Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold43
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: 2559314
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 13088 characters in sequence are not A, C, G, or T
File 17 of 19
Found at i:1988435 original size:13 final size:13
Alignment explanation
Indices: 1988417--1988462 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
1988407 ATTTTAAATT
1988417 TTTATTATTAATA
1 TTTATTATTAATA
1988430 TTTATTA-TAATTA
1 TTTATTATTAA-TA
* *
1988443 ATTA-TAATAATA
1 TTTATTATTAATA
1988455 TTTATTAT
1 TTTATTAT
1988463 ATTTATAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTATTATTAATA
Found at i:1988437 original size:16 final size:16
Alignment explanation
Indices: 1988366--1988444 Score: 51
Period size: 16 Copynumber: 5.2 Consensus size: 16
1988356 CGACAACTTA
* *
1988366 AATAATTATTATAATAT
1 AATATTTATTATTAT-T
*
1988383 AAT-TTTATGATTATT
1 AATATTTATTATTATT
* * *
1988398 -TTTTTTATAATT-TT
1 AATATTTATTATTATT
1988412 AA-ATTT-TTATTATT
1 AATATTTATTATTATT
*
1988426 AATATTTATTATAATT
1 AATATTTATTATTATT
1988442 AAT
1 AAT
1988445 TATAATAATA
Statistics
Matches: 48, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
13 4 0.08
14 10 0.21
15 13 0.27
16 18 0.38
17 3 0.06
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (16 bp):
AATATTTATTATTATT
Found at i:1988441 original size:25 final size:25
Alignment explanation
Indices: 1988425--1988478 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
1988415 TTTTTATTAT
1988425 TAATATTTATTATAATTAATTATAA
1 TAATATTTATTATAATTAATTATAA
*
1988450 TAATATTTATTATATTTATAATTATAA
1 TAATATTTATTATA-AT-TAATTATAA
1988477 TA
1 TA
1988479 CATACGATCC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 14 0.54
26 1 0.04
27 11 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TAATATTTATTATAATTAATTATAA
Found at i:1991891 original size:48 final size:49
Alignment explanation
Indices: 1991839--1991931 Score: 125
Period size: 48 Copynumber: 1.9 Consensus size: 49
1991829 ACCTAAAAAA
*
1991839 TAATACTTGTAATATTTAAATTTTAATATATT-TATTTATATTATTTTT
1 TAATACTTATAATATTTAAATTTTAATATATTATATTTATATTATTTTT
* * * **
1991887 TAATATTTATTATATTTTAATTTTTTTATATTATATTTATATTAT
1 TAATACTTATAATATTTAAATTTTAATATATTATATTTATATTAT
1991932 GTAATTATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
48 26 0.68
49 12 0.32
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (49 bp):
TAATACTTATAATATTTAAATTTTAATATATTATATTTATATTATTTTT
Found at i:1991892 original size:25 final size:24
Alignment explanation
Indices: 1991859--1991931 Score: 87
Period size: 25 Copynumber: 3.0 Consensus size: 24
1991849 AATATTTAAA
*
1991859 TTTTAATATATTTATTTATATTAT
1 TTTTTATATATTTATTTATATTAT
*
1991883 TTTTTA-ATATTTATTATATTTTAAT
1 TTTTTATATATTTATT-TATATT-AT
1991908 TTTTT-TATATTATATTTATATTAT
1 TTTTTATATATT-TATTTATATTAT
1991932 GTAATTATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
23 9 0.21
24 12 0.29
25 17 0.40
26 4 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (24 bp):
TTTTTATATATTTATTTATATTAT
Found at i:1992426 original size:31 final size:30
Alignment explanation
Indices: 1992345--1992452 Score: 83
Period size: 33 Copynumber: 3.4 Consensus size: 30
1992335 GATTTGAATT
* **
1992345 ATTAA-TTAAATAATAAAATTATTTTTTAAA
1 ATTAATTTAAATAATAAAATAAAATTTT-AA
* *
1992375 ATTTAATTATAAATATTAATATAAATAATTTTTAA
1 A-TTAATT-TAAATAATAAAAT-AA-AA-TTTTAA
* *
1992410 TATTATTTTAAATAATAAATTAAAATTTTAA
1 -ATTAATTTAAATAATAAAATAAAATTTTAA
1992441 ATTAATTTAAAT
1 ATTAATTTAAAT
1992453 CAATTCGAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
30 12 0.20
31 10 0.16
32 3 0.05
33 13 0.21
34 11 0.18
35 7 0.11
36 5 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
ATTAATTTAAATAATAAAATAAAATTTTAA
Found at i:1993172 original size:31 final size:31
Alignment explanation
Indices: 1993131--1993189 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1993121 ACTTTAGACA
* * *
1993131 TCATCCATTTCTTGCTTGTTTAACTAAAACT
1 TCATCAATTTCTTGCTTATGTAACTAAAACT
1993162 TCATCAATTTCTTGCTTATGTAACTAAA
1 TCATCAATTTCTTGCTTATGTAACTAAA
1993190 TTAAGCTCAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.29, C:0.20, G:0.07, T:0.44
Consensus pattern (31 bp):
TCATCAATTTCTTGCTTATGTAACTAAAACT
Found at i:2000788 original size:2 final size:2
Alignment explanation
Indices: 2000783--2000812 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2000773 TACTCAGCTA
2000783 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2000813 ATCTTAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2001160 original size:2 final size:2
Alignment explanation
Indices: 2001153--2001183 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2001143 TAAGGGCTTT
2001153 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 T
2001184 GATGAAAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2003966 original size:28 final size:28
Alignment explanation
Indices: 2003916--2003969 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
2003906 GTAGAAGCGT
*
2003916 AAAAATTAGTTAAAATTAATTTAATTGA
1 AAAAATTAGATAAAATTAATTTAATTGA
*
2003944 AAAAATTA-ATAAAATTTAGTTTAATT
1 AAAAATTAGATAAAA-TTAATTTAATT
2003970 AATTTAGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.41
Consensus pattern (28 bp):
AAAAATTAGATAAAATTAATTTAATTGA
Found at i:2004093 original size:11 final size:12
Alignment explanation
Indices: 2004075--2004112 Score: 51
Period size: 11 Copynumber: 3.1 Consensus size: 12
2004065 ATAATTGAAT
2004075 TAATATTTAAAA
1 TAATATTTAAAA
2004087 T-ATATTTAAAAA
1 TAATATTT-AAAA
2004099 TAAATATTTAAAA
1 T-AATATTTAAAA
2004112 T
1 T
2004113 TTAAAAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 6 0.26
12 6 0.26
13 5 0.22
14 6 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAATATTTAAAA
Found at i:2004107 original size:14 final size:13
Alignment explanation
Indices: 2004075--2004111 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
2004065 ATAATTGAAT
2004075 TAATATTT-AAAA
1 TAATATTTAAAAA
2004087 T-ATATTTAAAAA
1 TAATATTTAAAAA
2004099 TAAATATTTAAAA
1 T-AATATTTAAAA
2004112 TTTAAAAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 6 0.27
12 6 0.27
14 10 0.45
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TAATATTTAAAAA
Found at i:2004900 original size:18 final size:20
Alignment explanation
Indices: 2004877--2004925 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
2004867 TCATATTGCA
2004877 TATTTTTTATA-CA-TATAT
1 TATTTTTTATATCATTATAT
* *
2004895 TATTTTTGATATCATTATTT
1 TATTTTTTATATCATTATAT
*
2004915 TATCTTTTATA
1 TATTTTTTATA
2004926 ATTCTTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 10 0.40
19 2 0.08
20 13 0.52
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (20 bp):
TATTTTTTATATCATTATAT
Found at i:2004994 original size:17 final size:17
Alignment explanation
Indices: 2004974--2005008 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2004964 TCCTTTTAAG
* *
2004974 AAATATTTATCCATGCA
1 AAATAATTATCAATGCA
2004991 AAATAATTATCAATGCA
1 AAATAATTATCAATGCA
2005008 A
1 A
2005009 GCCATTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.31
Consensus pattern (17 bp):
AAATAATTATCAATGCA
Found at i:2007215 original size:18 final size:19
Alignment explanation
Indices: 2007192--2007243 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
2007182 GAATATGATA
* *
2007192 AATAAATATGAAA-ATTTT
1 AATAAATATGAAATAATAT
2007210 AATAAATATGATAATAATAT
1 AATAAATATGA-AATAATAT
2007230 AATAAATATGAAAT
1 AATAAATATGAAAT
2007244 GATAGTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 11 0.37
19 5 0.17
20 14 0.47
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.35
Consensus pattern (19 bp):
AATAAATATGAAATAATAT
Found at i:2012735 original size:20 final size:19
Alignment explanation
Indices: 2012711--2012757 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
2012701 TATTTTTTTA
2012711 AATTTTATTATAATTTATG
1 AATTTTATTATAATTTATG
* *
2012730 AGATTTTAATATAATTTATT
1 A-ATTTTATTATAATTTATG
2012750 AATTTTAT
1 AATTTTAT
2012758 ATTAAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (19 bp):
AATTTTATTATAATTTATG
Found at i:2012815 original size:21 final size:20
Alignment explanation
Indices: 2012778--2012834 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
2012768 ATACTATTAA
2012778 ATAAATATATATTTTTAATT
1 ATAAATATATATTTTTAATT
2012798 ATAAATCATAT-TTATTTAA-T
1 ATAAAT-ATATATT-TTTAATT
2012818 ATCAAA-AT-TATTTTTAA
1 AT-AAATATATATTTTTAA
2012835 AATATTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
18 6 0.18
19 4 0.12
20 11 0.33
21 12 0.36
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (20 bp):
ATAAATATATATTTTTAATT
Found at i:2014422 original size:15 final size:15
Alignment explanation
Indices: 2014402--2014431 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2014392 AATGGCATCC
2014402 AATGTGCAGTTTTTT
1 AATGTGCAGTTTTTT
*
2014417 AATGTGGAGTTTTTT
1 AATGTGCAGTTTTTT
2014432 TTTTTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.03, G:0.23, T:0.53
Consensus pattern (15 bp):
AATGTGCAGTTTTTT
Found at i:2014621 original size:22 final size:22
Alignment explanation
Indices: 2014595--2014637 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2014585 ATTATATAAA
2014595 TTAATTA-AATTTAATTTAATTT
1 TTAATTATAATTT-ATTTAATTT
*
2014617 TTAATTATACTTTATTTAATT
1 TTAATTATAATTTATTTAATT
2014638 AAAAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TTAATTATAATTTATTTAATTT
Found at i:2015051 original size:19 final size:20
Alignment explanation
Indices: 2015012--2015055 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2015002 TATAAATATG
*
2015012 ATATACTATAAAAATTACAA
1 ATATAATATAAAAATTACAA
*
2015032 ATATAATATAAATA-TACAA
1 ATATAATATAAAAATTACAA
2015051 ATATA
1 ATATA
2015056 TTAAAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (20 bp):
ATATAATATAAAAATTACAA
Found at i:2015097 original size:32 final size:33
Alignment explanation
Indices: 2015032--2015106 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 33
2015022 AAAATTACAA
*
2015032 ATATAATATAAATATACAAATATATTAAAATTT
1 ATATAATATAAATATACAAATATAATAAAATTT
* ** *
2015065 ATATTATATAAAT-TATTAATATAATAATATTT
1 ATATAATATAAATATACAAATATAATAAAATTT
*
2015097 ATAAAATATA
1 ATATAATATA
2015107 TATTTTAAAC
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
32 23 0.66
33 12 0.34
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (33 bp):
ATATAATATAAATATACAAATATAATAAAATTT
Found at i:2015176 original size:3 final size:3
Alignment explanation
Indices: 2015168--2015215 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
2015158 TCCAAAGAAA
2015168 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2015216 ATCATCAGTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2015441 original size:21 final size:22
Alignment explanation
Indices: 2015400--2015462 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 22
2015390 TACTACTTTC
2015400 AAATATGATATAATA-ATATTAAA
1 AAATAT-ATA-AATATATATTAAA
2015423 AAATATATAAATATA-ATTAAA
1 AAATATATAAATATATATTAAA
*
2015444 ATATAATATAAAATATATA
1 AAAT-ATAT-AAATATATA
2015463 ATACAAATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
21 13 0.37
22 8 0.23
23 13 0.37
24 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
AAATATATAAATATATATTAAA
Found at i:2015445 original size:11 final size:12
Alignment explanation
Indices: 2015412--2015460 Score: 59
Period size: 11 Copynumber: 4.2 Consensus size: 12
2015402 ATATGATATA
*
2015412 ATAATATTAAA-
1 ATAATATAAAAT
2015423 A-AATATATAAAT
1 ATAATATA-AAAT
2015435 ATAAT-TAAAAT
1 ATAATATAAAAT
2015446 ATAATATAAAAT
1 ATAATATAAAAT
2015458 ATA
1 ATA
2015461 TAATACAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
10 5 0.15
11 13 0.39
12 12 0.36
13 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAATATAAAAT
Found at i:2015484 original size:42 final size:43
Alignment explanation
Indices: 2015400--2015505 Score: 105
Period size: 42 Copynumber: 2.5 Consensus size: 43
2015390 TACTACTTTC
*
2015400 AAATATGATATAATAATAT-TAA-AAAATATATAAATATAATTA
1 AAATATAATATAA-AATATATAATAAAATATATAAATATAATTA
* *
2015442 AAATATAATATAAAATATATAATACAAAT-TATTAAT-TTATTA
1 AAATATAATATAAAATATATAATA-AAATATATAAATATAATTA
* * *
2015484 AATTTTATTAT-AAATATATAAT
1 AAATATAATATAAAATATATAAT
2015506 TATTATGAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
41 16 0.29
42 28 0.51
43 7 0.13
44 4 0.07
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.41
Consensus pattern (43 bp):
AAATATAATATAAAATATATAATAAAATATATAAATATAATTA
Found at i:2016412 original size:35 final size:35
Alignment explanation
Indices: 2016357--2016427 Score: 83
Period size: 35 Copynumber: 2.0 Consensus size: 35
2016347 TATATTAATA
*
2016357 TTTATATATAAAATTAAATTTA-AATAAATAAAAT
1 TTTATATATAAAAATAAATTTATAATAAATAAAAT
* *
2016391 TTTATTATATAAATAAT-AATTTATATTAAATCAAAT
1 TTTA-TATATAAA-AATAAATTTATAATAAATAAAAT
2016427 T
1 T
2016428 AAAAAATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
34 4 0.13
35 14 0.45
36 13 0.42
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (35 bp):
TTTATATATAAAAATAAATTTATAATAAATAAAAT
Found at i:2016427 original size:16 final size:17
Alignment explanation
Indices: 2016356--2016427 Score: 69
Period size: 19 Copynumber: 4.2 Consensus size: 17
2016346 TTATATTAAT
*
2016356 ATTTATATATAAAATTAA
1 ATTTATATAT-AAATAAA
2016374 ATTTA-A-ATAAATAAA
1 ATTTATATATAAATAAA
2016389 ATTTTATTATATAAATAATA
1 A-TTTA-TATATAAATAA-A
*
2016409 ATTTATAT-TAAATCAA
1 ATTTATATATAAATAAA
2016425 ATT
1 ATT
2016428 AAAAAATTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
15 7 0.15
16 10 0.21
17 7 0.15
18 9 0.19
19 12 0.26
20 2 0.04
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTATATATAAATAAA
Found at i:2017214 original size:13 final size:15
Alignment explanation
Indices: 2017191--2017222 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2017181 TTTTCACTTC
2017191 TTTTTTCTTTC-TGG
1 TTTTTTCTTTCTTGG
2017205 TTTTTT-TTTCTTGG
1 TTTTTTCTTTCTTGG
2017219 TTTT
1 TTTT
2017223 GTAATATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.00, C:0.09, G:0.12, T:0.78
Consensus pattern (15 bp):
TTTTTTCTTTCTTGG
Found at i:2022749 original size:21 final size:21
Alignment explanation
Indices: 2022725--2022766 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2022715 ATTTTAAAAA
*
2022725 AAAATTTTTTAACATAAATTT
1 AAAATTATTTAACATAAATTT
* *
2022746 AAAATTATTTAAGATATATTT
1 AAAATTATTTAACATAAATTT
2022767 TTGGTTTCGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
AAAATTATTTAACATAAATTT
Found at i:2025047 original size:21 final size:21
Alignment explanation
Indices: 2024990--2025039 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
2024980 AATTAATGAA
*
2024990 TTAAAAGAAAACCAAGCTCAG
1 TTAAAAGAAAACCAAGCTCAC
* * *
2025011 TTAAAGGATAACCAAGCTCTC
1 TTAAAAGAAAACCAAGCTCAC
2025032 TTAAAAGA
1 TTAAAAGA
2025040 GAATCAAGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (21 bp):
TTAAAAGAAAACCAAGCTCAC
Found at i:2025923 original size:21 final size:21
Alignment explanation
Indices: 2025897--2025939 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2025887 TTTCTGTGGT
*
2025897 TAATATTGTTTAGGATACTTA
1 TAATATTATTTAGGATACTTA
2025918 TAATATTATTTAGGATACTTA
1 TAATATTATTTAGGATACTTA
2025939 T
1 T
2025940 TATCTGTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.49
Consensus pattern (21 bp):
TAATATTATTTAGGATACTTA
Found at i:2028209 original size:14 final size:13
Alignment explanation
Indices: 2028195--2028239 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 13
2028185 AAATATTATT
2028195 TTTAT-ATTAAAA
1 TTTATAATTAAAA
2028207 TTTATAATT-AAA
1 TTTATAATTAAAA
2028219 TTTA-AA-TAAAA
1 TTTATAATTAAAA
*
2028230 TTTTTAATTA
1 TTTATAATTA
2028240 TTTAAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
10 1 0.04
11 8 0.29
12 14 0.50
13 5 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TTTATAATTAAAA
Found at i:2028244 original size:21 final size:22
Alignment explanation
Indices: 2028202--2028255 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 22
2028192 ATTTTTATAT
2028202 TAAAATTTATAATTAAATTTAAA
1 TAAAATTTATAATT-AATTTAAA
*
2028225 TAAAATTTTTAATT-ATTTAAA
1 TAAAATTTATAATTAATTTAAA
2028246 TAATAATTTA
1 TAA-AATTTA
2028256 GATTATTCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 10 0.36
22 5 0.18
23 13 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAAAATTTATAATTAATTTAAA
Found at i:2028262 original size:21 final size:20
Alignment explanation
Indices: 2028202--2028254 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 20
2028192 ATTTTTATAT
2028202 TAAAATTTATAATTAAATTTAAA
1 TAAAATTT-TAATT--ATTTAAA
2028225 TAAAATTTTTAATTATTTAAA
1 TAAAA-TTTTAATTATTTAAA
2028246 TAATAATTT
1 TAA-AATTT
2028255 AGATTATTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 13 0.46
22 2 0.07
23 10 0.36
24 3 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAAATTTTAATTATTTAAA
Found at i:2028837 original size:7 final size:7
Alignment explanation
Indices: 2028819--2028850 Score: 50
Period size: 6 Copynumber: 4.9 Consensus size: 7
2028809 TTATTTTTTA
2028819 TAATATT
1 TAATATT
2028826 T-ATATT
1 TAATATT
2028832 TAATATT
1 TAATATT
2028839 T-ATATT
1 TAATATT
2028845 TAATAT
1 TAATAT
2028851 ATATTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 12 0.52
7 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TAATATT
Found at i:2028837 original size:13 final size:13
Alignment explanation
Indices: 2028819--2028858 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
2028809 TTATTTTTTA
2028819 TAATATTTATATT
1 TAATATTTATATT
2028832 TAATATTTATATT
1 TAATATTTATATT
2028845 TAATA--TATATT
1 TAATATTTATATT
2028856 TAA
1 TAA
2028859 ATATAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 9 0.33
13 18 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TAATATTTATATT
Found at i:2028855 original size:11 final size:11
Alignment explanation
Indices: 2028826--2028863 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 11
2028816 TTATAATATT
2028826 TATATTTAATA
1 TATATTTAATA
2028837 TTTATATTTAATA
1 --TATATTTAATA
2028850 TATATTTAA-A
1 TATATTTAATA
2028860 TATA
1 TATA
2028864 AATAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 5 0.20
11 9 0.36
13 11 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TATATTTAATA
Found at i:2029108 original size:89 final size:89
Alignment explanation
Indices: 2028968--2029216 Score: 445
Period size: 89 Copynumber: 2.9 Consensus size: 89
2028958 AAGGCGTCAG
*
2028968 CACTCATTTGCATTCATGTGTGATCCTCCAAAGTCAAGCGGTAACATCATTGATTCATTTTCATG
1 CACTCATTTGCATTCATGTGTGATCCTCCAAAGTCAAGTGGTAACATCATTGATTCATTTTCATG
2029033 GGACATATAAATGCAAGGGATCAC
66 GGACATATAAATGCAAGGGATCAC
2029057 CACTCATTTGCATTCATGTGTGATCCTCCAAAGTCAAGTGGTAACATCATTGATTCATTTTCATG
1 CACTCATTTGCATTCATGTGTGATCCTCCAAAGTCAAGTGGTAACATCATTGATTCATTTTCATG
2029122 GGACATATAAATGCAAGGGATCAC
66 GGACATATAAATGCAAGGGATCAC
*
2029146 CACTCA--T---TTCATGTGTGATCCTCGAAAGTCAAGTGGTAACATCATTGATTCATTTTCATG
1 CACTCATTTGCATTCATGTGTGATCCTCCAAAGTCAAGTGGTAACATCATTGATTCATTTTCATG
2029206 GGACATATAAA
66 GGACATATAAA
2029217 CGCAGTGACA
Statistics
Matches: 158, Mismatches: 2, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
84 63 0.40
87 1 0.01
89 94 0.59
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Consensus pattern (89 bp):
CACTCATTTGCATTCATGTGTGATCCTCCAAAGTCAAGTGGTAACATCATTGATTCATTTTCATG
GGACATATAAATGCAAGGGATCAC
Found at i:2029696 original size:14 final size:14
Alignment explanation
Indices: 2029661--2029696 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2029651 AAATATCAAA
2029661 TTATTTAAATTTAT
1 TTATTTAAATTTAT
2029675 TT-TGTTAAATTTAT
1 TTAT-TTAAATTTAT
2029689 TTATTTAA
1 TTATTTAA
2029697 TAAAAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 1 0.05
14 18 0.90
15 1 0.05
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (14 bp):
TTATTTAAATTTAT
Found at i:2029905 original size:11 final size:11
Alignment explanation
Indices: 2029891--2029930 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
2029881 TCGATAATAA
*
2029891 TTAAATGAAAT
1 TTAAATTAAAT
**
2029902 TTAAATTATTT
1 TTAAATTAAAT
2029913 TTAAATTAAAT
1 TTAAATTAAAT
2029924 TTAAATT
1 TTAAATT
2029931 TAAAAACTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:2031572 original size:38 final size:39
Alignment explanation
Indices: 2031471--2031585 Score: 144
Period size: 40 Copynumber: 2.9 Consensus size: 39
2031461 TATGTCTGTT
* *
2031471 AGGGGGATGGTTTGAATTATTGCGTGTCAGTGTCAATGAG
1 AGGGGGATGGTTTGAATTATTGCATGTCA-TGTCAATGAA
* * *
2031511 GGGGGGATGGTTTGAACTGTTGCATGTCATCGTCAAT-AA
1 AGGGGGATGGTTTGAATTATTGCATGTCAT-GTCAATGAA
2031550 AGGGGGAT-GTTTGAATTATTGCATGTCATTGTCAAT
1 AGGGGGATGGTTTGAATTATTGCATGTCA-TGTCAAT
2031586 CTAGAGTATG
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
38 24 0.37
39 10 0.15
40 31 0.48
ACGTcount: A:0.23, C:0.10, G:0.33, T:0.34
Consensus pattern (39 bp):
AGGGGGATGGTTTGAATTATTGCATGTCATGTCAATGAA
Found at i:2034054 original size:25 final size:22
Alignment explanation
Indices: 2034018--2034075 Score: 64
Period size: 25 Copynumber: 2.5 Consensus size: 22
2034008 TGTTTAAATA
2034018 ATATTAAAAATTAAAAATTATTCAT
1 ATATT-AAAATTAAAAATT-TT-AT
*
2034043 ATATTAATAATTATAAATTTTAT
1 ATATTAA-AATTAAAAATTTTAT
2034066 A-ATTAAAATT
1 ATATTAAAATT
2034076 TTTATTATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
21 4 0.13
22 5 0.16
23 3 0.10
24 4 0.13
25 15 0.48
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATTAAAATTAAAAATTTTAT
Found at i:2034080 original size:15 final size:15
Alignment explanation
Indices: 2034049--2034077 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2034039 TCATATATTA
2034049 ATAATTATAAATTTT
1 ATAATTATAAATTTT
2034064 ATAATTA-AAATTTT
1 ATAATTATAAATTTT
2034078 TATTATGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATAATTATAAATTTT
Found at i:2036854 original size:19 final size:20
Alignment explanation
Indices: 2036832--2036871 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
2036822 ATTGAATACA
*
2036832 TATATTTTTATAAT-ATAGT
1 TATATATTTATAATAATAGT
2036851 TATATATTTATAATAATAGT
1 TATATATTTATAATAATAGT
2036871 T
1 T
2036872 GTAATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
TATATATTTATAATAATAGT
Found at i:2036857 original size:21 final size:22
Alignment explanation
Indices: 2036831--2036880 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 22
2036821 TATTGAATAC
2036831 ATATATTTTTATAAT-ATAGTT
1 ATATATTTTTATAATAATAGTT
2036852 ATATA--TTTATAATAATAGTT
1 ATATATTTTTATAATAATAGTT
*
2036872 GTA-ATTTTT
1 ATATATTTTT
2036881 TTATTTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 9 0.36
20 8 0.32
21 8 0.32
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (22 bp):
ATATATTTTTATAATAATAGTT
Found at i:2037031 original size:25 final size:26
Alignment explanation
Indices: 2036967--2037032 Score: 64
Period size: 24 Copynumber: 2.6 Consensus size: 26
2036957 AAAACTTATT
* * *
2036967 AAAAATATATATTTAATTATTAAAATT
1 AAAAATATATA-ATATTTATTAAAATA
* *
2036994 TAAATTATA-AATATTTA-TAAAATA
1 AAAAATATATAATATTTATTAAAATA
2037018 AAAAATATATAATAT
1 AAAAATATATAATAT
2037033 GAGTGAAGCT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
24 13 0.42
25 10 0.32
26 1 0.03
27 7 0.23
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
AAAAATATATAATATTTATTAAAATA
Found at i:2038557 original size:14 final size:14
Alignment explanation
Indices: 2038510--2038564 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
2038500 GTGAATTTAA
*
2038510 ATTTTAAATTTATT
1 ATTTTATATTTATT
*
2038524 ATTTTTAATAAATT-TT
1 A-TTTT-AT-ATTTATT
2038540 ATTTTATATTTATT
1 ATTTTATATTTATT
2038554 ATTTTA-ATTTA
1 ATTTTATATTTA
2038565 AATATTTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
13 8 0.24
14 11 0.32
15 8 0.24
16 4 0.12
17 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
ATTTTATATTTATT
Found at i:2038896 original size:14 final size:14
Alignment explanation
Indices: 2038865--2038907 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
2038855 ATTTAATGTT
*
2038865 AATTAATTTTAATAA
1 AATTAATTTAAAT-A
2038880 AATTTAA-TTAAATA
1 AA-TTAATTTAAATA
2038894 AATTAATTTAAATA
1 AATTAATTTAAATA
2038908 TTTTTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 4 0.16
14 10 0.40
15 7 0.28
16 4 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATTAATTTAAATA
Found at i:2039356 original size:16 final size:16
Alignment explanation
Indices: 2039335--2039412 Score: 54
Period size: 16 Copynumber: 4.9 Consensus size: 16
2039325 AATGTAATAT
2039335 TTATAATTTTATTATA
1 TTATAATTTTATTATA
* *
2039351 TTATAATTATATTTTA
1 TTATAATTTTATTATA
* *
2039367 -AAT-ATTTTA-TATT
1 TTATAATTTTATTATA
**
2039380 TATATAATTTTAAAATA
1 T-TATAATTTTATTATA
2039397 TTAATAATTTATATTA
1 TT-ATAATTT-TATTA
2039413 AATAAATTTT
Statistics
Matches: 45, Mismatches: 11, Indels: 10
0.68 0.17 0.15
Matches are distributed among these distances:
13 2 0.04
14 5 0.11
15 4 0.09
16 21 0.47
17 10 0.22
18 3 0.07
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATAATTTTATTATA
Found at i:2039406 original size:26 final size:25
Alignment explanation
Indices: 2039361--2039410 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
2039351 TTATAATTAT
*
2039361 ATTTTAAATATTTTATATTTATATA
1 ATTTTAAATATTATATATTTATATA
2039386 ATTTTAAAATATTA-ATAATTTATAT
1 ATTTT-AAATATTATAT-ATTTATAT
2039411 TAAATAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
ATTTTAAATATTATATATTTATATA
Found at i:2039482 original size:19 final size:19
Alignment explanation
Indices: 2039431--2039487 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 19
2039421 TTAAAAATAA
*
2039431 ATTTATATAAGATTATATTTTT
1 ATTTATATAA-A-TATA-TTAT
* *
2039453 ATTAATTTAAATATATTAT
1 ATTTATATAAATATATTAT
2039472 ATTTATATAAATATAT
1 ATTTATATAAATATAT
2039488 ATTTAATATT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 17 0.57
20 4 0.13
21 1 0.03
22 8 0.27
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
ATTTATATAAATATATTAT
Found at i:2041671 original size:22 final size:22
Alignment explanation
Indices: 2041641--2041692 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
2041631 AGTCAAATTG
* * *
2041641 ATAAGATTTTAATTATTAATTTA
1 ATAA-ATTTAAATAATTAATTAA
*
2041664 ATTAATTTAAATAATTAATTAA
1 ATAAATTTAAATAATTAATTAA
2041686 ATAAATT
1 ATAAATT
2041693 ATATTAGTGA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
ATAAATTTAAATAATTAATTAA
Found at i:2045196 original size:24 final size:24
Alignment explanation
Indices: 2045162--2045208 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
2045152 GCAACAACAA
*
2045162 CAACAAACACAGCAAAATCAGCAT
1 CAACAAACACAGCAAAACCAGCAT
*
2045186 CAACAACCACAGCAAAACCAGCA
1 CAACAAACACAGCAAAACCAGCA
2045209 ACAGCAAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.53, C:0.34, G:0.09, T:0.04
Consensus pattern (24 bp):
CAACAAACACAGCAAAACCAGCAT
Found at i:2045939 original size:16 final size:16
Alignment explanation
Indices: 2045918--2045963 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
2045908 AAAATTATTA
2045918 TTATATTAAA-ATAAAT
1 TTATA-TAAATATAAAT
2045934 TTATATAAATATAAAT
1 TTATATAAATATAAAT
* *
2045950 TTTTTTAAATATAA
1 TTATATAAATATAA
2045964 TTATAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 4 0.15
16 23 0.85
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTATATAAATATAAAT
Found at i:2048962 original size:42 final size:41
Alignment explanation
Indices: 2048890--2048994 Score: 117
Period size: 42 Copynumber: 2.5 Consensus size: 41
2048880 ATTAAAACTT
* **
2048890 TTTTTA-TTAATATTTCAA-TTAAATTTAAATAAAATA-ATTT
1 TTTTTATTTAA-ATTT-AATTTAAATTAAAATAAAATATATAA
*
2048930 TTTATTATTTAAATATTAATTTAAATTAAAATAAATTATATAA
1 TTT-TTATTTAAAT-TTAATTTAAATTAAAATAAAATATATAA
2048973 TTTTTATTTAAATTTAATTTAA
1 TTTTTATTTAAATTTAATTTAA
2048995 TACAAATCTG
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
40 3 0.05
41 16 0.29
42 32 0.57
43 5 0.09
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (41 bp):
TTTTTATTTAAATTTAATTTAAATTAAAATAAAATATATAA
Found at i:2048987 original size:36 final size:38
Alignment explanation
Indices: 2048907--2048994 Score: 94
Period size: 36 Copynumber: 2.4 Consensus size: 38
2048897 TAATATTTCA
* * *
2048907 ATTAAATTTAAA-TAAAATAATTTTTTATTATTTAAAT
1 ATTAAATTTAAATTAAAATAATATTATATAATTTAAAT
**
2048944 ATT-AATTTAAATTAAAATAA-ATTATATAATTTTTAT
1 ATTAAATTTAAATTAAAATAATATTATATAATTTAAAT
*
2048980 -TTAAATTTAATTTAA
1 ATTAAATTTAAATTAA
2048995 TACAAATCTG
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
35 2 0.05
36 30 0.70
37 11 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (38 bp):
ATTAAATTTAAATTAAAATAATATTATATAATTTAAAT
Found at i:2049561 original size:13 final size:15
Alignment explanation
Indices: 2049534--2049572 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
2049524 AAGGGTCAAA
2049534 AGAAAAAGAAGAAAG
1 AGAAAAAGAAGAAAG
2049549 AGAAAAAGAAAAGAAA-
1 AGAAAAAG--AAGAAAG
2049565 AGAAAAAG
1 AGAAAAAG
2049573 TGGTCTAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.36
16 8 0.36
17 6 0.27
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AGAAAAAGAAGAAAG
Found at i:2057772 original size:19 final size:18
Alignment explanation
Indices: 2057718--2057775 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
2057708 AGTTTCATTT
*
2057718 ATAATAAATTAAATTTAA
1 ATAATAAATAAAATTTAA
* * *
2057736 ATAAAAAATATTATTTTAA
1 ATAATAAATA-AAATTTAA
2057755 ATAATTAAATAAAATTTAA
1 ATAA-TAAATAAAATTTAA
2057774 AT
1 AT
2057776 TTAAATTTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
18 8 0.26
19 18 0.58
20 5 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAATAAATAAAATTTAA
Found at i:2059262 original size:15 final size:18
Alignment explanation
Indices: 2059247--2059282 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2059237 TGAATTTTTA
2059247 TTAA-AAAT-TATATTAT
1 TTAATAAATATATATTAT
2059263 TTAATAAATATATATT-T
1 TTAATAAATATATATTAT
2059280 TTA
1 TTA
2059283 TTTAATGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.22
17 8 0.44
18 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAATAAATATATATTAT
Found at i:2059303 original size:14 final size:14
Alignment explanation
Indices: 2059277--2059310 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
2059267 TAAATATATA
2059277 TTTTTATTTAATGT
1 TTTTTATTTAATGT
2059291 TTATTTA-TTAATGT
1 TT-TTTATTTAATGT
2059305 TTTTTA
1 TTTTTA
2059311 ATATAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.21
14 11 0.58
15 4 0.21
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (14 bp):
TTTTTATTTAATGT
Found at i:2061001 original size:4 final size:4
Alignment explanation
Indices: 2060992--2061018 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2060982 CCAAGTACTG
2060992 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
2061019 TGCTATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:2064958 original size:23 final size:23
Alignment explanation
Indices: 2064928--2064973 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2064918 ATTCATTTCC
2064928 TAAATCAGATGTTAATCTCACAT
1 TAAATCAGATGTTAATCTCACAT
2064951 TAAATCAGATGTTAATCTCACAT
1 TAAATCAGATGTTAATCTCACAT
2064974 CAGTTGTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (23 bp):
TAAATCAGATGTTAATCTCACAT
Found at i:2067000 original size:23 final size:24
Alignment explanation
Indices: 2066933--2067006 Score: 60
Period size: 23 Copynumber: 3.0 Consensus size: 24
2066923 TAAAATAATA
* *
2066933 TTATATAAATATATAAATAGATCAAATT
1 TTATAT-AA-ATAT-AATATAT-AAAAT
* * *
2066961 TTATATTATTATTATAT-TAAAAT
1 TTATATAAATATAATATATAAAAT
2066984 TTATATAAATATAATATATAAAA
1 TTATATAAATATAATATATAAAA
2067007 ATACACTATA
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
23 18 0.49
24 6 0.16
25 3 0.08
26 3 0.08
27 1 0.03
28 6 0.16
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (24 bp):
TTATATAAATATAATATATAAAAT
Found at i:2068126 original size:26 final size:28
Alignment explanation
Indices: 2068076--2068132 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 28
2068066 TAATTTATAA
2068076 TTAATATTAATTATATTATTAAAAAT-T
1 TTAATATTAATTATATTATTAAAAATAT
2068103 TTAAT-TTAATTA-ATT-TATACAAAATAT
1 TTAATATTAATTATATTAT-TA-AAAATAT
2068130 TTA
1 TTA
2068133 TTAGATTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
24 1 0.04
25 5 0.19
26 12 0.44
27 9 0.33
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (28 bp):
TTAATATTAATTATATTATTAAAAATAT
Found at i:2069920 original size:20 final size:19
Alignment explanation
Indices: 2069883--2069922 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
2069873 ATTTTTATAT
* *
2069883 TAATATTTATATATTTTTA
1 TAATATTTAAATAATTTTA
2069902 TAATAATTTAAATAATTTTA
1 TAAT-ATTTAAATAATTTTA
2069922 T
1 T
2069923 TATTAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TAATATTTAAATAATTTTA
Found at i:2069944 original size:16 final size:16
Alignment explanation
Indices: 2069901--2069949 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
2069891 ATATATTTTT
2069901 ATAATAATTTAAAT-A
1 ATAATAATTTAAATAA
** *
2069916 ATTTTATTATTAAATAA
1 ATAATAAT-TTAAATAA
2069933 ATAATAATTTAAATAA
1 ATAATAATTTAAATAA
2069949 A
1 A
2069950 ACAAATTACA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
15 5 0.19
16 15 0.58
17 6 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATAATAATTTAAATAA
Found at i:2073713 original size:236 final size:237
Alignment explanation
Indices: 2073285--2073732 Score: 589
Period size: 236 Copynumber: 1.9 Consensus size: 237
2073275 TTATATATAC
* * * * * *
2073285 ATTATCAATGTATTAAATATAAATTATTATTATATATTATATGAAAAAAATCTAAATTGACATAC
1 ATTATCAATGCATCAAACATAAATTATTATTACATATTACATGAAAAAAATCTAAATTAACATAC
* * * * *
2073350 GAATCCTTAAAAATCACATATTAATTTGATCACATGAATACTAATTATCACACCTATTGTCTAAA
66 GAAACATAAAAAATCACATATTAAATTGATCACATGAATACTAATTACCACACCTATTGTCTAAA
* * *
2073415 GAAGAATCCTTCCAATGATATCACCATTTATCTTCTTTACTTTCATAATTTTTTTAAAA-TTTTA
131 GAAGAATCCTTCCAATGATATCACCATTTATCTTCTTTACTTCCACAATTTTCTTAAAATTTTTA
*
2073479 AAAACATCAAGAATTATTTAAATAAATTTAAAAAATATAGAT
196 AAAACATAAAGAATTATTTAAATAAATTTAAAAAATATAGAT
* * * *
2073521 ATTATCAATGCATCGAACATAAATTATTATTACATATTACATGAAAATAATTTAAATTAACAT-T
1 ATTATCAATGCATCAAACATAAATTATTATTACATATTACATGAAAAAAATCTAAATTAACATAC
* * * * * * *
2073585 TAAACAATAAAAAATTACATATTAAATTGATTATATGAATA-TCAATTACCACTCTTGTTGTCTA
66 GAAAC-ATAAAAAATCACATATTAAATTGATCACATGAATACT-AATTACCACACCTATTGTCTA
*
2073649 AAGAAGAATCCTTCCAATGATATCAACCATTTATCTTCTTTACTTCCACAA-TTTCTTCAAATTT
129 AAGAAGAATCCTTCCAATGATATC-ACCATTTATCTTCTTTACTTCCACAATTTTCTTAAAATTT
*
2073713 TTAAAAACATAAATAATTAT
193 TTAAAAACATAAAGAATTAT
2073733 ATAGATAATT
Statistics
Matches: 180, Mismatches: 28, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
235 4 0.02
236 132 0.73
237 44 0.24
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (237 bp):
ATTATCAATGCATCAAACATAAATTATTATTACATATTACATGAAAAAAATCTAAATTAACATAC
GAAACATAAAAAATCACATATTAAATTGATCACATGAATACTAATTACCACACCTATTGTCTAAA
GAAGAATCCTTCCAATGATATCACCATTTATCTTCTTTACTTCCACAATTTTCTTAAAATTTTTA
AAAACATAAAGAATTATTTAAATAAATTTAAAAAATATAGAT
Found at i:2074176 original size:6 final size:6
Alignment explanation
Indices: 2074165--2074194 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
2074155 TCAAATCAAA
2074165 TAAATT TAAATT TAAA-T TAAATT TAAATT T
1 TAAATT TAAATT TAAATT TAAATT TAAATT T
2074195 TAAAATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAAATT
Found at i:2076179 original size:3 final size:3
Alignment explanation
Indices: 2076171--2076197 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2076161 TTATTTTAGT
2076171 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
2076198 AATGTGACGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2083009 original size:20 final size:21
Alignment explanation
Indices: 2082986--2083040 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
2082976 ATAAATATTT
2082986 AAATAAATATAAATATAT-AA
1 AAATAAATATAAATATATAAA
* *
2083006 AAATAATTTTTTAAATATATAAA
1 AAATAA--ATATAAATATATAAA
2083029 AAATTAAATATA
1 AAA-TAAATATA
2083041 TTTATATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
20 6 0.22
22 13 0.48
23 5 0.19
24 3 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATAAATATAAATATATAAA
Found at i:2095554 original size:2 final size:2
Alignment explanation
Indices: 2095549--2095580 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2095539 ACACACACAC
2095549 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
2095581 CGTTGTTTAA
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:2095790 original size:2 final size:2
Alignment explanation
Indices: 2095783--2095808 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2095773 TATGTCTGAT
2095783 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2095809 AAAGTGAATG
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):
TA
Found at i:2096038 original size:91 final size:91
Alignment explanation
Indices: 2095883--2096065 Score: 294
Period size: 91 Copynumber: 2.0 Consensus size: 91
2095873 TTGCCCTGAA
* * *
2095883 TTTCTTACTCCCCAGGGCCAGCTTTCACATACATTGACATTGATCATAGATCATGTTTTGTATCC
1 TTTCTTACTCCCAAGGGCCAACTTTCACATACATTGACATTGATCATAGATCATGCTTTGTATCC
2095948 GTTTAGAAACTCAATACAATACTCTT
66 GTTTAGAAACTCAATACAATACTCTT
* *
2095974 TTTCTTACTCCCAAGTGCCAACTTTCACATACATTGATATTGATCATAGATCATGCTTTGTATCC
1 TTTCTTACTCCCAAGGGCCAACTTTCACATACATTGACATTGATCATAGATCATGCTTTGTATCC
* * *
2096039 GTTTGGAAATTCAGTACAATACTCTT
66 GTTTAGAAACTCAATACAATACTCTT
2096065 T
1 T
2096066 CATTTTATCT
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 84 1.00
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (91 bp):
TTTCTTACTCCCAAGGGCCAACTTTCACATACATTGACATTGATCATAGATCATGCTTTGTATCC
GTTTAGAAACTCAATACAATACTCTT
Found at i:2099042 original size:12 final size:11
Alignment explanation
Indices: 2099017--2099055 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2099007 AATTTTCCCA
*
2099017 AAAAATAAATT
1 AAAAATAAAAT
*
2099028 AAAATTAAAACT
1 AAAAATAAAA-T
2099040 AAAAATAAAAT
1 AAAAATAAAAT
2099051 AAAAA
1 AAAAA
2099056 AATAAAGCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:2099087 original size:3 final size:3
Alignment explanation
Indices: 2099079--2099118 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
2099069 CTATGTACTA
*
2099079 TAT TAT TA- TACT CAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2099119 CGCTCCATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.91
4 1 0.03
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2103906 original size:20 final size:22
Alignment explanation
Indices: 2103864--2103919 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 22
2103854 AATTTATATG
*
2103864 AAATTGATTTTTTA-TAGATTT
1 AAATTAATTTTTTATTAGATTT
*
2103885 AATTTAATTTTTTATTA-A-TT
1 AAATTAATTTTTTATTAGATTT
2103905 AAATTAATTTTTTAT
1 AAATTAATTTTTTAT
2103920 ATATTGATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 16 0.52
21 13 0.42
22 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.61
Consensus pattern (22 bp):
AAATTAATTTTTTATTAGATTT
Found at i:2103929 original size:24 final size:25
Alignment explanation
Indices: 2103897--2103949 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 25
2103887 TTTAATTTTT
2103897 TATTAATTAAAT-T-AATTTTTTATA
1 TATTAATTAAATATCAATTTTTTA-A
*
2103921 TATTGATTAAATGATCAATTTTTTAA
1 TATTAATTAAAT-ATCAATTTTTTAA
2103947 TAT
1 TAT
2103950 GTATTAGATC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 11 0.44
26 5 0.20
27 9 0.36
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (25 bp):
TATTAATTAAATATCAATTTTTTAA
Found at i:2104557 original size:23 final size:24
Alignment explanation
Indices: 2104514--2104558 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
2104504 TCGATTTAAT
**
2104514 ATTTATATCATATTATTTAAAAGA
1 ATTTATATCATATTAAATAAAAGA
2104538 ATTTATAT-ATATTAAATAAAA
1 ATTTATATCATATTAAATAAAA
2104559 TTTTTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
ATTTATATCATATTAAATAAAAGA
Found at i:2105279 original size:9 final size:9
Alignment explanation
Indices: 2105267--2105291 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2105257 TATAATTTAT
2105267 TTAATATAA
1 TTAATATAA
2105276 TTAATATAA
1 TTAATATAA
2105285 TTAATAT
1 TTAATAT
2105292 GATATATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTAATATAA
Found at i:2105280 original size:18 final size:18
Alignment explanation
Indices: 2105261--2105320 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
2105251 AATAAATATA
2105261 ATTTATTTAATATAATTA-
1 ATTTATTTAATAT-ATTAT
* *
2105279 ATATAATTAATATGA-TAT
1 ATTTATTTAATAT-ATTAT
2105297 ATTTAATTT-ATATATTAT
1 ATTT-ATTTAATATATTAT
2105315 ATTTAT
1 ATTTAT
2105321 ATTTAAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
17 5 0.15
18 26 0.76
19 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
ATTTATTTAATATATTAT
Found at i:2105296 original size:23 final size:23
Alignment explanation
Indices: 2105255--2105303 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
2105245 ATTTTAAATA
* *
2105255 AATATAATTTATTTAATATAATT
1 AATATAATTAATATAATATAATT
* *
2105278 AATATAATTAATATGATATATTT
1 AATATAATTAATATAATATAATT
2105301 AAT
1 AAT
2105304 TTATATATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
AATATAATTAATATAATATAATT
Found at i:2106218 original size:21 final size:20
Alignment explanation
Indices: 2106191--2106247 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
2106181 TTTAATAAAA
*
2106191 AAATTAAATTATTTATTATT
1 AAATTTAATTATTTATTATT
* *
2106211 AAATTTAATTTTTTAATTTTT
1 AAATTTAATTATTT-ATTATT
*
2106232 TAATTTAATTATTTAT
1 AAATTTAATTATTTAT
2106248 ATTTAAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
AAATTTAATTATTTATTATT
Found at i:2106238 original size:13 final size:13
Alignment explanation
Indices: 2106222--2106269 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
2106212 AATTTAATTT
2106222 TTTAATTTTTTAA
1 TTTAATTTTTTAA
*
2106235 TTTAATTATTTATA
1 TTTAATTTTTTA-A
**
2106249 TTTAAAATTTTAA
1 TTTAATTTTTTAA
2106262 TATTAATT
1 T-TTAATT
2106270 AAAAATAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
13 13 0.48
14 14 0.52
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTAATTTTTTAA
Found at i:2106257 original size:21 final size:21
Alignment explanation
Indices: 2106190--2106258 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
2106180 ATTTAATAAA
*
2106190 AAAATTAAATTATTTAT-TATT
1 AAAATTTAATTATTTATAT-TT
*
2106211 -AAATTTAATTTTTTA-ATTTT
1 AAAATTTAATTATTTATA-TTT
**
2106231 TTAATTTAATTATTTATATTT
1 AAAATTTAATTATTTATATTT
2106252 AAAATTT
1 AAAATTT
2106259 TAATATTAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
20 15 0.39
21 22 0.58
22 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
AAAATTTAATTATTTATATTT
Found at i:2115512 original size:2 final size:2
Alignment explanation
Indices: 2115505--2115537 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2115495 AAGAAAATGA
2115505 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
2115538 ATAAAAATTG
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:2120458 original size:25 final size:24
Alignment explanation
Indices: 2120430--2120547 Score: 92
Period size: 27 Copynumber: 4.6 Consensus size: 24
2120420 AAGCCACCCA
2120430 TTTGTTTGTCAAAAATGGTGGTTATT
1 TTTGTTTGTCAAAAATGGTGG-T-TT
*
2120456 TTGTGTTTGTCAAAAATGGTAGTTT
1 TT-TGTTTGTCAAAAATGGTGGTTT
* * *
2120481 CCTTTGTATTTGTCAAATATGGAGGCTTG
1 --TTTG--TTTGTCAAAAATGGTGG-TTT
* * *
2120510 TTTATTTGTCAAAATTGGTGGCTT
1 TTTGTTTGTCAAAAATGGTGGTTT
*
2120534 GTTGTTTGTCAAAA
1 TTTGTTTGTCAAAA
2120548 TTAGTGGCTA
Statistics
Matches: 73, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
24 13 0.18
25 16 0.22
26 5 0.07
27 23 0.32
28 14 0.19
29 2 0.03
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.47
Consensus pattern (24 bp):
TTTGTTTGTCAAAAATGGTGGTTT
Found at i:2120541 original size:24 final size:25
Alignment explanation
Indices: 2120487--2120556 Score: 90
Period size: 24 Copynumber: 2.8 Consensus size: 25
2120477 GTTTCCTTTG
*
2120487 TATTTGTC-AAATATGGAGGCTTGTT
1 TATTTGTCAAAAT-TGGTGGCTTGTT
2120512 TATTTGTCAAAATTGGTGGCTTG-T
1 TATTTGTCAAAATTGGTGGCTTGTT
* *
2120536 TGTTTGTCAAAATTAGTGGCT
1 TATTTGTCAAAATTGGTGGCT
2120557 AATTTTTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
24 20 0.49
25 17 0.41
26 4 0.10
ACGTcount: A:0.23, C:0.09, G:0.24, T:0.44
Consensus pattern (25 bp):
TATTTGTCAAAATTGGTGGCTTGTT
Found at i:2123129 original size:21 final size:22
Alignment explanation
Indices: 2123100--2123145 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2123090 TGTTCAGACA
** *
2123100 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2123122 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2123143 AGT
1 AGT
2123146 TTCGACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:2125051 original size:25 final size:24
Alignment explanation
Indices: 2125023--2125147 Score: 106
Period size: 27 Copynumber: 4.9 Consensus size: 24
2125013 AAGCCACCCA
2125023 TTTGTTTGTCAAAAATGGTGGTTATT
1 TTTGTTTGTCAAAAATGGTGG-T-TT
2125049 TTGTGTTTGTCAAAAATGGTGGTTT
1 TT-TGTTTGTCAAAAATGGTGGTTT
* * *
2125074 CCTTTGTATTTGTCAAATATGGAGGCTTG
1 --TTTG--TTTGTCAAAAATGGTGG-TTT
* * *
2125103 TTTATTTGTCAAAATTGGTGGCTT
1 TTTGTTTGTCAAAAATGGTGGTTT
* *
2125127 GTTGTTTGTCAAAATTGGTGG
1 TTTGTTTGTCAAAAATGGTGG
2125148 CTAATTTTTA
Statistics
Matches: 82, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
24 20 0.24
25 16 0.20
26 5 0.06
27 24 0.29
28 15 0.18
29 2 0.02
ACGTcount: A:0.21, C:0.07, G:0.26, T:0.46
Consensus pattern (24 bp):
TTTGTTTGTCAAAAATGGTGGTTT
Found at i:2125134 original size:24 final size:25
Alignment explanation
Indices: 2125080--2125149 Score: 99
Period size: 24 Copynumber: 2.8 Consensus size: 25
2125070 GTTTCCTTTG
*
2125080 TATTTGTC-AAATATGGAGGCTTGTT
1 TATTTGTCAAAAT-TGGTGGCTTGTT
2125105 TATTTGTCAAAATTGGTGGCTTG-T
1 TATTTGTCAAAATTGGTGGCTTGTT
*
2125129 TGTTTGTCAAAATTGGTGGCT
1 TATTTGTCAAAATTGGTGGCT
2125150 AATTTTTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
24 21 0.50
25 17 0.40
26 4 0.10
ACGTcount: A:0.21, C:0.09, G:0.26, T:0.44
Consensus pattern (25 bp):
TATTTGTCAAAATTGGTGGCTTGTT
Found at i:2132631 original size:21 final size:21
Alignment explanation
Indices: 2132601--2132641 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2132591 AACATGCTGT
2132601 AAAAGCATGAAACAT-AGCTC
1 AAAAGCATGAAACATGAGCTC
*
2132621 AAAATGCATGAATCATGAGCT
1 AAAA-GCATGAAACATGAGCT
2132642 TTTAACATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 10 0.56
22 4 0.22
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.20
Consensus pattern (21 bp):
AAAAGCATGAAACATGAGCTC
Found at i:2133584 original size:13 final size:13
Alignment explanation
Indices: 2133566--2133595 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2133556 ATACAAAGAT
2133566 CAATGTATCGATA
1 CAATGTATCGATA
2133579 CAATGTATCGATA
1 CAATGTATCGATA
2133592 CAAT
1 CAAT
2133596 TTGAGTAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:2137173 original size:5 final size:5
Alignment explanation
Indices: 2137162--2137212 Score: 66
Period size: 5 Copynumber: 9.8 Consensus size: 5
2137152 GAGGGTGAGG
* *
2137162 GAAAA AAAAA AAAAA GAAAA GAAAA GAAAA GAAAA GAAAAA GAAAAA GAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA G-AAAA G-AAAA GAAA
2137213 TGTGACTTGG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
5 32 0.74
6 11 0.26
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:2137947 original size:2 final size:2
Alignment explanation
Indices: 2137940--2137969 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2137930 AAACCTGCAA
2137940 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
2137970 CTCATCATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2138946 original size:18 final size:17
Alignment explanation
Indices: 2138921--2138962 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
2138911 TTATAATATG
*
2138921 ATAT-AAAATAAAATAT
1 ATATAAAAATAAAATAA
*
2138937 ATATTAAAAATAATATAA
1 ATA-TAAAAATAAAATAA
2138955 ATATAAAA
1 ATATAAAA
2138963 TATTTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 3 0.14
17 6 0.27
18 13 0.59
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
ATATAAAAATAAAATAA
Found at i:2138951 original size:16 final size:16
Alignment explanation
Indices: 2138901--2138965 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 16
2138891 GAAAGAGGTG
*
2138901 ATATAAAAAATTATAAT
1 ATATATAAAA-TATAAT
*
2138918 ATGATATAAAATAAAAT
1 AT-ATATAAAATATAAT
2138935 ATATATTAAAA-ATAAT
1 ATATA-TAAAATATAAT
2138951 ATAAATATAAAATAT
1 AT--ATATAAAATAT
2138966 TTTAAATATA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
16 9 0.22
17 19 0.47
18 12 0.30
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
ATATATAAAATATAAT
Found at i:2138965 original size:27 final size:28
Alignment explanation
Indices: 2138921--2138982 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
2138911 TTATAATATG
2138921 ATATAAAATAAAATATATATTAAAAATA
1 ATATAAAATAAAATATATATTAAAAATA
*
2138949 ATATAAATATAAAATAT-T-TTAAATATA
1 ATATAAA-ATAAAATATATATTAAAAATA
2138976 ATTATAA
1 A-TATAA
2138983 TTTTAATATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 9 0.29
28 13 0.42
29 9 0.29
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (28 bp):
ATATAAAATAAAATATATATTAAAAATA
Found at i:2140766 original size:17 final size:17
Alignment explanation
Indices: 2140736--2140770 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2140726 AAAAGCCCTT
*
2140736 CTATGCTATTTGCACAA
1 CTATGCTATATGCACAA
*
2140753 CTATGTTATATGCACAA
1 CTATGCTATATGCACAA
2140770 C
1 C
2140771 CATGGCAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.34
Consensus pattern (17 bp):
CTATGCTATATGCACAA
Found at i:2143588 original size:18 final size:17
Alignment explanation
Indices: 2143565--2143619 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
2143555 CCAATATTAT
2143565 ATTATTATTTATTTTTTA
1 ATTATTATTT-TTTTTTA
*
2143583 ATTATT-TTTTGTTTCTTT
1 ATTATTATTTT-TTT-TTA
2143601 ATTATTA-TTTTTTTTA
1 ATTATTATTTTTTTTTA
2143617 ATT
1 ATT
2143620 TTTTTCCTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
16 6 0.19
17 9 0.28
18 17 0.53
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (17 bp):
ATTATTATTTTTTTTTA
Found at i:2148574 original size:17 final size:18
Alignment explanation
Indices: 2148538--2148599 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
2148528 AATATTATTA
* * *
2148538 TTTTATGTAAATTAATTT
1 TTTTATTTAAGTTAAATT
*
2148556 TTTTATTGTATG-T-AATT
1 TTTTATT-TAAGTTAAATT
*
2148573 TTATATTTAAGTTAAATT
1 TTTTATTTAAGTTAAATT
2148591 TTTTATTTA
1 TTTTATTTA
2148600 TTATTAATTA
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
16 3 0.09
17 10 0.29
18 19 0.56
19 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (18 bp):
TTTTATTTAAGTTAAATT
Found at i:2153205 original size:21 final size:22
Alignment explanation
Indices: 2153179--2153236 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
2153169 TTTAAAGAAA
*
2153179 TTAAAAATACT-AACATTATCT
1 TTAAAAATAATAAACATTATCT
* *
2153200 TTAAAAAGAATAAAATATTATCT
1 TTAAAAATAAT-AAACATTATCT
*
2153223 TTAAAAATATTAAA
1 TTAAAAATAATAAA
2153237 AATAAAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 9 0.30
22 3 0.10
23 18 0.60
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (22 bp):
TTAAAAATAATAAACATTATCT
Found at i:2158269 original size:14 final size:15
Alignment explanation
Indices: 2158212--2158273 Score: 51
Period size: 16 Copynumber: 4.3 Consensus size: 15
2158202 ATCGGATGCG
* * *
2158212 TATATATTTAATTTT
1 TATATTTTTAAATAT
*
2158227 TATATATTTTAAAAAT
1 TATAT-TTTTAAATAT
2158243 TATATTTTT--ATAT
1 TATATTTTTAAATAT
2158256 T-TATTTTTAAATA-
1 TATATTTTTAAATAT
2158269 TATAT
1 TATAT
2158274 AAGATATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
12 7 0.18
13 5 0.13
14 6 0.16
15 9 0.24
16 11 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TATATTTTTAAATAT
Found at i:2158882 original size:2 final size:2
Alignment explanation
Indices: 2158875--2158900 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2158865 GCACCTGTCA
2158875 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
2158901 GAATGCATGT
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:2160314 original size:18 final size:20
Alignment explanation
Indices: 2160271--2160314 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 20
2160261 GATTAATGTA
2160271 ATATTAT-TTATATAAATTT
1 ATATTATATTATATAAATTT
*
2160290 -TAATATATTA-AT-AATTT
1 ATATTATATTATATAAATTT
2160307 ATATTATA
1 ATATTATA
2160315 CATATAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
17 5 0.24
18 13 0.62
19 3 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATTATATTATATAAATTT
Found at i:2161011 original size:51 final size:51
Alignment explanation
Indices: 2160935--2161037 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
2160925 AATGATTTCT
*
2160935 AGCTACAGTAAAGACTTCGTTGCTACCAAAGTACGACCTAACAAAACTATC
1 AGCTACAGTAAAGACTTCGCTGCTACCAAAGTACGACCTAACAAAACTATC
2160986 AGCTACAGTAAAGACTTCGCTGCTACCAAAGTACGACCTAACAAAACTATC
1 AGCTACAGTAAAGACTTCGCTGCTACCAAAGTACGACCTAACAAAACTATC
2161037 A
1 A
2161038 CTTCAAATAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.40, C:0.26, G:0.14, T:0.20
Consensus pattern (51 bp):
AGCTACAGTAAAGACTTCGCTGCTACCAAAGTACGACCTAACAAAACTATC
Found at i:2161191 original size:19 final size:20
Alignment explanation
Indices: 2161153--2161192 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2161143 ATTAAATATA
*
2161153 TTAATTGAGATAAATTTTAAT
1 TTAATTGAGA-AAATATTAAT
2161174 TTAATTGAG-AAATATTAAT
1 TTAATTGAGAAAATATTAAT
2161193 AAAGTAGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (20 bp):
TTAATTGAGAAAATATTAAT
Found at i:2165969 original size:13 final size:12
Alignment explanation
Indices: 2165947--2165985 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
2165937 TGTACAATTA
2165947 ATTATAATAAAT
1 ATTATAATAAAT
2165959 ATTATTAATAAAT
1 ATTA-TAATAAAT
*
2165972 ATTAATAAAAAAT
1 ATT-ATAATAAAT
2165985 A
1 A
2165986 ATTAAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 4 0.17
13 19 0.79
14 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATTATAATAAAT
Found at i:2166133 original size:37 final size:38
Alignment explanation
Indices: 2166059--2166152 Score: 154
Period size: 38 Copynumber: 2.5 Consensus size: 38
2166049 TAATGATTTA
* *
2166059 ATATAACATGAGAGATCAGTGCCAAAAAAATATATTAT
1 ATATAACATGAGAGATTAGTACCAAAAAAATATATTAT
*
2166097 ATATAACATGAGATATTAGTACCAAAAAAA-ATATTAT
1 ATATAACATGAGAGATTAGTACCAAAAAAATATATTAT
2166134 ATATAACATGAGAGATTAG
1 ATATAACATGAGAGATTAG
2166153 AGGAAGTTGG
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
37 25 0.48
38 27 0.52
ACGTcount: A:0.51, C:0.09, G:0.13, T:0.28
Consensus pattern (38 bp):
ATATAACATGAGAGATTAGTACCAAAAAAATATATTAT
Found at i:2166795 original size:15 final size:16
Alignment explanation
Indices: 2166769--2166798 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2166759 TGAAAATTAA
2166769 TTAAGAAACTAGTTAT
1 TTAAGAAACTAGTTAT
2166785 TTAAG-AACTAGTTA
1 TTAAGAAACTAGTTA
2166799 GTTACAGGTT
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:0.07, G:0.13, T:0.37
Consensus pattern (16 bp):
TTAAGAAACTAGTTAT
Found at i:2167205 original size:20 final size:20
Alignment explanation
Indices: 2167180--2167222 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2167170 AATTAAAAAT
2167180 GGATACAAGAGAGGGATGAG
1 GGATACAAGAGAGGGATGAG
**
2167200 GGATACTTGAGAGGGATGAG
1 GGATACAAGAGAGGGATGAG
2167220 GGA
1 GGA
2167223 GCCTCTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.05, G:0.47, T:0.14
Consensus pattern (20 bp):
GGATACAAGAGAGGGATGAG
Found at i:2167359 original size:27 final size:28
Alignment explanation
Indices: 2167308--2167369 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
2167298 TCAATATTTA
*
2167308 ACAAATACAAAAGAAACCACCATTTTTG
1 ACAAACACAAAAGAAACCACCATTTTTG
* *
2167336 ACAAACACAAAA-TAACCACCATTTTTT
1 ACAAACACAAAAGAAACCACCATTTTTG
2167363 ACAAACA
1 ACAAACA
2167370 AATGGGTGGC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
27 20 0.65
28 11 0.35
ACGTcount: A:0.52, C:0.24, G:0.03, T:0.21
Consensus pattern (28 bp):
ACAAACACAAAAGAAACCACCATTTTTG
Found at i:2169287 original size:21 final size:22
Alignment explanation
Indices: 2169249--2169294 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2169239 ATCTGTTAAA
* **
2169249 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTACGGAGTACT
2169270 ACTCCACCTGCTACGGAGTACT
1 ACTCCACCTGCTACGGAGTACT
2169292 ACT
1 ACT
2169295 TGTCTGAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.22, C:0.30, G:0.17, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTACGGAGTACT
Found at i:2171931 original size:28 final size:28
Alignment explanation
Indices: 2171846--2171936 Score: 77
Period size: 28 Copynumber: 3.4 Consensus size: 28
2171836 TTAACCATAA
* * *
2171846 ATTTTGACAAAT--AAACAAGCCTCCAT
1 ATTTTGACAAATACAAAGAAACCACCAT
*
2171872 A-TTTGATAAATACAAAGGAAACCACCAT
1 ATTTTGACAAATACAAA-GAAACCACCAT
*
2171900 -TTTTGACAAATACAAA-ATAATCACCAT
1 ATTTTGACAAATACAAAGA-AACCACCAT
2171927 ATTTT-ACAAA
1 ATTTTGACAAA
2171937 CAAATGGGTG
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
25 9 0.17
26 2 0.04
27 16 0.30
28 26 0.49
ACGTcount: A:0.47, C:0.19, G:0.07, T:0.27
Consensus pattern (28 bp):
ATTTTGACAAATACAAAGAAACCACCAT
Found at i:2172172 original size:35 final size:35
Alignment explanation
Indices: 2172125--2172200 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
2172115 ATTAATTAAA
* * *
2172125 AAATAAATATATTTTATATTTTTATAATTA-AATTT
1 AAATAAAAATATTTTATATTATTA-AATAATAATTT
*
2172160 AAATAAAAATATTTTTTATTATTAAATAATAATTT
1 AAATAAAAATATTTTATATTATTAAATAATAATTT
2172195 AAATAA
1 AAATAA
2172201 TATTAATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
34 4 0.11
35 32 0.89
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (35 bp):
AAATAAAAATATTTTATATTATTAAATAATAATTT
Found at i:2172207 original size:15 final size:15
Alignment explanation
Indices: 2172184--2172213 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2172174 TTTATTATTA
2172184 AATAATAATTTAAAT
1 AATAATAATTTAAAT
*
2172199 AATATTAATTTAAAT
1 AATAATAATTTAAAT
2172214 TAAAAAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATAATAATTTAAAT
Found at i:2173363 original size:2 final size:2
Alignment explanation
Indices: 2173356--2173385 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2173346 GTTATATTTG
2173356 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
2173386 TTCGGATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2173697 original size:2 final size:2
Alignment explanation
Indices: 2173690--2173721 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2173680 TTTATGCTCA
2173690 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
2173722 GAATTGGATT
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:2176017 original size:25 final size:25
Alignment explanation
Indices: 2175989--2176064 Score: 77
Period size: 24 Copynumber: 3.0 Consensus size: 25
2175979 CGAAAAAATT
2175989 TAATATAAAAATATTAAAATTTATA
1 TAATATAAAAATATTAAAATTTATA
*
2176014 TAATAT-AAATTATT--AATTTATTA
1 TAATATAAAAATATTAAAATTTA-TA
* *
2176037 AAATATATAAATATATAAAAGTTTATA
1 TAATATAAAAATAT-TAAAA-TTTATA
2176064 T
1 T
2176065 TTAAAGCACT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
22 6 0.15
23 7 0.17
24 12 0.30
25 7 0.17
27 4 0.10
28 4 0.10
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (25 bp):
TAATATAAAAATATTAAAATTTATA
Found at i:2176025 original size:21 final size:22
Alignment explanation
Indices: 2175983--2176043 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 22
2175973 CTTATACGAA
2175983 AAAATTTAATATAA-A-AATATT
1 AAAATTT-ATATAATATAATATT
2176004 AAAATTTATATAATATAA-ATT
1 AAAATTTATATAATATAATATT
* *
2176025 ATTAATTTATTAAAATATA
1 A-AAATTTA-TATAATATA
2176044 TAAATATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 6 0.18
21 12 0.35
22 8 0.24
23 8 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAATTTATATAATATAATATT
Found at i:2176129 original size:23 final size:23
Alignment explanation
Indices: 2176080--2176129 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
2176070 GCACTTCATC
**
2176080 TAATTAAATTGTTTTAAACAATT
1 TAATTAAATTGTTTTAAACAAAA
* * *
2176103 TAATTATATTGTTTTTAATAAAA
1 TAATTAAATTGTTTTAAACAAAA
2176126 TAAT
1 TAAT
2176130 ATTTTTAATT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (23 bp):
TAATTAAATTGTTTTAAACAAAA
Done.