Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015333.1 Corchorus olitorius cultivar O-4 contig15366, 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: 150782
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:12660 original size:50 final size:50
Alignment explanation
Indices: 12585--12687 Score: 206
Period size: 50 Copynumber: 2.1 Consensus size: 50
12575 CTATTACATA
12585 AAATAAAATTTTACTCAGAATTGAAATTACTCAATTCTAATCCTAAATCG
1 AAATAAAATTTTACTCAGAATTGAAATTACTCAATTCTAATCCTAAATCG
12635 AAATAAAATTTTACTCAGAATTGAAATTACTCAATTCTAATCCTAAATCG
1 AAATAAAATTTTACTCAGAATTGAAATTACTCAATTCTAATCCTAAATCG
12685 AAA
1 AAA
12688 ACGTTCGCTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.46, C:0.16, G:0.06, T:0.33
Consensus pattern (50 bp):
AAATAAAATTTTACTCAGAATTGAAATTACTCAATTCTAATCCTAAATCG
Found at i:13827 original size:39 final size:37
Alignment explanation
Indices: 13775--13851 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 37
13765 AACACTCAAA
13775 TATATATATGCCTTATCTAGGGGAAGAGGGGGAAGGG
1 TATATATATGCCTTATCTAGGGGAAGAGGGGGAAGGG
* *
13812 TATATATATGCGCCTTATCTAGGGGAAGAGTGGGATGGG
1 TATATATAT--GCCTTATCTAGGGGAAGAGGGGGAAGGG
13851 T
1 T
13852 GGGTGGGAGC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 9 0.25
39 27 0.75
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.27
Consensus pattern (37 bp):
TATATATATGCCTTATCTAGGGGAAGAGGGGGAAGGG
Found at i:26807 original size:18 final size:18
Alignment explanation
Indices: 26774--26821 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
26764 CGATATAATA
26774 ATAATATATAGC-ATATAC
1 ATAATATATA-CAATATAC
*
26792 ATAATATATACAATATAT
1 ATAATATATACAATATAC
26810 AT-ATATACTACA
1 ATAATATA-TACA
26822 TATTATTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 6 0.22
18 21 0.78
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.35
Consensus pattern (18 bp):
ATAATATATACAATATAC
Found at i:27920 original size:90 final size:86
Alignment explanation
Indices: 27766--27976 Score: 246
Period size: 90 Copynumber: 2.4 Consensus size: 86
27756 AAGTGCGGAC
* * * * * *
27766 TATGTCAATGTTGCATCTGCATCTCAACAAGTCAATGTTCCTATTGCAGCAGCTAAGCCTGTGAA
1 TATGTCAATGCTGCATTTGCACCACAACAAGTCAATGTTCCAATTGCAGCAGC--AGCCGGTGAA
*
27831 ACGTGAGGTCACTGGCCAGGAC-
64 ACGTGAGGTCACTGGCCAAGACT
27853 TATGTCAATATTGCTGCATTTGCACCACAACAAGTCAATGTTCCAATTGCAGCTAAGGC-GCCGG
1 TATGTC-A-A-TGCTGCATTTGCACCACAACAAGTCAATGTTCCAATTGCAGC--A-GCAGCCGG
27917 TGAAACGTGAGGTCACTGGCCAAGACTAT
60 TGAAACGTGAGGTCACTGGCCAAGAC--T
*
27946 TATGTCAATGTTGCATTTGCACCACAACAAG
1 TATGTCAATGCTGCATTTGCACCACAACAAG
27977 CGAAGCCTGT
Statistics
Matches: 107, Mismatches: 8, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
87 6 0.06
88 1 0.01
89 1 0.01
90 88 0.82
91 1 0.01
92 2 0.02
93 8 0.07
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (86 bp):
TATGTCAATGCTGCATTTGCACCACAACAAGTCAATGTTCCAATTGCAGCAGCAGCCGGTGAAAC
GTGAGGTCACTGGCCAAGACT
Found at i:30358 original size:120 final size:118
Alignment explanation
Indices: 30147--30368 Score: 399
Period size: 120 Copynumber: 1.9 Consensus size: 118
30137 TGCAGTTTTC
30147 ATTTCCAATTCTGTTTCAAAAATGGTAAGCTACAGATAAACTTCCATGGCAGCATACATTTTATA
1 ATTTCCAATTCTGTTTCAAAAATGGTAAGCTACAGATAAACTTCCATGGCAGCATACATTTTATA
30212 AAATGCTTTGAATTGGATATAATTGAGATTATTATTAAGATACAGATAAGATT
66 AAATGCTTTGAATTGGATATAATTGAGATTATTATTAAGATACAGATAAGATT
* *
30265 ATTTCCAATTCTGTTTCAAAGATGGTAAGCTACACAGATAAGCTTCCATGGCAGCATACATTTTA
1 ATTTCCAATTCTGTTTCAAAAATGGTAAGCT--ACAGATAAACTTCCATGGCAGCATACATTTTA
*
30330 TGAAATGCTTTGAATTGGATATAATTGAGATTATTATTA
64 TAAAATGCTTTGAATTGGATATAATTGAGATTATTATTA
30369 TGTTTACCAA
Statistics
Matches: 99, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
118 30 0.30
120 69 0.70
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (118 bp):
ATTTCCAATTCTGTTTCAAAAATGGTAAGCTACAGATAAACTTCCATGGCAGCATACATTTTATA
AAATGCTTTGAATTGGATATAATTGAGATTATTATTAAGATACAGATAAGATT
Found at i:49204 original size:21 final size:21
Alignment explanation
Indices: 49178--49221 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
49168 AGATTCCCTT
49178 TGTTTTTTATATGCTGGAAAA
1 TGTTTTTTATATGCTGGAAAA
49199 TGTTTTTTATATGCTGGAAAA
1 TGTTTTTTATATGCTGGAAAA
49220 TG
1 TG
49222 CTGTTGCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.05, G:0.20, T:0.48
Consensus pattern (21 bp):
TGTTTTTTATATGCTGGAAAA
Found at i:49360 original size:20 final size:21
Alignment explanation
Indices: 49322--49362 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
49312 AGCGGATTCG
49322 TGCAAAGGTTGCTTCTCCAAC
1 TGCAAAGGTTGCTTCTCCAAC
* *
49343 TGCAAA-GTTGGTTTTCCAAC
1 TGCAAAGGTTGCTTCTCCAAC
49363 ATCATTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (21 bp):
TGCAAAGGTTGCTTCTCCAAC
Found at i:52659 original size:13 final size:13
Alignment explanation
Indices: 52641--52667 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
52631 TCATTCTCGA
52641 CACTACAAGCTGC
1 CACTACAAGCTGC
52654 CACTACAAGCTGC
1 CACTACAAGCTGC
52667 C
1 C
52668 GTGAGTTGTG
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:0.30, C:0.41, G:0.15, T:0.15
Consensus pattern (13 bp):
CACTACAAGCTGC
Found at i:57900 original size:7 final size:7
Alignment explanation
Indices: 57888--57912 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
57878 TTTTCATGAG
57888 TTGGCAT
1 TTGGCAT
57895 TTGGCAT
1 TTGGCAT
57902 TTGGCAT
1 TTGGCAT
57909 TTGG
1 TTGG
57913 TCGTCAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.32, T:0.44
Consensus pattern (7 bp):
TTGGCAT
Found at i:68266 original size:10 final size:10
Alignment explanation
Indices: 68251--68282 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
68241 GGGCATTTCA
68251 GTTTGAAAAG
1 GTTTGAAAAG
68261 GTTTGAAAAG
1 GTTTGAAAAG
68271 GTTTGAAAAG
1 GTTTGAAAAG
68281 GT
1 GT
68283 CTGCGTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (10 bp):
GTTTGAAAAG
Found at i:68447 original size:15 final size:16
Alignment explanation
Indices: 68424--68466 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
68414 ATAACAATGT
*
68424 TGCTGTTTCTGTTG-C
1 TGCTTTTTCTGTTGTC
68439 TGCTTTTTCTTGTTGTC
1 TGCTTTTTC-TGTTGTC
68456 TGCCTTTTTCT
1 TG-CTTTTTCT
68467 TCTGGTGTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 8 0.33
16 5 0.21
17 4 0.17
18 7 0.29
ACGTcount: A:0.00, C:0.21, G:0.19, T:0.60
Consensus pattern (16 bp):
TGCTTTTTCTGTTGTC
Found at i:68464 original size:18 final size:16
Alignment explanation
Indices: 68424--68467 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 16
68414 ATAACAATGT
*
68424 TGCTGTTTC-TGTTGC
1 TGCTTTTTCTTGTTGC
68439 TGCTTTTTCTTGTTGTC
1 TGCTTTTTCTTGTTG-C
68456 TGCCTTTTTCTT
1 TG-CTTTTTCTT
68468 CTGGTGTCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 8 0.32
16 5 0.20
17 3 0.12
18 9 0.36
ACGTcount: A:0.00, C:0.20, G:0.18, T:0.61
Consensus pattern (16 bp):
TGCTTTTTCTTGTTGC
Found at i:75958 original size:14 final size:14
Alignment explanation
Indices: 75939--75965 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
75929 TAAATTTCAA
75939 AACTCAAAATCTTT
1 AACTCAAAATCTTT
75953 AACTCAAAATCTT
1 AACTCAAAATCTT
75966 GTATAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (14 bp):
AACTCAAAATCTTT
Found at i:79222 original size:41 final size:41
Alignment explanation
Indices: 79177--79260 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
79167 TTAGAGTAAT
*
79177 AATACTCATAATCATAAAAGAACTAAGATGCTCATATTCCC
1 AATACTCATAATCATAAAAGAACTAAGATACTCATATTCCC
*
79218 AATACTCATAATCATAAAAGAATTAAGATACTCATATTCCC
1 AATACTCATAATCATAAAAGAACTAAGATACTCATATTCCC
79259 AA
1 AA
79261 ATCAACAACG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.46, C:0.20, G:0.06, T:0.27
Consensus pattern (41 bp):
AATACTCATAATCATAAAAGAACTAAGATACTCATATTCCC
Found at i:94422 original size:36 final size:39
Alignment explanation
Indices: 94365--94437 Score: 116
Period size: 36 Copynumber: 1.9 Consensus size: 39
94355 TTATGTGCAT
*
94365 TTTTTTTTTCTCTTTTGATGGATCGTTTTACGTCCATTG
1 TTTTTTTTTCTCTTTTGATGGATCGTTTTACGGCCATTG
94404 TTTTTTTTT-T-TTTT-ATGGATCGTTTTACGGCCAT
1 TTTTTTTTTCTCTTTTGATGGATCGTTTTACGGCCAT
94438 GGTATCCACA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
36 19 0.58
37 4 0.12
38 1 0.03
39 9 0.27
ACGTcount: A:0.11, C:0.14, G:0.15, T:0.60
Consensus pattern (39 bp):
TTTTTTTTTCTCTTTTGATGGATCGTTTTACGGCCATTG
Found at i:94532 original size:40 final size:40
Alignment explanation
Indices: 94488--94569 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
94478 CTCACTATAT
94488 AACCCAACAAACCTGTTTAATTTATGTTATAGTTACTAGA
1 AACCCAACAAACCTGTTTAATTTATGTTATAGTTACTAGA
94528 AACCCAACAAACCTGTTTAATTTATGTTATAGTTACTAGA
1 AACCCAACAAACCTGTTTAATTTATGTTATAGTTACTAGA
94568 AA
1 AA
94570 AACCAGAGCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (40 bp):
AACCCAACAAACCTGTTTAATTTATGTTATAGTTACTAGA
Found at i:94720 original size:13 final size:14
Alignment explanation
Indices: 94696--94724 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
94686 AAAAACAACC
94696 GAAAAGCACTTCTG
1 GAAAAGCACTTCTG
94710 GAAAA-CACTTCTG
1 GAAAAGCACTTCTG
94723 GA
1 GA
94725 TTTTCCGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (14 bp):
GAAAAGCACTTCTG
Found at i:119915 original size:122 final size:122
Alignment explanation
Indices: 119708--119932 Score: 369
Period size: 122 Copynumber: 1.8 Consensus size: 122
119698 TTGCTCTGAT
* ** *
119708 TTTCCTTTTTCTGCTCTGATGGTTTCTTGATAGTGTTTCTTCTCTTCTGCAGTTGTCTCCCAATT
1 TTTCCTTTTTCTGCTCTGATGGTTTCTGGATAACGTTTCTTCTCCTCTGCAGTTGTCTCCCAATT
* * *
119773 GGACCTGAGCGTATCGTTGTGGCAGCTAGGATTGCCTTCAGATTTGTTTGTTGTAAG
66 GGACCTGAGCATATCCTTGTGGCAGCAAGGATTGCCTTCAGATTTGTTTGTTGTAAG
*
119830 TTTCCTTTTTCTGCTCTGATGGTTTCTGGATAACGTTTCTTCTCCTCTGCAGTTGTCTCCCCATT
1 TTTCCTTTTTCTGCTCTGATGGTTTCTGGATAACGTTTCTTCTCCTCTGCAGTTGTCTCCCAATT
*
119895 GGAGCTGAGCATATCCTTGTGGCAGCAAGGATTGCCTT
66 GGACCTGAGCATATCCTTGTGGCAGCAAGGATTGCCTT
119933 ATTGTCTTGA
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
122 94 1.00
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.42
Consensus pattern (122 bp):
TTTCCTTTTTCTGCTCTGATGGTTTCTGGATAACGTTTCTTCTCCTCTGCAGTTGTCTCCCAATT
GGACCTGAGCATATCCTTGTGGCAGCAAGGATTGCCTTCAGATTTGTTTGTTGTAAG
Found at i:120055 original size:40 final size:40
Alignment explanation
Indices: 119999--120287 Score: 340
Period size: 40 Copynumber: 7.8 Consensus size: 40
119989 TTGAGGGCCA
119999 ATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTGG
1 ATGTG-ATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTGG
120040 ATGTGATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTGG
1 ATGTGATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTGG
120080 ATGTGATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTGG
1 ATGTGATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTGG
120120 ATGTGATTAAGGCAAGTTCAATGTCATTT-GG--A--T-G
1 ATGTGATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTGG
* *
120154 -TG-AATAAAGGCAAGTTCAATGTCATTT-GG--A--T-G
1 ATGTGATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTGG
*
120186 -TG-AATTAAGGCAAGTTCAATGTC--TT-------TTGG
1 ATGTGATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTGG
120215 ATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTGG
1 ATGTG-ATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTGG
*
120256 ATGTGAATAAAGGCAAGTTCAATGTCATTTGG
1 ATGTG-ATTAAGGCAAGTTCAATGTCATTTGG
120288 ATGTGAATTA
Statistics
Matches: 229, Mismatches: 5, Indels: 28
0.87 0.02 0.11
Matches are distributed among these distances:
28 1 0.00
29 1 0.00
30 4 0.02
32 70 0.31
33 2 0.01
34 3 0.01
35 1 0.00
37 1 0.00
39 2 0.01
40 104 0.45
41 40 0.17
ACGTcount: A:0.31, C:0.08, G:0.28, T:0.33
Consensus pattern (40 bp):
ATGTGATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTGG
Found at i:120136 original size:20 final size:20
Alignment explanation
Indices: 119997--120143 Score: 123
Period size: 20 Copynumber: 7.3 Consensus size: 20
119987 CATTGAGGGC
119997 CAATGTGAATTAAGGCAAGTT
1 CAATGTG-ATTAAGGCAAGTT
* ** *
120018 CAATGTCATTTGGGAAAGTT
1 CAATGTGATTAAGGCAAGTT
**
120038 GGATGTGATTAAGGCAAGTT
1 CAATGTGATTAAGGCAAGTT
* ** *
120058 CAATGTCATTTGGGAAAGTT
1 CAATGTGATTAAGGCAAGTT
**
120078 GGATGTGATTAAGGCAAGTT
1 CAATGTGATTAAGGCAAGTT
* ** *
120098 CAATGTCATTTGGGAAAGTT
1 CAATGTGATTAAGGCAAGTT
**
120118 GGATGTGATTAAGGCAAGTT
1 CAATGTGATTAAGGCAAGTT
120138 CAATGT
1 CAATGT
120144 CATTTGGATG
Statistics
Matches: 90, Mismatches: 36, Indels: 1
0.71 0.28 0.01
Matches are distributed among these distances:
20 84 0.93
21 6 0.07
ACGTcount: A:0.31, C:0.08, G:0.29, T:0.32
Consensus pattern (20 bp):
CAATGTGATTAAGGCAAGTT
Found at i:120169 original size:32 final size:32
Alignment explanation
Indices: 120116--120415 Score: 467
Period size: 32 Copynumber: 9.1 Consensus size: 32
120106 TTTGGGAAAG
120116 TTGGATGTG-ATTAAGGCAAGTTCAATGTCAT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
*
120147 TTGGATGTGAATAAAGGCAAGTTCAATGTCAT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
*
120179 TTGGATGTGAATTAAGGCAAGTTCAATGTCTT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
120211 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCA--T
*
120245 GGGAAAGTTGGATGTGAATAAAGGCAAGTTCAATGTCAT
1 -------TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
120284 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
*
120316 TTGGATGTGAATTAAGGCAAGTTCAATGTTAT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
*
120348 TTGGATGTGAATTAAGGCAAGTTCAATGTCTT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
120380 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
120412 TTGG
1 TTGG
120416 GAAAGTTAAA
Statistics
Matches: 249, Mismatches: 10, Indels: 19
0.90 0.04 0.07
Matches are distributed among these distances:
31 9 0.04
32 208 0.84
34 1 0.00
39 1 0.00
41 30 0.12
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.35
Consensus pattern (32 bp):
TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
Found at i:120280 original size:21 final size:21
Alignment explanation
Indices: 120215--120280 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
120205 TGTCTTTTGG
120215 ATGTGAATTAAGGCAAGTTCA
1 ATGTGAATTAAGGCAAGTTCA
* ** * **
120236 ATGT-CATTTGGGAAAGTTGG
1 ATGTGAATTAAGGCAAGTTCA
*
120256 ATGTGAATAAAGGCAAGTTCA
1 ATGTGAATTAAGGCAAGTTCA
120277 ATGT
1 ATGT
120281 CATTTGGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 2
0.67 0.28 0.04
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.30
Consensus pattern (21 bp):
ATGTGAATTAAGGCAAGTTCA
Found at i:120335 original size:169 final size:175
Alignment explanation
Indices: 120036--120432 Score: 666
Period size: 169 Copynumber: 2.3 Consensus size: 175
120026 TTTGGGAAAG
*
120036 TTGGATGTG-ATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGATGTG-ATTAAGGCAAGTTC
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGATGTGAATAAAGGCAAGTTC
*
120099 AATGTCATTTGGGAAAGTTGGATGTGATTAAGGCAAGTTCAATGTCATTTGGATGTGAATAAAGG
66 AATGTCATTTGGG-AAG-TGGATGTAATTAAGGCAAGTTCAATGTCATTTGGATGTGAATAAAGG
120164 CAAGTTCAATGTCATTTGGATGTGAATTAAGGCAAGTTCAATGTCTT
129 CAAGTTCAATGTCATTTGGATGTGAATTAAGGCAAGTTCAATGTCTT
120211 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGATGTGAATAAAGGCAAGTTC
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGATGTGAATAAAGGCAAGTTC
*
120276 AATGTCATTT-GG-A-T-G-TG-AATTAAGGCAAGTTCAATGTCATTTGGATGTGAATTAAGGCA
66 AATGTCATTTGGGAAGTGGATGTAATTAAGGCAAGTTCAATGTCATTTGGATGTGAATAAAGGCA
*
120335 AGTTCAATGTTATTTGGATGTGAATTAAGGCAAGTTCAATGTCTT
131 AGTTCAATGTCATTTGGATGTGAATTAAGGCAAGTTCAATGTCTT
**
120380 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTAAATGTGAAT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGATGTGAAT
120433 GTGCCGCGTG
Statistics
Matches: 214, Mismatches: 6, Indels: 10
0.93 0.03 0.04
Matches are distributed among these distances:
169 135 0.63
170 2 0.01
171 1 0.00
172 1 0.00
174 1 0.00
175 9 0.04
176 42 0.20
177 23 0.11
ACGTcount: A:0.31, C:0.08, G:0.27, T:0.34
Consensus pattern (175 bp):
TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGATGTGAATAAAGGCAAGTTC
AATGTCATTTGGGAAGTGGATGTAATTAAGGCAAGTTCAATGTCATTTGGATGTGAATAAAGGCA
AGTTCAATGTCATTTGGATGTGAATTAAGGCAAGTTCAATGTCTT
Found at i:120898 original size:7 final size:7
Alignment explanation
Indices: 120850--120897 Score: 78
Period size: 7 Copynumber: 6.9 Consensus size: 7
120840 TTTGCCAAAT
120850 TGTTTGC
1 TGTTTGC
120857 TGTTTGC
1 TGTTTGC
120864 TGTTTGC
1 TGTTTGC
120871 TGTTTGC
1 TGTTTGC
*
120878 TGTTTGT
1 TGTTTGC
*
120885 TGTTTGT
1 TGTTTGC
120892 TGTTTG
1 TGTTTG
120898 TGATTGGATG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.00, C:0.08, G:0.29, T:0.62
Consensus pattern (7 bp):
TGTTTGC
Found at i:123621 original size:25 final size:26
Alignment explanation
Indices: 123571--123626 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
123561 TTTTAATAAG
*
123571 TATTCTTTTTAGTCATTTAACTTTTT
1 TATTCTTTTTAGTCATTCAACTTTTT
*
123597 TATT-TTTTTAGATGATTCAACTTTTT
1 TATTCTTTTTAG-TCATTCAACTTTTT
123623 TATT
1 TATT
123627 AATTATGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 7 0.26
26 20 0.74
ACGTcount: A:0.21, C:0.09, G:0.05, T:0.64
Consensus pattern (26 bp):
TATTCTTTTTAGTCATTCAACTTTTT
Found at i:125548 original size:322 final size:327
Alignment explanation
Indices: 124609--126065 Score: 1328
Period size: 333 Copynumber: 4.5 Consensus size: 327
124599 CGAAATCGTG
** *
124609 TTGTTTCGATTTAATTAGAAATTAATTCAGAAAATAAATGGAAAAACGATATTAGAAGTGTGAAA
1 TTGTTTCGATTTAATTAGAAATTAATTTGGAAAA-AAATGGAAAAACGATATTAGAAGCGTGAAA
* * *
124674 A-CCCTTCAATCTTTTTGGCGTTGAATTAAATTTTTTTTTATTCTGAGTATTGTGGCAAAAAATT
65 AGCCCTTCAATATTTTTGGCGTTGAATT--A-TATATTTT-TTCTGAGTATTGTGGCAAAAAATT
* *
124738 GAGA-AAAAAATTTTCGTGTCAG-TTT--TTAGCCGAAATCATGTACTAACCATCACTGTTTTTG
126 GAGAGAAAAAATTTTCGTGTCAGTTTTAATTAGCCGAAATCGTGTACTAACCATCACGGTTTTTG
* * * ** * * * * * *
124799 GCTAAAAACGTG-TACTGAGGCCTCCACTCAGTTTTGAATGGTTTTTGGCATACAGAATCCTTGA
191 GCTAAAAACGCGTTCCGGAGGCCTCGGCTCAATTTTAAATGATTTTTGGCAAAAAGACTCCTTGA
* * * * *
124863 AAAATCTATACTAATGTAACCAAATCTCATCCACATTGGATTTAAAGATTTGTTTTTACGAGCAT
256 AATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAAGATTTGTTTTTACGAGCAT
124928 CTGAATC
321 CTGAATC
* * * ** ** *
124935 TTGTTTTGATTTTATT--AAGTTCAA---AAAAAAAAAAAGAAAAACGATATTA-AAGGAGTGAA
1 TTGTTTCGATTTAATTAGAAATT-AATTTGGAAAAAAATGGAAAAACGATATTAGAA-GCGTGAA
* *
124994 AAGCCCTTCAA-ATTTTTTGGCGTGGAATTATATATTTTTTCTGAGTATTGAGGCAAAAAATTGA
64 AAGCCCTTCAATA-TTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGA
** * *
125058 G-GAAAATCTTTTCGGGTCAGTTCTTTTACAAAATTTTAGCCGAAATCGTGTAC-ATA-TATCAC
128 GAGAAAAAATTTTCGTGTCAG---TTTT----AA--TTAGCCGAAATCGTGTACTA-ACCATCAC
* * * * **
125120 GGTTTTTGGCTAAAAACGCGTTCCAGA-GTCTCGGCTCAATTTTACATGATTTTTCGCGCAAAGA
183 GGTTTTTGGCTAAAAACGCGTTCCGGAGGCCTCGGCTCAATTTTAAATGATTTTTGGCAAAAAGA
*
125184 CTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCACATTGGATTTAAAGATTTGTTTTT
248 CTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAAGATTTGTTTTT
* *
125249 ACGAGCTTCTGAATT
313 ACGAGCATCTGAATC
* * **
125264 TTGTTTCGATTTAATTAAAAATTAATTTGGAAAAAAATGGAAAACCGATATTAGAAGCCCGAAAA
1 TTGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
* * * * * * *
125329 GCCCGTCAATATTTTTGGCATTGAATAATATATTTTTTCTAAATATT-TCGTAAAAAATTGAGAG
66 GCCCTTCAATATTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAG
* * *
125393 AAAAAATTTTCAATGTCAG-TTT-A-TAGCCGAAATCGTGTACTAACCATCACGATTCTTGGCTA
131 AAAAAATTTTC-GTGTCAGTTTTAATTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTA
* * ** *
125455 AAATCGCGTTTCGGA-TTCT-GGCTCAGTTTTAAATGATTTTTGGCAAAAAGACTCCTTGAAATA
195 AAAACGCGTTCCGGAGGCCTCGGCTCAATTTTAAATGATTTTTGGCAAAAAGACTCCTTGAAATA
* * * * ** *
125518 TCTACATTCATCTAACAAAATCTTAGCCACAATAAATTT-AAGAATTTGTTTTTACGAGCATCTC
260 TCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAAG-ATTTGTTTTTACGAGCATCTG
125582 AATC
324 AATC
* * * * * *
125586 TTTGTTTCGATTTAAATAGAAATAAATTCAGGAAAAAAAAGGAAAAACGATATTACAAACGTGAA
1 -TTGTTTCGATTTAATTAGAAATTAATT-TGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAA
* * * * * * *
125651 AAACCCTTCAATATTTTTGGCATTAAATTATATATTTATCCTGAGTATTATGGCAAAAAATGGAG
64 AAGCCCTTCAATATTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG
* * **
125716 -GAAAAACTTTTCGTGTCAGTTTTTACAAAATTTTAGCCTAAATCGTGTACTAATTATCACGGTT
129 AGAAAAAATTTTCGTGTCAG-TTTT----AA--TTAGCCGAAATCGTGTACTAACCATCACGGTT
* * * *** * * **
125780 TTTGGC-AAAAACGCCTTCCGGAGTCC-CGCCTCAATTTTGCCTAATTTTGGAGTTAAAA-ACTC
187 TTTGGCTAAAAACGCGTTCCGGAGGCCTCGGCTCAATTTTAAATGATTTTTG-GCAAAAAGACTC
** * * * * *
125842 CTTGAAACTATCTATATTCATGGAACCAAATCTTAGCCACATTGTATGTAAGGATTTGTTTTTAA
251 CTTGAAA-TATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAAGATTTGTTTTTAC
*
125907 GAGCATCCGAATC
315 GAGCATCTGAATC
* *
125920 TTATTTCGATTTAATTAGAAATTAATTTGG--AAAAATGGAAAAACGATATTAGAAGCGCGAAAA
1 TTGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
* * * * *
125983 GCCCGTCAAT-CTTTTGGCGTTGAATTATATA-TTTTTCTGAATATT-TTGTAAAAAATT--GAG
66 GCCCTTCAATATTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAG
* * *
126043 AAAAACTTTTCGGGTTAGTTTTA
131 AAAAAATTTTCGTGTCAGTTTTA
126066 GCCGAAATAG
Statistics
Matches: 920, Mismatches: 161, Indels: 105
0.78 0.14 0.09
Matches are distributed among these distances:
318 41 0.04
319 6 0.01
320 3 0.00
321 29 0.03
322 142 0.15
323 61 0.07
324 85 0.09
325 23 0.03
326 31 0.03
327 9 0.01
328 11 0.01
329 153 0.17
330 65 0.07
331 4 0.00
332 27 0.03
333 160 0.17
334 68 0.07
335 2 0.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (327 bp):
TTGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
GCCCTTCAATATTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAG
AAAAAATTTTCGTGTCAGTTTTAATTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAA
AAACGCGTTCCGGAGGCCTCGGCTCAATTTTAAATGATTTTTGGCAAAAAGACTCCTTGAAATAT
CTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTGAA
TC
Found at i:127049 original size:334 final size:330
Alignment explanation
Indices: 126076--127234 Score: 1288
Period size: 333 Copynumber: 3.5 Consensus size: 330
126066 GCCGAAATAG
* * *
126076 TTTG-TTTTACGAGCATCTAAATATTGTTTCGATTTAATTAGAAATAAATTCGGGAAAAAAAGGA
1 TTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAAGGA
* * *
126140 AAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTG
66 AAAACGATATTAGAAGCGTGAAAAACCCGTCAATATTTTTGGCATTGAATTATATATTTTTTCTG
* ** * * * * *
126205 AGTATTCTGGCAAATAAAAAGAGGAGAAACTTTTAGGGTCAATTTTTGCAAAATTTTAGCCGAAA
131 AATATT-TGGCAAA-AAATTGAGGAAAAACTTTTCGGGTCAGTTTTTGCTAAATTTTAGCCAAAA
* *
126270 TCGTATACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGTGCCAGCTCAATTTTGCAG
194 TCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGT-CCAGCTCAATTTTGCAT
* * * *
126335 GATTTTTGGCACAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATGTCAACCACATTGGA
258 GATTTTTGGCAAAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGAA
126400 TATAAGAA
323 TATAAGAA
** * * * * * * *
126408 TTTGTTTTTATTAGCATCTCGATCTTGTTTTGATTTTATTAGAAATTAATTCTGAAACAAATGGA
1 TTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAAGGA
* * *
126473 AAAACGATATTGGAAGGGTGAAAAGCCCGTCAATATTTTTGGCATTGAATTATATATTTTTTCTG
66 AAAACGATATTAGAAGCGTGAAAAACCCGTCAATATTTTTGGCATTGAATTATATATTTTTTCTG
* * * * * ** **
126538 AATGTTTCGTAAAAAATTAAGAAAAAAAATTT----TCA----TT-C-AGTTTTTAGCCAAAATC
131 AATATTTGGCAAAAAATTGAGGAAAAACTTTTCGGGTCAGTTTTTGCTAAATTTTAGCCAAAATC
* * * * * ** * **
126593 GTGTACTAACCATCACGATTCTTGGCTAAAATCGCGTTTCGGATTCTGGCTCAGTTTTAAATGAT
196 GTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGTCCAGCTCAATTTTGCATGAT
* * * * * *
126658 TTTTGGCAAAAAGAACTCCTTGAAATATCTATATTCATCTAACAAAATCTTAGCCACAATAAATT
261 TTTTGGCAAAAA-AACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGAATA
126723 TAAGAA
325 TAAGAA
*
126729 TTTGTTTTTACGAGCATCTCAATCTTTGTTTCGATTTAAATAGAAATAAATTCAGGAAAAAAAAG
1 TTTGTTTTTACGAGCATCTCAATC-TTGTTTCGATTTAATTAGAAATAAATTC-GGAAAAAAAAG
* * * * *
126794 GAAAAACGATATTACAAACGTGAAAAACCCTTCAATATTTTTGGCATTAAATTATATATTTATTC
64 GAAAAACGATATTAGAAGCGTGAAAAACCCGTCAATATTTTTGGCATTGAATTATATATTTTTTC
* * * *
126859 TGAGTATTATGGCAAAAAATTGAGGCAAAACTTTTCGTGTCAGTTTTTGCTAAATTTTAGCCTAA
129 TGAATATT-TGGCAAAAAATTGAGGAAAAACTTTTCGGGTCAGTTTTTGCTAAATTTTAGCCAAA
* * * * *
126924 ATCGTGTACTAACTATCACGGTTTTTGGCAAAAAACGCCTTCCGGAGTCCCGCCTCAATTTTGCC
193 ATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGTCCAG-CTCAATTTTGCA
* * *
126989 TAATTTTTGG-AGTAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCTGAGCCACATTG
257 TGATTTTTGGCA-AAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTG
* * *
127053 TATGTAAGGA
321 AATATAAGAA
* * * * *
127063 TTTGTTTTTAAGAGCATC-CGAATCTTATTTCGATTTAATTAGAAATTAATTTGG--AAAAATGG
1 TTTGTTTTTACGAGCATCTC-AATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAAGG
* * * * * *
127125 AAAAACGATATTGGAAGCGCGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTAT
65 AAAAACGATATTAGAAGCGTGAAAAACCCGTCAATATTTTTGGCATTGAATTATATATTTTTTCT
* * *
127190 GAATATTTTGCAAAATATTGA-GAAAAACTTTTCGGGTTAGTTTTT
130 GAATATTTGGCAAAAAATTGAGGAAAAACTTTTCGGGTCAGTTTTT
127235 AGCCGAAATA
Statistics
Matches: 678, Mismatches: 131, Indels: 40
0.80 0.15 0.05
Matches are distributed among these distances:
320 25 0.04
321 123 0.18
322 25 0.04
323 73 0.11
324 19 0.03
327 3 0.00
328 24 0.04
329 12 0.02
330 67 0.10
331 12 0.02
332 13 0.02
333 137 0.20
334 125 0.18
335 20 0.03
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (330 bp):
TTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAAGGA
AAAACGATATTAGAAGCGTGAAAAACCCGTCAATATTTTTGGCATTGAATTATATATTTTTTCTG
AATATTTGGCAAAAAATTGAGGAAAAACTTTTCGGGTCAGTTTTTGCTAAATTTTAGCCAAAATC
GTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGTCCAGCTCAATTTTGCATGAT
TTTTGGCAAAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGAATAT
AAGAA
Found at i:129187 original size:311 final size:314
Alignment explanation
Indices: 128607--129223 Score: 814
Period size: 321 Copynumber: 2.0 Consensus size: 314
128597 TTTCGCAAAA
* *
128607 TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGTGCCGGC
1 TTTTAGCCGAAATCGTGTACTAACCATCACGATTCTTGGCTAAAAACGCGTTCCGGAGTGCCGGC
** * *
128672 TCAATTTTGCAGGATTTTTGGCACAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATGTC
66 TCAATTTTAAAGGATTTTTGGCACAAAAACTCCTTGAAATATCTATATTCATCGAACAAAATCTC
* * ** * * * *
128737 AACCACATTAGATATAAGGATTTGTTTTTATTAGCATCTCGATCTTGTTTTGATTTTATTATAAA
131 AACCACAATAAATATAAGGATTTGTTTTTACGAGCATCTCGATCTTATTTCGATTTAATTAGAAA
* * *
128802 CTAATTCTGAAACAAATGGAAAAACGATATTAGAAGGGTGAAAAGCCCGTCAATATTTTTGGCAT
196 CTAATTCT-------ATGGAAAAACGATATTAGAAGCGCGAAAAGCCCGTCAATATTTTTAGCAT
*
128867 TGAATTATATATTTTTTCTAAATATTTCGTAAAAAATTGAGAGAAAAAATATTCATGTCAGT
254 TGAATTATATATTTTTTCTAAATATTTCGCAAAAAATTGAGA-AAAAAATATTCATGTCAGT
* * * *
128929 TTTTAGCCGAAATCGTGTACTAACCATCACGATTCTTGGCTAAAATCGCGTTTCGGA-TTCTGGC
1 TTTTAGCCGAAATCGTGTACTAACCATCACGATTCTTGGCTAAAAACGCGTTCCGGAGTGCCGGC
* * *
128993 TCAGTTTTAAATGATTTTTGGCA-AAAAGACTCCTTGAAATATCTATATTCATCTAACAAAATCT
66 TCAATTTTAAAGGATTTTTGGCACAAAA-ACTCCTTGAAATATCTATATTCATCGAACAAAATCT
* * *
129057 TAGCCACAATAAATTTAAGGATTTGTTTTTACGAGCATC-CGAATCTTATTTCGATTTAATTAGA
130 CAACCACAATAAATATAAGGATTTGTTTTTACGAGCATCTCG-ATCTTATTTCGATTTAATTAGA
* *
129121 AATTAA-T-T-TGGAAAAACGATATTAGAAGCGCGAAAAGCCCGTCAATATTTTTAGCGTTGAAT
194 AACTAATTCTATGGAAAAACGATATTAGAAGCGCGAAAAGCCCGTCAATATTTTTAGCATTGAAT
* *
129183 TATATATTTTTTCTGAATATTTTGCAAAAAATTGAGAAAAA
259 TATATATTTTTTCTAAATATTTCGCAAAAAATTGAGAAAAA
129224 CTTTTCGGGT
Statistics
Matches: 261, Mismatches: 32, Indels: 16
0.84 0.10 0.05
Matches are distributed among these distances:
310 4 0.02
311 84 0.32
319 1 0.00
320 7 0.03
321 112 0.43
322 53 0.20
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (314 bp):
TTTTAGCCGAAATCGTGTACTAACCATCACGATTCTTGGCTAAAAACGCGTTCCGGAGTGCCGGC
TCAATTTTAAAGGATTTTTGGCACAAAAACTCCTTGAAATATCTATATTCATCGAACAAAATCTC
AACCACAATAAATATAAGGATTTGTTTTTACGAGCATCTCGATCTTATTTCGATTTAATTAGAAA
CTAATTCTATGGAAAAACGATATTAGAAGCGCGAAAAGCCCGTCAATATTTTTAGCATTGAATTA
TATATTTTTTCTAAATATTTCGCAAAAAATTGAGAAAAAAATATTCATGTCAGT
Found at i:129891 original size:821 final size:826
Alignment explanation
Indices: 127753--129959 Score: 3067
Period size: 821 Copynumber: 2.6 Consensus size: 826
127743 TCATGTCAGT
* * * * * * ***
127753 TTTTAGCCGAAATCGTGTACTAACCATCAAGATTCTTGGCTAAAATCGCGTTTCGGA-TTATGGC
1 TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCAAAAAACGCGTTCCGGAGTGCCGGC
* ** * * * * *
127817 TCAGTTTTAAATGATTTTTGGCA-AAAAGACTACTTGAAATATCTATATTCATCTAACAAAATCT
66 TCAATTTTGCAGGATTTTTGGCACAAAA-ACTCCTTGAAATATCTATATTCATCGAACCAAATGT
* * * * * * ** * * *
127881 TAGCCACAATAAATTTAAGAATTTGTTTTTACAAGCATCTCAATCTT-TGTTTCGATTTAAATAG
130 CAACCACATTAGATATAAGGATTTGTTTTTATTAGCATCTCGATCTTCT-TTT-GATTTTATTAG
* * * * ** * *
127945 AAA-TAAATTCAGGAAAAAAAAAAAGGGAAAAACGATATTACAAACGTGAAAAACCCTTCAATAT
193 AAACT-AATTC-TG----AAACAAATGGAAAAACGATATTAGAAGGGTGAAAAGCCCGTCAATAT
* * * * * * * * * * * *
128009 TTTTGGCATTAAATTATATATTTATTCTGAGTATTATGGCAAAAAATGGAG-GAAAAACTTTTCG
252 TTTTAGCATTGAATTATATATTTTTTCTAAATATT-TCGTAAAAAATTGAGAAAAAAAATATTCA
* * * * * **
128073 TGTCAGTTTTTGCAAAATTTTAGCCTAAATCGTGTACTAACTATCACGGTTTTTGGCAAAAAAAG
316 TGTCAG----T------TTTTAGCCGAAATCGTGTACTAACAATCACGATTCTTGGC-TAAAATC
* * * * * * *** * * *
128138 GCCTTCCGGAGTCCCGCCTCAATTTTGCCTAATTTTTGGAG-TAAAA-ACTCCTTGAAATGTCTA
370 GCGTTTCGGA-TTCTGGCTCAGTTTTAAATGA-TTTTGG-GCAAAAAGACTCCTTGAAATATCTA
* * * * ** *
128201 TATTCATCGAACCAAATCTGAGCCACATTGTATTTAAGGATTTGTTTTTAAGAGCATCCGAATCT
432 TATTCATCTAACAAAATCTTAGCCACAATAAATTTAAGGATTTGTTTTTACGAGCATCCGAATCT
128266 TATTTCGATTTAATTAGAAATTAATTTGGAAAAATGGAAAAACGATATTAGAAGCGCGAAAAGAC
497 TATTTCGATTTAATTAGAAATTAA-TT------ATGGAAAAACGATATTAGAAGCGCGAAAAGAC
* * *
128331 CGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAATATTTTGTAAAAAATTGAGAAAAAC
555 CGTCAATATTTTTAGCGTTGAATTATATATTTTTTCTGAATATTTTGCAAAAAATTGAGAAAAAC
128396 TTTTCGGGTTAGTTTTTAGCCGAAATAGTTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTA
620 TTTTCGGGTTAGTTTTTAGCCGAAATAGTTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTA
*
128461 ATTAGAAATAAATTCGGGAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAATCCTTCAATTTT
685 ATTAGAAATAAATTCGGG---AAAA-GAAAAACAATATTAGAAGCGTGAAAAATCCTTCAATTTT
*
128526 TTTGGCGTTGAATTATATATTTTTTCTGAGTATTCTGACAAAAAAAAAGAGGAAATACTTTTAGG
746 TTTGGCGTTGAATTATATATTTTTTCTGAGTATTCTGACAAAAAAAAAGAGGAAAAACTTTTAGG
128591 GTCAATTTTCGCAAAA
811 GTCAATTTTCGCAAAA
*
128607 TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGTGCCGGC
1 TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCAAAAAACGCGTTCCGGAGTGCCGGC
128672 TCAATTTTGCAGGATTTTTGGCACAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATGTC
66 TCAATTTTGCAGGATTTTTGGCACAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATGTC
* *
128737 AACCACATTAGATATAAGGATTTGTTTTTATTAGCATCTCGATCTTGTTTTGATTTTATTATAAA
131 AACCACATTAGATATAAGGATTTGTTTTTATTAGCATCTCGATCTTCTTTTGATTTTATTAGAAA
*
128802 CTAATTCTGAAACAAATGGAAAAACGATATTAGAAGGGTGAAAAGCCCGTCAATATTTTTGGCAT
196 CTAATTCTGAAACAAATGGAAAAACGATATTAGAAGGGTGAAAAGCCCGTCAATATTTTTAGCAT
*
128867 TGAATTATATATTTTTTCTAAATATTTCGTAAAAAATTGAGAGAAAAAATATTCATGTCAGTTTT
261 TGAATTATATATTTTTTCTAAATATTTCGTAAAAAATTGAGAAAAAAAATATTCATGTCAGTTTT
*
128932 TAGCCGAAATCGTGTACTAACCATCACGATTCTTGGCTAAAATCGCGTTTCGGATTCTGGCTCAG
326 TAGCCGAAATCGTGTACTAACAATCACGATTCTTGGCTAAAATCGCGTTTCGGATTCTGGCTCAG
*
128997 TTTTAAATGATTTTTGGCAAAAAGACTCCTTGAAATATCTATATTCATCTAACAAAATCTTAGCC
391 TTTTAAATGATTTTGGGCAAAAAGACTCCTTGAAATATCTATATTCATCTAACAAAATCTTAGCC
129062 ACAATAAATTTAAGGATTTGTTTTTACGAGCATCCGAATCTTATTTCGATTTAATTAGAAATTAA
456 ACAATAAATTTAAGGATTTGTTTTTACGAGCATCCGAATCTTATTTCGATTTAATTAGAAATTAA
*
129127 TT-TGGAAAAACGATATTAGAAGCGCGAAAAGCCCGTCAATATTTTTAGCGTTGAATTATATATT
521 TTATGGAAAAACGATATTAGAAGCGCGAAAAGACCGTCAATATTTTTAGCGTTGAATTATATATT
* *
129191 TTTTCTGAATATTTTGCAAAAAATTGAGAAAAACTTTTCGGGTTTGTTTTTATCCGAAATAGTTT
586 TTTTCTGAATATTTTGCAAAAAATTGAGAAAAACTTTTCGGGTTAGTTTTTAGCCGAAATAGTTT
129256 GTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATAAATTC-GG-AAA-AAAAACAA
651 GTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATAAATTCGGGAAAAGAAAAACAA
129318 TATTAGAAGCGTGAAAAATCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTC
716 TATTAGAAGCGTGAAAAATCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTC
* * *
129383 TGGCAAATAAAAAGAGGAAAAACTTTTAGGGTCAATTTTTGCAAAA
781 TGACAAAAAAAAAGAGGAAAAACTTTTAGGGTCAATTTTCGCAAAA
129429 -TTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCAAAAAACGCGTTCCGGAGTGCCGGC
1 TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCAAAAAACGCGTTCCGGAGTGCCGGC
129493 TCAATTTTGCAGGATTTTTGGCACAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATGTC
66 TCAATTTTGCAGGATTTTTGGCACAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATGTC
*
129558 AACCACATTGGATATAAGGATTTGTTTTTATTAGCATCTCGATCTTCTTTTGATTTTATTAGAAA
131 AACCACATTAGATATAAGGATTTGTTTTTATTAGCATCTCGATCTTCTTTTGATTTTATTAGAAA
*
129623 TTAATTCTGAAACAAATGGAAAAACGATATTAGAAGGGTGAAAAGCCCGTCAATATTTTTAGCAT
196 CTAATTCTGAAACAAATGGAAAAACGATATTAGAAGGGTGAAAAGCCCGTCAATATTTTTAGCAT
*
129688 TGAATTATATATTTTTTCTAAATATTTCGTAAAAATTTGAGAAAAAAAA-ATTTCATGTCAGTTT
261 TGAATTATATATTTTTTCTAAATATTTCGTAAAAAATTGAGAAAAAAAATA-TTCATGTCAGTTT
*
129752 TTAGCCGAAATCGTGTACTAACAATCACGATTCTTGGCTAAAATCGTGTTTCGGATTCTGGCTCA
325 TTAGCCGAAATCGTGTACTAACAATCACGATTCTTGGCTAAAATCGCGTTTCGGATTCTGGCTCA
129817 GTTTTAAATGATTTTGGGCAAAAAGACTCCTTGAAATATCTATATTCATCTAACAAAATCTTAGC
390 GTTTTAAATGATTTTGGGCAAAAAGACTCCTTGAAATATCTATATTCATCTAACAAAATCTTAGC
* *
129882 CACAATAAATTTAAGAATTTGTTTTTACGAGCATCTC-AATCTTTATTTCGATTTAAATAGAAAT
455 CACAATAAATTTAAGGATTTGTTTTTACGAGCATC-CGAATC-TTATTTCGATTTAATTAGAAAT
*
129946 AAATTCA-GGAAAAA
518 TAATT-ATGGAAAAA
129960 AAAAAGAAAA
Statistics
Matches: 1243, Mismatches: 98, Indels: 55
0.89 0.07 0.04
Matches are distributed among these distances:
820 1 0.00
821 478 0.38
822 140 0.11
823 7 0.01
824 3 0.00
828 2 0.00
829 170 0.14
835 1 0.00
836 11 0.01
837 111 0.09
838 12 0.01
839 36 0.03
845 1 0.00
848 12 0.01
849 87 0.07
853 1 0.00
854 68 0.05
855 97 0.08
856 5 0.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (826 bp):
TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCAAAAAACGCGTTCCGGAGTGCCGGC
TCAATTTTGCAGGATTTTTGGCACAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATGTC
AACCACATTAGATATAAGGATTTGTTTTTATTAGCATCTCGATCTTCTTTTGATTTTATTAGAAA
CTAATTCTGAAACAAATGGAAAAACGATATTAGAAGGGTGAAAAGCCCGTCAATATTTTTAGCAT
TGAATTATATATTTTTTCTAAATATTTCGTAAAAAATTGAGAAAAAAAATATTCATGTCAGTTTT
TAGCCGAAATCGTGTACTAACAATCACGATTCTTGGCTAAAATCGCGTTTCGGATTCTGGCTCAG
TTTTAAATGATTTTGGGCAAAAAGACTCCTTGAAATATCTATATTCATCTAACAAAATCTTAGCC
ACAATAAATTTAAGGATTTGTTTTTACGAGCATCCGAATCTTATTTCGATTTAATTAGAAATTAA
TTATGGAAAAACGATATTAGAAGCGCGAAAAGACCGTCAATATTTTTAGCGTTGAATTATATATT
TTTTCTGAATATTTTGCAAAAAATTGAGAAAAACTTTTCGGGTTAGTTTTTAGCCGAAATAGTTT
GTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATAAATTCGGGAAAAGAAAAACAA
TATTAGAAGCGTGAAAAATCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTC
TGACAAAAAAAAAGAGGAAAAACTTTTAGGGTCAATTTTCGCAAAA
Found at i:131348 original size:30 final size:30
Alignment explanation
Indices: 131312--131372 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
131302 TTAGTAAGAT
*
131312 ATTAAAATTTGAGAGTATAAGAGGAAAGTC
1 ATTAAAAGTTGAGAGTATAAGAGGAAAGTC
* *
131342 ATTAAAAGTTGAGGGTATAATAGGAAAGTC
1 ATTAAAAGTTGAGAGTATAAGAGGAAAGTC
131372 A
1 A
131373 AGATAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.46, C:0.03, G:0.25, T:0.26
Consensus pattern (30 bp):
ATTAAAAGTTGAGAGTATAAGAGGAAAGTC
Found at i:137550 original size:27 final size:24
Alignment explanation
Indices: 137511--137563 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
137501 CCCCGGTGGA
137511 GGGTAACCATAACCAGGCGGTGGAGGC
1 GGGTAACCATAACC---CGGTGGAGGC
* *
137538 GGGTAGCCGTAACCCGGTGGAGGC
1 GGGTAACCATAACCCGGTGGAGGC
137562 GG
1 GG
137564 TCCCTGTGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 12 0.50
27 12 0.50
ACGTcount: A:0.21, C:0.23, G:0.45, T:0.11
Consensus pattern (24 bp):
GGGTAACCATAACCCGGTGGAGGC
Done.