGCACACGAAGT-CCACTATACAG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCC-CTATACGG
*
454656 AAATTCGTACACTTAGTATGAATTTCTTAACATTTTAGCACAC
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACAC
454699 TTAGTGACAT
Statistics
Matches: 578, Mismatches: 52, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
58 55 0.10
59 523 0.90
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (59 bp):
AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
Found at i:455667 original size:14 final size:15
Alignment explanation
Indices: 455642--455670 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
455632 ACCTGACCCA
455642 TTGACTCGTTGACCG
1 TTGACTCGTTGACCG
455657 TTGAC-CGTTGACCG
1 TTGACTCGTTGACCG
455671 GCGTTGACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.14, C:0.28, G:0.28, T:0.31
Consensus pattern (15 bp):
TTGACTCGTTGACCG
Found at i:458174 original size:48 final size:48
Alignment explanation
Indices: 458115--458243 Score: 179
Period size: 48 Copynumber: 2.7 Consensus size: 48
458105 ATTTGATTTT
458115 TGATATGATACTTGACATGGATTCTGATTTGATA-TCTAACATGGATTC
1 TGATATGATACTTGACATGGATTCTGATTTGATACT-TAACATGGATTC
* * * * *
458163 TGATCTGATACTTGACTTGGATTCTGATCTGATACTTGACATGGATTT
1 TGATATGATACTTGACATGGATTCTGATTTGATACTTAACATGGATTC
* *
458211 TGATATGATACTTGACATGAATTATGATTTGAT
1 TGATATGATACTTGACATGGATTCTGATTTGAT
458244 TTTTGATATA
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
48 69 0.99
49 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (48 bp):
TGATATGATACTTGACATGGATTCTGATTTGATACTTAACATGGATTC
Found at i:458249 original size:24 final size:24
Alignment explanation
Indices: 458115--458243 Score: 161
Period size: 24 Copynumber: 5.4 Consensus size: 24
458105 ATTTGATTTT
*
458115 TGATATGATACTTGACATGGATTC
1 TGATCTGATACTTGACATGGATTC
* *
458139 TGATTTGATA-TCTAACATGGATTC
1 TGATCTGATACT-TGACATGGATTC
*
458163 TGATCTGATACTTGACTTGGATTC
1 TGATCTGATACTTGACATGGATTC
*
458187 TGATCTGATACTTGACATGGATTT
1 TGATCTGATACTTGACATGGATTC
* * *
458211 TGATATGATACTTGACATGAATTA
1 TGATCTGATACTTGACATGGATTC
*
458235 TGATTTGAT
1 TGATCTGAT
458244 TTTTGATATA
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
23 1 0.01
24 90 0.98
25 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (24 bp):
TGATCTGATACTTGACATGGATTC
Found at i:462822 original size:24 final size:24
Alignment explanation
Indices: 462795--462885 Score: 114
Period size: 24 Copynumber: 3.8 Consensus size: 24
462785 TCGATTTAAT
*
462795 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATATGATACT-TGACATGGA
*
462819 TTCTGATTTGATACTTGA-ATTGGA
1 TTCTGATATGATACTTGACA-TGGA
*
462843 TTCTGATATGATACTTGACCTGGA
1 TTCTGATATGATACTTGACATGGA
*
462867 TTTTGATATGATACTTGAC
1 TTCTGATATGATACTTGAC
462886 GTGAATTATG
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
23 1 0.02
24 58 0.97
25 1 0.02
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (24 bp):
TTCTGATATGATACTTGACATGGA
Found at i:462897 original size:24 final size:24
Alignment explanation
Indices: 462810--462902 Score: 96
Period size: 24 Copynumber: 3.9 Consensus size: 24
462800 ATCTGATATC
* * *
462810 TGACATGGATTCTGATTTGATACT
1 TGACCTGGATTATGATATGATACT
** *
462834 TGAATTGGATTCTGATATGATACT
1 TGACCTGGATTATGATATGATACT
*
462858 TGACCTGGATTTTGATATGATACT
1 TGACCTGGATTATGATATGATACT
* * *
462882 TGACGTGAATTATGATTTGAT
1 TGACCTGGATTATGATATGAT
462903 TTTTGATATA
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.42
Consensus pattern (24 bp):
TGACCTGGATTATGATATGATACT
Found at i:464008 original size:95 final size:95
Alignment explanation
Indices: 463871--464042 Score: 272
Period size: 95 Copynumber: 1.8 Consensus size: 95
463861 AGATACTTCT
* * * *
463871 ATACCATGGTACTGACACCCCCTTCCGGTATCGATACCAAATTTAGGTTCAATGTTTCCTGGTAT
1 ATACCATGGTACCGACACCCCCTTCCGGTATCGATACAAAATTTAGATTCAATGTTGCCTGGTAT
463936 CGATACCCTTACCATGGTATCGATTCTATA
66 CGATACCCTTACCATGGTATCGATTCTATA
* * * *
463966 ATACTATGGTACCGATACCCCCTTCCGGTATCGATACAAAATTTAGATTCGATGTTGCTTGGTAT
1 ATACCATGGTACCGACACCCCCTTCCGGTATCGATACAAAATTTAGATTCAATGTTGCCTGGTAT
464031 CGATACCCTTAC
66 CGATACCCTTAC
464043 TATGATATTG
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
95 69 1.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.33
Consensus pattern (95 bp):
ATACCATGGTACCGACACCCCCTTCCGGTATCGATACAAAATTTAGATTCAATGTTGCCTGGTAT
CGATACCCTTACCATGGTATCGATTCTATA
Found at i:484714 original size:178 final size:181
Alignment explanation
Indices: 484398--484755 Score: 591
Period size: 178 Copynumber: 2.0 Consensus size: 181
484388 ATAGTCTTTA
*
484398 TAGTGCAACCAGTTACGGAGCATGTTTAACTGTATAAAAAAATACAACAATTTATGTTGGGATAA
1 TAGTGCAACCAGTTAAGGAGCATGTTTAACTGTATAAAAAAATACAACAATTTATGTTGGGATAA
484463 CATTGATCTCAAGTCTGAGGATCATACATATAGTCATTACCATGAGAAATGTCATAGTCGTCAAA
66 CATTGATCTCAAGTCTGAGGATCATACATATAGTCATTACCATGAGAAATGTCATAGTCGTCAAA
484528 TAATAATCCAAGATATATGCTCA-AG-GTAGGTCAATCCGATACATTGTTCTC
131 TAATAATCCAAGATATATGCTCATAGCG-A-GTCAATCCGATACATTGTTCTC
* * * *
484579 TAGT-CAA-CAGTTAAGGAGCATGTTTAACTGTATCAACATATATAACAATTTATGTTGGGAT-A
1 TAGTGCAACCAGTTAAGGAGCATGTTTAACTGTATAAAAAAATACAACAATTTATGTTGGGATAA
* *
484641 CATTGATCTCAAGTCTGAGGATCATACATATAGTCATTACCATGAGCAATGTCATAGTCGTCACA
66 CATTGATCTCAAGTCTGAGGATCATACATATAGTCATTACCATGAGAAATGTCATAGTCGTCAAA
*
484706 TAATAATCCAAGATATATGCTCATAGCGAGTCAATCCGATTCATTGTTCT
131 TAATAATCCAAGATATATGCTCATAGCGAGTCAATCCGATACATTGTTCT
484756 TTAATAATAT
Statistics
Matches: 167, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
178 107 0.64
179 52 0.31
180 4 0.02
181 4 0.02
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (181 bp):
TAGTGCAACCAGTTAAGGAGCATGTTTAACTGTATAAAAAAATACAACAATTTATGTTGGGATAA
CATTGATCTCAAGTCTGAGGATCATACATATAGTCATTACCATGAGAAATGTCATAGTCGTCAAA
TAATAATCCAAGATATATGCTCATAGCGAGTCAATCCGATACATTGTTCTC
Found at i:486849 original size:17 final size:17
Alignment explanation
Indices: 486815--486856 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
486805 CCCTTACCTT
* *
486815 TCTTT-GAGAGAAATTC
1 TCTTTCGAGAAAAACTC
486831 TCTTTCGAGAAAAACTC
1 TCTTTCGAGAAAAACTC
*
486848 TCATTCGAG
1 TCTTTCGAG
486857 CAACAAACAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (17 bp):
TCTTTCGAGAAAAACTC
Found at i:488451 original size:15 final size:16
Alignment explanation
Indices: 488431--488460 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
488421 TATGACAAAG
488431 TCATG-TAAATTTAAT
1 TCATGTTAAATTTAAT
488446 TCATGTTAAATTTAA
1 TCATGTTAAATTTAA
488461 GGACAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (16 bp):
TCATGTTAAATTTAAT
Found at i:502760 original size:20 final size:21
Alignment explanation
Indices: 502735--502782 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
502725 AAATGAGTAG
502735 TATCGATAC-CCTACATGC-AA
1 TATCGATACTCCTACAT-CAAA
*
502755 TATCGATACTCCTACCTCAAA
1 TATCGATACTCCTACATCAAA
502776 TATCGAT
1 TATCGAT
502783 GCCCCTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.33, C:0.29, G:0.08, T:0.29
Consensus pattern (21 bp):
TATCGATACTCCTACATCAAA
Found at i:503199 original size:18 final size:19
Alignment explanation
Indices: 503155--503200 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
503145 GAAACAAAAA
503155 ACCCCAAATATGCTCAAAT
1 ACCCCAAATATGCTCAAAT
503174 ACCCCAAATATGCTCAAAT
1 ACCCCAAATATGCTCAAAT
503193 A-CCCAAAT
1 ACCCCAAAT
503201 CCCTATACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 7 0.26
19 20 0.74
ACGTcount: A:0.43, C:0.33, G:0.04, T:0.20
Consensus pattern (19 bp):
ACCCCAAATATGCTCAAAT
Found at i:505414 original size:21 final size:21
Alignment explanation
Indices: 505389--505428 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
505379 CGGTAAAATT
* *
505389 TACCTAAAATATTATTATTTC
1 TACCTAAAACATTAATATTTC
505410 TACCTAAAACATTAATATT
1 TACCTAAAACATTAATATT
505429 CTTTAACAAT
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:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (21 bp):
TACCTAAAACATTAATATTTC
Found at i:509215 original size:31 final size:31
Alignment explanation
Indices: 509180--509242 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
509170 TTTGACTTAA
*
509180 GGAAGATGATAAGGTTGAGGTGTCTTGGTTT
1 GGAAGATGATAAGGTTGAGATGTCTTGGTTT
*
509211 GGAAGATTATAAGGTTGAGATGTCTTGGTTT
1 GGAAGATGATAAGGTTGAGATGTCTTGGTTT
509242 G
1 G
509243 ATGGTAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.24, C:0.03, G:0.37, T:0.37
Consensus pattern (31 bp):
GGAAGATGATAAGGTTGAGATGTCTTGGTTT
Found at i:516663 original size:27 final size:27
Alignment explanation
Indices: 516614--516665 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
516604 CTCTTTCTCC
* * *
516614 TCACATTCCTCTCGAATTATCTCTTCT
1 TCACACTCCTCTCAAATGATCTCTTCT
*
516641 TCACACTCCTCTCAAATGCTCTCTT
1 TCACACTCCTCTCAAATGATCTCTT
516666 TACACTCTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.19, C:0.37, G:0.04, T:0.40
Consensus pattern (27 bp):
TCACACTCCTCTCAAATGATCTCTTCT
Found at i:519728 original size:10 final size:10
Alignment explanation
Indices: 519710--519778 Score: 58
Period size: 10 Copynumber: 7.1 Consensus size: 10
519700 TTTAAGCATC
519710 TCTCATTTTT
1 TCTCATTTTT
*
519720 TCTCCTTTTT
1 TCTCATTTTT
519730 T-T-ATTTTT
1 TCTCATTTTT
519738 T-TCATTTTT
1 TCTCATTTTT
*
519747 T-TTATTTTT
1 TCTCATTTTT
519756 TCTTC-TTTTT
1 TC-TCATTTTT
519766 TCTTCTATTTTT
1 TC-TC-ATTTTT
519778 T
1 T
519779 AGCTCTTACG
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
8 7 0.14
9 16 0.32
10 20 0.40
11 1 0.02
12 6 0.12
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.78
Consensus pattern (10 bp):
TCTCATTTTT
Found at i:519736 original size:17 final size:18
Alignment explanation
Indices: 519714--519766 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
519704 AGCATCTCTC
519714 ATTTTTTCTCCTTTTTTT
1 ATTTTTTCTCCTTTTTTT
*
519732 ATTTTTT-TCATTTTTTTT
1 ATTTTTTCTC-CTTTTTTT
*
519750 ATTTTTTCTTCTTTTTT
1 ATTTTTTCTCCTTTTTT
519767 CTTCTATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 2 0.07
18 27 0.90
19 1 0.03
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (18 bp):
ATTTTTTCTCCTTTTTTT
Found at i:519737 original size:9 final size:9
Alignment explanation
Indices: 519725--519766 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
519715 TTTTTTCTCC
519725 TTTTTTTAT
1 TTTTTTTAT
*
519734 TTTTTTCAT
1 TTTTTTTAT
519743 TTTTTTTAT
1 TTTTTTTAT
*
519752 TTTTTCTTCT
1 TTTTT-TTAT
519762 TTTTT
1 TTTTT
519767 CTTCTATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
9 21 0.72
10 8 0.28
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:522133 original size:20 final size:20
Alignment explanation
Indices: 522108--522157 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
522098 ACAGTGATGT
522108 TATCGGTACCTGTAGTAGGG
1 TATCGGTACCTGTAGTAGGG
522128 TATCGGTACCTGTAGTAGGG
1 TATCGGTACCTGTAGTAGGG
522148 TATCGGTACC
1 TATCGGTACC
522158 CCTGTAGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.20, C:0.18, G:0.32, T:0.30
Consensus pattern (20 bp):
TATCGGTACCTGTAGTAGGG
Found at i:522650 original size:45 final size:45
Alignment explanation
Indices: 522596--522772 Score: 273
Period size: 45 Copynumber: 3.9 Consensus size: 45
522586 AATTTATTAT
* * * *
522596 CAATTTACTTACCAGTTATCTCATAAGCTCCTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTTCATAAGCTCGTAAGCTTATTTTAC
522641 CAATATACTTACCATTTATTTCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTTCATAAGCTCGTAAGCTTATTTTAC
* * *
522686 CAGTATACTTACCATTTATTCCATAATCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTTCATAAGCTCGTAAGCTTATTTTAC
* *
522731 CAATATACTTACCATTTATTTCATAAGCTCATAAGCATATTT
1 CAATATACTTACCATTTATTTCATAAGCTCGTAAGCTTATTT
522773 GCATGGTTAC
Statistics
Matches: 120, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 120 1.00
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.41
Consensus pattern (45 bp):
CAATATACTTACCATTTATTTCATAAGCTCGTAAGCTTATTTTAC
Found at i:524714 original size:30 final size:30
Alignment explanation
Indices: 524678--524744 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
524668 AAAATTACAT
* * * * *
524678 TTTGGTCTATAAACTTTTCAAAGTTTATAC
1 TTTGGTCGACAAACTTTACAAAATTTATAA
*
524708 TTTGGTCGCCAAACTTTACAAAATTTATAA
1 TTTGGTCGACAAACTTTACAAAATTTATAA
524738 TTTGGTC
1 TTTGGTC
524745 ACTAAATAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (30 bp):
TTTGGTCGACAAACTTTACAAAATTTATAA
Found at i:527573 original size:11 final size:11
Alignment explanation
Indices: 527557--527590 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
527547 CTTTTCCCAA
527557 TTAAATTAATT
1 TTAAATTAATT
527568 TTAAATTAATT
1 TTAAATTAATT
527579 TTAAATTAATT
1 TTAAATTAATT
527590 T
1 T
527591 AAACTCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TTAAATTAATT
Found at i:528309 original size:39 final size:39
Alignment explanation
Indices: 528255--528332 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
528245 TTGAAGCTAG
528255 AGTGATTGTGCCACATCATGTTAAACCACCAATGTCCTA
1 AGTGATTGTGCCACATCATGTTAAACCACCAATGTCCTA
528294 AGTGATTGTGCCACATCATGTTAAACCACCAATGTCCTA
1 AGTGATTGTGCCACATCATGTTAAACCACCAATGTCCTA
528333 TATCTAAGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (39 bp):
AGTGATTGTGCCACATCATGTTAAACCACCAATGTCCTA
Found at i:531270 original size:18 final size:17
Alignment explanation
Indices: 531216--531271 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 17
531206 ATATCAAAAG
* *
531216 AAAAGAAAAAATAAAAA
1 AAAAGAAAAAAGAGAAA
531233 TAAAAGATAAAAAG-GCAAA
1 -AAAAGA-AAAAAGAG-AAA
531252 AAAAGAGAAAAAGAGAAA
1 AAAAGA-AAAAAGAGAAA
531270 AA
1 AA
531272 GCCGAATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
18 23 0.72
19 9 0.28
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (17 bp):
AAAAGAAAAAAGAGAAA
Found at i:539621 original size:51 final size:51
Alignment explanation
Indices: 539557--539674 Score: 146
Period size: 51 Copynumber: 2.3 Consensus size: 51
539547 TTTAGAATTA
* * * * *
539557 TATTCATTATTTTATTAGGAATTAAGATAGAGTTAAAATATTACCTTTGGCT
1 TATT-ATTATTTTATTAGGAATTAAGATAAAATCAAAACATTACCTTTAGCT
* * **
539609 TATTATTATTTTATTAGGAATTAGGATAAAATCAAAACATTATCTTTATTT
1 TATTATTATTTTATTAGGAATTAAGATAAAATCAAAACATTACCTTTAGCT
539660 TATTATTATTTTATT
1 TATTATTATTTTATT
539675 CAGTAGTTAC
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
51 53 0.93
52 4 0.07
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.49
Consensus pattern (51 bp):
TATTATTATTTTATTAGGAATTAAGATAAAATCAAAACATTACCTTTAGCT
Found at i:554779 original size:137 final size:135
Alignment explanation
Indices: 554526--554802 Score: 376
Period size: 137 Copynumber: 2.0 Consensus size: 135
554516 GTCATAGGTG
* * *
554526 CATTTCGACATACTTTGTATATGACGGTTATCGATCGATTTTGTGTAATGCATATGTTGCATTTT
1 CATTTCAACATACTTTGTATATGACGGGTATCAATCGATTTTGTGTAATGCATATGTTGCATTTT
* * * *
554591 CATATCAGTACTATGTGTACTTTTGGCACTATATGTGCATCCATGGTATTCATAATGAGTTTGTG
66 CATATCAGTACTATATGTACTTTTGGCACTATATCTGCATCCATGGAATTCATAATGAG-TTATG
554656 AATTAC
130 AATTAC
* * *
554662 CATTTCAACATACATTTGTGTATGA-GGGTATCAATCGATTTTGTTTAATGCATATGTTGTATTT
1 CATTTCAACATAC-TTTGTATATGACGGGTATCAATCGATTTTGTGTAATGCATATGTTGCA-TT
** * * *
554726 TTTGTATCGGTACTATATGTACTTTTGGCATTATGTCTGCATCCATGGAATTCATAATGAGTTAT
64 TTCATATCAGTACTATATGTACTTTTGGCACTATATCTGCATCCATGGAATTCATAATGAGTTAT
*
554791 GAATTTC
129 GAATTAC
554798 CATTT
1 CATTT
554803 GGCACTTAGG
Statistics
Matches: 123, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
136 58 0.47
137 65 0.53
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (135 bp):
CATTTCAACATACTTTGTATATGACGGGTATCAATCGATTTTGTGTAATGCATATGTTGCATTTT
CATATCAGTACTATATGTACTTTTGGCACTATATCTGCATCCATGGAATTCATAATGAGTTATGA
ATTAC
Found at i:556769 original size:15 final size:15
Alignment explanation
Indices: 556729--556761 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
556719 TTATCCATCT
556729 ATTTCCATCATATCC
1 ATTTCCATCATATCC
556744 ATTTCCATCATATCC
1 ATTTCCATCATATCC
556759 ATT
1 ATT
556762 ATCATCATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTTCCATCATATCC
Found at i:559905 original size:21 final size:20
Alignment explanation
Indices: 559877--559915 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
559867 CATTGTAGGA
*
559877 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCCACAAAAG
*
559897 ATTTCATGGCTTCCACAAA
1 ATTT-ATGGCCTCCACAAA
559916 GACCTTGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCCACAAAAG
Found at i:571104 original size:12 final size:12
Alignment explanation
Indices: 571087--571111 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
571077 AAGCATATAT
571087 CTAAAATAACAC
1 CTAAAATAACAC
571099 CTAAAATAACAC
1 CTAAAATAACAC
571111 C
1 C
571112 GAAGATCCAA
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:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (12 bp):
CTAAAATAACAC
Found at i:573244 original size:28 final size:28
Alignment explanation
Indices: 573179--573246 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
573169 TGTAAAATAA
573179 ATAAAAGTATTAAAATTAAGGACTAAATT
1 ATAAAA-TATTAAAATTAAGGACTAAATT
* *
573208 ATAACATATTAAAATTAAAAGGTCT-AATT
1 ATAAAATATTAAAATT--AAGGACTAAATT
573237 -TAAAATATTA
1 ATAAAATATTA
573247 TAAAAACTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 19 0.56
29 9 0.26
30 6 0.18
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.34
Consensus pattern (28 bp):
ATAAAATATTAAAATTAAGGACTAAATT
Found at i:574210 original size:3 final size:3
Alignment explanation
Indices: 574202--574233 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
574192 AGGGGAAAAC
574202 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
574234 ATTTTATGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:579673 original size:22 final size:21
Alignment explanation
Indices: 579639--579692 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
579629 TACTAAAAAT
*
579639 GAGTATC-AGTACCATATTATA
1 GAGTATCGA-TACCATAGTATA
*
579660 GAAGTATCGATACCATGGTATA
1 G-AGTATCGATACCATAGTATA
579682 G-GTATCGATAC
1 GAGTATCGATAC
579693 TATTGAGCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 10 0.34
21 1 0.03
22 17 0.59
23 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (21 bp):
GAGTATCGATACCATAGTATA
Found at i:580205 original size:81 final size:80
Alignment explanation
Indices: 580089--580244 Score: 197
Period size: 81 Copynumber: 1.9 Consensus size: 80
580079 TTTTAAAATG
* * * * * * *
580089 AAAGATTAATGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAA-TTTGATGAAAGGT
1 AAAGATTAATACCTAACTGTGCATTTGGAAAAAAGGTGCCAATCATG-CAAGTTAGACGAAAGGT
580153 TAAATGCCTTTGGGTA
65 TAAATGCCTTTGGGTA
* *
580169 AAAGATTAAATACCTAACTGTGTATTTGGAAAAAAGGTGTCAATCATGCAAGTTAGACGAAAGGT
1 AAAGATT-AATACCTAACTGTGCATTTGGAAAAAAGGTGCCAATCATGCAAGTTAGACGAAAGGT
*
580234 TAATTGCCTTT
65 TAAATGCCTTT
580245 AGAGGAAATA
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
80 10 0.16
81 54 0.84
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (80 bp):
AAAGATTAATACCTAACTGTGCATTTGGAAAAAAGGTGCCAATCATGCAAGTTAGACGAAAGGTT
AAATGCCTTTGGGTA
Found at i:580260 original size:81 final size:80
Alignment explanation
Indices: 580100--580274 Score: 183
Period size: 81 Copynumber: 2.2 Consensus size: 80
580090 AAGATTAATG
* * * * * * *
580100 CCTAGCTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAATTTGATGAAAGGTTAAATGCCTTTG
1 CCTAACTGTGTATTTGGAAAAAAGGTGCCAATCATGCCAATTAGACGAAAGGTTAAATGCCTTTG
*
580165 GGTAAAAGATTAAATA
66 GG-AAAAGACTAAATA
* *
580181 CCTAACTGTGTATTTGGAAAAAAGGTGTCAATCATG-CAAGTTAGACGAAAGGTTAATTGCCTTT
1 CCTAACTGTGTATTTGGAAAAAAGGTGCCAATCATGCCAA-TTAGACGAAAGGTTAAATGCCTTT
*
580245 AGAGG-AAATACTAAATA
65 -G-GGAAAAGACTAAATA
* *
580262 CTTAACTATGTAT
1 CCTAACTGTGTAT
580275 GTTAACATAA
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
80 3 0.04
81 72 0.92
82 1 0.01
83 2 0.03
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.30
Consensus pattern (80 bp):
CCTAACTGTGTATTTGGAAAAAAGGTGCCAATCATGCCAATTAGACGAAAGGTTAAATGCCTTTG
GGAAAAGACTAAATA
Found at i:582200 original size:511 final size:511
Alignment explanation
Indices: 581239--582263 Score: 1836
Period size: 511 Copynumber: 2.0 Consensus size: 511
581229 ATGAAAAAGA
*
581239 GGAGGAATGCCCTATGGAGGCTGACTTATGGTTGAATGATGTAATGATAATACTTAACAATCTTC
1 GGAGGAATGCCCTATGGAGGCTGACTTATGGCTGAATGATGTAATGATAATACTTAACAATCTTC
581304 ACTGCTTGGATTTAGAGAATCTAGGAGGAGCTGTATCGTTAATAAAGGGATCAACTCGAGTGAGG
66 ACTGCTTGGATTTAGAGAATCTAGGAGGAGCTGTATCGTTAATAAAGGGATCAACTCGAGTGAGG
*
581369 TGGACAAATACTGCAATGTATGCACCACCATAACAATTGACATGGTAGTTCTTTCAAAAAGAATT
131 TGGACAAATACTGCAATGTATGCACCACCATAACAATTGACATGGTAGTTCTTTCAAAAACAATT
*
581434 TAACAATAAGTATATTGGTGAGCAGTTCAGAGGAGAGATACTGATGAAGTTTCTCAATTTGAAAC
196 TAACAATAAGTATATTGGTGAGCACTTCAGAGGAGAGATACTGATGAAGTTTCTCAATTTGAAAC
* **
581499 AAGGAGACTGATGAGTACATGAGTACGAGGCTGAGTATAATAAGTTGAGTTGTTTTGCTACTAAG
261 AAGGAGACTGAGGAGTACATGAGTACGAGGCTGAGTATAATAAGTTGAGCCGTTTTGCTACTAAG
*
581564 GTGGTTTCCAATGGCAAGGCCCGACGTGATTGGTTTATTGAGGGATTGAGGCCAAAGTTAAAAGA
326 GTGGTTTCCAATGGCAAGGCCCGACGCGATTGGTTTATTGAGGGATTGAGGCCAAAGTTAAAAGA
581629 ATTGATGTTGGCTTTGAGTGTGCCTAGCTTGCAAGAAGTTATAAACTGAGAAAAAGCTATTGAAA
391 ATTGATGTTGGCTTTGAGTGTGCCTAGCTTGCAAGAAGTTATAAACTGAGAAAAAGCTATTGAAA
* * * * *
581694 TAGCTCAAACGGAGACATTAGTAGTATAACAGAGTTTATAGATGGGGAAAAGGGTT
456 GAGCTCAAACGGAGACATTAGCAGTAGAACAGAGTTTACAGATGAGGAAAAGGGTT
* * *
581750 GGAGGAATGCCCTATGGAGGCTGACTTATGGCTGAATGTTGTAGTGATAATGCTTAACAATCTTC
1 GGAGGAATGCCCTATGGAGGCTGACTTATGGCTGAATGATGTAATGATAATACTTAACAATCTTC
*
581815 ACTGCTTGGATTTAGAGAATCTAGGAGGAGCTGTATCGTTAATAAAGGGATCAGCTCGAGTGAGG
66 ACTGCTTGGATTTAGAGAATCTAGGAGGAGCTGTATCGTTAATAAAGGGATCAACTCGAGTGAGG
581880 TGGACAAATACTGCAATGTATGCACCACCGA-AACAATTGACATGGTAGTTCTTTCAAAAACAAT
131 TGGACAAATACTGCAATGTATGCACCACC-ATAACAATTGACATGGTAGTTCTTTCAAAAACAAT
581944 TTAACAATAAGTATATTGGTGAGCACTTCAGAGGAGAGATACTGATGAAGTTTCTCAATTTGAAA
195 TTAACAATAAGTATATTGGTGAGCACTTCAGAGGAGAGATACTGATGAAGTTTCTCAATTTGAAA
* * *
582009 CAAGGAGACTGAGGAGTACATGAGTACGAGGCTGAGTATAATACGTTGAGCCGTTTTGCTATTGA
260 CAAGGAGACTGAGGAGTACATGAGTACGAGGCTGAGTATAATAAGTTGAGCCGTTTTGCTACTAA
*
582074 GGTGGTTTCCAATGGCAAGGCCTGACGCGATTGGTTTATTGAGGGATTGAGGCCAAAGTTAAAAG
325 GGTGGTTTCCAATGGCAAGGCCCGACGCGATTGGTTTATTGAGGGATTGAGGCCAAAGTTAAAAG
**
582139 AATTGATGTTGGCTTTGAGTGTGCCTAGCTTGCAAGAAGTTATAAACTGAGCCAAAGCTATTGAA
390 AATTGATGTTGGCTTTGAGTGTGCCTAGCTTGCAAGAAGTTATAAACTGAGAAAAAGCTATTGAA
582204 AGAGCTCAAACGGAGACATTAGCAGTAGAACAGAGTTTACAGATGAGGAAAAGGGTT
455 AGAGCTCAAACGGAGACATTAGCAGTAGAACAGAGTTTACAGATGAGGAAAAGGGTT
582261 GGA
1 GGA
582264 ATGCCTTCAA
Statistics
Matches: 491, Mismatches: 22, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
511 490 1.00
512 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (511 bp):
GGAGGAATGCCCTATGGAGGCTGACTTATGGCTGAATGATGTAATGATAATACTTAACAATCTTC
ACTGCTTGGATTTAGAGAATCTAGGAGGAGCTGTATCGTTAATAAAGGGATCAACTCGAGTGAGG
TGGACAAATACTGCAATGTATGCACCACCATAACAATTGACATGGTAGTTCTTTCAAAAACAATT
TAACAATAAGTATATTGGTGAGCACTTCAGAGGAGAGATACTGATGAAGTTTCTCAATTTGAAAC
AAGGAGACTGAGGAGTACATGAGTACGAGGCTGAGTATAATAAGTTGAGCCGTTTTGCTACTAAG
GTGGTTTCCAATGGCAAGGCCCGACGCGATTGGTTTATTGAGGGATTGAGGCCAAAGTTAAAAGA
ATTGATGTTGGCTTTGAGTGTGCCTAGCTTGCAAGAAGTTATAAACTGAGAAAAAGCTATTGAAA
GAGCTCAAACGGAGACATTAGCAGTAGAACAGAGTTTACAGATGAGGAAAAGGGTT
Found at i:594936 original size:15 final size:13
Alignment explanation
Indices: 594908--594942 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
594898 TTTGACTATA
594908 GGAAATTTTTAAT
1 GGAAATTTTTAAT
594921 GGAATATTTTTCAAT
1 GGAA-ATTTTT-AAT
594936 GGAAATT
1 GGAAATT
594943 AGTAATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 9 0.45
15 7 0.35
ACGTcount: A:0.37, C:0.03, G:0.17, T:0.43
Consensus pattern (13 bp):
GGAAATTTTTAAT
Found at i:596561 original size:14 final size:14
Alignment explanation
Indices: 596542--596569 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
596532 ACCTCGTATT
596542 ATTTTAAAGTATGA
1 ATTTTAAAGTATGA
596556 ATTTTAAAGTATGA
1 ATTTTAAAGTATGA
596570 TATAATTCTA
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:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (14 bp):
ATTTTAAAGTATGA
Found at i:597075 original size:16 final size:17
Alignment explanation
Indices: 597050--597085 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
597040 GAAAGTTATA
*
597050 AAAAGTATATGAAAA-G
1 AAAAGAATATGAAAATG
597066 AAAAGAATATGAAAATG
1 AAAAGAATATGAAAATG
597083 AAA
1 AAA
597086 TATGAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (17 bp):
AAAAGAATATGAAAATG
Found at i:606766 original size:17 final size:19
Alignment explanation
Indices: 606738--606786 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
606728 TATTTTGAAA
606738 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
606756 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
606775 CACCGATGCACT
1 CATCGATGCACT
606787 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:608455 original size:21 final size:22
Alignment explanation
Indices: 608414--608458 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
608404 CCAAAGTAAG
*
608414 ATTCATAATAAACATCATATAT
1 ATTCATAATAAACAGCATATAT
*
608436 ATTCATGATAAA-AGCATATAT
1 ATTCATAATAAACAGCATATAT
608457 AT
1 AT
608459 AATAACCATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (22 bp):
ATTCATAATAAACAGCATATAT
Found at i:614879 original size:20 final size:20
Alignment explanation
Indices: 614851--614889 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
614841 TTCTGAAAAT
*
614851 TAGGTGCAATAATGATACTA
1 TAGGGGCAATAATGATACTA
*
614871 TAGGGGCAATATTGATACT
1 TAGGGGCAATAATGATACT
614890 CTCCCTAGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (20 bp):
TAGGGGCAATAATGATACTA
Found at i:619178 original size:61 final size:61
Alignment explanation
Indices: 619100--619324 Score: 306
Period size: 61 Copynumber: 3.7 Consensus size: 61
619090 GGTTAATCCT
* * *
619100 ACCATATGCACTGAGTGTCATTTATATACACTGTAATTCTAATACACATAAGGTCGTGCCC
1 ACCATATGCACTAAGTGTCCTTTATATACACTGTAATGCTAATACACATAAGGTCGTGCCC
* * **
619161 ACCATATGCACTAAGTGTCCTTTATATACACTGTAGTGCTAATACACATAAGGTCGGGCTT
1 ACCATATGCACTAAGTGTCCTTTATATACACTGTAATGCTAATACACATAAGGTCGTGCCC
** * * *
619222 GTCATATGCACTAAGTGTCTTTTATATACATTGTAATGCTAATATACATAAGGTCGTGCCC
1 ACCATATGCACTAAGTGTCCTTTATATACACTGTAATGCTAATACACATAAGGTCGTGCCC
* * * *
619283 ACCCTATGCACTAAGTGTCCTCTATATACACTATAGTGCTAA
1 ACCATATGCACTAAGTGTCCTTTATATACACTGTAATGCTAA
619325 ATCGAATATG
Statistics
Matches: 140, Mismatches: 24, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 140 1.00
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (61 bp):
ACCATATGCACTAAGTGTCCTTTATATACACTGTAATGCTAATACACATAAGGTCGTGCCC
Found at i:619291 original size:122 final size:122
Alignment explanation
Indices: 619102--619324 Score: 374
Period size: 122 Copynumber: 1.8 Consensus size: 122
619092 TTAATCCTAC
* *
619102 CATATGCACTGAGTGTCATTTATATACACTGTAATTCTAATACACATAAGGTCGTGCCCACCATA
1 CATATGCACTAAGTGTCATTTATATACACTGTAATGCTAATACACATAAGGTCGTGCCCACCATA
* *
619167 TGCACTAAGTGTCCTTTATATACACTGTAGTGCTAATACACATAAGGTCGGGCTTGT
66 TGCACTAAGTGTCCTCTATATACACTATAGTGCTAATACACATAAGGTCGGGCTTGT
* * * *
619224 CATATGCACTAAGTGTCTTTTATATACATTGTAATGCTAATATACATAAGGTCGTGCCCACCCTA
1 CATATGCACTAAGTGTCATTTATATACACTGTAATGCTAATACACATAAGGTCGTGCCCACCATA
619289 TGCACTAAGTGTCCTCTATATACACTATAGTGCTAA
66 TGCACTAAGTGTCCTCTATATACACTATAGTGCTAA
619325 ATCGAATATG
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
122 93 1.00
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.33
Consensus pattern (122 bp):
CATATGCACTAAGTGTCATTTATATACACTGTAATGCTAATACACATAAGGTCGTGCCCACCATA
TGCACTAAGTGTCCTCTATATACACTATAGTGCTAATACACATAAGGTCGGGCTTGT
Found at i:621141 original size:20 final size:20
Alignment explanation
Indices: 621071--621131 Score: 122
Period size: 20 Copynumber: 3.0 Consensus size: 20
621061 TAAGATGTTG
621071 GTATCGATACTTTAGTGGAC
1 GTATCGATACTTTAGTGGAC
621091 GTATCGATACTTTAGTGGAC
1 GTATCGATACTTTAGTGGAC
621111 GTATCGATACTTTAGTGGAC
1 GTATCGATACTTTAGTGGAC
621131 G
1 G
621132 ACTCAATACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (20 bp):
GTATCGATACTTTAGTGGAC
Found at i:625659 original size:19 final size:19
Alignment explanation
Indices: 625635--625672 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
625625 TCGATACTCC
625635 TAAGTCAGTATCAATACTA
1 TAAGTCAGTATCAATACTA
*
625654 TAAGTCAGTATCTATACTA
1 TAAGTCAGTATCAATACTA
625673 CCTCAGTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (19 bp):
TAAGTCAGTATCAATACTA
Found at i:635310 original size:20 final size:21
Alignment explanation
Indices: 635266--635317 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
635256 TGATTCAATC
* *
635266 GGTATCGATATCGAAGGGGTA
1 GGTATCGATACCGAAGGGGAA
635287 -GTATCGATACCGAA-GGGAA
1 GGTATCGATACCGAAGGGGAA
635306 GGTATCGATACC
1 GGTATCGATACC
635318 ATTTCAAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.31, C:0.15, G:0.33, T:0.21
Consensus pattern (21 bp):
GGTATCGATACCGAAGGGGAA
Found at i:635894 original size:45 final size:45
Alignment explanation
Indices: 635826--636158 Score: 273
Period size: 45 Copynumber: 7.9 Consensus size: 45
635816 CTAAAAGAAT
* *
635826 AATGCATATGGGTGCATTATTGGCGTGAAAGGATGCCATAGCTGA
1 AATGCATATGAGTGCATTATTGGCATGAAAGGATGCCATAGCTGA
* *
635871 AATACATATGAGTGTATTATTGGCATGAAAGGATGCCATAGCTGA
1 AATGCATATGAGTGCATTATTGGCATGAAAGGATGCCATAGCTGA
* * *
635916 AATGCATATGGGTGCATTATCT-G-TTTAAA--A-G--A-A--T--
1 AATGCATATGAGTGCATTAT-TGGCATGAAAGGATGCCATAGCTGA
*
635950 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGA
1 AATGCATATGAGTGCATTATTGGCATGAAAGGATGCCATAGCTGA
* * **
635995 AATGCATAT-AGGTGCATTATTGGCATGAAATGATGTCATATTTGA
1 AATGCATATGA-GTGCATTATTGGCATGAAAGGATGCCATAGCTGA
* * *
636040 AATGCATATGAGTGCATTATCGACCT-AAA--A-G--A-A--T--
1 AATGCATATGAGTGCATTATTGGCATGAAAGGATGCCATAGCTGA
* * * *
636074 AATGCATTTGGGTGCATAATTGGCATAAAAGGATGCCATAGCTGA
1 AATGCATATGAGTGCATTATTGGCATGAAAGGATGCCATAGCTGA
* * * *
636119 AATGCATATGGGTGCATTATTTGAATGAAAGGATCCCATA
1 AATGCATATGAGTGCATTATTGGCATGAAAGGATGCCATA
636159 AATAAAATCA
Statistics
Matches: 231, Mismatches: 31, Indels: 52
0.74 0.10 0.17
Matches are distributed among these distances:
33 1 0.00
34 41 0.18
35 7 0.03
36 2 0.01
37 2 0.01
38 4 0.02
39 2 0.01
40 2 0.01
41 4 0.02
42 2 0.01
43 2 0.01
44 7 0.03
45 153 0.66
46 2 0.01
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (45 bp):
AATGCATATGAGTGCATTATTGGCATGAAAGGATGCCATAGCTGA
Found at i:636041 original size:124 final size:123
Alignment explanation
Indices: 635816--636158 Score: 499
Period size: 124 Copynumber: 2.8 Consensus size: 123
635806 GAACTAATGA
* *
635816 CTAAAAGAATAATGCATATGGGTGCATTATTGGCGTGAAAGGATGCCATAGCTGAAATACATATG
1 CTAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
* * *
635881 AGTGTATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTATCTG-T
66 -GTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGAGTGCATTATC-GAC
*
635940 TTAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATA
1 CTAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATAT-
* * **
636005 GGTGCATTATTGGCATGAAATGATGTCATATTTGAAATGCATATGAGTGCATTATCGAC
65 GGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGAGTGCATTATCGAC
* * *
636064 CTAAAAGAATAATGCATTTGGGTGCATAATTGGCATAAAAGGATGCCATAGCTGAAATGCATATG
1 CTAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATAT-
* * *
636129 GGTGCATTATTTGAATGAAAGGATCCCATA
65 GGTGCATTATTGGCATGAAAGGATGCCATA
636159 AATAAAATCA
Statistics
Matches: 197, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
123 1 0.01
124 195 0.99
125 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (123 bp):
CTAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
GTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGAGTGCATTATCGAC
Found at i:641219 original size:44 final size:43
Alignment explanation
Indices: 641169--641386 Score: 170
Period size: 34 Copynumber: 5.4 Consensus size: 43
641159 CATAAAAGAA
* *
641169 AAATGCACATGGGTTCATATTGGCATGAAAGGATGCCATAGCTG
1 AAATGCATATGGGTGCATATTGGCATGAAAGGATG-CATAGCTG
*
641213 AAATGCATATGGGTGCATTATTGACAT-AAA--A-G-A-A--TG
1 AAATGCATATGGGTGCA-TATTGGCATGAAAGGATGCATAGCTG
641249 --ATGCATATGGGTGCATATTGGCATGAAAGGATGTCATAGCTG
1 AAATGCATATGGGTGCATATTGGCATGAAAGGATG-CATAGCTG
* *
641291 AAATGCATATGGGTGTATTATCGGCAT-AAA--A-G-A-A--T-
1 AAATGCATATGGGTGCA-TATTGGCATGAAAGGATGCATAGCTG
* * *
641326 -AATGCTTATGGGTGCATAATTGGCATAAAAGGATACCATAGCTG
1 AAATGCATATGGGTGCAT-ATTGGCATGAAAGGAT-GCATAGCTG
641370 AAATGCATATGGGTGCA
1 AAATGCATATGGGTGCA
641387 AAGGATGCCA
Statistics
Matches: 138, Mismatches: 11, Indels: 49
0.70 0.06 0.25
Matches are distributed among these distances:
33 9 0.07
34 39 0.28
35 3 0.02
36 4 0.03
37 2 0.01
38 2 0.01
39 3 0.02
40 2 0.01
41 3 0.02
42 4 0.03
43 1 0.01
44 35 0.25
45 31 0.22
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.27
Consensus pattern (43 bp):
AAATGCATATGGGTGCATATTGGCATGAAAGGATGCATAGCTG
Found at i:641223 original size:78 final size:78
Alignment explanation
Indices: 641004--641386 Score: 545
Period size: 78 Copynumber: 4.9 Consensus size: 78
640994 AAAATAATGA
* * *
641004 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAATGATGCCATACCTGAAATGAATATG
1 ATAAAAGAATAATGCATATGGGTGCA-TATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
* *
641069 GGAGCATTATCGTC
65 GGTGCATTATCGAC
* * *
641083 ATAAAAGAATAATGCATA--GGTGCATTATTGGCATGAGAGGATGTCATATCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCA-TATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
*
641146 GGTGCATTATCAAC
65 GGTGCATTATCGAC
* * *
641160 ATAAAAGAAAAATGCACATGGGTTCATATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGG
1 ATAAAAGAATAATGCATATGGGTGCATATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGG
*
641225 GTGCATTATTGAC
66 GTGCATTATCGAC
* *
641238 ATAAAAGAATGATGCATATGGGTGCATATTGGCATGAAAGGATGTCATAGCTGAAATGCATATGG
1 ATAAAAGAATAATGCATATGGGTGCATATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGG
* *
641303 GTGTATTATCGGC
66 GTGCATTATCGAC
* * *
641316 ATAAAAGAATAATGCTTATGGGTGCATAATTGGCATAAAAGGATACCATAGCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCAT-ATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
641381 GGTGCA
65 GGTGCA
641387 AAGGATGCCA
Statistics
Matches: 271, Mismatches: 30, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
77 67 0.25
78 142 0.52
79 62 0.23
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.27
Consensus pattern (78 bp):
ATAAAAGAATAATGCATATGGGTGCATATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGG
GTGCATTATCGAC
Found at i:642425 original size:45 final size:45
Alignment explanation
Indices: 642376--642464 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
642366 TTTCATATCA
* *
642376 ATAATACACCCATATGCATTTCAATTATGGCATTCTTTCATGCCG
1 ATAATACACCCATATGCATTTAAATTATGGCATCCTTTCATGCCG
* *
642421 ATAATGCACCCTTATGCATTTAAATTATGGCATCCTTTCATGCC
1 ATAATACACCCATATGCATTTAAATTATGGCATCCTTTCATGCC
642465 TTTTATACAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (45 bp):
ATAATACACCCATATGCATTTAAATTATGGCATCCTTTCATGCCG
Found at i:642481 original size:45 final size:45
Alignment explanation
Indices: 642388--642485 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 45
642378 AATACACCCA
* * * * *
642388 TATGCATTTCAATTATGGCATTCTTTCATGCCGATAATGCACCCT
1 TATGCATTTAAATTATGGCATCCTTTCATGCCGATAATACAACAT
** *
642433 TATGCATTTAAATTATGGCATCCTTTCATGCCTTTTATACAACAT
1 TATGCATTTAAATTATGGCATCCTTTCATGCCGATAATACAACAT
642478 TATGCATT
1 TATGCATT
642486 GTTATACATC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.41
Consensus pattern (45 bp):
TATGCATTTAAATTATGGCATCCTTTCATGCCGATAATACAACAT
Found at i:642707 original size:68 final size:68
Alignment explanation
Indices: 642603--643061 Score: 515
Period size: 68 Copynumber: 6.8 Consensus size: 68
642593 TATTTAACCG
** * * * ** * * *
642603 TTCATCTAACTATCATCATTTACACA-TTCTTGTCAAATGCACAAACAGACCTCAAAGGAACTCA
1 TTCATCTAACTGGCATGATTGACACATTTC-TATCAAATGCACAATTAGGCCTCAAAGGCACTTA
642667 GCCT
65 GCCT
* ** * * * * *
642671 TTCAACTATTTGGCATGATTGACACATTTATATCAAATACACAGTCAAGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATGATTGACACATTTCTATCAAATGCACAATTAGGCCTCAAAGGCACTTAG
642736 CCT
66 CCT
* * * * * *
642739 TTCATCTAATTGGCATTATGGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATGATTGACACATTTCTATCAAATGCACAATTAGGCCTCAAAGGCACTTAG
642804 CCT
66 CCT
* * * * *
642807 TTCATCTAACTGGCATGATTGACACATTTCTGTAAAATGCACAAGTAGGCGTCAAAGGCATTTAG
1 TTCATCTAACTGGCATGATTGACACATTTCTATCAAATGCACAATTAGGCCTCAAAGGCACTTAG
642872 CCT
66 CCT
* * * * *
642875 TTCATCTAACTGGTATGATTGACACCTTTCTATCAAATGCACAGTTAGGCCTCAAAGGAACTTGG
1 TTCATCTAACTGGCATGATTGACACATTTCTATCAAATGCACAATTAGGCCTCAAAGGCACTTAG
642940 CCT
66 CCT
* * * * *
642943 TTCATCTAACTGACATGATTGACATATTTCTGTCAAATTCACAATTAGGCATCAAAGGCACTTAG
1 TTCATCTAACTGGCATGATTGACACATTTCTATCAAATGCACAATTAGGCCTCAAAGGCACTTAG
643008 CCT
66 CCT
* * * *
643011 TTCATCTAACTGGCATGATTGACACCTTTATATTAAATGCACAGTTAGGCC
1 TTCATCTAACTGGCATGATTGACACATTTCTATCAAATGCACAATTAGGCC
643062 ATAATCTTGT
Statistics
Matches: 326, Mismatches: 64, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
68 324 0.99
69 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (68 bp):
TTCATCTAACTGGCATGATTGACACATTTCTATCAAATGCACAATTAGGCCTCAAAGGCACTTAG
CCT
Found at i:642829 original size:136 final size:135
Alignment explanation
Indices: 642652--643061 Score: 568
Period size: 136 Copynumber: 3.0 Consensus size: 135
642642 CACAAACAGA
* * ** * *
642652 CCTCAAAGGAACTCAGCCTTTCAACTATTTGGCATGATTGACACATTTATATCAAATACACAGTC
1 CCTCAAAGGAACTTAGCCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATACACAGT-
* * * * * *
642717 AAGCCTCAAAGGCACTTAGCCTTTCATCTAATTGGCATTATGGACACCTTTCTGTCAAATGCACA
65 AGGCATCAAAGGCACTTAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTATCAAATGCACA
642782 GTTAGG
130 GTTAGG
* * *
642788 CCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATGATTGACACATTTCTGTAAAATGCACAAGT
1 CCTCAAAGGAACTTAGCCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATACAC-AGT
* * *
642853 AGGCGTCAAAGGCATTTAGCCTTTCATCTAACTGGTATGATTGACACCTTTCTATCAAATGCACA
65 AGGCATCAAAGGCACTTAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTATCAAATGCACA
642918 GTTAGG
130 GTTAGG
* * * * *
642924 CCTCAAAGGAACTTGGCCTTTCATCTAACTGACATGATTGACATATTTCTGTCAAATTCACAATT
1 CCTCAAAGGAACTTAGCCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATACAC-AGT
* *
642989 AGGCATCAAAGGCACTTAGCCTTTCATCTAACTGGCATGATTGACACCTTTATATTAAATGCACA
65 AGGCATCAAAGGCACTTAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTATCAAATGCACA
643054 GTTAGG
130 GTTAGG
643060 CC
1 CC
643062 ATAATCTTGT
Statistics
Matches: 244, Mismatches: 29, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
136 241 0.99
137 3 0.01
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (135 bp):
CCTCAAAGGAACTTAGCCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATACACAGTA
GGCATCAAAGGCACTTAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTATCAAATGCACAG
TTAGG
Found at i:643347 original size:58 final size:57
Alignment explanation
Indices: 643282--643497 Score: 315
Period size: 58 Copynumber: 3.7 Consensus size: 57
643272 TCCCACATGA
* *
643282 AAATTCATACACCTAGTATGAATTTCTTAACTTTTTGTACACAAAGTGCCCAATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAATA-GG
* *
643340 AAATTCATACACTTAGTATGAACTTCTTAAATTTTTGCACACAAAGTGCCCAATAGGG
1 AAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAATA-GG
* * * * *
643398 AACTTCATACACTTAGAATGAATTTCATAACTTTTTGCACACAAAGTGACCAATAGAT
1 AAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAATAG-G
*
643456 AAATTCATACACTTCGTATGAATTTCTTAACTTTTTGCACAC
1 AAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACAC
643498 TTAGTGCCAT
Statistics
Matches: 141, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
57 1 0.01
58 140 0.99
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (57 bp):
AAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAATAGG
Found at i:647649 original size:45 final size:45
Alignment explanation
Indices: 647589--647695 Score: 142
Period size: 45 Copynumber: 2.4 Consensus size: 45
647579 GCCATTACAT
* * * *
647589 TTATAGCATTTTTTCATACTAATAATGCACTCATATACATTTCAA
1 TTATGGCATTCTTTCATACCAATAATGCACCCATATACATTTCAA
* * *
647634 TTATGGCATTCTTTCATGCCGATAATGCACCCATATGCATTTCAA
1 TTATGGCATTCTTTCATACCAATAATGCACCCATATACATTTCAA
*
647679 TTATGGCATCCTTTCAT
1 TTATGGCATTCTTTCAT
647696 GCCTTTTATA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.40
Consensus pattern (45 bp):
TTATGGCATTCTTTCATACCAATAATGCACCCATATACATTTCAA
Found at i:647696 original size:45 final size:45
Alignment explanation
Indices: 647610--647698 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
647600 TTTCATACTA
* *
647610 ATAATGCACTCATATACATTTCAATTATGGCATTCTTTCATGCCG
1 ATAATGCACCCATATACATTTCAATTATGGCATCCTTTCATGCCG
*
647655 ATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATGCC
1 ATAATGCACCCATATACATTTCAATTATGGCATCCTTTCATGCC
647699 TTTTATACAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (45 bp):
ATAATGCACCCATATACATTTCAATTATGGCATCCTTTCATGCCG
Found at i:647929 original size:68 final size:68
Alignment explanation
Indices: 647838--648296 Score: 650
Period size: 68 Copynumber: 6.8 Consensus size: 68
647828 TTTTTAACCG
* * * * * *
647838 TTCATCTAACTGGCATTATTGACACCTTCCTATCAAATGCAAAGTCAGACCTCAAAGGAACTTAG
1 TTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGAACTTAG
647903 CCT
66 CCT
* * * * *
647906 TTTATCTAACTGGCATGATTGACACCTTTCTGTCAAATTCACAGTTAGACCACAAAGGAACCTAG
1 TTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGAACTTAG
647971 CCT
66 CCT
* ** * *
647974 TTCATCTAACTGGCATGATTGACACCTTTCTATCAAATAAACAATTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGAACTTAG
648039 CCT
66 CCT
*
648042 TTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATACACAGTTAGGCCTCAAAGGAACTTAG
1 TTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGAACTTAG
648107 CCT
66 CCT
* * *
648110 TTCATCTAACTGGCATGATTGACACCATTCTATCAAATGCACAGTTAGTCCTCAAA-GACACTTA
1 TTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGA-ACTTA
*
648174 GTCT
65 GCCT
* * * *
648178 TTCATCTAACTGACATGATTGACACCTTTCTGTCAAATGCACAGATAGGCCTGAAAGGCACTTAG
1 TTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGAACTTAG
648243 CCT
66 CCT
** *
648246 TTTGTCTAACTGGCATGATTGACACCTTTCTGTCAAATGCAAAGTTAGGCC
1 TTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGCC
648297 ATAATCTTGT
Statistics
Matches: 349, Mismatches: 40, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
67 2 0.01
68 346 0.99
69 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (68 bp):
TTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGAACTTAG
CCT
Found at i:648643 original size:58 final size:57
Alignment explanation
Indices: 648524--648731 Score: 274
Period size: 57 Copynumber: 3.6 Consensus size: 57
648514 GGAAAAAATA
* * * *
648524 ATACACTTAATATGAATTTCTTAATTTTTTGCATACAAAG-TTCCAATACAGAAATTA
1 ATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTTTCCAATA-AGAAATTC
* * *
648581 ATACACTTAGTATGAACTTCTTAACTTTTTGCACACGAAGTTTCCAACAAGAAAATTC
1 ATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTTTCCAATAAG-AAATTC
* * * * *
648639 ATACACTTAGTATGAATTTCATAGCTTTTTGCACACAAAGTGTCCAATACGAAATGC
1 ATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTTTCCAATAAGAAATTC
*
648696 ATATACTTAGTATGAATTTCTTAACTTTTTGCACAC
1 ATACACTTAGTATGAATTTCTTAACTTTTTGCACAC
648732 TTAGTGCCAT
Statistics
Matches: 131, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
57 75 0.57
58 56 0.43
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (57 bp):
ATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTTTCCAATAAGAAATTC
Found at i:648671 original size:115 final size:115
Alignment explanation
Indices: 648524--648731 Score: 319
Period size: 115 Copynumber: 1.8 Consensus size: 115
648514 GGAAAAAATA
* * * *
648524 ATACACTTAATATGAATTTCTTAATTTTTTGCATACAAAGT-TCCAATACAGAAATTAATACACT
1 ATACACTTAATATGAATTTCATAACTTTTTGCACACAAAGTGTCCAATAC-GAAATGAATACACT
648588 TAGTATGAACTTCTTAACTTTTTGCACACGAAGTTTCCAACAAGAAAATTC
65 TAGTATGAACTTCTTAACTTTTTGCACACGAAGTTTCCAACAAGAAAATTC
* * * *
648639 ATACACTTAGTATGAATTTCATAGCTTTTTGCACACAAAGTGTCCAATACGAAATGCATATACTT
1 ATACACTTAATATGAATTTCATAACTTTTTGCACACAAAGTGTCCAATACGAAATGAATACACTT
*
648704 AGTATGAATTTCTTAACTTTTTGCACAC
66 AGTATGAACTTCTTAACTTTTTGCACAC
648732 TTAGTGCCAT
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
115 75 0.90
116 8 0.10
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (115 bp):
ATACACTTAATATGAATTTCATAACTTTTTGCACACAAAGTGTCCAATACGAAATGAATACACTT
AGTATGAACTTCTTAACTTTTTGCACACGAAGTTTCCAACAAGAAAATTC
Found at i:649180 original size:20 final size:20
Alignment explanation
Indices: 649155--649210 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
649145 TCTGTGTTCA
* *
649155 ATGGTACCGATACCATCCTC
1 ATGGTATCGATACCACCCTC
649175 ATGGTATCGATACTC-CCCTC
1 ATGGTATCGATAC-CACCCTC
*
649195 TTGGTATCGATACCAC
1 ATGGTATCGATACCAC
649211 TTAAATCGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.23, C:0.32, G:0.16, T:0.29
Consensus pattern (20 bp):
ATGGTATCGATACCACCCTC
Found at i:654951 original size:40 final size:40
Alignment explanation
Indices: 654907--654994 Score: 158
Period size: 40 Copynumber: 2.2 Consensus size: 40
654897 ATTCAAAGTT
*
654907 TCGATACTCTTGAAAGAGTATCAATACTAGCCCTATAGTA
1 TCGATACTCTTGAAAAAGTATCAATACTAGCCCTATAGTA
*
654947 TCGATACTCTTGAAAAAGTATCAATACTAGCCTTATAGTA
1 TCGATACTCTTGAAAAAGTATCAATACTAGCCCTATAGTA
654987 TCGATACT
1 TCGATACT
654995 TGACCTATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (40 bp):
TCGATACTCTTGAAAAAGTATCAATACTAGCCCTATAGTA
Found at i:654986 original size:20 final size:20
Alignment explanation
Indices: 654923--654994 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
654913 CTCTTGAAAG
*
654923 AGTATCAATACTAGCCCTAT
1 AGTATCAATACTAGCCTTAT
* *
654943 AGTATCGATACT---CTTGAAAA
1 AGTATCAATACTAGCCTT---AT
654963 AGTATCAATACTAGCCTTAT
1 AGTATCAATACTAGCCTTAT
*
654983 AGTATCGATACT
1 AGTATCAATACT
654995 TGACCTATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
17 2 0.05
20 35 0.88
23 3 0.08
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.32
Consensus pattern (20 bp):
AGTATCAATACTAGCCTTAT
Found at i:655003 original size:20 final size:20
Alignment explanation
Indices: 654923--655003 Score: 51
Period size: 20 Copynumber: 4.0 Consensus size: 20
654913 CTCTTGAAAG
*
654923 AGTATCAATACTAGCCCTAT
1 AGTATCAATACTAGACCTAT
* * * *
654943 AGTATCGATACTCTTGA--AAA
1 AGTATCAATA--CTAGACCTAT
654963 AGTATCAATACTAG-CCTTAT
1 AGTATCAATACTAGACC-TAT
* *
654983 AGTATCGATACTTGACCTAT
1 AGTATCAATACTAGACCTAT
655003 A
1 A
655004 AAAGACTTAA
Statistics
Matches: 44, Mismatches: 11, Indels: 12
0.66 0.16 0.18
Matches are distributed among these distances:
18 3 0.07
20 36 0.82
21 2 0.05
22 3 0.07
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (20 bp):
AGTATCAATACTAGACCTAT
Found at i:670033 original size:20 final size:20
Alignment explanation
Indices: 669968--670045 Score: 63
Period size: 22 Copynumber: 3.9 Consensus size: 20
669958 TTTGGTGCAG
* *
669968 AGGGAATCGA-TCCCCCT-G
1 AGGGAACCGATTCCCCCTCA
*
669986 AGGGAACCGATTCCCCCTTTGA
1 AGGGAACCGATTCCCCC--TCA
670008 AGGGAACCGATTCCCCC-CA
1 AGGGAACCGATTCCCCCTCA
* *
670027 CAGGGAATCGATACCCCCT
1 -AGGGAACCGATTCCCCCT
670046 GGGGTTCTGC
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
18 9 0.18
19 7 0.14
20 15 0.31
21 1 0.02
22 17 0.35
ACGTcount: A:0.24, C:0.36, G:0.23, T:0.17
Consensus pattern (20 bp):
AGGGAACCGATTCCCCCTCA
Found at i:692328 original size:18 final size:18
Alignment explanation
Indices: 692305--692350 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 18
692295 AGGCATTTGA
692305 TCCTCTGGCT-GTGCTTGT
1 TCCTCT-GCTCGTGCTTGT
692323 TCCTCTGCTCGTGCTTGT
1 TCCTCTGCTCGTGCTTGT
692341 TCCTCGTGCT
1 TCCTC-TGCT
692351 GTTTTGGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.12
18 19 0.73
19 4 0.15
ACGTcount: A:0.00, C:0.33, G:0.24, T:0.43
Consensus pattern (18 bp):
TCCTCTGCTCGTGCTTGT
Found at i:694002 original size:23 final size:22
Alignment explanation
Indices: 693925--694014 Score: 92
Period size: 23 Copynumber: 4.0 Consensus size: 22
693915 TAGAACCCTC
* *
693925 AGGGGGTATCGATTCCCCTG-T
1 AGGGGGAATCGATTCCCCTGCA
* * *
693946 GGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGATTCCCCTGC-A
693969 AGGGGGAATCGATTCCCCTGCA
1 AGGGGGAATCGATTCCCCTGCA
*
693991 AGGGTGGTATCGATTCCCTCTGCA
1 AGGG-GGAATCGATTCCC-CTGCA
694015 CTAAAATTCT
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
21 16 0.29
22 5 0.09
23 30 0.54
24 5 0.09
ACGTcount: A:0.18, C:0.26, G:0.32, T:0.24
Consensus pattern (22 bp):
AGGGGGAATCGATTCCCCTGCA
Done.