Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 180 of 199
Found at i:52042530 original size:24 final size:24
Alignment explanation
Indices: 52042468--52042535 Score: 79
Period size: 24 Copynumber: 2.8 Consensus size: 24
52042458 CCAAAATGTC
52042468 ATTAAATTTCTTTAATTATAAAAA
1 ATTAAATTTCTTTAATTATAAAAA
*
52042492 A-GAAATTTAAC-TTAATCTA-AAAAA
1 ATTAAATTT--CTTTAAT-TATAAAAA
52042516 ATTAAATTTCTTTAATTATA
1 ATTAAATTTCTTTAATTATA
52042536 TCAATTCATT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
23 9 0.25
24 18 0.50
25 9 0.25
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.43
Consensus pattern (24 bp):
ATTAAATTTCTTTAATTATAAAAA
Found at i:52045348 original size:4 final size:4
Alignment explanation
Indices: 52045339--52045370 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
52045329 AATGATAATG
52045339 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
52045371 GCGAATGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:52045460 original size:2 final size:2
Alignment explanation
Indices: 52045448--52045515 Score: 77
Period size: 2 Copynumber: 35.0 Consensus size: 2
52045438 ATAAAATAGG
* * * * *
52045448 TA TA TA GA TA TA TG TA GA TA TG TA TA TA AA T- TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52045488 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52045516 AAACATGAGT
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
1 2 0.04
2 52 0.96
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (2 bp):
TA
Found at i:52046215 original size:11 final size:13
Alignment explanation
Indices: 52046199--52046232 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
52046189 AATTTTATGG
52046199 AAAAATTTCG-T-
1 AAAAATTTCGTTC
52046210 AAAAATTTCGTTC
1 AAAAATTTCGTTC
52046223 AAAAATTTCG
1 AAAAATTTCG
52046233 ACGTTTGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 1 0.05
13 10 0.48
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (13 bp):
AAAAATTTCGTTC
Found at i:52047332 original size:33 final size:33
Alignment explanation
Indices: 52047290--52047445 Score: 144
Period size: 33 Copynumber: 4.6 Consensus size: 33
52047280 AATATGAAGG
52047290 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
* *
52047323 GGTTGCTAAGTGCTGATTCCACCGTATCCTTAAATATAAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--C-T-CAT-T---GGT
*
52047366 GGTTGCTAAGTGCTGATT-CCC--C-CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
*
52047393 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
52047426 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
52047446 ACCGTATCTT
Statistics
Matches: 101, Mismatches: 6, Indels: 32
0.73 0.04 0.23
Matches are distributed among these distances:
27 18 0.18
28 5 0.05
31 2 0.02
32 2 0.02
33 41 0.41
34 3 0.03
35 1 0.01
36 1 0.01
37 1 0.01
38 1 0.01
39 2 0.02
40 1 0.01
41 2 0.02
42 1 0.01
43 20 0.20
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
Found at i:52047471 original size:103 final size:103
Alignment explanation
Indices: 52047286--52047515 Score: 415
Period size: 103 Copynumber: 2.2 Consensus size: 103
52047276 ATTGAATATG
52047286 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
52047351 CTTAAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCC
66 CTTAAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCC
*
52047389 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* * * *
52047454 TTTAAATGTGAATGGGGTTGCTAAGTGCTGATTCCCCC
66 CTTAAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCC
52047492 AAGGGGTTGCTAAGTGCTGATTCC
1 AAGGGGTTGCTAAGTGCTGATTCC
52047516 ACCATATCTT
Statistics
Matches: 122, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 122 1.00
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.31
Consensus pattern (103 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
CTTAAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:52047524 original size:70 final size:73
Alignment explanation
Indices: 52047389--52047594 Score: 276
Period size: 70 Copynumber: 2.8 Consensus size: 73
52047379 TGATTCCCCC
* *
52047389 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCC---TCATAGGTGGTTGCTAAGTGCTGATTCCACCATATC
52047454 TTTAAATGTGA
63 TTTAAATGTGA
*
52047465 ATGGGGTTGCTAAGTGCTGATTCCCC-CA-AGG-GGTTGCTAAGTGCTGATTCCACCATATCTTT
1 AAGGGGTTGCTAAGTGCTGATTCCCCTCATAGGTGGTTGCTAAGTGCTGATTCCACCATATCTTT
*
52047527 GAATGTGA
66 AAATGTGA
*
52047535 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACT-GGTGGTTGCTAAGTGCTGAATCCACC
1 AAGGGGTTGCTAAGTGCTGATTCCCC---TCA-TAGGTGGTTGCTAAGTGCTGATTCCACC
52047595 GATAACGGTT
Statistics
Matches: 117, Mismatches: 6, Indels: 14
0.85 0.04 0.10
Matches are distributed among these distances:
70 62 0.53
71 2 0.02
72 2 0.02
74 2 0.02
75 2 0.02
76 47 0.40
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.31
Consensus pattern (73 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCTCATAGGTGGTTGCTAAGTGCTGATTCCACCATATCTTT
AAATGTGA
Found at i:52052750 original size:33 final size:33
Alignment explanation
Indices: 52052704--52052897 Score: 177
Period size: 33 Copynumber: 5.7 Consensus size: 33
52052694 TTAACCGTTA
* *
52052704 TCGGTGGATTCAGCACTTAGCAACCACCAGTGAT
1 TCGG-GGAATCAGCACTTAGCAACCACCAATGAT
*
52052738 TCGGGGAATCAGCACTTAGCAACCCCTTTCACATTCAAAGAT
1 TCGGGGAATCAGCACTTAGCAA---C---CAC---CAATGAT
52052780 AT-GGTGGAATCAGCACTTAGCAACCACCAATGAT
1 -TCGG-GGAATCAGCACTTAGCAACCACCAATGAT
*
52052814 TCGGGGAATCAGCACTTAACAACC-CC-----T
1 TCGGGGAATCAGCACTTAGCAACCACCAATGAT
* *
52052841 TGGGGGAATCAGCACTTAGCAACCACCAATGAG
1 TCGGGGAATCAGCACTTAGCAACCACCAATGAT
52052874 TCGGGGAATCAGCACTTAGCAACC
1 TCGGGGAATCAGCACTTAGCAACC
52052898 CCTTCATATT
Statistics
Matches: 133, Mismatches: 9, Indels: 37
0.74 0.05 0.21
Matches are distributed among these distances:
27 23 0.17
28 2 0.02
32 2 0.02
33 60 0.45
34 12 0.09
36 1 0.01
37 3 0.02
39 3 0.02
40 1 0.01
42 7 0.05
43 19 0.14
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (33 bp):
TCGGGGAATCAGCACTTAGCAACCACCAATGAT
Found at i:52052878 original size:60 final size:60
Alignment explanation
Indices: 52052785--52052901 Score: 216
Period size: 60 Copynumber: 1.9 Consensus size: 60
52052775 AAGATATGGT
*
52052785 GGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAACAACCCCTTGGG
1 GGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAACAACCCCTTGGG
*
52052845 GGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTT
1 GGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAACAACCCCTT
52052902 CATATTCAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.18
Consensus pattern (60 bp):
GGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAACAACCCCTTGGG
Found at i:52068450 original size:3 final size:3
Alignment explanation
Indices: 52068442--52068467 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
52068432 CTTCCCCATC
52068442 CTG CTG CTG CTG CTG CTG CTG CTG CT
1 CTG CTG CTG CTG CTG CTG CTG CTG CT
52068468 TCAAATTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.31, T:0.35
Consensus pattern (3 bp):
CTG
Found at i:52096853 original size:2 final size:2
Alignment explanation
Indices: 52096846--52096877 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
52096836 GATTCTTTTG
52096846 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52096878 ATTCATATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52105776 original size:22 final size:22
Alignment explanation
Indices: 52105744--52105785 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
52105734 TATACATGTA
* *
52105744 ATATTACTTGAATAGTTATGAG
1 ATATTAATTGAATAATTATGAG
*
52105766 ATATTAATTGAGTAATTATG
1 ATATTAATTGAATAATTATG
52105786 TCTCCTTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.02, G:0.17, T:0.43
Consensus pattern (22 bp):
ATATTAATTGAATAATTATGAG
Found at i:52108421 original size:16 final size:17
Alignment explanation
Indices: 52108400--52108440 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
52108390 TGATAGTAAG
52108400 AAAACAATACATATA-T
1 AAAACAATACATATATT
52108416 AAAAC-ATAACATATATT
1 AAAACAAT-ACATATATT
52108433 AAAA-AATA
1 AAAACAATA
52108441 GATTCCATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 2 0.09
16 13 0.59
17 7 0.32
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAACAATACATATATT
Found at i:52110964 original size:108 final size:107
Alignment explanation
Indices: 52110776--52111053 Score: 327
Period size: 108 Copynumber: 2.6 Consensus size: 107
52110766 CCATCAGAGT
* * * * ** *
52110776 CTTTGTCTCGTTGAGTATATAATACCCAACCAAACTCATAGAGGAGCACGCGCTTTGGGACATAT
1 CTTTGTCTCATTGAGTACATAATACCCAACCGAACTCACAGAGGAGCACGTACTTTGAGACATAT
* * *
52110841 CACATTAGCTCATATACAGAGCT-GGTTTCACTCAGGAGAAAA
66 CACATTAGCTCATATACAGAGCTGGGCTT-ACTAAAGAGAAAA
* *
52110883 CTTTGTCTTATTGAGTACATAATTACCCATCCGAACTCACAGAGGAGCACGTACTTTGAGACATA
1 CTTTGTCTCATTGAGTACATAA-TACCCAACCGAACTCACAGAGGAGCACGTACTTTGAGACATA
* *
52110948 TCACTTTAGCTCATATACAGAGCTGGGCTTACTAAAGAGCAAA
65 TCACATTAGCTCATATACAGAGCTGGGCTTACTAAAGAGAAAA
* *
52110991 CTTTGTCTCATTGAG--CAT-AT-CCCAACCGAACTCACAAAAGAGCA--TACGTTTTGAGACAT
1 CTTTGTCTCATTGAGTACATAATACCCAACCGAACTCACAGAGGAGCACGTAC--TTTGAGACAT
52111050 ATCA
64 ATCA
52111054 TGAGTGAGTA
Statistics
Matches: 149, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
101 3 0.02
103 35 0.23
104 1 0.01
105 1 0.01
106 3 0.02
107 19 0.13
108 83 0.56
109 4 0.03
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (107 bp):
CTTTGTCTCATTGAGTACATAATACCCAACCGAACTCACAGAGGAGCACGTACTTTGAGACATAT
CACATTAGCTCATATACAGAGCTGGGCTTACTAAAGAGAAAA
Found at i:52112182 original size:8 final size:8
Alignment explanation
Indices: 52112130--52112184 Score: 58
Period size: 8 Copynumber: 6.8 Consensus size: 8
52112120 TTTTTTGAAG
52112130 TATATTAT
1 TATATTAT
*
52112138 TATTTTAT
1 TATATTAT
*
52112146 TATATT-G
1 TATATTAT
*
52112153 TAAATTATAT
1 TATA-T-TAT
52112163 TATATTAT
1 TATATTAT
52112171 TATATTAT
1 TATATTAT
52112179 TATATT
1 TATATT
52112185 TTAAATAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
7 3 0.08
8 30 0.79
9 2 0.05
10 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (8 bp):
TATATTAT
Found at i:52113214 original size:8 final size:8
Alignment explanation
Indices: 52113201--52113246 Score: 50
Period size: 8 Copynumber: 6.5 Consensus size: 8
52113191 TATGATTATG
52113201 TGTGAATA
1 TGTGAATA
52113209 TGTGAAT-
1 TGTGAATA
52113216 TGTG-A-A
1 TGTGAATA
52113222 T-TG-ATA
1 TGTGAATA
52113228 TGTGAATA
1 TGTGAATA
52113236 TGTGAAT-
1 TGTGAATA
52113243 TGTG
1 TGTG
52113247 TATTGATTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
5 3 0.09
6 4 0.12
7 10 0.29
8 17 0.50
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.41
Consensus pattern (8 bp):
TGTGAATA
Found at i:52113230 original size:19 final size:20
Alignment explanation
Indices: 52113206--52113244 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
52113196 TTATGTGTGA
52113206 ATATGTGAAT-TGTGAATTG
1 ATATGTGAATATGTGAATTG
52113225 ATATGTGAATATGTGAATTG
1 ATATGTGAATATGTGAATTG
52113245 TGTATTGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.41
Consensus pattern (20 bp):
ATATGTGAATATGTGAATTG
Found at i:52113234 original size:27 final size:27
Alignment explanation
Indices: 52113201--52113253 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
52113191 TATGATTATG
52113201 TGTGAATATGTGAATTGTGAATTGATA
1 TGTGAATATGTGAATTGTGAATTGATA
*
52113228 TGTGAATATGTGAATTGTGTATTGAT
1 TGTGAATATGTGAATTGTGAATTGAT
52113254 TGAAAAGTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.43
Consensus pattern (27 bp):
TGTGAATATGTGAATTGTGAATTGATA
Found at i:52113540 original size:41 final size:37
Alignment explanation
Indices: 52113492--52113591 Score: 92
Period size: 41 Copynumber: 2.6 Consensus size: 37
52113482 TCGACCTTGA
52113492 GTCGATGAGACACTGGGTGTCATACTGTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCA-AC--TTACTTCGGATAG
* ** ** * *
52113532 ATTCGATGAGGTACTGGGTACCAACTTACTTCGGCTTG
1 -GTCGATGAGACACTGGGTGTCAACTTACTTCGGATAG
*
52113570 GCCGATGAGACACTGGGTGTCA
1 GTCGATGAGACACTGGGTGTCA
52113592 CTATATTGCT
Statistics
Matches: 46, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
37 16 0.35
38 11 0.24
40 2 0.04
41 17 0.37
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (37 bp):
GTCGATGAGACACTGGGTGTCAACTTACTTCGGATAG
Found at i:52115792 original size:67 final size:67
Alignment explanation
Indices: 52115682--52115988 Score: 337
Period size: 67 Copynumber: 4.6 Consensus size: 67
52115672 CACGTCAAGA
* * * * * * *
52115682 CATTAAACATGGGGTATGATGTATAAAATCAGAGCTCAACTATAACAACATAGAGAGCCCGCTTG
1 CATTAAACATGGGGTATGATGTGTAAGACCATAGCTCAGCTATAACAACATAAAGAGCCCGCTAG
52115747 GG
66 GG
* *
52115749 CATTAAACATGGGGTATGATGCGTAAGACCATAGCTCAGCTATAACAACATAAAGAGCTCGCTAG
1 CATTAAACATGGGGTATGATGTGTAAGACCATAGCTCAGCTATAACAACATAAAGAGCCCGCTAG
*
52115814 GA
66 GG
* * * * *
52115816 CATTAAACATGTGGTATGATGTGTAAGGCCATAGCTCAGCTATGACAACATAAAGAGTCCG-TCG
1 CATTAAACATGGGGTATGATGTGTAAGACCATAGCTCAGCTATAACAACATAAAGAGCCCGCTAG
52115880 GG
66 GG
* * * * * *
52115882 ACATTAAACATGGGGTATGATGTGTAAGACCATAACTCGGCTATGACAACATAAAAAGTCCACTA
1 -CATTAAACATGGGGTATGATGTGTAAGACCATAGCTCAGCTATAACAACATAAAGAGCCCGCTA
**
52115947 GAA
65 GGG
** ** * *
52115950 CATTAAATGTAAGGTATGATGTGTAAGATCATAACTCAG
1 CATTAAACATGGGGTATGATGTGTAAGACCATAGCTCAG
52115989 TTTTATGATG
Statistics
Matches: 205, Mismatches: 33, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
66 3 0.01
67 200 0.98
68 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.23
Consensus pattern (67 bp):
CATTAAACATGGGGTATGATGTGTAAGACCATAGCTCAGCTATAACAACATAAAGAGCCCGCTAG
GG
Found at i:52115988 original size:134 final size:134
Alignment explanation
Indices: 52115681--52115988 Score: 381
Period size: 134 Copynumber: 2.3 Consensus size: 134
52115671 ACACGTCAAG
* * * * * * *
52115681 ACATTAAACATGGGGTATGATGTATAAAATCAGAGCTCAACTATAACAACATAGAGAGCCCGCTT
1 ACATTAAACATGTGGTATGATGTGTAAGATCATAGCTCAGCTATAACAACATAAAGAGCCCGCTC
* * *
52115746 GGGCATTAAACATGGGGTATGATGCGTAAGACCATAGCTCAGCTATAACAACATAAAGAGCTCGC
66 GGGCATTAAACATGGGGTATGATGCGTAAGACCATAACTCAGCTATAACAACATAAAAAGCTCAC
*
52115811 TAGG
131 TAGA
** * *
52115815 ACATTAAACATGTGGTATGATGTGTAAGGCCATAGCTCAGCTATGACAACATAAAGAGTCCG-TC
1 ACATTAAACATGTGGTATGATGTGTAAGATCATAGCTCAGCTATAACAACATAAAGAGCCCGCTC
* * *
52115879 GGGACATTAAACATGGGGTATGATGTGTAAGACCATAACTCGGCTATGACAACATAAAAAG-TCC
66 GGG-CATTAAACATGGGGTATGATGCGTAAGACCATAACTCAGCTATAACAACATAAAAAGCT-C
52115943 ACTAGA
129 ACTAGA
*
52115949 ACATT-AA-ATGTAAGGTATGATGTGTAAGATCATAACTCAG
1 ACATTAAACATGT--GGTATGATGTGTAAGATCATAGCTCAG
52115989 TTTTATGATG
Statistics
Matches: 149, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
132 4 0.03
133 7 0.05
134 138 0.93
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.23
Consensus pattern (134 bp):
ACATTAAACATGTGGTATGATGTGTAAGATCATAGCTCAGCTATAACAACATAAAGAGCCCGCTC
GGGCATTAAACATGGGGTATGATGCGTAAGACCATAACTCAGCTATAACAACATAAAAAGCTCAC
TAGA
Found at i:52116858 original size:9 final size:9
Alignment explanation
Indices: 52116836--52116868 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
52116826 GGCCTATTTG
52116836 TTTATTTA-
1 TTTATTTAT
52116844 TTTATTTAT
1 TTTATTTAT
*
52116853 TTTATTTCT
1 TTTATTTAT
52116862 TTTATTT
1 TTTATTT
52116869 TGAAAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTATTTAT
Found at i:52117834 original size:25 final size:26
Alignment explanation
Indices: 52117796--52117849 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
52117786 TTATTTATAC
52117796 ATTTGTTTTAAAATCTATTATGTATT
1 ATTTGTTTTAAAATCTATTATGTATT
* *
52117822 ATTT-TTTTGAAATTTATTATGTATT
1 ATTTGTTTTAAAATCTATTATGTATT
52117847 ATT
1 ATT
52117850 CACTATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 22 0.85
26 4 0.15
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (26 bp):
ATTTGTTTTAAAATCTATTATGTATT
Found at i:52122207 original size:30 final size:29
Alignment explanation
Indices: 52122145--52122207 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
52122135 CCATTTTGGC
*
52122145 AAAATACAAAGGCAATAAAATTTCCTTCA
1 AAAATACAAAGGCAATAAAATTTCCTTAA
**
52122174 AAAATACAAAGGCAATAAGTTATTCCTTAA
1 AAAATACAAAGGCAATAAAAT-TTCCTTAA
52122204 AAAA
1 AAAA
52122208 GCCAATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 19 0.63
30 11 0.37
ACGTcount: A:0.54, C:0.14, G:0.08, T:0.24
Consensus pattern (29 bp):
AAAATACAAAGGCAATAAAATTTCCTTAA
Found at i:52122859 original size:12 final size:12
Alignment explanation
Indices: 52122781--52122859 Score: 56
Period size: 12 Copynumber: 6.4 Consensus size: 12
52122771 TGAATGAAGT
52122781 GAAAAAGTAAAAG
1 GAAAAAG-AAAAG
**
52122794 GAAATAGAGGGAAG
1 GAAA-A-AGAAAAG
52122808 GAAGAAAGAAAAG
1 GAA-AAAGAAAAG
*
52122821 GCAAAAGAAAAG
1 GAAAAAGAAAAG
52122833 AGAAAAA-AAAA-
1 -GAAAAAGAAAAG
*
52122844 -AAAAAGAAGAG
1 GAAAAAGAAAAG
52122855 GAAAA
1 GAAAA
52122860 TCTCCCATAC
Statistics
Matches: 52, Mismatches: 7, Indels: 15
0.70 0.09 0.20
Matches are distributed among these distances:
9 5 0.10
10 3 0.06
12 17 0.33
13 16 0.31
14 8 0.15
15 3 0.06
ACGTcount: A:0.70, C:0.01, G:0.27, T:0.03
Consensus pattern (12 bp):
GAAAAAGAAAAG
Found at i:52123438 original size:18 final size:18
Alignment explanation
Indices: 52123415--52123450 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
52123405 TAGTTAAATA
*
52123415 AATATGTTTTATGAAAGT
1 AATATGTTATATGAAAGT
52123433 AATATGTTATATGAAAGT
1 AATATGTTATATGAAAGT
52123451 GAATTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.42
Consensus pattern (18 bp):
AATATGTTATATGAAAGT
Found at i:52126496 original size:22 final size:21
Alignment explanation
Indices: 52126470--52126510 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
52126460 ACCCTAATTT
52126470 CCAAACGCACACGCCCGTGTAA
1 CCAAA-GCACACGCCCGTGTAA
* *
52126492 CCAAAGGACACGGCCGTGT
1 CCAAAGCACACGCCCGTGT
52126511 GAAAATCGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.29, C:0.37, G:0.24, T:0.10
Consensus pattern (21 bp):
CCAAAGCACACGCCCGTGTAA
Found at i:52128963 original size:16 final size:16
Alignment explanation
Indices: 52128942--52128973 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
52128932 AGATAATAAG
52128942 CAAAGTGCGAGCCTGT
1 CAAAGTGCGAGCCTGT
*
52128958 CAAAGTGTGAGCCTGT
1 CAAAGTGCGAGCCTGT
52128974 TGAATTGCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.22
Consensus pattern (16 bp):
CAAAGTGCGAGCCTGT
Found at i:52129027 original size:44 final size:44
Alignment explanation
Indices: 52128979--52129073 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 44
52128969 CCTGTTGAAT
**
52128979 TGCAAGCCAAAGTGGTGGACA-GTCTAAATGCAAACCCGAATGGG
1 TGCAAGCCAAAGTGACGGA-AGGTCTAAATGCAAACCCGAATGGG
* * * *
52129023 TGCAAGCCAAAGTGACGGAAGGTTTAAATGCAAGCTCGAGTGGG
1 TGCAAGCCAAAGTGACGGAAGGTCTAAATGCAAACCCGAATGGG
52129067 TGCAAGC
1 TGCAAGC
52129074 TAAAATGGCA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
43 1 0.02
44 43 0.98
ACGTcount: A:0.33, C:0.19, G:0.32, T:0.17
Consensus pattern (44 bp):
TGCAAGCCAAAGTGACGGAAGGTCTAAATGCAAACCCGAATGGG
Found at i:52131280 original size:34 final size:34
Alignment explanation
Indices: 52131237--52131303 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
52131227 TTTAAGCCCC
52131237 CTTACTTACTATAAGTTTGGAAAACTACTCAACA
1 CTTACTTACTATAAGTTTGGAAAACTACTCAACA
*
52131271 CTTATTTACTATAAGTTTGGAAAACTACTCAAC
1 CTTACTTACTATAAGTTTGGAAAACTACTCAAC
52131304 TGGAAAGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.34
Consensus pattern (34 bp):
CTTACTTACTATAAGTTTGGAAAACTACTCAACA
Found at i:52139139 original size:23 final size:23
Alignment explanation
Indices: 52139112--52139210 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
52139102 AGTGTTATTG
*
52139112 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
52139135 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
52139158 AACAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
52139181 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
52139204 ATCAGTG
1 ATCAGTG
52139211 TTGCACTTAT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 69 1.00
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:52142528 original size:17 final size:17
Alignment explanation
Indices: 52142506--52142558 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
52142496 AATGCCTTAT
52142506 TTTCAAGTTAATGATAA
1 TTTCAAGTTAATGATAA
* **
52142523 TTTC-A---AATCATTC
1 TTTCAAGTTAATGATAA
52142536 TTTCAAGTTAATGATAA
1 TTTCAAGTTAATGATAA
52142553 TTTCAA
1 TTTCAA
52142559 ATCATTCTTG
Statistics
Matches: 26, Mismatches: 6, Indels: 8
0.65 0.15 0.20
Matches are distributed among these distances:
13 9 0.35
14 1 0.04
16 1 0.04
17 15 0.58
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (17 bp):
TTTCAAGTTAATGATAA
Found at i:52142540 original size:30 final size:30
Alignment explanation
Indices: 52142506--52142567 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
52142496 AATGCCTTAT
52142506 TTTCAAGTTAATGATAATTTCAAATCATTC
1 TTTCAAGTTAATGATAATTTCAAATCATTC
52142536 TTTCAAGTTAATGATAATTTCAAATCATTC
1 TTTCAAGTTAATGATAATTTCAAATCATTC
52142566 TT
1 TT
52142568 GATTAAAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.45
Consensus pattern (30 bp):
TTTCAAGTTAATGATAATTTCAAATCATTC
Found at i:52147864 original size:29 final size:29
Alignment explanation
Indices: 52147814--52147892 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
52147804 TGCGAGTTGT
* * *
52147814 AAAGTTGCAAGCTTATTAAAGACAGTGAGC
1 AAAG-TGCAAGCCTGTTAAAGACAGTAAGC
*
52147844 AAAGTGCAAGCCTGTTGAAGACAGTAAGC
1 AAAGTGCAAGCCTGTTAAAGACAGTAAGC
* * *
52147873 AAGGTGCAAGTCTGTCAAAG
1 AAAGTGCAAGCCTGTTAAAG
52147893 TGTGAGCCTG
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 37 0.90
30 4 0.10
ACGTcount: A:0.38, C:0.15, G:0.27, T:0.20
Consensus pattern (29 bp):
AAAGTGCAAGCCTGTTAAAGACAGTAAGC
Found at i:52147959 original size:44 final size:44
Alignment explanation
Indices: 52147909--52148004 Score: 138
Period size: 44 Copynumber: 2.2 Consensus size: 44
52147899 CCTGTCAAAT
* *
52147909 TGCAAGCCGAAGTGGTGGACAGTCTAAATGCAAACCCGAATGGG
1 TGCAAGCCGAAGTGGAGAACAGTCTAAATGCAAACCCGAATGGG
* * * *
52147953 TGCAAGCCGAAGTGGAGAACGGTCTAAATGCAAGCTCGAGTGGG
1 TGCAAGCCGAAGTGGAGAACAGTCTAAATGCAAACCCGAATGGG
52147997 TGCAAGCC
1 TGCAAGCC
52148005 AAAATGGTAG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.30, C:0.21, G:0.33, T:0.16
Consensus pattern (44 bp):
TGCAAGCCGAAGTGGAGAACAGTCTAAATGCAAACCCGAATGGG
Found at i:52150409 original size:24 final size:23
Alignment explanation
Indices: 52150353--52150409 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 23
52150343 AAGAACTTCT
*
52150353 ATTTTATTAAAAATATAAAAATA
1 ATTTTATTAAAAATATAAAAACA
52150376 ATTTACTATT-AAAATATTAAAAACA
1 ATTT--TATTAAAAATA-TAAAAACA
52150401 ACTTTTATT
1 A-TTTTATT
52150410 TTATTAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 4 0.14
24 10 0.34
25 12 0.41
26 3 0.10
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTTTATTAAAAATATAAAAACA
Found at i:52150835 original size:18 final size:18
Alignment explanation
Indices: 52150812--52150849 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
52150802 GGAAAATGAA
*
52150812 ACATATAAGGGTTAGGAT
1 ACATATAAGGGCTAGGAT
52150830 ACATATAAGGGCTAGGAT
1 ACATATAAGGGCTAGGAT
52150848 AC
1 AC
52150850 GCACCTGGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (18 bp):
ACATATAAGGGCTAGGAT
Found at i:52152636 original size:30 final size:30
Alignment explanation
Indices: 52152602--52152670 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
52152592 ATTAATTAAA
52152602 GAGAGTTTTGAGAAATTTAAAGAGAAATTT
1 GAGAGTTTTGAGAAATTTAAAGAGAAATTT
**
52152632 GAGAGTTTTGAGAAATTTAGGGAGAAATTT
1 GAGAGTTTTGAGAAATTTAAAGAGAAATTT
* *
52152662 AAGATTTTT
1 GAGAGTTTT
52152671 TGCTAAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (30 bp):
GAGAGTTTTGAGAAATTTAAAGAGAAATTT
Found at i:52155645 original size:26 final size:25
Alignment explanation
Indices: 52155616--52155728 Score: 95
Period size: 26 Copynumber: 4.4 Consensus size: 25
52155606 AAATGAAACA
*
52155616 AAATAATATATAGAACAATTTGAAGT
1 AAATAATATATA-AACAATTTAAAGT
*
52155642 AAATAGA-ATA-AAATAATTTAAAGT
1 AAATA-ATATATAAACAATTTAAAGT
* * *
52155666 AAATAATATGTAAAACAAATTAAAAT
1 AAATAATATAT-AAACAATTTAAAGT
* * *
52155692 AAATAATACACAAAGCAATTTAAAAT
1 AAATAATATATAAA-CAATTTAAAGT
*
52155718 AAATAACATAT
1 AAATAATATAT
52155729 CAGACAATAA
Statistics
Matches: 69, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
23 1 0.01
24 18 0.26
25 4 0.06
26 45 0.65
27 1 0.01
ACGTcount: A:0.61, C:0.05, G:0.06, T:0.27
Consensus pattern (25 bp):
AAATAATATATAAACAATTTAAAGT
Found at i:52155793 original size:28 final size:27
Alignment explanation
Indices: 52155658--52155878 Score: 96
Period size: 26 Copynumber: 7.9 Consensus size: 27
52155648 AATAAAATAA
* **
52155658 TTTAAAGTAAATAATATGTAAAACAAA-
1 TTTAAAATAAATAATATACAAAA-AAAG
* **
52155685 -TTAAAATAAATAATACACAAAGCAA-
1 TTTAAAATAAATAATATACAAAAAAAG
52155710 TTTAAAATAAATAACATATCAGACAATAAAAAG
1 TTTAAAATAAAT-A-ATAT---ACAA-AAAAAG
* **
52155743 TTTAAAATAAATTATATGTAAAAAGAAG
1 TTTAAAATAAATAATATACAAAAA-AAG
* *
52155771 TTTCAAATAAATAATATAC-AAAATAG
1 TTTAAAATAAATAATATACAAAAAAAG
* * *
52155797 TTTACAAAATAAATGATGTATATATAAATAA-
1 TTT--AAAATAAAT-A-ATATACA-AAAAAAG
* * * *
52155828 TTCAAAATAAATAATATA-TATAACAG
1 TTTAAAATAAATAATATACAAAAAAAG
*
52155854 TTTTAAAA-AAATAATATATAAAAAA
1 -TTTAAAATAAATAATATACAAAAAA
52155879 TGGATAATAG
Statistics
Matches: 144, Mismatches: 32, Indels: 36
0.68 0.15 0.17
Matches are distributed among these distances:
25 5 0.03
26 43 0.30
27 21 0.15
28 32 0.22
29 10 0.07
30 4 0.03
31 10 0.07
32 7 0.05
33 12 0.08
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.29
Consensus pattern (27 bp):
TTTAAAATAAATAATATACAAAAAAAG
Found at i:52155978 original size:27 final size:25
Alignment explanation
Indices: 52155927--52156011 Score: 77
Period size: 25 Copynumber: 3.3 Consensus size: 25
52155917 TGGAAACTTG
*
52155927 AAATAAATAATAATAAAACAATTTA
1 AAATAAATAATAATAAAAAAATTTA
52155952 AAATAAATAAT-ATAAGAAAAAGGTTTA
1 AAATAAATAATAATAA-AAAAA--TTTA
* *
52155979 AAATATA-AATGAAT-AAAAAATTCGA
1 AAATAAATAAT-AATAAAAAAATT-TA
52156004 AAATAAAT
1 AAATAAAT
52156012 TGAAATCAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
24 6 0.12
25 22 0.45
26 8 0.16
27 11 0.22
28 2 0.04
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (25 bp):
AAATAAATAATAATAAAAAAATTTA
Found at i:52156552 original size:12 final size:12
Alignment explanation
Indices: 52156537--52156567 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
52156527 ATCCAGCCAT
52156537 CAGCCACTGCAC
1 CAGCCACTGCAC
52156549 CAGCCACTGCAC
1 CAGCCACTGCAC
52156561 CAGCCAC
1 CAGCCAC
52156568 CGGTCACCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.52, G:0.16, T:0.06
Consensus pattern (12 bp):
CAGCCACTGCAC
Found at i:52157597 original size:19 final size:19
Alignment explanation
Indices: 52157573--52157611 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
52157563 TAATAACATA
52157573 AAAATAA-AATAAGTTAATC
1 AAAATAATAATAA-TTAATC
*
52157592 AAAATAATTATAATTAATC
1 AAAATAATAATAATTAATC
52157611 A
1 A
52157612 TGAATTAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.31
Consensus pattern (19 bp):
AAAATAATAATAATTAATC
Found at i:52159814 original size:11 final size:11
Alignment explanation
Indices: 52159798--52159824 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
52159788 TAAGATAATG
52159798 ATGAAGAATAA
1 ATGAAGAATAA
52159809 ATGAAGAATAA
1 ATGAAGAATAA
52159820 ATGAA
1 ATGAA
52159825 AAAACAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.19, T:0.19
Consensus pattern (11 bp):
ATGAAGAATAA
Found at i:52167086 original size:12 final size:12
Alignment explanation
Indices: 52167069--52167096 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
52167059 ATAAATCCTT
52167069 TCTCTAATATTC
1 TCTCTAATATTC
52167081 TCTCTAATATTC
1 TCTCTAATATTC
52167093 TCTC
1 TCTC
52167097 AATTTCCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.29, G:0.00, T:0.50
Consensus pattern (12 bp):
TCTCTAATATTC
Found at i:52169668 original size:7 final size:7
Alignment explanation
Indices: 52169653--52169706 Score: 54
Period size: 7 Copynumber: 7.7 Consensus size: 7
52169643 TAACGTATTG
52169653 TAAACCC
1 TAAACCC
*
52169660 TAAATCC
1 TAAACCC
52169667 TAAACCC
1 TAAACCC
* *
52169674 TAAATCA
1 TAAACCC
*
52169681 TAAACCT
1 TAAACCC
**
52169688 TAAACAT
1 TAAACCC
52169695 TAAACCC
1 TAAACCC
52169702 TAAAC
1 TAAAC
52169707 TTGTACCGAA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (7 bp):
TAAACCC
Found at i:52169706 original size:14 final size:14
Alignment explanation
Indices: 52169653--52169705 Score: 72
Period size: 14 Copynumber: 3.8 Consensus size: 14
52169643 TAACGTATTG
*
52169653 TAAACCCTAAATCC
1 TAAACCCTAAATCA
52169667 TAAACCCTAAATCA
1 TAAACCCTAAATCA
*
52169681 TAAACCTTAAA-CA
1 TAAACCCTAAATCA
52169694 TTAAACCCTAAA
1 -TAAACCCTAAA
52169706 CTTGTACCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
13 2 0.06
14 33 0.94
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACCCTAAATCA
Found at i:52170953 original size:126 final size:125
Alignment explanation
Indices: 52170728--52170995 Score: 473
Period size: 126 Copynumber: 2.1 Consensus size: 125
52170718 TGCGCCACTG
*
52170728 TAGCAAAAGCGCGTCCACGTAGGAGCTTTTTTCAGTACTTCTGCTGACAAAGCATCCTGCTTAAA
1 TAGCAAAAGCGCGTCCACGTAGGAGCTTTTTTCAATACTTCTGCTGACAAAGCATCCTGCTTAAA
*
52170793 CCGTTTTTGACACTGTTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGAGCTACTA
66 CCGTTTTTGACACTGTTTGCTCAAAAACGTCTACTCGAAATTA-TTTTTCAGGAGCTACTA
* *
52170854 TAGCAAAGGCGCGTCCACGTGGGAGCTTTTTTCAATACTTCTGCTGACAAAGCATCCTGCTTAAA
1 TAGCAAAAGCGCGTCCACGTAGGAGCTTTTTTCAATACTTCTGCTGACAAAGCATCCTGCTTAAA
* *
52170919 GCGTTTTTGACACTGTTTGCTCAAAAACGTCTACTCGAAATTATTTTTCAGGAGCTACTG
66 CCGTTTTTGACACTGTTTGCTCAAAAACGTCTACTCGAAATTATTTTTCAGGAGCTACTA
52170979 TAGCAAAAGCGCGTCCA
1 TAGCAAAAGCGCGTCCA
52170996 ACCCTAATCT
Statistics
Matches: 135, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
125 32 0.24
126 103 0.76
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (125 bp):
TAGCAAAAGCGCGTCCACGTAGGAGCTTTTTTCAATACTTCTGCTGACAAAGCATCCTGCTTAAA
CCGTTTTTGACACTGTTTGCTCAAAAACGTCTACTCGAAATTATTTTTCAGGAGCTACTA
Found at i:52171735 original size:12 final size:12
Alignment explanation
Indices: 52171714--52171743 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
52171704 AAAAAATTTT
52171714 GCCC-AGGCCCG
1 GCCCGAGGCCCG
52171725 GCCCGAGGCCCG
1 GCCCGAGGCCCG
52171737 GCCCGAG
1 GCCCGAG
52171744 AAAAAATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.10, C:0.50, G:0.40, T:0.00
Consensus pattern (12 bp):
GCCCGAGGCCCG
Found at i:52171823 original size:22 final size:21
Alignment explanation
Indices: 52171793--52171854 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 21
52171783 CAAAATTTTG
52171793 TTTTAAAAATTAAAAAAAAAGTA
1 TTTT-AAAATTAAAAAAAAA-TA
52171816 TTTTAAAA--AAAATTTAAAAATA
1 TTTTAAAATTAAAA---AAAAATA
52171838 TTTTAAAATTAAAAAAA
1 TTTTAAAATTAAAAAAA
52171855 TTAAAAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
20 4 0.12
21 3 0.09
22 14 0.41
23 9 0.26
24 4 0.12
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
TTTTAAAATTAAAAAAAAATA
Found at i:52172164 original size:21 final size:19
Alignment explanation
Indices: 52172126--52172165 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
52172116 TTGTAAATTT
52172126 TATTTTTAAAAATTATATA
1 TATTTTTAAAAATTATATA
*
52172145 TATTTTTATAATATT-TATA
1 TATTTTTA-AAAATTATATA
52172164 TA
1 TA
52172166 CCTTTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTTTTAAAAATTATATA
Found at i:52173555 original size:6 final size:6
Alignment explanation
Indices: 52173544--52173589 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
52173534 AGTAGCAATG
* *
52173544 GCAGGA GCAGGA GCAGGA GCAGGA GCAGGA GAAGAA GCAGGA GCAG
1 GCAGGA GCAGGA GCAGGA GCAGGA GCAGGA GCAGGA GCAGGA GCAG
52173590 TCGCAGGCCC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.37, C:0.15, G:0.48, T:0.00
Consensus pattern (6 bp):
GCAGGA
Found at i:52179714 original size:6 final size:6
Alignment explanation
Indices: 52179699--52179734 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
52179689 CCCGCCCCGC
*
52179699 CCTGCA CCTGCT CCTGCT CCTGCT CCTGCT -CTGCT C
1 CCTGCT CCTGCT CCTGCT CCTGCT CCTGCT CCTGCT C
52179735 TTCATATCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.03, C:0.50, G:0.17, T:0.31
Consensus pattern (6 bp):
CCTGCT
Found at i:52192310 original size:30 final size:31
Alignment explanation
Indices: 52192286--52192344 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
52192276 GTAAATACTC
* **
52192286 AAAATTTGAGGGATTAA-AGTGTAAATATGA
1 AAAATTTGAAGGACCAATAGTGTAAATATGA
52192316 AAAATTTGAAGGACCAATAGTGTAAATAT
1 AAAATTTGAAGGACCAATAGTGTAAATAT
52192345 TTTAAGGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.47, C:0.03, G:0.20, T:0.29
Consensus pattern (31 bp):
AAAATTTGAAGGACCAATAGTGTAAATATGA
Found at i:52196208 original size:20 final size:21
Alignment explanation
Indices: 52196166--52196211 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
52196156 AAGAAAATAG
52196166 CAATAAAACAATAAAATACAA
1 CAATAAAACAATAAAATACAA
*
52196187 CAATAAAGCAATAAAA-ACAA
1 CAATAAAACAATAAAATACAA
52196207 CAATA
1 CAATA
52196212 GTTTTCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.70, C:0.15, G:0.02, T:0.13
Consensus pattern (21 bp):
CAATAAAACAATAAAATACAA
Found at i:52200587 original size:50 final size:50
Alignment explanation
Indices: 52200524--52201087 Score: 335
Period size: 50 Copynumber: 11.3 Consensus size: 50
52200514 GATTTGCCAT
* *
52200524 TGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGT
1 TGTGGCTTTAATCTTTTTAACTGCAATGCCGGGGAAGCAAGATTCACCGC
** * * * * * * **
52200574 TGTGGCTTTAATCTGCTTCACTGCACTGCCTGGGAAGTAACACTCGTCGC
1 TGTGGCTTTAATCTTTTTAACTGCAATGCCGGGGAAGCAAGATTCACCGC
* * * * * **
52200624 TGTGGCTTTAGTCTTTTTAATTGCAATGTCGGGGAAGCAAGATACGCCAA
1 TGTGGCTTTAATCTTTTTAACTGCAATGCCGGGGAAGCAAGATTCACCGC
** ** * ** * * *
52200674 TGTGGCTTTAATCTGATCCACTGC-ATCACCTAGGAGGTAAGATTCACTGC
1 TGTGGCTTTAATCTTTTTAACTGCAAT-GCCGGGGAAGCAAGATTCACCGC
* * * * * * * **
52200724 TATAGCTTTAATCTTCTGAAATGCACA-GACGGGGGAGCAAGATTCACCAA
1 TGTGGCTTTAATCTTTTTAACTGCA-ATGCCGGGGAAGCAAGATTCACCGC
** * * * * *
52200774 TGTGGCTTTAAT-TTGTTCCACTGTACTGCCTGAGG-AGTAAGATTCACCGT
1 TGTGGCTTTAATCTT-TTTAACTGCAATGCC-GGGGAAGCAAGATTCACCGC
* * ** *
52200824 TATAGCTTTAATCTTTTTAACTGCAATGTTGGGGAAGCAAGATTCACCGT
1 TGTGGCTTTAATCTTTTTAACTGCAATGCCGGGGAAGCAAGATTCACCGC
* ** ** * * * * *
52200874 TGTGGCTTTAATCTGTTCCACTGCACCGCCTGGGAGGTAAGATTCGCTGC
1 TGTGGCTTTAATCTTTTTAACTGCAATGCCGGGGAAGCAAGATTCACCGC
* * * * * *
52200924 TGTAGCTTTAACCTTTTTAACTGTAATGTCAGGGAGGCAAGATTCACCGC
1 TGTGGCTTTAATCTTTTTAACTGCAATGCCGGGGAAGCAAGATTCACCGC
** * ** * * * * * *
52200974 TCAGGCTTTAATCTGTTCCACTGCACTGCCTGGGAGGTAAGATTCGCTGC
1 TGTGGCTTTAATCTTTTTAACTGCAATGCCGGGGAAGCAAGATTCACCGC
* * * *
52201024 TGTAGCTTTAATCTTTTTAATTGCAATGCCGGGGAAGCAAGATTCGCCGT
1 TGTGGCTTTAATCTTTTTAACTGCAATGCCGGGGAAGCAAGATTCACCGC
52201074 TGTGGCTTTAATCT
1 TGTGGCTTTAATCT
52201088 GTTCCACTAC
Statistics
Matches: 366, Mismatches: 140, Indels: 16
0.70 0.27 0.03
Matches are distributed among these distances:
49 7 0.02
50 353 0.96
51 5 0.01
52 1 0.00
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (50 bp):
TGTGGCTTTAATCTTTTTAACTGCAATGCCGGGGAAGCAAGATTCACCGC
Found at i:52200681 original size:100 final size:100
Alignment explanation
Indices: 52200528--52201116 Score: 702
Period size: 100 Copynumber: 5.9 Consensus size: 100
52200518 TGCCATTGTG
52200528 GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGCTT-
1 GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTG-TTC
* * * *
52200592 CACTGCACTGCCTGGGAAGTAACACTCG-TCGCTGTG
65 CACTGCACTGCCTGGGAGGTAAGATTCGCT-GCTGTA
* * * * ** *
52200628 GCTTTAGTCTTTTTAATTGCAATGTCGGGGAAGCAAGATACGCCAATGTGGCTTTAATCTGATCC
1 GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
* * * *
52200693 ACTGCA-TCACCTAGGAGGTAAGATTCACTGCTATA
66 ACTGCACT-GCCTGGGAGGTAAGATTCGCTGCTGTA
* * * * * ** *
52200728 GCTTTAATCTTCTGAAATGCACA-GACGGGGGAGCAAGATTCACCAATGTGGCTTTAATTTGTTC
1 GCTTTAATCTTTTTAACTGCA-ATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTC
* * * * *
52200792 CACTGTACTGCCTGAGGA-GTAAGATTCACCGTTATA
65 CACTGCACTGCCTG-GGAGGTAAGATTCGCTGCTGTA
*
52200828 GCTTTAATCTTTTTAACTGCAATGTTGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
*
52200893 ACTGCACCGCCTGGGAGGTAAGATTCGCTGCTGTA
66 ACTGCACTGCCTGGGAGGTAAGATTCGCTGCTGTA
* * * * * **
52200928 GCTTTAACCTTTTTAACTGTAATGTCAGGGAGGCAAGATTCACCGCTCAGGCTTTAATCTGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
52200993 ACTGCACTGCCTGGGAGGTAAGATTCGCTGCTGTA
66 ACTGCACTGCCTGGGAGGTAAGATTCGCTGCTGTA
* * *
52201028 GCTTTAATCTTTTTAATTGCAATGCCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
* * * *
52201093 ACTACACCGCTTGGGAGATAAGAT
66 ACTGCACTGCCTGGGAGGTAAGAT
52201117 CTGTAATTCT
Statistics
Matches: 413, Mismatches: 68, Indels: 16
0.83 0.14 0.03
Matches are distributed among these distances:
99 6 0.01
100 401 0.97
101 6 0.01
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (100 bp):
GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
ACTGCACTGCCTGGGAGGTAAGATTCGCTGCTGTA
Found at i:52201296 original size:98 final size:98
Alignment explanation
Indices: 52201170--52201513 Score: 544
Period size: 98 Copynumber: 3.5 Consensus size: 98
52201160 GATTACTGGC
* * * * * *
52201170 TTTAATCTGTTCCGCTGTAATCTTAGGGAGATAAGATTTCTGGCTTCAATCTGATGCGATTTACT
1 TTTAATCCGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGATGCGATTTACT
* *
52201235 CTATTGTAACTTCAGAGAGATAAGATCCTTTAT
66 CTACTGTAACTTCAGAGAGATAAGATCATTTAT
* *
52201268 TTTAATCCGCTCCACTGTAATCTCAGGGAGATGAGATTACTAGCTTCAATCTGCTGCGATTTACT
1 TTTAATCCGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGATGCGATTTACT
*
52201333 CTACTGTAACTTCAGAAAGATAAGATCATTTAT
66 CTACTGTAACTTCAGAGAGATAAGATCATTTAT
* * *
52201366 TTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGTTGCGATCTACT
1 TTTAATCCGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGATGCGATTTACT
52201431 CTACTGTAACTTCAGAGAGATAAGATCATTTAT
66 CTACTGTAACTTCAGAGAGATAAGATCATTTAT
* *
52201464 TTTAATCCGCTCTACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAAT
1 TTTAATCCGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAAT
52201514 ATGCTCTACT
Statistics
Matches: 229, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 229 1.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.35
Consensus pattern (98 bp):
TTTAATCCGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGATGCGATTTACT
CTACTGTAACTTCAGAGAGATAAGATCATTTAT
Found at i:52201398 original size:44 final size:44
Alignment explanation
Indices: 52201331--52201540 Score: 138
Period size: 44 Copynumber: 4.5 Consensus size: 44
52201321 CTGCGATTTA
**
52201331 CTCTACTGTAA-CTTCAGAAAGATAAGATCATTTATTTTAATCCG
1 CTCTACTGTAATC-TCAGGGAGATAAGATCATTTATTTTAATCCG
* * * * **
52201375 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGTTGCGATCTA
1 CTCTACTGTAATCTCAGGGAGATAAGA-T-C-A--TT-TAT-T-TT--AATCCG
*
52201429 CTCTACTGTAA-CTTCAGAGAGATAAGATCATTTATTTTAATCCG
1 CTCTACTGTAATC-TCAGGGAGATAAGATCATTTATTTTAATCCG
* * * * * **
52201473 CTCTACTGTAATCTCAGGGAGATAGGATTA-CTAGCTTCAATATG
1 CTCTACTGTAATCTCAGGGAGATAAGATCATTTA-TTTTAATCCG
52201517 CTCTACTGTAATCTCAGGGAGATA
1 CTCTACTGTAATCTCAGGGAGATA
52201541 GGATTACTAG
Statistics
Matches: 129, Mismatches: 23, Indels: 28
0.72 0.13 0.16
Matches are distributed among these distances:
43 2 0.02
44 79 0.61
45 3 0.02
46 3 0.02
47 2 0.02
48 2 0.02
49 4 0.03
50 2 0.02
51 2 0.02
52 3 0.02
53 2 0.02
54 25 0.19
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (44 bp):
CTCTACTGTAATCTCAGGGAGATAAGATCATTTATTTTAATCCG
Found at i:52201541 original size:44 final size:44
Alignment explanation
Indices: 52201472--52201633 Score: 200
Period size: 44 Copynumber: 3.7 Consensus size: 44
52201462 ATTTTAATCC
* *
52201472 GCTCTACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATAT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATAT
* *
52201516 GCTCTACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATAT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATAT
* * * ** * *
52201560 GCTCCGCTGTAATATTAGGGAGATAAGATTTTTGGCTTCAATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATAT
*
52201604 GCTCCACTGTAA-CATTAGGGAGATAAGATT
1 GCTCCACTGTAATC-TCAGGGAGATAAGATT
52201634 CACCATTTCC
Statistics
Matches: 106, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
44 106 1.00
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (44 bp):
GCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATAT
Found at i:52201830 original size:44 final size:43
Alignment explanation
Indices: 52201801--52202064 Score: 147
Period size: 44 Copynumber: 5.8 Consensus size: 43
52201791 CCTTTATTTT
*
52201801 AATCCGTTCCACTGTAATCTCAGGAAGATAAGATTACTAACTTC
1 AATCCGCTCCACTGTAATCTCAGGAAGATAAGA-TACTAACTTC
* * * * *
52201845 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTAGCTTC
1 AATCCGCTCCACTGTAATCTCAGGAAGATAAGA-TACTAACTTC
* * * *
52201889 AATCTGCTGCGATCTACTCTACTGTAA-CTTCA-GAGAGATAAGATCATTTATTTT
1 AA--T-C--CG--CT-C-C-ACTGTAATC-TCAGGA-AGATAAGAT-ACTAACTTC
* * * *
52201943 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTAATAGCTTC
1 AATCCGCTCCACTGTAATCTCAGGAAGATAAGA-TACTAACTTC
* * * * * *
52201987 AATCTGCTCCGCTCTAATCTCAGGGAGATAAGATTTCTAGCTTC
1 AATCCGCTCCACTGTAATCTCAGGAAGATAAGA-TACTAACTTC
* *
52202031 AATCTGCTCCACTGTAA-CATCAGGGAGATAAGAT
1 AATCCGCTCCACTGTAATC-TCAGGAAGATAAGAT
52202065 TCACCATTTT
Statistics
Matches: 173, Mismatches: 30, Indels: 35
0.73 0.13 0.15
Matches are distributed among these distances:
43 2 0.01
44 128 0.74
45 4 0.02
46 2 0.01
47 3 0.02
49 3 0.02
51 3 0.02
52 2 0.01
53 4 0.02
54 22 0.13
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.31
Consensus pattern (43 bp):
AATCCGCTCCACTGTAATCTCAGGAAGATAAGATACTAACTTC
Found at i:52201913 original size:98 final size:91
Alignment explanation
Indices: 52201811--52202065 Score: 252
Period size: 98 Copynumber: 2.8 Consensus size: 91
52201801 AATCCGTTCC
*
52201811 ACTGTAATCTCAGGAAGATAAGATTACTAACTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAA
1 ACTGTAATCTCAGGAAGATAAGATTACTAACTTCAATCTGCTCCACTGTAATCTCAGGGAGATAA
** *
52201876 GATTTCTAGCTTCAATCTGCTGCGATCTACTCT
66 GATTAATAGCTTCAA--T-CTGC--TC--CGCT
* * * * * *
52201909 ACTGTAA-CTTCA-GAGAGATAAGATCATTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGAT
1 ACTGTAATC-TCAGGA-AGATAAGATTACTAACTTCAATCTGCTCCACTGTAATCTCAGGGAGAT
*
52201972 AGGATTAATAGCTTCAATCTGCTCCGCT
64 AAGATTAATAGCTTCAATCTGCTCCGCT
* * *
52202000 -C--TAATCTCAGGGAGATAAGATTTCTAGCTTCAATCTGCTCCACTGTAA-CATCAGGGAGATA
1 ACTGTAATCTCAGGAAGATAAGATTACTAACTTCAATCTGCTCCACTGTAATC-TCAGGGAGATA
52202061 AGATT
65 AGATT
52202066 CACCATTTTC
Statistics
Matches: 131, Mismatches: 21, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
87 1 0.01
88 49 0.37
89 2 0.02
90 1 0.01
91 3 0.02
93 2 0.02
95 4 0.03
96 1 0.01
97 3 0.02
98 65 0.50
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (91 bp):
ACTGTAATCTCAGGAAGATAAGATTACTAACTTCAATCTGCTCCACTGTAATCTCAGGGAGATAA
GATTAATAGCTTCAATCTGCTCCGCT
Found at i:52202037 original size:142 final size:142
Alignment explanation
Indices: 52201271--52202038 Score: 693
Period size: 142 Copynumber: 5.4 Consensus size: 142
52201261 CCTTTATTTT
* * * * *
52201271 AATCCGCTCCACTGTAATCTCAGGGAGATGAGATTACTAGCTTCAATCTGCTGCGATTTACTCTA
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAATCTGCTGCGATCTACTCTA
*
52201336 CTGTAACTTCAGAAAGATAAGATCATTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGG
66 CTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGG
52201401 ATTACTAGCTTC
131 ATTACTAGCTTC
* * * *
52201413 AATCTGTTGCGATCTACTCTACTGTAA-CTTCAGAGAGATAAGA--TC-A--TT-TAT-T--T-T
1 AATC---T--G--CT-C-C-GCTGTAATC-TCAGGGAGATAAGATTTCTAGCTTCAATCTGCTGC
* ** * * * * * * ** *
52201467 AATCCGCTCTACTGTAA-TCTCAGGGAGATAGGATTA-CTAGCTTCAATATGCTCTACTGTAATC
55 GATCTACTCTACTGTAACT-TCAGAGAGATAAGATCATTTA-TTTTAATCCGCTCCACTGTAATC
52201530 TCAGGGAGATAGGATTACTAGCTTC
118 TCAGGGAGATAGGATTACTAGCTTC
* * * * *
52201555 AATATGCTCCGCTGTAATATTAGGGAGATAAGATTTTTGGCTTCAA--T-CT--G--CT-C-C-A
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAATCTGCTGCGATCTACTCTA
* ** *
52201610 CTGTAACATT-AGGGAGATAAGATTCACCATTTCCGATTAGAAATTCTTTGGTCTAATCCACTGT
66 CTGTAAC-TTCAGAGAGATAAGA-T---CATTT---ATT-TTAA-TC---CG-C---TCCACTGT
* * * *
52201674 AATCTTAGGGAAATAGAATTACTGGCTTC
114 AATCTCAGGGAGATAGGATTACTAGCTTC
* * *
52201703 AATCTGCTCCGCTGTAATATCAGGGAGATAAGATTTCTGGCTTCAATCTGATGCGATCTACTCTA
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAATCTGCTGCGATCTACTCTA
* * * *
52201768 CTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTGTAATCTCAGGAAGATAAG
66 CTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGG
*
52201833 ATTACTAACTTC
131 ATTACTAGCTTC
52201845 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAATCTGCTGCGATCTACTCTA
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAATCTGCTGCGATCTACTCTA
52201910 CTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGG
66 CTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGG
*
52201975 ATTAATAGCTTC
131 ATTACTAGCTTC
*
52201987 AATCTGCTCCGCTCTAATCTCAGGGAGATAAGATTTCTAGCTTCAATCTGCT
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAATCTGCT
52202039 CCACTGTAAC
Statistics
Matches: 505, Mismatches: 70, Indels: 102
0.75 0.10 0.15
Matches are distributed among these distances:
132 36 0.07
133 4 0.01
134 4 0.01
135 3 0.01
136 1 0.00
137 5 0.01
138 2 0.00
139 2 0.00
140 3 0.01
141 4 0.01
142 290 0.57
143 1 0.00
144 1 0.00
145 2 0.00
146 3 0.01
147 3 0.01
148 75 0.15
149 5 0.01
150 5 0.01
151 6 0.01
152 19 0.04
153 1 0.00
154 4 0.01
155 2 0.00
156 1 0.00
157 4 0.01
158 19 0.04
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (142 bp):
AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAATCTGCTGCGATCTACTCTA
CTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGG
ATTACTAGCTTC
Found at i:52202065 original size:44 final size:43
Alignment explanation
Indices: 52201900--52202065 Score: 167
Period size: 44 Copynumber: 3.8 Consensus size: 43
52201890 ATCTGCTGCG
* * * * *
52201900 ATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCATTTA-TTTTA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT--TTTAGCTTCA
* * *
52201944 ATCCGCTCCACTGTAATCTCAGGGAGATAGGATTAATAGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATT-TTAGCTTCA
* *
52201988 ATCTGCTCCGCTCTAATCTCAGGGAGATAAGATTTCTAGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTT-TAGCTTCA
52202032 ATCTGCTCCACTGTAA-CATCAGGGAGATAAGATT
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATT
52202066 CACCATTTTC
Statistics
Matches: 102, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
42 1 0.01
43 3 0.03
44 97 0.95
45 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (43 bp):
ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTTAGCTTCA
Found at i:52202089 original size:432 final size:428
Alignment explanation
Indices: 52201271--52202110 Score: 1088
Period size: 432 Copynumber: 1.9 Consensus size: 428
52201261 CCTTTATTTT
* * * *
52201271 AATCCGCTCCACTGTAATCTCAGGGAGATGAGATTACTAGCTTCAATCTGCTGCGATTTACTCTA
1 AATCCGCTCCACTGTAATATCAGGGAGATAAGATTACTAGCTTCAATCTGATGCGATCTACTCTA
* *
52201336 CTGTAACTTCAGAAAGATAAGATCATTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGG
66 CTGTAACTTCAGAAAGATAAGATCATTTATTTTAATCCGCTCCACTGTAATCTCAGGAAGATAAG
* *
52201401 ATTACTAGCTTCAATCTGTTGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTT
131 ATTACTAACTTCAATC--TT-CGA-CTACTCTACTGTAACTTCAGAGAGATAAGATCATTAATTT
* * * * * * *
52201466 TAATCCGCTCTACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATATGCTCTACTGTAATCT
192 CAATCCACTCTACTGTAATCTCAGAGAGATAAGATCACTAGCTTCAATACGCTCCACTGTAATCT
* * * * *
52201531 CAGGGAGATAGGATTACTAGCTTCAATATGCTCCGCTGTAATATTAGGGAGATAAGATTTTTGGC
257 CAGGGAGATAGGATTAATAGCTTCAATATGCTCCGCTCTAATATCAGGGAGATAAGATTTCTAGC
* *
52201596 TTCAATCTGCTCCACTGTAACATTAGGGAGATAAGATTCACCATTTCCGATTAGAAATTCTTTGG
322 TTCAATCTGCTCCACTGTAACATCAGGGAGATAAGATTCACCATTTCCGATTAGAAATTCTTCGG
52201661 TCTAATCCACTGTAATCTTAGGGAAATAGAATTACTGGCTTC
387 TCTAATCCACTGTAATCTTAGGGAAATAGAATTACTGGCTTC
* * * *
52201703 AATCTGCTCCGCTGTAATATCAGGGAGATAAGATTTCTGGCTTCAATCTGATGCGATCTACTCTA
1 AATCCGCTCCACTGTAATATCAGGGAGATAAGATTACTAGCTTCAATCTGATGCGATCTACTCTA
* * *
52201768 CTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGTTCCACTGTAATCTCAGGAAGATAAG
66 CTGTAACTTCAGAAAGATAAGATCATTTATTTTAATCCGCTCCACTGTAATCTCAGGAAGATAAG
* *
52201833 ATTACTAACTTCAATC-T-G-CT-C-C-GCTGTAA-TCTCAGGGAGATAAGATTTCTAGCTTCAA
131 ATTACTAACTTCAATCTTCGACTACTCTACTGTAACT-TCAGAGAGATAAGA--TC-A--TT-AA
* * * * * *
52201891 TCTGCTGCGATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCATTTA-TTTTAATCCGCTCCA
189 T-T--T-CAATCCACTCTACTGTAATC-TCAGAGAGATAAGATCA-CTAGCTTCAATACGCTCCA
* *
52201954 CTGTAATCTCAGGGAGATAGGATTAATAGCTTCAATCTGCTCCGCTCTAATCTCAGGGAGATAAG
248 CTGTAATCTCAGGGAGATAGGATTAATAGCTTCAATATGCTCCGCTCTAATATCAGGGAGATAAG
*
52202019 ATTTCTAGCTTCAATCTGCTCCACTGTAACATCAGGGAGATAAGATTCACCATTTTCGATTA-AG
313 ATTTCTAGCTTCAATCTGCTCCACTGTAACATCAGGGAGATAAGATTCACCATTTCCGATTAGA-
52202083 AATTCTTCGGTCTAATCCACTGTAATCT
377 AATTCTTCGGTCTAATCCACTGTAATCT
52202111 CAAGGAGATA
Statistics
Matches: 354, Mismatches: 40, Indels: 28
0.84 0.09 0.07
Matches are distributed among these distances:
421 1 0.00
422 19 0.05
423 1 0.00
424 3 0.01
425 3 0.01
427 3 0.01
428 2 0.01
429 2 0.01
431 3 0.01
432 315 0.89
433 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (428 bp):
AATCCGCTCCACTGTAATATCAGGGAGATAAGATTACTAGCTTCAATCTGATGCGATCTACTCTA
CTGTAACTTCAGAAAGATAAGATCATTTATTTTAATCCGCTCCACTGTAATCTCAGGAAGATAAG
ATTACTAACTTCAATCTTCGACTACTCTACTGTAACTTCAGAGAGATAAGATCATTAATTTCAAT
CCACTCTACTGTAATCTCAGAGAGATAAGATCACTAGCTTCAATACGCTCCACTGTAATCTCAGG
GAGATAGGATTAATAGCTTCAATATGCTCCGCTCTAATATCAGGGAGATAAGATTTCTAGCTTCA
ATCTGCTCCACTGTAACATCAGGGAGATAAGATTCACCATTTCCGATTAGAAATTCTTCGGTCTA
ATCCACTGTAATCTTAGGGAAATAGAATTACTGGCTTC
Found at i:52204464 original size:6 final size:6
Alignment explanation
Indices: 52204455--52204503 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
52204445 CATTTTGGCC
*
52204455 TTGATT TTGATT TTGATTT TTTATT CTT--TT TT-ATT TTGATT TTGATT
1 TTGATT TTGATT TTGA-TT TTGATT -TTGATT TTGATT TTGATT TTGATT
52204502 TT
1 TT
52204504 TTTGAGCTCA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
4 2 0.05
5 6 0.16
6 23 0.61
7 7 0.18
ACGTcount: A:0.14, C:0.02, G:0.10, T:0.73
Consensus pattern (6 bp):
TTGATT
Found at i:52205712 original size:28 final size:26
Alignment explanation
Indices: 52205648--52205715 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 26
52205638 AATACCAAAA
*
52205648 AAATATTTTAAAATTAAAAAATTATTT
1 AAATATTTT-AAATTAAAAAATTATTC
52205675 AAATATTTTTAAATTAAAAAAATT-TTAC
1 AAATA-TTTTAAATT-AAAAAATTATT-C
52205703 AAAGTATTTTAAA
1 AAA-TATTTTAAA
52205716 AATATTTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
27 12 0.33
28 22 0.61
29 2 0.06
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (26 bp):
AAATATTTTAAATTAAAAAATTATTC
Found at i:52205723 original size:11 final size:11
Alignment explanation
Indices: 52205688--52205767 Score: 71
Period size: 11 Copynumber: 7.5 Consensus size: 11
52205678 TATTTTTAAA
*
52205688 TTAAAAAAATT
1 TTAAAAATATT
*
52205699 TTACAAAGTATT
1 TTA-AAAATATT
52205711 TTAAAAATATT
1 TTAAAAATATT
52205722 TT--AAA-A-T
1 TTAAAAATATT
52205729 TTAAAAA-ATT
1 TTAAAAATATT
*
52205739 TAAAAAAGTATT
1 TTAAAAA-TATT
*
52205751 TTAAAAGTATT
1 TTAAAAATATT
52205762 TTAAAA
1 TTAAAA
52205768 TTAAAAAAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
7 3 0.05
8 1 0.02
9 7 0.12
10 7 0.12
11 22 0.39
12 17 0.30
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (11 bp):
TTAAAAATATT
Found at i:52205729 original size:40 final size:40
Alignment explanation
Indices: 52205675--52205777 Score: 161
Period size: 40 Copynumber: 2.6 Consensus size: 40
52205665 AAAATTATTT
* * *
52205675 AAATATTTTTAAATTAAAAAAATTTTACAAAGTATTTTAA
1 AAATATTTTAAAATTAAAAAAATTTAAAAAAGTATTTTAA
*
52205715 AAATATTTTAAAATTTAAAAAATTTAAAAAAGTATTTTAA
1 AAATATTTTAAAATTAAAAAAATTTAAAAAAGTATTTTAA
*
52205755 AAGTATTTTAAAATTAAAAAAAT
1 AAATATTTTAAAATTAAAAAAAT
52205778 AAAAAATAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (40 bp):
AAATATTTTAAAATTAAAAAAATTTAAAAAAGTATTTTAA
Found at i:52205733 original size:18 final size:16
Alignment explanation
Indices: 52205710--52205743 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
52205700 TACAAAGTAT
52205710 TTTAAAAATATTTTAAAA
1 TTTAAAAA-A-TTTAAAA
52205728 TTTAAAAAATTTAAAA
1 TTTAAAAAATTTAAAA
52205744 AAGTATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 1 0.06
18 8 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTAAAAAATTTAAAA
Found at i:52205745 original size:18 final size:18
Alignment explanation
Indices: 52205710--52205744 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
52205700 TACAAAGTAT
*
52205710 TTTAAAAATATTTTAAAA
1 TTTAAAAATATTTAAAAA
52205728 TTTAAAAA-ATTTAAAAA
1 TTTAAAAATATTTAAAAA
52205745 AGTATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TTTAAAAATATTTAAAAA
Found at i:52213170 original size:13 final size:13
Alignment explanation
Indices: 52213152--52213230 Score: 80
Period size: 13 Copynumber: 6.5 Consensus size: 13
52213142 TCGATTTTTC
52213152 CTAAATATTATCA
1 CTAAATATTATCA
*
52213165 CTAAATA--AT-T
1 CTAAATATTATCA
52213175 CTAAATATTATCA
1 CTAAATATTATCA
*
52213188 CTAAATATTATAA
1 CTAAATATTATCA
* *
52213201 GTAAATA--AT-T
1 CTAAATATTATCA
52213211 CTAAATATTATCA
1 CTAAATATTATCA
52213224 CTAAATA
1 CTAAATA
52213231 ATTCTAAATT
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
10 13 0.25
11 4 0.08
12 4 0.08
13 32 0.60
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.38
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:52213192 original size:36 final size:36
Alignment explanation
Indices: 52213152--52213230 Score: 140
Period size: 36 Copynumber: 2.2 Consensus size: 36
52213142 TCGATTTTTC
*
52213152 CTAAATATTATCACTAAATAATTCTAAATATTATCA
1 CTAAATATTATAACTAAATAATTCTAAATATTATCA
*
52213188 CTAAATATTATAAGTAAATAATTCTAAATATTATCA
1 CTAAATATTATAACTAAATAATTCTAAATATTATCA
52213224 CTAAATA
1 CTAAATA
52213231 ATTCTAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.38
Consensus pattern (36 bp):
CTAAATATTATAACTAAATAATTCTAAATATTATCA
Found at i:52213214 original size:23 final size:23
Alignment explanation
Indices: 52213188--52213239 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
52213178 AATATTATCA
*
52213188 CTAAATATTATAAGTAAATAATT
1 CTAAATATTATAACTAAATAATT
*
52213211 CTAAATATTATCACTAAATAATT
1 CTAAATATTATAACTAAATAATT
52213234 CTAAAT
1 CTAAAT
52213240 TTAAAAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.38
Consensus pattern (23 bp):
CTAAATATTATAACTAAATAATT
Found at i:52213252 original size:23 final size:23
Alignment explanation
Indices: 52213188--52213252 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
52213178 AATATTATCA
* *
52213188 CTAAATATTATAAGTAAATAATT
1 CTAAATATTAAAAATAAATAATT
** *
52213211 CTAAATATTATCACTAAATAATT
1 CTAAATATTAAAAATAAATAATT
52213234 CTAAAT-TTAAAAATCAAAT
1 CTAAATATTAAAAAT-AAAT
52213253 TTAAACTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
22 5 0.14
23 31 0.86
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.37
Consensus pattern (23 bp):
CTAAATATTAAAAATAAATAATT
Found at i:52217611 original size:18 final size:18
Alignment explanation
Indices: 52217574--52217609 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
52217564 ACTTGAAATC
52217574 ATAAAAAAAATAAAGGGG
1 ATAAAAAAAATAAAGGGG
*
52217592 ATAAACAAAAATATAGGG
1 ATAAA-AAAAATAAAGGG
52217610 ATTTTTATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.64, C:0.03, G:0.19, T:0.14
Consensus pattern (18 bp):
ATAAAAAAAATAAAGGGG
Found at i:52217748 original size:13 final size:13
Alignment explanation
Indices: 52217732--52217756 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52217722 ATAATACTTT
52217732 TTATATTTAATTA
1 TTATATTTAATTA
52217745 TTATATTTAATT
1 TTATATTTAATT
52217757 TTAAAAATAT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATATTTAATTA
Found at i:52230304 original size:20 final size:20
Alignment explanation
Indices: 52230266--52230304 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
52230256 GGTTCATGCC
* *
52230266 TTTCAGTTACGTATTTCATA
1 TTTCAGTTACATATATCATA
*
52230286 TTTCAGTTATATATATCAT
1 TTTCAGTTACATATATCAT
52230305 TCATGTCACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.51
Consensus pattern (20 bp):
TTTCAGTTACATATATCATA
Found at i:52232933 original size:21 final size:21
Alignment explanation
Indices: 52232908--52232947 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
52232898 TTAAAAATAT
*
52232908 AATTTAGTATATTT-TGTAAGA
1 AATTTACTA-ATTTGTGTAAGA
52232929 AATTTACTAATTTGTGTAA
1 AATTTACTAATTTGTGTAA
52232948 AGTATAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (21 bp):
AATTTACTAATTTGTGTAAGA
Found at i:52258729 original size:30 final size:31
Alignment explanation
Indices: 52258687--52258756 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
52258677 CGTCAAAGGG
* *
52258687 CAAACC-TTTCAAAA-TGATTAAATAATGGC
1 CAAACCTTTTCAAAATTGATCAAACAATGGC
* *
52258716 CAAATCTTTTCAAAATTGCTCAAACAATGGC
1 CAAACCTTTTCAAAATTGATCAAACAATGGC
52258747 CAAACCTTTT
1 CAAACCTTTT
52258757 TGAAAGTGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 5 0.15
30 8 0.24
31 21 0.62
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (31 bp):
CAAACCTTTTCAAAATTGATCAAACAATGGC
Found at i:52258748 original size:31 final size:30
Alignment explanation
Indices: 52258687--52258770 Score: 89
Period size: 31 Copynumber: 2.8 Consensus size: 30
52258677 CGTCAAAGGG
* * *
52258687 CAAACC-TTTCAAAATGATTAAATAATGGC
1 CAAACCTTTTCAAAATGCTCAAACAATGGC
*
52258716 CAAATCTTTTCAAAATTGCTCAAACAATGGC
1 CAAACCTTTTCAAAA-TGCTCAAACAATGGC
* *
52258747 CAAACCTTTTTGAAAGTGCTCAAA
1 CAAACC-TTTTCAAAATGCTCAAA
52258771 TAAGGATTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
29 5 0.11
30 8 0.18
31 25 0.56
32 7 0.16
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (30 bp):
CAAACCTTTTCAAAATGCTCAAACAATGGC
Found at i:52261453 original size:24 final size:24
Alignment explanation
Indices: 52261421--52261467 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
52261411 ATGTAACCAC
52261421 CCTTCAATTGAACTATACATGATT
1 CCTTCAATTGAACTATACATGATT
* *
52261445 CCTTCAATTGAGCTTTACATGAT
1 CCTTCAATTGAACTATACATGAT
52261468 GCATTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (24 bp):
CCTTCAATTGAACTATACATGATT
Found at i:52264715 original size:46 final size:46
Alignment explanation
Indices: 52264663--52264757 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 46
52264653 ACAAAGATAG
*
52264663 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
52264709 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
52264755 AAA
1 AAA
52264758 AGAAAATAGA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.42, C:0.22, G:0.02, T:0.34
Consensus pattern (46 bp):
AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATATCCTAATT
Found at i:52264748 original size:24 final size:24
Alignment explanation
Indices: 52264675--52264748 Score: 57
Period size: 24 Copynumber: 3.2 Consensus size: 24
52264665 ACCAAAATAT
52264675 TATCTCCTAAACTTTAGCATCT-A
1 TATCTCCTAAACTTTAGCATCTAA
* * ** *
52264698 -ATCTCCT-AA-TTAAACCAAAATAT
1 TATCTCCTAAACTT-TAGC-ATCTAA
52264721 TATCTCCTAAACTTTAGCATCTAA
1 TATCTCCTAAACTTTAGCATCTAA
52264745 TATC
1 TATC
52264749 CTAATTAAAA
Statistics
Matches: 35, Mismatches: 10, Indels: 11
0.62 0.18 0.20
Matches are distributed among these distances:
20 2 0.06
21 4 0.11
22 9 0.26
24 14 0.40
25 4 0.11
26 2 0.06
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.36
Consensus pattern (24 bp):
TATCTCCTAAACTTTAGCATCTAA
Found at i:52269357 original size:84 final size:84
Alignment explanation
Indices: 52269216--52269384 Score: 329
Period size: 84 Copynumber: 2.0 Consensus size: 84
52269206 TTTTGTTGAT
*
52269216 CAATGGGATGATTACAATGCTTCTTCAAAGACTCTATTTATAGGTATAAGAAGTATAAATGAAGT
1 CAATGGGATGATTACAATGCTTCTTCAAAGACTCTATTTATAGGTATAAGAAGTATAAATAAAGT
52269281 AGAGATCTAATTCTAATGA
66 AGAGATCTAATTCTAATGA
52269300 CAATGGGATGATTACAATGCTTCTTCAAAGACTCTATTTATAGGTATAAGAAGTATAAATAAAGT
1 CAATGGGATGATTACAATGCTTCTTCAAAGACTCTATTTATAGGTATAAGAAGTATAAATAAAGT
52269365 AGAGATCTAATTCTAATGA
66 AGAGATCTAATTCTAATGA
52269384 C
1 C
52269385 TATTAGAATT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (84 bp):
CAATGGGATGATTACAATGCTTCTTCAAAGACTCTATTTATAGGTATAAGAAGTATAAATAAAGT
AGAGATCTAATTCTAATGA
Found at i:52269513 original size:20 final size:18
Alignment explanation
Indices: 52269488--52269526 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
52269478 TTATATATGT
52269488 TTCAAAAAATAATTTTTTTG
1 TTCAAAAAAT--TTTTTTTG
*
52269508 TTCAAATAATTTTTTTTG
1 TTCAAAAAATTTTTTTTG
52269526 T
1 T
52269527 AAAATTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
20 9 0.50
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.56
Consensus pattern (18 bp):
TTCAAAAAATTTTTTTTG
Found at i:52269531 original size:17 final size:18
Alignment explanation
Indices: 52269493--52269538 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
52269483 TATGTTTCAA
52269493 AAAATAA-TTTTTTTGTT
1 AAAATAATTTTTTTTGTT
*
52269510 CAAATAATTTTTTTTG-T
1 AAAATAATTTTTTTTGTT
*
52269527 AAAATTATTTTT
1 AAAATAATTTTT
52269539 CGAAAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (18 bp):
AAAATAATTTTTTTTGTT
Found at i:52269662 original size:13 final size:13
Alignment explanation
Indices: 52269644--52269669 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52269634 CAAAAAATAC
52269644 TTTTCAGTAGAAA
1 TTTTCAGTAGAAA
52269657 TTTTCAGTAGAAA
1 TTTTCAGTAGAAA
52269670 AAACTTTTTG
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:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
TTTTCAGTAGAAA
Found at i:52270604 original size:14 final size:14
Alignment explanation
Indices: 52270585--52270614 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
52270575 GATTAGTTAC
52270585 TTAATTCTTTAAAT
1 TTAATTCTTTAAAT
52270599 TTAATTCTTTAAAT
1 TTAATTCTTTAAAT
52270613 TT
1 TT
52270615 TTATAACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (14 bp):
TTAATTCTTTAAAT
Found at i:52272196 original size:21 final size:21
Alignment explanation
Indices: 52272172--52272217 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
52272162 AAAAGCGTAA
52272172 ATTAAAACAA-CAAAATTTATT
1 ATTAAAACAATC-AAATTTATT
* *
52272193 ATTATACCAATCAAATTTATT
1 ATTAAAACAATCAAATTTATT
52272214 -TTAA
1 ATTAA
52272218 TTGATAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 3 0.14
21 17 0.81
22 1 0.05
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTAAAACAATCAAATTTATT
Found at i:52272233 original size:62 final size:62
Alignment explanation
Indices: 52272154--52272271 Score: 191
Period size: 62 Copynumber: 1.9 Consensus size: 62
52272144 ATCATGATCA
* *
52272154 AATTGATAAAAAGCGTAAATTAAAACAACAAAATTTATTATTATACCAATCAAATTTATTTT
1 AATTGATAAAAAACGTAAAATAAAACAACAAAATTTATTATTATACCAATCAAATTTATTTT
* * *
52272216 AATTGATAAAAAACGTAAAATATAACAACCAAATTTGTTATTATACCAATCAAATT
1 AATTGATAAAAAACGTAAAATAAAACAACAAAATTTATTATTATACCAATCAAATT
52272272 GACCGAAATG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 51 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.33
Consensus pattern (62 bp):
AATTGATAAAAAACGTAAAATAAAACAACAAAATTTATTATTATACCAATCAAATTTATTTT
Found at i:52276295 original size:29 final size:30
Alignment explanation
Indices: 52276253--52276311 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
52276243 GATGGTTCAA
*
52276253 TGTGTAATTATATATATG-AATTTTAATTT
1 TGTGTAATTATATACATGAAATTTTAATTT
* *
52276282 TGTGTAATTTTATACATGAAATTTTGATTT
1 TGTGTAATTATATACATGAAATTTTAATTT
52276312 GATCCAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.54
Consensus pattern (30 bp):
TGTGTAATTATATACATGAAATTTTAATTT
Found at i:52285244 original size:21 final size:22
Alignment explanation
Indices: 52285214--52285256 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
52285204 ATTTTAACTT
52285214 TTTTTAAATAACAAAATAATTA
1 TTTTTAAATAACAAAATAATTA
* *
52285236 TTTTT-AATAATACAATAATTA
1 TTTTTAAATAACAAAATAATTA
52285257 AATTATTCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (22 bp):
TTTTTAAATAACAAAATAATTA
Found at i:52287380 original size:18 final size:17
Alignment explanation
Indices: 52287342--52287390 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
52287332 ACTCTCTCTC
*
52287342 TTTTTCTAATTTTCATA
1 TTTTTCTAATTTTAATA
52287359 TTTTTCTAAATTTTAAT-
1 TTTTTCT-AATTTTAATA
* *
52287376 TTTTTATTATTTTAA
1 TTTTTCTAATTTTAA
52287391 AATATTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 7 0.25
17 13 0.46
18 8 0.29
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTCTAATTTTAATA
Found at i:52293031 original size:45 final size:45
Alignment explanation
Indices: 52292963--52293051 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 45
52292953 AACAGATACT
* * * *
52292963 CGGTGGATTTAACACATAACAACCACCTTATTGATCAATGATGTC
1 CGGTGGAATCAACACATAACAACCACCTTACTAATCAATGATGTC
* *
52293008 CGGTGGAATCAACACATAGCAACCACTTTACTAATCAATGATGT
1 CGGTGGAATCAACACATAACAACCACCTTACTAATCAATGATGT
52293052 TCAGTTCACA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (45 bp):
CGGTGGAATCAACACATAACAACCACCTTACTAATCAATGATGTC
Found at i:52293120 original size:51 final size:50
Alignment explanation
Indices: 52293062--52293248 Score: 234
Period size: 51 Copynumber: 3.7 Consensus size: 50
52293052 TCAGTTCACA
*
52293062 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATTCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATTCGATACACG
* * * * *
52293113 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTA-TCTGATACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATTC-GATACACG
* * * *
52293164 TAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATACCATT-CGATACACG
52293214 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
52293249 CACTTTAGTA
Statistics
Matches: 114, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
49 2 0.02
50 40 0.35
51 70 0.61
52 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATACCATTCGATACACG
Found at i:52293237 original size:101 final size:101
Alignment explanation
Indices: 52293060--52293244 Score: 318
Period size: 101 Copynumber: 1.8 Consensus size: 101
52293050 GTTCAGTTCA
*
52293060 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATTCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCA-TACCATTCGATACACGTAGTAGCCTGCA
52293125 CATAGTACTACACACGTGATCGAAACTATCTGATACG
65 CATAGTACTACACACGTGATCGAAACTATCTGATACG
* *
52293162 CATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATT-CGATACACGTAGTAGCCTGCA
52293226 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
52293245 CCATCACTTT
Statistics
Matches: 79, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
100 6 0.08
101 39 0.49
102 34 0.43
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATTCGATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATCTGATACG
Found at i:52293257 original size:26 final size:26
Alignment explanation
Indices: 52293228--52293280 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
52293218 AGCCTGCACA
52293228 TAGTACTACACACGTGACCATCACTT
1 TAGTACTACACACGTGACCATCACTT
52293254 TAGTACTACACACGTGACCATCACTT
1 TAGTACTACACACGTGACCATCACTT
52293280 T
1 T
52293281 CACTTTTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.30, G:0.11, T:0.28
Consensus pattern (26 bp):
TAGTACTACACACGTGACCATCACTT
Found at i:52295731 original size:62 final size:56
Alignment explanation
Indices: 52295655--52295794 Score: 154
Period size: 57 Copynumber: 2.4 Consensus size: 56
52295645 AATTGACGGT
* *
52295655 AAAAAGGATCTAGCCTGGACGGATGATCCTATCCTGATATAGTCCTCCCGAAGAATGTGTGTG
1 AAAAA-GATCTAGCCTGGACGGATGAT-C--T--TGATATAGCCCTCCCGAAGAATATGTG-G
* *
52295718 AAAAAGATCTAGCCCGGACGGGTGATCTTGATATAGCCCTCCCGAAGAATATGTGG
1 AAAAAGATCTAGCCTGGACGGATGATCTTGATATAGCCCTCCCGAAGAATATGTGG
** *
52295774 AAATGGATTTAGCCTGGACGG
1 AAAAAGATCTAGCCTGGACGG
52295795 GTAATCCGAA
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
56 18 0.26
57 25 0.36
59 1 0.01
61 1 0.01
62 19 0.28
63 5 0.07
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (56 bp):
AAAAAGATCTAGCCTGGACGGATGATCTTGATATAGCCCTCCCGAAGAATATGTGG
Found at i:52303147 original size:13 final size:11
Alignment explanation
Indices: 52303111--52303141 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
52303101 CCGCCTGTAT
52303111 TAATTTTTATA
1 TAATTTTTATA
*
52303122 TTATTTTTATA
1 TAATTTTTATA
52303133 TAATTTTTA
1 TAATTTTTA
52303142 GATATATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TAATTTTTATA
Found at i:52303153 original size:22 final size:22
Alignment explanation
Indices: 52303111--52303154 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
52303101 CCGCCTGTAT
* *
52303111 TAATTTTTATATTATTTTTATA
1 TAATTTTTAGATTATTATTATA
52303133 TAATTTTTAGA-TATATATTATA
1 TAATTTTTAGATTAT-TATTATA
52303155 CATCAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TAATTTTTAGATTATTATTATA
Found at i:52305967 original size:18 final size:18
Alignment explanation
Indices: 52305944--52305980 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
52305934 ATTTTTGTAC
* *
52305944 ATAAAATTATCTTATAAA
1 ATAAAATAATCCTATAAA
52305962 ATAAAATAATCCTATAAA
1 ATAAAATAATCCTATAAA
52305980 A
1 A
52305981 AATATCTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAAAATAATCCTATAAA
Found at i:52306925 original size:9 final size:9
Alignment explanation
Indices: 52306911--52306986 Score: 109
Period size: 9 Copynumber: 8.4 Consensus size: 9
52306901 TTTAGTGAAA
52306911 AATTAACCG
1 AATTAACCG
*
52306920 AATTAACCT
1 AATTAACCG
52306929 AATTAACCG
1 AATTAACCG
* *
52306938 GATTACCCG
1 AATTAACCG
52306947 AATTAACCG
1 AATTAACCG
52306956 AATT-ACCTG
1 AATTAACC-G
52306965 AATTAACCG
1 AATTAACCG
52306974 AATTAACCG
1 AATTAACCG
52306983 AATT
1 AATT
52306987 GAATCACTAC
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
8 3 0.05
9 53 0.90
10 3 0.05
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:52307128 original size:18 final size:18
Alignment explanation
Indices: 52307089--52307131 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
52307079 TATGATTGGG
**
52307089 TTGGGTTGGGTTGGGTAA
1 TTGGGTTGGGTTGAATAA
*
52307107 TTGGGTTGGGTTGAATAC
1 TTGGGTTGGGTTGAATAA
52307125 TTGGGTT
1 TTGGGTT
52307132 TGGATTGGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.12, C:0.02, G:0.44, T:0.42
Consensus pattern (18 bp):
TTGGGTTGGGTTGAATAA
Found at i:52313884 original size:27 final size:27
Alignment explanation
Indices: 52313844--52313929 Score: 165
Period size: 27 Copynumber: 3.2 Consensus size: 27
52313834 ATTATATTAA
52313844 GTGC-TTAAAATCATTCTAGATATGTC
1 GTGCTTTAAAATCATTCTAGATATGTC
52313870 GTGCTTTAAAATCATTCTAGATATGTC
1 GTGCTTTAAAATCATTCTAGATATGTC
52313897 GTGCTTTAAAATCATTCTAGATATGTC
1 GTGCTTTAAAATCATTCTAGATATGTC
52313924 GTGCTT
1 GTGCTT
52313930 GAGTTGTGAT
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
26 4 0.07
27 55 0.93
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (27 bp):
GTGCTTTAAAATCATTCTAGATATGTC
Found at i:52315195 original size:40 final size:39
Alignment explanation
Indices: 52315142--52315281 Score: 106
Period size: 40 Copynumber: 3.6 Consensus size: 39
52315132 AACACACCAG
*
52315142 TTTGGCACCCAGTGCCTCATCGGATAATTGGAAGTAATAA
1 TTTGACACCCAGTGCCTCATCGGATAATT-GAAGTAATAA
* * * **
52315182 TTTGACACTCAGTGTCTCATCGGCTAAACCGAAGT-A-AA
1 TTTGACACCCAGTGCCTCATCGGAT-AATTGAAGTAATAA
* * * *
52315220 -TTGGCACCCAGTGCCTTATCGAATTAATCTGAAGTAGTAA
1 TTTGACACCCAGTGCCTCATCGGA-TAAT-TGAAGTAATAA
* * *
52315260 ATTGACACTCAGTGTCTCATCG
1 TTTGACACCCAGTGCCTCATCG
52315282 ACTCGAAGTT
Statistics
Matches: 75, Mismatches: 19, Indels: 11
0.71 0.18 0.10
Matches are distributed among these distances:
37 19 0.25
38 8 0.11
39 1 0.01
40 28 0.37
41 19 0.25
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (39 bp):
TTTGACACCCAGTGCCTCATCGGATAATTGAAGTAATAA
Found at i:52316165 original size:5 final size:4
Alignment explanation
Indices: 52316127--52316203 Score: 68
Period size: 4 Copynumber: 18.2 Consensus size: 4
52316117 AACCCTTGCG
* *
52316127 TCTT TCTT TCTCT TTTT TCTT T-TT TCTT TCTT TCATT TCTG T-TT TCGTT
1 TCTT TCTT TCT-T TCTT TCTT TCTT TCTT TCTT TC-TT TCTT TCTT TC-TT
52316176 TGGCTT TCTTT TCTT TCTT TCTT TCTT T
1 T--CTT TC-TT TCTT TCTT TCTT TCTT T
52316204 TTTATTTGTT
Statistics
Matches: 61, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
3 5 0.08
4 38 0.62
5 14 0.23
6 3 0.05
7 1 0.02
ACGTcount: A:0.01, C:0.21, G:0.05, T:0.73
Consensus pattern (4 bp):
TCTT
Found at i:52341346 original size:13 final size:14
Alignment explanation
Indices: 52341328--52341363 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
52341318 AGTAGGATTG
52341328 AAAACAAAAA-AAA
1 AAAACAAAAACAAA
52341341 AAAACAAAAACAAA
1 AAAACAAAAACAAA
52341355 AAAATCAAA
1 AAAA-CAAA
52341364 TATAGCAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 10 0.48
14 7 0.33
15 4 0.19
ACGTcount: A:0.86, C:0.11, G:0.00, T:0.03
Consensus pattern (14 bp):
AAAACAAAAACAAA
Found at i:52347998 original size:10 final size:10
Alignment explanation
Indices: 52347983--52348007 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
52347973 ACTTTTTAAG
52347983 AAATTATTAT
1 AAATTATTAT
52347993 AAATTATTAT
1 AAATTATTAT
52348003 AAATT
1 AAATT
52348008 TAAATTGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
AAATTATTAT
Found at i:52352806 original size:24 final size:24
Alignment explanation
Indices: 52352778--52352829 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
52352768 TTTCTAGAAG
* *
52352778 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
*
52352802 ATTTAGCATTTATTAGCATAATTT
1 ATTTAGCATTTATTAGCATAATAT
52352826 ATTT
1 ATTT
52352830 GACCTATGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.54
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:52361573 original size:50 final size:50
Alignment explanation
Indices: 52361470--52361701 Score: 189
Period size: 50 Copynumber: 4.5 Consensus size: 50
52361460 AAAAAGATCT
* * *
52361470 CATGTAAGACCATGTTTGGGACATGGCATTGGCATCATTGAGGTTATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGATATGGCATTGGCA-C--CGA-G--ATGAGAGGTCC
* *
52361526 CATGTAACACCATGTCTGGGATATGGCGTTGGCACCGAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGATATGGCATTGGCACCGAGATGAGAGGTCC
** * * ** * ** *
52361576 CCCGTAAGACCATGTCTGGGACATGACAAGGGCACCGATATGAGAACTCT
1 CATGTAAGACCATGTCTGGGATATGGCATTGGCACCGAGATGAGAGGTCC
* * * * **
52361626 CATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACAAGAAACATCC
1 CATGTAAGACCATGTCTGGGATATGGCATTGGCACCG-AGATGAGAGGTCC
*
52361675 CATGTAAGACCATGTCTGGGACATGGC
1 CATGTAAGACCATGTCTGGGATATGGC
52361702 TCTGGTATGT
Statistics
Matches: 143, Mismatches: 32, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
48 1 0.01
49 32 0.22
50 76 0.53
52 1 0.01
53 2 0.01
55 1 0.01
56 30 0.21
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGATATGGCATTGGCACCGAGATGAGAGGTCC
Found at i:52366235 original size:29 final size:26
Alignment explanation
Indices: 52366183--52366236 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
52366173 CTATTAATTA
* *
52366183 AATAATAAAATATCTTATATTAAAAT
1 AATAATAAAATATCTTACAATAAAAT
52366209 AATAATAAAATAATCTTAACCAATAAAA
1 AATAATAAAAT-ATCTT-A-CAATAAAA
52366237 ATCTAACACC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 11 0.48
27 5 0.22
28 1 0.04
29 6 0.26
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (26 bp):
AATAATAAAATATCTTACAATAAAAT
Found at i:52369913 original size:25 final size:25
Alignment explanation
Indices: 52369863--52369914 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
52369853 TGTAATTTTT
* *
52369863 AATTAAATAAAATATTTAAAATTAA
1 AATTAAATAAAATATTAAAAAATAA
*
52369888 AATTAAGTAAAA-ATTAAAGAAATAA
1 AATTAAATAAAATATTAAA-AAATAA
52369913 AA
1 AA
52369915 AAAACAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (25 bp):
AATTAAATAAAATATTAAAAAATAA
Found at i:52370090 original size:20 final size:21
Alignment explanation
Indices: 52370048--52370091 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
52370038 TTGAAGGATG
**
52370048 ATATTGTTATTTCAATTTTAA
1 ATATTGTTATTTCAATTAAAA
*
52370069 ATATTTTTATTT-AATTAAAA
1 ATATTGTTATTTCAATTAAAA
52370089 ATA
1 ATA
52370092 CCACATGTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (21 bp):
ATATTGTTATTTCAATTAAAA
Found at i:52370654 original size:22 final size:22
Alignment explanation
Indices: 52370624--52370669 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
52370614 ATAAGAGATT
*
52370624 AATTGGGAGCGAAGAA-AAGAAG
1 AATTAGGAG-GAAGAAGAAGAAG
*
52370646 AATTAGGAGGAAGAAGAGGAAG
1 AATTAGGAGGAAGAAGAAGAAG
52370668 AA
1 AA
52370670 AAAGATCAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.52, C:0.02, G:0.37, T:0.09
Consensus pattern (22 bp):
AATTAGGAGGAAGAAGAAGAAG
Found at i:52372469 original size:100 final size:100
Alignment explanation
Indices: 52372281--52372472 Score: 285
Period size: 100 Copynumber: 1.9 Consensus size: 100
52372271 ATTGAACATT
* * *
52372281 AACATCATTTACAGTCTTGAGCAATTAGTTTGAATGCCCCTAATGTTTAAAATTCTACCTTTCTG
1 AACATCATTTACAGTCTTGAACAATTAGTCTGAATGCCCCTAATATTTAAAATTCTACCTTTCTG
* *
52372346 AGCTGAAAACTTAAATGGGGATTTAAATTGTGATC
66 AGCTGAAAACTCAAATGGAGATTTAAATTGTGATC
* * * *
52372381 AACATCATTTTCAGTCTTTAACAATTAGTCTGAATGCCCTTAATATTTAAAATTCTACCTTTTTG
1 AACATCATTTACAGTCTTGAACAATTAGTCTGAATGCCCCTAATATTTAAAATTCTACCTTTCTG
* *
52372446 AGCTGACAACTCAATTGGAGATTTAAA
66 AGCTGAAAACTCAAATGGAGATTTAAA
52372473 GTGCAATCAA
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
100 81 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.37
Consensus pattern (100 bp):
AACATCATTTACAGTCTTGAACAATTAGTCTGAATGCCCCTAATATTTAAAATTCTACCTTTCTG
AGCTGAAAACTCAAATGGAGATTTAAATTGTGATC
Found at i:52379392 original size:30 final size:28
Alignment explanation
Indices: 52379355--52379446 Score: 103
Period size: 30 Copynumber: 3.1 Consensus size: 28
52379345 TAAATATATT
52379355 TATTTTTTAAAATTTTTTAATTTTAAAA
1 TATTTTTTAAAATTTTTTAATTTTAAAA
**
52379383 TACTTTTTTTATTATTTTTTAATTTTAAAA
1 TA--TTTTTTAAAATTTTTTAATTTTAAAA
*
52379413 TATTTTTAAAATACTTTTTTTAATTTTTAAAA
1 TATTTTTTAAA-A--TTTTTTAA-TTTTAAAA
52379445 TA
1 TA
52379447 AATTTTTGGT
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
28 8 0.15
29 1 0.02
30 26 0.49
31 8 0.15
32 10 0.19
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (28 bp):
TATTTTTTAAAATTTTTTAATTTTAAAA
Found at i:52379398 original size:40 final size:41
Alignment explanation
Indices: 52379354--52379445 Score: 106
Period size: 41 Copynumber: 2.3 Consensus size: 41
52379344 ATAAATATAT
*
52379354 TTATTTTTTAAAATTTT-TTAATTTTAAAATACTTTTTTTA
1 TTATTTTTTAAAATTTTAATAATTTTAAAATACTTTTTTTA
*
52379394 TTATTTTTT--AATTTTAAAATATTTTTAAAATACTTTTTTTA
1 TTATTTTTTAAAATTTT--AATAATTTTAAAATACTTTTTTTA
52379435 --A-TTTTTAAAAT
1 TTATTTTTTAAAAT
52379446 AAATTTTTGG
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
38 11 0.24
39 1 0.02
40 12 0.27
41 21 0.47
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (41 bp):
TTATTTTTTAAAATTTTAATAATTTTAAAATACTTTTTTTA
Found at i:52379452 original size:21 final size:21
Alignment explanation
Indices: 52379414--52379453 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
52379404 ATTTTAAAAT
**
52379414 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
52379435 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
52379454 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:52379460 original size:22 final size:21
Alignment explanation
Indices: 52379413--52379471 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
52379403 AATTTTAAAA
* *
52379413 TATTTTTAAAAT-ACTTTTTT
1 TATTTTTAAAATAAATTTTTG
52379433 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAATAAATTTTT-G
52379456 TATTTATTAAAA-AAAT
1 TATTT-TTAAAATAAAT
52379472 GGGTCGGGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.03
21 11 0.33
22 14 0.42
23 7 0.21
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (21 bp):
TATTTTTAAAATAAATTTTTG
Done.