Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 98 of 230
Found at i:27697506 original size:49 final size:49
Alignment explanation
Indices: 27697434--27697580 Score: 170
Period size: 49 Copynumber: 3.0 Consensus size: 49
27697424 AGGGATTACT
* * * *
27697434 GATTGTAGCTGGTGAGAGCTTACCGATTCTCAGCTCGTATGAGCATATC
1 GATTGCAGCTCGTGAGAGCTTACCGATTCTCAGCTAGTATGAGCATACC
* * * *
27697483 GATTGCAGCTTGTGAGAGCTTACCAATTCTCAGCTTGTATGAGCTTACC
1 GATTGCAGCTCGTGAGAGCTTACCGATTCTCAGCTAGTATGAGCATACC
* * *
27697532 GATTTACAGCTCGTGAGAGCATATCGATTCAT-AGCTAGTATGAGCATAC
1 GA-TTGCAGCTCGTGAGAGCTTACCGATTC-TCAGCTAGTATGAGCATAC
27697581 ATGTACAGGA
Statistics
Matches: 83, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
49 45 0.54
50 37 0.45
51 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (49 bp):
GATTGCAGCTCGTGAGAGCTTACCGATTCTCAGCTAGTATGAGCATACC
Found at i:27702442 original size:78 final size:75
Alignment explanation
Indices: 27702355--27702530 Score: 199
Period size: 78 Copynumber: 2.3 Consensus size: 75
27702345 AAATTATATA
* * * * *
27702355 AATTGAATTAAAGTTATGAATTTTATATATTTATATGTGAGGTTCGAATATATATGTATATACAT
1 AATTAAATTAAAG-TATGAATTTTACATATGTATATGTGAGATTCG-A-ATAGATGTATATACAT
* * *
27702420 GTATAAGTTCTTG
63 ATACAAGTACTTG
* *
27702433 AATTAAATTAAAGGTATGAATTTTACATATGTATGTGTGTGATTCGAATAGATGTATATACATAT
1 AATTAAATTAAA-GTATGAATTTTACATATGTATATGTGAGATTCGAATAGATGTATATACATAT
27702498 ACAAGTACTTG
65 ACAAGTACTTG
* *
27702509 AGTTGAATTTAAAGTATGAATT
1 AATT-AAATTAAAGTATGAATT
27702531 GTAAATACTT
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
76 37 0.44
77 8 0.10
78 38 0.45
79 1 0.01
ACGTcount: A:0.38, C:0.05, G:0.16, T:0.41
Consensus pattern (75 bp):
AATTAAATTAAAGTATGAATTTTACATATGTATATGTGAGATTCGAATAGATGTATATACATATA
CAAGTACTTG
Found at i:27702526 original size:76 final size:77
Alignment explanation
Indices: 27702355--27702530 Score: 212
Period size: 76 Copynumber: 2.3 Consensus size: 77
27702345 AAATTATATA
* * * *
27702355 AATTGAATTAAAGTTATGAATTTTATATATTTATATGTGAGGTTCGAATATATATGTATATACAT
1 AATTGAATTAAAG-TATGAATTTTACATATGTATATGTGAGATTCGAATATAGATGTATATACAT
* * *
27702420 GTATAAGTTCTTG
65 ATACAAGTACTTG
* * *
27702433 AATTAAATTAAAGGTATGAATTTTACATATGTATGTGTGTGATTCG-A-ATAGATGTATATACAT
1 AATTGAATTAAA-GTATGAATTTTACATATGTATATGTGAGATTCGAATATAGATGTATATACAT
27702496 ATACAAGTACTTG
65 ATACAAGTACTTG
*
27702509 AGTTGAATTTAAAGTATGAATT
1 AATTGAA-TTAAAGTATGAATT
27702531 GTAAATACTT
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
76 39 0.46
77 6 0.07
78 38 0.45
79 1 0.01
ACGTcount: A:0.38, C:0.05, G:0.16, T:0.41
Consensus pattern (77 bp):
AATTGAATTAAAGTATGAATTTTACATATGTATATGTGAGATTCGAATATAGATGTATATACATA
TACAAGTACTTG
Found at i:27703029 original size:33 final size:32
Alignment explanation
Indices: 27702875--27703116 Score: 212
Period size: 33 Copynumber: 7.4 Consensus size: 32
27702865 ATTTATATCT
27702875 TATTTGATAAGTATTTATATGCATTCGGTTAT-A-
1 TATTTGAT-AGTA--TATATGCATTCGGTTATAAG
** * *
27702908 TACCTTTGA-AGCGTATATGCTTTCGATTATAAG
1 TA--TTTGATAGTATATATGCATTCGGTTATAAG
27702941 TATTTGATAGGTATATATATGCATTCGGTTAT-A-
1 TATTTGATA-G--TATATATGCATTCGGTTATAAG
* *
27702974 TACCTTTGAT-GTGTATATGCATTCGATTATAAG
1 TA--TTTGATAGTATATATGCATTCGGTTATAAG
*
27703007 TATTTGATAGGTATATATGCATTCGGTTGTATA-
1 TATTTGATA-GTATATATGCATTCGGTTATA-AG
* *
27703040 CATTTGAT-GTGTATATGCATTCGGTTATAAG
1 TATTTGATAGTATATATGCATTCGGTTATAAG
*
27703071 TAGTTGATAAGTATATATGCATTCGGTTATAAG
1 TATTTGAT-AGTATATATGCATTCGGTTATAAG
27703104 TATTTGATGAGTA
1 TATTTGAT-AGTA
27703117 GATACATACA
Statistics
Matches: 170, Mismatches: 21, Indels: 36
0.75 0.09 0.16
Matches are distributed among these distances:
30 1 0.01
31 68 0.40
32 3 0.02
33 70 0.41
34 2 0.01
35 26 0.15
ACGTcount: A:0.29, C:0.08, G:0.19, T:0.43
Consensus pattern (32 bp):
TATTTGATAGTATATATGCATTCGGTTATAAG
Found at i:27703055 original size:64 final size:64
Alignment explanation
Indices: 27702875--27703101 Score: 337
Period size: 64 Copynumber: 3.5 Consensus size: 64
27702865 ATTTATATCT
* * *
27702875 TATTTGATAAGTATTTATATGCATTCGGTTATATACCTTTGAAGCGTATATGCTTTCGATTATAA
1 TATTTGATAAGTA--TATATGCATTCGGTTATATACCTTTGATGTGTATATGCATTCGATTATAA
27702940 G
64 G
*
27702941 TATTTGATAGGTATATATATGCATTCGGTTATATACCTTTGATGTGTATATGCATTCGATTATAA
1 TATTTGATAAG--TATATATGCATTCGGTTATATACCTTTGATGTGTATATGCATTCGATTATAA
27703006 G
64 G
* * * *
27703007 TATTTGATAGGTATATATGCATTCGGTTGTATACATTTGATGTGTATATGCATTCGGTTATAAG
1 TATTTGATAAGTATATATGCATTCGGTTATATACCTTTGATGTGTATATGCATTCGATTATAAG
*
27703071 TAGTTGATAAGTATATATGCATTCGGTTATA
1 TATTTGATAAGTATATATGCATTCGGTTATA
27703102 AGTATTTGAT
Statistics
Matches: 149, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
64 78 0.52
66 69 0.46
68 2 0.01
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.44
Consensus pattern (64 bp):
TATTTGATAAGTATATATGCATTCGGTTATATACCTTTGATGTGTATATGCATTCGATTATAAG
Found at i:27703078 original size:31 final size:31
Alignment explanation
Indices: 27702890--27703112 Score: 195
Period size: 31 Copynumber: 6.9 Consensus size: 31
27702880 GATAAGTATT
* **
27702890 TATATGCATTCGGTTAT-A-TACCTTTGAAGCG
1 TATATGCATTCGGTTATAAGTA--TTTGATGTA
* *
27702921 TATATGCTTTCGATTATAAGTATTTGATAGGTATA
1 TATATGCATTCGGTTATAAGTATTTGAT--G--TA
*
27702956 TATATGCATTCGGTTAT-A-TACCTTTGATGTG
1 TATATGCATTCGGTTATAAGTA--TTTGATGTA
*
27702987 TATATGCATTCGATTATAAGTATTTGATAGGTA
1 TATATGCATTCGGTTATAAGTATTTGAT--GTA
* * *
27703020 TATATGCATTCGGTTGTATA-CATTTGATGTG
1 TATATGCATTCGGTTATA-AGTATTTGATGTA
*
27703051 TATATGCATTCGGTTATAAGTAGTTGATAAGTA
1 TATATGCATTCGGTTATAAGTATTTGAT--GTA
27703084 TATATGCATTCGGTTATAAGTATTTGATG
1 TATATGCATTCGGTTATAAGTATTTGATG
27703113 AGTAGATACA
Statistics
Matches: 157, Mismatches: 19, Indels: 32
0.75 0.09 0.15
Matches are distributed among these distances:
30 1 0.01
31 69 0.44
32 2 0.01
33 62 0.39
34 2 0.01
35 21 0.13
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.43
Consensus pattern (31 bp):
TATATGCATTCGGTTATAAGTATTTGATGTA
Found at i:27708505 original size:19 final size:18
Alignment explanation
Indices: 27708481--27708573 Score: 54
Period size: 20 Copynumber: 5.2 Consensus size: 18
27708471 ATTACAAAAT
*
27708481 AATTCAAAATCATTTTTAA
1 AATTCAAAAT-ATTTATAA
*
27708500 AATTCAGAATATTTATAAAA
1 AATTCAAAATATTTAT--AA
*
27708520 AATT-AAAA-A-TTAAAA
1 AATTCAAAATATTTATAA
*
27708535 AATTAAAAATATATATATAA
1 AATTCAAAATAT-T-TATAA
27708555 AAGTT-AAAAT-TTTA-AA
1 AA-TTCAAAATATTTATAA
27708571 AAT
1 AAT
27708574 GTTCTAAAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
15 7 0.11
16 8 0.13
17 6 0.10
18 7 0.11
19 14 0.23
20 17 0.28
21 2 0.03
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.35
Consensus pattern (18 bp):
AATTCAAAATATTTATAA
Found at i:27708518 original size:18 final size:19
Alignment explanation
Indices: 27708481--27708519 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
27708471 ATTACAAAAT
*
27708481 AATTCAAAATCATTTTTAA
1 AATTCAAAATCATTTATAA
*
27708500 AATTCAGAAT-ATTTATAA
1 AATTCAAAATCATTTATAA
27708518 AA
1 AA
27708520 AATTAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (19 bp):
AATTCAAAATCATTTATAA
Found at i:27708528 original size:8 final size:8
Alignment explanation
Indices: 27708515--27708543 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
27708505 AGAATATTTA
27708515 TAAAAAAT
1 TAAAAAAT
27708523 T-AAAAAT
1 TAAAAAAT
27708530 TAAAAAAT
1 TAAAAAAT
27708538 TAAAAA
1 TAAAAA
27708544 TATATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
TAAAAAAT
Found at i:27708535 original size:15 final size:15
Alignment explanation
Indices: 27708515--27708544 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
27708505 AGAATATTTA
27708515 TAAAAAATTAAAAAT
1 TAAAAAATTAAAAAT
27708530 TAAAAAATTAAAAAT
1 TAAAAAATTAAAAAT
27708545 ATATATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
TAAAAAATTAAAAAT
Found at i:27708538 original size:35 final size:36
Alignment explanation
Indices: 27708498--27708573 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
27708488 AATCATTTTT
* * *
27708498 AAAATTCAGAATATTTATA-AAAAATTAAAAATTAA
1 AAAATTAAAAATATATATATAAAAATTAAAAATTAA
* * *
27708533 AAAATTAAAAATATATATATAAAAGTTAAAATTTTA
1 AAAATTAAAAATATATATATAAAAATTAAAAATTAA
27708569 AAAAT
1 AAAAT
27708574 GTTCTAAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
35 16 0.47
36 18 0.53
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (36 bp):
AAAATTAAAAATATATATATAAAAATTAAAAATTAA
Found at i:27711393 original size:4 final size:4
Alignment explanation
Indices: 27711384--27711408 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
27711374 ACCAAATCTT
27711384 CATA CATA CATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA C
27711409 CACCAAGCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:27714338 original size:22 final size:22
Alignment explanation
Indices: 27714310--27714354 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
27714300 CGTTCTGGAG
27714310 TTAGCGTGCATTCCAGAATACA
1 TTAGCGTGCATTCCAGAATACA
27714332 TTAGCGTGCATTCCAGAATACA
1 TTAGCGTGCATTCCAGAATACA
27714354 T
1 T
27714355 GCCATGGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (22 bp):
TTAGCGTGCATTCCAGAATACA
Found at i:27714655 original size:18 final size:18
Alignment explanation
Indices: 27714628--27714667 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
27714618 CAGGTGCGTT
*
27714628 TCCTAGCCCTTATATGTA
1 TCCTAACCCTTATATGTA
*
27714646 TCCTAACCCTTATGTGTA
1 TCCTAACCCTTATATGTA
27714664 TCCT
1 TCCT
27714668 TTTCCGAGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.30, G:0.10, T:0.40
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:27715124 original size:25 final size:25
Alignment explanation
Indices: 27715096--27715212 Score: 113
Period size: 25 Copynumber: 4.9 Consensus size: 25
27715086 TATTTTGATA
27715096 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
* *
27715121 TTATTTGAAGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAGT
* ** *
27715146 TT-TTTTA-GT--T-ATTTTG-A-T
1 TTATTTGATGTAATAAAATAGAAGT
*
27715164 ATTATTTGATATAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
27715190 TTATTTGATGTAATAAAATAGAA
1 TTATTTGATGTAATAAAATAGAA
27715213 TTTTTTTTAG
Statistics
Matches: 72, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
18 1 0.01
19 3 0.04
20 7 0.10
21 2 0.03
23 3 0.04
24 7 0.10
25 48 0.67
26 1 0.01
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.44
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:27715168 original size:69 final size:69
Alignment explanation
Indices: 27715086--27715256 Score: 315
Period size: 69 Copynumber: 2.5 Consensus size: 69
27715076 ATATTTTGAA
27715086 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGAAGTAATAAAATAGAAATTTTTT
1 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGAAGTAATAAAATAGAAATTTTTT
27715151 TAGT
66 TAGT
* * *
27715155 TATTTTGATATTATTTGATATAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAATTTTTTT
1 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGAAGTAATAAAATAGAAATTTTTT
27715220 TAGT
66 TAGT
27715224 TATTTTGATATTATTTGATGTAATAAAATAGAA
1 TATTTTGATATTATTTGATGTAATAAAATAGAA
27715257 ATTTTTGAAT
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 98 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.47
Consensus pattern (69 bp):
TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGAAGTAATAAAATAGAAATTTTTT
TAGT
Found at i:27715273 original size:9 final size:9
Alignment explanation
Indices: 27715259--27715295 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
27715249 AAATAGAAAT
27715259 TTTTGAATA
1 TTTTGAATA
27715268 TTTTGAATA
1 TTTTGAATA
27715277 TTTTGAATA
1 TTTTGAATA
27715286 TTTTG-ATA
1 TTTTGAATA
27715294 TT
1 TT
27715296 ATTTGAGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 5 0.18
9 23 0.82
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (9 bp):
TTTTGAATA
Found at i:27715362 original size:23 final size:23
Alignment explanation
Indices: 27715326--27715414 Score: 142
Period size: 23 Copynumber: 3.8 Consensus size: 23
27715316 ATTAATACCC
*
27715326 TTAACTTAACAACCCTAACCTAAT
1 TTAA-TTAAAAACCCTAACCTAAT
27715350 TTAATTAAAAACCCTAACCTAAT
1 TTAATTAAAAACCCTAACCTAAT
* *
27715373 TAAATTAACAACCCTAACCTAAT
1 TTAATTAAAAACCCTAACCTAAT
27715396 TTAATTAAAAACCCTAACC
1 TTAATTAAAAACCCTAACC
27715415 CTAAAACCCT
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
23 56 0.93
24 4 0.07
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (23 bp):
TTAATTAAAAACCCTAACCTAAT
Found at i:27715398 original size:46 final size:46
Alignment explanation
Indices: 27715326--27715863 Score: 466
Period size: 46 Copynumber: 12.4 Consensus size: 46
27715316 ATTAATACCC
* *
27715326 TTAACTTAACAACCCTAACCTAATTTAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAA
*
27715372 TTAAATTAACAACCCTAACCTAATTTAATTAAAAACCCTAACC---
1 TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAA
* * *
27715415 -----CT-AAAACCCTAACCTAATTAAATAAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAA
* * *
27715455 TTTAATT-AAAACCTTAACC--------CT-AAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAA
*
27715491 TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACC--C
1 TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAA
** *
27715535 TTAACCCT-AAAATCCTAACCTAATTTAATTAAAAACCCTAACCTAA
1 TTAA-ATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAA
* * *
27715581 TTTAATTAAAAACCCTAACC-CA--TAACCCT-AAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAATTTAA--TTAAAAACCCTAACCTAA
*
27715625 TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCATAACCTAA
1 TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAA
*
27715671 TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACTC-AACCCT--
1 TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAA-CCTAA
* *** * *
27715715 TCACCCT-AAAACCCTAACCTAATTAAATTGAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAA
** * *
27715760 TTAAATTAAAAACCCTAACC--CGTTACTTAAAAACCCTAACC--C
1 TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAA
* *** *
27715802 TTAACTTAAAAACCCTAACC-CCCTTAACTTAAAAACCCTAACC--C
1 TTAAATTAAAAACCCTAACCTAATTTAA-TTAAAAACCCTAACCTAA
*
27715846 TTAACTTAAAAACCCTAA
1 TTAAATTAAAAACCCTAA
27715864 ACCCTTAACT
Statistics
Matches: 408, Mismatches: 49, Indels: 72
0.77 0.09 0.14
Matches are distributed among these distances:
36 21 0.05
37 43 0.11
38 1 0.00
42 19 0.05
43 37 0.09
44 127 0.31
45 24 0.06
46 133 0.33
47 3 0.01
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.26
Consensus pattern (46 bp):
TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAA
Found at i:27715444 original size:23 final size:22
Alignment explanation
Indices: 27715417--27715844 Score: 216
Period size: 23 Copynumber: 19.5 Consensus size: 22
27715407 CCCTAACCCT
27715417 AAAACCCTAACCTAATTAAATAA
1 AAAACCCTAACCTAATTAAAT-A
* *
27715440 AAAACCCTAACCTAATTTAATT
1 AAAACCCTAACCTAATTAAATA
* **
27715462 AAAACCTTAACCCT-A--AAACC
1 AAAACCCTAA-CCTAATTAAATA
** *
27715482 CTAA-CCTAA-TTAAATT--A-A
1 AAAACCCTAACCT-AATTAAATA
*
27715500 A-AACCCTAACCTAATTTAATTA
1 AAAACCCTAACCTAA-TTAAATA
* *
27715522 AAAACCCTAACC--CTTAACCCT-
1 AAAACCCTAACCTAATTAA--ATA
* *
27715543 AAAATCCTAACCTAATTTAATTA
1 AAAACCCTAACCTAA-TTAAATA
*
27715566 AAAACCCTAACCTAATTTAATTA
1 AAAACCCTAACCTAA-TTAAATA
* *
27715589 AAAACCCTAACC-CA-TAACCCT-
1 AAAACCCTAACCTAATTAA--ATA
27715610 AAAACCCTAACCTAATTAAATTA
1 AAAACCCTAACCTAATTAAA-TA
*
27715633 AAAACCCTAACCTAATTTAATTA
1 AAAACCCTAACCTAA-TTAAATA
*
27715656 AAAACCATAACCTAATTAAATTA
1 AAAACCCTAACCTAATTAAA-TA
*
27715679 AAAACCCTAACCTAATTTAATTA
1 AAAACCCTAACCTAA-TTAAATA
* * **
27715702 AAAACTC-AACCCT--TCACCCT-
1 AAAACCCTAA-CCTAATTA-AATA
*
27715722 AAAACCCTAACCTAATTAAATTG
1 AAAACCCTAACCTAATTAAA-TA
27715745 AAAACCCTAACCTAATTAAATTA
1 AAAACCCTAACCTAATTAAA-TA
** **
27715768 AAAACCCTAACC-CGTTACTTA
1 AAAACCCTAACCTAATTAAATA
* *
27715789 AAAACCCTAACC--CTTAACTTA
1 AAAACCCTAACCTAATTAA-ATA
*** *
27715810 AAAACCCTAACCCCCTTAACTTA
1 AAAACCCTAACCTAATTAA-ATA
27715833 AAAACCCTAACC
1 AAAACCCTAACC
27715845 CTTAACTTAA
Statistics
Matches: 324, Mismatches: 44, Indels: 74
0.73 0.10 0.17
Matches are distributed among these distances:
17 3 0.01
18 7 0.02
19 9 0.03
20 25 0.08
21 55 0.17
22 30 0.09
23 183 0.56
24 12 0.04
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (22 bp):
AAAACCCTAACCTAATTAAATA
Found at i:27715480 original size:36 final size:37
Alignment explanation
Indices: 27715440--27715510 Score: 117
Period size: 36 Copynumber: 1.9 Consensus size: 37
27715430 AATTAAATAA
* *
27715440 AAAACCCTAACCTAATTTAATT-AAAACCTTAACCCT
1 AAAACCCTAACCTAATTAAATTAAAAACCCTAACCCT
27715476 AAAACCCTAACCTAATTAAATTAAAAACCCTAACC
1 AAAACCCTAACCTAATTAAATTAAAAACCCTAACC
27715511 TAATTTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 21 0.66
37 11 0.34
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (37 bp):
AAAACCCTAACCTAATTAAATTAAAAACCCTAACCCT
Found at i:27715546 original size:67 final size:67
Alignment explanation
Indices: 27715357--27715872 Score: 510
Period size: 67 Copynumber: 8.0 Consensus size: 67
27715347 AATTTAATTA
*
27715357 AAAACCCTAACCTAATTAAATTAACAACCCTAACCTAATTTAATT--AAA----AACCC-TAACC
1 AAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTTAACC
27715415 CT
66 CT
*
27715417 AAAACCCTAACCTAATTAAATAAAAAACCCTAACCTAATTTAATT---AA----AA-CCTTAACC
1 AAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTTAACC
27715474 CT
66 CT
27715476 AAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTTAACC
1 AAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTTAACC
27715541 CT
66 CT
* * *
27715543 AAAATCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCCATAACC
1 AAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTTAACC
27715608 CT
66 CT
* *
27715610 AAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCATAACCTAATTAA
1 AAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACC--CTTAA
**
27715675 -ATT
64 CCCT
* * * * ** *
27715678 AAAAACCCTAACCTAATTTAATTAAAAACTC-AACC--CTTCACCCT-AAAACCCTAACCTAATT
1 -AAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTTA-ATTAAAAACCCTAACC--CTT
**
27715739 AA-ATT
62 AACCCT
** *
27715744 GAAAACCCTAACCTAATTAAATTAAAAACCCTAACC--CGTTACTTAAAAACCCTAACCCTTAA-
1 -AAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTTAAC
*
27715806 CTT
65 CCT
*** * *
27715809 AAAAACCCTAACCCCCTTAACTTAAAAACCCTAACC---CTTAACTTAAAAACCCTAAACCCTTA
1 -AAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTTAA-TTAAAAACCCT-AACCCTTA
27715871 AC
63 AC
27715873 TTAAAAACTC
Statistics
Matches: 403, Mismatches: 35, Indels: 29
0.86 0.07 0.06
Matches are distributed among these distances:
58 2 0.00
59 55 0.14
60 43 0.11
62 2 0.00
64 3 0.01
65 48 0.12
66 65 0.16
67 149 0.37
68 5 0.01
69 31 0.08
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (67 bp):
AAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTTAACC
CT
Found at i:27715557 original size:44 final size:45
Alignment explanation
Indices: 27715476--27715863 Score: 354
Period size: 44 Copynumber: 8.7 Consensus size: 45
27715466 CCTTAACCCT
*
27715476 AAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTTAATTA
1 AAAACCCTAACC-ACTTAAATTAAAAACCCTAACCTAATTTAATTA
** *
27715522 AAAACCCTAACC-CTTAACCCT-AAAATCCTAACCTAATTTAATTA
1 AAAACCCTAACCACTTAA-ATTAAAAACCCTAACCTAATTTAATTA
* * * *
27715566 AAAACCCTAACCTAATTTAATTAAAAACCCTAACC-CA--TAACCCT-
1 AAAACCCTAACC-ACTTAAATTAAAAACCCTAACCTAATTTAA--TTA
*
27715610 AAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTTAATTA
1 AAAACCCTAACC-ACTTAAATTAAAAACCCTAACCTAATTTAATTA
* *
27715656 AAAACCATAACCTAATTAAATTAAAAACCCTAACCTAATTTAATTA
1 AAAACCCTAACC-ACTTAAATTAAAAACCCTAACCTAATTTAATTA
* *** * *
27715702 AAAACTC-AACC-CTTCACCCT-AAAACCCTAACCTAATTAAATTG
1 AAAACCCTAACCACTT-AAATTAAAAACCCTAACCTAATTTAATTA
* ** *
27715745 AAAACCCTAACCTAATTAAATTAAAAACCCTAACC--CGTTACTTA
1 AAAACCCTAACC-ACTTAAATTAAAAACCCTAACCTAATTTAATTA
* ***
27715789 AAAACCCTAACC-CTTAACTTAAAAACCCTAACC-CCCTTAACTTA
1 AAAACCCTAACCACTTAAATTAAAAACCCTAACCTAATTTAA-TTA
*
27715833 AAAACCCTAACC-CTTAACTTAAAAACCCTAA
1 AAAACCCTAACCACTTAAATTAAAAACCCTAA
27715864 ACCCTTAACT
Statistics
Matches: 288, Mismatches: 37, Indels: 36
0.80 0.10 0.10
Matches are distributed among these distances:
42 19 0.07
43 36 0.12
44 128 0.44
45 12 0.04
46 90 0.31
47 3 0.01
ACGTcount: A:0.46, C:0.28, G:0.01, T:0.25
Consensus pattern (45 bp):
AAAACCCTAACCACTTAAATTAAAAACCCTAACCTAATTTAATTA
Found at i:27715588 original size:90 final size:89
Alignment explanation
Indices: 27715476--27715917 Score: 440
Period size: 90 Copynumber: 5.0 Consensus size: 89
27715466 CCTTAACCCT
27715476 AAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTTAACC
1 AAAACCCTAACCTAATTAAATTAAAAACCCTAACC-AATTTAATTAAAAACCCTAACCCTTAACC
*
27715541 CTAAAATCCTAACCTAATTTAATTA
65 CTAAAACCCTAACCTAATTTAATTA
* * * *
27715566 AAAACCCTAACCTAATTTAATTAAAAACCCTAACCCA--TAACCCT-AAAACCCTAACCTAATTA
1 AAAACCCTAACCTAATTAAATTAAAAACCCTAACCAATTTAA--TTAAAAACCCTAACC--CTTA
**
27715628 A-ATTAAAAACCCTAACCTAATTTAATTA
62 ACCCT-AAAACCCTAACCTAATTTAATTA
* * *
27715656 AAAACCATAACCTAATTAAATTAAAAACCCTAACCTAATTTAATTAAAAACTC-AACCCTTCACC
1 AAAACCCTAACCTAATTAAATTAAAAACCCTAACC-AATTTAATTAAAAACCCTAACCCTTAACC
* *
27715720 CTAAAACCCTAACCTAATTAAATTG
65 CTAAAACCCTAACCTAATTTAATTA
** * *
27715745 AAAACCCTAACCTAATTAAATTAAAAACCCTAACC-CGTTACTTAAAAACCCTAACCCTTAA-CT
1 AAAACCCTAACCTAATTAAATTAAAAACCCTAACCAATTTAATTAAAAACCCTAACCCTTAACCC
***
27715808 TAAAAACCCTAACC-CCCTTAACTTA
66 T-AAAACCCTAACCTAATTTAA-TTA
* * * * *
27715833 AAAACCCTAACC--CTTAACTTAAAAACCCTAAACC--CTTAACTTAAAAACTCTTACCCTTAAC
1 AAAACCCTAACCTAATTAAATTAAAAACCCT-AACCAATTTAA-TTAAAAACCCTAACCCTTAAC
** * * *
27715894 TTTAAAACCTTAAACTAAGTTAAT
64 CCTAAAACCCTAACCTAATTTAAT
27715918 AATTTTACTT
Statistics
Matches: 293, Mismatches: 42, Indels: 37
0.79 0.11 0.10
Matches are distributed among these distances:
86 18 0.06
87 53 0.18
88 52 0.18
89 61 0.21
90 94 0.32
91 6 0.02
92 6 0.02
93 3 0.01
ACGTcount: A:0.46, C:0.27, G:0.01, T:0.26
Consensus pattern (89 bp):
AAAACCCTAACCTAATTAAATTAAAAACCCTAACCAATTTAATTAAAAACCCTAACCCTTAACCC
TAAAACCCTAACCTAATTTAATTA
Found at i:27715845 original size:23 final size:23
Alignment explanation
Indices: 27715476--27715902 Score: 263
Period size: 23 Copynumber: 19.3 Consensus size: 23
27715466 CCTTAACCCT
* * *
27715476 AAAACCCTAACCTAATTAAATTA
1 AAAACCCTAACCCACTTAACTTA
* *
27715499 AAAACCCTAACCTAATTTAA-TTA
1 AAAACCCTAACC-CACTTAACTTA
*
27715522 AAAACCCTAA-CC-CTTAACCCT-
1 AAAACCCTAACCCACTTAA-CTTA
* * *
27715543 AAAATCCTAACCTAATTTAA-TTA
1 AAAACCCTAACC-CACTTAACTTA
* *
27715566 AAAACCCTAACCTAATTTAA-TTA
1 AAAACCCTAACC-CACTTAACTTA
*
27715589 AAAACCCTAACCCA--TAACCCT-
1 AAAACCCTAACCCACTTAA-CTTA
* * *
27715610 AAAACCCTAACCTAATTAAATTA
1 AAAACCCTAACCCACTTAACTTA
* *
27715633 AAAACCCTAACCTAATTTAA-TTA
1 AAAACCCTAACC-CACTTAACTTA
* * * *
27715656 AAAACCATAACCTAATTAAATTA
1 AAAACCCTAACCCACTTAACTTA
* *
27715679 AAAACCCTAACCTAATTTAA-TTA
1 AAAACCCTAACC-CACTTAACTTA
* * *
27715702 AAAACTC-AA-CC-CTTCACCCT-
1 AAAACCCTAACCCACTT-AACTTA
* * * *
27715722 AAAACCCTAACCTAATTAAATTG
1 AAAACCCTAACCCACTTAACTTA
* * *
27715745 AAAACCCTAACCTAATTAAATTA
1 AAAACCCTAACCCACTTAACTTA
*
27715768 AAAACCCTAACCC-GTT-ACTTA
1 AAAACCCTAACCCACTTAACTTA
27715789 AAAACCCTAA-CC-CTTAACTTA
1 AAAACCCTAACCCACTTAACTTA
*
27715810 AAAACCCTAACCCCCTTAACTTA
1 AAAACCCTAACCCACTTAACTTA
27715833 AAAACCCTAA-CC-CTTAACTTA
1 AAAACCCTAACCCACTTAACTTA
*
27715854 AAAACCCTAAACC-CTTAACTTA
1 AAAACCCTAACCCACTTAACTTA
* * *
27715876 AAAACTCTTA-CC-CTTAACTTT
1 AAAACCCTAACCCACTTAACTTA
27715897 AAAACC
1 AAAACC
27715903 TTAAACTAAG
Statistics
Matches: 336, Mismatches: 43, Indels: 52
0.78 0.10 0.12
Matches are distributed among these distances:
19 2 0.01
20 18 0.05
21 89 0.26
22 42 0.12
23 166 0.49
24 19 0.06
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (23 bp):
AAAACCCTAACCCACTTAACTTA
Found at i:27715899 original size:44 final size:43
Alignment explanation
Indices: 27715515--27715908 Score: 217
Period size: 44 Copynumber: 9.0 Consensus size: 43
27715505 CTAACCTAAT
* * *
27715515 TTAA-TTAAAAACCCTAACCCTTAACCCT-AAAATCCT-AACCTAAT
1 TTAACTTAAAAACCCTAACCCTTAA-CTTAAAAACCCTAAACC---C
*
27715559 TTAA-TTAAAAACCCTAACCTAATTTAA-TTAAAAACCCT-AACCC
1 TTAACTTAAAAACCCTAACC---CTTAACTTAAAAACCCTAAACCC
* * * * *
27715602 ATAACCCT-AAAACCCTAACCTAATTAAATTAAAAACCCT-AACCTAAT
1 TTAA-CTTAAAAACCCTAACC--CTTAACTTAAAAACCCTAAACC---C
* * * *
27715649 TTAA-TTAAAAACCATAACCTAATTAAATTAAAAACCCT-AACCTAAT
1 TTAACTTAAAAACCCTAACC--CTTAACTTAAAAACCCTAAACC---C
* * * *
27715695 TTAA-TTAAAAACTC-AACCCTTCACCCT-AAAACCCT-AACCTAA
1 TTAACTTAAAAACCCTAACCCTT-AACTTAAAAACCCTAAACC--C
* * * *
27715737 TTAAATTGAAAACCCTAACCTAATTAAATTAAAAACCCT-AACCC
1 TTAACTTAAAAACCCTAACC--CTTAACTTAAAAACCCTAAACCC
*
27715781 GTT-ACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCCCC
1 -TTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAA-ACCC
27715825 TTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCC
1 TTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCC
* * * *
27715868 TTAACTTAAAAACTCTTACCCTTAACTTTAAAACCTTAAAC
1 TTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAAAC
27715909 TAAGTTAATA
Statistics
Matches: 292, Mismatches: 37, Indels: 43
0.78 0.10 0.12
Matches are distributed among these distances:
42 20 0.07
43 73 0.25
44 106 0.36
45 11 0.04
46 75 0.26
47 7 0.02
ACGTcount: A:0.45, C:0.28, G:0.01, T:0.26
Consensus pattern (43 bp):
TTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCC
Found at i:27716149 original size:115 final size:116
Alignment explanation
Indices: 27715913--27716153 Score: 344
Period size: 115 Copynumber: 2.1 Consensus size: 116
27715903 TTAAACTAAG
* * **
27715913 TTAATAATTTTACTTTCATGTAATGTTAGATTTGGAAAATTGGTTTTTCCTAGTACTAACAATTA
1 TTAATAATTTTACTTTCATATAATGTTAGATTTGGAAAAATGGTTTTGACTAGTACTAACAATTA
* *
27715978 ATAACCCTAACCTAATTTGATAATTTTACTAACCATTAATACAATTTATCAC
66 ATAACCCTAA-CTAATTTGATAATTTTACTAACCATTAATACAAGTTATCAA
*
27716030 TTAATAATTTTACTTTCATATAATGTTAGATTTGGAAAAAT-GTTTTGACTGGTACTAACAATTA
1 TTAATAATTTTACTTTCATATAATGTTAGATTTGGAAAAATGGTTTTGACTAGTACTAACAATTA
***
27716094 ATAATTTTATA-TAATTTGA-AATTTTTACTAACCATTAATACAAGTTATCAA
66 ATAACCCTA-ACTAATTTGATAA-TTTTACTAACCATTAATACAAGTTATCAA
27716145 TTAATAATT
1 TTAATAATT
27716154 CACAAACTTA
Statistics
Matches: 112, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
114 2 0.02
115 44 0.39
116 26 0.23
117 40 0.36
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (116 bp):
TTAATAATTTTACTTTCATATAATGTTAGATTTGGAAAAATGGTTTTGACTAGTACTAACAATTA
ATAACCCTAACTAATTTGATAATTTTACTAACCATTAATACAAGTTATCAA
Found at i:27719387 original size:125 final size:124
Alignment explanation
Indices: 27719164--27719513 Score: 592
Period size: 124 Copynumber: 2.8 Consensus size: 124
27719154 CAAACATGCT
* *
27719164 ACTGTAGCAAAAGCGCGTCCACAAGGGCGCAATTTTCACAAATTCTTCTCAAATAGCATCCTGCT
1 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTT-ACAAATTCTTCTCAAATAGCATCCTGCT
*
27719229 AGAAGCGATTTTAGACTATTTGCTCAGAAACGTCAAAGAAAAATTATTTCTTCCATGACCG
65 AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAA-AAAAATTATTTCTTCCATGACCG
27719290 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTGCTA
1 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTGCTA
*
27719355 GAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGACCT
66 GAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGACCG
* * *
27719414 ATTATAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTA
1 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTGCTA
* * *
27719479 GAAGCGATTTTATACTATTCGATCAGAAATGTCAA
66 GAAGCGATTTTATACTATTTGCTCAGAAACGTCAA
27719514 CTCGAAATTA
Statistics
Matches: 214, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
124 116 0.54
125 64 0.30
126 34 0.16
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.28
Consensus pattern (124 bp):
ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTGCTA
GAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGACCG
Found at i:27719838 original size:10 final size:9
Alignment explanation
Indices: 27719824--27719856 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
27719814 CATTTTTTAT
27719824 TAAAAATCA
1 TAAAAATCA
27719833 TAAAAATCA
1 TAAAAATCA
27719842 TTAAAAAT-A
1 -TAAAAATCA
27719851 TAAAAA
1 TAAAAA
27719857 ATATATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 10 0.43
10 7 0.30
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (9 bp):
TAAAAATCA
Found at i:27720645 original size:29 final size:28
Alignment explanation
Indices: 27720603--27720731 Score: 122
Period size: 29 Copynumber: 4.5 Consensus size: 28
27720593 TTTATGATTC
*
27720603 TTTTTATATTTTTATAAGTTTATATATA
1 TTTTTATATTTTTATAAGTTTATATAAA
*
27720631 TTTTTATTACTTTTATAA-TTTAT-TAAAA
1 TTTTTA-TATTTTTATAAGTTTATAT-AAA
* *
27720659 TTTATTAGAATTTTTATAAGTTTGTATAAA
1 TTT-TTA-TATTTTTATAAGTTTATATAAA
* *
27720689 TATTTAATATTTTTATAA-TTT-TAAAATA
1 T-TTTTATATTTTTATAAGTTTATATAA-A
27720717 TTTTTATATTTTTAT
1 TTTTTATATTTTTAT
27720732 GATTTTTAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
27 18 0.21
28 21 0.25
29 32 0.38
30 10 0.12
31 3 0.04
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (28 bp):
TTTTTATATTTTTATAAGTTTATATAAA
Found at i:27720651 original size:58 final size:56
Alignment explanation
Indices: 27720603--27720731 Score: 161
Period size: 58 Copynumber: 2.3 Consensus size: 56
27720593 TTTATGATTC
* * *
27720603 TTTTTATATTTTTATAAGTTTATATATATTTTTATTACTTTTATAATTTATTAAAAT
1 TTTTTATATTTTTATAAGTTTATATAAATATTTAATACTTTTATAATTT-TTAAAAT
* * * *
27720660 TTATTAGAATTTTTATAAGTTTGTATAAATATTTAATATTTTTATAA-TTTTAAAAT
1 TTTTTA-TATTTTTATAAGTTTATATAAATATTTAATACTTTTATAATTTTTAAAAT
27720716 ATTTTTATATTTTTAT
1 -TTTTTATATTTTTAT
27720732 GATTTTTAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
56 15 0.25
57 12 0.20
58 34 0.56
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (56 bp):
TTTTTATATTTTTATAAGTTTATATAAATATTTAATACTTTTATAATTTTTAAAAT
Found at i:27720716 original size:19 final size:19
Alignment explanation
Indices: 27720694--27720730 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
27720684 ATAAATATTT
27720694 AATATTTTTATAATTTTAA
1 AATATTTTTATAATTTTAA
*
27720713 AATATTTTTATATTTTTA
1 AATATTTTTATAATTTTA
27720731 TGATTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
AATATTTTTATAATTTTAA
Found at i:27723008 original size:21 final size:21
Alignment explanation
Indices: 27722984--27723023 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
27722974 TAATTTAGCC
*
27722984 ATTTTTGTTTTTATTTTAAAT
1 ATTTTTGTTTTTAATTTAAAT
27723005 ATTTTTGTTTTTAATTTAA
1 ATTTTTGTTTTTAATTTAA
27723024 TTTTTACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (21 bp):
ATTTTTGTTTTTAATTTAAAT
Found at i:27729789 original size:22 final size:23
Alignment explanation
Indices: 27729764--27729807 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
27729754 CTTAGTTTAG
* *
27729764 TTAAATGATTTCTAA-TATGTTT
1 TTAAATGAATTCAAATTATGTTT
27729786 TTAAATGAATTCAAATTATGTT
1 TTAAATGAATTCAAATTATGTT
27729808 AGCACCACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50
Consensus pattern (23 bp):
TTAAATGAATTCAAATTATGTTT
Found at i:27740911 original size:18 final size:18
Alignment explanation
Indices: 27740888--27740924 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
27740878 TAGAATAAAA
27740888 AATATAATCAATATTCAT
1 AATATAATCAATATTCAT
27740906 AATATAATCAATATTCAT
1 AATATAATCAATATTCAT
27740924 A
1 A
27740925 CAAAATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (18 bp):
AATATAATCAATATTCAT
Found at i:27741183 original size:24 final size:22
Alignment explanation
Indices: 27741127--27741189 Score: 56
Period size: 24 Copynumber: 2.8 Consensus size: 22
27741117 TGGACCTTTC
**
27741127 AATTTGATA-ATTTTTTAATTT
1 AATTTGATATATTTTTTAATGG
* *
27741148 AATTTCAAATATTTATTTATATGG
1 AATTTGATATATTT-TTTA-ATGG
27741172 AATTTGATATATATTTTT
1 AATTTGATATAT-TTTTT
27741190 TAATTTTGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
21 7 0.22
22 4 0.12
23 4 0.12
24 15 0.47
25 2 0.06
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (22 bp):
AATTTGATATATTTTTTAATGG
Found at i:27741585 original size:43 final size:43
Alignment explanation
Indices: 27741514--27741605 Score: 166
Period size: 43 Copynumber: 2.1 Consensus size: 43
27741504 AAACTTAAAG
*
27741514 TTATACCTTATCTTATTACTATTATTAATAATTGACATCATCT
1 TTATCCCTTATCTTATTACTATTATTAATAATTGACATCATCT
*
27741557 TTATCCCTTTTCTTATTACTATTATTAATAATTGACATCATCT
1 TTATCCCTTATCTTATTACTATTATTAATAATTGACATCATCT
27741600 TTATCC
1 TTATCC
27741606 GGTAGTCTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.29, C:0.18, G:0.02, T:0.50
Consensus pattern (43 bp):
TTATCCCTTATCTTATTACTATTATTAATAATTGACATCATCT
Found at i:27756185 original size:23 final size:22
Alignment explanation
Indices: 27756134--27756185 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
27756124 CCTCGTCTTT
*
27756134 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
27756156 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
27756179 TTCTTTT
1 TTCTTTT
27756186 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:27756200 original size:18 final size:18
Alignment explanation
Indices: 27756179--27756217 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
27756169 TTTCTTCAAC
*
27756179 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTTCTT
*
27756197 TTCTGTTTCACATTTCTT
1 TTCTGTTTCAAATTTCTT
27756215 TTC
1 TTC
27756218 ACTCTCAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.13, C:0.21, G:0.03, T:0.64
Consensus pattern (18 bp):
TTCTGTTTCAAATTTCTT
Found at i:27761519 original size:54 final size:53
Alignment explanation
Indices: 27761453--27761714 Score: 238
Period size: 54 Copynumber: 4.8 Consensus size: 53
27761443 ATGACTTTTT
* *
27761453 ACTTTGCGAGATTTTACGAATCTCGCAGTTCGCTGATTTACGATCATGACATTC
1 ACTTT-CGAGATTTTACGAATCTCACAGTCCGCTGATTTACGATCATGACATTC
* * * * ** * *
27761507 AGCTTTTGAGATTTTACGAATTTCATAGTCCGTTGATTTACGATCACCACCTTTT
1 A-CTTTCGAGATTTTACGAATCTCACAGTCCGCTGATTTACGATCATGA-CATTC
* * ** * *
27761562 ACTTTCGAAATTTTACGAATCTTATGGTCCGCTGATTTATGATCATGACCTTCC
1 ACTTTCGAGATTTTACGAATCTCACAGTCCGCTGATTTACGATCATGACATT-C
* ** * *
27761616 ACTTTCGAGATTTTACGAATTTCACAGTTTGCTAATTTACAATCATGA-ACTTC
1 ACTTTCGAGATTTTACGAATCTCACAGTCCGCTGATTTACGATCATGACA-TTC
* * * *
27761669 TACTTTCGAGATTTTATGAATCTCACGGTCCACTGATTGACGATCA
1 -ACTTTCGAGATTTTACGAATCTCACAGTCCGCTGATTTACGATCA
27761715 CGACCTTTGT
Statistics
Matches: 162, Mismatches: 41, Indels: 10
0.76 0.19 0.05
Matches are distributed among these distances:
53 4 0.02
54 150 0.93
55 8 0.05
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (53 bp):
ACTTTCGAGATTTTACGAATCTCACAGTCCGCTGATTTACGATCATGACATTC
Found at i:27761654 original size:108 final size:108
Alignment explanation
Indices: 27761449--27761721 Score: 314
Period size: 108 Copynumber: 2.5 Consensus size: 108
27761439 GCTAATGACT
* * * * *
27761449 TTTTACTTTGCGAGATTTTACGAATCTCGCAGTTCGCTGATTTACGATCATGACATTCAGCTTTT
1 TTTTACTTT-CGAGATTTTACGAATCTCACGGTCCGCTGATTTACGATCATGACCTTCAGCTTTC
* * * * *
27761514 GAGATTTTACGAATTTCATAGTCCGTTGATTTACGATCACCACC
65 GAGATTTTACGAATTTCACAGTCCGCTAATTTACAATCACCAAC
* * * *
27761558 TTTTACTTTCGAAATTTTACGAATCTTATGGTCCGCTGATTTATGATCATGACCTTCCA-CTTTC
1 TTTTACTTTCGAGATTTTACGAATCTCACGGTCCGCTGATTTACGATCATGACCTT-CAGCTTTC
** **
27761622 GAGATTTTACGAATTTCACAGTTTGCTAATTTACAATCATGAAC
65 GAGATTTTACGAATTTCACAGTCCGCTAATTTACAATCACCAAC
* * * * *
27761666 TTCTACTTTCGAGATTTTATGAATCTCACGGTCCACTGATTGACGATCACGACCTT
1 TTTTACTTTCGAGATTTTACGAATCTCACGGTCCGCTGATTTACGATCATGACCTT
27761722 TGTAACAACT
Statistics
Matches: 136, Mismatches: 27, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
108 125 0.92
109 11 0.08
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (108 bp):
TTTTACTTTCGAGATTTTACGAATCTCACGGTCCGCTGATTTACGATCATGACCTTCAGCTTTCG
AGATTTTACGAATTTCACAGTCCGCTAATTTACAATCACCAAC
Found at i:27765411 original size:79 final size:79
Alignment explanation
Indices: 27765250--27765473 Score: 226
Period size: 79 Copynumber: 2.8 Consensus size: 79
27765240 TTGAATGATG
* * * * * *
27765250 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATATCCGGACTAAGAT-CCGAAGGCA
1 TCCGGACTAAGTCCCGAAGGCAATTGTGCGAGA-T-ACTATAACCGGGCTAAG-TCCCGAAGGCA
*
27765312 TTTGTGCGAGATACATA
63 TTTGTGCGAGATACAAA
* *
27765329 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATTCCGGGCTAAG-CCCGAAGGCAT
1 TCCGGACTAAG-TCCCGAAGGCAATTGTGCGAGATACTATA-ACCGGGCTAAGTCCCGAAGGCAT
*
27765391 TTGTGCGAGTTACTAAA
64 TTGTGCGAGATAC-AAA
** * *
27765408 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGACTAAGTCCCGAAGGCAATTGTGCGAGATACTATAACCGGGCTAAGTCCCGAAGGCATTT
27765473 G
66 G
27765474 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 12, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
78 24 0.19
79 74 0.60
80 25 0.20
81 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (79 bp):
TCCGGACTAAGTCCCGAAGGCAATTGTGCGAGATACTATAACCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACAAA
Found at i:27765487 original size:40 final size:40
Alignment explanation
Indices: 27765251--27765473 Score: 235
Period size: 40 Copynumber: 5.6 Consensus size: 40
27765241 TGAATGATGT
* * * *
27765251 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
27765291 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-ATAT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA
* * *
27765330 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
27765370 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
27765408 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
27765449 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
27765474 AACGAGTAGC
Statistics
Matches: 163, Mismatches: 12, Indels: 16
0.85 0.06 0.08
Matches are distributed among these distances:
39 74 0.45
40 79 0.48
41 10 0.06
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:27765495 original size:79 final size:77
Alignment explanation
Indices: 27765303--27765506 Score: 225
Period size: 79 Copynumber: 2.6 Consensus size: 77
27765293 GGACTAAGAT
* *
27765303 CCGAAGGCATTTGTGCGAGATAC-ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTA
1 CCGAAGGCATTTGTGCGAGATACTATATCCGG-TTAAG-TCCGAAGGCAATTGTGCGAGATACTA
*
27765367 ATTCCGGGCTAAGC
64 ATACCGGGCTAAGC
* * *
27765381 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACT-
1 CCGAAGGCATTTGTGCGAGATACTATATCC-GGTTAAGT-CCGAAGGCAATTGTGCGAGATACTA
*
27765445 ATAACCGGGCTATGTC
64 AT-ACCGGGCTAAG-C
** *
27765461 CCGAAGGCATTTGAACGAG-TAGCTATATCCGGTTAAATTCCGAAGG
1 CCGAAGGCATTTGTGCGAGATA-CTATATCCGGTT-AAGTCCGAAGG
27765507 TACGTGATTT
Statistics
Matches: 108, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
78 25 0.23
79 53 0.49
80 30 0.28
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (77 bp):
CCGAAGGCATTTGTGCGAGATACTATATCCGGTTAAGTCCGAAGGCAATTGTGCGAGATACTAAT
ACCGGGCTAAGC
Found at i:27769213 original size:12 final size:12
Alignment explanation
Indices: 27769183--27769215 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
27769173 ATGCAACAGG
27769183 AAACCAGCA-GC
1 AAACCAGCATGC
27769194 AAACCAGCATGC
1 AAACCAGCATGC
*
27769206 AGACCAGCAT
1 AAACCAGCAT
27769216 CCAAGCTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.42, C:0.33, G:0.18, T:0.06
Consensus pattern (12 bp):
AAACCAGCATGC
Found at i:27770236 original size:20 final size:20
Alignment explanation
Indices: 27770213--27770251 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
27770203 AAATTTAAAA
27770213 TATAAAAAATTATTAATATG
1 TATAAAAAATTATTAATATG
* *
27770233 TATATAAATTTATTAATAT
1 TATAAAAAATTATTAATAT
27770252 ATGTAAAAAC
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:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
TATAAAAAATTATTAATATG
Found at i:27770313 original size:32 final size:32
Alignment explanation
Indices: 27770272--27770358 Score: 106
Period size: 33 Copynumber: 2.7 Consensus size: 32
27770262 AACTTTTTCG
27770272 GAAAATATTTTCAAGAAATC-TGCCAAACAACA
1 GAAAATATTTTCAAGAAATCAT-CCAAACAACA
* *
27770304 GAAAATATTTTACACAG-ATTCATCCAAACACCA
1 GAAAATATTTT-CA-AGAAATCATCCAAACAACA
*
27770337 GAAAATATTTTCAATAAATCAT
1 GAAAATATTTTCAAGAAATCAT
27770359 TTTCCAGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
31 1 0.02
32 18 0.38
33 25 0.53
34 3 0.06
ACGTcount: A:0.48, C:0.18, G:0.07, T:0.26
Consensus pattern (32 bp):
GAAAATATTTTCAAGAAATCATCCAAACAACA
Found at i:27770409 original size:20 final size:20
Alignment explanation
Indices: 27770351--27770402 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
27770341 ATATTTTCAA
27770351 TAAATCATTTTCCAGAAAAG
1 TAAATCATTTTCCAGAAAAG
*
27770371 TAAATCATTTTCCAAAAAAG
1 TAAATCATTTTCCAGAAAAG
27770391 TAAATCATTTTC
1 TAAATCATTTTC
27770403 TGGAAAACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (20 bp):
TAAATCATTTTCCAGAAAAG
Found at i:27770853 original size:21 final size:22
Alignment explanation
Indices: 27770801--27770853 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
27770791 ACCGCTGTTT
*
27770801 CTAATCTCA-CTGCTACAGTAT
1 CTAATCTCACCTGCTACAGTAA
*
27770822 CCAATCTCACCT-CTACAGTAA
1 CTAATCTCACCTGCTACAGTAA
27770843 CTAATCTCACC
1 CTAATCTCACC
27770854 GCCACCGCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.30, C:0.36, G:0.06, T:0.28
Consensus pattern (22 bp):
CTAATCTCACCTGCTACAGTAA
Found at i:27776359 original size:45 final size:44
Alignment explanation
Indices: 27776310--27776429 Score: 143
Period size: 45 Copynumber: 2.7 Consensus size: 44
27776300 ATACCAGAAA
* * *
27776310 CGAGTAAGACCGTAGCTACAAGACGTTATGGTATTACG-ATTCTAT
1 CGAGTAAGACCATAGCTA-AAGACGTTATGGCA-TAAGAATTCTAT
*
27776355 CGAGTAAGACCATAGCTAAAAGACGTTATGGCATAAGAATTTTAT
1 CGAGTAAGACCATAGCT-AAAGACGTTATGGCATAAGAATTCTAT
* *
27776400 CAAGTAAGACCATAGCTGAAAGACGCTATG
1 CGAGTAAGACCATAGCT-AAAGACGTTATG
27776430 ACATCATTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
44 3 0.05
45 62 0.94
46 1 0.02
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.25
Consensus pattern (44 bp):
CGAGTAAGACCATAGCTAAAGACGTTATGGCATAAGAATTCTAT
Found at i:27776510 original size:46 final size:46
Alignment explanation
Indices: 27776446--27776660 Score: 272
Period size: 46 Copynumber: 4.7 Consensus size: 46
27776436 TTAATCAAAC
*
27776446 GAATAAGACCACAGTTGAAAGACACTATGGCAACACGACGAAAAAT
1 GAATAAGACCATAGTTGAAAGACACTATGGCAACACGACGAAAAAT
* * *
27776492 GAATAAGACCATATTTGAAAGACACTATGGCAACATGAAGAAAAAT
1 GAATAAGACCATAGTTGAAAGACACTATGGCAACACGACGAAAAAT
* *
27776538 GAATAAGACCATAGTTGAAAGACACTATGGCAACACGATGGAAAAT
1 GAATAAGACCATAGTTGAAAGACACTATGGCAACACGACGAAAAAT
* * * * * *
27776584 GAATAAGGA-TATTGTTGAAAGACACTATGGCATCAAGTCG-AGAAT
1 GAATAA-GACCATAGTTGAAAGACACTATGGCAACACGACGAAAAAT
* * *
27776629 AAATAAGACCATGGTTGAAAGACACCATGGCA
1 GAATAAGACCATAGTTGAAAGACACTATGGCA
27776661 CCCTTCGGTC
Statistics
Matches: 148, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
44 2 0.01
45 29 0.20
46 115 0.78
47 2 0.01
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.18
Consensus pattern (46 bp):
GAATAAGACCATAGTTGAAAGACACTATGGCAACACGACGAAAAAT
Found at i:27779651 original size:79 final size:81
Alignment explanation
Indices: 27779509--27779691 Score: 216
Period size: 79 Copynumber: 2.3 Consensus size: 81
27779499 TCCTCGTTCA
* *
27779509 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
* *
27779573 T-TTAGTAAC-TCGCACG
66 TATT-GTAACTTAGC-CC
* **
27779589 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
*
27779651 ATATTGTCACTTAGCCC
65 ATATTGTAACTTAGCCC
*
27779668 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
27779692 CATCATTCAA
Statistics
Matches: 89, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
78 3 0.03
79 57 0.64
80 29 0.33
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
TATTGTAACTTAGCCC
Found at i:27779691 original size:40 final size:41
Alignment explanation
Indices: 27779507--27779691 Score: 222
Period size: 40 Copynumber: 4.6 Consensus size: 41
27779497 GCTCCTCGTT
* *
27779507 CAAATGCCTTCGGGACATAGCCCGGTTA-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATTAGTAACTCGCA
*
27779547 CAAATGCCTTCGGGACTTAACCCGGAT-TTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATTAGTAACTCGCA
* *
27779587 CGAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATTAGTAACTCGCA
* * * *
27779626 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATTAGTAAC-TCGCA
27779667 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
27779692 CATCATTCAA
Statistics
Matches: 125, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 78 0.62
41 13 0.10
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (41 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATTAGTAACTCGCA
Found at i:27787482 original size:39 final size:40
Alignment explanation
Indices: 27787365--27787549 Score: 218
Period size: 40 Copynumber: 4.7 Consensus size: 40
27787355 GCTCCTCGTT
*
27787365 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
27787405 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
27787445 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
27787484 CAAATGCCTTC-GGATCTTAGTCCAGATATT-GTCACTTAGCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TTAGTAAC-TCGCA
27787525 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
27787550 CATCATTCAA
Statistics
Matches: 125, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.02
39 33 0.26
40 76 0.61
41 14 0.11
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:27787533 original size:79 final size:81
Alignment explanation
Indices: 27787365--27787549 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 81
27787355 GCTCCTCGTT
* * *
27787365 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCA
*
27787429 GATTTAGTAACTCGCA
66 GATTTAGTAACTAGCA
* **
27787445 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* *
27787507 AGATATT-GTCACTTAGCC
65 AGAT-TTAGTAAC-TAGCA
27787525 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
27787550 CATCATTCAA
Statistics
Matches: 91, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
78 3 0.03
79 53 0.58
80 35 0.38
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCA
GATTTAGTAACTAGCA
Found at i:27790925 original size:20 final size:20
Alignment explanation
Indices: 27790902--27790988 Score: 70
Period size: 20 Copynumber: 4.3 Consensus size: 20
27790892 AGGCACAAAT
27790902 GTGCAAACAGGGGCAC-CATA
1 GTGCAAACAGGGGCACTCA-A
* * * * *
27790922 GTGCGAATAGAGACACTGAA
1 GTGCAAACAGGGGCACTCAA
* * *
27790942 GTGTATACAGGGGCACTGAA
1 GTGCAAACAGGGGCACTCAA
27790962 GTGCAAACAGGGGCAC-CGAA
1 GTGCAAACAGGGGCACTC-AA
27790982 GTGCAAA
1 GTGCAAA
27790989 TCTCGTACAA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
20 50 0.98
21 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.32, T:0.13
Consensus pattern (20 bp):
GTGCAAACAGGGGCACTCAA
Found at i:27791552 original size:13 final size:13
Alignment explanation
Indices: 27791534--27791577 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
27791524 AATTAATAAT
27791534 TTAATTCAATCTA
1 TTAATTCAATCTA
*
27791547 TTAATT-AAT-AA
1 TTAATTCAATCTA
27791558 TTTAATTCAATCTA
1 -TTAATTCAATCTA
27791572 TTAATT
1 TTAATT
27791578 TAGAAGGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 1 0.04
12 9 0.35
13 15 0.58
14 1 0.04
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (13 bp):
TTAATTCAATCTA
Found at i:27791553 original size:25 final size:25
Alignment explanation
Indices: 27791524--27791577 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
27791514 TCTTGATCTA
27791524 AATTAATAATTTAATTCAATCTATT
1 AATTAATAATTTAATTCAATCTATT
27791549 AATTAATAATTTAATTCAATCTATT
1 AATTAATAATTTAATTCAATCTATT
27791574 AATT
1 AATT
27791578 TAGAAGGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (25 bp):
AATTAATAATTTAATTCAATCTATT
Found at i:27796920 original size:15 final size:16
Alignment explanation
Indices: 27796900--27796929 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
27796890 TAACAACTAG
27796900 TATATAAT-TATATTT
1 TATATAATATATATTT
27796915 TATATAATATATATT
1 TATATAATATATATT
27796930 AATTGTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATAATATATATTT
Found at i:27816853 original size:18 final size:18
Alignment explanation
Indices: 27816830--27816865 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
27816820 TAAATTGAGT
27816830 TTAATTAAAGTAATTGTC
1 TTAATTAAAGTAATTGTC
27816848 TTAATTAAAGTAATTGTC
1 TTAATTAAAGTAATTGTC
27816866 CTACTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (18 bp):
TTAATTAAAGTAATTGTC
Found at i:27819938 original size:27 final size:27
Alignment explanation
Indices: 27819900--27819952 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
27819890 TCATCCTAAG
27819900 AGAAATTCAAAACTATGTCGCTAGACC
1 AGAAATTCAAAACTATGTCGCTAGACC
*
27819927 AGAAATTCAAAACTGTGTCGCTAGAC
1 AGAAATTCAAAACTATGTCGCTAGAC
27819953 ATTCTGGTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.23
Consensus pattern (27 bp):
AGAAATTCAAAACTATGTCGCTAGACC
Found at i:27825457 original size:25 final size:25
Alignment explanation
Indices: 27825425--27825700 Score: 390
Period size: 25 Copynumber: 11.0 Consensus size: 25
27825415 AATCGGATAA
* * *
27825425 CACTAACGTGCTAATAACCAAATAG
1 CACTAACGTGCTAATAATCAGAGAG
27825450 CACTAACGTGCTAATAATCAGAGAG
1 CACTAACGTGCTAATAATCAGAGAG
27825475 CACTAACGTGCTAATAATCAGAGAG
1 CACTAACGTGCTAATAATCAGAGAG
* *
27825500 CACTGATGTGCTAATAATCAGAGAG
1 CACTAACGTGCTAATAATCAGAGAG
* *
27825525 AACTAACGTGCTAATAATCAAAGAG
1 CACTAACGTGCTAATAATCAGAGAG
* *
27825550 CACTAACATGCTAATAATTAGAGAG
1 CACTAACGTGCTAATAATCAGAGAG
* * * *
27825575 CATTGATGTGCTAGTAATCAGAGAG
1 CACTAACGTGCTAATAATCAGAGAG
27825600 CACTAACGTGCTAATAATCAGAGAG
1 CACTAACGTGCTAATAATCAGAGAG
27825625 CACTAACGTGCTAATAATCAGAGAG
1 CACTAACGTGCTAATAATCAGAGAG
* * * *
27825650 GATTGAGGTGCTAATAATCAGAGAG
1 CACTAACGTGCTAATAATCAGAGAG
*
27825675 CACTAATGTGCTAATAATCAGAGAG
1 CACTAACGTGCTAATAATCAGAGAG
27825700 C
1 C
27825701 GCGCTAAGGT
Statistics
Matches: 220, Mismatches: 31, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 220 1.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (25 bp):
CACTAACGTGCTAATAATCAGAGAG
Found at i:27825530 original size:75 final size:75
Alignment explanation
Indices: 27825432--27825700 Score: 430
Period size: 75 Copynumber: 3.6 Consensus size: 75
27825422 TAACACTAAC
* * *
27825432 GTGCTAATAACCAAATAGCACTAACGTGCTAATAATCAGAGAGCACTAACGTGCTAATAATCAGA
1 GTGCTAATAATCAGAGAGCACTAACGTGCTAATAATCAGAGAGCACTAACGTGCTAATAATCAGA
*
27825497 GAGCACTGAT
66 GAGCATTGAT
* * * *
27825507 GTGCTAATAATCAGAGAGAACTAACGTGCTAATAATCAAAGAGCACTAACATGCTAATAATTAGA
1 GTGCTAATAATCAGAGAGCACTAACGTGCTAATAATCAGAGAGCACTAACGTGCTAATAATCAGA
27825572 GAGCATTGAT
66 GAGCATTGAT
*
27825582 GTGCTAGTAATCAGAGAGCACTAACGTGCTAATAATCAGAGAGCACTAACGTGCTAATAATCAGA
1 GTGCTAATAATCAGAGAGCACTAACGTGCTAATAATCAGAGAGCACTAACGTGCTAATAATCAGA
* *
27825647 GAGGATTGAG
66 GAGCATTGAT
*
27825657 GTGCTAATAATCAGAGAGCACTAATGTGCTAATAATCAGAGAGC
1 GTGCTAATAATCAGAGAGCACTAACGTGCTAATAATCAGAGAGC
27825701 GCGCTAAGGT
Statistics
Matches: 177, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 177 1.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (75 bp):
GTGCTAATAATCAGAGAGCACTAACGTGCTAATAATCAGAGAGCACTAACGTGCTAATAATCAGA
GAGCATTGAT
Found at i:27826316 original size:49 final size:47
Alignment explanation
Indices: 27826244--27826368 Score: 142
Period size: 49 Copynumber: 2.6 Consensus size: 47
27826234 CAGAGTTTAA
* * * *
27826244 CTATGGTCTTGCACATAATCACATATCATACACCAAAGCCATAGCCCAG
1 CTATGGTCTTACACAAAATCACATATCAGACA--AAAGCCAAAGCCCAG
* * * *
27826293 CTATGGTCTTACACAGAAGCACATATCAGACAGATGCCAAAGCCCAG
1 CTATGGTCTTACACAAAATCACATATCAGACAAAAGCCAAAGCCCAG
*
27826340 CTATGGTCTTATACAAAAATCACATATCA
1 CTATGGTCTTACAC-AAAATCACATATCA
27826369 CATATTGCCA
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
47 25 0.38
48 12 0.18
49 28 0.43
ACGTcount: A:0.37, C:0.27, G:0.14, T:0.22
Consensus pattern (47 bp):
CTATGGTCTTACACAAAATCACATATCAGACAAAAGCCAAAGCCCAG
Found at i:27833036 original size:5 final size:5
Alignment explanation
Indices: 27833026--27833053 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
27833016 TTTATTTGAC
27833026 ATTAA ATTAA ATTAA ATTAA ATTAA ATT
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATT
27833054 CTAAAATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
ATTAA
Found at i:27849795 original size:39 final size:39
Alignment explanation
Indices: 27849678--27849901 Score: 242
Period size: 40 Copynumber: 5.7 Consensus size: 39
27849668 GCTACTCGTT
* *
27849678 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAT-TAGTAACTCGCA
* *
27849718 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGA-TTAGTAACTCGCA
*
27849758 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-ATTAGTAACTCGCA
* *
27849797 CAAATGCCTTC-GGATCTTAGTCCGGA-TATGTATCTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTA-GTAACTCGCA
* * * *
27849836 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TAGTAAC-TCGCA
27849877 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
27849902 CATCATTCAA
Statistics
Matches: 162, Mismatches: 13, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
38 4 0.02
39 69 0.43
40 76 0.47
41 13 0.08
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTAGTAACTCGCA
Found at i:27849795 original size:79 final size:79
Alignment explanation
Indices: 27849678--27849901 Score: 226
Period size: 79 Copynumber: 2.8 Consensus size: 79
27849668 GCTACTCGTT
* *
27849678 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCG
*
27849742 GATTTAGTAACTCGCA
65 GATAT-GTAACTCGCA
* * **
27849758 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
*
27849821 GATATGTATCTCGCA
65 GATATGTAACTCGCA
* * * * * *
27849836 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGA-CTTAGCC
1 CAAATGCCTTCGGGA-CATAGCCCGGATATAGTAAC-TCGCACAAATGCCTTC-GGATCTTAACC
27849898 CGGA
63 CGGA
27849902 CATCATTCAA
Statistics
Matches: 123, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
77 2 0.02
78 24 0.20
79 71 0.58
80 26 0.21
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATGTAACTCGCA
Found at i:27857903 original size:39 final size:39
Alignment explanation
Indices: 27857786--27858009 Score: 242
Period size: 40 Copynumber: 5.7 Consensus size: 39
27857776 GCTACTCGTT
* *
27857786 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAT-TAGTAACTCGCA
* *
27857826 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGA-TTAGTAACTCGCA
*
27857866 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-ATTAGTAACTCGCA
* *
27857905 CAAATGCCTTC-GGATCTTAGTCCGGA-TATGTATCTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTA-GTAACTCGCA
* * * *
27857944 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TAGTAAC-TCGCA
27857985 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
27858010 CATCATTCAA
Statistics
Matches: 162, Mismatches: 13, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
38 4 0.02
39 69 0.43
40 76 0.47
41 13 0.08
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTAGTAACTCGCA
Found at i:27857903 original size:79 final size:79
Alignment explanation
Indices: 27857786--27858009 Score: 226
Period size: 79 Copynumber: 2.8 Consensus size: 79
27857776 GCTACTCGTT
* *
27857786 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCG
*
27857850 GATTTAGTAACTCGCA
65 GATAT-GTAACTCGCA
* * **
27857866 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
*
27857929 GATATGTATCTCGCA
65 GATATGTAACTCGCA
* * * * * *
27857944 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGA-CTTAGCC
1 CAAATGCCTTCGGGA-CATAGCCCGGATATAGTAAC-TCGCACAAATGCCTTC-GGATCTTAACC
27858006 CGGA
63 CGGA
27858010 CATCATTCAA
Statistics
Matches: 123, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
77 2 0.02
78 24 0.20
79 71 0.58
80 26 0.21
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATGTAACTCGCA
Found at i:27860999 original size:40 final size:40
Alignment explanation
Indices: 27860946--27861134 Score: 193
Period size: 40 Copynumber: 4.8 Consensus size: 40
27860936 GAGTTACTAG
* * * * *
27860946 AGTATAAATAGGGGCACGAAAGTGCATTTAGGGGTAACAA
1 AGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTAACAA
* * * *
27860986 AGTACAAACAGGGGCACGTATGTGCATTCAAGGGT-ACTGA
1 AGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTAAC-AA
* * * * *
27861026 AGTACAAACAAGGGCATGTAAGTGCAATCAGAGGTACCGA
1 AGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTAACAA
* *
27861066 AGTACAAATAGGGGCACGTAAGTGCAATCAGGGGTACCAA
1 AGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTAACAA
* *
27861106 AGTACATACA-AGGCACGTAAGTGCAATCA
1 AGTACAAACAGGGGCACGTAAGTGCAATCA
27861135 TCAATAATTA
Statistics
Matches: 125, Mismatches: 22, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
39 20 0.16
40 104 0.83
41 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.28, T:0.17
Consensus pattern (40 bp):
AGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTAACAA
Found at i:27861091 original size:80 final size:79
Alignment explanation
Indices: 27860958--27861134 Score: 219
Period size: 80 Copynumber: 2.2 Consensus size: 79
27860948 TATAAATAGG
* * * * * * * *
27860958 GGCACGAAAGTGCATTTAGGGGTAACAAAGTACAAACAGGGGCACGTATGTGCATTCAAGGGTAC
1 GGCACGTAAGTGCAATCAGAGGTACCGAAGTACAAACAGGGGCACGTAAGTGCAATCAAGGGTAC
**
27861023 TGAAGTACAAACAA
66 CAAAGTACAAACAA
* * *
27861037 GGGCATGTAAGTGCAATCAGAGGTACCGAAGTACAAATAGGGGCACGTAAGTGCAATCAGGGGTA
1 -GGCACGTAAGTGCAATCAGAGGTACCGAAGTACAAACAGGGGCACGTAAGTGCAATCAAGGGTA
*
27861102 CCAAAGTACATACAA
65 CCAAAGTACAAACAA
27861117 GGCACGTAAGTGCAATCA
1 GGCACGTAAGTGCAATCA
27861135 TCAATAATTA
Statistics
Matches: 82, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
79 17 0.21
80 65 0.79
ACGTcount: A:0.37, C:0.18, G:0.28, T:0.17
Consensus pattern (79 bp):
GGCACGTAAGTGCAATCAGAGGTACCGAAGTACAAACAGGGGCACGTAAGTGCAATCAAGGGTAC
CAAAGTACAAACAA
Found at i:27861098 original size:20 final size:20
Alignment explanation
Indices: 27860994--27861134 Score: 67
Period size: 20 Copynumber: 7.1 Consensus size: 20
27860984 AAAGTACAAA
* *
27860994 CAGGGGCACGTATGTGCATT
1 CAGGGGCACGTAAGTGCAAT
* * * *
27861014 CAAGGGTAC-TGAAGTACAAA
1 CAGGGGCACGT-AAGTGCAAT
* *
27861034 CAAGGGCATGTAAGTGCAAT
1 CAGGGGCACGTAAGTGCAAT
* * *
27861054 CAGAGGTACCG-AAGTACAAAT
1 CAGGGGCA-CGTAAGTGC-AAT
27861075 -AGGGGCACGTAAGTGCAAT
1 CAGGGGCACGTAAGTGCAAT
* ** *
27861094 CAGGGGTACCAAAGTAC-AT
1 CAGGGGCACGTAAGTGCAAT
*
27861113 ACA-AGGCACGTAAGTGCAAT
1 -CAGGGGCACGTAAGTGCAAT
27861133 CA
1 CA
27861135 TCAATAATTA
Statistics
Matches: 86, Mismatches: 27, Indels: 17
0.66 0.21 0.13
Matches are distributed among these distances:
19 19 0.22
20 62 0.72
21 5 0.06
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.17
Consensus pattern (20 bp):
CAGGGGCACGTAAGTGCAAT
Found at i:27872597 original size:23 final size:21
Alignment explanation
Indices: 27872548--27872598 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
27872538 AAAAACTTAT
27872548 TTATGTATGAAATTTTATATA
1 TTATGTATGAAATTTTATATA
**
27872569 TATATGTATGGTATATTTATATGA
1 T-TATGTATGAAAT-TTTATAT-A
27872593 TTATGT
1 TTATGT
27872599 TGTATACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 1 0.04
22 10 0.40
23 12 0.48
24 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (21 bp):
TTATGTATGAAATTTTATATA
Found at i:27874638 original size:39 final size:41
Alignment explanation
Indices: 27874543--27874726 Score: 208
Period size: 40 Copynumber: 4.6 Consensus size: 41
27874533 TTGAATGATG
*
27874543 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATA
*
27874582 TCCGGACTAAGAT-CCGAAGGCATTTGTGCG-AGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAAG-TACTAATA
27874622 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATA
* *
27874661 TCCGGGGTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
* *
27874701 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
27874727 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 9, Indels: 19
0.82 0.06 0.12
Matches are distributed among these distances:
39 54 0.43
40 61 0.48
41 11 0.09
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
Found at i:27874678 original size:79 final size:81
Alignment explanation
Indices: 27874543--27874726 Score: 222
Period size: 79 Copynumber: 2.3 Consensus size: 81
27874533 TTGAATGATG
27874543 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
27874606 TGTGCGAGA-TACTA-A
66 TGTGCGA-ATTACTATA
* * **
27874621 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAA-ATCCGGGGTAAG-TCCCGAAGGC
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGC
27874682 ATTTGTGCGAATTACTATA
63 ATTTGTGCGAATTACTATA
* *
27874701 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
27874727 AACGAGGAGC
Statistics
Matches: 92, Mismatches: 6, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
78 11 0.12
79 58 0.63
80 23 0.25
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
TGTGCGAATTACTATA
Found at i:27874757 original size:79 final size:79
Alignment explanation
Indices: 27874594--27874759 Score: 178
Period size: 79 Copynumber: 2.1 Consensus size: 79
27874584 CGGACTAAGA
* ** *
27874594 TCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTA
1 TCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTA
* *
27874659 AATCCGGGGTAAGT
66 AATCCGAGGTAAAT
* *
27874673 CCCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GA
1 TCCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA
* *
27874735 GCTATATCC-AGTTAAAT
63 -CTAAATCCGAGGTAAAT
27874752 TCCGAAGG
1 TCCGAAGG
27874760 TACGTGATTT
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
78 3 0.04
79 44 0.61
80 25 0.35
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
TCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTA
AATCCGAGGTAAAT
Found at i:27882500 original size:39 final size:40
Alignment explanation
Indices: 27882405--27882627 Score: 257
Period size: 39 Copynumber: 5.7 Consensus size: 40
27882395 TTGAATGATG
*
27882405 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
27882443 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
27882484 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
27882523 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
27882562 TCCGGGTTAAGTCCTGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
27882601 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
27882628 AACGAGGAGC
Statistics
Matches: 162, Mismatches: 13, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
39 93 0.57
40 57 0.35
41 11 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:27882599 original size:79 final size:81
Alignment explanation
Indices: 27882405--27882627 Score: 273
Period size: 79 Copynumber: 2.8 Consensus size: 81
27882395 TTGAATGATG
* * * *
27882405 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAA-TTACTAATATCCGGGCTAAGACCCGAAGGCAT
*
27882467 TTGTGCGAGATACTAAT
65 TTGTGCGAGATACTAAA
27882484 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-TACTAAT-TCCGGGCTAAG-CCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGA-ATTACTAATATCCGGGCTAAGACCCGAAGGCAT
*
27882545 TTGTGCGAGTTACTAAA
65 TTGTGCGAGATACTAAA
* * * * *
27882562 TCCGGGTTAAGTCCTGAAGGCATTTGTGCGAATTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAATTACTAATATCCGGGCTAAGACCCGAAGGCATT
27882626 TG
66 TG
27882628 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
78 47 0.37
79 54 0.43
80 24 0.19
81 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAATTACTAATATCCGGGCTAAGACCCGAAGGCATT
TGTGCGAGATACTAAA
Found at i:27882649 original size:79 final size:79
Alignment explanation
Indices: 27882457--27882650 Score: 202
Period size: 79 Copynumber: 2.5 Consensus size: 79
27882447 GGACTAAGAT
** * * *
27882457 CCGAAGGCATTTGTGCGAGAT-ACTAATTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACT
1 CCGAAGGCATTTGAACGAG-TGACTAAATCCGGGTTAAGTCCTGAAGGCATTTGTGCGAGATACT
*
27882520 AATTCCGGGCTAAGC
65 AATACCGGGCTAAGC
** *
27882535 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCTGAAGGCATTTGTGCGA-ATTACT
1 CCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAGTCCTGAAGGCATTTGTGCGAGA-TACT
*
27882599 -ATAACCGGGCTATGTC
65 AAT-ACCGGGCTAAG-C
*
27882615 CCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAA
1 CCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAA
27882651 ATTCCGAAGG
Statistics
Matches: 101, Mismatches: 9, Indels: 11
0.83 0.07 0.09
Matches are distributed among these distances:
77 1 0.01
78 37 0.37
79 38 0.38
80 25 0.25
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAGTCCTGAAGGCATTTGTGCGAGATACTA
ATACCGGGCTAAGC
Found at i:27882660 original size:79 final size:78
Alignment explanation
Indices: 27882457--27882660 Score: 202
Period size: 78 Copynumber: 2.6 Consensus size: 78
27882447 GGACTAAGAT
** * * *
27882457 CCGAAGGCATTTGTGCGAGAT-ACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTA
1 CCGAAGGCATTTGAACGAG-TGACTAAATCCGGGTTAAGTCCGAAGGCATTTGTGCGAGATACTA
*
27882521 ATTCCGGGCTAAGC
65 ATACCGGGCTAAGC
** *
27882535 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCTGAAGGCATTTGTGCGA-ATTACT
1 CCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAGTCC-GAAGGCATTTGTGCGAGA-TACT
*
27882599 -ATAACCGGGCTATGTC
64 AAT-ACCGGGCTAAG-C
* *
27882615 CCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTT-AAGTCCGAAGG
27882661 TACGTGATTT
Statistics
Matches: 109, Mismatches: 10, Indels: 13
0.83 0.08 0.10
Matches are distributed among these distances:
77 1 0.01
78 39 0.36
79 39 0.36
80 30 0.28
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (78 bp):
CCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAGTCCGAAGGCATTTGTGCGAGATACTAA
TACCGGGCTAAGC
Found at i:27888739 original size:14 final size:14
Alignment explanation
Indices: 27888715--27888757 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 14
27888705 AAGACAATGA
27888715 ATTGCAAAAAAAAAT
1 ATTG-AAAAAAAAAT
*
27888730 ATTGAAAAAAATAT
1 ATTGAAAAAAAAAT
27888744 ATTGAAAAAGAAAA
1 ATTGAAAAA-AAAA
27888758 AAGAGATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 18 0.72
15 7 0.28
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.21
Consensus pattern (14 bp):
ATTGAAAAAAAAAT
Found at i:27888779 original size:13 final size:13
Alignment explanation
Indices: 27888763--27888798 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
27888753 GAAAAAAGAG
27888763 ATGAAAAATGAAA
1 ATGAAAAATGAAA
27888776 ATGAAAAATGAAA
1 ATGAAAAATGAAA
27888789 A-GTAAAAATG
1 ATG-AAAAATG
27888799 GAGAGGCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 1 0.05
13 21 0.95
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (13 bp):
ATGAAAAATGAAA
Found at i:27890183 original size:50 final size:50
Alignment explanation
Indices: 27890109--27890426 Score: 192
Period size: 50 Copynumber: 6.4 Consensus size: 50
27890099 CCACATCGGT
* *
27890109 GAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGC
1 GAATCTTACTTCCCCGACAGTGCAGTTAAAAAGATTAAAGCTACAACAGC
* * * * ** * * * * *
27890159 GAATGTTACTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGT
1 GAATCTTACTTCCCCGACAGTGCAGTTAAAAAGATTAAAGCTACAACAGC
* *
27890209 GAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGC
1 GAATCTTACTTCCCCGACAGTGCAGTTAAAAAGATTAAAGCTACAACAGC
* * * ** * * * * * *
27890259 G-A-CTTACTT-CTCAAGCGGTGCAGTGGAATAGATTAACGCCATAGCGGC
1 GAATCTTACTTCCCCGA-CAGTGCAGTTAAAAAGATTAAAGCTACAACAGC
* ** * * * * * *
27890307 GAACCTTGTTTCCCCAACATTGCAGTTAAAAAGACTAAAGCCACAACGGG
1 GAATCTTACTTCCCCGACAGTGCAGTTAAAAAGATTAAAGCTACAACAGC
* *** ** * *
27890357 GAATCTTACTTTCCCAGGTGGTGCAGTGGAACAGATTGAAGCTACAACAGC
1 GAATCTTAC-TTCCCCGACAGTGCAGTTAAAAAGATTAAAGCTACAACAGC
* *
27890408 AAATCTCACTTCCCCGACA
1 GAATCTTACTTCCCCGACA
27890427 TCACAGTTAA
Statistics
Matches: 188, Mismatches: 75, Indels: 10
0.69 0.27 0.04
Matches are distributed among these distances:
47 3 0.02
48 30 0.16
49 2 0.01
50 115 0.61
51 38 0.20
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (50 bp):
GAATCTTACTTCCCCGACAGTGCAGTTAAAAAGATTAAAGCTACAACAGC
Found at i:27890254 original size:100 final size:100
Alignment explanation
Indices: 27890081--27890398 Score: 442
Period size: 100 Copynumber: 3.2 Consensus size: 100
27890071 TCTGAGATTA
*
27890081 CAGTGGAACAGATTAAAACCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTA
1 CAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTA
* *
27890146 AAGCTACAACAGCGAATGTTACTTCCCTGGCGGTG
66 AAGCTACAACAGCGAATCTTACTTCCCAGGCGGTG
27890181 CAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTA
1 CAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTA
* *
27890246 AAGCTACAACAGCG-A-CTTACTTCTCAAGCGGTG
66 AAGCTACAACAGCGAATCTTACTTCCCAGGCGGTG
* * * * * * * * *
27890279 CAGTGGAATAGATTAACGCCATAGCGGCGAACCTTGTTTCCCCAACATTGCAGTTAAAAAGACTA
1 CAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTA
* * * *
27890344 AAGCCACAACGGGGAATCTTACTTTCCCAGGTGGTG
66 AAGCTACAACAGCGAATCTTAC-TTCCCAGGCGGTG
*
27890380 CAGTGGAACAGATTGAAGC
1 CAGTGGAACAGATTAAAGC
27890399 TACAACAGCA
Statistics
Matches: 192, Mismatches: 23, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
98 81 0.42
99 2 0.01
100 83 0.43
101 26 0.14
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (100 bp):
CAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTA
AAGCTACAACAGCGAATCTTACTTCCCAGGCGGTG
Found at i:27896087 original size:50 final size:50
Alignment explanation
Indices: 27895793--27896071 Score: 319
Period size: 50 Copynumber: 5.5 Consensus size: 50
27895783 ACATTAAGAG
* * *
27895793 GATGAGA--TCCCTTGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C--CGA
* *
27895844 GATTATGAGAGGTCCCATGTAAGACCATGTTTGGGACTTGGCGTTGGCACCGA
1 G---ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
* *
27895897 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCAA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
* *
27895947 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATAGTGTTGGCACCGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
* ** * * * *
27895997 GATGAGAGTTCCCCCGTAAGACCATATCTGGGACATGGCATGGGCACCTA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
* **
27896047 TATGAGAACTCCCATGTAAGACCAT
1 GATGAGAGGTCCCATGTAAGACCAT
27896072 ATTTGGGATG
Statistics
Matches: 198, Mismatches: 25, Indels: 11
0.85 0.11 0.05
Matches are distributed among these distances:
50 154 0.78
51 1 0.01
53 3 0.02
54 6 0.03
55 1 0.01
56 33 0.17
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (50 bp):
GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
Found at i:27907616 original size:50 final size:50
Alignment explanation
Indices: 27907513--27907705 Score: 172
Period size: 50 Copynumber: 3.7 Consensus size: 50
27907503 GGGAATGAGA
* **
27907513 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGAGATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGC---A---CCGAGATGAGAGG
*
27907569 TCCCACGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * * * **
27907619 TCCC-CTATAAGACCATGTCTGAGACATAGCATGGGCACCGATATGAGAAC
1 TCCCAC-GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * ** *
27907669 TGCCATGTAAGACCATACCTGGGATATGGCATTGGCA
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
27907706 GTACAGGAAA
Statistics
Matches: 114, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
49 1 0.01
50 78 0.68
53 1 0.01
56 34 0.30
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (50 bp):
TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:27912043 original size:21 final size:21
Alignment explanation
Indices: 27912017--27912059 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
27912007 TCATGCATAT
27912017 ATCGGTTAAGCAATTTACCTA
1 ATCGGTTAAGCAATTTACCTA
27912038 ATCGGTTAAGCAATTTACCTA
1 ATCGGTTAAGCAATTTACCTA
27912059 A
1 A
27912060 ATCTAACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (21 bp):
ATCGGTTAAGCAATTTACCTA
Found at i:27913873 original size:21 final size:22
Alignment explanation
Indices: 27913848--27913898 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
27913838 AAAATATATT
27913848 AAATCAATTTTTAAA-AATTTG
1 AAATCAATTTTTAAATAATTTG
* * *
27913869 AAATC-TTTTTTAAATCATTTT
1 AAATCAATTTTTAAATAATTTG
27913890 AAATCAATT
1 AAATCAATT
27913899 CACGAGTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 8 0.33
21 14 0.58
22 2 0.08
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (22 bp):
AAATCAATTTTTAAATAATTTG
Found at i:27917998 original size:4 final size:4
Alignment explanation
Indices: 27917991--27918015 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
27917981 AAAAAAAAAA
27917991 GAGG GAGG GAGG GAGG GAGG GAGG G
1 GAGG GAGG GAGG GAGG GAGG GAGG G
27918016 GTCGGGGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.76, T:0.00
Consensus pattern (4 bp):
GAGG
Found at i:27920129 original size:18 final size:17
Alignment explanation
Indices: 27920100--27920142 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
27920090 TCTCTCAATT
27920100 CTTTCT-AATCTCCTAA
1 CTTTCTCAATCTCCTAA
*
27920116 CTTTCTCAACTCTCTTAA
1 CTTTCTCAA-TCTCCTAA
*
27920134 ATTTCTCAA
1 CTTTCTCAA
27920143 GTTCTTGTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 6 0.26
17 2 0.09
18 15 0.65
ACGTcount: A:0.26, C:0.30, G:0.00, T:0.44
Consensus pattern (17 bp):
CTTTCTCAATCTCCTAA
Found at i:27924665 original size:11 final size:11
Alignment explanation
Indices: 27924649--27924687 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
27924639 TGTCCTTAAG
27924649 AAAACTAAATA
1 AAAACTAAATA
27924660 AAAACTAAA-A
1 AAAACTAAATA
27924670 ATAAACTAAACTA
1 A-AAACTAAA-TA
27924683 AAAAC
1 AAAAC
27924688 AGAAAATAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.08
11 17 0.68
12 4 0.16
13 2 0.08
ACGTcount: A:0.72, C:0.13, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAACTAAATA
Found at i:27924693 original size:23 final size:22
Alignment explanation
Indices: 27924650--27924696 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
27924640 GTCCTTAAGA
27924650 AAACTAAATAAAAACTAAAAAT
1 AAACTAAATAAAAACTAAAAAT
27924672 AAACTAAACTAAAAAC-AGAAAAT
1 AAACTAAA-TAAAAACTA-AAAAT
27924695 AA
1 AA
27924697 CATGCAAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.72, C:0.11, G:0.02, T:0.15
Consensus pattern (22 bp):
AAACTAAATAAAAACTAAAAAT
Found at i:27926311 original size:20 final size:21
Alignment explanation
Indices: 27926272--27926311 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
27926262 TACATCAATT
*
27926272 AGTTCATGCATTCTTTCCATA
1 AGTTCATGCATTCATTCCATA
*
27926293 AGTTCATGC-TTGATTCCAT
1 AGTTCATGCATTCATTCCAT
27926312 TTGAATACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (21 bp):
AGTTCATGCATTCATTCCATA
Found at i:27931125 original size:40 final size:40
Alignment explanation
Indices: 27930773--27931123 Score: 585
Period size: 40 Copynumber: 8.8 Consensus size: 40
27930763 CAGCCGCAAA
* * * *
27930773 CATATTTGCCTTCGGGTCTTAACCCGGACATATGAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
* *
27930813 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCATCCCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
*
27930853 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
*
27930893 CATAATTGCCTTCGGGTCTTAGCCCGGATATGTCAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
*
27930933 CATAATTGCCTTCGGGTCTTAGCCCGGATATGTCAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
* * *
27930973 CATAATTGCCTTCGGGTCATAACTCGGATATATCAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
27931013 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
*
27931053 CATAATTGCCTTCGGGTCTTAGCCCGGATATGTCAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
27931093 CATAATTGCCTTCGGGTCTTAGCCCGGATAT
1 CATAATTGCCTTCGGGTCTTAGCCCGGATAT
27931124 GTTCCAATGT
Statistics
Matches: 292, Mismatches: 19, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 292 1.00
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (40 bp):
CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
Found at i:27938467 original size:40 final size:40
Alignment explanation
Indices: 27938115--27938465 Score: 594
Period size: 40 Copynumber: 8.8 Consensus size: 40
27938105 CAGCCGCAAA
* * * *
27938115 CATATTTGCCTTCGGGTCTTAACCCGGACATATGAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
* *
27938155 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCATCCCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
*
27938195 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
*
27938235 CATAATTGCCTTCGGGTCTTAGCCCGGATATGTCAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
*
27938275 CATAATTGCCTTCGGGTCTTAGCCCGGATATGTCAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
* *
27938315 CATAATTGCCTTCGGGTCATAACCCGGATATATCAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
27938355 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
*
27938395 CATAATTGCCTTCGGGTCTTAGCCCGGATATGTCAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
27938435 CATAATTGCCTTCGGGTCTTAGCCCGGATAT
1 CATAATTGCCTTCGGGTCTTAGCCCGGATAT
27938466 GTTCCAATGT
Statistics
Matches: 294, Mismatches: 17, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 294 1.00
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.30
Consensus pattern (40 bp):
CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
Found at i:27942045 original size:504 final size:503
Alignment explanation
Indices: 27941066--27942048 Score: 1815
Period size: 502 Copynumber: 2.0 Consensus size: 503
27941056 TCACCTTTGT
*
27941066 AATTTTTTTCACTCATCCCTCCATCAATCCTAGCATCTAAAACCCACCAAGTACCAAATCACCTA
1 AATTTTTTTCACTCATCCCTCCATCAATCCTAGCATCCAAAACCCACCAAGTACCAAATCACCTA
27941131 GTGCCGAACTCTCTAGCCCGCAACACCGCCCAGCTTCGCACGTCACCTTTACGCCTAGCAACAGC
66 GTGCCGAACTCTCTAGCCCGCAACACCGCCCAGCTTCGCACGTCACCTTTACGCCTAGCAACAGC
*
27941196 CCCATTTGGCCAGCAGCCCAAGCACGCACCAGTAGCTTACGCCGCTACTGCCGCTCCCATCAGAC
131 CCCATTTGGCCAGCAGCCCAAGCACGCACCAGTAGCTTACACCGCTACTGCCGCTCCCATCAGAC
*
27941261 CTACACTCACGCACCCGCTCATGTGCACCAATGCACCAGCCCTACCATTCGCCCGACAATGCCAC
196 CTACACTCACGCACCCGCTCATGTGCACCAACGCACCAGCCCTACCATTCGCCCGACAATGCCAC
*
27941326 CTGCTGTTCACACATCTGCTCACATCGCCTTGCTACTCGGACCAACACCCTTTCCTATCGTACCA
261 CTGCTGTTCACACATCTGCTCACATCGCCTTGCTACTCGGACCAACACCCTTTCCTATCGCACCA
*
27941391 TACCATCAAGAAACCCTACAACCATCCCTAAACCAAACCCTTTTGCTTTATATTTATTTTCTTTG
326 CACCATCAAGAAACCCTACAACCATCCCTAAACCAAACCCTTTTGCTTTATATTTATTTTCTTTG
27941456 AGTTCTTACCAAAGTGAGATACGAAAGCGTTTTCAAGAATCAACAGACGCACCTAGAAAAAGGCT
391 AGTTCTTACCAAAGTGAGATACGAAAGCGTTTTCAAGAATCAACAGACGCACCTAGAAAAAGGCT
27941521 TTACGCTGAAAGAAAACAACTATAAAGAAAACAACGAAAGTCTGATGC
456 TTACGCTGAAAGAAAACAACTATAAAGAAAACAACGAAAGTCTGATGC
27941569 AATTTTTTTCACTCATCCCTCCATCAATCCTAGCATCCAAAACCCACCAAGTACCAAATCACCTA
1 AATTTTTTTCACTCATCCCTCCATCAATCCTAGCATCCAAAACCCACCAAGTACCAAATCACCTA
*
27941634 GTGCCGAACTCTCTAG-CCGCAACACCGCCCAGCTTCGCACGTCACCTTTACGCCTAGCAATAGC
66 GTGCCGAACTCTCTAGCCCGCAACACCGCCCAGCTTCGCACGTCACCTTTACGCCTAGCAACAGC
* * *
27941698 CCCATTTGGCTAGCAGCCCAAGCACGCACCAGTAGCTTACACTGCTACTGCCGCTCGCATCAGAC
131 CCCATTTGGCCAGCAGCCCAAGCACGCACCAGTAGCTTACACCGCTACTGCCGCTCCCATCAGAC
* * * *
27941763 CTACTCTCACGCACCCGCTCATGTGCACCAACGCACCAGCCCTACTATTCGCTCGACAGTGCCAC
196 CTACACTCACGCACCCGCTCATGTGCACCAACGCACCAGCCCTACCATTCGCCCGACAATGCCAC
27941828 CTGCTGTTCACACATCTGCTCACATCGCGCCTTGCTACTCGGACCAACACCCTTTCCTATCGCAC
261 CTGCTGTTCACACATCTGCTCACAT--CGCCTTGCTACTCGGACCAACACCCTTTCCTATCGCAC
27941893 CACACCATCAAGAAACCCTACAACCATCCCTAAACCAAACCCTTTTGCTTTATATTTATTTTCTT
324 CACACCATCAAGAAACCCTACAACCATCCCTAAACCAAACCCTTTTGCTTTATATTTATTTTCTT
*
27941958 TGAGTTCTTACCAAAGTGAGATACGAAAGCGTTTTCAAGAATCAACAGATGCACCTAGAAAAAGG
389 TGAGTTCTTACCAAAGTGAGATACGAAAGCGTTTTCAAGAATCAACAGACGCACCTAGAAAAAGG
27942023 CTTTACGCTGAAAGAAAACAACTATA
454 CTTTACGCTGAAAGAAAACAACTATA
27942049 TTGATTTCAT
Statistics
Matches: 464, Mismatches: 14, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
502 193 0.42
503 80 0.17
504 191 0.41
ACGTcount: A:0.29, C:0.35, G:0.14, T:0.23
Consensus pattern (503 bp):
AATTTTTTTCACTCATCCCTCCATCAATCCTAGCATCCAAAACCCACCAAGTACCAAATCACCTA
GTGCCGAACTCTCTAGCCCGCAACACCGCCCAGCTTCGCACGTCACCTTTACGCCTAGCAACAGC
CCCATTTGGCCAGCAGCCCAAGCACGCACCAGTAGCTTACACCGCTACTGCCGCTCCCATCAGAC
CTACACTCACGCACCCGCTCATGTGCACCAACGCACCAGCCCTACCATTCGCCCGACAATGCCAC
CTGCTGTTCACACATCTGCTCACATCGCCTTGCTACTCGGACCAACACCCTTTCCTATCGCACCA
CACCATCAAGAAACCCTACAACCATCCCTAAACCAAACCCTTTTGCTTTATATTTATTTTCTTTG
AGTTCTTACCAAAGTGAGATACGAAAGCGTTTTCAAGAATCAACAGACGCACCTAGAAAAAGGCT
TTACGCTGAAAGAAAACAACTATAAAGAAAACAACGAAAGTCTGATGC
Found at i:27944033 original size:12 final size:12
Alignment explanation
Indices: 27944018--27944058 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
27944008 ATGCTCGTGA
27944018 AAAAAAGAAAAG
1 AAAAAAGAAAAG
27944030 AAAAAAGAAAAG
1 AAAAAAGAAAAG
*
27944042 AAAAGA-AAAAG
1 AAAAAAGAAAAG
27944053 AAAAAA
1 AAAAAA
27944059 TGAAGAAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:27944042 original size:17 final size:16
Alignment explanation
Indices: 27944020--27944056 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 16
27944010 GCTCGTGAAA
27944020 AAAAGAAAAGAAAAAAG
1 AAAAGAAAAG-AAAAAG
27944037 AAAAGAAAAGAAAAAG
1 AAAAGAAAAGAAAAAG
27944053 AAAA
1 AAAA
27944057 AATGAAGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAGAAAAAG
Found at i:27944048 original size:22 final size:25
Alignment explanation
Indices: 27944020--27944067 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 25
27944010 GCTCGTGAAA
27944020 AAAAG-AAAAGAAAAAA-GAA-AAG
1 AAAAGAAAAAGAAAAAATGAAGAAG
27944042 AAAAGAAAAAGAAAAAATGAAGAAG
1 AAAAGAAAAAGAAAAAATGAAGAAG
27944067 A
1 A
27944068 GAACAACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.22
23 11 0.48
24 3 0.13
25 4 0.17
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (25 bp):
AAAAGAAAAAGAAAAAATGAAGAAG
Found at i:27944057 original size:17 final size:16
Alignment explanation
Indices: 27944017--27944057 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 16
27944007 AATGCTCGTG
27944017 AAAAAAAGAAAAGAAA
1 AAAAAAAGAAAAGAAA
27944033 AAAGAAAAGAAAAGAAA
1 AAA-AAAAGAAAAGAAA
27944050 AAGAAAAA
1 AA-AAAAA
27944058 ATGAAGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.13
17 19 0.83
18 1 0.04
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAAAAGAAA
Found at i:27945620 original size:20 final size:18
Alignment explanation
Indices: 27945589--27945625 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
27945579 TGTAATGCTG
27945589 ATATGCTTAATTTAATTA
1 ATATGCTTAATTTAATTA
27945607 ATATGGCTTAAATTTAATT
1 ATAT-GCTT-AATTTAATT
27945626 TCTGTTAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 4 0.24
20 9 0.53
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (18 bp):
ATATGCTTAATTTAATTA
Found at i:27952833 original size:51 final size:49
Alignment explanation
Indices: 27952771--27953008 Score: 260
Period size: 51 Copynumber: 4.7 Consensus size: 49
27952761 ATACTCGGTT
* * *
27952771 CACATAGTAGCCTGCACATAGTACTACACATGTGAGCGTTTTCATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-C-CTATCATCCGATA
* * * *
27952822 CACGTAGTAGCCTGCACATAGTACTACACACGTGATCCAAGCTATCCGCTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CCTATC-ATCCGATA
* * * *
27952873 CGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCTATCA-TCCGATA
* * * * *
27952923 CACGTAGTAGACTACACATAGTACTATACACGTGACCATTTTCATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACC--TATCATCCGATA
*
27952974 CACATAGTAGCCTACACATAGTACTACACACGTGA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA
27953009 TCTAGCAACT
Statistics
Matches: 156, Mismatches: 27, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
49 1 0.01
50 41 0.26
51 110 0.71
52 4 0.03
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.24
Consensus pattern (49 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCTATCATCCGATA
Found at i:27952955 original size:101 final size:102
Alignment explanation
Indices: 27952771--27953003 Score: 310
Period size: 101 Copynumber: 2.3 Consensus size: 102
27952761 ATACTCGGTT
* * * * *
27952771 CACATAGTAGCCTGCACATAGTACTACACATGTGAGCGTTTTCATCCGATACACGTAGTAGCCTG
1 CACATAGTAGCCTGCACATAGTACTACACATGCGAGCGCTATCATCCGATACACGTAGTAGACTA
*
27952836 CACATAGTACTACACACGTGATCCAAGCT-ATCCGCTA
66 CACATAGTACTACACACGTGA-CCAAGCTCATCCGATA
* *
27952873 CGCATAGTAGCCTGCACATAGTACTACACATGCGA-C-CTATCATTCCGGTACACGTAGTAGACT
1 CACATAGTAGCCTGCACATAGTACTACACATGCGAGCGCTATCA-TCCGATACACGTAGTAGACT
* ***
27952936 ACACATAGTACTATACACGTGACCATTTTCATCCGATA
65 ACACATAGTACTACACACGTGACCAAGCTCATCCGATA
*
27952974 CACATAGTAGCCTACACATAGTACTACACA
1 CACATAGTAGCCTGCACATAGTACTACACA
27953004 CGTGATCTAG
Statistics
Matches: 115, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
100 8 0.07
101 74 0.64
102 33 0.29
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.24
Consensus pattern (102 bp):
CACATAGTAGCCTGCACATAGTACTACACATGCGAGCGCTATCATCCGATACACGTAGTAGACTA
CACATAGTACTACACACGTGACCAAGCTCATCCGATA
Found at i:27958648 original size:23 final size:23
Alignment explanation
Indices: 27958618--27958661 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
27958608 GTTACTGAGT
27958618 ATGACGTTATGCATACATGTAAA
1 ATGACGTTATGCATACATGTAAA
27958641 ATGACGTTATGCATACATGTA
1 ATGACGTTATGCATACATGTA
27958662 TGATTTATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (23 bp):
ATGACGTTATGCATACATGTAAA
Found at i:27958718 original size:26 final size:25
Alignment explanation
Indices: 27958678--27958733 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
27958668 ATGACACGAC
* *
27958678 ATACTGTATTGGCAGCTTTGCTGCG
1 ATACTGTACTGGCAGCTTTACTGCG
27958703 ATACTGATACTGGCAGCTTTACTGCG
1 ATACTG-TACTGGCAGCTTTACTGCG
*
27958729 TTACT
1 ATACT
27958734 ATTACGAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (25 bp):
ATACTGTACTGGCAGCTTTACTGCG
Found at i:27958905 original size:28 final size:26
Alignment explanation
Indices: 27958865--27958924 Score: 93
Period size: 28 Copynumber: 2.2 Consensus size: 26
27958855 ACTGTACTGA
27958865 TACTGTAATGGGCTAAGGCCCACATTG
1 TACTGTAATGGGCTAAGG-CCACATTG
*
27958892 TTACTGTATTGGGCTAAGGCCACATTG
1 -TACTGTAATGGGCTAAGGCCACATTG
27958919 TACTGT
1 TACTGT
27958925 GACTAAATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 6 0.19
27 8 0.26
28 17 0.55
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (26 bp):
TACTGTAATGGGCTAAGGCCACATTG
Found at i:27965886 original size:13 final size:12
Alignment explanation
Indices: 27965849--27965901 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 12
27965839 CTAATCTTTG
*
27965849 ATTTATTTTTCT
1 ATTTATTTTTTT
27965861 ATTTTATTTATTTT
1 A-TTTATTT-TTTT
27965875 ATTTATTTATTTT
1 ATTTATTT-TTTT
* *
27965888 AATTAATTTTTT
1 ATTTATTTTTTT
27965900 AT
1 AT
27965902 CTGACTTGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
12 6 0.17
13 25 0.71
14 4 0.11
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (12 bp):
ATTTATTTTTTT
Found at i:27966313 original size:14 final size:14
Alignment explanation
Indices: 27966274--27966314 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
27966264 AATTCATGAG
27966274 TATCTCTTTCCTTTA
1 TATCTCTTT-CTTTA
*
27966289 T-TCT-ATTCTTTA
1 TATCTCTTTCTTTA
27966301 TATCTCTTTCTTTA
1 TATCTCTTTCTTTA
27966315 ACATTGTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
12 6 0.27
13 5 0.23
14 10 0.45
15 1 0.05
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.63
Consensus pattern (14 bp):
TATCTCTTTCTTTA
Found at i:27971034 original size:24 final size:24
Alignment explanation
Indices: 27971007--27971099 Score: 132
Period size: 24 Copynumber: 3.9 Consensus size: 24
27970997 ACACACCACG
*
27971007 TTGTGGCCAAGCCACTCCATAGCA
1 TTGTGGCCAAGCCACTCAATAGCA
* *
27971031 TTGTGGCCAAGCAACTCAATAGCG
1 TTGTGGCCAAGCCACTCAATAGCA
* * *
27971055 TTTTGGTCAAGCCACTCAATAACA
1 TTGTGGCCAAGCCACTCAATAGCA
27971079 TTGTGGCCAAGCCACTCAATA
1 TTGTGGCCAAGCCACTCAATA
27971100 TTGCAGATAA
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:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (24 bp):
TTGTGGCCAAGCCACTCAATAGCA
Found at i:27979222 original size:50 final size:50
Alignment explanation
Indices: 27979147--27979336 Score: 164
Period size: 50 Copynumber: 3.7 Consensus size: 50
27979137 TTTCTTGTAC
* * * * **
27979147 TGCCAATGTCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGAGACCTCTCATATCGG
* * * ** * *
27979197 TGCCCATGTCTTGTCCCAAACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGAGACCTCTCATATCGG
* * *
27979247 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGAGACCTCTCAT-A--TC---GG
* *
27979303 TGCCAATGCCATCTCCCAGACATGGTCTTACATG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATG
27979337 GGATCTCTTT
Statistics
Matches: 114, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
50 78 0.68
53 2 0.02
56 34 0.30
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAAACATGGTCTTACATGAGACCTCTCATATCGG
Found at i:27983517 original size:50 final size:50
Alignment explanation
Indices: 27983404--27983596 Score: 224
Period size: 50 Copynumber: 3.8 Consensus size: 50
27983394 GATAATAACA
* * * * ** *
27983404 TGCCAAAGCCATGTCCCAGGCATGGTATTAAATGGGATGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * * ** * *
27983455 TGCCCATGCCATGCCCCAAACATGGTCTTACGGGGGACCTTTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
27983505 TGCCAACGCCATGTCCCAGACATGGTATTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
27983555 TGCCAACGCCATGTCCCAGACATGATCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
27983597 TTACCCAAAT
Statistics
Matches: 117, Mismatches: 25, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
50 89 0.76
51 28 0.24
ACGTcount: A:0.22, C:0.30, G:0.23, T:0.25
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:27983592 original size:100 final size:101
Alignment explanation
Indices: 27983404--27983594 Score: 258
Period size: 100 Copynumber: 1.9 Consensus size: 101
27983394 GATAATAACA
* ** * *
27983404 TGCCAAAGCCATGTCCCAGGCATGGTATTAAATGGGATGTTCTCATATCGGTGCCCATGCCATGC
1 TGCCAAAGCCATGTCCCAGACATGGTATTAAATGGGATCCTCTCATATCGGTGCCAACGCCATGC
* *
27983469 CCCAAACATGGTCTTACGGGGGACCTTTCATCTTGG
66 CCCAAACATGATCTTACAGGGGACCTTTCATCTTGG
* * * *
27983505 TGCCAACGCCATGTCCCAGACATGGTATTACATGGGA-CCTCTCATCTCGGTGCCAACGCCATGT
1 TGCCAAAGCCATGTCCCAGACATGGTATTAAATGGGATCCTCTCATATCGGTGCCAACGCCATGC
* *
27983569 CCCAGACATGATCTTACATGGGACCT
66 CCCAAACATGATCTTACAGGGGACCT
27983595 CTTTACCCAA
Statistics
Matches: 77, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
100 43 0.56
101 34 0.44
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.25
Consensus pattern (101 bp):
TGCCAAAGCCATGTCCCAGACATGGTATTAAATGGGATCCTCTCATATCGGTGCCAACGCCATGC
CCCAAACATGATCTTACAGGGGACCTTTCATCTTGG
Found at i:27987422 original size:50 final size:50
Alignment explanation
Indices: 27987360--27987490 Score: 138
Period size: 50 Copynumber: 2.6 Consensus size: 50
27987350 CAATGTCATA
* ** * * * *
27987360 TCCCAGATATGGTCTTACATGGGAGTTCTCAGATCGGTGCTC-ATGTCTTG
1 TCCCAGACATGGTCTTACATGGGACCTCTCAGATCGGTAC-CAACGCCATG
* ** **
27987410 TCCCAGACATGGTCATACGGGGGACCTCTCATCTCGGTACCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCAGATCGGTACCAACGCCATG
27987460 TCCCAGACATGGTCTTACATGGGACCTCTCA
1 TCCCAGACATGGTCTTACATGGGACCTCTCA
27987491 TAACCTCAAT
Statistics
Matches: 65, Mismatches: 15, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
49 1 0.02
50 64 0.98
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACATGGGACCTCTCAGATCGGTACCAACGCCATG
Found at i:28000605 original size:25 final size:25
Alignment explanation
Indices: 28000577--28000629 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
28000567 TAACCACAAT
28000577 TATTACAAGCCACTATTCAAAAAAC
1 TATTACAAGCCACTATTCAAAAAAC
28000602 TATTACAAGCCACTATTCAAAAAAC
1 TATTACAAGCCACTATTCAAAAAAC
28000627 TAT
1 TAT
28000630 GGTCTATTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.47, C:0.23, G:0.04, T:0.26
Consensus pattern (25 bp):
TATTACAAGCCACTATTCAAAAAAC
Found at i:28000618 original size:13 final size:13
Alignment explanation
Indices: 28000577--28000618 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
28000567 TAACCACAAT
28000577 TATTACAAGCCAC
1 TATTACAAGCCAC
***
28000590 TATT-CAAAAAAC
1 TATTACAAGCCAC
28000602 TATTACAAGCCAC
1 TATTACAAGCCAC
28000615 TATT
1 TATT
28000619 CAAAAAACTA
Statistics
Matches: 22, Mismatches: 6, Indels: 2
0.73 0.20 0.07
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.43, C:0.24, G:0.05, T:0.29
Consensus pattern (13 bp):
TATTACAAGCCAC
Found at i:28002509 original size:186 final size:183
Alignment explanation
Indices: 28002161--28002519 Score: 454
Period size: 186 Copynumber: 1.9 Consensus size: 183
28002151 GGGTTTAGGT
* * * * * *
28002161 TGTAACAACCTATTTTCAGTGAAATCGAAACAGTGGTTTTGGGACCACAAATCTGACGTGAAAAT
1 TGTAACAACCCATTTTCAGTGAAATCAAAACAGTGGTTTTGAGACCACAAATCTAAAGTAAAAAT
** * *
28002226 ATTTTATTTATTATTTTAATGTCTACCACATGCTAGTACTGCCCTATAAAAATTTCATTAAAAAA
66 ATTTTATTTATTATTTTAATGTCTACCACATGCTAGTAAAGCCATAGAAAAATTTCATTAAAAAA
28002291 TTTTATCATTTGCATGCTTAATTAAGTAAAAAGGACTAAATCGTAAAAGGTGA
131 TTTTATCATTTGCATGCTTAATTAAGTAAAAAGGACTAAATCGTAAAAGGTGA
* ** *
28002344 TGTAACATCCCATTTTTGGTGAAATCAAAATAGTGGTTTTGAGACCACAAATAC-AAAGTAAAAA
1 TGTAACAACCCATTTTCAGTGAAATCAAAACAGTGGTTTTGAGACCACAAAT-CTAAAGTAAAAA
* * * * *
28002408 TATTTATTTTATTATTATTTTAATGTTTA-CAGCATGTTAGTAAAGTCATAGAAAAATTTCGTTA
65 TA-TT-TTAT-TTATTATTTTAATGTCTACCA-CATGCTAGTAAAGCCATAGAAAAATTTCATTA
* *
28002472 AGAAATTTTATCATTTGCATGCTTAATT-CGATAAAAAGGACTAAATCG
126 AAAAATTTTATCATTTGCATGCTTAATTAAG-TAAAAAGGACTAAATCG
28002520 CTTAAAATGT
Statistics
Matches: 149, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
183 54 0.36
184 3 0.02
185 6 0.04
186 86 0.58
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.36
Consensus pattern (183 bp):
TGTAACAACCCATTTTCAGTGAAATCAAAACAGTGGTTTTGAGACCACAAATCTAAAGTAAAAAT
ATTTTATTTATTATTTTAATGTCTACCACATGCTAGTAAAGCCATAGAAAAATTTCATTAAAAAA
TTTTATCATTTGCATGCTTAATTAAGTAAAAAGGACTAAATCGTAAAAGGTGA
Found at i:28023300 original size:26 final size:26
Alignment explanation
Indices: 28023244--28023300 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
28023234 CTTTTATGAT
*
28023244 TTTTTTATAAATTTTTTTAATTTTAA
1 TTTTTTATAAATTTTTTTAATTATAA
28023270 TTTTTTATAAATTTTTATTAAATTAT-A
1 TTTTTTATAAATTTTT-TT-AATTATAA
28023297 TTTT
1 TTTT
28023301 GATATAACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 16 0.57
27 7 0.25
28 5 0.18
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (26 bp):
TTTTTTATAAATTTTTTTAATTATAA
Found at i:28027941 original size:113 final size:113
Alignment explanation
Indices: 28027723--28028060 Score: 574
Period size: 113 Copynumber: 3.0 Consensus size: 113
28027713 ATACAGTGTT
* * *
28027723 TTGTGATAGTCA-A-TGTTATTTTCCTTACGAATGATCAAATGTTTCACTAGAGAACAAATCACA
1 TTGTGATAGTCAGAGTGTCATCTTCCTTACAAATGATCAAATGTTTCACTAGAGAACAAATCACA
28027786 TCGATGTTCAATGTCATTTTATACGTGATATTATTGCTCATGTTGATG
66 TCGATGTTCAATGTCATTTTATACGTGATATTATTGCTCATGTTGATG
28027834 TTGTGATAGTCAGAGTGTCATCTTCCTTACAAATGATCAAATGTTTCACTAGAGAACAAATCACA
1 TTGTGATAGTCAGAGTGTCATCTTCCTTACAAATGATCAAATGTTTCACTAGAGAACAAATCACA
28027899 TCGATGTTCAATGTCATTTTATACGTGATATTATTGCTCATGTTGATG
66 TCGATGTTCAATGTCATTTTATACGTGATATTATTGCTCATGTTGATG
28027947 TTGTGATAGTCAGAGTGTCATCTTCCTTACAAATGATCAAATGTTTCA-TGAGAGAACAAATCAC
1 TTGTGATAGTCAGAGTGTCATCTTCCTTACAAATGATCAAATGTTTCACT-AGAGAACAAATCAC
** * * *
28028011 ATCGATGTTCGGTGTCATTTTATGCATGATATTATTGCTCATGGTGATG
65 ATCGATGTTCAATGTCATTTTATACGTGATATTATTGCTCATGTTGATG
28028060 T
1 T
28028061 GAGCAAAGTT
Statistics
Matches: 216, Mismatches: 8, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
111 12 0.06
112 2 0.01
113 202 0.94
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (113 bp):
TTGTGATAGTCAGAGTGTCATCTTCCTTACAAATGATCAAATGTTTCACTAGAGAACAAATCACA
TCGATGTTCAATGTCATTTTATACGTGATATTATTGCTCATGTTGATG
Found at i:28037893 original size:25 final size:25
Alignment explanation
Indices: 28037840--28037926 Score: 99
Period size: 25 Copynumber: 3.5 Consensus size: 25
28037830 TACCAGTTTT
* *
28037840 AGCTCTTATGAGCTTACCGATACTT-
1 AGCTCGTATGAGCTTACCGTTA-TTC
28037865 AGCTCGTATGAGCTTACCGTTATTC
1 AGCTCGTATGAGCTTACCGTTATTC
* *
28037890 AGCTCAG-AGGAGCTTACCGTTA-AC
1 AGCTC-GTATGAGCTTACCGTTATTC
28037914 AGCTCGTATGAGC
1 AGCTCGTATGAGC
28037927 ATACATGTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
23 1 0.02
24 13 0.24
25 39 0.72
26 1 0.02
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (25 bp):
AGCTCGTATGAGCTTACCGTTATTC
Found at i:28044801 original size:140 final size:141
Alignment explanation
Indices: 28044541--28044863 Score: 576
Period size: 140 Copynumber: 2.3 Consensus size: 141
28044531 GAAATGATAG
*
28044541 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCAAATAGCCGAT
*
28044606 GTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
66 GTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
*
28044671 TATATGTGTGA
131 TATATATGTGA
* * *
28044682 TAAGGCC-AATGGTCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCAAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCAAATAGCCGAT
28044746 GTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
66 GTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
28044811 TATATATGTGA
131 TATATATGTGA
*
28044822 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
28044864 GTTGATGAAT
Statistics
Matches: 172, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
140 134 0.78
141 38 0.22
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (141 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCAAATAGCCGAT
GTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
TATATATGTGA
Done.