Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 138 of 144
Found at i:42673485 original size:21 final size:19
Alignment explanation
Indices: 42673459--42673503 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
42673449 CCAAAGTTTA
*
42673459 AAAATGTAAGTAGAACATTTT
1 AAAATGT-AG-AGAACAATTT
*
42673480 AAAATGTAGAGACCAATTT
1 AAAATGTAGAGAACAATTT
42673499 AAAAT
1 AAAAT
42673504 ATCAGTCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 13 0.59
20 2 0.09
21 7 0.32
ACGTcount: A:0.51, C:0.07, G:0.13, T:0.29
Consensus pattern (19 bp):
AAAATGTAGAGAACAATTT
Found at i:42703520 original size:40 final size:40
Alignment explanation
Indices: 42703469--42703757 Score: 299
Period size: 40 Copynumber: 7.2 Consensus size: 40
42703459 AATTATTATA
* ** * *
42703469 TGATTGTACATACGTGTTCTTGTTTATACTTCGGTACCCT
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCT
* *
42703509 TGATTGCACATACGTGTCCCTGTTTGTACTTTGGTACCCT
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCT
* * ** * *
42703549 TAATTGCACATAAGTGATCCTGTTTGTACTTCAGTGCCCT
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCT
** * *
42703589 TGATTGCACATGTGTGCCCCTGTTTGTACTTTGGTACCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCT
* * * *
42703629 TGATTGCACATACATGCCCTTATTTGTACTTCGGTACTCT
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCT
* * * *
42703669 TGATGGCACATACGTGCCCCTGTTCGTACTTTGGTAGCCT
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCT
* * * * *
42703709 TGATTTCACATATGTGCCCCTATTTGTACTTTGGTACACT
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCT
*
42703749 TGAATGCAC
1 TGATTGCAC
42703758 TTTCGTGCAC
Statistics
Matches: 203, Mismatches: 46, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 203 1.00
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.39
Consensus pattern (40 bp):
TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCT
Found at i:42710555 original size:40 final size:40
Alignment explanation
Indices: 42710498--42710746 Score: 309
Period size: 40 Copynumber: 6.2 Consensus size: 40
42710488 GATTATTGTA
* * * * *
42710498 TGATTGCACATACGTGTCCTTGTTTGTACTTCGGTACACC
1 TGATTGCACATATGTGCCCCTATTTGTACTTCGGTACCCC
* ***
42710538 TGATTGCACATATGTGTCCCTATTTGTACTTTAATACCCC
1 TGATTGCACATATGTGCCCCTATTTGTACTTCGGTACCCC
* * * *
42710578 TGATTGCACATACGTGCTCCTGTTTGTACTTCAGTACCCC
1 TGATTGCACATATGTGCCCCTATTTGTACTTCGGTACCCC
* *
42710618 TGATTGCACATATATGCCCCTATTTGTACTTCGGTACTCC
1 TGATTGCACATATGTGCCCCTATTTGTACTTCGGTACCCC
* ***
42710658 TGATTGCACATATGTCCCCCTATTCACACTTCGGTACCCC
1 TGATTGCACATATGTGCCCCTATTTGTACTTCGGTACCCC
*
42710698 TAATTGCACATATGTGCCCCTATTTGTACTTCGGTACCCC
1 TGATTGCACATATGTGCCCCTATTTGTACTTCGGTACCCC
*
42710738 TGAATGCAC
1 TGATTGCAC
42710747 TTTCATGCCC
Statistics
Matches: 177, Mismatches: 32, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 177 1.00
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.35
Consensus pattern (40 bp):
TGATTGCACATATGTGCCCCTATTTGTACTTCGGTACCCC
Found at i:42710717 original size:20 final size:20
Alignment explanation
Indices: 42710611--42710719 Score: 62
Period size: 20 Copynumber: 5.5 Consensus size: 20
42710601 TTGTACTTCA
*
42710611 GTACCCCTGATTGCACATAT
1 GTACCCCTAATTGCACATAT
* * * * * **
42710631 ATGCCCCTATTTGTACTTCG
1 GTACCCCTAATTGCACATAT
* *
42710651 GTACTCCTGATTGCACATAT
1 GTACCCCTAATTGCACATAT
*
42710671 GTCCCCCT-ATT-CACACT-T
1 GTACCCCTAATTGCACA-TAT
42710689 CGGTACCCCTAATTGCACATAT
1 --GTACCCCTAATTGCACATAT
*
42710711 GTGCCCCTA
1 GTACCCCTA
42710720 TTTGTACTTC
Statistics
Matches: 62, Mismatches: 21, Indels: 12
0.65 0.22 0.13
Matches are distributed among these distances:
18 5 0.08
19 4 0.06
20 44 0.71
21 4 0.06
22 5 0.08
ACGTcount: A:0.21, C:0.33, G:0.14, T:0.32
Consensus pattern (20 bp):
GTACCCCTAATTGCACATAT
Found at i:42710737 original size:20 final size:20
Alignment explanation
Indices: 42710634--42710738 Score: 68
Period size: 20 Copynumber: 5.2 Consensus size: 20
42710624 CACATATATG
*
42710634 CCCCTATTTGTACTTCGGTA
1 CCCCTATTTGCACTTCGGTA
* * ** *
42710654 CTCCTGA-TTGCACATATGTC
1 CCCCT-ATTTGCACTTCGGTA
**
42710674 CCCCTATTCACACTTCGGTA
1 CCCCTATTTGCACTTCGGTA
* * ** *
42710694 CCCCTAATTGCACATATGTG
1 CCCCTATTTGCACTTCGGTA
*
42710714 CCCCTATTTGTACTTCGGTA
1 CCCCTATTTGCACTTCGGTA
42710734 CCCCT
1 CCCCT
42710739 GAATGCACTT
Statistics
Matches: 57, Mismatches: 26, Indels: 4
0.66 0.30 0.05
Matches are distributed among these distances:
19 1 0.02
20 55 0.96
21 1 0.02
ACGTcount: A:0.18, C:0.34, G:0.13, T:0.34
Consensus pattern (20 bp):
CCCCTATTTGCACTTCGGTA
Found at i:42717220 original size:10 final size:10
Alignment explanation
Indices: 42717207--42717300 Score: 63
Period size: 10 Copynumber: 9.5 Consensus size: 10
42717197 TTTTAAATAA
42717207 ATATAAAATT
1 ATATAAAATT
42717217 ATATAAAATT
1 ATATAAAATT
42717227 AT-TCAAAATT
1 ATAT-AAAATT
42717237 -TATTAAGAATT
1 ATA-TAA-AATT
*
42717248 ATAAAAAATT
1 ATATAAAATT
* *
42717258 ATAAAAAATC
1 ATATAAAATT
42717268 AT-T-AAATT
1 ATATAAAATT
* *
42717276 TTTTAAAAATT
1 ATAT-AAAATT
*
42717287 AT-TAAAACT
1 ATATAAAATT
42717296 ATATA
1 ATATA
42717301 TATATACCCG
Statistics
Matches: 68, Mismatches: 7, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
8 5 0.07
9 10 0.15
10 38 0.56
11 13 0.19
12 2 0.03
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.39
Consensus pattern (10 bp):
ATATAAAATT
Found at i:42717275 original size:39 final size:40
Alignment explanation
Indices: 42717211--42717293 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 40
42717201 AAATAAATAT
* * *
42717211 AAAATTATATAAAATTATTCAAAATTTATTAAGAATTATAA
1 AAAATTATAAAAAATCATT-AAAATTTATTAAAAATTATAA
* *
42717252 AAAATTATAAAAAATCATT-AAATTTTTTAAAAATTATTA
1 AAAATTATAAAAAATCATTAAAATTTATTAAAAATTATAA
42717291 AAA
1 AAA
42717294 CTATATATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 20 0.54
41 17 0.46
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (40 bp):
AAAATTATAAAAAATCATTAAAATTTATTAAAAATTATAA
Found at i:42719161 original size:31 final size:31
Alignment explanation
Indices: 42719126--42719211 Score: 118
Period size: 31 Copynumber: 2.8 Consensus size: 31
42719116 AAGTTATGGA
* *
42719126 TTTAGTCCTTGTACTTTTTGAATTGGTTAAT
1 TTTAGTCCTTATACTTTTTGAATTGGTCAAT
* *
42719157 TTTAGTCATTATACTTTTTTAATTGGTCAAT
1 TTTAGTCCTTATACTTTTTGAATTGGTCAAT
* *
42719188 TTTGGTCCCTATACTTTTTGAATT
1 TTTAGTCCTTATACTTTTTGAATT
42719212 TTGAATTTTG
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.21, C:0.12, G:0.13, T:0.55
Consensus pattern (31 bp):
TTTAGTCCTTATACTTTTTGAATTGGTCAAT
Found at i:42719219 original size:30 final size:30
Alignment explanation
Indices: 42719137--42719224 Score: 97
Period size: 31 Copynumber: 2.9 Consensus size: 30
42719127 TTAGTCCTTG
* *
42719137 TACTTTTTGAATTGGTTAATTTTAGTCATTA
1 TACTTTTTGAATT-GTTAATTTTGGTCACTA
* * *
42719168 TACTTTTTTAATTGGTCAATTTTGGTCCCTA
1 TACTTTTTGAATT-GTTAATTTTGGTCACTA
42719199 TACTTTTTGAATT-TTGAATTTTGGTC
1 TACTTTTTGAATTGTT-AATTTTGGTC
42719225 TTGATTCAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
29 1 0.02
30 10 0.20
31 38 0.78
ACGTcount: A:0.22, C:0.10, G:0.14, T:0.55
Consensus pattern (30 bp):
TACTTTTTGAATTGTTAATTTTGGTCACTA
Found at i:42727793 original size:10 final size:10
Alignment explanation
Indices: 42727780--42727810 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
42727770 ATTTAAAATT
42727780 TATAAAAAAA
1 TATAAAAAAA
*
42727790 TATAAAAAAT
1 TATAAAAAAA
42727800 TATAAAAAAA
1 TATAAAAAAA
42727810 T
1 T
42727811 TACAAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
TATAAAAAAA
Found at i:42727796 original size:9 final size:10
Alignment explanation
Indices: 42727774--42727808 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
42727764 TAAACAATTT
*
42727774 AAAATTTATA
1 AAAAATTATA
*
42727784 AAAAAATATA
1 AAAAATTATA
42727794 AAAAATTATA
1 AAAAATTATA
42727804 AAAAA
1 AAAAA
42727809 ATTACAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAAATTATA
Found at i:42727810 original size:11 final size:11
Alignment explanation
Indices: 42727774--42727812 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
42727764 TAAACAATTT
*
42727774 AAAATTTATAA
1 AAAAATTATAA
42727785 AAAAA-TAT-A
1 AAAAATTATAA
42727794 AAAAATTATAA
1 AAAAATTATAA
42727805 AAAAATTA
1 AAAAATTA
42727813 CAAATTATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 6 0.24
10 6 0.24
11 13 0.52
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:42729856 original size:40 final size:40
Alignment explanation
Indices: 42729811--42729937 Score: 118
Period size: 39 Copynumber: 3.1 Consensus size: 40
42729801 CACGTAAGCA
* *
42729811 CGATTTGCTT-CCACGTCAGCAAATCGCGCTTACGTGGACG
1 CGATTTGCTTGCCACGTAAG-AAATCGCGCTGACGTGGACG
* *
42729851 TGATTTG-TTGCCACGTAAGTAATCGCGCTGACGTGGACG
1 CGATTTGCTTGCCACGTAAGAAATCGCGCTGACGTGGACG
** *
42729890 CGATTTGC-TGACACATC-TCCTGACATCGCGCTGACGTGGACG
1 CGATTTGCTTG-C-CA-CGT-AAGAAATCGCGCTGACGTGGACG
42729932 CGATTT
1 CGATTT
42729938 CGGGGAAAAT
Statistics
Matches: 72, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
39 28 0.39
40 15 0.21
41 3 0.04
42 26 0.36
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (40 bp):
CGATTTGCTTGCCACGTAAGAAATCGCGCTGACGTGGACG
Found at i:42734071 original size:21 final size:21
Alignment explanation
Indices: 42734047--42734089 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
42734037 GACTTTTTTA
42734047 GCATCAAACAGAACAAGGTGT
1 GCATCAAACAGAACAAGGTGT
*
42734068 GCATCAAACAGAACTAGGTGT
1 GCATCAAACAGAACAAGGTGT
42734089 G
1 G
42734090 TACCTGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.19, G:0.26, T:0.16
Consensus pattern (21 bp):
GCATCAAACAGAACAAGGTGT
Found at i:42736218 original size:7 final size:7
Alignment explanation
Indices: 42736204--42736277 Score: 67
Period size: 7 Copynumber: 10.6 Consensus size: 7
42736194 TTAAAAAAAT
42736204 AATTGAG
1 AATTGAG
*
42736211 ATTTGAG
1 AATTGAG
42736218 AATTGAG
1 AATTGAG
**
42736225 AATCAAG
1 AATTGAG
**
42736232 AAGCGAG
1 AATTGAG
42736239 AATTGAG
1 AATTGAG
*
42736246 AATCGAG
1 AATTGAG
**
42736253 AACCGAG
1 AATTGAG
42736260 AATTGAG
1 AATTGAG
*
42736267 AATCGAG
1 AATTGAG
42736274 AATT
1 AATT
42736278 TGGGATTGAG
Statistics
Matches: 53, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 53 1.00
ACGTcount: A:0.43, C:0.08, G:0.27, T:0.22
Consensus pattern (7 bp):
AATTGAG
Found at i:42736233 original size:14 final size:14
Alignment explanation
Indices: 42736204--42736277 Score: 76
Period size: 14 Copynumber: 5.3 Consensus size: 14
42736194 TTAAAAAAAT
* *
42736204 AATTGAGATTTGAG
1 AATTGAGAATCGAG
*
42736218 AATTGAGAATCAAG
1 AATTGAGAATCGAG
** *
42736232 AAGCGAGAATTGAG
1 AATTGAGAATCGAG
* *
42736246 AATCGAGAACCGAG
1 AATTGAGAATCGAG
42736260 AATTGAGAATCGAG
1 AATTGAGAATCGAG
42736274 AATT
1 AATT
42736278 TGGGATTGAG
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 48 1.00
ACGTcount: A:0.43, C:0.08, G:0.27, T:0.22
Consensus pattern (14 bp):
AATTGAGAATCGAG
Found at i:42736241 original size:21 final size:21
Alignment explanation
Indices: 42736215--42736275 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
42736205 ATTGAGATTT
* *
42736215 GAGAATTGAGAATCAAGAAGC
1 GAGAATTGAGAATCGAGAACC
42736236 GAGAATTGAGAATCGAGAACC
1 GAGAATTGAGAATCGAGAACC
42736257 GAGAATTGAGAATCGAGAA
1 GAGAATTGAGAATCGAGAA
42736276 TTTGGGATTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.46, C:0.10, G:0.30, T:0.15
Consensus pattern (21 bp):
GAGAATTGAGAATCGAGAACC
Found at i:42742050 original size:19 final size:19
Alignment explanation
Indices: 42742026--42742098 Score: 119
Period size: 19 Copynumber: 3.8 Consensus size: 19
42742016 AATCATATTT
42742026 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
** *
42742045 TCTAAGATTAAATATTATA
1 TCTAAGATTGCATATCATA
42742064 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
42742083 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
42742099 CCTGAAGATT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:42763907 original size:50 final size:51
Alignment explanation
Indices: 42763851--42763955 Score: 160
Period size: 50 Copynumber: 2.1 Consensus size: 51
42763841 TATAAATAAA
*
42763851 ATATTTATTAATTAAAAAGATGAATTAAAAATAAAA-AA-CTTGAAAACAAT
1 ATATTTATTAATTAAAAACATGAATTAAAAATAAAAGAAGCTTG-AAACAAT
*
42763901 ATATTTATTAATTAAAAACATTAATTAAAAATAAAAGAAGGCTTGAAACAAT
1 ATATTTATTAATTAAAAACATGAATTAAAAATAAAAGAA-GCTTGAAACAAT
42763953 ATA
1 ATA
42763956 GAATAAAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
50 34 0.68
51 2 0.04
52 10 0.20
53 4 0.08
ACGTcount: A:0.58, C:0.05, G:0.07, T:0.30
Consensus pattern (51 bp):
ATATTTATTAATTAAAAACATGAATTAAAAATAAAAGAAGCTTGAAACAAT
Found at i:42763925 original size:13 final size:13
Alignment explanation
Indices: 42763907--42763931 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42763897 CAATATATTT
42763907 ATTAATTAAAAAC
1 ATTAATTAAAAAC
42763920 ATTAATTAAAAA
1 ATTAATTAAAAA
42763932 TAAAAGAAGG
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:42765885 original size:21 final size:21
Alignment explanation
Indices: 42765852--42765896 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
42765842 TAAAAATATT
*
42765852 AATAATTAATTTTATTTATCA
1 AATAATTAATTTTAGTTATCA
* * *
42765873 AATATTTATTTTTAGTTATTA
1 AATAATTAATTTTAGTTATCA
42765894 AAT
1 AAT
42765897 TGAATTCTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
AATAATTAATTTTAGTTATCA
Found at i:42784551 original size:20 final size:20
Alignment explanation
Indices: 42784526--42784566 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
42784516 GCATGCAGAA
42784526 AATTACTCAACAAATTTGAT
1 AATTACTCAACAAATTTGAT
42784546 AATTACTCAACAAATTTGAT
1 AATTACTCAACAAATTTGAT
42784566 A
1 A
42784567 TTTTTACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (20 bp):
AATTACTCAACAAATTTGAT
Found at i:42785846 original size:15 final size:15
Alignment explanation
Indices: 42785826--42785873 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
42785816 TTTATGGAAA
42785826 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
42785841 ATCAAATA-ATGGAA
1 ATCAAAGATATGGGT
42785855 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
42785871 ATC
1 ATC
42785874 GAGATATTGG
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
14 5 0.20
15 15 0.60
16 5 0.20
ACGTcount: A:0.44, C:0.08, G:0.23, T:0.25
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:42790480 original size:15 final size:15
Alignment explanation
Indices: 42790460--42790537 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
42790450 TTTATGGAAA
42790460 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
42790475 ATCAAATA-ATGGAA
1 ATCAAAGATATGGGT
42790489 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
42790505 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
42790519 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
42790535 ATC
1 ATC
42790538 GAGATATTGG
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 9 0.19
15 29 0.62
16 9 0.19
ACGTcount: A:0.44, C:0.08, G:0.23, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:42790489 original size:30 final size:30
Alignment explanation
Indices: 42790453--42790537 Score: 152
Period size: 30 Copynumber: 2.8 Consensus size: 30
42790443 ATCCATATTT
*
42790453 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
42790483 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
42790513 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
42790538 GAGATATTGG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.45, C:0.07, G:0.24, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:42795226 original size:15 final size:14
Alignment explanation
Indices: 42795204--42795246 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 14
42795194 AAATATGTTA
42795204 TTTTTATTTAATAT
1 TTTTTATTTAATAT
42795218 TTATTTATTTCATATAT
1 TT-TTTATTT-A-ATAT
42795235 TTTTTATATTAA
1 TTTTTAT-TTAA
42795247 AAATTTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
14 2 0.08
15 8 0.32
16 7 0.28
17 8 0.32
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTTATTTAATAT
Found at i:42796183 original size:27 final size:27
Alignment explanation
Indices: 42796145--42796199 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
42796135 GATTACAGAT
42796145 TTTGAGAACCTTTGGCTATCATGCACC
1 TTTGAGAACCTTTGGCTATCATGCACC
*
42796172 TTTGGGAACCTTTGGCTATCATGCACC
1 TTTGAGAACCTTTGGCTATCATGCACC
42796199 T
1 T
42796200 GAGTATGCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (27 bp):
TTTGAGAACCTTTGGCTATCATGCACC
Found at i:42799075 original size:22 final size:22
Alignment explanation
Indices: 42799033--42799080 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
42799023 ATCCCATAAG
* * *
42799033 AAAAGTTACCAAGCCACAAACT
1 AAAAGTCACCAAACCACAAACC
42799055 AAAAGTCACCAAAACCA-AAACC
1 AAAAGTCACC-AAACCACAAACC
42799077 AAAA
1 AAAA
42799081 CCAATAGAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.58, C:0.27, G:0.06, T:0.08
Consensus pattern (22 bp):
AAAAGTCACCAAACCACAAACC
Found at i:42806204 original size:24 final size:25
Alignment explanation
Indices: 42806154--42806208 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
42806144 TTGGGTTTTA
42806154 GGTGACCAAAAATCCAAGATAGTTT
1 GGTGACCAAAAATCCAAGATAGTTT
*
42806179 GGTGACCAAAAATCCAAGATAGTTG
1 GGTGACCAAAAATCCAAGATAGTTT
42806204 GGTGA
1 GGTGA
42806209 AAAAAAAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (25 bp):
GGTGACCAAAAATCCAAGATAGTTT
Found at i:42806213 original size:24 final size:25
Alignment explanation
Indices: 42806154--42806215 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
42806144 TTGGGTTTTA
* *
42806154 GGTGACCAAAAATCCAAGATAGTTT
1 GGTGACAAAAAATCCAAGATAGTTG
*
42806179 GGTGACCAAAAATCCAAGATAGTTG
1 GGTGACAAAAAATCCAAGATAGTTG
*
42806204 GGTGAAAAAAAA
1 GGTGACAAAAAA
42806216 AGACAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.45, C:0.13, G:0.23, T:0.19
Consensus pattern (25 bp):
GGTGACAAAAAATCCAAGATAGTTG
Found at i:42807524 original size:27 final size:27
Alignment explanation
Indices: 42807494--42807550 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
42807484 AATTACATAC
42807494 CATTACAAAAGCTACTTAATCAGCAGT
1 CATTACAAAAGCTACTTAATCAGCAGT
42807521 CATTACAAAAGCTACTTAATCAGCAGT
1 CATTACAAAAGCTACTTAATCAGCAGT
42807548 CAT
1 CAT
42807551 CCAATGACCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (27 bp):
CATTACAAAAGCTACTTAATCAGCAGT
Found at i:42808825 original size:43 final size:43
Alignment explanation
Indices: 42808737--42808818 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
42808727 GTTTGATTAG
* * *
42808737 TGGTGGCCAATGGTGGTTCAACTGATAGTGGTCAGACGACCGA
1 TGGTGGCCAATGGTGGTTCAACAGACAGTGGCCAGACGACCGA
42808780 TGGTGGCCAATGGTGG-TCTAATCAG-CAGTGGCCAGACGA
1 TGGTGGCCAATGGTGGTTC-AA-CAGACAGTGGCCAGACGA
42808819 TTGATGGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 2 0.06
43 30 0.88
44 2 0.06
ACGTcount: A:0.23, C:0.20, G:0.35, T:0.22
Consensus pattern (43 bp):
TGGTGGCCAATGGTGGTTCAACAGACAGTGGCCAGACGACCGA
Found at i:42815985 original size:32 final size:33
Alignment explanation
Indices: 42815913--42815985 Score: 87
Period size: 32 Copynumber: 2.2 Consensus size: 33
42815903 TTTTTTTCAG
* * *
42815913 AACCTCTAAACCCTAAAAATTAAATATAACCCTA
1 AACC-CTAAACACTAAAAATTAAATAAAAACCTA
*
42815947 AA-CCTAAACACTTAAAATTAAA-AAAAACCTA
1 AACCCTAAACACTAAAAATTAAATAAAAACCTA
42815978 AACCCTAA
1 AACCCTAA
42815986 TTGGCCCTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
31 9 0.26
32 22 0.65
33 1 0.03
34 2 0.06
ACGTcount: A:0.55, C:0.25, G:0.00, T:0.21
Consensus pattern (33 bp):
AACCCTAAACACTAAAAATTAAATAAAAACCTA
Found at i:42816643 original size:15 final size:15
Alignment explanation
Indices: 42816623--42816679 Score: 96
Period size: 15 Copynumber: 3.8 Consensus size: 15
42816613 CAATGGCGAA
42816623 AAATCAAAAGATGAC
1 AAATCAAAAGATGAC
42816638 AAATCAAAAGATGAC
1 AAATCAAAAGATGAC
* *
42816653 AAATCAAAAGACGAA
1 AAATCAAAAGATGAC
42816668 AAATCAAAAGAT
1 AAATCAAAAGAT
42816680 AGCAAGTCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.63, C:0.12, G:0.12, T:0.12
Consensus pattern (15 bp):
AAATCAAAAGATGAC
Found at i:42818792 original size:11 final size:10
Alignment explanation
Indices: 42818765--42818794 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
42818755 TAATTTAGGA
42818765 ATTTAAATTC
1 ATTTAAATTC
42818775 ATTTAAATTC
1 ATTTAAATTC
42818785 ATTTTAAATT
1 A-TTTAAATT
42818795 ATACTCTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (10 bp):
ATTTAAATTC
Found at i:42820886 original size:22 final size:25
Alignment explanation
Indices: 42820860--42820933 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 25
42820850 TTATAATGAT
42820860 TTAATTTA-AAAATATA-TA-TAAA
1 TTAATTTATAAAATATACTATTAAA
*
42820882 TTAA-TTATAAAGTATACTATTAAA
1 TTAATTTATAAAATATACTATTAAA
42820906 TTAATTATATTATAAATATTA-TATTAAA
1 TTAATT-TA-TA-AAATA-TACTATTAAA
42820934 AAATAAATGA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
21 3 0.07
22 11 0.26
23 2 0.05
24 8 0.19
25 1 0.02
26 2 0.05
27 2 0.05
28 11 0.26
29 2 0.05
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (25 bp):
TTAATTTATAAAATATACTATTAAA
Found at i:42820930 original size:28 final size:28
Alignment explanation
Indices: 42820880--42820933 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
42820870 AATATATATA
42820880 AATTAATTATAAAGTATACTATTAAATT
1 AATTAATTATAAAGTATACTATTAAATT
42820908 AATTATATTATAAA-TATTA-TATTAAA
1 AATTA-ATTATAAAGTA-TACTATTAAA
42820934 AAATAAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (28 bp):
AATTAATTATAAAGTATACTATTAAATT
Found at i:42829259 original size:32 final size:32
Alignment explanation
Indices: 42829223--42829285 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
42829213 CATCACATAG
42829223 AAACAATTAATAAATTTAAAATATTAACATTA
1 AAACAATTAATAAATTTAAAATATTAACATTA
*
42829255 AAACAATTAATCAATTTAAAATATTAACATT
1 AAACAATTAATAAATTTAAAATATTAACATT
42829286 CAATTCCAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (32 bp):
AAACAATTAATAAATTTAAAATATTAACATTA
Found at i:42831877 original size:109 final size:106
Alignment explanation
Indices: 42831683--42831882 Score: 337
Period size: 109 Copynumber: 1.9 Consensus size: 106
42831673 TTACCTTTTT
42831683 TTAAAATCAATTTTTATAAAATGATGCATAATTTCATTACCATACTCATGAATTTATGAAATCTT
1 TTAAAATCAATTTTTATAAAATGATGCATAATTTCATTACCATACTCATGAATTTATGAAATCTT
42831748 ATACACATCATAAGCCCCACAAGTTATGAATTTATGAAATC
66 ATACACATCATAAGCCCCACAAGTTATGAATTTATGAAATC
* *
42831789 TTAAACTCAATTTTTATAAAATGATGCATAATTTCATTATCAATATACTCATGAATTTATGAAAT
1 TTAAAATCAATTTTTATAAAATGATGCATAATTTCATTA-C--CATACTCATGAATTTATGAAAT
**
42831854 CTTATACACATCATAAGTTCCACAAGTTA
63 CTTATACACATCATAAGCCCCACAAGTTA
42831883 GTGAGCTCAA
Statistics
Matches: 87, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
106 38 0.44
107 1 0.01
109 48 0.55
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (106 bp):
TTAAAATCAATTTTTATAAAATGATGCATAATTTCATTACCATACTCATGAATTTATGAAATCTT
ATACACATCATAAGCCCCACAAGTTATGAATTTATGAAATC
Found at i:42834850 original size:5 final size:5
Alignment explanation
Indices: 42834840--42834874 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
42834830 TAATAGAATT
42834840 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
42834875 ACCCCATGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:42835576 original size:20 final size:20
Alignment explanation
Indices: 42835542--42835591 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
42835532 ATTTTATAAA
*
42835542 TATTTTG-AGTTTTGAAAAT
1 TATTTTGAATTTTTGAAAAT
42835561 TATTTTGAATTTTTGAAAAT
1 TATTTTGAATTTTTGAAAAT
42835581 TATTTTGAATT
1 TATTTTGAATT
42835592 ATTTTGTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 7 0.24
20 22 0.76
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (20 bp):
TATTTTGAATTTTTGAAAAT
Found at i:42845104 original size:3 final size:3
Alignment explanation
Indices: 42845096--42845136 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
42845086 GACCACTGCT
42845096 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
42845137 TAAGTGAGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:42846175 original size:31 final size:31
Alignment explanation
Indices: 42846133--42846191 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
42846123 CAATTTGGTC
*
42846133 ACTAAATTATTCAAAAGTTTTCATTTAAGTA
1 ACTAAACTATTCAAAAGTTTTCATTTAAGTA
*
42846164 ACTAAACTATTCAAAAGTTTTTATTTAA
1 ACTAAACTATTCAAAAGTTTTCATTTAA
42846192 TTCACTATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.42
Consensus pattern (31 bp):
ACTAAACTATTCAAAAGTTTTCATTTAAGTA
Found at i:42846575 original size:18 final size:19
Alignment explanation
Indices: 42846540--42846575 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
42846530 GTCCTTCCCT
42846540 GCGCGTGCTGCGCCTCCAC
1 GCGCGTGCTGCGCCTCCAC
*
42846559 GCGCGTGC-GCTCCTCCA
1 GCGCGTGCTGCGCCTCCA
42846576 GGAATGTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.06, C:0.47, G:0.31, T:0.17
Consensus pattern (19 bp):
GCGCGTGCTGCGCCTCCAC
Found at i:42847746 original size:9 final size:8
Alignment explanation
Indices: 42847734--42847799 Score: 50
Period size: 7 Copynumber: 8.1 Consensus size: 8
42847724 TTTCATAGTT
42847734 TTTATATA
1 TTTATATA
42847742 CTTTATATACA
1 -TTTATAT--A
42847753 TTTATAT-
1 TTTATATA
42847760 TTTATAATA
1 TTTAT-ATA
42847769 TTTATAT-
1 TTTATATA
42847776 TTTCATAT-
1 TTT-ATATA
42847784 TTTATA-A
1 TTTATATA
*
42847791 TCTATATA
1 TTTATATA
42847799 T
1 T
42847800 GCTTATACAT
Statistics
Matches: 49, Mismatches: 1, Indels: 15
0.75 0.02 0.23
Matches are distributed among these distances:
7 16 0.33
8 13 0.27
9 12 0.24
10 7 0.14
11 1 0.02
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (8 bp):
TTTATATA
Found at i:42847763 original size:17 final size:17
Alignment explanation
Indices: 42847738--42847783 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
42847728 ATAGTTTTTA
*
42847738 TATACTTTATATACATT
1 TATATTTTATATACATT
*
42847755 TATATTTTATA-ATATT
1 TATATTTTATATACATT
42847771 TATATTTTCATAT
1 TATATTTT-ATAT
42847784 TTTATAATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.59
Consensus pattern (17 bp):
TATATTTTATATACATT
Found at i:42847785 original size:14 final size:16
Alignment explanation
Indices: 42847703--42847778 Score: 64
Period size: 16 Copynumber: 4.5 Consensus size: 16
42847693 ATATTATGTA
*
42847703 TATATTTTATTATTATT
1 TATATTTTA-TAATATT
* *
42847720 T-TATTTTCATAGTTTT
1 TATATTTT-ATAATATT
*
42847736 TATATACTTTATATACATT
1 TATAT--TTTATA-ATATT
42847755 TATATTTTATAATATT
1 TATATTTTATAATATT
42847771 TATATTTT
1 TATATTTT
42847779 CATATTTTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
16 24 0.50
17 11 0.23
18 3 0.06
19 10 0.21
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (16 bp):
TATATTTTATAATATT
Found at i:42847798 original size:24 final size:23
Alignment explanation
Indices: 42847704--42847799 Score: 68
Period size: 24 Copynumber: 3.8 Consensus size: 23
42847694 TATTATGTAT
* *
42847704 ATATTTTATTATTATTTTATTTTC
1 ATATTTTATAATTA-TATATTTTC
*
42847728 ATAGTTTTTATATACTTTATATACATTT-
1 ATA--TTTTATA-A--TTATATA-TTTTC
*
42847756 ATATTTTATAATATTTATATTTTC
1 ATATTTTATAAT-TATATATTTTC
42847780 ATATTTTATAATCTATATAT
1 ATATTTTATAAT-TATATAT
42847800 GCTTATACAT
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
23 4 0.07
24 26 0.46
25 1 0.02
26 13 0.23
27 1 0.02
28 6 0.11
29 6 0.11
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.61
Consensus pattern (23 bp):
ATATTTTATAATTATATATTTTC
Found at i:42851246 original size:20 final size:19
Alignment explanation
Indices: 42851223--42851304 Score: 58
Period size: 19 Copynumber: 4.2 Consensus size: 19
42851213 TTAATTTTTA
*
42851223 AAATATTTTTTATAATGTTT
1 AAATATTTTTAAT-ATGTTT
* *
42851243 AAATAATTTTAATATTTTT
1 AAATATTTTTAATATGTTT
*
42851262 AAA-ATTTTTAAAATAATTTTT
1 AAATATTTTT--AAT-ATGTTT
* * *
42851283 ATATATTTTTAAAATTTTT
1 AAATATTTTTAATATGTTT
42851302 AAA
1 AAA
42851305 ATTAATTAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
18 5 0.10
19 16 0.31
20 16 0.31
21 8 0.16
22 6 0.12
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (19 bp):
AAATATTTTTAATATGTTT
Found at i:42851261 original size:40 final size:40
Alignment explanation
Indices: 42851215--42851307 Score: 116
Period size: 40 Copynumber: 2.3 Consensus size: 40
42851205 GCATTTAATT
**
42851215 AATTTTTAAAATATTTT-TTATAATGTTTAAATAATTTTAA
1 AATTTTTAAAAT-TTTTAAAATAATGTTTAAATAATTTTAA
* * * *
42851255 TATTTTTAAAATTTTTAAAATAATTTTTATATATTTTTAA
1 AATTTTTAAAATTTTTAAAATAATGTTTAAATAATTTTAA
42851295 AATTTTTAAAATT
1 AATTTTTAAAATT
42851308 AATTAAATAC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.09
40 41 0.91
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (40 bp):
AATTTTTAAAATTTTTAAAATAATGTTTAAATAATTTTAA
Found at i:42851290 original size:22 final size:21
Alignment explanation
Indices: 42851214--42851297 Score: 68
Period size: 21 Copynumber: 4.0 Consensus size: 21
42851204 AGCATTTAAT
**
42851214 TAATTTTTAAAATATTTT-TTA
1 TAATTTTTAAAAT-TTTTAAAA
* *
42851235 TAATGTTTAAATAATTTT--AA
1 TAATTTTTAAA-ATTTTTAAAA
42851255 T-ATTTTTAAAATTTTTAAAA
1 TAATTTTTAAAATTTTTAAAA
*
42851275 TAATTTTTATATATTTTTAAAA
1 TAATTTTTA-AAATTTTTAAAA
42851297 T
1 T
42851298 TTTTAAAATT
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
18 5 0.10
19 8 0.15
20 5 0.10
21 21 0.40
22 13 0.25
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (21 bp):
TAATTTTTAAAATTTTTAAAA
Found at i:42851292 original size:31 final size:30
Alignment explanation
Indices: 42851243--42851311 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 30
42851233 TATAATGTTT
42851243 AAATAA-TTTTAATATTTTTAAAATTTTTA
1 AAATAATTTTTAATATTTTTAAAATTTTTA
42851272 AAATAATTTTTATATATTTTTAAAATTTTTA
1 AAATAATTTTTA-ATATTTTTAAAATTTTTA
42851303 AAATTAATT
1 AAA-TAATT
42851312 AAATACTGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
29 6 0.16
30 5 0.14
31 21 0.57
32 5 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
AAATAATTTTTAATATTTTTAAAATTTTTA
Found at i:42851301 original size:9 final size:9
Alignment explanation
Indices: 42851215--42851307 Score: 69
Period size: 9 Copynumber: 9.4 Consensus size: 9
42851205 GCATTTAATT
42851215 AATTTTTAAA
1 AATTTTT-AA
*
42851225 ATATTTTTTAT
1 A-A-TTTTTAA
*
42851236 AATGTTTAA
1 AATTTTTAA
*
42851245 ATAATTTTAA
1 A-ATTTTTAA
*
42851255 TATTTTTAA
1 AATTTTTAA
42851264 AATTTTTAAAA
1 AATTTTT--AA
42851275 TAATTTTTATA
1 -AATTTTTA-A
*
42851286 TATTTTTAA
1 AATTTTTAA
42851295 AATTTTTAA
1 AATTTTTAA
42851304 AATT
1 AATT
42851308 AATTAAATAC
Statistics
Matches: 66, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
9 32 0.48
10 16 0.24
11 6 0.09
12 12 0.18
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (9 bp):
AATTTTTAA
Found at i:42855699 original size:109 final size:109
Alignment explanation
Indices: 42855379--42855719 Score: 542
Period size: 109 Copynumber: 3.1 Consensus size: 109
42855369 TGGATTAAGA
* * *
42855379 TTTAAGAGGATATTTGGCTATTTGGTCCAACGAG--AAATCGAAACCCAGCACATTAGGGCATGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
* *
42855442 TTTCTCGAATTTTCAAACGCAAAACATTGCCTTATTTTAAAATT
66 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
* *
42855486 TCTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCATATTAGGGCACGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
42855551 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
66 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
* * *
42855595 TTTGAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAACCCCAGCACATTAGGGCACGC
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
* *
42855660 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTACTTTGAATTTTT
66 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAA--ATT
42855706 TTTAAAAGGATATT
1 TTTAAAAGGATATT
42855720 AATATGCACA
Statistics
Matches: 215, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
107 31 0.14
109 169 0.79
111 15 0.07
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (109 bp):
TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
Found at i:42855940 original size:7 final size:7
Alignment explanation
Indices: 42855928--42855977 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
42855918 TAATGAGAAT
42855928 AAATAAA
1 AAATAAA
42855935 AAAT-AA
1 AAATAAA
*
42855941 AAGT-AA
1 AAATAAA
*
42855947 AAATGAA
1 AAATAAA
*
42855954 AAATGAA
1 AAATAAA
42855961 AAATAAAA
1 AAAT-AAA
42855969 AAATAAA
1 AAATAAA
42855976 AA
1 AA
42855978 GCTATGTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
6 10 0.26
7 22 0.58
8 6 0.16
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (7 bp):
AAATAAA
Found at i:42855956 original size:14 final size:13
Alignment explanation
Indices: 42855928--42855969 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
42855918 TAATGAGAAT
42855928 AAATAAAAAATAA
1 AAATAAAAAATAA
*
42855941 AAGT-AAAAATGAA
1 AAATAAAAAAT-AA
*
42855954 AAATGAAAAATAA
1 AAATAAAAAATAA
42855967 AAA
1 AAA
42855970 AATAAAAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 6 0.24
13 13 0.52
14 6 0.24
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (13 bp):
AAATAAAAAATAA
Found at i:42856262 original size:29 final size:29
Alignment explanation
Indices: 42856230--42856310 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 29
42856220 AATATATATG
* *
42856230 AATATGTATCTATATATATAAGTTAT-AAA
1 AATATATATGTATATATATAA-TTATGAAA
*
42856259 AATATATATGTACATATATATATTATGAAA
1 AATATATATGTATATATATA-ATTATGAAA
* *
42856289 ATGTATTTATGTATATATATAA
1 A-ATATATATGTATATATATAA
42856311 CAAAATTTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 21 0.49
30 6 0.14
31 16 0.37
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.43
Consensus pattern (29 bp):
AATATATATGTATATATATAATTATGAAA
Found at i:42860752 original size:29 final size:29
Alignment explanation
Indices: 42860711--42860788 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
42860701 AGCCTTTCAC
* *
42860711 ATATAACATATTCTGCCAC-TAAGGCTCAT
1 ATATAACAGATTCAGCCACAT-AGGCTCAT
* * *
42860740 ATATAATAGATTCAGGCACATAGGCTTAT
1 ATATAACAGATTCAGCCACATAGGCTCAT
*
42860769 ATATAACAGATTTAGCCACA
1 ATATAACAGATTCAGCCACA
42860789 AAAGCATCAC
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 39 0.98
30 1 0.03
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.29
Consensus pattern (29 bp):
ATATAACAGATTCAGCCACATAGGCTCAT
Found at i:42861066 original size:15 final size:15
Alignment explanation
Indices: 42861046--42861083 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
42861036 ACTTATGCAA
42861046 CTCATGCACAGACTC
1 CTCATGCACAGACTC
*
42861061 CTCATGTACAGACTC
1 CTCATGCACAGACTC
42861076 CATCATGC
1 C-TCATGC
42861084 TTTCAGGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.26, C:0.37, G:0.13, T:0.24
Consensus pattern (15 bp):
CTCATGCACAGACTC
Found at i:42865469 original size:12 final size:10
Alignment explanation
Indices: 42865439--42865474 Score: 54
Period size: 10 Copynumber: 3.4 Consensus size: 10
42865429 TAGACCCAGG
42865439 CAAACAAACC
1 CAAACAAACC
42865449 CAAACAAACC
1 CAAACAAACC
42865459 CAATTACAAACC
1 CAA--ACAAACC
42865471 CAAA
1 CAAA
42865475 TCAGATGGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 14 0.58
12 10 0.42
ACGTcount: A:0.58, C:0.36, G:0.00, T:0.06
Consensus pattern (10 bp):
CAAACAAACC
Found at i:42866556 original size:3 final size:3
Alignment explanation
Indices: 42866550--42866608 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
42866540 TAATGTTACC
42866550 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
42866598 ATT ATT ATT AT
1 ATT ATT ATT AT
42866609 ACTTCCATTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:42866741 original size:14 final size:15
Alignment explanation
Indices: 42866680--42866742 Score: 62
Period size: 14 Copynumber: 4.3 Consensus size: 15
42866670 ATATAAGTGC
42866680 TTATATATATA-TAT
1 TTATATATATATTAT
42866694 TTCATATA-AT-TTAT
1 TT-ATATATATATTAT
*
42866708 TTAATATATATATTGCT
1 TT-ATATATATATT-AT
42866725 TTATATATATATT-T
1 TTATATATATATTAT
42866739 TTAT
1 TTAT
42866743 TTACATATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
14 19 0.45
15 7 0.17
16 13 0.31
17 3 0.07
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.59
Consensus pattern (15 bp):
TTATATATATATTAT
Found at i:42866745 original size:18 final size:17
Alignment explanation
Indices: 42866697--42866752 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
42866687 TATATATTTC
42866697 ATATA-ATTTATTTAAT
1 ATATATATTTATTTAAT
**
42866713 ATATATATTGCTTTATAT
1 ATATATATTTATTTA-AT
*
42866731 ATATATTTTTATTTACAT
1 ATATATATTTATTTA-AT
42866749 ATAT
1 ATAT
42866753 CTATGTACTC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
16 5 0.16
17 7 0.22
18 20 0.62
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (17 bp):
ATATATATTTATTTAAT
Found at i:42867334 original size:109 final size:109
Alignment explanation
Indices: 42867053--42867433 Score: 620
Period size: 109 Copynumber: 3.5 Consensus size: 109
42867043 TTTTTAATTG
42867053 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCAATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCAATTTTTCT
* * * * ** *
42867118 CGTTCAACCAAATGACTTAATATCCTTTTAAATTTTTTTTAAAATA
66 CGTTCAACGAAATAACTAAATATCCTTTCAAA--AATTTCAAAATA
* * *
42867164 AGGCAATGTTTTGCGTTTGAAAACTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCTATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCAATTTTTCT
42867229 CGTTCAACGAAATAACTAAATATCCTTTCAAAAATTTCAAAATA
66 CGTTCAACGAAATAACTAAATATCCTTTCAAAAATTTCAAAATA
42867273 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCAATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCAATTTTTCT
42867338 CGTTCAACGAAATAACTAAATATCCTTTCAAAAATTTCAAAATA
66 CGTTCAACGAAATAACTAAATATCCTTTCAAAAATTTCAAAATA
* * *
42867382 AGGCAATGTTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAAGGCGCTGGGT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGT
42867434 TTCGATTTCT
Statistics
Matches: 254, Mismatches: 16, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
108 20 0.08
109 144 0.57
111 90 0.35
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (109 bp):
AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCAATTTTTCT
CGTTCAACGAAATAACTAAATATCCTTTCAAAAATTTCAAAATA
Found at i:42871454 original size:20 final size:20
Alignment explanation
Indices: 42871420--42871461 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
42871410 AACTATTTAA
** *
42871420 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
42871440 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
42871460 AT
1 AT
42871462 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:42876560 original size:20 final size:20
Alignment explanation
Indices: 42876526--42876567 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
42876516 AACTATTTAA
** *
42876526 ATAATATTATTTGAATATTT
1 ATAATATTAAATGAATAATT
42876546 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
42876566 AT
1 AT
42876568 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:42883369 original size:29 final size:30
Alignment explanation
Indices: 42883312--42883373 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 30
42883302 ATCTTAAAAT
*
42883312 TATATATGAATTTTGATTTAATATGTAATTA
1 TATATATGAATTTTAATTTAATA-GTAATTA
*
42883343 TATATATGAATTTTAATTTGATA-TAATTA
1 TATATATGAATTTTAATTTAATAGTAATTA
42883372 TA
1 TA
42883374 CACGTGAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 8 0.28
31 21 0.72
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (30 bp):
TATATATGAATTTTAATTTAATAGTAATTA
Found at i:42884091 original size:22 final size:21
Alignment explanation
Indices: 42884039--42884092 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
42884029 AAAAAACCAA
*
42884039 CTGTTTTTTTACTGTTATTTG
1 CTGTTTTTTTACTGCTATTTG
*
42884060 CTGTTCTTTTT-CTTGCTATTTT
1 CTGTT-TTTTTAC-TGCTATTTG
42884082 CTTGTTTTTTT
1 C-TGTTTTTTT
42884093 TTCCACTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 6 0.21
22 18 0.64
23 4 0.14
ACGTcount: A:0.06, C:0.13, G:0.11, T:0.70
Consensus pattern (21 bp):
CTGTTTTTTTACTGCTATTTG
Found at i:42888883 original size:17 final size:17
Alignment explanation
Indices: 42888857--42888898 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
42888847 GGCTTACACT
*
42888857 TTTGGTTTGTTCGCCAC
1 TTTGGCTTGTTCGCCAC
*
42888874 TTTGGCTTGTTCGTCAC
1 TTTGGCTTGTTCGCCAC
42888891 TTTGGCTT
1 TTTGGCTT
42888899 ACATTTTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.05, C:0.21, G:0.24, T:0.50
Consensus pattern (17 bp):
TTTGGCTTGTTCGCCAC
Found at i:42902296 original size:28 final size:28
Alignment explanation
Indices: 42902265--42902319 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
42902255 ACCAAATATT
*
42902265 TTGAGAAAATTTAAAGATGATTTATGAC
1 TTGAGAAAATTTAAAAATGATTTATGAC
42902293 TTGAGAAAATTTAAAAATGATTTATGA
1 TTGAGAAAATTTAAAAATGATTTATGA
42902320 ACTTACCGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.45, C:0.02, G:0.16, T:0.36
Consensus pattern (28 bp):
TTGAGAAAATTTAAAAATGATTTATGAC
Found at i:42906306 original size:23 final size:23
Alignment explanation
Indices: 42906279--42906369 Score: 137
Period size: 23 Copynumber: 4.0 Consensus size: 23
42906269 TGTGTATCCT
* * *
42906279 TTCATATTCAAGCCTCTTAACTT
1 TTCATATTCAAGTCTCTTCACTA
*
42906302 TTCATCTTCAAGTCTCTTCACTA
1 TTCATATTCAAGTCTCTTCACTA
*
42906325 TTCATATTCAAGTCTTTTCACTA
1 TTCATATTCAAGTCTCTTCACTA
42906348 TTCATATTCAAGTCTCTTCACT
1 TTCATATTCAAGTCTCTTCACT
42906370 CTTCTAACTT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.24, C:0.26, G:0.04, T:0.45
Consensus pattern (23 bp):
TTCATATTCAAGTCTCTTCACTA
Found at i:42909541 original size:23 final size:23
Alignment explanation
Indices: 42909513--42909604 Score: 121
Period size: 23 Copynumber: 4.0 Consensus size: 23
42909503 GTGTGTATCC
* *
42909513 TTTCATATTCAAGCCTCTTAACT
1 TTTCATATTCAAGTCTCTTCACT
*
42909536 TTTCATCTTCAAGTCTCTTCACT
1 TTTCATATTCAAGTCTCTTCACT
* *
42909559 ATTCATATTCAAGTCTTTTCACT
1 TTTCATATTCAAGTCTCTTCACT
* *
42909582 CTTCATACTCAAGTCTCTTCACT
1 TTTCATATTCAAGTCTCTTCACT
42909605 CTTCTAACTT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.23, C:0.28, G:0.04, T:0.45
Consensus pattern (23 bp):
TTTCATATTCAAGTCTCTTCACT
Found at i:42913935 original size:20 final size:20
Alignment explanation
Indices: 42913910--42913951 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
42913900 ATTATTTAGA
42913910 TTTTATTTCAAATTATATCT
1 TTTTATTTCAAATTATATCT
42913930 TTTTATTTCAAATTATATCT
1 TTTTATTTCAAATTATATCT
42913950 TT
1 TT
42913952 ACTTATCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTATTTCAAATTATATCT
Found at i:42924973 original size:40 final size:40
Alignment explanation
Indices: 42924908--42925115 Score: 202
Period size: 40 Copynumber: 5.2 Consensus size: 40
42924898 GGGCATGAAA
* * * ** *
42924908 GTGCATTCAGGCGTACCGAATTACAAACATCGGCACATAT
1 GTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGTAT
* * * *
42924948 GTGCAATCAGGGGTACTGAAGTACAAATAGGGGAACATAT
1 GTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGTAT
* ** * * * *
42924988 GTGCAATTAGGACTACCAAAGTAAAAATAGGGGCATGTAT
1 GTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGTAT
* ** *
42925028 GTGTAATCAGGGGTACTAAAGTATAAACAGGGGCACGTAT
1 GTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGTAT
* *
42925068 GTGCAATTAGGGGTACCGAAGTACAAA-AGGGACACGTAT
1 GTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGTAT
42925107 GTGCAATCA
1 GTGCAATCA
42925116 TACAATAATT
Statistics
Matches: 136, Mismatches: 32, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
39 19 0.14
40 117 0.86
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.21
Consensus pattern (40 bp):
GTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGTAT
Found at i:42924998 original size:20 final size:20
Alignment explanation
Indices: 42924942--42924998 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
42924932 AAACATCGGC
* *
42924942 ACATATGTGCAATCAGGGGT
1 ACATATGTGCAATTAGGGGA
* * *
42924962 AC-TGAAGTACAAATAGGGGA
1 ACAT-ATGTGCAATTAGGGGA
42924982 ACATATGTGCAATTAGG
1 ACATATGTGCAATTAGG
42924999 ACTACCAAAG
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
19 1 0.04
20 25 0.93
21 1 0.04
ACGTcount: A:0.37, C:0.12, G:0.28, T:0.23
Consensus pattern (20 bp):
ACATATGTGCAATTAGGGGA
Found at i:42925050 original size:80 final size:79
Alignment explanation
Indices: 42924945--42925115 Score: 225
Period size: 80 Copynumber: 2.2 Consensus size: 79
42924935 CATCGGCACA
* *
42924945 TATGTGCAATCAGGGGTACTGAAGTACAAATAGGGGAACATATGTGCAATTAGGACTACCAAAGT
1 TATGTGCAATCAGGGGTACTAAAGTACAAACAGGGGAACATATGTGCAATTAGGACTACCAAAGT
* *
42925010 AAAAATAGGGGCATG
66 AAAAA-AGGGACACG
* * * * ** *
42925025 TATGTGTAATCAGGGGTACTAAAGTATAAACAGGGGCACGTATGTGCAATTAGGGGTACCGAAGT
1 TATGTGCAATCAGGGGTACTAAAGTACAAACAGGGGAACATATGTGCAATTAGGACTACCAAAGT
*
42925090 ACAAAAGGGACACG
66 AAAAAAGGGACACG
42925104 TATGTGCAATCA
1 TATGTGCAATCA
42925116 TACAATAATT
Statistics
Matches: 78, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
79 18 0.23
80 60 0.77
ACGTcount: A:0.37, C:0.13, G:0.28, T:0.22
Consensus pattern (79 bp):
TATGTGCAATCAGGGGTACTAAAGTACAAACAGGGGAACATATGTGCAATTAGGACTACCAAAGT
AAAAAAGGGACACG
Found at i:42932106 original size:40 final size:39
Alignment explanation
Indices: 42932062--42932266 Score: 169
Period size: 40 Copynumber: 5.1 Consensus size: 39
42932052 ATGTTTGTAT
* *
42932062 AATCAAGAGTACCGAAGTACAAACATGGGAACATATGTGC
1 AATCAAGGGTACCGAAGTACAAACA-GGGAACGTATGTGC
* * * * *
42932102 AATC-AGTGGTACTGAAGTATAAACAGGGGCACGCATATGC
1 AATCAAG-GGTACCGAAGTACAAACA-GGGAACGTATGTGC
* * * * * *
42932142 AATCAGGGGCACTGAAGTAGAAACAGGAGCACGTGTGTGC
1 AATCAAGGGTACCGAAGTACAAACAGG-GAACGTATGTGC
* *
42932182 AATCAAGGGAACCGAAGTACAAACAGGGACACGTATGTAC
1 AATCAAGGGTACCGAAGTACAAACAGGGA-ACGTATGTGC
* * * * *
42932222 AACCAGGGGTATCGAAGTATAAATAGGGACACGTATGTGC
1 AATCAAGGGTACCGAAGTACAAACAGGGA-ACGTATGTGC
42932262 AATCA
1 AATCA
42932267 TACAATAATT
Statistics
Matches: 132, Mismatches: 29, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
39 5 0.04
40 126 0.95
41 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.17
Consensus pattern (39 bp):
AATCAAGGGTACCGAAGTACAAACAGGGAACGTATGTGC
Found at i:42932159 original size:80 final size:78
Alignment explanation
Indices: 42932074--42932266 Score: 190
Period size: 80 Copynumber: 2.4 Consensus size: 78
42932064 TCAAGAGTAC
* * * * *
42932074 CGAAGTACAAACATGGGAACATATGTGCAATCAGTGGTACTGAAGTATAAACAGGGGCACGCATA
1 CGAAGTACAAACA-GGGAACGTATGTGCAATCAG-GGAACCGAAGTACAAACAGGGACACGCATA
* *
42932139 TGCAATCAGGGGCA-
64 TACAACCAGGGGCAT
* * * *
42932153 CTGAAGTAGAAACAGGAGCACGTGTGTGCAATCAAGGGAACCGAAGTACAAACAGGGACACGTAT
1 C-GAAGTACAAACAGG-GAACGTATGTGCAATC-AGGGAACCGAAGTACAAACAGGGACACGCAT
* *
42932218 GTACAACCAGGGGTAT
63 ATACAACCAGGGGCAT
* *
42932234 CGAAGTATAAATAGGGACACGTATGTGCAATCA
1 CGAAGTACAAACAGGGA-ACGTATGTGCAATCA
42932267 TACAATAATT
Statistics
Matches: 92, Mismatches: 17, Indels: 10
0.77 0.14 0.08
Matches are distributed among these distances:
79 5 0.05
80 84 0.91
81 3 0.03
ACGTcount: A:0.37, C:0.18, G:0.28, T:0.17
Consensus pattern (78 bp):
CGAAGTACAAACAGGGAACGTATGTGCAATCAGGGAACCGAAGTACAAACAGGGACACGCATATA
CAACCAGGGGCAT
Found at i:42932168 original size:20 final size:20
Alignment explanation
Indices: 42932112--42932173 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
42932102 AATCAGTGGT
*
42932112 ACTGAAGTATAAACAGGGGC
1 ACTGAAGTAGAAACAGGGGC
* *
42932132 AC-GCA-TATGCAATCAGGGGC
1 ACTGAAGTA-G-AAACAGGGGC
*
42932152 ACTGAAGTAGAAACAGGAGC
1 ACTGAAGTAGAAACAGGGGC
42932172 AC
1 AC
42932174 GTGTGTGCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
18 2 0.06
19 2 0.06
20 23 0.72
21 3 0.09
22 2 0.06
ACGTcount: A:0.39, C:0.19, G:0.29, T:0.13
Consensus pattern (20 bp):
ACTGAAGTAGAAACAGGGGC
Found at i:42934312 original size:18 final size:18
Alignment explanation
Indices: 42934274--42934317 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
42934264 TTTTTATTTT
42934274 TTAAATATTAATATAATTA
1 TTAAAT-TTAATATAATTA
*
42934293 TTTAATTTAATATTAA-TA
1 TTAAATTTAATA-TAATTA
42934311 TTAAATT
1 TTAAATT
42934318 ATTTTTAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTAAATTTAATATAATTA
Found at i:42936785 original size:33 final size:35
Alignment explanation
Indices: 42936748--42936818 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 35
42936738 ACTACTTTTT
* *
42936748 TGTCACTG-TACTGAGATGGGATAAGGCCCAA-AC
1 TGTCACTGATACTGAAAAGGGATAAGGCCCAAGAC
* *
42936781 TGTCACTGATACTGAAAAGGGCTTAGGCCCAAGAC
1 TGTCACTGATACTGAAAAGGGATAAGGCCCAAGAC
42936816 TGT
1 TGT
42936819 TCAACTGTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 8 0.25
34 19 0.59
35 5 0.16
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.23
Consensus pattern (35 bp):
TGTCACTGATACTGAAAAGGGATAAGGCCCAAGAC
Found at i:42940399 original size:14 final size:15
Alignment explanation
Indices: 42940382--42940410 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42940372 AATTTTAATT
42940382 AAATAA-ATTATTAA
1 AAATAAGATTATTAA
42940396 AAATAAGATTATTAA
1 AAATAAGATTATTAA
42940411 CATCAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
AAATAAGATTATTAA
Found at i:42946301 original size:19 final size:18
Alignment explanation
Indices: 42946261--42946303 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
42946251 TTTTTGTTAC
**
42946261 ATATCTTATTTTTTTATTT
1 ATAT-TTATTTTTTTAAAT
42946280 ATATTTATATTTTTTAAAT
1 ATATTTAT-TTTTTTAAAT
42946299 ATATT
1 ATATT
42946304 CTAAGATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
ATATTTATTTTTTTAAAT
Found at i:42948625 original size:3 final size:3
Alignment explanation
Indices: 42948617--42948654 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
42948607 CATGGACAAA
42948617 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
42948655 CTTGTACATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:42949891 original size:24 final size:23
Alignment explanation
Indices: 42949824--42949891 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 23
42949814 TTTTAAATAT
* *
42949824 ATATAAAATATTGATAAATATCAA
1 ATATAAAATA-TAATAAATTTCAA
42949848 ATAATAAAAT-TAAATAAATTTCAA
1 AT-ATAAAATAT-AATAAATTTCAA
*
42949872 ATATAAAATAGTAATCAATT
1 ATATAAAATA-TAATAAATT
42949892 ATATAAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
23 8 0.22
24 21 0.57
25 8 0.22
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.34
Consensus pattern (23 bp):
ATATAAAATATAATAAATTTCAA
Found at i:42955176 original size:19 final size:19
Alignment explanation
Indices: 42955152--42955191 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
42955142 TTTACTCACA
42955152 AACTATTCAAATTCAACTC
1 AACTATTCAAATTCAACTC
*
42955171 AACTATTCGAATTCAACTC
1 AACTATTCAAATTCAACTC
42955190 AA
1 AA
42955192 ATCATTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.42, C:0.25, G:0.03, T:0.30
Consensus pattern (19 bp):
AACTATTCAAATTCAACTC
Found at i:42976759 original size:6 final size:6
Alignment explanation
Indices: 42976748--42976822 Score: 77
Period size: 6 Copynumber: 12.7 Consensus size: 6
42976738 CCAATCTTTC
* *
42976748 TTTTTA TTTTTA TTTTTA TTTTTA TTTATTA -TTTT- TCTTTC TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT-TTA TTTTTA TTTTTA TTTTTA
42976795 TTTATTA TTTATTA -TTTTA -TTTTA TTTT
1 TTT-TTA TTT-TTA TTTTTA TTTTTA TTTT
42976823 AGTTAAATAT
Statistics
Matches: 61, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
5 13 0.21
6 35 0.57
7 13 0.21
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:42976764 original size:7 final size:7
Alignment explanation
Indices: 42976748--42976812 Score: 55
Period size: 7 Copynumber: 9.4 Consensus size: 7
42976738 CCAATCTTTC
42976748 TTTTTA-
1 TTTTTAT
42976754 TTTTTA-
1 TTTTTAT
42976760 TTTTTA-
1 TTTTTAT
42976766 TTTTTAT
1 TTTTTAT
*
42976773 TTATTAT
1 TTTTTAT
*
42976780 TTTTCTTT
1 TTTT-TAT
42976788 CTTTTTAT
1 -TTTTTAT
*
42976796 TTATTAT
1 TTTTTAT
*
42976803 TTATTAT
1 TTTTTAT
42976810 TTT
1 TTT
42976813 ATTTTATTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
6 18 0.36
7 24 0.48
8 4 0.08
9 4 0.08
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTAT
Found at i:42976777 original size:10 final size:10
Alignment explanation
Indices: 42976756--42976822 Score: 61
Period size: 10 Copynumber: 6.8 Consensus size: 10
42976746 TCTTTTTATT
42976756 TTTATTTTTA
1 TTTATTTTTA
42976766 TTT-TTATTTA
1 TTTATT-TTTA
*
42976776 -TTATTTTTC
1 TTTATTTTTA
*
42976785 TTTCTTTTTA
1 TTTATTTTTA
42976795 TTTATTATTTA
1 TTTATT-TTTA
42976806 -TTA-TTTTA
1 TTTATTTTTA
42976814 TTTTATTTT
1 -TTTATTTT
42976823 AGTTAAATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
8 4 0.09
9 8 0.17
10 27 0.59
11 7 0.15
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:42976956 original size:20 final size:20
Alignment explanation
Indices: 42976931--42976972 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
42976921 ATCCATGGTA
* *
42976931 CCAAACAGTTCTATTCCAGC
1 CCAAACAATCCTATTCCAGC
42976951 CCAAACAATCCTATTCCAGC
1 CCAAACAATCCTATTCCAGC
42976971 CC
1 CC
42976973 TAGAATCCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.40, G:0.07, T:0.21
Consensus pattern (20 bp):
CCAAACAATCCTATTCCAGC
Found at i:42977960 original size:118 final size:118
Alignment explanation
Indices: 42977749--42977978 Score: 361
Period size: 118 Copynumber: 1.9 Consensus size: 118
42977739 TGTTTCCATT
* * *
42977749 GTTATGAGTACAGCTTAGATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATTC
1 GTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGCAGGGTGCTTGGGTTGTCATTC
*
42977814 TACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGAG
66 TACTTCGCGTCAAAAGGTTGTGTAACGTGACAAGTAAAACTCCGCTAGCCGAG
* *
42977867 GTTATGAGTATAGCTCAAATCGTGACTGACTGAGTAACTGGGGCAGGGTGCTTGGGTTGTCATTC
1 GTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGCAGGGTGCTTGGGTTGTCATTC
* ****
42977932 TACTTCGCGTCAAAAGTTTGTGTAACGTGTTGGGTAAAACTCCGCTA
66 TACTTCGCGTCAAAAGGTTGTGTAACGTGACAAGTAAAACTCCGCTA
42977979 ACCGGAAATA
Statistics
Matches: 101, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
118 101 1.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (118 bp):
GTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGCAGGGTGCTTGGGTTGTCATTC
TACTTCGCGTCAAAAGGTTGTGTAACGTGACAAGTAAAACTCCGCTAGCCGAG
Found at i:42982181 original size:45 final size:44
Alignment explanation
Indices: 42981981--42982193 Score: 151
Period size: 45 Copynumber: 4.8 Consensus size: 44
42981971 ACCAGGAGTA
* ** * * *
42981981 AGTAAGACCATAGCTGAAACATACTATGCCATAATGATGATAATA-
1 AGTAAGACCATAGCTGAAAGACGCTATGACATCATGAT-A-AAAAG
* * *
42982026 AGTAAGACCATAGCTGAAAGATGCTACGATATCATGATAAAAATG
1 AGTAAGACCATAGCTGAAAGACGCTATGACATCATGATAAAAA-G
* * * * ***
42982071 AGTAAGACAATAGTTGAAAGACGCTATGGCATAATGATAAGGGTG
1 AGTAAGACCATAGCTGAAAGACGCTATGACATCATGATAA-AAAG
* * * *
42982116 AGTAAGACTATGGCTAAAAGACGCTATGGCATCAT-AGTAAATAAG
1 AGTAAGACCATAGCTGAAAGACGCTATGACATCATGA-TAAA-AAG
* * *
42982161 ACTAAGACCATAGTTGAAAGACACTATGACATC
1 AGTAAGACCATAGCTGAAAGACGCTATGACATC
42982194 CTTTGATAGT
Statistics
Matches: 131, Mismatches: 32, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
43 3 0.02
44 2 0.02
45 126 0.96
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.23
Consensus pattern (44 bp):
AGTAAGACCATAGCTGAAAGACGCTATGACATCATGATAAAAAG
Found at i:42983162 original size:17 final size:17
Alignment explanation
Indices: 42983135--42983178 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
42983125 TCTGATACCA
* *
42983135 ATGGCGGATACCTATCT
1 ATGGCGAATACCTATCC
*
42983152 ATGGTGAATACCTATCC
1 ATGGCGAATACCTATCC
42983169 ATGGCGAATA
1 ATGGCGAATA
42983179 GTTTTTCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (17 bp):
ATGGCGAATACCTATCC
Found at i:42991216 original size:129 final size:126
Alignment explanation
Indices: 42990964--42991292 Score: 385
Period size: 130 Copynumber: 2.6 Consensus size: 126
42990954 TTTTAAAATG
* ** * * * * *
42990964 ATATTCGATTGTTTGGTCAAACGGTAAATCGAAACCCAGCACG-TAGGGCACGTTTTCTCGGATT
1 ATATTCGATTATTTGAACAAACGGGAAATTGAAACCCAGCACGATAGGGCACGATTTCCCGAATT
* * *
42991028 CCCAAACATTGAACATTGCCTTGTTTTAGAATTTAGAAAACATGAGTGAAATTCTAAAGGA
66 TCCAAACATTGAACATTACCTTGTTTTAGAATTTAGAAAACATGAGTGAAATTCCAAAGGA
*
42991089 ATATTCGATTATTTGAACAAACGGGAAATTGTAACCCAGCACGATAGGGCACGATTTCCCGAATT
1 ATATTCGATTATTTGAACAAACGGGAAATTGAAACCCAGCACGATAGGGCACGATTTCCCGAATT
* ** *
42991154 TCCAAAC-TTCGAACGTTACCTTCGTTTTAAAGAATTTTTAAAACATGTGTGAAATTCCAAAGGA
66 TCCAAACATT-GAACATTACCTT-GTTTT--AGAATTTAGAAAACATGAGTGAAATTCCAAAGGA
* * * * *
42991218 ATATTCGATCATTTTGAACAAACGAGAAATTGCAACCCAGTACGACAGGGCACGA-TTCCTCGAA
1 ATATTCGATTA-TTTGAACAAACGGGAAATTGAAACCCAGCACGATAGGGCACGATTTCC-CGAA
*
42991282 TTTCTAAACAT
64 TTTCCAAACAT
42991293 CAAACATCGT
Statistics
Matches: 174, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
125 39 0.22
126 34 0.20
127 5 0.03
129 44 0.25
130 51 0.29
131 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (126 bp):
ATATTCGATTATTTGAACAAACGGGAAATTGAAACCCAGCACGATAGGGCACGATTTCCCGAATT
TCCAAACATTGAACATTACCTTGTTTTAGAATTTAGAAAACATGAGTGAAATTCCAAAGGA
Found at i:42991742 original size:24 final size:20
Alignment explanation
Indices: 42991699--42991747 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 20
42991689 TTAAAATCAT
42991699 TAATATAAAAGATAACAAAA
1 TAATATAAAAGATAACAAAA
42991719 TAATATAAATAGAATAACTTAAAA
1 TAATATAAA-AG-ATAAC--AAAA
42991743 TAATA
1 TAATA
42991748 ATTAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.36
21 2 0.08
22 5 0.20
24 9 0.36
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (20 bp):
TAATATAAAAGATAACAAAA
Found at i:42993838 original size:35 final size:33
Alignment explanation
Indices: 42993786--42993854 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 33
42993776 TTTTAACCTT
*
42993786 AAAAAAAATTTAGAACACCCAAAAATTTAAAGC
1 AAAAAAAATTTAAAACACCCAAAAATTTAAAGC
*
42993819 AAAAAAAACTTTTAAAACACTCAAAAATTTAAAGC
1 AAAAAAAA--TTTAAAACACCCAAAAATTTAAAGC
42993854 A
1 A
42993855 TCACCCTCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 8 0.25
35 24 0.75
ACGTcount: A:0.61, C:0.14, G:0.04, T:0.20
Consensus pattern (33 bp):
AAAAAAAATTTAAAACACCCAAAAATTTAAAGC
Found at i:42998395 original size:42 final size:43
Alignment explanation
Indices: 42998297--42998402 Score: 121
Period size: 43 Copynumber: 2.5 Consensus size: 43
42998287 AAATTTTAGC
* *
42998297 CTGTTACCCTACTGCTTAGGGAGTTAAGGCGTGTATCTTTAAT
1 CTGTTACCCTATTGCTTAGGGAGATAAGGCGTGTATCTTTAAT
* *
42998340 CTGCT-CCACTATTGCTTAGGGAGATAAGATC-TGTA-CTTTATAT
1 CTGTTACC-CTATTGCTTAGGGAGATAAG-GCGTGTATCTTTA-AT
42998383 -TGTTACCCTATTGCTTAGGG
1 CTGTTACCCTATTGCTTAGGG
42998403 GGTTAAAGCC
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
42 23 0.43
43 30 0.56
44 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.38
Consensus pattern (43 bp):
CTGTTACCCTATTGCTTAGGGAGATAAGGCGTGTATCTTTAAT
Found at i:42998496 original size:85 final size:85
Alignment explanation
Indices: 42997688--42998493 Score: 1005
Period size: 85 Copynumber: 9.5 Consensus size: 85
42997678 AAGCTAAGAC
*
42997688 CTGT-AATTTTAGCCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCTTCGACCTGCTCCACC
1 CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTCCACC
*
42997752 ACTGCTCGGAGAG-CCAGGAT
66 ACTGCTCGGCGAGCCCA-GAT
* * * *** * * * * *
42997772 CTGTAAATTTTAGCCTGCT-CCATTCTTGCTTAGTAAAGATAAGGCTAGTCTTCAACTTGCTCCG
1 CTGTAAATTTTAGCCTGTTACCCTAC-TGCTTAG-GGGGTTAAGGCGAGTCTTCGACCTGCTCCA
* *
42997836 CCACTGTTCGGCGAGCCTAGAT
64 CCACTGCTCGGCGAGCCCAGAT
* *
42997858 CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCAAATCTTCGACCTGCTCCACC
1 CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTCCACC
*
42997923 ACTACTCGGCGAGCCCAGAT
66 ACTGCTCGGCGAGCCCAGAT
* *
42997943 CTGTAAATTTTAGCCTGTTACCCTACTGTTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTCTACC
1 CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTCCACC
* *
42998008 ACTACTCGGCGAGCCCAAAT
66 ACTGCTCGGCGAGCCCAGAT
* * * *
42998028 CTGTAAATTTTAGCCTGTTACCCTATTGCTTAGGGGGTTAAGGCAAGTCTTCGATCTACTCCACC
1 CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTCCACC
*
42998093 ACTGCTCCGCGAGCCCAGAT
66 ACTGCTCGGCGAGCCCAGAT
* * *
42998113 CTGTAAATTTTAGCCTATTACCCTACTACTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTCCGCC
1 CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTCCACC
*
42998178 ACTACTCGGCGAGCCCAGAT
66 ACTGCTCGGCGAGCCCAGAT
* ** *
42998198 CTGTAAATTTTAGCCTGTTACCTTACTATTTAGGGGGTTAAGGCAAGTCTTCGACCTGCTCCACC
1 CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTCCACC
*
42998263 ACTACTCGGCGAGCCCAGAT
66 ACTGCTCGGCGAGCCCAGAT
* * ** *
42998283 CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGAGTTAAGGCGTGTATCTTTAATCTGCTCCA
1 CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAG--TCTTCGACCTGCTCCA
* * * ***
42998348 CTATTGCTTAGG-GAGATAAGAT
64 CCACTGC-TCGGCGAGCCCAGAT
* * * * **
42998370 CTGT-ACTTTATA--TTGTTACCCTATTGCTTAGGGGGTTAAAGCCTGTCTTCGACCTGCTCCAC
1 CTGTAAATTT-TAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTCCAC
*
42998432 CACTGCTCGACGAGCCCAGAT
65 CACTGCTCGGCGAGCCCAGAT
*
42998453 CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGAGTTAA
1 CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAA
42998494 AGCTTGCTGA
Statistics
Matches: 615, Mismatches: 94, Indels: 25
0.84 0.13 0.03
Matches are distributed among these distances:
82 2 0.00
83 31 0.05
84 12 0.02
85 465 0.76
86 66 0.11
87 36 0.06
88 3 0.00
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (85 bp):
CTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTCCACC
ACTGCTCGGCGAGCCCAGAT
Found at i:43006294 original size:21 final size:21
Alignment explanation
Indices: 43006268--43006312 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
43006258 GCTGGCTCAT
*
43006268 CATGTTGTTCTGTGACTCCAG
1 CATGTTGTTCTGGGACTCCAG
*
43006289 CATGTTTTTCTGGGACTCCAG
1 CATGTTGTTCTGGGACTCCAG
43006310 CAT
1 CAT
43006313 TTGATCCCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (21 bp):
CATGTTGTTCTGGGACTCCAG
Found at i:43011208 original size:35 final size:35
Alignment explanation
Indices: 43011162--43011232 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
43011152 TTTAACCTTA
*
43011162 AAAAAAAACTTTTAGAACACCCAAAAATTTAAAGC
1 AAAAAAAACTTTTAAAACACCCAAAAATTTAAAGC
*
43011197 AAAAAAAACTTTTAAAACACTCAAAAATTTAAAGC
1 AAAAAAAACTTTTAAAACACCCAAAAATTTAAAGC
43011232 A
1 A
43011233 TCACCCTCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.59, C:0.15, G:0.04, T:0.21
Consensus pattern (35 bp):
AAAAAAAACTTTTAAAACACCCAAAAATTTAAAGC
Found at i:43012215 original size:3 final size:3
Alignment explanation
Indices: 43012197--43012336 Score: 94
Period size: 3 Copynumber: 46.7 Consensus size: 3
43012187 TGACGATAGC
* * *
43012197 AAT AGT AAT AAT -AT AAT AAT AA- AGT AGAA AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
* * * * * *
43012241 AAT ACGTT AAT GAG AAT AAT AAT AGT -AT ATT AAT AAT AAC AAT AAT
1 AAT A--AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
43012287 AGA- AAGT AAT GAT AA- AAT AAT AAT AAAT AAT AAT AAT AAT AAT AA-
1 A-AT AA-T AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT
43012332 AAT AA
1 AAT AA
43012337 AGAATAGTGC
Statistics
Matches: 105, Mismatches: 20, Indels: 24
0.70 0.13 0.16
Matches are distributed among these distances:
2 9 0.09
3 87 0.83
4 7 0.07
5 2 0.02
ACGTcount: A:0.62, C:0.01, G:0.07, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:43012279 original size:43 final size:41
Alignment explanation
Indices: 43012225--43012330 Score: 115
Period size: 43 Copynumber: 2.5 Consensus size: 41
43012215 ATAAAGTAGA
* *
43012225 AAATAATAATAATAATAATACG-TTAATGAGAATAATAATAGT
1 AAATAATAATAATAATAATA-GAGTAATGAGAA-AATAATAAT
* * *
43012267 ATATTAATAATAACAATAATAGAAAGTAATGATAAAATAATAAT
1 A-AATAATAATAATAATAATAG--AGTAATGAGAAAATAATAAT
43012311 AAATAATAATAATAATAATA
1 AAATAATAATAATAATAATA
43012331 AAATAAAGAA
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
42 2 0.04
43 34 0.64
44 9 0.17
45 8 0.15
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (41 bp):
AAATAATAATAATAATAATAGAGTAATGAGAAAATAATAAT
Found at i:43012320 original size:24 final size:24
Alignment explanation
Indices: 43012293--43012342 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
43012283 TAATAGAAAG
* *
43012293 TAATGATAA-AATAATAATAAATAA
1 TAATAATAATAATAA-AATAAAGAA
43012317 TAATAATAATAATAAAATAAAGAA
1 TAATAATAATAATAAAATAAAGAA
43012341 TA
1 TA
43012343 GTGCCAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (24 bp):
TAATAATAATAATAAAATAAAGAA
Found at i:43023393 original size:24 final size:21
Alignment explanation
Indices: 43023366--43023412 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
43023356 CCCTTATGTT
43023366 CTTTCTCTATACTATTTCTCATCA
1 CTTTCTCT-TA-T-TTTCTCATCA
*
43023390 CTTTCTCTTATTTTCTCTTCA
1 CTTTCTCTTATTTTCTCATCA
43023411 CT
1 CT
43023413 AACATATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 11 0.50
22 1 0.05
23 2 0.09
24 8 0.36
ACGTcount: A:0.15, C:0.30, G:0.00, T:0.55
Consensus pattern (21 bp):
CTTTCTCTTATTTTCTCATCA
Found at i:43023841 original size:8 final size:8
Alignment explanation
Indices: 43023828--43023852 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
43023818 ATATAGACTA
43023828 AATAAAAT
1 AATAAAAT
43023836 AATAAAAT
1 AATAAAAT
43023844 AATAAAAT
1 AATAAAAT
43023852 A
1 A
43023853 TCTTATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:43023872 original size:29 final size:30
Alignment explanation
Indices: 43023831--43023904 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 30
43023821 TAGACTAAAT
*
43023831 AAAATAATAAAATAATAAAAT-ATCTTATTA
1 AAAATAATAAAATAA-AAAATAATCTAATTA
* *
43023861 AAAAT-ATTAAATAAATAATAATCTAATTA
1 AAAATAATAAAATAAAAAATAATCTAATTA
43023890 AATAACT-ATAAAATA
1 AA-AA-TAATAAAATA
43023905 TCACCAACAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 4 0.11
29 18 0.49
30 7 0.19
31 8 0.22
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (30 bp):
AAAATAATAAAATAAAAAATAATCTAATTA
Found at i:43023893 original size:16 final size:15
Alignment explanation
Indices: 43023849--43023894 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
43023839 AAAATAATAA
*
43023849 AATATCTTATTAAA-
1 AATATCTAATTAAAT
*
43023863 AATAT-TAAATAAAT
1 AATATCTAATTAAAT
43023877 AATAATCTAATTAAAT
1 AAT-ATCTAATTAAAT
43023893 AA
1 AA
43023895 CTATAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 6 0.23
14 8 0.31
15 2 0.08
16 10 0.38
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (15 bp):
AATATCTAATTAAAT
Found at i:43025242 original size:14 final size:15
Alignment explanation
Indices: 43025216--43025244 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
43025206 CAAAGGTGAT
43025216 TCTTTTCATTTTTTA
1 TCTTTTCATTTTTTA
43025231 TCTTTT-ATTTTTTA
1 TCTTTTCATTTTTTA
43025245 GAAAAAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (15 bp):
TCTTTTCATTTTTTA
Found at i:43052648 original size:96 final size:92
Alignment explanation
Indices: 43052423--43052932 Score: 335
Period size: 89 Copynumber: 5.5 Consensus size: 92
43052413 GTCACCATAG
* * *
43052423 CAAATCTTATCTTCCTGAAGTTGCAGTGGAGTAGATTGAAGTTACCATGGCGAATCTTATCTCCC
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG----CATAGCGAATCTTATCTCCC
* * *
43052488 TGAAGTTGCAGTGGAAAAGGTTAAAGCTACA
62 TAAAGTTGCAGTAGAAAAGATTAAAGCTACA
* * *
43052519 -AAA-CTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAG-ATAGCGAATCTTATTTTCCTAAA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCATAGCGAATCTTATCTCCCTAAA
*
43052581 GTTGCAGTAGAACAGATTAAAGCTACAAGTTA
66 GTTGCAGTAGAAAAGATTAAAGCTAC-----A
* * * *
43052613 CAAATCTAATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG--T-GACAAATCTTATAC-CTCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCATAG-CGAATCTTAT-CTCCCTA
** * **** *
43052674 AAGTTATAGTGGGTCGGATTAAATCTACCA
64 AAGTTGCAGTAGAAAAGATTAAAGCTA-CA
* * * * * * * *
43052704 TAACGAGTCTTATTTCCTTGAAGTTGCAGTGGAACTGATTAAAGCTACAAGTCACAAATCTTATC
1 CAA--A-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGC-A-TAG---CGAATCTTATC
* * ** *
43052769 TCCCTGAAGTTGCAGTGGAGTAGATTGAAGCT--A
58 TCCCTAAAGTTGCAGTAGAAAAGATTAAAGCTACA
*
43052802 CAAATCTTATCCCCCTGAAGTTGCAGTGGAGCAGATTGAAGC-TA-C-AGATCTTATCTCCCTAA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCATAGCGA-ATCTTATCTCCCTAA
* * * * *
43052864 AGTTGCAGTGGAGAAGATTGAAGAT-GA
65 AGTTGCAGTAGAAAAGATTAAAGCTACA
* * * *
43052891 CAAATCTTATCTCTCTAAAGTTGCAATGAAGCAGATTGAAGC
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGC
43052933 GACAAATCCT
Statistics
Matches: 334, Mismatches: 57, Indels: 53
0.75 0.13 0.12
Matches are distributed among these distances:
87 1 0.00
88 38 0.11
89 80 0.24
91 3 0.01
92 1 0.00
93 1 0.00
94 67 0.20
95 71 0.21
96 35 0.10
98 3 0.01
99 1 0.00
100 1 0.00
101 32 0.10
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.29
Consensus pattern (92 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCATAGCGAATCTTATCTCCCTAAA
GTTGCAGTAGAAAAGATTAAAGCTACA
Found at i:43052678 original size:44 final size:44
Alignment explanation
Indices: 43052423--43052963 Score: 281
Period size: 44 Copynumber: 11.6 Consensus size: 44
43052413 GTCACCATAG
* * *
43052423 CAAATCTTATCTTCCTGAAGTTGCAGTGGAGTAGATTGAAGTTACCATGG
1 CAAATCTTATCCT-CTGAAGTTGCAGTGGAGCAGATTGAAG----C-TGA
* * ** * *
43052473 CGAATCTTATCTCCCTGAAGTTGCAGTGGAAAAGGTTAAAGCT-A
1 CAAATCTTATC-CTCTGAAGTTGCAGTGGAGCAGATTGAAGCTGA
* * * *
43052517 CAAAACTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGAT-A
1 CAAATCTTATC-CTCTGAAGTTGCAGTGGAGCAGATTGAAGCTGA
* ** * * * *
43052561 GCGAATCTTATTTTCCTAAAGTTGCAGTAGAACAGATTAAAGCTACAAGTTA
1 -CAAATCTTATCCT-CTGAAGTTGCAGTGGAGCAGATTGAAGCT----G--A
* * *
43052613 CAAATCTAATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TGA
1 CAAATCTTATC-CTCTGAAGTTGCAGTGGAGCAGATTGAAGCTGA
* ** * * *
43052657 CAAATCTTATACCTCTAAAGTTATAGTGG-GTCGGATTAAATCT-A
1 CAAATCTTAT-CCTCTGAAGTTGCAGTGGAG-CAGATTGAAGCTGA
* * *
43052701 CCATAACGAGTCTTATTTCCT-TGAAGTTGCAGTGGAACTGATTAAAGCTACAAGTCA
1 -C--AA--A-TCTTA--TCCTCTGAAGTTGCAGTGGAGCAGATTGAAGCT----G--A
* *
43052758 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCT-A
1 CAAATCTTATC-CTCTGAAGTTGCAGTGGAGCAGATTGAAGCTGA
*
43052802 CAAATCTTATCCCCCTGAAGTTGCAGTGGAGCAGATTGAAGCT-A
1 CAAATCTTAT-CCTCTGAAGTTGCAGTGGAGCAGATTGAAGCTGA
* * * * *
43052846 CAGATCTTATCTCCCTAAAGTTGCAGTGGAGAAGATTGAAGATGA
1 CAAATCTTATC-CTCTGAAGTTGCAGTGGAGCAGATTGAAGCTGA
* * *
43052891 CAAATCTTATCTCTCTAAAGTTGCAATGAAGCAGATTGAAGC-GA
1 CAAATCTTATC-CTCTGAAGTTGCAGTGGAGCAGATTGAAGCTGA
*
43052935 CAAATCCTATACCTCTGAAGTTGCAGTGG
1 CAAATCTTAT-CCTCTGAAGTTGCAGTGG
43052964 GTAAGAATGA
Statistics
Matches: 387, Mismatches: 68, Indels: 78
0.73 0.13 0.15
Matches are distributed among these distances:
43 2 0.01
44 172 0.44
45 74 0.19
46 2 0.01
47 2 0.01
49 3 0.01
50 61 0.16
51 64 0.17
52 3 0.01
54 2 0.01
56 1 0.00
57 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (44 bp):
CAAATCTTATCCTCTGAAGTTGCAGTGGAGCAGATTGAAGCTGA
Found at i:43052830 original size:145 final size:140
Alignment explanation
Indices: 43052475--43052872 Score: 439
Period size: 145 Copynumber: 2.8 Consensus size: 140
43052465 TACCATGGCG
* * * *
43052475 AATCTTATCTCCCTGAAGTTGCAGTGGAAAAGGTTAAAGCTACAAAACTTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAGCTACAAATCTTATCCCCCTGAAGTTG
* * *
43052540 TAGTGGAGCAGATTGAAGATAGCGAATCTTATTTTCCTAAAGTTGCAGTAGAACAGATTAAAGCT
66 TAGTGGAGCAGATTAAACATAACGAATCTTATTTTCCTAAAGTTGCAGTAGAACAGATTAAAGCT
*
43052605 ACAAGTTACA
131 ACAAGTCACA
* * * * *
43052615 AATCTAATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TGACAAATCTTATACCTCTAAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAGCT-ACAAATCTTATCCCCCTGAAGTT
* * * * * *
43052679 ATAGTGG-GTCGGATTAAATCTACCATAACGAGTCTTA-TTTCCTTGAAGTTGCAGTGGAACTGA
65 GTAGTGGAG-CAGATT-AA---A-CATAACGAATCTTATTTTCC-TAAAGTTGCAGTAGAACAGA
43052742 TTAAAGCTACAAGTCACA
123 TTAAAGCTACAAGTCACA
* *
43052760 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACAAATCTTATCCCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAGCTACAAATCTTATCCCCCTGAAGTTG
* * * *
43052825 CAGTGGAGCAGATTGAAGC-T-AC-AGATCTTATCTCCCTAAAGTTGCAGT
66 TAGTGGAGCAGATT-AAACATAACGA-ATCTTATTTTCCTAAAGTTGCAGT
43052873 GGAGAAGATT
Statistics
Matches: 212, Mismatches: 34, Indels: 25
0.78 0.13 0.09
Matches are distributed among these distances:
138 1 0.00
139 20 0.09
140 68 0.32
141 2 0.01
144 6 0.03
145 113 0.53
146 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (140 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAGCTACAAATCTTATCCCCCTGAAGTTG
TAGTGGAGCAGATTAAACATAACGAATCTTATTTTCCTAAAGTTGCAGTAGAACAGATTAAAGCT
ACAAGTCACA
Found at i:43052956 original size:89 final size:88
Alignment explanation
Indices: 43052757--43052963 Score: 272
Period size: 89 Copynumber: 2.3 Consensus size: 88
43052747 GCTACAAGTC
* * * *
43052757 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACAAATCTTATCCCCCTGAAG
1 ACAAATCCTATCTCCCTGAAGTTGCAGTGGAGAAGATTGAAGATACAAATCTTATCCCCCTAAAG
* * *
43052822 TTGCAGTGGAGCAGATTGAAGCT
66 TTGCAATGAAGCAGATTGAAGCG
* * * * *
43052845 ACAGATCTTATCTCCCTAAAGTTGCAGTGGAGAAGATTGAAGATGACAAATCTTATCTCTCTAAA
1 ACAAATCCTATCTCCCTGAAGTTGCAGTGGAGAAGATTGAAGAT-ACAAATCTTATCCCCCTAAA
43052910 GTTGCAATGAAGCAGATTGAAGCG
65 GTTGCAATGAAGCAGATTGAAGCG
*
43052934 ACAAATCCTATAC-CTCTGAAGTTGCAGTGG
1 ACAAATCCTAT-CTCCCTGAAGTTGCAGTGG
43052964 GTAAGAATGA
Statistics
Matches: 103, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
88 40 0.39
89 62 0.60
90 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (88 bp):
ACAAATCCTATCTCCCTGAAGTTGCAGTGGAGAAGATTGAAGATACAAATCTTATCCCCCTAAAG
TTGCAATGAAGCAGATTGAAGCG
Found at i:43056645 original size:9 final size:9
Alignment explanation
Indices: 43056631--43056658 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
43056621 AATCAACCTT
43056631 AAAACGAAA
1 AAAACGAAA
43056640 AAAACGAAA
1 AAAACGAAA
43056649 AAAACGAAA
1 AAAACGAAA
43056658 A
1 A
43056659 CCTTAGAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.79, C:0.11, G:0.11, T:0.00
Consensus pattern (9 bp):
AAAACGAAA
Found at i:43060356 original size:29 final size:30
Alignment explanation
Indices: 43060324--43060389 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
43060314 AAATAATATG
43060324 ATATAT-AAATTTTGA-TTTAATTTAATTAT
1 ATATATGAAATTTT-ATTTTAATTTAATTAT
*
43060353 ATATATGAAATTTTATTTTTTATTTAATTAT
1 ATATATGAAATTTTA-TTTTAATTTAATTAT
*
43060384 ACATAT
1 ATATAT
43060390 TTTAAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 7 0.22
30 7 0.22
31 18 0.56
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (30 bp):
ATATATGAAATTTTATTTTAATTTAATTAT
Found at i:43061989 original size:84 final size:84
Alignment explanation
Indices: 43061809--43061991 Score: 219
Period size: 84 Copynumber: 2.2 Consensus size: 84
43061799 CGGCGTTTTT
* *
43061809 GCTAATGCCCCTAAATCTCCAATTAAAACCACGTCGTTTTTATTAAACTATAATGCTTTTTACAG
1 GCTAATGCCCCTAAATCTCAAATTAAAACAACGTCGTTTTTATTAAACTATAATGCTTTTTACAG
** *
43061874 CGTTTATTTACAAAACGCC
66 CGTTTATGCAAAAAACGCC
* * * *
43061893 GCTAATGCCCCTAAATCTGAAATTAAAACAATGTCG-TTTTAGTTAAACTATAATGTTTTTTTGC
1 GCTAATGCCCCTAAATCTCAAATTAAAACAACGTCGTTTTTA-TTAAACTATAATG-CTTTTTAC
* *
43061957 GGCGTTT-TGCAAATAAATGCC
64 AGCGTTTATGCAAA-AAACGCC
43061978 GCTAATG-CCCTAAA
1 GCTAATGCCCCTAAA
43061992 GTTATATGCT
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
83 5 0.06
84 55 0.65
85 25 0.29
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (84 bp):
GCTAATGCCCCTAAATCTCAAATTAAAACAACGTCGTTTTTATTAAACTATAATGCTTTTTACAG
CGTTTATGCAAAAAACGCC
Found at i:43062866 original size:18 final size:19
Alignment explanation
Indices: 43062843--43062888 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
43062833 ACCTTAAACA
*
43062843 CTAAACCCTAAAGTA-CCT
1 CTAAACCCTAAAATATCCT
*
43062861 CTAAACCTTAAAATATCCT
1 CTAAACCCTAAAATATCCT
43062880 -TAAACCCTA
1 CTAAACCCTA
43062889 GACATAAACC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 21 0.88
19 3 0.12
ACGTcount: A:0.41, C:0.30, G:0.02, T:0.26
Consensus pattern (19 bp):
CTAAACCCTAAAATATCCT
Found at i:43062872 original size:7 final size:7
Alignment explanation
Indices: 43062807--43062854 Score: 60
Period size: 7 Copynumber: 6.7 Consensus size: 7
43062797 ATTAATTAAT
43062807 CTAAACC
1 CTAAACC
43062814 CTAAACC
1 CTAAACC
43062821 TCTAAACC
1 -CTAAACC
*
43062829 CTATACC
1 CTAAACC
* *
43062836 TTAAACA
1 CTAAACC
43062843 CTAAACC
1 CTAAACC
43062850 CTAAA
1 CTAAA
43062855 GTACCTCTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
7 27 0.79
8 7 0.21
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:43062912 original size:13 final size:13
Alignment explanation
Indices: 43062880--43062913 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
43062870 AAAATATCCT
* *
43062880 TAAACCCTAGACA
1 TAAACCTTAAACA
43062893 TAAACCTTAAACA
1 TAAACCTTAAACA
43062906 TAAACCTT
1 TAAACCTT
43062914 CCACTCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.47, C:0.26, G:0.03, T:0.24
Consensus pattern (13 bp):
TAAACCTTAAACA
Found at i:43062971 original size:15 final size:14
Alignment explanation
Indices: 43062934--43062968 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
43062924 CCATAAACAT
43062934 CTAACCCTTGACCC
1 CTAACCCTTGACCC
*
43062948 TTAACCCTTGACCC
1 CTAACCCTTGACCC
43062962 CTAACCC
1 CTAACCC
43062969 CTTAAACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.23, C:0.49, G:0.06, T:0.23
Consensus pattern (14 bp):
CTAACCCTTGACCC
Found at i:43063474 original size:40 final size:40
Alignment explanation
Indices: 43063376--43063497 Score: 158
Period size: 40 Copynumber: 3.0 Consensus size: 40
43063366 CGGGGTTTTC
*
43063376 TTTAAAAA-CGCCACTAATGCTCGATCTACAGCGGCGTTT
1 TTTAAAAAGCGCCACTAATGCTCGATCTATAGCGGCGTTT
* * * *
43063415 TTCAAAAAAGCGCCGCTAATGGTCGA-CATATAGCAGCGTTT
1 TT-TAAAAAGCGCCACTAATGCTCGATC-TATAGCGGCGTTT
*
43063456 TTTAAAAAGCGCCACTAATGCTTGATCTATAGCGGCGTTT
1 TTTAAAAAGCGCCACTAATGCTCGATCTATAGCGGCGTTT
43063496 TT
1 TT
43063498 CGTAAAGCGA
Statistics
Matches: 69, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
39 2 0.03
40 39 0.57
41 28 0.41
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.30
Consensus pattern (40 bp):
TTTAAAAAGCGCCACTAATGCTCGATCTATAGCGGCGTTT
Done.