Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015369.1 Kokia drynarioides strain JFW-HI SEQ_130416, 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: 307577
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 160 characters in sequence are not A, C, G, or T
Found at i:589 original size:29 final size:29
Alignment explanation
Indices: 542--811 Score: 292
Period size: 30 Copynumber: 9.1 Consensus size: 29
532 CCTTAGAGGT
**
542 CCCTAAACTGTCCAAAAATTTTATTTTTAC
1 CCCTAAACT-TCCAAAAATTCCATTTTTAC
*
572 CCCTAAACTTCCAAAAATCCCATTTTTTA-
1 CCCTAAACTTCCAAAAATTCCA-TTTTTAC
*
601 CCCTCAAACTTCCAAAAATCCCATTTTTGAC
1 CCCT-AAACTTCCAAAAATTCCATTTTT-AC
*
632 CCCAAAACTTCCAAAAATTCCATTTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
661 CCCTAAACTTCCAAAAATTCCATTTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
** *
690 CCCCGAACTTCCAAAAATCCCATTTTTGAC
1 CCCTAAACTTCCAAAAATTCCATTTTT-AC
* * * *
720 CTCAAAACTTCCAAAAATACCATTTTTAA
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
* * *
749 CCTTAAAACTTCCAAAAATGCTATTTTTGA-
1 CCCT-AAACTTCCAAAAATTCCATTTTT-AC
* * *
779 CCCTAAAATTTCTAAAAATTCTATTTTTAC
1 CCCT-AAACTTCCAAAAATTCCATTTTTAC
809 CCC
1 CCC
812 CGAACCTCTA
Statistics
Matches: 209, Mismatches: 23, Indels: 16
0.84 0.09 0.06
Matches are distributed among these distances:
29 76 0.36
30 129 0.62
31 4 0.02
ACGTcount: A:0.35, C:0.29, G:0.02, T:0.34
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTCCATTTTTAC
Found at i:760 original size:118 final size:118
Alignment explanation
Indices: 542--816 Score: 383
Period size: 118 Copynumber: 2.3 Consensus size: 118
532 CCTTAGAGGT
* ** *
542 CCCTAAACTGTCCAAAAATTTTATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTTACCCTCA
1 CCCTAAACT-TCCAAAAATTCTATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTCA
* * *
607 AACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTT-A
65 AACTTCCAAAAATACCATTTTTAACCCCAAAACTTCCAAAAATGCCATTTTTGA
*
660 CCCCTAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCTCA
1 -CCCTAAACTTCCAAAAATTCTATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTC-
** *
724 AAACTTCCAAAAATACCATTTTTAACCTTAAAACTTCCAAAAATGCTATTTTTGA
64 AAACTTCCAAAAATACCATTTTTAACCCCAAAACTTCCAAAAATGCCATTTTTGA
* *
779 CCCTAAAATTTCTAAAAATTCTATTTTTACCCCCGAAC
1 CCCT-AAACTTCCAAAAATTCTATTTTTACCCCCGAAC
817 CTCTAAAACC
Statistics
Matches: 139, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
117 4 0.03
118 95 0.68
119 40 0.29
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (118 bp):
CCCTAAACTTCCAAAAATTCTATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTCAA
ACTTCCAAAAATACCATTTTTAACCCCAAAACTTCCAAAAATGCCATTTTTGA
Found at i:16859 original size:4 final size:5
Alignment explanation
Indices: 16830--16858 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
16820 AATTCTTGAA
16830 TATTT TATTT TATTT TATTT TA-TT TATTT
1 TATTT TATTT TATTT TATTT TATTT TATTT
16859 ACTCGCACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:27342 original size:21 final size:22
Alignment explanation
Indices: 27296--27344 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
27286 TTTTTCTTGC
*
27296 TTTAAATAATTTTCAATACTCT
1 TTTAAATAATTTTCAATAATCT
*
27318 TTTAAATTATTTT-AATAAT-T
1 TTTAAATAATTTTCAATAATCT
27338 ATTTAAA
1 -TTTAAA
27345 AATCACATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 11 0.46
22 12 0.50
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTAAATAATTTTCAATAATCT
Found at i:27472 original size:21 final size:21
Alignment explanation
Indices: 27431--27472 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
27421 TTATGGTTTT
**
27431 ATATTTTTTAGTGATTATTAA
1 ATATTTTTTAGAAATTATTAA
27452 ATATTCTTTTAGAAATT-TTAA
1 ATATT-TTTTAGAAATTATTAA
27473 TAACCTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (21 bp):
ATATTTTTTAGAAATTATTAA
Found at i:35460 original size:3 final size:3
Alignment explanation
Indices: 35452--35478 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
35442 AAGAAGCATA
35452 GGT GGT GGT GGT GGT GGT GGT GGT GGT
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT
35479 TGTGTAGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (3 bp):
GGT
Found at i:35910 original size:14 final size:14
Alignment explanation
Indices: 35887--35919 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
35877 ACGTGTTTCA
35887 TTTA-TTTAATATT
1 TTTATTTTAATATT
*
35900 TTTATTTTAATTTT
1 TTTATTTTAATATT
35914 TTTATT
1 TTTATT
35920 ATATGTATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTATTTTAATATT
Found at i:42730 original size:14 final size:14
Alignment explanation
Indices: 42693--42722 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
42683 GGGCGACAAA
42693 GAAAAAATAAAAAAG
1 GAAAAAA-AAAAAAG
42708 GAAAAAAAAAAAAG
1 GAAAAAAAAAAAAG
42722 G
1 G
42723 TAAGAAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (14 bp):
GAAAAAAAAAAAAG
Found at i:43998 original size:6 final size:6
Alignment explanation
Indices: 43987--44011 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
43977 TCCGGTTATA
43987 GATGTT GATGTT GATGTT GATGTT G
1 GATGTT GATGTT GATGTT GATGTT G
44012 GAGTAGGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.36, T:0.48
Consensus pattern (6 bp):
GATGTT
Found at i:46687 original size:22 final size:21
Alignment explanation
Indices: 46662--46720 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 21
46652 CCCACATAAC
46662 ATTTTTATTAAATATTTTTATG
1 ATTTTTATTAAATA-TTTTATG
*
46684 ATTTTTA-CAGAATATTTTATG
1 ATTTTTATTA-AATATTTTATG
46705 ATATTTGATATTAAAT
1 AT-TTT--TATTAAAT
46721 TTAATACTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
21 10 0.33
22 14 0.47
24 5 0.17
25 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.56
Consensus pattern (21 bp):
ATTTTTATTAAATATTTTATG
Found at i:53646 original size:64 final size:64
Alignment explanation
Indices: 53545--53673 Score: 240
Period size: 64 Copynumber: 2.0 Consensus size: 64
53535 AAATTGATAA
*
53545 TATTAGTATATAAATCAAAATACAATGGGGCCGTGTACAAGATTTTTATCATGCAGAAACAAAG
1 TATTAGTATATAAATCAAAATACAATGGGGCCATGTACAAGATTTTTATCATGCAGAAACAAAG
*
53609 TATTAGTATATAAATCAAAATACAATGGGGCCATGTACAAGATTTTTATCATGGAGAAACAAAG
1 TATTAGTATATAAATCAAAATACAATGGGGCCATGTACAAGATTTTTATCATGCAGAAACAAAG
53673 T
1 T
53674 CAATAAGGGC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.29
Consensus pattern (64 bp):
TATTAGTATATAAATCAAAATACAATGGGGCCATGTACAAGATTTTTATCATGCAGAAACAAAG
Found at i:54150 original size:20 final size:20
Alignment explanation
Indices: 54109--54150 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
54099 TTTTATTTTG
**
54109 AATTTCAAAATTTTCATTTA
1 AATTTCAAAATTTTCAGATA
54129 AATTT-AAAATTTTCAAGATA
1 AATTTCAAAATTTTC-AGATA
54149 AA
1 AA
54151 AATACTTACG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (20 bp):
AATTTCAAAATTTTCAGATA
Found at i:56629 original size:22 final size:20
Alignment explanation
Indices: 56588--56627 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
56578 AAATATGTTA
56588 TTTTTATTTTCAATATATAT
1 TTTTTATTTTCAATATATAT
56608 TTTTTATTTTCAATATATAT
1 TTTTTATTTTCAATATATAT
56628 ATATATATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTTATTTTCAATATATAT
Found at i:63493 original size:9 final size:9
Alignment explanation
Indices: 63479--63503 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
63469 ATCGGCTGAA
63479 GCCTTTGAT
1 GCCTTTGAT
63488 GCCTTTGAT
1 GCCTTTGAT
63497 GCCTTTG
1 GCCTTTG
63504 TTAGTTACTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.24, G:0.24, T:0.44
Consensus pattern (9 bp):
GCCTTTGAT
Found at i:73196 original size:10 final size:10
Alignment explanation
Indices: 73183--73224 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
73173 AAAAAATGGG
73183 AAATTATATA
1 AAATTATATA
*
73193 AAATTTTA-A
1 AAATTATATA
73202 AATATTAT-TA
1 AA-ATTATATA
73212 AAATTATATA
1 AAATTATATA
73222 AAA
1 AAA
73225 GAAGTACTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
9 8 0.30
10 19 0.70
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
AAATTATATA
Found at i:77232 original size:23 final size:23
Alignment explanation
Indices: 77179--77252 Score: 123
Period size: 23 Copynumber: 3.3 Consensus size: 23
77169 CTAATACAAT
77179 GTAAGCACACACAGTGCTGAA-A
1 GTAAGCACACACAGTGCTGAACA
* *
77201 GTAATCACACACAGTGCTAAACA
1 GTAAGCACACACAGTGCTGAACA
77224 GTAAGCACACACAGTGCTGAACA
1 GTAAGCACACACAGTGCTGAACA
77247 GTAAGC
1 GTAAGC
77253 GCGCTAATGT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
22 19 0.40
23 28 0.60
ACGTcount: A:0.41, C:0.24, G:0.20, T:0.15
Consensus pattern (23 bp):
GTAAGCACACACAGTGCTGAACA
Found at i:84156 original size:13 final size:13
Alignment explanation
Indices: 84138--84163 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
84128 GAGTTATTGA
84138 CAAATGAACTTCG
1 CAAATGAACTTCG
84151 CAAATGAACTTCG
1 CAAATGAACTTCG
84164 AAGATACAAT
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:0.23, G:0.15, T:0.23
Consensus pattern (13 bp):
CAAATGAACTTCG
Found at i:88760 original size:16 final size:17
Alignment explanation
Indices: 88732--88763 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
88722 TGAGTTTGAA
88732 AATTTATAGTGTAATTG
1 AATTTATAGTGTAATTG
88749 AATTTA-AGTGTAATT
1 AATTTATAGTGTAATT
88764 ACTCTCTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.47
Consensus pattern (17 bp):
AATTTATAGTGTAATTG
Found at i:102204 original size:30 final size:30
Alignment explanation
Indices: 102111--102204 Score: 84
Period size: 31 Copynumber: 3.1 Consensus size: 30
102101 TAAGAACTAA
* *
102111 AAGGATCAAATTGATAGAATATGTTAGTGTT
1 AAGGATCAAATT-ATAGAATATGTTAATATT
* * *
102142 AAGGATTAAATGTATTGAATGATG-TAAAATT
1 AAGGATCAAAT-TATAGAAT-ATGTTAATATT
*
102173 AA-GATCAAATTAATGGAATATGTTAATATT
1 AAGGATCAAATT-ATAGAATATGTTAATATT
102203 AA
1 AA
102205 AGATTAGATG
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
29 4 0.08
30 21 0.41
31 22 0.43
32 4 0.08
ACGTcount: A:0.45, C:0.02, G:0.18, T:0.35
Consensus pattern (30 bp):
AAGGATCAAATTATAGAATATGTTAATATT
Found at i:103021 original size:23 final size:24
Alignment explanation
Indices: 102995--103057 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 24
102985 TTAACTTAGT
102995 CGAACATGTTCACGAACAT-TAAA
1 CGAACATGTTCACGAACATATAAA
* * *
103018 CGAACATGTTCATGAGCATATAAT
1 CGAACATGTTCACGAACATATAAA
* *
103042 TGAACACGTTCACGAA
1 CGAACATGTTCACGAA
103058 TAATGTTAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 17 0.53
24 15 0.47
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.24
Consensus pattern (24 bp):
CGAACATGTTCACGAACATATAAA
Found at i:106826 original size:2 final size:2
Alignment explanation
Indices: 106819--106853 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
106809 GCTACTAACT
106819 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
106854 GTATGTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:112848 original size:20 final size:20
Alignment explanation
Indices: 112792--112855 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
112782 CTAAAGGAAA
112792 TTAT-TAATAGTCTAATAATT
1 TTATATAATAGT-TAATAATT
*
112812 TTATATAA-ACTTCAATAATT
1 TTATATAATAGTT-AATAATT
*
112832 TT-TATAATTAGTTAATAACT
1 TTATATAA-TAGTTAATAATT
112852 TTAT
1 TTAT
112856 TTTAACCTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
19 6 0.17
20 23 0.64
21 7 0.19
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (20 bp):
TTATATAATAGTTAATAATT
Found at i:115150 original size:24 final size:24
Alignment explanation
Indices: 115087--115154 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 24
115077 ATATTAGGAT
*
115087 TATCATAAT-T-TTTTTAATATAAC
1 TATCATAATCTATTTTTAA-AAAAC
* *
115110 TATCCTAATCTA-CTTTAAAAAAC
1 TATCATAATCTATTTTTAAAAAAC
*
115133 TATCATTATCTATTTTTAAAAA
1 TATCATAATCTATTTTTAAAAA
115155 GTTTTTTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
23 22 0.61
24 14 0.39
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (24 bp):
TATCATAATCTATTTTTAAAAAAC
Found at i:120095 original size:18 final size:18
Alignment explanation
Indices: 120072--120107 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
120062 GACAGTGTAA
*
120072 AAGTTGTTGAGTAGAATT
1 AAGTTGTGGAGTAGAATT
*
120090 AAGTTGTGGAGTTGAATT
1 AAGTTGTGGAGTAGAATT
120108 TCGGGCTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.39
Consensus pattern (18 bp):
AAGTTGTGGAGTAGAATT
Found at i:125127 original size:13 final size:13
Alignment explanation
Indices: 125109--125135 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
125099 AAAACAAACC
125109 AAAATAAAGAAAA
1 AAAATAAAGAAAA
125122 AAAATAAAGAAAA
1 AAAATAAAGAAAA
125135 A
1 A
125136 TTATTTTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.07
Consensus pattern (13 bp):
AAAATAAAGAAAA
Found at i:125127 original size:33 final size:34
Alignment explanation
Indices: 125072--125135 Score: 112
Period size: 33 Copynumber: 1.9 Consensus size: 34
125062 AATATCAATC
*
125072 ACCAAAATCAAGAAAAAAAAATAAAGAAAAACAA
1 ACCAAAATAAAGAAAAAAAAATAAAGAAAAACAA
125106 ACCAAAATAAAG-AAAAAAAATAAAGAAAAA
1 ACCAAAATAAAGAAAAAAAAATAAAGAAAAA
125136 TTATTTTGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 18 0.62
34 11 0.38
ACGTcount: A:0.78, C:0.09, G:0.06, T:0.06
Consensus pattern (34 bp):
ACCAAAATAAAGAAAAAAAAATAAAGAAAAACAA
Found at i:125268 original size:35 final size:34
Alignment explanation
Indices: 125170--125268 Score: 110
Period size: 36 Copynumber: 2.8 Consensus size: 34
125160 TTTGGAAGAC
* *
125170 AAAAAACAAAAATGAACAGAATTGATTCTCTCGAA
1 AAAAAACAGAAATGAACA-AAATGATTCTCTCGAA
* *
125205 AAAAATACAGAGATGAACAATAAAGATTCTCTACG-A
1 AAAAA-ACAGAAATGAACAA-AATGATTCTCT-CGAA
125241 AAAAAACAGAAATGAACAAAAGTGATTC
1 AAAAAACAGAAATGAACAAAA-TGATTC
125269 CTTACAAAGA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
34 2 0.04
35 24 0.44
36 26 0.48
37 2 0.04
ACGTcount: A:0.56, C:0.13, G:0.13, T:0.18
Consensus pattern (34 bp):
AAAAAACAGAAATGAACAAAATGATTCTCTCGAA
Found at i:129450 original size:37 final size:36
Alignment explanation
Indices: 129408--129535 Score: 132
Period size: 37 Copynumber: 3.5 Consensus size: 36
129398 TTTGGAAGAC
*
129408 AAAAGACAGAGATGAACATGAGTGATTCTCTACAAAG
1 AAAAGACAGAGATGAACA-GAATGATTCTCTACAAAG
*
129445 AAAAGACAAAGAT-AATCAGGAATGATTCTCTACAAAG
1 AAAAGACAGAGATGAA-CA-GAATGATTCTCTACAAAG
* ** ** *
129482 AAAAGAAAGATCTGAGTAGTAAAGATTCTCTACAAAG
1 AAAAGACAGAGATGAACAG-AATGATTCTCTACAAAG
*
129519 AAAAAACAGAGATGAAC
1 AAAAGACAGAGATGAAC
129536 GGTAACGATT
Statistics
Matches: 72, Mismatches: 16, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
36 3 0.04
37 68 0.94
38 1 0.01
ACGTcount: A:0.51, C:0.12, G:0.19, T:0.18
Consensus pattern (36 bp):
AAAAGACAGAGATGAACAGAATGATTCTCTACAAAG
Found at i:129546 original size:37 final size:37
Alignment explanation
Indices: 129431--129547 Score: 105
Period size: 37 Copynumber: 3.2 Consensus size: 37
129421 GAACATGAGT
* * *
129431 GATTCTCTACAAAGAAAAGACAAAGAT-AATCAGG-AAT
1 GATTCTCTACAAAGAAAAAACAGAGATGAA-C-GGTAAA
** ***
129468 GATTCTCTACAAAGAAAAGAA-AGATCTGAGTAGTAAA
1 GATTCTCTACAAAGAAAA-AACAGAGATGAACGGTAAA
*
129505 GATTCTCTACAAAGAAAAAACAGAGATGAACGGTAAC
1 GATTCTCTACAAAGAAAAAACAGAGATGAACGGTAAA
129542 GATTCT
1 GATTCT
129548 TGGGTAAAGC
Statistics
Matches: 62, Mismatches: 14, Indels: 8
0.74 0.17 0.10
Matches are distributed among these distances:
36 3 0.05
37 57 0.92
38 2 0.03
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.21
Consensus pattern (37 bp):
GATTCTCTACAAAGAAAAAACAGAGATGAACGGTAAA
Found at i:144258 original size:6 final size:6
Alignment explanation
Indices: 144244--144284 Score: 64
Period size: 6 Copynumber: 6.7 Consensus size: 6
144234 ATTGAGACTG
*
144244 ATAGATC ATAGTC ATAGCC ATAGTC ATAGTC ATAGTC ATAG
1 ATAG-TC ATAGTC ATAGTC ATAGTC ATAGTC ATAGTC ATAG
144285 ATCACGAGCG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 28 0.88
7 4 0.12
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (6 bp):
ATAGTC
Found at i:144272 original size:18 final size:19
Alignment explanation
Indices: 144244--144288 Score: 74
Period size: 18 Copynumber: 2.4 Consensus size: 19
144234 ATTGAGACTG
144244 ATAGATCATAGTCATAGCC
1 ATAGATCATAGTCATAGCC
*
144263 ATAG-TCATAGTCATAGTC
1 ATAGATCATAGTCATAGCC
144281 ATAGATCA
1 ATAGATCA
144289 CGAGCGCTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.29
Consensus pattern (19 bp):
ATAGATCATAGTCATAGCC
Found at i:145437 original size:30 final size:29
Alignment explanation
Indices: 145384--145573 Score: 197
Period size: 29 Copynumber: 6.5 Consensus size: 29
145374 GATAGTTGTC
* * *
145384 AAATTTTATTTTTACCCCTAAACTTTTAA
1 AAATTTCATTTTTACCCCAAAACTTTCAA
*
145413 AAATTTTATTTTTAACCCCAAAACTTTCAA
1 AAATTTCATTTTT-ACCCCAAAACTTTCAA
* *
145443 AAATCTCATTTTTACCCCAAAACCTTCAA
1 AAATTTCATTTTTACCCCAAAACTTTCAA
* ** *
145472 AAATTCCATTTTTACCCCCGAACTTCCAA
1 AAATTTCATTTTTACCCCAAAACTTTCAA
*
145501 AAATCTCATTTTTACCCCCAAAACTTTCAA
1 AAATTTCATTTTTA-CCCCAAAACTTTCAA
145531 AAA-TTCTATTTTTACCCTC-AAAC-TTCTAA
1 AAATTTC-ATTTTTACCC-CAAAACTTTC-AA
**
145560 AAATCCCATTTTTA
1 AAATTTCATTTTTA
145574 ACCTCAAATT
Statistics
Matches: 136, Mismatches: 19, Indels: 12
0.81 0.11 0.07
Matches are distributed among these distances:
28 3 0.02
29 84 0.62
30 49 0.36
ACGTcount: A:0.36, C:0.26, G:0.01, T:0.38
Consensus pattern (29 bp):
AAATTTCATTTTTACCCCAAAACTTTCAA
Found at i:145474 original size:59 final size:57
Alignment explanation
Indices: 145391--145573 Score: 233
Period size: 59 Copynumber: 3.1 Consensus size: 57
145381 GTCAAATTTT
* * *
145391 ATTTTTACCCCTAAACTTTTAAAAATTTTATTTTTAACCCCAAAACTTTCAAAAATCTC
1 ATTTTTACCCCAAAACTTTCAAAAATTCTATTTTT-ACCCC-AAACTTTCAAAAATCTC
* * * *
145450 ATTTTTACCCCAAAACCTTCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCTC
1 ATTTTTACCCCAAAACTTTCAAAAATTCTATTTTTA-CCCCAAACTTTCAAAAATCTC
*
145508 ATTTTTACCCCCAAAACTTTCAAAAATTCTATTTTTACCCTCAAAC-TTCTAAAAATCCC
1 ATTTTTA-CCCCAAAACTTTCAAAAATTCTATTTTTACCC-CAAACTTTC-AAAAATCTC
145567 ATTTTTA
1 ATTTTTA
145574 ACCTCAAATT
Statistics
Matches: 108, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
58 28 0.26
59 80 0.74
ACGTcount: A:0.36, C:0.27, G:0.01, T:0.37
Consensus pattern (57 bp):
ATTTTTACCCCAAAACTTTCAAAAATTCTATTTTTACCCCAAACTTTCAAAAATCTC
Found at i:145620 original size:28 final size:30
Alignment explanation
Indices: 145588--145652 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 30
145578 CAAATTTTCT
145588 CAAAATTATC-GTTTTG-CCCCCGAGAATC
1 CAAAATTATCAGTTTTGCCCCCCGAGAATC
*
145616 CAAAATTATCATTTTTTGCCCCCCGAGAATC
1 CAAAATTATCA-GTTTTGCCCCCCGAGAATC
145647 CGAAAA
1 C-AAAA
145653 GTCTCATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 10 0.31
30 5 0.16
31 13 0.41
32 4 0.12
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.28
Consensus pattern (30 bp):
CAAAATTATCAGTTTTGCCCCCCGAGAATC
Found at i:145635 original size:30 final size:32
Alignment explanation
Indices: 145599--145662 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 32
145589 AAAATTATCG
*
145599 TTTTG-CCCCCGAGAATCC-AAAATTATCATT
1 TTTTGCCCCCCGAGAATCCGAAAAGTATCATT
*
145629 TTTTGCCCCCCGAGAATCCGAAAAGTCTCATT
1 TTTTGCCCCCCGAGAATCCGAAAAGTATCATT
145661 TT
1 TT
145663 GAACTCCGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 5 0.17
31 13 0.43
32 12 0.40
ACGTcount: A:0.27, C:0.28, G:0.12, T:0.33
Consensus pattern (32 bp):
TTTTGCCCCCCGAGAATCCGAAAAGTATCATT
Found at i:154263 original size:7 final size:7
Alignment explanation
Indices: 154251--154285 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
154241 GGGTGTAACT
154251 AAATGAG
1 AAATGAG
154258 AAATGAG
1 AAATGAG
154265 AAATGAG
1 AAATGAG
154272 AAATGAG
1 AAATGAG
154279 AAATGAG
1 AAATGAG
154286 GAAAAAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.29, T:0.14
Consensus pattern (7 bp):
AAATGAG
Found at i:155118 original size:3 final size:3
Alignment explanation
Indices: 155110--155136 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
155100 TTTTTATTCC
155110 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
155137 GTAGTAGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:155820 original size:24 final size:24
Alignment explanation
Indices: 155793--155840 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
155783 ATGTGGAACT
*
155793 AGTAGAAAATGAAAATCTAACTCC
1 AGTAGAAAATGAAAATCCAACTCC
* *
155817 AGTAGAAATTGAAGATCCAACTCC
1 AGTAGAAAATGAAAATCCAACTCC
155841 GTGTATGGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.21
Consensus pattern (24 bp):
AGTAGAAAATGAAAATCCAACTCC
Found at i:156589 original size:58 final size:58
Alignment explanation
Indices: 156523--156642 Score: 197
Period size: 58 Copynumber: 2.1 Consensus size: 58
156513 ACCTATCAAC
*
156523 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCTTCAAA-AACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCT-AAATAACACTCAT
* *
156581 AAACTAAACCCAAATATTTTTAAACTCAAATATAATTTTATTCCTAAATAACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTAAATAACACTCAT
156639 AAAC
1 AAAC
156643 AACTTTTTTC
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
57 3 0.05
58 55 0.95
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (58 bp):
AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTAAATAACACTCAT
Found at i:156891 original size:21 final size:20
Alignment explanation
Indices: 156860--156902 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
156850 TGTTCGTTTA
156860 TTTGATTTTTGTTGTGTTGT
1 TTTGATTTTTGTTGTGTTGT
*
156880 TTTGATTTTTTGTTTTGTTGT
1 TTTGA-TTTTTGTTGTGTTGT
156901 TT
1 TT
156903 GGAATGGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.05, C:0.00, G:0.21, T:0.74
Consensus pattern (20 bp):
TTTGATTTTTGTTGTGTTGT
Found at i:159574 original size:16 final size:15
Alignment explanation
Indices: 159554--159600 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
159544 ATTATTTAGG
159554 GTTTAAGGTTTTTAA
1 GTTTAAGGTTTTTAA
* *
159569 GATTTAATGTTTTCAA
1 G-TTTAAGGTTTTTAA
*
159585 GTTTTAGGTTTTTAA
1 GTTTAAGGTTTTTAA
159600 G
1 G
159601 GTTATAAGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.26, C:0.02, G:0.19, T:0.53
Consensus pattern (15 bp):
GTTTAAGGTTTTTAA
Found at i:163457 original size:26 final size:26
Alignment explanation
Indices: 163417--163468 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
163407 ATGAATTTGG
*
163417 AATTAATTATGTTTAAATTTGTATTT
1 AATTAATAATGTTTAAATTTGTATTT
* **
163443 AATTAATAATTTTTATGTTTGTATTT
1 AATTAATAATGTTTAAATTTGTATTT
163469 TGGTTTAGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.60
Consensus pattern (26 bp):
AATTAATAATGTTTAAATTTGTATTT
Found at i:163660 original size:16 final size:16
Alignment explanation
Indices: 163639--163690 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
163629 TTTATGATTA
163639 TTTAAGGTTTAAGGTT
1 TTTAAGGTTTAAGGTT
* * *
163655 TTTAAGATTTCATG-T
1 TTTAAGGTTTAAGGTT
*
163670 TTTAAGGTTTTAGGTT
1 TTTAAGGTTTAAGGTT
163686 TTTAA
1 TTTAA
163691 TGTTATAGGT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
15 12 0.41
16 17 0.59
ACGTcount: A:0.25, C:0.02, G:0.19, T:0.54
Consensus pattern (16 bp):
TTTAAGGTTTAAGGTT
Found at i:163699 original size:16 final size:16
Alignment explanation
Indices: 163639--163701 Score: 51
Period size: 16 Copynumber: 4.0 Consensus size: 16
163629 TTTATGATTA
163639 TTTAAGGTT-TAAGGTT
1 TTTAAGGTTAT-AGGTT
* *
163655 TTTAAGATT-TCATG-T
1 TTTAAGGTTAT-AGGTT
*
163670 TTTAAGGTTTTAGGTT
1 TTTAAGGTTATAGGTT
*
163686 TTTAATGTTATAGGTT
1 TTTAAGGTTATAGGTT
163702 ATAGGTTTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
15 11 0.29
16 27 0.71
ACGTcount: A:0.24, C:0.02, G:0.21, T:0.54
Consensus pattern (16 bp):
TTTAAGGTTATAGGTT
Found at i:163840 original size:60 final size:60
Alignment explanation
Indices: 163765--163885 Score: 233
Period size: 60 Copynumber: 2.0 Consensus size: 60
163755 GCATAATCCT
*
163765 TGTTGAATTTGTGGGTTGGGTCGTTTAAGTAGAAAATCAAAGTCAAACCTTTGTTAATTA
1 TGTTGAATTTATGGGTTGGGTCGTTTAAGTAGAAAATCAAAGTCAAACCTTTGTTAATTA
163825 TGTTGAATTTATGGGTTGGGTCGTTTAAGTAGAAAATCAAAGTCAAACCTTTGTTAATTA
1 TGTTGAATTTATGGGTTGGGTCGTTTAAGTAGAAAATCAAAGTCAAACCTTTGTTAATTA
163885 T
1 T
163886 TAGGTTAAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (60 bp):
TGTTGAATTTATGGGTTGGGTCGTTTAAGTAGAAAATCAAAGTCAAACCTTTGTTAATTA
Found at i:164811 original size:16 final size:17
Alignment explanation
Indices: 164778--164814 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
164768 ATAAAATTAG
*
164778 CTTT-CTCTCTTTCTTT
1 CTTTCCTCTCCTTCTTT
164794 CTTTCCTCTCCTTC-TT
1 CTTTCCTCTCCTTCTTT
164810 CTTTC
1 CTTTC
164815 TTTGTTTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (17 bp):
CTTTCCTCTCCTTCTTT
Found at i:164813 original size:24 final size:25
Alignment explanation
Indices: 164780--164827 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
164770 AAAATTAGCT
164780 TTCTCTCTTTCTTTCTTTCCTCTCC
1 TTCTCTCTTTCTTTCTTTCCTCTCC
*
164805 TTCT-TCTTTCTTTGTTTCCTCTC
1 TTCTCTCTTTCTTTCTTTCCTCTC
164828 TCTACTGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.00, C:0.35, G:0.02, T:0.62
Consensus pattern (25 bp):
TTCTCTCTTTCTTTCTTTCCTCTCC
Found at i:165572 original size:5 final size:5
Alignment explanation
Indices: 165562--165589 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
165552 ACTACTAACA
165562 AAATT AAATT AAATT AAATT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAA
165590 AATAACCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AAATT
Found at i:165806 original size:12 final size:12
Alignment explanation
Indices: 165789--165844 Score: 60
Period size: 12 Copynumber: 4.6 Consensus size: 12
165779 TTTACTCAAC
165789 TAAATAAAAAAT
1 TAAATAAAAAAT
*
165801 TAAATAACAAAT
1 TAAATAAAAAAT
*
165813 CAAAT-AAAAAT
1 TAAATAAAAAAT
*
165824 TAAATTAAACAAAA
1 TAAA-TAAA-AAAT
165838 TAAATAA
1 TAAATAA
165845 CTTAAAATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
11 8 0.22
12 16 0.44
13 5 0.14
14 7 0.19
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.23
Consensus pattern (12 bp):
TAAATAAAAAAT
Found at i:165834 original size:25 final size:23
Alignment explanation
Indices: 165789--165844 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 23
165779 TTTACTCAAC
165789 TAAATAAAAAATTAAATAAC-AAA
1 TAAAT-AAAAATTAAATAACAAAA
165812 TCAAATAAAAATTAAATTAAACAAAA
1 T-AAATAAAAATTAAA-T-AACAAAA
165838 TAAATAA
1 TAAATAA
165845 CTTAAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.38
24 5 0.17
25 9 0.31
26 4 0.14
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.23
Consensus pattern (23 bp):
TAAATAAAAATTAAATAACAAAA
Found at i:166642 original size:23 final size:24
Alignment explanation
Indices: 166597--166642 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
166587 ATTAAACTAT
*
166597 TTTTATAAAATAATATAATTTTAA
1 TTTTATAAAATAATATAAATTTAA
166621 TTTTA-AAAATAAT-TAAAATTTA
1 TTTTATAAAATAATAT-AAATTTA
166643 CCTAGCATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 14 0.70
24 5 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTTATAAAATAATATAAATTTAA
Found at i:166824 original size:33 final size:33
Alignment explanation
Indices: 166776--166839 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
166766 CTTTTAAAAC
*
166776 TACCCTAAATAGTAGGGGCACTATTCTAAAGAT
1 TACCCTAAATAGTAGGGGCACCATTCTAAAGAT
* *
166809 TACCCTAAGTGGTAGGGGCACCATTCTAAAG
1 TACCCTAAATAGTAGGGGCACCATTCTAAAG
166840 CATCAAGTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (33 bp):
TACCCTAAATAGTAGGGGCACCATTCTAAAGAT
Found at i:169462 original size:11 final size:11
Alignment explanation
Indices: 169448--169472 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
169438 GTATTGCTTT
169448 TTTTTTTTTTA
1 TTTTTTTTTTA
169459 TTTTTTTTTTA
1 TTTTTTTTTTA
169470 TTT
1 TTT
169473 ATAGAAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTTA
Found at i:169463 original size:15 final size:15
Alignment explanation
Indices: 169445--169474 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
169435 TTTGTATTGC
169445 TTTTTTTTTT-TTTA
1 TTTTTTTTTTATTTA
169459 TTTTTTTTTTATTTA
1 TTTTTTTTTTATTTA
169474 T
1 T
169475 AGAAAATGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTTTTTTATTTA
Found at i:178655 original size:31 final size:32
Alignment explanation
Indices: 178593--178656 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
178583 TTTTTTGTCC
** *
178593 AATTAGGTACTTGAACTTAGCTTTTTGGTTCA
1 AATTAGGTACTTGAACTTAGCTTCATAGTTCA
*
178625 AATTA-GTACTTGAACTTGGCTTCATAGTTCA
1 AATTAGGTACTTGAACTTAGCTTCATAGTTCA
178656 A
1 A
178657 GTTGATTCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (32 bp):
AATTAGGTACTTGAACTTAGCTTCATAGTTCA
Found at i:186948 original size:9 final size:9
Alignment explanation
Indices: 186936--187037 Score: 57
Period size: 9 Copynumber: 11.3 Consensus size: 9
186926 TTAACTGATT
186936 TTTTTAAAA
1 TTTTTAAAA
186945 -TTTTAATAA
1 TTTTTAA-AA
*
186954 TATTTAAAA
1 TTTTTAAAA
* *
186963 ATTTTATAA
1 TTTTTAAAA
* *
186972 TTTTTATAC
1 TTTTTAAAA
186981 TTTTTAAATA
1 TTTTTAAA-A
* *
186991 ATTTTAATA
1 TTTTTAAAA
*
187000 TTTTT--TA
1 TTTTTAAAA
187007 TTTTTAAAA
1 TTTTTAAAA
* *
187016 ATTTAAAAA
1 TTTTTAAAA
*
187025 TTAATTAAAA
1 TT-TTTAAAA
187035 TTT
1 TTT
187038 GACATGTCAT
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
7 7 0.10
8 6 0.09
9 38 0.55
10 18 0.26
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:186974 original size:27 final size:28
Alignment explanation
Indices: 186937--187003 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
186927 TAACTGATTT
186937 TTTTAAAATTTTAATAATATTTAAA-AA
1 TTTTAAAATTTTAATAATATTTAAATAA
* * * *
186964 TTTTATAATTTTTATACTTTTTAAATAA
1 TTTTAAAATTTTAATAATATTTAAATAA
*
186992 TTTTAATATTTT
1 TTTTAAAATTTT
187004 TTATTTTTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 21 0.64
28 12 0.36
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (28 bp):
TTTTAAAATTTTAATAATATTTAAATAA
Found at i:186993 original size:20 final size:20
Alignment explanation
Indices: 186968--187006 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
186958 TAAAAATTTT
*
186968 ATAATTTTTATACTTTTTAA
1 ATAATTTTAATACTTTTTAA
*
186988 ATAATTTTAATATTTTTTA
1 ATAATTTTAATACTTTTTA
187007 TTTTTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
ATAATTTTAATACTTTTTAA
Found at i:190548 original size:23 final size:23
Alignment explanation
Indices: 190518--190574 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
190508 CACACAGTGC
190518 AATCAGTAGGCGCACATAGCGCA
1 AATCAGTAGGCGCACATAGCGCA
190541 AATCAGTAGGCGCACATAGCGCA
1 AATCAGTAGGCGCACATAGCGCA
190564 AATCAGTAGGC
1 AATCAGTAGGC
190575 ACACGAGGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.35, C:0.25, G:0.26, T:0.14
Consensus pattern (23 bp):
AATCAGTAGGCGCACATAGCGCA
Found at i:190593 original size:23 final size:23
Alignment explanation
Indices: 190582--190666 Score: 154
Period size: 23 Copynumber: 3.7 Consensus size: 23
190572 GGCACACGAG
190582 GTGCGAAACAGTAAGCACACACA
1 GTGCGAAACAGTAAGCACACACA
190605 GTGCGAAACAGTAAGCACACACA
1 GTGCGAAACAGTAAGCACACACA
190628 GTGCGAAACAGTAAGCACACACA
1 GTGCGAAACAGTAAGCACACACA
190651 GTGCTG-AACAGTAAGC
1 GTGC-GAAACAGTAAGC
190667 GCGCTAGCGT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
23 60 0.98
24 1 0.02
ACGTcount: A:0.41, C:0.25, G:0.24, T:0.11
Consensus pattern (23 bp):
GTGCGAAACAGTAAGCACACACA
Found at i:190594 original size:46 final size:46
Alignment explanation
Indices: 190472--190666 Score: 150
Period size: 46 Copynumber: 4.3 Consensus size: 46
190462 AAGTGCTAGG
* * * * *
190472 GAAATAGTAAGCACACACAATGC-AATCCAATAAGCACACACAGTGC
1 GAAACAGTAAGCACACACAGTGCGAA-ACAGTAAGCACACACAGCGC
* * * * * * * *
190518 -AATCAGTAGGCGCACATAGCGC-AAATCAGTAGGCGCACATAGCGC
1 GAAACAGTAAGCACACACAGTGCGAAA-CAGTAAGCACACACAGCGC
* * *
190563 -AAATCAGTAGGCACACGA-GGTGCGAAACAGTAAGCACACACAGTGC
1 GAAA-CAGTAAGCACAC-ACAGTGCGAAACAGTAAGCACACACAGCGC
*
190609 GAAACAGTAAGCACACACAGTGCGAAACAGTAAGCACACACAGTGC
1 GAAACAGTAAGCACACACAGTGCGAAACAGTAAGCACACACAGCGC
190655 TG-AACAGTAAGC
1 -GAAACAGTAAGC
190667 GCGCTAGCGT
Statistics
Matches: 119, Mismatches: 23, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
45 34 0.29
46 77 0.65
47 8 0.07
ACGTcount: A:0.41, C:0.25, G:0.23, T:0.12
Consensus pattern (46 bp):
GAAACAGTAAGCACACACAGTGCGAAACAGTAAGCACACACAGCGC
Found at i:190661 original size:69 final size:66
Alignment explanation
Indices: 190448--190666 Score: 174
Period size: 69 Copynumber: 3.2 Consensus size: 66
190438 CGAAGTACTT
* * * *
190448 AACAGTAAGCACACAAGTGCTAGGGAAATAGTAAGCACACACAATGCAATCCAATAAGCACACAC
1 AACAGTAAGCACACAAGTGC----GAAACAGTAAGCACACACAGTGCAA-ACAGTAAGCACACAC
190513 AGTGC-
61 AGTGCG
* * * * * * * *
190518 AATCAGTAGGCGCACATAGCGC-AAATCAGTAGGCGCACATAGCGCAAATCAGTAGGCACACGA-
1 AA-CAGTAAGCACACA-AGTGCGAAA-CAGTAAGCACACACAGTGCAAA-CAGTAAGCACAC-AC
*
190581 GGTGCG
61 AGTGCG
190587 AAACAGTAAGCACACACAGTGCGAAACAGTAAGCACACACAGTGCGAAACAGTAAGCACACACAG
1 -AACAGTAAGCACACA-AGTGCGAAACAGTAAGCACACACAGTGC-AAACAGTAAGCACACACAG
190652 TGCTG
63 TGC-G
190657 AACAGTAAGC
1 AACAGTAAGC
190667 GCGCTAGCGT
Statistics
Matches: 115, Mismatches: 23, Indels: 23
0.71 0.14 0.14
Matches are distributed among these distances:
67 3 0.03
68 30 0.26
69 56 0.49
70 11 0.10
71 11 0.10
72 4 0.03
ACGTcount: A:0.41, C:0.25, G:0.23, T:0.12
Consensus pattern (66 bp):
AACAGTAAGCACACAAGTGCGAAACAGTAAGCACACACAGTGCAAACAGTAAGCACACACAGTGC
G
Found at i:192866 original size:29 final size:30
Alignment explanation
Indices: 192834--192890 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
192824 TTATCTTTTA
192834 AAAATAAAAATAACAGAATT-AAATTTATT
1 AAAATAAAAATAACAGAATTAAAATTTATT
*
192863 AAAATAAAAATAAGAGAATTAAAATTTA
1 AAAATAAAAATAACAGAATTAAAATTTA
192891 AATATAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (30 bp):
AAAATAAAAATAACAGAATTAAAATTTATT
Found at i:200688 original size:60 final size:61
Alignment explanation
Indices: 200465--200736 Score: 309
Period size: 61 Copynumber: 4.5 Consensus size: 61
200455 TCAAAAAAAA
* * * * **
200465 TTTGTGTTAGCCATGCAATGGCCGACA-CCCCTTGTTCTCGGATAAAAAAATTTTAATTTTTT
1 TTTGTGTTGGCTATGCAATGGCCGACACCCCCTT-TT-TCAGATAAAAAAATTTCAAAATTTT
** * *
200527 TTTGTGTTGG-TCATGCAATGATCGACACCCCCTTTTTTAGCTAAAAAAATTTCAAAATTTT
1 TTTGTGTTGGCT-ATGCAATGGCCGACACCCCCTTTTTCAGATAAAAAAATTTCAAAATTTT
* * * ** * *
200588 TTTATGTTGACCATGCAATAACCGACACCCTCTTTTTTCAGATAAAAAAAATTC-AAATTTT
1 TTTGTGTTGGCTATGCAATGGCCGACACCC-CCTTTTTCAGATAAAAAAATTTCAAAATTTT
* *
200649 TTGGTGTTGGCTATGCAGTGGCCGACACCCCCTTTTTCAGAT-AAAAAATTTCAAAATTTT
1 TTTGTGTTGGCTATGCAATGGCCGACACCCCCTTTTTCAGATAAAAAAATTTCAAAATTTT
200709 TTTGTGTTGGCTATGCAATGGCCGACAC
1 TTTGTGTTGGCTATGCAATGGCCGACAC
200737 TAACTTCCCC
Statistics
Matches: 175, Mismatches: 30, Indels: 12
0.81 0.14 0.06
Matches are distributed among these distances:
59 9 0.05
60 44 0.25
61 73 0.42
62 43 0.25
63 6 0.03
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (61 bp):
TTTGTGTTGGCTATGCAATGGCCGACACCCCCTTTTTCAGATAAAAAAATTTCAAAATTTT
Found at i:206125 original size:30 final size:30
Alignment explanation
Indices: 206091--206182 Score: 105
Period size: 30 Copynumber: 3.1 Consensus size: 30
206081 TCCGTTTGCT
* *
206091 TTTTAAATTTAATTTGTAATTTCATT-TTTA
1 TTTTAAATTTAATTTCTAATTTC-TTGTATA
206121 TTTTAAATTTAATTTCTAATTTCTTGTATA
1 TTTTAAATTTAATTTCTAATTTCTTGTATA
* ** * *
206151 TTTTAATTTTTTTTTCTAACTTCATGTATA
1 TTTTAAATTTAATTTCTAATTTCTTGTATA
206181 TT
1 TT
206183 CTAATTATTT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
29 2 0.04
30 52 0.96
ACGTcount: A:0.27, C:0.07, G:0.03, T:0.63
Consensus pattern (30 bp):
TTTTAAATTTAATTTCTAATTTCTTGTATA
Found at i:206188 original size:30 final size:31
Alignment explanation
Indices: 206133--206196 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
206123 TTAAATTTAA
* * *
206133 TTTCTAATTTCTTGTATATTTTAATT-TTTT
1 TTTCTAACTTCATGTATATTCTAATTATTTT
206163 TTTCTAACTTCATGTATATTCTAATTATTTT
1 TTTCTAACTTCATGTATATTCTAATTATTTT
206194 TTT
1 TTT
206197 TAAAAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 23 0.77
31 7 0.23
ACGTcount: A:0.22, C:0.09, G:0.03, T:0.66
Consensus pattern (31 bp):
TTTCTAACTTCATGTATATTCTAATTATTTT
Found at i:207026 original size:61 final size:60
Alignment explanation
Indices: 206945--207646 Score: 443
Period size: 61 Copynumber: 11.7 Consensus size: 60
206935 ACTTATAAAT
* * *
206945 AAAAAAAGGGTGTCGGCCATTGCATGGGCAACACAAAAAAATTTTGAAATTTTTTTATCTG
1 AAAAAAGGGGTGTCGACCATTGCATGGCCAACACAAAAAAA-TTTGAAATTTTTTTATCTG
* * * * *
207006 ATAACAGGGGTGTCGACCATTGCATAGCCAACACCAAAAAAATTTAAAATTTTTTTATCCG
1 AAAAAAGGGGTGTCGACCATTGCATGGCCAACA-CAAAAAAATTTGAAATTTTTTTATCTG
* * * *
207067 AGAAAAGGAGGTATCGACCATTGCATGGCCAATACAAAAAAATTTTGAATTTTTTTTATCTG
1 AAAAAAGG-GGTGTCGACCATTGCATGGCCAACACAAAAAAA-TTTGAAATTTTTTTATCTG
207129 AAAAAAGGGGAAAGGGGCTGTCGACCATTGCATGGCCAACACCAAAAAAATTTGAAATTTTTTTA
1 ---AAA----AAAGGGG-TGTCGACCATTGCATGGCCAACA-CAAAAAAATTTGAAATTTTTTTA
207194 TCTG
57 TCTG
* * ** *
207198 ATAACAGGGGGTGTCGACCATTGCATAACCAACACCAAATAAAA-TTAAAATTTTTTTATCTG
1 A-AAAAAGGGGTGTCGACCATTGCATGGCCAACA-CAAA-AAAATTTGAAATTTTTTTATCTG
* * * *
207260 AAAAAGGGGGTGTCGACCATTGCATAGCCAATACCAAAAAAATTAGAAA-TTTTTTATCTG
1 AAAAAAGGGGTGTCGACCATTGCATGGCCAACA-CAAAAAAATTTGAAATTTTTTTATCTG
* * * * *****
207320 AGAAAAATGGGTGTCG----GT-CAT-G------CAAAAAAATTTAAAATTTTTATCCAAA
1 A-AAAAAGGGGTGTCGACCATTGCATGGCCAACACAAAAAAATTTGAAATTTTTTTATCTG
* * * * * * * * * *
207369 AAAAGAAAGTGTCGGCCATTACA-TG-A--CCAAAAC-CAAAAAATTTTAAATTTTTT-TATCTG
1 AAAA-AAGGGGT-GTCGA--CCATTGCATGGC-CAACACAAAAAAATTTGAAATTTTTTTATCTG
** * * *
207428 -AAAAAGGGGTGTCGACCATTGCATGGCCAACACCCAAAAA--TGCAACTTTTTTATCCG
1 AAAAAAGGGGTGTCGACCATTGCATGGCCAACACAAAAAAATTTGAAATTTTTTTATCTG
* * * * *
207485 AGAAAAGGGGGTGTCG-CTATTGCATGACCAACACCAAAAAATTTTAAATTTTTTTA-CTTG
1 A-AAAAAGGGGTGTCGACCATTGCATGGCCAACACAAAAAAATTTGAAATTTTTTTATC-TG
* ** * *
207545 AAAAAAGGGGTGTCGACCATTGGATGGCCAACACCCAAAAA--TAAAATTTTTTTATC-A
1 AAAAAAGGGGTGTCGACCATTGCATGGCCAACACAAAAAAATTTGAAATTTTTTTATCTG
* * *
207602 AATAAATAAGGGTGTCGACCATTGTATGCCCAACACAAAAAAATT
1 AA-AAA-AGGGGTGTCGACCATTGCATGGCCAACACAAAAAAATT
207647 ATATTTTTAT
Statistics
Matches: 504, Mismatches: 88, Indels: 98
0.73 0.13 0.14
Matches are distributed among these distances:
48 16 0.03
49 11 0.02
50 2 0.00
54 2 0.00
55 5 0.01
56 13 0.03
57 16 0.03
58 46 0.09
59 60 0.12
60 67 0.13
61 108 0.21
62 90 0.18
63 9 0.02
65 2 0.00
66 1 0.00
67 2 0.00
68 2 0.00
69 44 0.09
70 8 0.02
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (60 bp):
AAAAAAGGGGTGTCGACCATTGCATGGCCAACACAAAAAAATTTGAAATTTTTTTATCTG
Found at i:207084 original size:62 final size:62
Alignment explanation
Indices: 206953--207325 Score: 409
Period size: 62 Copynumber: 6.0 Consensus size: 62
206943 ATAAAAAAAG
* * * * * *
206953 GGTGTCGGCCATTGCATGGGCAACA-CAAAAAAATTTTGAAATTTTTTTATCTGATAACAGG-
1 GGTGTCGACCATTGCATAGCCAACACCAAAAAAA-TTTAAAATTTTTTTATCTGAGAAAAGGA
*
207014 GGTGTCGACCATTGCATAGCCAACACCAAAAAAATTTAAAATTTTTTTATCCGAGAAAAGGA
1 GGTGTCGACCATTGCATAGCCAACACCAAAAAAATTTAAAATTTTTTTATCTGAGAAAAGGA
* * * * * *
207076 GGTATCGACCATTGCATGGCCAATA-CAAAAAAATTTTGAATTTTTTTTATCTGAAAAAAGGGGA
1 GGTGTCGACCATTGCATAGCCAACACCAAAAAAA-TTTAAAATTTTTTTATCTGAGAAAA--GG-
207140 AA
62 -A
* * * * *
207142 GGGGCTGTCGACCATTGCATGGCCAACACCAAAAAAATTTGAAATTTTTTTATCTGATAACAGGG
1 --GG-TGTCGACCATTGCATAGCCAACACCAAAAAAATTTAAAATTTTTTTATCTGAGAAAAGGA
* *
207207 GGTGTCGACCATTGCATAACCAACACCAAATAAAA-TTAAAATTTTTTTATCTGA-AAAAGGG
1 GGTGTCGACCATTGCATAGCCAACACCAAA-AAAATTTAAAATTTTTTTATCTGAGAAAAGGA
*
207268 GGTGTCGACCATTGCATAGCCAATACCAAAAAAA-TTAGAAA-TTTTTTATCTGAGAAAA
1 GGTGTCGACCATTGCATAGCCAACACCAAAAAAATTTA-AAATTTTTTTATCTGAGAAAA
207326 ATGGGTGTCG
Statistics
Matches: 272, Mismatches: 26, Indels: 28
0.83 0.08 0.09
Matches are distributed among these distances:
60 19 0.07
61 94 0.35
62 95 0.35
63 6 0.02
64 2 0.01
66 1 0.00
67 2 0.01
68 2 0.01
69 43 0.16
70 8 0.03
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (62 bp):
GGTGTCGACCATTGCATAGCCAACACCAAAAAAATTTAAAATTTTTTTATCTGAGAAAAGGA
Found at i:207292 original size:192 final size:192
Alignment explanation
Indices: 206955--207326 Score: 583
Period size: 192 Copynumber: 1.9 Consensus size: 192
206945 AAAAAAAGGG
* *
206955 TGTCGGCCATTGCATGGGCAACACAAAAAAATTTTGAAATTTTTTTATCTGATAACAGGGGTGTC
1 TGTCGACCATTGCATGGCCAACACAAAAAAATTTTGAAATTTTTTTATCTGATAACAGGGGTGTC
*
207020 GACCATTGCATAGCCAACACCAAAAAAATTTAAAATTTTTTTATCCGAGAAAAGGAGGTATCGAC
66 GACCATTGCATAACCAACACCAAAAAAATTTAAAATTTTTTTATCCGAGAAAAGGAGGTATCGAC
* * *
207085 CATTGCATGGCCAATA-CAAAAAAATTTTGAATTTTTTTTATCTGA-AAAAAGGGGAAAGGGGC
131 CATTGCATAGCCAATACCAAAAAAA-TTAGAA-ATTTTTTATCTGAGAAAAAGGGGAAAGGGGC
207147 TGTCGACCATTGCATGGCCAACACCAAAAAAA-TTTGAAATTTTTTTATCTGATAACAGGGGGTG
1 TGTCGACCATTGCATGGCCAACA-CAAAAAAATTTTGAAATTTTTTTATCTGATAACA-GGGGTG
* * *
207211 TCGACCATTGCATAACCAACACCAAATAAAA-TTAAAATTTTTTTATCTGA-AAAAGGGGGTGTC
64 TCGACCATTGCATAACCAACACCAAA-AAAATTTAAAATTTTTTTATCCGAGAAAAGGAGGTATC
207274 GACCATTGCATAGCCAATACCAAAAAAATTAGAAATTTTTTATCTGAGAAAAA
128 GACCATTGCATAGCCAATACCAAAAAAATTAGAAATTTTTTATCTGAGAAAAA
207327 TGGGTGTCGG
Statistics
Matches: 166, Mismatches: 9, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
191 12 0.07
192 85 0.51
193 65 0.39
194 4 0.02
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.28
Consensus pattern (192 bp):
TGTCGACCATTGCATGGCCAACACAAAAAAATTTTGAAATTTTTTTATCTGATAACAGGGGTGTC
GACCATTGCATAACCAACACCAAAAAAATTTAAAATTTTTTTATCCGAGAAAAGGAGGTATCGAC
CATTGCATAGCCAATACCAAAAAAATTAGAAATTTTTTATCTGAGAAAAAGGGGAAAGGGGC
Found at i:207440 original size:59 final size:57
Alignment explanation
Indices: 207377--207654 Score: 263
Period size: 59 Copynumber: 4.7 Consensus size: 57
207367 AAAAAAGAAA
* * *
207377 GTGTCGGCCATTACATGACCAAAACCAAAAAATTTTAAATTTTTTTATCTGAAAAAGGG
1 GTGTCGACCATTGCATGACCAACACCAAAAAA--TTAAATTTTTTTATCTGAAAAAGGG
* * ** * *
207436 GTGTCGACCATTGCATGGCCAACACCCAAAAATGCAACTTTTTTATCCGAGAAAAGGGG
1 GTGTCGACCATTGCATGACCAACACCAAAAAATTAAATTTTTTTATCTGA-AAAA-GGG
*
207495 GTGTCG-CTATTGCATGACCAACACCAAAAAATTTTAAATTTTTTTA-CTTGAAAAAAGGG
1 GTGTCGACCATTGCATGACCAACACCAAAAAA--TTAAATTTTTTTATC-TG-AAAAAGGG
* * * * ** *
207554 GTGTCGACCATTGGATGGCCAACACCCAAAAATAAAATTTTTTTATCAAATAAATAAGG
1 GTGTCGACCATTGCATGACCAACACCAAAAAATTAAATTTTTTTATCTGA-AAA-AGGG
* * * *
207613 GTGTCGACCATTGTATGCCCAACACAAAAAAATTATATTTTT
1 GTGTCGACCATTGCATGACCAACACCAAAAAATTAAATTTTT
207655 ATCTGACAAA
Statistics
Matches: 179, Mismatches: 30, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
57 15 0.08
58 41 0.23
59 86 0.48
60 36 0.20
61 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (57 bp):
GTGTCGACCATTGCATGACCAACACCAAAAAATTAAATTTTTTTATCTGAAAAAGGG
Found at i:207615 original size:118 final size:118
Alignment explanation
Indices: 207357--207646 Score: 363
Period size: 118 Copynumber: 2.5 Consensus size: 118
207347 AAATTTAAAA
** * * *
207357 TTTTTATCCAAA-AAAAGAAAGTGTCGGCCATTACATGACCAAAACCAAAAAATTTTAAATTTTT
1 TTTTTAT-CAAAGAAAAGAGGGTGTCGACCATTGCATGACCAACACCAAAAAATTTTAAATTTTT
**
207421 TTATCTGAAAAAGGGGTGTCGACCATTGCATGGCCAACACCCAAAAATGCAACT
65 TTATCTGAAAAAGGGGTGTCGACCATTGCATGGCCAACACCCAAAAATAAAACT
** * *
207475 TTTTTATCCGAGAAAAGGGGGTGTCG-CTATTGCATGACCAACACCAAAAAATTTTAAATTTTTT
1 TTTTTATCAAAGAAAAGAGGGTGTCGACCATTGCATGACCAACACCAAAAAATTTTAAATTTTTT
* *
207539 TA-CTTGAAAAAAGGGGTGTCGACCATTGGATGGCCAACACCCAAAAATAAAATT
66 TATC-TG-AAAAAGGGGTGTCGACCATTGCATGGCCAACACCCAAAAATAAAACT
* * * *
207593 TTTTTATCAAATAAATA-AGGGTGTCGACCATTGTATGCCCAACACAAAAAAATT
1 TTTTTATCAAAGAAA-AGAGGGTGTCGACCATTGCATGACCAACACCAAAAAATT
207647 ATATTTTTAT
Statistics
Matches: 147, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
116 1 0.01
117 41 0.28
118 81 0.55
119 24 0.16
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.28
Consensus pattern (118 bp):
TTTTTATCAAAGAAAAGAGGGTGTCGACCATTGCATGACCAACACCAAAAAATTTTAAATTTTTT
TATCTGAAAAAGGGGTGTCGACCATTGCATGGCCAACACCCAAAAATAAAACT
Found at i:213245 original size:3 final size:3
Alignment explanation
Indices: 213239--213263 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
213229 GTTTGAACAC
213239 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
213264 TTTGTACTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:217462 original size:6 final size:6
Alignment explanation
Indices: 217451--217483 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
217441 CCACAGTCAT
217451 ATATAC ATATAC ATATAC ATATAC ATATAC ATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATA
217484 CAAAAAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAC
Found at i:221757 original size:24 final size:26
Alignment explanation
Indices: 221715--221762 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
221705 GGGTGGAACA
*
221715 GAAGAGAGAAAGAATGGAGGGTTTTG
1 GAAGAGAGAAAGAATGGAGCGTTTTG
*
221741 GAAGAGAGGAAG-A-GGAGCGTTT
1 GAAGAGAGAAAGAATGGAGCGTTT
221763 AATAGAGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 1 0.05
26 11 0.55
ACGTcount: A:0.38, C:0.02, G:0.44, T:0.17
Consensus pattern (26 bp):
GAAGAGAGAAAGAATGGAGCGTTTTG
Found at i:226149 original size:11 final size:12
Alignment explanation
Indices: 226119--226153 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
226109 GTCCGGTTCG
226119 TATTAATTTTTTA
1 TATTAA-TTTTTA
226132 TATTAATTTTTA
1 TATTAATTTTTA
226144 TA-TAATTTTT
1 TATTAATTTTT
226154 TGAAATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 8 0.36
12 8 0.36
13 6 0.27
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TATTAATTTTTA
Found at i:226154 original size:12 final size:13
Alignment explanation
Indices: 226119--226154 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
226109 GTCCGGTTCG
226119 TATTAATTTTTTA
1 TATTAATTTTTTA
226132 TATTAA-TTTTTA
1 TATTAATTTTTTA
226144 TA-TAATTTTTT
1 TATTAATTTTTT
226155 GAAATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 3 0.14
12 13 0.59
13 6 0.27
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TATTAATTTTTTA
Found at i:226960 original size:23 final size:23
Alignment explanation
Indices: 226909--226960 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
226899 AATGTGAAAC
226909 TTTTTTCATTTCTCTACAAAAAA
1 TTTTTTCATTTCTCTACAAAAAA
** *
226932 AATTTTCATTTCTCT-CGAAATAA
1 TTTTTTCATTTCTCTAC-AAAAAA
226955 TTTTTT
1 TTTTTT
226961 TTTGAATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.31, C:0.15, G:0.02, T:0.52
Consensus pattern (23 bp):
TTTTTTCATTTCTCTACAAAAAA
Found at i:234074 original size:13 final size:13
Alignment explanation
Indices: 234056--234080 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
234046 GTTTTAGTTT
234056 AATTTTATTTTCG
1 AATTTTATTTTCG
234069 AATTTTATTTTC
1 AATTTTATTTTC
234081 CAACTTCACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.04, T:0.64
Consensus pattern (13 bp):
AATTTTATTTTCG
Found at i:236048 original size:25 final size:25
Alignment explanation
Indices: 236014--236062 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
236004 ACTTTGTATG
236014 TCACCTTTGTGGCGTATTCTATATA
1 TCACCTTTGTGGCGTATTCTATATA
**
236039 TCACCTTTGTGTTGTATTCTATAT
1 TCACCTTTGTGGCGTATTCTATAT
236063 GTTGTGCTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.14, T:0.49
Consensus pattern (25 bp):
TCACCTTTGTGGCGTATTCTATATA
Found at i:238216 original size:23 final size:22
Alignment explanation
Indices: 238186--238308 Score: 120
Period size: 23 Copynumber: 5.4 Consensus size: 22
238176 GCTAGCGCGT
238186 TTACTGTTTCGCACTTTGTGTGC
1 TTACTGTTT-GCACTTTGTGTGC
*
238209 TTACTGTTTCGCACTTCGTGTGC
1 TTACTGTTT-GCACTTTGTGTGC
* * *
238232 TTACTGATTTGCGCTATGTGCGC
1 TTACTG-TTTGCACTTTGTGTGC
* *
238255 TTACTGATTGCACTGTGTGTGC
1 TTACTGTTTGCACTTTGTGTGC
* * * *
238277 CTACTGGATTGCACTGTGTGTGT
1 TTACT-GTTTGCACTTTGTGTGC
238300 TTACTGTTT
1 TTACTGTTT
238309 CCCCAACACT
Statistics
Matches: 85, Mismatches: 13, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
22 19 0.22
23 63 0.74
24 3 0.04
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.44
Consensus pattern (22 bp):
TTACTGTTTGCACTTTGTGTGC
Found at i:238304 original size:45 final size:46
Alignment explanation
Indices: 238187--238305 Score: 120
Period size: 45 Copynumber: 2.6 Consensus size: 46
238177 CTAGCGCGTT
* * *
238187 TACTG-TTTCGCACTTTGTGTGCTTACTGTTTCGCACTTCGTGTGCT
1 TACTGATTT-GCACTATGTGTGCTTACTGATTCGCACTTCGTGTGCC
* *
238233 TACTGATTTGCGCTATGTGCGCTTACTGATT-GCACTGT-GTGTGCC
1 TACTGATTTGCACTATGTGTGCTTACTGATTCGCACT-TCGTGTGCC
* *
238278 TACTGGA-TTGCACTGTGTGTGTTTACTG
1 TACT-GATTTGCACTATGTGTGCTTACTG
238306 TTTCCCCAAC
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
45 32 0.52
46 26 0.43
47 3 0.05
ACGTcount: A:0.12, C:0.21, G:0.25, T:0.42
Consensus pattern (46 bp):
TACTGATTTGCACTATGTGTGCTTACTGATTCGCACTTCGTGTGCC
Found at i:254789 original size:22 final size:21
Alignment explanation
Indices: 254764--254821 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
254754 TTGGTGCTTT
254764 TTTTTTACTATTTTAATTGCTA
1 TTTTTTACTATTTTAA-TGCTA
* * *
254786 TTTTTTACTGTTTTGATGCTT
1 TTTTTTACTATTTTAATGCTA
*
254807 TTTTATTATTATTTT
1 TTTT-TTACTATTTT
254822 GGTGTTGTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 8 0.27
22 22 0.73
ACGTcount: A:0.17, C:0.07, G:0.07, T:0.69
Consensus pattern (21 bp):
TTTTTTACTATTTTAATGCTA
Found at i:263102 original size:82 final size:84
Alignment explanation
Indices: 262953--263122 Score: 281
Period size: 82 Copynumber: 2.0 Consensus size: 84
262943 ATAGTGGAGT
262953 GACTTTTAACCAATTCTAATGTAAATGAAAAAAACCACTTAAGTTTACAACTTTATTCTTTGATT
1 GACTTTTAACCAATTCTAATGTAAATG--AAAAACCACTTAAGTTTACAACTTTATTCTTTGATT
263018 CATGATTAGAATTGATAATGG
64 CATGATTAGAATTGATAATGG
* * *
263039 GACTTTTAACCAATTCTAATGTAAATG-AGAA-TACTTAAGTTTGCAACTTTATTCTTTGATTCA
1 GACTTTTAACCAATTCTAATGTAAATGAAAAACCACTTAAGTTTACAACTTTATTCTTTGATTCA
263102 TGATTAGAATTGATAATGG
66 TGATTAGAATTGATAATGG
263121 GA
1 GA
263123 TAGGACATCG
Statistics
Matches: 81, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
82 51 0.63
83 3 0.04
86 27 0.33
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (84 bp):
GACTTTTAACCAATTCTAATGTAAATGAAAAACCACTTAAGTTTACAACTTTATTCTTTGATTCA
TGATTAGAATTGATAATGG
Found at i:263723 original size:28 final size:29
Alignment explanation
Indices: 263656--263731 Score: 70
Period size: 28 Copynumber: 2.6 Consensus size: 29
263646 ACATTAAAAT
263656 AATATTAAAATACTATATAAAAACTTTCAATA
1 AATATTAAAA-A-TATAT-AAAACTTTCAATA
* *
263688 AATA--AAAAATATATAAAA-TTTTATTA
1 AATATTAAAAATATATAAAACTTTCAATA
263714 AATATT-AAAATAATATAA
1 AATATTAAAAAT-ATATAA
263732 TATAAATAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
26 10 0.26
27 9 0.23
28 11 0.28
29 1 0.03
30 4 0.10
32 4 0.10
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.36
Consensus pattern (29 bp):
AATATTAAAAATATATAAAACTTTCAATA
Found at i:264434 original size:16 final size:16
Alignment explanation
Indices: 264413--264452 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
264403 TGGAGCAGTT
264413 GAGGCATTGAAAGACC
1 GAGGCATTGAAAGACC
264429 GAGGCATTGAAAGACC
1 GAGGCATTGAAAGACC
*
264445 AAGGCATT
1 GAGGCATT
264453 TGCAGGTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.38, C:0.17, G:0.30, T:0.15
Consensus pattern (16 bp):
GAGGCATTGAAAGACC
Found at i:265998 original size:24 final size:23
Alignment explanation
Indices: 265944--265996 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
265934 TTTTGGTTGC
*
265944 TATTTTGGTGTTTTTTTTTTAAAT
1 TATTTTGGTGTTTTTTTTCT-AAT
265968 TATTTTGGTGTTTTTTTTGCT-AT
1 TATTTTGGTGTTTTTTTT-CTAAT
265991 TATTTT
1 TATTTT
265997 TGTTGATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 8 0.30
24 18 0.67
25 1 0.04
ACGTcount: A:0.13, C:0.02, G:0.13, T:0.72
Consensus pattern (23 bp):
TATTTTGGTGTTTTTTTTCTAAT
Found at i:266040 original size:22 final size:22
Alignment explanation
Indices: 266005--266076 Score: 99
Period size: 22 Copynumber: 3.3 Consensus size: 22
265995 TTTGTTGATA
* * *
266005 TTTTTGTTGTTGTTTTGCTTTT
1 TTTTTTTTGCTGTTTTGCTGTT
266027 TTTTTTTTGCTGTTTTGCTGTT
1 TTTTTTTTGCTGTTTTGCTGTT
*
266049 TTTTTTTTGCTGTTTTGATGTT
1 TTTTTTTTGCTGTTTTGCTGTT
*
266071 ATTTTT
1 TTTTTT
266077 ATGCATTTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.03, C:0.06, G:0.17, T:0.75
Consensus pattern (22 bp):
TTTTTTTTGCTGTTTTGCTGTT
Found at i:266120 original size:22 final size:23
Alignment explanation
Indices: 266069--266120 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
266059 TGTTTTGATG
*
266069 TTATTT-TTATGCATTTTTACTA
1 TTATTTGTTATGCATTTTTAATA
* *
266091 TTGTTTTGTTAT-CTTTTTTAATA
1 TT-ATTTGTTATGCATTTTTAATA
266114 TTATTTG
1 TTATTTG
266121 AATATTGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
22 6 0.25
23 14 0.58
24 4 0.17
ACGTcount: A:0.19, C:0.06, G:0.08, T:0.67
Consensus pattern (23 bp):
TTATTTGTTATGCATTTTTAATA
Found at i:273809 original size:7 final size:7
Alignment explanation
Indices: 273797--273821 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
273787 GTCCACATCA
273797 ACTAGCC
1 ACTAGCC
273804 ACTAGCC
1 ACTAGCC
273811 ACTAGCC
1 ACTAGCC
273818 ACTA
1 ACTA
273822 AAGTAATGGC
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:0.32, C:0.40, G:0.12, T:0.16
Consensus pattern (7 bp):
ACTAGCC
Found at i:275092 original size:2 final size:2
Alignment explanation
Indices: 275085--275113 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
275075 CAAATCACCC
275085 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
275114 ACCACTCACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:275439 original size:21 final size:20
Alignment explanation
Indices: 275415--275458 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
275405 TAAAAGAAAT
275415 TAATTA-AAAGTAGAAATATAA
1 TAATTATAAA-TAGAAATA-AA
*
275436 TAATTATAAATATAAATAAA
1 TAATTATAAATAGAAATAAA
275456 TAA
1 TAA
275459 CTATTATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
21 13 0.62
22 3 0.14
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (20 bp):
TAATTATAAATAGAAATAAA
Found at i:277575 original size:22 final size:22
Alignment explanation
Indices: 277535--277594 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
277525 TGATTTGAGG
* *
277535 AAAAATAGAAG-AAACATAATT
1 AAAAATAAAAGAAAATATAATT
277556 AAAAATAAAAGAAAATATAATT
1 AAAAATAAAAGAAAATATAATT
*
277578 AAAAGA-AATAGAAAATA
1 AAAA-ATAAAAGAAAATA
277595 AGGAAGTCGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.29
22 23 0.68
23 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.08, T:0.18
Consensus pattern (22 bp):
AAAAATAAAAGAAAATATAATT
Found at i:278445 original size:22 final size:22
Alignment explanation
Indices: 278417--278458 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
278407 TGCTCGGAAA
278417 GAATAGAAGCACACACAGTGTT
1 GAATAGAAGCACACACAGTGTT
278439 GAATAGAAGCACACACAGTG
1 GAATAGAAGCACACACAGTG
278459 CTAAACAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.14
Consensus pattern (22 bp):
GAATAGAAGCACACACAGTGTT
Found at i:283181 original size:139 final size:139
Alignment explanation
Indices: 282963--283240 Score: 547
Period size: 139 Copynumber: 2.0 Consensus size: 139
282953 GTCATTTTAC
282963 TTCAAAGTAAATTACTTAAACTTGAGCTTCAAGAGTGATGTGATGTGATGTGATGAGAGGTCCCT
1 TTCAAAGTAAATTACTTAAACTTGAGCTTCAAGAGTGATGTGATGTGATGTGATGAGAGGTCCCT
283028 TGCTCGACTCTAGCTTTTCGTAGCTTTTGTACCTACACGTTAAAATAAAAGCGTTAAGCCAGTGA
66 TGCTCGACTCTAGCTTTTCGTAGCTTTTGTACCTACACGTTAAAATAAAAGCGTTAAGCCAGTGA
283093 AGGCTTAGT
131 AGGCTTAGT
*
283102 TTCAAAGTAAATTACTTAAACTTGAGCTTCAAGAGTGATGTGATGTGATGTGATGAGAGGTCTCT
1 TTCAAAGTAAATTACTTAAACTTGAGCTTCAAGAGTGATGTGATGTGATGTGATGAGAGGTCCCT
283167 TGCTCGACTCTAGCTTTTCGTAGCTTTTGTACCTACACGTTAAAATAAAAGCGTTAAGCCAGTGA
66 TGCTCGACTCTAGCTTTTCGTAGCTTTTGTACCTACACGTTAAAATAAAAGCGTTAAGCCAGTGA
283232 AGGCTTAGT
131 AGGCTTAGT
283241 AAGCACTACA
Statistics
Matches: 138, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 138 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (139 bp):
TTCAAAGTAAATTACTTAAACTTGAGCTTCAAGAGTGATGTGATGTGATGTGATGAGAGGTCCCT
TGCTCGACTCTAGCTTTTCGTAGCTTTTGTACCTACACGTTAAAATAAAAGCGTTAAGCCAGTGA
AGGCTTAGT
Found at i:283470 original size:25 final size:25
Alignment explanation
Indices: 283442--283501 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
283432 AGAAGCCCAT
283442 AAGTGCTGGGGAAACAAAAGCACAG
1 AAGTGCTGGGGAAACAAAAGCACAG
* * *
283467 AAGTACTGGGGAAACAGAAGCACAT
1 AAGTGCTGGGGAAACAAAAGCACAG
*
283492 AAGTGTTGGG
1 AAGTGCTGGG
283502 AAATAGTAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.33, T:0.13
Consensus pattern (25 bp):
AAGTGCTGGGGAAACAAAAGCACAG
Found at i:299571 original size:16 final size:16
Alignment explanation
Indices: 299550--299586 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
299540 TATTTTTTTA
299550 AAATTATT-TCACAATT
1 AAATTATTGTC-CAATT
299566 AAATTATTGTCCAATT
1 AAATTATTGTCCAATT
299582 AAATT
1 AAATT
299587 GTGATAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.43
Consensus pattern (16 bp):
AAATTATTGTCCAATT
Found at i:302147 original size:30 final size:29
Alignment explanation
Indices: 302113--302177 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 29
302103 ATTGAAAATT
302113 AAAATTA-GTTAATAATTTTATTATTTCAAA
1 AAAATTATGTTAATAATTTTA-TATTT-AAA
* *
302143 AAAATAATTTTAATAATTTTATATTTAAA
1 AAAATTATGTTAATAATTTTATATTTAAA
302172 AAAATT
1 AAAATT
302178 TATATTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 8 0.26
30 11 0.35
31 12 0.39
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (29 bp):
AAAATTATGTTAATAATTTTATATTTAAA
Found at i:302179 original size:16 final size:16
Alignment explanation
Indices: 302160--302192 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
302150 TTTTAATAAT
302160 TTTATATTTAAAAAAA
1 TTTATATTTAAAAAAA
302176 TTTATATTTAAAAAAA
1 TTTATATTTAAAAAAA
302192 T
1 T
302193 AATTTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTATATTTAAAAAAA
Found at i:303034 original size:22 final size:21
Alignment explanation
Indices: 303009--303050 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
302999 AAGATAAAAA
303009 TATTGATGTGACTATATAATAG
1 TATTGATGTGAC-ATATAATAG
* *
303031 TATTTATGTTACATATAATA
1 TATTGATGTGACATATAATA
303051 CTTTCTTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (21 bp):
TATTGATGTGACATATAATAG
Found at i:303556 original size:17 final size:18
Alignment explanation
Indices: 303534--303567 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
303524 TAAATCAATA
*
303534 AAATTTTAA-TCATAATC
1 AAATTTAAACTCATAATC
303551 AAATTTAAACTCATAAT
1 AAATTTAAACTCATAAT
303568 ATTGGGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATTTAAACTCATAATC
Found at i:303780 original size:21 final size:20
Alignment explanation
Indices: 303730--303781 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
303720 TTGAACTAGA
*
303730 TTAAGGTTTGAGGTTCGATAT
1 TTAAGGTTT-AGGTTCGAGAT
* * *
303751 TCAAAGTTTATGGTTCGAGGT
1 TTAAGGTTTA-GGTTCGAGAT
303772 TTAAGGTTTA
1 TTAAGGTTTA
303782 AAGTTGAGGG
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.25, C:0.06, G:0.27, T:0.42
Consensus pattern (20 bp):
TTAAGGTTTAGGTTCGAGAT
Done.