Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009587.1 Hibiscus syriacus cultivar Beakdansim tig00116965_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: 6483253
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 29
Found at i:4166073 original size:22 final size:23
Alignment explanation
Indices: 4166045--4166106 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 23
4166035 TCTATATAAT
4166045 TAATATTTTATAATAAGA-TTAA
1 TAATATTTTATAATAAGATTTAA
* * *
4166067 TAATA-TTTATATTAGATATTTAG
1 TAATATTTTATAATA-AGATTTAA
*
4166090 TAATTTTTTATAATAAG
1 TAATATTTTATAATAAG
4166107 TCATTAAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
21 8 0.26
22 7 0.23
23 8 0.26
24 8 0.26
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (23 bp):
TAATATTTTATAATAAGATTTAA
Found at i:4172731 original size:22 final size:22
Alignment explanation
Indices: 4172703--4172792 Score: 119
Period size: 22 Copynumber: 4.1 Consensus size: 22
4172693 TATATATCTA
*
4172703 CTTTCTGCAAGAATAATAGATT
1 CTTTCTGCAAGAATGATAGATT
4172725 CTTTCTGCAAGAATGATAGATT
1 CTTTCTGCAAGAATGATAGATT
*
4172747 CTTTATGCAAGAATGATAGATT
1 CTTTCTGCAAGAATGATAGATT
** *
4172769 CTCTT-TTAAAGGATGATAGATT
1 CT-TTCTGCAAGAATGATAGATT
4172791 CT
1 CT
4172793 CTTTTCAAAG
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
22 60 0.97
23 2 0.03
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (22 bp):
CTTTCTGCAAGAATGATAGATT
Found at i:4172793 original size:22 final size:22
Alignment explanation
Indices: 4172737--4172810 Score: 89
Period size: 22 Copynumber: 3.4 Consensus size: 22
4172727 TTCTGCAAGA
** *
4172737 ATGATAGATTCT-TTATGCAAGA
1 ATGATAGATTCTCTT-TTAAAGG
4172759 ATGATAGATTCTCTTTTAAAGG
1 ATGATAGATTCTCTTTTAAAGG
4172781 ATGATAGATTCTCTTTTCAAA-G
1 ATGATAGATTCTCTTTT-AAAGG
4172803 ATGATAGA
1 ATGATAGA
4172811 AATTGGATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
22 42 0.89
23 5 0.11
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (22 bp):
ATGATAGATTCTCTTTTAAAGG
Found at i:4174945 original size:22 final size:23
Alignment explanation
Indices: 4174918--4174979 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 23
4174908 TCTATATAGT
4174918 TAATATTTTATAATAAGA-TTAA
1 TAATATTTTATAATAAGATTTAA
* * *
4174940 TAATA-TTTATATTAGATATTTAG
1 TAATATTTTATAATA-AGATTTAA
*
4174963 TAATTTTTTATAATAAG
1 TAATATTTTATAATAAG
4174980 TTATTACATT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
21 8 0.26
22 7 0.23
23 8 0.26
24 8 0.26
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (23 bp):
TAATATTTTATAATAAGATTTAA
Found at i:4175553 original size:23 final size:22
Alignment explanation
Indices: 4175507--4175553 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
4175497 TTTATAATCG
* *
4175507 TAAAACATAAAAAATAGTACAT
1 TAAAACATAAAAAATAATAAAT
*
4175529 TAAAATATAATAAAATAATAAAT
1 TAAAACATAA-AAAATAATAAAT
4175552 TA
1 TA
4175554 TTTAATGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (22 bp):
TAAAACATAAAAAATAATAAAT
Found at i:4178530 original size:15 final size:15
Alignment explanation
Indices: 4178510--4178546 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
4178500 ATATTTAGTT
*
4178510 GGGCGGGCGGATGCG
1 GGGCGGGCGGATACG
*
4178525 GGGCGGGCTGATACG
1 GGGCGGGCGGATACG
4178540 GGGCGGG
1 GGGCGGG
4178547 TAATGTCTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.08, C:0.19, G:0.65, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATACG
Found at i:4182090 original size:82 final size:83
Alignment explanation
Indices: 4181938--4182368 Score: 432
Period size: 83 Copynumber: 5.2 Consensus size: 83
4181928 AAACACTTAA
* *
4181938 ACTTTAGTTG-CGTTTTT-GTAA-AAACGCCGCTAAAGACTA-TACTTTAGTGTCGTTTTTATGC
1 ACTTTAG-TGACGTTTTTAG-AACAAACGCCGCTAAAGACTAGTACTTTAGTGGCGTTTTTATAC
*
4181999 AAACACCGCTAAAGAAT-GT
64 AAACACCGCTAAAGACTCGT
* * *
4182018 ACTTTAGTGACGTTATTAGAACAAACGCTGCTAAAGACTAGTACTTTAGTGGCGTTCTTATACAA
1 ACTTTAGTGACGTTTTTAGAACAAACGCCGCTAAAGACTAGTACTTTAGTGGCGTTTTTATACAA
* * *
4182083 ACGCCGCTATATACTCGT
66 ACACCGCTAAAGACTCGT
* * *
4182101 ACTTTAGTGGA-GTTTTTAGAATAAACGCTGCTATAGACTAGTACTTTAGTGGCGTTTTTATACA
1 ACTTTAGT-GACGTTTTTAGAACAAACGCCGCTAAAGACTAGTACTTTAGTGGCGTTTTTATACA
*
4182165 AACACCGCCAAAGACT-GT
65 AACACCGCTAAAGACTCGT
* * * *
4182183 ACTTTAGTGGCGTTTTTTA-TACAAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTTAGAA
1 ACTTTAGTGACG-TTTTTAGAACAAACGCCGCTAAAGACTAGTACTTTAGTGGCG-TTTTTA-TA
* *
4182247 CAAACGCCGCTATAGACTCGT
63 CAAACACCGCTAAAGACTCGT
* * * * * * * *
4182268 ACTTTAGTGGCGTTTGTA-TACAGACGCCGTTAAAGACTCA-TAACTTTAATGGCATTTTTGTAA
1 ACTTTAGTGACGTTTTTAGAACAAACGCCGCTAAAGACT-AGT-ACTTTAGTGGCGTTTTTAT-A
* * *
4182331 AAAATACCGCTATAGACTCGT
63 CAAACACCGCTAAAGACTCGT
*
4182352 ACTTTAGTGGCGTTTTT
1 ACTTTAGTGACGTTTTT
4182369 GTTTACAAAC
Statistics
Matches: 300, Mismatches: 37, Indels: 24
0.83 0.10 0.07
Matches are distributed among these distances:
79 2 0.01
80 15 0.05
81 19 0.06
82 75 0.25
83 83 0.28
84 81 0.27
85 25 0.08
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (83 bp):
ACTTTAGTGACGTTTTTAGAACAAACGCCGCTAAAGACTAGTACTTTAGTGGCGTTTTTATACAA
ACACCGCTAAAGACTCGT
Found at i:4182135 original size:42 final size:41
Alignment explanation
Indices: 4181938--4182368 Score: 406
Period size: 41 Copynumber: 10.4 Consensus size: 41
4181928 AAACACTTAA
* * *
4181938 ACTTTAGTTGCGTTTTTGTAA-AAACGCCGCTAAAGACTA-T
1 ACTTTAGTGGCGTTTTT-AAACAAACGCCGCTATAGACTAGT
* ** * * *
4181978 ACTTTAGTGTCGTTTTTATGCAAACACCGCTAAAGAAT-GT
1 ACTTTAGTGGCGTTTTTAAACAAACGCCGCTATAGACTAGT
* * * *
4182018 ACTTTAGTGACGTTATTAGAACAAACGCTGCTAAAGACTAGT
1 ACTTTAGTGGCGTTTTTA-AACAAACGCCGCTATAGACTAGT
* * * *
4182060 ACTTTAGTGGCGTTCTTATACAAACGCCGCTATATACTCGT
1 ACTTTAGTGGCGTTTTTAAACAAACGCCGCTATAGACTAGT
* * *
4182101 ACTTTAGTGGAGTTTTTAGAATAAACGCTGCTATAGACTAGT
1 ACTTTAGTGGCGTTTTTA-AACAAACGCCGCTATAGACTAGT
* * * *
4182143 ACTTTAGTGGCGTTTTTATACAAACACCGCCAAAGACT-GT
1 ACTTTAGTGGCGTTTTTAAACAAACGCCGCTATAGACTAGT
*
4182183 ACTTTAGTGGCGTTTTTTATACAAACGCCGCTATAGACTAGT
1 ACTTTAGTGGCG-TTTTTAAACAAACGCCGCTATAGACTAGT
*
4182225 ACTTTAGTGGCGTTTTTTAGAACAAACGCCGCTATAGACTCGT
1 ACTTTAGTGGCG-TTTTTA-AACAAACGCCGCTATAGACTAGT
* * * * *
4182268 ACTTTAGTGGCGTTTGTATACAGACGCCGTTAAAGACTCA-T
1 ACTTTAGTGGCGTTTTTAAACAAACGCCGCTATAGACT-AGT
* * ** *
4182309 AACTTTAATGGCATTTTTGTAAA-AAATACCGCTATAGACTCGT
1 -ACTTTAGTGGC-GTTTT-TAAACAAACGCCGCTATAGACTAGT
4182352 ACTTTAGTGGCGTTTTT
1 ACTTTAGTGGCGTTTTT
4182369 GTTTACAAAC
Statistics
Matches: 320, Mismatches: 58, Indels: 26
0.79 0.14 0.06
Matches are distributed among these distances:
40 62 0.19
41 107 0.33
42 99 0.31
43 49 0.15
44 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (41 bp):
ACTTTAGTGGCGTTTTTAAACAAACGCCGCTATAGACTAGT
Found at i:4182186 original size:165 final size:165
Alignment explanation
Indices: 4181938--4182326 Score: 489
Period size: 165 Copynumber: 2.3 Consensus size: 165
4181928 AAACACTTAA
* * *
4181938 ACTTTAGTTGCGTTTTTGTAAAAACGCCGCTAAAGACTATACTTTAGTGTCGTTTTTATGCAAAC
1 ACTTTAGTGGCGTTTTTGTAAAAACGCCGCTAAAGACTATACTTTAGTGGCGTTTTTATACAAAC
* *
4182003 ACCGCTAAAGAATGTACTTTAGTGACG-TTATTAGAACAAACGCTGCTAAAGACTAGTACTTTAG
66 ACCGCCAAAGAATGTACTTTAGTGACGTTTATTA-AACAAACGCCGCTAAAGACTAGTACTTTAG
* *
4182067 TGGCG-TTCTTA-TACAAACGCCGCTATATACTCGT
130 TGGCGTTTCTTAGAACAAACGCCGCTATAGACTCGT
* * *
4182101 ACTTTAGTGGAGTTTTTAG-AATAAACGCTGCTATAGACTAGTACTTTAGTGGCGTTTTTATACA
1 ACTTTAGTGGCGTTTTT-GTAA-AAACGCCGCTAAAGACTA-TACTTTAGTGGCGTTTTTATACA
* * * * *
4182165 AACACCGCCAAAGACTGTACTTTAGTGGCGTTTTTTATACAAACGCCGCTATAGACTAGTACTTT
63 AACACCGCCAAAGAATGTACTTTAGTGACGTTTATTAAACAAACGCCGCTAAAGACTAGTACTTT
*
4182230 AGTGGCGTTTTTTAGAACAAACGCCGCTATAGACTCGT
128 AGTGGCGTTTCTTAGAACAAACGCCGCTATAGACTCGT
* * * * * * *
4182268 ACTTTAGTGGCGTTTGTATACAGACGCCGTTAAAGACTCATAACTTTAATGGCATTTTT
1 ACTTTAGTGGCGTTTTTGTAAAAACGCCGCTAAAGACT-AT-ACTTTAGTGGCGTTTTT
4182327 GTAAAAAATA
Statistics
Matches: 191, Mismatches: 26, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
163 17 0.09
164 17 0.09
165 80 0.42
166 24 0.13
167 53 0.28
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (165 bp):
ACTTTAGTGGCGTTTTTGTAAAAACGCCGCTAAAGACTATACTTTAGTGGCGTTTTTATACAAAC
ACCGCCAAAGAATGTACTTTAGTGACGTTTATTAAACAAACGCCGCTAAAGACTAGTACTTTAGT
GGCGTTTCTTAGAACAAACGCCGCTATAGACTCGT
Found at i:4182400 original size:84 final size:85
Alignment explanation
Indices: 4182079--4182400 Score: 229
Period size: 84 Copynumber: 3.8 Consensus size: 85
4182069 GCGTTCTTAT
* * * * * * *
4182079 ACAAACGCCGCTATATACTCGTACTTTAGTGGAGTTTTTAG-A-ATAAACGCTGC-TATAGACTA
1 ACAAACACCGCTATAGACTCGTACTTTAGTGGCGTTTTT-GTATACAAACGCCGCAAATATAC-A
* * * *
4182141 GTACTTTAGTGGC-GTTTTTA-T
64 AT-CTTTAATGGCATTTTTTAGA
* * * * *
4182162 ACAAACACCGCCAAAGACT-GTACTTTAGTGGCGTTTTT-TATACAAACGCCGC-TATAGACTAG
1 ACAAACACCGCTATAGACTCGTACTTTAGTGGCGTTTTTGTATACAAACGCCGCAAATATAC-AA
* *
4182224 TACTTTAGTGGCGTTTTTTAGA
65 T-CTTTAATGGCATTTTTTAGA
* * * *
4182246 ACAAACGCCGCTATAGACTCGTACTTTAGTGGCG--TTTGTATACAGACGCCGTTAAAGACT-CA
1 ACAAACACCGCTATAGACTCGTACTTTAGTGGCGTTTTTGTATACAAACGCCG-CAAATA-TACA
*
4182308 TAACTTTAATGGCATTTTTGTA-A
64 -ATCTTTAATGGCATTTTT-TAGA
* * *
4182331 A-AAATACCGCTATAGACTCGTACTTTAGTGGCGTTTTTGTTTACAAACGCCGCAAATTTACAAT
1 ACAAACACCGCTATAGACTCGTACTTTAGTGGCGTTTTTGTATACAAACGCCGCAAATATACAAT
*
4182395 TTTTAA
66 CTTTAA
4182401 ATCCCACACC
Statistics
Matches: 195, Mismatches: 30, Indels: 27
0.77 0.12 0.11
Matches are distributed among these distances:
81 1 0.01
82 49 0.25
83 24 0.12
84 65 0.33
85 36 0.18
86 20 0.10
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (85 bp):
ACAAACACCGCTATAGACTCGTACTTTAGTGGCGTTTTTGTATACAAACGCCGCAAATATACAAT
CTTTAATGGCATTTTTTAGA
Found at i:4182450 original size:18 final size:18
Alignment explanation
Indices: 4182427--4182474 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
4182417 ACCCTATTTC
4182427 ATTTTTCTCATTTCACCT
1 ATTTTTCTCATTTCACCT
* *
4182445 ATTTTTCCCACTTCACCT
1 ATTTTTCTCATTTCACCT
*
4182463 ATTTTTTTCATT
1 ATTTTTCTCATT
4182475 CTCTTGCTCG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.17, C:0.27, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTTCTCATTTCACCT
Found at i:4184370 original size:13 final size:13
Alignment explanation
Indices: 4184352--4184379 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4184342 CTTGTAATTG
4184352 TTATAATAATGAC
1 TTATAATAATGAC
4184365 TTATAATAATGAC
1 TTATAATAATGAC
4184378 TT
1 TT
4184380 GGTGCATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (13 bp):
TTATAATAATGAC
Found at i:4185839 original size:43 final size:43
Alignment explanation
Indices: 4185791--4186010 Score: 282
Period size: 42 Copynumber: 5.1 Consensus size: 43
4185781 CGTTTATTTA
*
4185791 AAAAAACGCCGTTATAGATCTGACATTTTACGGCGTTTGTTCC
1 AAAAAACGCCGCTATAGATCTGACATTTTACGGCGTTTGTTCC
* **
4185834 AAAAAATGCCGCTATAGATCTGACATTTTGTGGCGTTTGTTCC
1 AAAAAACGCCGCTATAGATCTGACATTTTACGGCGTTTGTTCC
* * *
4185877 -AAAAATGCCGCTATATATATGACATTTTACGGCGTTTGTTCC
1 AAAAAACGCCGCTATAGATCTGACATTTTACGGCGTTTGTTCC
* **
4185919 -AAAAACGCCGCTATAGATCTTACCCTTTACGGCGTTTGTTCC
1 AAAAAACGCCGCTATAGATCTGACATTTTACGGCGTTTGTTCC
* * * *
4185961 AAAAAAACGCCGCTATAGATATCGACCTTTTGCGGCGTTTGTTAC
1 -AAAAAACGCCGCTATAGATCT-GACATTTTACGGCGTTTGTTCC
4186006 AAAAA
1 AAAAA
4186011 TGCTAATATA
Statistics
Matches: 155, Mismatches: 19, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
42 74 0.48
43 39 0.25
44 24 0.15
45 18 0.12
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (43 bp):
AAAAAACGCCGCTATAGATCTGACATTTTACGGCGTTTGTTCC
Found at i:4185962 original size:84 final size:85
Alignment explanation
Indices: 4185791--4186010 Score: 289
Period size: 85 Copynumber: 2.6 Consensus size: 85
4185781 CGTTTATTTA
* * *
4185791 AAAAAACGCCGTTATAGATCTGACATTTTACGGCGTTTGTTCCAAAAAATGCCGCTATAGATCTG
1 AAAAAACGCCGCTATAGATATGACATTTTACGGCGTTTGTTCC-AAAAACGCCGCTATAGATCTG
* **
4185856 ACATTTTGTGGCGTTTGTTCC
65 ACACTTTACGGCGTTTGTTCC
* * *
4185877 -AAAAATGCCGCTATATATATGACATTTTACGGCGTTTGTTCCAAAAACGCCGCTATAGATCTTA
1 AAAAAACGCCGCTATAGATATGACATTTTACGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGA
*
4185941 CCCTTTACGGCGTTTGTTCC
66 CACTTTACGGCGTTTGTTCC
* * *
4185961 AAAAAAACGCCGCTATAGATATCGACCTTTTGCGGCGTTTGTTACAAAAA
1 -AAAAAACGCCGCTATAGATAT-GACATTTTACGGCGTTTGTTCCAAAAA
4186011 TGCTAATATA
Statistics
Matches: 116, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
84 36 0.31
85 38 0.33
86 18 0.16
87 24 0.21
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (85 bp):
AAAAAACGCCGCTATAGATATGACATTTTACGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGA
CACTTTACGGCGTTTGTTCC
Found at i:4186027 original size:43 final size:43
Alignment explanation
Indices: 4185974--4186055 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
4185964 AAAACGCCGC
* *
4185974 TATAGATATCGACCTTTTGCGGCGTTTGTTACAAAAATGCTAA
1 TATAGATATCGACCTTTTGCGACATTTGTTACAAAAATGCTAA
* * *
4186017 TATAGGTATCGACCTTTTGTGACATTTTTTACAAAAATG
1 TATAGATATCGACCTTTTGCGACATTTGTTACAAAAATG
4186056 TCGCTATAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (43 bp):
TATAGATATCGACCTTTTGCGACATTTGTTACAAAAATGCTAA
Found at i:4186064 original size:43 final size:42
Alignment explanation
Indices: 4185826--4186066 Score: 119
Period size: 42 Copynumber: 5.6 Consensus size: 42
4185816 TTTTACGGCG
* * * * * *
4185826 TTTGTTCCAAAAAATGCCGCTATAGATCT-GACATTTTGTGGCG
1 TTTGTTAC-AAAAATG-CGCTATAGATATCGACCTTTTGCGACA
* * * * * *
4185869 TTTGTTCCAAAAATGCCGCTATATATAT-GACATTTTACGGCG
1 TTTGTTACAAAAATG-CGCTATAGATATCGACCTTTTGCGACA
* * * * * * * *
4185911 TTTGTTCCAAAAACGCCGCTATAGATCT-TACCCTTTACGGCG
1 TTTGTTACAAAAATG-CGCTATAGATATCGACCTTTTGCGACA
* * * *
4185953 TTTGTTCCAAAAAAACGCCGCTATAGATATCGACCTTTTGCGGCG
1 TTTGTT--ACAAAAATG-CGCTATAGATATCGACCTTTTGCGACA
** * *
4185998 TTTGTTACAAAAATGCTAATATAGGTATCGACCTTTTGTGACA
1 TTTGTTACAAAAATGC-GCTATAGATATCGACCTTTTGCGACA
*
4186041 TTTTTTACAAAAATGTCGCTATAGAT
1 TTTGTTACAAAAATG-CGCTATAGAT
4186067 CTTGACATAT
Statistics
Matches: 165, Mismatches: 28, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
42 73 0.44
43 55 0.33
44 20 0.12
45 17 0.10
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (42 bp):
TTTGTTACAAAAATGCGCTATAGATATCGACCTTTTGCGACA
Found at i:4190706 original size:2 final size:2
Alignment explanation
Indices: 4190699--4190726 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4190689 TAAAATTCTA
4190699 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4190727 TGACCCAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4190820 original size:17 final size:17
Alignment explanation
Indices: 4190800--4190834 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
4190790 AATATGACAA
4190800 CTAACAAAATAAATTTT
1 CTAACAAAATAAATTTT
4190817 CTAACAAAATAAATTTT
1 CTAACAAAATAAATTTT
4190834 C
1 C
4190835 ATCATCTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.34
Consensus pattern (17 bp):
CTAACAAAATAAATTTT
Found at i:4193141 original size:37 final size:39
Alignment explanation
Indices: 4193089--4193449 Score: 379
Period size: 37 Copynumber: 9.7 Consensus size: 39
4193079 AAAAATTGGT
* *
4193089 TTTTGAAAAAGTATATATATTATATAG-TTTT-AAAACA
1 TTTTGAAAAAATATATATAATATATAGTTTTTAAAAACA
*
4193126 TTTTGAAAAAATATATATAATATATAGTTTTTGAAAACA
1 TTTTGAAAAAATATATATAATATATAGTTTTTAAAAACA
* *
4193165 TTTTGAAAACGTATATATATAATATATAG-TTTTAAAAATA
1 TTTTGAAAA--AATATATATAATATATAGTTTTTAAAAACA
* * *
4193205 TTTTGAAAACATATATATATTATATAGTTTTTTAAAACA
1 TTTTGAAAAAATATATATAATATATAGTTTTTAAAAACA
*
4193244 TTTTG--AAAACATATATAATATATAGTTTTT-AAAACA
1 TTTTGAAAAAATATATATAATATATAGTTTTTAAAAACA
4193280 TTTTG-----A-ATATAT-ATATATAGTTTTTAAAAACA
1 TTTTGAAAAAATATATATAATATATAGTTTTTAAAAACA
**
4193312 TTTTGAAAGTATATATATAATATAT-GTTTTTTAAAAACA
1 TTTTGAAAAAATATATATAATATATAG-TTTTTAAAAACA
4193351 TTTTG--AAAATATATATAATATAT-GATTTTT-AAAACA
1 TTTTGAAAAAATATATATAATATATAG-TTTTTAAAAACA
* *
4193387 TTTTG--AAAA-ATATATAATATATAG-TTTTGAAAACT
1 TTTTGAAAAAATATATATAATATATAGTTTTTAAAAACA
* *
4193422 TTTTTAATATATATATATATAATATATA
1 TTTTGAA-A-AAATATATATAATATATA
4193450 TAGTTTTAAA
Statistics
Matches: 285, Mismatches: 18, Indels: 39
0.83 0.05 0.11
Matches are distributed among these distances:
31 13 0.05
32 17 0.06
33 1 0.00
34 4 0.01
35 22 0.08
36 27 0.09
37 70 0.25
38 28 0.10
39 54 0.19
40 32 0.11
41 17 0.06
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (39 bp):
TTTTGAAAAAATATATATAATATATAGTTTTTAAAAACA
Found at i:4193143 original size:39 final size:36
Alignment explanation
Indices: 4193089--4193492 Score: 382
Period size: 39 Copynumber: 10.9 Consensus size: 36
4193079 AAAAATTGGT
4193089 TTTTGAAAA-AGTATATATATTATATAGTTTTAAAACA
1 TTTTGAAAATA-TATATATA-TATATAGTTTTAAAACA
*
4193126 TTTTGAAAAAATATATATAATATATAGTTTTTGAAAACA
1 TTTTGAAAATATATATAT-ATATATAG-TTTT-AAAACA
*
4193165 TTTTGAAAACGTATATATATAATATATAGTTTTAAAAATA
1 TTTTGAAAA--TATATATAT-ATATATAGTTTT-AAAACA
*
4193205 TTTTGAAAACATATATATATTATATAGTTTTTTAAAACA
1 TTTTGAAAATATATATATA-TATATAG--TTTTAAAACA
*
4193244 TTTTGAAAACATATATA-ATATATAGTTTTTAAAACA
1 TTTTGAAAATATATATATATATATAG-TTTTAAAACA
*
4193280 TTTTG--AATATATATATATAGT-T--TTTAAAAACA
1 TTTTGAAAATATATATATATA-TATAGTTTTAAAACA
*
4193312 TTTTGAAAGTATATATATA-ATATATGTTTTTTAAAAACA
1 TTTTGAAAATATATATATATATATA-G--TTTT-AAAACA
*
4193351 TTTTGAAAATATATATA-ATATATGATTTTTAAAACA
1 TTTTGAAAATATATATATATATAT-AGTTTTAAAACA
*
4193387 TTTTGAAAA-ATATATA-ATATATAGTTTTGAAAACTT
1 TTTTGAAAATATATATATATATATAGTTTT-AAAAC-A
* *
4193423 TTTTAATATATATATATATAATATATATAGTTTTAAAATA
1 TTTTGA-A-A-ATATATAT-ATATATATAGTTTTAAAACA
* * *
4193463 TTTTTAAAATATAAATATATAT-TATTTTTA
1 TTTTGAAAATATATATATATATATAGTTTTA
4193493 TTTATTTTAT
Statistics
Matches: 318, Mismatches: 19, Indels: 62
0.80 0.05 0.16
Matches are distributed among these distances:
32 15 0.05
33 2 0.01
34 25 0.08
35 29 0.09
36 43 0.14
37 43 0.14
38 28 0.09
39 65 0.20
40 34 0.11
41 22 0.07
42 12 0.04
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (36 bp):
TTTTGAAAATATATATATATATATAGTTTTAAAACA
Found at i:4193277 original size:25 final size:28
Alignment explanation
Indices: 4193254--4193313 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 28
4193244 TTTTGAAAAC
4193254 ATATATAATATATAGTTTTTAAAACATTTTGA
1 ATATAT-ATATATAGTTTTTAAAACA--TT-A
4193286 ATATATATATATAGTTTTTAAAAACATT
1 ATATATATATATAGTTTTT-AAAACATT
4193314 TTGAAAGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 2 0.07
31 13 0.48
32 12 0.44
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (28 bp):
ATATATATATATAGTTTTTAAAACATTA
Found at i:4193305 original size:107 final size:109
Alignment explanation
Indices: 4193179--4193492 Score: 371
Period size: 107 Copynumber: 2.9 Consensus size: 109
4193169 GAAAACGTAT
*
4193179 ATATATAATATATAG-TTTTAAAAATATTTTGAAAACATATATATATTATATAGTTTTTTAAAAC
1 ATATATAATATATAGTTTTTAAAAATATTTTGAAAATATATATATATTATATAGTTTTTTAAAAC
4193243 ATTTTGAAAACATATATAATATATAG-TTTTTAAAACATTTTG-A
66 ATTTTGAAAA-ATATATAATATATAGATTTTTAAAACATTTTGAA
* * *
4193286 ATATAT-ATATATAGTTTTTAAAAACATTTTGAAAGTATATATATAATATAT-GTTTTTTAAAAA
1 ATATATAATATATAGTTTTTAAAAATATTTTGAAAATATATATATATTATATAGTTTTTT-AAAA
4193349 CATTTTGAAAATATATATAATATAT-GATTTTTAAAACATTTTGAAAA
65 CATTTTGAAAA-ATATATAATATATAGATTTTTAAAACATTTTG--AA
* * *
4193396 ATATATAATATATAGTTTTGAAAACT-TTTTTAATATATATATATATAATATATATAG--TTTTA
1 ATATATAATATATAGTTTTTAAAAATATTTTGAA-A-ATATATATAT-AT-TATATAGTTTTTTA
* * *
4193458 AAATATTTT-TAAAATATA-AATATATATTATTTTTA
62 AAACATTTTGAAAAATATATAATATATA-GATTTTTA
4193493 TTTATTTTAT
Statistics
Matches: 179, Mismatches: 14, Indels: 24
0.82 0.06 0.11
Matches are distributed among these distances:
106 16 0.09
107 82 0.46
109 7 0.04
110 18 0.10
111 27 0.15
112 18 0.10
113 5 0.03
114 5 0.03
115 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (109 bp):
ATATATAATATATAGTTTTTAAAAATATTTTGAAAATATATATATATTATATAGTTTTTTAAAAC
ATTTTGAAAAATATATAATATATAGATTTTTAAAACATTTTGAA
Found at i:4193442 original size:42 final size:42
Alignment explanation
Indices: 4193396--4193484 Score: 121
Period size: 41 Copynumber: 2.1 Consensus size: 42
4193386 ATTTTGAAAA
* *
4193396 ATATATA-ATATATAGTTTTGAAAACT-TTTTTAATATATATAT
1 ATATATATATATATAGTTTT-AAAA-TATTTTTAAAATATAAAT
4193438 ATATA-ATATATATAGTTTTAAAATATTTTTAAAATATAAAT
1 ATATATATATATATAGTTTTAAAATATTTTTAAAATATAAAT
4193479 ATATAT
1 ATATAT
4193485 TATTTTTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
40 1 0.02
41 24 0.57
42 17 0.40
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.48
Consensus pattern (42 bp):
ATATATATATATATAGTTTTAAAATATTTTTAAAATATAAAT
Found at i:4194309 original size:12 final size:12
Alignment explanation
Indices: 4194292--4194324 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
4194282 TTTCGACCAG
4194292 ATGAGAGAGAGA
1 ATGAGAGAGAGA
4194304 ATGAGAGAGAGA
1 ATGAGAGAGAGA
4194316 ATGAGAGAG
1 ATGAGAGAG
4194325 TTAGAGAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.42, T:0.09
Consensus pattern (12 bp):
ATGAGAGAGAGA
Found at i:4194356 original size:7 final size:7
Alignment explanation
Indices: 4194346--4194370 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4194336 GGAGATGATG
4194346 TGAGAAA
1 TGAGAAA
4194353 TGAGAAA
1 TGAGAAA
4194360 TGAGAAA
1 TGAGAAA
4194367 TGAG
1 TGAG
4194371 GGGAATGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.32, T:0.16
Consensus pattern (7 bp):
TGAGAAA
Found at i:4194821 original size:17 final size:18
Alignment explanation
Indices: 4194799--4194849 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
4194789 TTTATGTGTC
4194799 TTTA-TTTATCTATT-TTA
1 TTTATTTTAT-TATTATTA
4194816 TTTATTTTATTATTATTA
1 TTTATTTTATTATTATTA
* *
4194834 -TTATTATATTAATATT
1 TTTATTTTATTATTATT
4194850 TTTTGTAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 22 0.73
18 8 0.27
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTATTTTATTATTATTA
Found at i:4196409 original size:18 final size:18
Alignment explanation
Indices: 4196386--4196420 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4196376 AGGGATTAAC
* *
4196386 AGTGGTCCTTCGGGACAT
1 AGTGGTCATTCAGGACAT
4196404 AGTGGTCATTCAGGACA
1 AGTGGTCATTCAGGACA
4196421 AATATTTAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.26
Consensus pattern (18 bp):
AGTGGTCATTCAGGACAT
Found at i:4199111 original size:13 final size:13
Alignment explanation
Indices: 4199093--4199118 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4199083 GTATTGGTAT
4199093 GTTTTAAAAGAGG
1 GTTTTAAAAGAGG
4199106 GTTTTAAAAGAGG
1 GTTTTAAAAGAGG
4199119 AAATACAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (13 bp):
GTTTTAAAAGAGG
Found at i:4204100 original size:39 final size:39
Alignment explanation
Indices: 4204041--4204145 Score: 140
Period size: 39 Copynumber: 2.7 Consensus size: 39
4204031 ATTCATAAGT
* * *
4204041 TTAACTATGATCATTCGATTAATAAATTTAT-TTTCTATA
1 TTAATTATGATCATTAGATTAAAAAATTT-TCTTTCTATA
* *
4204080 TTAATTATGATCACTAGATTAACAAATTTTCTTTCTATA
1 TTAATTATGATCATTAGATTAAAAAATTTTCTTTCTATA
*
4204119 TTAATTATGATCATTAGGTTAAAAAAT
1 TTAATTATGATCATTAGATTAAAAAAT
4204146 ATAATTATAA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
38 1 0.02
39 57 0.98
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.46
Consensus pattern (39 bp):
TTAATTATGATCATTAGATTAAAAAATTTTCTTTCTATA
Found at i:4205986 original size:15 final size:16
Alignment explanation
Indices: 4205966--4205995 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4205956 ACATGTACAT
4205966 ATGTATGTAT-TATTA
1 ATGTATGTATATATTA
4205981 ATGTATGTATATATT
1 ATGTATGTATATATT
4205996 TATGCACATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (16 bp):
ATGTATGTATATATTA
Found at i:4206021 original size:4 final size:4
Alignment explanation
Indices: 4206012--4206370 Score: 495
Period size: 4 Copynumber: 90.8 Consensus size: 4
4206002 CATTTTGATG
4206012 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
4206060 CATGA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CAT-A CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
4206109 CATA CACTA CA-A CATA CATA CATA CATA C-TA CATA CATA CATA CATA
1 CATA CA-TA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
4206156 CATA CATA CAGA CATA C-T- CATA CATA CA-A CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
4206201 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
4206249 CATA CATA CATA CATA CATA CATA CATA CATA CATGTT C-TA TATGA -AGA
1 CATA CATA CATA CATA CATA CATA CATA CATA CA--TA CATA CAT-A CATA
* * * * *
4206298 CATA TATA CATA CATTA CGTA -ATA TATG CATA CAT- TATA CATA CATA
1 CATA CATA CATA CA-TA CATA CATA CATA CATA CATA CATA CATA CATA
* *
4206345 CAT- TATA CATA CATA CATA TATA CAT
1 CATA CATA CATA CATA CATA CATA CAT
4206371 GCATTACTAT
Statistics
Matches: 319, Mismatches: 20, Indels: 32
0.86 0.05 0.09
Matches are distributed among these distances:
2 1 0.00
3 19 0.06
4 285 0.89
5 12 0.04
6 2 0.01
ACGTcount: A:0.48, C:0.23, G:0.02, T:0.27
Consensus pattern (4 bp):
CATA
Found at i:4209162 original size:18 final size:18
Alignment explanation
Indices: 4209141--4209184 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
4209131 AAGAAAATTG
*
4209141 ATAAAGAAAATAATAAAA-
1 ATAAA-AAAATAACAAAAT
4209159 ATAATAAAAATAACAAAAT
1 ATAA-AAAAATAACAAAAT
4209178 ATAAAAA
1 ATAAAAA
4209185 TAAAAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.18
Consensus pattern (18 bp):
ATAAAAAAATAACAAAAT
Found at i:4209167 original size:8 final size:9
Alignment explanation
Indices: 4209147--4209187 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
4209137 ATTGATAAAG
4209147 AAAATAATA
1 AAAATAATA
4209156 AAAATAATA
1 AAAATAATA
*
4209165 AAAATAA-C
1 AAAATAATA
4209173 AAAAT-ATA
1 AAAATAATA
4209181 AAAATAA
1 AAAATAA
4209188 AAATAATTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 1 0.04
8 10 0.36
9 17 0.61
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAATAATA
Found at i:4209183 original size:16 final size:17
Alignment explanation
Indices: 4209156--4209187 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
4209146 GAAAATAATA
4209156 AAAATAATAAAAATAAC
1 AAAATAATAAAAATAAC
4209173 AAAAT-ATAAAAATAA
1 AAAATAATAAAAATAA
4209188 AAATAATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (17 bp):
AAAATAATAAAAATAAC
Found at i:4209364 original size:47 final size:47
Alignment explanation
Indices: 4209291--4209388 Score: 189
Period size: 47 Copynumber: 2.1 Consensus size: 47
4209281 TTTTCATCAT
4209291 TTTC-CCATTAAACTTTCTCCAACCTTTATCTAATGGTTCTTGCTCC
1 TTTCTCCATTAAACTTTCTCCAACCTTTATCTAATGGTTCTTGCTCC
4209337 TTTCTCCATTAAACTTTCTCCAACCTTTATCTAATGGTTCTTGCTCC
1 TTTCTCCATTAAACTTTCTCCAACCTTTATCTAATGGTTCTTGCTCC
4209384 TTTCT
1 TTTCT
4209389 TTCGATAATG
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 4 0.08
47 47 0.92
ACGTcount: A:0.18, C:0.30, G:0.06, T:0.46
Consensus pattern (47 bp):
TTTCTCCATTAAACTTTCTCCAACCTTTATCTAATGGTTCTTGCTCC
Found at i:4215072 original size:53 final size:52
Alignment explanation
Indices: 4214973--4215085 Score: 120
Period size: 53 Copynumber: 2.2 Consensus size: 52
4214963 ATAAAAAAAA
* * * * * *
4214973 TTCAAGGTGGACACCATCAATAGAATATATCACTAATCGAAGAAAATTTAGAT
1 TTCAGGGTAGACACCATCAATAAAATATATCACTAATAGAA-AAAAATCAGAT
* *
4215026 TTCAGGGTAGACACCATTAATAAAATA-AGTGACTAATAGAAAAAAATCAGAT
1 TTCAGGGTAGACACCATCAATAAAATATA-TCACTAATAGAAAAAAATCAGAT
*
4215078 TTTAGGGT
1 TTCAGGGT
4215086 GGGCACGTGC
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
52 17 0.34
53 33 0.66
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (52 bp):
TTCAGGGTAGACACCATCAATAAAATATATCACTAATAGAAAAAAATCAGAT
Found at i:4220437 original size:55 final size:55
Alignment explanation
Indices: 4220353--4220462 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
4220343 ACATCATCCC
4220353 GATTCTCATTTATCACATTCAAACTAAAGAATAGTCCACTTTTGTCAAAATCAAT
1 GATTCTCATTTATCACATTCAAACTAAAGAATAGTCCACTTTTGTCAAAATCAAT
4220408 GATTCTCATTTATCACATTCAAACTAAAGAATAGTCCACTTTTGTCAAAATCAAT
1 GATTCTCATTTATCACATTCAAACTAAAGAATAGTCCACTTTTGTCAAAATCAAT
4220463 TTTCTACCCT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.35
Consensus pattern (55 bp):
GATTCTCATTTATCACATTCAAACTAAAGAATAGTCCACTTTTGTCAAAATCAAT
Found at i:4220563 original size:2 final size:2
Alignment explanation
Indices: 4220556--4220591 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4220546 AAGGTGCAGA
4220556 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4220592 TATGGTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4227147 original size:37 final size:37
Alignment explanation
Indices: 4227103--4227207 Score: 131
Period size: 37 Copynumber: 2.8 Consensus size: 37
4227093 CATTTTTGTC
4227103 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT-AAATTT
* * *
4227141 -TGCTAGGATTCAAACTCCTAAAAATATGATAGATTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAATTT
* * * *
4227177 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
4227208 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
36 5 0.09
37 52 0.91
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAATTT
Found at i:4227455 original size:18 final size:18
Alignment explanation
Indices: 4227434--4227506 Score: 58
Period size: 18 Copynumber: 4.1 Consensus size: 18
4227424 AATTTATTAT
4227434 TTTTTTTTATCTTATTTA
1 TTTTTTTTATCTTATTTA
* *
4227452 TTTTATTTATTTTATTT-
1 TTTTTTTTATCTTATTTA
* * *
4227469 TTCCTTTGTATCTTATTTG
1 TT-TTTTTTATCTTATTTA
* * *
4227488 TTTTCTTTACCTTGTTTA
1 TTTTTTTTATCTTATTTA
4227506 T
1 T
4227507 CTAACACATT
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
17 2 0.05
18 37 0.90
19 2 0.05
ACGTcount: A:0.14, C:0.10, G:0.04, T:0.73
Consensus pattern (18 bp):
TTTTTTTTATCTTATTTA
Found at i:4227457 original size:9 final size:9
Alignment explanation
Indices: 4227434--4227468 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
4227424 AATTTATTAT
*
4227434 TTTTTTTTA
1 TTTTATTTA
*
4227443 TCTTATTTA
1 TTTTATTTA
4227452 TTTTATTTA
1 TTTTATTTA
4227461 TTTTATTT
1 TTTTATTT
4227469 TTCCTTTGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTATTTA
Found at i:4227457 original size:14 final size:14
Alignment explanation
Indices: 4227426--4227469 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
4227416 ATATTATTAA
*
4227426 TTTA-TTATTTTTT
1 TTTATTTATTTTAT
4227439 TTTATCTTA-TTTAT
1 TTTAT-TTATTTTAT
4227453 TTTATTTATTTTAT
1 TTTATTTATTTTAT
4227467 TTT
1 TTT
4227470 TCCTTTGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 7 0.26
14 17 0.63
15 3 0.11
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTATTTATTTTAT
Found at i:4227466 original size:36 final size:36
Alignment explanation
Indices: 4227430--4227496 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
4227420 TATTAATTTA
4227430 TTATTTTT--TTT-TATCTTATTTATTTTATTTATT
1 TTATTTTTCCTTTGTATCTTATTTATTTTATTTATT
* *
4227463 TTATTTTTCCTTTGTATCTTATTTGTTTTCTTTA
1 TTATTTTTCCTTTGTATCTTATTTATTTTATTTA
4227497 CCTTGTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 8 0.28
35 3 0.10
36 18 0.62
ACGTcount: A:0.15, C:0.07, G:0.03, T:0.75
Consensus pattern (36 bp):
TTATTTTTCCTTTGTATCTTATTTATTTTATTTATT
Found at i:4232281 original size:183 final size:183
Alignment explanation
Indices: 4231967--4232496 Score: 909
Period size: 183 Copynumber: 2.9 Consensus size: 183
4231957 ATTAAATCCG
*
4231967 TAAAGATGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
4232032 ATAGATTATGTTCAAACTATAACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
* *
4232097 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTAAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTAAGTGATTTATCCCTA
4232150 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
4232215 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCTGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
4232280 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTATCCCTA
131 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTAAGTGATTTATCCCTA
4232333 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** * * * *
4232398 ATAGATTACATTCAAA-TCATGACATTGCTTGGATACTTGGCAATTCGGTGTTTGCTTCACTGCT
66 ATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
* * *
4232462 TTTTTCAGGTCAAAGACTTTGTGATGAGATGAACC
130 TTTGTCAGGCCAAAGACTTTGTGATGAGACGAACC
4232497 ATTCAGTTAA
Statistics
Matches: 330, Mismatches: 16, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
182 1 0.00
183 329 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTAAGTGATTTATCCCTA
Found at i:4233724 original size:35 final size:35
Alignment explanation
Indices: 4233685--4233800 Score: 88
Period size: 36 Copynumber: 3.1 Consensus size: 35
4233675 ATACTTTGTC
4233685 TCACTTGAGACTGTTTTCTCGAAAGAAGATTTATT
1 TCACTTGAGACTGTTTTCTCGAAAGAAGATTTATT
** * ** * * *
4233720 TCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTC
1 TCACTTGAGACTG-TTTTCTCGAAAGAAGATTTATT
* *
4233756 TCGCTTGAGACCGTTTTCACTCGAAAGAAGGCATTTCATT
1 TCACTTGAGACTGTTTT--CTCGAAAGAA-G-ATTT-ATT
4233796 TCACT
1 TCACT
4233801 CAAGGCTGTT
Statistics
Matches: 56, Mismatches: 19, Indels: 7
0.68 0.23 0.09
Matches are distributed among these distances:
35 14 0.25
36 25 0.45
37 7 0.12
38 1 0.02
39 4 0.07
40 5 0.09
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.38
Consensus pattern (35 bp):
TCACTTGAGACTGTTTTCTCGAAAGAAGATTTATT
Found at i:4233735 original size:71 final size:74
Alignment explanation
Indices: 4233644--4233818 Score: 216
Period size: 71 Copynumber: 2.4 Consensus size: 74
4233634 ATGCAGATGA
* * *
4233644 TTATCTCACTCAA-ATTTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTT-CTCG
1 TTATTTCACTCAAGA-TTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACCGTTTTACTCG
4233706 AAAGAA-G-AT
64 AAAGAAGGCAT
*
4233715 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGA
1 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTT-ACTCGA
4233780 AAGAAGGCAT
65 AAGAAGGCAT
** *
4233790 TTCATTTCACTCAAGGCTGTTTTTTTTAA
1 TT-ATTTCACTCAAGATTGTTTTTCTTAA
4233819 GAAGATTTTA
Statistics
Matches: 90, Mismatches: 7, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
70 1 0.01
71 50 0.56
72 1 0.01
73 10 0.11
74 1 0.01
75 4 0.04
76 23 0.26
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (74 bp):
TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTACTCGAA
AGAAGGCAT
Found at i:4233750 original size:36 final size:36
Alignment explanation
Indices: 4233644--4233757 Score: 99
Period size: 36 Copynumber: 3.2 Consensus size: 36
4233634 ATGCAGATGA
*
4233644 TTATCTCACTCAA-ATTTGTTTTTCTTAAAACATA-CT
1 TTATCTCACTCAAGA-TTGTTTTTCTTAAAACA-AGAT
* ** * ** *
4233680 TTGTCTCACTTGAGACTG-TTTTCTCGAAAGAAGAT
1 TTATCTCACTCAAGATTGTTTTTCTTAAAACAAGAT
*
4233715 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGAT
1 TTATCTCACTCAAGATTGTTTTTCTTAAAACAAGAT
*
4233751 TTGTCTC
1 TTATCTC
4233758 GCTTGAGACC
Statistics
Matches: 57, Mismatches: 18, Indels: 6
0.70 0.22 0.07
Matches are distributed among these distances:
34 1 0.02
35 24 0.42
36 31 0.54
37 1 0.02
ACGTcount: A:0.28, C:0.18, G:0.11, T:0.44
Consensus pattern (36 bp):
TTATCTCACTCAAGATTGTTTTTCTTAAAACAAGAT
Found at i:4233772 original size:36 final size:36
Alignment explanation
Indices: 4233660--4233772 Score: 104
Period size: 36 Copynumber: 3.2 Consensus size: 36
4233650 CACTCAAATT
*
4233660 TGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGAC
1 TGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGAC
** * * * ** *
4233696 TG-TTTTCTCGAAAGAAGATTTATTTCACTCAAGAT
1 TGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGAC
*
4233731 TGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGAC
1 TGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGAC
*
4233767 CGTTTT
1 TGTTTT
4233773 CACTCGAAAG
Statistics
Matches: 56, Mismatches: 19, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
34 1 0.02
35 24 0.43
36 31 0.55
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (36 bp):
TGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGAC
Found at i:4233877 original size:39 final size:39
Alignment explanation
Indices: 4233834--4233973 Score: 104
Period size: 39 Copynumber: 3.4 Consensus size: 39
4233824 TTTTATCTTG
*
4233834 CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
* * * *
4233873 CTTGAGACAGTTTCTCTTGAAAATTTCCCTTGAAATTAATTTT-TTTCTC
1 CTTGAGACAGTTTCCCTCG-AAA-----C-AG-AA--AATTTTGTCTC-C
* *
4233922 C-TGAGATAGTTTCCCTCGAAACATAAAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
4233960 CTTGAGACAGTTTC
1 CTTGAGACAGTTTC
4233974 TCTTAAAACA
Statistics
Matches: 76, Mismatches: 12, Indels: 26
0.67 0.11 0.23
Matches are distributed among these distances:
38 8 0.11
39 30 0.39
40 5 0.07
42 1 0.01
45 1 0.01
46 1 0.01
47 5 0.07
48 17 0.22
49 8 0.11
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (39 bp):
CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
Found at i:4234104 original size:103 final size:102
Alignment explanation
Indices: 4233895--4234201 Score: 433
Period size: 102 Copynumber: 3.0 Consensus size: 102
4233885 TCTCTTGAAA
* * * *
4233895 ATTTCCCTTGAAATTAATTTTTTTCTCCTGAGATAGTTTCCCTCGAAACATAAAATTTTGTCTCC
1 ATTTCCCTTGAAATGATTTTTTTTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA-TTTGTCTCC
4233960 CTTGAGACAGTTTCTCTTAAAACATAAACATTG-AAAC
65 CTTGAGACAGTTTCTCTTAAAACATAAACATTGAAAAC
4233997 ATTT-CCTTGAAATGATTTTTTTTTCTCTTGAGAATAGTTTCCCTCGAAACAGAAAATTTGTCTC
1 ATTTCCCTTGAAATGA-TTTTTTTTCTCTTGAG-ATAGTTTCCCTCGAAACAGAAAATTTGTCTC
*
4234061 CCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
64 CCTTGAGACAGTTTCTCTTAAAACATAAACATTGAAAAC
* * * * *
4234100 ATTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-G-AATTTTGTCTCC
1 ATTTCCCTTGAAATG-ATTTTTTTTCTCTTGAGATAGTTTCCCTCGAAACAGAAAATTTGTCTCC
** *
4234163 CTTGAGACAGTTTCTCTCCAAACATAAACTTTGAAAAC
65 CTTGAGACAGTTTCTCTTAAAACATAAACATTGAAAAC
4234201 A
1 A
4234202 ATTTAACGAA
Statistics
Matches: 187, Mismatches: 13, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
101 57 0.30
102 60 0.32
103 46 0.25
104 23 0.12
105 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (102 bp):
ATTTCCCTTGAAATGATTTTTTTTCTCTTGAGATAGTTTCCCTCGAAACAGAAAATTTGTCTCCC
TTGAGACAGTTTCTCTTAAAACATAAACATTGAAAAC
Found at i:4234148 original size:36 final size:36
Alignment explanation
Indices: 4234101--4234176 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
4234091 ATTGAAAACA
* * *
4234101 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
*
4234137 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
4234173 TTTC
1 TTTC
4234177 TCTCCAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
Found at i:4234199 original size:101 final size:101
Alignment explanation
Indices: 4233895--4234201 Score: 424
Period size: 101 Copynumber: 3.0 Consensus size: 101
4233885 TCTCTTGAAA
* *
4233895 ATTTCCCTTGAAATTAATTTTTTTCTCC-TGAGATAGTTTCCCTCGAAACATAAAATTTTGTCTC
1 ATTTCCCTTGAAATGAA-TTTTTTCTCCTTGAGATAGTTTCCCTCGAAAC--AGAATTTTGTCTC
4233959 CCTTGAGACAGTTTCTCTTAAAACATAAACATTG-AAAC
63 CCTTGAGACAGTTTCTCTTAAAACATAAACATTGAAAAC
* * *
4233997 ATTT-CCTTGAAATGATTTTTTTTTCTCTTGAGAATAGTTTCCCTCGAAACAGAAAATTTGTCTC
1 ATTTCCCTTGAAATGAATTTTTTCTC-CTTGAG-ATAGTTTCCCTCGAAACAG-AATTTTGTCTC
*
4234061 CCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
63 CCTTGAGACAGTTTCTCTTAAAACATAAACATTGAAAAC
* *
4234100 ATTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-GAATTTTGTCTCCC
1 ATTTCCCTTGAAATGAATTTTTTCTC-CTTGAGATAGTTTCCCTCGAAACAGAATTTTGTCTCCC
** *
4234164 TTGAGACAGTTTCTCTCCAAACATAAACTTTGAAAAC
65 TTGAGACAGTTTCTCTTAAAACATAAACATTGAAAAC
4234201 A
1 A
4234202 ATTTAACGAA
Statistics
Matches: 184, Mismatches: 15, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
100 8 0.04
101 59 0.32
102 52 0.28
103 41 0.22
104 24 0.13
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (101 bp):
ATTTCCCTTGAAATGAATTTTTTCTCCTTGAGATAGTTTCCCTCGAAACAGAATTTTGTCTCCCT
TGAGACAGTTTCTCTTAAAACATAAACATTGAAAAC
Found at i:4234574 original size:105 final size:105
Alignment explanation
Indices: 4234376--4234997 Score: 913
Period size: 105 Copynumber: 6.0 Consensus size: 105
4234366 GTGACACTTG
* * * *
4234376 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTT
4234441 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
65 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
4234482 AGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTC
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTC
* *
4234547 AGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTTC
66 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
4234587 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTC
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTC
4234652 -GAGCCAATTTCAAC-TCACAACGAAGGATA-TGGACTCC
66 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
4234689 AGAAAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATCTC
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTC
4234754 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
4234794 AGACAACGCAAGTTCAACTCCACGACGAAGGGACCGCT-CTTGTCAACAA-AA-TT-TC-A-TTC
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTC
* * *
4234853 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCG
66 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * * * * * **
4234893 AGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTCTCAACAAACAATTTCCCGGTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAAC-AACAACTTCTCAATT
* * *
4234957 CCAGAGCCAATTTCAACTTCACGACGGAGGATATTGGACTC
64 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
4234998 GGAACAATGC
Statistics
Matches: 473, Mismatches: 32, Indels: 22
0.90 0.06 0.04
Matches are distributed among these distances:
98 2 0.00
99 71 0.15
100 8 0.02
101 4 0.01
102 74 0.16
103 32 0.07
104 41 0.09
105 161 0.34
106 80 0.17
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.22
Consensus pattern (105 bp):
AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTC
AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
Found at i:4234724 original size:207 final size:209
Alignment explanation
Indices: 4234371--4234996 Score: 910
Period size: 207 Copynumber: 3.0 Consensus size: 209
4234361 ATATCGTGAC
* * * * *
4234371 ACTTGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTC
1 ACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTC
4234436 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
65 AA-TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
*
4234501 TCACGATGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCA
129 TCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCA
*
4234566 CAATGAAGGATATTGG
194 CAACGAAGGATATTGG
*
4234582 ACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
*
4234647 ATCTC-GAGCCAATTTCAAC-TCACAACGAAGGATA-TGGACTCCAGAAAACGCAAGTTCAACTT
66 AT-TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
*
4234709 CACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATCTCAGAGCCAATTTCAACTTCAC
130 CACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCAC
4234774 AACGAAGGATATTGG
195 AACGAAGGATATTGG
* *
4234789 ACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGGACCGCT-CTTGTCAACAA-AA-TT-TC-
1 ACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
* * * *
4234849 ATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTC
66 ATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
* * * * * ** *
4234914 ACAACGAAGGGA-CGACTGGTTCTCAACAAACAATTTCCCGGTTCCAGAGCCAATTTCAACTTCA
131 ACGACGAAGGGACCG-CTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCAATTTCAACTTCA
* *
4234978 CGACGGAGGATATTGG
194 CAACGAAGGATATTGG
4234994 ACT
1 ACT
4234997 CGGAACAATG
Statistics
Matches: 380, Mismatches: 29, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
201 2 0.01
202 15 0.04
203 17 0.04
204 49 0.13
205 49 0.13
206 11 0.03
207 145 0.38
208 15 0.04
209 15 0.04
210 14 0.04
211 48 0.13
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.22
Consensus pattern (209 bp):
ACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
ATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
ACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
ACGAAGGATATTGG
Found at i:4235591 original size:37 final size:37
Alignment explanation
Indices: 4235538--4235642 Score: 131
Period size: 37 Copynumber: 2.8 Consensus size: 37
4235528 CATTTTCGTC
4235538 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT-AAATTT
* * *
4235576 -TGCTAGGATTCAAACTCCTAAAAATATGATAGATTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAATTT
* * * *
4235612 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
4235643 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
36 5 0.09
37 52 0.91
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAATTT
Found at i:4235841 original size:2 final size:2
Alignment explanation
Indices: 4235834--4235865 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4235824 CAATACTTTG
4235834 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4235866 TTATTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4235927 original size:13 final size:12
Alignment explanation
Indices: 4235911--4235949 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 12
4235901 TAATTATTAA
4235911 TTTATTATATTTT
1 TTTATT-TATTTT
4235924 TTTATCTTATTTAT
1 TTTAT-TTATTT-T
4235938 TTTATTTATTTT
1 TTTATTTATTTT
4235950 ATTTTTCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.04
13 16 0.67
14 7 0.29
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTATTTATTTT
Found at i:4235942 original size:14 final size:13
Alignment explanation
Indices: 4235911--4235954 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 13
4235901 TAATTATTAA
4235911 TTTATTATATTT-T
1 TTTATT-TATTTAT
4235924 TTTATCTTATTTAT
1 TTTAT-TTATTTAT
4235938 TTTATTTATTTTAT
1 TTTATTTA-TTTAT
4235952 TTT
1 TTT
4235955 TCCTTTGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 13 0.46
14 15 0.54
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTATTTATTTAT
Found at i:4235945 original size:18 final size:17
Alignment explanation
Indices: 4235912--4235991 Score: 63
Period size: 18 Copynumber: 4.5 Consensus size: 17
4235902 AATTATTAAT
4235912 TTATTATATTTTTTTATC
1 TTATT-TATTTTTTTATC
*
4235930 TTATTTATTTTATTTATT
1 TTATTTATTTT-TTTATC
*
4235948 TTATTT-TTCCTTTGTATC
1 TTATTTATT--TTTTTATC
* *
4235966 TTATTTGTTTTCTTTACC
1 TTATTTATTTT-TTTATC
*
4235984 TTGTTTAT
1 TTATTTAT
4235992 CTAACACATT
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
17 10 0.20
18 36 0.72
19 4 0.08
ACGTcount: A:0.16, C:0.09, G:0.04, T:0.71
Consensus pattern (17 bp):
TTATTTATTTTTTTATC
Found at i:4239501 original size:2 final size:2
Alignment explanation
Indices: 4239494--4239546 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
4239484 GTTGTAACTT
4239494 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4239536 TA TA TA TA TA T
1 TA TA TA TA TA T
4239547 TATTCTAATT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4243966 original size:13 final size:13
Alignment explanation
Indices: 4243950--4243994 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
4243940 AAAGTAAACG
4243950 GTCAACAATCAAA
1 GTCAACAATCAAA
* *
4243963 GTCAACGATCGAA
1 GTCAACAATCAAA
*
4243976 GTCCACTAATCAAA
1 GTCAAC-AATCAAA
4243990 GTCAA
1 GTCAA
4243995 TGGGTTGACT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
13 16 0.64
14 9 0.36
ACGTcount: A:0.44, C:0.24, G:0.13, T:0.18
Consensus pattern (13 bp):
GTCAACAATCAAA
Found at i:4247119 original size:13 final size:13
Alignment explanation
Indices: 4247103--4247147 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
4247093 AAAGTAAACG
4247103 GTCAACAATCAAA
1 GTCAACAATCAAA
* *
4247116 GTCAACGATCGAA
1 GTCAACAATCAAA
*
4247129 GTCCACTAATCAAA
1 GTCAAC-AATCAAA
4247143 GTCAA
1 GTCAA
4247148 TGGGTTGACT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
13 16 0.64
14 9 0.36
ACGTcount: A:0.44, C:0.24, G:0.13, T:0.18
Consensus pattern (13 bp):
GTCAACAATCAAA
Found at i:4254574 original size:149 final size:151
Alignment explanation
Indices: 4254332--4254633 Score: 574
Period size: 149 Copynumber: 2.0 Consensus size: 151
4254322 GTGGCATTAC
4254332 TTCTGATAACTTAGGCTTGAAGTTATTCTAGTTCCTTTAGAGCTAGGAGTACTTTGTTCATTTGA
1 TTCTGATAACTTAGGCTTGAAGTTATTCTAGTTCCTTTAGAGCTAGGAGTACTTTGTTCATTTGA
4254397 TCACTGGACGTTATTTTCACCACAGGGGAAGTCTTGGTTATTTTACAGTATAAGGGCATTTTCTT
66 TCACTGGACGTTATTTTCACCACAGGGGAAGTCTTGGTTATTTTACAGTATAAGGGCATTTTCTT
4254462 AATTTTAGCCTATAGTACTAT
131 AATTTTAGCCTATAGTACTAT
4254483 TTCTGATAACTTAGGCTT-AAGTTATTCTAGTTCCTTTAGAGCTAGG-GTACTTTGGTTCA-TTG
1 TTCTGATAACTTAGGCTTGAAGTTATTCTAGTTCCTTTAGAGCTAGGAGTACTTT-GTTCATTTG
4254545 ATCACTGGACGTTATTTTCACCACAGGGGAAGTCTTGGTTATTTTACAGTATAAGGGCATTTTCT
65 ATCACTGGACGTTATTTTCACCACAGGGGAAGTCTTGGTTATTTTACAGTATAAGGGCATTTTCT
4254610 TAATTTTAGCCTATAGTACTAT
130 TAATTTTAGCCTATAGTACTAT
4254632 TT
1 TT
4254634 TTGGTAATTT
Statistics
Matches: 150, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
149 99 0.66
150 33 0.22
151 18 0.12
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.41
Consensus pattern (151 bp):
TTCTGATAACTTAGGCTTGAAGTTATTCTAGTTCCTTTAGAGCTAGGAGTACTTTGTTCATTTGA
TCACTGGACGTTATTTTCACCACAGGGGAAGTCTTGGTTATTTTACAGTATAAGGGCATTTTCTT
AATTTTAGCCTATAGTACTAT
Found at i:4257094 original size:16 final size:16
Alignment explanation
Indices: 4257043--4257095 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
4257033 GTTTGGTTTG
4257043 TTTTAGTTCGGGTTAT
1 TTTTAGTTCGGGTTAT
*
4257059 TTTCAGTTCGGGTTAT
1 TTTTAGTTCGGGTTAT
* *
4257075 TTTTGGTTCGGGTTGT
1 TTTTAGTTCGGGTTAT
4257091 TTTTA
1 TTTTA
4257096 ATTCAGGTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.09, C:0.08, G:0.26, T:0.57
Consensus pattern (16 bp):
TTTTAGTTCGGGTTAT
Found at i:4258319 original size:19 final size:18
Alignment explanation
Indices: 4258295--4258342 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 18
4258285 ATAAATTAAA
4258295 TTATTAAAACTATAATATT
1 TTATTAAAACTATAA-ATT
*
4258314 TTATTAAAA-GATAAATT
1 TTATTAAAACTATAAATT
4258331 TTA-T-AAACTATA
1 TTATTAAAACTATA
4258343 TTAATTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 3 0.12
16 4 0.15
17 6 0.23
18 4 0.15
19 9 0.35
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (18 bp):
TTATTAAAACTATAAATT
Found at i:4258400 original size:13 final size:13
Alignment explanation
Indices: 4258373--4258431 Score: 52
Period size: 12 Copynumber: 4.6 Consensus size: 13
4258363 AATAAAATAC
4258373 TATATT-ATTAAT
1 TATATTAATTAAT
*
4258385 TATATTAATTATT
1 TATATTAATTAAT
*
4258398 TATAATAA-TAAT
1 TATATTAATTAAT
*
4258410 AATATT-ATTATTAT
1 TATATTAATTA--AT
4258424 TATATTAA
1 TATATTAA
4258432 AAATATATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
11 1 0.03
12 15 0.42
13 12 0.33
14 7 0.19
15 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATTAATTAAT
Found at i:4260495 original size:19 final size:20
Alignment explanation
Indices: 4260446--4260488 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
4260436 TTGAACACGG
*
4260446 TTTATAAAATAAATAATTAA
1 TTTAAAAAATAAATAATTAA
*
4260466 TTTAAAAAATAAAT-TTTAA
1 TTTAAAAAATAAATAATTAA
4260485 TTTA
1 TTTA
4260489 GTAAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTAAAAAATAAATAATTAA
Found at i:4260567 original size:25 final size:25
Alignment explanation
Indices: 4260533--4260581 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
4260523 TAGTGCTTAC
*
4260533 AAACATAATTATT-TTTTTATAAAAT
1 AAACATAATT-TTATTTTTAAAAAAT
4260558 AAACATAATTTTATTTTTAAAAAA
1 AAACATAATTTTATTTTTAAAAAA
4260582 AAATTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (25 bp):
AAACATAATTTTATTTTTAAAAAAT
Found at i:4267511 original size:15 final size:15
Alignment explanation
Indices: 4267493--4267574 Score: 103
Period size: 15 Copynumber: 5.5 Consensus size: 15
4267483 TTCCGGAAAA
4267493 TGAATTACTGGAATT
1 TGAATTACTGGAATT
*
4267508 TGAACTACTGGAATT
1 TGAATTACTGGAATT
**
4267523 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
*
4267538 TGAATTACTAGAATT
1 TGAATTACTGGAATT
**
4267553 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
4267567 TGAATTAC
1 TGAATTAC
4267575 ATTTCTGGAA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
14 11 0.20
15 45 0.80
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:4267552 original size:45 final size:44
Alignment explanation
Indices: 4267487--4267574 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 44
4267477 TTGGTTTTCC
* **
4267487 GGAAAATGAATTACTGGAATTTGAACTACTGGAATTTGAATTACT
1 GGAAAATGAATTACTAGAATTTGAA-TACTGGAAAATGAATTACT
*
4267532 GGAAAATGAATTACTAGAATTTGAATTCTGGAAAATGAATTAC
1 GGAAAATGAATTACTAGAATTTGAATACTGGAAAATGAATTAC
4267575 ATTTCTGGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 15 0.38
45 24 0.62
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (44 bp):
GGAAAATGAATTACTAGAATTTGAATACTGGAAAATGAATTACT
Found at i:4267615 original size:14 final size:14
Alignment explanation
Indices: 4267576--4267616 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
4267566 ATGAATTACA
* *
4267576 TTTCTGGAAAACGT
1 TTTCCGGAAAATGT
4267590 TTTCCGGAAAATGT
1 TTTCCGGAAAATGT
*
4267604 TTTCCGTAAAATG
1 TTTCCGGAAAATG
4267617 AATTACATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.37
Consensus pattern (14 bp):
TTTCCGGAAAATGT
Found at i:4267805 original size:17 final size:18
Alignment explanation
Indices: 4267744--4267807 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 18
4267734 TACAATAAAT
*
4267744 AATA-TTATTTATCA-TA
1 AATACTTATTTATTATTA
4267760 AA-ACTTATTTATTATTAAA
1 AATACTTATTTATTATT--A
*
4267779 AATAATTTATTTATTATTA
1 AAT-ACTTATTTATTATTA
4267798 AATA-TTATTT
1 AATACTTATTT
4267808 TAATAATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
15 1 0.03
16 11 0.28
17 7 0.17
18 1 0.03
19 7 0.17
21 13 0.32
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
AATACTTATTTATTATTA
Found at i:4267957 original size:23 final size:23
Alignment explanation
Indices: 4267908--4267970 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
4267898 GTGTTATATT
* **
4267908 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
4267931 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
4267954 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
4267971 AAATAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 21 0.66
24 1 0.03
25 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:4267994 original size:28 final size:27
Alignment explanation
Indices: 4267956--4268008 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 27
4267946 TTATTAAAAT
4267956 ATTATTTAAATATATAAATAATATTATTC
1 ATTATTTAAATATATAAA-AAT-TTATTC
4267985 ATTA-TTAAATATATAAAAATTTAT
1 ATTATTTAAATATATAAAAATTTAT
4268009 ATTATATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 4 0.17
27 3 0.12
28 13 0.54
29 4 0.17
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
ATTATTTAAATATATAAAAATTTATTC
Found at i:4267998 original size:19 final size:20
Alignment explanation
Indices: 4267946--4267998 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
4267936 TTAAATATCT
4267946 TTATTAAA-ATATTATTTAA
1 TTATTAAATATATTATTTAA
* *
4267965 ATATATAAATAATATTA-TTCA
1 TTAT-TAAAT-ATATTATTTAA
4267986 TTATTAAATATAT
1 TTATTAAATATAT
4267999 AAAAATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 6 0.21
22 6 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTAAATATATTATTTAA
Found at i:4268011 original size:28 final size:27
Alignment explanation
Indices: 4267955--4268120 Score: 81
Period size: 29 Copynumber: 5.8 Consensus size: 27
4267945 TTTATTAAAA
4267955 TATTATTTAAATATATAAATAATATTAT
1 TATTA-TTAAATATATAAATAATATTAT
*
4267983 TCATTATTAAATATATAAAAATTTATATTAT
1 T-ATTATTAAATATAT--AAA-TAATATTAT
*
4268014 ATATTATTAAA-ATAAAAATATAATATCT-T
1 -TATTATTAAATAT-ATAA-ATAATAT-TAT
** * *
4268043 ATATTATTATAATATAATTGATTATTTTAT
1 -TATTATTA-AATAT-ATAAATAATATTAT
* * *
4268073 ATAATATTAAAAATAT-AATATTA-TAT
1 -TATTATTAAATATATAAATAATATTAT
4268099 TATTA-TAAATATTAATAAATAA
1 TATTATTAAATA-T-ATAAATAA
4268121 ATAAATAATA
Statistics
Matches: 107, Mismatches: 17, Indels: 29
0.70 0.11 0.19
Matches are distributed among these distances:
24 5 0.05
25 5 0.05
26 5 0.05
27 7 0.07
28 13 0.12
29 26 0.24
30 23 0.21
31 22 0.21
32 1 0.01
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (27 bp):
TATTATTAAATATATAAATAATATTAT
Found at i:4268045 original size:29 final size:28
Alignment explanation
Indices: 4267954--4268056 Score: 86
Period size: 29 Copynumber: 3.5 Consensus size: 28
4267944 CTTTATTAAA
*
4267954 ATATTATTTAAATATATAAA-TAATATTAT
1 ATATTA-TTAAA-ATAAAAATTAATATTAT
*
4267983 -TCATTATTAAATATATAAAAATTTATATTAT
1 AT-ATTATT-AA-A-ATAAAAATTAATATTAT
4268014 ATATTATTAAAATAAAAATATAATATCT-T
1 ATATTATTAAAATAAAAAT-TAATAT-TAT
*
4268043 ATATTATTATAATA
1 ATATTATTAAAATA
4268057 TAATTGATTA
Statistics
Matches: 63, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
28 11 0.17
29 26 0.41
30 11 0.17
31 14 0.22
32 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (28 bp):
ATATTATTAAAATAAAAATTAATATTAT
Found at i:4268097 original size:22 final size:23
Alignment explanation
Indices: 4268072--4268115 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
4268062 GATTATTTTA
4268072 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
4268094 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
4268116 AATAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:4268369 original size:42 final size:41
Alignment explanation
Indices: 4268310--4268413 Score: 136
Period size: 42 Copynumber: 2.5 Consensus size: 41
4268300 CCCGAATTCT
*
4268310 CGTGTTTGTTTCACGTAATTCATTTTCCGGAAAATATTTTTC
1 CGTGTTTGTTTCACGTAATTCATTTTCCGGAAAAT-GTTTTC
**
4268352 CGTGTTTGTTTCACGTAATTTGTTTTCCGGAAAATGTTTTC
1 CGTGTTTGTTTCACGTAATTCATTTTCCGGAAAATGTTTTC
* **
4268393 CAGTTTTTGCCTCACGTAATT
1 C-GTGTTTGTTTCACGTAATT
4268414 GGTTTTCCTG
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 6 0.11
42 49 0.89
ACGTcount: A:0.19, C:0.17, G:0.16, T:0.47
Consensus pattern (41 bp):
CGTGTTTGTTTCACGTAATTCATTTTCCGGAAAATGTTTTC
Found at i:4268646 original size:22 final size:23
Alignment explanation
Indices: 4268616--4268659 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
4268606 TTTATTAATT
4268616 TATTAATATTTATAATAATATAA
1 TATTAATATTTATAATAATATAA
* *
4268639 TATT-ATATTTTTAATATTATA
1 TATTAATATTTATAATAATATA
4268660 TAAAATAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAATATTTATAATAATATAA
Found at i:4268676 original size:17 final size:17
Alignment explanation
Indices: 4268654--4268688 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4268644 TATTTTTAAT
4268654 ATTATATAAAATAATCA
1 ATTATATAAAATAATCA
* *
4268671 ATTATATTATATAATCA
1 ATTATATAAAATAATCA
4268688 A
1 A
4268689 AATTATATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTATATAAAATAATCA
Found at i:4268678 original size:31 final size:32
Alignment explanation
Indices: 4268608--4268666 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
4268598 AAATATTATT
4268608 TATTA-ATTTATTAATATTTATAATAATATAA
1 TATTATATTTATTAATATTTATAATAATATAA
4268639 TATTATATTT-TTAATATTATATAA-AATA
1 TATTATATTTATTAATATT-TATAATAATA
4268667 ATCAATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
31 17 0.65
32 9 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
TATTATATTTATTAATATTTATAATAATATAA
Found at i:4270366 original size:23 final size:23
Alignment explanation
Indices: 4270340--4270384 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
4270330 AATAATATTT
4270340 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
4270363 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
4270385 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:4270503 original size:19 final size:19
Alignment explanation
Indices: 4270481--4270543 Score: 60
Period size: 21 Copynumber: 3.3 Consensus size: 19
4270471 ATAAAAATAC
4270481 TATTTAATAATAAATAAAT
1 TATTTAATAATAAATAAAT
*
4270500 TATTTTTAATAATAAA-AAAG
1 TA--TTTAATAATAAATAAAT
*
4270520 T-TTT-ATGATAAATAATAT
1 TATTTAATAATAAATAA-AT
4270538 TATTTA
1 TATTTA
4270544 TTGTATTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
16 7 0.20
17 5 0.14
18 2 0.06
19 5 0.14
20 4 0.11
21 12 0.34
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
TATTTAATAATAAATAAAT
Found at i:4270700 original size:14 final size:14
Alignment explanation
Indices: 4270667--4270702 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
4270657 AATTGTAATT
*
4270667 CATTTTACGGAAAA
1 CATTTTCCGGAAAA
4270681 CATTTTCCGGAAAA
1 CATTTTCCGGAAAA
*
4270695 CTTTTTCC
1 CATTTTCC
4270703 AGAATTCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (14 bp):
CATTTTCCGGAAAA
Found at i:4270746 original size:15 final size:15
Alignment explanation
Indices: 4270699--4270740 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
4270689 GGAAAACTTT
4270699 TTCCAG-AATTCAAA
1 TTCCAGTAATTCAAA
* *
4270713 GTACAGTAATTCAAA
1 TTCCAGTAATTCAAA
4270728 TTCCAGTAATTCA
1 TTCCAGTAATTCA
4270741 TTTTCCGGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (15 bp):
TTCCAGTAATTCAAA
Found at i:4270889 original size:42 final size:42
Alignment explanation
Indices: 4270830--4270949 Score: 177
Period size: 42 Copynumber: 2.9 Consensus size: 42
4270820 ATGACTTACG
* * *
4270830 TTCCGGAAAACCAATTACGTAAAACAAACACTGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
* *
4270872 TTCCGAAAAACGAATTACGTGAAACAAACGCGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
* *
4270914 TTCCGGAAAATGAATTACGTGAAATAAACACGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
4270950 TTCGGGGAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.46, C:0.18, G:0.17, T:0.18
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:4278332 original size:170 final size:168
Alignment explanation
Indices: 4277915--4278335 Score: 585
Period size: 169 Copynumber: 2.5 Consensus size: 168
4277905 ATATGTTGTT
* *
4277915 CTTCCCCTGGAACGAGCCTTTCCTTTTTGTCAAATTTTATCAGCATACGTCACTAAATTATGTTG
1 CTTCCCCTGGAACGAGCCTTTCCTTTTTGTCAAATTTTATCAGCATGCCTCACTAAATTATGTTG
* * * *
4277980 AATTAATGATGTTGGTAGTCGGGGAAATATTCTCGTCAACCCAATTTATGTTTGATGGATGAGAC
66 AATT-ATGATGTTGGCAGTAGGGGAAATATTCCCGTCAACCCAATTTATATTTGATGGATGAGAC
*
4278045 ACTATGACATGGCAGAGATTCTCTAAGAAAAGGAAAACA
130 ACTATGACATGGCAGAGATCCTCTAAGAAAAGGAAAACA
* * *
4278084 CTTCCCCTGGAACGAGCCTTTCCTTTTTGTCAGATTTGAT-ATGTATGCCTCACTAAATTATGTT
1 CTTCCCCTGGAACGAGCCTTTCCTTTTTGTCAAATTTTATCA-GCATGCCTCACTAAATTATGTT
* * *
4278148 AAATTTATGATGTTGGCAGTTATGGG-ACTATTCCCGTCAACCCAATTTATATTTGATGGATGAG
65 GAA-TTATGATGTTGGCAG-TAGGGGAAATATTCCCGTCAACCCAATTTATATTTGATGGATGAG
* * * *
4278212 ACACTATGACATGGTAGAGATCCTTTAAGAAATGGAAAAACG
128 ACACTATGACATGGCAGAGATCCTCTAAGAAAAGG-AAAACA
* * *
4278254 CTTCCCCTGGAACAAGCTTTTCCTTTTTGTCAAATTTTATCGGCATGCCTCACTAAATTATGTTG
1 CTTCCCCTGGAACGAGCCTTTCCTTTTTGTCAAATTTTATCAGCATGCCTCACTAAATTATGTTG
*
4278319 AAGGTATGATGTTGGCA
66 AA-TTATGATGTTGGCA
4278336 ATCTGGAACT
Statistics
Matches: 221, Mismatches: 26, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
168 1 0.00
169 137 0.62
170 83 0.38
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (168 bp):
CTTCCCCTGGAACGAGCCTTTCCTTTTTGTCAAATTTTATCAGCATGCCTCACTAAATTATGTTG
AATTATGATGTTGGCAGTAGGGGAAATATTCCCGTCAACCCAATTTATATTTGATGGATGAGACA
CTATGACATGGCAGAGATCCTCTAAGAAAAGGAAAACA
Found at i:4278400 original size:20 final size:21
Alignment explanation
Indices: 4278375--4278418 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
4278365 GTCTTCACTA
*
4278375 TTTTATT-TGTTATCTATCAT
1 TTTTATTATCTTATCTATCAT
4278395 TTTTATTATCTTATCTATCAT
1 TTTTATTATCTTATCTATCAT
4278416 TTT
1 TTT
4278419 CAATGACAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.20, C:0.11, G:0.02, T:0.66
Consensus pattern (21 bp):
TTTTATTATCTTATCTATCAT
Found at i:4281168 original size:26 final size:28
Alignment explanation
Indices: 4281137--4281201 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 28
4281127 TCATTTCCCT
*
4281137 AATTAATAAATAATA-T-ACA-AATTTA
1 AATTAATAAATAATACTAAAAGAATTTA
*
4281162 AATTTA-AAATAATACTAAAAGAATTTA
1 AATTAATAAATAATACTAAAAGAATTTA
4281189 AATTAATATAATA
1 AATTAATA-AATA
4281202 TTCACAACAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
24 8 0.25
25 6 0.19
26 2 0.06
27 11 0.34
28 1 0.03
29 4 0.12
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (28 bp):
AATTAATAAATAATACTAAAAGAATTTA
Found at i:4281368 original size:7 final size:7
Alignment explanation
Indices: 4281348--4281392 Score: 65
Period size: 7 Copynumber: 6.4 Consensus size: 7
4281338 AAAATCTTAG
4281348 AAAATAA
1 AAAATAA
4281355 TAAAATAA
1 -AAAATAA
4281363 AAAAT-A
1 AAAATAA
*
4281369 AATATAA
1 AAAATAA
4281376 AAAATAA
1 AAAATAA
4281383 AAAATAA
1 AAAATAA
4281390 AAA
1 AAA
4281393 TTTTTACCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
6 5 0.15
7 22 0.65
8 7 0.21
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (7 bp):
AAAATAA
Found at i:4281381 original size:20 final size:21
Alignment explanation
Indices: 4281351--4281390 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
4281341 ATCTTAGAAA
4281351 ATAATAAAATAAAAAATAAAT
1 ATAATAAAATAAAAAATAAAT
4281372 ATAA-AAAATAAAAAATAAA
1 ATAATAAAATAAAAAATAAA
4281391 AATTTTTACC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (21 bp):
ATAATAAAATAAAAAATAAAT
Found at i:4281393 original size:13 final size:14
Alignment explanation
Indices: 4281348--4281392 Score: 65
Period size: 13 Copynumber: 3.2 Consensus size: 14
4281338 AAAATCTTAG
4281348 AAAATAATAAAATAA
1 AAAATAA-AAAATAA
*
4281363 AAAAT-AAATATAA
1 AAAATAAAAAATAA
4281376 AAAATAAAAAATAA
1 AAAATAAAAAATAA
4281390 AAA
1 AAA
4281393 TTTTTACCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 11 0.41
14 11 0.41
15 5 0.19
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (14 bp):
AAAATAAAAAATAA
Found at i:4288752 original size:23 final size:23
Alignment explanation
Indices: 4288726--4288780 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
4288716 TTATAATTGT
*
4288726 TTAATTGTAGCCGTTATACCAAC
1 TTAATTGCAGCCGTTATACCAAC
4288749 TTAATTGCAGCCGTTATACCAAC
1 TTAATTGCAGCCGTTATACCAAC
4288772 TTAATTGCA
1 TTAATTGCA
4288781 CTTGAATTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.35
Consensus pattern (23 bp):
TTAATTGCAGCCGTTATACCAAC
Found at i:4293475 original size:25 final size:25
Alignment explanation
Indices: 4293447--4293507 Score: 113
Period size: 25 Copynumber: 2.4 Consensus size: 25
4293437 AGTTTCGTCT
4293447 ATCTTCTAGAAATGCTGACTGTACC
1 ATCTTCTAGAAATGCTGACTGTACC
*
4293472 ATCTTCTAGAAATGTTGACTGTACC
1 ATCTTCTAGAAATGCTGACTGTACC
4293497 ATCTTCTAGAA
1 ATCTTCTAGAA
4293508 GCTATTGACT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (25 bp):
ATCTTCTAGAAATGCTGACTGTACC
Found at i:4300350 original size:17 final size:19
Alignment explanation
Indices: 4300330--4300375 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
4300320 ATTAAAAGAG
4300330 AAATAAAAT-A-AATAAAT
1 AAATAAAATAACAATAAAT
4300347 AAATAAACCATAACAATAAAT
1 AAATAAA--ATAACAATAAAT
4300368 AAATAAAA
1 AAATAAAA
4300376 AGAAACTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 7 0.28
19 3 0.12
20 1 0.04
21 14 0.56
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.20
Consensus pattern (19 bp):
AAATAAAATAACAATAAAT
Found at i:4304814 original size:12 final size:11
Alignment explanation
Indices: 4304796--4304847 Score: 54
Period size: 12 Copynumber: 4.7 Consensus size: 11
4304786 TTTTCAAGTG
4304796 TTTATTTTTCC
1 TTTATTTTTCC
*
4304807 TCTTATTTTTTC
1 T-TTATTTTTCC
*
4304819 TTTCAATTTTCC
1 TTT-ATTTTTCC
4304831 TTTA--TTTCC
1 TTTATTTTTCC
4304840 TTTATTTT
1 TTTATTTT
4304848 CATTTTTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
9 9 0.26
11 6 0.18
12 19 0.56
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTATTTTTCC
Found at i:4309687 original size:14 final size:14
Alignment explanation
Indices: 4309668--4309699 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
4309658 AGGTATCAAA
4309668 GGATTCAAGTTATG
1 GGATTCAAGTTATG
*
4309682 GGATTCAAGTTCTG
1 GGATTCAAGTTATG
4309696 GGAT
1 GGAT
4309700 CCAGGTGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.25, C:0.09, G:0.31, T:0.34
Consensus pattern (14 bp):
GGATTCAAGTTATG
Found at i:4312672 original size:41 final size:40
Alignment explanation
Indices: 4312553--4312674 Score: 172
Period size: 41 Copynumber: 3.0 Consensus size: 40
4312543 AAAACTTCGT
* * *
4312553 TAAATACTCATACTTTAATGGTGTTTTTATACAAACGACGT
1 TAAA-ACTCATACTTTAGTGGTGTTTTTATACAAACGCCGC
*
4312594 TATAAACTCATACTTTAGTGGTATTTTTATACAAACGCCGC
1 TA-AAACTCATACTTTAGTGGTGTTTTTATACAAACGCCGC
*
4312635 TAAAGACTCGTACTTTAGTGGTGTTTTTATACAAACGCCG
1 TAAA-ACTCATACTTTAGTGGTGTTTTTATACAAACGCCG
4312675 TAATAAAAAT
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
40 2 0.03
41 69 0.95
42 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (40 bp):
TAAAACTCATACTTTAGTGGTGTTTTTATACAAACGCCGC
Found at i:4313378 original size:21 final size:21
Alignment explanation
Indices: 4313352--4313410 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
4313342 TGATTTATTA
4313352 TTATGGATTTCAAGTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
* *
4313373 TTATGGACTTCAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
*
4313394 TTATGGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
4313411 ATTGGATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.20, C:0.08, G:0.22, T:0.49
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:4324607 original size:27 final size:27
Alignment explanation
Indices: 4324569--4324633 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
4324559 TTTGTTAAAC
* *
4324569 GAGC-CGAGTCGAACTCGAGTATTGCT
1 GAGCTCGACTCGAACTCAAGTATTGCT
4324595 GAGCTCGACTCGAACTCAAGTATTGCT
1 GAGCTCGACTCGAACTCAAGTATTGCT
4324622 GAGCTCGACTCG
1 GAGCTCGACTCG
4324634 TTCTCGAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 4 0.11
27 32 0.89
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.23
Consensus pattern (27 bp):
GAGCTCGACTCGAACTCAAGTATTGCT
Found at i:4325771 original size:24 final size:25
Alignment explanation
Indices: 4325742--4325791 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
4325732 TCAATTCATT
4325742 ATTTA-TTTAAGTCAATTTTT-GATC
1 ATTTATTTTAAGTC-ATTTTTCGATC
4325766 ATTTATTTTAAGTCATTTTTCGATC
1 ATTTATTTTAAGTCATTTTTCGATC
4325791 A
1 A
4325792 AGTTTGAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.28, C:0.10, G:0.08, T:0.54
Consensus pattern (25 bp):
ATTTATTTTAAGTCATTTTTCGATC
Found at i:4326830 original size:21 final size:21
Alignment explanation
Indices: 4326804--4326853 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
4326794 CATGCAAAAG
4326804 TCAAACAAATTAAAAAGACAA
1 TCAAACAAATTAAAAAGACAA
*
4326825 TCAAACAAATTAAAAAGACGA
1 TCAAACAAATTAAAAAGACAA
4326846 TCAAACAA
1 TCAAACAA
4326854 TCAATTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.64, C:0.16, G:0.06, T:0.14
Consensus pattern (21 bp):
TCAAACAAATTAAAAAGACAA
Found at i:4328734 original size:111 final size:111
Alignment explanation
Indices: 4328540--4328880 Score: 454
Period size: 111 Copynumber: 3.1 Consensus size: 111
4328530 CCCAGGAAAT
* * * * *
4328540 ATTGAATCGAGGTAGACTTGTTCC-ATTGTCACTCATGGAATATCAAATCTTGAAAGAGAAAGAT
1 ATTGAATCGGGGTAGACTTGTTCCGCTT-TCACTCAGGGAATATCAAATCTTGGAAGAGAAGGAT
4328604 ATGTTCTGCTTCTTCTAAGGGAATATCAGATCTGGGAAAATTGATCC
65 ATGTTCTGCTTCTTCTAAGGGAATATCAGATCTGGGAAAATTGATCC
* * *
4328651 ATTGAATTGGGGTAGACTTGTTCCGCTTTCACTCAGGGAATATCAAATCTTGGAAGAGATGGATC
1 ATTGAATCGGGGTAGACTTGTTCCGCTTTCACTCAGGGAATATCAAATCTTGGAAGAGAAGGATA
* ** *
4328716 TATTCTGCTTCTTCTAAGGGAATATCAGATCTTAGAAAGTTGATCC
66 TGTTCTGCTTCTTCTAAGGGAATATCAGATCTGGGAAAATTGATCC
* * * *
4328762 ATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAGAGAGGGATT
1 ATTGAATCGGGGTAGACTTGTTCCGCTTTCACTCAGGGAATATCAAATCTTGGAAGAGAAGGATA
* * *
4328827 TGTTCCGCTTCTT-TGAAAGGGAATATCAGATCTGTGG-GAATTAATCC
66 TGTTCTGCTTCTTCT--AAGGGAATATCAGATCTG-GGAAAATTGATCC
4328874 ATTGAAT
1 ATTGAAT
4328881 TGGGATCGAA
Statistics
Matches: 202, Mismatches: 24, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
110 1 0.00
111 167 0.83
112 33 0.16
113 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Consensus pattern (111 bp):
ATTGAATCGGGGTAGACTTGTTCCGCTTTCACTCAGGGAATATCAAATCTTGGAAGAGAAGGATA
TGTTCTGCTTCTTCTAAGGGAATATCAGATCTGGGAAAATTGATCC
Found at i:4341273 original size:24 final size:25
Alignment explanation
Indices: 4341235--4341283 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
4341225 ATATATATCA
*
4341235 TTTTATTTCTCTTTTT-CTTTGTTT
1 TTTTATTTCTATTTTTGCTTTGTTT
* *
4341259 TTTTATTTTTATTTTTGTTTTGTTT
1 TTTTATTTCTATTTTTGCTTTGTTT
4341284 GTTAGAGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.06, C:0.06, G:0.06, T:0.82
Consensus pattern (25 bp):
TTTTATTTCTATTTTTGCTTTGTTT
Found at i:4341683 original size:18 final size:18
Alignment explanation
Indices: 4341650--4341684 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4341640 CCCCTTTGTT
*
4341650 TTTATTTTATTGTATTTA
1 TTTATTTTATTATATTTA
*
4341668 TTTATTTTTTTATATTT
1 TTTATTTTATTATATTT
4341685 CAAATGATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTATTTTATTATATTTA
Found at i:4346458 original size:21 final size:21
Alignment explanation
Indices: 4346341--4346478 Score: 68
Period size: 21 Copynumber: 6.7 Consensus size: 21
4346331 ACGCGAAATA
**
4346341 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
4346361 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
* *
4346381 AAAATCGCAACACGATTCTT-T
1 AAAATCGCAACGCGATT-TTCC
* ** *
4346402 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* **
4346423 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
* * * *
4346444 AGAATCGCAACGCGAATAT-G
1 AAAATCGCAACGCGATTTTCC
4346464 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
4346479 ACACATAAAT
Statistics
Matches: 86, Mismatches: 28, Indels: 8
0.70 0.23 0.07
Matches are distributed among these distances:
19 1 0.01
20 38 0.44
21 45 0.52
22 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:4346471 original size:20 final size:20
Alignment explanation
Indices: 4346446--4346639 Score: 87
Period size: 20 Copynumber: 9.7 Consensus size: 20
4346436 GATTTTCCAG
* *
4346446 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
4346466 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
4346486 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
4346506 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
4346526 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
4346546 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
4346566 TATCGCAACGCGTATC-CATA
1 AATCGCAACGCG-AACACATA
* ** *
4346586 AATCGCAGCGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
4346607 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
4346627 AATCGCAACGCGA
1 AATCGCAACGCGA
4346640 TATTTAAAGC
Statistics
Matches: 147, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
19 3 0.02
20 129 0.88
21 14 0.10
22 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:4346493 original size:40 final size:40
Alignment explanation
Indices: 4346446--4346638 Score: 133
Period size: 40 Copynumber: 4.8 Consensus size: 40
4346436 GATTTTCCAG
*
4346446 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACACATA
1 AATCGCAACGCGAATACGAAAATCGCAACGCGTAAC-CATA
* * * * * *
4346486 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGAATACGAAAATCGCAACGCGTAACCATA
* * * * * *
4346526 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAAAATCGCAACGCGTAACCATA
* * * *
4346566 TATCGCAACGCGTAT-CCATAAATCGC-A-GCGATAATACATAA
1 AATCGCAACGCGAATACGA-AAATCGCAACGCG-TAA-CCAT-A
* * *
4346607 AATCGCAACGCGTATCCGTAAATCGCAACGCG
1 AATCGCAACGCGAATACGAAAATCGCAACGCG
4346639 ATATTTAAAG
Statistics
Matches: 127, Mismatches: 18, Indels: 13
0.80 0.11 0.08
Matches are distributed among these distances:
38 3 0.02
39 4 0.03
40 91 0.72
41 24 0.19
42 2 0.02
43 3 0.02
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (40 bp):
AATCGCAACGCGAATACGAAAATCGCAACGCGTAACCATA
Found at i:4346515 original size:60 final size:60
Alignment explanation
Indices: 4346446--4346639 Score: 205
Period size: 60 Copynumber: 3.2 Consensus size: 60
4346436 GATTTTCCAG
4346446 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
* * ** * * * *
4346506 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATC-CGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACACATAAATCGCAACGCGTATCCGTA
* * * ** *
4346566 TATCGCAACGCG--TATCCATAAATCGCAGCGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATAT-GA-AAATCGCAACGCGAACACAT-AAATCGCAACGCGTATCCGTA
4346627 AATCGCAACGCGA
1 AATCGCAACGCGA
4346640 TATTTAAAGC
Statistics
Matches: 106, Mismatches: 22, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
58 1 0.01
59 1 0.01
60 71 0.67
61 33 0.31
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
Found at i:4347057 original size:33 final size:33
Alignment explanation
Indices: 4347018--4347088 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
4347008 TTCACTTAGA
4347018 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
***
4347051 TTTCATTTCGCGTTGTTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
4347084 TTTCA
1 TTTCA
4347089 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.17, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:4347194 original size:21 final size:20
Alignment explanation
Indices: 4347168--4347273 Score: 91
Period size: 21 Copynumber: 5.5 Consensus size: 20
4347158 TGCAGAAGAG
4347168 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
4347189 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
4347209 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
4347230 TCACAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
4347244 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
4347263 TCGCAACGAGA
1 TCGCAACGAGA
4347274 GAATCGCAAC
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 2 0.03
19 11 0.17
20 16 0.24
21 25 0.38
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:4347225 original size:41 final size:38
Alignment explanation
Indices: 4347161--4347277 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
4347151 TTCAATTTGC
* *
4347161 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
4347199 AGAATGACTGTCGCAACGAGAGAAATGAAAATCACAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
4347240 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
4347273 AGAAT
1 AGAAT
4347278 CGCAACGCGA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
33 22 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.47, C:0.17, G:0.25, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:4347250 original size:14 final size:14
Alignment explanation
Indices: 4347228--4347284 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
4347218 GAGAAATGAA
*
4347228 AATCACAACGAGAG
1 AATCGCAACGAGAG
*
4347242 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
4347261 AATCGCAACGAGAG
1 AATCGCAACGAGAG
4347275 AATCGCAACG
1 AATCGCAACG
4347285 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:4347260 original size:33 final size:33
Alignment explanation
Indices: 4347220--4347289 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
4347210 CGCAACGAGA
4347220 GAAATGAAAATCACAACGAGAGAATCGCAACGC
1 GAAATGAAAATCACAACGAGAGAATCGCAACGC
*
4347253 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCACAACGAGAGAATCGCAACGC
4347286 GAAA
1 GAAA
4347290 CCAAAATCGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.49, C:0.20, G:0.23, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCACAACGAGAGAATCGCAACGC
Found at i:4347296 original size:33 final size:33
Alignment explanation
Indices: 4347226--4347300 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
4347216 GAGAGAAATG
* **
4347226 AAAATCACAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
4347259 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
4347292 AAAATCGCA
1 AAAATCGCA
4347301 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.48, C:0.24, G:0.20, T:0.08
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:4347318 original size:19 final size:19
Alignment explanation
Indices: 4347296--4347421 Score: 110
Period size: 19 Copynumber: 7.1 Consensus size: 19
4347286 GAAACCAAAA
*
4347296 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
4347315 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
4347329 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
4347348 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
4347362 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
***
4347381 TCGCGTTGCGACAGTCATT
1 TCGCGTTGCGATTTTCATT
*
4347400 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
4347420 TC
1 TC
4347422 AACCAAAAGA
Statistics
Matches: 84, Mismatches: 12, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
14 20 0.24
16 6 0.07
17 6 0.07
19 37 0.44
20 15 0.18
ACGTcount: A:0.11, C:0.25, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:4347337 original size:14 final size:14
Alignment explanation
Indices: 4347318--4347374 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
4347308 TTTCATTTCG
4347318 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
4347332 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
4347351 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
4347365 CGTTGCGATT
1 CGTTGCGATT
4347375 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:4347412 original size:39 final size:33
Alignment explanation
Indices: 4347301--4347421 Score: 188
Period size: 33 Copynumber: 3.5 Consensus size: 33
4347291 CAAAATCGCA
4347301 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
4347334 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
4347367 TTGCGATTTTCATTTCGCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCATTTCGCGTT--G-C-G--ATTCTCTCG
4347406 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
4347422 AACCAAAAGA
Statistics
Matches: 82, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
33 54 0.66
35 1 0.01
36 1 0.01
37 1 0.01
39 25 0.30
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:4347848 original size:12 final size:12
Alignment explanation
Indices: 4347831--4347855 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4347821 TCTTCGGGGA
4347831 CTTTTTCTTCTT
1 CTTTTTCTTCTT
4347843 CTTTTTCTTCTT
1 CTTTTTCTTCTT
4347855 C
1 C
4347856 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Done.