Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008303.1 Hibiscus syriacus cultivar Beakdansim tig00110989_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: 1196166
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:227496 original size:21 final size:20
Alignment explanation
Indices: 227452--227525 Score: 58
Period size: 21 Copynumber: 3.6 Consensus size: 20
227442 ATAGTCAGAT
* *
227452 TCGCATTGCGATTTATGTAA
1 TCGCATTGCGATTTACGAAA
*
227472 TCGCGTTGCGATTTACGAAAA
1 TCGCATTGCGATTTACG-AAA
** **
227493 TCGCAACGCGAATTTGGGAAA
1 TCGCATTGCG-ATTTACGAAA
*
227514 TCGCAATGCGAT
1 TCGCATTGCGAT
227526 AGTCAGAATC
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 17 0.40
21 21 0.49
22 5 0.12
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.28
Consensus pattern (20 bp):
TCGCATTGCGATTTACGAAA
Found at i:228424 original size:5 final size:5
Alignment explanation
Indices: 228414--228438 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
228404 ACTTTTCTCT
228414 CAACA CAACA CAACA CAACA CAACA
1 CAACA CAACA CAACA CAACA CAACA
228439 GAGCTGGTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.40, G:0.00, T:0.00
Consensus pattern (5 bp):
CAACA
Found at i:231041 original size:18 final size:19
Alignment explanation
Indices: 231018--231055 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
231008 TATTAATATT
231018 TCTGAAGCATATA-TTCAA
1 TCTGAAGCATATATTTCAA
*
231036 TCTGAAGCATGTATTTCAA
1 TCTGAAGCATATATTTCAA
231055 T
1 T
231056 TCCAATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (19 bp):
TCTGAAGCATATATTTCAA
Found at i:236078 original size:30 final size:30
Alignment explanation
Indices: 236044--236132 Score: 88
Period size: 32 Copynumber: 2.9 Consensus size: 30
236034 AAAGGACCTA
*
236044 TCCATATATTCCGAAGAACATAGGTAACTG
1 TCCATATATCCCGAAGAACATAGGTAACTG
* *
236074 TCCATATGTCCCGAAGGACATAGGTAATCCTG
1 TCCATATATCCCGAAGAACATAGGTAA--CTG
** * * *
236106 TTAATATGTCCCGAAGGATATAGGTAA
1 TCCATATATCCCGAAGAACATAGGTAA
236133 ACTATTCATA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
30 24 0.47
32 27 0.53
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (30 bp):
TCCATATATCCCGAAGAACATAGGTAACTG
Found at i:236160 original size:31 final size:31
Alignment explanation
Indices: 236054--236163 Score: 123
Period size: 32 Copynumber: 3.5 Consensus size: 31
236044 TCCATATATT
* *
236054 CCGAAGAACATAGGT-AACTGTCCATATGTC
1 CCGAAGGACATAGGTAAACTGTTCATATGTC
* *
236084 CCGAAGGACATAGGTAATCCTGTTAATATGTC
1 CCGAAGGACATAGGTAA-ACTGTTCATATGTC
* *
236116 CCGAAGGATATAGGTAAACTATTCATATGTC
1 CCGAAGGACATAGGTAAACTGTTCATATGTC
* * *
236147 TCAAAAGACATAGGTAA
1 CCGAAGGACATAGGTAA
236164 CCCTTGACTC
Statistics
Matches: 66, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
30 14 0.21
31 25 0.38
32 27 0.41
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.25
Consensus pattern (31 bp):
CCGAAGGACATAGGTAAACTGTTCATATGTC
Found at i:236945 original size:18 final size:16
Alignment explanation
Indices: 236922--236955 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
236912 ACGTTTAATG
236922 TATACATAATCATATATT
1 TATACAT-ATCA-ATATT
236940 TATACATATCAATATT
1 TATACATATCAATATT
236956 CTAAATAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 4 0.25
18 7 0.44
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (16 bp):
TATACATATCAATATT
Found at i:239184 original size:18 final size:18
Alignment explanation
Indices: 239160--239209 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
239150 ATAATATTTA
239160 TGAAGCATATATTTAATTC
1 TGAAGCATATATTT-ATTC
*
239179 -GAAGCATATATTTGTTC
1 TGAAGCATATATTTATTC
*
239196 TGAAGCATGTATTT
1 TGAAGCATATATTT
239210 CGATTCCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 3 0.11
18 25 0.89
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (18 bp):
TGAAGCATATATTTATTC
Found at i:241864 original size:14 final size:15
Alignment explanation
Indices: 241835--241868 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
241825 ACCAATTTGA
241835 CATATTTCATACTTTT
1 CATATTTCA-ACTTTT
241851 CATATTTC-ACTTTT
1 CATATTTCAACTTTT
241865 CATA
1 CATA
241869 GTCCAATGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
16 8 0.44
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.53
Consensus pattern (15 bp):
CATATTTCAACTTTT
Found at i:244761 original size:314 final size:314
Alignment explanation
Indices: 244192--244821 Score: 1143
Period size: 314 Copynumber: 2.0 Consensus size: 314
244182 TTCCTACTAA
* *
244192 AACCTTAATTTCAAACTAAATTATTTTCTTATGACAAAAATATATAACTTTTAAAATTATATTTT
1 AACCTTAATTCCAAACTAAATTATTTGCTTATGACAAAAATATATAACTTTTAAAATTATATTTT
* *
244257 TGGTTCCTATACTTTGACAACTTTGTACTTCGGCCACTAAACTTTCCAAACTCATATTTTAGTCA
66 TAGTTCCTATACTTTGACAACTTTGTACTTCAGCCACTAAACTTTCCAAACTCATATTTTAGTCA
*
244322 CTAACCAAAATTTAGGATATTACATGTGACGGAAGCGATAACTCGATTCCCAGTTCGATATTTCC
131 CTAACCAAAATTTAGGATATTACACGTGACGGAAGCGATAACTCGATTCCCAGTTCGATATTTCC
244387 TACAACAACACGATGTCGAATCAAATTCCCAATAAACACCCAATAAATAATTTCTATATCACTAT
196 TACAACAACACGATGTCGAATCAAATTCCCAATAAACACCCAATAAATAATTTCTATATCACTAT
244452 TAGGGATGGGCATGAGATCCGAACCCGACCTAACCCGATCGGGTTTGGTTTTTT
261 TAGGGATGGGCATGAGATCCGAACCCGACCTAACCCGATCGGGTTTGGTTTTTT
*
244506 AACCTTAATTCCGAACTAAATTATTTGCTTATGACAAAAATATATAACTTTTAAAATTATATTTT
1 AACCTTAATTCCAAACTAAATTATTTGCTTATGACAAAAATATATAACTTTTAAAATTATATTTT
* *
244571 TAGTTCCTATACTTTTATAACTTTGTACTTCAGCCACTAAACTTTCCAAACTCATATTTTAGTCA
66 TAGTTCCTATACTTTGACAACTTTGTACTTCAGCCACTAAACTTTCCAAACTCATATTTTAGTCA
*
244636 CTAACCAAAATTTGGGATATTACACGTGACGGAAGCGATAACTCGATTCCCAGTTCGATATTTCC
131 CTAACCAAAATTTAGGATATTACACGTGACGGAAGCGATAACTCGATTCCCAGTTCGATATTTCC
* *
244701 TACAACAACACGATGTCGAATCAAATTCCCAATAAACACCCAATAAGTAATTTCTATATCACTGT
196 TACAACAACACGATGTCGAATCAAATTCCCAATAAACACCCAATAAATAATTTCTATATCACTAT
* *
244766 TAGGGATGGGCATGGGATCCGAACCCGACCTGACCCGATCGGGTTTGGTTTTTT
261 TAGGGATGGGCATGAGATCCGAACCCGACCTAACCCGATCGGGTTTGGTTTTTT
244820 AA
1 AA
244822 ATGTGATATT
Statistics
Matches: 303, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
314 303 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (314 bp):
AACCTTAATTCCAAACTAAATTATTTGCTTATGACAAAAATATATAACTTTTAAAATTATATTTT
TAGTTCCTATACTTTGACAACTTTGTACTTCAGCCACTAAACTTTCCAAACTCATATTTTAGTCA
CTAACCAAAATTTAGGATATTACACGTGACGGAAGCGATAACTCGATTCCCAGTTCGATATTTCC
TACAACAACACGATGTCGAATCAAATTCCCAATAAACACCCAATAAATAATTTCTATATCACTAT
TAGGGATGGGCATGAGATCCGAACCCGACCTAACCCGATCGGGTTTGGTTTTTT
Found at i:250823 original size:22 final size:22
Alignment explanation
Indices: 250795--250836 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
250785 CAAATCCATA
250795 ACTTTAATAAAATAATAATTTC
1 ACTTTAATAAAATAATAATTTC
*
250817 ACTTTAATATAATAATAATT
1 ACTTTAATAAAATAATAATT
250837 GCATGATTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (22 bp):
ACTTTAATAAAATAATAATTTC
Found at i:252113 original size:21 final size:21
Alignment explanation
Indices: 252084--252130 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
252074 ATTCTGACTA
252084 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* *
252105 TCGCGTTGCGATTTCCCTAAT
1 TCGCATTGCGATTTCCCAAAT
252126 TCGCA
1 TCGCA
252131 ACGCGAATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.19, C:0.30, G:0.17, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:252136 original size:21 final size:21
Alignment explanation
Indices: 252091--252136 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
252081 CTATCGCATT
***
252091 GCGATTTCCCAAATTCGCGTT
1 GCGATTTCCCAAATTCGCAAC
*
252112 GCGATTTCCCTAATTCGCAAC
1 GCGATTTCCCAAATTCGCAAC
252133 GCGA
1 GCGA
252137 ATACGTAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (21 bp):
GCGATTTCCCAAATTCGCAAC
Found at i:253039 original size:24 final size:24
Alignment explanation
Indices: 253012--253065 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
253002 GTATTCGAAA
253012 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
253036 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
253060 TTTGAT
1 TTTGAT
253066 GATTTTCAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:253270 original size:14 final size:14
Alignment explanation
Indices: 253251--253285 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
253241 TAAAAAGAAG
253251 AAGAAAAATCCCCA
1 AAGAAAAATCCCCA
* *
253265 AAGAAAAGTCCCCG
1 AAGAAAAATCCCCA
253279 AAGAAAA
1 AAGAAAA
253286 TGCCACGGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.57, C:0.23, G:0.14, T:0.06
Consensus pattern (14 bp):
AAGAAAAATCCCCA
Found at i:255631 original size:33 final size:33
Alignment explanation
Indices: 255594--255774 Score: 200
Period size: 33 Copynumber: 5.3 Consensus size: 33
255584 GGAAATTACT
255594 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
* * ** *
255627 ATCGCAACGTGAAAATCGCAACACGAATATGAAT
1 ATCGCAACGAGAGAATCGCAATGCGAA-ATGAAA
*
255661 ATCGCAACGCGGAAATGACTATCGCAATGCGAAATGAAA
1 ATCGCAA--C-GAGA-GA--ATCGCAATGCGAAATGAAA
* * *
255700 ATCGTAACTAGAGAATCACAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
* *
255733 ATCGCAACGAGGGAATCGCAAAGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
255766 ATCGCAACG
1 ATCGCAACG
255775 CGAATTTAGT
Statistics
Matches: 121, Mismatches: 20, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
33 78 0.64
34 12 0.10
35 2 0.02
36 3 0.02
37 3 0.02
38 1 0.01
39 11 0.09
40 11 0.09
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
Found at i:255641 original size:14 final size:14
Alignment explanation
Indices: 255622--255648 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
255612 CAATGCGAAA
255622 TGAAAATCGCAACG
1 TGAAAATCGCAACG
255636 TGAAAATCGCAAC
1 TGAAAATCGCAAC
255649 ACGAATATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (14 bp):
TGAAAATCGCAACG
Found at i:255659 original size:20 final size:19
Alignment explanation
Indices: 255607--255778 Score: 95
Period size: 19 Copynumber: 9.7 Consensus size: 19
255597 GCAACGAGAG
*
255607 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
255626 AATCGCAA--CG---TGAA
1 AATCGCAACGCGAAATGAA
*
255640 AATCGCAACACGAATATGAA
1 AATCGCAACGCGAA-ATGAA
* *
255660 TATCGCAACGCGGAAATGAC
1 AATCGCAACGC-GAAATGAA
* *
255680 TATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* * *
255699 AATCGTAA--C--TA-GAG
1 AATCGCAACGCGAAATGAA
* *
255713 AATCACAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
**
255732 AATCGCAA--CG--A-GGG
1 AATCGCAACGCGAAATGAA
*
255746 AATCGCAAAGCGAAATGAA
1 AATCGCAACGCGAAATGAA
255765 AATCGCAACGCGAA
1 AATCGCAACGCGAA
255779 TTTAGTTTCG
Statistics
Matches: 117, Mismatches: 19, Indels: 34
0.69 0.11 0.20
Matches are distributed among these distances:
14 29 0.25
15 2 0.02
16 5 0.04
17 5 0.04
18 2 0.02
19 44 0.38
20 27 0.23
21 3 0.03
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:255698 original size:73 final size:67
Alignment explanation
Indices: 255594--255774 Score: 204
Period size: 73 Copynumber: 2.6 Consensus size: 67
255584 GGAAATTACT
* *
255594 ATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGT-GAAAATCGCAACACGAATATG
1 ATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGTAGAAAATCACAACACGAA-ATG
*
255658 AAT
65 AAA
* * * **
255661 ATCGCAACGCGGAAATGACTATCGCAATGCGAAATGAAAATCGTAAC-TAGAGAATCACAATGCG
1 ATCGCAACGAGG----GA--ATCGCAATGCGAAATGAAAATCGCAACGTAGAAAATCACAACACG
255725 AAATGAAA
60 AAATGAAA
*
255733 ATCGCAACGAGGGAATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACG
255775 CGAATTTAGT
Statistics
Matches: 95, Mismatches: 11, Indels: 16
0.78 0.09 0.13
Matches are distributed among these distances:
66 25 0.26
67 10 0.11
68 2 0.02
71 2 0.02
72 17 0.18
73 39 0.41
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.14
Consensus pattern (67 bp):
ATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGTAGAAAATCACAACACGAAATGA
AA
Found at i:255722 original size:106 final size:106
Alignment explanation
Indices: 255567--255776 Score: 280
Period size: 106 Copynumber: 2.0 Consensus size: 106
255557 CAATCATCTT
* * ** *
255567 AATGTCTATCGCAACGCGGAAATTACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC
1 AATGACTATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGC
* *
255632 AACGTGAAAATCGCAACA-CGAATATGAATATCGCAACGCGGA
66 AACGAGAAAATCGCAA-AGCGAA-ATGAAAATCGCAACGCGGA
* * *
255674 AATGACTATCGCAATGC-GAAATGAAAATCGTAACTAGAGAATCACAATGCGAAATGAAAATCGC
1 AATGACTATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGC
**
255738 AACGAGGGAATCGCAAAGCGAAATGAAAATCGCAACGCG
66 AACGAGAAAATCGCAAAGCGAAATGAAAATCGCAACGCG
255777 AATTTAGTTT
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
105 17 0.19
106 58 0.64
107 15 0.17
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.16
Consensus pattern (106 bp):
AATGACTATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGC
AACGAGAAAATCGCAAAGCGAAATGAAAATCGCAACGCGGA
Found at i:255839 original size:33 final size:33
Alignment explanation
Indices: 255784--255863 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
255774 GCGAATTTAG
* * *
255784 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
*
255817 TTTCGCATTGTGATTCTCTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
255850 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
255864 AGTCATTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
Found at i:255862 original size:19 final size:19
Alignment explanation
Indices: 255805--255863 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
255795 GATTTTGTCG
255805 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
255824 TTGTGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
255838 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
255857 TTGCGAT
1 TTGCGAT
255864 AGTCATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 5 0.16
16 7 0.23
17 7 0.23
19 12 0.39
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:255989 original size:14 final size:14
Alignment explanation
Indices: 255970--256006 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
255960 CATCAATTAA
255970 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
255984 ACAAATCATCTTTT
1 ACAAATCAACTTTT
255998 ACAAATCAA
1 ACAAATCAA
256007 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:257387 original size:21 final size:20
Alignment explanation
Indices: 257354--257414 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
257344 ATGAATCGGG
*
257354 CTCTTGAATGATGGGAGGGAC
1 CTCTTGAACGATGGGAGGG-C
* **
257375 CTCTTCAACGATGACAGTGGC
1 CTCTTGAACGATGGGAG-GGC
*
257396 CTCTTGAACGGTGGGAGGG
1 CTCTTGAACGATGGGAGGG
257415 GACTCTCGAG
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.20, G:0.36, T:0.23
Consensus pattern (20 bp):
CTCTTGAACGATGGGAGGGC
Found at i:257439 original size:42 final size:42
Alignment explanation
Indices: 257393--257472 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
257383 CGATGACAGT
* * *
257393 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
257435 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
257473 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:259328 original size:20 final size:20
Alignment explanation
Indices: 259305--259360 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
259295 TGAAATGAAA
259305 ATCGCAACGAGAGAATGACT
1 ATCGCAACGAGAGAATGACT
*
259325 ATCGCAACGCG-GAAATGACT
1 ATCGCAACGAGAG-AATGACT
259345 ATCGCAACGAGAGAAT
1 ATCGCAACGAGAGAAT
259361 CGCAACGCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.14
Consensus pattern (20 bp):
ATCGCAACGAGAGAATGACT
Found at i:259382 original size:19 final size:19
Alignment explanation
Indices: 259358--259405 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
259348 GCAACGAGAG
259358 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATAAA
*
259377 AATCGCAACGCGAAATTAA
1 AATCGCAACGCGAAATAAA
259396 AATCGCAACG
1 AATCGCAACG
259406 AGAGAATCGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.48, C:0.23, G:0.17, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:259402 original size:52 final size:52
Alignment explanation
Indices: 259325--259441 Score: 171
Period size: 52 Copynumber: 2.2 Consensus size: 52
259315 GAGAATGACT
** *
259325 ATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCGCAACGCGAAATAAAA
1 ATCGCAACGC-GAAATGAAAATCGCAACGAGAGAATCGCAACACGAAATAAAA
* *
259378 ATCGCAACGCGAAATTAAAATCGCAACGAGAGAATCGCAACACGAAATGAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACACGAAATAAAA
*
259430 ATCGCAATGCGA
1 ATCGCAACGCGA
259442 TTTTGGTTTC
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
52 48 0.83
53 10 0.17
ACGTcount: A:0.44, C:0.22, G:0.21, T:0.12
Consensus pattern (52 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACACGAAATAAAA
Found at i:259434 original size:19 final size:19
Alignment explanation
Indices: 259296--259436 Score: 79
Period size: 19 Copynumber: 7.8 Consensus size: 19
259286 TCTTTTGGTT
259296 GAAATGAAAATCGCAACGA-
1 GAAATGAAAATCGCAAC-AC
** *
259315 GAGAATGACTATCGCAACGC
1 GA-AATGAAAATCGCAACAC
**
259335 GGAAATGACTATCGC-A-AC
1 -GAAATGAAAATCGCAACAC
* *
259353 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACAC
* *
259369 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACAC
*
259388 GAAATTAAAATCGC-A-AC
1 GAAATGAAAATCGCAACAC
*
259405 G--A-GAGAATCGCAACAC
1 GAAATGAAAATCGCAACAC
259421 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
259437 TGCGATTTTG
Statistics
Matches: 95, Mismatches: 14, Indels: 26
0.70 0.10 0.19
Matches are distributed among these distances:
14 14 0.15
15 4 0.04
16 5 0.05
17 3 0.03
18 4 0.04
19 38 0.40
20 25 0.26
21 2 0.02
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACAC
Found at i:259485 original size:33 final size:33
Alignment explanation
Indices: 259437--259517 Score: 117
Period size: 33 Copynumber: 2.5 Consensus size: 33
259427 AAAATCGCAA
** *
259437 TGCGATTTTGGTTTCGCGTTACGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTACGATTATCTCAT
* *
259470 TGCGATTTTCATTTCGCGTTGCGATTCTCTCAT
1 TGCGATTTTCATTTCGCGTTACGATTATCTCAT
259503 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
259518 TCTCGTTGCG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.12, C:0.21, G:0.20, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTACGATTATCTCAT
Found at i:259518 original size:21 final size:21
Alignment explanation
Indices: 259494--259572 Score: 85
Period size: 20 Copynumber: 3.9 Consensus size: 21
259484 CGCGTTGCGA
*
259494 TTCTCTCATTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
259515 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
259536 TT-TCGT-GTTGCGATTTTCAT
1 TTCTC-TCGTTGCGATTTTCAT
259556 TT-TCAT-GTTGCGATTTT
1 TTCTC-TCGTTGCGATTTT
259573 AAGTTTAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
20 30 0.59
21 21 0.41
ACGTcount: A:0.13, C:0.19, G:0.16, T:0.52
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:259570 original size:20 final size:19
Alignment explanation
Indices: 259502--259572 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 19
259492 GATTCTCTCA
259502 TTGCGATTTTCATTTCTCTCG
1 TTGCGATTTTCATTT-TCT-G
**
259523 TTGCGATAGTCATTTTCGTG
1 TTGCGATTTTCATTTTC-TG
259543 TTGCGATTTTCATTTTCATG
1 TTGCGATTTTCATTTTC-TG
259563 TTGCGATTTT
1 TTGCGATTTT
259573 AAGTTTAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
20 30 0.68
21 14 0.32
ACGTcount: A:0.13, C:0.17, G:0.18, T:0.52
Consensus pattern (19 bp):
TTGCGATTTTCATTTTCTG
Found at i:260154 original size:20 final size:20
Alignment explanation
Indices: 260129--260240 Score: 152
Period size: 20 Copynumber: 5.5 Consensus size: 20
260119 GCTATGTAAA
260129 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* *
260149 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
* *
260170 TCGCATTACGATTTACGTAA
1 TCGCATTGCGATTTACGTAT
*
260190 TCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAT
*
260210 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
*
260230 TCACATTGCGA
1 TCGCATTGCGA
260241 ATTAGGAAAA
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
20 63 0.79
21 17 0.21
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:260186 original size:41 final size:40
Alignment explanation
Indices: 260127--260240 Score: 165
Period size: 41 Copynumber: 2.8 Consensus size: 40
260117 GCGCTATGTA
*
260127 AATCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCT
1 AATCGCATTGCGATTTACGTATTCGCATTGCGATTTACCT
* * *
260167 AATTCGCATTACGATTTACGTAATCGCATTGCGATTTACGT
1 AA-TCGCATTGCGATTTACGTATTCGCATTGCGATTTACCT
* *
260208 AATCGCGTTGCGATTTACGTATTCACATTGCGA
1 AATCGCATTGCGATTTACGTATTCGCATTGCGA
260241 ATTAGGAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
40 29 0.45
41 36 0.55
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (40 bp):
AATCGCATTGCGATTTACGTATTCGCATTGCGATTTACCT
Found at i:260253 original size:61 final size:61
Alignment explanation
Indices: 260126--260255 Score: 163
Period size: 61 Copynumber: 2.1 Consensus size: 61
260116 GGCGCTATGT
* * * *
260126 AAATCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTAATTCGCATTACGATTTACG
1 AAATCGCATTGCGATTTACGTAATCGCATTGCGATTTACCTAATTCACATTACGAATTACG
* * * * *
260187 TAATCGCATTGCGATTTACGTAATCGCGTTGCGATTTACGT-ATTCACATTGCGAATTAGG
1 AAATCGCATTGCGATTTACGTAATCGCATTGCGATTTACCTAATTCACATTACGAATTACG
260247 AAAATCGCA
1 -AAATCGCA
260256 ACGCGAATTT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 15 0.26
61 43 0.74
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (61 bp):
AAATCGCATTGCGATTTACGTAATCGCATTGCGATTTACCTAATTCACATTACGAATTACG
Found at i:260263 original size:21 final size:21
Alignment explanation
Indices: 260237--260282 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
260227 TATTCACATT
260237 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
260258 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
260279 GCGA
1 GCGA
260283 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:268566 original size:20 final size:20
Alignment explanation
Indices: 268541--268581 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
268531 GAGGGGATGG
268541 TGATATGCACATAGAATTCT
1 TGATATGCACATAGAATTCT
268561 TGATATGCACATAGAATTCT
1 TGATATGCACATAGAATTCT
268581 T
1 T
268582 TCACCAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (20 bp):
TGATATGCACATAGAATTCT
Found at i:270655 original size:23 final size:23
Alignment explanation
Indices: 270622--270682 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
270612 CTCGTATAAA
*
270622 TGCACCAAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* * *
270645 TGTACCGAAGTGTCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
270668 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
270683 TATAAGCTTG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:270949 original size:31 final size:30
Alignment explanation
Indices: 270905--270964 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
270895 TATTGTATAG
*
270905 ACATATAATTTCCATACCTT-TATCACATAA
1 ACATATAATTTCCAT-CATTGTATCACATAA
*
270935 ACATATCATGTTCCATCATTGTATCACATA
1 ACATATAAT-TTCCATCATTGTATCACATA
270965 GCTTATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (30 bp):
ACATATAATTTCCATCATTGTATCACATAA
Found at i:277686 original size:104 final size:104
Alignment explanation
Indices: 277536--277744 Score: 409
Period size: 104 Copynumber: 2.0 Consensus size: 104
277526 GACTTTGAAC
*
277536 TCCTTTTGCATGTTTGTTATACTGCCACCGAGTGTCACGCCAGAGCCTTTATCGTGTGCGGTTAT
1 TCCTTTTGCATGTTCGTTATACTGCCACCGAGTGTCACGCCAGAGCCTTTATCGTGTGCGGTTAT
277601 GCACCAATTGACGAGACAAGCGCTTAATGAGTCATAAAA
66 GCACCAATTGACGAGACAAGCGCTTAATGAGTCATAAAA
277640 TCCTTTTGCATGTTCGTTATACTGCCACCGAGTGTCACGCCAGAGCCTTTATCGTGTGCGGTTAT
1 TCCTTTTGCATGTTCGTTATACTGCCACCGAGTGTCACGCCAGAGCCTTTATCGTGTGCGGTTAT
277705 GCACCAATTGACGAGACAAGCGCTTAATGAGTCATAAAA
66 GCACCAATTGACGAGACAAGCGCTTAATGAGTCATAAAA
277744 T
1 T
277745 AACCAAACTT
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 104 1.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (104 bp):
TCCTTTTGCATGTTCGTTATACTGCCACCGAGTGTCACGCCAGAGCCTTTATCGTGTGCGGTTAT
GCACCAATTGACGAGACAAGCGCTTAATGAGTCATAAAA
Found at i:279113 original size:19 final size:19
Alignment explanation
Indices: 279089--279197 Score: 92
Period size: 19 Copynumber: 5.4 Consensus size: 19
279079 TTATTTTGGA
279089 TTTTTCACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
279108 TTTTTCACTATCGCAACAACAC
1 TTTTTCACTATCG---CAACAC
*
279130 ATTTTTCAAACTCTCGCAACAC
1 -TTTTTC--ACTATCGCAACAC
* * *
279152 ATTTTAACTATCACAACAC
1 TTTTTCACTATCGCAACAC
* * *
279171 ATTTTAATTATCGCAACAC
1 TTTTTCACTATCGCAACAC
279190 ATTTTTCA
1 -TTTTTCA
279198 AAATCGCGTT
Statistics
Matches: 74, Mismatches: 9, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
19 41 0.55
20 5 0.07
21 4 0.05
22 12 0.16
23 6 0.08
25 6 0.08
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.36
Consensus pattern (19 bp):
TTTTTCACTATCGCAACAC
Found at i:280662 original size:16 final size:16
Alignment explanation
Indices: 280641--280671 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
280631 ATATATTAAA
280641 TTTGTAAGATAAATAT
1 TTTGTAAGATAAATAT
280657 TTTGTAAGATAAATA
1 TTTGTAAGATAAATA
280672 AATTTGTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (16 bp):
TTTGTAAGATAAATAT
Found at i:280978 original size:28 final size:29
Alignment explanation
Indices: 280954--281009 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
280944 ATTTTTATAA
280954 AGTATA-TAGATGAATTTGACCTTTAAAG
1 AGTATATTAGATGAATTTGACCTTTAAAG
* *
280982 TGTATATTTAGATTAATTTGACCTTTAA
1 AGTATA-TTAGATGAATTTGACCTTTAA
281010 TGTTTTAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.21
30 19 0.79
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (29 bp):
AGTATATTAGATGAATTTGACCTTTAAAG
Found at i:282583 original size:30 final size:29
Alignment explanation
Indices: 282547--282607 Score: 113
Period size: 30 Copynumber: 2.1 Consensus size: 29
282537 CTACAGTGGT
282547 CTTGGAGGTCGCCATGGCATCCCGGGCGAC
1 CTTGGAGGTCGCCATGGCAT-CCGGGCGAC
282577 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
282606 CT
1 CT
282608 GTGTGTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.35
30 20 0.65
ACGTcount: A:0.13, C:0.33, G:0.36, T:0.18
Consensus pattern (29 bp):
CTTGGAGGTCGCCATGGCATCCGGGCGAC
Found at i:282669 original size:17 final size:16
Alignment explanation
Indices: 282647--282717 Score: 90
Period size: 17 Copynumber: 4.4 Consensus size: 16
282637 ATGCAATCAA
282647 CATGGGACGTGGGAATG
1 CATGGG-CGTGGGAATG
* * *
282664 CATGGGGGAGGGGATG
1 CATGGGCGTGGGAATG
282680 CATGGGACGTGGGAATG
1 CATGGG-CGTGGGAATG
282697 CATGGG-GTGGGAATG
1 CATGGGCGTGGGAATG
282712 CATGGG
1 CATGGG
282718 GGAGGGGATG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
15 15 0.32
16 13 0.28
17 19 0.40
ACGTcount: A:0.21, C:0.10, G:0.52, T:0.17
Consensus pattern (16 bp):
CATGGGCGTGGGAATG
Found at i:282682 original size:16 final size:16
Alignment explanation
Indices: 282657--282723 Score: 82
Period size: 16 Copynumber: 4.2 Consensus size: 16
282647 CATGGGACGT
282657 GGGAATGCATGGGGGA
1 GGGAATGCATGGGGGA
* * *
282673 GGGGATGCATGGGACGT
1 GGGAATGCATGGG-GGA
*
282690 GGGAATGCAT-GGGGT
1 GGGAATGCATGGGGGA
282705 GGGAATGCATGGGGGA
1 GGGAATGCATGGGGGA
282721 GGG
1 GGG
282724 GATGGTGCAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
15 12 0.28
16 21 0.49
17 10 0.23
ACGTcount: A:0.21, C:0.07, G:0.57, T:0.15
Consensus pattern (16 bp):
GGGAATGCATGGGGGA
Found at i:282684 original size:33 final size:32
Alignment explanation
Indices: 282647--282717 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 32
282637 ATGCAATCAA
*
282647 CATGGGACGTGGGAATGCATGGGGGAGGGGATG
1 CATGGGACGTGGGAATGCAT-GGGGAGGGAATG
*
282680 CATGGGACGTGGGAATGCATGGGGTGGGAATG
1 CATGGGACGTGGGAATGCATGGGGAGGGAATG
282712 CATGGG
1 CATGGG
282718 GGAGGGGATG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 16 0.44
33 20 0.56
ACGTcount: A:0.21, C:0.10, G:0.52, T:0.17
Consensus pattern (32 bp):
CATGGGACGTGGGAATGCATGGGGAGGGAATG
Found at i:282708 original size:15 final size:15
Alignment explanation
Indices: 282655--282718 Score: 83
Period size: 15 Copynumber: 4.1 Consensus size: 15
282645 AACATGGGAC
282655 GTGGGAATGCATGGGG
1 GTGGGAATGCAT-GGG
* *
282671 GAGGGGATGCATGGG
1 GTGGGAATGCATGGG
282686 ACGTGGGAATGCATGGG
1 --GTGGGAATGCATGGG
282703 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
282718 G
1 G
282719 GAGGGGATGG
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
15 19 0.45
16 10 0.24
17 13 0.31
ACGTcount: A:0.20, C:0.08, G:0.55, T:0.17
Consensus pattern (15 bp):
GTGGGAATGCATGGG
Found at i:282753 original size:60 final size:58
Alignment explanation
Indices: 282688--282808 Score: 224
Period size: 60 Copynumber: 2.1 Consensus size: 58
282678 TGCATGGGAC
282688 GTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAACT
1 GTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGGTGC-TTGGACGTGGGAA-T
282748 GTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGGTGCTTGGACGTGGGAAT
1 GTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGGTGCTTGGACGTGGGAAT
282806 GTG
1 GTG
282809 CTGGCCATGC
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
58 4 0.07
59 13 0.21
60 44 0.72
ACGTcount: A:0.19, C:0.07, G:0.53, T:0.21
Consensus pattern (58 bp):
GTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGGTGCTTGGACGTGGGAAT
Found at i:282768 original size:15 final size:15
Alignment explanation
Indices: 282748--282778 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
282738 CGTGGGAACT
282748 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
282763 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
282778 G
1 G
282779 GAGGGGATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.55, T:0.19
Consensus pattern (15 bp):
GTGGGAATGCATGGG
Found at i:283265 original size:21 final size:21
Alignment explanation
Indices: 283240--283283 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
283230 AATCTAGTTA
283240 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
283261 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
283282 AT
1 AT
283284 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:283293 original size:28 final size:30
Alignment explanation
Indices: 283260--283322 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
283250 TAGTATAAAT
*
283260 TATTAGTTTGTTAGTTTAAG-T-TATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
283288 TATTAGTTTATTAGTTTAAGTTATATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
283318 TATTA
1 TATTA
283323 TATATAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (30 bp):
TATTAGTTTATTAGTTTAAGTTATATATTA
Found at i:283950 original size:14 final size:14
Alignment explanation
Indices: 283918--283956 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
283908 CCGGACAACG
*
283918 CATTATCTCGCGAA
1 CATTATCTCGAGAA
* *
283932 AATTATTTCGAGAA
1 CATTATCTCGAGAA
283946 CATTATCTCGA
1 CATTATCTCGA
283957 CAGTTTTGCC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (14 bp):
CATTATCTCGAGAA
Found at i:284144 original size:26 final size:25
Alignment explanation
Indices: 284115--284173 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
284105 AAATCATATT
*
284115 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
284141 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
284167 ATTATTA
1 ATTATTA
284174 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:287001 original size:22 final size:19
Alignment explanation
Indices: 286969--287017 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 19
286959 TATTTCTATG
*
286969 TATTTATTAATCATTATAAAA
1 TATTTAATAATCATT-T-AAA
*
286990 TGATTTAATAATGATTTAAA
1 T-ATTTAATAATCATTTAAA
287010 TATTTAAT
1 TATTTAAT
287018 GATTTGATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 7 0.28
20 4 0.16
21 2 0.08
22 12 0.48
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (19 bp):
TATTTAATAATCATTTAAA
Found at i:287059 original size:26 final size:26
Alignment explanation
Indices: 287030--287235 Score: 199
Period size: 26 Copynumber: 8.4 Consensus size: 26
287020 TTTGATGATT
287030 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
287056 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
287082 TAATAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** *
287108 TAAAAATGA-TT--T-ATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * * *
287129 TA--AAT-TTTTAAT-TTGATGATT-
1 TAGTAATGATTTGATAATAATCATTA
287150 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
287176 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
287202 -A-TAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
*
287226 TA-AAATGATT
1 TAGTAATGATT
287236 AATAATGATT
Statistics
Matches: 157, Mismatches: 12, Indels: 23
0.82 0.06 0.12
Matches are distributed among these distances:
19 5 0.03
21 12 0.08
22 8 0.05
23 5 0.03
24 26 0.17
25 18 0.11
26 83 0.53
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (26 bp):
TAGTAATGATTTGATAATAATCATTA
Found at i:287170 original size:14 final size:14
Alignment explanation
Indices: 287153--287196 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
287143 GATGATTTAG
287153 TAATGATTTGATAA
1 TAATGATTTGATAA
* *
287167 TAATCA-TT-ATAG
1 TAATGATTTGATAA
287179 TAATGATTTGATAA
1 TAATGATTTGATAA
287193 TAAT
1 TAAT
287197 CATTAATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
12 8 0.33
13 4 0.17
14 12 0.50
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.43
Consensus pattern (14 bp):
TAATGATTTGATAA
Found at i:287183 original size:120 final size:120
Alignment explanation
Indices: 286976--287352 Score: 567
Period size: 120 Copynumber: 3.2 Consensus size: 120
286966 ATGTATTTAT
286976 TAATCATTATAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATT
1 TAATCATTATAAAATGATTT-ATAATGATTTAAATATTT-ATGATTTGATGATTTAGTAATGATT
287041 TGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
64 TGATAATAATCATTATAGTAATGATTTGATAATAATCATT-TAATAATGATTTAGTAA
*
287099 TAATCATTATAAAAATGATTTATAATGATTTAAAT-TTT-TAATTTGATGATTTAGTAATGATTT
1 TAATCATTAT-AAAATGATTTATAATGATTTAAATATTTATGATTTGATGATTTAGTAATGATTT
287162 GATAATAATCATTATAGTAATGATTTGATAATAATCA-TTAATAATGATTTAGTAA
65 GATAATAATCATTATAGTAATGATTTGATAATAATCATTTAATAATGATTTAGTAA
*
287217 TAATCATTATAAAATGATTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTT
1 TAATCATTATAAAATGATTTATAATGATTTAAATATTT-ATGATTTGATGATTTAGTAATGATTT
* * * *
287282 GATAAT-ATCA-T-TA-TAATGATTTTATAATAATTATTTAGT-ATTATTTAGTAA
65 GATAATAATCATTATAGTAATGATTTGATAATAATCATTTAATAATGATTTAGTAA
*
287333 TTAT--TTATAATAATGATTTA
1 TAATCATTATAA-AATGATTTA
287353 ATACTAATGA
Statistics
Matches: 239, Mismatches: 9, Indels: 20
0.89 0.03 0.07
Matches are distributed among these distances:
114 6 0.03
115 8 0.03
116 32 0.13
117 29 0.12
118 31 0.13
119 5 0.02
120 91 0.38
122 3 0.01
123 24 0.10
124 10 0.04
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (120 bp):
TAATCATTATAAAATGATTTATAATGATTTAAATATTTATGATTTGATGATTTAGTAATGATTTG
ATAATAATCATTATAGTAATGATTTGATAATAATCATTTAATAATGATTTAGTAA
Found at i:287217 original size:35 final size:34
Alignment explanation
Indices: 287164--287247 Score: 96
Period size: 35 Copynumber: 2.4 Consensus size: 34
287154 AATGATTTGA
* * * *
287164 TAATAATCATTATAGTAATGATTTGATAATAATCAT
1 TAATAATGATT-TAGTAATAATATTATAA-AATCAT
*
287200 TAATAATGATTTAGTAATAATCATTATAAAATGAT
1 TAATAATGATTTAGTAATAAT-ATTATAAAATCAT
287235 TAATAATGATTTA
1 TAATAATGATTTA
287248 AATATTTAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
35 27 0.64
36 15 0.36
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (34 bp):
TAATAATGATTTAGTAATAATATTATAAAATCAT
Found at i:287326 original size:10 final size:11
Alignment explanation
Indices: 287309--287343 Score: 56
Period size: 10 Copynumber: 3.4 Consensus size: 11
287299 GATTTTATAA
287309 TAATTATTTAG
1 TAATTATTTAG
287320 T-ATTATTTAG
1 TAATTATTTAG
287330 TAATTATTTA-
1 TAATTATTTAG
287340 TAAT
1 TAAT
287344 AATGATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (11 bp):
TAATTATTTAG
Found at i:287362 original size:14 final size:14
Alignment explanation
Indices: 287330--287370 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
287320 TATTATTTAG
*
287330 TAATTATTT-ATAA
1 TAATGATTTAATAA
*
287343 TAATGATTTAATAC
1 TAATGATTTAATAA
287357 TAATGA-TTAATAA
1 TAATGATTTAATAA
287370 T
1 T
287371 TATTACTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 15 0.62
14 9 0.38
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:287602 original size:17 final size:17
Alignment explanation
Indices: 287577--287609 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
287567 ACTAAATATT
*
287577 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
287594 TAATGATTTGATACTA
1 TAATGATTTGATACTA
287610 AAATCATTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:289762 original size:15 final size:14
Alignment explanation
Indices: 289739--289769 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
289729 TACAACACTA
289739 AACTTTAATATAAT
1 AACTTTAATATAAT
289753 AACTTATAATATAAT
1 AACTT-TAATATAAT
289768 AA
1 AA
289770 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:289777 original size:16 final size:16
Alignment explanation
Indices: 289744--289790 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
289734 CACTAAACTT
*
289744 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
289759 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
289775 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
289791 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:290029 original size:43 final size:48
Alignment explanation
Indices: 289950--290038 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 48
289940 CAACAAACAA
*
289950 ATATAACTTAACTATTTAACTAACACAAACTAAATTAATAATTTTTTT
1 ATATAACTTAACTATTTAACTAACAAAAACTAAATTAATAATTTTTTT
*
289998 ATATAAC-TAACTA-TTAAC-AA-AAAAACT-AATTAATTATTTTT
1 ATATAACTTAACTATTTAACTAACAAAAACTAAATTAATAATTTTT
290039 AACTATATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
43 13 0.33
44 6 0.15
45 2 0.05
46 5 0.13
47 6 0.15
48 7 0.18
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.40
Consensus pattern (48 bp):
ATATAACTTAACTATTTAACTAACAAAAACTAAATTAATAATTTTTTT
Found at i:290107 original size:41 final size:39
Alignment explanation
Indices: 289971--290107 Score: 89
Period size: 41 Copynumber: 3.3 Consensus size: 39
289961 CTATTTAACT
* *
289971 AACACAAACTAAATTAATAATTTTTTTA-TATAACTAACTATTA
1 AACATAAACT-AATTAATAA-TTTTTAACTAT-A-TAACTA-TA
* * *
290014 ACAAAAAAACTAATTAATTATTTTTAACTATATAACTATCA
1 A-ACATAAACTAATTAATAATTTTTAACTATATAACTAT-A
* * *
290055 AACATATACTAATTAAATAATTTTTAATTTATGTATACTAT-
1 AACATAAACTAATT-AATAATTTTTAA-CTATATA-ACTATA
*
290096 AACTTAAACTAA
1 AACATAAACTAA
290108 CAATCATATA
Statistics
Matches: 76, Mismatches: 12, Indels: 14
0.75 0.12 0.14
Matches are distributed among these distances:
40 11 0.14
41 29 0.38
42 12 0.16
43 17 0.22
44 7 0.09
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.39
Consensus pattern (39 bp):
AACATAAACTAATTAATAATTTTTAACTATATAACTATA
Found at i:290266 original size:17 final size:17
Alignment explanation
Indices: 290244--290288 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
290234 CTTCTTCTTA
290244 CTTTCCTTTCTCCCTTT
1 CTTTCCTTTCTCCCTTT
290261 CTTTCCTTTCTCCCTTT
1 CTTTCCTTTCTCCCTTT
290278 CTTT-CTTTCTC
1 CTTTCCTTTCTC
290289 GGCTGCAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 7 0.25
17 21 0.75
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (17 bp):
CTTTCCTTTCTCCCTTT
Found at i:290321 original size:23 final size:23
Alignment explanation
Indices: 290291--290336 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
290281 TCTTTCTCGG
290291 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
290314 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
290337 TCTTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.09, C:0.39, G:0.04, T:0.48
Consensus pattern (23 bp):
CTGCAATCTCTTCTCCCTTTCTT
Found at i:290377 original size:25 final size:25
Alignment explanation
Indices: 290349--290400 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
290339 TTTCTTTTAT
290349 AACCAGCTGCCTCAATTATTTCACC
1 AACCAGCTGCCTCAATTATTTCACC
*
290374 AACCGGCTGCCTCAATTATTTCACC
1 AACCAGCTGCCTCAATTATTTCACC
290399 AA
1 AA
290401 TAATTGTACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.35, G:0.10, T:0.27
Consensus pattern (25 bp):
AACCAGCTGCCTCAATTATTTCACC
Found at i:290623 original size:29 final size:30
Alignment explanation
Indices: 290589--290666 Score: 124
Period size: 29 Copynumber: 2.7 Consensus size: 30
290579 GGGAATGGTG
290589 CTGGGACTACATGGCGACCTACAAGGTCGC
1 CTGGGACTACATGGCGACCTACAAGGTCGC
290619 C-GGGACTACATGGCGACCTACAAGGTCGC
1 CTGGGACTACATGGCGACCTACAAGGTCGC
* *
290648 CTAGG-CTGCATGGCGACCT
1 CTGGGACTACATGGCGACCT
290667 CTCTATTCCT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
29 42 0.93
30 3 0.07
ACGTcount: A:0.22, C:0.31, G:0.31, T:0.17
Consensus pattern (30 bp):
CTGGGACTACATGGCGACCTACAAGGTCGC
Found at i:290740 original size:35 final size:35
Alignment explanation
Indices: 290701--290923 Score: 248
Period size: 35 Copynumber: 6.0 Consensus size: 35
290691 TGGCGACCTC
*
290701 GCATGGGGAGAACCATTGGCTTGTATGGCTCGTAT
1 GCATGGGGAGAACCATTGGCTCGTATGGCTCGTAT
290736 GCATGGGGAGAACCATTGGCTCGTATGGCTCGTAT
1 GCATGGGGAGAACCATTGGCTCGTATGGCTCGTAT
290771 GCATGGGGAGAACCATTGGCTCGTATGGCTCGTAT
1 GCATGGGGAGAACCATTGGCTCGTATGGCTCGTAT
* ** * ** * **
290806 GTCACCCCGTATGTCACCGGAGAACCATTGGCTCGTATGGCTCGTAT
1 G-CA-----T-GGGGA---GA-ACCATTGGCT-CGTATGGCTCGTAT
290853 GCATGGGGAGAACCATTGGCTCGTATGGCTCGTAT
1 GCATGGGGAGAACCATTGGCTCGTATGGCTCGTAT
290888 GCATGGGGAGAACCATTGGCTCGTATGGCTCGTAT
1 GCATGGGGAGAACCATTGGCTCGTATGGCTCGTAT
290923 G
1 G
290924 TCACCCCGTA
Statistics
Matches: 157, Mismatches: 19, Indels: 24
0.79 0.09 0.12
Matches are distributed among these distances:
35 120 0.76
36 6 0.04
37 2 0.01
40 2 0.01
41 2 0.01
42 2 0.01
45 2 0.01
46 6 0.04
47 15 0.10
ACGTcount: A:0.20, C:0.22, G:0.33, T:0.26
Consensus pattern (35 bp):
GCATGGGGAGAACCATTGGCTCGTATGGCTCGTAT
Found at i:290913 original size:117 final size:117
Alignment explanation
Indices: 290707--290940 Score: 459
Period size: 117 Copynumber: 2.0 Consensus size: 117
290697 CCTCGCATGG
*
290707 GGAGAACCATTGGCTTGTATGGCTCGTATGCATGGGGAGAACCATTGGCTCGTATGGCTCGTATG
1 GGAGAACCATTGGCTCGTATGGCTCGTATGCATGGGGAGAACCATTGGCTCGTATGGCTCGTATG
290772 CATGGGGAGAACCATTGGCTCGTATGGCTCGTATGTCACCCCGTATGTCACC
66 CATGGGGAGAACCATTGGCTCGTATGGCTCGTATGTCACCCCGTATGTCACC
290824 GGAGAACCATTGGCTCGTATGGCTCGTATGCATGGGGAGAACCATTGGCTCGTATGGCTCGTATG
1 GGAGAACCATTGGCTCGTATGGCTCGTATGCATGGGGAGAACCATTGGCTCGTATGGCTCGTATG
290889 CATGGGGAGAACCATTGGCTCGTATGGCTCGTATGTCACCCCGTATGTCACC
66 CATGGGGAGAACCATTGGCTCGTATGGCTCGTATGTCACCCCGTATGTCACC
290941 CCGTATGTCG
Statistics
Matches: 116, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
117 116 1.00
ACGTcount: A:0.20, C:0.24, G:0.31, T:0.26
Consensus pattern (117 bp):
GGAGAACCATTGGCTCGTATGGCTCGTATGCATGGGGAGAACCATTGGCTCGTATGGCTCGTATG
CATGGGGAGAACCATTGGCTCGTATGGCTCGTATGTCACCCCGTATGTCACC
Found at i:290935 original size:12 final size:12
Alignment explanation
Indices: 290918--290949 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
290908 TCGTATGGCT
290918 CGTATGTCACCC
1 CGTATGTCACCC
290930 CGTATGTCACCC
1 CGTATGTCACCC
290942 CGTATGTC
1 CGTATGTC
290950 GCCTGGATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.16, C:0.38, G:0.19, T:0.28
Consensus pattern (12 bp):
CGTATGTCACCC
Found at i:290992 original size:29 final size:29
Alignment explanation
Indices: 290947--291005 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
290937 CACCCCGTAT
* *
290947 GTCGCCTGGATTGCATGGCGTCCTACAAG
1 GTCGCCCGGATTGCATGGCGACCTACAAG
*
290976 GTCGCCCGGA-TGCCATGGCGACCTCCAAG
1 GTCGCCCGGATTG-CATGGCGACCTACAAG
291005 G
1 G
291006 CCACTGTAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 2 0.08
29 24 0.92
ACGTcount: A:0.17, C:0.32, G:0.32, T:0.19
Consensus pattern (29 bp):
GTCGCCCGGATTGCATGGCGACCTACAAG
Found at i:299825 original size:20 final size:20
Alignment explanation
Indices: 299800--299851 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
299790 GTGTATCAAA
299800 CATTTTTAATGATGTTTTAC
1 CATTTTTAATGATGTTTTAC
*
299820 CATTTTTAATGTTGTTTTAC
1 CATTTTTAATGATGTTTTAC
299840 CATTTTTAATGA
1 CATTTTTAATGA
299852 AAATATCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.56
Consensus pattern (20 bp):
CATTTTTAATGATGTTTTAC
Found at i:300621 original size:26 final size:26
Alignment explanation
Indices: 300585--300668 Score: 89
Period size: 26 Copynumber: 3.3 Consensus size: 26
300575 TATTGTATTG
* * *
300585 TAATGCAATGTAGGAGTTAATGCTTA
1 TAATGTAATGTACGAGTTAATGCTTC
*
300611 TAATGTAATGTACGAGTTAATGTTTC
1 TAATGTAATGTACGAGTTAATGCTTC
* * * *
300637 TAGTGTAAT-AATGAGTTACTGCTTC
1 TAATGTAATGTACGAGTTAATGCTTC
300662 TAATGTA
1 TAATGTA
300669 TGAGTTAAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
25 18 0.38
26 30 0.62
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.39
Consensus pattern (26 bp):
TAATGTAATGTACGAGTTAATGCTTC
Found at i:300993 original size:15 final size:15
Alignment explanation
Indices: 300973--301009 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
300963 CTTAAGTTCA
300973 AGTCGAGTCAACTCG
1 AGTCGAGTCAACTCG
300988 AGTCGAGTCAACTCG
1 AGTCGAGTCAACTCG
301003 AGTCGAG
1 AGTCGAG
301010 CTTTTATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.27, C:0.24, G:0.30, T:0.19
Consensus pattern (15 bp):
AGTCGAGTCAACTCG
Found at i:313995 original size:21 final size:21
Alignment explanation
Indices: 313970--314029 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
313960 ATTTACATAC
* *
313970 AAAATACAGAGGAAATCATGA
1 AAAATACAGAGGAAAGCACGA
313991 AAAATACAGAGGAAAGCACGA
1 AAAATACAGAGGAAAGCACGA
*
314012 AAAATACAAAGGCAAAGC
1 AAAATACAGAGG-AAAGC
314030 TATTGTAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
21 30 0.86
22 5 0.14
ACGTcount: A:0.58, C:0.13, G:0.20, T:0.08
Consensus pattern (21 bp):
AAAATACAGAGGAAAGCACGA
Found at i:314536 original size:30 final size:27
Alignment explanation
Indices: 314483--314553 Score: 81
Period size: 26 Copynumber: 2.5 Consensus size: 27
314473 TTTCTAGTAT
*
314483 TTTATTTATTTCATTTGCTTTTATGGACTTTA
1 TTTATTTATTT-ATGTGCTTTTAT----TTTA
314515 TTTATTTATTTATGT-CTTTTATTTTA
1 TTTATTTATTTATGTGCTTTTATTTTA
314541 TTTATTTATTTAT
1 TTTATTTATTTAT
314554 TTTTCTTTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
26 17 0.45
30 7 0.18
31 3 0.08
32 11 0.29
ACGTcount: A:0.20, C:0.06, G:0.06, T:0.69
Consensus pattern (27 bp):
TTTATTTATTTATGTGCTTTTATTTTA
Found at i:314541 original size:5 final size:4
Alignment explanation
Indices: 314511--314555 Score: 56
Period size: 4 Copynumber: 10.8 Consensus size: 4
314501 TTTTATGGAC
314511 TTTA TTTA TTTA TTTA TGTCT- TTTA TTTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA T-T-TA TTTA -TTTA TTTA TTTA TTTA TTT
314556 TTCTTTTCGT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
3 1 0.03
4 29 0.78
5 6 0.16
6 1 0.03
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:314544 original size:9 final size:9
Alignment explanation
Indices: 314480--314556 Score: 61
Period size: 9 Copynumber: 8.7 Consensus size: 9
314470 TATTTTCTAG
314480 TATTTTATT
1 TATTTTATT
*
314489 TATTTCATT
1 TATTTTATT
* *
314498 TGCTTTTATG
1 T-ATTTTATT
* *
314508 GACTTTATT
1 TATTTTATT
314517 TA-TTTATT
1 TATTTTATT
*
314525 TATGTCT-TT
1 TAT-TTTATT
314534 TATTTTATT
1 TATTTTATT
314543 TA-TTTATT
1 TATTTTATT
314551 TATTTT
1 TATTTT
314557 TCTTTTCGTT
Statistics
Matches: 52, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
8 18 0.35
9 27 0.52
10 7 0.13
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.70
Consensus pattern (9 bp):
TATTTTATT
Found at i:314579 original size:30 final size:30
Alignment explanation
Indices: 314511--314582 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
314501 TTTTATGGAC
*
314511 TTTATTTATTTATTTATGTCTTTTATTTTA
1 TTTATTTATTTATTTATGTCTTTTAGTTTA
* *
314541 TTTATTTATTTATTT-T-TCTTTTCGTTTC
1 TTTATTTATTTATTTATGTCTTTTAGTTTA
314569 TTTA-TT-TTTATTTA
1 TTTATTTATTTATTTA
314583 ATTTACTTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
26 7 0.18
27 2 0.05
28 13 0.34
29 1 0.03
30 15 0.39
ACGTcount: A:0.17, C:0.06, G:0.03, T:0.75
Consensus pattern (30 bp):
TTTATTTATTTATTTATGTCTTTTAGTTTA
Found at i:316137 original size:33 final size:33
Alignment explanation
Indices: 316095--316161 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
316085 ATCTTGGGAG
316095 TCCCTTCGAAGACAACAATGGAAAAACGATAGC
1 TCCCTTCGAAGACAACAATGGAAAAACGATAGC
* *
316128 TCCCTTCGAAGACAACAATGGCAAAATGATAGC
1 TCCCTTCGAAGACAACAATGGAAAAACGATAGC
316161 T
1 T
316162 GAAATTGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.18
Consensus pattern (33 bp):
TCCCTTCGAAGACAACAATGGAAAAACGATAGC
Found at i:320834 original size:21 final size:21
Alignment explanation
Indices: 320807--320847 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
320797 CATAACCCCA
320807 GGGGGGGTATCGATTCCCCTGT
1 GGGGGGG-ATCGATTCCCCTGT
*
320829 GGGGGGGATCGGTTCCCCT
1 GGGGGGGATCGATTCCCCT
320848 TCAAAGGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.07, C:0.24, G:0.44, T:0.24
Consensus pattern (21 bp):
GGGGGGGATCGATTCCCCTGT
Found at i:320878 original size:22 final size:23
Alignment explanation
Indices: 320807--320882 Score: 63
Period size: 21 Copynumber: 3.5 Consensus size: 23
320797 CATAACCCCA
* *
320807 GGGGGGGTATCGATTCCCC-T-GT
1 GGGGGGG-ATCGGTTCCCCTTCAT
*
320829 GGGGGGGATCGGTTCCCCTTCAA
1 GGGGGGGATCGGTTCCCCTTCAT
* *
320852 AGGGGGAATCGGTT-CCC-TCAT
1 GGGGGGGATCGGTTCCCCTTCAT
320873 -GGGGGGATCG
1 GGGGGGGATCG
320883 ATTACCTCTG
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
20 9 0.20
21 13 0.29
22 11 0.24
23 12 0.27
ACGTcount: A:0.13, C:0.22, G:0.42, T:0.22
Consensus pattern (23 bp):
GGGGGGGATCGGTTCCCCTTCAT
Found at i:322248 original size:21 final size:21
Alignment explanation
Indices: 322222--322269 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
322212 TAAGCTCTAG
322222 GAGCTTGTTTTAAACCATAAA
1 GAGCTTGTTTTAAACCATAAA
322243 GAGCTTGTTTTAAACCATAAA
1 GAGCTTGTTTTAAACCATAAA
322264 GAGCTT
1 GAGCTT
322270 TTGTCAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (21 bp):
GAGCTTGTTTTAAACCATAAA
Found at i:328588 original size:183 final size:183
Alignment explanation
Indices: 328279--328632 Score: 627
Period size: 183 Copynumber: 1.9 Consensus size: 183
328269 ATTAAATCTA
* *
328279 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCTCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCAAAAGCCCTGGCTTTATGA
*
328344 ATAGATTACATTCAAACCATGATATTGCTCGGACACTTGGAAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTACATTCAAACCATGACATTGCTCGGACACTTGGAAATTCGGTGTTTGCTCCACTGCTT
* *
328409 TTTTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTATGATGAGACGAACCCTTCAGTGATTTGTCCCTC
*
328462 TAAAGCTGAGTTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCAAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCAAAAGCCCTGGCTTTATGA
* * *
328527 ATAGATTACATTCAAACCATGACATTGTTCGGACACTTGGTAATTCGGTGTTTGTTCCACTGCTT
66 ATAGATTACATTCAAACCATGACATTGCTCGGACACTTGGAAATTCGGTGTTTGCTCCACTGCTT
328592 TTGTCAGGCCAAAGACTTTATGATGAGACGAACCCTTCAGT
131 TTGTCAGGCCAAAGACTTTATGATGAGACGAACCCTTCAGT
328633 TAAACTTGGT
Statistics
Matches: 162, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
183 162 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCAAAAGCCCTGGCTTTATGA
ATAGATTACATTCAAACCATGACATTGCTCGGACACTTGGAAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTATGATGAGACGAACCCTTCAGTGATTTGTCCCTC
Found at i:329844 original size:72 final size:71
Alignment explanation
Indices: 329758--330014 Score: 270
Period size: 72 Copynumber: 3.5 Consensus size: 71
329748 ATCTCACTTG
* *
329758 AGATTGTTTTTCTTAAAGCATACTTTGTCTCACTTGAGACTGTTTTACTCGAAAGAAGATTTATT
1 AGATTGATTTTCTTAAAACA-ACTTTGTCTCACTTGAGACTGTTTTACTCGAAAGAAGATTTATT
329823 TCACTCA
65 TCACTCA
* * * * * *
329830 AGTTTGCTTTTCTTAAAACAAACTTTGTCTTACTTGAGACTATTTTACTTGGAAGAAGATTTATT
1 AGATTGATTTTCTTAAAAC-AACTTTGTCTCACTTGAGACTGTTTTACTCGAAAGAAGATTTATT
329895 TCACTCA
65 TCACTCA
* * * *
329902 AGATT-ATTTTTCTTAAAACAAGATTTGTCTCTCTTGGGATTGTTTTCACTCGAAAGAAGGCATT
1 AGATTGA-TTTTCTTAAAACAA-CTTTGTCTCACTTGAGACTGTTTT-ACTCGAAAGAA-G-ATT
329966 TCATTTCACTCA
61 T-ATTTCACTCA
* *
329978 AGACTGATTTT-TTAAAGA-AGA-TTTGTCTCTCTTGAGA
1 AGATTGATTTTCTTAAA-ACA-ACTTTGTCTCACTTGAGA
330015 TAGTTTCTCT
Statistics
Matches: 156, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
71 2 0.01
72 97 0.62
73 10 0.06
74 16 0.10
75 10 0.06
76 20 0.13
77 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (71 bp):
AGATTGATTTTCTTAAAACAACTTTGTCTCACTTGAGACTGTTTTACTCGAAAGAAGATTTATTT
CACTCA
Found at i:329925 original size:36 final size:36
Alignment explanation
Indices: 329813--329927 Score: 99
Period size: 36 Copynumber: 3.2 Consensus size: 36
329803 TACTCGAAAG
* **
329813 AAGATTTATTTCACTCAAGTTTGCTTTTCTTAAAAC
1 AAGATTTATTTCACTCAAGATTATTTTTCTTAAAAC
* ** * * ** *
329849 AA-ACTTTGTCTT-ACTTGAGACTATTTTACTTGGAAG
1 AAGA-TTTAT-TTCACTCAAGATTATTTTTCTTAAAAC
329885 AAGATTTATTTCACTCAAGATTATTTTTCTTAAAAC
1 AAGATTTATTTCACTCAAGATTATTTTTCTTAAAAC
329921 AAGATTT
1 AAGATTT
329928 GTCTCTCTTG
Statistics
Matches: 56, Mismatches: 19, Indels: 8
0.67 0.23 0.10
Matches are distributed among these distances:
35 3 0.05
36 50 0.89
37 3 0.05
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.43
Consensus pattern (36 bp):
AAGATTTATTTCACTCAAGATTATTTTTCTTAAAAC
Found at i:330045 original size:21 final size:21
Alignment explanation
Indices: 330020--330069 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
330010 TGAGATAGTT
*
330020 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTCGTC
330041 TCTCTTGAAACAAATTTCGTC
1 TCTCTTGAAACAAATTTCGTC
*
330062 TCCCTTGA
1 TCTCTTGA
330070 GACATTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.40
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTCGTC
Found at i:330209 original size:37 final size:37
Alignment explanation
Indices: 330142--330228 Score: 104
Period size: 37 Copynumber: 2.4 Consensus size: 37
330132 TTGAAAAAAA
** * *
330142 GTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 GTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
330178 GTTCCCTTGAAACAAAATTTTGTGTCCCTTGAGACAG
1 GTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
* *
330215 TTTCTCTTGAAACA
1 GTTCCCTTGAAACA
330229 TAAACATTGA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 12 0.28
37 31 0.72
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (37 bp):
GTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:330284 original size:65 final size:65
Alignment explanation
Indices: 330179--330349 Score: 202
Period size: 65 Copynumber: 2.6 Consensus size: 65
330169 TTGAGATAGG
*
330179 TTCCCTTGAAACAAAATTTTGTGTCCCTTGAGACAGTTTCTCTTGAAACATAAA-CATTGAAAAC
1 TTCCCTTGAAA-AAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA-AAATCATTG-AAAC
330243 -AT
63 TAT
* * * * * *
330245 TTCCCTTGAAATAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCTTTGAATCTGT
1 TTCCCTTGAAAAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCATTGAAACTAT
* ** *
330310 TTCCCTTGAAACAAATTTCATCTCCCTTGAGACATTTTCT
1 TTCCCTTGAAAAAAATTTTGTCTCCCTTGAGACAGTTTCT
330350 TTTGGAACTA
Statistics
Matches: 90, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 6 0.07
65 73 0.81
66 11 0.12
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (65 bp):
TTCCCTTGAAAAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCATTGAAACTAT
Found at i:330289 original size:102 final size:104
Alignment explanation
Indices: 330102--330302 Score: 343
Period size: 102 Copynumber: 2.0 Consensus size: 104
330092 TTTCATCTCT
*
330102 CTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAAAAGTTCCCTTGAAATGAATTTTGTCTC
1 CTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAAAAGTTCCCTTGAAATAAATTTTGTCTC
330167 TCTTGAGATAGGTTCCCTTGAAACAAAAT-TTTGTGTCC
66 TCTTGAGATAGGTTCCCTTGAAACAAAATCTTTGTGTCC
* *
330205 CTTGAGACAGTTTCTCTTGAAACATAAACATTG-AAAACATTTCCCTTGAAATAAATTTTGTCTC
1 CTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAAAAGTTCCCTTGAAATAAATTTTGTCTC
* *
330269 TCTTGAGATAGTTTCTCTTGAAACAAAATCTTTG
66 TCTTGAGATAGGTTCCCTTGAAACAAAATCTTTG
330303 AATCTGTTTC
Statistics
Matches: 92, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
102 55 0.60
103 37 0.40
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.36
Consensus pattern (104 bp):
CTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAAAAGTTCCCTTGAAATAAATTTTGTCTC
TCTTGAGATAGGTTCCCTTGAAACAAAATCTTTGTGTCC
Found at i:330366 original size:102 final size:99
Alignment explanation
Indices: 330244--330726 Score: 410
Period size: 102 Copynumber: 4.8 Consensus size: 99
330234 ATTGAAAACA
* * * * *
330244 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA-AAATCTTTGAATCT
1 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA-CTTTGAAAC-
* * * *
330308 GTTTCCCTTGAAACAAATTTCATCTCCCTTGAGACAT
64 ATTTCCCTTGAAACAAATTTC-TCTCTCTTGAGATAG
* * * * * **
330345 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTAAAAAC
1 TTTCTCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC-TTTGAAAC
* * *
330410 ATTTCCCTTAAAATGAATTTTCTCTCTCTTGAGATAG
64 ATTTCCCTTGAAA-CAAATTTCTCTCTCTTGAGATAG
* * * *
330447 GTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAGCATTGAAAAC
1 TTTCTCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTG-AAAC
** *
330512 ATTTCCCTTGAAATGAATTATGTCTCTCTTGAGATAG
64 ATTTCCCTTGAAACAAATT-TCTCTCTCTTGAGATAG
* *
330549 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAGCATAAACTTTGAAAATA
1 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTG-AAACA
* * *
330614 GTTTTCTTTGAAACAAA-----ATCT-TTGA-ATATG
65 -TTTCCCTTGAAACAAATTTCTCTCTCTTGAGATA-G
* * * * *
330644 TTT-TACGTT-AAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACTTCAATCTTTGAAT
1 TTTCT-C-TTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAT-AAACTTTGAA-
*
330707 ACAGTTTCTCTTGAAACAAA
62 ACA-TTTCCCTTGAAACAAA
330727 AAAAACCTTT
Statistics
Matches: 317, Mismatches: 53, Indels: 29
0.79 0.13 0.07
Matches are distributed among these distances:
94 4 0.01
95 48 0.15
96 28 0.09
101 61 0.19
102 162 0.51
103 14 0.04
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (99 bp):
TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAACAT
TTCCCTTGAAACAAATTTCTCTCTCTTGAGATAG
Found at i:330478 original size:37 final size:37
Alignment explanation
Indices: 330425--330497 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
330415 CCTTAAAATG
* *
330425 AATTTTCTCTCTCTTGAGATAGGTTCCCTTGAAACAA
1 AATTTTCTCTCCCTTGAGACAGGTTCCCTTGAAACAA
* * *
330462 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AATTTTCTCTCCCTTGAGACAGGTTCCCTTGAAACA
330498 TAAGCATTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (37 bp):
AATTTTCTCTCCCTTGAGACAGGTTCCCTTGAAACAA
Found at i:330499 original size:269 final size:263
Alignment explanation
Indices: 329999--330579 Score: 952
Period size: 269 Copynumber: 2.2 Consensus size: 263
329989 TTAAAGAAGA
* *
329999 TTTGTCTCTCTTGAGATAGTTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAAACAAATTTCGTCT
1 TTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATTTTGTCTCCCTTGAAACAAATTTCATCT
330063 CCCTTGAGACATTTTCTTTTAGAACTAAGTTTCATCTCTCTTGAGACAGTTTCTCTTGAAACATA
66 CCCTTGAGACATTTTCTTTTAGAACTAAGTTTCATCTCTCTTGAGACAGTTTCTCTTGAAACATA
* *
330128 AACATTGAAAAAAAGTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGGTTCCCTTGAAACAA
131 AACATTGAAAAAAAGTTCCCTTAAAATGAATTTTCTCTCTCTTGAGATAGGTTCCCTTGAAACAA
*
330193 AATTTTGTGTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATA
196 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATA
330258 AAT
261 AAT
330261 TTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCTTTGAATCTGTTTCCCTTGAAACAAAT
1 TTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAAT-TTTG--TC----TCCCTTGAAACAAAT
* ** *
330326 TTCATCTCCCTTGAGACATTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTG
59 TTCATCTCCCTTGAGACATTTTCTTTTAGAACTAAGTTTCATCTCTCTTGAGACAGTTTCTCTTG
* *
330391 AAACATAAACATT-AAAAACATTTCCCTTAAAATGAATTTTCTCTCTCTTGAGATAGGTTCCCTT
124 AAACATAAACATTGAAAAAAAGTTCCCTTAAAATGAATTTTCTCTCTCTTGAGATAGGTTCCCTT
*
330455 GAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAGCATTGAAAACATTTCCCT
189 GAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCT
*
330520 TGAAATGAAT
254 TGAAATAAAT
*
330530 TATGTCTCTCTTGAGATAGTTTCTCTTGAAAC-AAATTTTGTCTCCCTTGA
1 TTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATTTTGTCTCCCTTGA
330580 GACAGTTTCT
Statistics
Matches: 297, Mismatches: 14, Indels: 17
0.91 0.04 0.05
Matches are distributed among these distances:
261 8 0.03
262 32 0.11
263 4 0.01
264 4 0.01
265 2 0.01
266 2 0.01
267 4 0.01
268 4 0.01
269 150 0.51
270 87 0.29
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (263 bp):
TTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATTTTGTCTCCCTTGAAACAAATTTCATCT
CCCTTGAGACATTTTCTTTTAGAACTAAGTTTCATCTCTCTTGAGACAGTTTCTCTTGAAACATA
AACATTGAAAAAAAGTTCCCTTAAAATGAATTTTCTCTCTCTTGAGATAGGTTCCCTTGAAACAA
AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATA
AAT
Found at i:330572 original size:36 final size:36
Alignment explanation
Indices: 330513--330595 Score: 112
Period size: 36 Copynumber: 2.3 Consensus size: 36
330503 ATTGAAAACA
* ** * *
330513 TTTCCCTTGAAATGAATTATGTCTCTCTTGAGATAG
1 TTTCTCTTGAAACAAATTATGTCTCCCTTGAGACAG
*
330549 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAG
1 TTTCTCTTGAAACAAATTATGTCTCCCTTGAGACAG
330585 TTTCTCTTGAA
1 TTTCTCTTGAA
330596 GCATAAACTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTATGTCTCCCTTGAGACAG
Found at i:330621 original size:29 final size:30
Alignment explanation
Indices: 330585--330647 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
330575 CTTGAGACAG
*
330585 TTTCTCTTGAAGCATAAA-CTTTGAAAATAGT
1 TTTCT-TTGAAACA-AAATCTTTGAAAATAGT
*
330616 TTTCTTTGAAACAAAATCTTTGAATAT-GT
1 TTTCTTTGAAACAAAATCTTTGAAAATAGT
330645 TTT
1 TTT
330648 ACGTTAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 8 0.28
30 16 0.55
31 5 0.17
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (30 bp):
TTTCTTTGAAACAAAATCTTTGAAAATAGT
Found at i:330772 original size:35 final size:35
Alignment explanation
Indices: 330710--330793 Score: 136
Period size: 35 Copynumber: 2.5 Consensus size: 35
330700 TTTGAATACA
* *
330710 GTTTCTCTTG-AA-ACAAAAAAAACCTTTGAAATT
1 GTTTCTCTTGAAACACAAAAAAAAACTTTGAAAAT
330743 GTTTCTCTTGAAACACAAAAAAAAACTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAAAAACTTTGAAAAT
330778 GTTTCTCTTGAAACAC
1 GTTTCTCTTGAAACAC
330794 CAAGCCCTCG
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
33 10 0.21
34 2 0.04
35 35 0.74
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.32
Consensus pattern (35 bp):
GTTTCTCTTGAAACACAAAAAAAAACTTTGAAAAT
Found at i:330945 original size:84 final size:84
Alignment explanation
Indices: 330801--330954 Score: 227
Period size: 84 Copynumber: 1.8 Consensus size: 84
330791 CACCAAGCCC
* * * * * * * * *
330801 TCGAGTTCGACTATGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCT
1 TCGAGTTCAACTACGCTCAGCTCCAAGGCACATCATTTACAGCACAACTCAAGGCAAGAAGGGCT
330866 ATCTGCCAACCAAAGACCT
66 ATCTGCCAACCAAAGACCT
330885 TCGAGTTCAACTACGCTCAGCTCCAAGGCACATCATTTACAGCACAACTCAAGGCAAGAAGGGCT
1 TCGAGTTCAACTACGCTCAGCTCCAAGGCACATCATTTACAGCACAACTCAAGGCAAGAAGGGCT
330950 ATCTG
66 ATCTG
330955 TCAAAAAAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
84 61 1.00
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (84 bp):
TCGAGTTCAACTACGCTCAGCTCCAAGGCACATCATTTACAGCACAACTCAAGGCAAGAAGGGCT
ATCTGCCAACCAAAGACCT
Found at i:332291 original size:10 final size:10
Alignment explanation
Indices: 332215--332291 Score: 54
Period size: 10 Copynumber: 7.8 Consensus size: 10
332205 TTTTATGGAC
332215 TTTATTTATT
1 TTTATTTATT
*
332225 TTT-TATATAT
1 TTTATTTAT-T
*
332235 TTTATTT-TA
1 TTTATTTATT
332244 TTTATTTATT
1 TTTATTTATT
*
332254 TTTCTTT-TCT
1 TTTATTTAT-T
*
332264 TTTCTTT-TT
1 TTTATTTATT
*
332273 GTTTCTTTATT
1 -TTTATTTATT
332284 TTTATTTA
1 TTTATTTA
332292 ATTTACTTGT
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
9 13 0.24
10 38 0.69
11 4 0.07
ACGTcount: A:0.16, C:0.05, G:0.01, T:0.78
Consensus pattern (10 bp):
TTTATTTATT
Found at i:333655 original size:10 final size:10
Alignment explanation
Indices: 333640--333670 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
333630 TATCGATAAA
333640 GATACAACAT
1 GATACAACAT
333650 GATACAACAT
1 GATACAACAT
333660 GATACAACAT
1 GATACAACAT
333670 G
1 G
333671 CCGCACGCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.48, C:0.19, G:0.13, T:0.19
Consensus pattern (10 bp):
GATACAACAT
Found at i:333871 original size:25 final size:24
Alignment explanation
Indices: 333830--333876 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
333820 AGTATGTTAT
333830 ATTTTTAAGAGAAAATATATATTCA
1 ATTTTTAAGAGAAAATAT-TATTCA
*
333855 ATTTTTAA-ATAATAATATTATT
1 ATTTTTAAGAGAA-AATATTATT
333877 AAAAATAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (24 bp):
ATTTTTAAGAGAAAATATTATTCA
Found at i:334638 original size:39 final size:39
Alignment explanation
Indices: 334534--334639 Score: 153
Period size: 39 Copynumber: 2.7 Consensus size: 39
334524 CATAATCCTG
* *
334534 AAATTATTTCAC-TCTAACATTCTAAAATCTTAATTTCTT
1 AAATTATTTCACAT-TAACGTTCTAAATTCTTAATTTCTT
*
334573 AAATT-TTGACACATTAACGTTCTAAATTCTTAATTTCTT
1 AAATTATT-TCACATTAACGTTCTAAATTCTTAATTTCTT
334612 AAATTATTTCACATTAACGTTCTAAATT
1 AAATTATTTCACATTAACGTTCTAAATT
334640 ATTTTTTAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
38 2 0.03
39 55 0.92
40 3 0.05
ACGTcount: A:0.36, C:0.16, G:0.03, T:0.45
Consensus pattern (39 bp):
AAATTATTTCACATTAACGTTCTAAATTCTTAATTTCTT
Found at i:334659 original size:39 final size:38
Alignment explanation
Indices: 334534--334655 Score: 110
Period size: 39 Copynumber: 3.2 Consensus size: 38
334524 CATAATCCTG
* * * *
334534 AAATTATTTCAC-TCTAACATTCTAAAATCTTAATTTCTT
1 AAATTATTTCACAT-TAACGTTCTAAATTATT-ATTTCTA
* * *
334573 AAATT-TTGACACATTAACGTTCTAAATTCTTAATTTCTT
1 AAATTATT-TCACATTAACGTTCTAAATTATT-ATTTCTA
334612 AAATTATTTCACATTAACGTTCTAAATTATT-TTT-TA
1 AAATTATTTCACATTAACGTTCTAAATTATTATTTCTA
334648 AAA-TATTT
1 AAATTATTT
334656 ATTTTAACTC
Statistics
Matches: 74, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
35 5 0.07
36 4 0.05
37 3 0.04
38 2 0.03
39 57 0.77
40 3 0.04
ACGTcount: A:0.36, C:0.14, G:0.02, T:0.48
Consensus pattern (38 bp):
AAATTATTTCACATTAACGTTCTAAATTATTATTTCTA
Found at i:335600 original size:2 final size:2
Alignment explanation
Indices: 335593--335618 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
335583 ATTTTATAAA
335593 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
335619 GAATTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:335681 original size:18 final size:18
Alignment explanation
Indices: 335637--335684 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
335627 ATTTTTAAAA
* *
335637 AAATATATAAATATTTTTC
1 AAATATAT-AATATTATAC
*
335656 AACT-TATAATATTATAC
1 AAATATATAATATTATAC
335673 AAATATATAATA
1 AAATATATAATA
335685 AGGAGAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 11 0.46
18 10 0.42
19 3 0.12
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATATAATATTATAC
Found at i:337249 original size:40 final size:40
Alignment explanation
Indices: 337205--337295 Score: 119
Period size: 40 Copynumber: 2.3 Consensus size: 40
337195 ATAAGTTTCC
**
337205 TTTTCGCAACAAGATTTTTTAAATCGCAACACGAATTTTA
1 TTTTCGCAACAAGATTTTCGAAATCGCAACACGAATTTTA
*** *
337245 TTTTCGCAACTCTATTTTCGAATTCGCAACACGAATTTTA
1 TTTTCGCAACAAGATTTTCGAAATCGCAACACGAATTTTA
*
337285 ATTTCGCAACA
1 TTTTCGCAACA
337296 GTTTTTATTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (40 bp):
TTTTCGCAACAAGATTTTCGAAATCGCAACACGAATTTTA
Found at i:337251 original size:20 final size:20
Alignment explanation
Indices: 337167--337314 Score: 85
Period size: 20 Copynumber: 7.5 Consensus size: 20
337157 GATTTTTGAA
* * *
337167 TTCGCAACGCTAATTTTTTT
1 TTCGCAACACGAATTTTATT
* **
337187 TTCGCAACA-TAAGTTTCCTT
1 TTCGCAACACGAA-TTTTATT
*
337207 TTCGCAACAAG-ATTTT-TT
1 TTCGCAACACGAATTTTATT
*
337225 AAATCGCAACACGAATTTTATT
1 --TTCGCAACACGAATTTTATT
* * *
337247 TTCGCAACTC-TATTTTCGA-A
1 TTCGCAACACGAATTTT--ATT
*
337267 TTCGCAACACGAATTTTAAT
1 TTCGCAACACGAATTTTATT
*
337287 TTCGCAACA-G-TTTTTATT
1 TTCGCAACACGAATTTTATT
337305 TTCGCAACAC
1 TTCGCAACAC
337315 AAATGTTTTG
Statistics
Matches: 101, Mismatches: 16, Indels: 23
0.72 0.11 0.16
Matches are distributed among these distances:
18 17 0.17
19 13 0.13
20 58 0.57
21 11 0.11
22 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.40
Consensus pattern (20 bp):
TTCGCAACACGAATTTTATT
Found at i:337305 original size:17 final size:18
Alignment explanation
Indices: 337280--337313 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
337270 GCAACACGAA
337280 TTTTAA-TTTCGCAACAG
1 TTTTAATTTTCGCAACAG
*
337297 TTTTTATTTTCGCAACA
1 TTTTAATTTTCGCAACA
337314 CAAATGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.26, C:0.18, G:0.09, T:0.47
Consensus pattern (18 bp):
TTTTAATTTTCGCAACAG
Found at i:337497 original size:22 final size:23
Alignment explanation
Indices: 337472--337514 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
337462 ACATAATTTT
*
337472 ATTTCTATAT-AAATTTTCAATG
1 ATTTCTATATCAAATTATCAATG
*
337494 ATTTCTCTATCAAATTATCAA
1 ATTTCTATATCAAATTATCAA
337515 CTATCAACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.37, C:0.14, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTTCTATATCAAATTATCAATG
Found at i:340570 original size:6 final size:6
Alignment explanation
Indices: 340548--340594 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
340538 AGCAAAAAGG
* * * *
340548 AAATCA AAATCG CAATCA AAATCA AAATCC CAATCA AAATCA AAATC
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATC
340595 CCAATCACAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.57, C:0.23, G:0.02, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:340571 original size:18 final size:18
Alignment explanation
Indices: 340548--340601 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
340538 AGCAAAAAGG
*
340548 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
340566 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
340584 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
340602 CAACCGGCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.56, C:0.26, G:0.02, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:340854 original size:29 final size:29
Alignment explanation
Indices: 340812--340886 Score: 123
Period size: 29 Copynumber: 2.6 Consensus size: 29
340802 GAATTCGCAA
*
340812 TGCGAAAGTCAAATTCGCGTTGCGATTGC
1 TGCGAAAGTTAAATTCGCGTTGCGATTGC
* *
340841 TGCGAAAGTTAAATTCGTGTTGCGATTGT
1 TGCGAAAGTTAAATTCGCGTTGCGATTGC
340870 TGCGAAAGTTAAATTCG
1 TGCGAAAGTTAAATTCG
340887 AAATACGAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.32
Consensus pattern (29 bp):
TGCGAAAGTTAAATTCGCGTTGCGATTGC
Found at i:340959 original size:20 final size:20
Alignment explanation
Indices: 340934--340978 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
340924 CAATTGCAAC
340934 GCGAATTTGACTTCCGCGTT
1 GCGAATTTGACTTCCGCGTT
* * *
340954 GCGAATTTGATTTTCGTGTT
1 GCGAATTTGACTTCCGCGTT
340974 GCGAA
1 GCGAA
340979 AGTGTACCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.38
Consensus pattern (20 bp):
GCGAATTTGACTTCCGCGTT
Found at i:341048 original size:16 final size:16
Alignment explanation
Indices: 341027--341062 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
341017 TGCAAATTGA
* *
341027 AATTAAACAACAAATC
1 AATTAAACAAAAAAAC
341043 AATTAAACAAAAAAAC
1 AATTAAACAAAAAAAC
341059 AATT
1 AATT
341063 CTTATTTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.67, C:0.14, G:0.00, T:0.19
Consensus pattern (16 bp):
AATTAAACAAAAAAAC
Found at i:342488 original size:21 final size:21
Alignment explanation
Indices: 342448--342544 Score: 115
Period size: 21 Copynumber: 4.6 Consensus size: 21
342438 TGAATCGGGT
* * *
342448 TCTTGAACGGTGGGAGGGGCC
1 TCTTGAACGATGAGAAGGGCC
* *
342469 TGTTGAATGATGAGAAGGGCC
1 TCTTGAACGATGAGAAGGGCC
* *
342490 TCTTGAACGATGGGAGGGGCC
1 TCTTGAACGATGAGAAGGGCC
342511 TCTTGAACGAT-AGAAGGGGCC
1 TCTTGAACGATGAGAA-GGGCC
342532 TCTTGAACGATGA
1 TCTTGAACGATGA
342545 CAGGTGAATC
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
20 2 0.03
21 60 0.95
22 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.38, T:0.22
Consensus pattern (21 bp):
TCTTGAACGATGAGAAGGGCC
Found at i:342507 original size:42 final size:42
Alignment explanation
Indices: 342448--342543 Score: 149
Period size: 42 Copynumber: 2.3 Consensus size: 42
342438 TGAATCGGGT
* * *
342448 TCTTGAACGGTGGGAGGGGCCTGTTGAATGATGAGAA-GGGCC
1 TCTTGAACGATGGGAGGGGCCTCTTGAACGAT-AGAAGGGGCC
342490 TCTTGAACGATGGGAGGGGCCTCTTGAACGATAGAAGGGGCC
1 TCTTGAACGATGGGAGGGGCCTCTTGAACGATAGAAGGGGCC
342532 TCTTGAACGATG
1 TCTTGAACGATG
342544 ACAGGTGAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
41 4 0.08
42 46 0.92
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.22
Consensus pattern (42 bp):
TCTTGAACGATGGGAGGGGCCTCTTGAACGATAGAAGGGGCC
Found at i:342838 original size:21 final size:21
Alignment explanation
Indices: 342814--342867 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
342804 TGAAACAATC
* * *
342814 TCACGTAGAGCGGCTACCTCA
1 TCACGTAAAGCAGATACCTCA
*
342835 TCACGTAAAGTAGATACCTCA
1 TCACGTAAAGCAGATACCTCA
342856 TCACGTAAAGCA
1 TCACGTAAAGCA
342868 TCATTGTCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.20
Consensus pattern (21 bp):
TCACGTAAAGCAGATACCTCA
Found at i:342878 original size:42 final size:41
Alignment explanation
Indices: 342832--342912 Score: 99
Period size: 42 Copynumber: 2.0 Consensus size: 41
342822 AGCGGCTACC
** *
342832 TCATCACGTAAAGTAGATACCTCATCACGTAAAGCATCATTG
1 TCATCACGTAAAACAGATACCTCACCACGTAAAG-ATCATTG
* **
342874 TCATCGCGTAAAACATCTACCTCACCACGTAAAGATCAT
1 TCATCACGTAAAACAGATACCTCACCACGTAAAGATCAT
342913 ACCTCATCAC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
41 5 0.15
42 28 0.85
ACGTcount: A:0.36, C:0.27, G:0.12, T:0.25
Consensus pattern (41 bp):
TCATCACGTAAAACAGATACCTCACCACGTAAAGATCATTG
Found at i:342904 original size:21 final size:21
Alignment explanation
Indices: 342848--342923 Score: 57
Period size: 21 Copynumber: 3.6 Consensus size: 21
342838 CGTAAAGTAG
*
342848 ATACCTCATCACGTAAAGCATC
1 ATACCTCACCACGTAAA-CATC
** * *
342870 AT-TGTCATCGCGTAAAACATC
1 ATACCTCACCACGT-AAACATC
*
342891 -TACCTCACCACGTAAAGATC
1 ATACCTCACCACGTAAACATC
*
342911 ATACCTCATCACG
1 ATACCTCACCACG
342924 CCATGCACCA
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
20 7 0.17
21 30 0.71
22 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.11, T:0.24
Consensus pattern (21 bp):
ATACCTCACCACGTAAACATC
Done.