Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 140 of 161
Found at i:43591781 original size:18 final size:16
Alignment explanation
Indices: 43591748--43591782 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
43591738 TTTGTTTATA
43591748 ATTTTAAAAATTAATT
1 ATTTTAAAAATTAATT
43591764 ATTTTAAATAATTTAATT
1 ATTTTAAA-AA-TTAATT
43591782 A
1 A
43591783 AAGTTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 2 0.12
18 7 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTTAAAAATTAATT
Found at i:43596496 original size:19 final size:19
Alignment explanation
Indices: 43596474--43596511 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
43596464 ATGGGAAAAT
43596474 AAAGAA-AAAAAGAAAATTA
1 AAAGAACAAAAA-AAAATTA
*
43596493 AAAGAACATAAAAAAATTA
1 AAAGAACAAAAAAAAATTA
43596512 TTAAATTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.76, C:0.03, G:0.08, T:0.13
Consensus pattern (19 bp):
AAAGAACAAAAAAAAATTA
Found at i:43598283 original size:58 final size:58
Alignment explanation
Indices: 43598153--43598289 Score: 170
Period size: 58 Copynumber: 2.4 Consensus size: 58
43598143 TATTGTTATT
*
43598153 AAATTTTAATA-AGATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACC
1 AAATTTTAATATA-ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACA
* * * * * * *
43598211 ATACTTTAACATAATTATTATTAAATATAATTTAAT-AAAATAATATATACTTTAATA
1 AAATTTTAATATAATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACA
43598268 AAATTCTTAATATAATTATTAT
1 AAATT-TTAATATAATTATTAT
43598290 ATGAATTAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
57 20 0.30
58 45 0.68
59 1 0.02
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (58 bp):
AAATTTTAATATAATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACA
Found at i:43610301 original size:22 final size:21
Alignment explanation
Indices: 43610263--43610303 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
43610253 TTAAAAATAT
*
43610263 GATTTTTTAAATGTTTTTACA
1 GATTTTTTAAATATTTTTACA
*
43610284 GATTTTTTTAATAATTTTTA
1 GATTTTTTAAAT-ATTTTTA
43610304 ATCTAAGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.61
Consensus pattern (21 bp):
GATTTTTTAAATATTTTTACA
Found at i:43616987 original size:15 final size:14
Alignment explanation
Indices: 43616966--43617001 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
43616956 ATAATCCTTA
*
43616966 ATAATTATCTTAAT
1 ATAATTATCCTAAT
43616980 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
43616995 ATAATTA
1 ATAATTA
43617002 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:43617289 original size:15 final size:15
Alignment explanation
Indices: 43617269--43617298 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
43617259 TGTTATCACA
43617269 TTGTTATGTTCTTGT
1 TTGTTATGTTCTTGT
43617284 TTGTTATGTTCTTGT
1 TTGTTATGTTCTTGT
43617299 CAAAATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.07, G:0.20, T:0.67
Consensus pattern (15 bp):
TTGTTATGTTCTTGT
Found at i:43618258 original size:69 final size:69
Alignment explanation
Indices: 43618147--43618356 Score: 235
Period size: 69 Copynumber: 3.0 Consensus size: 69
43618137 CGACCTTCTA
* * *
43618147 TATAAAGGCTCATTGATTTAAAATCGCA--ACCTCAAAAGCAGCTTGCGGACCTACGTTCCTAGT
1 TATAAAGGCTCATTGATTTAAAATCGCAGCCCCTC-AAA-CAGCTTGCGGACCTACGTTCCCAGC
43618210 TGATAT
64 TGATAT
* *
43618216 TATAAAGGCTCATTGATTTAAGATCGCAGCCCCTCAAACAGCTTACGGACCTACGTTCCCAGCTG
1 TATAAAGGCTCATTGATTTAAAATCGCAGCCCCTCAAACAGCTTGCGGACCTACGTTCCCAGCTG
43618281 ATAT
66 ATAT
** * * ** * * * * *
43618285 TATAAAGGCTCGCTGATTTAATATCGTAGCCTTTAAAATAGCTCGCGGACTTACGTTCCCAACTG
1 TATAAAGGCTCATTGATTTAAAATCGCAGCCCCTCAAACAGCTTGCGGACCTACGTTCCCAGCTG
43618350 ATGAT
66 AT-AT
43618355 TA
1 TA
43618357 AATGTTAGCT
Statistics
Matches: 121, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
69 110 0.91
70 7 0.06
71 4 0.03
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (69 bp):
TATAAAGGCTCATTGATTTAAAATCGCAGCCCCTCAAACAGCTTGCGGACCTACGTTCCCAGCTG
ATAT
Found at i:43618543 original size:103 final size:104
Alignment explanation
Indices: 43618324--43618693 Score: 471
Period size: 104 Copynumber: 3.6 Consensus size: 104
43618314 CCTTTAAAAT
* * *
43618324 AGCTCGCGGACTTACGTTCCCAACTGATGATTAAATGTTAGCTGAGTTAAGCTCGA-AACCACCA
1 AGCTCGCTGACCTACGTTCCCAACTGATGATTAAATGTTAGCTGAGTTAAGCTC-ACAACCTCCA
* * *
43618388 GTTATTTGAGTTAGCTGAGTTAAGCTCACAACT-CTAAAGT
65 GTTATTTGAGTTAGCCGAGTTAAGCTCACAACTCCGAAA-C
* * * *
43618428 AGCTCG-TGGACCTATGTTCCCAATTGATGATTAAATGTTGGATGAGTTAAGCTCACAA-CTCCA
1 AGCTCGCT-GACCTACGTTCCCAACTGATGATTAAATGTTAGCTGAGTTAAGCTCACAACCTCCA
* *
43618491 ATTATTTGAGTTAGCCGAGTTAAGCTCATAACTCCGAAAC
65 GTTATTTGAGTTAGCCGAGTTAAGCTCACAACTCCGAAAC
* * * * *
43618531 AACTTGCTGACCTACGTTCCCAACTAATGATTAAAGGTTAGCTGAGTTAAGCTCGCAACCTCCAG
1 AGCTCGCTGACCTACGTTCCCAACTGATGATTAAATGTTAGCTGAGTTAAGCTCACAACCTCCAG
*
43618596 TTATTTGAGTTAGCCGAGTTAAGCTCGCAACTCCGAAAC
66 TTATTTGAGTTAGCCGAGTTAAGCTCACAACTCCGAAAC
* * * *
43618635 AGCTCGC-GAACCTACATTCCCAGCTGATGATTAAAAGTTAGCTGAGTTAAGCTCGCAAC
1 AGCTCGCTG-ACCTACGTTCCCAACTGATGATTAAATGTTAGCTGAGTTAAGCTCACAAC
43618694 TAAGTTCTTT
Statistics
Matches: 230, Mismatches: 30, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
103 83 0.36
104 147 0.64
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.28
Consensus pattern (104 bp):
AGCTCGCTGACCTACGTTCCCAACTGATGATTAAATGTTAGCTGAGTTAAGCTCACAACCTCCAG
TTATTTGAGTTAGCCGAGTTAAGCTCACAACTCCGAAAC
Found at i:43618628 original size:104 final size:103
Alignment explanation
Indices: 43618326--43618744 Score: 470
Period size: 104 Copynumber: 4.0 Consensus size: 103
43618316 TTTAAAATAG
* * * *
43618326 CTCGCGGACTTACGTTCCCAACTGATGATTAAATGTTAGCTGAGTTAAGCTCGAAACCACCAGTT
1 CTCGCTGACCTACGTTCCCAACTGATGATTAAATGTTAGCTGAGTTAAGCTCGCAA-CTCCAGTT
* * * *
43618391 ATTTGAGTTAGCTGAGTTAAGCTCACAACT-CTAAAGTAG
65 ATTTGAGTTAGCCGAGTTAAGCTCACAACTCCGAAA-CAA
* * * * * *
43618430 CTCG-TGGACCTATGTTCCCAATTGATGATTAAATGTTGGATGAGTTAAGCTCACAACTCCAATT
1 CTCGCT-GACCTACGTTCCCAACTGATGATTAAATGTTAGCTGAGTTAAGCTCGCAACTCCAGTT
*
43618494 ATTTGAGTTAGCCGAGTTAAGCTCATAACTCCGAAACAA
65 ATTTGAGTTAGCCGAGTTAAGCTCACAACTCCGAAACAA
* * *
43618533 CTTGCTGACCTACGTTCCCAACTAATGATTAAAGGTTAGCTGAGTTAAGCTCGCAACCTCCAGTT
1 CTCGCTGACCTACGTTCCCAACTGATGATTAAATGTTAGCTGAGTTAAGCTCGCAA-CTCCAGTT
* *
43618598 ATTTGAGTTAGCCGAGTTAAGCTCGCAACTCCGAAACAG
65 ATTTGAGTTAGCCGAGTTAAGCTCACAACTCCGAAACAA
* * * *
43618637 CTCGC-GAACCTACATTCCCAGCTGATGATTAAAAGTTAGCTGAGTTAAGCTCGCAACT-AAGTT
1 CTCGCTG-ACCTACGTTCCCAACTGATGATTAAATGTTAGCTGAGTTAAGCTCGCAACTCCAGTT
* * * * *
43618700 CTTTTGAGTTAGCTGATTTAAAGATCGCAACTCTC-AAACAA
65 -ATTTGAGTTAGCCGAGTT-AAGCTCACAACTC-CGAAACAA
43618741 CTCG
1 CTCG
43618745 TTGATTTAAA
Statistics
Matches: 269, Mismatches: 38, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
102 4 0.01
103 99 0.37
104 165 0.61
105 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (103 bp):
CTCGCTGACCTACGTTCCCAACTGATGATTAAATGTTAGCTGAGTTAAGCTCGCAACTCCAGTTA
TTTGAGTTAGCCGAGTTAAGCTCACAACTCCGAAACAA
Found at i:43618708 original size:207 final size:206
Alignment explanation
Indices: 43618336--43618712 Score: 533
Period size: 207 Copynumber: 1.8 Consensus size: 206
43618326 CTCGCGGACT
* *
43618336 TACGTTCCCAACTGATGATTAAATGTTAGCTGAGTTAAGCTCGAAACCACCAGTTATTTGAGTTA
1 TACGTTCCCAACTAATGATTAAAGGTTAGCTGAGTTAAGCTCGAAACCACCAGTTATTTGAGTTA
* * * * * ** * *
43618401 GCTGAGTTAAGCTCACAACTCTAAAGTAGCTCGTGGACCTATGTTCCCAATTGATGATTAAATGT
66 GCCGAGTTAAGCTCACAACTCGAAAGCAGCTCGCGAACCTACATTCCCAACTGATGATTAAAAGT
*
43618466 TGGATGAGTTAAGCTCACAACTCCAATTATTTGAGTTAGCCGAGTTAAGCTCATAACTCCGAAAC
131 TAGATGAGTTAAGCTCACAACT-CAATTATTTGAGTTAGCCGAGTTAAGCTCATAACTCCGAAAC
43618531 AACTTGCTGACC
195 AACTTGCTGACC
* *
43618543 TACGTTCCCAACTAATGATTAAAGGTTAGCTGAGTTAAGCTCGCAACCTCCAGTTATTTGAGTTA
1 TACGTTCCCAACTAATGATTAAAGGTTAGCTGAGTTAAGCTCGAAACCACCAGTTATTTGAGTTA
* *
43618608 GCCGAGTTAAGCTCGCAACTCCGAAA-CAGCTCGCGAACCTACATTCCCAGCTGATGATTAAAAG
66 GCCGAGTTAAGCTCACAACT-CGAAAGCAGCTCGCGAACCTACATTCCCAACTGATGATTAAAAG
* * *
43618672 TTAGCTGAGTTAAGCTCGCAACT-AAGTTCTTTTGAGTTAGC
130 TTAGATGAGTTAAGCTCACAACTCAA-TT-ATTTGAGTTAGC
43618713 TGATTTAAAG
Statistics
Matches: 148, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
205 2 0.01
206 2 0.01
207 140 0.95
208 4 0.03
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (206 bp):
TACGTTCCCAACTAATGATTAAAGGTTAGCTGAGTTAAGCTCGAAACCACCAGTTATTTGAGTTA
GCCGAGTTAAGCTCACAACTCGAAAGCAGCTCGCGAACCTACATTCCCAACTGATGATTAAAAGT
TAGATGAGTTAAGCTCACAACTCAATTATTTGAGTTAGCCGAGTTAAGCTCATAACTCCGAAACA
ACTTGCTGACC
Found at i:43621621 original size:13 final size:13
Alignment explanation
Indices: 43621599--43621628 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
43621589 TTGTTCTGTG
43621599 TTTT-TTTATTTA
1 TTTTATTTATTTA
43621611 TTTTATTTATTTA
1 TTTTATTTATTTA
43621624 TTTTA
1 TTTTA
43621629 AACTATGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTATTTATTTA
Found at i:43621833 original size:8 final size:8
Alignment explanation
Indices: 43621820--43621884 Score: 67
Period size: 8 Copynumber: 7.9 Consensus size: 8
43621810 GGTGTTGTTG
43621820 GTTTATTT
1 GTTTATTT
43621828 GTTTATTT
1 GTTTATTT
* *
43621836 GTATGTTT
1 GTTTATTT
43621844 GTTTATTT
1 GTTTATTT
* *
43621852 GTTCAATT
1 GTTTATTT
*
43621860 ATTTCATTT
1 GTTT-ATTT
43621869 CGTTTATTT
1 -GTTTATTT
43621878 GTTTATT
1 GTTTATT
43621885 AAATTGTGAT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
8 35 0.78
9 7 0.16
10 3 0.07
ACGTcount: A:0.15, C:0.05, G:0.12, T:0.68
Consensus pattern (8 bp):
GTTTATTT
Found at i:43623910 original size:18 final size:18
Alignment explanation
Indices: 43623887--43623929 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
43623877 GAATAGGTTT
43623887 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
43623905 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
43623923 TTAATTA
1 TTAATTA
43623930 CACATTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:43636212 original size:3 final size:3
Alignment explanation
Indices: 43636204--43636236 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
43636194 ATAATTAAAT
43636204 AGA AGA AGA AGA AGA AGA AGA AGA AGA A-A AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
43636237 ACTCACCGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:43641236 original size:50 final size:50
Alignment explanation
Indices: 43641161--43641348 Score: 259
Period size: 50 Copynumber: 3.6 Consensus size: 50
43641151 GATAATAACA
* *
43641161 TGCCAAAGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
43641211 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
43641261 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
43641316 ATGCCAATGCCATGTCCCAGACATGGTCTTACA
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACA
43641349 TGATTCGTAT
Statistics
Matches: 122, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
50 86 0.70
53 2 0.02
54 1 0.01
55 2 0.02
56 31 0.25
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.24
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:43641448 original size:13 final size:13
Alignment explanation
Indices: 43641427--43641458 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
43641417 GCTTGGATCA
*
43641427 TCATCAAATAAAT
1 TCATAAAATAAAT
43641440 TCATAAAATAAAT
1 TCATAAAATAAAT
43641453 TCATAA
1 TCATAA
43641459 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:43641705 original size:30 final size:30
Alignment explanation
Indices: 43641670--43641727 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
43641660 CCTCGACTCT
*
43641670 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
43641700 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
43641728 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:43653014 original size:17 final size:18
Alignment explanation
Indices: 43652992--43653027 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
43652982 TATATTTGTC
43652992 ATATATTATAAA-AATTA
1 ATATATTATAAATAATTA
*
43653009 ATATATTTTAAATAATTA
1 ATATATTATAAATAATTA
43653027 A
1 A
43653028 AAAATAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATATTATAAATAATTA
Found at i:43653728 original size:34 final size:30
Alignment explanation
Indices: 43653682--43653749 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
43653672 ATAAAAAATA
* *
43653682 ACCAAAATATT-ATA-AATTTTTTTTATTT
1 ACCAAAATATTAATATTATTTTTATTATTT
43653710 ACCAAAATATTAATATTATTTTTATTATTT
1 ACCAAAATATTAATATTATTTTTATTATTT
43653740 ACCAAAATAT
1 ACCAAAATAT
43653750 ATAAAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 11 0.31
29 3 0.08
30 22 0.61
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (30 bp):
ACCAAAATATTAATATTATTTTTATTATTT
Found at i:43653882 original size:27 final size:27
Alignment explanation
Indices: 43653818--43653883 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
43653808 AGGCCAATGG
*
43653818 CATTGGCGACACCAAAGGTGCCAAAAC
1 CATTGGCGGCACCAAAGGTGCCAAAAC
* *
43653845 CATTGGTGGCACCAATGGTGCCAAAAC
1 CATTGGCGGCACCAAAGGTGCCAAAAC
43653872 CATTGGCGGCAC
1 CATTGGCGGCAC
43653884 TACTCGTGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.30, C:0.29, G:0.26, T:0.15
Consensus pattern (27 bp):
CATTGGCGGCACCAAAGGTGCCAAAAC
Found at i:43654129 original size:3 final size:3
Alignment explanation
Indices: 43654121--43654145 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
43654111 TTTTAGTTAG
43654121 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
43654146 GTAGAAGCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:43657918 original size:17 final size:18
Alignment explanation
Indices: 43657896--43657931 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
43657886 TATACTTGTT
43657896 ATATATTATAAA-AATTA
1 ATATATTATAAATAATTA
*
43657913 ATATATTTTAAATAATTA
1 ATATATTATAAATAATTA
43657931 A
1 A
43657932 AAAATAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATATTATAAATAATTA
Found at i:43659266 original size:18 final size:18
Alignment explanation
Indices: 43659186--43659273 Score: 70
Period size: 18 Copynumber: 4.6 Consensus size: 18
43659176 TACATTTTCA
*
43659186 TTTCATTTAAATTAATTT-T
1 TTTCATTTAAGTT--TTTAT
*
43659205 TTTCATTTAAATTTAATTAT
1 TTTCATTTAAGTTT--TTAT
*
43659225 TTCTCATTTCAAAATTTTTAT
1 TT-TCATTT--AAGTTTTTAT
*
43659246 TTTCATTTAAGTTTTTGT
1 TTTCATTTAAGTTTTTAT
43659264 TTTCATTTAA
1 TTTCATTTAA
43659274 ATTTATAATT
Statistics
Matches: 61, Mismatches: 2, Indels: 13
0.80 0.03 0.17
Matches are distributed among these distances:
17 1 0.02
18 18 0.30
19 15 0.25
20 9 0.15
21 12 0.20
23 6 0.10
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTCATTTAAGTTTTTAT
Found at i:43659814 original size:6 final size:6
Alignment explanation
Indices: 43659791--43659853 Score: 57
Period size: 5 Copynumber: 11.5 Consensus size: 6
43659781 TCTTCTTTTT
* * *
43659791 TTTC-A TTTC-A TTTCAA TTTTAA TTTCAA TTTC-A TTTGAA TTTCCA
1 TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
43659836 TTTC-A TTTC-A TTT-AA TTT
1 TTTCAA TTTCAA TTTCAA TTT
43659854 ATATTTTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
5 26 0.52
6 24 0.48
ACGTcount: A:0.25, C:0.14, G:0.02, T:0.59
Consensus pattern (6 bp):
TTTCAA
Found at i:43659841 original size:17 final size:17
Alignment explanation
Indices: 43659795--43659843 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
43659785 CTTTTTTTTC
*
43659795 ATTT-CATTTCAATTTTA
1 ATTTCCATTTC-ATTTGA
*
43659812 ATTTCAATTTCATTTGA
1 ATTTCCATTTCATTTGA
43659829 ATTTCCATTTCATTT
1 ATTTCCATTTCATTT
43659844 CATTTAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 23 0.82
18 5 0.18
ACGTcount: A:0.27, C:0.14, G:0.02, T:0.57
Consensus pattern (17 bp):
ATTTCCATTTCATTTGA
Found at i:43659877 original size:22 final size:21
Alignment explanation
Indices: 43659844--43659918 Score: 100
Period size: 21 Copynumber: 3.6 Consensus size: 21
43659834 CATTTCATTT
43659844 CATTT-AATTTATATTTTTTTC
1 CATTTAAATTTAT-TTTTTTTC
*
43659865 CATTTAAATTTATTTTTTATTT
1 CATTTAAATTTATTTTTT-TTC
*
43659887 CATTTAAA-TTATCTTTTTTC
1 CATTTAAATTTATTTTTTTTC
43659907 CATTTAAATTTA
1 CATTTAAATTTA
43659919 ATTTCTTCCC
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.21
21 21 0.44
22 17 0.35
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (21 bp):
CATTTAAATTTATTTTTTTTC
Found at i:43659939 original size:27 final size:26
Alignment explanation
Indices: 43659907--43660155 Score: 172
Period size: 27 Copynumber: 10.0 Consensus size: 26
43659897 ATCTTTTTTC
* *
43659907 CATTTAAATTTAATTTCTTCCCCATTT
1 CATTTAAATTT-ATTTCTTTCTCATTT
**
43659934 CATTTAAA-TTA--TCTTTCT--TCC
1 CATTTAAATTTATTTCTTTCTCATTT
* *
43659955 CATTTTAATTTATTTTTTTCTCATTT
1 CATTTAAATTTATTTCTTTCTCATTT
* *
43659981 CATTTAAATTTTATTTTTTTCTTATTT
1 CATTTAAA-TTTATTTCTTTCTCATTT
*
43660008 CATTTAAA-TTA--TCTTT-T--TTGC
1 CATTTAAATTTATTTCTTTCTCATT-T
*
43660029 CATTTAAATTTAATTTCTTCCTCATTT
1 CATTTAAATTT-ATTTCTTTCTCATTT
* *
43660056 CATTTAAA-TTA--TCCTTCT--TTC
1 CATTTAAATTTATTTCTTTCTCATTT
*
43660077 CATTTTAATTTATTTCTTTCTCATTT
1 CATTTAAATTTATTTCTTTCTCATTT
* *
43660103 CATTTAAATTTAATTTTTTTCTCTTTT
1 CATTTAAATTT-ATTTCTTTCTCATTT
* *
43660130 CATTTAAGTTATCTTTCTTT-TCATTT
1 CATTTAAATT-TATTTCTTTCTCATTT
43660156 TAATTTACAT
Statistics
Matches: 174, Mismatches: 27, Indels: 43
0.71 0.11 0.18
Matches are distributed among these distances:
20 2 0.01
21 25 0.14
22 9 0.05
23 15 0.09
24 12 0.07
25 9 0.05
26 30 0.17
27 69 0.40
28 3 0.02
ACGTcount: A:0.22, C:0.16, G:0.01, T:0.61
Consensus pattern (26 bp):
CATTTAAATTTATTTCTTTCTCATTT
Found at i:43659939 original size:47 final size:43
Alignment explanation
Indices: 43659839--43659999 Score: 171
Period size: 47 Copynumber: 3.6 Consensus size: 43
43659829 ATTTCCATTT
* *
43659839 CATTTCATTTAATTTATATTTTTTTCCATTTAAATTTATTTTT-
1 CATTTCATTTAAATTAT-CTTTTTTCCATTTAAATTTATTTTTC
*
43659882 TATTTCATTTAAATTATCTTTTTTCCATTTAAATTTAATTTCTTCCC
1 CATTTCATTTAAATTATCTTTTTTCCATTTAAATTT-ATTT-TT--C
* *
43659929 CATTTCATTTAAATTATCTTTCTTCCCATTTTAATTTATTTTTTTC
1 CATTTCATTTAAATTATCTTT-TTTCCATTTAAATTTA--TTTTTC
* *
43659975 TCATTTCATTTAAATTTTATTTTTT
1 -CATTTCATTTAAATTATCTTTTTT
43660000 TCTTATTTCA
Statistics
Matches: 100, Mismatches: 9, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
42 18 0.18
43 19 0.19
44 2 0.02
46 3 0.03
47 40 0.40
48 15 0.15
49 3 0.03
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (43 bp):
CATTTCATTTAAATTATCTTTTTTCCATTTAAATTTATTTTTC
Found at i:43659979 original size:21 final size:22
Alignment explanation
Indices: 43659846--43659980 Score: 66
Period size: 21 Copynumber: 6.1 Consensus size: 22
43659836 TTTCATTTCA
*
43659846 TTTAATTTATATTTTTT-TCCAT
1 TTTAATTTATCTTTTTTCT-CAT
* *
43659868 TTAAATTTAT-TTTTTATTTCA-
1 TTTAATTTATCTTTTT-TCTCAT
*
43659889 TTTAAATTATCTTTTTTC-CAT
1 TTTAATTTATCTTTTTTCTCAT
* * * *
43659910 TTAAATTTAAT-TTCTTCCCCATTT
1 TTTAATTT-ATCTTTTTTCTCA--T
* * *
43659934 CATTTAAATTATCTTTCTTCCCAT
1 --TTTAATTTATCTTTTTTCTCAT
43659958 TTTAATTTAT-TTTTTTCTCAT
1 TTTAATTTATCTTTTTTCTCAT
43659979 TT
1 TT
43659981 CATTTAAATT
Statistics
Matches: 86, Mismatches: 16, Indels: 23
0.69 0.13 0.18
Matches are distributed among these distances:
20 2 0.02
21 36 0.42
22 30 0.35
23 1 0.01
24 2 0.02
25 2 0.02
26 13 0.15
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTAATTTATCTTTTTTCTCAT
Found at i:43660012 original size:74 final size:75
Alignment explanation
Indices: 43659907--43660065 Score: 221
Period size: 74 Copynumber: 2.1 Consensus size: 75
43659897 ATCTTTTTTC
* *
43659907 CATTTAAATTTAATTTCTTCCCCATTTCATTTAAATTATCTTTCTTCCCATTTTAATTT-ATTTT
1 CATTTAAATTTAATTTCTTCCCCATTTCATTTAAATTATCTTTCTTCCCATTTAAATTTAATTTC
*
43659971 TTTCTCATTT
66 TTCCTCATTT
* * * ** * *
43659981 CATTTAAATTTTATTTTTTTCTTATTTCATTTAAATTATCTTTTTTGCCATTTAAATTTAATTTC
1 CATTTAAATTTAATTTCTTCCCCATTTCATTTAAATTATCTTTCTTCCCATTTAAATTTAATTTC
43660046 TTCCTCATTT
66 TTCCTCATTT
43660056 CATTTAAATT
1 CATTTAAATT
43660066 ATCCTTCTTT
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
74 51 0.69
75 23 0.31
ACGTcount: A:0.25, C:0.16, G:0.01, T:0.59
Consensus pattern (75 bp):
CATTTAAATTTAATTTCTTCCCCATTTCATTTAAATTATCTTTCTTCCCATTTAAATTTAATTTC
TTCCTCATTT
Found at i:43660055 original size:122 final size:121
Alignment explanation
Indices: 43659866--43660167 Score: 464
Period size: 122 Copynumber: 2.5 Consensus size: 121
43659856 ATTTTTTTCC
43659866 ATTTAAATTTATTTT-TTATTTCATTTAAATTATCTTTTTTCCATTTAAATTTAATTTCTTCCCC
1 ATTT-AATTT-TTTTCTTATTTCATTTAAATTATCTTTTTTCCATTTAAATTTAATTTCTTCCCC
* *
43659930 ATTTCATTTAAATTATCTTTCTTCCCATTTTAATTTATTTTTTTCTCATTTCATTTAA
64 ATTTCATTTAAATTATCCTTCTTCCCATTTTAATTTATTTCTTTCTCATTTCATTTAA
* *
43659988 ATTTTATTTTTTTCTTATTTCATTTAAATTATCTTTTTTGCCATTTAAATTTAATTTCTTCCTCA
1 ATTTAATTTTTTTCTTATTTCATTTAAATTATCTTTTTT-CCATTTAAATTTAATTTCTTCCCCA
*
43660053 TTTCATTTAAATTATCCTTCTTTCCATTTTAATTTATTTCTTTCTCATTTCATTTAA
65 TTTCATTTAAATTATCCTTCTTCCCATTTTAATTTATTTCTTTCTCATTTCATTTAA
* * *
43660110 ATTTAATTTTTTTCTCT-TTTCATTTAAGTTATCTTTCTTTTCATTTTAATTTACATTT
1 ATTTAATTTTTTTCT-TATTTCATTTAAATTATCTTT-TTTCCATTTAAATTTA-ATTT
43660168 TTTTCATATT
Statistics
Matches: 166, Mismatches: 9, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
120 4 0.02
121 29 0.17
122 125 0.75
123 8 0.05
ACGTcount: A:0.24, C:0.15, G:0.01, T:0.61
Consensus pattern (121 bp):
ATTTAATTTTTTTCTTATTTCATTTAAATTATCTTTTTTCCATTTAAATTTAATTTCTTCCCCAT
TTCATTTAAATTATCCTTCTTCCCATTTTAATTTATTTCTTTCTCATTTCATTTAA
Found at i:43660061 original size:21 final size:21
Alignment explanation
Indices: 43660036--43660109 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 21
43660026 TGCCATTTAA
43660036 ATTTAATTTCTTCCTCATTTC
1 ATTTAATTTCTTCCTCATTTC
* *
43660057 ATTTAAATTATCCTTCTTTCCATTTTA
1 ATTT-AATT-T-CTTC-CT-CA-TTTC
*
43660084 ATTT-ATTTCTTTCTCATTTC
1 ATTTAATTTCTTCCTCATTTC
43660104 ATTTAA
1 ATTTAA
43660110 ATTTAATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 14
0.68 0.08 0.23
Matches are distributed among these distances:
20 7 0.17
21 7 0.17
22 5 0.12
23 4 0.10
24 5 0.12
25 4 0.10
26 2 0.05
27 7 0.17
ACGTcount: A:0.23, C:0.19, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTTAATTTCTTCCTCATTTC
Found at i:43660110 original size:47 final size:47
Alignment explanation
Indices: 43659981--43660112 Score: 185
Period size: 48 Copynumber: 2.8 Consensus size: 47
43659971 TTTCTCATTT
* * *
43659981 CATTTAAATTTTATTTTTTTCTTATTTCATTTAAATTATCTTTTTTGC
1 CATTTAAA-TTTATTTCTTTCTCATTTCATTTAAATTATCTTCTTTGC
*
43660029 CATTTAAATTTAATTTCTTCCTCATTTCATTTAAATTATCCTTCTTT-C
1 CATTTAAATTT-ATTTCTTTCTCATTTCATTTAAATTAT-CTTCTTTGC
*
43660077 CATTTTAATTTATTTCTTTCTCATTTCATTTAAATT
1 CATTTAAATTTATTTCTTTCTCATTTCATTTAAATT
43660113 TAATTTTTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
47 27 0.36
48 43 0.57
49 6 0.08
ACGTcount: A:0.24, C:0.15, G:0.01, T:0.60
Consensus pattern (47 bp):
CATTTAAATTTATTTCTTTCTCATTTCATTTAAATTATCTTCTTTGC
Found at i:43660134 original size:21 final size:20
Alignment explanation
Indices: 43660110--43660183 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 20
43660100 TTTCATTTAA
*
43660110 ATTTAATTTTTTTCTCTTTTC
1 ATTTAATTTTCTT-TCTTTTC
*
43660131 ATTTAAGTTATCTTTCTTTTC
1 ATTTAA-TTTTCTTTCTTTTC
*
43660152 ATTTTAATTTACATTT-TTTTC
1 A-TTTAATTTTC-TTTCTTTTC
43660173 ATATTAATTTT
1 AT-TTAATTTT
43660184 TCTCTCATTG
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
20 1 0.02
21 30 0.68
22 13 0.30
ACGTcount: A:0.22, C:0.11, G:0.01, T:0.66
Consensus pattern (20 bp):
ATTTAATTTTCTTTCTTTTC
Found at i:43663356 original size:113 final size:113
Alignment explanation
Indices: 43663152--43663356 Score: 272
Period size: 114 Copynumber: 1.8 Consensus size: 113
43663142 GCCGGCCATT
* **
43663152 TACTGGCTAGCACCAAATTTTTTTTTAAAATATACACTGGTGTTAGCCATCAGTGTCCCAAAGTA
1 TACTGGCTAGCACCAAATTTTTTTTTAAAAAATACACCAGTGTTAGCCATCAGTGTCCCAAAGTA
* * * *
43663217 AAAAAAAATTGCGTTGGGGGCTGAAAATTGTACCTGGTGCTAGCTCTC
66 AAAAAAAATTGCGCTCGGGACCGAAAATTGTACCTGGTGCTAGCTCTC
* * *
43663265 TACTGGC-AGGCATCAAATTTTTTTTTAAAAAAATTCACCAGTGTTGGCCATCAGTGTCCCAAAG
1 TACTGGCTA-GCACCAAATTTTTTTTT-AAAAAATACACCAGTGTTAGCCATCAGTGTCCCAAAG
43663329 TAAAAAAAAATT-C-CTCGGGACACGAAAA
64 TAAAAAAAAATTGCGCTCGGGAC-CGAAAA
43663357 AAGTGCCTGT
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
112 6 0.08
113 29 0.37
114 44 0.56
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (113 bp):
TACTGGCTAGCACCAAATTTTTTTTTAAAAAATACACCAGTGTTAGCCATCAGTGTCCCAAAGTA
AAAAAAAATTGCGCTCGGGACCGAAAATTGTACCTGGTGCTAGCTCTC
Found at i:43674117 original size:16 final size:14
Alignment explanation
Indices: 43674096--43674134 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 14
43674086 AATGAACTTT
43674096 AGAAAAAAGTTTGACA
1 AGAAAAAAG-TTGA-A
43674112 AGAAAAAAAGTTGAA
1 AG-AAAAAAGTTGAA
43674127 AGAAAAAA
1 AGAAAAAA
43674135 ATATTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 6 0.27
15 3 0.14
16 6 0.27
17 7 0.32
ACGTcount: A:0.67, C:0.03, G:0.18, T:0.13
Consensus pattern (14 bp):
AGAAAAAAGTTGAA
Found at i:43674135 original size:16 final size:17
Alignment explanation
Indices: 43674098--43674135 Score: 62
Period size: 15 Copynumber: 2.4 Consensus size: 17
43674088 TGAACTTTAG
43674098 AAAAAAGTTTGACAAGA
1 AAAAAAGTTTGACAAGA
43674115 AAAAAAG-TTGA-AAGA
1 AAAAAAGTTTGACAAGA
43674130 AAAAAA
1 AAAAAA
43674136 TATTTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 10 0.48
16 4 0.19
17 7 0.33
ACGTcount: A:0.68, C:0.03, G:0.16, T:0.13
Consensus pattern (17 bp):
AAAAAAGTTTGACAAGA
Found at i:43674586 original size:3 final size:3
Alignment explanation
Indices: 43674578--43674602 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
43674568 TTTTAGTTAG
43674578 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
43674603 GTAGAAGCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:43680895 original size:5 final size:6
Alignment explanation
Indices: 43680865--43680895 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
43680855 ATAAAAATTT
43680865 ATTTAA ATTTAA ATTTAA ATTTAA A-TTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT
43680896 ATTATTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTTAA
Found at i:43682084 original size:18 final size:17
Alignment explanation
Indices: 43682047--43682086 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
43682037 AATTTTGGAA
*
43682047 ATTTTATAAATATTTGG
1 ATTTTAAAAATATTTGG
*
43682064 ATTTTAAAAATTATTTTG
1 ATTTTAAAAA-TATTTGG
43682082 ATTTT
1 ATTTT
43682087 TTTTTGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (17 bp):
ATTTTAAAAATATTTGG
Found at i:43686959 original size:3 final size:3
Alignment explanation
Indices: 43686953--43687009 Score: 87
Period size: 3 Copynumber: 19.0 Consensus size: 3
43686943 TACCATCATC
* *
43686953 ATT ATT ATT GTT ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
43687001 ATT AAT ATT
1 ATT ATT ATT
43687010 CTATGGTATA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:43690663 original size:21 final size:22
Alignment explanation
Indices: 43690615--43690665 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
43690605 CTTGAACCTT
43690615 AATT-ATAATTTATAAAAATTA
1 AATTAATAATTTATAAAAATTA
*
43690636 AA-AAATAATTTATAAAAA-TA
1 AATTAATAATTTATAAAAATTA
43690656 AATTAATAAT
1 AATTAATAAT
43690666 AAAATTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AATTAATAATTTATAAAAATTA
Found at i:43690667 original size:17 final size:18
Alignment explanation
Indices: 43690647--43690683 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
43690637 AAAATAATTT
43690647 ATAAAAATAAAT-TAATA
1 ATAAAAATAAATATAATA
*
43690664 ATAAAATTAAATATAATA
1 ATAAAAATAAATATAATA
43690682 AT
1 AT
43690684 TAATAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAAAAATAAATATAATA
Found at i:43718000 original size:23 final size:23
Alignment explanation
Indices: 43717968--43718022 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
43717958 TCAAATCGAT
*
43717968 TGAACTAATTGAATTGGACGAGA
1 TGAACCAATTGAATTGGACGAGA
43717991 TGAACCAATTGAATTGGACGAGA
1 TGAACCAATTGAATTGGACGAGA
43718014 TGAACCAAT
1 TGAACCAAT
43718023 AACTTGATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.24
Consensus pattern (23 bp):
TGAACCAATTGAATTGGACGAGA
Found at i:43718461 original size:6 final size:6
Alignment explanation
Indices: 43718450--43718474 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
43718440 TTGTCAGACA
43718450 GCACAT GCACAT GCACAT GCACAT G
1 GCACAT GCACAT GCACAT GCACAT G
43718475 GAACATGGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.32, G:0.20, T:0.16
Consensus pattern (6 bp):
GCACAT
Found at i:43722414 original size:35 final size:35
Alignment explanation
Indices: 43722368--43722434 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
43722358 TTTCTCATTC
43722368 TTTTATTTCTTTCTTTCAGTCTTTATGTTAATTGA
1 TTTTATTTCTTTCTTTCAGTCTTTATGTTAATTGA
43722403 TTTTATTTCTTTCTTTCAGTCTTTATGTTAAT
1 TTTTATTTCTTTCTTTCAGTCTTTATGTTAAT
43722435 CTGTCAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.16, C:0.12, G:0.07, T:0.64
Consensus pattern (35 bp):
TTTTATTTCTTTCTTTCAGTCTTTATGTTAATTGA
Found at i:43725646 original size:55 final size:55
Alignment explanation
Indices: 43725579--43725689 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
43725569 GCCCTAATCT
43725579 TTCCCAAATTTCAGGATTTGGGTTCCCTACATATCCTTTATTTATTTCTTTATGA
1 TTCCCAAATTTCAGGATTTGGGTTCCCTACATATCCTTTATTTATTTCTTTATGA
*
43725634 TTCCCTAATTTCAGGATTTGGGTTCCCTACATATCCTTTATTTATTTCTTTATGA
1 TTCCCAAATTTCAGGATTTGGGTTCCCTACATATCCTTTATTTATTTCTTTATGA
43725689 T
1 T
43725690 GTTACGAGCT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.21, C:0.20, G:0.11, T:0.49
Consensus pattern (55 bp):
TTCCCAAATTTCAGGATTTGGGTTCCCTACATATCCTTTATTTATTTCTTTATGA
Found at i:43747554 original size:20 final size:20
Alignment explanation
Indices: 43747526--43747590 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 20
43747516 GGGAAAGAGG
*
43747526 AGCACAGAGCATTCCAAGCT
1 AGCAAAGAGCATTCCAAGCT
*
43747546 AGCAAAGAG-A----AAGAGT
1 AGCAAAGAGCATTCCAAG-CT
*
43747562 AGCACAGAGCATTCCAAGCT
1 AGCAAAGAGCATTCCAAGCT
43747582 AGCAAAGAG
1 AGCAAAGAG
43747591 ATGCAAAGCA
Statistics
Matches: 34, Mismatches: 5, Indels: 12
0.67 0.10 0.24
Matches are distributed among these distances:
15 3 0.09
16 9 0.26
17 1 0.03
19 1 0.03
20 17 0.50
21 3 0.09
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.11
Consensus pattern (20 bp):
AGCAAAGAGCATTCCAAGCT
Found at i:43747566 original size:36 final size:36
Alignment explanation
Indices: 43747518--43747591 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
43747508 ACAGAAATGG
43747518 GAAAGAGGAGCACAGAGCATTCCAAGCTAGCAAAGA
1 GAAAGAGGAGCACAGAGCATTCCAAGCTAGCAAAGA
*
43747554 GAAAGAGTAGCACAGAGCATTCCAAGCTAGCAAAGA
1 GAAAGAGGAGCACAGAGCATTCCAAGCTAGCAAAGA
43747590 GA
1 GA
43747592 TGCAAAGCAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.45, C:0.19, G:0.27, T:0.09
Consensus pattern (36 bp):
GAAAGAGGAGCACAGAGCATTCCAAGCTAGCAAAGA
Found at i:43754209 original size:511 final size:511
Alignment explanation
Indices: 43753246--43754269 Score: 1904
Period size: 511 Copynumber: 2.0 Consensus size: 511
43753236 TTTCTACATA
43753246 ATGTTTTGGTTTTAAACATGTGAAACAGGATATTTGGATGAAAATGAGTGGATGAGTTAATGCTA
1 ATGTTTTGGTTTTAAACATGTGAAACAGGATATTTGGATGAAAATGAGTGGATGAGTTAATGCTA
* * * *
43753311 TTGTTTATTACGACGATGAAATTCATGACACCAATATCGAGTTCATTTTTTCATCAGCCTACATA
66 TTGTTTATTACGACGATGAAATTCATGACACCAACATCAAGTTCATTTTTTCATCAACCTACACA
*
43753376 ACGTAATTGGCTTTCAACCCGGACATTCAATTGTCGGAGCTCCGATCAAGAATTAGGTGGAAAAT
131 ACGTAATTGGCTTTCAACCCGAACATTCAATTGTCGGAGCTCCGATCAAGAATTAGGTGGAAAAT
43753441 GAGCAATTCAAGCCACAGAATATAGTCGTTGAAGTATAGATATTTAGCGTCAGAGAACCCCGTAA
196 GAGCAATTCAAGCCACAGAATATAGTCGTTGAAGTATAGATATTTAGCGTCAGAGAACCCCGTAA
*
43753506 AAGATGAAATATTTAATGTCATAGGCCCAATAGCGATCGGTGTAATGGTCTAGACGCATAATGCT
261 AAGATGAAATATTTAATGTCATAAGCCCAATAGCGATCGGTGTAATGGTCTAGACGCATAATGCT
*
43753571 ACTGAACCACCTATACTTGAGTTATATACCGAGTTTATCAACGTCGATGAAGGTGCTTGGAGGTT
326 ACTGAACCACCTATACTTGAGTTATATACCGAGTTTATCAACATCGATGAAGGTGCTTGGAGGTT
* *
43753636 AAAAATTTTTCTCATTCATGCTAGAACAGAATAAGAAGCTGGAAGTCCAACCACATAGTTATGCA
391 AAAAATTGTTCTCATTCATGCTAGAACAGAATAAGAAGCTGGAAGTCCAACCACACAGTTATGCA
*
43753701 GTGGGGTCACAGCTTTGTTAGAAAGCTCTCATTATGAAATCCCGGAATCATACTTC
456 GTGGGGTCACAGCTTTGTTAGAAAGCTCTCATTATGAAATCCCAGAATCATACTTC
*
43753757 ATGTTTTGGTTTTAAACATGTGAAACAGGATATTTGGATGAAAATGAGTGTATGAGTTAATGCTA
1 ATGTTTTGGTTTTAAACATGTGAAACAGGATATTTGGATGAAAATGAGTGGATGAGTTAATGCTA
43753822 TTGTTTATTACGACGATGAAATTCATGACACCAACATCAAGTTCATTTTTTCATCAACCTACACA
66 TTGTTTATTACGACGATGAAATTCATGACACCAACATCAAGTTCATTTTTTCATCAACCTACACA
43753887 ACGTAATTGGCTTTCAACCCGAACATTCAATTGTCGGAGCTCCGATCAAGAATTAGGTGGAAAAT
131 ACGTAATTGGCTTTCAACCCGAACATTCAATTGTCGGAGCTCCGATCAAGAATTAGGTGGAAAAT
*
43753952 GCGCAATTCAAGCCACAGAATATAGTCGTTGAAGTATAGATATTTAGCGTCAGAGAACCCCGTAA
196 GAGCAATTCAAGCCACAGAATATAGTCGTTGAAGTATAGATATTTAGCGTCAGAGAACCCCGTAA
* *
43754017 AAGATGAAATATTTAATGTTATAAGCCCAATAGTGATCGGTGTAATGGTCTAGACGCATAATGCT
261 AAGATGAAATATTTAATGTCATAAGCCCAATAGCGATCGGTGTAATGGTCTAGACGCATAATGCT
*
43754082 ACTGAACCACCTATACTTGAGTTATATACCGAGTTTATCGACATCGATGAAGGTGCTTGGAGGTT
326 ACTGAACCACCTATACTTGAGTTATATACCGAGTTTATCAACATCGATGAAGGTGCTTGGAGGTT
*
43754147 AAAAGTTGTTCTCATTCATGCTAGAACAGAATAAGAAGCTGGAAGTCCAACCACACAGTTATGCA
391 AAAAATTGTTCTCATTCATGCTAGAACAGAATAAGAAGCTGGAAGTCCAACCACACAGTTATGCA
43754212 GTGGGGTCACAGCTTTGTTAGAAAGCTCTCATTATGAAATCCCAGAATCATACTTC
456 GTGGGGTCACAGCTTTGTTAGAAAGCTCTCATTATGAAATCCCAGAATCATACTTC
43754268 AT
1 AT
43754270 TACCCAAATT
Statistics
Matches: 497, Mismatches: 16, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
511 497 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.29
Consensus pattern (511 bp):
ATGTTTTGGTTTTAAACATGTGAAACAGGATATTTGGATGAAAATGAGTGGATGAGTTAATGCTA
TTGTTTATTACGACGATGAAATTCATGACACCAACATCAAGTTCATTTTTTCATCAACCTACACA
ACGTAATTGGCTTTCAACCCGAACATTCAATTGTCGGAGCTCCGATCAAGAATTAGGTGGAAAAT
GAGCAATTCAAGCCACAGAATATAGTCGTTGAAGTATAGATATTTAGCGTCAGAGAACCCCGTAA
AAGATGAAATATTTAATGTCATAAGCCCAATAGCGATCGGTGTAATGGTCTAGACGCATAATGCT
ACTGAACCACCTATACTTGAGTTATATACCGAGTTTATCAACATCGATGAAGGTGCTTGGAGGTT
AAAAATTGTTCTCATTCATGCTAGAACAGAATAAGAAGCTGGAAGTCCAACCACACAGTTATGCA
GTGGGGTCACAGCTTTGTTAGAAAGCTCTCATTATGAAATCCCAGAATCATACTTC
Found at i:43759952 original size:15 final size:15
Alignment explanation
Indices: 43759932--43759961 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43759922 AGTATTAAAT
43759932 AAATTTAAATTGTAC
1 AAATTTAAATTGTAC
*
43759947 AAATTTAACTTGTAC
1 AAATTTAAATTGTAC
43759962 TATAAGCTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (15 bp):
AAATTTAAATTGTAC
Found at i:43762977 original size:44 final size:45
Alignment explanation
Indices: 43762910--43763005 Score: 133
Period size: 44 Copynumber: 2.2 Consensus size: 45
43762900 ATTTTCTCTC
* * *
43762910 AACTCAAATATTGCCTTTCACCAGTTCTTACTTGTTTAAATACAG
1 AACTCAAACATTGCCTTTCACCAGTTATTACATGTTTAAATACAG
* *
43762955 AACTCAAACATTGGC-TTCACCAGTTATTACATGTTTAAATACTG
1 AACTCAAACATTGCCTTTCACCAGTTATTACATGTTTAAATACAG
43762999 AA-TCAAA
1 AACTCAAA
43763006 GAATATACGA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 5 0.11
44 28 0.61
45 13 0.28
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.34
Consensus pattern (45 bp):
AACTCAAACATTGCCTTTCACCAGTTATTACATGTTTAAATACAG
Found at i:43767198 original size:19 final size:20
Alignment explanation
Indices: 43767152--43767203 Score: 79
Period size: 21 Copynumber: 2.6 Consensus size: 20
43767142 TTCAAGGATG
43767152 TGCAATCTTAGATATGATATA
1 TGCAATCTTAGATATGA-ATA
*
43767173 TGAAATCTTAGATATG-ATA
1 TGCAATCTTAGATATGAATA
43767192 TGCAATCTTAGA
1 TGCAATCTTAGA
43767204 AGATATGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 14 0.48
21 15 0.52
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (20 bp):
TGCAATCTTAGATATGAATA
Found at i:43768820 original size:71 final size:71
Alignment explanation
Indices: 43768704--43768863 Score: 275
Period size: 71 Copynumber: 2.3 Consensus size: 71
43768694 AATACTTCGT
* *
43768704 TTTTGTCTTCGCATCATAACTCATAAGCTACTAGATTGTGATGAAGTCAGACTATAAATAACAAT
1 TTTTGTCTTTGCATCTTAACTCATAAGCTACTAGATTGTGATGAAGTCAGACTATAAATAACAAT
43768769 GTTGGA
66 GTTGGA
* *
43768775 TTTTGTCTTTGCATCTTAACTCATAAGCTAGTAGATTGTGATGAAGTCAGACTTTAAATAACAAT
1 TTTTGTCTTTGCATCTTAACTCATAAGCTACTAGATTGTGATGAAGTCAGACTATAAATAACAAT
43768840 GTTGGA
66 GTTGGA
*
43768846 TTTTGACTTTGCATCTTA
1 TTTTGTCTTTGCATCTTA
43768864 TTGTATCAGT
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 84 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (71 bp):
TTTTGTCTTTGCATCTTAACTCATAAGCTACTAGATTGTGATGAAGTCAGACTATAAATAACAAT
GTTGGA
Found at i:43770654 original size:21 final size:21
Alignment explanation
Indices: 43770615--43770678 Score: 83
Period size: 21 Copynumber: 2.9 Consensus size: 21
43770605 ACAAATGAAA
*
43770615 TAAAATAATATACAAAAAAAATT
1 TAAAATAA-ATA-ATAAAAAATT
*
43770638 TAAAGTAAATAATAAAAAATT
1 TAAAATAAATAATAAAAAATT
43770659 TAAAATAAATAATATAAAAA
1 TAAAATAAATAATA-AAAAA
43770679 AAAGGTTCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.59
22 8 0.22
23 7 0.19
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (21 bp):
TAAAATAAATAATAAAAAATT
Found at i:43770675 original size:26 final size:25
Alignment explanation
Indices: 43770612--43770980 Score: 170
Period size: 26 Copynumber: 14.6 Consensus size: 25
43770602 AAGACAAATG
*
43770612 AAATAAAATAATATACAAAAAAAATTTA
1 AAAT-AAATAATAT--ATAAAAAATTTA
*
43770640 AAGT--A-AATA-ATAAAAAATTTA
1 AAATAAATAATATATAAAAAATTTA
* *
43770661 AAATAAATAATATAAAAAAAAGGTTCA
1 AAATAAATAATATATAAAAAA--TTTA
* * *
43770688 AAATAAA-AAAATGTAAAAAAATTA
1 AAATAAATAATATATAAAAAATTTA
* * * *
43770712 ACATAAATAAAATATAAAATAGTTTG
1 AAATAAATAATATATAAAA-AATTTA
*
43770738 AAATAAATAAT-T-TAAAGCAATTTA
1 AAATAAATAATATATAAA-AAATTTA
* * * *
43770762 AAATAAACATTACATAAAATAGTTTA
1 AAATAAATAATATATAAAA-AATTTA
* * *
43770788 AAAGAAATAATATGTAAAAAAATCTA
1 AAATAAATAATATAT-AAAAAATTTA
* *
43770814 AAATAAATAA-ATATATAACAGTTTA
1 AAATAAATAATATATA-AAAAATTTA
* * * *
43770839 AGATAAAAATAATATATAAAGCAGTTCA
1 A-A-ATAAATAATATATAAA-AAATTTA
** * *
43770867 AAATAAATAATACGTGAAACAATTTG
1 AAATAAATAATATAT-AAAAAATTTA
** * * *
43770893 AAATAAATAATA-CCAAATAGTATA
1 AAATAAATAATATATAAAAAATTTA
*
43770917 ATATAAATAATATAT--AAAATTTA
1 AAATAAATAATATATAAAAAATTTA
* *
43770940 AAATAAATAAAATAT-AAAACTGTTA
1 AAATAAATAATATATAAAAAAT-TTA
43770965 AAA-ATAATAATATATA
1 AAATA-AATAATATATA
43770981 TAAAGAAATT
Statistics
Matches: 256, Mismatches: 61, Indels: 50
0.70 0.17 0.14
Matches are distributed among these distances:
21 14 0.05
23 19 0.07
24 56 0.22
25 44 0.17
26 81 0.32
27 27 0.11
28 15 0.06
ACGTcount: A:0.63, C:0.04, G:0.05, T:0.28
Consensus pattern (25 bp):
AAATAAATAATATATAAAAAATTTA
Found at i:43770764 original size:101 final size:104
Alignment explanation
Indices: 43770655--43770879 Score: 255
Period size: 101 Copynumber: 2.2 Consensus size: 104
43770645 AATAATAAAA
* * *
43770655 AATTTAAAATAAATAATATAAAAAAAAGGTTCAAAATAAA-AAAATGTAAAAAAAT-TAACATAA
1 AATTTAAAATAAATAATACAAAAAAAA-GTTCAAAAGAAATAAAATGTAAAAAAATCTAAAATAA
*
43770718 ATAAAATATAAAATAGTTTGAA-AT-AAATAAT-T-TAAAGC
65 AT-AAATATAAAACAGTTT-AAGATAAAATAATATATAAAGC
* * * * * *
43770756 AATTTAAAATAAACATTACATAAAATAGTTTAAAAGAAATAATATGTAAAAAAATCTAAAATAAA
1 AATTTAAAATAAATAATACAAAAAAAAGTTCAAAAGAAATAAAATGTAAAAAAATCTAAAATAAA
*
43770821 TAAATATATAACAGTTTAAGATAAAAATAATATATAAAGC
66 TAAATATAAAACAGTTTAAGAT-AAAATAATATATAAAGC
* *
43770861 AGTTCAAAATAAATAATAC
1 AATTTAAAATAAATAATAC
43770880 GTGAAACAAT
Statistics
Matches: 102, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
100 12 0.12
101 52 0.51
102 9 0.09
103 7 0.07
104 1 0.01
105 21 0.21
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (104 bp):
AATTTAAAATAAATAATACAAAAAAAAGTTCAAAAGAAATAAAATGTAAAAAAATCTAAAATAAA
TAAATATAAAACAGTTTAAGATAAAATAATATATAAAGC
Found at i:43770863 original size:28 final size:27
Alignment explanation
Indices: 43770818--43770878 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
43770808 AATCTAAAAT
* *
43770818 AAATAAATATATAACAGTTTAAGATAA
1 AAATAAATATATAACAGTTCAAAATAA
43770845 AAAT-AATATATAAAGCAGTTCAAAATAA
1 AAATAAATATAT-AA-CAGTTCAAAATAA
43770873 ATAATA
1 A-AATA
43770879 CGTGAAACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
26 7 0.25
27 6 0.21
28 12 0.43
29 3 0.11
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.28
Consensus pattern (27 bp):
AAATAAATATATAACAGTTCAAAATAA
Found at i:43770944 original size:16 final size:16
Alignment explanation
Indices: 43770925--43770958 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
43770915 TAATATAAAT
* *
43770925 AATATATAAAATTTAA
1 AATAAATAAAATATAA
43770941 AATAAATAAAATATAA
1 AATAAATAAAATATAA
43770957 AA
1 AA
43770959 CTGTTAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAAATAAAATATAA
Found at i:43772400 original size:2 final size:2
Alignment explanation
Indices: 43772393--43772417 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43772383 TGAATCTTAC
43772393 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 A
43772418 AGCATGCCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43774789 original size:25 final size:25
Alignment explanation
Indices: 43774761--43774811 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
43774751 AAAAAAGAAA
43774761 GAACGTACTAAAACAAACATCCTAT
1 GAACGTACTAAAACAAACATCCTAT
*
43774786 GAACGTAGTAAAACAAACATCCTAT
1 GAACGTACTAAAACAAACATCCTAT
43774811 G
1 G
43774812 TTGTCTTGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.47, C:0.22, G:0.12, T:0.20
Consensus pattern (25 bp):
GAACGTACTAAAACAAACATCCTAT
Found at i:43775354 original size:2 final size:2
Alignment explanation
Indices: 43775347--43775375 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
43775337 TCAATGTCAA
43775347 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
43775376 CTATGTCTTT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:43782131 original size:13 final size:13
Alignment explanation
Indices: 43782113--43782137 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43782103 CTTGCCTCCT
43782113 TTTTCTTTTCACG
1 TTTTCTTTTCACG
43782126 TTTTCTTTTCAC
1 TTTTCTTTTCAC
43782138 CTCATGAAAT
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:0.08, C:0.24, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTCTTTTCACG
Found at i:43782918 original size:3 final size:3
Alignment explanation
Indices: 43782910--43782942 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
43782900 CCCTCACCTA
43782910 CGC CGC CGC CGC CGC CGC CGC CGC CGC CGC CGC
1 CGC CGC CGC CGC CGC CGC CGC CGC CGC CGC CGC
43782943 TACCTTTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.67, G:0.33, T:0.00
Consensus pattern (3 bp):
CGC
Found at i:43784249 original size:71 final size:71
Alignment explanation
Indices: 43784133--43784268 Score: 254
Period size: 71 Copynumber: 1.9 Consensus size: 71
43784123 AGTTTGGATG
*
43784133 GGCGGTGTGTTTAGCTCCGGTGAGGTTAAAAACAGCGGTGGCGGTGAAATTAGTTACTGTAGCGG
1 GGCGGTGTGTTTAGCTCCGGTGAGGTTAAAAACAGCGGTGGCGGTGAAATTAGGTACTGTAGCGG
43784198 GAAGAT
66 GAAGAT
*
43784204 GGCGGTGTGTTTAGCTCCGGTGAGGTTAAAAACAGCGGTGGCGGTGAGATTAGGTACTGTAGCGG
1 GGCGGTGTGTTTAGCTCCGGTGAGGTTAAAAACAGCGGTGGCGGTGAAATTAGGTACTGTAGCGG
43784269 TGAGATTGGG
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 63 1.00
ACGTcount: A:0.22, C:0.13, G:0.40, T:0.25
Consensus pattern (71 bp):
GGCGGTGTGTTTAGCTCCGGTGAGGTTAAAAACAGCGGTGGCGGTGAAATTAGGTACTGTAGCGG
GAAGAT
Found at i:43784270 original size:21 final size:21
Alignment explanation
Indices: 43784244--43784298 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
43784234 AACAGCGGTG
43784244 GCGGTGAGATTAGGTACTGTA
1 GCGGTGAGATTAGGTACTGTA
*
43784265 GCGGTGAGATTGGGTACTGTA
1 GCGGTGAGATTAGGTACTGTA
*
43784286 GCAGTGAGATTAG
1 GCGGTGAGATTAG
43784299 AAACAGCGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.24, C:0.09, G:0.40, T:0.27
Consensus pattern (21 bp):
GCGGTGAGATTAGGTACTGTA
Found at i:43792960 original size:13 final size:14
Alignment explanation
Indices: 43792944--43792980 Score: 58
Period size: 13 Copynumber: 2.6 Consensus size: 14
43792934 AAACAAAATA
43792944 AAAAAATAAATT-T
1 AAAAAATAAATTAT
43792957 AAAAAATAAATTAAT
1 AAAAAATAAATT-AT
43792972 AAAAAATAA
1 AAAAAATAA
43792981 GTAAATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 12 0.55
15 10 0.45
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAAAAATAAATTAT
Found at i:43793408 original size:92 final size:92
Alignment explanation
Indices: 43793242--43793423 Score: 240
Period size: 92 Copynumber: 2.0 Consensus size: 92
43793232 TCAATTGTTA
* * *
43793242 TAATAAAAGACATATTGGTAGTTTAGGTGCCAAATTGGATATTTTCAAAGTACACGTACCACATT
1 TAATAAAACACATATTGATAGTTTAGGTGCCAAATTGGATATTTTCAAAGCACACGTACCACATT
**
43793307 AAATATTTTATGAAAGTAAAAGTACCT
66 AAATATTTTACAAAAGTAAAAGTACCT
* * * * *
43793334 TAATAAAACACATATTGATAGTTTAGGTGCTACATTGGATATTTTCAAAGCATAGGTGCCACATT
1 TAATAAAACACATATTGATAGTTTAGGTGCCAAATTGGATATTTTCAAAGCACACGTACCACATT
* *
43793399 -GATATTTTTACAAAAGTACAAGTAC
66 AAATA-TTTTACAAAAGTAAAAGTAC
43793424 TAAATTTGAC
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
91 3 0.04
92 74 0.96
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (92 bp):
TAATAAAACACATATTGATAGTTTAGGTGCCAAATTGGATATTTTCAAAGCACACGTACCACATT
AAATATTTTACAAAAGTAAAAGTACCT
Found at i:43805046 original size:11 final size:11
Alignment explanation
Indices: 43805030--43805054 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
43805020 AGGATTATGC
43805030 AAAGTGACCAT
1 AAAGTGACCAT
43805041 AAAGTGACCAT
1 AAAGTGACCAT
43805052 AAA
1 AAA
43805055 TAGAGATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (11 bp):
AAAGTGACCAT
Found at i:43833687 original size:38 final size:38
Alignment explanation
Indices: 43833645--43833718 Score: 148
Period size: 38 Copynumber: 1.9 Consensus size: 38
43833635 ATTGAATACG
43833645 TAGAATATGAGAAAGCATGTAATACTTTCATTTCATCT
1 TAGAATATGAGAAAGCATGTAATACTTTCATTTCATCT
43833683 TAGAATATGAGAAAGCATGTAATACTTTCATTTCAT
1 TAGAATATGAGAAAGCATGTAATACTTTCATTTCAT
43833719 GAGGGAGAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (38 bp):
TAGAATATGAGAAAGCATGTAATACTTTCATTTCATCT
Found at i:43837854 original size:1 final size:1
Alignment explanation
Indices: 43837839--43837872 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
43837829 AATTCTATTG
* *
43837839 TTTTGTTTTTGTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
43837873 GTTCATATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.06, T:0.94
Consensus pattern (1 bp):
T
Found at i:43851900 original size:9 final size:9
Alignment explanation
Indices: 43851886--43851913 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
43851876 CAAATGTTAG
43851886 TTATTAAGT
1 TTATTAAGT
43851895 TTATTAAGT
1 TTATTAAGT
43851904 TTATTAAGT
1 TTATTAAGT
43851913 T
1 T
43851914 ATGTTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TTATTAAGT
Found at i:43852242 original size:31 final size:30
Alignment explanation
Indices: 43852199--43852266 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
43852189 AACTTTTAAA
*
43852199 AATTAAAAAATATAGGGATTAAACTTGACC
1 AATTAAAAAATATAGAGATTAAACTTGACC
* * *
43852229 AATTCAAAGAATATAGAGATTAAATTTGATCA
1 AATT-AAAAAATATAGAGATTAAACTTGA-CC
43852261 AATTAA
1 AATTAA
43852267 CGTATATGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 4 0.12
31 23 0.72
32 5 0.16
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.29
Consensus pattern (30 bp):
AATTAAAAAATATAGAGATTAAACTTGACC
Found at i:43854364 original size:28 final size:28
Alignment explanation
Indices: 43854332--43854389 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
43854322 GCTTCACCCC
43854332 TGTCTCAAATATATTTAGTAACTCTGGA
1 TGTCTCAAATATATTTAGTAACTCTGGA
43854360 TGTCTCAAATATATTTAGTAACTCTGGA
1 TGTCTCAAATATATTTAGTAACTCTGGA
43854388 TG
1 TG
43854390 AGATGATTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.40
Consensus pattern (28 bp):
TGTCTCAAATATATTTAGTAACTCTGGA
Found at i:43858685 original size:29 final size:29
Alignment explanation
Indices: 43858646--43858702 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
43858636 ATTAGAAATC
* * *
43858646 ATAAAATTTTATTTTAATTTTTTAAAAAG
1 ATAAAAATTTAATTTAATTTTATAAAAAG
43858675 ATAAAAATTTAATTTAATTTTATAAAAA
1 ATAAAAATTTAATTTAATTTTATAAAAA
43858703 TAATAAAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
ATAAAAATTTAATTTAATTTTATAAAAAG
Found at i:43858709 original size:30 final size:30
Alignment explanation
Indices: 43858641--43858709 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
43858631 TTTAAATTAG
* * * *
43858641 AAATCATAAAATTTTATTTTAATTTTTTAA
1 AAATAATAAAAATTTAATTTAATTTTATAA
*
43858671 AAA-GATAAAAATTTAATTTAATTTTATAA
1 AAATAATAAAAATTTAATTTAATTTTATAA
43858700 AAATAATAAA
1 AAATAATAAA
43858710 GATATAGATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 25 0.76
30 8 0.24
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (30 bp):
AAATAATAAAAATTTAATTTAATTTTATAA
Found at i:43861082 original size:22 final size:22
Alignment explanation
Indices: 43861041--43861082 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
43861031 ACACCAAAAC
* *
43861041 AGGCTTTTAGCGGCATTTTTTT
1 AGGCATTTAGCGGCACTTTTTT
*
43861063 AGGCATTTAGCGGCGCTTTT
1 AGGCATTTAGCGGCACTTTT
43861083 CCTAGCGCCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.14, C:0.17, G:0.26, T:0.43
Consensus pattern (22 bp):
AGGCATTTAGCGGCACTTTTTT
Found at i:43861236 original size:43 final size:43
Alignment explanation
Indices: 43861173--43861259 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
43861163 ATGCTTTTCC
* * *
43861173 ACAAACGCCGCTAAAGAACATGAGCTTTAGCGGTACTTTACCA
1 ACAAACGCCGCTAAAAAACATGACCTTTAGCGGCACTTTACCA
* *
43861216 ACAAACGTCGCTAAAAAACATGACCTTTAGCGGCGCTTTACCA
1 ACAAACGCCGCTAAAAAACATGACCTTTAGCGGCACTTTACCA
43861259 A
1 A
43861260 TTATTAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (43 bp):
ACAAACGCCGCTAAAAAACATGACCTTTAGCGGCACTTTACCA
Found at i:43864599 original size:23 final size:23
Alignment explanation
Indices: 43864564--43864608 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
43864554 TGGAGTATAA
* *
43864564 AAGTTTTATATTTTTATATGTAC
1 AAGTTTTATATTTATACATGTAC
43864587 AAGTTTTGA-ATTTATACATGTA
1 AAGTTTT-ATATTTATACATGTA
43864609 TATACAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.51
Consensus pattern (23 bp):
AAGTTTTATATTTATACATGTAC
Found at i:43865245 original size:42 final size:42
Alignment explanation
Indices: 43865184--43865368 Score: 191
Period size: 41 Copynumber: 4.5 Consensus size: 42
43865174 CAGTGCCTAT
* * *
43865184 CAGGTTTATTGCCAGTGAAACAATATCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
* *
43865226 CAGGCTTAATGCCGGTGAAATAATTTCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
* * *
43865268 CAGGCTTAATGCCGGTGAAAC-ATTTCAGACTATATGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
* * * *
43865309 CAGGC-TAAGTGCCGGTG-TACTGA-ATCAGGCTTTAAGTCTAG
1 CAGGCTTAA-TGCCGGTGAAAC-AATATCAGACTTTACGTCTAG
*
43865350 CAGGC-TAAGTGCCAGTGAA
1 CAGGCTTAA-TGCCGGTGAA
43865369 TCTGTTTAAA
Statistics
Matches: 124, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
40 5 0.04
41 61 0.49
42 58 0.47
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (42 bp):
CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
Found at i:43865307 original size:41 final size:41
Alignment explanation
Indices: 43865184--43865325 Score: 187
Period size: 42 Copynumber: 3.4 Consensus size: 41
43865174 CAGTGCCTAT
* * * *
43865184 CAGGTTTATTGCCAGTGAAACAATATCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAAC-ATTTCAGACTTTACGTCTAG
*
43865226 CAGGCTTAATGCCGGTGAAATAATTTCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAA-CATTTCAGACTTTACGTCTAG
* *
43865268 CAGGCTTAATGCCGGTGAAACATTTCAGACTATATGTCTAG
1 CAGGCTTAATGCCGGTGAAACATTTCAGACTTTACGTCTAG
43865309 CAGGC-TAAGTGCCGGTG
1 CAGGCTTAA-TGCCGGTG
43865326 TACTGAATCA
Statistics
Matches: 90, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
40 3 0.03
41 31 0.34
42 56 0.62
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (41 bp):
CAGGCTTAATGCCGGTGAAACATTTCAGACTTTACGTCTAG
Found at i:43871181 original size:21 final size:21
Alignment explanation
Indices: 43871155--43871209 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
43871145 AACAGCGGTG
*
43871155 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGGTACTGTA
*
43871176 GCGGTGAGATTGGGTACTGTA
1 GCGGTGAGATTAGGTACTGTA
43871197 GCGGTGAGATTAG
1 GCGGTGAGATTAG
43871210 AAACAATGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.22, C:0.09, G:0.40, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGGTACTGTA
Found at i:43879005 original size:23 final size:23
Alignment explanation
Indices: 43878970--43879014 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
43878960 TGGAGTATAA
* *
43878970 AAGTTTTATATTTTTATATGTAC
1 AAGTTTTATATTTATACATGTAC
43878993 AAGTTTTGA-ATTTATACATGTA
1 AAGTTTT-ATATTTATACATGTA
43879015 TATACAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.51
Consensus pattern (23 bp):
AAGTTTTATATTTATACATGTAC
Found at i:43882379 original size:16 final size:16
Alignment explanation
Indices: 43882358--43882426 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
43882348 TTTGGTTCGC
43882358 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
43882374 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
43882390 TGTATTGAGATTAGAGG
1 TGTATTG-GATTAGAGG
43882407 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
43882423 TGTA
1 TGTA
43882427 ATAGCTAATC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.26, C:0.00, G:0.36, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:43882404 original size:33 final size:32
Alignment explanation
Indices: 43882358--43882426 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
43882348 TTTGGTTCGC
43882358 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
43882390 TGTATTGAGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTG-GATTAGAGGTGTATTGGATTAGAGG
43882423 TGTA
1 TGTA
43882427 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 7 0.19
33 29 0.81
ACGTcount: A:0.26, C:0.00, G:0.36, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGATTAGAGG
Found at i:43882491 original size:44 final size:45
Alignment explanation
Indices: 43882407--43882497 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
43882397 AGATTAGAGG
* * *
43882407 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
43882452 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
43882496 TG
1 TG
43882498 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:43882787 original size:177 final size:177
Alignment explanation
Indices: 43882491--43882845 Score: 683
Period size: 177 Copynumber: 2.0 Consensus size: 177
43882481 TTGTGTTTGG
43882491 TTGAATGGAATAGAGGTGTAATAGCATAATGGAAAAAACTAAAATGACTAGAATACCCTTAGCAT
1 TTGAATGGAATAGAGGTGTAATAGCATAATGGAAAAAACTAAAATGACTAGAATACCCTTAGCAT
* *
43882556 AAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTATCAG
66 AAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
*
43882621 TAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATAT
131 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATAT
43882668 TTGAATGGAATAGAGGTGTAATAGCATAATGGAAAAAACTAAAATGACTAGAATACCCTTAGCAT
1 TTGAATGGAATAGAGGTGTAATAGCATAATGGAAAAAACTAAAATGACTAGAATACCCTTAGCAT
43882733 AAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
66 AAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
43882798 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATAT
131 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATAT
43882845 T
1 T
43882846 ATAATTAAAA
Statistics
Matches: 175, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
177 175 1.00
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.40
Consensus pattern (177 bp):
TTGAATGGAATAGAGGTGTAATAGCATAATGGAAAAAACTAAAATGACTAGAATACCCTTAGCAT
AAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATAT
Found at i:43882856 original size:16 final size:16
Alignment explanation
Indices: 43882819--43882860 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
43882809 TTAATCATAT
*
43882819 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
43882835 TT-AAATATATTATAA
1 TTAAAATATATTATAA
43882850 TTAAAATATAT
1 TTAAAATATAT
43882861 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:43882867 original size:14 final size:15
Alignment explanation
Indices: 43882828--43882869 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
43882818 TTTAAACATA
*
43882828 ATTATTATTAAATAT
1 ATTATAATTAAATAT
43882843 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
43882857 A-TATAATTTAATA
1 ATTATAATTAAATA
43882870 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:43886539 original size:6 final size:6
Alignment explanation
Indices: 43886530--43886564 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
43886520 TTGATGTTGG
43886530 GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA GAGGG
1 GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA GAGGG
43886565 TGGGGAGAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (6 bp):
GAGGGA
Found at i:43887458 original size:21 final size:21
Alignment explanation
Indices: 43887395--43887464 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
43887385 ACCCTTAAAT
*
43887395 CCCTAAATCCTTAACTCTTAAC
1 CCCTAAA-CCTTAACTCATAAC
* * *
43887417 CCCTAACCCCTAACTCCTAAC
1 CCCTAAACCTTAACTCATAAC
*
43887438 CCCTAAACCTTAAATCATAA-
1 CCCTAAACCTTAACTCATAAC
43887458 CCCTAAA
1 CCCTAAA
43887465 ACCATAATCC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 7 0.17
21 28 0.68
22 6 0.15
ACGTcount: A:0.36, C:0.40, G:0.00, T:0.24
Consensus pattern (21 bp):
CCCTAAACCTTAACTCATAAC
Found at i:43887805 original size:15 final size:15
Alignment explanation
Indices: 43887785--43887814 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43887775 AAGCCATAAA
*
43887785 CATAATCCCTAAACC
1 CATAATCCATAAACC
43887800 CATAATCCATAAACC
1 CATAATCCATAAACC
43887815 TTAAAATGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.20
Consensus pattern (15 bp):
CATAATCCATAAACC
Found at i:43887848 original size:7 final size:7
Alignment explanation
Indices: 43887832--43887877 Score: 56
Period size: 7 Copynumber: 6.4 Consensus size: 7
43887822 GGTAACACCT
43887832 AACCCTTA
1 AACCC-TA
*
43887840 AACTCTA
1 AACCCTA
*
43887847 AACCATA
1 AACCCTA
*
43887854 TACCCTA
1 AACCCTA
43887861 AACCCTA
1 AACCCTA
43887868 AACCCTA
1 AACCCTA
43887875 AAC
1 AAC
43887878 TATAGTGATA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
7 28 0.88
8 4 0.12
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.20
Consensus pattern (7 bp):
AACCCTA
Found at i:43888126 original size:41 final size:40
Alignment explanation
Indices: 43888051--43888225 Score: 172
Period size: 41 Copynumber: 4.3 Consensus size: 40
43888041 TAAATTATTT
* * * *
43888051 TAAATCCCTGAGCATTCGAGGCGCTTTATAAAAAATGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCT-AAAAATGCCGC
** * *
43888092 TAAAGCCCTGAGCATTAGCGGTACTTTCTCAAAAATGCTGA
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCT-AAAAATGCCGC
*
43888133 TAAAGCCCTGAGCATTCGCGGCGCTTTCTAAAAA-GCGCTGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTAAAAATGC-C-GC
* * * * *
43888174 TAAAGCACTGAGTATTAGCGACGCTTTTTTAAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGC-TTTCTAAAAATGCCGC
43888215 TAAAGCCCTGA
1 TAAAGCCCTGA
43888226 AAGATAGAAA
Statistics
Matches: 110, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
39 2 0.02
40 5 0.05
41 91 0.83
42 10 0.09
43 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (40 bp):
TAAAGCCCTGAGCATTAGCGGCGCTTTCTAAAAATGCCGC
Found at i:43888208 original size:82 final size:82
Alignment explanation
Indices: 43888051--43888225 Score: 206
Period size: 82 Copynumber: 2.1 Consensus size: 82
43888041 TAAATTATTT
* * * **
43888051 TAAATCCCTGAGCATTCGAGGCGCTTTATAAAAAATGCCGCTAAAGCCCTGAGCATTAGCGGTAC
1 TAAAGCCCTGAGCATTCGAGGCGCTTTATAAAAAACGCCGCTAAAGCACTGAGCATTAGCGACAC
* *
43888116 TTTCTCAAAAATGCTGA
66 TTTCTCAAAAACGCCGA
* * * * * *
43888133 TAAAGCCCTGAGCATTCGCGGCGCTTTCTAAAAAGCGCTGCTAAAGCACTGAGTATTAGCGACGC
1 TAAAGCCCTGAGCATTCGAGGCGCTTTATAAAAAACGCCGCTAAAGCACTGAGCATTAGCGACAC
* * *
43888198 TTTTTTAAAAACGCCGC
66 TTTCTCAAAAACGCCGA
43888215 TAAAGCCCTGA
1 TAAAGCCCTGA
43888226 AAGATAGAAA
Statistics
Matches: 77, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
82 77 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (82 bp):
TAAAGCCCTGAGCATTCGAGGCGCTTTATAAAAAACGCCGCTAAAGCACTGAGCATTAGCGACAC
TTTCTCAAAAACGCCGA
Found at i:43892993 original size:31 final size:29
Alignment explanation
Indices: 43892929--43892997 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
43892919 GTGATAACGT
*
43892929 AAGTGACTAAAATGTAACCTTTCAAACAT
1 AAGTGACTAAAATGTAACCTTTCAAACAA
*
43892958 AAGTGACTAGAATGTAACCTGATGT-AAACAA
1 AAGTGACTAAAATGTAACCT--T-TCAAACAA
43892989 AAGTGACTA
1 AAGTGACTA
43892998 TTTTAGTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 19 0.54
31 15 0.43
32 1 0.03
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.25
Consensus pattern (29 bp):
AAGTGACTAAAATGTAACCTTTCAAACAA
Found at i:43893647 original size:20 final size:21
Alignment explanation
Indices: 43893607--43893647 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
43893597 ATTTCAACTC
**
43893607 TAAATTTATTTATTTAATATT
1 TAAATTTATTTATAAAATATT
43893628 TAAATTTATTT-TAAAATATT
1 TAAATTTATTTATAAAATATT
43893648 GAAAATAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAAATTTATTTATAAAATATT
Found at i:43893844 original size:28 final size:29
Alignment explanation
Indices: 43893813--43893885 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 29
43893803 AATTAACAAA
* *
43893813 AATTAAAGAAAATATTACTATTTACTA-T
1 AATTAAATAAAATATTAATATTTACTATT
* *
43893841 AATTTAAATAAAA-ATTAATTTTTATTATT
1 AA-TTAAATAAAATATTAATATTTACTATT
*
43893870 AATTAAATAAATTATT
1 AATTAAATAAAATATT
43893886 TAAAAATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
28 22 0.59
29 15 0.41
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (29 bp):
AATTAAATAAAATATTAATATTTACTATT
Found at i:43901544 original size:14 final size:14
Alignment explanation
Indices: 43901525--43901556 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
43901515 AGTTTGTTAC
43901525 AAAATAATAATAAT
1 AAAATAATAATAAT
43901539 AAAATAATAATAAT
1 AAAATAATAATAAT
43901553 AAAA
1 AAAA
43901557 CATCAAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (14 bp):
AAAATAATAATAAT
Found at i:43901625 original size:68 final size:68
Alignment explanation
Indices: 43901535--43901747 Score: 399
Period size: 68 Copynumber: 3.1 Consensus size: 68
43901525 AAAATAATAA
* *
43901535 TAATAAAATAATAATAATAAAACATCAAGTTTGTTTTACTAATCAAATGTTAGATTTTGTTACAA
1 TAATACAA-AATAATAATAAAACATCAAGTTTATTTTACTAATCAAATGTTAGATTTTGTTACAA
43901600 CAAT
65 CAAT
43901604 TAATACAAAATAATAATAAAACATCAAGTTTATTTTACTAATCAAATGTTAGATTTTGTTACAAC
1 TAATACAAAATAATAATAAAACATCAAGTTTATTTTACTAATCAAATGTTAGATTTTGTTACAAC
43901669 AAT
66 AAT
43901672 TAATACAAAATAATAATAAAACATCAAGTTTATTTTACTAATCAAATGTTAGATTTTGTTACAAC
1 TAATACAAAATAATAATAAAACATCAAGTTTATTTTACTAATCAAATGTTAGATTTTGTTACAAC
43901737 AAT
66 AAT
43901740 TAATACAA
1 TAATACAA
43901748 TTATTTCAAT
Statistics
Matches: 142, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
68 135 0.95
69 7 0.05
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (68 bp):
TAATACAAAATAATAATAAAACATCAAGTTTATTTTACTAATCAAATGTTAGATTTTGTTACAAC
AAT
Found at i:43901749 original size:9 final size:9
Alignment explanation
Indices: 43901735--43901778 Score: 56
Period size: 9 Copynumber: 5.1 Consensus size: 9
43901725 TTTTGTTACA
43901735 ACAATTAAT
1 ACAATTAAT
*
43901744 ACAATTATT
1 ACAATTAAT
*
43901753 TCAATT-A-
1 ACAATTAAT
43901760 ACAATTAAT
1 ACAATTAAT
43901769 ACAATTAAT
1 ACAATTAAT
43901778 A
1 A
43901779 ATTTGATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 5 0.17
8 1 0.03
9 23 0.79
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (9 bp):
ACAATTAAT
Found at i:43901872 original size:16 final size:16
Alignment explanation
Indices: 43901851--43901892 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
43901841 AATAATTTGA
*
43901851 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
43901867 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
43901883 TAGTTTTAAT
1 TAATTTTAAT
43901893 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:43901876 original size:22 final size:23
Alignment explanation
Indices: 43901866--43901926 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
43901856 TTACTAACAA
* * *
43901866 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
43901888 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
*
43901911 TTAATTTTAATTAAAA
1 TTAATTTTAATAAAAA
43901927 TTGAGCCGGG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.31
23 22 0.69
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:43902592 original size:26 final size:26
Alignment explanation
Indices: 43902562--43902616 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
43902552 TTTTTTTTTC
43902562 AAAACAAGATCTTGGTTGTGATATCT
1 AAAACAAGATCTTGGTTGTGATATCT
43902588 AAAACAAGATCTTGGTTGTGATATCT
1 AAAACAAGATCTTGGTTGTGATATCT
43902614 AAA
1 AAA
43902617 GTACTAAACA
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:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (26 bp):
AAAACAAGATCTTGGTTGTGATATCT
Found at i:43902999 original size:17 final size:17
Alignment explanation
Indices: 43902979--43903022 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
43902969 TATTTAAATT
*
43902979 GATATAATATTTATTAA
1 GATATAATATTGATTAA
43902996 GATA-AATACTTGATTAA
1 GATATAATA-TTGATTAA
43903013 -ATATAATATT
1 GATATAATATT
43903023 AAATTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (17 bp):
GATATAATATTGATTAA
Found at i:43904714 original size:20 final size:20
Alignment explanation
Indices: 43904689--43904732 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
43904679 CATAGAATCC
43904689 ATCTTGGCATCCATACTCAG
1 ATCTTGGCATCCATACTCAG
43904709 ATCTTGGCATCCATACTCAG
1 ATCTTGGCATCCATACTCAG
43904729 ATCT
1 ATCT
43904733 CATACCCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.25, C:0.30, G:0.14, T:0.32
Consensus pattern (20 bp):
ATCTTGGCATCCATACTCAG
Found at i:43906753 original size:28 final size:28
Alignment explanation
Indices: 43906719--43906808 Score: 119
Period size: 28 Copynumber: 3.2 Consensus size: 28
43906709 ATAATAGTAC
43906719 AGTGTGGGCCATAGCCCGATACAGTAAT
1 AGTGTGGGCCATAGCCCGATACAGTAAT
* *
43906747 AGTGTGGG-TATTAGCCCAATACAGTAAT
1 AGTGTGGGCCA-TAGCCCGATACAGTAAT
* * *
43906775 AGTGTGGACCTTAGCCCGATACAGTAAC
1 AGTGTGGGCCATAGCCCGATACAGTAAT
43906803 AGTGTG
1 AGTGTG
43906809 ATAATGTAAC
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
27 1 0.02
28 52 0.98
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (28 bp):
AGTGTGGGCCATAGCCCGATACAGTAAT
Found at i:43907162 original size:27 final size:27
Alignment explanation
Indices: 43907132--43907206 Score: 64
Period size: 27 Copynumber: 2.8 Consensus size: 27
43907122 TTTCGACTCC
43907132 TAGGAGTATAAT-AGACATTTTACCCTA
1 TAGGAGTAT-ATCAGACATTTTACCCTA
* * *
43907159 TAGGGGTATTTCAGTCATTTTACCCT-
1 TAGGAGTATATCAGACATTTTACCCTA
* * * *
43907185 TTGGGGTATATCGGTCATTTTA
1 TAGGAGTATATCAGACATTTTA
43907207 TCCTTCGAGG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
26 20 0.49
27 21 0.51
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (27 bp):
TAGGAGTATATCAGACATTTTACCCTA
Found at i:43907226 original size:27 final size:26
Alignment explanation
Indices: 43907147--43907241 Score: 118
Period size: 27 Copynumber: 3.6 Consensus size: 26
43907137 GTATAATAGA
* *
43907147 CATTTTACCCTATAGGGGTATTTCAGT
1 CATTTTACCCT-TCGGGGTATTTCGGT
* *
43907174 CATTTTACCCTTTGGGGTATATCGGT
1 CATTTTACCCTTCGGGGTATTTCGGT
*
43907200 CATTTTATCCTTCGAGGGTATTTCGGT
1 CATTTTACCCTTCG-GGGTATTTCGGT
*
43907227 TATTTTACCCTTCGG
1 CATTTTACCCTTCGG
43907242 TCGTAAGTTG
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
26 25 0.42
27 34 0.58
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.43
Consensus pattern (26 bp):
CATTTTACCCTTCGGGGTATTTCGGT
Found at i:43914709 original size:13 final size:13
Alignment explanation
Indices: 43914691--43914716 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43914681 AGTTAGTCCA
43914691 TTAATCCAAAAAC
1 TTAATCCAAAAAC
43914704 TTAATCCAAAAAC
1 TTAATCCAAAAAC
43914717 ACCATTCTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (13 bp):
TTAATCCAAAAAC
Found at i:43920632 original size:22 final size:22
Alignment explanation
Indices: 43920607--43920656 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
43920597 ATCAGATCCA
*
43920607 ACTCCACCTCCACTGA-TTCACG
1 ACTCCACCTCCA-TGACTCCACG
*
43920629 ACTCCACGTCCATGACTCCACG
1 ACTCCACCTCCATGACTCCACG
43920651 ACTCCA
1 ACTCCA
43920657 TGGTGCTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.24, C:0.46, G:0.10, T:0.20
Consensus pattern (22 bp):
ACTCCACCTCCATGACTCCACG
Found at i:43921603 original size:7 final size:8
Alignment explanation
Indices: 43921577--43921601 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
43921567 TAAAATATTT
43921577 AAGTTAAA
1 AAGTTAAA
43921585 AAGTTAAA
1 AAGTTAAA
43921593 AAGTTAAA
1 AAGTTAAA
43921601 A
1 A
43921602 GTAATTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (8 bp):
AAGTTAAA
Found at i:43921702 original size:25 final size:25
Alignment explanation
Indices: 43921667--43921714 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
43921657 TTAAGATTTG
*
43921667 ATTGTTTGTAATTAAATTCAAATTA
1 ATTGTTAGTAATTAAATTCAAATTA
43921692 ATTGTTAGTAATTAAATTCAAAT
1 ATTGTTAGTAATTAAATTCAAAT
43921715 AAGTAATCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (25 bp):
ATTGTTAGTAATTAAATTCAAATTA
Found at i:43921806 original size:16 final size:16
Alignment explanation
Indices: 43921785--43921818 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
43921775 ATATAAATTC
43921785 AATAACAATTAATTTT
1 AATAACAATTAATTTT
*
43921801 AATAACAATTAGTTTT
1 AATAACAATTAATTTT
43921817 AA
1 AA
43921819 CTTTTAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (16 bp):
AATAACAATTAATTTT
Found at i:43925735 original size:43 final size:43
Alignment explanation
Indices: 43925687--43925838 Score: 159
Period size: 43 Copynumber: 3.6 Consensus size: 43
43925677 TGTTTTTGTG
*
43925687 TAAGACCACGTCTGGGACGATGACATCAACTTGTATTTTCATA
1 TAAGACCACGTCTGGGACGATGACATCGACTTGTATTTTCATA
* *
43925730 TAAGACCACGTTTGGGACGATGGCATCGACTTGTATTTTCA-A
1 TAAGACCACGTCTGGGACGATGACATCGACTTGTATTTTCATA
* * * * * *
43925772 GTAAGACC-CTATCTAGGAAG-TGACATCGATTTGTGA-TTGCATG
1 -TAAGACCAC-GTCTGGGACGATGACATCGACTTGT-ATTTTCATA
*
43925815 TAAGACCACGTCTGGGACGTTGAC
1 TAAGACCACGTCTGGGACGATGAC
43925839 GTTGTACAAA
Statistics
Matches: 89, Mismatches: 14, Indels: 12
0.77 0.12 0.10
Matches are distributed among these distances:
42 32 0.36
43 57 0.64
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.29
Consensus pattern (43 bp):
TAAGACCACGTCTGGGACGATGACATCGACTTGTATTTTCATA
Found at i:43928760 original size:9 final size:9
Alignment explanation
Indices: 43928746--43928777 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
43928736 TATAGTTTGA
43928746 TATTCGAGT
1 TATTCGAGT
*
43928755 TATTCGAAT
1 TATTCGAGT
43928764 TATTCGAGT
1 TATTCGAGT
43928773 TATTC
1 TATTC
43928778 AAATTCGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.47
Consensus pattern (9 bp):
TATTCGAGT
Found at i:43928769 original size:18 final size:18
Alignment explanation
Indices: 43928746--43928782 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
43928736 TATAGTTTGA
*
43928746 TATTCGAGTTATTCGAAT
1 TATTCGAGTTATTCAAAT
43928764 TATTCGAGTTATTCAAAT
1 TATTCGAGTTATTCAAAT
43928782 T
1 T
43928783 CGAAAACTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (18 bp):
TATTCGAGTTATTCAAAT
Found at i:43939545 original size:6 final size:6
Alignment explanation
Indices: 43939498--43939547 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
43939488 AAAAAAATCC
*
43939498 TATTAT TATTATT TA-TTT TACTATTT TA-TTT TATTTT TATTTT TATTTT
1 TATTTT TATT-TT TATTTT TA-T-TTT TATTTT TATTTT TATTTT TATTTT
43939547 T
1 T
43939548 GCATGAAAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
5 9 0.24
6 21 0.55
7 3 0.08
8 5 0.13
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (6 bp):
TATTTT
Found at i:43939547 original size:18 final size:17
Alignment explanation
Indices: 43939500--43939546 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
43939490 AAAAATCCTA
*
43939500 TTATTATTA-TTTA-TT
1 TTATTTTTATTTTATTT
43939515 TTACTATTTTATTTTATTT
1 TTA-T-TTTTATTTTATTT
43939534 TTATTTTTATTTT
1 TTATTTTTATTTT
43939547 TGCATGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 3 0.11
16 1 0.04
17 13 0.48
18 5 0.19
19 5 0.19
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (17 bp):
TTATTTTTATTTTATTT
Found at i:43944198 original size:24 final size:24
Alignment explanation
Indices: 43944166--43944214 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
43944156 AAAATGAGAC
*
43944166 TAAATTAATAATTTAAATATCTAAA
1 TAAATTAATAATTTAAAGAT-TAAA
43944191 TAAA-TAATAATTTAAAGATTAAA
1 TAAATTAATAATTTAAAGATTAAA
43944214 T
1 T
43944215 TTGAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.22
24 14 0.61
25 4 0.17
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (24 bp):
TAAATTAATAATTTAAAGATTAAA
Done.