Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold11
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: 5230303
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 140504 characters in sequence are not A, C, G, or T
File 15 of 29
Found at i:2008321 original size:28 final size:27
Alignment explanation
Indices: 2008290--2008370 Score: 67
Period size: 28 Copynumber: 2.9 Consensus size: 27
2008280 GGTATATTTT
2008290 TATTAATTAATTATAATTATATTTAAAA
1 TATTAATTAATTATAATTATATTT-AAA
* * *
2008318 TATTATTTATTTATATATTAACATTT-AA
1 TATTAATTAATTATA-ATT-ATATTTAAA
* *
2008346 TATTATATAAATTTTAA-TATATTTA
1 TATTA-ATTAATTATAATTATATTTA
2008371 TTTTTTATTA
Statistics
Matches: 41, Mismatches: 8, Indels: 9
0.71 0.14 0.16
Matches are distributed among these distances:
26 5 0.12
27 1 0.02
28 21 0.51
29 9 0.22
30 5 0.12
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (27 bp):
TATTAATTAATTATAATTATATTTAAA
Found at i:2008385 original size:18 final size:18
Alignment explanation
Indices: 2008357--2008412 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
2008347 ATTATATAAA
*
2008357 TTTTAATATATTTATT-T
1 TTTTTATATATTTATTAT
2008374 TTTATTATATATTTTTATTAT
1 TTT-TTATATA--TTTATTAT
*
2008395 TTTTTATATATTTTTTAT
1 TTTTTATATATTTATTAT
2008413 ATTTATATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
17 3 0.09
18 13 0.39
20 13 0.39
21 4 0.12
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTATATATTTATTAT
Found at i:2008385 original size:20 final size:20
Alignment explanation
Indices: 2008362--2008425 Score: 76
Period size: 20 Copynumber: 3.1 Consensus size: 20
2008352 ATAAATTTTA
*
2008362 ATATATTTATTTTTTATTAT
1 ATATTTTTATTTTTTATTAT
2008382 ATATTTTTATTATTTT-TTAT
1 ATATTTTTATT-TTTTATTAT
*
2008402 ATATTTTTTATATTTATATTAT
1 ATA-TTTTTAT-TTTTTATTAT
2008424 AT
1 AT
2008426 CATCAAACCA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
20 17 0.45
21 14 0.37
22 7 0.18
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
ATATTTTTATTTTTTATTAT
Found at i:2008394 original size:16 final size:15
Alignment explanation
Indices: 2008316--2008425 Score: 51
Period size: 14 Copynumber: 7.7 Consensus size: 15
2008306 TTATATTTAA
*
2008316 AATATTATTTA-TTT
1 AATATTATATATTTT
*
2008330 ATATATTA-ACA-TTT
1 A-ATATTATATATTTT
2008344 AATATTATATAAATTTT
1 AATATTATAT--ATTTT
*
2008361 AATA-TATTTATTTT
1 AATATTATATATTTT
*
2008375 -TTATTATATATTTT
1 AATATTATATATTTT
2008389 --TATTAT-T-TTTT
1 AATATTATATATTTT
* *
2008400 ATATATTTTTTATATTT
1 A-ATATTATATAT-TTT
2008417 -ATATTATAT
1 AATATTATAT
2008426 CATCAAACCA
Statistics
Matches: 75, Mismatches: 9, Indels: 23
0.70 0.08 0.21
Matches are distributed among these distances:
11 4 0.05
12 1 0.01
13 14 0.19
14 26 0.35
15 14 0.19
16 6 0.08
17 10 0.13
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (15 bp):
AATATTATATATTTT
Found at i:2008406 original size:11 final size:11
Alignment explanation
Indices: 2008369--2008414 Score: 67
Period size: 11 Copynumber: 4.1 Consensus size: 11
2008359 TTAATATATT
2008369 TATTTTTTATTA
1 TATTTTTTA-TA
2008381 TATATTTTTAT-
1 TAT-TTTTTATA
2008392 TATTTTTTATA
1 TATTTTTTATA
2008403 TATTTTTTATA
1 TATTTTTTATA
2008414 T
1 T
2008415 TTATATTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 7 0.22
11 15 0.47
12 4 0.12
13 6 0.19
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TATTTTTTATA
Found at i:2008423 original size:11 final size:11
Alignment explanation
Indices: 2008368--2008425 Score: 54
Period size: 9 Copynumber: 5.5 Consensus size: 11
2008358 TTTAATATAT
2008368 TTAT-TTTTTA
1 TTATATTTTTA
2008378 TTATATATTTTTA
1 -T-TATATTTTTA
2008391 TTAT-TTTTTA
1 TTATATTTTTA
2008401 -TATA-TTTT-
1 TTATATTTTTA
*
2008409 TTATATTTATA
1 TTATATTTTTA
2008420 TTATAT
1 TTATAT
2008426 CATCAAACCA
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
9 11 0.28
10 9 0.22
11 10 0.25
12 4 0.10
13 6 0.15
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATATTTTTA
Found at i:2008711 original size:20 final size:23
Alignment explanation
Indices: 2008686--2008733 Score: 75
Period size: 20 Copynumber: 2.2 Consensus size: 23
2008676 TAATAATAAA
2008686 TAATATTTTAA-TA-TTTTCTT-
1 TAATATTTTAATTATTTTTCTTG
2008706 TAATATTTTAATTATTTTTCTTG
1 TAATATTTTAATTATTTTTCTTG
2008729 TAATA
1 TAATA
2008734 AAACTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.44
21 2 0.08
22 7 0.28
23 5 0.20
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (23 bp):
TAATATTTTAATTATTTTTCTTG
Found at i:2009545 original size:6 final size:6
Alignment explanation
Indices: 2009507--2009552 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
2009497 TTTTTTAATT
* *
2009507 ATATAA ATATAT ATAT-A ATATAA ATTTTAA ATATAA ATA-AA ATATA
1 ATATAA ATATAA ATATAA ATATAA A-TATAA ATATAA ATATAA ATATA
2009553 TGTATTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
5 9 0.27
6 19 0.58
7 5 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (6 bp):
ATATAA
Found at i:2009560 original size:24 final size:24
Alignment explanation
Indices: 2009510--2009562 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2009500 TTTAATTATA
* * *
2009510 TAAATATATATATAATATAAATTT
1 TAAATATAAATAAAATATAAATAT
**
2009534 TAAATATAAATAAAATATATGTAT
1 TAAATATAAATAAAATATAAATAT
2009558 TAAAT
1 TAAAT
2009563 GCATCATATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (24 bp):
TAAATATAAATAAAATATAAATAT
Found at i:2010290 original size:15 final size:16
Alignment explanation
Indices: 2010270--2010299 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2010260 ATTAAATTAA
2010270 ATAAAT-AATTTAATT
1 ATAAATAAATTTAATT
2010285 ATAAATAAATTTAAT
1 ATAAATAAATTTAAT
2010300 GCAAAATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATAAATAAATTTAATT
Found at i:2011349 original size:15 final size:15
Alignment explanation
Indices: 2011331--2011375 Score: 90
Period size: 15 Copynumber: 3.0 Consensus size: 15
2011321 ATAATTTCAT
2011331 ATAAAAATAAAAATA
1 ATAAAAATAAAAATA
2011346 ATAAAAATAAAAATA
1 ATAAAAATAAAAATA
2011361 ATAAAAATAAAAATA
1 ATAAAAATAAAAATA
2011376 TAATATTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (15 bp):
ATAAAAATAAAAATA
Found at i:2011350 original size:9 final size:9
Alignment explanation
Indices: 2011336--2011380 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
2011326 TTCATATAAA
2011336 AATAAAAAT
1 AATAAAAAT
2011345 AAT--AAA-
1 AATAAAAAT
2011351 AATAAAAAT
1 AATAAAAAT
2011360 AATAAAAAT
1 AATAAAAAT
*
2011369 AA-AAATAT
1 AATAAAAAT
2011377 AATA
1 AATA
2011381 TTTATTTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
6 3 0.10
7 3 0.10
8 10 0.32
9 15 0.48
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
AATAAAAAT
Found at i:2011355 original size:21 final size:21
Alignment explanation
Indices: 2011331--2011375 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 21
2011321 ATAATTTCAT
2011331 ATAAAAATAAAAATAATAAAA
1 ATAAAAATAAAAATAATAAAA
2011352 ATAAAAATAATAAA-AATAAAA
1 ATAAAAATAA-AAATAATAAAA
2011373 ATA
1 ATA
2011376 TAATATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (21 bp):
ATAAAAATAAAAATAATAAAA
Found at i:2011441 original size:37 final size:33
Alignment explanation
Indices: 2011369--2011430 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 33
2011359 TAATAAAAAT
2011369 AAAAATATAATATTTATTTAATATAAATTATTA
1 AAAAATATAATATTTATTTAATATAAATTATTA
2011402 AAATAATATAATA-TT-TTTAATAT-AATTAT
1 AAA-AATATAATATTTATTTAATATAAATTAT
2011431 CATATATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 6 0.21
32 8 0.29
33 5 0.18
34 9 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (33 bp):
AAAAATATAATATTTATTTAATATAAATTATTA
Found at i:2011816 original size:20 final size:20
Alignment explanation
Indices: 2011791--2011829 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2011781 ATTTTAATAT
*
2011791 TAAATAAATATTAAATATAG
1 TAAATAAATAATAAATATAG
*
2011811 TAAATAATTAATAAATATA
1 TAAATAAATAATAAATATA
2011830 TGTTTTACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
TAAATAAATAATAAATATAG
Found at i:2011878 original size:15 final size:14
Alignment explanation
Indices: 2011858--2011900 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
2011848 GACCTTCAAC
2011858 TTAAAATTAAAATAT
1 TTAAAATTAAAA-AT
*
2011873 TTAAAATTTAAAAT
1 TTAAAATTAAAAAT
*
2011887 TTATTAATTAAAAA
1 TTA-AAATTAAAAA
2011901 AATAAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 5 0.21
15 19 0.79
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTAAAATTAAAAAT
Found at i:2012285 original size:23 final size:23
Alignment explanation
Indices: 2012258--2012305 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
2012248 TTTTTAAAAA
*
2012258 TATTAAAGACATTTA-AATATTAG
1 TATTAAA-AAATTTATAATATTAG
*
2012281 TATTAAAAAATTTATAATTTTAG
1 TATTAAAAAATTTATAATATTAG
2012304 TA
1 TA
2012306 ACTAAAGCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (23 bp):
TATTAAAAAATTTATAATATTAG
Found at i:2012816 original size:3 final size:3
Alignment explanation
Indices: 2012808--2012833 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2012798 GTGATGGTTC
2012808 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
2012834 GTGAAGTTCA
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:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2013587 original size:17 final size:17
Alignment explanation
Indices: 2013565--2013604 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
2013555 AAAATTGGTA
2013565 ATATTAAATATAAATAT
1 ATATTAAATATAAATAT
*
2013582 ATATTACATATAAATAT
1 ATATTAAATATAAATAT
2013599 AT-TTAA
1 ATATTAA
2013605 TTTTTTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATTAAATATAAATAT
Found at i:2019799 original size:15 final size:15
Alignment explanation
Indices: 2019779--2019897 Score: 66
Period size: 15 Copynumber: 7.6 Consensus size: 15
2019769 AATTAAATAA
2019779 TTAAATAATTTAATT
1 TTAAATAATTTAATT
2019794 TT--A-AA-TTAATTT
1 TTAAATAATTTAA-TT
2019806 TTAAATCAAGTATTACAAATT
1 TTAAAT-AA-T-TT--AA-TT
2019827 TTAAATAATTTAATT
1 TTAAATAATTTAATT
* * * *
2019842 TGAATTAGTTTTTAAAT
1 TTAAATA--ATTTAATT
2019859 TTAAATAATTTAATT
1 TTAAATAATTTAATT
* *
2019874 TTAAATTATTTAAAT
1 TTAAATAATTTAATT
*
2019889 TTGAATAAT
1 TTAAATAAT
2019898 ATGATTTTTA
Statistics
Matches: 79, Mismatches: 13, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
11 4 0.05
12 6 0.08
13 1 0.01
14 1 0.01
15 35 0.44
16 4 0.05
17 11 0.14
18 2 0.03
19 3 0.04
20 2 0.03
21 10 0.13
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (15 bp):
TTAAATAATTTAATT
Found at i:2019874 original size:47 final size:46
Alignment explanation
Indices: 2019779--2019894 Score: 126
Period size: 47 Copynumber: 2.4 Consensus size: 46
2019769 AATTAAATAA
* *
2019779 TTAAATAATTTAATTTTAAATTAATTTTTAAATCAAGTATTACAAATT
1 TTAAATAATTTAA-TTTGAATTAATTTTTAAATCAAATATTA-AAATT
* * *
2019827 TTAAATAATTTAATTTGAATTAGTTTTTAAATTTAAATAATT-TAATT
1 TTAAATAATTTAATTTGAATTAATTTTTAAA-TCAAAT-ATTAAAATT
*
2019874 TTAAATTATTTAAATTTGAAT
1 TTAAATAATTT-AATTTGAAT
2019895 AATATGATTT
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
47 30 0.51
48 26 0.44
49 3 0.05
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (46 bp):
TTAAATAATTTAATTTGAATTAATTTTTAAATCAAATATTAAAATT
Found at i:2019888 original size:30 final size:30
Alignment explanation
Indices: 2019826--2019916 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
2019816 TATTACAAAT
*
2019826 TTTAAATAATTTAA-TTTGAATTAGTTTTTAAA
1 TTTAAATAATTTAATTTTAAATTA---TTTAAA
2019858 TTTAAATAATTTAATTTTAAATTATTTAAA
1 TTTAAATAATTTAATTTTAAATTATTTAAA
* * * * *
2019888 TTTGAATAATATGATTTTTAATTTTTTAA
1 TTTAAATAATTTAATTTTAAATTATTTAA
2019917 TTATTTTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
30 30 0.58
32 14 0.27
33 8 0.15
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (30 bp):
TTTAAATAATTTAATTTTAAATTATTTAAA
Found at i:2021004 original size:30 final size:30
Alignment explanation
Indices: 2020954--2021015 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
2020944 AAAATATATA
2020954 AAAATAATATTAAAATTAATTCA-AAATAC
1 AAAATAATATTAAAATTAATTCATAAATAC
* * *
2020983 AAAATAATGTTTAATATTAATTTATAAATAC
1 AAAATAAT-ATTAAAATTAATTCATAAATAC
2021014 AA
1 AA
2021016 TTTATTTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 8 0.29
30 12 0.43
31 8 0.29
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (30 bp):
AAAATAATATTAAAATTAATTCATAAATAC
Found at i:2031931 original size:34 final size:34
Alignment explanation
Indices: 2031876--2032092 Score: 276
Period size: 34 Copynumber: 6.4 Consensus size: 34
2031866 ACAGTAATAA
*
2031876 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * * *
2031909 TATTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* *
2031943 TGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* **
2031977 TGTTGATTAAATGAGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* *
2032011 TATTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * *
2032045 TGTTGACTAAAT-GGTAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGT-GATTTGGTAGCTTACCAT
2032079 TGTTGATTAAATGG
1 TGTTGATTAAATGG
2032093 TGGTTTTTAC
Statistics
Matches: 158, Mismatches: 23, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
33 14 0.09
34 143 0.91
35 1 0.01
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
Found at i:2032068 original size:102 final size:101
Alignment explanation
Indices: 2031876--2032092 Score: 353
Period size: 102 Copynumber: 2.1 Consensus size: 101
2031866 ACAGTAATAA
** * * *
2031876 TGTTGATTAAATGGTGATTTGGTAGTTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTACC
2031941 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
66 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
2031977 TGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
1 TGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
* * *
2032042 CATTGTTGACTAAATGGTAGATTTGGTAGGTTGCCAT
65 CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
2032079 TGTTGATTAAATGG
1 TGTTGATTAAATGG
2032093 TGGTTTTTAC
Statistics
Matches: 107, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
101 14 0.13
102 93 0.87
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
TGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTACC
ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:2032454 original size:19 final size:19
Alignment explanation
Indices: 2032398--2032460 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
2032388 TGGTTGTCGA
**
2032398 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
2032417 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
2032436 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
2032455 GTTACT
1 GGTACT
2032461 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:2036583 original size:34 final size:34
Alignment explanation
Indices: 2036526--2036744 Score: 280
Period size: 34 Copynumber: 6.5 Consensus size: 34
2036516 AAGTGGGAGA
*
2036526 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * * *
2036559 ATTATTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
2036593 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
2036627 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
2036661 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
2036695 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
2036729 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2036745 TGGTTTTTAC
Statistics
Matches: 160, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
33 16 0.10
34 143 0.89
35 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:2036666 original size:102 final size:101
Alignment explanation
Indices: 2036526--2036744 Score: 357
Period size: 102 Copynumber: 2.2 Consensus size: 101
2036516 AAGTGGGAGA
** * * *
2036526 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
2036591 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
2036627 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
* * *
2036692 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
2036729 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2036745 TGGTTTTTAC
Statistics
Matches: 109, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
101 16 0.15
102 93 0.85
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:2041987 original size:2 final size:2
Alignment explanation
Indices: 2041980--2042006 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2041970 GAAGATCAAC
2041980 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
2042007 CGGGACTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2042399 original size:3 final size:3
Alignment explanation
Indices: 2042393--2042418 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2042383 TTATCTTATT
2042393 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
2042419 CACTTATATT
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):
ATA
Found at i:2042944 original size:21 final size:22
Alignment explanation
Indices: 2042901--2042946 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2042891 TGAATAGACA
* * *
2042901 AAAAATAAAATAGTTATTCAAT
1 AAAAATAAAATAATAAATCAAT
2042923 AAAAATAAAATAATAAAT-AAT
1 AAAAATAAAATAATAAATCAAT
2042944 AAA
1 AAA
2042947 TATTATATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (22 bp):
AAAAATAAAATAATAAATCAAT
Found at i:2058207 original size:5 final size:5
Alignment explanation
Indices: 2058199--2058300 Score: 70
Period size: 5 Copynumber: 20.8 Consensus size: 5
2058189 ATTCATTACA
* * * *
2058199 TTAAT TTAA- TTAAG TTACT TTAAT TTAA- TTAAG TTACT TTAAT TTAA-
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT
* * *
2058246 TTAGA- TTACT TTAAT TTATT TTAAT TT-AT TTAATTT TTAAA TTAAT
1 TTA-AT TTAAT TTAAT TTAAT TTAAT TTAAT TTAA--T TTAAT TTAAT
*
2058292 TTATT TTAA
1 TTAAT TTAA
2058301 AATAAATTTA
Statistics
Matches: 76, Mismatches: 14, Indels: 14
0.73 0.13 0.13
Matches are distributed among these distances:
4 15 0.20
5 56 0.74
7 5 0.07
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (5 bp):
TTAAT
Found at i:2058221 original size:19 final size:19
Alignment explanation
Indices: 2058183--2058281 Score: 123
Period size: 19 Copynumber: 5.3 Consensus size: 19
2058173 GTCATTAATC
* *
2058183 AATTTAATTCA-TTACATT
1 AATTTAATTAAGTTACTTT
2058201 AATTTAATTAAGTTACTTT
1 AATTTAATTAAGTTACTTT
2058220 AATTTAATTAAGTTACTTT
1 AATTTAATTAAGTTACTTT
2058239 AATTTAATT-AGATTACTTT
1 AATTTAATTAAG-TTACTTT
* *
2058258 AATTTATTTTAATTTA-TTT
1 AATTTA-ATTAAGTTACTTT
2058277 AATTT
1 AATTT
2058282 TTAAATTAAT
Statistics
Matches: 73, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
18 12 0.16
19 55 0.75
20 5 0.07
21 1 0.01
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (19 bp):
AATTTAATTAAGTTACTTT
Found at i:2058240 original size:10 final size:9
Alignment explanation
Indices: 2058199--2058299 Score: 71
Period size: 9 Copynumber: 10.9 Consensus size: 9
2058189 ATTCATTACA
*
2058199 TTAATTTAA
1 TTAATTTAT
*
2058208 TTAAGTTACT
1 TTAATTTA-T
*
2058218 TTAATTTAA
1 TTAATTTAT
*
2058227 TTAAGTTACT
1 TTAATTTA-T
*
2058237 TTAATTTAA
1 TTAATTTAT
2058246 TTAGA-TTACT
1 TTA-ATTTA-T
2058256 TTAATTTATT
1 TTAATTTA-T
2058266 TTAATTTAT
1 TTAATTTAT
2058275 TTAATTT-T
1 TTAATTTAT
* *
2058283 TAAATTAAT
1 TTAATTTAT
*
2058292 TTATTTTA
1 TTAATTTA
2058300 AAATAAATTT
Statistics
Matches: 71, Mismatches: 15, Indels: 12
0.72 0.15 0.12
Matches are distributed among these distances:
8 6 0.08
9 35 0.49
10 30 0.42
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (9 bp):
TTAATTTAT
Found at i:2058285 original size:16 final size:16
Alignment explanation
Indices: 2058256--2058312 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
2058246 TTAGATTACT
2058256 TTAATTTA-TTTT-AA
1 TTAATTTATTTTTAAA
*
2058270 TTTATTTAATTTTTAAA
1 TTAATTT-ATTTTTAAA
*
2058287 TTAATTTATTTTAAAA
1 TTAATTTATTTTTAAA
*
2058303 TAAATTTATT
1 TTAATTTATT
2058313 CAGTTAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
14 6 0.17
15 1 0.03
16 21 0.58
17 8 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTAATTTATTTTTAAA
Found at i:2058516 original size:22 final size:23
Alignment explanation
Indices: 2058485--2058531 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
2058475 TTATATAACA
2058485 TATAAAATATAAAT-ATTT-TTT
1 TATAAAATATAAATAATTTATTT
2058506 TATAATAATATAAATAATTTATTT
1 TATAA-AATATAAATAATTTATTT
2058530 TA
1 TA
2058532 AGGCTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.22
22 9 0.39
23 4 0.17
24 5 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATAAAATATAAATAATTTATTT
Found at i:2058730 original size:14 final size:16
Alignment explanation
Indices: 2058694--2058729 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
2058684 CAAAATCTAC
2058694 AATATAAAAAAATTAA
1 AATATAAAAAAATTAA
*
2058710 AATATAAAAAAATAAA
1 AATATAAAAAAATTAA
2058726 AATA
1 AATA
2058730 ATATAATTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
AATATAAAAAAATTAA
Found at i:2059578 original size:20 final size:19
Alignment explanation
Indices: 2059544--2059589 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
2059534 CTCATTTTAT
*
2059544 TATTTAAAATTTATTAAAA
1 TATTAAAAATTTATTAAAA
**
2059563 TATTAAAAATTTTATTTTAA
1 TATTAAAAA-TTTATTAAAA
2059583 TATTAAA
1 TATTAAA
2059590 TTTAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TATTAAAAATTTATTAAAA
Found at i:2060376 original size:6 final size:6
Alignment explanation
Indices: 2060361--2060423 Score: 65
Period size: 6 Copynumber: 10.3 Consensus size: 6
2060351 ATTCTACAAA
* * * *
2060361 TTTATT TTTGTT TTTGTT TTTATT TTTATT TTTATT TTCTTTT TTTATAG
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TT-TATT TTTAT-T
2060411 TTT-TT TTTATT TT
1 TTTATT TTTATT TT
2060424 CATTAATTGG
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
5 3 0.06
6 37 0.77
7 8 0.17
ACGTcount: A:0.11, C:0.02, G:0.05, T:0.83
Consensus pattern (6 bp):
TTTATT
Found at i:2060405 original size:25 final size:26
Alignment explanation
Indices: 2060361--2060424 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 26
2060351 ATTCTACAAA
* *
2060361 TTTATTTTTGTTTT-TGTTTTTAT-T
1 TTTATTTTTATTTTCTGTTTTTATAG
*
2060385 TTTATTTTTATTTTCTTTTTTTATAG
1 TTTATTTTTATTTTCTGTTTTTATAG
2060411 TTT-TTTTTATTTTC
1 TTTATTTTTATTTTC
2060425 ATTAATTGGC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
24 13 0.37
25 19 0.54
26 3 0.09
ACGTcount: A:0.11, C:0.03, G:0.05, T:0.81
Consensus pattern (26 bp):
TTTATTTTTATTTTCTGTTTTTATAG
Found at i:2060558 original size:20 final size:20
Alignment explanation
Indices: 2060512--2060575 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
2060502 ACTAATAAAG
*
2060512 TTAATTAATATATTATT-TA
1 TTAAATAATATATTATTATA
*
2060531 TAATAATAATATATTATTATA
1 TTA-AATAATATATTATTATA
*
2060552 TTAAATATTATTATTATTAT-
1 TTAAATAATA-TATTATTATA
2060572 TTAA
1 TTAA
2060576 TTCATGAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
19 2 0.05
20 23 0.61
21 13 0.34
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTAAATAATATATTATTATA
Found at i:2060561 original size:15 final size:16
Alignment explanation
Indices: 2060541--2060570 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2060531 TAATAATAAT
2060541 ATATTATTA-TATTAA
1 ATATTATTATTATTAA
2060556 ATATTATTATTATTA
1 ATATTATTATTATTA
2060571 TTTAATTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATATTATTATTATTAA
Found at i:2060902 original size:30 final size:30
Alignment explanation
Indices: 2060847--2060912 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
2060837 AAAGTTTAAT
* *
2060847 ATATAAATTAAATATTAAGATTTTATTTGA-
1 ATATAAATTAAATATTAAAAATTTATTT-AC
2060877 ATATAAATTAAA-AGTTAAAAATTTATTTAC
1 ATATAAATTAAATA-TTAAAAATTTATTTAC
2060907 ATATAA
1 ATATAA
2060913 TTTATTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 2 0.06
30 30 0.94
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (30 bp):
ATATAAATTAAATATTAAAAATTTATTTAC
Found at i:2061357 original size:18 final size:19
Alignment explanation
Indices: 2061320--2061360 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
2061310 TTTATAATTA
2061320 ATTTTAAATAAAATATATT
1 ATTTTAAATAAAATATATT
*
2061339 ATTTTAATTAAAA-ATATT
1 ATTTTAAATAAAATATATT
2061357 ATTT
1 ATTT
2061361 CAGGCGAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTTAAATAAAATATATT
Found at i:2062007 original size:15 final size:15
Alignment explanation
Indices: 2061984--2062029 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
2061974 TCTCAAAATT
*
2061984 TTTTTAAAAATATTA
1 TTTTAAAAAATATTA
2061999 TTTTAAAAAATATTA
1 TTTTAAAAAATATTA
*
2062014 -TTAAAAATAATATTA
1 TTTTAAAA-AATATTA
2062029 T
1 T
2062030 AAATAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 6 0.22
15 21 0.78
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTTAAAAAATATTA
Found at i:2062017 original size:27 final size:27
Alignment explanation
Indices: 2061978--2062044 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
2061968 ATGTTATCTC
* * * *
2061978 AAAATTTTTTTAAAAATATTATTTTAA
1 AAAATATTATTAAAAATAATATTATAA
2062005 AAAATATTATTAAAAATAATATTATAA
1 AAAATATTATTAAAAATAATATTATAA
2062032 ATAAA-ATTATTAA
1 A-AAATATTATTAA
2062045 TTATTTTCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 32 0.91
28 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
AAAATATTATTAAAAATAATATTATAA
Found at i:2062021 original size:12 final size:12
Alignment explanation
Indices: 2061987--2062034 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
2061977 CAAAATTTTT
2061987 TTAAAAATATTA
1 TTAAAAATATTA
2061999 TTTTAAAAAATATTA
1 --TT-AAAAATATTA
*
2062014 TTAAAAATAATA
1 TTAAAAATATTA
*
2062026 TTATAAATA
1 TTAAAAATA
2062035 AAATTATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 17 0.55
13 2 0.06
14 2 0.06
15 10 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TTAAAAATATTA
Found at i:2062042 original size:15 final size:14
Alignment explanation
Indices: 2061978--2062043 Score: 55
Period size: 14 Copynumber: 4.7 Consensus size: 14
2061968 ATGTTATCTC
* *
2061978 AAAATTTTTTTAAA
1 AAAATTATTATAAA
* *
2061992 AATATTATTTTAAA
1 AAAATTATTATAAA
2062006 AAATATTATTA-AAA
1 AAA-ATTATTATAAA
*
2062020 ATAA-TATTATAAA
1 AAAATTATTATAAA
2062033 TAAAATTATTA
1 -AAAATTATTA
2062044 ATTATTTTCA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
12 5 0.12
13 4 0.10
14 22 0.52
15 11 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAATTATTATAAA
Found at i:2063647 original size:12 final size:12
Alignment explanation
Indices: 2063630--2063661 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
2063620 AGTCGAAGAA
2063630 AAGAAAGATGAG
1 AAGAAAGATGAG
2063642 AAGAAAGATGAG
1 AAGAAAGATGAG
2063654 AAGAAAGA
1 AAGAAAGA
2063662 CGTGGTAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.31, T:0.06
Consensus pattern (12 bp):
AAGAAAGATGAG
Found at i:2064694 original size:13 final size:13
Alignment explanation
Indices: 2064678--2064708 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2064668 TTTATTTTTT
*
2064678 TATTTTTAATATC
1 TATTTTTAATATA
2064691 TATTTTTAATATA
1 TATTTTTAATATA
2064704 TATTT
1 TATTT
2064709 AAATATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (13 bp):
TATTTTTAATATA
Found at i:2066019 original size:2 final size:2
Alignment explanation
Indices: 2066012--2066064 Score: 79
Period size: 2 Copynumber: 26.0 Consensus size: 2
2066002 CTATCAACCC
*
2066012 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AG
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
*
2066055 GT AT AT AT AT
1 AT AT AT AT AT
2066065 GGTATTCTAC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 44 0.96
3 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2067238 original size:13 final size:14
Alignment explanation
Indices: 2067215--2067243 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2067205 AAAGTAATCG
2067215 ATAAAAGAAATAAA
1 ATAAAAGAAATAAA
2067229 ATAAAA-AAATAAA
1 ATAAAAGAAATAAA
2067242 AT
1 AT
2067244 TTCAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.17
Consensus pattern (14 bp):
ATAAAAGAAATAAA
Found at i:2068111 original size:13 final size:14
Alignment explanation
Indices: 2068095--2068124 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2068085 TTTATTCTTT
2068095 AAAAAT-ATTTTTA
1 AAAAATCATTTTTA
2068108 AAAAATCATTTTTA
1 AAAAATCATTTTTA
2068122 AAA
1 AAA
2068125 TTTATTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (14 bp):
AAAAATCATTTTTA
Found at i:2068663 original size:13 final size:14
Alignment explanation
Indices: 2068643--2068679 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
2068633 TAATTAAAAA
2068643 ATTAAATTGAATTG
1 ATTAAATTGAATTG
*
2068657 ATT-AATTAAATTG
1 ATTAAATTGAATTG
2068670 ATTAAATTGA
1 ATTAAATTGA
2068680 GAATTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (14 bp):
ATTAAATTGAATTG
Found at i:2068736 original size:22 final size:22
Alignment explanation
Indices: 2068711--2068757 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2068701 TTATACATAT
*
2068711 ATTAAAATTAAAAAT-TAATTGA
1 ATTAAAA-TAAAAATCGAATTGA
*
2068733 ATTAATATAAAAATCGAATTGA
1 ATTAAAATAAAAATCGAATTGA
2068755 ATT
1 ATT
2068758 GGTAAATAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.36
Consensus pattern (22 bp):
ATTAAAATAAAAATCGAATTGA
Found at i:2068927 original size:23 final size:23
Alignment explanation
Indices: 2068888--2068933 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2068878 TTAAGTATAT
** *
2068888 TTAATATTTATTTAATATTAAAA
1 TTAATATTTATAAAATACTAAAA
2068911 TTAATATTTATAAAATACTAAAA
1 TTAATATTTATAAAATACTAAAA
2068934 AAATTATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
TTAATATTTATAAAATACTAAAA
Found at i:2070461 original size:16 final size:16
Alignment explanation
Indices: 2070442--2070473 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2070432 TATGATATAA
*
2070442 TTATATATTTTAAAAT
1 TTATATATTATAAAAT
2070458 TTATATATTATAAAAT
1 TTATATATTATAAAAT
2070474 ATTAAAGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATATATTATAAAAT
Found at i:2070546 original size:23 final size:23
Alignment explanation
Indices: 2070515--2070565 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
2070505 TATTTTAAAA
* *
2070515 ATAATTATATTATAATAAAATAT
1 ATAAATATAATATAATAAAATAT
* *
2070538 ATAAATATAATATGATAATATAT
1 ATAAATATAATATAATAAAATAT
2070561 A-AAAT
1 ATAAAT
2070566 CACATGGACG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
ATAAATATAATATAATAAAATAT
Found at i:2071099 original size:18 final size:17
Alignment explanation
Indices: 2071072--2071105 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2071062 TTTTGTTTTA
2071072 ATTTTAAAAAATAAAATT
1 ATTTTAAAAAA-AAAATT
*
2071090 ATTTTTAAAAAAAAAT
1 ATTTTAAAAAAAAAAT
2071106 ATGATTTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTTTAAAAAAAAAATT
Found at i:2071112 original size:19 final size:19
Alignment explanation
Indices: 2071073--2071112 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2071063 TTTGTTTTAA
*
2071073 TTTTAAAAAATAAAATTAT
1 TTTTAAAAAATAAAATGAT
2071092 TTTTAAAAAA-AAATATGAT
1 TTTTAAAAAATAAA-ATGAT
2071111 TT
1 TT
2071113 AAGTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 3 0.16
19 16 0.84
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TTTTAAAAAATAAAATGAT
Found at i:2078748 original size:2 final size:2
Alignment explanation
Indices: 2078741--2078769 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2078731 ATGGCAACTT
2078741 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2078770 TCTTTCTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2088078 original size:34 final size:36
Alignment explanation
Indices: 2088040--2088113 Score: 84
Period size: 33 Copynumber: 2.2 Consensus size: 36
2088030 TTAATATTTA
* *
2088040 TAAATATTTAATTA-ATTTAATAATTA-CATAAATT
1 TAAATATTAAATTATATTAAATAATTATCATAAATT
**
2088074 T-AA-ATTAAATTATATTAAATAATTATCATTTATT
1 TAAATATTAAATTATATTAAATAATTATCATAAATT
2088108 TAAATA
1 TAAATA
2088114 AATTTTATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
32 8 0.25
33 13 0.41
34 8 0.25
35 2 0.06
36 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (36 bp):
TAAATATTAAATTATATTAAATAATTATCATAAATT
Found at i:2088095 original size:33 final size:32
Alignment explanation
Indices: 2088049--2088117 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 32
2088039 ATAAATATTT
*
2088049 AATTAATTTAATAATTA-CATAAATTTAAATTA
1 AATTAATTAAATAATTATCATAAATTTAAA-TA
**
2088081 AATTATATTAAATAATTATCATTTATTTAAATA
1 AATTA-ATTAAATAATTATCATAAATTTAAATA
2088114 AATT
1 AATT
2088118 TTATAATTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 5 0.16
33 17 0.53
34 10 0.31
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (32 bp):
AATTAATTAAATAATTATCATAAATTTAAATA
Found at i:2088509 original size:24 final size:23
Alignment explanation
Indices: 2088435--2088520 Score: 79
Period size: 23 Copynumber: 3.7 Consensus size: 23
2088425 TTTAGTATTT
2088435 TAAATATATAAAAAATAAA-ATGAA
1 TAAA-ATAT-AAAAATAAATATGAA
* * *
2088459 TACAATATTAAAAATTAAT-TAAAA
1 TAAAATA-TAAAAATAAATAT-GAA
2088483 TAAAATATAAAAATAAATATGACA
1 TAAAATATAAAAATAAATATGA-A
2088507 T-AAATATAAAAATA
1 TAAAATATAAAAATA
2088521 TAAAAAATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
23 36 0.71
24 15 0.29
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (23 bp):
TAAAATATAAAAATAAATATGAA
Found at i:2088533 original size:19 final size:19
Alignment explanation
Indices: 2088511--2088553 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2088501 ATGACATAAA
2088511 TATAAAAA-TATAAAAAATT
1 TATAAAAATTAT-AAAAATT
* *
2088530 TATAAATATTATATAAATT
1 TATAAAAATTATAAAAATT
2088549 TATAA
1 TATAA
2088554 TATTTTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TATAAAAATTATAAAAATT
Found at i:2088779 original size:23 final size:23
Alignment explanation
Indices: 2088753--2088818 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 23
2088743 AATATACTAT
*
2088753 TAAAAATTAAT-TAAAATAAAATA
1 TAAAAATAAATATAAAAT-AAATA
*
2088776 TAAAAAATAAATATAACATAAATA
1 T-AAAAATAAATATAAAATAAATA
2088800 TAAAAAT--ATATAAAA-AAAT
1 TAAAAATAAATATAAAATAAAT
2088819 TTATACGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
20 4 0.11
21 7 0.18
23 7 0.18
24 15 0.39
25 5 0.13
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (23 bp):
TAAAAATAAATATAAAATAAATA
Found at i:2088781 original size:24 final size:24
Alignment explanation
Indices: 2088726--2088805 Score: 78
Period size: 24 Copynumber: 3.5 Consensus size: 24
2088716 TTAATATTTT
2088726 AAATATAAAAAATT-A-T-AAATA
1 AAATATAAAAAATTAATTAAAATA
* * *
2088747 TACTATTAAAAATTAATTAAAATA
1 AAATATAAAAAATTAATTAAAATA
* *
2088771 AAATATAAAAAATAAATATAACAT-
1 AAATATAAAAAATTAAT-TAAAATA
2088795 AAATATAAAAA
1 AAATATAAAAA
2088806 TATATAAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
21 11 0.23
22 1 0.02
23 1 0.02
24 29 0.62
25 5 0.11
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (24 bp):
AAATATAAAAAATTAATTAAAATA
Found at i:2088784 original size:14 final size:13
Alignment explanation
Indices: 2088765--2088818 Score: 53
Period size: 12 Copynumber: 4.4 Consensus size: 13
2088755 AAAATTAATT
2088765 AAAATAAAATATAA
1 AAAAT-AAATATAA
2088779 AAAATAAATAT--
1 AAAATAAATATAA
*
2088790 AACATAAATAT-A
1 AAAATAAATATAA
*
2088802 AAAATATATA-AA
1 AAAATAAATATAA
2088814 AAAAT
1 AAAAT
2088819 TTATACGTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
11 10 0.29
12 14 0.40
13 6 0.17
14 5 0.14
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAATAAATATAA
Found at i:2092151 original size:1 final size:1
Alignment explanation
Indices: 2092145--2092172 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
2092135 TGAATATTGC
2092145 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
2092173 CAGATCATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2092547 original size:3 final size:3
Alignment explanation
Indices: 2092541--2092566 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2092531 ATTGTTATCG
2092541 TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TC
2092567 CTCCAATAAA
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:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:2092867 original size:9 final size:8
Alignment explanation
Indices: 2092852--2092880 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
2092842 TGTTATTTGG
2092852 ATTTTTTT
1 ATTTTTTT
2092860 ATTTTTTT
1 ATTTTTTT
2092868 A-TTTTTT
1 ATTTTTTT
2092875 ATTTTT
1 ATTTTT
2092881 AAAGTATTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (8 bp):
ATTTTTTT
Found at i:2093270 original size:2 final size:2
Alignment explanation
Indices: 2093263--2093288 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2093253 GCATGCATGC
2093263 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2093289 GATCTGAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2094556 original size:3 final size:3
Alignment explanation
Indices: 2094548--2094593 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
2094538 GGAAGGGTCT
2094548 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2094594 CCAATAAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2096253 original size:13 final size:13
Alignment explanation
Indices: 2096235--2096259 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2096225 AAAACTACAA
2096235 TATATATATATAT
1 TATATATATATAT
2096248 TATATATATATA
1 TATATATATATA
2096260 ATTAATATGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TATATATATATAT
Found at i:2096465 original size:32 final size:32
Alignment explanation
Indices: 2096424--2096497 Score: 105
Period size: 32 Copynumber: 2.3 Consensus size: 32
2096414 GATACGATAA
*
2096424 AAATATATTAATGTATTAAAATTTATATAAAAT
1 AAATATATTAATATATTAAAATTTATAT-AAAT
*
2096457 AAAT-TATTATTATATTAAAATTTATATAAAT
1 AAATATATTAATATATTAAAATTTATATAAAT
2096488 AAATAATATT
1 AAAT-ATATT
2096498 TTAAATATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
31 8 0.22
32 21 0.57
33 8 0.22
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (32 bp):
AAATATATTAATATATTAAAATTTATATAAAT
Found at i:2096490 original size:15 final size:15
Alignment explanation
Indices: 2096440--2096490 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
2096430 ATTAATGTAT
2096440 TAAAATTTATATAAAA
1 TAAAATTTATAT-AAA
* *
2096456 TAAATTATTAT-TATAT
1 TAAAAT-TTATATA-AA
2096472 TAAAATTTATATAAA
1 TAAAATTTATATAAA
2096487 TAAA
1 TAAA
2096491 TAATATTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
15 10 0.36
16 14 0.50
17 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAAAATTTATATAAA
Found at i:2097286 original size:30 final size:30
Alignment explanation
Indices: 2097250--2097309 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
2097240 TACTTACATT
2097250 GCTCTATGTTCTTGGGCATGTTGATTGATC
1 GCTCTATGTTCTTGGGCATGTTGATTGATC
2097280 GCTCTATGTTCTTGGGCATGTTGATTGATC
1 GCTCTATGTTCTTGGGCATGTTGATTGATC
2097310 AAAGCTGCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.13, C:0.17, G:0.27, T:0.43
Consensus pattern (30 bp):
GCTCTATGTTCTTGGGCATGTTGATTGATC
Found at i:2111384 original size:11 final size:13
Alignment explanation
Indices: 2111352--2111377 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2111342 TGTATGAATA
2111352 TGAATTCAAAATT
1 TGAATTCAAAATT
2111365 TGAATTCAAAATT
1 TGAATTCAAAATT
2111378 AATTCAATCA
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:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
TGAATTCAAAATT
Found at i:2111741 original size:15 final size:17
Alignment explanation
Indices: 2111700--2111735 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2111690 TTTCTAACTT
2111700 TATATA-TAAATATAAA
1 TATATATTAAATATAAA
*
2111716 TATATATTAAATAAAAA
1 TATATATTAAATATAAA
2111733 TAT
1 TAT
2111736 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TATATATTAAATATAAA
Found at i:2111787 original size:20 final size:19
Alignment explanation
Indices: 2111742--2111790 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
2111732 ATATTTTAAA
2111742 ATTTTTAAAATTTTTTTAC
1 ATTTTTAAAATTTTTTTAC
* *
2111761 ATATTTAAAAGTTTTATTT-T
1 ATTTTTAAAA-TTTT-TTTAC
2111781 ATTTTTAAAA
1 ATTTTTAAAA
2111791 AATCAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 9 0.36
20 13 0.52
21 3 0.12
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
ATTTTTAAAATTTTTTTAC
Found at i:2116002 original size:4 final size:4
Alignment explanation
Indices: 2115993--2116046 Score: 81
Period size: 4 Copynumber: 13.5 Consensus size: 4
2115983 CACTTGTTCG
* *
2115993 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT TTAT AAAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
2116041 AAAT AT
1 ATAT AT
2116047 GCCAAAGAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
ATAT
Found at i:2116004 original size:6 final size:6
Alignment explanation
Indices: 2115993--2116046 Score: 81
Period size: 6 Copynumber: 9.0 Consensus size: 6
2115983 CACTTGTTCG
* *
2115993 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT TTATAA ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
*
2116041 AAATAT
1 ATATAT
2116047 GCCAAAGAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATAT
Found at i:2117265 original size:2 final size:2
Alignment explanation
Indices: 2117258--2117300 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
2117248 CAGGAAATTT
2117258 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2117299 TA
1 TA
2117301 GTTCTAGGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2118652 original size:4 final size:4
Alignment explanation
Indices: 2118643--2118672 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
2118633 GACTGCAGAT
*
2118643 CTTG CTTG CTTG CTTG CTTG CTTT CTTG CT
1 CTTG CTTG CTTG CTTG CTTG CTTG CTTG CT
2118673 AATAACTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.27, G:0.20, T:0.53
Consensus pattern (4 bp):
CTTG
Found at i:2136297 original size:20 final size:20
Alignment explanation
Indices: 2136273--2136321 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
2136263 TATTTAAATT
2136273 TAATTAAAAAATATAAATAAA
1 TAATTAAAAAATAT-AATAAA
* *
2136294 -AATTTAATAATATAATAAA
1 TAATTAAAAAATATAATAAA
2136313 TAA-TAAAAA
1 TAATTAAAAA
2136322 TATTTAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
TAATTAAAAAATATAATAAA
Found at i:2136300 original size:25 final size:28
Alignment explanation
Indices: 2136268--2136333 Score: 77
Period size: 25 Copynumber: 2.5 Consensus size: 28
2136258 AAATTTATTT
*
2136268 AAATTTAATTAA-AAAATATA-AAT-AA
1 AAATTTAATTAATAAAATAAATAATAAA
*
2136293 AAATTTAA-TAATATAATAAATAATAAA
1 AAATTTAATTAATAAAATAAATAATAAA
2136320 AATATTTAATTAAT
1 AA-ATTTAATTAAT
2136334 TGAATTATCC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 3 0.09
25 14 0.41
26 3 0.09
27 4 0.12
28 6 0.18
29 4 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (28 bp):
AAATTTAATTAATAAAATAAATAATAAA
Found at i:2140360 original size:20 final size:20
Alignment explanation
Indices: 2140308--2140365 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
2140298 TAATTTTAAT
* *
2140308 ATTAAATATTATAAATATTTA
1 ATTAAATAATAT-TATATTTA
2140329 A-T-AA-AATA-TATATTTA
1 ATTAAATAATATTATATTTA
*
2140345 ATTAAATAATATTATAGTTA
1 ATTAAATAATATTATATTTA
2140365 A
1 A
2140366 CATAAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
16 8 0.27
17 1 0.03
18 5 0.17
19 6 0.20
20 9 0.30
21 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
ATTAAATAATATTATATTTA
Found at i:2140365 original size:16 final size:15
Alignment explanation
Indices: 2140321--2140357 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
2140311 AAATATTATA
*
2140321 AATATTTAATAAAAT
1 AATATTTAATTAAAT
2140336 ATATATTTAATTAAAT
1 A-ATATTTAATTAAAT
2140352 AATATT
1 AATATT
2140358 ATAGTTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATTTAATTAAAT
Found at i:2143063 original size:24 final size:24
Alignment explanation
Indices: 2143036--2143083 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2143026 GAATGCAATT
2143036 TAGCTGTTACTACATAAAATACTA
1 TAGCTGTTACTACATAAAATACTA
2143060 TAGCTGTTACTACATAAAATACTA
1 TAGCTGTTACTACATAAAATACTA
2143084 CACAAGAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (24 bp):
TAGCTGTTACTACATAAAATACTA
Found at i:2148959 original size:2 final size:2
Alignment explanation
Indices: 2148952--2148984 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2148942 ATTGACAAAA
2148952 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2148985 AGGAGGGAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2150873 original size:30 final size:29
Alignment explanation
Indices: 2150834--2150907 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 29
2150824 TATATTAAAT
2150834 TAAAAAAAA-TATTATCTAAATCTTAAAAGA
1 TAAAAAAAATTATT-TCTAAAT-TTAAAAGA
* *
2150864 TAAATAAAATTATTTTTAAATTT-AAA-A
1 TAAAAAAAATTATTTCTAAATTTAAAAGA
2150891 TAATAAAAAATT-TTTCT
1 TAA-AAAAAATTATTTCT
2150908 TATATAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
27 8 0.21
28 10 0.26
29 2 0.05
30 14 0.37
31 4 0.11
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.39
Consensus pattern (29 bp):
TAAAAAAAATTATTTCTAAATTTAAAAGA
Found at i:2151605 original size:20 final size:19
Alignment explanation
Indices: 2151558--2151605 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
2151548 TTGAATTAAT
2151558 TTAAATTA-AATTTAAAAA
1 TTAAATTATAATTTAAAAA
**
2151576 TATATTTTATAATTTAAAATA
1 T-TAAATTATAATTTAAAA-A
2151597 TTAAATTAT
1 TTAAATTAT
2151606 GAAATAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
18 1 0.04
19 5 0.22
20 15 0.65
21 2 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTAAATTATAATTTAAAAA
Found at i:2153754 original size:21 final size:21
Alignment explanation
Indices: 2153727--2153782 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
2153717 ATTTTTATAT
2153727 TTTTATAATTAAATTAAAAT-
1 TTTTATAATTAAATTAAAATA
* *
2153747 TATTTAT-ATTAATATTTATATA
1 T-TTTATAATTAA-ATTAAAATA
2153769 TTTTATAATTAAAT
1 TTTTATAATTAAAT
2153783 ATTTATTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
20 6 0.20
21 18 0.60
22 6 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTATAATTAAATTAAAATA
Found at i:2153763 original size:35 final size:36
Alignment explanation
Indices: 2153723--2153795 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 36
2153713 TAATATTTTT
*
2153723 ATATTTTTATA-ATTA-AATTAAAATTATTTA-TATTA
1 ATATTTATATATATTATAATT-AAA-TATTTATTATTA
*
2153758 ATATTTATATATTTTATAATTAAATATTTATTATTA
1 ATATTTATATATATTATAATTAAATATTTATTATTA
2153794 AT
1 AT
2153796 TCAATAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
35 16 0.48
36 13 0.39
37 4 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (36 bp):
ATATTTATATATATTATAATTAAATATTTATTATTA
Found at i:2154062 original size:19 final size:17
Alignment explanation
Indices: 2154027--2154062 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2154017 TAAAAATAAA
*
2154027 TTTAATATATCAATTTT
1 TTTAATATATAAATTTT
2154044 TTTAATATATAAATGTTT
1 TTTAATATATAAAT-TTT
2154062 T
1 T
2154063 AAAAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (17 bp):
TTTAATATATAAATTTT
Found at i:2155958 original size:15 final size:16
Alignment explanation
Indices: 2155938--2155979 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
2155928 GAGCAATTAT
*
2155938 TATTTTTAAATATTAA
1 TATTTTTAAATATAAA
2155954 T-TTTTTAAATATAAA
1 TATTTTTAAATATAAA
*
2155969 TAATTTTAAAT
1 TATTTTTAAAT
2155980 TACACCTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTTTTAAATATAAA
Found at i:2156629 original size:21 final size:19
Alignment explanation
Indices: 2156601--2156652 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 19
2156591 TTATAAAATA
2156601 ATTT-TTTTATTATATATTTT
1 ATTTATTTTATTAT-TA-TTT
2156621 ATTTATTTTTAATTATTATTT
1 ATTTA-TTTT-ATTATTATTT
2156642 ATTTGATTTTA
1 ATTT-ATTTTA
2156653 AATTAATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
20 5 0.18
21 11 0.39
22 7 0.25
23 5 0.18
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (19 bp):
ATTTATTTTATTATTATTT
Found at i:2156653 original size:21 final size:23
Alignment explanation
Indices: 2156603--2156657 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
2156593 ATAAAATAAT
*
2156603 TTTTTTATTATATATTTTATTTA
1 TTTTTAATTATATATTTTATTTA
2156626 TTTTTAATTAT-TA-TTTATTTGA
1 TTTTTAATTATATATTTTATTT-A
*
2156648 TTTTAAATTA
1 TTTTTAATTA
2156658 ATTAAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 7 0.24
22 12 0.41
23 10 0.34
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTTTAATTATATATTTTATTTA
Found at i:2158591 original size:2 final size:2
Alignment explanation
Indices: 2158584--2158615 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2158574 CATTTTCTTC
2158584 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2158616 GAAACATGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2160319 original size:13 final size:13
Alignment explanation
Indices: 2160301--2160326 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2160291 TAATTAAAAA
2160301 TATTTATTTATTT
1 TATTTATTTATTT
2160314 TATTTATTTATTT
1 TATTTATTTATTT
2160327 CACTTACAAA
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TATTTATTTATTT
Found at i:2162189 original size:12 final size:13
Alignment explanation
Indices: 2162166--2162190 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2162156 CAGAATCGAT
2162166 TTTACTTTTTTTG
1 TTTACTTTTTTTG
2162179 TTTACTTTTTTT
1 TTTACTTTTTTT
2162191 AATGTTAGAT
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:0.08, C:0.08, G:0.04, T:0.80
Consensus pattern (13 bp):
TTTACTTTTTTTG
Found at i:2162710 original size:2 final size:2
Alignment explanation
Indices: 2162705--2162739 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2162695 TCTCTCTCTC
2162705 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2162740 TGTTAAAACC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2164962 original size:18 final size:18
Alignment explanation
Indices: 2164905--2165025 Score: 81
Period size: 18 Copynumber: 6.8 Consensus size: 18
2164895 GATCAGCATA
* * *
2164905 AATCACAGATTTTTTAGG
1 AATCATAGATTTTCTAAG
* * *
2164923 AATCTTAAATTTTTTGAA-
1 AATCATAGATTTTCT-AAG
*
2164941 AATCATATATTTTCTAAG
1 AATCATAGATTTTCTAAG
*
2164959 AATCATTAGATTTT-TTAG
1 AATCA-TAGATTTTCTAAG
* *
2164977 AAATCACAAATTTTCTAAG
1 -AATCATAGATTTTCTAAG
2164996 AATCATAGA-TTTCT--G
1 AATCATAGATTTTCTAAG
2165011 TAATCATAGATTTTC
1 -AATCATAGATTTTC
2165026 AACCTCAATA
Statistics
Matches: 82, Mismatches: 14, Indels: 15
0.74 0.13 0.14
Matches are distributed among these distances:
15 1 0.01
16 9 0.11
17 11 0.13
18 45 0.55
19 16 0.20
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (18 bp):
AATCATAGATTTTCTAAG
Found at i:2164981 original size:37 final size:37
Alignment explanation
Indices: 2164904--2165007 Score: 124
Period size: 37 Copynumber: 2.9 Consensus size: 37
2164894 AGATCAGCAT
* * * *
2164904 AAATCACAGATTTTTTAGGAATC-TTAAATTTTTTGA
1 AAATCACAAATTTTCTAAGAATCATTAGATTTTTTGA
* *
2164940 AAATCATATATTTTCTAAGAATCATTAGATTTTTT-A
1 AAATCACAAATTTTCTAAGAATCATTAGATTTTTTGA
2164976 GAAATCACAAATTTTCTAAGAATCA-TAGATTT
1 -AAATCACAAATTTTCTAAGAATCATTAGATTT
2165008 CTGTAATCAT
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
36 27 0.46
37 32 0.54
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.42
Consensus pattern (37 bp):
AAATCACAAATTTTCTAAGAATCATTAGATTTTTTGA
Found at i:2165751 original size:21 final size:21
Alignment explanation
Indices: 2165713--2165753 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2165703 TTCTGATGAG
* *
2165713 GATGATGATTAAGCTGCTGAA
1 GATGATGATGAAGATGCTGAA
*
2165734 GATGATGATGATGATGCTGA
1 GATGATGATGAAGATGCTGA
2165754 GAATGAGAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.07, G:0.32, T:0.29
Consensus pattern (21 bp):
GATGATGATGAAGATGCTGAA
Found at i:2165759 original size:21 final size:21
Alignment explanation
Indices: 2165709--2165759 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
2165699 ATGATTCTGA
* * *
2165709 TGAGGATGATGATTAAGCTGC
1 TGAGAATGATGATGAAGATGC
*
2165730 TGA-AGATGATGATGATGATGC
1 TGAGA-ATGATGATGAAGATGC
2165751 TGAGAATGA
1 TGAGAATGA
2165760 GAAATATGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.33, C:0.06, G:0.33, T:0.27
Consensus pattern (21 bp):
TGAGAATGATGATGAAGATGC
Found at i:2168081 original size:2 final size:2
Alignment explanation
Indices: 2168076--2168110 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2168066 CCCCCAACAA
2168076 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2168111 AGAAATAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2173410 original size:16 final size:16
Alignment explanation
Indices: 2173375--2173410 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2173365 ATGAAATTCT
* *
2173375 TAGTCATACTCCGTGT
1 TAGTCATACTCCATGA
2173391 TAGTCATACTCCATGA
1 TAGTCATACTCCATGA
2173407 TAGT
1 TAGT
2173411 GCTCCACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (16 bp):
TAGTCATACTCCATGA
Found at i:2177531 original size:28 final size:28
Alignment explanation
Indices: 2177499--2177557 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
2177489 TTTTGAAGAA
2177499 CAAAATAAGTAAAGACTCTTATTAGGAC
1 CAAAATAAGTAAAGACTCTTATTAGGAC
2177527 CAAAATAAGTAAAGACTCTTATTAGGAC
1 CAAAATAAGTAAAGACTCTTATTAGGAC
2177555 CAA
1 CAA
2177558 GCAGCACCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.47, C:0.15, G:0.14, T:0.24
Consensus pattern (28 bp):
CAAAATAAGTAAAGACTCTTATTAGGAC
Found at i:2182589 original size:4 final size:4
Alignment explanation
Indices: 2182580--2182616 Score: 56
Period size: 4 Copynumber: 9.0 Consensus size: 4
2182570 CATAAGAATT
*
2182580 TAAA TAAA TAAA TAAA TAAA CAAA TAAGA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAA-A TAAA TAAA
2182617 CCCCCACTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.22
Consensus pattern (4 bp):
TAAA
Found at i:2188121 original size:15 final size:14
Alignment explanation
Indices: 2188101--2188134 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2188091 GAATTCGGTG
2188101 TTTCTTTCTTTTCTT
1 TTTCTTT-TTTTCTT
*
2188116 TTTCTTTTTTTTTT
1 TTTCTTTTTTTCTT
2188130 TTTCT
1 TTTCT
2188135 CCCTTAGTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTCTTTTTTTCTT
Found at i:2188584 original size:31 final size:31
Alignment explanation
Indices: 2188523--2188586 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 31
2188513 TTTATTTAAT
2188523 ATAGTGTTAGTTTTTTATGACAAATAATTTTA
1 ATAGTGTTAGTTTTTTATGAC-AATAATTTTA
*
2188555 ATAGTGTTAGTTTTTTTATGAC-ATGATTTTA
1 ATAGTGTTAG-TTTTTTATGACAATAATTTTA
2188586 A
1 A
2188587 AAAAATGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 9 0.30
32 10 0.33
33 11 0.37
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.52
Consensus pattern (31 bp):
ATAGTGTTAGTTTTTTATGACAATAATTTTA
Found at i:2189284 original size:49 final size:49
Alignment explanation
Indices: 2189225--2189324 Score: 137
Period size: 49 Copynumber: 2.0 Consensus size: 49
2189215 AAACAAAATG
* * * * *
2189225 TTTCTTAAACATCTTTATAAAGAAATTGATTTACTACTTGGATTAATAT
1 TTTCTGAAACATCTCTATAAAGAAATTAATCTACTACTTGAATTAATAT
* *
2189274 TTTCTGAAACATCTCTATAAAGAAATTAATCTATTACTTGAATTTATAT
1 TTTCTGAAACATCTCTATAAAGAAATTAATCTACTACTTGAATTAATAT
2189323 TT
1 TT
2189325 GAATGATTAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.45
Consensus pattern (49 bp):
TTTCTGAAACATCTCTATAAAGAAATTAATCTACTACTTGAATTAATAT
Found at i:2189796 original size:30 final size:30
Alignment explanation
Indices: 2189709--2189821 Score: 79
Period size: 30 Copynumber: 3.7 Consensus size: 30
2189699 AAAATTAGGG
* * * *
2189709 AAAAAGATATTTA-CTTTTTAAAATTTTATA
1 AAAAATATATTTATCTCTTT-AAAGTTTAGA
* * * * *
2189739 AAAAATACAATTATTTTTTTAACGTTT--A
1 AAAAATATATTTATCTCTTTAAAGTTTAGA
2189767 AAAAATATTCATTTATCTCTTTAAAGTTTAGTA
1 AAAAATA-T-ATTTATCTCTTTAAAGTTTAG-A
*
2189800 AAAAATATATTTATCTCGTTAA
1 AAAAATATATTTATCTCTTTAA
2189822 GTTATTATTT
Statistics
Matches: 65, Mismatches: 12, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
28 8 0.12
30 30 0.46
31 18 0.28
32 1 0.02
33 8 0.12
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.45
Consensus pattern (30 bp):
AAAAATATATTTATCTCTTTAAAGTTTAGA
Found at i:2189978 original size:16 final size:16
Alignment explanation
Indices: 2189957--2189988 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2189947 AATGATCTTT
*
2189957 AATTATTGTTAAATTA
1 AATTATTATTAAATTA
2189973 AATTATTATTAAATTA
1 AATTATTATTAAATTA
2189989 TATTCTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
AATTATTATTAAATTA
Found at i:2190295 original size:18 final size:17
Alignment explanation
Indices: 2190257--2190295 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
2190247 AAAAATATTA
2190257 TTTTTTATTTTAATCAAT
1 TTTTTTATTTTAA-CAAT
2190275 TTTTTTATTTTTAA-AAT
1 TTTTTTA-TTTTAACAAT
2190292 TTTT
1 TTTT
2190296 AAAATAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 7 0.35
19 6 0.30
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTTATTTTAACAAT
Found at i:2190390 original size:17 final size:17
Alignment explanation
Indices: 2190348--2190381 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2190338 ATATATTAAT
*
2190348 ATTAAAATTAATATATA
1 ATTAAATTTAATATATA
2190365 ATTAAATTTAA-ATATA
1 ATTAAATTTAATATATA
2190381 A
1 A
2190382 GTTCAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTAAATTTAATATATA
Found at i:2195287 original size:22 final size:20
Alignment explanation
Indices: 2195245--2195310 Score: 71
Period size: 22 Copynumber: 3.1 Consensus size: 20
2195235 TATGTGATAG
*
2195245 AATTTTATAAAAGATAAAAAA
1 AATTTTATAAAATAT-AAAAA
2195266 AATTTTATTAAAATATATAAAA
1 AATTTTA-TAAAATATA-AAAA
*
2195288 AATAGTTATAAAAT-TAAAAA
1 AAT-TTTATAAAATATAAAAA
2195308 AAT
1 AAT
2195311 ATATCAATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
20 7 0.17
21 10 0.25
22 20 0.50
23 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
AATTTTATAAAATATAAAAA
Found at i:2195987 original size:20 final size:20
Alignment explanation
Indices: 2195962--2196005 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2195952 GTAAATTATT
2195962 AAATTATTATTTAT-TATTTA
1 AAATTATT-TTTATATATTTA
*
2195982 AAATTATTTTTTTATATTTA
1 AAATTATTTTTATATATTTA
2196002 AAAT
1 AAAT
2196006 AAACTATACG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
AAATTATTTTTATATATTTA
Found at i:2197193 original size:51 final size:51
Alignment explanation
Indices: 2197138--2197316 Score: 189
Period size: 51 Copynumber: 3.5 Consensus size: 51
2197128 AATTAGTATG
*
2197138 ATAATTAAATAATCATTAATTAATGTATCCCACCATTAATTAACTTTTTGA
1 ATAATTAAATAATCATTAATTAATGTATCCCACCATTAATTAACTTTTTAA
* ** * *
2197189 ATAATTAAATAATTATTAATTGGTGTATCTCATCATTAATTAACTTTTTAA
1 ATAATTAAATAATCATTAATTAATGTATCCCACCATTAATTAACTTTTTAA
* * ** * * *
2197240 ATAACTAAATCATCATTAATTGGTGTA-CCACACCATGACTTACCTTTTTTAA
1 ATAATTAAATAATCATTAATTAATGTATCC-CACCATTAATTAAC-TTTTTAA
* *
2197292 ATAAATAAATAAATAATTAATTAAT
1 ATAATTAAAT-AATCATTAATTAAT
2197317 TAAATTTTAT
Statistics
Matches: 106, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
50 1 0.01
51 79 0.75
52 16 0.15
53 10 0.09
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.41
Consensus pattern (51 bp):
ATAATTAAATAATCATTAATTAATGTATCCCACCATTAATTAACTTTTTAA
Done.