Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 125 of 297
Found at i:43926273 original size:16 final size:16
Alignment explanation
Indices: 43926252--43926293 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
43926242 TTATTAAATT
*
43926252 ATATATTTTAATTATA
1 ATATATTTTAATAATA
43926268 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
43926283 AT-TATGTTTAA
1 ATATAT-TTTAA
43926294 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:43926278 original size:15 final size:15
Alignment explanation
Indices: 43926243--43926284 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
43926233 TTAAGAATTT
*
43926243 TATTAAATTAT-ATA
1 TATTTAATTATAATA
43926257 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
43926271 TATTTAATAATAAT
1 TATTTAATTATAAT
43926285 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:43926519 original size:45 final size:43
Alignment explanation
Indices: 43926419--43926528 Score: 120
Period size: 45 Copynumber: 2.6 Consensus size: 43
43926409 TTTTCCATTA
43926419 TGCTATTACACCTCTATT-C---CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
* * ***
43926458 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCA-TACATTCAACCAAACACAAGA-T
43926503 TGCTATTACACCTCTATTCCAATACA
1 TGCTATTACACCTCTATTCC-ATACA
43926529 CCTCTAATCC
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 23 0.40
46 1 0.02
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (43 bp):
TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
Found at i:43926530 original size:16 final size:16
Alignment explanation
Indices: 43926509--43926608 Score: 164
Period size: 16 Copynumber: 6.2 Consensus size: 16
43926499 GATTTGCTAT
*
43926509 TACACCTCTATTCCAA
1 TACACCTCTAATCCAA
*
43926525 TACACCTCTAATCCAT
1 TACACCTCTAATCCAA
*
43926541 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
*
43926557 TACACCTCTAATCCAT
1 TACACCTCTAATCCAA
43926573 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
43926589 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
43926605 TACA
1 TACA
43926609 GCGAACCAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 77 1.00
ACGTcount: A:0.35, C:0.36, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:43929314 original size:11 final size:11
Alignment explanation
Indices: 43929300--43929329 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
43929290 ATAATACTAG
43929300 AATATATATAC
1 AATATATATAC
*
43929311 AATATATATAT
1 AATATATATAC
43929322 AATATATA
1 AATATATA
43929330 AAATGAACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (11 bp):
AATATATATAC
Found at i:43929402 original size:12 final size:10
Alignment explanation
Indices: 43929344--43929403 Score: 52
Period size: 9 Copynumber: 6.0 Consensus size: 10
43929334 GAACGTATAC
43929344 AATATATATT
1 AATATATATT
*
43929354 -ATAAATATT
1 AATATATATT
*
43929363 AATA-ATATA
1 AATATATATT
*
43929372 AAAATATATT
1 AATATATATT
*
43929382 AATAAATATCT
1 AATATATAT-T
43929393 ACATATATATT
1 A-ATATATATT
43929404 GAAAATAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
9 15 0.38
10 14 0.36
11 3 0.08
12 7 0.18
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (10 bp):
AATATATATT
Found at i:43929593 original size:20 final size:20
Alignment explanation
Indices: 43929555--43929593 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
43929545 TGATATTAAT
*
43929555 AATAAATATAATAGGAATAA
1 AATAAATATAATAAGAATAA
* *
43929575 AATAAATGTAATAATAATA
1 AATAAATATAATAAGAATA
43929594 TATACACAAT
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:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (20 bp):
AATAAATATAATAAGAATAA
Found at i:43929691 original size:25 final size:23
Alignment explanation
Indices: 43929662--43929751 Score: 101
Period size: 23 Copynumber: 3.7 Consensus size: 23
43929652 GCATAAGATG
43929662 ATATAAAAAATATATACATGGAATA
1 ATATAAAAAATATATACAT--AATA
*
43929687 GTATAAAAAAATATATA-ACTAATA
1 ATAT-AAAAAATATATACA-TAATA
*
43929711 ATATTAAAAATATATACATAATA
1 ATATAAAAAATATATACATAATA
43929734 TATATAAAAACATATATA
1 -ATATAAAAA-ATATATA
43929752 TTAGACATGA
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
23 16 0.29
24 16 0.29
25 11 0.20
26 13 0.23
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.31
Consensus pattern (23 bp):
ATATAAAAAATATATACATAATA
Found at i:43929723 original size:23 final size:25
Alignment explanation
Indices: 43929645--43929751 Score: 100
Period size: 25 Copynumber: 4.3 Consensus size: 25
43929635 AGTGTTTAAG
* *
43929645 AATATAT-GCATAAGATGATATAAAA
1 AATATATAACATAATAT-ATATAAAA
43929670 AATATAT-ACATGGAATAGTATA-AAAA
1 AATATATAACAT--AATA-TATATAAAA
*
43929696 AATATATAAC-TAATA-ATATTAAA
1 AATATATAACATAATATATATAAAA
43929719 AATATAT-ACATAATATATATAAAA
1 AATATATAACATAATATATATAAAA
43929743 ACATATATA
1 A-ATATATA
43929752 TTAGACATGA
Statistics
Matches: 69, Mismatches: 4, Indels: 17
0.77 0.04 0.19
Matches are distributed among these distances:
22 5 0.07
23 15 0.22
24 12 0.17
25 16 0.23
26 12 0.17
27 8 0.12
28 1 0.01
ACGTcount: A:0.59, C:0.05, G:0.06, T:0.31
Consensus pattern (25 bp):
AATATATAACATAATATATATAAAA
Found at i:43929859 original size:3 final size:3
Alignment explanation
Indices: 43929851--43929876 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
43929841 ATACTAGTAC
43929851 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
43929877 TGTGCATATA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:43929940 original size:3 final size:3
Alignment explanation
Indices: 43929927--43929975 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
43929917 ATAACTAAAT
* * *
43929927 ATA AT- ATA ATA ATA ATA ATA AT- ATA AAA ATA ATA ATG ATA ACA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
43929973 ATA
1 ATA
43929976 TGTCAAATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:43929949 original size:17 final size:17
Alignment explanation
Indices: 43929927--43929962 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
43929917 ATAACTAAAT
*
43929927 ATAATATAATAATAATA
1 ATAATATAAAAATAATA
43929944 ATAATATAAAAATAATA
1 ATAATATAAAAATAATA
43929961 AT
1 AT
43929963 GATAACAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAATATAAAAATAATA
Found at i:43930334 original size:3 final size:3
Alignment explanation
Indices: 43930077--43930323 Score: 95
Period size: 3 Copynumber: 81.7 Consensus size: 3
43930067 ATAGTAAGTG
* * * *
43930077 ATA ATA AAA ATA ATA ATA ATCA GTA ATA A-A AGA ATG ATA ATA GGA-A
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA --ATA
* * * *
43930123 ATA ATA ATA ATA GT- ATA CACTA ATA ACA GTA ATA AT- ATGA AAA ATA
1 ATA ATA ATA ATA ATA ATA -A-TA ATA ATA ATA ATA ATA AT-A ATA ATA
* * * *
43930169 AGAA ATA ACA GTA AT- ATA A-A ATA ATA ATAA ATA CATGT ATA ATA A-A
1 A-TA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA -AT-A ATA ATA ATA
* * * * *
43930215 ACA TATA CTA ATA A-A A-A AAA ATA ATA ATA ATA ATA ACA ATA ACA
1 ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
43930259 ATA AT- ATA GTA GTA ACA ATA ATA A-A AGTA GA-A ATA ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA -ATA ATA ATA ATA ATA
43930303 ATAA ATA ATA ATA ATA ATA AT
1 AT-A ATA ATA ATA ATA ATA AT
43930324 CCCAATAATA
Statistics
Matches: 182, Mismatches: 37, Indels: 50
0.68 0.14 0.19
Matches are distributed among these distances:
2 21 0.12
3 136 0.75
4 21 0.12
5 4 0.02
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.26
Consensus pattern (3 bp):
ATA
Found at i:43934492 original size:10 final size:11
Alignment explanation
Indices: 43934466--43934494 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
43934456 GCCCGTAATA
43934466 ATTTTTATATT
1 ATTTTTATATT
43934477 ATTTTTATATT
1 ATTTTTATATT
43934488 ATTTTTA
1 ATTTTTA
43934495 AATATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTTTTATATT
Found at i:43934653 original size:31 final size:31
Alignment explanation
Indices: 43934616--43934674 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
43934606 ACTTAACAAG
43934616 CAAATGCCTCTAAAATAATAAAAAAATTTAA
1 CAAATGCCTCTAAAATAATAAAAAAATTTAA
* *
43934647 CAAATGCCTTTAAAATAATAAGAAAATT
1 CAAATGCCTCTAAAATAATAAAAAAATT
43934675 AAAAATAAAA
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:0.56, C:0.12, G:0.05, T:0.27
Consensus pattern (31 bp):
CAAATGCCTCTAAAATAATAAAAAAATTTAA
Found at i:43935205 original size:22 final size:20
Alignment explanation
Indices: 43935158--43935206 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 20
43935148 ATTCAAATAT
43935158 TATAATTAAAAAATTTTAAA
1 TATAATTAAAAAATTTTAAA
*
43935178 TCATAATTAAATAATTTTTAACA
1 T-ATAATTAAA-AAATTTTAA-A
43935201 TATAAT
1 TATAAT
43935207 ATTAATTAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 1 0.04
21 9 0.36
22 13 0.52
23 2 0.08
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (20 bp):
TATAATTAAAAAATTTTAAA
Found at i:43936205 original size:28 final size:28
Alignment explanation
Indices: 43936142--43936229 Score: 86
Period size: 28 Copynumber: 3.0 Consensus size: 28
43936132 TATTTTTTTT
* *
43936142 GAGAATTGGACCAAATAAAATTTCATGTA
1 GAGAATTGCACAAAATAAAA-TTCATGTA
* * *
43936171 TAAAATTGTACAAAATAAAATTCATGTA
1 GAGAATTGCACAAAATAAAATTCATGTA
*
43936199 GAGAATTACACATTAAACTAAAATTCATGTA
1 GAGAATTGCACA--AAA-TAAAATTCATGTA
43936230 TAATTTTGAG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
28 16 0.33
29 16 0.33
30 3 0.06
31 13 0.27
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.30
Consensus pattern (28 bp):
GAGAATTGCACAAAATAAAATTCATGTA
Found at i:43937842 original size:6 final size:6
Alignment explanation
Indices: 43937831--43937857 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
43937821 TAGGGACAGA
43937831 TGGTAT TGGTAT TGGTAT TGGTAT TGG
1 TGGTAT TGGTAT TGGTAT TGGTAT TGG
43937858 ATCACGAGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.37, T:0.48
Consensus pattern (6 bp):
TGGTAT
Found at i:43943361 original size:21 final size:19
Alignment explanation
Indices: 43943337--43943383 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
43943327 TTATAATCAA
*
43943337 TGTATTTTTACATATTCTTGG
1 TGTATTTTTA-AAATT-TTGG
43943358 TGTATTATTTAAAATTTTGG
1 TGTATT-TTTAAAATTTTGG
43943378 TG-ATTT
1 TGTATTT
43943384 GATATCCCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 1 0.04
19 3 0.12
20 6 0.25
21 10 0.42
22 4 0.17
ACGTcount: A:0.23, C:0.04, G:0.15, T:0.57
Consensus pattern (19 bp):
TGTATTTTTAAAATTTTGG
Found at i:43943947 original size:20 final size:21
Alignment explanation
Indices: 43943922--43943966 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
43943912 ATATTTTTAA
43943922 TTTTAA-AA-TTACATTATATT
1 TTTTAATAAGTTA-ATTATATT
*
43943942 TTTTAATAAGTTAATTCTATT
1 TTTTAATAAGTTAATTATATT
43943963 TTTT
1 TTTT
43943967 TTATAATTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 13 0.59
22 3 0.14
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTTAATAAGTTAATTATATT
Found at i:43944084 original size:22 final size:22
Alignment explanation
Indices: 43944059--43944103 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
43944049 CTAACATAAT
43944059 TGTTATTTATTAA-TATTTCACA
1 TGTTATTTATTAATTA-TTCACA
* *
43944081 TGTTTTTTTTTAATTATTCACA
1 TGTTATTTATTAATTATTCACA
43944103 T
1 T
43944104 ACAACATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.27, C:0.09, G:0.04, T:0.60
Consensus pattern (22 bp):
TGTTATTTATTAATTATTCACA
Found at i:43948028 original size:32 final size:31
Alignment explanation
Indices: 43947978--43948038 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
43947968 TGTTTCAATC
*
43947978 TTGTAACACATCCATTAAATTTTTATCATAATA
1 TTGTAACACAT-CATTAAATTATT-TCATAATA
43948011 TTGTAATCACAT-ATTAAATTATTTCATA
1 TTGTAA-CACATCATTAAATTATTTCATA
43948039 CTTAAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 5 0.19
32 10 0.38
33 6 0.23
34 5 0.19
ACGTcount: A:0.39, C:0.13, G:0.03, T:0.44
Consensus pattern (31 bp):
TTGTAACACATCATTAAATTATTTCATAATA
Found at i:43948848 original size:15 final size:16
Alignment explanation
Indices: 43948816--43948851 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
43948806 ATTTAAAAAA
*
43948816 AATTACAATTCTTTAT
1 AATTACAATTCTTAAT
43948832 AATTACAA-TCTTAAT
1 AATTACAATTCTTAAT
43948847 AATTA
1 AATTA
43948852 TACTTTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTACAATTCTTAAT
Found at i:43950019 original size:18 final size:18
Alignment explanation
Indices: 43949998--43950048 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
43949988 AATTTTGAAG
43949998 AAATATATAAAAATACAT
1 AAATATATAAAAATACAT
* *
43950016 AAATATTTTCAAAA-ACAT
1 AAATA-TATAAAAATACAT
43950034 ATAAT-TATAAAAATA
1 A-AATATATAAAAATA
43950049 AAAAATATCG
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
17 6 0.23
18 11 0.42
19 9 0.35
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATATATAAAAATACAT
Found at i:43950073 original size:3 final size:3
Alignment explanation
Indices: 43950065--43950097 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
43950055 ATCGTTCACA
43950065 AAT AAT AAT AAT AAT AAT AAT AAT AAT ATAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AA
43950098 AATTTTCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:43950073 original size:35 final size:35
Alignment explanation
Indices: 43950003--43950093 Score: 85
Period size: 35 Copynumber: 2.5 Consensus size: 35
43949993 TGAAGAAATA
* *
43950003 TATAAAAATACATAAATATTTTCAAAAACATATAAT
1 TATAAAAATA-AAAAATATGTTCAAAAACATATAAT
* *
43950039 TATAAAAATAAAAAATATCGTTCACAAATA-ATAAT
1 TATAAAAATAAAAAATAT-GTTCAAAAACATATAAT
* *
43950074 AATAATAATAATAATAATAT
1 TATAAAAATAA-AA-AATAT
43950094 ATAAAATTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
35 21 0.46
36 20 0.43
37 5 0.11
ACGTcount: A:0.60, C:0.07, G:0.01, T:0.32
Consensus pattern (35 bp):
TATAAAAATAAAAAATATGTTCAAAAACATATAAT
Found at i:43955595 original size:19 final size:19
Alignment explanation
Indices: 43955571--43955626 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 19
43955561 AAAAAAATTC
43955571 AAAAAAAATTATTTGAACAA
1 AAAAAAAATTATTTGAA-AA
* *
43955591 AAAAATAATTTTTTGAAAA
1 AAAAAAAATTATTTGAAAA
43955610 ATAAATAAAATTTATTT
1 A-AAA-AAAA-TTATTT
43955627 TTAGGTGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.10
20 18 0.62
21 3 0.10
22 5 0.17
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.36
Consensus pattern (19 bp):
AAAAAAAATTATTTGAAAA
Found at i:43955600 original size:20 final size:19
Alignment explanation
Indices: 43955571--43955617 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
43955561 AAAAAAATTC
43955571 AAAAAA-AATTATTTGAACA
1 AAAAAATAATTATTTGAA-A
*
43955590 AAAAAATAATTTTTTGAAA
1 AAAAAATAATTATTTGAAA
*
43955609 AATAAATAA
1 AAAAAATAA
43955618 AATTTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (19 bp):
AAAAAATAATTATTTGAAA
Found at i:43965132 original size:6 final size:6
Alignment explanation
Indices: 43965123--43965150 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
43965113 AAAAATCGAC
43965123 AAACCA AAACCA AAACCA AAACCA AAAC
1 AAACCA AAACCA AAACCA AAACCA AAAC
43965151 ACAGCCCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (6 bp):
AAACCA
Found at i:43967307 original size:19 final size:19
Alignment explanation
Indices: 43967280--43967352 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
43967270 GGGATTGCAC
*
43967280 TTCGGTGTCTCTGTTACAG
1 TTCGATGTCTCTGTTACAG
* *
43967299 TTCGATGTCTCTGTTTGCAC
1 TTCGATGTCTCTG-TTACAG
*
43967319 TTCGGTGTCTCTGTTACAG
1 TTCGATGTCTCTGTTACAG
**
43967338 TTTAATGTCTCTGTT
1 TTCGATGTCTCTGTT
43967353 TGCACTTCGG
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 28 0.64
20 16 0.36
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.47
Consensus pattern (19 bp):
TTCGATGTCTCTGTTACAG
Found at i:43967317 original size:39 final size:39
Alignment explanation
Indices: 43967274--43967364 Score: 164
Period size: 39 Copynumber: 2.3 Consensus size: 39
43967264 TTATACGGGA
*
43967274 TTGCACTTCGGTGTCTCTGTTACAGTTCGATGTCTCTGT
1 TTGCACTTCGGTGTCTCTGTTACAGTTCAATGTCTCTGT
*
43967313 TTGCACTTCGGTGTCTCTGTTACAGTTTAATGTCTCTGT
1 TTGCACTTCGGTGTCTCTGTTACAGTTCAATGTCTCTGT
43967352 TTGCACTTCGGTG
1 TTGCACTTCGGTG
43967365 CCTTTGATTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.11, C:0.22, G:0.23, T:0.44
Consensus pattern (39 bp):
TTGCACTTCGGTGTCTCTGTTACAGTTCAATGTCTCTGT
Found at i:43967327 original size:20 final size:20
Alignment explanation
Indices: 43967274--43967418 Score: 107
Period size: 20 Copynumber: 7.2 Consensus size: 20
43967264 TTATACGGGA
43967274 TTGCACTTCGGTGTCTCTG-
1 TTGCACTTCGGTGTCTCTGT
* * *
43967293 TTACAGTTCGATGTCTCTGT
1 TTGCACTTCGGTGTCTCTGT
43967313 TTGCACTTCGGTGTCTCTG-
1 TTGCACTTCGGTGTCTCTGT
* * ***
43967332 TTACAGTTTAATGTCTCTGT
1 TTGCACTTCGGTGTCTCTGT
* *
43967352 TTGCACTTCGGTGCCTTTGAT
1 TTGCACTTCGGTGTCTCTG-T
* *
43967373 TTGCACAATC-GTGTCTTTGT
1 TTGCAC-TTCGGTGTCTCTGT
* * *
43967393 CTGCACTTTGGTGCCTCTGT
1 TTGCACTTCGGTGTCTCTGT
43967413 TATGCA
1 T-TGCA
43967419 TTTACGATGG
Statistics
Matches: 94, Mismatches: 26, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
19 31 0.33
20 42 0.45
21 19 0.20
22 2 0.02
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (20 bp):
TTGCACTTCGGTGTCTCTGT
Found at i:43967377 original size:21 final size:20
Alignment explanation
Indices: 43967349--43967418 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 20
43967339 TTAATGTCTC
43967349 TGTTTGCACTTCGGTGCCTT
1 TGTTTGCACTTCGGTGCCTT
* *
43967369 TGATTTGCACAATC-GTGTCTT
1 TG-TTTGCAC-TTCGGTGCCTT
* * *
43967390 TGTCTGCACTTTGGTGCCTC
1 TGTTTGCACTTCGGTGCCTT
43967410 TGTTATGCA
1 TGTT-TGCA
43967419 TTTACGATGG
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
19 1 0.03
20 16 0.42
21 19 0.50
22 2 0.05
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (20 bp):
TGTTTGCACTTCGGTGCCTT
Found at i:43967716 original size:21 final size:21
Alignment explanation
Indices: 43967691--43967757 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
43967681 TGTGATTGGT
43967691 GAATTTGTATTTAATGATCAA
1 GAATTTGTATTTAATGATCAA
** * *
43967712 GAATTATAAATTATATTGGT---
1 GAATT-TGTATT-TAATGATCAA
43967732 GAATTTGTATTTAATGATCAA
1 GAATTTGTATTTAATGATCAA
43967753 GAATT
1 GAATT
43967758 ATAAATTATC
Statistics
Matches: 33, Mismatches: 8, Indels: 10
0.65 0.16 0.20
Matches are distributed among these distances:
18 5 0.15
19 4 0.12
20 5 0.15
21 10 0.30
22 4 0.12
23 5 0.15
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.43
Consensus pattern (21 bp):
GAATTTGTATTTAATGATCAA
Found at i:43967766 original size:41 final size:41
Alignment explanation
Indices: 43967685--43967766 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
43967675 TACTAATGTG
43967685 ATTGGTGAATTTGTATTTAATGATCAAGAATTATAAATTAT
1 ATTGGTGAATTTGTATTTAATGATCAAGAATTATAAATTAT
43967726 ATTGGTGAATTTGTATTTAATGATCAAGAATTATAAATTAT
1 ATTGGTGAATTTGTATTTAATGATCAAGAATTATAAATTAT
43967767 CTCTTAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.44
Consensus pattern (41 bp):
ATTGGTGAATTTGTATTTAATGATCAAGAATTATAAATTAT
Found at i:43969874 original size:13 final size:13
Alignment explanation
Indices: 43969856--43969881 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43969846 TGTGAAAAAT
43969856 AAAATAAAATAAA
1 AAAATAAAATAAA
43969869 AAAATAAAATAAA
1 AAAATAAAATAAA
43969882 GAACACACAA
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAATAAAATAAA
Found at i:43974595 original size:12 final size:12
Alignment explanation
Indices: 43974578--43974602 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43974568 TGTGAAAAAT
43974578 AAAATAAAATAA
1 AAAATAAAATAA
43974590 AAAATAAAATAA
1 AAAATAAAATAA
43974602 A
1 A
43974603 GAACACACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:43975735 original size:13 final size:13
Alignment explanation
Indices: 43975717--43975742 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43975707 ATGTATGCAA
43975717 ATTGCTCAGTTGC
1 ATTGCTCAGTTGC
43975730 ATTGCTCAGTTGC
1 ATTGCTCAGTTGC
43975743 GCATTTTTCA
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:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (13 bp):
ATTGCTCAGTTGC
Found at i:43981751 original size:25 final size:26
Alignment explanation
Indices: 43981681--43981751 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 26
43981671 ATTAATAGAA
* *
43981681 AAGCTCATGAGAGCCAAAT-ATCGGG
1 AAGCTCATAAGAGCTAAATAATCGGG
* *
43981706 AAGCTCGTAAGAGCTATATAAT-GGG
1 AAGCTCATAAGAGCTAAATAATCGGG
*
43981731 ATGCTCATAAGAGCTAAATAA
1 AAGCTCATAAGAGCTAAATAA
43981752 CCAGACGCTC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
25 36 0.95
26 2 0.05
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.21
Consensus pattern (26 bp):
AAGCTCATAAGAGCTAAATAATCGGG
Found at i:43984235 original size:7 final size:8
Alignment explanation
Indices: 43984220--43984251 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
43984210 TGCATTTCAA
43984220 TATTTTTT
1 TATTTTTT
43984228 TATTTTTT
1 TATTTTTT
43984236 TATTTTTT
1 TATTTTTT
43984244 TATATTTT
1 TAT-TTTT
43984252 AATATAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 19 0.83
9 4 0.17
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (8 bp):
TATTTTTT
Found at i:43988015 original size:18 final size:18
Alignment explanation
Indices: 43987992--43988027 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
43987982 ACTAGATAGT
43987992 GTTTGCAATATATATATA
1 GTTTGCAATATATATATA
43988010 GTTTGCAATATATATATA
1 GTTTGCAATATATATATA
43988028 TATATAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (18 bp):
GTTTGCAATATATATATA
Found at i:43996224 original size:20 final size:19
Alignment explanation
Indices: 43996199--43996273 Score: 59
Period size: 20 Copynumber: 3.9 Consensus size: 19
43996189 AAAATAAAAA
43996199 TAAAATAATTTTCAAAATTT
1 TAAAAT-ATTTTCAAAATTT
43996219 TAAAATATTTAT-AAAATTT
1 TAAAATATTT-TCAAAATTT
*
43996238 CT--AAT-TTTTTAATAATTT
1 -TAAAATATTTTCAA-AATTT
*
43996256 TAAAAAATTTTCTAAAAT
1 TAAAATATTTTC-AAAAT
43996274 AATAATTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 16
0.71 0.03 0.25
Matches are distributed among these distances:
16 1 0.02
17 6 0.13
18 8 0.18
19 13 0.29
20 15 0.33
21 2 0.04
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (19 bp):
TAAAATATTTTCAAAATTT
Found at i:43998417 original size:20 final size:22
Alignment explanation
Indices: 43998377--43998422 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 22
43998367 TTTAGTGATA
*
43998377 TAATAAATATAATTTATTATTT
1 TAATAAATATAATTTAATATTT
43998399 TAATAAAT-T-ATTTAATATTT
1 TAATAAATATAATTTAATATTT
43998419 TAAT
1 TAAT
43998423 TTTATTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.61
21 1 0.04
22 8 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TAATAAATATAATTTAATATTT
Found at i:43998442 original size:13 final size:14
Alignment explanation
Indices: 43998426--43998472 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
43998416 TTTTAATTTT
43998426 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
43998439 ATTTTAAGAATAATA
1 ATTTTAATAAT-ATA
*
43998454 ATTTTAAATAATATT
1 ATTTT-AATAATATA
43998469 ATTT
1 ATTT
43998473 ACATATAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 10 0.36
14 1 0.04
15 12 0.43
16 5 0.18
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:43998458 original size:15 final size:16
Alignment explanation
Indices: 43998431--43998460 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
43998421 ATTTTATTTT
43998431 AATAATAAATTTTAAG
1 AATAATAAATTTTAAG
43998447 AATAAT-AATTTTAA
1 AATAATAAATTTTAA
43998461 ATAATATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (16 bp):
AATAATAAATTTTAAG
Found at i:43998519 original size:15 final size:15
Alignment explanation
Indices: 43998499--43998555 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
43998489 ATTCTATATT
43998499 AATATTTTAATAATA
1 AATATTTTAATAATA
*
43998514 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
43998533 AATATATTAATAATA
1 AATATTTTAATAATA
43998548 AATATTTT
1 AATATTTT
43998556 GTAGTATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 17 0.50
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:44002517 original size:43 final size:43
Alignment explanation
Indices: 44002469--44002610 Score: 189
Period size: 43 Copynumber: 3.3 Consensus size: 43
44002459 TTATTTAAAA
*
44002469 AAACGCCACTAAAGACCATGACCTTTAGCGGCACTTTTTTCAC
1 AAACGCCACTAAAGACCATGACCTTTAGCGGCGCTTTTTTCAC
*
44002512 AAACGCCACTAAAGACCATGACCTTCAGCGGCGCTTTTTT-AC
1 AAACGCCACTAAAGACCATGACCTTTAGCGGCGCTTTTTTCAC
* ** * * * *
44002554 AAACGCCGCTACGGAACA-AACCTTTAGCAGCGCTTTTCTCAC
1 AAACGCCACTAAAGACCATGACCTTTAGCGGCGCTTTTTTCAC
44002596 AAACGCCACTAAAGA
1 AAACGCCACTAAAGA
44002611 ATATAAGCTT
Statistics
Matches: 85, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
41 17 0.20
42 30 0.35
43 38 0.45
ACGTcount: A:0.32, C:0.31, G:0.15, T:0.22
Consensus pattern (43 bp):
AAACGCCACTAAAGACCATGACCTTTAGCGGCGCTTTTTTCAC
Found at i:44002856 original size:18 final size:18
Alignment explanation
Indices: 44002833--44002869 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
44002823 TACCAGCAAC
44002833 AGATAATACAATTTATGA
1 AGATAATACAATTTATGA
44002851 AGATAATACAATTTATGA
1 AGATAATACAATTTATGA
44002869 A
1 A
44002870 AATTTATGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.32
Consensus pattern (18 bp):
AGATAATACAATTTATGA
Found at i:44006027 original size:15 final size:15
Alignment explanation
Indices: 44006007--44006036 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
44005997 CGTTTCTTGT
44006007 AAAAAATTTTGCGGC
1 AAAAAATTTTGCGGC
44006022 AAAAAATTTTGCGGC
1 AAAAAATTTTGCGGC
44006037 GTTTTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (15 bp):
AAAAAATTTTGCGGC
Found at i:44006719 original size:7 final size:7
Alignment explanation
Indices: 44006707--44006819 Score: 54
Period size: 7 Copynumber: 15.9 Consensus size: 7
44006697 ACTAATTAAT
44006707 CTAAACC
1 CTAAACC
44006714 CTAAACC
1 CTAAACC
*
44006721 TCTTAACC
1 -CTAAACC
*
44006729 C-ATATCC
1 CTA-AACC
*
44006736 CATAAACA
1 C-TAAACC
44006744 CTAAACC
1 CTAAACC
*
44006751 CTTAACC
1 CTAAACC
44006758 CTAAACC
1 CTAAACC
*
44006765 CTTACACC
1 C-TAAACC
*
44006773 TTAAACTC
1 CTAAAC-C
44006781 C--AACC
1 CTAAACC
44006786 CT-AACC
1 CTAAACC
44006792 CTTAAACC
1 C-TAAACC
* *
44006800 TTAAATC
1 CTAAACC
* *
44006807 ATAATCC
1 CTAAACC
44006814 CTAAAC
1 CTAAAC
44006820 TCATAATTCA
Statistics
Matches: 78, Mismatches: 19, Indels: 18
0.68 0.17 0.16
Matches are distributed among these distances:
5 2 0.03
6 8 0.10
7 48 0.62
8 19 0.24
9 1 0.01
ACGTcount: A:0.39, C:0.38, G:0.00, T:0.23
Consensus pattern (7 bp):
CTAAACC
Found at i:44006763 original size:14 final size:14
Alignment explanation
Indices: 44006710--44006796 Score: 65
Period size: 15 Copynumber: 6.1 Consensus size: 14
44006700 AATTAATCTA
44006710 AACCCTAAACCTCTT
1 AACCCTAAACC-CTT
* *
44006725 AACCC-ATATCCCATA
1 AACCCTA-AACCC-TT
*
44006740 AACACTAAACCCTT
1 AACCCTAAACCCTT
44006754 AACCCTAAACCCTT
1 AACCCTAAACCCTT
*
44006768 ACACCTTAAACTCC--
1 A-ACCCTAAAC-CCTT
44006782 AACCCT-AACCCTT
1 AACCCTAAACCCTT
44006795 AA
1 AA
44006797 ACCTTAAATC
Statistics
Matches: 57, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
11 2 0.04
12 3 0.05
13 6 0.11
14 18 0.32
15 25 0.44
16 3 0.05
ACGTcount: A:0.38, C:0.40, G:0.00, T:0.22
Consensus pattern (14 bp):
AACCCTAAACCCTT
Found at i:44006914 original size:15 final size:15
Alignment explanation
Indices: 44006859--44006931 Score: 69
Period size: 14 Copynumber: 4.8 Consensus size: 15
44006849 AGTTAACTCT
44006859 TAAACCTTAAACCC-
1 TAAACCTTAAACCCA
* *
44006873 TAAACCATAGTTAACTCA
1 TAAACC-T--TAAACCCA
44006891 TAAACCTTAAACCCA
1 TAAACCTTAAACCCA
* *
44006906 TATATCTTAAA-CCA
1 TAAACCTTAAACCCA
44006920 TAAACCTTAAAC
1 TAAACCTTAAAC
44006932 TATAATGATA
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
14 18 0.39
15 16 0.35
17 6 0.13
18 6 0.13
ACGTcount: A:0.45, C:0.27, G:0.01, T:0.26
Consensus pattern (15 bp):
TAAACCTTAAACCCA
Found at i:44007157 original size:41 final size:41
Alignment explanation
Indices: 44007095--44007296 Score: 282
Period size: 41 Copynumber: 4.9 Consensus size: 41
44007085 TTATATGACT
*
44007095 TTTAACGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
*
44007136 TATAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
** * *
44007177 TTTAGCGTTGTTTTACCAAAAGCCCCGCTAATGCTCGGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
* *
44007218 TTTAGCGGCGTTTTACCAAAAGCGCCGTTAATGCTCT-GTT
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
* *
44007258 TTTAGCGGCGTTTTTTACTAAAA-CGCCGCTATTGCTCTG
1 TTTAGCGGCG--TTTTACCAAAAGCGCCGCTAATGCTCTG
44007297 TGTTTTACAA
Statistics
Matches: 142, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
40 12 0.08
41 120 0.85
42 10 0.07
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.32
Consensus pattern (41 bp):
TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
Found at i:44011814 original size:3 final size:3
Alignment explanation
Indices: 44011806--44011858 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
44011796 AAAATAAAGG
44011806 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
44011854 AAT AA
1 AAT AA
44011859 GGAAAATGGG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:44016159 original size:14 final size:15
Alignment explanation
Indices: 44016130--44016163 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
44016120 ATTCGAGCAA
44016130 AAAGAAAAGAAGAAG
1 AAAGAAAAGAAGAAG
44016145 AAAGAAAACAGAAGAAG
1 AAAG-AAA-AGAAGAAG
44016162 AA
1 AA
44016164 GCAATGGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 3 0.18
17 10 0.59
ACGTcount: A:0.74, C:0.03, G:0.24, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAGAAG
Found at i:44018630 original size:14 final size:15
Alignment explanation
Indices: 44018601--44018634 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
44018591 ATTCGAGCAA
44018601 AAAGAAAAGAAGAAG
1 AAAGAAAAGAAGAAG
44018616 AAAGAAAACAGAAGAAG
1 AAAG-AAA-AGAAGAAG
44018633 AA
1 AA
44018635 GCAATGGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 3 0.18
17 10 0.59
ACGTcount: A:0.74, C:0.03, G:0.24, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAGAAG
Found at i:44029090 original size:21 final size:21
Alignment explanation
Indices: 44029064--44029109 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
44029054 AATAATTTAT
44029064 TTAAAGTGATTGATCTACAAG
1 TTAAAGTGATTGATCTACAAG
44029085 TTAAAGTGATTGATCTACAAG
1 TTAAAGTGATTGATCTACAAG
44029106 TTAA
1 TTAA
44029110 GTCAGGCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (21 bp):
TTAAAGTGATTGATCTACAAG
Found at i:44029573 original size:27 final size:27
Alignment explanation
Indices: 44029504--44029574 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
44029494 TTAATATACA
*
44029504 AATATTTTTATTATT-TTTTTAAAAAGT
1 AATAATTTTATT-TTATTTTTAAAAAGT
** *
44029531 AATAATAATATATTATTTTTAAACAA-T
1 AATAATTTTATTTTATTTTTAAA-AAGT
44029558 AATAATTTTATTTTATT
1 AATAATTTTATTTTATT
44029575 GTTTTAATAT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
26 2 0.06
27 31 0.89
28 2 0.06
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (27 bp):
AATAATTTTATTTTATTTTTAAAAAGT
Found at i:44030080 original size:26 final size:26
Alignment explanation
Indices: 44030051--44030107 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
44030041 AGTTTTTTTT
44030051 TAAAATTAGAAAATCT-TAAAAATACA
1 TAAAATTAGAAAAT-TATAAAAATACA
* *
44030077 T-AAATTTGAAAATTAATAAAAATAGA
1 TAAAATTAGAAAATT-ATAAAAATACA
44030103 TAAAA
1 TAAAA
44030108 AATTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 1 0.04
25 11 0.42
26 11 0.42
27 3 0.12
ACGTcount: A:0.63, C:0.04, G:0.05, T:0.28
Consensus pattern (26 bp):
TAAAATTAGAAAATTATAAAAATACA
Found at i:44030087 original size:25 final size:25
Alignment explanation
Indices: 44030053--44030106 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
44030043 TTTTTTTTTA
44030053 AAATTAGAAAATCT-TAAAAATACAT
1 AAATTAGAAAAT-TATAAAAATACAT
* *
44030078 AAATTTGAAAATTAATAAAAATAGAT
1 AAATTAGAAAATT-ATAAAAATACAT
44030104 AAA
1 AAA
44030107 AAATTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 1 0.04
25 11 0.44
26 13 0.52
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.28
Consensus pattern (25 bp):
AAATTAGAAAATTATAAAAATACAT
Found at i:44030111 original size:21 final size:21
Alignment explanation
Indices: 44030085--44030126 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
44030075 CATAAATTTG
44030085 AAAATTA-ATAAAAATAGATAA
1 AAAATTATA-AAAAATAGATAA
*
44030106 AAAATTTTAAAAAATAGATAA
1 AAAATTATAAAAAATAGATAA
44030127 GTGAGAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (21 bp):
AAAATTATAAAAAATAGATAA
Found at i:44031943 original size:18 final size:18
Alignment explanation
Indices: 44031920--44031957 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
44031910 TTATTAATTT
44031920 AAAATTTTATAAATTATA
1 AAAATTTTATAAATTATA
44031938 AAAATTTTATAAATTATA
1 AAAATTTTATAAATTATA
44031956 AA
1 AA
44031958 GGGCCTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAATTTTATAAATTATA
Found at i:44033744 original size:26 final size:26
Alignment explanation
Indices: 44033715--44033789 Score: 84
Period size: 25 Copynumber: 3.0 Consensus size: 26
44033705 AAGAAATTTT
44033715 TTTTTTATTATTATTTATTTTAAGTC
1 TTTTTTATTATTATTTATTTTAAGTC
* *
44033741 TTTTCTTA-TATTA-TCATTTTAA-AC
1 TTTT-TTATTATTATTTATTTTAAGTC
* *
44033765 TGTTTTATTATTATATATTTTAAGT
1 TTTTTTATTATTATTTATTTTAAGT
44033790 TTTCCCTGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
23 3 0.08
24 9 0.23
25 15 0.38
26 9 0.23
27 3 0.08
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.64
Consensus pattern (26 bp):
TTTTTTATTATTATTTATTTTAAGTC
Found at i:44033771 original size:50 final size:50
Alignment explanation
Indices: 44033717--44033838 Score: 156
Period size: 50 Copynumber: 2.4 Consensus size: 50
44033707 GAAATTTTTT
* * **
44033717 TTTTATTATTATTTATTTTAAGTCTTTTCTTATATTA-TCATTTTAAACTG
1 TTTTATTATTATTTATTTTAAGT-TTTCCCTATATTACTCATTTTAAACAC
* * *
44033767 TTTTATTATTATATATTTTAAGTTTTCCCTGTATTACTTATTTTAAACAC
1 TTTTATTATTATTTATTTTAAGTTTTCCCTATATTACTCATTTTAAACAC
44033817 TTTTATTATTTATTTATTTTAA
1 TTTTATTA-TTATTTATTTTAA
44033839 ATTATTATAT
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
49 10 0.16
50 40 0.65
51 12 0.19
ACGTcount: A:0.27, C:0.08, G:0.03, T:0.61
Consensus pattern (50 bp):
TTTTATTATTATTTATTTTAAGTTTTCCCTATATTACTCATTTTAAACAC
Found at i:44033890 original size:28 final size:26
Alignment explanation
Indices: 44033798--44033878 Score: 85
Period size: 26 Copynumber: 3.1 Consensus size: 26
44033788 GTTTTCCCTG
* *
44033798 TATTACTTATTTTAAAC-ACTTTTAT-
1 TATTATTTATTTTAAACTA-TTATATA
*
44033823 TATTTATTTATTTTAAATTATTATATA
1 TA-TTATTTATTTTAAACTATTATATA
* *
44033850 TATTATTTGTTTTGAACTATTATATA
1 TATTATTTATTTTAAACTATTATATA
44033876 TAT
1 TAT
44033879 ATCTTTTATT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
25 2 0.04
26 42 0.89
27 3 0.06
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.59
Consensus pattern (26 bp):
TATTATTTATTTTAAACTATTATATA
Found at i:44033891 original size:6 final size:6
Alignment explanation
Indices: 44033882--44033913 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
44033872 TATATATATC
44033882 TTTTAT TTTTAT TTTT-T TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
44033914 AAAAAAACTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (6 bp):
TTTTAT
Found at i:44034016 original size:26 final size:26
Alignment explanation
Indices: 44033987--44034115 Score: 77
Period size: 26 Copynumber: 5.0 Consensus size: 26
44033977 TTATATGTTC
44033987 TTTTAAAGTGTCTTGTA-A-ATTATTTA
1 TTTTAAAGTG-CTT-TATATATTATTTA
* *
44034013 TTTTGAATTGCTTTATATATTATTTA
1 TTTTAAAGTGCTTTATATATTATTTA
* * * *
44034039 TTTTAATATTTGTTTTACATATTATTCA
1 TTTTAA-A-GTGCTTTATATATTATTTA
* *
44034067 TTTTAAATTG-TTT-TATACTATTTA
1 TTTTAAAGTGCTTTATATATTATTTA
* * * * *
44034091 CTTCAAATTGTTTTATATGTTATTT
1 TTTTAAAGTGCTTTATATATTATTT
44034116 TGTTTTGTTT
Statistics
Matches: 84, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
24 18 0.21
25 10 0.12
26 32 0.38
27 2 0.02
28 22 0.26
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (26 bp):
TTTTAAAGTGCTTTATATATTATTTA
Found at i:44034064 original size:28 final size:26
Alignment explanation
Indices: 44034005--44034115 Score: 109
Period size: 26 Copynumber: 4.3 Consensus size: 26
44033995 TGTCTTGTAA
* * *
44034005 ATTATTTATTTTGAATTGCTTTATAT
1 ATTATTTATTTTAAATTGTTTTACAT
44034031 ATTATTTATTTTAATATTTGTTTTACAT
1 ATTATTTATTTTAA-A-TTGTTTTACAT
*
44034059 ATTATTCATTTTAAATTGTTTT--AT
1 ATTATTTATTTTAAATTGTTTTACAT
* * * *
44034083 ACTATTTACTTCAAATTGTTTTATAT
1 ATTATTTATTTTAAATTGTTTTACAT
*
44034109 GTTATTT
1 ATTATTT
44034116 TGTTTTGTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
24 20 0.28
26 27 0.38
27 2 0.03
28 22 0.31
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.61
Consensus pattern (26 bp):
ATTATTTATTTTAAATTGTTTTACAT
Found at i:44042185 original size:16 final size:16
Alignment explanation
Indices: 44042164--44042214 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
44042154 ATCATGTTTA
44042164 AAATTAAGTAAAACTG
1 AAATTAAGTAAAACTG
**
44042180 AAATT-A--AAAACAA
1 AAATTAAGTAAAACTG
44042193 AAATTAAGTAAAACTG
1 AAATTAAGTAAAACTG
44042209 AAATTA
1 AAATTA
44042215 TAAAAAAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
13 10 0.36
14 1 0.04
15 1 0.04
16 16 0.57
ACGTcount: A:0.63, C:0.06, G:0.08, T:0.24
Consensus pattern (16 bp):
AAATTAAGTAAAACTG
Found at i:44042204 original size:29 final size:28
Alignment explanation
Indices: 44042163--44042223 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 28
44042153 AATCATGTTT
44042163 AAAATTAAGTAAAACTGAAATTAAAAACA
1 AAAATTAAGTAAAACTGAAATTAAAAA-A
*
44042192 AAAATTAAGTAAAACTGAAATTATAAAA
1 AAAATTAAGTAAAACTGAAATTAAAAAA
44042220 AAAA
1 AAAA
44042224 GAACGTCAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 5 0.16
29 26 0.84
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (28 bp):
AAAATTAAGTAAAACTGAAATTAAAAAA
Found at i:44043087 original size:19 final size:20
Alignment explanation
Indices: 44043041--44043087 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
44043031 ATCGAGTGGT
*
44043041 TAATTAGGCTTTAATTAAGTG
1 TAATTA-GCTTTAATTAAGAG
44043062 -AATTTAGC-TTAATTAAGAG
1 TAA-TTAGCTTTAATTAAGAG
44043081 TAATTAG
1 TAATTAG
44043088 GAAGAAAGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
19 14 0.61
20 6 0.26
21 3 0.13
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.40
Consensus pattern (20 bp):
TAATTAGCTTTAATTAAGAG
Found at i:44043430 original size:35 final size:30
Alignment explanation
Indices: 44043390--44043464 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 30
44043380 ATTGTGATAC
44043390 ATTTATTTAATTACATTTAATTTAAGTAAATAGAT
1 ATTTA-TTAATTACA-TT-A-TTAAGTAAA-AGAT
*
44043425 ATTTATT-ATT-TATTATTAAGTAAAAGAT
1 ATTTATTAATTACATTATTAAGTAAAAGAT
44043453 ATTTATTAATTA
1 ATTTATTAATTA
44043465 AATAATTATA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
28 11 0.30
29 12 0.32
30 1 0.03
31 2 0.05
32 1 0.03
33 3 0.08
34 2 0.05
35 5 0.14
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (30 bp):
ATTTATTAATTACATTATTAAGTAAAAGAT
Found at i:44044915 original size:18 final size:18
Alignment explanation
Indices: 44044893--44044989 Score: 86
Period size: 18 Copynumber: 5.4 Consensus size: 18
44044883 AACGACTGAC
*
44044893 TGTTACTGAATAATTGAT
1 TGTTACTGAATAAATGAT
* *
44044911 CGTTACTGAATAACTGAT
1 TGTTACTGAATAAATGAT
* **
44044929 TGCTACTGAGCAAATGAT
1 TGTTACTGAATAAATGAT
* *
44044947 TGTTACTGAATAACTAAT
1 TGTTACTGAATAAATGAT
* * * *
44044965 TGCTACTGAATGATTGAA
1 TGTTACTGAATAAATGAT
44044983 TGTTACT
1 TGTTACT
44044990 AAATGAAATT
Statistics
Matches: 61, Mismatches: 18, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 61 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (18 bp):
TGTTACTGAATAAATGAT
Found at i:44044918 original size:36 final size:36
Alignment explanation
Indices: 44044878--44044974 Score: 95
Period size: 36 Copynumber: 2.7 Consensus size: 36
44044868 TAAATAAAAA
* * * *
44044878 TACTGAACGACTGACTGTTACTGAATAATTGATCGT
1 TACTGAACAACTGACTGCTACTGAACAAATGATCGT
* * * *
44044914 TACTGAATAACTGATTGCTACTGAGCAAATGATTGT
1 TACTGAACAACTGACTGCTACTGAACAAATGATCGT
* * *
44044950 TACTGAATAACTAATTGCTACTGAA
1 TACTGAACAACTGACTGCTACTGAA
44044975 TGATTGAATG
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (36 bp):
TACTGAACAACTGACTGCTACTGAACAAATGATCGT
Found at i:44044987 original size:36 final size:36
Alignment explanation
Indices: 44044896--44044989 Score: 118
Period size: 36 Copynumber: 2.6 Consensus size: 36
44044886 GACTGACTGT
*
44044896 TACTGAATAATTG-ATCGTTACTGAATAACTGATTGC
1 TACTGAATAATTGAAT-GTTACTGAATAACTAATTGC
** * *
44044932 TACTGAGCAAATGATTGTTACTGAATAACTAATTGC
1 TACTGAATAATTGAATGTTACTGAATAACTAATTGC
*
44044968 TACTGAATGATTGAATGTTACT
1 TACTGAATAATTGAATGTTACT
44044990 AAATGAAATT
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
36 46 0.98
37 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (36 bp):
TACTGAATAATTGAATGTTACTGAATAACTAATTGC
Found at i:44048972 original size:24 final size:24
Alignment explanation
Indices: 44048928--44048973 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
44048918 TGAAACTTAG
*
44048928 ATAGATTACTCTGAAATACTATAA
1 ATAGATTACTCTGAAACACTATAA
*
44048952 ATAG-TTACTTTGAAAACACTAT
1 ATAGATTACTCTG-AAACACTAT
44048974 TAGTTAGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (24 bp):
ATAGATTACTCTGAAACACTATAA
Found at i:44061960 original size:28 final size:28
Alignment explanation
Indices: 44061928--44061997 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
44061918 AATGAGATTG
*
44061928 GCACTAAGTGTGCGAGTTTAATT-GTATA
1 GCACTAAGTGTGCGAGTTTAATTATTA-A
*
44061956 GCACTAAGTGTGCGAGTTTGATTATTAA
1 GCACTAAGTGTGCGAGTTTAATTATTAA
44061984 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
44061998 GACTTACTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 37 0.95
29 2 0.05
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAATTATTAA
Found at i:44065017 original size:32 final size:32
Alignment explanation
Indices: 44064981--44065046 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
44064971 AAGGTTTCGA
*
44064981 GTAGAAAAATTCATTTCTTTGGTTTAACAAGT
1 GTAGAAAAATTCATTTATTTGGTTTAACAAGT
44065013 GTAGAAAAATTCATTTATTTGGTTTAACAAGT
1 GTAGAAAAATTCATTTATTTGGTTTAACAAGT
44065045 GT
1 GT
44065047 TAACGAAGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.41
Consensus pattern (32 bp):
GTAGAAAAATTCATTTATTTGGTTTAACAAGT
Found at i:44066599 original size:29 final size:30
Alignment explanation
Indices: 44066534--44066614 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
44066524 GGGTGTTACA
* *
44066534 GCTTTTTCCCTTTTAAAAAAATGTCCCCAT
1 GCTTTTTCCTTTTTAACAAAATGTCCCCAT
*
44066564 GCTTTTTCCTTTTTGACAAAATGTCCCCAT
1 GCTTTTTCCTTTTTAACAAAATGTCCCCAT
*
44066594 GCTTTTTCCTTTTTTACAAAA
1 GCTTTTTCCTTTTTAACAAAA
44066615 AAAATGAAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.23, C:0.25, G:0.07, T:0.44
Consensus pattern (30 bp):
GCTTTTTCCTTTTTAACAAAATGTCCCCAT
Found at i:44067560 original size:17 final size:16
Alignment explanation
Indices: 44067538--44067580 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
44067528 TAATAAAAAT
44067538 ATAATTTTATTATTTAA
1 ATAATTTTATT-TTTAA
*
44067555 ATAATTTATATTTTTAT
1 ATAATTT-TATTTTTAA
44067572 A-AATTTTAT
1 ATAATTTTAT
44067581 AGGGTTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 3 0.12
16 5 0.21
17 12 0.50
18 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATAATTTTATTTTTAA
Found at i:44068104 original size:63 final size:63
Alignment explanation
Indices: 44068028--44068192 Score: 321
Period size: 63 Copynumber: 2.6 Consensus size: 63
44068018 GAAGGGTAAG
*
44068028 ACATATGCGTCACTTTGTTCTTTTCTTACAGCTCAATAAATTTCAGATTAATTAGCAGAATTC
1 ACATATGCATCACTTTGTTCTTTTCTTACAGCTCAATAAATTTCAGATTAATTAGCAGAATTC
44068091 ACATATGCATCACTTTGTTCTTTTCTTACAGCTCAATAAATTTCAGATTAATTAGCAGAATTC
1 ACATATGCATCACTTTGTTCTTTTCTTACAGCTCAATAAATTTCAGATTAATTAGCAGAATTC
44068154 ACATATGCATCACTTTGTTCTTTTCTTACAGCTCAATAA
1 ACATATGCATCACTTTGTTCTTTTCTTACAGCTCAATAA
44068193 TTTTGTCTTC
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 101 1.00
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (63 bp):
ACATATGCATCACTTTGTTCTTTTCTTACAGCTCAATAAATTTCAGATTAATTAGCAGAATTC
Found at i:44069936 original size:161 final size:162
Alignment explanation
Indices: 44069667--44069965 Score: 474
Period size: 161 Copynumber: 1.9 Consensus size: 162
44069657 TAACAACACA
* * *
44069667 CATTGGAAAGAGATATTTCAAATTATTGCAGCCTGTAACTTGTACTTCTCTTAGGCATTGAAAGC
1 CATTGGAAAGAGATATTTCAAATTATTACAGCCTGTAACTTGTACTTCTCTTAAGCACTGAAAGC
* * * *
44069732 TTATGTTTGATATTTGTGAGTCTTAGATTATTTCTTTCAATCCAAAGCACCTCTCTATCTTCAGG
66 TTATGATTGATATTTGAGAGTCTTAGATTATTTCTTCCAATCCAAAGCACCTCTCTATCTTCAGC
44069797 GTTTGTAATTGCCTAAGGTTATTAGAAGCAGG
131 GTTTGTAATTGCCTAAGGTTATTAGAAGCAGG
** *
44069829 CATTGGAAAGAGATATTTCAAATTATTACATTCTGTAACTTGTACTTC-CTTAAGCGCTGAAAGC
1 CATTGGAAAGAGATATTTCAAATTATTACAGCCTGTAACTTGTACTTCTCTTAAGCACTGAAAGC
* * *
44069893 TTATGATTGATATTTGAGGGTCTTAGATTATTTCTTCCAATCCAAAGCACTTCTCTATCTTTAGC
66 TTATGATTGATATTTGAGAGTCTTAGATTATTTCTTCCAATCCAAAGCACCTCTCTATCTTCAGC
44069958 GTTTGTAA
131 GTTTGTAA
44069966 ATTGGGCACA
Statistics
Matches: 124, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
161 79 0.64
162 45 0.36
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (162 bp):
CATTGGAAAGAGATATTTCAAATTATTACAGCCTGTAACTTGTACTTCTCTTAAGCACTGAAAGC
TTATGATTGATATTTGAGAGTCTTAGATTATTTCTTCCAATCCAAAGCACCTCTCTATCTTCAGC
GTTTGTAATTGCCTAAGGTTATTAGAAGCAGG
Found at i:44071453 original size:162 final size:162
Alignment explanation
Indices: 44071108--44071682 Score: 675
Period size: 162 Copynumber: 3.6 Consensus size: 162
44071098 TAGACATATG
** *
44071108 TATGGCACTTGTGGGTCTTGGATTACATCTTCCAATTGCGAGCAACTCTTTATTTTCAAAGTATG
1 TATGGCACTTGTGGGTCTTGGATTATGTCTTCCAATTGCGAGCAACTCTTTATCTTCAAAGTATG
* ** * * *
44071173 CAATTGCCCAAGGGTATTAGTAGCAGATAGTGG-AAGAGATATTTTAAATTATCACATTTTTCAA
66 CAATTGTCCAAGACTATTAGCAACAGATAGTGGAAAGAGATACTTTAAATTATCACATTTTTCAA
* * **
44071237 CTTTTATTTCCCTTAAACTTTGGAGGCTTATG
131 CTTTTACTTCCCATAAACTTTGGAGGCTTACA
* ** * * * * *
44071269 TATGACACTTGCAGGTCTTGGATTATGTTTTCCAATTGAGTGCAACTTTTTATCTTCTAAGTATG
1 TATGGCACTTGTGGGTCTTGGATTATGTCTTCCAATTGCGAGCAACTCTTTATCTTCAAAGTATG
* *
44071334 CAATTGTCTAAGACTATTAGCAACAGATAGTGGAAAGAGATACTTTAAGTTATCACATTTTTCAA
66 CAATTGTCCAAGACTATTAGCAACAGATAGTGGAAAGAGATACTTTAAATTATCACATTTTTCAA
44071399 CTTTTACTTCCCATAAACTTTGGAGGCTTACA
131 CTTTTACTTCCCATAAACTTTGGAGGCTTACA
* * *
44071431 TATGGCAGTTGTGGGCCTTGGATTATGTCTTCCAATTGCGAGCAACTCTTTATCTCCAAAGTATG
1 TATGGCACTTGTGGGTCTTGGATTATGTCTTCCAATTGCGAGCAACTCTTTATCTTCAAAGTATG
* * * ** * *
44071496 CAATTGTCCAAGACCATTATCAACAGAAAGACGAAAGAGATACTTTAACTTATCGCATTTTTCAA
66 CAATTGTCCAAGACTATTAGCAACAGATAGTGGAAAGAGATACTTTAAATTATCACATTTTTCAA
*** * * **
44071561 CTTTTACTTCTTTTAGACTTTGGAGTCTTATT
131 CTTTTACTTCCCATAAACTTTGGAGGCTTACA
* * * * * ** * *
44071593 TTTGGCACTTATGAGTCTTAGATTATTTCTTTTAATTGCGAGCAGCTCTTTATTTTCAAAGTATG
1 TATGGCACTTGTGGGTCTTGGATTATGTCTTCCAATTGCGAGCAACTCTTTATCTTCAAAGTATG
* * *
44071658 CAATTGCCCAAGGCTGTTAGCAACA
66 CAATTGTCCAAGACTATTAGCAACA
44071683 AACATATATT
Statistics
Matches: 347, Mismatches: 66, Indels: 1
0.84 0.16 0.00
Matches are distributed among these distances:
161 81 0.23
162 266 0.77
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (162 bp):
TATGGCACTTGTGGGTCTTGGATTATGTCTTCCAATTGCGAGCAACTCTTTATCTTCAAAGTATG
CAATTGTCCAAGACTATTAGCAACAGATAGTGGAAAGAGATACTTTAAATTATCACATTTTTCAA
CTTTTACTTCCCATAAACTTTGGAGGCTTACA
Found at i:44074030 original size:18 final size:18
Alignment explanation
Indices: 44073994--44074030 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
44073984 TGAGTTTTCG
* *
44073994 AATTCGAATAACTCGAAT
1 AATTCGAATAAATCAAAT
44074012 AATTCGAATAAATCAAAT
1 AATTCGAATAAATCAAAT
44074030 A
1 A
44074031 TCAAACTATA
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:0.51, C:0.14, G:0.08, T:0.27
Consensus pattern (18 bp):
AATTCGAATAAATCAAAT
Found at i:44074113 original size:30 final size:30
Alignment explanation
Indices: 44074079--44074170 Score: 123
Period size: 30 Copynumber: 3.0 Consensus size: 30
44074069 AAACCTTTTT
*
44074079 ACTTTTCCCTCAAAACTTTTACTTCTTCCC
1 ACTTTTCCCTCAAAACTTTTACTCCTTCCC
*
44074109 AC-TTTCCCTCCAAAACTTTCACTCCTTCCC
1 ACTTTTCCCT-CAAAACTTTTACTCCTTCCC
* *
44074139 ACTTTCCCCCCAAAACTTTTACTCCCTTCCC
1 ACTTTTCCCTCAAAACTTTTACT-CCTTCCC
44074170 A
1 A
44074171 TCCTAACCCG
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
29 7 0.13
30 34 0.63
31 13 0.24
ACGTcount: A:0.21, C:0.43, G:0.00, T:0.36
Consensus pattern (30 bp):
ACTTTTCCCTCAAAACTTTTACTCCTTCCC
Found at i:44075798 original size:31 final size:31
Alignment explanation
Indices: 44075763--44075838 Score: 102
Period size: 30 Copynumber: 2.5 Consensus size: 31
44075753 TTTAATATTT
44075763 TTATTTTATTATTTTTTAAA-AAGTAATAATA
1 TTATTTTATTATTTTTTAAACAA-TAATAATA
* *
44075794 TTATTATATTA-TTTTTAAACAATAATAATT
1 TTATTTTATTATTTTTTAAACAATAATAATA
*
44075824 TTATTTTATTGTTTT
1 TTATTTTATTATTTT
44075839 AATATTTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 24 0.62
31 15 0.38
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (31 bp):
TTATTTTATTATTTTTTAAACAATAATAATA
Found at i:44082687 original size:24 final size:24
Alignment explanation
Indices: 44082655--44082708 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
44082645 GTACCTGTTT
44082655 ATCTTCATATTCAAAATCACTTTC
1 ATCTTCATATTCAAAATCACTTTC
44082679 ATCTTCATATTCAAAATCACTTTC
1 ATCTTCATATTCAAAATCACTTTC
44082703 ATCTTC
1 ATCTTC
44082709 CTCTTTGGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.31, C:0.26, G:0.00, T:0.43
Consensus pattern (24 bp):
ATCTTCATATTCAAAATCACTTTC
Found at i:44083215 original size:24 final size:24
Alignment explanation
Indices: 44083181--44083271 Score: 101
Period size: 24 Copynumber: 3.5 Consensus size: 24
44083171 TGTACCTGTG
*
44083181 CTTTCACCTTCATATTCAAAATCA
1 CTTTCATCTTCATATTCAAAATCA
44083205 CTTTCATCTTCATATTCAAAATCA
1 CTTTCATCTTCATATTCAAAATCA
44083229 CTTCATCACTTTCATCTTCATATTCAAAATCA
1 CTT--TCA---TC---TTCATATTCAAAATCA
44083261 CTTTCATCTTC
1 CTTTCATCTTC
44083272 CTCTTTGGAT
Statistics
Matches: 58, Mismatches: 1, Indels: 16
0.77 0.01 0.21
Matches are distributed among these distances:
24 29 0.50
26 3 0.05
27 2 0.03
29 2 0.03
30 3 0.05
32 19 0.33
ACGTcount: A:0.30, C:0.29, G:0.00, T:0.42
Consensus pattern (24 bp):
CTTTCATCTTCATATTCAAAATCA
Found at i:44083242 original size:32 final size:32
Alignment explanation
Indices: 44083201--44083586 Score: 706
Period size: 32 Copynumber: 12.1 Consensus size: 32
44083191 CATATTCAAA
44083201 ATCACTTTCATCTTCATATTCAAAATCACTTC
1 ATCACTTTCATCTTCATATTCAAAATCACTTC
44083233 ATCACTTTCATCTTCATATTCAAAATCACTT-
1 ATCACTTTCATCTTCATATTCAAAATCACTTC
* *
44083264 -TCA-TCTTCCTCTTTGGATATTCAAAATCACTTC
1 ATCACT-TTCATC-TT-CATATTCAAAATCACTTC
44083297 ATCACTTTCATCTTCATATTCAAAATCACTTC
1 ATCACTTTCATCTTCATATTCAAAATCACTTC
44083329 ATCACTTTCATCTTCATATTCAAAATCACTTC
1 ATCACTTTCATCTTCATATTCAAAATCACTTC
44083361 ATCACTTTCATCTTCATATTCAAAATCACTTC
1 ATCACTTTCATCTTCATATTCAAAATCACTTC
44083393 ATCACTTTCATCTTCATATTCAAAATCACTTC
1 ATCACTTTCATCTTCATATTCAAAATCACTTC
44083425 ATCACTTTCATCTTCATATTCAAAATCACTTC
1 ATCACTTTCATCTTCATATTCAAAATCACTTC
44083457 ATCACTTTCATCTTCATATTCAAAATCACTTC
1 ATCACTTTCATCTTCATATTCAAAATCACTTC
44083489 ATCACTTTCATCTTCATATTCAAAATCACTTC
1 ATCACTTTCATCTTCATATTCAAAATCACTTC
44083521 ATCACTTTCATCTTCATATTCAAAATCACTTC
1 ATCACTTTCATCTTCATATTCAAAATCACTTC
44083553 ATCACTTTCATCTTCATATTCAAAATCACTTC
1 ATCACTTTCATCTTCATATTCAAAATCACTTC
44083585 AT
1 AT
44083587 TCTTCCTCTT
Statistics
Matches: 344, Mismatches: 4, Indels: 12
0.96 0.01 0.03
Matches are distributed among these distances:
29 1 0.00
30 8 0.02
31 2 0.01
32 322 0.94
33 2 0.01
34 8 0.02
35 1 0.00
ACGTcount: A:0.31, C:0.28, G:0.01, T:0.41
Consensus pattern (32 bp):
ATCACTTTCATCTTCATATTCAAAATCACTTC
Found at i:44085788 original size:162 final size:162
Alignment explanation
Indices: 44085594--44086262 Score: 1014
Period size: 162 Copynumber: 4.1 Consensus size: 162
44085584 GGGAACAGCT
* * * * *
44085594 CTCTATCTTTAGAATTTGCAATTGCTCAAGACTATTAGCAACACACATTGGGAAGAGATATTTCA
1 CTCTATCTTCAGAGTTTGCAATTTCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTTCA
* * * * **
44085659 AATTATTGCATTCCGTGACTTGTACTTCCCTTAGGCATTGGAATTTTATGGTTGATACTTGTGAG
66 AATTATTGCATTCTGTGACTTGTACTTCCCTAAGACATTGAAAGCTTATGGTTGATACTTGTGAG
* *
44085724 TGTTGGATTATTTCTTCAATTCTAAAGCACCA
131 TGTTGGATTATTTCTTCCATTCCAAAGCACCA
44085756 CTCTATCTTCAGAGTTTGCAATTTCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTTCA
1 CTCTATCTTCAGAGTTTGCAATTTCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTTCA
** * * * * *
44085821 AATTATTGCATTCAATGACTTGTACTTCCGTAAGGCATTGGAAGTTTGTGGTTGATACTTGTGAG
66 AATTATTGCATTCTGTGACTTGTACTTCCCTAAGACATTGAAAGCTTATGGTTGATACTTGTGAG
44085886 TGTTGGATTATTTCTTCCATTCCAAAGCACCA
131 TGTTGGATTATTTCTTCCATTCCAAAGCACCA
*
44085918 CTCTATCTTCAGAGTTTGCAATTTCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATATCA
1 CTCTATCTTCAGAGTTTGCAATTTCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTTCA
* * * * *
44085983 ATTTATAGCATTCTTTGACTTGTACTTTCCTAAGACATTGAAAGCTTACGGTTGATACTTGTGAG
66 AATTATTGCATTCTGTGACTTGTACTTCCCTAAGACATTGAAAGCTTATGGTTGATACTTGTGAG
*
44086048 TGTTGGATTATTTCTTCCATTCCAAAGCACCT
131 TGTTGGATTATTTCTTCCATTCCAAAGCACCA
*
44086080 CTCTATCTTTAGAGTTTGCAATTTCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTTCA
1 CTCTATCTTCAGAGTTTGCAATTTCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTTCA
* * * *
44086145 ATTTATTGCACTCTGTGACTTGTACTTCCCTTAGACATTGAAAGCTTATCGTTGATACTTGTGAG
66 AATTATTGCATTCTGTGACTTGTACTTCCCTAAGACATTGAAAGCTTATGGTTGATACTTGTGAG
* *
44086210 TCTTGGATTATTTCTTCCATTCCAAAGCACCT
131 TGTTGGATTATTTCTTCCATTCCAAAGCACCA
* *
44086242 CTCTATGTTCAAAGTTTGCAA
1 CTCTATCTTCAGAGTTTGCAA
44086263 ATTGGGCGCA
Statistics
Matches: 468, Mismatches: 39, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
162 468 1.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (162 bp):
CTCTATCTTCAGAGTTTGCAATTTCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTTCA
AATTATTGCATTCTGTGACTTGTACTTCCCTAAGACATTGAAAGCTTATGGTTGATACTTGTGAG
TGTTGGATTATTTCTTCCATTCCAAAGCACCA
Found at i:44095407 original size:148 final size:148
Alignment explanation
Indices: 44095210--44095496 Score: 468
Period size: 148 Copynumber: 1.9 Consensus size: 148
44095200 TTAACAACAC
* *
44095210 ACATTGGGAAGAGATATTTCAAATTATTGCAGCCTGTAACTTGTACTTCCCTTAGGCATTGAAAG
1 ACATTGGAAAGAGATATTTCAAATTATTGCAGCCTGTAACTTGTACTTCCCTTAAGCATTGAAAG
* *
44095275 CTTATGTTTGATACTTGAGA-GTCTTGGATTATTTCTTTCAATCCAAAGCACCTCTCTATCTTCA
66 CTTATGATTGATACTTGA-ATGTCTTGGATTATTTCTTCCAATCCAAAGCACCTCTCTATCTTCA
44095339 GAGTTTGTAATTGCCAAAG
130 GAGTTTGTAATTGCCAAAG
**
44095358 ACATTGGAAAGAGATATTTCAAATTATTGCATTCTGTAACTTGTACTTCCCTTAAGCATTGAAAG
1 ACATTGGAAAGAGATATTTCAAATTATTGCAGCCTGTAACTTGTACTTCCCTTAAGCATTGAAAG
* * *
44095423 TTTATGATTGATATTTGAATGTCTTGGATTATTTCTTCCAATCCAAAGCACCTCTCTATCTTTAG
66 CTTATGATTGATACTTGAATGTCTTGGATTATTTCTTCCAATCCAAAGCACCTCTCTATCTTCAG
*
44095488 CGTTTGTAA
131 AGTTTGTAA
44095497 ATTGAGCGCA
Statistics
Matches: 128, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
147 1 0.01
148 127 0.99
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.38
Consensus pattern (148 bp):
ACATTGGAAAGAGATATTTCAAATTATTGCAGCCTGTAACTTGTACTTCCCTTAAGCATTGAAAG
CTTATGATTGATACTTGAATGTCTTGGATTATTTCTTCCAATCCAAAGCACCTCTCTATCTTCAG
AGTTTGTAATTGCCAAAG
Found at i:44097037 original size:165 final size:162
Alignment explanation
Indices: 44096639--44097053 Score: 506
Period size: 162 Copynumber: 2.5 Consensus size: 162
44096629 ACTTTGGAGT
* * * ** * *
44096639 AGGCATATGTATGGCACTTGTAGGTCTTAGATTACATCTTCCAATTGCAAGCAACTCTTTATTTT
1 AGGCTTATATATGGCACTTGTAGGTCTTGGATTATGTCTTCCAATTGCGAGCAACTCTTTATCTT
* ** * * * * * * * *
44096704 CAAAGTATGCAATTGCCCAAGGGTATTAGTAGCAGATAGTGGGAAGAGATATTTTAATTTATCAC
66 CAAAGTATGCAATTGTCCAAGACTATTAGCAACAAACAGTGGAAAAAGATACTTTAAATTATCAC
* *
44096769 ATTTTTTAACCTTTACTTCCCTTAAACTTTGG
131 ATTTTTCAACCTTTACTTCCCATAAACTTTGG
* ** * * * *
44096801 AGGCTTATGTATGGCACTTGCGGGTCTTGGATTATGTTTTCTAATTGAGAGCAACTTTTTATCTT
1 AGGCTTATATATGGCACTTGTAGGTCTTGGATTATGTCTTCCAATTGCGAGCAACTCTTTATCTT
*
44096866 CAAAGTATGCAATTGTCCAAGACTATTTAGCAACAAACAGTGGAAAAAGATACTTTAAATTATCG
66 CAAAGTATGCAATTGTCCAAGACTA-TTAGCAACAAACAGTGGAAAAAGATACTTTAAATTATCA
*
44096931 CATTTTTCAACTTTTACTTCCCATAAACTTTGG
130 CATTTTTCAACCTTTACTTCCCATAAACTTTGG
*
44096964 AGGCTTACGTATATGGCACTTGTAGGCCTTGGATTATGTCTTCCAATTGCGAGCAACTCTTTATC
1 AGGCTTA--TATATGGCACTTGTAGGTCTTGGATTATGTCTTCCAATTGCGAGCAACTCTTTATC
** *
44097029 CCCAAAGTATGCAATTGTCTAAGAC
64 TTCAAAGTATGCAATTGTCCAAGAC
44097054 CAAAAAATCA
Statistics
Matches: 212, Mismatches: 38, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
162 75 0.35
163 67 0.32
165 70 0.33
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (162 bp):
AGGCTTATATATGGCACTTGTAGGTCTTGGATTATGTCTTCCAATTGCGAGCAACTCTTTATCTT
CAAAGTATGCAATTGTCCAAGACTATTAGCAACAAACAGTGGAAAAAGATACTTTAAATTATCAC
ATTTTTCAACCTTTACTTCCCATAAACTTTGG
Found at i:44098138 original size:26 final size:27
Alignment explanation
Indices: 44098090--44098151 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 27
44098080 AATATATATA
*
44098090 ATAATAATATAAAAAGTAGATAA-AAT
1 ATAATAATATAAAAAGTAAATAAGAAT
*
44098116 ATAATGATATAAAAA-TAAAATAAGAAT
1 ATAATAATATAAAAAGT-AAATAAGAAT
44098143 A-AAGTAATA
1 ATAA-TAATA
44098152 GGTAATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 1 0.03
26 21 0.70
27 8 0.27
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (27 bp):
ATAATAATATAAAAAGTAAATAAGAAT
Found at i:44099346 original size:13 final size:13
Alignment explanation
Indices: 44099330--44099355 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44099320 TTTATTTGGT
44099330 TTATTGGGTTTTG
1 TTATTGGGTTTTG
44099343 TTATTGGGTTTTG
1 TTATTGGGTTTTG
44099356 GGGGTGGCCC
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:0.08, C:0.00, G:0.31, T:0.62
Consensus pattern (13 bp):
TTATTGGGTTTTG
Found at i:44100288 original size:217 final size:201
Alignment explanation
Indices: 44100146--44100931 Score: 517
Period size: 216 Copynumber: 3.7 Consensus size: 201
44100136 ATTTGCCAAA
*
44100146 CAGATTTTGAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
1 CAGAATTTGAAAATACCTCGGC--GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
* * * * *
44100210 AATTAAAACACACAAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCACAACTCACCTCTAGCAA
64 AATTAAAA-A-AC-AAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAA
*
44100275 TATGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGAT
126 TATGAGTTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGAT
44100340 TTTTTTGAAAG
191 TTTTTTGAAAG
* * * **
44100351 TAGAATTTGAAAATACCTCGGCGTGCCCCGATGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 CAGAATTTGAAAATACCTCGGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATAA
* *
44100416 TTGAAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
66 TTAAAAAACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
* * * **
44100481 GTTGATTTTTG-AAAAGCAAAAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCT
131 GTTGA-TTTTGAAAAAG-TAGAAATT----A-A----AA-G-G---T-----TCAACCCACCTCT
* *
44100545 CGCAATATGAGTTGA--ATTTTGAAAA
175 CGCAATATGAGTTGATTTTTTTGAAAG
* * ** * ** ** *
44100570 CAGAAATTGAAACTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-AT
1 CAGAATTTGAAAATACCTCGGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATAA
** * * * * **
44100634 TTTGAAAACAGAAATTGAAACTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGA
66 TTAAAAAACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
* * * * **
44100699 GTTGAATTTTGAAAACAGAAATTGAAACTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGC
131 GTTG-ATTTTGAAAA-AG---TAGAAA-T---T-AA--------AAGGTTCAACCCACCTCTCGC
* *
44100764 AATATGAGTTGA--ATTTTGAAAA
178 AATATGAGTTGATTTTTTTGAAAG
* * ** * ** ** *
44100786 CAGAAATTGAAACTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-AT
1 CAGAATTTGAAAATACCTCGGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATAA
** * * * * **
44100850 TTTGAAAACAGAAATTGAAACTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGA
66 TTAAAAAACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
44100915 GTTGAATTTTTGAAAAA
131 GTTG-A-TTTTGAAAAA
44100932 CAAAAATTGA
Statistics
Matches: 496, Mismatches: 49, Indels: 61
0.82 0.08 0.10
Matches are distributed among these distances:
201 59 0.12
202 13 0.03
203 39 0.08
204 5 0.01
205 20 0.04
206 1 0.00
207 1 0.00
211 2 0.00
212 1 0.00
213 1 0.00
216 175 0.35
217 9 0.02
218 68 0.14
219 63 0.13
220 2 0.00
221 25 0.05
222 4 0.01
223 2 0.00
224 1 0.00
225 1 0.00
226 4 0.01
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (201 bp):
CAGAATTTGAAAATACCTCGGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATAA
TTAAAAAACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTTTTT
TGAAAG
Found at i:44100618 original size:72 final size:72
Alignment explanation
Indices: 44100321--44101088 Score: 1088
Period size: 72 Copynumber: 10.5 Consensus size: 72
44100311 TCAACCCACC
* ** * * ** * ** *
44100321 TCTCGCAATATGAGTTGATTTTTTTGAAAGTAGAATTTGAAAATACCTCGGCGTGCCCCGATGCT
1 TCTCGCAATATGAGTTGA--ATTTTGAAAACAGAAATTGAAACTACCTCAACGTGTCTTGAGGCT
**
44100386 CAACTCACC
64 CAACTCATT
* * * *
44100395 TCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTC
1 TCTCGCAATATGAGTTGAATTTTG-AAAACAGAAATTGAAACTACCTCAACGTGTCTTGAGGCTC
**
44100460 AACTCACC
65 AACTCATT
* * * *
44100468 TCTCGCAATATGAGTTGATTTTTGAAAAGCAAAAAATTGAAAATACCTCAATGTGTCTTGAGGCT
1 TCTCGCAATATGAGTTGAATTTTGAAAA-C-AGAAATTGAAACTACCTCAACGTGTCTTGAGGCT
44100533 CAACTCATT
64 CAACTCATT
44100542 TCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAACTACCTCAACGTGTCTTGAGGCTCA
1 TCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAACTACCTCAACGTGTCTTGAGGCTCA
44100607 ACTCATT
66 ACTCATT
44100614 TCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAACTACCTCAACGTGTCTTGAGGCTCA
1 TCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAACTACCTCAACGTGTCTTGAGGCTCA
44100679 ACTCATT
66 ACTCATT
44100686 TCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAACTACCTCAACGTGTCTTGAGGCTCA
1 TCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAACTACCTCAACGTGTCTTGAGGCTCA
44100751 ACTCATT
66 ACTCATT
44100758 TCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAACTACCTCAACGTGTCTTGAGGCTCA
1 TCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAACTACCTCAACGTGTCTTGAGGCTCA
44100823 ACTCATT
66 ACTCATT
44100830 TCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAACTACCTCAACGTGTCTTGAGGCTCA
1 TCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAACTACCTCAACGTGTCTTGAGGCTCA
44100895 ACTCATT
66 ACTCATT
* * * *
44100902 TCTCGCAATATGAGTTGAATTTTTGAAAAACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCT
1 TCTCGCAATATGAGTTGAA-TTTTG-AAAACAGAAATTGAAACTACCTCAACGTGTCTTGAGGCT
44100967 CAACTCATT
64 CAACTCATT
* * * * *
44100976 TCTCGCAATATGAGTTGATTTTTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAG
1 TCTCGCAATATGAGTTGA-----ATTTTGAAAACAGAAATTGAAACTACCTCAACGTGTCTTGAG
**
44101041 GCTCAACTCACC
61 GCTCAACTCATT
* *
44101053 TCTAGCAATATGAGTTG-ATTTTGAAAAACAAAAATT
1 TCTCGCAATATGAGTTGAATTTTG-AAAACAGAAATT
44101089 AAAAGGCTTA
Statistics
Matches: 651, Mismatches: 32, Indels: 24
0.92 0.05 0.03
Matches are distributed among these distances:
71 5 0.01
72 367 0.56
73 71 0.11
74 143 0.22
77 60 0.09
78 5 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (72 bp):
TCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAACTACCTCAACGTGTCTTGAGGCTCA
ACTCATT
Found at i:44114112 original size:13 final size:13
Alignment explanation
Indices: 44114096--44114121 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44114086 TTTATTTGGT
44114096 TTATTGGGTTTTG
1 TTATTGGGTTTTG
44114109 TTATTGGGTTTTG
1 TTATTGGGTTTTG
44114122 GGGGTGGCCC
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:0.08, C:0.00, G:0.31, T:0.62
Consensus pattern (13 bp):
TTATTGGGTTTTG
Found at i:44115669 original size:56 final size:57
Alignment explanation
Indices: 44115557--44115669 Score: 201
Period size: 56 Copynumber: 2.0 Consensus size: 57
44115547 TTCTAACGCT
*
44115557 GGGGAGAGTCTCTATTCGCTGGGAAAATGGGCAAAGACTTTGTTATCTTTTGGAAGG
1 GGGGAGACTCTCTATTCGCTGGGAAAATGGGCAAAGACTTTGTTATCTTTTGGAAGG
*
44115614 GGGGAGACTCTCTGTTCGCTGGGAAAAT-GGCAAAGACTTTGTTATCTTTTGGAAGG
1 GGGGAGACTCTCTATTCGCTGGGAAAATGGGCAAAGACTTTGTTATCTTTTGGAAGG
44115670 ACTTGTAAAG
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
56 28 0.52
57 26 0.48
ACGTcount: A:0.24, C:0.13, G:0.33, T:0.30
Consensus pattern (57 bp):
GGGGAGACTCTCTATTCGCTGGGAAAATGGGCAAAGACTTTGTTATCTTTTGGAAGG
Found at i:44116974 original size:27 final size:27
Alignment explanation
Indices: 44116936--44116990 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
44116926 TAGTAATACG
*
44116936 TAAATATAAACAAATGCGTGAGAAAAA
1 TAAACATAAACAAATGCGTGAGAAAAA
44116963 TAAACATAAACAAATGCGTGAGAAAAA
1 TAAACATAAACAAATGCGTGAGAAAAA
44116990 T
1 T
44116991 GAAATGATCG
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:0.58, C:0.09, G:0.15, T:0.18
Consensus pattern (27 bp):
TAAACATAAACAAATGCGTGAGAAAAA
Found at i:44117245 original size:12 final size:12
Alignment explanation
Indices: 44117126--44117266 Score: 61
Period size: 12 Copynumber: 11.3 Consensus size: 12
44117116 AATATTGATG
* *
44117126 ATAATAAAAATA
1 ATAATAATAGTA
*
44117138 ATAATAAGAGTA
1 ATAATAATAGTA
* * *
44117150 TTAATATTTGTA
1 ATAATAATAGTA
* *
44117162 TTAATAATAGTG
1 ATAATAATAGTA
*
44117174 ATAATAATAGAA
1 ATAATAATAGTA
*
44117186 AGTAATAA-AGGA
1 A-TAATAATAGTA
* *
44117198 ATGATATTAGTA
1 ATAATAATAGTA
* **
44117210 ATAGTAATAAAAA
1 ATAATAAT-AGTA
44117223 ATGAAAATAATAGTA
1 AT---AATAATAGTA
*
44117238 ATAATAATGGTAA
1 ATAATAATAGT-A
44117251 ATACA-AATAGTA
1 ATA-ATAATAGTA
44117263 ATAA
1 ATAA
44117267 CAAAATACAA
Statistics
Matches: 95, Mismatches: 26, Indels: 17
0.69 0.19 0.12
Matches are distributed among these distances:
11 5 0.05
12 61 0.64
13 19 0.20
14 1 0.01
15 4 0.04
16 5 0.05
ACGTcount: A:0.57, C:0.01, G:0.12, T:0.30
Consensus pattern (12 bp):
ATAATAATAGTA
Found at i:44117556 original size:25 final size:26
Alignment explanation
Indices: 44117528--44117580 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
44117518 ATGATGGTAA
44117528 TAAAGATAC-AATAATAATAATA-TAT
1 TAAAGA-ACAAATAATAATAATATTAT
*
44117553 TAAATAACAAATAATAATAATATTAT
1 TAAAGAACAAATAATAATAATATTAT
44117579 TA
1 TA
44117581 TTAAATATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 2 0.08
25 18 0.72
26 5 0.20
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (26 bp):
TAAAGAACAAATAATAATAATATTAT
Found at i:44117607 original size:20 final size:20
Alignment explanation
Indices: 44117582--44117625 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
44117572 ATATTATTAT
44117582 TAAATATTAAATTAAAATAA
1 TAAATATTAAATTAAAATAA
44117602 TAAATATTAAATTAAAATAA
1 TAAATATTAAATTAAAATAA
44117622 TAAA
1 TAAA
44117626 AATCACTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAATATTAAATTAAAATAA
Found at i:44117636 original size:28 final size:28
Alignment explanation
Indices: 44117605--44117699 Score: 66
Period size: 28 Copynumber: 3.1 Consensus size: 28
44117595 AAAATAATAA
44117605 ATATTAAATTAAAATAATAAAAATCACT
1 ATATTAAATTAAAATAATAAAAATCACT
** * * *
44117633 ATA-TATTTTAATAATATGAAAAGCAAATATATT
1 ATATTAAATTAA-AATA--ATAA--AAAT-CACT
44117666 AAATATTAAATTAAAATAATAAAAATCACT
1 --ATATTAAATTAAAATAATAAAAATCACT
44117696 ATAT
1 ATAT
44117700 ATATATCTAT
Statistics
Matches: 48, Mismatches: 10, Indels: 18
0.63 0.13 0.24
Matches are distributed among these distances:
27 6 0.12
28 11 0.23
30 5 0.10
31 4 0.08
32 4 0.08
33 5 0.10
35 7 0.15
36 6 0.12
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (28 bp):
ATATTAAATTAAAATAATAAAAATCACT
Found at i:44117979 original size:22 final size:22
Alignment explanation
Indices: 44117952--44117994 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
44117942 ATACTAAGGC
*
44117952 TAATAAATAAT-AAGTATAATAA
1 TAAT-AATAATGAAATATAATAA
44117974 TAATAATAATGAAATATAATA
1 TAATAATAATGAAATATAATA
44117995 GTATGTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (22 bp):
TAATAATAATGAAATATAATAA
Found at i:44118083 original size:19 final size:19
Alignment explanation
Indices: 44118056--44118092 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
44118046 GACGAAAATA
*
44118056 AAAAGGGAAACGAATTTTC
1 AAAACGGAAACGAATTTTC
44118075 AAAACGGAAACGAATTTT
1 AAAACGGAAACGAATTTT
44118093 GGGACAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.11, G:0.19, T:0.22
Consensus pattern (19 bp):
AAAACGGAAACGAATTTTC
Found at i:44120199 original size:13 final size:13
Alignment explanation
Indices: 44120141--44120206 Score: 62
Period size: 13 Copynumber: 5.1 Consensus size: 13
44120131 CTTAAACCAA
*
44120141 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
* *
44120154 ACTTCTCAAAAAC
1 ACTTTTCAAAAGC
*
44120167 ACTTTTCCACAA-C
1 ACTTTT-CAAAAGC
* *
44120180 ACCTTTCAAAAGT
1 ACTTTTCAAAAGC
44120193 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
44120206 A
1 A
44120207 TTGTTAAACT
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
12 4 0.10
13 33 0.80
14 4 0.10
ACGTcount: A:0.39, C:0.26, G:0.05, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:44122093 original size:40 final size:41
Alignment explanation
Indices: 44122046--44122125 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
44122036 GTAACGGTTT
44122046 GGCCTTAGCCCATC-TCAGTA-CAGTATCAAATATGCAGTAG
1 GGCCTTAGCCCATCAT-AGTATCAGTATCAAATATGCAGTAG
*
44122086 GGCCTTAGCCTATCATAGTATCAGTATCAAATATGCAGTA
1 GGCCTTAGCCCATCATAGTATCAGTATCAAATATGCAGTA
44122126 TTCAGTAACA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
40 17 0.46
41 20 0.54
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (41 bp):
GGCCTTAGCCCATCATAGTATCAGTATCAAATATGCAGTAG
Found at i:44122421 original size:18 final size:17
Alignment explanation
Indices: 44122378--44122423 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 17
44122368 CACAGGTTTA
44122378 TCAGATACATATATAGT
1 TCAGATACATATATAGT
44122395 TCAAGATACATATATAGT
1 TC-AGATACATATATAGT
44122413 TCAGTATACAT
1 TCAG-ATACAT
44122424 GCTTATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.15
18 23 0.85
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (17 bp):
TCAGATACATATATAGT
Found at i:44130800 original size:20 final size:20
Alignment explanation
Indices: 44130775--44130814 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
44130765 TTTCTGCATT
*
44130775 TTAATATTTACATTAATATA
1 TTAATATTAACATTAATATA
*
44130795 TTAATATTAATATTAATATA
1 TTAATATTAACATTAATATA
44130815 AAAACATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAATATTAACATTAATATA
Found at i:44134547 original size:26 final size:26
Alignment explanation
Indices: 44134518--44134575 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
44134508 CATGAAATTC
44134518 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
44134544 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
44134570 TTATCA
1 TTATCA
44134576 ATTTGTATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:44135505 original size:15 final size:15
Alignment explanation
Indices: 44135485--44135542 Score: 71
Period size: 15 Copynumber: 3.7 Consensus size: 15
44135475 CATTAAACTA
*
44135485 ATTTTAAAATTATGC
1 ATTTTAATATTATGC
**
44135500 ATTTTAATATTAAAC
1 ATTTTAATATTATGC
44135515 TAATTTTAATATTATGC
1 --ATTTTAATATTATGC
44135532 ATTTTAATATT
1 ATTTTAATATT
44135543 TTAAAATTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 23 0.64
17 13 0.36
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (15 bp):
ATTTTAATATTATGC
Found at i:44135513 original size:32 final size:32
Alignment explanation
Indices: 44135476--44135614 Score: 134
Period size: 32 Copynumber: 4.1 Consensus size: 32
44135466 TTTTATGTAC
44135476 ATTAAACTAATTTTAAAATTATGCATTTTAAT
1 ATTAAACTAATTTTAAAATTATGCATTTTAAT
*
44135508 ATTAAACTAATTTTAATATTATGCATTTTAAT
1 ATTAAACTAATTTTAAAATTATGCATTTTAAT
* * * * ** *
44135540 ATTTTAAAATTATGCATGTGACAATTAAACTAATTTTAAA
1 A--TT-AAACTA---ATTTTAAAATTATGC--ATTTTAAT
44135580 ATTAAACTAATTTTAAAATTATGCATTTTAAT
1 ATTAAACTAATTTTAAAATTATGCATTTTAAT
44135612 ATT
1 ATT
44135615 TATATTAATA
Statistics
Matches: 83, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
32 42 0.51
34 12 0.14
35 5 0.06
37 5 0.06
38 11 0.13
40 8 0.10
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.46
Consensus pattern (32 bp):
ATTAAACTAATTTTAAAATTATGCATTTTAAT
Found at i:44135522 original size:17 final size:17
Alignment explanation
Indices: 44135476--44135528 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
44135466 TTTTATGTAC
*
44135476 ATTAAACTAATTTTAAA
1 ATTAAACTAATTTTAAT
**
44135493 ATTATGC--ATTTTAAT
1 ATTAAACTAATTTTAAT
44135508 ATTAAACTAATTTTAAT
1 ATTAAACTAATTTTAAT
44135525 ATTA
1 ATTA
44135529 TGCATTTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
15 12 0.41
17 17 0.59
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (17 bp):
ATTAAACTAATTTTAAT
Found at i:44135548 original size:55 final size:49
Alignment explanation
Indices: 44135476--44135614 Score: 163
Period size: 55 Copynumber: 2.7 Consensus size: 49
44135466 TTTTATGTAC
*
44135476 ATTAAACTAATTTTAAAATTATGCATTTTAATATTAAACTAATTTTAAT
1 ATTAAACTAATTTTAAAATTATGCATTTTAATATTAAACTAATTTTAAA
** * *
44135525 ATTATGCATTTTAATATTTTAAAATTATGCATGTGACA-ATTAAACTAATTTTAAA
1 ATTA---A-ACT-A-ATTTTAAAATTATGCATTTTA-ATATTAAACTAATTTTAAA
44135580 ATTAAACTAATTTTAAAATTATGCATTTTAATATT
1 ATTAAACTAATTTTAAAATTATGCATTTTAATATT
44135615 TATATTAATA
Statistics
Matches: 73, Mismatches: 9, Indels: 16
0.74 0.09 0.16
Matches are distributed among these distances:
48 1 0.01
49 26 0.36
50 1 0.01
51 1 0.01
52 2 0.03
53 1 0.01
54 1 0.01
55 39 0.53
56 1 0.01
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.46
Consensus pattern (49 bp):
ATTAAACTAATTTTAAAATTATGCATTTTAATATTAAACTAATTTTAAA
Found at i:44135584 original size:17 final size:17
Alignment explanation
Indices: 44135562--44135600 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
44135552 TGCATGTGAC
44135562 AATTAAACTAATTTTAA
1 AATTAAACTAATTTTAA
44135579 AATTAAACTAATTTTAA
1 AATTAAACTAATTTTAA
44135596 AATTA
1 AATTA
44135601 TGCATTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTAAACTAATTTTAA
Found at i:44135633 original size:14 final size:13
Alignment explanation
Indices: 44135607--44135640 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
44135597 ATTATGCATT
44135607 TTAATAT-TTATA
1 TTAATATATTATA
44135619 TTAATATATTAATA
1 TTAATATATT-ATA
44135633 TTAATATA
1 TTAATATA
44135641 AAAACATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 7 0.35
13 2 0.10
14 11 0.55
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTAATATATTATA
Found at i:44136318 original size:27 final size:27
Alignment explanation
Indices: 44136261--44136318 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
44136251 TTAGAAAATC
* * *
44136261 ATAAAAATACATAAATTTAAAAATTAA
1 ATAAAAATACAAAAAATTAAAAAATAA
* *
44136288 ATAAAAATAGAAAAAATTAAAAAATAG
1 ATAAAAATACAAAAAATTAAAAAATAA
44136315 ATAA
1 ATAA
44136319 GTAAGAGAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.24
Consensus pattern (27 bp):
ATAAAAATACAAAAAATTAAAAAATAA
Found at i:44138033 original size:25 final size:23
Alignment explanation
Indices: 44138000--44138051 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
44137990 AGAAACAAAA
* * *
44138000 TTTTTATATTTACGTTCTGTGATG
1 TTTTTATATTAACATTAT-TGATG
44138024 TTTTTCATATTAACATTATTGATG
1 TTTTT-ATATTAACATTATTGATG
44138048 TTTT
1 TTTT
44138052 GAAATTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.21, C:0.08, G:0.12, T:0.60
Consensus pattern (23 bp):
TTTTTATATTAACATTATTGATG
Found at i:44146467 original size:35 final size:35
Alignment explanation
Indices: 44146426--44146495 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
44146416 TTTTCCTTAT
** *
44146426 TCATTTTTATACATTTAAATTGAATTTTCTGTTTA
1 TCATTTTTATACATTTAAAGAGAATTTTCTATTTA
44146461 TCATTTTTATACATTTAAAGAGAATTTTCTATTTA
1 TCATTTTTATACATTTAAAGAGAATTTTCTATTTA
44146496 AAATAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.54
Consensus pattern (35 bp):
TCATTTTTATACATTTAAAGAGAATTTTCTATTTA
Found at i:44159176 original size:12 final size:12
Alignment explanation
Indices: 44159156--44159216 Score: 61
Period size: 12 Copynumber: 5.1 Consensus size: 12
44159146 TATTTTACAG
*
44159156 CTTGATGTACCT
1 CTTGTTGTACCT
*
44159168 CTTGTTGTACAT
1 CTTGTTGTACCT
* *
44159180 CCTATTGTACC-
1 CTTGTTGTACCT
*
44159191 CTTTATTGTACCT
1 C-TTGTTGTACCT
44159204 CTTGTTGTACCT
1 CTTGTTGTACCT
44159216 C
1 C
44159217 CTTTGATACA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
11 1 0.03
12 38 0.95
13 1 0.03
ACGTcount: A:0.15, C:0.26, G:0.13, T:0.46
Consensus pattern (12 bp):
CTTGTTGTACCT
Done.