Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 131 of 132
Found at i:40736647 original size:2 final size:2
Alignment explanation
Indices: 40736640--40736690 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
40736630 CCAGCACTAT
40736640 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40736682 TA TA TA TA T
1 TA TA TA TA T
40736691 GAAAGTGCAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40738865 original size:34 final size:34
Alignment explanation
Indices: 40738822--40738890 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
40738812 AATAATATAA
* *
40738822 TTTATTTTGTAAACAAAAATTTATTTTAATAATT
1 TTTACTTTGTAAACAAAAATTTATTCTAATAATT
* * *
40738856 TTTACTTTGTAAATAAAAGTTTGTTCTAATAATT
1 TTTACTTTGTAAACAAAAATTTATTCTAATAATT
40738890 T
1 T
40738891 CTCAATTGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (34 bp):
TTTACTTTGTAAACAAAAATTTATTCTAATAATT
Found at i:40751607 original size:2 final size:2
Alignment explanation
Indices: 40751557--40751588 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
40751547 TCATGATTAA
40751557 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
40751589 TTAGCGATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40753127 original size:44 final size:44
Alignment explanation
Indices: 40753064--40753152 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
40753054 ATATATAGAC
40753064 ATACATAAAGATTGATTATTGATAGAGGACAATAGAAGGGAGCT
1 ATACATAAAGATTGATTATTGATAGAGGACAATAGAAGGGAGCT
40753108 ATACATAAAGATTGATTATTGATAGAGGACAATAGAAGGGAGCT
1 ATACATAAAGATTGATTATTGATAGAGGACAATAGAAGGGAGCT
40753152 A
1 A
40753153 AAAATCAAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.44, C:0.07, G:0.25, T:0.25
Consensus pattern (44 bp):
ATACATAAAGATTGATTATTGATAGAGGACAATAGAAGGGAGCT
Found at i:40753885 original size:12 final size:12
Alignment explanation
Indices: 40753868--40753898 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
40753858 CCCATTTCCG
40753868 CCGCCGTTTGCA
1 CCGCCGTTTGCA
40753880 CCGCCGTTTGCA
1 CCGCCGTTTGCA
*
40753892 CCACCGT
1 CCGCCGT
40753899 CATCTTCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.45, G:0.23, T:0.23
Consensus pattern (12 bp):
CCGCCGTTTGCA
Found at i:40756665 original size:45 final size:45
Alignment explanation
Indices: 40756614--40756707 Score: 188
Period size: 45 Copynumber: 2.1 Consensus size: 45
40756604 TATGAAGTGC
40756614 TATAAAAGGAAATATGGGTTATGTTCCTTTTTTAGATATTCATAA
1 TATAAAAGGAAATATGGGTTATGTTCCTTTTTTAGATATTCATAA
40756659 TATAAAAGGAAATATGGGTTATGTTCCTTTTTTAGATATTCATAA
1 TATAAAAGGAAATATGGGTTATGTTCCTTTTTTAGATATTCATAA
40756704 TATA
1 TATA
40756708 TGATTTTTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.43
Consensus pattern (45 bp):
TATAAAAGGAAATATGGGTTATGTTCCTTTTTTAGATATTCATAA
Found at i:40759075 original size:19 final size:19
Alignment explanation
Indices: 40759047--40759087 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
40759037 TTCATCCAAA
* *
40759047 AAAATCATATGTGATTCTT
1 AAAATAATATGTGATTATT
40759066 AAAATAATATGTGATTATT
1 AAAATAATATGTGATTATT
40759085 AAA
1 AAA
40759088 TATTCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (19 bp):
AAAATAATATGTGATTATT
Found at i:40763203 original size:6 final size:6
Alignment explanation
Indices: 40763192--40763223 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
40763182 AGATTGCAAA
40763192 TGGCAG TGGCAG TGGCAG TGGCAG T-GCAG TGG
1 TGGCAG TGGCAG TGGCAG TGGCAG TGGCAG TGG
40763224 GCAGGGGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.16, C:0.16, G:0.50, T:0.19
Consensus pattern (6 bp):
TGGCAG
Found at i:40763232 original size:18 final size:18
Alignment explanation
Indices: 40763193--40763232 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
40763183 GATTGCAAAT
*
40763193 GGCAGTGGCAGTGGCAGT
1 GGCAGTGGCAGTGGCAGG
40763211 GGCAGT-GCAGTGGGCAGG
1 GGCAGTGGCAGT-GGCAGG
40763229 GGCA
1 GGCA
40763233 TATGAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.17, C:0.17, G:0.53, T:0.12
Consensus pattern (18 bp):
GGCAGTGGCAGTGGCAGG
Found at i:40763711 original size:21 final size:21
Alignment explanation
Indices: 40763686--40763733 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
40763676 TGGTAGTAAT
*
40763686 ATTAATTATTGTAATAATAAA
1 ATTAAATATTGTAATAATAAA
*
40763707 ATTAAATATTGTAATAATAAG
1 ATTAAATATTGTAATAATAAA
40763728 ATTAAA
1 ATTAAA
40763734 AACAGTGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (21 bp):
ATTAAATATTGTAATAATAAA
Found at i:40775751 original size:21 final size:22
Alignment explanation
Indices: 40775727--40775769 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
40775717 AATTATAAAA
*
40775727 AAATTAAAATTAT-TAAATATT
1 AAATTAAAATAATGTAAATATT
40775748 AAATTAAAATAATGTAAATATT
1 AAATTAAAATAATGTAAATATT
40775770 TTTAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AAATTAAAATAATGTAAATATT
Found at i:40783368 original size:29 final size:29
Alignment explanation
Indices: 40783335--40783406 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 29
40783325 ATTACATTAG
*
40783335 TAGTCACTCAACTATAAAAAGTTAGAAAA
1 TAGTCACTCAACTATAAAAAGTTACAAAA
* * *
40783364 TAGTCACCCAACTATTAAAAGTTACAAAT
1 TAGTCACTCAACTATAAAAAGTTACAAAA
*
40783393 TGGTCACTCAACTA
1 TAGTCACTCAACTA
40783407 CTCAATTTTG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.26
Consensus pattern (29 bp):
TAGTCACTCAACTATAAAAAGTTACAAAA
Found at i:40783997 original size:2 final size:2
Alignment explanation
Indices: 40783992--40784032 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
40783982 ACATAAATAC
*
40783992 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40784033 TTGTGGTCCA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:40783999 original size:8 final size:8
Alignment explanation
Indices: 40783982--40784028 Score: 58
Period size: 8 Copynumber: 5.9 Consensus size: 8
40783972 TAATATTCAC
*
40783982 ACATAAAT
1 ACATATAT
40783990 ACATATAT
1 ACATATAT
40783998 ACATATAT
1 ACATATAT
*
40784006 ATATATAT
1 ACATATAT
*
40784014 ATATATAT
1 ACATATAT
*
40784022 ATATATA
1 ACATATA
40784029 ATATTTGTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 37 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (8 bp):
ACATATAT
Found at i:40785910 original size:18 final size:18
Alignment explanation
Indices: 40785884--40785937 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 18
40785874 TATTAAAAAG
40785884 TATATTTTTTATATTTTA
1 TATATTTTTTATATTTTA
* *
40785902 TATACTTTTAATGATTTTA
1 TATATTTTTTAT-ATTTTA
40785921 -ATGATTTTTTAT-TTTTA
1 TAT-ATTTTTTATATTTTA
40785938 AAAATAGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
17 5 0.17
18 12 0.40
19 13 0.43
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (18 bp):
TATATTTTTTATATTTTA
Found at i:40791679 original size:105 final size:105
Alignment explanation
Indices: 40791497--40791707 Score: 422
Period size: 105 Copynumber: 2.0 Consensus size: 105
40791487 CTTTGAGTTT
40791497 TAGGGTCATATTTAATTTCTGGGTTTGGTTTTTAATGTTATGTAATTGTAATTGTGTTGTTTAAG
1 TAGGGTCATATTTAATTTCTGGGTTTGGTTTTTAATGTTATGTAATTGTAATTGTGTTGTTTAAG
40791562 GATTTGGGTGTGTTTTGGTTTTGATTAATACTATGGATTG
66 GATTTGGGTGTGTTTTGGTTTTGATTAATACTATGGATTG
40791602 TAGGGTCATATTTAATTTCTGGGTTTGGTTTTTAATGTTATGTAATTGTAATTGTGTTGTTTAAG
1 TAGGGTCATATTTAATTTCTGGGTTTGGTTTTTAATGTTATGTAATTGTAATTGTGTTGTTTAAG
40791667 GATTTGGGTGTGTTTTGGTTTTGATTAATACTATGGATTG
66 GATTTGGGTGTGTTTTGGTTTTGATTAATACTATGGATTG
40791707 T
1 T
40791708 GGCTTGGATT
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 106 1.00
ACGTcount: A:0.20, C:0.03, G:0.26, T:0.52
Consensus pattern (105 bp):
TAGGGTCATATTTAATTTCTGGGTTTGGTTTTTAATGTTATGTAATTGTAATTGTGTTGTTTAAG
GATTTGGGTGTGTTTTGGTTTTGATTAATACTATGGATTG
Found at i:40810222 original size:20 final size:20
Alignment explanation
Indices: 40810197--40810236 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
40810187 ATACTTACCC
40810197 TAAA-TTAAAATTTTTAATAT
1 TAAATTTAAAA-TTTTAATAT
*
40810217 TAAATTTAGAATTTTAATAT
1 TAAATTTAAAATTTTAATAT
40810237 AAACAACACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TAAATTTAAAATTTTAATAT
Found at i:40813131 original size:16 final size:16
Alignment explanation
Indices: 40813110--40813142 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
40813100 AAGATTTAAG
40813110 TCATTTGATA-TTGAAA
1 TCATTT-ATATTTGAAA
40813126 TCATTTATATTTGAAA
1 TCATTTATATTTGAAA
40813142 T
1 T
40813143 AGAGGACACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.48
Consensus pattern (16 bp):
TCATTTATATTTGAAA
Found at i:40821816 original size:2 final size:2
Alignment explanation
Indices: 40821809--40821853 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
40821799 CATTGCATAG
*
40821809 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40821851 TA T
1 TA T
40821854 CGATGATGCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40826688 original size:5 final size:5
Alignment explanation
Indices: 40826678--40826708 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
40826668 TAGAAAAGCT
40826678 TATAA TATAA TATAA TATAA TATAA TATAA T
1 TATAA TATAA TATAA TATAA TATAA TATAA T
40826709 TCCGAATAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:40832367 original size:23 final size:23
Alignment explanation
Indices: 40832315--40832368 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 23
40832305 TATATTTAAT
40832315 TATTTTAA-AAATGATAAAATCA
1 TATTTTAATAAATGATAAAATCA
** * * *
40832337 TAAATTAATATATTATAAAATTA
1 TATTTTAATAAATGATAAAATCA
40832360 TATTTTAAT
1 TATTTTAAT
40832369 CTCTCAAATT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
TATTTTAATAAATGATAAAATCA
Found at i:40842889 original size:31 final size:31
Alignment explanation
Indices: 40842851--40842909 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
40842841 ATATGGTCAT
* **
40842851 TGAACTATTCGAAAGTTTTTATTTAAGTTAC
1 TGAACTATTCAAAAAATTTTATTTAAGTTAC
40842882 TGAACTATTCAAAAAATTTTATTTAAGT
1 TGAACTATTCAAAAAATTTTATTTAAGT
40842910 CACCAAATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.44
Consensus pattern (31 bp):
TGAACTATTCAAAAAATTTTATTTAAGTTAC
Found at i:40849493 original size:6 final size:6
Alignment explanation
Indices: 40849482--40849527 Score: 83
Period size: 6 Copynumber: 7.7 Consensus size: 6
40849472 AAGAGAATAC
*
40849482 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACACAT ACAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACAT
40849528 CTCCATTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (6 bp):
ACATAT
Found at i:40849655 original size:68 final size:66
Alignment explanation
Indices: 40849504--40849703 Score: 248
Period size: 68 Copynumber: 3.0 Consensus size: 66
40849494 ACATATACAT
* * * *
40849504 ATACATATACATATACACATACATCTCCATTATATAGCTTAAGGCCAGTAGTTACACAAACAAGA
1 ATACACATACACATA-ACATACATCTCCATTATATAACTTAAGGCCAGTAGTTACACAAATAAGA
*
40849569 GG
65 GA
* * * *
40849571 ATACACAT--ACAT---ATACATCTTCATTATAAAACTTAAGGATCAGCAGTTACACAAATAAGA
1 ATACACATACACATAACATACATCTCCATTATATAACTTAAGG-CCAGTAGTTACACAAATAAGA
40849631 GA
65 GA
40849633 ATACACATACACATAGACATACATCTCCATTATATAACTTAAAGGCCAGTAGTTACACAAATAAG
1 ATACACATACACATA-ACATACATCTCCATTATATAACTT-AAGGCCAGTAGTTACACAAATAAG
40849698 AGA
64 AGA
40849701 ATA
1 ATA
40849704 TATATACATA
Statistics
Matches: 112, Mismatches: 13, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
61 23 0.21
62 27 0.24
64 4 0.04
65 3 0.03
67 7 0.06
68 44 0.39
69 4 0.04
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.25
Consensus pattern (66 bp):
ATACACATACACATAACATACATCTCCATTATATAACTTAAGGCCAGTAGTTACACAAATAAGAG
A
Found at i:40849795 original size:20 final size:22
Alignment explanation
Indices: 40849770--40849813 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
40849760 GGCTATTAGT
40849770 TATACAAATA-AGA-GTATACA
1 TATACAAATACAGATGTATACA
*
40849790 TATACAAATACATATGTATACA
1 TATACAAATACAGATGTATACA
40849812 TA
1 TA
40849814 GAAAAAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
21 2 0.10
22 9 0.43
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (22 bp):
TATACAAATACAGATGTATACA
Found at i:40852112 original size:6 final size:6
Alignment explanation
Indices: 40852101--40852137 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
40852091 TCGCCTTTGG
40852101 TGTATA TGTATA --TATA TGTATA TGTATA TGTATA TGT
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGT
40852138 GTAAAAGTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.14
6 25 0.86
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.51
Consensus pattern (6 bp):
TGTATA
Found at i:40852301 original size:144 final size:147
Alignment explanation
Indices: 40852119--40852430 Score: 443
Period size: 144 Copynumber: 2.1 Consensus size: 147
40852109 TATATATATG
* * * * * *
40852119 TATATGTATATGTATATGTGTAAAAGTACGTATATTGCAATGCAACATAATTCTAATTATGCCAT
1 TATATG-ATATGTGTATGTATATATGTACATATATTGCAATGCAACATAATTCTAATAATGCCAT
* * * *
40852184 GGACATGAAGGATATGA-A-GGATAGATGATTCTTTTCGTAAATGTGTTATTGTTGGTGGTATG-
65 GGACATGAAGGATATGAGAGGGATAGATGATTCTTTTCCTAAATGTGCTATAG-TGATGGTATGA
40852246 TTTACAGCCAAGTGAATCC
129 TTTACAGCCAAGTGAATCC
* *
40852265 TTTATG-TATGTGTATGTATATATGTACATATATTGCAATGCAACATAATTCTAATAATGTCATG
1 TATATGATATGTGTATGTATATATGTACATATATTGCAATGCAACATAATTCTAATAATGCCATG
40852329 GACATGAAGGATATGAGGAGGGATAGATGATTCTTTTCCTAAATGTGCTATAGTGATGGTATGAT
66 GACATGAAGGATATGA-GAGGGATAGATGATTCTTTTCCTAAATGTGCTATAGTGATGGTATGAT
*
40852394 TTGCAGCCAAGTGAATCC
130 TTACAGCCAAGTGAATCC
40852412 TATATGTATATGTGTATGT
1 TATATG-ATATGTGTATGT
40852431 GTATCCTTTT
Statistics
Matches: 146, Mismatches: 14, Indels: 9
0.86 0.08 0.05
Matches are distributed among these distances:
144 67 0.46
146 15 0.10
147 53 0.36
149 11 0.08
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.37
Consensus pattern (147 bp):
TATATGATATGTGTATGTATATATGTACATATATTGCAATGCAACATAATTCTAATAATGCCATG
GACATGAAGGATATGAGAGGGATAGATGATTCTTTTCCTAAATGTGCTATAGTGATGGTATGATT
TACAGCCAAGTGAATCC
Found at i:40854991 original size:16 final size:17
Alignment explanation
Indices: 40854970--40855002 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40854960 AATGTTTTGG
*
40854970 TTATTTG-TTTTCTTTT
1 TTATTTGATTTTATTTT
40854986 TTATTTGATTTTATTTT
1 TTATTTGATTTTATTTT
40855003 ATGTGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.12, C:0.03, G:0.06, T:0.79
Consensus pattern (17 bp):
TTATTTGATTTTATTTT
Found at i:40859927 original size:31 final size:29
Alignment explanation
Indices: 40859892--40859954 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 29
40859882 AATATTTCTG
* * *
40859892 AAAGTTTTGAGGGGTCTAATTGCATTTTTCA
1 AAAGTTTTGAAGGGTATAA-TGAATTTTT-A
40859923 AAAGTTTTGAAGGGTATAATGAATTTTTA
1 AAAGTTTTGAAGGGTATAATGAATTTTTA
40859952 AAA
1 AAA
40859955 TTTGTTTGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 4 0.14
30 8 0.28
31 17 0.59
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.40
Consensus pattern (29 bp):
AAAGTTTTGAAGGGTATAATGAATTTTTA
Found at i:40861529 original size:24 final size:24
Alignment explanation
Indices: 40861492--40861554 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
40861482 TTCTGCATGT
** * *
40861492 GCACCTCCTGCACCATATACACCA
1 GCACCTCCACCACCAGAGACACCA
*
40861516 GCACCTCCACCACCAGAGCCACCA
1 GCACCTCCACCACCAGAGACACCA
* *
40861540 CCACCACCACCACCA
1 GCACCTCCACCACCA
40861555 CCACCGTGAC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.30, C:0.54, G:0.08, T:0.08
Consensus pattern (24 bp):
GCACCTCCACCACCAGAGACACCA
Found at i:40861530 original size:3 final size:3
Alignment explanation
Indices: 40861511--40861559 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
40861501 GCACCATATA
* * *
40861511 CAC CAG CAC CTC CAC CAC CA- GAGC CAC CAC CAC CAC CAC CAC CAC
1 CAC CAC CAC CAC CAC CAC CAC CA-C CAC CAC CAC CAC CAC CAC CAC
40861556 CAC C
1 CAC C
40861560 GTGACCACCT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
2 1 0.03
3 36 0.95
4 1 0.03
ACGTcount: A:0.31, C:0.61, G:0.06, T:0.02
Consensus pattern (3 bp):
CAC
Found at i:40861661 original size:30 final size:30
Alignment explanation
Indices: 40861598--40861676 Score: 90
Period size: 30 Copynumber: 2.6 Consensus size: 30
40861588 CCAGCTCCTT
*
40861598 CTCCACCGCCATATCCACCTGCATGAGCCC
1 CTCCACCACCATATCCACCTGCATGAGCCC
* * *
40861628 CTCCACCACCATATCCTCCTGCACT-TGCTC
1 CTCCACCACCATATCCACCTGCA-TGAGCCC
40861658 CTCCACCACCACT-TCCACC
1 CTCCACCACCA-TATCCACC
40861677 ACCACCTCCA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 40 0.95
31 2 0.05
ACGTcount: A:0.19, C:0.53, G:0.08, T:0.20
Consensus pattern (30 bp):
CTCCACCACCATATCCACCTGCATGAGCCC
Found at i:40861674 original size:12 final size:12
Alignment explanation
Indices: 40861657--40861686 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
40861647 TGCACTTGCT
40861657 CCTCCACCACCA
1 CCTCCACCACCA
*
40861669 CTTCCACCACCA
1 CCTCCACCACCA
40861681 CCTCCA
1 CCTCCA
40861687 TGTCCACCGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.23, C:0.63, G:0.00, T:0.13
Consensus pattern (12 bp):
CCTCCACCACCA
Found at i:40861742 original size:66 final size:66
Alignment explanation
Indices: 40861672--40862310 Score: 230
Period size: 66 Copynumber: 9.3 Consensus size: 66
40861662 ACCACCACTT
* * *
40861672 CCACCACCACCTCCATGTCCACCGGCGCCTCCATACCCGCCAGCACCACCAGCTCCGGCTCCTTC
1 CCACCACCACCTCCATGTCCACCGGCACCTCCATACCCACCAGCACCACCAGCTCCGCCTCCTTC
40861737 A
66 A
* * * * ** * * * * * ** * *
40861738 CCACCTCCACCACCATATCCAGAAGCTCCACCACCATATCCACCTGCACTAGCTCCGCCGCCACC
1 CCACCACCACCTCCATGTCC---ACCGGCACCTCCATACCCACCAGCACCACCAGCTCCGCCTCC
*
40861803 -ACTA
63 TTC-A
* *
40861807 CCACCACCACCTCCATGTCCACCGGCTCCTCCATACCCACTAGCACCACCAGCTCCGCCTCCTTC
1 CCACCACCACCTCCATGTCCACCGGCACCTCCATACCCACCAGCACCACCAGCTCCGCCTCCTTC
40861872 A
66 A
** * * * ** * * * * * * *
40861873 CCACTTCCACCACCATATCCAGAAGCTCCACCACCATATCCACCTGCACTAGCTCCACCGCCACC
1 CCACCACCACCTCCATGTCC---ACCGGCACCTCCATACCCACCAGCAC---CACCAGCTCC-GC
**
40861938 TCTACCACCA
59 -CT-CCTTCA
* * ** *
40861948 CCACCACCACCTCCAAT-TCCACCCGCTCCTCCATACCCGTCGGCACCACCAGCTCCGCCTCCTT
1 CCACCACCACCTCC-ATGTCCACCGGCACCTCCATACCCACCAGCACCACCAGCTCCGCCTCCTT
*
40862012 CG
65 CA
* * * ** * * * * * *
40862014 CCACCTCCACCTCCATATCCAGAAGCTCCACCACCATATCCACCTGCACTTGCTCC-GCCGCCAC
1 CCACCACCACCTCCATGTCC---ACCGGCACCTCCATACCCACCAGCAC---CACCAG-CTCC-G
*
40862078 CACTACC-ACTA
58 C-CT-CCTTC-A
* ** *
40862089 CCACCACCACCTCCATGTCCACCAGCTGCTCCATACCCACCGGCACCACCAGCTCCGCCTCCTTC
1 CCACCACCACCTCCATGTCCACCGGCACCTCCATACCCACCAGCACCACCAGCTCCGCCTCCTTC
40862154 A
66 A
* * * * ** * * * ** *
40862155 CCACCTCCACCACCATATCCAGAAGCTCCACCACCATATCCACCTG---CACTTGCTCCGCCACC
1 CCACCACCACCTCCATGTCC---ACCGGCACCTCCATACCCACCAGCACCACCAGCTCCGCC-TC
**
40862217 ACCACTA
62 -CTTC-A
* * **
40862224 CCACCACCACCTCCATGTCCACCAGCTCCTCCATACCCACTGGCACCACCAGCTCCGCCTCCTTC
1 CCACCACCACCTCCATGTCCACCGGCACCTCCATACCCACCAGCACCACCAGCTCCGCCTCCTTC
40862289 A
66 A
* * *
40862290 CCACCTCCACCACCATATCCA
1 CCACCACCACCTCCATGTCCA
40862311 GAAGCTTCAC
Statistics
Matches: 397, Mismatches: 138, Indels: 76
0.65 0.23 0.12
Matches are distributed among these distances:
65 2 0.01
66 146 0.37
67 9 0.02
68 6 0.02
69 137 0.35
70 1 0.00
71 1 0.00
72 48 0.12
73 2 0.01
74 5 0.01
75 38 0.10
76 2 0.01
ACGTcount: A:0.22, C:0.53, G:0.09, T:0.16
Consensus pattern (66 bp):
CCACCACCACCTCCATGTCCACCGGCACCTCCATACCCACCAGCACCACCAGCTCCGCCTCCTTC
A
Found at i:40861784 original size:135 final size:135
Alignment explanation
Indices: 40861628--40862355 Score: 1098
Period size: 135 Copynumber: 5.3 Consensus size: 135
40861618 GCATGAGCCC
* * * *
40861628 CTCCACCACCATATCCTCCTGCACTTGCTCCTCCACCACCACTTCCACCACCACCTCCATGTCCA
1 CTCCACCACCATATCCACCTGCACTAGCTCCGCCACCACCACTACCACCACCACCTCCATGTCCA
* * * * *
40861693 CCGGCGCCTCCATACCCGCCAGCACCACCAGCTCCGGCTCCTTCACCACCTCCACCACCATATCC
66 CCAGCTCCTCCATACCCACCGGCACCACCAGCTCCGCCTCCTTCACCACCTCCACCACCATATCC
40861758 AGAAG
131 AGAAG
*
40861763 CTCCACCACCATATCCACCTGCACTAGCTCCGCCGCCACCACTACCACCACCACCTCCATGTCCA
1 CTCCACCACCATATCCACCTGCACTAGCTCCGCCACCACCACTACCACCACCACCTCCATGTCCA
* ** *
40861828 CCGGCTCCTCCATACCCACTAGCACCACCAGCTCCGCCTCCTTCACCACTTCCACCACCATATCC
66 CCAGCTCCTCCATACCCACCGGCACCACCAGCTCCGCCTCCTTCACCACCTCCACCACCATATCC
40861893 AGAAG
131 AGAAG
*
40861898 CTCCACCACCATATCCACCTGCACTAGCTCCACCGCCACCTCTACCACCACCACCACCACCTCCA
1 CTCCACCACCATATCCACCTGCACTAGCT---CCGCCA-C-C-ACCACTACCACCACCACCTCC-
* ** * *
40861963 AT-TCCACCCGCTCCTCCATACCCGTCGGCACCACCAGCTCCGCCTCCTTCGCCACCTCCACCTC
59 ATGTCCACCAGCTCCTCCATACCCACCGGCACCACCAGCTCCGCCTCCTTCACCACCTCCACCAC
40862027 CATATCCAGAAG
124 CATATCCAGAAG
*
40862039 CTCCACCACCATATCCACCTGCACTTGCTCCGCCGCCACCACTACCACTACCACCACCACCTCCA
1 CTCCACCACCATATCCACCTGCACTAGCT---CCGCCA-C-C-ACCACTACCACCACCACCTCCA
*
40862104 TGTCCACCAGCTGCTCCATACCCACCGGCACCACCAGCTCCGCCTCCTTCACCACCTCCACCACC
60 TGTCCACCAGCTCCTCCATACCCACCGGCACCACCAGCTCCGCCTCCTTCACCACCTCCACCACC
40862169 ATATCCAGAAG
125 ATATCCAGAAG
*
40862180 CTCCACCACCATATCCACCTGCACTTGCTCCGCCACCACCACTACCACCACCACCTCCATGTCCA
1 CTCCACCACCATATCCACCTGCACTAGCTCCGCCACCACCACTACCACCACCACCTCCATGTCCA
*
40862245 CCAGCTCCTCCATACCCACTGGCACCACCAGCTCCGCCTCCTTCACCACCTCCACCACCATATCC
66 CCAGCTCCTCCATACCCACCGGCACCACCAGCTCCGCCTCCTTCACCACCTCCACCACCATATCC
40862310 AGAAG
131 AGAAG
* *
40862315 CTTCACCACCATATCCACCTGCACTAGCTCCACCACCACCA
1 CTCCACCACCATATCCACCTGCACTAGCTCCGCCACCACCA
40862356 TTGCCACCTC
Statistics
Matches: 550, Mismatches: 35, Indels: 16
0.92 0.06 0.03
Matches are distributed among these distances:
135 288 0.52
136 1 0.00
137 1 0.00
138 11 0.02
139 1 0.00
140 3 0.01
141 243 0.44
142 2 0.00
ACGTcount: A:0.22, C:0.53, G:0.09, T:0.16
Consensus pattern (135 bp):
CTCCACCACCATATCCACCTGCACTAGCTCCGCCACCACCACTACCACCACCACCTCCATGTCCA
CCAGCTCCTCCATACCCACCGGCACCACCAGCTCCGCCTCCTTCACCACCTCCACCACCATATCC
AGAAG
Found at i:40861981 original size:276 final size:270
Alignment explanation
Indices: 40861628--40862355 Score: 1116
Period size: 276 Copynumber: 2.7 Consensus size: 270
40861618 GCATGAGCCC
* * *
40861628 CTCCACCACCATATCCTCCTGCACTTGCTCCTCCACCACCACTTCCACCACCACCTCCATGTCCA
1 CTCCACCACCATATCCACCTGCACTTGCTCCGCCACCACCACTACCACCACCACCTCCATGTCCA
* * * *
40861693 CCGGCGCCTCCATACCCGCCAGCACCACCAGCTCCGGCTCCTTCACCACCTCCACCACCATATCC
66 CCAGCTCCTCCATACCCGCCGGCACCACCAGCTCCGCCTCCTTCACCACCTCCACCACCATATCC
40861758 AGAAGCTCCACCACCATATCCACCTGCACTAGCTCCGCCGCCACCACTACCACCACCACCTCCAT
131 AGAAGCTCCACCACCATATCCACCTGCACTAGCTCCGCCGCCACCACTACCACCACCACCTCCAT
* * *
40861823 GTCCACCGGCTCCTCCATACCCACTAGCACCACCAGCTCCGCCTCCTTCACCACTTCCACCACCA
196 GTCCACCAGCTCCTCCATACCCACCAGCACCACCAGCTCCGCCTCCTTCACCACCTCCACCACCA
40861888 TATCCAGAAG
261 TATCCAGAAG
* *
40861898 CTCCACCACCATATCCACCTGCACTAGCTCCACCGCCACCTCTACCACCACCACCACCACCTCCA
1 CTCCACCACCATATCCACCTGCACTTGCT---CCGCCA-C-C-ACCACTACCACCACCACCTCC-
* * * *
40861963 AT-TCCACCCGCTCCTCCATACCCGTCGGCACCACCAGCTCCGCCTCCTTCGCCACCTCCACCTC
59 ATGTCCACCAGCTCCTCCATACCCGCCGGCACCACCAGCTCCGCCTCCTTCACCACCTCCACCAC
*
40862027 CATATCCAGAAGCTCCACCACCATATCCACCTGCACTTGCTCCGCCGCCACCACTACCACTACCA
124 CATATCCAGAAGCTCCACCACCATATCCACCTGCACTAGCTCCGCCG----C-C-ACCACTACCA
* *
40862092 CCACCACCTCCATGTCCACCAGCTGCTCCATACCCACCGGCACCACCAGCTCCGCCTCCTTCACC
183 CCACCACCTCCATGTCCACCAGCTCCTCCATACCCACCAGCACCACCAGCTCCGCCTCCTTCACC
40862157 ACCTCCACCACCATATCCAGAAG
248 ACCTCCACCACCATATCCAGAAG
40862180 CTCCACCACCATATCCACCTGCACTTGCTCCGCCACCACCACTACCACCACCACCTCCATGTCCA
1 CTCCACCACCATATCCACCTGCACTTGCTCCGCCACCACCACTACCACCACCACCTCCATGTCCA
* *
40862245 CCAGCTCCTCCATACCCACTGGCACCACCAGCTCCGCCTCCTTCACCACCTCCACCACCATATCC
66 CCAGCTCCTCCATACCCGCCGGCACCACCAGCTCCGCCTCCTTCACCACCTCCACCACCATATCC
* * *
40862310 AGAAGCTTCACCACCATATCCACCTGCACTAGCTCCACCACCACCA
131 AGAAGCTCCACCACCATATCCACCTGCACTAGCTCCGCCGCCACCA
40862356 TTGCCACCTC
Statistics
Matches: 414, Mismatches: 30, Indels: 28
0.88 0.06 0.06
Matches are distributed among these distances:
270 31 0.07
271 1 0.00
272 1 0.00
273 5 0.01
274 1 0.00
275 3 0.01
276 239 0.58
277 3 0.01
278 1 0.00
279 6 0.01
280 1 0.00
281 1 0.00
282 121 0.29
ACGTcount: A:0.22, C:0.53, G:0.09, T:0.16
Consensus pattern (270 bp):
CTCCACCACCATATCCACCTGCACTTGCTCCGCCACCACCACTACCACCACCACCTCCATGTCCA
CCAGCTCCTCCATACCCGCCGGCACCACCAGCTCCGCCTCCTTCACCACCTCCACCACCATATCC
AGAAGCTCCACCACCATATCCACCTGCACTAGCTCCGCCGCCACCACTACCACCACCACCTCCAT
GTCCACCAGCTCCTCCATACCCACCAGCACCACCAGCTCCGCCTCCTTCACCACCTCCACCACCA
TATCCAGAAG
Found at i:40869966 original size:81 final size:82
Alignment explanation
Indices: 40869878--40870038 Score: 218
Period size: 81 Copynumber: 1.9 Consensus size: 82
40869868 ACCAGCTCAT
* * *
40869878 CCTCCATTTCCATACCCAGAAGCGCCATCTGCA-CTAGCTCCA-CCTCCACCACTGCCGCCACCA
1 CCTCCATTGCCATACCCAGAAGCACCACCTGCAGC-AGCTCCACCCTCCACCACTGCCGCCACCA
*
40869941 GCACCACCTCCTGCGCCA
65 ACACCACCTCCTGCGCCA
40869959 CCTCCATTGCCATACCCAGAAGCACCACCTGCAGCAGCTCCACCTTCGCCTCCACCACTGCCGCC
1 CCTCCATTGCCATACCCAGAAGCACCACCTGCAGCAGCTCCA----C-CCTCCACCACTGCCGCC
40870024 ACCAACACCACCTCC
61 ACCAACACCACCTCC
40870039 ATGCCCATTG
Statistics
Matches: 69, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
81 37 0.54
82 1 0.01
87 31 0.45
ACGTcount: A:0.22, C:0.52, G:0.12, T:0.15
Consensus pattern (82 bp):
CCTCCATTGCCATACCCAGAAGCACCACCTGCAGCAGCTCCACCCTCCACCACTGCCGCCACCAA
CACCACCTCCTGCGCCA
Found at i:40870349 original size:56 final size:55
Alignment explanation
Indices: 40870185--40870353 Score: 130
Period size: 56 Copynumber: 3.0 Consensus size: 55
40870175 CCTCCATAGG
* * *
40870185 CACCACCTCCAACACCATATCCAGAAGCTCCACCATCA-GCTCCACCTACACTACCT
1 CACCACCTCCACCACCGTATCCAGAAGCT-CACCACCATG-TCCACCTACACTACCT
* * * * * * * * *
40870241 CCCCACCACCACTACCGCCA-CCAGCA-C-CACCTCCTTGTCCACCGGCTCCACTACTT
1 CACCACCTCCACCACCG-TATCCAGAAGCTCACCACCATGTCCA-C--CTACACTACCT
*
40870297 CACCACCTCCACCACCGTATCCAGAAGCTTCACCACCATGTCCACCTGCACTACCT
1 CACCACCTCCACCACCGTATCCAGAAGC-TCACCACCATGTCCACCTACACTACCT
40870353 C
1 C
40870354 CCCCACCACC
Statistics
Matches: 83, Mismatches: 21, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
53 9 0.11
54 2 0.02
55 2 0.02
56 55 0.66
57 2 0.02
58 1 0.01
59 12 0.14
ACGTcount: A:0.25, C:0.51, G:0.08, T:0.17
Consensus pattern (55 bp):
CACCACCTCCACCACCGTATCCAGAAGCTCACCACCATGTCCACCTACACTACCT
Found at i:40874161 original size:22 final size:24
Alignment explanation
Indices: 40874114--40874168 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
40874104 TATTTATTAG
*
40874114 ATATTAATAATATTTTATATACAA
1 ATATTAATAATATTTTATATAAAA
40874138 ATATTCAATAAT-TTTT-TA-AAAA
1 ATATT-AATAATATTTTATATAAAA
*
40874160 ATATGAATA
1 ATATTAATA
40874169 TCAATACATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 4 0.14
22 7 0.25
23 2 0.07
24 9 0.32
25 6 0.21
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (24 bp):
ATATTAATAATATTTTATATAAAA
Found at i:40882686 original size:15 final size:15
Alignment explanation
Indices: 40882668--40882700 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
40882658 AATATCTTCT
40882668 CTTTTTGATAAAATG
1 CTTTTTGATAAAATG
*
40882683 CTTTTTGATAGAATG
1 CTTTTTGATAAAATG
40882698 CTT
1 CTT
40882701 AGAACTATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.09, G:0.15, T:0.48
Consensus pattern (15 bp):
CTTTTTGATAAAATG
Found at i:40883916 original size:24 final size:24
Alignment explanation
Indices: 40883889--40883934 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
40883879 ACTAATGTGG
*
40883889 TTAAAATGTTAGCACTATTAATCT
1 TTAAAATGATAGCACTATTAATCT
* *
40883913 TTAATATGATAGCATTATTAAT
1 TTAAAATGATAGCACTATTAAT
40883935 AATTTTATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (24 bp):
TTAAAATGATAGCACTATTAATCT
Found at i:40887243 original size:2 final size:2
Alignment explanation
Indices: 40887236--40887267 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
40887226 GCAAGGGTTG
40887236 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40887268 AATAAAATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40890406 original size:2 final size:2
Alignment explanation
Indices: 40890399--40890434 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
40890389 ATAATCACTC
40890399 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40890435 ATTAAATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40891422 original size:29 final size:30
Alignment explanation
Indices: 40891389--40891446 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
40891379 TCATGTATAT
40891389 AATTGCATCAA-A-TCAAAGTCCATATATTA
1 AATTGCA-CAAGATTCAAAGTCCATATATTA
*
40891418 AATTGCACAATGATTCAAAGTTCATATAT
1 AATTGCACAA-GATTCAAAGTCCATATAT
40891447 AATTTTGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 3 0.12
29 7 0.28
30 1 0.04
31 14 0.56
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.33
Consensus pattern (30 bp):
AATTGCACAAGATTCAAAGTCCATATATTA
Found at i:40891450 original size:29 final size:27
Alignment explanation
Indices: 40891384--40891450 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 27
40891374 AAGTTTCATG
40891384 TATATAATTGCATCAAATCAAAGTCCA
1 TATATAATTGCATCAAATCAAAGTCCA
*
40891411 TATATTAAATTGCA-CAATGATTCAAAGTTCA
1 TATA-T-AATTGCATCAA--A-TCAAAGTCCA
40891442 TATATAATT
1 TATATAATT
40891451 TTGAGATGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
27 4 0.12
28 4 0.12
29 11 0.32
30 2 0.06
31 13 0.38
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.36
Consensus pattern (27 bp):
TATATAATTGCATCAAATCAAAGTCCA
Found at i:40891849 original size:31 final size:30
Alignment explanation
Indices: 40891776--40891850 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 30
40891766 AAGTTTCTAT
*
40891776 AAATTCTTATTAAACCTCTAAAATTTTTGA
1 AAATTCTTATTAAACCTCTAAAATTTTTAA
* *
40891806 AAGTT-TTAATTAAACCTATTAAAATTTTTAA
1 AAATTCTT-ATTAAACCT-CTAAAATTTTTAA
40891837 AAATTCTTATTAAA
1 AAATTCTTATTAAA
40891851 TCCCAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
29 2 0.05
30 13 0.34
31 21 0.55
32 2 0.05
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (30 bp):
AAATTCTTATTAAACCTCTAAAATTTTTAA
Found at i:40900383 original size:2 final size:2
Alignment explanation
Indices: 40900378--40900402 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40900368 AAACCATTAT
40900378 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
40900403 TCTCCATTGC
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:40902014 original size:36 final size:34
Alignment explanation
Indices: 40901928--40902023 Score: 119
Period size: 30 Copynumber: 2.9 Consensus size: 34
40901918 AGAGGGATCG
*
40901928 AAATTAAATTATTTTTATTTTTATAATTTTTAAA
1 AAATTAAATTAATTTTATTTTTATAATTTTTAAA
*
40901962 AAATTAAATTAA----ATTTTTATCATTTTTAAA
1 AAATTAAATTAATTTTATTTTTATAATTTTTAAA
40901992 AAATTAAAATATAATTTTATTTTTATTAATTT
1 AAATT-AAAT-TAATTTTATTTTTA-TAATTT
40902024 AAAATTTTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
30 22 0.42
31 4 0.08
32 3 0.06
34 11 0.21
36 7 0.13
37 5 0.10
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (34 bp):
AAATTAAATTAATTTTATTTTTATAATTTTTAAA
Found at i:40909952 original size:81 final size:81
Alignment explanation
Indices: 40909817--40909978 Score: 202
Period size: 81 Copynumber: 2.0 Consensus size: 81
40909807 ATTCTGAAAT
* * * * ** * *
40909817 CAACAGCCAAGATACACAAGCATGTGATAAACATCTGCAAAGTTTTCCCACTGAAAATTTATTAC
1 CAACAGCCAAGATACACAAGCAAGTGACAAAAATATGCAAAGAATTCCCACTGAAAATCTATCAC
*
40909882 AAATTAAAAAATGTAC
66 AAATTAAAAAAGGTAC
40909898 CAACAGCCAAGATACACAAGCAAGTGACAAAGAATAT-CAATA-AATTCCCACTGAAAATCTATC
1 CAACAGCCAAGATACACAAGCAAGTGACAAA-AATATGCAA-AGAATTCCCACTGAAAATCTATC
*
40909961 ACAAATTCAAAAAGGTAC
64 ACAAATTAAAAAAGGTAC
40909979 ATTAAGCAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
81 65 0.94
82 4 0.06
ACGTcount: A:0.47, C:0.21, G:0.11, T:0.21
Consensus pattern (81 bp):
CAACAGCCAAGATACACAAGCAAGTGACAAAAATATGCAAAGAATTCCCACTGAAAATCTATCAC
AAATTAAAAAAGGTAC
Found at i:40924122 original size:28 final size:29
Alignment explanation
Indices: 40924096--40924460 Score: 178
Period size: 29 Copynumber: 12.5 Consensus size: 29
40924086 ACCCGGGGGC
*
40924096 AAAATGGTGATTTTGGTGAAATCGGGGTT
1 AAAATGGTAATTTTGGTGAAATCGGGGTT
40924125 AAAATGG-AATTTT-G-GAAAGTTCGAGGG-T
1 AAAATGGTAATTTTGGTGAAA--TCG-GGGTT
* *
40924153 AAAATGGTTATTTTTGGTGAAATCGGGGTG
1 AAAATGG-TAATTTTGGTGAAATCGGGGTT
*** * *
40924183 AAAATGG-AATTTTAAAAGATATGGGGGTT
1 AAAATGGTAATTTT-GGTGAAATCGGGGTT
* *
40924212 -AAATAGTAATTTTCGGTAAAATCGGGGTT
1 AAAATGGTAATTTT-GGTGAAATCGGGGTT
**
40924241 AAAAATGG-AATTTT--AAAAGATTCAGGGG-T
1 -AAAATGGTAATTTTGGTGAA-A-TC-GGGGTT
*
40924270 AAAATGGTAATTTTCGGTGAAATCGAGGTT
1 AAAATGGTAATTTT-GGTGAAATCGGGGTT
* *
40924300 AAAAATGG-AATTTT--AGAAGATTCGGGGGT
1 -AAAATGGTAATTTTGGTGAA-A-TCGGGGTT
* *
40924329 AAAAGGGTAATTTTCGATGAAATCGGGGTT
1 AAAATGGTAATTTT-GGTGAAATCGGGGTT
**
40924359 AAAAATGG-AATTTT--AAAAGATTCAGGGG-T
1 -AAAATGGTAATTTTGGTGAA-A-TC-GGGGTT
*
40924388 AAAATGGTAATTTTCGATGAAATCGGGGTT
1 AAAATGGTAATTTT-GGTGAAATCGGGGTT
*
40924418 AAAAATGG-AATTTT--AGAATATTCAGGGG-T
1 -AAAATGGTAATTTTGGTGAA-A-TC-GGGGTT
40924447 AAAATGGTAATTTT
1 AAAATGGTAATTTT
40924461 TGGAAGTTTT
Statistics
Matches: 260, Mismatches: 35, Indels: 82
0.69 0.09 0.22
Matches are distributed among these distances:
26 4 0.02
27 12 0.05
28 57 0.22
29 83 0.32
30 64 0.25
31 29 0.11
32 11 0.04
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.32
Consensus pattern (29 bp):
AAAATGGTAATTTTGGTGAAATCGGGGTT
Found at i:40924256 original size:59 final size:59
Alignment explanation
Indices: 40924089--40924460 Score: 511
Period size: 59 Copynumber: 6.4 Consensus size: 59
40924079 TTTGGATACC
* * *
40924089 CGGGGGCAAAATGGTGATTTT-GGTGAAATCGGGGTT-AAAATGGAATTTTGGAAAG-TT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTT-AAAAGATT
* * * *
40924146 CGAGGGTAAAATGGTTATTTTTGGTGAAATCGGGG-TGAAAATGGAATTTTAAAAGATAT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGAT-T
* * *
40924205 -GGGGGTTAAATAGTAATTTTCGGTAAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* * *
40924263 CAGGGGTAAAATGGTAATTTTCGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* *
40924322 CGGGGGTAAAAGGGTAATTTTCGATGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* * * *
40924381 CAGGGGTAAAATGGTAATTTTCGATGAAATCGGGGTTAAAAATGGAATTTTAGAATATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
*
40924440 CAGGGGTAAAATGGTAATTTT
1 CGGGGGTAAAATGGTAATTTT
40924461 TGGAAGTTTT
Statistics
Matches: 283, Mismatches: 26, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
57 23 0.08
58 56 0.20
59 204 0.72
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.31
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
Found at i:40924760 original size:162 final size:162
Alignment explanation
Indices: 40924592--40924930 Score: 448
Period size: 162 Copynumber: 2.1 Consensus size: 162
40924582 AGGCATCCAG
* * *** * *
40924592 CAGTCAAAGGATTAAGTTGTAAATTTTGAAAAAAAT-TTGGGCCAATTTCGTATTTAAATAAAAG
1 CAGTCAAAGGACTAAGTTATAAACCATG-AAAAAATCTTGGGCCAATTTCATAATTAAATAAAAG
* *
40924656 TTGATTTGGGGATTAAATTAAGACAAATTAAAAATAAAAAGGACTAAATGCATAAATAAACCAAA
65 TTGATTTGGGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAACCAAA
*** *
40924721 AGGTGACACGTGGTAG-CTCCTGGTACAGTCAAA
130 AAAAGACACGTGGCAGCCT-CTGGTACAGTCAAA
* *
40924754 CAGTCAAAGGACTAATTTATAAACCATGAAAAATTCTTGGGCCAATTTCATAATTAAATAAAAGT
1 CAGTCAAAGGACTAAGTTATAAACCATGAAAAAATCTTGGGCCAATTTCATAATTAAATAAAAGT
*** * * * *
40924819 TGATTTGGGGATTAAATTAAAACAAATTAAAAATGTCAGGGATTCAATGCAGAAATAATCCAAAA
66 TGATTTGGGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAACCAAAA
40924884 AAAGACACGTGGCAGCCTCTGGTACAGTCAAA
131 AAAGACACGTGGCAGCCTCTGGTACAGTCAAA
40924916 CAGTCAAAGGACTAA
1 CAGTCAAAGGACTAA
40924931 ATTGAAAAGC
Statistics
Matches: 153, Mismatches: 22, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
161 6 0.04
162 145 0.95
163 2 0.01
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.26
Consensus pattern (162 bp):
CAGTCAAAGGACTAAGTTATAAACCATGAAAAAATCTTGGGCCAATTTCATAATTAAATAAAAGT
TGATTTGGGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAACCAAAA
AAAGACACGTGGCAGCCTCTGGTACAGTCAAA
Found at i:40925584 original size:16 final size:16
Alignment explanation
Indices: 40925563--40925593 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
40925553 TTGATTTTTC
40925563 AAAACCCAGATCTGGG
1 AAAACCCAGATCTGGG
40925579 AAAACCCAGATCTGG
1 AAAACCCAGATCTGG
40925594 AAACATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.13
Consensus pattern (16 bp):
AAAACCCAGATCTGGG
Found at i:40926397 original size:20 final size:20
Alignment explanation
Indices: 40926359--40926397 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40926349 CAGGGCATGG
*
40926359 TGGAGCTTGGTGGTGGCAGA
1 TGGAGCTTGGTGGTAGCAGA
40926379 TGGAGC-TGGTGGTCAGCAG
1 TGGAGCTTGGTGGT-AGCAG
40926398 CATAGGCACG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.15, C:0.13, G:0.49, T:0.23
Consensus pattern (20 bp):
TGGAGCTTGGTGGTAGCAGA
Found at i:40926643 original size:6 final size:6
Alignment explanation
Indices: 40926626--40926724 Score: 85
Period size: 6 Copynumber: 16.2 Consensus size: 6
40926616 ACTTTTAATT
* * ** *
40926626 TTTAAA TGTTAAA TTTAATG TTTTAA TTTTTA TTTAAA TTTAAA TTCAAA
1 TTTAAA T-TTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
40926676 -GTAAA TTTAAA TAATTAAA TTTAAA TTTAAA -ATAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA T--TTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
40926724 T
1 T
40926725 AGAATTAAAA
Statistics
Matches: 75, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
5 7 0.09
6 52 0.69
7 10 0.13
8 6 0.08
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:40926680 original size:17 final size:16
Alignment explanation
Indices: 40926660--40926730 Score: 74
Period size: 17 Copynumber: 4.4 Consensus size: 16
40926650 AATTTTTATT
*
40926660 TAAATTTAAATTCAAAG
1 TAAATTTAAATT-AAAA
*
40926677 TAAATTTAAA-T-AAT
1 TAAATTTAAATTAAAA
40926691 TAAATTTAAATTTAAAA
1 TAAATTTAAA-TTAAAA
*
40926708 TAAATTTAAATTTAAA
1 TAAATTTAAATTAAAA
40926724 TAGAATT
1 TA-AATT
40926731 AAAAATCAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
14 12 0.26
16 9 0.19
17 26 0.55
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (16 bp):
TAAATTTAAATTAAAA
Found at i:40926694 original size:31 final size:31
Alignment explanation
Indices: 40926659--40926718 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
40926649 TAATTTTTAT
*
40926659 TTAAATTTAAATTCAAAGTAAATTTAAATAA
1 TTAAATTTAAATTCAAAATAAATTTAAATAA
*
40926690 TTAAATTTAAATTTAAAATAAATTTAAAT
1 TTAAATTTAAATTCAAAATAAATTTAAAT
40926719 TTAAATAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (31 bp):
TTAAATTTAAATTCAAAATAAATTTAAATAA
Found at i:40926751 original size:28 final size:28
Alignment explanation
Indices: 40926699--40926752 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
40926689 ATTAAATTTA
* *
40926699 AATTTAAAATAAATTTAAATTTAAATAG
1 AATTAAAAATAAATTTAAATCTAAATAG
* *
40926727 AATTAAAAATCAATTTAACTCTAAAT
1 AATTAAAAATAAATTTAAATCTAAAT
40926753 TAAACGAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (28 bp):
AATTAAAAATAAATTTAAATCTAAATAG
Found at i:40938708 original size:26 final size:27
Alignment explanation
Indices: 40938679--40938740 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
40938669 CAAACTTTGA
*
40938679 TTTAA-TGTATAATGTTATACATGAAT
1 TTTAATTGAATAATGTTATACATGAAT
*
40938705 TTTAATTTGAATAATTTTATACATGAAAT
1 TTTAA-TTGAATAATGTTATACATG-AAT
*
40938734 ATTAATT
1 TTTAATT
40938741 TAATTTAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 5 0.17
28 18 0.60
29 7 0.23
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.48
Consensus pattern (27 bp):
TTTAATTGAATAATGTTATACATGAAT
Found at i:40938724 original size:28 final size:29
Alignment explanation
Indices: 40938687--40938741 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
40938677 GATTTAATGT
*
40938687 ATAATGTTATACATG-AATTTTAATTTGA
1 ATAATGTTATACATGAAATATTAATTTGA
*
40938715 ATAATTTTATACATGAAATATTAATTT
1 ATAATGTTATACATGAAATATTAATTT
40938742 AATTTAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (29 bp):
ATAATGTTATACATGAAATATTAATTTGA
Found at i:40938839 original size:24 final size:24
Alignment explanation
Indices: 40938791--40938839 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
40938781 AGCATCATTT
* *
40938791 TAAGTATACATATTGTAATACAAA
1 TAAGTATACATATTCTAATAAAAA
40938815 TAAGTATACATA-TCTAATATAAAA
1 TAAGTATACATATTCTAATA-AAAA
40938839 T
1 T
40938840 TAAATTGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (24 bp):
TAAGTATACATATTCTAATAAAAA
Found at i:40944049 original size:6 final size:6
Alignment explanation
Indices: 40944040--40944090 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
40944030 CCAAAAAACT
40944040 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
40944088 TAT
1 TAT
40944091 GGCTAAAACT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:40944393 original size:6 final size:6
Alignment explanation
Indices: 40944382--40944435 Score: 81
Period size: 6 Copynumber: 9.0 Consensus size: 6
40944372 ACAACATCAC
* * *
40944382 TATATG TATATG TATATG CATATG CATATG TATATG TATATG CATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
40944430 TATATG
1 TATATG
40944436 AATGGTGGGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (6 bp):
TATATG
Found at i:40947930 original size:29 final size:28
Alignment explanation
Indices: 40947861--40947943 Score: 69
Period size: 29 Copynumber: 2.9 Consensus size: 28
40947851 TAAGTTTTAG
* * *
40947861 AAATGCTCATTAGGCTCTTAAAATTTTGA
1 AAAT-CTCATTAGACCCTCAAAATTTTGA
* *
40947890 AAATTTGAATTAGACCCTCAAAATTTTGA
1 AAATCT-CATTAGACCCTCAAAATTTTGA
*
40947919 AAACTCTCATTAAACACC-CAAAATT
1 AAA-TCTCATTAGAC-CCTCAAAATT
40947944 AAAAATCCCA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
28 1 0.02
29 38 0.88
30 4 0.09
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (28 bp):
AAATCTCATTAGACCCTCAAAATTTTGA
Found at i:40955085 original size:24 final size:24
Alignment explanation
Indices: 40955038--40955085 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
40955028 ATGGATGTTC
*
40955038 AACCTTCCATCTTTTTTGACCTTT
1 AACCTTCCATCTTTTTTAACCTTT
*
40955062 AACCTTCCATCTTTTTTAATCTTT
1 AACCTTCCATCTTTTTTAACCTTT
40955086 TATATTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.19, C:0.27, G:0.02, T:0.52
Consensus pattern (24 bp):
AACCTTCCATCTTTTTTAACCTTT
Found at i:40958187 original size:15 final size:16
Alignment explanation
Indices: 40958163--40958200 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
40958153 ATTTTAATAA
40958163 ATAA-TTTCTTTTGAT
1 ATAATTTTCTTTTGAT
*
40958178 AT-ATTTTCTTTTTAT
1 ATAATTTTCTTTTGAT
40958193 ATAATTTT
1 ATAATTTT
40958201 TATATGTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 14 0.70
16 5 0.25
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (16 bp):
ATAATTTTCTTTTGAT
Found at i:40967773 original size:16 final size:16
Alignment explanation
Indices: 40967752--40967783 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
40967742 TCTGCAAGAA
40967752 GAAGATTTTCAAAACT
1 GAAGATTTTCAAAACT
40967768 GAAGATTTTCAAAACT
1 GAAGATTTTCAAAACT
40967784 AAGGCCATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (16 bp):
GAAGATTTTCAAAACT
Found at i:40972487 original size:16 final size:16
Alignment explanation
Indices: 40972466--40972497 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
40972456 TCTGCAAGAA
40972466 GAAGATTTTCAAAACT
1 GAAGATTTTCAAAACT
40972482 GAAGATTTTCAAAACT
1 GAAGATTTTCAAAACT
40972498 AAGGCCATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (16 bp):
GAAGATTTTCAAAACT
Found at i:40977808 original size:16 final size:16
Alignment explanation
Indices: 40977787--40977822 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
40977777 TACTTTCGTA
40977787 TTCATGTTA-TTTTGGG
1 TTCATGTTAGTTTT-GG
40977803 TTCATGTTAGTTTTGG
1 TTCATGTTAGTTTTGG
40977819 TTCA
1 TTCA
40977823 AGTCGTTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.14, C:0.08, G:0.22, T:0.56
Consensus pattern (16 bp):
TTCATGTTAGTTTTGG
Found at i:40980259 original size:31 final size:30
Alignment explanation
Indices: 40980194--40980267 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
40980184 CTCTTAAAAA
* * **
40980194 TTTTGAAATTTAATTTTTTTATTTTTTTAT
1 TTTTAAAATTTAATTCTTTTATTTTCATAT
*
40980224 TTTTAGGAATTTAATTCTTTTACTTTTCATA-
1 TTTTA-AAATTTAATTCTTTTA-TTTTCATAT
40980255 TTTTAAAATTTAA
1 TTTTAAAATTTAA
40980268 ATTTAATTGC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
30 11 0.31
31 19 0.53
32 6 0.17
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (30 bp):
TTTTAAAATTTAATTCTTTTATTTTCATAT
Found at i:40982478 original size:96 final size:95
Alignment explanation
Indices: 40982327--40982880 Score: 701
Period size: 95 Copynumber: 5.9 Consensus size: 95
40982317 TTGGGTTCTT
* * *
40982327 TTTTTTTTCTGTTTTTAATCGGCTGTGTTTTCCATTGAATTTGAATATGTATATATAACTTCGAA
1 TTTTTTTTCT-TCTTTAATCGGCTGTATTTTCCATTGAATTTGAATATGTATATATAACTTTGAA
40982392 TCGATTTTTCAGCTTCATTGGGATTTTGGGG
65 TCGATTTTTCAGCTTCATTGGGATTTTGGGG
* * *
40982423 TTCTTTTTTCTTCTTTAATTGGTTGTATTTTCCATTGAATTTGAATATGTATATATAACTTTGAG
1 TT-TTTTTTCTTCTTTAATCGGCTGTATTTTCCATTGAATTTGAATATGTATATATAACTTTGAA
* * *
40982488 TCGATTTTTCAGATTTATTGGGATTTTTGGG
65 TCGATTTTTCAGCTTCATTGGGATTTTGGGG
** * *
40982519 TTCATTTTCTTCTTTAGTCGGCTGTATTTTCCATTGAATATGAATATGTATATATAACTTTGAAT
1 TTTTTTTTCTTCTTTAATCGGCTGTATTTTCCATTGAATTTGAATATGTATATATAACTTTGAAT
*
40982584 CGACTTTTCAGCTTCATTGGGATTTTGGGG
66 CGATTTTTCAGCTTCATTGGGATTTTGGGG
* **** * *
40982614 GTTTCCCCCTTCTTTAATCGGCTGCATTTTCCATTGAATTTG-A-ATGTATATATAACTTTTAAT
1 TTTTTTTTCTTCTTTAATCGGCTGTATTTTCCATTGAATTTGAATATGTATATATAACTTTGAAT
* *
40982677 CGATTTTTCGGCTTCATTGGGATTTT--TG
66 CGATTTTTCAGCTTCATTGGGATTTTGGGG
* * * * * * *
40982705 TTTTTTCTC-CCTTTAATTGGCTGTATTTTTCATTGAATTTGAATGTGTATATATAAATATGAAT
1 TTTTTTTTCTTCTTTAATCGGCTGTATTTTCCATTGAATTTGAATATGTATATATAACTTTGAAT
* *
40982769 TGATTTTTCAGCTTCATTGGGATTTTTGGG
66 CGATTTTTCAGCTTCATTGGGATTTTGGGG
* *
40982799 TTTTCTTTT-TTCCTTTAGTCGGCTGTATTTTTCATTGAATTTG-A-ATGTATATATAACTTTGA
1 TTTT-TTTTCTT-CTTTAATCGGCTGTATTTTCCATTGAATTTGAATATGTATATATAACTTTGA
*
40982861 ATCGATGTTTCAGCTTCATT
64 ATCGATTTTTCAGCTTCATT
40982881 TGCATGCGGG
Statistics
Matches: 392, Mismatches: 58, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
90 28 0.07
91 7 0.02
92 40 0.10
93 43 0.11
94 39 0.10
95 118 0.30
96 109 0.28
97 8 0.02
ACGTcount: A:0.21, C:0.12, G:0.17, T:0.50
Consensus pattern (95 bp):
TTTTTTTTCTTCTTTAATCGGCTGTATTTTCCATTGAATTTGAATATGTATATATAACTTTGAAT
CGATTTTTCAGCTTCATTGGGATTTTGGGG
Found at i:40982579 original size:95 final size:94
Alignment explanation
Indices: 40982331--40982880 Score: 686
Period size: 96 Copynumber: 5.8 Consensus size: 94
40982321 GTTCTTTTTT
* * *
40982331 TTTTCTGTTTTTAATCGGCTGTGTTTTCCATTGAATTTGAATATGTATATATAACTTCGAATCGA
1 TTTTCT-TCTTTAATCGGCTGTATTTTCCATTGAATTTGAATATGTATATATAACTTTGAATCGA
*
40982396 TTTTTCAGCTTCATTGGGATTTTGGGGTTC
65 TTTTTCAGCTTCATTGGGATTTTTGGGTTC
* * *
40982426 TTTTTTCTTCTTTAATTGGTTGTATTTTCCATTGAATTTGAATATGTATATATAACTTTGAGTCG
1 --TTTTCTTCTTTAATCGGCTGTATTTTCCATTGAATTTGAATATGTATATATAACTTTGAATCG
* *
40982491 ATTTTTCAGATTTATTGGGATTTTTGGGTTC
64 ATTTTTCAGCTTCATTGGGATTTTTGGGTTC
* *
40982522 ATTTTCTTCTTTAGTCGGCTGTATTTTCCATTGAATATGAATATGTATATATAACTTTGAATCGA
1 -TTTTCTTCTTTAATCGGCTGTATTTTCCATTGAATTTGAATATGTATATATAACTTTGAATCGA
* *
40982587 CTTTTCAGCTTCATTGGGATTTTGGGGGTT-
65 TTTTTCAGCTTCATTGGGATTTT-TGGGTTC
*** * *
40982617 TCCCCCTTCTTTAATCGGCTGCATTTTCCATTGAATTTG-A-ATGTATATATAACTTTTAATCGA
1 T-TTTCTTCTTTAATCGGCTGTATTTTCCATTGAATTTGAATATGTATATATAACTTTGAATCGA
*
40982680 TTTTTCGGCTTCATTGGGATTTTT--GTT-
65 TTTTTCAGCTTCATTGGGATTTTTGGGTTC
* * * * * * *
40982707 TTTTCTCCCTTTAATTGGCTGTATTTTTCATTGAATTTGAATGTGTATATATAAATATGAATTGA
1 TTTTCT-TCTTTAATCGGCTGTATTTTCCATTGAATTTGAATATGTATATATAACTTTGAATCGA
40982772 TTTTTCAGCTTCATTGGGATTTTTGGGTTTTC
65 TTTTTCAGCTTCATTGGGATTTTTGGG--TTC
* *
40982804 TTTT-TTCCTTTAGTCGGCTGTATTTTTCATTGAATTTG-A-ATGTATATATAACTTTGAATCGA
1 TTTTCTT-CTTTAATCGGCTGTATTTTCCATTGAATTTGAATATGTATATATAACTTTGAATCGA
*
40982866 TGTTTCAGCTTCATT
65 TTTTTCAGCTTCATT
40982881 TGCATGCGGG
Statistics
Matches: 392, Mismatches: 50, Indels: 25
0.84 0.11 0.05
Matches are distributed among these distances:
89 2 0.01
90 32 0.08
91 1 0.00
92 41 0.10
93 43 0.11
94 36 0.09
95 111 0.28
96 116 0.30
97 10 0.03
ACGTcount: A:0.21, C:0.12, G:0.17, T:0.50
Consensus pattern (94 bp):
TTTTCTTCTTTAATCGGCTGTATTTTCCATTGAATTTGAATATGTATATATAACTTTGAATCGAT
TTTTCAGCTTCATTGGGATTTTTGGGTTC
Found at i:40987721 original size:23 final size:24
Alignment explanation
Indices: 40987660--40987746 Score: 67
Period size: 23 Copynumber: 3.8 Consensus size: 24
40987650 TATTTTAAAA
* * **
40987660 ATTATAAAAATATAAATTATTAAA
1 ATTATAAAAATATATATTTTTATT
*
40987684 ATTATCAAAAT-TATATTTTTATT
1 ATTATAAAAATATATATTTTTATT
* *
40987707 ATTAT-AAAATATATAATTTAATT
1 ATTATAAAAATATATATTTTTATT
*
40987730 -TCATAAAAA-ATAT-TTTT
1 ATTATAAAAATATATATTTT
40987747 CTAACTCCAC
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
21 3 0.06
22 12 0.23
23 27 0.52
24 10 0.19
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTATAAAAATATATATTTTTATT
Found at i:40992464 original size:21 final size:22
Alignment explanation
Indices: 40992440--40992481 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
40992430 AAAATATTAC
*
40992440 AAAATAATTTTTTA-ATTTTTA
1 AAAATAATTTTATATATTTTTA
*
40992461 AAAATAGTTTTATATATTTTT
1 AAAATAATTTTATATATTTTT
40992482 TGAATTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
AAAATAATTTTATATATTTTTA
Found at i:40999129 original size:35 final size:35
Alignment explanation
Indices: 40999073--40999139 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
40999063 AATTCCTGAC
* *
40999073 AAAATTTGAGATTTAATTTTTTGTGTTTAAAAAATT
1 AAAATTTCAGATTTAATTTTTT-TATTTAAAAAATT
*
40999109 AAAATTTCAG-TTTTATTTTTTTATTTAAAAA
1 AAAATTTCAGATTTAATTTTTTTATTTAAAAA
40999140 TTTCAGCTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 9 0.32
35 10 0.36
36 9 0.32
ACGTcount: A:0.39, C:0.01, G:0.07, T:0.52
Consensus pattern (35 bp):
AAAATTTCAGATTTAATTTTTTTATTTAAAAAATT
Found at i:41010657 original size:2 final size:2
Alignment explanation
Indices: 41010652--41010680 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
41010642 CCCCCCCCCC
41010652 CT CT CT CT CT CT CT CT CT CT CT -T CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
41010681 TCTGCTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:41017327 original size:22 final size:21
Alignment explanation
Indices: 41017285--41017328 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
41017275 CTAGAGACCC
* * *
41017285 AAAAAAAGTCTTTATAGACCT
1 AAAAAAAGTCGTTAAAAACCT
41017306 AAAAAAACGTCGTTAAAAACCT
1 AAAAAAA-GTCGTTAAAAACCT
41017328 A
1 A
41017329 TTTTTCTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.52, C:0.16, G:0.09, T:0.23
Consensus pattern (21 bp):
AAAAAAAGTCGTTAAAAACCT
Found at i:41023536 original size:23 final size:20
Alignment explanation
Indices: 41023487--41023534 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
41023477 ACTATTATAT
* *
41023487 TTATTTATTAATTTTTAAAT
1 TTATTTATTAATTGTTAAAA
41023507 TTATTTATTAACTTGTTAATAA
1 TTATTTATTAA-TTGTTAA-AA
41023529 TTATTT
1 TTATTT
41023535 TAATATTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 11 0.46
21 6 0.25
22 7 0.29
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
TTATTTATTAATTGTTAAAA
Found at i:41031616 original size:10 final size:9
Alignment explanation
Indices: 41031595--41031638 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 9
41031585 TCAATAAATA
41031595 AAAAGAAAAG
1 AAAA-AAAAG
41031605 AAAAAAAGAG
1 AAAAAAA-AG
41031615 AAAAAAAAGG
1 AAAAAAAA-G
41031625 AAAAAAAAAG
1 -AAAAAAAAG
41031635 AAAA
1 AAAA
41031639 TGAGAGGTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
9 8 0.26
10 15 0.48
11 8 0.26
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:41031619 original size:11 final size:11
Alignment explanation
Indices: 41031605--41031638 Score: 54
Period size: 10 Copynumber: 3.3 Consensus size: 11
41031595 AAAAGAAAAG
41031605 AAAAAAAGAGA
1 AAAAAAAGAGA
41031616 AAAAAAAG-GA
1 AAAAAAAGAGA
41031626 AAAAAAA-AGA
1 AAAAAAAGAGA
41031636 AAA
1 AAA
41031639 TGAGAGGTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 14 0.64
11 8 0.36
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAGA
Found at i:41031627 original size:20 final size:21
Alignment explanation
Indices: 41031594--41031638 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
41031584 TTCAATAAAT
*
41031594 AAAAAGAAAAGAAAAAAAGAG
1 AAAAAGAAAAGAAAAAAAAAG
*
41031615 AAAAA-AAAGGAAAAAAAAAG
1 AAAAAGAAAAGAAAAAAAAAG
41031635 AAAA
1 AAAA
41031639 TGAGAGGTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (21 bp):
AAAAAGAAAAGAAAAAAAAAG
Found at i:41033046 original size:51 final size:50
Alignment explanation
Indices: 41032891--41033048 Score: 142
Period size: 50 Copynumber: 3.1 Consensus size: 50
41032881 CAGGTTTGAC
* * *
41032891 GGGAAAGATCTAAGACCACAATGGCGGATCCAGTATCGCAAAGATACTAAA
1 GGGAAAGATCTAAGACCACAATGGCGGATCCAGTACCACAAA-ATACAAAA
* * * * * * * * *
41032942 GGGAAAGGTCTAAG-TCGCAACGGCGGA-CCGTGTACCTCAGAA-GCATGAA
1 GGGAAAGATCTAAGACCACAATGGCGGATCC-AGTACCACAAAATACA-AAA
*
41032991 GGGAAAGATCTAAGACCACAATGGCAGATCCAGTACCACAAATATACAAAA
1 GGGAAAGATCTAAGACCACAATGGCGGATCCAGTACCACAAA-ATACAAAA
41033042 GGGAAAG
1 GGGAAAG
41033049 GTTTAAGTCG
Statistics
Matches: 80, Mismatches: 21, Indels: 12
0.71 0.19 0.11
Matches are distributed among these distances:
48 1 0.01
49 18 0.22
50 34 0.43
51 25 0.31
52 2 0.03
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14
Consensus pattern (50 bp):
GGGAAAGATCTAAGACCACAATGGCGGATCCAGTACCACAAAATACAAAA
Found at i:41033077 original size:100 final size:101
Alignment explanation
Indices: 41032891--41033093 Score: 293
Period size: 100 Copynumber: 2.0 Consensus size: 101
41032881 CAGGTTTGAC
* * * *
41032891 GGGAAAGATCTAAGACCACAATGGCGGATCCAGTATCGCAAAGATACTAAAGGGAAAGGTCTAAG
1 GGGAAAGATCTAAGACCACAATGGCAGATCCAGTACCACAAAGATACAAAAGGGAAAGGTCTAAG
* * *
41032956 TCGCAACGGCGGACCGTGTACCTCAGAAGCAT-GAA
66 TCGCAACGACGAACCGTGTACCTCAGAAACATGGAA
* *
41032991 GGGAAAGATCTAAGACCACAATGGCAGATCCAGTACCACAAATATACAAAAGGGAAAGGTTTAAG
1 GGGAAAGATCTAAGACCACAATGGCAGATCCAGTACCACAAAGATACAAAAGGGAAAGGTCTAAG
*
41033056 TCGCAACGACGAACCCG-GTACCTTAGAAACATGGAA
66 TCGCAACGACGAA-CCGTGTACCTCAGAAACATGGAA
41033092 GG
1 GG
41033094 TCAAATCCAC
Statistics
Matches: 91, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
100 83 0.91
101 8 0.09
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.15
Consensus pattern (101 bp):
GGGAAAGATCTAAGACCACAATGGCAGATCCAGTACCACAAAGATACAAAAGGGAAAGGTCTAAG
TCGCAACGACGAACCGTGTACCTCAGAAACATGGAA
Found at i:41033225 original size:52 final size:51
Alignment explanation
Indices: 41033160--41033417 Score: 174
Period size: 52 Copynumber: 5.4 Consensus size: 51
41033150 TAGCGAACCT
41033160 TTAT-CTCTCTGAAGTTATAGTAGGAGCAAGATGAAGTTTCAAATGTCAATTC
1 TTATCCTCT-TGAAGTTATAGTA-GAGCAAGATGAAGTTTCAAATGTCAATTC
* * * *
41033212 TTATCCCCTTGAAGTTATAGT--A--AAGTTG--G-AT--AATG--AA-CC
1 TTATCCTCTTGAAGTTATAGTAGAGCAAGATGAAGTTTCAAATGTCAATTC
*
41033251 TTTAT-CTCTCTGAAGTTATAGTAAGAGCAAGATGAAGTTTCAAACGTCAATTC
1 -TTATCCTCT-TGAAGTTATAGT-AGAGCAAGATGAAGTTTCAAATGTCAATTC
* * *
41033304 TTATCCTCTTGAAGTTATAGT--A--AAGTTG--G-AT--AATG--AA-CC
1 TTATCCTCTTGAAGTTATAGTAGAGCAAGATGAAGTTTCAAATGTCAATTC
*
41033343 TTTAT-CTCTCTGAAGTTATAGTAAGAGCAAGATGAAGTTTCAAACGTCAATTC
1 -TTATCCTCT-TGAAGTTATAGT-AGAGCAAGATGAAGTTTCAAATGTCAATTC
41033396 TTATCCTCTTGAAGTTATAGTA
1 TTATCCTCTTGAAGTTATAGTA
41033418 AAGTTGGATA
Statistics
Matches: 156, Mismatches: 17, Indels: 67
0.65 0.07 0.28
Matches are distributed among these distances:
39 9 0.06
40 36 0.23
42 7 0.04
43 2 0.01
44 2 0.01
45 12 0.08
47 12 0.08
48 2 0.01
49 2 0.01
50 6 0.04
51 1 0.01
52 52 0.33
53 13 0.08
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.35
Consensus pattern (51 bp):
TTATCCTCTTGAAGTTATAGTAGAGCAAGATGAAGTTTCAAATGTCAATTC
Found at i:41033256 original size:40 final size:40
Alignment explanation
Indices: 41033221--41033366 Score: 132
Period size: 40 Copynumber: 3.4 Consensus size: 40
41033211 CTTATCCCCT
41033221 TGAAGTTATAGTAAAGTTGGATAATGAACCTTTATCTCTC
1 TGAAGTTATAGTAAAGTTGGATAATGAACCTTTATCTCTC
*** *
41033261 TGAAGTTATAGTAAGAGCAAGATGAAGTTTCAAACGTCAATTCTTATC-CTC
1 TGAAGTTATAGTAA-AGTTGGAT-AA---T-GAAC--C---T-TTATCTCTC
41033312 TTGAAGTTATAGTAAAGTTGGATAATGAACCTTTATCTCTC
1 -TGAAGTTATAGTAAAGTTGGATAATGAACCTTTATCTCTC
41033353 TGAAGTTATAGTAA
1 TGAAGTTATAGTAA
41033367 GAGCAAGATG
Statistics
Matches: 84, Mismatches: 8, Indels: 28
0.70 0.07 0.23
Matches are distributed among these distances:
40 33 0.39
41 9 0.11
42 2 0.02
44 1 0.01
45 1 0.01
46 6 0.07
47 1 0.01
48 1 0.01
50 2 0.02
51 9 0.11
52 19 0.23
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (40 bp):
TGAAGTTATAGTAAAGTTGGATAATGAACCTTTATCTCTC
Found at i:41033315 original size:92 final size:91
Alignment explanation
Indices: 41033158--41033741 Score: 762
Period size: 92 Copynumber: 6.4 Consensus size: 91
41033148 AATAGCGAAC
* ** *
41033158 CTTTATCTCTCTGAAGTTATAGTAGGAGCAAGATGAAGTTTCAAATGTCAATTCTTATCCCCTTG
1 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCTTATCCTCTTG
*
41033223 AAGTTATAGTAAAGTTGGATAATGAAC
66 AAGTTATAGTAAAGTTGGATAA-GAAT
*
41033250 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGTTTCAAACGTCAATTCTTATCCTCTTG
1 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCTTATCCTCTTG
*
41033315 AAGTTATAGTAAAGTTGGATAATGAAC
66 AAGTTATAGTAAAGTTGGATAA-GAAT
*
41033342 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGTTTCAAACGTCAATTCTTATCCTCTTG
1 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCTTATCCTCTTG
41033407 AAGTTATAGTAAAGTTGGATAACGAAT
66 AAGTTATAGTAAAGTTGGATAA-GAAT
* ** * * *
41033434 CTTTATCTCTCTAAAGTTATAGTAAGAGCAAGATGAAG-CACCAACATCATTTCCTATCCTCTTG
1 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCTTATCCTCTTG
* *
41033498 AAGTTGTAGTAAAGCTGGAT-AGCAAGT
66 AAGTTATAGTAAAGTTGGATAAG-AA-T
* * * ** ** *
41033525 CTTTATCTCTCTGAACTTGTAATAAGAGCAAGATGAAG-CACCGACATCAATTCTTATTCTCTTG
1 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCTTATCCTCTTG
*
41033589 AAGTTATAGTAAAGTTGGATAACAATT
66 AAGTTATAGTAAAGTTGGATAAGAA-T
* ** *
41033616 CTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCTCTTG
1 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCTTATCCTCTTG
**
41033681 AAGTTGCAGTAAAGTTGGAT-AGCAAGT
66 AAGTTATAGTAAAGTTGGATAAG-AA-T
* * *
41033708 CTTTATATCTCTGAAGTTGTAGTAAAAGCAAGAT
1 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGAT
41033742 AAAGCCTCGA
Statistics
Matches: 447, Mismatches: 40, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
89 1 0.00
90 3 0.01
91 153 0.34
92 290 0.65
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (91 bp):
CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCTTATCCTCTTG
AAGTTATAGTAAAGTTGGATAAGAAT
Found at i:41033649 original size:274 final size:275
Alignment explanation
Indices: 41033153--41033746 Score: 777
Period size: 274 Copynumber: 2.2 Consensus size: 275
41033143 TCAAAAATAG
* * *** *
41033153 CGAACCTTTATCTCTCTGAAGTTATAGTAGGAGCAAGATGAAGTTTCAAATGTCAATTCTTATCC
1 CGAATCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCACCAAA-GTCAATTCCTATCC
* * *
41033218 CCTTGAAGTTATAGTAAAGTTGGATAATGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGA
65 CCTTGAAGTTATAGTAAAGCTGGATAATGAACCTTTATCTCTCTGAACTTATAATAAGAGCAAGA
** * *
41033283 TGAAGTTTCAAACGTCAATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAATGAACCTTTAT
130 TGAAGTCACAAACATCAATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAATCAACCTTTAT
** * *
41033348 CTCTCTGAAGTTATAGTAAGAGCAAGATGAAGTTTCAAACGTCAATTCTTATCCTCTTGAAGTTA
195 CTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCTCTTGAAGTTA
*
41033413 TAGTAAAGTTGGATAA
260 CAGTAAAGTTGGATAA
* *
41033429 CGAATCTTTATCTCTCTAAAGTTATAGTAAGAGCAAGATGAAGCACCAACA-TCATTTCCTATCC
1 CGAATCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCACCAA-AGTCAATTCCTATCC
* * * *
41033493 TCTTGAAGTTGTAGTAAAGCTGGAT-A-GCAAGTCTTTATCTCTCTGAACTTGTAATAAGAGCAA
65 CCTTGAAGTTATAGTAAAGCTGGATAATG-AA-CCTTTATCTCTCTGAACTTATAATAAGAGCAA
** * *
41033556 GATGAAG-CACCGACATCAATTCTTATTCTCTTGAAGTTATAGTAAAGTTGGATAA-CAATTCTT
128 GATGAAGTCACAAACATCAATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAATCAA-CCTT
*
41033619 TATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCTCTTGAAG
192 TATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCTCTTGAAG
* *
41033684 TTGCAGTAAAGTTGGATAG
257 TTACAGTAAAGTTGGATAA
* * * *
41033703 C-AAGTCTTTATATCTCTGAAGTTGTAGTAAAAGCAAGATAAAGC
1 CGAA-TCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGC
41033747 CTCGACATCA
Statistics
Matches: 277, Mismatches: 36, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
273 5 0.02
274 160 0.58
275 68 0.25
276 43 0.16
277 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Consensus pattern (275 bp):
CGAATCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCACCAAAGTCAATTCCTATCCC
CTTGAAGTTATAGTAAAGCTGGATAATGAACCTTTATCTCTCTGAACTTATAATAAGAGCAAGAT
GAAGTCACAAACATCAATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAATCAACCTTTATC
TCTCTGAAGTTATAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCTCTTGAAGTTAC
AGTAAAGTTGGATAA
Found at i:41034018 original size:11 final size:11
Alignment explanation
Indices: 41034002--41034083 Score: 73
Period size: 11 Copynumber: 7.5 Consensus size: 11
41033992 TCAAATCATT
*
41034002 TTAAATTTATA
1 TTAAATTTAAA
41034013 TTAAATTTAAA
1 TTAAATTTAAA
* *
41034024 TTTATTTTAAA
1 TTAAATTTAAA
41034035 TTTAAATTT--A
1 -TTAAATTTAAA
41034045 TTAAATTTAAA
1 TTAAATTTAAA
*
41034056 TTTAGATTT-AA
1 -TTAAATTTAAA
41034067 TATAAATTT-AA
1 T-TAAATTTAAA
41034078 TTAAAT
1 TTAAAT
41034084 GAAGTCCAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
9 8 0.14
10 7 0.12
11 31 0.53
12 13 0.22
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:41034022 original size:6 final size:6
Alignment explanation
Indices: 41034001--41034077 Score: 76
Period size: 6 Copynumber: 13.8 Consensus size: 6
41033991 ATCAAATCAT
* *
41034001 TTTAAA TTTATA -TTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTT--A
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
41034045 -TTAAA TTTAAA TTTAGA TTT-AA TATAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
41034078 TTAAATGAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
3 2 0.04
4 1 0.02
5 12 0.21
6 42 0.74
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:41034023 original size:17 final size:17
Alignment explanation
Indices: 41034001--41034083 Score: 109
Period size: 17 Copynumber: 5.1 Consensus size: 17
41033991 ATCAAATCAT
41034001 TTTAAATTTATATTAAA
1 TTTAAATTTATATTAAA
*
41034018 TTTAAATTTATTTTAAA
1 TTTAAATTTATATTAAA
41034035 TTTAAA-TT-TATTAAA
1 TTTAAATTTATATTAAA
* *
41034050 TTTAAATTTAGATTTAA
1 TTTAAATTTATATTAAA
*
41034067 TATAAATTTA-ATTAAA
1 TTTAAATTTATATTAAA
41034083 T
1 T
41034084 GAAGTCCAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
15 12 0.21
16 10 0.17
17 36 0.62
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATATTAAA
Found at i:41034742 original size:3 final size:3
Alignment explanation
Indices: 41034734--41034777 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
41034724 GCATTAATTT
**
41034734 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GCA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
41034778 GAAGTTATTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:41035187 original size:11 final size:10
Alignment explanation
Indices: 41035173--41035215 Score: 50
Period size: 11 Copynumber: 4.0 Consensus size: 10
41035163 AATGAAAATA
41035173 AAAGAACAAAG
1 AAAGAA-AAAG
41035184 AAAGAAAAATG
1 AAAGAAAAA-G
41035195 AAAGAAGAAAG
1 AAAGAA-AAAG
*
41035206 AATGAAAAAG
1 AAAGAAAAAG
41035216 GTGACTTTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 7 0.24
11 19 0.66
12 3 0.10
ACGTcount: A:0.72, C:0.02, G:0.21, T:0.05
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:41035193 original size:22 final size:22
Alignment explanation
Indices: 41035167--41035214 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
41035157 AAAATAAATG
41035167 AAAATAAAAGAACAAAGAAAGA
1 AAAATAAAAGAACAAAGAAAGA
* * *
41035189 AAAATGAAAGAAGAAAGAATGA
1 AAAATAAAAGAACAAAGAAAGA
41035211 AAAA
1 AAAA
41035215 GGTGACTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.75, C:0.02, G:0.17, T:0.06
Consensus pattern (22 bp):
AAAATAAAAGAACAAAGAAAGA
Found at i:41035200 original size:15 final size:15
Alignment explanation
Indices: 41035180--41035212 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
41035170 ATAAAAGAAC
41035180 AAAGAAAGAAA-AATG
1 AAAG-AAGAAAGAATG
41035195 AAAGAAGAAAGAATG
1 AAAGAAGAAAGAATG
41035210 AAA
1 AAA
41035213 AAGGTGACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (15 bp):
AAAGAAGAAAGAATG
Found at i:41035948 original size:30 final size:30
Alignment explanation
Indices: 41035904--41036086 Score: 208
Period size: 30 Copynumber: 6.1 Consensus size: 30
41035894 AAAATTGGTG
*
41035904 TTTTGACCCTAAAACTTTCTAAAAATTACA
1 TTTTGACCCCAAAACTTTCTAAAAATTACA
* * *
41035934 TTTTAACCCCAAAACTTTTTAAAAATTATA
1 TTTTGACCCCAAAACTTTCTAAAAATTACA
* ** *
41035964 TTTTAACCTTAAAACATTCTAAAAATTACA
1 TTTTGACCCCAAAACTTTCTAAAAATTACA
* * *
41035994 TTTTGACCCCCAAACTTT-TCCAAAATTATA
1 TTTTGACCCCAAAACTTTCT-AAAAATTACA
** *
41036024 TTTTGACCCTGAAACTTTCTAAAAATTATA
1 TTTTGACCCCAAAACTTTCTAAAAATTACA
*
41036054 TTTTGACCCCAAAACTTTCT-AAAATGACA
1 TTTTGACCCCAAAACTTTCTAAAAATTACA
41036083 TTTT
1 TTTT
41036087 ATCCCTAAAT
Statistics
Matches: 128, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
29 12 0.09
30 115 0.90
31 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.03, T:0.38
Consensus pattern (30 bp):
TTTTGACCCCAAAACTTTCTAAAAATTACA
Found at i:41035978 original size:60 final size:60
Alignment explanation
Indices: 41035904--41036077 Score: 258
Period size: 60 Copynumber: 2.9 Consensus size: 60
41035894 AAAATTGGTG
*
41035904 TTTTGACCCTAAAACTTTCTAAAAATTACATTTTAACCCCAAAACTTTTTAAAAATTATA
1 TTTTGACCCTAAAACTTTCTAAAAATTACATTTTGACCCCAAAACTTTTTAAAAATTATA
* * * * **
41035964 TTTTAACCTTAAAACATTCTAAAAATTACATTTTGACCCCCAAACTTTTCCAAAATTATA
1 TTTTGACCCTAAAACTTTCTAAAAATTACATTTTGACCCCAAAACTTTTTAAAAATTATA
* * *
41036024 TTTTGACCCTGAAACTTTCTAAAAATTATATTTTGACCCCAAAACTTTCTAAAA
1 TTTTGACCCTAAAACTTTCTAAAAATTACATTTTGACCCCAAAACTTTTTAAAA
41036078 TGACATTTTA
Statistics
Matches: 98, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 98 1.00
ACGTcount: A:0.40, C:0.20, G:0.03, T:0.37
Consensus pattern (60 bp):
TTTTGACCCTAAAACTTTCTAAAAATTACATTTTGACCCCAAAACTTTTTAAAAATTATA
Found at i:41036057 original size:90 final size:87
Alignment explanation
Indices: 41035925--41036114 Score: 236
Period size: 90 Copynumber: 2.1 Consensus size: 87
41035915 AAACTTTCTA
* **
41035925 AAAATTACATTTTAACCCCAAAACTTTTTAAAAATTATATTTTAACCTTAAAACATTCTAAAAAT
1 AAAATTACATTTTAACCCCAAAACTTTCTAAAAATTATATTTTAACCCCAAAACATTCT-AAAAT
*
41035990 TACATTTTGACCCCCAAACTTTTCC
65 GACATTTT-ACCCCCAAA-TTTTCC
* * ** * *
41036015 AAAATTATATTTTGACCCTGAAACTTTCTAAAAATTATATTTTGACCCCAAAACTTTCTAAAATG
1 AAAATTACATTTTAACCCCAAAACTTTCTAAAAATTATATTTTAACCCCAAAACATTCTAAAATG
* *
41036080 ACATTTTATCCCTAAATTTTCC
66 ACATTTTACCCCCAAATTTTCC
*
41036102 AAAATTTCATTTT
1 AAAATTACATTTT
41036115 TGACCTCGAT
Statistics
Matches: 86, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
87 17 0.20
88 7 0.08
89 12 0.14
90 50 0.58
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39
Consensus pattern (87 bp):
AAAATTACATTTTAACCCCAAAACTTTCTAAAAATTATATTTTAACCCCAAAACATTCTAAAATG
ACATTTTACCCCCAAATTTTCC
Found at i:41036413 original size:14 final size:15
Alignment explanation
Indices: 41036394--41036423 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
41036384 AAAATCGCAT
41036394 ATTTGTTTTCA-AAA
1 ATTTGTTTTCATAAA
41036408 ATTTGTTTTCATAAA
1 ATTTGTTTTCATAAA
41036423 A
1 A
41036424 ATTTAAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (15 bp):
ATTTGTTTTCATAAA
Found at i:41039481 original size:21 final size:22
Alignment explanation
Indices: 41039437--41039481 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
41039427 TTTAATTAAC
*
41039437 ATTTTTATTAAAAAATTATTTG
1 ATTTTTATTAAAAAATTATATG
41039459 ATTTTT-TTAAAAAAATTA-ATG
1 ATTTTTATT-AAAAAATTATATG
41039480 AT
1 AT
41039482 CAAATTTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (22 bp):
ATTTTTATTAAAAAATTATATG
Found at i:41050160 original size:20 final size:20
Alignment explanation
Indices: 41050135--41050176 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
41050125 CACTAAAGCT
41050135 CAGTGGAGCTGGTCCCCAAA
1 CAGTGGAGCTGGTCCCCAAA
41050155 CAGTGGAGCTGGTCCCCAAA
1 CAGTGGAGCTGGTCCCCAAA
41050175 CA
1 CA
41050177 TCAGCTGCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.31, G:0.29, T:0.14
Consensus pattern (20 bp):
CAGTGGAGCTGGTCCCCAAA
Found at i:41050628 original size:30 final size:31
Alignment explanation
Indices: 41050594--41050651 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
41050584 CAATGCAATT
41050594 ATATATACA-TAAATTTTTATTGTAATTTAA
1 ATATATACATTAAATTTTTATTGTAATTTAA
* *
41050624 ATATATACATTATATTTTTATTTTAATT
1 ATATATACATTAAATTTTTATTGTAATT
41050652 CAATTGTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 9 0.36
31 16 0.64
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (31 bp):
ATATATACATTAAATTTTTATTGTAATTTAA
Found at i:41053869 original size:10 final size:10
Alignment explanation
Indices: 41053854--41053896 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
41053844 CAATATATAC
*
41053854 TTTTTATAAT
1 TTTTTAAAAT
41053864 TTTTTAAAAT
1 TTTTTAAAAT
** *
41053874 CATTTATAAT
1 TTTTTAAAAT
41053884 TTTTTAAAAT
1 TTTTTAAAAT
41053894 TTT
1 TTT
41053897 AAAAGATTTT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (10 bp):
TTTTTAAAAT
Found at i:41053881 original size:20 final size:20
Alignment explanation
Indices: 41053856--41053893 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
41053846 ATATATACTT
41053856 TTTATAATTTTTTAAAATCA
1 TTTATAATTTTTTAAAATCA
41053876 TTTATAATTTTTTAAAAT
1 TTTATAATTTTTTAAAAT
41053894 TTTAAAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTATAATTTTTTAAAATCA
Found at i:41055102 original size:12 final size:12
Alignment explanation
Indices: 41055085--41055111 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
41055075 AATTACTGAG
41055085 TTTAAGATCTAA
1 TTTAAGATCTAA
41055097 TTTAAGATCTAA
1 TTTAAGATCTAA
41055109 TTT
1 TTT
41055112 GAAAAAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.48
Consensus pattern (12 bp):
TTTAAGATCTAA
Found at i:41057901 original size:14 final size:14
Alignment explanation
Indices: 41057882--41057910 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41057872 TACGATATAT
41057882 ATAAGAATTATACG
1 ATAAGAATTATACG
41057896 ATAAGAATTATACG
1 ATAAGAATTATACG
41057910 A
1 A
41057911 ATCCATCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.28
Consensus pattern (14 bp):
ATAAGAATTATACG
Found at i:41059184 original size:29 final size:28
Alignment explanation
Indices: 41059126--41059182 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
41059116 TTATATGAGT
41059126 TAGATCAAATTAGTCATGCTATTATTAAA
1 TAGATCAAATTAGTCA-GCTATTATTAAA
* *
41059155 TAGATCAATTTAGTC-GTTATATATTAAA
1 TAGATCAAATTAGTCAGCTAT-TATTAAA
41059183 ATGAATCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 4 0.16
28 7 0.28
29 14 0.56
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (28 bp):
TAGATCAAATTAGTCAGCTATTATTAAA
Found at i:41066982 original size:3 final size:3
Alignment explanation
Indices: 41066974--41067007 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
41066964 TTGAGTTCAG
*
41066974 GTT GTT GTT GTT GTT GTT GTT GTT GTT GGT GTT G
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT G
41067008 GTTTTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.38, T:0.62
Consensus pattern (3 bp):
GTT
Found at i:41087061 original size:23 final size:24
Alignment explanation
Indices: 41086997--41087073 Score: 84
Period size: 23 Copynumber: 3.2 Consensus size: 24
41086987 TTTATTATTC
41086997 ATTAACATAGTTCGTGAACATGTTCA
1 ATTAA-AT-GTTCGTGAACATGTTCA
* * *
41087023 ATTATATGTCCATGAACATGTTC-
1 ATTAAATGTTCGTGAACATGTTCA
* *
41087046 GTTAAATGTTCGTGAACATTTTCA
1 ATTAAATGTTCGTGAACATGTTCA
41087070 ATTA
1 ATTA
41087074 CGTTAAATGA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
23 18 0.44
24 17 0.41
25 2 0.05
26 4 0.10
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (24 bp):
ATTAAATGTTCGTGAACATGTTCA
Found at i:41088003 original size:3 final size:3
Alignment explanation
Indices: 41087995--41088020 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
41087985 TTGTCTTACC
41087995 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
41088021 ATGTTGTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:41088960 original size:21 final size:21
Alignment explanation
Indices: 41088933--41088988 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
41088923 ACATTTTTAC
41088933 ATAAAATATATAAGTAT-CAA
1 ATAAAATATATAAGTATACAA
* * * *
41088953 AGTAAAATTTGTTATTATACAA
1 A-TAAAATATATAAGTATACAA
41088975 ATAAAATATATAAG
1 ATAAAATATATAAG
41088989 AAAAATATTC
Statistics
Matches: 26, Mismatches: 8, Indels: 3
0.70 0.22 0.08
Matches are distributed among these distances:
20 1 0.04
21 21 0.81
22 4 0.15
ACGTcount: A:0.55, C:0.04, G:0.07, T:0.34
Consensus pattern (21 bp):
ATAAAATATATAAGTATACAA
Found at i:41092860 original size:5 final size:5
Alignment explanation
Indices: 41092845--41092882 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
41092835 CTTTGTGGAC
41092845 TTCTCT TTCTT TTCTT TTCTT TTCTT TT-TT TTCATT TT
1 TTCT-T TTCTT TTCTT TTCTT TTCTT TTCTT TTC-TT TT
41092883 TCTGGATTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.13
5 18 0.60
6 8 0.27
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (5 bp):
TTCTT
Found at i:41093819 original size:17 final size:17
Alignment explanation
Indices: 41093797--41093830 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
41093787 GTAGTAAAAA
41093797 GAAAAAGTATCATCACC
1 GAAAAAGTATCATCACC
41093814 GAAAAAGTATCATCACC
1 GAAAAAGTATCATCACC
41093831 CCAACCATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.24, G:0.12, T:0.18
Consensus pattern (17 bp):
GAAAAAGTATCATCACC
Found at i:41093991 original size:44 final size:43
Alignment explanation
Indices: 41093930--41094016 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 43
41093920 ACCTGTGCAT
41093930 ACTTACCCTTCTTTCAACAAAGAAAGGTATCACATTCACATAC
1 ACTTACCCTTCTTTCAACAAAGAAAGGTATCACATTCACATAC
41093973 ACTTACCCTTTCTTTCAACAAAGAAAGGTATCACATTCACATAC
1 ACTTACCC-TTCTTTCAACAAAGAAAGGTATCACATTCACATAC
41094017 TCATATAGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 8 0.19
44 35 0.81
ACGTcount: A:0.37, C:0.28, G:0.07, T:0.29
Consensus pattern (43 bp):
ACTTACCCTTCTTTCAACAAAGAAAGGTATCACATTCACATAC
Found at i:41099451 original size:30 final size:29
Alignment explanation
Indices: 41099400--41099467 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
41099390 TGATATTGTT
41099400 ATTTTTTAATAAAATTTTATAAT-TTTA-A
1 ATTTTTT-ATAAAATTTTATAATGTTTATA
*
41099428 ATTTTTTATAAAATTTATTTATAATGTTTATG
1 ATTTTTTATAAAA--T-TTTATAATGTTTATA
41099460 ATTTTTTA
1 ATTTTTTA
41099468 ATAATCTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
27 6 0.18
28 7 0.21
29 1 0.03
30 8 0.24
31 4 0.12
32 8 0.24
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (29 bp):
ATTTTTTATAAAATTTTATAATGTTTATA
Found at i:41103019 original size:39 final size:40
Alignment explanation
Indices: 41102976--41103051 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
41102966 ATTAAGCCCG
41102976 ATAAACATATCGGT-CTAAGCCTGCTAGGCACAAGGCTCA
1 ATAAACATATCGGTACTAAGCCTGCTAGGCACAAGGCTCA
41103015 ATAAACATATCGGTACTAAGCCTGCTAGGCACAAGGC
1 ATAAACATATCGGTACTAAGCCTGCTAGGCACAAGGC
41103052 CCGATATAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
39 14 0.39
40 22 0.61
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (40 bp):
ATAAACATATCGGTACTAAGCCTGCTAGGCACAAGGCTCA
Found at i:41103106 original size:41 final size:41
Alignment explanation
Indices: 41103032--41103175 Score: 155
Period size: 41 Copynumber: 3.5 Consensus size: 41
41103022 TATCGGTACT
* * * * *
41103032 AAGCCTGCTAGGCACAAGGCCCGATATAGTACATTGGCATA
1 AAGCTTGCTAGGCTCAAGGCCAGATACAATACATTGGCATA
* **
41103073 TAGCTTGCTAGGCTCAAGGCCAGATACAATACATCAGCATA
1 AAGCTTGCTAGGCTCAAGGCCAGATACAATACATTGGCATA
* * * **
41103114 AAGCCTGCTTGGCTCAAGGCCCA-ATACAACACATTGATATA
1 AAGCTTGCTAGGCTCAAGG-CCAGATACAATACATTGGCATA
41103155 AAGCTTGCTAGGCTCAAGGCC
1 AAGCTTGCTAGGCTCAAGGCC
41103176 CGAATCATTG
Statistics
Matches: 84, Mismatches: 18, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
40 2 0.02
41 79 0.94
42 3 0.04
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.21
Consensus pattern (41 bp):
AAGCTTGCTAGGCTCAAGGCCAGATACAATACATTGGCATA
Found at i:41103176 original size:41 final size:41
Alignment explanation
Indices: 41102992--41103176 Score: 146
Period size: 41 Copynumber: 4.5 Consensus size: 41
41102982 ATATCGGTCT
* * * *
41102992 AAGCCTGCTAGGCACAAGGCTCAATA-AACATATCGGTAC-T-
1 AAGCCTGCTAGGCTCAAGGCCCAATACAACACAT-TG-ACATA
* * * ** *
41103032 AAGCCTGCTAGGCACAAGGCCCGATATAGTACATTGGCATA
1 AAGCCTGCTAGGCTCAAGGCCCAATACAACACATTGACATA
* * * *
41103073 TAGCTTGCTAGGCTCAAGG-CCAGATACAATACA-TCAGCATA
1 AAGCCTGCTAGGCTCAAGGCCCA-ATACAACACATTGA-CATA
* *
41103114 AAGCCTGCTTGGCTCAAGGCCCAATACAACACATTGATATA
1 AAGCCTGCTAGGCTCAAGGCCCAATACAACACATTGACATA
*
41103155 AAGCTTGCTAGGCTCAAGGCCC
1 AAGCCTGCTAGGCTCAAGGCCC
41103177 GAATCATTGC
Statistics
Matches: 115, Mismatches: 23, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
39 1 0.01
40 29 0.25
41 80 0.70
42 5 0.04
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (41 bp):
AAGCCTGCTAGGCTCAAGGCCCAATACAACACATTGACATA
Found at i:41104459 original size:19 final size:19
Alignment explanation
Indices: 41104431--41104469 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
41104421 GACCATGTGG
*
41104431 CCAAGTCGTGTGGCTTAAC
1 CCAAGCCGTGTGGCTTAAC
41104450 CCAAGCCGTGTGGCTTAAC
1 CCAAGCCGTGTGGCTTAAC
41104469 C
1 C
41104470 TAGGTCATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.31, G:0.26, T:0.23
Consensus pattern (19 bp):
CCAAGCCGTGTGGCTTAAC
Found at i:41106119 original size:76 final size:75
Alignment explanation
Indices: 41105936--41106176 Score: 250
Period size: 76 Copynumber: 3.2 Consensus size: 75
41105926 GTCAAATGTA
* * * * * *
41105936 TGCCCAACACTAGTTAGTTAAACTGACAAAAGTTGTGTCCAGCGCTAGTCGA-ATAACAGACTAA
1 TGCCCAACACTAGTCAGATAAACTGACAAAAGTTGCGCCCAGCGCTAGTCGATA-AACCGACAAA
41106000 TATAAAAAGTG
65 TATAAAAAGTG
* * ** * * *
41106011 TGCCCAACACTGGTCAGATAAACTAATGAAAGTTGCGCCCAGCTCTAGTCAGATAAACCGGCGAA
1 TGCCCAACACTAGTCAGATAAACTGACAAAAGTTGCGCCCAGCGCTAGTC-GATAAACCGACAAA
*
41106076 TATAAGAAGTG
65 TATAAAAAGTG
* * * * * * *
41106087 TGCCCAGCACTAGTCAAATAAATTGACAAAAGTTGCACCCAGCGCAAATCGAATAAATCGACAAA
1 TGCCCAACACTAGTCAGATAAACTGACAAAAGTTGCGCCCAGCGCTAGTCG-ATAAACCGACAAA
41106152 TATAAAAAGTG
65 TATAAAAAGTG
*
41106163 TGCCCAGCACTAGT
1 TGCCCAACACTAGT
41106177 TGGATATACC
Statistics
Matches: 135, Mismatches: 28, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
75 42 0.31
76 92 0.68
77 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.21
Consensus pattern (75 bp):
TGCCCAACACTAGTCAGATAAACTGACAAAAGTTGCGCCCAGCGCTAGTCGATAAACCGACAAAT
ATAAAAAGTG
Found at i:41137198 original size:12 final size:12
Alignment explanation
Indices: 41137163--41137198 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
41137153 GTTCACGAAC
* *
41137163 AAGCTCGTTTAA
1 AAGCTTGTTTAT
41137175 AAGCTTGTTTAT
1 AAGCTTGTTTAT
41137187 AAGCTTGTTTAT
1 AAGCTTGTTTAT
41137199 TTATTAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.44
Consensus pattern (12 bp):
AAGCTTGTTTAT
Done.