Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007418.1 Hibiscus syriacus cultivar Beakdansim tig00020063_pilon, whole genome shotgun sequence
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: 1198774
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1103316 original size:24 final size:23
Alignment explanation
Indices: 1103288--1103337 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 23
1103278 TATGTTTCAA
1103288 AAATA-CGTTTCCAAAAACTATATT
1 AAATATCGTTTCCAAAAA-TAT-TT
* *
1103312 AAATATTGTTTTCAAAAATATTT
1 AAATATCGTTTCCAAAAATATTT
1103335 AAA
1 AAA
1103338 AATTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 5 0.22
24 8 0.35
25 10 0.43
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.38
Consensus pattern (23 bp):
AAATATCGTTTCCAAAAATATTT
Found at i:1103478 original size:36 final size:36
Alignment explanation
Indices: 1103263--1103489 Score: 180
Period size: 36 Copynumber: 6.3 Consensus size: 36
1103253 ATAATTTAAA
* **
1103263 AAAAACTTTATATTATATG-TTTCAAAAATACGTTTCC
1 AAAAACTATATATTATATGTTTTCAAAAATA--TTTTT
*
1103300 AAAAACTATAT-TAAATATTGTTTTCAAAAATA--TTT
1 AAAAACTATATAT-TATA-TGTTTTCAAAAATATTTTT
* * *
1103335 AAAAATTATATATTATA-CTTTTCAAAAATGTGTTTT
1 AAAAACTATATATTATATGTTTTCAAAAATAT-TTTT
** * *
1103371 CGAAACTATATATTATAAGTTTTCAAAAATGTGTTTT
1 AAAAACTATATATTATATGTTTTCAAAAATAT-TTTT
* * **
1103408 CAAAAC--CATATTATATGTTTTCCAAAACCGATTTTT
1 AAAAACTATATATTATATGTTTT-CAAAA-ATATTTTT
* *
1103444 AAAAACTATATATTATCTGTTTTCAAAAATATTTTC
1 AAAAACTATATATTATATGTTTTCAAAAATATTTTT
1103480 AAAAACTATA
1 AAAAACTATA
1103490 CTATATTATT
Statistics
Matches: 154, Mismatches: 24, Indels: 25
0.76 0.12 0.12
Matches are distributed among these distances:
33 11 0.07
35 27 0.18
36 48 0.31
37 42 0.27
38 15 0.10
39 11 0.07
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (36 bp):
AAAAACTATATATTATATGTTTTCAAAAATATTTTT
Found at i:1104461 original size:14 final size:14
Alignment explanation
Indices: 1104436--1104472 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 14
1104426 TCCCTGCCAA
1104436 TCTTGAATTTTGGAT
1 TCTTG-ATTTTGGAT
1104451 TCTTGATTTTGGAT
1 TCTTGATTTTGGAT
1104465 TCTCTGAT
1 TCT-TGAT
1104473 CCTCGACGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.16, C:0.11, G:0.19, T:0.54
Consensus pattern (14 bp):
TCTTGATTTTGGAT
Found at i:1104749 original size:19 final size:19
Alignment explanation
Indices: 1104716--1104754 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1104706 ATGTTAGATT
1104716 ATAAAATTAAATAAA-CAA
1 ATAAAATTAAATAAATCAA
*
1104734 ATAAATATTAAGTAAATCAA
1 ATAAA-ATTAAATAAATCAA
1104754 A
1 A
1104755 GAGAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 9 0.50
20 4 0.22
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.26
Consensus pattern (19 bp):
ATAAAATTAAATAAATCAA
Found at i:1106221 original size:22 final size:22
Alignment explanation
Indices: 1106183--1106234 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 22
1106173 TTTGGACCTG
1106183 AAAATAAAAAATAAAATGA-AAT
1 AAAATAAAAAATAAAAT-ATAAT
*
1106205 AAAATAAATAACT-AAATATAAT
1 AAAATAAA-AAATAAAATATAAT
1106227 AATAATAA
1 AA-AATAA
1106235 CTATATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 1 0.04
22 17 0.65
23 8 0.31
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (22 bp):
AAAATAAAAAATAAAATATAAT
Found at i:1106306 original size:23 final size:22
Alignment explanation
Indices: 1106261--1106304 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1106251 ATTTTCCAAA
1106261 ATATGTTTTCAAAAATTATTTT
1 ATATGTTTTCAAAAATTATTTT
*
1106283 ATATGTTTTCAAAAATTGTTTT
1 ATATGTTTTCAAAAATTATTTT
1106305 TAAAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.55
Consensus pattern (22 bp):
ATATGTTTTCAAAAATTATTTT
Found at i:1106331 original size:37 final size:35
Alignment explanation
Indices: 1106233--1106652 Score: 409
Period size: 35 Copynumber: 11.7 Consensus size: 35
1106223 TAATAATAAT
* *
1106233 AACTATATATAATACTATATTTTCCAAAATATGTTTTCAAA
1 AACTATATAT--TA-TATGTTTT-CAAAAT-TATTTT-AAA
* *
1106274 AA-T-TATTTTATATGTTTTCAAAAATTGTTTTTAAA
1 AACTATATATTATATGTTTTC-AAAATT-ATTTTAAA
* *
1106309 AAATATAAATTATATGTTTTCAAAATTATTTTAAAA
1 AACTATATATTATATGTTTTCAAAATTATTTT-AAA
** ***
1106345 AACTATATACCATATGTTTTCAAAACCGTTTTAAA
1 AACTATATATTATATGTTTTCAAAATTATTTTAAA
*
1106380 AACTATATATTATACGTTTTCAAAATTATTTTAAA
1 AACTATATATTATATGTTTTCAAAATTATTTTAAA
* *
1106415 AA-T-TATATTATACGTTTTCAAAATTA-TTAAAA
1 AACTATATATTATATGTTTTCAAAATTATTTTAAA
* * *
1106447 AATTATATACTATATGTTTTCAAAACTATTTTAAA
1 AACTATATATTATATGTTTTCAAAATTATTTTAAA
* *
1106482 AACTATATATTATACGTTTTTAAAATTATTTTTAAA
1 AACTATATATTATATGTTTTCAAAATTA-TTTTAAA
* *
1106518 AAGCTATATATTATACGTTTTCAAAATTATTTTGAA
1 AA-CTATATATTATATGTTTTCAAAATTATTTTAAA
* * **
1106554 AACTATTTACTATATGTTTTCAAAACCATTTTAAA
1 AACTATATATTATATGTTTTCAAAATTATTTTAAA
* * *
1106589 AACTATATATTATATGTTTTTAAAAAATAAGTTTCCAAA
1 AACTATATATTATATG-TTTT-CAAAATTA-TTT-TAAA
*
1106628 AACTATATATTATATATTTTCAAAA
1 AACTATATATTATATGTTTTCAAAA
1106653 ACTATATTTG
Statistics
Matches: 320, Mismatches: 45, Indels: 32
0.81 0.11 0.08
Matches are distributed among these distances:
32 7 0.02
33 24 0.08
34 21 0.07
35 114 0.36
36 72 0.22
37 50 0.16
38 7 0.02
39 22 0.07
40 1 0.00
41 2 0.01
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.45
Consensus pattern (35 bp):
AACTATATATTATATGTTTTCAAAATTATTTTAAA
Found at i:1106333 original size:72 final size:70
Alignment explanation
Indices: 1106305--1106652 Score: 355
Period size: 72 Copynumber: 4.9 Consensus size: 70
1106295 AAATTGTTTT
* **
1106305 TAAAAAATATAAATTATATGTTTTCAAAATTATTTTAAAAAACTATATACCATATGTTTTCAAAA
1 TAAAAAATATATATTATATGTTTTCAAAATTATTTT-AAAAACTATATATTATATGTTTTCAAAA
1106370 CCG-TTT
65 -CGTTTT
* * *
1106376 TAAAAACTATATATTATACGTTTTCAAAATTATTTTAAAAA-T-TATATTATACGTTTTCAAAA-
1 TAAAAAATATATATTATATGTTTTCAAAATTATTTTAAAAACTATATATTATATGTTTTCAAAAC
*
1106438 -TTAT
66 GTTTT
* * * *
1106442 TAAAAAATTATATACTATATGTTTTCAAAACTATTTTAAAAACTATATATTATACGTTTTTAAAA
1 TAAAAAA-TATATATTATATGTTTTCAAAATTATTTTAAAAACTATATATTATATGTTTTCAAAA
**
1106507 TTATTTT
65 -CGTTTT
* * * * *
1106514 TAAAAAGCTATATATTATACGTTTTCAAAATTATTTTGAAAACTATTTACTATATGTTTTCAAAA
1 TAAAAA-ATATATATTATATGTTTTCAAAATTATTTTAAAAACTATATATTATATGTTTTCAAAA
**
1106579 CCATTT
65 CGTTTT
* * * * *
1106585 TAAAAACTATATATTATATGTTTTTAAAAAATAAGTTTCCAAAAACTATATATTATATATTTTCA
1 TAAAAAATATATATTATATG-TTTT-CAAAATTA-TTT-TAAAAACTATATATTATATGTTTTCA
1106650 AAA
62 AAA
1106653 ACTATATTTG
Statistics
Matches: 232, Mismatches: 33, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
66 8 0.03
67 31 0.13
68 18 0.08
69 20 0.09
70 18 0.08
71 46 0.20
72 64 0.28
73 3 0.01
74 24 0.10
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.44
Consensus pattern (70 bp):
TAAAAAATATATATTATATGTTTTCAAAATTATTTTAAAAACTATATATTATATGTTTTCAAAAC
GTTTT
Found at i:1107578 original size:9 final size:10
Alignment explanation
Indices: 1107553--1107581 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1107543 AATACATATT
1107553 TATTTTTTCG
1 TATTTTTTCG
1107563 TATTTTTTCG
1 TATTTTTTCG
1107573 TATTTTTTC
1 TATTTTTTC
1107582 ATATGTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.10, G:0.07, T:0.72
Consensus pattern (10 bp):
TATTTTTTCG
Found at i:1109242 original size:40 final size:40
Alignment explanation
Indices: 1109198--1109276 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
1109188 TGGGAAGTTC
* * *
1109198 ATGAACAAGGTTTTATGTTTGTTTAATTAAATGAATGAAT
1 ATGAACAAAGTTTTATGCTCGTTTAATTAAATGAATGAAT
*
1109238 ATGAACAAAGTTTTCTGCTCGTTTAATTAAATGAATGAA
1 ATGAACAAAGTTTTATGCTCGTTTAATTAAATGAATGAA
1109277 CACAAACAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.39
Consensus pattern (40 bp):
ATGAACAAAGTTTTATGCTCGTTTAATTAAATGAATGAAT
Found at i:1112961 original size:22 final size:22
Alignment explanation
Indices: 1112916--1113010 Score: 85
Period size: 22 Copynumber: 4.5 Consensus size: 22
1112906 AGGCTCAATA
* *
1112916 GTATCGATAC-CCT-TACCATG
1 GTATCGATACTTCTATACTATG
1112936 GTATCGATACTTCTATACTATG
1 GTATCGATACTTCTATACTATG
*
1112958 GTATCGATACCTT-TCT-CTCA--
1 GTATCGATA-CTTCTATACT-ATG
* *
1112978 GTATCGATACTACTACACTATG
1 GTATCGATACTTCTATACTATG
1113000 GTATCGATACT
1 GTATCGATACT
1113011 CCCTTTCAGT
Statistics
Matches: 61, Mismatches: 6, Indels: 14
0.75 0.07 0.17
Matches are distributed among these distances:
19 2 0.03
20 21 0.34
21 6 0.10
22 29 0.48
23 3 0.05
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (22 bp):
GTATCGATACTTCTATACTATG
Found at i:1112982 original size:42 final size:41
Alignment explanation
Indices: 1112936--1113028 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 41
1112926 CCTTACCATG
* * **
1112936 GTATCGATACTTCTATACTATGGTATCGATACCTTTCTCTCA
1 GTATCGATACTACTACACTATGGTATCGATA-CTCCCTCTCA
*
1112978 GTATCGATACTACTACACTATGGTATCGATACTCCCTTTCA
1 GTATCGATACTACTACACTATGGTATCGATACTCCCTCTCA
1113019 GTATCGATAC
1 GTATCGATAC
1113029 CATTTTGGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 17 0.37
42 29 0.63
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.37
Consensus pattern (41 bp):
GTATCGATACTACTACACTATGGTATCGATACTCCCTCTCA
Found at i:1114222 original size:48 final size:47
Alignment explanation
Indices: 1114164--1114328 Score: 194
Period size: 44 Copynumber: 3.5 Consensus size: 47
1114154 ACCATTTAAC
*
1114164 CCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCGTTTAAAATT
1 CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACC-TTTAAAATT
*
1114212 CCATAAGCTCGTAAGCTTATATTTTTTTCCAATATACTTACCATTT-AAATT
1 CCATAAGCTCGTAAGC-T-TA--TTTTACCAATATACTTACC-TTTAAAATT
* * *
1114263 CCATAAGCTCGTAAGCTTATTTTACCCATATACTTGCC---AATATT
1 CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCTTTAAAATT
*
1114307 CCAAAAGCTCGTAAGCTTATTT
1 CCATAAGCTCGTAAGCTTATTT
1114329 GTATGCTTAC
Statistics
Matches: 104, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
44 25 0.24
47 16 0.15
48 16 0.15
49 3 0.03
50 3 0.03
51 21 0.20
52 20 0.19
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (47 bp):
CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCTTTAAAATT
Found at i:1114277 original size:51 final size:49
Alignment explanation
Indices: 1114151--1114326 Score: 181
Period size: 51 Copynumber: 3.7 Consensus size: 49
1114141 TATAAAATCC
*
1114151 CTTACCATTT-AA-CCCATAAGCTCGTAAGC-T-TATTTTACCAAAATA
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATATTTTACCAAAATA
* * *
1114196 CTTACCGTTTAAAATTCCATAAGCTCGTAAGCTTATATTTTTTTCCAATATA
1 CTTACCATTT-AAATTCCATAAGCTCGTAAGCTTATA--TTTTACCAAAATA
* *
1114248 CTTACCATTTAAATTCCATAAGCTCGTAAGC-T-TATTTTACCCATATA
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATATTTTACCAAAATA
* * *
1114295 CTTGCCA---ATATTCCAAAAGCTCGTAAGCTTAT
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTAT
1114327 TTGTATGCTT
Statistics
Matches: 112, Mismatches: 10, Indels: 17
0.81 0.07 0.12
Matches are distributed among these distances:
44 19 0.17
45 10 0.09
46 1 0.01
47 19 0.17
48 16 0.14
49 3 0.03
50 3 0.03
51 21 0.19
52 20 0.18
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.37
Consensus pattern (49 bp):
CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATATTTTACCAAAATA
Found at i:1114277 original size:99 final size:93
Alignment explanation
Indices: 1114151--1114326 Score: 244
Period size: 99 Copynumber: 1.8 Consensus size: 93
1114141 TATAAAATCC
*
1114151 CTTACCATTTAACCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCGTTTAAAATTCCAT
1 CTTACCATTTAACCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACC----AAAATTCCAA
1114216 AAGCTCGTAAGCTTATATTTTTTTCCAATATA
62 AAGCTCGTAAGCTTATATTTTTTTCCAATATA
* * * * *
1114248 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATACTTGCCAATATTCCAAAA
1 CTTACCATTT-AA-CCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCAAAATTCCAAAA
1114313 GCTCGTAAGCTTAT
64 GCTCGTAAGCTTAT
1114327 TTGTATGCTT
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
95 24 0.34
97 10 0.14
98 2 0.03
99 35 0.49
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.37
Consensus pattern (93 bp):
CTTACCATTTAACCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCAAAATTCCAAAAGC
TCGTAAGCTTATATTTTTTTCCAATATA
Found at i:1114489 original size:40 final size:40
Alignment explanation
Indices: 1114433--1114514 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
1114423 ACCTTAGTGC
1114433 TACACATAAGGGCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGGCGTGCCCACCATATACACCGAAGTGTAT
*
1114473 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGGCGTGCCCACCATATACACCGAAGTGTAT
1114513 TA
1 TA
1114515 TAAACCTACA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (40 bp):
TACACATAAGGGCGTGCCCACCATATACACCGAAGTGTAT
Found at i:1114821 original size:15 final size:17
Alignment explanation
Indices: 1114801--1114838 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1114791 CTTCCTTATG
1114801 ATGTATAAA-A-CATCC
1 ATGTATAAATATCATCC
*
1114816 ATGTATAAATATCATGC
1 ATGTATAAATATCATCC
1114833 ATGTAT
1 ATGTAT
1114839 TGCACTCACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
16 1 0.05
17 10 0.50
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (17 bp):
ATGTATAAATATCATCC
Found at i:1121334 original size:99 final size:93
Alignment explanation
Indices: 1121212--1121387 Score: 244
Period size: 99 Copynumber: 1.8 Consensus size: 93
1121202 TATAAAATCC
* *
1121212 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCGTTTAAAATTCCAT
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACC-ATT---ATTCCAA
1121277 AAGCTCGTAAGCTTATATTTTTTTCCAATATA
62 AAGCTCGTAAGCTTATATTTTTTTCCAATATA
* * * *
1121309 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATACTTGCCATTATTCCAAAA
1 CTTACCATTT--ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTATTCCAAAA
1121374 GCTCGTAAGCTTAT
64 GCTCGTAAGCTTAT
1121388 TTGTATGTTT
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
95 22 0.31
97 10 0.14
98 2 0.03
99 37 0.52
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (93 bp):
CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTATTCCAAAAGC
TCGTAAGCTTATATTTTTTTCCAATATA
Found at i:1121338 original size:51 final size:45
Alignment explanation
Indices: 1121212--1121389 Score: 205
Period size: 44 Copynumber: 3.8 Consensus size: 45
1121202 TATAAAATCC
* *
1121212 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
1121257 CTTACCGTTTAAAATTCCATAAGCTCGTAAGCTTATATTTTTTTCCAATATA
1 CTTACCATTT---ATTCCATAAGCTCGTAAGC-T-TA--TTTTACCAATATA
*
1121309 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
1121356 CTTGCCA-TTATTCCAAAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
1121390 GTATGTTTAC
Statistics
Matches: 117, Mismatches: 9, Indels: 15
0.83 0.06 0.11
Matches are distributed among these distances:
44 24 0.21
45 9 0.08
46 2 0.02
47 17 0.15
48 18 0.15
49 3 0.03
50 3 0.03
51 21 0.18
52 20 0.17
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:1121538 original size:40 final size:40
Alignment explanation
Indices: 1121494--1121615 Score: 235
Period size: 40 Copynumber: 3.0 Consensus size: 40
1121484 ACCGTAGTGC
*
1121494 TACACATAAGATCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1121534 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1121574 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1121614 TA
1 TA
1121616 TAAACCTGCA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:1139041 original size:81 final size:81
Alignment explanation
Indices: 1138929--1139211 Score: 327
Period size: 81 Copynumber: 3.5 Consensus size: 81
1138919 CAATACACCA
** * * *
1138929 ATTTCTATCAAATGCAAAACTAGGCTATTAATCTTTTAATCAAAGGTATTTAACCTTTTATCTAA
1 ATTTCTATCAAATGCACGACTAAGCTATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAA
**
1138994 CTGGCATAATTGATGC
66 CTGGCATAATTGACAC
* * * * *
1139010 CTTTCTATCAAATGC-CTAGCTAAGTTGTTAATCTTTTACTCAAAGGTATTTAACATTTCATCTA
1 ATTTCTATCAAATGCACGA-CTAAGCTATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTA
* *
1139074 ACTAGCATAATTGACAT
65 ACTGGCATAATTGACAC
* * * *
1139091 ATTTCTGTCAAATGCACGACTAGGCTACTAATATTTTACTCAAAGGTATTTAACCTTTCATCTAA
1 ATTTCTATCAAATGCACGACTAAGCTATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAA
*
1139156 CTGGCATAATTGGCAC
66 CTGGCATAATTGACAC
* * * *
1139172 ATTTCTGTCAAATACAC-ATCTAGGCTATTCATCTTTTACT
1 ATTTCTATCAAATGCACGA-CTAAGCTATTAATCTTTTACT
1139212 TTAAAACATT
Statistics
Matches: 170, Mismatches: 29, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
80 2 0.01
81 166 0.98
82 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (81 bp):
ATTTCTATCAAATGCACGACTAAGCTATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAA
CTGGCATAATTGACAC
Found at i:1139673 original size:42 final size:41
Alignment explanation
Indices: 1139627--1139717 Score: 101
Period size: 42 Copynumber: 2.2 Consensus size: 41
1139617 CTTACCATAC
** * *
1139627 TATCGATAATTTTATACTATGGTATCGATACCTTTCTCTCAG
1 TATCGATAATACTACACTATGGTATCGATA-CTCTCTCTCAG
* * * *
1139669 TATCGATACTACTACACTATGGTATTGATACTCTCTTTCGG
1 TATCGATAATACTACACTATGGTATCGATACTCTCTCTCAG
1139710 TATCGATA
1 TATCGATA
1139718 CCATTTTGGA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 16 0.39
42 25 0.61
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (41 bp):
TATCGATAATACTACACTATGGTATCGATACTCTCTCTCAG
Found at i:1143322 original size:24 final size:24
Alignment explanation
Indices: 1143295--1143377 Score: 96
Period size: 24 Copynumber: 3.5 Consensus size: 24
1143285 ATTTCAAATT
* *
1143295 TGAATTCTGCTCTGATATCTGATA
1 TGAATTCTGTTCTGATATCTGATC
*
1143319 TGAATTCTGTTCTGAT-TCTTGACC
1 TGAATTCTGTTCTGATATC-TGATC
* *
1143343 TGGATTCTGTTATGATATCTGATC
1 TGAATTCTGTTCTGATATCTGATC
*
1143367 TGAATTATGTT
1 TGAATTCTGTT
1143378 TTGTTTTCAA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
23 2 0.04
24 45 0.92
25 2 0.04
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.46
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATC
Found at i:1146121 original size:40 final size:40
Alignment explanation
Indices: 1146077--1146157 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
1146067 TCTTTTATCA
*
1146077 TTTTCCTAAAAGCAGAAAT-CCAATGCTATCCATCTCTTCT
1 TTTTCCTAAAAGCAGAAATACC-ATGCTATCCATCTCATCT
* *
1146117 TTTTCCTAAAAGCAGAAATACCATGCTCTCTATCTCATCT
1 TTTTCCTAAAAGCAGAAATACCATGCTATCCATCTCATCT
1146157 T
1 T
1146158 CTCTTCCATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 35 0.95
41 2 0.05
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (40 bp):
TTTTCCTAAAAGCAGAAATACCATGCTATCCATCTCATCT
Found at i:1148973 original size:192 final size:193
Alignment explanation
Indices: 1148630--1149015 Score: 756
Period size: 192 Copynumber: 2.0 Consensus size: 193
1148620 AAAATATTGT
1148630 TTTGATTAAATAACATATTTAATTTAGACTCAATAAAATGAAAGTAAAATTTATTACTTTGATAA
1 TTTGATTAAATAACA-ATTTAATTTAGACTCAATAAAATGAAAGTAAAATTTATTACTTTGATAA
1148695 TTATATAAAAAAACCTATATCAGGAACTCCCGATTATAAATGTAAAAAAACAGATCATTAAAAAC
65 TTATATAAAAAAACCTATATCAGGAACTCCCGATTATAAATGTAAAAAAACAGATCATTAAAAAC
1148760 CTCAATGTTAGAAATTGAGAATGAGTATAGATTGTAAATTTAATACTTGTGTTATCTTCATTAG
130 CTCAATGTTAGAAATTGAGAATGAGTATAGATTGTAAATTTAATACTTGTGTTATCTTCATTAG
1148824 TTTGATTAAATAAC-ATTTAATTTAGACTCAATAAAATGAAAGTAAAATTTATTACTTTGATAAT
1 TTTGATTAAATAACAATTTAATTTAGACTCAATAAAATGAAAGTAAAATTTATTACTTTGATAAT
1148888 TATATAAAAAAACCTATATCAGGAACTCCCGATTATAAATGTAAAAAAACAGATCATTAAAAACC
66 TATATAAAAAAACCTATATCAGGAACTCCCGATTATAAATGTAAAAAAACAGATCATTAAAAACC
1148953 TCAATGTTAGAAATTGAGAATGAGTATAGATTGTAAATTTAATACTTGTGTTATCTTCATTAG
131 TCAATGTTAGAAATTGAGAATGAGTATAGATTGTAAATTTAATACTTGTGTTATCTTCATTAG
1149016 ACATCCCTAA
Statistics
Matches: 192, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
192 178 0.93
194 14 0.07
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (193 bp):
TTTGATTAAATAACAATTTAATTTAGACTCAATAAAATGAAAGTAAAATTTATTACTTTGATAAT
TATATAAAAAAACCTATATCAGGAACTCCCGATTATAAATGTAAAAAAACAGATCATTAAAAACC
TCAATGTTAGAAATTGAGAATGAGTATAGATTGTAAATTTAATACTTGTGTTATCTTCATTAG
Found at i:1153647 original size:24 final size:24
Alignment explanation
Indices: 1153620--1153668 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
1153610 TGCATGACAT
*
1153620 TGTACATAGATGTTATATACATCA
1 TGTACACAGATGTTATATACATCA
*
1153644 TGTACACAGATGTTTTATACATCA
1 TGTACACAGATGTTATATACATCA
1153668 T
1 T
1153669 CAGGAAGACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (24 bp):
TGTACACAGATGTTATATACATCA
Found at i:1154761 original size:22 final size:22
Alignment explanation
Indices: 1154708--1154761 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 22
1154698 GGTACACTGT
*
1154708 TCACTATTCATGGTACCATTCA
1 TCACTATTCACGGTACCATTCA
* * * **
1154730 TCAATGTTCACGTTACTGTTCA
1 TCACTATTCACGGTACCATTCA
1154752 TCACTATTCA
1 TCACTATTCA
1154762 TAAAAAATAT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.09, T:0.39
Consensus pattern (22 bp):
TCACTATTCACGGTACCATTCA
Found at i:1168189 original size:45 final size:45
Alignment explanation
Indices: 1168140--1168231 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 45
1168130 ATCGACAAGA
* *
1168140 TTTCATTAGTGGCACCTTTTATGTTGATAATGCATCGTTATGCAT
1 TTTCATTAGTGGCACCTTTTATGTCGATAATGCACCGTTATGCAT
1168185 TTTCATTAGTGGCACCTTTTATGTCGATAATGCACCGTTATGCAT
1 TTTCATTAGTGGCACCTTTTATGTCGATAATGCACCGTTATGCAT
1168230 TT
1 TT
1168232 AACTTGTATT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.43
Consensus pattern (45 bp):
TTTCATTAGTGGCACCTTTTATGTCGATAATGCACCGTTATGCAT
Found at i:1168380 original size:49 final size:49
Alignment explanation
Indices: 1168189--1168531 Score: 341
Period size: 49 Copynumber: 7.0 Consensus size: 49
1168179 ATGCATTTTC
* * * * *
1168189 ATTAGTGGCACCTTTTATGTCGATAATGCACCGTTATGCATTTAACTTGT
1 ATTAGTGGCACC-TTTCTGTCAAAAATGCACCATTATGCATTTAACTTGA
* ** ** *
1168239 ATTAGTGGTACCTTTCTGTCAAAAA-GACACTTTTAAACATTTAATTTGA
1 ATTAGTGGCACCTTTCTGTCAAAAATG-CACCATTATGCATTTAACTTGA
* * * *
1168288 GTTAGTGGCACATTTCTATCAAAAAATGCACCATAATGCATTTAACTTGA
1 ATTAGTGGCACCTTTCTGTC-AAAAATGCACCATTATGCATTTAACTTGA
* * * *
1168338 ATTAGTGGAACCTTTCTGTCAATAATGCACCATTATGCATTTAGCTTGC
1 ATTAGTGGCACCTTTCTGTCAAAAATGCACCATTATGCATTTAACTTGA
* * * *
1168387 ATTAGTGACACCTTTCTGCCAAAAATGCACCATTATGTATTTAACTTGT
1 ATTAGTGGCACCTTTCTGTCAAAAATGCACCATTATGCATTTAACTTGA
* ** * *
1168436 ATTAGTGGCACATTTCTG-CAAAAAGTGCACTTTTAAGCATTTAACTTGC
1 ATTAGTGGCACCTTTCTGTCAAAAA-TGCACCATTATGCATTTAACTTGA
* * *
1168485 ACTACTGGCACCTTTCTG-CAAAAAATGTACCATTATGCATTTAACTT
1 ATTAGTGGCACCTTTCTGTC-AAAAATGCACCATTATGCATTTAACTT
1168532 TCATTATAAA
Statistics
Matches: 239, Mismatches: 49, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
48 7 0.03
49 178 0.74
50 53 0.22
51 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (49 bp):
ATTAGTGGCACCTTTCTGTCAAAAATGCACCATTATGCATTTAACTTGA
Found at i:1168452 original size:98 final size:97
Alignment explanation
Indices: 1168213--1168531 Score: 381
Period size: 98 Copynumber: 3.2 Consensus size: 97
1168203 TTATGTCGAT
* * * *
1168213 AATGCACCGTTATGCATTTAACTTGTATTAGTGGTACCTTTCTGTCAAAAAGACACTTTTAAACA
1 AATGCACCATTATGCATTTAACTTGTATTAGTGGAACCTTTCTGTCAAAATG-CACTTTTAAGCA
* * *
1168278 TTTAATTTG-AGTTAGTGGCACATTTCTATCAAAA
65 TTTAACTTGCA-TTAGTGGCACCTTTCT-GCAAAA
* * ** *
1168312 AATGCACCATAATGCATTTAACTTGAATTAGTGGAACCTTTCTGTCAATAATGCACCATTATGCA
1 AATGCACCATTATGCATTTAACTTGTATTAGTGGAACCTTTCTGTCAA-AATGCACTTTTAAGCA
* * *
1168377 TTTAGCTTGCATTAGTGACACCTTTCTGCCAAA
65 TTTAACTTGCATTAGTGGCACCTTTCTGCAAAA
* * *
1168410 AATGCACCATTATGTATTTAACTTGTATTAGTGGCACATTTCTG-CAAAAAGTGCACTTTTAAGC
1 AATGCACCATTATGCATTTAACTTGTATTAGTGGAACCTTTCTGTC-AAAA-TGCACTTTTAAGC
* *
1168474 ATTTAACTTGCACTACTGGCACCTTTCTGCAAAA
64 ATTTAACTTGCATTAGTGGCACCTTTCTGCAAAA
*
1168508 AATGTACCATTATGCATTTAACTT
1 AATGCACCATTATGCATTTAACTT
1168532 TCATTATAAA
Statistics
Matches: 186, Mismatches: 30, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
97 3 0.02
98 106 0.57
99 73 0.39
100 4 0.02
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (97 bp):
AATGCACCATTATGCATTTAACTTGTATTAGTGGAACCTTTCTGTCAAAATGCACTTTTAAGCAT
TTAACTTGCATTAGTGGCACCTTTCTGCAAAA
Found at i:1169277 original size:14 final size:14
Alignment explanation
Indices: 1169258--1169299 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
1169248 GTTAACCTGC
1169258 ACTGAGTCAACTCA
1 ACTGAGTCAACTCA
*
1169272 ACTGAGTCAACTCG
1 ACTGAGTCAACTCA
*
1169286 ATTGAGTCAACTCA
1 ACTGAGTCAACTCA
1169300 TTGGGTTAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (14 bp):
ACTGAGTCAACTCA
Found at i:1169310 original size:13 final size:14
Alignment explanation
Indices: 1169260--1169316 Score: 64
Period size: 14 Copynumber: 4.2 Consensus size: 14
1169250 TAACCTGCAC
* *
1169260 TGAGTCAACTCAAC
1 TGAGTCAACTCGAT
1169274 TGAGTCAACTCGAT
1 TGAGTCAACTCGAT
1169288 TGAGTCAACTC-AT
1 TGAGTCAACTCGAT
* *
1169301 TGGGTTAACTCG-T
1 TGAGTCAACTCGAT
1169314 TGA
1 TGA
1169317 CATTGACCGA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
13 14 0.38
14 23 0.62
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (14 bp):
TGAGTCAACTCGAT
Found at i:1169411 original size:17 final size:18
Alignment explanation
Indices: 1169389--1169422 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1169379 TTGACTTTGA
*
1169389 TAAAAAAGTCA-ATTTTT
1 TAAAAAAATCATATTTTT
1169406 TAAAAAAATCATATTTT
1 TAAAAAAATCATATTTT
1169423 ATGTTTTTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (18 bp):
TAAAAAAATCATATTTTT
Found at i:1172070 original size:44 final size:44
Alignment explanation
Indices: 1172018--1172490 Score: 371
Period size: 44 Copynumber: 10.8 Consensus size: 44
1172008 ACCATTTTCT
* * * * *
1172018 CAGGCTCCTCTGCTATGTGCAAGGGTATGTCATTACTGTTATCG
1 CAGGCTCCTCTACTATGTGCAAGGGTAAGTCCTTACCGTTACCG
* * * * * *
1172062 CCGGCTCCTATACTATATGCTAGAGTAAGTCCTTACTGTTACCG
1 CAGGCTCCTCTACTATGTGCAAGGGTAAGTCCTTACCGTTACCG
* * *
1172106 TAAGCTCCTCTACTATGTGTAAGGGTAAGTCCTTACCGTTACCG
1 CAGGCTCCTCTACTATGTGCAAGGGTAAGTCCTTACCGTTACCG
* * * *
1172150 CAGGCTCCGCTGCTATGTACAAGGGTAAGTCTTTACCGTTACCG
1 CAGGCTCCTCTACTATGTGCAAGGGTAAGTCCTTACCGTTACCG
* *
1172194 TAGGCTCCTCTACTATGTGCATGGGTAAGTCCTTACCGTTACCG
1 CAGGCTCCTCTACTATGTGCAAGGGTAAGTCCTTACCGTTACCG
* * * * * *
1172238 TAGTCTCCTATGCTATGTGCAATGGTAAGTTCTTACCGTTACCG
1 CAGGCTCCTCTACTATGTGCAAGGGTAAGTCCTTACCGTTACCG
* ** * *
1172282 CAGGCTCCTCTTCTATGTGCAAGGAAAAGACCTTACCGTTTCTC-
1 CAGGCTCCTCTACTATGTGCAAGGGTAAGTCCTTACCGTTAC-CG
* * ** * * * *
1172326 C-GGCTCATTTGTTATGTGCAAGGATAAGACCTTACCGTT-TCT
1 CAGGCTCCTCTACTATGTGCAAGGGTAAGTCCTTACCGTTACCG
* * * ** * * **
1172368 CAGGATCCTTTGCTATGTGCAAGGAAAAGACCTTACCATTTTC-
1 CAGGCTCCTCTACTATGTGCAAGGGTAAGTCCTTACCGTTACCG
* * * * * **
1172411 CAGGCTCTTTTGCTATGTGCAAGGGTAAGACCTTACCATTTTC-
1 CAGGCTCCTCTACTATGTGCAAGGGTAAGTCCTTACCGTTACCG
* * * *
1172454 CAGGCTCTTTTGCTATGTGCAAGGGTAAGACCTTACC
1 CAGGCTCCTCTACTATGTGCAAGGGTAAGTCCTTACC
1172491 ATTTTTGCAG
Statistics
Matches: 363, Mismatches: 62, Indels: 9
0.84 0.14 0.02
Matches are distributed among these distances:
41 1 0.00
42 1 0.00
43 142 0.39
44 218 0.60
45 1 0.00
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (44 bp):
CAGGCTCCTCTACTATGTGCAAGGGTAAGTCCTTACCGTTACCG
Found at i:1172345 original size:43 final size:43
Alignment explanation
Indices: 1172294--1172504 Score: 282
Period size: 43 Copynumber: 4.9 Consensus size: 43
1172284 GGCTCCTCTT
* * *
1172294 CTATGTGCAAGGAAAAGACCTTACCGTTTCTCC-GGCTCATTTG
1 CTATGTGCAAGGATAAGACCTTACCATTT-TCCAGGCTCTTTTG
* * * *
1172337 TTATGTGCAAGGATAAGACCTTACC-GTTTCTCAGGATCCTTTG
1 CTATGTGCAAGGATAAGACCTTACCATTTTC-CAGGCTCTTTTG
*
1172380 CTATGTGCAAGGAAAAGACCTTACCATTTTCCAGGCTCTTTTG
1 CTATGTGCAAGGATAAGACCTTACCATTTTCCAGGCTCTTTTG
*
1172423 CTATGTGCAAGGGTAAGACCTTACCATTTTCCAGGCTCTTTTG
1 CTATGTGCAAGGATAAGACCTTACCATTTTCCAGGCTCTTTTG
* *
1172466 CTATGTGCAAGGGTAAGACCTTACCATTTTTGCAGGCTC
1 CTATGTGCAAGGATAAGACCTTACCA-TTTTCCAGGCTC
1172505 ATCTGCTTTA
Statistics
Matches: 151, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
41 2 0.01
42 3 0.02
43 131 0.87
44 15 0.10
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (43 bp):
CTATGTGCAAGGATAAGACCTTACCATTTTCCAGGCTCTTTTG
Found at i:1172397 original size:86 final size:85
Alignment explanation
Indices: 1172248--1172511 Score: 309
Period size: 86 Copynumber: 3.0 Consensus size: 85
1172238 TAGTCTCCTA
** * *
1172248 TGCTATGTGCAATGGTAAGTTCTTACCGTTACCGCAGGCTCCTCTT-CTATGTGCAAGGAAAAGA
1 TGCTATGTGCAA-GGTAAGACCTTACCGTT-TCTCAGGCTCCT-TTGCTATGTGCAAGGAAAAGA
*
1172312 CCTTACCGTTTCTCC-GGCTCATT
63 CCTTACCATTT-TCCAGGCTCATT
* *
1172335 TGTTATGTGCAAGGATAAGACCTTACCGTTTCTCAGGATCCTTTGCTATGTGCAAGGAAAAGACC
1 TGCTATGTGCAAGG-TAAGACCTTACCGTTTCTCAGGCTCCTTTGCTATGTGCAAGGAAAAGACC
*
1172400 TTACCATTTTCCAGGCTCTTT
65 TTACCATTTTCCAGGCTCATT
* * **
1172421 TGCTATGTGCAAGGGTAAGACCTTACCATTT-TCCAGGCTCTTTTGCTATGTGCAAGGGTAAGAC
1 TGCTATGTGCAA-GGTAAGACCTTACCGTTTCT-CAGGCTCCTTTGCTATGTGCAAGGAAAAGAC
* *
1172485 CTTACCATTTTTGCAGGCTCATC
64 CTTACCA-TTTTCCAGGCTCATT
1172508 TGCT
1 TGCT
1172512 TTATGCACAG
Statistics
Matches: 154, Mismatches: 17, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
85 6 0.04
86 106 0.69
87 42 0.27
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (85 bp):
TGCTATGTGCAAGGTAAGACCTTACCGTTTCTCAGGCTCCTTTGCTATGTGCAAGGAAAAGACCT
TACCATTTTCCAGGCTCATT
Found at i:1175291 original size:18 final size:18
Alignment explanation
Indices: 1175264--1175298 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1175254 TTATAAAGGA
*
1175264 TTGAAATAAATGATAAGT
1 TTGAAATAAATAATAAGT
*
1175282 TTGAATTAAATAATAAG
1 TTGAAATAAATAATAAG
1175299 ACCGGGCCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.34
Consensus pattern (18 bp):
TTGAAATAAATAATAAGT
Found at i:1177021 original size:44 final size:44
Alignment explanation
Indices: 1176958--1177343 Score: 389
Period size: 44 Copynumber: 8.8 Consensus size: 44
1176948 CCGTTTTCTC
* * *
1176958 AGGCTCCTCTGTTATGTGCAAGGGTAAGTCATTATCGTTACCGT
1 AGGCTCCTCTGCTATGTGCAAGGGTAAGTCCTTACCGTTACCGT
* *
1177002 AGGCTCCTCTGCTATGTGCAAGGGTAAGTCCTTACCATTGCCGT
1 AGGCTCCTCTGCTATGTGCAAGGGTAAGTCCTTACCGTTACCGT
* * * *
1177046 AGGCTCCTCTGCTATATGCAAAGGTAAATCCTTACCGTTACCAT
1 AGGCTCCTCTGCTATGTGCAAGGGTAAGTCCTTACCGTTACCGT
*
1177090 AGGCTCCTCTGCTATATGCAAGGGTAAGTCCTTACCGTTACCGT
1 AGGCTCCTCTGCTATGTGCAAGGGTAAGTCCTTACCGTTACCGT
* * * * * *
1177134 ATGATCCTCTGTTATGTTCAAGGGTAAGTCCTTATCGTTACCGC
1 AGGCTCCTCTGCTATGTGCAAGGGTAAGTCCTTACCGTTACCGT
* * ** * * *
1177178 AAGCTCTTCTATTTTATGCAAGGGTAAGTCCTTACCATTACCGT
1 AGGCTCCTCTGCTATGTGCAAGGGTAAGTCCTTACCGTTACCGT
* * * * *
1177222 AGGCTCCTCTGCTATGTACAAGGATAAGACCTTACCGTTTCC-C
1 AGGCTCCTCTGCTATGTGCAAGGGTAAGTCCTTACCGTTACCGT
* * * * * * *
1177265 AGGATCCTTTGCTATGTGTAAGGATAAGACCTTACCGTTTCC-C
1 AGGCTCCTCTGCTATGTGCAAGGGTAAGTCCTTACCGTTACCGT
* * * * * *
1177308 AGTCTGCTTTGTTATGTGCAAGGATAAGACCTTACC
1 AGGCTCCTCTGCTATGTGCAAGGGTAAGTCCTTACC
1177344 ATTTTCTAGG
Statistics
Matches: 290, Mismatches: 52, Indels: 1
0.85 0.15 0.00
Matches are distributed among these distances:
43 70 0.24
44 220 0.76
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.32
Consensus pattern (44 bp):
AGGCTCCTCTGCTATGTGCAAGGGTAAGTCCTTACCGTTACCGT
Found at i:1177288 original size:43 final size:43
Alignment explanation
Indices: 1176945--1177386 Score: 242
Period size: 44 Copynumber: 10.1 Consensus size: 43
1176935 AATGGATTAG
* * * * * *
1176945 TTACCGTTTTCTCAGGCTCCTCTGTTATGTGCAAGGGTAAGTCA
1 TTACCG-TTTCCCAGGCTCCTTTGCTATGTGCAAGGATAAGACC
* * * * * *
1176989 TTATCGTTACCGTAGGCTCCTCTGCTATGTGCAAGGGTAAGTCC
1 TTACCGTTTCC-CAGGCTCCTTTGCTATGTGCAAGGATAAGACC
* * * * *
1177033 TTACCATTGCCGTAGGCTCCTCTGCTATATGCAAAGG-TAA-ATCC
1 TTACCGTTTCC-CAGGCTCCTTTGCTATGTGC-AAGGATAAGA-CC
* * * * * *
1177077 TTACCGTTACCATAGGCTCCTCTGCTATATGCAAGGGTAAGTCC
1 TTACCGTTTCC-CAGGCTCCTTTGCTATGTGCAAGGATAAGACC
* * * * * * * * *
1177121 TTACCGTTACCGTATGATCCTCTGTTATGTTCAAGGGTAAGTCC
1 TTACCGTTTCC-CAGGCTCCTTTGCTATGTGCAAGGATAAGACC
* * * ** * * * *
1177165 TTATCGTTACCGCAAGCT-CTTCTATTTTATGCAAGGGTAAGTCC
1 TTACCGTTTCC-CAGGCTCCTT-TGCTATGTGCAAGGATAAGACC
* * * * *
1177209 TTACCATTACCGTAGGCTCCTCTGCTATGTACAAGGATAAGACC
1 TTACCGTTTCC-CAGGCTCCTTTGCTATGTGCAAGGATAAGACC
* *
1177253 TTACCGTTTCCCAGGATCCTTTGCTATGTGTAAGGATAAGACC
1 TTACCGTTTCCCAGGCTCCTTTGCTATGTGCAAGGATAAGACC
* * *
1177296 TTACCGTTTCCCAGTCTGCTTTGTTATGTGCAAGGATAAGACC
1 TTACCGTTTCCCAGGCTCCTTTGCTATGTGCAAGGATAAGACC
* * * * * * *
1177339 TTACCATTTTCTAGGCTCTTTTGCTATATGAAATGATAAGACC
1 TTACCGTTTCCCAGGCTCCTTTGCTATGTGCAAGGATAAGACC
*
1177382 ATACC
1 TTACC
1177387 ATTTTTGTAG
Statistics
Matches: 326, Mismatches: 65, Indels: 15
0.80 0.16 0.04
Matches are distributed among these distances:
43 111 0.34
44 209 0.64
45 6 0.02
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (43 bp):
TTACCGTTTCCCAGGCTCCTTTGCTATGTGCAAGGATAAGACC
Found at i:1192781 original size:20 final size:20
Alignment explanation
Indices: 1192753--1192795 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1192743 TCTAAGAGCT
*
1192753 CATTCAGAACCATGTAGATG
1 CATTCAGAACCATATAGATG
* * *
1192773 CATTTAGAAGCATATAGTTG
1 CATTCAGAACCATATAGATG
1192793 CAT
1 CAT
1192796 GTGGTGGAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (20 bp):
CATTCAGAACCATATAGATG
Found at i:1194324 original size:20 final size:22
Alignment explanation
Indices: 1194295--1194336 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1194285 TATACTACCA
1194295 CCATTCCA-TTT-CCACAATAT
1 CCATTCCATTTTGCCACAATAT
*
1194315 CCATTTCATTTTGCCACAATAT
1 CCATTCCATTTTGCCACAATAT
1194337 TCTCATTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 3 0.16
22 9 0.47
ACGTcount: A:0.29, C:0.31, G:0.02, T:0.38
Consensus pattern (22 bp):
CCATTCCATTTTGCCACAATAT
Found at i:1195265 original size:19 final size:19
Alignment explanation
Indices: 1195241--1195288 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
1195231 TCCTGAGTGG
1195241 ATCGATGCATGGTCTGTGC
1 ATCGATGCATGGTCTGTGC
1195260 ATCGATGCATGGTCTGTGC
1 ATCGATGCATGGTCTGTGC
1195279 ATCGATGCAT
1 ATCGATGCAT
1195289 CAAATGCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.31
Consensus pattern (19 bp):
ATCGATGCATGGTCTGTGC
Found at i:1195353 original size:84 final size:83
Alignment explanation
Indices: 1195195--1195353 Score: 228
Period size: 84 Copynumber: 1.9 Consensus size: 83
1195185 ACTAAGAGTA
* * * * * *
1195195 CATCGATGTATAAAATGCATTCGATGTTTTGAAAAATCCTGAGTGGATCGATGCATGGTCTGTGC
1 CATCGATGCATAAAATGCATTCGATGTTTTCAAAAACCCTAAGTGCATCGATGCATGGTCTATGC
1195260 ATCGATGCATGGTCTGTG
66 ATCGATGCATGGTCTGTG
* **
1195278 CATCGATGCATCAAATGCATTCGATGTTTTCATAAAACCCTAAGTGCATCGATGTGTGGTCTATG
1 CATCGATGCATAAAATGCATTCGATGTTTTCA-AAAACCCTAAGTGCATCGATGCATGGTCTATG
1195343 CATCGATGCAT
65 CATCGATGCAT
1195354 CAAATGCATT
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
83 29 0.44
84 37 0.56
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.32
Consensus pattern (83 bp):
CATCGATGCATAAAATGCATTCGATGTTTTCAAAAACCCTAAGTGCATCGATGCATGGTCTATGC
ATCGATGCATGGTCTGTG
Found at i:1195409 original size:65 final size:65
Alignment explanation
Indices: 1195256--1195418 Score: 179
Period size: 65 Copynumber: 2.5 Consensus size: 65
1195246 TGCATGGTCT
* *
1195256 GTGCATCGATGCATGGTCTG-TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACCCTA
1 GTGCATCGATGTATGGTCTGATGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAACCATA
1195320 A
65 A
* * * ** *
1195321 GTGCATCGATGTGTGGTCT-ATGCATCGATGCATCAAATGCATTTGATG-TTCAATTAATTCATC
1 GTGCATCGATGTATGGTCTGATGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAACCATA
*
1195384 G
65 A
* * *
1195385 GTGCATCGATGTATAGTTTGATGCATCGGTGCAT
1 GTGCATCGATGTATGGTCTGATGCATCGATGCAT
1195419 GCCTTTGAAT
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
63 3 0.04
64 22 0.27
65 57 0.70
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (65 bp):
GTGCATCGATGTATGGTCTGATGCATCGATGCATCAAATGCATTCGATGTTTCATAAAACCATAA
Found at i:1196535 original size:21 final size:21
Alignment explanation
Indices: 1196511--1196554 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1196501 CCAGAGCCGG
* *
1196511 AGGAGGAGCACGAGAGGAGCT
1 AGGAGCAGCACGAGAGGAACT
* *
1196532 AGGAGCAGCTCGTGAGGAACT
1 AGGAGCAGCACGAGAGGAACT
1196553 AG
1 AG
1196555 CTCCCGGAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.43, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAGGAACT
Done.