Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009343.1 Hibiscus syriacus cultivar Beakdansim tig00113123_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2141224
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 11
Found at i:1999379 original size:84 final size:82
Alignment explanation
Indices: 1999276--1999891 Score: 584
Period size: 81 Copynumber: 7.5 Consensus size: 82
1999266 CTCGGGAGTC
* * *
1999276 TTTGGCAGATGGCCCTTCTTGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
1 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
*
1999341 TCAAACTCGAAGGTCTT
66 TCGAACTCGAAGGTCTT
* * * * * *
1999358 TGATTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGCGCCCTCGAAGCTGAGCG
1 T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCG
* **
1999423 TAATCGAACTCGGGGGTC--
63 TAGTCGAACTCGAAGGTCTT
*
1999441 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
1 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
*
1999506 TCGAACTCAAAGGTCTT
66 TCGAACTCGAAGGTCTT
* ** * * * * * * * * * *
1999523 TGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGT
1 T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGT
* * *
1999588 AATCAAACT-TAAGGGTC--
64 AGTCGAACTCGAA-GGTCTT
* *
1999605 TTTGGCAGATAGCTCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
1 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
*
1999670 TCGAACTCAAAGGTCTT
66 TCGAACTCGAAGGTCTT
** * * * * * * * * * *
1999687 TTCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGT
1 TT-TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGT
* *
1999752 AATCGAACT-TAAGGGTC--
64 AGTCGAACTCGAA-GGTCTT
*
1999769 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
1 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
1999834 TCGAACTCGAAGGT-TT
66 TCGAACTCGAAGGTCTT
* * * * * *
1999850 TGGTGGCAGGTAGCCCTTCTGGCCTTGAGCTAAGCTGCAAAT
1 T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAAT
1999892 AGTTTGTTTA
Statistics
Matches: 421, Mismatches: 95, Indels: 36
0.76 0.17 0.07
Matches are distributed among these distances:
80 77 0.18
81 113 0.27
82 40 0.10
83 72 0.17
84 92 0.22
85 27 0.06
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (82 bp):
TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
TCGAACTCGAAGGTCTT
Found at i:1999625 original size:164 final size:164
Alignment explanation
Indices: 1999207--1999878 Score: 925
Period size: 164 Copynumber: 4.1 Consensus size: 164
1999197 TGACAAATAG
* * * * * * * **
1999207 CCCTTCTTGCCATGAGCTATGTTGTAAATGATATGACCTCGAAGTTGAGTGTAATTGAAC-TCGG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTTAAG
* * * *
1999271 GAGTCTTTGGCAGATGGCCCTTCTTGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAG
66 G-GTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAG
* * * **
1999336 CGTAGTCAAACTCGAAGGTCTTTGATTGGCAGATAA
130 CGTAGTCGAACTCAAAGGTCTTTG-CTAACAGATAA
* * * * ** * ***
1999372 CCCTTCTTGACTTAAGTTATGCTGCAAATGATGCGCCCTCGAAGCTGAGCGTAATCGAACTCGGG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTTAAG
1999437 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGC
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGC
1999502 GTAGTCGAACTCAAAGGTCTTTGCTAACAGATAA
131 GTAGTCGAACTCAAAGGTCTTTGCTAACAGATAA
* * *
1999536 CCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCAAACTTAAG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTTAAG
* *
1999601 GGTCTTTGGCAGATAGCTCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGC
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGC
*
1999666 GTAGTCGAACTCAAAGGTCTTTTCTAACAGATAA
131 GTAGTCGAACTCAAAGGTCTTTGCTAACAGATAA
* *
1999700 CCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTTAAG
1999765 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGC
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGC
* * ** * *
1999830 GTAGTCGAACTCGAAGGT-TTTGGTGGCAGGTAG
131 GTAGTCGAACTCAAAGGTCTTTGCTAACAGATAA
*
1999863 CCCTTCTGGCCTTGAG
1 CCCTTCTAGCCTTGAG
1999879 CTAAGCTGCA
Statistics
Matches: 456, Mismatches: 50, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
163 24 0.05
164 300 0.66
165 129 0.28
166 3 0.01
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.31
Consensus pattern (164 bp):
CCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTTAAG
GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGC
GTAGTCGAACTCAAAGGTCTTTGCTAACAGATAA
Found at i:2005032 original size:8 final size:8
Alignment explanation
Indices: 2004976--2005034 Score: 50
Period size: 8 Copynumber: 7.2 Consensus size: 8
2004966 AAAATGCTAA
2004976 AAAATAA-
1 AAAATAAT
*
2004983 AAAATATAA
1 AAAATA-AT
2004992 AAAATAAT
1 AAAATAAT
2005000 AATAATAAT
1 AA-AATAAT
* *
2005009 GAAAGAA-
1 AAAATAAT
2005016 AGAAATAAT
1 A-AAATAAT
2005025 AAAATAAT
1 AAAATAAT
2005033 AA
1 AA
2005035 TAAAAGGTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
7 6 0.14
8 22 0.52
9 14 0.33
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (8 bp):
AAAATAAT
Found at i:2006227 original size:16 final size:16
Alignment explanation
Indices: 2006208--2006244 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
2006198 AGACCAAAAC
2006208 AATAAAATAAAATAA-A
1 AATAAAAT-AAATAATA
2006224 AATAAAATAAATAATA
1 AATAAAATAAATAATA
2006240 AATAA
1 AATAA
2006245 TATATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
AATAAAATAAATAATA
Found at i:2006244 original size:11 final size:11
Alignment explanation
Indices: 2006211--2006241 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
2006201 CCAAAACAAT
2006211 AAAATAAAATA
1 AAAATAAAATA
2006222 AAAATAAAATA
1 AAAATAAAATA
2006233 AATAATAAA
1 AA-AATAAA
2006242 TAATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.68
12 6 0.32
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:2006393 original size:36 final size:36
Alignment explanation
Indices: 2006258--2006523 Score: 206
Period size: 36 Copynumber: 7.2 Consensus size: 36
2006248 ATATATACAT
*
2006258 AAATATTTTCAAAAAC-ATATAATATATAAA-TTT-CA
1 AAATGTTTT-AAAAACTATAT-ATATATAAATTTTCCA
* * *
2006293 AAATGTTTT-TAAACTATATAATATATGAATTTTTTCA
1 AAATGTTTTAAAAACTATAT-ATATAT-AAATTTTCCA
* * * *
2006330 ACATGTTTTCAAAAA-AAAAGATTATATAAATTTTCCCA
1 AAATGTTTT-AAAAACTATATA-TATATAAATTTT-CCA
* *
2006368 AAACGTTTTAAAAACTATATA-ATATAAATGTTTTCA
1 AAATGTTTTAAAAACTATATATATATAAAT-TTTCCA
* ** *
2006404 AAATGTTTTCAAAACTATA-ATATATATGTTTTCAA
1 AAATGTTTTAAAAACTATATATATATAAATTTTCCA
2006439 AAATGTTTTCAAAAACTATATATATATATAAGTTTT-CA
1 AAATGTTTT-AAAAACTATATATATATA-AA-TTTTCCA
* * *
2006477 AAATGATTTTAAAAATTATATATTATATATATTTTCTA
1 AAATG-TTTTAAAAACTATATA-TATATAAATTTTCCA
2006515 AAATGTTTT
1 AAATGTTTT
2006524 CTTTTAAAAC
Statistics
Matches: 184, Mismatches: 29, Indels: 34
0.74 0.12 0.14
Matches are distributed among these distances:
33 4 0.02
34 11 0.06
35 24 0.13
36 45 0.24
37 40 0.22
38 43 0.23
39 17 0.09
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (36 bp):
AAATGTTTTAAAAACTATATATATATAAATTTTCCA
Found at i:2006402 original size:38 final size:36
Alignment explanation
Indices: 2006258--2006523 Score: 206
Period size: 38 Copynumber: 7.2 Consensus size: 36
2006248 ATATATACAT
* *
2006258 AAATATTTTCAAAAAC-ATATAATATATAA--ATTTCA
1 AAATGTTTT-AAAAACTATATAATATA-AATGTTTTCA
* *
2006293 AAATGTTTT-TAAACTATATAATATATGAATTTTTTCA
1 AAATGTTTTAAAAACTATATAATATA--AATGTTTTCA
* ** * * *
2006330 ACATGTTTTCAAAAAAAAAGATTATATAAAT-TTTCCCA
1 AAATGTTTT--AAAAACTATATAATATAAATGTTT-TCA
*
2006368 AAACGTTTTAAAAACTATATAATATAAATGTTTTCA
1 AAATGTTTTAAAAACTATATAATATAAATGTTTTCA
* *
2006404 AAATGTTTTCAAAAC--TATAATATATATGTTTTCAA
1 AAATGTTTTAAAAACTATATAATATAAATGTTTTC-A
2006439 AAATGTTTTCAAAAACTATATATATATATAA-GTTTTCA
1 AAATGTTTT-AAAAACTATATA-ATATA-AATGTTTTCA
* * * *
2006477 AAATGATTTTAAAAATTATATATTATATATATTTTCTA
1 AAATG-TTTTAAAAACTATATAATATAAATGTTTTC-A
2006515 AAATGTTTT
1 AAATGTTTT
2006524 CTTTTAAAAC
Statistics
Matches: 186, Mismatches: 27, Indels: 34
0.75 0.11 0.14
Matches are distributed among these distances:
33 4 0.02
34 27 0.15
35 20 0.11
36 37 0.20
37 32 0.17
38 39 0.21
39 15 0.08
40 12 0.06
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (36 bp):
AAATGTTTTAAAAACTATATAATATAAATGTTTTCA
Found at i:2006402 original size:74 final size:72
Alignment explanation
Indices: 2006258--2006523 Score: 238
Period size: 72 Copynumber: 3.6 Consensus size: 72
2006248 ATATATACAT
* * *
2006258 AAATATTTTCAAAAACATATAATATATAAA-TTT-CAAAATGTTTT-TAAACTATATAATATATG
1 AAATGTTTTCAAAAA-A-AAAATATATAAATTTTCCAAAATGTTTTAAAAACTATATAATATAT-
*
2006320 AATTTTTTCA
63 AATGTTTTCA
* *
2006330 ACATGTTTTCAAAAAAAAAGATTATATAAATTTTCCCAAAACGTTTTAAAAACTATATAATATA-
1 AAATGTTTTCAAAAAAAAA-A-TATATAAATTTT-CCAAAATGTTTTAAAAACTATATAATATAT
2006394 AATGTTTTCA
63 AATGTTTTCA
** * ** *
2006404 AAATGTTTTCAAAACTATAATATATATGTTTTCAAAAATGTTTTCAAAAACTATATATATATATA
1 AAATGTTTTCAAAAAAAAAATATATAAATTTTCCAAAATGTTTT-AAAAACTATATA-ATATATA
2006469 A-GTTTTCA
64 ATGTTTTCA
* * * *
2006477 AAATGATTTT-AAAAATTATATATTATATATATTTTCTAAAATGTTTT
1 AAATG-TTTTCAAAAA--A-AAAATATATAAATTTTCCAAAATGTTTT
2006524 CTTTTAAAAC
Statistics
Matches: 162, Mismatches: 19, Indels: 22
0.80 0.09 0.11
Matches are distributed among these distances:
70 2 0.01
71 12 0.07
72 43 0.27
73 25 0.15
74 30 0.19
75 10 0.06
76 40 0.25
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (72 bp):
AAATGTTTTCAAAAAAAAAATATATAAATTTTCCAAAATGTTTTAAAAACTATATAATATATAAT
GTTTTCA
Found at i:2006409 original size:11 final size:11
Alignment explanation
Indices: 2006393--2006417 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2006383 TATATAATAT
2006393 AAATGTTTTCA
1 AAATGTTTTCA
2006404 AAATGTTTTCA
1 AAATGTTTTCA
2006415 AAA
1 AAA
2006418 CTATAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:2006446 original size:12 final size:12
Alignment explanation
Indices: 2006429--2006453 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2006419 TATAATATAT
2006429 ATGTTTTCAAAA
1 ATGTTTTCAAAA
2006441 ATGTTTTCAAAA
1 ATGTTTTCAAAA
2006453 A
1 A
2006454 CTATATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:2006491 original size:110 final size:109
Alignment explanation
Indices: 2006258--2006524 Score: 271
Period size: 110 Copynumber: 2.4 Consensus size: 109
2006248 ATATATACAT
* *
2006258 AAAT-ATTTTCAAAAAC-ATATAATATATAA-ATTTCAAAATGTTTT-TAAACTATATAATATAT
1 AAATGATTTT-AAAAACTATATAATATA-AATTTTTCAAAATGTTTTCAAAAC-ATATAATATAT
* *
2006319 GAATTTTTTCAACATGTTTTCAAAAAAAAAGATTATATAAATTTTCCCA
63 -AATGTTTTCAAAATGTTTTCAAAAAAAAAGATTATATAAATTTT-CCA
*
2006368 AAACG-TTTTAAAAACTATATAATATAAATGTTTTCAAAATGTTTTCAAAAC-TATAATATAT-A
1 AAATGATTTTAAAAACTATATAATATAAAT-TTTTCAAAATGTTTTCAAAACATATAATATATAA
* * * *
2006430 TGTTTTCAAAAATGTTTTCAAAAACTATATATATATATAAGTTTT-CA
65 TGTTTTC-AAAATGTTTTCAAAAA-AAAAGAT-TATATAAATTTTCCA
* * *
2006477 AAATGATTTTAAAAATTATATATTATATATATTTTCTAAAATGTTTTC
1 AAATGATTTTAAAAACTATATAATATAAAT-TTTTC-AAAATGTTTTC
2006525 TTTTAAAACT
Statistics
Matches: 133, Mismatches: 14, Indels: 19
0.80 0.08 0.11
Matches are distributed among these distances:
108 7 0.05
109 29 0.22
110 57 0.43
111 36 0.27
112 4 0.03
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.42
Consensus pattern (109 bp):
AAATGATTTTAAAAACTATATAATATAAATTTTTCAAAATGTTTTCAAAACATATAATATATAAT
GTTTTCAAAATGTTTTCAAAAAAAAAGATTATATAAATTTTCCA
Found at i:2011483 original size:40 final size:40
Alignment explanation
Indices: 2011428--2011506 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
2011418 GGACTTTTTT
2011428 TTGCTAATTCTAATGTCAAACTTTTCTCACACTACTGTAC
1 TTGCTAATTCTAATGTCAAACTTTTCTCACACTACTGTAC
**
2011468 TTGCTAATTCTAATGTCAAACTTTTCTCACTGTACTGTA
1 TTGCTAATTCTAATGTCAAACTTTTCTCACACTACTGTA
2011507 TTACCACACA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.27, C:0.23, G:0.09, T:0.42
Consensus pattern (40 bp):
TTGCTAATTCTAATGTCAAACTTTTCTCACACTACTGTAC
Found at i:2011953 original size:2 final size:2
Alignment explanation
Indices: 2011948--2011978 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2011938 CAAAGGAATT
2011948 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2011979 TTTAAAAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2013922 original size:24 final size:25
Alignment explanation
Indices: 2013890--2013936 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
2013880 CTATTCTTTC
2013890 ACTTCAATCAAGC-TCGAATTTTAG
1 ACTTCAATCAAGCTTCGAATTTTAG
* *
2013914 ACTTCAATCGAGCTTCTAATTTT
1 ACTTCAATCAAGCTTCGAATTTT
2013937 TTTTTGAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (25 bp):
ACTTCAATCAAGCTTCGAATTTTAG
Found at i:2020932 original size:28 final size:28
Alignment explanation
Indices: 2020891--2021002 Score: 215
Period size: 28 Copynumber: 4.0 Consensus size: 28
2020881 ATTGTTACTC
2020891 TATTTCACCTTTTTATATGATAATTCAA
1 TATTTCACCTTTTTATATGATAATTCAA
*
2020919 CATTTCACCTTTTTATATGATAATTCAA
1 TATTTCACCTTTTTATATGATAATTCAA
2020947 TATTTCACCTTTTTATATGATAATTCAA
1 TATTTCACCTTTTTATATGATAATTCAA
2020975 TATTTCACCTTTTTATATGATAATTCAA
1 TATTTCACCTTTTTATATGATAATTCAA
2021003 GTGATTTCTC
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 82 1.00
ACGTcount: A:0.32, C:0.15, G:0.04, T:0.49
Consensus pattern (28 bp):
TATTTCACCTTTTTATATGATAATTCAA
Found at i:2025617 original size:16 final size:14
Alignment explanation
Indices: 2025588--2025621 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
2025578 AACTTAAAAA
2025588 TATAAATTTAAAGG
1 TATAAATTTAAAGG
2025602 TATAATATTATAAAGG
1 TATAA-ATT-TAAAGG
2025618 TATA
1 TATA
2025622 CAAACTAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 3 0.17
16 10 0.56
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (14 bp):
TATAAATTTAAAGG
Found at i:2029423 original size:14 final size:15
Alignment explanation
Indices: 2029391--2029423 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
2029381 AAAAAAAATT
2029391 AAAATTAGAACTTATA
1 AAAATTAGAAC-TATA
2029407 AAAATTAGAAC-ATA
1 AAAATTAGAACTATA
2029421 AAA
1 AAA
2029424 GAACACATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
16 11 0.65
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.24
Consensus pattern (15 bp):
AAAATTAGAACTATA
Found at i:2030507 original size:21 final size:21
Alignment explanation
Indices: 2030483--2030527 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2030473 ATTTGTAATT
*
2030483 AACCTTAAATCC-TAAATCATA
1 AACCTTAAA-CCATAAACCATA
*
2030504 AACCTTAGACCATAAACCATA
1 AACCTTAAACCATAAACCATA
2030525 AAC
1 AAC
2030528 TCAAAACTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.49, C:0.27, G:0.02, T:0.22
Consensus pattern (21 bp):
AACCTTAAACCATAAACCATA
Found at i:2039283 original size:4 final size:4
Alignment explanation
Indices: 2039269--2039308 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
2039259 AATAACTTGG
*
2039269 ATGT GTGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2039309 GTATACAGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:2049817 original size:16 final size:16
Alignment explanation
Indices: 2049796--2049847 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 16
2049786 TATTTTAATT
2049796 ATATATTAATAAAAAA
1 ATATATTAATAAAAAA
2049812 ATATA-TAATGTCAAAAAA
1 ATATATTAA--T-AAAAAA
2049830 AT-TATTAATAAAATAA
1 ATATATTAATAAAA-AA
2049846 AT
1 AT
2049848 TAGAGTGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
15 7 0.23
16 10 0.32
17 3 0.10
18 11 0.35
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (16 bp):
ATATATTAATAAAAAA
Found at i:2055119 original size:37 final size:36
Alignment explanation
Indices: 2055060--2055179 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
2055050 ATCCCATTAT
* *
2055060 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
2055096 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
2055132 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
2055167 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
2055180 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
35 35 0.45
36 13 0.17
37 29 0.38
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:2055135 original size:21 final size:21
Alignment explanation
Indices: 2055111--2055171 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
2055101 TTCAAAGAAA
2055111 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
2055132 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
2055146 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
2055167 CATTT
1 CATTT
2055172 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:2055188 original size:35 final size:36
Alignment explanation
Indices: 2055062--2055206 Score: 142
Period size: 35 Copynumber: 4.1 Consensus size: 36
2055052 CCCATTATCA
*
2055062 TTTTTCAACA-AACA-TCTACCAAACTTTGAAAAAC-T
1 TTTTTCAA-AGAACAGT-TACCAAACTTTGAAAACCAT
*
2055097 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 -TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
*
2055134 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1 TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
***
2055170 TTTTTCAAAG-TTGGTTACCAAAC-TTGAAAACCAT
1 TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
2055204 TTT
1 TTT
2055207 AATACTTTCA
Statistics
Matches: 98, Mismatches: 5, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
34 14 0.14
35 45 0.46
36 8 0.08
37 30 0.31
38 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.33
Consensus pattern (36 bp):
TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
Found at i:2059270 original size:16 final size:16
Alignment explanation
Indices: 2059246--2059277 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2059236 TATCGCCGAT
*
2059246 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
2059262 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
2059278 TATGAATAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:2059764 original size:36 final size:37
Alignment explanation
Indices: 2059687--2059771 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 37
2059677 ATCCCATTAT
* *
2059687 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAT
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
* *
2059723 TATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
2059759 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
2059772 TTGGTTACCA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
36 12 0.29
37 30 0.71
ACGTcount: A:0.42, C:0.19, G:0.05, T:0.34
Consensus pattern (37 bp):
CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
Found at i:2059771 original size:37 final size:37
Alignment explanation
Indices: 2059688--2059757 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
2059678 TCCCATTATC
*
2059688 ATTTTTC-AACAAACATCTACCAAACTTTGAAAAATT
1 ATTTTTCAAAGAAACATCTACCAAACTTTGAAAAATT
*
2059724 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAA
1 ATTTTTCAAAGAAACATCTACCAAACTTTGAAAA
2059758 CCATTTTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 7 0.23
37 24 0.77
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (37 bp):
ATTTTTCAAAGAAACATCTACCAAACTTTGAAAAATT
Found at i:2063609 original size:7 final size:7
Alignment explanation
Indices: 2063597--2063797 Score: 191
Period size: 7 Copynumber: 28.1 Consensus size: 7
2063587 TGTAACATAC
2063597 ATTATAT
1 ATTATAT
2063604 ATTATAT
1 ATTATAT
*
2063611 ATTACAT
1 ATTATAT
2063618 ATTATAT
1 ATTATAT
*
2063625 AGTATAT
1 ATTATAT
*
2063632 AGTATAT
1 ATTATAT
*
2063639 ATTATGGT
1 ATTAT-AT
*
2063647 AGTATAT
1 ATTATAT
2063654 ATTATAT
1 ATTATAT
2063661 ATAGTATAT
1 AT--TATAT
*
2063670 AGTATAT
1 ATTATAT
2063677 ATTATA-
1 ATTATAT
2063683 A-TAGTAT
1 ATTA-TAT
2063690 ATTATAT
1 ATTATAT
2063697 ATTATAAT
1 ATTAT-AT
2063705 ATATATAT
1 AT-TATAT
2063713 ATT-TAT
1 ATTATAT
2063719 A-TATAT
1 ATTATAT
2063725 A-TATAT
1 ATTATAT
2063731 ATATATTAT
1 AT-TA-TAT
2063740 ATTATAGT
1 ATTATA-T
2063748 ATTATAT
1 ATTATAT
2063755 ATTAT-T
1 ATTATAT
*
2063761 ATCATAT
1 ATTATAT
2063768 ATTAT-T
1 ATTATAT
2063774 ATTATTATT
1 ATTA-TA-T
2063783 ATTATAT
1 ATTATAT
2063790 ATTATAT
1 ATTATAT
2063797 A
1 A
2063798 ATTTTTAACG
Statistics
Matches: 165, Mismatches: 12, Indels: 34
0.78 0.06 0.16
Matches are distributed among these distances:
5 3 0.02
6 27 0.16
7 88 0.53
8 28 0.17
9 19 0.12
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (7 bp):
ATTATAT
Found at i:2063611 original size:2 final size:2
Alignment explanation
Indices: 2063599--2063797 Score: 136
Period size: 2 Copynumber: 106.0 Consensus size: 2
2063589 TAACATACAT
*
2063599 TA TA TA T- TA TA TA T- TA CA TA T- TA TA TA GTA TA TA GTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
*
2063640 T- TA TGG TA GTA TA TA T- TA TA TA TA GTA TA TA GTA TA TA T- TA
1 TA TA T-A TA -TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA
*
2063681 TA -A TA GTA TA T- TA TA TA T- TA TA -A TA TA TA TA TA TT TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2063720 TA TA TA TA TA TA TA TA T- TA TA T- TA TA GTA T- TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
2063759 T- TA TCA TA TA T- TA T- TA T- TA T- TA T- TA T- TA TA TA T- TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2063794 TA TA
1 TA TA
2063798 ATTTTTAACG
Statistics
Matches: 160, Mismatches: 6, Indels: 62
0.70 0.03 0.27
Matches are distributed among these distances:
1 22 0.14
2 121 0.76
3 17 0.11
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2063653 original size:50 final size:50
Alignment explanation
Indices: 2063599--2063799 Score: 186
Period size: 50 Copynumber: 4.0 Consensus size: 50
2063589 TAACATACAT
* * * *
2063599 TATATATTATATATTACATATTATATAGTATATAGTATATATTATGGTAG
1 TATATATTATATATTATATATTATATATTATATAGTATATATTATAGTAA
*
2063649 TATATATTATATATAGTATATAGTATATATTATAATAGTATATTATATATTA-TAA
1 TATATATTATATAT--TATATATTATATATTAT-ATAGTATA-TAT-TA-TAGTAA
*
2063704 TATATA-TATAT-TTATATA-TATATA-TATATA-TATTATATTATAGTAT
1 TATATATTATATATTATATATTATATATTATATAGTA-TATATTATAGTAA
* *
2063750 TATATATTAT-TATCATATATTAT-TATTATTATTATTATATATTATA-TAA
1 TATATATTATATATTATATATTATATATTA-TA-TAGTATATATTATAGTAA
2063799 T
1 T
2063800 TTTTAACGTT
Statistics
Matches: 128, Mismatches: 8, Indels: 31
0.77 0.05 0.19
Matches are distributed among these distances:
45 2 0.02
46 11 0.09
47 16 0.12
48 10 0.08
49 8 0.06
50 31 0.24
51 8 0.06
52 14 0.11
53 9 0.07
54 8 0.06
55 10 0.08
56 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (50 bp):
TATATATTATATATTATATATTATATATTATATAGTATATATTATAGTAA
Found at i:2063667 original size:38 final size:37
Alignment explanation
Indices: 2063599--2063797 Score: 170
Period size: 38 Copynumber: 5.5 Consensus size: 37
2063589 TAACATACAT
* *
2063599 TATATATTATATATTACATA-T-TATATAGTATATAG
1 TATATATTATATAGTATATATTATATATAGTATATAG
*
2063634 TATATATTATGGTAGTATATATTATATATAGTATATAG
1 TATATATTAT-ATAGTATATATTATATATAGTATATAG
*
2063672 TATATATTATAATAGTATAT-TATATATTATAATATATA-
1 TATATATTAT-ATAGTATATAT-TATA-TATAGTATATAG
*
2063710 TATAT-TTATATA-TATATA-TATATATA-T-TATAT
1 TATATATTATATAGTATATATTATATATAGTATATAG
* * * *
2063742 TATAGTATTATATATTAT-TATCATATATTATTAT-TAT
1 TATA-TATTATATAGTATATATTATATA-TAGTATATAG
*
2063779 TAT-TATTATATATTATATA
1 TATATATTATATAGTATATA
2063798 ATTTTTAACG
Statistics
Matches: 142, Mismatches: 7, Indels: 29
0.80 0.04 0.16
Matches are distributed among these distances:
31 4 0.03
32 5 0.04
33 5 0.04
34 13 0.09
35 36 0.25
36 14 0.10
37 13 0.09
38 42 0.30
39 10 0.07
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (37 bp):
TATATATTATATAGTATATATTATATATAGTATATAG
Found at i:2063762 original size:3 final size:3
Alignment explanation
Indices: 2063734--2063794 Score: 63
Period size: 3 Copynumber: 20.0 Consensus size: 3
2063724 TATATATATA
* *
2063734 TAT TA- TAT TA- TAG TAT TAT ATAT TAT TAT CAT ATAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT -TAT TAT TAT TAT
2063779 TAT TAT TAT ATAT TAT
1 TAT TAT TAT -TAT TAT
2063795 ATAATTTTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
2 4 0.08
3 38 0.76
4 8 0.16
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:2069810 original size:33 final size:31
Alignment explanation
Indices: 2069740--2069811 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
2069730 TAAAGGAATC
*
2069740 AAGTG-ATCCTTGTTGATCAACATAATTTAA
1 AAGTGCATCCTTGTTGATCAACATAAGTTAA
** *
2069770 ATTTGCATCCTTGTTGATCAACTGATCAGTTAA
1 AAGTGCATCCTTGTTGATCAAC--ATAAGTTAA
2069803 AAGTGCATC
1 AAGTGCATC
2069812 TTTTGGATGA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
30 3 0.09
31 16 0.48
33 14 0.42
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (31 bp):
AAGTGCATCCTTGTTGATCAACATAAGTTAA
Found at i:2073018 original size:11 final size:11
Alignment explanation
Indices: 2072998--2073028 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
2072988 TTAGTTATTT
2072998 TTAAACAATAAA
1 TTAAA-AATAAA
2073010 TTAAAAATAAA
1 TTAAAAATAAA
2073021 TTAAAAAT
1 TTAAAAAT
2073029 GGTAAACTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (11 bp):
TTAAAAATAAA
Found at i:2074744 original size:3 final size:3
Alignment explanation
Indices: 2074736--2074770 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
2074726 TTATTTATAT
* *
2074736 TTA TTA TTA TTA TTA TTA TTT TTA TTT TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2074771 TTGAATTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (3 bp):
TTA
Found at i:2074770 original size:9 final size:9
Alignment explanation
Indices: 2074724--2074772 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
2074714 TTTTTTTTCA
2074724 TTTTATTTAT
1 TTTTA-TTAT
*
2074734 ATTTATTAT
1 TTTTATTAT
*
2074743 TATTATTAT
1 TTTTATTAT
2074752 TATTT-TTAT
1 T-TTTATTAT
2074761 TTTTATTAT
1 TTTTATTAT
2074770 TTT
1 TTT
2074773 GAATTTTACA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
8 3 0.09
9 24 0.73
10 6 0.18
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTATTAT
Found at i:2074771 original size:15 final size:15
Alignment explanation
Indices: 2074724--2074772 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
2074714 TTTTTTTTCA
*
2074724 TTTTATTTATATTTAT
1 TTTTATTTTTA-TTAT
* *
2074740 TATTATTATTATTAT
1 TTTTATTTTTATTAT
2074755 TTTTATTTTTATTAT
1 TTTTATTTTTATTAT
2074770 TTT
1 TTT
2074773 GAATTTTACA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 20 0.71
16 8 0.29
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTATTTTTATTAT
Found at i:2079194 original size:21 final size:20
Alignment explanation
Indices: 2079156--2079195 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2079146 GATCAATATT
*
2079156 TTTGCATCTGCATTTGCATC
1 TTTGCATCTGCATATGCATC
*
2079176 TTTGCATTTTGCATATGCAT
1 TTTGCA-TCTGCATATGCAT
2079196 TTCATTATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.17, C:0.20, G:0.15, T:0.47
Consensus pattern (20 bp):
TTTGCATCTGCATATGCATC
Found at i:2081430 original size:24 final size:23
Alignment explanation
Indices: 2081377--2081433 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
2081367 TGAAAGGGGT
2081377 AATATTTTCAAAATCTTTGATTA
1 AATATTTTCAAAATCTTTGATTA
* *
2081400 AACATTTTTAAAACTCTTTTGA-TA
1 AATATTTTCAAAA-TC-TTTGATTA
*
2081424 GATATTTTCA
1 AATATTTTCA
2081434 GACTTTTGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
23 11 0.41
24 11 0.41
25 5 0.19
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (23 bp):
AATATTTTCAAAATCTTTGATTA
Found at i:2082249 original size:106 final size:107
Alignment explanation
Indices: 2082120--2082329 Score: 332
Period size: 106 Copynumber: 2.0 Consensus size: 107
2082110 GCTTGAGATA
*
2082120 ATTTCTCTTAAAAATAAACTTCGTCTCGCTTGAGACATTTTTTTCTTTGAGATACAAATTTCGAA
1 ATTTCTCTTAAAAACAAACTTCGTCTCGCTTGAGACATTTTTTTCTTTGAGATACAAATTTCGAA
*
2082185 TTCGATTCACTTGAAACAAAATTAATCTCACTTGAGATTGTT
66 TTCGATTCACTTGAAACAAAAGTAATCTCACTTGAGATTGTT
* * * * *
2082227 ATTTCT-TTCAAAACAAATTTCGTCTCGTTTGAGACATTTTTTTCTTTGATATACAAATTTTGAA
1 ATTTCTCTTAAAAACAAACTTCGTCTCGCTTGAGACATTTTTTTCTTTGAGATACAAATTTCGAA
* *
2082291 TTTGATTCACTTGAGACAAAAGTAATCTCACTTGAGATT
66 TTCGATTCACTTGAAACAAAAGTAATCTCACTTGAGATT
2082330 TTCAAAACCG
Statistics
Matches: 94, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
106 88 0.94
107 6 0.06
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.41
Consensus pattern (107 bp):
ATTTCTCTTAAAAACAAACTTCGTCTCGCTTGAGACATTTTTTTCTTTGAGATACAAATTTCGAA
TTCGATTCACTTGAAACAAAAGTAATCTCACTTGAGATTGTT
Found at i:2083189 original size:31 final size:31
Alignment explanation
Indices: 2083151--2083211 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
2083141 CAAAACAAAC
* *
2083151 AAAATCTTTGAGTATGTTTTTCTTGAAACAA
1 AAAATCTTTGAGTATGTTTCTCTCGAAACAA
*
2083182 AAAATCTTTGAGTTTGTTTCTCTCGAAACA
1 AAAATCTTTGAGTATGTTTCTCTCGAAACA
2083212 CCGATCTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (31 bp):
AAAATCTTTGAGTATGTTTCTCTCGAAACAA
Found at i:2083375 original size:29 final size:29
Alignment explanation
Indices: 2083338--2083395 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
2083328 TTGCTTTTGA
2083338 AAAACATCATCCGTGAGTCT-GTTTCTTTT
1 AAAACATCATCCGTGAGT-TGGTTTCTTTT
**
2083367 AAAACATCATCTTTGAGTTGGTTTCTTTT
1 AAAACATCATCCGTGAGTTGGTTTCTTTT
2083396 GAAATCAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 25 0.96
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.45
Consensus pattern (29 bp):
AAAACATCATCCGTGAGTTGGTTTCTTTT
Found at i:2083651 original size:134 final size:134
Alignment explanation
Indices: 2083408--2083758 Score: 551
Period size: 134 Copynumber: 2.6 Consensus size: 134
2083398 AATCAGTATC
* *
2083408 CCTAATGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCACCGACCAGATCTCTTCAT
1 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCACCGACCAGATCTCTTCAT
*
2083473 CACGTAGGAGCCGTGTCAACCATAGATAATAAGCCGTCCACATCACGTAGGAACCATGTTATCGC
66 CACGTAGGAGCCGTGTCAACCATAGATAACAAGCCGTCCACATCACGTAGGAACCATGTTATCGC
2083538 CCTT
131 CCTT
*
2083542 CCTAAAGATGGCTAGAACTCTTCATCACGTATGAGCCGTGTCATCCACCGACCAGATCTCTTCAT
1 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCACCGACCAGATCTCTTCAT
* * *
2083607 CACGTAGGAGTCGTGTCAACCATAGATAACAAGCCGTCCTCATCACGTAGGAACCGTGTTATCGC
66 CACGTAGGAGCCGTGTCAACCATAGATAACAAGCCGTCCACATCACGTAGGAACCATGTTATCGC
2083672 CCTT
131 CCTT
* * * * * * *
2083676 CCTAAAGATGACCAGAACT-TTGCATCACGTATGAGCTGTGTCATCCGCTGACCAAATTTCCTCA
1 CCTAAAGATGGCCAGAACTCTT-CATCACGTATGAGCCGTGTCATCCACCGACCAGATCTCTTCA
*
2083740 TCACGTAGGAACCGTGTCA
65 TCACGTAGGAGCCGTGTCA
2083759 CCCTTGGACG
Statistics
Matches: 199, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
133 2 0.01
134 197 0.99
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (134 bp):
CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCACCGACCAGATCTCTTCAT
CACGTAGGAGCCGTGTCAACCATAGATAACAAGCCGTCCACATCACGTAGGAACCATGTTATCGC
CCTT
Found at i:2083970 original size:3 final size:3
Alignment explanation
Indices: 2083964--2084001 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2083954 TTCATTTTAT
2083964 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2084002 TTGAATTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2086963 original size:42 final size:41
Alignment explanation
Indices: 2086872--2087118 Score: 255
Period size: 42 Copynumber: 5.8 Consensus size: 41
2086862 CTATACACCA
* * *
2086872 GTAAGGCTTAACCTATGCACAAAGC-AGAGGAGCCTAGGAAAACT
1 GTAAGGCTT-ACCT-TGCACACAGCAAAAGGA-CCT-GGGAAACT
*
2086916 GTAAGGTTTATCCTTGCACACAGCAAAAGGACCTGGGAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAAGGACCTGGGAAACT
* * *
2086958 GTAAGGCTTACCCTTGCACACGGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAAGGACCTGGGAAACT
* * *
2087000 GTAAAGCTTACCTTCGCACACAGCAAAGGGACCTGGGAAGCT
1 GTAAGGCTTACCTT-GCACACAGCAAAAGGACCTGGGAAACT
* * * * *
2087042 GTAAGGTTTACCCTTGCACACAACAAATGGACTTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAAGGACCTGGGAAACT
2087084 GTAAGGCTTACCTTCGCACACAGC-AAAGAGACCTG
1 GTAAGGCTTACCTT-GCACACAGCAAAAG-GACCTG
2087119 ATAATACTTC
Statistics
Matches: 173, Mismatches: 24, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
41 11 0.06
42 129 0.75
43 17 0.10
44 16 0.09
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.19
Consensus pattern (41 bp):
GTAAGGCTTACCTTGCACACAGCAAAAGGACCTGGGAAACT
Found at i:2087019 original size:84 final size:84
Alignment explanation
Indices: 2086872--2087118 Score: 304
Period size: 84 Copynumber: 2.9 Consensus size: 84
2086862 CTATACACCA
* * * *
2086872 GTAAGGCTTAACCTATGCACA-AAGCAGA-GGAGCCTAGGAAAACTGTAAGGTTTATCCTT-GCA
1 GTAAGGCTTACCCT-TGCACACAA-CAAAGGGA-CCT-GGTAAACTGTAAGGCTTA-CCTTCGCA
2086934 CACAGCAAAAGGACCTGGGAAACT
61 CACAGCAAAAGGACCTGGGAAACT
** *
2086958 GTAAGGCTTACCCTTGCACACGGCAAAGGGACCTGGTAAACTGTAAAGCTTACCTTCGCACACAG
1 GTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
* *
2087023 CAAAGGGACCTGGGAAGCT
66 CAAAAGGACCTGGGAAACT
* * *
2087042 GTAAGGTTTACCCTTGCACACAACAAATGGACTTGGTAAACTGTAAGGCTTACCTTCGCACACAG
1 GTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
2087107 C-AAAGAGACCTG
66 CAAAAG-GACCTG
2087119 ATAATACTTC
Statistics
Matches: 141, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
83 7 0.05
84 106 0.75
85 12 0.09
86 16 0.11
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.19
Consensus pattern (84 bp):
GTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
CAAAAGGACCTGGGAAACT
Found at i:2088100 original size:29 final size:28
Alignment explanation
Indices: 2088059--2088114 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
2088049 AACACCCTTT
*
2088059 TTTTTTAATAATTACCAAAATAGCACCC
1 TTTTTGAATAATTACCAAAATAGCACCC
*
2088087 TTTTTGAATTAATTCCCAAAATAGCACC
1 TTTTTGAA-TAATTACCAAAATAGCACC
2088115 AATTTCAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (28 bp):
TTTTTGAATAATTACCAAAATAGCACCC
Found at i:2088125 original size:29 final size:29
Alignment explanation
Indices: 2088067--2088228 Score: 114
Period size: 29 Copynumber: 5.7 Consensus size: 29
2088057 TTTTTTTTAA
* ** *
2088067 TAATTACCAAAATAGCACCCTTTTTGAAT
1 TAATTCCCAAAATAGCACCAATTTCGAAT
*
2088096 TAATTCCCAAAATAGCACCAATTTCAAAT
1 TAATTCCCAAAATAGCACCAATTTCGAAT
* * * * **
2088125 TAATTCTCAGAATA-TAACTTTTTCGAA-
1 TAATTCCCAAAATAGCACCAATTTCGAAT
* * *
2088152 AAATTACCAAAATAACACTC-ATTTCGAAT
1 TAATTCCCAAAATAGCAC-CAATTTCGAAT
* * **
2088181 TAATTTCTAAAATAGCACCAAAATCGAAT
1 TAATTCCCAAAATAGCACCAATTTCGAAT
* *
2088210 AAATTCCCAGAATAGCACC
1 TAATTCCCAAAATAGCACC
2088229 GGTCAACGGG
Statistics
Matches: 100, Mismatches: 29, Indels: 8
0.73 0.21 0.06
Matches are distributed among these distances:
27 10 0.10
28 17 0.17
29 73 0.73
ACGTcount: A:0.43, C:0.21, G:0.06, T:0.30
Consensus pattern (29 bp):
TAATTCCCAAAATAGCACCAATTTCGAAT
Found at i:2088215 original size:85 final size:85
Alignment explanation
Indices: 2088068--2088223 Score: 213
Period size: 85 Copynumber: 1.8 Consensus size: 85
2088058 TTTTTTTAAT
* * * ** * *
2088068 AATTACCAAAATAGCACCCTTTTTGAATTAATTCCCAAAATAGCACCAATTTCAAATTAATTCTC
1 AATTACCAAAATAACACCCATTTCGAATTAATTCCCAAAATAGCACCAAAATCAAATAAATTCCC
2088133 AGAATATAACTTTTTCGAAA
66 AGAATATAACTTTTTCGAAA
* * * *
2088153 AATTACCAAAATAACACTCATTTCGAATTAATTTCTAAAATAGCACCAAAATCGAATAAATTCCC
1 AATTACCAAAATAACACCCATTTCGAATTAATTCCCAAAATAGCACCAAAATCAAATAAATTCCC
2088218 AGAATA
66 AGAATA
2088224 GCACCGGTCA
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
85 60 1.00
ACGTcount: A:0.44, C:0.20, G:0.06, T:0.30
Consensus pattern (85 bp):
AATTACCAAAATAACACCCATTTCGAATTAATTCCCAAAATAGCACCAAAATCAAATAAATTCCC
AGAATATAACTTTTTCGAAA
Found at i:2088253 original size:18 final size:18
Alignment explanation
Indices: 2088230--2088278 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
2088220 AATAGCACCG
2088230 GTCAACGGGTCGGATCGA
1 GTCAACGGGTCGGATCGA
* *
2088248 GTCAACGGATCGGATCGG
1 GTCAACGGGTCGGATCGA
2088266 GTCAACGGGTCGG
1 GTCAACGGGTCGG
2088279 GTCGTGACCG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.20, C:0.22, G:0.41, T:0.16
Consensus pattern (18 bp):
GTCAACGGGTCGGATCGA
Found at i:2092898 original size:30 final size:30
Alignment explanation
Indices: 2092863--2092937 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 30
2092853 TAATTTGATC
*
2092863 TTATATAAACTATTAATTCAACTCTT-AACT
1 TTATATAAA-TATTAATTCAACCCTTAAACT
* *
2092893 TTATATTAAATGTTAATTTAACCCTTAAACT
1 TTATA-TAAATATTAATTCAACCCTTAAACT
*
2092924 TTTTATAAAATATT
1 TTATAT-AAATATT
2092938 TGTTTTATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
30 19 0.51
31 18 0.49
ACGTcount: A:0.40, C:0.12, G:0.01, T:0.47
Consensus pattern (30 bp):
TTATATAAATATTAATTCAACCCTTAAACT
Found at i:2103074 original size:16 final size:16
Alignment explanation
Indices: 2103055--2103100 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
2103045 AATCATATTT
2103055 TCCATACTCATAATTA
1 TCCATACTCATAATTA
2103071 TCCATACTCATAATTA
1 TCCATACTCATAATTA
* *
2103087 TCCGTATTCATAAT
1 TCCATACTCATAAT
2103101 GTTTCCACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (16 bp):
TCCATACTCATAATTA
Found at i:2103854 original size:21 final size:21
Alignment explanation
Indices: 2103830--2103882 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
2103820 ACACTTAGGG
2103830 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
*
2103851 AACCGATTCCCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
2103872 TACCGATTCCC
1 AACCGATTCCC
2103883 CCACGCTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:2104099 original size:13 final size:13
Alignment explanation
Indices: 2104078--2104132 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
2104068 AAGTTCGATA
*
2104078 AATTCAAATACTT
1 AATTGAAATACTT
2104091 AATTGAAATACTT
1 AATTGAAATACTT
* *
2104104 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
2104118 AATTGAAATACTT
1 AATTGAAATACTT
2104131 AA
1 AA
2104133 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:2104214 original size:32 final size:33
Alignment explanation
Indices: 2104118--2104216 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
2104108 AACTCAACAT
* * *
2104118 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
2104151 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
2104184 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
2104216 A
1 A
2104217 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:2104235 original size:21 final size:21
Alignment explanation
Indices: 2104211--2104250 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2104201 ACTTCAAGTT
2104211 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
2104232 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
2104251 ATAAAATAAA
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:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:2106616 original size:14 final size:13
Alignment explanation
Indices: 2106581--2106619 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
2106571 GGTTTTTTAT
2106581 CCGG-TAAAAAAA
1 CCGGTTAAAAAAA
*
2106593 CCGGTTAAAATAA
1 CCGGTTAAAAAAA
2106606 CCGGTTTAAAAAAA
1 CCGG-TTAAAAAAA
2106620 ATCTGATCCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 4 0.17
13 11 0.48
14 8 0.35
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.18
Consensus pattern (13 bp):
CCGGTTAAAAAAA
Found at i:2117209 original size:20 final size:21
Alignment explanation
Indices: 2117184--2117230 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2117174 GCTTCTAGGG
*
2117184 TAAACTAGGCG-TTTAATACC
1 TAAACTAGCCGTTTTAATACC
* *
2117204 TAAACTATCCGTTTTAGTACC
1 TAAACTAGCCGTTTTAATACC
2117225 TAAACT
1 TAAACT
2117231 TTCAATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (21 bp):
TAAACTAGCCGTTTTAATACC
Found at i:2117239 original size:21 final size:21
Alignment explanation
Indices: 2117195--2117239 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2117185 AAACTAGGCG
**
2117195 TTTAATACCTAAACTATCCGT
1 TTTAATACCTAAACTATCAAT
* *
2117216 TTTAGTACCTAAACTTTCAAT
1 TTTAATACCTAAACTATCAAT
2117237 TTT
1 TTT
2117240 TTCAAAATCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.20, G:0.04, T:0.44
Consensus pattern (21 bp):
TTTAATACCTAAACTATCAAT
Found at i:2118432 original size:23 final size:23
Alignment explanation
Indices: 2118390--2118451 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
2118380 AAATATTTAA
2118390 TAAATATTTATA-TTTTTTAATT
1 TAAATATTTATATTTTTTTAATT
*
2118412 TAAATGTTTATATTTTTTTAATT
1 TAAATATTTATATTTTTTTAATT
2118435 TAAATATTTAT-TTTTTT
1 TAAATATTTATATTTTTT
2118452 ACATGAACCA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 17 0.46
23 20 0.54
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (23 bp):
TAAATATTTATATTTTTTTAATT
Found at i:2121289 original size:84 final size:84
Alignment explanation
Indices: 2121148--2121316 Score: 329
Period size: 84 Copynumber: 2.0 Consensus size: 84
2121138 TAGTCACAAG
*
2121148 TAAGCTAACGGAGTCCGATTGCCAATCTTTTCTTAATAATATTAGTAGCAGGTTGGAGCAGTGGG
1 TAAGCTAACGGAGTCCGATTGCCAATCTTTGCTTAATAATATTAGTAGCAGGTTGGAGCAGTGGG
2121213 CCAAGCATAGGTTGAGTTA
66 CCAAGCATAGGTTGAGTTA
2121232 TAAGCTAACGGAGTCCGATTGCCAATCTTTGCTTAATAATATTAGTAGCAGGTTGGAGCAGTGGG
1 TAAGCTAACGGAGTCCGATTGCCAATCTTTGCTTAATAATATTAGTAGCAGGTTGGAGCAGTGGG
2121297 CCAAGCATAGGTTGAGTTA
66 CCAAGCATAGGTTGAGTTA
2121316 T
1 T
2121317 GTGGGGGGGG
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (84 bp):
TAAGCTAACGGAGTCCGATTGCCAATCTTTGCTTAATAATATTAGTAGCAGGTTGGAGCAGTGGG
CCAAGCATAGGTTGAGTTA
Found at i:2123182 original size:2 final size:2
Alignment explanation
Indices: 2123175--2123214 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2123165 TTAAAACCAT
*
2123175 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2123215 AAAGCTATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2128005 original size:13 final size:13
Alignment explanation
Indices: 2127987--2128013 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2127977 TATGAACGAA
2127987 AAAAAATAAAAAT
1 AAAAAATAAAAAT
2128000 AAAAAATAAAAAT
1 AAAAAATAAAAAT
2128013 A
1 A
2128014 TTAACATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:2129898 original size:55 final size:56
Alignment explanation
Indices: 2129828--2130189 Score: 263
Period size: 55 Copynumber: 6.7 Consensus size: 56
2129818 ATCTTCAAAT
* * * *
2129828 AACGGGTCTGCTCCCTTTTCTTTCAAGGAGTATAAGACTCGAACAATCCTT-GGCA
1 AACGGGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGAACAATCCTTCGACA
* *
2129883 AACGTGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGAATAAT-CTTCGACA
1 AACGGGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGAACAATCCTTCGACA
* * * *
2129938 AACGGGTCCGCTCCCTATCCGTTCAGGGAGTAT-AGAACTCGAACAAT-CTTC-ATAA
1 AACGGGTCTGCTCCCTATTCATTCAGGGAGTATAAG-ACTCGAACAATCCTTCGA-CA
* * * * *
2129993 AACGGGTCCGCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAACAAT-CTTCAACA
1 AACGGGTCTGCTCCCTATTCATTCAGGGAGTATAAG-ACTCGAACAATCCTTCGACA
** * * * * * *
2130048 AACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAAT-CTTCAACG
1 AACGGGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGAACAATCCTTCGACA
** * * * * *
2130099 AACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAAT-CTTCAACA
1 AACGGGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGAACAATCCTTCGACA
** * * *
2130150 AACTTGTCTGCTCCCTATTCCTTCAGAGAGTATAGGACTC
1 AACGGGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTC
2130190 AATCTTCAAC
Statistics
Matches: 277, Mismatches: 24, Indels: 15
0.88 0.08 0.05
Matches are distributed among these distances:
51 99 0.36
54 6 0.02
55 170 0.61
56 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.28
Consensus pattern (56 bp):
AACGGGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGAACAATCCTTCGACA
Found at i:2130011 original size:110 final size:109
Alignment explanation
Indices: 2129817--2130291 Score: 323
Period size: 102 Copynumber: 4.5 Consensus size: 109
2129807 ATACTTGAAA
* * * * *
2129817 AATCTTCAA-ATAACGGGTCTGCTCCCTTTTCTTTCAAGGAGTATA-AGACTCGAACAATCCTTG
1 AATCTTCAACA-AACGGGTCCGCTCCC-TATCCTTCAGGGAGTATAGA-ACTCGAACAATCCTTA
* * * * *
2129880 GCAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATA-AGACTCGAAT
63 GAAAACGGGTCCGCTCCCTATTCATTCAGAGAGTATAGA-ACTCGAAC
* *
2129927 AATCTTCGACAAACGGGTCCGCTCCCTATCCGTTCAGGGAGTATAGAACTCGAACAAT-CTTCAT
1 AATCTTCAACAAACGGGTCCGCTCCCTATCC-TTCAGGGAGTATAGAACTCGAACAATCCTT-AG
* *
2129991 AAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
64 AAAACGGGTCCGCTCCCTATTCATTCAGAGAGTATAGAACTCGAAC
** * *
2130037 AATCTTCAACAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAAT-CTTCA-
1 AATCTTCAACAAACGGGTCCGCTCCCTA-TCCTTCAGGGAGTATAGAACTCGAACAATCCTT-AG
* ** * *
2130096 ACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----C
64 A-AAACGGGTCCGCTCCCTATTCATTCAGAGAGTATAGAACTCGAAC
** * * *
2130139 AATCTTCAACAAACTTGTCTGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAAT-CTTCA-
1 AATCTTCAACAAACGGGTCCGCTCCCTA-TCCTTCAGGGAGTATAGAACTCGAACAATCCTT-AG
* ** * *
2130198 ACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----C
64 A-AAACGGGTCCGCTCCCTATTCATTCAGAGAGTATAGAACTCGAAC
* ** * *
2130241 AATCTTCAACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTC
1 AATCTTCAACAAACGGGTCCGCTCCCTA-TCCTTCAGGGAGTATAGAACTC
2130292 AATCTTCAAC
Statistics
Matches: 330, Mismatches: 27, Indels: 23
0.87 0.07 0.06
Matches are distributed among these distances:
102 150 0.45
105 1 0.00
106 44 0.13
109 6 0.02
110 123 0.37
111 6 0.02
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (109 bp):
AATCTTCAACAAACGGGTCCGCTCCCTATCCTTCAGGGAGTATAGAACTCGAACAATCCTTAGAA
AACGGGTCCGCTCCCTATTCATTCAGAGAGTATAGAACTCGAAC
Found at i:2130112 original size:51 final size:51
Alignment explanation
Indices: 2129881--2130305 Score: 548
Period size: 51 Copynumber: 8.1 Consensus size: 51
2129871 CAATCCTTGG
* * * * * *
2129881 CAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGAATAATCTTCGA
1 CAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTC----AATCTTCAA
** * *
2129936 CAAACGGGTCCGCTCCCTA-TCCGTTCAGGGAGTATAGAACTCGAACAATCTTCATA
1 CAAACTTGTCCGCTCCCTATTCC-TTCAGAGAGTATAGGACT----CAATCTTCA-A
** * *
2129992 -AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAA
1 CAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAA
2130046 CAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAA
1 CAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAA
*
2130097 CGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAA
1 CAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAA
*
2130148 CAAACTTGTCTGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAA
1 CAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAA
*
2130199 CGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAA
1 CAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAA
*
2130250 CGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAA
1 CAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAA
2130301 CAAAC
1 CAAAC
2130306 GAATTTGCTT
Statistics
Matches: 344, Mismatches: 18, Indels: 20
0.90 0.05 0.05
Matches are distributed among these distances:
51 213 0.62
54 3 0.01
55 123 0.36
56 4 0.01
59 1 0.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (51 bp):
CAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAA
Found at i:2131641 original size:15 final size:14
Alignment explanation
Indices: 2131610--2131685 Score: 75
Period size: 14 Copynumber: 5.3 Consensus size: 14
2131600 TGAACCCTCC
* *
2131610 TTTTATTTCTCTTT
1 TTTTATTTTTCTAT
2131624 TTTTCATTTTTCTAT
1 TTTT-ATTTTTCTAT
2131639 TTTTATTTTTCT-T
1 TTTTATTTTTCTAT
*
2131652 TCTTTTTTTTTC-AT
1 T-TTTATTTTTCTAT
2131666 TTTTATTTTTTCTCAT
1 TTTTA-TTTTTCT-AT
2131682 TTTT
1 TTTT
2131686 TCTTTTCTTC
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
13 5 0.10
14 29 0.56
15 12 0.23
16 6 0.12
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTATTTTTCTAT
Found at i:2131743 original size:8 final size:7
Alignment explanation
Indices: 2131622--2131762 Score: 87
Period size: 7 Copynumber: 19.6 Consensus size: 7
2131612 TTATTTCTCT
2131622 TTTTTTC
1 TTTTTTC
*
2131629 ATTTTTC
1 TTTTTTC
2131636 TATTTTT-
1 T-TTTTTC
*
2131643 ATTTTTC
1 TTTTTTC
2131650 TTTCTTT-
1 TTT-TTTC
2131657 TTTTTTC
1 TTTTTTC
2131664 ATTTTTAT-
1 -TTTTT-TC
2131672 TTTTTCTC
1 TTTTT-TC
2131680 ATTTTTTC
1 -TTTTTTC
2131688 TTTTCTTC
1 TTTT-TTC
2131696 TTTTCTTC
1 TTTT-TTC
2131704 -TTTTTC
1 TTTTTTC
2131710 TTTTTCTC
1 TTTTT-TC
* *
2131718 ATTTTTA
1 TTTTTTC
2131725 TTATTTT-
1 TT-TTTTC
2131732 TTTTTTC
1 TTTTTTC
*
2131739 ATTTTTC
1 TTTTTTC
*
2131746 GTTTTT-
1 TTTTTTC
*
2131752 TTTTCTC
1 TTTTTTC
2131759 TTTT
1 TTTT
2131763 ATTTCTTCTT
Statistics
Matches: 108, Mismatches: 12, Indels: 28
0.73 0.08 0.19
Matches are distributed among these distances:
6 19 0.18
7 47 0.44
8 36 0.33
9 6 0.06
ACGTcount: A:0.07, C:0.13, G:0.01, T:0.79
Consensus pattern (7 bp):
TTTTTTC
Found at i:2131750 original size:15 final size:15
Alignment explanation
Indices: 2131610--2131753 Score: 93
Period size: 15 Copynumber: 9.3 Consensus size: 15
2131600 TGAACCCTCC
*
2131610 TTTT-ATTTCTCTTT
1 TTTTCATTTTTCTTT
2131624 TTTTCATTTTTCTATT
1 TTTTCATTTTTCT-TT
**
2131640 TTTATTTTTCTTTCTTTTT
1 TTT-TCATT-TTTC--TTT
*
2131659 TTTTCATTTTTATTT
1 TTTTCATTTTTCTTT
2131674 TTTCTCATTTTTTCTTT
1 TTT-TCA-TTTTTCTTT
*
2131691 TCTTC--TTTTCTTCT
1 TTTTCATTTTTCTT-T
*
2131705 TTTTC-TTTTTCTCAT
1 TTTTCATTTTTCT-TT
2131720 TTTT-ATTATTT-TTT
1 TTTTCATT-TTTCTTT
2131734 TTTTCATTTTTCGTTT
1 TTTTCATTTTTC-TTT
2131750 TTTT
1 TTTT
2131754 TTCTCTTTTA
Statistics
Matches: 103, Mismatches: 11, Indels: 30
0.72 0.08 0.21
Matches are distributed among these distances:
13 7 0.07
14 17 0.17
15 30 0.29
16 20 0.19
17 16 0.16
18 7 0.07
19 5 0.05
20 1 0.01
ACGTcount: A:0.08, C:0.13, G:0.01, T:0.78
Consensus pattern (15 bp):
TTTTCATTTTTCTTT
Found at i:2131768 original size:75 final size:74
Alignment explanation
Indices: 2131609--2131772 Score: 185
Period size: 75 Copynumber: 2.2 Consensus size: 74
2131599 TTGAACCCTC
* *
2131609 CTTTTATTTC-TCTTTTTTTCATTTTTCTATTTTTATTTTTCTTTCTTTTTTTTTCATTTTTATT
1 CTTTTATTTCTTCTTTTCTTCATTTTTCTATTTTTATTTTTATTTCTTTTTTTTTCATTTTTATT
2131673 TTTTCTCAT
66 TTTTCTCAT
* *
2131682 TTTTTCTTTTCTTCTTTTCTTC-TTTTTCT-TTTTCTCATTTTTATTAT-TTTTTTTTTCATTTT
1 CTTTT-ATTTCTTCTTTTCTTCATTTTTCTATTTT-T-ATTTTTATT-TCTTTTTTTTTCATTTT
* *
2131744 TCGTTTTTTTTTC-T
62 T--ATTTTTTCTCAT
2131758 CTTTTATTTCTTCTT
1 CTTTTATTTCTTCTT
2131773 CAAGCGAAAT
Statistics
Matches: 76, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
73 8 0.11
74 12 0.16
75 42 0.55
76 6 0.08
77 8 0.11
ACGTcount: A:0.07, C:0.15, G:0.01, T:0.77
Consensus pattern (74 bp):
CTTTTATTTCTTCTTTTCTTCATTTTTCTATTTTTATTTTTATTTCTTTTTTTTTCATTTTTATT
TTTTCTCAT
Done.