Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 80 of 203
Found at i:25432330 original size:37 final size:37
Alignment explanation
Indices: 25432267--25432358 Score: 98
Period size: 37 Copynumber: 2.4 Consensus size: 37
25432257 ATTTTATAAA
*
25432267 TAATATTATTTTAATAGTTTAATATTAAATTAA-ATT
1 TAATATTATCTTAATAGTTTAATATTAAATTAATATT
* *
25432303 TAATACTTATCTTAATAGTATT-TTATTAATTTAATATT
1 TAATA-TTATCTTAATAGT-TTAATATTAAATTAATATT
*
25432341 AAAGTGATTATCTTAATA
1 TAA-T-ATTATCTTAATA
25432359 TTAAATTTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
36 5 0.11
37 22 0.47
38 7 0.15
39 12 0.26
40 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.51
Consensus pattern (37 bp):
TAATATTATCTTAATAGTTTAATATTAAATTAATATT
Found at i:25432552 original size:25 final size:26
Alignment explanation
Indices: 25432502--25432552 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
25432492 AGTTATAGAG
*
25432502 AGAAAATTCTCTAAAGAGATTATTCT
1 AGAAAATTCTCTAAAGACATTATTCT
* *
25432528 AGAAAATT-TCTAGAGACATTTTTCT
1 AGAAAATTCTCTAAAGACATTATTCT
25432553 GATTTACAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (26 bp):
AGAAAATTCTCTAAAGACATTATTCT
Found at i:25436246 original size:21 final size:20
Alignment explanation
Indices: 25436220--25436280 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 20
25436210 CCAAGATTAC
25436220 ATATCATATCCAAGATTGCAT
1 ATATCATAT-CAAGATTGCAT
25436241 ATATCATATCTAAGATTGCAT
1 ATATCATATC-AAGATTGCAT
25436262 ATCAT-ATAT-AAGATTGCAT
1 AT-ATCATATCAAGATTGCAT
25436281 GTCCTTGAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.26
20 1 0.03
21 25 0.66
22 2 0.05
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (20 bp):
ATATCATATCAAGATTGCAT
Found at i:25436273 original size:19 final size:19
Alignment explanation
Indices: 25436212--25436280 Score: 93
Period size: 19 Copynumber: 3.5 Consensus size: 19
25436202 CATATCTTCC
* *
25436212 AAGATTACATATCATATCC
1 AAGATTGCATATCATATCT
25436231 AAGATTGCATATATCATATCT
1 AAGATTGC--ATATCATATCT
*
25436252 AAGATTGCATATCATATAT
1 AAGATTGCATATCATATCT
25436271 AAGATTGCAT
1 AAGATTGCAT
25436281 GTCCTTGAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
19 27 0.60
21 18 0.40
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (19 bp):
AAGATTGCATATCATATCT
Found at i:25439661 original size:3 final size:3
Alignment explanation
Indices: 25439641--25439691 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
25439631 AATGTAGATA
* * *
25439641 AAG ATG AAG AAT AAG AAG AAG AAG AAG AAA AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
25439689 AAG
1 AAG
25439692 GAGGAGATTG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.29, T:0.04
Consensus pattern (3 bp):
AAG
Found at i:25442237 original size:16 final size:16
Alignment explanation
Indices: 25442216--25442248 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
25442206 TTTTTAAAAA
25442216 TTATTTATATTTTTTC
1 TTATTTATATTTTTTC
*
25442232 TTATTTCTATTTTTTC
1 TTATTTATATTTTTTC
25442248 T
1 T
25442249 GATGTTCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTATATTTTTTC
Found at i:25445057 original size:29 final size:30
Alignment explanation
Indices: 25444999--25445057 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
25444989 GTTGAGGGAG
* * *
25444999 AAAAAGTTTAAGTACCAATATGGGGTTAAA
1 AAAAACTTTAAGTACCAATATGAGGATAAA
*
25445029 AAAAACTTTAAGTACCAATCT-AGGATAAA
1 AAAAACTTTAAGTACCAATATGAGGATAAA
25445058 TGAATAAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 6 0.24
30 19 0.76
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.25
Consensus pattern (30 bp):
AAAAACTTTAAGTACCAATATGAGGATAAA
Found at i:25452065 original size:23 final size:23
Alignment explanation
Indices: 25452029--25452074 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
25452019 AATGTCAAAT
* * *
25452029 ATATTATGCTAATAAATGCTAAA
1 ATATTATACCAATAAATACTAAA
25452052 ATATTATACCAATAAATACTAAA
1 ATATTATACCAATAAATACTAAA
25452075 TCTTCTAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.52, C:0.11, G:0.04, T:0.33
Consensus pattern (23 bp):
ATATTATACCAATAAATACTAAA
Found at i:25456512 original size:24 final size:24
Alignment explanation
Indices: 25456481--25456544 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
25456471 AAATCTATTT
*
25456481 CTAATAAATG-TCAAATATATTATG
1 CTAATAAATGCT-AAATATATTATA
25456505 CTAATAAATGCTAAATATATTATA
1 CTAATAAATGCTAAATATATTATA
*
25456529 CTAATAAATACTAAAT
1 CTAATAAATGCTAAAT
25456545 CTTCTAGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 36 0.97
25 1 0.03
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (24 bp):
CTAATAAATGCTAAATATATTATA
Found at i:25461644 original size:10 final size:10
Alignment explanation
Indices: 25461629--25461681 Score: 61
Period size: 10 Copynumber: 5.1 Consensus size: 10
25461619 AAAAGTACAG
25461629 AGAAAACTAA
1 AGAAAACTAA
*
25461639 AGAAAACCTAG
1 AGAAAA-CTAA
25461650 AGAAAACTAA
1 AGAAAACTAA
**
25461660 AGAAAACCTCG
1 AGAAAA-CTAA
25461671 AGAAAACTAA
1 AGAAAACTAA
25461681 A
1 A
25461682 CCTAAAACTA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
10 18 0.51
11 17 0.49
ACGTcount: A:0.62, C:0.15, G:0.13, T:0.09
Consensus pattern (10 bp):
AGAAAACTAA
Found at i:25461653 original size:21 final size:21
Alignment explanation
Indices: 25461627--25461681 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
25461617 AGAAAAGTAC
25461627 AGAGAAAACTAAAGAAAACCT
1 AGAGAAAACTAAAGAAAACCT
25461648 AGAGAAAACTAAAGAAAACCT
1 AGAGAAAACTAAAGAAAACCT
*
25461669 CGAGAAAACTAAA
1 AGAGAAAACTAAA
25461682 CCTAAAACTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.62, C:0.15, G:0.15, T:0.09
Consensus pattern (21 bp):
AGAGAAAACTAAAGAAAACCT
Found at i:25461655 original size:11 final size:11
Alignment explanation
Indices: 25461627--25461677 Score: 61
Period size: 11 Copynumber: 4.8 Consensus size: 11
25461617 AGAAAAGTAC
25461627 AGAGAAAA-CT
1 AGAGAAAACCT
*
25461637 AAAGAAAACCT
1 AGAGAAAACCT
25461648 AGAGAAAA-CT
1 AGAGAAAACCT
*
25461658 AAAGAAAACCT
1 AGAGAAAACCT
*
25461669 CGAGAAAAC
1 AGAGAAAAC
25461678 TAAACCTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
10 16 0.47
11 18 0.53
ACGTcount: A:0.61, C:0.16, G:0.16, T:0.08
Consensus pattern (11 bp):
AGAGAAAACCT
Found at i:25463936 original size:13 final size:14
Alignment explanation
Indices: 25463918--25463946 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
25463908 TAATTTGTTG
25463918 CACAT-AAGAAAAA
1 CACATAAAGAAAAA
25463931 CACATAAAGAAAAA
1 CACATAAAGAAAAA
25463945 CA
1 CA
25463947 AACAACAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.69, C:0.17, G:0.07, T:0.07
Consensus pattern (14 bp):
CACATAAAGAAAAA
Found at i:25470624 original size:26 final size:26
Alignment explanation
Indices: 25470578--25470637 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
25470568 TTATTCTCTA
25470578 AAAATTTTACCAGAGGCAAAATCATC
1 AAAATTTTACCAGAGGCAAAATCATC
* *
25470604 AAAATTTTACTAG-GAGTAAAATCATC
1 AAAATTTTACCAGAG-GCAAAATCATC
25470630 AAAATTTT
1 AAAATTTT
25470638 GCTGGGGGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 1 0.03
26 30 0.97
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (26 bp):
AAAATTTTACCAGAGGCAAAATCATC
Found at i:25470650 original size:26 final size:26
Alignment explanation
Indices: 25470578--25470651 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
25470568 TTATTCTCTA
* *
25470578 AAAATTTTACCA-GAGGCAAAATCATC
1 AAAATTTTACTAGGA-GAAAAATCATC
*
25470604 AAAATTTTACTAGGAGTAAAATCATC
1 AAAATTTTACTAGGAGAAAAATCATC
* * *
25470630 AAAATTTTGCTGGGGGAAAAAT
1 AAAATTTTACTAGGAGAAAAAT
25470652 AGGGATGAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 39 0.95
27 2 0.05
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (26 bp):
AAAATTTTACTAGGAGAAAAATCATC
Found at i:25475034 original size:78 final size:80
Alignment explanation
Indices: 25474944--25475104 Score: 213
Period size: 80 Copynumber: 2.0 Consensus size: 80
25474934 TTTTATAGAC
*
25474944 ATTGGTATATATAAATTATAATACATAT-ATCAACACTTAC-ATGTCAT-A-ATACATATATCAT
1 ATTGGTATATATAAATCATAATACATATCAT--ACACTTACTATGTCATCATATACATATATCAT
25475005 TCAAGACAACTCTCGAT
64 TCAAGACAACTCTCGAT
* * * * * *
25475022 ATTGGTATATATATATCATAATACATGTCATTCTCTTACTATTTCTTCATATACATATATCATTC
1 ATTGGTATATATAAATCATAATACATATCATACACTTACTATGTCATCATATACATATATCATTC
25475087 AAGACAACTCTCGAT
66 AAGACAACTCTCGAT
25475102 ATT
1 ATT
25475105 TTACCTTTCG
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
77 6 0.08
78 30 0.42
79 3 0.04
80 33 0.46
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.39
Consensus pattern (80 bp):
ATTGGTATATATAAATCATAATACATATCATACACTTACTATGTCATCATATACATATATCATTC
AAGACAACTCTCGAT
Found at i:25475105 original size:40 final size:40
Alignment explanation
Indices: 25474986--25475105 Score: 102
Period size: 42 Copynumber: 3.0 Consensus size: 40
25474976 ACACTTACAT
*
25474986 GTCATAATACATATATCATTCAAGACAACTCTCGATA-TTG
1 GTCAT-ATACATATATCATTCAAGACAACTCTCGATATTTC
* * * * * * *
25475026 GT-ATATATATATCATAATACATGTC-ATTCTCTTACTATTTC
1 GTCATATACATAT-ATCATTCAAGACAACTCTC-GA-TATTTC
*
25475067 TTCATATACATATATCATTCAAGACAACTCTCGATATTT
1 GTCATATACATATATCATTCAAGACAACTCTCGATATTT
25475106 TACCTTTCGA
Statistics
Matches: 58, Mismatches: 16, Indels: 12
0.67 0.19 0.14
Matches are distributed among these distances:
38 12 0.21
39 11 0.19
40 9 0.16
41 12 0.21
42 14 0.24
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.39
Consensus pattern (40 bp):
GTCATATACATATATCATTCAAGACAACTCTCGATATTTC
Found at i:25475222 original size:21 final size:21
Alignment explanation
Indices: 25475163--25475331 Score: 83
Period size: 21 Copynumber: 8.0 Consensus size: 21
25475153 GTTCGAAAGC
* *
25475163 TGAACAGAAGCTCATGAGAGCT
1 TGAACAGAAGCTCATAAG-GGT
* * *
25475185 T-AATAGAAACCCATAAGGGT
1 TGAACAGAAGCTCATAAGGGT
* * *
25475205 TGAACAGAAGCTCGTAAGAGC
1 TGAACAGAAGCTCATAAGGGT
* * *
25475226 TGAATAGAAACCCATAAGGGT
1 TGAACAGAAGCTCATAAGGGT
* * *
25475247 TAAACAGAAGCTCAAAAGAGCT
1 TGAACAGAAGCTCATAAG-GGT
** * *
25475269 T-AATGGAAACCCATAAGGGT
1 TGAACAGAAGCTCATAAGGGT
* * *
25475289 TAAACAGAAGCTCAAAAGAGT
1 TGAACAGAAGCTCATAAGGGT
* *
25475310 TGAAC-GAAAACCCATAAGGGT
1 TGAACAG-AAGCTCATAAGGGT
25475331 T
1 T
25475332 AAATAGAAAC
Statistics
Matches: 103, Mismatches: 40, Indels: 9
0.68 0.26 0.06
Matches are distributed among these distances:
20 7 0.07
21 92 0.89
22 4 0.04
ACGTcount: A:0.43, C:0.17, G:0.23, T:0.17
Consensus pattern (21 bp):
TGAACAGAAGCTCATAAGGGT
Found at i:25475225 original size:42 final size:42
Alignment explanation
Indices: 25475165--25475361 Score: 245
Period size: 42 Copynumber: 4.7 Consensus size: 42
25475155 TCGAAAGCTG
* *
25475165 AACAGAAGCTCATGAGAGCTTAATAGAAACCCATAAGGGTTG
1 AACAGAAGCTCATAAGAGCTTAATAGAAACCCATAAGGGTTA
* *
25475207 AACAGAAGCTCGTAAGAGCTGAATAGAAACCCATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTTAATAGAAACCCATAAGGGTTA
* *
25475249 AACAGAAGCTCAAAAGAGCTTAATGGAAACCCATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTTAATAGAAACCCATAAGGGTTA
* *
25475291 AACAGAAGCTCAAAAGAG-TTGAA-CGAAAACCCATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTT-AATAG-AAACCCATAAGGGTTA
* * * * *
25475333 AATAGAAACTCGTAAGAGCTAAACAGAAA
1 AACAGAAGCTCATAAGAGCTTAATAGAAA
25475362 GTAAAACACG
Statistics
Matches: 136, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
41 3 0.02
42 131 0.96
43 2 0.01
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.16
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTTAATAGAAACCCATAAGGGTTA
Found at i:25475348 original size:21 final size:21
Alignment explanation
Indices: 25475186--25475341 Score: 91
Period size: 21 Copynumber: 7.4 Consensus size: 21
25475176 ATGAGAGCTT
*
25475186 AATAGAAACCCATAAGGGTTG
1 AATAGAAACCCATAAGGGTTA
* * * * * * *
25475207 AACAGAAGCTCGTAAGAGCTG
1 AATAGAAACCCATAAGGGTTA
25475228 AATAGAAACCCATAAGGGTTA
1 AATAGAAACCCATAAGGGTTA
* * * * *
25475249 AACAGAAGCTCAAAAGAGCTT-
1 AATAGAAACCCATAAG-GGTTA
*
25475270 AATGGAAACCCATAAGGGTTA
1 AATAGAAACCCATAAGGGTTA
* * * * * *
25475291 AACAGAAGCTCAAAAGAGTTG
1 AATAGAAACCCATAAGGGTTA
*
25475312 AA-CGAAAACCCATAAGGGTTA
1 AATAG-AAACCCATAAGGGTTA
25475333 AATAGAAAC
1 AATAGAAAC
25475342 TCGTAAGAGC
Statistics
Matches: 93, Mismatches: 38, Indels: 8
0.67 0.27 0.06
Matches are distributed among these distances:
20 4 0.04
21 85 0.91
22 4 0.04
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.16
Consensus pattern (21 bp):
AATAGAAACCCATAAGGGTTA
Found at i:25477950 original size:8 final size:8
Alignment explanation
Indices: 25477932--25477967 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
25477922 TAGGGTTTGC
25477932 AAAAGAAAG
1 AAAA-AAAG
*
25477941 AAGAAAAG
1 AAAAAAAG
25477949 AAAAAAAG
1 AAAAAAAG
25477957 AAAAAAAG
1 AAAAAAAG
25477965 AAA
1 AAA
25477968 GGAAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 22 0.88
9 3 0.12
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:25477957 original size:20 final size:19
Alignment explanation
Indices: 25477932--25477993 Score: 70
Period size: 20 Copynumber: 3.2 Consensus size: 19
25477922 TAGGGTTTGC
25477932 AAAAGAAAGAAGAAAAGAAA
1 AAAAGAAA-AAGAAAAGAAA
* *
25477952 AAAAGAAAAAAAGAAAGGAA
1 AAAAGAAAAAGA-AAAGAAA
* *
25477972 AAAATAAAAAGGAAAGAAA
1 AAAAGAAAAAGAAAAGAAA
25477991 AAA
1 AAA
25477994 TAAAAATATA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
19 12 0.34
20 23 0.66
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.02
Consensus pattern (19 bp):
AAAAGAAAAAGAAAAGAAA
Found at i:25477958 original size:16 final size:17
Alignment explanation
Indices: 25477932--25477990 Score: 66
Period size: 16 Copynumber: 3.5 Consensus size: 17
25477922 TAGGGTTTGC
*
25477932 AAAAGAAAGAAGAAAAG
1 AAAAGAAAGAAAAAAAG
25477949 AAAA-AAAGAAAAAAAG
1 AAAAGAAAGAAAAAAAG
* *
25477965 AAAGGAAAAAATAAAAAG
1 AAAAGAAAGAA-AAAAAG
*
25477983 GAAAGAAA
1 AAAAGAAA
25477991 AAATAAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
16 14 0.40
17 9 0.26
18 12 0.34
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.02
Consensus pattern (17 bp):
AAAAGAAAGAAAAAAAG
Found at i:25477968 original size:12 final size:13
Alignment explanation
Indices: 25477945--25477993 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 13
25477935 AGAAAGAAGA
25477945 AAAGAAAAAAA-G
1 AAAGAAAAAAAGG
25477957 AAA-AAAAGAAAGG
1 AAAGAAAA-AAAGG
*
25477970 AAAAAATAAAAAGG
1 AAAGAA-AAAAAGG
25477984 AAAGAAAAAA
1 AAAGAAAAAA
25477994 TAAAAATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
11 4 0.12
12 6 0.19
13 8 0.25
14 12 0.38
15 2 0.06
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (13 bp):
AAAGAAAAAAAGG
Found at i:25477973 original size:19 final size:18
Alignment explanation
Indices: 25477945--25477999 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 18
25477935 AGAAAGAAGA
25477945 AAAGAAAAAAAGAAAAAAAG
1 AAAG-AAAAAA-AAAAAAAG
* *
25477965 AAAGGAAAAAATAAAAAGG
1 AAA-GAAAAAAAAAAAAAG
25477984 AAAGAAAAAATAAAAA
1 AAAGAAAAAA-AAAAA
25478000 TATATAATAG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 7 0.23
19 13 0.43
20 9 0.30
21 1 0.03
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.04
Consensus pattern (18 bp):
AAAGAAAAAAAAAAAAAG
Found at i:25477980 original size:18 final size:18
Alignment explanation
Indices: 25477958--25477999 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
25477948 GAAAAAAAGA
*
25477958 AAAAAAGAAAGGAAAAAAT
1 AAAAAGGAAA-GAAAAAAT
25477977 AAAAAGGAAAGAAAAAAT
1 AAAAAGGAAAGAAAAAAT
25477995 AAAAA
1 AAAAA
25478000 TATATAATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (18 bp):
AAAAAGGAAAGAAAAAAT
Found at i:25478117 original size:14 final size:14
Alignment explanation
Indices: 25478098--25478156 Score: 64
Period size: 14 Copynumber: 4.2 Consensus size: 14
25478088 CCCACAGCAA
25478098 GCCACCAGCAACAG
1 GCCACCAGCAACAG
*
25478112 GCCACCAGCAATAG
1 GCCACCAGCAACAG
* * *
25478126 GCCATCGGCATCAG
1 GCCACCAGCAACAG
* *
25478140 GCCATCAGCAGCAG
1 GCCACCAGCAACAG
25478154 GCC
1 GCC
25478157 CAGTCCCTAC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 38 1.00
ACGTcount: A:0.29, C:0.39, G:0.25, T:0.07
Consensus pattern (14 bp):
GCCACCAGCAACAG
Found at i:25478302 original size:8 final size:8
Alignment explanation
Indices: 25478289--25478342 Score: 53
Period size: 8 Copynumber: 7.2 Consensus size: 8
25478279 CAATAAGCAG
25478289 AAAAAGAA
1 AAAAAGAA
*
25478297 AAAAAGAG
1 AAAAAGAA
25478305 AAAAAG--
1 AAAAAGAA
*
25478311 -AAAAGGA
1 AAAAAGAA
*
25478318 AAAAAGAG
1 AAAAAGAA
25478326 AAAAA-AA
1 AAAAAGAA
25478333 AAAAAGAA
1 AAAAAGAA
25478341 AA
1 AA
25478343 GGGATCCCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
5 5 0.13
7 6 0.16
8 27 0.71
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:25478319 original size:22 final size:21
Alignment explanation
Indices: 25478287--25478342 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 21
25478277 CCCAATAAGC
25478287 AGAAAAAGAAAAAAAGAGAAAA
1 AGAAAAAG-AAAAAAGAGAAAA
*
25478309 AGAAAAGGAAAAAAGAGAAAAA
1 AGAAAAAGAAAAAAGAG-AAAA
*
25478331 AAAAAAAGAAAA
1 AGAAAAAGAAAA
25478343 GGGATCCCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 9 0.30
22 21 0.70
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (21 bp):
AGAAAAAGAAAAAAGAGAAAA
Found at i:25478320 original size:21 final size:21
Alignment explanation
Indices: 25478289--25478343 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
25478279 CAATAAGCAG
25478289 AAAAAGAAAAAAAGAGAAAAA
1 AAAAAGAAAAAAAGAGAAAAA
* *
25478310 GAAAAGGAAAAAAGAGAAAAA
1 AAAAAGAAAAAAAGAGAAAAA
*
25478331 AAAAA-AAGAAAAG
1 AAAAAGAAAAAAAG
25478344 GGATCCCAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 6 0.21
21 23 0.79
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (21 bp):
AAAAAGAAAAAAAGAGAAAAA
Found at i:25478321 original size:13 final size:14
Alignment explanation
Indices: 25478305--25478344 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
25478295 AAAAAAAGAG
25478305 AAAAAGAAAAGGAA
1 AAAAAGAAAAGGAA
*
25478319 AAAAGAGAAAA-AAA
1 AAAA-AGAAAAGGAA
25478333 AAAAAGAAAAGG
1 AAAAAGAAAAGG
25478345 GATCCCAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 6 0.27
14 10 0.45
15 6 0.27
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAGGAA
Found at i:25478329 original size:28 final size:29
Alignment explanation
Indices: 25478289--25478344 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
25478279 CAATAAGCAG
* *
25478289 AAAAAGAAAAAAAGAGAAAAAGAAAAGGA
1 AAAAAGAAAAAAAAAAAAAAAGAAAAGGA
*
25478318 AAAAAG-AGAAAAAAAAAAAAGAAAAGG
1 AAAAAGAAAAAAAAAAAAAAAGAAAAGG
25478345 GATCCCAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (29 bp):
AAAAAGAAAAAAAAAAAAAAAGAAAAGGA
Found at i:25478979 original size:12 final size:13
Alignment explanation
Indices: 25478962--25478990 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
25478952 AAATCGACTT
25478962 TTTTAAAAGA-AA
1 TTTTAAAAGATAA
25478974 TTTTAAAAGATAA
1 TTTTAAAAGATAA
25478987 TTTT
1 TTTT
25478991 TCTTTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (13 bp):
TTTTAAAAGATAA
Found at i:25481116 original size:42 final size:42
Alignment explanation
Indices: 25481064--25481256 Score: 296
Period size: 42 Copynumber: 4.6 Consensus size: 42
25481054 GCTCGAAAGC
* * *
25481064 TAAACAGAAGCTCATGAGAGCTTAACAGAAACCCATAAGGGT
1 TAAACAGAAGCTCATAAGAGCTAAATAGAAACCCATAAGGGT
* * * *
25481106 TGAACAGAAGCTCGTAAGAGCTGAATGGAAACCCATAAGGGT
1 TAAACAGAAGCTCATAAGAGCTAAATAGAAACCCATAAGGGT
*
25481148 TAAACAGAAGCTCAAAAGAGCTAAATAGAAACCCATAAGGGT
1 TAAACAGAAGCTCATAAGAGCTAAATAGAAACCCATAAGGGT
*
25481190 TAAACAGAAGCTCAAAAGAGCTAAATAGAAACCCATAAGGGT
1 TAAACAGAAGCTCATAAGAGCTAAATAGAAACCCATAAGGGT
*
25481232 TAAACAGAAGCTCTTAAGAGCTAAA
1 TAAACAGAAGCTCATAAGAGCTAAA
25481257 CGGAAAGTAA
Statistics
Matches: 138, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 138 1.00
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.16
Consensus pattern (42 bp):
TAAACAGAAGCTCATAAGAGCTAAATAGAAACCCATAAGGGT
Found at i:25481256 original size:21 final size:21
Alignment explanation
Indices: 25481047--25481257 Score: 147
Period size: 21 Copynumber: 10.1 Consensus size: 21
25481037 GTACATCATT
*
25481047 AACAGAAGCTC-GAA-AGCTA
1 AACAGAAGCTCATAAGAGCTA
* *
25481066 AACAGAAGCTCATGAGAGCTT
1 AACAGAAGCTCATAAGAGCTA
* * * * *
25481087 AACAGAAACCCATAAGGGTTG
1 AACAGAAGCTCATAAGAGCTA
* *
25481108 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCATAAGAGCTA
** * * * *
25481129 AATGGAAACCCATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTA
*
25481150 AACAGAAGCTCAAAAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
* * * * *
25481171 AATAGAAACCCATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTA
*
25481192 AACAGAAGCTCAAAAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
* * * * *
25481213 AATAGAAACCCATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTA
*
25481234 AACAGAAGCTCTTAAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
25481255 AAC
1 AAC
25481258 GGAAAGTAAA
Statistics
Matches: 137, Mismatches: 53, Indels: 2
0.71 0.28 0.01
Matches are distributed among these distances:
19 11 0.08
20 1 0.01
21 125 0.91
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.15
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTA
Found at i:25494114 original size:42 final size:41
Alignment explanation
Indices: 25494052--25494140 Score: 106
Period size: 41 Copynumber: 2.1 Consensus size: 41
25494042 TTCAATTTTC
* * * *
25494052 AATTTTTATATTTTTTTTGTTAATAAAATTTATTTAATCTAA
1 AATTTTAATAGTTTTATTGTT-ATAAAAGTTATTTAATCTAA
* * *
25494094 ACTTTTAATAGTTTTATTGTTATTAACGTTATTTAATCTAA
1 AATTTTAATAGTTTTATTGTTATAAAAGTTATTTAATCTAA
25494135 AATTTT
1 AATTTT
25494141 TAGAATAATA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
41 22 0.56
42 17 0.44
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.57
Consensus pattern (41 bp):
AATTTTAATAGTTTTATTGTTATAAAAGTTATTTAATCTAA
Found at i:25496819 original size:18 final size:18
Alignment explanation
Indices: 25496793--25496828 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
25496783 TGAGTTAAAC
*
25496793 TAATCGAGTTATTTGAGT
1 TAATCGAGTTATTCGAGT
*
25496811 TAATTGAGTTATTCGAGT
1 TAATCGAGTTATTCGAGT
25496829 CAAATCAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.06, G:0.22, T:0.44
Consensus pattern (18 bp):
TAATCGAGTTATTCGAGT
Found at i:25497544 original size:28 final size:28
Alignment explanation
Indices: 25497513--25497613 Score: 82
Period size: 28 Copynumber: 3.5 Consensus size: 28
25497503 ATCTCGTCGA
25497513 ACTTATCCCATGTTTATTGTCCCAACG-G
1 ACTTAT-CCATGTTTATTGTCCCAACGAG
* * *
25497541 ACTTTATCCATGTTAATTGTCCTAACAGATT
1 AC-TTATCCATGTTTATTGTCCCAAC-GA-G
25497572 ATCTCTATTCCATGTTTATTGTCCCAACGA-
1 A-CT-TA-TCCATGTTTATTGTCCCAACGAG
*
25497602 AC-TATCTATGTT
1 ACTTATCCATGTT
25497614 CTGTGCTTAC
Statistics
Matches: 60, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
26 7 0.12
27 2 0.03
28 19 0.32
29 6 0.10
30 1 0.02
31 2 0.03
32 5 0.08
33 18 0.30
ACGTcount: A:0.25, C:0.24, G:0.11, T:0.41
Consensus pattern (28 bp):
ACTTATCCATGTTTATTGTCCCAACGAG
Found at i:25497608 original size:33 final size:33
Alignment explanation
Indices: 25497520--25497643 Score: 91
Period size: 33 Copynumber: 3.9 Consensus size: 33
25497510 CGAACTTATC
*
25497520 CCATGTTTATTGTCCCAACGGAC--T-T-TA-T
1 CCATGTTTATTGTCCCAACGAACTATCTCTATT
* * *
25497548 CCATGTTAATTGTCCTAAC-AGATTATCTCTATT
1 CCATGTTTATTGTCCCAACGA-ACTATCTCTATT
* *
25497581 CCATGTTTATTGTCCCAACGAACTATCTATGTT
1 CCATGTTTATTGTCCCAACGAACTATCTCTATT
** * *
25497614 CTGTGCTTACTGTCCCAACCG-ACTATCTCT
1 CCATGTTTATTGTCCCAA-CGAACTATCTCT
25497644 GTTATGTGGA
Statistics
Matches: 74, Mismatches: 14, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
28 18 0.24
30 1 0.01
31 1 0.01
32 2 0.03
33 49 0.66
34 3 0.04
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.39
Consensus pattern (33 bp):
CCATGTTTATTGTCCCAACGAACTATCTCTATT
Found at i:25500179 original size:26 final size:26
Alignment explanation
Indices: 25500104--25500189 Score: 90
Period size: 26 Copynumber: 3.4 Consensus size: 26
25500094 AAGTTCAAGC
*
25500104 GAGCCA-T-ATCGGGAAGCTC-CGGA
1 GAGCCATTAATCGGGAAGCTCACGAA
* *
25500127 GAGTCATTAA-CGGGAAGCTCACAAA
1 GAGCCATTAATCGGGAAGCTCACGAA
* *
25500152 GAGCCTTTAATCGGAAAGCTCACGAA
1 GAGCCATTAATCGGGAAGCTCACGAA
25500178 GAGCCATATAAT
1 GAGCCAT-TAAT
25500190 AGGACGCTCA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
23 5 0.10
24 11 0.22
25 11 0.22
26 19 0.38
27 4 0.08
ACGTcount: A:0.35, C:0.22, G:0.26, T:0.17
Consensus pattern (26 bp):
GAGCCATTAATCGGGAAGCTCACGAA
Found at i:25500278 original size:24 final size:23
Alignment explanation
Indices: 25500245--25500327 Score: 69
Period size: 24 Copynumber: 3.4 Consensus size: 23
25500235 CACAACCAAT
*
25500245 CGGGATGCTCCGAAAAGCTATTAA
1 CGGGAAGCT-CGAAAAGCTATTAA
25500269 CGGGAAGCTCGCAAGAA-CTATATAA
1 CGGGAAGCTCG-AA-AAGCTAT-TAA
* **
25500294 TGGGAAGCTCGAGAGGGCTATTAA
1 CGGGAAGCTCGA-AAAGCTATTAA
*
25500318 CGGGATGCTC
1 CGGGAAGCTC
25500328 ATGAGAGCTA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
23 2 0.04
24 26 0.54
25 20 0.42
ACGTcount: A:0.31, C:0.19, G:0.30, T:0.19
Consensus pattern (23 bp):
CGGGAAGCTCGAAAAGCTATTAA
Found at i:25500314 original size:25 final size:24
Alignment explanation
Indices: 25500260--25500327 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 24
25500250 TGCTCCGAAA
25500260 AGCTATTAACGGGAAGCTCGCAAG
1 AGCTATTAACGGGAAGCTCGCAAG
* *
25500284 AACTATATAATGGGAAGCTCG-AGAG
1 AGCTAT-TAACGGGAAGCTCGCA-AG
* *
25500309 GGCTATTAACGGGATGCTC
1 AGCTATTAACGGGAAGCTC
25500328 ATGAGAGCTA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
24 17 0.47
25 19 0.53
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (24 bp):
AGCTATTAACGGGAAGCTCGCAAG
Found at i:25500337 original size:24 final size:23
Alignment explanation
Indices: 25500260--25500337 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 23
25500250 TGCTCCGAAA
25500260 AGCTATTAACGGGAAGCTC-GCAAG
1 AGCTATTAACGGGAAGCTCAG--AG
* *
25500284 AACTATATAATGGGAAGCTCGAGAG
1 AGCTAT-TAACGGGAAGCTC-AGAG
* *
25500309 GGCTATTAACGGGATGCTCATGAG
1 AGCTATTAACGGGAAGCTCA-GAG
25500333 AGCTA
1 AGCTA
25500338 ACAATGGGAC
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
23 1 0.02
24 23 0.53
25 18 0.42
27 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (23 bp):
AGCTATTAACGGGAAGCTCAGAG
Found at i:25502471 original size:17 final size:16
Alignment explanation
Indices: 25502438--25502470 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
25502428 TCTTTTTCCG
25502438 TCCCTAAGAATTTTTT
1 TCCCTAAGAATTTTTT
25502454 TCCCATAAG-ATTTTTT
1 TCCC-TAAGAATTTTTT
25502470 T
1 T
25502471 TATCTTCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.52
Consensus pattern (16 bp):
TCCCTAAGAATTTTTT
Found at i:25506077 original size:25 final size:26
Alignment explanation
Indices: 25506029--25506077 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
25506019 TATTTGAGAT
*
25506029 ATTTTATTAAATTTTTTTTGTTTTTA
1 ATTTTATTAAATTTTTTTTATTTTTA
25506055 ATTTTA-T-AATTATTTTTTATTTT
1 ATTTTATTAAATT-TTTTTTATTTT
25506078 AAATCATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 11 0.52
26 6 0.29
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (26 bp):
ATTTTATTAAATTTTTTTTATTTTTA
Found at i:25506303 original size:69 final size:68
Alignment explanation
Indices: 25506192--25506323 Score: 246
Period size: 69 Copynumber: 1.9 Consensus size: 68
25506182 TGAAAACGAT
25506192 TTATTTACATATTTCTTTTAAATGATAATCAATATTATTATGGTGATACTTTTTGTATTTTCATG
1 TTATTTACATATTTCTTTTAAATGATAATCAATATTATTATGGTGATAC-TTTTGTATTTTCATG
25506257 CGAC
65 CGAC
*
25506261 TTATTTTCATATTTCTTTTAAATGATAATCAATATTATTATGGTGATACTTTTGTATTTTCAT
1 TTATTTACATATTTCTTTTAAATGATAATCAATATTATTATGGTGATACTTTTGTATTTTCAT
25506324 ACTTTTATAT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
68 14 0.23
69 48 0.77
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (68 bp):
TTATTTACATATTTCTTTTAAATGATAATCAATATTATTATGGTGATACTTTTGTATTTTCATGC
GAC
Found at i:25530834 original size:31 final size:29
Alignment explanation
Indices: 25530764--25530837 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
25530754 ACCTTAGGTT
*
25530764 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTGAAATGTA
* ***
25530793 ACGTTTTAGTCACTTATGTTATCGTGTTGTA
1 ACATTTTAGTCACTTATGTT-T-GAAATGTA
25530824 ACATTTTAGTCACT
1 ACATTTTAGTCACT
25530838 GATCGTTAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 19 0.51
30 1 0.03
31 17 0.46
ACGTcount: A:0.24, C:0.14, G:0.15, T:0.47
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTGAAATGTA
Found at i:25532784 original size:19 final size:20
Alignment explanation
Indices: 25532745--25532784 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
25532735 ACTATTTCTA
25532745 CTTTCTTCCCATTTTCTCTT
1 CTTTCTTCCCATTTTCTCTT
25532765 CTTT-TTCCCTATTTTC-CTT
1 CTTTCTTCCC-ATTTTCTCTT
25532784 C
1 C
25532785 ATCCCAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.05, C:0.35, G:0.00, T:0.60
Consensus pattern (20 bp):
CTTTCTTCCCATTTTCTCTT
Found at i:25534579 original size:14 final size:14
Alignment explanation
Indices: 25534562--25534589 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
25534552 CTCACATTTC
25534562 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
25534576 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
25534590 GATTTCTGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTCTTTTCTCCA
Found at i:25534580 original size:19 final size:18
Alignment explanation
Indices: 25534542--25534586 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
25534532 TACGGTACGC
25534542 TTCTTTTC-TTCTCACAT
1 TTCTTTTCTTTCTCACAT
25534559 TTCTTTTCTTTTCTC-CATT
1 TTCTTTTC-TTTCTCACA-T
25534578 TTCTTTTCT
1 TTCTTTTCT
25534587 CCAGATTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.32
18 3 0.12
19 14 0.56
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.67
Consensus pattern (18 bp):
TTCTTTTCTTTCTCACAT
Found at i:25534664 original size:6 final size:6
Alignment explanation
Indices: 25534655--25534696 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
25534645 GTTAAATCGA
* *
25534655 TTTTGA TTTTG- TTTTGC TTTTGC TTTTGC TTTTGC TTGTGC T
1 TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC T
25534697 CAAATCTGGA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
5 5 0.15
6 29 0.85
ACGTcount: A:0.02, C:0.12, G:0.19, T:0.67
Consensus pattern (6 bp):
TTTTGC
Found at i:25535517 original size:30 final size:28
Alignment explanation
Indices: 25535465--25535537 Score: 112
Period size: 30 Copynumber: 2.6 Consensus size: 28
25535455 TAAAAAAATA
*
25535465 ACCAAAATATTATAACTTTTTATTATTT
1 ACCAAAATATTATAAATTTTTATTATTT
25535493 ACCAAAATATTATAATTATTTTTATTATTT
1 ACCAAAATATTATAA--ATTTTTATTATTT
25535523 ACCAAAATA-TATAAA
1 ACCAAAATATTATAAA
25535538 AAAATGCAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
27 1 0.02
28 15 0.36
29 5 0.12
30 21 0.50
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (28 bp):
ACCAAAATATTATAAATTTTTATTATTT
Found at i:25535658 original size:27 final size:27
Alignment explanation
Indices: 25535589--25535659 Score: 115
Period size: 27 Copynumber: 2.6 Consensus size: 27
25535579 AGGCCAATGG
* *
25535589 CATTGGCGGCACCAAAGGTGCCAAAGC
1 CATTGGCGGCACCAATGGTGCCAAAAC
*
25535616 CATTGGTGGCACCAATGGTGCCAAAAC
1 CATTGGCGGCACCAATGGTGCCAAAAC
25535643 CATTGGCGGCACCAATG
1 CATTGGCGGCACCAATG
25535660 CCATAATAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.15
Consensus pattern (27 bp):
CATTGGCGGCACCAATGGTGCCAAAAC
Found at i:25535722 original size:13 final size:13
Alignment explanation
Indices: 25535698--25535739 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
25535688 AGAAGGAGAG
25535698 GGAAAGAAAGGAA
1 GGAAAGAAAGGAA
* *
25535711 GGAATGAGAGGAA
1 GGAAAGAAAGGAA
*
25535724 AGAAAGAAAGGAA
1 GGAAAGAAAGGAA
25535737 GGA
1 GGA
25535740 GAGGAAAGAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.40, T:0.02
Consensus pattern (13 bp):
GGAAAGAAAGGAA
Found at i:25535730 original size:26 final size:22
Alignment explanation
Indices: 25535689--25535754 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
25535679 GGTGGGCGGA
*
25535689 GAAGGAGAGGGAAAGAAAGGAAG
1 GAAGGAGA-GGAAAGAAAGAAAG
*
25535712 GAATGAGAGGAAAGAAAGAAAG
1 GAAGGAGAGGAAAGAAAGAAAG
25535734 GAAGGAGAGGAAAGAAAGAAA
1 GAAGGAGAGGAAAGAAAGAAA
25535755 AAGAAGAAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 33 0.82
23 7 0.17
ACGTcount: A:0.58, C:0.00, G:0.41, T:0.02
Consensus pattern (22 bp):
GAAGGAGAGGAAAGAAAGAAAG
Found at i:25535767 original size:18 final size:18
Alignment explanation
Indices: 25535746--25535868 Score: 81
Period size: 18 Copynumber: 6.6 Consensus size: 18
25535736 AGGAGAGGAA
25535746 AGAAAGAAAAAGAAGAAG
1 AGAAAGAAAAAGAAGAAG
* *
25535764 AGAAA-AGGAAAGGAGAAG
1 AGAAAGA-AAAAGAAGAAG
*
25535782 AGAAAAAAAAAGGAAAGAAG
1 AGAAAGAAAAA-G-AAGAAG
* * *
25535802 AAAAAGAGGAAAGGAGAAG
1 AGAAAGA-AAAAGAAGAAG
*
25535821 AAGAAAGAAAGAAAAAGAAG
1 -AGAAAGAAA-AAGAAGAAG
* *
25535841 -GAAAGAAAAGGAA-AGG
1 AGAAAGAAAAAGAAGAAG
25535857 AGAAGAGAAAAA
1 AGAA-AGAAAAA
25535869 AAAAAGAAGA
Statistics
Matches: 80, Mismatches: 16, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
16 2 0.03
17 7 0.09
18 36 0.45
19 8 0.10
20 24 0.30
21 3 0.04
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (18 bp):
AGAAAGAAAAAGAAGAAG
Found at i:25535809 original size:44 final size:41
Alignment explanation
Indices: 25535748--25535884 Score: 181
Period size: 41 Copynumber: 3.3 Consensus size: 41
25535738 GAGAGGAAAG
25535748 AAAGAAAAAGAAGAAGAGAAAAGGAAAGGAGAAGAGAAAAAA
1 AAAGAAAAAGAAGAA-AGAAAAGGAAAGGAGAAGAGAAAAAA
* * * *
25535790 AAAG-GAAAGAAGAAA-AAGAGGAAAGGAGAAGA-AGAAAG
1 AAAGAAAAAGAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAA
25535828 AAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAA
1 AAAGAAAAAGAA-GAAAGAAAAGGAAAGGAGAAGAG-AAAAAA
*
25535871 AAAGAAGAAGAAGA
1 AAAGAAAAAGAAGA
25535885 GGGAAGGAAG
Statistics
Matches: 81, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
38 8 0.10
39 22 0.27
40 5 0.06
41 25 0.31
42 6 0.07
43 15 0.19
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (41 bp):
AAAGAAAAAGAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAA
Found at i:25535812 original size:76 final size:75
Alignment explanation
Indices: 25535723--25535909 Score: 240
Period size: 80 Copynumber: 2.5 Consensus size: 75
25535713 AATGAGAGGA
25535723 AAGAAAGAA-AGGAAGGAGAGGAAAGAAAGAAAAAGAA-GAAGAGAAAAGGAAAGGAGAAGAGAA
1 AAGAAA-AAGAGGAAGGAGAGGAAAGAAAGAAAAAGAAGGAA-AGAAAAGGAAAGGAGAAGAGAA
*
25535786 AAAAAAAGGAAAG
64 AAAAAAAAG-AAG
25535799 AAGAAAAAGAGGAAAGGAGAAGAAGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAG
1 AAGAAAAAGAGG-AAGGAG-AG--GAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAG
25535864 AAAAAAAAAAGAAG
62 AAAAAAAAAAGAAG
* *
25535878 AAG-AAGAG-GGAAGGA-AGGAAAAAAAAGAAAAA
1 AAGAAAAAGAGGAAGGAGAGG-AAAGAAAGAAAAA
25535910 AGGTAATTTT
Statistics
Matches: 101, Mismatches: 3, Indels: 17
0.83 0.02 0.14
Matches are distributed among these distances:
72 1 0.01
73 12 0.12
74 2 0.02
75 2 0.02
76 14 0.14
77 8 0.08
78 6 0.06
79 6 0.06
80 47 0.47
81 3 0.03
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (75 bp):
AAGAAAAAGAGGAAGGAGAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAA
AAAAAAGAAG
Found at i:25535848 original size:80 final size:80
Alignment explanation
Indices: 25535729--25535882 Score: 249
Period size: 80 Copynumber: 1.9 Consensus size: 80
25535719 AGGAAAGAAA
* * *
25535729 GAAAGGAAGGAGAGGAAAGAAAGAAAAAGAAGAAGAGAAAAGGAAAGGAGAAGAGAAAAAAAAAG
1 GAAAGGAAGAAGAAGAAAGAAAGAAAAAGAAGAAGAGAAAAGGAAAGGAGAAGAGAAAAAAAAAA
25535794 GAAAGAAGAAAAAGAG
66 G-AAGAAGAAAAAGAG
25535810 GAAAGG-AGAAGAAGAAAGAAAGAAAAAGAAGGAA-AGAAAAGGAAAGGAGAAGAGAAAAAAAAA
1 GAAAGGAAGAAGAAGAAAGAAAGAAAAAGAA-GAAGAGAAAAGGAAAGGAGAAGAGAAAAAAAAA
25535873 AGAAGAAGAA
65 AGAAGAAGAA
25535883 GAGGGAAGGA
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
79 8 0.12
80 52 0.75
81 9 0.13
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (80 bp):
GAAAGGAAGAAGAAGAAAGAAAGAAAAAGAAGAAGAGAAAAGGAAAGGAGAAGAGAAAAAAAAAA
GAAGAAGAAAAAGAG
Found at i:25535876 original size:29 final size:28
Alignment explanation
Indices: 25535842--25535908 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 28
25535832 AAAAAGAAGG
25535842 AAAGAAAAGGAA-AGGAGAAGAGAA-AAAAA
1 AAAGAAAA-GAAGAGG-GAAG-GAAGAAAAA
25535871 AAAGAAGAAGAAGAGGGAAGGAAGGAAAAA
1 AAAGAA-AAGAAGAGGGAAGGAA-GAAAAA
25535901 AAAGAAAA
1 AAAGAAAA
25535909 AAGGTAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
28 3 0.09
29 15 0.44
30 16 0.47
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (28 bp):
AAAGAAAAGAAGAGGGAAGGAAGAAAAA
Found at i:25537807 original size:14 final size:14
Alignment explanation
Indices: 25537785--25537851 Score: 57
Period size: 14 Copynumber: 4.7 Consensus size: 14
25537775 TATCAGCGAN
*
25537785 AGAAGAAGAAAGAA
1 AGAAAAAGAAAGAA
*
25537799 AGAAAAAGAAGGAA
1 AGAAAAAGAAAGAA
*
25537813 AGAAAAGGAAAGGAGA
1 AGAAAAAGAAA-GA-A
25537829 AGAGAAAA-AAA-AA
1 AGA-AAAAGAAAGAA
*
25537842 AGAAGAAGAA
1 AGAAAAAGAA
25537852 GAGGGAAGGA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
12 3 0.07
13 6 0.14
14 22 0.51
15 2 0.05
16 7 0.16
17 3 0.07
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (14 bp):
AGAAAAAGAAAGAA
Found at i:25537851 original size:35 final size:36
Alignment explanation
Indices: 25537788--25537872 Score: 90
Period size: 35 Copynumber: 2.4 Consensus size: 36
25537778 CAGCGANAGA
25537788 AGAAGA-AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGG
1 AGAAGAGAA-AAA-AAAAAGAAGGAAAGAAAAGGAAA-G
* *
25537826 AGAAGAGAAAAAAAAAAGAA-G-AAGAAGAGGGAAG
1 AGAAGAGAAAAAAAAAAGAAGGAAAGAAAAGGAAAG
25537860 -GAAG-GAAAAAAAA
1 AGAAGAGAAAAAAAA
25537873 GAAAAAAGGT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
32 9 0.20
33 4 0.09
34 1 0.02
35 10 0.23
36 1 0.02
37 8 0.18
38 9 0.20
39 2 0.05
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (36 bp):
AGAAGAGAAAAAAAAAAGAAGGAAAGAAAAGGAAAG
Found at i:25545260 original size:29 final size:29
Alignment explanation
Indices: 25545213--25545270 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
25545203 TATCTTTTAT
*
25545213 TAGGAATAGAGTTTTGATATGATAATAAA
1 TAGGAATAGAGTTTCGATATGATAATAAA
25545242 TAGGAATAGCA-TTTCGATATGATAATAAA
1 TAGGAATAG-AGTTTCGATATGATAATAAA
25545271 AATGGGTTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 26 0.96
30 1 0.04
ACGTcount: A:0.45, C:0.03, G:0.19, T:0.33
Consensus pattern (29 bp):
TAGGAATAGAGTTTCGATATGATAATAAA
Found at i:25548551 original size:16 final size:16
Alignment explanation
Indices: 25548526--25548558 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
25548516 ACGGTATTCT
*
25548526 ATATTTTATAGTAGCA
1 ATATTCTATAGTAGCA
25548542 ATATTCTATAGTAGCA
1 ATATTCTATAGTAGCA
25548558 A
1 A
25548559 AACAATAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (16 bp):
ATATTCTATAGTAGCA
Found at i:25552246 original size:27 final size:27
Alignment explanation
Indices: 25552216--25552271 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
25552206 ATTATATTTT
25552216 TTCTATTCTATTAGTATTAGATTAGTA
1 TTCTATTCTATTAGTATTAGATTAGTA
*
25552243 TTCTATTCTATTTGTATTAGATTAGTA
1 TTCTATTCTATTAGTATTAGATTAGTA
25552270 TT
1 TT
25552272 AGTTAGTGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.07, G:0.11, T:0.55
Consensus pattern (27 bp):
TTCTATTCTATTAGTATTAGATTAGTA
Found at i:25561725 original size:41 final size:41
Alignment explanation
Indices: 25561668--25561750 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
25561658 TCTCCTCAAG
25561668 TAGGATTCGAACCTACGACCAGTCAGTTAACAATCGACTGC
1 TAGGATTCGAACCTACGACCAGTCAGTTAACAATCGACTGC
25561709 TAGGATTCGAACCTACGACCAGTCAGTTAACAATCGACTGC
1 TAGGATTCGAACCTACGACCAGTCAGTTAACAATCGACTGC
25561750 T
1 T
25561751 CTATCGCTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (41 bp):
TAGGATTCGAACCTACGACCAGTCAGTTAACAATCGACTGC
Found at i:25562084 original size:76 final size:77
Alignment explanation
Indices: 25561958--25562110 Score: 281
Period size: 76 Copynumber: 2.0 Consensus size: 77
25561948 TCCATTTTTA
25561958 TATTGTCATTGACATGACATAAGAGATGTCGATTCTAGTCTATCCTTTTCTATTTCTATATAT-T
1 TATTGTCATTGACATGACATAAGAGATGTCGATTCTAGTCTATCCTTTTCTATTTCTATATATGT
25562022 ATATGGAAAGTT
66 ATATGGAAAGTT
* *
25562034 TATTGTCATTGACATGACATAAGAGATGTCGGTTCTAGTCTATCTTTTTCTATTTCTATATATGT
1 TATTGTCATTGACATGACATAAGAGATGTCGATTCTAGTCTATCCTTTTCTATTTCTATATATGT
25562099 ATATGGAAAGTT
66 ATATGGAAAGTT
25562111 CAAAAATCAT
Statistics
Matches: 74, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
76 61 0.82
77 13 0.18
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (77 bp):
TATTGTCATTGACATGACATAAGAGATGTCGATTCTAGTCTATCCTTTTCTATTTCTATATATGT
ATATGGAAAGTT
Found at i:25563925 original size:21 final size:20
Alignment explanation
Indices: 25563884--25563925 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
25563874 CCAATTATCC
*
25563884 AATAAAAACCTAAGATTCCT
1 AATAAAAACCTAAAATTCCT
25563904 AATAATAAACC-AAAATTGCCT
1 AATAA-AAACCTAAAATT-CCT
25563925 A
1 A
25563926 TCCGATTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.52, C:0.19, G:0.05, T:0.24
Consensus pattern (20 bp):
AATAAAAACCTAAAATTCCT
Found at i:25568926 original size:22 final size:21
Alignment explanation
Indices: 25568891--25568948 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
25568881 AAAGGGTATG
* *
25568891 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
25568912 TACAAAATCATATCTTCTCAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
25568935 TGCATATCATATCT
1 TACAAATCATATCT
25568949 AAGATTGCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 4 0.13
22 17 0.57
23 9 0.30
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:25571722 original size:48 final size:48
Alignment explanation
Indices: 25571643--25571736 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
25571633 AGGGAATTCT
* *
25571643 GTTGAATCCTTTATTGTTGCGAGTTGAGCTGACTTAGGCGTTTTTACG
1 GTTGAATCCATTATTGGTGCGAGTTGAGCTGACTTAGGCGTTTTTACG
25571691 GTTGAATCCATTATTGGTG-GAAGTT-AGGCTGACTTAGGCGTTTTTA
1 GTTGAATCCATTATTGGTGCG-AGTTGA-GCTGACTTAGGCGTTTTTA
25571737 AGCCAAGAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 2 0.05
48 40 0.95
ACGTcount: A:0.19, C:0.13, G:0.28, T:0.40
Consensus pattern (48 bp):
GTTGAATCCATTATTGGTGCGAGTTGAGCTGACTTAGGCGTTTTTACG
Found at i:25572912 original size:3 final size:3
Alignment explanation
Indices: 25572904--25572940 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
25572894 ATTCCCGCTC
25572904 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC- TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
25572941 AAATTTCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:25593818 original size:7 final size:7
Alignment explanation
Indices: 25593808--25593835 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
25593798 CTTATCCTTT
25593808 CCCCTCG
1 CCCCTCG
25593815 CCCCTCG
1 CCCCTCG
25593822 CCCCTCG
1 CCCCTCG
25593829 CCCCTCG
1 CCCCTCG
25593836 TTGCTCCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.71, G:0.14, T:0.14
Consensus pattern (7 bp):
CCCCTCG
Found at i:25594187 original size:7 final size:7
Alignment explanation
Indices: 25594170--25594200 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
25594160 CCCTTCTTAT
25594170 TTTATTTA
1 TTTA-TTA
25594178 TTTATTA
1 TTTATTA
25594185 TTTATTA
1 TTTATTA
25594192 TTTATTA
1 TTTATTA
25594199 TT
1 TT
25594201 ATTGTTATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.83
8 4 0.17
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTATTA
Found at i:25597321 original size:25 final size:24
Alignment explanation
Indices: 25597171--25597322 Score: 169
Period size: 25 Copynumber: 6.1 Consensus size: 24
25597161 CCTGACACAC
25597171 CACAGCTCGTATGAGCTTACCGATT
1 CACAGCTCGTA-GAGCTTACCGATT
** *
25597196 TGCAGCTCGTGAGAGCTTATCGATT
1 CACAGCTCGT-AGAGCTTACCGATT
*
25597221 CTCAGCTCGTATGAGCTTACCGATT
1 CACAGCTCGTA-GAGCTTACCGATT
** *
25597246 TGCAGCTCGTGAGAGCTTATCGATT
1 CACAGCTCGT-AGAGCTTACCGATT
*
25597271 CTCAGCTCGTATGAGCTTACCGATT
1 CACAGCTCGTA-GAGCTTACCGATT
*
25597296 CACAGCTCGTGAGAGCATACCGATT
1 CACAGCTCGT-AGAGCTTACCGATT
25597321 CA
1 CA
25597323 TTGCTCGTTT
Statistics
Matches: 108, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
24 2 0.02
25 103 0.95
26 3 0.03
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (24 bp):
CACAGCTCGTAGAGCTTACCGATT
Found at i:25597330 original size:75 final size:75
Alignment explanation
Indices: 25597173--25597320 Score: 196
Period size: 75 Copynumber: 2.0 Consensus size: 75
25597163 TGACACACCA
* * *
25597173 CAGCTCGTATGAGCTTACCGATTTGCAGCTCGTGAGAGCTTATCGATTCTCAGCTCGTATGAGCT
1 CAGCTCGTATGAGCTTACCGATTTGCAGCTCGTGAGAGCTTACCGATTCACAGCTCGTATGAGCA
25597238 TACCGATTTG
66 TACCGATTTG
*
25597248 CAGCTCGTGA-GAGCTTATCGATTCT-CAGCTCGT-ATGAGCTTACCGATTCACAGCTCGTGA-G
1 CAGCTCGT-ATGAGCTTACCGATT-TGCAGCTCGTGA-GAGCTTACCGATTCACAGCTCGT-ATG
25597309 AGCATACCGATT
62 AGCATACCGATT
25597321 CATTGCTCGT
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
74 1 0.02
75 61 0.94
76 3 0.05
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.30
Consensus pattern (75 bp):
CAGCTCGTATGAGCTTACCGATTTGCAGCTCGTGAGAGCTTACCGATTCACAGCTCGTATGAGCA
TACCGATTTG
Found at i:25597336 original size:25 final size:25
Alignment explanation
Indices: 25597171--25597340 Score: 148
Period size: 25 Copynumber: 6.8 Consensus size: 25
25597161 CCTGACACAC
*
25597171 CACAGCTCGTATGAGCTTACCGATT
1 CACAGCTCGTATGAGCATACCGATT
** * *
25597196 TGCAGCTCGTGA-GAGCTTATCGATT
1 CACAGCTCGT-ATGAGCATACCGATT
* *
25597221 CTCAGCTCGTATGAGCTTACCGATT
1 CACAGCTCGTATGAGCATACCGATT
** * *
25597246 TGCAGCTCGTGA-GAGCTTATCGATT
1 CACAGCTCGT-ATGAGCATACCGATT
* *
25597271 CTCAGCTCGTATGAGCTTACCGATT
1 CACAGCTCGTATGAGCATACCGATT
25597296 CACAGCTCGTGA-GAGCATACCGATT
1 CACAGCTCGT-ATGAGCATACCGATT
** *
25597321 CATTGCTCGTTTGAGCATAC
1 CACAGCTCGTATGAGCATAC
25597341 ATGTATATGA
Statistics
Matches: 122, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
24 2 0.02
25 117 0.96
26 3 0.02
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (25 bp):
CACAGCTCGTATGAGCATACCGATT
Found at i:25597336 original size:50 final size:50
Alignment explanation
Indices: 25597173--25597321 Score: 262
Period size: 50 Copynumber: 3.0 Consensus size: 50
25597163 TGACACACCA
25597173 CAGCTCGTATGAGCTTACCGATTTGCAGCTCGTGAGAGCTTATCGATTCT
1 CAGCTCGTATGAGCTTACCGATTTGCAGCTCGTGAGAGCTTATCGATTCT
25597223 CAGCTCGTATGAGCTTACCGATTTGCAGCTCGTGAGAGCTTATCGATTCT
1 CAGCTCGTATGAGCTTACCGATTTGCAGCTCGTGAGAGCTTATCGATTCT
** * *
25597273 CAGCTCGTATGAGCTTACCGATTCACAGCTCGTGAGAGCATACCGATTC
1 CAGCTCGTATGAGCTTACCGATTTGCAGCTCGTGAGAGCTTATCGATTC
25597322 ATTGCTCGTT
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 95 1.00
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (50 bp):
CAGCTCGTATGAGCTTACCGATTTGCAGCTCGTGAGAGCTTATCGATTCT
Found at i:25606875 original size:19 final size:18
Alignment explanation
Indices: 25606853--25606904 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
25606843 GCAAAAAAGC
*
25606853 AAAAAAACATAAAAGTAAA
1 AAAAAAACAAAAAAG-AAA
25606872 AAAAAAACAAAAAAGAAA
1 AAAAAAACAAAAAAGAAA
*
25606890 ATAAAAAAGAAAAAA
1 A-AAAAAACAAAAAA
25606905 AACCTCTACC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 4 0.13
19 26 0.87
ACGTcount: A:0.85, C:0.04, G:0.06, T:0.06
Consensus pattern (18 bp):
AAAAAAACAAAAAAGAAA
Found at i:25608459 original size:33 final size:33
Alignment explanation
Indices: 25608422--25608642 Score: 132
Period size: 33 Copynumber: 6.3 Consensus size: 33
25608412 CCCAAGGGGC
*
25608422 TGCTAAGTGTTGATTCCCCGATTCATTGGTGGT
1 TGCTAAGTGCTGATTCCCCGATTCATTGGTGGT
* *
25608455 TGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGGGGGT
1 TGCTAAGTGCTGATTCC-CCG-A--TT-CAT-T---GGTGGT
25608497 TGCTAAGTGCTGATTCCCC----CGA--GG-GGT
1 TGCTAAGTGCTGATTCCCCGATTC-ATTGGTGGT
* * *
25608524 TGCTAAGTGCTGATTCCCTGAATCACTGGTGGT
1 TGCTAAGTGCTGATTCCCCGATTCATTGGTGGT
* *
25608557 TGCTAAGTGCTGATCCCACCGTATCTTCAATGTGAAAGGGGT
1 TGCTAAGTGCTGATTCC-CCG-A--TTC-AT-TG---GTGGT
* *
25608599 TGCTAAGTGCTGATTCCCTGACTCATTGGTGGT
1 TGCTAAGTGCTGATTCCCCGATTCATTGGTGGT
25608632 TGCTAAGTGCT
1 TGCTAAGTGCT
25608643 AAATCCACCG
Statistics
Matches: 148, Mismatches: 14, Indels: 52
0.69 0.07 0.24
Matches are distributed among these distances:
27 21 0.14
28 2 0.01
30 1 0.01
31 1 0.01
32 2 0.01
33 50 0.34
34 6 0.04
35 2 0.01
36 2 0.01
37 6 0.04
38 5 0.03
39 3 0.02
40 1 0.01
41 4 0.03
42 42 0.28
ACGTcount: A:0.19, C:0.20, G:0.28, T:0.33
Consensus pattern (33 bp):
TGCTAAGTGCTGATTCCCCGATTCATTGGTGGT
Found at i:25608563 original size:102 final size:102
Alignment explanation
Indices: 25608388--25608616 Score: 361
Period size: 102 Copynumber: 2.3 Consensus size: 102
25608378 TTTGAATATA
* * * *
25608388 AAGGGGTTTGCTAAGTGCTGATT-CCCCAAGGGGCTGCTAAGTGTTGATTCCCCGATTCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGCTGCTAAGTGCTGATTCCCCGAATCACTGGT
*
25608452 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTG
66 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTG
* * *
25608489 AAGGGGGTTGCTAAGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCTGAATCACTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGCTGCTAAGTGCTGATTCCCCGAATCACTGGT
*
25608554 GGTTGCTAAGTGCTGATCCCACCGTATCTTCAATGTG
66 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTG
*
25608591 AAAGGGGTTGCTAAGTGCTGATTCCC
1 AAGGGGGTTGCTAAGTGCTGATTCCC
25608617 TGACTCATTG
Statistics
Matches: 117, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
101 22 0.19
102 95 0.81
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.31
Consensus pattern (102 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGCTGCTAAGTGCTGATTCCCCGAATCACTGGT
GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTG
Found at i:25610974 original size:50 final size:50
Alignment explanation
Indices: 25610916--25611327 Score: 292
Period size: 50 Copynumber: 8.2 Consensus size: 50
25610906 ACGGTTAAAA
* ***
25610916 AGATTGAAGCCGCAACGGTGAATCTTACTTCCCTGGTGGTGCAGTGGAAC
1 AGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCATTGCAGTGGAAC
* * * *** * * *
25610966 AGATTGAAGCTACAACGGCGAATCTT-GTTCCCCAACATTGCAATTGAAA
1 AGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCATTGCAGTGGAAC
* * * *
25611015 AGATTGAAGCCGCAACGGCGAATCTTACTTCCTTGGCA-TGCAGTGGAGC
1 AGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCATTGCAGTGGAAC
* * * * * * ** *
25611064 AGATTGAAGCTACGACGGTGAATCTTGCTTCCCCCGACATTGCATTCTAAA
1 AGATTGAAGCCACAACGGTGAATCTTACTT-CCCTGGCATTGCAGTGGAAC
* ** *
25611115 AGATTGAAGCCACAACGGTGAATCTTACTTTCCTGGCGGTGCAGTGGAGC
1 AGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCATTGCAGTGGAAC
* ** * * ** * ** *
25611165 AGATTGAAGCTACGCCGGTGAATCTTGCTTCCCCGATATTGCAATTTAAA
1 AGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCATTGCAGTGGAAC
* * *
25611215 AGATTGAAGCCACGACGGTGAATCTTACCTCCCT-G-AGTTCGCAGTGGAGC
1 AGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCA-TT-GCAGTGGAAC
* * * * * ** *
25611265 AGATTGAAGCTACAACGGTGAGTCTTGCTTCCCCTGACATTGCATTTTAAA
1 AGATTGAAGCCACAACGGTGAATCTTACTT-CCCTGGCATTGCAGTGGAAC
25611316 AGATTGAAGCCA
1 AGATTGAAGCCA
25611328 TACACCACAG
Statistics
Matches: 266, Mismatches: 88, Indels: 15
0.72 0.24 0.04
Matches are distributed among these distances:
48 1 0.00
49 71 0.27
50 138 0.52
51 53 0.20
52 2 0.01
53 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.25
Consensus pattern (50 bp):
AGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCATTGCAGTGGAAC
Found at i:25611188 original size:101 final size:100
Alignment explanation
Indices: 25610913--25611327 Score: 577
Period size: 100 Copynumber: 4.2 Consensus size: 100
25610903 ATTACGGTTA
* * *
25610913 AAAAGATTGAAGCCGCAACGGTGAATCTTACTTCCCTGGTGGTGCAGTGGAACAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATTGAAGCTA
* * *
25610978 CAACGGCGAATCTTG-TTCCCCAACATTGCAATTG
66 CAACGGTGAATCTTGCTTCCCCGACATTGCAATTT
* * * *
25611012 AAAAGATTGAAGCCGCAACGGCGAATCTTACTTCCTTGGC-ATGCAGTGGAGCAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATTGAAGCTA
*
25611076 CGACGGTGAATCTTGCTTCCCCCGACATTGC-ATTCT
66 CAACGGTGAATCTTGCTT-CCCCGACATTGCAATT-T
*
25611112 AAAAGATTGAAGCCACAACGGTGAATCTTACTTTCCTGGCGGTGCAGTGGAGCAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATTGAAGCTA
** *
25611177 CGCCGGTGAATCTTGCTTCCCCGATATTGCAATTT
66 CAACGGTGAATCTTGCTTCCCCGACATTGCAATTT
* * * *
25611212 AAAAGATTGAAGCCACGACGGTGAATCTTACCTCCCT-GAGTTCGCAGTGGAGCAGATTGAAGCT
1 AAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGGT-GCAGTGGAGCAGATTGAAGCT
* *
25611276 ACAACGGTGAGTCTTGCTTCCCCTGACATTGCATTTT
65 ACAACGGTGAATCTTGCTTCCCC-GACATTGCAATTT
25611313 AAAAGATTGAAGCCA
1 AAAAGATTGAAGCCA
25611328 TACACCACAG
Statistics
Matches: 283, Mismatches: 26, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
98 35 0.12
99 45 0.16
100 134 0.47
101 69 0.24
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (100 bp):
AAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATTGAAGCTA
CAACGGTGAATCTTGCTTCCCCGACATTGCAATTT
Found at i:25611439 original size:44 final size:42
Alignment explanation
Indices: 25611331--25611967 Score: 401
Period size: 44 Copynumber: 14.8 Consensus size: 42
25611321 GAAGCCATAC
* * * ***
25611331 ACCACAGATCTTGTCTCTCTGAGGTTGCAGTAGAGCAGACCGCA
1 ACCACA-ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGA-TAAA
* * *
25611375 TCCAC--TCCTATCTC-CTTGAAGTTGCAGTGGAGCGGATTAAA
1 ACCACAATCTTATCTCTC-TGAAGTTGCAGTGGAGCAGA-TAAA
* * ***
25611416 ACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGAAGATCGT
1 ACCACA-ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATAAA
* * * *
25611459 ATCA-AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAA
1 ACCACAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATAAA
** * * *
25611500 AGAAACCAATCCTATCTCCCGGAAGTTGCAGTGGAGCAGATTAAA
1 A-CCA-CAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGA-TAAA
* * ***
25611545 ACCACATATCTTATCTCTCTGAAGTTGCAATAGAGCAGATCGC
1 ACCACA-ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATAAA
* * *
25611588 ATC-CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-AAA
1 ACCACAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATAAA
** * * **
25611628 AAAATCAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAA
1 ACCA-CAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGA-TAAA
* * ***
25611672 ACCACAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGC
1 ACCACA-ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATAAA
* * * *
25611715 ATC-CAATCTTATCTCTCTGAAGTTGCAGTAGATCAGACAAA
1 ACCACAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATAAA
** * *
25611756 AGAAACCAATCCTATCTCTCGGAAGTTGCAGTGGAGC-GAATTAAA
1 A-CCA-CAATCTTATCTCTCTGAAGTTGCAGTGGAGCAG-A-TAAA
* * * *
25611801 ATCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCAC
1 ACCACA-ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATAAA
* * * *
25611844 ACCATAACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAG
1 ACC---AC-AATCTTATCTCTCTGAAGTTGCAGTGGAGCA-GAT-AAA
* *
25611892 A-TATCAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAA
1 ACCA-CAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGA-TAAA
* * * *
25611935 GCTACTAATCCTATCTCCCTGAAGTTGCAGTGG
1 ACCAC-AATCTTATCTCTCTGAAGTTGCAGTGG
25611968 GGCGGATTAA
Statistics
Matches: 456, Mismatches: 105, Indels: 64
0.73 0.17 0.10
Matches are distributed among these distances:
40 2 0.00
41 117 0.26
42 36 0.08
43 24 0.05
44 232 0.51
45 11 0.02
46 29 0.06
47 3 0.01
48 2 0.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (42 bp):
ACCACAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATAAA
Found at i:25611474 original size:85 final size:83
Alignment explanation
Indices: 25611331--25611965 Score: 354
Period size: 85 Copynumber: 7.4 Consensus size: 83
25611321 GAAGCCATAC
* * * * * *
25611331 ACCACAGATCTTGTCTCTCTGAGGTTGCAGTAGAGCAGACCGCATCCACTCCTATCTCCTTGAAG
1 ACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGAAT-CAATCTTATCTCCTTGAAG
*
25611396 TTGCAGTGGAGCGGATTAAA
65 TTGCAGTGGAGCAGA-TAAA
* * *
25611416 ACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGAAGATCGTATCAAGTCTTATCTCCCTGAAG
1 ACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGAATCAA-TCTTATCTCCTTGAAG
*
25611481 TTGCAGTGGAGCAGACAAA
65 TTGCAGTGGAGCAGATAAA
** * * * * ** *
25611500 AGAAACCA-ATCCTATCTCCCGGAAGTTGCAGTGGAGCAGATTAAAACCACATATCTTATCT-CT
1 A-CCA-CAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-TCGAA--TCA-ATCTTATCTCCT
* * ***
25611563 CTGAAGTTGCAATAGAGCAGATCGC
60 -TGAAGTTGCAGTGGAGCAGATAAA
* * * *** * *
25611588 ATC-CAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAAAAAAAATCAATCCTATCTCCCTGAA
1 ACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAG--ATCGAATCAATCTTATCTCCTTGAA
**
25611651 GTTGCAGTGGAGTGGATTAAA
64 GTTGCAGTGGAGCAGA-TAAA
* *
25611672 ACCACAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCATCCAATCTTATCT-CTCTGAA
1 ACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGAAT-CAATCTTATCTCCT-TGAA
* * *
25611736 GTTGCAGTAGATCAGACAAA
64 GTTGCAGTGGAGCAGATAAA
** * * * **
25611756 AGAAACCA-ATCCTATCTCTCGGAAGTTGCAGTGGAGC-GAATTAAAATCACAGATCTTATCT-C
1 A-CCA-CAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAG-A-TCGAAT--CA-ATCTTATCTCC
* * *
25611818 TCTGAAGTTGCAGTAGAGCAGATCAC
59 T-TGAAGTTGCAGTGGAGCAGATAAA
* * * * * *
25611844 ACCATAACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATATCAATCTTATCT-C
1 ACC---ACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCA-GAT--CGA-ATCAATCTTATCTCC
*
25611908 TCTGAAGTTGCAGTGGAGCAGATTGAA
59 T-TGAAGTTGCAGTGGAGCAGA-TAAA
* * * *
25611935 GCTACTA-ATCCTATCTCCCTGAAGTTGCAGT
1 ACCAC-AGATCTTATCTCTCTGAAGTTGCAGT
25611966 GGGGCGGATT
Statistics
Matches: 429, Mismatches: 87, Indels: 65
0.74 0.15 0.11
Matches are distributed among these distances:
83 24 0.06
84 21 0.05
85 182 0.42
86 40 0.09
87 4 0.01
88 86 0.20
89 4 0.01
90 58 0.14
91 5 0.01
92 3 0.01
93 2 0.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (83 bp):
ACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGAATCAATCTTATCTCCTTGAAGT
TGCAGTGGAGCAGATAAA
Found at i:25611610 original size:129 final size:129
Alignment explanation
Indices: 25611380--25611965 Score: 757
Period size: 129 Copynumber: 4.5 Consensus size: 129
25611370 CCGCATCCAC
* *
25611380 TCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCA
1 TCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCA
* * *
25611445 GTAGAGAAGATCGTATCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAA
66 GTAGAGCAGATCGCATCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAA
* *
25611509 TCCTATCTCCCGGAAGTTGCAGTGGAGCAGATTAAAACCACATATCTTATCTCTCTGAAGTTGCA
1 TCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCA
* * * *
25611574 ATAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-AAAA-AAATCAA
66 GTAGAGCAGATCGCATCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAA
** *
25611636 TCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTTACA
1 TCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCA
* * * *
25611701 GTAGAGCAGATCGCATCCAATCTTATCTCTCTGAAGTTGCAGTAGATCAGACAAAAGAAACCAA
66 GTAGAGCAGATCGCATCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAA
* * *
25611765 TCCTATCTCTCGGAAGTTGCAGTGGAGC-GAATTAAAATCACAGATCTTATCTCTCTGAAGTTGC
1 TCCTATCTCCCTGAAGTTGCAGTGGAGCAG-ATTAAAACCACAGATCTTATCTCTCTGAAGTTGC
* * **** *
25611829 AGTAGAGCAGATCACACCATAACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGAT
65 AGTAGAGCAGAT--C-GCAT--CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAA
*
25611894 ATCAA
125 ACCAA
* * * * * * *
25611899 TCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGCTACTA-ATCCTATCTCCCTGAAGTTGC
1 TCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCAC-AGATCTTATCTCTCTGAAGTTGC
25611963 AGT
65 AGT
25611966 GGGGCGGATT
Statistics
Matches: 402, Mismatches: 45, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
127 112 0.28
128 9 0.02
129 183 0.46
131 1 0.00
132 3 0.01
134 92 0.23
135 2 0.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (129 bp):
TCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCA
GTAGAGCAGATCGCATCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAA
Found at i:25611837 original size:256 final size:261
Alignment explanation
Indices: 25611380--25611931 Score: 812
Period size: 256 Copynumber: 2.1 Consensus size: 261
25611370 CCGCATCCAC
* *
25611380 TCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCA
1 TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTACA
* *
25611445 GTAGAGAAGATCGTATCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAAT
66 GTAGAGAAGATCGCATCAAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGACAAAAGAAACCAAT
*
25611510 CCTATCTCCCGGAAGTTGCAGTGGAGCAGATTAAAACCACATATCTTATCTCTCTGAAGTTGCAA
131 CCTATCTCCCGGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAA
* * **
25611575 TAGAGCAGAT-C-GCAT-CCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCA-G-AAAAAAAATCA
196 TAGAGCAGATACACCATACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTAAAAAAAATCA
25611635 A
261 A
*
25611636 TCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTTACA
1 TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTACA
* * *
25611701 GTAGAGCAGATCGCATCCAA-TCTTATCTCTCTGAAGTTGCAGTAGATCAGACAAAAGAAACCAA
66 GTAGAGAAGATCGCAT-CAAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGACAAAAGAAACCAA
* *
25611765 TCCTATCTCTCGGAAGTTGCAGTGGAGC-GAATTAAAATCACAGATCTTATCTCTCTGAAGTTGC
130 TCCTATCTCCCGGAAGTTGCAGTGGAGCAG-ATTAAAACCACAGATCTTATCTCTCTGAAGTTGC
* ** * *
25611829 AGTAGAGCAGATCACACCATAACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGAT
194 AATAGAGCAGAT-ACACCAT-ACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTAAAAAAA
25611894 ATCAA
257 ATCAA
* * *
25611899 TCTTATCTCTCTGAAGTTGCAGTGGAGCAGATT
1 TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATT
25611932 GAAGCTACTA
Statistics
Matches: 263, Mismatches: 24, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
255 1 0.00
256 187 0.71
257 3 0.01
258 1 0.00
259 3 0.01
261 30 0.11
262 1 0.00
263 37 0.14
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.26
Consensus pattern (261 bp):
TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTACA
GTAGAGAAGATCGCATCAAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGACAAAAGAAACCAAT
CCTATCTCCCGGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAA
TAGAGCAGATACACCATACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTAAAAAAAATCA
A
Found at i:25615665 original size:13 final size:13
Alignment explanation
Indices: 25615647--25615671 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25615637 CAAGGCTCCT
25615647 TTGCTTCTTTGCG
1 TTGCTTCTTTGCG
25615660 TTGCTTCTTTGC
1 TTGCTTCTTTGC
25615672 TGATCGCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.24, G:0.20, T:0.56
Consensus pattern (13 bp):
TTGCTTCTTTGCG
Found at i:25619932 original size:25 final size:25
Alignment explanation
Indices: 25619869--25619967 Score: 69
Period size: 25 Copynumber: 4.0 Consensus size: 25
25619859 GGACACACCA
*
25619869 CAGCTCGT-ATGAGCTTATCGATT-T
1 CAGCTCGTGA-GAGCTTACCGATTCT
* *
25619893 GTAGCTCATGAGAGCTTACCGATTCT
1 -CAGCTCGTGAGAGCTTACCGATTCT
** * *
25619919 CAGCTCGT-ATGAGCCGACTGATTCA
1 CAGCTCGTGA-GAGCTTACCGATTCT
* *
25619944 CAACTCGTGAGAGCATACCGATTC
1 CAGCTCGTGAGAGCTTACCGATTC
25619968 ATAACTCATA
Statistics
Matches: 57, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
24 1 0.02
25 53 0.93
26 3 0.05
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.28
Consensus pattern (25 bp):
CAGCTCGTGAGAGCTTACCGATTCT
Found at i:25624100 original size:28 final size:28
Alignment explanation
Indices: 25624068--25624123 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
25624058 CCTAGTATTA
25624068 TTACTACAACTACGTACTAAATTTCATC
1 TTACTACAACTACGTACTAAATTTCATC
25624096 TTACTACAACTACGTACTAAATTTCATC
1 TTACTACAACTACGTACTAAATTTCATC
25624124 AAATGGAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.36
Consensus pattern (28 bp):
TTACTACAACTACGTACTAAATTTCATC
Found at i:25632306 original size:18 final size:18
Alignment explanation
Indices: 25632283--25632318 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
25632273 GTGATATCTG
*
25632283 CATTACTCTCTCCAAGGA
1 CATTACTCTCTACAAGGA
25632301 CATTACTCTCTACAAGGA
1 CATTACTCTCTACAAGGA
25632319 AAAAAACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.31, G:0.11, T:0.28
Consensus pattern (18 bp):
CATTACTCTCTACAAGGA
Found at i:25636060 original size:14 final size:14
Alignment explanation
Indices: 25636026--25636053 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
25636016 AGTACTTCCT
25636026 AGACTTTTAACCCA
1 AGACTTTTAACCCA
25636040 AGACTTTTAACCCA
1 AGACTTTTAACCCA
25636054 GTACTTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (14 bp):
AGACTTTTAACCCA
Found at i:25637612 original size:19 final size:19
Alignment explanation
Indices: 25637588--25637628 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
25637578 AAGAAGAATA
25637588 GATCCTAAATTCGTTTATG
1 GATCCTAAATTCGTTTATG
25637607 GATCCTAAATTCGTTTATG
1 GATCCTAAATTCGTTTATG
25637626 GAT
1 GAT
25637629 TTATTCACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (19 bp):
GATCCTAAATTCGTTTATG
Found at i:25638393 original size:6 final size:6
Alignment explanation
Indices: 25638377--25638425 Score: 62
Period size: 6 Copynumber: 7.8 Consensus size: 6
25638367 TGGTTTTCTC
* *
25638377 AAAATG GAAATG AAAATG AAAATG AAAATG AAAATT AGAAATG AGAAAT
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG A-AAATG A-AAAT
25638426 TATTCATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
6 28 0.74
7 10 0.26
ACGTcount: A:0.63, C:0.00, G:0.18, T:0.18
Consensus pattern (6 bp):
AAAATG
Found at i:25642055 original size:27 final size:27
Alignment explanation
Indices: 25642017--25642106 Score: 128
Period size: 27 Copynumber: 3.3 Consensus size: 27
25642007 AGAGGTCAAT
25642017 AAATGA-TCGAATTACCCCCATAGGATA
1 AAATGACT-GAATTACCCCCATAGGATA
25642044 AAATGACTGAATTACCCCCATAGGATA
1 AAATGACTGAATTACCCCCATAGGATA
* * *
25642071 AAATGACCGAAATACCCTCATAGGATA
1 AAATGACTGAATTACCCCCATAGGATA
*
25642098 AAATAACTG
1 AAATGACTG
25642107 TTATACCCCT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
27 56 0.98
28 1 0.02
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.21
Consensus pattern (27 bp):
AAATGACTGAATTACCCCCATAGGATA
Found at i:25642112 original size:27 final size:27
Alignment explanation
Indices: 25642029--25642145 Score: 110
Period size: 27 Copynumber: 4.2 Consensus size: 27
25642019 ATGATCGAAT
*
25642029 TACCCCCATAGGATAAAATGACTG-AA
1 TACCCCCATAGGATAAAATAACTGTAA
* * *
25642055 TTACCCCCATAGGATAAAATGACCGAAA
1 -TACCCCCATAGGATAAAATAACTGTAA
* *
25642083 TACCCTCATAGGATAAAATAACTGTTA
1 TACCCCCATAGGATAAAATAACTGTAA
* * *
25642110 TACCCCTAGGAGATGATAAAATAACTGTTA
1 TACCCCCA-TAG--GATAAAATAACTGTAA
25642140 TACCCC
1 TACCCC
25642146 TAGGAGATGA
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
27 51 0.66
28 4 0.05
30 22 0.29
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (27 bp):
TACCCCCATAGGATAAAATAACTGTAA
Found at i:25642129 original size:30 final size:30
Alignment explanation
Indices: 25642094--25642155 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
25642084 ACCCTCATAG
25642094 GATAAAATAACTGTTATACCCCTAGGAGAT
1 GATAAAATAACTGTTATACCCCTAGGAGAT
25642124 GATAAAATAACTGTTATACCCCTAGGAGAT
1 GATAAAATAACTGTTATACCCCTAGGAGAT
25642154 GA
1 GA
25642156 AATGCCTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (30 bp):
GATAAAATAACTGTTATACCCCTAGGAGAT
Found at i:25649420 original size:22 final size:23
Alignment explanation
Indices: 25649370--25649428 Score: 84
Period size: 26 Copynumber: 2.5 Consensus size: 23
25649360 AAAGTACAAG
25649370 TTTAATGTGTCTTGCTGCTGCCAGAT
1 TTTAATGTGTCTTGCTGCT--C-GAT
25649396 TTTAATGTGTCTTGCTGCT-GAT
1 TTTAATGTGTCTTGCTGCTCGAT
25649418 TTTAATGTGTC
1 TTTAATGTGTC
25649429 ATGACCTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
22 14 0.42
26 19 0.58
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.47
Consensus pattern (23 bp):
TTTAATGTGTCTTGCTGCTCGAT
Found at i:25649439 original size:21 final size:21
Alignment explanation
Indices: 25649393--25649440 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
25649383 GCTGCTGCCA
*
25649393 GATTTTAATGTGTCTTGCTGCT
1 GATTTTAATGTGTCATGC-GCT
25649415 GATTTTAATGTGTCATGAC-CT
1 GATTTTAATGTGTCATG-CGCT
25649436 GATTT
1 GATTT
25649441 AATTTGTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 7 0.29
22 16 0.67
23 1 0.04
ACGTcount: A:0.19, C:0.12, G:0.21, T:0.48
Consensus pattern (21 bp):
GATTTTAATGTGTCATGCGCT
Found at i:25665823 original size:18 final size:18
Alignment explanation
Indices: 25665777--25665832 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
25665767 TTTAAAAAAT
*
25665777 ATTTTTTAAAAATA-TAA
1 ATTTTATAAAAATATTAA
25665794 A-TTTATAAAAAATTATTAA
1 ATTTTAT-AAAAA-TATTAA
25665813 ATTTTATAAAAATATTAA
1 ATTTTATAAAAATATTAA
25665831 AT
1 AT
25665833 AAAGTTCAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
16 4 0.12
17 6 0.18
18 10 0.29
19 9 0.26
20 5 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTTTATAAAAATATTAA
Found at i:25666409 original size:6 final size:6
Alignment explanation
Indices: 25666370--25666409 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
25666360 TGGGACCTCG
* *
25666370 TTTCTAT TTCCAT TTCCAT TTTCAT TTTCAT TTTCAT TTT
1 TTTC-AT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTT
25666410 TGAAAATCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 28 0.90
7 3 0.10
ACGTcount: A:0.15, C:0.20, G:0.00, T:0.65
Consensus pattern (6 bp):
TTTCAT
Found at i:25670281 original size:49 final size:49
Alignment explanation
Indices: 25670160--25670297 Score: 140
Period size: 49 Copynumber: 2.8 Consensus size: 49
25670150 GCTATTTGGG
* * ** *
25670160 GCTTCCCATTAATGGCTCTTCA-GAGCTACCCGTTAT-TAGCTCGCATGA
1 GCTTCCCATTAATGGCTC-TCATGAGCTTCCCGTTATATAGCCCAAATAA
* * *
25670208 GCTTTCCGATT-ATGGCTCTTATGAGCTTCCCGTTGTATAGCCCAAATAA
1 GC-TTCCCATTAATGGCTCTCATGAGCTTCCCGTTATATAGCCCAAATAA
*
25670257 GCTTCCCATTAATGGCT-TACATGAGCTTCCTGTTATATAGC
1 GCTTCCCATTAATGGCTCT-CATGAGCTTCCCGTTATATAGC
25670298 TCAAGAGAGA
Statistics
Matches: 73, Mismatches: 12, Indels: 9
0.78 0.13 0.10
Matches are distributed among these distances:
47 2 0.03
48 29 0.40
49 42 0.58
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (49 bp):
GCTTCCCATTAATGGCTCTCATGAGCTTCCCGTTATATAGCCCAAATAA
Found at i:25685869 original size:16 final size:17
Alignment explanation
Indices: 25685850--25685883 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
25685840 AAATATTACG
25685850 AAATAAAAAT-AAACAA
1 AAATAAAAATCAAACAA
*
25685866 AAATAAACATCAAACAA
1 AAATAAAAATCAAACAA
25685883 A
1 A
25685884 CGCAATCCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (17 bp):
AAATAAAAATCAAACAA
Found at i:25689170 original size:26 final size:26
Alignment explanation
Indices: 25689141--25689207 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 26
25689131 TTACCCCCAG
25689141 TAAAATTTTGATG-ATTTTACCCTCGA
1 TAAAATTTTGA-GAATTTTACCCTCGA
* *
25689167 TAAAATTTTTGAGAATTTTACCCTTGG
1 TAAAA-TTTTGAGAATTTTACCCTCGA
*
25689194 TAAAATTTCGAGAA
1 TAAAATTTTGAGAA
25689208 AATATGCTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 14 0.39
27 22 0.61
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (26 bp):
TAAAATTTTGAGAATTTTACCCTCGA
Found at i:25689356 original size:6 final size:6
Alignment explanation
Indices: 25689345--25689378 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
25689335 AATTGCAATA
*
25689345 ATTTCC ATTTCC ATTTCC ATTTCG ATTTCC ATTT
1 ATTTCC ATTTCC ATTTCC ATTTCC ATTTCC ATTT
25689379 TTGCAAACCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.18, C:0.26, G:0.03, T:0.53
Consensus pattern (6 bp):
ATTTCC
Found at i:25696707 original size:16 final size:17
Alignment explanation
Indices: 25696676--25696709 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
25696666 AAATTTAGTC
*
25696676 CAAAATTCATACTTTTG
1 CAAAATTCACACTTTTG
25696693 CAAAATT-ACACTTTTG
1 CAAAATTCACACTTTTG
25696709 C
1 C
25696710 CCCTAACATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.38
Consensus pattern (17 bp):
CAAAATTCACACTTTTG
Found at i:25699889 original size:33 final size:33
Alignment explanation
Indices: 25699847--25699912 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
25699837 ACGTGTATGG
*
25699847 CCCTAGGGAAAAATCCTGAGTTTGGGGCCCACA
1 CCCTAGGGAAAAATCCTAAGTTTGGGGCCCACA
25699880 CCCTAGGGAAAAATCCTAAGTTTGGGGCCCACA
1 CCCTAGGGAAAAATCCTAAGTTTGGGGCCCACA
25699913 TGATCCAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.29, C:0.27, G:0.26, T:0.18
Consensus pattern (33 bp):
CCCTAGGGAAAAATCCTAAGTTTGGGGCCCACA
Found at i:25701205 original size:278 final size:276
Alignment explanation
Indices: 25700666--25701220 Score: 1047
Period size: 278 Copynumber: 2.0 Consensus size: 276
25700656 AGTTTTTTTT
*
25700666 AAAAAAAATTTTGAATTTACTCCAAACTCAACCACTTAAACAACACACACCTAAAAATTTATTAT
1 AAAAAAAAATTTGAATTTACTCCAAACTCAACCACTTAAACAACACACACCTAAAAATTTATTAT
25700731 CATAAGACTAATGAAGGAACTTGAACCCCCGACCCACCATACACAGTCCAACCTTTAACCACTAA
66 CATAAGACTAATGAAGGAACTTGAACCCCCGACCCACCATACACAGTCCAACCTTTAACCACTAA
*
25700796 ACAGGTGCTAAATTATATGATAATATTTGACAAATCCCGTATATAAACTTTGGGGCGTTACAAGT
131 ACAGGTGCTAAATTATATGATAATATTCGACAAATCCCGTATATAAACTTTGGGGCGTTACAAGT
* *
25700861 AACCCTGTTCTGATATTATGAATGAAGTACTAATACATTTTTTTAAATCATAAATTCACTTTAAA
196 AACCCTGTTCTGATACTATGAATAAAGTACTAATACATTTTTTTAAATCATAAATTCACTTTAAA
25700926 ATATTTTGGGAAAATA
261 ATATTTTGGGAAAATA
25700942 AAAAAAAACATTTGAATTTACTCCAAACTCAACCACTTAAACAACACACACCTAAAAATTTATTA
1 AAAAAAAA-ATTTGAATTTACTCCAAACTCAACCACTTAAACAACACACACCTAAAAATTTATTA
*
25701007 TCATAAGACTCATGAAGGAACTTGAACCCCCGACCCACCATACACAGTCCAACCTTTAACCACTA
65 TCATAAGACTAATGAAGGAACTTGAACCCCCGACCCACCATACACAGTCCAACCTTTAACCACTA
25701072 AAGCAGGTGCTAAATTATATGATAATATTCGACAAATCCCGTATATAAACTTTGGGGCGTTACAA
130 AA-CAGGTGCTAAATTATATGATAATATTCGACAAATCCCGTATATAAACTTTGGGGCGTTACAA
25701137 GTAACCCTGTTCTGATACTATGAATAAAGTACTAATACATTTTTTTAAATCATAAATTCACTTTA
194 GTAACCCTGTTCTGATACTATGAATAAAGTACTAATACATTTTTTTAAATCATAAATTCACTTTA
25701202 AAATATTTTGGGAAAATA
259 AAATATTTTGGGAAAATA
25701220 A
1 A
25701221 TTTAGGATTC
Statistics
Matches: 272, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
276 8 0.03
277 121 0.44
278 143 0.53
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (276 bp):
AAAAAAAAATTTGAATTTACTCCAAACTCAACCACTTAAACAACACACACCTAAAAATTTATTAT
CATAAGACTAATGAAGGAACTTGAACCCCCGACCCACCATACACAGTCCAACCTTTAACCACTAA
ACAGGTGCTAAATTATATGATAATATTCGACAAATCCCGTATATAAACTTTGGGGCGTTACAAGT
AACCCTGTTCTGATACTATGAATAAAGTACTAATACATTTTTTTAAATCATAAATTCACTTTAAA
ATATTTTGGGAAAATA
Found at i:25704627 original size:39 final size:39
Alignment explanation
Indices: 25704566--25704741 Score: 176
Period size: 39 Copynumber: 4.5 Consensus size: 39
25704556 AACATGTTTT
* * *
25704566 TGAGTATTGCGACATATACTTGAATGATATGTGATTATA
1 TGAGTATTGCGATATATGCTTGAATGTTATGTGATTATA
* * *
25704605 TGAATATTGCGATATATGCTTGAATGTTACGTGAATATA
1 TGAGTATTGCGATATATGCTTGAATGTTATGTGATTATA
* * * * *
25704644 TGAGTATTAC-ATATGTGCTTGAACGTTATGTAAGTATA
1 TGAGTATTGCGATATATGCTTGAATGTTATGTGATTATA
* * *
25704682 TGAGTATTGTGATATATG-TTAAAATGCTATGTGATTATA
1 TGAGTATTGCGATATATGCTT-GAATGTTATGTGATTATA
* * *
25704721 TGTGTAATGTGATATATGCTT
1 TGAGTATTGCGATATATGCTT
25704742 AAAAGTGAAT
Statistics
Matches: 111, Mismatches: 23, Indels: 5
0.80 0.17 0.04
Matches are distributed among these distances:
38 33 0.30
39 76 0.68
40 2 0.02
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.41
Consensus pattern (39 bp):
TGAGTATTGCGATATATGCTTGAATGTTATGTGATTATA
Found at i:25705594 original size:22 final size:22
Alignment explanation
Indices: 25705550--25705594 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
25705540 TTTCTATGGT
* * *
25705550 TGCTCATTAAGTTTTATTTTTG
1 TGCTCATTAAATTTCATTGTTG
*
25705572 TGCTCGTTAAATTTCATTGTTG
1 TGCTCATTAAATTTCATTGTTG
25705594 T
1 T
25705595 TATCGATAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.18, C:0.11, G:0.16, T:0.56
Consensus pattern (22 bp):
TGCTCATTAAATTTCATTGTTG
Found at i:25706207 original size:63 final size:63
Alignment explanation
Indices: 25706083--25706229 Score: 170
Period size: 63 Copynumber: 2.3 Consensus size: 63
25706073 GTCGTGTGGC
* * **
25706083 AGACCGTGTAACTCACTATTTATGAATTAGAGTCACATGGGCTAGGGATACGGGGGCGTGTCT
1 AGACCGTGTAACTCACTATTTATGAATTAGAGTCACACGGGCTAGGGACACGGGCACGTGTCT
* * * * * *
25706146 AGACCGTGTGATTCACTGTTTAT-AGATTAGAGTCACACGGGCTTGGGACACGGGCATGTGTCC
1 AGACCGTGTAACTCACTATTTATGA-ATTAGAGTCACACGGGCTAGGGACACGGGCACGTGTCT
* *
25706209 AAACCATGTAACTCACTATTT
1 AGACCGTGTAACTCACTATTT
25706230 TGGTGCAGAG
Statistics
Matches: 68, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
62 1 0.01
63 67 0.99
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.28
Consensus pattern (63 bp):
AGACCGTGTAACTCACTATTTATGAATTAGAGTCACACGGGCTAGGGACACGGGCACGTGTCT
Found at i:25708737 original size:13 final size:13
Alignment explanation
Indices: 25708719--25708744 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25708709 GAGTTGATAG
25708719 CAAAATATTTGAC
1 CAAAATATTTGAC
25708732 CAAAATATTTGAC
1 CAAAATATTTGAC
25708745 TATGTAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
CAAAATATTTGAC
Found at i:25711270 original size:25 final size:25
Alignment explanation
Indices: 25711216--25711273 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
25711206 GACACAGCGC
*
25711216 AGCTCTTATGAGCGTCCCGATATAT
1 AGCTCTTAGGAGCGTCCCGATATAT
* * *
25711241 GGCTCTTCGGAGCTTCCCGATA-ACT
1 AGCTCTTAGGAGCGTCCCGATATA-T
25711266 AGCTCTTA
1 AGCTCTTA
25711274 TGGCTTTCTG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 1 0.04
25 25 0.96
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.31
Consensus pattern (25 bp):
AGCTCTTAGGAGCGTCCCGATATAT
Found at i:25713967 original size:183 final size:182
Alignment explanation
Indices: 25713720--25714070 Score: 596
Period size: 183 Copynumber: 1.9 Consensus size: 182
25713710 TTAACCTCTT
*
25713720 CCTCTCAATTGAGCTGAATTTTCCTAAATTAACACATTATCAATCACTTTAAACTACTTTATAAC
1 CCTCTCAATTGAGCTGAATTTTCCTAAATTAACACATTATCAATCACTTTAAACTACCTTATAAC
*
25713785 CTTTGGAAATCAAAATTTTAGCATTAGACTTTAATTCCAAACTTTTTCACAATTAGGTCCTACAA
66 CTTTAGAAATCAAAATTTTAGCATTAGACTTTAATTCCAAACTTTTTCACAATTAGGTCCTACAA
25713850 ATCAATTTCTATTGAAATCACCTAGTAAAACCATCTCGNCCCTGCTCAATTAA
131 ATCAATTTCTATTGAAATCACCTAGTAAAACCATCTCG-CCCTGCTCAATTAA
* * ** * *
25713903 CCTCTTAATTGAGCTG-ATTTTTCTCCATTAACACTTTATTCTATCACTTTAAACTACCTTATAA
1 CCTCTCAATTGAGCTGAATTTTCCTAAATTAACACATTA-TCAATCACTTTAAACTACCTTATAA
*
25713967 CCTTTAGAATTCAAAATTTTAGCATTAGACTTTAATTCCAAACTTTTTCACAATTAGGTCCTACA
65 CCTTTAGAAATCAAAATTTTAGCATTAGACTTTAATTCCAAACTTTTTCACAATTAGGTCCTACA
25714032 AATCAATTTCTATTGAAATCACCTAGTAAAACCATCTCG
130 AATCAATTTCTATTGAAATCACCTAGTAAAACCATCTCG
25714071 TAAACAAATT
Statistics
Matches: 158, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
182 18 0.11
183 140 0.89
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (182 bp):
CCTCTCAATTGAGCTGAATTTTCCTAAATTAACACATTATCAATCACTTTAAACTACCTTATAAC
CTTTAGAAATCAAAATTTTAGCATTAGACTTTAATTCCAAACTTTTTCACAATTAGGTCCTACAA
ATCAATTTCTATTGAAATCACCTAGTAAAACCATCTCGCCCTGCTCAATTAA
Found at i:25720592 original size:6 final size:6
Alignment explanation
Indices: 25720581--25720608 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
25720571 CACGTGACCA
25720581 TCACTT TCACTT TCACTT TCACTT TCAC
1 TCACTT TCACTT TCACTT TCACTT TCAC
25720609 ATAGTAGCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.36, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:25721213 original size:18 final size:18
Alignment explanation
Indices: 25721190--25721247 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
25721180 ACCGGGACTC
25721190 TAAAAACGTAAAGAACAT
1 TAAAAACGTAAAGAACAT
*
25721208 TAAAAACG----GGAC-T
1 TAAAAACGTAAAGAACAT
25721221 CTAAAAACGTAAAGAACAT
1 -TAAAAACGTAAAGAACAT
25721240 TAAAAACG
1 TAAAAACG
25721248 GGGCTTGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
13 1 0.03
14 11 0.34
18 19 0.59
19 1 0.03
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.16
Consensus pattern (18 bp):
TAAAAACGTAAAGAACAT
Found at i:25721218 original size:32 final size:32
Alignment explanation
Indices: 25721182--25721249 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
25721172 ATCAAGTTAC
25721182 CGGGACTCTAAAAACGTAAAGAACATTAAAAA
1 CGGGACTCTAAAAACGTAAAGAACATTAAAAA
25721214 CGGGACTCTAAAAACGTAAAGAACATTAAAAA
1 CGGGACTCTAAAAACGTAAAGAACATTAAAAA
25721246 CGGG
1 CGGG
25721250 GCTTGGAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.50, C:0.16, G:0.19, T:0.15
Consensus pattern (32 bp):
CGGGACTCTAAAAACGTAAAGAACATTAAAAA
Found at i:25723325 original size:152 final size:152
Alignment explanation
Indices: 25723049--25723353 Score: 565
Period size: 152 Copynumber: 2.0 Consensus size: 152
25723039 TGTCAGAATT
* *
25723049 AATTCAGTTGAAAAACATATCTCTCTCATCAAGATAATTTTCATCATAAAACAGTACTGATGAGG
1 AATTCAGTTGAAAAACATATCTCTCTCATCAAGATAATTTTCATCATAAAACAATACTGATGAAG
25723114 GGGTGATGGCGAGGACATAAAGCTTTTAACTTACTCTCATAGATACACATATATATATGACTTTG
66 GGGTGATGGCGAGGACATAAAGCTTTTAACTTACTCTCATAGATACACATATATATATGACTTTG
25723179 CATTCATCATCAATGTAATACC
131 CATTCATCATCAATGTAATACC
* *
25723201 AATTCAGTTGAAAAACATATCTGTCTCATCAAGATAATTTTCGTCATAAAACAATACTGATGAAG
1 AATTCAGTTGAAAAACATATCTCTCTCATCAAGATAATTTTCATCATAAAACAATACTGATGAAG
*
25723266 GGGTGATGGTGAGGACATAAAGCTTTTAACTTACTCTCATAGATACACATATATATATGACTTTG
66 GGGTGATGGCGAGGACATAAAGCTTTTAACTTACTCTCATAGATACACATATATATATGACTTTG
25723331 CATTCATCATCAATGTAATACC
131 CATTCATCATCAATGTAATACC
25723353 A
1 A
25723354 TCATAACCAC
Statistics
Matches: 148, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
152 148 1.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (152 bp):
AATTCAGTTGAAAAACATATCTCTCTCATCAAGATAATTTTCATCATAAAACAATACTGATGAAG
GGGTGATGGCGAGGACATAAAGCTTTTAACTTACTCTCATAGATACACATATATATATGACTTTG
CATTCATCATCAATGTAATACC
Found at i:25723422 original size:90 final size:90
Alignment explanation
Indices: 25723319--25723499 Score: 308
Period size: 90 Copynumber: 2.0 Consensus size: 90
25723309 TACACATATA
* * *
25723319 TATATGACTTTGCATTCATCATCAATGTAATACCATCATAACCACGTACTTCATTCCAAACAAAT
1 TATATGACTTTGCATTCATCATCAATGTAATACCAACATAACCACGAAATTCATTCCAAACAAAT
25723384 TAACACATCTATTTATTATGAATAC
66 TAACACATCTATTTATTATGAATAC
* * *
25723409 TATATGACTTTGCATTCATCATCAATGTAATACCAACATAACTATGAAATTCATTCCAAGCAAAT
1 TATATGACTTTGCATTCATCATCAATGTAATACCAACATAACCACGAAATTCATTCCAAACAAAT
25723474 TAACACATCTATTTATTATGAATAC
66 TAACACATCTATTTATTATGAATAC
25723499 T
1 T
25723500 TTCTATCACC
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 85 1.00
ACGTcount: A:0.39, C:0.20, G:0.06, T:0.35
Consensus pattern (90 bp):
TATATGACTTTGCATTCATCATCAATGTAATACCAACATAACCACGAAATTCATTCCAAACAAAT
TAACACATCTATTTATTATGAATAC
Found at i:25723729 original size:42 final size:42
Alignment explanation
Indices: 25723649--25723730 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
25723639 CATTTTCTCT
* * **
25723649 ATGCCATAGTCCAACTATGGTCTTACACATATTTACATATTG
1 ATGCCATAGCCCAACTATGGCCTTACACATATGCACATATTG
*
25723691 ATGCCATAGCCCAGCTATGGCCTTACACAGTA-GCACATAT
1 ATGCCATAGCCCAACTATGGCCTTACACA-TATGCACATAT
25723731 CACACCGATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 32 0.94
43 2 0.06
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (42 bp):
ATGCCATAGCCCAACTATGGCCTTACACATATGCACATATTG
Found at i:25726536 original size:16 final size:16
Alignment explanation
Indices: 25726515--25726546 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
25726505 GTTTTGTTGC
*
25726515 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
25726531 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
25726547 CTTTCAATTA
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:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Done.