Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 105 of 438
Found at i:30082166 original size:2 final size:2
Alignment explanation
Indices: 30082161--30082186 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30082151 ACACACACAC
30082161 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
30082187 TCACATGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30100321 original size:51 final size:51
Alignment explanation
Indices: 30100209--30100341 Score: 137
Period size: 51 Copynumber: 2.6 Consensus size: 51
30100199 ATGCGTACCC
* * * * *
30100209 GATAACTTCGATCACATGTGTGGTACTAAGTATAGGCCACTATGTGTAAGA
1 GATAGCTTTGATCACAAGTGTGGTACTATGTAAAGGCCACTATGTGTAAGA
* * *
30100260 GATGGTTTTGATCACAAGTGTGGTACTATGTAAAGGCCACTTTGTG-AAGA
1 GATAGCTTTGATCACAAGTGTGGTACTATGTAAAGGCCACTATGTGTAAGA
*
30100310 TGGTAGCTTTGA-CTACAA-TGGTGGTACTATGT
1 -GATAGCTTTGATC-ACAAGT-GTGGTACTATGT
30100342 GCTGGCCACC
Statistics
Matches: 68, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
50 6 0.09
51 62 0.91
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (51 bp):
GATAGCTTTGATCACAAGTGTGGTACTATGTAAAGGCCACTATGTGTAAGA
Found at i:30102966 original size:16 final size:16
Alignment explanation
Indices: 30102947--30102977 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30102937 CTTCTTCACT
30102947 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
30102963 TACTTACTTACTTAA
1 TACTCACTTACTTAA
30102978 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:30102983 original size:20 final size:20
Alignment explanation
Indices: 30102944--30102983 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
30102934 AAACTTCTTC
* *
30102944 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
30102964 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
30102984 TTATTTATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:30103358 original size:55 final size:54
Alignment explanation
Indices: 30103216--30103421 Score: 265
Period size: 55 Copynumber: 3.8 Consensus size: 54
30103206 ATCCTTTTGA
* * *
30103216 AACTTACCATTGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTAT-G
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * * *
30103269 AACTCACCAATGCCATGCCTTGGCATGCTCTTACATGGGA-CCTTTGCCTTATAG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTATAG
* *
30103323 TAACTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAGA-
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
*
30103377 AACCTTACCAATTGCCATGCCTTGGCATGGTCTTACATGGTATCC
1 AA-CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTATCC
30103422 GTAAACCCTA
Statistics
Matches: 132, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
52 2 0.02
53 44 0.33
54 9 0.07
55 75 0.57
56 2 0.02
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.33
Consensus pattern (54 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
Found at i:30115874 original size:45 final size:45
Alignment explanation
Indices: 30115810--30115899 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
30115800 ATCACAGCAA
30115810 GCTAGGTCTCGTATAGTGTTCAAGCAATTACAACCATGCTTCTTG
1 GCTAGGTCTCGTATAGTGTTCAAGCAATTACAACCATGCTTCTTG
30115855 GCTAGGTCTCGTATAGTGTTCAAGCAATTACAACCATGCTTCTTG
1 GCTAGGTCTCGTATAGTGTTCAAGCAATTACAACCATGCTTCTTG
30115900 ATGCTAAAGC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.33
Consensus pattern (45 bp):
GCTAGGTCTCGTATAGTGTTCAAGCAATTACAACCATGCTTCTTG
Found at i:30135229 original size:19 final size:20
Alignment explanation
Indices: 30135195--30135236 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
30135185 ATAATTAATG
30135195 TTTATAATATTATTTAATGTT
1 TTTATAATATTATTTAAT-TT
30135216 TTTATAA-ATT-TTTAATTT
1 TTTATAATATTATTTAATTT
30135234 TTT
1 TTT
30135237 TCCTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.24
19 6 0.29
20 3 0.14
21 7 0.33
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTATAATATTATTTAATTT
Found at i:30135237 original size:19 final size:21
Alignment explanation
Indices: 30135195--30135237 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
30135185 ATAATTAATG
30135195 TTTATAATATTATTTAATGTT
1 TTTATAATATTATTTAATGTT
*
30135216 TTTATAA-ATT-TTTAATTTT
1 TTTATAATATTATTTAATGTT
30135235 TTT
1 TTT
30135238 CCTTTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.52
20 3 0.14
21 7 0.33
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTATAATATTATTTAATGTT
Found at i:30138995 original size:69 final size:69
Alignment explanation
Indices: 30138879--30139017 Score: 233
Period size: 69 Copynumber: 2.0 Consensus size: 69
30138869 AGAAGACGAG
* * *
30138879 TGGGTTTAAACCGGGCTTAAACCCAAATTGGACCGGATTTTAGATTTATTAAGAAAACATATTCA
1 TGGGTTTAAACCGGGCTCAAACCCAAATTAGACCGGATTTTAGATTTATTAAGAAAACACATTCA
30138944 AATC
66 AATC
* *
30138948 TGGGTTTAAACCGGGCTCAAATCCAAATTAGACCGGATTTTATATTTATTAAGAAAACACATTCA
1 TGGGTTTAAACCGGGCTCAAACCCAAATTAGACCGGATTTTAGATTTATTAAGAAAACACATTCA
30139013 AATC
66 AATC
30139017 T
1 T
30139018 AGTCTTAGTT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.31
Consensus pattern (69 bp):
TGGGTTTAAACCGGGCTCAAACCCAAATTAGACCGGATTTTAGATTTATTAAGAAAACACATTCA
AATC
Found at i:30140633 original size:25 final size:25
Alignment explanation
Indices: 30140599--30140655 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
30140589 TCATCTTTGG
*
30140599 AACTGATCAATCTATTATTTATTCT
1 AACTAATCAATCTATTATTTATTCT
30140624 AACTAATCAATCTATTATTTATTCT
1 AACTAATCAATCTATTATTTATTCT
30140649 AACTAAT
1 AACTAAT
30140656 TGTCCTACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.37, C:0.16, G:0.02, T:0.46
Consensus pattern (25 bp):
AACTAATCAATCTATTATTTATTCT
Found at i:30143415 original size:28 final size:28
Alignment explanation
Indices: 30143346--30143446 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
30143336 GACAAGATTG
* * * *
30143346 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
30143376 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
30143404 GCACTAAGTGTGCGAG-CTGAATGTATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
30143433 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
30143447 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.03
28 24 0.38
29 20 0.31
30 18 0.28
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:30143440 original size:29 final size:28
Alignment explanation
Indices: 30143375--30143446 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 28
30143365 AAAATTGTAC
*
30143375 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTCTGATTATAT
30143403 AGCACTAAGTGTGCGAG-CTGAATGTATAT
1 AGCACTAAGTGTGCGAGTCTG-AT-TATAT
30143432 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
30143447 GATTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 2 0.05
28 19 0.46
29 20 0.49
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTCTGATTATAT
Found at i:30147675 original size:19 final size:18
Alignment explanation
Indices: 30147662--30147739 Score: 77
Period size: 21 Copynumber: 4.2 Consensus size: 18
30147652 CTTAAAATAA
30147662 ATAAAAATATTT-AAATT
1 ATAAAAATATTTAAAATT
*
30147679 ATAAAAATAATTAAAATCT
1 ATAAAAATATTTAAAAT-T
30147698 ATAAAAATATTAATACAAATT
1 ATAAAAATATT--TA-AAATT
* * *
30147719 CTAAAAATATTAAAAAAT
1 ATAAAAATATTTAAAATT
30147737 ATA
1 ATA
30147740 TAAACAATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
17 11 0.22
18 10 0.20
19 12 0.24
21 13 0.26
22 4 0.08
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (18 bp):
ATAAAAATATTTAAAATT
Found at i:30147685 original size:18 final size:18
Alignment explanation
Indices: 30147662--30147710 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
30147652 CTTAAAATAA
*
30147662 ATAAAAATATTTAAAT-T
1 ATAAAAATATTAAAATCT
30147679 ATAAAAATAATTAAAATCT
1 ATAAAAAT-ATTAAAATCT
30147698 ATAAAAATATTAA
1 ATAAAAATATTAA
30147711 TACAAATTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 8 0.28
18 12 0.41
19 9 0.31
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAAAAATATTAAAATCT
Found at i:30152447 original size:47 final size:48
Alignment explanation
Indices: 30152388--30152486 Score: 184
Period size: 47 Copynumber: 2.1 Consensus size: 48
30152378 CATTCATAAG
30152388 CAAA-AAATTTAATCAATAGTATAAAGTATTTCAAAAATTAAATAGCA
1 CAAACAAATTTAATCAATAGTATAAAGTATTTCAAAAATTAAATAGCA
30152435 CAAACAAA-TTAATCAATAGTATAAAGTATTTCAAAAATTAAATAGCA
1 CAAACAAATTTAATCAATAGTATAAAGTATTTCAAAAATTAAATAGCA
30152482 CAAAC
1 CAAAC
30152487 CAATAACTCA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
47 48 0.94
48 3 0.06
ACGTcount: A:0.56, C:0.11, G:0.06, T:0.27
Consensus pattern (48 bp):
CAAACAAATTTAATCAATAGTATAAAGTATTTCAAAAATTAAATAGCA
Found at i:30153218 original size:120 final size:120
Alignment explanation
Indices: 30152991--30153231 Score: 295
Period size: 120 Copynumber: 2.0 Consensus size: 120
30152981 ACAATAAACC
* * * ** * *
30152991 TTGGGTAAAATTACCCCATAAACCTTTTTTTTCTTTCCTTACTAAAAACTAATACTTTATAGAAT
1 TTGGGAAAAATCACCCCATAAACCCTTTCCTTCTTTCATTACTAAAAACTAATACTTTATACAAT
* ** **
30153056 TAACCACTTAATTTGACTTTTCTTGCAACTTTGTCCACAGCCTAATTTAATAAAA
66 TAACCACTCAATTTGACTTTTCTTGCAAAATAATCCACAGCCTAATTTAATAAAA
* * * *
30153111 TTGGGAAAAATCACCTCATAAACCCTTTCCTTCTTTTATTACTAAAAA-TCAGTACTTTATACTA
1 TTGGGAAAAATCACCCCATAAACCCTTTCCTTCTTTCATTACTAAAAACT-AATACTTTATACAA
* * *
30153175 TTAACCACTCAATTTGACTTTTCTTGCAAAATAATCTATAGCCTAATTTAATGAAA
65 TTAACCACTCAATTTGACTTTTCTTGCAAAATAATCCACAGCCTAATTTAATAAAA
30153231 T
1 T
30153232 CCTTTATCTA
Statistics
Matches: 101, Mismatches: 19, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
119 1 0.01
120 100 0.99
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (120 bp):
TTGGGAAAAATCACCCCATAAACCCTTTCCTTCTTTCATTACTAAAAACTAATACTTTATACAAT
TAACCACTCAATTTGACTTTTCTTGCAAAATAATCCACAGCCTAATTTAATAAAA
Found at i:30155203 original size:28 final size:28
Alignment explanation
Indices: 30155166--30155219 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
30155156 ACTCTGGATG
30155166 TTAGCACGTCCGGAGGTGGTCAAGTTGT
1 TTAGCACGTCCGGAGGTGGTCAAGTTGT
* * *
30155194 TTAGTACGTCTGGAGTTGGTCAAGTT
1 TTAGCACGTCCGGAGGTGGTCAAGTT
30155220 TTTGGTGCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.19, C:0.15, G:0.33, T:0.33
Consensus pattern (28 bp):
TTAGCACGTCCGGAGGTGGTCAAGTTGT
Found at i:30157089 original size:20 final size:20
Alignment explanation
Indices: 30157064--30157102 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
30157054 AAATAAGGTC
30157064 ACACGCCCATGTGGCTTGGG
1 ACACGCCCATGTGGCTTGGG
* *
30157084 ACACGCTCATGTGGGTTGG
1 ACACGCCCATGTGGCTTGG
30157103 CATGTGGTCA
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:0.15, C:0.26, G:0.36, T:0.23
Consensus pattern (20 bp):
ACACGCCCATGTGGCTTGGG
Found at i:30158891 original size:29 final size:29
Alignment explanation
Indices: 30158853--30158910 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
30158843 ATGCATTTTC
30158853 ACTAAAAATCACTTAGTAAAAGTTATTCA
1 ACTAAAAATCACTTAGTAAAAGTTATTCA
*
30158882 ACTAAAAATCACTTAGTAAAAGTTGTTCA
1 ACTAAAAATCACTTAGTAAAAGTTATTCA
30158911 TTACACCTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.31
Consensus pattern (29 bp):
ACTAAAAATCACTTAGTAAAAGTTATTCA
Found at i:30165456 original size:17 final size:19
Alignment explanation
Indices: 30165429--30165465 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
30165419 TTAGTATTCT
30165429 TACCAAAAGTTCAT-CTCA
1 TACCAAAAGTTCATACTCA
30165447 TACC-AAAGTTCATACTCA
1 TACCAAAAGTTCATACTCA
30165465 T
1 T
30165466 GGGTTTTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.38, C:0.27, G:0.05, T:0.30
Consensus pattern (19 bp):
TACCAAAAGTTCATACTCA
Found at i:30175003 original size:18 final size:19
Alignment explanation
Indices: 30174961--30175004 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
30174951 CCGAAAAATA
*
30174961 ATTTTTGAAAAATGATTTAT
1 ATTTTTGAAAAA-GATTAAT
*
30174981 TTTTTTGAAAAA-ATTAAT
1 ATTTTTGAAAAAGATTAAT
30174999 ATTTTT
1 ATTTTT
30175005 TCGTGTTTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 10 0.48
20 11 0.52
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.55
Consensus pattern (19 bp):
ATTTTTGAAAAAGATTAAT
Found at i:30175540 original size:22 final size:22
Alignment explanation
Indices: 30175496--30175555 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
30175486 TTAAAATAAA
*
30175496 ATTAAAATATTAAA-TA-ATTT
1 ATTAAAATAATAAATTATATTT
30175516 ATTAAAATAATAAATTATATTT
1 ATTAAAATAATAAATTATATTT
* * *
30175538 ATTATATTAATAATTTAT
1 ATTAAAATAATAAATTAT
30175556 TATATGACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.38
21 2 0.06
22 19 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTAAAATAATAAATTATATTT
Found at i:30180442 original size:21 final size:21
Alignment explanation
Indices: 30180416--30180468 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
30180406 AGCAGTGGCG
*
30180416 GTGAGATTAGTTACTATAGCA
1 GTGAGATTAGATACTATAGCA
* * *
30180437 GTGAGATTGGATACTGTAGCG
1 GTGAGATTAGATACTATAGCA
30180458 GTGAGATTAGA
1 GTGAGATTAGA
30180469 AACAGCGGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.08, G:0.32, T:0.30
Consensus pattern (21 bp):
GTGAGATTAGATACTATAGCA
Found at i:30183568 original size:45 final size:46
Alignment explanation
Indices: 30183472--30183644 Score: 207
Period size: 45 Copynumber: 3.9 Consensus size: 46
30183462 TTTTCTCAAA
* * * *
30183472 TCACCGGCATT-TTGCCTGCTAGGATCG--AGGCCCGATTA-TCATT
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAAGGCCCGAATAGT-ATC
*
30183515 TCATCGGCATTATAGCCTGCTAGGCTCGAAA-GCCCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAAGGCCCGAATAGTATC
* *
30183560 TCACCGGCATTATAGCCTGCTAGGC-CCAAAGGCCCGAATAGTGTC
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAAGGCCCGAATAGTATC
* *
30183605 TCACCGGCATAATAGCTTGCTAGGCTC-AAAGGCCCGAATA
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAAGGCCCGAATA
30183645 TAATACCAGC
Statistics
Matches: 114, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
43 10 0.09
44 18 0.16
45 83 0.73
46 3 0.03
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (46 bp):
TCACCGGCATTATAGCCTGCTAGGCTCGAAAGGCCCGAATAGTATC
Found at i:30183788 original size:38 final size:38
Alignment explanation
Indices: 30183637--30183781 Score: 186
Period size: 38 Copynumber: 3.8 Consensus size: 38
30183627 GGCTCAAAGG
* *
30183637 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACTAAGCCTGCGGGATTTAA
* * *
30183675 CCCGGATAAAATACCAGCACGAAGCCTGCGGGAATTAA
1 CCCGGATATAATACCAGCACTAAGCCTGCGGGATTTAA
* *
30183713 CCCGGATATATTACCAGCA-TGAAGCCTGCAGGATTTAA
1 CCCGGATATAATACCAGCACT-AAGCCTGCGGGATTTAA
*
30183751 CCCGGATATAATTCCAGCA-TATAGCCTGCGG
1 CCCGGATATAATACCAGCACTA-AGCCTGCGG
30183782 TCTTTAAGCT
Statistics
Matches: 92, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
37 1 0.01
38 91 0.99
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.20
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACTAAGCCTGCGGGATTTAA
Found at i:30184174 original size:43 final size:44
Alignment explanation
Indices: 30184066--30184200 Score: 184
Period size: 43 Copynumber: 3.1 Consensus size: 44
30184056 ACATAACATT
*
30184066 TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGGCTCGAATAA
1 TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAA-GCCCGAAT-A
* * *
30184112 T-ATTTCACCGGCATCATAGCCTACTAAGCTCAAAGCCCG-ATA
1 TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGCCCGAATA
* *
30184154 TCATTTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGAATA
1 TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGCCCGAATA
30184198 TCA
1 TCA
30184201 CATTTCGATA
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
42 2 0.03
43 35 0.45
44 10 0.13
45 30 0.38
46 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (44 bp):
TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGCCCGAATA
Found at i:30185573 original size:2 final size:2
Alignment explanation
Indices: 30185561--30185607 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
30185551 CACTTTCAAA
30185561 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30185602 AT AT AT
1 AT AT AT
30185608 TCGAATTTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30196735 original size:43 final size:43
Alignment explanation
Indices: 30196688--30196769 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
30196678 ATTGATTAAT
* *
30196688 AATGCAAATGTCCCAGACATGGTCTTACACGTAATCACAATAC
1 AATGCAAATGTCCCAAACATGGTCTTACACGTAACCACAATAC
* *
30196731 AATGCCAATGTCCCAAACATGGTCTTACATGTAACCACA
1 AATGCAAATGTCCCAAACATGGTCTTACACGTAACCACA
30196770 TCTCAGTAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.23
Consensus pattern (43 bp):
AATGCAAATGTCCCAAACATGGTCTTACACGTAACCACAATAC
Found at i:30204454 original size:39 final size:39
Alignment explanation
Indices: 30204323--30204513 Score: 172
Period size: 40 Copynumber: 4.8 Consensus size: 39
30204313 GGATATAACG
* ** **
30204323 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGG-TTATAGCG
1 ACTCGCAC-AATGCCTTCGGGACTTAGCCCGGATT-TAGTA
* *
30204363 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCAC-AATGCCTTCGGGACTTAGCCCGGATTTAGTA
* *
30204403 ACTTGCACAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * * *
30204441 ACTCGCACGAATGCCTTC-GGATCCTAGTCCGGATATAGTC
1 ACTCGCAC-AATGCCTTCGGGA-CTTAGCCCGGATTTAGTA
* *
30204481 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAATGCCTTCGGGACTTAGCCCGGA
30204514 CATCATTCGA
Statistics
Matches: 124, Mismatches: 21, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
38 24 0.19
39 21 0.17
40 69 0.56
41 10 0.08
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.24
Consensus pattern (39 bp):
ACTCGCACAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:30204458 original size:78 final size:80
Alignment explanation
Indices: 30204363--30204513 Score: 209
Period size: 78 Copynumber: 1.9 Consensus size: 80
30204353 GGTTATAGCG
* * * *
30204363 ACTCGCACGAATGCCTTCGGGA-CTTAACCCGGGTTTAGTAACTT-GCACAATGCCTTCGGG-CT
1 ACTCGCACGAATGCCTTC-GGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACT
30204425 TAGCCCGGATTTATTA
65 TAGCCCGGATTTATTA
** *
30204441 ACTCGCACGAATGCCTTCGGATCCTAGTCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTT
1 ACTCGCACGAATGCCTTCGGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTT
30204506 AGCCCGGA
66 AGCCCGGA
30204514 CATCATTCGA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
77 3 0.05
78 34 0.54
79 15 0.24
80 11 0.17
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.25
Consensus pattern (80 bp):
ACTCGCACGAATGCCTTCGGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTT
AGCCCGGATTTATTA
Found at i:30212493 original size:39 final size:39
Alignment explanation
Indices: 30212362--30212552 Score: 172
Period size: 40 Copynumber: 4.8 Consensus size: 39
30212352 GGATATAACG
* ** **
30212362 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGG-TTATAGCG
1 ACTCGCAC-AATGCCTTCGGGACTTAGCCCGGATT-TAGTA
* *
30212402 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCAC-AATGCCTTCGGGACTTAGCCCGGATTTAGTA
* *
30212442 ACTTGCACAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * * *
30212480 ACTCGCACGAATGCCTTC-GGATCCTAGTCCGGATATAGTC
1 ACTCGCAC-AATGCCTTCGGGA-CTTAGCCCGGATTTAGTA
* *
30212520 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAATGCCTTCGGGACTTAGCCCGGA
30212553 CATCATTCGA
Statistics
Matches: 124, Mismatches: 21, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
38 24 0.19
39 21 0.17
40 69 0.56
41 10 0.08
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.24
Consensus pattern (39 bp):
ACTCGCACAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:30212497 original size:78 final size:80
Alignment explanation
Indices: 30212402--30212552 Score: 209
Period size: 78 Copynumber: 1.9 Consensus size: 80
30212392 GGTTATAGCG
* * * *
30212402 ACTCGCACGAATGCCTTCGGGA-CTTAACCCGGGTTTAGTAACTT-GCACAATGCCTTCGGG-CT
1 ACTCGCACGAATGCCTTC-GGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACT
30212464 TAGCCCGGATTTATTA
65 TAGCCCGGATTTATTA
** *
30212480 ACTCGCACGAATGCCTTCGGATCCTAGTCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTT
1 ACTCGCACGAATGCCTTCGGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTT
30212545 AGCCCGGA
66 AGCCCGGA
30212553 CATCATTCGA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
77 3 0.05
78 34 0.54
79 15 0.24
80 11 0.17
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.25
Consensus pattern (80 bp):
ACTCGCACGAATGCCTTCGGATCCTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTT
AGCCCGGATTTATTA
Found at i:30219687 original size:27 final size:28
Alignment explanation
Indices: 30219631--30219700 Score: 133
Period size: 27 Copynumber: 2.5 Consensus size: 28
30219621 AAATTTGTAC
30219631 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
30219659 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
30219686 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
30219701 GACTCACTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 25 0.60
28 17 0.40
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATAT
Found at i:30223941 original size:39 final size:40
Alignment explanation
Indices: 30223798--30223943 Score: 138
Period size: 40 Copynumber: 3.7 Consensus size: 40
30223788 GCGACTCGCT
* * * * *
30223798 CAAAAGCCTTCGGGACATAGCCCGG-TTATAATAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTAGCA
* * * *
30223838 CAAATGCCTTCGGGACTTAACCCGGTTTTGGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTAGCA
* *
30223878 CAAATGCCTTCGGGAATT-GACCCGGATTTAGTCACTTAG-A
1 CAAATGCCTTCGGGACTTAG-CCCGGATTTAGTAAC-TAGCA
30223918 CAAA-GCCTTCGGGACTTAGCCCGGAT
1 CAAATGCCTTCGGGACTTAGCCCGGAT
30223944 ACCATTCGAA
Statistics
Matches: 89, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
39 19 0.21
40 66 0.74
41 4 0.04
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTAGCA
Found at i:30231895 original size:39 final size:39
Alignment explanation
Indices: 30231800--30231898 Score: 119
Period size: 40 Copynumber: 2.5 Consensus size: 39
30231790 GGATATAGCG
* * *
30231800 ACTCGCTCAAAAGCCTTCGGGACATAGCCCGGTTATAAT
1 ACTCGCACAAATGCCTTCGGGACATAACCCGGTTATAAT
* * *
30231839 AGCTCGCACAAATGCCTTCGGGACTTAACCCGGTTTTGGA-
1 A-CTCGCACAAATGCCTTCGGGACATAACCCGGTTAT-AAT
30231879 ACTCGCACAAATGCCTTCGG
1 ACTCGCACAAATGCCTTCGG
30231899 AATTGACCCG
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 20 0.38
40 31 0.60
41 1 0.02
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.23
Consensus pattern (39 bp):
ACTCGCACAAATGCCTTCGGGACATAACCCGGTTATAAT
Found at i:30241495 original size:40 final size:38
Alignment explanation
Indices: 30241439--30241591 Score: 137
Period size: 40 Copynumber: 3.8 Consensus size: 38
30241429 GGATATAGCG
* *
30241439 ACTCGCTCAAAAGCCTTCGGGACATAGCCCGGTTATAAT
1 ACTCGCACAAAAGCCTTCGGGACATAGCCCGGTT-TAGT
* * * *
30241478 AGCTCGCACAAATGCCTTCGGGACTTAACCCGGTTTTGGT
1 A-CTCGCACAAAAGCCTTCGGGACATAGCCCGG-TTTAGT
* *
30241518 AACTCGCACAAATGCCTTCGGGA-ATTGACCCGGATTTAGT
1 -ACTCGCACAAAAGCCTTCGGGACATAG-CCCGG-TTTAGT
* *
30241558 CACTTAGCACAAAAGCCTTCGGGACTTAGCCCGG
1 -AC-TCGCACAAAAGCCTTCGGGACATAGCCCGG
30241592 ATACCATTCG
Statistics
Matches: 92, Mismatches: 16, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
39 2 0.02
40 62 0.67
41 26 0.28
42 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (38 bp):
ACTCGCACAAAAGCCTTCGGGACATAGCCCGGTTTAGT
Found at i:30248477 original size:27 final size:28
Alignment explanation
Indices: 30248421--30248490 Score: 133
Period size: 27 Copynumber: 2.5 Consensus size: 28
30248411 AAATTTGTAC
30248421 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
30248449 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
30248476 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
30248491 GACTCACTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 25 0.60
28 17 0.40
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATAT
Found at i:30254094 original size:45 final size:45
Alignment explanation
Indices: 30254029--30254119 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
30254019 CCTATCTTAA
* * *
30254029 AAGCTTGGTAAATATAGAAGGTGATCTTCAAATATATGCGATCCT
1 AAGCTTGGCAAATATAGAAGGTGATCTTCAAAGATATACGATCCT
* *
30254074 AAGCTTGGCAAATATGGAAGGTGATCTTCAAAGATATATGATCCT
1 AAGCTTGGCAAATATAGAAGGTGATCTTCAAAGATATACGATCCT
30254119 A
1 A
30254120 GACATTAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (45 bp):
AAGCTTGGCAAATATAGAAGGTGATCTTCAAAGATATACGATCCT
Found at i:30259149 original size:40 final size:40
Alignment explanation
Indices: 30259100--30259215 Score: 196
Period size: 40 Copynumber: 2.9 Consensus size: 40
30259090 CGATATATTG
30259100 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAAGT
1 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAAGT
* *
30259140 ATATTCGGGTTAAATCCCGCAGGCTTCGTACTGGTAAAGT
1 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAAGT
* *
30259180 ATATCCGGGTTAATTCCCGCAGGCTTAGTGCTGGTA
1 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTA
30259216 CTATATCTGG
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 70 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (40 bp):
ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAAGT
Found at i:30267971 original size:40 final size:40
Alignment explanation
Indices: 30267926--30268092 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
30267916 CGGAATATAA
30267926 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
30267966 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
30268006 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
30268046 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
30268085 CCGGATAT
1 CCGGATAT
30268093 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:30268076 original size:80 final size:79
Alignment explanation
Indices: 30267926--30268092 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
30267916 CGGAATATAA
* *
30267926 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
30267991 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
30268006 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
30268068 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
30268085 CCGGATAT
1 CCGGATAT
30268093 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:30268941 original size:17 final size:19
Alignment explanation
Indices: 30268918--30268963 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
30268908 AAGAAGCATG
30268918 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
30268936 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
30268954 AATCATGCTC
1 AATCATGCTC
30268964 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:30277230 original size:20 final size:20
Alignment explanation
Indices: 30277202--30277255 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
30277192 AAAAGGGGTC
*
30277202 ACACGCCCGTGTGGCTTGGG
1 ACACACCCGTGTGGCTTGGG
30277222 ACACACCCGTGTGGCTTGGG
1 ACACACCCGTGTGGCTTGGG
30277242 ACACACCCGTGTGG
1 ACACACCCGTGTGG
30277256 GAAGGCCGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.15, C:0.31, G:0.35, T:0.19
Consensus pattern (20 bp):
ACACACCCGTGTGGCTTGGG
Found at i:30279277 original size:28 final size:29
Alignment explanation
Indices: 30279246--30279376 Score: 131
Period size: 29 Copynumber: 4.6 Consensus size: 29
30279236 GTGACGAGAT
30279246 TGGCACTAAGTGTGCGTGCTGGAAA-ATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
30279274 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * ****
30279303 TGGCACTAAGTGTGCGAGCTCGAAGGGCA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * * **
30279332 TGGCACTATGTGTGCGGGCT-TAAATCGCA
1 TGGCACTAAGTGTGCGTGCTGGAAAT-ATA
30279361 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
30279377 AAATCGAGTA
Statistics
Matches: 87, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
28 26 0.30
29 61 0.70
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.24
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:30279313 original size:29 final size:28
Alignment explanation
Indices: 30279246--30279317 Score: 126
Period size: 28 Copynumber: 2.5 Consensus size: 28
30279236 GTGACGAGAT
*
30279246 TGGCACTAAGTGTGCGTGCTGGAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAAATA
30279274 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAA-ATA
30279303 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
30279318 GAGCTCGAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
28 24 0.57
29 18 0.43
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (28 bp):
TGGCACTAAGTGTGCATGCTGGAAAATA
Found at i:30287009 original size:28 final size:29
Alignment explanation
Indices: 30286978--30287108 Score: 131
Period size: 29 Copynumber: 4.6 Consensus size: 29
30286968 GTGACGAGAT
30286978 TGGCACTAAGTGTGCGTGCTGGAAA-ATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
30287006 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * ****
30287035 TGGCACTAAGTGTGCGAGCTCGAAGGGCA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * * **
30287064 TGGCACTATGTGTGCGGGCT-TAAATCGCA
1 TGGCACTAAGTGTGCGTGCTGGAAAT-ATA
30287093 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
30287109 AAATCGAGTA
Statistics
Matches: 87, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
28 26 0.30
29 61 0.70
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.24
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:30287045 original size:29 final size:28
Alignment explanation
Indices: 30286978--30287049 Score: 126
Period size: 28 Copynumber: 2.5 Consensus size: 28
30286968 GTGACGAGAT
*
30286978 TGGCACTAAGTGTGCGTGCTGGAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAAATA
30287006 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAA-ATA
30287035 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
30287050 GAGCTCGAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
28 24 0.57
29 18 0.43
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (28 bp):
TGGCACTAAGTGTGCATGCTGGAAAATA
Found at i:30293847 original size:47 final size:47
Alignment explanation
Indices: 30293789--30293898 Score: 130
Period size: 47 Copynumber: 2.3 Consensus size: 47
30293779 TGGCCACGGA
* * * * * *
30293789 CCATGGTATAGGTATTTAGAGAGGAGTTACCTTGATTTGGCTACGTG
1 CCATGGTATAGGTACTCAGAGAGAAGTTACCTTGATTTGACTAAGGG
* * *
30293836 CCATGGTATAGGTACTCCGAGATAAGTTACCTTGGTTTGACTAAGGG
1 CCATGGTATAGGTACTCAGAGAGAAGTTACCTTGATTTGACTAAGGG
*
30293883 CAATGGTATAGGTACT
1 CCATGGTATAGGTACT
30293899 TATCGATTGT
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
47 53 1.00
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (47 bp):
CCATGGTATAGGTACTCAGAGAGAAGTTACCTTGATTTGACTAAGGG
Found at i:30296451 original size:29 final size:29
Alignment explanation
Indices: 30296412--30296491 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 29
30296402 CTTAATAATC
*
30296412 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
30296442 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
30296471 AGCCCGCACACTTAGTGCCAT
1 AACCCGCACACTTAGTGCCAT
30296492 TCTCTCAACC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 39 0.87
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.25
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:30297038 original size:2 final size:2
Alignment explanation
Indices: 30297031--30297058 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
30297021 CCGAATATGC
30297031 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30297059 CAACTATACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30304357 original size:29 final size:29
Alignment explanation
Indices: 30304318--30304397 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 29
30304308 CTTAATAATC
*
30304318 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
30304348 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
30304377 AGCCCGCACACTTAGTGCCAT
1 AACCCGCACACTTAGTGCCAT
30304398 TCTCTCAACC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 39 0.87
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.25
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:30306322 original size:81 final size:81
Alignment explanation
Indices: 30306184--30306416 Score: 308
Period size: 81 Copynumber: 2.9 Consensus size: 81
30306174 TTAGTTTACC
* * * * **
30306184 AAATTACCAAAATACCCTTAATTTAAAAAATTACCAAAATACCCTTGGTTTAAAAAATTACCAAA
1 AAATTACTAAAATACCCTTAGTTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAA
*
30306249 ATACCCCTGGTTTGTA
66 ATACCCCTAGTTTGTA
*
30306265 AAATTACTAAAATACCCTTTGTTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAA
1 AAATTACTAAAATACCCTTAGTTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAA
30306330 ATACCCCTAGTTTGTA
66 ATACCCCTAGTTTGTA
* * * * **
30306346 AAATTA-TCAAAATACCCCTAGTTT-TACAAATTACCAAAATCCCCCTGATTTGTGAAATTACTG
1 AAATTACT-AAAATACCCTTAGTTTATA-AAATTACCAAAATACCCCTGGTTTGTAAAATTACCA
30306409 AAATACCC
64 AAATACCC
30306417 TCGACCTGTA
Statistics
Matches: 135, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
80 3 0.02
81 132 0.98
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (81 bp):
AAATTACTAAAATACCCTTAGTTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAA
ATACCCCTAGTTTGTA
Found at i:30306403 original size:27 final size:27
Alignment explanation
Indices: 30306184--30306476 Score: 258
Period size: 27 Copynumber: 10.9 Consensus size: 27
30306174 TTAGTTTACC
* * **
30306184 AAATTACCAAAATACCCTTAATTTAAA
1 AAATTACCAAAATACCCCTGATTTGTA
* * **
30306211 AAATTACCAAAATACCCTTGGTTTAAA
1 AAATTACCAAAATACCCCTGATTTGTA
*
30306238 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
* * *
30306265 AAATTACTAAAATACCCTTTG-TTTATA
1 AAATTACCAAAATACCC-CTGATTTGTA
*
30306292 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
30306319 AAATTACCAAAATACCCCT-AGTTTGTA
1 AAATTACCAAAATACCCCTGA-TTTGTA
*
30306346 AAATTATCAAAATACCCCT-AGTTT-TA
1 AAATTACCAAAATACCCCTGA-TTTGTA
* *
30306372 CAAATTACCAAAATCCCCCTGATTTGTG
1 -AAATTACCAAAATACCCCTGATTTGTA
** **
30306400 AAATTACTGAAATA-CCCTCGACCTGTA
1 AAATTACCAAAATACCCCT-GATTTGTA
*** *
30306427 AAATTATTGAAATA-CCCTCGACTTGTA
1 AAATTACCAAAATACCCCT-GATTTGTA
*
30306454 AAATTACCAAAGTA-CCCTGATTT
1 AAATTACCAAAATACCCCTGATTT
30306477 ACAGAATTAC
Statistics
Matches: 230, Mismatches: 29, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
26 12 0.05
27 214 0.93
28 4 0.02
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGATTTGTA
Found at i:30306518 original size:27 final size:27
Alignment explanation
Indices: 30306466--30306658 Score: 244
Period size: 27 Copynumber: 7.2 Consensus size: 27
30306456 ATTACCAAAG
* *
30306466 TACCCT-GATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
* * *
30306492 TACCCTCGACTTAAAAAATTATTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
* * *
30306519 TACCCTCGATTGACAGAATAACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
30306546 TACCCTCGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
*
30306573 TACCCTCGATTTACAAAATTACTATTT
1 TACCCTCGATTTACAAAATTACTGTTT
* * *
30306600 TATCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
* **
30306627 TACCCTCGATTTATAAAATTACCATTT
1 TACCCTCGATTTACAAAATTACTGTTT
30306654 TACCC
1 TACCC
30306659 CTAGGGTGTT
Statistics
Matches: 143, Mismatches: 23, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
26 6 0.04
27 137 0.96
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACTGTTT
Found at i:30306581 original size:81 final size:81
Alignment explanation
Indices: 30306466--30306658 Score: 271
Period size: 81 Copynumber: 2.4 Consensus size: 81
30306456 ATTACCAAAG
* * *
30306466 TACCCT-GATTTACAGAATTACCGTTTTACCCTCGACTTAAAAAATTATTGTTTTACCCTCGATT
1 TACCCTCGATTTACAAAATTACCGTTTTACCCTCGACTTAAAAAATTACTATTTTACCCTCGATT
*
30306530 GACAGAATAACTGTTT
66 GACAGAATAACCGTTT
* * * *
30306546 TACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTACAAAATTACTATTTTATCCTCGATT
1 TACCCTCGATTTACAAAATTACCGTTTTACCCTCGACTTAAAAAATTACTATTTTACCCTCGATT
* *
30306611 TACAGAATTACCGTTT
66 GACAGAATAACCGTTT
* *
30306627 TACCCTCGATTTATAAAATTACCATTTTACCC
1 TACCCTCGATTTACAAAATTACCGTTTTACCC
30306659 CTAGGGTGTT
Statistics
Matches: 99, Mismatches: 13, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
80 6 0.06
81 93 0.94
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (81 bp):
TACCCTCGATTTACAAAATTACCGTTTTACCCTCGACTTAAAAAATTACTATTTTACCCTCGATT
GACAGAATAACCGTTT
Found at i:30306939 original size:27 final size:26
Alignment explanation
Indices: 30306895--30306946 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
30306885 CTCGCTGCAA
*
30306895 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
30306922 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
30306947 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:30307014 original size:26 final size:27
Alignment explanation
Indices: 30306985--30307044 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
30306975 CCACATATAT
*
30306985 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
30307011 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
30307038 ATATCTG
1 ATATCTG
30307045 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:30307230 original size:6 final size:6
Alignment explanation
Indices: 30307219--30307259 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
30307209 GTGTCACCTA
* *
30307219 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTC ATTTTG ATTCT
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCT
30307260 AGTTTTGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.17, C:0.17, G:0.12, T:0.54
Consensus pattern (6 bp):
ATTCTG
Found at i:30312105 original size:38 final size:38
Alignment explanation
Indices: 30312062--30312140 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
30312052 ACCTACTAGT
30312062 TCATCTACACAACATTTACATACTCATGCAAACATATA
1 TCATCTACACAACATTTACATACTCATGCAAACATATA
*
30312100 TCATCTACACAACATTTACATACTCATGCAAGCATATA
1 TCATCTACACAACATTTACATACTCATGCAAACATATA
30312138 TCA
1 TCA
30312141 CATTTCACGC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.41, C:0.27, G:0.04, T:0.29
Consensus pattern (38 bp):
TCATCTACACAACATTTACATACTCATGCAAACATATA
Found at i:30314028 original size:48 final size:48
Alignment explanation
Indices: 30313920--30314191 Score: 413
Period size: 48 Copynumber: 5.7 Consensus size: 48
30313910 TAAAGTACGA
* ** *
30313920 ATGCCATGTCCCTGACATGGTCTTACATTGGCACACATATCATCG-CG
1 ATGCCATGTCCCAGACATGGTCTTACACAGGCACATATATCATCGTCG
* *
30313967 ATGCCATGTCCCAGACATGGT-TTGACACAGGCACATATATTATCGTCA
1 ATGCCATGTCCCAGACATGGTCTT-ACACAGGCACATATATCATCGTCG
* *
30314015 ATGCCATGTCCCAGGCATGGTCTTACACAGGCACATATATCATCGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACAGGCACATATATCATCGTCG
* * *
30314063 ATGCCATGTCCTAGACATGGTCTTACACAGGCACATTTATCATTGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACAGGCACATATATCATCGTCG
*
30314111 ATGCCATGTCCTAGACATGGTCTTACACAGGCACATATATCATCGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACAGGCACATATATCATCGTCG
30314159 ATGCCATGTCCCAGACATGGTCTTACACAGGCA
1 ATGCCATGTCCCAGACATGGTCTTACACAGGCA
30314192 TATTAGCACA
Statistics
Matches: 204, Mismatches: 18, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
46 2 0.01
47 37 0.18
48 163 0.80
49 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.26
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACAGGCACATATATCATCGTCG
Found at i:30318743 original size:47 final size:47
Alignment explanation
Indices: 30318673--30318968 Score: 466
Period size: 47 Copynumber: 6.3 Consensus size: 47
30318663 CCCTTCGGGA
* * * *
30318673 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTTGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
**
30318720 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCAAC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
* *
30318767 CGTATCAACATATATACACATTCACATTCGTCACATTGGCCATTCGGC
1 CTTATC-ACATATATACACATTCACATTCATCACATTGGCCATTCGGC
*
30318815 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTTGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
* *
30318862 CTTATCACATATATACATATTCACATTCGTCACATTGGCCATTCGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
30318909 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
* *
30318956 TTTACCACATATA
1 CTTATCACATATA
30318969 CATATCTTAT
Statistics
Matches: 228, Mismatches: 20, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
47 185 0.81
48 43 0.19
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
Found at i:30318822 original size:22 final size:22
Alignment explanation
Indices: 30318797--30318871 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
30318787 TTCACATTCG
30318797 TCACATTGGCCATTCGGCCTTA
1 TCACATTGGCCATTCGGCCTTA
** * *
30318819 TCACATATATACACATTC-ACATTCA
1 TCACAT-T-GGC-CATTCGGCCTT-A
*
30318844 TCACATTGGCCATTTGGCCTTA
1 TCACATTGGCCATTCGGCCTTA
30318866 TCACAT
1 TCACAT
30318872 ATATACATAT
Statistics
Matches: 39, Mismatches: 9, Indels: 10
0.67 0.16 0.17
Matches are distributed among these distances:
22 17 0.44
23 5 0.13
24 5 0.13
25 12 0.31
ACGTcount: A:0.27, C:0.29, G:0.11, T:0.33
Consensus pattern (22 bp):
TCACATTGGCCATTCGGCCTTA
Found at i:30320743 original size:40 final size:40
Alignment explanation
Indices: 30320677--30320843 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
30320667 AAATTGAATG
* * *
30320677 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
30320716 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
30320756 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
30320796 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
30320836 ATATCCGG
1 ATATCCGG
30320844 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:30328731 original size:40 final size:40
Alignment explanation
Indices: 30328665--30328831 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
30328655 AAATTGAATG
* * *
30328665 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
30328704 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
30328744 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
30328784 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
30328824 ATATCCGG
1 ATATCCGG
30328832 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:30333832 original size:35 final size:35
Alignment explanation
Indices: 30333776--30333844 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
30333766 CATTCTCGCG
*
30333776 TATCTTTGAAGATCCCCTTCCACATTTGCCAAGCA
1 TATCTTTGAAGATCACCTTCCACATTTGCCAAGCA
* * * *
30333811 TATCTTTGAAGATTACTTTCCATATTTGGCAAGC
1 TATCTTTGAAGATCACCTTCCACATTTGCCAAGC
30333845 TCCGGAGATG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (35 bp):
TATCTTTGAAGATCACCTTCCACATTTGCCAAGCA
Found at i:30342570 original size:24 final size:24
Alignment explanation
Indices: 30342522--30342581 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
30342512 TAAGTTTGTG
* *
30342522 AAATTA-AATAT-ATAATACTTTA
1 AAATTATAATATAATAATACCTAA
30342544 AAATT-TAGATATAATAATACCTAA
1 AAATTATA-ATATAATAATACCTAA
30342568 AAATTATAATATAA
1 AAATTATAATATAA
30342582 CATCTTTGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 6 0.19
23 4 0.12
24 20 0.62
25 2 0.06
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.37
Consensus pattern (24 bp):
AAATTATAATATAATAATACCTAA
Found at i:30348198 original size:44 final size:44
Alignment explanation
Indices: 30348135--30348241 Score: 187
Period size: 44 Copynumber: 2.4 Consensus size: 44
30348125 TCTCAGATAG
30348135 GGTCTTACTCGCACACATATATCAGAGTCACATATCGATGCCAT
1 GGTCTTACTCGCACACATATATCAGAGTCACATATCGATGCCAT
* *
30348179 GGTCTTACTTGCACACATATATCGGAGTCACATATCGATGCCAT
1 GGTCTTACTCGCACACATATATCAGAGTCACATATCGATGCCAT
*
30348223 GGTCTTACTCGTACACATA
1 GGTCTTACTCGCACACATA
30348242 AATTGGAATC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 59 1.00
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (44 bp):
GGTCTTACTCGCACACATATATCAGAGTCACATATCGATGCCAT
Found at i:30352348 original size:2 final size:2
Alignment explanation
Indices: 30352341--30352394 Score: 65
Period size: 2 Copynumber: 27.0 Consensus size: 2
30352331 AGATTGACAA
* * *
30352341 AT AT AT AT AT AT AT AT AG AT -T GAC AA 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 AT
30352383 AT AT AT AT AT AT
1 AT AT AT AT AT AT
30352395 TCCGAAAAGG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:30352365 original size:26 final size:26
Alignment explanation
Indices: 30352329--30352383 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
30352319 ACTTGAAGAA
30352329 ATAGATTGACAAATATATATATATAT
1 ATAGATTGACAAATATATATATATAT
30352355 ATAGATTGACAAATATATATATATAT
1 ATAGATTGACAAATATATATATATAT
30352381 ATA
1 ATA
30352384 TATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (26 bp):
ATAGATTGACAAATATATATATATAT
Found at i:30352837 original size:22 final size:20
Alignment explanation
Indices: 30352811--30352853 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
30352801 AAATAACACA
30352811 AATATGAAAGCAATACAAAAAT
1 AATATGAAA--AATACAAAAAT
*
30352833 AATATTAAAAATACAAAAAT
1 AATATGAAAAATACAAAAAT
30352853 A
1 A
30352854 TAAGACGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
22 8 0.40
ACGTcount: A:0.67, C:0.07, G:0.05, T:0.21
Consensus pattern (20 bp):
AATATGAAAAATACAAAAAT
Found at i:30356387 original size:43 final size:43
Alignment explanation
Indices: 30356337--30356518 Score: 165
Period size: 43 Copynumber: 4.3 Consensus size: 43
30356327 TATCTCGGAT
* *
30356337 ATGGTCTTACATGTTATCATATATCGATGCCACTATCCCAGAC
1 ATGGTCTTACATGTAATCATATATCGATGCCAATATCCCAGAC
* * * * * * * *
30356380 AAGGTCTTATACGAAACCATATAACGATGCCAATGTCCTAGAC
1 ATGGTCTTACATGTAATCATATATCGATGCCAATATCCCAGAC
* * *
30356423 ATGGTCTTACATGTAATCACA-ATACAATGCCAATGTCCCA-AGC
1 ATGGTCTTACATGTAATCATATAT-CGATGCCAATATCCCAGA-C
* * *
30356466 ATGGTCTTACATGTAAT-ATCATACCGATGCC-ATATCCTAGAT
1 ATGGTCTTACATGTAATCAT-ATATCGATGCCAATATCCCAGAC
30356508 ATGGTCTTACA
1 ATGGTCTTACA
30356519 CGTATTCTCA
Statistics
Matches: 109, Mismatches: 25, Indels: 11
0.75 0.17 0.08
Matches are distributed among these distances:
42 20 0.18
43 88 0.81
44 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (43 bp):
ATGGTCTTACATGTAATCATATATCGATGCCAATATCCCAGAC
Found at i:30357848 original size:23 final size:25
Alignment explanation
Indices: 30357822--30357868 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
30357812 TACCAAGCTT
30357822 TAAGCTAAAC-A-CATACCAAACAC
1 TAAGCTAAACTATCATACCAAACAC
*
30357845 TAAGCTAAGCTATCATACCAAACA
1 TAAGCTAAACTATCATACCAAACA
30357869 TAGCCTCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.43
24 1 0.05
25 11 0.52
ACGTcount: A:0.49, C:0.28, G:0.06, T:0.17
Consensus pattern (25 bp):
TAAGCTAAACTATCATACCAAACAC
Found at i:30360380 original size:34 final size:32
Alignment explanation
Indices: 30360342--30360407 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 32
30360332 ATTATTTCAA
30360342 TCATTGTAAAACGCAATCCAAA-TATATAAACAAT
1 TCATT-TAAAAC-CAA-CCAAATTATATAAACAAT
* *
30360376 TCATTTTAAACCAACCAAATTATATTAACAAT
1 TCATTTAAAACCAACCAAATTATATAAACAAT
30360408 ATAAGCTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 5 0.17
32 14 0.48
33 5 0.17
34 5 0.17
ACGTcount: A:0.48, C:0.18, G:0.03, T:0.30
Consensus pattern (32 bp):
TCATTTAAAACCAACCAAATTATATAAACAAT
Found at i:30367885 original size:34 final size:32
Alignment explanation
Indices: 30367847--30367912 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 32
30367837 ATTATTTCAA
30367847 TCATTGTAAAACGCAATCCAAA-TATATAAACAAT
1 TCATT-TAAAAC-CAA-CCAAATTATATAAACAAT
* *
30367881 TCATTTTAAACCAACCAAATTATATTAACAAT
1 TCATTTAAAACCAACCAAATTATATAAACAAT
30367913 ATAAGCTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 5 0.17
32 14 0.48
33 5 0.17
34 5 0.17
ACGTcount: A:0.48, C:0.18, G:0.03, T:0.30
Consensus pattern (32 bp):
TCATTTAAAACCAACCAAATTATATAAACAAT
Found at i:30373729 original size:28 final size:27
Alignment explanation
Indices: 30373666--30373735 Score: 131
Period size: 27 Copynumber: 2.6 Consensus size: 27
30373656 ATAGTGAGTC
30373666 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
30373693 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
30373721 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
30373736 GTACAAATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 23 0.55
28 19 0.45
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:30375467 original size:80 final size:80
Alignment explanation
Indices: 30375312--30375472 Score: 261
Period size: 80 Copynumber: 2.0 Consensus size: 80
30375302 GGCTGTCACA
* * *
30375312 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGC
1 GGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTCGAGC
30375377 GAGTTACTATATCCG
66 GAGTTACTATATCCG
*
30375392 GGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATATCCGGGCTATGTCCCGAAGGCATTCGAGC
1 GGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTCGAGC
*
30375457 TAG-TAGCTATATCCG
66 GAGTTA-CTATATCCG
30375472 G
1 G
30375473 TGAAATCCCG
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
79 2 0.03
80 73 0.97
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26
Consensus pattern (80 bp):
GGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTCGAGC
GAGTTACTATATCCG
Found at i:30375472 original size:40 final size:40
Alignment explanation
Indices: 30375312--30375451 Score: 262
Period size: 40 Copynumber: 3.5 Consensus size: 40
30375302 GGCTGTCACA
30375312 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
30375352 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
*
30375392 GGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
*
30375432 GGCTATGTCCCGAAGGCATT
1 GGCTAAGTCCCGAAGGCATT
30375452 CGAGCTAGTA
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 98 1.00
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
Found at i:30383060 original size:31 final size:31
Alignment explanation
Indices: 30383019--30383190 Score: 163
Period size: 31 Copynumber: 5.6 Consensus size: 31
30383009 TAAGGTGTCC
30383019 ATCACCGGTACATAGTACCTGATAAGATATA
1 ATCACCGGTACATAGTACCTGATAAGATATA
* *
30383050 ATCACTGGTACATAATACCTGATAAGATATA
1 ATCACCGGTACATAGTACCTGATAAGATATA
* * * * *
30383081 AACACTGGCACATAGTGCATGAT-AGAATATA
1 ATCACCGGTACATAGTACCTGATAAG-ATATA
* * * *
30383112 AACATCGGTATAAAGTACCTGAT-A-ATATA
1 ATCACCGGTACATAGTACCTGATAAGATATA
* * * *
30383141 GTCACCAGTATATAATACCTGATAAGATATA
1 ATCACCGGTACATAGTACCTGATAAGATATA
*
30383172 ATCACCGGCACATA-TACCT
1 ATCACCGGTACATAGTACCT
30383191 AATACTTTAA
Statistics
Matches: 114, Mismatches: 24, Indels: 7
0.79 0.17 0.05
Matches are distributed among these distances:
29 22 0.19
30 8 0.07
31 84 0.74
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.26
Consensus pattern (31 bp):
ATCACCGGTACATAGTACCTGATAAGATATA
Found at i:30384916 original size:57 final size:57
Alignment explanation
Indices: 30384821--30384952 Score: 178
Period size: 57 Copynumber: 2.3 Consensus size: 57
30384811 AGTATTTTTA
*
30384821 ATTTTTCATTTTCATTTTGGAGAAAACCACATTAATTTCCAAATGATTT-CATTTCTCC
1 ATTTTT-ATTTTCATTTTGGAGAAAACCACAATAATTTCCAAATG-TTTCCATTTCTCC
* * *
30384879 ATTTTTATTTTCATTTTGGTA-AAAATCATAATCATTTCCAAATGTTTCCATTTCTCC
1 ATTTTTATTTTCATTTTGG-AGAAAACCACAATAATTTCCAAATGTTTCCATTTCTCC
*
30384936 ATTTTCATTTTCATTTT
1 ATTTTTATTTTCATTTT
30384953 CATTCTCATT
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
56 3 0.04
57 57 0.85
58 7 0.10
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.50
Consensus pattern (57 bp):
ATTTTTATTTTCATTTTGGAGAAAACCACAATAATTTCCAAATGTTTCCATTTCTCC
Found at i:30384944 original size:6 final size:6
Alignment explanation
Indices: 30384935--30384964 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
30384925 TCCATTTCTC
*
30384935 CATTTT CATTTT CATTTT CATTCT CATTTT
1 CATTTT CATTTT CATTTT CATTTT CATTTT
30384965 GGATAAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.20, G:0.00, T:0.63
Consensus pattern (6 bp):
CATTTT
Found at i:30384952 original size:12 final size:12
Alignment explanation
Indices: 30384930--30384964 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
30384920 ATGTTTCCAT
30384930 TTCTCCATTTTCA
1 TTCT-CATTTTCA
*
30384943 TTTTCATTTTCA
1 TTCTCATTTTCA
30384955 TTCTCATTTT
1 TTCTCATTTT
30384965 GGATAAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 17 0.85
13 3 0.15
ACGTcount: A:0.14, C:0.23, G:0.00, T:0.63
Consensus pattern (12 bp):
TTCTCATTTTCA
Found at i:30384966 original size:69 final size:73
Alignment explanation
Indices: 30384867--30385019 Score: 208
Period size: 74 Copynumber: 2.1 Consensus size: 73
30384857 TTCCAAATGA
* * *
30384867 TTTCATTTCTCCATTTTTATTTTCATTTTGG-T-AAA-A-ATCATAATCATTTCCAAATGTTTCC
1 TTTCATTT-TCCATTTTCATTCTCATTTTGGATAAAACATATCATAATCATTTCCAAATGATTCC
30384928 ATTTCTCCAT
65 -TTTCTCCAT
*
30384938 TTTCATTTT-CATTTTCATTCTCATTTTGGATAAAATCATATCATAATCATTTCCTAATGATTCC
1 TTTCATTTTCCATTTTCATTCTCATTTTGGATAAAA-CATATCATAATCATTTCCAAATGATTCC
30385002 TTTCTCCAT
65 TTTCTCCAT
30385011 TTTCATTTT
1 TTTCATTTT
30385020 TGAGAAAAGC
Statistics
Matches: 73, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
69 18 0.25
70 2 0.03
71 11 0.15
73 19 0.26
74 23 0.32
ACGTcount: A:0.25, C:0.20, G:0.04, T:0.52
Consensus pattern (73 bp):
TTTCATTTTCCATTTTCATTCTCATTTTGGATAAAACATATCATAATCATTTCCAAATGATTCCT
TTCTCCAT
Found at i:30389496 original size:27 final size:26
Alignment explanation
Indices: 30389448--30389630 Score: 226
Period size: 27 Copynumber: 6.8 Consensus size: 26
30389438 GTGAGGCTGC
* *
30389448 CAGATATTGTGAC-GAAGTCACCAGAT
1 CAGATATTGTGGCAG-AGCCACCAGAT
*
30389474 ACAGATATTGTGGCAGAGCCACCAGAA
1 -CAGATATTGTGGCAGAGCCACCAGAT
30389501 CAGATATATGTGGCAGAGCCACCAGAT
1 CAGATAT-TGTGGCAGAGCCACCAGAT
30389528 CAGATATATGTGGCAGAGCCACCAGAT
1 CAGATAT-TGTGGCAGAGCCACCAGAT
* *
30389555 CAAATAATTGTGGCATAGCCACCAGGA-
1 CAGAT-ATTGTGGCAGAGCCACCA-GAT
30389582 CAGATATATGTGGCAGAGCCACCAGAT
1 CAGATAT-TGTGGCAGAGCCACCAGAT
*
30389609 CAGATAATTGTGGCATAGCCAC
1 CAGAT-ATTGTGGCAGAGCCAC
30389631 TAGGACGCTT
Statistics
Matches: 140, Mismatches: 9, Indels: 14
0.86 0.06 0.09
Matches are distributed among these distances:
26 11 0.08
27 122 0.87
28 7 0.05
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGAT
Found at i:30389541 original size:54 final size:54
Alignment explanation
Indices: 30389466--30389630 Score: 255
Period size: 54 Copynumber: 3.1 Consensus size: 54
30389456 GTGACGAAGT
* *
30389466 CACCAGATACAGATAT-TGTGGCAGAGCCACCAGAACAGAT-ATATGTGGCAGAGC
1 CACCAGAT-CAGATATATGTGGCAGAGCCACCAGATCAGATAAT-TGTGGCATAGC
*
30389520 CACCAGATCAGATATATGTGGCAGAGCCACCAGATCAAATAATTGTGGCATAGC
1 CACCAGATCAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGC
30389574 CACCAGGA-CAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGC
1 CACCA-GATCAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGC
30389628 CAC
1 CAC
30389631 TAGGACGCTT
Statistics
Matches: 104, Mismatches: 4, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
53 7 0.07
54 93 0.89
55 4 0.04
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (54 bp):
CACCAGATCAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGC
Found at i:30389569 original size:81 final size:81
Alignment explanation
Indices: 30389466--30389630 Score: 262
Period size: 81 Copynumber: 2.0 Consensus size: 81
30389456 GTGACGAAGT
*
30389466 CACCAGATACAGATATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGCCACCAGATCAG
1 CACCAGATACAAATATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGCCACCAGATCAG
30389531 AT-ATATGTGGCAGAGC
66 ATAAT-TGTGGCAGAGC
* *
30389547 CACCAGAT-CAAATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGCCACCAGATCA
1 CACCAGATACAAAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGCCACCAGATCA
*
30389611 GATAATTGTGGCATAGC
65 GATAATTGTGGCAGAGC
30389628 CAC
1 CAC
30389631 TAGGACGCTT
Statistics
Matches: 78, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
80 4 0.05
81 72 0.92
82 2 0.03
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (81 bp):
CACCAGATACAAATATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGCCACCAGATCAG
ATAATTGTGGCAGAGC
Found at i:30397387 original size:21 final size:22
Alignment explanation
Indices: 30397361--30397422 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 22
30397351 CTTTTACATA
30397361 TATGCTCACACGAGCT-AGAAG
1 TATGCTCACACGAGCTAAGAAG
* *
30397382 TATGCTTACACGAGTTCTGAATAAG
1 TATGCTCACACGAG--CT-AAGAAG
30397407 TATGCTCACACGAGCT
1 TATGCTCACACGAGCT
30397423 GTGGGTCGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 13 0.38
23 4 0.12
25 17 0.50
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (22 bp):
TATGCTCACACGAGCTAAGAAG
Found at i:30400478 original size:39 final size:40
Alignment explanation
Indices: 30400420--30400520 Score: 132
Period size: 39 Copynumber: 2.5 Consensus size: 40
30400410 AAATTGAATG
* *
30400420 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * * *
30400459 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
30400499 ATATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
30400521 GCATTCGTGC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 29 0.55
40 24 0.45
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:30400513 original size:40 final size:40
Alignment explanation
Indices: 30400420--30400602 Score: 181
Period size: 40 Copynumber: 4.6 Consensus size: 40
30400410 AAATTGAATG
* * * * *
30400420 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
30400459 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
30400499 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* * * * * *
30400539 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTG
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* * *
30400579 ATATCCGGGTTAAGTCCCGTAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
30400603 CTTGGTGCGG
Statistics
Matches: 121, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
39 32 0.26
40 87 0.72
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:30404760 original size:17 final size:19
Alignment explanation
Indices: 30404737--30404782 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
30404727 AAGAAGCATG
30404737 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
30404755 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
30404773 AATCATGCTC
1 AATCATGCTC
30404783 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:30411799 original size:40 final size:40
Alignment explanation
Indices: 30411754--30411920 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
30411744 CGGAATATAA
30411754 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
30411794 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
30411834 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
30411874 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
30411913 CCGGATAT
1 CCGGATAT
30411921 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:30411904 original size:80 final size:79
Alignment explanation
Indices: 30411754--30411920 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
30411744 CGGAATATAA
* *
30411754 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
30411819 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
30411834 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
30411896 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
30411913 CCGGATAT
1 CCGGATAT
30411921 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:30412769 original size:17 final size:19
Alignment explanation
Indices: 30412746--30412791 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
30412736 AAGAAGCATG
30412746 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
30412764 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
30412782 AATCATGCTC
1 AATCATGCTC
30412792 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:30414021 original size:40 final size:40
Alignment explanation
Indices: 30413977--30414094 Score: 191
Period size: 40 Copynumber: 3.0 Consensus size: 40
30413967 TTGATATATT
*
30413977 GTATATCCGGGTTAAATCTCGCAGGCTTCGTGCTGGTAAA
1 GTATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAA
*
30414017 GTATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAG
1 GTATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAA
* * *
30414057 GTATATCCGGGTTAATTCCCACAGGCTTAGTGCTGGTA
1 GTATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTA
30414095 CTATATCCGG
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 73 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (40 bp):
GTATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAA
Found at i:30415484 original size:13 final size:14
Alignment explanation
Indices: 30415460--30415490 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
30415450 CCAGAATTGA
30415460 AGAAGAAAAAGAAG
1 AGAAGAAAAAGAAG
30415474 AGAAG-AAAAGAAG
1 AGAAGAAAAAGAAG
30415487 AGAA
1 AGAA
30415491 AGAATAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (14 bp):
AGAAGAAAAAGAAG
Found at i:30417023 original size:43 final size:42
Alignment explanation
Indices: 30416877--30417023 Score: 154
Period size: 44 Copynumber: 3.4 Consensus size: 42
30416867 TGATTTCGTG
* * *
30416877 TAAGACCACGTCTGGGACATTGACATCG-ATTTGAGATTTATGT
1 TAAGACCACGTCTGGGACATTGGCATCGTATTTGATA-TCAT-T
* * * *
30416920 GTAAGACCATGTCTGGGACATTGGCATCGTATATGATTTCATG
1 -TAAGACCACGTCTGGGACATTGGCATCGTATTTGATATCATT
* *
30416963 TAAGACC-CTGTCTGGGACAGTGGCATCGATATTTGATAACATT
1 TAAGACCAC-GTCTGGGACATTGGCATCG-TATTTGATATCATT
30417006 TAAGACCACGTCTGGGAC
1 TAAGACCACGTCTGGGAC
30417024 GTTGTCATTG
Statistics
Matches: 86, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
42 25 0.29
43 26 0.30
44 30 0.35
45 5 0.06
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.30
Consensus pattern (42 bp):
TAAGACCACGTCTGGGACATTGGCATCGTATTTGATATCATT
Found at i:30421952 original size:13 final size:13
Alignment explanation
Indices: 30421934--30421960 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
30421924 TAGGAAAAAC
30421934 TTGAAAAATTTCA
1 TTGAAAAATTTCA
30421947 TTGAAAAATTTCA
1 TTGAAAAATTTCA
30421960 T
1 T
30421961 GCTTTAAGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (13 bp):
TTGAAAAATTTCA
Found at i:30437853 original size:20 final size:20
Alignment explanation
Indices: 30437825--30437878 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
30437815 AAAAGGGGTC
*
30437825 ACACGCCCGTGTGGCTTGGG
1 ACACACCCGTGTGGCTTGGG
30437845 ACACACCCGTGTGGCTTGGG
1 ACACACCCGTGTGGCTTGGG
30437865 ACACACCCGTGTGG
1 ACACACCCGTGTGG
30437879 GAAGGCCGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.15, C:0.31, G:0.35, T:0.19
Consensus pattern (20 bp):
ACACACCCGTGTGGCTTGGG
Found at i:30439911 original size:27 final size:29
Alignment explanation
Indices: 30439879--30440008 Score: 131
Period size: 29 Copynumber: 4.6 Consensus size: 29
30439869 GTGACGAGAT
30439879 TGGCACTAAGTGTGCGTGCTGGAAA-A-A
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
30439906 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * ****
30439935 TGGCACTAAGTGTGCGAGCTCGAAGGGCA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * * *
30439964 TGGCACTATGTGTGCGGGCT-TAAATCTCA
1 TGGCACTAAGTGTGCGTGCTGGAAATAT-A
30439993 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
30440009 AAATCGAGTA
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
27 24 0.29
28 3 0.04
29 57 0.68
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:30439947 original size:29 final size:27
Alignment explanation
Indices: 30439879--30439949 Score: 115
Period size: 27 Copynumber: 2.6 Consensus size: 27
30439869 GTGACGAGAT
*
30439879 TGGCACTAAGTGTGCGTGCTGGAAAAA
1 TGGCACTAAGTGTGCATGCTGGAAAAA
30439906 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAA-A-A
30439935 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
30439950 GAGCTCGAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 24 0.59
28 1 0.02
29 16 0.39
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.25
Consensus pattern (27 bp):
TGGCACTAAGTGTGCATGCTGGAAAAA
Found at i:30446708 original size:40 final size:40
Alignment explanation
Indices: 30446585--30446793 Score: 296
Period size: 40 Copynumber: 5.2 Consensus size: 40
30446575 CGGGATTTAA
* * * * *
30446585 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
30446625 CCGGATTTGGT-GACTTGCACAAAGGCCTTC-GGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
30446664 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
30446704 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
30446744 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
30446784 CCGGATATAT
1 CCGGATATAT
30446794 TTCCAATGTT
Statistics
Matches: 151, Mismatches: 15, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
38 1 0.01
39 29 0.19
40 121 0.80
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:30453910 original size:40 final size:40
Alignment explanation
Indices: 30453802--30454011 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
30453792 CGGGATTTAA
* * * * *
30453802 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
30453842 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
30453882 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
30453922 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
30453962 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
30454002 CCGGATATAT
1 CCGGATATAT
30454012 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:30455463 original size:28 final size:28
Alignment explanation
Indices: 30455365--30455463 Score: 101
Period size: 28 Copynumber: 3.5 Consensus size: 28
30455355 TCACAAATTG
* * * *
30455365 GCACTAAGTGTGCGGGTTCAATTTGTATA
1 GCACTAAGTGTGCGAGTTCGA-CTATATA
* * *
30455394 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTCGACTATATA
30455422 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCGAGTTCGACTATAT-A
*
30455450 GCACTATGTGTGCG
1 GCACTAAGTGTGCG
30455464 GGCTTATTAC
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
27 1 0.02
28 42 0.70
29 17 0.28
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTCGACTATATA
Found at i:30457815 original size:10 final size:10
Alignment explanation
Indices: 30457800--30457824 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
30457790 CCATTTTCAC
30457800 CATTTCTATT
1 CATTTCTATT
30457810 CATTTCTATT
1 CATTTCTATT
30457820 CATTT
1 CATTT
30457825 GATTTAACAT
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:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (10 bp):
CATTTCTATT
Found at i:30463694 original size:40 final size:40
Alignment explanation
Indices: 30463631--30463771 Score: 133
Period size: 40 Copynumber: 3.5 Consensus size: 40
30463621 TGAATGATAC
* ** * *
30463631 CCGGGCTAAGCCCCGAAAACAATTATGCTGGAAATTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATTATAT
* * *** *
30463671 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATTATAT
* *
30463711 CCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTCATTCTAT
1 CCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATTATAT
30463751 CCGGGCTAAGACCCGAAGGCA
1 CCGGGCTAAGACCCGAAGGCA
30463772 TTCGTGCACG
Statistics
Matches: 80, Mismatches: 18, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
39 3 0.04
40 77 0.96
ACGTcount: A:0.28, C:0.26, G:0.27, T:0.20
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATTATAT
Found at i:30463792 original size:40 final size:40
Alignment explanation
Indices: 30463665--30463792 Score: 161
Period size: 40 Copynumber: 3.2 Consensus size: 40
30463655 ATGCTGGAAA
* *
30463665 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * **
30463705 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
30463745 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
30463785 TTATATCC
1 TTATATCC
30463793 AGTTGTATTC
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
39 4 0.05
40 70 0.95
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:30466566 original size:8 final size:9
Alignment explanation
Indices: 30466530--30466563 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
30466520 TTAATTGAAA
30466530 AATTAATTT
1 AATTAATTT
*
30466539 AGTTAATTT
1 AATTAATTT
30466548 AATTAA-TT
1 AATTAATTT
30466556 AATTAATT
1 AATTAATT
30466564 AATATTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (9 bp):
AATTAATTT
Found at i:30486728 original size:29 final size:29
Alignment explanation
Indices: 30486693--30486766 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
30486683 GTTGTGAGAT
* *
30486693 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
30486722 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
30486751 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
30486767 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:30490747 original size:16 final size:17
Alignment explanation
Indices: 30490711--30490749 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
30490701 CAACTTGGGC
*
30490711 CGTGTGGGCCACACGGG
1 CGTGTGGGCCACACAGG
30490728 CGTGTGGGCC-CACAGG
1 CGTGTGGGCCACACAGG
30490744 CGTGTG
1 CGTGTG
30490750 AGATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.10, C:0.28, G:0.46, T:0.15
Consensus pattern (17 bp):
CGTGTGGGCCACACAGG
Found at i:30495613 original size:83 final size:83
Alignment explanation
Indices: 30495471--30495636 Score: 278
Period size: 83 Copynumber: 2.0 Consensus size: 83
30495461 TGTTTATGAG
* *
30495471 AACGCGCCGAAGTCCACGATCACCAACTTTGGTACATCCTACATTGAATCTTAATCACTTCCCCC
1 AACGCGCCGAAGTCCACGATCACCAACTTTGGCACATCCTACATTGAATCTTAACCACTTCCCCC
30495536 CTCACCAACTCATCTGGT
66 CTCACCAACTCATCTGGT
* * * *
30495554 AACGCGCTGAAGTCCACGATCACCAACTTTGGCACATCCTGCATTGAGTCTTAACCACTTTCCCC
1 AACGCGCCGAAGTCCACGATCACCAACTTTGGCACATCCTACATTGAATCTTAACCACTTCCCCC
30495619 CTCACCAACTCATCTGGT
66 CTCACCAACTCATCTGGT
30495637 TCGCTCTATT
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 77 1.00
ACGTcount: A:0.25, C:0.36, G:0.13, T:0.25
Consensus pattern (83 bp):
AACGCGCCGAAGTCCACGATCACCAACTTTGGCACATCCTACATTGAATCTTAACCACTTCCCCC
CTCACCAACTCATCTGGT
Found at i:30506902 original size:44 final size:44
Alignment explanation
Indices: 30506836--30506922 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
30506826 CTATTTTTTA
*
30506836 TTTCCCACTTAAACTCTGATTAGTATAGGTTATTTTAATATTAG
1 TTTCCCACTAAAACTCTGATTAGTATAGGTTATTTTAATATTAG
*
30506880 TTTCCCACTAAAACTCTTATTAGTATAGGTTATTTTAATATTA
1 TTTCCCACTAAAACTCTGATTAGTATAGGTTATTTTAATATTA
30506923 TTTGACTTAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.46
Consensus pattern (44 bp):
TTTCCCACTAAAACTCTGATTAGTATAGGTTATTTTAATATTAG
Found at i:30507665 original size:17 final size:17
Alignment explanation
Indices: 30507645--30507693 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
30507635 AAATACATAC
30507645 AATTACTTTATATAATT
1 AATTACTTTATATAATT
*
30507662 AATTACATTAGTA-AATT
1 AATTACTTTA-TATAATT
*
30507679 AA--ATTTTATATAATT
1 AATTACTTTATATAATT
30507694 TTAACTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
14 2 0.07
15 8 0.30
17 15 0.56
18 2 0.07
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (17 bp):
AATTACTTTATATAATT
Found at i:30517311 original size:35 final size:35
Alignment explanation
Indices: 30517265--30517337 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
30517255 GAGCTAAGAT
30517265 GGTACATAACATTTAAACTTCAAGATTATATGAAA
1 GGTACATAACATTTAAACTTCAAGATTATATGAAA
30517300 GGTACATAACATTTAAACTTCAAGATTATATGAAA
1 GGTACATAACATTTAAACTTCAAGATTATATGAAA
30517335 GGT
1 GGT
30517338 TAACCTAGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.32
Consensus pattern (35 bp):
GGTACATAACATTTAAACTTCAAGATTATATGAAA
Found at i:30525118 original size:28 final size:30
Alignment explanation
Indices: 30525060--30525119 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 30
30525050 TATCTCTACT
* * *
30525060 TTTTATTTTTAAAAATATTATTTTTATTTA
1 TTTTATTTTTAAAAATATTAGTTCTAGTTA
*
30525090 TTTTA-TTTT-AAAATTTTAGTTCTAGTTA
1 TTTTATTTTTAAAAATATTAGTTCTAGTTA
30525118 TT
1 TT
30525120 ACCACTTTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 17 0.65
29 4 0.15
30 5 0.19
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (30 bp):
TTTTATTTTTAAAAATATTAGTTCTAGTTA
Found at i:30529512 original size:279 final size:279
Alignment explanation
Indices: 30529012--30529577 Score: 1080
Period size: 279 Copynumber: 2.0 Consensus size: 279
30529002 GTCAATAATG
*
30529012 TGCTCAATTTAAAGTGCCAAAATGCATATGTGAATCATGTAACATAGCCATTTTAATATCAAATT
1 TGCTCAATTTAAAGTGCCAAAATGCATATGTAAATCATGTAACATAGCCATTTTAATATCAAATT
30529077 AAATCTAGCATACCAATTAACTATTATCAATGTTCATTTATCAATTGAAATATCAACATACCATG
66 AAATCTAGCATACCAATTAACTATTATCAATGTTCATTTATCAATTGAAATATCAACATACCATG
* *
30529142 GACCAAAAACTCTAGCATACTTGCTTAGTTCACCATTATAATCAACCAAATCATGCACATAAAAT
131 GACCAAAAACTCTAACATACTTGCTTAGTTCACCATTATAATCAACCAAATCAAGCACATAAAAT
30529207 CACTAGATGTTCACTTACCAACACTTAACAAAAAATTCATCACTTAAACATATATCAACAATCTT
196 CACTAGATGTTCACTTACCAACACTTAACAAAAAATTCATCACTTAAACATATATCAACAATCTT
30529272 GCAAAATTAACCACCCAAA
261 GCAAAATTAACCACCCAAA
30529291 TGCTCAATTTAAAGTGCCAAAATGCATATGTAAATCATGTAACATAGCCATTTTAATATCAAATT
1 TGCTCAATTTAAAGTGCCAAAATGCATATGTAAATCATGTAACATAGCCATTTTAATATCAAATT
30529356 AAATCTAGCATACCAATTAACTATTATCAATGTTCATTTATCAATTGAAATATCAACATACCATG
66 AAATCTAGCATACCAATTAACTATTATCAATGTTCATTTATCAATTGAAATATCAACATACCATG
30529421 GACCAAAAACTCTAACATACTTGCTTAGTTCACCATTATAATCAACCAAATCAAGCACATAAAAT
131 GACCAAAAACTCTAACATACTTGCTTAGTTCACCATTATAATCAACCAAATCAAGCACATAAAAT
*
30529486 CACTAGATGTTCACTTACCAACACTTAACAAAAAATTCATCACTTAAACATATATCAATAATCTT
196 CACTAGATGTTCACTTACCAACACTTAACAAAAAATTCATCACTTAAACATATATCAACAATCTT
30529551 GCAAAATTAACCACCCAAA
261 GCAAAATTAACCACCCAAA
*
30529570 -ACTCAATT
1 TGCTCAATT
30529578 AAATATTTGC
Statistics
Matches: 282, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
278 7 0.02
279 275 0.98
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (279 bp):
TGCTCAATTTAAAGTGCCAAAATGCATATGTAAATCATGTAACATAGCCATTTTAATATCAAATT
AAATCTAGCATACCAATTAACTATTATCAATGTTCATTTATCAATTGAAATATCAACATACCATG
GACCAAAAACTCTAACATACTTGCTTAGTTCACCATTATAATCAACCAAATCAAGCACATAAAAT
CACTAGATGTTCACTTACCAACACTTAACAAAAAATTCATCACTTAAACATATATCAACAATCTT
GCAAAATTAACCACCCAAA
Found at i:30531778 original size:7 final size:6
Alignment explanation
Indices: 30531770--30531838 Score: 77
Period size: 7 Copynumber: 10.8 Consensus size: 6
30531760 GGAAGTTATC
*
30531770 ATTTTT CATTTTT ATTTTGT ATTTTT A-TTTT ATCCTTT ATTTTT CATTTTT
1 ATTTTT -ATTTTT ATTTT-T ATTTTT ATTTTT AT-TTTT ATTTTT -ATTTTT
30531821 ATTTTGT ATTTTT ATTTT
1 ATTTT-T ATTTTT ATTTT
30531839 ATCCTTTTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
5 5 0.09
6 21 0.38
7 29 0.53
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.75
Consensus pattern (6 bp):
ATTTTT
Found at i:30531793 original size:13 final size:12
Alignment explanation
Indices: 30531770--30531838 Score: 77
Period size: 13 Copynumber: 5.4 Consensus size: 12
30531760 GGAAGTTATC
30531770 ATTTTTCATTTTT
1 ATTTTT-ATTTTT
30531783 ATTTTGTATTTTT
1 ATTTT-TATTTTT
*
30531796 A-TTTTATCCTTT
1 ATTTTTAT-TTTT
30531808 ATTTTTCATTTTT
1 ATTTTT-ATTTTT
30531821 ATTTTGTATTTTT
1 ATTTT-TATTTTT
30531834 ATTTT
1 ATTTT
30531839 ATCCTTTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
11 3 0.06
12 7 0.14
13 35 0.71
14 4 0.08
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.75
Consensus pattern (12 bp):
ATTTTTATTTTT
Found at i:30531812 original size:38 final size:38
Alignment explanation
Indices: 30531770--30531851 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
30531760 GGAAGTTATC
30531770 ATTTTTCATTTTTATTTTGTATTTTTATTTTATCCTTT
1 ATTTTTCATTTTTATTTTGTATTTTTATTTTATCCTTT
30531808 ATTTTTCATTTTTATTTTGTATTTTTATTTTATCCTTT
1 ATTTTTCATTTTTATTTTGTATTTTTATTTTATCCTTT
*
30531846 TTTTTT
1 ATTTTT
30531852 AAATTTCAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (38 bp):
ATTTTTCATTTTTATTTTGTATTTTTATTTTATCCTTT
Found at i:30531846 original size:13 final size:13
Alignment explanation
Indices: 30531792--30531852 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 13
30531782 TATTTTGTAT
30531792 TTTTATTTTATCC
1 TTTTATTTTATCC
*
30531805 -TTTATTTT-TCAT
1 TTTTATTTTATC-C
* **
30531817 TTTTATTTTGTAT
1 TTTTATTTTATCC
30531830 TTTTATTTTATCC
1 TTTTATTTTATCC
*
30531843 TTTTTTTTTA
1 TTTTATTTTA
30531853 AATTTCAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
11 2 0.05
12 8 0.21
13 28 0.72
14 1 0.03
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (13 bp):
TTTTATTTTATCC
Found at i:30531857 original size:26 final size:26
Alignment explanation
Indices: 30531777--30531857 Score: 71
Period size: 25 Copynumber: 3.2 Consensus size: 26
30531767 ATCATTTTTC
30531777 ATTTTTATTTTGT-ATTTTTATTTT--
1 ATTTTTATTTT-TCATTTTTATTTTAA
* **
30531801 ATCCTTTATTTTTCATTTTTATTTTGT
1 AT-TTTTATTTTTCATTTTTATTTTAA
*
30531828 ATTTTTATTTTATCCTTTTT-TTTTAA
1 ATTTTTATTTT-TCATTTTTATTTTAA
30531854 ATTT
1 ATTT
30531858 CAATTTTCTT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
24 3 0.06
25 19 0.40
26 16 0.34
27 9 0.19
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.74
Consensus pattern (26 bp):
ATTTTTATTTTTCATTTTTATTTTAA
Found at i:30539840 original size:30 final size:30
Alignment explanation
Indices: 30539768--30539845 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 30
30539758 CGTATGTTTT
* * *
30539768 AACTCAGTGTGTTACACGGTCGTGTGTCAC
1 AACTCAGTGAGTTACACAGTCGTGTGGCAC
* * *
30539798 AAGTCAGAGAGTTACACAGTCGTGTGGCCC
1 AACTCAGTGAGTTACACAGTCGTGTGGCAC
*
30539828 AACTTAGTGAGTTACACA
1 AACTCAGTGAGTTACACA
30539846 AGTAGGGACA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.26
Consensus pattern (30 bp):
AACTCAGTGAGTTACACAGTCGTGTGGCAC
Done.