Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009145.1 Hibiscus syriacus cultivar Beakdansim tig00112657_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 440284
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:1280 original size:16 final size:16
Alignment explanation
Indices: 1259--1290 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1249 AAGATCTATG
1259 ATATGAACATAAGATA
1 ATATGAACATAAGATA
*
1275 ATATGAACATGAGATA
1 ATATGAACATAAGATA
1291 TGTGATTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.06, G:0.16, T:0.25
Consensus pattern (16 bp):
ATATGAACATAAGATA
Found at i:1529 original size:17 final size:18
Alignment explanation
Indices: 1496--1529 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1486 AGGGTTCTGC
1496 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
1514 GTGGTCCTTC-GGACAT
1 GTGGTCCTTCGGGACAT
1530 TTCATAGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.15, C:0.24, G:0.32, T:0.29
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:3574 original size:41 final size:40
Alignment explanation
Indices: 3524--3620 Score: 106
Period size: 40 Copynumber: 2.4 Consensus size: 40
3514 TATGAGCCTA
3524 AAAAGTGCCCCAACATTATACTTCTGGCTG-AATCGGGCCTTC
1 AAAA-TGCCCCAACATTA-ACTTCTGGCTGAAAT-GGGCCTTC
* * **
3566 AAAATGCCCCAATATTAATTTCTTTCTGAAATGGGCCTTC
1 AAAATGCCCCAACATTAACTTCTGGCTGAAATGGGCCTTC
**
3606 AAAACACCCCAACAT
1 AAAATGCCCCAACAT
3621 GATATAGATC
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
40 28 0.60
41 15 0.32
42 4 0.09
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.27
Consensus pattern (40 bp):
AAAATGCCCCAACATTAACTTCTGGCTGAAATGGGCCTTC
Found at i:3602 original size:40 final size:42
Alignment explanation
Indices: 3500--3609 Score: 111
Period size: 40 Copynumber: 2.7 Consensus size: 42
3490 TGTTCAAAAT
* * *
3500 TATTTCTTTCCTGATATGAGCC-TAAAAAGTGCCCCAACATTA
1 TATTTCTTT-CTGAAATGGGCCTTCAAAAGTGCCCCAACATTA
* ** *
3542 TACTTCTGGCTG-AATCGGGCCTTCAAAA-TGCCCCAATATTA
1 TATTTCTTTCTGAAAT-GGGCCTTCAAAAGTGCCCCAACATTA
3583 -ATTTCTTTCTGAAATGGGCCTTCAAAA
1 TATTTCTTTCTGAAATGGGCCTTCAAAA
3610 CACCCCAACA
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
40 22 0.40
41 22 0.40
42 11 0.20
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.33
Consensus pattern (42 bp):
TATTTCTTTCTGAAATGGGCCTTCAAAAGTGCCCCAACATTA
Found at i:9753 original size:15 final size:15
Alignment explanation
Indices: 9730--9763 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
9720 ATTTTAATAT
*
9730 AATTTAAAGAAAAAA
1 AATTAAAAGAAAAAA
*
9745 AATTAAAAGATAAAA
1 AATTAAAAGAAAAAA
9760 AATT
1 AATT
9764 GATTTGCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (15 bp):
AATTAAAAGAAAAAA
Found at i:10195 original size:7 final size:7
Alignment explanation
Indices: 10180--10226 Score: 67
Period size: 7 Copynumber: 6.4 Consensus size: 7
10170 AACCAAAAAT
10180 AATATTA
1 AATATTA
*
10187 AAAATTAAA
1 AATATT--A
10196 AATATTA
1 AATATTA
10203 AATATTA
1 AATATTA
10210 AATATTA
1 AATATTA
10217 AATATTA
1 AATATTA
10224 AAT
1 AAT
10227 TAGAGGATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
7 30 0.83
9 6 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AATATTA
Found at i:11561 original size:25 final size:25
Alignment explanation
Indices: 11515--11562 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
11505 CTTCGGGTTC
* *
11515 TTGTAAATGGGCCTTCATATTTGCT
1 TTGTAAATGGGCCTCCAGATTTGCT
* *
11540 TTGTAACTGGGGCTCCAGATTTG
1 TTGTAAATGGGCCTCCAGATTTG
11563 TCTTCAATTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.40
Consensus pattern (25 bp):
TTGTAAATGGGCCTCCAGATTTGCT
Found at i:12974 original size:3 final size:3
Alignment explanation
Indices: 12966--13033 Score: 73
Period size: 3 Copynumber: 22.7 Consensus size: 3
12956 CGTCACTGCC
* * * * * *
12966 ACA ACA ACA AGA ACA TCG ACA ACA ACA ACA GCG ACA ACA TCA ACA ACA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
*
13014 TCA ACA ACA ACA ACA ACA AC
1 ACA ACA ACA ACA ACA ACA AC
13034 GAAAAAAAAT
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.57, C:0.32, G:0.06, T:0.04
Consensus pattern (3 bp):
ACA
Found at i:13072 original size:24 final size:24
Alignment explanation
Indices: 13055--13115 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
13045 GCAATGGCAG
13055 CAAAAACAACAACAGCAACGGTAA
1 CAAAAACAACAACAGCAACGGTAA
*
13079 CAAAAACAACAACAACAACGGTAA
1 CAAAAACAACAACAGCAACGGTAA
13103 CAAAAACAACAAC
1 CAAAAACAACAAC
13116 GGCATGGATA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.62, C:0.26, G:0.08, T:0.03
Consensus pattern (24 bp):
CAAAAACAACAACAGCAACGGTAA
Found at i:13104 original size:18 final size:18
Alignment explanation
Indices: 13083--13117 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
13073 CGGTAACAAA
*
13083 AACAACAACAACAACGGT
1 AACAAAAACAACAACGGT
13101 AACAAAAACAACAACGG
1 AACAAAAACAACAACGG
13118 CATGGATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.26, G:0.11, T:0.03
Consensus pattern (18 bp):
AACAAAAACAACAACGGT
Found at i:13168 original size:25 final size:25
Alignment explanation
Indices: 13139--13187 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
13129 TTATTATTTG
* *
13139 AATTTAAATACAATCATTTTAATAT
1 AATTTAAAAAAAATCATTTTAATAT
13164 AATTTAAAAAAAATCATTTTAATA
1 AATTTAAAAAAAATCATTTTAATA
13188 CAATGTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (25 bp):
AATTTAAAAAAAATCATTTTAATAT
Found at i:15104 original size:18 final size:19
Alignment explanation
Indices: 15081--15124 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
15071 CCAGTAATCC
*
15081 TATTCC-CTGGTAATCTTT
1 TATTCCACTGGTAATCTTA
15099 TATTCCCACTGGTAATCTTA
1 TATT-CCACTGGTAATCTTA
15119 TATTCC
1 TATTCC
15125 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 15 0.65
ACGTcount: A:0.20, C:0.25, G:0.09, T:0.45
Consensus pattern (19 bp):
TATTCCACTGGTAATCTTA
Found at i:15112 original size:20 final size:20
Alignment explanation
Indices: 15087--15124 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
15077 ATCCTATTCC
*
15087 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTATATTCCCA
15107 CTGGTAATCTTATATTCC
1 CTGGTAATCTTATATTCC
15125 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTATATTCCCA
Found at i:21237 original size:23 final size:24
Alignment explanation
Indices: 21205--21252 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
21195 CGATACCACC
21205 TTGAAGGGGAACTGATTCCC-CCT
1 TTGAAGGGGAACTGATTCCCTCCT
*
21228 TTGAATGGGAACTGATTCCCTCCT
1 TTGAAGGGGAACTGATTCCCTCCT
21252 T
1 T
21253 GAGGGAATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (24 bp):
TTGAAGGGGAACTGATTCCCTCCT
Found at i:25100 original size:20 final size:20
Alignment explanation
Indices: 25075--25120 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
25065 TAAATCGTTG
25075 TGCAAATATTTTCAATTTTC
1 TGCAAATATTTTCAATTTTC
25095 TGCAAATATTTTCAATTTTC
1 TGCAAATATTTTCAATTTTC
25115 TGCAAA
1 TGCAAA
25121 AGCTTCCACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.46
Consensus pattern (20 bp):
TGCAAATATTTTCAATTTTC
Found at i:25240 original size:13 final size:13
Alignment explanation
Indices: 25222--25255 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
25212 GAGTTAGGAC
25222 AATAGATGAGTGA
1 AATAGATGAGTGA
*
25235 AATAGATTAGTGA
1 AATAGATGAGTGA
25248 AATAGATG
1 AATAGATG
25256 GTTGAGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.26
Consensus pattern (13 bp):
AATAGATGAGTGA
Found at i:25741 original size:2 final size:2
Alignment explanation
Indices: 25734--25767 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
25724 AACTTCTTTA
25734 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25768 TCTAAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29999 original size:36 final size:36
Alignment explanation
Indices: 29958--30033 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
29948 ATTTTCGGGA
*
29958 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
29994 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
30030 TTTT
1 TTTT
30034 TTAGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:30474 original size:15 final size:15
Alignment explanation
Indices: 30454--30483 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
30444 TATCACAATC
30454 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
30469 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
30484 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:34997 original size:36 final size:36
Alignment explanation
Indices: 34956--35031 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
34946 ATTTTCGGGA
*
34956 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
34992 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
35028 TTTT
1 TTTT
35032 TTAGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:44122 original size:40 final size:39
Alignment explanation
Indices: 44047--44134 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 39
44037 CCTAATATTT
* *
44047 TAAATTCTTAATTTCTTAAACCATTTCACTATAACATTC
1 TAAATTATTAATTTCTTAAACCATTTCACTATAACAATC
* ** * *
44086 TAAATTATTAATTTTTTTAAATTATTTCATTGTAACAATC
1 TAAATTATTAA-TTTCTTAAACCATTTCACTATAACAATC
44126 TAAATTATT
1 TAAATTATT
44135 TCTTTTAACT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
39 10 0.24
40 31 0.76
ACGTcount: A:0.38, C:0.12, G:0.01, T:0.49
Consensus pattern (39 bp):
TAAATTATTAATTTCTTAAACCATTTCACTATAACAATC
Found at i:48068 original size:3 final size:3
Alignment explanation
Indices: 48060--48121 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
48050 CTGGGTTTTG
48060 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
48108 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
48122 CGTAAACTCG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:48616 original size:41 final size:42
Alignment explanation
Indices: 48566--48668 Score: 127
Period size: 42 Copynumber: 2.5 Consensus size: 42
48556 ACCCAAAGGT
* * * * *
48566 CTGAAAGATGGCCCTAAGGACTT-ATCATCTTGCTCAAAAGA
1 CTGACAGATGACCCTAAGGACTTAAGCACCATGCTCAAAAGA
*
48607 CTGACAGATGACCCTAAGGATTTAAGCACCATGCTCAAAAGA
1 CTGACAGATGACCCTAAGGACTTAAGCACCATGCTCAAAAGA
* *
48649 CTGACGGATGACCCCAAGGA
1 CTGACAGATGACCCTAAGGA
48669 TTTACAAATT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 20 0.38
42 33 0.62
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.19
Consensus pattern (42 bp):
CTGACAGATGACCCTAAGGACTTAAGCACCATGCTCAAAAGA
Found at i:48783 original size:260 final size:260
Alignment explanation
Indices: 48311--49523 Score: 1899
Period size: 260 Copynumber: 4.7 Consensus size: 260
48301 CTCGTCTTAT
* * * *
48311 GGATGACCATAAGGACTTATCATCTTACTTAAAAGACTGACAGATGACCCTAAGGATTTAAGCAT
1 GGATGGCCCTAAGGACTTATCATCTTGCTCAAAAGACTGACAGATGACCCTAAGGATTTAAGCAT
* * * *
48376 CATGCTCGAAAGACTGACAGATGACCCTAAAGATTTACAAATTTGAGAAATAATTTACTGGGTAA
66 CATGCTCGAAAGACTGACAGATGACCCGAAGGATTTACAAATTTGGGAAATAATTTACTAGGTAA
* *
48441 GAAACTTTGGAAATTGA-TTTCTTACTTTTCAAGAATTTCATTTTCTTGAACATTAAATGATAAA
131 GAAACTTTGGAAA-TCACTTTCTTACTTTTCAAGAATTTCATTTTCTTGAACATTAAATGAGAAA
* * *
48505 CTTTGAAAATCACTTTCTCATTTTCATGTGAAAATCATGTGTAAACATCATACCCAAAGGTCTGA
195 CTTTGAAAATCACTTTCTCATTTTCATATGAAAATCACGTGTAAACATCCTACCCAAAGGTCTGA
48570 A
260 A
* *
48571 AGATGGCCCTAAGGACTTATCATCTTGCTCAAAAGACTGACAGATGACCCTAAGGATTTAAGCAC
1 GGATGGCCCTAAGGACTTATCATCTTGCTCAAAAGACTGACAGATGACCCTAAGGATTTAAGCAT
* * *
48636 CATGCTCAAAAGACTGACGGATGACCCCAAGGATTTACAAATTTGGGAAATAATTTACTAGGTAA
66 CATGCTCGAAAGACTGACAGATGACCCGAAGGATTTACAAATTTGGGAAATAATTTACTAGGTAA
*
48701 GAAACTTTGGAAATCACTTTCTTACTTTTCAAGAATTTCATTTTCTTGAACATTAAATGAGGAAC
131 GAAACTTTGGAAATCACTTTCTTACTTTTCAAGAATTTCATTTTCTTGAACATTAAATGAGAAAC
* * ** *
48766 TTTGAAAATCGCTTTCTCATTTTCATGTGAAAATCATTTGTAAACATCCTACCCAAAGGTCTGAC
196 TTTGAAAATCACTTTCTCATTTTCATATGAAAATCACGTGTAAACATCCTACCCAAAGGTCTGAA
* *
48831 GGATGGCCCTAAGGACTTATTATCTTGCTCAAAAGACTAACAGATGACCCTAAGGATTTAAGCAT
1 GGATGGCCCTAAGGACTTATCATCTTGCTCAAAAGACTGACAGATGACCCTAAGGATTTAAGCAT
* * *
48896 CATGCTCGAAAGACTGACATATGACCCAAAGAATTTACAAATTTGGGAAATAATTTACT-GGTAA
66 CATGCTCGAAAGACTGACAGATGACCCGAAGGATTTACAAATTTGGGAAATAATTTACTAGGTAA
* *
48960 GAAACTTTGGAAATCGCTTTCTTACTTTTCAATAATTTCATTTTCTTGAACATTAAATGAGAAAC
131 GAAACTTTGGAAATCACTTTCTTACTTTTCAAGAATTTCATTTTCTTGAACATTAAATGAGAAAC
**
49025 TTTGAAAATCACTTTCTCATTTTCATATGAAAATCACGTGTAAACATCCTACCCAATTGTCTGAA
196 TTTGAAAATCACTTTCTCATTTTCATATGAAAATCACGTGTAAACATCCTACCCAAAGGTCTGAA
* **
49090 GGATGGCCCTAATGACTTATCATCTTATTCAAAAGACTGACAGATGACCCTAAGGATTTAAGCAT
1 GGATGGCCCTAAGGACTTATCATCTTGCTCAAAAGACTGACAGATGACCCTAAGGATTTAAGCAT
* *
49155 CATGCTCGAAAGACTGACAGATGATCCGAAGGGTTTACAAATTTGGGAAATAATTTACTAGGTAA
66 CATGCTCGAAAGACTGACAGATGACCCGAAGGATTTACAAATTTGGGAAATAATTTACTAGGTAA
* *
49220 GACACTTTGGAAATCACTTTCTTACTTTTCAAGAATTTCATTTTATTGAACATTAAATGAGAAAC
131 GAAACTTTGGAAATCACTTTCTTACTTTTCAAGAATTTCATTTTCTTGAACATTAAATGAGAAAC
* * * *
49285 TTTGAAAATCGCTTTCTCATTTTCATATGAAAATCACGTGTAAAAATCCTACCCAATGGTCTGAC
196 TTTGAAAATCACTTTCTCATTTTCATATGAAAATCACGTGTAAACATCCTACCCAAAGGTCTGAA
* * *
49350 GGATGGCCCTAAGGACTTATCATCTTGCTCAAAAGACTGACAAATGACCATAAGGATTTAAGTAT
1 GGATGGCCCTAAGGACTTATCATCTTGCTCAAAAGACTGACAGATGACCCTAAGGATTTAAGCAT
* * * *
49415 CACGCTCGAAAGACTGACAGATGATCAGAAGGATTTACAAATTTGGGAAATAATTTACTGGGTAA
66 CATGCTCGAAAGACTGACAGATGACCCGAAGGATTTACAAATTTGGGAAATAATTTACTAGGTAA
* * * * *
49480 GAAATTTTGAAAATCGCTTTCTTACTTTTCAAAAATTTTATTTT
131 GAAACTTTGGAAATCACTTTCTTACTTTTCAAGAATTTCATTTT
49524 TCAAAAAGGA
Statistics
Matches: 879, Mismatches: 72, Indels: 4
0.92 0.08 0.00
Matches are distributed among these distances:
259 241 0.27
260 638 0.73
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Consensus pattern (260 bp):
GGATGGCCCTAAGGACTTATCATCTTGCTCAAAAGACTGACAGATGACCCTAAGGATTTAAGCAT
CATGCTCGAAAGACTGACAGATGACCCGAAGGATTTACAAATTTGGGAAATAATTTACTAGGTAA
GAAACTTTGGAAATCACTTTCTTACTTTTCAAGAATTTCATTTTCTTGAACATTAAATGAGAAAC
TTTGAAAATCACTTTCTCATTTTCATATGAAAATCACGTGTAAACATCCTACCCAAAGGTCTGAA
Found at i:49271 original size:519 final size:519
Alignment explanation
Indices: 48311--49523 Score: 1980
Period size: 519 Copynumber: 2.3 Consensus size: 519
48301 CTCGTCTTAT
* * * *
48311 GGATGACCATAAGGACTTATCATCTTACTTAAAAGACTGACAGATGACCCTAAGGATTTAAGCAT
1 GGATGGCCCTAAGGACTTATCATCTTGCTCAAAAGACTGACAGATGACCCTAAGGATTTAAGCAT
*
48376 CATGCTCGAAAGACTGACAGATGACCCTAAAGATTTACAAATTTGAGAAATAATTTACTGGGTAA
66 CATGCTCGAAAGACTGACAGATGACCC-AAAGATTTACAAATTTGGGAAATAATTTACTGGGTAA
* * * *
48441 GAAACTTTGGAAATTGATTTCTTACTTTTCAAGAATTTCATTTTCTTGAACATTAAATGATAAAC
130 GAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTTGAACATTAAATGAGAAAC
* *
48506 TTTGAAAATCACTTTCTCATTTTCATGTGAAAATCATGTGTAAACATCATACCCAAAGGTCTGAA
195 TTTGAAAATCACTTTCTCATTTTCATATGAAAATCACGTGTAAACATCATACCCAAAGGTCTGAA
*
48571 AGATGGCCCTAAGGACTTATCATCTTGCTCAAAAGACTGACAGATGACCCTAAGGATTTAAGCAC
260 AGATGGCCCTAAGGACTTATCATCTTACTCAAAAGACTGACAGATGACCCTAAGGATTTAAGCAC
*
48636 CATGCTCAAAAGACTGACGGATGACCCCAAGGATTTACAAATTTGGGAAATAATTTACTAGGTAA
325 CATGCTCAAAAGACTGACAGATGACCCCAAGGATTTACAAATTTGGGAAATAATTTACTAGGTAA
* *
48701 GAAACTTTGGAAATCACTTTCTTACTTTTCAAGAATTTCATTTTCTTGAACATTAAATGAGGAAC
390 GAAACTTTGGAAATCACTTTCTTACTTTTCAAGAATTTCATTTTATTGAACATTAAATGAGAAAC
* ** *
48766 TTTGAAAATCGCTTTCTCATTTTCATGTGAAAATCATTTGTAAACATCCTACCCAAAGGTCTGAC
455 TTTGAAAATCGCTTTCTCATTTTCATATGAAAATCACGTGTAAAAATCCTACCCAAAGGTCTGAC
* *
48831 GGATGGCCCTAAGGACTTATTATCTTGCTCAAAAGACTAACAGATGACCCTAAGGATTTAAGCAT
1 GGATGGCCCTAAGGACTTATCATCTTGCTCAAAAGACTGACAGATGACCCTAAGGATTTAAGCAT
*
48896 CATGCTCGAAAGACTGACATATGACCCAAAGAATTTACAAATTTGGGAAATAATTTACT-GGTAA
66 CATGCTCGAAAGACTGACAGATGACCCAAAG-ATTTACAAATTTGGGAAATAATTTACTGGGTAA
*
48960 GAAACTTTGGAAATCGCTTTCTTACTTTTCAATAATTTCATTTTCTTGAACATTAAATGAGAAAC
130 GAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTTGAACATTAAATGAGAAAC
* **
49025 TTTGAAAATCACTTTCTCATTTTCATATGAAAATCACGTGTAAACATCCTACCCAATTGTCTGAA
195 TTTGAAAATCACTTTCTCATTTTCATATGAAAATCACGTGTAAACATCATACCCAAAGGTCTGAA
* * * *
49090 GGATGGCCCTAATGACTTATCATCTTATTCAAAAGACTGACAGATGACCCTAAGGATTTAAGCAT
260 AGATGGCCCTAAGGACTTATCATCTTACTCAAAAGACTGACAGATGACCCTAAGGATTTAAGCAC
* * * *
49155 CATGCTCGAAAGACTGACAGATGATCCGAAGGGTTTACAAATTTGGGAAATAATTTACTAGGTAA
325 CATGCTCAAAAGACTGACAGATGACCCCAAGGATTTACAAATTTGGGAAATAATTTACTAGGTAA
*
49220 GACACTTTGGAAATCACTTTCTTACTTTTCAAGAATTTCATTTTATTGAACATTAAATGAGAAAC
390 GAAACTTTGGAAATCACTTTCTTACTTTTCAAGAATTTCATTTTATTGAACATTAAATGAGAAAC
*
49285 TTTGAAAATCGCTTTCTCATTTTCATATGAAAATCACGTGTAAAAATCCTACCCAATGGTCTGAC
455 TTTGAAAATCGCTTTCTCATTTTCATATGAAAATCACGTGTAAAAATCCTACCCAAAGGTCTGAC
* * *
49350 GGATGGCCCTAAGGACTTATCATCTTGCTCAAAAGACTGACAAATGACCATAAGGATTTAAGTAT
1 GGATGGCCCTAAGGACTTATCATCTTGCTCAAAAGACTGACAGATGACCCTAAGGATTTAAGCAT
* *
49415 CACGCTCGAAAGACTGACAGATGA-TCAGAAGGATTTACAAATTTGGGAAATAATTTACTGGGTA
66 CATGCTCGAAAGACTGACAGATGACCCA-AA-GATTTACAAATTTGGGAAATAATTTACTGGGTA
* * *
49479 AGAAATTTTGAAAATCGCTTTCTTACTTTTCAAAAATTTTATTTT
129 AGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTT
49524 TCAAAAAGGA
Statistics
Matches: 642, Mismatches: 47, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
518 2 0.00
519 483 0.75
520 157 0.24
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Consensus pattern (519 bp):
GGATGGCCCTAAGGACTTATCATCTTGCTCAAAAGACTGACAGATGACCCTAAGGATTTAAGCAT
CATGCTCGAAAGACTGACAGATGACCCAAAGATTTACAAATTTGGGAAATAATTTACTGGGTAAG
AAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTTGAACATTAAATGAGAAACT
TTGAAAATCACTTTCTCATTTTCATATGAAAATCACGTGTAAACATCATACCCAAAGGTCTGAAA
GATGGCCCTAAGGACTTATCATCTTACTCAAAAGACTGACAGATGACCCTAAGGATTTAAGCACC
ATGCTCAAAAGACTGACAGATGACCCCAAGGATTTACAAATTTGGGAAATAATTTACTAGGTAAG
AAACTTTGGAAATCACTTTCTTACTTTTCAAGAATTTCATTTTATTGAACATTAAATGAGAAACT
TTGAAAATCGCTTTCTCATTTTCATATGAAAATCACGTGTAAAAATCCTACCCAAAGGTCTGAC
Found at i:58873 original size:64 final size:67
Alignment explanation
Indices: 58787--58932 Score: 176
Period size: 64 Copynumber: 2.2 Consensus size: 67
58777 TGCACTAAGA
* *
58787 GTGCATCGATGCAT-GAAGTGCATTCGATGTTTAAAAA-ATAGC-CTGGTGCATCGATGCATGG-
1 GTGCATCGGTGCATGGAAGTGCATTCGATGTTTAAAAATAT-GCACTGATGCATCGATGCATGGT
58848 ATT
65 ATT
* ** * *
58851 GTGCATCGGTGCATGGAA-TGCATTCGATGTTTCAATTTATTCATTGATGCATCGATGCATGGTA
1 GTGCATCGGTGCATGGAAGTGCATTCGATGTTTAAAAATATGCACTGATGCATCGATGCATGGTA
58915 TT
66 TT
58917 GATGCATCGGTGCATG
1 G-TGCATCGGTGCATG
58933 CATTTGAAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
64 30 0.43
65 22 0.31
66 4 0.06
67 14 0.20
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.33
Consensus pattern (67 bp):
GTGCATCGGTGCATGGAAGTGCATTCGATGTTTAAAAATATGCACTGATGCATCGATGCATGGTA
TT
Found at i:58917 original size:21 final size:21
Alignment explanation
Indices: 58893--58932 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
58883 CAATTTATTC
58893 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
58914 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
58933 CATTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:82357 original size:30 final size:30
Alignment explanation
Indices: 82317--82377 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
82307 GTCCCGAAGG
82317 ACCTATCCATATGTCCCAAAGAACATAGGT
1 ACCTATCCATATGTCCCAAAGAACATAGGT
* *
82347 ACCTGTCCATATGTCCCGAAGAACATAGGT
1 ACCTATCCATATGTCCCAAAGAACATAGGT
82377 A
1 A
82378 ACTCCCGACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.23
Consensus pattern (30 bp):
ACCTATCCATATGTCCCAAAGAACATAGGT
Found at i:86314 original size:14 final size:14
Alignment explanation
Indices: 86295--86327 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
86285 AAGTCGTCTT
86295 GATCTATCTCTATA
1 GATCTATCTCTATA
86309 GATCTATCTCTATA
1 GATCTATCTCTATA
86323 GATCT
1 GATCT
86328 TAACTCTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.42
Consensus pattern (14 bp):
GATCTATCTCTATA
Found at i:98776 original size:3 final size:3
Alignment explanation
Indices: 98768--98813 Score: 83
Period size: 3 Copynumber: 15.0 Consensus size: 3
98758 ATTTTGTAAC
98768 AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
98814 TATTATTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:98818 original size:3 final size:3
Alignment explanation
Indices: 98812--98874 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
98802 AATAATAATA
98812 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
98860 ATT ATT ATT A-T ATT A
1 ATT ATT ATT ATT ATT A
98875 CTACGTAAAC
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 57 0.97
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:101280 original size:22 final size:22
Alignment explanation
Indices: 101252--101305 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
101242 TTCCCGGAGA
101252 ACTCCTTATCCTATGCCCTCCC
1 ACTCCTTATCCTATGCCCTCCC
*
101274 ACTCCTTGTCCTATGCCCTCCC
1 ACTCCTTATCCTATGCCCTCCC
*
101296 AC-ACTTATCC
1 ACTCCTTATCC
101306 AGTTGGTTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 6 0.21
22 23 0.79
ACGTcount: A:0.15, C:0.48, G:0.06, T:0.31
Consensus pattern (22 bp):
ACTCCTTATCCTATGCCCTCCC
Found at i:103605 original size:141 final size:140
Alignment explanation
Indices: 103359--103616 Score: 419
Period size: 141 Copynumber: 1.8 Consensus size: 140
103349 GTGTTTTTCA
103359 TTTGACTCGTGAGTTGGTCACAATTTCGATGATCAGATTATTGAATGGATGTTATATCAAGTCGA
1 TTTGACTCGTGAGTTGGTCACAATTTCGATGATCAGATTATTGAATGGATGTTATATCAAGTCGA
* *
103424 ACCTTCCGTTATAGCTGCTATCGATACCCAGACAATTCTCACCAATTTCTCCGCTCGTGGTTTTT
66 ACCTTCCGTTATAGCTGCTACCAATACCCAGACAATTCTCACCAATTTCTCCGCTCGTGGTTTTT
103489 TTTTTTTTTT
131 TTTTTTTTTT
* * * * *
103499 TTTGACTCGTGAGTTGGGTCACGATTTCGATGGTCAGATTTTTGAATGGATTTTATGTCAAGTC-
1 TTTGACTCGTGAGTT-GGTCACAATTTCGATGATCAGATTATTGAATGGATGTTATATCAAGTCG
*
103563 AAGCCTTCCGTTATAGCTGCTACCAATACCGAGACAATTCTCACCAATTTCTCC
65 AA-CCTTCCGTTATAGCTGCTACCAATACCCAGACAATTCTCACCAATTTCTCC
103617 ACTATGTCAG
Statistics
Matches: 108, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
140 17 0.16
141 91 0.84
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (140 bp):
TTTGACTCGTGAGTTGGTCACAATTTCGATGATCAGATTATTGAATGGATGTTATATCAAGTCGA
ACCTTCCGTTATAGCTGCTACCAATACCCAGACAATTCTCACCAATTTCTCCGCTCGTGGTTTTT
TTTTTTTTTT
Found at i:104146 original size:26 final size:26
Alignment explanation
Indices: 104117--104176 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
104107 TAATCTGGTT
*
104117 TGATACCAATACTCATTCTTGAGTAG
1 TGATACCAATACTCATTCTTAAGTAG
* *
104143 TGATACCATTACTCATTCTTAAGTAT
1 TGATACCAATACTCATTCTTAAGTAG
*
104169 TAATACCA
1 TGATACCA
104177 TCAAAGTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (26 bp):
TGATACCAATACTCATTCTTAAGTAG
Found at i:107224 original size:18 final size:18
Alignment explanation
Indices: 107191--107225 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
107181 GGGTCCTGGC
* *
107191 TTTGTTTATTATCTTTGA
1 TTTGTTTATCAGCTTTGA
107209 TTTGTTTATCAGCTTTG
1 TTTGTTTATCAGCTTTG
107226 CATTAGGAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.09, G:0.14, T:0.63
Consensus pattern (18 bp):
TTTGTTTATCAGCTTTGA
Found at i:118084 original size:22 final size:21
Alignment explanation
Indices: 118043--118084 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
118033 CATTCAATTC
*
118043 TTTTTTCATTTTGAGTCCACT
1 TTTTTTCATTTTGAGACCACT
118064 TTTTTATCAATTTTGA-ACCAC
1 TTTTT-TC-ATTTTGAGACCAC
118085 ATACTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 5 0.28
22 6 0.33
23 7 0.39
ACGTcount: A:0.21, C:0.19, G:0.07, T:0.52
Consensus pattern (21 bp):
TTTTTTCATTTTGAGACCACT
Found at i:122640 original size:23 final size:23
Alignment explanation
Indices: 122569--122644 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
122559 TGTGACAAGT
* *
122569 TATGTGAAACTGAACTAAGTGAA
1 TATGTGAAACTGAACTATGTGAC
* **
122592 TATATGAAACTAGAA-TATAAG-C
1 TATGTGAAACT-GAACTATGTGAC
*
122614 TATGTGAAAGTGAACTATGTGAC
1 TATGTGAAACTGAACTATGTGAC
122637 TATGTGAA
1 TATGTGAA
122645 CATGTGGATA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
21 3 0.07
22 13 0.32
23 22 0.54
24 3 0.07
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.29
Consensus pattern (23 bp):
TATGTGAAACTGAACTATGTGAC
Found at i:122662 original size:23 final size:21
Alignment explanation
Indices: 122604--122663 Score: 57
Period size: 23 Copynumber: 2.7 Consensus size: 21
122594 TATGAAACTA
*
122604 GAATATAAGCTATGTGAAAGT
1 GAATATATGCTATGTGAAAGT
*
122625 GAACTATGTGACTATGTGAACATGT
1 GAA-TATATG-CTATGTGAA-A-GT
*
122650 GGATATATGCTATG
1 GAATATATGCTATG
122664 AGATATGATC
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
21 3 0.10
22 4 0.13
23 14 0.45
24 6 0.19
25 4 0.13
ACGTcount: A:0.35, C:0.08, G:0.25, T:0.32
Consensus pattern (21 bp):
GAATATATGCTATGTGAAAGT
Found at i:123896 original size:90 final size:90
Alignment explanation
Indices: 123782--123963 Score: 294
Period size: 90 Copynumber: 2.0 Consensus size: 90
123772 TTAATAATCC
* * *
123782 GGATTATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAATCCTTAATA
1 GGATTATTTAAATTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCCTAATA
*
123847 TGATTAGGGTAACTTGGATATAAAA
66 TGATTAGGATAACTTGGATATAAAA
*
123872 GGATTA-TTAAATTCAAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAAT
1 GGATTATTTAAATTC-AATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCCTAAT
*
123936 ATGATTAGGATAACTTGGTTATAAAA
65 ATGATTAGGATAACTTGGATATAAAA
123962 GG
1 GG
123964 GTGTGTTAGG
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
89 7 0.08
90 78 0.92
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (90 bp):
GGATTATTTAAATTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCCTAATA
TGATTAGGATAACTTGGATATAAAA
Found at i:125688 original size:14 final size:14
Alignment explanation
Indices: 125669--125697 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
125659 TTCAATTGTT
125669 ATAGATTTAATGGC
1 ATAGATTTAATGGC
125683 ATAGATTTAATGGC
1 ATAGATTTAATGGC
125697 A
1 A
125698 AACAACACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (14 bp):
ATAGATTTAATGGC
Found at i:136081 original size:20 final size:20
Alignment explanation
Indices: 136056--136096 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
136046 TATATTGGGC
* *
136056 TATTGTCTATTGTTTATGGT
1 TATTGTCTATGGTATATGGT
136076 TATTGTCTATGGTATATGGT
1 TATTGTCTATGGTATATGGT
136096 T
1 T
136097 TGGAATAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.05, G:0.22, T:0.56
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGT
Found at i:136163 original size:45 final size:44
Alignment explanation
Indices: 136097--136200 Score: 163
Period size: 45 Copynumber: 2.3 Consensus size: 44
136087 GTATATGGTT
* * *
136097 TGGAATAATGGCAAGTGTATTGGTAAAATAAGCTTACGAGCTTA
1 TGGATTAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
136141 TGGTATTAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
1 TGG-ATTAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
*
136186 TGGATAAATGGTAAG
1 TGGATTAATGGTAAG
136201 AGATCTTATA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
44 14 0.25
45 41 0.75
ACGTcount: A:0.37, C:0.07, G:0.25, T:0.32
Consensus pattern (44 bp):
TGGATTAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
Found at i:136583 original size:12 final size:12
Alignment explanation
Indices: 136568--136601 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
136558 CGAAAGTTAC
136568 TGTAGCAGTTGT
1 TGTAGCAGTTGT
136580 TGTAGCAGTTGT
1 TGTAGCAGTTGT
136592 TGTAGCAGTT
1 TGTAGCAGTT
136602 ACTGTAGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.18, C:0.09, G:0.32, T:0.41
Consensus pattern (12 bp):
TGTAGCAGTTGT
Found at i:136607 original size:12 final size:12
Alignment explanation
Indices: 136562--136610 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
136552 TATTTTCGAA
136562 AGTTACTGTAGC
1 AGTTACTGTAGC
**
136574 AGTTGTTGTAGC
1 AGTTACTGTAGC
**
136586 AGTTGTTGTAGC
1 AGTTACTGTAGC
136598 AGTTACTGTAGC
1 AGTTACTGTAGC
136610 A
1 A
136611 TGAACAGTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.22, C:0.12, G:0.29, T:0.37
Consensus pattern (12 bp):
AGTTACTGTAGC
Found at i:139101 original size:21 final size:21
Alignment explanation
Indices: 139075--139148 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 21
139065 TACACGGTTC
*
139075 TTCGGGACATATACGTGGTCA
1 TTCGGGACATATATGTGGTCA
* * *
139096 TTCGGGATAATTCTATGAGGTCCA
1 TTCGGGA-CA-TATATGTGGT-CA
*
139120 -TCGGGACATATATGTGGTCT
1 TTCGGGACATATATGTGGTCA
139140 TTCGGGACA
1 TTCGGGACA
139149 ATTTTATATG
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
20 1 0.02
21 23 0.56
22 2 0.05
23 13 0.32
24 2 0.05
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (21 bp):
TTCGGGACATATATGTGGTCA
Found at i:143256 original size:23 final size:23
Alignment explanation
Indices: 143222--143290 Score: 88
Period size: 23 Copynumber: 3.1 Consensus size: 23
143212 GAGTCGAGGG
143222 TTCTATGTGGTCCTTCGGGACAA
1 TTCTATGTGGTCCTTCGGGACAA
* *
143245 TTCTATGAGGTCCTTCAGGAC-A
1 TTCTATGTGGTCCTTCGGGACAA
* *
143267 -TATATGTGGTCCTTCGGGATAA
1 TTCTATGTGGTCCTTCGGGACAA
143289 TT
1 TT
143291 TTATATGGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
21 16 0.42
22 2 0.05
23 20 0.53
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (23 bp):
TTCTATGTGGTCCTTCGGGACAA
Found at i:146249 original size:6 final size:6
Alignment explanation
Indices: 146240--146303 Score: 58
Period size: 6 Copynumber: 10.8 Consensus size: 6
146230 AGGAAAATCA
* * * * * **
146240 AAAAAT AAAAAT AAAATT AATAAT AATAAT AATAAT AATAAT ATGAA-
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
146287 AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAA
146304 ATGGAACCAT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
5 3 0.06
6 47 0.94
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (6 bp):
AAAAAT
Found at i:146265 original size:3 final size:3
Alignment explanation
Indices: 146243--146282 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
146233 AAAATCAAAA
*
146243 AAT AAA AAT AA- AATT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT A
146283 TGAAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.88
4 2 0.06
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:147423 original size:23 final size:20
Alignment explanation
Indices: 147391--147437 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
147381 GATCAAATAG
147391 ATAAAAAATATATATATATATTA
1 ATAAAAAATA-A-ATA-ATATTA
*
147414 ATAAACAATAAATAATATTA
1 ATAAAAAATAAATAATATTA
147434 ATAA
1 ATAA
147438 TATTAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 10 0.43
21 3 0.13
22 1 0.04
23 9 0.39
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
ATAAAAAATAAATAATATTA
Found at i:147438 original size:23 final size:23
Alignment explanation
Indices: 147386--147439 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
147376 GACCTGATCA
*
147386 AATAGATAAAAAATATATATATAT
1 AATA-ATAAAAAATAAATATATAT
* *
147410 ATTAATAAACAATAAATA-ATATT
1 AATAATAAAAAATAAATATATA-T
147433 AATAATA
1 AATAATA
147440 TTAATAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 3 0.12
23 19 0.76
24 3 0.12
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
AATAATAAAAAATAAATATATAT
Found at i:147536 original size:38 final size:36
Alignment explanation
Indices: 147472--147561 Score: 92
Period size: 38 Copynumber: 2.4 Consensus size: 36
147462 ATATATTATT
* * *
147472 TATTTTCAAAAACCTTGTTTTCAAAACCATACTATATA
1 TATTTTCAAAAACATTATTTTCAAAACCATA-TA-ACA
* *
147510 TATTTTCCAAAAA-ATTATTTTTAAAACTATATAACA
1 TATTTT-CAAAAACATTATTTTCAAAACCATATAACA
*
147546 TATTTTCAAAAGCATT
1 TATTTTCAAAAACATT
147562 TTCAAAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
35 5 0.11
36 11 0.25
37 2 0.05
38 20 0.45
39 6 0.14
ACGTcount: A:0.42, C:0.14, G:0.02, T:0.41
Consensus pattern (36 bp):
TATTTTCAAAAACATTATTTTCAAAACCATATAACA
Found at i:147576 original size:13 final size:13
Alignment explanation
Indices: 147560--147584 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
147550 TTCAAAAGCA
147560 TTTTCAAAAAATG
1 TTTTCAAAAAATG
147573 TTTTCAAAAAAT
1 TTTTCAAAAAAT
147585 TATATATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (13 bp):
TTTTCAAAAAATG
Found at i:147656 original size:36 final size:36
Alignment explanation
Indices: 147567--147754 Score: 159
Period size: 37 Copynumber: 5.1 Consensus size: 36
147557 GCATTTTCAA
* * *
147567 AAAATGTTTTCAAAAAAT-TATATATATATATATATTA
1 AAAATGTTTT-AAAAACTATATA-ATATATATATTTTC
* * *
147604 AAATATTTTTTAAAAACTATATAGTATATATGTTTTC
1 AAA-ATGTTTTAAAAACTATATAATATATATATTTTC
* *
147641 AAAATGCTTTT-AAAACTATATAATATACATGTCTTTC
1 AAAATG-TTTTAAAAACTATATAATATATATAT-TTTC
* *
147678 AAAATGTTTTTAAAAAAACCATATATTATATA-ATTTTC
1 AAAATG-TTTT--AAAAACTATATAATATATATATTTTC
* * *
147716 AAAATGATTT-CAAACTATATAATATATACATTTTC
1 AAAATGTTTTAAAAACTATATAATATATATATTTTC
147751 AAAA
1 AAAA
147755 CTATATATAT
Statistics
Matches: 125, Mismatches: 18, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
34 15 0.12
35 10 0.08
36 21 0.17
37 43 0.34
38 20 0.16
39 1 0.01
40 15 0.12
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (36 bp):
AAAATGTTTTAAAAACTATATAATATATATATTTTC
Found at i:147764 original size:24 final size:25
Alignment explanation
Indices: 147722--147778 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
147712 TTTCAAAATG
147722 ATTTC-AAACTATATAATATATACAT
1 ATTTCAAAACTATATAATAT-TACAT
*
147747 -TTTCAAAACTATAT-ATATTATAT
1 ATTTCAAAACTATATAATATTACAT
147770 ATTTCAAAA
1 ATTTCAAAA
147779 TCATTTGCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 4 0.14
24 16 0.55
25 9 0.31
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTTCAAAACTATATAATATTACAT
Found at i:148334 original size:84 final size:82
Alignment explanation
Indices: 148205--150252 Score: 1360
Period size: 84 Copynumber: 24.6 Consensus size: 82
148195 AGTTGAATGG
* * ** *
148205 AATCGAACTCGACGGT-TTTTATTGACAGATAACCCTTCTTTCCTTGAGATATGCTGTAAATGAT
1 AATCGAACTCGA-GGTCTTTTGTTGGCAGATAACCCTTC-CGCCTTGAGATATGCTGCAAATGAT
*
148269 GTGCCTTTGACCTGAGTGT
64 GTGCCTTTGAGCTGAGTGT
* * **
148288 AATCGAACTCGCAGTTCTTTTGTTGGCAGATAACCCTTCCAGCCTTGAGTTATGCTGCAAATGGC
1 AATCGAACTCG-AGGTCTTTTGTTGGCAGATAACCCTTCC-GCCTTGAGATATGCTGCAAATGAT
* * *
148353 GTGCCTTTGAGCTCAATGG
64 GTGCCTTTGAGCTGAGTGT
* * * * * * *
148372 AATCGAACTCGAAGGTCTTTGGTTAGCAGATAGCCTTTCTCGACTTAAGCTATGCTGCAAATGAT
1 AATCGAACTCG-AGGTCTTTTGTTGGCAGATAACCCTTC-CGCCTTGAGATATGCTGCAAATGAT
148437 GTGCCTTTGAGCTGAGTG-
64 GTGCCTTTGAGCTGAGTGT
* * * * * * * *
148455 --T---A----A-GTC-TTTATTGACATATAACCCTTCTAGACTTGAGTTATGCTGTAAATGATA
1 AATCGAACTCGAGGTCTTTTGTTGGCAGATAACCCTTC-CGCCTTGAGATATGCTGCAAATGATG
* *
148509 TGCCTTGGAGCTGAGCGT
65 TGCCTTTGAGCTGAGTGT
* * * * * *
148527 AGTCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTT-AAATTATGTTGCAAATGA
1 AATCGAACTCG-AGGTCTTTTGTTGGCAGATAACCCTTC-CGCCTTGAGA-TATGCTGCAAATGA
*
148591 TGTGCCTTTGAGCTAAGTGT
63 TGTGCCTTTGAGCTGAGTGT
* * * ** *
148611 AATCGAATTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGATTTATGCTGTAAATGAT
1 AATCGAACTC-GAGGTCTTTTGTTGGCAGATAACCCTTC-CGCCTTGAGATATGCTGCAAATGAT
* * * * *
148676 ATTCCTTGGAACTGAGCGT
64 GTGCCTTTGAGCTGAGTGT
* * * * * * *
148695 AGTCGAACTCGAAGGTCTTTGGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGAT
1 AATCGAACTCG-AGGTCTTTTGTTGGCAGATAACCCTTC-CGCCTTGAGATATGCTGCAAATGAT
* * *
148760 GTGTCTTAGAGCTGAGCGT
64 GTGCCTTTGAGCTGAGTGT
* * * * * * * ** * *
148779 AGTCAAACTTGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCGATGTTGCAGATGAT
1 AATCGAACTCG-AGGTCTTTTGTTGGCAGATAACCCTTC-CGCCTTGAGATATGCTGCAAATGAT
148844 GTGCCTTTGAGCTGAGTGT
64 GTGCCTTTGAGCTGAGTGT
* * * * *
148863 AATCGAACTCGAAGGTCTTTTATTGACAGATAACCCTTCTAGCCTTGAGTTATGATGCAAATGAT
1 AATCGAACTCG-AGGTCTTTTGTTGGCAGATAACCCTTC-CGCCTTGAGATATGCTGCAAATGAT
* * * *
148928 ATGCCTTGGATCTGAGTAT
64 GTGCCTTTGAGCTGAGTGT
* * * ** * *
148947 AGTCGAACTTGAAGGTCTTTTGTTGGCAAATAACCCTTTTTGCCTTGAGCTATGTTGCAAATGAT
1 AATCGAACTCG-AGGTCTTTTGTTGGCAGATAACCC-TTCCGCCTTGAGATATGCTGCAAATGAT
* * *
149012 GTG-TTTTGGAACTGAGCGT
64 GTGCCTTT-GAGCTGAGTGT
* * * * *
149031 AGTCGAACTCGAAGGTCTTTTATTAGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT
1 AATCGAACTCG-AGGTCTTTTGTTGGCAGATAACCCTTC-CGCCTTGAGATATGCTGCAAATGAT
* * * * *
149096 ATTCCTTGGAGCTGAATGG
64 GTGCCTTTGAGCTGAGTGT
* * * * * * *
149115 AATCGAACTCAAATGT-ATTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGCAAATGAT
1 AATCGAACTC-GAGGTCTTTTGTTGGCAGATAACCCTTC-CGCCTTGAGATATGCTGCAAATGAT
* ** **
149179 ATGCCTCGGAGCTGAGCCT
64 GTGCCTTTGAGCTGAGTGT
* * * * * *
149198 AATCGAACTCGAAGGTCTTTTGTAGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGAT
1 AATCGAACTCG-AGGTCTTTTGTTGGCAGATAACCCTTC-CGCCTTGAGATATGCTGCAAATGAT
* * *
149263 GTGTCTTGGAGCTGAGCGT
64 GTGCCTTTGAGCTGAGTGT
* * ** * * * *
149282 AGTCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTAACCGTGAGTTATTCTACAAATGAT
1 AATCGAACTCG-AGGTCTTTTGTTGGCAGATAACCCTTC-CGCCTTGAGATATGCTGCAAATGAT
* *
149347 GTGCCTTGGAGCTGAGCGT
64 GTGCCTTTGAGCTGAGTGT
* * * * * *
149366 AGA-CGAACTCTAAGGTCTTTT-TTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGA
1 A-ATCGAACTC-GAGGTCTTTTGTTGGCAGATAACCCTTC-CGCCTTGAGATATGCTGCAAATGA
* *
149429 TGTGCC-TTGGGCCTGAGCGT
63 TGTGCCTTTGAG-CTGAGTGT
* * * * * ** * *
149449 AGTCAAACTCGAAGGTCTTTTGTTGACAGATAACTCTTCTAGCAATGAGTTATGTTGCAAATGAT
1 AATCGAACTCG-AGGTCTTTTGTTGGCAGATAACCCTTC-CGCCTTGAGATATGCTGCAAATGAT
* * * *
149514 ATGCCTTGGATCTGAGCGT
64 GTGCCTTTGAGCTGAGTGT
* * * * * * * *
149533 AGTCAAACTCGAAGGCCTTTTGATGGAAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGAT
1 AATCGAACTCG-AGGTCTTTTGTTGGCAGATAACCCTTC-CGCCTTGAGATATGCTGCAAATGAT
* *
149598 GTGCCTTGGAGCTGAGCGT
64 GTGCCTTTGAGCTGAGTGT
* * ** *
149617 AGTCGAACTCGAAGGTCTCTTGTTGGCAGATAACCCTTCTAACCTTGAGTTATGCTGCAAATGAT
1 AATCGAACTCG-AGGTCTTTTGTTGGCAGATAACCCTTC-CGCCTTGAGATATGCTGCAAATGAT
* * *
149682 GTGCCTTGGAACTGAGCGT
64 GTGCCTTTGAGCTGAGTGT
* * * * *
149701 AGTCGAACTCAAAGGTC-TTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGAT
1 AATCGAACTC-GAGGTCTTTTGTTGGCAGATAACCCTTC-CGCCTTGAGATATGCTGCAAATGAT
* * *
149765 ATG-CTTTGGAGCTAAGCGT
64 GTGCCTTT-GAGCTGAGTGT
* * * * * * * * *
149784 AGTCAAATTCAAAGGTCTTTTGATGGAAAATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGAT
1 AATCGAACTC-GAGGTCTTTTGTTGGCAGATAACCCTTC-CGCCTTGAGATATGCTGCAAATGAT
* ** *
149849 GTGCCTTAGAGCTTCGCGT
64 GTGCCTTTGAGCTGAGTGT
* * * * *
149868 AATCGAACTCGAAGGTC---T-TTGGCAGATAGCCTTTCTTGCCTTGAGCTATGCTACAAATGAT
1 AATCGAACTCG-AGGTCTTTTGTTGGCAGATAACCCTTC-CGCCTTGAGATATGCTGCAAATGAT
*
149929 GTGCCTTTGAGTTGAGTGT
64 GTGCCTTTGAGCTGAGTGT
* * * * *
149948 AATCAAACTCAAAGGTCTTTTGTTGGCAGATAGCCATTCTCGCCTTGAGCTATGCTGCAAATGAT
1 AATCGAACTC-GAGGTCTTTTGTTGGCAGATAACCCTTC-CGCCTTGAGATATGCTGCAAATGAT
150013 GTGCCTTTGAGCTGAGTGT
64 GTGCCTTTGAGCTGAGTGT
* * * * * *
150032 AATCGAA-TGCAAATGTCTTTGGTTGGCAGATAACCCTTCTAGCTTTGAGTTATGCTGCAAATGA
1 AATCGAACT-C-GAGGTCTTTTGTTGGCAGATAACCCTTC-CGCCTTGAGATATGCTGCAAATGA
* * **
150096 TATGCCTTGGAGCTGAACGT
63 TGTGCCTTTGAGCTGAGTGT
* * * * * * * * *
150116 AGTCAAACTTGAAGGTCTTTTGGTGGAAAATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGAT
1 AATCGAACTCG-AGGTCTTTTGTTGGCAGATAACCCTTC-CGCCTTGAGATATGCTGCAAATGAT
* *
150181 GTGCCTTGGAGCTGAGCGT
64 GTGCCTTTGAGCTGAGTGT
* * * * * * *
150200 AGTCGAACTCAAAGGTC-TTTGCTGACAGATAACTCTTCTCGTCTTGAGTTATG
1 AATCGAACTC-GAGGTCTTTTGTTGGCAGATAACCCTTC-CGCCTTGAGATATG
150253 TTACAGATAG
Statistics
Matches: 1604, Mismatches: 312, Indels: 98
0.80 0.15 0.05
Matches are distributed among these distances:
71 51 0.03
72 3 0.00
73 1 0.00
74 1 0.00
77 1 0.00
78 1 0.00
80 64 0.04
81 2 0.00
82 7 0.00
83 253 0.16
84 1208 0.75
85 12 0.01
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (82 bp):
AATCGAACTCGAGGTCTTTTGTTGGCAGATAACCCTTCCGCCTTGAGATATGCTGCAAATGATGT
GCCTTTGAGCTGAGTGT
Found at i:148751 original size:168 final size:168
Alignment explanation
Indices: 148472--150220 Score: 1977
Period size: 168 Copynumber: 10.5 Consensus size: 168
148462 TTATTGACAT
* * *
148472 ATAACCCTTCTAGACTTGAGTTATGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * ** * *
148537 GAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAATTATGTTGCAAATGATGTGCCTTTGA
66 GAAGGTCTTTGGTTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGA
* * * * * *
148602 GCTAAGTGTAATCGAATTCAAAGGTCTTTTGTTGGCAG
131 GCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTGGCAG
* * * * *
148640 ATAACCCTTCTAGCCTTGATTTATGCTGTAAATGATATTCCTTGGAACTGAGCGTAGTCGAACTC
1 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * * *
148705 GAAGGTCTTTGGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGTCTTAGA
66 GAAGGTCTTTGGTTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGA
* *
148770 GCTGAGCGTAGTCAAACTTGAAGGTCTTTGGTTGGCAG
131 GCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTGGCAG
* * * * ** * * * * *
148808 ATAGCCCTTCTCGACTTAAGCGATGTTGCAGATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
** * * * * *
148873 GAAGGTCTTTTATTGACAGATAACCCTTCTAGCCTTGAGTTATGATGCAAATGATATGCCTTGGA
66 GAAGGTCTTTGGTTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGA
* ** * * *
148938 TCTGAGTATAGTCGAACTTGAAGGTCTTTTGTTGGCAA
131 GCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTGGCAG
* * * * ** *
148976 ATAACCCTTTTTGCCTTGAGCTATGTTGCAAATGATGTGTTTTGGAACTGAGCGTAGTCGAACTC
1 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
** * * * * *
149041 GAAGGTCTTTTATTAGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATTCCTTGGA
66 GAAGGTCTTTGGTTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGA
** * * * * * * *
149106 GCTGAATGGAATCGAACTCAAATGT-ATTTGTTGACAG
131 GCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTGGCAG
* * * * *
149143 ATAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATATGCCTCGGAGCTGAGCCTAATCGAACTC
1 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * * * *
149208 GAAGGTCTTTTGTAGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGTCTTGGA
66 GAAGGTCTTTGGTTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGA
*
149273 GCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAG
131 GCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTGGCAG
* * * * * *
149311 ATAGCCCTTCTAACCGTGAGTTATTCTACAAATGATGTGCCTTGGAGCTGAGCGTAGACGAACTC
1 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * * *
149376 TAAGGTCTTT-TTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGG-
66 GAAGGTCTTTGGTTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGA
*
149439 GCCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTGACAG
131 G-CTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTGGCAG
* ** * * * *
149478 ATAACTCTTCTAGCAATGAGTTATGTTGCAAATGATATGCCTTGGATCTGAGCGTAGTCAAACTC
1 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * *
149543 GAAGGCCTTTTGATGGAAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGA
66 GAAGGTCTTTGGTTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGA
* *
149608 GCTGAGCGTAGTCGAACTCGAAGGTCTCTTGTTGGCAG
131 GCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTGGCAG
* *
149646 ATAACCCTTCTAACCTTGAGTTATGCTGCAAATGATGTGCCTTGGAACTGAGCGTAGTCGAACTC
1 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * * * *
149711 AAAGGTCTTT-GTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATATGCTTTGGA
66 GAAGGTCTTTGGTTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGA
* * * * * *
149775 GCTAAGCGTAGTCAAATTCAAAGGTCTTTTGATGGAAA
131 GCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTGGCAG
* * ** *
149813 ATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTAGAGCTTCGCGTAATCGAACTC
1 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * *
149878 GAAGGTC--T--TTGGCAGATAGCCTTTCTTGCCTTGAGCTATGCTACAAATGATGTGCCTTTGA
66 GAAGGTCTTTGGTTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGA
* * * *
149939 GTTGAGTGTAATCAAACTCAAAGGTCTTTTGTTGGCAG
131 GCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTGGCAG
* * * * * * *
149977 ATAGCCATTCTCGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA-TG
1 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACT-
* * * * * *
150041 CAAATGTCTTTGGTTGGCAGATAACCCTTCTAGCTTTGAGTTATGCTGCAAATGATATGCCTTGG
65 CGAAGGTCTTTGGTTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGG
* * * * *
150106 AGCTGAACGTAGTCAAACTTGAAGGTCTTTTGGTGGAAA
130 AGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTGGCAG
* *
150145 ATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
*
150210 AAAGGTCTTTG
66 GAAGGTCTTTG
150221 CTGACAGATA
Statistics
Matches: 1341, Mismatches: 230, Indels: 20
0.84 0.14 0.01
Matches are distributed among these distances:
163 1 0.00
164 137 0.10
165 1 0.00
166 2 0.00
167 424 0.32
168 774 0.58
169 2 0.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (168 bp):
ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
GAAGGTCTTTGGTTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGA
GCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTGGCAG
Found at i:149243 original size:251 final size:251
Alignment explanation
Indices: 148472--150254 Score: 1982
Period size: 251 Copynumber: 7.1 Consensus size: 251
148462 TTATTGACAT
* * * * *
148472 ATAACCCTTCTAGACTTGAGTTATGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAACCCTTCTAGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * * * * *
148537 GAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAATTATGTTGCAAATGATGTGCCTTTGA
66 GAAGGTCTTTTGTTGGCAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGA
* * * * * *
148602 GCTAAGTGTAATCGAATTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGATTTATGCT
131 GCTGAGCGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCT
* * * * *
148667 GTAAATGATATTCCTTGGAACTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAA
195 GCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAA
* * * * * *
148724 ATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGTCTTAGAGCTGAGCGTAGTCAAACTT
1 ATAACCCTTCTAGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * * ** * * *
148789 GAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCGATGTTGCAGATGATGTGCCTTTGA
66 GAAGGTCTTTTGTTGGCAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGA
* * *
148854 GCTGAGTGTAATCGAACTCGAAGGTCTTTTATTGACAGATAACCCTTCTAGCCTTGAGTTATGAT
131 GCTGAGCGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCT
* * ** *
148919 GCAAATGATATGCCTTGGATCTGAGTATAGTCGAACTTGAAGGTCTTTTGTTGGCAA
195 GCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAA
* * ** *
148976 ATAACCCTTTTTGCCTTGAGCTATGTTGCAAATGATGTGTTTTGGAACTGAGCGTAGTCGAACTC
1 ATAACCCTTCTAGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * * *
149041 GAAGGTCTTTTATTAGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATTCCTTGGA
66 GAAGGTCTTTTGTTGGCAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGA
** * * * * *
149106 GCTGAATGGAATCGAACTCAAATGTATTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGTTG
131 GCTGAGCGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTG
* * * * *
149171 CAAATGATATGCCTCGGAGCTGAGCCTAATCGAACTCGAAGGTCTTTTGTAGGCAA
196 CAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAA
* * *
149227 ATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGTCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAACCCTTCTAGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * *
149292 GAAGGTCTTTTGTTGGCAGATAGCCCTTCTAACCGTGAGTTATTCTACAAATGATGTGCCTTGGA
66 GAAGGTCTTTTGTTGGCAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGA
* * * * * * * *
149357 GCTGAGCGTAGA-CGAACTCTAAGGTCTTTTTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTT
131 GCTGAGCGTA-ATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCT
* * *
149421 GCAAATGATGTGCCTTGG-GCCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTGACAG
195 GCAAATGATGTGCCTTGGAG-CTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAA
* ** * * * *
149478 ATAACTCTTCTAGCAATGAGTTATGTTGCAAATGATATGCCTTGGATCTGAGCGTAGTCAAACTC
1 ATAACCCTTCTAGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * *
149543 GAAGGCCTTTTGATGGAAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGA
66 GAAGGTCTTTTGTTGGCAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGA
* * *
149608 GCTGAGCGTAGTCGAACTCGAAGGTCTCTTGTTGGCAGATAACCCTTCTAACCTTGAGTTATGCT
131 GCTGAGCGTAATCGAACTCGAAGGTCT-TTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCT
* * *
149673 GCAAATGATGTGCCTTGGAACTGAGCGTAGTCGAACTCAAAGGTC-TTTGTTGGCAG
195 GCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAA
* * * * * * * *
149729 ATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATATGCTTTGGAGCTAAGCGTAGTCAAATTC
1 ATAACCCTTCTAGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * * * * *
149794 AAAGGTCTTTTGATGGAAAATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTAGA
66 GAAGGTCTTTTGTTGGCAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGA
** * * * * *
149859 GCTTCGCGTAATCGAACTCGAAGGTCTTTG--G-CAGATAGCCTTTCTTGCCTTGAGCTATGCTA
131 GCTGAGCGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTG
* * * * * * *
149921 CAAATGATGTGCCTTTGAGTTGAGTGTAATCAAACTCAAAGGTCTTTTGTTGGCAG
196 CAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAA
* * * * * * *
149977 ATAGCCATTCTCGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA-TG
1 ATAACCCTTCTAGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACT-
* * * * * *
150041 CAAATGTCTTTGGTTGGCAGATAACCCTTCTAGCTTTGAGTTATGCTGCAAATGATATGCCTTGG
65 CGAAGGTCTTTTGTTGGCAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGG
* * * * * * * *
150106 AGCTGAACGTAGTCAAACTTGAAGGTCTTTTGGTGGA-AAATAGCCCTTCTAGCCTTGAGCTATG
130 AGCTGAGCGTAATCGAACTCGAAGGTC-TTT-GTTGACAGATAACCCTTCTAGCCTTGAGTTATG
* * * *
150170 CTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGCTGACAG
193 CTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAA
* * * *
150228 ATAACTCTTCTCGTCTTGAGTTATGTT
1 ATAACCCTTCTAGCCTTGAGCTATGTT
150255 ACAGATAGTT
Statistics
Matches: 1318, Mismatches: 201, Indels: 25
0.85 0.13 0.02
Matches are distributed among these distances:
247 64 0.05
248 139 0.11
249 3 0.00
250 5 0.00
251 616 0.47
252 491 0.37
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (251 bp):
ATAACCCTTCTAGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
GAAGGTCTTTTGTTGGCAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGA
GCTGAGCGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTG
CAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAA
Found at i:151551 original size:95 final size:95
Alignment explanation
Indices: 151374--151633 Score: 317
Period size: 95 Copynumber: 2.7 Consensus size: 95
151364 GACTAGCTGG
* * * ** * *
151374 ATCCATAAAGTC-GGGTGTTTAACCAATTGCTCTAAAGGGACCGCTTAATATCATTGTA-TATAT
1 ATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAGAGGGACAAC-TCA-AGC-TT-TATTATAT
**
151437 ATTATAATCACCTTTATCAGGCTCGCTGAATATT
62 ATTATAATCACCTTTATCAGGCTAACTGAATATT
* * *
151471 ATCCATAAAGCCGGGGCGTTTAACCAGTTGCTCTAGAGGGACAACTCAAGCTTTATTTTATATTA
1 ATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTATATATTA
*
151536 TAATCACCTTTATCAGGCTAATTGAATATT
66 TAATCACCTTTATCAGGCTAACTGAATATT
* * *
151566 ATCCATAAAGCCAGGGTGTTTATCCAATTGCTCTAGTGGGACAACTCAAGCTTTATTATATATAT
1 ATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTATATAT-T
151631 ATA
65 ATA
151634 TATATATAAT
Statistics
Matches: 142, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
94 2 0.01
95 94 0.66
96 6 0.04
97 13 0.09
98 27 0.19
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.34
Consensus pattern (95 bp):
ATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTATATATTA
TAATCACCTTTATCAGGCTAACTGAATATT
Found at i:155719 original size:32 final size:31
Alignment explanation
Indices: 155671--155742 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 31
155661 AAAAGGAAAC
* *
155671 AAAAAAATAGAAAATAAGA-GAAAAGGAAAAT
1 AAAAAAATAAAAAATAAGATGAAAA-AAAAAT
* *
155702 CAAAAAATAAAATAATAATATGAAAAAAAAAT
1 AAAAAAATAAAA-AATAAGATGAAAAAAAAAT
155734 AAAAAAATA
1 AAAAAAATA
155743 GAACCATGCA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 10 0.29
32 19 0.56
33 5 0.15
ACGTcount: A:0.76, C:0.01, G:0.08, T:0.14
Consensus pattern (31 bp):
AAAAAAATAAAAAATAAGATGAAAAAAAAAT
Found at i:156996 original size:38 final size:36
Alignment explanation
Indices: 156932--157021 Score: 92
Period size: 38 Copynumber: 2.4 Consensus size: 36
156922 ATATATTATT
* * *
156932 TATTTTCAAAAACCTTGTTTTCAAAACCATACTACATA
1 TATTTTCAAAAACATTATTTTCAAAACCATA-TA-ACA
* *
156970 TATTTTCCAAAAA-ATTATTTTTAAAACTATATAACA
1 TATTTT-CAAAAACATTATTTTCAAAACCATATAACA
*
157006 TATTTTCAAAAGCATT
1 TATTTTCAAAAACATT
157022 TTCAAAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
35 5 0.11
36 11 0.25
37 2 0.05
38 20 0.45
39 6 0.14
ACGTcount: A:0.42, C:0.16, G:0.02, T:0.40
Consensus pattern (36 bp):
TATTTTCAAAAACATTATTTTCAAAACCATATAACA
Found at i:157036 original size:13 final size:13
Alignment explanation
Indices: 157020--157044 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
157010 TTCAAAAGCA
157020 TTTTCAAAAAATG
1 TTTTCAAAAAATG
157033 TTTTCAAAAAAT
1 TTTTCAAAAAAT
157045 TATATATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (13 bp):
TTTTCAAAAAATG
Found at i:157089 original size:25 final size:24
Alignment explanation
Indices: 157053--157100 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
157043 ATTATATATA
*
157053 TATATATATATATTTTTTAAAAAC
1 TATATATATATATGTTTTAAAAAC
*
157077 TATATAGTATATATGTTTTCAAAA
1 TATATA-TATATATGTTTTAAAAA
157101 TGCTTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (24 bp):
TATATATATATATGTTTTAAAAAC
Found at i:157219 original size:24 final size:25
Alignment explanation
Indices: 157177--157233 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
157167 TTTCAAAATG
157177 ATTTC-AAACTATATAATATATACAT
1 ATTTCAAAACTATATAATAT-TACAT
*
157202 -TTTCAAAACTATAT-ATATTATAT
1 ATTTCAAAACTATATAATATTACAT
157225 ATTTCAAAA
1 ATTTCAAAA
157234 TAATTTGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 4 0.14
24 16 0.55
25 9 0.31
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTTCAAAACTATATAATATTACAT
Found at i:157257 original size:2 final size:2
Alignment explanation
Indices: 157246--157285 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
157236 ATTTGAAAAC
157246 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
157286 GAAAAAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:163062 original size:184 final size:180
Alignment explanation
Indices: 162796--163138 Score: 485
Period size: 184 Copynumber: 1.9 Consensus size: 180
162786 ATTCTAAGGA
** * *
162796 AAAATATATTAAAATAATTTTTATAAAAACTAAAGTAAATATATATATTTTTAGGGTTTTATAAG
1 AAAATATATTAAAATAATTTGAATAAAAACTAAAGTAAATATATATATATATA-GGTTTTATAAG
162861 TAAGGTATTTATTATTTA-AAAATATCAGAAAATAACATCTAGTTACTTTAAGACAACCTCTTTC
65 TAAGGTATTTATTATTTATAAAATATCAGAAAATAACATCTAGTTACTTTAAGACAACCTCTTT-
*
162925 TTATTATATATAAAAAATAAAAAAATATTAATAAAATATGATAATTATTCCTAAG
129 TT-TAATAT-TAAAAAATAAAAAAAT-TTAATAAAATATGATAATTATTCCTAAG
*
162980 AAAATCATATTAAAATAATTTGAAT-AAAACTAAAGTAAATATATATATATATA-TTCTTTATAA
1 AAAAT-ATATTAAAATAATTTGAATAAAAACTAAAGTAAATATATATATATATAGGT-TTTATAA
* * *
163043 GTAGGGTATTTATTTATTTATTTAAAATATCAGAAAATGACATCTAGTTACTTTAAGACAACTTC
64 GTAAGGTATTTA-TTATTTA--TAAAATATCAGAAAATAACATCTAGTTACTTTAAGACAACCTC
*
163108 TTTTTTAATATTAAAAAATAAATAAATTTAA
126 TTTTTTAATATTAAAAAATAAAAAAATTTAA
163139 ATCTTTCACA
Statistics
Matches: 143, Mismatches: 10, Indels: 13
0.86 0.06 0.08
Matches are distributed among these distances:
182 1 0.01
183 22 0.15
184 53 0.37
185 22 0.15
186 2 0.01
187 43 0.30
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (180 bp):
AAAATATATTAAAATAATTTGAATAAAAACTAAAGTAAATATATATATATATAGGTTTTATAAGT
AAGGTATTTATTATTTATAAAATATCAGAAAATAACATCTAGTTACTTTAAGACAACCTCTTTTT
TAATATTAAAAAATAAAAAAATTTAATAAAATATGATAATTATTCCTAAG
Found at i:164468 original size:3 final size:3
Alignment explanation
Indices: 164460--164563 Score: 73
Period size: 3 Copynumber: 34.0 Consensus size: 3
164450 AATGGGCATG
** * * **
164460 TAA TAA TAA TATA TTT TAT TAA TAA TATA TAC TAA TAA TAA TTT TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
* * * * * * *
164507 TAA TAA TAA AAA TAA TAT TAA TAT TAA TAT TAA TAT TAA TAA AAA GAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
164555 TAA TAA TAA
1 TAA TAA TAA
164564 ATAAATAACA
Statistics
Matches: 76, Mismatches: 23, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
3 71 0.93
4 5 0.07
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:164484 original size:16 final size:16
Alignment explanation
Indices: 164460--164514 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 16
164450 AATGGGCATG
164460 TAATAATAATATATTT
1 TAATAATAATATATTT
*
164476 TATTAATAATATA---
1 TAATAATAATATATTT
*
164489 TACTAATAATA-ATTT
1 TAATAATAATATATTT
164504 TAATAATAATA
1 TAATAATAATA
164515 AAAATAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 1 0.03
13 10 0.30
15 10 0.30
16 12 0.36
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATAATAATATATTT
Found at i:164540 original size:33 final size:33
Alignment explanation
Indices: 164483--164563 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 33
164473 TTTTATTAAT
* *
164483 AATATATACTAATAATAATTTTAATAATAATAAA
1 AATA-ATAATAATAATAATATTAATAATAATAAA
* * *
164517 AATAATATTAATATTAATATTAATATTAATAAA
1 AATAATAATAATAATAATATTAATAATAATAAA
*
164550 AAGAATAATAATAA
1 AATAATAATAATAA
164564 ATAAATAACA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 36 0.90
34 4 0.10
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (33 bp):
AATAATAATAATAATAATATTAATAATAATAAA
Found at i:164915 original size:123 final size:122
Alignment explanation
Indices: 164694--165808 Score: 1425
Period size: 123 Copynumber: 9.1 Consensus size: 122
164684 TTGATTAAGA
* * * * *
164694 TGGAAATGTTGATGTTGATCTATCTCCTTCTGTGAT-GAATCGAGC-TAAGGTTGAACAAGTTCT
1 TGGAAATGTT-ATGTTGCTCTATCTCCTTCTGCGATAGAATCAAGCAAAAGGTTGAATAAGTTCT
*
164757 TCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTC
65 TCAGACTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTC
* * *
164815 TGGAAATGTTAATGTTTCTCTATCTCCTTCTGCGATAGAATCGAGTAAAAGGTTGAATAAGTTCT
1 TGGAAATGTT-ATGTTGCTCTATCTCCTTCTGCGATAGAATCAAGCAAAAGGTTGAATAAGTTCT
* *
164880 TCAGATTATGAACTTCTTCTTCCTCTTCA-ATTGAGTTCTTCTTATTACGAAGTCCTTC
65 TCAGACTATGAACTTCTTCTTCCTCTTCAGA-TGAGTTCTTCTTATTACGAACTCCTTC
** * * * * *
164938 TGGAAACCTTGATGATGTTATATCTCCTTCTGCGATAGAATCGAGAAAAAGGTTGAATAAGTTCT
1 TGGAAATGTT-ATGTTGCTCTATCTCCTTCTGCGATAGAATCAAGCAAAAGGTTGAATAAGTTCT
* *
165003 TCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCATTC
65 TCAGACTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTC
* * * ** *
165061 TGGAAACGTTGATGCTGCTCTACCTCCTTCTATGATAGAATCGAGCAAAAGGTTGAATAAGTTCT
1 TGGAAATGTT-ATGTTGCTCTATCTCCTTCTGCGATAGAATCAAGCAAAAGGTTGAATAAGTTCT
* * * * *
165126 TCATATTATGAACTTTTTCTTCCTCTTCAAATGAGTTCTTCCTATTACGAACTCCTTC
65 TCAGACTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTC
* * * * *
165184 TAGAAATGGTTCTGCTGCTCTATCTCCTTCTGCGATAGAGTCAAGAAAAAGGTTGAATAAGTTCT
1 TGGAAAT-GTTATGTTGCTCTATCTCCTTCTGCGATAGAATCAAGCAAAAGGTTGAATAAGTTCT
* * * *
165249 TCAGAGTATGAACTTCTTCTTCATCTTCAGAGGAGTTCTTCTTATTACGAACT-TTGTC
65 TCAGACTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCT-TC
* *
165307 TGGAAATGGTTATGATGCTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGTTGAATAAGTTCT
1 TGGAAAT-GTTATGTTGCTCTATCTCCTTCTGCGATAGAATCAAGCAAAAGGTTGAATAAGTTCT
* * * *
165372 TCATACTATGAACTTCTTCTTCCTCTTCAGAGGAGTTCTTCTTATTACGAACTCTTTT
65 TCAGACTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTC
* * * *
165430 TGGAAATGGTTATGTTGCTCTATCTTCTTCTGTGATA-AAGTCAAACAAAACGTTGAATAAGTTC
1 TGGAAAT-GTTATGTTGCTCTATCTCCTTCTGCGATAGAA-TCAAGCAAAAGGTTGAATAAGTTC
*
165494 TTCAGACTATGAACTTCTTCTTACTCTTCAGATGAGTTCTTCTTATTACGAACT-CTATC
64 TTCAGACTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCT-TC
* * * * * *
165553 TAGAAATGATTATGCTGCTCTATCTCCTTCTACGATAGAGTCAAGCAAAAGTTTAAATAAGTTCT
1 TGGAAATG-TTATGTTGCTCTATCTCCTTCTGCGATAGAATCAAGCAAAAGGTTGAATAAGTTCT
* * * * *
165618 TCAGACTATGAACATCTTCTTCCTATTCAAAGGAGTTCTTATTATTACGAACT-CTGTC
65 TCAGACTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCT-TC
* * * *
165676 TGGAAATGATTTTGTTGATCTATCTCCTTCTACGATAGAGTCAAGCAAAAGGTTGAATAAGTTCT
1 TGGAAATG-TTATGTTGCTCTATCTCCTTCTGCGATAGAATCAAGCAAAAGGTTGAATAAGTTCT
* * * *
165741 TCATACTATGAACTTCTTCTTTCTCTTCAGAGGAGTTCTTCTTATTACGAACTCTTTC
65 TCAGACTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTC
165799 TGGAAATGTT
1 TGGAAATGTT
165809 GATCCCTCAA
Statistics
Matches: 885, Mismatches: 97, Indels: 23
0.88 0.10 0.02
Matches are distributed among these distances:
121 32 0.04
122 15 0.02
123 830 0.94
124 8 0.01
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.38
Consensus pattern (122 bp):
TGGAAATGTTATGTTGCTCTATCTCCTTCTGCGATAGAATCAAGCAAAAGGTTGAATAAGTTCTT
CAGACTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTC
Found at i:165419 original size:369 final size:368
Alignment explanation
Indices: 164694--165811 Score: 1595
Period size: 369 Copynumber: 3.0 Consensus size: 368
164684 TTGATTAAGA
* * *
164694 TGGAAATGTTGATGTTGATCTATCTCCTTCTGTGAT-GAATCGAGC-TAAGGTTGAACAAGTTCT
1 TGGAAATGTTGATGTTGCTCTATCTCCTTCTGTGATAGAATCGAGCAAAAGGTTGAATAAGTTCT
*
164757 TCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAAT
66 TCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTAGAAAT
* * * * * *
164822 -GTTAATGTTTCTCTATCTCCTTCTGCGATAGAATCGAGTAAAAGGTTGAATAAGTTCTTCAGAT
131 GGTT-ATGCTGCTCTATCTCCTTCTGCGATAGAGTCAAGAAAAAGGTTGAATAAGTTCTTCAGAC
* * **
164886 TATGAACTTCTTCTTCCTCTTCAATTGAGTTCTTCTTATTACGAAGTCCT-TCTGGAAA-CCTTG
195 TATGAACTTCTTCTTCCTCTTCAA-GGAGTTCTTCTTATTACGAACT-CTGTCTGGAAATGATT-
* * * * * * *
164949 ATGATGTTATATCTCCTTCTGCGATAGAATCGAGAAAAAGGTTGAATAAGTTCTTCAGATTATGA
257 ATGATGATCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGTTGAATAAGTTCTTCATACTATGA
* *
165014 ACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCATTC
322 ACTTCTTCTTCCTCTTCAGAGGAGTTCTTCTTATTACGAACTCTTTC
* * * *
165061 TGGAAACGTTGATGCTGCTCTACCTCCTTCTATGATAGAATCGAGCAAAAGGTTGAATAAGTTCT
1 TGGAAATGTTGATGTTGCTCTATCTCCTTCTGTGATAGAATCGAGCAAAAGGTTGAATAAGTTCT
* * * *
165126 TCATATTATGAACTTTTTCTTCCTCTTCAAATGAGTTCTTCCTATTACGAACTCCTTCTAGAAAT
66 TCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTAGAAAT
* *
165191 GGTTCTGCTGCTCTATCTCCTTCTGCGATAGAGTCAAGAAAAAGGTTGAATAAGTTCTTCAGAGT
131 GGTTATGCTGCTCTATCTCCTTCTGCGATAGAGTCAAGAAAAAGGTTGAATAAGTTCTTCAGACT
* * *
165256 ATGAACTTCTTCTTCATCTTCAGAGGAGTTCTTCTTATTACGAACTTTGTCTGGAAATGGTTATG
196 ATGAACTTCTTCTTCCTCTTCA-AGGAGTTCTTCTTATTACGAACTCTGTCTGGAAATGATTATG
*
165321 ATGCTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGTTGAATAAGTTCTTCATACTATGAACT
260 ATGATCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGTTGAATAAGTTCTTCATACTATGAACT
*
165386 TCTTCTTCCTCTTCAGAGGAGTTCTTCTTATTACGAACTCTTTT
325 TCTTCTTCCTCTTCAGAGGAGTTCTTCTTATTACGAACTCTTTC
* * * *
165430 TGGAAATGGTT-ATGTTGCTCTATCTTCTTCTGTGATA-AAGTCAAACAAAACGTTGAATAAGTT
1 TGGAAAT-GTTGATGTTGCTCTATCTCCTTCTGTGATAGAA-TCGAGCAAAAGGTTGAATAAGTT
* *
165493 CTTCAGACTATGAACTTCTTCTTACTCTTCAGATGAGTTCTTCTTATTACGAACT-CTATCTAGA
64 CTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCT-TCTAGA
* * * * *
165557 AATGATTATGCTGCTCTATCTCCTTCTACGATAGAGTCAAGCAAAAGTTTAAATAAGTTCTTCAG
128 AATGGTTATGCTGCTCTATCTCCTTCTGCGATAGAGTCAAGAAAAAGGTTGAATAAGTTCTTCAG
* * *
165622 ACTATGAACATCTTCTTCCTATTCAAAGGAGTTCTTATTATTACGAACTCTGTCTGGAAATGATT
193 ACTATGAACTTCTTCTTCCTCTTC-AAGGAGTTCTTCTTATTACGAACTCTGTCTGGAAATGATT
* * *
165687 TTGTTGATCTATCTCCTTCTACGATAGAGTCAAGCAAAAGGTTGAATAAGTTCTTCATACTATGA
257 ATGATGATCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGTTGAATAAGTTCTTCATACTATGA
*
165752 ACTTCTTCTTTCTCTTCAGAGGAGTTCTTCTTATTACGAACTCTTTC
322 ACTTCTTCTTCCTCTTCAGAGGAGTTCTTCTTATTACGAACTCTTTC
165799 TGGAAATGTTGAT
1 TGGAAATGTTGAT
165812 CCCTCAAGTG
Statistics
Matches: 672, Mismatches: 68, Indels: 20
0.88 0.09 0.03
Matches are distributed among these distances:
367 31 0.05
368 17 0.03
369 614 0.91
370 10 0.01
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.38
Consensus pattern (368 bp):
TGGAAATGTTGATGTTGCTCTATCTCCTTCTGTGATAGAATCGAGCAAAAGGTTGAATAAGTTCT
TCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTAGAAAT
GGTTATGCTGCTCTATCTCCTTCTGCGATAGAGTCAAGAAAAAGGTTGAATAAGTTCTTCAGACT
ATGAACTTCTTCTTCCTCTTCAAGGAGTTCTTCTTATTACGAACTCTGTCTGGAAATGATTATGA
TGATCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGTTGAATAAGTTCTTCATACTATGAACTT
CTTCTTCCTCTTCAGAGGAGTTCTTCTTATTACGAACTCTTTC
Found at i:167793 original size:19 final size:19
Alignment explanation
Indices: 167769--167807 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
167759 TAGTAACTTC
167769 TTTTTCT-TTTTCATTTCTT
1 TTTTTCTCTTTTC-TTTCTT
167788 TTTTTCTCTTTTCTTTCTT
1 TTTTTCTCTTTTCTTTCTT
167807 T
1 T
167808 CCTTTTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTCTCTTTTCTTTCTT
Found at i:167802 original size:15 final size:14
Alignment explanation
Indices: 167782--167820 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
167772 TTCTTTTTCA
*
167782 TTTCTTTTTTTCTCT
1 TTTCTTTCTTTC-CT
167797 TTTCTTTCTTTCCT
1 TTTCTTTCTTTCCT
167811 TTT-TTTCTTT
1 TTTCTTTCTTT
167821 TTTATATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 7 0.30
14 5 0.22
15 11 0.48
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTCTTTCTTTCCT
Found at i:167812 original size:24 final size:24
Alignment explanation
Indices: 167777--167823 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
167767 TCTTTTTCTT
167777 TTTCATTTCTTTTTTTCTCTTTTC
1 TTTCATTTCTTTTTTTCTCTTTTC
*
167801 TTTC-TTTCCTTTTTTTCTTTTTT
1 TTTCATTT-CTTTTTTTCTCTTTT
167824 ATATTTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (24 bp):
TTTCATTTCTTTTTTTCTCTTTTC
Found at i:167823 original size:8 final size:8
Alignment explanation
Indices: 167782--167823 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
167772 TTCTTTTTCA
167782 TTTCTTTT
1 TTTCTTTT
*
167790 TTTC-TCT
1 TTTCTTTT
167797 TTTCTTTCT
1 TTTCTTT-T
*
167806 TTCCTTTT
1 TTTCTTTT
167814 TTTCTTTT
1 TTTCTTTT
167822 TT
1 TT
167824 ATATTTGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 6 0.21
8 15 0.54
9 7 0.25
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTCTTTT
Found at i:168715 original size:18 final size:18
Alignment explanation
Indices: 168692--168726 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
168682 TGTAATGTTG
*
168692 GGTGTGTAATCTGACCAA
1 GGTGTGTAATCAGACCAA
168710 GGTGTGTAATCAGACCA
1 GGTGTGTAATCAGACCA
168727 GGATTTTGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.26
Consensus pattern (18 bp):
GGTGTGTAATCAGACCAA
Found at i:170307 original size:14 final size:14
Alignment explanation
Indices: 170288--170317 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
170278 AATGCAACTG
*
170288 TGCAAAAATGCAAA
1 TGCAAAAATGAAAA
170302 TGCAAAAATGAAAA
1 TGCAAAAATGAAAA
170316 TG
1 TG
170318 TAAATGCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.10, G:0.17, T:0.17
Consensus pattern (14 bp):
TGCAAAAATGAAAA
Found at i:170317 original size:20 final size:20
Alignment explanation
Indices: 170292--170359 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
170282 CAACTGTGCA
170292 AAAATGCAAATGCAAAAATG
1 AAAATGCAAATGCAAAAATG
* **
170312 AAAATGTAAATGCAAACGT-
1 AAAATGCAAATGCAAAAATG
* *
170331 AAAAGTACATATGC-AAAATG
1 AAAA-TGCAAATGCAAAAATG
170351 AAAATGCAA
1 AAAATGCAA
170360 CGAAGGAGTT
Statistics
Matches: 36, Mismatches: 10, Indels: 5
0.71 0.20 0.10
Matches are distributed among these distances:
19 10 0.28
20 26 0.72
ACGTcount: A:0.57, C:0.10, G:0.15, T:0.18
Consensus pattern (20 bp):
AAAATGCAAATGCAAAAATG
Found at i:171869 original size:36 final size:36
Alignment explanation
Indices: 171822--171892 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
171812 GACGTTTTTT
171822 AAAATTACTCCCCCTTACTTTAACACTTACTCCTCG
1 AAAATTACTCCCCCTTACTTTAACACTTACTCCTCG
171858 AAAATTACTCCCCCTTACTTTAACACTTACTCCTC
1 AAAATTACTCCCCCTTACTTTAACACTTACTCCTC
171893 TTTAAAACTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.28, C:0.37, G:0.01, T:0.34
Consensus pattern (36 bp):
AAAATTACTCCCCCTTACTTTAACACTTACTCCTCG
Found at i:177932 original size:91 final size:91
Alignment explanation
Indices: 177775--177957 Score: 357
Period size: 91 Copynumber: 2.0 Consensus size: 91
177765 ACCTCTATGA
177775 TTGTAGTTTTTAAAACTTTTTCTAGCAAAGTTGGATTTTGAATTTTCTCCACTTTCAAAACATTT
1 TTGTAGTTTTTAAAACTTTTTCTAGCAAAGTTGGATTTTGAATTTTCTCCACTTTCAAAACATTT
177840 TGTTCCAACTTTATCAAAAGAAGCTT
66 TGTTCCAACTTTATCAAAAGAAGCTT
*
177866 TTGTAGTTTTTAAAACTTTTTCTAGCAAAGTTGGATTTTGAATTTTCTCCACTTTCAAAACGTTT
1 TTGTAGTTTTTAAAACTTTTTCTAGCAAAGTTGGATTTTGAATTTTCTCCACTTTCAAAACATTT
177931 TGTTCCAACTTTATCAAAAGAAGCTT
66 TGTTCCAACTTTATCAAAAGAAGCTT
177957 T
1 T
177958 AAGATCATCA
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.44
Consensus pattern (91 bp):
TTGTAGTTTTTAAAACTTTTTCTAGCAAAGTTGGATTTTGAATTTTCTCCACTTTCAAAACATTT
TGTTCCAACTTTATCAAAAGAAGCTT
Found at i:182759 original size:64 final size:64
Alignment explanation
Indices: 182628--182786 Score: 178
Period size: 64 Copynumber: 2.5 Consensus size: 64
182618 ATGCACACCC
* * ** * *
182628 AACATCGAA-GCTATTTTATATACCGATGCACAGCCATGCATCGATACACTTCTATTTTTATTGA
1 AACATCGAATGC-ATTTTGTATACCGATACACAGCCATGCATCGATACACTTCTAGCTTTAATAA
* * *
182692 AACATCGAATGCATTTTGTGTACCGATACACATCCTATGCATCGATACAC-TCTGGCTTTAATAA
1 AACATCGAATGCATTTTGTATACCGATACACAGCC-ATGCATCGATACACTTCTAGCTTTAATAA
* * *
182756 AACATCGAATGCAATTAGTTTACCGATACAC
1 AACATCGAATGCATTTTGTATACCGATACAC
182787 CCCAAGTGTA
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
64 65 0.80
65 16 0.20
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (64 bp):
AACATCGAATGCATTTTGTATACCGATACACAGCCATGCATCGATACACTTCTAGCTTTAATAA
Found at i:188605 original size:44 final size:43
Alignment explanation
Indices: 188538--188658 Score: 179
Period size: 44 Copynumber: 2.8 Consensus size: 43
188528 TTTGTGCAAA
* *
188538 GTGCATCGATACACTATCGAAGTGTACCTATGCATTCCTTGAAT
1 GTGCATCGATACACTAT-GAAGTGTACCGATACATTCCTTGAAT
*
188582 GTGCATCGATACACTATGTAAGTGCACCGATACATTCCTTGAAT
1 GTGCATCGATACACTATG-AAGTGTACCGATACATTCCTTGAAT
* *
188626 GTGTATCGATACACTATGCAGTGTACCGATACA
1 GTGCATCGATACACTATGAAGTGTACCGATACA
188659 CTATGTAGTG
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
43 14 0.20
44 56 0.80
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (43 bp):
GTGCATCGATACACTATGAAGTGTACCGATACATTCCTTGAAT
Found at i:188655 original size:20 final size:20
Alignment explanation
Indices: 188626--188679 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
188616 TTCCTTGAAT
188626 GTGTATCGATACACTATGCA
1 GTGTATCGATACACTATGCA
* *
188646 GTGTACCGATACACTATGTA
1 GTGTATCGATACACTATGCA
188666 GTGTATCGATACAC
1 GTGTATCGATACAC
188680 GCATCGGGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (20 bp):
GTGTATCGATACACTATGCA
Found at i:188679 original size:40 final size:42
Alignment explanation
Indices: 188542--188679 Score: 131
Period size: 44 Copynumber: 3.2 Consensus size: 42
188532 TGCAAAGTGC
* * * *
188542 ATCGATACACTATCG-AAGTGTACCTATGCATTCCTTGAATGTGC
1 ATCGATACACTAT-GTAAGTGCACCGATACA-T-CTTGAATGTGT
188586 ATCGATACACTATGTAAGTGCACCGATACATTCCTTGAATGTGT
1 ATCGATACACTATGTAAGTGCACCGATACA-T-CTTGAATGTGT
* * *
188630 ATCGATACACTATG-CAGTGTACCGATACA-CTATGTA-GTGT
1 ATCGATACACTATGTAAGTGCACCGATACATCT-TGAATGTGT
188670 ATCGATACAC
1 ATCGATACAC
188680 GCATCGGGTT
Statistics
Matches: 85, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
40 16 0.19
41 3 0.04
43 14 0.16
44 52 0.61
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (42 bp):
ATCGATACACTATGTAAGTGCACCGATACATCTTGAATGTGT
Found at i:193369 original size:2 final size:2
Alignment explanation
Indices: 193362--193395 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
193352 TTTTACCCTA
193362 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
193396 GGTAGGGACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:194060 original size:22 final size:22
Alignment explanation
Indices: 194035--194093 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
194025 AGTGGCCCTC
194035 GGTGAGTCACCGAAGCTACAAT
1 GGTGAGTCACCGAAGCTACAAT
194057 GGTGAGTCACCGAAGCTACAAT
1 GGTGAGTCACCGAAGCTACAAT
* *
194079 TGTGACTCACCGAAG
1 GGTGAGTCACCGAAG
194094 GGATACAACG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.19
Consensus pattern (22 bp):
GGTGAGTCACCGAAGCTACAAT
Found at i:194439 original size:3 final size:3
Alignment explanation
Indices: 194431--194530 Score: 69
Period size: 3 Copynumber: 33.0 Consensus size: 3
194421 AATGGGCCTG
** * * *
194431 TAA TAA TAA TATA TTT TAT TAA TAA TATA TAC TAA TAA TAA TAT TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
* * * * *
194478 TAA TAA -AA AAA TAA TGA TAA TAA TAT TAA TAT TAA CAA -AA TGAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
194522 TAA TAA TAA
1 TAA TAA TAA
194531 ATAAATAAAT
Statistics
Matches: 76, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
2 4 0.05
3 64 0.84
4 8 0.11
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:194455 original size:16 final size:16
Alignment explanation
Indices: 194431--194483 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
194421 AATGGGCCTG
**
194431 TAATAATAATATATTT
1 TAATAATAATATATAC
*
194447 TATTAATAATATATAC
1 TAATAATAATATATAC
*
194463 TAATAATAATAT-TAA
1 TAATAATAATATATAC
194478 TAATAA
1 TAATAA
194484 AAAAATAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
15 8 0.25
16 24 0.75
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAATAATATATAC
Found at i:194497 original size:29 final size:30
Alignment explanation
Indices: 194463--194538 Score: 102
Period size: 29 Copynumber: 2.6 Consensus size: 30
194453 TAATATATAC
194463 TAATAATAATATTAATAATAAAAAAAT-AA
1 TAATAATAATATTAATAATAAAAAAATGAA
* * *
194492 TGATAATAATATTAATATTAACAAAATGAA
1 TAATAATAATATTAATAATAAAAAAATGAA
*
194522 TAATAATAA-ATAAATAA
1 TAATAATAATATTAATAA
194539 ATAATGGATA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 30 0.75
30 10 0.25
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (30 bp):
TAATAATAATATTAATAATAAAAAAATGAA
Found at i:197375 original size:23 final size:23
Alignment explanation
Indices: 197349--197394 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
197339 ATTTGCGTAA
*
197349 AATAATTTGCTATTTAGAAACAT
1 AATAATTTACTATTTAGAAACAT
197372 AATAATTTACTATTTAGAAACAT
1 AATAATTTACTATTTAGAAACAT
197395 GCATTGCGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.39
Consensus pattern (23 bp):
AATAATTTACTATTTAGAAACAT
Found at i:199281 original size:3 final size:3
Alignment explanation
Indices: 199273--199299 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
199263 AATGTAAAAT
199273 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
199300 TTTTTATAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:201735 original size:17 final size:17
Alignment explanation
Indices: 201710--201761 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
201700 CCGGTTTCGG
201710 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
201727 TTTTTAAAAAACCGG-T
1 TTTTAAAAAAACCGGTT
* * *
201743 TATAAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
201760 TT
1 TT
201762 AATATTCCAG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
16 12 0.43
17 16 0.57
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:201958 original size:21 final size:21
Alignment explanation
Indices: 201934--201986 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
201924 ACACTTAGGG
201934 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
*
201955 AACCGATTCCCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
201976 TACCGATTCCC
1 AACCGATTCCC
201987 CCACGCTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:202203 original size:13 final size:13
Alignment explanation
Indices: 202182--202236 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
202172 AAGTTCGATA
*
202182 AATTCAAATACTT
1 AATTGAAATACTT
202195 AATTGAAATACTT
1 AATTGAAATACTT
* *
202208 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
202222 AATTGAAATACTT
1 AATTGAAATACTT
202235 AA
1 AA
202237 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:202318 original size:32 final size:33
Alignment explanation
Indices: 202222--202320 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
202212 AACTCAACAT
* * *
202222 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
202255 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
202288 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
202320 A
1 A
202321 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:202339 original size:21 final size:21
Alignment explanation
Indices: 202315--202354 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
202305 ACTTCAAGTT
202315 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
202336 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
202355 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:204679 original size:11 final size:12
Alignment explanation
Indices: 204658--204703 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
204648 TCCGGATAAA
204658 AACCGGTTTTTT
1 AACCGGTTTTTT
204670 AACCGGTTTTTTT
1 AACCGG-TTTTTT
204683 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
204697 ATCCGGT
1 AACCGGT
204704 AAAAAAACAG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 6 0.20
15 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:204688 original size:15 final size:14
Alignment explanation
Indices: 204657--204696 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
204647 TTCCGGATAA
204657 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
204670 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
204683 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
204697 ATCCGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:204979 original size:28 final size:29
Alignment explanation
Indices: 204934--204989 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
204924 CATCGTAGGG
*
204934 TTATTATTTTTTTAATAGTCTGGGCGATA
1 TTATTATTTTTTTAATAGTCTGAGCGATA
*
204963 TTATT-TTTTTTTAATAGTGTGAGCGAT
1 TTATTATTTTTTTAATAGTCTGAGCGAT
204990 TATAAGATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.23, C:0.05, G:0.18, T:0.54
Consensus pattern (29 bp):
TTATTATTTTTTTAATAGTCTGAGCGATA
Found at i:205833 original size:32 final size:32
Alignment explanation
Indices: 205792--205890 Score: 153
Period size: 32 Copynumber: 3.1 Consensus size: 32
205782 ATCCAACAAA
* *
205792 CACACTATCCTTGAGTGAAGTTCATACAATAT
1 CACACTATCCTTAAGTGAAGTTCATACAAGAT
205824 CACACTATCCTTAAGTGAAGTTCATACAAGAT
1 CACACTATCCTTAAGTGAAGTTCATACAAGAT
* * *
205856 CACACTATCCTTAAGTGAAATTCGTATAAGAT
1 CACACTATCCTTAAGTGAAGTTCATACAAGAT
205888 CAC
1 CAC
205891 GTGTGTTCGT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.29
Consensus pattern (32 bp):
CACACTATCCTTAAGTGAAGTTCATACAAGAT
Found at i:209933 original size:26 final size:26
Alignment explanation
Indices: 209899--209952 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
209889 TTTCAGGTCA
209899 AACATGATGGGCTAAAAACCCGACTC
1 AACATGATGGGCTAAAAACCCGACTC
209925 AACATGATGGGCTAAAAACCCGACTC
1 AACATGATGGGCTAAAAACCCGACTC
209951 AA
1 AA
209953 ACTAACCTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.41, C:0.26, G:0.19, T:0.15
Consensus pattern (26 bp):
AACATGATGGGCTAAAAACCCGACTC
Found at i:220337 original size:2 final size:2
Alignment explanation
Indices: 220330--220364 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
220320 TTTAGTCCAT
220330 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
220365 GGAGAAAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:225093 original size:2 final size:2
Alignment explanation
Indices: 225086--225112 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
225076 TTTTACCGAA
225086 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
225113 CAATTGGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:234314 original size:21 final size:23
Alignment explanation
Indices: 234269--234318 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
234259 AGGGGTTATT
234269 AAAAATAAAAGTAATAAACTCAC
1 AAAAATAAAAGTAATAAACTCAC
* *
234292 AAAAATACAATTAA-AAA-TCAC
1 AAAAATAAAAGTAATAAACTCAC
234313 AAAAAT
1 AAAAAT
234319 TTAAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.40
22 3 0.12
23 12 0.48
ACGTcount: A:0.68, C:0.12, G:0.02, T:0.18
Consensus pattern (23 bp):
AAAAATAAAAGTAATAAACTCAC
Found at i:235763 original size:10 final size:10
Alignment explanation
Indices: 235748--235777 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
235738 TGAAATATAT
235748 TTTATTAATA
1 TTTATTAATA
235758 TTTATTAATA
1 TTTATTAATA
235768 TTTATTAATA
1 TTTATTAATA
235778 ATATAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTATTAATA
Found at i:235789 original size:23 final size:21
Alignment explanation
Indices: 235741--235790 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
235731 ACATATTTGA
235741 AATAT-AT-TTTATTAATATT
1 AATATAATATTTATTAATATT
*
235760 TAT-TAATATTTATTAATAATAT
1 AATATAATATTTATTAAT-AT-T
235782 AATATAATA
1 AATATAATA
235791 ATATACTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
18 1 0.04
19 4 0.17
20 9 0.38
21 2 0.08
22 3 0.12
23 5 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AATATAATATTTATTAATATT
Found at i:240443 original size:32 final size:30
Alignment explanation
Indices: 240386--240462 Score: 79
Period size: 32 Copynumber: 2.6 Consensus size: 30
240376 TCATGTGCCT
**
240386 TTCACTTTA-TTCATTTCATAGACTATATCA
1 TTCACTTTATTTCATAGCATAGACTAT-TCA
*
240416 TTCACTTTCATTTCATAGCATATACTATTCA
1 TTCACTTT-ATTTCATAGCATAGACTATTCA
*
240447 --CATTTTATTTCATAGC
1 TTCACTTTATTTCATAGC
240463 CCAATGTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 10 0.24
29 5 0.12
30 8 0.20
31 4 0.10
32 14 0.34
ACGTcount: A:0.29, C:0.21, G:0.04, T:0.47
Consensus pattern (30 bp):
TTCACTTTATTTCATAGCATAGACTATTCA
Found at i:240462 original size:28 final size:28
Alignment explanation
Indices: 240395--240462 Score: 88
Period size: 27 Copynumber: 2.5 Consensus size: 28
240385 TTTCACTTTA
240395 TTCATTTCATAG-ACTATATCATTCACT
1 TTCATTTCATAGCACTATATCATTCACT
240422 TTCATTTCATAGCA-TATA-CTATTCACAT
1 TTCATTTCATAGCACTATATC-ATTCAC-T
*
240450 TTTATTTCATAGC
1 TTCATTTCATAGC
240463 CCAATGTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
26 1 0.03
27 22 0.59
28 14 0.38
ACGTcount: A:0.29, C:0.21, G:0.04, T:0.46
Consensus pattern (28 bp):
TTCATTTCATAGCACTATATCATTCACT
Found at i:244009 original size:13 final size:13
Alignment explanation
Indices: 243993--244019 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
243983 AAAAAAGAGG
243993 AAAAAAACAAAAA
1 AAAAAAACAAAAA
244006 AAAAAAACAAAAA
1 AAAAAAACAAAAA
244019 A
1 A
244020 GCCAAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAA
Found at i:251663 original size:25 final size:25
Alignment explanation
Indices: 251613--251664 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
251603 ACACCAATAG
*
251613 AAAACAGAAAAGAAAAATCGAGAGA
1 AAAACAGAAAAGAAAAATCGAAAGA
251638 AAAAC-GAAAAGAATAAAAT-GAAAGA
1 AAAACAGAAAAG-A-AAAATCGAAAGA
251663 AA
1 AA
251665 GAAAGAGAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 6 0.25
25 13 0.54
26 5 0.21
ACGTcount: A:0.71, C:0.06, G:0.17, T:0.06
Consensus pattern (25 bp):
AAAACAGAAAAGAAAAATCGAAAGA
Found at i:255209 original size:76 final size:76
Alignment explanation
Indices: 255083--255235 Score: 297
Period size: 76 Copynumber: 2.0 Consensus size: 76
255073 TGAAAATGAT
*
255083 CCTGCGATGTCAAATACACAAGGGACTACTTTAGAAGAAGCTAATCCTAGCCAATGTGGTAAATC
1 CCTGCGATGTCAAATACACAAGGGACTACTTTAGAAGAAGCTAATCCTAGCCAATGTGATAAATC
255148 ACAAACAATCA
66 ACAAACAATCA
255159 CCTGCGATGTCAAATACACAAGGGACTACTTTAGAAGAAGCTAATCCTAGCCAATGTGATAAATC
1 CCTGCGATGTCAAATACACAAGGGACTACTTTAGAAGAAGCTAATCCTAGCCAATGTGATAAATC
255224 ACAAACAATCA
66 ACAAACAATCA
255235 C
1 C
255236 TATTCGTATC
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (76 bp):
CCTGCGATGTCAAATACACAAGGGACTACTTTAGAAGAAGCTAATCCTAGCCAATGTGATAAATC
ACAAACAATCA
Found at i:257683 original size:6 final size:6
Alignment explanation
Indices: 257674--257757 Score: 64
Period size: 6 Copynumber: 13.0 Consensus size: 6
257664 ATATAAAGAG
* *
257674 AGAAAA AG--AA AGAAAA AGAGAAA AGATAGA AGAAGAA GGAAAAAA AGAAAA
1 AGAAAA AGAAAA AGAAAA AGA-AAA AGA-AAA AGAA-AA --AGAAAA AGAAAA
257725 AGAGGAAA AGAAAAA AGAAAA AGAAAA AGAAAA
1 AGA--AAA AG-AAAA AGAAAA AGAAAA AGAAAA
257758 TAAATCAAGT
Statistics
Matches: 64, Mismatches: 5, Indels: 18
0.74 0.06 0.21
Matches are distributed among these distances:
4 4 0.06
6 32 0.50
7 17 0.27
8 7 0.11
9 4 0.06
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (6 bp):
AGAAAA
Found at i:257709 original size:27 final size:27
Alignment explanation
Indices: 257668--257754 Score: 95
Period size: 27 Copynumber: 3.2 Consensus size: 27
257658 ATACATATAT
*
257668 AAAGAGAGAAAAAGAAAGAAAAAGAGA
1 AAAGAGAGAAGAAGAAAGAAAAAGAGA
* * *
257695 AAAGATAGAAGAAGAAGGAAAAAAAGAA
1 AAAGAGAGAAGAAGAAAGAAAAAGAG-A
* *
257723 AAAGAGGAAAAGAAAAAAGAAAAAGA-A
1 AAAGA-GAGAAGAAGAAAGAAAAAGAGA
257750 AAAGA
1 AAAGA
257755 AAATAAATCA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
27 28 0.57
28 6 0.12
29 15 0.31
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (27 bp):
AAAGAGAGAAGAAGAAAGAAAAAGAGA
Found at i:257727 original size:21 final size:20
Alignment explanation
Indices: 257674--257757 Score: 69
Period size: 21 Copynumber: 3.9 Consensus size: 20
257664 ATATAAAGAG
*
257674 AGAAAAAGAAAGAAAAAGAGAAA
1 AGAAAAAG-AAGAAGAA-A-AAA
*
257697 AGATAGAAGAAGAAGGAAAAAA
1 AGA-AAAAGAAGAA-GAAAAAA
* *
257719 AGAAAAAGAGGAAAAGAAAAA
1 AGAAAAAGAAGAAGA-AAAAA
*
257740 AGAAAAAGAAAAAGAAAA
1 AGAAAAAGAAGAAGAAAA
257758 TAAATCAAGT
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
20 4 0.08
21 25 0.50
22 6 0.12
23 9 0.18
24 6 0.12
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (20 bp):
AGAAAAAGAAGAAGAAAAAA
Found at i:261881 original size:53 final size:53
Alignment explanation
Indices: 261822--261998 Score: 219
Period size: 53 Copynumber: 3.3 Consensus size: 53
261812 AGGGATTAAG
* * * * *
261822 GAACTCGAATAATCCTCTAAAAATGGGTTCGCTCCCTATTGCTTCAGGGAGTA
1 GAACTCGAACAATCTTCTACAAACGGGTTCGCTCCCTCTTGCTTCAGGGAGTA
* * * *
261875 GAACTCGAACAATCTTCGACCAGCGGGTTCACTCCCTCTTGCTTCAGGGAGTA
1 GAACTCGAACAATCTTCTACAAACGGGTTCGCTCCCTCTTGCTTCAGGGAGTA
* * ** *
261928 GAACTCGAACGATCTTCTGCTTACGGGTTCGCTCCCTCTTGCTTTAGGGAGTA
1 GAACTCGAACAATCTTCTACAAACGGGTTCGCTCCCTCTTGCTTCAGGGAGTA
*
261981 AAACTCGAACAATCTTCT
1 GAACTCGAACAATCTTCT
261999 GGTTTGATTC
Statistics
Matches: 105, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
53 105 1.00
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (53 bp):
GAACTCGAACAATCTTCTACAAACGGGTTCGCTCCCTCTTGCTTCAGGGAGTA
Found at i:261999 original size:53 final size:54
Alignment explanation
Indices: 261846--261999 Score: 224
Period size: 53 Copynumber: 2.9 Consensus size: 54
261836 CTCTAAAAAT
*
261846 GGGTTCGCTCCCTATTGCTTCAGGGAGTAGAACTCGAACAATCTTC-GACCAGC
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGACCAGC
* * *
261899 GGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCGAACGATCTTCTG-CTTA-C
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGAC-CAGC
* *
261952 GGGTTCGCTCCCTCTTGCTTTAGGGAGTAAAACTCGAACAATCTTCTG
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
262000 GTTTGATTCT
Statistics
Matches: 91, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
53 89 0.98
54 2 0.02
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (54 bp):
GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGACCAGC
Found at i:262548 original size:42 final size:42
Alignment explanation
Indices: 262502--262626 Score: 214
Period size: 42 Copynumber: 3.0 Consensus size: 42
262492 TTACAAATTA
* *
262502 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGG
*
262544 CCCGAAGGACTTCATCATCATACTCGAAAGACTTACTGATGG
1 CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGG
*
262586 CCCAAAGGACTTCATCATCATGCTCGAAAGACTTACTGATG
1 CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATG
262627 AATTTGCTTC
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 78 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (42 bp):
CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGG
Found at i:262554 original size:20 final size:20
Alignment explanation
Indices: 262526--262626 Score: 64
Period size: 22 Copynumber: 4.8 Consensus size: 20
262516 TCATCATGCT
262526 CGAAAGACTTACTGATGGCC
1 CGAAAGACTTACTGATGGCC
* * * *
262546 CGAAGGACTTCATCATCAT-ACT
1 CGAAAGACTT-A-C-TGATGGCC
262568 CGAAAGACTTACTGATGGCC
1 CGAAAGACTTACTGATGGCC
* *
262588 C-AAAGGACTTCATCATCAT-GCT
1 CGAAA-GACTT-A-C-TGATGGCC
262610 CGAAAGACTTACTGATG
1 CGAAAGACTTACTGATG
262627 AATTTGCTTC
Statistics
Matches: 60, Mismatches: 11, Indels: 20
0.66 0.12 0.22
Matches are distributed among these distances:
19 9 0.15
20 18 0.30
21 4 0.07
22 20 0.33
23 9 0.15
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.24
Consensus pattern (20 bp):
CGAAAGACTTACTGATGGCC
Found at i:262559 original size:122 final size:120
Alignment explanation
Indices: 262360--262585 Score: 310
Period size: 122 Copynumber: 1.9 Consensus size: 120
262350 TCCAACACTA
* * *
262360 TTCCGAGAAGGCTTAAAATGGCCCGAAGGACTTATCAACTTGCTTGAAAGACTTACAAATGACCC
1 TTCCGAGAAGGCTTAAAATGACCCGAAGGACTTATCAACATGCTCGAAAGACTTACAAATGACCC
* *
262425 GAAGGATTTCATCATCA-AGCTCGAAAGACTTATTGATGGATTTGCTTCTCTACTC
66 GAAGGACTTCATCATCATA-CTCGAAAGACTTACTGATGGATTTGCTTCTCTACTC
* * * * ** *
262480 TTCCGTGAAGGCTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGC
1 TTCCGAGAAGGCTTA-AAATGACCCGAAGGACTT-ATCAACATGCTCGAAAGACTTACAAATGAC
262545 CCGAAGGACTTCATCATCATACTCGAAAGACTTACTGATGG
64 CCGAAGGACTTCATCATCATACTCGAAAGACTTACTGATGG
262586 CCCAAAGGAC
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
120 14 0.15
121 15 0.16
122 61 0.67
123 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.27
Consensus pattern (120 bp):
TTCCGAGAAGGCTTAAAATGACCCGAAGGACTTATCAACATGCTCGAAAGACTTACAAATGACCC
GAAGGACTTCATCATCATACTCGAAAGACTTACTGATGGATTTGCTTCTCTACTC
Found at i:262576 original size:22 final size:22
Alignment explanation
Indices: 262515--262619 Score: 80
Period size: 20 Copynumber: 5.0 Consensus size: 22
262505 GAAGGATTTA
262515 ATCATCATGCTCGAAAGACTT-
1 ATCATCATGCTCGAAAGACTTC
* * *
262536 A-C-TGATGGCCCGAAGGACTTC
1 ATCATCAT-GCTCGAAAGACTTC
*
262557 ATCATCATACTCGAAAGACTT-
1 ATCATCATGCTCGAAAGACTTC
* *
262578 A-C-TGATGGC-CCAAAGGACTTC
1 ATCATCAT-GCTCGAAA-GACTTC
262599 ATCATCATGCTCGAAAGACTT
1 ATCATCATGCTCGAAAGACTT
262620 ACTGATGAAT
Statistics
Matches: 62, Mismatches: 12, Indels: 19
0.67 0.13 0.20
Matches are distributed among these distances:
19 10 0.16
20 19 0.31
21 4 0.06
22 19 0.31
23 10 0.16
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (22 bp):
ATCATCATGCTCGAAAGACTTC
Found at i:262654 original size:164 final size:163
Alignment explanation
Indices: 262377--262708 Score: 529
Period size: 164 Copynumber: 2.0 Consensus size: 163
262367 AAGGCTTAAA
* * * * *
262377 ATGGCCCGAAGGACTTATCAACTTGCTTGAAAGACTTACAAATGACCCGAAGGATTTCATCATCA
1 ATGGCCCGAAGGACTTATCAACATACTCGAAAGACTTACAAATGACCCAAAGGACTTCATCATCA
* * *
262442 AGCTCGAAAGACTTATTGATGGATTTGCTTCTCTACTCTTCCGTGAAGGCTTACAAATTACCCGA
66 AGCTCGAAAGACTTACTGATGAATTTGCTTCACTACTCTTCCGTGAAGGCTTACAAATTACCCGA
262507 AGGATTTAATCATCATGCTCGAAAGACTTACTG
131 AGGATTTAATCATCATGCTCGAAAGACTTACTG
* ** *
262540 ATGGCCCGAAGGACTTCATCATCATACTCGAAAGACTTACTGATGGCCCAAAGGACTTCATCATC
1 ATGGCCCGAAGGACTT-ATCAACATACTCGAAAGACTTACAAATGACCCAAAGGACTTCATCATC
* *
262605 ATGCTCGAAAGACTTACTGATGAATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCCG
65 AAGCTCGAAAGACTTACTGATGAATTTGCTTCACTACTCTTCCGTGAAGGCTTACAAATTACCCG
262670 AAGGATTTAATCATCATGCTCGAAAGACTTACTG
130 AAGGATTTAATCATCATGCTCGAAAGACTTACTG
262704 ATGGC
1 ATGGC
262709 ACTTACTGAT
Statistics
Matches: 154, Mismatches: 14, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
163 16 0.10
164 138 0.90
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (163 bp):
ATGGCCCGAAGGACTTATCAACATACTCGAAAGACTTACAAATGACCCAAAGGACTTCATCATCA
AGCTCGAAAGACTTACTGATGAATTTGCTTCACTACTCTTCCGTGAAGGCTTACAAATTACCCGA
AGGATTTAATCATCATGCTCGAAAGACTTACTG
Done.