Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold140
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: 3130556
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82166 characters in sequence are not A, C, G, or T
File 7 of 20
Found at i:1087426 original size:16 final size:17
Alignment explanation
Indices: 1087407--1087443 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1087397 TAAATTATTT
1087407 TAATTTTAAAATT-AAA
1 TAATTTTAAAATTAAAA
*
1087423 TAA-TTTAAATTTAAAA
1 TAATTTTAAAATTAAAA
1087439 TAATT
1 TAATT
1087444 CATAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 8 0.44
16 9 0.50
17 1 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAATTTTAAAATTAAAA
Found at i:1087431 original size:15 final size:16
Alignment explanation
Indices: 1087411--1087443 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1087401 TTATTTTAAT
1087411 TTTAAAATT-AAATAA
1 TTTAAAATTAAAATAA
*
1087426 TTTAAATTTAAAATAA
1 TTTAAAATTAAAATAA
1087442 TT
1 TT
1087444 CATAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTAAAATTAAAATAA
Found at i:1088223 original size:34 final size:33
Alignment explanation
Indices: 1088156--1088375 Score: 242
Period size: 34 Copynumber: 6.5 Consensus size: 33
1088146 ATATGTCACG
* *
1088156 TGTTGATTAAATGGTGATGTGGTAGTTTACCAT
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCAT
* * *
1088189 TGTTGATTAAATGAGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATG-GTGATTTGGTAGCTTACCAT
* *
1088223 TGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAAT-GGTGATTTGGTAGCTTACCAT
** *
1088257 TGTTGATTAAATGAGAAATTTGGTAGCTTACTAT
1 TGTTGATTAAATG-GTGATTTGGTAGCTTACCAT
* *
1088291 TATTGATTAAATAGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAAT--GGTGATTTGGTAGCTTACCAT
* * *
1088326 TGTTGACTAAATGGTAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGT-GATTTGGTAGCTTACCAT
*
1088360 TATTGATTAAATGGTG
1 TGTTGATTAAATGGTG
1088376 GTTTTTACCA
Statistics
Matches: 158, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
33 18 0.11
34 112 0.71
35 27 0.17
36 1 0.01
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.40
Consensus pattern (33 bp):
TGTTGATTAAATGGTGATTTGGTAGCTTACCAT
Found at i:1088333 original size:103 final size:101
Alignment explanation
Indices: 1088156--1088373 Score: 301
Period size: 103 Copynumber: 2.1 Consensus size: 101
1088146 ATATGTCACG
** * * * *
1088156 TGTTGATTAAATGGTGATGTGGTAGTTTACCATTGTTGATTAAATGAGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGAAATGTGGTAGCTTACCATTATTGATTAAATGAGTGATTTGGTGGCTTACC
1088221 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
66 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
* * *
1088257 TGTTGATTAAATGAGAAATTTGGTAGCTTACTATTATTGATTAAATAGGGTGATTTGGTGGCTTA
1 TGTTGATTAAATG-GAAATGTGGTAGCTTACCATTATTGATTAAAT-GAGTGATTTGGTGGCTTA
* * *
1088322 CCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCCAT
64 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
*
1088360 TATTGATTAAATGG
1 TGTTGATTAAATGG
1088374 TGGTTTTTAC
Statistics
Matches: 102, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
101 13 0.13
102 27 0.26
103 62 0.61
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.40
Consensus pattern (101 bp):
TGTTGATTAAATGGAAATGTGGTAGCTTACCATTATTGATTAAATGAGTGATTTGGTGGCTTACC
ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:1088347 original size:69 final size:69
Alignment explanation
Indices: 1088158--1088373 Score: 278
Period size: 68 Copynumber: 3.2 Consensus size: 69
1088148 ATGTCACGTG
* * * *
1088158 TTGATTAAAT-GGTGATGTGGTAGTTTACCATTGTTGATTAAATGAGT-GATTTGGTGGTTTGCC
1 TTGATTAAATGGGTGATTTGGTAGCTTACCATTGTTGATTAAATGAGTAGATTTGGTAGCTTGCC
*
1088221 ATTG
66 ATTA
* * * * *
1088225 TTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGAG-AAATTTGGTAGCTTACT
1 TTGATTAAATGGGTGATTTGGTAGCTTACCATTGTTGATTAAATGAGTAGATTTGGTAGCTTGCC
1088289 ATTA
66 ATTA
* * *
1088293 TTGATTAAATAGGGTGATTTGGTGGCTTACCATTGTTGACTAAATG-GTAGATTTGGTAGGTTGC
1 TTGATTAAAT-GGGTGATTTGGTAGCTTACCATTGTTGATTAAATGAGTAGATTTGGTAGCTTGC
1088357 CATTA
65 CATTA
1088362 TTGATTAAATGG
1 TTGATTAAATGG
1088374 TGGTTTTTAC
Statistics
Matches: 127, Mismatches: 18, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
67 9 0.07
68 59 0.46
69 59 0.46
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.40
Consensus pattern (69 bp):
TTGATTAAATGGGTGATTTGGTAGCTTACCATTGTTGATTAAATGAGTAGATTTGGTAGCTTGCC
ATTA
Found at i:1092852 original size:34 final size:34
Alignment explanation
Indices: 1092783--1093001 Score: 271
Period size: 34 Copynumber: 6.5 Consensus size: 34
1092773 AAGTGAGAGA
* * *
1092783 ATTGTTGATTAAAT-GGTGATGTAGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
1092816 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
1092850 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
1092884 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
1092918 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
1092952 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
1092986 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1093002 TGGTTTTTAT
Statistics
Matches: 160, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
33 17 0.11
34 142 0.89
35 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:1092933 original size:102 final size:101
Alignment explanation
Indices: 1092783--1093001 Score: 330
Period size: 102 Copynumber: 2.2 Consensus size: 101
1092773 AAGTGAGAGA
** * * * *
1092783 ATTGTTGATTAAATGGTGATGTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATGTAGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
1092848 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
* *
1092884 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATGTAGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
* * *
1092949 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1092986 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1093002 TGGTTTTTAT
Statistics
Matches: 106, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 16 0.15
102 90 0.85
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATGTAGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:1094207 original size:14 final size:14
Alignment explanation
Indices: 1094169--1094208 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
1094159 AGTTCGGTTA
*
1094169 TTAAATTAATTAAAT
1 TTAAA-TAATTTAAT
1094184 TTAAAT-ATTTAAT
1 TTAAATAATTTAAT
1094197 TTAAATAATTTA
1 TTAAATAATTTA
1094209 TAAATTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 12 0.52
14 6 0.26
15 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAAATAATTTAAT
Found at i:1095341 original size:21 final size:21
Alignment explanation
Indices: 1095317--1095374 Score: 77
Period size: 19 Copynumber: 2.9 Consensus size: 21
1095307 CAATCAAAAT
1095317 TTATATAAATATA-AAATATTA
1 TTATATAAATATATAAATA-TA
*
1095338 TTATAAAAATATATAAATATA
1 TTATATAAATATATAAATATA
1095359 --ATATAAATATATAAAT
1 TTATATAAATATATAAAT
1095375 TATCAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.44
21 14 0.41
22 5 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TTATATAAATATATAAATATA
Found at i:1095371 original size:29 final size:29
Alignment explanation
Indices: 1095318--1095373 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
1095308 AATCAAAATT
*
1095318 TATATAAATATAAAATATTATTATAAAAA
1 TATATAAATATAAAATAATATTATAAAAA
*
1095347 TATATAAATATAATATAA-ATATATAAA
1 TATATAAATATAAAATAATAT-TATAAA
1095374 TTATCAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (29 bp):
TATATAAATATAAAATAATATTATAAAAA
Found at i:1096831 original size:6 final size:7
Alignment explanation
Indices: 1096810--1096834 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1096800 TTGATAACTT
1096810 AAATAAA
1 AAATAAA
1096817 AAATAAA
1 AAATAAA
1096824 AAATAAA
1 AAATAAA
1096831 AAAT
1 AAAT
1096835 TTATGATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AAATAAA
Found at i:1102885 original size:21 final size:21
Alignment explanation
Indices: 1102859--1102968 Score: 73
Period size: 21 Copynumber: 5.0 Consensus size: 21
1102849 TTTAATTTTG
1102859 ATATATTATTAATATATAAAT
1 ATATATTATTAATATATAAAT
*
1102880 ATATATTATCAATAAATTATATAAT
1 ATATATTATTAAT--A-TATA-AAT
* * *
1102905 ATTTTTTATTAATAAATAAAT
1 ATATATTATTAATATATAAAT
*
1102926 ATAATATT-TTAA-AAATAAAT
1 AT-ATATTATTAATATATAAAT
* *
1102946 ACATATAACTTAACT-TATAAAT
1 ATATATTA-TTAA-TATATAAAT
1102968 A
1 A
1102969 AATTTACTAT
Statistics
Matches: 70, Mismatches: 10, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
19 4 0.06
20 9 0.13
21 25 0.36
22 13 0.19
23 2 0.03
24 4 0.06
25 13 0.19
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (21 bp):
ATATATTATTAATATATAAAT
Found at i:1102886 original size:18 final size:18
Alignment explanation
Indices: 1102859--1102906 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
1102849 TTTAATTTTG
1102859 ATATATTATTAATATATAA
1 ATATA-TATTAATATATAA
1102878 ATATATATT-ATCA-ATAA
1 ATATATATTAAT-ATATAA
1102895 AT-TATA-TAATAT
1 ATATATATTAATAT
1102907 TTTTTATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
15 2 0.08
16 6 0.23
17 8 0.31
18 5 0.19
19 5 0.19
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATATATTAATATATAA
Found at i:1102913 original size:25 final size:26
Alignment explanation
Indices: 1102869--1102935 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 26
1102859 ATATATTATT
* *
1102869 AATATATA-AATATATATTATCAATA
1 AATATATATAATATTTTTTATCAATA
*
1102894 AAT-TATATAATATTTTTTATTAATA
1 AATATATATAATATTTTTTATCAATA
*
1102919 AATAAATATAATATTTT
1 AATATATATAATATTTT
1102936 AAAAATAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 4 0.11
25 20 0.56
26 12 0.33
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (26 bp):
AATATATATAATATTTTTTATCAATA
Found at i:1102927 original size:26 final size:25
Alignment explanation
Indices: 1102885--1102935 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
1102875 TAAATATATA
*
1102885 TTATCAATAAATTATATAATATTTT
1 TTATCAATAAATAATATAATATTTT
*
1102910 TTATTAATAAATAAATATAATATTTT
1 TTATCAATAAAT-AATATAATATTTT
1102936 AAAAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (25 bp):
TTATCAATAAATAATATAATATTTT
Found at i:1103320 original size:17 final size:17
Alignment explanation
Indices: 1103298--1103341 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
1103288 TTATTTTTAT
1103298 AAAAATTATAAATATAA
1 AAAAATTATAAATATAA
* *
1103315 AAAAATTACAATTATAA
1 AAAAATTATAAATATAA
* *
1103332 TAATATTATA
1 AAAAATTATA
1103342 TTTATATAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAAATTATAAATATAA
Found at i:1104039 original size:22 final size:21
Alignment explanation
Indices: 1104000--1104040 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
1103990 TATTAAAAAT
1104000 TATTTTTTATTAATATTTATA
1 TATTTTTTATTAATATTTATA
1104021 TATTTTTATAATTAA-ATTTA
1 TATTTTT-T-ATTAATATTTA
1104041 AATAAAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 6 0.33
23 5 0.28
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TATTTTTTATTAATATTTATA
Found at i:1105319 original size:9 final size:9
Alignment explanation
Indices: 1105305--1105333 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1105295 TAAGGTTGAG
1105305 AAAAAAATT
1 AAAAAAATT
1105314 AAAAAAA-T
1 AAAAAAATT
1105322 AAAAAAATT
1 AAAAAAATT
1105331 AAA
1 AAA
1105334 TTAAATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (9 bp):
AAAAAAATT
Found at i:1105460 original size:3 final size:3
Alignment explanation
Indices: 1105452--1105485 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1105442 AAATTAAAAA
1105452 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1105486 ACCATAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1106153 original size:17 final size:17
Alignment explanation
Indices: 1106131--1106186 Score: 50
Period size: 16 Copynumber: 3.5 Consensus size: 17
1106121 AATAATTTTT
1106131 TTATATTTAAAAAATTA
1 TTATATTTAAAAAATTA
*
1106148 TTATATGTT--AAATTTA
1 TTATAT-TTAAAAAATTA
*
1106164 TT-TA-TTAAAAAAATA
1 TTATATTTAAAAAATTA
1106179 TTAT-TTTA
1 TTATATTTA
1106187 TTAATAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 11
0.69 0.07 0.24
Matches are distributed among these distances:
13 2 0.06
15 9 0.29
16 12 0.39
17 6 0.19
18 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
TTATATTTAAAAAATTA
Found at i:1107002 original size:32 final size:32
Alignment explanation
Indices: 1106951--1107034 Score: 90
Period size: 32 Copynumber: 2.8 Consensus size: 32
1106941 AAAATAATAA
1106951 AAATATATAAATATTTAAAATATATATAACAT
1 AAATATATAAATATTTAAAATATATATAACAT
* *
1106983 AAAT-TATTAATATATTAAAAT-T-TAT-ATA-
1 AAATATATAAATAT-TTAAAATATATATAACAT
*
1107011 AAATATA-AAATATTTTAAATATAT
1 AAATATATAAATATTTAAAATATAT
1107035 TTATAATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
27 6 0.14
28 10 0.23
29 5 0.11
30 3 0.07
31 9 0.20
32 11 0.25
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (32 bp):
AAATATATAAATATTTAAAATATATATAACAT
Found at i:1107007 original size:18 final size:19
Alignment explanation
Indices: 1106985--1107035 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
1106975 TATAACATAA
1106985 ATTATTAATATATTAAAAT
1 ATTATTAATATATTAAAAT
*
1107004 -TTATATAAAATA-TAAAAT
1 ATTAT-TAATATATTAAAAT
1107022 ATT-TTAAATATATT
1 ATTATT-AATATATT
1107036 TATAATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
17 1 0.04
18 16 0.62
19 9 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTATTAATATATTAAAAT
Found at i:1107042 original size:11 final size:10
Alignment explanation
Indices: 1106948--1107055 Score: 53
Period size: 10 Copynumber: 10.9 Consensus size: 10
1106938 TAAAAAATAA
* *
1106948 TAAAAATATA
1 TAAATATATT
1106958 TAAATAT-TT
1 TAAATATATT
* *
1106967 AAAATATATA
1 TAAATATATT
*
1106977 TAACATAAATT
1 TAA-ATATATT
*
1106988 ATTAATATATT
1 -TAAATATATT
* * *
1106999 AAAATTTATA
1 TAAATATATT
1107009 TAAA-ATA-T
1 TAAATATATT
*
1107017 AAAATAT-TT
1 TAAATATATT
1107026 TAAATATATT
1 TAAATATATT
*
1107036 TATAATATAAT
1 TA-AATATATT
*
1107047 AAAATATAT
1 TAAATATAT
1107056 AAATATAATA
Statistics
Matches: 70, Mismatches: 21, Indels: 14
0.67 0.20 0.13
Matches are distributed among these distances:
8 3 0.04
9 18 0.26
10 28 0.40
11 19 0.27
12 2 0.03
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (10 bp):
TAAATATATT
Found at i:1107078 original size:48 final size:48
Alignment explanation
Indices: 1106944--1107092 Score: 128
Period size: 48 Copynumber: 3.0 Consensus size: 48
1106934 ATAATAAAAA
* *
1106944 ATAATAAAAATATATAAATAT-T-TAAAATATATATAACATAAATTATTAAT
1 ATAAT-AAAATATATAAATATATATAAAAT-TATA-AATAT-ATTTATTAAT
* *
1106994 ATATTAAAATTTATATAAA-ATATA-AAATATTTTAAATATATTTA-TAAT
1 ATAATAAAA--TATATAAATATATATAAA-ATTATAAATATATTTATTAAT
1107042 ATAATAAAATATATAAATATAATATAAAATTATAAATTATTATTTTATTAA
1 ATAATAAAATATATAAATAT-ATATAAAATTATAAA-TA-TA-TTTATTAA
1107093 GAGCAGTGAT
Statistics
Matches: 81, Mismatches: 6, Indels: 22
0.74 0.06 0.20
Matches are distributed among these distances:
46 8 0.10
47 2 0.02
48 22 0.27
49 13 0.16
50 12 0.15
51 19 0.23
52 5 0.06
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (48 bp):
ATAATAAAATATATAAATATATATAAAATTATAAATATATTTATTAAT
Found at i:1107893 original size:26 final size:26
Alignment explanation
Indices: 1107829--1107893 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
1107819 ATTGATAGTG
1107829 AAATAAAAAATATTTTACAAATAATT
1 AAATAAAAAATATTTTACAAATAATT
* * *
1107855 TAGTAAAATATATTTTA-AAA-AATAT
1 AAATAAAAAATATTTTACAAATAAT-T
1107880 AAATAAATAAATAT
1 AAATAAA-AAATAT
1107894 GGCACTCGTG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
24 3 0.10
25 9 0.29
26 19 0.61
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (26 bp):
AAATAAAAAATATTTTACAAATAATT
Found at i:1108125 original size:14 final size:14
Alignment explanation
Indices: 1108103--1108171 Score: 52
Period size: 14 Copynumber: 4.7 Consensus size: 14
1108093 GTTATAATTT
1108103 ATTTA-AAATAAAA
1 ATTTATAAATAAAA
1108116 ATTTATAAATATAAA
1 ATTTATAAATA-AAA
1108131 ATTTTATCATTAA-AAAA
1 A-TTTAT-A--AATAAAA
* *
1108148 ATTTTTAAATATAA
1 ATTTATAAATAAAA
*
1108162 ATTTTTAAAT
1 ATTTATAAAT
1108172 TTTTATTATT
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
13 7 0.15
14 18 0.38
15 5 0.11
16 9 0.19
17 5 0.11
18 1 0.02
19 2 0.04
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (14 bp):
ATTTATAAATAAAA
Found at i:1108131 original size:16 final size:16
Alignment explanation
Indices: 1108106--1108162 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
1108096 ATAATTTATT
1108106 TAAA-ATAAAAATTTA
1 TAAATATAAAAATTTA
*
1108121 TAAATATAAAATTTTA
1 TAAATATAAAAATTTA
* * * *
1108137 TCATTAAAAAAATTTT
1 TAAATATAAAAATTTA
1108153 TAAATATAAA
1 TAAATATAAA
1108163 TTTTTAAATT
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
15 4 0.12
16 28 0.88
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAATATAAAAATTTA
Found at i:1109799 original size:16 final size:17
Alignment explanation
Indices: 1109768--1109804 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
1109758 CGTCTATCTA
1109768 TATATCTATATTATATT
1 TATATCTATATTATATT
*
1109785 TATAT-TATTTTATATT
1 TATATCTATATTATATT
1109801 TATA
1 TATA
1109805 GCTTTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATCTATATTATATT
Found at i:1109803 original size:11 final size:11
Alignment explanation
Indices: 1109768--1109800 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1109758 CGTCTATCTA
*
1109768 TATATCTATAT
1 TATATTTATAT
1109779 TATATTTATAT
1 TATATTTATAT
1109790 TAT-TTTATAT
1 TATATTTATAT
1109800 T
1 T
1109801 TATAGCTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1110345 original size:26 final size:26
Alignment explanation
Indices: 1110303--1110352 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
1110293 AAAAAACATG
1110303 TAAATATAAAAAAAATATTTTATTCT
1 TAAATATAAAAAAAATATTTTATTCT
*
1110329 TAAAT-TAAATAATAATATTTTATT
1 TAAATATAAA-AAAAATATTTTATT
1110353 TACAAAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (26 bp):
TAAATATAAAAAAAATATTTTATTCT
Found at i:1110864 original size:28 final size:28
Alignment explanation
Indices: 1110792--1110864 Score: 67
Period size: 30 Copynumber: 2.5 Consensus size: 28
1110782 ATTTCTATTA
*
1110792 ATAATCTTTAAAATTTACATTTATCCATTC
1 ATAATCTTTAAAA-TTACATTTAT-CAATC
* * *
1110822 ATGATTTTTAAAAATTATATTTAT-AATC
1 ATAATCTTT-AAAATTACATTTATCAATC
1110850 ATAATCTTTCAAAAT
1 ATAATCTTT-AAAAT
1110865 ATTTAATTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
28 15 0.43
30 16 0.46
31 4 0.11
ACGTcount: A:0.41, C:0.11, G:0.01, T:0.47
Consensus pattern (28 bp):
ATAATCTTTAAAATTACATTTATCAATC
Found at i:1113843 original size:22 final size:21
Alignment explanation
Indices: 1113810--1113856 Score: 76
Period size: 22 Copynumber: 2.2 Consensus size: 21
1113800 TTATAATTTT
*
1113810 TAATTATTAAATATTTTTAAA
1 TAATTATTAAATAATTTTAAA
1113831 TAATTAATTAAATAATTTTAAA
1 TAATT-ATTAAATAATTTTAAA
1113853 TAAT
1 TAAT
1113857 AAAATTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAATTATTAAATAATTTTAAA
Found at i:1113855 original size:10 final size:11
Alignment explanation
Indices: 1113810--1113856 Score: 62
Period size: 10 Copynumber: 4.4 Consensus size: 11
1113800 TTATAATTTT
1113810 TAATTATTAAA
1 TAATTATTAAA
*
1113821 T-ATTTTTAAA
1 TAATTATTAAA
1113831 TAATTAATTAAA
1 TAATT-ATTAAA
1113843 TAATT-TTAAA
1 TAATTATTAAA
1113853 TAAT
1 TAAT
1113857 AAAATTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 18 0.56
11 4 0.12
12 10 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
TAATTATTAAA
Found at i:1113879 original size:20 final size:22
Alignment explanation
Indices: 1113824--1113898 Score: 75
Period size: 22 Copynumber: 3.4 Consensus size: 22
1113814 TATTAAATAT
* *
1113824 TTTTAAATAAT-TAATTAAATAA
1 TTTTAAATAATAAAATT-ATTAA
1113846 TTTTAAATAATAAAATT-TTAA
1 TTTTAAATAATAAAATTATTAA
*
1113867 TTTTATA-AATAAAATTATTAAA
1 TTTTAAATAATAAAATTATT-AA
1113889 TTATTAAATA
1 TT-TTAAATA
1113899 TTTTATTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
20 9 0.20
21 11 0.25
22 15 0.34
23 8 0.18
24 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TTTTAAATAATAAAATTATTAA
Found at i:1113952 original size:39 final size:38
Alignment explanation
Indices: 1113903--1113993 Score: 94
Period size: 39 Copynumber: 2.3 Consensus size: 38
1113893 TAAATATTTT
*
1113903 ATTTATTATTTTTTAAATAAATAATAAAA-ATATATAATA
1 ATTTTTTATTTTTT-AATAAA-AATAAAATATATATAATA
* * * *
1113942 ATTTTTTATTTTATTTATAAAATTAAAATATTTATAATT
1 ATTTTTTATTTT-TTAATAAAAATAAAATATATATAATA
*
1113981 ATATTTTATTTTT
1 ATTTTTTATTTTT
1113994 AATTTATTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
38 7 0.16
39 35 0.80
40 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (38 bp):
ATTTTTTATTTTTTAATAAAAATAAAATATATATAATA
Found at i:1113990 original size:17 final size:16
Alignment explanation
Indices: 1113946--1114002 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
1113936 ATAATAATTT
1113946 TTTATTTTATTTATAAA
1 TTTATTTTATTTAT-AA
* ***
1113963 ATTAAAATATTTATAA
1 TTTATTTTATTTATAA
*
1113979 TTATATTTTATTTTTAA
1 TT-TATTTTATTTATAA
1113996 TTTATTT
1 TTTATTT
1114003 AAAATTTAAT
Statistics
Matches: 30, Mismatches: 9, Indels: 3
0.71 0.21 0.07
Matches are distributed among these distances:
16 8 0.27
17 22 0.73
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTATTTTATTTATAA
Found at i:1114607 original size:30 final size:30
Alignment explanation
Indices: 1114571--1114631 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
1114561 TTAGGGGTTT
*
1114571 AGGAATTCTGGGTTTCATAGGTACTGCTTA
1 AGGAATTCTGGGTTTCATAGGTACTCCTTA
1114601 AGGAATTCTGGGTTTCATAGGTACTCCTTA
1 AGGAATTCTGGGTTTCATAGGTACTCCTTA
1114631 A
1 A
1114632 ACAGGATGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.36
Consensus pattern (30 bp):
AGGAATTCTGGGTTTCATAGGTACTCCTTA
Found at i:1115603 original size:261 final size:263
Alignment explanation
Indices: 1115104--1115633 Score: 780
Period size: 261 Copynumber: 2.0 Consensus size: 263
1115094 AGTAAGTGCG
* * * *
1115104 TTTTGGGTGAAAGCAATAGACAGAGGCAATGTTCCCTGAACCTGGCTGAACTCAGCAATGTTTCT
1 TTTTGGGTGAAAGCAATAGACAGAGGCAACGTTCCCTGAAACTGGCTGAACTAAGCAATGTTTAT
* **
1115169 TTTGCAGATCCATTTGCTTTTGAAAATGCAGCCTCAGCTGCATCTATGAGTGCAGCAACGGAGGG
66 TTTGCAGATCCATTGGCACTTGAAAATGCAGCCTCAGCTGCATCTATGAGTGCAGCAACGGAGGG
* * * * * *
1115234 GATTAATGGGCACCGTTCCGAATGCAGCTCTGCTGGGCTCTTTCCTGTGCATATAAATTTATCAG
131 GATTAATAGACACCATTCCGAATGCAACTCTGATGGGCTCTTTCCTGTGCATATAAATTTATCAA
* *
1115299 CTCAACCAAACATATGGATTGATGGCAATTGCACGCTGAGAAAAAACCAAAGTAAGAATAAGTT-
196 CTCAACAAAACATATGGATTGATGGCAATTGCACGCCGAGAAAAAACCAAAGTAAG-ATAAGTTA
1115363 AGAC
260 AGAC
*
1115367 TTTTGGGT-AATAGCAATAGAC-G-GGCAACGTTCCCTGAAACTGGCTGAACTAAGCAATTTTTA
1 TTTTGGGTGAA-AGCAATAGACAGAGGCAACGTTCCCTGAAACTGGCTGAACTAAGCAATGTTTA
* * *
1115429 TTTTGCAGATCTATTGGCACTTGAAAATGCAGCCTCAGCTGCATCTATGAGTGCGGCATCGGAGG
65 TTTTGCAGATCCATTGGCACTTGAAAATGCAGCCTCAGCTGCATCTATGAGTGCAGCAACGGAGG
* * * *
1115494 GGATTAATAGACATCATTCTGAATGCAACTCTGATGGGCTCTTTCCTGTGTATGTAAATTTATCA
130 GGATTAATAGACACCATTCCGAATGCAACTCTGATGGGCTCTTTCCTGTGCATATAAATTTATCA
* *
1115559 ACTCAACAAAACATATGGATTGATGGCAATTGCACGCCGAGAAAACAGCAAAGTAAGATAAGTTA
195 ACTCAACAAAACATATGGATTGATGGCAATTGCACGCCGAGAAAAAACCAAAGTAAGATAAGTT-
1115624 AAGAC
259 AAGAC
1115629 TTTTG
1 TTTTG
1115634 TGAATTCACT
Statistics
Matches: 239, Mismatches: 25, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
260 7 0.03
261 202 0.85
262 12 0.05
263 18 0.08
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (263 bp):
TTTTGGGTGAAAGCAATAGACAGAGGCAACGTTCCCTGAAACTGGCTGAACTAAGCAATGTTTAT
TTTGCAGATCCATTGGCACTTGAAAATGCAGCCTCAGCTGCATCTATGAGTGCAGCAACGGAGGG
GATTAATAGACACCATTCCGAATGCAACTCTGATGGGCTCTTTCCTGTGCATATAAATTTATCAA
CTCAACAAAACATATGGATTGATGGCAATTGCACGCCGAGAAAAAACCAAAGTAAGATAAGTTAA
GAC
Found at i:1126625 original size:2 final size:2
Alignment explanation
Indices: 1126618--1126649 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1126608 CAAACGACTC
1126618 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1126650 GTGTGGATAA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1127392 original size:18 final size:19
Alignment explanation
Indices: 1127351--1127393 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
1127341 CCTGTGACGA
1127351 TAAAATAATATAAATATAT
1 TAAAATAATATAAATATAT
* *
1127370 AAAAAT-ATATAAATATTT
1 TAAAATAATATAAATATAT
1127388 TAAAAT
1 TAAAAT
1127394 TTATGTAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAAATAATATAAATATAT
Found at i:1127758 original size:18 final size:18
Alignment explanation
Indices: 1127711--1127759 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
1127701 TCTTTTTATT
*
1127711 TTAATTATTTTAAATTAA
1 TTAATTATTTTAAATAAA
* *
1127729 TT-ATTTTCTTTATATAAA
1 TTAATTAT-TTTAAATAAA
1127747 TTAATTATTTTAA
1 TTAATTATTTTAA
1127760 TTTTGTAAGG
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
17 4 0.17
18 16 0.67
19 4 0.17
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAATTATTTTAAATAAA
Found at i:1128494 original size:15 final size:14
Alignment explanation
Indices: 1128474--1128503 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1128464 AAAAATTAAA
1128474 TAAATTTTTATCATT
1 TAAATTTTTAT-ATT
1128489 TAAATTTTTATATT
1 TAAATTTTTATATT
1128503 T
1 T
1128504 GCTTTGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (14 bp):
TAAATTTTTATATT
Found at i:1128696 original size:21 final size:21
Alignment explanation
Indices: 1128664--1128725 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
1128654 ATTAAAAATC
*
1128664 ATAAAA-TTTAATTAATTTTAA
1 ATAAAATTTTAATTAA-ATTAA
*
1128685 A-AATATTTTAATTACAATTAA
1 ATAAAATTTTAATTA-AATTAA
1128706 ATAAAATTTTAATTAAATTA
1 ATAAAATTTTAATTAAATTA
1128726 TATCTTACTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
20 3 0.09
21 19 0.54
22 13 0.37
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
ATAAAATTTTAATTAAATTAA
Found at i:1128897 original size:17 final size:16
Alignment explanation
Indices: 1128875--1128923 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 16
1128865 ATAATAAATT
1128875 AATATTTGTTAATAATA
1 AATATTT-TTAATAATA
1128892 AATATTTTT--TAA-A
1 AATATTTTTAATAATA
1128905 AAT-TTTATTAATAATA
1 AATATTT-TTAATAATA
1128921 AAT
1 AAT
1128924 TTTATATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
12 3 0.11
13 6 0.21
14 3 0.11
15 3 0.11
16 6 0.21
17 7 0.25
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
AATATTTTTAATAATA
Found at i:1128903 original size:27 final size:28
Alignment explanation
Indices: 1128872--1128953 Score: 73
Period size: 29 Copynumber: 3.0 Consensus size: 28
1128862 ATAATAATAA
1128872 ATTAATATTTGTTAATAATAAATATTT-T
1 ATTAATATTTGTTAATAATAAAT-TTTAT
* *
1128900 -TTAAAAATTTTATTAATAATAAATTTTAT
1 ATT-AATA-TTTGTTAATAATAAATTTTAT
* *
1128929 ATT-TTATTTGATAATAAT-AATTTTA
1 ATTAATATTTGTTAATAATAAATTTTA
1128954 AATTTTATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
26 7 0.16
27 12 0.27
28 7 0.16
29 16 0.36
30 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
ATTAATATTTGTTAATAATAAATTTTAT
Found at i:1128923 original size:16 final size:16
Alignment explanation
Indices: 1128883--1128928 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
1128873 TTAATATTTG
1128883 TTAATAATAAATATTT-
1 TTAATAATAAAT-TTTA
1128899 TT--TAA-AAATTTTA
1 TTAATAATAAATTTTA
1128912 TTAATAATAAATTTTA
1 TTAATAATAAATTTTA
1128928 T
1 T
1128929 ATTTTATTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
12 3 0.12
13 6 0.23
14 3 0.12
15 3 0.12
16 11 0.42
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAATAATAAATTTTA
Found at i:1128950 original size:26 final size:27
Alignment explanation
Indices: 1128913--1128963 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
1128903 AAAATTTTAT
*
1128913 TAATAATAAATTTTATATTTTATTTGA
1 TAATAATAAATTTTAAATTTTATTTGA
1128940 TAATAAT-AATTTTAAATTTTATTT
1 TAATAATAAATTTTAAATTTTATTT
1128964 TAATATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (27 bp):
TAATAATAAATTTTAAATTTTATTTGA
Found at i:1128967 original size:24 final size:25
Alignment explanation
Indices: 1128904--1128968 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 25
1128894 TATTTTTTAA
1128904 AAATTTTA--TTAATAATAAATTTT
1 AAATTTTATTTTAATAATAAATTTT
*
1128927 ATATTTTATTTGATAATAAT-AATTTT
1 AAATTTTATTT--TAATAATAAATTTT
1128953 AAATTTTATTTTAATA
1 AAATTTTATTTTAATA
1128969 TTTTTAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
23 7 0.19
24 5 0.14
25 1 0.03
26 16 0.44
27 7 0.19
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
AAATTTTATTTTAATAATAAATTTT
Found at i:1128977 original size:33 final size:33
Alignment explanation
Indices: 1128919--1128987 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 33
1128909 TTATTAATAA
1128919 TAAATTTTATATTTTATTTGATAATAATAAT-TT
1 TAAATTTTATATTTTATTTGATAATAA-AATATT
*
1128952 TAAATTTTAT-TTTAATATTT-TTAATAAAATATT
1 TAAATTTTATATTT--TATTTGATAATAAAATATT
1128985 TAA
1 TAA
1128988 TAAATCAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
32 6 0.19
33 21 0.66
34 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (33 bp):
TAAATTTTATATTTTATTTGATAATAAAATATT
Found at i:1129107 original size:17 final size:16
Alignment explanation
Indices: 1129065--1129107 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1129055 ATATTAAATA
1129065 TAATAATAT-TATTTT
1 TAATAATATATATTTT
*
1129080 TAAAAAATATATATTTT
1 T-AATAATATATATTTT
1129097 TAATAAT-TATA
1 TAATAATATATA
1129108 CTTCATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 5 0.21
16 12 0.50
17 7 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TAATAATATATATTTT
Found at i:1136033 original size:58 final size:58
Alignment explanation
Indices: 1135947--1136318 Score: 388
Period size: 58 Copynumber: 6.4 Consensus size: 58
1135937 GCATAGTAAA
* * * * * *
1135947 TGATGCCAAATCACCCAAACTCAGATCGCCACCAAGGTGACCAGATCTACGCGCTAAA
1 TGATGACAAGTCACCCAAACTCAGATCGCCACCAAGGCGACCAGATCCACGCACTAAG
* ** *
1136005 TGATGACAAATCACTTAAACTCAGATCGCCACCAAGGCGACCAGATCCATGCACTAAG
1 TGATGACAAGTCACCCAAACTCAGATCGCCACCAAGGCGACCAGATCCACGCACTAAG
* * *
1136063 TGATGCCAAGTCACCCAAACTCAGATCGCCACCAAAGCGACCAGATCCACGCGCTAAG
1 TGATGACAAGTCACCCAAACTCAGATCGCCACCAAGGCGACCAGATCCACGCACTAAG
* * * * * *
1136121 TAACGACAAGTCATCCAAACTCAGATCGCCATCAAGGCGATC-GAATCCATGCACTAAG
1 TGATGACAAGTCACCCAAACTCAGATCGCCACCAAGGCGACCAG-ATCCACGCACTAAG
** * * * *
1136179 TGACAACAAGTCACCCAAACTCAGATCGCCACCAAGGTGACCGGATTCACACACTAAG
1 TGATGACAAGTCACCCAAACTCAGATCGCCACCAAGGCGACCAGATCCACGCACTAAG
* * * * * * * *
1136237 TGATGCCAAGTTACCAAAACTTAGCTCGCCACCAAGGCGACCA-AACTCACACACTAGG
1 TGATGACAAGTCACCCAAACTCAGATCGCCACCAAGGCGACCAGATC-CACGCACTAAG
** *
1136295 TGGCGCCAAGTCACCCAAACTCAG
1 TGATGACAAGTCACCCAAACTCAG
1136319 GTTGCTACTA
Statistics
Matches: 261, Mismatches: 50, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
57 2 0.01
58 258 0.99
59 1 0.00
ACGTcount: A:0.35, C:0.33, G:0.18, T:0.15
Consensus pattern (58 bp):
TGATGACAAGTCACCCAAACTCAGATCGCCACCAAGGCGACCAGATCCACGCACTAAG
Found at i:1136151 original size:116 final size:115
Alignment explanation
Indices: 1135951--1136318 Score: 436
Period size: 116 Copynumber: 3.2 Consensus size: 115
1135941 AGTAAATGAT
* * * *
1135951 GCCAAATCACCCAAACTCAGATCGCCACCAAGGTGACCAGATCTACGCGCTAAATGATGACAAAT
1 GCCAAGTCACCCAAACTCAGATCGCCACCAAGGTGACCAGATCCACGCGCTAAGTGATGACAAGT
* *
1136016 CACTTAAACTCAGATCGCCACCAAGGCGACCAGATCCATGCACTAAGTGAT
66 CAC-CAAACTCAGATCGCCACCAAGGCGACCAGATCCATGCACTAAGTGAC
* * * *
1136067 GCCAAGTCACCCAAACTCAGATCGCCACCAAAGCGACCAGATCCACGCGCTAAGTAACGACAAGT
1 GCCAAGTCACCCAAACTCAGATCGCCACCAAGGTGACCAGATCCACGCGCTAAGTGATGACAAGT
* *
1136132 CATCCAAACTCAGATCGCCATCAAGGCGATC-GAATCCATGCACTAAGTGAC
66 CA-CCAAACTCAGATCGCCACCAAGGCGACCAG-ATCCATGCACTAAGTGAC
** * * * * *
1136183 AACAAGTCACCCAAACTCAGATCGCCACCAAGGTGACCGGATTCACACACTAAGTGATGCCAAGT
1 GCCAAGTCACCCAAACTCAGATCGCCACCAAGGTGACCAGATCCACGCGCTAAGTGATGACAAGT
* * * * * *
1136248 TACCAAAACTTAGCTCGCCACCAAGGCGACCAAACTCACA--CACTAGGTGGC
66 CACC-AAACTCAGATCGCCACCAAGGCGACCAGA-TC-CATGCACTAAGTGAC
1136299 GCCAAGTCACCCAAACTCAG
1 GCCAAGTCACCCAAACTCAG
1136319 GTTGCTACTA
Statistics
Matches: 213, Mismatches: 33, Indels: 12
0.83 0.13 0.05
Matches are distributed among these distances:
115 3 0.01
116 205 0.96
117 3 0.01
118 2 0.01
ACGTcount: A:0.35, C:0.33, G:0.18, T:0.15
Consensus pattern (115 bp):
GCCAAGTCACCCAAACTCAGATCGCCACCAAGGTGACCAGATCCACGCGCTAAGTGATGACAAGT
CACCAAACTCAGATCGCCACCAAGGCGACCAGATCCATGCACTAAGTGAC
Found at i:1140344 original size:26 final size:26
Alignment explanation
Indices: 1140310--1140361 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
1140300 AATATCATCA
1140310 TTAAATTAA-A-TATAAATTTATTAATT
1 TTAAATTAATATTA-AAATTT-TTAATT
*
1140336 TTAATTTAATATTAAAATTTTTAATT
1 TTAAATTAATATTAAAATTTTTAATT
1140362 AAATCGATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 14 0.61
27 7 0.30
28 2 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TTAAATTAATATTAAAATTTTTAATT
Found at i:1140591 original size:2 final size:2
Alignment explanation
Indices: 1140584--1140611 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1140574 AGATGATTTA
1140584 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
1140612 TATTTTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1141739 original size:20 final size:20
Alignment explanation
Indices: 1141714--1141752 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1141704 TGAATTTGAT
* *
1141714 TTTAAATTTTATTTTTAAAA
1 TTTAAATTTAATTTATAAAA
1141734 TTTAAATTTAATTTATAAA
1 TTTAAATTTAATTTATAAA
1141753 TAAATTATTT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTAAATTTAATTTATAAAA
Found at i:1141762 original size:26 final size:26
Alignment explanation
Indices: 1141729--1141802 Score: 82
Period size: 26 Copynumber: 2.8 Consensus size: 26
1141719 ATTTTATTTT
1141729 TAAA-ATTTAAATTTAATTTAT-AAA
1 TAAATATTTAAATTTAATTTATAAAA
*
1141753 TAAATTATTTAAATAT-ATTTATTAAAA
1 TAAA-TATTTAAATTTAATTTA-TAAAA
*
1141780 TAAATATTAAAATTTATATTTAT
1 TAAATATTTAAATTTA-ATTTAT
1141803 TTTTAAATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
24 4 0.10
25 5 0.12
26 19 0.46
27 8 0.20
28 5 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
TAAATATTTAAATTTAATTTATAAAA
Found at i:1141809 original size:26 final size:26
Alignment explanation
Indices: 1141729--1141827 Score: 71
Period size: 26 Copynumber: 3.8 Consensus size: 26
1141719 ATTTTATTTT
* *
1141729 TAAA-ATTTAAATTTA-ATTTATAAA
1 TAAATATTAAAATTTATATTTATTAA
*
1141753 TAAATTATTTAAA--TATATTTATTAAAA
1 TAAA-TATTAAAATTTATATTTATT--AA
**
1141780 TAAATATTAAAATTTATATTTATTTT
1 TAAATATTAAAATTTATATTTATTAA
* **
1141806 TAAATTTTATTATTTATATTTA
1 TAAATATTAAAATTTATATTTA
1141828 AATTTAAAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
24 6 0.10
25 6 0.10
26 33 0.54
27 6 0.10
28 10 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TAAATATTAAAATTTATATTTATTAA
Found at i:1141821 original size:20 final size:19
Alignment explanation
Indices: 1141786--1141832 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1141776 AAAATAAATA
* *
1141786 TTAAAATTTATATTTATTT
1 TTAAATTTTATATTTATAT
1141805 TTAAATTTTATTATTTATAT
1 TTAAATTTTA-TATTTATAT
1141825 TTAAATTT
1 TTAAATTT
1141833 AAAATTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTAAATTTTATATTTATAT
Found at i:1147364 original size:23 final size:23
Alignment explanation
Indices: 1147338--1147385 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1147328 TTGATTAGCA
1147338 AACAATCTTCAATTATGCCAACT
1 AACAATCTTCAATTATGCCAACT
1147361 AACAATCTTCAATTATGCCAACT
1 AACAATCTTCAATTATGCCAACT
1147384 AA
1 AA
1147386 GAATATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.42, C:0.25, G:0.04, T:0.29
Consensus pattern (23 bp):
AACAATCTTCAATTATGCCAACT
Found at i:1158069 original size:18 final size:18
Alignment explanation
Indices: 1158029--1158071 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1158019 AATTTTTAAA
1158029 ATTTTAAA-ATATTTATT
1 ATTTTAAATATATTTATT
*
1158046 AATTTATAATATATTT-TT
1 ATTTTA-AATATATTTATT
1158064 ATTTTAAA
1 ATTTTAAA
1158072 ATAAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 7 0.32
18 9 0.41
19 6 0.27
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTTAAATATATTTATT
Found at i:1158074 original size:18 final size:17
Alignment explanation
Indices: 1158029--1158074 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
1158019 AATTTTTAAA
1158029 ATTTTAAAATATTTATT
1 ATTTTAAAATATTTATT
*
1158046 AATTTATAATATATTT-TT
1 -ATTT-TAAAATATTTATT
1158064 ATTTTAAAATA
1 ATTTTAAAATA
1158075 AATAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 6 0.24
17 4 0.16
18 6 0.24
19 9 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTTAAAATATTTATT
Found at i:1158274 original size:21 final size:20
Alignment explanation
Indices: 1158250--1158290 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1158240 ATGAGATGAA
1158250 TTAAATTGTGATTTTAATTTT
1 TTAAATTGTGA-TTTAATTTT
* *
1158271 TTAAATTTTTATTTAATTTT
1 TTAAATTGTGATTTAATTTT
1158291 AATTTGAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (20 bp):
TTAAATTGTGATTTAATTTT
Found at i:1158401 original size:26 final size:27
Alignment explanation
Indices: 1158357--1158408 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
1158347 AAATATAATT
** *
1158357 TTAAATTTTAAATTTATATATTTTTAA
1 TTAAATTTTAAATAAATATATATTTAA
1158384 TTAAA-TTTAAATAAATATATATTTA
1 TTAAATTTTAAATAAATATATATTTA
1158409 TTTATTAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TTAAATTTTAAATAAATATATATTTAA
Found at i:1163228 original size:24 final size:24
Alignment explanation
Indices: 1163200--1163249 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1163190 GAATGTTGGG
1163200 TCTCATAAACACTCTCCTCAGTCT
1 TCTCATAAACACTCTCCTCAGTCT
1163224 TCTCATAAACACTCTCCTCAGTCT
1 TCTCATAAACACTCTCCTCAGTCT
1163248 TC
1 TC
1163250 ATCTGCTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.38, G:0.04, T:0.34
Consensus pattern (24 bp):
TCTCATAAACACTCTCCTCAGTCT
Found at i:1164017 original size:117 final size:116
Alignment explanation
Indices: 1163864--1164100 Score: 332
Period size: 117 Copynumber: 2.0 Consensus size: 116
1163854 GCTGTATCTG
*
1163864 TCCCATCTCTTCAGACGCGTACCCAAATGCAGAAGAAGAGCCTGGAAATTGAGAAGCCAACTGAG
1 TCCCATCTCTTCAGACGCCTACCCAAATGCAGAAGAAGAGCCTGGAAATTGAGAAGCCAACTGAG
*
1163929 AAACTGAACAAGAGCTCAGACATT-CTGAGTTCATCAGATGCTCCTTATTCTC
66 AAACTGAACAAGAGCTCAGACATTCCAG-GTTCATCAGATGCTCCTTATTC-C
* * * *
1163981 TCCCATCTCTTCAGATGCCTACCCAAATGCATAAGAAGAGCTTGGGAATTGAGAAGCCAACTGAG
1 TCCCATCTCTTCAGACGCCTACCCAAATGCAGAAGAAGAGCCTGGAAATTGAGAAGCCAACTGAG
*** * * * *
1164046 TCGCTGAGCAAGAGCTTAGACATTCCAGGTTCATCTGATGCTCCTTGTTCC
66 AAACTGAACAAGAGCTCAGACATTCCAGGTTCATCAGATGCTCCTTATTCC
1164097 TCCC
1 TCCC
1164101 CTATGGATGA
Statistics
Matches: 106, Mismatches: 13, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
116 5 0.05
117 99 0.93
118 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (116 bp):
TCCCATCTCTTCAGACGCCTACCCAAATGCAGAAGAAGAGCCTGGAAATTGAGAAGCCAACTGAG
AAACTGAACAAGAGCTCAGACATTCCAGGTTCATCAGATGCTCCTTATTCC
Found at i:1166046 original size:25 final size:29
Alignment explanation
Indices: 1166011--1166078 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 29
1166001 CGATTTTGAG
1166011 TTTATTCATTATTAT-TAATTATAAT-AATA
1 TTTATT-A-TATTATATAATTATAATAAATA
*
1166040 TTTATTATATTTTATAATTATAATAAATA
1 TTTATTATATTATATAATTATAATAAATA
1166069 TTT-TTA-ATTA
1 TTTATTATATTA
1166079 AATTTAAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 8 0.23
28 14 0.40
29 13 0.37
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (29 bp):
TTTATTATATTATATAATTATAATAAATA
Found at i:1167776 original size:20 final size:20
Alignment explanation
Indices: 1167753--1167792 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1167743 TTATAATTAA
1167753 TATTTGTTTAACA-TTAAAAT
1 TATTT-TTTAACATTTAAAAT
*
1167773 TATTTTTTAATATTTAAAAT
1 TATTTTTTAACATTTAAAAT
1167793 CTCATTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (20 bp):
TATTTTTTAACATTTAAAAT
Found at i:1168693 original size:15 final size:15
Alignment explanation
Indices: 1168673--1168711 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1168663 AAATATAATT
1168673 ATATATTTAATATAA
1 ATATATTTAATATAA
* *
1168688 ATATATTTAATTTAT
1 ATATATTTAATATAA
1168703 ATAT-TTTAA
1 ATATATTTAA
1168712 ATTTTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATATATTTAATATAA
Found at i:1168752 original size:30 final size:31
Alignment explanation
Indices: 1168672--1168753 Score: 78
Period size: 31 Copynumber: 2.7 Consensus size: 31
1168662 TAAATATAAT
* *
1168672 TATATATTTAATA-TAAATATATTTAATTTA
1 TATAAATTAAATATTAAATATATTTAATTTA
** * *
1168702 TATATTTTAAATTTTAAA-ATATTTTATTTTA
1 TATAAATTAAATATTAAATATA-TTTAATTTA
*
1168733 TGTAAATTAAATATTAAATAT
1 TATAAATTAAATATTAAATAT
1168754 GAATATTTAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
30 13 0.32
31 26 0.63
32 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (31 bp):
TATAAATTAAATATTAAATATATTTAATTTA
Found at i:1169326 original size:20 final size:21
Alignment explanation
Indices: 1169284--1169328 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
1169274 ATTGGTTAGA
1169284 ATTAAATTAATTTTAATTAATT
1 ATTAAATT-ATTTTAATTAATT
* *
1169306 ATTAAATT-TTTTGATTTATT
1 ATTAAATTATTTTAATTAATT
1169326 ATT
1 ATT
1169329 GGTATAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.62
22 8 0.38
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
ATTAAATTATTTTAATTAATT
Found at i:1172841 original size:18 final size:19
Alignment explanation
Indices: 1172814--1172855 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
1172804 TATAATTAAA
1172814 TTTAAATAAAAA-TATTAT
1 TTTAAATAAAAATTATTAT
*
1172832 TTTAATTAAAAATTATTAT
1 TTTAAATAAAAATTATTAT
*
1172851 GTTAA
1 TTTAA
1172856 GTTTAGTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TTTAAATAAAAATTATTAT
Found at i:1174177 original size:21 final size:21
Alignment explanation
Indices: 1174153--1174217 Score: 82
Period size: 20 Copynumber: 3.1 Consensus size: 21
1174143 TTGTGTTTAA
1174153 AATATTAAAAT-ATTTTATATT
1 AATATTAAAATAATTTT-TATT
1174174 AATATTAAAATAATTCTTT-TT
1 AATATTAAAATAATT-TTTATT
*
1174195 AA-AATAAAATAATTTTTATT
1 AATATTAAAATAATTTTTATT
1174215 AAT
1 AAT
1174218 TAAATTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
19 3 0.08
20 15 0.38
21 15 0.38
22 4 0.10
23 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
AATATTAAAATAATTTTTATT
Found at i:1177579 original size:25 final size:23
Alignment explanation
Indices: 1177551--1177615 Score: 60
Period size: 25 Copynumber: 2.7 Consensus size: 23
1177541 GATAAAGAGA
*
1177551 TAAATATTTTTAATTTTATATCTAT
1 TAAATATTTTTAATTTAATAT-T-T
*
1177576 TAAAATAATTTT-ATTTAATATTT
1 T-AAATATTTTTAATTTAATATTT
1177599 TAATATATATTTTAATT
1 TAA-ATAT-TTTTAATT
1177616 AAATTAATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
22 2 0.06
23 5 0.15
24 5 0.15
25 12 0.36
26 9 0.27
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
TAAATATTTTTAATTTAATATTT
Found at i:1178074 original size:2 final size:2
Alignment explanation
Indices: 1178067--1178093 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1178057 CTCAGTTCCG
1178067 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 T
1178094 ATCTTCCCTT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1185783 original size:2 final size:2
Alignment explanation
Indices: 1185770--1185799 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1185760 AAGTTTCACT
*
1185770 AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1185800 GCAGACTGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1188970 original size:21 final size:21
Alignment explanation
Indices: 1188940--1188987 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1188930 CTAAAAAATG
*
1188940 AAAATAATTAATAATTATCTCT
1 AAAA-AATTAAAAATTATCTCT
* *
1188962 AAAAAATTAAAAATTATTTTT
1 AAAAAATTAAAAATTATCTCT
1188983 AAAAA
1 AAAAA
1188988 TTTTAGAACC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAAAATTAAAAATTATCTCT
Found at i:1189683 original size:20 final size:19
Alignment explanation
Indices: 1189660--1189723 Score: 50
Period size: 20 Copynumber: 3.6 Consensus size: 19
1189650 TATAAATATG
1189660 ATATAAATATATTAAAATTT
1 ATAT-AATATATTAAAATTT
* *
1189680 ATAT--TATGTT--AA-TA
1 ATATAATATATTAAAATTT
1189694 AT-TAATATATTAAAATTT
1 ATATAATATATTAAAATTT
1189712 ATATAAATATAT
1 ATAT-AATATAT
1189724 AATATCTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
13 1 0.03
14 3 0.09
15 7 0.21
17 7 0.21
18 3 0.09
19 1 0.03
20 11 0.33
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
ATATAATATATTAAAATTT
Found at i:1189771 original size:20 final size:19
Alignment explanation
Indices: 1189746--1189785 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
1189736 TAATTAATAA
1189746 AATATAAATAATATAAATTT
1 AATATAAATAAT-TAAATTT
*
1189766 AATATAAATTATTAAATTT
1 AATATAAATAATTAAATTT
1189785 A
1 A
1189786 CCAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATATAAATAATTAAATTT
Found at i:1189776 original size:35 final size:35
Alignment explanation
Indices: 1189712--1189781 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
1189702 ATTAAAATTT
*
1189712 ATATAAATATATAATATCTTAAATTAATTAATAAA
1 ATATAAATATATAATATCTTAAATAAATTAATAAA
*
1189747 ATATAAATAATATAA-AT-TTAATATAAATTATTAAA
1 ATATAAAT-ATATAATATCTTAA-ATAAATTAATAAA
1189782 TTTACCAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 4 0.13
35 21 0.68
36 6 0.19
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (35 bp):
ATATAAATATATAATATCTTAAATAAATTAATAAA
Found at i:1190039 original size:15 final size:16
Alignment explanation
Indices: 1190018--1190055 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1190008 TAAAAAATTT
*
1190018 AATTTAATTAA-TTAA
1 AATTTAATAAATTTAA
*
1190033 TATTTAATAAATTTAA
1 AATTTAATAAATTTAA
1190049 AATTTAA
1 AATTTAA
1190056 AATTTTATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTTAATAAATTTAA
Found at i:1190389 original size:14 final size:14
Alignment explanation
Indices: 1190347--1190390 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1190337 TTATTAGATA
*
1190347 TAAAACATATTTTT
1 TAAAACATATTATT
*
1190361 TAAAAAATATATATT
1 TAAAACATAT-TATT
*
1190376 TAAATCATATTATT
1 TAAAACATATTATT
1190390 T
1 T
1190391 GATTTATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (14 bp):
TAAAACATATTATT
Found at i:1190965 original size:23 final size:25
Alignment explanation
Indices: 1190902--1190966 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 25
1190892 AAACAGTTTA
1190902 ATATATTTATATTAATTTTTTATCAT
1 ATATATTTATATT-ATTTTTTATCAT
*
1190928 ATCACATATTA-ATTATTTTTTAT-AT
1 AT-ATAT-TTATATTATTTTTTATCAT
1190953 -TATATTTATATTAT
1 ATATATTTATATTAT
1190967 ATAATCATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
22 3 0.09
23 8 0.24
24 1 0.03
25 2 0.06
26 11 0.32
27 6 0.18
28 3 0.09
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (25 bp):
ATATATTTATATTATTTTTTATCAT
Found at i:1191662 original size:2 final size:2
Alignment explanation
Indices: 1191651--1191693 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1191641 CACTTCACAT
1191651 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1191692 TA
1 TA
1191694 AAATGAATGA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1192109 original size:15 final size:16
Alignment explanation
Indices: 1192089--1192135 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
1192079 TAAACTTTTT
1192089 TAAATATTAATTTA-A
1 TAAATATTAATTTACA
*
1192104 TAAATAATAATTATAACA
1 TAAATATTAATT-T-ACA
*
1192122 TAAATATTATTTTA
1 TAAATATTAATTTA
1192136 TTTTAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 11 0.42
16 2 0.08
17 2 0.08
18 11 0.42
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAATATTAATTTACA
Found at i:1192156 original size:30 final size:29
Alignment explanation
Indices: 1192114--1192178 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 29
1192104 TAAATAATAA
**
1192114 TTATAACATAAATATTATT-TTATTTTAATT
1 TTAT-ACATAAAT-TTATTATTATTAAAATT
*
1192144 TTATACATTAAATTTTTTATTATTAAAATT
1 TTATACA-TAAATTTATTATTATTAAAATT
1192174 TTATA
1 TTATA
1192179 TAATTTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 7 0.23
30 23 0.77
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (29 bp):
TTATACATAAATTTATTATTATTAAAATT
Found at i:1193174 original size:16 final size:16
Alignment explanation
Indices: 1193149--1193183 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1193139 TTTAAAAATT
1193149 AATAAATTAAATATAA
1 AATAAATTAAATATAA
* *
1193165 AATAACTTAAATTTAA
1 AATAAATTAAATATAA
1193181 AAT
1 AAT
1193184 TAAAATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (16 bp):
AATAAATTAAATATAA
Found at i:1193246 original size:22 final size:25
Alignment explanation
Indices: 1193197--1193246 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 25
1193187 AATTATTCTA
*
1193197 AAAATAAACTAATCAAATTTATATTT
1 AAAATAAACTAA-CAAATTTATAATT
1193223 AAAAT-AACTAA-AAA-TTATAATT
1 AAAATAAACTAACAAATTTATAATT
1193245 AA
1 AA
1193247 TTTAAGACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 9 0.39
23 3 0.13
25 6 0.26
26 5 0.22
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (25 bp):
AAAATAAACTAACAAATTTATAATT
Found at i:1195498 original size:43 final size:43
Alignment explanation
Indices: 1195437--1195519 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
1195427 ATAGAATGAG
* *
1195437 GAAGATCATACCGACAGAATAGCTTCTAGTTTCAGTACTACAC
1 GAAGATCATACCGACAGAAGAACTTCTAGTTTCAGTACTACAC
1195480 GAAGATCATACCGACAGAAGAACTTCTAGTTTCAGTACTA
1 GAAGATCATACCGACAGAAGAACTTCTAGTTTCAGTACTA
1195520 TTTGCTGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (43 bp):
GAAGATCATACCGACAGAAGAACTTCTAGTTTCAGTACTACAC
Found at i:1198267 original size:11 final size:11
Alignment explanation
Indices: 1198231--1198271 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
1198221 ATAATATAAA
1198231 ATAAGATATGAT
1 ATAA-ATATGAT
*
1198243 ATAAAAAT-AT
1 ATAAATATGAT
1198253 ATAAATATGAT
1 ATAAATATGAT
1198264 ATAAATAT
1 ATAAATAT
1198272 ATAAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 9 0.35
11 13 0.50
12 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (11 bp):
ATAAATATGAT
Found at i:1198271 original size:19 final size:19
Alignment explanation
Indices: 1198219--1198278 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
1198209 CAATATAATT
* *
1198219 ATATAATATAAA-ATA-AG
1 ATATGATATAAATATATAA
1198236 ATATGATATAAAAATATATAA
1 ATATGATAT--AAATATATAA
1198257 ATATGATATAAATATATAA
1 ATATGATATAAATATATAA
1198276 ATA
1 ATA
1198279 ATTTAAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
17 8 0.22
19 16 0.43
20 3 0.08
21 10 0.27
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (19 bp):
ATATGATATAAATATATAA
Found at i:1198271 original size:27 final size:25
Alignment explanation
Indices: 1198223--1198278 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
1198213 ATAATTATAT
*
1198223 AATATAAAATAAGATATGATATAAA
1 AATATAAAATAAGATATAATATAAA
* *
1198248 AATATATAAATATGATATAAATATATA
1 AATATA-AAATAAGATAT-AATATAAA
1198275 AATA
1 AATA
1198279 ATTTAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 6 0.23
26 10 0.38
27 10 0.38
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (25 bp):
AATATAAAATAAGATATAATATAAA
Found at i:1198355 original size:16 final size:15
Alignment explanation
Indices: 1198328--1198366 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
1198318 AATTATTAAT
1198328 ATATGA-ATATATAA
1 ATATGATATATATAA
1198342 ATATGATATAATATAA
1 ATATGATAT-ATATAA
*
1198358 ATATAATAT
1 ATATGATAT
1198367 TTTAAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.27
15 2 0.09
16 14 0.64
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (15 bp):
ATATGATATATATAA
Found at i:1199393 original size:14 final size:16
Alignment explanation
Indices: 1199364--1199405 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 16
1199354 AATAATATTA
* *
1199364 AATATATATTAATTTT
1 AATATTTATAAATTTT
1199380 AA-ATTT-TAAATTTT
1 AATATTTATAAATTTT
1199394 AATATTTATAAA
1 AATATTTATAAA
1199406 CCTGCAACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 9 0.41
15 7 0.32
16 6 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATATTTATAAATTTT
Found at i:1201911 original size:2 final size:2
Alignment explanation
Indices: 1201904--1201940 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1201894 TATGCTTTTA
1201904 TC TC TC TC 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 TC TC TC TC T
1201941 GCTGCTGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1202008 original size:2 final size:2
Alignment explanation
Indices: 1202001--1202032 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1201991 TCTTTTGAAA
1202001 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
1202033 TGTGTGGACG
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:1203099 original size:13 final size:13
Alignment explanation
Indices: 1203081--1203115 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1203071 ATAAAAATAT
1203081 TAAATTTAAAAAA
1 TAAATTTAAAAAA
*
1203094 TAAATTAAAAAAA
1 TAAATTTAAAAAA
*
1203107 TAAAATTAA
1 TAAATTTAA
1203116 TTTAAAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
TAAATTTAAAAAA
Found at i:1203105 original size:14 final size:14
Alignment explanation
Indices: 1203072--1203115 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
1203062 AAGTTTTGAA
* *
1203072 TAAAAATATTAAAT
1 TAAAAAAATAAAAT
*
1203086 TTAAAAAAT-AAAT
1 TAAAAAAATAAAAT
1203099 TAAAAAAATAAAAT
1 TAAAAAAATAAAAT
1203113 TAA
1 TAA
1203116 TTTAAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 12 0.46
14 14 0.54
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
TAAAAAAATAAAAT
Found at i:1203973 original size:21 final size:21
Alignment explanation
Indices: 1203949--1204005 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
1203939 ACTATTCTTC
1203949 TTTTCTTTTCTTTTTTTAATT
1 TTTTCTTTTCTTTTTTTAATT
* *
1203970 TTTT-TCTTCCTTTTTTTACTT
1 TTTTCT-TTTCTTTTTTTAATT
*
1203991 TCCTTCTTTT-TTTTT
1 T-TTTCTTTTCTTTTT
1204006 AATGTATGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
20 1 0.03
21 23 0.79
22 4 0.14
23 1 0.03
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTCTTTTCTTTTTTTAATT
Found at i:1204078 original size:25 final size:26
Alignment explanation
Indices: 1204032--1204102 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
1204022 ATAATTGAAT
*
1204032 ATTTATAATTTTTATAA-T-TTTT-AA
1 ATTT-TAATTTATATAATTATTTTAAA
1204056 ATTTTAATTTATATAATTATTTTAAA
1 ATTTTAATTTATATAATTATTTTAAA
* *
1204082 ATTTAAATTTAT-TTATTATTT
1 ATTTTAATTTATATAATTATTT
1204103 ACGTTAAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
23 11 0.27
24 5 0.12
25 12 0.29
26 13 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
ATTTTAATTTATATAATTATTTTAAA
Found at i:1204118 original size:17 final size:18
Alignment explanation
Indices: 1204092--1204131 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
1204082 ATTTAAATTT
*
1204092 ATTTATTATTTACGTTAA
1 ATTTATTATTTAAGTTAA
*
1204110 ATTTA-TATTTAATTTAA
1 ATTTATTATTTAAGTTAA
1204127 ATTTA
1 ATTTA
1204132 AATTAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (18 bp):
ATTTATTATTTAAGTTAA
Found at i:1204124 original size:22 final size:22
Alignment explanation
Indices: 1204084--1204125 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1204074 ATTTTAAAAT
*
1204084 TTAAATTTATTTATTATTTACG
1 TTAAATTTATTTATAATTTACG
1204106 TTAAATTTATATT-TAATTTA
1 TTAAATTTAT-TTATAATTTA
1204126 AATTTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
TTAAATTTATTTATAATTTACG
Found at i:1204313 original size:14 final size:15
Alignment explanation
Indices: 1204286--1204315 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1204276 TTATTCACAA
1204286 AAATAATATAAATTT
1 AAATAATATAAATTT
1204301 AAATAAT-TAAATTT
1 AAATAATATAAATTT
1204315 A
1 A
1204316 TTACCGATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATAATATAAATTT
Found at i:1209064 original size:21 final size:21
Alignment explanation
Indices: 1209013--1209053 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1209003 TAAAAAAAAT
*
1209013 TAAGATTAATTATTATAATAA
1 TAAGATTAAATATTATAATAA
1209034 TAAGATTAAATATTATAATA
1 TAAGATTAAATATTATAATA
1209054 GTGAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (21 bp):
TAAGATTAAATATTATAATAA
Found at i:1209202 original size:19 final size:21
Alignment explanation
Indices: 1209180--1209226 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
1209170 TAAATAATCT
1209180 AAATTTATT-AAATA-ATTAA
1 AAATTTATTAAAATATATTAA
*
1209199 AAATTAATTAAAATATATTAA
1 AAATTTATTAAAATATATTAA
1209220 ATAATTT
1 A-AATTT
1209227 TTTATTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 8 0.35
20 5 0.22
21 6 0.26
22 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AAATTTATTAAAATATATTAA
Found at i:1209356 original size:24 final size:25
Alignment explanation
Indices: 1209320--1209369 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
1209310 TTAAATTACT
1209320 ATATAAAAGTAAAATA-TATATTTA
1 ATATAAAAGTAAAATATTATATTTA
* * *
1209344 ATATATAATTAAAATATTATGTTTA
1 ATATAAAAGTAAAATATTATATTTA
1209369 A
1 A
1209370 AAAAAAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (25 bp):
ATATAAAAGTAAAATATTATATTTA
Found at i:1213594 original size:15 final size:13
Alignment explanation
Indices: 1213574--1213611 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
1213564 TTATTTTTTA
1213574 TAATTTAAATTAATT
1 TAATTTAAATT-A-T
1213589 TAATTTAAATTAT
1 TAATTTAAATTAT
1213602 T-ATTTAAATT
1 TAATTTAAATT
1213612 TAATAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.39
13 2 0.09
14 1 0.04
15 11 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TAATTTAAATTAT
Found at i:1214347 original size:14 final size:14
Alignment explanation
Indices: 1214315--1214341 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1214305 CCATTGATTA
1214315 AATTTGATTTATTC
1 AATTTGATTTATTC
1214329 AATTTGATTTATT
1 AATTTGATTTATT
1214342 TGATTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.59
Consensus pattern (14 bp):
AATTTGATTTATTC
Found at i:1214513 original size:18 final size:18
Alignment explanation
Indices: 1214474--1214513 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1214464 TTGATTAAGT
* **
1214474 TAATTTTTAAAATTTATT
1 TAATTTTTAAAATTAAAC
1214492 TAATTTTTAAAATTAAAC
1 TAATTTTTAAAATTAAAC
1214510 TAAT
1 TAAT
1214514 CCTCTTTAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTTTTAAAATTAAAC
Found at i:1214616 original size:14 final size:14
Alignment explanation
Indices: 1214594--1214644 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
1214584 ATATTATTTA
*
1214594 TTTATAAAATAATT
1 TTTAAAAAATAATT
*
1214608 TTTAAAAAATAATA
1 TTTAAAAAATAATT
*
1214622 TTTAAAAATATAAAAT
1 TTTAAAAA-AT-AATT
1214638 TTTAAAA
1 TTTAAAA
1214645 TTTAACATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 20 0.65
15 2 0.06
16 9 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTTAAAAAATAATT
Found at i:1214634 original size:15 final size:15
Alignment explanation
Indices: 1214592--1214662 Score: 65
Period size: 15 Copynumber: 4.9 Consensus size: 15
1214582 AAATATTATT
*
1214592 TATTTATAAA-ATAA
1 TATTTAAAAATATAA
*
1214606 TTTTTAAAAA-ATAA
1 TATTTAAAAATATAA
1214620 TATTTAAAAATATAA
1 TATTTAAAAATATAA
* * *
1214635 AATTTTAAAATTTAA
1 TATTTAAAAATATAA
* *
1214650 CATTTATAAATAT
1 TATTTAAAAATAT
1214663 CTTATTTTAT
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
14 21 0.46
15 25 0.54
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (15 bp):
TATTTAAAAATATAA
Found at i:1215294 original size:6 final size:6
Alignment explanation
Indices: 1215285--1215312 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1215275 GTAAAAGTTT
1215285 TTTTTA TTTTTA TTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTT
1215313 GATTCGGTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:1215669 original size:2 final size:2
Alignment explanation
Indices: 1215662--1215692 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1215652 CCTCCACCAA
1215662 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1215693 ACAAATTCAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1215824 original size:27 final size:27
Alignment explanation
Indices: 1215794--1215852 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
1215784 GGTGATAACG
* *
1215794 TTAATTATTATAATGATGAT-ATTAATA
1 TTAATTATTATAAT-ATAATAATTAAAA
*
1215821 TTAAATATTATAATATAATAATTAAAA
1 TTAATTATTATAATATAATAATTAAAA
1215848 TTAAT
1 TTAAT
1215853 AATAAAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (27 bp):
TTAATTATTATAATATAATAATTAAAA
Found at i:1215836 original size:21 final size:21
Alignment explanation
Indices: 1215816--1215861 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1215806 ATGATGATAT
1215816 TAAT-ATTAAATATT-ATAATA
1 TAATAATTAAA-ATTAATAATA
1215836 TAATAATTAAAATTAATAATA
1 TAATAATTAAAATTAATAATA
*
1215857 AAATA
1 TAATA
1215862 TATATTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAATAATTAAAATTAATAATA
Found at i:1216001 original size:33 final size:33
Alignment explanation
Indices: 1215958--1216056 Score: 101
Period size: 36 Copynumber: 2.8 Consensus size: 33
1215948 TTTATAATTT
*
1215958 ATAATTAAAAAATATTAAAATTATATATATTAA
1 ATAATAAAAAAATATTAAAATTATATATATTAA
* *
1215991 ATAATAAAAAATATAATAATATATTATATATGTTAA
1 ATAATAAAAAA-ATATTAA-A-ATTATATATATTAA
*
1216027 ATAAAAAATAAAATTTATTAAAA-TATATAT
1 ATAATAAA-AAAA--TATTAAAATTATATAT
1216057 TTATGCTAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
33 10 0.18
34 6 0.11
35 8 0.15
36 22 0.40
37 4 0.07
38 5 0.09
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (33 bp):
ATAATAAAAAAATATTAAAATTATATATATTAA
Found at i:1217881 original size:16 final size:16
Alignment explanation
Indices: 1217860--1217890 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1217850 CCTTAAAACT
1217860 AAAATTTTCATTTTTC
1 AAAATTTTCATTTTTC
*
1217876 AAAATTTTTATTTTT
1 AAAATTTTCATTTTT
1217891 GAAACTTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (16 bp):
AAAATTTTCATTTTTC
Found at i:1218359 original size:19 final size:17
Alignment explanation
Indices: 1218333--1218367 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 17
1218323 TTATATCAAA
1218333 TAAATATTTAAATATTTT
1 TAAATATTTAAA-ATTTT
1218351 TAAATTATTTAAAATTT
1 TAAA-TATTTAAAATTT
1218368 AACGTACATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TAAATATTTAAAATTTT
Found at i:1218445 original size:31 final size:30
Alignment explanation
Indices: 1218385--1218446 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 30
1218375 ATGATTTACA
*
1218385 TAAATAAAATATAAAATATACTAATTTAAT
1 TAAATAAAATATAAAATATACTAACTTAAT
1218415 TAAAT-AAATATAAATAATATA-TAAACTTAAT
1 TAAATAAAATAT-AA-AATATACT-AACTTAAT
1218446 T
1 T
1218447 TAATTTTATC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 6 0.21
30 8 0.29
31 14 0.50
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (30 bp):
TAAATAAAATATAAAATATACTAACTTAAT
Found at i:1218862 original size:2 final size:2
Alignment explanation
Indices: 1218855--1218889 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1218845 ACGTACATAC
1218855 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1218890 GATAATTATC
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:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1218992 original size:13 final size:13
Alignment explanation
Indices: 1218974--1218999 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1218964 TTTATTTTTT
1218974 AAATATATAATAA
1 AAATATATAATAA
1218987 AAATATATAATAA
1 AAATATATAATAA
1219000 TTTTTTAATT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATATATAATAA
Done.