Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D01
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: 62811768
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 736185 characters in sequence are not A, C, G, or T
File 10 of 211
Found at i:2975525 original size:4 final size:4
Alignment explanation
Indices: 2975511--2975551 Score: 64
Period size: 4 Copynumber: 10.2 Consensus size: 4
2975501 ATGTATATGC
* *
2975511 AATG CATG AATG AATG AATG AATG AATG AATG GATG AATG A
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG A
2975552 CAAGTGAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.46, C:0.02, G:0.27, T:0.24
Consensus pattern (4 bp):
AATG
Found at i:2977679 original size:106 final size:106
Alignment explanation
Indices: 2977493--2977810 Score: 438
Period size: 106 Copynumber: 3.0 Consensus size: 106
2977483 AGGAAACCAT
* * * * * * *
2977493 ACTTTGAAGTTTGAAGAGGGTATTTAGCTATTTAGTCGAACGAGAAATCAAAACCCAGCACGTTA
1 ACTTTGAAATTTAAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTA
* * *
2977558 GGGCATGTTTTCTCGAATTTCCAAACGCAAAATATTGCCTC
66 GGGCACGTTTCCTCGATTTTCCAAACGCAAAATATTGCCTC
* * * * * *
2977599 ACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCAAACAAGGAGTCGAAACCCAACACGTTA
1 ACTTTGAAATTTAAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTA
* *
2977664 GGGCACGTTTCCTCGATTTTCCAAATGCAAAATATTGCCTT
66 GGGCACGTTTCCTCGATTTTCCAAACGCAAAATATTGCCTC
* *
2977705 ATTTTAAAAGTTTAAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTT
1 ACTTTGAAA-TTTAAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTT
*
2977770 AGGGCACGTTTCCTCGATTTTCCAAACGCGAAATATTGCCT
65 AGGGCACGTTTCCTCGATTTTCCAAACGCAAAATATTGCCT
2977811 TATTTAAAAA
Statistics
Matches: 184, Mismatches: 27, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
106 96 0.52
107 88 0.48
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (106 bp):
ACTTTGAAATTTAAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTA
GGGCACGTTTCCTCGATTTTCCAAACGCAAAATATTGCCTC
Found at i:2977774 original size:107 final size:107
Alignment explanation
Indices: 2977499--2977820 Score: 448
Period size: 107 Copynumber: 3.0 Consensus size: 107
2977489 CCATACTTTG
* * * * * * *
2977499 AAGTTTGAAGAGGGTATTTAGCTATTTAGTCGAACGAGAAATCAAAACCCAGCACGTTAGGGCAT
1 AAGTTTAAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
* * * * *
2977564 GTTTTCTCGAATTTCCAAACGCAAAATATTGCCTCACTTTGA
66 GTTTCCTCGATTTTCCAAACGCAAAATATTGCCTTATTTTAA
* * * * * *
2977606 AA-TTTTAAAAGGATATTTGGCTATTTGGTCAAACAAGGAGTCGAAACCCAACACGTTAGGGCAC
1 AAGTTTAAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
*
2977670 GTTTCCTCGATTTTCCAAATGCAAAATATTGCCTTATTTTAA
66 GTTTCCTCGATTTTCCAAACGCAAAATATTGCCTTATTTTAA
2977712 AAGTTTAAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
1 AAGTTTAAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
* *
2977777 GTTTCCTCGATTTTCCAAACGCGAAATATTGCCTTATTTAAA
66 GTTTCCTCGATTTTCCAAACGCAAAATATTGCCTTATTTTAA
2977819 AA
1 AA
2977821 AAACCTTCCT
Statistics
Matches: 187, Mismatches: 27, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
106 88 0.47
107 99 0.53
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (107 bp):
AAGTTTAAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
GTTTCCTCGATTTTCCAAACGCAAAATATTGCCTTATTTTAA
Found at i:2980269 original size:14 final size:14
Alignment explanation
Indices: 2980231--2980283 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
2980221 AATAATTAAT
*
2980231 TAAACATAAAAGAAA
1 TAAA-ATAAAGGAAA
2980246 TAAAATAAAGGAAA
1 TAAAATAAAGGAAA
* * *
2980260 TAAAGTAAAGTAAGT
1 TAAAATAAAGGAA-A
2980275 TAAAATAAA
1 TAAAATAAA
2980284 AAGGAAAAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.68, C:0.02, G:0.11, T:0.19
Consensus pattern (14 bp):
TAAAATAAAGGAAA
Found at i:2981011 original size:3 final size:3
Alignment explanation
Indices: 2981003--2981035 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2980993 GTGAGGTAAG
2981003 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2981036 GAGTGTGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2981204 original size:23 final size:24
Alignment explanation
Indices: 2981188--2981233 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2981178 TGGATTAATT
2981188 ATTG-ATTGAAAGATGGAGAAATG
1 ATTGAATTGAAAGATGGAGAAATG
2981211 ATTGAATTGAAA-ATGTGAGAAAT
1 ATTGAATTGAAAGATG-GAGAAAT
2981234 TGTGATTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.46, C:0.00, G:0.26, T:0.28
Consensus pattern (24 bp):
ATTGAATTGAAAGATGGAGAAATG
Found at i:2981414 original size:34 final size:34
Alignment explanation
Indices: 2981371--2981438 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
2981361 TGGGTGTCAC
2981371 TATATTTCTTCGGATAGATTCGATGAGGTACTGG
1 TATATTTCTTCGGATAGATTCGATGAGGTACTGG
2981405 TATATTTCTTCGGATAGATTCGATGAGGTACTGG
1 TATATTTCTTCGGATAGATTCGATGAGGTACTGG
2981439 GTACCAACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.38
Consensus pattern (34 bp):
TATATTTCTTCGGATAGATTCGATGAGGTACTGG
Found at i:2982919 original size:17 final size:18
Alignment explanation
Indices: 2982879--2983170 Score: 194
Period size: 18 Copynumber: 16.2 Consensus size: 18
2982869 AATTATTTTC
2982879 TTTGAAAAACACGAAAATT
1 TTTG-AAAACACGAAAATT
*
2982898 TTTGAAAACACGACAA-T
1 TTTGAAAACACGAAAATT
2982915 TTTG-AAACACGCAAAATTTT
1 TTTGAAAACACG-AAAA--TT
* ***
2982935 TTTGAAAACCCGATTTTTT
1 TTTGAAAACACGA-AAATT
*
2982954 TTTG-AAACGCGAAAATT
1 TTTGAAAACACGAAAATT
* *
2982971 TGTG-AAACACGAGAATT
1 TTTGAAAACACGAAAATT
*
2982988 GTTGAAAACAC-ACAAATT
1 TTTGAAAACACGA-AAATT
2983006 TTTGAAAACACGAAAATT
1 TTTGAAAACACGAAAATT
*
2983024 TTTG-AAACACGAAAGTT
1 TTTGAAAACACGAAAATT
* * **
2983041 TTTAGGAAACATGAAAAAAAAAA
1 TTT-GAAAACACG----AAAATT
*
2983064 TTTG--ATCATCG-AAATT
1 TTTGAAAACA-CGAAAATT
*
2983080 TTTTAAAACACGAAAATT
1 TTTGAAAACACGAAAATT
*
2983098 TTTG-AAACACGGAAATT
1 TTTGAAAACACGAAAATT
*
2983115 TTTGAAAACACGGAAATTT
1 TTTGAAAACAC-GAAAATT
**
2983134 TTTGAAAACGTGAAAATT
1 TTTGAAAACACGAAAATT
*
2983152 TTTG-AAACAC-CAAATT
1 TTTGAAAACACGAAAATT
2983168 TTT
1 TTT
2983171 TTTAAACACA
Statistics
Matches: 214, Mismatches: 38, Indels: 45
0.72 0.13 0.15
Matches are distributed among these distances:
16 21 0.10
17 64 0.30
18 75 0.35
19 31 0.14
20 9 0.04
21 7 0.03
22 1 0.00
23 6 0.03
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (18 bp):
TTTGAAAACACGAAAATT
Found at i:2983020 original size:53 final size:53
Alignment explanation
Indices: 2982884--2983134 Score: 167
Period size: 53 Copynumber: 4.6 Consensus size: 53
2982874 TTTTCTTTGA
* *
2982884 AAAACACGAAAATTTTTGAAAACACGACAATTTTGAAACACGCAAAATTTTTTTG
1 AAAACACGAAAATTTTTGAAAACACGAAAATTTTGAAACACG-AAAA-TTTGTTG
* *** * *
2982939 AAAACCCGATTTTTTTTTG-AAACGCGAAAATTTGTGAAACACGAGAA-TTGTTG
1 AAAACACGA-AAATTTTTGAAAACACGAAAATTT-TGAAACACGAAAATTTGTTG
*
2982992 AAAACAC-ACAAATTTTTGAAAACACGAAAATTTTTGAAACACGAAAGTTT-TTAG
1 AAAACACGA-AAATTTTTGAAAACACGAAAA-TTTTGAAACACGAAAATTTGTT-G
* * ** * * *
2983046 GAAACATGAAAAAAAAAATTTG--ATCATCGAAATTTTTTAAAACACGAAAATTT-TTG
1 AAAACACG----AAAATTTTTGAAAACA-CGAAA-ATTTTGAAACACGAAAATTTGTTG
* *
2983102 -AAACACGGAAATTTTTGAAAACACGGAAATTTT
1 AAAACACGAAAATTTTTGAAAACACGAAAATTTT
2983135 TTGAAAACGT
Statistics
Matches: 150, Mismatches: 31, Indels: 34
0.70 0.14 0.16
Matches are distributed among these distances:
51 11 0.07
52 11 0.07
53 37 0.25
54 11 0.07
55 29 0.19
56 19 0.13
57 24 0.16
58 7 0.05
59 1 0.01
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.29
Consensus pattern (53 bp):
AAAACACGAAAATTTTTGAAAACACGAAAATTTTGAAACACGAAAATTTGTTG
Found at i:2983171 original size:17 final size:18
Alignment explanation
Indices: 2983074--2983171 Score: 114
Period size: 17 Copynumber: 5.6 Consensus size: 18
2983064 TTTGATCATC
*
2983074 GAAATTTTTTAAAACAC-
1 GAAATTTTTTGAAACACG
*
2983091 GAAAATTTTTGAAACACG
1 GAAATTTTTTGAAACACG
2983109 GAAA-TTTTTGAAAACACG
1 GAAATTTTTTG-AAACACG
2983127 GAAATTTTTTGAAA-ACG
1 GAAATTTTTTGAAACACG
*
2983144 TGAAAATTTTTGAAACAC-
1 -GAAATTTTTTGAAACACG
*
2983162 CAAATTTTTT
1 GAAATTTTTT
2983172 TTAAACACAA
Statistics
Matches: 71, Mismatches: 5, Indels: 10
0.83 0.06 0.12
Matches are distributed among these distances:
17 32 0.45
18 31 0.44
19 8 0.11
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (18 bp):
GAAATTTTTTGAAACACG
Found at i:2983182 original size:17 final size:18
Alignment explanation
Indices: 2983150--2983187 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2983140 AACGTGAAAA
2983150 TTTTTGAAACACCAAATT
1 TTTTTGAAACACCAAATT
*
2983168 TTTTTTAAACA-CAAATT
1 TTTTTGAAACACCAAATT
2983185 TTT
1 TTT
2983188 CGATTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.37, C:0.13, G:0.03, T:0.47
Consensus pattern (18 bp):
TTTTTGAAACACCAAATT
Found at i:2983320 original size:20 final size:20
Alignment explanation
Indices: 2983295--2983360 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
2983285 GCCTTATTAT
2983295 TATTTTTTTGAAAACGCGAA
1 TATTTTTTTGAAAACGCGAA
*
2983315 TA-TTTTTTGAAACACGAGAA
1 TATTTTTTTGAAA-ACGCGAA
* * *
2983335 TTTTTTTTTGAAGACACGAA
1 TATTTTTTTGAAAACGCGAA
*
2983355 AATTTT
1 TATTTT
2983361 GAAGCACGAG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 10 0.27
20 18 0.49
21 9 0.24
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (20 bp):
TATTTTTTTGAAAACGCGAA
Found at i:2983327 original size:18 final size:19
Alignment explanation
Indices: 2983298--2983340 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
2983288 TTATTATTAT
*
2983298 TTTTTTGAAAACGCGA-ATA
1 TTTTTTGAAAACACGAGA-A
2983317 TTTTTTG-AAACACGAGAA
1 TTTTTTGAAAACACGAGAA
2983335 TTTTTT
1 TTTTTT
2983341 TTTGAAGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (19 bp):
TTTTTTGAAAACACGAGAA
Found at i:2983360 original size:40 final size:38
Alignment explanation
Indices: 2983297--2983387 Score: 110
Period size: 40 Copynumber: 2.3 Consensus size: 38
2983287 CTTATTATTA
* *
2983297 TTTTTTTGAAAACGCGAATATTTTTTGAAACACGAGAATT
1 TTTTTTTGAAAACACGAA-A-ATTTTGAAACACGAGAATT
* * *
2983337 TTTTTTTGAAGACACGAAAATTTTGAAGCACGAGATTTT
1 TTTTTTTGAAAACACGAAAATTTTGAAACACGAGA-ATT
2983376 TTTTTTTGAAAA
1 TTTTTTTGAAAA
2983388 TATGAATTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
38 14 0.32
39 14 0.32
40 16 0.36
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (38 bp):
TTTTTTTGAAAACACGAAAATTTTGAAACACGAGAATT
Found at i:2983376 original size:16 final size:17
Alignment explanation
Indices: 2983339--2983376 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
2983329 CGAGAATTTT
2983339 TTTTTGAAGACACGAAA
1 TTTTTGAAGACACGAAA
* *
2983356 ATTTTGAAG-CACGAGA
1 TTTTTGAAGACACGAAA
2983372 TTTTT
1 TTTTT
2983377 TTTTTTGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (17 bp):
TTTTTGAAGACACGAAA
Found at i:2983549 original size:21 final size:21
Alignment explanation
Indices: 2983525--2983570 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2983515 AAAAATATTA
* *
2983525 AAAATAAAATTAATTTGAATT
1 AAAATAAAATTAAATTAAATT
*
2983546 AAAATTAAATTAAATTAAATT
1 AAAATAAAATTAAATTAAATT
2983567 AAAA
1 AAAA
2983571 ATATAAATGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
AAAATAAAATTAAATTAAATT
Found at i:2983550 original size:16 final size:16
Alignment explanation
Indices: 2983529--2983569 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
2983519 ATATTAAAAA
* *
2983529 TAAAATTAATTTGAAT
1 TAAAATTAAATTAAAT
2983545 TAAAATTAAATTAAAT
1 TAAAATTAAATTAAAT
2983561 T-AAATTAAA
1 TAAAATTAAA
2983570 AATATAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
TAAAATTAAATTAAAT
Found at i:2983557 original size:5 final size:5
Alignment explanation
Indices: 2983526--2983569 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
2983516 AAAATATTAA
* * *
2983526 AAATA AAATT AATTT GAATT AAAATT AAATT AAATT AAATT AAA
1 AAATT AAATT AAATT AAATT -AAATT AAATT AAATT AAATT AAA
2983570 AATATAAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
5 29 0.88
6 4 0.12
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (5 bp):
AAATT
Found at i:2983728 original size:9 final size:9
Alignment explanation
Indices: 2983716--2983754 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
2983706 ACATTTTTTC
2983716 TTTTTTCCT
1 TTTTTTCCT
2983725 TTTTTTCCT
1 TTTTTTCCT
*
2983734 TTTCTTTCTT
1 TTT-TTTCCT
*
2983744 TTTTTTTCT
1 TTTTTTCCT
2983753 TT
1 TT
2983755 CTCTCTCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTCCT
Found at i:2983749 original size:20 final size:20
Alignment explanation
Indices: 2983724--2983771 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
2983714 TCTTTTTTCC
* *
2983724 TTTTTTTCCTTT-TCTTTCT
1 TTTTTTTTCTTTCTCTCTCT
2983743 TTTTTTTTCTTTCTCTCTCT
1 TTTTTTTTCTTTCTCTCTCT
2983763 TTCTTTTTT
1 TT-TTTTTT
2983772 TTGTTCGGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 11 0.44
20 8 0.32
21 6 0.24
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTTTTCTTTCTCTCTCT
Found at i:2984051 original size:15 final size:14
Alignment explanation
Indices: 2984030--2984075 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 14
2984020 TTTTTGATTT
2984030 TTTTTCTCTTTTTC
1 TTTTTCTCTTTTTC
2984044 TCTTTTCTCTTTTTC
1 T-TTTTCTCTTTTTC
*
2984059 TTCTTTCTCTTCTTC
1 TT-TTTCTCTTTTTC
2984074 TT
1 TT
2984076 CCCCTCCCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 2 0.07
15 27 0.93
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTCTCTTTTTC
Found at i:2984069 original size:9 final size:8
Alignment explanation
Indices: 2984030--2984074 Score: 58
Period size: 8 Copynumber: 5.9 Consensus size: 8
2984020 TTTTTGATTT
2984030 TTTTTCTC
1 TTTTTCTC
2984038 TTTTTCTC
1 TTTTTCTC
2984046 -TTTTCTC
1 TTTTTCTC
2984053 TTTTTCT-
1 TTTTTCTC
*
2984060 TCTTTCTC
1 TTTTTCTC
*
2984068 TTCTTCT
1 TTTTTCT
2984075 TCCCCTCCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
7 13 0.41
8 19 0.59
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTTTCTC
Found at i:2984095 original size:10 final size:10
Alignment explanation
Indices: 2984056--2984113 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
2984046 TTTTCTCTTT
*
2984056 TTCTTCTTTC
1 TTCTTCTTCC
2984066 -TCTTCTT-C
1 TTCTTCTTCC
** *
2984074 TTCCCCTCCC
1 TTCTTCTTCC
2984084 TTCTTCTTCC
1 TTCTTCTTCC
2984094 TTCTTCCTT-C
1 TTCTT-CTTCC
2984104 TTCTTCTTCC
1 TTCTTCTTCC
2984114 AGTTCTCCTA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
8 1 0.03
9 14 0.37
10 20 0.53
11 3 0.08
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (10 bp):
TTCTTCTTCC
Found at i:2984614 original size:30 final size:30
Alignment explanation
Indices: 2984580--2984662 Score: 116
Period size: 29 Copynumber: 2.8 Consensus size: 30
2984570 CAAAACTTTT
*
2984580 GGGGTTGAAACGTAATTTTGAGAAA-GTTTA
1 GGGGTTGAAATGTAATTTTGA-AAATGTTTA
* *
2984610 GGGGTTAAAATGTAA-TTTCAAAATGTTTA
1 GGGGTTGAAATGTAATTTTGAAAATGTTTA
2984639 GGGGTTGAAATGTAATTTTGAAAA
1 GGGGTTGAAATGTAATTTTGAAAA
2984663 AAAATTAGGG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
28 3 0.07
29 23 0.50
30 20 0.43
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.35
Consensus pattern (30 bp):
GGGGTTGAAATGTAATTTTGAAAATGTTTA
Found at i:2984699 original size:60 final size:59
Alignment explanation
Indices: 2984548--2984717 Score: 160
Period size: 60 Copynumber: 2.8 Consensus size: 59
2984538 TGGCTGTCAG
* ** * * * * **
2984548 AGGGACCAAAATGTAATGGCAGCAAAACTTTTGGGGTTGAAACGTAATTTTGAGAAAGTTT
1 AGGGATCAAAATGTAATTTCA--AAAAATTTAGGGGTTGAAATGTAATTTTGAAAAAAATT
* * **
2984609 AGGGGTTAAAATGTAATTTCAAAATGTTTAGGGGTTGAAATGTAATTTTGAAAAAAAATT
1 AGGGATCAAAATGTAATTTCAAAAAATTTAGGGGTTGAAATGTAATTTTG-AAAAAAATT
* ** *
2984669 AGGGATCAAAATGTAATTTTAAAAAATTTAGGGGTCAAAATATAATTTT
1 AGGGATCAAAATGTAATTTCAAAAAATTTAGGGGTTGAAATGTAATTTT
2984718 TTTAAACACA
Statistics
Matches: 88, Mismatches: 20, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
59 25 0.28
60 47 0.53
61 16 0.18
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (59 bp):
AGGGATCAAAATGTAATTTCAAAAAATTTAGGGGTTGAAATGTAATTTTGAAAAAAATT
Found at i:2984706 original size:29 final size:30
Alignment explanation
Indices: 2984591--2984717 Score: 132
Period size: 29 Copynumber: 4.3 Consensus size: 30
2984581 GGGTTGAAAC
* * *
2984591 GTAATTTTGAGAAAGTTTAGGGGTTAAAAT
1 GTAATTTTGAAAAAATTTAGGGGTCAAAAT
* ** **
2984621 GTAA-TTTCAAAATGTTTAGGGGTTGAAAT
1 GTAATTTTGAAAAAATTTAGGGGTCAAAAT
* *
2984650 GTAATTTTGAAAAAAAATTAGGGATCAAAAT
1 GTAATTTTG-AAAAAATTTAGGGGTCAAAAT
2984681 GTAATTTT-AAAAAATTTAGGGGTCAAAAT
1 GTAATTTTGAAAAAATTTAGGGGTCAAAAT
*
2984710 ATAATTTT
1 GTAATTTT
2984718 TTTAAACACA
Statistics
Matches: 81, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
29 51 0.63
30 7 0.09
31 23 0.28
ACGTcount: A:0.42, C:0.02, G:0.20, T:0.36
Consensus pattern (30 bp):
GTAATTTTGAAAAAATTTAGGGGTCAAAAT
Found at i:2985066 original size:43 final size:43
Alignment explanation
Indices: 2984982--2985067 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 43
2984972 CAATCATGTG
* * **
2984982 AGCTAAATTTAAGAATATTAATACTTGAATTATTTTTCTTGCA
1 AGCTAAATTTAAGAAAATTAATACTTGAATTATGTAGCTTGCA
* *
2985025 AGCTGAATTTGAGAAAATTAATACTTGAATTGA-GTAGCTTGCA
1 AGCTAAATTTAAGAAAATTAATACTTGAATT-ATGTAGCTTGCA
2985068 GTTTAACTCG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
43 35 0.97
44 1 0.03
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.38
Consensus pattern (43 bp):
AGCTAAATTTAAGAAAATTAATACTTGAATTATGTAGCTTGCA
Found at i:2986178 original size:7 final size:7
Alignment explanation
Indices: 2986166--2986191 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2986156 ATCCATGATA
2986166 AAACCCT
1 AAACCCT
2986173 AAACCCT
1 AAACCCT
2986180 AAACCCT
1 AAACCCT
2986187 AAACC
1 AAACC
2986192 AAATAATCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.42, G:0.00, T:0.12
Consensus pattern (7 bp):
AAACCCT
Found at i:2991360 original size:3 final size:3
Alignment explanation
Indices: 2991352--2991387 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2991342 CAAAAATATG
2991352 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2991388 GTAAACAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2994583 original size:126 final size:126
Alignment explanation
Indices: 2994431--2994953 Score: 913
Period size: 126 Copynumber: 4.2 Consensus size: 126
2994421 CCACTAATGC
* * * *
2994431 CAGGGAGATAGGATTAGGTT-TTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTAATGT
1 CAGGGAGATAGGATT-GGTTCTTCAGTCTACTCCACTGCAACTTCAGAGAGATAAGACTTGATGC
*
2994495 GATCTGCTCTCTGCAACCTCAGAGAGATAAGATCCGTGATTTAATCCACTCCACTGCAACTT
65 GATCTGCTCTCTGCAACCTCAGAGAGATAAGATCTGTGATTTAATCCACTCCACTGCAACTT
*
2994557 CAGGGAGATAGGATTGGTTCTTCAGTCTACTCCACTGCAACTTCAGAGAGATAAGACTTGATACG
1 CAGGGAGATAGGATTGGTTCTTCAGTCTACTCCACTGCAACTTCAGAGAGATAAGACTTGATGCG
**
2994622 ATCTGCTCTCTGCAACCTTGGAGAGATAAGATCTGTGATTTAATCCACTCCACTGCAACTT
66 ATCTGCTCTCTGCAACCTCAGAGAGATAAGATCTGTGATTTAATCCACTCCACTGCAACTT
2994683 CAGGGAGATAGGATTGGTTCTTCAGTCTACTCCACTGCAACTTCAGAGAGATAAGACTTGATGCG
1 CAGGGAGATAGGATTGGTTCTTCAGTCTACTCCACTGCAACTTCAGAGAGATAAGACTTGATGCG
*
2994748 ATCTGCTCTCTGCAACCTCAGAGAGATAAGATCTTTGATTTAATCCACTCCACTGCAACTT
66 ATCTGCTCTCTGCAACCTCAGAGAGATAAGATCTGTGATTTAATCCACTCCACTGCAACTT
* *
2994809 CAGAGAGATAGGATTGGTTCTTCAGTCTACTTCACTGCAACTTCAGAGAGATAAGACTTGATGCG
1 CAGGGAGATAGGATTGGTTCTTCAGTCTACTCCACTGCAACTTCAGAGAGATAAGACTTGATGCG
* *
2994874 ATCTGCTCTCTGCAACCTCGGAGAGATAAGATCTGTGATTTAATCCACTCCACTACAACTT
66 ATCTGCTCTCTGCAACCTCAGAGAGATAAGATCTGTGATTTAATCCACTCCACTGCAACTT
2994935 CAGGGAGATAGGATTGGTT
1 CAGGGAGATAGGATTGGTT
2994954 TTTCGGTTTC
Statistics
Matches: 378, Mismatches: 18, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
125 4 0.01
126 374 0.99
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (126 bp):
CAGGGAGATAGGATTGGTTCTTCAGTCTACTCCACTGCAACTTCAGAGAGATAAGACTTGATGCG
ATCTGCTCTCTGCAACCTCAGAGAGATAAGATCTGTGATTTAATCCACTCCACTGCAACTT
Found at i:2994934 original size:83 final size:84
Alignment explanation
Indices: 2994505--2994944 Score: 324
Period size: 83 Copynumber: 5.2 Consensus size: 84
2994495 GATCTGCTCT
* * ** * * * *
2994505 CTGCAACCTCAGAGAGATAAGATCCGTGATTTAATCCACTCCACTGCAACTTCAGGGAGATAGGA
1 CTGCAACTTCAGAGAGATAAGA--CTTGATTCGATCTACTCCACTGCAACCTCAGAGAGATAAGA
* * *
2994570 T-TG-GTTCTTCAGTCTACTCCA
64 TCTGTGAT-TT-AATCCACTCCA
* * * **
2994591 CTGCAACTTCAGAGAGATAAGACTTGATACGATCTGCT-CTCTGCAACCTTGGAGAGATAAGATC
1 CTGCAACTTCAGAGAGATAAGACTTGATTCGATCTACTCCACTGCAACCTCAGAGAGATAAGATC
2994655 TGTGATTTAATCCACTCCA
66 TGTGATTTAATCCACTCCA
* * * * *
2994674 CTGCAACTTCAGGGAGATAGGA-TTGGTTCTTCAGTCTACTCCACTGCAACTTCAGAGAGATAAG
1 CTGCAACTTCAGAGAGATAAGACTTGATTC--GA-TCTACTCCACTGCAACCTCAGAGAGATAAG
*** ** *
2994738 A-CT-TGATGCGATCTGCT-CT
63 ATCTGTGATTTAATCCACTCCA
* ** * * *
2994757 CTGCAACCTCAGAGAGATAAGATCTTTGATTTAATCCACTCCACTGCAACTTCAGAGAGATAGGA
1 CTGCAACTTCAGAGAGATAAGA-C-TTGATTCGATCTACTCCACTGCAACCTCAGAGAGATAAGA
* * * *
2994822 T-TG-GTTCTTCAGTCTACTTCA
64 TCTGTGAT-TT-AATCCACTCCA
* * * *
2994843 CTGCAACTTCAGAGAGATAAGACTTGATGCGATCTGCT-CTCTGCAACCTCGGAGAGATAAGATC
1 CTGCAACTTCAGAGAGATAAGACTTGATTCGATCTACTCCACTGCAACCTCAGAGAGATAAGATC
2994907 TGTGATTTAATCCACTCCA
66 TGTGATTTAATCCACTCCA
* *
2994926 CTACAACTTCAGGGAGATA
1 CTGCAACTTCAGAGAGATA
2994945 GGATTGGTTT
Statistics
Matches: 275, Mismatches: 63, Indels: 35
0.74 0.17 0.09
Matches are distributed among these distances:
82 5 0.02
83 146 0.53
84 39 0.14
85 17 0.06
86 68 0.25
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.28
Consensus pattern (84 bp):
CTGCAACTTCAGAGAGATAAGACTTGATTCGATCTACTCCACTGCAACCTCAGAGAGATAAGATC
TGTGATTTAATCCACTCCA
Found at i:2996049 original size:14 final size:14
Alignment explanation
Indices: 2996032--2996080 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
2996022 CCTTAGCCTC
2996032 TTCATTTTTACTTT
1 TTCATTTTTACTTT
2996046 TTCATTTTT--TATT
1 TTCATTTTTACT-TT
2996059 TTCATTTTTACATTT
1 TTCATTTTTAC-TTT
2996074 TT-ATTTT
1 TTCATTTT
2996081 CACATATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
12 1 0.03
13 11 0.35
14 14 0.45
15 4 0.13
16 1 0.03
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.73
Consensus pattern (14 bp):
TTCATTTTTACTTT
Found at i:2996076 original size:8 final size:7
Alignment explanation
Indices: 2996032--2996080 Score: 50
Period size: 7 Copynumber: 7.1 Consensus size: 7
2996022 CCTTAGCCTC
2996032 TTCATTT
1 TTCATTT
2996039 TT-ACTTT
1 TTCA-TTT
2996046 TTCATTT
1 TTCATTT
*
2996053 TTTA-TT
1 TTCATTT
2996059 TTCATTT
1 TTCATTT
2996066 TTACATTT
1 TT-CATTT
2996074 TT-ATTT
1 TTCATTT
2996080 T
1 T
2996081 CACATATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
6 11 0.31
7 17 0.47
8 8 0.22
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.73
Consensus pattern (7 bp):
TTCATTT
Found at i:2996602 original size:13 final size:12
Alignment explanation
Indices: 2996579--2996622 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 12
2996569 CGGTAGAAGT
2996579 TTTTTTCTTTTTG
1 TTTTTT-TTTTTG
2996592 TTTTTATTTTTTG
1 TTTTT-TTTTTTG
*
2996605 TTCTTTTTTTATG
1 TT-TTTTTTTTTG
2996618 TTTTT
1 TTTTT
2996623 CTTCTCTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 3 0.11
13 21 0.75
14 4 0.14
ACGTcount: A:0.05, C:0.05, G:0.07, T:0.84
Consensus pattern (12 bp):
TTTTTTTTTTTG
Found at i:2996603 original size:19 final size:18
Alignment explanation
Indices: 2996579--2996633 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
2996569 CGGTAGAAGT
*
2996579 TTTTTTCTTTTTGTTTTTA
1 TTTTTTCTTCTT-TTTTTA
*
2996598 TTTTTTGTTCTTTTTTTA
1 TTTTTTCTTCTTTTTTTA
2996616 TGTTTTTCTTCTCTTTTT
1 T-TTTTTCTTCT-TTTTT
2996634 CCTTTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.23
19 19 0.61
20 5 0.16
ACGTcount: A:0.04, C:0.09, G:0.05, T:0.82
Consensus pattern (18 bp):
TTTTTTCTTCTTTTTTTA
Found at i:2997347 original size:13 final size:12
Alignment explanation
Indices: 2997317--2997341 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2997307 AATATCAAAG
2997317 AATATACAAAAA
1 AATATACAAAAA
2997329 AATATACAAAAA
1 AATATACAAAAA
2997341 A
1 A
2997342 TGTATAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AATATACAAAAA
Found at i:3003460 original size:43 final size:43
Alignment explanation
Indices: 3003411--3003802 Score: 150
Period size: 43 Copynumber: 9.3 Consensus size: 43
3003401 CCACTAATGC
* *
3003411 CAGGGAGATAGGATTAGG-TCTTCAGTCTGCTCCACTGCAACTT
1 CAGGGAGATAAGATTAGGAT-TTCAGTCTACTCCACTGCAACTT
* * * * *
3003454 CAGGGAGATAAGACTTA--ATGTGA-TCTGCT-CTCTGCAACCT
1 CAGGGAGATAAGA-TTAGGATTTCAGTCTACTCCACTGCAACTT
* ** * *
3003494 CAGAGAGATAAGATCCGCGATTT-AATCCACTCCACTGCAACTT
1 CAGGGAGATAAGATTAG-GATTTCAGTCTACTCCACTGCAACTT
* *
3003537 CAGGGAGATAGGATT-GGTTCTTCAGTCTACTCCACTGCAACTT
1 CAGGGAGATAAGATTAGGAT-TTCAGTCTACTCCACTGCAACTT
* * * * *
3003580 CAGAGAGATAAGCTTGATGCGA--TCTG-CT-CTCTACAGC--CTT
1 CAGGGAGATAAGATT-A-G-GATTTCAGTCTACTCCACTGCAACTT
* * *
3003620 --GGAGAGATAAGATCT-GTGATTT-AATCCACTCCACTGTAACTT
1 CAGG-GAGATAAGAT-TAG-GATTTCAGTCTACTCCACTGCAACTT
* * * *
3003662 CAGAGAGATAGGATT-GGTTCTTCAGTATACTCCACTGCAACTT
1 CAGGGAGATAAGATTAGGAT-TTCAGTCTACTCCACTGCAACTT
* * * * *
3003705 CAGAGAGATAAGACTT--GA-TGC-GATCTGCT-CTCTGCAACCT
1 CAGGGAGATAAGA-TTAGGATTTCAG-TCTACTCCACTGCAACTT
* * * *
3003745 CAGAGAGATAAGATCT-GTGATTT-AATCCACTCCACTGTAACTT
1 CAGGGAGATAAGAT-TAG-GATTTCAGTCTACTCCACTGCAACTT
*
3003788 CAGGGAGATAGGATT
1 CAGGGAGATAAGATT
3003803 GGTTCTTCGG
Statistics
Matches: 258, Mismatches: 58, Indels: 67
0.67 0.15 0.17
Matches are distributed among these distances:
37 3 0.01
38 1 0.00
39 13 0.05
40 55 0.21
41 17 0.07
42 33 0.13
43 125 0.48
44 9 0.03
46 1 0.00
47 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (43 bp):
CAGGGAGATAAGATTAGGATTTCAGTCTACTCCACTGCAACTT
Found at i:3003662 original size:125 final size:126
Alignment explanation
Indices: 3003411--3003810 Score: 660
Period size: 126 Copynumber: 3.2 Consensus size: 126
3003401 CCACTAATGC
* * * *
3003411 CAGGGAGATAGGATTAGG-TCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTAATGT
1 CAGGGAGATAGGATT-GGTTCTTCAGTCTACTCCACTGCAACTTCAGAGAGATAAGACTTGATGC
* * *
3003475 GATCTGCTCTCTGCAACCTCAGAGAGATAAGATCCGCGATTTAATCCACTCCACTGCAACTT
65 GATCTGCTCTCTGCAACCTCAGAGAGATAAGATCTGTGATTTAATCCACTCCACTGTAACTT
3003537 CAGGGAGATAGGATTGGTTCTTCAGTCTACTCCACTGCAACTTCAGAGAGATAAG-CTTGATGCG
1 CAGGGAGATAGGATTGGTTCTTCAGTCTACTCCACTGCAACTTCAGAGAGATAAGACTTGATGCG
* * **
3003601 ATCTGCTCTCTACAGCCTTGGAGAGATAAGATCTGTGATTTAATCCACTCCACTGTAACTT
66 ATCTGCTCTCTGCAACCTCAGAGAGATAAGATCTGTGATTTAATCCACTCCACTGTAACTT
* *
3003662 CAGAGAGATAGGATTGGTTCTTCAGTATACTCCACTGCAACTTCAGAGAGATAAGACTTGATGCG
1 CAGGGAGATAGGATTGGTTCTTCAGTCTACTCCACTGCAACTTCAGAGAGATAAGACTTGATGCG
3003727 ATCTGCTCTCTGCAACCTCAGAGAGATAAGATCTGTGATTTAATCCACTCCACTGTAACTT
66 ATCTGCTCTCTGCAACCTCAGAGAGATAAGATCTGTGATTTAATCCACTCCACTGTAACTT
3003788 CAGGGAGATAGGATTGGTTCTTC
1 CAGGGAGATAGGATTGGTTCTTC
3003811 GGTTTGTTCT
Statistics
Matches: 254, Mismatches: 18, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
125 116 0.46
126 138 0.54
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (126 bp):
CAGGGAGATAGGATTGGTTCTTCAGTCTACTCCACTGCAACTTCAGAGAGATAAGACTTGATGCG
ATCTGCTCTCTGCAACCTCAGAGAGATAAGATCTGTGATTTAATCCACTCCACTGTAACTT
Found at i:3005037 original size:7 final size:7
Alignment explanation
Indices: 3005016--3005064 Score: 50
Period size: 7 Copynumber: 7.1 Consensus size: 7
3005006 CCTTAGCCTC
3005016 TTCATTT
1 TTCATTT
3005023 TT-ACTTT
1 TTCA-TTT
3005030 TTCATTT
1 TTCATTT
*
3005037 TTTA-TT
1 TTCATTT
3005043 TTCATTT
1 TTCATTT
3005050 TTCCATTT
1 TT-CATTT
3005058 TT-ATTT
1 TTCATTT
3005064 T
1 T
3005065 CACATATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
6 11 0.31
7 17 0.47
8 8 0.22
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.73
Consensus pattern (7 bp):
TTCATTT
Found at i:3011048 original size:22 final size:22
Alignment explanation
Indices: 3011020--3011063 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3011010 CGTTTATCTT
3011020 CAAAACAAGGGAAAA-AAAAGAA
1 CAAAAC-AGGGAAAAGAAAAGAA
*
3011042 CAAAACAGTGAAAAGAAAAGAA
1 CAAAACAGGGAAAAGAAAAGAA
3011064 AAATGGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.70, C:0.09, G:0.18, T:0.02
Consensus pattern (22 bp):
CAAAACAGGGAAAAGAAAAGAA
Found at i:3013574 original size:59 final size:59
Alignment explanation
Indices: 3013508--3013634 Score: 229
Period size: 58 Copynumber: 2.2 Consensus size: 59
3013498 AAAGTAAGAA
3013508 GAAAAAATTAAAGAGGTGCTTAGTGCTCCAAGAAATTTCAAATCTTGATGTAAACATTT
1 GAAAAAATTAAAGAGGTGCTTAGTGCTCCAAGAAATTTCAAATCTTGATGTAAACATTT
*
3013567 GAAAAAA-TAAAGAGGTGCTTAGTGCTCCTAGAAATTTCAAATCTTGATGTAAACATTT
1 GAAAAAATTAAAGAGGTGCTTAGTGCTCCAAGAAATTTCAAATCTTGATGTAAACATTT
3013625 GAAGAAAATT
1 GAA-AAAATT
3013635 GAGTTGAGTT
Statistics
Matches: 65, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
58 53 0.82
59 11 0.17
60 1 0.02
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (59 bp):
GAAAAAATTAAAGAGGTGCTTAGTGCTCCAAGAAATTTCAAATCTTGATGTAAACATTT
Found at i:3013897 original size:21 final size:21
Alignment explanation
Indices: 3013871--3013913 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3013861 TCCGATTGGG
*
3013871 ATTCTTTAGCTTGGCTAACTC
1 ATTCTTCAGCTTGGCTAACTC
3013892 ATTCTTCAGCTTGGCTAACTC
1 ATTCTTCAGCTTGGCTAACTC
3013913 A
1 A
3013914 AGCAATCGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.40
Consensus pattern (21 bp):
ATTCTTCAGCTTGGCTAACTC
Found at i:3020430 original size:14 final size:14
Alignment explanation
Indices: 3020402--3020443 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
3020392 TACAACCACC
3020402 TTAACTGCT-ACTG
1 TTAACTGCTAACTG
3020415 TTAACTGCTAACTG
1 TTAACTGCTAACTG
*
3020429 TTAACTACTAACTG
1 TTAACTGCTAACTG
3020443 T
1 T
3020444 AATAACAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
13 9 0.33
14 18 0.67
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (14 bp):
TTAACTGCTAACTG
Found at i:3026619 original size:15 final size:15
Alignment explanation
Indices: 3026595--3026624 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3026585 TGGAGATCGA
*
3026595 GGAAATGGTCGTGGT
1 GGAAAAGGTCGTGGT
3026610 GGAAAAGGTCGTGGT
1 GGAAAAGGTCGTGGT
3026625 CAAGAAGGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.07, G:0.47, T:0.23
Consensus pattern (15 bp):
GGAAAAGGTCGTGGT
Found at i:3034070 original size:15 final size:16
Alignment explanation
Indices: 3034052--3034083 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3034042 AAAATACTTT
3034052 AAAATAAAAAA-ATAA
1 AAAATAAAAAATATAA
3034067 AAAATAAAAAATATAA
1 AAAATAAAAAATATAA
3034083 A
1 A
3034084 TACTAAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAATAAAAAATATAA
Found at i:3038579 original size:21 final size:20
Alignment explanation
Indices: 3038551--3038589 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3038541 GAATTTTTTT
* *
3038551 AATTGAGTCGAGTGAAATGA
1 AATTGAGTCAAGTCAAATGA
3038571 AATTCGAGTCAAGTCAAAT
1 AATT-GAGTCAAGTCAAAT
3038590 AGAATCAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26
Consensus pattern (20 bp):
AATTGAGTCAAGTCAAATGA
Found at i:3038834 original size:19 final size:19
Alignment explanation
Indices: 3038803--3038914 Score: 70
Period size: 19 Copynumber: 5.7 Consensus size: 19
3038793 ATATTAACTC
3038803 TTTTTATATATTTTTTAGAA
1 TTTTTATA-ATTTTTTAGAA
3038823 TTTTTATAATTTTTTTA-AA
1 TTTTTATAA-TTTTTTAGAA
** * *
3038842 AATATATAATTTTTGA-AA
1 TTTTTATAATTTTTTAGAA
*
3038860 TTTTTATAAATATTTT-GAA
1 TTTTTAT-AATTTTTTAGAA
* *
3038879 TTTTAAAAATTATTTT-GAA
1 TTTTTATAATT-TTTTAGAA
3038898 TTCTATTTATAATTTTT
1 -T-T-TTTATAATTTTT
3038915 ATTGAGGGAG
Statistics
Matches: 71, Mismatches: 14, Indels: 13
0.72 0.14 0.13
Matches are distributed among these distances:
18 15 0.21
19 29 0.41
20 16 0.23
21 4 0.06
22 7 0.10
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.60
Consensus pattern (19 bp):
TTTTTATAATTTTTTAGAA
Found at i:3038888 original size:28 final size:28
Alignment explanation
Indices: 3038803--3038889 Score: 77
Period size: 28 Copynumber: 3.1 Consensus size: 28
3038793 ATATTAACTC
* * *
3038803 TTTTTATATATTTTTTAGAATTTTTATAA
1 TTTTTATAAATATTTT-GAATTTTTAAAA
* * * *
3038832 TTTTTTTAAAAATATAT-AATTTTTGAAA
1 TTTTTATAAATAT-TTTGAATTTTTAAAA
*
3038860 TTTTTATAAATATTTTGAATTTTAAAAA
1 TTTTTATAAATATTTTGAATTTTTAAAA
3038888 TT
1 TT
3038890 ATTTTGAATT
Statistics
Matches: 44, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
27 2 0.05
28 31 0.70
29 9 0.20
30 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (28 bp):
TTTTTATAAATATTTTGAATTTTTAAAA
Found at i:3042653 original size:16 final size:17
Alignment explanation
Indices: 3042616--3042657 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
3042606 GCTAGCTAGG
3042616 TACA-ATAT-ATATGTA
1 TACATATATAATATGTA
3042631 TACATATATAATATGT-
1 TACATATATAATATGTA
*
3042647 TATATATATAA
1 TACATATATAA
3042658 GTAAAAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 14 0.58
17 6 0.25
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (17 bp):
TACATATATAATATGTA
Found at i:3045400 original size:14 final size:14
Alignment explanation
Indices: 3045381--3045411 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3045371 TAACCGCTAT
*
3045381 TGTTAACTGCTAAC
1 TGTTAACTACTAAC
3045395 TGTTAACTACTAAC
1 TGTTAACTACTAAC
3045409 TGT
1 TGT
3045412 CATAACAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (14 bp):
TGTTAACTACTAAC
Found at i:3056130 original size:12 final size:12
Alignment explanation
Indices: 3056113--3056139 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3056103 ACAAAATTAT
3056113 ATTATATCAATA
1 ATTATATCAATA
3056125 ATTATATCAATA
1 ATTATATCAATA
3056137 ATT
1 ATT
3056140 TATAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (12 bp):
ATTATATCAATA
Found at i:3059496 original size:27 final size:27
Alignment explanation
Indices: 3059381--3059502 Score: 104
Period size: 27 Copynumber: 4.5 Consensus size: 27
3059371 TGGAGGGGTT
* * *
3059381 CTGATTGGCGGCACCAAAGGTGCCAAA
1 CTGATTGGCGGCACCGATGGTGCCATA
*
3059408 CTGATTGGCGGCATCGATGGTGCCA-A
1 CTGATTGGCGGCACCGATGGTGCCATA
** * *
3059434 -TGAGGTTGGAAGCACTGATGATGCCATA
1 CTGA--TTGGCGGCACCGATGGTGCCATA
* * * *
3059462 CAGGTTGGCAGCACCGACGGTGCCATA
1 CTGATTGGCGGCACCGATGGTGCCATA
3059489 CTGATTGGCGGCAC
1 CTGATTGGCGGCAC
3059503 TACTCGTCTT
Statistics
Matches: 74, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
25 3 0.04
26 1 0.01
27 68 0.92
28 1 0.01
29 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.33, T:0.20
Consensus pattern (27 bp):
CTGATTGGCGGCACCGATGGTGCCATA
Found at i:3059726 original size:3 final size:3
Alignment explanation
Indices: 3059718--3059769 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
3059708 GATAGTTTTA
* *
3059718 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT AGT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3059766 ATT A
1 ATT A
3059770 AGATGTTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:3060632 original size:15 final size:18
Alignment explanation
Indices: 3060604--3060648 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
3060594 TTGATATGGT
* *
3060604 TGGTGGTGAAGAAGAAAG
1 TGGTGGCGAAGAAGAAGG
3060622 TGGTGGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
3060640 TGGTGGCGA
1 TGGTGGCGA
3060649 TCATTGGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.31, C:0.04, G:0.49, T:0.16
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:3063575 original size:317 final size:316
Alignment explanation
Indices: 3063000--3063771 Score: 1318
Period size: 317 Copynumber: 2.4 Consensus size: 316
3062990 AAGTTGAAAA
3063000 AAAAAGTTAGTAAAAAACTCTTACTTCGGCCATTTGTTCGTA-TTTTTTCTCCGCATTTTATTAC
1 AAAAAGTTAGTAAAAAACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA-
*
3063064 TTTAAAAAATATCTTAATTTCTAATTTTATAAGTTTACATTATTTCAGTGCATAATGTTTGAAAT
65 TTTAAAAAATAT-TTAATTT-TAATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAAT
3063129 TTATTAATTTAGTGTGTTTTTAAATTAAGTTGGTGTAAGAAAAAAACCCTTATCCCTGCCCTTTG
128 TTATTAATTTAGTGTGTTTTTAAATTAAGTTGGTGTAAGAAAAAAACCCTTATCCCTGCCCTTTG
*
3063194 CTCGTATTATTTTCCCAATTTTTATTACTTTCAATAAAAATATTTTATTTTCGTATTTTATTATT
193 CTCGTATTATTTTCCCAATTTTTATTACTTTCAATAAAAATATTTTATTTTCGAATTTTATTATT
3063259 TTATATTATTCCAGTGCATTTTGTTTGAAATATTTGTATTAATTAT-TCCTGAA-TTTTT
258 TTATATTATTCCAGTGCATTTTGTTTGAAATATTTGTATTAATTATCT-CTGAATTTTTT
*
3063317 AAAAAGTTAGTAAAAAACTCTTACTTCGGCCATTTGTTTGTATTTTTTTCTCCGCATTTT-TTAT
1 AAAAAGTTAGTAAAAAACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTAT
*
3063381 TATAGAAAATATTATAATTTTAATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAATT
66 T-TAAAAAATATT-TAATTTTAATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAATT
*
3063446 TATTAATTTAGTGTGTTTTTTAAATTAATTTGGTGTAAGAAAAAAACCCTTATCCCTGCCCTTTG
129 TATTAATTTAGTGTG-TTTTTAAATTAAGTTGGTGTAAGAAAAAAACCCTTATCCCTGCCCTTTG
*
3063511 CTCGTATTATTTTCCCGATTTTTATTACTTTCAATAAAAATATTTTATTTTCGAATTTTATTATT
193 CTCGTATTATTTTCCCAATTTTTATTACTTTCAATAAAAATATTTTATTTTCGAATTTTATTATT
3063576 TTATATTATTCCAGTGCATTTTGTTTGAAATATTTGTATTAATTATCTCTGAATTTTTT
258 TTATATTATTCCAGTGCATTTTGTTTGAAATATTTGTATTAATTATCTCTGAATTTTTT
* * *
3063635 AAAAAGTTAGTAAAAAACTCTTATTTCGACCATTTGTTCGTATTTTTTTATCCGCATTTTATTAT
1 AAAAAGTTAGTAAAAAACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA-
* * *
3063700 TTTAAAAAATATCGTAATTTTTAATTTTATCATTTTACATTATTTCAGTGCATTATGTTTGAAAT
65 TTTAAAAAATAT-TTAA-TTTTAATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAAT
3063765 TTATTAA
128 TTATTAA
3063772 ATATACAATT
Statistics
Matches: 431, Mismatches: 14, Indels: 17
0.93 0.03 0.04
Matches are distributed among these distances:
316 62 0.14
317 221 0.51
318 79 0.18
319 15 0.03
320 54 0.13
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.49
Consensus pattern (316 bp):
AAAAAGTTAGTAAAAAACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTAT
TTAAAAAATATTTAATTTTAATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAATTTA
TTAATTTAGTGTGTTTTTAAATTAAGTTGGTGTAAGAAAAAAACCCTTATCCCTGCCCTTTGCTC
GTATTATTTTCCCAATTTTTATTACTTTCAATAAAAATATTTTATTTTCGAATTTTATTATTTTA
TATTATTCCAGTGCATTTTGTTTGAAATATTTGTATTAATTATCTCTGAATTTTTT
Found at i:3063735 original size:158 final size:149
Alignment explanation
Indices: 3063000--3063771 Score: 587
Period size: 158 Copynumber: 4.9 Consensus size: 149
3062990 AAGTTGAAAA
* * *
3063000 AAAAAGTTAGTAAAAAACTCTTACTTCGGCCATTTGTTCGTATTTTTTCTCCGCATTTTATTACT
1 AAAAAGTTAGTAAAAAACTCTTATTTC-GCCATTTGTTCGTATTTTTTTTCCGCATTTTATTATT
* * *
3063065 TTAAAAAATATCTTAATTTCTAATTTTATAAGTTTACATTATTTCAGTGCATAATGTTTG-AA-A
65 TTAAAAAATAT-TTAATTTTTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAATA
**
3063128 TTTATTAATTTAGTGTGTTTTT
129 TTTATTAATTTTCTGT-TTTTT
* * ** * * *
3063150 AAATTAAGTTGGTGTAAGAAAAAAACCCTTATCCCTGCCCTTTGCTCGTA-TTATTTTCC-CAAT
1 AAA--AA----GT-T-AGTAAAAAACTCTTATTTC-GCCATTTGTTCGTATTTTTTTTCCGC-A-
* * * * *
3063213 TTTTATTACTTTCAATAAAAATATTTTATTTTCGT-ATTTTATTATTTTATATTATTCCAGTGCA
55 TTTTATTA-TTT-TA-AAAAATATTTAATTTT--TAATTTTATAATTTTACATTATTTCAGTGCA
* *
3063277 TTTTGTTTGAAATATTTGTATTAATTATTCCTGAATTTTT
115 TTATGTTTGAAATA-TT-TATTAATT-TT-CTG-TTTTTT
* *
3063317 AAAAAGTTAGTAAAAAACTCTTACTTCGGCCATTTGTTTGTATTTTTTTCTCCGCATTTT-TTAT
1 AAAAAGTTAGTAAAAAACTCTTATTTC-GCCATTTGTTCGTATTTTTTT-TCCGCATTTTATTAT
* * *
3063381 TATAGAAAATATTATAA-TTTTAATTTTATAATTTTACATTATTTCAGTGCATAATGTTTG-AA-
64 TTTAAAAAATATT-TAATTTTTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAAT
*
3063443 ATTTATTAATTTAGTGTGTTTTTT
128 ATTTATTAATTT--TCTGTTTTTT
* * ** * * * *
3063467 AAATTAATTTGGTGTAAGAAAAAAACCCTTATCCCTGCCCTTTGCTCGTATTATTTTCCCG-ATT
1 AAA--AA----GT-T-AGTAAAAAACTCTTATTTC-GCCATTTGTTCGTATTTTTTTTCCGCA-T
* * * * * *
3063531 TTTATTACTTTCAATAAAAATATTTTATTTTCGAATTTTATTATTTTATATTATTCCAGTGCATT
56 TTTATTA-TTT-TA-AAAAATATTTAATTTT-TAATTTTATAATTTTACATTATTTCAGTGCATT
*
3063596 TTGTTTGAAATATTTGTATTAATTATCTCTGAATTTTTT
117 ATGTTTGAAATA-TT-TATTAATT-T-TCTG--TTTTTT
3063635 AAAAAGTTAGTAAAAAACTCTTATTTCGACCATTTGTTCGTATTTTTTTATCCGCATTTTATTAT
1 AAAAAGTTAGTAAAAAACTCTTATTTCG-CCATTTGTTCGTATTTTTTT-TCCGCATTTTATTAT
* *
3063700 TTTAAAAAATATCGTAATTTTTAATTTTATCATTTTACATTATTTCAGTGCATTATGTTTG-AA-
64 TTTAAAAAATAT-TTAATTTTTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAAT
3063763 ATTTATTAA
128 ATTTATTAA
3063772 ATATACAATT
Statistics
Matches: 484, Mismatches: 83, Indels: 106
0.72 0.12 0.16
Matches are distributed among these distances:
150 12 0.02
151 10 0.02
152 7 0.01
153 1 0.00
154 9 0.02
155 35 0.07
156 18 0.04
157 22 0.05
158 113 0.23
159 40 0.08
160 55 0.11
161 69 0.14
162 41 0.08
163 3 0.01
164 3 0.01
165 12 0.02
166 14 0.03
167 11 0.02
168 9 0.02
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.49
Consensus pattern (149 bp):
AAAAAGTTAGTAAAAAACTCTTATTTCGCCATTTGTTCGTATTTTTTTTCCGCATTTTATTATTT
TAAAAAATATTTAATTTTTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAATATT
TATTAATTTTCTGTTTTTT
Found at i:3064133 original size:4 final size:4
Alignment explanation
Indices: 3064126--3064226 Score: 63
Period size: 4 Copynumber: 25.8 Consensus size: 4
3064116 TTCCCTCTTC
* *
3064126 TTCT TTCT TT-T TTTT TCTCT TTCT TCTCCT TTCTT TTCT TTCC TTC-
1 TTCT TTCT TTCT TTCT T-TCT TTCT T-T-CT TTC-T TTCT TTCT TTCT
* * *
3064172 TT-T TTCT TTCT TT-T TTCC TTC- TTCT TCCTT TTCT TTCC TTC- TT-T
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC-T TTCT TTCT TTCT TTCT
3064216 TTCT TTCT TTC
1 TTCT TTCT TTC
3064227 CTCTCCTGTC
Statistics
Matches: 79, Mismatches: 6, Indels: 24
0.72 0.06 0.22
Matches are distributed among these distances:
3 17 0.22
4 47 0.59
5 12 0.15
6 3 0.04
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
TTCT
Found at i:3064134 original size:10 final size:10
Alignment explanation
Indices: 3064121--3064272 Score: 91
Period size: 10 Copynumber: 16.2 Consensus size: 10
3064111 CTTCCTTCCC
3064121 TCTTCTTCTT
1 TCTTCTTCTT
3064131 TCTT-TT-TT
1 TCTTCTTCTT
3064139 T-TTC-TCTT
1 TCTTCTTCTT
*
3064147 TCTTCTCCTT
1 TCTTCTTCTT
3064157 TCTT-TTCTT
1 TCTTCTTCTT
3064166 TCCTTCTT-TT
1 T-CTTCTTCTT
*
3064176 TCTTTCTTTTT
1 TC-TTCTTCTT
3064187 TCCTTCTTCTT
1 T-CTTCTTCTT
*
3064198 CCTT-TTCTT
1 TCTTCTTCTT
3064207 TC--CTTCTT
1 TCTTCTTCTT
3064215 T-TTCTTTCTT
1 TCTTC-TTCTT
* *
3064225 TCCTCTCCTGT
1 TCTTCTTCT-T
*
3064236 CCTT-TTC-T
1 TCTTCTTCTT
*
3064244 TCTTTTTCTT
1 TCTTCTTCTT
3064254 TC-TCTTC-T
1 TCTTCTTCTT
3064262 TCTTCTT-TT
1 TCTTCTTCTT
3064271 TC
1 TC
3064273 CCTCTCCTTC
Statistics
Matches: 111, Mismatches: 12, Indels: 39
0.69 0.07 0.24
Matches are distributed among these distances:
7 3 0.03
8 19 0.17
9 32 0.29
10 39 0.35
11 17 0.15
12 1 0.01
ACGTcount: A:0.00, C:0.30, G:0.01, T:0.70
Consensus pattern (10 bp):
TCTTCTTCTT
Found at i:3064135 original size:30 final size:28
Alignment explanation
Indices: 3064099--3064228 Score: 88
Period size: 30 Copynumber: 4.5 Consensus size: 28
3064089 ATTACCTTTT
*
3064099 TTTCTTTTTTTCCTTC-CTTCCCTCTTCTTC
1 TTTCTTTTTTTCCTTCTCTT---TCTTCTCC
3064129 TTTCTTTTTTT--TTCTCTTTCTTCTCC
1 TTTCTTTTTTTCCTTCTCTTTCTTCTCC
* **
3064155 TTTCTTTTCTTTCCTTCTTTTTCTTTCTTT
1 TTTCTTTT-TTTCCTTCTCTTTC-TTCTCC
* * *
3064185 TTTCCTTCTTCTTCCTTTTCTTTCCTTCT-T
1 TTT-CTT-TTTTTCCTTCTCTTT-CTTCTCC
*
3064215 TTTCTTTCTTTCCT
1 TTTCTTTTTTTCCT
3064229 CTCCTGTCCT
Statistics
Matches: 83, Mismatches: 9, Indels: 18
0.75 0.08 0.16
Matches are distributed among these distances:
26 15 0.18
27 3 0.04
28 9 0.11
29 14 0.17
30 22 0.27
31 17 0.20
32 3 0.04
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (28 bp):
TTTCTTTTTTTCCTTCTCTTTCTTCTCC
Found at i:3064149 original size:23 final size:24
Alignment explanation
Indices: 3064123--3064226 Score: 89
Period size: 23 Copynumber: 4.6 Consensus size: 24
3064113 TCCTTCCCTC
3064123 TTCTTCTTTCTTT-TTTTTTCTCT
1 TTCTTCTTTCTTTCTTTTTTCTCT
* *
3064146 TTCTTC-TCCTTTCTTTTCTT-TCC
1 TTCTTCTTTCTTTCTTTT-TTCTCT
3064169 TTCTT-TTTCTTTCTTTTTTC-C-
1 TTCTTCTTTCTTTCTTTTTTCTCT
* * *
3064190 TTCTTCTTCCTTT-TCTTTCCTTCT
1 TTCTTCTTTCTTTCTTTTTTC-TCT
3064214 TT-TTCTTTCTTTC
1 TTCTTCTTTCTTTC
3064227 CTCTCCTGTC
Statistics
Matches: 65, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
21 10 0.15
22 14 0.22
23 37 0.57
24 4 0.06
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (24 bp):
TTCTTCTTTCTTTCTTTTTTCTCT
Found at i:3064252 original size:74 final size:71
Alignment explanation
Indices: 3064093--3064273 Score: 183
Period size: 74 Copynumber: 2.5 Consensus size: 71
3064083 TAAAAAATTA
* * * *
3064093 CCTTTTTTTCTTTTT-TTCCTTCCTTCCCTCTTCTT-CTTTCTTTTTTTTTCTCTTTCTTCTCCT
1 CCTTTTCTTCTTTTTCTTTCTTTCTTCCTTCTTCTTCCTTTCTTTTTTTTTCTCTTTCTTCTCCT
* *
3064156 TTCTTT
66 TCCTGT
* * *
3064162 TCTTTCCTTCTTTTTCTTTCTTTTTTCCTTCTTCTTCCTTTTCTTTCCTTCTTTT-TCTTTCTT-
1 CCTTTTCTTCTTTTTCTTTCTTTCTTCCTTCTTCTTCC-TTTCTTT--TT-TTTTCTCTTTCTTC
3064225 TCCTCTCCTGT
62 TCCT-TCCTGT
*
3064236 CCTTTTCTTCTTTTTCTTTCTCTTCTT-CTTCTTTTTCC
1 CCTTTTCTTCTTTTTCTTTCT-TTCTTCCTTCTTCTTCC
3064274 CTCTCCTTCT
Statistics
Matches: 91, Mismatches: 13, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
69 12 0.13
70 16 0.18
71 1 0.01
72 7 0.08
73 4 0.04
74 43 0.47
75 8 0.09
ACGTcount: A:0.00, C:0.31, G:0.01, T:0.69
Consensus pattern (71 bp):
CCTTTTCTTCTTTTTCTTTCTTTCTTCCTTCTTCTTCCTTTCTTTTTTTTTCTCTTTCTTCTCCT
TCCTGT
Found at i:3064277 original size:47 final size:48
Alignment explanation
Indices: 3064187--3064280 Score: 138
Period size: 47 Copynumber: 2.0 Consensus size: 48
3064177 CTTTCTTTTT
* *
3064187 TCCTTCTTCTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCCTG
1 TCCTTCTTCTTCCTTTTCTTTCCTTCTTCTTCTTTCTTCCCTCTCCTG
*
3064235 TCCTT-TTCTTCTTTTTCTTTCTCTTCTTCTTCTTT-TTCCCTCTCCT
1 TCCTTCTTCTTCCTTTTCTTTC-CTTCTTCTTCTTTCTTCCCTCTCCT
3064281 TCTCCCCCCG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
47 25 0.60
48 17 0.40
ACGTcount: A:0.00, C:0.35, G:0.01, T:0.64
Consensus pattern (48 bp):
TCCTTCTTCTTCCTTTTCTTTCCTTCTTCTTCTTTCTTCCCTCTCCTG
Found at i:3064278 original size:21 final size:22
Alignment explanation
Indices: 3064187--3064283 Score: 74
Period size: 21 Copynumber: 4.3 Consensus size: 22
3064177 CTTTCTTTTT
* *
3064187 TCCTTCTTCTTCCTTTT--CTT
1 TCCTTCTTCTTCTTTTTCCCTC
* *
3064207 TCCTTCTTTTTCTTTCTTTCCTC
1 TCCTTCTTCTTCTTT-TTCCCTC
**
3064230 TCCTGTCCTTTTCTTCTTTTTCTTTC
1 TCCT-T-C--TTCTTCTTTTTCCCTC
3064256 T-CTTCTTCTTCTTTTTCCCTC
1 TCCTTCTTCTTCTTTTTCCCTC
3064277 TCCTTCT
1 TCCTTCT
3064284 CCCCCCGATG
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
20 13 0.22
21 17 0.28
22 5 0.08
23 7 0.12
24 2 0.03
25 3 0.05
26 5 0.08
27 8 0.13
ACGTcount: A:0.00, C:0.35, G:0.01, T:0.64
Consensus pattern (22 bp):
TCCTTCTTCTTCTTTTTCCCTC
Found at i:3067400 original size:41 final size:40
Alignment explanation
Indices: 3067302--3067442 Score: 95
Period size: 40 Copynumber: 3.5 Consensus size: 40
3067292 CCGCAAATAA
* * **
3067302 TCCGATCTATAGCGGCGTTTTTATAAACCGCCGCTGGTGC
1 TCCGATCTATAGCGGCGTTTATAGAAACCGCCGCTAATGC
* * * * * *
3067342 TCCGCTCTAAAGTGGCGTTTATGGAGAATCGCCGCTAATGT
1 TCCGATCTATAGCGGCGTTTATAGA-AACCGCCGCTAATGC
* * * * * *
3067383 TCCGGTCTATAGCGGCGTTTGT-GTAACAGCCCGGTAATTC
1 TCCGATCTATAGCGGCGTTTATAGAAACCG-CCGCTAATGC
* *
3067423 TTCGGTCTATAGCGGCGTTT
1 TCCGATCTATAGCGGCGTTT
3067443 GTGTAAAAAC
Statistics
Matches: 78, Mismatches: 21, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
39 3 0.04
40 46 0.59
41 29 0.37
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (40 bp):
TCCGATCTATAGCGGCGTTTATAGAAACCGCCGCTAATGC
Found at i:3069340 original size:790 final size:785
Alignment explanation
Indices: 3067925--3069503 Score: 2776
Period size: 790 Copynumber: 2.0 Consensus size: 785
3067915 CCGCAAAATG
* *
3067925 TGTAACCGAAACGACTTCGTTTTTATACTGTTTATTGGTATTAGCGGCGTTTTTTGTAAAAACGC
1 TGTAACCGAAAAGACTTCGTTTTTATACTGTTTATTGGTATTAGCGGCATTTTTTGTAAAAACGC
* *
3067990 CGCAAATGAAAGTTATGTATTTTAGGGTTTTGGGATTAATATTTAAGTTTTATTGTATACGGTTT
66 CGCAAATGAAAGTTATGTATTTTAGGGTATTGGGATTAATATTTAAGTTTTATTGCATACGGTTT
*
3068055 GGGGTTTTAGGGTTTAATACATAATGTTTATTAATTTAGGATTACAATTTTATGTTTAGGGTTTT
131 GGGGTTTTAGGGTTCAATACATAATGTTTATTAATTTAGGATTACAATTTTATGTTTAGGGTTTT
3068120 GGGTTTAGGTTTACGCTTGAGGAATGGGGTTTAGGGTTTGAGTTTACATGTTAGTTTTAATGCGA
196 GGGTTTAGGTTTACGCTTGAGGAATGGGGTTTAGGGTTTGAGTTTACATGTTAGTTTTAATGCGA
* * * *
3068185 GGTTTACGGCTTATAAGATATATTAATGATCAAATTTATTGTTTTACGGCTTGATGTTTATGGTT
261 GGTTTACAGCTTATAAGA-ATAGTAATGATCAAATTTACTATTTTACGGCTTGATGTTTATGGTT
* *
3068250 TATGGTTTACCCTTATTGATTTGAATGTTACAATGCTTGGTTTTGTGTTCGGATTTGCATGAAGA
325 TATGGTTCACCCTTATTGATTTGAATGTTACAATGCTTGGTTTTGCGTTCGGATTTGCATGAAGA
*
3068315 ATATGAGTTAGCTAGGGTTTAGCCTTTAATTTTAATGTTTACGGGTTATAGGGATTAATAGCTTC
390 ATACGAGTTAGCTAGGGTTTAGCCTTTAATTTTAATGTTTACGGGTTATAGGGATTAATAGCTTC
3068380 GGGTTTTAGGGTACAAAAGCAAAAAAAAAATTAAAATTCTTTCTGCTTTTTACTTCTTATTATGT
455 GGGTTTTAGGGTACAAAAGCAAAAAAAAAATTAAAATTCTTTCTGCTTTTTACTTCTTATTATGT
*
3068445 CACTAGTATATAGGATTATAAGAGACAGGGTTATATATATTATATAATATGTCACGATATATATC
520 CACTAGTATATAGGATTATAAGAGACAGGGTTATATATATTATATAATATGCCACGATATATATC
*
3068510 TATGCATATAGTTATATATATACATACTGCATAAAATTGAAATAATTTTATAAATTCATATTAAT
585 TATGCATATAGTTATATATATACATACTGCATAAAATTGAAATAATTTTATAAATGCATATTAAT
*
3068575 GTATCAATTTAAAATAATGTCATAACAATTATCAAAATAAAAAATCTACTAAAAATCATTAGACT
650 GTATCAATTTAAAATAATGTCATAACAATTA-C--AA-AAAAAATCTACTAAAAATCATTAAACT
*
3068640 TATAAATAAAGACAAATAAAATAAATTGAAAAATTAGCGGCGTTTATACAGAAAACGCCGCTATA
711 TATAAATAAAGACAAATAAAATAAATTGAAAAATTAGCGGCGCTTATACAGAAAACGCCGCTATA
3068705 GAACAAGATT
776 GAACAAGATT
3068715 TGTAACCGAAAAGACTTCGTTTTTATACTGTTTATTGGTATTAGCGGCATTTTTTGTAAAAACGC
1 TGTAACCGAAAAGACTTCGTTTTTATACTGTTTATTGGTATTAGCGGCATTTTTTGTAAAAACGC
* *
3068780 CGCAAATGAAAGTTATGTATTTTAGGGTATTGGGATTAATATTTAAGTTTTGTTGCATATGGTTT
66 CGCAAATGAAAGTTATGTATTTTAGGGTATTGGGATTAATATTTAAGTTTTATTGCATACGGTTT
* *
3068845 GGGGTTTTAGGGTTCGATACATAATGTTTATTAATTTAGGATTATAATTTTATGTTTAGGGTTTT
131 GGGGTTTTAGGGTTCAATACATAATGTTTATTAATTTAGGATTACAATTTTATGTTTAGGGTTTT
3068910 GGGTTTAGGTTTACGGCTTGAGGAATGGGGTTTAGGGTTTGAGTTTACATGTTAGTTTTAATGCG
196 GGGTTTAGGTTTAC-GCTTGAGGAATGGGGTTTAGGGTTTGAGTTTACATGTTAGTTTTAATGCG
3068975 AGGTTTACAGCTTATAAG-AT-GTAATGATCAAATTTACTATTTTACGGCTTGATGTTTATGGTT
260 AGGTTTACAGCTTATAAGAATAGTAATGATCAAATTTACTATTTTACGGCTTGATGTTTATGGTT
3069038 TATGGTTCACCCTTATTGATTTGAATGTTACAATGCTTGGTTTTTGCGTTC-GATTTGCATGAAG
325 TATGGTTCACCCTTATTGATTTGAATGTTACAATGCTTGG-TTTTGCGTTCGGATTTGCATGAAG
3069102 AATACGAGTTAGCTAGGGTTTAGCCTTTAATTTTAATGTTTACGGGTTATAAGGGATTAATAGCT
389 AATACGAGTTAGCTAGGGTTTAGCCTTTAATTTTAATGTTTACGGGTTAT-AGGGATTAATAGCT
3069167 TCGGGTTTTAGGGTACAAAAGCAAAAAAATTAAAATTAAAATTCTTTCTGCTTTTTACTTCTTAT
453 TCGGGTTTTAGGGTACAAAAGC-AAAAAA--AAAATTAAAATTCTTTCTGCTTTTTACTTCTTAT
*
3069232 TATGTCACTAGTATATAGGATTATAAGTGACAGGG-T-TATATA-TATAT-ATATGCCACGATAT
515 TATGTCACTAGTATATAGGATTATAAGAGACAGGGTTATATATATTATATAATATGCCACGATAT
*
3069293 ATATCTATGCATATATGTTATATATTATATATACTGCATAAAATTGAAATAATTTTATAAATGCA
580 ATATCTATGCATATA-GTTATATA-TATACATACTGCATAAAATTGAAATAATTTTATAAATGCA
* *
3069358 TATTAATGTATCAATTTAAAATAATGTCATAACAATTACCAAAAAAATCTATTAAAAATCATTAA
643 TATTAATGTATCAATTTAAAATAATGTCATAACAATTACAAAAAAAATCTACTAAAAATCATTAA
3069423 ACTTATAAATAAAGACAAATAAAATAAATTGAAAAATTAGCGGCGCTTATACAGAAAACGCCGCT
708 ACTTATAAATAAAGACAAATAAAATAAATTGAAAAATTAGCGGCGCTTATACAGAAAACGCCGCT
3069488 ATAGAACAAGATT
773 ATAGAACAAGATT
3069501 TGT
1 TGT
3069504 GGCGTTTATT
Statistics
Matches: 757, Mismatches: 24, Indels: 20
0.95 0.03 0.02
Matches are distributed among these distances:
786 102 0.13
787 1 0.00
788 169 0.22
789 61 0.08
790 288 0.38
791 68 0.09
792 68 0.09
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.39
Consensus pattern (785 bp):
TGTAACCGAAAAGACTTCGTTTTTATACTGTTTATTGGTATTAGCGGCATTTTTTGTAAAAACGC
CGCAAATGAAAGTTATGTATTTTAGGGTATTGGGATTAATATTTAAGTTTTATTGCATACGGTTT
GGGGTTTTAGGGTTCAATACATAATGTTTATTAATTTAGGATTACAATTTTATGTTTAGGGTTTT
GGGTTTAGGTTTACGCTTGAGGAATGGGGTTTAGGGTTTGAGTTTACATGTTAGTTTTAATGCGA
GGTTTACAGCTTATAAGAATAGTAATGATCAAATTTACTATTTTACGGCTTGATGTTTATGGTTT
ATGGTTCACCCTTATTGATTTGAATGTTACAATGCTTGGTTTTGCGTTCGGATTTGCATGAAGAA
TACGAGTTAGCTAGGGTTTAGCCTTTAATTTTAATGTTTACGGGTTATAGGGATTAATAGCTTCG
GGTTTTAGGGTACAAAAGCAAAAAAAAAATTAAAATTCTTTCTGCTTTTTACTTCTTATTATGTC
ACTAGTATATAGGATTATAAGAGACAGGGTTATATATATTATATAATATGCCACGATATATATCT
ATGCATATAGTTATATATATACATACTGCATAAAATTGAAATAATTTTATAAATGCATATTAATG
TATCAATTTAAAATAATGTCATAACAATTACAAAAAAAATCTACTAAAAATCATTAAACTTATAA
ATAAAGACAAATAAAATAAATTGAAAAATTAGCGGCGCTTATACAGAAAACGCCGCTATAGAACA
AGATT
Found at i:3069924 original size:16 final size:16
Alignment explanation
Indices: 3069900--3069930 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3069890 ATTTTTCCTC
3069900 TTCTAAAATCCCTAAG
1 TTCTAAAATCCCTAAG
*
3069916 TTCTGAAATCCCTAA
1 TTCTAAAATCCCTAA
3069931 CTCCATTTAC
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:0.35, C:0.26, G:0.06, T:0.32
Consensus pattern (16 bp):
TTCTAAAATCCCTAAG
Found at i:3072089 original size:14 final size:15
Alignment explanation
Indices: 3072072--3072109 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
3072062 GTTTAGTCAC
*
3072072 TAGGGTTTTT-GGTT
1 TAGGGTTTTTAGGGT
3072086 TAGGGTTTTTAGGGT
1 TAGGGTTTTTAGGGT
3072101 TAGGGTTTT
1 TAGGGTTTT
3072110 GTTAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.11, C:0.00, G:0.37, T:0.53
Consensus pattern (15 bp):
TAGGGTTTTTAGGGT
Found at i:3072277 original size:34 final size:32
Alignment explanation
Indices: 3072151--3072285 Score: 101
Period size: 34 Copynumber: 4.0 Consensus size: 32
3072141 AGGTTTAGGG
*
3072151 AATAAATCAAGGTTTAGAGTTTTTTTAAAAAAATT-
1 AATAAAT-TAGGTTTAGAG--TTTTT-AAAAAATTA
* * *
3072186 ATTAAATTAGGTTTTAGAGGTTTTAAATAAATAA
1 AATAAATTAGG-TTTAGAGTTTTTAAA-AAATTA
*
3072220 AATAAATTAGGGCTTAGAGTTTTTAAGAAAATTA
1 AATAAATTA-GGTTTAGAGTTTTTAA-AAAATTA
* ** *
3072254 ACTAAATTATGGTTTAGTTTTTTTAAATAATT
1 AATAAATTA-GGTTTAGAGTTTTTAAAAAATT
3072286 TTGTCTTTAG
Statistics
Matches: 81, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
32 3 0.04
33 13 0.16
34 49 0.60
35 16 0.20
ACGTcount: A:0.42, C:0.02, G:0.13, T:0.42
Consensus pattern (32 bp):
AATAAATTAGGTTTAGAGTTTTTAAAAAATTA
Found at i:3076505 original size:21 final size:19
Alignment explanation
Indices: 3076456--3076511 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 19
3076446 AATTTTCGAG
3076456 GATATACAATCTTAGATAT
1 GATATACAATCTTAGATAT
*
3076475 GATATGCAATCTTAGATAT
1 GATATACAATCTTAGATAT
3076494 GATATATACAATCTTAGA
1 G--ATATACAATCTTAGA
3076512 AGATACGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 19 0.58
21 14 0.42
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (19 bp):
GATATACAATCTTAGATAT
Found at i:3079247 original size:140 final size:140
Alignment explanation
Indices: 3078995--3079275 Score: 562
Period size: 140 Copynumber: 2.0 Consensus size: 140
3078985 TTTATTGTTT
3078995 AATTTTTGTAATCGATCCAGCTAAACAAGATGTTTTGGATTGGAGAAAACGCTTCAACATTATTA
1 AATTTTTGTAATCGATCCAGCTAAACAAGATGTTTTGGATTGGAGAAAACGCTTCAACATTATTA
3079060 AAGGGATTAAGCAAGGATTGCTTTATCTTCATAGAGATTCAAGACTAAGGATTATACATAGAGAT
66 AAGGGATTAAGCAAGGATTGCTTTATCTTCATAGAGATTCAAGACTAAGGATTATACATAGAGAT
3079125 TTAAAAGTAA
131 TTAAAAGTAA
3079135 AATTTTTGTAATCGATCCAGCTAAACAAGATGTTTTGGATTGGAGAAAACGCTTCAACATTATTA
1 AATTTTTGTAATCGATCCAGCTAAACAAGATGTTTTGGATTGGAGAAAACGCTTCAACATTATTA
3079200 AAGGGATTAAGCAAGGATTGCTTTATCTTCATAGAGATTCAAGACTAAGGATTATACATAGAGAT
66 AAGGGATTAAGCAAGGATTGCTTTATCTTCATAGAGATTCAAGACTAAGGATTATACATAGAGAT
3079265 TTAAAAGTAA
131 TTAAAAGTAA
3079275 A
1 A
3079276 TAATATTTTA
Statistics
Matches: 141, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
140 141 1.00
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (140 bp):
AATTTTTGTAATCGATCCAGCTAAACAAGATGTTTTGGATTGGAGAAAACGCTTCAACATTATTA
AAGGGATTAAGCAAGGATTGCTTTATCTTCATAGAGATTCAAGACTAAGGATTATACATAGAGAT
TTAAAAGTAA
Found at i:3081419 original size:40 final size:40
Alignment explanation
Indices: 3081274--3081422 Score: 194
Period size: 40 Copynumber: 3.7 Consensus size: 40
3081264 GCTCCTCGTT
* *
3081274 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
3081314 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * * *
3081354 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
3081395 CAAA-GCCTTCGGGACTTAGCCCGGATAT
1 CAAATGCCTTCGGGACTTAGCCCGGATAT
3081423 CATTCAAATA
Statistics
Matches: 95, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
39 3 0.03
40 81 0.85
41 11 0.12
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:3083059 original size:13 final size:13
Alignment explanation
Indices: 3083041--3083065 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3083031 GGATGAGCAT
3083041 TTTTTTTTCTTTG
1 TTTTTTTTCTTTG
3083054 TTTTTTTTCTTT
1 TTTTTTTTCTTT
3083066 CTAGTTTCGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.08, G:0.04, T:0.88
Consensus pattern (13 bp):
TTTTTTTTCTTTG
Found at i:3087965 original size:18 final size:17
Alignment explanation
Indices: 3087937--3087971 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3087927 ATTATTAAGA
*
3087937 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
3087954 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
3087972 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:3088109 original size:18 final size:17
Alignment explanation
Indices: 3088081--3088115 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3088071 ATTATTAAGA
*
3088081 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
3088098 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
3088116 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:3088328 original size:44 final size:45
Alignment explanation
Indices: 3088279--3088371 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 45
3088269 ACACCTCTAA
* *
3088279 TACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCCAT
1 TACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCCAT
** *
3088323 TACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCCAT
1 TACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCCAT
3088368 TACA
1 TACA
3088372 CCTCTAATCC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 16 0.37
45 27 0.63
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.34
Consensus pattern (45 bp):
TACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCCAT
Found at i:3088371 original size:16 final size:16
Alignment explanation
Indices: 3088350--3088387 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
3088340 TTGATTTGCT
*
3088350 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
3088366 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
3088382 AATACA
1 ATTACA
3088388 ATACACCTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:3088394 original size:21 final size:21
Alignment explanation
Indices: 3088368--3088408 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
3088358 TCTATTCCAT
3088368 TACACCTCTAATCCAATACAA
1 TACACCTCTAATCCAATACAA
3088389 TACACCTCTAATCCAATACA
1 TACACCTCTAATCCAATACA
3088409 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.34, G:0.00, T:0.24
Consensus pattern (21 bp):
TACACCTCTAATCCAATACAA
Found at i:3088965 original size:28 final size:30
Alignment explanation
Indices: 3088925--3088982 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
3088915 AGACCCTAAG
3088925 AGTCAATTTC-T-GTAGAAGGTCCTTTAAT
1 AGTCAATTTCGTAGTAGAAGGTCCTTTAAT
3088953 AGTCAATTTCTGTAGTAGAAGGTCCTTTAA
1 AGTCAATTTC-GTAGTAGAAGGTCCTTTAA
3088983 CTTCTCCCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 10 0.37
30 1 0.04
31 16 0.59
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (30 bp):
AGTCAATTTCGTAGTAGAAGGTCCTTTAAT
Found at i:3091233 original size:24 final size:24
Alignment explanation
Indices: 3091206--3091257 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3091196 TTAGTAAGTC
*
3091206 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
3091230 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
3091254 AAAT
1 AAAT
3091258 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:3093203 original size:24 final size:24
Alignment explanation
Indices: 3093176--3093227 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3093166 TTAGTAAGTC
*
3093176 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
3093200 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
3093224 AAAT
1 AAAT
3093228 CTTCTAGGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:3096673 original size:34 final size:33
Alignment explanation
Indices: 3096623--3096719 Score: 104
Period size: 34 Copynumber: 2.8 Consensus size: 33
3096613 TTTAGAGTTT
* *
3096623 TTTTAAAAAAAATAATTAAATTAGGTTTTAGGGG
1 TTTT-AAAAAATTAATTAAATTAGGTTTTAGAGG
** *
3096657 TTTTAAATAAATTAATTAAATTAGGGCTTAGAGT
1 TTTTAAA-AAATTAATTAAATTAGGTTTTAGAGG
*
3096691 TTTTAAGAAAATTAACTAAATTATGGTTT
1 TTTTAA-AAAATTAATTAAATTA-GGTTT
3096720 AGTTTTTTAA
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
33 3 0.06
34 45 0.87
35 4 0.08
ACGTcount: A:0.42, C:0.02, G:0.14, T:0.41
Consensus pattern (33 bp):
TTTTAAAAAATTAATTAAATTAGGTTTTAGAGG
Found at i:3097916 original size:16 final size:16
Alignment explanation
Indices: 3097892--3097929 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
3097882 ATCTAAACTC
* *
3097892 AAATGATTCAAACTTG
1 AAATAATTCAAACTTA
3097908 AAATAATTCAAACTTA
1 AAATAATTCAAACTTA
3097924 AAATAA
1 AAATAA
3097930 GTCGAATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.29
Consensus pattern (16 bp):
AAATAATTCAAACTTA
Found at i:3103223 original size:17 final size:17
Alignment explanation
Indices: 3103190--3103223 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3103180 AATGGAATTT
*
3103190 TAAATTTTGAGATATAA
1 TAAATTTTGAGAGATAA
*
3103207 TAAATTTTGTGAGATAA
1 TAAATTTTGAGAGATAA
3103224 GATTAGAATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (17 bp):
TAAATTTTGAGAGATAA
Found at i:3103966 original size:24 final size:24
Alignment explanation
Indices: 3103907--3103969 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 24
3103897 AAAATTTATT
3103907 TTAAAAA-TAAAAA-A-TTTAAAA
1 TTAAAAATTAAAAATATTTTAAAA
* *
3103928 -AAAAAGTATTTAAAATATTTTAAAA
1 TTAAAA--ATTAAAAATATTTTAAAA
3103953 TTAAAAATTAAAAATAT
1 TTAAAAATTAAAAATAT
3103970 ATATTTATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
20 4 0.12
22 1 0.03
23 5 0.16
24 11 0.34
25 7 0.22
26 4 0.12
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (24 bp):
TTAAAAATTAAAAATATTTTAAAA
Found at i:3104852 original size:15 final size:16
Alignment explanation
Indices: 3104824--3104882 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 16
3104814 TTAAAAAAAA
3104824 AAACACGAAAATTTTG
1 AAACACGAAAATTTTG
**
3104840 AAACACGAGATTTTTTTTTG
1 AAACACGA-A---AATTTTG
3104860 AAACACGAAAATTTATG
1 AAACACGAAAATTT-TG
3104877 AAACAC
1 AAACAC
3104883 AGTTTTCTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
16 11 0.32
17 9 0.26
19 1 0.03
20 13 0.38
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.29
Consensus pattern (16 bp):
AAACACGAAAATTTTG
Found at i:3105184 original size:16 final size:16
Alignment explanation
Indices: 3105163--3105208 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
3105153 TATTAAAATT
3105163 AATTAAAATAAAATAA
1 AATTAAAATAAAATAA
** *
3105179 AATTAAAATGGAATTA
1 AATTAAAATAAAATAA
3105195 AATTAAAGATAAAA
1 AATTAAA-ATAAAA
3105209 ATATAAAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 20 0.83
17 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (16 bp):
AATTAAAATAAAATAA
Found at i:3105374 original size:8 final size:7
Alignment explanation
Indices: 3105350--3105387 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
3105340 GAATTGAACC
3105350 TCTTTTT
1 TCTTTTT
3105357 TC-TTTT
1 TCTTTTT
3105363 TCTTTTT
1 TCTTTTT
3105370 CTCTTTTTT
1 -TC-TTTTT
3105379 TCTTTTT
1 TCTTTTT
3105386 TC
1 TC
3105388 CTCCTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
6 6 0.21
7 13 0.46
8 4 0.14
9 5 0.18
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (7 bp):
TCTTTTT
Found at i:3105374 original size:14 final size:13
Alignment explanation
Indices: 3105350--3105425 Score: 57
Period size: 13 Copynumber: 5.6 Consensus size: 13
3105340 GAATTGAACC
3105350 TCTTTTTTCTTTT
1 TCTTTTTTCTTTT
3105363 TCTTTTTCTCTTTT
1 TCTTTTT-TCTTTT
*
3105377 T-TTCTTTT-TTCCT
1 TCTT-TTTTCTT-TT
* * *
3105390 CCTTTTTTCCTTC
1 TCTTTTTTCTTTT
3105403 TCTTTCTCTTCTTTT
1 TCTTT-T-TTCTTTT
3105418 TCTTTTTT
1 TCTTTTTT
3105426 TTTCTCTGCT
Statistics
Matches: 48, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
12 2 0.04
13 21 0.44
14 15 0.31
15 10 0.21
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TCTTTTTTCTTTT
Found at i:3105379 original size:11 final size:11
Alignment explanation
Indices: 3105352--3105432 Score: 50
Period size: 10 Copynumber: 7.9 Consensus size: 11
3105342 ATTGAACCTC
3105352 TTTTTTCT-TT
1 TTTTTTCTCTT
*
3105362 TTCTTTT-TCTC
1 TT-TTTTCTCTT
3105373 TTTTTT-TC-T
1 TTTTTTCTCTT
* *
3105382 TTTTTCCTC-C
1 TTTTTTCTCTT
3105392 TTTTTTC-CTT
1 TTTTTTCTCTT
* *
3105402 CTCTTTCTCTT
1 TTTTTTCTCTT
*
3105413 CTTTTTCT-TT
1 TTTTTTCTCTT
3105423 TTTTTTCTCT
1 TTTTTTCTCT
3105433 GCTGGGCCAA
Statistics
Matches: 55, Mismatches: 10, Indels: 11
0.72 0.13 0.14
Matches are distributed among these distances:
9 6 0.11
10 31 0.56
11 18 0.33
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTTCTCTT
Found at i:3105380 original size:10 final size:10
Alignment explanation
Indices: 3105365--3105432 Score: 61
Period size: 10 Copynumber: 6.9 Consensus size: 10
3105355 TTTCTTTTTC
3105365 TTTTTCTC-T
1 TTTTTCTCTT
3105374 TTTTT-TCTT
1 TTTTTCTCTT
* *
3105383 TTTTCCTCCT
1 TTTTTCTCTT
3105393 TTTTTC-CTT
1 TTTTTCTCTT
*
3105402 CTCTTTCTCTT
1 -TTTTTCTCTT
*
3105413 CTTTTTCTTTT
1 -TTTTTCTCTT
3105424 TTTTTCTCT
1 TTTTTCTCT
3105433 GCTGGGCCAA
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
8 2 0.04
9 12 0.26
10 21 0.45
11 12 0.26
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTTCTCTT
Found at i:3105416 original size:22 final size:21
Alignment explanation
Indices: 3105350--3105418 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 21
3105340 GAATTGAACC
* *
3105350 TCTTTTTTCTTTTTCTTTTTC-
1 TCTTTTTTC-CTTTCTTTCTCT
*
3105371 TCTTTTTTTCTTT-TTTC-CT
1 TCTTTTTTCCTTTCTTTCTCT
*
3105390 CCTTTTTTCCTTCTCTTTCTCT
1 TCTTTTTTCCTT-TCTTTCTCT
3105412 TCTTTTT
1 TCTTTTT
3105419 CTTTTTTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
18 1 0.03
19 13 0.34
20 4 0.11
21 12 0.32
22 8 0.21
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (21 bp):
TCTTTTTTCCTTTCTTTCTCT
Found at i:3105704 original size:7 final size:7
Alignment explanation
Indices: 3105694--3105750 Score: 91
Period size: 7 Copynumber: 8.3 Consensus size: 7
3105684 TTTATTATTA
3105694 TTTTTTC
1 TTTTTTC
3105701 -TTTTTC
1 TTTTTTC
3105707 TTTTTTC
1 TTTTTTC
3105714 TTTTTTC
1 TTTTTTC
3105721 TTTTTTC
1 TTTTTTC
3105728 TTTTTTC
1 TTTTTTC
3105735 TTTTTT-
1 TTTTTTC
3105741 TTTCTTTC
1 TTT-TTTC
3105749 TT
1 TT
3105751 CTTCTTCTTC
Statistics
Matches: 47, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
6 9 0.19
7 36 0.77
8 2 0.04
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTC
Found at i:3105718 original size:21 final size:23
Alignment explanation
Indices: 3105694--3105807 Score: 114
Period size: 24 Copynumber: 5.0 Consensus size: 23
3105684 TTTATTATTA
3105694 TTTTTTCTTTTTCTT-TT-TTC-
1 TTTTTTCTTTTTCTTCTTCTTCT
3105714 TTTTTTCTTTTTTCTT-TT-TTCT
1 TTTTTTC-TTTTTCTTCTTCTTCT
3105736 TTTTTT-TTCTTTCTTCTTCTTCT
1 TTTTTTCTT-TTTCTTCTTCTTCT
* *
3105759 TCTTCTTCTTCTTCTTCTTCTTCT
1 T-TTTTTCTTTTTCTTCTTCTTCT
* *
3105783 TCTTCTTCTTCTTCTTCTTCTTCT
1 T-TTTTTCTTTTTCTTCTTCTTCT
3105807 T
1 T
3105808 ATTCTTCAAA
Statistics
Matches: 85, Mismatches: 2, Indels: 10
0.88 0.02 0.10
Matches are distributed among these distances:
20 9 0.11
21 19 0.22
22 8 0.09
23 5 0.06
24 42 0.49
25 2 0.02
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTTTTCTTTTTCTTCTTCTTCT
Found at i:3105752 original size:3 final size:3
Alignment explanation
Indices: 3105746--3105814 Score: 129
Period size: 3 Copynumber: 23.0 Consensus size: 3
3105736 TTTTTTTTCT
3105746 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
3105794 TTC TTC TTC TTC TTA TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC
3105815 AAAAACCCTA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:3106253 original size:29 final size:30
Alignment explanation
Indices: 3106154--3106284 Score: 156
Period size: 30 Copynumber: 4.4 Consensus size: 30
3106144 GAAAAATTTT
* * * *
3106154 GGGGCCAAAACGTAATTTCGAGGAAGTTTA
1 GGGGTCAAAATGTAATTTTGAGAAAGTTTA
*
3106184 GGGGTCAAAATGTAATTTTGAGAAAGTTTC
1 GGGGTCAAAATGTAATTTTGAGAAAGTTTA
*
3106214 GGGGTCAAAATGTAATTTAGA-AAAGTTTA
1 GGGGTCAAAATGTAATTTTGAGAAAGTTTA
** * **
3106243 GGGGTTGAAATATAATTTTGAGAAAGTACA
1 GGGGTCAAAATGTAATTTTGAGAAAGTTTA
3106273 GGGGTCAAAATG
1 GGGGTCAAAATG
3106285 CAATGTTTAT
Statistics
Matches: 84, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
29 24 0.29
30 60 0.71
ACGTcount: A:0.37, C:0.07, G:0.28, T:0.28
Consensus pattern (30 bp):
GGGGTCAAAATGTAATTTTGAGAAAGTTTA
Found at i:3106259 original size:59 final size:60
Alignment explanation
Indices: 3106154--3106284 Score: 167
Period size: 59 Copynumber: 2.2 Consensus size: 60
3106144 GAAAAATTTT
* * * * * *
3106154 GGGGCCAAAACGTAATTTCGAGGAAGTTTAGGGGTCAAAATGTAATTTTGAGAAAGTTTC-
1 GGGGTCAAAATGTAATTTAGAGAAAGTTTAGGGGTCAAAATATAATTTTGAGAAAG-TACA
**
3106214 GGGGTCAAAATGTAATTTAGA-AAAGTTTAGGGGTTGAAATATAATTTTGAGAAAGTACA
1 GGGGTCAAAATGTAATTTAGAGAAAGTTTAGGGGTCAAAATATAATTTTGAGAAAGTACA
3106273 GGGGTCAAAATG
1 GGGGTCAAAATG
3106285 CAATGTTTAT
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
58 2 0.03
59 42 0.68
60 18 0.29
ACGTcount: A:0.37, C:0.07, G:0.28, T:0.28
Consensus pattern (60 bp):
GGGGTCAAAATGTAATTTAGAGAAAGTTTAGGGGTCAAAATATAATTTTGAGAAAGTACA
Found at i:3106735 original size:81 final size:80
Alignment explanation
Indices: 3106487--3106941 Score: 598
Period size: 81 Copynumber: 5.8 Consensus size: 80
3106477 TGCTTCGGCG
* * *
3106487 TGTGACCCGAGGCTCAACTCACCTCTCACAATATGAGTTGA--TTTTTGAAAAATAGAAA-TT-G
1 TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTTAA
3106548 AA-AAATACCTCG-A
66 AAGAAATACCTCGCA
* * *
3106561 CGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAA-TT-G
1 TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTTAA
3106622 AA-AAATACCTCG-A
66 AAGAAATACCTCGCA
* * *
3106635 CGTGACTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATAC-GAAATTTA
1 TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAA-ACAGAAATTTA
3106699 AAAGAAATACCTCGGCA
65 AAAGAAATACCTC-GCA
* *
3106716 TGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAGATTTAA
1 TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTTAA
3106781 AAGAAATACCTCAGC-
66 AAGAAATACCTC-GCA
* *
3106796 -GTGACCCGAGGCTCAACTCATCTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTTAA
1 TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTTAA
*
3106860 AAGAAATACCTCAGCG
66 AAGAAATACCTC-GCA
** * * *
3106876 TGCAACCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAAAACAAAAATTTAA
1 TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTTAA
3106941 A
66 A
3106942 CCCGAGGCTT
Statistics
Matches: 349, Mismatches: 21, Indels: 15
0.91 0.05 0.04
Matches are distributed among these distances:
74 110 0.32
76 14 0.04
77 4 0.01
78 2 0.01
79 86 0.25
80 3 0.01
81 130 0.37
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.28
Consensus pattern (80 bp):
TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTTAA
AAGAAATACCTCGCA
Found at i:3106981 original size:61 final size:62
Alignment explanation
Indices: 3106879--3107003 Score: 198
Period size: 61 Copynumber: 2.0 Consensus size: 62
3106869 CTCAGCGTGC
* *
3106879 AACCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTT-GAAAAACAAAAATTTA
1 AACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTAATTTTTTTCGAAAAACAAAAATTTA
* * *
3106940 AACCCGAGGCTTAACTCACTTCTCGCAATATGAGTTAATTTTTTTCGAAAAACAGAGATTTA
1 AACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTAATTTTTTTCGAAAAACAAAAATTTA
3107002 AA
1 AA
3107004 AGAAATACCT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
61 42 0.72
62 16 0.28
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (62 bp):
AACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTAATTTTTTTCGAAAAACAAAAATTTA
Found at i:3107056 original size:141 final size:141
Alignment explanation
Indices: 3106799--3107082 Score: 439
Period size: 141 Copynumber: 2.0 Consensus size: 141
3106789 CCTCAGCGTG
* *
3106799 ACCCGAGGCTCAACTCATCTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTTAAAAGA
1 ACCCGAGGCTCAACTCATCTCTCGCAATATGAGTTAATTTTTTTGAAAAACAGAAATTTAAAAGA
*
3106864 AATACCTCAGCGTGCAACCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAAA
66 AATACCTCAGCGTG-AACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAAA
3106929 ACAAAAATTTAA
130 ACAAAAATTTAA
* *
3106941 ACCCGAGGCTTAACTCA-CTTCTCGCAATATGAGTTAATTTTTTTCGAAAAACAGAGATTTAAAA
1 ACCCGAGGCTCAACTCATC-TCTCGCAATATGAGTTAATTTTTTT-GAAAAACAGAAATTTAAAA
*
3107005 GAAATACCTCAGCGTG-ACCCGAGGCTCAACTCA-TCTCTCGCATTATGAGTTGATTTTTTTGAA
64 GAAATACCTCAGCGTGAACCCGAGGCTCAACTCACT-TCTCGCAATATGAGTTGATTTTTTTGAA
* *
3107068 AAATAGAAATTTAA
128 AAACAAAAATTTAA
3107082 A
1 A
3107083 AGAAATACCT
Statistics
Matches: 131, Mismatches: 8, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
140 1 0.01
141 57 0.44
142 39 0.30
143 34 0.26
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (141 bp):
ACCCGAGGCTCAACTCATCTCTCGCAATATGAGTTAATTTTTTTGAAAAACAGAAATTTAAAAGA
AATACCTCAGCGTGAACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAAAA
CAAAAATTTAA
Found at i:3107525 original size:82 final size:82
Alignment explanation
Indices: 3106941--3107908 Score: 1540
Period size: 83 Copynumber: 11.8 Consensus size: 82
3106931 AAAAATTTAA
* * * *
3106941 ACCCGAGGCTTAACTCACTTCTCGCAATATGAGTTAATTTTTTTCGAAAAACAGAGATTTAAAAG
1 ACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTTAAAAG
3107006 AAATACCTCAGCGT--G
66 AAATACCTCAGCGTGCG
* *
3107021 ACCCGAGGCTCAACTCA-TCTCTCGCATTATGAGTTGA-TTTTTTTGAAAAATAGAAATTTAAAA
1 ACCCGAGGCTCAACTCACT-TCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTTAAAA
3107084 GAAATACCTCAGCGTGCG
65 GAAATACCTCAGCGTGCG
3107102 ACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTTTGAAAAACAGAAATTTAAAAG
1 ACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTTAAAAG
* *
3107166 AAATACTTCAGCGTGCA
66 AAATACCTCAGCGTGCG
*
3107183 ACCCGAGGCTCAACTTACTTCTCGCAATATGAGTTGA--TTTTTTGAAAAACAGAAATTTAAAAG
1 ACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTTAAAAG
3107246 AAATACCTCAGCGTGCG
66 AAATACCTCAGCGTGCG
3107263 ACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTTGAAAAACAGAAATTTAAA
1 ACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA--TTTTTTTTGAAAAACAGAAATTTAAA
3107328 AGAAATACCTCAGCGTGCG
64 AGAAATACCTCAGCGTGCG
* *
3107347 ACCCGAGGATCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTGAAAAACATAAATTTAAAA
1 ACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTTTTGAAAAACAGAAATTTAAAA
3107412 GAAATACCTCAGCGTGCG
65 GAAATACCTCAGCGTGCG
* * *
3107430 ACCCGAGGATCAACTCACTTCTCGCAATATGAGTTGATTTTTTTCGAAAAACAGAGATTTAAAAG
1 ACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTTAAAAG
*
3107495 AAACACCTCAGCGTGCG
66 AAATACCTCAGCGTGCG
3107512 ACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTTTTGAAAAGACAGAAATTT
1 ACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA----TTTTTTTTGAAAA-ACAGAAATTT
* *
3107577 AAAAGAAATATCTCAGCGTGAG
61 AAAAGAAATACCTCAGCGTGCG
3107599 ACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTGAAAAACAGAAATTTAAAA
1 ACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTTTTGAAAAACAGAAATTTAAAA
3107664 GAAATACCTCAGCGTGCG
65 GAAATACCTCAGCGTGCG
* * *
3107682 ACCCGAGGATCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAAAACATAAATTTAAAA
1 ACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTT-GAAAAACAGAAATTTAAAA
3107747 GAAATACCTCAGCGTGCG
65 GAAATACCTCAGCGTGCG
* * *
3107765 ACCCGAGGATCAACTCACTTCTCGCAATATGAGTTGATTTTTTTCGAAAAACAGAGATTTAAAAG
1 ACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTTAAAAG
*
3107830 AAACACCTCAGCGTGCG
66 AAATACCTCAGCGTGCG
* *
3107847 ACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA--TTTTTTGAAAAATAGAAATTGAAAA
1 ACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTTAAAA
3107909 ATATTTCTTG
Statistics
Matches: 833, Mismatches: 41, Indels: 28
0.92 0.05 0.03
Matches are distributed among these distances:
79 39 0.05
80 130 0.16
81 112 0.13
82 155 0.19
83 227 0.27
84 93 0.11
86 12 0.01
87 65 0.08
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.29
Consensus pattern (82 bp):
ACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTTAAAAG
AAATACCTCAGCGTGCG
Found at i:3107708 original size:335 final size:334
Alignment explanation
Indices: 3106941--3107889 Score: 1618
Period size: 335 Copynumber: 2.9 Consensus size: 334
3106931 AAAAATTTAA
* * * *
3106941 ACCCGAGGCTTAACTCACTTCTCGCAATATGAGTT-AATTTTTTTCGAAAAACAGAGATTTAAAA
1 ACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTGAAAAACAGAAATTTAAAA
* *
3107005 GAAATACCTCAGCGT--GACCCGAGGCTCAACTCA-TCTCTCGCATTATGAGTTGA--TTTTTTT
66 GAAATACCTCAGCGTGCGACCCGAGGATCAACTCACT-TCTCGCAATATGAGTTGATTTTTTTTT
* * *
3107065 GAAAAATAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAAT
130 GAAAAACATAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGATCAACTCACTTCTCGCAAT
* * * *
3107130 ATGAGTTGATTTTTTT-GAAAAACAGAAATTTAAAAGAAATACTTCAGCGTGCAACCCGAGGCTC
195 ATGAGTTGATTTTTTTCGAAAAACAGAGATTTAAAAGAAACACCTCAGCGTGCGACCCGAGGCTC
*
3107194 AACTTACTTCTCGCAATATGAGTTGA------TTTTTTGAAAAACAGAAATTTAAAAGAAATACC
260 AACTCACTTCTCGCAATATGAGTTGATTTTTTTTTTTTGAAAAACAGAAATTTAAAAGAAATACC
*
3107253 TCAGCGTGCG
325 TCAGCGTGAG
3107263 ACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTTGAAAAACAGAAATTTAAA
1 ACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTTTTTGAAAAACAGAAATTTAAA
3107328 AGAAATACCTCAGCGTGCGACCCGAGGATCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTT
65 AGAAATACCTCAGCGTGCGACCCGAGGATCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTT
3107393 GAAAAACATAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGATCAACTCACTTCTCGCAAT
130 GAAAAACATAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGATCAACTCACTTCTCGCAAT
3107458 ATGAGTTGATTTTTTTCGAAAAACAGAGATTTAAAAGAAACACCTCAGCGTGCGACCCGAGGCTC
195 ATGAGTTGATTTTTTTCGAAAAACAGAGATTTAAAAGAAACACCTCAGCGTGCGACCCGAGGCTC
*
3107523 AACTCACTTCTCGCAATATGAGTTGATTTTTTTTTTTTGAAAAGACAGAAATTTAAAAGAAATAT
260 AACTCACTTCTCGCAATATGAGTTGATTTTTTTTTTTTGAAAA-ACAGAAATTTAAAAGAAATAC
3107588 CTCAGCGTGAG
324 CTCAGCGTGAG
3107599 ACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTGAAAAACAGAAATTTAAAA
1 ACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTGAAAAACAGAAATTTAAAA
**
3107664 GAAATACCTCAGCGTGCGACCCGAGGATCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTAA
66 GAAATACCTCAGCGTGCGACCCGAGGATCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTG
3107729 AAAAACATAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGATCAACTCACTTCTCGCAATA
131 AAAAACATAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGATCAACTCACTTCTCGCAATA
3107794 TGAGTTGATTTTTTTCGAAAAACAGAGATTTAAAAGAAACACCTCAGCGTGCGACCCGAGGCTCA
196 TGAGTTGATTTTTTTCGAAAAACAGAGATTTAAAAGAAACACCTCAGCGTGCGACCCGAGGCTCA
3107859 ACTCACTTCTCGCAATATGAGTTGATTTTTT
261 ACTCACTTCTCGCAATATGAGTTGATTTTTT
3107890 GAAAAATAGA
Statistics
Matches: 594, Mismatches: 18, Indels: 17
0.94 0.03 0.03
Matches are distributed among these distances:
322 34 0.06
323 1 0.00
324 40 0.07
326 34 0.06
327 1 0.00
328 85 0.14
329 69 0.12
335 263 0.44
336 67 0.11
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (334 bp):
ACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTGAAAAACAGAAATTTAAAA
GAAATACCTCAGCGTGCGACCCGAGGATCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTG
AAAAACATAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGATCAACTCACTTCTCGCAATA
TGAGTTGATTTTTTTCGAAAAACAGAGATTTAAAAGAAACACCTCAGCGTGCGACCCGAGGCTCA
ACTCACTTCTCGCAATATGAGTTGATTTTTTTTTTTTGAAAAACAGAAATTTAAAAGAAATACCT
CAGCGTGAG
Found at i:3108190 original size:33 final size:33
Alignment explanation
Indices: 3108148--3108215 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
3108138 TTCGTAAGGA
*
3108148 TCCGCATTCATTTCCTCAATTCTTGACTTTTTC
1 TCCGCATTCATTTCCTCAATTCTTGACTTTCTC
3108181 TCCGCATTCATTTCCTCAATTCTTGACTTTCTC
1 TCCGCATTCATTTCCTCAATTCTTGACTTTCTC
3108214 TC
1 TC
3108216 AAGTTTTGTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.15, C:0.32, G:0.06, T:0.47
Consensus pattern (33 bp):
TCCGCATTCATTTCCTCAATTCTTGACTTTCTC
Found at i:3108824 original size:11 final size:11
Alignment explanation
Indices: 3108796--3108845 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
3108786 TTCATCTTGA
*
3108796 TTTTTCTTTTTC
1 TTTTT-TTTTTG
*
3108808 TATTTTTTTTG
1 TTTTTTTTTTG
*
3108819 TTTTTTTCTTG
1 TTTTTTTTTTG
*
3108830 TTTTTTTGTTG
1 TTTTTTTTTTG
3108841 TTTTT
1 TTTTT
3108846 ATTGTCTCTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
11 29 0.88
12 4 0.12
ACGTcount: A:0.02, C:0.06, G:0.08, T:0.84
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:3108824 original size:19 final size:20
Alignment explanation
Indices: 3108802--3108850 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
3108792 TTGATTTTTC
3108802 TTTTTCTAT-TTTTTTTGTT-
1 TTTTTCT-TGTTTTTTTGTTG
3108821 TTTTTCTTGTTTTTTTGTTG
1 TTTTTCTTGTTTTTTTGTTG
*
3108841 TTTTTATTGT
1 TTTTTCTTGT
3108851 CTCTTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 1 0.04
19 17 0.63
20 9 0.33
ACGTcount: A:0.04, C:0.04, G:0.10, T:0.82
Consensus pattern (20 bp):
TTTTTCTTGTTTTTTTGTTG
Found at i:3108833 original size:20 final size:21
Alignment explanation
Indices: 3108810--3108859 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
3108800 TCTTTTTCTA
*
3108810 TTTTTTTTGTT-TTTTTCTTG
1 TTTTTTTTGTTGTTTTTATTG
3108830 -TTTTTTTGTTGTTTTTATTG
1 TTTTTTTTGTTGTTTTTATTG
3108850 TCTCTTTTTT
1 T-T-TTTTTT
3108860 TCAGGCATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 10 0.40
20 8 0.32
22 1 0.04
23 6 0.24
ACGTcount: A:0.02, C:0.06, G:0.10, T:0.82
Consensus pattern (21 bp):
TTTTTTTTGTTGTTTTTATTG
Found at i:3108850 original size:12 final size:11
Alignment explanation
Indices: 3108810--3108860 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
3108800 TCTTTTTCTA
3108810 TTTTTT-TTGT
1 TTTTTTGTTGT
*
3108820 TTTTTTCTTGT
1 TTTTTTGTTGT
3108831 TTTTTTGTTGT
1 TTTTTTGTTGT
*
3108842 TTTTATTGTCTCT
1 TTTT-TTGT-TGT
3108855 TTTTTT
1 TTTTTT
3108861 CAGGCATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
10 6 0.17
11 18 0.50
12 6 0.17
13 6 0.17
ACGTcount: A:0.02, C:0.06, G:0.10, T:0.82
Consensus pattern (11 bp):
TTTTTTGTTGT
Found at i:3114984 original size:15 final size:15
Alignment explanation
Indices: 3114964--3115018 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
3114954 CAACAACTTT
3114964 TTTTTAAAACACGAA
1 TTTTTAAAACACGAA
*
3114979 TTTTTAAAATACAAGAA
1 TTTTT-AAA-ACACGAA
3114996 -TTTTAGAAACAC-AA
1 TTTTTA-AAACACGAA
*
3115010 ATTTTAAAA
1 TTTTTAAAA
3115019 AAAACACGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
14 5 0.15
15 14 0.41
16 9 0.26
17 6 0.18
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.35
Consensus pattern (15 bp):
TTTTTAAAACACGAA
Found at i:3115558 original size:7 final size:7
Alignment explanation
Indices: 3115546--3115576 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
3115536 GAATTGAACC
3115546 TCTTTTT
1 TCTTTTT
3115553 TCTTTTT
1 TCTTTTT
3115560 CTCTTTTT
1 -TCTTTTT
3115568 TCTTTTT
1 TCTTTTT
3115575 TC
1 TC
3115577 CTCCTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (7 bp):
TCTTTTT
Found at i:3115565 original size:15 final size:15
Alignment explanation
Indices: 3115545--3115615 Score: 74
Period size: 15 Copynumber: 4.6 Consensus size: 15
3115535 CGAATTGAAC
3115545 CTCTTTTTTCTTTTT
1 CTCTTTTTTCTTTTT
3115560 CTCTTTTTTCTTTTTT
1 CTCTTTTTTC-TTTTT
* *
3115576 CCTCCTTTTTTCCTTCT
1 -CT-CTTTTTTCTTTTT
3115593 CT-TTTTCTTCTTTTT
1 CTCTTTT-TTCTTTTT
3115608 CT-TTTTTT
1 CTCTTTTTT
3115616 TTCTCTGCTG
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
14 6 0.12
15 22 0.46
16 7 0.15
17 5 0.10
18 8 0.17
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
CTCTTTTTTCTTTTT
Found at i:3115796 original size:11 final size:10
Alignment explanation
Indices: 3115778--3115807 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
3115768 TTCTTTTCTC
3115778 TTTTTTTTGT
1 TTTTTTTTGT
3115788 TTTTGTTTTGT
1 TTTT-TTTTGT
3115799 TTTTTTTTG
1 TTTTTTTTG
3115808 GGCTGCTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (10 bp):
TTTTTTTTGT
Found at i:3115893 original size:6 final size:6
Alignment explanation
Indices: 3115884--3115967 Score: 69
Period size: 6 Copynumber: 13.3 Consensus size: 6
3115874 TTATTATTAT
* * *
3115884 TTTTTC TTTTTC TTTTTTC TTTTTTC TTTTTTT TTCTTTC TTCTTC TTCTTC
1 TTTTTC TTTTTC -TTTTTC -TTTTTC -TTTTTC TT-TTTC TTTTTC TTTTTC
* * * *
3115936 TTCTTC TTTTTC TTCTTC TTCTTC TTCTTC TT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT
3115968 CAAAAACCCT
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
6 47 0.66
7 24 0.34
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTTC
Found at i:3115918 original size:17 final size:17
Alignment explanation
Indices: 3115886--3115961 Score: 70
Period size: 17 Copynumber: 4.5 Consensus size: 17
3115876 ATTATTATTT
3115886 TTTCTT-TTTCTTTTTTC
1 TTTCTTCTTT-TTTTTTC
*
3115903 TTTTTTCTTTTTTTTTC
1 TTTCTTCTTTTTTTTTC
* *
3115920 TTTCTTC-TTCTTCTTC
1 TTTCTTCTTTTTTTTTC
3115936 -TTCTTCTTTTTCTTCTTC
1 TTTCTTCTTTTT-TT-TTC
3115954 -TTCTTCTT
1 TTTCTTCTT
3115962 CTTCTTCAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
15 6 0.12
16 10 0.20
17 19 0.39
18 14 0.29
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTCTTCTTTTTTTTTC
Found at i:3115927 original size:3 final size:3
Alignment explanation
Indices: 3115921--3115968 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
3115911 TTTTTTTTCT
*
3115921 TTC TTC TTC TTC TTC TTC TTC TTT TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
3115969 AAAAACCCTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:3115950 original size:9 final size:9
Alignment explanation
Indices: 3115883--3115968 Score: 74
Period size: 9 Copynumber: 9.9 Consensus size: 9
3115873 ATTATTATTA
3115883 TTTT-TTCT
1 TTTTCTTCT
3115891 TTTTC-T-T
1 TTTTCTTCT
3115898 TTTTC-T-T
1 TTTTCTTCT
*
3115905 TTTTCTTTTT
1 TTTTC-TTCT
3115915 TTTTCTTTCT
1 TTTTC-TTCT
*
3115925 TCTTCTTCT
1 TTTTCTTCT
*
3115934 TCTTCTTCT
1 TTTTCTTCT
3115943 TTTTCTTCT
1 TTTTCTTCT
*
3115952 TCTTCTTCT
1 TTTTCTTCT
*
3115961 TCTTCTTC
1 TTTTCTTC
3115969 AAAAACCCTA
Statistics
Matches: 70, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
7 13 0.19
8 5 0.07
9 38 0.54
10 14 0.20
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTCTTCT
Found at i:3116345 original size:30 final size:30
Alignment explanation
Indices: 3116311--3116446 Score: 150
Period size: 30 Copynumber: 4.6 Consensus size: 30
3116301 GAAAAATTTT
* *
3116311 GGGGTCGAAATGTAATTTCGAGGAAGTTTA
1 GGGGTCAAAATGTAATTTCGAGAAAGTTTA
* *
3116341 GGGGTCAAAATGTAATTTTGAGAAAGTTTC
1 GGGGTCAAAATGTAATTTCGAGAAAGTTTA
* **
3116371 GAGGTCAAAATGTAATTTATA-AAAGTTTA
1 GGGGTCAAAATGTAATTTCGAGAAAGTTTA
** * **
3116400 GGGGTTGAAATGTAATTTCAAGAAAGTACA
1 GGGGTCAAAATGTAATTTCGAGAAAGTTTA
3116430 -GGGTCAAAATGTAATTT
1 GGGGTCAAAATGTAATTT
3116447 TTATTTTTTG
Statistics
Matches: 88, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
29 38 0.43
30 50 0.57
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.32
Consensus pattern (30 bp):
GGGGTCAAAATGTAATTTCGAGAAAGTTTA
Found at i:3116411 original size:59 final size:58
Alignment explanation
Indices: 3116334--3116446 Score: 156
Period size: 59 Copynumber: 1.9 Consensus size: 58
3116324 AATTTCGAGG
** *
3116334 AAGTTTAGGGGTCAAAATGTAATTTTGAGAAAGTTTC-GAGGTCAAAATGTAATTTATAA
1 AAGTTTAGGGGTCAAAATGTAATTTCAAGAAAG-TACAG-GGTCAAAATGTAATTTATAA
**
3116393 AAGTTTAGGGGTTGAAATGTAATTTCAAGAAAGTACAGGGTCAAAATGTAATTT
1 AAGTTTAGGGGTCAAAATGTAATTTCAAGAAAGTACAGGGTCAAAATGTAATTT
3116447 TTATTTTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
58 18 0.38
59 30 0.62
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.33
Consensus pattern (58 bp):
AAGTTTAGGGGTCAAAATGTAATTTCAAGAAAGTACAGGGTCAAAATGTAATTTATAA
Found at i:3116463 original size:16 final size:17
Alignment explanation
Indices: 3116439--3116472 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3116429 AGGGTCAAAA
3116439 TGTAATTTTT-ATTTTT
1 TGTAATTTTTGATTTTT
*
3116455 TGTATTTTTTGATTTTT
1 TGTAATTTTTGATTTTT
3116472 T
1 T
3116473 TTAAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76
Consensus pattern (17 bp):
TGTAATTTTTGATTTTT
Found at i:3122616 original size:18 final size:19
Alignment explanation
Indices: 3122581--3122618 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3122571 ATCGTGTTTG
*
3122581 TTTTTTATTTCTAAATTTA
1 TTTTTGATTTCTAAATTTA
*
3122600 TTTTTGATTT-TAGATTTA
1 TTTTTGATTTCTAAATTTA
3122618 T
1 T
3122619 CCTTAACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTTTGATTTCTAAATTTA
Found at i:3127317 original size:23 final size:25
Alignment explanation
Indices: 3127274--3127335 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 25
3127264 TTAACAATAC
3127274 TGAAGTTTATTTTTATATTTTGT-TT
1 TGAA-TTTATTTTTATATTTTGTATT
* * *
3127299 TG-ATTTATTTTTGTCTTTTTTATT
1 TGAATTTATTTTTATATTTTGTATT
*
3127323 TGAATTTTTTTTT
1 TGAATTTATTTTT
3127336 TCATTTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
23 15 0.48
24 5 0.16
25 11 0.35
ACGTcount: A:0.16, C:0.02, G:0.10, T:0.73
Consensus pattern (25 bp):
TGAATTTATTTTTATATTTTGTATT
Found at i:3127342 original size:24 final size:23
Alignment explanation
Indices: 3127279--3127347 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
3127269 AATACTGAAG
* *
3127279 TTTATTTTTAT-ATTTTGTTTTGA
1 TTTATTTTTGTCATTTT-ATTTGA
*
3127302 TTTATTTTTGTCTTTTTTATTTGAA
1 TTTATTTTTGTC-ATTTTATTTG-A
*
3127327 TTT-TTTTTTTCATTTTATTTG
1 TTTATTTTTGTCATTTTATTTG
3127348 TACCATTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
23 19 0.50
24 11 0.29
25 8 0.21
ACGTcount: A:0.14, C:0.03, G:0.07, T:0.75
Consensus pattern (23 bp):
TTTATTTTTGTCATTTTATTTGA
Done.