Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 47 of 208
Found at i:18184151 original size:20 final size:20
Alignment explanation
Indices: 18184128--18184193 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 20
18184118 TATTATATTA
18184128 ATTATATAAGTTTAATAATT
1 ATTATATAAGTTTAATAATT
**
18184148 ATTATATATA-TTTATATTTTCGTT
1 ATTATATA-AGTTTA-A---TAATT
18184172 ATTATATAAGTTTAATAATT
1 ATTATATAAGTTTAATAATT
18184192 AT
1 AT
18184194 ATTTATAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
20 17 0.47
21 2 0.06
23 2 0.06
24 15 0.42
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (20 bp):
ATTATATAAGTTTAATAATT
Found at i:18184847 original size:18 final size:17
Alignment explanation
Indices: 18184824--18184857 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
18184814 AAGGTTTTAC
18184824 TAATTTAAAATAAAACTG
1 TAATTT-AAATAAAACTG
*
18184842 TAATTTTAATAAAACT
1 TAATTTAAATAAAACT
18184858 TTAAGCGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (17 bp):
TAATTTAAATAAAACTG
Found at i:18202660 original size:84 final size:86
Alignment explanation
Indices: 18202485--18202660 Score: 196
Period size: 86 Copynumber: 2.1 Consensus size: 86
18202475 TTTTTTAAAT
* * *
18202485 AAAATATATTTAAGATAATGATAAATATAAAAATATATATTATATAATTATTATTTTATTTATAT
1 AAAATATATTTAACATAATGATAAATATAAAAATATATATTACATAATTATTATTTGATTTATAT
* *
18202550 AAATAAAGTAGTTGTTAATTT
66 AAATAAAATAGTTGTTAATTA
* * * * * ** *
18202571 CAAATATTTTTAACATAATGATATATTTTATTATATA-ATTACATATTTATTATTTGATTT-TAT
1 AAAATATATTTAACATAATGATAAATATAAAAATATATATTACATAATTATTATTTGATTTATAT
*
18202634 AAATAAAATATTTAG-TAATTA
66 AAATAAAATAGTT-GTTAATTA
18202655 AAAATA
1 AAAATA
18202661 AAAAATTTGA
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
84 24 0.32
85 21 0.28
86 29 0.39
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (86 bp):
AAAATATATTTAACATAATGATAAATATAAAAATATATATTACATAATTATTATTTGATTTATAT
AAATAAAATAGTTGTTAATTA
Found at i:18207044 original size:2 final size:2
Alignment explanation
Indices: 18207037--18207065 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18207027 GATCCTGCGA
18207037 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18207066 AGTCAATCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18207448 original size:46 final size:46
Alignment explanation
Indices: 18207381--18207566 Score: 327
Period size: 46 Copynumber: 4.0 Consensus size: 46
18207371 ACAATGCTAT
* *
18207381 AACTCAGTATGGTTTCCTTCACTGAAACAACATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
*
18207427 AACTCAGTATAGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
*
18207473 AACTCAGTATGATTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
*
18207519 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTATTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
18207565 AA
1 AA
18207567 TTTGCCATGG
Statistics
Matches: 133, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 133 1.00
ACGTcount: A:0.31, C:0.28, G:0.08, T:0.33
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
Found at i:18208837 original size:16 final size:17
Alignment explanation
Indices: 18208791--18208838 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
18208781 AAATTCTTTT
*
18208791 TAAATCGCAAAATTCAC
1 TAAATCACAAAATTCAC
*
18208808 TAAATCACAAAATTTAC
1 TAAATCACAAAATTCAC
*
18208825 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
18208839 TTATAAATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 6 0.22
17 21 0.78
ACGTcount: A:0.50, C:0.19, G:0.02, T:0.29
Consensus pattern (17 bp):
TAAATCACAAAATTCAC
Found at i:18208969 original size:42 final size:42
Alignment explanation
Indices: 18208917--18208996 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
18208907 GATCTCGAAT
*
18208917 CACTGTTTCCGACACCACTGAAAATTAGGCTGTTACATGAAC
1 CACTATTTCCGACACCACTGAAAATTAGGCTGTTACATGAAC
* *
18208959 CACTATTTCCGACGCCACTGAAAATTGGGCTGTTACAT
1 CACTATTTCCGACACCACTGAAAATTAGGCTGTTACAT
18208997 TTACTTAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (42 bp):
CACTATTTCCGACACCACTGAAAATTAGGCTGTTACATGAAC
Found at i:18217377 original size:20 final size:20
Alignment explanation
Indices: 18217336--18217386 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
18217326 AAACTTGGGG
18217336 TTTTATAGGAAATTAACTGAT
1 TTTTATAGGAAATTAAC-GAT
*
18217357 TTTTATAGGAAAATTTA-GAT
1 TTTTATAGG-AAATTAACGAT
18217377 TTTTACTAGG
1 TTTTA-TAGG
18217387 GTTGTTTGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 8 0.30
21 13 0.48
22 6 0.22
ACGTcount: A:0.35, C:0.04, G:0.16, T:0.45
Consensus pattern (20 bp):
TTTTATAGGAAATTAACGAT
Found at i:18220625 original size:16 final size:16
Alignment explanation
Indices: 18220604--18220651 Score: 87
Period size: 16 Copynumber: 3.0 Consensus size: 16
18220594 TTTTACATGG
18220604 AATTGTTATTAAAATT
1 AATTGTTATTAAAATT
*
18220620 AATTGTTATCAAAATT
1 AATTGTTATTAAAATT
18220636 AATTGTTATTAAAATT
1 AATTGTTATTAAAATT
18220652 GTATTAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (16 bp):
AATTGTTATTAAAATT
Found at i:18220806 original size:93 final size:93
Alignment explanation
Indices: 18220697--18220880 Score: 332
Period size: 93 Copynumber: 2.0 Consensus size: 93
18220687 TTTGTAAAAT
* *
18220697 CTAACATTTTGCTAGTAAAATTATTAATTGTTACTTGTATTAATTGTTATTAAAATTATCAAATT
1 CTAACATTTTGCTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATCAAATT
18220762 ATATCAAATTATTAATTATTAATTGTTA
66 ATATCAAATTATTAATTATTAATTGTTA
*
18220790 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATCAAATT
1 CTAACATTTTGCTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATCAAATT
*
18220855 ATATCAAATTATTAATTGTTAATTGT
66 ATATCAAATTATTAATTATTAATTGT
18220881 ATTAATTGTT
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 87 1.00
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (93 bp):
CTAACATTTTGCTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATCAAATT
ATATCAAATTATTAATTATTAATTGTTA
Found at i:18223736 original size:18 final size:18
Alignment explanation
Indices: 18223690--18223736 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
18223680 GCTTACTTAA
*
18223690 TATTTGATTTA-TTATTT
1 TATTTTATTTATTTATTT
*
18223707 TATTTTAGTTATTTATTT
1 TATTTTATTTATTTATTT
18223725 TAATTTT-TTTAT
1 T-ATTTTATTTAT
18223737 CTGACTTGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 9 0.36
18 11 0.44
19 5 0.20
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.72
Consensus pattern (18 bp):
TATTTTATTTATTTATTT
Found at i:18225830 original size:40 final size:39
Alignment explanation
Indices: 18225768--18225884 Score: 121
Period size: 40 Copynumber: 3.0 Consensus size: 39
18225758 TTGGCACCTA
* *
18225768 GTGCCTCATCTGATAATTCGAAGTAATAATTTGACACCCG
1 GTGCCTCATCGGATAATCCGAAGTAATAA-TTGACACCCG
* * * *
18225808 GTGCCTCATCGGCTAAACCGAAGT-A-AATTGGCACCCT
1 GTGCCTCATCGGATAATCCGAAGTAATAATTGACACCCG
* *
18225845 GTGCCTCATTGAATTAATCCGAAGTAATGAATTGACACCC
1 GTGCCTCATCGGA-TAATCCGAAGTAAT-AATTGACACCC
18225885 AGTGTCTTAT
Statistics
Matches: 62, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
37 18 0.29
38 12 0.19
39 2 0.03
40 20 0.32
41 10 0.16
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (39 bp):
GTGCCTCATCGGATAATCCGAAGTAATAATTGACACCCG
Found at i:18226057 original size:17 final size:16
Alignment explanation
Indices: 18226019--18226076 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 16
18226009 TATTCATTTC
18226019 AATTCAA-ATAATCAATA
1 AATTCAATATAAT--ATA
*
18226036 TATTCAATAT-ATATA
1 AATTCAATATAATATA
18226051 CCAATTCAAT-TAATATA
1 --AATTCAATATAATATA
18226068 AATTCAATA
1 AATTCAATA
18226077 AATTCATCAC
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
15 11 0.32
16 1 0.03
17 20 0.59
18 2 0.06
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (16 bp):
AATTCAATATAATATA
Found at i:18226917 original size:21 final size:21
Alignment explanation
Indices: 18226878--18226919 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
18226868 AATACATATT
*
18226878 TTATTATTAAATATATATTTA
1 TTATTATTAAACATATATTTA
* *
18226899 TTATTATTACACATGTATTTA
1 TTATTATTAAACATATATTTA
18226920 CCAACACCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (21 bp):
TTATTATTAAACATATATTTA
Found at i:18232302 original size:31 final size:32
Alignment explanation
Indices: 18232267--18232329 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
18232257 TTAGCATTTC
18232267 ATTAATGATTTAACAA-ATAAATGACTAAAAT
1 ATTAATGATTTAACAATATAAATGACTAAAAT
** * *
18232298 ATTAATTTTTTAATAATATTAATGACTAAAAT
1 ATTAATGATTTAACAATATAAATGACTAAAAT
18232330 TGCCAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 13 0.48
32 14 0.52
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.40
Consensus pattern (32 bp):
ATTAATGATTTAACAATATAAATGACTAAAAT
Found at i:18232465 original size:54 final size:54
Alignment explanation
Indices: 18232393--18232497 Score: 156
Period size: 54 Copynumber: 1.9 Consensus size: 54
18232383 GCTAAAACAA
* **
18232393 TTTTGGGCACAGTGAAGTTTCGTCCGTTCCAAACTTGCCGCAGCCTAACACGAC
1 TTTTGGGCACAGTCAAGTTTCACCCGTTCCAAACTTGCCGCAGCCTAACACGAC
* **
18232447 TTTTGGGCAGAGTCAAGTTTCACCCGTTCCAATTTTGCCGCAGCCTAACAC
1 TTTTGGGCACAGTCAAGTTTCACCCGTTCCAAACTTGCCGCAGCCTAACAC
18232498 TGAATTCTCC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.28
Consensus pattern (54 bp):
TTTTGGGCACAGTCAAGTTTCACCCGTTCCAAACTTGCCGCAGCCTAACACGAC
Found at i:18232899 original size:7 final size:7
Alignment explanation
Indices: 18232887--18232912 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
18232877 CTCATCTTTC
18232887 AAATTTT
1 AAATTTT
18232894 AAATTTT
1 AAATTTT
18232901 AAATTTT
1 AAATTTT
18232908 AAATT
1 AAATT
18232913 ATATTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
AAATTTT
Found at i:18234914 original size:88 final size:88
Alignment explanation
Indices: 18234765--18234936 Score: 299
Period size: 88 Copynumber: 2.0 Consensus size: 88
18234755 AATTCAGATG
**
18234765 CTTCCAATTATACTCAACATGGTTTTCATGAATACTTGTTTATTCCAACTCCAAACTTTCACCAT
1 CTTCCAATTATACTCAACATGGTTTTCATGAATACTTGTTTAGCCCAACTCCAAACTTTCACCAT
18234830 CCAACAAAGCACAACCATGAACA
66 CCAACAAAGCACAACCATGAACA
* *
18234853 CTTCCAATTATACTCAGCATTGTTTTCATGAATACTTGTTTAGCCCAACTCCAAACTTTCACCAT
1 CTTCCAATTATACTCAACATGGTTTTCATGAATACTTGTTTAGCCCAACTCCAAACTTTCACCAT
*
18234918 CCAACAAAGGACAACCATG
66 CCAACAAAGCACAACCATG
18234937 GACAATCATG
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 79 1.00
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.30
Consensus pattern (88 bp):
CTTCCAATTATACTCAACATGGTTTTCATGAATACTTGTTTAGCCCAACTCCAAACTTTCACCAT
CCAACAAAGCACAACCATGAACA
Found at i:18239881 original size:40 final size:41
Alignment explanation
Indices: 18239822--18239901 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 41
18239812 TATAAAAGAA
*
18239822 AGAAAGAAAATAAACAGAGAGCAAAACAAAACAGAGAAGGG
1 AGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGGG
*
18239863 AGAAAG-AAAGAAACAGAGAGCAAAACGAAACAGAGAAGG
1 AGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
18239902 AAGGAAGGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
40 31 0.84
41 6 0.16
ACGTcount: A:0.62, C:0.10, G:0.26, T:0.01
Consensus pattern (41 bp):
AGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGGG
Found at i:18247988 original size:16 final size:17
Alignment explanation
Indices: 18247957--18247991 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
18247947 TAAAAAAATC
*
18247957 CAATTATCATATTTACA
1 CAATTATCACATTTACA
18247974 CAATT-TCACATTTACA
1 CAATTATCACATTTACA
18247990 CA
1 CA
18247992 CACATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (17 bp):
CAATTATCACATTTACA
Found at i:18248000 original size:2 final size:2
Alignment explanation
Indices: 18247995--18248033 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
18247985 TTACACACAC
18247995 AT AT AT AT AT -T CAT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18248034 TCCAATTCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 31 0.91
3 1 0.03
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18248797 original size:16 final size:17
Alignment explanation
Indices: 18248770--18248801 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
18248760 CGTTTTAAGC
18248770 TTTCTGTTTCTTTCTTA
1 TTTCTGTTTCTTTCTTA
18248787 TTTCT-TTTCTTTCTT
1 TTTCTGTTTCTTTCTT
18248802 TTGTTTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (17 bp):
TTTCTGTTTCTTTCTTA
Found at i:18250446 original size:23 final size:24
Alignment explanation
Indices: 18250410--18250478 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 24
18250400 GGACTCACCA
*
18250410 CAGCTCGTATGAGCTTACCGTT-T
1 CAGCTCGAATGAGCTTACCGTTAT
*
18250433 CAGCTC-AATAGAGCTTACCATTTAT
1 CAGCTCGAAT-GAGCTTACC-GTTAT
18250458 CAGCTCGGAATGAGCTTACCG
1 CAGCTC-GAATGAGCTTACCG
18250479 ATCATGGCTC
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
22 2 0.05
23 15 0.39
24 2 0.05
25 7 0.18
26 9 0.24
27 3 0.08
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (24 bp):
CAGCTCGAATGAGCTTACCGTTAT
Found at i:18251337 original size:7 final size:7
Alignment explanation
Indices: 18251320--18251348 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
18251310 AATTTTTAAA
18251320 AAAAAAG
1 AAAAAAG
18251327 -AAAAAG
1 AAAAAAG
18251333 AAAAAAG
1 AAAAAAG
18251340 AAAAAAG
1 AAAAAAG
18251347 AA
1 AA
18251349 TGAAGTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:18251338 original size:13 final size:13
Alignment explanation
Indices: 18251320--18251344 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18251310 AATTTTTAAA
18251320 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
18251333 AAAAAAGAAAAA
1 AAAAAAGAAAAA
18251345 AGAATGAAGT
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:18264788 original size:9 final size:9
Alignment explanation
Indices: 18264774--18264803 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
18264764 TAACAATTTC
18264774 GAAATGGTG
1 GAAATGGTG
18264783 GAAATGGTG
1 GAAATGGTG
18264792 GAAATGGTG
1 GAAATGGTG
18264801 GAA
1 GAA
18264804 GAGGAGAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.43, T:0.20
Consensus pattern (9 bp):
GAAATGGTG
Found at i:18271007 original size:7 final size:7
Alignment explanation
Indices: 18270992--18271040 Score: 55
Period size: 7 Copynumber: 7.1 Consensus size: 7
18270982 TAAAGCTACT
18270992 ACTTATC
1 ACTTATC
*
18270999 ACTTGTC
1 ACTTATC
18271006 ACTTATC
1 ACTTATC
*
18271013 AC-TACC
1 ACTTATC
18271019 ACTTATC
1 ACTTATC
*
18271026 ACTTGTC
1 ACTTATC
*
18271033 ACTGATC
1 ACTTATC
18271040 A
1 A
18271041 AAAGTACTCA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
6 5 0.15
7 29 0.85
ACGTcount: A:0.27, C:0.31, G:0.06, T:0.37
Consensus pattern (7 bp):
ACTTATC
Found at i:18271011 original size:14 final size:14
Alignment explanation
Indices: 18270992--18271040 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
18270982 TAAAGCTACT
18270992 ACTTATCACTTGTC
1 ACTTATCACTTGTC
**
18271006 ACTTATCAC-TACC
1 ACTTATCACTTGTC
18271019 ACTTATCACTTGTC
1 ACTTATCACTTGTC
*
18271033 ACTGATCA
1 ACTTATCA
18271041 AAAGTACTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
13 11 0.38
14 18 0.62
ACGTcount: A:0.27, C:0.31, G:0.06, T:0.37
Consensus pattern (14 bp):
ACTTATCACTTGTC
Found at i:18271024 original size:27 final size:27
Alignment explanation
Indices: 18270987--18271040 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
18270977 GTAGCTAAAG
* *
18270987 CTACTACTTATCACTTGTCACTTATCA
1 CTACCACTTATCACTTGTCACTGATCA
18271014 CTACCACTTATCACTTGTCACTGATCA
1 CTACCACTTATCACTTGTCACTGATCA
18271041 AAAGTACTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.26, C:0.31, G:0.06, T:0.37
Consensus pattern (27 bp):
CTACCACTTATCACTTGTCACTGATCA
Found at i:18271027 original size:20 final size:20
Alignment explanation
Indices: 18270998--18271035 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
18270988 TACTACTTAT
*
18270998 CACTTGTCACTTATCACTAC
1 CACTTATCACTTATCACTAC
*
18271018 CACTTATCACTTGTCACT
1 CACTTATCACTTATCACT
18271036 GATCAAAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.05, T:0.37
Consensus pattern (20 bp):
CACTTATCACTTATCACTAC
Found at i:18274347 original size:2 final size:2
Alignment explanation
Indices: 18274340--18274368 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18274330 CTCCTTGTAA
18274340 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18274369 ATAGTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18275581 original size:9 final size:9
Alignment explanation
Indices: 18275541--18275635 Score: 68
Period size: 9 Copynumber: 10.4 Consensus size: 9
18275531 GTAAATATAT
*
18275541 TAAAAATAA
1 TAAAAATTA
* *
18275550 AAAAAAATA
1 TAAAAATTA
18275559 -AAAAATTA
1 TAAAAATTA
*
18275567 T-TAAATTA
1 TAAAAATTA
*
18275575 TAAAAATGA
1 TAAAAATTA
*
18275584 TAAAAATGA
1 TAAAAATTA
*
18275593 TAAAAAAATA
1 T-AAAAATTA
* *
18275603 TAATAATTTT
1 TAA-AAATTA
18275613 TAATAAATTA
1 TAA-AAATTA
18275623 TAAAAATTA
1 TAAAAATTA
18275632 TAAA
1 TAAA
18275636 TGTAATAAAC
Statistics
Matches: 68, Mismatches: 14, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
8 14 0.21
9 33 0.49
10 21 0.31
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (9 bp):
TAAAAATTA
Found at i:18280219 original size:19 final size:18
Alignment explanation
Indices: 18280195--18280233 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
18280185 AGTCTAATAA
18280195 TTTC-TTTCTTTCTTTCCTT
1 TTTCTTTTCTTT-TTT-CTT
18280214 TTTCTTTTCTTTTTTCTT
1 TTTCTTTTCTTTTTTCTT
18280232 TT
1 TT
18280234 AAATTTCAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 7 0.37
20 7 0.37
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTCTTTTCTTTTTTCTT
Found at i:18280960 original size:156 final size:157
Alignment explanation
Indices: 18280647--18280968 Score: 610
Period size: 156 Copynumber: 2.1 Consensus size: 157
18280637 CGCAGTTTAT
*
18280647 TTCTGACAGCTTTGCTGATATTAAATGGACTTCACATATGGTTCTGATTTAGATTGTTTTTCATA
1 TTCTGA-ACCTTTGCTGATATTAAATGGACTTCACATATGGTTCTGATTTAGATTGTTTTTCATA
18280712 CATAATGTAACTAAGGAAAATTTTCCACAAAGGGTTTTACATTAATGCTTTTACTGTCAATTTTT
65 CATAATGTAACTAAGGAAAATTTTCCACAAAGGGTTTTACATTAATGCTTTTACTGTCAATTTTT
*
18280777 ATCCATCAGCCTCAAGCTTTGTTCAAAG
130 ATCCATCAGCCTCAAGCCTTGTTCAAAG
18280805 TTCTGAACCTTTGCTGATATTAAATGGACTTCACATATGGTTCTGATTTAGATTGTTTTTCATAC
1 TTCTGAACCTTTGCTGATATTAAATGGACTTCACATATGGTTCTGATTTAGATTGTTTTTCATAC
18280870 ATAATGTAACTAAGG-AAATTTTCCACAAAGGGTTTTACATTAATGCTTTTACTGTCAATTTTTA
66 ATAATGTAACTAAGGAAAATTTTCCACAAAGGGTTTTACATTAATGCTTTTACTGTCAATTTTTA
18280934 TCCATCAGCCTCAAGCCTTGTTCAAAG
131 TCCATCAGCCTCAAGCCTTGTTCAAAG
18280961 TTCTGAAC
1 TTCTGAAC
18280969 AAAACCCCGC
Statistics
Matches: 162, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
156 83 0.51
157 73 0.45
158 6 0.04
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (157 bp):
TTCTGAACCTTTGCTGATATTAAATGGACTTCACATATGGTTCTGATTTAGATTGTTTTTCATAC
ATAATGTAACTAAGGAAAATTTTCCACAAAGGGTTTTACATTAATGCTTTTACTGTCAATTTTTA
TCCATCAGCCTCAAGCCTTGTTCAAAG
Found at i:18282068 original size:31 final size:29
Alignment explanation
Indices: 18282033--18282109 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
18282023 TTAATAGCTC
*
18282033 AGTGACTAAAATGTTACAACACGATAACATA
1 AGTGACTAAAATGTAACAACAC-A-AACATA
* * ***
18282064 AGTGACAAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACAACACAAACATA
18282093 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
18282110 CTAAGGTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 21 0.55
30 1 0.03
31 16 0.42
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.22
Consensus pattern (29 bp):
AGTGACTAAAATGTAACAACACAAACATA
Found at i:18282957 original size:1 final size:1
Alignment explanation
Indices: 18282951--18282975 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
18282941 ACCATTCACC
18282951 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
18282976 GTTATTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:18286433 original size:2 final size:2
Alignment explanation
Indices: 18286426--18286464 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
18286416 TCTTTTCCTT
18286426 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
18286465 TTGGGGTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:18307749 original size:13 final size:12
Alignment explanation
Indices: 18307707--18307749 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 12
18307697 ATTCTTAGTT
18307707 TTTTTTATATTAA
1 TTTTTTAT-TTAA
18307720 TTTTTTATTTAAA
1 TTTTTTATTT-AA
18307733 TTTTTTGATTT-A
1 TTTTTT-ATTTAA
18307745 TTTTT
1 TTTTT
18307750 ACAAAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 8 0.29
13 16 0.57
14 4 0.14
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (12 bp):
TTTTTTATTTAA
Found at i:18324050 original size:31 final size:31
Alignment explanation
Indices: 18323992--18324051 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
18323982 TGTGTCAATA
* *
18323992 ATTTATAAAATTTAAATCAAACCAAATTTTC
1 ATTTATAAAATTTAAATAAAACAAAATTTTC
*
18324023 ATTTATAAAA-TTATATAAAATCAAAATTT
1 ATTTATAAAATTTAAATAAAA-CAAAATTT
18324052 ATGTATGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (31 bp):
ATTTATAAAATTTAAATAAAACAAAATTTTC
Found at i:18333181 original size:56 final size:59
Alignment explanation
Indices: 18333072--18333218 Score: 194
Period size: 56 Copynumber: 2.5 Consensus size: 59
18333062 AATTGACAAT
*
18333072 AAAAAGGATCTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCCTGAAGAATATGTGTG
1 AAAAA-GATCTAGCCCGGACGGGTGATCC-AT-CTGATATAGCCCTCCCGAAGAATATGTG-G
18333135 AAAAAGATCTAG-CCGGACGGGTGAT-C-T-TGATATAGCCCTCCCGAAGAATATGTGG
1 AAAAAGATCTAGCCCGGACGGGTGATCCATCTGATATAGCCCTCCCGAAGAATATGTGG
* *
18333190 AAAATAGATTTAGCCCGGACGGGTAATCC
1 AAAA-AGATCTAGCCCGGACGGGTGATCC
18333219 GAATTAGGGT
Statistics
Matches: 78, Mismatches: 3, Indels: 11
0.85 0.03 0.12
Matches are distributed among these distances:
55 5 0.06
56 33 0.42
57 12 0.15
58 2 0.03
60 1 0.01
61 13 0.17
62 7 0.09
63 5 0.06
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.22
Consensus pattern (59 bp):
AAAAAGATCTAGCCCGGACGGGTGATCCATCTGATATAGCCCTCCCGAAGAATATGTGG
Found at i:18333447 original size:66 final size:66
Alignment explanation
Indices: 18333340--18333465 Score: 234
Period size: 66 Copynumber: 1.9 Consensus size: 66
18333330 GTTTATATTA
*
18333340 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAAGATGAGGTTCGCGGGAGTGTGCTATCTT
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAAGATGAGGTTCGCAGGAGTGTGCTATCTT
18333405 G
66 G
*
18333406 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGGATGAGGTTCGCAGGAGTGTGCT
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAAGATGAGGTTCGCAGGAGTGTGCT
18333466 CTCTGAAATG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.20, C:0.18, G:0.36, T:0.26
Consensus pattern (66 bp):
CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAAGATGAGGTTCGCAGGAGTGTGCTATCTT
G
Found at i:18336047 original size:7 final size:7
Alignment explanation
Indices: 18336023--18336071 Score: 62
Period size: 7 Copynumber: 7.0 Consensus size: 7
18336013 AAAAATAATA
*
18336023 ATTGAGG
1 ATTGAGT
* *
18336030 ATTTAGG
1 ATTGAGT
18336037 ATTGAGT
1 ATTGAGT
*
18336044 ATTGAAT
1 ATTGAGT
18336051 ATTGAGT
1 ATTGAGT
18336058 ATTGAGT
1 ATTGAGT
18336065 ATTGAGT
1 ATTGAGT
18336072 TGAAAAGAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.31, C:0.00, G:0.29, T:0.41
Consensus pattern (7 bp):
ATTGAGT
Found at i:18336526 original size:15 final size:15
Alignment explanation
Indices: 18336506--18336541 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
18336496 ATTAAAAAAA
*
18336506 TTAAAAATTTAAACT
1 TTAAAAATTCAAACT
18336521 TTAAAAATTCAAACT
1 TTAAAAATTCAAACT
*
18336536 CTAAAA
1 TTAAAA
18336542 GGCTCGAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (15 bp):
TTAAAAATTCAAACT
Found at i:18336552 original size:31 final size:31
Alignment explanation
Indices: 18336517--18336589 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
18336507 TAAAAATTTA
* * **
18336517 AACTTTAAAAAT-TCAAACTCTAAAAGGCTCG
1 AACTTAAAAAATAT-AAACTCGAAAAAACTCG
18336548 AACTTAAAAAATATAAACTCGAAAAAACTCG
1 AACTTAAAAAATATAAACTCGAAAAAACTCG
18336579 AACTTAAAAAA
1 AACTTAAAAAA
18336590 AATCGAACTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 36 0.97
32 1 0.03
ACGTcount: A:0.55, C:0.16, G:0.07, T:0.22
Consensus pattern (31 bp):
AACTTAAAAAATATAAACTCGAAAAAACTCG
Found at i:18336599 original size:16 final size:16
Alignment explanation
Indices: 18336545--18336599 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
18336535 TCTAAAAGGC
*
18336545 TCGAACTTAAAAAATA
1 TCGAACTTAAAAAAAA
* ** *
18336561 T-AAACTCGAAAAAAC
1 TCGAACTTAAAAAAAA
18336576 TCGAACTTAAAAAAAA
1 TCGAACTTAAAAAAAA
18336592 TCGAACTT
1 TCGAACTT
18336600 GAGACTGACC
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
15 10 0.34
16 19 0.66
ACGTcount: A:0.55, C:0.16, G:0.07, T:0.22
Consensus pattern (16 bp):
TCGAACTTAAAAAAAA
Found at i:18337600 original size:25 final size:21
Alignment explanation
Indices: 18337561--18337612 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 21
18337551 AACAAATTTT
18337561 AATT-TTAATTAAAATATAATTAA
1 AATTATTAATTAAAATA-AA--AA
18337584 AATTATTATATTAAAATAAAAA
1 AATTATTA-ATTAAAATAAAAA
18337606 AATTATT
1 AATTATT
18337613 TAAAATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 9 0.33
23 4 0.15
24 5 0.19
25 9 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTATTAATTAAAATAAAAA
Found at i:18337610 original size:19 final size:20
Alignment explanation
Indices: 18337588--18337631 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
18337578 AATTAAAATT
18337588 ATTATATTAAAATA-AAAAA
1 ATTATATTAAAATATAAAAA
*
18337607 ATTAT-TTAAAATATAATAA
1 ATTATATTAAAATATAAAAA
18337626 ATTATA
1 ATTATA
18337632 AATTTATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTATATTAAAATATAAAAA
Found at i:18337624 original size:23 final size:22
Alignment explanation
Indices: 18337568--18337626 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 22
18337558 TTTAATTTTA
*
18337568 ATTAAAATATAAT--TAAAATT
1 ATTAAAATATAATAAAAAAATT
* * *
18337588 ATTATATTAAAATAAAAAAATT
1 ATTAAAATATAATAAAAAAATT
18337610 ATTTAAAATATAATAAA
1 A-TTAAAATATAATAAA
18337627 TTATAAATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
20 10 0.34
22 7 0.24
23 12 0.41
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
ATTAAAATATAATAAAAAAATT
Found at i:18339425 original size:28 final size:28
Alignment explanation
Indices: 18339383--18339437 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
18339373 TCTGATTTGA
18339383 AATTTCAAATCAAATTGATAATACTATG
1 AATTTCAAATCAAATTGATAATACTATG
*
18339411 AATTTCAAATGAAATTGATAATACTAT
1 AATTTCAAATCAAATTGATAATACTAT
18339438 TAAATAATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.36
Consensus pattern (28 bp):
AATTTCAAATCAAATTGATAATACTATG
Found at i:18347062 original size:9 final size:9
Alignment explanation
Indices: 18347045--18347081 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
18347035 TATAGTTTGA
*
18347045 TATTTGAAT
1 TATTCGAAT
18347054 TATTCGAAT
1 TATTCGAAT
*
18347063 TATTCGAGT
1 TATTCGAAT
18347072 TATTCGAAT
1 TATTCGAAT
18347081 T
1 T
18347082 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:18347473 original size:9 final size:9
Alignment explanation
Indices: 18347461--18347515 Score: 51
Period size: 9 Copynumber: 5.8 Consensus size: 9
18347451 TATTTAGGAA
18347461 TTTTAAAAC
1 TTTTAAAAC
18347470 TTTTAAAA-
1 TTTTAAAAC
18347478 TTTTAAATTAGGAC
1 TTTT-AA--A--AC
18347492 TTTTAAAAC
1 TTTTAAAAC
18347501 TTTTAAAA-
1 TTTTAAAAC
18347509 TTTTAAA
1 TTTTAAA
18347516 TTAATAATGA
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
8 11 0.28
9 20 0.50
11 2 0.05
13 3 0.08
14 4 0.10
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (9 bp):
TTTTAAAAC
Found at i:18347490 original size:31 final size:31
Alignment explanation
Indices: 18347454--18347518 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
18347444 TTTTTCTTAT
18347454 TTAGGAATTTTAAAACTTTTAAAATTTTAAA
1 TTAGGAATTTTAAAACTTTTAAAATTTTAAA
*
18347485 TTAGGACTTTTAAAACTTTTAAAATTTTAAA
1 TTAGGAATTTTAAAACTTTTAAAATTTTAAA
18347516 TTA
1 TTA
18347519 ATAATGATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (31 bp):
TTAGGAATTTTAAAACTTTTAAAATTTTAAA
Found at i:18347859 original size:12 final size:12
Alignment explanation
Indices: 18347842--18347884 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 12
18347832 AACTAATCCT
18347842 CTCTCAAATTTC
1 CTCTCAAATTTC
18347854 CTCTCAAA-TTC
1 CTCTCAAATTTC
18347865 CT-TCAAAATTT-
1 CTCTC-AAATTTC
18347876 CTCTCAAAT
1 CTCTCAAAT
18347885 CCATATTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
10 2 0.07
11 14 0.50
12 12 0.43
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:18347957 original size:10 final size:10
Alignment explanation
Indices: 18347942--18347966 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
18347932 AAATCTCTAT
18347942 TTTTAAATAA
1 TTTTAAATAA
18347952 TTTTAAATAA
1 TTTTAAATAA
18347962 TTTTA
1 TTTTA
18347967 TTTTTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTTAAATAA
Found at i:18348760 original size:7 final size:7
Alignment explanation
Indices: 18348748--18348773 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
18348738 TAGTCGATTG
18348748 GTATTTA
1 GTATTTA
18348755 GTATTTA
1 GTATTTA
18348762 GTATTTA
1 GTATTTA
18348769 GTATT
1 GTATT
18348774 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:18351057 original size:125 final size:124
Alignment explanation
Indices: 18350760--18351136 Score: 585
Period size: 125 Copynumber: 3.0 Consensus size: 124
18350750 CCCAAACATG
* * * *
18350760 CTACAGTAGCAAAAACGCGTCCACAAGGGCGCGATTTCACAAATTCTTCTTAAATAACATCCT-G
1 CTACTGTAGCAAAAACGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCAT-CTAG
* *
18350824 CTAGAAGTGATTTTATACTATTTGCTCACAAACGTCAAAAAAAATTATTTCTTCCATGAC
65 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
*
18350884 CTACTGTAGCAAAAACGTGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCTAGC
1 CTACTGTAGCAAAAACGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCTAGC
*
18350949 TAGAAGCGATTTTATACTATTTCCTCAGAAACGTCAAAAAAAATTTATTTCTTCCATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAA-TTATTTCTTCCATGAC
* *
18351009 CTACTGTAGCAAAAGCGCGTTCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCTAGC
1 CTACTGTAGCAAAAACGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCTAGC
* *** *
18351074 TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAACTCGAAATTATTTCTTCCAAGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA-AAAAAATTATTTCTTCCATGAC
18351134 CTA
1 CTA
18351137 AAAACCCTAA
Statistics
Matches: 233, Mismatches: 17, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
123 2 0.01
124 97 0.42
125 131 0.56
126 3 0.01
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.29
Consensus pattern (124 bp):
CTACTGTAGCAAAAACGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCTAGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
Found at i:18356998 original size:24 final size:24
Alignment explanation
Indices: 18356966--18357038 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 24
18356956 TAAGTGATCA
18356966 TTATTTCTCATGTTCTTTTACCTT
1 TTATTTCTCATGTTCTTTTACCTT
* *
18356990 TTATTTCTCATCCTTTGCCCTTTACCTT
1 TTATTTCTCAT--GTT--CTTTTACCTT
18357018 TTATTTCTCATGTTCTTTTAC
1 TTATTTCTCATGTTCTTTTAC
18357039 TCTCTTATGG
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
24 17 0.41
26 4 0.10
28 20 0.49
ACGTcount: A:0.12, C:0.25, G:0.04, T:0.59
Consensus pattern (24 bp):
TTATTTCTCATGTTCTTTTACCTT
Found at i:18362419 original size:6 final size:6
Alignment explanation
Indices: 18362408--18362435 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
18362398 CCGAAATAGT
18362408 TTCCAA TTCCAA TTCCAA TTCCAA TTCC
1 TTCCAA TTCCAA TTCCAA TTCCAA TTCC
18362436 CTTTCCTCTT
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:0.29, C:0.36, G:0.00, T:0.36
Consensus pattern (6 bp):
TTCCAA
Found at i:18364559 original size:20 final size:20
Alignment explanation
Indices: 18364534--18364583 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
18364524 TGGCTTAAAA
18364534 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
18364554 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
18364571 GTGGTAGTGGATT
1 TTGGTAGTGGATT
18364584 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:18369198 original size:20 final size:20
Alignment explanation
Indices: 18369173--18369222 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
18369163 TGGCTTAAAA
18369173 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
18369193 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
18369210 GTGGTAGTGGATT
1 TTGGTAGTGGATT
18369223 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:18370468 original size:33 final size:33
Alignment explanation
Indices: 18370431--18370498 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
18370421 AAACTGTAAC
18370431 ATGTGTTTTAGCTAAAATATCTATGGATTATTG
1 ATGTGTTTTAGCTAAAATATCTATGGATTATTG
*
18370464 ATGTGTTTTAGCTAAAATTTCTATGGATTATTG
1 ATGTGTTTTAGCTAAAATATCTATGGATTATTG
18370497 AT
1 AT
18370499 TTTGGATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (33 bp):
ATGTGTTTTAGCTAAAATATCTATGGATTATTG
Found at i:18377694 original size:21 final size:21
Alignment explanation
Indices: 18377658--18377700 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
18377648 TTAATTTTTT
18377658 AAAATTTTAAAAATATTCAAAA
1 AAAATTTTAAAAATATT-AAAA
*
18377680 AAAATTTT-AATATATTAAAA
1 AAAATTTTAAAAATATTAAAA
18377700 A
1 A
18377701 TATATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 7 0.35
22 8 0.40
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAATTTTAAAAATATTAAAA
Found at i:18377699 original size:19 final size:20
Alignment explanation
Indices: 18377658--18377714 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 20
18377648 TTAATTTTTT
18377658 AAAATTTTAAAAATATTCAAAA
1 AAAATTTT-AAAATATT-AAAA
*
18377680 AAAATTTTAATATATT-AAA
1 AAAATTTTAAAATATTAAAA
* *
18377699 AATATATTAAAATATT
1 AAAATTTTAAAATATT
18377715 TTTATACTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 16 0.52
21 7 0.23
22 8 0.26
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAATTTTAAAATATTAAAA
Found at i:18383818 original size:16 final size:17
Alignment explanation
Indices: 18383783--18383820 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
18383773 CTTAAATTTT
* *
18383783 TTTTAATATGTTTAATA
1 TTTTAATATGATTAAAA
18383800 TTTTAATAT-ATTAAAA
1 TTTTAATATGATTAAAA
18383816 TTTTA
1 TTTTA
18383821 GAATTAGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TTTTAATATGATTAAAA
Found at i:18383828 original size:60 final size:61
Alignment explanation
Indices: 18383764--18383880 Score: 166
Period size: 61 Copynumber: 1.9 Consensus size: 61
18383754 CATTAGTTAT
* * * *
18383764 TTAGTTATACTTAA-ATTTTTTTTAATATGTTTA-ATATTTTAATATATTAAAATTTTAGAA
1 TTAGTTATACTCAACATTTTCTTTAACATATTTAGA-ATTTTAATATATTAAAATTTTAGAA
*
18383824 TTAGTTATACTCAACATTTTCTTTAACATATTTAGAATTTTAATATATTTAAATTTT
1 TTAGTTATACTCAACATTTTCTTTAACATATTTAGAATTTTAATATATTAAAATTTT
18383881 TTAAAGTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
60 13 0.26
61 36 0.72
62 1 0.02
ACGTcount: A:0.37, C:0.05, G:0.04, T:0.54
Consensus pattern (61 bp):
TTAGTTATACTCAACATTTTCTTTAACATATTTAGAATTTTAATATATTAAAATTTTAGAA
Found at i:18383881 original size:17 final size:17
Alignment explanation
Indices: 18383845--18383880 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
18383835 CAACATTTTC
18383845 TTTAACATATTTAGAAT
1 TTTAACATATTTAGAAT
*
18383862 TTTAATATATTTA-AAT
1 TTTAACATATTTAGAAT
18383878 TTT
1 TTT
18383881 TTAAAGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTAACATATTTAGAAT
Found at i:18384063 original size:70 final size:70
Alignment explanation
Indices: 18383972--18384128 Score: 210
Period size: 70 Copynumber: 2.3 Consensus size: 70
18383962 TTTAAAATAT
* * **
18383972 ATTTTAAAAATATATTGAATATATTGAA-AGTTTAAAATTGATTATACTTAGTATTTTTTAATAT
1 ATTTTTAAAATATATTAAATATATT-AACAGTTTAAAATTGATTATACTTAACATTTTTTAATAT
18384036 ATTTAA
65 ATTTAA
* * *
18384042 TTTTTTAAAATATATTAAATATATTAACATTTTAAAATTGGTTATACTTAACATTTTTTAATATA
1 ATTTTTAAAATATATTAAATATATTAACAGTTTAAAATTGATTATACTTAACATTTTTTAATATA
18384107 TTTAA
66 TTTAA
* *
18384112 AATTTTAATATAT-TTAA
1 ATTTTTAAAATATATTAA
18384129 TTTTTTAAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
69 6 0.08
70 70 0.92
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (70 bp):
ATTTTTAAAATATATTAAATATATTAACAGTTTAAAATTGATTATACTTAACATTTTTTAATATA
TTTAA
Found at i:18384111 original size:19 final size:18
Alignment explanation
Indices: 18384024--18384160 Score: 90
Period size: 17 Copynumber: 7.8 Consensus size: 18
18384014 TATACTTAGT
18384024 ATTTTTTAATATATTT-A
1 ATTTTTTAATATATTTAA
*
18384041 ATTTTTTAAAATATATTAA
1 ATTTTTTAATATAT-TTAA
* * *
18384060 ATATATTAACAT-TTTAA
1 ATTTTTTAATATATTTAA
* ** *
18384077 AATTGGT--TATACTTAA
1 ATTTTTTAATATATTTAA
18384093 CATTTTTTAATATATTTAA
1 -ATTTTTTAATATATTTAA
*
18384112 A-ATTTTAATATATTT-A
1 ATTTTTTAATATATTTAA
*
18384128 ATTTTTTAA-ATTTTTTAA
1 ATTTTTTAATA-TATTTAA
* *
18384146 AGTTTTAAATATATT
1 ATTTTTTAATATATT
18384161 AAGAAAATCT
Statistics
Matches: 90, Mismatches: 20, Indels: 19
0.70 0.16 0.15
Matches are distributed among these distances:
15 2 0.02
16 7 0.08
17 47 0.52
18 15 0.17
19 19 0.21
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
ATTTTTTAATATATTTAA
Found at i:18384256 original size:20 final size:21
Alignment explanation
Indices: 18384223--18384262 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
18384213 AATTTTAAAA
*
18384223 TTAATTATACTTAACATTTTT
1 TTAATTATACTTAAAATTTTT
*
18384244 TTAA-TATATTTAAAATTTT
1 TTAATTATACTTAAAATTTT
18384263 AAAAAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAATTATACTTAAAATTTTT
Found at i:18393594 original size:16 final size:18
Alignment explanation
Indices: 18393573--18393611 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
18393563 ATAATCTATA
18393573 ATATAATAATAGT-TA-T
1 ATATAATAATAGTATATT
*
18393589 ATATAATAGTAGTATATT
1 ATATAATAATAGTATATT
18393607 ATATA
1 ATATA
18393612 TAAATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 2 0.10
18 6 0.30
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.44
Consensus pattern (18 bp):
ATATAATAATAGTATATT
Found at i:18393865 original size:22 final size:21
Alignment explanation
Indices: 18393814--18393875 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
18393804 CTATCTTTTT
*
18393814 ATTATAATCTATAATA-TAATA
1 ATTAT-ATATATAATATTAATA
*
18393835 ATATTTATATATAATATTAATA
1 AT-TATATATATAATATTAATA
18393857 CATTATATAT-TACATATTA
1 -ATTATATATATA-ATATTA
18393876 TTATATATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 13 0.38
22 19 0.56
23 2 0.06
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTATATATATAATATTAATA
Found at i:18394090 original size:256 final size:251
Alignment explanation
Indices: 18393532--18394353 Score: 935
Period size: 256 Copynumber: 3.2 Consensus size: 251
18393522 TACTATATTA
*
18393532 TATAATATCATGTAATACTATATATTTTATTATAATCTATAATATAATAATAGTTATATATAATA
1 TATAATATCATGTAATACTATATTTTTTATTATAATCTATAATATAATAATAGTTATATATAATA
* * * ** *
18393597 GTAGTATATTATATA-TA-A-ATTATTATACATTATTGTTTATTATTACACAAGGTTGAAATATG
66 GTAGTACATTATATATTACATATTATTATATATTATTGTTTATTATTATA-GTGGTTAAAATATG
* * * *
18393659 CTCCAAGTCCCTATACTTTTTGTACATTTAAAAGTTAACCCTCCTACTATATTATAT-ATATATA
130 CTCTAAGTCTCTAT-CTTTTTGTACATTTGAAAGTTAGCCCTCCTACTATATTATATAATATAT-
* * * * *
18393723 ATGCTATATCATATAGAATATAATATATTAATA-ATTTTATACATGCATCAATGATTGAACAT
193 AT-C-ATATCATATA-AATATATTATATTATTATA-TATATATATGCATCAATGATTAAACAT
* * * ** * *
18393785 TAAAACATTATGTAATTTTCTATCTTTTTATTATAATCTATAATATAATAATATTTATATATAAT
1 TATAATATCATGTAATACTATAT-TTTTTATTATAATCTATAATATAATAATAGTTATATATAAT
* * *
18393850 ATTAATACATTATATATTACATATTATTATATATTATTGTTTATTATTATAGTGGTTAAAATTTG
65 AGTAGTACATTATATATTACATATTATTATATATTATTGTTTATTATTATAGTGGTTAAAATATG
* * * * *
18393915 CTCTAAGTTTCTATGCTTTTTATGCATTTGAAAGTTAGCCTTCCTACTATATTATATAATGCTAT
130 CTCTAAGTCTCTAT-CTTTTTGTACATTTGAAAGTTAGCCCTCCTACTATATTATATAAT-ATAT
* * *
18393980 ATCATATCATATATTAATATTTTATATATATGTATATATATATATGCATAAATGATT-AATAT
193 ATCATATCATATA--AATATATTATAT-TAT-TATATATATATATGCATCAATGATTAAACAT
*
18394042 TATAATATCATGTAATACTATATTTTTTATTATAATCTATATTATAATAATAGTTATATATAATA
1 TATAATATCATGTAATACTATATTTTTTATTATAATCTATAATATAATAATAGTTATATATAATA
* * * * *
18394107 GTAGTACACTATATATTACTTATTATTGTATATTATTGTTTATTGTTATAGTAGTTAAAATATGC
66 GTAGTACATTATATATTACATATTATTATATATTATTGTTTATTATTATAGTGGTTAAAATATGC
* * **
18394172 TTTAAGTCTCTATATTTTTCGTACATTTGAAAGTTAGCCCTATTACTATATTATATAATATTATA
131 TCTAAGTCTCTATCTTTTT-GTACATTTGAAAGTTAGCCCTCCTACTATATTATATAATA-TATA
* * *
18394237 TCATATCATA-AAATATATTA-ATGGT-TTATATATATATATGTATCGATAATTAAACAT
194 TCATATCATATAAATATATTATAT--TATTATATATATATATGCATCAATGATTAAACAT
* ** * *
18394294 TACAATATCATGTAATTTTATATCTTTTATTATAATCTAT-ATAAAAATAATAGTTATATA
1 TATAATATCATGTAATACTATATTTTTTATTATAATCTATAAT-ATAATAATAGTTATATA
18394354 CGTGTTAATA
Statistics
Matches: 481, Mismatches: 73, Indels: 31
0.82 0.12 0.05
Matches are distributed among these distances:
251 22 0.05
252 59 0.12
253 26 0.05
254 52 0.11
255 18 0.04
256 226 0.47
257 54 0.11
258 23 0.05
259 1 0.00
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (251 bp):
TATAATATCATGTAATACTATATTTTTTATTATAATCTATAATATAATAATAGTTATATATAATA
GTAGTACATTATATATTACATATTATTATATATTATTGTTTATTATTATAGTGGTTAAAATATGC
TCTAAGTCTCTATCTTTTTGTACATTTGAAAGTTAGCCCTCCTACTATATTATATAATATATATC
ATATCATATAAATATATTATATTATTATATATATATATGCATCAATGATTAAACAT
Found at i:18394105 original size:16 final size:17
Alignment explanation
Indices: 18394079--18394111 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
18394069 TATTATAATC
18394079 TATATTATAATAATAGT
1 TATATTATAATAATAGT
*
18394096 TATA-TATAATAGTAGT
1 TATATTATAATAATAGT
18394112 ACACTATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (17 bp):
TATATTATAATAATAGT
Found at i:18397555 original size:29 final size:27
Alignment explanation
Indices: 18397491--18397555 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 27
18397481 ATTTTTTGCA
*
18397491 AAATTTTAATTTTTTTAAATTTTCATT
1 AAATTTTAATTTTTTTAAATTTTAATT
*
18397518 ATACCTTTTAATTTTTTTAAATATTTTAATT
1 A-A-ATTTTAATTTTTTT-AA-ATTTTAATT
18397549 AAATTTT
1 AAATTTT
18397556 CTTAAATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 1 0.03
28 1 0.03
29 17 0.55
30 3 0.10
31 9 0.29
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.62
Consensus pattern (27 bp):
AAATTTTAATTTTTTTAAATTTTAATT
Found at i:18398458 original size:12 final size:12
Alignment explanation
Indices: 18398443--18398478 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
18398433 AAATTTTATG
18398443 TTTTATTTTTAC
1 TTTTATTTTTAC
*
18398455 TTTTACTTTTAC
1 TTTTATTTTTAC
18398467 TTTTACTTTTTA
1 TTTTA-TTTTTA
18398479 TAATTATGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 16 0.76
13 5 0.24
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTTATTTTTAC
Found at i:18401407 original size:251 final size:249
Alignment explanation
Indices: 18400947--18401449 Score: 934
Period size: 251 Copynumber: 2.0 Consensus size: 249
18400937 AATTCATGGC
*
18400947 TTTGTAACCCCCCTCTGTCACCCCCTTCCCAGAAATGTATGTAAAATGTGTCAAAGATATTTTGA
1 TTTGTAACCCCCCTCTGTCACCCCCTTCCCAGAAATATATGTAAAATGTGTCAAAGATATTTTGA
*
18401012 GTATATAAGAGTTAATAAATATTGTAATGGCTCGAATTATCAATGTAGGTTATTAAATATTATAC
66 GTATATAAGAGTTAATAAATATTGTAATGGCTCAAATTATCAATGTAGGTTATTAAATATTATAC
*
18401077 TAGTGCATATTCAAGGCCAAATAAGTTTTGGTACTTGCTTTTTTCCTATCCTATGTCGTTTGGCT
131 TAGTGCATATTCAAGGCCAAATAAGTTTTGGTACTTGCTTTTTTCCTATCCTATGTCATTTGGCT
18401142 TATTTTTACCGTTTCAATCTTTTCAAGCGAAGACCATTTCAATGGTTATATTGT
196 TATTTTTACCGTTTCAATCTTTTCAAGCGAAGACCATTTCAATGGTTATATTGT
18401196 TTTGTAACCCCCCTCTCTGTCACCCCCTTCCCAGAAATATATGTAAAATGTGTCAAAGATATTTT
1 TTTGTAA-CCCCC-CTCTGTCACCCCCTTCCCAGAAATATATGTAAAATGTGTCAAAGATATTTT
*
18401261 GAGTATATAAGAGTTGATAAATATTGTAATGGCTCAAATTATCAATGTAGGTTATTAAATATTAT
64 GAGTATATAAGAGTTAATAAATATTGTAATGGCTCAAATTATCAATGTAGGTTATTAAATATTAT
18401326 ACTAGTGCATATTCAAGGCCAAATAAGTTTTGGTACTTGCTTTTTTCCTATCCTATGTCATTTGG
129 ACTAGTGCATATTCAAGGCCAAATAAGTTTTGGTACTTGCTTTTTTCCTATCCTATGTCATTTGG
* *
18401391 CTTATTTTTTCCGTTTCAATCTTTTCAAGTGAAGACCATTTCAATGGTTATATTGT
194 CTTATTTTTACCGTTTCAATCTTTTCAAGCGAAGACCATTTCAATGGTTATATTGT
18401447 TTT
1 TTT
18401450 TTGTTACTGT
Statistics
Matches: 246, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
249 7 0.03
250 5 0.02
251 234 0.95
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (249 bp):
TTTGTAACCCCCCTCTGTCACCCCCTTCCCAGAAATATATGTAAAATGTGTCAAAGATATTTTGA
GTATATAAGAGTTAATAAATATTGTAATGGCTCAAATTATCAATGTAGGTTATTAAATATTATAC
TAGTGCATATTCAAGGCCAAATAAGTTTTGGTACTTGCTTTTTTCCTATCCTATGTCATTTGGCT
TATTTTTACCGTTTCAATCTTTTCAAGCGAAGACCATTTCAATGGTTATATTGT
Found at i:18406168 original size:20 final size:20
Alignment explanation
Indices: 18406143--18406181 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18406133 TGTAGGAACT
* *
18406143 TGCATTTTGGCTTTTTTTAG
1 TGCATTTTAGCTTGTTTTAG
18406163 TGCATTTTAGCTTGTTTTA
1 TGCATTTTAGCTTGTTTTA
18406182 TTTGTTTATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.10, G:0.18, T:0.59
Consensus pattern (20 bp):
TGCATTTTAGCTTGTTTTAG
Found at i:18408234 original size:20 final size:21
Alignment explanation
Indices: 18408187--18408237 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
18408177 TTATATATTT
18408187 TTTATAAAA-TTAATAAAACA
1 TTTATAAAATTTAATAAAACA
*
18408207 TATT-TAAAATTTTATAAAA-A
1 T-TTATAAAATTTAATAAAACA
18408227 TTTATAAAATT
1 TTTATAAAATT
18408238 CAAAAATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 2 0.07
20 15 0.56
21 10 0.37
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TTTATAAAATTTAATAAAACA
Found at i:18408270 original size:20 final size:19
Alignment explanation
Indices: 18408212--18408274 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 19
18408202 AAACATATTT
*
18408212 AAAATTTTATAAAAATT-TA
1 AAAATTCTA-AAAAATTATA
*
18408231 TAAAATTC-AAAAATAATATA
1 -AAAATTCTAAAAA-ATTATA
18408251 ATAAATTCTAAAAAATTATA
1 A-AAATTCTAAAAAATTATA
18408271 AAAA
1 AAAA
18408275 AAAGTCAACT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
18 4 0.11
19 7 0.19
20 20 0.56
21 5 0.14
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATTCTAAAAAATTATA
Found at i:18412143 original size:9 final size:9
Alignment explanation
Indices: 18412129--18412159 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
18412119 GTTAAACGAA
18412129 TCGAGTTAT
1 TCGAGTTAT
*
18412138 TCGAGTTAA
1 TCGAGTTAT
18412147 TCGAGTTAT
1 TCGAGTTAT
18412156 TCGA
1 TCGA
18412160 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:18418184 original size:26 final size:25
Alignment explanation
Indices: 18418155--18418213 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
18418145 CTTCGTAAGT
*
18418155 TTCCCGATTAAAGGCTCTTTATGAGC
1 TTCCCGATTAAAGGCTCTCTA-GAGC
* *
18418181 TTCCTGATTAATGGCTCTCTAGAGC
1 TTCCCGATTAAAGGCTCTCTAGAGC
18418206 TTCCCGAT
1 TTCCCGAT
18418214 ATGGCTCGCT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 11 0.38
26 18 0.62
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.36
Consensus pattern (25 bp):
TTCCCGATTAAAGGCTCTCTAGAGC
Found at i:18418231 original size:23 final size:23
Alignment explanation
Indices: 18418191--18418238 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
18418181 TTCCTGATTA
* * *
18418191 ATGGCTCTCTAGAGCTTCCCGAT
1 ATGGCTCGCTAGAACTTCCAGAT
*
18418214 ATGGCTCGCTTGAACTTCCAGAT
1 ATGGCTCGCTAGAACTTCCAGAT
18418237 AT
1 AT
18418239 ATGGCTATCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.31
Consensus pattern (23 bp):
ATGGCTCGCTAGAACTTCCAGAT
Found at i:18418327 original size:72 final size:72
Alignment explanation
Indices: 18418155--18418331 Score: 164
Period size: 72 Copynumber: 2.4 Consensus size: 72
18418145 CTTCGTAAGT
*
18418155 TTCCCGATTAAAGGCTCTTTATGAGCTTCCTGATTAATGGCTCTCTAGAGCTTCCCGATATGGCT
1 TTCCCGATTATA-GCTC-TTATGAGCTTCCTGATTAATGGCTCTCTAGAGCTTCCCGATATGGCT
*
18418220 CGCTTGAAC
64 CGCATGAAC
* * * ** * * *
18418229 TTCCAGATATATGGCT-ATCCGAAGCTT-CTCG-TTAATGGCTCTTTGGAGCTAT-CCGTTATTG
1 TTCCCGAT-TATAGCTCTTATG-AGCTTCCT-GATTAATGGCTCTCTAGAGCT-TCCCGATA-TG
*
18418290 GCTCGCATGAGC
61 GCTCGCATGAAC
18418302 TTCCCGATTATAGCTCTTATGAGCTTCCTG
1 TTCCCGATTATAGCTCTTATGAGCTTCCTG
18418332 TTATACAACC
Statistics
Matches: 80, Mismatches: 16, Indels: 16
0.71 0.14 0.14
Matches are distributed among these distances:
72 38 0.47
73 30 0.38
74 10 0.12
75 2 0.03
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (72 bp):
TTCCCGATTATAGCTCTTATGAGCTTCCTGATTAATGGCTCTCTAGAGCTTCCCGATATGGCTCG
CATGAAC
Found at i:18418406 original size:25 final size:25
Alignment explanation
Indices: 18418345--18418409 Score: 112
Period size: 25 Copynumber: 2.6 Consensus size: 25
18418335 TACAACCCGG
*
18418345 ATAAGCTTCCCATTACAAGACTCAC
1 ATAAGCTTCCCGTTACAAGACTCAC
*
18418370 ATAAGCTTCCCGTTACACGACTCAC
1 ATAAGCTTCCCGTTACAAGACTCAC
18418395 ATAAGCTTCCCGTTA
1 ATAAGCTTCCCGTTA
18418410 TATGGCTCGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.31, C:0.32, G:0.11, T:0.26
Consensus pattern (25 bp):
ATAAGCTTCCCGTTACAAGACTCAC
Found at i:18420540 original size:10 final size:9
Alignment explanation
Indices: 18420523--18420667 Score: 77
Period size: 9 Copynumber: 15.7 Consensus size: 9
18420513 TTATTAAAAA
18420523 TTAT-ATTT
1 TTATAATTT
18420531 TTAATAATTT
1 TT-ATAATTT
* *
18420541 ATTAGAACTTA
1 -TTATAA-TTT
18420552 TTATGAATTT
1 TTAT-AATTT
18420562 TTATAA-TT
1 TTATAATTT
18420570 TTATAATTAT
1 TTATAATT-T
*
18420580 TGATAA-TT
1 TTATAATTT
18420588 TTATAA-TT
1 TTATAATTT
18420596 TTAT-ATTT
1 TTATAATTT
*
18420604 TATTTGAATTT
1 T-TAT-AATTT
18420615 TT-TATATGTT
1 TTATA-AT-TT
*
18420625 CTTATAATGT
1 -TTATAATTT
*
18420635 TTATTATTT
1 TTATAATTT
*
18420644 TTATAATAT
1 TTATAATTT
* *
18420653 TTACAAATT
1 TTATAATTT
18420662 TTATAA
1 TTATAA
18420668 GTTCACAGAA
Statistics
Matches: 106, Mismatches: 16, Indels: 29
0.70 0.11 0.19
Matches are distributed among these distances:
7 1 0.01
8 26 0.25
9 36 0.34
10 26 0.25
11 15 0.14
12 2 0.02
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.59
Consensus pattern (9 bp):
TTATAATTT
Found at i:18420573 original size:8 final size:8
Alignment explanation
Indices: 18420560--18420606 Score: 69
Period size: 8 Copynumber: 5.8 Consensus size: 8
18420550 TATTATGAAT
18420560 TTTTATAA
1 TTTTATAA
18420568 TTTTATAA
1 TTTTATAA
18420576 TTATTGATAA
1 TT-TT-ATAA
18420586 TTTTATAA
1 TTTTATAA
18420594 TTTTAT-A
1 TTTTATAA
18420601 TTTTAT
1 TTTTAT
18420607 TTGAATTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
7 7 0.19
8 20 0.54
9 4 0.11
10 6 0.16
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (8 bp):
TTTTATAA
Found at i:18420613 original size:26 final size:25
Alignment explanation
Indices: 18420549--18420615 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 25
18420539 TTATTAGAAC
18420549 TTATTATGAATTTTTATAATTTTATAA
1 TTATT-TGAA-TTTTATAATTTTATAA
*
18420576 TTA-TTGATAATTTTATAATTTTATATT
1 TTATTTG--AATTTTATAATTTTATA-A
18420603 TTATTTGAATTTT
1 TTATTTGAATTTT
18420616 TTATATGTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
25 2 0.06
26 22 0.63
27 8 0.23
28 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (25 bp):
TTATTTGAATTTTATAATTTTATAA
Found at i:18420740 original size:29 final size:30
Alignment explanation
Indices: 18420704--18420773 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 30
18420694 AACATGTTTT
* * *
18420704 ATTTTTTATTTTTTTTATAATTAATTA-GA
1 ATTTTTTATTATATTTATAAATAATTATGA
* *
18420733 ATTTTTTATAATATTTATAAATATTTATGA
1 ATTTTTTATTATATTTATAAATAATTATGA
18420763 ATTTTTTATTA
1 ATTTTTTATTA
18420774 GTTTTGTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 22 0.65
30 12 0.35
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (30 bp):
ATTTTTTATTATATTTATAAATAATTATGA
Found at i:18421308 original size:15 final size:16
Alignment explanation
Indices: 18421280--18421310 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
18421270 ACCAATTTGG
18421280 TTAATTTCAGTTAATT
1 TTAATTTCAGTTAATT
18421296 TTAATTT-AGTTAATT
1 TTAATTTCAGTTAATT
18421311 CGGTTAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.58
Consensus pattern (16 bp):
TTAATTTCAGTTAATT
Found at i:18433066 original size:24 final size:24
Alignment explanation
Indices: 18433038--18433103 Score: 62
Period size: 25 Copynumber: 2.7 Consensus size: 24
18433028 TATCAAAGAA
18433038 TATATTTTTTTATTAAAAAATTAT
1 TATATTTTTTTATTAAAAAATTAT
* * *
18433062 TATATTTAATTTTA-GAAAACATTTT
1 TATATTT--TTTTATTAAAAAATTAT
*
18433087 TATATGTTGTTTATTAA
1 TATAT-TTTTTTATTAA
18433104 TTTGTGGAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
24 11 0.33
25 15 0.45
26 7 0.21
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.56
Consensus pattern (24 bp):
TATATTTTTTTATTAAAAAATTAT
Found at i:18437243 original size:17 final size:18
Alignment explanation
Indices: 18437215--18437249 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
18437205 AATCTTTAAA
18437215 AAAATAATATATTCATAT
1 AAAATAATATATTCATAT
*
18437233 AAAAT-ATATATTTATAT
1 AAAATAATATATTCATAT
18437250 CAATCATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
AAAATAATATATTCATAT
Found at i:18440166 original size:2 final size:2
Alignment explanation
Indices: 18440161--18440213 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
18440151 TCTACATTGA
18440161 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
18440203 CT CT CT CT CT C
1 CT CT CT CT CT C
18440214 GTTTTTGATG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:18459494 original size:10 final size:10
Alignment explanation
Indices: 18459479--18459507 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
18459469 ATGTGGGATT
18459479 TTTTTTTTAA
1 TTTTTTTTAA
18459489 TTTTTTTTAA
1 TTTTTTTTAA
18459499 TTTTTTTTA
1 TTTTTTTTA
18459508 TCCTCAGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTTTAA
Found at i:18461312 original size:26 final size:26
Alignment explanation
Indices: 18461283--18461332 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
18461273 AAAACCTATT
*
18461283 TGTACCTAAAA-AAAGTTAACAAATGA
1 TGTACC-AAAATAAAGCTAACAAATGA
18461309 TGTACCAAAATAAAGCTAACAAAT
1 TGTACCAAAATAAAGCTAACAAAT
18461333 TAAGAGGTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.54, C:0.14, G:0.10, T:0.22
Consensus pattern (26 bp):
TGTACCAAAATAAAGCTAACAAATGA
Found at i:18466446 original size:13 final size:15
Alignment explanation
Indices: 18466423--18466459 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
18466413 TTAATATAAT
*
18466423 TGAAATGTTTTTAT-
1 TGAAATTTTTTTATG
18466437 T-AAATTTTTTTATG
1 TGAAATTTTTTTATG
18466451 TGAAATTTT
1 TGAAATTTT
18466460 GAAATAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 11 0.55
14 2 0.10
15 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (15 bp):
TGAAATTTTTTTATG
Found at i:18466976 original size:21 final size:21
Alignment explanation
Indices: 18466952--18467016 Score: 55
Period size: 24 Copynumber: 3.1 Consensus size: 21
18466942 GCTTAATATG
18466952 TTTA-ATAAGTATATTAATCTT
1 TTTAGATAAGTATATTAAT-TT
*
18466973 TTTAAAGATAATTATATTAATTT
1 TTT--AGATAAGTATATTAATTT
* *
18466996 TTTAGTTAA-TATA-AAATTT
1 TTTAGATAAGTATATTAATTT
18467015 TT
1 TT
18467017 AAAGAAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
19 7 0.18
20 4 0.11
21 8 0.21
23 6 0.16
24 13 0.34
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.54
Consensus pattern (21 bp):
TTTAGATAAGTATATTAATTT
Found at i:18467756 original size:44 final size:44
Alignment explanation
Indices: 18467706--18467796 Score: 132
Period size: 44 Copynumber: 2.1 Consensus size: 44
18467696 GTAGGTAAAA
*
18467706 TAATATTAAAATAACATATACTAATCAGAA-TTTA-AGTGAGAAAC
1 TAATATTAAAATAACATACACTAATCA-AATTTTATA-TGAGAAAC
*
18467750 TAATATTAAAATAACTTACACTAATCAAATTTTATATGAGAAAC
1 TAATATTAAAATAACATACACTAATCAAATTTTATATGAGAAAC
18467794 TAA
1 TAA
18467797 AAACATAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
43 2 0.05
44 40 0.93
45 1 0.02
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.32
Consensus pattern (44 bp):
TAATATTAAAATAACATACACTAATCAAATTTTATATGAGAAAC
Found at i:18469293 original size:26 final size:26
Alignment explanation
Indices: 18469263--18469336 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 26
18469253 GCAACTCTTA
*
18469263 TGAGCGTCCCGA-TATATGGCTCTTTG
1 TGAGCGTCCCGATTA-AAGGCTCTTTG
* *
18469289 TGAGCTTCTCGATTAAAGGCTCTTTG
1 TGAGCGTCCCGATTAAAGGCTCTTTG
** * *
18469315 TGAGATTCCTGATTAATGGCTC
1 TGAGCGTCCCGATTAAAGGCTC
18469337 CCCGGAGCTT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 38 0.95
27 2 0.05
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.36
Consensus pattern (26 bp):
TGAGCGTCCCGATTAAAGGCTCTTTG
Found at i:18469357 original size:23 final size:23
Alignment explanation
Indices: 18469330--18469377 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
18469320 TTCCTGATTA
*
18469330 ATGGCTCCCCGGAGCTTCCCGAT
1 ATGGCTCCCCGGAACTTCCCGAT
**
18469353 ATGGCTCCCTTGAACTTCCCGAT
1 ATGGCTCCCCGGAACTTCCCGAT
18469376 AT
1 AT
18469378 ATGGCTATCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.17, C:0.35, G:0.21, T:0.27
Consensus pattern (23 bp):
ATGGCTCCCCGGAACTTCCCGAT
Found at i:18470817 original size:43 final size:43
Alignment explanation
Indices: 18470756--18470838 Score: 125
Period size: 43 Copynumber: 1.9 Consensus size: 43
18470746 GACTCCGATA
18470756 TGTGTTTTCGTGTAAGACCAC-GTCTGGGAC-GTCGGCATCGACT
1 TGTGTTTTCGTGTAAGACC-CTGTCTGGGACAGT-GGCATCGACT
*
18470799 TGTGTTTTTGTGTAAGACCCTGTCTGGGACAGTGGCATCG
1 TGTGTTTTCGTGTAAGACCCTGTCTGGGACAGTGGCATCG
18470839 GTATCTGATT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
42 1 0.03
43 34 0.92
44 2 0.05
ACGTcount: A:0.16, C:0.20, G:0.31, T:0.33
Consensus pattern (43 bp):
TGTGTTTTCGTGTAAGACCCTGTCTGGGACAGTGGCATCGACT
Found at i:18471552 original size:14 final size:15
Alignment explanation
Indices: 18471528--18471562 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
18471518 TACTTTAATC
18471528 ATGGATTAGTATTT-T
1 ATGG-TTAGTATTTAT
18471543 ATGGTTAGTATTTAT
1 ATGGTTAGTATTTAT
18471558 ATGGT
1 ATGGT
18471563 AATGTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (15 bp):
ATGGTTAGTATTTAT
Found at i:18471870 original size:47 final size:47
Alignment explanation
Indices: 18471816--18472164 Score: 533
Period size: 47 Copynumber: 7.5 Consensus size: 47
18471806 GAGTAAATGA
*
18471816 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATAT
1 ATGTATATGCTGTCAATTTTTGATGTACAAATGCAGTCCAATTATAT
* *
18471863 ATGTATATGCTGTCAATTTTTGATGTA-TAAGGCAGTCCAATTATAT
1 ATGTATATGCTGTCAATTTTTGATGTACAAATGCAGTCCAATTATAT
* * *
18471909 ATGTATATGCTATCAATTTTTGACGTATAAATGCAGTCCAATTATAT
1 ATGTATATGCTGTCAATTTTTGATGTACAAATGCAGTCCAATTATAT
* * *
18471956 ATGTATATACTGTCAAATTTTGATGTACAAATGCAGTCCAAATATAT
1 ATGTATATGCTGTCAATTTTTGATGTACAAATGCAGTCCAATTATAT
* *
18472003 ATGTATATGCTGTCAATTTTTTATGTATAAATGCAGTCCAATTATAT
1 ATGTATATGCTGTCAATTTTTGATGTACAAATGCAGTCCAATTATAT
18472050 ATGTATATGCTGTCAATTTTTGATGTACAAATGCAGTCCAATTATAT
1 ATGTATATGCTGTCAATTTTTGATGTACAAATGCAGTCCAATTATAT
*
18472097 ATGTATATGCTGTCAATTTTTGATGTATAAATGCAGTCCAATT-T-T
1 ATGTATATGCTGTCAATTTTTGATGTACAAATGCAGTCCAATTATAT
* * *
18472142 GTATATATGCTGTCCAAATTTTG
1 ATGTATATGCTGT-CAATTTTTG
18472165 GTGTGAAAAT
Statistics
Matches: 276, Mismatches: 24, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
45 12 0.04
46 51 0.18
47 213 0.77
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (47 bp):
ATGTATATGCTGTCAATTTTTGATGTACAAATGCAGTCCAATTATAT
Found at i:18472146 original size:21 final size:22
Alignment explanation
Indices: 18472120--18472164 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
18472110 CAATTTTTGA
18472120 TGTATAAATGCAGTCC-AATTT
1 TGTATAAATGCAGTCCAAATTT
* *
18472141 TGTATATATGCTGTCCAAATTT
1 TGTATAAATGCAGTCCAAATTT
18472163 TG
1 TG
18472165 GTGTGAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (22 bp):
TGTATAAATGCAGTCCAAATTT
Found at i:18477118 original size:19 final size:21
Alignment explanation
Indices: 18477062--18477124 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
18477052 TTTCTTTTTA
18477062 TTCAGCTCTTACGAGCTTCTG
1 TTCAGCTCTTACGAGCTTCTG
*
18477083 TTAAGCTCTTACGAGCTTCTG
1 TTCAGCTCTTACGAGCTTCTG
18477104 TTCAGCT-TT-CGAGCTTCTG
1 TTCAGCTCTTACGAGCTTCTG
18477123 TT
1 TT
18477125 GGCGTATTCG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
19 12 0.30
20 2 0.05
21 26 0.65
ACGTcount: A:0.14, C:0.25, G:0.19, T:0.41
Consensus pattern (21 bp):
TTCAGCTCTTACGAGCTTCTG
Found at i:18478597 original size:11 final size:11
Alignment explanation
Indices: 18478583--18478620 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
18478573 ATATCTTAAT
18478583 TATTAAGTATA
1 TATTAAGTATA
18478594 TATTAAGTATA
1 TATTAAGTATA
*
18478605 TATTATATTATA
1 TATTA-AGTATA
18478617 TATT
1 TATT
18478621 GTAATAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (11 bp):
TATTAAGTATA
Found at i:18478611 original size:18 final size:17
Alignment explanation
Indices: 18478545--18478612 Score: 52
Period size: 18 Copynumber: 3.9 Consensus size: 17
18478535 AAACTTAAAG
*
18478545 TTAATCTATATTATAATA
1 TTAATATATATTAT-ATA
*
18478563 TT-ATA-ATATTATATC
1 TTAATATATATTATATA
*
18478578 TTAAT-TATTAAGTATATA
1 TTAATATA-T-ATTATATA
18478596 TTAAGTATATATTATAT
1 TTAA-TATATATTATAT
18478613 TATATATTGT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
15 4 0.10
16 10 0.26
17 3 0.08
18 18 0.46
19 2 0.05
20 2 0.05
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (17 bp):
TTAATATATATTATATA
Found at i:18479038 original size:41 final size:41
Alignment explanation
Indices: 18478993--18479091 Score: 162
Period size: 41 Copynumber: 2.4 Consensus size: 41
18478983 TGAAATTTAA
**
18478993 GAATTTATGTGAAAATAGGGAGTTGAATTTATTCTAAAGTG
1 GAATTTACATGAAAATAGGGAGTTGAATTTATTCTAAAGTG
*
18479034 GAATTTGCATGAAAATAGGGAGTTGAATTTATTCTAAAGTG
1 GAATTTACATGAAAATAGGGAGTTGAATTTATTCTAAAGTG
*
18479075 GAATTTGCATGAAAATA
1 GAATTTACATGAAAATA
18479092 AAGAATTAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.34
Consensus pattern (41 bp):
GAATTTACATGAAAATAGGGAGTTGAATTTATTCTAAAGTG
Found at i:18499940 original size:23 final size:24
Alignment explanation
Indices: 18499909--18499955 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
18499899 TAATATATGT
* * *
18499909 GAACGTAAAGATTTAAAT-TTTCA
1 GAACATAAAAATTGAAATGTTTCA
18499932 GAACATAAAAATTGAAATGTTTCA
1 GAACATAAAAATTGAAATGTTTCA
18499956 CAGCAACTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.32
Consensus pattern (24 bp):
GAACATAAAAATTGAAATGTTTCA
Found at i:18503655 original size:22 final size:22
Alignment explanation
Indices: 18503627--18503668 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
18503617 ATAGCTAATG
18503627 GAATTTATTCCAAAATTAAAAA
1 GAATTTATTCCAAAATTAAAAA
*
18503649 GAATTTATTTCAAAATTAAA
1 GAATTTATTCCAAAATTAAA
18503669 GCATATTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (22 bp):
GAATTTATTCCAAAATTAAAAA
Found at i:18511757 original size:7 final size:7
Alignment explanation
Indices: 18511745--18511791 Score: 94
Period size: 7 Copynumber: 6.7 Consensus size: 7
18511735 ATCACATTTA
18511745 TCACTTG
1 TCACTTG
18511752 TCACTTG
1 TCACTTG
18511759 TCACTTG
1 TCACTTG
18511766 TCACTTG
1 TCACTTG
18511773 TCACTTG
1 TCACTTG
18511780 TCACTTG
1 TCACTTG
18511787 TCACT
1 TCACT
18511792 GATCAGATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.15, C:0.30, G:0.13, T:0.43
Consensus pattern (7 bp):
TCACTTG
Found at i:18511831 original size:58 final size:57
Alignment explanation
Indices: 18511760--18511950 Score: 328
Period size: 58 Copynumber: 3.3 Consensus size: 57
18511750 TGTCACTTGT
* *
18511760 CACTTGTCACTTGTCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGTTAC
1 CACTTATCACTTGTCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAA-CTAC
18511818 CACTTATCACTTGTCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTAC
1 CACTTATCACTTGTCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCT-AAACTAC
**
18511876 CACTTATCACTTGTCACTTGTCACTTGTCACCAATCAGATAAGTGTAGCTAAACTAC
1 CACTTATCACTTGTCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAACTAC
18511933 CACTTATCACTTGTCACT
1 CACTTATCACTTGTCACT
18511951 AATCAAAAGT
Statistics
Matches: 128, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
57 25 0.20
58 100 0.78
59 3 0.02
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.34
Consensus pattern (57 bp):
CACTTATCACTTGTCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAACTAC
Found at i:18511834 original size:7 final size:7
Alignment explanation
Indices: 18511818--18511849 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
18511808 CTAAAGTTAC
*
18511818 CACTTAT
1 CACTTGT
18511825 CACTTGT
1 CACTTGT
18511832 CACTTGT
1 CACTTGT
18511839 CACTTGT
1 CACTTGT
18511846 CACT
1 CACT
18511850 GATCAGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.19, C:0.31, G:0.09, T:0.41
Consensus pattern (7 bp):
CACTTGT
Found at i:18511841 original size:14 final size:14
Alignment explanation
Indices: 18511818--18511854 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
18511808 CTAAAGTTAC
18511818 CACTTATCACTTGT
1 CACTTATCACTTGT
*
18511832 CACTTGTCACTTGT
1 CACTTATCACTTGT
*
18511846 CACTGATCA
1 CACTTATCA
18511855 GATAAGTGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.22, C:0.30, G:0.11, T:0.38
Consensus pattern (14 bp):
CACTTATCACTTGT
Found at i:18511892 original size:7 final size:7
Alignment explanation
Indices: 18511876--18511906 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
18511866 CTAAAACTAC
*
18511876 CACTTAT
1 CACTTGT
18511883 CACTTGT
1 CACTTGT
18511890 CACTTGT
1 CACTTGT
18511897 CACTTGT
1 CACTTGT
18511904 CAC
1 CAC
18511907 CAATCAGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.19, C:0.32, G:0.10, T:0.39
Consensus pattern (7 bp):
CACTTGT
Found at i:18519203 original size:19 final size:18
Alignment explanation
Indices: 18519176--18519213 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
18519166 TCTCATTTTA
*
18519176 TCATTTCATATTTCATTTC
1 TCATCTCATA-TTCATTTC
18519195 TCATCTCATATTCATTTC
1 TCATCTCATATTCATTTC
18519213 T
1 T
18519214 TAACTTTGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.55
Consensus pattern (18 bp):
TCATCTCATATTCATTTC
Found at i:18528656 original size:23 final size:23
Alignment explanation
Indices: 18528630--18528727 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
18528620 ATAAGTGCCA
18528630 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
18528653 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
18528676 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
18528698 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
18528721 CACTGAT
1 CACTGAT
18528728 CAATAACACT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:18528695 original size:45 final size:45
Alignment explanation
Indices: 18528637--18528725 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
18528627 CCACACTGAT
* *
18528637 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
18528682 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
18528726 ATCAATAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.19
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:18536031 original size:23 final size:23
Alignment explanation
Indices: 18536002--18536099 Score: 144
Period size: 23 Copynumber: 4.3 Consensus size: 23
18535992 ATAAGTGCCA
*
18536002 CACTGATATGTAACCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
18536025 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
18536048 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
18536070 CACTGAAATGTAGTCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
18536093 CACTGAT
1 CACTGAT
18536100 CAATAACACT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
22 20 0.30
23 47 0.70
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:18536067 original size:45 final size:45
Alignment explanation
Indices: 18536009--18536097 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
18535999 CCACACTGAT
* *
18536009 ATGTAACCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAACCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
* *
18536054 ATGTAGCCAAAGCTACCACTGAAATGTAGTCGAAGCTACCACTG
1 ATGTAACCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
18536098 ATCAATAACA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (45 bp):
ATGTAACCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:18545875 original size:7 final size:7
Alignment explanation
Indices: 18545863--18545888 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
18545853 GGCCTGTCAT
18545863 CCATTAC
1 CCATTAC
18545870 CCATTAC
1 CCATTAC
18545877 CCATTAC
1 CCATTAC
18545884 CCATT
1 CCATT
18545889 TTCCATAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.42, G:0.00, T:0.31
Consensus pattern (7 bp):
CCATTAC
Done.